From 3e8ab3354e265635e7f6948d363bac49667a0071 Mon Sep 17 00:00:00 2001
From: plumedbot <giovanni.bussi+plumedbot@gmail.com>
Date: Wed, 9 Oct 2024 13:38:18 +0000
Subject: [PATCH] Update to plumed/plumed2@941986b

---
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+Coverage scan for PLUMED v2.9
+-----------------------------
+
+This repository hosts the coverage scan for [PLUMED](http://www.plumed.org) v2.9,
+git revision [941986b](https://github.com/plumed/plumed2/commit/941986b).
+
+Coverage scan done on [GiHub actions](http://github.com/plumed/plumed2/actions) on Wed Oct  9 13:38:17 UTC 2024.
+
+To browse the scan you should go [here](http://plumed.github.io/coverage-v2.9).
+
+You can also download a full copy of the scan for offline access
+at [this link](http://github.com/plumed/coverage-v2.9/archive/gh-pages.zip).
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/arch.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - arch.cpp<span style="font-size: 80%;"> (<a href="arch.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
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+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="arch.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="arch.cpp.gcov.html#59">_ZN4PLMD6asmjit8ArchInfo4initEjj</a></td>
+              <td class="coverFnHi">70</td>
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+    <tr>
+              <td class="coverFn"><a href="arch.cpp.gcov.html#76">_ZN4PLMD6asmjit9ArchUtils15typeIdToRegInfoEjRjRNS0_7RegInfoE</a></td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/arch.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - arch.cpp<span style="font-size: 80%;"> (<a href="arch.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
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+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="arch.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="arch.cpp.gcov.html#59">_ZN4PLMD6asmjit8ArchInfo4initEjj</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="arch.cpp.gcov.html#76">_ZN4PLMD6asmjit9ArchUtils15typeIdToRegInfoEjRjRNS0_7RegInfoE</a></td>
+              <td class="coverFnHi">23788</td>
+            </tr>
+  </table>
+  <br>
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+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/arch.cpp.gcov.html b/coverage-libs/asmjit/arch.cpp.gcov.html
new file mode 100644
index 0000000000..89b53c34b6
--- /dev/null
+++ b/coverage-libs/asmjit/arch.cpp.gcov.html
@@ -0,0 +1,263 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/arch.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - arch.cpp<span style="font-size: 80%;"> (source / <a href="arch.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // ============================================================================</a>
+<a name="46"><span class="lineNum">      46 </span>            : // [asmjit::ArchInfo]</a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : static const uint32_t archInfoTable[] = {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   // &lt;-------------+---------------------+-----------------------+-------+</a>
+<a name="51"><span class="lineNum">      51 </span>            :   //               | Type                | SubType               | GPInfo|</a>
+<a name="52"><span class="lineNum">      52 </span>            :   // &lt;-------------+---------------------+-----------------------+-------+</a>
+<a name="53"><span class="lineNum">      53 </span>            :   ASMJIT_PACK32_4x8(ArchInfo::kTypeNone  , ArchInfo::kSubTypeNone, 0,  0),</a>
+<a name="54"><span class="lineNum">      54 </span>            :   ASMJIT_PACK32_4x8(ArchInfo::kTypeX86   , ArchInfo::kSubTypeNone, 4,  8),</a>
+<a name="55"><span class="lineNum">      55 </span>            :   ASMJIT_PACK32_4x8(ArchInfo::kTypeX64   , ArchInfo::kSubTypeNone, 8, 16),</a>
+<a name="56"><span class="lineNum">      56 </span>            :   ASMJIT_PACK32_4x8(ArchInfo::kTypeX32   , ArchInfo::kSubTypeNone, 8, 16),</a>
+<a name="57"><span class="lineNum">      57 </span>            :   ASMJIT_PACK32_4x8(ArchInfo::kTypeA32   , ArchInfo::kSubTypeNone, 4, 16),</a>
+<a name="58"><span class="lineNum">      58 </span>            :   ASMJIT_PACK32_4x8(ArchInfo::kTypeA64   , ArchInfo::kSubTypeNone, 8, 32)</a>
+<a name="59"><span class="lineNum">      59 </span>            : };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         70 : ASMJIT_FAVOR_SIZE void ArchInfo::init(uint32_t type, uint32_t subType) noexcept {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         70 :   uint32_t index = type &lt; ASMJIT_ARRAY_SIZE(archInfoTable) ? type : uint32_t(0);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   // Make sure the `archInfoTable` array is correctly indexed.</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         70 :   _signature = archInfoTable[index];</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   ASMJIT_ASSERT(_type == index);</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   // Even if the architecture is not known we setup its type and sub-type,</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // however, such architecture is not really useful.</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         70 :   _type = type;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         70 :   _subType = subType;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         70 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : // ============================================================================</a>
+<a name="75"><span class="lineNum">      75 </span>            : // [asmjit::ArchUtils]</a>
+<a name="76"><span class="lineNum">      76 </span>            : // ============================================================================</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      23788 : ASMJIT_FAVOR_SIZE Error ArchUtils::typeIdToRegInfo(uint32_t archType, uint32_t&amp; typeIdInOut, RegInfo&amp; regInfo) noexcept {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      23788 :   uint32_t typeId = typeIdInOut;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   // Zero the signature so it's clear in case that typeId is not invalid.</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      23788 :   regInfo._signature = 0;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      23788 :   if (ArchInfo::isX86Family(archType)) {</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     // Passed RegType instead of TypeId?</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      23788 :     if (typeId &lt;= Reg::kRegMax)</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :       typeId = x86OpData.archRegs.regTypeToTypeId[typeId];</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      23788 :     if (ASMJIT_UNLIKELY(!TypeId::isValid(typeId)))</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :       return DebugUtils::errored(kErrorInvalidTypeId);</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :     // First normalize architecture dependent types.</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      23788 :     if (TypeId::isAbstract(typeId)) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       7268 :       if (typeId == TypeId::kIntPtr)</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       7268 :         typeId = (archType == ArchInfo::kTypeX86) ? TypeId::kI32 : TypeId::kI64;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :       else</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :         typeId = (archType == ArchInfo::kTypeX86) ? TypeId::kU32 : TypeId::kU64;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :     }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :     // Type size helps to construct all kinds of registers. If the size is zero</a>
+<a name="102"><span class="lineNum">     102 </span>            :     // then the TypeId is invalid.</a>
+<a name="103"><span class="lineNum">     103 </span>            :     uint32_t size = TypeId::sizeOf(typeId);</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      23788 :     if (ASMJIT_UNLIKELY(!size))</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :       return DebugUtils::errored(kErrorInvalidTypeId);</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      23788 :     if (ASMJIT_UNLIKELY(typeId == TypeId::kF80))</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :       return DebugUtils::errored(kErrorInvalidUseOfF80);</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :     uint32_t regType = 0;</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      23788 :     switch (typeId) {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :       case TypeId::kI8:</a>
+<a name="114"><span class="lineNum">     114 </span>            :       case TypeId::kU8:</a>
+<a name="115"><span class="lineNum">     115 </span>            :         regType = X86Reg::kRegGpbLo;</a>
+<a name="116"><span class="lineNum">     116 </span>            :         break;</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :       case TypeId::kI16:</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       case TypeId::kU16:</a>
+<a name="120"><span class="lineNum">     120 </span>            :         regType = X86Reg::kRegGpw;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :       case TypeId::kI32:</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :       case TypeId::kU32:</a>
+<a name="125"><span class="lineNum">     125 </span>            :         regType = X86Reg::kRegGpd;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       7268 :       case TypeId::kI64:</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :       case TypeId::kU64:</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       7268 :         if (archType == ArchInfo::kTypeX86)</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :           return DebugUtils::errored(kErrorInvalidUseOfGpq);</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :         regType = X86Reg::kRegGpq;</a>
+<a name="134"><span class="lineNum">     134 </span>            :         break;</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :       // F32 and F64 are always promoted to use vector registers.</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :       case TypeId::kF32:</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :         typeId = TypeId::kF32x1;</a>
+<a name="139"><span class="lineNum">     139 </span>            :         regType = X86Reg::kRegXmm;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :       case TypeId::kF64:</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :         typeId = TypeId::kF64x1;</a>
+<a name="144"><span class="lineNum">     144 </span>            :         regType = X86Reg::kRegXmm;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :       // Mask registers {k}.</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :       case TypeId::kMask8:</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :       case TypeId::kMask16:</a>
+<a name="150"><span class="lineNum">     150 </span>            :       case TypeId::kMask32:</a>
+<a name="151"><span class="lineNum">     151 </span>            :       case TypeId::kMask64:</a>
+<a name="152"><span class="lineNum">     152 </span>            :         regType = X86Reg::kRegK;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :       // MMX registers.</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :       case TypeId::kMmx32:</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       case TypeId::kMmx64:</a>
+<a name="158"><span class="lineNum">     158 </span>            :         regType = X86Reg::kRegMm;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            :       // XMM|YMM|ZMM registers.</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      16520 :       default:</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      16520 :         if (size &lt;= 16)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :           regType = X86Reg::kRegXmm;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :         else if (size == 32)</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :           regType = X86Reg::kRegYmm;</a>
+<a name="167"><span class="lineNum">     167 </span>            :         else</a>
+<a name="168"><span class="lineNum">     168 </span>            :           regType = X86Reg::kRegZmm;</a>
+<a name="169"><span class="lineNum">     169 </span>            :         break;</a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      23788 :     typeIdInOut = typeId;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      23788 :     regInfo._signature = x86OpData.archRegs.regInfo[regType].getSignature();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      23788 :     return kErrorOk;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : } // asmjit namespace</a>
+<a name="182"><span class="lineNum">     182 </span>            : } // namespace PLMD</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : // [Api-End]</a>
+<a name="185"><span class="lineNum">     185 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="186"><span class="lineNum">     186 </span>            : #pragma GCC diagnostic pop</a>
+<a name="187"><span class="lineNum">     187 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/arch.h.func-sort-c.html b/coverage-libs/asmjit/arch.h.func-sort-c.html
new file mode 100644
index 0000000000..e80475eec9
--- /dev/null
+++ b/coverage-libs/asmjit/arch.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/arch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - arch.h<span style="font-size: 80%;"> (<a href="arch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="arch.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/arch.h.func.html b/coverage-libs/asmjit/arch.h.func.html
new file mode 100644
index 0000000000..9c7dc6def1
--- /dev/null
+++ b/coverage-libs/asmjit/arch.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/arch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - arch.h<span style="font-size: 80%;"> (<a href="arch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="arch.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/arch.h.gcov.html b/coverage-libs/asmjit/arch.h.gcov.html
new file mode 100644
index 0000000000..3cf75cdefb
--- /dev/null
+++ b/coverage-libs/asmjit/arch.h.gcov.html
@@ -0,0 +1,304 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/arch.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - arch.h<span style="font-size: 80%;"> (source / <a href="arch.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_arch_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_arch_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_ARCH_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_ARCH_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./globals.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \addtogroup asmjit_base</a>
+<a name="46"><span class="lineNum">      46 </span>            : //! \{</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // ============================================================================</a>
+<a name="49"><span class="lineNum">      49 </span>            : // [asmjit::ArchInfo]</a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : class ArchInfo {</a>
+<a name="53"><span class="lineNum">      53 </span>            : public:</a>
+<a name="54"><span class="lineNum">      54 </span>            :   //! Architecture type.</a>
+<a name="55"><span class="lineNum">      55 </span>            :   ASMJIT_ENUM(Type) {</a>
+<a name="56"><span class="lineNum">      56 </span>            :     kTypeNone  = 0,                      //!&lt; No/Unknown architecture.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :     // X86 architectures.</a>
+<a name="59"><span class="lineNum">      59 </span>            :     kTypeX86   = 1,                      //!&lt; X86 architecture (32-bit).</a>
+<a name="60"><span class="lineNum">      60 </span>            :     kTypeX64   = 2,                      //!&lt; X64 architecture (64-bit) (AMD64).</a>
+<a name="61"><span class="lineNum">      61 </span>            :     kTypeX32   = 3,                      //!&lt; X32 architecture (DEAD-END).</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            :     // ARM architectures.</a>
+<a name="64"><span class="lineNum">      64 </span>            :     kTypeA32   = 4,                      //!&lt; ARM 32-bit architecture (AArch32/ARM/THUMB).</a>
+<a name="65"><span class="lineNum">      65 </span>            :     kTypeA64   = 5,                      //!&lt; ARM 64-bit architecture (AArch64).</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            :     //! Architecture detected at compile-time (architecture of the host).</a>
+<a name="68"><span class="lineNum">      68 </span>            :     kTypeHost  = ASMJIT_ARCH_X86   ? kTypeX86 :</a>
+<a name="69"><span class="lineNum">      69 </span>            :                  ASMJIT_ARCH_X64   ? kTypeX64 :</a>
+<a name="70"><span class="lineNum">      70 </span>            :                  ASMJIT_ARCH_ARM32 ? kTypeA32 :</a>
+<a name="71"><span class="lineNum">      71 </span>            :                  ASMJIT_ARCH_ARM64 ? kTypeA64 : kTypeNone</a>
+<a name="72"><span class="lineNum">      72 </span>            :   };</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   //! Architecture sub-type or execution mode.</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ASMJIT_ENUM(SubType) {</a>
+<a name="76"><span class="lineNum">      76 </span>            :     kSubTypeNone         = 0,            //!&lt; Default mode (or no specific mode).</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :     // X86 sub-types.</a>
+<a name="79"><span class="lineNum">      79 </span>            :     kSubTypeX86_AVX      = 1,            //!&lt; Code generation uses AVX         by default (VEC instructions).</a>
+<a name="80"><span class="lineNum">      80 </span>            :     kSubTypeX86_AVX2     = 2,            //!&lt; Code generation uses AVX2        by default (VEC instructions).</a>
+<a name="81"><span class="lineNum">      81 </span>            :     kSubTypeX86_AVX512   = 3,            //!&lt; Code generation uses AVX-512F    by default (+32 vector regs).</a>
+<a name="82"><span class="lineNum">      82 </span>            :     kSubTypeX86_AVX512VL = 4,            //!&lt; Code generation uses AVX-512F-VL by default (+VL extensions).</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :     // ARM sub-types.</a>
+<a name="85"><span class="lineNum">      85 </span>            :     kSubTypeA32_Thumb    = 8,            //!&lt; THUMB|THUMB2 sub-type (only ARM in 32-bit mode).</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : #if   (ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64) &amp;&amp; defined(__AVX512VL__)</a>
+<a name="88"><span class="lineNum">      88 </span>            :     kSubTypeHost = kSubTypeX86_AVX512VL</a>
+<a name="89"><span class="lineNum">      89 </span>            : #elif (ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64) &amp;&amp; defined(__AVX512F__)</a>
+<a name="90"><span class="lineNum">      90 </span>            :     kSubTypeHost = kSubTypeX86_AVX512</a>
+<a name="91"><span class="lineNum">      91 </span>            : #elif (ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64) &amp;&amp; defined(__AVX2__)</a>
+<a name="92"><span class="lineNum">      92 </span>            :     kSubTypeHost = kSubTypeX86_AVX2</a>
+<a name="93"><span class="lineNum">      93 </span>            : #elif (ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64) &amp;&amp; defined(__AVX__)</a>
+<a name="94"><span class="lineNum">      94 </span>            :     kSubTypeHost = kSubTypeX86_AVX</a>
+<a name="95"><span class="lineNum">      95 </span>            : #elif (ASMJIT_ARCH_ARM32) &amp;&amp; (defined(_M_ARMT) || defined(__thumb__) || defined(__thumb2__))</a>
+<a name="96"><span class="lineNum">      96 </span>            :     kSubTypeHost = kSubTypeA32_Thumb</a>
+<a name="97"><span class="lineNum">      97 </span>            : #else</a>
+<a name="98"><span class="lineNum">      98 </span>            :     kSubTypeHost = 0</a>
+<a name="99"><span class="lineNum">      99 </span>            : #endif</a>
+<a name="100"><span class="lineNum">     100 </span>            :   };</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="103"><span class="lineNum">     103 </span>            :   // [Utilities]</a>
+<a name="104"><span class="lineNum">     104 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      31580 :   static ASMJIT_INLINE bool isX86Family(uint32_t archType) noexcept { return archType &gt;= kTypeX86 &amp;&amp; archType &lt;= kTypeX32; }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   static ASMJIT_INLINE bool isArmFamily(uint32_t archType) noexcept { return archType &gt;= kTypeA32 &amp;&amp; archType &lt;= kTypeA64; }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // [Construction / Destruction]</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       7890 :   ASMJIT_INLINE ArchInfo() noexcept : _signature(0) {}</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_INLINE ArchInfo(const ArchInfo&amp; other) noexcept = default;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   explicit ASMJIT_INLINE ArchInfo(uint32_t type, uint32_t subType = kSubTypeNone) noexcept { init(type, subType); }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   ASMJIT_INLINE static ArchInfo host() noexcept { return ArchInfo(kTypeHost, kSubTypeHost); }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="120"><span class="lineNum">     120 </span>            :   // [Init / Reset]</a>
+<a name="121"><span class="lineNum">     121 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   ASMJIT_INLINE bool isInitialized() const noexcept { return _type != kTypeNone; }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   ASMJIT_API void init(uint32_t type, uint32_t subType = kSubTypeNone) noexcept;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void reset() noexcept { _signature = 0; }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="129"><span class="lineNum">     129 </span>            :   // [Accessors]</a>
+<a name="130"><span class="lineNum">     130 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   //! Get if the architecture is 32-bit.</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool is32Bit() const noexcept { return _gpSize == 4; }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   //! Get if the architecture is 64-bit.</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool is64Bit() const noexcept { return _gpSize == 8; }</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            :   //! Get architecture type, see \ref Type.</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      31580 :   ASMJIT_INLINE uint32_t getType() const noexcept { return _type; }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   //! Get architecture sub-type, see \ref SubType.</a>
+<a name="141"><span class="lineNum">     141 </span>            :   //!</a>
+<a name="142"><span class="lineNum">     142 </span>            :   //! X86 &amp; X64</a>
+<a name="143"><span class="lineNum">     143 </span>            :   //! ---------</a>
+<a name="144"><span class="lineNum">     144 </span>            :   //!</a>
+<a name="145"><span class="lineNum">     145 </span>            :   //! Architecture subtype describe the highest instruction-set level that can</a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! be used.</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //!</a>
+<a name="148"><span class="lineNum">     148 </span>            :   //! ARM32</a>
+<a name="149"><span class="lineNum">     149 </span>            :   //! -----</a>
+<a name="150"><span class="lineNum">     150 </span>            :   //!</a>
+<a name="151"><span class="lineNum">     151 </span>            :   //! Architecture mode means the instruction encoding to be used when generating</a>
+<a name="152"><span class="lineNum">     152 </span>            :   //! machine code, thus mode can be used to force generation of THUMB and THUMB2</a>
+<a name="153"><span class="lineNum">     153 </span>            :   //! encoding or regular ARM encoding.</a>
+<a name="154"><span class="lineNum">     154 </span>            :   //!</a>
+<a name="155"><span class="lineNum">     155 </span>            :   //! ARM64</a>
+<a name="156"><span class="lineNum">     156 </span>            :   //! -----</a>
+<a name="157"><span class="lineNum">     157 </span>            :   //!</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //! No meaning yet.</a>
+<a name="159"><span class="lineNum">     159 </span>            :   ASMJIT_INLINE uint32_t getSubType() const noexcept { return _subType; }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            :   //! Get if the architecture is X86, X64, or X32.</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       3896 :   ASMJIT_INLINE bool isX86Family() const noexcept { return isX86Family(_type); }</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   //! Get if the architecture is ARM32 or ARM64.</a>
+<a name="164"><span class="lineNum">     164 </span>            :   ASMJIT_INLINE bool isArmFamily() const noexcept { return isArmFamily(_type); }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   //! Get a size of a general-purpose register.</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getGpSize() const noexcept { return _gpSize; }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   //! Get number of general-purpose registers.</a>
+<a name="169"><span class="lineNum">     169 </span>            :   ASMJIT_INLINE uint32_t getGpCount() const noexcept { return _gpCount; }</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="172"><span class="lineNum">     172 </span>            :   // [Operator Overload]</a>
+<a name="173"><span class="lineNum">     173 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   ASMJIT_INLINE ArchInfo&amp; operator=(const ArchInfo&amp; other) noexcept = default;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   ASMJIT_INLINE bool operator==(const ArchInfo&amp; other) const noexcept { return _signature == other._signature; }</a>
+<a name="177"><span class="lineNum">     177 </span>            :   ASMJIT_INLINE bool operator!=(const ArchInfo&amp; other) const noexcept { return _signature != other._signature; }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="180"><span class="lineNum">     180 </span>            :   // [Members]</a>
+<a name="181"><span class="lineNum">     181 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   union {</a>
+<a name="184"><span class="lineNum">     184 </span>            :     struct {</a>
+<a name="185"><span class="lineNum">     185 </span>            :       uint8_t _type;                     //!&lt; Architecture type.</a>
+<a name="186"><span class="lineNum">     186 </span>            :       uint8_t _subType;                  //!&lt; Architecture sub-type.</a>
+<a name="187"><span class="lineNum">     187 </span>            :       uint8_t _gpSize;                   //!&lt; Default size of a general purpose register.</a>
+<a name="188"><span class="lineNum">     188 </span>            :       uint8_t _gpCount;                  //!&lt; Count of all general purpose registers.</a>
+<a name="189"><span class="lineNum">     189 </span>            :     };</a>
+<a name="190"><span class="lineNum">     190 </span>            :     uint32_t _signature;                 //!&lt; Architecture signature (32-bit int).</a>
+<a name="191"><span class="lineNum">     191 </span>            :   };</a>
+<a name="192"><span class="lineNum">     192 </span>            : };</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : // ============================================================================</a>
+<a name="195"><span class="lineNum">     195 </span>            : // [asmjit::ArchRegs]</a>
+<a name="196"><span class="lineNum">     196 </span>            : // ============================================================================</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : //! Information about all architecture registers.</a>
+<a name="199"><span class="lineNum">     199 </span>            : struct ArchRegs {</a>
+<a name="200"><span class="lineNum">     200 </span>            :   //! Register information and signatures indexed by \ref Reg::Type.</a>
+<a name="201"><span class="lineNum">     201 </span>            :   RegInfo regInfo[Reg::kRegMax + 1];</a>
+<a name="202"><span class="lineNum">     202 </span>            :   //! Count (maximum) of registers per \ref Reg::Type.</a>
+<a name="203"><span class="lineNum">     203 </span>            :   uint8_t regCount[Reg::kRegMax + 1];</a>
+<a name="204"><span class="lineNum">     204 </span>            :   //! Converts RegType to TypeId, see \ref TypeId::Id.</a>
+<a name="205"><span class="lineNum">     205 </span>            :   uint8_t regTypeToTypeId[Reg::kRegMax + 1];</a>
+<a name="206"><span class="lineNum">     206 </span>            : };</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            : // ============================================================================</a>
+<a name="209"><span class="lineNum">     209 </span>            : // [asmjit::ArchUtils]</a>
+<a name="210"><span class="lineNum">     210 </span>            : // ============================================================================</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            : struct ArchUtils {</a>
+<a name="213"><span class="lineNum">     213 </span>            :   ASMJIT_API static Error typeIdToRegInfo(uint32_t archType, uint32_t&amp; typeIdInOut, RegInfo&amp; regInfo) noexcept;</a>
+<a name="214"><span class="lineNum">     214 </span>            : };</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : //! \}</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : } // asmjit namespace</a>
+<a name="219"><span class="lineNum">     219 </span>            : } // namespace PLMD</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : // [Api-End]</a>
+<a name="222"><span class="lineNum">     222 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : // [Guard]</a>
+<a name="225"><span class="lineNum">     225 </span>            : #endif // _ASMJIT_BASE_ARCH_H</a>
+<a name="226"><span class="lineNum">     226 </span>            : #pragma GCC diagnostic pop</a>
+<a name="227"><span class="lineNum">     227 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="228"><span class="lineNum">     228 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/assembler.cpp.func-sort-c.html b/coverage-libs/asmjit/assembler.cpp.func-sort-c.html
new file mode 100644
index 0000000000..aa7b517198
--- /dev/null
+++ b/coverage-libs/asmjit/assembler.cpp.func-sort-c.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/assembler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - assembler.cpp<span style="font-size: 80%;"> (<a href="assembler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">174</td>
+            <td class="headerCovTableEntryLo">23.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="assembler.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#307">_ZN4PLMD6asmjit9Assembler10embedLabelERKNS0_5LabelE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#430">_ZN4PLMD6asmjit9Assembler11_emitFailedEjjjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#199">_ZN4PLMD6asmjit9Assembler13newNamedLabelEPKcmjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#354">_ZN4PLMD6asmjit9Assembler14embedConstPoolERKNS0_5LabelERKNS0_9ConstPoolE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#94">_ZN4PLMD6asmjit9Assembler5_emitEjRKNS0_8Operand_ES4_S4_S4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#288">_ZN4PLMD6asmjit9Assembler5embedEPKvj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#167">_ZN4PLMD6asmjit9Assembler7commentEPKcm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#386">_ZN4PLMD6asmjit9Assembler8_emitLogEjjRKNS0_8Operand_ES4_S4_S4_jjPh</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#189">_ZN4PLMD6asmjit9Assembler8newLabelEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#78">_ZN4PLMD6asmjit9Assembler8onDetachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#146">_ZN4PLMD6asmjit9Assembler9setOffsetEm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#55">_ZN4PLMD6asmjit9AssemblerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#63">_ZN4PLMD6asmjit9Assembler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#46">_ZN4PLMD6asmjit9AssemblerC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#55">_ZN4PLMD6asmjit9AssemblerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#209">_ZN4PLMD6asmjit9Assembler4bindERKNS0_5LabelE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#131">_ZN4PLMD6asmjit9Assembler4syncEv</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#101">_ZN4PLMD6asmjit9Assembler12_emitOpArrayEjPKNS0_8Operand_Em</a></td>
+              <td class="coverFnHi">48362</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/assembler.cpp.func.html b/coverage-libs/asmjit/assembler.cpp.func.html
new file mode 100644
index 0000000000..dd7ab87aec
--- /dev/null
+++ b/coverage-libs/asmjit/assembler.cpp.func.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/assembler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - assembler.cpp<span style="font-size: 80%;"> (<a href="assembler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">174</td>
+            <td class="headerCovTableEntryLo">23.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="assembler.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#307">_ZN4PLMD6asmjit9Assembler10embedLabelERKNS0_5LabelE</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="assembler.cpp.gcov.html#430">_ZN4PLMD6asmjit9Assembler11_emitFailedEjjjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#101">_ZN4PLMD6asmjit9Assembler12_emitOpArrayEjPKNS0_8Operand_Em</a></td>
+              <td class="coverFnHi">48362</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#199">_ZN4PLMD6asmjit9Assembler13newNamedLabelEPKcmjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#354">_ZN4PLMD6asmjit9Assembler14embedConstPoolERKNS0_5LabelERKNS0_9ConstPoolE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#209">_ZN4PLMD6asmjit9Assembler4bindERKNS0_5LabelE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#131">_ZN4PLMD6asmjit9Assembler4syncEv</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#94">_ZN4PLMD6asmjit9Assembler5_emitEjRKNS0_8Operand_ES4_S4_S4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#288">_ZN4PLMD6asmjit9Assembler5embedEPKvj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#167">_ZN4PLMD6asmjit9Assembler7commentEPKcm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#386">_ZN4PLMD6asmjit9Assembler8_emitLogEjjRKNS0_8Operand_ES4_S4_S4_jjPh</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#189">_ZN4PLMD6asmjit9Assembler8newLabelEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#63">_ZN4PLMD6asmjit9Assembler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#78">_ZN4PLMD6asmjit9Assembler8onDetachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#146">_ZN4PLMD6asmjit9Assembler9setOffsetEm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#46">_ZN4PLMD6asmjit9AssemblerC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#55">_ZN4PLMD6asmjit9AssemblerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="assembler.cpp.gcov.html#55">_ZN4PLMD6asmjit9AssemblerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/assembler.cpp.gcov.html b/coverage-libs/asmjit/assembler.cpp.gcov.html
new file mode 100644
index 0000000000..c70de8c287
--- /dev/null
+++ b/coverage-libs/asmjit/assembler.cpp.gcov.html
@@ -0,0 +1,549 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/assembler.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - assembler.cpp<span style="font-size: 80%;"> (source / <a href="assembler.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">174</td>
+            <td class="headerCovTableEntryLo">23.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./constpool.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./vmem.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // ============================================================================</a>
+<a name="45"><span class="lineNum">      45 </span>            : // [asmjit::Assembler - Construction / Destruction]</a>
+<a name="46"><span class="lineNum">      46 </span>            : // ============================================================================</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1948 : Assembler::Assembler() noexcept</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   : CodeEmitter(kTypeAssembler),</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1948 :     _section(nullptr),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1948 :     _bufferData(nullptr),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       1948 :     _bufferEnd(nullptr),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       1948 :     _bufferPtr(nullptr),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1948 :     _op4(),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1948 :     _op5() {}</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1948 : Assembler::~Assembler() noexcept {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       1948 :   if (_code) sync();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       1948 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // ============================================================================</a>
+<a name="62"><span class="lineNum">      62 </span>            : // [asmjit::Assembler - Events]</a>
+<a name="63"><span class="lineNum">      63 </span>            : // ============================================================================</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1948 : Error Assembler::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   // Attach to the end of the .text section.</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       1948 :   _section = code-&gt;_sections[0];</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       1948 :   uint8_t* p = _section-&gt;_buffer._data;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       1948 :   _bufferData = p;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1948 :   _bufferEnd  = p + _section-&gt;_buffer._capacity;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       1948 :   _bufferPtr  = p + _section-&gt;_buffer._length;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   _op4.reset();</a>
+<a name="75"><span class="lineNum">      75 </span>            :   _op5.reset();</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1948 :   return Base::onAttach(code);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 : Error Assembler::onDetach(CodeHolder* code) noexcept {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   _section    = nullptr;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   _bufferData = nullptr;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   _bufferEnd  = nullptr;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   _bufferPtr  = nullptr;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   _op4.reset();</a>
+<a name="87"><span class="lineNum">      87 </span>            :   _op5.reset();</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   return Base::onDetach(code);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : // ============================================================================</a>
+<a name="93"><span class="lineNum">      93 </span>            : // [asmjit::Assembler - Code-Generation]</a>
+<a name="94"><span class="lineNum">      94 </span>            : // ============================================================================</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 : Error Assembler::_emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, const Operand_&amp; o5) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   _op4 = o4;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   _op5 = o5;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   _options |= kOptionOp4Op5Used;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   return _emit(instId, o0, o1, o2, o3);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      48362 : Error Assembler::_emitOpArray(uint32_t instId, const Operand_* opArray, size_t opCount) {</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   const Operand_* op = opArray;</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      48362 :   switch (opCount) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1948 :     case 0: return _emit(instId, _none, _none, _none, _none);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       3888 :     case 1: return _emit(instId, op[0], _none, _none, _none);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      42406 :     case 2: return _emit(instId, op[0], op[1], _none, _none);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        120 :     case 3: return _emit(instId, op[0], op[1], op[2], _none);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     case 4: return _emit(instId, op[0], op[1], op[2], op[3]);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     case 5:</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       _op4 = op[4];</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :       _op5.reset();</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :       _options |= kOptionOp4Op5Used;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :       return _emit(instId, op[0], op[1], op[2], op[3]);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     case 6:</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :       _op4 = op[4];</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       _op5 = op[5];</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       _options |= kOptionOp4Op5Used;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :       return _emit(instId, op[0], op[1], op[2], op[3]);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :     default:</a>
+<a name="125"><span class="lineNum">     125 </span>            :       return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : // ============================================================================</a>
+<a name="130"><span class="lineNum">     130 </span>            : // [asmjit::Assembler - Sync]</a>
+<a name="131"><span class="lineNum">     131 </span>            : // ============================================================================</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       3896 : void Assembler::sync() noexcept {</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   ASMJIT_ASSERT(_code != nullptr);                       // Only called by CodeHolder, so we must be attached.</a>
+<a name="135"><span class="lineNum">     135 </span>            :   ASMJIT_ASSERT(_section != nullptr);                    // One section must always be active, no matter what.</a>
+<a name="136"><span class="lineNum">     136 </span>            :   ASMJIT_ASSERT(_bufferData == _section-&gt;_buffer._data); // `_bufferStart` is a shortcut to `_section-&gt;buffer.data`.</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Update only if the current offset is greater than the section length.</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       3896 :   size_t offset = (size_t)(_bufferPtr - _bufferData);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       3896 :   if (_section-&gt;getBuffer().getLength() &lt; offset)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1948 :     _section-&gt;_buffer._length = offset;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       3896 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : // ============================================================================</a>
+<a name="145"><span class="lineNum">     145 </span>            : // [asmjit::Assembler - Code-Buffer]</a>
+<a name="146"><span class="lineNum">     146 </span>            : // ============================================================================</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 : Error Assembler::setOffset(size_t offset) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   size_t length = std::max(_section-&gt;getBuffer().getLength(), getOffset());</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(offset &gt; length))</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidArgument));</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   // If the `Assembler` generated any code the `_bufferPtr` may be higher than</a>
+<a name="156"><span class="lineNum">     156 </span>            :   // the section length stored in `CodeHolder` as it doesn't update it each</a>
+<a name="157"><span class="lineNum">     157 </span>            :   // time it generates machine code. This is the same as calling `sync()`.</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :   if (_section-&gt;_buffer._length &lt; length)</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     _section-&gt;_buffer._length = length;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   _bufferPtr = _bufferData + offset;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : // ============================================================================</a>
+<a name="166"><span class="lineNum">     166 </span>            : // [asmjit::Assembler - Comment]</a>
+<a name="167"><span class="lineNum">     167 </span>            : // ============================================================================</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 : Error Assembler::comment(const char* s, size_t len) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :     Logger* logger = _code-&gt;getLogger();</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     logger-&gt;log(s, len);</a>
+<a name="176"><span class="lineNum">     176 </span>            :     logger-&gt;log(&quot;\n&quot;, 1);</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            : #else</a>
+<a name="180"><span class="lineNum">     180 </span>            :   ASMJIT_UNUSED(s);</a>
+<a name="181"><span class="lineNum">     181 </span>            :   ASMJIT_UNUSED(len);</a>
+<a name="182"><span class="lineNum">     182 </span>            : #endif</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :   return kErrorOk;</a>
+<a name="185"><span class="lineNum">     185 </span>            : }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : // ============================================================================</a>
+<a name="188"><span class="lineNum">     188 </span>            : // [asmjit::Assembler - Building Blocks]</a>
+<a name="189"><span class="lineNum">     189 </span>            : // ============================================================================</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 : Label Assembler::newLabel() {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :   uint32_t id = 0;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :   if (!_lastError) {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     Error err = _code-&gt;newLabelId(id);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(err)) setLastError(err);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :   return Label(id);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 : Label Assembler::newNamedLabel(const char* name, size_t nameLength, uint32_t type, uint32_t parentId) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   uint32_t id = 0;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :   if (!_lastError) {</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :     ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :     Error err = _code-&gt;newNamedLabelId(id, name, nameLength, type, parentId);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(err)) setLastError(err);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :   return Label(id);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       3896 : Error Assembler::bind(const Label&amp; label) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       3896 :   if (_lastError) return _lastError;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       3896 :   LabelEntry* le = _code-&gt;getLabelEntry(label);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       3896 :   if (ASMJIT_UNLIKELY(!le))</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidLabel));</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :   // Label can be bound only once.</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       3896 :   if (ASMJIT_UNLIKELY(le-&gt;isBound()))</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorLabelAlreadyBound));</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       3896 :   if (_globalOptions &amp; kOptionLoggingEnabled) {</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     if (le-&gt;hasName())</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       sb.setFormat(&quot;%s:&quot;, le-&gt;getName());</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     else</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       sb.setFormat(&quot;L%u:&quot;, Operand::unpackId(label.getId()));</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :     size_t binSize = 0;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     if (!_code-&gt;_logger-&gt;hasOption(Logger::kOptionBinaryForm))</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :       binSize = Globals::kInvalidIndex;</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :     Logging::formatLine(sb, nullptr, binSize, 0, 0, getInlineComment());</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :     _code-&gt;_logger-&gt;log(sb.getData(), sb.getLength());</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   Error err = kErrorOk;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   size_t pos = getOffset();</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       3896 :   LabelLink* link = le-&gt;_links;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   LabelLink* prev = nullptr;</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">       3896 :   while (link) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :     intptr_t offset = link-&gt;offset;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :     uint32_t relocId = link-&gt;relocId;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :     if (relocId != RelocEntry::kInvalidId) {</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :       // Adjust relocation data.</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :       RelocEntry* re = _code-&gt;_relocations[relocId];</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :       re-&gt;_data += static_cast&lt;uint64_t&gt;(pos);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :     }</a>
+<a name="255"><span class="lineNum">     255 </span>            :     else {</a>
+<a name="256"><span class="lineNum">     256 </span>            :       // Not using relocId, this means that we are overwriting a real</a>
+<a name="257"><span class="lineNum">     257 </span>            :       // displacement in the CodeBuffer.</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :       int32_t patchedValue = static_cast&lt;int32_t&gt;(</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :         static_cast&lt;intptr_t&gt;(pos) - offset + link-&gt;rel);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :       // Size of the value we are going to patch. Only BYTE/DWORD is allowed.</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :       uint32_t size = _bufferData[offset];</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :       if (size == 4)</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :         Utils::writeI32u(_bufferData + offset, static_cast&lt;int32_t&gt;(patchedValue));</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :       else if (size == 1 &amp;&amp; Utils::isInt8(patchedValue))</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :         _bufferData[offset] = static_cast&lt;uint8_t&gt;(patchedValue &amp; 0xFF);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :       else</a>
+<a name="268"><span class="lineNum">     268 </span>            :         err = DebugUtils::errored(kErrorInvalidDisplacement);</a>
+<a name="269"><span class="lineNum">     269 </span>            :     }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :     prev = link-&gt;prev;</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     _code-&gt;_unresolvedLabelsCount--;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :     _code-&gt;_baseHeap.release(link, sizeof(LabelLink));</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :     link = prev;</a>
+<a name="276"><span class="lineNum">     276 </span>            :   }</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   // Set as bound.</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       3896 :   le-&gt;_sectionId = _section-&gt;getId();</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       3896 :   le-&gt;_offset = pos;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       3896 :   le-&gt;_links = nullptr;</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :   resetInlineComment();</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       3896 :   if (err != kErrorOk)</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :     return setLastError(err);</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :   return kErrorOk;</a>
+<a name="288"><span class="lineNum">     288 </span>            : }</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 : Error Assembler::embed(const void* data, uint32_t size) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :   if (getRemainingSpace() &lt; size) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :     Error err = _code-&gt;growBuffer(&amp;_section-&gt;_buffer, size);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(err != kErrorOk)) return setLastError(err);</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :   }</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :   ::memcpy(_bufferPtr, data, size);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :   _bufferPtr += size;</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled)</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :     _code-&gt;_logger-&gt;logBinary(data, size);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :   return kErrorOk;</a>
+<a name="307"><span class="lineNum">     307 </span>            : }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 : Error Assembler::embedLabel(const Label&amp; label) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   RelocEntry* re;</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :   LabelEntry* le = _code-&gt;getLabelEntry(label);</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!le))</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidLabel));</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :   Error err;</a>
+<a name="320"><span class="lineNum">     320 </span>            :   uint32_t gpSize = getGpSize();</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :   if (getRemainingSpace() &lt; gpSize) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     err = _code-&gt;growBuffer(&amp;_section-&gt;_buffer, gpSize);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :   }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled)</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :     _code-&gt;_logger-&gt;logf(gpSize == 4 ? &quot;.dd L%u\n&quot; : &quot;.dq L%u\n&quot;, Operand::unpackId(label.getId()));</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :   err = _code-&gt;newRelocEntry(&amp;re, RelocEntry::kTypeRelToAbs, gpSize);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :   re-&gt;_sourceSectionId = _section-&gt;getId();</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :   re-&gt;_sourceOffset = static_cast&lt;uint64_t&gt;(getOffset());</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :   if (le-&gt;isBound()) {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :     re-&gt;_targetSectionId = le-&gt;getSectionId();</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :     re-&gt;_data = static_cast&lt;uint64_t&gt;(static_cast&lt;int64_t&gt;(le-&gt;getOffset()));</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :   }</a>
+<a name="342"><span class="lineNum">     342 </span>            :   else {</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :     LabelLink* link = _code-&gt;newLabelLink(le, _section-&gt;getId(), getOffset(), 0);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!link))</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :       return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :     link-&gt;relocId = re-&gt;getId();</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   // Emit dummy DWORD/QWORD depending on the address size.</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :   ::memset(_bufferPtr, 0, gpSize);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :   _bufferPtr += gpSize;</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 : Error Assembler::embedConstPool(const Label&amp; label, const ConstPool&amp; pool) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :   if (!isLabelValid(label))</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :     return DebugUtils::errored(kErrorInvalidLabel);</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(align(kAlignData, static_cast&lt;uint32_t&gt;(pool.getAlignment())));</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(bind(label));</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            :   size_t size = pool.getSize();</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :   if (getRemainingSpace() &lt; size) {</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :     Error err = _code-&gt;growBuffer(&amp;_section-&gt;_buffer, size);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :   }</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :   uint8_t* p = _bufferPtr;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :   pool.fill(p);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled)</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :     _code-&gt;_logger-&gt;logBinary(p, size);</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   _bufferPtr += size;</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : }</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            : // ============================================================================</a>
+<a name="384"><span class="lineNum">     384 </span>            : // [asmjit::Assembler - Emit-Helpers]</a>
+<a name="385"><span class="lineNum">     385 </span>            : // ============================================================================</a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 : void Assembler::_emitLog(</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   uint32_t instId, uint32_t options, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3,</a>
+<a name="390"><span class="lineNum">     390 </span>            :   uint32_t relSize, uint32_t imLen, uint8_t* afterCursor) {</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :   Logger* logger = _code-&gt;getLogger();</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   ASMJIT_ASSERT(logger != nullptr);</a>
+<a name="394"><span class="lineNum">     394 </span>            :   ASMJIT_ASSERT(options &amp; CodeEmitter::kOptionLoggingEnabled);</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="397"><span class="lineNum">     397 </span>            :   uint32_t logOptions = logger-&gt;getOptions();</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :   uint8_t* beforeCursor = _bufferPtr;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :   intptr_t emittedSize = (intptr_t)(afterCursor - beforeCursor);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            :   sb.appendString(logger-&gt;getIndentation());</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            :   Operand_ opArray[6];</a>
+<a name="405"><span class="lineNum">     405 </span>            :   opArray[0].copyFrom(o0);</a>
+<a name="406"><span class="lineNum">     406 </span>            :   opArray[1].copyFrom(o1);</a>
+<a name="407"><span class="lineNum">     407 </span>            :   opArray[2].copyFrom(o2);</a>
+<a name="408"><span class="lineNum">     408 </span>            :   opArray[3].copyFrom(o3);</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :   if (options &amp; kOptionOp4Op5Used) {</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :     opArray[4].copyFrom(_op4);</a>
+<a name="412"><span class="lineNum">     412 </span>            :     opArray[5].copyFrom(_op5);</a>
+<a name="413"><span class="lineNum">     413 </span>            :   }</a>
+<a name="414"><span class="lineNum">     414 </span>            :   else {</a>
+<a name="415"><span class="lineNum">     415 </span>            :     opArray[4].reset();</a>
+<a name="416"><span class="lineNum">     416 </span>            :     opArray[5].reset();</a>
+<a name="417"><span class="lineNum">     417 </span>            :   }</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :   Logging::formatInstruction(</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :     sb, logOptions,</a>
+<a name="421"><span class="lineNum">     421 </span>            :     this, getArchType(),</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :     Inst::Detail(instId, options, _extraReg), opArray, 6);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :   if ((logOptions &amp; Logger::kOptionBinaryForm) != 0)</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :     Logging::formatLine(sb, _bufferPtr, emittedSize, relSize, imLen, getInlineComment());</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :   else</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :     Logging::formatLine(sb, nullptr, Globals::kInvalidIndex, 0, 0, getInlineComment());</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            :   logger-&gt;log(sb.getData(), sb.getLength());</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 : Error Assembler::_emitFailed(</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :   Error err,</a>
+<a name="434"><span class="lineNum">     434 </span>            :   uint32_t instId, uint32_t options, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) {</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            :   StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :   sb.appendString(DebugUtils::errorAsString(err));</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :   sb.appendString(&quot;: &quot;);</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span>            :   Operand_ opArray[6];</a>
+<a name="441"><span class="lineNum">     441 </span>            :   opArray[0].copyFrom(o0);</a>
+<a name="442"><span class="lineNum">     442 </span>            :   opArray[1].copyFrom(o1);</a>
+<a name="443"><span class="lineNum">     443 </span>            :   opArray[2].copyFrom(o2);</a>
+<a name="444"><span class="lineNum">     444 </span>            :   opArray[3].copyFrom(o3);</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :   if (options &amp; kOptionOp4Op5Used) {</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :     opArray[4].copyFrom(_op4);</a>
+<a name="448"><span class="lineNum">     448 </span>            :     opArray[5].copyFrom(_op5);</a>
+<a name="449"><span class="lineNum">     449 </span>            :   }</a>
+<a name="450"><span class="lineNum">     450 </span>            :   else {</a>
+<a name="451"><span class="lineNum">     451 </span>            :     opArray[4].reset();</a>
+<a name="452"><span class="lineNum">     452 </span>            :     opArray[5].reset();</a>
+<a name="453"><span class="lineNum">     453 </span>            :   }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :   Logging::formatInstruction(</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :     sb, 0,</a>
+<a name="457"><span class="lineNum">     457 </span>            :     this, getArchType(),</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 :     Inst::Detail(instId, options, _extraReg), opArray, 6);</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   resetOptions();</a>
+<a name="461"><span class="lineNum">     461 </span>            :   resetExtraReg();</a>
+<a name="462"><span class="lineNum">     462 </span>            :   resetInlineComment();</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :   return setLastError(err, sb.getData());</span></a>
+<a name="464"><span class="lineNum">     464 </span>            : }</a>
+<a name="465"><span class="lineNum">     465 </span>            : #endif</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span>            : } // asmjit namespace</a>
+<a name="468"><span class="lineNum">     468 </span>            : } // namespace PLMD</a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            : // [Api-End]</a>
+<a name="471"><span class="lineNum">     471 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="472"><span class="lineNum">     472 </span>            : #pragma GCC diagnostic pop</a>
+<a name="473"><span class="lineNum">     473 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/assembler.h.func-sort-c.html b/coverage-libs/asmjit/assembler.h.func-sort-c.html
new file mode 100644
index 0000000000..bff6ac86d4
--- /dev/null
+++ b/coverage-libs/asmjit/assembler.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/assembler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - assembler.h<span style="font-size: 80%;"> (<a href="assembler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="assembler.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/assembler.h.func.html b/coverage-libs/asmjit/assembler.h.func.html
new file mode 100644
index 0000000000..f441cdb02c
--- /dev/null
+++ b/coverage-libs/asmjit/assembler.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/assembler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - assembler.h<span style="font-size: 80%;"> (<a href="assembler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="assembler.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/assembler.h.gcov.html b/coverage-libs/asmjit/assembler.h.gcov.html
new file mode 100644
index 0000000000..64cd1b026c
--- /dev/null
+++ b/coverage-libs/asmjit/assembler.h.gcov.html
@@ -0,0 +1,259 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/assembler.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - assembler.h<span style="font-size: 80%;"> (source / <a href="assembler.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_assembler_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_assembler_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_ASSEMBLER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_ASSEMBLER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./codeemitter.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./codeholder.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./simdtypes.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : // [Api-Begin]</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace asmjit {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : //! \addtogroup asmjit_base</a>
+<a name="48"><span class="lineNum">      48 </span>            : //! \{</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : // [asmjit::Assembler]</a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : //! Base assembler.</a>
+<a name="55"><span class="lineNum">      55 </span>            : //!</a>
+<a name="56"><span class="lineNum">      56 </span>            : //! This class implements a base interface that is used by architecture</a>
+<a name="57"><span class="lineNum">      57 </span>            : //! specific assemblers.</a>
+<a name="58"><span class="lineNum">      58 </span>            : //!</a>
+<a name="59"><span class="lineNum">      59 </span>            : //! \sa CodeCompiler.</a>
+<a name="60"><span class="lineNum">      60 </span>            : class ASMJIT_VIRTAPI Assembler : public CodeEmitter {</a>
+<a name="61"><span class="lineNum">      61 </span>            : public:</a>
+<a name="62"><span class="lineNum">      62 </span>            :   ASMJIT_NONCOPYABLE(Assembler)</a>
+<a name="63"><span class="lineNum">      63 </span>            :   typedef CodeEmitter Base;</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="66"><span class="lineNum">      66 </span>            :   // [Construction / Destruction]</a>
+<a name="67"><span class="lineNum">      67 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            :   //! Create a new `Assembler` instance.</a>
+<a name="70"><span class="lineNum">      70 </span>            :   ASMJIT_API Assembler() noexcept;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   //! Destroy the `Assembler` instance.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   ASMJIT_API virtual ~Assembler() noexcept;</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="75"><span class="lineNum">      75 </span>            :   // [Events]</a>
+<a name="76"><span class="lineNum">      76 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   ASMJIT_API Error onAttach(CodeHolder* code) noexcept override;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ASMJIT_API Error onDetach(CodeHolder* code) noexcept override;</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="82"><span class="lineNum">      82 </span>            :   // [Code-Generation]</a>
+<a name="83"><span class="lineNum">      83 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   using CodeEmitter::_emit;</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   ASMJIT_API Error _emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, const Operand_&amp; o5) override;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ASMJIT_API Error _emitOpArray(uint32_t instId, const Operand_* opArray, size_t opCount) override;</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // [Code-Buffer]</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Called by \ref CodeHolder::sync().</a>
+<a name="95"><span class="lineNum">      95 </span>            :   ASMJIT_API virtual void sync() noexcept;</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   //! Get the capacity of the current CodeBuffer.</a>
+<a name="98"><span class="lineNum">      98 </span>            :   ASMJIT_INLINE size_t getBufferCapacity() const noexcept { return (size_t)(_bufferEnd - _bufferData); }</a>
+<a name="99"><span class="lineNum">      99 </span>            :   //! Get the number of remaining bytes in the current CodeBuffer.</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE size_t getRemainingSpace() const noexcept { return (size_t)(_bufferEnd - _bufferPtr); }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   //! Get the current position in the CodeBuffer.</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       5844 :   ASMJIT_INLINE size_t getOffset() const noexcept { return (size_t)(_bufferPtr - _bufferData); }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   //! Set the current position in the CodeBuffer to `offset`.</a>
+<a name="105"><span class="lineNum">     105 </span>            :   //!</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //! NOTE: The `offset` cannot be outside of the buffer length (even if it's</a>
+<a name="107"><span class="lineNum">     107 </span>            :   //! within buffer's capacity).</a>
+<a name="108"><span class="lineNum">     108 </span>            :   ASMJIT_API Error setOffset(size_t offset);</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   //! Get start of the CodeBuffer of the current section.</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ASMJIT_INLINE uint8_t* getBufferData() const noexcept { return _bufferData; }</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //! Get end (first invalid byte) of the current section.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ASMJIT_INLINE uint8_t* getBufferEnd() const noexcept { return _bufferEnd; }</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //! Get pointer in the CodeBuffer of the current section.</a>
+<a name="115"><span class="lineNum">     115 </span>            :   ASMJIT_INLINE uint8_t* getBufferPtr() const noexcept { return _bufferPtr; }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="118"><span class="lineNum">     118 </span>            :   // [Code-Generation]</a>
+<a name="119"><span class="lineNum">     119 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   ASMJIT_API Label newLabel() override;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   ASMJIT_API Label newNamedLabel(</a>
+<a name="123"><span class="lineNum">     123 </span>            :     const char* name,</a>
+<a name="124"><span class="lineNum">     124 </span>            :     size_t nameLength = Globals::kInvalidIndex,</a>
+<a name="125"><span class="lineNum">     125 </span>            :     uint32_t type = Label::kTypeGlobal,</a>
+<a name="126"><span class="lineNum">     126 </span>            :     uint32_t parentId = 0) override;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   ASMJIT_API Error bind(const Label&amp; label) override;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   ASMJIT_API Error embed(const void* data, uint32_t size) override;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   ASMJIT_API Error embedLabel(const Label&amp; label) override;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   ASMJIT_API Error embedConstPool(const Label&amp; label, const ConstPool&amp; pool) override;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   ASMJIT_API Error comment(const char* s, size_t len = Globals::kInvalidIndex) override;</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="134"><span class="lineNum">     134 </span>            :   // [Emit-Helpers]</a>
+<a name="135"><span class="lineNum">     135 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : protected:</a>
+<a name="138"><span class="lineNum">     138 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void _emitLog(</a>
+<a name="140"><span class="lineNum">     140 </span>            :     uint32_t instId, uint32_t options, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3,</a>
+<a name="141"><span class="lineNum">     141 </span>            :     uint32_t relSize, uint32_t imLen, uint8_t* afterCursor);</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   Error _emitFailed(</a>
+<a name="144"><span class="lineNum">     144 </span>            :     Error err,</a>
+<a name="145"><span class="lineNum">     145 </span>            :     uint32_t instId, uint32_t options, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3);</a>
+<a name="146"><span class="lineNum">     146 </span>            : #else</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ASMJIT_INLINE Error _emitFailed(</a>
+<a name="148"><span class="lineNum">     148 </span>            :     uint32_t err,</a>
+<a name="149"><span class="lineNum">     149 </span>            :     uint32_t instId, uint32_t options, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) {</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :     resetOptions();</a>
+<a name="152"><span class="lineNum">     152 </span>            :     resetInlineComment();</a>
+<a name="153"><span class="lineNum">     153 </span>            :     return setLastError(err);</a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span>            : #endif</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="158"><span class="lineNum">     158 </span>            :   // [Members]</a>
+<a name="159"><span class="lineNum">     159 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : public:</a>
+<a name="162"><span class="lineNum">     162 </span>            :   SectionEntry* _section;                //!&lt; Current section where the assembling happens.</a>
+<a name="163"><span class="lineNum">     163 </span>            :   uint8_t* _bufferData;                  //!&lt; Start of the CodeBuffer of the current section.</a>
+<a name="164"><span class="lineNum">     164 </span>            :   uint8_t* _bufferEnd;                   //!&lt; End (first invalid byte) of the current section.</a>
+<a name="165"><span class="lineNum">     165 </span>            :   uint8_t* _bufferPtr;                   //!&lt; Pointer in the CodeBuffer of the current section.</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   Operand_ _op4;                         //!&lt; 5th operand data, used only temporarily.</a>
+<a name="168"><span class="lineNum">     168 </span>            :   Operand_ _op5;                         //!&lt; 6th operand data, used only temporarily.</a>
+<a name="169"><span class="lineNum">     169 </span>            : };</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : //! \}</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : } // asmjit namespace</a>
+<a name="174"><span class="lineNum">     174 </span>            : } // namespace PLMD</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : // [Api-End]</a>
+<a name="177"><span class="lineNum">     177 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : // [Guard]</a>
+<a name="180"><span class="lineNum">     180 </span>            : #endif // _ASMJIT_BASE_ASSEMBLER_H</a>
+<a name="181"><span class="lineNum">     181 </span>            : #pragma GCC diagnostic pop</a>
+<a name="182"><span class="lineNum">     182 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="183"><span class="lineNum">     183 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codebuilder.cpp.func-sort-c.html b/coverage-libs/asmjit/codebuilder.cpp.func-sort-c.html
new file mode 100644
index 0000000000..91b7acfaac
--- /dev/null
+++ b/coverage-libs/asmjit/codebuilder.cpp.func-sort-c.html
@@ -0,0 +1,204 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codebuilder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codebuilder.cpp<span style="font-size: 80%;"> (<a href="codebuilder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">257</td>
+            <td class="headerCovTableEntryLo">23.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryLo">30.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#135">_ZN4PLMD6asmjit11CodeBuilder12newLabelNodeEv</a></td>
+              <td class="coverFnHi">1948</td>
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+              <td class="coverFnHi">1948</td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage-libs/asmjit/codebuilder.cpp.func.html b/coverage-libs/asmjit/codebuilder.cpp.func.html
new file mode 100644
index 0000000000..b05795b601
--- /dev/null
+++ b/coverage-libs/asmjit/codebuilder.cpp.func.html
@@ -0,0 +1,204 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codebuilder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codebuilder.cpp<span style="font-size: 80%;"> (<a href="codebuilder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">257</td>
+            <td class="headerCovTableEntryLo">23.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryLo">30.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codebuilder.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#502">_ZN4PLMD6asmjit11CodeBuilder10deletePassEPNS0_6CBPassE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#255">_ZN4PLMD6asmjit11CodeBuilder10embedLabelERKNS0_5LabelE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#93">_ZN4PLMD6asmjit11CodeBuilder10getCBLabelEPPNS0_7CBLabelEj</a></td>
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+    <tr>
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+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#233">_ZN4PLMD6asmjit11CodeBuilder5alignEjj</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#244">_ZN4PLMD6asmjit11CodeBuilder5embedEPKvj</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#299">_ZN4PLMD6asmjit11CodeBuilder7addNodeEPNS0_6CBNodeE</a></td>
+              <td class="coverFnHi">56154</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#484">_ZN4PLMD6asmjit11CodeBuilder7addPassEPNS0_6CBPassE</a></td>
+              <td class="coverFnHi">1948</td>
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+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#284">_ZN4PLMD6asmjit11CodeBuilder7commentEPKcm</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#333">_ZN4PLMD6asmjit11CodeBuilder8addAfterEPNS0_6CBNodeES3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#181">_ZN4PLMD6asmjit11CodeBuilder8newLabelEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#66">_ZN4PLMD6asmjit11CodeBuilder8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#70">_ZN4PLMD6asmjit11CodeBuilder8onDetachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#355">_ZN4PLMD6asmjit11CodeBuilder9addBeforeEPNS0_6CBNodeES3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#525">_ZN4PLMD6asmjit11CodeBuilder9serializeEPNS0_11CodeEmitterE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#464">_ZN4PLMD6asmjit11CodeBuilder9setCursorEPNS0_6CBNodeE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#47">_ZN4PLMD6asmjit11CodeBuilderC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#60">_ZN4PLMD6asmjit11CodeBuilderD0Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#60">_ZN4PLMD6asmjit11CodeBuilderD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#594">_ZN4PLMD6asmjit6CBPassC2EPKc</a></td>
+              <td class="coverFnHi">1948</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#597">_ZN4PLMD6asmjit6CBPassD0Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#597">_ZN4PLMD6asmjit6CBPassD2Ev</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codebuilder.cpp.gcov.html#474">_ZNK4PLMD6asmjit11CodeBuilder13getPassByNameEPKc</a></td>
+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codebuilder.cpp.gcov.html b/coverage-libs/asmjit/codebuilder.cpp.gcov.html
new file mode 100644
index 0000000000..ebe70271a6
--- /dev/null
+++ b/coverage-libs/asmjit/codebuilder.cpp.gcov.html
@@ -0,0 +1,686 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codebuilder.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codebuilder.cpp<span style="font-size: 80%;"> (source / <a href="codebuilder.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">257</td>
+            <td class="headerCovTableEntryLo">23.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryLo">30.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if !defined(ASMJIT_DISABLE_BUILDER)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./codebuilder.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // ============================================================================</a>
+<a name="46"><span class="lineNum">      46 </span>            : // [asmjit::CodeBuilder - Construction / Destruction]</a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       1948 : CodeBuilder::CodeBuilder() noexcept</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   : CodeEmitter(kTypeBuilder),</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1948 :     _cbBaseZone(32768 - Zone::kZoneOverhead),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       1948 :     _cbDataZone(16384 - Zone::kZoneOverhead),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       1948 :     _cbPassZone(32768 - Zone::kZoneOverhead),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1948 :     _cbHeap(&amp;_cbBaseZone),</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     _cbPasses(),</a>
+<a name="56"><span class="lineNum">      56 </span>            :     _cbLabels(),</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1948 :     _firstNode(nullptr),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       1948 :     _lastNode(nullptr),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       1948 :     _cursor(nullptr),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       1948 :     _position(0),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1948 :     _nodeFlags(0) {}</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       1948 : CodeBuilder::~CodeBuilder() noexcept {}</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : // ============================================================================</a>
+<a name="65"><span class="lineNum">      65 </span>            : // [asmjit::CodeBuilder - Events]</a>
+<a name="66"><span class="lineNum">      66 </span>            : // ============================================================================</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       1948 : Error CodeBuilder::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1948 :   return Base::onAttach(code);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 : Error CodeBuilder::onDetach(CodeHolder* code) noexcept {</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   _cbPasses.reset();</a>
+<a name="74"><span class="lineNum">      74 </span>            :   _cbLabels.reset();</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   _cbHeap.reset(&amp;_cbBaseZone);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :   _cbBaseZone.reset(false);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   _cbDataZone.reset(false);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   _cbPassZone.reset(false);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   _position = 0;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   _nodeFlags = 0;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   _firstNode = nullptr;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   _lastNode = nullptr;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   _cursor = nullptr;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :   return Base::onDetach(code);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : // ============================================================================</a>
+<a name="92"><span class="lineNum">      92 </span>            : // [asmjit::CodeBuilder - Node-Factory]</a>
+<a name="93"><span class="lineNum">      93 </span>            : // ============================================================================</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 : Error CodeBuilder::getCBLabel(CBLabel** pOut, uint32_t id) noexcept {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   size_t index = Operand::unpackId(id);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(index &gt;= _code-&gt;getLabelsCount()))</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     return DebugUtils::errored(kErrorInvalidLabel);</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   if (index &gt;= _cbLabels.getLength())</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(_cbLabels.resize(&amp;_cbHeap, index + 1));</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   CBLabel* node = _cbLabels[index];</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   if (!node) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :     node = newNodeT&lt;CBLabel&gt;(id);</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :       return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     _cbLabels[index] = node;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   *pOut = node;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       3896 : Error CodeBuilder::registerLabelNode(CBLabel* node) noexcept {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       3896 :   if (_lastError) return _lastError;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   // Don't call setLastError() from here, we are noexcept and we are called</a>
+<a name="123"><span class="lineNum">     123 </span>            :   // by `newLabelNode()` and `newFuncNode()`, which are noexcept as well.</a>
+<a name="124"><span class="lineNum">     124 </span>            :   uint32_t id;</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       3896 :   ASMJIT_PROPAGATE(_code-&gt;newLabelId(id));</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       3896 :   size_t index = Operand::unpackId(id);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   // We just added one label so it must be true.</a>
+<a name="129"><span class="lineNum">     129 </span>            :   ASMJIT_ASSERT(_cbLabels.getLength() &lt; index + 1);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       3896 :   ASMJIT_PROPAGATE(_cbLabels.resize(&amp;_cbHeap, index + 1));</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       3896 :   _cbLabels[index] = node;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       3896 :   node-&gt;_id = id;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       3896 :   return kErrorOk;</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1948 : CBLabel* CodeBuilder::newLabelNode() noexcept {</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   CBLabel* node = newNodeT&lt;CBLabel&gt;();</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       1948 :   if (!node || registerLabelNode(node) != kErrorOk)</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   return node;</a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 : CBAlign* CodeBuilder::newAlignNode(uint32_t mode, uint32_t alignment) noexcept {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   return newNodeT&lt;CBAlign&gt;(mode, alignment);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 : CBData* CodeBuilder::newDataNode(const void* data, uint32_t size) noexcept {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   if (size &gt; CBData::kInlineBufferSize) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :     void* cloned = _cbDataZone.alloc(size);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     if (!cloned) return nullptr;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :     if (data) ::memcpy(cloned, data, size);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     data = cloned;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   return newNodeT&lt;CBData&gt;(const_cast&lt;void*&gt;(data), size);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 : CBConstPool* CodeBuilder::newConstPool() noexcept {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   CBConstPool* node = newNodeT&lt;CBConstPool&gt;();</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :   if (!node || registerLabelNode(node) != kErrorOk)</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   return node;</a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 : CBComment* CodeBuilder::newCommentNode(const char* s, size_t len) noexcept {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :   if (s) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     if (len == Globals::kInvalidIndex) len = ::strlen(s);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     if (len &gt; 0) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :       s = static_cast&lt;char*&gt;(_cbDataZone.dup(s, len, true));</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :       if (!s) return nullptr;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     }</a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :   return newNodeT&lt;CBComment&gt;(s);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : // ============================================================================</a>
+<a name="180"><span class="lineNum">     180 </span>            : // [asmjit::CodeBuilder - Code-Emitter]</a>
+<a name="181"><span class="lineNum">     181 </span>            : // ============================================================================</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 : Label CodeBuilder::newLabel() {</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   uint32_t id = kInvalidValue;</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   if (!_lastError) {</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     CBLabel* node = newNodeT&lt;CBLabel&gt;(id);</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!node)) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :       setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :     }</a>
+<a name="191"><span class="lineNum">     191 </span>            :     else {</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :       Error err = registerLabelNode(node);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(err))</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :         setLastError(err);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :       else</a>
+<a name="196"><span class="lineNum">     196 </span>            :         id = node-&gt;getId();</a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :   return Label(id);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 : Label CodeBuilder::newNamedLabel(const char* name, size_t nameLength, uint32_t type, uint32_t parentId) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   uint32_t id = kInvalidValue;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :   if (!_lastError) {</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     CBLabel* node = newNodeT&lt;CBLabel&gt;(id);</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!node)) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     }</a>
+<a name="211"><span class="lineNum">     211 </span>            :     else {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       Error err = _code-&gt;newNamedLabelId(id, name, nameLength, type, parentId);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(err))</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :         setLastError(err);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :       else</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :         id = node-&gt;getId();</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     }</a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :   return Label(id);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 : Error CodeBuilder::bind(const Label&amp; label) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            :   CBLabel* node;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   Error err = getCBLabel(&amp;node, label);</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(err))</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     return setLastError(err);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 : Error CodeBuilder::align(uint32_t mode, uint32_t alignment) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :   CBAlign* node = newAlignNode(mode, alignment);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 : Error CodeBuilder::embed(const void* data, uint32_t size) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   CBData* node = newDataNode(data, size);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 : Error CodeBuilder::embedLabel(const Label&amp; label) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            :   CBLabelData* node = newNodeT&lt;CBLabelData&gt;(label.getId());</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 : Error CodeBuilder::embedConstPool(const Label&amp; label, const ConstPool&amp; pool) {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :   if (!isLabelValid(label))</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidLabel));</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(align(kAlignData, static_cast&lt;uint32_t&gt;(pool.getAlignment())));</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(bind(label));</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :   CBData* node = newDataNode(nullptr, static_cast&lt;uint32_t&gt;(pool.getSize()));</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :   pool.fill(node-&gt;getData());</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            : }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 : Error CodeBuilder::comment(const char* s, size_t len) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :   if (_lastError) return _lastError;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :   CBComment* node = newCommentNode(s, len);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : // ============================================================================</a>
+<a name="298"><span class="lineNum">     298 </span>            : // [asmjit::CodeBuilder - Node-Management]</a>
+<a name="299"><span class="lineNum">     299 </span>            : // ============================================================================</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">      56154 : CBNode* CodeBuilder::addNode(CBNode* node) noexcept {</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   ASMJIT_ASSERT(node);</a>
+<a name="303"><span class="lineNum">     303 </span>            :   ASMJIT_ASSERT(node-&gt;_prev == nullptr);</a>
+<a name="304"><span class="lineNum">     304 </span>            :   ASMJIT_ASSERT(node-&gt;_next == nullptr);</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">      56154 :   if (!_cursor) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       1948 :     if (!_firstNode) {</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       1948 :       _firstNode = node;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1948 :       _lastNode = node;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     }</a>
+<a name="311"><span class="lineNum">     311 </span>            :     else {</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :       node-&gt;_next = _firstNode;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :       _firstNode-&gt;_prev = node;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :       _firstNode = node;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :     }</a>
+<a name="316"><span class="lineNum">     316 </span>            :   }</a>
+<a name="317"><span class="lineNum">     317 </span>            :   else {</a>
+<a name="318"><span class="lineNum">     318 </span>            :     CBNode* prev = _cursor;</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">      54206 :     CBNode* next = _cursor-&gt;_next;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">      54206 :     node-&gt;_prev = prev;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      54206 :     node-&gt;_next = next;</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      54206 :     prev-&gt;_next = node;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      54206 :     if (next)</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">      50310 :       next-&gt;_prev = node;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     else</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       3896 :       _lastNode = node;</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   }</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">      56154 :   _cursor = node;</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      56154 :   return node;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 : CBNode* CodeBuilder::addAfter(CBNode* node, CBNode* ref) noexcept {</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   ASMJIT_ASSERT(node);</a>
+<a name="337"><span class="lineNum">     337 </span>            :   ASMJIT_ASSERT(ref);</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            :   ASMJIT_ASSERT(node-&gt;_prev == nullptr);</a>
+<a name="340"><span class="lineNum">     340 </span>            :   ASMJIT_ASSERT(node-&gt;_next == nullptr);</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            :   CBNode* prev = ref;</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :   CBNode* next = ref-&gt;_next;</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   node-&gt;_prev = prev;</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   node-&gt;_next = next;</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :   prev-&gt;_next = node;</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   if (next)</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :     next-&gt;_prev = node;</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :   else</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :     _lastNode = node;</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :   return node;</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 : CBNode* CodeBuilder::addBefore(CBNode* node, CBNode* ref) noexcept {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   ASMJIT_ASSERT(node != nullptr);</a>
+<a name="359"><span class="lineNum">     359 </span>            :   ASMJIT_ASSERT(node-&gt;_prev == nullptr);</a>
+<a name="360"><span class="lineNum">     360 </span>            :   ASMJIT_ASSERT(node-&gt;_next == nullptr);</a>
+<a name="361"><span class="lineNum">     361 </span>            :   ASMJIT_ASSERT(ref != nullptr);</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   CBNode* prev = ref-&gt;_prev;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   CBNode* next = ref;</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :   node-&gt;_prev = prev;</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :   node-&gt;_next = next;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :   next-&gt;_prev = node;</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :   if (prev)</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :     prev-&gt;_next = node;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   else</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :     _firstNode = node;</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :   return node;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : static ASMJIT_INLINE void CodeBuilder_nodeRemoved(CodeBuilder* self, CBNode* node_) noexcept {</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   if (node_-&gt;isJmpOrJcc()) {</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :     CBJump* node = static_cast&lt;CBJump*&gt;(node_);</a>
+<a name="381"><span class="lineNum">     381 </span>            :     CBLabel* label = node-&gt;getTarget();</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :     if (label) {</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :       // Disconnect.</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :       CBJump** pPrev = &amp;label-&gt;_from;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :       for (;;) {</a>
+<a name="387"><span class="lineNum">     387 </span>            :         ASMJIT_ASSERT(*pPrev != nullptr);</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :         CBJump* current = *pPrev;</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :         if (!current) break;</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :         if (current == node) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :           *pPrev = node-&gt;_jumpNext;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :           break;</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :         }</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :         pPrev = &amp;current-&gt;_jumpNext;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :       label-&gt;subNumRefs();</a>
+<a name="401"><span class="lineNum">     401 </span>            :     }</a>
+<a name="402"><span class="lineNum">     402 </span>            :   }</a>
+<a name="403"><span class="lineNum">     403 </span>            : }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 : CBNode* CodeBuilder::removeNode(CBNode* node) noexcept {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineNoCov">          0 :   CBNode* prev = node-&gt;_prev;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :   CBNode* next = node-&gt;_next;</span></a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :   if (_firstNode == node)</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :     _firstNode = next;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :   else</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :     prev-&gt;_next = next;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :   if (_lastNode == node)</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :     _lastNode  = prev;</span></a>
+<a name="416"><span class="lineNum">     416 </span>            :   else</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :     next-&gt;_prev = prev;</span></a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :   node-&gt;_prev = nullptr;</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :   node-&gt;_next = nullptr;</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :   if (_cursor == node)</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :     _cursor = prev;</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :   CodeBuilder_nodeRemoved(this, node);</a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :   return node;</span></a>
+<a name="427"><span class="lineNum">     427 </span>            : }</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 : void CodeBuilder::removeNodes(CBNode* first, CBNode* last) noexcept {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :   if (first == last) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :     removeNode(first);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :   }</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :   CBNode* prev = first-&gt;_prev;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :   CBNode* next = last-&gt;_next;</span></a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :   if (_firstNode == first)</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :     _firstNode = next;</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   else</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :     prev-&gt;_next = next;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :   if (_lastNode == last)</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :     _lastNode  = prev;</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   else</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     next-&gt;_prev = prev;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            :   CBNode* node = first;</a>
+<a name="449"><span class="lineNum">     449 </span>            :   for (;;) {</a>
+<a name="450"><span class="lineNum">     450 </span>            :     CBNode* next = node-&gt;getNext();</a>
+<a name="451"><span class="lineNum">     451 </span>            :     ASMJIT_ASSERT(next != nullptr);</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :     node-&gt;_prev = nullptr;</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :     node-&gt;_next = nullptr;</span></a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :     if (_cursor == node)</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :       _cursor = prev;</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :     CodeBuilder_nodeRemoved(this, node);</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :     if (node == last)</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :       break;</a>
+<a name="462"><span class="lineNum">     462 </span>            :     node = next;</a>
+<a name="463"><span class="lineNum">     463 </span>            :   }</a>
+<a name="464"><span class="lineNum">     464 </span>            : }</a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">       3896 : CBNode* CodeBuilder::setCursor(CBNode* node) noexcept {</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">       3896 :   CBNode* old = _cursor;</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">       3896 :   _cursor = node;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">       3896 :   return old;</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : }</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            : // ============================================================================</a>
+<a name="473"><span class="lineNum">     473 </span>            : // [asmjit::CodeBuilder - Passes]</a>
+<a name="474"><span class="lineNum">     474 </span>            : // ============================================================================</a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE CBPass* CodeBuilder::getPassByName(const char* name) const noexcept {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   for (size_t i = 0, len = _cbPasses.getLength(); i &lt; len; i++) {</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :     CBPass* pass = _cbPasses[i];</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :     if (::strcmp(pass-&gt;getName(), name) == 0)</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 :       return pass;</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :   }</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            :   return nullptr;</a>
+<a name="484"><span class="lineNum">     484 </span>            : }</a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error CodeBuilder::addPass(CBPass* pass) noexcept {</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(pass == nullptr)) {</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :     // Since this is directly called by `addPassT()` we treat `null` argument</a>
+<a name="489"><span class="lineNum">     489 </span>            :     // as out-of-memory condition. Otherwise it would be API misuse.</a>
+<a name="490"><span class="lineNum">     490 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="491"><span class="lineNum">     491 </span>            :   }</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">       1948 :   else if (ASMJIT_UNLIKELY(pass-&gt;_cb)) {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :     // Kind of weird, but okay...</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :     if (pass-&gt;_cb == this)</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineNoCov">          0 :       return kErrorOk;</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="497"><span class="lineNum">     497 </span>            :   }</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">       1948 :   ASMJIT_PROPAGATE(_cbPasses.append(&amp;_cbHeap, pass));</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">       1948 :   pass-&gt;_cb = this;</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : }</a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error CodeBuilder::deletePass(CBPass* pass) noexcept {</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(pass == nullptr))</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineNoCov">          0 :   if (pass-&gt;_cb != nullptr) {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :     if (pass-&gt;_cb != this)</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :       return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            :     size_t index = _cbPasses.indexOf(pass);</a>
+<a name="513"><span class="lineNum">     513 </span>            :     ASMJIT_ASSERT(index != Globals::kInvalidIndex);</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :     pass-&gt;_cb = nullptr;</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :     _cbPasses.removeAt(index);</a>
+<a name="517"><span class="lineNum">     517 </span>            :   }</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :   pass-&gt;~CBPass();</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="521"><span class="lineNum">     521 </span>            : }</a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span>            : // ============================================================================</a>
+<a name="524"><span class="lineNum">     524 </span>            : // [asmjit::CodeBuilder - Serialization]</a>
+<a name="525"><span class="lineNum">     525 </span>            : // ============================================================================</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">       1948 : Error CodeBuilder::serialize(CodeEmitter* dst) {</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :   Error err = kErrorOk;</a>
+<a name="529"><span class="lineNum">     529 </span>            :   CBNode* node_ = getFirstNode();</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   do {</a>
+<a name="532"><span class="lineNum">     532 </span>            :     dst-&gt;setInlineComment(node_-&gt;getInlineComment());</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">      56154 :     switch (node_-&gt;getType()) {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :       case CBNode::kNodeAlign: {</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :         CBAlign* node = static_cast&lt;CBAlign*&gt;(node_);</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :         err = dst-&gt;align(node-&gt;getMode(), node-&gt;getAlignment());</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :       }</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :       case CBNode::kNodeData: {</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :         CBData* node = static_cast&lt;CBData*&gt;(node_);</a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :         err = dst-&gt;embed(node-&gt;getData(), node-&gt;getSize());</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :       }</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">       3896 :       case CBNode::kNodeFunc:</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :       case CBNode::kNodeLabel: {</a>
+<a name="549"><span class="lineNum">     549 </span>            :         CBLabel* node = static_cast&lt;CBLabel*&gt;(node_);</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">       3896 :         err = dst-&gt;bind(node-&gt;getLabel());</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">       3896 :         break;</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :       }</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :       case CBNode::kNodeLabelData: {</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :         CBLabelData* node = static_cast&lt;CBLabelData*&gt;(node_);</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineNoCov">          0 :         err = dst-&gt;embedLabel(node-&gt;getLabel());</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :       }</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineNoCov">          0 :       case CBNode::kNodeConstPool: {</span></a>
+<a name="561"><span class="lineNum">     561 </span>            :         CBConstPool* node = static_cast&lt;CBConstPool*&gt;(node_);</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :         err = dst-&gt;embedConstPool(node-&gt;getLabel(), node-&gt;getConstPool());</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :       }</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span>            :       case CBNode::kNodeInst:</a>
+<a name="567"><span class="lineNum">     567 </span>            :       case CBNode::kNodeFuncCall: {</a>
+<a name="568"><span class="lineNum">     568 </span>            :         CBInst* node = node_-&gt;as&lt;CBInst&gt;();</a>
+<a name="569"><span class="lineNum">     569 </span>            :         dst-&gt;setOptions(node-&gt;getOptions());</a>
+<a name="570"><span class="lineNum">     570 </span>            :         dst-&gt;setExtraReg(node-&gt;getExtraReg());</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">      48362 :         err = dst-&gt;emitOpArray(node-&gt;getInstId(), node-&gt;getOpArray(), node-&gt;getOpCount());</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">      48362 :         break;</span></a>
+<a name="573"><span class="lineNum">     573 </span>            :       }</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :       case CBNode::kNodeComment: {</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :         CBComment* node = static_cast&lt;CBComment*&gt;(node_);</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :         err = dst-&gt;comment(node-&gt;getInlineComment());</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :       }</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            :       default:</a>
+<a name="582"><span class="lineNum">     582 </span>            :         break;</a>
+<a name="583"><span class="lineNum">     583 </span>            :     }</a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">      56154 :     if (err) break;</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :     node_ = node_-&gt;getNext();</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">      56154 :   } while (node_);</span></a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">       1948 :   return err;</span></a>
+<a name="590"><span class="lineNum">     590 </span>            : }</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            : // ============================================================================</a>
+<a name="593"><span class="lineNum">     593 </span>            : // [asmjit::CBPass]</a>
+<a name="594"><span class="lineNum">     594 </span>            : // ============================================================================</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">       1948 : CBPass::CBPass(const char* name) noexcept</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">       1948 :   : _cb(nullptr),</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">       1948 :     _name(name) {}</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 : CBPass::~CBPass() noexcept {}</span></a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span>            : } // asmjit namespace</a>
+<a name="602"><span class="lineNum">     602 </span>            : } // namespace PLMD</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span>            : // [Api-End]</a>
+<a name="605"><span class="lineNum">     605 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span>            : // [Guard]</a>
+<a name="608"><span class="lineNum">     608 </span>            : #endif // !ASMJIT_DISABLE_BUILDER</a>
+<a name="609"><span class="lineNum">     609 </span>            : #pragma GCC diagnostic pop</a>
+<a name="610"><span class="lineNum">     610 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codebuilder.h.func-sort-c.html b/coverage-libs/asmjit/codebuilder.h.func-sort-c.html
new file mode 100644
index 0000000000..fd8d9c153c
--- /dev/null
+++ b/coverage-libs/asmjit/codebuilder.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codebuilder.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codebuilder.h<span style="font-size: 80%;"> (<a href="codebuilder.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryLo">53.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="codebuilder.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codebuilder.h.func.html b/coverage-libs/asmjit/codebuilder.h.func.html
new file mode 100644
index 0000000000..097da50f4a
--- /dev/null
+++ b/coverage-libs/asmjit/codebuilder.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codebuilder.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codebuilder.h<span style="font-size: 80%;"> (<a href="codebuilder.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryLo">53.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codebuilder.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codebuilder.h.gcov.html b/coverage-libs/asmjit/codebuilder.h.gcov.html
new file mode 100644
index 0000000000..9b4e92a202
--- /dev/null
+++ b/coverage-libs/asmjit/codebuilder.h.gcov.html
@@ -0,0 +1,1020 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codebuilder.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codebuilder.h<span style="font-size: 80%;"> (source / <a href="codebuilder.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryLo">53.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_codebuilder_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_codebuilder_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_CODEBUILDER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_CODEBUILDER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if !defined(ASMJIT_DISABLE_BUILDER)</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Dependencies]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./codeholder.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./constpool.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./inst.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;./zone.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // [Api-Begin]</a>
+<a name="48"><span class="lineNum">      48 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace PLMD {</a>
+<a name="51"><span class="lineNum">      51 </span>            : namespace asmjit {</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : // [Forward Declarations]</a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : class CBNode;</a>
+<a name="58"><span class="lineNum">      58 </span>            : class CBPass;</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : class CBAlign;</a>
+<a name="61"><span class="lineNum">      61 </span>            : class CBComment;</a>
+<a name="62"><span class="lineNum">      62 </span>            : class CBConstPool;</a>
+<a name="63"><span class="lineNum">      63 </span>            : class CBData;</a>
+<a name="64"><span class="lineNum">      64 </span>            : class CBInst;</a>
+<a name="65"><span class="lineNum">      65 </span>            : class CBJump;</a>
+<a name="66"><span class="lineNum">      66 </span>            : class CBLabel;</a>
+<a name="67"><span class="lineNum">      67 </span>            : class CBLabelData;</a>
+<a name="68"><span class="lineNum">      68 </span>            : class CBSentinel;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : //! \addtogroup asmjit_base</a>
+<a name="71"><span class="lineNum">      71 </span>            : //! \{</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : // ============================================================================</a>
+<a name="74"><span class="lineNum">      74 </span>            : // [asmjit::CodeBuilder]</a>
+<a name="75"><span class="lineNum">      75 </span>            : // ============================================================================</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : class ASMJIT_VIRTAPI CodeBuilder : public CodeEmitter {</a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ASMJIT_NONCOPYABLE(CodeBuilder)</a>
+<a name="80"><span class="lineNum">      80 </span>            :   typedef CodeEmitter Base;</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="83"><span class="lineNum">      83 </span>            :   // [Construction / Destruction]</a>
+<a name="84"><span class="lineNum">      84 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   //! Create a new `CodeBuilder` instance.</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ASMJIT_API CodeBuilder() noexcept;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   //! Destroy the `CodeBuilder` instance.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   ASMJIT_API virtual ~CodeBuilder() noexcept;</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // [Events]</a>
+<a name="93"><span class="lineNum">      93 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   ASMJIT_API virtual Error onAttach(CodeHolder* code) noexcept override;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   ASMJIT_API virtual Error onDetach(CodeHolder* code) noexcept override;</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="99"><span class="lineNum">      99 </span>            :   // [Accessors]</a>
+<a name="100"><span class="lineNum">     100 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   //! Get a vector of CBPass objects that will be executed by `process()`.</a>
+<a name="103"><span class="lineNum">     103 </span>            :   ASMJIT_INLINE const ZoneVector&lt;CBPass*&gt;&amp; getPasses() const noexcept { return _cbPasses; }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   //! Get a vector of CBLabel nodes.</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //!</a>
+<a name="107"><span class="lineNum">     107 </span>            :   //! NOTE: If a label of some index is not associated with `CodeBuilder` it</a>
+<a name="108"><span class="lineNum">     108 </span>            :   //! would be null, so always check for nulls if you iterate over the vector.</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ASMJIT_INLINE const ZoneVector&lt;CBLabel*&gt;&amp; getLabels() const noexcept { return _cbLabels; }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   //! Get the first node.</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       3896 :   ASMJIT_INLINE CBNode* getFirstNode() const noexcept { return _firstNode; }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Get the last node.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_INLINE CBNode* getLastNode() const noexcept { return _lastNode; }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="117"><span class="lineNum">     117 </span>            :   // [Node-Management]</a>
+<a name="118"><span class="lineNum">     118 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   //! \internal</a>
+<a name="121"><span class="lineNum">     121 </span>            :   template&lt;typename T&gt;</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       3896 :   ASMJIT_INLINE T* newNodeT() noexcept { return new(_cbHeap.alloc(sizeof(T))) T(this); }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   //! \internal</a>
+<a name="125"><span class="lineNum">     125 </span>            :   template&lt;typename T, typename P0&gt;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE T* newNodeT(P0 p0) noexcept { return new(_cbHeap.alloc(sizeof(T))) T(this, p0); }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   //! \internal</a>
+<a name="129"><span class="lineNum">     129 </span>            :   template&lt;typename T, typename P0, typename P1&gt;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       1948 :   ASMJIT_INLINE T* newNodeT(P0 p0, P1 p1) noexcept { return new(_cbHeap.alloc(sizeof(T))) T(this, p0, p1); }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   //! \internal</a>
+<a name="133"><span class="lineNum">     133 </span>            :   template&lt;typename T, typename P0, typename P1, typename P2&gt;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE T* newNodeT(P0 p0, P1 p1, P2 p2) noexcept { return new(_cbHeap.alloc(sizeof(T))) T(this, p0, p1, p2); }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   ASMJIT_API Error registerLabelNode(CBLabel* node) noexcept;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   //! Get `CBLabel` by `id`.</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ASMJIT_API Error getCBLabel(CBLabel** pOut, uint32_t id) noexcept;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   //! Get `CBLabel` by `label`.</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Error getCBLabel(CBLabel** pOut, const Label&amp; label) noexcept { return getCBLabel(pOut, label.getId()); }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   //! Create a new \ref CBLabel node.</a>
+<a name="143"><span class="lineNum">     143 </span>            :   ASMJIT_API CBLabel* newLabelNode() noexcept;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   //! Create a new \ref CBAlign node.</a>
+<a name="145"><span class="lineNum">     145 </span>            :   ASMJIT_API CBAlign* newAlignNode(uint32_t mode, uint32_t alignment) noexcept;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! Create a new \ref CBData node.</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ASMJIT_API CBData* newDataNode(const void* data, uint32_t size) noexcept;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   //! Create a new \ref CBConstPool node.</a>
+<a name="149"><span class="lineNum">     149 </span>            :   ASMJIT_API CBConstPool* newConstPool() noexcept;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   //! Create a new \ref CBComment node.</a>
+<a name="151"><span class="lineNum">     151 </span>            :   ASMJIT_API CBComment* newCommentNode(const char* s, size_t len) noexcept;</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="154"><span class="lineNum">     154 </span>            :   // [Code-Emitter]</a>
+<a name="155"><span class="lineNum">     155 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   ASMJIT_API virtual Label newLabel() override;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   ASMJIT_API virtual Label newNamedLabel(const char* name, size_t nameLength = Globals::kInvalidIndex, uint32_t type = Label::kTypeGlobal, uint32_t parentId = kInvalidValue) override;</a>
+<a name="159"><span class="lineNum">     159 </span>            :   ASMJIT_API virtual Error bind(const Label&amp; label) override;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   ASMJIT_API virtual Error align(uint32_t mode, uint32_t alignment) override;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   ASMJIT_API virtual Error embed(const void* data, uint32_t size) override;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   ASMJIT_API virtual Error embedLabel(const Label&amp; label) override;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   ASMJIT_API virtual Error embedConstPool(const Label&amp; label, const ConstPool&amp; pool) override;</a>
+<a name="164"><span class="lineNum">     164 </span>            :   ASMJIT_API virtual Error comment(const char* s, size_t len = Globals::kInvalidIndex) override;</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="167"><span class="lineNum">     167 </span>            :   // [Node-Management]</a>
+<a name="168"><span class="lineNum">     168 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            :   //! Add `node` after the current and set current to `node`.</a>
+<a name="171"><span class="lineNum">     171 </span>            :   ASMJIT_API CBNode* addNode(CBNode* node) noexcept;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   //! Insert `node` after `ref`.</a>
+<a name="173"><span class="lineNum">     173 </span>            :   ASMJIT_API CBNode* addAfter(CBNode* node, CBNode* ref) noexcept;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   //! Insert `node` before `ref`.</a>
+<a name="175"><span class="lineNum">     175 </span>            :   ASMJIT_API CBNode* addBefore(CBNode* node, CBNode* ref) noexcept;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   //! Remove `node`.</a>
+<a name="177"><span class="lineNum">     177 </span>            :   ASMJIT_API CBNode* removeNode(CBNode* node) noexcept;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   //! Remove multiple nodes.</a>
+<a name="179"><span class="lineNum">     179 </span>            :   ASMJIT_API void removeNodes(CBNode* first, CBNode* last) noexcept;</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   //! Get current node.</a>
+<a name="182"><span class="lineNum">     182 </span>            :   //!</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //! \note If this method returns null it means that nothing has been</a>
+<a name="184"><span class="lineNum">     184 </span>            :   //! emitted yet.</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       1948 :   ASMJIT_INLINE CBNode* getCursor() const noexcept { return _cursor; }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   //! Set the current node without returning the previous node.</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       9440 :   ASMJIT_INLINE void _setCursor(CBNode* node) noexcept { _cursor = node; }</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   //! Set the current node to `node` and return the previous one.</a>
+<a name="189"><span class="lineNum">     189 </span>            :   ASMJIT_API CBNode* setCursor(CBNode* node) noexcept;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="192"><span class="lineNum">     192 </span>            :   // [Passes]</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            :   template&lt;typename T&gt;</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       1948 :   ASMJIT_INLINE T* newPassT() noexcept { return new(_cbBaseZone.alloc(sizeof(T))) T(); }</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   template&lt;typename T, typename P0&gt;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   ASMJIT_INLINE T* newPassT(P0 p0) noexcept { return new(_cbBaseZone.alloc(sizeof(T))) T(p0); }</a>
+<a name="199"><span class="lineNum">     199 </span>            :   template&lt;typename T, typename P0, typename P1&gt;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   ASMJIT_INLINE T* newPassT(P0 p0, P1 p1) noexcept { return new(_cbBaseZone.alloc(sizeof(T))) T(p0, p1); }</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   template&lt;typename T&gt;</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       1948 :   ASMJIT_INLINE Error addPassT() noexcept { return addPass(newPassT&lt;T&gt;()); }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   template&lt;typename T, typename P0&gt;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   ASMJIT_INLINE Error addPassT(P0 p0) noexcept { return addPass(newPassT&lt;P0&gt;(p0)); }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   template&lt;typename T, typename P0, typename P1&gt;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   ASMJIT_INLINE Error addPassT(P0 p0, P1 p1) noexcept { return addPass(newPassT&lt;P0, P1&gt;(p0, p1)); }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   //! Get a `CBPass` by name.</a>
+<a name="210"><span class="lineNum">     210 </span>            :   ASMJIT_API CBPass* getPassByName(const char* name) const noexcept;</a>
+<a name="211"><span class="lineNum">     211 </span>            :   //! Add `pass` to the list of passes.</a>
+<a name="212"><span class="lineNum">     212 </span>            :   ASMJIT_API Error addPass(CBPass* pass) noexcept;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   //! Remove `pass` from the list of passes and delete it.</a>
+<a name="214"><span class="lineNum">     214 </span>            :   ASMJIT_API Error deletePass(CBPass* pass) noexcept;</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="217"><span class="lineNum">     217 </span>            :   // [Serialization]</a>
+<a name="218"><span class="lineNum">     218 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :   ASMJIT_API virtual Error serialize(CodeEmitter* dst);</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="223"><span class="lineNum">     223 </span>            :   // [Members]</a>
+<a name="224"><span class="lineNum">     224 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            :   Zone _cbBaseZone;                      //!&lt; Base zone used to allocate nodes and `CBPass`.</a>
+<a name="227"><span class="lineNum">     227 </span>            :   Zone _cbDataZone;                      //!&lt; Data zone used to allocate data and names.</a>
+<a name="228"><span class="lineNum">     228 </span>            :   Zone _cbPassZone;                      //!&lt; Zone passed to `CBPass::process()`.</a>
+<a name="229"><span class="lineNum">     229 </span>            :   ZoneHeap _cbHeap;                      //!&lt; ZoneHeap that uses `_cbBaseZone`.</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :   ZoneVector&lt;CBPass*&gt; _cbPasses;         //!&lt; Array of `CBPass` objects.</a>
+<a name="232"><span class="lineNum">     232 </span>            :   ZoneVector&lt;CBLabel*&gt; _cbLabels;        //!&lt; Maps label indexes to `CBLabel` nodes.</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            :   CBNode* _firstNode;                    //!&lt; First node of the current section.</a>
+<a name="235"><span class="lineNum">     235 </span>            :   CBNode* _lastNode;                     //!&lt; Last node of the current section.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   CBNode* _cursor;                       //!&lt; Current node (cursor).</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            :   uint32_t _position;                    //!&lt; Flow-id assigned to each new node.</a>
+<a name="239"><span class="lineNum">     239 </span>            :   uint32_t _nodeFlags;                   //!&lt; Flags assigned to each new node.</a>
+<a name="240"><span class="lineNum">     240 </span>            : };</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : // ============================================================================</a>
+<a name="243"><span class="lineNum">     243 </span>            : // [asmjit::CBPass]</a>
+<a name="244"><span class="lineNum">     244 </span>            : // ============================================================================</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : //! `CodeBuilder` pass used to  code transformations, analysis, and lowering.</a>
+<a name="247"><span class="lineNum">     247 </span>            : class ASMJIT_VIRTAPI CBPass {</a>
+<a name="248"><span class="lineNum">     248 </span>            : public:</a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_NONCOPYABLE(CBPass);</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="252"><span class="lineNum">     252 </span>            :   // [Construction / Destruction]</a>
+<a name="253"><span class="lineNum">     253 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   ASMJIT_API CBPass(const char* name) noexcept;</a>
+<a name="256"><span class="lineNum">     256 </span>            :   ASMJIT_API virtual ~CBPass() noexcept;</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="259"><span class="lineNum">     259 </span>            :   // [Interface]</a>
+<a name="260"><span class="lineNum">     260 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :   //! Process the code stored in CodeBuffer `cb`.</a>
+<a name="263"><span class="lineNum">     263 </span>            :   //!</a>
+<a name="264"><span class="lineNum">     264 </span>            :   //! This is the only function that is called by the `CodeBuilder` to process</a>
+<a name="265"><span class="lineNum">     265 </span>            :   //! the code. It passes the CodeBuilder itself (`cb`) and also a zone memory</a>
+<a name="266"><span class="lineNum">     266 </span>            :   //! allocator `zone`, which will be reset after the `process()` returns. The</a>
+<a name="267"><span class="lineNum">     267 </span>            :   //! allocator should be used for all allocations as it's fast and everything</a>
+<a name="268"><span class="lineNum">     268 </span>            :   //! it allocates will be released at once when `process()` returns.</a>
+<a name="269"><span class="lineNum">     269 </span>            :   virtual Error process(Zone* zone) noexcept = 0;</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="272"><span class="lineNum">     272 </span>            :   // [Accessors]</a>
+<a name="273"><span class="lineNum">     273 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1948 :   ASMJIT_INLINE const CodeBuilder* cb() const noexcept { return _cb; }</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const char* getName() const noexcept { return _name; }</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="279"><span class="lineNum">     279 </span>            :   // [Members]</a>
+<a name="280"><span class="lineNum">     280 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   CodeBuilder* _cb;                      //!&lt; CodeBuilder this pass is assigned to.</a>
+<a name="283"><span class="lineNum">     283 </span>            :   const char* _name;                     //!&lt; Name of the pass.</a>
+<a name="284"><span class="lineNum">     284 </span>            : };</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : // ============================================================================</a>
+<a name="287"><span class="lineNum">     287 </span>            : // [asmjit::CBNode]</a>
+<a name="288"><span class="lineNum">     288 </span>            : // ============================================================================</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : //! Node (CodeBuilder).</a>
+<a name="291"><span class="lineNum">     291 </span>            : //!</a>
+<a name="292"><span class="lineNum">     292 </span>            : //! Every node represents a building-block used by \ref CodeBuilder. It can be</a>
+<a name="293"><span class="lineNum">     293 </span>            : //! instruction, data, label, comment, directive, or any other high-level</a>
+<a name="294"><span class="lineNum">     294 </span>            : //! representation that can be transformed to the building blocks mentioned.</a>
+<a name="295"><span class="lineNum">     295 </span>            : //! Every class that inherits \ref CodeBuilder can define its own nodes that it</a>
+<a name="296"><span class="lineNum">     296 </span>            : //! can lower to basic nodes.</a>
+<a name="297"><span class="lineNum">     297 </span>            : class CBNode {</a>
+<a name="298"><span class="lineNum">     298 </span>            : public:</a>
+<a name="299"><span class="lineNum">     299 </span>            :   ASMJIT_NONCOPYABLE(CBNode)</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="302"><span class="lineNum">     302 </span>            :   // [Type]</a>
+<a name="303"><span class="lineNum">     303 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! Type of \ref CBNode.</a>
+<a name="306"><span class="lineNum">     306 </span>            :   ASMJIT_ENUM(NodeType) {</a>
+<a name="307"><span class="lineNum">     307 </span>            :     kNodeNone       = 0,                 //!&lt; Invalid node (internal, don't use).</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :     // [CodeBuilder]</a>
+<a name="310"><span class="lineNum">     310 </span>            :     kNodeInst       = 1,                 //!&lt; Node is \ref CBInst or \ref CBJump.</a>
+<a name="311"><span class="lineNum">     311 </span>            :     kNodeData       = 2,                 //!&lt; Node is \ref CBData.</a>
+<a name="312"><span class="lineNum">     312 </span>            :     kNodeAlign      = 3,                 //!&lt; Node is \ref CBAlign.</a>
+<a name="313"><span class="lineNum">     313 </span>            :     kNodeLabel      = 4,                 //!&lt; Node is \ref CBLabel.</a>
+<a name="314"><span class="lineNum">     314 </span>            :     kNodeLabelData  = 5,                 //!&lt; Node is \ref CBLabelData.</a>
+<a name="315"><span class="lineNum">     315 </span>            :     kNodeConstPool  = 6,                 //!&lt; Node is \ref CBConstPool.</a>
+<a name="316"><span class="lineNum">     316 </span>            :     kNodeComment    = 7,                 //!&lt; Node is \ref CBComment.</a>
+<a name="317"><span class="lineNum">     317 </span>            :     kNodeSentinel   = 8,                 //!&lt; Node is \ref CBSentinel.</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :     // [CodeCompiler]</a>
+<a name="320"><span class="lineNum">     320 </span>            :     kNodeFunc       = 16,                //!&lt; Node is \ref CCFunc (considered as \ref CBLabel by \ref CodeBuilder).</a>
+<a name="321"><span class="lineNum">     321 </span>            :     kNodeFuncExit   = 17,                //!&lt; Node is \ref CCFuncRet.</a>
+<a name="322"><span class="lineNum">     322 </span>            :     kNodeFuncCall   = 18,                //!&lt; Node is \ref CCFuncCall.</a>
+<a name="323"><span class="lineNum">     323 </span>            :     kNodePushArg    = 19,                //!&lt; Node is \ref CCPushArg.</a>
+<a name="324"><span class="lineNum">     324 </span>            :     kNodeHint       = 20,                //!&lt; Node is \ref CCHint.</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :     // [UserDefined]</a>
+<a name="327"><span class="lineNum">     327 </span>            :     kNodeUser       = 32                 //!&lt; First id of a user-defined node.</a>
+<a name="328"><span class="lineNum">     328 </span>            :   };</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="331"><span class="lineNum">     331 </span>            :   // [Flags]</a>
+<a name="332"><span class="lineNum">     332 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            :   ASMJIT_ENUM(Flags) {</a>
+<a name="335"><span class="lineNum">     335 </span>            :     //! The node has been translated by the CodeCompiler.</a>
+<a name="336"><span class="lineNum">     336 </span>            :     kFlagIsTranslated = 0x0001,</a>
+<a name="337"><span class="lineNum">     337 </span>            :     //! If the node can be safely removed (has no effect).</a>
+<a name="338"><span class="lineNum">     338 </span>            :     kFlagIsRemovable = 0x0004,</a>
+<a name="339"><span class="lineNum">     339 </span>            :     //! If the node is informative only and can be safely removed.</a>
+<a name="340"><span class="lineNum">     340 </span>            :     kFlagIsInformative = 0x0008,</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            :     //! If the `CBInst` is a jump.</a>
+<a name="343"><span class="lineNum">     343 </span>            :     kFlagIsJmp = 0x0010,</a>
+<a name="344"><span class="lineNum">     344 </span>            :     //! If the `CBInst` is a conditional jump.</a>
+<a name="345"><span class="lineNum">     345 </span>            :     kFlagIsJcc = 0x0020,</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :     //! If the `CBInst` is an unconditional jump or conditional jump that is</a>
+<a name="348"><span class="lineNum">     348 </span>            :     //! likely to be taken.</a>
+<a name="349"><span class="lineNum">     349 </span>            :     kFlagIsTaken = 0x0040,</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :     //! If the `CBNode` will return from a function.</a>
+<a name="352"><span class="lineNum">     352 </span>            :     //!</a>
+<a name="353"><span class="lineNum">     353 </span>            :     //! This flag is used by both `CBSentinel` and `CCFuncRet`.</a>
+<a name="354"><span class="lineNum">     354 </span>            :     kFlagIsRet = 0x0080,</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            :     //! Whether the instruction is special.</a>
+<a name="357"><span class="lineNum">     357 </span>            :     kFlagIsSpecial = 0x0100,</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            :     //! Whether the instruction is an FPU instruction.</a>
+<a name="360"><span class="lineNum">     360 </span>            :     kFlagIsFp = 0x0200</a>
+<a name="361"><span class="lineNum">     361 </span>            :   };</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="364"><span class="lineNum">     364 </span>            :   // [Construction / Destruction]</a>
+<a name="365"><span class="lineNum">     365 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :   //! Create a new \ref CBNode - always use \ref CodeBuilder to allocate nodes.</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">      56154 :   ASMJIT_INLINE CBNode(CodeBuilder* cb, uint32_t type) noexcept {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">      56154 :     _prev = nullptr;</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      56154 :     _next = nullptr;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      54206 :     _type = static_cast&lt;uint8_t&gt;(type);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">       7792 :     _opCount = 0;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">      56154 :     _flags = static_cast&lt;uint16_t&gt;(cb-&gt;_nodeFlags);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      56154 :     _position = cb-&gt;_position;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      56154 :     _inlineComment = nullptr;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      50610 :     _passData = nullptr;</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :   }</a>
+<a name="378"><span class="lineNum">     378 </span>            :   //! Destroy the `CBNode` instance (NEVER CALLED).</a>
+<a name="379"><span class="lineNum">     379 </span>            :   ASMJIT_INLINE ~CBNode() noexcept {}</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="382"><span class="lineNum">     382 </span>            :   // [Accessors]</a>
+<a name="383"><span class="lineNum">     383 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            :   template&lt;typename T&gt;</a>
+<a name="386"><span class="lineNum">     386 </span>            :   ASMJIT_INLINE T* as() noexcept { return static_cast&lt;T*&gt;(this); }</a>
+<a name="387"><span class="lineNum">     387 </span>            :   template&lt;typename T&gt;</a>
+<a name="388"><span class="lineNum">     388 </span>            :   ASMJIT_INLINE const T* as() const noexcept { return static_cast&lt;const T*&gt;(this); }</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :   //! Get previous node in the compiler stream.</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">      73404 :   ASMJIT_INLINE CBNode* getPrev() const noexcept { return _prev; }</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   //! Get next node in the compiler stream.</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">     144906 :   ASMJIT_INLINE CBNode* getNext() const noexcept { return _next; }</span></a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            :   //! Get the node type, see \ref Type.</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">     251416 :   ASMJIT_INLINE uint32_t getType() const noexcept { return _type; }</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   //! Get the node flags.</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">      31158 :   ASMJIT_INLINE uint32_t getFlags() const noexcept { return _flags; }</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :   //! Get whether the instruction has flag `flag`.</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">     171098 :   ASMJIT_INLINE bool hasFlag(uint32_t flag) const noexcept { return (static_cast&lt;uint32_t&gt;(_flags) &amp; flag) != 0; }</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :   //! Set node flags to `flags`.</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">      31158 :   ASMJIT_INLINE void setFlags(uint32_t flags) noexcept { _flags = static_cast&lt;uint16_t&gt;(flags); }</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :   //! Add instruction `flags`.</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void orFlags(uint32_t flags) noexcept { _flags |= static_cast&lt;uint16_t&gt;(flags); }</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :   //! And instruction `flags`.</a>
+<a name="407"><span class="lineNum">     407 </span>            :   ASMJIT_INLINE void andFlags(uint32_t flags) noexcept { _flags &amp;= static_cast&lt;uint16_t&gt;(flags); }</a>
+<a name="408"><span class="lineNum">     408 </span>            :   //! Clear instruction `flags`.</a>
+<a name="409"><span class="lineNum">     409 </span>            :   ASMJIT_INLINE void andNotFlags(uint32_t flags) noexcept { _flags &amp;= ~static_cast&lt;uint16_t&gt;(flags); }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            :   //! Get whether the node has been translated.</a>
+<a name="412"><span class="lineNum">     412 </span>            :   ASMJIT_INLINE bool isTranslated() const noexcept { return hasFlag(kFlagIsTranslated); }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :   //! Get whether the node is removable if it's in unreachable code block.</a>
+<a name="415"><span class="lineNum">     415 </span>            :   ASMJIT_INLINE bool isRemovable() const noexcept { return hasFlag(kFlagIsRemovable); }</a>
+<a name="416"><span class="lineNum">     416 </span>            :   //! Get whether the node is informative only (comment, hint).</a>
+<a name="417"><span class="lineNum">     417 </span>            :   ASMJIT_INLINE bool isInformative() const noexcept { return hasFlag(kFlagIsInformative); }</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span>            :   //! Whether the node is `CBLabel`.</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool isLabel() const noexcept { return _type == kNodeLabel; }</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :   //! Whether the `CBInst` node is an unconditional jump.</a>
+<a name="422"><span class="lineNum">     422 </span>            :   ASMJIT_INLINE bool isJmp() const noexcept { return hasFlag(kFlagIsJmp); }</a>
+<a name="423"><span class="lineNum">     423 </span>            :   //! Whether the `CBInst` node is a conditional jump.</a>
+<a name="424"><span class="lineNum">     424 </span>            :   ASMJIT_INLINE bool isJcc() const noexcept { return hasFlag(kFlagIsJcc); }</a>
+<a name="425"><span class="lineNum">     425 </span>            :   //! Whether the `CBInst` node is a conditional/unconditional jump.</a>
+<a name="426"><span class="lineNum">     426 </span>            :   ASMJIT_INLINE bool isJmpOrJcc() const noexcept { return hasFlag(kFlagIsJmp | kFlagIsJcc); }</a>
+<a name="427"><span class="lineNum">     427 </span>            :   //! Whether the `CBInst` node is a return.</a>
+<a name="428"><span class="lineNum">     428 </span>            :   ASMJIT_INLINE bool isRet() const noexcept { return hasFlag(kFlagIsRet); }</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span>            :   //! Get whether the node is `CBInst` and the instruction is special.</a>
+<a name="431"><span class="lineNum">     431 </span>            :   ASMJIT_INLINE bool isSpecial() const noexcept { return hasFlag(kFlagIsSpecial); }</a>
+<a name="432"><span class="lineNum">     432 </span>            :   //! Get whether the node is `CBInst` and the instruction uses x87-FPU.</a>
+<a name="433"><span class="lineNum">     433 </span>            :   ASMJIT_INLINE bool isFp() const noexcept { return hasFlag(kFlagIsFp); }</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasPosition() const noexcept { return _position != 0; }</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :   //! Get flow index.</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getPosition() const noexcept { return _position; }</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :   //! Set flow index.</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">      40598 :   ASMJIT_INLINE void setPosition(uint32_t position) noexcept { _position = position; }</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            :   //! Get if the node has an inline comment.</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasInlineComment() const noexcept { return _inlineComment != nullptr; }</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :   //! Get an inline comment string.</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">      56154 :   ASMJIT_INLINE const char* getInlineComment() const noexcept { return _inlineComment; }</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   //! Set an inline comment string to `s`.</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setInlineComment(const char* s) noexcept { _inlineComment = s; }</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   //! Set an inline comment string to null.</a>
+<a name="448"><span class="lineNum">     448 </span>            :   ASMJIT_INLINE void resetInlineComment() noexcept { _inlineComment = nullptr; }</a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span>            :   //! Get if the node has associated work-data.</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">     112054 :   ASMJIT_INLINE bool hasPassData() const noexcept { return _passData != nullptr; }</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :   //! Get work-data - data used during processing &amp; transformations.</a>
+<a name="453"><span class="lineNum">     453 </span>            :   template&lt;typename T&gt;</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">     330596 :   ASMJIT_INLINE T* getPassData() const noexcept { return (T*)_passData; }</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :   //! Set work-data to `data`.</a>
+<a name="456"><span class="lineNum">     456 </span>            :   template&lt;typename T&gt;</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">      40598 :   ASMJIT_INLINE void setPassData(T* data) noexcept { _passData = (void*)data; }</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :   //! Reset work-data to null.</a>
+<a name="459"><span class="lineNum">     459 </span>            :   ASMJIT_INLINE void resetPassData() noexcept { _passData = nullptr; }</a>
+<a name="460"><span class="lineNum">     460 </span>            : </a>
+<a name="461"><span class="lineNum">     461 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="462"><span class="lineNum">     462 </span>            :   // [Members]</a>
+<a name="463"><span class="lineNum">     463 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span>            :   CBNode* _prev;                         //!&lt; Previous node.</a>
+<a name="466"><span class="lineNum">     466 </span>            :   CBNode* _next;                         //!&lt; Next node.</a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   uint8_t _type;                         //!&lt; Node type, see \ref NodeType.</a>
+<a name="469"><span class="lineNum">     469 </span>            :   uint8_t _opCount;                      //!&lt; Count of operands or zero.</a>
+<a name="470"><span class="lineNum">     470 </span>            :   uint16_t _flags;                       //!&lt; Flags, different meaning for every type of the node.</a>
+<a name="471"><span class="lineNum">     471 </span>            :   uint32_t _position;                    //!&lt; Flow index.</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            :   const char* _inlineComment;            //!&lt; Inline comment or null if not used.</a>
+<a name="474"><span class="lineNum">     474 </span>            :   void* _passData;                       //!&lt; Data used exclusively by the current `CBPass`.</a>
+<a name="475"><span class="lineNum">     475 </span>            : };</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span>            : // ============================================================================</a>
+<a name="478"><span class="lineNum">     478 </span>            : // [asmjit::CBInst]</a>
+<a name="479"><span class="lineNum">     479 </span>            : // ============================================================================</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            : //! Instruction (CodeBuilder).</a>
+<a name="482"><span class="lineNum">     482 </span>            : //!</a>
+<a name="483"><span class="lineNum">     483 </span>            : //! Wraps an instruction with its options and operands.</a>
+<a name="484"><span class="lineNum">     484 </span>            : class CBInst : public CBNode {</a>
+<a name="485"><span class="lineNum">     485 </span>            : public:</a>
+<a name="486"><span class="lineNum">     486 </span>            :   ASMJIT_NONCOPYABLE(CBInst)</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="489"><span class="lineNum">     489 </span>            :   // [Construction / Destruction]</a>
+<a name="490"><span class="lineNum">     490 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            :   //! Create a new `CBInst` instance.</a>
+<a name="493"><span class="lineNum">     493 </span>            :   ASMJIT_INLINE CBInst(CodeBuilder* cb, uint32_t instId, uint32_t options, Operand* opArray, uint32_t opCount) noexcept</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">      48362 :     : CBNode(cb, kNodeInst) {</span></a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            :     orFlags(kFlagIsRemovable);</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">      48362 :     _instDetail.instId = static_cast&lt;uint16_t&gt;(instId);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">      48362 :     _instDetail.options = options;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">      48362 :     _opCount = static_cast&lt;uint8_t&gt;(opCount);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">      48362 :     _opArray = opArray;</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            :     _updateMemOp();</a>
+<a name="504"><span class="lineNum">     504 </span>            :   }</a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span>            :   //! Destroy the `CBInst` instance (NEVER CALLED).</a>
+<a name="507"><span class="lineNum">     507 </span>            :   ASMJIT_INLINE ~CBInst() noexcept {}</a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="510"><span class="lineNum">     510 </span>            :   // [Accessors]</a>
+<a name="511"><span class="lineNum">     511 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Inst::Detail&amp; getInstDetail() noexcept { return _instDetail; }</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const Inst::Detail&amp; getInstDetail() const noexcept { return _instDetail; }</span></a>
+<a name="515"><span class="lineNum">     515 </span>            : </a>
+<a name="516"><span class="lineNum">     516 </span>            :   //! Get the instruction id, see \ref Inst::Id.</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">      79520 :   ASMJIT_INLINE uint32_t getInstId() const noexcept { return _instDetail.instId; }</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :   //! Set the instruction id to `instId`, see \ref Inst::Id.</a>
+<a name="519"><span class="lineNum">     519 </span>            :   ASMJIT_INLINE void setInstId(uint32_t instId) noexcept { _instDetail.instId = instId; }</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            :   //! Whether the instruction is either a jump or a conditional jump likely to be taken.</a>
+<a name="522"><span class="lineNum">     522 </span>            :   ASMJIT_INLINE bool isTaken() const noexcept { return hasFlag(kFlagIsTaken); }</a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            :   //! Get emit options.</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">      79254 :   ASMJIT_INLINE uint32_t getOptions() const noexcept { return _instDetail.options; }</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :   //! Set emit options.</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setOptions(uint32_t options) noexcept { _instDetail.options = options; }</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :   //! Add emit options.</a>
+<a name="529"><span class="lineNum">     529 </span>            :   ASMJIT_INLINE void addOptions(uint32_t options) noexcept { _instDetail.options |= options; }</a>
+<a name="530"><span class="lineNum">     530 </span>            :   //! Mask emit options.</a>
+<a name="531"><span class="lineNum">     531 </span>            :   ASMJIT_INLINE void andOptions(uint32_t options) noexcept { _instDetail.options &amp;= options; }</a>
+<a name="532"><span class="lineNum">     532 </span>            :   //! Clear emit options.</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void delOptions(uint32_t options) noexcept { _instDetail.options &amp;= ~options; }</span></a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            :   //! Get if the node has an extra register operand.</a>
+<a name="536"><span class="lineNum">     536 </span>            :   ASMJIT_INLINE bool hasExtraReg() const noexcept { return _instDetail.hasExtraReg(); }</a>
+<a name="537"><span class="lineNum">     537 </span>            :   //! Get extra register operand.</a>
+<a name="538"><span class="lineNum">     538 </span>            :   ASMJIT_INLINE RegOnly&amp; getExtraReg() noexcept { return _instDetail.extraReg; }</a>
+<a name="539"><span class="lineNum">     539 </span>            :   //! \overload</a>
+<a name="540"><span class="lineNum">     540 </span>            :   ASMJIT_INLINE const RegOnly&amp; getExtraReg() const noexcept { return _instDetail.extraReg; }</a>
+<a name="541"><span class="lineNum">     541 </span>            :   //! Set extra register operand to `reg`.</a>
+<a name="542"><span class="lineNum">     542 </span>            :   ASMJIT_INLINE void setExtraReg(const Reg&amp; reg) noexcept { _instDetail.extraReg.init(reg); }</a>
+<a name="543"><span class="lineNum">     543 </span>            :   //! Set extra register operand to `reg`.</a>
+<a name="544"><span class="lineNum">     544 </span>            :   ASMJIT_INLINE void setExtraReg(const RegOnly&amp; reg) noexcept { _instDetail.extraReg.init(reg); }</a>
+<a name="545"><span class="lineNum">     545 </span>            :   //! Reset extra register operand.</a>
+<a name="546"><span class="lineNum">     546 </span>            :   ASMJIT_INLINE void resetExtraReg() noexcept { _instDetail.extraReg.reset(); }</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            :   //! Get operands count.</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">      48362 :   ASMJIT_INLINE uint32_t getOpCount() const noexcept { return _opCount; }</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :   //! Get operands list.</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">     112326 :   ASMJIT_INLINE Operand* getOpArray() noexcept { return _opArray; }</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   //! \overload</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const Operand* getOpArray() const noexcept { return _opArray; }</span></a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            :   //! Get whether the instruction contains a memory operand.</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">      40910 :   ASMJIT_INLINE bool hasMemOp() const noexcept { return _memOpIndex != 0xFF; }</span></a>
+<a name="557"><span class="lineNum">     557 </span>            :   //! Get memory operand.</a>
+<a name="558"><span class="lineNum">     558 </span>            :   //!</a>
+<a name="559"><span class="lineNum">     559 </span>            :   //! NOTE: Can only be called if the instruction has such operand,</a>
+<a name="560"><span class="lineNum">     560 </span>            :   //! see `hasMemOp()`.</a>
+<a name="561"><span class="lineNum">     561 </span>            :   ASMJIT_INLINE Mem* getMemOp() const noexcept {</a>
+<a name="562"><span class="lineNum">     562 </span>            :     ASMJIT_ASSERT(hasMemOp());</a>
+<a name="563"><span class="lineNum">     563 </span>            :     return static_cast&lt;Mem*&gt;(&amp;_opArray[_memOpIndex]);</a>
+<a name="564"><span class="lineNum">     564 </span>            :   }</a>
+<a name="565"><span class="lineNum">     565 </span>            :   //! \overload</a>
+<a name="566"><span class="lineNum">     566 </span>            :   template&lt;typename T&gt;</a>
+<a name="567"><span class="lineNum">     567 </span>            :   ASMJIT_INLINE T* getMemOp() const noexcept {</a>
+<a name="568"><span class="lineNum">     568 </span>            :     ASMJIT_ASSERT(hasMemOp());</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">      14528 :     return static_cast&lt;T*&gt;(&amp;_opArray[_memOpIndex]);</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :   }</a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span>            :   //! Set memory operand index, `0xFF` means no memory operand.</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">      54462 :   ASMJIT_INLINE void setMemOpIndex(uint32_t index) noexcept { _memOpIndex = static_cast&lt;uint8_t&gt;(index); }</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :   //! Reset memory operand index to `0xFF` (no operand).</a>
+<a name="575"><span class="lineNum">     575 </span>            :   ASMJIT_INLINE void resetMemOpIndex() noexcept { _memOpIndex = 0xFF; }</a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="578"><span class="lineNum">     578 </span>            :   // [Utils]</a>
+<a name="579"><span class="lineNum">     579 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            :   ASMJIT_INLINE void _updateMemOp() noexcept {</a>
+<a name="582"><span class="lineNum">     582 </span>            :     Operand* opArray = getOpArray();</a>
+<a name="583"><span class="lineNum">     583 </span>            :     uint32_t opCount = getOpCount();</a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span>            :     uint32_t i;</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">     118624 :     for (i = 0; i &lt; opCount; i++)</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">      84790 :       if (opArray[i].isMem())</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">      14528 :         goto Update;</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :     i = 0xFF;</a>
+<a name="590"><span class="lineNum">     590 </span>            : </a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">      48362 : Update:</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :     setMemOpIndex(i);</a>
+<a name="593"><span class="lineNum">     593 </span>            :   }</a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="596"><span class="lineNum">     596 </span>            :   // [Members]</a>
+<a name="597"><span class="lineNum">     597 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="598"><span class="lineNum">     598 </span>            : </a>
+<a name="599"><span class="lineNum">     599 </span>            :   Inst::Detail _instDetail;              //!&lt; Instruction id, options, and extra register.</a>
+<a name="600"><span class="lineNum">     600 </span>            :   uint8_t _memOpIndex;                   //!&lt; \internal</a>
+<a name="601"><span class="lineNum">     601 </span>            :   uint8_t _reserved[7];                  //!&lt; \internal</a>
+<a name="602"><span class="lineNum">     602 </span>            :   Operand* _opArray;                     //!&lt; Instruction operands.</a>
+<a name="603"><span class="lineNum">     603 </span>            : };</a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span>            : // ============================================================================</a>
+<a name="606"><span class="lineNum">     606 </span>            : // [asmjit::CBInstEx]</a>
+<a name="607"><span class="lineNum">     607 </span>            : // ============================================================================</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            : struct CBInstEx : public CBInst {</a>
+<a name="610"><span class="lineNum">     610 </span>            :   Operand _op4;</a>
+<a name="611"><span class="lineNum">     611 </span>            :   Operand _op5;</a>
+<a name="612"><span class="lineNum">     612 </span>            : };</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            : // ============================================================================</a>
+<a name="615"><span class="lineNum">     615 </span>            : // [asmjit::CBJump]</a>
+<a name="616"><span class="lineNum">     616 </span>            : // ============================================================================</a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span>            : //! Asm jump (conditional or direct).</a>
+<a name="619"><span class="lineNum">     619 </span>            : //!</a>
+<a name="620"><span class="lineNum">     620 </span>            : //! Extension of `CBInst` node, which stores more information about the jump.</a>
+<a name="621"><span class="lineNum">     621 </span>            : class CBJump : public CBInst {</a>
+<a name="622"><span class="lineNum">     622 </span>            : public:</a>
+<a name="623"><span class="lineNum">     623 </span>            :   ASMJIT_NONCOPYABLE(CBJump)</a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="626"><span class="lineNum">     626 </span>            :   // [Construction / Destruction]</a>
+<a name="627"><span class="lineNum">     627 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="628"><span class="lineNum">     628 </span>            : </a>
+<a name="629"><span class="lineNum">     629 </span>            :   ASMJIT_INLINE CBJump(CodeBuilder* cb, uint32_t instId, uint32_t options, Operand* opArray, uint32_t opCount) noexcept</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :     : CBInst(cb, instId, options, opArray, opCount),</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :       _target(nullptr),</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :       _jumpNext(nullptr) {}</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :   ASMJIT_INLINE ~CBJump() noexcept {}</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="636"><span class="lineNum">     636 </span>            :   // [Accessors]</a>
+<a name="637"><span class="lineNum">     637 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CBLabel* getTarget() const noexcept { return _target; }</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CBJump* getJumpNext() const noexcept { return _jumpNext; }</span></a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="643"><span class="lineNum">     643 </span>            :   // [Members]</a>
+<a name="644"><span class="lineNum">     644 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="645"><span class="lineNum">     645 </span>            : </a>
+<a name="646"><span class="lineNum">     646 </span>            :   CBLabel* _target;                     //!&lt; Target node.</a>
+<a name="647"><span class="lineNum">     647 </span>            :   CBJump* _jumpNext;                    //!&lt; Next jump to the same target in a single linked-list.</a>
+<a name="648"><span class="lineNum">     648 </span>            : };</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span>            : // ============================================================================</a>
+<a name="651"><span class="lineNum">     651 </span>            : // [asmjit::CBData]</a>
+<a name="652"><span class="lineNum">     652 </span>            : // ============================================================================</a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span>            : //! Asm data (CodeBuilder).</a>
+<a name="655"><span class="lineNum">     655 </span>            : //!</a>
+<a name="656"><span class="lineNum">     656 </span>            : //! Wraps `.data` directive. The node contains data that will be placed at the</a>
+<a name="657"><span class="lineNum">     657 </span>            : //! node's position in the assembler stream. The data is considered to be RAW;</a>
+<a name="658"><span class="lineNum">     658 </span>            : //! no analysis nor byte-order conversion is performed on RAW data.</a>
+<a name="659"><span class="lineNum">     659 </span>            : class CBData : public CBNode {</a>
+<a name="660"><span class="lineNum">     660 </span>            : public:</a>
+<a name="661"><span class="lineNum">     661 </span>            :   ASMJIT_NONCOPYABLE(CBData)</a>
+<a name="662"><span class="lineNum">     662 </span>            :   enum { kInlineBufferSize = static_cast&lt;int&gt;(64 - sizeof(CBNode) - 4) };</a>
+<a name="663"><span class="lineNum">     663 </span>            : </a>
+<a name="664"><span class="lineNum">     664 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="665"><span class="lineNum">     665 </span>            :   // [Construction / Destruction]</a>
+<a name="666"><span class="lineNum">     666 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="667"><span class="lineNum">     667 </span>            : </a>
+<a name="668"><span class="lineNum">     668 </span>            :   //! Create a new `CBData` instance.</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CBData(CodeBuilder* cb, void* data, uint32_t size) noexcept : CBNode(cb, kNodeData) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :     if (size &lt;= kInlineBufferSize) {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :       if (data) ::memcpy(_buf, data, size);</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :     }</a>
+<a name="673"><span class="lineNum">     673 </span>            :     else {</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :       _externalPtr = static_cast&lt;uint8_t*&gt;(data);</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :     }</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :     _size = size;</span></a>
+<a name="677"><span class="lineNum">     677 </span>            :   }</a>
+<a name="678"><span class="lineNum">     678 </span>            : </a>
+<a name="679"><span class="lineNum">     679 </span>            :   //! Destroy the `CBData` instance (NEVER CALLED).</a>
+<a name="680"><span class="lineNum">     680 </span>            :   ASMJIT_INLINE ~CBData() noexcept {}</a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="683"><span class="lineNum">     683 </span>            :   // [Accessors]</a>
+<a name="684"><span class="lineNum">     684 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="685"><span class="lineNum">     685 </span>            : </a>
+<a name="686"><span class="lineNum">     686 </span>            :   //! Get size of the data.</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :   uint32_t getSize() const noexcept { return _size; }</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :   //! Get pointer to the data.</a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :   uint8_t* getData() const noexcept { return _size &lt;= kInlineBufferSize ? const_cast&lt;uint8_t*&gt;(_buf) : _externalPtr; }</span></a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="692"><span class="lineNum">     692 </span>            :   // [Members]</a>
+<a name="693"><span class="lineNum">     693 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span>            :   union {</a>
+<a name="696"><span class="lineNum">     696 </span>            :     struct {</a>
+<a name="697"><span class="lineNum">     697 </span>            :       uint8_t _buf[kInlineBufferSize];   //!&lt; Embedded data buffer.</a>
+<a name="698"><span class="lineNum">     698 </span>            :       uint32_t _size;                    //!&lt; Size of the data.</a>
+<a name="699"><span class="lineNum">     699 </span>            :     };</a>
+<a name="700"><span class="lineNum">     700 </span>            :     struct {</a>
+<a name="701"><span class="lineNum">     701 </span>            :       uint8_t* _externalPtr;             //!&lt; Pointer to external data.</a>
+<a name="702"><span class="lineNum">     702 </span>            :     };</a>
+<a name="703"><span class="lineNum">     703 </span>            :   };</a>
+<a name="704"><span class="lineNum">     704 </span>            : };</a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            : // ============================================================================</a>
+<a name="707"><span class="lineNum">     707 </span>            : // [asmjit::CBAlign]</a>
+<a name="708"><span class="lineNum">     708 </span>            : // ============================================================================</a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span>            : //! Align directive (CodeBuilder).</a>
+<a name="711"><span class="lineNum">     711 </span>            : //!</a>
+<a name="712"><span class="lineNum">     712 </span>            : //! Wraps `.align` directive.</a>
+<a name="713"><span class="lineNum">     713 </span>            : class CBAlign : public CBNode {</a>
+<a name="714"><span class="lineNum">     714 </span>            : public:</a>
+<a name="715"><span class="lineNum">     715 </span>            :   ASMJIT_NONCOPYABLE(CBAlign)</a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="718"><span class="lineNum">     718 </span>            :   // [Construction / Destruction]</a>
+<a name="719"><span class="lineNum">     719 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span>            :   //! Create a new `CBAlign` instance.</a>
+<a name="722"><span class="lineNum">     722 </span>            :   ASMJIT_INLINE CBAlign(CodeBuilder* cb, uint32_t mode, uint32_t alignment) noexcept</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :     : CBNode(cb, kNodeAlign),</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineNoCov">          0 :       _mode(mode),</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineNoCov">          0 :       _alignment(alignment) {}</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :   //! Destroy the `CBAlign` instance (NEVER CALLED).</a>
+<a name="727"><span class="lineNum">     727 </span>            :   ASMJIT_INLINE ~CBAlign() noexcept {}</a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="730"><span class="lineNum">     730 </span>            :   // [Accessors]</a>
+<a name="731"><span class="lineNum">     731 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span>            :   //! Get align mode.</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getMode() const noexcept { return _mode; }</span></a>
+<a name="735"><span class="lineNum">     735 </span>            :   //! Set align mode.</a>
+<a name="736"><span class="lineNum">     736 </span>            :   ASMJIT_INLINE void setMode(uint32_t mode) noexcept { _mode = mode; }</a>
+<a name="737"><span class="lineNum">     737 </span>            : </a>
+<a name="738"><span class="lineNum">     738 </span>            :   //! Get align offset in bytes.</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getAlignment() const noexcept { return _alignment; }</span></a>
+<a name="740"><span class="lineNum">     740 </span>            :   //! Set align offset in bytes to `offset`.</a>
+<a name="741"><span class="lineNum">     741 </span>            :   ASMJIT_INLINE void setAlignment(uint32_t alignment) noexcept { _alignment = alignment; }</a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="744"><span class="lineNum">     744 </span>            :   // [Members]</a>
+<a name="745"><span class="lineNum">     745 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span>            :   uint32_t _mode;                        //!&lt; Align mode, see \ref AlignMode.</a>
+<a name="748"><span class="lineNum">     748 </span>            :   uint32_t _alignment;                   //!&lt; Alignment (in bytes).</a>
+<a name="749"><span class="lineNum">     749 </span>            : };</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            : // ============================================================================</a>
+<a name="752"><span class="lineNum">     752 </span>            : // [asmjit::CBLabel]</a>
+<a name="753"><span class="lineNum">     753 </span>            : // ============================================================================</a>
+<a name="754"><span class="lineNum">     754 </span>            : </a>
+<a name="755"><span class="lineNum">     755 </span>            : //! Label (CodeBuilder).</a>
+<a name="756"><span class="lineNum">     756 </span>            : class CBLabel : public CBNode {</a>
+<a name="757"><span class="lineNum">     757 </span>            : public:</a>
+<a name="758"><span class="lineNum">     758 </span>            :   ASMJIT_NONCOPYABLE(CBLabel)</a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="761"><span class="lineNum">     761 </span>            :   // [Construction / Destruction]</a>
+<a name="762"><span class="lineNum">     762 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span>            :   //! Create a new `CBLabel` instance.</a>
+<a name="765"><span class="lineNum">     765 </span>            :   ASMJIT_INLINE CBLabel(CodeBuilder* cb, uint32_t id = kInvalidValue) noexcept</a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">       3896 :     : CBNode(cb, kNodeLabel),</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       3896 :       _id(id),</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">       3896 :       _numRefs(0),</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">       3896 :       _from(nullptr) {}</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :   //! Destroy the `CBLabel` instance (NEVER CALLED).</a>
+<a name="771"><span class="lineNum">     771 </span>            :   ASMJIT_INLINE ~CBLabel() noexcept {}</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="774"><span class="lineNum">     774 </span>            :   // [Accessors]</a>
+<a name="775"><span class="lineNum">     775 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="776"><span class="lineNum">     776 </span>            : </a>
+<a name="777"><span class="lineNum">     777 </span>            :   //! Get the label id.</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</span></a>
+<a name="779"><span class="lineNum">     779 </span>            :   //! Get the label as `Label` operand.</a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">       3896 :   ASMJIT_INLINE Label getLabel() const noexcept { return Label(_id); }</span></a>
+<a name="781"><span class="lineNum">     781 </span>            : </a>
+<a name="782"><span class="lineNum">     782 </span>            :   //! Get first jmp instruction.</a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CBJump* getFrom() const noexcept { return _from; }</span></a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            :   //! Get number of jumps to this target.</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getNumRefs() const noexcept { return _numRefs; }</span></a>
+<a name="787"><span class="lineNum">     787 </span>            :   //! Set number of jumps to this target.</a>
+<a name="788"><span class="lineNum">     788 </span>            :   ASMJIT_INLINE void setNumRefs(uint32_t i) noexcept { _numRefs = i; }</a>
+<a name="789"><span class="lineNum">     789 </span>            : </a>
+<a name="790"><span class="lineNum">     790 </span>            :   //! Add number of jumps to this target.</a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void addNumRefs(uint32_t i = 1) noexcept { _numRefs += i; }</span></a>
+<a name="792"><span class="lineNum">     792 </span>            :   //! Subtract number of jumps to this target.</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void subNumRefs(uint32_t i = 1) noexcept { _numRefs -= i; }</span></a>
+<a name="794"><span class="lineNum">     794 </span>            : </a>
+<a name="795"><span class="lineNum">     795 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="796"><span class="lineNum">     796 </span>            :   // [Members]</a>
+<a name="797"><span class="lineNum">     797 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span>            :   uint32_t _id;                          //!&lt; Label id.</a>
+<a name="800"><span class="lineNum">     800 </span>            :   uint32_t _numRefs;                     //!&lt; Count of jumps here.</a>
+<a name="801"><span class="lineNum">     801 </span>            :   CBJump* _from;                         //!&lt; Linked-list of nodes that can jump here.</a>
+<a name="802"><span class="lineNum">     802 </span>            : };</a>
+<a name="803"><span class="lineNum">     803 </span>            : </a>
+<a name="804"><span class="lineNum">     804 </span>            : // ============================================================================</a>
+<a name="805"><span class="lineNum">     805 </span>            : // [asmjit::CBLabelData]</a>
+<a name="806"><span class="lineNum">     806 </span>            : // ============================================================================</a>
+<a name="807"><span class="lineNum">     807 </span>            : </a>
+<a name="808"><span class="lineNum">     808 </span>            : class CBLabelData : public CBNode {</a>
+<a name="809"><span class="lineNum">     809 </span>            : public:</a>
+<a name="810"><span class="lineNum">     810 </span>            :   ASMJIT_NONCOPYABLE(CBLabelData)</a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="813"><span class="lineNum">     813 </span>            :   // [Construction / Destruction]</a>
+<a name="814"><span class="lineNum">     814 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="815"><span class="lineNum">     815 </span>            : </a>
+<a name="816"><span class="lineNum">     816 </span>            :   //! Create a new `CBLabelData` instance.</a>
+<a name="817"><span class="lineNum">     817 </span>            :   ASMJIT_INLINE CBLabelData(CodeBuilder* cb, uint32_t id = kInvalidValue) noexcept</a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineNoCov">          0 :     : CBNode(cb, kNodeLabelData),</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineNoCov">          0 :       _id(id) {}</span></a>
+<a name="820"><span class="lineNum">     820 </span>            : </a>
+<a name="821"><span class="lineNum">     821 </span>            :   //! Destroy the `CBLabelData` instance (NEVER CALLED).</a>
+<a name="822"><span class="lineNum">     822 </span>            :   ASMJIT_INLINE ~CBLabelData() noexcept {}</a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="825"><span class="lineNum">     825 </span>            :   // [Interface]</a>
+<a name="826"><span class="lineNum">     826 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="827"><span class="lineNum">     827 </span>            : </a>
+<a name="828"><span class="lineNum">     828 </span>            :   //! Get the label id.</a>
+<a name="829"><span class="lineNum">     829 </span>            :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</a>
+<a name="830"><span class="lineNum">     830 </span>            :   //! Get the label as `Label` operand.</a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Label getLabel() const noexcept { return Label(_id); }</span></a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="834"><span class="lineNum">     834 </span>            :   // [Members]</a>
+<a name="835"><span class="lineNum">     835 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            :   uint32_t _id;</a>
+<a name="838"><span class="lineNum">     838 </span>            : };</a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span>            : // ============================================================================</a>
+<a name="841"><span class="lineNum">     841 </span>            : // [asmjit::CBConstPool]</a>
+<a name="842"><span class="lineNum">     842 </span>            : // ============================================================================</a>
+<a name="843"><span class="lineNum">     843 </span>            : </a>
+<a name="844"><span class="lineNum">     844 </span>            : class CBConstPool : public CBLabel {</a>
+<a name="845"><span class="lineNum">     845 </span>            : public:</a>
+<a name="846"><span class="lineNum">     846 </span>            :   ASMJIT_NONCOPYABLE(CBConstPool)</a>
+<a name="847"><span class="lineNum">     847 </span>            : </a>
+<a name="848"><span class="lineNum">     848 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="849"><span class="lineNum">     849 </span>            :   // [Construction / Destruction]</a>
+<a name="850"><span class="lineNum">     850 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="851"><span class="lineNum">     851 </span>            : </a>
+<a name="852"><span class="lineNum">     852 </span>            :   //! Create a new `CBConstPool` instance.</a>
+<a name="853"><span class="lineNum">     853 </span>            :   ASMJIT_INLINE CBConstPool(CodeBuilder* cb, uint32_t id = kInvalidValue) noexcept</a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :     : CBLabel(cb, id),</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineNoCov">          0 :       _constPool(&amp;cb-&gt;_cbBaseZone) { _type = kNodeConstPool; }</span></a>
+<a name="856"><span class="lineNum">     856 </span>            : </a>
+<a name="857"><span class="lineNum">     857 </span>            :   //! Destroy the `CBConstPool` instance (NEVER CALLED).</a>
+<a name="858"><span class="lineNum">     858 </span>            :   ASMJIT_INLINE ~CBConstPool() noexcept {}</a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="861"><span class="lineNum">     861 </span>            :   // [Interface]</a>
+<a name="862"><span class="lineNum">     862 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE ConstPool&amp; getConstPool() noexcept { return _constPool; }</span></a>
+<a name="865"><span class="lineNum">     865 </span>            :   ASMJIT_INLINE const ConstPool&amp; getConstPool() const noexcept { return _constPool; }</a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span>            :   //! Get whether the constant-pool is empty.</a>
+<a name="868"><span class="lineNum">     868 </span>            :   ASMJIT_INLINE bool isEmpty() const noexcept { return _constPool.isEmpty(); }</a>
+<a name="869"><span class="lineNum">     869 </span>            :   //! Get the size of the constant-pool in bytes.</a>
+<a name="870"><span class="lineNum">     870 </span>            :   ASMJIT_INLINE size_t getSize() const noexcept { return _constPool.getSize(); }</a>
+<a name="871"><span class="lineNum">     871 </span>            :   //! Get minimum alignment.</a>
+<a name="872"><span class="lineNum">     872 </span>            :   ASMJIT_INLINE size_t getAlignment() const noexcept { return _constPool.getAlignment(); }</a>
+<a name="873"><span class="lineNum">     873 </span>            : </a>
+<a name="874"><span class="lineNum">     874 </span>            :   //! See \ref ConstPool::add().</a>
+<a name="875"><span class="lineNum">     875 </span>            :   ASMJIT_INLINE Error add(const void* data, size_t size, size_t&amp; dstOffset) noexcept {</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineNoCov">          0 :     return _constPool.add(data, size, dstOffset);</span></a>
+<a name="877"><span class="lineNum">     877 </span>            :   }</a>
+<a name="878"><span class="lineNum">     878 </span>            : </a>
+<a name="879"><span class="lineNum">     879 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="880"><span class="lineNum">     880 </span>            :   // [Members]</a>
+<a name="881"><span class="lineNum">     881 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="882"><span class="lineNum">     882 </span>            : </a>
+<a name="883"><span class="lineNum">     883 </span>            :   ConstPool _constPool;</a>
+<a name="884"><span class="lineNum">     884 </span>            : };</a>
+<a name="885"><span class="lineNum">     885 </span>            : </a>
+<a name="886"><span class="lineNum">     886 </span>            : // ============================================================================</a>
+<a name="887"><span class="lineNum">     887 </span>            : // [asmjit::CBComment]</a>
+<a name="888"><span class="lineNum">     888 </span>            : // ============================================================================</a>
+<a name="889"><span class="lineNum">     889 </span>            : </a>
+<a name="890"><span class="lineNum">     890 </span>            : //! Comment (CodeBuilder).</a>
+<a name="891"><span class="lineNum">     891 </span>            : class CBComment : public CBNode {</a>
+<a name="892"><span class="lineNum">     892 </span>            : public:</a>
+<a name="893"><span class="lineNum">     893 </span>            :   ASMJIT_NONCOPYABLE(CBComment)</a>
+<a name="894"><span class="lineNum">     894 </span>            : </a>
+<a name="895"><span class="lineNum">     895 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="896"><span class="lineNum">     896 </span>            :   // [Construction / Destruction]</a>
+<a name="897"><span class="lineNum">     897 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="898"><span class="lineNum">     898 </span>            : </a>
+<a name="899"><span class="lineNum">     899 </span>            :   //! Create a new `CBComment` instance.</a>
+<a name="900"><span class="lineNum">     900 </span>            :   ASMJIT_INLINE CBComment(CodeBuilder* cb, const char* comment) noexcept : CBNode(cb, kNodeComment) {</a>
+<a name="901"><span class="lineNum">     901 </span>            :     orFlags(kFlagIsRemovable | kFlagIsInformative);</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineNoCov">          0 :     _inlineComment = comment;</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :   }</a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span>            :   //! Destroy the `CBComment` instance (NEVER CALLED).</a>
+<a name="906"><span class="lineNum">     906 </span>            :   ASMJIT_INLINE ~CBComment() noexcept {}</a>
+<a name="907"><span class="lineNum">     907 </span>            : };</a>
+<a name="908"><span class="lineNum">     908 </span>            : </a>
+<a name="909"><span class="lineNum">     909 </span>            : // ============================================================================</a>
+<a name="910"><span class="lineNum">     910 </span>            : // [asmjit::CBSentinel]</a>
+<a name="911"><span class="lineNum">     911 </span>            : // ============================================================================</a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span>            : //! Sentinel (CodeBuilder).</a>
+<a name="914"><span class="lineNum">     914 </span>            : //!</a>
+<a name="915"><span class="lineNum">     915 </span>            : //! Sentinel is a marker that is completely ignored by the code builder. It's</a>
+<a name="916"><span class="lineNum">     916 </span>            : //! used to remember a position in a code as it never gets removed by any pass.</a>
+<a name="917"><span class="lineNum">     917 </span>            : class CBSentinel : public CBNode {</a>
+<a name="918"><span class="lineNum">     918 </span>            : public:</a>
+<a name="919"><span class="lineNum">     919 </span>            :   ASMJIT_NONCOPYABLE(CBSentinel)</a>
+<a name="920"><span class="lineNum">     920 </span>            : </a>
+<a name="921"><span class="lineNum">     921 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="922"><span class="lineNum">     922 </span>            :   // [Construction / Destruction]</a>
+<a name="923"><span class="lineNum">     923 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span>            :   //! Create a new `CBSentinel` instance.</a>
+<a name="926"><span class="lineNum">     926 </span>            :   ASMJIT_INLINE CBSentinel(CodeBuilder* cb) noexcept : CBNode(cb, kNodeSentinel) {}</a>
+<a name="927"><span class="lineNum">     927 </span>            :   //! Destroy the `CBSentinel` instance (NEVER CALLED).</a>
+<a name="928"><span class="lineNum">     928 </span>            :   ASMJIT_INLINE ~CBSentinel() noexcept {}</a>
+<a name="929"><span class="lineNum">     929 </span>            : };</a>
+<a name="930"><span class="lineNum">     930 </span>            : </a>
+<a name="931"><span class="lineNum">     931 </span>            : //! \}</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span>            : } // asmjit namespace</a>
+<a name="934"><span class="lineNum">     934 </span>            : } // namespace PLMD</a>
+<a name="935"><span class="lineNum">     935 </span>            : </a>
+<a name="936"><span class="lineNum">     936 </span>            : // [Api-End]</a>
+<a name="937"><span class="lineNum">     937 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="938"><span class="lineNum">     938 </span>            : </a>
+<a name="939"><span class="lineNum">     939 </span>            : // [Guard]</a>
+<a name="940"><span class="lineNum">     940 </span>            : #endif // !ASMJIT_DISABLE_BUILDER</a>
+<a name="941"><span class="lineNum">     941 </span>            : #endif // _ASMJIT_BASE_CODEBUILDER_H</a>
+<a name="942"><span class="lineNum">     942 </span>            : #pragma GCC diagnostic pop</a>
+<a name="943"><span class="lineNum">     943 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="944"><span class="lineNum">     944 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codecompiler.cpp.func-sort-c.html b/coverage-libs/asmjit/codecompiler.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4bfbc52ea6
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codecompiler.cpp - functions</title>
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+</head>
+
+<body>
+
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codecompiler.cpp<span style="font-size: 80%;"> (<a href="codecompiler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">239</td>
+            <td class="headerCovTableEntryLo">37.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">36</td>
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+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#89">_ZN4PLMD6asmjit12CodeCompilerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#319">_ZN4PLMD6asmjit12CodeCompiler10newVirtRegEjjPKc</a></td>
+              <td class="coverFnHi">23788</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#351">_ZN4PLMD6asmjit12CodeCompiler7_newRegERNS0_3RegEjPKc</a></td>
+              <td class="coverFnHi">23788</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codecompiler.cpp.func.html b/coverage-libs/asmjit/codecompiler.cpp.func.html
new file mode 100644
index 0000000000..657988c7ac
--- /dev/null
+++ b/coverage-libs/asmjit/codecompiler.cpp.func.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codecompiler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codecompiler.cpp<span style="font-size: 80%;"> (<a href="codecompiler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">239</td>
+            <td class="headerCovTableEntryLo">37.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">41.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codecompiler.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#59">_ZN4PLMD6asmjit10CCFuncCall7_setArgEjRKNS0_8Operand_E</a></td>
+              <td class="coverFnHi">1870</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#67">_ZN4PLMD6asmjit10CCFuncCall7_setRetEjRKNS0_8Operand_E</a></td>
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+    <tr>
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+              <td class="coverFnHi">23788</td>
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+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#115">_ZN4PLMD6asmjit12CodeCompiler11newHintNodeERNS0_3RegEjj</a></td>
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+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#173">_ZN4PLMD6asmjit12CodeCompiler7addFuncEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
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+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#186">_ZN4PLMD6asmjit12CodeCompiler7addFuncERKNS0_13FuncSignatureE</a></td>
+              <td class="coverFnHi">1948</td>
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+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#197">_ZN4PLMD6asmjit12CodeCompiler7endFuncEv</a></td>
+              <td class="coverFnHi">1948</td>
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+              <td class="coverFnHi">1648</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#126">_ZN4PLMD6asmjit12CodeCompiler7newFuncERKNS0_13FuncSignatureE</a></td>
+              <td class="coverFnHi">1948</td>
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+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#95">_ZN4PLMD6asmjit12CodeCompiler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
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+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#99">_ZN4PLMD6asmjit12CodeCompiler8onDetachEPNS0_10CodeHolderE</a></td>
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+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#479">_ZN4PLMD6asmjit12CodeCompiler9_newConstERNS0_3MemEjPKvm</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#454">_ZN4PLMD6asmjit12CodeCompiler9_newStackERNS0_3MemEjjPKc</a></td>
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+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#79">_ZN4PLMD6asmjit12CodeCompilerC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
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+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#89">_ZN4PLMD6asmjit12CodeCompilerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#89">_ZN4PLMD6asmjit12CodeCompilerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#538">_ZNK4PLMD6asmjit12CodeCompiler11getPriorityERNS0_3RegE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codecompiler.cpp.gcov.html#551">_ZNK4PLMD6asmjit12CodeCompiler14getSaveOnUnuseERNS0_3RegE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codecompiler.cpp.gcov.html b/coverage-libs/asmjit/codecompiler.cpp.gcov.html
new file mode 100644
index 0000000000..4d2d0986f4
--- /dev/null
+++ b/coverage-libs/asmjit/codecompiler.cpp.gcov.html
@@ -0,0 +1,675 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codecompiler.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codecompiler.cpp<span style="font-size: 80%;"> (source / <a href="codecompiler.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">239</td>
+            <td class="headerCovTableEntryLo">37.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">41.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./codecompiler.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./logging.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./regalloc_p.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &lt;stdarg.h&gt;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // [Api-Begin]</a>
+<a name="46"><span class="lineNum">      46 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : namespace PLMD {</a>
+<a name="49"><span class="lineNum">      49 </span>            : namespace asmjit {</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : // [Constants]</a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : static const char noName[1] = { '\0' };</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : // [asmjit::CCFuncCall - Arg / Ret]</a>
+<a name="59"><span class="lineNum">      59 </span>            : // ============================================================================</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1870 : bool CCFuncCall::_setArg(uint32_t i, const Operand_&amp; op) noexcept {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       1870 :   if ((i &amp; ~kFuncArgHi) &gt;= _funcDetail.getArgCount())</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     return false;</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1870 :   _args[i] = op;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1870 :   return true;</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1648 : bool CCFuncCall::_setRet(uint32_t i, const Operand_&amp; op) noexcept {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       1648 :   if (i &gt;= 2)</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :     return false;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       1648 :   _ret[i] = op;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       1648 :   return true;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : // ============================================================================</a>
+<a name="78"><span class="lineNum">      78 </span>            : // [asmjit::CodeCompiler - Construction / Destruction]</a>
+<a name="79"><span class="lineNum">      79 </span>            : // ============================================================================</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1948 : CodeCompiler::CodeCompiler() noexcept</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   : CodeBuilder(),</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1948 :     _func(nullptr),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1948 :     _vRegZone(4096 - Zone::kZoneOverhead),</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :     _vRegArray(),</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1948 :     _localConstPool(nullptr),</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1948 :     _globalConstPool(nullptr) {</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1948 :   _type = kTypeCompiler;</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1948 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1948 : CodeCompiler::~CodeCompiler() noexcept {}</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : // ============================================================================</a>
+<a name="94"><span class="lineNum">      94 </span>            : // [asmjit::CodeCompiler - Events]</a>
+<a name="95"><span class="lineNum">      95 </span>            : // ============================================================================</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1948 : Error CodeCompiler::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1948 :   return Base::onAttach(code);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : Error CodeCompiler::onDetach(CodeHolder* code) noexcept {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   _func = nullptr;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   _localConstPool = nullptr;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   _globalConstPool = nullptr;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   _vRegArray.reset();</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :   _vRegZone.reset(false);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   return Base::onDetach(code);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : // ============================================================================</a>
+<a name="114"><span class="lineNum">     114 </span>            : // [asmjit::CodeCompiler - Node-Factory]</a>
+<a name="115"><span class="lineNum">     115 </span>            : // ============================================================================</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 : CCHint* CodeCompiler::newHintNode(Reg&amp; r, uint32_t hint, uint32_t value) noexcept {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   if (!r.isVirtReg()) return nullptr;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   VirtReg* vr = getVirtReg(r);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :   return newNodeT&lt;CCHint&gt;(vr, hint, value);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : // ============================================================================</a>
+<a name="125"><span class="lineNum">     125 </span>            : // [asmjit::CodeCompiler - Func]</a>
+<a name="126"><span class="lineNum">     126 </span>            : // ============================================================================</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       1948 : CCFunc* CodeCompiler::newFunc(const FuncSignature&amp; sign) noexcept {</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   Error err;</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   CCFunc* func = newNodeT&lt;CCFunc&gt;();</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       1948 :   if (!func) goto _NoMemory;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1948 :   err = registerLabelNode(func);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(err)) {</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :     // TODO: Calls setLastError, maybe rethink noexcept?</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     setLastError(err);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // Create helper nodes.</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       1948 :   func-&gt;_exitNode = newLabelNode();</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1948 :   func-&gt;_end = newNodeT&lt;CBSentinel&gt;();</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1948 :   if (!func-&gt;_exitNode || !func-&gt;_end)</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     goto _NoMemory;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :   // Function prototype.</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1948 :   err = func-&gt;getDetail().init(sign);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       1948 :   if (err != kErrorOk) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     setLastError(err);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   // If the CodeInfo guarantees higher alignment honor it.</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       1948 :   if (_codeInfo.getStackAlignment() &gt; func-&gt;_funcDetail._callConv.getNaturalStackAlignment())</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     func-&gt;_funcDetail._callConv.setNaturalStackAlignment(_codeInfo.getStackAlignment());</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Allocate space for function arguments.</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1948 :   func-&gt;_args = nullptr;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1948 :   if (func-&gt;getArgCount() != 0) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     func-&gt;_args = _cbHeap.allocT&lt;VirtReg*&gt;(func-&gt;getArgCount() * sizeof(VirtReg*));</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     if (!func-&gt;_args) goto _NoMemory;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     ::memset(func-&gt;_args, 0, func-&gt;getArgCount() * sizeof(VirtReg*));</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   return func;</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 : _NoMemory:</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   return nullptr;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1948 : CCFunc* CodeCompiler::addFunc(CCFunc* func) {</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   ASMJIT_ASSERT(_func == nullptr);</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       1948 :   _func = func;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       1948 :   addNode(func);                 // Function node.</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   CBNode* cursor = getCursor();  // {CURSOR}.</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       1948 :   addNode(func-&gt;getExitNode());  // Function exit label.</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       1948 :   addNode(func-&gt;getEnd());       // Function end marker.</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :   _setCursor(cursor);</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       1948 :   return func;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       1948 : CCFunc* CodeCompiler::addFunc(const FuncSignature&amp; sign) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       1948 :   CCFunc* func = newFunc(sign);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1948 :   if (!func) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       1948 :   return addFunc(func);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       1948 : CBSentinel* CodeCompiler::endFunc() {</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   CCFunc* func = getFunc();</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1948 :   if (!func) {</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :     // TODO:</a>
+<a name="203"><span class="lineNum">     203 </span>            :     return nullptr;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   // Add the local constant pool at the end of the function (if exists).</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       1948 :   if (_localConstPool) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     setCursor(func-&gt;getEnd()-&gt;getPrev());</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :     addNode(_localConstPool);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :     _localConstPool = nullptr;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            :   // Mark as finished.</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1948 :   func-&gt;_isFinished = true;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1948 :   _func = nullptr;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   CBSentinel* end = func-&gt;getEnd();</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       1948 :   setCursor(end);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1948 :   return end;</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : // ============================================================================</a>
+<a name="223"><span class="lineNum">     223 </span>            : // [asmjit::CodeCompiler - Ret]</a>
+<a name="224"><span class="lineNum">     224 </span>            : // ============================================================================</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       1948 : CCFuncRet* CodeCompiler::newRet(const Operand_&amp; o0, const Operand_&amp; o1) noexcept {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       1948 :   CCFuncRet* node = newNodeT&lt;CCFuncRet&gt;(o0, o1);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       1948 :   if (!node) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   }</a>
+<a name="232"><span class="lineNum">     232 </span>            :   return node;</a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       1948 : CCFuncRet* CodeCompiler::addRet(const Operand_&amp; o0, const Operand_&amp; o1) noexcept {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       1948 :   CCFuncRet* node = newRet(o0, o1);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       1948 :   if (!node) return nullptr;</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       1948 :   return static_cast&lt;CCFuncRet*&gt;(addNode(node));</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : }</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : // ============================================================================</a>
+<a name="242"><span class="lineNum">     242 </span>            : // [asmjit::CodeCompiler - Call]</a>
+<a name="243"><span class="lineNum">     243 </span>            : // ============================================================================</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       1648 : CCFuncCall* CodeCompiler::newCall(uint32_t instId, const Operand_&amp; o0, const FuncSignature&amp; sign) noexcept {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   Error err;</a>
+<a name="247"><span class="lineNum">     247 </span>            :   uint32_t nArgs;</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       1648 :   CCFuncCall* node = _cbHeap.allocT&lt;CCFuncCall&gt;(sizeof(CCFuncCall) + sizeof(Operand));</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       1648 :   Operand* opArray = reinterpret_cast&lt;Operand*&gt;(reinterpret_cast&lt;uint8_t*&gt;(node) + sizeof(CCFuncCall));</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       1648 :   if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :     goto _NoMemory;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">       1648 :   opArray[0].copyFrom(o0);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   new (node) CCFuncCall(this, instId, 0, opArray, 1);</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       1648 :   if ((err = node-&gt;getDetail().init(sign)) != kErrorOk) {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     setLastError(err);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   // If there are no arguments skip the allocation.</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       1648 :   if ((nArgs = sign.getArgCount()) == 0)</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     return node;</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       1648 :   node-&gt;_args = static_cast&lt;Operand*&gt;(_cbHeap.alloc(nArgs * sizeof(Operand)));</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       1648 :   if (!node-&gt;_args) goto _NoMemory;</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   ::memset(node-&gt;_args, 0, nArgs * sizeof(Operand));</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       1648 :   return node;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 : _NoMemory:</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :   setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   return nullptr;</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : }</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       1648 : CCFuncCall* CodeCompiler::addCall(uint32_t instId, const Operand_&amp; o0, const FuncSignature&amp; sign) noexcept {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       1648 :   CCFuncCall* node = newCall(instId, o0, sign);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       1648 :   if (!node) return nullptr;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       1648 :   return static_cast&lt;CCFuncCall*&gt;(addNode(node));</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : // ============================================================================</a>
+<a name="285"><span class="lineNum">     285 </span>            : // [asmjit::CodeCompiler - Vars]</a>
+<a name="286"><span class="lineNum">     286 </span>            : // ============================================================================</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 : Error CodeCompiler::setArg(uint32_t argIndex, const Reg&amp; r) {</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   CCFunc* func = getFunc();</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   if (!func)</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidState));</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :   if (!isVirtRegValid(r))</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidVirtId));</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   VirtReg* vr = getVirtReg(r);</a>
+<a name="298"><span class="lineNum">     298 </span>            :   func-&gt;setArg(argIndex, vr);</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : // ============================================================================</a>
+<a name="304"><span class="lineNum">     304 </span>            : // [asmjit::CodeCompiler - Hint]</a>
+<a name="305"><span class="lineNum">     305 </span>            : // ============================================================================</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 : Error CodeCompiler::_hint(Reg&amp; r, uint32_t hint, uint32_t value) {</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :   if (!r.isVirtReg()) return kErrorOk;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :   CCHint* node = newHintNode(r, hint, value);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :   if (!node) return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :   addNode(node);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : // ============================================================================</a>
+<a name="318"><span class="lineNum">     318 </span>            : // [asmjit::CodeCompiler - Vars]</a>
+<a name="319"><span class="lineNum">     319 </span>            : // ============================================================================</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">      23788 : VirtReg* CodeCompiler::newVirtReg(uint32_t typeId, uint32_t signature, const char* name) noexcept {</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   size_t index = _vRegArray.getLength();</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">      23788 :   if (ASMJIT_UNLIKELY(index &gt; Operand::kPackedIdCount))</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :     return nullptr;</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   VirtReg* vreg;</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      29036 :   if (_vRegArray.willGrow(&amp;_cbHeap, 1) != kErrorOk || !(vreg = _vRegZone.allocZeroedT&lt;VirtReg&gt;()))</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">      23788 :   vreg-&gt;_id = Operand::packId(static_cast&lt;uint32_t&gt;(index));</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">      23788 :   vreg-&gt;_regInfo._signature = signature;</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      23788 :   vreg-&gt;_name = noName;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      23788 :   if (name &amp;&amp; name[0] != '\0')</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :     vreg-&gt;_name = static_cast&lt;char*&gt;(_cbDataZone.dup(name, ::strlen(name), true));</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      23788 :   vreg-&gt;_size = TypeId::sizeOf(typeId);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      23788 :   vreg-&gt;_typeId = typeId;</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      23788 :   vreg-&gt;_alignment = static_cast&lt;uint8_t&gt;(std::min&lt;uint32_t&gt;(vreg-&gt;_size, 64));</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">      23788 :   vreg-&gt;_priority = 10;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :   // The following are only used by `RAPass`.</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">      23788 :   vreg-&gt;_raId = kInvalidValue;</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">      23788 :   vreg-&gt;_state = VirtReg::kStateNone;</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">      23788 :   vreg-&gt;_physId = Globals::kInvalidRegId;</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   _vRegArray.appendUnsafe(vreg);</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">      23788 :   return vreg;</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : }</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">      23788 : Error CodeCompiler::_newReg(Reg&amp; out, uint32_t typeId, const char* name) {</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :   RegInfo regInfo;</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">      23788 :   Error err = ArchUtils::typeIdToRegInfo(getArchType(), typeId, regInfo);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">      23788 :   if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">      23788 :   VirtReg* vReg = newVirtReg(typeId, regInfo.getSignature(), name);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">      23788 :   if (ASMJIT_UNLIKELY(!vReg)) {</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :     out.reset();</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :   }</a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            :   out._initReg(regInfo.getSignature(), vReg-&gt;getId());</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">      23788 :   return kErrorOk;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 : Error CodeCompiler::_newReg(Reg&amp; out, uint32_t typeId, const char* nameFmt, va_list ap) {</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="371"><span class="lineNum">     371 </span>            :   sb.appendFormatVA(nameFmt, ap);</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :   return _newReg(out, typeId, sb.getData());</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 : Error CodeCompiler::_newReg(Reg&amp; out, const Reg&amp; ref, const char* name) {</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   RegInfo regInfo;</a>
+<a name="377"><span class="lineNum">     377 </span>            :   uint32_t typeId;</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   if (isVirtRegValid(ref)) {</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :     VirtReg* vRef = getVirtReg(ref);</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :     typeId = vRef-&gt;getTypeId();</span></a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            :     // NOTE: It's possible to cast one register type to another if it's the</a>
+<a name="384"><span class="lineNum">     384 </span>            :     // same register kind. However, VirtReg always contains the TypeId that</a>
+<a name="385"><span class="lineNum">     385 </span>            :     // was used to create the register. This means that in some cases we may</a>
+<a name="386"><span class="lineNum">     386 </span>            :     // end up having different size of `ref` and `vRef`. In such case we</a>
+<a name="387"><span class="lineNum">     387 </span>            :     // adjust the TypeId to match the `ref` register type instead of the</a>
+<a name="388"><span class="lineNum">     388 </span>            :     // original register type, which should be the expected behavior.</a>
+<a name="389"><span class="lineNum">     389 </span>            :     uint32_t typeSize = TypeId::sizeOf(typeId);</a>
+<a name="390"><span class="lineNum">     390 </span>            :     uint32_t refSize = ref.getSize();</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :     if (typeSize != refSize) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(typeId)) {</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :         // GP register - change TypeId to match `ref`, but keep sign of `vRef`.</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :         switch (refSize) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :           case  1: typeId = TypeId::kI8  | (typeId &amp; 1); break;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :           case  2: typeId = TypeId::kI16 | (typeId &amp; 1); break;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :           case  4: typeId = TypeId::kI32 | (typeId &amp; 1); break;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :           case  8: typeId = TypeId::kI64 | (typeId &amp; 1); break;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :           default: typeId = TypeId::kVoid; break;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :         }</a>
+<a name="402"><span class="lineNum">     402 </span>            :       }</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :       else if (TypeId::isMmx(typeId)) {</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :         // MMX register - always use 64-bit.</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :         typeId = TypeId::kMmx64;</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :       }</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :       else if (TypeId::isMask(typeId)) {</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :         // Mask register - change TypeId to match `ref` size.</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :         switch (refSize) {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :           case  1: typeId = TypeId::kMask8; break;</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :           case  2: typeId = TypeId::kMask16; break;</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :           case  4: typeId = TypeId::kMask32; break;</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :           case  8: typeId = TypeId::kMask64; break;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :           default: typeId = TypeId::kVoid; break;</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :         }</a>
+<a name="416"><span class="lineNum">     416 </span>            :       }</a>
+<a name="417"><span class="lineNum">     417 </span>            :       else {</a>
+<a name="418"><span class="lineNum">     418 </span>            :         // VEC register - change TypeId to match `ref` size, keep vector metadata.</a>
+<a name="419"><span class="lineNum">     419 </span>            :         uint32_t elementTypeId = TypeId::elementOf(typeId);</a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :         switch (refSize) {</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :           case 16: typeId = TypeId::_kVec128Start + (elementTypeId - TypeId::kI8); break;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :           case 32: typeId = TypeId::_kVec256Start + (elementTypeId - TypeId::kI8); break;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :           case 64: typeId = TypeId::_kVec512Start + (elementTypeId - TypeId::kI8); break;</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :           default: typeId = TypeId::kVoid; break;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :         }</a>
+<a name="427"><span class="lineNum">     427 </span>            :       }</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :       if (typeId == TypeId::kVoid)</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :         return setLastError(DebugUtils::errored(kErrorInvalidState));</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :     }</a>
+<a name="432"><span class="lineNum">     432 </span>            :   }</a>
+<a name="433"><span class="lineNum">     433 </span>            :   else {</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     typeId = ref.getType();</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :   }</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :   Error err = ArchUtils::typeIdToRegInfo(getArchType(), typeId, regInfo);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :   VirtReg* vReg = newVirtReg(typeId, regInfo.getSignature(), name);</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!vReg)) {</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :     out.reset();</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            :   out._initReg(regInfo.getSignature(), vReg-&gt;getId());</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="448"><span class="lineNum">     448 </span>            : }</a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 : Error CodeCompiler::_newReg(Reg&amp; out, const Reg&amp; ref, const char* nameFmt, va_list ap) {</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :   StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="452"><span class="lineNum">     452 </span>            :   sb.appendFormatVA(nameFmt, ap);</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :   return _newReg(out, ref, sb.getData());</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 : Error CodeCompiler::_newStack(Mem&amp; out, uint32_t size, uint32_t alignment, const char* name) {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :   if (size == 0)</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidArgument));</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   if (alignment == 0) alignment = 1;</a>
+<a name="461"><span class="lineNum">     461 </span>            :   if (!Utils::isPowerOf2(alignment))</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidArgument));</span></a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            :   if (alignment &gt; 64) alignment = 64;</a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :   VirtReg* vReg = newVirtReg(0, 0, name);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!vReg)) {</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :     out.reset();</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :   }</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :   vReg-&gt;_size = size;</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :   vReg-&gt;_isStack = true;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :   vReg-&gt;_alignment = static_cast&lt;uint8_t&gt;(alignment);</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            :   // Set the memory operand to GPD/GPQ and its id to VirtReg.</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   out = Mem(Init, _nativeGpReg.getType(), vReg-&gt;getId(), Reg::kRegNone, kInvalidValue, 0, 0, Mem::kSignatureMemRegHomeFlag);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : }</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 : Error CodeCompiler::_newConst(Mem&amp; out, uint32_t scope, const void* data, size_t size) {</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   CBConstPool** pPool;</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineNoCov">          0 :   if (scope == kConstScopeLocal)</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineNoCov">          0 :     pPool = &amp;_localConstPool;</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :   else if (scope == kConstScopeGlobal)</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :     pPool = &amp;_globalConstPool;</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :   else</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidArgument));</span></a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineNoCov">          0 :   if (!*pPool &amp;&amp; !(*pPool = newConstPool()))</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :   CBConstPool* pool = *pPool;</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :   size_t off;</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            :   Error err = pool-&gt;add(data, size, off);</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :   out = Mem(Init,</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :     Label::kLabelTag,             // Base type.</a>
+<a name="501"><span class="lineNum">     501 </span>            :     pool-&gt;getId(),                // Base id.</a>
+<a name="502"><span class="lineNum">     502 </span>            :     0,                            // Index type.</a>
+<a name="503"><span class="lineNum">     503 </span>            :     kInvalidValue,                // Index id.</a>
+<a name="504"><span class="lineNum">     504 </span>            :     static_cast&lt;int32_t&gt;(off),    // Offset.</a>
+<a name="505"><span class="lineNum">     505 </span>            :     static_cast&lt;uint32_t&gt;(size),  // Size.</a>
+<a name="506"><span class="lineNum">     506 </span>            :     0);                           // Flags.</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 : Error CodeCompiler::alloc(Reg&amp; reg) {</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return kErrorOk;</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :   return _hint(reg, CCHint::kHintAlloc, kInvalidValue);</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 : Error CodeCompiler::alloc(Reg&amp; reg, uint32_t physId) {</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return kErrorOk;</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :   return _hint(reg, CCHint::kHintAlloc, physId);</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : }</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 : Error CodeCompiler::alloc(Reg&amp; reg, const Reg&amp; physReg) {</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return kErrorOk;</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 :   return _hint(reg, CCHint::kHintAlloc, physReg.getId());</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : }</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 : Error CodeCompiler::save(Reg&amp; reg) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return kErrorOk;</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :   return _hint(reg, CCHint::kHintSave, kInvalidValue);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            : }</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 : Error CodeCompiler::spill(Reg&amp; reg) {</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return kErrorOk;</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :   return _hint(reg, CCHint::kHintSpill, kInvalidValue);</span></a>
+<a name="533"><span class="lineNum">     533 </span>            : }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 : Error CodeCompiler::unuse(Reg&amp; reg) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return kErrorOk;</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :   return _hint(reg, CCHint::kHintUnuse, kInvalidValue);</span></a>
+<a name="538"><span class="lineNum">     538 </span>            : }</a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 : uint32_t CodeCompiler::getPriority(Reg&amp; reg) const {</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return 0;</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :   return getVirtRegById(reg.getId())-&gt;getPriority();</span></a>
+<a name="543"><span class="lineNum">     543 </span>            : }</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 : void CodeCompiler::setPriority(Reg&amp; reg, uint32_t priority) {</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return;</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :   if (priority &gt; 255) priority = 255;</a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span>            :   VirtReg* vreg = getVirtRegById(reg.getId());</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :   if (vreg) vreg-&gt;_priority = static_cast&lt;uint8_t&gt;(priority);</span></a>
+<a name="551"><span class="lineNum">     551 </span>            : }</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 : bool CodeCompiler::getSaveOnUnuse(Reg&amp; reg) const {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return false;</span></a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            :   VirtReg* vreg = getVirtRegById(reg.getId());</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :   return static_cast&lt;bool&gt;(vreg-&gt;_saveOnUnuse);</span></a>
+<a name="558"><span class="lineNum">     558 </span>            : }</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineNoCov">          0 : void CodeCompiler::setSaveOnUnuse(Reg&amp; reg, bool value) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return;</span></a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span>            :   VirtReg* vreg = getVirtRegById(reg.getId());</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :   if (!vreg) return;</span></a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineNoCov">          0 :   vreg-&gt;_saveOnUnuse = value;</span></a>
+<a name="567"><span class="lineNum">     567 </span>            : }</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 : void CodeCompiler::rename(Reg&amp; reg, const char* fmt, ...) {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :   if (!reg.isVirtReg()) return;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span>            :   VirtReg* vreg = getVirtRegById(reg.getId());</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :   if (!vreg) return;</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :   vreg-&gt;_name = noName;</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :   if (fmt &amp;&amp; fmt[0] != '\0') {</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :     char buf[64];</a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span>            :     va_list ap;</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :     va_start(ap, fmt);</span></a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span>            :     vsnprintf(buf, ASMJIT_ARRAY_SIZE(buf), fmt, ap);</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :     buf[ASMJIT_ARRAY_SIZE(buf) - 1] = '\0';</span></a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineNoCov">          0 :     vreg-&gt;_name = static_cast&lt;char*&gt;(_cbDataZone.dup(buf, ::strlen(buf), true));</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 :     va_end(ap);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :   }</a>
+<a name="588"><span class="lineNum">     588 </span>            : }</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span>            : } // asmjit namespace</a>
+<a name="591"><span class="lineNum">     591 </span>            : } // namespace PLMD</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span>            : // [Api-End]</a>
+<a name="594"><span class="lineNum">     594 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            : // [Guard]</a>
+<a name="597"><span class="lineNum">     597 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="598"><span class="lineNum">     598 </span>            : #pragma GCC diagnostic pop</a>
+<a name="599"><span class="lineNum">     599 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codecompiler.h.func-sort-c.html b/coverage-libs/asmjit/codecompiler.h.func-sort-c.html
new file mode 100644
index 0000000000..872f801646
--- /dev/null
+++ b/coverage-libs/asmjit/codecompiler.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codecompiler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codecompiler.h<span style="font-size: 80%;"> (<a href="codecompiler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntryLo">64.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="codecompiler.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codecompiler.h.func.html b/coverage-libs/asmjit/codecompiler.h.func.html
new file mode 100644
index 0000000000..20ccf4cd0d
--- /dev/null
+++ b/coverage-libs/asmjit/codecompiler.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codecompiler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codecompiler.h<span style="font-size: 80%;"> (<a href="codecompiler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntryLo">64.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codecompiler.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codecompiler.h.gcov.html b/coverage-libs/asmjit/codecompiler.h.gcov.html
new file mode 100644
index 0000000000..f240ee3f9e
--- /dev/null
+++ b/coverage-libs/asmjit/codecompiler.h.gcov.html
@@ -0,0 +1,843 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codecompiler.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codecompiler.h<span style="font-size: 80%;"> (source / <a href="codecompiler.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntryLo">64.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_codecompiler_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_codecompiler_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_CODECOMPILER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_CODECOMPILER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Dependencies]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./codebuilder.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./constpool.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./func.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;./zone.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // [Api-Begin]</a>
+<a name="48"><span class="lineNum">      48 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace PLMD {</a>
+<a name="51"><span class="lineNum">      51 </span>            : namespace asmjit {</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : // [Forward Declarations]</a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : struct VirtReg;</a>
+<a name="58"><span class="lineNum">      58 </span>            : struct TiedReg;</a>
+<a name="59"><span class="lineNum">      59 </span>            : struct RAState;</a>
+<a name="60"><span class="lineNum">      60 </span>            : struct RACell;</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : //! \addtogroup asmjit_base</a>
+<a name="63"><span class="lineNum">      63 </span>            : //! \{</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : // ============================================================================</a>
+<a name="66"><span class="lineNum">      66 </span>            : // [asmjit::ConstScope]</a>
+<a name="67"><span class="lineNum">      67 </span>            : // ============================================================================</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : //! Scope of the constant.</a>
+<a name="70"><span class="lineNum">      70 </span>            : ASMJIT_ENUM(ConstScope) {</a>
+<a name="71"><span class="lineNum">      71 </span>            :   //! Local constant, always embedded right after the current function.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   kConstScopeLocal = 0,</a>
+<a name="73"><span class="lineNum">      73 </span>            :   //! Global constant, embedded at the end of the currently compiled code.</a>
+<a name="74"><span class="lineNum">      74 </span>            :   kConstScopeGlobal = 1</a>
+<a name="75"><span class="lineNum">      75 </span>            : };</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : // ============================================================================</a>
+<a name="78"><span class="lineNum">      78 </span>            : // [asmjit::VirtReg]</a>
+<a name="79"><span class="lineNum">      79 </span>            : // ============================================================================</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : //! Virtual register data (CodeCompiler).</a>
+<a name="82"><span class="lineNum">      82 </span>            : struct VirtReg {</a>
+<a name="83"><span class="lineNum">      83 </span>            :   //! A state of a virtual register (used during register allocation).</a>
+<a name="84"><span class="lineNum">      84 </span>            :   ASMJIT_ENUM(State) {</a>
+<a name="85"><span class="lineNum">      85 </span>            :     kStateNone = 0,                      //!&lt; Not allocated, not used.</a>
+<a name="86"><span class="lineNum">      86 </span>            :     kStateReg = 1,                       //!&lt; Allocated in register.</a>
+<a name="87"><span class="lineNum">      87 </span>            :     kStateMem = 2                        //!&lt; Allocated in memory or spilled.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   };</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // [Accessors]</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Get the virtual-register id.</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      32216 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   //! Get virtual-register's name.</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const char* getName() const noexcept { return _name; }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   //! Get a physical register type.</a>
+<a name="100"><span class="lineNum">     100 </span>            :   ASMJIT_INLINE uint32_t getType() const noexcept { return _regInfo.getType(); }</a>
+<a name="101"><span class="lineNum">     101 </span>            :   //! Get a physical register kind.</a>
+<a name="102"><span class="lineNum">     102 </span>            :   ASMJIT_INLINE uint32_t getKind() const noexcept { return _regInfo.getKind(); }</a>
+<a name="103"><span class="lineNum">     103 </span>            :   //! Get a physical register size.</a>
+<a name="104"><span class="lineNum">     104 </span>            :   ASMJIT_INLINE uint32_t getRegSize() const noexcept { return _regInfo.getSize(); }</a>
+<a name="105"><span class="lineNum">     105 </span>            :   //! Get a register signature of this virtual register.</a>
+<a name="106"><span class="lineNum">     106 </span>            :   ASMJIT_INLINE uint32_t getSignature() const noexcept { return _regInfo.getSignature(); }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   //! Get a register's type-id, see \ref TypeId.</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       9084 :   ASMJIT_INLINE uint32_t getTypeId() const noexcept { return _typeId; }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   //! Get virtual-register's size.</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      25896 :   ASMJIT_INLINE uint32_t getSize() const noexcept { return _size; }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Get virtual-register's alignment.</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getAlignment() const noexcept { return _alignment; }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   //! Get the virtual-register  priority, used by compiler to decide which variable to spill.</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getPriority() const noexcept { return _priority; }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   //! Set the virtual-register  priority.</a>
+<a name="119"><span class="lineNum">     119 </span>            :   ASMJIT_INLINE void setPriority(uint32_t priority) noexcept {</a>
+<a name="120"><span class="lineNum">     120 </span>            :     ASMJIT_ASSERT(priority &lt;= 0xFF);</a>
+<a name="121"><span class="lineNum">     121 </span>            :     _priority = static_cast&lt;uint8_t&gt;(priority);</a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   //! Get variable state, only used by `RAPass`.</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       4972 :   ASMJIT_INLINE uint32_t getState() const noexcept { return _state; }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   //! Set variable state, only used by `RAPass`.</a>
+<a name="127"><span class="lineNum">     127 </span>            :   ASMJIT_INLINE void setState(uint32_t state) {</a>
+<a name="128"><span class="lineNum">     128 </span>            :     ASMJIT_ASSERT(state &lt;= 0xFF);</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     _state = static_cast&lt;uint8_t&gt;(state);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      24746 :   }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   //! Get register index.</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">     181634 :   ASMJIT_INLINE uint32_t getPhysId() const noexcept { return _physId; }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   //! Set register index.</a>
+<a name="135"><span class="lineNum">     135 </span>            :   ASMJIT_INLINE void setPhysId(uint32_t physId) {</a>
+<a name="136"><span class="lineNum">     136 </span>            :     ASMJIT_ASSERT(physId &lt;= Globals::kInvalidRegId);</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        656 :     _physId = static_cast&lt;uint8_t&gt;(physId);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   //! Reset register index.</a>
+<a name="140"><span class="lineNum">     140 </span>            :   ASMJIT_INLINE void resetPhysId() {</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      50052 :     _physId = static_cast&lt;uint8_t&gt;(Globals::kInvalidRegId);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   //! Get home registers mask.</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      26412 :   ASMJIT_INLINE uint32_t getHomeMask() const { return _homeMask; }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! Add a home register index to the home registers mask.</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       4424 :   ASMJIT_INLINE void addHomeId(uint32_t physId) { _homeMask |= Utils::mask(physId); }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      27940 :   ASMJIT_INLINE bool isFixed() const noexcept { return static_cast&lt;bool&gt;(_isFixed); }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   //! Get whether the VirtReg is only memory allocated on the stack.</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      10104 :   ASMJIT_INLINE bool isStack() const noexcept { return static_cast&lt;bool&gt;(_isStack); }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   //! Get whether to save variable when it's unused (spill).</a>
+<a name="155"><span class="lineNum">     155 </span>            :   ASMJIT_INLINE bool saveOnUnuse() const noexcept { return static_cast&lt;bool&gt;(_saveOnUnuse); }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   //! Get whether the variable was changed.</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      10462 :   ASMJIT_INLINE bool isModified() const noexcept { return static_cast&lt;bool&gt;(_modified); }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   //! Set whether the variable was changed.</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      88836 :   ASMJIT_INLINE void setModified(bool modified) noexcept { _modified = modified; }</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! Get home memory offset.</a>
+<a name="163"><span class="lineNum">     163 </span>            :   ASMJIT_INLINE int32_t getMemOffset() const noexcept { return _memOffset; }</a>
+<a name="164"><span class="lineNum">     164 </span>            :   //! Set home memory offset.</a>
+<a name="165"><span class="lineNum">     165 </span>            :   ASMJIT_INLINE void setMemOffset(int32_t offset) noexcept { _memOffset = offset; }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   //! Get home memory cell.</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       8428 :   ASMJIT_INLINE RACell* getMemCell() const noexcept { return _memCell; }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   //! Set home memory cell.</a>
+<a name="170"><span class="lineNum">     170 </span>            :   ASMJIT_INLINE void setMemCell(RACell* cell) noexcept { _memCell = cell; }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="173"><span class="lineNum">     173 </span>            :   // [Members]</a>
+<a name="174"><span class="lineNum">     174 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   uint32_t _id;                          //!&lt; Virtual register id.</a>
+<a name="177"><span class="lineNum">     177 </span>            :   RegInfo _regInfo;                      //!&lt; Physical register info &amp; signature.</a>
+<a name="178"><span class="lineNum">     178 </span>            :   const char* _name;                     //!&lt; Virtual name (user provided).</a>
+<a name="179"><span class="lineNum">     179 </span>            :   uint32_t _size;                        //!&lt; Virtual size (can be smaller than `regInfo._size`).</a>
+<a name="180"><span class="lineNum">     180 </span>            :   uint8_t _typeId;                       //!&lt; Type-id.</a>
+<a name="181"><span class="lineNum">     181 </span>            :   uint8_t _alignment;                    //!&lt; Register's natural alignment (for spilling).</a>
+<a name="182"><span class="lineNum">     182 </span>            :   uint8_t _priority;                     //!&lt; Allocation priority (hint for RAPass that can be ignored).</a>
+<a name="183"><span class="lineNum">     183 </span>            :   uint8_t _isFixed : 1;                  //!&lt; True if this is a fixed register, never reallocated.</a>
+<a name="184"><span class="lineNum">     184 </span>            :   uint8_t _isStack : 1;                  //!&lt; True if the virtual register is only used as a stack.</a>
+<a name="185"><span class="lineNum">     185 </span>            :   uint8_t _isMaterialized : 1;           //!&lt; Register is constant that is easily created by a single instruction.</a>
+<a name="186"><span class="lineNum">     186 </span>            :   uint8_t _saveOnUnuse : 1;              //!&lt; Save on unuse (at end of the variable scope).</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // The following members are used exclusively by RAPass. They are initialized</a>
+<a name="190"><span class="lineNum">     190 </span>            :   // when the VirtReg is created and then changed during RAPass.</a>
+<a name="191"><span class="lineNum">     191 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   uint32_t _raId;                        //!&lt; Register allocator work-id (used by RAPass).</a>
+<a name="194"><span class="lineNum">     194 </span>            :   int32_t _memOffset;                    //!&lt; Home memory offset.</a>
+<a name="195"><span class="lineNum">     195 </span>            :   uint32_t _homeMask;                    //!&lt; Mask of all registers variable has been allocated to.</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   uint8_t _state;                        //!&lt; Variable state (connected with actual `RAState)`.</a>
+<a name="198"><span class="lineNum">     198 </span>            :   uint8_t _physId;                       //!&lt; Actual register index (only used by `RAPass)`, during translate.</a>
+<a name="199"><span class="lineNum">     199 </span>            :   uint8_t _modified;                     //!&lt; Whether variable was changed (connected with actual `RAState)`.</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :   RACell* _memCell;                      //!&lt; Home memory cell, used by `RAPass` (initially nullptr).</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   //! Temporary link to TiedReg* used by the `RAPass` used in</a>
+<a name="204"><span class="lineNum">     204 </span>            :   //! various phases, but always set back to nullptr when finished.</a>
+<a name="205"><span class="lineNum">     205 </span>            :   //!</a>
+<a name="206"><span class="lineNum">     206 </span>            :   //! This temporary data is designed to be used by algorithms that need to</a>
+<a name="207"><span class="lineNum">     207 </span>            :   //! store some data into variables themselves during compilation. But it's</a>
+<a name="208"><span class="lineNum">     208 </span>            :   //! expected that after variable is compiled &amp; translated the data is set</a>
+<a name="209"><span class="lineNum">     209 </span>            :   //! back to zero/null. Initial value is nullptr.</a>
+<a name="210"><span class="lineNum">     210 </span>            :   TiedReg* _tied;</a>
+<a name="211"><span class="lineNum">     211 </span>            : };</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : // ============================================================================</a>
+<a name="214"><span class="lineNum">     214 </span>            : // [asmjit::CCHint]</a>
+<a name="215"><span class="lineNum">     215 </span>            : // ============================================================================</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : //! Hint for register allocator (CodeCompiler).</a>
+<a name="218"><span class="lineNum">     218 </span>            : class CCHint : public CBNode {</a>
+<a name="219"><span class="lineNum">     219 </span>            : public:</a>
+<a name="220"><span class="lineNum">     220 </span>            :   ASMJIT_NONCOPYABLE(CCHint)</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   //! Hint type.</a>
+<a name="223"><span class="lineNum">     223 </span>            :   ASMJIT_ENUM(Hint) {</a>
+<a name="224"><span class="lineNum">     224 </span>            :     //! Alloc to physical reg.</a>
+<a name="225"><span class="lineNum">     225 </span>            :     kHintAlloc = 0,</a>
+<a name="226"><span class="lineNum">     226 </span>            :     //! Spill to memory.</a>
+<a name="227"><span class="lineNum">     227 </span>            :     kHintSpill = 1,</a>
+<a name="228"><span class="lineNum">     228 </span>            :     //! Save if modified.</a>
+<a name="229"><span class="lineNum">     229 </span>            :     kHintSave = 2,</a>
+<a name="230"><span class="lineNum">     230 </span>            :     //! Save if modified and mark it as unused.</a>
+<a name="231"><span class="lineNum">     231 </span>            :     kHintSaveAndUnuse = 3,</a>
+<a name="232"><span class="lineNum">     232 </span>            :     //! Mark as unused.</a>
+<a name="233"><span class="lineNum">     233 </span>            :     kHintUnuse = 4</a>
+<a name="234"><span class="lineNum">     234 </span>            :   };</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="237"><span class="lineNum">     237 </span>            :   // [Construction / Destruction]</a>
+<a name="238"><span class="lineNum">     238 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   //! Create a new `CCHint` instance.</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CCHint(CodeBuilder* cb, VirtReg* vreg, uint32_t hint, uint32_t value) noexcept : CBNode(cb, kNodeHint) {</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     orFlags(kFlagIsRemovable | kFlagIsInformative);</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :     _vreg = vreg;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :     _hint = hint;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :     _value = value;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   //! Destroy the `CCHint` instance (NEVER CALLED).</a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_INLINE ~CCHint() noexcept {}</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="252"><span class="lineNum">     252 </span>            :   // [Accessors]</a>
+<a name="253"><span class="lineNum">     253 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   //! Get variable.</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE VirtReg* getVReg() const noexcept { return _vreg; }</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   //! Get hint it, see \ref Hint.</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getHint() const noexcept { return _hint; }</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   //! Set hint it, see \ref Hint.</a>
+<a name="261"><span class="lineNum">     261 </span>            :   ASMJIT_INLINE void setHint(uint32_t hint) noexcept { _hint = hint; }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   //! Get hint value.</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getValue() const noexcept { return _value; }</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   //! Set hint value.</a>
+<a name="266"><span class="lineNum">     266 </span>            :   ASMJIT_INLINE void setValue(uint32_t value) noexcept { _value = value; }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="269"><span class="lineNum">     269 </span>            :   // [Members]</a>
+<a name="270"><span class="lineNum">     270 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :   //! Variable.</a>
+<a name="273"><span class="lineNum">     273 </span>            :   VirtReg* _vreg;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   //! Hint id.</a>
+<a name="275"><span class="lineNum">     275 </span>            :   uint32_t _hint;</a>
+<a name="276"><span class="lineNum">     276 </span>            :   //! Value.</a>
+<a name="277"><span class="lineNum">     277 </span>            :   uint32_t _value;</a>
+<a name="278"><span class="lineNum">     278 </span>            : };</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            : // ============================================================================</a>
+<a name="281"><span class="lineNum">     281 </span>            : // [asmjit::CCFunc]</a>
+<a name="282"><span class="lineNum">     282 </span>            : // ============================================================================</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : //! Function entry (CodeCompiler).</a>
+<a name="285"><span class="lineNum">     285 </span>            : class CCFunc : public CBLabel {</a>
+<a name="286"><span class="lineNum">     286 </span>            : public:</a>
+<a name="287"><span class="lineNum">     287 </span>            :   ASMJIT_NONCOPYABLE(CCFunc)</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="290"><span class="lineNum">     290 </span>            :   // [Construction / Destruction]</a>
+<a name="291"><span class="lineNum">     291 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            :   //! Create a new `CCFunc` instance.</a>
+<a name="294"><span class="lineNum">     294 </span>            :   //!</a>
+<a name="295"><span class="lineNum">     295 </span>            :   //! Always use `CodeCompiler::addFunc()` to create \ref CCFunc.</a>
+<a name="296"><span class="lineNum">     296 </span>            :   ASMJIT_INLINE CCFunc(CodeBuilder* cb) noexcept</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       1948 :     : CBLabel(cb),</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1948 :       _funcDetail(),</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       1948 :       _frameInfo(),</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1948 :       _exitNode(nullptr),</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       1948 :       _end(nullptr),</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       1948 :       _args(nullptr),</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       1948 :       _isFinished(false) {</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1948 :     _type = kNodeFunc;</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            :   //! Destroy the `CCFunc` instance (NEVER CALLED).</a>
+<a name="309"><span class="lineNum">     309 </span>            :   ASMJIT_INLINE ~CCFunc() noexcept {}</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="312"><span class="lineNum">     312 </span>            :   // [Accessors]</a>
+<a name="313"><span class="lineNum">     313 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            :   //! Get function exit `CBLabel`.</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       7792 :   ASMJIT_INLINE CBLabel* getExitNode() const noexcept { return _exitNode; }</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :   //! Get function exit label.</a>
+<a name="318"><span class="lineNum">     318 </span>            :   ASMJIT_INLINE Label getExitLabel() const noexcept { return _exitNode-&gt;getLabel(); }</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :   //! Get &quot;End of Func&quot; sentinel.</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       7792 :   ASMJIT_INLINE CBSentinel* getEnd() const noexcept { return _end; }</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :   //! Get function declaration.</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">       1948 :   ASMJIT_INLINE FuncDetail&amp; getDetail() noexcept { return _funcDetail; }</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :   //! Get function declaration.</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const FuncDetail&amp; getDetail() const noexcept { return _funcDetail; }</span></a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            :   //! Get function declaration.</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       1948 :   ASMJIT_INLINE FuncFrameInfo&amp; getFrameInfo() noexcept { return _frameInfo; }</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :   //! Get function declaration.</a>
+<a name="331"><span class="lineNum">     331 </span>            :   ASMJIT_INLINE const FuncFrameInfo&amp; getFrameInfo() const noexcept { return _frameInfo; }</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   //! Get arguments count.</a>
+<a name="334"><span class="lineNum">     334 </span>            :   ASMJIT_INLINE uint32_t getArgCount() const noexcept { return _funcDetail.getArgCount(); }</a>
+<a name="335"><span class="lineNum">     335 </span>            :   //! Get returns count.</a>
+<a name="336"><span class="lineNum">     336 </span>            :   ASMJIT_INLINE uint32_t getRetCount() const noexcept { return _funcDetail.getRetCount(); }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            :   //! Get arguments list.</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE VirtReg** getArgs() const noexcept { return _args; }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   //! Get argument at `i`.</a>
+<a name="342"><span class="lineNum">     342 </span>            :   ASMJIT_INLINE VirtReg* getArg(uint32_t i) const noexcept {</a>
+<a name="343"><span class="lineNum">     343 </span>            :     ASMJIT_ASSERT(i &lt; getArgCount());</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :     return _args[i];</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :   //! Set argument at `i`.</a>
+<a name="348"><span class="lineNum">     348 </span>            :   ASMJIT_INLINE void setArg(uint32_t i, VirtReg* vreg) noexcept {</a>
+<a name="349"><span class="lineNum">     349 </span>            :     ASMJIT_ASSERT(i &lt; getArgCount());</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :     _args[i] = vreg;</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :   }</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            :   //! Reset argument at `i`.</a>
+<a name="354"><span class="lineNum">     354 </span>            :   ASMJIT_INLINE void resetArg(uint32_t i) noexcept {</a>
+<a name="355"><span class="lineNum">     355 </span>            :     ASMJIT_ASSERT(i &lt; getArgCount());</a>
+<a name="356"><span class="lineNum">     356 </span>            :     _args[i] = nullptr;</a>
+<a name="357"><span class="lineNum">     357 </span>            :   }</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            :   ASMJIT_INLINE uint32_t getAttributes() const noexcept { return _frameInfo.getAttributes(); }</a>
+<a name="360"><span class="lineNum">     360 </span>            :   ASMJIT_INLINE void addAttributes(uint32_t attrs) noexcept { _frameInfo.addAttributes(attrs); }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="363"><span class="lineNum">     363 </span>            :   // [Members]</a>
+<a name="364"><span class="lineNum">     364 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            :   FuncDetail _funcDetail;                //!&lt; Function detail.</a>
+<a name="367"><span class="lineNum">     367 </span>            :   FuncFrameInfo _frameInfo;              //!&lt; Function frame information.</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            :   CBLabel* _exitNode;                    //!&lt; Function exit.</a>
+<a name="370"><span class="lineNum">     370 </span>            :   CBSentinel* _end;                      //!&lt; Function end.</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            :   VirtReg** _args;                       //!&lt; Arguments array as `VirtReg`.</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            :   //! Function was finished by `Compiler::endFunc()`.</a>
+<a name="375"><span class="lineNum">     375 </span>            :   uint8_t _isFinished;</a>
+<a name="376"><span class="lineNum">     376 </span>            : };</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : // ============================================================================</a>
+<a name="379"><span class="lineNum">     379 </span>            : // [asmjit::CCFuncRet]</a>
+<a name="380"><span class="lineNum">     380 </span>            : // ============================================================================</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            : //! Function return (CodeCompiler).</a>
+<a name="383"><span class="lineNum">     383 </span>            : class CCFuncRet : public CBNode {</a>
+<a name="384"><span class="lineNum">     384 </span>            : public:</a>
+<a name="385"><span class="lineNum">     385 </span>            :   ASMJIT_NONCOPYABLE(CCFuncRet)</a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="388"><span class="lineNum">     388 </span>            :   // [Construction / Destruction]</a>
+<a name="389"><span class="lineNum">     389 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            :   //! Create a new `CCFuncRet` instance.</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       1948 :   ASMJIT_INLINE CCFuncRet(CodeBuilder* cb, const Operand_&amp; o0, const Operand_&amp; o1) noexcept : CBNode(cb, kNodeFuncExit) {</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :     orFlags(kFlagIsRet);</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       1948 :     _ret[0].copyFrom(o0);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       1948 :     _ret[1].copyFrom(o1);</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :   }</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            :   //! Destroy the `CCFuncRet` instance (NEVER CALLED).</a>
+<a name="399"><span class="lineNum">     399 </span>            :   ASMJIT_INLINE ~CCFuncRet() noexcept {}</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="402"><span class="lineNum">     402 </span>            :   // [Accessors]</a>
+<a name="403"><span class="lineNum">     403 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            :   //! Get the first return operand.</a>
+<a name="406"><span class="lineNum">     406 </span>            :   ASMJIT_INLINE Operand&amp; getFirst() noexcept { return static_cast&lt;Operand&amp;&gt;(_ret[0]); }</a>
+<a name="407"><span class="lineNum">     407 </span>            :   //! \overload</a>
+<a name="408"><span class="lineNum">     408 </span>            :   ASMJIT_INLINE const Operand&amp; getFirst() const noexcept { return static_cast&lt;const Operand&amp;&gt;(_ret[0]); }</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :   //! Get the second return operand.</a>
+<a name="411"><span class="lineNum">     411 </span>            :   ASMJIT_INLINE Operand&amp; getSecond() noexcept { return static_cast&lt;Operand&amp;&gt;(_ret[1]); }</a>
+<a name="412"><span class="lineNum">     412 </span>            :    //! \overload</a>
+<a name="413"><span class="lineNum">     413 </span>            :   ASMJIT_INLINE const Operand&amp; getSecond() const noexcept { return static_cast&lt;const Operand&amp;&gt;(_ret[1]); }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="416"><span class="lineNum">     416 </span>            :   // [Members]</a>
+<a name="417"><span class="lineNum">     417 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span>            :   //! Return operands.</a>
+<a name="420"><span class="lineNum">     420 </span>            :   Operand_ _ret[2];</a>
+<a name="421"><span class="lineNum">     421 </span>            : };</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span>            : // ============================================================================</a>
+<a name="424"><span class="lineNum">     424 </span>            : // [asmjit::CCFuncCall]</a>
+<a name="425"><span class="lineNum">     425 </span>            : // ============================================================================</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            : //! Function call (CodeCompiler).</a>
+<a name="428"><span class="lineNum">     428 </span>            : class CCFuncCall : public CBInst {</a>
+<a name="429"><span class="lineNum">     429 </span>            : public:</a>
+<a name="430"><span class="lineNum">     430 </span>            :   ASMJIT_NONCOPYABLE(CCFuncCall)</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="433"><span class="lineNum">     433 </span>            :   // [Construction / Destruction]</a>
+<a name="434"><span class="lineNum">     434 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            :   //! Create a new `CCFuncCall` instance.</a>
+<a name="437"><span class="lineNum">     437 </span>            :   ASMJIT_INLINE CCFuncCall(CodeBuilder* cb, uint32_t instId, uint32_t options, Operand* opArray, uint32_t opCount) noexcept</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">       1648 :     : CBInst(cb, instId, options, opArray, opCount),</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">       1648 :       _funcDetail(),</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">       1648 :       _args(nullptr) {</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">       1648 :     _type = kNodeFuncCall;</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     _ret[0].reset();</a>
+<a name="444"><span class="lineNum">     444 </span>            :     _ret[1].reset();</a>
+<a name="445"><span class="lineNum">     445 </span>            :     orFlags(kFlagIsRemovable);</a>
+<a name="446"><span class="lineNum">     446 </span>            :   }</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            :   //! Destroy the `CCFuncCall` instance (NEVER CALLED).</a>
+<a name="449"><span class="lineNum">     449 </span>            :   ASMJIT_INLINE ~CCFuncCall() noexcept {}</a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="452"><span class="lineNum">     452 </span>            :   // [Signature]</a>
+<a name="453"><span class="lineNum">     453 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            :   //! Set function signature.</a>
+<a name="456"><span class="lineNum">     456 </span>            :   ASMJIT_INLINE Error setSignature(const FuncSignature&amp; sign) noexcept {</a>
+<a name="457"><span class="lineNum">     457 </span>            :     return _funcDetail.init(sign);</a>
+<a name="458"><span class="lineNum">     458 </span>            :   }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="461"><span class="lineNum">     461 </span>            :   // [Accessors]</a>
+<a name="462"><span class="lineNum">     462 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            :   //! Get function declaration.</a>
+<a name="465"><span class="lineNum">     465 </span>            :   ASMJIT_INLINE FuncDetail&amp; getDetail() noexcept { return _funcDetail; }</a>
+<a name="466"><span class="lineNum">     466 </span>            :   //! Get function declaration.</a>
+<a name="467"><span class="lineNum">     467 </span>            :   ASMJIT_INLINE const FuncDetail&amp; getDetail() const noexcept { return _funcDetail; }</a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span>            :   //! Get target operand.</a>
+<a name="470"><span class="lineNum">     470 </span>            :   ASMJIT_INLINE Operand&amp; getTarget() noexcept { return static_cast&lt;Operand&amp;&gt;(_opArray[0]); }</a>
+<a name="471"><span class="lineNum">     471 </span>            :   //! \overload</a>
+<a name="472"><span class="lineNum">     472 </span>            :   ASMJIT_INLINE const Operand&amp; getTarget() const noexcept { return static_cast&lt;const Operand&amp;&gt;(_opArray[0]); }</a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span>            :   //! Get return at `i`.</a>
+<a name="475"><span class="lineNum">     475 </span>            :   ASMJIT_INLINE Operand&amp; getRet(uint32_t i = 0) noexcept {</a>
+<a name="476"><span class="lineNum">     476 </span>            :     ASMJIT_ASSERT(i &lt; 2);</a>
+<a name="477"><span class="lineNum">     477 </span>            :     return static_cast&lt;Operand&amp;&gt;(_ret[i]);</a>
+<a name="478"><span class="lineNum">     478 </span>            :   }</a>
+<a name="479"><span class="lineNum">     479 </span>            :   //! \overload</a>
+<a name="480"><span class="lineNum">     480 </span>            :   ASMJIT_INLINE const Operand&amp; getRet(uint32_t i = 0) const noexcept {</a>
+<a name="481"><span class="lineNum">     481 </span>            :     ASMJIT_ASSERT(i &lt; 2);</a>
+<a name="482"><span class="lineNum">     482 </span>            :     return static_cast&lt;const Operand&amp;&gt;(_ret[i]);</a>
+<a name="483"><span class="lineNum">     483 </span>            :   }</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            :   //! Get argument at `i`.</a>
+<a name="486"><span class="lineNum">     486 </span>            :   ASMJIT_INLINE Operand&amp; getArg(uint32_t i) noexcept {</a>
+<a name="487"><span class="lineNum">     487 </span>            :     ASMJIT_ASSERT(i &lt; kFuncArgCountLoHi);</a>
+<a name="488"><span class="lineNum">     488 </span>            :     return static_cast&lt;Operand&amp;&gt;(_args[i]);</a>
+<a name="489"><span class="lineNum">     489 </span>            :   }</a>
+<a name="490"><span class="lineNum">     490 </span>            :   //! \overload</a>
+<a name="491"><span class="lineNum">     491 </span>            :   ASMJIT_INLINE const Operand&amp; getArg(uint32_t i) const noexcept {</a>
+<a name="492"><span class="lineNum">     492 </span>            :     ASMJIT_ASSERT(i &lt; kFuncArgCountLoHi);</a>
+<a name="493"><span class="lineNum">     493 </span>            :     return static_cast&lt;const Operand&amp;&gt;(_args[i]);</a>
+<a name="494"><span class="lineNum">     494 </span>            :   }</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            :   //! Set argument at `i` to `op`.</a>
+<a name="497"><span class="lineNum">     497 </span>            :   ASMJIT_API bool _setArg(uint32_t i, const Operand_&amp; op) noexcept;</a>
+<a name="498"><span class="lineNum">     498 </span>            :   //! Set return at `i` to `op`.</a>
+<a name="499"><span class="lineNum">     499 </span>            :   ASMJIT_API bool _setRet(uint32_t i, const Operand_&amp; op) noexcept;</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            :   //! Set argument at `i` to `reg`.</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">       1438 :   ASMJIT_INLINE bool setArg(uint32_t i, const Reg&amp; reg) noexcept { return _setArg(i, reg); }</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   //! Set argument at `i` to `imm`.</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        210 :   ASMJIT_INLINE bool setArg(uint32_t i, const Imm&amp; imm) noexcept { return _setArg(i, imm); }</span></a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span>            :   //! Set return at `i` to `var`.</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">       1648 :   ASMJIT_INLINE bool setRet(uint32_t i, const Reg&amp; reg) noexcept { return _setRet(i, reg); }</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="510"><span class="lineNum">     510 </span>            :   // [Members]</a>
+<a name="511"><span class="lineNum">     511 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span>            :   FuncDetail _funcDetail;                //!&lt; Function detail.</a>
+<a name="514"><span class="lineNum">     514 </span>            :   Operand_ _ret[2];                      //!&lt; Return.</a>
+<a name="515"><span class="lineNum">     515 </span>            :   Operand_* _args;                       //!&lt; Arguments.</a>
+<a name="516"><span class="lineNum">     516 </span>            : };</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : // ============================================================================</a>
+<a name="519"><span class="lineNum">     519 </span>            : // [asmjit::CCPushArg]</a>
+<a name="520"><span class="lineNum">     520 </span>            : // ============================================================================</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            : //! Push argument before a function call (CodeCompiler).</a>
+<a name="523"><span class="lineNum">     523 </span>            : class CCPushArg : public CBNode {</a>
+<a name="524"><span class="lineNum">     524 </span>            : public:</a>
+<a name="525"><span class="lineNum">     525 </span>            :   ASMJIT_NONCOPYABLE(CCPushArg)</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="528"><span class="lineNum">     528 </span>            :   // [Construction / Destruction]</a>
+<a name="529"><span class="lineNum">     529 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   //! Create a new `CCPushArg` instance.</a>
+<a name="532"><span class="lineNum">     532 </span>            :   ASMJIT_INLINE CCPushArg(CodeBuilder* cb, CCFuncCall* call, VirtReg* src, VirtReg* cvt) noexcept</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :     : CBNode(cb, kNodePushArg),</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :       _call(call),</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :       _src(src),</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :       _cvt(cvt),</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :       _args(0) {</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :     orFlags(kFlagIsRemovable);</a>
+<a name="539"><span class="lineNum">     539 </span>            :   }</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span>            :   //! Destroy the `CCPushArg` instance.</a>
+<a name="542"><span class="lineNum">     542 </span>            :   ASMJIT_INLINE ~CCPushArg() noexcept {}</a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="545"><span class="lineNum">     545 </span>            :   // [Accessors]</a>
+<a name="546"><span class="lineNum">     546 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            :   //! Get the associated function-call.</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CCFuncCall* getCall() const noexcept { return _call; }</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :   //! Get source variable.</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE VirtReg* getSrcReg() const noexcept { return _src; }</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   //! Get conversion variable.</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE VirtReg* getCvtReg() const noexcept { return _cvt; }</span></a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="556"><span class="lineNum">     556 </span>            :   // [Members]</a>
+<a name="557"><span class="lineNum">     557 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span>            :   CCFuncCall* _call;                     //!&lt; Associated `CCFuncCall`.</a>
+<a name="560"><span class="lineNum">     560 </span>            :   VirtReg* _src;                         //!&lt; Source variable.</a>
+<a name="561"><span class="lineNum">     561 </span>            :   VirtReg* _cvt;                         //!&lt; Temporary variable used for conversion (or null).</a>
+<a name="562"><span class="lineNum">     562 </span>            :   uint32_t _args;                        //!&lt; Affected arguments bit-array.</a>
+<a name="563"><span class="lineNum">     563 </span>            : };</a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span>            : // ============================================================================</a>
+<a name="566"><span class="lineNum">     566 </span>            : // [asmjit::CodeCompiler]</a>
+<a name="567"><span class="lineNum">     567 </span>            : // ============================================================================</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span>            : //! Code emitter that uses virtual registers and performs register allocation.</a>
+<a name="570"><span class="lineNum">     570 </span>            : //!</a>
+<a name="571"><span class="lineNum">     571 </span>            : //! Compiler is a high-level code-generation tool that provides register</a>
+<a name="572"><span class="lineNum">     572 </span>            : //! allocation and automatic handling of function calling conventions. It was</a>
+<a name="573"><span class="lineNum">     573 </span>            : //! primarily designed for merging multiple parts of code into a function</a>
+<a name="574"><span class="lineNum">     574 </span>            : //! without worrying about registers and function calling conventions.</a>
+<a name="575"><span class="lineNum">     575 </span>            : //!</a>
+<a name="576"><span class="lineNum">     576 </span>            : //! CodeCompiler can be used, with a minimum effort, to handle 32-bit and 64-bit</a>
+<a name="577"><span class="lineNum">     577 </span>            : //! code at the same time.</a>
+<a name="578"><span class="lineNum">     578 </span>            : //!</a>
+<a name="579"><span class="lineNum">     579 </span>            : //! CodeCompiler is based on CodeBuilder and contains all the features it</a>
+<a name="580"><span class="lineNum">     580 </span>            : //! provides. It means that the code it stores can be modified (removed, added,</a>
+<a name="581"><span class="lineNum">     581 </span>            : //! injected) and analyzed. When the code is finalized the compiler can emit</a>
+<a name="582"><span class="lineNum">     582 </span>            : //! the code into an Assembler to translate the abstract representation into a</a>
+<a name="583"><span class="lineNum">     583 </span>            : //! machine code.</a>
+<a name="584"><span class="lineNum">     584 </span>            : class ASMJIT_VIRTAPI CodeCompiler : public CodeBuilder {</a>
+<a name="585"><span class="lineNum">     585 </span>            : public:</a>
+<a name="586"><span class="lineNum">     586 </span>            :   ASMJIT_NONCOPYABLE(CodeCompiler)</a>
+<a name="587"><span class="lineNum">     587 </span>            :   typedef CodeBuilder Base;</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="590"><span class="lineNum">     590 </span>            :   // [Construction / Destruction]</a>
+<a name="591"><span class="lineNum">     591 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span>            :   //! Create a new `CodeCompiler` instance.</a>
+<a name="594"><span class="lineNum">     594 </span>            :   ASMJIT_API CodeCompiler() noexcept;</a>
+<a name="595"><span class="lineNum">     595 </span>            :   //! Destroy the `CodeCompiler` instance.</a>
+<a name="596"><span class="lineNum">     596 </span>            :   ASMJIT_API virtual ~CodeCompiler() noexcept;</a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="599"><span class="lineNum">     599 </span>            :   // [Events]</a>
+<a name="600"><span class="lineNum">     600 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span>            :   ASMJIT_API virtual Error onAttach(CodeHolder* code) noexcept override;</a>
+<a name="603"><span class="lineNum">     603 </span>            :   ASMJIT_API virtual Error onDetach(CodeHolder* code) noexcept override;</a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="606"><span class="lineNum">     606 </span>            :   // [Node-Factory]</a>
+<a name="607"><span class="lineNum">     607 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            :   //! \internal</a>
+<a name="610"><span class="lineNum">     610 </span>            :   //!</a>
+<a name="611"><span class="lineNum">     611 </span>            :   //! Create a new `CCHint`.</a>
+<a name="612"><span class="lineNum">     612 </span>            :   ASMJIT_API CCHint* newHintNode(Reg&amp; reg, uint32_t hint, uint32_t value) noexcept;</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="615"><span class="lineNum">     615 </span>            :   // [Func]</a>
+<a name="616"><span class="lineNum">     616 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span>            :   //! Get the current function.</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">       1948 :   ASMJIT_INLINE CCFunc* getFunc() const noexcept { return _func; }</span></a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span>            :   //! Create a new `CCFunc`.</a>
+<a name="622"><span class="lineNum">     622 </span>            :   ASMJIT_API CCFunc* newFunc(const FuncSignature&amp; sign) noexcept;</a>
+<a name="623"><span class="lineNum">     623 </span>            :   //! Add a function `node` to the stream.</a>
+<a name="624"><span class="lineNum">     624 </span>            :   ASMJIT_API CCFunc* addFunc(CCFunc* func);</a>
+<a name="625"><span class="lineNum">     625 </span>            :   //! Add a new function.</a>
+<a name="626"><span class="lineNum">     626 </span>            :   ASMJIT_API CCFunc* addFunc(const FuncSignature&amp; sign);</a>
+<a name="627"><span class="lineNum">     627 </span>            :   //! Emit a sentinel that marks the end of the current function.</a>
+<a name="628"><span class="lineNum">     628 </span>            :   ASMJIT_API CBSentinel* endFunc();</a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="631"><span class="lineNum">     631 </span>            :   // [Ret]</a>
+<a name="632"><span class="lineNum">     632 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :   //! Create a new `CCFuncRet`.</a>
+<a name="635"><span class="lineNum">     635 </span>            :   ASMJIT_API CCFuncRet* newRet(const Operand_&amp; o0, const Operand_&amp; o1) noexcept;</a>
+<a name="636"><span class="lineNum">     636 </span>            :   //! Add a new `CCFuncRet`.</a>
+<a name="637"><span class="lineNum">     637 </span>            :   ASMJIT_API CCFuncRet* addRet(const Operand_&amp; o0, const Operand_&amp; o1) noexcept;</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="640"><span class="lineNum">     640 </span>            :   // [Call]</a>
+<a name="641"><span class="lineNum">     641 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span>            :   //! Create a new `CCFuncCall`.</a>
+<a name="644"><span class="lineNum">     644 </span>            :   ASMJIT_API CCFuncCall* newCall(uint32_t instId, const Operand_&amp; o0, const FuncSignature&amp; sign) noexcept;</a>
+<a name="645"><span class="lineNum">     645 </span>            :   //! Add a new `CCFuncCall`.</a>
+<a name="646"><span class="lineNum">     646 </span>            :   ASMJIT_API CCFuncCall* addCall(uint32_t instId, const Operand_&amp; o0, const FuncSignature&amp; sign) noexcept;</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="649"><span class="lineNum">     649 </span>            :   // [Args]</a>
+<a name="650"><span class="lineNum">     650 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :   //! Set a function argument at `argIndex` to `reg`.</a>
+<a name="653"><span class="lineNum">     653 </span>            :   ASMJIT_API Error setArg(uint32_t argIndex, const Reg&amp; reg);</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="656"><span class="lineNum">     656 </span>            :   // [Hint]</a>
+<a name="657"><span class="lineNum">     657 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            :   //! Emit a new hint (purely informational node).</a>
+<a name="660"><span class="lineNum">     660 </span>            :   ASMJIT_API Error _hint(Reg&amp; reg, uint32_t hint, uint32_t value);</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="663"><span class="lineNum">     663 </span>            :   // [VirtReg / Stack]</a>
+<a name="664"><span class="lineNum">     664 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span>            :   //! Create a new virtual register representing the given `vti` and `signature`.</a>
+<a name="667"><span class="lineNum">     667 </span>            :   //!</a>
+<a name="668"><span class="lineNum">     668 </span>            :   //! This function accepts either register type representing a machine-specific</a>
+<a name="669"><span class="lineNum">     669 </span>            :   //! register, like `X86Reg`, or RegTag representation, which represents</a>
+<a name="670"><span class="lineNum">     670 </span>            :   //! machine independent register, and from the machine-specific register</a>
+<a name="671"><span class="lineNum">     671 </span>            :   //! is deduced.</a>
+<a name="672"><span class="lineNum">     672 </span>            :   ASMJIT_API VirtReg* newVirtReg(uint32_t typeId, uint32_t signature, const char* name) noexcept;</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :   ASMJIT_API Error _newReg(Reg&amp; out, uint32_t typeId, const char* name);</a>
+<a name="675"><span class="lineNum">     675 </span>            :   ASMJIT_API Error _newReg(Reg&amp; out, uint32_t typeId, const char* nameFmt, va_list ap);</a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span>            :   ASMJIT_API Error _newReg(Reg&amp; out, const Reg&amp; ref, const char* name);</a>
+<a name="678"><span class="lineNum">     678 </span>            :   ASMJIT_API Error _newReg(Reg&amp; out, const Reg&amp; ref, const char* nameFmt, va_list ap);</a>
+<a name="679"><span class="lineNum">     679 </span>            : </a>
+<a name="680"><span class="lineNum">     680 </span>            :   ASMJIT_API Error _newStack(Mem&amp; out, uint32_t size, uint32_t alignment, const char* name);</a>
+<a name="681"><span class="lineNum">     681 </span>            :   ASMJIT_API Error _newConst(Mem&amp; out, uint32_t scope, const void* data, size_t size);</a>
+<a name="682"><span class="lineNum">     682 </span>            : </a>
+<a name="683"><span class="lineNum">     683 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="684"><span class="lineNum">     684 </span>            :   // [VirtReg]</a>
+<a name="685"><span class="lineNum">     685 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span>            :   //! Get whether the virtual register `r` is valid.</a>
+<a name="688"><span class="lineNum">     688 </span>            :   ASMJIT_INLINE bool isVirtRegValid(const Reg&amp; reg) const noexcept {</a>
+<a name="689"><span class="lineNum">     689 </span>            :     return isVirtRegValid(reg.getId());</a>
+<a name="690"><span class="lineNum">     690 </span>            :   }</a>
+<a name="691"><span class="lineNum">     691 </span>            :   //! \overload</a>
+<a name="692"><span class="lineNum">     692 </span>            :   ASMJIT_INLINE bool isVirtRegValid(uint32_t id) const noexcept {</a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">      12200 :     size_t index = Operand::unpackId(id);</span></a>
+<a name="694"><span class="lineNum">     694 </span>            :     return index &lt; _vRegArray.getLength();</a>
+<a name="695"><span class="lineNum">     695 </span>            :   }</a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span>            :   //! Get \ref VirtReg associated with the given `r`.</a>
+<a name="698"><span class="lineNum">     698 </span>            :   ASMJIT_INLINE VirtReg* getVirtReg(const Reg&amp; reg) const noexcept {</a>
+<a name="699"><span class="lineNum">     699 </span>            :     return getVirtRegById(reg.getId());</a>
+<a name="700"><span class="lineNum">     700 </span>            :   }</a>
+<a name="701"><span class="lineNum">     701 </span>            :   //! Get \ref VirtReg associated with the given `id`.</a>
+<a name="702"><span class="lineNum">     702 </span>            :   ASMJIT_INLINE VirtReg* getVirtRegById(uint32_t id) const noexcept {</a>
+<a name="703"><span class="lineNum">     703 </span>            :     ASMJIT_ASSERT(id != kInvalidValue);</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">     116314 :     size_t index = Operand::unpackId(id);</span></a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            :     ASMJIT_ASSERT(index &lt; _vRegArray.getLength());</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">     128514 :     return _vRegArray[index];</span></a>
+<a name="708"><span class="lineNum">     708 </span>            :   }</a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span>            :   //! Get an array of all virtual registers managed by CodeCompiler.</a>
+<a name="711"><span class="lineNum">     711 </span>            :   ASMJIT_INLINE const ZoneVector&lt;VirtReg*&gt;&amp; getVirtRegArray() const noexcept { return _vRegArray; }</a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span>            :   //! Alloc a virtual register `reg`.</a>
+<a name="714"><span class="lineNum">     714 </span>            :   ASMJIT_API Error alloc(Reg&amp; reg);</a>
+<a name="715"><span class="lineNum">     715 </span>            :   //! Alloc a virtual register `reg` using `physId` as a register id.</a>
+<a name="716"><span class="lineNum">     716 </span>            :   ASMJIT_API Error alloc(Reg&amp; reg, uint32_t physId);</a>
+<a name="717"><span class="lineNum">     717 </span>            :   //! Alloc a virtual register `reg` using `ref` as a register operand.</a>
+<a name="718"><span class="lineNum">     718 </span>            :   ASMJIT_API Error alloc(Reg&amp; reg, const Reg&amp; ref);</a>
+<a name="719"><span class="lineNum">     719 </span>            :   //! Spill a virtual register `reg`.</a>
+<a name="720"><span class="lineNum">     720 </span>            :   ASMJIT_API Error spill(Reg&amp; reg);</a>
+<a name="721"><span class="lineNum">     721 </span>            :   //! Save a virtual register `reg` if the status is `modified` at this point.</a>
+<a name="722"><span class="lineNum">     722 </span>            :   ASMJIT_API Error save(Reg&amp; reg);</a>
+<a name="723"><span class="lineNum">     723 </span>            :   //! Unuse a virtual register `reg`.</a>
+<a name="724"><span class="lineNum">     724 </span>            :   ASMJIT_API Error unuse(Reg&amp; reg);</a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            :   //! Get priority of a virtual register `reg`.</a>
+<a name="727"><span class="lineNum">     727 </span>            :   ASMJIT_API uint32_t getPriority(Reg&amp; reg) const;</a>
+<a name="728"><span class="lineNum">     728 </span>            :   //! Set priority of variable `reg` to `priority`.</a>
+<a name="729"><span class="lineNum">     729 </span>            :   ASMJIT_API void setPriority(Reg&amp; reg, uint32_t priority);</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span>            :   //! Get save-on-unuse `reg` property.</a>
+<a name="732"><span class="lineNum">     732 </span>            :   ASMJIT_API bool getSaveOnUnuse(Reg&amp; reg) const;</a>
+<a name="733"><span class="lineNum">     733 </span>            :   //! Set save-on-unuse `reg` property to `value`.</a>
+<a name="734"><span class="lineNum">     734 </span>            :   ASMJIT_API void setSaveOnUnuse(Reg&amp; reg, bool value);</a>
+<a name="735"><span class="lineNum">     735 </span>            : </a>
+<a name="736"><span class="lineNum">     736 </span>            :   //! Rename variable `reg` to `name`.</a>
+<a name="737"><span class="lineNum">     737 </span>            :   //!</a>
+<a name="738"><span class="lineNum">     738 </span>            :   //! NOTE: Only new name will appear in the logger.</a>
+<a name="739"><span class="lineNum">     739 </span>            :   ASMJIT_API void rename(Reg&amp; reg, const char* fmt, ...);</a>
+<a name="740"><span class="lineNum">     740 </span>            : </a>
+<a name="741"><span class="lineNum">     741 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="742"><span class="lineNum">     742 </span>            :   // [Members]</a>
+<a name="743"><span class="lineNum">     743 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="744"><span class="lineNum">     744 </span>            : </a>
+<a name="745"><span class="lineNum">     745 </span>            :   CCFunc* _func;                         //!&lt; Current function.</a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span>            :   Zone _vRegZone;                        //!&lt; Allocates \ref VirtReg objects.</a>
+<a name="748"><span class="lineNum">     748 </span>            :   ZoneVector&lt;VirtReg*&gt; _vRegArray;       //!&lt; Stores array of \ref VirtReg pointers.</a>
+<a name="749"><span class="lineNum">     749 </span>            : </a>
+<a name="750"><span class="lineNum">     750 </span>            :   CBConstPool* _localConstPool;          //!&lt; Local constant pool, flushed at the end of each function.</a>
+<a name="751"><span class="lineNum">     751 </span>            :   CBConstPool* _globalConstPool;         //!&lt; Global constant pool, flushed at the end of the compilation.</a>
+<a name="752"><span class="lineNum">     752 </span>            : };</a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span>            : //! \}</a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span>            : } // asmjit namespace</a>
+<a name="757"><span class="lineNum">     757 </span>            : } // namespace PLMD</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            : // [Api-End]</a>
+<a name="760"><span class="lineNum">     760 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="761"><span class="lineNum">     761 </span>            : </a>
+<a name="762"><span class="lineNum">     762 </span>            : // [Guard]</a>
+<a name="763"><span class="lineNum">     763 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="764"><span class="lineNum">     764 </span>            : #endif // _ASMJIT_BASE_CODECOMPILER_H</a>
+<a name="765"><span class="lineNum">     765 </span>            : #pragma GCC diagnostic pop</a>
+<a name="766"><span class="lineNum">     766 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="767"><span class="lineNum">     767 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeemitter.cpp.func-sort-c.html b/coverage-libs/asmjit/codeemitter.cpp.func-sort-c.html
new file mode 100644
index 0000000000..dbcbb8f911
--- /dev/null
+++ b/coverage-libs/asmjit/codeemitter.cpp.func-sort-c.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeemitter.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeemitter.cpp<span style="font-size: 80%;"> (<a href="codeemitter.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryLo">33.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryLo">29.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="codeemitter.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#116">_ZN4PLMD6asmjit11CodeEmitter12_emitOpArrayEjPKNS0_8Operand_Em</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#153">_ZN4PLMD6asmjit11CodeEmitter12setLastErrorEjPKc</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#136">_ZN4PLMD6asmjit11CodeEmitter14getLabelByNameEPKcmj</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#240">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_ES4_S4_i</a></td>
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+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#239">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_ES4_i</a></td>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#237">_ZN4PLMD6asmjit11CodeEmitter4emitEji</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#190">_ZN4PLMD6asmjit11CodeEmitter8commentfEPKcz</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#208">_ZN4PLMD6asmjit11CodeEmitter8commentvEPKcP13__va_list_tag</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#144">_ZN4PLMD6asmjit11CodeEmitter8finalizeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#93">_ZN4PLMD6asmjit11CodeEmitter8onDetachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#72">_ZN4PLMD6asmjit11CodeEmitterD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#185">_ZNK4PLMD6asmjit11CodeEmitter12isLabelValidEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#232">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_ES4_S4_</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#238">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_Ei</a></td>
+              <td class="coverFnHi">932</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#245">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_El</a></td>
+              <td class="coverFnHi">932</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#229">_ZN4PLMD6asmjit11CodeEmitter4emitEj</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#230">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_E</a></td>
+              <td class="coverFnHi">2240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#83">_ZN4PLMD6asmjit11CodeEmitter8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#53">_ZN4PLMD6asmjit11CodeEmitterC2Ej</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#72">_ZN4PLMD6asmjit11CodeEmitterD2Ev</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#231">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_ES4_</a></td>
+              <td class="coverFnHi">40542</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeemitter.cpp.func.html b/coverage-libs/asmjit/codeemitter.cpp.func.html
new file mode 100644
index 0000000000..88cad71306
--- /dev/null
+++ b/coverage-libs/asmjit/codeemitter.cpp.func.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeemitter.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeemitter.cpp<span style="font-size: 80%;"> (<a href="codeemitter.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryLo">33.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryLo">29.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codeemitter.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#116">_ZN4PLMD6asmjit11CodeEmitter12_emitOpArrayEjPKNS0_8Operand_Em</a></td>
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+    <tr>
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+              <td class="coverFnHi">1948</td>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#246">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_ES4_l</a></td>
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+              <td class="coverFnHi">932</td>
+            </tr>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#245">_ZN4PLMD6asmjit11CodeEmitter4emitEjRKNS0_8Operand_El</a></td>
+              <td class="coverFnHi">932</td>
+            </tr>
+    <tr>
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+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#244">_ZN4PLMD6asmjit11CodeEmitter4emitEjl</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#190">_ZN4PLMD6asmjit11CodeEmitter8commentfEPKcz</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#144">_ZN4PLMD6asmjit11CodeEmitter8finalizeEv</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#83">_ZN4PLMD6asmjit11CodeEmitter8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">3896</td>
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+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#93">_ZN4PLMD6asmjit11CodeEmitter8onDetachEPNS0_10CodeHolderE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#53">_ZN4PLMD6asmjit11CodeEmitterC2Ej</a></td>
+              <td class="coverFnHi">3896</td>
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+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#72">_ZN4PLMD6asmjit11CodeEmitterD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#72">_ZN4PLMD6asmjit11CodeEmitterD2Ev</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeemitter.cpp.gcov.html#185">_ZNK4PLMD6asmjit11CodeEmitter12isLabelValidEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeemitter.cpp.gcov.html b/coverage-libs/asmjit/codeemitter.cpp.gcov.html
new file mode 100644
index 0000000000..4df71ae81a
--- /dev/null
+++ b/coverage-libs/asmjit/codeemitter.cpp.gcov.html
@@ -0,0 +1,338 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeemitter.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeemitter.cpp<span style="font-size: 80%;"> (source / <a href="codeemitter.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryLo">33.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryLo">29.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./vmem.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./x86inst.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./arminst.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // [Api-Begin]</a>
+<a name="46"><span class="lineNum">      46 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : namespace PLMD {</a>
+<a name="49"><span class="lineNum">      49 </span>            : namespace asmjit {</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : // [asmjit::CodeEmitter - Construction / Destruction]</a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       3896 : CodeEmitter::CodeEmitter(uint32_t type) noexcept</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   : _codeInfo(),</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       3896 :     _code(nullptr),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       3896 :     _nextEmitter(nullptr),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       3896 :     _type(static_cast&lt;uint8_t&gt;(type)),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       3896 :     _destroyed(false),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       3896 :     _finalized(false),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       3896 :     _reserved(false),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       3896 :     _lastError(kErrorNotInitialized),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       3896 :     _privateData(0),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       3896 :     _globalHints(0),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       3896 :     _globalOptions(kOptionMaybeFailureCase),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       3896 :     _options(0),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       3896 :     _extraReg(),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       3896 :     _inlineComment(nullptr),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       3896 :     _none(),</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :     _nativeGpReg(),</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       3896 :     _nativeGpArray(nullptr) {}</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       3896 : CodeEmitter::~CodeEmitter() noexcept {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       3896 :   if (_code) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       3896 :     _destroyed = true;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       3896 :     _code-&gt;detach(this);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       3896 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : // ============================================================================</a>
+<a name="82"><span class="lineNum">      82 </span>            : // [asmjit::CodeEmitter - Events]</a>
+<a name="83"><span class="lineNum">      83 </span>            : // ============================================================================</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       3896 : Error CodeEmitter::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   _codeInfo = code-&gt;getCodeInfo();</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       3896 :   _lastError = kErrorOk;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       3896 :   _globalHints = code-&gt;getGlobalHints();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       3896 :   _globalOptions = code-&gt;getGlobalOptions();</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       3896 :   return kErrorOk;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 : Error CodeEmitter::onDetach(CodeHolder* code) noexcept {</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   _codeInfo.reset();</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   _finalized = false;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   _lastError = kErrorNotInitialized;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   _privateData = 0;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   _globalHints = 0;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   _globalOptions = kOptionMaybeFailureCase;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   _options = 0;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   _extraReg.reset();</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   _inlineComment = nullptr;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   _nativeGpReg.reset();</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :   _nativeGpArray = nullptr;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : // ============================================================================</a>
+<a name="115"><span class="lineNum">     115 </span>            : // [asmjit::CodeEmitter - Code-Generation]</a>
+<a name="116"><span class="lineNum">     116 </span>            : // ============================================================================</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 : Error CodeEmitter::_emitOpArray(uint32_t instId, const Operand_* opArray, size_t opCount) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   const Operand_* op = opArray;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   switch (opCount) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     case 0: return _emit(instId, _none, _none, _none, _none);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     case 1: return _emit(instId, op[0], _none, _none, _none);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     case 2: return _emit(instId, op[0], op[1], _none, _none);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     case 3: return _emit(instId, op[0], op[1], op[2], _none);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     case 4: return _emit(instId, op[0], op[1], op[2], op[3]);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     case 5: return _emit(instId, op[0], op[1], op[2], op[3], op[4], _none);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     case 6: return _emit(instId, op[0], op[1], op[2], op[3], op[4], op[5]);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :     default:</a>
+<a name="130"><span class="lineNum">     130 </span>            :       return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : // ============================================================================</a>
+<a name="135"><span class="lineNum">     135 </span>            : // [asmjit::CodeEmitter - Finalize]</a>
+<a name="136"><span class="lineNum">     136 </span>            : // ============================================================================</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 : Label CodeEmitter::getLabelByName(const char* name, size_t nameLength, uint32_t parentId) noexcept {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   return Label(_code ? _code-&gt;getLabelIdByName(name, nameLength, parentId) : static_cast&lt;uint32_t&gt;(0));</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : // ============================================================================</a>
+<a name="143"><span class="lineNum">     143 </span>            : // [asmjit::CodeEmitter - Finalize]</a>
+<a name="144"><span class="lineNum">     144 </span>            : // ============================================================================</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 : Error CodeEmitter::finalize() {</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   // Finalization does nothing by default, overridden by `CodeBuilder`.</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : // ============================================================================</a>
+<a name="152"><span class="lineNum">     152 </span>            : // [asmjit::CodeEmitter - Error Handling]</a>
+<a name="153"><span class="lineNum">     153 </span>            : // ============================================================================</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 : Error CodeEmitter::setLastError(Error error, const char* message) {</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   // This is fatal, CodeEmitter can't set error without being attached to `CodeHolder`.</a>
+<a name="157"><span class="lineNum">     157 </span>            :   ASMJIT_ASSERT(_code != nullptr);</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Special case used to reset the last error.</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :   if (error == kErrorOk) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     _lastError = kErrorOk;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     _globalOptions &amp;= ~kOptionMaybeFailureCase;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   if (!message)</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     message = DebugUtils::errorAsString(error);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   // Logging is skipped if the error is handled by `ErrorHandler`.</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :   ErrorHandler* handler = _code-&gt;_errorHandler;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   if (handler &amp;&amp; handler-&gt;handleError(error, message, this))</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     return error;</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // The handler-&gt;handleError() function may throw an exception or longjmp()</a>
+<a name="175"><span class="lineNum">     175 </span>            :   // to terminate the execution of `setLastError()`. This is the reason why</a>
+<a name="176"><span class="lineNum">     176 </span>            :   // we have delayed changing the `_error` member until now.</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   _lastError = error;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :   _globalOptions |= kOptionMaybeFailureCase;</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   return error;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : // ============================================================================</a>
+<a name="184"><span class="lineNum">     184 </span>            : // [asmjit::CodeEmitter - Helpers]</a>
+<a name="185"><span class="lineNum">     185 </span>            : // ============================================================================</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 : bool CodeEmitter::isLabelValid(uint32_t id) const noexcept {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   size_t index = Operand::unpackId(id);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   return _code &amp;&amp; index &lt; _code-&gt;_labels.getLength();</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 : Error CodeEmitter::commentf(const char* fmt, ...) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :   Error err = _lastError;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   if (err) return err;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled) {</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     va_list ap;</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :     va_start(ap, fmt);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :     err = _code-&gt;_logger-&gt;logv(fmt, ap);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     va_end(ap);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span>            : #else</a>
+<a name="204"><span class="lineNum">     204 </span>            :   ASMJIT_UNUSED(fmt);</a>
+<a name="205"><span class="lineNum">     205 </span>            : #endif</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   return err;</a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 : Error CodeEmitter::commentv(const char* fmt, va_list ap) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :   Error err = _lastError;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   if (err) return err;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled)</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :     err = _code-&gt;_logger-&gt;logv(fmt, ap);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : #else</a>
+<a name="218"><span class="lineNum">     218 </span>            :   ASMJIT_UNUSED(fmt);</a>
+<a name="219"><span class="lineNum">     219 </span>            :   ASMJIT_UNUSED(ap);</a>
+<a name="220"><span class="lineNum">     220 </span>            : #endif</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   return err;</a>
+<a name="223"><span class="lineNum">     223 </span>            : }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : // ============================================================================</a>
+<a name="226"><span class="lineNum">     226 </span>            : // [asmjit::CodeEmitter - Emit]</a>
+<a name="227"><span class="lineNum">     227 </span>            : // ============================================================================</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : #define OP const Operand_&amp;</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       1948 : Error CodeEmitter::emit(uint32_t instId) { return _emit(instId, _none, _none, _none, _none); }</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       2240 : Error CodeEmitter::emit(uint32_t instId, OP o0) { return _emit(instId, o0, _none, _none, _none); }</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      40542 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1) { return _emit(instId, o0, o1, _none, _none); }</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        120 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2) { return _emit(instId, o0, o1, o2, _none); }</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3) { return _emit(instId, o0, o1, o2, o3); }</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3, OP o4) { return _emit(instId, o0, o1, o2, o3, o4, _none); }</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3, OP o4, OP o5) { return _emit(instId, o0, o1, o2, o3, o4, o5); }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, int o0) { return _emit(instId, Imm(o0), _none, _none, _none); }</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        932 : Error CodeEmitter::emit(uint32_t instId, OP o0, int o1) { return _emit(instId, o0, Imm(o1), _none, _none); }</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, int o2) { return _emit(instId, o0, o1, Imm(o2), _none); }</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, int o3) { return _emit(instId, o0, o1, o2, Imm(o3)); }</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3, int o4) { return _emit(instId, o0, o1, o2, o3, Imm(o4), _none); }</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3, OP o4, int o5) { return _emit(instId, o0, o1, o2, o3, o4, Imm(o5)); }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, int64_t o0) { return _emit(instId, Imm(o0), _none, _none, _none); }</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        932 : Error CodeEmitter::emit(uint32_t instId, OP o0, int64_t o1) { return _emit(instId, o0, Imm(o1), _none, _none); }</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, int64_t o2) { return _emit(instId, o0, o1, Imm(o2), _none); }</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, int64_t o3) { return _emit(instId, o0, o1, o2, Imm(o3)); }</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3, int64_t o4) { return _emit(instId, o0, o1, o2, o3, Imm(o4), _none); }</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 : Error CodeEmitter::emit(uint32_t instId, OP o0, OP o1, OP o2, OP o3, OP o4, int64_t o5) { return _emit(instId, o0, o1, o2, o3, o4, Imm(o5)); }</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : #undef OP</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            : } // asmjit namespace</a>
+<a name="257"><span class="lineNum">     257 </span>            : } // namespace PLMD</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : // [Api-End]</a>
+<a name="260"><span class="lineNum">     260 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="261"><span class="lineNum">     261 </span>            : #pragma GCC diagnostic pop</a>
+<a name="262"><span class="lineNum">     262 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeemitter.h.func-sort-c.html b/coverage-libs/asmjit/codeemitter.h.func-sort-c.html
new file mode 100644
index 0000000000..48ebd2764d
--- /dev/null
+++ b/coverage-libs/asmjit/codeemitter.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeemitter.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeemitter.h<span style="font-size: 80%;"> (<a href="codeemitter.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="codeemitter.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeemitter.h.func.html b/coverage-libs/asmjit/codeemitter.h.func.html
new file mode 100644
index 0000000000..0b03abbd9c
--- /dev/null
+++ b/coverage-libs/asmjit/codeemitter.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeemitter.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeemitter.h<span style="font-size: 80%;"> (<a href="codeemitter.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codeemitter.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
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+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeemitter.h.gcov.html b/coverage-libs/asmjit/codeemitter.h.gcov.html
new file mode 100644
index 0000000000..cb08501a01
--- /dev/null
+++ b/coverage-libs/asmjit/codeemitter.h.gcov.html
@@ -0,0 +1,604 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeemitter.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeemitter.h<span style="font-size: 80%;"> (source / <a href="codeemitter.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_codeemitter_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_codeemitter_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_CODEEMITTER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_CODEEMITTER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./codeholder.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : // [Api-Begin]</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace PLMD {</a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace asmjit {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : //! \addtogroup asmjit_base</a>
+<a name="47"><span class="lineNum">      47 </span>            : //! \{</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : // [Forward Declarations]</a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : class ConstPool;</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : // [asmjit::CodeEmitter]</a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : //! Provides a base foundation to emit code - specialized by \ref Assembler and</a>
+<a name="60"><span class="lineNum">      60 </span>            : //! \ref CodeBuilder.</a>
+<a name="61"><span class="lineNum">      61 </span>            : class ASMJIT_VIRTAPI CodeEmitter {</a>
+<a name="62"><span class="lineNum">      62 </span>            : public:</a>
+<a name="63"><span class="lineNum">      63 </span>            :   //! CodeEmitter type.</a>
+<a name="64"><span class="lineNum">      64 </span>            :   ASMJIT_ENUM(Type) {</a>
+<a name="65"><span class="lineNum">      65 </span>            :     kTypeNone       = 0,</a>
+<a name="66"><span class="lineNum">      66 </span>            :     kTypeAssembler  = 1,</a>
+<a name="67"><span class="lineNum">      67 </span>            :     kTypeBuilder    = 2,</a>
+<a name="68"><span class="lineNum">      68 </span>            :     kTypeCompiler   = 3,</a>
+<a name="69"><span class="lineNum">      69 </span>            :     kTypeCount      = 4</a>
+<a name="70"><span class="lineNum">      70 </span>            :   };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :   //! CodeEmitter hints - global settings that affect machine-code generation.</a>
+<a name="73"><span class="lineNum">      73 </span>            :   ASMJIT_ENUM(Hints) {</a>
+<a name="74"><span class="lineNum">      74 </span>            :     //! Emit optimized code-alignment sequences.</a>
+<a name="75"><span class="lineNum">      75 </span>            :     //!</a>
+<a name="76"><span class="lineNum">      76 </span>            :     //! Default `true`.</a>
+<a name="77"><span class="lineNum">      77 </span>            :     //!</a>
+<a name="78"><span class="lineNum">      78 </span>            :     //! X86/X64 Specific</a>
+<a name="79"><span class="lineNum">      79 </span>            :     //! ----------------</a>
+<a name="80"><span class="lineNum">      80 </span>            :     //!</a>
+<a name="81"><span class="lineNum">      81 </span>            :     //! Default align sequence used by X86/X64 architecture is one-byte (0x90)</a>
+<a name="82"><span class="lineNum">      82 </span>            :     //! opcode that is often shown by disassemblers as nop. However there are</a>
+<a name="83"><span class="lineNum">      83 </span>            :     //! more optimized align sequences for 2-11 bytes that may execute faster.</a>
+<a name="84"><span class="lineNum">      84 </span>            :     //! If this feature is enabled AsmJit will generate specialized sequences</a>
+<a name="85"><span class="lineNum">      85 </span>            :     //! for alignment between 2 to 11 bytes.</a>
+<a name="86"><span class="lineNum">      86 </span>            :     kHintOptimizedAlign = 0x00000001U,</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :     //! Emit jump-prediction hints.</a>
+<a name="89"><span class="lineNum">      89 </span>            :     //!</a>
+<a name="90"><span class="lineNum">      90 </span>            :     //! Default `false`.</a>
+<a name="91"><span class="lineNum">      91 </span>            :     //!</a>
+<a name="92"><span class="lineNum">      92 </span>            :     //! X86/X64 Specific</a>
+<a name="93"><span class="lineNum">      93 </span>            :     //! ----------------</a>
+<a name="94"><span class="lineNum">      94 </span>            :     //!</a>
+<a name="95"><span class="lineNum">      95 </span>            :     //! Jump prediction is usually based on the direction of the jump. If the</a>
+<a name="96"><span class="lineNum">      96 </span>            :     //! jump is backward it is usually predicted as taken; and if the jump is</a>
+<a name="97"><span class="lineNum">      97 </span>            :     //! forward it is usually predicted as not-taken. The reason is that loops</a>
+<a name="98"><span class="lineNum">      98 </span>            :     //! generally use backward jumps and conditions usually use forward jumps.</a>
+<a name="99"><span class="lineNum">      99 </span>            :     //! However this behavior can be overridden by using instruction prefixes.</a>
+<a name="100"><span class="lineNum">     100 </span>            :     //! If this option is enabled these hints will be emitted.</a>
+<a name="101"><span class="lineNum">     101 </span>            :     //!</a>
+<a name="102"><span class="lineNum">     102 </span>            :     //! This feature is disabled by default, because the only processor that</a>
+<a name="103"><span class="lineNum">     103 </span>            :     //! used to take into consideration prediction hints was P4. Newer processors</a>
+<a name="104"><span class="lineNum">     104 </span>            :     //! implement heuristics for branch prediction that ignores any static hints.</a>
+<a name="105"><span class="lineNum">     105 </span>            :     kHintPredictedJumps = 0x00000002U</a>
+<a name="106"><span class="lineNum">     106 </span>            :   };</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   //! CodeEmitter options that are merged with instruction options.</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ASMJIT_ENUM(Options) {</a>
+<a name="110"><span class="lineNum">     110 </span>            :     //! Reserved, used to check for errors in `Assembler::_emit()`. In addition,</a>
+<a name="111"><span class="lineNum">     111 </span>            :     //! if an emitter is in error state it will have `kOptionMaybeFailureCase`</a>
+<a name="112"><span class="lineNum">     112 </span>            :     //! set</a>
+<a name="113"><span class="lineNum">     113 </span>            :     kOptionMaybeFailureCase = 0x00000001U,</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :     //! Perform a strict validation before the instruction is emitted.</a>
+<a name="116"><span class="lineNum">     116 </span>            :     kOptionStrictValidation = 0x00000002U,</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :     //! Logging is enabled and `CodeHolder::getLogger()` should return a valid</a>
+<a name="119"><span class="lineNum">     119 </span>            :     //! \ref Logger pointer.</a>
+<a name="120"><span class="lineNum">     120 </span>            :     kOptionLoggingEnabled   = 0x00000004U,</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :     //! Mask of all internal options that are not used to represent instruction</a>
+<a name="123"><span class="lineNum">     123 </span>            :     //! options, but are used to instrument Assembler and CodeBuilder. These</a>
+<a name="124"><span class="lineNum">     124 </span>            :     //! options are internal and should not be used outside of AsmJit itself.</a>
+<a name="125"><span class="lineNum">     125 </span>            :     //!</a>
+<a name="126"><span class="lineNum">     126 </span>            :     //! NOTE: Reserved options should never appear in `CBInst` options.</a>
+<a name="127"><span class="lineNum">     127 </span>            :     kOptionReservedMask = 0x00000007U,</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :     //! Used only by Assembler to mark `_op4` and `_op5` are used.</a>
+<a name="130"><span class="lineNum">     130 </span>            :     kOptionOp4Op5Used = 0x00000008U,</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :     //! Prevents following a jump during compilation (CodeCompiler).</a>
+<a name="133"><span class="lineNum">     133 </span>            :     kOptionUnfollow = 0x00000010U,</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :     //! Overwrite the destination operand (CodeCompiler).</a>
+<a name="136"><span class="lineNum">     136 </span>            :     //!</a>
+<a name="137"><span class="lineNum">     137 </span>            :     //! Hint that is important for register liveness analysis. It tells the</a>
+<a name="138"><span class="lineNum">     138 </span>            :     //! compiler that the destination operand will be overwritten now or by</a>
+<a name="139"><span class="lineNum">     139 </span>            :     //! adjacent instructions. CodeCompiler knows when a register is completely</a>
+<a name="140"><span class="lineNum">     140 </span>            :     //! overwritten by a single instruction, for example you don't have to</a>
+<a name="141"><span class="lineNum">     141 </span>            :     //! mark &quot;movaps&quot; or &quot;pxor x, x&quot;, however, if a pair of instructions is</a>
+<a name="142"><span class="lineNum">     142 </span>            :     //! used and the first of them doesn't completely overwrite the content</a>
+<a name="143"><span class="lineNum">     143 </span>            :     //! of the destination, CodeCompiler fails to mark that register as dead.</a>
+<a name="144"><span class="lineNum">     144 </span>            :     //!</a>
+<a name="145"><span class="lineNum">     145 </span>            :     //! X86/X64 Specific</a>
+<a name="146"><span class="lineNum">     146 </span>            :     //! ----------------</a>
+<a name="147"><span class="lineNum">     147 </span>            :     //!</a>
+<a name="148"><span class="lineNum">     148 </span>            :     //!   - All instructions that always overwrite at least the size of the</a>
+<a name="149"><span class="lineNum">     149 </span>            :     //!     register the virtual-register uses , for example &quot;mov&quot;, &quot;movq&quot;,</a>
+<a name="150"><span class="lineNum">     150 </span>            :     //!     &quot;movaps&quot; don't need the overwrite option to be used - conversion,</a>
+<a name="151"><span class="lineNum">     151 </span>            :     //!     shuffle, and other miscellaneous instructions included.</a>
+<a name="152"><span class="lineNum">     152 </span>            :     //!</a>
+<a name="153"><span class="lineNum">     153 </span>            :     //!   - All instructions that clear the destination register if all operands</a>
+<a name="154"><span class="lineNum">     154 </span>            :     //!     are the same, for example &quot;xor x, x&quot;, &quot;pcmpeqb x x&quot;, etc...</a>
+<a name="155"><span class="lineNum">     155 </span>            :     //!</a>
+<a name="156"><span class="lineNum">     156 </span>            :     //!   - Consecutive instructions that partially overwrite the variable until</a>
+<a name="157"><span class="lineNum">     157 </span>            :     //!     there is no old content require the `overwrite()` to be used. Some</a>
+<a name="158"><span class="lineNum">     158 </span>            :     //!     examples (not always the best use cases thought):</a>
+<a name="159"><span class="lineNum">     159 </span>            :     //!</a>
+<a name="160"><span class="lineNum">     160 </span>            :     //!     - `movlps xmm0, ?` followed by `movhps xmm0, ?` and vice versa</a>
+<a name="161"><span class="lineNum">     161 </span>            :     //!     - `movlpd xmm0, ?` followed by `movhpd xmm0, ?` and vice versa</a>
+<a name="162"><span class="lineNum">     162 </span>            :     //!     - `mov al, ?` followed by `and ax, 0xFF`</a>
+<a name="163"><span class="lineNum">     163 </span>            :     //!     - `mov al, ?` followed by `mov ah, al`</a>
+<a name="164"><span class="lineNum">     164 </span>            :     //!     - `pinsrq xmm0, ?, 0` followed by `pinsrq xmm0, ?, 1`</a>
+<a name="165"><span class="lineNum">     165 </span>            :     //!</a>
+<a name="166"><span class="lineNum">     166 </span>            :     //!   - If allocated variable is used temporarily for scalar operations. For</a>
+<a name="167"><span class="lineNum">     167 </span>            :     //!     example if you allocate a full vector like `X86Compiler::newXmm()`</a>
+<a name="168"><span class="lineNum">     168 </span>            :     //!     and then use that vector for scalar operations you should use</a>
+<a name="169"><span class="lineNum">     169 </span>            :     //!     `overwrite()` directive:</a>
+<a name="170"><span class="lineNum">     170 </span>            :     //!</a>
+<a name="171"><span class="lineNum">     171 </span>            :     //!     - `sqrtss x, y` - only LO element of `x` is changed, if you don't use</a>
+<a name="172"><span class="lineNum">     172 </span>            :     //!       HI elements, use `X86Compiler.overwrite().sqrtss(x, y)`.</a>
+<a name="173"><span class="lineNum">     173 </span>            :     kOptionOverwrite = 0x00000020U</a>
+<a name="174"><span class="lineNum">     174 </span>            :   };</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="177"><span class="lineNum">     177 </span>            :   // [Construction / Destruction]</a>
+<a name="178"><span class="lineNum">     178 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   ASMJIT_API CodeEmitter(uint32_t type) noexcept;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   ASMJIT_API virtual ~CodeEmitter() noexcept;</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="184"><span class="lineNum">     184 </span>            :   // [Events]</a>
+<a name="185"><span class="lineNum">     185 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   //! Called after the \ref CodeEmitter was attached to the \ref CodeHolder.</a>
+<a name="188"><span class="lineNum">     188 </span>            :   virtual Error onAttach(CodeHolder* code) noexcept = 0;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //! Called after the \ref CodeEmitter was detached from the \ref CodeHolder.</a>
+<a name="190"><span class="lineNum">     190 </span>            :   virtual Error onDetach(CodeHolder* code) noexcept = 0;</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // [Code-Generation]</a>
+<a name="194"><span class="lineNum">     194 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   //! Emit instruction having max 4 operands.</a>
+<a name="197"><span class="lineNum">     197 </span>            :   virtual Error _emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) = 0;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   //! Emit instruction having max 6 operands.</a>
+<a name="199"><span class="lineNum">     199 </span>            :   virtual Error _emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, const Operand_&amp; o5) = 0;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   //! Emit instruction having operands stored in array.</a>
+<a name="201"><span class="lineNum">     201 </span>            :   virtual Error _emitOpArray(uint32_t instId, const Operand_* opArray, size_t opCount);</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   //! Create a new label.</a>
+<a name="204"><span class="lineNum">     204 </span>            :   virtual Label newLabel() = 0;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   //! Create a new named label.</a>
+<a name="206"><span class="lineNum">     206 </span>            :   virtual Label newNamedLabel(</a>
+<a name="207"><span class="lineNum">     207 </span>            :     const char* name,</a>
+<a name="208"><span class="lineNum">     208 </span>            :     size_t nameLength = Globals::kInvalidIndex,</a>
+<a name="209"><span class="lineNum">     209 </span>            :     uint32_t type = Label::kTypeGlobal,</a>
+<a name="210"><span class="lineNum">     210 </span>            :     uint32_t parentId = 0) = 0;</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   //! Get a label by name.</a>
+<a name="213"><span class="lineNum">     213 </span>            :   //!</a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! Returns invalid Label in case that the name is invalid or label was not found.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   //!</a>
+<a name="216"><span class="lineNum">     216 </span>            :   //! NOTE: This function doesn't trigger ErrorHandler in case the name is</a>
+<a name="217"><span class="lineNum">     217 </span>            :   //! invalid or no such label exist. You must always check the validity of the</a>
+<a name="218"><span class="lineNum">     218 </span>            :   //! \ref Label returned.</a>
+<a name="219"><span class="lineNum">     219 </span>            :   ASMJIT_API Label getLabelByName(</a>
+<a name="220"><span class="lineNum">     220 </span>            :     const char* name,</a>
+<a name="221"><span class="lineNum">     221 </span>            :     size_t nameLength = Globals::kInvalidIndex,</a>
+<a name="222"><span class="lineNum">     222 </span>            :     uint32_t parentId = 0) noexcept;</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   //! Bind the `label` to the current position of the current section.</a>
+<a name="225"><span class="lineNum">     225 </span>            :   //!</a>
+<a name="226"><span class="lineNum">     226 </span>            :   //! NOTE: Attempt to bind the same label multiple times will return an error.</a>
+<a name="227"><span class="lineNum">     227 </span>            :   virtual Error bind(const Label&amp; label) = 0;</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :   //! Align to the `alignment` specified.</a>
+<a name="230"><span class="lineNum">     230 </span>            :   //!</a>
+<a name="231"><span class="lineNum">     231 </span>            :   //! The sequence that is used to fill the gap between the aligned location</a>
+<a name="232"><span class="lineNum">     232 </span>            :   //! and the current location depends on the align `mode`, see \ref AlignMode.</a>
+<a name="233"><span class="lineNum">     233 </span>            :   virtual Error align(uint32_t mode, uint32_t alignment) = 0;</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   //! Embed raw data into the code-buffer.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   virtual Error embed(const void* data, uint32_t size) = 0;</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            :   //! Embed absolute label address as data (4 or 8 bytes).</a>
+<a name="239"><span class="lineNum">     239 </span>            :   virtual Error embedLabel(const Label&amp; label) = 0;</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   //! Embed a constant pool into the code-buffer in the following steps:</a>
+<a name="242"><span class="lineNum">     242 </span>            :   //!   1. Align by using kAlignData to the minimum `pool` alignment.</a>
+<a name="243"><span class="lineNum">     243 </span>            :   //!   2. Bind `label` so it's bound to an aligned location.</a>
+<a name="244"><span class="lineNum">     244 </span>            :   //!   3. Emit constant pool data.</a>
+<a name="245"><span class="lineNum">     245 </span>            :   virtual Error embedConstPool(const Label&amp; label, const ConstPool&amp; pool) = 0;</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :   //! Emit a comment string `s` with an optional `len` parameter.</a>
+<a name="248"><span class="lineNum">     248 </span>            :   virtual Error comment(const char* s, size_t len = Globals::kInvalidIndex) = 0;</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="251"><span class="lineNum">     251 </span>            :   // [Code-Generation Status]</a>
+<a name="252"><span class="lineNum">     252 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   //! Get if the CodeEmitter is initialized (i.e. attached to a \ref CodeHolder).</a>
+<a name="255"><span class="lineNum">     255 </span>            :   ASMJIT_INLINE bool isInitialized() const noexcept { return _code != nullptr; }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :   ASMJIT_API virtual Error finalize();</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="260"><span class="lineNum">     260 </span>            :   // [Code Information]</a>
+<a name="261"><span class="lineNum">     261 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   //! Get information about the code, see \ref CodeInfo.</a>
+<a name="264"><span class="lineNum">     264 </span>            :   ASMJIT_INLINE const CodeInfo&amp; getCodeInfo() const noexcept { return _codeInfo; }</a>
+<a name="265"><span class="lineNum">     265 </span>            :   //! Get \ref CodeHolder this CodeEmitter is attached to.</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE CodeHolder* getCode() const noexcept { return _code; }</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   //! Get information about the architecture, see \ref ArchInfo.</a>
+<a name="269"><span class="lineNum">     269 </span>            :   ASMJIT_INLINE const ArchInfo&amp; getArchInfo() const noexcept { return _codeInfo.getArchInfo(); }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   //! Get if the target architecture is 32-bit.</a>
+<a name="272"><span class="lineNum">     272 </span>            :   ASMJIT_INLINE bool is32Bit() const noexcept { return getArchInfo().is32Bit(); }</a>
+<a name="273"><span class="lineNum">     273 </span>            :   //! Get if the target architecture is 64-bit.</a>
+<a name="274"><span class="lineNum">     274 </span>            :   ASMJIT_INLINE bool is64Bit() const noexcept { return getArchInfo().is64Bit(); }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   //! Get the target architecture type.</a>
+<a name="277"><span class="lineNum">     277 </span>            :   ASMJIT_INLINE uint32_t getArchType() const noexcept { return getArchInfo().getType(); }</a>
+<a name="278"><span class="lineNum">     278 </span>            :   //! Get the target architecture sub-type.</a>
+<a name="279"><span class="lineNum">     279 </span>            :   ASMJIT_INLINE uint32_t getArchSubType() const noexcept { return getArchInfo().getSubType(); }</a>
+<a name="280"><span class="lineNum">     280 </span>            :   //! Get the target architecture's GP register size (4 or 8 bytes).</a>
+<a name="281"><span class="lineNum">     281 </span>            :   ASMJIT_INLINE uint32_t getGpSize() const noexcept { return getArchInfo().getGpSize(); }</a>
+<a name="282"><span class="lineNum">     282 </span>            :   //! Get the number of target GP registers.</a>
+<a name="283"><span class="lineNum">     283 </span>            :   ASMJIT_INLINE uint32_t getGpCount() const noexcept { return getArchInfo().getGpCount(); }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="286"><span class="lineNum">     286 </span>            :   // [Code-Emitter Type]</a>
+<a name="287"><span class="lineNum">     287 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   //! Get the type of this CodeEmitter, see \ref Type.</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       7792 :   ASMJIT_INLINE uint32_t getType() const noexcept { return _type; }</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            :   ASMJIT_INLINE bool isAssembler() const noexcept { return _type == kTypeAssembler; }</a>
+<a name="293"><span class="lineNum">     293 </span>            :   ASMJIT_INLINE bool isCodeBuilder() const noexcept { return _type == kTypeBuilder; }</a>
+<a name="294"><span class="lineNum">     294 </span>            :   ASMJIT_INLINE bool isCodeCompiler() const noexcept { return _type == kTypeCompiler; }</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="297"><span class="lineNum">     297 </span>            :   // [Global Information]</a>
+<a name="298"><span class="lineNum">     298 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :   //! Get global hints.</a>
+<a name="301"><span class="lineNum">     301 </span>            :   ASMJIT_INLINE uint32_t getGlobalHints() const noexcept { return _globalHints; }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            :   //! Get global options.</a>
+<a name="304"><span class="lineNum">     304 </span>            :   //!</a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! Global options are merged with instruction options before the instruction</a>
+<a name="306"><span class="lineNum">     306 </span>            :   //! is encoded. These options have some bits reserved that are used for error</a>
+<a name="307"><span class="lineNum">     307 </span>            :   //! checking, logging, and strict validation. Other options are globals that</a>
+<a name="308"><span class="lineNum">     308 </span>            :   //! affect each instruction, for example if VEX3 is set globally, it will all</a>
+<a name="309"><span class="lineNum">     309 </span>            :   //! instructions, even those that don't have such option set.</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      98972 :   ASMJIT_INLINE uint32_t getGlobalOptions() const noexcept { return _globalOptions; }</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="313"><span class="lineNum">     313 </span>            :   // [Error Handling]</a>
+<a name="314"><span class="lineNum">     314 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            :   //! Get if the object is in error state.</a>
+<a name="317"><span class="lineNum">     317 </span>            :   //!</a>
+<a name="318"><span class="lineNum">     318 </span>            :   //! Error state means that it does not consume anything unless the error</a>
+<a name="319"><span class="lineNum">     319 </span>            :   //! state is reset by calling `resetLastError()`. Use `getLastError()` to</a>
+<a name="320"><span class="lineNum">     320 </span>            :   //! get the last error that put the object into the error state.</a>
+<a name="321"><span class="lineNum">     321 </span>            :   ASMJIT_INLINE bool isInErrorState() const noexcept { return _lastError != kErrorOk; }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :   //! Get the last error code.</a>
+<a name="324"><span class="lineNum">     324 </span>            :   ASMJIT_INLINE Error getLastError() const noexcept { return _lastError; }</a>
+<a name="325"><span class="lineNum">     325 </span>            :   //! Set the last error code and propagate it through the error handler.</a>
+<a name="326"><span class="lineNum">     326 </span>            :   ASMJIT_API Error setLastError(Error error, const char* message = nullptr);</a>
+<a name="327"><span class="lineNum">     327 </span>            :   //! Clear the last error code and return `kErrorOk`.</a>
+<a name="328"><span class="lineNum">     328 </span>            :   ASMJIT_INLINE Error resetLastError() noexcept { return setLastError(kErrorOk); }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="331"><span class="lineNum">     331 </span>            :   // [Accessors That Affect the Next Instruction]</a>
+<a name="332"><span class="lineNum">     332 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            :   //! Get options of the next instruction.</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      95076 :   ASMJIT_INLINE uint32_t getOptions() const noexcept { return _options; }</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   //! Set options of the next instruction.</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      48362 :   ASMJIT_INLINE void setOptions(uint32_t options) noexcept { _options = options; }</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   //! Add options of the next instruction.</a>
+<a name="339"><span class="lineNum">     339 </span>            :   ASMJIT_INLINE void addOptions(uint32_t options) noexcept { _options |= options; }</a>
+<a name="340"><span class="lineNum">     340 </span>            :   //! Reset options of the next instruction.</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      95076 :   ASMJIT_INLINE void resetOptions() noexcept { _options = 0; }</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :   //! Get if the extra register operand is valid.</a>
+<a name="344"><span class="lineNum">     344 </span>            :   ASMJIT_INLINE bool hasExtraReg() const noexcept { return _extraReg.isValid(); }</a>
+<a name="345"><span class="lineNum">     345 </span>            :   //! Get an extra operand that will be used by the next instruction (architecture specific).</a>
+<a name="346"><span class="lineNum">     346 </span>            :   ASMJIT_INLINE const RegOnly&amp; getExtraReg() const noexcept { return _extraReg; }</a>
+<a name="347"><span class="lineNum">     347 </span>            :   //! Set an extra operand that will be used by the next instruction (architecture specific).</a>
+<a name="348"><span class="lineNum">     348 </span>            :   ASMJIT_INLINE void setExtraReg(const Reg&amp; reg) noexcept { _extraReg.init(reg); }</a>
+<a name="349"><span class="lineNum">     349 </span>            :   //! Set an extra operand that will be used by the next instruction (architecture specific).</a>
+<a name="350"><span class="lineNum">     350 </span>            :   ASMJIT_INLINE void setExtraReg(const RegOnly&amp; reg) noexcept { _extraReg.init(reg); }</a>
+<a name="351"><span class="lineNum">     351 </span>            :   //! Reset an extra operand that will be used by the next instruction (architecture specific).</a>
+<a name="352"><span class="lineNum">     352 </span>            :   ASMJIT_INLINE void resetExtraReg() noexcept { _extraReg.reset(); }</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            :   //! Get annotation of the next instruction.</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      46714 :   ASMJIT_INLINE const char* getInlineComment() const noexcept { return _inlineComment; }</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :   //! Set annotation of the next instruction.</a>
+<a name="357"><span class="lineNum">     357 </span>            :   //!</a>
+<a name="358"><span class="lineNum">     358 </span>            :   //! NOTE: This string is set back to null by `_emit()`, but until that it has</a>
+<a name="359"><span class="lineNum">     359 </span>            :   //! to remain valid as `CodeEmitter` is not required to make a copy of it (and</a>
+<a name="360"><span class="lineNum">     360 </span>            :   //! it would be slow to do that for each instruction).</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">      65238 :   ASMJIT_INLINE void setInlineComment(const char* s) noexcept { _inlineComment = s; }</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :   //! Reset annotation of the next instruction to null.</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">      98972 :   ASMJIT_INLINE void resetInlineComment() noexcept { _inlineComment = nullptr; }</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="366"><span class="lineNum">     366 </span>            :   // [Helpers]</a>
+<a name="367"><span class="lineNum">     367 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            :   //! Get if the `label` is valid (i.e. registered).</a>
+<a name="370"><span class="lineNum">     370 </span>            :   ASMJIT_INLINE bool isLabelValid(const Label&amp; label) const noexcept {</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :     return isLabelValid(label.getId());</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            :   //! Get if the label `id` is valid (i.e. registered).</a>
+<a name="375"><span class="lineNum">     375 </span>            :   ASMJIT_API bool isLabelValid(uint32_t id) const noexcept;</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            :   //! Emit a formatted string `fmt`.</a>
+<a name="378"><span class="lineNum">     378 </span>            :   ASMJIT_API Error commentf(const char* fmt, ...);</a>
+<a name="379"><span class="lineNum">     379 </span>            :   //! Emit a formatted string `fmt` (va_list version).</a>
+<a name="380"><span class="lineNum">     380 </span>            :   ASMJIT_API Error commentv(const char* fmt, va_list ap);</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="383"><span class="lineNum">     383 </span>            :   // [Emit]</a>
+<a name="384"><span class="lineNum">     384 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            :   // NOTE: These `emit()` helpers are designed to address a code-bloat generated</a>
+<a name="387"><span class="lineNum">     387 </span>            :   // by C++ compilers to call a function having many arguments. Each parameter to</a>
+<a name="388"><span class="lineNum">     388 </span>            :   // `_emit()` requires code to pass it, which means that if we default to 4</a>
+<a name="389"><span class="lineNum">     389 </span>            :   // operand parameters in `_emit()` and instId the C++ compiler would have to</a>
+<a name="390"><span class="lineNum">     390 </span>            :   // generate a virtual function call having 5 parameters, which is quite a lot.</a>
+<a name="391"><span class="lineNum">     391 </span>            :   // Since by default asm instructions have 2 to 3 operands it's better to</a>
+<a name="392"><span class="lineNum">     392 </span>            :   // introduce helpers that pass those and fill all the remaining with `_none`.</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            :   //! Emit an instruction.</a>
+<a name="395"><span class="lineNum">     395 </span>            :   ASMJIT_API Error emit(uint32_t instId);</a>
+<a name="396"><span class="lineNum">     396 </span>            :   //! \overload</a>
+<a name="397"><span class="lineNum">     397 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0);</a>
+<a name="398"><span class="lineNum">     398 </span>            :   //! \overload</a>
+<a name="399"><span class="lineNum">     399 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1);</a>
+<a name="400"><span class="lineNum">     400 </span>            :   //! \overload</a>
+<a name="401"><span class="lineNum">     401 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2);</a>
+<a name="402"><span class="lineNum">     402 </span>            :   //! \overload</a>
+<a name="403"><span class="lineNum">     403 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3);</a>
+<a name="404"><span class="lineNum">     404 </span>            :   //! \overload</a>
+<a name="405"><span class="lineNum">     405 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4);</a>
+<a name="406"><span class="lineNum">     406 </span>            :   //! \overload</a>
+<a name="407"><span class="lineNum">     407 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, const Operand_&amp; o5);</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            :   //! Emit an instruction that has a 32-bit signed immediate operand.</a>
+<a name="410"><span class="lineNum">     410 </span>            :   ASMJIT_API Error emit(uint32_t instId, int o0);</a>
+<a name="411"><span class="lineNum">     411 </span>            :   //! \overload</a>
+<a name="412"><span class="lineNum">     412 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, int o1);</a>
+<a name="413"><span class="lineNum">     413 </span>            :   //! \overload</a>
+<a name="414"><span class="lineNum">     414 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, int o2);</a>
+<a name="415"><span class="lineNum">     415 </span>            :   //! \overload</a>
+<a name="416"><span class="lineNum">     416 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, int o3);</a>
+<a name="417"><span class="lineNum">     417 </span>            :   //! \overload</a>
+<a name="418"><span class="lineNum">     418 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, int o4);</a>
+<a name="419"><span class="lineNum">     419 </span>            :   //! \overload</a>
+<a name="420"><span class="lineNum">     420 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, int o5);</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            :   //! Emit an instruction that has a 64-bit signed immediate operand.</a>
+<a name="423"><span class="lineNum">     423 </span>            :   ASMJIT_API Error emit(uint32_t instId, int64_t o0);</a>
+<a name="424"><span class="lineNum">     424 </span>            :   //! \overload</a>
+<a name="425"><span class="lineNum">     425 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, int64_t o1);</a>
+<a name="426"><span class="lineNum">     426 </span>            :   //! \overload</a>
+<a name="427"><span class="lineNum">     427 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, int64_t o2);</a>
+<a name="428"><span class="lineNum">     428 </span>            :   //! \overload</a>
+<a name="429"><span class="lineNum">     429 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, int64_t o3);</a>
+<a name="430"><span class="lineNum">     430 </span>            :   //! \overload</a>
+<a name="431"><span class="lineNum">     431 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, int64_t o4);</a>
+<a name="432"><span class="lineNum">     432 </span>            :   //! \overload</a>
+<a name="433"><span class="lineNum">     433 </span>            :   ASMJIT_API Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, int64_t o5);</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :   //! \overload</a>
+<a name="436"><span class="lineNum">     436 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, unsigned int o0) {</a>
+<a name="437"><span class="lineNum">     437 </span>            :     return emit(instId, static_cast&lt;int64_t&gt;(o0));</a>
+<a name="438"><span class="lineNum">     438 </span>            :   }</a>
+<a name="439"><span class="lineNum">     439 </span>            :   //! \overload</a>
+<a name="440"><span class="lineNum">     440 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, unsigned int o1) {</a>
+<a name="441"><span class="lineNum">     441 </span>            :     return emit(instId, o0, static_cast&lt;int64_t&gt;(o1));</a>
+<a name="442"><span class="lineNum">     442 </span>            :   }</a>
+<a name="443"><span class="lineNum">     443 </span>            :   //! \overload</a>
+<a name="444"><span class="lineNum">     444 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, unsigned int o2) {</a>
+<a name="445"><span class="lineNum">     445 </span>            :     return emit(instId, o0, o1, static_cast&lt;int64_t&gt;(o2));</a>
+<a name="446"><span class="lineNum">     446 </span>            :   }</a>
+<a name="447"><span class="lineNum">     447 </span>            :   //! \overload</a>
+<a name="448"><span class="lineNum">     448 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, unsigned int o3) {</a>
+<a name="449"><span class="lineNum">     449 </span>            :     return emit(instId, o0, o1, o2, static_cast&lt;int64_t&gt;(o3));</a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span>            :   //! \overload</a>
+<a name="452"><span class="lineNum">     452 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, unsigned int o4) {</a>
+<a name="453"><span class="lineNum">     453 </span>            :     return emit(instId, o0, o1, o2, o3, static_cast&lt;int64_t&gt;(o4));</a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span>            :   //! \overload</a>
+<a name="456"><span class="lineNum">     456 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, unsigned int o5) {</a>
+<a name="457"><span class="lineNum">     457 </span>            :     return emit(instId, o0, o1, o2, o3, o4, static_cast&lt;int64_t&gt;(o5));</a>
+<a name="458"><span class="lineNum">     458 </span>            :   }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   //! \overload</a>
+<a name="461"><span class="lineNum">     461 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, uint64_t o0) {</a>
+<a name="462"><span class="lineNum">     462 </span>            :     return emit(instId, static_cast&lt;int64_t&gt;(o0));</a>
+<a name="463"><span class="lineNum">     463 </span>            :   }</a>
+<a name="464"><span class="lineNum">     464 </span>            :   //! \overload</a>
+<a name="465"><span class="lineNum">     465 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, uint64_t o1) {</a>
+<a name="466"><span class="lineNum">     466 </span>            :     return emit(instId, o0, static_cast&lt;int64_t&gt;(o1));</a>
+<a name="467"><span class="lineNum">     467 </span>            :   }</a>
+<a name="468"><span class="lineNum">     468 </span>            :   //! \overload</a>
+<a name="469"><span class="lineNum">     469 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, uint64_t o2) {</a>
+<a name="470"><span class="lineNum">     470 </span>            :     return emit(instId, o0, o1, static_cast&lt;int64_t&gt;(o2));</a>
+<a name="471"><span class="lineNum">     471 </span>            :   }</a>
+<a name="472"><span class="lineNum">     472 </span>            :   //! \overload</a>
+<a name="473"><span class="lineNum">     473 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, uint64_t o3) {</a>
+<a name="474"><span class="lineNum">     474 </span>            :     return emit(instId, o0, o1, o2, static_cast&lt;int64_t&gt;(o3));</a>
+<a name="475"><span class="lineNum">     475 </span>            :   }</a>
+<a name="476"><span class="lineNum">     476 </span>            :   //! \overload</a>
+<a name="477"><span class="lineNum">     477 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, uint64_t o4) {</a>
+<a name="478"><span class="lineNum">     478 </span>            :     return emit(instId, o0, o1, o2, o3, static_cast&lt;int64_t&gt;(o4));</a>
+<a name="479"><span class="lineNum">     479 </span>            :   }</a>
+<a name="480"><span class="lineNum">     480 </span>            :   //! \overload</a>
+<a name="481"><span class="lineNum">     481 </span>            :   ASMJIT_INLINE Error emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, uint64_t o5) {</a>
+<a name="482"><span class="lineNum">     482 </span>            :     return emit(instId, o0, o1, o2, o3, o4, static_cast&lt;int64_t&gt;(o5));</a>
+<a name="483"><span class="lineNum">     483 </span>            :   }</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            :   ASMJIT_INLINE Error emitOpArray(uint32_t instId, const Operand_* opArray, size_t opCount) {</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">      48362 :     return _emitOpArray(instId, opArray, opCount);</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :   }</a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="490"><span class="lineNum">     490 </span>            :   // [Members]</a>
+<a name="491"><span class="lineNum">     491 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            :   CodeInfo _codeInfo;                    //!&lt; Basic information about the code (matches CodeHolder::_codeInfo).</a>
+<a name="494"><span class="lineNum">     494 </span>            :   CodeHolder* _code;                     //!&lt; CodeHolder the CodeEmitter is attached to.</a>
+<a name="495"><span class="lineNum">     495 </span>            :   CodeEmitter* _nextEmitter;             //!&lt; Linked list of `CodeEmitter`s attached to the same \ref CodeHolder.</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span>            :   uint8_t _type;                         //!&lt; See CodeEmitter::Type.</a>
+<a name="498"><span class="lineNum">     498 </span>            :   uint8_t _destroyed;                    //!&lt; Set by ~CodeEmitter() before calling `_code-&gt;detach()`.</a>
+<a name="499"><span class="lineNum">     499 </span>            :   uint8_t _finalized;                    //!&lt; True if the CodeEmitter is finalized (CodeBuilder &amp; CodeCompiler).</a>
+<a name="500"><span class="lineNum">     500 </span>            :   uint8_t _reserved;                     //!&lt; \internal</a>
+<a name="501"><span class="lineNum">     501 </span>            :   Error _lastError;                      //!&lt; Last error code.</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            :   uint32_t _privateData;                 //!&lt; Internal private data used freely by any CodeEmitter.</a>
+<a name="504"><span class="lineNum">     504 </span>            :   uint32_t _globalHints;                 //!&lt; Global hints, always in sync with CodeHolder.</a>
+<a name="505"><span class="lineNum">     505 </span>            :   uint32_t _globalOptions;               //!&lt; Global options, combined with `_options` before used by each instruction.</a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span>            :   uint32_t _options;                     //!&lt; Used to pass instruction options        (affects the next instruction).</a>
+<a name="508"><span class="lineNum">     508 </span>            :   RegOnly _extraReg;                     //!&lt; Extra register (op-mask {k} on AVX-512) (affects the next instruction).</a>
+<a name="509"><span class="lineNum">     509 </span>            :   const char* _inlineComment;            //!&lt; Inline comment of the next instruction  (affects the next instruction).</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            :   Operand_ _none;                        //!&lt; Used to pass unused operands to `_emit()` instead of passing null.</a>
+<a name="512"><span class="lineNum">     512 </span>            :   Reg _nativeGpReg;                      //!&lt; Native GP register with zero id.</a>
+<a name="513"><span class="lineNum">     513 </span>            :   const Reg* _nativeGpArray;             //!&lt; Array of native registers indexed from zero.</a>
+<a name="514"><span class="lineNum">     514 </span>            : };</a>
+<a name="515"><span class="lineNum">     515 </span>            : </a>
+<a name="516"><span class="lineNum">     516 </span>            : //! \}</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : } // asmjit namespace</a>
+<a name="519"><span class="lineNum">     519 </span>            : } // namespace PLMD</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            : // [Api-End]</a>
+<a name="522"><span class="lineNum">     522 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            : // [Guard]</a>
+<a name="525"><span class="lineNum">     525 </span>            : #endif // _ASMJIT_BASE_CODEEMITTER_H</a>
+<a name="526"><span class="lineNum">     526 </span>            : #pragma GCC diagnostic pop</a>
+<a name="527"><span class="lineNum">     527 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="528"><span class="lineNum">     528 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeholder.cpp.func-sort-c.html b/coverage-libs/asmjit/codeholder.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3402c63b77
--- /dev/null
+++ b/coverage-libs/asmjit/codeholder.cpp.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeholder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeholder.cpp<span style="font-size: 80%;"> (<a href="codeholder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">259</td>
+            <td class="headerCovTableEntryLo">46.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">48.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="codeholder.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#431">_ZN4PLMD6asmjit10CodeHolder12newLabelLinkEPNS0_10LabelEntryEjml</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#543">_ZN4PLMD6asmjit10CodeHolder16getLabelIdByNameEPKcmj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#161">_ZN4PLMD6asmjit10CodeHolder5resetEb</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#273">_ZN4PLMD6asmjit10CodeHolder9setLoggerEPNS0_6LoggerE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#45">_ZN4PLMD6asmjit12ErrorHandlerC2Ev</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#46">_ZN4PLMD6asmjit12ErrorHandlerD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#407">_ZN4PLMD6asmjit12_GLOBAL__N_1L28CodeHolder_hashNameAndFixLenEPKcRm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#52">_ZN4PLMD6asmjitL26CodeHolder_setGlobalOptionEPNS0_10CodeHolderEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#321">_ZN4PLMD6asmjit10CodeHolder10growBufferEPNS0_10CodeBufferEm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#128">_ZN4PLMD6asmjit10CodeHolder4initERKNS0_8CodeInfoE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#105">_ZN4PLMD6asmjit10CodeHolderC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#120">_ZN4PLMD6asmjit10CodeHolderD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#64">_ZN4PLMD6asmjitL24CodeHolder_resetInternalEPNS0_10CodeHolderEb</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#291">_ZN4PLMD6asmjitL26CodeHolder_reserveInternalEPNS0_10CodeHolderEPNS0_10CodeBufferEm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#585">_ZNK4PLMD6asmjit10CodeHolder8relocateEPvm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#447">_ZN4PLMD6asmjit10CodeHolder10newLabelIdERj</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#252">_ZN4PLMD6asmjit10CodeHolder4syncEv</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#169">_ZN4PLMD6asmjit10CodeHolder6attachEPNS0_11CodeEmitterE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#205">_ZN4PLMD6asmjit10CodeHolder6detachEPNS0_11CodeEmitterE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#260">_ZNK4PLMD6asmjit10CodeHolder11getCodeSizeEv</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeholder.cpp.func.html b/coverage-libs/asmjit/codeholder.cpp.func.html
new file mode 100644
index 0000000000..fe81eac53e
--- /dev/null
+++ b/coverage-libs/asmjit/codeholder.cpp.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeholder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeholder.cpp<span style="font-size: 80%;"> (<a href="codeholder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">259</td>
+            <td class="headerCovTableEntryLo">46.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">48.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codeholder.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#321">_ZN4PLMD6asmjit10CodeHolder10growBufferEPNS0_10CodeBufferEm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#447">_ZN4PLMD6asmjit10CodeHolder10newLabelIdERj</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#431">_ZN4PLMD6asmjit10CodeHolder12newLabelLinkEPNS0_10LabelEntryEjml</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#560">_ZN4PLMD6asmjit10CodeHolder13newRelocEntryEPPNS0_10RelocEntryEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#367">_ZN4PLMD6asmjit10CodeHolder13reserveBufferEPNS0_10CodeBufferEm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#471">_ZN4PLMD6asmjit10CodeHolder15newNamedLabelIdERjPKcmjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#282">_ZN4PLMD6asmjit10CodeHolder15setErrorHandlerEPNS0_12ErrorHandlerE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#543">_ZN4PLMD6asmjit10CodeHolder16getLabelIdByNameEPKcmj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#128">_ZN4PLMD6asmjit10CodeHolder4initERKNS0_8CodeInfoE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#252">_ZN4PLMD6asmjit10CodeHolder4syncEv</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#161">_ZN4PLMD6asmjit10CodeHolder5resetEb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#169">_ZN4PLMD6asmjit10CodeHolder6attachEPNS0_11CodeEmitterE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#205">_ZN4PLMD6asmjit10CodeHolder6detachEPNS0_11CodeEmitterE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#273">_ZN4PLMD6asmjit10CodeHolder9setLoggerEPNS0_6LoggerE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#105">_ZN4PLMD6asmjit10CodeHolderC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#120">_ZN4PLMD6asmjit10CodeHolderD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#45">_ZN4PLMD6asmjit12ErrorHandlerC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#46">_ZN4PLMD6asmjit12ErrorHandlerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#46">_ZN4PLMD6asmjit12ErrorHandlerD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#407">_ZN4PLMD6asmjit12_GLOBAL__N_1L28CodeHolder_hashNameAndFixLenEPKcRm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#64">_ZN4PLMD6asmjitL24CodeHolder_resetInternalEPNS0_10CodeHolderEb</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#291">_ZN4PLMD6asmjitL26CodeHolder_reserveInternalEPNS0_10CodeHolderEPNS0_10CodeBufferEm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#52">_ZN4PLMD6asmjitL26CodeHolder_setGlobalOptionEPNS0_10CodeHolderEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#260">_ZNK4PLMD6asmjit10CodeHolder11getCodeSizeEv</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="codeholder.cpp.gcov.html#585">_ZNK4PLMD6asmjit10CodeHolder8relocateEPvm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeholder.cpp.gcov.html b/coverage-libs/asmjit/codeholder.cpp.gcov.html
new file mode 100644
index 0000000000..d39ae65ddf
--- /dev/null
+++ b/coverage-libs/asmjit/codeholder.cpp.gcov.html
@@ -0,0 +1,799 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeholder.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeholder.cpp<span style="font-size: 80%;"> (source / <a href="codeholder.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">259</td>
+            <td class="headerCovTableEntryLo">46.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">48.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./vmem.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : // [Api-Begin]</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace asmjit {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : // ============================================================================</a>
+<a name="44"><span class="lineNum">      44 </span>            : // [asmjit::ErrorHandler]</a>
+<a name="45"><span class="lineNum">      45 </span>            : // ============================================================================</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 : ErrorHandler::ErrorHandler() noexcept {}</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 : ErrorHandler::~ErrorHandler() noexcept {}</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : // [asmjit::CodeHolder - Utilities]</a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 : static void CodeHolder_setGlobalOption(CodeHolder* self, uint32_t clear, uint32_t add) noexcept {</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   // Modify global options of `CodeHolder` itself.</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   self-&gt;_globalOptions = (self-&gt;_globalOptions &amp; ~clear) | add;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   // Modify all global options of all `CodeEmitter`s attached.</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   CodeEmitter* emitter = self-&gt;_emitters;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :   while (emitter) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :     emitter-&gt;_globalOptions = (emitter-&gt;_globalOptions &amp; ~clear) | add;</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :     emitter = emitter-&gt;_nextEmitter;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1948 : static void CodeHolder_resetInternal(CodeHolder* self, bool releaseMemory) noexcept {</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   // Detach all `CodeEmitter`s.</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       1948 :   while (self-&gt;_emitters)</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :     self-&gt;detach(self-&gt;_emitters);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   // Reset everything into its construction state.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   self-&gt;_codeInfo.reset();</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       1948 :   self-&gt;_globalHints = 0;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       1948 :   self-&gt;_globalOptions = 0;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       1948 :   self-&gt;_logger = nullptr;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       1948 :   self-&gt;_errorHandler = nullptr;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       1948 :   self-&gt;_unresolvedLabelsCount = 0;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       1948 :   self-&gt;_trampolinesSize = 0;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   // Reset all sections.</a>
+<a name="82"><span class="lineNum">      82 </span>            :   size_t numSections = self-&gt;_sections.getLength();</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       3896 :   for (size_t i = 0; i &lt; numSections; i++) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1948 :     SectionEntry* section = self-&gt;_sections[i];</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1948 :     if (section-&gt;_buffer.hasData() &amp;&amp; !section-&gt;_buffer.isExternal())</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :       Internal::releaseMemory(section-&gt;_buffer._data);</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1948 :     section-&gt;_buffer._data = nullptr;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1948 :     section-&gt;_buffer._capacity = 0;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   // Reset zone allocator and all containers using it.</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1948 :   ZoneHeap* heap = &amp;self-&gt;_baseHeap;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1948 :   self-&gt;_namedLabels.reset(heap);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   self-&gt;_relocations.reset();</a>
+<a name="96"><span class="lineNum">      96 </span>            :   self-&gt;_labels.reset();</a>
+<a name="97"><span class="lineNum">      97 </span>            :   self-&gt;_sections.reset();</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1948 :   heap-&gt;reset(&amp;self-&gt;_baseZone);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1948 :   self-&gt;_baseZone.reset(releaseMemory);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1948 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : // ============================================================================</a>
+<a name="104"><span class="lineNum">     104 </span>            : // [asmjit::CodeHolder - Construction / Destruction]</a>
+<a name="105"><span class="lineNum">     105 </span>            : // ============================================================================</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1948 : CodeHolder::CodeHolder() noexcept</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   : _codeInfo(),</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1948 :     _globalHints(0),</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       1948 :     _globalOptions(0),</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1948 :     _emitters(nullptr),</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1948 :     _cgAsm(nullptr),</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1948 :     _logger(nullptr),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1948 :     _errorHandler(nullptr),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1948 :     _unresolvedLabelsCount(0),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       1948 :     _trampolinesSize(0),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       1948 :     _baseZone(16384 - Zone::kZoneOverhead),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1948 :     _dataZone(16384 - Zone::kZoneOverhead),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1948 :     _baseHeap(&amp;_baseZone),</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1948 :     _namedLabels(&amp;_baseHeap) {}</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       1948 : CodeHolder::~CodeHolder() noexcept {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       1948 :   CodeHolder_resetInternal(this, true);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       1948 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : // ============================================================================</a>
+<a name="127"><span class="lineNum">     127 </span>            : // [asmjit::CodeHolder - Init / Reset]</a>
+<a name="128"><span class="lineNum">     128 </span>            : // ============================================================================</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       1948 : Error CodeHolder::init(const CodeInfo&amp; info) noexcept {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Cannot reinitialize if it's locked or there is one or more CodeEmitter</a>
+<a name="132"><span class="lineNum">     132 </span>            :   // attached.</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       1948 :   if (isInitialized())</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     return DebugUtils::errored(kErrorAlreadyInitialized);</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // If we are just initializing there should be no emitters attached).</a>
+<a name="137"><span class="lineNum">     137 </span>            :   ASMJIT_ASSERT(_emitters == nullptr);</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   // Create the default section and insert it to the `_sections` array.</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1948 :   Error err = _sections.willGrow(&amp;_baseHeap);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1948 :   if (err == kErrorOk) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       1948 :     SectionEntry* se = _baseZone.allocZeroedT&lt;SectionEntry&gt;();</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1948 :     if (ASMJIT_LIKELY(se)) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       1948 :       se-&gt;_flags = SectionEntry::kFlagExec | SectionEntry::kFlagConst;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :       se-&gt;_setDefaultName('.', 't', 'e', 'x', 't');</a>
+<a name="146"><span class="lineNum">     146 </span>            :       _sections.appendUnsafe(se);</a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span>            :     else {</a>
+<a name="149"><span class="lineNum">     149 </span>            :       err = DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="150"><span class="lineNum">     150 </span>            :     }</a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(err)) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :     _baseZone.reset(false);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     return err;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            :   else {</a>
+<a name="158"><span class="lineNum">     158 </span>            :     _codeInfo = info;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       1948 :     return kErrorOk;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 : void CodeHolder::reset(bool releaseMemory) noexcept {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   CodeHolder_resetInternal(this, releaseMemory);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : // ============================================================================</a>
+<a name="168"><span class="lineNum">     168 </span>            : // [asmjit::CodeHolder - Attach / Detach]</a>
+<a name="169"><span class="lineNum">     169 </span>            : // ============================================================================</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       3896 : Error CodeHolder::attach(CodeEmitter* emitter) noexcept {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   // Catch a possible misuse of the API.</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       3896 :   if (!emitter)</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   uint32_t type = emitter-&gt;getType();</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       3896 :   if (type == CodeEmitter::kTypeNone || type &gt;= CodeEmitter::kTypeCount)</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   // This is suspicious, but don't fail if `emitter` matches.</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       3896 :   if (emitter-&gt;_code != nullptr) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     if (emitter-&gt;_code == this) return kErrorOk;</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // Special case - attach `Assembler`.</a>
+<a name="187"><span class="lineNum">     187 </span>            :   CodeEmitter** pSlot = nullptr;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       3896 :   if (type == CodeEmitter::kTypeAssembler) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       1948 :     if (_cgAsm)</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :       return DebugUtils::errored(kErrorSlotOccupied);</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1948 :     pSlot = reinterpret_cast&lt;CodeEmitter**&gt;(&amp;_cgAsm);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       3896 :   Error err = emitter-&gt;onAttach(this);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       3896 :   if (err != kErrorOk) return err;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   // Add to a single-linked list of `CodeEmitter`s.</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       3896 :   emitter-&gt;_nextEmitter = _emitters;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       3896 :   _emitters = emitter;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       3896 :   if (pSlot) *pSlot = emitter;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   // Establish the connection.</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       3896 :   emitter-&gt;_code = this;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       3896 :   return kErrorOk;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       3896 : Error CodeHolder::detach(CodeEmitter* emitter) noexcept {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       3896 :   if (!emitter)</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       3896 :   if (emitter-&gt;_code != this)</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   uint32_t type = emitter-&gt;getType();</a>
+<a name="215"><span class="lineNum">     215 </span>            :   Error err = kErrorOk;</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // NOTE: We always detach if we were asked to, if error happens during</a>
+<a name="218"><span class="lineNum">     218 </span>            :   // `emitter-&gt;onDetach()` we just propagate it, but the CodeEmitter will</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // be detached.</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       3896 :   if (!emitter-&gt;_destroyed) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     if (type == CodeEmitter::kTypeAssembler)</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :       static_cast&lt;Assembler*&gt;(emitter)-&gt;sync();</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :     err = emitter-&gt;onDetach(this);</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            :   // Special case - detach `Assembler`.</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       3896 :   if (type == CodeEmitter::kTypeAssembler)</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       1948 :     _cgAsm = nullptr;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   // Remove from a single-linked list of `CodeEmitter`s.</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       3896 :   CodeEmitter** pPrev = &amp;_emitters;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   for (;;) {</a>
+<a name="233"><span class="lineNum">     233 </span>            :     ASMJIT_ASSERT(*pPrev != nullptr);</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       3896 :     CodeEmitter* cur = *pPrev;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       3896 :     if (cur == emitter) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       3896 :       *pPrev = emitter-&gt;_nextEmitter;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :       break;</a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :     pPrev = &amp;cur-&gt;_nextEmitter;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">       3896 :   emitter-&gt;_code = nullptr;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       3896 :   emitter-&gt;_nextEmitter = nullptr;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       3896 :   return err;</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : // ============================================================================</a>
+<a name="251"><span class="lineNum">     251 </span>            : // [asmjit::CodeHolder - Sync]</a>
+<a name="252"><span class="lineNum">     252 </span>            : // ============================================================================</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       3896 : void CodeHolder::sync() noexcept {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">       3896 :   if (_cgAsm) _cgAsm-&gt;sync();</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       3896 : }</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : // ============================================================================</a>
+<a name="259"><span class="lineNum">     259 </span>            : // [asmjit::CodeHolder - Result Information]</a>
+<a name="260"><span class="lineNum">     260 </span>            : // ============================================================================</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       3896 : size_t CodeHolder::getCodeSize() const noexcept {</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   // Reflect all changes first.</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       3896 :   const_cast&lt;CodeHolder*&gt;(this)-&gt;sync();</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :   // TODO: Support sections.</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       3896 :   return _sections[0]-&gt;_buffer._length + getTrampolinesSize();</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            : // ============================================================================</a>
+<a name="271"><span class="lineNum">     271 </span>            : // [asmjit::CodeHolder - Logging &amp; Error Handling]</a>
+<a name="272"><span class="lineNum">     272 </span>            : // ============================================================================</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 : void CodeHolder::setLogger(Logger* logger) noexcept {</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :   uint32_t opt = 0;</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :   if (logger) opt = CodeEmitter::kOptionLoggingEnabled;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   _logger = logger;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :   CodeHolder_setGlobalOption(this, CodeEmitter::kOptionLoggingEnabled, opt);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 : Error CodeHolder::setErrorHandler(ErrorHandler* handler) noexcept {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :   _errorHandler = handler;</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : // ============================================================================</a>
+<a name="290"><span class="lineNum">     290 </span>            : // [asmjit::CodeHolder - Sections]</a>
+<a name="291"><span class="lineNum">     291 </span>            : // ============================================================================</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1948 : static Error CodeHolder_reserveInternal(CodeHolder* self, CodeBuffer* cb, size_t n) noexcept {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       1948 :   uint8_t* oldData = cb-&gt;_data;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   uint8_t* newData;</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       1948 :   if (oldData &amp;&amp; !cb-&gt;isExternal())</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     newData = static_cast&lt;uint8_t*&gt;(Internal::reallocMemory(oldData, n));</a>
+<a name="299"><span class="lineNum">     299 </span>            :   else</a>
+<a name="300"><span class="lineNum">     300 </span>            :     newData = static_cast&lt;uint8_t*&gt;(Internal::allocMemory(n));</a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(!newData))</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1948 :   cb-&gt;_data = newData;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       1948 :   cb-&gt;_capacity = n;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            :   // Update the `Assembler` pointers if attached. Maybe we should introduce an</a>
+<a name="309"><span class="lineNum">     309 </span>            :   // event for this, but since only one Assembler can be attached at a time it</a>
+<a name="310"><span class="lineNum">     310 </span>            :   // should not matter how these pointers are updated.</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       1948 :   Assembler* a = self-&gt;_cgAsm;</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       1948 :   if (a &amp;&amp; &amp;a-&gt;_section-&gt;_buffer == cb) {</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :     size_t offset = a-&gt;getOffset();</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       1948 :     a-&gt;_bufferData = newData;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       1948 :     a-&gt;_bufferEnd  = newData + n;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       1948 :     a-&gt;_bufferPtr  = newData + offset;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :   return kErrorOk;</a>
+<a name="321"><span class="lineNum">     321 </span>            : }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       1948 : Error CodeHolder::growBuffer(CodeBuffer* cb, size_t n) noexcept {</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   // This is most likely called by `Assembler` so `sync()` shouldn't be needed,</a>
+<a name="325"><span class="lineNum">     325 </span>            :   // however, if this is called by the user and the currently attached Assembler</a>
+<a name="326"><span class="lineNum">     326 </span>            :   // did generate some code we could lose that, so sync now and make sure the</a>
+<a name="327"><span class="lineNum">     327 </span>            :   // section length is updated.</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       1948 :   if (_cgAsm) _cgAsm-&gt;sync();</span></a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :   // Now the length of the section must be valid.</a>
+<a name="331"><span class="lineNum">     331 </span>            :   size_t length = cb-&gt;getLength();</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(n &gt; IntTraits&lt;uintptr_t&gt;::maxValue() - length))</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :   // We can now check if growing the buffer is really necessary. It's unlikely</a>
+<a name="336"><span class="lineNum">     336 </span>            :   // that this function is called while there is still room for `n` bytes.</a>
+<a name="337"><span class="lineNum">     337 </span>            :   size_t capacity = cb-&gt;getCapacity();</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">       1948 :   size_t required = cb-&gt;getLength() + n;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(required &lt;= capacity)) return kErrorOk;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       1948 :   if (cb-&gt;isFixedSize())</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :     return DebugUtils::errored(kErrorCodeTooLarge);</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">       1948 :   if (capacity &lt; 8096)</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :     capacity = 8096;</a>
+<a name="346"><span class="lineNum">     346 </span>            :   else</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :     capacity += Globals::kAllocOverhead;</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   do {</a>
+<a name="350"><span class="lineNum">     350 </span>            :     size_t old = capacity;</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">       1948 :     if (capacity &lt; Globals::kAllocThreshold)</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       1948 :       capacity *= 2;</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :     else</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :       capacity += Globals::kAllocThreshold;</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       1948 :     if (capacity &lt; Globals::kAllocThreshold)</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       1948 :       capacity *= 2;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :     else</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :       capacity += Globals::kAllocThreshold;</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            :     // Overflow.</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       1948 :     if (ASMJIT_UNLIKELY(old &gt; capacity))</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :       return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">       1948 :   } while (capacity - Globals::kAllocOverhead &lt; required);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       1948 :   return CodeHolder_reserveInternal(this, cb, capacity - Globals::kAllocOverhead);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 : Error CodeHolder::reserveBuffer(CodeBuffer* cb, size_t n) noexcept {</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   size_t capacity = cb-&gt;getCapacity();</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :   if (n &lt;= capacity) return kErrorOk;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :   if (cb-&gt;isFixedSize())</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :     return DebugUtils::errored(kErrorCodeTooLarge);</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            :   // We must sync, as mentioned in `growBuffer()` as well.</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :   if (_cgAsm) _cgAsm-&gt;sync();</span></a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   return CodeHolder_reserveInternal(this, cb, n);</span></a>
+<a name="380"><span class="lineNum">     380 </span>            : }</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            : // ============================================================================</a>
+<a name="383"><span class="lineNum">     383 </span>            : // [asmjit::CodeHolder - Labels &amp; Symbols]</a>
+<a name="384"><span class="lineNum">     384 </span>            : // ============================================================================</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            : namespace {</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            : //! \internal</a>
+<a name="389"><span class="lineNum">     389 </span>            : //!</a>
+<a name="390"><span class="lineNum">     390 </span>            : //! Only used to lookup a label from `_namedLabels`.</a>
+<a name="391"><span class="lineNum">     391 </span>            : class LabelByName {</a>
+<a name="392"><span class="lineNum">     392 </span>            : public:</a>
+<a name="393"><span class="lineNum">     393 </span>            :   ASMJIT_INLINE LabelByName(const char* name, size_t nameLength, uint32_t hVal) noexcept</a>
+<a name="394"><span class="lineNum">     394 </span>            :     : name(name),</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :       nameLength(static_cast&lt;uint32_t&gt;(nameLength)),</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :       hVal(hVal) {}</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            :   ASMJIT_INLINE bool matches(const LabelEntry* entry) const noexcept {</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :     return static_cast&lt;uint32_t&gt;(entry-&gt;getNameLength()) == nameLength &amp;&amp;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :            ::memcmp(entry-&gt;getName(), name, nameLength) == 0;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   }</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            :   const char* name;</a>
+<a name="404"><span class="lineNum">     404 </span>            :   uint32_t nameLength;</a>
+<a name="405"><span class="lineNum">     405 </span>            :   uint32_t hVal;</a>
+<a name="406"><span class="lineNum">     406 </span>            : };</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : // Returns a hash of `name` and fixes `nameLength` if it's `Globals::kInvalidIndex`.</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 : static uint32_t CodeHolder_hashNameAndFixLen(const char* name, size_t&amp; nameLength) noexcept {</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   uint32_t hVal = 0;</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :   if (nameLength == Globals::kInvalidIndex) {</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :     size_t i = 0;</a>
+<a name="413"><span class="lineNum">     413 </span>            :     for (;;) {</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :       uint8_t c = static_cast&lt;uint8_t&gt;(name[i]);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :       if (!c) break;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :       hVal = Utils::hashRound(hVal, c);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :     nameLength = i;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span>            :   else {</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :     for (size_t i = 0; i &lt; nameLength; i++) {</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :       uint8_t c = static_cast&lt;uint8_t&gt;(name[i]);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!c)) return DebugUtils::errored(kErrorInvalidLabelName);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :       hVal = Utils::hashRound(hVal, c);</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     }</a>
+<a name="427"><span class="lineNum">     427 </span>            :   }</a>
+<a name="428"><span class="lineNum">     428 </span>            :   return hVal;</a>
+<a name="429"><span class="lineNum">     429 </span>            : }</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            : } // anonymous namespace</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 : LabelLink* CodeHolder::newLabelLink(LabelEntry* le, uint32_t sectionId, size_t offset, intptr_t rel) noexcept {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :   LabelLink* link = _baseHeap.allocT&lt;LabelLink&gt;();</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!link)) return nullptr;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :   link-&gt;prev = le-&gt;_links;</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :   le-&gt;_links = link;</span></a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :   link-&gt;sectionId = sectionId;</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :   link-&gt;relocId = RelocEntry::kInvalidId;</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :   link-&gt;offset = offset;</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :   link-&gt;rel = rel;</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :   _unresolvedLabelsCount++;</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :   return link;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : }</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">       3896 : Error CodeHolder::newLabelId(uint32_t&amp; idOut) noexcept {</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">       3896 :   idOut = 0;</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :   size_t index = _labels.getLength();</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">       3896 :   if (ASMJIT_LIKELY(index &gt;= Operand::kPackedIdCount))</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :     return DebugUtils::errored(kErrorLabelIndexOverflow);</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">       5844 :   ASMJIT_PROPAGATE(_labels.willGrow(&amp;_baseHeap));</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">       3896 :   LabelEntry* le = _baseHeap.allocZeroedT&lt;LabelEntry&gt;();</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">       3896 :   if (ASMJIT_UNLIKELY(!le))</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);;</a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">       3896 :   uint32_t id = Operand::packId(static_cast&lt;uint32_t&gt;(index));</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   le-&gt;_setId(id);</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">       3896 :   le-&gt;_parentId = 0;</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">       3896 :   le-&gt;_sectionId = SectionEntry::kInvalidId;</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">       3896 :   le-&gt;_offset = 0;</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   _labels.appendUnsafe(le);</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">       3896 :   idOut = id;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">       3896 :   return kErrorOk;</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : }</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 : Error CodeHolder::newNamedLabelId(uint32_t&amp; idOut, const char* name, size_t nameLength, uint32_t type, uint32_t parentId) noexcept {</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :   idOut = 0;</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :   uint32_t hVal = CodeHolder_hashNameAndFixLen(name, nameLength);</span></a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(nameLength == 0))</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :     return DebugUtils::errored(kErrorInvalidLabelName);</a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(nameLength &gt; Globals::kMaxLabelLength))</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :     return DebugUtils::errored(kErrorLabelNameTooLong);</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineNoCov">          0 :   switch (type) {</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :     case Label::kTypeLocal:</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(Operand::unpackId(parentId) &gt;= _labels.getLength()))</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :         return DebugUtils::errored(kErrorInvalidParentLabel);</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :       hVal ^= parentId;</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineNoCov">          0 :     case Label::kTypeGlobal:</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(parentId != 0))</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :         return DebugUtils::errored(kErrorNonLocalLabelCantHaveParent);</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :       break;</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span>            :     default:</a>
+<a name="498"><span class="lineNum">     498 </span>            :       return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="499"><span class="lineNum">     499 </span>            :   }</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            :   // Don't allow to insert duplicates. Local labels allow duplicates that have</a>
+<a name="502"><span class="lineNum">     502 </span>            :   // different id, this is already accomplished by having a different hashes</a>
+<a name="503"><span class="lineNum">     503 </span>            :   // between the same label names having different parent labels.</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :   LabelEntry* le = _namedLabels.get(LabelByName(name, nameLength, hVal));</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(le))</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     return DebugUtils::errored(kErrorLabelAlreadyDefined);</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span>            :   Error err = kErrorOk;</a>
+<a name="509"><span class="lineNum">     509 </span>            :   size_t index = _labels.getLength();</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(index &gt;= Operand::kPackedIdCount))</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :     return DebugUtils::errored(kErrorLabelIndexOverflow);</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(_labels.willGrow(&amp;_baseHeap));</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :   le = _baseHeap.allocZeroedT&lt;LabelEntry&gt;();</span></a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!le))</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :     return  DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   uint32_t id = Operand::packId(static_cast&lt;uint32_t&gt;(index));</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :   le-&gt;_hVal = hVal;</span></a>
+<a name="522"><span class="lineNum">     522 </span>            :   le-&gt;_setId(id);</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :   le-&gt;_type = static_cast&lt;uint8_t&gt;(type);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :   le-&gt;_parentId = 0;</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :   le-&gt;_sectionId = SectionEntry::kInvalidId;</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   le-&gt;_offset = 0;</span></a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 :   if (le-&gt;_name.mustEmbed(nameLength)) {</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :     le-&gt;_name.setEmbedded(name, nameLength);</a>
+<a name="530"><span class="lineNum">     530 </span>            :   }</a>
+<a name="531"><span class="lineNum">     531 </span>            :   else {</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :     char* nameExternal = static_cast&lt;char*&gt;(_dataZone.dup(name, nameLength, true));</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!nameExternal))</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :       return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :     le-&gt;_name.setExternal(nameExternal, nameLength);</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :   }</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            :   _labels.appendUnsafe(le);</a>
+<a name="539"><span class="lineNum">     539 </span>            :   _namedLabels.put(le);</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :   idOut = id;</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :   return err;</span></a>
+<a name="543"><span class="lineNum">     543 </span>            : }</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 : uint32_t CodeHolder::getLabelIdByName(const char* name, size_t nameLength, uint32_t parentId) noexcept {</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :   uint32_t hVal = CodeHolder_hashNameAndFixLen(name, nameLength);</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!nameLength)) return 0;</span></a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span>            :   LabelEntry* le = _namedLabels.get(LabelByName(name, nameLength, hVal));</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :   return le ? le-&gt;getId() : static_cast&lt;uint32_t&gt;(0);</span></a>
+<a name="551"><span class="lineNum">     551 </span>            : }</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span>            : // ============================================================================</a>
+<a name="554"><span class="lineNum">     554 </span>            : // [asmjit::CodeEmitter - Relocations]</a>
+<a name="555"><span class="lineNum">     555 </span>            : // ============================================================================</a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span>            : //! Encode MOD byte.</a>
+<a name="558"><span class="lineNum">     558 </span>            : static ASMJIT_INLINE uint32_t x86EncodeMod(uint32_t m, uint32_t o, uint32_t rm) noexcept {</a>
+<a name="559"><span class="lineNum">     559 </span>            :   return (m &lt;&lt; 6) | (o &lt;&lt; 3) | rm;</a>
+<a name="560"><span class="lineNum">     560 </span>            : }</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 : Error CodeHolder::newRelocEntry(RelocEntry** dst, uint32_t type, uint32_t size) noexcept {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(_relocations.willGrow(&amp;_baseHeap));</span></a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span>            :   size_t index = _relocations.getLength();</a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(index &gt; size_t(0xFFFFFFFFU)))</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :     return DebugUtils::errored(kErrorRelocIndexOverflow);</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :   RelocEntry* re = _baseHeap.allocZeroedT&lt;RelocEntry&gt;();</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!re))</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :   re-&gt;_id = static_cast&lt;uint32_t&gt;(index);</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineNoCov">          0 :   re-&gt;_type = static_cast&lt;uint8_t&gt;(type);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :   re-&gt;_size = static_cast&lt;uint8_t&gt;(size);</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :   re-&gt;_sourceSectionId = SectionEntry::kInvalidId;</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :   re-&gt;_targetSectionId = SectionEntry::kInvalidId;</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :   _relocations.appendUnsafe(re);</a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :   *dst = re;</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : }</a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span>            : // TODO: Support multiple sections, this only relocates the first.</a>
+<a name="585"><span class="lineNum">     585 </span>            : // TODO: This should go to Runtime as it's responsible for relocating the</a>
+<a name="586"><span class="lineNum">     586 </span>            : //       code, CodeHolder should just hold it.</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">       1948 : size_t CodeHolder::relocate(void* _dst, uint64_t baseAddress) const noexcept {</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">       1948 :   SectionEntry* section = _sections[0];</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :   ASMJIT_ASSERT(section != nullptr);</a>
+<a name="590"><span class="lineNum">     590 </span>            : </a>
+<a name="591"><span class="lineNum">     591 </span>            :   uint8_t* dst = static_cast&lt;uint8_t*&gt;(_dst);</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">       1948 :   if (baseAddress == Globals::kNoBaseAddress)</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">       1948 :     baseAddress = static_cast&lt;uint64_t&gt;((uintptr_t)dst);</span></a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="596"><span class="lineNum">     596 </span>            :   Logger* logger = getLogger();</a>
+<a name="597"><span class="lineNum">     597 </span>            : #endif // ASMJIT_DISABLE_LOGGING</a>
+<a name="598"><span class="lineNum">     598 </span>            : </a>
+<a name="599"><span class="lineNum">     599 </span>            :   size_t minCodeSize = section-&gt;getBuffer().getLength(); // Minimum code size.</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">       1948 :   size_t maxCodeSize = getCodeSize();                    // Includes all possible trampolines.</span></a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span>            :   // We will copy the exact size of the generated code. Extra code for trampolines</a>
+<a name="603"><span class="lineNum">     603 </span>            :   // is generated on-the-fly by the relocator (this code doesn't exist at the moment).</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">       1948 :   ::memcpy(dst, section-&gt;_buffer._data, minCodeSize);</span></a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            :   // Trampoline offset from the beginning of dst/baseAddress.</a>
+<a name="607"><span class="lineNum">     607 </span>            :   size_t trampOffset = minCodeSize;</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            :   // Relocate all recorded locations.</a>
+<a name="610"><span class="lineNum">     610 </span>            :   size_t numRelocs = _relocations.getLength();</a>
+<a name="611"><span class="lineNum">     611 </span>            :   const RelocEntry* const* reArray = _relocations.getData();</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       1948 :   for (size_t i = 0; i &lt; numRelocs; i++) {</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineNoCov">          0 :     const RelocEntry* re = reArray[i];</span></a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span>            :     // Possibly deleted or optimized out relocation entry.</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :     if (re-&gt;getType() == RelocEntry::kTypeNone)</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="619"><span class="lineNum">     619 </span>            : </a>
+<a name="620"><span class="lineNum">     620 </span>            :     uint64_t ptr = re-&gt;getData();</a>
+<a name="621"><span class="lineNum">     621 </span>            :     size_t codeOffset = static_cast&lt;size_t&gt;(re-&gt;getSourceOffset());</a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span>            :     // Make sure that the `RelocEntry` is correct, we don't want to write</a>
+<a name="624"><span class="lineNum">     624 </span>            :     // out of bounds in `dst`.</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(codeOffset + re-&gt;getSize() &gt; maxCodeSize))</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :       return DebugUtils::errored(kErrorInvalidRelocEntry);</a>
+<a name="627"><span class="lineNum">     627 </span>            : </a>
+<a name="628"><span class="lineNum">     628 </span>            :     // Whether to use trampoline, can be only used if relocation type is `kRelocTrampoline`.</a>
+<a name="629"><span class="lineNum">     629 </span>            :     bool useTrampoline = false;</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :     switch (re-&gt;getType()) {</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :       case RelocEntry::kTypeAbsToAbs: {</a>
+<a name="633"><span class="lineNum">     633 </span>            :         break;</a>
+<a name="634"><span class="lineNum">     634 </span>            :       }</a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :       case RelocEntry::kTypeRelToAbs: {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :         ptr += baseAddress;</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="639"><span class="lineNum">     639 </span>            :       }</a>
+<a name="640"><span class="lineNum">     640 </span>            : </a>
+<a name="641"><span class="lineNum">     641 </span>            :       case RelocEntry::kTypeAbsToRel: {</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :         ptr -= baseAddress + re-&gt;getSourceOffset() + re-&gt;getSize();</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :       }</a>
+<a name="645"><span class="lineNum">     645 </span>            : </a>
+<a name="646"><span class="lineNum">     646 </span>            :       case RelocEntry::kTypeTrampoline: {</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineNoCov">          0 :         if (re-&gt;getSize() != 4)</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :           return DebugUtils::errored(kErrorInvalidRelocEntry);</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineNoCov">          0 :         ptr -= baseAddress + re-&gt;getSourceOffset() + re-&gt;getSize();</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 :         if (!Utils::isInt32(static_cast&lt;int64_t&gt;(ptr))) {</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineNoCov">          0 :           ptr = (uint64_t)trampOffset - re-&gt;getSourceOffset() - re-&gt;getSize();</span></a>
+<a name="653"><span class="lineNum">     653 </span>            :           useTrampoline = true;</a>
+<a name="654"><span class="lineNum">     654 </span>            :         }</a>
+<a name="655"><span class="lineNum">     655 </span>            :         break;</a>
+<a name="656"><span class="lineNum">     656 </span>            :       }</a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span>            :       default:</a>
+<a name="659"><span class="lineNum">     659 </span>            :         return DebugUtils::errored(kErrorInvalidRelocEntry);</a>
+<a name="660"><span class="lineNum">     660 </span>            :     }</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :     switch (re-&gt;getSize()) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :       case 1:</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :         Utils::writeU8(dst + codeOffset, static_cast&lt;uint32_t&gt;(ptr &amp; 0xFFU));</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :         break;</a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :       case 4:</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :         Utils::writeU32u(dst + codeOffset, static_cast&lt;uint32_t&gt;(ptr &amp; 0xFFFFFFFFU));</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :         break;</a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :       case 8:</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :         Utils::writeU64u(dst + codeOffset, ptr);</span></a>
+<a name="673"><span class="lineNum">     673 </span>            :         break;</a>
+<a name="674"><span class="lineNum">     674 </span>            : </a>
+<a name="675"><span class="lineNum">     675 </span>            :       default:</a>
+<a name="676"><span class="lineNum">     676 </span>            :         return DebugUtils::errored(kErrorInvalidRelocEntry);</a>
+<a name="677"><span class="lineNum">     677 </span>            :     }</a>
+<a name="678"><span class="lineNum">     678 </span>            : </a>
+<a name="679"><span class="lineNum">     679 </span>            :     // Handle the trampoline case.</a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :     if (useTrampoline) {</span></a>
+<a name="681"><span class="lineNum">     681 </span>            :       // Bytes that replace [REX, OPCODE] bytes.</a>
+<a name="682"><span class="lineNum">     682 </span>            :       uint32_t byte0 = 0xFF;</a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :       uint32_t byte1 = dst[codeOffset - 1];</span></a>
+<a name="684"><span class="lineNum">     684 </span>            : </a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :       if (byte1 == 0xE8) {</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :         // Patch CALL/MOD byte to FF/2 (-&gt; 0x15).</a>
+<a name="687"><span class="lineNum">     687 </span>            :         byte1 = x86EncodeMod(0, 2, 5);</a>
+<a name="688"><span class="lineNum">     688 </span>            :       }</a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :       else if (byte1 == 0xE9) {</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :         // Patch JMP/MOD byte to FF/4 (-&gt; 0x25).</a>
+<a name="691"><span class="lineNum">     691 </span>            :         byte1 = x86EncodeMod(0, 4, 5);</a>
+<a name="692"><span class="lineNum">     692 </span>            :       }</a>
+<a name="693"><span class="lineNum">     693 </span>            :       else {</a>
+<a name="694"><span class="lineNum">     694 </span>            :         return DebugUtils::errored(kErrorInvalidRelocEntry);</a>
+<a name="695"><span class="lineNum">     695 </span>            :       }</a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span>            :       // Patch `jmp/call` instruction.</a>
+<a name="698"><span class="lineNum">     698 </span>            :       ASMJIT_ASSERT(codeOffset &gt;= 2);</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :       dst[codeOffset - 2] = static_cast&lt;uint8_t&gt;(byte0);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :       dst[codeOffset - 1] = static_cast&lt;uint8_t&gt;(byte1);</span></a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            :       // Store absolute address and advance the trampoline pointer.</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :       Utils::writeU64u(dst + trampOffset, re-&gt;getData());</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineNoCov">          0 :       trampOffset += 8;</span></a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineNoCov">          0 :       if (logger)</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :         logger-&gt;logf(&quot;[reloc] dq 0x%016llX ; Trampoline\n&quot;, re-&gt;getData());</span></a>
+<a name="709"><span class="lineNum">     709 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="710"><span class="lineNum">     710 </span>            :     }</a>
+<a name="711"><span class="lineNum">     711 </span>            :   }</a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span>            :   // If there are no trampolines this is the same as `minCodeSize`.</a>
+<a name="714"><span class="lineNum">     714 </span>            :   return trampOffset;</a>
+<a name="715"><span class="lineNum">     715 </span>            : }</a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            : } // asmjit namespace</a>
+<a name="718"><span class="lineNum">     718 </span>            : } // namespace PLMD</a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span>            : // [Api-End]</a>
+<a name="721"><span class="lineNum">     721 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="722"><span class="lineNum">     722 </span>            : #pragma GCC diagnostic pop</a>
+<a name="723"><span class="lineNum">     723 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeholder.h.func-sort-c.html b/coverage-libs/asmjit/codeholder.h.func-sort-c.html
new file mode 100644
index 0000000000..aed1ed53d8
--- /dev/null
+++ b/coverage-libs/asmjit/codeholder.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeholder.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeholder.h<span style="font-size: 80%;"> (<a href="codeholder.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="codeholder.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeholder.h.func.html b/coverage-libs/asmjit/codeholder.h.func.html
new file mode 100644
index 0000000000..5c88151dc8
--- /dev/null
+++ b/coverage-libs/asmjit/codeholder.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeholder.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeholder.h<span style="font-size: 80%;"> (<a href="codeholder.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="codeholder.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/codeholder.h.gcov.html b/coverage-libs/asmjit/codeholder.h.gcov.html
new file mode 100644
index 0000000000..95b98f1dc5
--- /dev/null
+++ b/coverage-libs/asmjit/codeholder.h.gcov.html
@@ -0,0 +1,853 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/codeholder.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - codeholder.h<span style="font-size: 80%;"> (source / <a href="codeholder.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_codeholder_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_codeholder_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_CODEHOLDER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_CODEHOLDER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./func.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./logging.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./simdtypes.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./zone.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // [Api-Begin]</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : namespace PLMD {</a>
+<a name="48"><span class="lineNum">      48 </span>            : namespace asmjit {</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : //! \addtogroup asmjit_base</a>
+<a name="51"><span class="lineNum">      51 </span>            : //! \{</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : // [Forward Declarations]</a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : class Assembler;</a>
+<a name="58"><span class="lineNum">      58 </span>            : class CodeEmitter;</a>
+<a name="59"><span class="lineNum">      59 </span>            : class CodeHolder;</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // ============================================================================</a>
+<a name="62"><span class="lineNum">      62 </span>            : // [asmjit::AlignMode]</a>
+<a name="63"><span class="lineNum">      63 </span>            : // ============================================================================</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : //! Align mode.</a>
+<a name="66"><span class="lineNum">      66 </span>            : ASMJIT_ENUM(AlignMode) {</a>
+<a name="67"><span class="lineNum">      67 </span>            :   kAlignCode = 0,                        //!&lt; Align executable code.</a>
+<a name="68"><span class="lineNum">      68 </span>            :   kAlignData = 1,                        //!&lt; Align non-executable code.</a>
+<a name="69"><span class="lineNum">      69 </span>            :   kAlignZero = 2,                        //!&lt; Align by a sequence of zeros.</a>
+<a name="70"><span class="lineNum">      70 </span>            :   kAlignCount                            //!&lt; Count of alignment modes.</a>
+<a name="71"><span class="lineNum">      71 </span>            : };</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : // ============================================================================</a>
+<a name="74"><span class="lineNum">      74 </span>            : // [asmjit::ErrorHandler]</a>
+<a name="75"><span class="lineNum">      75 </span>            : // ============================================================================</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : //! Error handler can be used to override the default behavior of error handling</a>
+<a name="78"><span class="lineNum">      78 </span>            : //! available to all classes that inherit \ref CodeEmitter. See \ref handleError().</a>
+<a name="79"><span class="lineNum">      79 </span>            : class ASMJIT_VIRTAPI ErrorHandler {</a>
+<a name="80"><span class="lineNum">      80 </span>            : public:</a>
+<a name="81"><span class="lineNum">      81 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="82"><span class="lineNum">      82 </span>            :   // [Construction / Destruction]</a>
+<a name="83"><span class="lineNum">      83 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   //! Create a new `ErrorHandler` instance.</a>
+<a name="86"><span class="lineNum">      86 </span>            :   ASMJIT_API ErrorHandler() noexcept;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //! Destroy the `ErrorHandler` instance.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ASMJIT_API virtual ~ErrorHandler() noexcept;</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // [Handle Error]</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Error handler (abstract).</a>
+<a name="95"><span class="lineNum">      95 </span>            :   //!</a>
+<a name="96"><span class="lineNum">      96 </span>            :   //! Error handler is called after an error happened and before it's propagated</a>
+<a name="97"><span class="lineNum">      97 </span>            :   //! to the caller. There are multiple ways how the error handler can be used:</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //!</a>
+<a name="99"><span class="lineNum">      99 </span>            :   //! 1. Returning `true` or `false` from `handleError()`. If `true` is returned</a>
+<a name="100"><span class="lineNum">     100 </span>            :   //!    it means that the error was reported and AsmJit can continue execution.</a>
+<a name="101"><span class="lineNum">     101 </span>            :   //!    The reported error still be propagated to the caller, but won't put the</a>
+<a name="102"><span class="lineNum">     102 </span>            :   //!    CodeEmitter into an error state (it won't set last-error). However,</a>
+<a name="103"><span class="lineNum">     103 </span>            :   //!    returning `false` means that the error cannot be handled - in such case</a>
+<a name="104"><span class="lineNum">     104 </span>            :   //!    it stores the error, which can be then retrieved by using `getLastError()`.</a>
+<a name="105"><span class="lineNum">     105 </span>            :   //!    Returning `false` is the default behavior when no error handler is present.</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //!    To put the assembler into a non-error state again a `resetLastError()` must</a>
+<a name="107"><span class="lineNum">     107 </span>            :   //!    be called.</a>
+<a name="108"><span class="lineNum">     108 </span>            :   //!</a>
+<a name="109"><span class="lineNum">     109 </span>            :   //! 2. Throwing an exception. AsmJit doesn't use exceptions and is completely</a>
+<a name="110"><span class="lineNum">     110 </span>            :   //!    exception-safe, but you can throw exception from your error handler if</a>
+<a name="111"><span class="lineNum">     111 </span>            :   //!    this way is the preferred way of handling errors in your project. Throwing</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //!    an exception acts virtually as returning `true` as AsmJit won't be able</a>
+<a name="113"><span class="lineNum">     113 </span>            :   //!    to store the error because the exception changes execution path.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //!</a>
+<a name="115"><span class="lineNum">     115 </span>            :   //! 3. Using plain old C's `setjmp()` and `longjmp()`. Asmjit always puts</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //!    `CodeEmitter` to a consistent state before calling the `handleError()`</a>
+<a name="117"><span class="lineNum">     117 </span>            :   //!    so `longjmp()` can be used without any issues to cancel the code</a>
+<a name="118"><span class="lineNum">     118 </span>            :   //!    generation if an error occurred. There is no difference between</a>
+<a name="119"><span class="lineNum">     119 </span>            :   //!    exceptions and longjmp() from AsmJit's perspective.</a>
+<a name="120"><span class="lineNum">     120 </span>            :   virtual bool handleError(Error err, const char* message, CodeEmitter* origin) = 0;</a>
+<a name="121"><span class="lineNum">     121 </span>            : };</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : // ============================================================================</a>
+<a name="124"><span class="lineNum">     124 </span>            : // [asmjit::CodeInfo]</a>
+<a name="125"><span class="lineNum">     125 </span>            : // ============================================================================</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : //! Basic information about a code (or target). It describes its architecture,</a>
+<a name="128"><span class="lineNum">     128 </span>            : //! code generation mode (or optimization level), and base address.</a>
+<a name="129"><span class="lineNum">     129 </span>            : class CodeInfo {</a>
+<a name="130"><span class="lineNum">     130 </span>            : public:</a>
+<a name="131"><span class="lineNum">     131 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="132"><span class="lineNum">     132 </span>            :   // [Construction / Destruction]</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   ASMJIT_INLINE CodeInfo() noexcept</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       7820 :     : _archInfo(),</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       7820 :       _stackAlignment(0),</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       7820 :       _cdeclCallConv(CallConv::kIdNone),</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       7820 :       _stdCallConv(CallConv::kIdNone),</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       7820 :       _fastCallConv(CallConv::kIdNone),</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       7820 :       _baseAddress(Globals::kNoBaseAddress) {}</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   ASMJIT_INLINE CodeInfo(const CodeInfo&amp; other) noexcept { init(other); }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   explicit ASMJIT_INLINE CodeInfo(uint32_t archType, uint32_t archMode = 0, uint64_t baseAddress = Globals::kNoBaseAddress) noexcept</a>
+<a name="145"><span class="lineNum">     145 </span>            :     : _archInfo(archType, archMode),</a>
+<a name="146"><span class="lineNum">     146 </span>            :       _packedMiscInfo(0),</a>
+<a name="147"><span class="lineNum">     147 </span>            :       _baseAddress(baseAddress) {}</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="150"><span class="lineNum">     150 </span>            :   // [Init / Reset]</a>
+<a name="151"><span class="lineNum">     151 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   ASMJIT_INLINE bool isInitialized() const noexcept {</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1948 :     return _archInfo._type != ArchInfo::kTypeNone;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   ASMJIT_INLINE void init(const CodeInfo&amp; other) noexcept {</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       5844 :     _archInfo = other._archInfo;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       5844 :     _packedMiscInfo = other._packedMiscInfo;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       5844 :     _baseAddress = other._baseAddress;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   ASMJIT_INLINE void init(uint32_t archType, uint32_t archMode = 0, uint64_t baseAddress = Globals::kNoBaseAddress) noexcept {</a>
+<a name="164"><span class="lineNum">     164 </span>            :     _archInfo.init(archType, archMode);</a>
+<a name="165"><span class="lineNum">     165 </span>            :     _packedMiscInfo = 0;</a>
+<a name="166"><span class="lineNum">     166 </span>            :     _baseAddress = baseAddress;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="170"><span class="lineNum">     170 </span>            :     _archInfo.reset();</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1948 :     _stackAlignment = 0;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       1948 :     _cdeclCallConv = CallConv::kIdNone;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       1948 :     _stdCallConv = CallConv::kIdNone;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       1948 :     _fastCallConv = CallConv::kIdNone;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1948 :     _baseAddress = Globals::kNoBaseAddress;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="179"><span class="lineNum">     179 </span>            :   // [Architecture Information]</a>
+<a name="180"><span class="lineNum">     180 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :   //! Get architecture information, see \ref ArchInfo.</a>
+<a name="183"><span class="lineNum">     183 </span>            :   ASMJIT_INLINE const ArchInfo&amp; getArchInfo() const noexcept { return _archInfo; }</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   //! Get architecture type, see \ref ArchInfo::Type.</a>
+<a name="186"><span class="lineNum">     186 </span>            :   ASMJIT_INLINE uint32_t getArchType() const noexcept { return _archInfo.getType(); }</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //! Get architecture sub-type, see \ref ArchInfo::SubType.</a>
+<a name="188"><span class="lineNum">     188 </span>            :   ASMJIT_INLINE uint32_t getArchSubType() const noexcept { return _archInfo.getSubType(); }</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //! Get a size of a GP register of the architecture the code is using.</a>
+<a name="190"><span class="lineNum">     190 </span>            :   ASMJIT_INLINE uint32_t getGpSize() const noexcept { return _archInfo.getGpSize(); }</a>
+<a name="191"><span class="lineNum">     191 </span>            :   //! Get number of GP registers available of the architecture the code is using.</a>
+<a name="192"><span class="lineNum">     192 </span>            :   ASMJIT_INLINE uint32_t getGpCount() const noexcept { return _archInfo.getGpCount(); }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="195"><span class="lineNum">     195 </span>            :   // [High-Level Information]</a>
+<a name="196"><span class="lineNum">     196 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :   //! Get a natural stack alignment that must be honored (or 0 if not known).</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getStackAlignment() const noexcept { return _stackAlignment; }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   //! Set a natural stack alignment that must be honored.</a>
+<a name="201"><span class="lineNum">     201 </span>            :   ASMJIT_INLINE void setStackAlignment(uint8_t sa) noexcept { _stackAlignment = static_cast&lt;uint8_t&gt;(sa); }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   ASMJIT_INLINE uint32_t getCdeclCallConv() const noexcept { return _cdeclCallConv; }</a>
+<a name="204"><span class="lineNum">     204 </span>            :   ASMJIT_INLINE void setCdeclCallConv(uint32_t cc) noexcept { _cdeclCallConv = static_cast&lt;uint8_t&gt;(cc); }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   ASMJIT_INLINE uint32_t getStdCallConv() const noexcept { return _stdCallConv; }</a>
+<a name="207"><span class="lineNum">     207 </span>            :   ASMJIT_INLINE void setStdCallConv(uint32_t cc) noexcept { _stdCallConv = static_cast&lt;uint8_t&gt;(cc); }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   ASMJIT_INLINE uint32_t getFastCallConv() const noexcept { return _fastCallConv; }</a>
+<a name="210"><span class="lineNum">     210 </span>            :   ASMJIT_INLINE void setFastCallConv(uint32_t cc) noexcept { _fastCallConv = static_cast&lt;uint8_t&gt;(cc); }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="213"><span class="lineNum">     213 </span>            :   // [Addressing Information]</a>
+<a name="214"><span class="lineNum">     214 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :   ASMJIT_INLINE bool hasBaseAddress() const noexcept { return _baseAddress != Globals::kNoBaseAddress; }</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint64_t getBaseAddress() const noexcept { return _baseAddress; }</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   ASMJIT_INLINE void setBaseAddress(uint64_t p) noexcept { _baseAddress = p; }</a>
+<a name="219"><span class="lineNum">     219 </span>            :   ASMJIT_INLINE void resetBaseAddress() noexcept { _baseAddress = Globals::kNoBaseAddress; }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="222"><span class="lineNum">     222 </span>            :   // [Operator Overload]</a>
+<a name="223"><span class="lineNum">     223 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   ASMJIT_INLINE CodeInfo&amp; operator=(const CodeInfo&amp; other) noexcept { init(other); return *this; }</a>
+<a name="226"><span class="lineNum">     226 </span>            :   ASMJIT_INLINE bool operator==(const CodeInfo&amp; other) const noexcept { return ::memcmp(this, &amp;other, sizeof(*this)) == 0; }</a>
+<a name="227"><span class="lineNum">     227 </span>            :   ASMJIT_INLINE bool operator!=(const CodeInfo&amp; other) const noexcept { return ::memcmp(this, &amp;other, sizeof(*this)) != 0; }</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="230"><span class="lineNum">     230 </span>            :   // [Members]</a>
+<a name="231"><span class="lineNum">     231 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :   ArchInfo _archInfo;                    //!&lt; Architecture information.</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   union {</a>
+<a name="236"><span class="lineNum">     236 </span>            :     struct {</a>
+<a name="237"><span class="lineNum">     237 </span>            :       uint8_t _stackAlignment;           //!&lt; Natural stack alignment (ARCH+OS).</a>
+<a name="238"><span class="lineNum">     238 </span>            :       uint8_t _cdeclCallConv;            //!&lt; Default CDECL calling convention.</a>
+<a name="239"><span class="lineNum">     239 </span>            :       uint8_t _stdCallConv;              //!&lt; Default STDCALL calling convention.</a>
+<a name="240"><span class="lineNum">     240 </span>            :       uint8_t _fastCallConv;             //!&lt; Default FASTCALL calling convention.</a>
+<a name="241"><span class="lineNum">     241 </span>            :     };</a>
+<a name="242"><span class="lineNum">     242 </span>            :     uint32_t _packedMiscInfo;            //!&lt; \internal</a>
+<a name="243"><span class="lineNum">     243 </span>            :   };</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   uint64_t _baseAddress;                 //!&lt; Base address.</a>
+<a name="246"><span class="lineNum">     246 </span>            : };</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : // ============================================================================</a>
+<a name="249"><span class="lineNum">     249 </span>            : // [asmjit::CodeBuffer]</a>
+<a name="250"><span class="lineNum">     250 </span>            : // ============================================================================</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : //! Code or data buffer.</a>
+<a name="253"><span class="lineNum">     253 </span>            : struct CodeBuffer {</a>
+<a name="254"><span class="lineNum">     254 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="255"><span class="lineNum">     255 </span>            :   // [Accessors]</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasData() const noexcept { return _data != nullptr; }</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   ASMJIT_INLINE uint8_t* getData() noexcept { return _data; }</a>
+<a name="260"><span class="lineNum">     260 </span>            :   ASMJIT_INLINE const uint8_t* getData() const noexcept { return _data; }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       5844 :   ASMJIT_INLINE size_t getLength() const noexcept { return _length; }</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       1948 :   ASMJIT_INLINE size_t getCapacity() const noexcept { return _capacity; }</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool isExternal() const noexcept { return _isExternal; }</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool isFixedSize() const noexcept { return _isFixedSize; }</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="269"><span class="lineNum">     269 </span>            :   // [Members]</a>
+<a name="270"><span class="lineNum">     270 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :   uint8_t* _data;                        //!&lt; The content of the buffer (data).</a>
+<a name="273"><span class="lineNum">     273 </span>            :   size_t _length;                        //!&lt; Number of bytes of `data` used.</a>
+<a name="274"><span class="lineNum">     274 </span>            :   size_t _capacity;                      //!&lt; Buffer capacity (in bytes).</a>
+<a name="275"><span class="lineNum">     275 </span>            :   bool _isExternal;                      //!&lt; True if this is external buffer.</a>
+<a name="276"><span class="lineNum">     276 </span>            :   bool _isFixedSize;                     //!&lt; True if this buffer cannot grow.</a>
+<a name="277"><span class="lineNum">     277 </span>            : };</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : // ============================================================================</a>
+<a name="280"><span class="lineNum">     280 </span>            : // [asmjit::SectionEntry]</a>
+<a name="281"><span class="lineNum">     281 </span>            : // ============================================================================</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : //! Section entry.</a>
+<a name="284"><span class="lineNum">     284 </span>            : class SectionEntry {</a>
+<a name="285"><span class="lineNum">     285 </span>            : public:</a>
+<a name="286"><span class="lineNum">     286 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="287"><span class="lineNum">     287 </span>            :     kInvalidId       = 0xFFFFFFFFU       //!&lt; Invalid section id.</a>
+<a name="288"><span class="lineNum">     288 </span>            :   };</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            :   //! Section flags.</a>
+<a name="291"><span class="lineNum">     291 </span>            :   ASMJIT_ENUM(Flags) {</a>
+<a name="292"><span class="lineNum">     292 </span>            :     kFlagExec        = 0x00000001U,      //!&lt; Executable (.text sections).</a>
+<a name="293"><span class="lineNum">     293 </span>            :     kFlagConst       = 0x00000002U,      //!&lt; Read-only (.text and .data sections).</a>
+<a name="294"><span class="lineNum">     294 </span>            :     kFlagZero        = 0x00000004U,      //!&lt; Zero initialized by the loader (BSS).</a>
+<a name="295"><span class="lineNum">     295 </span>            :     kFlagInfo        = 0x00000008U,      //!&lt; Info / comment flag.</a>
+<a name="296"><span class="lineNum">     296 </span>            :     kFlagImplicit    = 0x80000000U       //!&lt; Section created implicitly (can be deleted by the Runtime).</a>
+<a name="297"><span class="lineNum">     297 </span>            :   };</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="300"><span class="lineNum">     300 </span>            :   // [Accessors]</a>
+<a name="301"><span class="lineNum">     301 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       3896 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :   ASMJIT_INLINE const char* getName() const noexcept { return _name; }</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :   ASMJIT_INLINE void _setDefaultName(</a>
+<a name="307"><span class="lineNum">     307 </span>            :       char c0 = 0, char c1 = 0, char c2 = 0, char c3 = 0,</a>
+<a name="308"><span class="lineNum">     308 </span>            :       char c4 = 0, char c5 = 0, char c6 = 0, char c7 = 0) noexcept {</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1948 :     _nameAsU32[0] = Utils::pack32_4x8(c0, c1, c2, c3);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">       1948 :     _nameAsU32[1] = Utils::pack32_4x8(c4, c5, c6, c7);</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   }</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   ASMJIT_INLINE uint32_t getFlags() const noexcept { return _flags; }</a>
+<a name="314"><span class="lineNum">     314 </span>            :   ASMJIT_INLINE bool hasFlag(uint32_t flag) const noexcept { return (_flags &amp; flag) != 0; }</a>
+<a name="315"><span class="lineNum">     315 </span>            :   ASMJIT_INLINE void addFlags(uint32_t flags) noexcept { _flags |= flags; }</a>
+<a name="316"><span class="lineNum">     316 </span>            :   ASMJIT_INLINE void clearFlags(uint32_t flags) noexcept { _flags &amp;= ~flags; }</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :   ASMJIT_INLINE uint32_t getAlignment() const noexcept { return _alignment; }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   ASMJIT_INLINE void setAlignment(uint32_t alignment) noexcept { _alignment = alignment; }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :   ASMJIT_INLINE size_t getPhysicalSize() const noexcept { return _buffer.getLength(); }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :   ASMJIT_INLINE size_t getVirtualSize() const noexcept { return _virtualSize; }</a>
+<a name="324"><span class="lineNum">     324 </span>            :   ASMJIT_INLINE void setVirtualSize(uint32_t size) noexcept { _virtualSize = size; }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   ASMJIT_INLINE CodeBuffer&amp; getBuffer() noexcept { return _buffer; }</a>
+<a name="327"><span class="lineNum">     327 </span>            :   ASMJIT_INLINE const CodeBuffer&amp; getBuffer() const noexcept { return _buffer; }</a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="330"><span class="lineNum">     330 </span>            :   // [Members]</a>
+<a name="331"><span class="lineNum">     331 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   uint32_t _id;                          //!&lt; Section id.</a>
+<a name="334"><span class="lineNum">     334 </span>            :   uint32_t _flags;                       //!&lt; Section flags.</a>
+<a name="335"><span class="lineNum">     335 </span>            :   uint32_t _alignment;                   //!&lt; Section alignment requirements (0 if no requirements).</a>
+<a name="336"><span class="lineNum">     336 </span>            :   uint32_t _virtualSize;                 //!&lt; Virtual size of the section (zero initialized mostly).</a>
+<a name="337"><span class="lineNum">     337 </span>            :   union {</a>
+<a name="338"><span class="lineNum">     338 </span>            :     char _name[36];                      //!&lt; Section name (max 35 characters, PE allows max 8).</a>
+<a name="339"><span class="lineNum">     339 </span>            :     uint32_t _nameAsU32[36 / 4];         //!&lt; Section name as `uint32_t[]` (only optimization).</a>
+<a name="340"><span class="lineNum">     340 </span>            :   };</a>
+<a name="341"><span class="lineNum">     341 </span>            :   CodeBuffer _buffer;                    //!&lt; Code or data buffer.</a>
+<a name="342"><span class="lineNum">     342 </span>            : };</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            : // ============================================================================</a>
+<a name="345"><span class="lineNum">     345 </span>            : // [asmjit::LabelLink]</a>
+<a name="346"><span class="lineNum">     346 </span>            : // ============================================================================</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            : //! Data structure used to link labels.</a>
+<a name="349"><span class="lineNum">     349 </span>            : struct LabelLink {</a>
+<a name="350"><span class="lineNum">     350 </span>            :   LabelLink* prev;                       //!&lt; Previous link (single-linked list).</a>
+<a name="351"><span class="lineNum">     351 </span>            :   uint32_t sectionId;                    //!&lt; Section id.</a>
+<a name="352"><span class="lineNum">     352 </span>            :   uint32_t relocId;                      //!&lt; Relocation id or RelocEntry::kInvalidId.</a>
+<a name="353"><span class="lineNum">     353 </span>            :   size_t offset;                         //!&lt; Label offset relative to the start of the section.</a>
+<a name="354"><span class="lineNum">     354 </span>            :   intptr_t rel;                          //!&lt; Inlined rel8/rel32.</a>
+<a name="355"><span class="lineNum">     355 </span>            : };</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : // ============================================================================</a>
+<a name="358"><span class="lineNum">     358 </span>            : // [asmjit::LabelEntry]</a>
+<a name="359"><span class="lineNum">     359 </span>            : // ============================================================================</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : //! Label entry.</a>
+<a name="362"><span class="lineNum">     362 </span>            : //!</a>
+<a name="363"><span class="lineNum">     363 </span>            : //! Contains the following properties:</a>
+<a name="364"><span class="lineNum">     364 </span>            : //!   * Label id - This is the only thing that is set to the `Label` operand.</a>
+<a name="365"><span class="lineNum">     365 </span>            : //!   * Label name - Optional, used mostly to create executables and libraries.</a>
+<a name="366"><span class="lineNum">     366 </span>            : //!   * Label type - Type of the label, default `Label::kTypeAnonymous`.</a>
+<a name="367"><span class="lineNum">     367 </span>            : //!   * Label parent id - Derived from many assemblers that allow to define a</a>
+<a name="368"><span class="lineNum">     368 </span>            : //!       local label that falls under a global label. This allows to define</a>
+<a name="369"><span class="lineNum">     369 </span>            : //!       many labels of the same name that have different parent (global) label.</a>
+<a name="370"><span class="lineNum">     370 </span>            : //!   * Offset - offset of the label bound by `Assembler`.</a>
+<a name="371"><span class="lineNum">     371 </span>            : //!   * Links - single-linked list that contains locations of code that has</a>
+<a name="372"><span class="lineNum">     372 </span>            : //!       to be patched when the label gets bound. Every use of unbound label</a>
+<a name="373"><span class="lineNum">     373 </span>            : //!       adds one link to `_links` list.</a>
+<a name="374"><span class="lineNum">     374 </span>            : //!   * HVal - Hash value of label's name and optionally parentId.</a>
+<a name="375"><span class="lineNum">     375 </span>            : //!   * HashNext - Hash-table implementation detail.</a>
+<a name="376"><span class="lineNum">     376 </span>            : class LabelEntry : public ZoneHashNode {</a>
+<a name="377"><span class="lineNum">     377 </span>            : public:</a>
+<a name="378"><span class="lineNum">     378 </span>            :   // NOTE: Label id is stored in `_customData`, which is provided by ZoneHashNode</a>
+<a name="379"><span class="lineNum">     379 </span>            :   // to fill a padding that a C++ compiler targeting 64-bit CPU will add to align</a>
+<a name="380"><span class="lineNum">     380 </span>            :   // the structure to 64-bits.</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :   //! Get label id.</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _customData; }</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   //! Set label id (internal, used only by \ref CodeHolder).</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       3896 :   ASMJIT_INLINE void _setId(uint32_t id) noexcept { _customData = id; }</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            :   //! Get label type, see \ref Label::Type.</a>
+<a name="388"><span class="lineNum">     388 </span>            :   ASMJIT_INLINE uint32_t getType() const noexcept { return _type; }</a>
+<a name="389"><span class="lineNum">     389 </span>            :   //! Get label flags, returns 0 at the moment.</a>
+<a name="390"><span class="lineNum">     390 </span>            :   ASMJIT_INLINE uint32_t getFlags() const noexcept { return _flags; }</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasParent() const noexcept { return _parentId != 0; }</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   //! Get label's parent id.</a>
+<a name="394"><span class="lineNum">     394 </span>            :   ASMJIT_INLINE uint32_t getParentId() const noexcept { return _parentId; }</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   //! Get label's section id where it's bound to (or `SectionEntry::kInvalidId` if it's not bound yet).</a>
+<a name="397"><span class="lineNum">     397 </span>            :   ASMJIT_INLINE uint32_t getSectionId() const noexcept { return _sectionId; }</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            :   //! Get if the label has name.</a>
+<a name="400"><span class="lineNum">     400 </span>            :   ASMJIT_INLINE bool hasName() const noexcept { return !_name.isEmpty(); }</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            :   //! Get the label's name.</a>
+<a name="403"><span class="lineNum">     403 </span>            :   //!</a>
+<a name="404"><span class="lineNum">     404 </span>            :   //! NOTE: Local labels will return their local name without their parent</a>
+<a name="405"><span class="lineNum">     405 </span>            :   //! part, for example &quot;.L1&quot;.</a>
+<a name="406"><span class="lineNum">     406 </span>            :   ASMJIT_INLINE const char* getName() const noexcept { return _name.getData(); }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :   //! Get length of label's name.</a>
+<a name="409"><span class="lineNum">     409 </span>            :   //!</a>
+<a name="410"><span class="lineNum">     410 </span>            :   //! NOTE: Label name is always null terminated, so you can use `strlen()` to</a>
+<a name="411"><span class="lineNum">     411 </span>            :   //! get it, however, it's also cached in `LabelEntry`, so if you want to know</a>
+<a name="412"><span class="lineNum">     412 </span>            :   //! the length the easiest way is to use `LabelEntry::getNameLength()`.</a>
+<a name="413"><span class="lineNum">     413 </span>            :   ASMJIT_INLINE size_t getNameLength() const noexcept { return _name.getLength(); }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            :   //! Get if the label is bound.</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       3896 :   ASMJIT_INLINE bool isBound() const noexcept { return _sectionId != SectionEntry::kInvalidId; }</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :   //! Get the label offset (only useful if the label is bound).</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE intptr_t getOffset() const noexcept { return _offset; }</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   //! Get the hash-value of label's name and its parent label (if any).</a>
+<a name="421"><span class="lineNum">     421 </span>            :   //!</a>
+<a name="422"><span class="lineNum">     422 </span>            :   //! Label hash is calculated as `HASH(Name) ^ ParentId`. The hash function</a>
+<a name="423"><span class="lineNum">     423 </span>            :   //! is implemented in `Utils::hashString()` and `Utils::hashRound()`.</a>
+<a name="424"><span class="lineNum">     424 </span>            :   ASMJIT_INLINE uint32_t getHVal() const noexcept { return _hVal; }</a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            :   // ------------------------------------------------------------------------</a>
+<a name="427"><span class="lineNum">     427 </span>            :   // [Members]</a>
+<a name="428"><span class="lineNum">     428 </span>            :   // ------------------------------------------------------------------------</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span>            :   // Let's round the size of `LabelEntry` to 64 bytes (as ZoneHeap has 32</a>
+<a name="431"><span class="lineNum">     431 </span>            :   // bytes granularity anyway). This gives `_name` the remaining space, which</a>
+<a name="432"><span class="lineNum">     432 </span>            :   // is roughly 16 bytes on 64-bit and 28 bytes on 32-bit architectures.</a>
+<a name="433"><span class="lineNum">     433 </span>            :   enum { kNameBytes = 64 - (sizeof(ZoneHashNode) + 16 + sizeof(intptr_t) + sizeof(LabelLink*)) };</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :   uint8_t _type;                         //!&lt; Label type, see Label::Type.</a>
+<a name="436"><span class="lineNum">     436 </span>            :   uint8_t _flags;                        //!&lt; Must be zero.</a>
+<a name="437"><span class="lineNum">     437 </span>            :   uint16_t _reserved16;                  //!&lt; Reserved.</a>
+<a name="438"><span class="lineNum">     438 </span>            :   uint32_t _parentId;                    //!&lt; Label parent id or zero.</a>
+<a name="439"><span class="lineNum">     439 </span>            :   uint32_t _sectionId;                   //!&lt; Section id or `SectionEntry::kInvalidId`.</a>
+<a name="440"><span class="lineNum">     440 </span>            :   uint32_t _reserved32;                  //!&lt; Reserved.</a>
+<a name="441"><span class="lineNum">     441 </span>            :   intptr_t _offset;                      //!&lt; Label offset.</a>
+<a name="442"><span class="lineNum">     442 </span>            :   LabelLink* _links;                     //!&lt; Label links.</a>
+<a name="443"><span class="lineNum">     443 </span>            :   SmallString&lt;kNameBytes&gt; _name;         //!&lt; Label name.</a>
+<a name="444"><span class="lineNum">     444 </span>            : };</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            : // ============================================================================</a>
+<a name="447"><span class="lineNum">     447 </span>            : // [asmjit::RelocEntry]</a>
+<a name="448"><span class="lineNum">     448 </span>            : // ============================================================================</a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span>            : //! Relocation entry.</a>
+<a name="451"><span class="lineNum">     451 </span>            : struct RelocEntry {</a>
+<a name="452"><span class="lineNum">     452 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="453"><span class="lineNum">     453 </span>            :     kInvalidId       = 0xFFFFFFFFU       //!&lt; Invalid relocation id.</a>
+<a name="454"><span class="lineNum">     454 </span>            :   };</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            :   //! Relocation type.</a>
+<a name="457"><span class="lineNum">     457 </span>            :   ASMJIT_ENUM(Type) {</a>
+<a name="458"><span class="lineNum">     458 </span>            :     kTypeNone        = 0,                //!&lt; Deleted entry (no relocation).</a>
+<a name="459"><span class="lineNum">     459 </span>            :     kTypeAbsToAbs    = 1,                //!&lt; Relocate absolute to absolute.</a>
+<a name="460"><span class="lineNum">     460 </span>            :     kTypeRelToAbs    = 2,                //!&lt; Relocate relative to absolute.</a>
+<a name="461"><span class="lineNum">     461 </span>            :     kTypeAbsToRel    = 3,                //!&lt; Relocate absolute to relative.</a>
+<a name="462"><span class="lineNum">     462 </span>            :     kTypeTrampoline  = 4                 //!&lt; Relocate absolute to relative or use trampoline.</a>
+<a name="463"><span class="lineNum">     463 </span>            :   };</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span>            :   // ------------------------------------------------------------------------</a>
+<a name="466"><span class="lineNum">     466 </span>            :   // [Accessors]</a>
+<a name="467"><span class="lineNum">     467 </span>            :   // ------------------------------------------------------------------------</a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getType() const noexcept { return _type; }</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getSize() const noexcept { return _size; }</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span>            :   ASMJIT_INLINE uint32_t getSourceSectionId() const noexcept { return _sourceSectionId; }</a>
+<a name="475"><span class="lineNum">     475 </span>            :   ASMJIT_INLINE uint32_t getTargetSectionId() const noexcept { return _targetSectionId; }</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint64_t getSourceOffset() const noexcept { return _sourceOffset; }</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint64_t getData() const noexcept { return _data; }</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span>            :   // ------------------------------------------------------------------------</a>
+<a name="481"><span class="lineNum">     481 </span>            :   // [Members]</a>
+<a name="482"><span class="lineNum">     482 </span>            :   // ------------------------------------------------------------------------</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :   uint32_t _id;                          //!&lt; Relocation id.</a>
+<a name="485"><span class="lineNum">     485 </span>            :   uint8_t _type;                         //!&lt; Type of the relocation.</a>
+<a name="486"><span class="lineNum">     486 </span>            :   uint8_t _size;                         //!&lt; Size of the relocation (1, 2, 4 or 8 bytes).</a>
+<a name="487"><span class="lineNum">     487 </span>            :   uint8_t _reserved[2];                  //!&lt; Reserved.</a>
+<a name="488"><span class="lineNum">     488 </span>            :   uint32_t _sourceSectionId;             //!&lt; Source section id.</a>
+<a name="489"><span class="lineNum">     489 </span>            :   uint32_t _targetSectionId;             //!&lt; Destination section id.</a>
+<a name="490"><span class="lineNum">     490 </span>            :   uint64_t _sourceOffset;                //!&lt; Source offset (relative to start of the section).</a>
+<a name="491"><span class="lineNum">     491 </span>            :   uint64_t _data;                        //!&lt; Relocation data (target offset, target address, etc).</a>
+<a name="492"><span class="lineNum">     492 </span>            : };</a>
+<a name="493"><span class="lineNum">     493 </span>            : </a>
+<a name="494"><span class="lineNum">     494 </span>            : // ============================================================================</a>
+<a name="495"><span class="lineNum">     495 </span>            : // [asmjit::CodeHolder]</a>
+<a name="496"><span class="lineNum">     496 </span>            : // ============================================================================</a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span>            : //! Contains basic information about the target architecture plus its settings,</a>
+<a name="499"><span class="lineNum">     499 </span>            : //! and holds code &amp; data (including sections, labels, and relocation information).</a>
+<a name="500"><span class="lineNum">     500 </span>            : //! CodeHolder can store both binary and intermediate representation of assembly,</a>
+<a name="501"><span class="lineNum">     501 </span>            : //! which can be generated by \ref Assembler and/or \ref CodeBuilder.</a>
+<a name="502"><span class="lineNum">     502 </span>            : //!</a>
+<a name="503"><span class="lineNum">     503 </span>            : //! NOTE: CodeHolder has ability to attach an \ref ErrorHandler, however, this</a>
+<a name="504"><span class="lineNum">     504 </span>            : //! error handler is not triggered by CodeHolder itself, it's only used by the</a>
+<a name="505"><span class="lineNum">     505 </span>            : //! attached code generators.</a>
+<a name="506"><span class="lineNum">     506 </span>            : class CodeHolder {</a>
+<a name="507"><span class="lineNum">     507 </span>            : public:</a>
+<a name="508"><span class="lineNum">     508 </span>            :   ASMJIT_NONCOPYABLE(CodeHolder)</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="511"><span class="lineNum">     511 </span>            :   // [Construction / Destruction]</a>
+<a name="512"><span class="lineNum">     512 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            :   //! Create an uninitialized CodeHolder (you must init() it before it can be used).</a>
+<a name="515"><span class="lineNum">     515 </span>            :   ASMJIT_API CodeHolder() noexcept;</a>
+<a name="516"><span class="lineNum">     516 </span>            :   //! Destroy the CodeHolder.</a>
+<a name="517"><span class="lineNum">     517 </span>            :   ASMJIT_API ~CodeHolder() noexcept;</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="520"><span class="lineNum">     520 </span>            :   // [Init / Reset]</a>
+<a name="521"><span class="lineNum">     521 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span>            :   ASMJIT_INLINE bool isInitialized() const noexcept { return _codeInfo.isInitialized(); }</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            :   //! Initialize to CodeHolder to hold code described by `codeInfo`.</a>
+<a name="526"><span class="lineNum">     526 </span>            :   ASMJIT_API Error init(const CodeInfo&amp; info) noexcept;</a>
+<a name="527"><span class="lineNum">     527 </span>            :   //! Detach all code-generators attached and reset the \ref CodeHolder.</a>
+<a name="528"><span class="lineNum">     528 </span>            :   ASMJIT_API void reset(bool releaseMemory = false) noexcept;</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="531"><span class="lineNum">     531 </span>            :   // [Attach / Detach]</a>
+<a name="532"><span class="lineNum">     532 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            :   //! Attach a \ref CodeEmitter to this \ref CodeHolder.</a>
+<a name="535"><span class="lineNum">     535 </span>            :   ASMJIT_API Error attach(CodeEmitter* emitter) noexcept;</a>
+<a name="536"><span class="lineNum">     536 </span>            :   //! Detach a \ref CodeEmitter from this \ref CodeHolder.</a>
+<a name="537"><span class="lineNum">     537 </span>            :   ASMJIT_API Error detach(CodeEmitter* emitter) noexcept;</a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="540"><span class="lineNum">     540 </span>            :   // [Sync]</a>
+<a name="541"><span class="lineNum">     541 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            :   //! Synchronize all states of all `CodeEmitter`s associated with the CodeHolder.</a>
+<a name="544"><span class="lineNum">     544 </span>            :   //! This is required as some code generators don't sync every time they do</a>
+<a name="545"><span class="lineNum">     545 </span>            :   //! something - for example \ref Assembler generally syncs when it needs to</a>
+<a name="546"><span class="lineNum">     546 </span>            :   //! reallocate the \ref CodeBuffer, but not each time it encodes instruction</a>
+<a name="547"><span class="lineNum">     547 </span>            :   //! or directive.</a>
+<a name="548"><span class="lineNum">     548 </span>            :   ASMJIT_API void sync() noexcept;</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="551"><span class="lineNum">     551 </span>            :   // [Code-Information]</a>
+<a name="552"><span class="lineNum">     552 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            :   //! Get code/target information, see \ref CodeInfo.</a>
+<a name="555"><span class="lineNum">     555 </span>            :   ASMJIT_INLINE const CodeInfo&amp; getCodeInfo() const noexcept { return _codeInfo; }</a>
+<a name="556"><span class="lineNum">     556 </span>            :   //! Get architecture information, see \ref ArchInfo.</a>
+<a name="557"><span class="lineNum">     557 </span>            :   ASMJIT_INLINE const ArchInfo&amp; getArchInfo() const noexcept { return _codeInfo.getArchInfo(); }</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span>            :   //! Get the target's architecture type.</a>
+<a name="560"><span class="lineNum">     560 </span>            :   ASMJIT_INLINE uint32_t getArchType() const noexcept { return getArchInfo().getType(); }</a>
+<a name="561"><span class="lineNum">     561 </span>            :   //! Get the target's architecture sub-type.</a>
+<a name="562"><span class="lineNum">     562 </span>            :   ASMJIT_INLINE uint32_t getArchSubType() const noexcept { return getArchInfo().getSubType(); }</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :   //! Get if a static base-address is set.</a>
+<a name="565"><span class="lineNum">     565 </span>            :   ASMJIT_INLINE bool hasBaseAddress() const noexcept { return _codeInfo.hasBaseAddress(); }</a>
+<a name="566"><span class="lineNum">     566 </span>            :   //! Get a static base-address (uint64_t).</a>
+<a name="567"><span class="lineNum">     567 </span>            :   ASMJIT_INLINE uint64_t getBaseAddress() const noexcept { return _codeInfo.getBaseAddress(); }</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="570"><span class="lineNum">     570 </span>            :   // [Global Information]</a>
+<a name="571"><span class="lineNum">     571 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span>            :   //! Get global hints, internally propagated to all `CodeEmitter`s attached.</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">       3896 :   ASMJIT_INLINE uint32_t getGlobalHints() const noexcept { return _globalHints; }</span></a>
+<a name="575"><span class="lineNum">     575 </span>            :   //! Get global options, internally propagated to all `CodeEmitter`s attached.</a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">       3896 :   ASMJIT_INLINE uint32_t getGlobalOptions() const noexcept { return _globalOptions; }</span></a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="579"><span class="lineNum">     579 </span>            :   // [Result Information]</a>
+<a name="580"><span class="lineNum">     580 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span>            :   //! Get the size code &amp; data of all sections.</a>
+<a name="583"><span class="lineNum">     583 </span>            :   ASMJIT_API size_t getCodeSize() const noexcept;</a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span>            :   //! Get size of all possible trampolines.</a>
+<a name="586"><span class="lineNum">     586 </span>            :   //!</a>
+<a name="587"><span class="lineNum">     587 </span>            :   //! Trampolines are needed to successfully generate relative jumps to absolute</a>
+<a name="588"><span class="lineNum">     588 </span>            :   //! addresses. This value is only non-zero if jmp of call instructions were</a>
+<a name="589"><span class="lineNum">     589 </span>            :   //! used with immediate operand (this means jumping or calling an absolute</a>
+<a name="590"><span class="lineNum">     590 </span>            :   //! address directly).</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">       3896 :   ASMJIT_INLINE size_t getTrampolinesSize() const noexcept { return _trampolinesSize; }</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="594"><span class="lineNum">     594 </span>            :   // [Logging &amp; Error Handling]</a>
+<a name="595"><span class="lineNum">     595 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="598"><span class="lineNum">     598 </span>            :   //! Get if a logger attached.</a>
+<a name="599"><span class="lineNum">     599 </span>            :   ASMJIT_INLINE bool hasLogger() const noexcept { return _logger != nullptr; }</a>
+<a name="600"><span class="lineNum">     600 </span>            :   //! Get the attached logger.</a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">       1948 :   ASMJIT_INLINE Logger* getLogger() const noexcept { return _logger; }</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :   //! Attach a `logger` to CodeHolder and propagate it to all attached `CodeEmitter`s.</a>
+<a name="603"><span class="lineNum">     603 </span>            :   ASMJIT_API void setLogger(Logger* logger) noexcept;</a>
+<a name="604"><span class="lineNum">     604 </span>            :   //! Reset the logger (does nothing if not attached).</a>
+<a name="605"><span class="lineNum">     605 </span>            :   ASMJIT_INLINE void resetLogger() noexcept { setLogger(nullptr); }</a>
+<a name="606"><span class="lineNum">     606 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span>            :   //! Get if error-handler is attached.</a>
+<a name="609"><span class="lineNum">     609 </span>            :   ASMJIT_INLINE bool hasErrorHandler() const noexcept { return _errorHandler != nullptr; }</a>
+<a name="610"><span class="lineNum">     610 </span>            :   //! Get the error-handler.</a>
+<a name="611"><span class="lineNum">     611 </span>            :   ASMJIT_INLINE ErrorHandler* getErrorHandler() const noexcept { return _errorHandler; }</a>
+<a name="612"><span class="lineNum">     612 </span>            :   //! Set the error handler, will affect all attached `CodeEmitter`s.</a>
+<a name="613"><span class="lineNum">     613 </span>            :   ASMJIT_API Error setErrorHandler(ErrorHandler* handler) noexcept;</a>
+<a name="614"><span class="lineNum">     614 </span>            :   //! Reset the error handler (does nothing if not attached).</a>
+<a name="615"><span class="lineNum">     615 </span>            :   ASMJIT_INLINE void resetErrorHandler() noexcept { setErrorHandler(nullptr); }</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="618"><span class="lineNum">     618 </span>            :   // [Sections]</a>
+<a name="619"><span class="lineNum">     619 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span>            :   //! Get array of `SectionEntry*` records.</a>
+<a name="622"><span class="lineNum">     622 </span>            :   ASMJIT_INLINE const ZoneVector&lt;SectionEntry*&gt;&amp; getSections() const noexcept { return _sections; }</a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            :   //! Get a section entry of the given index.</a>
+<a name="625"><span class="lineNum">     625 </span>            :   ASMJIT_INLINE SectionEntry* getSectionEntry(size_t index) const noexcept { return _sections[index]; }</a>
+<a name="626"><span class="lineNum">     626 </span>            : </a>
+<a name="627"><span class="lineNum">     627 </span>            :   ASMJIT_API Error growBuffer(CodeBuffer* cb, size_t n) noexcept;</a>
+<a name="628"><span class="lineNum">     628 </span>            :   ASMJIT_API Error reserveBuffer(CodeBuffer* cb, size_t n) noexcept;</a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="631"><span class="lineNum">     631 </span>            :   // [Labels &amp; Symbols]</a>
+<a name="632"><span class="lineNum">     632 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :   //! Create a new anonymous label and return its id in `idOut`.</a>
+<a name="635"><span class="lineNum">     635 </span>            :   //!</a>
+<a name="636"><span class="lineNum">     636 </span>            :   //! Returns `Error`, does not report error to \ref ErrorHandler.</a>
+<a name="637"><span class="lineNum">     637 </span>            :   ASMJIT_API Error newLabelId(uint32_t&amp; idOut) noexcept;</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            :   //! Create a new named label label-type `type`.</a>
+<a name="640"><span class="lineNum">     640 </span>            :   //!</a>
+<a name="641"><span class="lineNum">     641 </span>            :   //! Returns `Error`, does not report error to \ref ErrorHandler.</a>
+<a name="642"><span class="lineNum">     642 </span>            :   ASMJIT_API Error newNamedLabelId(uint32_t&amp; idOut, const char* name, size_t nameLength, uint32_t type, uint32_t parentId) noexcept;</a>
+<a name="643"><span class="lineNum">     643 </span>            : </a>
+<a name="644"><span class="lineNum">     644 </span>            :   //! Get a label id by name.</a>
+<a name="645"><span class="lineNum">     645 </span>            :   ASMJIT_API uint32_t getLabelIdByName(const char* name, size_t nameLength = Globals::kInvalidIndex, uint32_t parentId = 0) noexcept;</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            :   //! Create a new label-link used to store information about yet unbound labels.</a>
+<a name="648"><span class="lineNum">     648 </span>            :   //!</a>
+<a name="649"><span class="lineNum">     649 </span>            :   //! Returns `null` if the allocation failed.</a>
+<a name="650"><span class="lineNum">     650 </span>            :   ASMJIT_API LabelLink* newLabelLink(LabelEntry* le, uint32_t sectionId, size_t offset, intptr_t rel) noexcept;</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :   //! Get array of `LabelEntry*` records.</a>
+<a name="653"><span class="lineNum">     653 </span>            :   ASMJIT_INLINE const ZoneVector&lt;LabelEntry*&gt;&amp; getLabelEntries() const noexcept { return _labels; }</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :   //! Get number of labels created.</a>
+<a name="656"><span class="lineNum">     656 </span>            :   ASMJIT_INLINE size_t getLabelsCount() const noexcept { return _labels.getLength(); }</a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span>            :   //! Get number of label references, which are unresolved at the moment.</a>
+<a name="659"><span class="lineNum">     659 </span>            :   ASMJIT_INLINE size_t getUnresolvedLabelsCount() const noexcept { return _unresolvedLabelsCount; }</a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span>            :   //! Get if the `label` is valid (i.e. created by `newLabelId()`).</a>
+<a name="662"><span class="lineNum">     662 </span>            :   ASMJIT_INLINE bool isLabelValid(const Label&amp; label) const noexcept {</a>
+<a name="663"><span class="lineNum">     663 </span>            :     return isLabelValid(label.getId());</a>
+<a name="664"><span class="lineNum">     664 </span>            :   }</a>
+<a name="665"><span class="lineNum">     665 </span>            :   //! Get if the label having `id` is valid (i.e. created by `newLabelId()`).</a>
+<a name="666"><span class="lineNum">     666 </span>            :   ASMJIT_INLINE bool isLabelValid(uint32_t labelId) const noexcept {</a>
+<a name="667"><span class="lineNum">     667 </span>            :     size_t index = Operand::unpackId(labelId);</a>
+<a name="668"><span class="lineNum">     668 </span>            :     return index &lt; _labels.getLength();</a>
+<a name="669"><span class="lineNum">     669 </span>            :   }</a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span>            :   //! Get if the `label` is already bound.</a>
+<a name="672"><span class="lineNum">     672 </span>            :   //!</a>
+<a name="673"><span class="lineNum">     673 </span>            :   //! Returns `false` if the `label` is not valid.</a>
+<a name="674"><span class="lineNum">     674 </span>            :   ASMJIT_INLINE bool isLabelBound(const Label&amp; label) const noexcept {</a>
+<a name="675"><span class="lineNum">     675 </span>            :     return isLabelBound(label.getId());</a>
+<a name="676"><span class="lineNum">     676 </span>            :   }</a>
+<a name="677"><span class="lineNum">     677 </span>            :   //! \overload</a>
+<a name="678"><span class="lineNum">     678 </span>            :   ASMJIT_INLINE bool isLabelBound(uint32_t id) const noexcept {</a>
+<a name="679"><span class="lineNum">     679 </span>            :     size_t index = Operand::unpackId(id);</a>
+<a name="680"><span class="lineNum">     680 </span>            :     return index &lt; _labels.getLength() &amp;&amp; _labels[index]-&gt;isBound();</a>
+<a name="681"><span class="lineNum">     681 </span>            :   }</a>
+<a name="682"><span class="lineNum">     682 </span>            : </a>
+<a name="683"><span class="lineNum">     683 </span>            :   //! Get a `label` offset or -1 if the label is not yet bound.</a>
+<a name="684"><span class="lineNum">     684 </span>            :   ASMJIT_INLINE intptr_t getLabelOffset(const Label&amp; label) const noexcept {</a>
+<a name="685"><span class="lineNum">     685 </span>            :     return getLabelOffset(label.getId());</a>
+<a name="686"><span class="lineNum">     686 </span>            :   }</a>
+<a name="687"><span class="lineNum">     687 </span>            :   //! \overload</a>
+<a name="688"><span class="lineNum">     688 </span>            :   ASMJIT_INLINE intptr_t getLabelOffset(uint32_t id) const noexcept {</a>
+<a name="689"><span class="lineNum">     689 </span>            :     ASMJIT_ASSERT(isLabelValid(id));</a>
+<a name="690"><span class="lineNum">     690 </span>            :     return _labels[Operand::unpackId(id)]-&gt;getOffset();</a>
+<a name="691"><span class="lineNum">     691 </span>            :   }</a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :   //! Get information about the given `label`.</a>
+<a name="694"><span class="lineNum">     694 </span>            :   ASMJIT_INLINE LabelEntry* getLabelEntry(const Label&amp; label) const noexcept {</a>
+<a name="695"><span class="lineNum">     695 </span>            :     return getLabelEntry(label.getId());</a>
+<a name="696"><span class="lineNum">     696 </span>            :   }</a>
+<a name="697"><span class="lineNum">     697 </span>            :   //! Get information about a label having the given `id`.</a>
+<a name="698"><span class="lineNum">     698 </span>            :   ASMJIT_INLINE LabelEntry* getLabelEntry(uint32_t id) const noexcept {</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">       3896 :     size_t index = static_cast&lt;size_t&gt;(Operand::unpackId(id));</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">       3896 :     return index &lt; _labels.getLength() ? _labels[index] : static_cast&lt;LabelEntry*&gt;(nullptr);</span></a>
+<a name="701"><span class="lineNum">     701 </span>            :   }</a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="704"><span class="lineNum">     704 </span>            :   // [Relocations]</a>
+<a name="705"><span class="lineNum">     705 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="706"><span class="lineNum">     706 </span>            : </a>
+<a name="707"><span class="lineNum">     707 </span>            :   //! Create a new relocation entry of type `type` and size `size`.</a>
+<a name="708"><span class="lineNum">     708 </span>            :   //!</a>
+<a name="709"><span class="lineNum">     709 </span>            :   //! Additional fields can be set after the relocation entry was created.</a>
+<a name="710"><span class="lineNum">     710 </span>            :   ASMJIT_API Error newRelocEntry(RelocEntry** dst, uint32_t type, uint32_t size) noexcept;</a>
+<a name="711"><span class="lineNum">     711 </span>            : </a>
+<a name="712"><span class="lineNum">     712 </span>            :   //! Get if the code contains relocations.</a>
+<a name="713"><span class="lineNum">     713 </span>            :   ASMJIT_INLINE bool hasRelocations() const noexcept { return !_relocations.isEmpty(); }</a>
+<a name="714"><span class="lineNum">     714 </span>            :   //! Get array of `RelocEntry*` records.</a>
+<a name="715"><span class="lineNum">     715 </span>            :   ASMJIT_INLINE const ZoneVector&lt;RelocEntry*&gt;&amp; getRelocEntries() const noexcept { return _relocations; }</a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            :   ASMJIT_INLINE RelocEntry* getRelocEntry(uint32_t id) const noexcept { return _relocations[id]; }</a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            :   //! Relocate the code to `baseAddress` and copy it to `dst`.</a>
+<a name="720"><span class="lineNum">     720 </span>            :   //!</a>
+<a name="721"><span class="lineNum">     721 </span>            :   //! \param dst Contains the location where the relocated code should be</a>
+<a name="722"><span class="lineNum">     722 </span>            :   //! copied. The pointer can be address returned by virtual memory allocator</a>
+<a name="723"><span class="lineNum">     723 </span>            :   //! or any other address that has sufficient space.</a>
+<a name="724"><span class="lineNum">     724 </span>            :   //!</a>
+<a name="725"><span class="lineNum">     725 </span>            :   //! \param baseAddress Base address used for relocation. `JitRuntime` always</a>
+<a name="726"><span class="lineNum">     726 </span>            :   //! sets the `baseAddress` to be the same as `dst`.</a>
+<a name="727"><span class="lineNum">     727 </span>            :   //!</a>
+<a name="728"><span class="lineNum">     728 </span>            :   //! \return The number bytes actually used. If the code emitter reserved</a>
+<a name="729"><span class="lineNum">     729 </span>            :   //! space for possible trampolines, but didn't use it, the number of bytes</a>
+<a name="730"><span class="lineNum">     730 </span>            :   //! used can actually be less than the expected worst case. Virtual memory</a>
+<a name="731"><span class="lineNum">     731 </span>            :   //! allocator can shrink the memory it allocated initially.</a>
+<a name="732"><span class="lineNum">     732 </span>            :   //!</a>
+<a name="733"><span class="lineNum">     733 </span>            :   //! A given buffer will be overwritten, to get the number of bytes required,</a>
+<a name="734"><span class="lineNum">     734 </span>            :   //! use `getCodeSize()`.</a>
+<a name="735"><span class="lineNum">     735 </span>            :   ASMJIT_API size_t relocate(void* dst, uint64_t baseAddress = Globals::kNoBaseAddress) const noexcept;</a>
+<a name="736"><span class="lineNum">     736 </span>            : </a>
+<a name="737"><span class="lineNum">     737 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="738"><span class="lineNum">     738 </span>            :   // [Members]</a>
+<a name="739"><span class="lineNum">     739 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="740"><span class="lineNum">     740 </span>            : </a>
+<a name="741"><span class="lineNum">     741 </span>            :   CodeInfo _codeInfo;                    //!&lt; Basic information about the code (architecture and other info).</a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span>            :   uint32_t _globalHints;                 //!&lt; Global hints, propagated to all `CodeEmitter`s.</a>
+<a name="744"><span class="lineNum">     744 </span>            :   uint32_t _globalOptions;               //!&lt; Global options, propagated to all `CodeEmitter`s.</a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span>            :   CodeEmitter* _emitters;                //!&lt; Linked-list of all attached `CodeEmitter`s.</a>
+<a name="747"><span class="lineNum">     747 </span>            :   Assembler* _cgAsm;                     //!&lt; Attached \ref Assembler (only one at a time).</a>
+<a name="748"><span class="lineNum">     748 </span>            : </a>
+<a name="749"><span class="lineNum">     749 </span>            :   Logger* _logger;                       //!&lt; Attached \ref Logger, used by all consumers.</a>
+<a name="750"><span class="lineNum">     750 </span>            :   ErrorHandler* _errorHandler;           //!&lt; Attached \ref ErrorHandler.</a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span>            :   uint32_t _unresolvedLabelsCount;       //!&lt; Count of label references which were not resolved.</a>
+<a name="753"><span class="lineNum">     753 </span>            :   uint32_t _trampolinesSize;             //!&lt; Size of all possible trampolines.</a>
+<a name="754"><span class="lineNum">     754 </span>            : </a>
+<a name="755"><span class="lineNum">     755 </span>            :   Zone _baseZone;                        //!&lt; Base zone (used to allocate core structures).</a>
+<a name="756"><span class="lineNum">     756 </span>            :   Zone _dataZone;                        //!&lt; Data zone (used to allocate extra data like label names).</a>
+<a name="757"><span class="lineNum">     757 </span>            :   ZoneHeap _baseHeap;                    //!&lt; Zone allocator, used to manage internal containers.</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            :   ZoneVector&lt;SectionEntry*&gt; _sections;   //!&lt; Section entries.</a>
+<a name="760"><span class="lineNum">     760 </span>            :   ZoneVector&lt;LabelEntry*&gt; _labels;       //!&lt; Label entries (each label is stored here).</a>
+<a name="761"><span class="lineNum">     761 </span>            :   ZoneVector&lt;RelocEntry*&gt; _relocations;  //!&lt; Relocation entries.</a>
+<a name="762"><span class="lineNum">     762 </span>            :   ZoneHash&lt;LabelEntry&gt; _namedLabels;     //!&lt; Label name -&gt; LabelEntry (only named labels).</a>
+<a name="763"><span class="lineNum">     763 </span>            : };</a>
+<a name="764"><span class="lineNum">     764 </span>            : </a>
+<a name="765"><span class="lineNum">     765 </span>            : //! \}</a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            : } // asmjit namespace</a>
+<a name="768"><span class="lineNum">     768 </span>            : } // namespace PLMD</a>
+<a name="769"><span class="lineNum">     769 </span>            : </a>
+<a name="770"><span class="lineNum">     770 </span>            : // [Api-End]</a>
+<a name="771"><span class="lineNum">     771 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            : // [Guard]</a>
+<a name="774"><span class="lineNum">     774 </span>            : #endif // _ASMJIT_BASE_CODEHOLDER_H</a>
+<a name="775"><span class="lineNum">     775 </span>            : #pragma GCC diagnostic pop</a>
+<a name="776"><span class="lineNum">     776 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="777"><span class="lineNum">     777 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/constpool.cpp.func-sort-c.html b/coverage-libs/asmjit/constpool.cpp.func-sort-c.html
new file mode 100644
index 0000000000..30d0ec1720
--- /dev/null
+++ b/coverage-libs/asmjit/constpool.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/constpool.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - constpool.cpp<span style="font-size: 80%;"> (<a href="constpool.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">110</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="constpool.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#236">_ZN4PLMD6asmjit9ConstPool3addEPKvmRm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#85">_ZN4PLMD6asmjit9ConstPool4Tree3getEPKv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#99">_ZN4PLMD6asmjit9ConstPool4Tree3putEPNS1_4NodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#158">_ZN4PLMD6asmjit9ConstPool5resetEPNS0_4ZoneE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#151">_ZN4PLMD6asmjit9ConstPoolC2EPNS0_4ZoneE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#152">_ZN4PLMD6asmjit9ConstPoolD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#191">_ZN4PLMD6asmjitL16ConstPool_addGapEPNS0_9ConstPoolEmm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#353">_ZNK4PLMD6asmjit9ConstPool4fillEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/constpool.cpp.func.html b/coverage-libs/asmjit/constpool.cpp.func.html
new file mode 100644
index 0000000000..d22cfb21c0
--- /dev/null
+++ b/coverage-libs/asmjit/constpool.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/constpool.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - constpool.cpp<span style="font-size: 80%;"> (<a href="constpool.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">110</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="constpool.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#236">_ZN4PLMD6asmjit9ConstPool3addEPKvmRm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#85">_ZN4PLMD6asmjit9ConstPool4Tree3getEPKv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#99">_ZN4PLMD6asmjit9ConstPool4Tree3putEPNS1_4NodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#158">_ZN4PLMD6asmjit9ConstPool5resetEPNS0_4ZoneE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#151">_ZN4PLMD6asmjit9ConstPoolC2EPNS0_4ZoneE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#152">_ZN4PLMD6asmjit9ConstPoolD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#191">_ZN4PLMD6asmjitL16ConstPool_addGapEPNS0_9ConstPoolEmm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="constpool.cpp.gcov.html#353">_ZNK4PLMD6asmjit9ConstPool4fillEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/constpool.cpp.gcov.html b/coverage-libs/asmjit/constpool.cpp.gcov.html
new file mode 100644
index 0000000000..27538216cf
--- /dev/null
+++ b/coverage-libs/asmjit/constpool.cpp.gcov.html
@@ -0,0 +1,613 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/constpool.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - constpool.cpp<span style="font-size: 80%;"> (source / <a href="constpool.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">110</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./constpool.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;algorithm&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // Binary tree code is based on Julienne Walker's &quot;Andersson Binary Trees&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : // article and implementation. However, only three operations are implemented -</a>
+<a name="46"><span class="lineNum">      46 </span>            : // get, insert and traverse.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // ============================================================================</a>
+<a name="49"><span class="lineNum">      49 </span>            : // [asmjit::ConstPool::Tree - Ops]</a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : //! \internal</a>
+<a name="53"><span class="lineNum">      53 </span>            : //!</a>
+<a name="54"><span class="lineNum">      54 </span>            : //! Remove left horizontal links.</a>
+<a name="55"><span class="lineNum">      55 </span>            : static ASMJIT_INLINE ConstPool::Node* ConstPoolTree_skewNode(ConstPool::Node* node) noexcept {</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   ConstPool::Node* link = node-&gt;_link[0];</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   uint32_t level = node-&gt;_level;</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   if (level != 0 &amp;&amp; link &amp;&amp; link-&gt;_level == level) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :     node-&gt;_link[0] = link-&gt;_link[1];</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :     link-&gt;_link[1] = node;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            :     node = link;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            :   return node;</a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : //! \internal</a>
+<a name="70"><span class="lineNum">      70 </span>            : //!</a>
+<a name="71"><span class="lineNum">      71 </span>            : //! Remove consecutive horizontal links.</a>
+<a name="72"><span class="lineNum">      72 </span>            : static ASMJIT_INLINE ConstPool::Node* ConstPoolTree_splitNode(ConstPool::Node* node) noexcept {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   ConstPool::Node* link = node-&gt;_link[1];</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :   uint32_t level = node-&gt;_level;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   if (level != 0 &amp;&amp; link &amp;&amp; link-&gt;_link[1] &amp;&amp; link-&gt;_link[1]-&gt;_level == level) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :     node-&gt;_link[1] = link-&gt;_link[0];</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     link-&gt;_link[0] = node;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :     node = link;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :     node-&gt;_level++;</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   return node;</a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 : ConstPool::Node* ConstPool::Tree::get(const void* data) noexcept {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :   ConstPool::Node* node = _root;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   size_t dataSize = _dataSize;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   while (node) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     int c = ::memcmp(node-&gt;getData(), data, dataSize);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     if (c == 0)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :       return node;</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     node = node-&gt;_link[c &lt; 0];</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   return nullptr;</a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : void ConstPool::Tree::put(ConstPool::Node* newNode) noexcept {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   size_t dataSize = _dataSize;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   _length++;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   if (!_root) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     _root = newNode;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   ConstPool::Node* node = _root;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ConstPool::Node* stack[kHeightLimit];</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   unsigned int top = 0;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   unsigned int dir;</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   // Find a spot and save the stack.</a>
+<a name="117"><span class="lineNum">     117 </span>            :   for (;;) {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     stack[top++] = node;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     dir = ::memcmp(node-&gt;getData(), newNode-&gt;getData(), dataSize) &lt; 0;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     ConstPool::Node* link = node-&gt;_link[dir];</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     if (!link) break;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :     node = link;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // Link and rebalance.</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   node-&gt;_link[dir] = newNode;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :   while (top &gt; 0) {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     // Which child?</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     node = stack[--top];</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     if (top != 0) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :       dir = stack[top - 1]-&gt;_link[1] == node;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :     }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :     node = ConstPoolTree_skewNode(node);</a>
+<a name="139"><span class="lineNum">     139 </span>            :     node = ConstPoolTree_splitNode(node);</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :     // Fix the parent.</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     if (top != 0)</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :       stack[top - 1]-&gt;_link[dir] = node;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     else</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :       _root = node;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : // ============================================================================</a>
+<a name="150"><span class="lineNum">     150 </span>            : // [asmjit::ConstPool - Construction / Destruction]</a>
+<a name="151"><span class="lineNum">     151 </span>            : // ============================================================================</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 : ConstPool::ConstPool(Zone* zone) noexcept { reset(zone); }</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 : ConstPool::~ConstPool() noexcept {}</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : // ============================================================================</a>
+<a name="157"><span class="lineNum">     157 </span>            : // [asmjit::ConstPool - Reset]</a>
+<a name="158"><span class="lineNum">     158 </span>            : // ============================================================================</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 : void ConstPool::reset(Zone* zone) noexcept {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   _zone = zone;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   size_t dataSize = 1;</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   for (size_t i = 0; i &lt; ASMJIT_ARRAY_SIZE(_tree); i++) {</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     _tree[i].reset();</a>
+<a name="166"><span class="lineNum">     166 </span>            :     _tree[i].setDataSize(dataSize);</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     _gaps[i] = nullptr;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     dataSize &lt;&lt;= 1;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   _gapPool = nullptr;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   _size = 0;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   _alignment = 0;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : // ============================================================================</a>
+<a name="177"><span class="lineNum">     177 </span>            : // [asmjit::ConstPool - Ops]</a>
+<a name="178"><span class="lineNum">     178 </span>            : // ============================================================================</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : static ASMJIT_INLINE ConstPool::Gap* ConstPool_allocGap(ConstPool* self) noexcept {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :   ConstPool::Gap* gap = self-&gt;_gapPool;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   if (!gap) return self-&gt;_zone-&gt;allocT&lt;ConstPool::Gap&gt;();</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :   self-&gt;_gapPool = gap-&gt;_next;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   return gap;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : static ASMJIT_INLINE void ConstPool_freeGap(ConstPool* self,  ConstPool::Gap* gap) noexcept {</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   gap-&gt;_next = self-&gt;_gapPool;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   self-&gt;_gapPool = gap;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 : static void ConstPool_addGap(ConstPool* self, size_t offset, size_t length) noexcept {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   ASMJIT_ASSERT(length &gt; 0);</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   while (length &gt; 0) {</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     size_t gapIndex;</a>
+<a name="198"><span class="lineNum">     198 </span>            :     size_t gapLength;</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :       gapIndex = ConstPool::kIndex16;</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     if (length &gt;= 16 &amp;&amp; Utils::isAligned&lt;size_t&gt;(offset, 16)) {</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :       gapLength = 16;</a>
+<a name="203"><span class="lineNum">     203 </span>            :     }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     else if (length &gt;= 8 &amp;&amp; Utils::isAligned&lt;size_t&gt;(offset, 8)) {</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :       gapIndex = ConstPool::kIndex8;</a>
+<a name="206"><span class="lineNum">     206 </span>            :       gapLength = 8;</a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     else if (length &gt;= 4 &amp;&amp; Utils::isAligned&lt;size_t&gt;(offset, 4)) {</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :       gapIndex = ConstPool::kIndex4;</a>
+<a name="210"><span class="lineNum">     210 </span>            :       gapLength = 4;</a>
+<a name="211"><span class="lineNum">     211 </span>            :     }</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :     else if (length &gt;= 2 &amp;&amp; Utils::isAligned&lt;size_t&gt;(offset, 2)) {</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :       gapIndex = ConstPool::kIndex2;</a>
+<a name="214"><span class="lineNum">     214 </span>            :       gapLength = 2;</a>
+<a name="215"><span class="lineNum">     215 </span>            :     }</a>
+<a name="216"><span class="lineNum">     216 </span>            :     else {</a>
+<a name="217"><span class="lineNum">     217 </span>            :       gapIndex = ConstPool::kIndex1;</a>
+<a name="218"><span class="lineNum">     218 </span>            :       gapLength = 1;</a>
+<a name="219"><span class="lineNum">     219 </span>            :     }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :     // We don't have to check for errors here, if this failed nothing really</a>
+<a name="222"><span class="lineNum">     222 </span>            :     // happened (just the gap won't be visible) and it will fail again at</a>
+<a name="223"><span class="lineNum">     223 </span>            :     // place where checking will cause kErrorNoHeapMemory.</a>
+<a name="224"><span class="lineNum">     224 </span>            :     ConstPool::Gap* gap = ConstPool_allocGap(self);</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     if (!gap) return;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :     gap-&gt;_next = self-&gt;_gaps[gapIndex];</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     self-&gt;_gaps[gapIndex] = gap;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :     gap-&gt;_offset = offset;</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     gap-&gt;_length = gapLength;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :     offset += gapLength;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :     length -= gapLength;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 : Error ConstPool::add(const void* data, size_t size, size_t&amp; dstOffset) noexcept {</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   size_t treeIndex;</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   if (size == 32)</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     treeIndex = kIndex32;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   else if (size == 16)</a>
+<a name="244"><span class="lineNum">     244 </span>            :     treeIndex = kIndex16;</a>
+<a name="245"><span class="lineNum">     245 </span>            :   else if (size == 8)</a>
+<a name="246"><span class="lineNum">     246 </span>            :     treeIndex = kIndex8;</a>
+<a name="247"><span class="lineNum">     247 </span>            :   else if (size == 4)</a>
+<a name="248"><span class="lineNum">     248 </span>            :     treeIndex = kIndex4;</a>
+<a name="249"><span class="lineNum">     249 </span>            :   else if (size == 2)</a>
+<a name="250"><span class="lineNum">     250 </span>            :     treeIndex = kIndex2;</a>
+<a name="251"><span class="lineNum">     251 </span>            :   else if (size == 1)</a>
+<a name="252"><span class="lineNum">     252 </span>            :     treeIndex = kIndex1;</a>
+<a name="253"><span class="lineNum">     253 </span>            :   else</a>
+<a name="254"><span class="lineNum">     254 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   ConstPool::Node* node = _tree[treeIndex].get(data);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   if (node) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :     dstOffset = node-&gt;_offset;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :   // Before incrementing the current offset try if there is a gap that can</a>
+<a name="263"><span class="lineNum">     263 </span>            :   // be used for the requested data.</a>
+<a name="264"><span class="lineNum">     264 </span>            :   size_t offset = ~static_cast&lt;size_t&gt;(0);</a>
+<a name="265"><span class="lineNum">     265 </span>            :   size_t gapIndex = treeIndex;</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :   while (gapIndex != kIndexCount - 1) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :     ConstPool::Gap* gap = _gaps[treeIndex];</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :     // Check if there is a gap.</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :     if (gap) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :       size_t gapOffset = gap-&gt;_offset;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :       size_t gapLength = gap-&gt;_length;</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :       // Destroy the gap for now.</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :       _gaps[treeIndex] = gap-&gt;_next;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :       ConstPool_freeGap(this, gap);</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :       offset = gapOffset;</a>
+<a name="280"><span class="lineNum">     280 </span>            :       ASMJIT_ASSERT(Utils::isAligned&lt;size_t&gt;(offset, size));</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :       gapLength -= size;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :       if (gapLength &gt; 0)</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :         ConstPool_addGap(this, gapOffset, gapLength);</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     gapIndex++;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   }</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :   if (offset == ~static_cast&lt;size_t&gt;(0)) {</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :     // Get how many bytes have to be skipped so the address is aligned accordingly</a>
+<a name="292"><span class="lineNum">     292 </span>            :     // to the 'size'.</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :     size_t diff = Utils::alignDiff&lt;size_t&gt;(_size, size);</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     if (diff != 0) {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :       ConstPool_addGap(this, _size, diff);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :       _size += diff;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :     offset = _size;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :     _size += size;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   // Add the initial node to the right index.</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   node = ConstPool::Tree::_newNode(_zone, data, size, offset, false);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 :   if (!node) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :   _tree[treeIndex].put(node);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :   _alignment = std::max&lt;size_t&gt;(_alignment, size);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :   dstOffset = offset;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   // Now create a bunch of shared constants that are based on the data pattern.</a>
+<a name="314"><span class="lineNum">     314 </span>            :   // We stop at size 4, it probably doesn't make sense to split constants down</a>
+<a name="315"><span class="lineNum">     315 </span>            :   // to 1 byte.</a>
+<a name="316"><span class="lineNum">     316 </span>            :   size_t pCount = 1;</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :   while (size &gt; 4) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :     size &gt;&gt;= 1;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :     pCount &lt;&lt;= 1;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :     ASMJIT_ASSERT(treeIndex != 0);</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :     treeIndex--;</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            :     const uint8_t* pData = static_cast&lt;const uint8_t*&gt;(data);</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :     for (size_t i = 0; i &lt; pCount; i++, pData += size) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :       node = _tree[treeIndex].get(pData);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :       if (node) continue;</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :       node = ConstPool::Tree::_newNode(_zone, pData, size, offset + (i * size), true);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :       _tree[treeIndex].put(node);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :     }</a>
+<a name="332"><span class="lineNum">     332 </span>            :   }</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            :   return kErrorOk;</a>
+<a name="335"><span class="lineNum">     335 </span>            : }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            : // ============================================================================</a>
+<a name="338"><span class="lineNum">     338 </span>            : // [asmjit::ConstPool - Reset]</a>
+<a name="339"><span class="lineNum">     339 </span>            : // ============================================================================</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : struct ConstPoolFill {</a>
+<a name="342"><span class="lineNum">     342 </span>            :   ASMJIT_INLINE ConstPoolFill(uint8_t* dst, size_t dataSize) noexcept :</a>
+<a name="343"><span class="lineNum">     343 </span>            :     _dst(dst),</a>
+<a name="344"><span class="lineNum">     344 </span>            :     _dataSize(dataSize) {}</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            :   ASMJIT_INLINE void visit(const ConstPool::Node* node) noexcept {</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :     if (!node-&gt;_shared)</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :       ::memcpy(_dst + node-&gt;_offset, node-&gt;getData(), _dataSize);</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :   }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :   uint8_t* _dst;</a>
+<a name="352"><span class="lineNum">     352 </span>            :   size_t _dataSize;</a>
+<a name="353"><span class="lineNum">     353 </span>            : };</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 : void ConstPool::fill(void* dst) const noexcept {</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :   // Clears possible gaps, asmjit should never emit garbage to the output.</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :   ::memset(dst, 0, _size);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            :   ConstPoolFill filler(static_cast&lt;uint8_t*&gt;(dst), 1);</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :   for (size_t i = 0; i &lt; ASMJIT_ARRAY_SIZE(_tree); i++) {</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :     _tree[i].iterate(filler);</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :     filler._dataSize &lt;&lt;= 1;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :   }</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            : // ============================================================================</a>
+<a name="367"><span class="lineNum">     367 </span>            : // [asmjit::ConstPool - Test]</a>
+<a name="368"><span class="lineNum">     368 </span>            : // ============================================================================</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span>            : #if defined(ASMJIT_TEST)</a>
+<a name="371"><span class="lineNum">     371 </span>            : UNIT(base_constpool) {</a>
+<a name="372"><span class="lineNum">     372 </span>            :   Zone zone(32384 - Zone::kZoneOverhead);</a>
+<a name="373"><span class="lineNum">     373 </span>            :   ConstPool pool(&amp;zone);</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            :   uint32_t i;</a>
+<a name="376"><span class="lineNum">     376 </span>            :   uint32_t kCount = 1000000;</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :   INFO(&quot;Adding %u constants to the pool.&quot;, kCount);</a>
+<a name="379"><span class="lineNum">     379 </span>            :   {</a>
+<a name="380"><span class="lineNum">     380 </span>            :     size_t prevOffset;</a>
+<a name="381"><span class="lineNum">     381 </span>            :     size_t curOffset;</a>
+<a name="382"><span class="lineNum">     382 </span>            :     uint64_t c = ASMJIT_UINT64_C(0x0101010101010101);</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            :     EXPECT(pool.add(&amp;c, 8, prevOffset) == kErrorOk,</a>
+<a name="385"><span class="lineNum">     385 </span>            :       &quot;pool.add() - Returned error&quot;);</a>
+<a name="386"><span class="lineNum">     386 </span>            :     EXPECT(prevOffset == 0,</a>
+<a name="387"><span class="lineNum">     387 </span>            :       &quot;pool.add() - First constant should have zero offset&quot;);</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            :     for (i = 1; i &lt; kCount; i++) {</a>
+<a name="390"><span class="lineNum">     390 </span>            :       c++;</a>
+<a name="391"><span class="lineNum">     391 </span>            :       EXPECT(pool.add(&amp;c, 8, curOffset) == kErrorOk,</a>
+<a name="392"><span class="lineNum">     392 </span>            :         &quot;pool.add() - Returned error&quot;);</a>
+<a name="393"><span class="lineNum">     393 </span>            :       EXPECT(prevOffset + 8 == curOffset,</a>
+<a name="394"><span class="lineNum">     394 </span>            :         &quot;pool.add() - Returned incorrect curOffset&quot;);</a>
+<a name="395"><span class="lineNum">     395 </span>            :       EXPECT(pool.getSize() == (i + 1) * 8,</a>
+<a name="396"><span class="lineNum">     396 </span>            :         &quot;pool.getSize() - Reported incorrect size&quot;);</a>
+<a name="397"><span class="lineNum">     397 </span>            :       prevOffset = curOffset;</a>
+<a name="398"><span class="lineNum">     398 </span>            :     }</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :     EXPECT(pool.getAlignment() == 8,</a>
+<a name="401"><span class="lineNum">     401 </span>            :       &quot;pool.getAlignment() - Expected 8-byte alignment&quot;);</a>
+<a name="402"><span class="lineNum">     402 </span>            :   }</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            :   INFO(&quot;Retrieving %u constants from the pool.&quot;, kCount);</a>
+<a name="405"><span class="lineNum">     405 </span>            :   {</a>
+<a name="406"><span class="lineNum">     406 </span>            :     uint64_t c = ASMJIT_UINT64_C(0x0101010101010101);</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :     for (i = 0; i &lt; kCount; i++) {</a>
+<a name="409"><span class="lineNum">     409 </span>            :       size_t offset;</a>
+<a name="410"><span class="lineNum">     410 </span>            :       EXPECT(pool.add(&amp;c, 8, offset) == kErrorOk,</a>
+<a name="411"><span class="lineNum">     411 </span>            :         &quot;pool.add() - Returned error&quot;);</a>
+<a name="412"><span class="lineNum">     412 </span>            :       EXPECT(offset == i * 8,</a>
+<a name="413"><span class="lineNum">     413 </span>            :         &quot;pool.add() - Should have reused constant&quot;);</a>
+<a name="414"><span class="lineNum">     414 </span>            :       c++;</a>
+<a name="415"><span class="lineNum">     415 </span>            :     }</a>
+<a name="416"><span class="lineNum">     416 </span>            :   }</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            :   INFO(&quot;Checking if the constants were split into 4-byte patterns&quot;);</a>
+<a name="419"><span class="lineNum">     419 </span>            :   {</a>
+<a name="420"><span class="lineNum">     420 </span>            :     uint32_t c = 0x01010101;</a>
+<a name="421"><span class="lineNum">     421 </span>            :     for (i = 0; i &lt; kCount; i++) {</a>
+<a name="422"><span class="lineNum">     422 </span>            :       size_t offset;</a>
+<a name="423"><span class="lineNum">     423 </span>            :       EXPECT(pool.add(&amp;c, 4, offset) == kErrorOk,</a>
+<a name="424"><span class="lineNum">     424 </span>            :         &quot;pool.add() - Returned error&quot;);</a>
+<a name="425"><span class="lineNum">     425 </span>            :       EXPECT(offset == i * 8,</a>
+<a name="426"><span class="lineNum">     426 </span>            :         &quot;pool.add() - Should reuse existing constant&quot;);</a>
+<a name="427"><span class="lineNum">     427 </span>            :       c++;</a>
+<a name="428"><span class="lineNum">     428 </span>            :     }</a>
+<a name="429"><span class="lineNum">     429 </span>            :   }</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            :   INFO(&quot;Adding 2 byte constant to misalign the current offset&quot;);</a>
+<a name="432"><span class="lineNum">     432 </span>            :   {</a>
+<a name="433"><span class="lineNum">     433 </span>            :     uint16_t c = 0xFFFF;</a>
+<a name="434"><span class="lineNum">     434 </span>            :     size_t offset;</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            :     EXPECT(pool.add(&amp;c, 2, offset) == kErrorOk,</a>
+<a name="437"><span class="lineNum">     437 </span>            :       &quot;pool.add() - Returned error&quot;);</a>
+<a name="438"><span class="lineNum">     438 </span>            :     EXPECT(offset == kCount * 8,</a>
+<a name="439"><span class="lineNum">     439 </span>            :       &quot;pool.add() - Didn't return expected position&quot;);</a>
+<a name="440"><span class="lineNum">     440 </span>            :     EXPECT(pool.getAlignment() == 8,</a>
+<a name="441"><span class="lineNum">     441 </span>            :       &quot;pool.getAlignment() - Expected 8-byte alignment&quot;);</a>
+<a name="442"><span class="lineNum">     442 </span>            :   }</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            :   INFO(&quot;Adding 8 byte constant to check if pool gets aligned again&quot;);</a>
+<a name="445"><span class="lineNum">     445 </span>            :   {</a>
+<a name="446"><span class="lineNum">     446 </span>            :     uint64_t c = ASMJIT_UINT64_C(0xFFFFFFFFFFFFFFFF);</a>
+<a name="447"><span class="lineNum">     447 </span>            :     size_t offset;</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            :     EXPECT(pool.add(&amp;c, 8, offset) == kErrorOk,</a>
+<a name="450"><span class="lineNum">     450 </span>            :       &quot;pool.add() - Returned error&quot;);</a>
+<a name="451"><span class="lineNum">     451 </span>            :     EXPECT(offset == kCount * 8 + 8,</a>
+<a name="452"><span class="lineNum">     452 </span>            :       &quot;pool.add() - Didn't return aligned offset&quot;);</a>
+<a name="453"><span class="lineNum">     453 </span>            :   }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            :   INFO(&quot;Adding 2 byte constant to verify the gap is filled&quot;);</a>
+<a name="456"><span class="lineNum">     456 </span>            :   {</a>
+<a name="457"><span class="lineNum">     457 </span>            :     uint16_t c = 0xFFFE;</a>
+<a name="458"><span class="lineNum">     458 </span>            :     size_t offset;</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :     EXPECT(pool.add(&amp;c, 2, offset) == kErrorOk,</a>
+<a name="461"><span class="lineNum">     461 </span>            :       &quot;pool.add() - Returned error&quot;);</a>
+<a name="462"><span class="lineNum">     462 </span>            :     EXPECT(offset == kCount * 8 + 2,</a>
+<a name="463"><span class="lineNum">     463 </span>            :       &quot;pool.add() - Didn't fill the gap&quot;);</a>
+<a name="464"><span class="lineNum">     464 </span>            :     EXPECT(pool.getAlignment() == 8,</a>
+<a name="465"><span class="lineNum">     465 </span>            :       &quot;pool.getAlignment() - Expected 8-byte alignment&quot;);</a>
+<a name="466"><span class="lineNum">     466 </span>            :   }</a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   INFO(&quot;Checking reset functionality&quot;);</a>
+<a name="469"><span class="lineNum">     469 </span>            :   {</a>
+<a name="470"><span class="lineNum">     470 </span>            :     pool.reset(&amp;zone);</a>
+<a name="471"><span class="lineNum">     471 </span>            :     zone.reset();</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            :     EXPECT(pool.getSize() == 0,</a>
+<a name="474"><span class="lineNum">     474 </span>            :       &quot;pool.getSize() - Expected pool size to be zero&quot;);</a>
+<a name="475"><span class="lineNum">     475 </span>            :     EXPECT(pool.getAlignment() == 0,</a>
+<a name="476"><span class="lineNum">     476 </span>            :       &quot;pool.getSize() - Expected pool alignment to be zero&quot;);</a>
+<a name="477"><span class="lineNum">     477 </span>            :   }</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            :   INFO(&quot;Checking pool alignment when combined constants are added&quot;);</a>
+<a name="480"><span class="lineNum">     480 </span>            :   {</a>
+<a name="481"><span class="lineNum">     481 </span>            :     uint8_t bytes[32] = { 0 };</a>
+<a name="482"><span class="lineNum">     482 </span>            :     size_t offset;</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :     pool.add(bytes, 1, offset);</a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span>            :     EXPECT(pool.getSize() == 1,</a>
+<a name="487"><span class="lineNum">     487 </span>            :       &quot;pool.getSize() - Expected pool size to be 1 byte&quot;);</a>
+<a name="488"><span class="lineNum">     488 </span>            :     EXPECT(pool.getAlignment() == 1,</a>
+<a name="489"><span class="lineNum">     489 </span>            :       &quot;pool.getSize() - Expected pool alignment to be 1 byte&quot;);</a>
+<a name="490"><span class="lineNum">     490 </span>            :     EXPECT(offset == 0,</a>
+<a name="491"><span class="lineNum">     491 </span>            :       &quot;pool.getSize() - Expected offset returned to be zero&quot;);</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            :     pool.add(bytes, 2, offset);</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :     EXPECT(pool.getSize() == 4,</a>
+<a name="496"><span class="lineNum">     496 </span>            :       &quot;pool.getSize() - Expected pool size to be 4 bytes&quot;);</a>
+<a name="497"><span class="lineNum">     497 </span>            :     EXPECT(pool.getAlignment() == 2,</a>
+<a name="498"><span class="lineNum">     498 </span>            :       &quot;pool.getSize() - Expected pool alignment to be 2 bytes&quot;);</a>
+<a name="499"><span class="lineNum">     499 </span>            :     EXPECT(offset == 2,</a>
+<a name="500"><span class="lineNum">     500 </span>            :       &quot;pool.getSize() - Expected offset returned to be 2&quot;);</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            :     pool.add(bytes, 4, offset);</a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span>            :     EXPECT(pool.getSize() == 8,</a>
+<a name="505"><span class="lineNum">     505 </span>            :       &quot;pool.getSize() - Expected pool size to be 8 bytes&quot;);</a>
+<a name="506"><span class="lineNum">     506 </span>            :     EXPECT(pool.getAlignment() == 4,</a>
+<a name="507"><span class="lineNum">     507 </span>            :       &quot;pool.getSize() - Expected pool alignment to be 4 bytes&quot;);</a>
+<a name="508"><span class="lineNum">     508 </span>            :     EXPECT(offset == 4,</a>
+<a name="509"><span class="lineNum">     509 </span>            :       &quot;pool.getSize() - Expected offset returned to be 4&quot;);</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            :     pool.add(bytes, 4, offset);</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span>            :     EXPECT(pool.getSize() == 8,</a>
+<a name="514"><span class="lineNum">     514 </span>            :       &quot;pool.getSize() - Expected pool size to be 8 bytes&quot;);</a>
+<a name="515"><span class="lineNum">     515 </span>            :     EXPECT(pool.getAlignment() == 4,</a>
+<a name="516"><span class="lineNum">     516 </span>            :       &quot;pool.getSize() - Expected pool alignment to be 4 bytes&quot;);</a>
+<a name="517"><span class="lineNum">     517 </span>            :     EXPECT(offset == 4,</a>
+<a name="518"><span class="lineNum">     518 </span>            :       &quot;pool.getSize() - Expected offset returned to be 8&quot;);</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            :     pool.add(bytes, 32, offset);</a>
+<a name="521"><span class="lineNum">     521 </span>            :     EXPECT(pool.getSize() == 64,</a>
+<a name="522"><span class="lineNum">     522 </span>            :       &quot;pool.getSize() - Expected pool size to be 64 bytes&quot;);</a>
+<a name="523"><span class="lineNum">     523 </span>            :     EXPECT(pool.getAlignment() == 32,</a>
+<a name="524"><span class="lineNum">     524 </span>            :       &quot;pool.getSize() - Expected pool alignment to be 32 bytes&quot;);</a>
+<a name="525"><span class="lineNum">     525 </span>            :     EXPECT(offset == 32,</a>
+<a name="526"><span class="lineNum">     526 </span>            :       &quot;pool.getSize() - Expected offset returned to be 32&quot;);</a>
+<a name="527"><span class="lineNum">     527 </span>            :   }</a>
+<a name="528"><span class="lineNum">     528 </span>            : }</a>
+<a name="529"><span class="lineNum">     529 </span>            : #endif // ASMJIT_TEST</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            : } // asmjit namespace</a>
+<a name="532"><span class="lineNum">     532 </span>            : } // namespace PLMD</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            : // [Api-End]</a>
+<a name="535"><span class="lineNum">     535 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="536"><span class="lineNum">     536 </span>            : #pragma GCC diagnostic pop</a>
+<a name="537"><span class="lineNum">     537 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/constpool.h.func-sort-c.html b/coverage-libs/asmjit/constpool.h.func-sort-c.html
new file mode 100644
index 0000000000..8bd312855a
--- /dev/null
+++ b/coverage-libs/asmjit/constpool.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/constpool.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - constpool.h<span style="font-size: 80%;"> (<a href="constpool.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="constpool.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/constpool.h.func.html b/coverage-libs/asmjit/constpool.h.func.html
new file mode 100644
index 0000000000..5843700720
--- /dev/null
+++ b/coverage-libs/asmjit/constpool.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/constpool.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - constpool.h<span style="font-size: 80%;"> (<a href="constpool.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="constpool.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/constpool.h.gcov.html b/coverage-libs/asmjit/constpool.h.gcov.html
new file mode 100644
index 0000000000..dbc41592e0
--- /dev/null
+++ b/coverage-libs/asmjit/constpool.h.gcov.html
@@ -0,0 +1,362 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/constpool.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - constpool.h<span style="font-size: 80%;"> (source / <a href="constpool.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_constpool_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_constpool_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_CONSTPOOL_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_CONSTPOOL_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./zone.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::ConstPool]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! Constant pool.</a>
+<a name="52"><span class="lineNum">      52 </span>            : class ConstPool {</a>
+<a name="53"><span class="lineNum">      53 </span>            : public:</a>
+<a name="54"><span class="lineNum">      54 </span>            :   ASMJIT_NONCOPYABLE(ConstPool)</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   enum {</a>
+<a name="57"><span class="lineNum">      57 </span>            :     kIndex1 = 0,</a>
+<a name="58"><span class="lineNum">      58 </span>            :     kIndex2 = 1,</a>
+<a name="59"><span class="lineNum">      59 </span>            :     kIndex4 = 2,</a>
+<a name="60"><span class="lineNum">      60 </span>            :     kIndex8 = 3,</a>
+<a name="61"><span class="lineNum">      61 </span>            :     kIndex16 = 4,</a>
+<a name="62"><span class="lineNum">      62 </span>            :     kIndex32 = 5,</a>
+<a name="63"><span class="lineNum">      63 </span>            :     kIndexCount = 6</a>
+<a name="64"><span class="lineNum">      64 </span>            :   };</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="67"><span class="lineNum">      67 </span>            :   // [Gap]</a>
+<a name="68"><span class="lineNum">      68 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   //! \internal</a>
+<a name="71"><span class="lineNum">      71 </span>            :   //!</a>
+<a name="72"><span class="lineNum">      72 </span>            :   //! Zone-allocated const-pool gap.</a>
+<a name="73"><span class="lineNum">      73 </span>            :   struct Gap {</a>
+<a name="74"><span class="lineNum">      74 </span>            :     Gap* _next;                          //!&lt; Pointer to the next gap</a>
+<a name="75"><span class="lineNum">      75 </span>            :     size_t _offset;                      //!&lt; Offset of the gap.</a>
+<a name="76"><span class="lineNum">      76 </span>            :     size_t _length;                      //!&lt; Remaining bytes of the gap (basically a gap size).</a>
+<a name="77"><span class="lineNum">      77 </span>            :   };</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="80"><span class="lineNum">      80 </span>            :   // [Node]</a>
+<a name="81"><span class="lineNum">      81 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   //! \internal</a>
+<a name="84"><span class="lineNum">      84 </span>            :   //!</a>
+<a name="85"><span class="lineNum">      85 </span>            :   //! Zone-allocated const-pool node.</a>
+<a name="86"><span class="lineNum">      86 </span>            :   struct Node {</a>
+<a name="87"><span class="lineNum">      87 </span>            :     ASMJIT_INLINE void* getData() const noexcept {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :       return static_cast&lt;void*&gt;(const_cast&lt;ConstPool::Node*&gt;(this) + 1);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :     Node* _link[2];                      //!&lt; Left/Right nodes.</a>
+<a name="92"><span class="lineNum">      92 </span>            :     uint32_t _level : 31;                //!&lt; Horizontal level for balance.</a>
+<a name="93"><span class="lineNum">      93 </span>            :     uint32_t _shared : 1;                //!&lt; If this constant is shared with another.</a>
+<a name="94"><span class="lineNum">      94 </span>            :     uint32_t _offset;                    //!&lt; Data offset from the beginning of the pool.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="98"><span class="lineNum">      98 </span>            :   // [Tree]</a>
+<a name="99"><span class="lineNum">      99 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   //! \internal</a>
+<a name="102"><span class="lineNum">     102 </span>            :   //!</a>
+<a name="103"><span class="lineNum">     103 </span>            :   //! Zone-allocated const-pool tree.</a>
+<a name="104"><span class="lineNum">     104 </span>            :   struct Tree {</a>
+<a name="105"><span class="lineNum">     105 </span>            :     enum {</a>
+<a name="106"><span class="lineNum">     106 </span>            :       //! Maximum tree height == log2(1 &lt;&lt; 64).</a>
+<a name="107"><span class="lineNum">     107 </span>            :       kHeightLimit = 64</a>
+<a name="108"><span class="lineNum">     108 </span>            :     };</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="111"><span class="lineNum">     111 </span>            :     // [Construction / Destruction]</a>
+<a name="112"><span class="lineNum">     112 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :     ASMJIT_INLINE Tree(size_t dataSize = 0) noexcept</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :       : _root(nullptr),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :         _length(0),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :         _dataSize(dataSize) {}</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE ~Tree() {}</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="121"><span class="lineNum">     121 </span>            :     // [Reset]</a>
+<a name="122"><span class="lineNum">     122 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :     ASMJIT_INLINE void reset() noexcept {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :       _root = nullptr;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :       _length = 0;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="130"><span class="lineNum">     130 </span>            :     // [Accessors]</a>
+<a name="131"><span class="lineNum">     131 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :     ASMJIT_INLINE bool isEmpty() const noexcept { return _length == 0; }</a>
+<a name="134"><span class="lineNum">     134 </span>            :     ASMJIT_INLINE size_t getLength() const noexcept { return _length; }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :     ASMJIT_INLINE void setDataSize(size_t dataSize) noexcept {</a>
+<a name="137"><span class="lineNum">     137 </span>            :       ASMJIT_ASSERT(isEmpty());</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :       _dataSize = dataSize;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="142"><span class="lineNum">     142 </span>            :     // [Ops]</a>
+<a name="143"><span class="lineNum">     143 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :     ASMJIT_API Node* get(const void* data) noexcept;</a>
+<a name="146"><span class="lineNum">     146 </span>            :     ASMJIT_API void put(Node* node) noexcept;</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="149"><span class="lineNum">     149 </span>            :     // [Iterate]</a>
+<a name="150"><span class="lineNum">     150 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :     template&lt;typename Visitor&gt;</a>
+<a name="153"><span class="lineNum">     153 </span>            :     ASMJIT_INLINE void iterate(Visitor&amp; visitor) const noexcept {</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :       Node* node = const_cast&lt;Node*&gt;(_root);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :       if (!node) return;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :       Node* stack[kHeightLimit];</a>
+<a name="158"><span class="lineNum">     158 </span>            :       size_t top = 0;</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :       for (;;) {</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :         Node* left = node-&gt;_link[0];</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :         if (left != nullptr) {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :           ASMJIT_ASSERT(top != kHeightLimit);</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :           stack[top++] = node;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :           node = left;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :         }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 : Visit:</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :         visitor.visit(node);</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :         node = node-&gt;_link[1];</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :         if (node != nullptr)</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :         if (top == 0)</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :           return;</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :         node = stack[--top];</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :         goto Visit;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :       }</a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="185"><span class="lineNum">     185 </span>            :     // [Helpers]</a>
+<a name="186"><span class="lineNum">     186 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :     static ASMJIT_INLINE Node* _newNode(Zone* zone, const void* data, size_t size, size_t offset, bool shared) noexcept {</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :       Node* node = zone-&gt;allocT&lt;Node&gt;(sizeof(Node) + size);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!node)) return nullptr;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :       node-&gt;_link[0] = nullptr;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :       node-&gt;_link[1] = nullptr;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :       node-&gt;_level = 1;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :       node-&gt;_shared = shared;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       node-&gt;_offset = static_cast&lt;uint32_t&gt;(offset);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :       ::memcpy(node-&gt;getData(), data, size);</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :       return node;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="203"><span class="lineNum">     203 </span>            :     // [Members]</a>
+<a name="204"><span class="lineNum">     204 </span>            :     // --------------------------------------------------------------------------</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :     Node* _root;                         //!&lt; Root of the tree</a>
+<a name="207"><span class="lineNum">     207 </span>            :     size_t _length;                      //!&lt; Length of the tree (count of nodes).</a>
+<a name="208"><span class="lineNum">     208 </span>            :     size_t _dataSize;                    //!&lt; Size of the data.</a>
+<a name="209"><span class="lineNum">     209 </span>            :   };</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="212"><span class="lineNum">     212 </span>            :   // [Construction / Destruction]</a>
+<a name="213"><span class="lineNum">     213 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   ASMJIT_API ConstPool(Zone* zone) noexcept;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   ASMJIT_API ~ConstPool() noexcept;</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // [Reset]</a>
+<a name="220"><span class="lineNum">     220 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   ASMJIT_API void reset(Zone* zone) noexcept;</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="225"><span class="lineNum">     225 </span>            :   // [Ops]</a>
+<a name="226"><span class="lineNum">     226 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   //! Get whether the constant-pool is empty.</a>
+<a name="229"><span class="lineNum">     229 </span>            :   ASMJIT_INLINE bool isEmpty() const noexcept { return _size == 0; }</a>
+<a name="230"><span class="lineNum">     230 </span>            :   //! Get the size of the constant-pool in bytes.</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE size_t getSize() const noexcept { return _size; }</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   //! Get minimum alignment.</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE size_t getAlignment() const noexcept { return _alignment; }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   //! Add a constant to the constant pool.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   //!</a>
+<a name="237"><span class="lineNum">     237 </span>            :   //! The constant must have known size, which is 1, 2, 4, 8, 16 or 32 bytes.</a>
+<a name="238"><span class="lineNum">     238 </span>            :   //! The constant is added to the pool only if it doesn't not exist, otherwise</a>
+<a name="239"><span class="lineNum">     239 </span>            :   //! cached value is returned.</a>
+<a name="240"><span class="lineNum">     240 </span>            :   //!</a>
+<a name="241"><span class="lineNum">     241 </span>            :   //! AsmJit is able to subdivide added constants, so for example if you add</a>
+<a name="242"><span class="lineNum">     242 </span>            :   //! 8-byte constant 0x1122334455667788 it will create the following slots:</a>
+<a name="243"><span class="lineNum">     243 </span>            :   //!</a>
+<a name="244"><span class="lineNum">     244 </span>            :   //!   8-byte: 0x1122334455667788</a>
+<a name="245"><span class="lineNum">     245 </span>            :   //!   4-byte: 0x11223344, 0x55667788</a>
+<a name="246"><span class="lineNum">     246 </span>            :   //!</a>
+<a name="247"><span class="lineNum">     247 </span>            :   //! The reason is that when combining MMX/SSE/AVX code some patterns are used</a>
+<a name="248"><span class="lineNum">     248 </span>            :   //! frequently. However, AsmJit is not able to reallocate a constant that has</a>
+<a name="249"><span class="lineNum">     249 </span>            :   //! been already added. For example if you try to add 4-byte constant and then</a>
+<a name="250"><span class="lineNum">     250 </span>            :   //! 8-byte constant having the same 4-byte pattern as the previous one, two</a>
+<a name="251"><span class="lineNum">     251 </span>            :   //! independent slots will be generated by the pool.</a>
+<a name="252"><span class="lineNum">     252 </span>            :   ASMJIT_API Error add(const void* data, size_t size, size_t&amp; dstOffset) noexcept;</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="255"><span class="lineNum">     255 </span>            :   // [Fill]</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   //! Fill the destination with the constants from the pool.</a>
+<a name="259"><span class="lineNum">     259 </span>            :   ASMJIT_API void fill(void* dst) const noexcept;</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="262"><span class="lineNum">     262 </span>            :   // [Members]</a>
+<a name="263"><span class="lineNum">     263 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   Zone* _zone;                           //!&lt; Zone allocator.</a>
+<a name="266"><span class="lineNum">     266 </span>            :   Tree _tree[kIndexCount];               //!&lt; Tree per size.</a>
+<a name="267"><span class="lineNum">     267 </span>            :   Gap* _gaps[kIndexCount];               //!&lt; Gaps per size.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   Gap* _gapPool;                         //!&lt; Gaps pool</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   size_t _size;                          //!&lt; Size of the pool (in bytes).</a>
+<a name="271"><span class="lineNum">     271 </span>            :   size_t _alignment;                     //!&lt; Required pool alignment.</a>
+<a name="272"><span class="lineNum">     272 </span>            : };</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : //! \}</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : } // asmjit namespace</a>
+<a name="277"><span class="lineNum">     277 </span>            : } // namespace PLMD</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : // [Api-End]</a>
+<a name="280"><span class="lineNum">     280 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            : // [Guard]</a>
+<a name="283"><span class="lineNum">     283 </span>            : #endif // _ASMJIT_BASE_CONSTPOOL_H</a>
+<a name="284"><span class="lineNum">     284 </span>            : #pragma GCC diagnostic pop</a>
+<a name="285"><span class="lineNum">     285 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="286"><span class="lineNum">     286 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/cpuinfo.cpp.func-sort-c.html b/coverage-libs/asmjit/cpuinfo.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c0d8151355
--- /dev/null
+++ b/coverage-libs/asmjit/cpuinfo.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/cpuinfo.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - cpuinfo.cpp<span style="font-size: 80%;"> (<a href="cpuinfo.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">137</td>
+            <td class="headerCovTableEntry">149</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="cpuinfo.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="cpuinfo.cpp.gcov.html#665">_ZN4PLMD6asmjit7CpuInfo6detectEv</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="cpuinfo.cpp.gcov.html#409">_ZN4PLMD6asmjitL16x86DetectCpuInfoEPNS0_7CpuInfoE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="cpuinfo.cpp.gcov.html#687">_ZN4PLMD6asmjit7CpuInfo7getHostEv</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/cpuinfo.cpp.func.html b/coverage-libs/asmjit/cpuinfo.cpp.func.html
new file mode 100644
index 0000000000..890e516451
--- /dev/null
+++ b/coverage-libs/asmjit/cpuinfo.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/cpuinfo.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - cpuinfo.cpp<span style="font-size: 80%;"> (<a href="cpuinfo.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">137</td>
+            <td class="headerCovTableEntry">149</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="cpuinfo.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="cpuinfo.cpp.gcov.html#665">_ZN4PLMD6asmjit7CpuInfo6detectEv</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="cpuinfo.cpp.gcov.html#687">_ZN4PLMD6asmjit7CpuInfo7getHostEv</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="cpuinfo.cpp.gcov.html#409">_ZN4PLMD6asmjitL16x86DetectCpuInfoEPNS0_7CpuInfoE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/cpuinfo.cpp.gcov.html b/coverage-libs/asmjit/cpuinfo.cpp.gcov.html
new file mode 100644
index 0000000000..876d374362
--- /dev/null
+++ b/coverage-libs/asmjit/cpuinfo.cpp.gcov.html
@@ -0,0 +1,776 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/cpuinfo.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - cpuinfo.cpp<span style="font-size: 80%;"> (source / <a href="cpuinfo.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">137</td>
+            <td class="headerCovTableEntry">149</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #if ASMJIT_OS_POSIX</a>
+<a name="37"><span class="lineNum">      37 </span>            : # include &lt;errno.h&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : # include &lt;sys/utsname.h&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : # include &lt;unistd.h&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #endif // ASMJIT_OS_POSIX</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : #if ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="43"><span class="lineNum">      43 </span>            : # if ASMJIT_CC_MSC_GE(14, 0, 0)</a>
+<a name="44"><span class="lineNum">      44 </span>            :  # include &lt;intrin.h&gt;         // Required by `__cpuid()` and `_xgetbv()`.</a>
+<a name="45"><span class="lineNum">      45 </span>            : # endif // _MSC_VER &gt;= 1400</a>
+<a name="46"><span class="lineNum">      46 </span>            : #endif</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : #if ASMJIT_ARCH_ARM32 || ASMJIT_ARCH_ARM64</a>
+<a name="49"><span class="lineNum">      49 </span>            : # if ASMJIT_OS_LINUX</a>
+<a name="50"><span class="lineNum">      50 </span>            : #  include &lt;sys/auxv.h&gt;       // Required by `getauxval()`.</a>
+<a name="51"><span class="lineNum">      51 </span>            : # endif</a>
+<a name="52"><span class="lineNum">      52 </span>            : #endif</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : // [Api-Begin]</a>
+<a name="55"><span class="lineNum">      55 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : namespace PLMD {</a>
+<a name="58"><span class="lineNum">      58 </span>            : namespace asmjit {</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : // ============================================================================</a>
+<a name="61"><span class="lineNum">      61 </span>            : // [asmjit::CpuInfo - Detect ARM]</a>
+<a name="62"><span class="lineNum">      62 </span>            : // ============================================================================</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : // ARM information has to be retrieved by the OS (this is how ARM was designed).</a>
+<a name="65"><span class="lineNum">      65 </span>            : #if ASMJIT_ARCH_ARM32 || ASMJIT_ARCH_ARM64</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : #if ASMJIT_ARCH_ARM32</a>
+<a name="68"><span class="lineNum">      68 </span>            : static ASMJIT_INLINE void armPopulateBaselineA32Features(CpuInfo* cpuInfo) noexcept {</a>
+<a name="69"><span class="lineNum">      69 </span>            :   cpuInfo-&gt;_archInfo.init(ArchInfo::kTypeA32);</a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : #endif // ASMJIT_ARCH_ARM32</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : #if ASMJIT_ARCH_ARM64</a>
+<a name="74"><span class="lineNum">      74 </span>            : static ASMJIT_INLINE void armPopulateBaselineA64Features(CpuInfo* cpuInfo) noexcept {</a>
+<a name="75"><span class="lineNum">      75 </span>            :   cpuInfo-&gt;_archInfo.init(ArchInfo::kTypeA64);</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :   // Thumb (including all variations) is supported on A64 (but not accessible from A64).</a>
+<a name="78"><span class="lineNum">      78 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureTHUMB);</a>
+<a name="79"><span class="lineNum">      79 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureTHUMB2);</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   // A64 is based on ARMv8 and newer.</a>
+<a name="82"><span class="lineNum">      82 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV6);</a>
+<a name="83"><span class="lineNum">      83 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV7);</a>
+<a name="84"><span class="lineNum">      84 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV8);</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   // A64 comes with these features by default.</a>
+<a name="87"><span class="lineNum">      87 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureVFPv2);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureVFPv3);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureVFPv4);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureEDSP);</a>
+<a name="91"><span class="lineNum">      91 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureASIMD);</a>
+<a name="92"><span class="lineNum">      92 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureIDIVA);</a>
+<a name="93"><span class="lineNum">      93 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureIDIVT);</a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : #endif // ASMJIT_ARCH_ARM64</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="98"><span class="lineNum">      98 </span>            : //! \internal</a>
+<a name="99"><span class="lineNum">      99 </span>            : //!</a>
+<a name="100"><span class="lineNum">     100 </span>            : //! Detect ARM CPU features on Windows.</a>
+<a name="101"><span class="lineNum">     101 </span>            : //!</a>
+<a name="102"><span class="lineNum">     102 </span>            : //! The detection is based on `IsProcessorFeaturePresent()` API call.</a>
+<a name="103"><span class="lineNum">     103 </span>            : static ASMJIT_INLINE void armDetectCpuInfoOnWindows(CpuInfo* cpuInfo) noexcept {</a>
+<a name="104"><span class="lineNum">     104 </span>            : #if ASMJIT_ARCH_ARM32</a>
+<a name="105"><span class="lineNum">     105 </span>            :   armPopulateBaselineA32Features(cpuInfo);</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   // Windows for ARM requires at least ARMv7 with DSP extensions.</a>
+<a name="108"><span class="lineNum">     108 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV6);</a>
+<a name="109"><span class="lineNum">     109 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV7);</a>
+<a name="110"><span class="lineNum">     110 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureEDSP);</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   // Windows for ARM requires VFPv3.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureVFPv2);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureVFPv3);</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   // Windows for ARM requires and uses THUMB2.</a>
+<a name="117"><span class="lineNum">     117 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureTHUMB);</a>
+<a name="118"><span class="lineNum">     118 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureTHUMB2);</a>
+<a name="119"><span class="lineNum">     119 </span>            : #else</a>
+<a name="120"><span class="lineNum">     120 </span>            :   armPopulateBaselineA64Features(cpuInfo);</a>
+<a name="121"><span class="lineNum">     121 </span>            : #endif</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   // Windows for ARM requires ASIMD.</a>
+<a name="124"><span class="lineNum">     124 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureASIMD);</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   // Detect additional CPU features by calling `IsProcessorFeaturePresent()`.</a>
+<a name="127"><span class="lineNum">     127 </span>            :   struct WinPFPMapping {</a>
+<a name="128"><span class="lineNum">     128 </span>            :     uint32_t pfpId;</a>
+<a name="129"><span class="lineNum">     129 </span>            :     uint32_t featureId;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   };</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   static const WinPFPMapping mapping[] = {</a>
+<a name="133"><span class="lineNum">     133 </span>            :     { PF_ARM_FMAC_INSTRUCTIONS_AVAILABLE , CpuInfo::kArmFeatureVFPv4     },</a>
+<a name="134"><span class="lineNum">     134 </span>            :     { PF_ARM_VFP_32_REGISTERS_AVAILABLE  , CpuInfo::kArmFeatureVFP_D32   },</a>
+<a name="135"><span class="lineNum">     135 </span>            :     { PF_ARM_DIVIDE_INSTRUCTION_AVAILABLE, CpuInfo::kArmFeatureIDIVT     },</a>
+<a name="136"><span class="lineNum">     136 </span>            :     { PF_ARM_64BIT_LOADSTORE_ATOMIC      , CpuInfo::kArmFeatureAtomics64 }</a>
+<a name="137"><span class="lineNum">     137 </span>            :   };</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   for (uint32_t i = 0; i &lt; ASMJIT_ARRAY_SIZE(mapping); i++)</a>
+<a name="140"><span class="lineNum">     140 </span>            :     if (::IsProcessorFeaturePresent(mapping[i].pfpId))</a>
+<a name="141"><span class="lineNum">     141 </span>            :       cpuInfo-&gt;addFeature(mapping[i].featureId);</a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : #if ASMJIT_OS_LINUX</a>
+<a name="146"><span class="lineNum">     146 </span>            : struct LinuxHWCapMapping {</a>
+<a name="147"><span class="lineNum">     147 </span>            :   uint32_t hwcapMask;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   uint32_t featureId;</a>
+<a name="149"><span class="lineNum">     149 </span>            : };</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : static void armDetectHWCaps(CpuInfo* cpuInfo, unsigned long type, const LinuxHWCapMapping* mapping, size_t length) noexcept {</a>
+<a name="152"><span class="lineNum">     152 </span>            :   unsigned long mask = getauxval(type);</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   for (size_t i = 0; i &lt; length; i++)</a>
+<a name="155"><span class="lineNum">     155 </span>            :     if ((mask &amp; mapping[i].hwcapMask) == mapping[i].hwcapMask)</a>
+<a name="156"><span class="lineNum">     156 </span>            :       cpuInfo-&gt;addFeature(mapping[i].featureId);</a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : //! \internal</a>
+<a name="160"><span class="lineNum">     160 </span>            : //!</a>
+<a name="161"><span class="lineNum">     161 </span>            : //! Detect ARM CPU features on Linux.</a>
+<a name="162"><span class="lineNum">     162 </span>            : //!</a>
+<a name="163"><span class="lineNum">     163 </span>            : //! The detection is based on `getauxval()`.</a>
+<a name="164"><span class="lineNum">     164 </span>            : ASMJIT_FAVOR_SIZE static void armDetectCpuInfoOnLinux(CpuInfo* cpuInfo) noexcept {</a>
+<a name="165"><span class="lineNum">     165 </span>            : #if ASMJIT_ARCH_ARM32</a>
+<a name="166"><span class="lineNum">     166 </span>            :   armPopulateBaselineA32Features(cpuInfo);</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   // `AT_HWCAP` provides ARMv7 (and less) related flags.</a>
+<a name="169"><span class="lineNum">     169 </span>            :   static const LinuxHWCapMapping hwCapMapping[] = {</a>
+<a name="170"><span class="lineNum">     170 </span>            :     { /* HWCAP_VFP     */ (1 &lt;&lt;  6), CpuInfo::kArmFeatureVFPv2     },</a>
+<a name="171"><span class="lineNum">     171 </span>            :     { /* HWCAP_EDSP    */ (1 &lt;&lt;  7), CpuInfo::kArmFeatureEDSP      },</a>
+<a name="172"><span class="lineNum">     172 </span>            :     { /* HWCAP_NEON    */ (1 &lt;&lt; 12), CpuInfo::kArmFeatureASIMD     },</a>
+<a name="173"><span class="lineNum">     173 </span>            :     { /* HWCAP_VFPv3   */ (1 &lt;&lt; 13), CpuInfo::kArmFeatureVFPv3     },</a>
+<a name="174"><span class="lineNum">     174 </span>            :     { /* HWCAP_VFPv4   */ (1 &lt;&lt; 16), CpuInfo::kArmFeatureVFPv4     },</a>
+<a name="175"><span class="lineNum">     175 </span>            :     { /* HWCAP_IDIVA   */ (1 &lt;&lt; 17), CpuInfo::kArmFeatureIDIVA     },</a>
+<a name="176"><span class="lineNum">     176 </span>            :     { /* HWCAP_IDIVT   */ (1 &lt;&lt; 18), CpuInfo::kArmFeatureIDIVT     },</a>
+<a name="177"><span class="lineNum">     177 </span>            :     { /* HWCAP_VFPD32  */ (1 &lt;&lt; 19), CpuInfo::kArmFeatureVFP_D32   }</a>
+<a name="178"><span class="lineNum">     178 </span>            :   };</a>
+<a name="179"><span class="lineNum">     179 </span>            :   armDetectHWCaps(cpuInfo, AT_HWCAP, hwCapMapping, ASMJIT_ARRAY_SIZE(hwCapMapping));</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   // VFPv3 implies VFPv2.</a>
+<a name="182"><span class="lineNum">     182 </span>            :   if (cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureVFPv3)) {</a>
+<a name="183"><span class="lineNum">     183 </span>            :     cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureVFPv2);</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // VFPv2 implies ARMv6.</a>
+<a name="187"><span class="lineNum">     187 </span>            :   if (cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureVFPv2)) {</a>
+<a name="188"><span class="lineNum">     188 </span>            :     cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV6);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // VFPv3 or ASIMD implies ARMv7.</a>
+<a name="192"><span class="lineNum">     192 </span>            :   if (cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureVFPv3) ||</a>
+<a name="193"><span class="lineNum">     193 </span>            :       cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureASIMD)) {</a>
+<a name="194"><span class="lineNum">     194 </span>            :     cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV7);</a>
+<a name="195"><span class="lineNum">     195 </span>            :   }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   // `AT_HWCAP2` provides ARMv8+ related flags.</a>
+<a name="198"><span class="lineNum">     198 </span>            :   static const LinuxHWCapMapping hwCap2Mapping[] = {</a>
+<a name="199"><span class="lineNum">     199 </span>            :     { /* HWCAP2_AES    */ (1 &lt;&lt;  0), CpuInfo::kArmFeatureAES       },</a>
+<a name="200"><span class="lineNum">     200 </span>            :     { /* HWCAP2_PMULL  */ (1 &lt;&lt;  1), CpuInfo::kArmFeaturePMULL     },</a>
+<a name="201"><span class="lineNum">     201 </span>            :     { /* HWCAP2_SHA1   */ (1 &lt;&lt;  2), CpuInfo::kArmFeatureSHA1      },</a>
+<a name="202"><span class="lineNum">     202 </span>            :     { /* HWCAP2_SHA2   */ (1 &lt;&lt;  3), CpuInfo::kArmFeatureSHA256    },</a>
+<a name="203"><span class="lineNum">     203 </span>            :     { /* HWCAP2_CRC32  */ (1 &lt;&lt;  4), CpuInfo::kArmFeatureCRC32     }</a>
+<a name="204"><span class="lineNum">     204 </span>            :   };</a>
+<a name="205"><span class="lineNum">     205 </span>            :   armDetectHWCaps(cpuInfo, AT_HWCAP2, hwCap2Mapping, ASMJIT_ARRAY_SIZE(hwCap2Mapping));</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   if (cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureAES   ) ||</a>
+<a name="208"><span class="lineNum">     208 </span>            :       cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureCRC32 ) ||</a>
+<a name="209"><span class="lineNum">     209 </span>            :       cpuInfo-&gt;hasFeature(CpuInfo::kArmFeaturePMULL ) ||</a>
+<a name="210"><span class="lineNum">     210 </span>            :       cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureSHA1  ) ||</a>
+<a name="211"><span class="lineNum">     211 </span>            :       cpuInfo-&gt;hasFeature(CpuInfo::kArmFeatureSHA256)) {</a>
+<a name="212"><span class="lineNum">     212 </span>            :     cpuInfo-&gt;addFeature(CpuInfo::kArmFeatureV8);</a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span>            : #else</a>
+<a name="215"><span class="lineNum">     215 </span>            :   armPopulateBaselineA64Features(cpuInfo);</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // `AT_HWCAP` provides ARMv8+ related flags.</a>
+<a name="218"><span class="lineNum">     218 </span>            :   static const LinuxHWCapMapping hwCapMapping[] = {</a>
+<a name="219"><span class="lineNum">     219 </span>            :     { /* HWCAP_ASIMD   */ (1 &lt;&lt;  1), CpuInfo::kArmFeatureASIMD     },</a>
+<a name="220"><span class="lineNum">     220 </span>            :     { /* HWCAP_AES     */ (1 &lt;&lt;  3), CpuInfo::kArmFeatureAES       },</a>
+<a name="221"><span class="lineNum">     221 </span>            :     { /* HWCAP_CRC32   */ (1 &lt;&lt;  7), CpuInfo::kArmFeatureCRC32     },</a>
+<a name="222"><span class="lineNum">     222 </span>            :     { /* HWCAP_PMULL   */ (1 &lt;&lt;  4), CpuInfo::kArmFeaturePMULL     },</a>
+<a name="223"><span class="lineNum">     223 </span>            :     { /* HWCAP_SHA1    */ (1 &lt;&lt;  5), CpuInfo::kArmFeatureSHA1      },</a>
+<a name="224"><span class="lineNum">     224 </span>            :     { /* HWCAP_SHA2    */ (1 &lt;&lt;  6), CpuInfo::kArmFeatureSHA256    },</a>
+<a name="225"><span class="lineNum">     225 </span>            :     { /* HWCAP_ATOMICS */ (1 &lt;&lt;  8), CpuInfo::kArmFeatureAtomics64 }</a>
+<a name="226"><span class="lineNum">     226 </span>            :   };</a>
+<a name="227"><span class="lineNum">     227 </span>            :   armDetectHWCaps(cpuInfo, AT_HWCAP, hwCapMapping, ASMJIT_ARRAY_SIZE(hwCapMapping));</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :   // `AT_HWCAP2` is not used at the moment.</a>
+<a name="230"><span class="lineNum">     230 </span>            : #endif</a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : #endif // ASMJIT_OS_LINUX</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : ASMJIT_FAVOR_SIZE static void armDetectCpuInfo(CpuInfo* cpuInfo) noexcept {</a>
+<a name="235"><span class="lineNum">     235 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="236"><span class="lineNum">     236 </span>            :   armDetectCpuInfoOnWindows(cpuInfo);</a>
+<a name="237"><span class="lineNum">     237 </span>            : #elif ASMJIT_OS_LINUX</a>
+<a name="238"><span class="lineNum">     238 </span>            :   armDetectCpuInfoOnLinux(cpuInfo);</a>
+<a name="239"><span class="lineNum">     239 </span>            : #else</a>
+<a name="240"><span class="lineNum">     240 </span>            : # error &quot;[asmjit] armDetectCpuInfo() - Unsupported OS.&quot;</a>
+<a name="241"><span class="lineNum">     241 </span>            : #endif</a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : #endif // ASMJIT_ARCH_ARM32 || ASMJIT_ARCH_ARM64</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : // ============================================================================</a>
+<a name="246"><span class="lineNum">     246 </span>            : // [asmjit::CpuInfo - Detect X86]</a>
+<a name="247"><span class="lineNum">     247 </span>            : // ============================================================================</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : #if ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : //! \internal</a>
+<a name="252"><span class="lineNum">     252 </span>            : //!</a>
+<a name="253"><span class="lineNum">     253 </span>            : //! X86 CPUID result.</a>
+<a name="254"><span class="lineNum">     254 </span>            : struct CpuIdResult {</a>
+<a name="255"><span class="lineNum">     255 </span>            :   uint32_t eax, ebx, ecx, edx;</a>
+<a name="256"><span class="lineNum">     256 </span>            : };</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : //! \internal</a>
+<a name="259"><span class="lineNum">     259 </span>            : //!</a>
+<a name="260"><span class="lineNum">     260 </span>            : //! Content of XCR register, result of XGETBV instruction.</a>
+<a name="261"><span class="lineNum">     261 </span>            : struct XGetBVResult {</a>
+<a name="262"><span class="lineNum">     262 </span>            :   uint32_t eax, edx;</a>
+<a name="263"><span class="lineNum">     263 </span>            : };</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : #if ASMJIT_CC_MSC &amp;&amp; !ASMJIT_CC_MSC_GE(15, 0, 30729) &amp;&amp; ASMJIT_ARCH_X64</a>
+<a name="266"><span class="lineNum">     266 </span>            : //! \internal</a>
+<a name="267"><span class="lineNum">     267 </span>            : //!</a>
+<a name="268"><span class="lineNum">     268 </span>            : //! HACK: VS2008 or less, 64-bit mode - `__cpuidex` doesn't exist! However,</a>
+<a name="269"><span class="lineNum">     269 </span>            : //! 64-bit calling convention specifies the first parameter to be passed by</a>
+<a name="270"><span class="lineNum">     270 </span>            : //! ECX, so we may be lucky if compiler doesn't move the register, otherwise</a>
+<a name="271"><span class="lineNum">     271 </span>            : //! the result would be wrong.</a>
+<a name="272"><span class="lineNum">     272 </span>            : static void ASMJIT_NOINLINE void x86CallCpuIdWorkaround(uint32_t inEcx, uint32_t inEax, CpuIdResult* result) noexcept {</a>
+<a name="273"><span class="lineNum">     273 </span>            :   __cpuid(reinterpret_cast&lt;int*&gt;(result), inEax);</a>
+<a name="274"><span class="lineNum">     274 </span>            : }</a>
+<a name="275"><span class="lineNum">     275 </span>            : #endif</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            : //! \internal</a>
+<a name="278"><span class="lineNum">     278 </span>            : //!</a>
+<a name="279"><span class="lineNum">     279 </span>            : //! Wrapper to call `cpuid` instruction.</a>
+<a name="280"><span class="lineNum">     280 </span>            : static void ASMJIT_INLINE x86CallCpuId(CpuIdResult* result, uint32_t inEax, uint32_t inEcx = 0) noexcept {</a>
+<a name="281"><span class="lineNum">     281 </span>            : #if ASMJIT_CC_MSC &amp;&amp; ASMJIT_CC_MSC_GE(15, 0, 30729)</a>
+<a name="282"><span class="lineNum">     282 </span>            :   __cpuidex(reinterpret_cast&lt;int*&gt;(result), inEax, inEcx);</a>
+<a name="283"><span class="lineNum">     283 </span>            : #elif ASMJIT_CC_MSC &amp;&amp; ASMJIT_ARCH_X64</a>
+<a name="284"><span class="lineNum">     284 </span>            :   x86CallCpuIdWorkaround(inEcx, inEax, result);</a>
+<a name="285"><span class="lineNum">     285 </span>            : #elif ASMJIT_CC_MSC &amp;&amp; ASMJIT_ARCH_X86</a>
+<a name="286"><span class="lineNum">     286 </span>            :   uint32_t paramEax = inEax;</a>
+<a name="287"><span class="lineNum">     287 </span>            :   uint32_t paramEcx = inEcx;</a>
+<a name="288"><span class="lineNum">     288 </span>            :   uint32_t* out = reinterpret_cast&lt;uint32_t*&gt;(result);</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            :   __asm {</a>
+<a name="291"><span class="lineNum">     291 </span>            :     mov     eax, paramEax</a>
+<a name="292"><span class="lineNum">     292 </span>            :     mov     ecx, paramEcx</a>
+<a name="293"><span class="lineNum">     293 </span>            :     mov     edi, out</a>
+<a name="294"><span class="lineNum">     294 </span>            :     cpuid</a>
+<a name="295"><span class="lineNum">     295 </span>            :     mov     dword ptr[edi +  0], eax</a>
+<a name="296"><span class="lineNum">     296 </span>            :     mov     dword ptr[edi +  4], ebx</a>
+<a name="297"><span class="lineNum">     297 </span>            :     mov     dword ptr[edi +  8], ecx</a>
+<a name="298"><span class="lineNum">     298 </span>            :     mov     dword ptr[edi + 12], edx</a>
+<a name="299"><span class="lineNum">     299 </span>            :   }</a>
+<a name="300"><span class="lineNum">     300 </span>            : #elif (ASMJIT_CC_GCC || ASMJIT_CC_CLANG) &amp;&amp; ASMJIT_ARCH_X86</a>
+<a name="301"><span class="lineNum">     301 </span>            :   __asm__ __volatile__(</a>
+<a name="302"><span class="lineNum">     302 </span>            :     &quot;mov %%ebx, %%edi\n&quot;</a>
+<a name="303"><span class="lineNum">     303 </span>            :     &quot;cpuid\n&quot;</a>
+<a name="304"><span class="lineNum">     304 </span>            :     &quot;xchg %%edi, %%ebx\n&quot;</a>
+<a name="305"><span class="lineNum">     305 </span>            :       : &quot;=a&quot;(result-&gt;eax),</a>
+<a name="306"><span class="lineNum">     306 </span>            :         &quot;=D&quot;(result-&gt;ebx),</a>
+<a name="307"><span class="lineNum">     307 </span>            :         &quot;=c&quot;(result-&gt;ecx),</a>
+<a name="308"><span class="lineNum">     308 </span>            :         &quot;=d&quot;(result-&gt;edx)</a>
+<a name="309"><span class="lineNum">     309 </span>            :       : &quot;a&quot;(inEax),</a>
+<a name="310"><span class="lineNum">     310 </span>            :         &quot;c&quot;(inEcx));</a>
+<a name="311"><span class="lineNum">     311 </span>            : #elif (ASMJIT_CC_GCC || ASMJIT_CC_CLANG || ASMJIT_CC_INTEL) &amp;&amp; ASMJIT_ARCH_X64</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        770 :   __asm__ __volatile__(</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :     &quot;mov %%rbx, %%rdi\n&quot;</a>
+<a name="314"><span class="lineNum">     314 </span>            :     &quot;cpuid\n&quot;</a>
+<a name="315"><span class="lineNum">     315 </span>            :     &quot;xchg %%rdi, %%rbx\n&quot;</a>
+<a name="316"><span class="lineNum">     316 </span>            :       : &quot;=a&quot;(result-&gt;eax),</a>
+<a name="317"><span class="lineNum">     317 </span>            :         &quot;=D&quot;(result-&gt;ebx),</a>
+<a name="318"><span class="lineNum">     318 </span>            :         &quot;=c&quot;(result-&gt;ecx),</a>
+<a name="319"><span class="lineNum">     319 </span>            :         &quot;=d&quot;(result-&gt;edx)</a>
+<a name="320"><span class="lineNum">     320 </span>            :       : &quot;a&quot;(inEax),</a>
+<a name="321"><span class="lineNum">     321 </span>            :         &quot;c&quot;(inEcx));</a>
+<a name="322"><span class="lineNum">     322 </span>            : #else</a>
+<a name="323"><span class="lineNum">     323 </span>            : # error &quot;[asmjit] x86CallCpuid() - Unsupported compiler.&quot;</a>
+<a name="324"><span class="lineNum">     324 </span>            : #endif</a>
+<a name="325"><span class="lineNum">     325 </span>            : }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            : //! \internal</a>
+<a name="328"><span class="lineNum">     328 </span>            : //!</a>
+<a name="329"><span class="lineNum">     329 </span>            : //! Wrapper to call `xgetbv` instruction.</a>
+<a name="330"><span class="lineNum">     330 </span>            : static ASMJIT_INLINE void x86CallXGetBV(XGetBVResult* result, uint32_t inEcx) noexcept {</a>
+<a name="331"><span class="lineNum">     331 </span>            : #if ASMJIT_CC_MSC_GE(16, 0, 40219) // 2010SP1+</a>
+<a name="332"><span class="lineNum">     332 </span>            :   uint64_t value = _xgetbv(inEcx);</a>
+<a name="333"><span class="lineNum">     333 </span>            :   result-&gt;eax = static_cast&lt;uint32_t&gt;(value &amp; 0xFFFFFFFFU);</a>
+<a name="334"><span class="lineNum">     334 </span>            :   result-&gt;edx = static_cast&lt;uint32_t&gt;(value &gt;&gt; 32);</a>
+<a name="335"><span class="lineNum">     335 </span>            : #elif ASMJIT_CC_GCC || ASMJIT_CC_CLANG</a>
+<a name="336"><span class="lineNum">     336 </span>            :   uint32_t outEax;</a>
+<a name="337"><span class="lineNum">     337 </span>            :   uint32_t outEdx;</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            :   // Replaced, because the world is not perfect:</a>
+<a name="340"><span class="lineNum">     340 </span>            :   //   __asm__ __volatile__(&quot;xgetbv&quot; : &quot;=a&quot;(outEax), &quot;=d&quot;(outEdx) : &quot;c&quot;(inEcx));</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         70 :   __asm__ __volatile__(&quot;.byte 0x0F, 0x01, 0xd0&quot; : &quot;=a&quot;(outEax), &quot;=d&quot;(outEdx) : &quot;c&quot;(inEcx));</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :   result-&gt;eax = outEax;</a>
+<a name="344"><span class="lineNum">     344 </span>            :   result-&gt;edx = outEdx;</a>
+<a name="345"><span class="lineNum">     345 </span>            : #else</a>
+<a name="346"><span class="lineNum">     346 </span>            :   result-&gt;eax = 0;</a>
+<a name="347"><span class="lineNum">     347 </span>            :   result-&gt;edx = 0;</a>
+<a name="348"><span class="lineNum">     348 </span>            : #endif</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         70 : }</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            : //! \internal</a>
+<a name="352"><span class="lineNum">     352 </span>            : //!</a>
+<a name="353"><span class="lineNum">     353 </span>            : //! Map a 12-byte vendor string returned by `cpuid` into a `CpuInfo::Vendor` ID.</a>
+<a name="354"><span class="lineNum">     354 </span>            : static ASMJIT_INLINE uint32_t x86GetCpuVendorID(const char* vendorString) noexcept {</a>
+<a name="355"><span class="lineNum">     355 </span>            :   struct VendorData {</a>
+<a name="356"><span class="lineNum">     356 </span>            :     uint32_t id;</a>
+<a name="357"><span class="lineNum">     357 </span>            :     char text[12];</a>
+<a name="358"><span class="lineNum">     358 </span>            :   };</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            :   static const VendorData vendorList[] = {</a>
+<a name="361"><span class="lineNum">     361 </span>            :     { CpuInfo::kVendorIntel , { 'G', 'e', 'n', 'u', 'i', 'n', 'e', 'I', 'n', 't', 'e', 'l' } },</a>
+<a name="362"><span class="lineNum">     362 </span>            :     { CpuInfo::kVendorAMD   , { 'A', 'u', 't', 'h', 'e', 'n', 't', 'i', 'c', 'A', 'M', 'D' } },</a>
+<a name="363"><span class="lineNum">     363 </span>            :     { CpuInfo::kVendorVIA   , { 'V', 'I', 'A',  0 , 'V', 'I', 'A',  0 , 'V', 'I', 'A',  0  } },</a>
+<a name="364"><span class="lineNum">     364 </span>            :     { CpuInfo::kVendorVIA   , { 'C', 'e', 'n', 't', 'a', 'u', 'r', 'H', 'a', 'u', 'l', 's' } }</a>
+<a name="365"><span class="lineNum">     365 </span>            :   };</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         70 :   uint32_t dw0 = reinterpret_cast&lt;const uint32_t*&gt;(vendorString)[0];</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         70 :   uint32_t dw1 = reinterpret_cast&lt;const uint32_t*&gt;(vendorString)[1];</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         70 :   uint32_t dw2 = reinterpret_cast&lt;const uint32_t*&gt;(vendorString)[2];</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        140 :   for (uint32_t i = 0; i &lt; ASMJIT_ARRAY_SIZE(vendorList); i++) {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        140 :     if (dw0 == reinterpret_cast&lt;const uint32_t*&gt;(vendorList[i].text)[0] &amp;&amp;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         70 :         dw1 == reinterpret_cast&lt;const uint32_t*&gt;(vendorList[i].text)[1] &amp;&amp;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         70 :         dw2 == reinterpret_cast&lt;const uint32_t*&gt;(vendorList[i].text)[2])</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         70 :       return vendorList[i].id;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :   return CpuInfo::kVendorNone;</a>
+<a name="379"><span class="lineNum">     379 </span>            : }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            : static ASMJIT_INLINE void x86SimplifyBrandString(char* s) noexcept {</a>
+<a name="382"><span class="lineNum">     382 </span>            :   // Used to always clear the current character to ensure that the result</a>
+<a name="383"><span class="lineNum">     383 </span>            :   // doesn't contain garbage after the new zero terminator.</a>
+<a name="384"><span class="lineNum">     384 </span>            :   char* d = s;</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            :   char prev = 0;</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         70 :   char curr = s[0];</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         70 :   s[0] = '\0';</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :   for (;;) {</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">       3360 :     if (curr == 0)</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :       break;</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       3290 :     if (curr == ' ') {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       1400 :       if (prev == '@' || s[1] == ' ' || s[1] == '@')</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       1050 :         goto L_Skip;</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :     }</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       2240 :     d[0] = curr;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       2240 :     d++;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :     prev = curr;</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       3290 : L_Skip:</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       3290 :     curr = *++s;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       3290 :     s[0] = '\0';</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :   }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         70 :   d[0] = '\0';</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         70 : ASMJIT_FAVOR_SIZE static void x86DetectCpuInfo(CpuInfo* cpuInfo) noexcept {</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :   uint32_t i, maxId;</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :   CpuIdResult regs;</a>
+<a name="415"><span class="lineNum">     415 </span>            :   XGetBVResult xcr0 = { 0, 0 };</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         70 :   cpuInfo-&gt;_archInfo.init(ArchInfo::kTypeHost);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :   cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureI486);</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="421"><span class="lineNum">     421 </span>            :   // [CPUID EAX=0x0]</a>
+<a name="422"><span class="lineNum">     422 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span>            :   // Get vendor string/id.</a>
+<a name="425"><span class="lineNum">     425 </span>            :   x86CallCpuId(&amp;regs, 0x0);</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         70 :   maxId = regs.eax;</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         70 :   ::memcpy(cpuInfo-&gt;_vendorString + 0, &amp;regs.ebx, 4);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         70 :   ::memcpy(cpuInfo-&gt;_vendorString + 4, &amp;regs.edx, 4);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         70 :   ::memcpy(cpuInfo-&gt;_vendorString + 8, &amp;regs.ecx, 4);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         70 :   cpuInfo-&gt;_vendorId = x86GetCpuVendorID(cpuInfo-&gt;_vendorString);</span></a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="434"><span class="lineNum">     434 </span>            :   // [CPUID EAX=0x1]</a>
+<a name="435"><span class="lineNum">     435 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">         70 :   if (maxId &gt;= 0x1) {</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :     // Get feature flags in ECX/EDX and family/model in EAX.</a>
+<a name="439"><span class="lineNum">     439 </span>            :     x86CallCpuId(&amp;regs, 0x1);</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            :     // Fill family and model fields.</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         70 :     cpuInfo-&gt;_family   = (regs.eax &gt;&gt; 8) &amp; 0x0F;</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         70 :     cpuInfo-&gt;_model    = (regs.eax &gt;&gt; 4) &amp; 0x0F;</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         70 :     cpuInfo-&gt;_stepping = (regs.eax     ) &amp; 0x0F;</span></a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            :     // Use extended family and model fields.</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         70 :     if (cpuInfo-&gt;_family == 0x0F) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         70 :       cpuInfo-&gt;_family += ((regs.eax &gt;&gt; 20) &amp; 0xFF);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         70 :       cpuInfo-&gt;_model  += ((regs.eax &gt;&gt; 16) &amp; 0x0F) &lt;&lt; 4;</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :     }</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         70 :     cpuInfo-&gt;_x86Data._processorType        = ((regs.eax &gt;&gt; 12) &amp; 0x03);</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         70 :     cpuInfo-&gt;_x86Data._brandIndex           = ((regs.ebx      ) &amp; 0xFF);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">         70 :     cpuInfo-&gt;_x86Data._flushCacheLineSize   = ((regs.ebx &gt;&gt;  8) &amp; 0xFF) * 8;</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         70 :     cpuInfo-&gt;_x86Data._maxLogicalProcessors = ((regs.ebx &gt;&gt; 16) &amp; 0xFF);</span></a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00000001U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSE3);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00000002U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeaturePCLMULQDQ);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00000008U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMONITOR);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00000200U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSSE3);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00002000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCMPXCHG16B);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00080000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSE4_1);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00100000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSE4_2);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00400000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMOVBE);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00800000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeaturePOPCNT);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x02000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAESNI);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x04000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureXSAVE);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x08000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureOSXSAVE);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x40000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureRDRAND);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x00000010U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureRDTSC);</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x00000020U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMSR);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x00000100U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCMPXCHG8B);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x00008000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCMOV);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x00080000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCLFLUSH);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x00800000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMMX);</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x01000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureFXSR);</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x02000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSE)</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :                                         .addFeature(CpuInfo::kX86FeatureMMX2);</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x04000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSE)</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :                                         .addFeature(CpuInfo::kX86FeatureSSE2);</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         70 :     if (regs.edx &amp; 0x10000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMT);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            :     // Get the content of XCR0 if supported by CPU and enabled by OS.</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         70 :     if ((regs.ecx &amp; 0x0C000000U) == 0x0C000000U) {</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :       x86CallXGetBV(&amp;xcr0, 0);</a>
+<a name="486"><span class="lineNum">     486 </span>            :     }</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            :     // Detect AVX+.</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x10000000U) {</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :       // - XCR0[2:1] == 11b</a>
+<a name="491"><span class="lineNum">     491 </span>            :       //   XMM &amp; YMM states need to be enabled by OS.</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         70 :       if ((xcr0.eax &amp; 0x00000006U) == 0x00000006U) {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :         cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX);</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00001000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureFMA);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x20000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureF16C);</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :       }</a>
+<a name="498"><span class="lineNum">     498 </span>            :     }</a>
+<a name="499"><span class="lineNum">     499 </span>            :   }</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="502"><span class="lineNum">     502 </span>            :   // [CPUID EAX=0x7]</a>
+<a name="503"><span class="lineNum">     503 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            :   // Detect new features if the processor supports CPUID-07.</a>
+<a name="506"><span class="lineNum">     506 </span>            :   bool maybeMPX = false;</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         70 :   if (maxId &gt;= 0x7) {</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :     x86CallCpuId(&amp;regs, 0x7);</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000001U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureFSGSBASE);</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000008U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureBMI);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000010U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureHLE);</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000080U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSMEP);</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000100U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureBMI2);</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000200U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureERMS);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000800U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureRTM);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00004000U) maybeMPX = true;</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00040000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureRDSEED);</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00080000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureADX);</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00100000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSMAP);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00400000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeaturePCOMMIT);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00800000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCLFLUSHOPT);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x01000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCLWB);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x20000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSHA);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         70 :     if (regs.ecx &amp; 0x00000001U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeaturePREFETCHWT1);</span></a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span>            :     // TSX is supported if at least one of `HLE` and `RTM` is supported.</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00000810U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureTSX);</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :     // Detect AVX2.</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         70 :     if (cpuInfo-&gt;hasFeature(CpuInfo::kX86FeatureAVX)) {</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         70 :       if (regs.ebx &amp; 0x00000020U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX2);</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :     }</a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span>            :     // Detect AVX-512+.</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">         70 :     if (regs.ebx &amp; 0x00010000U) {</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :       // - XCR0[2:1] == 11b</a>
+<a name="539"><span class="lineNum">     539 </span>            :       //   XMM/YMM states need to be enabled by OS.</a>
+<a name="540"><span class="lineNum">     540 </span>            :       // - XCR0[7:5] == 111b</a>
+<a name="541"><span class="lineNum">     541 </span>            :       //   Upper 256-bit of ZMM0-XMM15 and ZMM16-ZMM31 need to be enabled by the OS.</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :       if ((xcr0.eax &amp; 0x000000E6U) == 0x000000E6U) {</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :         cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_F);</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x00020000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_DQ);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x00200000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_IFMA);</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x04000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_PFI);</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x08000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_ERI);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x10000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_CDI);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x40000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_BW);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :         if (regs.ebx &amp; 0x80000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_VL);</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :         if (regs.ecx &amp; 0x00000002U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_VBMI);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :         if (regs.ecx &amp; 0x00004000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_VPOPCNTDQ);</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :         if (regs.edx &amp; 0x00000004U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_4VNNIW);</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineNoCov">          0 :         if (regs.edx &amp; 0x00000008U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureAVX512_4FMAPS);</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :       }</a>
+<a name="557"><span class="lineNum">     557 </span>            :     }</a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="561"><span class="lineNum">     561 </span>            :   // [CPUID EAX=0xD]</a>
+<a name="562"><span class="lineNum">     562 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         70 :   if (maxId &gt;= 0xD) {</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :     x86CallCpuId(&amp;regs, 0xD, 0);</a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            :     // Both CPUID result and XCR0 has to be enabled to have support for MPX.</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         70 :     if (((regs.eax &amp; xcr0.eax) &amp; 0x00000018U) == 0x00000018U &amp;&amp; maybeMPX)</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :       cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMPX);</a>
+<a name="570"><span class="lineNum">     570 </span>            : </a>
+<a name="571"><span class="lineNum">     571 </span>            :     x86CallCpuId(&amp;regs, 0xD, 1);</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         70 :     if (regs.eax &amp; 0x00000001U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureXSAVEOPT);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         70 :     if (regs.eax &amp; 0x00000002U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureXSAVEC);</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         70 :     if (regs.eax &amp; 0x00000008U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureXSAVES);</span></a>
+<a name="575"><span class="lineNum">     575 </span>            :   }</a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="578"><span class="lineNum">     578 </span>            :   // [CPUID EAX=0x80000000...maxId]</a>
+<a name="579"><span class="lineNum">     579 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            :   // The highest EAX that we understand.</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         70 :   uint32_t kHighestProcessedEAX = 0x80000008U;</span></a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span>            :   // Several CPUID calls are required to get the whole branc string. It's easy</a>
+<a name="585"><span class="lineNum">     585 </span>            :   // to copy one DWORD at a time instead of performing a byte copy.</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         70 :   uint32_t* brand = reinterpret_cast&lt;uint32_t*&gt;(cpuInfo-&gt;_brandString);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span>            :   i = maxId = 0x80000000U;</a>
+<a name="589"><span class="lineNum">     589 </span>            :   do {</a>
+<a name="590"><span class="lineNum">     590 </span>            :     x86CallCpuId(&amp;regs, i);</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">        420 :     switch (i) {</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :       case 0x80000000U:</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         70 :         maxId = std::min&lt;uint32_t&gt;(regs.eax, kHighestProcessedEAX);</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         70 :         break;</span></a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         70 :       case 0x80000001U:</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00000001U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureLAHFSAHF);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00000020U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureLZCNT);</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00000040U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureSSE4A);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00000080U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMSSE);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00000100U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeaturePREFETCHW);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         70 :         if (regs.ecx &amp; 0x00200000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureTBM);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         70 :         if (regs.edx &amp; 0x00100000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureNX);</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         70 :         if (regs.edx &amp; 0x00200000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureFXSROPT);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">         70 :         if (regs.edx &amp; 0x00400000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureMMX2);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">         70 :         if (regs.edx &amp; 0x08000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureRDTSCP);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         70 :         if (regs.edx &amp; 0x40000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86Feature3DNOW2)</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :                                             .addFeature(CpuInfo::kX86FeatureMMX2);</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         70 :         if (regs.edx &amp; 0x80000000U) cpuInfo-&gt;addFeature(CpuInfo::kX86Feature3DNOW);</span></a>
+<a name="610"><span class="lineNum">     610 </span>            : </a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         70 :         if (cpuInfo-&gt;hasFeature(CpuInfo::kX86FeatureAVX)) {</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         70 :           if (regs.ecx &amp; 0x00000800U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureXOP);</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">         70 :           if (regs.ecx &amp; 0x00010000U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureFMA4);</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :         }</a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span>            :         // These seem to be only supported by AMD.</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         70 :         if (cpuInfo-&gt;getVendorId() == CpuInfo::kVendorAMD) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         70 :           if (regs.ecx &amp; 0x00000010U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureALTMOVCR8);</span></a>
+<a name="619"><span class="lineNum">     619 </span>            :         }</a>
+<a name="620"><span class="lineNum">     620 </span>            :         break;</a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        210 :       case 0x80000002U:</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :       case 0x80000003U:</a>
+<a name="624"><span class="lineNum">     624 </span>            :       case 0x80000004U:</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">        210 :         *brand++ = regs.eax;</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        210 :         *brand++ = regs.ebx;</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">        210 :         *brand++ = regs.ecx;</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">        210 :         *brand++ = regs.edx;</span></a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            :         // Go directly to the last one.</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">        210 :         if (i == 0x80000004U) i = 0x80000008U - 1;</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :         break;</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">         70 :       case 0x80000008U:</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">         70 :         if (regs.ebx &amp; 0x00000001U) cpuInfo-&gt;addFeature(CpuInfo::kX86FeatureCLZERO);</span></a>
+<a name="636"><span class="lineNum">     636 </span>            :         break;</a>
+<a name="637"><span class="lineNum">     637 </span>            :     }</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">        420 :   } while (++i &lt;= maxId);</span></a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span>            :   // Simplify CPU brand string by removing unnecessary spaces.</a>
+<a name="641"><span class="lineNum">     641 </span>            :   x86SimplifyBrandString(cpuInfo-&gt;_brandString);</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">         70 : }</span></a>
+<a name="643"><span class="lineNum">     643 </span>            : #endif // ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span>            : // ============================================================================</a>
+<a name="646"><span class="lineNum">     646 </span>            : // [asmjit::CpuInfo - Detect - HWThreadsCount]</a>
+<a name="647"><span class="lineNum">     647 </span>            : // ============================================================================</a>
+<a name="648"><span class="lineNum">     648 </span>            : </a>
+<a name="649"><span class="lineNum">     649 </span>            : static ASMJIT_INLINE uint32_t cpuDetectHWThreadsCount() noexcept {</a>
+<a name="650"><span class="lineNum">     650 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="651"><span class="lineNum">     651 </span>            :   SYSTEM_INFO info;</a>
+<a name="652"><span class="lineNum">     652 </span>            :   ::GetSystemInfo(&amp;info);</a>
+<a name="653"><span class="lineNum">     653 </span>            :   return info.dwNumberOfProcessors;</a>
+<a name="654"><span class="lineNum">     654 </span>            : #elif ASMJIT_OS_POSIX &amp;&amp; defined(_SC_NPROCESSORS_ONLN)</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         70 :   long res = ::sysconf(_SC_NPROCESSORS_ONLN);</span></a>
+<a name="656"><span class="lineNum">     656 </span>            :   if (res &lt;= 0) return 1;</a>
+<a name="657"><span class="lineNum">     657 </span>            :   return static_cast&lt;uint32_t&gt;(res);</a>
+<a name="658"><span class="lineNum">     658 </span>            : #else</a>
+<a name="659"><span class="lineNum">     659 </span>            :   return 1;</a>
+<a name="660"><span class="lineNum">     660 </span>            : #endif</a>
+<a name="661"><span class="lineNum">     661 </span>            : }</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span>            : // ============================================================================</a>
+<a name="664"><span class="lineNum">     664 </span>            : // [asmjit::CpuInfo - Detect]</a>
+<a name="665"><span class="lineNum">     665 </span>            : // ============================================================================</a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         70 : ASMJIT_FAVOR_SIZE void CpuInfo::detect() noexcept {</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :   reset();</a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span>            : #if ASMJIT_ARCH_ARM32 || ASMJIT_ARCH_ARM64</a>
+<a name="671"><span class="lineNum">     671 </span>            :   armDetectCpuInfo(this);</a>
+<a name="672"><span class="lineNum">     672 </span>            : #endif // ASMJIT_ARCH_ARM32 || ASMJIT_ARCH_ARM64</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            : #if ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">         70 :   x86DetectCpuInfo(this);</span></a>
+<a name="676"><span class="lineNum">     676 </span>            : #endif // ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="677"><span class="lineNum">     677 </span>            : </a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         70 :   _hwThreadsCount = cpuDetectHWThreadsCount();</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">         70 : }</span></a>
+<a name="680"><span class="lineNum">     680 </span>            : </a>
+<a name="681"><span class="lineNum">     681 </span>            : // ============================================================================</a>
+<a name="682"><span class="lineNum">     682 </span>            : // [asmjit::CpuInfo - GetHost]</a>
+<a name="683"><span class="lineNum">     683 </span>            : // ============================================================================</a>
+<a name="684"><span class="lineNum">     684 </span>            : </a>
+<a name="685"><span class="lineNum">     685 </span>            : struct HostCpuInfo : public CpuInfo {</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         70 :   ASMJIT_INLINE HostCpuInfo() noexcept : CpuInfo() { detect(); }</span></a>
+<a name="687"><span class="lineNum">     687 </span>            : };</a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">       1976 : const CpuInfo&amp; CpuInfo::getHost() noexcept {</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">       2046 :   static HostCpuInfo host;</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">       1976 :   return host;</span></a>
+<a name="692"><span class="lineNum">     692 </span>            : }</a>
+<a name="693"><span class="lineNum">     693 </span>            : </a>
+<a name="694"><span class="lineNum">     694 </span>            : } // asmjit namespace</a>
+<a name="695"><span class="lineNum">     695 </span>            : } // namespace PLMD</a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span>            : // [Api-End]</a>
+<a name="698"><span class="lineNum">     698 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="699"><span class="lineNum">     699 </span>            : #pragma GCC diagnostic pop</a>
+<a name="700"><span class="lineNum">     700 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/cpuinfo.h.func-sort-c.html b/coverage-libs/asmjit/cpuinfo.h.func-sort-c.html
new file mode 100644
index 0000000000..6cb346b5b7
--- /dev/null
+++ b/coverage-libs/asmjit/cpuinfo.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/cpuinfo.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - cpuinfo.h<span style="font-size: 80%;"> (<a href="cpuinfo.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">54.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="cpuinfo.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/cpuinfo.h.func.html b/coverage-libs/asmjit/cpuinfo.h.func.html
new file mode 100644
index 0000000000..68332641da
--- /dev/null
+++ b/coverage-libs/asmjit/cpuinfo.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/cpuinfo.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - cpuinfo.h<span style="font-size: 80%;"> (<a href="cpuinfo.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">54.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="cpuinfo.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/cpuinfo.h.gcov.html b/coverage-libs/asmjit/cpuinfo.h.gcov.html
new file mode 100644
index 0000000000..7f248a34ae
--- /dev/null
+++ b/coverage-libs/asmjit/cpuinfo.h.gcov.html
@@ -0,0 +1,478 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/cpuinfo.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - cpuinfo.h<span style="font-size: 80%;"> (source / <a href="cpuinfo.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">54.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_cpuinfo_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_cpuinfo_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_CPUINFO_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_CPUINFO_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::CpuFeatures]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : class CpuFeatures {</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   typedef uintptr_t BitWord;</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            :   enum {</a>
+<a name="56"><span class="lineNum">      56 </span>            :     kMaxFeatures = 128,</a>
+<a name="57"><span class="lineNum">      57 </span>            :     kBitWordSize = static_cast&lt;int&gt;(sizeof(BitWord)) * 8,</a>
+<a name="58"><span class="lineNum">      58 </span>            :     kNumBitWords = kMaxFeatures / kBitWordSize</a>
+<a name="59"><span class="lineNum">      59 </span>            :   };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="62"><span class="lineNum">      62 </span>            :   // [Construction / Destruction]</a>
+<a name="63"><span class="lineNum">      63 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         70 :   ASMJIT_INLINE CpuFeatures() noexcept { reset(); }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   ASMJIT_INLINE CpuFeatures(const CpuFeatures&amp; other) noexcept = default;</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // [Init / Reset]</a>
+<a name="70"><span class="lineNum">      70 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :   ASMJIT_INLINE void init(const CpuFeatures&amp; other) noexcept { ::memcpy(this, &amp;other, sizeof(*this)); }</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void reset() noexcept { ::memset(this, 0, sizeof(*this)); }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="76"><span class="lineNum">      76 </span>            :   // [Ops]</a>
+<a name="77"><span class="lineNum">      77 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   //! Get all features as `BitWord` array.</a>
+<a name="80"><span class="lineNum">      80 </span>            :   ASMJIT_INLINE BitWord* getBits() noexcept { return _bits; }</a>
+<a name="81"><span class="lineNum">      81 </span>            :   //! Get all features as `BitWord` array (const).</a>
+<a name="82"><span class="lineNum">      82 </span>            :   ASMJIT_INLINE const BitWord* getBits() const noexcept { return _bits; }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! Get if feature `feature` is present.</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ASMJIT_INLINE bool has(uint32_t feature) const noexcept {</a>
+<a name="86"><span class="lineNum">      86 </span>            :     ASMJIT_ASSERT(feature &lt; kMaxFeatures);</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :     uint32_t idx = feature / kBitWordSize;</a>
+<a name="89"><span class="lineNum">      89 </span>            :     uint32_t bit = feature % kBitWordSize;</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        140 :     return static_cast&lt;bool&gt;((_bits[idx] &gt;&gt; bit) &amp; 0x1);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Get if all features as defined by `other` are  present.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   ASMJIT_INLINE bool hasAll(const CpuFeatures&amp; other) const noexcept {</a>
+<a name="96"><span class="lineNum">      96 </span>            :     for (uint32_t i = 0; i &lt; kNumBitWords; i++)</a>
+<a name="97"><span class="lineNum">      97 </span>            :       if ((_bits[i] &amp; other._bits[i]) != other._bits[i])</a>
+<a name="98"><span class="lineNum">      98 </span>            :         return false;</a>
+<a name="99"><span class="lineNum">      99 </span>            :     return true;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   //! Add a CPU `feature`.</a>
+<a name="103"><span class="lineNum">     103 </span>            :   ASMJIT_INLINE CpuFeatures&amp; add(uint32_t feature) noexcept {</a>
+<a name="104"><span class="lineNum">     104 </span>            :     ASMJIT_ASSERT(feature &lt; kMaxFeatures);</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     uint32_t idx = feature / kBitWordSize;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     uint32_t bit = feature % kBitWordSize;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        140 :     _bits[idx] |= static_cast&lt;BitWord&gt;(1) &lt;&lt; bit;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     return *this;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Remove a CPU `feature`.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_INLINE CpuFeatures&amp; remove(uint32_t feature) noexcept {</a>
+<a name="115"><span class="lineNum">     115 </span>            :     ASMJIT_ASSERT(feature &lt; kMaxFeatures);</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :     uint32_t idx = feature / kBitWordSize;</a>
+<a name="118"><span class="lineNum">     118 </span>            :     uint32_t bit = feature % kBitWordSize;</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     _bits[idx] &amp;= ~(static_cast&lt;BitWord&gt;(1) &lt;&lt; bit);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     return *this;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="125"><span class="lineNum">     125 </span>            :   // [Members]</a>
+<a name="126"><span class="lineNum">     126 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   BitWord _bits[kNumBitWords];</a>
+<a name="129"><span class="lineNum">     129 </span>            : };</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : // ============================================================================</a>
+<a name="132"><span class="lineNum">     132 </span>            : // [asmjit::CpuInfo]</a>
+<a name="133"><span class="lineNum">     133 </span>            : // ============================================================================</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : //! CPU information.</a>
+<a name="136"><span class="lineNum">     136 </span>            : class CpuInfo {</a>
+<a name="137"><span class="lineNum">     137 </span>            : public:</a>
+<a name="138"><span class="lineNum">     138 </span>            :   //! CPU vendor ID.</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ASMJIT_ENUM(Vendor) {</a>
+<a name="140"><span class="lineNum">     140 </span>            :     kVendorNone  = 0,                    //!&lt; Generic or unknown.</a>
+<a name="141"><span class="lineNum">     141 </span>            :     kVendorIntel = 1,                    //!&lt; Intel vendor.</a>
+<a name="142"><span class="lineNum">     142 </span>            :     kVendorAMD   = 2,                    //!&lt; AMD vendor.</a>
+<a name="143"><span class="lineNum">     143 </span>            :     kVendorVIA   = 3                     //!&lt; VIA vendor.</a>
+<a name="144"><span class="lineNum">     144 </span>            :   };</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! ARM/ARM64 CPU features.</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ASMJIT_ENUM(ArmFeatures) {</a>
+<a name="148"><span class="lineNum">     148 </span>            :     kArmFeatureV6 = 1,                   //!&lt; ARMv6 instruction set.</a>
+<a name="149"><span class="lineNum">     149 </span>            :     kArmFeatureV7,                       //!&lt; ARMv7 instruction set.</a>
+<a name="150"><span class="lineNum">     150 </span>            :     kArmFeatureV8,                       //!&lt; ARMv8 instruction set.</a>
+<a name="151"><span class="lineNum">     151 </span>            :     kArmFeatureTHUMB,                    //!&lt; CPU provides THUMB v1 instruction set (THUMB mode).</a>
+<a name="152"><span class="lineNum">     152 </span>            :     kArmFeatureTHUMB2,                   //!&lt; CPU provides THUMB v2 instruction set (THUMB mode).</a>
+<a name="153"><span class="lineNum">     153 </span>            :     kArmFeatureVFPv2,                    //!&lt; CPU provides VFPv2 instruction set.</a>
+<a name="154"><span class="lineNum">     154 </span>            :     kArmFeatureVFPv3,                    //!&lt; CPU provides VFPv3 instruction set.</a>
+<a name="155"><span class="lineNum">     155 </span>            :     kArmFeatureVFPv4,                    //!&lt; CPU provides VFPv4 instruction set.</a>
+<a name="156"><span class="lineNum">     156 </span>            :     kArmFeatureVFP_D32,                  //!&lt; CPU provides 32 VFP-D (64-bit) registers.</a>
+<a name="157"><span class="lineNum">     157 </span>            :     kArmFeatureEDSP,                     //!&lt; CPU provides EDSP extensions.</a>
+<a name="158"><span class="lineNum">     158 </span>            :     kArmFeatureASIMD,                    //!&lt; CPU provides 'Advanced SIMD'.</a>
+<a name="159"><span class="lineNum">     159 </span>            :     kArmFeatureIDIVA,                    //!&lt; CPU provides hardware SDIV and UDIV (ARM mode).</a>
+<a name="160"><span class="lineNum">     160 </span>            :     kArmFeatureIDIVT,                    //!&lt; CPU provides hardware SDIV and UDIV (THUMB mode).</a>
+<a name="161"><span class="lineNum">     161 </span>            :     kArmFeatureAES,                      //!&lt; CPU provides AES instructions (ARM64 only).</a>
+<a name="162"><span class="lineNum">     162 </span>            :     kArmFeatureCRC32,                    //!&lt; CPU provides CRC32 instructions.</a>
+<a name="163"><span class="lineNum">     163 </span>            :     kArmFeaturePMULL,                    //!&lt; CPU provides PMULL instructions (ARM64 only).</a>
+<a name="164"><span class="lineNum">     164 </span>            :     kArmFeatureSHA1,                     //!&lt; CPU provides SHA1 instructions.</a>
+<a name="165"><span class="lineNum">     165 </span>            :     kArmFeatureSHA256,                   //!&lt; CPU provides SHA256 instructions.</a>
+<a name="166"><span class="lineNum">     166 </span>            :     kArmFeatureAtomics64,                //!&lt; CPU provides 64-bit load/store atomics (ARM64 only).</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :     kArmFeaturesCount                    //!&lt; Count of ARM/ARM64 CPU features.</a>
+<a name="169"><span class="lineNum">     169 </span>            :   };</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   //! X86/X64 CPU features.</a>
+<a name="172"><span class="lineNum">     172 </span>            :   ASMJIT_ENUM(X86Features) {</a>
+<a name="173"><span class="lineNum">     173 </span>            :     kX86FeatureI486 = 1,                 //!&lt; CPU is at least I486.</a>
+<a name="174"><span class="lineNum">     174 </span>            :     kX86FeatureNX,                       //!&lt; CPU has Not-Execute-Bit.</a>
+<a name="175"><span class="lineNum">     175 </span>            :     kX86FeatureMT,                       //!&lt; CPU has multi-threading.</a>
+<a name="176"><span class="lineNum">     176 </span>            :     kX86FeatureALTMOVCR8,                //!&lt; CPU supports `LOCK MOV CR8` (AMD CPUs).</a>
+<a name="177"><span class="lineNum">     177 </span>            :     kX86FeatureCMOV,                     //!&lt; CPU has CMOV.</a>
+<a name="178"><span class="lineNum">     178 </span>            :     kX86FeatureCMPXCHG8B,                //!&lt; CPU has CMPXCHG8B.</a>
+<a name="179"><span class="lineNum">     179 </span>            :     kX86FeatureCMPXCHG16B,               //!&lt; CPU has CMPXCHG16B (x64).</a>
+<a name="180"><span class="lineNum">     180 </span>            :     kX86FeatureMSR,                      //!&lt; CPU has RDMSR/WRMSR.</a>
+<a name="181"><span class="lineNum">     181 </span>            :     kX86FeatureRDTSC,                    //!&lt; CPU has RDTSC.</a>
+<a name="182"><span class="lineNum">     182 </span>            :     kX86FeatureRDTSCP,                   //!&lt; CPU has RDTSCP.</a>
+<a name="183"><span class="lineNum">     183 </span>            :     kX86FeatureCLFLUSH,                  //!&lt; CPU has CLFUSH.</a>
+<a name="184"><span class="lineNum">     184 </span>            :     kX86FeatureCLFLUSHOPT,               //!&lt; CPU has CLFUSHOPT.</a>
+<a name="185"><span class="lineNum">     185 </span>            :     kX86FeatureCLWB,                     //!&lt; CPU has CLWB.</a>
+<a name="186"><span class="lineNum">     186 </span>            :     kX86FeatureCLZERO,                   //!&lt; CPU has CLZERO.</a>
+<a name="187"><span class="lineNum">     187 </span>            :     kX86FeaturePCOMMIT,                  //!&lt; CPU has PCOMMIT.</a>
+<a name="188"><span class="lineNum">     188 </span>            :     kX86FeaturePREFETCHW,                //!&lt; CPU has PREFETCHW.</a>
+<a name="189"><span class="lineNum">     189 </span>            :     kX86FeaturePREFETCHWT1,              //!&lt; CPU has PREFETCHWT1.</a>
+<a name="190"><span class="lineNum">     190 </span>            :     kX86FeatureLAHFSAHF,                 //!&lt; CPU has LAHF/SAHF.</a>
+<a name="191"><span class="lineNum">     191 </span>            :     kX86FeatureFXSR,                     //!&lt; CPU has FXSAVE/FXRSTOR.</a>
+<a name="192"><span class="lineNum">     192 </span>            :     kX86FeatureFXSROPT,                  //!&lt; CPU has FXSAVE/FXRSTOR (optimized).</a>
+<a name="193"><span class="lineNum">     193 </span>            :     kX86FeatureMMX,                      //!&lt; CPU has MMX.</a>
+<a name="194"><span class="lineNum">     194 </span>            :     kX86FeatureMMX2,                     //!&lt; CPU has extended MMX.</a>
+<a name="195"><span class="lineNum">     195 </span>            :     kX86Feature3DNOW,                    //!&lt; CPU has 3DNOW.</a>
+<a name="196"><span class="lineNum">     196 </span>            :     kX86Feature3DNOW2,                   //!&lt; CPU has 3DNOW2 (enhanced).</a>
+<a name="197"><span class="lineNum">     197 </span>            :     kX86FeatureGEODE,                    //!&lt; CPU has GEODE extensions (few additions to 3DNOW).</a>
+<a name="198"><span class="lineNum">     198 </span>            :     kX86FeatureSSE,                      //!&lt; CPU has SSE.</a>
+<a name="199"><span class="lineNum">     199 </span>            :     kX86FeatureSSE2,                     //!&lt; CPU has SSE2.</a>
+<a name="200"><span class="lineNum">     200 </span>            :     kX86FeatureSSE3,                     //!&lt; CPU has SSE3.</a>
+<a name="201"><span class="lineNum">     201 </span>            :     kX86FeatureSSSE3,                    //!&lt; CPU has SSSE3.</a>
+<a name="202"><span class="lineNum">     202 </span>            :     kX86FeatureSSE4A,                    //!&lt; CPU has SSE4.A.</a>
+<a name="203"><span class="lineNum">     203 </span>            :     kX86FeatureSSE4_1,                   //!&lt; CPU has SSE4.1.</a>
+<a name="204"><span class="lineNum">     204 </span>            :     kX86FeatureSSE4_2,                   //!&lt; CPU has SSE4.2.</a>
+<a name="205"><span class="lineNum">     205 </span>            :     kX86FeatureMSSE,                     //!&lt; CPU has Misaligned SSE (MSSE).</a>
+<a name="206"><span class="lineNum">     206 </span>            :     kX86FeatureMONITOR,                  //!&lt; CPU has MONITOR and MWAIT.</a>
+<a name="207"><span class="lineNum">     207 </span>            :     kX86FeatureMOVBE,                    //!&lt; CPU has MOVBE.</a>
+<a name="208"><span class="lineNum">     208 </span>            :     kX86FeaturePOPCNT,                   //!&lt; CPU has POPCNT.</a>
+<a name="209"><span class="lineNum">     209 </span>            :     kX86FeatureLZCNT,                    //!&lt; CPU has LZCNT.</a>
+<a name="210"><span class="lineNum">     210 </span>            :     kX86FeatureAESNI,                    //!&lt; CPU has AESNI.</a>
+<a name="211"><span class="lineNum">     211 </span>            :     kX86FeaturePCLMULQDQ,                //!&lt; CPU has PCLMULQDQ.</a>
+<a name="212"><span class="lineNum">     212 </span>            :     kX86FeatureRDRAND,                   //!&lt; CPU has RDRAND.</a>
+<a name="213"><span class="lineNum">     213 </span>            :     kX86FeatureRDSEED,                   //!&lt; CPU has RDSEED.</a>
+<a name="214"><span class="lineNum">     214 </span>            :     kX86FeatureSMAP,                     //!&lt; CPU has SMAP (supervisor-mode access prevention).</a>
+<a name="215"><span class="lineNum">     215 </span>            :     kX86FeatureSMEP,                     //!&lt; CPU has SMEP (supervisor-mode execution prevention).</a>
+<a name="216"><span class="lineNum">     216 </span>            :     kX86FeatureSHA,                      //!&lt; CPU has SHA-1 and SHA-256.</a>
+<a name="217"><span class="lineNum">     217 </span>            :     kX86FeatureXSAVE,                    //!&lt; CPU has XSAVE support (XSAVE/XRSTOR, XSETBV/XGETBV, and XCR).</a>
+<a name="218"><span class="lineNum">     218 </span>            :     kX86FeatureXSAVEC,                   //!&lt; CPU has XSAVEC support (XSAVEC).</a>
+<a name="219"><span class="lineNum">     219 </span>            :     kX86FeatureXSAVES,                   //!&lt; CPU has XSAVES support (XSAVES/XRSTORS).</a>
+<a name="220"><span class="lineNum">     220 </span>            :     kX86FeatureXSAVEOPT,                 //!&lt; CPU has XSAVEOPT support (XSAVEOPT/XSAVEOPT64).</a>
+<a name="221"><span class="lineNum">     221 </span>            :     kX86FeatureOSXSAVE,                  //!&lt; CPU has XSAVE enabled by OS.</a>
+<a name="222"><span class="lineNum">     222 </span>            :     kX86FeatureAVX,                      //!&lt; CPU has AVX.</a>
+<a name="223"><span class="lineNum">     223 </span>            :     kX86FeatureAVX2,                     //!&lt; CPU has AVX2.</a>
+<a name="224"><span class="lineNum">     224 </span>            :     kX86FeatureF16C,                     //!&lt; CPU has F16C.</a>
+<a name="225"><span class="lineNum">     225 </span>            :     kX86FeatureFMA,                      //!&lt; CPU has FMA.</a>
+<a name="226"><span class="lineNum">     226 </span>            :     kX86FeatureFMA4,                     //!&lt; CPU has FMA4.</a>
+<a name="227"><span class="lineNum">     227 </span>            :     kX86FeatureXOP,                      //!&lt; CPU has XOP.</a>
+<a name="228"><span class="lineNum">     228 </span>            :     kX86FeatureBMI,                      //!&lt; CPU has BMI (bit manipulation instructions #1).</a>
+<a name="229"><span class="lineNum">     229 </span>            :     kX86FeatureBMI2,                     //!&lt; CPU has BMI2 (bit manipulation instructions #2).</a>
+<a name="230"><span class="lineNum">     230 </span>            :     kX86FeatureADX,                      //!&lt; CPU has ADX (multi-precision add-carry instruction extensions).</a>
+<a name="231"><span class="lineNum">     231 </span>            :     kX86FeatureTBM,                      //!&lt; CPU has TBM (trailing bit manipulation).</a>
+<a name="232"><span class="lineNum">     232 </span>            :     kX86FeatureMPX,                      //!&lt; CPU has MPX (memory protection extensions).</a>
+<a name="233"><span class="lineNum">     233 </span>            :     kX86FeatureHLE,                      //!&lt; CPU has HLE.</a>
+<a name="234"><span class="lineNum">     234 </span>            :     kX86FeatureRTM,                      //!&lt; CPU has RTM.</a>
+<a name="235"><span class="lineNum">     235 </span>            :     kX86FeatureTSX,                      //!&lt; CPU has TSX.</a>
+<a name="236"><span class="lineNum">     236 </span>            :     kX86FeatureERMS,                     //!&lt; CPU has ERMS (enhanced REP MOVSB/STOSB).</a>
+<a name="237"><span class="lineNum">     237 </span>            :     kX86FeatureFSGSBASE,                 //!&lt; CPU has FSGSBASE.</a>
+<a name="238"><span class="lineNum">     238 </span>            :     kX86FeatureAVX512_F,                 //!&lt; CPU has AVX512-F (foundation).</a>
+<a name="239"><span class="lineNum">     239 </span>            :     kX86FeatureAVX512_CDI,               //!&lt; CPU has AVX512-CDI (conflict detection).</a>
+<a name="240"><span class="lineNum">     240 </span>            :     kX86FeatureAVX512_PFI,               //!&lt; CPU has AVX512-PFI (prefetch instructions).</a>
+<a name="241"><span class="lineNum">     241 </span>            :     kX86FeatureAVX512_ERI,               //!&lt; CPU has AVX512-ERI (exponential and reciprocal).</a>
+<a name="242"><span class="lineNum">     242 </span>            :     kX86FeatureAVX512_DQ,                //!&lt; CPU has AVX512-DQ (DWORD/QWORD).</a>
+<a name="243"><span class="lineNum">     243 </span>            :     kX86FeatureAVX512_BW,                //!&lt; CPU has AVX512-BW (BYTE/WORD).</a>
+<a name="244"><span class="lineNum">     244 </span>            :     kX86FeatureAVX512_VL,                //!&lt; CPU has AVX512-VL (vector length extensions).</a>
+<a name="245"><span class="lineNum">     245 </span>            :     kX86FeatureAVX512_IFMA,              //!&lt; CPU has AVX512-IFMA (integer fused-multiply-add using 52-bit precision).</a>
+<a name="246"><span class="lineNum">     246 </span>            :     kX86FeatureAVX512_VBMI,              //!&lt; CPU has AVX512-VBMI (vector byte manipulation).</a>
+<a name="247"><span class="lineNum">     247 </span>            :     kX86FeatureAVX512_VPOPCNTDQ,         //!&lt; CPU has AVX512-VPOPCNTDQ (VPOPCNT[D|Q] instructions).</a>
+<a name="248"><span class="lineNum">     248 </span>            :     kX86FeatureAVX512_4VNNIW,            //!&lt; CPU has AVX512-VNNIW (vector NN instructions word variable precision).</a>
+<a name="249"><span class="lineNum">     249 </span>            :     kX86FeatureAVX512_4FMAPS,            //!&lt; CPU has AVX512-FMAPS (FMA packed single).</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :     kX86FeaturesCount                    //!&lt; Count of X86/X64 CPU features.</a>
+<a name="252"><span class="lineNum">     252 </span>            :   };</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="255"><span class="lineNum">     255 </span>            :   // [ArmInfo]</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   struct ArmData {</a>
+<a name="259"><span class="lineNum">     259 </span>            :   };</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="262"><span class="lineNum">     262 </span>            :   // [X86Info]</a>
+<a name="263"><span class="lineNum">     263 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   struct X86Data {</a>
+<a name="266"><span class="lineNum">     266 </span>            :     uint32_t _processorType;             //!&lt; Processor type.</a>
+<a name="267"><span class="lineNum">     267 </span>            :     uint32_t _brandIndex;                //!&lt; Brand index.</a>
+<a name="268"><span class="lineNum">     268 </span>            :     uint32_t _flushCacheLineSize;        //!&lt; Flush cache line size (in bytes).</a>
+<a name="269"><span class="lineNum">     269 </span>            :     uint32_t _maxLogicalProcessors;      //!&lt; Maximum number of addressable IDs for logical processors.</a>
+<a name="270"><span class="lineNum">     270 </span>            :   };</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="273"><span class="lineNum">     273 </span>            :   // [Construction / Destruction]</a>
+<a name="274"><span class="lineNum">     274 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         70 :   ASMJIT_INLINE CpuInfo() noexcept { reset(); }</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   ASMJIT_INLINE CpuInfo(const CpuInfo&amp; other) noexcept = default;</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="280"><span class="lineNum">     280 </span>            :   // [Init / Reset]</a>
+<a name="281"><span class="lineNum">     281 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            :   //! Initialize CpuInfo to the given architecture, see \ArchInfo.</a>
+<a name="284"><span class="lineNum">     284 </span>            :   ASMJIT_INLINE void initArch(uint32_t archType, uint32_t archMode = 0) noexcept {</a>
+<a name="285"><span class="lineNum">     285 </span>            :     _archInfo.init(archType, archMode);</a>
+<a name="286"><span class="lineNum">     286 </span>            :   }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   ASMJIT_INLINE void init(const CpuInfo&amp; other) noexcept { ::memcpy(this, &amp;other, sizeof(*this)); }</a>
+<a name="289"><span class="lineNum">     289 </span>            :   ASMJIT_INLINE void reset() noexcept { ::memset(this, 0, sizeof(*this)); }</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="292"><span class="lineNum">     292 </span>            :   // [Detect]</a>
+<a name="293"><span class="lineNum">     293 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            :   ASMJIT_API void detect() noexcept;</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="298"><span class="lineNum">     298 </span>            :   // [Accessors]</a>
+<a name="299"><span class="lineNum">     299 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   //! Get generic architecture information.</a>
+<a name="302"><span class="lineNum">     302 </span>            :   ASMJIT_INLINE const ArchInfo&amp; getArchInfo() const noexcept { return _archInfo; }</a>
+<a name="303"><span class="lineNum">     303 </span>            :   //! Get CPU architecture type, see \ArchInfo::Type.</a>
+<a name="304"><span class="lineNum">     304 </span>            :   ASMJIT_INLINE uint32_t getArchType() const noexcept { return _archInfo.getType(); }</a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! Get CPU architecture sub-type, see \ArchInfo::SubType.</a>
+<a name="306"><span class="lineNum">     306 </span>            :   ASMJIT_INLINE uint32_t getArchSubType() const noexcept { return _archInfo.getSubType(); }</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            :     //! Get CPU vendor ID.</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         70 :   ASMJIT_INLINE uint32_t getVendorId() const noexcept { return _vendorId; }</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   //! Get CPU family ID.</a>
+<a name="311"><span class="lineNum">     311 </span>            :   ASMJIT_INLINE uint32_t getFamily() const noexcept { return _family; }</a>
+<a name="312"><span class="lineNum">     312 </span>            :   //! Get CPU model ID.</a>
+<a name="313"><span class="lineNum">     313 </span>            :   ASMJIT_INLINE uint32_t getModel() const noexcept { return _model; }</a>
+<a name="314"><span class="lineNum">     314 </span>            :   //! Get CPU stepping.</a>
+<a name="315"><span class="lineNum">     315 </span>            :   ASMJIT_INLINE uint32_t getStepping() const noexcept { return _stepping; }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :   //! Get number of hardware threads available.</a>
+<a name="318"><span class="lineNum">     318 </span>            :   ASMJIT_INLINE uint32_t getHwThreadsCount() const noexcept {</a>
+<a name="319"><span class="lineNum">     319 </span>            :     return _hwThreadsCount;</a>
+<a name="320"><span class="lineNum">     320 </span>            :   }</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            :   //! Get all CPU features.</a>
+<a name="323"><span class="lineNum">     323 </span>            :   ASMJIT_INLINE const CpuFeatures&amp; getFeatures() const noexcept { return _features; }</a>
+<a name="324"><span class="lineNum">     324 </span>            :   //! Get whether CPU has a `feature`.</a>
+<a name="325"><span class="lineNum">     325 </span>            :   ASMJIT_INLINE bool hasFeature(uint32_t feature) const noexcept { return _features.has(feature); }</a>
+<a name="326"><span class="lineNum">     326 </span>            :   //! Add a CPU `feature`.</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">       3430 :   ASMJIT_INLINE CpuInfo&amp; addFeature(uint32_t feature) noexcept { _features.add(feature); return *this; }</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            :   //! Get CPU vendor string.</a>
+<a name="330"><span class="lineNum">     330 </span>            :   ASMJIT_INLINE const char* getVendorString() const noexcept { return _vendorString; }</a>
+<a name="331"><span class="lineNum">     331 </span>            :   //! Get CPU brand string.</a>
+<a name="332"><span class="lineNum">     332 </span>            :   ASMJIT_INLINE const char* getBrandString() const noexcept { return _brandString; }</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="335"><span class="lineNum">     335 </span>            :   // [Accessors - ARM]</a>
+<a name="336"><span class="lineNum">     336 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="339"><span class="lineNum">     339 </span>            :   // [Accessors - X86]</a>
+<a name="340"><span class="lineNum">     340 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            :   //! Get processor type.</a>
+<a name="343"><span class="lineNum">     343 </span>            :   ASMJIT_INLINE uint32_t getX86ProcessorType() const noexcept {</a>
+<a name="344"><span class="lineNum">     344 </span>            :     return _x86Data._processorType;</a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :   //! Get brand index.</a>
+<a name="348"><span class="lineNum">     348 </span>            :   ASMJIT_INLINE uint32_t getX86BrandIndex() const noexcept {</a>
+<a name="349"><span class="lineNum">     349 </span>            :     return _x86Data._brandIndex;</a>
+<a name="350"><span class="lineNum">     350 </span>            :   }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            :   //! Get flush cache line size.</a>
+<a name="353"><span class="lineNum">     353 </span>            :   ASMJIT_INLINE uint32_t getX86FlushCacheLineSize() const noexcept {</a>
+<a name="354"><span class="lineNum">     354 </span>            :     return _x86Data._flushCacheLineSize;</a>
+<a name="355"><span class="lineNum">     355 </span>            :   }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   //! Get maximum logical processors count.</a>
+<a name="358"><span class="lineNum">     358 </span>            :   ASMJIT_INLINE uint32_t getX86MaxLogicalProcessors() const noexcept {</a>
+<a name="359"><span class="lineNum">     359 </span>            :     return _x86Data._maxLogicalProcessors;</a>
+<a name="360"><span class="lineNum">     360 </span>            :   }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="363"><span class="lineNum">     363 </span>            :   // [Statics]</a>
+<a name="364"><span class="lineNum">     364 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            :   //! Get the host CPU information.</a>
+<a name="367"><span class="lineNum">     367 </span>            :   ASMJIT_API static const CpuInfo&amp; getHost() noexcept;</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="370"><span class="lineNum">     370 </span>            :   // [Members]</a>
+<a name="371"><span class="lineNum">     371 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            :   ArchInfo _archInfo;                    //!&lt; CPU architecture information.</a>
+<a name="374"><span class="lineNum">     374 </span>            :   uint32_t _vendorId;                    //!&lt; CPU vendor id, see \ref Vendor.</a>
+<a name="375"><span class="lineNum">     375 </span>            :   uint32_t _family;                      //!&lt; CPU family ID.</a>
+<a name="376"><span class="lineNum">     376 </span>            :   uint32_t _model;                       //!&lt; CPU model ID.</a>
+<a name="377"><span class="lineNum">     377 </span>            :   uint32_t _stepping;                    //!&lt; CPU stepping.</a>
+<a name="378"><span class="lineNum">     378 </span>            :   uint32_t _hwThreadsCount;              //!&lt; Number of hardware threads.</a>
+<a name="379"><span class="lineNum">     379 </span>            :   CpuFeatures _features;                 //!&lt; CPU features.</a>
+<a name="380"><span class="lineNum">     380 </span>            :   char _vendorString[16];                //!&lt; CPU vendor string.</a>
+<a name="381"><span class="lineNum">     381 </span>            :   char _brandString[64];                 //!&lt; CPU brand string.</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            :   // Architecture specific data.</a>
+<a name="384"><span class="lineNum">     384 </span>            :   union {</a>
+<a name="385"><span class="lineNum">     385 </span>            :     ArmData _armData;</a>
+<a name="386"><span class="lineNum">     386 </span>            :     X86Data _x86Data;</a>
+<a name="387"><span class="lineNum">     387 </span>            :   };</a>
+<a name="388"><span class="lineNum">     388 </span>            : };</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            : //! \}</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            : } // asmjit namespace</a>
+<a name="393"><span class="lineNum">     393 </span>            : } // namespace PLMD</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            : // [Api-End]</a>
+<a name="396"><span class="lineNum">     396 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            : // [Guard]</a>
+<a name="399"><span class="lineNum">     399 </span>            : #endif // _ASMJIT_BASE_CPUINFO_H</a>
+<a name="400"><span class="lineNum">     400 </span>            : #pragma GCC diagnostic pop</a>
+<a name="401"><span class="lineNum">     401 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="402"><span class="lineNum">     402 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/func.cpp.func-sort-c.html b/coverage-libs/asmjit/func.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4ed4d93eed
--- /dev/null
+++ b/coverage-libs/asmjit/func.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/func.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - func.cpp<span style="font-size: 80%;"> (<a href="func.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="func.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#190">_ZN4PLMD6asmjit9FuncUtils9allocArgsEPNS0_11CodeEmitterERKNS0_15FuncFrameLayoutERKNS0_14FuncArgsMapperE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#139">_ZNK4PLMD6asmjit14FuncArgsMapper15updateFrameInfoERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#119">_ZN4PLMD6asmjit15FuncFrameLayout4initERKNS0_10FuncDetailERKNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#176">_ZN4PLMD6asmjit9FuncUtils10emitEpilogEPNS0_11CodeEmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
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+              <td class="coverFn"><a href="func.cpp.gcov.html#162">_ZN4PLMD6asmjit9FuncUtils10emitPrologEPNS0_11CodeEmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#74">_ZN4PLMD6asmjit10FuncDetail4initERKNS0_13FuncSignatureE</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#54">_ZN4PLMD6asmjit8CallConv4initEj</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/func.cpp.func.html b/coverage-libs/asmjit/func.cpp.func.html
new file mode 100644
index 0000000000..334f54c900
--- /dev/null
+++ b/coverage-libs/asmjit/func.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/func.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - func.cpp<span style="font-size: 80%;"> (<a href="func.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="func.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#74">_ZN4PLMD6asmjit10FuncDetail4initERKNS0_13FuncSignatureE</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#119">_ZN4PLMD6asmjit15FuncFrameLayout4initERKNS0_10FuncDetailERKNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#54">_ZN4PLMD6asmjit8CallConv4initEj</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#176">_ZN4PLMD6asmjit9FuncUtils10emitEpilogEPNS0_11CodeEmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#162">_ZN4PLMD6asmjit9FuncUtils10emitPrologEPNS0_11CodeEmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#190">_ZN4PLMD6asmjit9FuncUtils9allocArgsEPNS0_11CodeEmitterERKNS0_15FuncFrameLayoutERKNS0_14FuncArgsMapperE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="func.cpp.gcov.html#139">_ZNK4PLMD6asmjit14FuncArgsMapper15updateFrameInfoERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/func.cpp.gcov.html b/coverage-libs/asmjit/func.cpp.gcov.html
new file mode 100644
index 0000000000..86fe1317ec
--- /dev/null
+++ b/coverage-libs/asmjit/func.cpp.gcov.html
@@ -0,0 +1,288 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/func.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - func.cpp<span style="font-size: 80%;"> (source / <a href="func.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./func.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./x86internal_p.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./arminternal_p.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./armoperand.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : // [Api-Begin]</a>
+<a name="47"><span class="lineNum">      47 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : namespace PLMD {</a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace asmjit {</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : // [asmjit::CallConv - Init / Reset]</a>
+<a name="54"><span class="lineNum">      54 </span>            : // ============================================================================</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       3596 : ASMJIT_FAVOR_SIZE Error CallConv::init(uint32_t ccId) noexcept {</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   reset();</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       3596 :   if (CallConv::isX86Family(ccId))</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       3596 :     return X86Internal::initCallConv(*this, ccId);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="65"><span class="lineNum">      65 </span>            :   if (CallConv::isArmFamily(ccId))</a>
+<a name="66"><span class="lineNum">      66 </span>            :     return ArmInternal::initCallConv(*this, ccId);</a>
+<a name="67"><span class="lineNum">      67 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            :   return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : // ============================================================================</a>
+<a name="73"><span class="lineNum">      73 </span>            : // [asmjit::FuncDetail - Init / Reset]</a>
+<a name="74"><span class="lineNum">      74 </span>            : // ============================================================================</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       3596 : ASMJIT_FAVOR_SIZE Error FuncDetail::init(const FuncSignature&amp; sign) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   uint32_t ccId = sign.getCallConv();</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       3596 :   CallConv&amp; cc = _callConv;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   uint32_t argCount = sign.getArgCount();</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       3596 :   if (ASMJIT_UNLIKELY(argCount &gt; kFuncArgCount))</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       3596 :   ASMJIT_PROPAGATE(cc.init(ccId));</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       3596 :   uint32_t gpSize = (cc.getArchType() == ArchInfo::kTypeX86) ? 4 : 8;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   uint32_t deabstractDelta = TypeId::deabstractDeltaOfSize(gpSize);</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   const uint8_t* args = sign.getArgs();</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       5466 :   for (uint32_t i = 0; i &lt; argCount; i++) {</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :     Value&amp; arg = _args[i];</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1870 :     arg.initTypeId(TypeId::deabstract(args[i], deabstractDelta));</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       3596 :   _argCount = static_cast&lt;uint8_t&gt;(argCount);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   uint32_t ret = sign.getRet();</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       3596 :   if (ret != TypeId::kVoid) {</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :     _rets[0].initTypeId(TypeId::deabstract(ret, deabstractDelta));</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       3596 :     _retCount = 1;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       3596 :   if (CallConv::isX86Family(ccId))</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       3596 :     return X86Internal::initFuncDetail(*this, sign, gpSize);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="108"><span class="lineNum">     108 </span>            :   if (CallConv::isArmFamily(ccId))</a>
+<a name="109"><span class="lineNum">     109 </span>            :     return ArmInternal::initFuncDetail(*this, sign, gpSize);</a>
+<a name="110"><span class="lineNum">     110 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   // We should never bubble here as if `cc.init()` succeeded then there has to</a>
+<a name="113"><span class="lineNum">     113 </span>            :   // be an implementation for the current architecture. However, stay safe.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : // ============================================================================</a>
+<a name="118"><span class="lineNum">     118 </span>            : // [asmjit::FuncFrameLayout - Init / Reset]</a>
+<a name="119"><span class="lineNum">     119 </span>            : // ============================================================================</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error FuncFrameLayout::init(const FuncDetail&amp; func, const FuncFrameInfo&amp; ffi) noexcept {</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   uint32_t ccId = func.getCallConv().getId();</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       1948 :   if (CallConv::isX86Family(ccId))</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       1948 :     return X86Internal::initFrameLayout(*this, func, ffi);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="130"><span class="lineNum">     130 </span>            :   if (CallConv::isArmFamily(ccId))</a>
+<a name="131"><span class="lineNum">     131 </span>            :     return ArmInternal::initFrameLayout(*this, func, ffi);</a>
+<a name="132"><span class="lineNum">     132 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : // ============================================================================</a>
+<a name="138"><span class="lineNum">     138 </span>            : // [asmjit::FuncArgsMapper]</a>
+<a name="139"><span class="lineNum">     139 </span>            : // ============================================================================</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error FuncArgsMapper::updateFrameInfo(FuncFrameInfo&amp; ffi) const noexcept {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   const FuncDetail* func = getFuncDetail();</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   if (!func) return DebugUtils::errored(kErrorInvalidState);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   uint32_t ccId = func-&gt;getCallConv().getId();</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   if (CallConv::isX86Family(ccId))</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     return X86Internal::argsToFrameInfo(*this, ffi);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="153"><span class="lineNum">     153 </span>            :   if (CallConv::isArmFamily(ccId))</a>
+<a name="154"><span class="lineNum">     154 </span>            :     return ArmInternal::argsToFrameInfo(*this, ffi);</a>
+<a name="155"><span class="lineNum">     155 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : // ============================================================================</a>
+<a name="161"><span class="lineNum">     161 </span>            : // [asmjit::FuncUtils]</a>
+<a name="162"><span class="lineNum">     162 </span>            : // ============================================================================</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error FuncUtils::emitProlog(CodeEmitter* emitter, const FuncFrameLayout&amp; layout) {</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       1948 :   if (emitter-&gt;getArchInfo().isX86Family())</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1948 :     return X86Internal::emitProlog(static_cast&lt;X86Emitter*&gt;(emitter), layout);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="171"><span class="lineNum">     171 </span>            :   if (emitter-&gt;getArchInfo().isArmFamily())</a>
+<a name="172"><span class="lineNum">     172 </span>            :     return ArmInternal::emitProlog(static_cast&lt;ArmEmitter*&gt;(emitter), layout);</a>
+<a name="173"><span class="lineNum">     173 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error FuncUtils::emitEpilog(CodeEmitter* emitter, const FuncFrameLayout&amp; layout) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       1948 :   if (emitter-&gt;getArchInfo().isX86Family())</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       1948 :     return X86Internal::emitEpilog(static_cast&lt;X86Emitter*&gt;(emitter), layout);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="185"><span class="lineNum">     185 </span>            :   if (emitter-&gt;getArchInfo().isArmFamily())</a>
+<a name="186"><span class="lineNum">     186 </span>            :     return ArmInternal::emitEpilog(static_cast&lt;ArmEmitter*&gt;(emitter), layout);</a>
+<a name="187"><span class="lineNum">     187 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error FuncUtils::allocArgs(CodeEmitter* emitter, const FuncFrameLayout&amp; layout, const FuncArgsMapper&amp; args) {</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   if (emitter-&gt;getArchInfo().isX86Family())</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     return X86Internal::allocArgs(static_cast&lt;X86Emitter*&gt;(emitter), layout, args);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="199"><span class="lineNum">     199 </span>            :   if (emitter-&gt;getArchInfo().isArmFamily())</a>
+<a name="200"><span class="lineNum">     200 </span>            :     return ArmInternal::allocArgs(static_cast&lt;ArmEmitter*&gt;(emitter), layout, args);</a>
+<a name="201"><span class="lineNum">     201 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : } // asmjit namespace</a>
+<a name="207"><span class="lineNum">     207 </span>            : } // namespace PLMD</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : // [Api-End]</a>
+<a name="210"><span class="lineNum">     210 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="211"><span class="lineNum">     211 </span>            : #pragma GCC diagnostic pop</a>
+<a name="212"><span class="lineNum">     212 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/func.h.func-sort-c.html b/coverage-libs/asmjit/func.h.func-sort-c.html
new file mode 100644
index 0000000000..6008055adb
--- /dev/null
+++ b/coverage-libs/asmjit/func.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/func.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - func.h<span style="font-size: 80%;"> (<a href="func.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryLo">70.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="func.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/func.h.func.html b/coverage-libs/asmjit/func.h.func.html
new file mode 100644
index 0000000000..5708a7d907
--- /dev/null
+++ b/coverage-libs/asmjit/func.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/func.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - func.h<span style="font-size: 80%;"> (<a href="func.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryLo">70.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="func.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/func.h.gcov.html b/coverage-libs/asmjit/func.h.gcov.html
new file mode 100644
index 0000000000..8fc4ade4c2
--- /dev/null
+++ b/coverage-libs/asmjit/func.h.gcov.html
@@ -0,0 +1,1403 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/func.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - func.h<span style="font-size: 80%;"> (source / <a href="func.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryLo">70.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_func_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_func_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_FUNC_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_FUNC_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : // [Dependencies]</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // [Api-Begin]</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace PLMD {</a>
+<a name="46"><span class="lineNum">      46 </span>            : namespace asmjit {</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : //! \addtogroup asmjit_base</a>
+<a name="49"><span class="lineNum">      49 </span>            : //! \{</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : // [Forward Declarations]</a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : class CodeEmitter;</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : // [asmjit::CallConv]</a>
+<a name="59"><span class="lineNum">      59 </span>            : // ============================================================================</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : //! Function calling convention.</a>
+<a name="62"><span class="lineNum">      62 </span>            : //!</a>
+<a name="63"><span class="lineNum">      63 </span>            : //! Function calling convention is a scheme that defines how function parameters</a>
+<a name="64"><span class="lineNum">      64 </span>            : //! are passed and how function returns its result. AsmJit defines a variety of</a>
+<a name="65"><span class="lineNum">      65 </span>            : //! architecture and OS specific calling conventions and also provides a compile</a>
+<a name="66"><span class="lineNum">      66 </span>            : //! time detection to make JIT code-generation easier.</a>
+<a name="67"><span class="lineNum">      67 </span>            : struct CallConv {</a>
+<a name="68"><span class="lineNum">      68 </span>            :   //! Calling convention id.</a>
+<a name="69"><span class="lineNum">      69 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="70"><span class="lineNum">      70 </span>            :     //! None or invalid (can't be used).</a>
+<a name="71"><span class="lineNum">      71 </span>            :     kIdNone = 0,</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="74"><span class="lineNum">      74 </span>            :     // [Universal]</a>
+<a name="75"><span class="lineNum">      75 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :     // TODO: To make this possible we need to know target ARCH and ABI.</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :     /*</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :     // Universal calling conventions are applicable to any target and are</a>
+<a name="82"><span class="lineNum">      82 </span>            :     // converted to target dependent conventions at runtime. The purpose of</a>
+<a name="83"><span class="lineNum">      83 </span>            :     // these conventions is to make using functions less target dependent.</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :     kIdCDecl = 1,</a>
+<a name="86"><span class="lineNum">      86 </span>            :     kIdStdCall = 2,</a>
+<a name="87"><span class="lineNum">      87 </span>            :     kIdFastCall = 3,</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :     //! AsmJit specific calling convention designed for calling functions</a>
+<a name="90"><span class="lineNum">      90 </span>            :     //! inside a multimedia code like that don't use many registers internally,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     //! but are long enough to be called and not inlined. These functions are</a>
+<a name="92"><span class="lineNum">      92 </span>            :     //! usually used to calculate trigonometric functions, logarithms, etc...</a>
+<a name="93"><span class="lineNum">      93 </span>            :     kIdFastEval2 = 10,</a>
+<a name="94"><span class="lineNum">      94 </span>            :     kIdFastEval3 = 11,</a>
+<a name="95"><span class="lineNum">      95 </span>            :     kIdFastEval4 = 12,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     */</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="99"><span class="lineNum">      99 </span>            :     // [X86]</a>
+<a name="100"><span class="lineNum">     100 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :     //! X86 `__cdecl` calling convention (used by C runtime and libraries).</a>
+<a name="103"><span class="lineNum">     103 </span>            :     kIdX86CDecl = 16,</a>
+<a name="104"><span class="lineNum">     104 </span>            :     //! X86 `__stdcall` calling convention (used mostly by WinAPI).</a>
+<a name="105"><span class="lineNum">     105 </span>            :     kIdX86StdCall = 17,</a>
+<a name="106"><span class="lineNum">     106 </span>            :     //! X86 `__thiscall` calling convention (MSVC/Intel).</a>
+<a name="107"><span class="lineNum">     107 </span>            :     kIdX86MsThisCall = 18,</a>
+<a name="108"><span class="lineNum">     108 </span>            :     //! X86 `__fastcall` convention (MSVC/Intel).</a>
+<a name="109"><span class="lineNum">     109 </span>            :     kIdX86MsFastCall = 19,</a>
+<a name="110"><span class="lineNum">     110 </span>            :     //! X86 `__fastcall` convention (GCC and Clang).</a>
+<a name="111"><span class="lineNum">     111 </span>            :     kIdX86GccFastCall = 20,</a>
+<a name="112"><span class="lineNum">     112 </span>            :     //! X86 `regparm(1)` convention (GCC and Clang).</a>
+<a name="113"><span class="lineNum">     113 </span>            :     kIdX86GccRegParm1 = 21,</a>
+<a name="114"><span class="lineNum">     114 </span>            :     //! X86 `regparm(2)` convention (GCC and Clang).</a>
+<a name="115"><span class="lineNum">     115 </span>            :     kIdX86GccRegParm2 = 22,</a>
+<a name="116"><span class="lineNum">     116 </span>            :     //! X86 `regparm(3)` convention (GCC and Clang).</a>
+<a name="117"><span class="lineNum">     117 </span>            :     kIdX86GccRegParm3 = 23,</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :     kIdX86FastEval2 = 29,</a>
+<a name="120"><span class="lineNum">     120 </span>            :     kIdX86FastEval3 = 30,</a>
+<a name="121"><span class="lineNum">     121 </span>            :     kIdX86FastEval4 = 31,</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :     //! X64 calling convention defined by WIN64-ABI.</a>
+<a name="124"><span class="lineNum">     124 </span>            :     //!</a>
+<a name="125"><span class="lineNum">     125 </span>            :     //! Links:</a>
+<a name="126"><span class="lineNum">     126 </span>            :     //!   * &lt;http://msdn.microsoft.com/en-us/library/9b372w95.aspx&gt;.</a>
+<a name="127"><span class="lineNum">     127 </span>            :     kIdX86Win64 = 32,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     //! X64 calling convention used by Unix platforms (SYSV/AMD64-ABI).</a>
+<a name="129"><span class="lineNum">     129 </span>            :     kIdX86SysV64 = 33,</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :     kIdX64FastEval2 = 45,</a>
+<a name="132"><span class="lineNum">     132 </span>            :     kIdX64FastEval3 = 46,</a>
+<a name="133"><span class="lineNum">     133 </span>            :     kIdX64FastEval4 = 47,</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="136"><span class="lineNum">     136 </span>            :     // [ARM]</a>
+<a name="137"><span class="lineNum">     137 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :     //! Legacy calling convention, floating point arguments are passed via GP registers.</a>
+<a name="140"><span class="lineNum">     140 </span>            :     kIdArm32SoftFP = 48,</a>
+<a name="141"><span class="lineNum">     141 </span>            :     //! Modern calling convention, uses VFP registers to pass floating point arguments.</a>
+<a name="142"><span class="lineNum">     142 </span>            :     kIdArm32HardFP = 49,</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="145"><span class="lineNum">     145 </span>            :     // [Internal]</a>
+<a name="146"><span class="lineNum">     146 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :     _kIdX86Start = 16,   //!&lt; \internal</a>
+<a name="149"><span class="lineNum">     149 </span>            :     _kIdX86End = 31,     //!&lt; \internal</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :     _kIdX64Start = 32,  //!&lt; \internal</a>
+<a name="152"><span class="lineNum">     152 </span>            :     _kIdX64End = 47,    //!&lt; \internal</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :     _kIdArmStart = 48,  //!&lt; \internal</a>
+<a name="155"><span class="lineNum">     155 </span>            :     _kIdArmEnd = 49,    //!&lt; \internal</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="158"><span class="lineNum">     158 </span>            :     // [Host]</a>
+<a name="159"><span class="lineNum">     159 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : #if defined(ASMJIT_DOCGEN)</a>
+<a name="162"><span class="lineNum">     162 </span>            :     //! Default calling convention based on the current C++ compiler's settings.</a>
+<a name="163"><span class="lineNum">     163 </span>            :     //!</a>
+<a name="164"><span class="lineNum">     164 </span>            :     //! NOTE: This should be always the same as `kIdHostCDecl`, but some</a>
+<a name="165"><span class="lineNum">     165 </span>            :     //! compilers allow to override the default calling convention. Overriding</a>
+<a name="166"><span class="lineNum">     166 </span>            :     //! is not detected at the moment.</a>
+<a name="167"><span class="lineNum">     167 </span>            :     kIdHost          = DETECTED_AT_COMPILE_TIME,</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :     //! Default CDECL calling convention based on the current C++ compiler's settings.</a>
+<a name="170"><span class="lineNum">     170 </span>            :     kIdHostCDecl     = DETECTED_AT_COMPILE_TIME,</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :     //! Default STDCALL calling convention based on the current C++ compiler's settings.</a>
+<a name="173"><span class="lineNum">     173 </span>            :     //!</a>
+<a name="174"><span class="lineNum">     174 </span>            :     //! NOTE: If not defined by the host then it's the same as `kIdHostCDecl`.</a>
+<a name="175"><span class="lineNum">     175 </span>            :     kIdHostStdCall   = DETECTED_AT_COMPILE_TIME,</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            :     //! Compatibility for `__fastcall` calling convention.</a>
+<a name="178"><span class="lineNum">     178 </span>            :     //!</a>
+<a name="179"><span class="lineNum">     179 </span>            :     //! NOTE: If not defined by the host then it's the same as `kIdHostCDecl`.</a>
+<a name="180"><span class="lineNum">     180 </span>            :     kIdHostFastCall  = DETECTED_AT_COMPILE_TIME</a>
+<a name="181"><span class="lineNum">     181 </span>            : #elif ASMJIT_ARCH_X86</a>
+<a name="182"><span class="lineNum">     182 </span>            :     kIdHost          = kIdX86CDecl,</a>
+<a name="183"><span class="lineNum">     183 </span>            :     kIdHostCDecl     = kIdX86CDecl,</a>
+<a name="184"><span class="lineNum">     184 </span>            :     kIdHostStdCall   = kIdX86StdCall,</a>
+<a name="185"><span class="lineNum">     185 </span>            :     kIdHostFastCall  = ASMJIT_CC_MSC   ? kIdX86MsFastCall  :</a>
+<a name="186"><span class="lineNum">     186 </span>            :                        ASMJIT_CC_GCC   ? kIdX86GccFastCall :</a>
+<a name="187"><span class="lineNum">     187 </span>            :                        ASMJIT_CC_CLANG ? kIdX86GccFastCall : kIdNone,</a>
+<a name="188"><span class="lineNum">     188 </span>            :     kIdHostFastEval2 = kIdX86FastEval2,</a>
+<a name="189"><span class="lineNum">     189 </span>            :     kIdHostFastEval3 = kIdX86FastEval3,</a>
+<a name="190"><span class="lineNum">     190 </span>            :     kIdHostFastEval4 = kIdX86FastEval4</a>
+<a name="191"><span class="lineNum">     191 </span>            : #elif ASMJIT_ARCH_X64</a>
+<a name="192"><span class="lineNum">     192 </span>            :     kIdHost          = ASMJIT_OS_WINDOWS ? kIdX86Win64 : kIdX86SysV64,</a>
+<a name="193"><span class="lineNum">     193 </span>            :     kIdHostCDecl     = kIdHost, // Doesn't exist, redirected to host.</a>
+<a name="194"><span class="lineNum">     194 </span>            :     kIdHostStdCall   = kIdHost, // Doesn't exist, redirected to host.</a>
+<a name="195"><span class="lineNum">     195 </span>            :     kIdHostFastCall  = kIdHost, // Doesn't exist, redirected to host.</a>
+<a name="196"><span class="lineNum">     196 </span>            :     kIdHostFastEval2 = kIdX64FastEval2,</a>
+<a name="197"><span class="lineNum">     197 </span>            :     kIdHostFastEval3 = kIdX64FastEval3,</a>
+<a name="198"><span class="lineNum">     198 </span>            :     kIdHostFastEval4 = kIdX64FastEval4</a>
+<a name="199"><span class="lineNum">     199 </span>            : #elif ASMJIT_ARCH_ARM32</a>
+<a name="200"><span class="lineNum">     200 </span>            : # if defined(__SOFTFP__)</a>
+<a name="201"><span class="lineNum">     201 </span>            :     kIdHost          = kIdArm32SoftFP,</a>
+<a name="202"><span class="lineNum">     202 </span>            : # else</a>
+<a name="203"><span class="lineNum">     203 </span>            :     kIdHost          = kIdArm32HardFP,</a>
+<a name="204"><span class="lineNum">     204 </span>            : # endif</a>
+<a name="205"><span class="lineNum">     205 </span>            :     // These don't exist on ARM.</a>
+<a name="206"><span class="lineNum">     206 </span>            :     kIdHostCDecl     = kIdHost, // Doesn't exist, redirected to host.</a>
+<a name="207"><span class="lineNum">     207 </span>            :     kIdHostStdCall   = kIdHost, // Doesn't exist, redirected to host.</a>
+<a name="208"><span class="lineNum">     208 </span>            :     kIdHostFastCall  = kIdHost  // Doesn't exist, redirected to host.</a>
+<a name="209"><span class="lineNum">     209 </span>            : #else</a>
+<a name="210"><span class="lineNum">     210 </span>            : # error &quot;[asmjit] Couldn't determine the target's calling convention.&quot;</a>
+<a name="211"><span class="lineNum">     211 </span>            : #endif</a>
+<a name="212"><span class="lineNum">     212 </span>            :   };</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! Calling convention algorithm.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   //!</a>
+<a name="216"><span class="lineNum">     216 </span>            :   //! This is AsmJit specific. It basically describes how should AsmJit convert</a>
+<a name="217"><span class="lineNum">     217 </span>            :   //! the function arguments defined by `FuncSignature` into register ids or</a>
+<a name="218"><span class="lineNum">     218 </span>            :   //! stack offsets. The default algorithm is a standard algorithm that assigns</a>
+<a name="219"><span class="lineNum">     219 </span>            :   //! registers first, and then assigns stack. The Win64 algorithm does register</a>
+<a name="220"><span class="lineNum">     220 </span>            :   //! shadowing as defined by `WIN64` calling convention - it applies to 64-bit</a>
+<a name="221"><span class="lineNum">     221 </span>            :   //! calling conventions only.</a>
+<a name="222"><span class="lineNum">     222 </span>            :   ASMJIT_ENUM(Algorithm) {</a>
+<a name="223"><span class="lineNum">     223 </span>            :     kAlgorithmDefault    = 0,            //!&lt; Default algorithm (cross-platform).</a>
+<a name="224"><span class="lineNum">     224 </span>            :     kAlgorithmWin64      = 1             //!&lt; WIN64 specific algorithm.</a>
+<a name="225"><span class="lineNum">     225 </span>            :   };</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :   //! Calling convention flags.</a>
+<a name="228"><span class="lineNum">     228 </span>            :   ASMJIT_ENUM(Flags) {</a>
+<a name="229"><span class="lineNum">     229 </span>            :     kFlagCalleePopsStack = 0x01,         //!&lt; Callee is responsible for cleaning up the stack.</a>
+<a name="230"><span class="lineNum">     230 </span>            :     kFlagPassFloatsByVec = 0x02,         //!&lt; Pass F32 and F64 arguments by VEC128 register.</a>
+<a name="231"><span class="lineNum">     231 </span>            :     kFlagVectorCall      = 0x04,         //!&lt; This is a '__vectorcall' calling convention.</a>
+<a name="232"><span class="lineNum">     232 </span>            :     kFlagIndirectVecArgs = 0x08          //!&lt; Pass vector arguments indirectly (as a pointer).</a>
+<a name="233"><span class="lineNum">     233 </span>            :   };</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   //! Internal limits of AsmJit/CallConv.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   ASMJIT_ENUM(Limits) {</a>
+<a name="237"><span class="lineNum">     237 </span>            :     kMaxVRegKinds        = Globals::kMaxVRegKinds,</a>
+<a name="238"><span class="lineNum">     238 </span>            :     kNumRegArgsPerKind   = 8</a>
+<a name="239"><span class="lineNum">     239 </span>            :   };</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   //! Passed registers' order.</a>
+<a name="242"><span class="lineNum">     242 </span>            :   union RegOrder {</a>
+<a name="243"><span class="lineNum">     243 </span>            :     uint8_t id[kNumRegArgsPerKind];      //!&lt; Passed registers, ordered.</a>
+<a name="244"><span class="lineNum">     244 </span>            :     uint32_t packed[(kNumRegArgsPerKind + 3) / 4];</a>
+<a name="245"><span class="lineNum">     245 </span>            :   };</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="248"><span class="lineNum">     248 </span>            :   // [Utilities]</a>
+<a name="249"><span class="lineNum">     249 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       3596 :   static ASMJIT_INLINE bool isX86Family(uint32_t ccId) noexcept { return ccId &gt;= _kIdX86Start &amp;&amp; ccId &lt;= _kIdX64End; }</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :   static ASMJIT_INLINE bool isArmFamily(uint32_t ccId) noexcept { return ccId &gt;= _kIdArmStart &amp;&amp; ccId &lt;= _kIdArmEnd; }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="255"><span class="lineNum">     255 </span>            :   // [Init / Reset]</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   ASMJIT_API Error init(uint32_t ccId) noexcept;</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="261"><span class="lineNum">     261 </span>            :     ::memset(this, 0, sizeof(*this));</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       3596 :     ::memset(_passedOrder, 0xFF, sizeof(_passedOrder));</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="266"><span class="lineNum">     266 </span>            :   // [Accessors]</a>
+<a name="267"><span class="lineNum">     267 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :   //! Get calling convention id, see \ref Id.</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :   //! Set calling convention id, see \ref Id.</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       3596 :   ASMJIT_INLINE void setId(uint32_t id) noexcept { _id = static_cast&lt;uint8_t&gt;(id); }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   //! Get architecture type.</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       5544 :   ASMJIT_INLINE uint32_t getArchType() const noexcept { return _archType; }</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :   //! Set architecture type.</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       3596 :   ASMJIT_INLINE void setArchType(uint32_t archType) noexcept { _archType = static_cast&lt;uint8_t&gt;(archType); }</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :   //! Get calling convention algorithm, see \ref Algorithm.</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       3596 :   ASMJIT_INLINE uint32_t getAlgorithm() const noexcept { return _algorithm; }</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   //! Set calling convention algorithm, see \ref Algorithm.</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setAlgorithm(uint32_t algorithm) noexcept { _algorithm = static_cast&lt;uint8_t&gt;(algorithm); }</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   //! Get if the calling convention has the given `flag` set.</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       5046 :   ASMJIT_INLINE bool hasFlag(uint32_t flag) const noexcept { return (_flags &amp; flag) != 0; }</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   //! Get calling convention flags, see \ref Flags.</a>
+<a name="287"><span class="lineNum">     287 </span>            :   ASMJIT_INLINE uint32_t getFlags() const noexcept { return _flags; }</a>
+<a name="288"><span class="lineNum">     288 </span>            :   //! Add calling convention flags, see \ref Flags.</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setFlags(uint32_t flag) noexcept { _flags = flag; };</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   //! Add calling convention flags, see \ref Flags.</a>
+<a name="291"><span class="lineNum">     291 </span>            :   ASMJIT_INLINE void addFlags(uint32_t flag) noexcept { _flags |= flag; };</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            :   //! Get a natural stack alignment.</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       5844 :   ASMJIT_INLINE uint32_t getNaturalStackAlignment() const noexcept { return _naturalStackAlignment; }</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   //! Set a natural stack alignment.</a>
+<a name="297"><span class="lineNum">     297 </span>            :   //!</a>
+<a name="298"><span class="lineNum">     298 </span>            :   //! This function can be used to override the default stack alignment in case</a>
+<a name="299"><span class="lineNum">     299 </span>            :   //! that you know that it's alignment is different. For example it allows to</a>
+<a name="300"><span class="lineNum">     300 </span>            :   //! implement custom calling conventions that guarantee higher stack alignment.</a>
+<a name="301"><span class="lineNum">     301 </span>            :   ASMJIT_INLINE void setNaturalStackAlignment(uint32_t value) noexcept {</a>
+<a name="302"><span class="lineNum">     302 </span>            :     ASMJIT_ASSERT(value &lt; 256);</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       3596 :     _naturalStackAlignment = static_cast&lt;uint8_t&gt;(value);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :   //! Get if this calling convention specifies 'SpillZone'.</a>
+<a name="307"><span class="lineNum">     307 </span>            :   ASMJIT_INLINE bool hasSpillZone() const noexcept { return _spillZoneSize != 0; }</a>
+<a name="308"><span class="lineNum">     308 </span>            :   //! Get size of 'SpillZone'.</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getSpillZoneSize() const noexcept { return _spillZoneSize; }</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   //! Set size of 'SpillZone'.</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setSpillZoneSize(uint32_t size) noexcept { _spillZoneSize = static_cast&lt;uint8_t&gt;(size); }</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   //! Get if this calling convention specifies 'RedZone'.</a>
+<a name="314"><span class="lineNum">     314 </span>            :   ASMJIT_INLINE bool hasRedZone() const noexcept { return _redZoneSize != 0; }</a>
+<a name="315"><span class="lineNum">     315 </span>            :   //! Get size of 'RedZone'.</a>
+<a name="316"><span class="lineNum">     316 </span>            :   ASMJIT_INLINE uint32_t getRedZoneSize() const noexcept { return _redZoneSize; }</a>
+<a name="317"><span class="lineNum">     317 </span>            :   //! Set size of 'RedZone'.</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       3596 :   ASMJIT_INLINE void setRedZoneSize(uint32_t size) noexcept { _redZoneSize = static_cast&lt;uint16_t&gt;(size); }</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :   ASMJIT_INLINE const uint8_t* getPassedOrder(uint32_t kind) const noexcept {</a>
+<a name="321"><span class="lineNum">     321 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="322"><span class="lineNum">     322 </span>            :     return _passedOrder[kind].id;</a>
+<a name="323"><span class="lineNum">     323 </span>            :   }</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :   ASMJIT_INLINE uint32_t getPassedRegs(uint32_t kind) const noexcept {</a>
+<a name="326"><span class="lineNum">     326 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      11388 :     return _passedRegs[kind];</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :   }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :   ASMJIT_INLINE void _setPassedPacked(uint32_t kind, uint32_t p0, uint32_t p1) noexcept {</a>
+<a name="331"><span class="lineNum">     331 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       3596 :     _passedOrder[kind].packed[0] = p0;</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       3596 :     _passedOrder[kind].packed[1] = p1;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :   }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            :   ASMJIT_INLINE void setPassedToNone(uint32_t kind) noexcept {</a>
+<a name="338"><span class="lineNum">     338 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            :     _setPassedPacked(kind, ASMJIT_PACK32_4x8(0xFF, 0xFF, 0xFF, 0xFF),</a>
+<a name="341"><span class="lineNum">     341 </span>            :                            ASMJIT_PACK32_4x8(0xFF, 0xFF, 0xFF, 0xFF));</a>
+<a name="342"><span class="lineNum">     342 </span>            :     _passedRegs[kind] = 0;</a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            :   ASMJIT_INLINE void setPassedOrder(uint32_t kind, uint32_t a0, uint32_t a1 = 0xFF, uint32_t a2 = 0xFF, uint32_t a3 = 0xFF, uint32_t a4 = 0xFF, uint32_t a5 = 0xFF, uint32_t a6 = 0xFF, uint32_t a7 = 0xFF) noexcept {</a>
+<a name="346"><span class="lineNum">     346 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            :     _setPassedPacked(kind, ASMJIT_PACK32_4x8(a0, a1, a2, a3),</a>
+<a name="349"><span class="lineNum">     349 </span>            :                            ASMJIT_PACK32_4x8(a4, a5, a6, a7));</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :     // NOTE: This should always be called with all arguments known at compile</a>
+<a name="352"><span class="lineNum">     352 </span>            :     // time, so even if it looks scary it should be translated to a single</a>
+<a name="353"><span class="lineNum">     353 </span>            :     // instruction.</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :     _passedRegs[kind] = (a0 != 0xFF ? 1U &lt;&lt; a0 : 0U) |</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :                         (a1 != 0xFF ? 1U &lt;&lt; a1 : 0U) |</a>
+<a name="356"><span class="lineNum">     356 </span>            :                         (a2 != 0xFF ? 1U &lt;&lt; a2 : 0U) |</a>
+<a name="357"><span class="lineNum">     357 </span>            :                         (a3 != 0xFF ? 1U &lt;&lt; a3 : 0U) |</a>
+<a name="358"><span class="lineNum">     358 </span>            :                         (a4 != 0xFF ? 1U &lt;&lt; a4 : 0U) |</a>
+<a name="359"><span class="lineNum">     359 </span>            :                         (a5 != 0xFF ? 1U &lt;&lt; a5 : 0U) |</a>
+<a name="360"><span class="lineNum">     360 </span>            :                         (a6 != 0xFF ? 1U &lt;&lt; a6 : 0U) |</a>
+<a name="361"><span class="lineNum">     361 </span>            :                         (a7 != 0xFF ? 1U &lt;&lt; a7 : 0U) ;</a>
+<a name="362"><span class="lineNum">     362 </span>            :   }</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :   ASMJIT_INLINE uint32_t getPreservedRegs(uint32_t kind) const noexcept {</a>
+<a name="365"><span class="lineNum">     365 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       9440 :     return _preservedRegs[kind];</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :   }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span>            :   ASMJIT_INLINE void setPreservedRegs(uint32_t kind, uint32_t regs) noexcept {</a>
+<a name="371"><span class="lineNum">     371 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     _preservedRegs[kind] = regs;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">       3596 :   }</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="376"><span class="lineNum">     376 </span>            :   // [Members]</a>
+<a name="377"><span class="lineNum">     377 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :   uint8_t _id;                           //!&lt; Calling convention id, see \ref Id.</a>
+<a name="380"><span class="lineNum">     380 </span>            :   uint8_t _archType;                     //!&lt; Architecture type (see \ref ArchInfo::Type).</a>
+<a name="381"><span class="lineNum">     381 </span>            :   uint8_t _algorithm;                    //!&lt; Calling convention algorithm.</a>
+<a name="382"><span class="lineNum">     382 </span>            :   uint8_t _flags;                        //!&lt; Calling convention flags.</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            :   uint8_t _naturalStackAlignment;        //!&lt; Natural stack alignment as defined by OS/ABI.</a>
+<a name="385"><span class="lineNum">     385 </span>            :   uint8_t _spillZoneSize;                //!&lt; Spill zone size (WIN64 == 32 bytes).</a>
+<a name="386"><span class="lineNum">     386 </span>            :   uint16_t _redZoneSize;                 //!&lt; Red zone size (AMD64 == 128 bytes).</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            :   RegOrder _passedOrder[kMaxVRegKinds];  //!&lt; Passed registers' order, per kind.</a>
+<a name="389"><span class="lineNum">     389 </span>            :   uint32_t _passedRegs[kMaxVRegKinds];   //!&lt; Mask of all passed registers, per kind.</a>
+<a name="390"><span class="lineNum">     390 </span>            :   uint32_t _preservedRegs[kMaxVRegKinds];//!&lt; Mask of all preserved registers, per kind.</a>
+<a name="391"><span class="lineNum">     391 </span>            : };</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span>            : // ============================================================================</a>
+<a name="394"><span class="lineNum">     394 </span>            : // [asmjit::FuncArgIndex]</a>
+<a name="395"><span class="lineNum">     395 </span>            : // ============================================================================</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            : //! Function argument index (lo/hi).</a>
+<a name="398"><span class="lineNum">     398 </span>            : ASMJIT_ENUM(FuncArgIndex) {</a>
+<a name="399"><span class="lineNum">     399 </span>            :   //! Maximum number of function arguments supported by AsmJit.</a>
+<a name="400"><span class="lineNum">     400 </span>            :   kFuncArgCount = 16,</a>
+<a name="401"><span class="lineNum">     401 </span>            :   //! Extended maximum number of arguments (used internally).</a>
+<a name="402"><span class="lineNum">     402 </span>            :   kFuncArgCountLoHi = kFuncArgCount * 2,</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            :   //! Index to the LO part of function argument (default).</a>
+<a name="405"><span class="lineNum">     405 </span>            :   //!</a>
+<a name="406"><span class="lineNum">     406 </span>            :   //! This value is typically omitted and added only if there is HI argument</a>
+<a name="407"><span class="lineNum">     407 </span>            :   //! accessed.</a>
+<a name="408"><span class="lineNum">     408 </span>            :   kFuncArgLo = 0,</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :   //! Index to the HI part of function argument.</a>
+<a name="411"><span class="lineNum">     411 </span>            :   //!</a>
+<a name="412"><span class="lineNum">     412 </span>            :   //! HI part of function argument depends on target architecture. On x86 it's</a>
+<a name="413"><span class="lineNum">     413 </span>            :   //! typically used to transfer 64-bit integers (they form a pair of 32-bit</a>
+<a name="414"><span class="lineNum">     414 </span>            :   //! integers).</a>
+<a name="415"><span class="lineNum">     415 </span>            :   kFuncArgHi = kFuncArgCount</a>
+<a name="416"><span class="lineNum">     416 </span>            : };</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            : // ============================================================================</a>
+<a name="419"><span class="lineNum">     419 </span>            : // [asmjit::FuncSignature]</a>
+<a name="420"><span class="lineNum">     420 </span>            : // ============================================================================</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            : //! Function signature.</a>
+<a name="423"><span class="lineNum">     423 </span>            : //!</a>
+<a name="424"><span class="lineNum">     424 </span>            : //! Contains information about function return type, count of arguments and</a>
+<a name="425"><span class="lineNum">     425 </span>            : //! their TypeIds. Function signature is a low level structure which doesn't</a>
+<a name="426"><span class="lineNum">     426 </span>            : //! contain platform specific or calling convention specific information.</a>
+<a name="427"><span class="lineNum">     427 </span>            : struct FuncSignature {</a>
+<a name="428"><span class="lineNum">     428 </span>            :   enum {</a>
+<a name="429"><span class="lineNum">     429 </span>            :     //! Doesn't have variable number of arguments (`...`).</a>
+<a name="430"><span class="lineNum">     430 </span>            :     kNoVarArgs = 0xFF</a>
+<a name="431"><span class="lineNum">     431 </span>            :   };</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="434"><span class="lineNum">     434 </span>            :   // [Init / Reset]</a>
+<a name="435"><span class="lineNum">     435 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            :   //! Initialize the function signature.</a>
+<a name="438"><span class="lineNum">     438 </span>            :   ASMJIT_INLINE void init(uint32_t ccId, uint32_t ret, const uint8_t* args, uint32_t argCount) noexcept {</a>
+<a name="439"><span class="lineNum">     439 </span>            :     ASMJIT_ASSERT(ccId &lt;= 0xFF);</a>
+<a name="440"><span class="lineNum">     440 </span>            :     ASMJIT_ASSERT(argCount &lt;= 0xFF);</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">       3596 :     _callConv = static_cast&lt;uint8_t&gt;(ccId);</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">       3596 :     _argCount = static_cast&lt;uint8_t&gt;(argCount);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">       3596 :     _vaIndex = kNoVarArgs;</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">       3596 :     _ret = ret;</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">       3596 :     _args = args;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   }</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="450"><span class="lineNum">     450 </span>            :     memset(this, 0, sizeof(*this));</a>
+<a name="451"><span class="lineNum">     451 </span>            :   }</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="454"><span class="lineNum">     454 </span>            :   // [Accessors]</a>
+<a name="455"><span class="lineNum">     455 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   //! Get the function's calling convention.</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">       3596 :   ASMJIT_INLINE uint32_t getCallConv() const noexcept { return _callConv; }</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   //! Get if the function has variable number of arguments (...).</a>
+<a name="461"><span class="lineNum">     461 </span>            :   ASMJIT_INLINE bool hasVarArgs() const noexcept { return _vaIndex != kNoVarArgs; }</a>
+<a name="462"><span class="lineNum">     462 </span>            :   //! Get the variable arguments (...) index, `kNoVarArgs` if none.</a>
+<a name="463"><span class="lineNum">     463 </span>            :   ASMJIT_INLINE uint32_t getVAIndex() const noexcept { return _vaIndex; }</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span>            :   //! Get the number of function arguments.</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">       5244 :   ASMJIT_INLINE uint32_t getArgCount() const noexcept { return _argCount; }</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   ASMJIT_INLINE bool hasRet() const noexcept { return _ret != TypeId::kVoid; }</a>
+<a name="469"><span class="lineNum">     469 </span>            :   //! Get the return value type.</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">       3596 :   ASMJIT_INLINE uint32_t getRet() const noexcept { return _ret; }</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :   //! Get the type of the argument at index `i`.</a>
+<a name="473"><span class="lineNum">     473 </span>            :   ASMJIT_INLINE uint32_t getArg(uint32_t i) const noexcept {</a>
+<a name="474"><span class="lineNum">     474 </span>            :     ASMJIT_ASSERT(i &lt; _argCount);</a>
+<a name="475"><span class="lineNum">     475 </span>            :     return _args[i];</a>
+<a name="476"><span class="lineNum">     476 </span>            :   }</a>
+<a name="477"><span class="lineNum">     477 </span>            :   //! Get the array of function arguments' types.</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">       3596 :   ASMJIT_INLINE const uint8_t* getArgs() const noexcept { return _args; }</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="481"><span class="lineNum">     481 </span>            :   // [Members]</a>
+<a name="482"><span class="lineNum">     482 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :   uint8_t _callConv;                     //!&lt; Calling convention id.</a>
+<a name="485"><span class="lineNum">     485 </span>            :   uint8_t _argCount;                     //!&lt; Count of arguments.</a>
+<a name="486"><span class="lineNum">     486 </span>            :   uint8_t _vaIndex;                      //!&lt; Index to a first vararg or `kNoVarArgs`.</a>
+<a name="487"><span class="lineNum">     487 </span>            :   uint8_t _ret;                          //!&lt; TypeId of a return value.</a>
+<a name="488"><span class="lineNum">     488 </span>            :   const uint8_t* _args;                  //!&lt; TypeIds of function arguments.</a>
+<a name="489"><span class="lineNum">     489 </span>            : };</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            : // ============================================================================</a>
+<a name="492"><span class="lineNum">     492 </span>            : // [asmjit::FuncSignatureT]</a>
+<a name="493"><span class="lineNum">     493 </span>            : // ============================================================================</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            : //! \internal</a>
+<a name="496"><span class="lineNum">     496 </span>            : #define T(TYPE) TypeIdOf&lt;TYPE&gt;::kTypeId</a>
+<a name="497"><span class="lineNum">     497 </span>            : namespace { // unnamed namespace to avoid unique global symbols</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            : //! Static function signature (no arguments).</a>
+<a name="500"><span class="lineNum">     500 </span>            : template&lt;typename RET&gt;</a>
+<a name="501"><span class="lineNum">     501 </span>            : class FuncSignature0 : public FuncSignature {</a>
+<a name="502"><span class="lineNum">     502 </span>            : public:</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">       1948 :   ASMJIT_INLINE FuncSignature0(uint32_t ccId = CallConv::kIdHost) noexcept {</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :     init(ccId, T(RET), nullptr, 0);</a>
+<a name="505"><span class="lineNum">     505 </span>            :   }</a>
+<a name="506"><span class="lineNum">     506 </span>            : };</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span>            : //! Static function signature (1 argument).</a>
+<a name="509"><span class="lineNum">     509 </span>            : template&lt;typename RET, typename A0&gt;</a>
+<a name="510"><span class="lineNum">     510 </span>            : class FuncSignature1 : public FuncSignature {</a>
+<a name="511"><span class="lineNum">     511 </span>            : public:</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">       1426 :   ASMJIT_INLINE FuncSignature1(uint32_t ccId = CallConv::kIdHost) noexcept {</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :     static const uint8_t args[] = { T(A0) };</a>
+<a name="514"><span class="lineNum">     514 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="515"><span class="lineNum">     515 </span>            :   }</a>
+<a name="516"><span class="lineNum">     516 </span>            : };</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : //! Static function signature (2 arguments).</a>
+<a name="519"><span class="lineNum">     519 </span>            : template&lt;typename RET, typename A0, typename A1&gt;</a>
+<a name="520"><span class="lineNum">     520 </span>            : class FuncSignature2 : public FuncSignature {</a>
+<a name="521"><span class="lineNum">     521 </span>            : public:</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        222 :   ASMJIT_INLINE FuncSignature2(uint32_t ccId = CallConv::kIdHost) noexcept {</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :     static const uint8_t args[] = { T(A0), T(A1) };</a>
+<a name="524"><span class="lineNum">     524 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="525"><span class="lineNum">     525 </span>            :   }</a>
+<a name="526"><span class="lineNum">     526 </span>            : };</a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span>            : //! Static function signature (3 arguments).</a>
+<a name="529"><span class="lineNum">     529 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2&gt;</a>
+<a name="530"><span class="lineNum">     530 </span>            : class FuncSignature3 : public FuncSignature {</a>
+<a name="531"><span class="lineNum">     531 </span>            : public:</a>
+<a name="532"><span class="lineNum">     532 </span>            :   ASMJIT_INLINE FuncSignature3(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="533"><span class="lineNum">     533 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2) };</a>
+<a name="534"><span class="lineNum">     534 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="535"><span class="lineNum">     535 </span>            :   }</a>
+<a name="536"><span class="lineNum">     536 </span>            : };</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            : //! Static function signature (4 arguments).</a>
+<a name="539"><span class="lineNum">     539 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3&gt;</a>
+<a name="540"><span class="lineNum">     540 </span>            : class FuncSignature4 : public FuncSignature {</a>
+<a name="541"><span class="lineNum">     541 </span>            : public:</a>
+<a name="542"><span class="lineNum">     542 </span>            :   ASMJIT_INLINE FuncSignature4(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="543"><span class="lineNum">     543 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3) };</a>
+<a name="544"><span class="lineNum">     544 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="545"><span class="lineNum">     545 </span>            :   }</a>
+<a name="546"><span class="lineNum">     546 </span>            : };</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            : //! Static function signature (5 arguments).</a>
+<a name="549"><span class="lineNum">     549 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3, typename A4&gt;</a>
+<a name="550"><span class="lineNum">     550 </span>            : class FuncSignature5 : public FuncSignature {</a>
+<a name="551"><span class="lineNum">     551 </span>            : public:</a>
+<a name="552"><span class="lineNum">     552 </span>            :   ASMJIT_INLINE FuncSignature5(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="553"><span class="lineNum">     553 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3), T(A4) };</a>
+<a name="554"><span class="lineNum">     554 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="555"><span class="lineNum">     555 </span>            :   }</a>
+<a name="556"><span class="lineNum">     556 </span>            : };</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            : //! Static function signature (6 arguments).</a>
+<a name="559"><span class="lineNum">     559 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3, typename A4, typename A5&gt;</a>
+<a name="560"><span class="lineNum">     560 </span>            : class FuncSignature6 : public FuncSignature {</a>
+<a name="561"><span class="lineNum">     561 </span>            : public:</a>
+<a name="562"><span class="lineNum">     562 </span>            :   ASMJIT_INLINE FuncSignature6(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="563"><span class="lineNum">     563 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3), T(A4), T(A5) };</a>
+<a name="564"><span class="lineNum">     564 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="565"><span class="lineNum">     565 </span>            :   }</a>
+<a name="566"><span class="lineNum">     566 </span>            : };</a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span>            : //! Static function signature (7 arguments).</a>
+<a name="569"><span class="lineNum">     569 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3, typename A4, typename A5, typename A6&gt;</a>
+<a name="570"><span class="lineNum">     570 </span>            : class FuncSignature7 : public FuncSignature {</a>
+<a name="571"><span class="lineNum">     571 </span>            : public:</a>
+<a name="572"><span class="lineNum">     572 </span>            :   ASMJIT_INLINE FuncSignature7(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="573"><span class="lineNum">     573 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3), T(A4), T(A5), T(A6) };</a>
+<a name="574"><span class="lineNum">     574 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="575"><span class="lineNum">     575 </span>            :   }</a>
+<a name="576"><span class="lineNum">     576 </span>            : };</a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span>            : //! Static function signature (8 arguments).</a>
+<a name="579"><span class="lineNum">     579 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3, typename A4, typename A5, typename A6, typename A7&gt;</a>
+<a name="580"><span class="lineNum">     580 </span>            : class FuncSignature8 : public FuncSignature {</a>
+<a name="581"><span class="lineNum">     581 </span>            : public:</a>
+<a name="582"><span class="lineNum">     582 </span>            :   ASMJIT_INLINE FuncSignature8(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="583"><span class="lineNum">     583 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3), T(A4), T(A5), T(A6), T(A7) };</a>
+<a name="584"><span class="lineNum">     584 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="585"><span class="lineNum">     585 </span>            :   }</a>
+<a name="586"><span class="lineNum">     586 </span>            : };</a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span>            : //! Static function signature (9 arguments).</a>
+<a name="589"><span class="lineNum">     589 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3, typename A4, typename A5, typename A6, typename A7, typename A8&gt;</a>
+<a name="590"><span class="lineNum">     590 </span>            : class FuncSignature9 : public FuncSignature {</a>
+<a name="591"><span class="lineNum">     591 </span>            : public:</a>
+<a name="592"><span class="lineNum">     592 </span>            :   ASMJIT_INLINE FuncSignature9(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="593"><span class="lineNum">     593 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3), T(A4), T(A5), T(A6), T(A7), T(A8) };</a>
+<a name="594"><span class="lineNum">     594 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="595"><span class="lineNum">     595 </span>            :   }</a>
+<a name="596"><span class="lineNum">     596 </span>            : };</a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span>            : //! Static function signature (10 arguments).</a>
+<a name="599"><span class="lineNum">     599 </span>            : template&lt;typename RET, typename A0, typename A1, typename A2, typename A3, typename A4, typename A5, typename A6, typename A7, typename A8, typename A9&gt;</a>
+<a name="600"><span class="lineNum">     600 </span>            : class FuncSignature10 : public FuncSignature {</a>
+<a name="601"><span class="lineNum">     601 </span>            : public:</a>
+<a name="602"><span class="lineNum">     602 </span>            :   ASMJIT_INLINE FuncSignature10(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="603"><span class="lineNum">     603 </span>            :     static const uint8_t args[] = { T(A0), T(A1), T(A2), T(A3), T(A4), T(A5), T(A6), T(A7), T(A8), T(A9) };</a>
+<a name="604"><span class="lineNum">     604 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="605"><span class="lineNum">     605 </span>            :   }</a>
+<a name="606"><span class="lineNum">     606 </span>            : };</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span>            : #if ASMJIT_CC_HAS_VARIADIC_TEMPLATES</a>
+<a name="609"><span class="lineNum">     609 </span>            : //! Static function signature (variadic).</a>
+<a name="610"><span class="lineNum">     610 </span>            : template&lt;typename RET, typename... ARGS&gt;</a>
+<a name="611"><span class="lineNum">     611 </span>            : class FuncSignatureT : public FuncSignature {</a>
+<a name="612"><span class="lineNum">     612 </span>            : public:</a>
+<a name="613"><span class="lineNum">     613 </span>            :   ASMJIT_INLINE FuncSignatureT(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="614"><span class="lineNum">     614 </span>            :     static const uint8_t args[] = { (T(ARGS))... };</a>
+<a name="615"><span class="lineNum">     615 </span>            :     init(ccId, T(RET), args, ASMJIT_ARRAY_SIZE(args));</a>
+<a name="616"><span class="lineNum">     616 </span>            :   }</a>
+<a name="617"><span class="lineNum">     617 </span>            : };</a>
+<a name="618"><span class="lineNum">     618 </span>            : #endif // ASMJIT_CC_HAS_VARIADIC_TEMPLATES</a>
+<a name="619"><span class="lineNum">     619 </span>            : </a>
+<a name="620"><span class="lineNum">     620 </span>            : }</a>
+<a name="621"><span class="lineNum">     621 </span>            : #undef T</a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span>            : // ============================================================================</a>
+<a name="624"><span class="lineNum">     624 </span>            : // [asmjit::FuncSignatureX]</a>
+<a name="625"><span class="lineNum">     625 </span>            : // ============================================================================</a>
+<a name="626"><span class="lineNum">     626 </span>            : </a>
+<a name="627"><span class="lineNum">     627 </span>            : //! Dynamic function signature.</a>
+<a name="628"><span class="lineNum">     628 </span>            : class FuncSignatureX : public FuncSignature {</a>
+<a name="629"><span class="lineNum">     629 </span>            : public:</a>
+<a name="630"><span class="lineNum">     630 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="631"><span class="lineNum">     631 </span>            :   // [Construction / Destruction]</a>
+<a name="632"><span class="lineNum">     632 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :   ASMJIT_INLINE FuncSignatureX(uint32_t ccId = CallConv::kIdHost) noexcept {</a>
+<a name="635"><span class="lineNum">     635 </span>            :     init(ccId, TypeId::kVoid, _builderArgList, 0);</a>
+<a name="636"><span class="lineNum">     636 </span>            :   }</a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="639"><span class="lineNum">     639 </span>            :   // [Accessors]</a>
+<a name="640"><span class="lineNum">     640 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span>            :   ASMJIT_INLINE void setCallConv(uint32_t ccId) noexcept {</a>
+<a name="643"><span class="lineNum">     643 </span>            :     ASMJIT_ASSERT(ccId &lt;= 0xFF);</a>
+<a name="644"><span class="lineNum">     644 </span>            :     _callConv = static_cast&lt;uint8_t&gt;(ccId);</a>
+<a name="645"><span class="lineNum">     645 </span>            :   }</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            :   //! Set the return type to `retType`.</a>
+<a name="648"><span class="lineNum">     648 </span>            :   ASMJIT_INLINE void setRet(uint32_t retType) noexcept { _ret = retType; }</a>
+<a name="649"><span class="lineNum">     649 </span>            :   //! Set the return type based on `T`.</a>
+<a name="650"><span class="lineNum">     650 </span>            :   template&lt;typename T&gt;</a>
+<a name="651"><span class="lineNum">     651 </span>            :   ASMJIT_INLINE void setRetT() noexcept { setRet(TypeIdOf&lt;T&gt;::kTypeId); }</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            :   //! Set the argument at index `i` to the `type`</a>
+<a name="654"><span class="lineNum">     654 </span>            :   ASMJIT_INLINE void setArg(uint32_t i, uint32_t type) noexcept {</a>
+<a name="655"><span class="lineNum">     655 </span>            :     ASMJIT_ASSERT(i &lt; _argCount);</a>
+<a name="656"><span class="lineNum">     656 </span>            :     _builderArgList[i] = type;</a>
+<a name="657"><span class="lineNum">     657 </span>            :   }</a>
+<a name="658"><span class="lineNum">     658 </span>            :   //! Set the argument at index `i` to the type based on `T`.</a>
+<a name="659"><span class="lineNum">     659 </span>            :   template&lt;typename T&gt;</a>
+<a name="660"><span class="lineNum">     660 </span>            :   ASMJIT_INLINE void setArgT(uint32_t i) noexcept { setArg(i, TypeIdOf&lt;T&gt;::kTypeId); }</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span>            :   //! Append an argument of `type` to the function prototype.</a>
+<a name="663"><span class="lineNum">     663 </span>            :   ASMJIT_INLINE void addArg(uint32_t type) noexcept {</a>
+<a name="664"><span class="lineNum">     664 </span>            :     ASMJIT_ASSERT(_argCount &lt; kFuncArgCount);</a>
+<a name="665"><span class="lineNum">     665 </span>            :     _builderArgList[_argCount++] = static_cast&lt;uint8_t&gt;(type);</a>
+<a name="666"><span class="lineNum">     666 </span>            :   }</a>
+<a name="667"><span class="lineNum">     667 </span>            :   //! Append an argument of type based on `T` to the function prototype.</a>
+<a name="668"><span class="lineNum">     668 </span>            :   template&lt;typename T&gt;</a>
+<a name="669"><span class="lineNum">     669 </span>            :   ASMJIT_INLINE void addArgT() noexcept { addArg(TypeIdOf&lt;T&gt;::kTypeId); }</a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="672"><span class="lineNum">     672 </span>            :   // [Members]</a>
+<a name="673"><span class="lineNum">     673 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="674"><span class="lineNum">     674 </span>            : </a>
+<a name="675"><span class="lineNum">     675 </span>            :   uint8_t _builderArgList[kFuncArgCount];</a>
+<a name="676"><span class="lineNum">     676 </span>            : };</a>
+<a name="677"><span class="lineNum">     677 </span>            : </a>
+<a name="678"><span class="lineNum">     678 </span>            : // ============================================================================</a>
+<a name="679"><span class="lineNum">     679 </span>            : // [asmjit::FuncDetail]</a>
+<a name="680"><span class="lineNum">     680 </span>            : // ============================================================================</a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span>            : //! Function detail - CallConv and expanded FuncSignature.</a>
+<a name="683"><span class="lineNum">     683 </span>            : //!</a>
+<a name="684"><span class="lineNum">     684 </span>            : //! Function details is architecture and OS dependent representation of function.</a>
+<a name="685"><span class="lineNum">     685 </span>            : //! It contains calling convention and expanded function signature so all</a>
+<a name="686"><span class="lineNum">     686 </span>            : //! arguments have assigned either register type &amp; id or stack address.</a>
+<a name="687"><span class="lineNum">     687 </span>            : class FuncDetail {</a>
+<a name="688"><span class="lineNum">     688 </span>            : public:</a>
+<a name="689"><span class="lineNum">     689 </span>            :   ASMJIT_ENUM(Limits) {</a>
+<a name="690"><span class="lineNum">     690 </span>            :     kMaxVRegKinds = Globals::kMaxVRegKinds</a>
+<a name="691"><span class="lineNum">     691 </span>            :   };</a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :   //! Argument or return value as defined by `FuncSignature`, but with register</a>
+<a name="694"><span class="lineNum">     694 </span>            :   //! or stack address (and other metadata) assigned.</a>
+<a name="695"><span class="lineNum">     695 </span>            :   struct Value {</a>
+<a name="696"><span class="lineNum">     696 </span>            :     ASMJIT_ENUM(Parts) {</a>
+<a name="697"><span class="lineNum">     697 </span>            :       kTypeIdShift      = 24,</a>
+<a name="698"><span class="lineNum">     698 </span>            :       kTypeIdMask       = 0xFF000000U,</a>
+<a name="699"><span class="lineNum">     699 </span>            : </a>
+<a name="700"><span class="lineNum">     700 </span>            :       kRegTypeShift     = 8,</a>
+<a name="701"><span class="lineNum">     701 </span>            :       kRegTypeMask      = 0x0000FF00U,</a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span>            :       kRegIdShift       = 0,</a>
+<a name="704"><span class="lineNum">     704 </span>            :       kRegIdMask        = 0x000000FFU,</a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            :       kStackOffsetShift = 0,</a>
+<a name="707"><span class="lineNum">     707 </span>            :       kStackOffsetMask  = 0x0000FFFFU,</a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span>            :       kIsByReg          = 0x00010000U,</a>
+<a name="710"><span class="lineNum">     710 </span>            :       kIsByStack        = 0x00020000U,</a>
+<a name="711"><span class="lineNum">     711 </span>            :       kIsIndirect       = 0x00040000U</a>
+<a name="712"><span class="lineNum">     712 </span>            :     };</a>
+<a name="713"><span class="lineNum">     713 </span>            : </a>
+<a name="714"><span class="lineNum">     714 </span>            :     //! Get if this value is initialized (i.e. contains a valid data).</a>
+<a name="715"><span class="lineNum">     715 </span>            :     ASMJIT_INLINE bool isInitialized() const noexcept { return _value != 0; }</a>
+<a name="716"><span class="lineNum">     716 </span>            :     //! Initialize this in/out by a given `typeId`.</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">       5466 :     ASMJIT_INLINE void initTypeId(uint32_t typeId) noexcept { _value = typeId &lt;&lt; kTypeIdShift; }</span></a>
+<a name="718"><span class="lineNum">     718 </span>            :     //! Initialize this in/out by a given `typeId`, `regType`, and `regId`.</a>
+<a name="719"><span class="lineNum">     719 </span>            :     ASMJIT_INLINE void initReg(uint32_t typeId, uint32_t regType, uint32_t regId) noexcept {</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">       1450 :       _value = (typeId &lt;&lt; kTypeIdShift) | (regType &lt;&lt; kRegTypeShift) | (regId &lt;&lt; kRegIdShift) | kIsByReg;</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="722"><span class="lineNum">     722 </span>            :     //! Initialize this in/out by a given `typeId` and `offset`.</a>
+<a name="723"><span class="lineNum">     723 </span>            :     ASMJIT_INLINE void initStack(uint32_t typeId, uint32_t stackOffset) noexcept {</a>
+<a name="724"><span class="lineNum">     724 </span>            :       _value = (typeId &lt;&lt; kTypeIdShift) | (stackOffset &lt;&lt; kStackOffsetShift) | kIsByStack;</a>
+<a name="725"><span class="lineNum">     725 </span>            :     }</a>
+<a name="726"><span class="lineNum">     726 </span>            :     //! Reset the value to its uninitialized and unassigned state.</a>
+<a name="727"><span class="lineNum">     727 </span>            :     ASMJIT_INLINE void reset() noexcept { _value = 0; }</a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span>            :     ASMJIT_INLINE void assignToReg(uint32_t regType, uint32_t regId) noexcept {</a>
+<a name="730"><span class="lineNum">     730 </span>            :       ASMJIT_ASSERT(!isAssigned());</a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">        420 :       _value |= (regType &lt;&lt; kRegTypeShift) | (regId &lt;&lt; kRegIdShift) | kIsByReg;</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">       3596 :     }</span></a>
+<a name="733"><span class="lineNum">     733 </span>            : </a>
+<a name="734"><span class="lineNum">     734 </span>            :     ASMJIT_INLINE void assignToStack(int32_t offset) noexcept {</a>
+<a name="735"><span class="lineNum">     735 </span>            :       ASMJIT_ASSERT(!isAssigned());</a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :       _value |= (offset &lt;&lt; kStackOffsetShift) | kIsByStack;</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :     }</a>
+<a name="738"><span class="lineNum">     738 </span>            : </a>
+<a name="739"><span class="lineNum">     739 </span>            :     //! Get if this argument is passed by register.</a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">       6394 :     ASMJIT_INLINE bool byReg() const noexcept { return (_value &amp; kIsByReg) != 0; }</span></a>
+<a name="741"><span class="lineNum">     741 </span>            :     //! Get if this argument is passed by stack.</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE bool byStack() const noexcept { return (_value &amp; kIsByStack) != 0; }</span></a>
+<a name="743"><span class="lineNum">     743 </span>            :     //! Get if this argument is passed by register.</a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE bool isAssigned() const noexcept { return (_value &amp; (kIsByReg | kIsByStack)) != 0; }</span></a>
+<a name="745"><span class="lineNum">     745 </span>            :     //! Get if this argument is passed through a pointer (used by WIN64 to pass XMM|YMM|ZMM).</a>
+<a name="746"><span class="lineNum">     746 </span>            :     ASMJIT_INLINE bool isIndirect() const noexcept { return (_value &amp; kIsIndirect) != 0; }</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span>            :     //! Get virtual type of this argument or return value.</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">       5886 :     ASMJIT_INLINE uint32_t getTypeId() const noexcept { return _value &gt;&gt; kTypeIdShift; }</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :     //! Get a register type of the register used to pass the argument or return the value.</a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">       6694 :     ASMJIT_INLINE uint32_t getRegType() const noexcept { return (_value &amp; kRegTypeMask) &gt;&gt; kRegTypeShift; }</span></a>
+<a name="752"><span class="lineNum">     752 </span>            :     //! Get a physical id of the register used to pass the argument or return the value.</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">       7114 :     ASMJIT_INLINE uint32_t getRegId() const noexcept { return (_value &amp; kRegIdMask) &gt;&gt; kRegIdShift; }</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :     //! Get a stack offset of this argument (always positive).</a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE int32_t getStackOffset() const noexcept { return (_value &amp; kStackOffsetMask) &gt;&gt; kStackOffsetShift; }</span></a>
+<a name="756"><span class="lineNum">     756 </span>            : </a>
+<a name="757"><span class="lineNum">     757 </span>            :     uint32_t _value;</a>
+<a name="758"><span class="lineNum">     758 </span>            :   };</a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="761"><span class="lineNum">     761 </span>            :   // [Construction / Destruction]</a>
+<a name="762"><span class="lineNum">     762 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">       3596 :   ASMJIT_INLINE FuncDetail() noexcept { reset(); }</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :   ASMJIT_INLINE FuncDetail(const FuncDetail&amp; other) noexcept {</a>
+<a name="766"><span class="lineNum">     766 </span>            :     ::memcpy(this, &amp;other, sizeof(*this));</a>
+<a name="767"><span class="lineNum">     767 </span>            :   }</a>
+<a name="768"><span class="lineNum">     768 </span>            : </a>
+<a name="769"><span class="lineNum">     769 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="770"><span class="lineNum">     770 </span>            :   // [Init / Reset]</a>
+<a name="771"><span class="lineNum">     771 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            :   //! Initialize this `FuncDetail` to the given signature.</a>
+<a name="774"><span class="lineNum">     774 </span>            :   ASMJIT_API Error init(const FuncSignature&amp; sign);</a>
+<a name="775"><span class="lineNum">     775 </span>            :   ASMJIT_INLINE void reset() noexcept { ::memset(this, 0, sizeof(*this)); }</a>
+<a name="776"><span class="lineNum">     776 </span>            : </a>
+<a name="777"><span class="lineNum">     777 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="778"><span class="lineNum">     778 </span>            :   // [Accessors - Calling Convention]</a>
+<a name="779"><span class="lineNum">     779 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="780"><span class="lineNum">     780 </span>            : </a>
+<a name="781"><span class="lineNum">     781 </span>            :   //! Get the function's calling convention, see `CallConv`.</a>
+<a name="782"><span class="lineNum">     782 </span>            :   ASMJIT_INLINE const CallConv&amp; getCallConv() const noexcept { return _callConv; }</a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span>            :   //! Get CallConv flags, see \ref CallConv::Flags.</a>
+<a name="785"><span class="lineNum">     785 </span>            :   ASMJIT_INLINE uint32_t getFlags() const noexcept { return _callConv.getFlags(); }</a>
+<a name="786"><span class="lineNum">     786 </span>            :   //! Check if a CallConv `flag` is set, see \ref CallConv::Flags.</a>
+<a name="787"><span class="lineNum">     787 </span>            :   ASMJIT_INLINE bool hasFlag(uint32_t ccFlag) const noexcept { return _callConv.hasFlag(ccFlag); }</a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="790"><span class="lineNum">     790 </span>            :   // [Accessors - Arguments and Return]</a>
+<a name="791"><span class="lineNum">     791 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span>            :   //! Get count of function return values.</a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">       3596 :   ASMJIT_INLINE uint32_t getRetCount() const noexcept { return _retCount; }</span></a>
+<a name="795"><span class="lineNum">     795 </span>            :   //! Get the number of function arguments.</a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">      12658 :   ASMJIT_INLINE uint32_t getArgCount() const noexcept { return _argCount; }</span></a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span>            :   //! Get whether the function has a return value.</a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasRet() const noexcept { return _retCount != 0; }</span></a>
+<a name="800"><span class="lineNum">     800 </span>            :   //! Get function return value.</a>
+<a name="801"><span class="lineNum">     801 </span>            :   ASMJIT_INLINE Value&amp; getRet(size_t index = 0) noexcept {</a>
+<a name="802"><span class="lineNum">     802 </span>            :     ASMJIT_ASSERT(index &lt; ASMJIT_ARRAY_SIZE(_rets));</a>
+<a name="803"><span class="lineNum">     803 </span>            :     return _rets[index];</a>
+<a name="804"><span class="lineNum">     804 </span>            :   }</a>
+<a name="805"><span class="lineNum">     805 </span>            :   //! Get function return value (const).</a>
+<a name="806"><span class="lineNum">     806 </span>            :   ASMJIT_INLINE const Value&amp; getRet(size_t index = 0) const noexcept {</a>
+<a name="807"><span class="lineNum">     807 </span>            :     ASMJIT_ASSERT(index &lt; ASMJIT_ARRAY_SIZE(_rets));</a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineNoCov">          0 :     return _rets[index];</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :   }</a>
+<a name="810"><span class="lineNum">     810 </span>            : </a>
+<a name="811"><span class="lineNum">     811 </span>            :   //! Get function arguments array.</a>
+<a name="812"><span class="lineNum">     812 </span>            :   ASMJIT_INLINE Value* getArgs() noexcept { return _args; }</a>
+<a name="813"><span class="lineNum">     813 </span>            :   //! Get function arguments array (const).</a>
+<a name="814"><span class="lineNum">     814 </span>            :   ASMJIT_INLINE const Value* getArgs() const noexcept { return _args; }</a>
+<a name="815"><span class="lineNum">     815 </span>            : </a>
+<a name="816"><span class="lineNum">     816 </span>            :   ASMJIT_INLINE bool hasArg(size_t index) const noexcept {</a>
+<a name="817"><span class="lineNum">     817 </span>            :     ASMJIT_ASSERT(index &lt; kFuncArgCountLoHi);</a>
+<a name="818"><span class="lineNum">     818 </span>            :     return _args[index].isInitialized();</a>
+<a name="819"><span class="lineNum">     819 </span>            :   }</a>
+<a name="820"><span class="lineNum">     820 </span>            : </a>
+<a name="821"><span class="lineNum">     821 </span>            :   //! Get function argument at index `index`.</a>
+<a name="822"><span class="lineNum">     822 </span>            :   ASMJIT_INLINE Value&amp; getArg(size_t index) noexcept {</a>
+<a name="823"><span class="lineNum">     823 </span>            :     ASMJIT_ASSERT(index &lt; kFuncArgCountLoHi);</a>
+<a name="824"><span class="lineNum">     824 </span>            :     return _args[index];</a>
+<a name="825"><span class="lineNum">     825 </span>            :   }</a>
+<a name="826"><span class="lineNum">     826 </span>            : </a>
+<a name="827"><span class="lineNum">     827 </span>            :   //! Get function argument at index `index`.</a>
+<a name="828"><span class="lineNum">     828 </span>            :   ASMJIT_INLINE const Value&amp; getArg(size_t index) const noexcept {</a>
+<a name="829"><span class="lineNum">     829 </span>            :     ASMJIT_ASSERT(index &lt; kFuncArgCountLoHi);</a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineNoCov">          0 :     return _args[index];</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :   }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            :   ASMJIT_INLINE void resetArg(size_t index) noexcept {</a>
+<a name="834"><span class="lineNum">     834 </span>            :     ASMJIT_ASSERT(index &lt; kFuncArgCountLoHi);</a>
+<a name="835"><span class="lineNum">     835 </span>            :     _args[index].reset();</a>
+<a name="836"><span class="lineNum">     836 </span>            :   }</a>
+<a name="837"><span class="lineNum">     837 </span>            : </a>
+<a name="838"><span class="lineNum">     838 </span>            :   //! Get if the function passes one or more argument by stack.</a>
+<a name="839"><span class="lineNum">     839 </span>            :   ASMJIT_INLINE bool hasStackArgs() const noexcept { return _argStackSize != 0; }</a>
+<a name="840"><span class="lineNum">     840 </span>            :   //! Get stack size needed for function arguments passed on the stack.</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getArgStackSize() const noexcept { return _argStackSize; }</span></a>
+<a name="842"><span class="lineNum">     842 </span>            : </a>
+<a name="843"><span class="lineNum">     843 </span>            :   ASMJIT_INLINE uint32_t getNaturalStackAlignment() const noexcept { return _callConv.getNaturalStackAlignment(); }</a>
+<a name="844"><span class="lineNum">     844 </span>            :   ASMJIT_INLINE uint32_t getSpillZoneSize() const noexcept { return _callConv.getSpillZoneSize(); }</a>
+<a name="845"><span class="lineNum">     845 </span>            :   ASMJIT_INLINE uint32_t getRedZoneSize() const noexcept { return _callConv.getRedZoneSize(); }</a>
+<a name="846"><span class="lineNum">     846 </span>            : </a>
+<a name="847"><span class="lineNum">     847 </span>            :   ASMJIT_INLINE uint32_t getPassedRegs(uint32_t kind) const noexcept { return _callConv.getPassedRegs(kind); }</a>
+<a name="848"><span class="lineNum">     848 </span>            :   ASMJIT_INLINE uint32_t getPreservedRegs(uint32_t kind) const noexcept { return _callConv.getPreservedRegs(kind); }</a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span>            :   ASMJIT_INLINE uint32_t getUsedRegs(uint32_t kind) const noexcept {</a>
+<a name="851"><span class="lineNum">     851 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">       5244 :     return _usedRegs[kind];</span></a>
+<a name="853"><span class="lineNum">     853 </span>            :   }</a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span>            :   ASMJIT_INLINE void addUsedRegs(uint32_t kind, uint32_t regs) noexcept {</a>
+<a name="856"><span class="lineNum">     856 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">       1870 :     _usedRegs[kind] |= regs;</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="861"><span class="lineNum">     861 </span>            :   // [Members]</a>
+<a name="862"><span class="lineNum">     862 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span>            :   CallConv _callConv;                    //!&lt; Calling convention.</a>
+<a name="865"><span class="lineNum">     865 </span>            :   uint8_t _argCount;                     //!&lt; Number of function arguments.</a>
+<a name="866"><span class="lineNum">     866 </span>            :   uint8_t _retCount;                     //!&lt; Number of function return values.</a>
+<a name="867"><span class="lineNum">     867 </span>            :   uint32_t _usedRegs[kMaxVRegKinds];     //!&lt; Registers that contains arguments (signature dependent).</a>
+<a name="868"><span class="lineNum">     868 </span>            :   uint32_t _argStackSize;                //!&lt; Size of arguments passed by stack.</a>
+<a name="869"><span class="lineNum">     869 </span>            :   Value _rets[2];                        //!&lt; Function return values.</a>
+<a name="870"><span class="lineNum">     870 </span>            :   Value _args[kFuncArgCountLoHi];        //!&lt; Function arguments.</a>
+<a name="871"><span class="lineNum">     871 </span>            : };</a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            : // ============================================================================</a>
+<a name="874"><span class="lineNum">     874 </span>            : // [asmjit::FuncFrameInfo]</a>
+<a name="875"><span class="lineNum">     875 </span>            : // ============================================================================</a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span>            : //! Function-frame information.</a>
+<a name="878"><span class="lineNum">     878 </span>            : //!</a>
+<a name="879"><span class="lineNum">     879 </span>            : //! This structure can be used to create a function frame in a cross-platform</a>
+<a name="880"><span class="lineNum">     880 </span>            : //! way. It contains information about the function's stack to be used and</a>
+<a name="881"><span class="lineNum">     881 </span>            : //! registers to be saved and restored. Based on this information in can</a>
+<a name="882"><span class="lineNum">     882 </span>            : //! calculate the optimal layout of a function as \ref FuncFrameLayout.</a>
+<a name="883"><span class="lineNum">     883 </span>            : struct FuncFrameInfo {</a>
+<a name="884"><span class="lineNum">     884 </span>            :   ASMJIT_ENUM(Limits) {</a>
+<a name="885"><span class="lineNum">     885 </span>            :     kMaxVRegKinds = Globals::kMaxVRegKinds</a>
+<a name="886"><span class="lineNum">     886 </span>            :   };</a>
+<a name="887"><span class="lineNum">     887 </span>            : </a>
+<a name="888"><span class="lineNum">     888 </span>            :   //! Attributes.</a>
+<a name="889"><span class="lineNum">     889 </span>            :   //!</a>
+<a name="890"><span class="lineNum">     890 </span>            :   //! Attributes are designed in a way that all are initially false, and user</a>
+<a name="891"><span class="lineNum">     891 </span>            :   //! or function-frame finalizer sets them when necessary. Architecture-specific</a>
+<a name="892"><span class="lineNum">     892 </span>            :   //! attributes are prefixed with the architecture name.</a>
+<a name="893"><span class="lineNum">     893 </span>            :   ASMJIT_ENUM(Attributes) {</a>
+<a name="894"><span class="lineNum">     894 </span>            :     kAttrPreserveFP       = 0x00000001U, //!&lt; Preserve frame pointer (EBP|RBP).</a>
+<a name="895"><span class="lineNum">     895 </span>            :     kAttrCompactPE        = 0x00000002U, //!&lt; Use smaller, but possibly slower prolog/epilog.</a>
+<a name="896"><span class="lineNum">     896 </span>            :     kAttrHasCalls         = 0x00000004U, //!&lt; Function calls other functions (is not leaf).</a>
+<a name="897"><span class="lineNum">     897 </span>            : </a>
+<a name="898"><span class="lineNum">     898 </span>            :     kX86AttrAlignedVecSR  = 0x00010000U, //!&lt; Use aligned save/restore of VEC regs.</a>
+<a name="899"><span class="lineNum">     899 </span>            :     kX86AttrMmxCleanup    = 0x00020000U, //!&lt; Emit EMMS instruction in epilog (X86).</a>
+<a name="900"><span class="lineNum">     900 </span>            :     kX86AttrAvxCleanup    = 0x00040000U, //!&lt; Emit VZEROUPPER instruction in epilog (X86).</a>
+<a name="901"><span class="lineNum">     901 </span>            :     kX86AttrAvxEnabled    = 0x00080000U  //!&lt; Use AVX instead of SSE for all operations (X86).</a>
+<a name="902"><span class="lineNum">     902 </span>            :   };</a>
+<a name="903"><span class="lineNum">     903 </span>            : </a>
+<a name="904"><span class="lineNum">     904 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="905"><span class="lineNum">     905 </span>            :   // [Construction / Destruction]</a>
+<a name="906"><span class="lineNum">     906 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">       1948 :   ASMJIT_INLINE FuncFrameInfo() noexcept { reset(); }</span></a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span>            :   ASMJIT_INLINE FuncFrameInfo(const FuncFrameInfo&amp; other) noexcept {</a>
+<a name="911"><span class="lineNum">     911 </span>            :     ::memcpy(this, &amp;other, sizeof(*this));</a>
+<a name="912"><span class="lineNum">     912 </span>            :   }</a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="915"><span class="lineNum">     915 </span>            :   // [Init / Reset]</a>
+<a name="916"><span class="lineNum">     916 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="919"><span class="lineNum">     919 </span>            :     ::memset(this, 0, sizeof(*this));</a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">       1948 :     _stackArgsRegId = Globals::kInvalidRegId;</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :   }</a>
+<a name="922"><span class="lineNum">     922 </span>            : </a>
+<a name="923"><span class="lineNum">     923 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="924"><span class="lineNum">     924 </span>            :   // [Accessors]</a>
+<a name="925"><span class="lineNum">     925 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="926"><span class="lineNum">     926 </span>            : </a>
+<a name="927"><span class="lineNum">     927 </span>            :   //! Get frame-info flags, see \ref Attributes.</a>
+<a name="928"><span class="lineNum">     928 </span>            :   ASMJIT_INLINE uint32_t getAttributes() const noexcept { return _attributes; }</a>
+<a name="929"><span class="lineNum">     929 </span>            :   //! Check if a frame-info `flag` is set, see \ref Attributes.</a>
+<a name="930"><span class="lineNum">     930 </span>            :   ASMJIT_INLINE bool hasAttribute(uint32_t attr) const noexcept { return (_attributes &amp; attr) != 0; }</a>
+<a name="931"><span class="lineNum">     931 </span>            :   //! Add `flags` to the frame-info, see \ref Attributes.</a>
+<a name="932"><span class="lineNum">     932 </span>            :   ASMJIT_INLINE void addAttributes(uint32_t attrs) noexcept { _attributes |= attrs; }</a>
+<a name="933"><span class="lineNum">     933 </span>            :   //! Clear `flags` from the frame-info, see \ref Attributes.</a>
+<a name="934"><span class="lineNum">     934 </span>            :   ASMJIT_INLINE void clearAttributes(uint32_t attrs) noexcept { _attributes &amp;= ~attrs; }</a>
+<a name="935"><span class="lineNum">     935 </span>            : </a>
+<a name="936"><span class="lineNum">     936 </span>            :   //! Get if the function preserves frame pointer (EBP|ESP on X86).</a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">       5844 :   ASMJIT_INLINE bool hasPreservedFP() const noexcept { return (_attributes &amp; kAttrPreserveFP) != 0; }</span></a>
+<a name="938"><span class="lineNum">     938 </span>            :   //! Enable preserved frame pointer.</a>
+<a name="939"><span class="lineNum">     939 </span>            :   ASMJIT_INLINE void enablePreservedFP() noexcept { _attributes |= kAttrPreserveFP; }</a>
+<a name="940"><span class="lineNum">     940 </span>            :   //! Disable preserved frame pointer.</a>
+<a name="941"><span class="lineNum">     941 </span>            :   ASMJIT_INLINE void disablePreservedFP() noexcept { _attributes &amp;= ~kAttrPreserveFP; }</a>
+<a name="942"><span class="lineNum">     942 </span>            : </a>
+<a name="943"><span class="lineNum">     943 </span>            :   //! Get if the function prolog and epilog should be compacted (as small as possible).</a>
+<a name="944"><span class="lineNum">     944 </span>            :   ASMJIT_INLINE bool hasCompactPE() const noexcept { return (_attributes &amp; kAttrCompactPE) != 0; }</a>
+<a name="945"><span class="lineNum">     945 </span>            :   //! Enable compact prolog/epilog.</a>
+<a name="946"><span class="lineNum">     946 </span>            :   ASMJIT_INLINE void enableCompactPE() noexcept { _attributes |= kAttrCompactPE; }</a>
+<a name="947"><span class="lineNum">     947 </span>            :   //! Disable compact prolog/epilog.</a>
+<a name="948"><span class="lineNum">     948 </span>            :   ASMJIT_INLINE void disableCompactPE() noexcept { _attributes &amp;= ~kAttrCompactPE; }</a>
+<a name="949"><span class="lineNum">     949 </span>            : </a>
+<a name="950"><span class="lineNum">     950 </span>            :   //! Get if the function calls other functions.</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">       1016 :   ASMJIT_INLINE bool hasCalls() const noexcept { return (_attributes &amp; kAttrHasCalls) != 0; }</span></a>
+<a name="952"><span class="lineNum">     952 </span>            :   //! Set `kFlagHasCalls` to true.</a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">       1648 :   ASMJIT_INLINE void enableCalls() noexcept { _attributes |= kAttrHasCalls; }</span></a>
+<a name="954"><span class="lineNum">     954 </span>            :   //! Set `kFlagHasCalls` to false.</a>
+<a name="955"><span class="lineNum">     955 </span>            :   ASMJIT_INLINE void disableCalls() noexcept { _attributes &amp;= ~kAttrHasCalls; }</a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            :   //! Get if the function contains MMX cleanup - 'emms' instruction in epilog.</a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasMmxCleanup() const noexcept { return (_attributes &amp; kX86AttrMmxCleanup) != 0; }</span></a>
+<a name="959"><span class="lineNum">     959 </span>            :   //! Enable MMX cleanup.</a>
+<a name="960"><span class="lineNum">     960 </span>            :   ASMJIT_INLINE void enableMmxCleanup() noexcept { _attributes |= kX86AttrMmxCleanup; }</a>
+<a name="961"><span class="lineNum">     961 </span>            :   //! Disable MMX cleanup.</a>
+<a name="962"><span class="lineNum">     962 </span>            :   ASMJIT_INLINE void disableMmxCleanup() noexcept { _attributes &amp;= ~kX86AttrMmxCleanup; }</a>
+<a name="963"><span class="lineNum">     963 </span>            : </a>
+<a name="964"><span class="lineNum">     964 </span>            :   //! Get if the function contains AVX cleanup - 'vzeroupper' instruction in epilog.</a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasAvxCleanup() const noexcept { return (_attributes &amp; kX86AttrAvxCleanup) != 0; }</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :   //! Enable AVX cleanup.</a>
+<a name="967"><span class="lineNum">     967 </span>            :   ASMJIT_INLINE void enableAvxCleanup() noexcept { _attributes |= kX86AttrAvxCleanup; }</a>
+<a name="968"><span class="lineNum">     968 </span>            :   //! Disable AVX cleanup.</a>
+<a name="969"><span class="lineNum">     969 </span>            :   ASMJIT_INLINE void disableAvxCleanup() noexcept { _attributes &amp;= ~kX86AttrAvxCleanup; }</a>
+<a name="970"><span class="lineNum">     970 </span>            : </a>
+<a name="971"><span class="lineNum">     971 </span>            :   //! Get if the function contains AVX cleanup - 'vzeroupper' instruction in epilog.</a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool isAvxEnabled() const noexcept { return (_attributes &amp; kX86AttrAvxEnabled) != 0; }</span></a>
+<a name="973"><span class="lineNum">     973 </span>            :   //! Enable AVX cleanup.</a>
+<a name="974"><span class="lineNum">     974 </span>            :   ASMJIT_INLINE void enableAvx() noexcept { _attributes |= kX86AttrAvxEnabled; }</a>
+<a name="975"><span class="lineNum">     975 </span>            :   //! Disable AVX cleanup.</a>
+<a name="976"><span class="lineNum">     976 </span>            :   ASMJIT_INLINE void disableAvx() noexcept { _attributes &amp;= ~kX86AttrAvxEnabled; }</a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span>            :   //! Get which registers (by `kind`) are saved/restored in prolog/epilog, respectively.</a>
+<a name="979"><span class="lineNum">     979 </span>            :   ASMJIT_INLINE uint32_t getDirtyRegs(uint32_t kind) const noexcept {</a>
+<a name="980"><span class="lineNum">     980 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">       7792 :     return _dirtyRegs[kind];</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :   }</a>
+<a name="983"><span class="lineNum">     983 </span>            : </a>
+<a name="984"><span class="lineNum">     984 </span>            :   //! Set which registers (by `kind`) are saved/restored in prolog/epilog, respectively.</a>
+<a name="985"><span class="lineNum">     985 </span>            :   ASMJIT_INLINE void setDirtyRegs(uint32_t kind, uint32_t regs) noexcept {</a>
+<a name="986"><span class="lineNum">     986 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">       1948 :     _dirtyRegs[kind] = regs;</span></a>
+<a name="988"><span class="lineNum">     988 </span>            :   }</a>
+<a name="989"><span class="lineNum">     989 </span>            : </a>
+<a name="990"><span class="lineNum">     990 </span>            :   //! Add registers (by `kind`) to saved/restored registers.</a>
+<a name="991"><span class="lineNum">     991 </span>            :   ASMJIT_INLINE void addDirtyRegs(uint32_t kind, uint32_t regs) noexcept {</a>
+<a name="992"><span class="lineNum">     992 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineNoCov">          0 :     _dirtyRegs[kind] |= regs;</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span>            :   ASMJIT_INLINE void setAllDirty() noexcept {</a>
+<a name="997"><span class="lineNum">     997 </span>            :     _dirtyRegs[0] = 0xFFFFFFFFU;</a>
+<a name="998"><span class="lineNum">     998 </span>            :     _dirtyRegs[1] = 0xFFFFFFFFU;</a>
+<a name="999"><span class="lineNum">     999 </span>            :     _dirtyRegs[2] = 0xFFFFFFFFU;</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :     _dirtyRegs[3] = 0xFFFFFFFFU;</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   }</a>
+<a name="1002"><span class="lineNum">    1002 </span>            : </a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   ASMJIT_INLINE void setAllDirty(uint32_t kind) noexcept {</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :     _dirtyRegs[kind] = 0xFFFFFFFFU;</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   }</a>
+<a name="1007"><span class="lineNum">    1007 </span>            : </a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   //! Get stack-frame size used by the function.</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   ASMJIT_INLINE uint32_t getStackFrameSize() const noexcept { return _stackFrameSize; }</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   //! Get call-frame size used by the function.</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :   ASMJIT_INLINE uint32_t getCallFrameSize() const noexcept { return _callFrameSize; }</a>
+<a name="1012"><span class="lineNum">    1012 </span>            : </a>
+<a name="1013"><span class="lineNum">    1013 </span>            :   //! Get minimum stack-frame alignment required by the function.</a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getStackFrameAlignment() const noexcept { return _stackFrameAlignment; }</span></a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   //! Get minimum call-frame alignment required by the function.</a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getCallFrameAlignment() const noexcept { return _callFrameAlignment; }</span></a>
+<a name="1017"><span class="lineNum">    1017 </span>            : </a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void setStackFrameSize(uint32_t size) noexcept { _stackFrameSize = size; }</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   ASMJIT_INLINE void setCallFrameSize(uint32_t size) noexcept { _callFrameSize = size; }</a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span>            :   ASMJIT_INLINE void setStackFrameAlignment(uint32_t value) noexcept {</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :     ASMJIT_ASSERT(value &lt; 256);</a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">       1948 :     _stackFrameAlignment = static_cast&lt;uint8_t&gt;(value);</span></a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   }</a>
+<a name="1025"><span class="lineNum">    1025 </span>            : </a>
+<a name="1026"><span class="lineNum">    1026 </span>            :   ASMJIT_INLINE void setCallFrameAlignment(uint32_t value) noexcept {</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :     ASMJIT_ASSERT(value &lt; 256);</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     _callFrameAlignment = static_cast&lt;uint8_t&gt;(value);</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :   }</a>
+<a name="1030"><span class="lineNum">    1030 </span>            : </a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   ASMJIT_INLINE void mergeStackFrameSize(uint32_t size) noexcept { _stackFrameSize = std::max&lt;uint32_t&gt;(_stackFrameSize, size); }</a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">       1648 :   ASMJIT_INLINE void mergeCallFrameSize(uint32_t size) noexcept { _callFrameSize = std::max&lt;uint32_t&gt;(_callFrameSize, size); }</span></a>
+<a name="1033"><span class="lineNum">    1033 </span>            : </a>
+<a name="1034"><span class="lineNum">    1034 </span>            :   ASMJIT_INLINE void mergeStackFrameAlignment(uint32_t value) noexcept {</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     ASMJIT_ASSERT(value &lt; 256);</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :     _stackFrameAlignment = static_cast&lt;uint8_t&gt;(std::max&lt;uint32_t&gt;(_stackFrameAlignment, value));</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :   }</a>
+<a name="1038"><span class="lineNum">    1038 </span>            : </a>
+<a name="1039"><span class="lineNum">    1039 </span>            :   ASMJIT_INLINE void mergeCallFrameAlignment(uint32_t value) noexcept {</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :     ASMJIT_ASSERT(value &lt; 256);</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     _callFrameAlignment = static_cast&lt;uint8_t&gt;(std::max&lt;uint32_t&gt;(_callFrameAlignment, value));</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :   }</a>
+<a name="1043"><span class="lineNum">    1043 </span>            : </a>
+<a name="1044"><span class="lineNum">    1044 </span>            :   ASMJIT_INLINE bool hasStackArgsRegId() const noexcept {</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     return _stackArgsRegId != Globals::kInvalidRegId;</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :   }</a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getStackArgsRegId() const noexcept { return _stackArgsRegId; }</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void setStackArgsRegId(uint32_t regId) { _stackArgsRegId = regId; }</span></a>
+<a name="1049"><span class="lineNum">    1049 </span>            : </a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   // [Members]</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1053"><span class="lineNum">    1053 </span>            : </a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   uint32_t _attributes;                  //!&lt; Function attributes.</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   uint32_t _dirtyRegs[kMaxVRegKinds];    //!&lt; Registers used by the function.</a>
+<a name="1056"><span class="lineNum">    1056 </span>            : </a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   uint8_t _stackFrameAlignment;          //!&lt; Minimum alignment of stack-frame.</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   uint8_t _callFrameAlignment;           //!&lt; Minimum alignment of call-frame.</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   uint8_t _stackArgsRegId;               //!&lt; Register that holds base-address to arguments passed by stack.</a>
+<a name="1060"><span class="lineNum">    1060 </span>            : </a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   uint32_t _stackFrameSize;              //!&lt; Size of a stack-frame used by the function.</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   uint32_t _callFrameSize;               //!&lt; Size of a call-frame (not part of _stackFrameSize).</a>
+<a name="1063"><span class="lineNum">    1063 </span>            : };</a>
+<a name="1064"><span class="lineNum">    1064 </span>            : </a>
+<a name="1065"><span class="lineNum">    1065 </span>            : // ============================================================================</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : // [asmjit::FuncFrameLayout]</a>
+<a name="1067"><span class="lineNum">    1067 </span>            : // ============================================================================</a>
+<a name="1068"><span class="lineNum">    1068 </span>            : </a>
+<a name="1069"><span class="lineNum">    1069 </span>            : //! Function-frame layout.</a>
+<a name="1070"><span class="lineNum">    1070 </span>            : //!</a>
+<a name="1071"><span class="lineNum">    1071 </span>            : //! Function layout is used directly by prolog and epilog insertion helpers. It</a>
+<a name="1072"><span class="lineNum">    1072 </span>            : //! contains only information necessary to insert proper prolog and epilog, and</a>
+<a name="1073"><span class="lineNum">    1073 </span>            : //! should be always calculated from \ref FuncDetail and \ref FuncFrameInfo, where</a>
+<a name="1074"><span class="lineNum">    1074 </span>            : //! \ref FuncDetail defines function's calling convention and signature, and \ref</a>
+<a name="1075"><span class="lineNum">    1075 </span>            : //! FuncFrameInfo specifies how much stack is used, and which registers are dirty.</a>
+<a name="1076"><span class="lineNum">    1076 </span>            : struct FuncFrameLayout {</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   ASMJIT_ENUM(Limits) {</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     kMaxVRegKinds = Globals::kMaxVRegKinds</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   };</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : </a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   // [Init / Reset]</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1084"><span class="lineNum">    1084 </span>            : </a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   ASMJIT_API Error init(const FuncDetail&amp; func, const FuncFrameInfo&amp; ffi) noexcept;</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   ASMJIT_INLINE void reset() noexcept { ::memset(this, 0, sizeof(*this)); }</a>
+<a name="1087"><span class="lineNum">    1087 </span>            : </a>
+<a name="1088"><span class="lineNum">    1088 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :   // [Accessors]</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1091"><span class="lineNum">    1091 </span>            : </a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">       7792 :   ASMJIT_INLINE bool hasPreservedFP() const noexcept { return static_cast&lt;bool&gt;(_preservedFP); }</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasDsaSlotUsed() const noexcept { return static_cast&lt;bool&gt;(_dsaSlotUsed); }</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasAlignedVecSR() const noexcept { return static_cast&lt;bool&gt;(_alignedVecSR); }</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">       5844 :   ASMJIT_INLINE bool hasDynamicAlignment() const noexcept { return static_cast&lt;bool&gt;(_dynamicAlignment); }</span></a>
+<a name="1096"><span class="lineNum">    1096 </span>            : </a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasMmxCleanup() const noexcept { return static_cast&lt;bool&gt;(_mmxCleanup); }</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasAvxCleanup() const noexcept { return static_cast&lt;bool&gt;(_avxCleanup); }</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool isAvxEnabled() const noexcept { return static_cast&lt;bool&gt;(_avxEnabled); }</span></a>
+<a name="1100"><span class="lineNum">    1100 </span>            : </a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   ASMJIT_INLINE uint32_t getSavedRegs(uint32_t kind) const noexcept {</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     ASMJIT_ASSERT(kind &lt; kMaxVRegKinds);</a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">       7792 :     return _savedRegs[kind];</span></a>
+<a name="1104"><span class="lineNum">    1104 </span>            :   }</a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   //! Get stack size.</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   ASMJIT_INLINE uint32_t getStackSize() const noexcept { return _stackSize; }</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   //! Get stack alignment.</a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getStackAlignment() const noexcept { return _stackAlignment; }</span></a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   //! Get the offset needed to access the function's stack (it skips call-stack).</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   ASMJIT_INLINE uint32_t getStackBaseOffset() const noexcept { return _stackBaseOffset; }</a>
+<a name="1112"><span class="lineNum">    1112 </span>            : </a>
+<a name="1113"><span class="lineNum">    1113 </span>            :   //! Get stack size required to save GP registers.</a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getGpStackSize() const noexcept { return _gpStackSize; }</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   //! Get stack size required to save VEC registers.</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :   ASMJIT_INLINE uint32_t getVecStackSize() const noexcept { return _vecStackSize; }</a>
+<a name="1117"><span class="lineNum">    1117 </span>            : </a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   ASMJIT_INLINE uint32_t getGpStackOffset() const noexcept { return _gpStackOffset; }</a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getVecStackOffset() const noexcept { return _vecStackOffset; }</span></a>
+<a name="1120"><span class="lineNum">    1120 </span>            : </a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getStackArgsRegId() const noexcept { return _stackArgsRegId; }</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getStackArgsOffset() const noexcept { return _stackArgsOffset; }</span></a>
+<a name="1123"><span class="lineNum">    1123 </span>            : </a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">       3896 :   ASMJIT_INLINE bool hasStackAdjustment() const noexcept { return _stackAdjustment != 0; }</span></a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   ASMJIT_INLINE uint32_t getStackAdjustment() const noexcept { return _stackAdjustment; }</a>
+<a name="1126"><span class="lineNum">    1126 </span>            : </a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool hasCalleeStackCleanup() const noexcept { return _calleeStackCleanup != 0; }</span></a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   ASMJIT_INLINE uint32_t getCalleeStackCleanup() const noexcept { return _calleeStackCleanup; }</a>
+<a name="1129"><span class="lineNum">    1129 </span>            : </a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   // [Members]</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1133"><span class="lineNum">    1133 </span>            : </a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   uint8_t _stackAlignment;               //!&lt; Final stack alignment of the functions.</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   uint8_t _stackBaseRegId;               //!&lt; GP register that holds address of base stack address.</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :   uint8_t _stackArgsRegId;               //!&lt; GP register that holds address of the first argument passed by stack.</a>
+<a name="1137"><span class="lineNum">    1137 </span>            : </a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   uint32_t _savedRegs[kMaxVRegKinds];    //!&lt; Registers that will be saved/restored in prolog/epilog.</a>
+<a name="1139"><span class="lineNum">    1139 </span>            : </a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   uint32_t _preservedFP : 1;             //!&lt; Function preserves frame-pointer.</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   uint32_t _dsaSlotUsed : 1;             //!&lt; True if `_dsaSlot` contains a valid memory slot/offset.</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :   uint32_t _alignedVecSR : 1;            //!&lt; Use instructions that perform aligned ops to save/restore XMM regs.</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :   uint32_t _dynamicAlignment : 1;        //!&lt; Function must dynamically align the stack.</a>
+<a name="1144"><span class="lineNum">    1144 </span>            : </a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   uint32_t _mmxCleanup : 1;              //!&lt; Emit 'emms' in epilog (X86).</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   uint32_t _avxCleanup : 1;              //!&lt; Emit 'vzeroupper' in epilog (X86).</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   uint32_t _avxEnabled : 1;              //!&lt; Use AVX instead of SSE for SIMD saves/restores (X86).</a>
+<a name="1148"><span class="lineNum">    1148 </span>            : </a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   uint32_t _stackSize;                   //!&lt; Stack size (sum of function's stack and call stack).</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :   uint32_t _stackBaseOffset;             //!&lt; Stack offset (non-zero if kFlagHasCalls is set).</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   uint32_t _stackAdjustment;             //!&lt; Stack adjustment in prolog/epilog.</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :   uint32_t _stackArgsOffset;             //!&lt; Offset to the first argument passed by stack of _stackArgsRegId.</a>
+<a name="1153"><span class="lineNum">    1153 </span>            : </a>
+<a name="1154"><span class="lineNum">    1154 </span>            :   uint32_t _dsaSlot;                     //!&lt; Memory slot where the prolog inserter stores previous (unaligned) ESP.</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :   uint16_t _calleeStackCleanup;          //!&lt; How many bytes the callee should add to the stack (X86 STDCALL).</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :   uint16_t _gpStackSize;                 //!&lt; Stack size required to save GP regs.</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :   uint16_t _vecStackSize;                //!&lt; Stack size required to save VEC regs.</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   uint32_t _gpStackOffset;               //!&lt; Offset where saved GP regs are stored.</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :   uint32_t _vecStackOffset;              //!&lt; Offset where saved GP regs are stored.</a>
+<a name="1160"><span class="lineNum">    1160 </span>            : };</a>
+<a name="1161"><span class="lineNum">    1161 </span>            : </a>
+<a name="1162"><span class="lineNum">    1162 </span>            : // ============================================================================</a>
+<a name="1163"><span class="lineNum">    1163 </span>            : // [asmjit::FuncArgsMapper]</a>
+<a name="1164"><span class="lineNum">    1164 </span>            : // ============================================================================</a>
+<a name="1165"><span class="lineNum">    1165 </span>            : </a>
+<a name="1166"><span class="lineNum">    1166 </span>            : //! Assign a physical register to each function argument.</a>
+<a name="1167"><span class="lineNum">    1167 </span>            : //!</a>
+<a name="1168"><span class="lineNum">    1168 </span>            : //! This is used to specify where each function argument should be shuffled</a>
+<a name="1169"><span class="lineNum">    1169 </span>            : //! or allocated (in case it's passed by stack).</a>
+<a name="1170"><span class="lineNum">    1170 </span>            : class FuncArgsMapper {</a>
+<a name="1171"><span class="lineNum">    1171 </span>            : public:</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :   struct Value {</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :     // NOTE: The layout is compatible with FuncDetail::Value except stack.</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :     ASMJIT_ENUM(Parts) {</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :       kTypeIdShift      = 24,</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :       kTypeIdMask       = 0xFF000000U,</a>
+<a name="1177"><span class="lineNum">    1177 </span>            : </a>
+<a name="1178"><span class="lineNum">    1178 </span>            :       kRegTypeShift     = 8,</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :       kRegTypeMask      = 0x0000FF00U,</a>
+<a name="1180"><span class="lineNum">    1180 </span>            : </a>
+<a name="1181"><span class="lineNum">    1181 </span>            :       kRegIdShift       = 0,</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :       kRegIdMask        = 0x000000FFU,</a>
+<a name="1183"><span class="lineNum">    1183 </span>            : </a>
+<a name="1184"><span class="lineNum">    1184 </span>            :       kIsAssigned       = 0x00010000U</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     };</a>
+<a name="1186"><span class="lineNum">    1186 </span>            : </a>
+<a name="1187"><span class="lineNum">    1187 </span>            :     //! Get if this value is initialized (i.e. contains a valid data).</a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE bool isAssigned() const noexcept { return _value != 0; }</span></a>
+<a name="1189"><span class="lineNum">    1189 </span>            :     //! Initialize this in/out by a given `typeId`, `regType`, and `regId`.</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     ASMJIT_INLINE void assign(uint32_t typeId, uint32_t regType, uint32_t regId) noexcept {</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :       _value = (typeId &lt;&lt; kTypeIdShift) | (regType &lt;&lt; kRegTypeShift) | (regId &lt;&lt; kRegIdShift) | kIsAssigned;</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :     }</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :     //! Reset the value to its unassigned state.</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :     ASMJIT_INLINE void reset() noexcept { _value = 0; }</a>
+<a name="1195"><span class="lineNum">    1195 </span>            : </a>
+<a name="1196"><span class="lineNum">    1196 </span>            :     //! Get virtual type of this argument or return value.</a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE uint32_t getTypeId() const noexcept { return _value &gt;&gt; kTypeIdShift; }</span></a>
+<a name="1198"><span class="lineNum">    1198 </span>            :     //! Get a register type of the register used to pass the argument or return the value.</a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE uint32_t getRegType() const noexcept { return (_value &amp; kRegTypeMask) &gt;&gt; kRegTypeShift; }</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            :     //! Get a physical id of the register used to pass the argument or return the value.</a>
+<a name="1201"><span class="lineNum">    1201 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE uint32_t getRegId() const noexcept { return (_value &amp; kRegIdMask) &gt;&gt; kRegIdShift; }</span></a>
+<a name="1202"><span class="lineNum">    1202 </span>            : </a>
+<a name="1203"><span class="lineNum">    1203 </span>            :     uint32_t _value;</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :   };</a>
+<a name="1205"><span class="lineNum">    1205 </span>            : </a>
+<a name="1206"><span class="lineNum">    1206 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1207"><span class="lineNum">    1207 </span>            :   // [Construction / Destruction]</a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1209"><span class="lineNum">    1209 </span>            : </a>
+<a name="1210"><span class="lineNum">    1210 </span>            :   explicit ASMJIT_INLINE FuncArgsMapper(const FuncDetail* fd) noexcept { reset(fd); }</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :   ASMJIT_INLINE FuncArgsMapper(const FuncArgsMapper&amp; other) noexcept {</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :     ::memcpy(this, &amp;other, sizeof(*this));</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :   }</a>
+<a name="1214"><span class="lineNum">    1214 </span>            : </a>
+<a name="1215"><span class="lineNum">    1215 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :   // [Reset]</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1218"><span class="lineNum">    1218 </span>            : </a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   ASMJIT_INLINE void reset(const FuncDetail* fd = nullptr) noexcept {</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :     _funcDetail = fd;</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :     ::memset(_args, 0, sizeof(_args));</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   }</a>
+<a name="1223"><span class="lineNum">    1223 </span>            : </a>
+<a name="1224"><span class="lineNum">    1224 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :   // [Accessors]</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1227"><span class="lineNum">    1227 </span>            : </a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const FuncDetail* getFuncDetail() const noexcept { return _funcDetail; }</span></a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   ASMJIT_INLINE void setFuncDetail(const FuncDetail* fd) noexcept { _funcDetail = fd; }</a>
+<a name="1230"><span class="lineNum">    1230 </span>            : </a>
+<a name="1231"><span class="lineNum">    1231 </span>            :   ASMJIT_INLINE Value&amp; getArg(size_t index) noexcept {</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :     ASMJIT_ASSERT(index &lt; ASMJIT_ARRAY_SIZE(_args));</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     return _args[index];</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :   }</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :   ASMJIT_INLINE const Value&amp; getArg(size_t index) const noexcept {</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     ASMJIT_ASSERT(index &lt; ASMJIT_ARRAY_SIZE(_args));</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :     return _args[index];</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :   }</a>
+<a name="1239"><span class="lineNum">    1239 </span>            : </a>
+<a name="1240"><span class="lineNum">    1240 </span>            :   ASMJIT_INLINE bool isAssigned(size_t index) const noexcept {</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :     ASMJIT_ASSERT(index &lt; ASMJIT_ARRAY_SIZE(_args));</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :     return _args[index].isAssigned();</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :   }</a>
+<a name="1244"><span class="lineNum">    1244 </span>            : </a>
+<a name="1245"><span class="lineNum">    1245 </span>            :   ASMJIT_INLINE void assign(size_t index, const Reg&amp; reg, uint32_t typeId = TypeId::kVoid) noexcept {</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :     // Not designed for virtual registers.</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :     ASMJIT_ASSERT(index &lt; ASMJIT_ARRAY_SIZE(_args));</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :     ASMJIT_ASSERT(reg.isPhysReg());</a>
+<a name="1249"><span class="lineNum">    1249 </span>            : </a>
+<a name="1250"><span class="lineNum">    1250 </span>            :     _args[index].assign(typeId, reg.getType(), reg.getId());</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :   }</a>
+<a name="1252"><span class="lineNum">    1252 </span>            : </a>
+<a name="1253"><span class="lineNum">    1253 </span>            :   // NOTE: All `assignAll()` methods are shortcuts to assign all arguments at</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   // once, however, since registers are passed all at once these initializers</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :   // don't provide any way to pass TypeId and/or to keep any argument between</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :   // the arguments passed uninitialized.</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0) noexcept {</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :     assign(0, a0);</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :   }</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1) noexcept {</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :     assign(0, a0); assign(1, a1);</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   }</a>
+<a name="1263"><span class="lineNum">    1263 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1, const Reg&amp; a2) noexcept {</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :     assign(0, a0); assign(1, a1); assign(2, a2);</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :   }</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1, const Reg&amp; a2, const Reg&amp; a3) noexcept {</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :     assign(0, a0); assign(1, a1); assign(2, a2); assign(3, a3);</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :   }</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1, const Reg&amp; a2, const Reg&amp; a3, const Reg&amp; a4) noexcept {</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :     assign(0, a0); assign(1, a1); assign(2, a2); assign(3, a3);</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :     assign(4, a4);</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :   }</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1, const Reg&amp; a2, const Reg&amp; a3, const Reg&amp; a4, const Reg&amp; a5) noexcept {</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :     assign(0, a0); assign(1, a1); assign(2, a2); assign(3, a3);</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :     assign(4, a4); assign(5, a5);</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :   }</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1, const Reg&amp; a2, const Reg&amp; a3, const Reg&amp; a4, const Reg&amp; a5, const Reg&amp; a6) noexcept {</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :     assign(0, a0); assign(1, a1); assign(2, a2); assign(3, a3);</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :     assign(4, a4); assign(5, a5); assign(6, a6);</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :   }</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :   ASMJIT_INLINE void assignAll(const Reg&amp; a0, const Reg&amp; a1, const Reg&amp; a2, const Reg&amp; a3, const Reg&amp; a4, const Reg&amp; a5, const Reg&amp; a6, const Reg&amp; a7) noexcept {</a>
+<a name="1282"><span class="lineNum">    1282 </span>            :     assign(0, a0); assign(1, a1); assign(2, a2); assign(3, a3);</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :     assign(4, a4); assign(5, a5); assign(6, a6); assign(7, a7);</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :   }</a>
+<a name="1285"><span class="lineNum">    1285 </span>            : </a>
+<a name="1286"><span class="lineNum">    1286 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :   // [Utilities]</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1289"><span class="lineNum">    1289 </span>            : </a>
+<a name="1290"><span class="lineNum">    1290 </span>            :   //! Update `FuncFrameInfo` accordingly to FuncArgsMapper.</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :   //!</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :   //! This method must be called if you use `FuncArgsMapper` and you plan to</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :   //! use `FuncUtils::allocArgs()` to remap all arguments after the prolog is</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :   //! inserted.</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :   ASMJIT_API Error updateFrameInfo(FuncFrameInfo&amp; ffi) const noexcept;</a>
+<a name="1296"><span class="lineNum">    1296 </span>            : </a>
+<a name="1297"><span class="lineNum">    1297 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :   // [Members]</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1300"><span class="lineNum">    1300 </span>            : </a>
+<a name="1301"><span class="lineNum">    1301 </span>            :   const FuncDetail* _funcDetail;         //!&lt; Function detail.</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :   Value _args[kFuncArgCountLoHi];        //!&lt; Mapping of each function argument.</a>
+<a name="1303"><span class="lineNum">    1303 </span>            : };</a>
+<a name="1304"><span class="lineNum">    1304 </span>            : </a>
+<a name="1305"><span class="lineNum">    1305 </span>            : // ============================================================================</a>
+<a name="1306"><span class="lineNum">    1306 </span>            : // [asmjit::FuncUtils]</a>
+<a name="1307"><span class="lineNum">    1307 </span>            : // ============================================================================</a>
+<a name="1308"><span class="lineNum">    1308 </span>            : </a>
+<a name="1309"><span class="lineNum">    1309 </span>            : struct FuncUtils {</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   ASMJIT_API static Error emitProlog(CodeEmitter* emitter, const FuncFrameLayout&amp; layout);</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :   ASMJIT_API static Error emitEpilog(CodeEmitter* emitter, const FuncFrameLayout&amp; layout);</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :   ASMJIT_API static Error allocArgs(CodeEmitter* emitter, const FuncFrameLayout&amp; layout, const FuncArgsMapper&amp; args);</a>
+<a name="1313"><span class="lineNum">    1313 </span>            : };</a>
+<a name="1314"><span class="lineNum">    1314 </span>            : </a>
+<a name="1315"><span class="lineNum">    1315 </span>            : //! \}</a>
+<a name="1316"><span class="lineNum">    1316 </span>            : </a>
+<a name="1317"><span class="lineNum">    1317 </span>            : } // asmjit namespace</a>
+<a name="1318"><span class="lineNum">    1318 </span>            : } // namespace PLMD</a>
+<a name="1319"><span class="lineNum">    1319 </span>            : </a>
+<a name="1320"><span class="lineNum">    1320 </span>            : // [Api-End]</a>
+<a name="1321"><span class="lineNum">    1321 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="1322"><span class="lineNum">    1322 </span>            : </a>
+<a name="1323"><span class="lineNum">    1323 </span>            : // [Guard]</a>
+<a name="1324"><span class="lineNum">    1324 </span>            : #endif // _ASMJIT_BASE_FUNC_H</a>
+<a name="1325"><span class="lineNum">    1325 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1326"><span class="lineNum">    1326 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="1327"><span class="lineNum">    1327 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/globals.cpp.func-sort-c.html b/coverage-libs/asmjit/globals.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3643615fcc
--- /dev/null
+++ b/coverage-libs/asmjit/globals.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/globals.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - globals.cpp<span style="font-size: 80%;"> (<a href="globals.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="globals.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="globals.cpp.gcov.html#114">_ZN4PLMD6asmjit10DebugUtils11debugOutputEPKc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="globals.cpp.gcov.html#105">_ZN4PLMD6asmjit10DebugUtils13errorAsStringEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="globals.cpp.gcov.html#122">_ZN4PLMD6asmjit10DebugUtils15assertionFailedEPKciS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/globals.cpp.func.html b/coverage-libs/asmjit/globals.cpp.func.html
new file mode 100644
index 0000000000..0c0d71d2c5
--- /dev/null
+++ b/coverage-libs/asmjit/globals.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/globals.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - globals.cpp<span style="font-size: 80%;"> (<a href="globals.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="globals.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="globals.cpp.gcov.html#114">_ZN4PLMD6asmjit10DebugUtils11debugOutputEPKc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="globals.cpp.gcov.html#105">_ZN4PLMD6asmjit10DebugUtils13errorAsStringEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="globals.cpp.gcov.html#122">_ZN4PLMD6asmjit10DebugUtils15assertionFailedEPKciS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/globals.cpp.gcov.html b/coverage-libs/asmjit/globals.cpp.gcov.html
new file mode 100644
index 0000000000..f1f239e5b8
--- /dev/null
+++ b/coverage-libs/asmjit/globals.cpp.gcov.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/globals.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - globals.cpp<span style="font-size: 80%;"> (source / <a href="globals.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./globals.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Api-Begin]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace asmjit {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // ============================================================================</a>
+<a name="43"><span class="lineNum">      43 </span>            : // [asmjit::DebugUtils]</a>
+<a name="44"><span class="lineNum">      44 </span>            : // ============================================================================</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : #if !defined(ASMJIT_DISABLE_TEXT)</a>
+<a name="47"><span class="lineNum">      47 </span>            : static const char errorMessages[] =</a>
+<a name="48"><span class="lineNum">      48 </span>            :   &quot;Ok\0&quot;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   &quot;No heap memory\0&quot;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   &quot;No virtual memory\0&quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   &quot;Invalid argument\0&quot;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   &quot;Invalid state\0&quot;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   &quot;Invalid architecture\0&quot;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   &quot;Not initialized\0&quot;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   &quot;Already initialized\0&quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   &quot;Feature not enabled\0&quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   &quot;Slot occupied\0&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   &quot;No code generated\0&quot;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   &quot;Code too large\0&quot;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   &quot;Invalid label\0&quot;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   &quot;Label index overflow\0&quot;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   &quot;Label already bound\0&quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   &quot;Label already defined\0&quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   &quot;Label name too long\0&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   &quot;Invalid label name\0&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   &quot;Invalid parent label\0&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   &quot;Non-local label can't have parent\0&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   &quot;Relocation index overflow\0&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   &quot;Invalid relocation entry\0&quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   &quot;Invalid instruction\0&quot;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   &quot;Invalid register type\0&quot;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   &quot;Invalid register kind\0&quot;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   &quot;Invalid register's physical id\0&quot;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   &quot;Invalid register's virtual id\0&quot;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   &quot;Invalid prefix combination\0&quot;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   &quot;Invalid lock prefix\0&quot;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   &quot;Invalid xacquire prefix\0&quot;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   &quot;Invalid xrelease prefix\0&quot;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   &quot;Invalid rep prefix\0&quot;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   &quot;Invalid rex prefix\0&quot;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   &quot;Invalid mask, expected {k}\0&quot;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   &quot;Invalid use of {k}\0&quot;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   &quot;Invalid use of {k}{z}\0&quot;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   &quot;Invalid broadcast {1tox}\0&quot;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   &quot;Invalid {er} or {sae} option\0&quot;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   &quot;Invalid address\0&quot;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   &quot;Invalid address index\0&quot;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   &quot;Invalid address scale\0&quot;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   &quot;Invalid use of 64-bit address\0&quot;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   &quot;Invalid displacement\0&quot;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   &quot;Invalid segment\0&quot;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   &quot;Invalid immediate value\0&quot;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   &quot;Invalid operand size\0&quot;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   &quot;Ambiguous operand size\0&quot;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   &quot;Operand size mismatch\0&quot;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   &quot;Invalid type-info\0&quot;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   &quot;Invalid use of a low 8-bit GPB register\0&quot;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   &quot;Invalid use of a 64-bit GPQ register in 32-bit mode\0&quot;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   &quot;Invalid use of an 80-bit float\0&quot;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   &quot;Not consecutive registers\0&quot;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   &quot;No more physical registers\0&quot;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   &quot;Overlapped registers\0&quot;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   &quot;Overlapping register and arguments base-address register\0&quot;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   &quot;Unknown error\0&quot;;</a>
+<a name="105"><span class="lineNum">     105 </span>            : #endif // ASMJIT_DISABLE_TEXT</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE const char* DebugUtils::errorAsString(Error err) noexcept {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : #if !defined(ASMJIT_DISABLE_TEXT)</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :   return Utils::findPackedString(errorMessages, std::min&lt;Error&gt;(err, kErrorCount));</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : #else</a>
+<a name="111"><span class="lineNum">     111 </span>            :   static const char noMessage[] = &quot;&quot;;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   return noMessage;</a>
+<a name="113"><span class="lineNum">     113 </span>            : #endif</a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE void DebugUtils::debugOutput(const char* str) noexcept {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="118"><span class="lineNum">     118 </span>            :   ::OutputDebugStringA(str);</a>
+<a name="119"><span class="lineNum">     119 </span>            : #else</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   ::fputs(str, stderr);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : #endif</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE void DebugUtils::assertionFailed(const char* file, int line, const char* msg) noexcept {</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   char str[1024];</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   snprintf(str, 1024,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     &quot;[asmjit] Assertion failed at %s (line %d):\n&quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :     &quot;[asmjit] %s\n&quot;, file, line, msg);</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Support buggy `snprintf` implementations.</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   str[1023] = '\0';</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   debugOutput(str);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :   ::abort();</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : } // asmjit namespace</a>
+<a name="139"><span class="lineNum">     139 </span>            : } // namespace PLMD</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : // [Api-End]</a>
+<a name="142"><span class="lineNum">     142 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="143"><span class="lineNum">     143 </span>            : #pragma GCC diagnostic pop</a>
+<a name="144"><span class="lineNum">     144 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/globals.h.func-sort-c.html b/coverage-libs/asmjit/globals.h.func-sort-c.html
new file mode 100644
index 0000000000..5221c4edce
--- /dev/null
+++ b/coverage-libs/asmjit/globals.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/globals.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - globals.h<span style="font-size: 80%;"> (<a href="globals.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="globals.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/globals.h.func.html b/coverage-libs/asmjit/globals.h.func.html
new file mode 100644
index 0000000000..ec47e94606
--- /dev/null
+++ b/coverage-libs/asmjit/globals.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/globals.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - globals.h<span style="font-size: 80%;"> (<a href="globals.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="globals.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/globals.h.gcov.html b/coverage-libs/asmjit/globals.h.gcov.html
new file mode 100644
index 0000000000..9587e0ce2c
--- /dev/null
+++ b/coverage-libs/asmjit/globals.h.gcov.html
@@ -0,0 +1,446 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/globals.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - globals.h<span style="font-size: 80%;"> (source / <a href="globals.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_globals_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_globals_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_GLOBALS_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_GLOBALS_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::Globals]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : enum { kInvalidValue = 0xFFFFFFFFU };</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : //! AsmJit globals.</a>
+<a name="54"><span class="lineNum">      54 </span>            : namespace Globals {</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : //! Invalid index</a>
+<a name="57"><span class="lineNum">      57 </span>            : //!</a>
+<a name="58"><span class="lineNum">      58 </span>            : //! Invalid index is the last possible index that is never used in practice. In</a>
+<a name="59"><span class="lineNum">      59 </span>            : //! AsmJit it is used exclusively with strings to indicate the the length of the</a>
+<a name="60"><span class="lineNum">      60 </span>            : //! string is not known and has to be determined.</a>
+<a name="61"><span class="lineNum">      61 </span>            : static const size_t kInvalidIndex = ~static_cast&lt;size_t&gt;(0);</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : //! Invalid base address.</a>
+<a name="64"><span class="lineNum">      64 </span>            : static const uint64_t kNoBaseAddress = ~static_cast&lt;uint64_t&gt;(0);</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : //! Global definitions.</a>
+<a name="67"><span class="lineNum">      67 </span>            : ASMJIT_ENUM(Defs) {</a>
+<a name="68"><span class="lineNum">      68 </span>            :   //! Invalid register id.</a>
+<a name="69"><span class="lineNum">      69 </span>            :   kInvalidRegId = 0xFF,</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   //! Host memory allocator overhead.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   kAllocOverhead = static_cast&lt;int&gt;(sizeof(intptr_t) * 4),</a>
+<a name="73"><span class="lineNum">      73 </span>            :   //! Aggressive growing strategy threshold.</a>
+<a name="74"><span class="lineNum">      74 </span>            :   kAllocThreshold = 8192 * 1024</a>
+<a name="75"><span class="lineNum">      75 </span>            : };</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : ASMJIT_ENUM(Limits) {</a>
+<a name="78"><span class="lineNum">      78 </span>            :   //! Count of register kinds that are important to Function API and CodeCompiler.</a>
+<a name="79"><span class="lineNum">      79 </span>            :   //! The target architecture can define more register kinds for special registers,</a>
+<a name="80"><span class="lineNum">      80 </span>            :   //! but these will never map to virtual registers and will never be used to pass</a>
+<a name="81"><span class="lineNum">      81 </span>            :   //! and return function arguments and function return values, respectively.</a>
+<a name="82"><span class="lineNum">      82 </span>            :   kMaxVRegKinds = 4,</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! Maximum number of physical registers of all kinds of all supported</a>
+<a name="85"><span class="lineNum">      85 </span>            :   //! architectures. This is only important for \ref CodeCompiler and its</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //! \ref RAPass (register allocator pass).</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //!</a>
+<a name="88"><span class="lineNum">      88 </span>            :   //! NOTE: The distribution of these registers is architecture specific.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   kMaxPhysRegs = 64,</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   //! Maximum alignment.</a>
+<a name="92"><span class="lineNum">      92 </span>            :   kMaxAlignment = 64,</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Maximum label or symbol length in bytes (take into consideration that a</a>
+<a name="95"><span class="lineNum">      95 </span>            :   //! single UTF-8 character can take more than single byte to encode it).</a>
+<a name="96"><span class="lineNum">      96 </span>            :   kMaxLabelLength = 2048</a>
+<a name="97"><span class="lineNum">      97 </span>            : };</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : } // Globals namespace</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : // ============================================================================</a>
+<a name="102"><span class="lineNum">     102 </span>            : // [asmjit::Error]</a>
+<a name="103"><span class="lineNum">     103 </span>            : // ============================================================================</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : //! AsmJit error type (uint32_t).</a>
+<a name="106"><span class="lineNum">     106 </span>            : typedef uint32_t Error;</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : //! AsmJit error codes.</a>
+<a name="109"><span class="lineNum">     109 </span>            : ASMJIT_ENUM(ErrorCode) {</a>
+<a name="110"><span class="lineNum">     110 </span>            :   //! No error (success).</a>
+<a name="111"><span class="lineNum">     111 </span>            :   //!</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //! This is default state and state you want.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   kErrorOk = 0,</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   //! Heap memory allocation failed.</a>
+<a name="116"><span class="lineNum">     116 </span>            :   kErrorNoHeapMemory,</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   //! Virtual memory allocation failed.</a>
+<a name="119"><span class="lineNum">     119 </span>            :   kErrorNoVirtualMemory,</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   //! Invalid argument.</a>
+<a name="122"><span class="lineNum">     122 </span>            :   kErrorInvalidArgument,</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   //! Invalid state.</a>
+<a name="125"><span class="lineNum">     125 </span>            :   //!</a>
+<a name="126"><span class="lineNum">     126 </span>            :   //! If this error is returned it means that either you are doing something</a>
+<a name="127"><span class="lineNum">     127 </span>            :   //! wrong or AsmJit caught itself by doing something wrong. This error should</a>
+<a name="128"><span class="lineNum">     128 </span>            :   //! not be underestimated.</a>
+<a name="129"><span class="lineNum">     129 </span>            :   kErrorInvalidState,</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   //! Invalid or incompatible architecture.</a>
+<a name="132"><span class="lineNum">     132 </span>            :   kErrorInvalidArch,</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   //! The object is not initialized.</a>
+<a name="135"><span class="lineNum">     135 </span>            :   kErrorNotInitialized,</a>
+<a name="136"><span class="lineNum">     136 </span>            :   //! The object is already initialized.</a>
+<a name="137"><span class="lineNum">     137 </span>            :   kErrorAlreadyInitialized,</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   //! Built-in feature was disabled at compile time and it's not available.</a>
+<a name="140"><span class="lineNum">     140 </span>            :   kErrorFeatureNotEnabled,</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   //! CodeHolder can't have attached more than one \ref Assembler at a time.</a>
+<a name="143"><span class="lineNum">     143 </span>            :   kErrorSlotOccupied,</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   //! No code generated.</a>
+<a name="146"><span class="lineNum">     146 </span>            :   //!</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //! Returned by runtime if the \ref CodeHolder contains no code.</a>
+<a name="148"><span class="lineNum">     148 </span>            :   kErrorNoCodeGenerated,</a>
+<a name="149"><span class="lineNum">     149 </span>            :   //! Code generated is larger than allowed.</a>
+<a name="150"><span class="lineNum">     150 </span>            :   kErrorCodeTooLarge,</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   //! Attempt to use uninitialized label.</a>
+<a name="153"><span class="lineNum">     153 </span>            :   kErrorInvalidLabel,</a>
+<a name="154"><span class="lineNum">     154 </span>            :   //! Label index overflow - a single `Assembler` instance can hold more than</a>
+<a name="155"><span class="lineNum">     155 </span>            :   //! 2 billion labels (2147483391 to be exact). If there is an attempt to</a>
+<a name="156"><span class="lineNum">     156 </span>            :   //! create more labels this error is returned.</a>
+<a name="157"><span class="lineNum">     157 </span>            :   kErrorLabelIndexOverflow,</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //! Label is already bound.</a>
+<a name="159"><span class="lineNum">     159 </span>            :   kErrorLabelAlreadyBound,</a>
+<a name="160"><span class="lineNum">     160 </span>            :   //! Label is already defined (named labels).</a>
+<a name="161"><span class="lineNum">     161 </span>            :   kErrorLabelAlreadyDefined,</a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! Label name is too long.</a>
+<a name="163"><span class="lineNum">     163 </span>            :   kErrorLabelNameTooLong,</a>
+<a name="164"><span class="lineNum">     164 </span>            :   //! Label must always be local if it's anonymous (without a name).</a>
+<a name="165"><span class="lineNum">     165 </span>            :   kErrorInvalidLabelName,</a>
+<a name="166"><span class="lineNum">     166 </span>            :   //! Parent id passed to `CodeHolder::newNamedLabelId()` was invalid.</a>
+<a name="167"><span class="lineNum">     167 </span>            :   kErrorInvalidParentLabel,</a>
+<a name="168"><span class="lineNum">     168 </span>            :   //! Parent id specified for a non-local (global) label.</a>
+<a name="169"><span class="lineNum">     169 </span>            :   kErrorNonLocalLabelCantHaveParent,</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   //! Relocation index overflow.</a>
+<a name="172"><span class="lineNum">     172 </span>            :   kErrorRelocIndexOverflow,</a>
+<a name="173"><span class="lineNum">     173 </span>            :   //! Invalid relocation entry.</a>
+<a name="174"><span class="lineNum">     174 </span>            :   kErrorInvalidRelocEntry,</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   //! Invalid instruction.</a>
+<a name="177"><span class="lineNum">     177 </span>            :   kErrorInvalidInstruction,</a>
+<a name="178"><span class="lineNum">     178 </span>            :   //! Invalid register type.</a>
+<a name="179"><span class="lineNum">     179 </span>            :   kErrorInvalidRegType,</a>
+<a name="180"><span class="lineNum">     180 </span>            :   //! Invalid register kind.</a>
+<a name="181"><span class="lineNum">     181 </span>            :   kErrorInvalidRegKind,</a>
+<a name="182"><span class="lineNum">     182 </span>            :   //! Invalid register's physical id.</a>
+<a name="183"><span class="lineNum">     183 </span>            :   kErrorInvalidPhysId,</a>
+<a name="184"><span class="lineNum">     184 </span>            :   //! Invalid register's virtual id.</a>
+<a name="185"><span class="lineNum">     185 </span>            :   kErrorInvalidVirtId,</a>
+<a name="186"><span class="lineNum">     186 </span>            :   //! Invalid prefix combination.</a>
+<a name="187"><span class="lineNum">     187 </span>            :   kErrorInvalidPrefixCombination,</a>
+<a name="188"><span class="lineNum">     188 </span>            :   //! Invalid LOCK prefix.</a>
+<a name="189"><span class="lineNum">     189 </span>            :   kErrorInvalidLockPrefix,</a>
+<a name="190"><span class="lineNum">     190 </span>            :   //! Invalid XACQUIRE prefix.</a>
+<a name="191"><span class="lineNum">     191 </span>            :   kErrorInvalidXAcquirePrefix,</a>
+<a name="192"><span class="lineNum">     192 </span>            :   //! Invalid XACQUIRE prefix.</a>
+<a name="193"><span class="lineNum">     193 </span>            :   kErrorInvalidXReleasePrefix,</a>
+<a name="194"><span class="lineNum">     194 </span>            :   //! Invalid REP prefix.</a>
+<a name="195"><span class="lineNum">     195 </span>            :   kErrorInvalidRepPrefix,</a>
+<a name="196"><span class="lineNum">     196 </span>            :   //! Invalid REX prefix.</a>
+<a name="197"><span class="lineNum">     197 </span>            :   kErrorInvalidRexPrefix,</a>
+<a name="198"><span class="lineNum">     198 </span>            :   //! Invalid mask register (not 'k').</a>
+<a name="199"><span class="lineNum">     199 </span>            :   kErrorInvalidKMaskReg,</a>
+<a name="200"><span class="lineNum">     200 </span>            :   //! Invalid {k} use (not supported by the instruction).</a>
+<a name="201"><span class="lineNum">     201 </span>            :   kErrorInvalidKMaskUse,</a>
+<a name="202"><span class="lineNum">     202 </span>            :   //! Invalid {k}{z} use (not supported by the instruction).</a>
+<a name="203"><span class="lineNum">     203 </span>            :   kErrorInvalidKZeroUse,</a>
+<a name="204"><span class="lineNum">     204 </span>            :   //! Invalid broadcast - Currently only related to invalid use of AVX-512 {1tox}.</a>
+<a name="205"><span class="lineNum">     205 </span>            :   kErrorInvalidBroadcast,</a>
+<a name="206"><span class="lineNum">     206 </span>            :   //! Invalid 'embedded-rounding' {er} or 'suppress-all-exceptions' {sae} (AVX-512).</a>
+<a name="207"><span class="lineNum">     207 </span>            :   kErrorInvalidEROrSAE,</a>
+<a name="208"><span class="lineNum">     208 </span>            :   //! Invalid address used (not encodable).</a>
+<a name="209"><span class="lineNum">     209 </span>            :   kErrorInvalidAddress,</a>
+<a name="210"><span class="lineNum">     210 </span>            :   //! Invalid index register used in memory address (not encodable).</a>
+<a name="211"><span class="lineNum">     211 </span>            :   kErrorInvalidAddressIndex,</a>
+<a name="212"><span class="lineNum">     212 </span>            :   //! Invalid address scale (not encodable).</a>
+<a name="213"><span class="lineNum">     213 </span>            :   kErrorInvalidAddressScale,</a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! Invalid use of 64-bit address.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   kErrorInvalidAddress64Bit,</a>
+<a name="216"><span class="lineNum">     216 </span>            :   //! Invalid displacement (not encodable).</a>
+<a name="217"><span class="lineNum">     217 </span>            :   kErrorInvalidDisplacement,</a>
+<a name="218"><span class="lineNum">     218 </span>            :   //! Invalid segment (X86).</a>
+<a name="219"><span class="lineNum">     219 </span>            :   kErrorInvalidSegment,</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   //! Invalid immediate (out of bounds on X86 and invalid pattern on ARM).</a>
+<a name="222"><span class="lineNum">     222 </span>            :   kErrorInvalidImmediate,</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   //! Invalid operand size.</a>
+<a name="225"><span class="lineNum">     225 </span>            :   kErrorInvalidOperandSize,</a>
+<a name="226"><span class="lineNum">     226 </span>            :   //! Ambiguous operand size (memory has zero size while it's required to determine the operation type.</a>
+<a name="227"><span class="lineNum">     227 </span>            :   kErrorAmbiguousOperandSize,</a>
+<a name="228"><span class="lineNum">     228 </span>            :   //! Mismatching operand size (size of multiple operands doesn't match the operation size).</a>
+<a name="229"><span class="lineNum">     229 </span>            :   kErrorOperandSizeMismatch,</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :   //! Invalid TypeId.</a>
+<a name="232"><span class="lineNum">     232 </span>            :   kErrorInvalidTypeId,</a>
+<a name="233"><span class="lineNum">     233 </span>            :   //! Invalid use of a 8-bit GPB-HIGH register.</a>
+<a name="234"><span class="lineNum">     234 </span>            :   kErrorInvalidUseOfGpbHi,</a>
+<a name="235"><span class="lineNum">     235 </span>            :   //! Invalid use of a 64-bit GPQ register in 32-bit mode.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   kErrorInvalidUseOfGpq,</a>
+<a name="237"><span class="lineNum">     237 </span>            :   //! Invalid use of an 80-bit float (TypeId::kF80).</a>
+<a name="238"><span class="lineNum">     238 </span>            :   kErrorInvalidUseOfF80,</a>
+<a name="239"><span class="lineNum">     239 </span>            :   //! Some registers in the instruction muse be consecutive (some ARM and AVX512 neural-net instructions).</a>
+<a name="240"><span class="lineNum">     240 </span>            :   kErrorNotConsecutiveRegs,</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :   //! AsmJit requires a physical register, but no one is available.</a>
+<a name="243"><span class="lineNum">     243 </span>            :   kErrorNoMorePhysRegs,</a>
+<a name="244"><span class="lineNum">     244 </span>            :   //! A variable has been assigned more than once to a function argument (CodeCompiler).</a>
+<a name="245"><span class="lineNum">     245 </span>            :   kErrorOverlappedRegs,</a>
+<a name="246"><span class="lineNum">     246 </span>            :   //! Invalid register to hold stack arguments offset.</a>
+<a name="247"><span class="lineNum">     247 </span>            :   kErrorOverlappingStackRegWithRegArg,</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   //! Count of AsmJit error codes.</a>
+<a name="250"><span class="lineNum">     250 </span>            :   kErrorCount</a>
+<a name="251"><span class="lineNum">     251 </span>            : };</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : // ============================================================================</a>
+<a name="254"><span class="lineNum">     254 </span>            : // [asmjit::Internal]</a>
+<a name="255"><span class="lineNum">     255 </span>            : // ============================================================================</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : namespace Internal {</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : #if defined(ASMJIT_CUSTOM_ALLOC)   &amp;&amp; \</a>
+<a name="260"><span class="lineNum">     260 </span>            :     defined(ASMJIT_CUSTOM_REALLOC) &amp;&amp; \</a>
+<a name="261"><span class="lineNum">     261 </span>            :     defined(ASMJIT_CUSTOM_FREE)</a>
+<a name="262"><span class="lineNum">     262 </span>            : static ASMJIT_INLINE void* allocMemory(size_t size) noexcept { return ASMJIT_CUSTOM_ALLOC(size); }</a>
+<a name="263"><span class="lineNum">     263 </span>            : static ASMJIT_INLINE void* reallocMemory(void* p, size_t size) noexcept { return ASMJIT_CUSTOM_REALLOC(p, size); }</a>
+<a name="264"><span class="lineNum">     264 </span>            : static ASMJIT_INLINE void releaseMemory(void* p) noexcept { ASMJIT_CUSTOM_FREE(p); }</a>
+<a name="265"><span class="lineNum">     265 </span>            : #elif !defined(ASMJIT_CUSTOM_ALLOC)   &amp;&amp; \</a>
+<a name="266"><span class="lineNum">     266 </span>            :       !defined(ASMJIT_CUSTOM_REALLOC) &amp;&amp; \</a>
+<a name="267"><span class="lineNum">     267 </span>            :       !defined(ASMJIT_CUSTOM_FREE)</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      11700 : static ASMJIT_INLINE void* allocMemory(size_t size) noexcept { return ::malloc(size); }</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 : static ASMJIT_INLINE void* reallocMemory(void* p, size_t size) noexcept { return ::realloc(p, size); }</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">      11700 : static ASMJIT_INLINE void releaseMemory(void* p) noexcept { ::free(p); }</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : #else</a>
+<a name="272"><span class="lineNum">     272 </span>            : # error &quot;[asmjit] You must provide either none or all of ASMJIT_CUSTOM_[ALLOC|REALLOC|FREE]&quot;</a>
+<a name="273"><span class="lineNum">     273 </span>            : #endif</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : //! Cast designed to cast between function and void* pointers.</a>
+<a name="276"><span class="lineNum">     276 </span>            : template&lt;typename Dst, typename Src&gt;</a>
+<a name="277"><span class="lineNum">     277 </span>            : static ASMJIT_INLINE Dst ptr_cast(Src p) noexcept { return (Dst)p; }</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : } // Internal namespace</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : template&lt;typename Func&gt;</a>
+<a name="282"><span class="lineNum">     282 </span>            : static ASMJIT_INLINE Func ptr_as_func(void* func) noexcept { return Internal::ptr_cast&lt;Func, void*&gt;(func); }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : template&lt;typename Func&gt;</a>
+<a name="285"><span class="lineNum">     285 </span>            : static ASMJIT_INLINE void* func_as_ptr(Func func) noexcept { return Internal::ptr_cast&lt;void*, Func&gt;(func); }</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : // ============================================================================</a>
+<a name="288"><span class="lineNum">     288 </span>            : // [asmjit::DebugUtils]</a>
+<a name="289"><span class="lineNum">     289 </span>            : // ============================================================================</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : namespace DebugUtils {</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            : //! Returns the error `err` passed.</a>
+<a name="294"><span class="lineNum">     294 </span>            : //!</a>
+<a name="295"><span class="lineNum">     295 </span>            : //! Provided for debugging purposes. Putting a breakpoint inside `errored` can</a>
+<a name="296"><span class="lineNum">     296 </span>            : //! help with tracing the origin of any error reported / returned by AsmJit.</a>
+<a name="297"><span class="lineNum">     297 </span>            : static ASMJIT_INLINE Error errored(Error err) noexcept { return err; }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : //! Get a printable version of `asmjit::Error` code.</a>
+<a name="300"><span class="lineNum">     300 </span>            : ASMJIT_API const char* errorAsString(Error err) noexcept;</a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : //! Called to output debugging message(s).</a>
+<a name="303"><span class="lineNum">     303 </span>            : ASMJIT_API void debugOutput(const char* str) noexcept;</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            : //! Called on assertion failure.</a>
+<a name="306"><span class="lineNum">     306 </span>            : //!</a>
+<a name="307"><span class="lineNum">     307 </span>            : //! \param file Source file name where it happened.</a>
+<a name="308"><span class="lineNum">     308 </span>            : //! \param line Line in the source file.</a>
+<a name="309"><span class="lineNum">     309 </span>            : //! \param msg Message to display.</a>
+<a name="310"><span class="lineNum">     310 </span>            : //!</a>
+<a name="311"><span class="lineNum">     311 </span>            : //! If you have problems with assertions put a breakpoint at assertionFailed()</a>
+<a name="312"><span class="lineNum">     312 </span>            : //! function (asmjit/base/globals.cpp) and check the call stack to locate the</a>
+<a name="313"><span class="lineNum">     313 </span>            : //! failing code.</a>
+<a name="314"><span class="lineNum">     314 </span>            : ASMJIT_API void ASMJIT_NORETURN assertionFailed(const char* file, int line, const char* msg) noexcept;</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : #if defined(ASMJIT_DEBUG)</a>
+<a name="317"><span class="lineNum">     317 </span>            : # define ASMJIT_ASSERT(exp)                                          \</a>
+<a name="318"><span class="lineNum">     318 </span>            :   do {                                                               \</a>
+<a name="319"><span class="lineNum">     319 </span>            :     if (ASMJIT_LIKELY(exp))                                          \</a>
+<a name="320"><span class="lineNum">     320 </span>            :       break;                                                         \</a>
+<a name="321"><span class="lineNum">     321 </span>            :     ::PLMD::asmjit::DebugUtils::assertionFailed(__FILE__, __LINE__, #exp); \</a>
+<a name="322"><span class="lineNum">     322 </span>            :   } while (0)</a>
+<a name="323"><span class="lineNum">     323 </span>            : # define ASMJIT_NOT_REACHED()                                        \</a>
+<a name="324"><span class="lineNum">     324 </span>            :   do {                                                               \</a>
+<a name="325"><span class="lineNum">     325 </span>            :     ::PLMD::asmjit::DebugUtils::assertionFailed(__FILE__, __LINE__,        \</a>
+<a name="326"><span class="lineNum">     326 </span>            :       &quot;ASMJIT_NOT_REACHED has been reached&quot;);                        \</a>
+<a name="327"><span class="lineNum">     327 </span>            :     ASMJIT_ASSUME(0);                                                \</a>
+<a name="328"><span class="lineNum">     328 </span>            :   } while (0)</a>
+<a name="329"><span class="lineNum">     329 </span>            : #else</a>
+<a name="330"><span class="lineNum">     330 </span>            : # define ASMJIT_ASSERT(exp) ASMJIT_NOP</a>
+<a name="331"><span class="lineNum">     331 </span>            : # define ASMJIT_NOT_REACHED() ASMJIT_ASSUME(0)</a>
+<a name="332"><span class="lineNum">     332 </span>            : #endif // DEBUG</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            : //! \internal</a>
+<a name="335"><span class="lineNum">     335 </span>            : //!</a>
+<a name="336"><span class="lineNum">     336 </span>            : //! Used by AsmJit to propagate a possible `Error` produced by `...` to the caller.</a>
+<a name="337"><span class="lineNum">     337 </span>            : #define ASMJIT_PROPAGATE(...)               \</a>
+<a name="338"><span class="lineNum">     338 </span>            :   do {                                      \</a>
+<a name="339"><span class="lineNum">     339 </span>            :     ::PLMD::asmjit::Error _err = __VA_ARGS__;     \</a>
+<a name="340"><span class="lineNum">     340 </span>            :     if (ASMJIT_UNLIKELY(_err))              \</a>
+<a name="341"><span class="lineNum">     341 </span>            :       return _err;                          \</a>
+<a name="342"><span class="lineNum">     342 </span>            :   } while (0)</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            : } // DebugUtils namespace</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            : // ============================================================================</a>
+<a name="347"><span class="lineNum">     347 </span>            : // [asmjit::Init / NoInit]</a>
+<a name="348"><span class="lineNum">     348 </span>            : // ============================================================================</a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : #if !defined(ASMJIT_DOCGEN)</a>
+<a name="351"><span class="lineNum">     351 </span>            : struct _Init {};</a>
+<a name="352"><span class="lineNum">     352 </span>            : static const _Init Init = {};</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : struct _NoInit {};</a>
+<a name="355"><span class="lineNum">     355 </span>            : static const _NoInit NoInit = {};</a>
+<a name="356"><span class="lineNum">     356 </span>            : #endif // !ASMJIT_DOCGEN</a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            : //! \}</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            : } // asmjit namespace</a>
+<a name="361"><span class="lineNum">     361 </span>            : } // namespace PLMD</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            : // [Api-End]</a>
+<a name="364"><span class="lineNum">     364 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            : // [Guard]</a>
+<a name="367"><span class="lineNum">     367 </span>            : #endif // _ASMJIT_BASE_GLOBALS_H</a>
+<a name="368"><span class="lineNum">     368 </span>            : #pragma GCC diagnostic pop</a>
+<a name="369"><span class="lineNum">     369 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="370"><span class="lineNum">     370 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - asmjit</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2235</td>
+            <td class="headerCovTableEntry">7124</td>
+            <td class="headerCovTableEntryLo">31.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">139</td>
+            <td class="headerCovTableEntry">352</td>
+            <td class="headerCovTableEntryLo">39.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86compiler.h.gcov.html">x86compiler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86inst.cpp.gcov.html">x86inst.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 24</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="inst.cpp.gcov.html">inst.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86instimpl.cpp.gcov.html">x86instimpl.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 170</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="globals.cpp.gcov.html">globals.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 9</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86builder.cpp.gcov.html">x86builder.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 15</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="constpool.cpp.gcov.html">constpool.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 110</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86logging.cpp.gcov.html">x86logging.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 203</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="string.cpp.gcov.html">string.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 138</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logging.cpp.gcov.html">logging.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 147</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeemitter.cpp.gcov.html">codeemitter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=34 height=10 alt="33.7%"><img src="../snow.png" width=66 height=10 alt="33.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.7&nbsp;%</td>
+      <td class="coverNumLo">32 / 95</td>
+      <td class="coverPerLo">29.0&nbsp;%</td>
+      <td class="coverNumLo">9 / 31</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codebuilder.cpp.gcov.html">codebuilder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="23.3%"><img src="../snow.png" width=77 height=10 alt="23.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">23.3&nbsp;%</td>
+      <td class="coverNumLo">60 / 257</td>
+      <td class="coverPerLo">30.3&nbsp;%</td>
+      <td class="coverNumLo">10 / 33</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="assembler.cpp.gcov.html">assembler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="23.0%"><img src="../snow.png" width=77 height=10 alt="23.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">23.0&nbsp;%</td>
+      <td class="coverNumLo">40 / 174</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">6 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codecompiler.cpp.gcov.html">codecompiler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=37 height=10 alt="37.2%"><img src="../snow.png" width=63 height=10 alt="37.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">37.2&nbsp;%</td>
+      <td class="coverNumLo">89 / 239</td>
+      <td class="coverPerLo">41.7&nbsp;%</td>
+      <td class="coverNumLo">15 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86internal.cpp.gcov.html">x86internal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=29 height=10 alt="28.7%"><img src="../snow.png" width=71 height=10 alt="28.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">28.7&nbsp;%</td>
+      <td class="coverNumLo">113 / 394</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">6 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeholder.cpp.gcov.html">codeholder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="46.3%"><img src="../snow.png" width=54 height=10 alt="46.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">46.3&nbsp;%</td>
+      <td class="coverNumLo">120 / 259</td>
+      <td class="coverPerLo">48.0&nbsp;%</td>
+      <td class="coverNumLo">12 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86assembler.cpp.gcov.html">x86assembler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=11 height=10 alt="10.7%"><img src="../snow.png" width=89 height=10 alt="10.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">10.7&nbsp;%</td>
+      <td class="coverNumLo">183 / 1705</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">4 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vmem.cpp.gcov.html">vmem.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=30 height=10 alt="30.2%"><img src="../snow.png" width=70 height=10 alt="30.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">30.2&nbsp;%</td>
+      <td class="coverNumLo">96 / 318</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">8 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86regalloc.cpp.gcov.html">x86regalloc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=44 height=10 alt="44.2%"><img src="../snow.png" width=56 height=10 alt="44.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">44.2&nbsp;%</td>
+      <td class="coverNumLo">466 / 1055</td>
+      <td class="coverPerLo">58.6&nbsp;%</td>
+      <td class="coverNumLo">17 / 29</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="zone.cpp.gcov.html">zone.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.6%"><img src="../snow.png" width=54 height=10 alt="45.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.6&nbsp;%</td>
+      <td class="coverNumLo">136 / 298</td>
+      <td class="coverPerLo">59.1&nbsp;%</td>
+      <td class="coverNumLo">13 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="regalloc.cpp.gcov.html">regalloc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=47 height=10 alt="47.3%"><img src="../snow.png" width=53 height=10 alt="47.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">47.3&nbsp;%</td>
+      <td class="coverNumLo">114 / 241</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="func.cpp.gcov.html">func.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">24 / 31</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86compiler.cpp.gcov.html">x86compiler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=32 height=10 alt="31.8%"><img src="../snow.png" width=68 height=10 alt="31.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.8&nbsp;%</td>
+      <td class="coverNumLo">48 / 151</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="runtime.cpp.gcov.html">runtime.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.7%"><img src="../snow.png" width=26 height=10 alt="73.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.7&nbsp;%</td>
+      <td class="coverNumLo">28 / 38</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="osutils.cpp.gcov.html">osutils.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="assembler.h.gcov.html">assembler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="runtime.h.gcov.html">runtime.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="globals.h.gcov.html">globals.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86inst.h.gcov.html">x86inst.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">10 / 15</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codebuilder.h.gcov.html">codebuilder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=53 height=10 alt="53.2%"><img src="../snow.png" width=47 height=10 alt="53.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">53.2&nbsp;%</td>
+      <td class="coverNumLo">50 / 94</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="func.h.gcov.html">func.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.1%"><img src="../snow.png" width=30 height=10 alt="70.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.1&nbsp;%</td>
+      <td class="coverNumLo">68 / 97</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logging.h.gcov.html">logging.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86regalloc_p.h.gcov.html">x86regalloc_p.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.4%"><img src="../snow.png" width=31 height=10 alt="69.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.4&nbsp;%</td>
+      <td class="coverNumLo">34 / 49</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeholder.h.gcov.html">codeholder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.0%"><img src="../snow.png" width=22 height=10 alt="78.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">32 / 41</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86misc.h.gcov.html">x86misc.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=59 height=10 alt="59.5%"><img src="../snow.png" width=41 height=10 alt="59.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">59.5&nbsp;%</td>
+      <td class="coverNumLo">22 / 37</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86assembler.h.gcov.html">x86assembler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86emitter.h.gcov.html">x86emitter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.0%"><img src="../snow.png" width=37 height=10 alt="63.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.0&nbsp;%</td>
+      <td class="coverNumLo">17 / 27</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="inst.h.gcov.html">inst.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=40 height=10 alt="40.0%"><img src="../snow.png" width=60 height=10 alt="40.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="constpool.h.gcov.html">constpool.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 31</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cpuinfo.h.gcov.html">cpuinfo.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.5%"><img src="../snow.png" width=45 height=10 alt="54.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="arch.h.gcov.html">arch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="utils.h.gcov.html">utils.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=49 height=10 alt="48.9%"><img src="../snow.png" width=51 height=10 alt="48.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">48.9&nbsp;%</td>
+      <td class="coverNumLo">22 / 45</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="osutils.h.gcov.html">osutils.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeemitter.h.gcov.html">codeemitter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codecompiler.h.gcov.html">codecompiler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=64 height=10 alt="64.1%"><img src="../snow.png" width=36 height=10 alt="64.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">64.1&nbsp;%</td>
+      <td class="coverNumLo">41 / 64</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86operand.h.gcov.html">x86operand.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.5%"><img src="../snow.png" width=45 height=10 alt="54.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="operand.h.gcov.html">operand.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=54 height=10 alt="54.4%"><img src="../snow.png" width=46 height=10 alt="54.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.4&nbsp;%</td>
+      <td class="coverNumLo">49 / 90</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="moved_string.h.gcov.html">moved_string.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">6 / 27</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="regalloc_p.h.gcov.html">regalloc_p.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">36 / 54</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="zone.h.gcov.html">zone.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.5%"><img src="../snow.png" width=22 height=10 alt="78.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.5&nbsp;%</td>
+      <td class="coverNumMed">73 / 93</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="arch.cpp.gcov.html">arch.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=62 height=10 alt="62.5%"><img src="../snow.png" width=38 height=10 alt="62.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">25 / 40</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cpuinfo.cpp.gcov.html">cpuinfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">137 / 149</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/index-sort-l.html b/coverage-libs/asmjit/index-sort-l.html
new file mode 100644
index 0000000000..9675dbf41c
--- /dev/null
+++ b/coverage-libs/asmjit/index-sort-l.html
@@ -0,0 +1,603 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - asmjit</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2235</td>
+            <td class="headerCovTableEntry">7124</td>
+            <td class="headerCovTableEntryLo">31.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">139</td>
+            <td class="headerCovTableEntry">352</td>
+            <td class="headerCovTableEntryLo">39.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logging.h.gcov.html">logging.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="inst.cpp.gcov.html">inst.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="globals.cpp.gcov.html">globals.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 9</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86builder.cpp.gcov.html">x86builder.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 15</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86inst.cpp.gcov.html">x86inst.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 24</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="constpool.h.gcov.html">constpool.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 31</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="constpool.cpp.gcov.html">constpool.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 110</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="string.cpp.gcov.html">string.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 138</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logging.cpp.gcov.html">logging.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 147</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86instimpl.cpp.gcov.html">x86instimpl.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 170</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86logging.cpp.gcov.html">x86logging.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 203</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86assembler.cpp.gcov.html">x86assembler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=11 height=10 alt="10.7%"><img src="../snow.png" width=89 height=10 alt="10.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">10.7&nbsp;%</td>
+      <td class="coverNumLo">183 / 1705</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">4 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="moved_string.h.gcov.html">moved_string.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">6 / 27</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="assembler.cpp.gcov.html">assembler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="23.0%"><img src="../snow.png" width=77 height=10 alt="23.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">23.0&nbsp;%</td>
+      <td class="coverNumLo">40 / 174</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">6 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codebuilder.cpp.gcov.html">codebuilder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="23.3%"><img src="../snow.png" width=77 height=10 alt="23.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">23.3&nbsp;%</td>
+      <td class="coverNumLo">60 / 257</td>
+      <td class="coverPerLo">30.3&nbsp;%</td>
+      <td class="coverNumLo">10 / 33</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86internal.cpp.gcov.html">x86internal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=29 height=10 alt="28.7%"><img src="../snow.png" width=71 height=10 alt="28.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">28.7&nbsp;%</td>
+      <td class="coverNumLo">113 / 394</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">6 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vmem.cpp.gcov.html">vmem.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=30 height=10 alt="30.2%"><img src="../snow.png" width=70 height=10 alt="30.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">30.2&nbsp;%</td>
+      <td class="coverNumLo">96 / 318</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">8 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86compiler.cpp.gcov.html">x86compiler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=32 height=10 alt="31.8%"><img src="../snow.png" width=68 height=10 alt="31.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.8&nbsp;%</td>
+      <td class="coverNumLo">48 / 151</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeemitter.cpp.gcov.html">codeemitter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=34 height=10 alt="33.7%"><img src="../snow.png" width=66 height=10 alt="33.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.7&nbsp;%</td>
+      <td class="coverNumLo">32 / 95</td>
+      <td class="coverPerLo">29.0&nbsp;%</td>
+      <td class="coverNumLo">9 / 31</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codecompiler.cpp.gcov.html">codecompiler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=37 height=10 alt="37.2%"><img src="../snow.png" width=63 height=10 alt="37.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">37.2&nbsp;%</td>
+      <td class="coverNumLo">89 / 239</td>
+      <td class="coverPerLo">41.7&nbsp;%</td>
+      <td class="coverNumLo">15 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="inst.h.gcov.html">inst.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=40 height=10 alt="40.0%"><img src="../snow.png" width=60 height=10 alt="40.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86regalloc.cpp.gcov.html">x86regalloc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=44 height=10 alt="44.2%"><img src="../snow.png" width=56 height=10 alt="44.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">44.2&nbsp;%</td>
+      <td class="coverNumLo">466 / 1055</td>
+      <td class="coverPerLo">58.6&nbsp;%</td>
+      <td class="coverNumLo">17 / 29</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="zone.cpp.gcov.html">zone.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.6%"><img src="../snow.png" width=54 height=10 alt="45.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.6&nbsp;%</td>
+      <td class="coverNumLo">136 / 298</td>
+      <td class="coverPerLo">59.1&nbsp;%</td>
+      <td class="coverNumLo">13 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeholder.cpp.gcov.html">codeholder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="46.3%"><img src="../snow.png" width=54 height=10 alt="46.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">46.3&nbsp;%</td>
+      <td class="coverNumLo">120 / 259</td>
+      <td class="coverPerLo">48.0&nbsp;%</td>
+      <td class="coverNumLo">12 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="regalloc.cpp.gcov.html">regalloc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=47 height=10 alt="47.3%"><img src="../snow.png" width=53 height=10 alt="47.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">47.3&nbsp;%</td>
+      <td class="coverNumLo">114 / 241</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="utils.h.gcov.html">utils.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=49 height=10 alt="48.9%"><img src="../snow.png" width=51 height=10 alt="48.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">48.9&nbsp;%</td>
+      <td class="coverNumLo">22 / 45</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="assembler.h.gcov.html">assembler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codebuilder.h.gcov.html">codebuilder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=53 height=10 alt="53.2%"><img src="../snow.png" width=47 height=10 alt="53.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">53.2&nbsp;%</td>
+      <td class="coverNumLo">50 / 94</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="operand.h.gcov.html">operand.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=54 height=10 alt="54.4%"><img src="../snow.png" width=46 height=10 alt="54.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.4&nbsp;%</td>
+      <td class="coverNumLo">49 / 90</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cpuinfo.h.gcov.html">cpuinfo.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.5%"><img src="../snow.png" width=45 height=10 alt="54.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86operand.h.gcov.html">x86operand.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.5%"><img src="../snow.png" width=45 height=10 alt="54.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86misc.h.gcov.html">x86misc.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=59 height=10 alt="59.5%"><img src="../snow.png" width=41 height=10 alt="59.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">59.5&nbsp;%</td>
+      <td class="coverNumLo">22 / 37</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="arch.cpp.gcov.html">arch.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=62 height=10 alt="62.5%"><img src="../snow.png" width=38 height=10 alt="62.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">25 / 40</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86emitter.h.gcov.html">x86emitter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.0%"><img src="../snow.png" width=37 height=10 alt="63.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.0&nbsp;%</td>
+      <td class="coverNumLo">17 / 27</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codecompiler.h.gcov.html">codecompiler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=64 height=10 alt="64.1%"><img src="../snow.png" width=36 height=10 alt="64.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">64.1&nbsp;%</td>
+      <td class="coverNumLo">41 / 64</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="globals.h.gcov.html">globals.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86compiler.h.gcov.html">x86compiler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86inst.h.gcov.html">x86inst.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">10 / 15</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="regalloc_p.h.gcov.html">regalloc_p.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">36 / 54</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86regalloc_p.h.gcov.html">x86regalloc_p.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.4%"><img src="../snow.png" width=31 height=10 alt="69.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.4&nbsp;%</td>
+      <td class="coverNumLo">34 / 49</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="func.h.gcov.html">func.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.1%"><img src="../snow.png" width=30 height=10 alt="70.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.1&nbsp;%</td>
+      <td class="coverNumLo">68 / 97</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="runtime.cpp.gcov.html">runtime.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.7%"><img src="../snow.png" width=26 height=10 alt="73.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.7&nbsp;%</td>
+      <td class="coverNumLo">28 / 38</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="arch.h.gcov.html">arch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="func.cpp.gcov.html">func.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">24 / 31</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeholder.h.gcov.html">codeholder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.0%"><img src="../snow.png" width=22 height=10 alt="78.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">32 / 41</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="zone.h.gcov.html">zone.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.5%"><img src="../snow.png" width=22 height=10 alt="78.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.5&nbsp;%</td>
+      <td class="coverNumMed">73 / 93</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeemitter.h.gcov.html">codeemitter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="osutils.cpp.gcov.html">osutils.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cpuinfo.cpp.gcov.html">cpuinfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">137 / 149</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86assembler.h.gcov.html">x86assembler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="runtime.h.gcov.html">runtime.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="osutils.h.gcov.html">osutils.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/index.html b/coverage-libs/asmjit/index.html
new file mode 100644
index 0000000000..c2296cad24
--- /dev/null
+++ b/coverage-libs/asmjit/index.html
@@ -0,0 +1,603 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - asmjit</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2235</td>
+            <td class="headerCovTableEntry">7124</td>
+            <td class="headerCovTableEntryLo">31.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">139</td>
+            <td class="headerCovTableEntry">352</td>
+            <td class="headerCovTableEntryLo">39.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="arch.cpp.gcov.html">arch.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=62 height=10 alt="62.5%"><img src="../snow.png" width=38 height=10 alt="62.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">25 / 40</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="arch.h.gcov.html">arch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="assembler.cpp.gcov.html">assembler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="23.0%"><img src="../snow.png" width=77 height=10 alt="23.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">23.0&nbsp;%</td>
+      <td class="coverNumLo">40 / 174</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">6 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="assembler.h.gcov.html">assembler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codebuilder.cpp.gcov.html">codebuilder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="23.3%"><img src="../snow.png" width=77 height=10 alt="23.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">23.3&nbsp;%</td>
+      <td class="coverNumLo">60 / 257</td>
+      <td class="coverPerLo">30.3&nbsp;%</td>
+      <td class="coverNumLo">10 / 33</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codebuilder.h.gcov.html">codebuilder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=53 height=10 alt="53.2%"><img src="../snow.png" width=47 height=10 alt="53.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">53.2&nbsp;%</td>
+      <td class="coverNumLo">50 / 94</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codecompiler.cpp.gcov.html">codecompiler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=37 height=10 alt="37.2%"><img src="../snow.png" width=63 height=10 alt="37.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">37.2&nbsp;%</td>
+      <td class="coverNumLo">89 / 239</td>
+      <td class="coverPerLo">41.7&nbsp;%</td>
+      <td class="coverNumLo">15 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codecompiler.h.gcov.html">codecompiler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=64 height=10 alt="64.1%"><img src="../snow.png" width=36 height=10 alt="64.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">64.1&nbsp;%</td>
+      <td class="coverNumLo">41 / 64</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeemitter.cpp.gcov.html">codeemitter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=34 height=10 alt="33.7%"><img src="../snow.png" width=66 height=10 alt="33.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.7&nbsp;%</td>
+      <td class="coverNumLo">32 / 95</td>
+      <td class="coverPerLo">29.0&nbsp;%</td>
+      <td class="coverNumLo">9 / 31</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeemitter.h.gcov.html">codeemitter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeholder.cpp.gcov.html">codeholder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="46.3%"><img src="../snow.png" width=54 height=10 alt="46.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">46.3&nbsp;%</td>
+      <td class="coverNumLo">120 / 259</td>
+      <td class="coverPerLo">48.0&nbsp;%</td>
+      <td class="coverNumLo">12 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="codeholder.h.gcov.html">codeholder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.0%"><img src="../snow.png" width=22 height=10 alt="78.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">32 / 41</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="constpool.cpp.gcov.html">constpool.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 110</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="constpool.h.gcov.html">constpool.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 31</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cpuinfo.cpp.gcov.html">cpuinfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">137 / 149</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cpuinfo.h.gcov.html">cpuinfo.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.5%"><img src="../snow.png" width=45 height=10 alt="54.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="func.cpp.gcov.html">func.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">24 / 31</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="func.h.gcov.html">func.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.1%"><img src="../snow.png" width=30 height=10 alt="70.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.1&nbsp;%</td>
+      <td class="coverNumLo">68 / 97</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="globals.cpp.gcov.html">globals.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 9</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="globals.h.gcov.html">globals.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="inst.cpp.gcov.html">inst.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="inst.h.gcov.html">inst.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=40 height=10 alt="40.0%"><img src="../snow.png" width=60 height=10 alt="40.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logging.cpp.gcov.html">logging.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 147</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logging.h.gcov.html">logging.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="moved_string.h.gcov.html">moved_string.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">6 / 27</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="operand.h.gcov.html">operand.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=54 height=10 alt="54.4%"><img src="../snow.png" width=46 height=10 alt="54.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.4&nbsp;%</td>
+      <td class="coverNumLo">49 / 90</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="osutils.cpp.gcov.html">osutils.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="osutils.h.gcov.html">osutils.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="regalloc.cpp.gcov.html">regalloc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=47 height=10 alt="47.3%"><img src="../snow.png" width=53 height=10 alt="47.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">47.3&nbsp;%</td>
+      <td class="coverNumLo">114 / 241</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="regalloc_p.h.gcov.html">regalloc_p.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">36 / 54</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="runtime.cpp.gcov.html">runtime.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.7%"><img src="../snow.png" width=26 height=10 alt="73.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.7&nbsp;%</td>
+      <td class="coverNumLo">28 / 38</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="runtime.h.gcov.html">runtime.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="string.cpp.gcov.html">string.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 138</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="utils.h.gcov.html">utils.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=49 height=10 alt="48.9%"><img src="../snow.png" width=51 height=10 alt="48.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">48.9&nbsp;%</td>
+      <td class="coverNumLo">22 / 45</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vmem.cpp.gcov.html">vmem.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=30 height=10 alt="30.2%"><img src="../snow.png" width=70 height=10 alt="30.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">30.2&nbsp;%</td>
+      <td class="coverNumLo">96 / 318</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">8 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86assembler.cpp.gcov.html">x86assembler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=11 height=10 alt="10.7%"><img src="../snow.png" width=89 height=10 alt="10.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">10.7&nbsp;%</td>
+      <td class="coverNumLo">183 / 1705</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">4 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86assembler.h.gcov.html">x86assembler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86builder.cpp.gcov.html">x86builder.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 15</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86compiler.cpp.gcov.html">x86compiler.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=32 height=10 alt="31.8%"><img src="../snow.png" width=68 height=10 alt="31.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.8&nbsp;%</td>
+      <td class="coverNumLo">48 / 151</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86compiler.h.gcov.html">x86compiler.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86emitter.h.gcov.html">x86emitter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.0%"><img src="../snow.png" width=37 height=10 alt="63.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.0&nbsp;%</td>
+      <td class="coverNumLo">17 / 27</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86inst.cpp.gcov.html">x86inst.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 24</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86inst.h.gcov.html">x86inst.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">10 / 15</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86instimpl.cpp.gcov.html">x86instimpl.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 170</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86internal.cpp.gcov.html">x86internal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=29 height=10 alt="28.7%"><img src="../snow.png" width=71 height=10 alt="28.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">28.7&nbsp;%</td>
+      <td class="coverNumLo">113 / 394</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">6 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86logging.cpp.gcov.html">x86logging.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 203</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86misc.h.gcov.html">x86misc.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=59 height=10 alt="59.5%"><img src="../snow.png" width=41 height=10 alt="59.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">59.5&nbsp;%</td>
+      <td class="coverNumLo">22 / 37</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86operand.h.gcov.html">x86operand.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.5%"><img src="../snow.png" width=45 height=10 alt="54.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 11</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86regalloc.cpp.gcov.html">x86regalloc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=44 height=10 alt="44.2%"><img src="../snow.png" width=56 height=10 alt="44.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">44.2&nbsp;%</td>
+      <td class="coverNumLo">466 / 1055</td>
+      <td class="coverPerLo">58.6&nbsp;%</td>
+      <td class="coverNumLo">17 / 29</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="x86regalloc_p.h.gcov.html">x86regalloc_p.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.4%"><img src="../snow.png" width=31 height=10 alt="69.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.4&nbsp;%</td>
+      <td class="coverNumLo">34 / 49</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="zone.cpp.gcov.html">zone.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.6%"><img src="../snow.png" width=54 height=10 alt="45.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.6&nbsp;%</td>
+      <td class="coverNumLo">136 / 298</td>
+      <td class="coverPerLo">59.1&nbsp;%</td>
+      <td class="coverNumLo">13 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="zone.h.gcov.html">zone.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.5%"><img src="../snow.png" width=22 height=10 alt="78.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.5&nbsp;%</td>
+      <td class="coverNumMed">73 / 93</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/inst.cpp.func-sort-c.html b/coverage-libs/asmjit/inst.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1c163b1aff
--- /dev/null
+++ b/coverage-libs/asmjit/inst.cpp.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/inst.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - inst.cpp<span style="font-size: 80%;"> (<a href="inst.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="inst.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="inst.cpp.gcov.html#77">_ZN4PLMD6asmjit4Inst13checkFeaturesEjRKNS1_6DetailEPKNS0_8Operand_EjRNS0_11CpuFeaturesE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="inst.cpp.gcov.html#57">_ZN4PLMD6asmjit4Inst8validateEjRKNS1_6DetailEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/inst.cpp.func.html b/coverage-libs/asmjit/inst.cpp.func.html
new file mode 100644
index 0000000000..85968b8337
--- /dev/null
+++ b/coverage-libs/asmjit/inst.cpp.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/inst.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - inst.cpp<span style="font-size: 80%;"> (<a href="inst.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="inst.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="inst.cpp.gcov.html#77">_ZN4PLMD6asmjit4Inst13checkFeaturesEjRKNS1_6DetailEPKNS0_8Operand_EjRNS0_11CpuFeaturesE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="inst.cpp.gcov.html#57">_ZN4PLMD6asmjit4Inst8validateEjRKNS1_6DetailEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/inst.cpp.gcov.html b/coverage-libs/asmjit/inst.cpp.gcov.html
new file mode 100644
index 0000000000..c042e40dab
--- /dev/null
+++ b/coverage-libs/asmjit/inst.cpp.gcov.html
@@ -0,0 +1,179 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/inst.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - inst.cpp<span style="font-size: 80%;"> (source / <a href="inst.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./inst.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="41"><span class="lineNum">      41 </span>            : # include &quot;./x86instimpl_p.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="45"><span class="lineNum">      45 </span>            : # include &quot;./arminstimpl_p.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // [Api-Begin]</a>
+<a name="49"><span class="lineNum">      49 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : namespace PLMD {</a>
+<a name="52"><span class="lineNum">      52 </span>            : namespace asmjit {</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : // ============================================================================</a>
+<a name="55"><span class="lineNum">      55 </span>            : // [asmjit::Inst - Validate]</a>
+<a name="56"><span class="lineNum">      56 </span>            : // ============================================================================</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 : Error Inst::validate(uint32_t archType, const Detail&amp; detail, const Operand_* operands, uint32_t count) noexcept {</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   #if defined(ASMJIT_BUILD_X86)</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   if (ArchInfo::isX86Family(archType))</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :     return X86InstImpl::validate(archType, detail, operands, count);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   #endif</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="66"><span class="lineNum">      66 </span>            :   if (ArchInfo::isArmFamily(archType))</a>
+<a name="67"><span class="lineNum">      67 </span>            :     return ArmInstImpl::validate(archType, detail, operands, count);</a>
+<a name="68"><span class="lineNum">      68 </span>            :   #endif</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : #endif</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : // ============================================================================</a>
+<a name="75"><span class="lineNum">      75 </span>            : // [asmjit::Inst - CheckFeatures]</a>
+<a name="76"><span class="lineNum">      76 </span>            : // ============================================================================</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : #if !defined(ASMJIT_DISABLE_EXTENSIONS)</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 : Error Inst::checkFeatures(uint32_t archType, const Detail&amp; detail, const Operand_* operands, uint32_t count, CpuFeatures&amp; out) noexcept {</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   #if defined(ASMJIT_BUILD_X86)</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   if (ArchInfo::isX86Family(archType))</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :     return X86InstImpl::checkFeatures(archType, detail, operands, count, out);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   #endif</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="86"><span class="lineNum">      86 </span>            :   if (ArchInfo::isArmFamily(archType))</a>
+<a name="87"><span class="lineNum">      87 </span>            :     return ArmInstImpl::checkFeatures(archType, detail, operands, count, out);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   #endif</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : #endif // !defined(ASMJIT_DISABLE_EXTENSIONS)</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : } // asmjit namespace</a>
+<a name="95"><span class="lineNum">      95 </span>            : } // namespace PLMD</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : // [Api-End]</a>
+<a name="98"><span class="lineNum">      98 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : // [Guard]</a>
+<a name="101"><span class="lineNum">     101 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="102"><span class="lineNum">     102 </span>            : #pragma GCC diagnostic pop</a>
+<a name="103"><span class="lineNum">     103 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/inst.h.func-sort-c.html b/coverage-libs/asmjit/inst.h.func-sort-c.html
new file mode 100644
index 0000000000..bd1508ef22
--- /dev/null
+++ b/coverage-libs/asmjit/inst.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/inst.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - inst.h<span style="font-size: 80%;"> (<a href="inst.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="inst.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/inst.h.func.html b/coverage-libs/asmjit/inst.h.func.html
new file mode 100644
index 0000000000..c4cf94a96a
--- /dev/null
+++ b/coverage-libs/asmjit/inst.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/inst.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - inst.h<span style="font-size: 80%;"> (<a href="inst.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="inst.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/inst.h.gcov.html b/coverage-libs/asmjit/inst.h.gcov.html
new file mode 100644
index 0000000000..adaaef8ab0
--- /dev/null
+++ b/coverage-libs/asmjit/inst.h.gcov.html
@@ -0,0 +1,213 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/inst.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - inst.h<span style="font-size: 80%;"> (source / <a href="inst.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_inst_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_inst_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_INST_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_INST_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \addtogroup asmjit_base</a>
+<a name="46"><span class="lineNum">      46 </span>            : //! \{</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // ============================================================================</a>
+<a name="49"><span class="lineNum">      49 </span>            : // [asmjit::Inst]</a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : //! Definitions and utilities related to instructions used by all architectures.</a>
+<a name="53"><span class="lineNum">      53 </span>            : struct Inst {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="55"><span class="lineNum">      55 </span>            :     kIdNone = 0                          //!&lt; Invalid or uninitialized instruction id.</a>
+<a name="56"><span class="lineNum">      56 </span>            :   };</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   //! Describes an instruction's jump type, if any.</a>
+<a name="59"><span class="lineNum">      59 </span>            :   ASMJIT_ENUM(JumpType) {</a>
+<a name="60"><span class="lineNum">      60 </span>            :     kJumpTypeNone        = 0,            //!&lt; Instruction doesn't jump (regular instruction).</a>
+<a name="61"><span class="lineNum">      61 </span>            :     kJumpTypeDirect      = 1,            //!&lt; Instruction is a unconditional (direct) jump.</a>
+<a name="62"><span class="lineNum">      62 </span>            :     kJumpTypeConditional = 2,            //!&lt; Instruction is a conditional jump.</a>
+<a name="63"><span class="lineNum">      63 </span>            :     kJumpTypeCall        = 3,            //!&lt; Instruction is a function call.</a>
+<a name="64"><span class="lineNum">      64 </span>            :     kJumpTypeReturn      = 4             //!&lt; Instruction is a function return.</a>
+<a name="65"><span class="lineNum">      65 </span>            :   };</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="68"><span class="lineNum">      68 </span>            :   // [Detail]</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   //! Instruction id, options, and extraReg packed in a single structure. This</a>
+<a name="72"><span class="lineNum">      72 </span>            :   //! structure exists to simplify analysis and validation API that requires a</a>
+<a name="73"><span class="lineNum">      73 </span>            :   //! lot of information about the instruction to be processed.</a>
+<a name="74"><span class="lineNum">      74 </span>            :   class Detail {</a>
+<a name="75"><span class="lineNum">      75 </span>            :   public:</a>
+<a name="76"><span class="lineNum">      76 </span>            :     ASMJIT_INLINE Detail() noexcept</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      48362 :       : instId(0),</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :         options(0),</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      48362 :         extraReg() {}</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :     explicit ASMJIT_INLINE Detail(uint32_t instId, uint32_t options = 0) noexcept</a>
+<a name="82"><span class="lineNum">      82 </span>            :       : instId(instId),</a>
+<a name="83"><span class="lineNum">      83 </span>            :         options(options),</a>
+<a name="84"><span class="lineNum">      84 </span>            :         extraReg() {}</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :     ASMJIT_INLINE Detail(uint32_t instId, uint32_t options, const RegOnly&amp; reg) noexcept</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :       : instId(instId),</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :         options(options),</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :         extraReg(reg) {}</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :     ASMJIT_INLINE Detail(uint32_t instId, uint32_t options, const Reg&amp; reg) noexcept</a>
+<a name="92"><span class="lineNum">      92 </span>            :       : instId(instId),</a>
+<a name="93"><span class="lineNum">      93 </span>            :         options(options) { extraReg.init(reg); }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="96"><span class="lineNum">      96 </span>            :     // [Accessors]</a>
+<a name="97"><span class="lineNum">      97 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :     ASMJIT_INLINE bool hasExtraReg() const noexcept { return extraReg.isValid(); }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="102"><span class="lineNum">     102 </span>            :     // [Members]</a>
+<a name="103"><span class="lineNum">     103 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :     uint32_t instId;</a>
+<a name="106"><span class="lineNum">     106 </span>            :     uint32_t options;</a>
+<a name="107"><span class="lineNum">     107 </span>            :     RegOnly extraReg;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   };</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // [API]</a>
+<a name="112"><span class="lineNum">     112 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="115"><span class="lineNum">     115 </span>            :   //! Validate the given instruction.</a>
+<a name="116"><span class="lineNum">     116 </span>            :   ASMJIT_API static Error validate(uint32_t archType, const Detail&amp; detail, const Operand_* operands, uint32_t count) noexcept;</a>
+<a name="117"><span class="lineNum">     117 </span>            : #endif // !ASMJIT_DISABLE_VALIDATION</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : #if !defined(ASMJIT_DISABLE_EXTENSIONS)</a>
+<a name="120"><span class="lineNum">     120 </span>            :   //! Check CPU features required to execute the given instruction.</a>
+<a name="121"><span class="lineNum">     121 </span>            :   ASMJIT_API static Error checkFeatures(uint32_t archType, const Detail&amp; detail, const Operand_* operands, uint32_t count, CpuFeatures&amp; out) noexcept;</a>
+<a name="122"><span class="lineNum">     122 </span>            : #endif // !defined(ASMJIT_DISABLE_EXTENSIONS)</a>
+<a name="123"><span class="lineNum">     123 </span>            : };</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : //! \}</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : } // asmjit namespace</a>
+<a name="128"><span class="lineNum">     128 </span>            : } // namespace PLMD</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : // [Api-End]</a>
+<a name="131"><span class="lineNum">     131 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : // [Guard]</a>
+<a name="134"><span class="lineNum">     134 </span>            : #endif // _ASMJIT_BASE_INST_H</a>
+<a name="135"><span class="lineNum">     135 </span>            : #pragma GCC diagnostic pop</a>
+<a name="136"><span class="lineNum">     136 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="137"><span class="lineNum">     137 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
+
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index 0000000000..bc341c9e2d
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/logging.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
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+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - logging.cpp<span style="font-size: 80%;"> (<a href="logging.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
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+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">147</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
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new file mode 100644
index 0000000000..5a9b81eefb
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/logging.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
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+          <tr>
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - logging.cpp<span style="font-size: 80%;"> (<a href="logging.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
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+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">147</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
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+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="logging.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
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diff --git a/coverage-libs/asmjit/logging.cpp.gcov.html b/coverage-libs/asmjit/logging.cpp.gcov.html
new file mode 100644
index 0000000000..697736da6a
--- /dev/null
+++ b/coverage-libs/asmjit/logging.cpp.gcov.html
@@ -0,0 +1,600 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/logging.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - logging.cpp<span style="font-size: 80%;"> (source / <a href="logging.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">147</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./codeholder.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./codeemitter.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./logging.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : #if !defined(ASMJIT_DISABLE_BUILDER)</a>
+<a name="43"><span class="lineNum">      43 </span>            : # include &quot;./codebuilder.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #endif // !ASMJIT_DISABLE_BUILDER</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="47"><span class="lineNum">      47 </span>            : # include &quot;./codecompiler.h&quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            : #else</a>
+<a name="49"><span class="lineNum">      49 </span>            : namespace PLMD {</a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace asmjit { class VirtReg; }</a>
+<a name="51"><span class="lineNum">      51 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="54"><span class="lineNum">      54 </span>            : # include &quot;./x86logging_p.h&quot;</a>
+<a name="55"><span class="lineNum">      55 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="58"><span class="lineNum">      58 </span>            : # include &quot;./armlogging_p.h&quot;</a>
+<a name="59"><span class="lineNum">      59 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // [Api-Begin]</a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : namespace PLMD {</a>
+<a name="65"><span class="lineNum">      65 </span>            : namespace asmjit {</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : // ============================================================================</a>
+<a name="68"><span class="lineNum">      68 </span>            : // [asmjit::Logger - Construction / Destruction]</a>
+<a name="69"><span class="lineNum">      69 </span>            : // ============================================================================</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 : Logger::Logger() noexcept {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   _options = 0;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   ::memset(_indentation, 0, ASMJIT_ARRAY_SIZE(_indentation));</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 : Logger::~Logger() noexcept {}</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : // ============================================================================</a>
+<a name="78"><span class="lineNum">      78 </span>            : // [asmjit::Logger - Logging]</a>
+<a name="79"><span class="lineNum">      79 </span>            : // ============================================================================</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 : Error Logger::logf(const char* fmt, ...) noexcept {</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   Error err;</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   va_list ap;</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   va_start(ap, fmt);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   err = logv(fmt, ap);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   va_end(ap);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   return err;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 : Error Logger::logv(const char* fmt, va_list ap) noexcept {</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   char buf[1024];</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   size_t len = vsnprintf(buf, sizeof(buf), fmt, ap);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   if (len &gt;= sizeof(buf))</a>
+<a name="97"><span class="lineNum">      97 </span>            :     len = sizeof(buf) - 1;</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   return log(buf, len);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : Error Logger::logBinary(const void* data, size_t size) noexcept {</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   static const char prefix[] = &quot;.data &quot;;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   static const char hex[16] = { '0', '1', '2', '3', '4', '5', '6', '7', '8', '9', 'A', 'B', 'C', 'D', 'E', 'F' };</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   const uint8_t* s = static_cast&lt;const uint8_t*&gt;(data);</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   size_t i = size;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   char buffer[128];</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ::memcpy(buffer, prefix, ASMJIT_ARRAY_SIZE(prefix) - 1);</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   while (i) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     uint32_t n = static_cast&lt;uint32_t&gt;(std::min&lt;size_t&gt;(i, 16));</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     char* p = buffer + ASMJIT_ARRAY_SIZE(prefix) - 1;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     i -= n;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     do {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :       uint32_t c = s[0];</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :       p[0] = hex[c &gt;&gt; 4];</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       p[1] = hex[c &amp; 15];</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :       p += 2;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :       s += 1;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     } while (--n);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     *p++ = '\n';</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(log(buffer, (size_t)(p - buffer)));</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :   return kErrorOk;</a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : // ============================================================================</a>
+<a name="134"><span class="lineNum">     134 </span>            : // [asmjit::Logger - Indentation]</a>
+<a name="135"><span class="lineNum">     135 </span>            : // ============================================================================</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 : void Logger::setIndentation(const char* indentation) noexcept {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   ::memset(_indentation, 0, ASMJIT_ARRAY_SIZE(_indentation));</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   if (!indentation)</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     return;</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   size_t length = Utils::strLen(indentation, ASMJIT_ARRAY_SIZE(_indentation) - 1);</a>
+<a name="143"><span class="lineNum">     143 </span>            :   ::memcpy(_indentation, indentation, length);</a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : // ============================================================================</a>
+<a name="147"><span class="lineNum">     147 </span>            : // [asmjit::FileLogger - Construction / Destruction]</a>
+<a name="148"><span class="lineNum">     148 </span>            : // ============================================================================</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 : FileLogger::FileLogger(FILE* stream) noexcept : _stream(nullptr) { setStream(stream); }</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 : FileLogger::~FileLogger() noexcept {}</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : // ============================================================================</a>
+<a name="154"><span class="lineNum">     154 </span>            : // [asmjit::FileLogger - Logging]</a>
+<a name="155"><span class="lineNum">     155 </span>            : // ============================================================================</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 : Error FileLogger::_log(const char* buf, size_t len) noexcept {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :   if (!_stream)</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     return kErrorOk;</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   if (len == Globals::kInvalidIndex)</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     len = strlen(buf);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   fwrite(buf, 1, len, _stream);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : // ============================================================================</a>
+<a name="169"><span class="lineNum">     169 </span>            : // [asmjit::StringLogger - Construction / Destruction]</a>
+<a name="170"><span class="lineNum">     170 </span>            : // ============================================================================</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 : StringLogger::StringLogger() noexcept {}</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 : StringLogger::~StringLogger() noexcept {}</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : // ============================================================================</a>
+<a name="176"><span class="lineNum">     176 </span>            : // [asmjit::StringLogger - Logging]</a>
+<a name="177"><span class="lineNum">     177 </span>            : // ============================================================================</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 : Error StringLogger::_log(const char* buf, size_t len) noexcept {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   return _stringBuilder.appendString(buf, len);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : // ============================================================================</a>
+<a name="184"><span class="lineNum">     184 </span>            : // [asmjit::Logging]</a>
+<a name="185"><span class="lineNum">     185 </span>            : // ============================================================================</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 : Error Logging::formatLabel(</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   StringBuilder&amp; sb,</a>
+<a name="189"><span class="lineNum">     189 </span>            :   uint32_t logOptions,</a>
+<a name="190"><span class="lineNum">     190 </span>            :   const CodeEmitter* emitter,</a>
+<a name="191"><span class="lineNum">     191 </span>            :   uint32_t labelId) noexcept {</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   const LabelEntry* le = emitter-&gt;getCode()-&gt;getLabelEntry(labelId);</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!le))</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     return sb.appendFormat(&quot;InvalidLabel[Id=%u]&quot;, static_cast&lt;unsigned int&gt;(labelId));</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   if (le-&gt;hasName()) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :     if (le-&gt;hasParent()) {</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :       uint32_t parentId = le-&gt;getParentId();</a>
+<a name="200"><span class="lineNum">     200 </span>            :       const LabelEntry* pe = emitter-&gt;getCode()-&gt;getLabelEntry(parentId);</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!pe))</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendFormat(&quot;InvalidLabel[Id=%u]&quot;, static_cast&lt;unsigned int&gt;(labelId)));</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :       else if (ASMJIT_UNLIKELY(!pe-&gt;hasName()))</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendFormat(&quot;L%u&quot;, Operand::unpackId(parentId)));</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :       else</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(pe-&gt;getName()));</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendChar('.'));</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     }</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :     return sb.appendString(le-&gt;getName());</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span>            :   else {</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     return sb.appendFormat(&quot;L%u&quot;, Operand::unpackId(labelId));</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 : Error Logging::formatRegister(</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   StringBuilder&amp; sb,</a>
+<a name="220"><span class="lineNum">     220 </span>            :   uint32_t logOptions,</a>
+<a name="221"><span class="lineNum">     221 </span>            :   const CodeEmitter* emitter,</a>
+<a name="222"><span class="lineNum">     222 </span>            :   uint32_t archType,</a>
+<a name="223"><span class="lineNum">     223 </span>            :   uint32_t regType,</a>
+<a name="224"><span class="lineNum">     224 </span>            :   uint32_t regId) noexcept {</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   return X86Logging::formatRegister(sb, logOptions, emitter, archType, regType, regId);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="231"><span class="lineNum">     231 </span>            :   return ArmLogging::formatRegister(sb, logOptions, emitter, archType, regType, regId);</a>
+<a name="232"><span class="lineNum">     232 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            :   return kErrorInvalidArch;</a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 : Error Logging::formatOperand(</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   StringBuilder&amp; sb,</a>
+<a name="239"><span class="lineNum">     239 </span>            :   uint32_t logOptions,</a>
+<a name="240"><span class="lineNum">     240 </span>            :   const CodeEmitter* emitter,</a>
+<a name="241"><span class="lineNum">     241 </span>            :   uint32_t archType,</a>
+<a name="242"><span class="lineNum">     242 </span>            :   const Operand_&amp; op) noexcept {</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :   return X86Logging::formatOperand(sb, logOptions, emitter, archType, op);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="249"><span class="lineNum">     249 </span>            :   return ArmLogging::formatOperand(sb, logOptions, emitter, archType, op);</a>
+<a name="250"><span class="lineNum">     250 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :   return kErrorInvalidArch;</a>
+<a name="253"><span class="lineNum">     253 </span>            : }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 : Error Logging::formatInstruction(</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   StringBuilder&amp; sb,</a>
+<a name="257"><span class="lineNum">     257 </span>            :   uint32_t logOptions,</a>
+<a name="258"><span class="lineNum">     258 </span>            :   const CodeEmitter* emitter,</a>
+<a name="259"><span class="lineNum">     259 </span>            :   uint32_t archType,</a>
+<a name="260"><span class="lineNum">     260 </span>            :   const Inst::Detail&amp; detail, const Operand_* opArray, uint32_t opCount) noexcept {</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :   return X86Logging::formatInstruction(sb, logOptions, emitter, archType, detail, opArray, opCount);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            : #if defined(ASMJIT_BUILD_ARM)</a>
+<a name="267"><span class="lineNum">     267 </span>            :   return ArmLogging::formatInstruction(sb, logOptions, emitter, archType, detail, opArray, opCount);</a>
+<a name="268"><span class="lineNum">     268 </span>            : #endif // ASMJIT_BUILD_ARM</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   return kErrorInvalidArch;</a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : #if !defined(ASMJIT_DISABLE_BUILDER)</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 : static Error formatTypeId(StringBuilder&amp; sb, uint32_t typeId) noexcept {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   if (typeId == TypeId::kVoid)</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     return sb.appendString(&quot;void&quot;);</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   if (!TypeId::isValid(typeId))</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :     return sb.appendString(&quot;unknown&quot;);</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            :   const char* typeName = &quot;unknown&quot;;</a>
+<a name="282"><span class="lineNum">     282 </span>            :   uint32_t typeSize = TypeId::sizeOf(typeId);</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   uint32_t elementId = TypeId::elementOf(typeId);</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :   switch (elementId) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :     case TypeId::kIntPtr : typeName = &quot;intptr&quot; ; break;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     case TypeId::kUIntPtr: typeName = &quot;uintptr&quot;; break;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :     case TypeId::kI8     : typeName = &quot;i8&quot;     ; break;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :     case TypeId::kU8     : typeName = &quot;u8&quot;     ; break;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :     case TypeId::kI16    : typeName = &quot;i16&quot;    ; break;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :     case TypeId::kU16    : typeName = &quot;u16&quot;    ; break;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     case TypeId::kI32    : typeName = &quot;i32&quot;    ; break;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :     case TypeId::kU32    : typeName = &quot;u32&quot;    ; break;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :     case TypeId::kI64    : typeName = &quot;i64&quot;    ; break;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     case TypeId::kU64    : typeName = &quot;u64&quot;    ; break;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     case TypeId::kF32    : typeName = &quot;f32&quot;    ; break;</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :     case TypeId::kF64    : typeName = &quot;f64&quot;    ; break;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :     case TypeId::kF80    : typeName = &quot;f80&quot;    ; break;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :     case TypeId::kMask8  : typeName = &quot;mask8&quot;  ; break;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :     case TypeId::kMask16 : typeName = &quot;mask16&quot; ; break;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :     case TypeId::kMask32 : typeName = &quot;mask32&quot; ; break;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :     case TypeId::kMask64 : typeName = &quot;mask64&quot; ; break;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :     case TypeId::kMmx32  : typeName = &quot;mmx32&quot;  ; break;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :     case TypeId::kMmx64  : typeName = &quot;mmx64&quot;  ; break;</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :   }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   uint32_t elementSize = TypeId::sizeOf(elementId);</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :   if (typeSize &gt; elementSize) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :     unsigned int numElements = typeSize / elementSize;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :     return sb.appendFormat(&quot;%sx%u&quot;, typeName, numElements);</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   }</a>
+<a name="312"><span class="lineNum">     312 </span>            :   else {</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     return sb.appendString(typeName);</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :   }</a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 : static Error formatFuncDetailValue(</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :   StringBuilder&amp; sb,</a>
+<a name="319"><span class="lineNum">     319 </span>            :   uint32_t logOptions,</a>
+<a name="320"><span class="lineNum">     320 </span>            :   const CodeEmitter* emitter,</a>
+<a name="321"><span class="lineNum">     321 </span>            :   FuncDetail::Value value) noexcept {</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :   uint32_t typeId = value.getTypeId();</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(formatTypeId(sb, typeId));</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :   if (value.byReg()) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendChar(':'));</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(Logging::formatRegister(sb, logOptions, emitter, emitter-&gt;getArchType(), value.getRegType(), value.getRegId()));</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   }</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :   if (value.byStack()) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendFormat(&quot;:[%d]&quot;, static_cast&lt;int&gt;(value.getStackOffset())));</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :   return kErrorOk;</a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 : static Error formatFuncRets(</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   StringBuilder&amp; sb,</a>
+<a name="340"><span class="lineNum">     340 </span>            :   uint32_t logOptions,</a>
+<a name="341"><span class="lineNum">     341 </span>            :   const CodeEmitter* emitter,</a>
+<a name="342"><span class="lineNum">     342 </span>            :   const FuncDetail&amp; fd,</a>
+<a name="343"><span class="lineNum">     343 </span>            :   VirtReg* const* vRegs) noexcept {</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   if (!fd.hasRet())</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :     return sb.appendString(&quot;void&quot;);</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; fd.getRetCount(); i++) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :     if (i) ASMJIT_PROPAGATE(sb.appendString(&quot;, &quot;));</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(formatFuncDetailValue(sb, logOptions, emitter, fd.getRet(i)));</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :     if (vRegs)</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot; {%s}&quot;, vRegs[i]-&gt;getName()));</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="356"><span class="lineNum">     356 </span>            :   }</a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            :   return kErrorOk;</a>
+<a name="359"><span class="lineNum">     359 </span>            : }</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 : static Error formatFuncArgs(</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :   StringBuilder&amp; sb,</a>
+<a name="363"><span class="lineNum">     363 </span>            :   uint32_t logOptions,</a>
+<a name="364"><span class="lineNum">     364 </span>            :   const CodeEmitter* emitter,</a>
+<a name="365"><span class="lineNum">     365 </span>            :   const FuncDetail&amp; fd,</a>
+<a name="366"><span class="lineNum">     366 </span>            :   VirtReg* const* vRegs) noexcept {</a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; fd.getArgCount(); i++) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     if (i) ASMJIT_PROPAGATE(sb.appendString(&quot;, &quot;));</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(formatFuncDetailValue(sb, logOptions, emitter, fd.getArg(i)));</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :     if (vRegs)</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot; {%s}&quot;, vRegs[i]-&gt;getName()));</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="376"><span class="lineNum">     376 </span>            :   }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :   return kErrorOk;</a>
+<a name="379"><span class="lineNum">     379 </span>            : }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 : Error Logging::formatNode(</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   StringBuilder&amp; sb,</a>
+<a name="383"><span class="lineNum">     383 </span>            :   uint32_t logOptions,</a>
+<a name="384"><span class="lineNum">     384 </span>            :   const CodeBuilder* cb,</a>
+<a name="385"><span class="lineNum">     385 </span>            :   const CBNode* node_) noexcept {</a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :   if (node_-&gt;hasPosition())</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendFormat(&quot;&lt;%04u&gt; &quot;, node_-&gt;getPosition()));</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :   switch (node_-&gt;getType()) {</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     case CBNode::kNodeInst: {</a>
+<a name="392"><span class="lineNum">     392 </span>            :       const CBInst* node = node_-&gt;as&lt;CBInst&gt;();</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :         Logging::formatInstruction(sb, logOptions, cb,</a>
+<a name="395"><span class="lineNum">     395 </span>            :           cb-&gt;getArchType(),</a>
+<a name="396"><span class="lineNum">     396 </span>            :           node-&gt;getInstDetail(), node-&gt;getOpArray(), node-&gt;getOpCount()));</a>
+<a name="397"><span class="lineNum">     397 </span>            :       break;</a>
+<a name="398"><span class="lineNum">     398 </span>            :     }</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :     case CBNode::kNodeLabel: {</a>
+<a name="401"><span class="lineNum">     401 </span>            :       const CBLabel* node = node_-&gt;as&lt;CBLabel&gt;();</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot;L%u:&quot;, Operand::unpackId(node-&gt;getId())));</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :       break;</a>
+<a name="404"><span class="lineNum">     404 </span>            :     }</a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            :     case CBNode::kNodeData: {</a>
+<a name="407"><span class="lineNum">     407 </span>            :       const CBData* node = node_-&gt;as&lt;CBData&gt;();</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot;.embed (%u bytes)&quot;, node-&gt;getSize()));</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :       break;</a>
+<a name="410"><span class="lineNum">     410 </span>            :     }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            :     case CBNode::kNodeAlign: {</a>
+<a name="413"><span class="lineNum">     413 </span>            :       const CBAlign* node = node_-&gt;as&lt;CBAlign&gt;();</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :         sb.appendFormat(&quot;.align %u (%s)&quot;,</a>
+<a name="416"><span class="lineNum">     416 </span>            :           node-&gt;getAlignment(),</a>
+<a name="417"><span class="lineNum">     417 </span>            :           node-&gt;getMode() == kAlignCode ? &quot;code&quot; : &quot;data&quot;));</a>
+<a name="418"><span class="lineNum">     418 </span>            :       break;</a>
+<a name="419"><span class="lineNum">     419 </span>            :     }</a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            :     case CBNode::kNodeComment: {</a>
+<a name="422"><span class="lineNum">     422 </span>            :       const CBComment* node = node_-&gt;as&lt;CBComment&gt;();</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot;; %s&quot;, node-&gt;getInlineComment()));</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :       break;</a>
+<a name="425"><span class="lineNum">     425 </span>            :     }</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :     case CBNode::kNodeSentinel: {</a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;[sentinel]&quot;));</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :       break;</a>
+<a name="430"><span class="lineNum">     430 </span>            :     }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="433"><span class="lineNum">     433 </span>            :     case CBNode::kNodeFunc: {</a>
+<a name="434"><span class="lineNum">     434 </span>            :       const CCFunc* node = node_-&gt;as&lt;CCFunc&gt;();</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(formatLabel(sb, logOptions, cb, node-&gt;getId()));</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;: [&quot;));</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(formatFuncRets(sb, logOptions, cb, node-&gt;getDetail(), nullptr));</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;]&quot;));</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;(&quot;));</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(formatFuncArgs(sb, logOptions, cb, node-&gt;getDetail(), node-&gt;getArgs()));</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;)&quot;));</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :       break;</a>
+<a name="445"><span class="lineNum">     445 </span>            :     }</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span>            :     case CBNode::kNodeFuncExit: {</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;[ret]&quot;));</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :       break;</a>
+<a name="450"><span class="lineNum">     450 </span>            :     }</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :     case CBNode::kNodeFuncCall: {</a>
+<a name="453"><span class="lineNum">     453 </span>            :       const CCFuncCall* node = node_-&gt;as&lt;CCFuncCall&gt;();</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :         Logging::formatInstruction(sb, logOptions, cb,</a>
+<a name="456"><span class="lineNum">     456 </span>            :           cb-&gt;getArchType(),</a>
+<a name="457"><span class="lineNum">     457 </span>            :           node-&gt;getInstDetail(), node-&gt;getOpArray(), node-&gt;getOpCount()));</a>
+<a name="458"><span class="lineNum">     458 </span>            :       break;</a>
+<a name="459"><span class="lineNum">     459 </span>            :     }</a>
+<a name="460"><span class="lineNum">     460 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            :     default: {</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot;[unknown (type=%u)]&quot;, node_-&gt;getType()));</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :       break;</a>
+<a name="465"><span class="lineNum">     465 </span>            :     }</a>
+<a name="466"><span class="lineNum">     466 </span>            :   }</a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   return kErrorOk;</a>
+<a name="469"><span class="lineNum">     469 </span>            : }</a>
+<a name="470"><span class="lineNum">     470 </span>            : #endif // !ASMJIT_DISABLE_BUILDER</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 : Error Logging::formatLine(StringBuilder&amp; sb, const uint8_t* binData, size_t binLen, size_t dispLen, size_t imLen, const char* comment) noexcept {</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :   size_t currentLen = sb.getLength();</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :   size_t commentLen = comment ? Utils::strLen(comment, kMaxCommentLength) : 0;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            :   ASMJIT_ASSERT(binLen &gt;= dispLen);</a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :   if ((binLen != 0 &amp;&amp; binLen != Globals::kInvalidIndex) || commentLen) {</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :     size_t align = kMaxInstLength;</a>
+<a name="480"><span class="lineNum">     480 </span>            :     char sep = ';';</a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :     for (size_t i = (binLen == Globals::kInvalidIndex); i &lt; 2; i++) {</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :       size_t begin = sb.getLength();</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            :       // Append align.</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :       if (currentLen &lt; align)</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendChars(' ', align - currentLen));</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            :       // Append separator.</a>
+<a name="490"><span class="lineNum">     490 </span>            :       if (sep) {</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendChar(sep));</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendChar(' '));</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :       }</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :       // Append binary data or comment.</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :       if (i == 0) {</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendHex(binData, binLen - dispLen - imLen));</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendChars('.', dispLen * 2));</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendHex(binData + binLen - imLen, imLen));</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :         if (commentLen == 0) break;</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :       }</a>
+<a name="502"><span class="lineNum">     502 </span>            :       else {</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(comment, commentLen));</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :       }</a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :       currentLen += sb.getLength() - begin;</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :       align += kMaxBinaryLength;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :       sep = '|';</a>
+<a name="509"><span class="lineNum">     509 </span>            :     }</a>
+<a name="510"><span class="lineNum">     510 </span>            :   }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :   return sb.appendChar('\n');</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : } // asmjit namespace</a>
+<a name="516"><span class="lineNum">     516 </span>            : } // namespace PLMD</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : // [Api-End]</a>
+<a name="519"><span class="lineNum">     519 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            : // [Guard]</a>
+<a name="522"><span class="lineNum">     522 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="523"><span class="lineNum">     523 </span>            : #pragma GCC diagnostic pop</a>
+<a name="524"><span class="lineNum">     524 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/logging.h.func-sort-c.html b/coverage-libs/asmjit/logging.h.func-sort-c.html
new file mode 100644
index 0000000000..8b42706c9c
--- /dev/null
+++ b/coverage-libs/asmjit/logging.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/logging.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - logging.h<span style="font-size: 80%;"> (<a href="logging.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="logging.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/logging.h.func.html b/coverage-libs/asmjit/logging.h.func.html
new file mode 100644
index 0000000000..cf26acc639
--- /dev/null
+++ b/coverage-libs/asmjit/logging.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/logging.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - logging.h<span style="font-size: 80%;"> (<a href="logging.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="logging.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/logging.h.gcov.html b/coverage-libs/asmjit/logging.h.gcov.html
new file mode 100644
index 0000000000..0acb61dc7d
--- /dev/null
+++ b/coverage-libs/asmjit/logging.h.gcov.html
@@ -0,0 +1,393 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/logging.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - logging.h<span style="font-size: 80%;"> (source / <a href="logging.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_logging_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_logging_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_LOGGING_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_LOGGING_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./inst.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./moved_string.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \addtogroup asmjit_base</a>
+<a name="46"><span class="lineNum">      46 </span>            : //! \{</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : // [Forward Declarations]</a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : class CodeEmitter;</a>
+<a name="55"><span class="lineNum">      55 </span>            : class Reg;</a>
+<a name="56"><span class="lineNum">      56 </span>            : struct Operand_;</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : #if !defined(ASMJIT_DISABLE_BUILDER)</a>
+<a name="59"><span class="lineNum">      59 </span>            : class CodeBuilder;</a>
+<a name="60"><span class="lineNum">      60 </span>            : class CBNode;</a>
+<a name="61"><span class="lineNum">      61 </span>            : #endif // !ASMJIT_DISABLE_BUILDER</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : // ============================================================================</a>
+<a name="64"><span class="lineNum">      64 </span>            : // [asmjit::Logger]</a>
+<a name="65"><span class="lineNum">      65 </span>            : // ============================================================================</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : //! Abstract logging interface and helpers.</a>
+<a name="68"><span class="lineNum">      68 </span>            : //!</a>
+<a name="69"><span class="lineNum">      69 </span>            : //! This class can be inherited and reimplemented to fit into your logging</a>
+<a name="70"><span class="lineNum">      70 </span>            : //! subsystem. When reimplementing use `Logger::_log()` method to log into</a>
+<a name="71"><span class="lineNum">      71 </span>            : //! a custom stream.</a>
+<a name="72"><span class="lineNum">      72 </span>            : //!</a>
+<a name="73"><span class="lineNum">      73 </span>            : //! There are two \ref Logger implementations offered by AsmJit:</a>
+<a name="74"><span class="lineNum">      74 </span>            : //!   - \ref FileLogger - allows to log into a `FILE*` stream.</a>
+<a name="75"><span class="lineNum">      75 </span>            : //!   - \ref StringLogger - logs into a \ref StringBuilder.</a>
+<a name="76"><span class="lineNum">      76 </span>            : class ASMJIT_VIRTAPI Logger {</a>
+<a name="77"><span class="lineNum">      77 </span>            : public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ASMJIT_NONCOPYABLE(Logger)</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="81"><span class="lineNum">      81 </span>            :   // [Options]</a>
+<a name="82"><span class="lineNum">      82 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! Logger options.</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ASMJIT_ENUM(Options) {</a>
+<a name="86"><span class="lineNum">      86 </span>            :     kOptionBinaryForm      = 0x00000001, //! Output instructions also in binary form.</a>
+<a name="87"><span class="lineNum">      87 </span>            :     kOptionImmExtended     = 0x00000002, //! Output a meaning of some immediates.</a>
+<a name="88"><span class="lineNum">      88 </span>            :     kOptionHexImmediate    = 0x00000004, //! Output constants in hexadecimal form.</a>
+<a name="89"><span class="lineNum">      89 </span>            :     kOptionHexDisplacement = 0x00000008  //! Output displacements in hexadecimal form.</a>
+<a name="90"><span class="lineNum">      90 </span>            :   };</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="93"><span class="lineNum">      93 </span>            :   // [Construction / Destruction]</a>
+<a name="94"><span class="lineNum">      94 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   //! Create a `Logger` instance.</a>
+<a name="97"><span class="lineNum">      97 </span>            :   ASMJIT_API Logger() noexcept;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //! Destroy the `Logger` instance.</a>
+<a name="99"><span class="lineNum">      99 </span>            :   ASMJIT_API virtual ~Logger() noexcept;</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="102"><span class="lineNum">     102 </span>            :   // [Logging]</a>
+<a name="103"><span class="lineNum">     103 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   //! Log `str` - must be reimplemented.</a>
+<a name="106"><span class="lineNum">     106 </span>            :   virtual Error _log(const char* str, size_t len) noexcept = 0;</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   //! Log a string `str`, which is either null terminated or having `len` length.</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Error log(const char* str, size_t len = Globals::kInvalidIndex) noexcept { return _log(str, len); }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   //! Log a content of a `StringBuilder` `str`.</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ASMJIT_INLINE Error log(const StringBuilder&amp; str) noexcept { return _log(str.getData(), str.getLength()); }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Format the message by using `sprintf()` and then send to `log()`.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_API Error logf(const char* fmt, ...) noexcept;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   //! Format the message by using `vsprintf()` and then send to `log()`.</a>
+<a name="116"><span class="lineNum">     116 </span>            :   ASMJIT_API Error logv(const char* fmt, va_list ap) noexcept;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   //! Log binary data.</a>
+<a name="118"><span class="lineNum">     118 </span>            :   ASMJIT_API Error logBinary(const void* data, size_t size) noexcept;</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="121"><span class="lineNum">     121 </span>            :   // [Options]</a>
+<a name="122"><span class="lineNum">     122 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   //! Get all logger options as a single integer.</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getOptions() const noexcept { return _options; }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   //! Get the given logger option.</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasOption(uint32_t option) const noexcept { return (_options &amp; option) != 0; }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   ASMJIT_INLINE void addOptions(uint32_t options) noexcept { _options |= options; }</a>
+<a name="129"><span class="lineNum">     129 </span>            :   ASMJIT_INLINE void clearOptions(uint32_t options) noexcept { _options &amp;= ~options; }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="132"><span class="lineNum">     132 </span>            :   // [Indentation]</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   //! Get indentation.</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE const char* getIndentation() const noexcept { return _indentation; }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   //! Set indentation.</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ASMJIT_API void setIndentation(const char* indentation) noexcept;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   //! Reset indentation.</a>
+<a name="140"><span class="lineNum">     140 </span>            :   ASMJIT_INLINE void resetIndentation() noexcept { setIndentation(nullptr); }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="143"><span class="lineNum">     143 </span>            :   // [Members]</a>
+<a name="144"><span class="lineNum">     144 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! Options, see \ref LoggerOption.</a>
+<a name="147"><span class="lineNum">     147 </span>            :   uint32_t _options;</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   //! Indentation.</a>
+<a name="150"><span class="lineNum">     150 </span>            :   char _indentation[12];</a>
+<a name="151"><span class="lineNum">     151 </span>            : };</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : // ============================================================================</a>
+<a name="154"><span class="lineNum">     154 </span>            : // [asmjit::FileLogger]</a>
+<a name="155"><span class="lineNum">     155 </span>            : // ============================================================================</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : //! Logger that can log to a `FILE*` stream.</a>
+<a name="158"><span class="lineNum">     158 </span>            : class ASMJIT_VIRTAPI FileLogger : public Logger {</a>
+<a name="159"><span class="lineNum">     159 </span>            : public:</a>
+<a name="160"><span class="lineNum">     160 </span>            :   ASMJIT_NONCOPYABLE(FileLogger)</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="163"><span class="lineNum">     163 </span>            :   // [Construction / Destruction]</a>
+<a name="164"><span class="lineNum">     164 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   //! Create a new `FileLogger` that logs to a `FILE` stream.</a>
+<a name="167"><span class="lineNum">     167 </span>            :   ASMJIT_API FileLogger(FILE* stream = nullptr) noexcept;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   //! Destroy the `FileLogger`.</a>
+<a name="169"><span class="lineNum">     169 </span>            :   ASMJIT_API virtual ~FileLogger() noexcept;</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="172"><span class="lineNum">     172 </span>            :   // [Accessors]</a>
+<a name="173"><span class="lineNum">     173 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   //! Get the logging out put stream or null.</a>
+<a name="176"><span class="lineNum">     176 </span>            :   ASMJIT_INLINE FILE* getStream() const noexcept { return _stream; }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   //! Set the logging output stream to `stream` or null.</a>
+<a name="179"><span class="lineNum">     179 </span>            :   //!</a>
+<a name="180"><span class="lineNum">     180 </span>            :   //! NOTE: If the `stream` is null it will disable logging, but it won't</a>
+<a name="181"><span class="lineNum">     181 </span>            :   //! stop calling `log()` unless the logger is detached from the</a>
+<a name="182"><span class="lineNum">     182 </span>            :   //! \ref Assembler.</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setStream(FILE* stream) noexcept { _stream = stream; }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="186"><span class="lineNum">     186 </span>            :   // [Logging]</a>
+<a name="187"><span class="lineNum">     187 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   ASMJIT_API Error _log(const char* buf, size_t len = Globals::kInvalidIndex) noexcept override;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="192"><span class="lineNum">     192 </span>            :   // [Members]</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            :   //! C file stream.</a>
+<a name="196"><span class="lineNum">     196 </span>            :   FILE* _stream;</a>
+<a name="197"><span class="lineNum">     197 </span>            : };</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : // ============================================================================</a>
+<a name="200"><span class="lineNum">     200 </span>            : // [asmjit::StringLogger]</a>
+<a name="201"><span class="lineNum">     201 </span>            : // ============================================================================</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : //! Logger that stores everything in an internal string buffer.</a>
+<a name="204"><span class="lineNum">     204 </span>            : class ASMJIT_VIRTAPI StringLogger : public Logger {</a>
+<a name="205"><span class="lineNum">     205 </span>            : public:</a>
+<a name="206"><span class="lineNum">     206 </span>            :   ASMJIT_NONCOPYABLE(StringLogger)</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="209"><span class="lineNum">     209 </span>            :   // [Construction / Destruction]</a>
+<a name="210"><span class="lineNum">     210 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   //! Create new `StringLogger`.</a>
+<a name="213"><span class="lineNum">     213 </span>            :   ASMJIT_API StringLogger() noexcept;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! Destroy the `StringLogger`.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   ASMJIT_API virtual ~StringLogger() noexcept;</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="218"><span class="lineNum">     218 </span>            :   // [Accessors]</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   //! Get `char*` pointer which represents the resulting string.</a>
+<a name="222"><span class="lineNum">     222 </span>            :   //!</a>
+<a name="223"><span class="lineNum">     223 </span>            :   //! The pointer is owned by `StringLogger`, it can't be modified or freed.</a>
+<a name="224"><span class="lineNum">     224 </span>            :   ASMJIT_INLINE const char* getString() const noexcept { return _stringBuilder.getData(); }</a>
+<a name="225"><span class="lineNum">     225 </span>            :   //! Clear the resulting string.</a>
+<a name="226"><span class="lineNum">     226 </span>            :   ASMJIT_INLINE void clearString() noexcept { _stringBuilder.clear(); }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   //! Get the length of the string returned by `getString()`.</a>
+<a name="229"><span class="lineNum">     229 </span>            :   ASMJIT_INLINE size_t getLength() const noexcept { return _stringBuilder.getLength(); }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="232"><span class="lineNum">     232 </span>            :   // [Logging]</a>
+<a name="233"><span class="lineNum">     233 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   ASMJIT_API Error _log(const char* buf, size_t len = Globals::kInvalidIndex) noexcept override;</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="238"><span class="lineNum">     238 </span>            :   // [Members]</a>
+<a name="239"><span class="lineNum">     239 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   //! Output string.</a>
+<a name="242"><span class="lineNum">     242 </span>            :   StringBuilder _stringBuilder;</a>
+<a name="243"><span class="lineNum">     243 </span>            : };</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : // ============================================================================</a>
+<a name="246"><span class="lineNum">     246 </span>            : // [asmjit::Logging]</a>
+<a name="247"><span class="lineNum">     247 </span>            : // ============================================================================</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : struct Logging {</a>
+<a name="250"><span class="lineNum">     250 </span>            :   ASMJIT_API static Error formatRegister(</a>
+<a name="251"><span class="lineNum">     251 </span>            :     StringBuilder&amp; sb,</a>
+<a name="252"><span class="lineNum">     252 </span>            :     uint32_t logOptions,</a>
+<a name="253"><span class="lineNum">     253 </span>            :     const CodeEmitter* emitter,</a>
+<a name="254"><span class="lineNum">     254 </span>            :     uint32_t archType,</a>
+<a name="255"><span class="lineNum">     255 </span>            :     uint32_t regType,</a>
+<a name="256"><span class="lineNum">     256 </span>            :     uint32_t regId) noexcept;</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   ASMJIT_API static Error formatLabel(</a>
+<a name="259"><span class="lineNum">     259 </span>            :     StringBuilder&amp; sb,</a>
+<a name="260"><span class="lineNum">     260 </span>            :     uint32_t logOptions,</a>
+<a name="261"><span class="lineNum">     261 </span>            :     const CodeEmitter* emitter,</a>
+<a name="262"><span class="lineNum">     262 </span>            :     uint32_t labelId) noexcept;</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   ASMJIT_API static Error formatOperand(</a>
+<a name="265"><span class="lineNum">     265 </span>            :     StringBuilder&amp; sb,</a>
+<a name="266"><span class="lineNum">     266 </span>            :     uint32_t logOptions,</a>
+<a name="267"><span class="lineNum">     267 </span>            :     const CodeEmitter* emitter,</a>
+<a name="268"><span class="lineNum">     268 </span>            :     uint32_t archType,</a>
+<a name="269"><span class="lineNum">     269 </span>            :     const Operand_&amp; op) noexcept;</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   ASMJIT_API static Error formatInstruction(</a>
+<a name="272"><span class="lineNum">     272 </span>            :     StringBuilder&amp; sb,</a>
+<a name="273"><span class="lineNum">     273 </span>            :     uint32_t logOptions,</a>
+<a name="274"><span class="lineNum">     274 </span>            :     const CodeEmitter* emitter,</a>
+<a name="275"><span class="lineNum">     275 </span>            :     uint32_t archType,</a>
+<a name="276"><span class="lineNum">     276 </span>            :     const Inst::Detail&amp; detail, const Operand_* opArray, uint32_t opCount) noexcept;</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : #if !defined(ASMJIT_DISABLE_BUILDER)</a>
+<a name="279"><span class="lineNum">     279 </span>            :   ASMJIT_API static Error formatNode(</a>
+<a name="280"><span class="lineNum">     280 </span>            :     StringBuilder&amp; sb,</a>
+<a name="281"><span class="lineNum">     281 </span>            :     uint32_t logOptions,</a>
+<a name="282"><span class="lineNum">     282 </span>            :     const CodeBuilder* cb,</a>
+<a name="283"><span class="lineNum">     283 </span>            :     const CBNode* node_) noexcept;</a>
+<a name="284"><span class="lineNum">     284 </span>            : #endif // !ASMJIT_DISABLE_BUILDER</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : // Only used by AsmJit internals, not available to users.</a>
+<a name="287"><span class="lineNum">     287 </span>            : #if defined(ASMJIT_EXPORTS)</a>
+<a name="288"><span class="lineNum">     288 </span>            :   enum {</a>
+<a name="289"><span class="lineNum">     289 </span>            :     // Has to be big to be able to hold all metadata compiler can assign to a</a>
+<a name="290"><span class="lineNum">     290 </span>            :     // single instruction.</a>
+<a name="291"><span class="lineNum">     291 </span>            :     kMaxCommentLength = 512,</a>
+<a name="292"><span class="lineNum">     292 </span>            :     kMaxInstLength = 40,</a>
+<a name="293"><span class="lineNum">     293 </span>            :     kMaxBinaryLength = 26</a>
+<a name="294"><span class="lineNum">     294 </span>            :   };</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   static Error formatLine(</a>
+<a name="297"><span class="lineNum">     297 </span>            :     StringBuilder&amp; sb,</a>
+<a name="298"><span class="lineNum">     298 </span>            :     const uint8_t* binData, size_t binLen, size_t dispLen, size_t imLen, const char* comment) noexcept;</a>
+<a name="299"><span class="lineNum">     299 </span>            : #endif // ASMJIT_EXPORTS</a>
+<a name="300"><span class="lineNum">     300 </span>            : };</a>
+<a name="301"><span class="lineNum">     301 </span>            : #else</a>
+<a name="302"><span class="lineNum">     302 </span>            : class Logger;</a>
+<a name="303"><span class="lineNum">     303 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            : //! \}</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : } // asmjit namespace</a>
+<a name="308"><span class="lineNum">     308 </span>            : } // namespace PLMD</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : // [Api-End]</a>
+<a name="311"><span class="lineNum">     311 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : // [Guard]</a>
+<a name="314"><span class="lineNum">     314 </span>            : #endif // _ASMJIT_BASE_LOGGER_H</a>
+<a name="315"><span class="lineNum">     315 </span>            : #pragma GCC diagnostic pop</a>
+<a name="316"><span class="lineNum">     316 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="317"><span class="lineNum">     317 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/moved_string.h.func-sort-c.html b/coverage-libs/asmjit/moved_string.h.func-sort-c.html
new file mode 100644
index 0000000000..77d71737db
--- /dev/null
+++ b/coverage-libs/asmjit/moved_string.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/moved_string.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - moved_string.h<span style="font-size: 80%;"> (<a href="moved_string.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="moved_string.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/moved_string.h.func.html b/coverage-libs/asmjit/moved_string.h.func.html
new file mode 100644
index 0000000000..d35a7d7d33
--- /dev/null
+++ b/coverage-libs/asmjit/moved_string.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/moved_string.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - moved_string.h<span style="font-size: 80%;"> (<a href="moved_string.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="moved_string.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+  </center>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/moved_string.h.gcov.html b/coverage-libs/asmjit/moved_string.h.gcov.html
new file mode 100644
index 0000000000..5a0fe0405f
--- /dev/null
+++ b/coverage-libs/asmjit/moved_string.h.gcov.html
@@ -0,0 +1,394 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/moved_string.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - moved_string.h<span style="font-size: 80%;"> (source / <a href="moved_string.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_moved_string_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_moved_string_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_STRING_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_STRING_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./globals.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::SmallString]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! Small string is a template that helps to create strings that can be either</a>
+<a name="52"><span class="lineNum">      52 </span>            : //! statically allocated if they are small, or externally allocated in case</a>
+<a name="53"><span class="lineNum">      53 </span>            : //! their length exceed the limit. The `WholeSize` represents the size of the</a>
+<a name="54"><span class="lineNum">      54 </span>            : //! whole `SmallString` structure, based on that size the maximum size of the</a>
+<a name="55"><span class="lineNum">      55 </span>            : //! internal buffer is determined.</a>
+<a name="56"><span class="lineNum">      56 </span>            : template&lt;size_t WholeSize&gt;</a>
+<a name="57"><span class="lineNum">      57 </span>            : class SmallString {</a>
+<a name="58"><span class="lineNum">      58 </span>            : public:</a>
+<a name="59"><span class="lineNum">      59 </span>            :   enum { kMaxEmbeddedLength = WholeSize - 5 };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   ASMJIT_INLINE SmallString() noexcept { reset(); }</a>
+<a name="62"><span class="lineNum">      62 </span>            :   ASMJIT_INLINE void reset() noexcept { ::memset(this, 0, sizeof(*this)); }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool isEmpty() const noexcept { return _length == 0; }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   ASMJIT_INLINE bool isEmbedded() const noexcept { return _length &lt;= kMaxEmbeddedLength; }</a>
+<a name="66"><span class="lineNum">      66 </span>            :   ASMJIT_INLINE bool mustEmbed(size_t len) const noexcept { return len &lt;= kMaxEmbeddedLength; }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getLength() const noexcept { return _length; }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   ASMJIT_INLINE char* getData() const noexcept {</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     return _length &lt;= kMaxEmbeddedLength ? const_cast&lt;char*&gt;(_embedded) : _external[1];</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   ASMJIT_INLINE void setEmbedded(const char* data, size_t len) noexcept {</a>
+<a name="74"><span class="lineNum">      74 </span>            :     ASMJIT_ASSERT(len &lt;= kMaxEmbeddedLength);</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :     _length = static_cast&lt;uint32_t&gt;(len);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :     ::memcpy(_embedded, data, len);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     _embedded[len] = '\0';</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   ASMJIT_INLINE void setExternal(const char* data, size_t len) noexcept {</a>
+<a name="82"><span class="lineNum">      82 </span>            :     ASMJIT_ASSERT(len &gt; kMaxEmbeddedLength);</a>
+<a name="83"><span class="lineNum">      83 </span>            :     ASMJIT_ASSERT(len &lt;= ~static_cast&lt;uint32_t&gt;(0));</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :     _length = static_cast&lt;uint32_t&gt;(len);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     _external[1] = const_cast&lt;char*&gt;(data);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   union {</a>
+<a name="90"><span class="lineNum">      90 </span>            :     struct {</a>
+<a name="91"><span class="lineNum">      91 </span>            :       uint32_t _length;</a>
+<a name="92"><span class="lineNum">      92 </span>            :       char _embedded[WholeSize - 4];</a>
+<a name="93"><span class="lineNum">      93 </span>            :     };</a>
+<a name="94"><span class="lineNum">      94 </span>            :     char* _external[2];</a>
+<a name="95"><span class="lineNum">      95 </span>            :   };</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : // ============================================================================</a>
+<a name="99"><span class="lineNum">      99 </span>            : // [asmjit::StringBuilder]</a>
+<a name="100"><span class="lineNum">     100 </span>            : // ============================================================================</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : //! String builder.</a>
+<a name="103"><span class="lineNum">     103 </span>            : //!</a>
+<a name="104"><span class="lineNum">     104 </span>            : //! String builder was designed to be able to build a string using append like</a>
+<a name="105"><span class="lineNum">     105 </span>            : //! operation to append numbers, other strings, or signle characters. It can</a>
+<a name="106"><span class="lineNum">     106 </span>            : //! allocate it's own buffer or use a buffer created on the stack.</a>
+<a name="107"><span class="lineNum">     107 </span>            : //!</a>
+<a name="108"><span class="lineNum">     108 </span>            : //! String builder contains method specific to AsmJit functionality, used for</a>
+<a name="109"><span class="lineNum">     109 </span>            : //! logging or HTML output.</a>
+<a name="110"><span class="lineNum">     110 </span>            : class StringBuilder {</a>
+<a name="111"><span class="lineNum">     111 </span>            : public:</a>
+<a name="112"><span class="lineNum">     112 </span>            :   ASMJIT_NONCOPYABLE(StringBuilder)</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   //! \internal</a>
+<a name="115"><span class="lineNum">     115 </span>            :   //!</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //! String operation.</a>
+<a name="117"><span class="lineNum">     117 </span>            :   ASMJIT_ENUM(OpType) {</a>
+<a name="118"><span class="lineNum">     118 </span>            :     kStringOpSet = 0,                    //!&lt; Replace the current string by a given content.</a>
+<a name="119"><span class="lineNum">     119 </span>            :     kStringOpAppend = 1                  //!&lt; Append a given content to the current string.</a>
+<a name="120"><span class="lineNum">     120 </span>            :   };</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   //! \internal</a>
+<a name="123"><span class="lineNum">     123 </span>            :   //!</a>
+<a name="124"><span class="lineNum">     124 </span>            :   //! String format flags.</a>
+<a name="125"><span class="lineNum">     125 </span>            :   ASMJIT_ENUM(StringFormatFlags) {</a>
+<a name="126"><span class="lineNum">     126 </span>            :     kStringFormatShowSign  = 0x00000001,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     kStringFormatShowSpace = 0x00000002,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     kStringFormatAlternate = 0x00000004,</a>
+<a name="129"><span class="lineNum">     129 </span>            :     kStringFormatSigned    = 0x80000000</a>
+<a name="130"><span class="lineNum">     130 </span>            :   };</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // [Construction / Destruction]</a>
+<a name="134"><span class="lineNum">     134 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   ASMJIT_API StringBuilder() noexcept;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   ASMJIT_API ~StringBuilder() noexcept;</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       1948 :   ASMJIT_INLINE StringBuilder(const _NoInit&amp;) noexcept {}</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="142"><span class="lineNum">     142 </span>            :   // [Accessors]</a>
+<a name="143"><span class="lineNum">     143 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   //! Get string builder capacity.</a>
+<a name="146"><span class="lineNum">     146 </span>            :   ASMJIT_INLINE size_t getCapacity() const noexcept { return _capacity; }</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //! Get length.</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE size_t getLength() const noexcept { return _length; }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   //! Get null-terminated string data.</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE char* getData() noexcept { return _data; }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   //! Get null-terminated string data (const).</a>
+<a name="153"><span class="lineNum">     153 </span>            :   ASMJIT_INLINE const char* getData() const noexcept { return _data; }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="156"><span class="lineNum">     156 </span>            :   // [Prepare / Reserve]</a>
+<a name="157"><span class="lineNum">     157 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   //! Prepare to set/append.</a>
+<a name="160"><span class="lineNum">     160 </span>            :   ASMJIT_API char* prepare(uint32_t op, size_t len) noexcept;</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! Reserve `to` bytes in string builder.</a>
+<a name="163"><span class="lineNum">     163 </span>            :   ASMJIT_API Error reserve(size_t to) noexcept;</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="166"><span class="lineNum">     166 </span>            :   // [Clear]</a>
+<a name="167"><span class="lineNum">     167 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   //! Clear the content in String builder.</a>
+<a name="170"><span class="lineNum">     170 </span>            :   ASMJIT_API void clear() noexcept;</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="173"><span class="lineNum">     173 </span>            :   // [Op]</a>
+<a name="174"><span class="lineNum">     174 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   ASMJIT_API Error _opString(uint32_t op, const char* str, size_t len = Globals::kInvalidIndex) noexcept;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   ASMJIT_API Error _opVFormat(uint32_t op, const char* fmt, va_list ap) noexcept;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   ASMJIT_API Error _opChar(uint32_t op, char c) noexcept;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   ASMJIT_API Error _opChars(uint32_t op, char c, size_t n) noexcept;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   ASMJIT_API Error _opNumber(uint32_t op, uint64_t i, uint32_t base = 0, size_t width = 0, uint32_t flags = 0) noexcept;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   ASMJIT_API Error _opHex(uint32_t op, const void* data, size_t len) noexcept;</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="184"><span class="lineNum">     184 </span>            :   // [Set]</a>
+<a name="185"><span class="lineNum">     185 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   //! Replace the current string with `str` having `len` characters (or `kInvalidIndex` if it's null terminated).</a>
+<a name="188"><span class="lineNum">     188 </span>            :   ASMJIT_INLINE Error setString(const char* str, size_t len = Globals::kInvalidIndex) noexcept { return _opString(kStringOpSet, str, len); }</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //! Replace the current content by a formatted string `fmt`.</a>
+<a name="190"><span class="lineNum">     190 </span>            :   ASMJIT_API Error setFormat(const char* fmt, ...) noexcept;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   //! Replace the current content by a formatted string `fmt` (va_list version).</a>
+<a name="192"><span class="lineNum">     192 </span>            :   ASMJIT_INLINE Error setFormatVA(const char* fmt, va_list ap) noexcept { return _opVFormat(kStringOpSet, fmt, ap); }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            :   //! Replace the current content by a single `c` character.</a>
+<a name="195"><span class="lineNum">     195 </span>            :   ASMJIT_INLINE Error setChar(char c) noexcept { return _opChar(kStringOpSet, c); }</a>
+<a name="196"><span class="lineNum">     196 </span>            :   //! Replace the current content by `c` character `n` times.</a>
+<a name="197"><span class="lineNum">     197 </span>            :   ASMJIT_INLINE Error setChars(char c, size_t n) noexcept { return _opChars(kStringOpSet, c, n); }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   //! Replace the current content by a formatted integer `i` (signed).</a>
+<a name="200"><span class="lineNum">     200 </span>            :   ASMJIT_INLINE Error setInt(uint64_t i, uint32_t base = 0, size_t width = 0, uint32_t flags = 0) noexcept {</a>
+<a name="201"><span class="lineNum">     201 </span>            :     return _opNumber(kStringOpSet, i, base, width, flags | kStringFormatSigned);</a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :   //! Replace the current content by a formatted integer `i` (unsigned).</a>
+<a name="205"><span class="lineNum">     205 </span>            :   ASMJIT_INLINE Error setUInt(uint64_t i, uint32_t base = 0, size_t width = 0, uint32_t flags = 0) noexcept {</a>
+<a name="206"><span class="lineNum">     206 </span>            :     return _opNumber(kStringOpSet, i, base, width, flags);</a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   //! Replace the current content by the given `data` converted to a HEX string.</a>
+<a name="210"><span class="lineNum">     210 </span>            :   ASMJIT_INLINE Error setHex(const void* data, size_t len) noexcept {</a>
+<a name="211"><span class="lineNum">     211 </span>            :     return _opHex(kStringOpSet, data, len);</a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="215"><span class="lineNum">     215 </span>            :   // [Append]</a>
+<a name="216"><span class="lineNum">     216 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   //! Append string `str` having `len` characters (or `kInvalidIndex` if it's null terminated).</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Error appendString(const char* str, size_t len = Globals::kInvalidIndex) noexcept { return _opString(kStringOpAppend, str, len); }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   //! Append a formatted string `fmt`.</a>
+<a name="221"><span class="lineNum">     221 </span>            :   ASMJIT_API Error appendFormat(const char* fmt, ...) noexcept;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   //! Append a formatted string `fmt` (va_list version).</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Error appendFormatVA(const char* fmt, va_list ap) noexcept { return _opVFormat(kStringOpAppend, fmt, ap); }</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   //! Append a single `c` character.</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Error appendChar(char c) noexcept { return _opChar(kStringOpAppend, c); }</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   //! Append `c` character `n` times.</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Error appendChars(char c, size_t n) noexcept { return _opChars(kStringOpAppend, c, n); }</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   //! Append `i`.</a>
+<a name="231"><span class="lineNum">     231 </span>            :   ASMJIT_INLINE Error appendInt(int64_t i, uint32_t base = 0, size_t width = 0, uint32_t flags = 0) noexcept {</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     return _opNumber(kStringOpAppend, static_cast&lt;uint64_t&gt;(i), base, width, flags | kStringFormatSigned);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   //! Append `i`.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   ASMJIT_INLINE Error appendUInt(uint64_t i, uint32_t base = 0, size_t width = 0, uint32_t flags = 0) noexcept {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :     return _opNumber(kStringOpAppend, i, base, width, flags);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   //! Append the given `data` converted to a HEX string.</a>
+<a name="241"><span class="lineNum">     241 </span>            :   ASMJIT_INLINE Error appendHex(const void* data, size_t len) noexcept {</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :     return _opHex(kStringOpAppend, data, len);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="246"><span class="lineNum">     246 </span>            :   // [Eq]</a>
+<a name="247"><span class="lineNum">     247 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   //! Check for equality with other `str` of length `len`.</a>
+<a name="250"><span class="lineNum">     250 </span>            :   ASMJIT_API bool eq(const char* str, size_t len = Globals::kInvalidIndex) const noexcept;</a>
+<a name="251"><span class="lineNum">     251 </span>            :   //! Check for equality with `other`.</a>
+<a name="252"><span class="lineNum">     252 </span>            :   ASMJIT_INLINE bool eq(const StringBuilder&amp; other) const noexcept { return eq(other._data, other._length); }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="255"><span class="lineNum">     255 </span>            :   // [Operator Overload]</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   ASMJIT_INLINE bool operator==(const StringBuilder&amp; other) const noexcept { return  eq(other); }</a>
+<a name="259"><span class="lineNum">     259 </span>            :   ASMJIT_INLINE bool operator!=(const StringBuilder&amp; other) const noexcept { return !eq(other); }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   ASMJIT_INLINE bool operator==(const char* str) const noexcept { return  eq(str); }</a>
+<a name="262"><span class="lineNum">     262 </span>            :   ASMJIT_INLINE bool operator!=(const char* str) const noexcept { return !eq(str); }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="265"><span class="lineNum">     265 </span>            :   // [Members]</a>
+<a name="266"><span class="lineNum">     266 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   char* _data;                           //!&lt; String data.</a>
+<a name="269"><span class="lineNum">     269 </span>            :   size_t _length;                        //!&lt; String length.</a>
+<a name="270"><span class="lineNum">     270 </span>            :   size_t _capacity;                      //!&lt; String capacity.</a>
+<a name="271"><span class="lineNum">     271 </span>            :   size_t _canFree;                       //!&lt; If the string data can be freed.</a>
+<a name="272"><span class="lineNum">     272 </span>            : };</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : // ============================================================================</a>
+<a name="275"><span class="lineNum">     275 </span>            : // [asmjit::StringBuilderTmp]</a>
+<a name="276"><span class="lineNum">     276 </span>            : // ============================================================================</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : //! Temporary string builder, has statically allocated `N` bytes.</a>
+<a name="279"><span class="lineNum">     279 </span>            : template&lt;size_t N&gt;</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 : class StringBuilderTmp : public StringBuilder {</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : public:</a>
+<a name="282"><span class="lineNum">     282 </span>            :   ASMJIT_NONCOPYABLE(StringBuilderTmp&lt;N&gt;)</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="285"><span class="lineNum">     285 </span>            :   // [Construction / Destruction]</a>
+<a name="286"><span class="lineNum">     286 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       1948 :   ASMJIT_INLINE StringBuilderTmp() noexcept : StringBuilder(NoInit) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       1948 :     _data = _embeddedData;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       1948 :     _data[0] = 0;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       1948 :     _length = 0;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1948 :     _capacity = N;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :     _canFree = false;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="298"><span class="lineNum">     298 </span>            :   // [Members]</a>
+<a name="299"><span class="lineNum">     299 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   //! Embedded data.</a>
+<a name="302"><span class="lineNum">     302 </span>            :   char _embeddedData[static_cast&lt;size_t&gt;(</a>
+<a name="303"><span class="lineNum">     303 </span>            :     N + 1 + sizeof(intptr_t)) &amp; ~static_cast&lt;size_t&gt;(sizeof(intptr_t) - 1)];</a>
+<a name="304"><span class="lineNum">     304 </span>            : };</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            : //! \}</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : } // asmjit namespace</a>
+<a name="309"><span class="lineNum">     309 </span>            : } // namespace PLMD</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            : // [Api-End]</a>
+<a name="312"><span class="lineNum">     312 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : // [Guard]</a>
+<a name="315"><span class="lineNum">     315 </span>            : #endif // _ASMJIT_BASE_STRING_H</a>
+<a name="316"><span class="lineNum">     316 </span>            : #pragma GCC diagnostic pop</a>
+<a name="317"><span class="lineNum">     317 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="318"><span class="lineNum">     318 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/operand.h.func-sort-c.html b/coverage-libs/asmjit/operand.h.func-sort-c.html
new file mode 100644
index 0000000000..f78539f2ba
--- /dev/null
+++ b/coverage-libs/asmjit/operand.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/operand.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - operand.h<span style="font-size: 80%;"> (<a href="operand.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryLo">54.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="operand.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/operand.h.func.html b/coverage-libs/asmjit/operand.h.func.html
new file mode 100644
index 0000000000..4a90ecf7d2
--- /dev/null
+++ b/coverage-libs/asmjit/operand.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/operand.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - operand.h<span style="font-size: 80%;"> (<a href="operand.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryLo">54.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="operand.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/operand.h.gcov.html b/coverage-libs/asmjit/operand.h.gcov.html
new file mode 100644
index 0000000000..3fcb743c1f
--- /dev/null
+++ b/coverage-libs/asmjit/operand.h.gcov.html
@@ -0,0 +1,1675 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/operand.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - operand.h<span style="font-size: 80%;"> (source / <a href="operand.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryLo">54.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_operand_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_operand_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_OPERAND_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_OPERAND_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::Operand_]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! Constructor-less \ref Operand.</a>
+<a name="52"><span class="lineNum">      52 </span>            : //!</a>
+<a name="53"><span class="lineNum">      53 </span>            : //! Contains no initialization code and can be used safely to define an array</a>
+<a name="54"><span class="lineNum">      54 </span>            : //! of operands that won't be initialized. This is a \ref Operand compatible</a>
+<a name="55"><span class="lineNum">      55 </span>            : //! data structure designed to be statically initialized or `static const`.</a>
+<a name="56"><span class="lineNum">      56 </span>            : struct Operand_ {</a>
+<a name="57"><span class="lineNum">      57 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="58"><span class="lineNum">      58 </span>            :   // [Operand Type]</a>
+<a name="59"><span class="lineNum">      59 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   //! Operand types that can be encoded in \ref Operand.</a>
+<a name="62"><span class="lineNum">      62 </span>            :   ASMJIT_ENUM(OpType) {</a>
+<a name="63"><span class="lineNum">      63 </span>            :     kOpNone  = 0,                        //!&lt; Not an operand or not initialized.</a>
+<a name="64"><span class="lineNum">      64 </span>            :     kOpReg   = 1,                        //!&lt; Operand is a register.</a>
+<a name="65"><span class="lineNum">      65 </span>            :     kOpMem   = 2,                        //!&lt; Operand is a memory.</a>
+<a name="66"><span class="lineNum">      66 </span>            :     kOpImm   = 3,                        //!&lt; Operand is an immediate value.</a>
+<a name="67"><span class="lineNum">      67 </span>            :     kOpLabel = 4                         //!&lt; Operand is a label.</a>
+<a name="68"><span class="lineNum">      68 </span>            :   };</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="71"><span class="lineNum">      71 </span>            :   // [Operand Signature (Bits)]</a>
+<a name="72"><span class="lineNum">      72 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   ASMJIT_ENUM(SignatureBits) {</a>
+<a name="75"><span class="lineNum">      75 </span>            :     // Operand type (3 least significant bits).</a>
+<a name="76"><span class="lineNum">      76 </span>            :     // |........|........|........|.....XXX|</a>
+<a name="77"><span class="lineNum">      77 </span>            :     kSignatureOpShift           = 0,</a>
+<a name="78"><span class="lineNum">      78 </span>            :     kSignatureOpBits            = 0x07U,</a>
+<a name="79"><span class="lineNum">      79 </span>            :     kSignatureOpMask            = kSignatureOpBits &lt;&lt; kSignatureOpShift,</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :     // Operand size (8 most significant bits).</a>
+<a name="82"><span class="lineNum">      82 </span>            :     // |XXXXXXXX|........|........|........|</a>
+<a name="83"><span class="lineNum">      83 </span>            :     kSignatureSizeShift         = 24,</a>
+<a name="84"><span class="lineNum">      84 </span>            :     kSignatureSizeBits          = 0xFFU,</a>
+<a name="85"><span class="lineNum">      85 </span>            :     kSignatureSizeMask          = kSignatureSizeBits &lt;&lt; kSignatureSizeShift,</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :     // Register type (5 bits).</a>
+<a name="88"><span class="lineNum">      88 </span>            :     // |........|........|........|XXXXX...|</a>
+<a name="89"><span class="lineNum">      89 </span>            :     kSignatureRegTypeShift      = 3,</a>
+<a name="90"><span class="lineNum">      90 </span>            :     kSignatureRegTypeBits       = 0x1FU,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     kSignatureRegTypeMask       = kSignatureRegTypeBits &lt;&lt; kSignatureRegTypeShift,</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :     // Register kind (4 bits).</a>
+<a name="94"><span class="lineNum">      94 </span>            :     // |........|........|....XXXX|........|</a>
+<a name="95"><span class="lineNum">      95 </span>            :     kSignatureRegKindShift      = 8,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     kSignatureRegKindBits       = 0x0FU,</a>
+<a name="97"><span class="lineNum">      97 </span>            :     kSignatureRegKindMask       = kSignatureRegKindBits &lt;&lt; kSignatureRegKindShift,</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :     // Memory base type (5 bits).</a>
+<a name="100"><span class="lineNum">     100 </span>            :     // |........|........|........|XXXXX...|</a>
+<a name="101"><span class="lineNum">     101 </span>            :     kSignatureMemBaseTypeShift  = 3,</a>
+<a name="102"><span class="lineNum">     102 </span>            :     kSignatureMemBaseTypeBits   = 0x1FU,</a>
+<a name="103"><span class="lineNum">     103 </span>            :     kSignatureMemBaseTypeMask   = kSignatureMemBaseTypeBits &lt;&lt; kSignatureMemBaseTypeShift,</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :     // Memory index type (5 bits).</a>
+<a name="106"><span class="lineNum">     106 </span>            :     // |........|........|...XXXXX|........|</a>
+<a name="107"><span class="lineNum">     107 </span>            :     kSignatureMemIndexTypeShift = 8,</a>
+<a name="108"><span class="lineNum">     108 </span>            :     kSignatureMemIndexTypeBits  = 0x1FU,</a>
+<a name="109"><span class="lineNum">     109 </span>            :     kSignatureMemIndexTypeMask  = kSignatureMemIndexTypeBits &lt;&lt; kSignatureMemIndexTypeShift,</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :     // Memory base+index combined (10 bits).</a>
+<a name="112"><span class="lineNum">     112 </span>            :     // |........|........|...XXXXX|XXXXX...|</a>
+<a name="113"><span class="lineNum">     113 </span>            :     kSignatureMemBaseIndexShift = 3,</a>
+<a name="114"><span class="lineNum">     114 </span>            :     kSignatureMemBaseIndexBits  = 0x3FFU,</a>
+<a name="115"><span class="lineNum">     115 </span>            :     kSignatureMemBaseIndexMask  = kSignatureMemBaseIndexBits &lt;&lt; kSignatureMemBaseIndexShift,</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :     // Memory should be encoded as absolute immediate (X86|X64).</a>
+<a name="118"><span class="lineNum">     118 </span>            :     // |........|........|.XX.....|........|</a>
+<a name="119"><span class="lineNum">     119 </span>            :     kSignatureMemAddrTypeShift  = 13,</a>
+<a name="120"><span class="lineNum">     120 </span>            :     kSignatureMemAddrTypeBits   = 0x03U,</a>
+<a name="121"><span class="lineNum">     121 </span>            :     kSignatureMemAddrTypeMask   = kSignatureMemAddrTypeBits &lt;&lt; kSignatureMemAddrTypeShift,</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :     // This memory operand represents a function argument's stack location (CodeCompiler)</a>
+<a name="124"><span class="lineNum">     124 </span>            :     // |........|........|.X......|........|</a>
+<a name="125"><span class="lineNum">     125 </span>            :     kSignatureMemArgHomeShift   = 15,</a>
+<a name="126"><span class="lineNum">     126 </span>            :     kSignatureMemArgHomeBits    = 0x01U,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     kSignatureMemArgHomeFlag    = kSignatureMemArgHomeBits &lt;&lt; kSignatureMemArgHomeShift,</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :     // This memory operand represents a virtual register's home-slot (CodeCompiler).</a>
+<a name="130"><span class="lineNum">     130 </span>            :     // |........|........|X.......|........|</a>
+<a name="131"><span class="lineNum">     131 </span>            :     kSignatureMemRegHomeShift   = 16,</a>
+<a name="132"><span class="lineNum">     132 </span>            :     kSignatureMemRegHomeBits    = 0x01U,</a>
+<a name="133"><span class="lineNum">     133 </span>            :     kSignatureMemRegHomeFlag    = kSignatureMemRegHomeBits &lt;&lt; kSignatureMemRegHomeShift</a>
+<a name="134"><span class="lineNum">     134 </span>            :   };</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="137"><span class="lineNum">     137 </span>            :   // [Operand Id]</a>
+<a name="138"><span class="lineNum">     138 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   //! Operand id helpers useful for id &lt;-&gt; index translation.</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ASMJIT_ENUM(PackedId) {</a>
+<a name="142"><span class="lineNum">     142 </span>            :     //! Minimum valid packed-id.</a>
+<a name="143"><span class="lineNum">     143 </span>            :     kPackedIdMin    = 0x00000100U,</a>
+<a name="144"><span class="lineNum">     144 </span>            :     //! Maximum valid packed-id.</a>
+<a name="145"><span class="lineNum">     145 </span>            :     kPackedIdMax    = 0xFFFFFFFFU,</a>
+<a name="146"><span class="lineNum">     146 </span>            :     //! Count of valid packed-ids.</a>
+<a name="147"><span class="lineNum">     147 </span>            :     kPackedIdCount  = kPackedIdMax - kPackedIdMin + 1</a>
+<a name="148"><span class="lineNum">     148 </span>            :   };</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="151"><span class="lineNum">     151 </span>            :   // [Operand Utilities]</a>
+<a name="152"><span class="lineNum">     152 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   //! Get if the given `id` is a valid packed-id that can be used by Operand.</a>
+<a name="155"><span class="lineNum">     155 </span>            :   //! Packed ids are those equal or greater than `kPackedIdMin` and lesser or</a>
+<a name="156"><span class="lineNum">     156 </span>            :   //! equal to `kPackedIdMax`. This concept was created to support virtual</a>
+<a name="157"><span class="lineNum">     157 </span>            :   //! registers and to make them distinguishable from physical ones. It allows</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //! a single uint32_t to contain either physical register id or virtual</a>
+<a name="159"><span class="lineNum">     159 </span>            :   //! register id represented as `packed-id`. This concept is used also for</a>
+<a name="160"><span class="lineNum">     160 </span>            :   //! labels to make the API consistent.</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     124078 :   static ASMJIT_INLINE bool isPackedId(uint32_t id) noexcept { return id - kPackedIdMin &lt; kPackedIdCount; }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! Convert a real-id into a packed-id that can be stored in Operand.</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      27684 :   static ASMJIT_INLINE uint32_t packId(uint32_t id) noexcept { return id + kPackedIdMin; }</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   //! Convert a packed-id back to real-id.</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      13892 :   static ASMJIT_INLINE uint32_t unpackId(uint32_t id) noexcept { return id - kPackedIdMin; }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="168"><span class="lineNum">     168 </span>            :   // [Operand Data]</a>
+<a name="169"><span class="lineNum">     169 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   //! Any operand.</a>
+<a name="172"><span class="lineNum">     172 </span>            :   struct AnyData {</a>
+<a name="173"><span class="lineNum">     173 </span>            :     uint32_t signature;                  //!&lt; Type of the operand (see \ref OpType) and other data.</a>
+<a name="174"><span class="lineNum">     174 </span>            :     uint32_t id;                         //!&lt; Operand id or `0`.</a>
+<a name="175"><span class="lineNum">     175 </span>            :     uint32_t reserved8_4;                //!&lt; \internal</a>
+<a name="176"><span class="lineNum">     176 </span>            :     uint32_t reserved12_4;               //!&lt; \internal</a>
+<a name="177"><span class="lineNum">     177 </span>            :   };</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   //! Register operand data.</a>
+<a name="180"><span class="lineNum">     180 </span>            :   struct RegData {</a>
+<a name="181"><span class="lineNum">     181 </span>            :     uint32_t signature;                  //!&lt; Type of the operand (always \ref kOpReg) and other data.</a>
+<a name="182"><span class="lineNum">     182 </span>            :     uint32_t id;                         //!&lt; Physical or virtual register id.</a>
+<a name="183"><span class="lineNum">     183 </span>            :     uint32_t reserved8_4;                //!&lt; \internal</a>
+<a name="184"><span class="lineNum">     184 </span>            :     uint32_t reserved12_4;               //!&lt; \internal</a>
+<a name="185"><span class="lineNum">     185 </span>            :   };</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   //! Memory operand data.</a>
+<a name="188"><span class="lineNum">     188 </span>            :   struct MemData {</a>
+<a name="189"><span class="lineNum">     189 </span>            :     uint32_t signature;                  //!&lt; Type of the operand (always \ref kOpMem) and other data.</a>
+<a name="190"><span class="lineNum">     190 </span>            :     uint32_t index;                      //!&lt; INDEX register id or `0`.</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :     // [BASE + OFF32] vs just [OFF64].</a>
+<a name="193"><span class="lineNum">     193 </span>            :     union {</a>
+<a name="194"><span class="lineNum">     194 </span>            :       uint64_t offset64;                 //!&lt; 64-bit offset, combining low and high 32-bit parts.</a>
+<a name="195"><span class="lineNum">     195 </span>            :       struct {</a>
+<a name="196"><span class="lineNum">     196 </span>            : #if ASMJIT_ARCH_LE</a>
+<a name="197"><span class="lineNum">     197 </span>            :         uint32_t offsetLo32;             //!&lt; 32-bit low offset part.</a>
+<a name="198"><span class="lineNum">     198 </span>            :         uint32_t base;                   //!&lt; 32-bit high offset part or BASE.</a>
+<a name="199"><span class="lineNum">     199 </span>            : #else</a>
+<a name="200"><span class="lineNum">     200 </span>            :         uint32_t base;                   //!&lt; 32-bit high offset part or BASE.</a>
+<a name="201"><span class="lineNum">     201 </span>            :         uint32_t offsetLo32;             //!&lt; 32-bit low offset part.</a>
+<a name="202"><span class="lineNum">     202 </span>            : #endif</a>
+<a name="203"><span class="lineNum">     203 </span>            :       };</a>
+<a name="204"><span class="lineNum">     204 </span>            :     };</a>
+<a name="205"><span class="lineNum">     205 </span>            :   };</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   //! Immediate operand data.</a>
+<a name="208"><span class="lineNum">     208 </span>            :   struct ImmData {</a>
+<a name="209"><span class="lineNum">     209 </span>            :     uint32_t signature;                  //!&lt; Type of the operand (always \ref kOpImm) and other data.</a>
+<a name="210"><span class="lineNum">     210 </span>            :     uint32_t id;                         //!&lt; Immediate id (always `0`).</a>
+<a name="211"><span class="lineNum">     211 </span>            :     UInt64 value;                        //!&lt; Immediate value.</a>
+<a name="212"><span class="lineNum">     212 </span>            :   };</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! Label operand data.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   struct LabelData {</a>
+<a name="216"><span class="lineNum">     216 </span>            :     uint32_t signature;                  //!&lt; Type of the operand (always \ref kOpLabel) and other data.</a>
+<a name="217"><span class="lineNum">     217 </span>            :     uint32_t id;                         //!&lt; Label id (`0` if not initialized).</a>
+<a name="218"><span class="lineNum">     218 </span>            :     uint32_t reserved8_4;                //!&lt; \internal</a>
+<a name="219"><span class="lineNum">     219 </span>            :     uint32_t reserved12_4;               //!&lt; \internal</a>
+<a name="220"><span class="lineNum">     220 </span>            :   };</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="223"><span class="lineNum">     223 </span>            :   // [Init &amp; Copy]</a>
+<a name="224"><span class="lineNum">     224 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            :   //! \internal</a>
+<a name="227"><span class="lineNum">     227 </span>            :   //!</a>
+<a name="228"><span class="lineNum">     228 </span>            :   //! Initialize the operand to `other` (used by constructors).</a>
+<a name="229"><span class="lineNum">     229 </span>            :   ASMJIT_INLINE void _init(const Operand_&amp; other) noexcept { ::memcpy(this, &amp;other, sizeof(Operand_)); }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :   //! \internal</a>
+<a name="232"><span class="lineNum">     232 </span>            :   ASMJIT_INLINE void _initReg(uint32_t signature, uint32_t rd) {</a>
+<a name="233"><span class="lineNum">     233 </span>            :     _init_packed_d0_d1(signature, rd);</a>
+<a name="234"><span class="lineNum">     234 </span>            :     _init_packed_d2_d3(0, 0);</a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   //! \internal</a>
+<a name="238"><span class="lineNum">     238 </span>            :   ASMJIT_INLINE void _init_packed_d0_d1(uint32_t d0, uint32_t d1) noexcept { _packed[0].setPacked_2x32(d0, d1); }</a>
+<a name="239"><span class="lineNum">     239 </span>            :   //! \internal</a>
+<a name="240"><span class="lineNum">     240 </span>            :   ASMJIT_INLINE void _init_packed_d2_d3(uint32_t d2, uint32_t d3) noexcept { _packed[1].setPacked_2x32(d2, d3); }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :   //! \internal</a>
+<a name="243"><span class="lineNum">     243 </span>            :   //!</a>
+<a name="244"><span class="lineNum">     244 </span>            :   //! Initialize the operand from `other` (used by operator overloads).</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      87412 :   ASMJIT_INLINE void copyFrom(const Operand_&amp; other) noexcept { ::memcpy(this, &amp;other, sizeof(Operand_)); }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="248"><span class="lineNum">     248 </span>            :   // [Accessors]</a>
+<a name="249"><span class="lineNum">     249 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :   //! Get if the operand matches the given signature `sign`.</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasSignature(uint32_t signature) const noexcept { return _signature == signature; }</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   //! Get if the operand matches a signature of the `other` operand.</a>
+<a name="255"><span class="lineNum">     255 </span>            :   ASMJIT_INLINE bool hasSignature(const Operand_&amp; other) const noexcept {</a>
+<a name="256"><span class="lineNum">     256 </span>            :     return _signature == other.getSignature();</a>
+<a name="257"><span class="lineNum">     257 </span>            :   }</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            :   //! Get a 32-bit operand signature.</a>
+<a name="260"><span class="lineNum">     260 </span>            :   //!</a>
+<a name="261"><span class="lineNum">     261 </span>            :   //! Signature is first 4 bytes of the operand data. It's used mostly for</a>
+<a name="262"><span class="lineNum">     262 </span>            :   //! operand checking as it's much faster to check 4 bytes at once than having</a>
+<a name="263"><span class="lineNum">     263 </span>            :   //! to check these bytes individually.</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getSignature() const noexcept { return _signature; }</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :   //! Set the operand signature (see \ref getSignature).</a>
+<a name="267"><span class="lineNum">     267 </span>            :   //!</a>
+<a name="268"><span class="lineNum">     268 </span>            :   //! Improper use of `setSignature()` can lead to hard-to-debug errors.</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        420 :   ASMJIT_INLINE void setSignature(uint32_t signature) noexcept { _signature = signature; }</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      41256 :   ASMJIT_INLINE bool _hasSignatureData(uint32_t bits) const noexcept { return (_signature &amp; bits) != 0; }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   //! \internal</a>
+<a name="274"><span class="lineNum">     274 </span>            :   //!</a>
+<a name="275"><span class="lineNum">     275 </span>            :   //! Unpacks information from operand's signature.</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">     297664 :   ASMJIT_INLINE uint32_t _getSignatureData(uint32_t bits, uint32_t shift) const noexcept { return (_signature &gt;&gt; shift) &amp; bits; }</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   //! \internal</a>
+<a name="279"><span class="lineNum">     279 </span>            :   //!</a>
+<a name="280"><span class="lineNum">     280 </span>            :   //! Packs information to operand's signature.</a>
+<a name="281"><span class="lineNum">     281 </span>            :   ASMJIT_INLINE void _setSignatureData(uint32_t value, uint32_t bits, uint32_t shift) noexcept {</a>
+<a name="282"><span class="lineNum">     282 </span>            :     ASMJIT_ASSERT(value &lt;= bits);</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       8428 :     _signature = (_signature &amp; ~(bits &lt;&lt; shift)) | (value &lt;&lt; shift);</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :   ASMJIT_INLINE void _addSignatureData(uint32_t data) noexcept { _signature |= data; }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   //! Clears specified bits in operand's signature.</a>
+<a name="289"><span class="lineNum">     289 </span>            :   ASMJIT_INLINE void _clearSignatureData(uint32_t bits, uint32_t shift) noexcept { _signature &amp;= ~(bits &lt;&lt; shift); }</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :   //! Get type of the operand, see \ref OpType.</a>
+<a name="292"><span class="lineNum">     292 </span>            :   ASMJIT_INLINE uint32_t getOp() const noexcept { return _getSignatureData(kSignatureOpBits, kSignatureOpShift); }</a>
+<a name="293"><span class="lineNum">     293 </span>            :   //! Get if the operand is none (\ref kOpNone).</a>
+<a name="294"><span class="lineNum">     294 </span>            :   ASMJIT_INLINE bool isNone() const noexcept { return getOp() == 0; }</a>
+<a name="295"><span class="lineNum">     295 </span>            :   //! Get if the operand is a register (\ref kOpReg).</a>
+<a name="296"><span class="lineNum">     296 </span>            :   ASMJIT_INLINE bool isReg() const noexcept { return getOp() == kOpReg; }</a>
+<a name="297"><span class="lineNum">     297 </span>            :   //! Get if the operand is a memory location (\ref kOpMem).</a>
+<a name="298"><span class="lineNum">     298 </span>            :   ASMJIT_INLINE bool isMem() const noexcept { return getOp() == kOpMem; }</a>
+<a name="299"><span class="lineNum">     299 </span>            :   //! Get if the operand is an immediate (\ref kOpImm).</a>
+<a name="300"><span class="lineNum">     300 </span>            :   ASMJIT_INLINE bool isImm() const noexcept { return getOp() == kOpImm; }</a>
+<a name="301"><span class="lineNum">     301 </span>            :   //! Get if the operand is a label (\ref kOpLabel).</a>
+<a name="302"><span class="lineNum">     302 </span>            :   ASMJIT_INLINE bool isLabel() const noexcept { return getOp() == kOpLabel; }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   //! Get if the operand is a physical register.</a>
+<a name="305"><span class="lineNum">     305 </span>            :   ASMJIT_INLINE bool isPhysReg() const noexcept { return isReg() &amp;&amp; _reg.id &lt; Globals::kInvalidRegId; }</a>
+<a name="306"><span class="lineNum">     306 </span>            :   //! Get if the operand is a virtual register.</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">     146394 :   ASMJIT_INLINE bool isVirtReg() const noexcept { return isReg() &amp;&amp; isPackedId(_reg.id); }</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :   //! Get if the operand specifies a size (i.e. the size is not zero).</a>
+<a name="310"><span class="lineNum">     310 </span>            :   ASMJIT_INLINE bool hasSize() const noexcept { return _hasSignatureData(kSignatureSizeMask); }</a>
+<a name="311"><span class="lineNum">     311 </span>            :   //! Get if the size of the operand matches `size`.</a>
+<a name="312"><span class="lineNum">     312 </span>            :   ASMJIT_INLINE bool hasSize(uint32_t size) const noexcept { return getSize() == size; }</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :   //! Get size of the operand (in bytes).</a>
+<a name="315"><span class="lineNum">     315 </span>            :   //!</a>
+<a name="316"><span class="lineNum">     316 </span>            :   //! The value returned depends on the operand type:</a>
+<a name="317"><span class="lineNum">     317 </span>            :   //!   * None  - Should always return zero size.</a>
+<a name="318"><span class="lineNum">     318 </span>            :   //!   * Reg   - Should always return the size of the register. If the register</a>
+<a name="319"><span class="lineNum">     319 </span>            :   //!             size depends on architecture (like \ref X86CReg and \ref X86DReg)</a>
+<a name="320"><span class="lineNum">     320 </span>            :   //!             the size returned should be the greatest possible (so it should</a>
+<a name="321"><span class="lineNum">     321 </span>            :   //!             return 64-bit size in such case).</a>
+<a name="322"><span class="lineNum">     322 </span>            :   //!   * Mem   - Size is optional and will be in most cases zero.</a>
+<a name="323"><span class="lineNum">     323 </span>            :   //!   * Imm   - Should always return zero size.</a>
+<a name="324"><span class="lineNum">     324 </span>            :   //!   * Label - Should always return zero size.</a>
+<a name="325"><span class="lineNum">     325 </span>            :   ASMJIT_INLINE uint32_t getSize() const noexcept { return _getSignatureData(kSignatureSizeBits, kSignatureSizeShift); }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            :   //! Get the operand id.</a>
+<a name="328"><span class="lineNum">     328 </span>            :   //!</a>
+<a name="329"><span class="lineNum">     329 </span>            :   //! The value returned should be interpreted accordingly to the operand type:</a>
+<a name="330"><span class="lineNum">     330 </span>            :   //!   * None  - Should be `0`.</a>
+<a name="331"><span class="lineNum">     331 </span>            :   //!   * Reg   - Physical or virtual register id.</a>
+<a name="332"><span class="lineNum">     332 </span>            :   //!   * Mem   - Multiple meanings - BASE address (register or label id), or</a>
+<a name="333"><span class="lineNum">     333 </span>            :   //!             high value of a 64-bit absolute address.</a>
+<a name="334"><span class="lineNum">     334 </span>            :   //!   * Imm   - Should be `0`.</a>
+<a name="335"><span class="lineNum">     335 </span>            :   //!   * Label - Label id if it was created by using `newLabel()` or `0`</a>
+<a name="336"><span class="lineNum">     336 </span>            :   //!             if the label is invalid or uninitialized.</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      54546 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _any.id; }</span></a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            :   //! Get if the operand is 100% equal to `other`.</a>
+<a name="340"><span class="lineNum">     340 </span>            :   ASMJIT_INLINE bool isEqual(const Operand_&amp; other) const noexcept {</a>
+<a name="341"><span class="lineNum">     341 </span>            :     return (_packed[0] == other._packed[0]) &amp;</a>
+<a name="342"><span class="lineNum">     342 </span>            :            (_packed[1] == other._packed[1]) ;</a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            :   //! Get if the operand is a register matching `rType`.</a>
+<a name="346"><span class="lineNum">     346 </span>            :   ASMJIT_INLINE bool isReg(uint32_t rType) const noexcept {</a>
+<a name="347"><span class="lineNum">     347 </span>            :     const uint32_t kMsk = (kSignatureOpBits &lt;&lt; kSignatureOpShift) | (kSignatureRegTypeBits &lt;&lt; kSignatureRegTypeShift);</a>
+<a name="348"><span class="lineNum">     348 </span>            :     const uint32_t kSgn = (kOpReg           &lt;&lt; kSignatureOpShift) | (rType                 &lt;&lt; kSignatureRegTypeShift);</a>
+<a name="349"><span class="lineNum">     349 </span>            :     return (_signature &amp; kMsk) == kSgn;</a>
+<a name="350"><span class="lineNum">     350 </span>            :   }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            :   //! Get whether the operand is register and of `type` and `id`.</a>
+<a name="353"><span class="lineNum">     353 </span>            :   ASMJIT_INLINE bool isReg(uint32_t rType, uint32_t rId) const noexcept {</a>
+<a name="354"><span class="lineNum">     354 </span>            :     return isReg(rType) &amp;&amp; getId() == rId;</a>
+<a name="355"><span class="lineNum">     355 </span>            :   }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   //! Get whether the operand is a register or memory.</a>
+<a name="358"><span class="lineNum">     358 </span>            :   ASMJIT_INLINE bool isRegOrMem() const noexcept {</a>
+<a name="359"><span class="lineNum">     359 </span>            :     ASMJIT_ASSERT(kOpMem - kOpReg == 1);</a>
+<a name="360"><span class="lineNum">     360 </span>            :     return Utils::inInterval&lt;uint32_t&gt;(getOp(), kOpReg, kOpMem);</a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            :   //! Cast this operand to `T` type.</a>
+<a name="364"><span class="lineNum">     364 </span>            :   template&lt;typename T&gt;</a>
+<a name="365"><span class="lineNum">     365 </span>            :   ASMJIT_INLINE T&amp; as() noexcept { return static_cast&lt;T&amp;&gt;(*this); }</a>
+<a name="366"><span class="lineNum">     366 </span>            :   //! Cast this operand to `T` type (const).</a>
+<a name="367"><span class="lineNum">     367 </span>            :   template&lt;typename T&gt;</a>
+<a name="368"><span class="lineNum">     368 </span>            :   ASMJIT_INLINE const T&amp; as() const noexcept { return static_cast&lt;const T&amp;&gt;(*this); }</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="371"><span class="lineNum">     371 </span>            :   // [Reset]</a>
+<a name="372"><span class="lineNum">     372 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            :   //! Reset the `Operand` to none.</a>
+<a name="375"><span class="lineNum">     375 </span>            :   //!</a>
+<a name="376"><span class="lineNum">     376 </span>            :   //! None operand is defined the following way:</a>
+<a name="377"><span class="lineNum">     377 </span>            :   //!   - Its signature is zero (kOpNone, and the rest zero as well).</a>
+<a name="378"><span class="lineNum">     378 </span>            :   //!   - Its id is `0`.</a>
+<a name="379"><span class="lineNum">     379 </span>            :   //!   - The reserved8_4 field is set to `0`.</a>
+<a name="380"><span class="lineNum">     380 </span>            :   //!   - The reserved12_4 field is set to zero.</a>
+<a name="381"><span class="lineNum">     381 </span>            :   //!</a>
+<a name="382"><span class="lineNum">     382 </span>            :   //! In other words, reset operands have all members set to zero. Reset operand</a>
+<a name="383"><span class="lineNum">     383 </span>            :   //! must match the Operand state right after its construction. Alternatively,</a>
+<a name="384"><span class="lineNum">     384 </span>            :   //! if you have an array of operands, you can simply use `memset()`.</a>
+<a name="385"><span class="lineNum">     385 </span>            :   //!</a>
+<a name="386"><span class="lineNum">     386 </span>            :   //! ```</a>
+<a name="387"><span class="lineNum">     387 </span>            :   //! using namespace asmjit;</a>
+<a name="388"><span class="lineNum">     388 </span>            :   //!</a>
+<a name="389"><span class="lineNum">     389 </span>            :   //! Operand a;</a>
+<a name="390"><span class="lineNum">     390 </span>            :   //! Operand b;</a>
+<a name="391"><span class="lineNum">     391 </span>            :   //! assert(a == b);</a>
+<a name="392"><span class="lineNum">     392 </span>            :   //!</a>
+<a name="393"><span class="lineNum">     393 </span>            :   //! b = x86::eax;</a>
+<a name="394"><span class="lineNum">     394 </span>            :   //! assert(a != b);</a>
+<a name="395"><span class="lineNum">     395 </span>            :   //!</a>
+<a name="396"><span class="lineNum">     396 </span>            :   //! b.reset();</a>
+<a name="397"><span class="lineNum">     397 </span>            :   //! assert(a == b);</a>
+<a name="398"><span class="lineNum">     398 </span>            :   //!</a>
+<a name="399"><span class="lineNum">     399 </span>            :   //! memset(&amp;b, 0, sizeof(Operand));</a>
+<a name="400"><span class="lineNum">     400 </span>            :   //! assert(a == b);</a>
+<a name="401"><span class="lineNum">     401 </span>            :   //! ```</a>
+<a name="402"><span class="lineNum">     402 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="403"><span class="lineNum">     403 </span>            :     _init_packed_d0_d1(kOpNone, 0);</a>
+<a name="404"><span class="lineNum">     404 </span>            :     _init_packed_d2_d3(0, 0);</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="408"><span class="lineNum">     408 </span>            :   // [Operator Overload]</a>
+<a name="409"><span class="lineNum">     409 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            :   template&lt;typename T&gt;</a>
+<a name="412"><span class="lineNum">     412 </span>            :   ASMJIT_INLINE bool operator==(const T&amp; other) const noexcept { return  isEqual(other); }</a>
+<a name="413"><span class="lineNum">     413 </span>            :   template&lt;typename T&gt;</a>
+<a name="414"><span class="lineNum">     414 </span>            :   ASMJIT_INLINE bool operator!=(const T&amp; other) const noexcept { return !isEqual(other); }</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="417"><span class="lineNum">     417 </span>            :   // [Members]</a>
+<a name="418"><span class="lineNum">     418 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   union {</a>
+<a name="421"><span class="lineNum">     421 </span>            :     AnyData _any;                        //!&lt; Generic data.</a>
+<a name="422"><span class="lineNum">     422 </span>            :     RegData _reg;                        //!&lt; Physical or virtual register data.</a>
+<a name="423"><span class="lineNum">     423 </span>            :     MemData _mem;                        //!&lt; Memory address data.</a>
+<a name="424"><span class="lineNum">     424 </span>            :     ImmData _imm;                        //!&lt; Immediate value data.</a>
+<a name="425"><span class="lineNum">     425 </span>            :     LabelData _label;                    //!&lt; Label data.</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :     uint32_t _signature;                 //!&lt; Operand signature (first 32-bits).</a>
+<a name="428"><span class="lineNum">     428 </span>            :     UInt64 _packed[2];                   //!&lt; Operand packed into two 64-bit integers.</a>
+<a name="429"><span class="lineNum">     429 </span>            :   };</a>
+<a name="430"><span class="lineNum">     430 </span>            : };</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            : // ============================================================================</a>
+<a name="433"><span class="lineNum">     433 </span>            : // [asmjit::Operand]</a>
+<a name="434"><span class="lineNum">     434 </span>            : // ============================================================================</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            : //! Operand can contain register, memory location, immediate, or label.</a>
+<a name="437"><span class="lineNum">     437 </span>            : class Operand : public Operand_ {</a>
+<a name="438"><span class="lineNum">     438 </span>            : public:</a>
+<a name="439"><span class="lineNum">     439 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="440"><span class="lineNum">     440 </span>            :   // [Construction / Destruction]</a>
+<a name="441"><span class="lineNum">     441 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            :   //! Create an uninitialized operand.</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">      24732 :   ASMJIT_INLINE Operand() noexcept { reset(); }</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   //! Create a reference to `other` operand.</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">       4316 :   ASMJIT_INLINE Operand(const Operand&amp; other) noexcept { _init(other); }</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   //! Create a reference to `other` operand.</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">       9084 :   explicit ASMJIT_INLINE Operand(const Operand_&amp; other) noexcept { _init(other); }</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   //! Create a completely uninitialized operand (dangerous).</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">       1984 :   explicit ASMJIT_INLINE Operand(const _NoInit&amp;) noexcept {}</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="453"><span class="lineNum">     453 </span>            :   // [Clone]</a>
+<a name="454"><span class="lineNum">     454 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            :   //! Clone the `Operand`.</a>
+<a name="457"><span class="lineNum">     457 </span>            :   ASMJIT_INLINE Operand clone() const noexcept { return Operand(*this); }</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            :   ASMJIT_INLINE Operand&amp; operator=(const Operand_&amp; other) noexcept { copyFrom(other); return *this; }</a>
+<a name="460"><span class="lineNum">     460 </span>            : };</a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            : // ============================================================================</a>
+<a name="463"><span class="lineNum">     463 </span>            : // [asmjit::Label]</a>
+<a name="464"><span class="lineNum">     464 </span>            : // ============================================================================</a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span>            : //! Label (jump target or data location).</a>
+<a name="467"><span class="lineNum">     467 </span>            : //!</a>
+<a name="468"><span class="lineNum">     468 </span>            : //! Label represents a location in code typically used as a jump target, but</a>
+<a name="469"><span class="lineNum">     469 </span>            : //! may be also a reference to some data or a static variable. Label has to be</a>
+<a name="470"><span class="lineNum">     470 </span>            : //! explicitly created by CodeEmitter.</a>
+<a name="471"><span class="lineNum">     471 </span>            : //!</a>
+<a name="472"><span class="lineNum">     472 </span>            : //! Example of using labels:</a>
+<a name="473"><span class="lineNum">     473 </span>            : //!</a>
+<a name="474"><span class="lineNum">     474 </span>            : //! ~~~</a>
+<a name="475"><span class="lineNum">     475 </span>            : //! // Create a CodeEmitter (for example X86Assembler).</a>
+<a name="476"><span class="lineNum">     476 </span>            : //! X86Assembler a;</a>
+<a name="477"><span class="lineNum">     477 </span>            : //!</a>
+<a name="478"><span class="lineNum">     478 </span>            : //! // Create Label instance.</a>
+<a name="479"><span class="lineNum">     479 </span>            : //! Label L1 = a.newLabel();</a>
+<a name="480"><span class="lineNum">     480 </span>            : //!</a>
+<a name="481"><span class="lineNum">     481 </span>            : //! // ... your code ...</a>
+<a name="482"><span class="lineNum">     482 </span>            : //!</a>
+<a name="483"><span class="lineNum">     483 </span>            : //! // Using label.</a>
+<a name="484"><span class="lineNum">     484 </span>            : //! a.jump(L1);</a>
+<a name="485"><span class="lineNum">     485 </span>            : //!</a>
+<a name="486"><span class="lineNum">     486 </span>            : //! // ... your code ...</a>
+<a name="487"><span class="lineNum">     487 </span>            : //!</a>
+<a name="488"><span class="lineNum">     488 </span>            : //! // Bind label to the current position, see `CodeEmitter::bind()`.</a>
+<a name="489"><span class="lineNum">     489 </span>            : //! a.bind(L1);</a>
+<a name="490"><span class="lineNum">     490 </span>            : //! ~~~</a>
+<a name="491"><span class="lineNum">     491 </span>            : class Label : public Operand {</a>
+<a name="492"><span class="lineNum">     492 </span>            : public:</a>
+<a name="493"><span class="lineNum">     493 </span>            :   //! Type of the Label.</a>
+<a name="494"><span class="lineNum">     494 </span>            :   enum Type {</a>
+<a name="495"><span class="lineNum">     495 </span>            :     kTypeAnonymous = 0,                  //!&lt; Anonymous (unnamed) label.</a>
+<a name="496"><span class="lineNum">     496 </span>            :     kTypeLocal     = 1,                  //!&lt; Local label (always has parentId).</a>
+<a name="497"><span class="lineNum">     497 </span>            :     kTypeGlobal    = 2,                  //!&lt; Global label (never has parentId).</a>
+<a name="498"><span class="lineNum">     498 </span>            :     kTypeCount     = 3                   //!&lt; Number of label types.</a>
+<a name="499"><span class="lineNum">     499 </span>            :   };</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            :   // TODO: Find a better place, find a better name.</a>
+<a name="502"><span class="lineNum">     502 </span>            :   enum {</a>
+<a name="503"><span class="lineNum">     503 </span>            :     //! Label tag is used as a sub-type, forming a unique signature across all</a>
+<a name="504"><span class="lineNum">     504 </span>            :     //! operand types as 0x1 is never associated with any register (reg-type).</a>
+<a name="505"><span class="lineNum">     505 </span>            :     //! This means that a memory operand's BASE register can be constructed</a>
+<a name="506"><span class="lineNum">     506 </span>            :     //! from virtually any operand (register vs. label) by just assigning its</a>
+<a name="507"><span class="lineNum">     507 </span>            :     //! type (reg type or label-tag) and operand id.</a>
+<a name="508"><span class="lineNum">     508 </span>            :     kLabelTag = 0x1</a>
+<a name="509"><span class="lineNum">     509 </span>            :   };</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="512"><span class="lineNum">     512 </span>            :   // [Construction / Destruction]</a>
+<a name="513"><span class="lineNum">     513 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :   //! Create new, unassociated label.</a>
+<a name="516"><span class="lineNum">     516 </span>            :   ASMJIT_INLINE Label() noexcept : Operand(NoInit) { reset(); }</a>
+<a name="517"><span class="lineNum">     517 </span>            :   //! Create a reference to another label.</a>
+<a name="518"><span class="lineNum">     518 </span>            :   ASMJIT_INLINE Label(const Label&amp; other) noexcept : Operand(other) {}</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            :   explicit ASMJIT_INLINE Label(uint32_t id) noexcept : Operand(NoInit) {</a>
+<a name="521"><span class="lineNum">     521 </span>            :     _init_packed_d0_d1(kOpLabel, id);</a>
+<a name="522"><span class="lineNum">     522 </span>            :     _init_packed_d2_d3(0, 0);</a>
+<a name="523"><span class="lineNum">     523 </span>            :   }</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            :   explicit ASMJIT_INLINE Label(const _NoInit&amp;) noexcept : Operand(NoInit) {}</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="528"><span class="lineNum">     528 </span>            :   // [Reset]</a>
+<a name="529"><span class="lineNum">     529 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   // TODO: I think that if operand is reset it shouldn't say it's a Label, it</a>
+<a name="532"><span class="lineNum">     532 </span>            :   // should be none like all other operands.</a>
+<a name="533"><span class="lineNum">     533 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="534"><span class="lineNum">     534 </span>            :     _init_packed_d0_d1(kOpLabel, 0);</a>
+<a name="535"><span class="lineNum">     535 </span>            :     _init_packed_d2_d3(0, 0);</a>
+<a name="536"><span class="lineNum">     536 </span>            :   }</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="539"><span class="lineNum">     539 </span>            :   // [Label Specific]</a>
+<a name="540"><span class="lineNum">     540 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span>            :   //! Get if the label was created by CodeEmitter and has an assigned id.</a>
+<a name="543"><span class="lineNum">     543 </span>            :   ASMJIT_INLINE bool isValid() const noexcept { return _label.id != 0; }</a>
+<a name="544"><span class="lineNum">     544 </span>            :   //! Set label id.</a>
+<a name="545"><span class="lineNum">     545 </span>            :   ASMJIT_INLINE void setId(uint32_t id) { _label.id = id; }</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="548"><span class="lineNum">     548 </span>            :   // [Operator Overload]</a>
+<a name="549"><span class="lineNum">     549 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span>            :   ASMJIT_INLINE Label&amp; operator=(const Label&amp; other) noexcept { copyFrom(other); return *this; }</a>
+<a name="552"><span class="lineNum">     552 </span>            : };</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            : // ============================================================================</a>
+<a name="555"><span class="lineNum">     555 </span>            : // [asmjit::Reg]</a>
+<a name="556"><span class="lineNum">     556 </span>            : // ============================================================================</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            : #define ASMJIT_DEFINE_REG_TRAITS(TRAITS_T, REG_T, TYPE, KIND, SIZE, COUNT, TYPE_ID) \</a>
+<a name="559"><span class="lineNum">     559 </span>            : template&lt;&gt;                                                                    \</a>
+<a name="560"><span class="lineNum">     560 </span>            : struct TRAITS_T &lt; TYPE &gt; {                                                    \</a>
+<a name="561"><span class="lineNum">     561 </span>            :   typedef REG_T Reg;                                                          \</a>
+<a name="562"><span class="lineNum">     562 </span>            :                                                                               \</a>
+<a name="563"><span class="lineNum">     563 </span>            :   enum {                                                                      \</a>
+<a name="564"><span class="lineNum">     564 </span>            :     kValid     = 1,                                                           \</a>
+<a name="565"><span class="lineNum">     565 </span>            :     kCount     = COUNT,                                                       \</a>
+<a name="566"><span class="lineNum">     566 </span>            :     kTypeId    = TYPE_ID,                                                     \</a>
+<a name="567"><span class="lineNum">     567 </span>            :                                                                               \</a>
+<a name="568"><span class="lineNum">     568 </span>            :     kType      = TYPE,                                                        \</a>
+<a name="569"><span class="lineNum">     569 </span>            :     kKind      = KIND,                                                        \</a>
+<a name="570"><span class="lineNum">     570 </span>            :     kSize      = SIZE,                                                        \</a>
+<a name="571"><span class="lineNum">     571 </span>            :     kSignature = (Operand::kOpReg &lt;&lt; Operand::kSignatureOpShift     ) |       \</a>
+<a name="572"><span class="lineNum">     572 </span>            :                  (kType           &lt;&lt; Operand::kSignatureRegTypeShift) |       \</a>
+<a name="573"><span class="lineNum">     573 </span>            :                  (kKind           &lt;&lt; Operand::kSignatureRegKindShift) |       \</a>
+<a name="574"><span class="lineNum">     574 </span>            :                  (kSize           &lt;&lt; Operand::kSignatureSizeShift   )         \</a>
+<a name="575"><span class="lineNum">     575 </span>            :   };                                                                          \</a>
+<a name="576"><span class="lineNum">     576 </span>            : }                                                                             \</a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span>            : #define ASMJIT_DEFINE_ABSTRACT_REG(REG_T, BASE_T)                             \</a>
+<a name="579"><span class="lineNum">     579 </span>            : public:                                                                       \</a>
+<a name="580"><span class="lineNum">     580 </span>            :   /*! Default constructor doesn't setup anything, it's like `Operand()`. */   \</a>
+<a name="581"><span class="lineNum">     581 </span>            :   ASMJIT_INLINE REG_T() ASMJIT_NOEXCEPT                                       \</a>
+<a name="582"><span class="lineNum">     582 </span>            :     : BASE_T() {}                                                             \</a>
+<a name="583"><span class="lineNum">     583 </span>            :                                                                               \</a>
+<a name="584"><span class="lineNum">     584 </span>            :   /*! Copy the `other` REG_T register operand. */                             \</a>
+<a name="585"><span class="lineNum">     585 </span>            :   ASMJIT_INLINE REG_T(const REG_T&amp; other) ASMJIT_NOEXCEPT                     \</a>
+<a name="586"><span class="lineNum">     586 </span>            :     : BASE_T(other) {}                                                        \</a>
+<a name="587"><span class="lineNum">     587 </span>            :                                                                               \</a>
+<a name="588"><span class="lineNum">     588 </span>            :   /*! Copy the `other` REG_T register operand having its id set to `rId` */   \</a>
+<a name="589"><span class="lineNum">     589 </span>            :   ASMJIT_INLINE REG_T(const Reg&amp; other, uint32_t rId) ASMJIT_NOEXCEPT         \</a>
+<a name="590"><span class="lineNum">     590 </span>            :     : BASE_T(other, rId) {}                                                   \</a>
+<a name="591"><span class="lineNum">     591 </span>            :                                                                               \</a>
+<a name="592"><span class="lineNum">     592 </span>            :   /*! Create a REG_T register operand based on `signature` and `rId`. */      \</a>
+<a name="593"><span class="lineNum">     593 </span>            :   ASMJIT_INLINE REG_T(const _Init&amp; init, uint32_t signature, uint32_t rId) ASMJIT_NOEXCEPT \</a>
+<a name="594"><span class="lineNum">     594 </span>            :     : BASE_T(init, signature, rId) {}                                         \</a>
+<a name="595"><span class="lineNum">     595 </span>            :                                                                               \</a>
+<a name="596"><span class="lineNum">     596 </span>            :   /*! Create a completely uninitialized REG_T register operand (garbage). */  \</a>
+<a name="597"><span class="lineNum">     597 </span>            :   explicit ASMJIT_INLINE REG_T(const _NoInit&amp;) ASMJIT_NOEXCEPT                \</a>
+<a name="598"><span class="lineNum">     598 </span>            :     : BASE_T(NoInit) {}                                                       \</a>
+<a name="599"><span class="lineNum">     599 </span>            :                                                                               \</a>
+<a name="600"><span class="lineNum">     600 </span>            :   /*! Clone the register operand. */                                          \</a>
+<a name="601"><span class="lineNum">     601 </span>            :   ASMJIT_INLINE REG_T clone() const ASMJIT_NOEXCEPT { return REG_T(*this); }  \</a>
+<a name="602"><span class="lineNum">     602 </span>            :                                                                               \</a>
+<a name="603"><span class="lineNum">     603 </span>            :   /*! Create a new register from register type and id. */                     \</a>
+<a name="604"><span class="lineNum">     604 </span>            :   static ASMJIT_INLINE REG_T fromTypeAndId(uint32_t rType, uint32_t rId) ASMJIT_NOEXCEPT { \</a>
+<a name="605"><span class="lineNum">     605 </span>            :     return REG_T(Init, signatureOf(rType), rId);                              \</a>
+<a name="606"><span class="lineNum">     606 </span>            :   }                                                                           \</a>
+<a name="607"><span class="lineNum">     607 </span>            :                                                                               \</a>
+<a name="608"><span class="lineNum">     608 </span>            :   /*! Create a new register from signature and id. */                         \</a>
+<a name="609"><span class="lineNum">     609 </span>            :   static ASMJIT_INLINE REG_T fromSignature(uint32_t signature, uint32_t rId) ASMJIT_NOEXCEPT { \</a>
+<a name="610"><span class="lineNum">     610 </span>            :     return REG_T(Init, signature, rId);                                       \</a>
+<a name="611"><span class="lineNum">     611 </span>            :   }                                                                           \</a>
+<a name="612"><span class="lineNum">     612 </span>            :                                                                               \</a>
+<a name="613"><span class="lineNum">     613 </span>            :   ASMJIT_INLINE REG_T&amp; operator=(const REG_T&amp; other) ASMJIT_NOEXCEPT {        \</a>
+<a name="614"><span class="lineNum">     614 </span>            :     copyFrom(other); return *this;                                            \</a>
+<a name="615"><span class="lineNum">     615 </span>            :   }</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            : #define ASMJIT_DEFINE_FINAL_REG(REG_T, BASE_T, TRAITS_T)                      \</a>
+<a name="618"><span class="lineNum">     618 </span>            :   ASMJIT_DEFINE_ABSTRACT_REG(REG_T, BASE_T)                                   \</a>
+<a name="619"><span class="lineNum">     619 </span>            :                                                                               \</a>
+<a name="620"><span class="lineNum">     620 </span>            :   /*! Create a REG_T register with `id`. */                                   \</a>
+<a name="621"><span class="lineNum">     621 </span>            :   explicit ASMJIT_INLINE REG_T(uint32_t rId) ASMJIT_NOEXCEPT                  \</a>
+<a name="622"><span class="lineNum">     622 </span>            :     : BASE_T(Init, kSignature, rId) {}                                        \</a>
+<a name="623"><span class="lineNum">     623 </span>            :                                                                               \</a>
+<a name="624"><span class="lineNum">     624 </span>            :   enum {                                                                      \</a>
+<a name="625"><span class="lineNum">     625 </span>            :     kThisType  = TRAITS_T::kType,                                             \</a>
+<a name="626"><span class="lineNum">     626 </span>            :     kThisKind  = TRAITS_T::kKind,                                             \</a>
+<a name="627"><span class="lineNum">     627 </span>            :     kThisSize  = TRAITS_T::kSize,                                             \</a>
+<a name="628"><span class="lineNum">     628 </span>            :     kSignature = TRAITS_T::kSignature                                         \</a>
+<a name="629"><span class="lineNum">     629 </span>            :   };</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            : //! Structure that contains core register information.</a>
+<a name="632"><span class="lineNum">     632 </span>            : //!</a>
+<a name="633"><span class="lineNum">     633 </span>            : //! This information is compatible with operand's signature (32-bit integer)</a>
+<a name="634"><span class="lineNum">     634 </span>            : //! and `RegInfo` just provides easy way to access it.</a>
+<a name="635"><span class="lineNum">     635 </span>            : struct RegInfo {</a>
+<a name="636"><span class="lineNum">     636 </span>            :   ASMJIT_INLINE uint32_t getSignature() const noexcept {</a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">      78684 :     return _signature;</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :   }</a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span>            :   ASMJIT_INLINE uint32_t getOp() const noexcept {</a>
+<a name="641"><span class="lineNum">     641 </span>            :     return (_signature &gt;&gt; Operand::kSignatureOpShift) &amp; Operand::kSignatureOpBits;</a>
+<a name="642"><span class="lineNum">     642 </span>            :   }</a>
+<a name="643"><span class="lineNum">     643 </span>            : </a>
+<a name="644"><span class="lineNum">     644 </span>            :   ASMJIT_INLINE uint32_t getType() const noexcept {</a>
+<a name="645"><span class="lineNum">     645 </span>            :     return (_signature &gt;&gt; Operand::kSignatureRegTypeShift) &amp; Operand::kSignatureRegTypeBits;</a>
+<a name="646"><span class="lineNum">     646 </span>            :   }</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            :   ASMJIT_INLINE uint32_t getKind() const noexcept {</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">     183032 :     return (_signature &gt;&gt; Operand::kSignatureRegKindShift) &amp; Operand::kSignatureRegKindBits;</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :   }</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :   ASMJIT_INLINE uint32_t getSize() const noexcept {</a>
+<a name="653"><span class="lineNum">     653 </span>            :     return (_signature &gt;&gt; Operand::kSignatureSizeShift) &amp; Operand::kSignatureSizeBits;</a>
+<a name="654"><span class="lineNum">     654 </span>            :   }</a>
+<a name="655"><span class="lineNum">     655 </span>            : </a>
+<a name="656"><span class="lineNum">     656 </span>            :   uint32_t _signature;</a>
+<a name="657"><span class="lineNum">     657 </span>            : };</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            : //! Physical/Virtual register operand.</a>
+<a name="660"><span class="lineNum">     660 </span>            : class Reg : public Operand {</a>
+<a name="661"><span class="lineNum">     661 </span>            : public:</a>
+<a name="662"><span class="lineNum">     662 </span>            :   //! Architecture neutral register types.</a>
+<a name="663"><span class="lineNum">     663 </span>            :   //!</a>
+<a name="664"><span class="lineNum">     664 </span>            :   //! These must be reused by any platform that contains that types. All GP</a>
+<a name="665"><span class="lineNum">     665 </span>            :   //! and VEC registers are also allowed by design to be part of a BASE|INDEX</a>
+<a name="666"><span class="lineNum">     666 </span>            :   //! of a memory operand.</a>
+<a name="667"><span class="lineNum">     667 </span>            :   ASMJIT_ENUM(RegType) {</a>
+<a name="668"><span class="lineNum">     668 </span>            :     kRegNone      = 0,                   //!&lt; No register - unused, invalid, multiple meanings.</a>
+<a name="669"><span class="lineNum">     669 </span>            :     // (1 is used as a LabelTag)</a>
+<a name="670"><span class="lineNum">     670 </span>            :     kRegGp8Lo     = 2,                   //!&lt; 8-bit low general purpose register (X86).</a>
+<a name="671"><span class="lineNum">     671 </span>            :     kRegGp8Hi     = 3,                   //!&lt; 8-bit high general purpose register (X86).</a>
+<a name="672"><span class="lineNum">     672 </span>            :     kRegGp16      = 4,                   //!&lt; 16-bit general purpose register (X86).</a>
+<a name="673"><span class="lineNum">     673 </span>            :     kRegGp32      = 5,                   //!&lt; 32-bit general purpose register (X86|ARM).</a>
+<a name="674"><span class="lineNum">     674 </span>            :     kRegGp64      = 6,                   //!&lt; 64-bit general purpose register (X86|ARM).</a>
+<a name="675"><span class="lineNum">     675 </span>            :     kRegVec32     = 7,                   //!&lt; 32-bit view of a vector register (ARM).</a>
+<a name="676"><span class="lineNum">     676 </span>            :     kRegVec64     = 8,                   //!&lt; 64-bit view of a vector register (ARM).</a>
+<a name="677"><span class="lineNum">     677 </span>            :     kRegVec128    = 9,                   //!&lt; 128-bit view of a vector register (X86|ARM).</a>
+<a name="678"><span class="lineNum">     678 </span>            :     kRegVec256    = 10,                  //!&lt; 256-bit view of a vector register (X86).</a>
+<a name="679"><span class="lineNum">     679 </span>            :     kRegVec512    = 11,                  //!&lt; 512-bit view of a vector register (X86).</a>
+<a name="680"><span class="lineNum">     680 </span>            :     kRegVec1024   = 12,                  //!&lt; 1024-bit view of a vector register (future).</a>
+<a name="681"><span class="lineNum">     681 </span>            :     kRegVec2048   = 13,                  //!&lt; 2048-bit view of a vector register (future).</a>
+<a name="682"><span class="lineNum">     682 </span>            :     kRegIP        = 14,                  //!&lt; Universal id of IP/PC register (if separate).</a>
+<a name="683"><span class="lineNum">     683 </span>            :     kRegCustom    = 15,                  //!&lt; Start of platform dependent register types (must be honored).</a>
+<a name="684"><span class="lineNum">     684 </span>            :     kRegMax       = 31                   //!&lt; Maximum possible register id of all architectures.</a>
+<a name="685"><span class="lineNum">     685 </span>            :   };</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span>            :   //! Architecture neutral register kinds.</a>
+<a name="688"><span class="lineNum">     688 </span>            :   ASMJIT_ENUM(Kind) {</a>
+<a name="689"><span class="lineNum">     689 </span>            :     kKindGp       = 0,                   //!&lt; General purpose register (X86|ARM).</a>
+<a name="690"><span class="lineNum">     690 </span>            :     kKindVec      = 1,                   //!&lt; Vector register (X86|ARM).</a>
+<a name="691"><span class="lineNum">     691 </span>            :     kKindMax      = 15                   //!&lt; Maximum possible register kind of all architectures.</a>
+<a name="692"><span class="lineNum">     692 </span>            :   };</a>
+<a name="693"><span class="lineNum">     693 </span>            : </a>
+<a name="694"><span class="lineNum">     694 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="695"><span class="lineNum">     695 </span>            :   // [Construction / Destruction]</a>
+<a name="696"><span class="lineNum">     696 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="697"><span class="lineNum">     697 </span>            : </a>
+<a name="698"><span class="lineNum">     698 </span>            :   //! Create a dummy register operand.</a>
+<a name="699"><span class="lineNum">     699 </span>            :   ASMJIT_INLINE Reg() noexcept : Operand() {}</a>
+<a name="700"><span class="lineNum">     700 </span>            :   //! Create a new register operand which is the same as `other` .</a>
+<a name="701"><span class="lineNum">     701 </span>            :   ASMJIT_INLINE Reg(const Reg&amp; other) noexcept : Operand(other) {}</a>
+<a name="702"><span class="lineNum">     702 </span>            :   //! Create a new register operand compatible with `other`, but with a different `rId`.</a>
+<a name="703"><span class="lineNum">     703 </span>            :   ASMJIT_INLINE Reg(const Reg&amp; other, uint32_t rId) noexcept : Operand(NoInit) {</a>
+<a name="704"><span class="lineNum">     704 </span>            :     _init_packed_d0_d1(other._signature, rId);</a>
+<a name="705"><span class="lineNum">     705 </span>            :     _packed[1] = other._packed[1];</a>
+<a name="706"><span class="lineNum">     706 </span>            :   }</a>
+<a name="707"><span class="lineNum">     707 </span>            : </a>
+<a name="708"><span class="lineNum">     708 </span>            :   //! Create a register initialized to `signature` and `rId`.</a>
+<a name="709"><span class="lineNum">     709 </span>            :   ASMJIT_INLINE Reg(const _Init&amp;, uint32_t signature, uint32_t rId) noexcept : Operand(NoInit) {</a>
+<a name="710"><span class="lineNum">     710 </span>            :     _initReg(signature, rId);</a>
+<a name="711"><span class="lineNum">     711 </span>            :   }</a>
+<a name="712"><span class="lineNum">     712 </span>            :   explicit ASMJIT_INLINE Reg(const _NoInit&amp;) noexcept : Operand(NoInit) {}</a>
+<a name="713"><span class="lineNum">     713 </span>            : </a>
+<a name="714"><span class="lineNum">     714 </span>            :   //! Create a new register based on `signature` and `rId`.</a>
+<a name="715"><span class="lineNum">     715 </span>            :   static ASMJIT_INLINE Reg fromSignature(uint32_t signature, uint32_t rId) noexcept { return Reg(Init, signature, rId); }</a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="718"><span class="lineNum">     718 </span>            :   // [Reg Specific]</a>
+<a name="719"><span class="lineNum">     719 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span>            :   //! Get if the register is valid (either virtual or physical).</a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">       1948 :   ASMJIT_INLINE bool isValid() const noexcept { return _signature != 0; }</span></a>
+<a name="723"><span class="lineNum">     723 </span>            :   //! Get if this is a physical register.</a>
+<a name="724"><span class="lineNum">     724 </span>            :   ASMJIT_INLINE bool isPhysReg() const noexcept { return _reg.id &lt; Globals::kInvalidRegId; }</a>
+<a name="725"><span class="lineNum">     725 </span>            :   //! Get if this is a virtual register (used by \ref CodeCompiler).</a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool isVirtReg() const noexcept { return isPackedId(_reg.id); }</span></a>
+<a name="727"><span class="lineNum">     727 </span>            : </a>
+<a name="728"><span class="lineNum">     728 </span>            :   //! Get if this register is the same as `other`.</a>
+<a name="729"><span class="lineNum">     729 </span>            :   //!</a>
+<a name="730"><span class="lineNum">     730 </span>            :   //! This is just an optimization. Registers by default only use the first</a>
+<a name="731"><span class="lineNum">     731 </span>            :   //! 8 bytes of the Operand, so this method takes advantage of this knowledge</a>
+<a name="732"><span class="lineNum">     732 </span>            :   //! and only compares these 8 bytes. If both operands were created correctly</a>
+<a name="733"><span class="lineNum">     733 </span>            :   //! then `isEqual()` and `isSame()` should give the same answer, however, if</a>
+<a name="734"><span class="lineNum">     734 </span>            :   //! some operands contains a garbage or other metadata in the upper 8 bytes</a>
+<a name="735"><span class="lineNum">     735 </span>            :   //! then `isSame()` may return `true` in cases where `isEqual()` returns</a>
+<a name="736"><span class="lineNum">     736 </span>            :   //! false. However. no such case is known at the moment.</a>
+<a name="737"><span class="lineNum">     737 </span>            :   ASMJIT_INLINE bool isSame(const Reg&amp; other) const noexcept { return _packed[0] == other._packed[0]; }</a>
+<a name="738"><span class="lineNum">     738 </span>            : </a>
+<a name="739"><span class="lineNum">     739 </span>            :   //! Get if the register type matches `rType` - same as `isReg(rType)`, provided for convenience.</a>
+<a name="740"><span class="lineNum">     740 </span>            :   ASMJIT_INLINE bool isType(uint32_t rType) const noexcept { return (_signature &amp; kSignatureRegTypeMask) == (rType &lt;&lt; kSignatureRegTypeShift); }</a>
+<a name="741"><span class="lineNum">     741 </span>            :   //! Get if the register kind matches `rKind`.</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">      21892 :   ASMJIT_INLINE bool isKind(uint32_t rKind) const noexcept { return (_signature &amp; kSignatureRegKindMask) == (rKind &lt;&lt; kSignatureRegKindShift); }</span></a>
+<a name="743"><span class="lineNum">     743 </span>            : </a>
+<a name="744"><span class="lineNum">     744 </span>            :   //! Get if the register is a general purpose register (any size).</a>
+<a name="745"><span class="lineNum">     745 </span>            :   ASMJIT_INLINE bool isGp() const noexcept { return isKind(kKindGp); }</a>
+<a name="746"><span class="lineNum">     746 </span>            :   //! Get if the register is a vector register.</a>
+<a name="747"><span class="lineNum">     747 </span>            :   ASMJIT_INLINE bool isVec() const noexcept { return isKind(kKindVec); }</a>
+<a name="748"><span class="lineNum">     748 </span>            : </a>
+<a name="749"><span class="lineNum">     749 </span>            :   using Operand_::isReg;</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            :   //! Same as `isType()`, provided for convenience.</a>
+<a name="752"><span class="lineNum">     752 </span>            :   ASMJIT_INLINE bool isReg(uint32_t rType) const noexcept { return isType(rType); }</a>
+<a name="753"><span class="lineNum">     753 </span>            :   //! Get if the register type matches `type` and register id matches `rId`.</a>
+<a name="754"><span class="lineNum">     754 </span>            :   ASMJIT_INLINE bool isReg(uint32_t rType, uint32_t rId) const noexcept { return isType(rType) &amp;&amp; getId() == rId; }</a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span>            :   //! Get the register type.</a>
+<a name="757"><span class="lineNum">     757 </span>            :   ASMJIT_INLINE uint32_t getType() const noexcept { return _getSignatureData(kSignatureRegTypeBits, kSignatureRegTypeShift); }</a>
+<a name="758"><span class="lineNum">     758 </span>            :   //! Get the register kind.</a>
+<a name="759"><span class="lineNum">     759 </span>            :   ASMJIT_INLINE uint32_t getKind() const noexcept { return _getSignatureData(kSignatureRegKindBits, kSignatureRegKindShift); }</a>
+<a name="760"><span class="lineNum">     760 </span>            : </a>
+<a name="761"><span class="lineNum">     761 </span>            :   //! Clone the register operand.</a>
+<a name="762"><span class="lineNum">     762 </span>            :   ASMJIT_INLINE Reg clone() const noexcept { return Reg(*this); }</a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span>            :   //! Cast this register to `RegT` by also changing its signature.</a>
+<a name="765"><span class="lineNum">     765 </span>            :   //!</a>
+<a name="766"><span class="lineNum">     766 </span>            :   //! NOTE: Improper use of `cloneAs()` can lead to hard-to-debug errors.</a>
+<a name="767"><span class="lineNum">     767 </span>            :   template&lt;typename RegT&gt;</a>
+<a name="768"><span class="lineNum">     768 </span>            :   ASMJIT_INLINE RegT cloneAs() const noexcept { return RegT(Init, RegT::kSignature, getId()); }</a>
+<a name="769"><span class="lineNum">     769 </span>            : </a>
+<a name="770"><span class="lineNum">     770 </span>            :   //! Cast this register to `other` by also changing its signature.</a>
+<a name="771"><span class="lineNum">     771 </span>            :   //!</a>
+<a name="772"><span class="lineNum">     772 </span>            :   //! NOTE: Improper use of `cloneAs()` can lead to hard-to-debug errors.</a>
+<a name="773"><span class="lineNum">     773 </span>            :   template&lt;typename RegT&gt;</a>
+<a name="774"><span class="lineNum">     774 </span>            :   ASMJIT_INLINE RegT cloneAs(const RegT&amp; other) const noexcept { return RegT(Init, other.getSignature(), getId()); }</a>
+<a name="775"><span class="lineNum">     775 </span>            : </a>
+<a name="776"><span class="lineNum">     776 </span>            :   //! Set the register id to `id`.</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">       2660 :   ASMJIT_INLINE void setId(uint32_t rId) noexcept { _reg.id = rId; }</span></a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span>            :   //! Set a 32-bit operand signature based on traits of `RegT`.</a>
+<a name="780"><span class="lineNum">     780 </span>            :   template&lt;typename RegT&gt;</a>
+<a name="781"><span class="lineNum">     781 </span>            :   ASMJIT_INLINE void setSignatureT() noexcept { _signature = RegT::kSignature; }</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            :   //! Set register's `signature` and `rId`.</a>
+<a name="784"><span class="lineNum">     784 </span>            :   ASMJIT_INLINE void setSignatureAndId(uint32_t signature, uint32_t rId) noexcept {</a>
+<a name="785"><span class="lineNum">     785 </span>            :     _signature = signature;</a>
+<a name="786"><span class="lineNum">     786 </span>            :     _reg.id = rId;</a>
+<a name="787"><span class="lineNum">     787 </span>            :   }</a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="790"><span class="lineNum">     790 </span>            :   // [Reg Statics]</a>
+<a name="791"><span class="lineNum">     791 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span>            :   static ASMJIT_INLINE bool isGp(const Operand_&amp; op) noexcept {</a>
+<a name="794"><span class="lineNum">     794 </span>            :     // Check operand type and register kind. Not interested in register type and size.</a>
+<a name="795"><span class="lineNum">     795 </span>            :     const uint32_t kSgn = (kOpReg  &lt;&lt; kSignatureOpShift     ) |</a>
+<a name="796"><span class="lineNum">     796 </span>            :                           (kKindGp &lt;&lt; kSignatureRegKindShift) ;</a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineNoCov">          0 :     return (op.getSignature() &amp; (kSignatureOpMask | kSignatureRegKindMask)) == kSgn;</span></a>
+<a name="798"><span class="lineNum">     798 </span>            :   }</a>
+<a name="799"><span class="lineNum">     799 </span>            : </a>
+<a name="800"><span class="lineNum">     800 </span>            :   //! Get if the `op` operand is either a low or high 8-bit GPB register.</a>
+<a name="801"><span class="lineNum">     801 </span>            :   static ASMJIT_INLINE bool isVec(const Operand_&amp; op) noexcept {</a>
+<a name="802"><span class="lineNum">     802 </span>            :     // Check operand type and register kind. Not interested in register type and size.</a>
+<a name="803"><span class="lineNum">     803 </span>            :     const uint32_t kSgn = (kOpReg   &lt;&lt; kSignatureOpShift     ) |</a>
+<a name="804"><span class="lineNum">     804 </span>            :                           (kKindVec &lt;&lt; kSignatureRegKindShift) ;</a>
+<a name="805"><span class="lineNum">     805 </span>            :     return (op.getSignature() &amp; (kSignatureOpMask | kSignatureRegKindMask)) == kSgn;</a>
+<a name="806"><span class="lineNum">     806 </span>            :   }</a>
+<a name="807"><span class="lineNum">     807 </span>            : </a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isGp(const Operand_&amp; op, uint32_t rId) noexcept { return isGp(op) &amp; (op.getId() == rId); }</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :   static ASMJIT_INLINE bool isVec(const Operand_&amp; op, uint32_t rId) noexcept { return isVec(op) &amp; (op.getId() == rId); }</a>
+<a name="810"><span class="lineNum">     810 </span>            : };</a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span>            : // ============================================================================</a>
+<a name="813"><span class="lineNum">     813 </span>            : // [asmjit::RegOnly]</a>
+<a name="814"><span class="lineNum">     814 </span>            : // ============================================================================</a>
+<a name="815"><span class="lineNum">     815 </span>            : </a>
+<a name="816"><span class="lineNum">     816 </span>            : //! RegOnly is 8-byte version of `Reg` that only allows to store either `Reg`</a>
+<a name="817"><span class="lineNum">     817 </span>            : //! or nothing. This class was designed to decrease the space consumed by each</a>
+<a name="818"><span class="lineNum">     818 </span>            : //! extra &quot;operand&quot; in `CodeEmitter` and `CBInst` classes.</a>
+<a name="819"><span class="lineNum">     819 </span>            : struct RegOnly {</a>
+<a name="820"><span class="lineNum">     820 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="821"><span class="lineNum">     821 </span>            :   // [Init / Reset]</a>
+<a name="822"><span class="lineNum">     822 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span>            :   //! Initialize the `RegOnly` instance to hold register `signature` and `id`.</a>
+<a name="825"><span class="lineNum">     825 </span>            :   ASMJIT_INLINE void init(uint32_t signature, uint32_t id) noexcept {</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">     143438 :     _signature = signature;</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">     143438 :     _id = id;</span></a>
+<a name="828"><span class="lineNum">     828 </span>            :   }</a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span>            :   ASMJIT_INLINE void init(const Reg&amp; reg) noexcept { init(reg.getSignature(), reg.getId()); }</a>
+<a name="831"><span class="lineNum">     831 </span>            :   ASMJIT_INLINE void init(const RegOnly&amp; reg) noexcept { init(reg.getSignature(), reg.getId()); }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            :   //! Reset the `RegOnly` to none.</a>
+<a name="834"><span class="lineNum">     834 </span>            :   ASMJIT_INLINE void reset() noexcept { init(0, 0); }</a>
+<a name="835"><span class="lineNum">     835 </span>            : </a>
+<a name="836"><span class="lineNum">     836 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="837"><span class="lineNum">     837 </span>            :   // [Accessors]</a>
+<a name="838"><span class="lineNum">     838 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span>            :   //! Get if the `ExtraReg` is none (same as calling `Operand_::isNone()`).</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool isNone() const noexcept { return _signature == 0; }</span></a>
+<a name="842"><span class="lineNum">     842 </span>            :   //! Get if the register is valid (either virtual or physical).</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">      62316 :   ASMJIT_INLINE bool isValid() const noexcept { return _signature != 0; }</span></a>
+<a name="844"><span class="lineNum">     844 </span>            : </a>
+<a name="845"><span class="lineNum">     845 </span>            :   //! Get if this is a physical register.</a>
+<a name="846"><span class="lineNum">     846 </span>            :   ASMJIT_INLINE bool isPhysReg() const noexcept { return _id &lt; Globals::kInvalidRegId; }</a>
+<a name="847"><span class="lineNum">     847 </span>            :   //! Get if this is a virtual register (used by \ref CodeCompiler).</a>
+<a name="848"><span class="lineNum">     848 </span>            :   ASMJIT_INLINE bool isVirtReg() const noexcept { return Operand::isPackedId(_id); }</a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span>            :   //! Get register signature or 0.</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">      48362 :   ASMJIT_INLINE uint32_t getSignature() const noexcept { return _signature; }</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :   //! Get register id or 0.</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">      48362 :   ASMJIT_INLINE uint32_t getId() const noexcept { return _id; }</span></a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span>            :   //! \internal</a>
+<a name="856"><span class="lineNum">     856 </span>            :   //!</a>
+<a name="857"><span class="lineNum">     857 </span>            :   //! Unpacks information from operand's signature.</a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t _getSignatureData(uint32_t bits, uint32_t shift) const noexcept { return (_signature &gt;&gt; shift) &amp; bits; }</span></a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :   //! Get the register type.</a>
+<a name="861"><span class="lineNum">     861 </span>            :   ASMJIT_INLINE uint32_t getType() const noexcept { return _getSignatureData(Operand::kSignatureRegTypeBits, Operand::kSignatureRegTypeShift); }</a>
+<a name="862"><span class="lineNum">     862 </span>            :   //! Get the register kind.</a>
+<a name="863"><span class="lineNum">     863 </span>            :   ASMJIT_INLINE uint32_t getKind() const noexcept { return _getSignatureData(Operand::kSignatureRegKindBits, Operand::kSignatureRegKindShift); }</a>
+<a name="864"><span class="lineNum">     864 </span>            : </a>
+<a name="865"><span class="lineNum">     865 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="866"><span class="lineNum">     866 </span>            :   // [ToReg]</a>
+<a name="867"><span class="lineNum">     867 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span>            :   //! Convert back to `RegT` operand.</a>
+<a name="870"><span class="lineNum">     870 </span>            :   template&lt;typename RegT&gt;</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE RegT toReg() const noexcept { return RegT(Init, _signature, _id); }</span></a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="874"><span class="lineNum">     874 </span>            :   // [Members]</a>
+<a name="875"><span class="lineNum">     875 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span>            :   //! Type of the operand, either `kOpNone` or `kOpReg`.</a>
+<a name="878"><span class="lineNum">     878 </span>            :   uint32_t _signature;</a>
+<a name="879"><span class="lineNum">     879 </span>            :   //! Physical or virtual register id.</a>
+<a name="880"><span class="lineNum">     880 </span>            :   uint32_t _id;</a>
+<a name="881"><span class="lineNum">     881 </span>            : };</a>
+<a name="882"><span class="lineNum">     882 </span>            : </a>
+<a name="883"><span class="lineNum">     883 </span>            : // ============================================================================</a>
+<a name="884"><span class="lineNum">     884 </span>            : // [asmjit::Mem]</a>
+<a name="885"><span class="lineNum">     885 </span>            : // ============================================================================</a>
+<a name="886"><span class="lineNum">     886 </span>            : </a>
+<a name="887"><span class="lineNum">     887 </span>            : //! Base class for all memory operands.</a>
+<a name="888"><span class="lineNum">     888 </span>            : //!</a>
+<a name="889"><span class="lineNum">     889 </span>            : //! NOTE: It's tricky to pack all possible cases that define a memory operand</a>
+<a name="890"><span class="lineNum">     890 </span>            : //! into just 16 bytes. The `Mem` splits data into the following parts:</a>
+<a name="891"><span class="lineNum">     891 </span>            : //!</a>
+<a name="892"><span class="lineNum">     892 </span>            : //!   BASE - Base register or label - requires 36 bits total. 4 bits are used</a>
+<a name="893"><span class="lineNum">     893 </span>            : //!     to encode the type of the BASE operand (label vs. register type) and</a>
+<a name="894"><span class="lineNum">     894 </span>            : //!     the remaining 32 bits define the BASE id, which can be a physical or</a>
+<a name="895"><span class="lineNum">     895 </span>            : //!     virtual register index. If BASE type is zero, which is never used as</a>
+<a name="896"><span class="lineNum">     896 </span>            : //!     a register-type and label doesn't use it as well then BASE field</a>
+<a name="897"><span class="lineNum">     897 </span>            : //!     contains a high DWORD of a possible 64-bit absolute address, which is</a>
+<a name="898"><span class="lineNum">     898 </span>            : //!     possible on X64.</a>
+<a name="899"><span class="lineNum">     899 </span>            : //!</a>
+<a name="900"><span class="lineNum">     900 </span>            : //!   INDEX - Index register (or theoretically Label, which doesn't make sense).</a>
+<a name="901"><span class="lineNum">     901 </span>            : //!     Encoding is similar to BASE - it also requires 36 bits and splits the</a>
+<a name="902"><span class="lineNum">     902 </span>            : //!     encoding to INDEX type (4 bits defining the register type) and id (32-bits).</a>
+<a name="903"><span class="lineNum">     903 </span>            : //!</a>
+<a name="904"><span class="lineNum">     904 </span>            : //!   OFFSET - A relative offset of the address. Basically if BASE is specified</a>
+<a name="905"><span class="lineNum">     905 </span>            : //!     the relative displacement adjusts BASE and an optional INDEX. if BASE is</a>
+<a name="906"><span class="lineNum">     906 </span>            : //!     not specified then the OFFSET should be considered as ABSOLUTE address</a>
+<a name="907"><span class="lineNum">     907 </span>            : //!     (at least on X86/X64). In that case its low 32 bits are stored in</a>
+<a name="908"><span class="lineNum">     908 </span>            : //!     DISPLACEMENT field and the remaining high 32 bits are stored in BASE.</a>
+<a name="909"><span class="lineNum">     909 </span>            : //!</a>
+<a name="910"><span class="lineNum">     910 </span>            : //!   OTHER FIELDS - There is rest 8 bits that can be used for whatever purpose.</a>
+<a name="911"><span class="lineNum">     911 </span>            : //!          The X86Mem operand uses these bits to store segment override</a>
+<a name="912"><span class="lineNum">     912 </span>            : //!          prefix and index shift (scale).</a>
+<a name="913"><span class="lineNum">     913 </span>            : class Mem : public Operand {</a>
+<a name="914"><span class="lineNum">     914 </span>            : public:</a>
+<a name="915"><span class="lineNum">     915 </span>            :   enum AddrType {</a>
+<a name="916"><span class="lineNum">     916 </span>            :     kAddrTypeDefault = 0,</a>
+<a name="917"><span class="lineNum">     917 </span>            :     kAddrTypeAbs     = 1,</a>
+<a name="918"><span class="lineNum">     918 </span>            :     kAddrTypeRel     = 2,</a>
+<a name="919"><span class="lineNum">     919 </span>            :     kAddrTypeWrt     = 3</a>
+<a name="920"><span class="lineNum">     920 </span>            :   };</a>
+<a name="921"><span class="lineNum">     921 </span>            : </a>
+<a name="922"><span class="lineNum">     922 </span>            :   // Shortcuts.</a>
+<a name="923"><span class="lineNum">     923 </span>            :   enum SignatureMem {</a>
+<a name="924"><span class="lineNum">     924 </span>            :     kSignatureMemAbs = kAddrTypeAbs &lt;&lt; kSignatureMemAddrTypeShift,</a>
+<a name="925"><span class="lineNum">     925 </span>            :     kSignatureMemRel = kAddrTypeRel &lt;&lt; kSignatureMemAddrTypeShift,</a>
+<a name="926"><span class="lineNum">     926 </span>            :     kSignatureMemWrt = kAddrTypeWrt &lt;&lt; kSignatureMemAddrTypeShift</a>
+<a name="927"><span class="lineNum">     927 </span>            :   };</a>
+<a name="928"><span class="lineNum">     928 </span>            : </a>
+<a name="929"><span class="lineNum">     929 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="930"><span class="lineNum">     930 </span>            :   // [Construction / Destruction]</a>
+<a name="931"><span class="lineNum">     931 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span>            :   //! Construct a default `Mem` operand, that points to [0].</a>
+<a name="934"><span class="lineNum">     934 </span>            :   ASMJIT_INLINE Mem() noexcept : Operand(NoInit) { reset(); }</a>
+<a name="935"><span class="lineNum">     935 </span>            :   ASMJIT_INLINE Mem(const Mem&amp; other) noexcept : Operand(other) {}</a>
+<a name="936"><span class="lineNum">     936 </span>            : </a>
+<a name="937"><span class="lineNum">     937 </span>            :   ASMJIT_INLINE Mem(const _Init&amp;,</a>
+<a name="938"><span class="lineNum">     938 </span>            :     uint32_t baseType, uint32_t baseId,</a>
+<a name="939"><span class="lineNum">     939 </span>            :     uint32_t indexType, uint32_t indexId,</a>
+<a name="940"><span class="lineNum">     940 </span>            :     int32_t off, uint32_t size, uint32_t flags) noexcept : Operand(NoInit) {</a>
+<a name="941"><span class="lineNum">     941 </span>            : </a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">       8428 :     uint32_t signature = (baseType  &lt;&lt; kSignatureMemBaseTypeShift ) |</span></a>
+<a name="943"><span class="lineNum">     943 </span>            :                          (indexType &lt;&lt; kSignatureMemIndexTypeShift) |</a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 :                          (size      &lt;&lt; kSignatureSizeShift        ) ;</span></a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">       8428 :     _init_packed_d0_d1(kOpMem | signature | flags, indexId);</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">       8428 :     _mem.base = baseId;</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">       8428 :     _mem.offsetLo32 = static_cast&lt;uint32_t&gt;(off);</span></a>
+<a name="949"><span class="lineNum">     949 </span>            :   }</a>
+<a name="950"><span class="lineNum">     950 </span>            :   explicit ASMJIT_INLINE Mem(const _NoInit&amp;) noexcept : Operand(NoInit) {}</a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="953"><span class="lineNum">     953 </span>            :   // [Mem Specific]</a>
+<a name="954"><span class="lineNum">     954 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="955"><span class="lineNum">     955 </span>            : </a>
+<a name="956"><span class="lineNum">     956 </span>            :   //! Clone `Mem` operand.</a>
+<a name="957"><span class="lineNum">     957 </span>            :   ASMJIT_INLINE Mem clone() const noexcept { return Mem(*this); }</a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span>            :   //! Reset the memory operand - after reset the memory points to [0].</a>
+<a name="960"><span class="lineNum">     960 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="961"><span class="lineNum">     961 </span>            :     _init_packed_d0_d1(kOpMem, 0);</a>
+<a name="962"><span class="lineNum">     962 </span>            :     _init_packed_d2_d3(0, 0);</a>
+<a name="963"><span class="lineNum">     963 </span>            :   }</a>
+<a name="964"><span class="lineNum">     964 </span>            : </a>
+<a name="965"><span class="lineNum">     965 </span>            :   ASMJIT_INLINE bool hasAddrType() const noexcept { return _hasSignatureData(kSignatureMemAddrTypeMask); }</a>
+<a name="966"><span class="lineNum">     966 </span>            :   ASMJIT_INLINE uint32_t getAddrType() const noexcept { return _getSignatureData(kSignatureMemAddrTypeBits, kSignatureMemAddrTypeShift); }</a>
+<a name="967"><span class="lineNum">     967 </span>            :   ASMJIT_INLINE void setAddrType(uint32_t addrType) noexcept { return _setSignatureData(addrType, kSignatureMemAddrTypeBits, kSignatureMemAddrTypeShift); }</a>
+<a name="968"><span class="lineNum">     968 </span>            :   ASMJIT_INLINE void resetAddrType() noexcept { return _clearSignatureData(kSignatureMemAddrTypeBits, kSignatureMemAddrTypeShift); }</a>
+<a name="969"><span class="lineNum">     969 </span>            : </a>
+<a name="970"><span class="lineNum">     970 </span>            :   ASMJIT_INLINE bool isAbs() const noexcept { return getAddrType() == kAddrTypeAbs; }</a>
+<a name="971"><span class="lineNum">     971 </span>            :   ASMJIT_INLINE bool isRel() const noexcept { return getAddrType() == kAddrTypeRel; }</a>
+<a name="972"><span class="lineNum">     972 </span>            :   ASMJIT_INLINE bool isWrt() const noexcept { return getAddrType() == kAddrTypeWrt; }</a>
+<a name="973"><span class="lineNum">     973 </span>            : </a>
+<a name="974"><span class="lineNum">     974 </span>            :   ASMJIT_INLINE void setAbs() noexcept { setAddrType(kAddrTypeAbs); }</a>
+<a name="975"><span class="lineNum">     975 </span>            :   ASMJIT_INLINE void setRel() noexcept { setAddrType(kAddrTypeRel); }</a>
+<a name="976"><span class="lineNum">     976 </span>            :   ASMJIT_INLINE void setWrt() noexcept { setAddrType(kAddrTypeWrt); }</a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span>            :   ASMJIT_INLINE bool isArgHome() const noexcept { return _hasSignatureData(kSignatureMemArgHomeFlag); }</a>
+<a name="979"><span class="lineNum">     979 </span>            :   ASMJIT_INLINE bool isRegHome() const noexcept { return _hasSignatureData(kSignatureMemRegHomeFlag); }</a>
+<a name="980"><span class="lineNum">     980 </span>            : </a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setArgHome() noexcept { _signature |= kSignatureMemArgHomeFlag; }</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :   ASMJIT_INLINE void setRegHome() noexcept { _signature |= kSignatureMemRegHomeFlag; }</a>
+<a name="983"><span class="lineNum">     983 </span>            : </a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void clearArgHome() noexcept { _signature &amp;= ~kSignatureMemArgHomeFlag; }</span></a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">       8428 :   ASMJIT_INLINE void clearRegHome() noexcept { _signature &amp;= ~kSignatureMemRegHomeFlag; }</span></a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span>            :   //! Get if the memory operand has a BASE register or label specified.</a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasBase() const noexcept { return (_signature &amp; kSignatureMemBaseTypeMask) != 0; }</span></a>
+<a name="989"><span class="lineNum">     989 </span>            :   //! Get if the memory operand has an INDEX register specified.</a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasIndex() const noexcept { return (_signature &amp; kSignatureMemIndexTypeMask) != 0; }</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :   //! Get whether the memory operand has BASE and INDEX register.</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE bool hasBaseOrIndex() const noexcept { return (_signature &amp; kSignatureMemBaseIndexMask) != 0; }</span></a>
+<a name="993"><span class="lineNum">     993 </span>            :   //! Get whether the memory operand has BASE and INDEX register.</a>
+<a name="994"><span class="lineNum">     994 </span>            :   ASMJIT_INLINE bool hasBaseAndIndex() const noexcept { return (_signature &amp; kSignatureMemBaseTypeMask) != 0 &amp;&amp; (_signature &amp; kSignatureMemIndexTypeMask) != 0; }</a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span>            :   //! Get if the BASE operand is a register (registers start after `kLabelTag`).</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">      12200 :   ASMJIT_INLINE bool hasBaseReg() const noexcept { return (_signature &amp; kSignatureMemBaseTypeMask) &gt; (Label::kLabelTag &lt;&lt; kSignatureMemBaseTypeShift); }</span></a>
+<a name="998"><span class="lineNum">     998 </span>            :   //! Get if the BASE operand is a label.</a>
+<a name="999"><span class="lineNum">     999 </span>            :   ASMJIT_INLINE bool hasBaseLabel() const noexcept { return (_signature &amp; kSignatureMemBaseTypeMask) == (Label::kLabelTag &lt;&lt; kSignatureMemBaseTypeShift); }</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :   //! Get if the INDEX operand is a register (registers start after `kLabelTag`).</a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">      12200 :   ASMJIT_INLINE bool hasIndexReg() const noexcept { return (_signature &amp; kSignatureMemIndexTypeMask) &gt; (Label::kLabelTag &lt;&lt; kSignatureMemIndexTypeShift); }</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            : </a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   //! Get type of a BASE register (0 if this memory operand doesn't use the BASE register).</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :   //!</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :   //! NOTE: If the returned type is one (a value never associated to a register</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   //! type) the BASE is not register, but it's a label. One equals to `kLabelTag`.</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :   //! You should always check `hasBaseLabel()` before using `getBaseId()` result.</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   ASMJIT_INLINE uint32_t getBaseType() const noexcept { return _getSignatureData(kSignatureMemBaseTypeBits, kSignatureMemBaseTypeShift); }</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   //! Get type of an INDEX register (0 if this memory operand doesn't use the INDEX register).</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   ASMJIT_INLINE uint32_t getIndexType() const noexcept { return _getSignatureData(kSignatureMemIndexTypeBits, kSignatureMemIndexTypeShift); }</a>
+<a name="1011"><span class="lineNum">    1011 </span>            : </a>
+<a name="1012"><span class="lineNum">    1012 </span>            :   //! Get both BASE (4:0 bits) and INDEX (9:5 bits) types combined into a single integer.</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :   //!</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   //! This is used internally for BASE+INDEX validation.</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   ASMJIT_INLINE uint32_t getBaseIndexType() const noexcept { return _getSignatureData(kSignatureMemBaseIndexBits, kSignatureMemBaseIndexShift); }</a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   //! Get id of the BASE register or label (if the BASE was specified as label).</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">      20628 :   ASMJIT_INLINE uint32_t getBaseId() const noexcept { return _mem.base; }</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   //! Get id of the INDEX register.</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">      14528 :   ASMJIT_INLINE uint32_t getIndexId() const noexcept { return _mem.index; }</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            : </a>
+<a name="1022"><span class="lineNum">    1022 </span>            :   ASMJIT_INLINE void _setBase(uint32_t rType, uint32_t rId) noexcept {</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :     _setSignatureData(rType, kSignatureMemBaseTypeBits, kSignatureMemBaseTypeShift);</a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">       8428 :     _mem.base = rId;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   }</a>
+<a name="1026"><span class="lineNum">    1026 </span>            : </a>
+<a name="1027"><span class="lineNum">    1027 </span>            :   ASMJIT_INLINE void _setIndex(uint32_t rType, uint32_t rId) noexcept {</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     _setSignatureData(rType, kSignatureMemIndexTypeBits, kSignatureMemIndexTypeShift);</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     _mem.index = rId;</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :   }</a>
+<a name="1031"><span class="lineNum">    1031 </span>            : </a>
+<a name="1032"><span class="lineNum">    1032 </span>            :   ASMJIT_INLINE void setBase(const Reg&amp; base) noexcept { return _setBase(base.getType(), base.getId()); }</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   ASMJIT_INLINE void setIndex(const Reg&amp; index) noexcept { return _setIndex(index.getType(), index.getId()); }</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : </a>
+<a name="1035"><span class="lineNum">    1035 </span>            :   //! Reset the memory operand's BASE register / label.</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   ASMJIT_INLINE void resetBase() noexcept { _setBase(0, 0); }</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :   //! Reset the memory operand's INDEX register.</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :   ASMJIT_INLINE void resetIndex() noexcept { _setIndex(0, 0); }</a>
+<a name="1039"><span class="lineNum">    1039 </span>            : </a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   //! Set memory operand size.</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   ASMJIT_INLINE void setSize(uint32_t size) noexcept {</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     _setSignatureData(size, kSignatureSizeBits, kSignatureSizeShift);</a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">       8428 :   }</span></a>
+<a name="1044"><span class="lineNum">    1044 </span>            : </a>
+<a name="1045"><span class="lineNum">    1045 </span>            :   ASMJIT_INLINE bool hasOffset() const noexcept {</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineNoCov">          0 :     int32_t lo = static_cast&lt;int32_t&gt;(_mem.offsetLo32);</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineNoCov">          0 :     int32_t hi = static_cast&lt;int32_t&gt;(_mem.base) &amp; -static_cast&lt;int32_t&gt;(getBaseType() == 0);</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineNoCov">          0 :     return (lo | hi) != 0;</span></a>
+<a name="1049"><span class="lineNum">    1049 </span>            :   }</a>
+<a name="1050"><span class="lineNum">    1050 </span>            : </a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   //! Get if the memory operand has 64-bit offset or absolute address.</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   //!</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   //! If this is true then `hasBase()` must always report false.</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   ASMJIT_INLINE bool has64BitOffset() const noexcept { return getBaseType() == 0; }</a>
+<a name="1055"><span class="lineNum">    1055 </span>            : </a>
+<a name="1056"><span class="lineNum">    1056 </span>            :   //! Get a 64-bit offset or absolute address.</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   ASMJIT_INLINE int64_t getOffset() const noexcept {</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :     return has64BitOffset()</a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineNoCov">          0 :       ? static_cast&lt;int64_t&gt;(_mem.offset64)</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineNoCov">          0 :       : static_cast&lt;int64_t&gt;(static_cast&lt;int32_t&gt;(_mem.offsetLo32)); // Sign-Extend.</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   }</a>
+<a name="1062"><span class="lineNum">    1062 </span>            : </a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   //! Get a lower part of a 64-bit offset or absolute address.</a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">      14528 :   ASMJIT_INLINE int32_t getOffsetLo32() const noexcept { return static_cast&lt;int32_t&gt;(_mem.offsetLo32); }</span></a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   //! Get a higher part of a 64-bit offset or absolute address.</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :   //!</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   //! NOTE: This function is UNSAFE and returns garbage if `has64BitOffset()`</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   //! returns false. Never use it blindly without checking it.</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE int32_t getOffsetHi32() const noexcept { return static_cast&lt;int32_t&gt;(_mem.base); }</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            : </a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   //! Set a 64-bit offset or an absolute address to `offset`.</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :   //!</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   //! NOTE: This functions attempts to set both high and low parts of a 64-bit</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   //! offset, however, if the operand has a BASE register it will store only the</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   //! low 32 bits of the offset / address as there is no way to store both BASE</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :   //! and 64-bit offset, and there is currently no architecture that has such</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   //! capability targeted by AsmJit.</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :   ASMJIT_INLINE void setOffset(int64_t offset) noexcept {</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     if (has64BitOffset())</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :       _mem.offset64 = static_cast&lt;uint64_t&gt;(offset);</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     else</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :       _mem.offsetLo32 = static_cast&lt;int32_t&gt;(offset &amp; 0xFFFFFFFF);</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   }</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :   //! Adjust the offset by a 64-bit `off`.</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   ASMJIT_INLINE void addOffset(int64_t off) noexcept {</a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineNoCov">          0 :     if (has64BitOffset())</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineNoCov">          0 :       _mem.offset64 += static_cast&lt;uint64_t&gt;(off);</span></a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     else</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :       _mem.offsetLo32 += static_cast&lt;uint32_t&gt;(off &amp; 0xFFFFFFFF);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   }</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   //! Reset the memory offset to zero.</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   ASMJIT_INLINE void resetOffset() noexcept { setOffset(0); }</a>
+<a name="1093"><span class="lineNum">    1093 </span>            : </a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   //! Set a low 32-bit offset to `off`.</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   ASMJIT_INLINE void setOffsetLo32(int32_t off) noexcept {</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :     _mem.offsetLo32 = static_cast&lt;uint32_t&gt;(off);</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   }</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   //! Adjust the offset by `off`.</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :   //!</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :   //! NOTE: This is a fast function that doesn't use the HI 32-bits of a</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   //! 64-bit offset. Use it only if you know that there is a BASE register</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   //! and the offset is only 32 bits anyway.</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   ASMJIT_INLINE void addOffsetLo32(int32_t off) noexcept {</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">       8428 :     _mem.offsetLo32 += static_cast&lt;uint32_t&gt;(off);</span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   //! Reset the memory offset to zero.</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   ASMJIT_INLINE void resetOffsetLo32() noexcept { setOffsetLo32(0); }</a>
+<a name="1108"><span class="lineNum">    1108 </span>            : </a>
+<a name="1109"><span class="lineNum">    1109 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   // [Operator Overload]</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1112"><span class="lineNum">    1112 </span>            : </a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Mem&amp; operator=(const Mem&amp; other) noexcept { copyFrom(other); return *this; }</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            : };</a>
+<a name="1115"><span class="lineNum">    1115 </span>            : </a>
+<a name="1116"><span class="lineNum">    1116 </span>            : // ============================================================================</a>
+<a name="1117"><span class="lineNum">    1117 </span>            : // [asmjit::Imm]</a>
+<a name="1118"><span class="lineNum">    1118 </span>            : // ============================================================================</a>
+<a name="1119"><span class="lineNum">    1119 </span>            : </a>
+<a name="1120"><span class="lineNum">    1120 </span>            : //! Immediate operand.</a>
+<a name="1121"><span class="lineNum">    1121 </span>            : //!</a>
+<a name="1122"><span class="lineNum">    1122 </span>            : //! Immediate operand is usually part of instruction itself. It's inlined after</a>
+<a name="1123"><span class="lineNum">    1123 </span>            : //! or before the instruction opcode. Immediates can be only signed or unsigned</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : //! integers.</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : //!</a>
+<a name="1126"><span class="lineNum">    1126 </span>            : //! To create immediate operand use `imm()` or `imm_u()` non-members or `Imm`</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : //! constructors.</a>
+<a name="1128"><span class="lineNum">    1128 </span>            : class Imm : public Operand {</a>
+<a name="1129"><span class="lineNum">    1129 </span>            : public:</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   // [Construction / Destruction]</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1133"><span class="lineNum">    1133 </span>            : </a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   //! Create a new immediate value (initial value is 0).</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   Imm() noexcept : Operand(NoInit) {</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :     _init_packed_d0_d1(kOpImm, 0);</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :     _imm.value.i64 = 0;</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   }</a>
+<a name="1139"><span class="lineNum">    1139 </span>            : </a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   //! Create a new signed immediate value, assigning the value to `val`.</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   explicit Imm(int64_t val) noexcept : Operand(NoInit) {</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :     _init_packed_d0_d1(kOpImm, 0);</a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">       9462 :     _imm.value.i64 = val;</span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : </a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   //! Create a new immediate value from `other`.</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   ASMJIT_INLINE Imm(const Imm&amp; other) noexcept : Operand(other) {}</a>
+<a name="1148"><span class="lineNum">    1148 </span>            : </a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   explicit ASMJIT_INLINE Imm(const _NoInit&amp;) noexcept : Operand(NoInit) {}</a>
+<a name="1150"><span class="lineNum">    1150 </span>            : </a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :   // [Immediate Specific]</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1154"><span class="lineNum">    1154 </span>            : </a>
+<a name="1155"><span class="lineNum">    1155 </span>            :   //! Clone `Imm` operand.</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :   ASMJIT_INLINE Imm clone() const noexcept { return Imm(*this); }</a>
+<a name="1157"><span class="lineNum">    1157 </span>            : </a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   //! Get whether the immediate can be casted to 8-bit signed integer.</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :   ASMJIT_INLINE bool isInt8() const noexcept { return Utils::isInt8(_imm.value.i64); }</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   //! Get whether the immediate can be casted to 8-bit unsigned integer.</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :   ASMJIT_INLINE bool isUInt8() const noexcept { return Utils::isUInt8(_imm.value.i64); }</a>
+<a name="1162"><span class="lineNum">    1162 </span>            : </a>
+<a name="1163"><span class="lineNum">    1163 </span>            :   //! Get whether the immediate can be casted to 16-bit signed integer.</a>
+<a name="1164"><span class="lineNum">    1164 </span>            :   ASMJIT_INLINE bool isInt16() const noexcept { return Utils::isInt16(_imm.value.i64); }</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :   //! Get whether the immediate can be casted to 16-bit unsigned integer.</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :   ASMJIT_INLINE bool isUInt16() const noexcept { return Utils::isUInt16(_imm.value.i64); }</a>
+<a name="1167"><span class="lineNum">    1167 </span>            : </a>
+<a name="1168"><span class="lineNum">    1168 </span>            :   //! Get whether the immediate can be casted to 32-bit signed integer.</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :   ASMJIT_INLINE bool isInt32() const noexcept { return Utils::isInt32(_imm.value.i64); }</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :   //! Get whether the immediate can be casted to 32-bit unsigned integer.</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :   ASMJIT_INLINE bool isUInt32() const noexcept { return Utils::isUInt32(_imm.value.i64); }</a>
+<a name="1172"><span class="lineNum">    1172 </span>            : </a>
+<a name="1173"><span class="lineNum">    1173 </span>            :   //! Get immediate value as 8-bit signed integer.</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :   ASMJIT_INLINE int8_t getInt8() const noexcept { return static_cast&lt;int8_t&gt;(_imm.value.i32Lo &amp; 0xFF); }</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :   //! Get immediate value as 8-bit unsigned integer.</a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint8_t getUInt8() const noexcept { return static_cast&lt;uint8_t&gt;(_imm.value.u32Lo &amp; 0xFFU); }</span></a>
+<a name="1177"><span class="lineNum">    1177 </span>            :   //! Get immediate value as 16-bit signed integer.</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :   ASMJIT_INLINE int16_t getInt16() const noexcept { return static_cast&lt;int16_t&gt;(_imm.value.i32Lo &amp; 0xFFFF);}</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :   //! Get immediate value as 16-bit unsigned integer.</a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint16_t getUInt16() const noexcept { return static_cast&lt;uint16_t&gt;(_imm.value.u32Lo &amp; 0xFFFFU);}</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            : </a>
+<a name="1182"><span class="lineNum">    1182 </span>            :   //! Get immediate value as 32-bit signed integer.</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :   ASMJIT_INLINE int32_t getInt32() const noexcept { return _imm.value.i32Lo; }</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :   //! Get low 32-bit signed integer.</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :   ASMJIT_INLINE int32_t getInt32Lo() const noexcept { return _imm.value.i32Lo; }</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   //! Get high 32-bit signed integer.</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :   ASMJIT_INLINE int32_t getInt32Hi() const noexcept { return _imm.value.i32Hi; }</a>
+<a name="1188"><span class="lineNum">    1188 </span>            : </a>
+<a name="1189"><span class="lineNum">    1189 </span>            :   //! Get immediate value as 32-bit unsigned integer.</a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getUInt32() const noexcept { return _imm.value.u32Lo; }</span></a>
+<a name="1191"><span class="lineNum">    1191 </span>            :   //! Get low 32-bit signed integer.</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :   ASMJIT_INLINE uint32_t getUInt32Lo() const noexcept { return _imm.value.u32Lo; }</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :   //! Get high 32-bit signed integer.</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :   ASMJIT_INLINE uint32_t getUInt32Hi() const noexcept { return _imm.value.u32Hi; }</a>
+<a name="1195"><span class="lineNum">    1195 </span>            : </a>
+<a name="1196"><span class="lineNum">    1196 </span>            :   //! Get immediate value as 64-bit signed integer.</a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineCov">       9672 :   ASMJIT_INLINE int64_t getInt64() const noexcept { return _imm.value.i64; }</span></a>
+<a name="1198"><span class="lineNum">    1198 </span>            :   //! Get immediate value as 64-bit unsigned integer.</a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint64_t getUInt64() const noexcept { return _imm.value.u64; }</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            : </a>
+<a name="1201"><span class="lineNum">    1201 </span>            :   //! Get immediate value as `intptr_t`.</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :   ASMJIT_INLINE intptr_t getIntPtr() const noexcept {</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :     if (sizeof(intptr_t) == sizeof(int64_t))</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :       return static_cast&lt;intptr_t&gt;(getInt64());</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :     else</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :       return static_cast&lt;intptr_t&gt;(getInt32());</a>
+<a name="1207"><span class="lineNum">    1207 </span>            :   }</a>
+<a name="1208"><span class="lineNum">    1208 </span>            : </a>
+<a name="1209"><span class="lineNum">    1209 </span>            :   //! Get immediate value as `uintptr_t`.</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :   ASMJIT_INLINE uintptr_t getUIntPtr() const noexcept {</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :     if (sizeof(uintptr_t) == sizeof(uint64_t))</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :       return static_cast&lt;uintptr_t&gt;(getUInt64());</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :     else</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :       return static_cast&lt;uintptr_t&gt;(getUInt32());</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :   }</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   //! Set immediate value to 8-bit signed integer `val`.</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   ASMJIT_INLINE void setInt8(int8_t val) noexcept { _imm.value.i64 = static_cast&lt;int64_t&gt;(val); }</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   //! Set immediate value to 8-bit unsigned integer `val`.</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :   ASMJIT_INLINE void setUInt8(uint8_t val) noexcept { _imm.value.u64 = static_cast&lt;uint64_t&gt;(val); }</a>
+<a name="1221"><span class="lineNum">    1221 </span>            : </a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   //! Set immediate value to 16-bit signed integer `val`.</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   ASMJIT_INLINE void setInt16(int16_t val) noexcept { _imm.value.i64 = static_cast&lt;int64_t&gt;(val); }</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :   //! Set immediate value to 16-bit unsigned integer `val`.</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :   ASMJIT_INLINE void setUInt16(uint16_t val) noexcept { _imm.value.u64 = static_cast&lt;uint64_t&gt;(val); }</a>
+<a name="1226"><span class="lineNum">    1226 </span>            : </a>
+<a name="1227"><span class="lineNum">    1227 </span>            :   //! Set immediate value to 32-bit signed integer `val`.</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :   ASMJIT_INLINE void setInt32(int32_t val) noexcept { _imm.value.i64 = static_cast&lt;int64_t&gt;(val); }</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   //! Set immediate value to 32-bit unsigned integer `val`.</a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setUInt32(uint32_t val) noexcept { _imm.value.u64 = static_cast&lt;uint64_t&gt;(val); }</span></a>
+<a name="1231"><span class="lineNum">    1231 </span>            : </a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   //! Set immediate value to 64-bit signed integer `val`.</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :   ASMJIT_INLINE void setInt64(int64_t val) noexcept { _imm.value.i64 = val; }</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :   //! Set immediate value to 64-bit unsigned integer `val`.</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :   ASMJIT_INLINE void setUInt64(uint64_t val) noexcept { _imm.value.u64 = val; }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :   //! Set immediate value to intptr_t `val`.</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :   ASMJIT_INLINE void setIntPtr(intptr_t val) noexcept { _imm.value.i64 = static_cast&lt;int64_t&gt;(val); }</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :   //! Set immediate value to uintptr_t `val`.</a>
+<a name="1239"><span class="lineNum">    1239 </span>            :   ASMJIT_INLINE void setUIntPtr(uintptr_t val) noexcept { _imm.value.u64 = static_cast&lt;uint64_t&gt;(val); }</a>
+<a name="1240"><span class="lineNum">    1240 </span>            : </a>
+<a name="1241"><span class="lineNum">    1241 </span>            :   //! Set immediate value as unsigned type to `val`.</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :   ASMJIT_INLINE void setPtr(void* p) noexcept { setIntPtr((uint64_t)p); }</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :   //! Set immediate value to `val`.</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :   template&lt;typename T&gt;</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :   ASMJIT_INLINE void setValue(T val) noexcept { setIntPtr((int64_t)val); }</a>
+<a name="1246"><span class="lineNum">    1246 </span>            : </a>
+<a name="1247"><span class="lineNum">    1247 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :   // [Float]</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1250"><span class="lineNum">    1250 </span>            : </a>
+<a name="1251"><span class="lineNum">    1251 </span>            :   ASMJIT_INLINE void setFloat(float f) noexcept {</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :     _imm.value.f32Lo = f;</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :     _imm.value.u32Hi = 0;</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   }</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : </a>
+<a name="1256"><span class="lineNum">    1256 </span>            :   ASMJIT_INLINE void setDouble(double d) noexcept {</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :     _imm.value.f64 = d;</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :   }</a>
+<a name="1259"><span class="lineNum">    1259 </span>            : </a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :   // [Truncate]</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1263"><span class="lineNum">    1263 </span>            : </a>
+<a name="1264"><span class="lineNum">    1264 </span>            :   ASMJIT_INLINE void truncateTo8Bits() noexcept {</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1266"><span class="lineNum">    1266 </span><span class="lineNoCov">          0 :       _imm.value.u64   &amp;= static_cast&lt;uint64_t&gt;(0x000000FFU);</span></a>
+<a name="1267"><span class="lineNum">    1267 </span>            :     }</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :     else {</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :       _imm.value.u32Lo &amp;= 0x000000FFU;</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :       _imm.value.u32Hi  = 0;</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :     }</a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            : </a>
+<a name="1274"><span class="lineNum">    1274 </span>            :   ASMJIT_INLINE void truncateTo16Bits() noexcept {</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineNoCov">          0 :       _imm.value.u64   &amp;= static_cast&lt;uint64_t&gt;(0x0000FFFFU);</span></a>
+<a name="1277"><span class="lineNum">    1277 </span>            :     }</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :     else {</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :       _imm.value.u32Lo &amp;= 0x0000FFFFU;</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :       _imm.value.u32Hi  = 0;</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :     }</a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            : </a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void truncateTo32Bits() noexcept { _imm.value.u32Hi = 0; }</span></a>
+<a name="1285"><span class="lineNum">    1285 </span>            : </a>
+<a name="1286"><span class="lineNum">    1286 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :   // [Operator Overload]</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1289"><span class="lineNum">    1289 </span>            : </a>
+<a name="1290"><span class="lineNum">    1290 </span>            :   //! Assign `other` to the immediate operand.</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :   ASMJIT_INLINE Imm&amp; operator=(const Imm&amp; other) noexcept { copyFrom(other); return *this; }</a>
+<a name="1292"><span class="lineNum">    1292 </span>            : };</a>
+<a name="1293"><span class="lineNum">    1293 </span>            : </a>
+<a name="1294"><span class="lineNum">    1294 </span>            : //! Create a signed immediate operand.</a>
+<a name="1295"><span class="lineNum">    1295 </span>            : static ASMJIT_INLINE Imm imm(int64_t val) noexcept { return Imm(val); }</a>
+<a name="1296"><span class="lineNum">    1296 </span>            : //! Create an unsigned immediate operand.</a>
+<a name="1297"><span class="lineNum">    1297 </span>            : static ASMJIT_INLINE Imm imm_u(uint64_t val) noexcept { return Imm(static_cast&lt;int64_t&gt;(val)); }</a>
+<a name="1298"><span class="lineNum">    1298 </span>            : //! Create an immediate operand from `p`.</a>
+<a name="1299"><span class="lineNum">    1299 </span>            : template&lt;typename T&gt;</a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">       7478 : static ASMJIT_INLINE Imm imm_ptr(T p) noexcept { return Imm(static_cast&lt;int64_t&gt;((intptr_t)p)); }</span></a>
+<a name="1301"><span class="lineNum">    1301 </span>            : </a>
+<a name="1302"><span class="lineNum">    1302 </span>            : // ============================================================================</a>
+<a name="1303"><span class="lineNum">    1303 </span>            : // [asmjit::TypeId]</a>
+<a name="1304"><span class="lineNum">    1304 </span>            : // ============================================================================</a>
+<a name="1305"><span class="lineNum">    1305 </span>            : </a>
+<a name="1306"><span class="lineNum">    1306 </span>            : //! Type-id.</a>
+<a name="1307"><span class="lineNum">    1307 </span>            : //!</a>
+<a name="1308"><span class="lineNum">    1308 </span>            : //! This is an additional information that can be used to describe a physical</a>
+<a name="1309"><span class="lineNum">    1309 </span>            : //! or virtual register. it's used mostly by CodeCompiler to describe register</a>
+<a name="1310"><span class="lineNum">    1310 </span>            : //! representation (the kind of data stored in the register and the width used)</a>
+<a name="1311"><span class="lineNum">    1311 </span>            : //! and it's also used by APIs that allow to describe and work with function</a>
+<a name="1312"><span class="lineNum">    1312 </span>            : //! signatures.</a>
+<a name="1313"><span class="lineNum">    1313 </span>            : struct TypeId {</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :   // [Id]</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1317"><span class="lineNum">    1317 </span>            : </a>
+<a name="1318"><span class="lineNum">    1318 </span>            :   enum Id {</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :     kVoid         = 0,</a>
+<a name="1320"><span class="lineNum">    1320 </span>            : </a>
+<a name="1321"><span class="lineNum">    1321 </span>            :     _kIntStart    = 32,</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :     _kIntEnd      = 41,</a>
+<a name="1323"><span class="lineNum">    1323 </span>            : </a>
+<a name="1324"><span class="lineNum">    1324 </span>            :     kIntPtr       = 32,</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :     kUIntPtr      = 33,</a>
+<a name="1326"><span class="lineNum">    1326 </span>            : </a>
+<a name="1327"><span class="lineNum">    1327 </span>            :     kI8           = 34,</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :     kU8           = 35,</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :     kI16          = 36,</a>
+<a name="1330"><span class="lineNum">    1330 </span>            :     kU16          = 37,</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :     kI32          = 38,</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :     kU32          = 39,</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :     kI64          = 40,</a>
+<a name="1334"><span class="lineNum">    1334 </span>            :     kU64          = 41,</a>
+<a name="1335"><span class="lineNum">    1335 </span>            : </a>
+<a name="1336"><span class="lineNum">    1336 </span>            :     _kFloatStart  = 42,</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :     _kFloatEnd    = 44,</a>
+<a name="1338"><span class="lineNum">    1338 </span>            : </a>
+<a name="1339"><span class="lineNum">    1339 </span>            :     kF32          = 42,</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :     kF64          = 43,</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :     kF80          = 44,</a>
+<a name="1342"><span class="lineNum">    1342 </span>            : </a>
+<a name="1343"><span class="lineNum">    1343 </span>            :     _kMaskStart   = 45,</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :     _kMaskEnd     = 48,</a>
+<a name="1345"><span class="lineNum">    1345 </span>            : </a>
+<a name="1346"><span class="lineNum">    1346 </span>            :     kMask8        = 45,</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :     kMask16       = 46,</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :     kMask32       = 47,</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :     kMask64       = 48,</a>
+<a name="1350"><span class="lineNum">    1350 </span>            : </a>
+<a name="1351"><span class="lineNum">    1351 </span>            :     _kMmxStart    = 49,</a>
+<a name="1352"><span class="lineNum">    1352 </span>            :     _kMmxEnd      = 50,</a>
+<a name="1353"><span class="lineNum">    1353 </span>            : </a>
+<a name="1354"><span class="lineNum">    1354 </span>            :     kMmx32        = 49,</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :     kMmx64        = 50,</a>
+<a name="1356"><span class="lineNum">    1356 </span>            : </a>
+<a name="1357"><span class="lineNum">    1357 </span>            :     _kVec32Start  = 51,</a>
+<a name="1358"><span class="lineNum">    1358 </span>            :     _kVec32End    = 60,</a>
+<a name="1359"><span class="lineNum">    1359 </span>            : </a>
+<a name="1360"><span class="lineNum">    1360 </span>            :     kI8x4         = 51,</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :     kU8x4         = 52,</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :     kI16x2        = 53,</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :     kU16x2        = 54,</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :     kI32x1        = 55,</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :     kU32x1        = 56,</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :     kF32x1        = 59,</a>
+<a name="1367"><span class="lineNum">    1367 </span>            : </a>
+<a name="1368"><span class="lineNum">    1368 </span>            :     _kVec64Start  = 61,</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :     _kVec64End    = 70,</a>
+<a name="1370"><span class="lineNum">    1370 </span>            : </a>
+<a name="1371"><span class="lineNum">    1371 </span>            :     kI8x8         = 61,</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :     kU8x8         = 62,</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :     kI16x4        = 63,</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :     kU16x4        = 64,</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :     kI32x2        = 65,</a>
+<a name="1376"><span class="lineNum">    1376 </span>            :     kU32x2        = 66,</a>
+<a name="1377"><span class="lineNum">    1377 </span>            :     kI64x1        = 67,</a>
+<a name="1378"><span class="lineNum">    1378 </span>            :     kU64x1        = 68,</a>
+<a name="1379"><span class="lineNum">    1379 </span>            :     kF32x2        = 69,</a>
+<a name="1380"><span class="lineNum">    1380 </span>            :     kF64x1        = 70,</a>
+<a name="1381"><span class="lineNum">    1381 </span>            : </a>
+<a name="1382"><span class="lineNum">    1382 </span>            :     _kVec128Start = 71,</a>
+<a name="1383"><span class="lineNum">    1383 </span>            :     _kVec128End   = 80,</a>
+<a name="1384"><span class="lineNum">    1384 </span>            : </a>
+<a name="1385"><span class="lineNum">    1385 </span>            :     kI8x16        = 71,</a>
+<a name="1386"><span class="lineNum">    1386 </span>            :     kU8x16        = 72,</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :     kI16x8        = 73,</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :     kU16x8        = 74,</a>
+<a name="1389"><span class="lineNum">    1389 </span>            :     kI32x4        = 75,</a>
+<a name="1390"><span class="lineNum">    1390 </span>            :     kU32x4        = 76,</a>
+<a name="1391"><span class="lineNum">    1391 </span>            :     kI64x2        = 77,</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :     kU64x2        = 78,</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :     kF32x4        = 79,</a>
+<a name="1394"><span class="lineNum">    1394 </span>            :     kF64x2        = 80,</a>
+<a name="1395"><span class="lineNum">    1395 </span>            : </a>
+<a name="1396"><span class="lineNum">    1396 </span>            :     _kVec256Start = 81,</a>
+<a name="1397"><span class="lineNum">    1397 </span>            :     _kVec256End   = 90,</a>
+<a name="1398"><span class="lineNum">    1398 </span>            : </a>
+<a name="1399"><span class="lineNum">    1399 </span>            :     kI8x32        = 81,</a>
+<a name="1400"><span class="lineNum">    1400 </span>            :     kU8x32        = 82,</a>
+<a name="1401"><span class="lineNum">    1401 </span>            :     kI16x16       = 83,</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :     kU16x16       = 84,</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :     kI32x8        = 85,</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :     kU32x8        = 86,</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :     kI64x4        = 87,</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :     kU64x4        = 88,</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :     kF32x8        = 89,</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :     kF64x4        = 90,</a>
+<a name="1409"><span class="lineNum">    1409 </span>            : </a>
+<a name="1410"><span class="lineNum">    1410 </span>            :     _kVec512Start = 91,</a>
+<a name="1411"><span class="lineNum">    1411 </span>            :     _kVec512End   = 100,</a>
+<a name="1412"><span class="lineNum">    1412 </span>            : </a>
+<a name="1413"><span class="lineNum">    1413 </span>            :     kI8x64        = 91,</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :     kU8x64        = 92,</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :     kI16x32       = 93,</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :     kU16x32       = 94,</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :     kI32x16       = 95,</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :     kU32x16       = 96,</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     kI64x8        = 97,</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :     kU64x8        = 98,</a>
+<a name="1421"><span class="lineNum">    1421 </span>            :     kF32x16       = 99,</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     kF64x8        = 100,</a>
+<a name="1423"><span class="lineNum">    1423 </span>            : </a>
+<a name="1424"><span class="lineNum">    1424 </span>            :     kCount        = 101</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :   };</a>
+<a name="1426"><span class="lineNum">    1426 </span>            : </a>
+<a name="1427"><span class="lineNum">    1427 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :   // [TypeName - Used by Templates]</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1430"><span class="lineNum">    1430 </span>            : </a>
+<a name="1431"><span class="lineNum">    1431 </span>            :   struct Int8    {};                     //!&lt; int8_t as C++ type-name.</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :   struct UInt8   {};                     //!&lt; uint8_t as C++ type-name.</a>
+<a name="1433"><span class="lineNum">    1433 </span>            :   struct Int16   {};                     //!&lt; int16_t as C++ type-name.</a>
+<a name="1434"><span class="lineNum">    1434 </span>            :   struct UInt16  {};                     //!&lt; uint16_t as C++ type-name.</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :   struct Int32   {};                     //!&lt; int32_t as C++ type-name.</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :   struct UInt32  {};                     //!&lt; uint32_t as C++ type-name.</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :   struct Int64   {};                     //!&lt; int64_t as C++ type-name.</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :   struct UInt64  {};                     //!&lt; uint64_t as C++ type-name.</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :   struct IntPtr  {};                     //!&lt; intptr_t as C++ type-name.</a>
+<a name="1440"><span class="lineNum">    1440 </span>            :   struct UIntPtr {};                     //!&lt; uintptr_t as C++ type-name.</a>
+<a name="1441"><span class="lineNum">    1441 </span>            :   struct Float   {};                     //!&lt; float as C++ type-name.</a>
+<a name="1442"><span class="lineNum">    1442 </span>            :   struct Double  {};                     //!&lt; double as C++ type-name.</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :   struct MmxReg  {};                     //!&lt; MMX register as C++ type-name.</a>
+<a name="1444"><span class="lineNum">    1444 </span>            :   struct Vec128  {};                     //!&lt; SIMD128/XMM register as C++ type-name.</a>
+<a name="1445"><span class="lineNum">    1445 </span>            :   struct Vec256  {};                     //!&lt; SIMD256/YMM register as C++ type-name.</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :   struct Vec512  {};                     //!&lt; SIMD512/ZMM register as C++ type-name.</a>
+<a name="1447"><span class="lineNum">    1447 </span>            : </a>
+<a name="1448"><span class="lineNum">    1448 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :   // [Utilities]</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1451"><span class="lineNum">    1451 </span>            : </a>
+<a name="1452"><span class="lineNum">    1452 </span>            :   struct Info {</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :     uint8_t sizeOf[128];</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :     uint8_t elementOf[128];</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :   };</a>
+<a name="1456"><span class="lineNum">    1456 </span>            : </a>
+<a name="1457"><span class="lineNum">    1457 </span>            :   ASMJIT_API static const Info _info;</a>
+<a name="1458"><span class="lineNum">    1458 </span>            : </a>
+<a name="1459"><span class="lineNum">    1459 </span>            :   static ASMJIT_INLINE bool isVoid(uint32_t typeId) noexcept { return typeId == 0; }</a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineCov">      23788 :   static ASMJIT_INLINE bool isValid(uint32_t typeId) noexcept { return typeId &gt;= _kIntStart &amp;&amp; typeId &lt;= _kVec512End; }</span></a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineCov">       5466 :   static ASMJIT_INLINE bool isAbstract(uint32_t typeId) noexcept { return typeId &gt;= kIntPtr &amp;&amp; typeId &lt;= kUIntPtr; }</span></a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">       1870 :   static ASMJIT_INLINE bool isInt(uint32_t typeId) noexcept { return typeId &gt;= _kIntStart &amp;&amp; typeId &lt;= _kIntEnd; }</span></a>
+<a name="1463"><span class="lineNum">    1463 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isGpb(uint32_t typeId) noexcept { return typeId &gt;= kI8 &amp;&amp; typeId &lt;= kU8; }</span></a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isGpw(uint32_t typeId) noexcept { return typeId &gt;= kI16 &amp;&amp; typeId &lt;= kU16; }</span></a>
+<a name="1465"><span class="lineNum">    1465 </span>            :   static ASMJIT_INLINE bool isGpd(uint32_t typeId) noexcept { return typeId &gt;= kI32 &amp;&amp; typeId &lt;= kU32; }</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :   static ASMJIT_INLINE bool isGpq(uint32_t typeId) noexcept { return typeId &gt;= kI64 &amp;&amp; typeId &lt;= kU64; }</a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">       1450 :   static ASMJIT_INLINE bool isFloat(uint32_t typeId) noexcept { return typeId &gt;= _kFloatStart &amp;&amp; typeId &lt;= _kFloatEnd; }</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isMask(uint32_t typeId) noexcept { return typeId &gt;= _kMaskStart &amp;&amp; typeId &lt;= _kMaskEnd; }</span></a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isMmx(uint32_t typeId) noexcept { return typeId &gt;= _kMmxStart &amp;&amp; typeId &lt;= _kMmxEnd; }</span></a>
+<a name="1470"><span class="lineNum">    1470 </span>            : </a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isVec(uint32_t typeId) noexcept { return typeId &gt;= _kVec32Start &amp;&amp; typeId &lt;= _kVec512End; }</span></a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineCov">       9084 :   static ASMJIT_INLINE bool isVec32(uint32_t typeId) noexcept { return typeId &gt;= _kVec32Start &amp;&amp; typeId &lt;= _kVec32End; }</span></a>
+<a name="1473"><span class="lineNum">    1473 </span><span class="lineCov">       9084 :   static ASMJIT_INLINE bool isVec64(uint32_t typeId) noexcept { return typeId &gt;= _kVec64Start &amp;&amp; typeId &lt;= _kVec64End; }</span></a>
+<a name="1474"><span class="lineNum">    1474 </span>            :   static ASMJIT_INLINE bool isVec128(uint32_t typeId) noexcept { return typeId &gt;= _kVec128Start &amp;&amp; typeId &lt;= _kVec128End; }</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :   static ASMJIT_INLINE bool isVec256(uint32_t typeId) noexcept { return typeId &gt;= _kVec256Start &amp;&amp; typeId &lt;= _kVec256End; }</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :   static ASMJIT_INLINE bool isVec512(uint32_t typeId) noexcept { return typeId &gt;= _kVec512Start &amp;&amp; typeId &lt;= _kVec512End; }</a>
+<a name="1477"><span class="lineNum">    1477 </span>            : </a>
+<a name="1478"><span class="lineNum">    1478 </span>            :   static ASMJIT_INLINE uint32_t sizeOf(uint32_t typeId) noexcept {</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :     ASMJIT_ASSERT(typeId &lt; ASMJIT_ARRAY_SIZE(_info.sizeOf));</a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">      47576 :     return _info.sizeOf[typeId];</span></a>
+<a name="1481"><span class="lineNum">    1481 </span>            :   }</a>
+<a name="1482"><span class="lineNum">    1482 </span>            : </a>
+<a name="1483"><span class="lineNum">    1483 </span>            :   static ASMJIT_INLINE uint32_t elementOf(uint32_t typeId) noexcept {</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :     ASMJIT_ASSERT(typeId &lt; ASMJIT_ARRAY_SIZE(_info.elementOf));</a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineCov">       9084 :     return _info.elementOf[typeId];</span></a>
+<a name="1486"><span class="lineNum">    1486 </span>            :   }</a>
+<a name="1487"><span class="lineNum">    1487 </span>            : </a>
+<a name="1488"><span class="lineNum">    1488 </span>            :   //! Get an offset to convert a `kIntPtr` and `kUIntPtr` TypeId into a</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :   //! type that matches `gpSize` (general-purpose register size). If you</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :   //! find such TypeId it's then only about adding the offset to it.</a>
+<a name="1491"><span class="lineNum">    1491 </span>            :   //!</a>
+<a name="1492"><span class="lineNum">    1492 </span>            :   //! For example:</a>
+<a name="1493"><span class="lineNum">    1493 </span>            :   //! ~~~</a>
+<a name="1494"><span class="lineNum">    1494 </span>            :   //! uint32_t gpSize = '4' or '8';</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :   //! uint32_t deabstractDelta = TypeId::deabstractDeltaOfSize(gpSize);</a>
+<a name="1496"><span class="lineNum">    1496 </span>            :   //!</a>
+<a name="1497"><span class="lineNum">    1497 </span>            :   //! uint32_t typeId = 'some type-id';</a>
+<a name="1498"><span class="lineNum">    1498 </span>            :   //!</a>
+<a name="1499"><span class="lineNum">    1499 </span>            :   //! // Normalize some typeId into a non-abstract typeId.</a>
+<a name="1500"><span class="lineNum">    1500 </span>            :   //! if (TypeId::isAbstract(typeId)) typeId += deabstractDelta;</a>
+<a name="1501"><span class="lineNum">    1501 </span>            :   //!</a>
+<a name="1502"><span class="lineNum">    1502 </span>            :   //! // The same, but by using TypeId::deabstract() function.</a>
+<a name="1503"><span class="lineNum">    1503 </span>            :   //! typeId = TypeId::deabstract(typeId, deabstractDelta);</a>
+<a name="1504"><span class="lineNum">    1504 </span>            :   //! ~~~</a>
+<a name="1505"><span class="lineNum">    1505 </span>            :   static ASMJIT_INLINE uint32_t deabstractDeltaOfSize(uint32_t gpSize) noexcept {</a>
+<a name="1506"><span class="lineNum">    1506 </span>            :     return gpSize &gt;= 8 ? kI64 - kIntPtr : kI32 - kIntPtr;</a>
+<a name="1507"><span class="lineNum">    1507 </span>            :   }</a>
+<a name="1508"><span class="lineNum">    1508 </span>            : </a>
+<a name="1509"><span class="lineNum">    1509 </span>            :   static ASMJIT_INLINE uint32_t deabstract(uint32_t typeId, uint32_t deabstractDelta) noexcept {</a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineCov">       5466 :     return TypeId::isAbstract(typeId) ? typeId += deabstractDelta : typeId;</span></a>
+<a name="1511"><span class="lineNum">    1511 </span>            :   }</a>
+<a name="1512"><span class="lineNum">    1512 </span>            : };</a>
+<a name="1513"><span class="lineNum">    1513 </span>            : </a>
+<a name="1514"><span class="lineNum">    1514 </span>            : //! TypeIdOf&lt;&gt; template allows to get a TypeId of a C++ type.</a>
+<a name="1515"><span class="lineNum">    1515 </span>            : template&lt;typename T&gt; struct TypeIdOf {</a>
+<a name="1516"><span class="lineNum">    1516 </span>            :   // Don't provide anything if not specialized.</a>
+<a name="1517"><span class="lineNum">    1517 </span>            : };</a>
+<a name="1518"><span class="lineNum">    1518 </span>            : template&lt;typename T&gt; struct TypeIdOf&lt;T*&gt; {</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :   enum { kTypeId = TypeId::kUIntPtr };</a>
+<a name="1520"><span class="lineNum">    1520 </span>            : };</a>
+<a name="1521"><span class="lineNum">    1521 </span>            : </a>
+<a name="1522"><span class="lineNum">    1522 </span>            : template&lt;typename T&gt;</a>
+<a name="1523"><span class="lineNum">    1523 </span>            : struct TypeIdOfInt {</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :   enum {</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :     kSigned = int(~T(0) &lt; T(0)),</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :     kTypeId = (sizeof(T) == 1) ? (int)(kSigned ? TypeId::kI8  : TypeId::kU8 ) :</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :               (sizeof(T) == 2) ? (int)(kSigned ? TypeId::kI16 : TypeId::kU16) :</a>
+<a name="1528"><span class="lineNum">    1528 </span>            :               (sizeof(T) == 4) ? (int)(kSigned ? TypeId::kI32 : TypeId::kU32) :</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :               (sizeof(T) == 8) ? (int)(kSigned ? TypeId::kI64 : TypeId::kU64) : (int)TypeId::kVoid</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :   };</a>
+<a name="1531"><span class="lineNum">    1531 </span>            : };</a>
+<a name="1532"><span class="lineNum">    1532 </span>            : </a>
+<a name="1533"><span class="lineNum">    1533 </span>            : #define ASMJIT_DEFINE_TYPE_ID(T, TYPE_ID) \</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :   template&lt;&gt; \</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :   struct TypeIdOf&lt;T&gt; { enum { kTypeId = TYPE_ID}; }</a>
+<a name="1536"><span class="lineNum">    1536 </span>            : </a>
+<a name="1537"><span class="lineNum">    1537 </span>            : ASMJIT_DEFINE_TYPE_ID(signed char       , TypeIdOfInt&lt; signed char        &gt;::kTypeId);</a>
+<a name="1538"><span class="lineNum">    1538 </span>            : ASMJIT_DEFINE_TYPE_ID(unsigned char     , TypeIdOfInt&lt; unsigned char      &gt;::kTypeId);</a>
+<a name="1539"><span class="lineNum">    1539 </span>            : ASMJIT_DEFINE_TYPE_ID(short             , TypeIdOfInt&lt; short              &gt;::kTypeId);</a>
+<a name="1540"><span class="lineNum">    1540 </span>            : ASMJIT_DEFINE_TYPE_ID(unsigned short    , TypeIdOfInt&lt; unsigned short     &gt;::kTypeId);</a>
+<a name="1541"><span class="lineNum">    1541 </span>            : ASMJIT_DEFINE_TYPE_ID(int               , TypeIdOfInt&lt; int                &gt;::kTypeId);</a>
+<a name="1542"><span class="lineNum">    1542 </span>            : ASMJIT_DEFINE_TYPE_ID(unsigned int      , TypeIdOfInt&lt; unsigned int       &gt;::kTypeId);</a>
+<a name="1543"><span class="lineNum">    1543 </span>            : ASMJIT_DEFINE_TYPE_ID(long              , TypeIdOfInt&lt; long               &gt;::kTypeId);</a>
+<a name="1544"><span class="lineNum">    1544 </span>            : ASMJIT_DEFINE_TYPE_ID(unsigned long     , TypeIdOfInt&lt; unsigned long      &gt;::kTypeId);</a>
+<a name="1545"><span class="lineNum">    1545 </span>            : #if ASMJIT_CC_MSC &amp;&amp; !ASMJIT_CC_MSC_GE(16, 0, 0)</a>
+<a name="1546"><span class="lineNum">    1546 </span>            : ASMJIT_DEFINE_TYPE_ID(__int64           , TypeIdOfInt&lt; __int64            &gt;::kTypeId);</a>
+<a name="1547"><span class="lineNum">    1547 </span>            : ASMJIT_DEFINE_TYPE_ID(unsigned __int64  , TypeIdOfInt&lt; unsigned __int64   &gt;::kTypeId);</a>
+<a name="1548"><span class="lineNum">    1548 </span>            : #else</a>
+<a name="1549"><span class="lineNum">    1549 </span>            : ASMJIT_DEFINE_TYPE_ID(long long         , TypeIdOfInt&lt; long long          &gt;::kTypeId);</a>
+<a name="1550"><span class="lineNum">    1550 </span>            : ASMJIT_DEFINE_TYPE_ID(unsigned long long, TypeIdOfInt&lt; unsigned long long &gt;::kTypeId);</a>
+<a name="1551"><span class="lineNum">    1551 </span>            : #endif</a>
+<a name="1552"><span class="lineNum">    1552 </span>            : #if ASMJIT_CC_HAS_NATIVE_CHAR</a>
+<a name="1553"><span class="lineNum">    1553 </span>            : ASMJIT_DEFINE_TYPE_ID(char              , TypeIdOfInt&lt; char               &gt;::kTypeId);</a>
+<a name="1554"><span class="lineNum">    1554 </span>            : #endif</a>
+<a name="1555"><span class="lineNum">    1555 </span>            : #if ASMJIT_CC_HAS_NATIVE_CHAR16_T</a>
+<a name="1556"><span class="lineNum">    1556 </span>            : ASMJIT_DEFINE_TYPE_ID(char16_t          , TypeIdOfInt&lt; char16_t           &gt;::kTypeId);</a>
+<a name="1557"><span class="lineNum">    1557 </span>            : #endif</a>
+<a name="1558"><span class="lineNum">    1558 </span>            : #if ASMJIT_CC_HAS_NATIVE_CHAR32_T</a>
+<a name="1559"><span class="lineNum">    1559 </span>            : ASMJIT_DEFINE_TYPE_ID(char32_t          , TypeIdOfInt&lt; char32_t           &gt;::kTypeId);</a>
+<a name="1560"><span class="lineNum">    1560 </span>            : #endif</a>
+<a name="1561"><span class="lineNum">    1561 </span>            : #if ASMJIT_CC_HAS_NATIVE_WCHAR_T</a>
+<a name="1562"><span class="lineNum">    1562 </span>            : ASMJIT_DEFINE_TYPE_ID(wchar_t           , TypeIdOfInt&lt; wchar_t            &gt;::kTypeId);</a>
+<a name="1563"><span class="lineNum">    1563 </span>            : #endif</a>
+<a name="1564"><span class="lineNum">    1564 </span>            : </a>
+<a name="1565"><span class="lineNum">    1565 </span>            : ASMJIT_DEFINE_TYPE_ID(void              , TypeId::kVoid);</a>
+<a name="1566"><span class="lineNum">    1566 </span>            : ASMJIT_DEFINE_TYPE_ID(bool              , TypeId::kI8);</a>
+<a name="1567"><span class="lineNum">    1567 </span>            : ASMJIT_DEFINE_TYPE_ID(float             , TypeId::kF32);</a>
+<a name="1568"><span class="lineNum">    1568 </span>            : ASMJIT_DEFINE_TYPE_ID(double            , TypeId::kF64);</a>
+<a name="1569"><span class="lineNum">    1569 </span>            : </a>
+<a name="1570"><span class="lineNum">    1570 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Int8      , TypeId::kI8);</a>
+<a name="1571"><span class="lineNum">    1571 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::UInt8     , TypeId::kU8);</a>
+<a name="1572"><span class="lineNum">    1572 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Int16     , TypeId::kI16);</a>
+<a name="1573"><span class="lineNum">    1573 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::UInt16    , TypeId::kU16);</a>
+<a name="1574"><span class="lineNum">    1574 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Int32     , TypeId::kI32);</a>
+<a name="1575"><span class="lineNum">    1575 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::UInt32    , TypeId::kU32);</a>
+<a name="1576"><span class="lineNum">    1576 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Int64     , TypeId::kI64);</a>
+<a name="1577"><span class="lineNum">    1577 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::UInt64    , TypeId::kU64);</a>
+<a name="1578"><span class="lineNum">    1578 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::IntPtr    , TypeId::kIntPtr);</a>
+<a name="1579"><span class="lineNum">    1579 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::UIntPtr   , TypeId::kUIntPtr);</a>
+<a name="1580"><span class="lineNum">    1580 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Float     , TypeId::kF32);</a>
+<a name="1581"><span class="lineNum">    1581 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Double    , TypeId::kF64);</a>
+<a name="1582"><span class="lineNum">    1582 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::MmxReg    , TypeId::kMmx64);</a>
+<a name="1583"><span class="lineNum">    1583 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Vec128    , TypeId::kI32x4);</a>
+<a name="1584"><span class="lineNum">    1584 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Vec256    , TypeId::kI32x8);</a>
+<a name="1585"><span class="lineNum">    1585 </span>            : ASMJIT_DEFINE_TYPE_ID(TypeId::Vec512    , TypeId::kI32x16);</a>
+<a name="1586"><span class="lineNum">    1586 </span>            : </a>
+<a name="1587"><span class="lineNum">    1587 </span>            : //! \}</a>
+<a name="1588"><span class="lineNum">    1588 </span>            : </a>
+<a name="1589"><span class="lineNum">    1589 </span>            : } // asmjit namespace</a>
+<a name="1590"><span class="lineNum">    1590 </span>            : } // namespace PLMD</a>
+<a name="1591"><span class="lineNum">    1591 </span>            : </a>
+<a name="1592"><span class="lineNum">    1592 </span>            : // [Api-End]</a>
+<a name="1593"><span class="lineNum">    1593 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="1594"><span class="lineNum">    1594 </span>            : </a>
+<a name="1595"><span class="lineNum">    1595 </span>            : // [Guard]</a>
+<a name="1596"><span class="lineNum">    1596 </span>            : #endif // _ASMJIT_BASE_OPERAND_H</a>
+<a name="1597"><span class="lineNum">    1597 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1598"><span class="lineNum">    1598 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="1599"><span class="lineNum">    1599 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/osutils.cpp.func-sort-c.html b/coverage-libs/asmjit/osutils.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7b642a7897
--- /dev/null
+++ b/coverage-libs/asmjit/osutils.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/osutils.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - osutils.cpp<span style="font-size: 80%;"> (<a href="osutils.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="osutils.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#232">_ZN4PLMD6asmjit7OSUtils12getTickCountEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#149">_ZN4PLMD6asmjit7OSUtils18allocVirtualMemoryEmPmj</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#165">_ZN4PLMD6asmjit7OSUtils20releaseVirtualMemoryEPvm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#147">_ZN4PLMD6asmjit7OSUtils20getVirtualMemoryInfoEv</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#137">_ZN4PLMD6asmjitL19OSUtils_GetVMemInfoEv</a></td>
+              <td class="coverFnHi">3924</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/osutils.cpp.func.html b/coverage-libs/asmjit/osutils.cpp.func.html
new file mode 100644
index 0000000000..013dcbb959
--- /dev/null
+++ b/coverage-libs/asmjit/osutils.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/osutils.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - osutils.cpp<span style="font-size: 80%;"> (<a href="osutils.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="osutils.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#232">_ZN4PLMD6asmjit7OSUtils12getTickCountEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#149">_ZN4PLMD6asmjit7OSUtils18allocVirtualMemoryEmPmj</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#147">_ZN4PLMD6asmjit7OSUtils20getVirtualMemoryInfoEv</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#165">_ZN4PLMD6asmjit7OSUtils20releaseVirtualMemoryEPvm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="osutils.cpp.gcov.html#137">_ZN4PLMD6asmjitL19OSUtils_GetVMemInfoEv</a></td>
+              <td class="coverFnHi">3924</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/osutils.cpp.gcov.html b/coverage-libs/asmjit/osutils.cpp.gcov.html
new file mode 100644
index 0000000000..24a26a9f6f
--- /dev/null
+++ b/coverage-libs/asmjit/osutils.cpp.gcov.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/osutils.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - osutils.cpp<span style="font-size: 80%;"> (source / <a href="osutils.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./osutils.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #if ASMJIT_OS_POSIX</a>
+<a name="37"><span class="lineNum">      37 </span>            : # include &lt;sys/types.h&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : # include &lt;sys/mman.h&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : # include &lt;time.h&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : # include &lt;unistd.h&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #endif // ASMJIT_OS_POSIX</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : #if ASMJIT_OS_MAC</a>
+<a name="44"><span class="lineNum">      44 </span>            : # include &lt;mach/mach_time.h&gt;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #endif // ASMJIT_OS_MAC</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="48"><span class="lineNum">      48 </span>            : # if defined(_MSC_VER) &amp;&amp; _MSC_VER &gt;= 1400</a>
+<a name="49"><span class="lineNum">      49 </span>            : #  include &lt;intrin.h&gt;</a>
+<a name="50"><span class="lineNum">      50 </span>            : # else</a>
+<a name="51"><span class="lineNum">      51 </span>            : #  define _InterlockedCompareExchange InterlockedCompareExchange</a>
+<a name="52"><span class="lineNum">      52 </span>            : # endif // _MSC_VER</a>
+<a name="53"><span class="lineNum">      53 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // [Api-Begin]</a>
+<a name="56"><span class="lineNum">      56 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : namespace PLMD {</a>
+<a name="59"><span class="lineNum">      59 </span>            : namespace asmjit {</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // ============================================================================</a>
+<a name="62"><span class="lineNum">      62 </span>            : // [asmjit::OSUtils - Virtual Memory]</a>
+<a name="63"><span class="lineNum">      63 </span>            : // ============================================================================</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : // Windows specific implementation using `VirtualAllocEx` and `VirtualFree`.</a>
+<a name="66"><span class="lineNum">      66 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="67"><span class="lineNum">      67 </span>            : static ASMJIT_NOINLINE const VMemInfo&amp; OSUtils_GetVMemInfo() noexcept {</a>
+<a name="68"><span class="lineNum">      68 </span>            :   static VMemInfo vmi;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   if (ASMJIT_UNLIKELY(!vmi.hCurrentProcess)) {</a>
+<a name="71"><span class="lineNum">      71 </span>            :     SYSTEM_INFO info;</a>
+<a name="72"><span class="lineNum">      72 </span>            :     ::GetSystemInfo(&amp;info);</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :     vmi.pageSize = Utils::alignToPowerOf2&lt;uint32_t&gt;(info.dwPageSize);</a>
+<a name="75"><span class="lineNum">      75 </span>            :     vmi.pageGranularity = info.dwAllocationGranularity;</a>
+<a name="76"><span class="lineNum">      76 </span>            :     vmi.hCurrentProcess = ::GetCurrentProcess();</a>
+<a name="77"><span class="lineNum">      77 </span>            :   }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   return vmi;</a>
+<a name="80"><span class="lineNum">      80 </span>            : };</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : VMemInfo OSUtils::getVirtualMemoryInfo() noexcept { return OSUtils_GetVMemInfo(); }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : void* OSUtils::allocVirtualMemory(size_t size, size_t* allocated, uint32_t flags) noexcept {</a>
+<a name="85"><span class="lineNum">      85 </span>            :   return allocProcessMemory(static_cast&lt;HANDLE&gt;(0), size, allocated, flags);</a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : Error OSUtils::releaseVirtualMemory(void* p, size_t size) noexcept {</a>
+<a name="89"><span class="lineNum">      89 </span>            :   return releaseProcessMemory(static_cast&lt;HANDLE&gt;(0), p, size);</a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : void* OSUtils::allocProcessMemory(HANDLE hProcess, size_t size, size_t* allocated, uint32_t flags) noexcept {</a>
+<a name="93"><span class="lineNum">      93 </span>            :   if (size == 0)</a>
+<a name="94"><span class="lineNum">      94 </span>            :     return nullptr;</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   const VMemInfo&amp; vmi = OSUtils_GetVMemInfo();</a>
+<a name="97"><span class="lineNum">      97 </span>            :   if (!hProcess) hProcess = vmi.hCurrentProcess;</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   // VirtualAllocEx rounds the allocated size to a page size automatically,</a>
+<a name="100"><span class="lineNum">     100 </span>            :   // but we need the `alignedSize` so we can store the real allocated size</a>
+<a name="101"><span class="lineNum">     101 </span>            :   // into `allocated` output.</a>
+<a name="102"><span class="lineNum">     102 </span>            :   size_t alignedSize = Utils::alignTo(size, vmi.pageSize);</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   // Windows XP SP2 / Vista+ allow data-execution-prevention (DEP).</a>
+<a name="105"><span class="lineNum">     105 </span>            :   DWORD protectFlags = 0;</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   if (flags &amp; kVMExecutable)</a>
+<a name="108"><span class="lineNum">     108 </span>            :     protectFlags |= (flags &amp; kVMWritable) ? PAGE_EXECUTE_READWRITE : PAGE_EXECUTE_READ;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   else</a>
+<a name="110"><span class="lineNum">     110 </span>            :     protectFlags |= (flags &amp; kVMWritable) ? PAGE_READWRITE : PAGE_READONLY;</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   LPVOID mBase = ::VirtualAllocEx(hProcess, nullptr, alignedSize, MEM_COMMIT | MEM_RESERVE, protectFlags);</a>
+<a name="113"><span class="lineNum">     113 </span>            :   if (ASMJIT_UNLIKELY(!mBase)) return nullptr;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   ASMJIT_ASSERT(Utils::isAligned&lt;size_t&gt;(reinterpret_cast&lt;size_t&gt;(mBase), vmi.pageSize));</a>
+<a name="116"><span class="lineNum">     116 </span>            :   if (allocated) *allocated = alignedSize;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   return mBase;</a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : Error OSUtils::releaseProcessMemory(HANDLE hProcess, void* p, size_t size) noexcept {</a>
+<a name="121"><span class="lineNum">     121 </span>            :   const VMemInfo&amp; vmi = OSUtils_GetVMemInfo();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   if (!hProcess) hProcess = vmi.hCurrentProcess;</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   if (ASMJIT_UNLIKELY(!::VirtualFreeEx(hProcess, p, 0, MEM_RELEASE)))</a>
+<a name="125"><span class="lineNum">     125 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   return kErrorOk;</a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : // Posix specific implementation using `mmap()` and `munmap()`.</a>
+<a name="132"><span class="lineNum">     132 </span>            : #if ASMJIT_OS_POSIX</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : // Mac uses MAP_ANON instead of MAP_ANONYMOUS.</a>
+<a name="135"><span class="lineNum">     135 </span>            : #if !defined(MAP_ANONYMOUS)</a>
+<a name="136"><span class="lineNum">     136 </span>            : # define MAP_ANONYMOUS MAP_ANON</a>
+<a name="137"><span class="lineNum">     137 </span>            : #endif // MAP_ANONYMOUS</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       3924 : static const VMemInfo&amp; OSUtils_GetVMemInfo() noexcept {</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   static VMemInfo vmi;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       3924 :   if (ASMJIT_UNLIKELY(!vmi.pageSize)) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         70 :     size_t pageSize = ::getpagesize();</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         70 :     vmi.pageSize = pageSize;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        140 :     vmi.pageGranularity = std::max&lt;size_t&gt;(pageSize, 65536);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       3924 :   return vmi;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : };</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1976 : VMemInfo OSUtils::getVirtualMemoryInfo() noexcept { return OSUtils_GetVMemInfo(); }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       1948 : void* OSUtils::allocVirtualMemory(size_t size, size_t* allocated, uint32_t flags) noexcept {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1948 :   const VMemInfo&amp; vmi = OSUtils_GetVMemInfo();</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1948 :   size_t alignedSize = Utils::alignTo&lt;size_t&gt;(size, vmi.pageSize);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   int protection = PROT_READ;</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1948 :   if (flags &amp; kVMWritable  ) protection |= PROT_WRITE;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1948 :   if (flags &amp; kVMExecutable) protection |= PROT_EXEC;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1948 :   void* mbase = ::mmap(nullptr, alignedSize, protection, MAP_PRIVATE | MAP_ANONYMOUS, -1, 0);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(mbase == MAP_FAILED)) return nullptr;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       1948 :   if (allocated) *allocated = alignedSize;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   return mbase;</a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1948 : Error OSUtils::releaseVirtualMemory(void* p, size_t size) noexcept {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(::munmap(p, size) != 0))</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : #endif // ASMJIT_OS_POSIX</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : // ============================================================================</a>
+<a name="176"><span class="lineNum">     176 </span>            : // [asmjit::OSUtils - GetTickCount]</a>
+<a name="177"><span class="lineNum">     177 </span>            : // ============================================================================</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="180"><span class="lineNum">     180 </span>            : static ASMJIT_INLINE uint32_t OSUtils_calcHiRes(const LARGE_INTEGER&amp; now, double freq) noexcept {</a>
+<a name="181"><span class="lineNum">     181 </span>            :   return static_cast&lt;uint32_t&gt;(</a>
+<a name="182"><span class="lineNum">     182 </span>            :     (int64_t)(double(now.QuadPart) / freq) &amp; 0xFFFFFFFF);</a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : uint32_t OSUtils::getTickCount() noexcept {</a>
+<a name="186"><span class="lineNum">     186 </span>            :   static volatile uint32_t _hiResTicks;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   static volatile double _hiResFreq;</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   do {</a>
+<a name="190"><span class="lineNum">     190 </span>            :     uint32_t hiResOk = _hiResTicks;</a>
+<a name="191"><span class="lineNum">     191 </span>            :     LARGE_INTEGER qpf, now;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :     // If for whatever reason this fails, bail to `GetTickCount()`.</a>
+<a name="194"><span class="lineNum">     194 </span>            :     if (!::QueryPerformanceCounter(&amp;now)) break;</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :     // Expected - if we ran through this at least once `hiResTicks` will be</a>
+<a name="197"><span class="lineNum">     197 </span>            :     // either 1 or 0xFFFFFFFF. If it's '1' then the Hi-Res counter is available</a>
+<a name="198"><span class="lineNum">     198 </span>            :     // and `QueryPerformanceCounter()` can be used.</a>
+<a name="199"><span class="lineNum">     199 </span>            :     if (hiResOk == 1) return OSUtils_calcHiRes(now, _hiResFreq);</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :     // Hi-Res counter is not available, bail to `GetTickCount()`.</a>
+<a name="202"><span class="lineNum">     202 </span>            :     if (hiResOk != 0) break;</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :     // Detect availability of Hi-Res counter, if not available, bail to `GetTickCount()`.</a>
+<a name="205"><span class="lineNum">     205 </span>            :     if (!::QueryPerformanceFrequency(&amp;qpf)) {</a>
+<a name="206"><span class="lineNum">     206 </span>            :       _InterlockedCompareExchange((LONG*)&amp;_hiResTicks, 0xFFFFFFFF, 0);</a>
+<a name="207"><span class="lineNum">     207 </span>            :       break;</a>
+<a name="208"><span class="lineNum">     208 </span>            :     }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            :     double freq = double(qpf.QuadPart) / 1000.0;</a>
+<a name="211"><span class="lineNum">     211 </span>            :     _hiResFreq = freq;</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            :     _InterlockedCompareExchange((LONG*)&amp;_hiResTicks, 1, 0);</a>
+<a name="214"><span class="lineNum">     214 </span>            :     return OSUtils_calcHiRes(now, freq);</a>
+<a name="215"><span class="lineNum">     215 </span>            :   } while (0);</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   return ::GetTickCount();</a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : #elif ASMJIT_OS_MAC</a>
+<a name="220"><span class="lineNum">     220 </span>            : uint32_t OSUtils::getTickCount() noexcept {</a>
+<a name="221"><span class="lineNum">     221 </span>            :   static mach_timebase_info_data_t _machTime;</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   // See Apple's QA1398.</a>
+<a name="224"><span class="lineNum">     224 </span>            :   if (ASMJIT_UNLIKELY(_machTime.denom == 0) || mach_timebase_info(&amp;_machTime) != KERN_SUCCESS)</a>
+<a name="225"><span class="lineNum">     225 </span>            :     return 0;</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :   // `mach_absolute_time()` returns nanoseconds, we want milliseconds.</a>
+<a name="228"><span class="lineNum">     228 </span>            :   uint64_t t = mach_absolute_time() / 1000000;</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   t = t * _machTime.numer / _machTime.denom;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   return static_cast&lt;uint32_t&gt;(t &amp; 0xFFFFFFFFU);</a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : #elif defined(_POSIX_MONOTONIC_CLOCK) &amp;&amp; _POSIX_MONOTONIC_CLOCK &gt;= 0</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 : uint32_t OSUtils::getTickCount() noexcept {</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   struct timespec ts;</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(clock_gettime(CLOCK_MONOTONIC, &amp;ts) != 0))</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :     return 0;</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :   uint64_t t = (uint64_t(ts.tv_sec ) * 1000) + (uint64_t(ts.tv_nsec) / 1000000);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   return static_cast&lt;uint32_t&gt;(t &amp; 0xFFFFFFFFU);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : #else</a>
+<a name="244"><span class="lineNum">     244 </span>            : #error &quot;[asmjit] OSUtils::getTickCount() is not implemented for your target OS.&quot;</a>
+<a name="245"><span class="lineNum">     245 </span>            : uint32_t OSUtils::getTickCount() noexcept { return 0; }</a>
+<a name="246"><span class="lineNum">     246 </span>            : #endif</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : } // asmjit namespace</a>
+<a name="249"><span class="lineNum">     249 </span>            : } // namespace PLMD</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : // [Api-End]</a>
+<a name="252"><span class="lineNum">     252 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="253"><span class="lineNum">     253 </span>            : #pragma GCC diagnostic pop</a>
+<a name="254"><span class="lineNum">     254 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/osutils.h.func-sort-c.html b/coverage-libs/asmjit/osutils.h.func-sort-c.html
new file mode 100644
index 0000000000..5f4c99343f
--- /dev/null
+++ b/coverage-libs/asmjit/osutils.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/osutils.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - osutils.h<span style="font-size: 80%;"> (<a href="osutils.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="osutils.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/osutils.h.func.html b/coverage-libs/asmjit/osutils.h.func.html
new file mode 100644
index 0000000000..579a7c5468
--- /dev/null
+++ b/coverage-libs/asmjit/osutils.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/osutils.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - osutils.h<span style="font-size: 80%;"> (<a href="osutils.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="osutils.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/osutils.h.gcov.html b/coverage-libs/asmjit/osutils.h.gcov.html
new file mode 100644
index 0000000000..5c81abaa77
--- /dev/null
+++ b/coverage-libs/asmjit/osutils.h.gcov.html
@@ -0,0 +1,283 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/osutils.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - osutils.h<span style="font-size: 80%;"> (source / <a href="osutils.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_osutils_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_osutils_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_OSUTILS_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_OSUTILS_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./globals.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::VMemInfo]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! Information about OS virtual memory.</a>
+<a name="52"><span class="lineNum">      52 </span>            : struct VMemInfo {</a>
+<a name="53"><span class="lineNum">      53 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="54"><span class="lineNum">      54 </span>            :   HANDLE hCurrentProcess;                //!&lt; Handle of the current process (Windows).</a>
+<a name="55"><span class="lineNum">      55 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="56"><span class="lineNum">      56 </span>            :   size_t pageSize;                       //!&lt; Virtual memory page size.</a>
+<a name="57"><span class="lineNum">      57 </span>            :   size_t pageGranularity;                //!&lt; Virtual memory page granularity.</a>
+<a name="58"><span class="lineNum">      58 </span>            : };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : // ============================================================================</a>
+<a name="61"><span class="lineNum">      61 </span>            : // [asmjit::OSUtils]</a>
+<a name="62"><span class="lineNum">      62 </span>            : // ============================================================================</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : //! OS utilities.</a>
+<a name="65"><span class="lineNum">      65 </span>            : //!</a>
+<a name="66"><span class="lineNum">      66 </span>            : //! Virtual Memory</a>
+<a name="67"><span class="lineNum">      67 </span>            : //! --------------</a>
+<a name="68"><span class="lineNum">      68 </span>            : //!</a>
+<a name="69"><span class="lineNum">      69 </span>            : //! Provides functions to allocate and release virtual memory that is required</a>
+<a name="70"><span class="lineNum">      70 </span>            : //! to execute dynamically generated code. If both processor and host OS support</a>
+<a name="71"><span class="lineNum">      71 </span>            : //! data-execution-prevention (DEP) then the only way to run machine code is to</a>
+<a name="72"><span class="lineNum">      72 </span>            : //! allocate virtual memory that has `OSUtils::kVMExecutable` flag enabled. All</a>
+<a name="73"><span class="lineNum">      73 </span>            : //! functions provides by OSUtils use internally platform specific API.</a>
+<a name="74"><span class="lineNum">      74 </span>            : //!</a>
+<a name="75"><span class="lineNum">      75 </span>            : //! Benchmarking</a>
+<a name="76"><span class="lineNum">      76 </span>            : //! ------------</a>
+<a name="77"><span class="lineNum">      77 </span>            : //!</a>
+<a name="78"><span class="lineNum">      78 </span>            : //! OSUtils also provide a function `getTickCount()` that can be used for</a>
+<a name="79"><span class="lineNum">      79 </span>            : //! benchmarking purposes. It's similar to Windows-only `GetTickCount()`, but</a>
+<a name="80"><span class="lineNum">      80 </span>            : //! it's cross-platform and tries to be the most reliable platform specific</a>
+<a name="81"><span class="lineNum">      81 </span>            : //! calls to make the result usable.</a>
+<a name="82"><span class="lineNum">      82 </span>            : struct OSUtils {</a>
+<a name="83"><span class="lineNum">      83 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="84"><span class="lineNum">      84 </span>            :   // [Virtual Memory]</a>
+<a name="85"><span class="lineNum">      85 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   //! Virtual memory flags.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ASMJIT_ENUM(VMFlags) {</a>
+<a name="89"><span class="lineNum">      89 </span>            :     kVMWritable   = 0x00000001U,         //!&lt; Virtual memory is writable.</a>
+<a name="90"><span class="lineNum">      90 </span>            :     kVMExecutable = 0x00000002U          //!&lt; Virtual memory is executable.</a>
+<a name="91"><span class="lineNum">      91 </span>            :   };</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   ASMJIT_API static VMemInfo getVirtualMemoryInfo() noexcept;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   //! Allocate virtual memory.</a>
+<a name="96"><span class="lineNum">      96 </span>            :   ASMJIT_API static void* allocVirtualMemory(size_t size, size_t* allocated, uint32_t flags) noexcept;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   //! Release virtual memory previously allocated by \ref allocVirtualMemory().</a>
+<a name="98"><span class="lineNum">      98 </span>            :   ASMJIT_API static Error releaseVirtualMemory(void* p, size_t size) noexcept;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="101"><span class="lineNum">     101 </span>            :   //! Allocate virtual memory of `hProcess` (Windows).</a>
+<a name="102"><span class="lineNum">     102 </span>            :   ASMJIT_API static void* allocProcessMemory(HANDLE hProcess, size_t size, size_t* allocated, uint32_t flags) noexcept;</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   //! Release virtual memory of `hProcess` (Windows).</a>
+<a name="105"><span class="lineNum">     105 </span>            :   ASMJIT_API static Error releaseProcessMemory(HANDLE hProcess, void* p, size_t size) noexcept;</a>
+<a name="106"><span class="lineNum">     106 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="109"><span class="lineNum">     109 </span>            :   // [GetTickCount]</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   //! Get the current CPU tick count, used for benchmarking (1ms resolution).</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ASMJIT_API static uint32_t getTickCount() noexcept;</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : // ============================================================================</a>
+<a name="117"><span class="lineNum">     117 </span>            : // [asmjit::Lock]</a>
+<a name="118"><span class="lineNum">     118 </span>            : // ============================================================================</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : //! \internal</a>
+<a name="121"><span class="lineNum">     121 </span>            : //!</a>
+<a name="122"><span class="lineNum">     122 </span>            : //! Lock.</a>
+<a name="123"><span class="lineNum">     123 </span>            : struct Lock {</a>
+<a name="124"><span class="lineNum">     124 </span>            :   ASMJIT_NONCOPYABLE(Lock)</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="127"><span class="lineNum">     127 </span>            :   // [Windows]</a>
+<a name="128"><span class="lineNum">     128 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="131"><span class="lineNum">     131 </span>            :   typedef CRITICAL_SECTION Handle;</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   //! Create a new `Lock` instance.</a>
+<a name="134"><span class="lineNum">     134 </span>            :   ASMJIT_INLINE Lock() noexcept { InitializeCriticalSection(&amp;_handle); }</a>
+<a name="135"><span class="lineNum">     135 </span>            :   //! Destroy the `Lock` instance.</a>
+<a name="136"><span class="lineNum">     136 </span>            :   ASMJIT_INLINE ~Lock() noexcept { DeleteCriticalSection(&amp;_handle); }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   //! Lock.</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ASMJIT_INLINE void lock() noexcept { EnterCriticalSection(&amp;_handle); }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   //! Unlock.</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ASMJIT_INLINE void unlock() noexcept { LeaveCriticalSection(&amp;_handle); }</a>
+<a name="142"><span class="lineNum">     142 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="145"><span class="lineNum">     145 </span>            :   // [Posix]</a>
+<a name="146"><span class="lineNum">     146 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : #if ASMJIT_OS_POSIX</a>
+<a name="149"><span class="lineNum">     149 </span>            :   typedef pthread_mutex_t Handle;</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   //! Create a new `Lock` instance.</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1976 :   ASMJIT_INLINE Lock() noexcept { pthread_mutex_init(&amp;_handle, nullptr); }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   //! Destroy the `Lock` instance.</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1976 :   ASMJIT_INLINE ~Lock() noexcept { pthread_mutex_destroy(&amp;_handle); }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :   //! Lock.</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void lock() noexcept { pthread_mutex_lock(&amp;_handle); }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   //! Unlock.</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void unlock() noexcept { pthread_mutex_unlock(&amp;_handle); }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : #endif // ASMJIT_OS_POSIX</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="163"><span class="lineNum">     163 </span>            :   // [Members]</a>
+<a name="164"><span class="lineNum">     164 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   //! Native handle.</a>
+<a name="167"><span class="lineNum">     167 </span>            :   Handle _handle;</a>
+<a name="168"><span class="lineNum">     168 </span>            : };</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : // ============================================================================</a>
+<a name="171"><span class="lineNum">     171 </span>            : // [asmjit::AutoLock]</a>
+<a name="172"><span class="lineNum">     172 </span>            : // ============================================================================</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : //! \internal</a>
+<a name="175"><span class="lineNum">     175 </span>            : //!</a>
+<a name="176"><span class="lineNum">     176 </span>            : //! Scoped lock.</a>
+<a name="177"><span class="lineNum">     177 </span>            : struct AutoLock {</a>
+<a name="178"><span class="lineNum">     178 </span>            :   ASMJIT_NONCOPYABLE(AutoLock)</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="181"><span class="lineNum">     181 </span>            :   // [Construction / Destruction]</a>
+<a name="182"><span class="lineNum">     182 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :   ASMJIT_INLINE AutoLock(Lock&amp; target) noexcept : _target(target) { _target.lock(); }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ~AutoLock() noexcept { _target.unlock(); }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="188"><span class="lineNum">     188 </span>            :   // [Members]</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   //! Reference to the `Lock`.</a>
+<a name="192"><span class="lineNum">     192 </span>            :   Lock&amp; _target;</a>
+<a name="193"><span class="lineNum">     193 </span>            : };</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : //! \}</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : } // asmjit namespace</a>
+<a name="198"><span class="lineNum">     198 </span>            : } // namespace PLMD</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : // [Api-End]</a>
+<a name="201"><span class="lineNum">     201 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : // [Guard]</a>
+<a name="204"><span class="lineNum">     204 </span>            : #endif // _ASMJIT_BASE_OSUTILS_H</a>
+<a name="205"><span class="lineNum">     205 </span>            : #pragma GCC diagnostic pop</a>
+<a name="206"><span class="lineNum">     206 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="207"><span class="lineNum">     207 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/regalloc.cpp.func-sort-c.html b/coverage-libs/asmjit/regalloc.cpp.func-sort-c.html
new file mode 100644
index 0000000000..16ec2dd53b
--- /dev/null
+++ b/coverage-libs/asmjit/regalloc.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/regalloc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - regalloc.cpp<span style="font-size: 80%;"> (<a href="regalloc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">114</td>
+            <td class="headerCovTableEntry">241</td>
+            <td class="headerCovTableEntryLo">47.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="regalloc.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#230">_ZN4PLMD6asmjit6RAPass13_newStackCellEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#560">_ZN4PLMD6asmjit6RAPass19formatInlineCommentERNS0_13StringBuilderEPNS0_6CBNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#51">_ZN4PLMD6asmjit6RAPassD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#51">_ZN4PLMD6asmjit6RAPassD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#382">_ZN4PLMD6asmjit6RAPass16livenessAnalysisEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#268">_ZN4PLMD6asmjit6RAPass18resolveCellOffsetsEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#324">_ZN4PLMD6asmjit6RAPass21removeUnreachableCodeEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#151">_ZN4PLMD6asmjit6RAPass7cleanupEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#86">_ZN4PLMD6asmjit6RAPass7compileEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#119">_ZN4PLMD6asmjit6RAPass7prepareEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#57">_ZN4PLMD6asmjit6RAPass7processEPNS0_4ZoneE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#48">_ZN4PLMD6asmjit6RAPassC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#185">_ZN4PLMD6asmjit6RAPass11_newVarCellEPNS0_7VirtRegE</a></td>
+              <td class="coverFnHi">4004</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/regalloc.cpp.func.html b/coverage-libs/asmjit/regalloc.cpp.func.html
new file mode 100644
index 0000000000..80385ec1d2
--- /dev/null
+++ b/coverage-libs/asmjit/regalloc.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/regalloc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - regalloc.cpp<span style="font-size: 80%;"> (<a href="regalloc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">114</td>
+            <td class="headerCovTableEntry">241</td>
+            <td class="headerCovTableEntryLo">47.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="regalloc.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#185">_ZN4PLMD6asmjit6RAPass11_newVarCellEPNS0_7VirtRegE</a></td>
+              <td class="coverFnHi">4004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#230">_ZN4PLMD6asmjit6RAPass13_newStackCellEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#382">_ZN4PLMD6asmjit6RAPass16livenessAnalysisEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#268">_ZN4PLMD6asmjit6RAPass18resolveCellOffsetsEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#560">_ZN4PLMD6asmjit6RAPass19formatInlineCommentERNS0_13StringBuilderEPNS0_6CBNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#324">_ZN4PLMD6asmjit6RAPass21removeUnreachableCodeEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#151">_ZN4PLMD6asmjit6RAPass7cleanupEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#86">_ZN4PLMD6asmjit6RAPass7compileEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#119">_ZN4PLMD6asmjit6RAPass7prepareEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#57">_ZN4PLMD6asmjit6RAPass7processEPNS0_4ZoneE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#48">_ZN4PLMD6asmjit6RAPassC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#51">_ZN4PLMD6asmjit6RAPassD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="regalloc.cpp.gcov.html#51">_ZN4PLMD6asmjit6RAPassD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/regalloc.cpp.gcov.html b/coverage-libs/asmjit/regalloc.cpp.gcov.html
new file mode 100644
index 0000000000..68aec31c8f
--- /dev/null
+++ b/coverage-libs/asmjit/regalloc.cpp.gcov.html
@@ -0,0 +1,696 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/regalloc.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - regalloc.cpp<span style="font-size: 80%;"> (source / <a href="regalloc.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">114</td>
+            <td class="headerCovTableEntry">241</td>
+            <td class="headerCovTableEntryLo">47.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./regalloc_p.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : // [Api-Begin]</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace PLMD {</a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace asmjit {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : // ============================================================================</a>
+<a name="47"><span class="lineNum">      47 </span>            : // [asmjit::RAPass - Construction / Destruction]</a>
+<a name="48"><span class="lineNum">      48 </span>            : // ============================================================================</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1948 : RAPass::RAPass() noexcept :</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   CBPass(&quot;RA&quot;),</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       1948 :   _varMapToVaListOffset(0) {}</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 : RAPass::~RAPass() noexcept {}</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : // [asmjit::RAPass - Interface]</a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       1948 : Error RAPass::process(Zone* zone) noexcept {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       1948 :   _zone = zone;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1948 :   _heap.reset(zone);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       1948 :   _emitComments = (cb()-&gt;getGlobalOptions() &amp; CodeEmitter::kOptionLoggingEnabled) != 0;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   Error err = kErrorOk;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   CBNode* node = cc()-&gt;getFirstNode();</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1948 :   if (!node) return err;</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   do {</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1948 :     if (node-&gt;getType() == CBNode::kNodeFunc) {</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :       CCFunc* func = static_cast&lt;CCFunc*&gt;(node);</a>
+<a name="71"><span class="lineNum">      71 </span>            :       node = func-&gt;getEnd();</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       1948 :       err = compile(func);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       1948 :       if (err) break;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :     // Find a function by skipping all nodes that are not `kNodeFunc`.</a>
+<a name="78"><span class="lineNum">      78 </span>            :     do {</a>
+<a name="79"><span class="lineNum">      79 </span>            :       node = node-&gt;getNext();</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       1948 :     } while (node &amp;&amp; node-&gt;getType() != CBNode::kNodeFunc);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1948 :   } while (node);</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1948 :   _heap.reset(nullptr);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1948 :   _zone = nullptr;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1948 :   return err;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1948 : Error RAPass::compile(CCFunc* func) noexcept {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1948 :   ASMJIT_PROPAGATE(prepare(func));</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   Error err;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   do {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       1948 :     err = fetch();</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1948 :     if (err) break;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1948 :     err = removeUnreachableCode();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1948 :     if (err) break;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1948 :     err = livenessAnalysis();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1948 :     if (err) break;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1948 :     if (cc()-&gt;getGlobalOptions() &amp; CodeEmitter::kOptionLoggingEnabled) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :       err = annotate();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :       if (err) break;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :     }</a>
+<a name="107"><span class="lineNum">     107 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1948 :     err = translate();</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   } while (false);</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1948 :   cleanup();</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   // We alter the compiler cursor, because it doesn't make sense to reference</a>
+<a name="115"><span class="lineNum">     115 </span>            :   // it after compilation - some nodes may disappear and it's forbidden to add</a>
+<a name="116"><span class="lineNum">     116 </span>            :   // new code after the compilation is done.</a>
+<a name="117"><span class="lineNum">     117 </span>            :   cc()-&gt;_setCursor(nullptr);</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1948 :   return err;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       1948 : Error RAPass::prepare(CCFunc* func) noexcept {</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   CBNode* end = func-&gt;getEnd();</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       1948 :   _func = func;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       1948 :   _stop = end-&gt;getNext();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   _unreachableList.reset();</a>
+<a name="128"><span class="lineNum">     128 </span>            :   _returningList.reset();</a>
+<a name="129"><span class="lineNum">     129 </span>            :   _jccList.reset();</a>
+<a name="130"><span class="lineNum">     130 </span>            :   _contextVd.reset();</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       1948 :   _memVarCells = nullptr;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       1948 :   _memStackCells = nullptr;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1948 :   _mem1ByteVarsUsed = 0;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1948 :   _mem2ByteVarsUsed = 0;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1948 :   _mem4ByteVarsUsed = 0;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       1948 :   _mem8ByteVarsUsed = 0;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       1948 :   _mem16ByteVarsUsed = 0;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1948 :   _mem32ByteVarsUsed = 0;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1948 :   _mem64ByteVarsUsed = 0;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       1948 :   _memStackCellsUsed = 0;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       1948 :   _memMaxAlign = 0;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1948 :   _memVarTotal = 0;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1948 :   _memStackTotal = 0;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1948 :   _memAllTotal = 0;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       1948 :   _annotationLength = 12;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       1948 : void RAPass::cleanup() noexcept {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   VirtReg** virtArray = _contextVd.getData();</a>
+<a name="155"><span class="lineNum">     155 </span>            :   size_t virtCount = _contextVd.getLength();</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      25736 :   for (size_t i = 0; i &lt; virtCount; i++) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      23788 :     VirtReg* vreg = virtArray[i];</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      23788 :     vreg-&gt;_raId = kInvalidValue;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     vreg-&gt;resetPhysId();</a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   _contextVd.reset();</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       1948 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : // ============================================================================</a>
+<a name="167"><span class="lineNum">     167 </span>            : // [asmjit::RAPass - Mem]</a>
+<a name="168"><span class="lineNum">     168 </span>            : // ============================================================================</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : static ASMJIT_INLINE uint32_t RAGetDefaultAlignment(uint32_t size) {</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   if (size &gt; 32)</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     return 64;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   else if (size &gt; 16)</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     return 32;</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :   else if (size &gt; 8)</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :     return 16;</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   else if (size &gt; 4)</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     return 8;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   else if (size &gt; 2)</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     return 4;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :   else if (size &gt; 1)</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     return 2;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   else</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :     return 1;</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       4004 : RACell* RAPass::_newVarCell(VirtReg* vreg) {</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   ASMJIT_ASSERT(vreg-&gt;_memCell == nullptr);</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   RACell* cell;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       4004 :   uint32_t size = vreg-&gt;getSize();</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       4004 :   if (vreg-&gt;isStack()) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     cell = _newStackCell(size, vreg-&gt;getAlignment());</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!cell)) return nullptr;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span>            :   else {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       4004 :     cell = static_cast&lt;RACell*&gt;(_zone-&gt;alloc(sizeof(RACell)));</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       4004 :     if (!cell) goto _NoMemory;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       4004 :     cell-&gt;next = _memVarCells;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       4004 :     cell-&gt;offset = 0;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       4004 :     cell-&gt;size = size;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       4004 :     cell-&gt;alignment = size;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       4004 :     _memVarCells = cell;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       4004 :     _memMaxAlign = std::max&lt;uint32_t&gt;(_memMaxAlign, size);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       4004 :     _memVarTotal += size;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       4004 :     switch (size) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       case  1: _mem1ByteVarsUsed++ ; break;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       case  2: _mem2ByteVarsUsed++ ; break;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :       case  4: _mem4ByteVarsUsed++ ; break;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       4004 :       case  8: _mem8ByteVarsUsed++ ; break;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :       case 16: _mem16ByteVarsUsed++; break;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :       case 32: _mem32ByteVarsUsed++; break;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :       case 64: _mem64ByteVarsUsed++; break;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :       default:</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :         ASMJIT_NOT_REACHED();</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     }</a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       4004 :   vreg-&gt;_memCell = cell;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       4004 :   return cell;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            : _NoMemory:</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   cc()-&gt;setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   return nullptr;</a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 : RACell* RAPass::_newStackCell(uint32_t size, uint32_t alignment) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :   RACell* cell = static_cast&lt;RACell*&gt;(_zone-&gt;alloc(sizeof(RACell)));</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!cell)) return nullptr;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   if (alignment == 0)</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :     alignment = RAGetDefaultAlignment(size);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   if (alignment &gt; 64)</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :     alignment = 64;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :   ASMJIT_ASSERT(Utils::isPowerOf2(alignment));</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   size = Utils::alignTo&lt;uint32_t&gt;(size, alignment);</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   // Insert it sorted according to the alignment and size.</a>
+<a name="246"><span class="lineNum">     246 </span>            :   {</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :     RACell** pPrev = &amp;_memStackCells;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :     RACell* cur = *pPrev;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :     while (cur &amp;&amp; ((cur-&gt;alignment &gt; alignment) || (cur-&gt;alignment == alignment &amp;&amp; cur-&gt;size &gt; size))) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :       pPrev = &amp;cur-&gt;next;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :       cur = *pPrev;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :     cell-&gt;next = cur;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :     cell-&gt;offset = 0;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :     cell-&gt;size = size;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :     cell-&gt;alignment = alignment;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :     *pPrev = cell;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :     _memStackCellsUsed++;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :     _memMaxAlign = std::max&lt;uint32_t&gt;(_memMaxAlign, alignment);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :     _memStackTotal += size;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :   return cell;</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       1948 : Error RAPass::resolveCellOffsets() {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       1948 :   RACell* varCell = _memVarCells;</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       1948 :   RACell* stackCell = _memStackCells;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   uint32_t pos64 = 0;</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1948 :   uint32_t pos32 = pos64 + _mem64ByteVarsUsed * 64;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       1948 :   uint32_t pos16 = pos32 + _mem32ByteVarsUsed * 32;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       1948 :   uint32_t pos8  = pos16 + _mem16ByteVarsUsed * 16;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       1948 :   uint32_t pos4  = pos8  + _mem8ByteVarsUsed  * 8 ;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       1948 :   uint32_t pos2  = pos4  + _mem4ByteVarsUsed  * 4 ;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       1948 :   uint32_t pos1  = pos2  + _mem2ByteVarsUsed  * 2 ;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   // Assign home slots.</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       5952 :   while (varCell) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       4004 :     uint32_t size = varCell-&gt;size;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     uint32_t offset = 0;</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       4004 :     switch (size) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :       case  1: offset = pos1 ; pos1  += 1 ; break;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :       case  2: offset = pos2 ; pos2  += 2 ; break;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :       case  4: offset = pos4 ; pos4  += 4 ; break;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       4004 :       case  8: offset = pos8 ; pos8  += 8 ; break;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :       case 16: offset = pos16; pos16 += 16; break;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :       case 32: offset = pos32; pos32 += 32; break;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :       case 64: offset = pos64; pos64 += 64; break;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :       default:</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :         ASMJIT_NOT_REACHED();</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       4004 :     varCell-&gt;offset = static_cast&lt;int32_t&gt;(offset);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       4004 :     varCell = varCell-&gt;next;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   // Assign stack slots.</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1948 :   uint32_t stackPos = pos1 + _mem1ByteVarsUsed;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       1948 :   while (stackCell) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :     uint32_t size = stackCell-&gt;size;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :     uint32_t alignment = stackCell-&gt;alignment;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :     ASMJIT_ASSERT(alignment != 0 &amp;&amp; Utils::isPowerOf2(alignment));</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :     stackPos = Utils::alignTo(stackPos, alignment);</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :     stackCell-&gt;offset = stackPos;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     stackCell = stackCell-&gt;next;</span></a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :     stackPos += size;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :   }</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       1948 :   _memAllTotal = stackPos;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : }</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : // ============================================================================</a>
+<a name="323"><span class="lineNum">     323 </span>            : // [asmjit::RAPass - RemoveUnreachableCode]</a>
+<a name="324"><span class="lineNum">     324 </span>            : // ============================================================================</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       1948 : Error RAPass::removeUnreachableCode() {</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :   ZoneList&lt;CBNode*&gt;::Link* link = _unreachableList.getFirst();</a>
+<a name="328"><span class="lineNum">     328 </span>            :   CBNode* stop = getStop();</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       3896 :   while (link) {</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :     CBNode* node = link-&gt;getValue();</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       1948 :     if (node &amp;&amp; node-&gt;getPrev() &amp;&amp; node != stop) {</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :       // Locate all unreachable nodes.</a>
+<a name="334"><span class="lineNum">     334 </span>            :       CBNode* first = node;</a>
+<a name="335"><span class="lineNum">     335 </span>            :       do {</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       1948 :         if (node-&gt;hasPassData()) break;</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :         node = node-&gt;getNext();</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :       } while (node != stop);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            :       // Remove unreachable nodes that are neither informative nor directives.</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       1948 :       if (node != first) {</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :         CBNode* end = node;</a>
+<a name="343"><span class="lineNum">     343 </span>            :         node = first;</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            :         // NOTE: The strategy is as follows:</a>
+<a name="346"><span class="lineNum">     346 </span>            :         // 1. The algorithm removes everything until it finds a first label.</a>
+<a name="347"><span class="lineNum">     347 </span>            :         // 2. After the first label is found it removes only removable nodes.</a>
+<a name="348"><span class="lineNum">     348 </span>            :         bool removeEverything = true;</a>
+<a name="349"><span class="lineNum">     349 </span>            :         do {</a>
+<a name="350"><span class="lineNum">     350 </span>            :           CBNode* next = node-&gt;getNext();</a>
+<a name="351"><span class="lineNum">     351 </span>            :           bool remove = node-&gt;isRemovable();</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :           if (!remove) {</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :             if (node-&gt;isLabel())</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :               removeEverything = false;</a>
+<a name="356"><span class="lineNum">     356 </span>            :             remove = removeEverything;</a>
+<a name="357"><span class="lineNum">     357 </span>            :           }</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :           if (remove)</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :             cc()-&gt;removeNode(node);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :           node = next;</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :         } while (node != end);</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :       }</a>
+<a name="365"><span class="lineNum">     365 </span>            :     }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :     link = link-&gt;getNext();</a>
+<a name="368"><span class="lineNum">     368 </span>            :   }</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : }</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            : // ============================================================================</a>
+<a name="374"><span class="lineNum">     374 </span>            : // [asmjit::RAPass - Liveness Analysis]</a>
+<a name="375"><span class="lineNum">     375 </span>            : // ============================================================================</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : //! \internal</a>
+<a name="378"><span class="lineNum">     378 </span>            : struct LivenessTarget {</a>
+<a name="379"><span class="lineNum">     379 </span>            :   LivenessTarget* prev;  //!&lt; Previous target.</a>
+<a name="380"><span class="lineNum">     380 </span>            :   CBLabel* node;         //!&lt; Target node.</a>
+<a name="381"><span class="lineNum">     381 </span>            :   CBJump* from;          //!&lt; Jumped from.</a>
+<a name="382"><span class="lineNum">     382 </span>            : };</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       1948 : Error RAPass::livenessAnalysis() {</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :   uint32_t bLen = static_cast&lt;uint32_t&gt;(</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       1948 :     ((_contextVd.getLength() + RABits::kEntityBits - 1) / RABits::kEntityBits));</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            :   // No variables.</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">       1948 :   if (bLen == 0)</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :     return kErrorOk;</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            :   CCFunc* func = getFunc();</a>
+<a name="393"><span class="lineNum">     393 </span>            :   CBJump* from = nullptr;</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            :   LivenessTarget* ltCur = nullptr;</a>
+<a name="396"><span class="lineNum">     396 </span>            :   LivenessTarget* ltUnused = nullptr;</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            :   ZoneList&lt;CBNode*&gt;::Link* retPtr = _returningList.getFirst();</a>
+<a name="399"><span class="lineNum">     399 </span>            :   ASMJIT_ASSERT(retPtr != nullptr);</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :   CBNode* node = retPtr-&gt;getValue();</a>
+<a name="402"><span class="lineNum">     402 </span>            :   RAData* wd;</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       1948 :   size_t varMapToVaListOffset = _varMapToVaListOffset;</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :   RABits* bCur = newBits(bLen);</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(!bCur)) goto NoMem;</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :   // Allocate bits for code visited first time.</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">      36702 : Visit:</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   for (;;) {</a>
+<a name="411"><span class="lineNum">     411 </span>            :     wd = node-&gt;getPassData&lt;RAData&gt;();</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">      36702 :     if (wd-&gt;liveness) {</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :       if (bCur-&gt;_addBitsDelSource(wd-&gt;liveness, bCur, bLen))</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :         goto Patch;</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :       else</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :         goto Done;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :     }</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span>            :     RABits* bTmp = copyBits(bCur, bLen);</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      36702 :     if (!bTmp) goto NoMem;</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            :     wd = node-&gt;getPassData&lt;RAData&gt;();</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">      36702 :     wd-&gt;liveness = bTmp;</span></a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">      36702 :     uint32_t tiedTotal = wd-&gt;tiedTotal;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     TiedReg* tiedArray = reinterpret_cast&lt;TiedReg*&gt;(((uint8_t*)wd) + varMapToVaListOffset);</a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">      98196 :     for (uint32_t i = 0; i &lt; tiedTotal; i++) {</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">      61494 :       TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">      61494 :       VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">      61494 :       uint32_t flags = tied-&gt;flags;</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">      61494 :       uint32_t raId = vreg-&gt;_raId;</span></a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">      61494 :       if ((flags &amp; TiedReg::kWAll) &amp;&amp; !(flags &amp; TiedReg::kRAll)) {</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :         // Write-Only.</a>
+<a name="437"><span class="lineNum">     437 </span>            :         bTmp-&gt;setBit(raId);</a>
+<a name="438"><span class="lineNum">     438 </span>            :         bCur-&gt;delBit(raId);</a>
+<a name="439"><span class="lineNum">     439 </span>            :       }</a>
+<a name="440"><span class="lineNum">     440 </span>            :       else {</a>
+<a name="441"><span class="lineNum">     441 </span>            :         // Read-Only or Read/Write.</a>
+<a name="442"><span class="lineNum">     442 </span>            :         bTmp-&gt;setBit(raId);</a>
+<a name="443"><span class="lineNum">     443 </span>            :         bCur-&gt;setBit(raId);</a>
+<a name="444"><span class="lineNum">     444 </span>            :       }</a>
+<a name="445"><span class="lineNum">     445 </span>            :     }</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">      36702 :     if (node-&gt;getType() == CBNode::kNodeLabel)</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :       goto Target;</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">      36702 :     if (node == func)</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">       1948 :       goto Done;</span></a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            :     ASMJIT_ASSERT(node-&gt;getPrev());</a>
+<a name="454"><span class="lineNum">     454 </span>            :     node = node-&gt;getPrev();</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">      34754 :   }</span></a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   // Patch already generated liveness bits.</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 : Patch:</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :   for (;;) {</a>
+<a name="460"><span class="lineNum">     460 </span>            :     ASMJIT_ASSERT(node-&gt;hasPassData());</a>
+<a name="461"><span class="lineNum">     461 </span>            :     ASMJIT_ASSERT(node-&gt;getPassData&lt;RAData&gt;()-&gt;liveness != nullptr);</a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :     RABits* bNode = node-&gt;getPassData&lt;RAData&gt;()-&gt;liveness;</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :     if (!bNode-&gt;_addBitsDelSource(bCur, bLen)) goto Done;</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 :     if (node-&gt;getType() == CBNode::kNodeLabel) goto Target;</span></a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :     if (node == func) goto Done;</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :     node = node-&gt;getPrev();</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 : Target:</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :   if (static_cast&lt;CBLabel*&gt;(node)-&gt;getNumRefs() != 0) {</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :     // Push a new LivenessTarget onto the stack if needed.</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :     if (!ltCur || ltCur-&gt;node != node) {</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :       // Allocate a new LivenessTarget object (from pool or zone).</a>
+<a name="476"><span class="lineNum">     476 </span>            :       LivenessTarget* ltTmp = ltUnused;</a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :       if (ltTmp) {</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :         ltUnused = ltUnused-&gt;prev;</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :       }</a>
+<a name="481"><span class="lineNum">     481 </span>            :       else {</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :         ltTmp = _zone-&gt;allocT&lt;LivenessTarget&gt;(</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineNoCov">          0 :           sizeof(LivenessTarget) - sizeof(RABits) + bLen * sizeof(uintptr_t));</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineNoCov">          0 :         if (!ltTmp) goto NoMem;</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :       }</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span>            :       // Initialize and make current - ltTmp-&gt;from will be set later on.</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :       ltTmp-&gt;prev = ltCur;</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :       ltTmp-&gt;node = static_cast&lt;CBLabel*&gt;(node);</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :       ltCur = ltTmp;</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            :       from = static_cast&lt;CBLabel*&gt;(node)-&gt;getFrom();</a>
+<a name="493"><span class="lineNum">     493 </span>            :       ASMJIT_ASSERT(from != nullptr);</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     else {</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :       from = ltCur-&gt;from;</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :       goto JumpNext;</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :     }</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            :     // Visit/Patch.</a>
+<a name="501"><span class="lineNum">     501 </span>            :     do {</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 :       ltCur-&gt;from = from;</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :       bCur-&gt;copyBits(node-&gt;getPassData&lt;RAData&gt;()-&gt;liveness, bLen);</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :       if (!from-&gt;getPassData&lt;RAData&gt;()-&gt;liveness) {</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :         node = from;</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :         goto Visit;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :       }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            :       // Issue #25: Moved 'JumpNext' here since it's important to patch</a>
+<a name="511"><span class="lineNum">     511 </span>            :       // code again if there are more live variables than before.</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 : JumpNext:</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :       if (bCur-&gt;delBits(from-&gt;getPassData&lt;RAData&gt;()-&gt;liveness, bLen)) {</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :         node = from;</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :         goto Patch;</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :       }</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            :       from = from-&gt;getJumpNext();</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :     } while (from);</span></a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            :     // Pop the current LivenessTarget from the stack.</a>
+<a name="522"><span class="lineNum">     522 </span>            :     {</a>
+<a name="523"><span class="lineNum">     523 </span>            :       LivenessTarget* ltTmp = ltCur;</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :       ltCur = ltCur-&gt;prev;</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :       ltTmp-&gt;prev = ltUnused;</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :       ltUnused = ltTmp;</a>
+<a name="527"><span class="lineNum">     527 </span>            :     }</a>
+<a name="528"><span class="lineNum">     528 </span>            :   }</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :   bCur-&gt;copyBits(node-&gt;getPassData&lt;RAData&gt;()-&gt;liveness, bLen);</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :   node = node-&gt;getPrev();</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :   if (node-&gt;isJmp() || !node-&gt;hasPassData()) goto Done;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            :   wd = node-&gt;getPassData&lt;RAData&gt;();</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :   if (!wd-&gt;liveness) goto Visit;</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :   if (bCur-&gt;delBits(wd-&gt;liveness, bLen)) goto Patch;</span></a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 : Done:</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">       1948 :   if (ltCur) {</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 :     node = ltCur-&gt;node;</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :     from = ltCur-&gt;from;</span></a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     goto JumpNext;</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :   }</a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span>            :   retPtr = retPtr-&gt;getNext();</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">       1948 :   if (retPtr) {</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :     node = retPtr-&gt;getValue();</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :     goto Visit;</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :   }</a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span>            :   return kErrorOk;</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            : NoMem:</a>
+<a name="555"><span class="lineNum">     555 </span>            :   return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="556"><span class="lineNum">     556 </span>            : }</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            : // ============================================================================</a>
+<a name="559"><span class="lineNum">     559 </span>            : // [asmjit::RAPass - Annotate]</a>
+<a name="560"><span class="lineNum">     560 </span>            : // ============================================================================</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 : Error RAPass::formatInlineComment(StringBuilder&amp; dst, CBNode* node) {</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="564"><span class="lineNum">     564 </span>            :   RAData* wd = node-&gt;getPassData&lt;RAData&gt;();</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineNoCov">          0 :   if (node-&gt;hasInlineComment())</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :     dst.appendString(node-&gt;getInlineComment());</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :   if (wd &amp;&amp; wd-&gt;liveness) {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :     if (dst.getLength() &lt; _annotationLength)</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineNoCov">          0 :       dst.appendChars(' ', _annotationLength - dst.getLength());</span></a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :     uint32_t vdCount = static_cast&lt;uint32_t&gt;(_contextVd.getLength());</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineNoCov">          0 :     size_t offset = dst.getLength() + 1;</span></a>
+<a name="575"><span class="lineNum">     575 </span>            : </a>
+<a name="576"><span class="lineNum">     576 </span>            :     dst.appendChar('[');</a>
+<a name="577"><span class="lineNum">     577 </span>            :     dst.appendChars(' ', vdCount);</a>
+<a name="578"><span class="lineNum">     578 </span>            :     dst.appendChar(']');</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineNoCov">          0 :     RABits* liveness = wd-&gt;liveness;</span></a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            :     uint32_t i;</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; vdCount; i++) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :       if (liveness-&gt;getBit(i))</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineNoCov">          0 :         dst.getData()[offset + i] = '.';</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :     }</a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineNoCov">          0 :     uint32_t tiedTotal = wd-&gt;tiedTotal;</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :     TiedReg* tiedArray = reinterpret_cast&lt;TiedReg*&gt;(((uint8_t*)wd) + _varMapToVaListOffset);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; tiedTotal; i++) {</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :       TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineNoCov">          0 :       VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 :       uint32_t flags = tied-&gt;flags;</span></a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span>            :       char c = 'u';</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :       if ( (flags &amp; TiedReg::kRAll) &amp;&amp; !(flags &amp; TiedReg::kWAll)) c = 'r';</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :       if (!(flags &amp; TiedReg::kRAll) &amp;&amp;  (flags &amp; TiedReg::kWAll)) c = 'w';</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :       if ( (flags &amp; TiedReg::kRAll) &amp;&amp;  (flags &amp; TiedReg::kWAll)) c = 'x';</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :       // Uppercase if unused.</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :       if ( (flags &amp; TiedReg::kUnuse)) c -= 'a' - 'A';</span></a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span>            :       ASMJIT_ASSERT(offset + vreg-&gt;_raId &lt; dst.getLength());</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :       dst._data[offset + vreg-&gt;_raId] = c;</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :     }</a>
+<a name="605"><span class="lineNum">     605 </span>            :   }</a>
+<a name="606"><span class="lineNum">     606 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="609"><span class="lineNum">     609 </span>            : }</a>
+<a name="610"><span class="lineNum">     610 </span>            : </a>
+<a name="611"><span class="lineNum">     611 </span>            : } // asmjit namespace</a>
+<a name="612"><span class="lineNum">     612 </span>            : } // namespace PLMD</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            : // [Api-End]</a>
+<a name="615"><span class="lineNum">     615 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            : // [Guard]</a>
+<a name="618"><span class="lineNum">     618 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="619"><span class="lineNum">     619 </span>            : #pragma GCC diagnostic pop</a>
+<a name="620"><span class="lineNum">     620 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/regalloc_p.h.func-sort-c.html b/coverage-libs/asmjit/regalloc_p.h.func-sort-c.html
new file mode 100644
index 0000000000..a79a04e706
--- /dev/null
+++ b/coverage-libs/asmjit/regalloc_p.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/regalloc_p.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - regalloc_p.h<span style="font-size: 80%;"> (<a href="regalloc_p.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="regalloc_p.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/regalloc_p.h.func.html b/coverage-libs/asmjit/regalloc_p.h.func.html
new file mode 100644
index 0000000000..205a32bf6b
--- /dev/null
+++ b/coverage-libs/asmjit/regalloc_p.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/regalloc_p.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - regalloc_p.h<span style="font-size: 80%;"> (<a href="regalloc_p.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="regalloc_p.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/regalloc_p.h.gcov.html b/coverage-libs/asmjit/regalloc_p.h.gcov.html
new file mode 100644
index 0000000000..e15ab289fa
--- /dev/null
+++ b/coverage-libs/asmjit/regalloc_p.h.gcov.html
@@ -0,0 +1,673 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/regalloc_p.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - regalloc_p.h<span style="font-size: 80%;"> (source / <a href="regalloc_p.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_regalloc_p_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_regalloc_p_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_REGALLOC_P_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_REGALLOC_P_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Dependencies]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./codecompiler.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./zone.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // [Api-Begin]</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace PLMD {</a>
+<a name="46"><span class="lineNum">      46 </span>            : namespace asmjit {</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : //! \addtogroup asmjit_base</a>
+<a name="49"><span class="lineNum">      49 </span>            : //! \{</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : // [asmjit::TiedReg]</a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : //! Tied register (CodeCompiler)</a>
+<a name="56"><span class="lineNum">      56 </span>            : //!</a>
+<a name="57"><span class="lineNum">      57 </span>            : //! Tied register is used to describe one ore more register operands that share</a>
+<a name="58"><span class="lineNum">      58 </span>            : //! the same virtual register. Tied register contains all the data that is</a>
+<a name="59"><span class="lineNum">      59 </span>            : //! essential for register allocation.</a>
+<a name="60"><span class="lineNum">      60 </span>            : struct TiedReg {</a>
+<a name="61"><span class="lineNum">      61 </span>            :   //! Flags.</a>
+<a name="62"><span class="lineNum">      62 </span>            :   ASMJIT_ENUM(Flags) {</a>
+<a name="63"><span class="lineNum">      63 </span>            :     kRReg        = 0x00000001U,          //!&lt; Register read.</a>
+<a name="64"><span class="lineNum">      64 </span>            :     kWReg        = 0x00000002U,          //!&lt; Register write.</a>
+<a name="65"><span class="lineNum">      65 </span>            :     kXReg        = 0x00000003U,          //!&lt; Register read-write.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            :     kRMem        = 0x00000004U,          //!&lt; Memory read.</a>
+<a name="68"><span class="lineNum">      68 </span>            :     kWMem        = 0x00000008U,          //!&lt; Memory write.</a>
+<a name="69"><span class="lineNum">      69 </span>            :     kXMem        = 0x0000000CU,          //!&lt; Memory read-write.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :     kRDecide     = 0x00000010U,          //!&lt; RA can decide between reg/mem read.</a>
+<a name="72"><span class="lineNum">      72 </span>            :     kWDecide     = 0x00000020U,          //!&lt; RA can decide between reg/mem write.</a>
+<a name="73"><span class="lineNum">      73 </span>            :     kXDecide     = 0x00000030U,          //!&lt; RA can decide between reg/mem read-write.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :     kRFunc       = 0x00000100U,          //!&lt; Function argument passed in register.</a>
+<a name="76"><span class="lineNum">      76 </span>            :     kWFunc       = 0x00000200U,          //!&lt; Function return value passed into register.</a>
+<a name="77"><span class="lineNum">      77 </span>            :     kXFunc       = 0x00000300U,          //!&lt; Function argument and return value.</a>
+<a name="78"><span class="lineNum">      78 </span>            :     kRCall       = 0x00000400U,          //!&lt; Function call operand.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :     kSpill       = 0x00000800U,          //!&lt; Variable should be spilled.</a>
+<a name="81"><span class="lineNum">      81 </span>            :     kUnuse       = 0x00001000U,          //!&lt; Variable should be unused at the end of the instruction/node.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :     kRAll        = kRReg | kRMem | kRDecide | kRFunc | kRCall, //!&lt; All in-flags.</a>
+<a name="84"><span class="lineNum">      84 </span>            :     kWAll        = kWReg | kWMem | kWDecide | kWFunc,          //!&lt; All out-flags.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :     kRDone       = 0x00400000U,          //!&lt; Already allocated on the input.</a>
+<a name="87"><span class="lineNum">      87 </span>            :     kWDone       = 0x00800000U,          //!&lt; Already allocated on the output.</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :     kX86GpbLo    = 0x10000000U,</a>
+<a name="90"><span class="lineNum">      90 </span>            :     kX86GpbHi    = 0x20000000U,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     kX86Fld4     = 0x40000000U,</a>
+<a name="92"><span class="lineNum">      92 </span>            :     kX86Fld8     = 0x80000000U</a>
+<a name="93"><span class="lineNum">      93 </span>            :   };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // [Init / Reset]</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   ASMJIT_INLINE void init(VirtReg* vreg, uint32_t flags = 0, uint32_t inRegs = 0, uint32_t allocableRegs = 0) noexcept {</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      61494 :     this-&gt;vreg = vreg;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      61494 :     this-&gt;flags = flags;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      61494 :     this-&gt;refCount = 0;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      61494 :     this-&gt;inPhysId = Globals::kInvalidRegId;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      61494 :     this-&gt;outPhysId = Globals::kInvalidRegId;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      61494 :     this-&gt;reserved = 0;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      61494 :     this-&gt;inRegs = inRegs;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1648 :     this-&gt;allocableRegs = allocableRegs;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // [Accessors]</a>
+<a name="112"><span class="lineNum">     112 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   //! Get whether the variable has to be allocated in a specific input register.</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4272 :   ASMJIT_INLINE uint32_t hasInPhysId() const { return inPhysId != Globals::kInvalidRegId; }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   //! Get whether the variable has to be allocated in a specific output register.</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      26412 :   ASMJIT_INLINE uint32_t hasOutPhysId() const { return outPhysId != Globals::kInvalidRegId; }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   //! Set the input register index.</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      37706 :   ASMJIT_INLINE void setInPhysId(uint32_t index) { inPhysId = static_cast&lt;uint8_t&gt;(index); }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   //! Set the output register index.</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      23788 :   ASMJIT_INLINE void setOutPhysId(uint32_t index) { outPhysId = static_cast&lt;uint8_t&gt;(index); }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="125"><span class="lineNum">     125 </span>            :   // [Operator Overload]</a>
+<a name="126"><span class="lineNum">     126 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   ASMJIT_INLINE TiedReg&amp; operator=(const TiedReg&amp; other) {</a>
+<a name="129"><span class="lineNum">     129 </span>            :     ::memcpy(this, &amp;other, sizeof(TiedReg));</a>
+<a name="130"><span class="lineNum">     130 </span>            :     return *this;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="134"><span class="lineNum">     134 </span>            :   // [Members]</a>
+<a name="135"><span class="lineNum">     135 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            :   //! Pointer to the associated \ref VirtReg.</a>
+<a name="138"><span class="lineNum">     138 </span>            :   VirtReg* vreg;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   //! Tied flags.</a>
+<a name="140"><span class="lineNum">     140 </span>            :   uint32_t flags;</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   union {</a>
+<a name="143"><span class="lineNum">     143 </span>            :     struct {</a>
+<a name="144"><span class="lineNum">     144 </span>            :       //! How many times the variable is used by the instruction/node.</a>
+<a name="145"><span class="lineNum">     145 </span>            :       uint8_t refCount;</a>
+<a name="146"><span class="lineNum">     146 </span>            :       //! Input register index or `kInvalidReg` if it's not given.</a>
+<a name="147"><span class="lineNum">     147 </span>            :       //!</a>
+<a name="148"><span class="lineNum">     148 </span>            :       //! Even if the input register index is not given (i.e. it may by any</a>
+<a name="149"><span class="lineNum">     149 </span>            :       //! register), register allocator should assign an index that will be</a>
+<a name="150"><span class="lineNum">     150 </span>            :       //! used to persist a variable into this specific index. It's helpful</a>
+<a name="151"><span class="lineNum">     151 </span>            :       //! in situations where one variable has to be allocated in multiple</a>
+<a name="152"><span class="lineNum">     152 </span>            :       //! registers to determine the register which will be persistent.</a>
+<a name="153"><span class="lineNum">     153 </span>            :       uint8_t inPhysId;</a>
+<a name="154"><span class="lineNum">     154 </span>            :       //! Output register index or `kInvalidReg` if it's not given.</a>
+<a name="155"><span class="lineNum">     155 </span>            :       //!</a>
+<a name="156"><span class="lineNum">     156 </span>            :       //! Typically `kInvalidReg` if variable is only used on input.</a>
+<a name="157"><span class="lineNum">     157 </span>            :       uint8_t outPhysId;</a>
+<a name="158"><span class="lineNum">     158 </span>            :       //! \internal</a>
+<a name="159"><span class="lineNum">     159 </span>            :       uint8_t reserved;</a>
+<a name="160"><span class="lineNum">     160 </span>            :     };</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :     //! \internal</a>
+<a name="163"><span class="lineNum">     163 </span>            :     //!</a>
+<a name="164"><span class="lineNum">     164 </span>            :     //! Packed data #0.</a>
+<a name="165"><span class="lineNum">     165 </span>            :     uint32_t packed;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   };</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   //! Mandatory input registers.</a>
+<a name="169"><span class="lineNum">     169 </span>            :   //!</a>
+<a name="170"><span class="lineNum">     170 </span>            :   //! Mandatory input registers are required by the instruction even if</a>
+<a name="171"><span class="lineNum">     171 </span>            :   //! there are duplicates. This schema allows us to allocate one variable</a>
+<a name="172"><span class="lineNum">     172 </span>            :   //! in one or more register when needed. Required mostly by instructions</a>
+<a name="173"><span class="lineNum">     173 </span>            :   //! that have implicit register operands (imul, cpuid, ...) and function</a>
+<a name="174"><span class="lineNum">     174 </span>            :   //! call.</a>
+<a name="175"><span class="lineNum">     175 </span>            :   uint32_t inRegs;</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            :   //! Allocable input registers.</a>
+<a name="178"><span class="lineNum">     178 </span>            :   //!</a>
+<a name="179"><span class="lineNum">     179 </span>            :   //! Optional input registers is a mask of all allocable registers for a given</a>
+<a name="180"><span class="lineNum">     180 </span>            :   //! variable where we have to pick one of them. This mask is usually not used</a>
+<a name="181"><span class="lineNum">     181 </span>            :   //! when _inRegs is set. If both masks are used then the register</a>
+<a name="182"><span class="lineNum">     182 </span>            :   //! allocator tries first to find an intersection between these and allocates</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //! an extra slot if not found.</a>
+<a name="184"><span class="lineNum">     184 </span>            :   uint32_t allocableRegs;</a>
+<a name="185"><span class="lineNum">     185 </span>            : };</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : // ============================================================================</a>
+<a name="188"><span class="lineNum">     188 </span>            : // [asmjit::RABits]</a>
+<a name="189"><span class="lineNum">     189 </span>            : // ============================================================================</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : //! Fixed size bit-array.</a>
+<a name="192"><span class="lineNum">     192 </span>            : //!</a>
+<a name="193"><span class="lineNum">     193 </span>            : //! Used by variable liveness analysis.</a>
+<a name="194"><span class="lineNum">     194 </span>            : struct RABits {</a>
+<a name="195"><span class="lineNum">     195 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="196"><span class="lineNum">     196 </span>            :   // [Enums]</a>
+<a name="197"><span class="lineNum">     197 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   enum {</a>
+<a name="200"><span class="lineNum">     200 </span>            :     kEntitySize = static_cast&lt;int&gt;(sizeof(uintptr_t)),</a>
+<a name="201"><span class="lineNum">     201 </span>            :     kEntityBits = kEntitySize * 8</a>
+<a name="202"><span class="lineNum">     202 </span>            :   };</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="205"><span class="lineNum">     205 </span>            :   // [Accessors]</a>
+<a name="206"><span class="lineNum">     206 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   ASMJIT_INLINE uintptr_t getBit(uint32_t index) const noexcept {</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     178746 :     return (data[index / kEntityBits] &gt;&gt; (index % kEntityBits)) &amp; 1;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   ASMJIT_INLINE void setBit(uint32_t index) noexcept {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      61494 :     data[index / kEntityBits] |= static_cast&lt;uintptr_t&gt;(1) &lt;&lt; (index % kEntityBits);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      37706 :   }</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :   ASMJIT_INLINE void delBit(uint32_t index) noexcept {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      23788 :     data[index / kEntityBits] &amp;= ~(static_cast&lt;uintptr_t&gt;(1) &lt;&lt; (index % kEntityBits));</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      23788 :   }</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="221"><span class="lineNum">     221 </span>            :   // [Interface]</a>
+<a name="222"><span class="lineNum">     222 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   //! Copy bits from `s0`, returns `true` if at least one bit is set in `s0`.</a>
+<a name="225"><span class="lineNum">     225 </span>            :   ASMJIT_INLINE bool copyBits(const RABits* s0, uint32_t len) noexcept {</a>
+<a name="226"><span class="lineNum">     226 </span>            :     uintptr_t r = 0;</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :     for (uint32_t i = 0; i &lt; len; i++) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :       uintptr_t t = s0-&gt;data[i];</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       data[i] = t;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       r |= t;</a>
+<a name="231"><span class="lineNum">     231 </span>            :     }</a>
+<a name="232"><span class="lineNum">     232 </span>            :     return r != 0;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   ASMJIT_INLINE bool addBits(const RABits* s0, uint32_t len) noexcept {</a>
+<a name="236"><span class="lineNum">     236 </span>            :     return addBits(this, s0, len);</a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            :   ASMJIT_INLINE bool addBits(const RABits* s0, const RABits* s1, uint32_t len) noexcept {</a>
+<a name="240"><span class="lineNum">     240 </span>            :     uintptr_t r = 0;</a>
+<a name="241"><span class="lineNum">     241 </span>            :     for (uint32_t i = 0; i &lt; len; i++) {</a>
+<a name="242"><span class="lineNum">     242 </span>            :       uintptr_t t = s0-&gt;data[i] | s1-&gt;data[i];</a>
+<a name="243"><span class="lineNum">     243 </span>            :       data[i] = t;</a>
+<a name="244"><span class="lineNum">     244 </span>            :       r |= t;</a>
+<a name="245"><span class="lineNum">     245 </span>            :     }</a>
+<a name="246"><span class="lineNum">     246 </span>            :     return r != 0;</a>
+<a name="247"><span class="lineNum">     247 </span>            :   }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_INLINE bool andBits(const RABits* s1, uint32_t len) noexcept {</a>
+<a name="250"><span class="lineNum">     250 </span>            :     return andBits(this, s1, len);</a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            :   ASMJIT_INLINE bool andBits(const RABits* s0, const RABits* s1, uint32_t len) noexcept {</a>
+<a name="254"><span class="lineNum">     254 </span>            :     uintptr_t r = 0;</a>
+<a name="255"><span class="lineNum">     255 </span>            :     for (uint32_t i = 0; i &lt; len; i++) {</a>
+<a name="256"><span class="lineNum">     256 </span>            :       uintptr_t t = s0-&gt;data[i] &amp; s1-&gt;data[i];</a>
+<a name="257"><span class="lineNum">     257 </span>            :       data[i] = t;</a>
+<a name="258"><span class="lineNum">     258 </span>            :       r |= t;</a>
+<a name="259"><span class="lineNum">     259 </span>            :     }</a>
+<a name="260"><span class="lineNum">     260 </span>            :     return r != 0;</a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   ASMJIT_INLINE bool delBits(const RABits* s1, uint32_t len) noexcept {</a>
+<a name="264"><span class="lineNum">     264 </span>            :     return delBits(this, s1, len);</a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            :   ASMJIT_INLINE bool delBits(const RABits* s0, const RABits* s1, uint32_t len) noexcept {</a>
+<a name="268"><span class="lineNum">     268 </span>            :     uintptr_t r = 0;</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :     for (uint32_t i = 0; i &lt; len; i++) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :       uintptr_t t = s0-&gt;data[i] &amp; ~s1-&gt;data[i];</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :       data[i] = t;</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :       r |= t;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span>            :     return r != 0;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :   ASMJIT_INLINE bool _addBitsDelSource(RABits* s1, uint32_t len) noexcept {</a>
+<a name="278"><span class="lineNum">     278 </span>            :     return _addBitsDelSource(this, s1, len);</a>
+<a name="279"><span class="lineNum">     279 </span>            :   }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            :   ASMJIT_INLINE bool _addBitsDelSource(const RABits* s0, RABits* s1, uint32_t len) noexcept {</a>
+<a name="282"><span class="lineNum">     282 </span>            :     uintptr_t r = 0;</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :     for (uint32_t i = 0; i &lt; len; i++) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :       uintptr_t a = s0-&gt;data[i];</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :       uintptr_t b = s1-&gt;data[i];</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :       this-&gt;data[i] = a | b;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :       b &amp;= ~a;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :       s1-&gt;data[i] = b;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :       r |= b;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :     }</a>
+<a name="293"><span class="lineNum">     293 </span>            :     return r != 0;</a>
+<a name="294"><span class="lineNum">     294 </span>            :   }</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="297"><span class="lineNum">     297 </span>            :   // [Members]</a>
+<a name="298"><span class="lineNum">     298 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :   uintptr_t data[1];</a>
+<a name="301"><span class="lineNum">     301 </span>            : };</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : // ============================================================================</a>
+<a name="304"><span class="lineNum">     304 </span>            : // [asmjit::RACell]</a>
+<a name="305"><span class="lineNum">     305 </span>            : // ============================================================================</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : //! Register allocator's (RA) memory cell.</a>
+<a name="308"><span class="lineNum">     308 </span>            : struct RACell {</a>
+<a name="309"><span class="lineNum">     309 </span>            :   RACell* next;                          //!&lt; Next active cell.</a>
+<a name="310"><span class="lineNum">     310 </span>            :   int32_t offset;                        //!&lt; Cell offset, relative to base-offset.</a>
+<a name="311"><span class="lineNum">     311 </span>            :   uint32_t size;                         //!&lt; Cell size.</a>
+<a name="312"><span class="lineNum">     312 </span>            :   uint32_t alignment;                    //!&lt; Cell alignment.</a>
+<a name="313"><span class="lineNum">     313 </span>            : };</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            : // ============================================================================</a>
+<a name="316"><span class="lineNum">     316 </span>            : // [asmjit::RAData]</a>
+<a name="317"><span class="lineNum">     317 </span>            : // ============================================================================</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            : //! Register allocator's (RA) data associated with each \ref CBNode.</a>
+<a name="320"><span class="lineNum">     320 </span>            : struct RAData {</a>
+<a name="321"><span class="lineNum">     321 </span>            :   ASMJIT_INLINE RAData(uint32_t tiedTotal) noexcept</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      40598 :     : liveness(nullptr),</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">      40598 :       state(nullptr),</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      40598 :       tiedTotal(tiedTotal) {}</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   RABits* liveness;                      //!&lt; Liveness bits (populated by liveness-analysis).</a>
+<a name="327"><span class="lineNum">     327 </span>            :   RAState* state;                        //!&lt; Optional saved \ref RAState.</a>
+<a name="328"><span class="lineNum">     328 </span>            :   uint32_t tiedTotal;                    //!&lt; Total count of \ref TiedReg regs.</a>
+<a name="329"><span class="lineNum">     329 </span>            : };</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            : // ============================================================================</a>
+<a name="332"><span class="lineNum">     332 </span>            : // [asmjit::RAState]</a>
+<a name="333"><span class="lineNum">     333 </span>            : // ============================================================================</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            : //! Variables' state.</a>
+<a name="336"><span class="lineNum">     336 </span>            : struct RAState {};</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : // ============================================================================</a>
+<a name="339"><span class="lineNum">     339 </span>            : // [asmjit::RAPass]</a>
+<a name="340"><span class="lineNum">     340 </span>            : // ============================================================================</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            : //! \internal</a>
+<a name="343"><span class="lineNum">     343 </span>            : //!</a>
+<a name="344"><span class="lineNum">     344 </span>            : //! Register allocator pipeline used by \ref CodeCompiler.</a>
+<a name="345"><span class="lineNum">     345 </span>            : struct RAPass : public CBPass {</a>
+<a name="346"><span class="lineNum">     346 </span>            : public:</a>
+<a name="347"><span class="lineNum">     347 </span>            :   ASMJIT_NONCOPYABLE(RAPass)</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   typedef void (ASMJIT_CDECL* TraceNodeFunc)(RAPass* self, CBNode* node_, const char* prefix);</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="352"><span class="lineNum">     352 </span>            :   // [Construction / Destruction]</a>
+<a name="353"><span class="lineNum">     353 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :   RAPass() noexcept;</a>
+<a name="356"><span class="lineNum">     356 </span>            :   virtual ~RAPass() noexcept;</a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="359"><span class="lineNum">     359 </span>            :   // [Interface]</a>
+<a name="360"><span class="lineNum">     360 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   virtual Error process(Zone* zone) noexcept override;</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :   //! Run the register allocator for a given function `func`.</a>
+<a name="365"><span class="lineNum">     365 </span>            :   virtual Error compile(CCFunc* func) noexcept;</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :   //! Called by `compile()` to prepare the register allocator to process the</a>
+<a name="368"><span class="lineNum">     368 </span>            :   //! given function. It should reset and set-up everything (i.e. no states</a>
+<a name="369"><span class="lineNum">     369 </span>            :   //! from a previous compilation should prevail).</a>
+<a name="370"><span class="lineNum">     370 </span>            :   virtual Error prepare(CCFunc* func) noexcept;</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            :   //! Called after `compile()` to clean everything up, no matter if it</a>
+<a name="373"><span class="lineNum">     373 </span>            :   //! succeeded or failed.</a>
+<a name="374"><span class="lineNum">     374 </span>            :   virtual void cleanup() noexcept;</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="377"><span class="lineNum">     377 </span>            :   // [Accessors]</a>
+<a name="378"><span class="lineNum">     378 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span>            :   //! Get the associated `CodeCompiler`.</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       3896 :   ASMJIT_INLINE CodeCompiler* cc() const noexcept { return static_cast&lt;CodeCompiler*&gt;(_cb); }</span></a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            :   //! Get function.</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       3896 :   ASMJIT_INLINE CCFunc* getFunc() const noexcept { return _func; }</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :   //! Get stop node.</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       5844 :   ASMJIT_INLINE CBNode* getStop() const noexcept { return _stop; }</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="389"><span class="lineNum">     389 </span>            :   // [State]</a>
+<a name="390"><span class="lineNum">     390 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            :   //! Get current state.</a>
+<a name="393"><span class="lineNum">     393 </span>            :   ASMJIT_INLINE RAState* getState() const { return _state; }</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            :   //! Load current state from `target` state.</a>
+<a name="396"><span class="lineNum">     396 </span>            :   virtual void loadState(RAState* src) = 0;</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            :   //! Save current state, returning new `RAState` instance.</a>
+<a name="399"><span class="lineNum">     399 </span>            :   virtual RAState* saveState() = 0;</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :   //! Change the current state to `target` state.</a>
+<a name="402"><span class="lineNum">     402 </span>            :   virtual void switchState(RAState* src) = 0;</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            :   //! Change the current state to the intersection of two states `a` and `b`.</a>
+<a name="405"><span class="lineNum">     405 </span>            :   virtual void intersectStates(RAState* a, RAState* b) = 0;</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="408"><span class="lineNum">     408 </span>            :   // [Context]</a>
+<a name="409"><span class="lineNum">     409 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            :   ASMJIT_INLINE Error assignRAId(VirtReg* vreg) noexcept {</a>
+<a name="412"><span class="lineNum">     412 </span>            :     // Likely as a single virtual register would be mostly used more than once,</a>
+<a name="413"><span class="lineNum">     413 </span>            :     // this means that each virtual register will hit one bad case (doesn't</a>
+<a name="414"><span class="lineNum">     414 </span>            :     // have id) and then all likely cases.</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">      61494 :     if (ASMJIT_LIKELY(vreg-&gt;_raId != kInvalidValue)) return kErrorOk;</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">      23788 :     uint32_t raId = static_cast&lt;uint32_t&gt;(_contextVd.getLength());</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">      23788 :     ASMJIT_PROPAGATE(_contextVd.append(&amp;_heap, vreg));</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      23788 :     vreg-&gt;_raId = raId;</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :   }</a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="425"><span class="lineNum">     425 </span>            :   // [Mem]</a>
+<a name="426"><span class="lineNum">     426 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span>            :   RACell* _newVarCell(VirtReg* vreg);</a>
+<a name="429"><span class="lineNum">     429 </span>            :   RACell* _newStackCell(uint32_t size, uint32_t alignment);</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            :   ASMJIT_INLINE RACell* getVarCell(VirtReg* vreg) {</a>
+<a name="432"><span class="lineNum">     432 </span>            :     RACell* cell = vreg-&gt;getMemCell();</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">       8428 :     return cell ? cell : _newVarCell(vreg);</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :   }</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            :   virtual Error resolveCellOffsets();</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="439"><span class="lineNum">     439 </span>            :   // [Bits]</a>
+<a name="440"><span class="lineNum">     440 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :   ASMJIT_INLINE RABits* newBits(uint32_t len) {</a>
+<a name="443"><span class="lineNum">     443 </span>            :     return static_cast&lt;RABits*&gt;(</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">       1948 :       _zone-&gt;allocZeroed(static_cast&lt;size_t&gt;(len) * RABits::kEntitySize));</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   }</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span>            :   ASMJIT_INLINE RABits* copyBits(const RABits* src, uint32_t len) {</a>
+<a name="448"><span class="lineNum">     448 </span>            :     return static_cast&lt;RABits*&gt;(</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">      36702 :       _zone-&gt;dup(src, static_cast&lt;size_t&gt;(len) * RABits::kEntitySize));</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="453"><span class="lineNum">     453 </span>            :   // [Fetch]</a>
+<a name="454"><span class="lineNum">     454 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            :   //! Fetch.</a>
+<a name="457"><span class="lineNum">     457 </span>            :   //!</a>
+<a name="458"><span class="lineNum">     458 </span>            :   //! Fetch iterates over all nodes and gathers information about all variables</a>
+<a name="459"><span class="lineNum">     459 </span>            :   //! used. The process generates information required by register allocator,</a>
+<a name="460"><span class="lineNum">     460 </span>            :   //! variable liveness analysis and translator.</a>
+<a name="461"><span class="lineNum">     461 </span>            :   virtual Error fetch() = 0;</a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="464"><span class="lineNum">     464 </span>            :   // [Unreachable Code]</a>
+<a name="465"><span class="lineNum">     465 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span>            :   //! Add unreachable-flow data to the unreachable flow list.</a>
+<a name="468"><span class="lineNum">     468 </span>            :   ASMJIT_INLINE Error addUnreachableNode(CBNode* node) {</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">       1948 :     ZoneList&lt;CBNode*&gt;::Link* link = _zone-&gt;allocT&lt;ZoneList&lt;CBNode*&gt;::Link&gt;();</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">       1948 :     if (!link) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :     link-&gt;setValue(node);</a>
+<a name="473"><span class="lineNum">     473 </span>            :     _unreachableList.append(link);</a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">       1948 :     return kErrorOk;</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :   }</a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span>            :   //! Remove unreachable code.</a>
+<a name="479"><span class="lineNum">     479 </span>            :   virtual Error removeUnreachableCode();</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="482"><span class="lineNum">     482 </span>            :   // [Code-Flow]</a>
+<a name="483"><span class="lineNum">     483 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            :   //! Add returning node (i.e. node that returns and where liveness analysis</a>
+<a name="486"><span class="lineNum">     486 </span>            :   //! should start).</a>
+<a name="487"><span class="lineNum">     487 </span>            :   ASMJIT_INLINE Error addReturningNode(CBNode* node) {</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">       1948 :     ZoneList&lt;CBNode*&gt;::Link* link = _zone-&gt;allocT&lt;ZoneList&lt;CBNode*&gt;::Link&gt;();</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">       1948 :     if (!link) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            :     link-&gt;setValue(node);</a>
+<a name="492"><span class="lineNum">     492 </span>            :     _returningList.append(link);</a>
+<a name="493"><span class="lineNum">     493 </span>            : </a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">       1948 :     return kErrorOk;</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :   }</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span>            :   //! Add jump-flow data to the jcc flow list.</a>
+<a name="498"><span class="lineNum">     498 </span>            :   ASMJIT_INLINE Error addJccNode(CBNode* node) {</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :     ZoneList&lt;CBNode*&gt;::Link* link = _zone-&gt;allocT&lt;ZoneList&lt;CBNode*&gt;::Link&gt;();</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :     if (!link) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            :     link-&gt;setValue(node);</a>
+<a name="503"><span class="lineNum">     503 </span>            :     _jccList.append(link);</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :   }</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="509"><span class="lineNum">     509 </span>            :   // [Analyze]</a>
+<a name="510"><span class="lineNum">     510 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            :   //! Perform variable liveness analysis.</a>
+<a name="513"><span class="lineNum">     513 </span>            :   //!</a>
+<a name="514"><span class="lineNum">     514 </span>            :   //! Analysis phase iterates over nodes in reverse order and generates a bit</a>
+<a name="515"><span class="lineNum">     515 </span>            :   //! array describing variables that are alive at every node in the function.</a>
+<a name="516"><span class="lineNum">     516 </span>            :   //! When the analysis start all variables are assumed dead. When a read or</a>
+<a name="517"><span class="lineNum">     517 </span>            :   //! read/write operations of a variable is detected the variable becomes</a>
+<a name="518"><span class="lineNum">     518 </span>            :   //! alive; when only write operation is detected the variable becomes dead.</a>
+<a name="519"><span class="lineNum">     519 </span>            :   //!</a>
+<a name="520"><span class="lineNum">     520 </span>            :   //! When a label is found all jumps to that label are followed and analysis</a>
+<a name="521"><span class="lineNum">     521 </span>            :   //! repeats until all variables are resolved.</a>
+<a name="522"><span class="lineNum">     522 </span>            :   virtual Error livenessAnalysis();</a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="525"><span class="lineNum">     525 </span>            :   // [Annotate]</a>
+<a name="526"><span class="lineNum">     526 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span>            :   virtual Error annotate() = 0;</a>
+<a name="529"><span class="lineNum">     529 </span>            :   virtual Error formatInlineComment(StringBuilder&amp; dst, CBNode* node);</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="532"><span class="lineNum">     532 </span>            :   // [Translate]</a>
+<a name="533"><span class="lineNum">     533 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            :   //! Translate code by allocating registers and handling state changes.</a>
+<a name="536"><span class="lineNum">     536 </span>            :   virtual Error translate() = 0;</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="539"><span class="lineNum">     539 </span>            :   // [Members]</a>
+<a name="540"><span class="lineNum">     540 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span>            :   Zone* _zone;                           //!&lt; Zone passed to `process()`.</a>
+<a name="543"><span class="lineNum">     543 </span>            :   ZoneHeap _heap;                        //!&lt; ZoneHeap that uses `_zone`.</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span>            :   CCFunc* _func;                         //!&lt; Function being processed.</a>
+<a name="546"><span class="lineNum">     546 </span>            :   CBNode* _stop;                         //!&lt; Stop node.</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            :   //! \internal</a>
+<a name="549"><span class="lineNum">     549 </span>            :   //!</a>
+<a name="550"><span class="lineNum">     550 </span>            :   //! Offset (how many bytes to add) to `VarMap` to get `TiedReg` array. Used</a>
+<a name="551"><span class="lineNum">     551 </span>            :   //! by liveness analysis shared across all backends. This is needed because</a>
+<a name="552"><span class="lineNum">     552 </span>            :   //! `VarMap` is a base class for a specialized version that liveness analysis</a>
+<a name="553"><span class="lineNum">     553 </span>            :   //! doesn't use, it just needs `TiedReg` array.</a>
+<a name="554"><span class="lineNum">     554 </span>            :   uint32_t _varMapToVaListOffset;</a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            :   uint8_t _emitComments;                 //!&lt; Whether to emit comments.</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            :   ZoneList&lt;CBNode*&gt; _unreachableList;     //!&lt; Unreachable nodes.</a>
+<a name="559"><span class="lineNum">     559 </span>            :   ZoneList&lt;CBNode*&gt; _returningList;       //!&lt; Returning nodes.</a>
+<a name="560"><span class="lineNum">     560 </span>            :   ZoneList&lt;CBNode*&gt; _jccList;             //!&lt; Jump nodes.</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span>            :   ZoneVector&lt;VirtReg*&gt; _contextVd;       //!&lt; All variables used by the current function.</a>
+<a name="563"><span class="lineNum">     563 </span>            :   RACell* _memVarCells;                  //!&lt; Memory used to spill variables.</a>
+<a name="564"><span class="lineNum">     564 </span>            :   RACell* _memStackCells;                //!&lt; Memory used to allocate memory on the stack.</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span>            :   uint32_t _mem1ByteVarsUsed;            //!&lt; Count of 1-byte cells.</a>
+<a name="567"><span class="lineNum">     567 </span>            :   uint32_t _mem2ByteVarsUsed;            //!&lt; Count of 2-byte cells.</a>
+<a name="568"><span class="lineNum">     568 </span>            :   uint32_t _mem4ByteVarsUsed;            //!&lt; Count of 4-byte cells.</a>
+<a name="569"><span class="lineNum">     569 </span>            :   uint32_t _mem8ByteVarsUsed;            //!&lt; Count of 8-byte cells.</a>
+<a name="570"><span class="lineNum">     570 </span>            :   uint32_t _mem16ByteVarsUsed;           //!&lt; Count of 16-byte cells.</a>
+<a name="571"><span class="lineNum">     571 </span>            :   uint32_t _mem32ByteVarsUsed;           //!&lt; Count of 32-byte cells.</a>
+<a name="572"><span class="lineNum">     572 </span>            :   uint32_t _mem64ByteVarsUsed;           //!&lt; Count of 64-byte cells.</a>
+<a name="573"><span class="lineNum">     573 </span>            :   uint32_t _memStackCellsUsed;           //!&lt; Count of stack memory cells.</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span>            :   uint32_t _memMaxAlign;                 //!&lt; Maximum memory alignment used by the function.</a>
+<a name="576"><span class="lineNum">     576 </span>            :   uint32_t _memVarTotal;                 //!&lt; Count of bytes used by variables.</a>
+<a name="577"><span class="lineNum">     577 </span>            :   uint32_t _memStackTotal;               //!&lt; Count of bytes used by stack.</a>
+<a name="578"><span class="lineNum">     578 </span>            :   uint32_t _memAllTotal;                 //!&lt; Count of bytes used by variables and stack after alignment.</a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span>            :   uint32_t _annotationLength;            //!&lt; Default length of an annotated instruction.</a>
+<a name="581"><span class="lineNum">     581 </span>            :   RAState* _state;                       //!&lt; Current RA state.</a>
+<a name="582"><span class="lineNum">     582 </span>            : };</a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span>            : //! \}</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span>            : } // asmjit namespace</a>
+<a name="587"><span class="lineNum">     587 </span>            : } // namespace PLMD</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span>            : // [Api-End]</a>
+<a name="590"><span class="lineNum">     590 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            : // [Guard]</a>
+<a name="593"><span class="lineNum">     593 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="594"><span class="lineNum">     594 </span>            : #endif // _ASMJIT_BASE_REGALLOC_P_H</a>
+<a name="595"><span class="lineNum">     595 </span>            : #pragma GCC diagnostic pop</a>
+<a name="596"><span class="lineNum">     596 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="597"><span class="lineNum">     597 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/runtime.cpp.func-sort-c.html b/coverage-libs/asmjit/runtime.cpp.func-sort-c.html
new file mode 100644
index 0000000000..745f50ee3c
--- /dev/null
+++ b/coverage-libs/asmjit/runtime.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/runtime.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - runtime.cpp<span style="font-size: 80%;"> (<a href="runtime.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryLo">73.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="runtime.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#161">_ZN4PLMD6asmjit10JitRuntime8_releaseEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#110">_ZN4PLMD6asmjit11HostRuntimeD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#94">_ZN4PLMD6asmjit7RuntimeD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#131">_ZN4PLMD6asmjit10JitRuntime4_addEPPvPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#116">_ZN4PLMD6asmjit11HostRuntime5flushEPKvm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#124">_ZN4PLMD6asmjit10JitRuntimeC2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#125">_ZN4PLMD6asmjit10JitRuntimeD0Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#125">_ZN4PLMD6asmjit10JitRuntimeD2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#100">_ZN4PLMD6asmjit11HostRuntimeC2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#110">_ZN4PLMD6asmjit11HostRuntimeD2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#90">_ZN4PLMD6asmjit7RuntimeC2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#94">_ZN4PLMD6asmjit7RuntimeD2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/runtime.cpp.func.html b/coverage-libs/asmjit/runtime.cpp.func.html
new file mode 100644
index 0000000000..7bea935f63
--- /dev/null
+++ b/coverage-libs/asmjit/runtime.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/runtime.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - runtime.cpp<span style="font-size: 80%;"> (<a href="runtime.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryLo">73.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="runtime.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="runtime.cpp.gcov.html#131">_ZN4PLMD6asmjit10JitRuntime4_addEPPvPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="runtime.cpp.gcov.html#116">_ZN4PLMD6asmjit11HostRuntime5flushEPKvm</a></td>
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+              <td class="coverFn"><a href="runtime.cpp.gcov.html#100">_ZN4PLMD6asmjit11HostRuntimeC2Ev</a></td>
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+              <td class="coverFn"><a href="runtime.cpp.gcov.html#110">_ZN4PLMD6asmjit11HostRuntimeD2Ev</a></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/runtime.cpp.gcov.html b/coverage-libs/asmjit/runtime.cpp.gcov.html
new file mode 100644
index 0000000000..e612720fd7
--- /dev/null
+++ b/coverage-libs/asmjit/runtime.cpp.gcov.html
@@ -0,0 +1,249 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/runtime.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - runtime.cpp<span style="font-size: 80%;"> (source / <a href="runtime.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryLo">73.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./runtime.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : // [Api-Begin]</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace asmjit {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : static ASMJIT_INLINE void hostFlushInstructionCache(const void* p, size_t size) noexcept {</a>
+<a name="44"><span class="lineNum">      44 </span>            :   // Only useful on non-x86 architectures.</a>
+<a name="45"><span class="lineNum">      45 </span>            : #if !ASMJIT_ARCH_X86 &amp;&amp; !ASMJIT_ARCH_X64</a>
+<a name="46"><span class="lineNum">      46 </span>            : # if ASMJIT_OS_WINDOWS</a>
+<a name="47"><span class="lineNum">      47 </span>            :   // Windows has a built-in support in kernel32.dll.</a>
+<a name="48"><span class="lineNum">      48 </span>            :   ::FlushInstructionCache(_memMgr.getProcessHandle(), p, size);</a>
+<a name="49"><span class="lineNum">      49 </span>            : # endif // ASMJIT_OS_WINDOWS</a>
+<a name="50"><span class="lineNum">      50 </span>            : #else</a>
+<a name="51"><span class="lineNum">      51 </span>            :   ASMJIT_UNUSED(p);</a>
+<a name="52"><span class="lineNum">      52 </span>            :   ASMJIT_UNUSED(size);</a>
+<a name="53"><span class="lineNum">      53 </span>            : #endif // !ASMJIT_ARCH_X86 &amp;&amp; !ASMJIT_ARCH_X64</a>
+<a name="54"><span class="lineNum">      54 </span>            : }</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : static ASMJIT_INLINE uint32_t hostDetectNaturalStackAlignment() noexcept {</a>
+<a name="57"><span class="lineNum">      57 </span>            :   // Alignment is assumed to match the pointer-size by default.</a>
+<a name="58"><span class="lineNum">      58 </span>            :   uint32_t alignment = sizeof(intptr_t);</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            :   // X86 &amp; X64</a>
+<a name="61"><span class="lineNum">      61 </span>            :   // ---------</a>
+<a name="62"><span class="lineNum">      62 </span>            :   //</a>
+<a name="63"><span class="lineNum">      63 </span>            :   //   - 32-bit X86 requires stack to be aligned to 4 bytes. Modern Linux, Mac</a>
+<a name="64"><span class="lineNum">      64 </span>            :   //     and UNIX guarantees 16-byte stack alignment even on 32-bit. I'm not</a>
+<a name="65"><span class="lineNum">      65 </span>            :   //     sure about all other UNIX operating systems, because 16-byte alignment</a>
+<a name="66"><span class="lineNum">      66 </span>            :   //!    is addition to an older specification.</a>
+<a name="67"><span class="lineNum">      67 </span>            :   //   - 64-bit X86 requires stack to be aligned to at least 16 bytes.</a>
+<a name="68"><span class="lineNum">      68 </span>            : #if ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="69"><span class="lineNum">      69 </span>            :   int kIsModernOS = ASMJIT_OS_LINUX  || // Linux &amp; ANDROID.</a>
+<a name="70"><span class="lineNum">      70 </span>            :                     ASMJIT_OS_MAC    || // OSX and iOS.</a>
+<a name="71"><span class="lineNum">      71 </span>            :                     ASMJIT_OS_BSD    ;  // BSD variants.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   alignment = ASMJIT_ARCH_X64 || kIsModernOS ? 16 : 4;</a>
+<a name="73"><span class="lineNum">      73 </span>            : #endif</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   // ARM32 &amp; ARM64</a>
+<a name="76"><span class="lineNum">      76 </span>            :   // -------------</a>
+<a name="77"><span class="lineNum">      77 </span>            :   //</a>
+<a name="78"><span class="lineNum">      78 </span>            :   //   - 32-bit ARM requires stack to be aligned to 8 bytes.</a>
+<a name="79"><span class="lineNum">      79 </span>            :   //   - 64-bit ARM requires stack to be aligned to 16 bytes.</a>
+<a name="80"><span class="lineNum">      80 </span>            : #if ASMJIT_ARCH_ARM32 || ASMJIT_ARCH_ARM64</a>
+<a name="81"><span class="lineNum">      81 </span>            :   alignment = ASMJIT_ARCH_ARM32 ? 8 : 16;</a>
+<a name="82"><span class="lineNum">      82 </span>            : #endif</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   return alignment;</a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : // ============================================================================</a>
+<a name="89"><span class="lineNum">      89 </span>            : // [asmjit::Runtime - Construction / Destruction]</a>
+<a name="90"><span class="lineNum">      90 </span>            : // ============================================================================</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1976 : Runtime::Runtime() noexcept</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   : _codeInfo(),</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1976 :     _runtimeType(kRuntimeNone),</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1976 :     _allocType(VMemMgr::kAllocFreeable) {}</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1976 : Runtime::~Runtime() noexcept {}</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : // ============================================================================</a>
+<a name="99"><span class="lineNum">      99 </span>            : // [asmjit::HostRuntime - Construction / Destruction]</a>
+<a name="100"><span class="lineNum">     100 </span>            : // ============================================================================</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       1976 : HostRuntime::HostRuntime() noexcept {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1976 :   _runtimeType = kRuntimeJit;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Setup the CodeInfo of this Runtime.</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1976 :   _codeInfo._archInfo       = CpuInfo::getHost().getArchInfo();</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1976 :   _codeInfo._stackAlignment = static_cast&lt;uint8_t&gt;(hostDetectNaturalStackAlignment());</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1976 :   _codeInfo._cdeclCallConv  = CallConv::kIdHostCDecl;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1976 :   _codeInfo._stdCallConv    = CallConv::kIdHostStdCall;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       1976 :   _codeInfo._fastCallConv   = CallConv::kIdHostFastCall;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1976 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1976 : HostRuntime::~HostRuntime() noexcept {}</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : // ============================================================================</a>
+<a name="115"><span class="lineNum">     115 </span>            : // [asmjit::HostRuntime - Interface]</a>
+<a name="116"><span class="lineNum">     116 </span>            : // ============================================================================</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1948 : void HostRuntime::flush(const void* p, size_t size) noexcept {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   hostFlushInstructionCache(p, size);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1948 : }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : // ============================================================================</a>
+<a name="123"><span class="lineNum">     123 </span>            : // [asmjit::JitRuntime - Construction / Destruction]</a>
+<a name="124"><span class="lineNum">     124 </span>            : // ============================================================================</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       1976 : JitRuntime::JitRuntime() noexcept {}</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       3952 : JitRuntime::~JitRuntime() noexcept {}</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : // ============================================================================</a>
+<a name="130"><span class="lineNum">     130 </span>            : // [asmjit::JitRuntime - Interface]</a>
+<a name="131"><span class="lineNum">     131 </span>            : // ============================================================================</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       1948 : Error JitRuntime::_add(void** dst, CodeHolder* code) noexcept {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1948 :   size_t codeSize = code-&gt;getCodeSize();</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(codeSize == 0)) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     *dst = nullptr;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     return DebugUtils::errored(kErrorNoCodeGenerated);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1948 :   void* p = _memMgr.alloc(codeSize, getAllocType());</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(!p)) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     *dst = nullptr;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     return DebugUtils::errored(kErrorNoVirtualMemory);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Relocate the code and release the unused memory back to `VMemMgr`.</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1948 :   size_t relocSize = code-&gt;relocate(p);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(relocSize == 0)) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     *dst = nullptr;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :     _memMgr.release(p);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     return DebugUtils::errored(kErrorInvalidState);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1948 :   if (relocSize &lt; codeSize)</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     _memMgr.shrink(p, relocSize);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1948 :   flush(p, relocSize);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1948 :   *dst = p;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 : Error JitRuntime::_release(void* p) noexcept {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   return _memMgr.release(p);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : } // asmjit namespace</a>
+<a name="168"><span class="lineNum">     168 </span>            : } // namespace PLMD</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : // [Api-End]</a>
+<a name="171"><span class="lineNum">     171 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="172"><span class="lineNum">     172 </span>            : #pragma GCC diagnostic pop</a>
+<a name="173"><span class="lineNum">     173 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/runtime.h.func-sort-c.html b/coverage-libs/asmjit/runtime.h.func-sort-c.html
new file mode 100644
index 0000000000..689bfa03ce
--- /dev/null
+++ b/coverage-libs/asmjit/runtime.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/runtime.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - runtime.h<span style="font-size: 80%;"> (<a href="runtime.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="runtime.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/runtime.h.func.html b/coverage-libs/asmjit/runtime.h.func.html
new file mode 100644
index 0000000000..e2defa812b
--- /dev/null
+++ b/coverage-libs/asmjit/runtime.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/runtime.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - runtime.h<span style="font-size: 80%;"> (<a href="runtime.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="runtime.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/runtime.h.gcov.html b/coverage-libs/asmjit/runtime.h.gcov.html
new file mode 100644
index 0000000000..29bae50954
--- /dev/null
+++ b/coverage-libs/asmjit/runtime.h.gcov.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/runtime.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - runtime.h<span style="font-size: 80%;"> (source / <a href="runtime.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_runtime_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_runtime_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_RUNTIME_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_RUNTIME_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./codeholder.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./vmem.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // ============================================================================</a>
+<a name="46"><span class="lineNum">      46 </span>            : // [Forward Declarations]</a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : class CodeHolder;</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! \addtogroup asmjit_base</a>
+<a name="52"><span class="lineNum">      52 </span>            : //! \{</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : // ============================================================================</a>
+<a name="55"><span class="lineNum">      55 </span>            : // [asmjit::Runtime]</a>
+<a name="56"><span class="lineNum">      56 </span>            : // ============================================================================</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : //! Base runtime.</a>
+<a name="59"><span class="lineNum">      59 </span>            : class ASMJIT_VIRTAPI Runtime {</a>
+<a name="60"><span class="lineNum">      60 </span>            : public:</a>
+<a name="61"><span class="lineNum">      61 </span>            :   ASMJIT_NONCOPYABLE(Runtime)</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            :   ASMJIT_ENUM(RuntimeType) {</a>
+<a name="64"><span class="lineNum">      64 </span>            :     kRuntimeNone = 0,</a>
+<a name="65"><span class="lineNum">      65 </span>            :     kRuntimeJit = 1,</a>
+<a name="66"><span class="lineNum">      66 </span>            :     kRuntimeRemote = 2</a>
+<a name="67"><span class="lineNum">      67 </span>            :   };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="70"><span class="lineNum">      70 </span>            :   // [Construction / Destruction]</a>
+<a name="71"><span class="lineNum">      71 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   //! Create a `Runtime` instance.</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ASMJIT_API Runtime() noexcept;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   //! Destroy the `Runtime` instance.</a>
+<a name="76"><span class="lineNum">      76 </span>            :   ASMJIT_API virtual ~Runtime() noexcept;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="79"><span class="lineNum">      79 </span>            :   // [Accessors]</a>
+<a name="80"><span class="lineNum">      80 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   //! Get CodeInfo of this runtime.</a>
+<a name="83"><span class="lineNum">      83 </span>            :   //!</a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! CodeInfo can be used to setup a CodeHolder in case you plan to generate a</a>
+<a name="85"><span class="lineNum">      85 </span>            :   //! code compatible and executable by this Runtime.</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1948 :   ASMJIT_INLINE const CodeInfo&amp; getCodeInfo() const noexcept { return _codeInfo; }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :   //! Get the Runtime's architecture type, see \ref ArchInfo::Type.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   ASMJIT_INLINE uint32_t getArchType() const noexcept { return _codeInfo.getArchType(); }</a>
+<a name="90"><span class="lineNum">      90 </span>            :   //! Get the Runtime's architecture sub-type, see \ref ArchInfo::SubType.</a>
+<a name="91"><span class="lineNum">      91 </span>            :   ASMJIT_INLINE uint32_t getArchSubType() const noexcept { return _codeInfo.getArchSubType(); }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   //! Get the runtime type, see \ref Type.</a>
+<a name="94"><span class="lineNum">      94 </span>            :   ASMJIT_INLINE uint32_t getRuntimeType() const noexcept { return _runtimeType; }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // [Interface]</a>
+<a name="98"><span class="lineNum">      98 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   // NOTE: To allow passing function pointers to `add()` and `release()` the</a>
+<a name="101"><span class="lineNum">     101 </span>            :   // virtual methods are prefixed with `_` and called from templates.</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   template&lt;typename Func&gt;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   ASMJIT_INLINE Error add(Func* dst, CodeHolder* code) noexcept {</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1948 :     return _add(Internal::ptr_cast&lt;void**, Func*&gt;(dst), code);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   template&lt;typename Func&gt;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ASMJIT_INLINE Error release(Func dst) noexcept {</a>
+<a name="110"><span class="lineNum">     110 </span>            :     return _release(Internal::ptr_cast&lt;void*, Func&gt;(dst));</a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Allocate a memory needed for a code stored in the \ref CodeHolder and</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //! relocate it to the target location.</a>
+<a name="115"><span class="lineNum">     115 </span>            :   //!</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //! The beginning of the memory allocated for the function is returned in</a>
+<a name="117"><span class="lineNum">     117 </span>            :   //! `dst`. If failed the \ref Error code is returned and `dst` is set to null</a>
+<a name="118"><span class="lineNum">     118 </span>            :   //! (this means that you don't have to set it to null before calling `add()`).</a>
+<a name="119"><span class="lineNum">     119 </span>            :   virtual Error _add(void** dst, CodeHolder* code) noexcept = 0;</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   //! Release `p` allocated by `add()`.</a>
+<a name="122"><span class="lineNum">     122 </span>            :   virtual Error _release(void* p) noexcept = 0;</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="125"><span class="lineNum">     125 </span>            :   // [Members]</a>
+<a name="126"><span class="lineNum">     126 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   CodeInfo _codeInfo;                    //!&lt; Basic information about the Runtime's code.</a>
+<a name="129"><span class="lineNum">     129 </span>            :   uint8_t _runtimeType;                  //!&lt; Type of the runtime.</a>
+<a name="130"><span class="lineNum">     130 </span>            :   uint8_t _allocType;                    //!&lt; Type of the allocator the Runtime uses.</a>
+<a name="131"><span class="lineNum">     131 </span>            :   uint8_t _reserved[6];                  //!&lt; \internal</a>
+<a name="132"><span class="lineNum">     132 </span>            : };</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : // ============================================================================</a>
+<a name="135"><span class="lineNum">     135 </span>            : // [asmjit::HostRuntime]</a>
+<a name="136"><span class="lineNum">     136 </span>            : // ============================================================================</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : //! Runtime designed to be used in the same process the code is generated in.</a>
+<a name="139"><span class="lineNum">     139 </span>            : class ASMJIT_VIRTAPI HostRuntime : public Runtime {</a>
+<a name="140"><span class="lineNum">     140 </span>            : public:</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ASMJIT_NONCOPYABLE(HostRuntime)</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="144"><span class="lineNum">     144 </span>            :   // [Construction / Destruction]</a>
+<a name="145"><span class="lineNum">     145 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   //! Create a `HostRuntime` instance.</a>
+<a name="148"><span class="lineNum">     148 </span>            :   ASMJIT_API HostRuntime() noexcept;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   //! Destroy the `HostRuntime` instance.</a>
+<a name="150"><span class="lineNum">     150 </span>            :   ASMJIT_API virtual ~HostRuntime() noexcept;</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="153"><span class="lineNum">     153 </span>            :   // [Interface]</a>
+<a name="154"><span class="lineNum">     154 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :   //! Flush an instruction cache.</a>
+<a name="157"><span class="lineNum">     157 </span>            :   //!</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //! This member function is called after the code has been copied to the</a>
+<a name="159"><span class="lineNum">     159 </span>            :   //! destination buffer. It is only useful for JIT code generation as it</a>
+<a name="160"><span class="lineNum">     160 </span>            :   //! causes a flush of the processor's cache.</a>
+<a name="161"><span class="lineNum">     161 </span>            :   //!</a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! Flushing is basically a NOP under X86/X64, but is needed by architectures</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //! that do not have a transparent instruction cache like ARM.</a>
+<a name="164"><span class="lineNum">     164 </span>            :   //!</a>
+<a name="165"><span class="lineNum">     165 </span>            :   //! This function can also be overridden to improve compatibility with tools</a>
+<a name="166"><span class="lineNum">     166 </span>            :   //! such as Valgrind, however, it's not an official part of AsmJit.</a>
+<a name="167"><span class="lineNum">     167 </span>            :   ASMJIT_API virtual void flush(const void* p, size_t size) noexcept;</a>
+<a name="168"><span class="lineNum">     168 </span>            : };</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : // ============================================================================</a>
+<a name="171"><span class="lineNum">     171 </span>            : // [asmjit::JitRuntime]</a>
+<a name="172"><span class="lineNum">     172 </span>            : // ============================================================================</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : //! Runtime designed to store and execute code generated at runtime (JIT).</a>
+<a name="175"><span class="lineNum">     175 </span>            : class ASMJIT_VIRTAPI JitRuntime : public HostRuntime {</a>
+<a name="176"><span class="lineNum">     176 </span>            : public:</a>
+<a name="177"><span class="lineNum">     177 </span>            :   ASMJIT_NONCOPYABLE(JitRuntime)</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="180"><span class="lineNum">     180 </span>            :   // [Construction / Destruction]</a>
+<a name="181"><span class="lineNum">     181 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   //! Create a `JitRuntime` instance.</a>
+<a name="184"><span class="lineNum">     184 </span>            :   ASMJIT_API JitRuntime() noexcept;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   //! Destroy the `JitRuntime` instance.</a>
+<a name="186"><span class="lineNum">     186 </span>            :   ASMJIT_API virtual ~JitRuntime() noexcept;</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // [Accessors]</a>
+<a name="190"><span class="lineNum">     190 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   //! Get the type of allocation.</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       1948 :   ASMJIT_INLINE uint32_t getAllocType() const noexcept { return _allocType; }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   //! Set the type of allocation.</a>
+<a name="195"><span class="lineNum">     195 </span>            :   ASMJIT_INLINE void setAllocType(uint32_t allocType) noexcept { _allocType = allocType; }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   //! Get the virtual memory manager.</a>
+<a name="198"><span class="lineNum">     198 </span>            :   ASMJIT_INLINE VMemMgr* getMemMgr() const noexcept { return const_cast&lt;VMemMgr*&gt;(&amp;_memMgr); }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="201"><span class="lineNum">     201 </span>            :   // [Interface]</a>
+<a name="202"><span class="lineNum">     202 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :   ASMJIT_API Error _add(void** dst, CodeHolder* code) noexcept override;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   ASMJIT_API Error _release(void* p) noexcept override;</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="208"><span class="lineNum">     208 </span>            :   // [Members]</a>
+<a name="209"><span class="lineNum">     209 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   //! Virtual memory manager.</a>
+<a name="212"><span class="lineNum">     212 </span>            :   VMemMgr _memMgr;</a>
+<a name="213"><span class="lineNum">     213 </span>            : };</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : //! \}</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : } // asmjit namespace</a>
+<a name="218"><span class="lineNum">     218 </span>            : } // namespace PLMD</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : // [Api-End]</a>
+<a name="221"><span class="lineNum">     221 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : // [Guard]</a>
+<a name="224"><span class="lineNum">     224 </span>            : #endif // _ASMJIT_BASE_RUNTIME_H</a>
+<a name="225"><span class="lineNum">     225 </span>            : #pragma GCC diagnostic pop</a>
+<a name="226"><span class="lineNum">     226 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="227"><span class="lineNum">     227 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/string.cpp.func-sort-c.html b/coverage-libs/asmjit/string.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5c57f600f1
--- /dev/null
+++ b/coverage-libs/asmjit/string.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/string.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - string.cpp<span style="font-size: 80%;"> (<a href="string.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="string.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="string.cpp.gcov.html#319">_ZN4PLMD6asmjit13StringBuilder10_opVFormatEjPKcP13__va_list_tag</a></td>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="string.cpp.gcov.html#47">_ZN4PLMD6asmjit13StringBuilderC2Ev</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="string.cpp.gcov.html#53">_ZN4PLMD6asmjit13StringBuilderD2Ev</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="string.cpp.gcov.html#350">_ZNK4PLMD6asmjit13StringBuilder2eqEPKcm</a></td>
+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/string.cpp.func.html b/coverage-libs/asmjit/string.cpp.func.html
new file mode 100644
index 0000000000..2c7f7cc7cb
--- /dev/null
+++ b/coverage-libs/asmjit/string.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/string.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - string.cpp<span style="font-size: 80%;"> (<a href="string.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="string.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/string.cpp.gcov.html b/coverage-libs/asmjit/string.cpp.gcov.html
new file mode 100644
index 0000000000..f3f649a3b6
--- /dev/null
+++ b/coverage-libs/asmjit/string.cpp.gcov.html
@@ -0,0 +1,455 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/string.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - string.cpp<span style="font-size: 80%;"> (source / <a href="string.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./moved_string.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Api-Begin]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace asmjit {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // ============================================================================</a>
+<a name="43"><span class="lineNum">      43 </span>            : // [asmjit::StringBuilder - Construction / Destruction]</a>
+<a name="44"><span class="lineNum">      44 </span>            : // ============================================================================</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : // Should be placed in read-only memory.</a>
+<a name="47"><span class="lineNum">      47 </span>            : static const char StringBuilder_empty[4] = { 0 };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 : StringBuilder::StringBuilder() noexcept</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :   : _data(const_cast&lt;char*&gt;(StringBuilder_empty)),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :     _length(0),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :     _capacity(0),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :     _canFree(false) {}</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 : StringBuilder::~StringBuilder() noexcept {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   if (_canFree)</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :     Internal::releaseMemory(_data);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : // ============================================================================</a>
+<a name="61"><span class="lineNum">      61 </span>            : // [asmjit::StringBuilder - Prepare / Reserve]</a>
+<a name="62"><span class="lineNum">      62 </span>            : // ============================================================================</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE char* StringBuilder::prepare(uint32_t op, size_t len) noexcept {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   if (op == kStringOpSet) {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :     // We don't care here, but we can't return a null pointer since it indicates</a>
+<a name="67"><span class="lineNum">      67 </span>            :     // failure in memory allocation.</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :     if (len == 0) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :       if (_data != StringBuilder_empty)</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :         _data[0] = 0;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :       _length = 0;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :       return _data;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :     }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :     if (_capacity &lt; len) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :       if (len &gt;= IntTraits&lt;size_t&gt;::maxValue() - sizeof(intptr_t) * 2)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :         return nullptr;</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :       size_t to = Utils::alignTo&lt;size_t&gt;(len, sizeof(intptr_t));</a>
+<a name="81"><span class="lineNum">      81 </span>            :       if (to &lt; 256 - sizeof(intptr_t))</a>
+<a name="82"><span class="lineNum">      82 </span>            :         to = 256 - sizeof(intptr_t);</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :       char* newData = static_cast&lt;char*&gt;(Internal::allocMemory(to + sizeof(intptr_t)));</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :       if (!newData) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :         clear();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :         return nullptr;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :       }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :       if (_canFree)</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :         Internal::releaseMemory(_data);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :       _data = newData;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :       _capacity = to + sizeof(intptr_t) - 1;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :       _canFree = true;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :     }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     _data[len] = 0;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     _length = len;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :     ASMJIT_ASSERT(_length &lt;= _capacity);</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :     return _data;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span>            :   else {</a>
+<a name="105"><span class="lineNum">     105 </span>            :     // We don't care here, but we can't return a null pointer since it indicates</a>
+<a name="106"><span class="lineNum">     106 </span>            :     // failure of memory allocation.</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     if (len == 0)</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :       return _data + _length;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :     // Overflow.</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     if (IntTraits&lt;size_t&gt;::maxValue() - sizeof(intptr_t) * 2 - _length &lt; len)</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :       return nullptr;</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     size_t after = _length + len;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     if (_capacity &lt; after) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :       size_t to = _capacity;</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :       if (to &lt; 256)</a>
+<a name="119"><span class="lineNum">     119 </span>            :         to = 256;</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       while (to &lt; 1024 * 1024 &amp;&amp; to &lt; after)</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :         to *= 2;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :       if (to &lt; after) {</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :         to = after;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :         if (to &lt; (IntTraits&lt;size_t&gt;::maxValue() - 1024 * 32))</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :           to = Utils::alignTo&lt;size_t&gt;(to, 1024 * 32);</a>
+<a name="128"><span class="lineNum">     128 </span>            :       }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :       to = Utils::alignTo&lt;size_t&gt;(to, sizeof(intptr_t));</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :       char* newData = static_cast&lt;char*&gt;(Internal::allocMemory(to + sizeof(intptr_t)));</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :       if (!newData) return nullptr;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :       ::memcpy(newData, _data, _length);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :       if (_canFree)</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :         Internal::releaseMemory(_data);</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :       _data = newData;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :       _capacity = to + sizeof(intptr_t) - 1;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       _canFree = true;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     char* ret = _data + _length;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :     _data[after] = 0;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     _length = after;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :     ASMJIT_ASSERT(_length &lt;= _capacity);</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :     return ret;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error StringBuilder::reserve(size_t to) noexcept {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   if (_capacity &gt;= to)</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     return kErrorOk;</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   if (to &gt;= IntTraits&lt;size_t&gt;::maxValue() - sizeof(intptr_t) * 2)</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   to = Utils::alignTo&lt;size_t&gt;(to, sizeof(intptr_t));</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :   char* newData = static_cast&lt;char*&gt;(Internal::allocMemory(to + sizeof(intptr_t)));</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :   if (!newData)</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :   ::memcpy(newData, _data, _length + 1);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   if (_canFree)</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :     Internal::releaseMemory(_data);</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :   _data = newData;</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :   _capacity = to + sizeof(intptr_t) - 1;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   _canFree = true;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : // ============================================================================</a>
+<a name="176"><span class="lineNum">     176 </span>            : // [asmjit::StringBuilder - Clear]</a>
+<a name="177"><span class="lineNum">     177 </span>            : // ============================================================================</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 : void StringBuilder::clear() noexcept {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   if (_data != StringBuilder_empty)</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     _data[0] = 0;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   _length = 0;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : // ============================================================================</a>
+<a name="186"><span class="lineNum">     186 </span>            : // [asmjit::StringBuilder - Methods]</a>
+<a name="187"><span class="lineNum">     187 </span>            : // ============================================================================</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 : Error StringBuilder::_opString(uint32_t op, const char* str, size_t len) noexcept {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   if (len == Globals::kInvalidIndex)</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     len = str ? ::strlen(str) : static_cast&lt;size_t&gt;(0);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :   char* p = prepare(op, len);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   if (!p) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   ::memcpy(p, str, len);</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 : Error StringBuilder::_opChar(uint32_t op, char c) noexcept {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   char* p = prepare(op, 1);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   if (!p) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   *p = c;</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 : Error StringBuilder::_opChars(uint32_t op, char c, size_t n) noexcept {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :   char* p = prepare(op, n);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   if (!p) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   ::memset(p, c, n);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : static const char StringBuilder_numbers[] = &quot;0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ&quot;;</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 : Error StringBuilder::_opNumber(uint32_t op, uint64_t i, uint32_t base, size_t width, uint32_t flags) noexcept {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   if (base &lt; 2 || base &gt; 36)</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :     base = 10;</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   char buf[128];</a>
+<a name="223"><span class="lineNum">     223 </span>            :   char* p = buf + ASMJIT_ARRAY_SIZE(buf);</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   uint64_t orig = i;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   char sign = '\0';</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="229"><span class="lineNum">     229 </span>            :   // [Sign]</a>
+<a name="230"><span class="lineNum">     230 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :   if ((flags &amp; kStringFormatSigned) != 0 &amp;&amp; static_cast&lt;int64_t&gt;(i) &lt; 0) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :     i = static_cast&lt;uint64_t&gt;(-static_cast&lt;int64_t&gt;(i));</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     sign = '-';</a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   else if ((flags &amp; kStringFormatShowSign) != 0) {</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     sign = '+';</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   else if ((flags &amp; kStringFormatShowSpace) != 0) {</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :     sign = ' ';</a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="244"><span class="lineNum">     244 </span>            :   // [Number]</a>
+<a name="245"><span class="lineNum">     245 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :   do {</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :     uint64_t d = i / base;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :     uint64_t r = i % base;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     *--p = StringBuilder_numbers[r];</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     i = d;</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :   } while (i);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :   size_t numberLength = (size_t)(buf + ASMJIT_ARRAY_SIZE(buf) - p);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="258"><span class="lineNum">     258 </span>            :   // [Alternate Form]</a>
+<a name="259"><span class="lineNum">     259 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   if ((flags &amp; kStringFormatAlternate) != 0) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :     if (base == 8) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :       if (orig != 0)</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :         *--p = '0';</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     }</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :     if (base == 16) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :       *--p = 'x';</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :       *--p = '0';</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     }</a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="273"><span class="lineNum">     273 </span>            :   // [Width]</a>
+<a name="274"><span class="lineNum">     274 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :   if (sign != 0)</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :     *--p = sign;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :   if (width &gt; 256)</a>
+<a name="280"><span class="lineNum">     280 </span>            :     width = 256;</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :   if (width &lt;= numberLength)</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     width = 0;</a>
+<a name="284"><span class="lineNum">     284 </span>            :   else</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :     width -= numberLength;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="288"><span class="lineNum">     288 </span>            :   // Write]</a>
+<a name="289"><span class="lineNum">     289 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   size_t prefixLength = (size_t)(buf + ASMJIT_ARRAY_SIZE(buf) - p) - numberLength;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   char* data = prepare(op, prefixLength + width + numberLength);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :   if (!data)</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   ::memcpy(data, p, prefixLength);</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :   data += prefixLength;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :   ::memset(data, '0', width);</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :   data += width;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :   ::memcpy(data, p + prefixLength, numberLength);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 : Error StringBuilder::_opHex(uint32_t op, const void* data, size_t len) noexcept {</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :   char* dst;</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :   if (len &gt;= IntTraits&lt;size_t&gt;::maxValue() / 2 || !(dst = prepare(op, len * 2)))</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);;</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   const char* src = static_cast&lt;const char*&gt;(data);</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :   for (size_t i = 0; i &lt; len; i++, dst += 2, src++) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :     dst[0] = StringBuilder_numbers[(src[0] &gt;&gt; 4) &amp; 0xF];</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :     dst[1] = StringBuilder_numbers[(src[0]     ) &amp; 0xF];</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :   }</a>
+<a name="318"><span class="lineNum">     318 </span>            :   return kErrorOk;</a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 : Error StringBuilder::_opVFormat(uint32_t op, const char* fmt, va_list ap) noexcept {</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   char buf[1024];</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            :   vsnprintf(buf, ASMJIT_ARRAY_SIZE(buf), fmt, ap);</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :   buf[ASMJIT_ARRAY_SIZE(buf) - 1] = '\0';</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :   return _opString(op, buf);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 : Error StringBuilder::setFormat(const char* fmt, ...) noexcept {</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   bool result;</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   va_list ap;</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :   va_start(ap, fmt);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :   result = _opVFormat(kStringOpSet, fmt, ap);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :   va_end(ap);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :   return result;</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : }</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 : Error StringBuilder::appendFormat(const char* fmt, ...) noexcept {</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :   bool result;</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :   va_list ap;</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   va_start(ap, fmt);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   result = _opVFormat(kStringOpAppend, fmt, ap);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :   va_end(ap);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   return result;</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 : bool StringBuilder::eq(const char* str, size_t len) const noexcept {</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :   const char* aData = _data;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :   const char* bData = str;</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :   size_t aLength = _length;</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   size_t bLength = len;</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :   if (bLength == Globals::kInvalidIndex) {</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :     size_t i;</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; aLength; i++)</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :       if (aData[i] != bData[i] || bData[i] == 0)</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :         return false;</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :     return bData[i] == 0;</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :   }</a>
+<a name="366"><span class="lineNum">     366 </span>            :   else {</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :     if (aLength != bLength)</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :       return false;</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     return ::memcmp(aData, bData, aLength) == 0;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span>            : }</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            : } // asmjit namespace</a>
+<a name="374"><span class="lineNum">     374 </span>            : } // namespace PLMD</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : // [Api-End]</a>
+<a name="377"><span class="lineNum">     377 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="378"><span class="lineNum">     378 </span>            : #pragma GCC diagnostic pop</a>
+<a name="379"><span class="lineNum">     379 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/utils.h.func-sort-c.html b/coverage-libs/asmjit/utils.h.func-sort-c.html
new file mode 100644
index 0000000000..24883963ba
--- /dev/null
+++ b/coverage-libs/asmjit/utils.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/utils.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - utils.h<span style="font-size: 80%;"> (<a href="utils.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryLo">48.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="utils.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/utils.h.func.html b/coverage-libs/asmjit/utils.h.func.html
new file mode 100644
index 0000000000..c042c017ea
--- /dev/null
+++ b/coverage-libs/asmjit/utils.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/utils.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - utils.h<span style="font-size: 80%;"> (<a href="utils.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryLo">48.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="utils.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/utils.h.gcov.html b/coverage-libs/asmjit/utils.h.gcov.html
new file mode 100644
index 0000000000..f75e600843
--- /dev/null
+++ b/coverage-libs/asmjit/utils.h.gcov.html
@@ -0,0 +1,1463 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/utils.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - utils.h<span style="font-size: 80%;"> (source / <a href="utils.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryLo">48.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_utils_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_utils_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_UTILS_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_UTILS_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./globals.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : #if ASMJIT_CC_MSC_GE(14, 0, 0)</a>
+<a name="39"><span class="lineNum">      39 </span>            : # include &lt;intrin.h&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // [Api-Begin]</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace PLMD {</a>
+<a name="46"><span class="lineNum">      46 </span>            : namespace asmjit {</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : //! \addtogroup asmjit_base</a>
+<a name="49"><span class="lineNum">      49 </span>            : //! \{</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : // [asmjit::IntTraits]</a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : //! \internal</a>
+<a name="56"><span class="lineNum">      56 </span>            : //! \{</a>
+<a name="57"><span class="lineNum">      57 </span>            : template&lt;size_t Size, int IsSigned&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : struct IntTraitsPrivate {}; // Let it fail if not specialized!</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;1, 0&gt; { typedef int     IntType; typedef int8_t  SignedType; typedef uint8_t  UnsignedType; };</a>
+<a name="61"><span class="lineNum">      61 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;1, 1&gt; { typedef int     IntType; typedef int8_t  SignedType; typedef uint8_t  UnsignedType; };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;2, 0&gt; { typedef int     IntType; typedef int16_t SignedType; typedef uint16_t UnsignedType; };</a>
+<a name="64"><span class="lineNum">      64 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;2, 1&gt; { typedef int     IntType; typedef int16_t SignedType; typedef uint16_t UnsignedType; };</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;4, 0&gt; { typedef int64_t IntType; typedef int32_t SignedType; typedef uint32_t UnsignedType; };</a>
+<a name="67"><span class="lineNum">      67 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;4, 1&gt; { typedef int     IntType; typedef int32_t SignedType; typedef uint32_t UnsignedType; };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;8, 0&gt; { typedef int64_t IntType; typedef int64_t SignedType; typedef uint64_t UnsignedType; };</a>
+<a name="70"><span class="lineNum">      70 </span>            : template&lt;&gt; struct IntTraitsPrivate&lt;8, 1&gt; { typedef int64_t IntType; typedef int64_t SignedType; typedef uint64_t UnsignedType; };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : //! \internal</a>
+<a name="73"><span class="lineNum">      73 </span>            : template&lt;typename T&gt;</a>
+<a name="74"><span class="lineNum">      74 </span>            : struct IntTraits {</a>
+<a name="75"><span class="lineNum">      75 </span>            :   enum {</a>
+<a name="76"><span class="lineNum">      76 </span>            :     kIsSigned   = static_cast&lt;T&gt;(~static_cast&lt;T&gt;(0)) &lt; static_cast&lt;T&gt;(0),</a>
+<a name="77"><span class="lineNum">      77 </span>            :     kIsUnsigned = !kIsSigned,</a>
+<a name="78"><span class="lineNum">      78 </span>            :     kIs8Bit     = sizeof(T) == 1,</a>
+<a name="79"><span class="lineNum">      79 </span>            :     kIs16Bit    = sizeof(T) == 2,</a>
+<a name="80"><span class="lineNum">      80 </span>            :     kIs32Bit    = sizeof(T) == 4,</a>
+<a name="81"><span class="lineNum">      81 </span>            :     kIs64Bit    = sizeof(T) == 8,</a>
+<a name="82"><span class="lineNum">      82 </span>            :     kIsIntPtr   = sizeof(T) == sizeof(intptr_t)</a>
+<a name="83"><span class="lineNum">      83 </span>            :   };</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   typedef typename IntTraitsPrivate&lt;sizeof(T), kIsSigned&gt;::IntType IntType;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   typedef typename IntTraitsPrivate&lt;sizeof(T), kIsSigned&gt;::SignedType SignedType;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   typedef typename IntTraitsPrivate&lt;sizeof(T), kIsSigned&gt;::UnsignedType UnsignedType;</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   //! Get a minimum value of `T`.</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static ASMJIT_INLINE T minValue() noexcept {</a>
+<a name="91"><span class="lineNum">      91 </span>            :     return kIsSigned ? T((~static_cast&lt;UnsignedType&gt;(0) &gt;&gt; 1) + static_cast&lt;UnsignedType&gt;(1)) : T(0);</a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Get a maximum value of `T`.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   static ASMJIT_INLINE T maxValue() noexcept {</a>
+<a name="96"><span class="lineNum">      96 </span>            :     return kIsSigned ? T(~static_cast&lt;UnsignedType&gt;(0) &gt;&gt; 1) : ~T(0);</a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span>            : };</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : //! \}</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : // ============================================================================</a>
+<a name="103"><span class="lineNum">     103 </span>            : // [asmjit::Utils]</a>
+<a name="104"><span class="lineNum">     104 </span>            : // ============================================================================</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : //! AsmJit utilities - integer, string, etc...</a>
+<a name="107"><span class="lineNum">     107 </span>            : namespace Utils {</a>
+<a name="108"><span class="lineNum">     108 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="109"><span class="lineNum">     109 </span>            :   // [Float &lt;-&gt; Int]</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   //! \internal</a>
+<a name="113"><span class="lineNum">     113 </span>            :   union FloatBits {</a>
+<a name="114"><span class="lineNum">     114 </span>            :     int32_t i;</a>
+<a name="115"><span class="lineNum">     115 </span>            :     float f;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   };</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   //! \internal</a>
+<a name="119"><span class="lineNum">     119 </span>            :   union DoubleBits {</a>
+<a name="120"><span class="lineNum">     120 </span>            :     int64_t i;</a>
+<a name="121"><span class="lineNum">     121 </span>            :     double d;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   };</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   //! Bit-cast `float` to a 32-bit integer.</a>
+<a name="125"><span class="lineNum">     125 </span>            :   static ASMJIT_INLINE int32_t floatAsInt(float f) noexcept { FloatBits m; m.f = f; return m.i; }</a>
+<a name="126"><span class="lineNum">     126 </span>            :   //! Bit-cast 32-bit integer to `float`.</a>
+<a name="127"><span class="lineNum">     127 </span>            :   static ASMJIT_INLINE float intAsFloat(int32_t i) noexcept { FloatBits m; m.i = i; return m.f; }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :   //! Bit-cast `double` to a 64-bit integer.</a>
+<a name="130"><span class="lineNum">     130 </span>            :   static ASMJIT_INLINE int64_t doubleAsInt(double d) noexcept { DoubleBits m; m.d = d; return m.i; }</a>
+<a name="131"><span class="lineNum">     131 </span>            :   //! Bit-cast 64-bit integer to `double`.</a>
+<a name="132"><span class="lineNum">     132 </span>            :   static ASMJIT_INLINE double intAsDouble(int64_t i) noexcept { DoubleBits m; m.i = i; return m.d; }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="135"><span class="lineNum">     135 </span>            :   // [Pack / Unpack]</a>
+<a name="136"><span class="lineNum">     136 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   //! Pack four 8-bit integer into a 32-bit integer as it is an array of `{b0,b1,b2,b3}`.</a>
+<a name="139"><span class="lineNum">     139 </span>            :   static ASMJIT_INLINE uint32_t pack32_4x8(uint32_t b0, uint32_t b1, uint32_t b2, uint32_t b3) noexcept {</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      36702 :     return ASMJIT_PACK32_4x8(b0, b1, b2, b3);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   //! Pack two 32-bit integer into a 64-bit integer as it is an array of `{u0,u1}`.</a>
+<a name="144"><span class="lineNum">     144 </span>            :   static ASMJIT_INLINE uint64_t pack64_2x32(uint32_t u0, uint32_t u1) noexcept {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      47292 :     return ASMJIT_ARCH_LE ? (static_cast&lt;uint64_t&gt;(u1) &lt;&lt; 32) + u0</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      27684 :                           : (static_cast&lt;uint64_t&gt;(u0) &lt;&lt; 32) + u1;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="150"><span class="lineNum">     150 </span>            :   // [Position of byte (in bit-shift)]</a>
+<a name="151"><span class="lineNum">     151 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   static ASMJIT_INLINE uint32_t byteShiftOfDWordStruct(uint32_t index) noexcept {</a>
+<a name="154"><span class="lineNum">     154 </span>            :     if (ASMJIT_ARCH_LE)</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">     122988 :       return index * 8;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     else</a>
+<a name="157"><span class="lineNum">     157 </span>            :       return (sizeof(uint32_t) - 1 - index) * 8;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="161"><span class="lineNum">     161 </span>            :   // [Lower/Upper]</a>
+<a name="162"><span class="lineNum">     162 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            :   template&lt;typename T&gt;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   static ASMJIT_INLINE T toLower(T c) noexcept { return c ^ (static_cast&lt;T&gt;(c &gt;= T('A') &amp;&amp; c &lt;= T('Z')) &lt;&lt; 5); }</a>
+<a name="166"><span class="lineNum">     166 </span>            :   template&lt;typename T&gt;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   static ASMJIT_INLINE T toUpper(T c) noexcept { return c ^ (static_cast&lt;T&gt;(c &gt;= T('a') &amp;&amp; c &lt;= T('z')) &lt;&lt; 5); }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="170"><span class="lineNum">     170 </span>            :   // [Hash]</a>
+<a name="171"><span class="lineNum">     171 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :   // \internal</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE uint32_t hashRound(uint32_t hash, uint32_t c) noexcept { return hash * 65599 + c; }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   // Get a hash of the given string `str` of `len` length. Length must be valid</a>
+<a name="177"><span class="lineNum">     177 </span>            :   // as this function doesn't check for a null terminator and allows it in the</a>
+<a name="178"><span class="lineNum">     178 </span>            :   // middle of the string.</a>
+<a name="179"><span class="lineNum">     179 </span>            :   static ASMJIT_INLINE uint32_t hashString(const char* str, size_t len) noexcept {</a>
+<a name="180"><span class="lineNum">     180 </span>            :     uint32_t hVal = 0;</a>
+<a name="181"><span class="lineNum">     181 </span>            :     for (uint32_t i = 0; i &lt; len; i++)</a>
+<a name="182"><span class="lineNum">     182 </span>            :       hVal = hashRound(hVal, str[i]);</a>
+<a name="183"><span class="lineNum">     183 </span>            :     return hVal;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="187"><span class="lineNum">     187 </span>            :   // [Swap]</a>
+<a name="188"><span class="lineNum">     188 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   template&lt;typename T&gt;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   static ASMJIT_INLINE void swap(T&amp; a, T&amp; b) noexcept {</a>
+<a name="192"><span class="lineNum">     192 </span>            :     T tmp = a;</a>
+<a name="193"><span class="lineNum">     193 </span>            :     a = b;</a>
+<a name="194"><span class="lineNum">     194 </span>            :     b = tmp;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="198"><span class="lineNum">     198 </span>            :   // [InInterval]</a>
+<a name="199"><span class="lineNum">     199 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :   //! Get whether `x` is greater than or equal to `a` and lesses than or equal to `b`.</a>
+<a name="202"><span class="lineNum">     202 </span>            :   template&lt;typename T&gt;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   static ASMJIT_INLINE bool inInterval(T x, T a, T b) noexcept {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      20198 :     return x &gt;= a &amp;&amp; x &lt;= b;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="208"><span class="lineNum">     208 </span>            :   // [AsInt]</a>
+<a name="209"><span class="lineNum">     209 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   //! Map an integer `x` of type `T` to `int` or `int64_t` depending on the</a>
+<a name="212"><span class="lineNum">     212 </span>            :   //! type. Used internally by AsmJit to dispatch arguments that can be of</a>
+<a name="213"><span class="lineNum">     213 </span>            :   //! arbitrary integer type into a function argument that is either `int` or</a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! `int64_t`.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   template&lt;typename T&gt;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   static ASMJIT_INLINE typename IntTraits&lt;T&gt;::IntType asInt(T x) noexcept {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        932 :     return static_cast&lt;typename IntTraits&lt;T&gt;::IntType&gt;(x);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="221"><span class="lineNum">     221 </span>            :   // [IsInt / IsUInt]</a>
+<a name="222"><span class="lineNum">     222 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   //! Get whether the given integer `x` can be casted to a 4-bit signed integer.</a>
+<a name="225"><span class="lineNum">     225 </span>            :   template&lt;typename T&gt;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   static ASMJIT_INLINE bool isInt4(T x) noexcept {</a>
+<a name="227"><span class="lineNum">     227 </span>            :     typedef typename IntTraits&lt;T&gt;::SignedType SignedType;</a>
+<a name="228"><span class="lineNum">     228 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="231"><span class="lineNum">     231 </span>            :       return inInterval&lt;SignedType&gt;(SignedType(x), -8, 7);</a>
+<a name="232"><span class="lineNum">     232 </span>            :     else</a>
+<a name="233"><span class="lineNum">     233 </span>            :       return UnsignedType(x) &lt;= UnsignedType(7U);</a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :   //! Get whether the given integer `x` can be casted to an 8-bit signed integer.</a>
+<a name="237"><span class="lineNum">     237 </span>            :   template&lt;typename T&gt;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   static ASMJIT_INLINE bool isInt8(T x) noexcept {</a>
+<a name="239"><span class="lineNum">     239 </span>            :     typedef typename IntTraits&lt;T&gt;::SignedType SignedType;</a>
+<a name="240"><span class="lineNum">     240 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="243"><span class="lineNum">     243 </span>            :       return sizeof(T) &lt;= 1 || inInterval&lt;SignedType&gt;(SignedType(x), -128, 127);</a>
+<a name="244"><span class="lineNum">     244 </span>            :     else</a>
+<a name="245"><span class="lineNum">     245 </span>            :       return UnsignedType(x) &lt;= UnsignedType(127U);</a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   //! Get whether the given integer `x` can be casted to a 16-bit signed integer.</a>
+<a name="249"><span class="lineNum">     249 </span>            :   template&lt;typename T&gt;</a>
+<a name="250"><span class="lineNum">     250 </span>            :   static ASMJIT_INLINE bool isInt16(T x) noexcept {</a>
+<a name="251"><span class="lineNum">     251 </span>            :     typedef typename IntTraits&lt;T&gt;::SignedType SignedType;</a>
+<a name="252"><span class="lineNum">     252 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="255"><span class="lineNum">     255 </span>            :       return sizeof(T) &lt;= 2 || inInterval&lt;SignedType&gt;(SignedType(x), -32768, 32767);</a>
+<a name="256"><span class="lineNum">     256 </span>            :     else</a>
+<a name="257"><span class="lineNum">     257 </span>            :       return sizeof(T) &lt;= 1 || UnsignedType(x) &lt;= UnsignedType(32767U);</a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            :   //! Get whether the given integer `x` can be casted to a 32-bit signed integer.</a>
+<a name="261"><span class="lineNum">     261 </span>            :   template&lt;typename T&gt;</a>
+<a name="262"><span class="lineNum">     262 </span>            :   static ASMJIT_INLINE bool isInt32(T x) noexcept {</a>
+<a name="263"><span class="lineNum">     263 </span>            :     typedef typename IntTraits&lt;T&gt;::SignedType SignedType;</a>
+<a name="264"><span class="lineNum">     264 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="267"><span class="lineNum">     267 </span>            :       return sizeof(T) &lt;= 4 || inInterval&lt;SignedType&gt;(SignedType(x), -2147483647 - 1, 2147483647);</a>
+<a name="268"><span class="lineNum">     268 </span>            :     else</a>
+<a name="269"><span class="lineNum">     269 </span>            :       return sizeof(T) &lt;= 2 || UnsignedType(x) &lt;= UnsignedType(2147483647U);</a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :   //! Get whether the given integer `x` can be casted to a 4-bit unsigned integer.</a>
+<a name="273"><span class="lineNum">     273 </span>            :   template&lt;typename T&gt;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   static ASMJIT_INLINE bool isUInt4(T x) noexcept {</a>
+<a name="275"><span class="lineNum">     275 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="278"><span class="lineNum">     278 </span>            :       return x &gt;= T(0) &amp;&amp; x &lt;= T(15);</a>
+<a name="279"><span class="lineNum">     279 </span>            :     else</a>
+<a name="280"><span class="lineNum">     280 </span>            :       return UnsignedType(x) &lt;= UnsignedType(15U);</a>
+<a name="281"><span class="lineNum">     281 </span>            :   }</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            :   //! Get whether the given integer `x` can be casted to an 8-bit unsigned integer.</a>
+<a name="284"><span class="lineNum">     284 </span>            :   template&lt;typename T&gt;</a>
+<a name="285"><span class="lineNum">     285 </span>            :   static ASMJIT_INLINE bool isUInt8(T x) noexcept {</a>
+<a name="286"><span class="lineNum">     286 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="289"><span class="lineNum">     289 </span>            :       return x &gt;= T(0) &amp;&amp; (sizeof(T) &lt;= 1 ? true : x &lt;= T(255));</a>
+<a name="290"><span class="lineNum">     290 </span>            :     else</a>
+<a name="291"><span class="lineNum">     291 </span>            :       return sizeof(T) &lt;= 1 || UnsignedType(x) &lt;= UnsignedType(255U);</a>
+<a name="292"><span class="lineNum">     292 </span>            :   }</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            :   //! Get whether the given integer `x` can be casted to a 12-bit unsigned integer (ARM specific).</a>
+<a name="295"><span class="lineNum">     295 </span>            :   template&lt;typename T&gt;</a>
+<a name="296"><span class="lineNum">     296 </span>            :   static ASMJIT_INLINE bool isUInt12(T x) noexcept {</a>
+<a name="297"><span class="lineNum">     297 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="300"><span class="lineNum">     300 </span>            :       return x &gt;= T(0) &amp;&amp; (sizeof(T) &lt;= 1 ? true : x &lt;= T(4095));</a>
+<a name="301"><span class="lineNum">     301 </span>            :     else</a>
+<a name="302"><span class="lineNum">     302 </span>            :       return sizeof(T) &lt;= 1 || UnsignedType(x) &lt;= UnsignedType(4095U);</a>
+<a name="303"><span class="lineNum">     303 </span>            :   }</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! Get whether the given integer `x` can be casted to a 16-bit unsigned integer.</a>
+<a name="306"><span class="lineNum">     306 </span>            :   template&lt;typename T&gt;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   static ASMJIT_INLINE bool isUInt16(T x) noexcept {</a>
+<a name="308"><span class="lineNum">     308 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="311"><span class="lineNum">     311 </span>            :       return x &gt;= T(0) &amp;&amp; (sizeof(T) &lt;= 2 ? true : x &lt;= T(65535));</a>
+<a name="312"><span class="lineNum">     312 </span>            :     else</a>
+<a name="313"><span class="lineNum">     313 </span>            :       return sizeof(T) &lt;= 2 || UnsignedType(x) &lt;= UnsignedType(65535U);</a>
+<a name="314"><span class="lineNum">     314 </span>            :   }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            :   //! Get whether the given integer `x` can be casted to a 32-bit unsigned integer.</a>
+<a name="317"><span class="lineNum">     317 </span>            :   template&lt;typename T&gt;</a>
+<a name="318"><span class="lineNum">     318 </span>            :   static ASMJIT_INLINE bool isUInt32(T x) noexcept {</a>
+<a name="319"><span class="lineNum">     319 </span>            :     typedef typename IntTraits&lt;T&gt;::UnsignedType UnsignedType;</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :     if (IntTraits&lt;T&gt;::kIsSigned)</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       9972 :       return x &gt;= T(0) &amp;&amp; (sizeof(T) &lt;= 4 ? true : x &lt;= T(4294967295U));</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :     else</a>
+<a name="324"><span class="lineNum">     324 </span>            :       return sizeof(T) &lt;= 4 || UnsignedType(x) &lt;= UnsignedType(4294967295U);</a>
+<a name="325"><span class="lineNum">     325 </span>            :   }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="328"><span class="lineNum">     328 </span>            :   // [IsPowerOf2]</a>
+<a name="329"><span class="lineNum">     329 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            :   //! Get whether the `n` value is a power of two (only one bit is set).</a>
+<a name="332"><span class="lineNum">     332 </span>            :   template&lt;typename T&gt;</a>
+<a name="333"><span class="lineNum">     333 </span>            :   static ASMJIT_INLINE bool isPowerOf2(T n) noexcept {</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      26412 :     return n != 0 &amp;&amp; (n &amp; (n - 1)) == 0;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :   }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="338"><span class="lineNum">     338 </span>            :   // [Mask]</a>
+<a name="339"><span class="lineNum">     339 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   //! Generate a bit-mask that has `x` bit set.</a>
+<a name="342"><span class="lineNum">     342 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x) noexcept {</a>
+<a name="343"><span class="lineNum">     343 </span>            :     ASMJIT_ASSERT(x &lt; 32);</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">     157552 :     return static_cast&lt;uint32_t&gt;(1) &lt;&lt; x;</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :   //! Generate a bit-mask that has `x0` and `x1` bits set.</a>
+<a name="348"><span class="lineNum">     348 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1) noexcept {</a>
+<a name="349"><span class="lineNum">     349 </span>            :     return mask(x0) | mask(x1);</a>
+<a name="350"><span class="lineNum">     350 </span>            :   }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            :   //! Generate a bit-mask that has `x0`, `x1` and `x2` bits set.</a>
+<a name="353"><span class="lineNum">     353 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2) noexcept {</a>
+<a name="354"><span class="lineNum">     354 </span>            :     return mask(x0, x1) | mask(x2);</a>
+<a name="355"><span class="lineNum">     355 </span>            :   }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2` and `x3` bits set.</a>
+<a name="358"><span class="lineNum">     358 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3) noexcept {</a>
+<a name="359"><span class="lineNum">     359 </span>            :     return mask(x0, x1) | mask(x2, x3);</a>
+<a name="360"><span class="lineNum">     360 </span>            :   }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2`, `x3` and `x4` bits set.</a>
+<a name="363"><span class="lineNum">     363 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3, uint32_t x4) noexcept {</a>
+<a name="364"><span class="lineNum">     364 </span>            :     return mask(x0, x1) | mask(x2, x3) | mask(x4);</a>
+<a name="365"><span class="lineNum">     365 </span>            :   }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2`, `x3`, `x4` and `x5` bits set.</a>
+<a name="368"><span class="lineNum">     368 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3, uint32_t x4, uint32_t x5) noexcept {</a>
+<a name="369"><span class="lineNum">     369 </span>            :     return mask(x0, x1) | mask(x2, x3) | mask(x4, x5);</a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2`, `x3`, `x4`, `x5` and `x6` bits set.</a>
+<a name="373"><span class="lineNum">     373 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3, uint32_t x4, uint32_t x5, uint32_t x6) noexcept {</a>
+<a name="374"><span class="lineNum">     374 </span>            :     return mask(x0, x1) | mask(x2, x3) | mask(x4, x5) | mask(x6);</a>
+<a name="375"><span class="lineNum">     375 </span>            :   }</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2`, `x3`, `x4`, `x5`, `x6` and `x7` bits set.</a>
+<a name="378"><span class="lineNum">     378 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3, uint32_t x4, uint32_t x5, uint32_t x6, uint32_t x7) noexcept {</a>
+<a name="379"><span class="lineNum">     379 </span>            :     return mask(x0, x1) | mask(x2, x3) | mask(x4, x5) | mask(x6, x7);</a>
+<a name="380"><span class="lineNum">     380 </span>            :   }</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2`, `x3`, `x4`, `x5`, `x6`, `x7` and `x8` bits set.</a>
+<a name="383"><span class="lineNum">     383 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3, uint32_t x4, uint32_t x5, uint32_t x6, uint32_t x7, uint32_t x8) noexcept {</a>
+<a name="384"><span class="lineNum">     384 </span>            :     return mask(x0, x1) | mask(x2, x3) | mask(x4, x5) | mask(x6, x7) | mask(x8);</a>
+<a name="385"><span class="lineNum">     385 </span>            :   }</a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            :   //! Generate a bit-mask that has `x0`, `x1`, `x2`, `x3`, `x4`, `x5`, `x6`, `x7`, `x8` and `x9` bits set.</a>
+<a name="388"><span class="lineNum">     388 </span>            :   static ASMJIT_INLINE uint32_t mask(uint32_t x0, uint32_t x1, uint32_t x2, uint32_t x3, uint32_t x4, uint32_t x5, uint32_t x6, uint32_t x7, uint32_t x8, uint32_t x9) noexcept {</a>
+<a name="389"><span class="lineNum">     389 </span>            :     return mask(x0, x1) | mask(x2, x3) | mask(x4, x5) | mask(x6, x7) | mask(x8, x9);</a>
+<a name="390"><span class="lineNum">     390 </span>            :   }</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="393"><span class="lineNum">     393 </span>            :   // [Bits]</a>
+<a name="394"><span class="lineNum">     394 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   //! Generate a bit-mask that has `x` least significant bits set.</a>
+<a name="397"><span class="lineNum">     397 </span>            :   static ASMJIT_INLINE uint32_t bits(uint32_t x) noexcept {</a>
+<a name="398"><span class="lineNum">     398 </span>            :     // Shifting more bits than the type has results in undefined behavior. In</a>
+<a name="399"><span class="lineNum">     399 </span>            :     // such case asmjit trashes the result by ORing with `overflow` mask, which</a>
+<a name="400"><span class="lineNum">     400 </span>            :     // discards the undefined value returned by the shift.</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       5544 :     uint32_t overflow = static_cast&lt;uint32_t&gt;(</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">       5544 :       -static_cast&lt;int32_t&gt;(x &gt;= sizeof(uint32_t) * 8));</span></a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       5544 :     return ((static_cast&lt;uint32_t&gt;(1) &lt;&lt; x) - 1U) | overflow;</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :   }</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="408"><span class="lineNum">     408 </span>            :   // [HasBit]</a>
+<a name="409"><span class="lineNum">     409 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            :   //! Get whether `x` has bit `n` set.</a>
+<a name="412"><span class="lineNum">     412 </span>            :   template&lt;typename T, typename Index&gt;</a>
+<a name="413"><span class="lineNum">     413 </span>            :   static ASMJIT_INLINE bool hasBit(T x, Index n) noexcept {</a>
+<a name="414"><span class="lineNum">     414 </span>            :     return (x &amp; (static_cast&lt;T&gt;(1) &lt;&lt; n)) != 0;</a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="418"><span class="lineNum">     418 </span>            :   // [BitCount]</a>
+<a name="419"><span class="lineNum">     419 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            :   static ASMJIT_INLINE uint32_t bitCountSlow(uint32_t x) noexcept {</a>
+<a name="422"><span class="lineNum">     422 </span>            :     // From: http://graphics.stanford.edu/~seander/bithacks.html</a>
+<a name="423"><span class="lineNum">     423 </span>            :     x = x - ((x &gt;&gt; 1) &amp; 0x55555555U);</a>
+<a name="424"><span class="lineNum">     424 </span>            :     x = (x &amp; 0x33333333U) + ((x &gt;&gt; 2) &amp; 0x33333333U);</a>
+<a name="425"><span class="lineNum">     425 </span>            :     return (((x + (x &gt;&gt; 4)) &amp; 0x0F0F0F0FU) * 0x01010101U) &gt;&gt; 24;</a>
+<a name="426"><span class="lineNum">     426 </span>            :   }</a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span>            :   //! Get count of bits in `x`.</a>
+<a name="429"><span class="lineNum">     429 </span>            :   static ASMJIT_INLINE uint32_t bitCount(uint32_t x) noexcept {</a>
+<a name="430"><span class="lineNum">     430 </span>            : #if ASMJIT_CC_GCC || ASMJIT_CC_CLANG</a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">       1948 :     return __builtin_popcount(x);</span></a>
+<a name="432"><span class="lineNum">     432 </span>            : #else</a>
+<a name="433"><span class="lineNum">     433 </span>            :     return bitCountSlow(x);</a>
+<a name="434"><span class="lineNum">     434 </span>            : #endif</a>
+<a name="435"><span class="lineNum">     435 </span>            :   }</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="438"><span class="lineNum">     438 </span>            :   // [FirstBitOf]</a>
+<a name="439"><span class="lineNum">     439 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            :   template&lt;uint64_t In&gt;</a>
+<a name="442"><span class="lineNum">     442 </span>            :   struct FirstBitOfTImpl {</a>
+<a name="443"><span class="lineNum">     443 </span>            :     enum {</a>
+<a name="444"><span class="lineNum">     444 </span>            :       _shift = (In &amp; ASMJIT_UINT64_C(0x0000FFFFFFFFFFFF)) == 0 ? 48 :</a>
+<a name="445"><span class="lineNum">     445 </span>            :                (In &amp; ASMJIT_UINT64_C(0x00000000FFFFFFFF)) == 0 ? 32 :</a>
+<a name="446"><span class="lineNum">     446 </span>            :                (In &amp; ASMJIT_UINT64_C(0x000000000000FFFF)) == 0 ? 16 : 0,</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            :       kValue = ((In &gt;&gt; _shift) &amp; 0x0001) ? (_shift +  0) :</a>
+<a name="449"><span class="lineNum">     449 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0002) ? (_shift +  1) :</a>
+<a name="450"><span class="lineNum">     450 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0004) ? (_shift +  2) :</a>
+<a name="451"><span class="lineNum">     451 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0008) ? (_shift +  3) :</a>
+<a name="452"><span class="lineNum">     452 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0010) ? (_shift +  4) :</a>
+<a name="453"><span class="lineNum">     453 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0020) ? (_shift +  5) :</a>
+<a name="454"><span class="lineNum">     454 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0040) ? (_shift +  6) :</a>
+<a name="455"><span class="lineNum">     455 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0080) ? (_shift +  7) :</a>
+<a name="456"><span class="lineNum">     456 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0100) ? (_shift +  8) :</a>
+<a name="457"><span class="lineNum">     457 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0200) ? (_shift +  9) :</a>
+<a name="458"><span class="lineNum">     458 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0400) ? (_shift + 10) :</a>
+<a name="459"><span class="lineNum">     459 </span>            :                ((In &gt;&gt; _shift) &amp; 0x0800) ? (_shift + 11) :</a>
+<a name="460"><span class="lineNum">     460 </span>            :                ((In &gt;&gt; _shift) &amp; 0x1000) ? (_shift + 12) :</a>
+<a name="461"><span class="lineNum">     461 </span>            :                ((In &gt;&gt; _shift) &amp; 0x2000) ? (_shift + 13) :</a>
+<a name="462"><span class="lineNum">     462 </span>            :                ((In &gt;&gt; _shift) &amp; 0x4000) ? (_shift + 14) :</a>
+<a name="463"><span class="lineNum">     463 </span>            :                ((In &gt;&gt; _shift) &amp; 0x8000) ? (_shift + 15) : 0</a>
+<a name="464"><span class="lineNum">     464 </span>            :     };</a>
+<a name="465"><span class="lineNum">     465 </span>            :   };</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span>            :   template&lt;&gt;</a>
+<a name="468"><span class="lineNum">     468 </span>            :   struct FirstBitOfTImpl&lt;0&gt; {};</a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            :   template&lt;uint64_t In&gt;</a>
+<a name="471"><span class="lineNum">     471 </span>            :   static ASMJIT_INLINE uint32_t firstBitOfT() noexcept { return FirstBitOfTImpl&lt;In&gt;::kValue; }</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="474"><span class="lineNum">     474 </span>            :   // [FindFirstBit]</a>
+<a name="475"><span class="lineNum">     475 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span>            :   //! \internal</a>
+<a name="478"><span class="lineNum">     478 </span>            :   static ASMJIT_INLINE uint32_t findFirstBitSlow(uint32_t mask) noexcept {</a>
+<a name="479"><span class="lineNum">     479 </span>            :     // This is a reference (slow) implementation of `findFirstBit()`, used when</a>
+<a name="480"><span class="lineNum">     480 </span>            :     // we don't have a C++ compiler support. The implementation speed has been</a>
+<a name="481"><span class="lineNum">     481 </span>            :     // improved to check for 2 bits per iteration.</a>
+<a name="482"><span class="lineNum">     482 </span>            :     uint32_t i = 1;</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :     while (mask != 0) {</a>
+<a name="485"><span class="lineNum">     485 </span>            :       uint32_t two = mask &amp; 0x3;</a>
+<a name="486"><span class="lineNum">     486 </span>            :       if (two != 0x0)</a>
+<a name="487"><span class="lineNum">     487 </span>            :         return i - (two &amp; 0x1);</a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            :       i += 2;</a>
+<a name="490"><span class="lineNum">     490 </span>            :       mask &gt;&gt;= 2;</a>
+<a name="491"><span class="lineNum">     491 </span>            :     }</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            :     return 0xFFFFFFFFU;</a>
+<a name="494"><span class="lineNum">     494 </span>            :   }</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            :   //! Find a first bit in `mask`.</a>
+<a name="497"><span class="lineNum">     497 </span>            :   static ASMJIT_INLINE uint32_t findFirstBit(uint32_t mask) noexcept {</a>
+<a name="498"><span class="lineNum">     498 </span>            : #if ASMJIT_CC_MSC_GE(14, 0, 0) &amp;&amp; (ASMJIT_ARCH_X86 || ASMJIT_ARCH_ARM32 || \</a>
+<a name="499"><span class="lineNum">     499 </span>            :                                    ASMJIT_ARCH_X64 || ASMJIT_ARCH_ARM64)</a>
+<a name="500"><span class="lineNum">     500 </span>            :     DWORD i;</a>
+<a name="501"><span class="lineNum">     501 </span>            :     if (_BitScanForward(&amp;i, mask))</a>
+<a name="502"><span class="lineNum">     502 </span>            :       return static_cast&lt;uint32_t&gt;(i);</a>
+<a name="503"><span class="lineNum">     503 </span>            :     else</a>
+<a name="504"><span class="lineNum">     504 </span>            :       return 0xFFFFFFFFU;</a>
+<a name="505"><span class="lineNum">     505 </span>            : #elif ASMJIT_CC_GCC_GE(3, 4, 6) || ASMJIT_CC_CLANG</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">      29716 :     if (mask)</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">      29716 :       return __builtin_ctz(mask);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :     else</a>
+<a name="509"><span class="lineNum">     509 </span>            :       return 0xFFFFFFFFU;</a>
+<a name="510"><span class="lineNum">     510 </span>            : #else</a>
+<a name="511"><span class="lineNum">     511 </span>            :     return findFirstBitSlow(mask);</a>
+<a name="512"><span class="lineNum">     512 </span>            : #endif</a>
+<a name="513"><span class="lineNum">     513 </span>            :   }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="516"><span class="lineNum">     516 </span>            :   // [Misc]</a>
+<a name="517"><span class="lineNum">     517 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span>            :   static ASMJIT_INLINE uint32_t keepNOnesFromRight(uint32_t mask, uint32_t nBits) noexcept {</a>
+<a name="520"><span class="lineNum">     520 </span>            :     uint32_t m = 0x1;</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            :     do {</a>
+<a name="523"><span class="lineNum">     523 </span>            :       nBits -= (mask &amp; m) != 0;</a>
+<a name="524"><span class="lineNum">     524 </span>            :       m &lt;&lt;= 1;</a>
+<a name="525"><span class="lineNum">     525 </span>            :       if (nBits == 0) {</a>
+<a name="526"><span class="lineNum">     526 </span>            :         m -= 1;</a>
+<a name="527"><span class="lineNum">     527 </span>            :         mask &amp;= m;</a>
+<a name="528"><span class="lineNum">     528 </span>            :         break;</a>
+<a name="529"><span class="lineNum">     529 </span>            :       }</a>
+<a name="530"><span class="lineNum">     530 </span>            :     } while (m);</a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span>            :     return mask;</a>
+<a name="533"><span class="lineNum">     533 </span>            :   }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            :   static ASMJIT_INLINE uint32_t indexNOnesFromRight(uint8_t* dst, uint32_t mask, uint32_t nBits) noexcept {</a>
+<a name="536"><span class="lineNum">     536 </span>            :     uint32_t totalBits = nBits;</a>
+<a name="537"><span class="lineNum">     537 </span>            :     uint8_t i = 0;</a>
+<a name="538"><span class="lineNum">     538 </span>            :     uint32_t m = 0x1;</a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span>            :     do {</a>
+<a name="541"><span class="lineNum">     541 </span>            :       if (mask &amp; m) {</a>
+<a name="542"><span class="lineNum">     542 </span>            :         *dst++ = i;</a>
+<a name="543"><span class="lineNum">     543 </span>            :         if (--nBits == 0)</a>
+<a name="544"><span class="lineNum">     544 </span>            :           break;</a>
+<a name="545"><span class="lineNum">     545 </span>            :       }</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :       m &lt;&lt;= 1;</a>
+<a name="548"><span class="lineNum">     548 </span>            :       i++;</a>
+<a name="549"><span class="lineNum">     549 </span>            :     } while (m);</a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span>            :     return totalBits - nBits;</a>
+<a name="552"><span class="lineNum">     552 </span>            :   }</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="555"><span class="lineNum">     555 </span>            :   // [Alignment]</a>
+<a name="556"><span class="lineNum">     556 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            :   template&lt;typename X, typename Y&gt;</a>
+<a name="559"><span class="lineNum">     559 </span>            :   static ASMJIT_INLINE bool isAligned(X base, Y alignment) noexcept {</a>
+<a name="560"><span class="lineNum">     560 </span>            :     typedef typename IntTraitsPrivate&lt;sizeof(X), 0&gt;::UnsignedType U;</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :     return ((U)base % (U)alignment) == 0;</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :   }</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :   template&lt;typename X, typename Y&gt;</a>
+<a name="565"><span class="lineNum">     565 </span>            :   static ASMJIT_INLINE X alignTo(X x, Y alignment) noexcept {</a>
+<a name="566"><span class="lineNum">     566 </span>            :     typedef typename IntTraitsPrivate&lt;sizeof(X), 0&gt;::UnsignedType U;</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">     171916 :     return (X)( ((U)x + (U)(alignment - 1)) &amp; ~(static_cast&lt;U&gt;(alignment) - 1) );</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :   }</a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span>            :   //! Get delta required to align `base` to `alignment`.</a>
+<a name="571"><span class="lineNum">     571 </span>            :   template&lt;typename X, typename Y&gt;</a>
+<a name="572"><span class="lineNum">     572 </span>            :   static ASMJIT_INLINE X alignDiff(X base, Y alignment) noexcept {</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">       1092 :     return alignTo(base, alignment) - base;</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :   }</a>
+<a name="575"><span class="lineNum">     575 </span>            : </a>
+<a name="576"><span class="lineNum">     576 </span>            :   template&lt;typename T&gt;</a>
+<a name="577"><span class="lineNum">     577 </span>            :   static ASMJIT_INLINE T alignToPowerOf2(T base) noexcept {</a>
+<a name="578"><span class="lineNum">     578 </span>            :     // Implementation is from &quot;Hacker's Delight&quot; by Henry S. Warren, Jr.</a>
+<a name="579"><span class="lineNum">     579 </span>            :     base -= 1;</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            : #if defined(_MSC_VER)</a>
+<a name="582"><span class="lineNum">     582 </span>            : # pragma warning(push)</a>
+<a name="583"><span class="lineNum">     583 </span>            : # pragma warning(disable: 4293)</a>
+<a name="584"><span class="lineNum">     584 </span>            : #endif // _MSC_VER</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span>            :     base = base | (base &gt;&gt; 1);</a>
+<a name="587"><span class="lineNum">     587 </span>            :     base = base | (base &gt;&gt; 2);</a>
+<a name="588"><span class="lineNum">     588 </span>            :     base = base | (base &gt;&gt; 4);</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span>            :     // 8/16/32 constants are multiplied by the condition to prevent a compiler</a>
+<a name="591"><span class="lineNum">     591 </span>            :     // complaining about the 'shift count &gt;= type width' (GCC).</a>
+<a name="592"><span class="lineNum">     592 </span>            :     if (sizeof(T) &gt;= 2) base = base | (base &gt;&gt; ( 8 * (sizeof(T) &gt;= 2))); // Base &gt;&gt;  8.</a>
+<a name="593"><span class="lineNum">     593 </span>            :     if (sizeof(T) &gt;= 4) base = base | (base &gt;&gt; (16 * (sizeof(T) &gt;= 4))); // Base &gt;&gt; 16.</a>
+<a name="594"><span class="lineNum">     594 </span>            :     if (sizeof(T) &gt;= 8) base = base | (base &gt;&gt; (32 * (sizeof(T) &gt;= 8))); // Base &gt;&gt; 32.</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            : #if defined(_MSC_VER)</a>
+<a name="597"><span class="lineNum">     597 </span>            : # pragma warning(pop)</a>
+<a name="598"><span class="lineNum">     598 </span>            : #endif // _MSC_VER</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span>            :     return base + 1;</a>
+<a name="601"><span class="lineNum">     601 </span>            :   }</a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="604"><span class="lineNum">     604 </span>            :   // [String]</a>
+<a name="605"><span class="lineNum">     605 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span>            :   static ASMJIT_INLINE size_t strLen(const char* s, size_t maxlen) noexcept {</a>
+<a name="608"><span class="lineNum">     608 </span>            :     size_t i;</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; maxlen; i++)</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 :       if (!s[i])</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :         break;</a>
+<a name="612"><span class="lineNum">     612 </span>            :     return i;</a>
+<a name="613"><span class="lineNum">     613 </span>            :   }</a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span>            :   static ASMJIT_INLINE const char* findPackedString(const char* p, uint32_t id) noexcept {</a>
+<a name="616"><span class="lineNum">     616 </span>            :     uint32_t i = 0;</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :     while (i &lt; id) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :       while (p[0])</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :         p++;</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :       p++;</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :     }</a>
+<a name="623"><span class="lineNum">     623 </span>            :     return p;</a>
+<a name="624"><span class="lineNum">     624 </span>            :   }</a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span>            :   //! \internal</a>
+<a name="627"><span class="lineNum">     627 </span>            :   //!</a>
+<a name="628"><span class="lineNum">     628 </span>            :   //! Compare two instruction names.</a>
+<a name="629"><span class="lineNum">     629 </span>            :   //!</a>
+<a name="630"><span class="lineNum">     630 </span>            :   //! `a` is a null terminated instruction name from `???InstDB::nameData[]` table.</a>
+<a name="631"><span class="lineNum">     631 </span>            :   //! `b` is a non-null terminated instruction name passed to `???Inst::getIdByName()`.</a>
+<a name="632"><span class="lineNum">     632 </span>            :   static ASMJIT_INLINE int cmpInstName(const char* a, const char* b, size_t len) noexcept {</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineNoCov">          0 :     for (size_t i = 0; i &lt; len; i++) {</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :       int c = static_cast&lt;int&gt;(static_cast&lt;uint8_t&gt;(a[i])) -</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineNoCov">          0 :               static_cast&lt;int&gt;(static_cast&lt;uint8_t&gt;(b[i])) ;</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :       if (c != 0) return c;</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :     }</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :     return static_cast&lt;int&gt;(a[len]);</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :   }</a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="643"><span class="lineNum">     643 </span>            :   // [BSwap]</a>
+<a name="644"><span class="lineNum">     644 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="645"><span class="lineNum">     645 </span>            : </a>
+<a name="646"><span class="lineNum">     646 </span>            :   static ASMJIT_INLINE uint32_t byteswap32(uint32_t x) noexcept {</a>
+<a name="647"><span class="lineNum">     647 </span>            : #if ASMJIT_CC_MSC</a>
+<a name="648"><span class="lineNum">     648 </span>            :     return static_cast&lt;uint32_t&gt;(_byteswap_ulong(x));</a>
+<a name="649"><span class="lineNum">     649 </span>            : #elif ASMJIT_CC_GCC_GE(4, 3, 0) || ASMJIT_CC_CLANG_GE(2, 6, 0)</a>
+<a name="650"><span class="lineNum">     650 </span>            :     return __builtin_bswap32(x);</a>
+<a name="651"><span class="lineNum">     651 </span>            : #else</a>
+<a name="652"><span class="lineNum">     652 </span>            :     uint32_t y = x &amp; 0x00FFFF00U;</a>
+<a name="653"><span class="lineNum">     653 </span>            :     x = (x &lt;&lt; 24) + (x &gt;&gt; 24);</a>
+<a name="654"><span class="lineNum">     654 </span>            :     y = (y &lt;&lt;  8) + (y &gt;&gt;  8);</a>
+<a name="655"><span class="lineNum">     655 </span>            :     return x + (y &amp; 0x00FFFF00U);</a>
+<a name="656"><span class="lineNum">     656 </span>            : #endif</a>
+<a name="657"><span class="lineNum">     657 </span>            :   }</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="660"><span class="lineNum">     660 </span>            :   // [ReadMem]</a>
+<a name="661"><span class="lineNum">     661 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span>            :   static ASMJIT_INLINE uint32_t readU8(const void* p) noexcept {</a>
+<a name="664"><span class="lineNum">     664 </span>            :     return static_cast&lt;uint32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[0]);</a>
+<a name="665"><span class="lineNum">     665 </span>            :   }</a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span>            :   static ASMJIT_INLINE int32_t readI8(const void* p) noexcept {</a>
+<a name="668"><span class="lineNum">     668 </span>            :     return static_cast&lt;int32_t&gt;(static_cast&lt;const int8_t*&gt;(p)[0]);</a>
+<a name="669"><span class="lineNum">     669 </span>            :   }</a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="672"><span class="lineNum">     672 </span>            :   static ASMJIT_INLINE uint32_t readU16xLE(const void* p) noexcept {</a>
+<a name="673"><span class="lineNum">     673 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="674"><span class="lineNum">     674 </span>            :     if (ASMJIT_ARCH_LE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_16 || Alignment &gt;= 2)) {</a>
+<a name="675"><span class="lineNum">     675 </span>            :       return static_cast&lt;uint32_t&gt;(static_cast&lt;const uint16_t*&gt;(p)[0]);</a>
+<a name="676"><span class="lineNum">     676 </span>            :     }</a>
+<a name="677"><span class="lineNum">     677 </span>            :     else {</a>
+<a name="678"><span class="lineNum">     678 </span>            :       uint32_t x = static_cast&lt;uint32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[0]);</a>
+<a name="679"><span class="lineNum">     679 </span>            :       uint32_t y = static_cast&lt;uint32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[1]);</a>
+<a name="680"><span class="lineNum">     680 </span>            :       return x + (y &lt;&lt; 8);</a>
+<a name="681"><span class="lineNum">     681 </span>            :     }</a>
+<a name="682"><span class="lineNum">     682 </span>            :   }</a>
+<a name="683"><span class="lineNum">     683 </span>            : </a>
+<a name="684"><span class="lineNum">     684 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="685"><span class="lineNum">     685 </span>            :   static ASMJIT_INLINE uint32_t readU16xBE(const void* p) noexcept {</a>
+<a name="686"><span class="lineNum">     686 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="687"><span class="lineNum">     687 </span>            :     if (ASMJIT_ARCH_BE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_16 || Alignment &gt;= 2)) {</a>
+<a name="688"><span class="lineNum">     688 </span>            :       return static_cast&lt;uint32_t&gt;(static_cast&lt;const uint16_t*&gt;(p)[0]);</a>
+<a name="689"><span class="lineNum">     689 </span>            :     }</a>
+<a name="690"><span class="lineNum">     690 </span>            :     else {</a>
+<a name="691"><span class="lineNum">     691 </span>            :       uint32_t x = static_cast&lt;uint32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[0]);</a>
+<a name="692"><span class="lineNum">     692 </span>            :       uint32_t y = static_cast&lt;uint32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[1]);</a>
+<a name="693"><span class="lineNum">     693 </span>            :       return (x &lt;&lt; 8) + y;</a>
+<a name="694"><span class="lineNum">     694 </span>            :     }</a>
+<a name="695"><span class="lineNum">     695 </span>            :   }</a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="698"><span class="lineNum">     698 </span>            :   static ASMJIT_INLINE uint32_t readU16x(const void* p) noexcept {</a>
+<a name="699"><span class="lineNum">     699 </span>            :     return ASMJIT_ARCH_LE ? readU16xLE&lt;Alignment&gt;(p) : readU16xBE&lt;Alignment&gt;(p);</a>
+<a name="700"><span class="lineNum">     700 </span>            :   }</a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="703"><span class="lineNum">     703 </span>            :   static ASMJIT_INLINE int32_t readI16xLE(const void* p) noexcept {</a>
+<a name="704"><span class="lineNum">     704 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="705"><span class="lineNum">     705 </span>            :     if (ASMJIT_ARCH_LE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_16 || Alignment &gt;= 2)) {</a>
+<a name="706"><span class="lineNum">     706 </span>            :       return static_cast&lt;int32_t&gt;(static_cast&lt;const int16_t*&gt;(p)[0]);</a>
+<a name="707"><span class="lineNum">     707 </span>            :     }</a>
+<a name="708"><span class="lineNum">     708 </span>            :     else {</a>
+<a name="709"><span class="lineNum">     709 </span>            :       int32_t x = static_cast&lt;int32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[0]);</a>
+<a name="710"><span class="lineNum">     710 </span>            :       int32_t y = static_cast&lt;int32_t&gt;(static_cast&lt;const int8_t*&gt;(p)[1]);</a>
+<a name="711"><span class="lineNum">     711 </span>            :       return x + (y &lt;&lt; 8);</a>
+<a name="712"><span class="lineNum">     712 </span>            :     }</a>
+<a name="713"><span class="lineNum">     713 </span>            :   }</a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="716"><span class="lineNum">     716 </span>            :   static ASMJIT_INLINE int32_t readI16xBE(const void* p) noexcept {</a>
+<a name="717"><span class="lineNum">     717 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="718"><span class="lineNum">     718 </span>            :     if (ASMJIT_ARCH_BE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_16 || Alignment &gt;= 2)) {</a>
+<a name="719"><span class="lineNum">     719 </span>            :       return static_cast&lt;int32_t&gt;(static_cast&lt;const int16_t*&gt;(p)[0]);</a>
+<a name="720"><span class="lineNum">     720 </span>            :     }</a>
+<a name="721"><span class="lineNum">     721 </span>            :     else {</a>
+<a name="722"><span class="lineNum">     722 </span>            :       int32_t x = static_cast&lt;int32_t&gt;(static_cast&lt;const int8_t*&gt;(p)[0]);</a>
+<a name="723"><span class="lineNum">     723 </span>            :       int32_t y = static_cast&lt;int32_t&gt;(static_cast&lt;const uint8_t*&gt;(p)[1]);</a>
+<a name="724"><span class="lineNum">     724 </span>            :       return (x &lt;&lt; 8) + y;</a>
+<a name="725"><span class="lineNum">     725 </span>            :     }</a>
+<a name="726"><span class="lineNum">     726 </span>            :   }</a>
+<a name="727"><span class="lineNum">     727 </span>            : </a>
+<a name="728"><span class="lineNum">     728 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="729"><span class="lineNum">     729 </span>            :   static ASMJIT_INLINE int32_t readI16x(const void* p) noexcept {</a>
+<a name="730"><span class="lineNum">     730 </span>            :     return ASMJIT_ARCH_LE ? readI16xLE&lt;Alignment&gt;(p) : readI16xBE&lt;Alignment&gt;(p);</a>
+<a name="731"><span class="lineNum">     731 </span>            :   }</a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span>            :   static ASMJIT_INLINE uint32_t readU16aLE(const void* p) noexcept { return readU16xLE&lt;2&gt;(p); }</a>
+<a name="734"><span class="lineNum">     734 </span>            :   static ASMJIT_INLINE uint32_t readU16uLE(const void* p) noexcept { return readU16xLE&lt;0&gt;(p); }</a>
+<a name="735"><span class="lineNum">     735 </span>            : </a>
+<a name="736"><span class="lineNum">     736 </span>            :   static ASMJIT_INLINE uint32_t readU16aBE(const void* p) noexcept { return readU16xBE&lt;2&gt;(p); }</a>
+<a name="737"><span class="lineNum">     737 </span>            :   static ASMJIT_INLINE uint32_t readU16uBE(const void* p) noexcept { return readU16xBE&lt;0&gt;(p); }</a>
+<a name="738"><span class="lineNum">     738 </span>            : </a>
+<a name="739"><span class="lineNum">     739 </span>            :   static ASMJIT_INLINE uint32_t readU16a(const void* p) noexcept { return readU16x&lt;2&gt;(p); }</a>
+<a name="740"><span class="lineNum">     740 </span>            :   static ASMJIT_INLINE uint32_t readU16u(const void* p) noexcept { return readU16x&lt;0&gt;(p); }</a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span>            :   static ASMJIT_INLINE int32_t readI16aLE(const void* p) noexcept { return readI16xLE&lt;2&gt;(p); }</a>
+<a name="743"><span class="lineNum">     743 </span>            :   static ASMJIT_INLINE int32_t readI16uLE(const void* p) noexcept { return readI16xLE&lt;0&gt;(p); }</a>
+<a name="744"><span class="lineNum">     744 </span>            : </a>
+<a name="745"><span class="lineNum">     745 </span>            :   static ASMJIT_INLINE int32_t readI16aBE(const void* p) noexcept { return readI16xBE&lt;2&gt;(p); }</a>
+<a name="746"><span class="lineNum">     746 </span>            :   static ASMJIT_INLINE int32_t readI16uBE(const void* p) noexcept { return readI16xBE&lt;0&gt;(p); }</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span>            :   static ASMJIT_INLINE int32_t readI16a(const void* p) noexcept { return readI16x&lt;2&gt;(p); }</a>
+<a name="749"><span class="lineNum">     749 </span>            :   static ASMJIT_INLINE int32_t readI16u(const void* p) noexcept { return readI16x&lt;0&gt;(p); }</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="752"><span class="lineNum">     752 </span>            :   static ASMJIT_INLINE uint32_t readU32xLE(const void* p) noexcept {</a>
+<a name="753"><span class="lineNum">     753 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="754"><span class="lineNum">     754 </span>            :     if (ASMJIT_ARCH_UNALIGNED_32 || Alignment &gt;= 4) {</a>
+<a name="755"><span class="lineNum">     755 </span>            :       uint32_t x = static_cast&lt;const uint32_t*&gt;(p)[0];</a>
+<a name="756"><span class="lineNum">     756 </span>            :       return ASMJIT_ARCH_LE ? x : byteswap32(x);</a>
+<a name="757"><span class="lineNum">     757 </span>            :     }</a>
+<a name="758"><span class="lineNum">     758 </span>            :     else {</a>
+<a name="759"><span class="lineNum">     759 </span>            :       uint32_t x = readU16xLE&lt;Alignment&gt;(static_cast&lt;const uint8_t*&gt;(p) + 0);</a>
+<a name="760"><span class="lineNum">     760 </span>            :       uint32_t y = readU16xLE&lt;Alignment&gt;(static_cast&lt;const uint8_t*&gt;(p) + 2);</a>
+<a name="761"><span class="lineNum">     761 </span>            :       return x + (y &lt;&lt; 16);</a>
+<a name="762"><span class="lineNum">     762 </span>            :     }</a>
+<a name="763"><span class="lineNum">     763 </span>            :   }</a>
+<a name="764"><span class="lineNum">     764 </span>            : </a>
+<a name="765"><span class="lineNum">     765 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="766"><span class="lineNum">     766 </span>            :   static ASMJIT_INLINE uint32_t readU32xBE(const void* p) noexcept {</a>
+<a name="767"><span class="lineNum">     767 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="768"><span class="lineNum">     768 </span>            :     if (ASMJIT_ARCH_UNALIGNED_32 || Alignment &gt;= 4) {</a>
+<a name="769"><span class="lineNum">     769 </span>            :       uint32_t x = static_cast&lt;const uint32_t*&gt;(p)[0];</a>
+<a name="770"><span class="lineNum">     770 </span>            :       return ASMJIT_ARCH_BE ? x : byteswap32(x);</a>
+<a name="771"><span class="lineNum">     771 </span>            :     }</a>
+<a name="772"><span class="lineNum">     772 </span>            :     else {</a>
+<a name="773"><span class="lineNum">     773 </span>            :       uint32_t x = readU16xBE&lt;Alignment&gt;(static_cast&lt;const uint8_t*&gt;(p) + 0);</a>
+<a name="774"><span class="lineNum">     774 </span>            :       uint32_t y = readU16xBE&lt;Alignment&gt;(static_cast&lt;const uint8_t*&gt;(p) + 2);</a>
+<a name="775"><span class="lineNum">     775 </span>            :       return (x &lt;&lt; 16) + y;</a>
+<a name="776"><span class="lineNum">     776 </span>            :     }</a>
+<a name="777"><span class="lineNum">     777 </span>            :   }</a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="780"><span class="lineNum">     780 </span>            :   static ASMJIT_INLINE uint32_t readU32x(const void* p) noexcept {</a>
+<a name="781"><span class="lineNum">     781 </span>            :     return ASMJIT_ARCH_LE ? readU32xLE&lt;Alignment&gt;(p) : readU32xBE&lt;Alignment&gt;(p);</a>
+<a name="782"><span class="lineNum">     782 </span>            :   }</a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="785"><span class="lineNum">     785 </span>            :   static ASMJIT_INLINE int32_t readI32xLE(const void* p) noexcept {</a>
+<a name="786"><span class="lineNum">     786 </span>            :     return static_cast&lt;int32_t&gt;(readU32xLE&lt;Alignment&gt;(p));</a>
+<a name="787"><span class="lineNum">     787 </span>            :   }</a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="790"><span class="lineNum">     790 </span>            :   static ASMJIT_INLINE int32_t readI32xBE(const void* p) noexcept {</a>
+<a name="791"><span class="lineNum">     791 </span>            :     return static_cast&lt;int32_t&gt;(readU32xBE&lt;Alignment&gt;(p));</a>
+<a name="792"><span class="lineNum">     792 </span>            :   }</a>
+<a name="793"><span class="lineNum">     793 </span>            : </a>
+<a name="794"><span class="lineNum">     794 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="795"><span class="lineNum">     795 </span>            :   static ASMJIT_INLINE int32_t readI32x(const void* p) noexcept {</a>
+<a name="796"><span class="lineNum">     796 </span>            :     return ASMJIT_ARCH_LE ? readI32xLE&lt;Alignment&gt;(p) : readI32xBE&lt;Alignment&gt;(p);</a>
+<a name="797"><span class="lineNum">     797 </span>            :   }</a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span>            :   static ASMJIT_INLINE uint32_t readU32a(const void* p) noexcept { return readU32x&lt;4&gt;(p); }</a>
+<a name="800"><span class="lineNum">     800 </span>            :   static ASMJIT_INLINE uint32_t readU32u(const void* p) noexcept { return readU32x&lt;0&gt;(p); }</a>
+<a name="801"><span class="lineNum">     801 </span>            : </a>
+<a name="802"><span class="lineNum">     802 </span>            :   static ASMJIT_INLINE uint32_t readU32aLE(const void* p) noexcept { return readU32xLE&lt;4&gt;(p); }</a>
+<a name="803"><span class="lineNum">     803 </span>            :   static ASMJIT_INLINE uint32_t readU32uLE(const void* p) noexcept { return readU32xLE&lt;0&gt;(p); }</a>
+<a name="804"><span class="lineNum">     804 </span>            : </a>
+<a name="805"><span class="lineNum">     805 </span>            :   static ASMJIT_INLINE uint32_t readU32aBE(const void* p) noexcept { return readU32xBE&lt;4&gt;(p); }</a>
+<a name="806"><span class="lineNum">     806 </span>            :   static ASMJIT_INLINE uint32_t readU32uBE(const void* p) noexcept { return readU32xBE&lt;0&gt;(p); }</a>
+<a name="807"><span class="lineNum">     807 </span>            : </a>
+<a name="808"><span class="lineNum">     808 </span>            :   static ASMJIT_INLINE int32_t readI32a(const void* p) noexcept { return readI32x&lt;4&gt;(p); }</a>
+<a name="809"><span class="lineNum">     809 </span>            :   static ASMJIT_INLINE int32_t readI32u(const void* p) noexcept { return readI32x&lt;0&gt;(p); }</a>
+<a name="810"><span class="lineNum">     810 </span>            : </a>
+<a name="811"><span class="lineNum">     811 </span>            :   static ASMJIT_INLINE int32_t readI32aLE(const void* p) noexcept { return readI32xLE&lt;4&gt;(p); }</a>
+<a name="812"><span class="lineNum">     812 </span>            :   static ASMJIT_INLINE int32_t readI32uLE(const void* p) noexcept { return readI32xLE&lt;0&gt;(p); }</a>
+<a name="813"><span class="lineNum">     813 </span>            : </a>
+<a name="814"><span class="lineNum">     814 </span>            :   static ASMJIT_INLINE int32_t readI32aBE(const void* p) noexcept { return readI32xBE&lt;4&gt;(p); }</a>
+<a name="815"><span class="lineNum">     815 </span>            :   static ASMJIT_INLINE int32_t readI32uBE(const void* p) noexcept { return readI32xBE&lt;0&gt;(p); }</a>
+<a name="816"><span class="lineNum">     816 </span>            : </a>
+<a name="817"><span class="lineNum">     817 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="818"><span class="lineNum">     818 </span>            :   static ASMJIT_INLINE uint64_t readU64xLE(const void* p) noexcept {</a>
+<a name="819"><span class="lineNum">     819 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="820"><span class="lineNum">     820 </span>            :     if (ASMJIT_ARCH_LE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_64 || Alignment &gt;= 8)) {</a>
+<a name="821"><span class="lineNum">     821 </span>            :       return static_cast&lt;const uint64_t*&gt;(p)[0];</a>
+<a name="822"><span class="lineNum">     822 </span>            :     }</a>
+<a name="823"><span class="lineNum">     823 </span>            :     else {</a>
+<a name="824"><span class="lineNum">     824 </span>            :       uint32_t x = readU32xLE&lt;Alignment / 2U&gt;(static_cast&lt;const uint8_t*&gt;(p) + 0);</a>
+<a name="825"><span class="lineNum">     825 </span>            :       uint32_t y = readU32xLE&lt;Alignment / 2U&gt;(static_cast&lt;const uint8_t*&gt;(p) + 4);</a>
+<a name="826"><span class="lineNum">     826 </span>            :       return static_cast&lt;uint64_t&gt;(x) + (static_cast&lt;uint64_t&gt;(y) &lt;&lt; 32);</a>
+<a name="827"><span class="lineNum">     827 </span>            :     }</a>
+<a name="828"><span class="lineNum">     828 </span>            :   }</a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="831"><span class="lineNum">     831 </span>            :   static ASMJIT_INLINE uint64_t readU64xBE(const void* p) noexcept {</a>
+<a name="832"><span class="lineNum">     832 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="833"><span class="lineNum">     833 </span>            :     if (ASMJIT_ARCH_BE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_64 || Alignment &gt;= 8)) {</a>
+<a name="834"><span class="lineNum">     834 </span>            :       return static_cast&lt;const uint64_t*&gt;(p)[0];</a>
+<a name="835"><span class="lineNum">     835 </span>            :     }</a>
+<a name="836"><span class="lineNum">     836 </span>            :     else {</a>
+<a name="837"><span class="lineNum">     837 </span>            :       uint32_t x = readU32xLE&lt;Alignment / 2U&gt;(static_cast&lt;const uint8_t*&gt;(p) + 0);</a>
+<a name="838"><span class="lineNum">     838 </span>            :       uint32_t y = readU32xLE&lt;Alignment / 2U&gt;(static_cast&lt;const uint8_t*&gt;(p) + 4);</a>
+<a name="839"><span class="lineNum">     839 </span>            :       return (static_cast&lt;uint64_t&gt;(x) &lt;&lt; 32) + static_cast&lt;uint64_t&gt;(y);</a>
+<a name="840"><span class="lineNum">     840 </span>            :     }</a>
+<a name="841"><span class="lineNum">     841 </span>            :   }</a>
+<a name="842"><span class="lineNum">     842 </span>            : </a>
+<a name="843"><span class="lineNum">     843 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="844"><span class="lineNum">     844 </span>            :   static ASMJIT_INLINE uint64_t readU64x(const void* p) noexcept {</a>
+<a name="845"><span class="lineNum">     845 </span>            :     return ASMJIT_ARCH_LE ? readU64xLE&lt;Alignment&gt;(p) : readU64xBE&lt;Alignment&gt;(p);</a>
+<a name="846"><span class="lineNum">     846 </span>            :   }</a>
+<a name="847"><span class="lineNum">     847 </span>            : </a>
+<a name="848"><span class="lineNum">     848 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="849"><span class="lineNum">     849 </span>            :   static ASMJIT_INLINE int64_t readI64xLE(const void* p) noexcept {</a>
+<a name="850"><span class="lineNum">     850 </span>            :     return static_cast&lt;int64_t&gt;(readU64xLE&lt;Alignment&gt;(p));</a>
+<a name="851"><span class="lineNum">     851 </span>            :   }</a>
+<a name="852"><span class="lineNum">     852 </span>            : </a>
+<a name="853"><span class="lineNum">     853 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="854"><span class="lineNum">     854 </span>            :   static ASMJIT_INLINE int64_t readI64xBE(const void* p) noexcept {</a>
+<a name="855"><span class="lineNum">     855 </span>            :     return static_cast&lt;int64_t&gt;(readU64xBE&lt;Alignment&gt;(p));</a>
+<a name="856"><span class="lineNum">     856 </span>            :   }</a>
+<a name="857"><span class="lineNum">     857 </span>            : </a>
+<a name="858"><span class="lineNum">     858 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="859"><span class="lineNum">     859 </span>            :   static ASMJIT_INLINE int64_t readI64x(const void* p) noexcept {</a>
+<a name="860"><span class="lineNum">     860 </span>            :     return ASMJIT_ARCH_LE ? readI64xLE&lt;Alignment&gt;(p) : readI64xBE&lt;Alignment&gt;(p);</a>
+<a name="861"><span class="lineNum">     861 </span>            :   }</a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span>            :   static ASMJIT_INLINE uint64_t readU64a(const void* p) noexcept { return readU64x&lt;8&gt;(p); }</a>
+<a name="864"><span class="lineNum">     864 </span>            :   static ASMJIT_INLINE uint64_t readU64u(const void* p) noexcept { return readU64x&lt;0&gt;(p); }</a>
+<a name="865"><span class="lineNum">     865 </span>            : </a>
+<a name="866"><span class="lineNum">     866 </span>            :   static ASMJIT_INLINE uint64_t readU64aLE(const void* p) noexcept { return readU64xLE&lt;8&gt;(p); }</a>
+<a name="867"><span class="lineNum">     867 </span>            :   static ASMJIT_INLINE uint64_t readU64uLE(const void* p) noexcept { return readU64xLE&lt;0&gt;(p); }</a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span>            :   static ASMJIT_INLINE uint64_t readU64aBE(const void* p) noexcept { return readU64xBE&lt;8&gt;(p); }</a>
+<a name="870"><span class="lineNum">     870 </span>            :   static ASMJIT_INLINE uint64_t readU64uBE(const void* p) noexcept { return readU64xBE&lt;0&gt;(p); }</a>
+<a name="871"><span class="lineNum">     871 </span>            : </a>
+<a name="872"><span class="lineNum">     872 </span>            :   static ASMJIT_INLINE int64_t readI64a(const void* p) noexcept { return readI64x&lt;8&gt;(p); }</a>
+<a name="873"><span class="lineNum">     873 </span>            :   static ASMJIT_INLINE int64_t readI64u(const void* p) noexcept { return readI64x&lt;0&gt;(p); }</a>
+<a name="874"><span class="lineNum">     874 </span>            : </a>
+<a name="875"><span class="lineNum">     875 </span>            :   static ASMJIT_INLINE int64_t readI64aLE(const void* p) noexcept { return readI64xLE&lt;8&gt;(p); }</a>
+<a name="876"><span class="lineNum">     876 </span>            :   static ASMJIT_INLINE int64_t readI64uLE(const void* p) noexcept { return readI64xLE&lt;0&gt;(p); }</a>
+<a name="877"><span class="lineNum">     877 </span>            : </a>
+<a name="878"><span class="lineNum">     878 </span>            :   static ASMJIT_INLINE int64_t readI64aBE(const void* p) noexcept { return readI64xBE&lt;8&gt;(p); }</a>
+<a name="879"><span class="lineNum">     879 </span>            :   static ASMJIT_INLINE int64_t readI64uBE(const void* p) noexcept { return readI64xBE&lt;0&gt;(p); }</a>
+<a name="880"><span class="lineNum">     880 </span>            : </a>
+<a name="881"><span class="lineNum">     881 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="882"><span class="lineNum">     882 </span>            :   // [WriteMem]</a>
+<a name="883"><span class="lineNum">     883 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="884"><span class="lineNum">     884 </span>            : </a>
+<a name="885"><span class="lineNum">     885 </span>            :   static ASMJIT_INLINE void writeU8(void* p, uint32_t x) noexcept {</a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineNoCov">          0 :     static_cast&lt;uint8_t*&gt;(p)[0] = static_cast&lt;uint8_t&gt;(x &amp; 0xFFU);</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span>            :   static ASMJIT_INLINE void writeI8(void* p, int32_t x) noexcept {</a>
+<a name="890"><span class="lineNum">     890 </span>            :     static_cast&lt;uint8_t*&gt;(p)[0] = static_cast&lt;uint8_t&gt;(x &amp; 0xFF);</a>
+<a name="891"><span class="lineNum">     891 </span>            :   }</a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="894"><span class="lineNum">     894 </span>            :   static ASMJIT_INLINE void writeU16xLE(void* p, uint32_t x) noexcept {</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineNoCov">          0 :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</span></a>
+<a name="896"><span class="lineNum">     896 </span>            :     if (ASMJIT_ARCH_LE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_16 || Alignment &gt;= 2)) {</a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineNoCov">          0 :       static_cast&lt;uint16_t*&gt;(p)[0] = static_cast&lt;uint16_t&gt;(x &amp; 0xFFFFU);</span></a>
+<a name="898"><span class="lineNum">     898 </span>            :     }</a>
+<a name="899"><span class="lineNum">     899 </span>            :     else {</a>
+<a name="900"><span class="lineNum">     900 </span>            :       static_cast&lt;uint8_t*&gt;(p)[0] = static_cast&lt;uint8_t&gt;((x     ) &amp; 0xFFU);</a>
+<a name="901"><span class="lineNum">     901 </span>            :       static_cast&lt;uint8_t*&gt;(p)[1] = static_cast&lt;uint8_t&gt;((x &gt;&gt; 8) &amp; 0xFFU);</a>
+<a name="902"><span class="lineNum">     902 </span>            :     }</a>
+<a name="903"><span class="lineNum">     903 </span>            :   }</a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="906"><span class="lineNum">     906 </span>            :   static ASMJIT_INLINE void writeU16xBE(void* p, uint32_t x) noexcept {</a>
+<a name="907"><span class="lineNum">     907 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="908"><span class="lineNum">     908 </span>            :     if (ASMJIT_ARCH_BE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_16 || Alignment &gt;= 2)) {</a>
+<a name="909"><span class="lineNum">     909 </span>            :       static_cast&lt;uint16_t*&gt;(p)[0] = static_cast&lt;uint16_t&gt;(x &amp; 0xFFFFU);</a>
+<a name="910"><span class="lineNum">     910 </span>            :     }</a>
+<a name="911"><span class="lineNum">     911 </span>            :     else {</a>
+<a name="912"><span class="lineNum">     912 </span>            :       static_cast&lt;uint8_t*&gt;(p)[0] = static_cast&lt;uint8_t&gt;((x &gt;&gt; 8) &amp; 0xFFU);</a>
+<a name="913"><span class="lineNum">     913 </span>            :       static_cast&lt;uint8_t*&gt;(p)[1] = static_cast&lt;uint8_t&gt;((x     ) &amp; 0xFFU);</a>
+<a name="914"><span class="lineNum">     914 </span>            :     }</a>
+<a name="915"><span class="lineNum">     915 </span>            :   }</a>
+<a name="916"><span class="lineNum">     916 </span>            : </a>
+<a name="917"><span class="lineNum">     917 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="918"><span class="lineNum">     918 </span>            :   static ASMJIT_INLINE void writeU16x(void* p, uint32_t x) noexcept {</a>
+<a name="919"><span class="lineNum">     919 </span>            :     if (ASMJIT_ARCH_LE)</a>
+<a name="920"><span class="lineNum">     920 </span>            :       writeU16xLE&lt;Alignment&gt;(p, x);</a>
+<a name="921"><span class="lineNum">     921 </span>            :     else</a>
+<a name="922"><span class="lineNum">     922 </span>            :       writeU16xBE&lt;Alignment&gt;(p, x);</a>
+<a name="923"><span class="lineNum">     923 </span>            :   }</a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="926"><span class="lineNum">     926 </span>            :   static ASMJIT_INLINE void writeI16xLE(void* p, int32_t x) noexcept {</a>
+<a name="927"><span class="lineNum">     927 </span>            :     writeU16xLE&lt;Alignment&gt;(p, static_cast&lt;uint32_t&gt;(x));</a>
+<a name="928"><span class="lineNum">     928 </span>            :   }</a>
+<a name="929"><span class="lineNum">     929 </span>            : </a>
+<a name="930"><span class="lineNum">     930 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="931"><span class="lineNum">     931 </span>            :   static ASMJIT_INLINE void writeI16xBE(void* p, int32_t x) noexcept {</a>
+<a name="932"><span class="lineNum">     932 </span>            :     writeU16xBE&lt;Alignment&gt;(p, static_cast&lt;uint32_t&gt;(x));</a>
+<a name="933"><span class="lineNum">     933 </span>            :   }</a>
+<a name="934"><span class="lineNum">     934 </span>            : </a>
+<a name="935"><span class="lineNum">     935 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="936"><span class="lineNum">     936 </span>            :   static ASMJIT_INLINE void writeI16x(void* p, int32_t x) noexcept {</a>
+<a name="937"><span class="lineNum">     937 </span>            :     writeU16x&lt;Alignment&gt;(p, static_cast&lt;uint32_t&gt;(x));</a>
+<a name="938"><span class="lineNum">     938 </span>            :   }</a>
+<a name="939"><span class="lineNum">     939 </span>            : </a>
+<a name="940"><span class="lineNum">     940 </span>            :   static ASMJIT_INLINE void writeU16aLE(void* p, uint32_t x) noexcept { writeU16xLE&lt;2&gt;(p, x); }</a>
+<a name="941"><span class="lineNum">     941 </span>            :   static ASMJIT_INLINE void writeU16uLE(void* p, uint32_t x) noexcept { writeU16xLE&lt;0&gt;(p, x); }</a>
+<a name="942"><span class="lineNum">     942 </span>            : </a>
+<a name="943"><span class="lineNum">     943 </span>            :   static ASMJIT_INLINE void writeU16aBE(void* p, uint32_t x) noexcept { writeU16xBE&lt;2&gt;(p, x); }</a>
+<a name="944"><span class="lineNum">     944 </span>            :   static ASMJIT_INLINE void writeU16uBE(void* p, uint32_t x) noexcept { writeU16xBE&lt;0&gt;(p, x); }</a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span>            :   static ASMJIT_INLINE void writeU16a(void* p, uint32_t x) noexcept { writeU16x&lt;2&gt;(p, x); }</a>
+<a name="947"><span class="lineNum">     947 </span>            :   static ASMJIT_INLINE void writeU16u(void* p, uint32_t x) noexcept { writeU16x&lt;0&gt;(p, x); }</a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span>            :   static ASMJIT_INLINE void writeI16aLE(void* p, int32_t x) noexcept { writeI16xLE&lt;2&gt;(p, x); }</a>
+<a name="950"><span class="lineNum">     950 </span>            :   static ASMJIT_INLINE void writeI16uLE(void* p, int32_t x) noexcept { writeI16xLE&lt;0&gt;(p, x); }</a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span>            :   static ASMJIT_INLINE void writeI16aBE(void* p, int32_t x) noexcept { writeI16xBE&lt;2&gt;(p, x); }</a>
+<a name="953"><span class="lineNum">     953 </span>            :   static ASMJIT_INLINE void writeI16uBE(void* p, int32_t x) noexcept { writeI16xBE&lt;0&gt;(p, x); }</a>
+<a name="954"><span class="lineNum">     954 </span>            : </a>
+<a name="955"><span class="lineNum">     955 </span>            :   static ASMJIT_INLINE void writeI16a(void* p, int32_t x) noexcept { writeI16x&lt;2&gt;(p, x); }</a>
+<a name="956"><span class="lineNum">     956 </span>            :   static ASMJIT_INLINE void writeI16u(void* p, int32_t x) noexcept { writeI16x&lt;0&gt;(p, x); }</a>
+<a name="957"><span class="lineNum">     957 </span>            : </a>
+<a name="958"><span class="lineNum">     958 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="959"><span class="lineNum">     959 </span>            :   static ASMJIT_INLINE void writeU32xLE(void* p, uint32_t x) noexcept {</a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">       7700 :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</span></a>
+<a name="961"><span class="lineNum">     961 </span>            :     if (ASMJIT_ARCH_UNALIGNED_32 || Alignment &gt;= 4) {</a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">       7700 :       static_cast&lt;uint32_t*&gt;(p)[0] = ASMJIT_ARCH_LE ? x : byteswap32(x);</span></a>
+<a name="963"><span class="lineNum">     963 </span>            :     }</a>
+<a name="964"><span class="lineNum">     964 </span>            :     else {</a>
+<a name="965"><span class="lineNum">     965 </span>            :       writeU16xLE&lt;Alignment&gt;(static_cast&lt;uint8_t*&gt;(p) + 0, x &gt;&gt; 16);</a>
+<a name="966"><span class="lineNum">     966 </span>            :       writeU16xLE&lt;Alignment&gt;(static_cast&lt;uint8_t*&gt;(p) + 2, x);</a>
+<a name="967"><span class="lineNum">     967 </span>            :     }</a>
+<a name="968"><span class="lineNum">     968 </span>            :   }</a>
+<a name="969"><span class="lineNum">     969 </span>            : </a>
+<a name="970"><span class="lineNum">     970 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="971"><span class="lineNum">     971 </span>            :   static ASMJIT_INLINE void writeU32xBE(void* p, uint32_t x) noexcept {</a>
+<a name="972"><span class="lineNum">     972 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="973"><span class="lineNum">     973 </span>            :     if (ASMJIT_ARCH_UNALIGNED_32 || Alignment &gt;= 4) {</a>
+<a name="974"><span class="lineNum">     974 </span>            :       static_cast&lt;uint32_t*&gt;(p)[0] = ASMJIT_ARCH_BE ? x : byteswap32(x);</a>
+<a name="975"><span class="lineNum">     975 </span>            :     }</a>
+<a name="976"><span class="lineNum">     976 </span>            :     else {</a>
+<a name="977"><span class="lineNum">     977 </span>            :       writeU16xBE&lt;Alignment&gt;(static_cast&lt;uint8_t*&gt;(p) + 0, x);</a>
+<a name="978"><span class="lineNum">     978 </span>            :       writeU16xBE&lt;Alignment&gt;(static_cast&lt;uint8_t*&gt;(p) + 2, x &gt;&gt; 16);</a>
+<a name="979"><span class="lineNum">     979 </span>            :     }</a>
+<a name="980"><span class="lineNum">     980 </span>            :   }</a>
+<a name="981"><span class="lineNum">     981 </span>            : </a>
+<a name="982"><span class="lineNum">     982 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="983"><span class="lineNum">     983 </span>            :   static ASMJIT_INLINE void writeU32x(void* p, uint32_t x) noexcept {</a>
+<a name="984"><span class="lineNum">     984 </span>            :     if (ASMJIT_ARCH_LE)</a>
+<a name="985"><span class="lineNum">     985 </span>            :       writeU32xLE&lt;Alignment&gt;(p, x);</a>
+<a name="986"><span class="lineNum">     986 </span>            :     else</a>
+<a name="987"><span class="lineNum">     987 </span>            :       writeU32xBE&lt;Alignment&gt;(p, x);</a>
+<a name="988"><span class="lineNum">     988 </span>            :   }</a>
+<a name="989"><span class="lineNum">     989 </span>            : </a>
+<a name="990"><span class="lineNum">     990 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="991"><span class="lineNum">     991 </span>            :   static ASMJIT_INLINE void writeI32xLE(void* p, int32_t x) noexcept {</a>
+<a name="992"><span class="lineNum">     992 </span>            :     writeU32xLE&lt;Alignment&gt;(p, static_cast&lt;uint32_t&gt;(x));</a>
+<a name="993"><span class="lineNum">     993 </span>            :   }</a>
+<a name="994"><span class="lineNum">     994 </span>            : </a>
+<a name="995"><span class="lineNum">     995 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="996"><span class="lineNum">     996 </span>            :   static ASMJIT_INLINE void writeI32xBE(void* p, int32_t x) noexcept {</a>
+<a name="997"><span class="lineNum">     997 </span>            :     writeU32xBE&lt;Alignment&gt;(p, static_cast&lt;uint32_t&gt;(x));</a>
+<a name="998"><span class="lineNum">     998 </span>            :   }</a>
+<a name="999"><span class="lineNum">     999 </span>            : </a>
+<a name="1000"><span class="lineNum">    1000 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   static ASMJIT_INLINE void writeI32x(void* p, int32_t x) noexcept {</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     writeU32x&lt;Alignment&gt;(p, static_cast&lt;uint32_t&gt;(x));</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   }</a>
+<a name="1004"><span class="lineNum">    1004 </span>            : </a>
+<a name="1005"><span class="lineNum">    1005 </span>            :   static ASMJIT_INLINE void writeU32aLE(void* p, uint32_t x) noexcept { writeU32xLE&lt;4&gt;(p, x); }</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   static ASMJIT_INLINE void writeU32uLE(void* p, uint32_t x) noexcept { writeU32xLE&lt;0&gt;(p, x); }</a>
+<a name="1007"><span class="lineNum">    1007 </span>            : </a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   static ASMJIT_INLINE void writeU32aBE(void* p, uint32_t x) noexcept { writeU32xBE&lt;4&gt;(p, x); }</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   static ASMJIT_INLINE void writeU32uBE(void* p, uint32_t x) noexcept { writeU32xBE&lt;0&gt;(p, x); }</a>
+<a name="1010"><span class="lineNum">    1010 </span>            : </a>
+<a name="1011"><span class="lineNum">    1011 </span>            :   static ASMJIT_INLINE void writeU32a(void* p, uint32_t x) noexcept { writeU32x&lt;4&gt;(p, x); }</a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE void writeU32u(void* p, uint32_t x) noexcept { writeU32x&lt;0&gt;(p, x); }</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   static ASMJIT_INLINE void writeI32aLE(void* p, int32_t x) noexcept { writeI32xLE&lt;4&gt;(p, x); }</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   static ASMJIT_INLINE void writeI32uLE(void* p, int32_t x) noexcept { writeI32xLE&lt;0&gt;(p, x); }</a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   static ASMJIT_INLINE void writeI32aBE(void* p, int32_t x) noexcept { writeI32xBE&lt;4&gt;(p, x); }</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :   static ASMJIT_INLINE void writeI32uBE(void* p, int32_t x) noexcept { writeI32xBE&lt;0&gt;(p, x); }</a>
+<a name="1019"><span class="lineNum">    1019 </span>            : </a>
+<a name="1020"><span class="lineNum">    1020 </span>            :   static ASMJIT_INLINE void writeI32a(void* p, int32_t x) noexcept { writeI32x&lt;4&gt;(p, x); }</a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE void writeI32u(void* p, int32_t x) noexcept { writeI32x&lt;0&gt;(p, x); }</span></a>
+<a name="1022"><span class="lineNum">    1022 </span>            : </a>
+<a name="1023"><span class="lineNum">    1023 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   static ASMJIT_INLINE void writeU64xLE(void* p, uint64_t x) noexcept {</a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineNoCov">          0 :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</span></a>
+<a name="1026"><span class="lineNum">    1026 </span>            :     if (ASMJIT_ARCH_LE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_64 || Alignment &gt;= 8)) {</a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineNoCov">          0 :       static_cast&lt;uint64_t*&gt;(p)[0] = x;</span></a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     }</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     else {</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :       writeU32xLE&lt;Alignment / 2U&gt;(static_cast&lt;uint8_t*&gt;(p) + 0, static_cast&lt;uint32_t&gt;(x &gt;&gt; 32));</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :       writeU32xLE&lt;Alignment / 2U&gt;(static_cast&lt;uint8_t*&gt;(p) + 4, static_cast&lt;uint32_t&gt;(x &amp; 0xFFFFFFFFU));</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :     }</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   }</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : </a>
+<a name="1035"><span class="lineNum">    1035 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   static ASMJIT_INLINE void writeU64xBE(void* p, uint64_t x) noexcept {</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     ASMJIT_ASSUME_ALIGNED(p, Alignment &gt; 1 ? Alignment : 1U);</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :     if (ASMJIT_ARCH_BE &amp;&amp; (ASMJIT_ARCH_UNALIGNED_64 || Alignment &gt;= 8)) {</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :       static_cast&lt;uint64_t*&gt;(p)[0] = x;</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :     }</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     else {</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :       writeU32xBE&lt;Alignment / 2U&gt;(static_cast&lt;uint8_t*&gt;(p) + 0, static_cast&lt;uint32_t&gt;(x &amp; 0xFFFFFFFFU));</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :       writeU32xBE&lt;Alignment / 2U&gt;(static_cast&lt;uint8_t*&gt;(p) + 4, static_cast&lt;uint32_t&gt;(x &gt;&gt; 32));</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     }</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :   }</a>
+<a name="1046"><span class="lineNum">    1046 </span>            : </a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :   static ASMJIT_INLINE void writeU64x(void* p, uint64_t x) noexcept {</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :     if (ASMJIT_ARCH_LE)</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :       writeU64xLE&lt;Alignment&gt;(p, x);</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     else</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :       writeU64xBE&lt;Alignment&gt;(p, x);</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   }</a>
+<a name="1054"><span class="lineNum">    1054 </span>            : </a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :   static ASMJIT_INLINE void writeI64xLE(void* p, int64_t x) noexcept {</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :     writeU64xLE&lt;Alignment&gt;(p, static_cast&lt;uint64_t&gt;(x));</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   }</a>
+<a name="1059"><span class="lineNum">    1059 </span>            : </a>
+<a name="1060"><span class="lineNum">    1060 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   static ASMJIT_INLINE void writeI64xBE(void* p, int64_t x) noexcept {</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     writeU64xBE&lt;Alignment&gt;(p, static_cast&lt;uint64_t&gt;(x));</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   }</a>
+<a name="1064"><span class="lineNum">    1064 </span>            : </a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   template&lt;unsigned int Alignment&gt;</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :   static ASMJIT_INLINE void writeI64x(void* p, int64_t x) noexcept {</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :     writeU64x&lt;Alignment&gt;(p, static_cast&lt;uint64_t&gt;(x));</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   }</a>
+<a name="1069"><span class="lineNum">    1069 </span>            : </a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   static ASMJIT_INLINE void writeU64aLE(void* p, uint64_t x) noexcept { writeU64xLE&lt;8&gt;(p, x); }</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   static ASMJIT_INLINE void writeU64uLE(void* p, uint64_t x) noexcept { writeU64xLE&lt;0&gt;(p, x); }</a>
+<a name="1072"><span class="lineNum">    1072 </span>            : </a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   static ASMJIT_INLINE void writeU64aBE(void* p, uint64_t x) noexcept { writeU64xBE&lt;8&gt;(p, x); }</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   static ASMJIT_INLINE void writeU64uBE(void* p, uint64_t x) noexcept { writeU64xBE&lt;0&gt;(p, x); }</a>
+<a name="1075"><span class="lineNum">    1075 </span>            : </a>
+<a name="1076"><span class="lineNum">    1076 </span>            :   static ASMJIT_INLINE void writeU64a(void* p, uint64_t x) noexcept { writeU64x&lt;8&gt;(p, x); }</a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE void writeU64u(void* p, uint64_t x) noexcept { writeU64x&lt;0&gt;(p, x); }</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            : </a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   static ASMJIT_INLINE void writeI64aLE(void* p, int64_t x) noexcept { writeI64xLE&lt;8&gt;(p, x); }</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :   static ASMJIT_INLINE void writeI64uLE(void* p, int64_t x) noexcept { writeI64xLE&lt;0&gt;(p, x); }</a>
+<a name="1081"><span class="lineNum">    1081 </span>            : </a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   static ASMJIT_INLINE void writeI64aBE(void* p, int64_t x) noexcept { writeI64xBE&lt;8&gt;(p, x); }</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   static ASMJIT_INLINE void writeI64uBE(void* p, int64_t x) noexcept { writeI64xBE&lt;0&gt;(p, x); }</a>
+<a name="1084"><span class="lineNum">    1084 </span>            : </a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   static ASMJIT_INLINE void writeI64a(void* p, int64_t x) noexcept { writeI64x&lt;8&gt;(p, x); }</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   static ASMJIT_INLINE void writeI64u(void* p, int64_t x) noexcept { writeI64x&lt;0&gt;(p, x); }</a>
+<a name="1087"><span class="lineNum">    1087 </span>            : } // Utils namespace</a>
+<a name="1088"><span class="lineNum">    1088 </span>            : </a>
+<a name="1089"><span class="lineNum">    1089 </span>            : // ============================================================================</a>
+<a name="1090"><span class="lineNum">    1090 </span>            : // [asmjit::UInt64]</a>
+<a name="1091"><span class="lineNum">    1091 </span>            : // ============================================================================</a>
+<a name="1092"><span class="lineNum">    1092 </span>            : </a>
+<a name="1093"><span class="lineNum">    1093 </span>            : union UInt64 {</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   // [Construction / Destruction]</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : </a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   ASMJIT_INLINE UInt64 fromUInt64(uint64_t val) noexcept {</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :     UInt64 data;</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :     data.setUInt64(val);</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :     return data;</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   }</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : </a>
+<a name="1104"><span class="lineNum">    1104 </span>            :   ASMJIT_INLINE UInt64 fromUInt64(const UInt64&amp; val) noexcept {</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :     UInt64 data;</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :     data.setUInt64(val);</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :     return data;</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   }</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   // [Reset]</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1113"><span class="lineNum">    1113 </span>            : </a>
+<a name="1114"><span class="lineNum">    1114 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">      80896 :       u64 = 0;</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     }</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :     else {</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :       u32[0] = 0;</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :       u32[1] = 0;</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     }</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   }</a>
+<a name="1123"><span class="lineNum">    1123 </span>            : </a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   // [Accessors]</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : </a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   ASMJIT_INLINE uint64_t getUInt64() const noexcept {</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :     return u64;</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   }</a>
+<a name="1131"><span class="lineNum">    1131 </span>            : </a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   ASMJIT_INLINE UInt64&amp; setUInt64(uint64_t val) noexcept {</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     u64 = val;</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     return *this;</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   }</a>
+<a name="1136"><span class="lineNum">    1136 </span>            : </a>
+<a name="1137"><span class="lineNum">    1137 </span>            :   ASMJIT_INLINE UInt64&amp; setUInt64(const UInt64&amp; val) noexcept {</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :       u64 = val.u64;</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :     }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     else {</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :       u32[0] = val.u32[0];</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :       u32[1] = val.u32[1];</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :     }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :     return *this;</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   }</a>
+<a name="1147"><span class="lineNum">    1147 </span>            : </a>
+<a name="1148"><span class="lineNum">    1148 </span>            :   ASMJIT_INLINE UInt64&amp; setPacked_2x32(uint32_t u0, uint32_t u1) noexcept {</a>
+<a name="1149"><span class="lineNum">    1149 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">      74716 :       u64 = Utils::pack64_2x32(u0, u1);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span>            :     }</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :     else {</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :       u32[0] = u0;</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :       u32[1] = u1;</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :     }</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     return *this;</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :   }</a>
+<a name="1158"><span class="lineNum">    1158 </span>            : </a>
+<a name="1159"><span class="lineNum">    1159 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   // [Add]</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1162"><span class="lineNum">    1162 </span>            : </a>
+<a name="1163"><span class="lineNum">    1163 </span>            :   ASMJIT_INLINE UInt64&amp; add(uint64_t val) noexcept {</a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     u64 += val;</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :     return *this;</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :   }</a>
+<a name="1167"><span class="lineNum">    1167 </span>            : </a>
+<a name="1168"><span class="lineNum">    1168 </span>            :   ASMJIT_INLINE UInt64&amp; add(const UInt64&amp; val) noexcept {</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :       u64 += val.u64;</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :     }</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :     else {</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :       u32[0] += val.u32[0];</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :       u32[1] += val.u32[1];</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :     }</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     return *this;</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :   }</a>
+<a name="1178"><span class="lineNum">    1178 </span>            : </a>
+<a name="1179"><span class="lineNum">    1179 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1180"><span class="lineNum">    1180 </span>            :   // [Sub]</a>
+<a name="1181"><span class="lineNum">    1181 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1182"><span class="lineNum">    1182 </span>            : </a>
+<a name="1183"><span class="lineNum">    1183 </span>            :   ASMJIT_INLINE UInt64&amp; sub(uint64_t val) noexcept {</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :     u64 -= val;</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     return *this;</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   }</a>
+<a name="1187"><span class="lineNum">    1187 </span>            : </a>
+<a name="1188"><span class="lineNum">    1188 </span>            :   ASMJIT_INLINE UInt64&amp; sub(const UInt64&amp; val) noexcept {</a>
+<a name="1189"><span class="lineNum">    1189 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :       u64 -= val.u64;</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :     }</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :     else {</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :       u32[0] -= val.u32[0];</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :       u32[1] -= val.u32[1];</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :     }</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :     return *this;</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :   }</a>
+<a name="1198"><span class="lineNum">    1198 </span>            : </a>
+<a name="1199"><span class="lineNum">    1199 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :   // [And]</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1202"><span class="lineNum">    1202 </span>            : </a>
+<a name="1203"><span class="lineNum">    1203 </span>            :   ASMJIT_INLINE UInt64&amp; and_(uint64_t val) noexcept {</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     u64 &amp;= val;</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :     return *this;</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :   }</a>
+<a name="1207"><span class="lineNum">    1207 </span>            : </a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   ASMJIT_INLINE UInt64&amp; and_(const UInt64&amp; val) noexcept {</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :       u64 &amp;= val.u64;</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :     }</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :     else {</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :       u32[0] &amp;= val.u32[0];</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :       u32[1] &amp;= val.u32[1];</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :     }</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :     return *this;</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   }</a>
+<a name="1218"><span class="lineNum">    1218 </span>            : </a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :   // [AndNot]</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1222"><span class="lineNum">    1222 </span>            : </a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   ASMJIT_INLINE UInt64&amp; andNot(uint64_t val) noexcept {</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :     u64 &amp;= ~val;</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :     return *this;</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :   }</a>
+<a name="1227"><span class="lineNum">    1227 </span>            : </a>
+<a name="1228"><span class="lineNum">    1228 </span>            :   ASMJIT_INLINE UInt64&amp; andNot(const UInt64&amp; val) noexcept {</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :       u64 &amp;= ~val.u64;</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :     }</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :     else {</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :       u32[0] &amp;= ~val.u32[0];</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :       u32[1] &amp;= ~val.u32[1];</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :     }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     return *this;</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :   }</a>
+<a name="1238"><span class="lineNum">    1238 </span>            : </a>
+<a name="1239"><span class="lineNum">    1239 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :   // [Or]</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1242"><span class="lineNum">    1242 </span>            : </a>
+<a name="1243"><span class="lineNum">    1243 </span>            :   ASMJIT_INLINE UInt64&amp; or_(uint64_t val) noexcept {</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :     u64 |= val;</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :     return *this;</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :   }</a>
+<a name="1247"><span class="lineNum">    1247 </span>            : </a>
+<a name="1248"><span class="lineNum">    1248 </span>            :   ASMJIT_INLINE UInt64&amp; or_(const UInt64&amp; val) noexcept {</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">      68160 :       u64 |= val.u64;</span></a>
+<a name="1251"><span class="lineNum">    1251 </span>            :     }</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :     else {</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :       u32[0] |= val.u32[0];</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :       u32[1] |= val.u32[1];</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :     }</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :     return *this;</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :   }</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : </a>
+<a name="1259"><span class="lineNum">    1259 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   // [Xor]</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span>            :   ASMJIT_INLINE UInt64&amp; xor_(uint64_t val) noexcept {</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :     u64 ^= val;</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :     return *this;</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   }</a>
+<a name="1267"><span class="lineNum">    1267 </span>            : </a>
+<a name="1268"><span class="lineNum">    1268 </span>            :   ASMJIT_INLINE UInt64&amp; xor_(const UInt64&amp; val) noexcept {</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :     if (ASMJIT_ARCH_64BIT) {</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :       u64 ^= val.u64;</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :     }</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :     else {</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :       u32[0] ^= val.u32[0];</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :       u32[1] ^= val.u32[1];</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :     }</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :     return *this;</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :   }</a>
+<a name="1278"><span class="lineNum">    1278 </span>            : </a>
+<a name="1279"><span class="lineNum">    1279 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :   // [Eq]</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1282"><span class="lineNum">    1282 </span>            : </a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   ASMJIT_INLINE bool isZero() const noexcept {</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :     if (ASMJIT_ARCH_64BIT)</a>
+<a name="1285"><span class="lineNum">    1285 </span>            :       return u64 == 0;</a>
+<a name="1286"><span class="lineNum">    1286 </span>            :     else</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :       return (u32[0] | u32[1]) == 0;</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :   }</a>
+<a name="1289"><span class="lineNum">    1289 </span>            : </a>
+<a name="1290"><span class="lineNum">    1290 </span>            :   ASMJIT_INLINE bool isNonZero() const noexcept {</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     if (ASMJIT_ARCH_64BIT)</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :       return u64 != 0;</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :     else</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :       return (u32[0] | u32[1]) != 0;</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :   }</a>
+<a name="1296"><span class="lineNum">    1296 </span>            : </a>
+<a name="1297"><span class="lineNum">    1297 </span>            :   ASMJIT_INLINE bool eq(uint64_t val) const noexcept {</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :     return u64 == val;</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :   }</a>
+<a name="1300"><span class="lineNum">    1300 </span>            : </a>
+<a name="1301"><span class="lineNum">    1301 </span>            :   ASMJIT_INLINE bool eq(const UInt64&amp; val) const noexcept {</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :     if (ASMJIT_ARCH_64BIT)</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :       return u64 == val.u64;</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :     else</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :       return u32[0] == val.u32[0] &amp;&amp; u32[1] == val.u32[1];</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :   }</a>
+<a name="1307"><span class="lineNum">    1307 </span>            : </a>
+<a name="1308"><span class="lineNum">    1308 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :   // [Operator Overload]</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1311"><span class="lineNum">    1311 </span>            : </a>
+<a name="1312"><span class="lineNum">    1312 </span>            :   ASMJIT_INLINE UInt64&amp; operator+=(uint64_t val) noexcept { return add(val); }</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :   ASMJIT_INLINE UInt64&amp; operator+=(const UInt64&amp; val) noexcept { return add(val); }</a>
+<a name="1314"><span class="lineNum">    1314 </span>            : </a>
+<a name="1315"><span class="lineNum">    1315 </span>            :   ASMJIT_INLINE UInt64&amp; operator-=(uint64_t val) noexcept { return sub(val); }</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :   ASMJIT_INLINE UInt64&amp; operator-=(const UInt64&amp; val) noexcept { return sub(val); }</a>
+<a name="1317"><span class="lineNum">    1317 </span>            : </a>
+<a name="1318"><span class="lineNum">    1318 </span>            :   ASMJIT_INLINE UInt64&amp; operator&amp;=(uint64_t val) noexcept { return and_(val); }</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :   ASMJIT_INLINE UInt64&amp; operator&amp;=(const UInt64&amp; val) noexcept { return and_(val); }</a>
+<a name="1320"><span class="lineNum">    1320 </span>            : </a>
+<a name="1321"><span class="lineNum">    1321 </span>            :   ASMJIT_INLINE UInt64&amp; operator|=(uint64_t val) noexcept { return or_(val); }</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :   ASMJIT_INLINE UInt64&amp; operator|=(const UInt64&amp; val) noexcept { return or_(val); }</a>
+<a name="1323"><span class="lineNum">    1323 </span>            : </a>
+<a name="1324"><span class="lineNum">    1324 </span>            :   ASMJIT_INLINE UInt64&amp; operator^=(uint64_t val) noexcept { return xor_(val); }</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :   ASMJIT_INLINE UInt64&amp; operator^=(const UInt64&amp; val) noexcept { return xor_(val); }</a>
+<a name="1326"><span class="lineNum">    1326 </span>            : </a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   ASMJIT_INLINE bool operator==(uint64_t val) const noexcept { return eq(val); }</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :   ASMJIT_INLINE bool operator==(const UInt64&amp; val) const noexcept { return eq(val); }</a>
+<a name="1329"><span class="lineNum">    1329 </span>            : </a>
+<a name="1330"><span class="lineNum">    1330 </span>            :   ASMJIT_INLINE bool operator!=(uint64_t val) const noexcept { return !eq(val); }</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :   ASMJIT_INLINE bool operator!=(const UInt64&amp; val) const noexcept { return !eq(val); }</a>
+<a name="1332"><span class="lineNum">    1332 </span>            : </a>
+<a name="1333"><span class="lineNum">    1333 </span>            :   ASMJIT_INLINE bool operator&lt;(uint64_t val) const noexcept { return u64 &lt; val; }</a>
+<a name="1334"><span class="lineNum">    1334 </span>            :   ASMJIT_INLINE bool operator&lt;(const UInt64&amp; val) const noexcept { return u64 &lt; val.u64; }</a>
+<a name="1335"><span class="lineNum">    1335 </span>            : </a>
+<a name="1336"><span class="lineNum">    1336 </span>            :   ASMJIT_INLINE bool operator&lt;=(uint64_t val) const noexcept { return u64 &lt;= val; }</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   ASMJIT_INLINE bool operator&lt;=(const UInt64&amp; val) const noexcept { return u64 &lt;= val.u64; }</a>
+<a name="1338"><span class="lineNum">    1338 </span>            : </a>
+<a name="1339"><span class="lineNum">    1339 </span>            :   ASMJIT_INLINE bool operator&gt;(uint64_t val) const noexcept { return u64 &gt; val; }</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :   ASMJIT_INLINE bool operator&gt;(const UInt64&amp; val) const noexcept { return u64 &gt; val.u64; }</a>
+<a name="1341"><span class="lineNum">    1341 </span>            : </a>
+<a name="1342"><span class="lineNum">    1342 </span>            :   ASMJIT_INLINE bool operator&gt;=(uint64_t val) const noexcept { return u64 &gt;= val; }</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :   ASMJIT_INLINE bool operator&gt;=(const UInt64&amp; val) const noexcept { return u64 &gt;= val.u64; }</a>
+<a name="1344"><span class="lineNum">    1344 </span>            : </a>
+<a name="1345"><span class="lineNum">    1345 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1346"><span class="lineNum">    1346 </span>            :   // [Members]</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1348"><span class="lineNum">    1348 </span>            : </a>
+<a name="1349"><span class="lineNum">    1349 </span>            :   int8_t   i8[8];                        //!&lt; 8-bit signed integer (8x).</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :   uint8_t  u8[8];                        //!&lt; 8-bit unsigned integer (8x).</a>
+<a name="1351"><span class="lineNum">    1351 </span>            : </a>
+<a name="1352"><span class="lineNum">    1352 </span>            :   int16_t  i16[4];                       //!&lt; 16-bit signed integer (4x).</a>
+<a name="1353"><span class="lineNum">    1353 </span>            :   uint16_t u16[4];                       //!&lt; 16-bit unsigned integer (4x).</a>
+<a name="1354"><span class="lineNum">    1354 </span>            : </a>
+<a name="1355"><span class="lineNum">    1355 </span>            :   int32_t  i32[2];                       //!&lt; 32-bit signed integer (2x).</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :   uint32_t u32[2];                       //!&lt; 32-bit unsigned integer (2x).</a>
+<a name="1357"><span class="lineNum">    1357 </span>            : </a>
+<a name="1358"><span class="lineNum">    1358 </span>            :   int64_t  i64;                          //!&lt; 64-bit signed integer.</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :   uint64_t u64;                          //!&lt; 64-bit unsigned integer.</a>
+<a name="1360"><span class="lineNum">    1360 </span>            : </a>
+<a name="1361"><span class="lineNum">    1361 </span>            :   float    f32[2];                       //!&lt; 32-bit floating point (2x).</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :   double   f64;                          //!&lt; 64-bit floating point.</a>
+<a name="1363"><span class="lineNum">    1363 </span>            : </a>
+<a name="1364"><span class="lineNum">    1364 </span>            : #if ASMJIT_ARCH_LE</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :   struct { float    f32Lo, f32Hi; };</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :   struct { int32_t  i32Lo, i32Hi; };</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :   struct { uint32_t u32Lo, u32Hi; };</a>
+<a name="1368"><span class="lineNum">    1368 </span>            : #else</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :   struct { float    f32Hi, f32Lo; };</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :   struct { int32_t  i32Hi, i32Lo; };</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :   struct { uint32_t u32Hi, u32Lo; };</a>
+<a name="1372"><span class="lineNum">    1372 </span>            : #endif // ASMJIT_ARCH_LE</a>
+<a name="1373"><span class="lineNum">    1373 </span>            : };</a>
+<a name="1374"><span class="lineNum">    1374 </span>            : </a>
+<a name="1375"><span class="lineNum">    1375 </span>            : //! \}</a>
+<a name="1376"><span class="lineNum">    1376 </span>            : </a>
+<a name="1377"><span class="lineNum">    1377 </span>            : } // asmjit namespace</a>
+<a name="1378"><span class="lineNum">    1378 </span>            : } // namespace PLMD</a>
+<a name="1379"><span class="lineNum">    1379 </span>            : </a>
+<a name="1380"><span class="lineNum">    1380 </span>            : // [Api-End]</a>
+<a name="1381"><span class="lineNum">    1381 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="1382"><span class="lineNum">    1382 </span>            : </a>
+<a name="1383"><span class="lineNum">    1383 </span>            : // [Guard]</a>
+<a name="1384"><span class="lineNum">    1384 </span>            : #endif // _ASMJIT_BASE_UTILS_H</a>
+<a name="1385"><span class="lineNum">    1385 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1386"><span class="lineNum">    1386 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="1387"><span class="lineNum">    1387 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/vmem.cpp.func-sort-c.html b/coverage-libs/asmjit/vmem.cpp.func-sort-c.html
new file mode 100644
index 0000000000..506e56ff03
--- /dev/null
+++ b/coverage-libs/asmjit/vmem.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/vmem.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - vmem.cpp<span style="font-size: 80%;"> (<a href="vmem.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">318</td>
+            <td class="headerCovTableEntryLo">30.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="vmem.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#784">_ZN4PLMD6asmjit7VMemMgr5resetEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#883">_ZN4PLMD6asmjit7VMemMgr6shrinkEPvm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#799">_ZN4PLMD6asmjit7VMemMgr7releaseEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#416">_ZN4PLMD6asmjitL17vMemMgrRemoveNodeEPNS0_7VMemMgrEPNS1_7MemNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#515">_ZN4PLMD6asmjitL20vMemMgrFindNodeByPtrEPNS0_7VMemMgrEPh</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#539">_ZN4PLMD6asmjitL21vMemMgrAllocPermanentEPNS0_7VMemMgrEm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#792">_ZN4PLMD6asmjit7VMemMgr5allocEmj</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#291">_ZN4PLMD6asmjitL17vMemMgrCreateNodeEPNS0_7VMemMgrEmm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#333">_ZN4PLMD6asmjitL17vMemMgrInsertNodeEPNS0_7VMemMgrEPNS1_7MemNodeE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#582">_ZN4PLMD6asmjitL20vMemMgrAllocFreeableEPNS0_7VMemMgrEm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#741">_ZN4PLMD6asmjit7VMemMgrC2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#767">_ZN4PLMD6asmjit7VMemMgrD2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#712">_ZN4PLMD6asmjitL12vMemMgrResetEPNS0_7VMemMgrEb</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#91">_ZN4PLMD6asmjitL8_SetBitsEPmmm</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/vmem.cpp.func.html b/coverage-libs/asmjit/vmem.cpp.func.html
new file mode 100644
index 0000000000..ad3f59acf8
--- /dev/null
+++ b/coverage-libs/asmjit/vmem.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/vmem.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - vmem.cpp<span style="font-size: 80%;"> (<a href="vmem.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">318</td>
+            <td class="headerCovTableEntryLo">30.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="vmem.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#792">_ZN4PLMD6asmjit7VMemMgr5allocEmj</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#784">_ZN4PLMD6asmjit7VMemMgr5resetEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#883">_ZN4PLMD6asmjit7VMemMgr6shrinkEPvm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#799">_ZN4PLMD6asmjit7VMemMgr7releaseEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#741">_ZN4PLMD6asmjit7VMemMgrC2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#767">_ZN4PLMD6asmjit7VMemMgrD2Ev</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#712">_ZN4PLMD6asmjitL12vMemMgrResetEPNS0_7VMemMgrEb</a></td>
+              <td class="coverFnHi">1976</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#291">_ZN4PLMD6asmjitL17vMemMgrCreateNodeEPNS0_7VMemMgrEmm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#333">_ZN4PLMD6asmjitL17vMemMgrInsertNodeEPNS0_7VMemMgrEPNS1_7MemNodeE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#416">_ZN4PLMD6asmjitL17vMemMgrRemoveNodeEPNS0_7VMemMgrEPNS1_7MemNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#582">_ZN4PLMD6asmjitL20vMemMgrAllocFreeableEPNS0_7VMemMgrEm</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#515">_ZN4PLMD6asmjitL20vMemMgrFindNodeByPtrEPNS0_7VMemMgrEPh</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#539">_ZN4PLMD6asmjitL21vMemMgrAllocPermanentEPNS0_7VMemMgrEm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="vmem.cpp.gcov.html#91">_ZN4PLMD6asmjitL8_SetBitsEPmmm</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/vmem.cpp.gcov.html b/coverage-libs/asmjit/vmem.cpp.gcov.html
new file mode 100644
index 0000000000..aeae52860c
--- /dev/null
+++ b/coverage-libs/asmjit/vmem.cpp.gcov.html
@@ -0,0 +1,1179 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/vmem.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - vmem.cpp<span style="font-size: 80%;"> (source / <a href="vmem.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">318</td>
+            <td class="headerCovTableEntryLo">30.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./osutils.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./vmem.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : // [Api-Begin]</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : // This file contains implementation of virtual memory management for AsmJit</a>
+<a name="41"><span class="lineNum">      41 </span>            : // library. There are several goals I decided to write implementation myself:</a>
+<a name="42"><span class="lineNum">      42 </span>            : //</a>
+<a name="43"><span class="lineNum">      43 </span>            : // - Granularity of allocated blocks is different than granularity for a typical</a>
+<a name="44"><span class="lineNum">      44 </span>            : //   C malloc. It is at least 64-bytes so CodeEmitter can guarantee the alignment</a>
+<a name="45"><span class="lineNum">      45 </span>            : //   up to 64 bytes, which is the size of a cache-line and it's also required by</a>
+<a name="46"><span class="lineNum">      46 </span>            : //   AVX-512 aligned loads and stores. Alignment requirements can grow in the future,</a>
+<a name="47"><span class="lineNum">      47 </span>            : //   but at the moment 64 bytes is safe (we may jump to 128 bytes if necessary or</a>
+<a name="48"><span class="lineNum">      48 </span>            : //   make it configurable).</a>
+<a name="49"><span class="lineNum">      49 </span>            : //</a>
+<a name="50"><span class="lineNum">      50 </span>            : // - Keep memory manager information outside of the allocated virtual memory</a>
+<a name="51"><span class="lineNum">      51 </span>            : //   pages, because these pages allow machine code execution and there should</a>
+<a name="52"><span class="lineNum">      52 </span>            : //   be not data required to keep track of these blocks. Another reason is that</a>
+<a name="53"><span class="lineNum">      53 </span>            : //   some environments (i.e. iOS) allow to generate and run JIT code, but this</a>
+<a name="54"><span class="lineNum">      54 </span>            : //   code has to be set to [Executable, but not Writable].</a>
+<a name="55"><span class="lineNum">      55 </span>            : //</a>
+<a name="56"><span class="lineNum">      56 </span>            : // - Keep implementation simple and easy to follow.</a>
+<a name="57"><span class="lineNum">      57 </span>            : //</a>
+<a name="58"><span class="lineNum">      58 </span>            : // Implementation is based on bit arrays and binary trees. Bit arrays contain</a>
+<a name="59"><span class="lineNum">      59 </span>            : // information related to allocated and unused blocks of memory. The size of</a>
+<a name="60"><span class="lineNum">      60 </span>            : // a block is described by `MemNode::density`. Count of blocks is stored in</a>
+<a name="61"><span class="lineNum">      61 </span>            : // `MemNode::blocks`. For example if density is 64 and count of blocks is 20,</a>
+<a name="62"><span class="lineNum">      62 </span>            : // memory node contains 64*20 bytes of memory and the smallest possible allocation</a>
+<a name="63"><span class="lineNum">      63 </span>            : // (and also alignment) is 64 bytes. So density is also related to memory</a>
+<a name="64"><span class="lineNum">      64 </span>            : // alignment. Binary trees (RB) are used to enable fast lookup into all addresses</a>
+<a name="65"><span class="lineNum">      65 </span>            : // allocated by memory manager instance. This is used mainly by `VMemPrivate::release()`.</a>
+<a name="66"><span class="lineNum">      66 </span>            : //</a>
+<a name="67"><span class="lineNum">      67 </span>            : // Bit array looks like this (empty = unused, X = used) - Size of block 64:</a>
+<a name="68"><span class="lineNum">      68 </span>            : //</a>
+<a name="69"><span class="lineNum">      69 </span>            : //   -------------------------------------------------------------------------</a>
+<a name="70"><span class="lineNum">      70 </span>            : //   | |X|X| | | | | |X|X|X|X|X|X| | | | | | | | | | | | |X| | | | |X|X|X| | |</a>
+<a name="71"><span class="lineNum">      71 </span>            : //   -------------------------------------------------------------------------</a>
+<a name="72"><span class="lineNum">      72 </span>            : //                               (Maximum continuous block)</a>
+<a name="73"><span class="lineNum">      73 </span>            : //</a>
+<a name="74"><span class="lineNum">      74 </span>            : // These bits show that there are 12 allocated blocks (X) of 64 bytes, so total</a>
+<a name="75"><span class="lineNum">      75 </span>            : // size allocated is 768 bytes. Maximum count of continuous memory is 12 * 64.</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : namespace PLMD {</a>
+<a name="78"><span class="lineNum">      78 </span>            : namespace asmjit {</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : // ============================================================================</a>
+<a name="81"><span class="lineNum">      81 </span>            : // [asmjit::VMemMgr - BitOps]</a>
+<a name="82"><span class="lineNum">      82 </span>            : // ============================================================================</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : #define M_DIV(x, y) ((x) / (y))</a>
+<a name="85"><span class="lineNum">      85 </span>            : #define M_MOD(x, y) ((x) % (y))</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : //! \internal</a>
+<a name="88"><span class="lineNum">      88 </span>            : enum { kBitsPerEntity = (sizeof(size_t) * 8) };</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : //! \internal</a>
+<a name="91"><span class="lineNum">      91 </span>            : //!</a>
+<a name="92"><span class="lineNum">      92 </span>            : //! Set `len` bits in `buf` starting at `index` bit index.</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       3896 : static void _SetBits(size_t* buf, size_t index, size_t len) noexcept {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       3896 :   if (len == 0)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     return;</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       3152 :   size_t i = index / kBitsPerEntity; // size_t[]</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       3152 :   size_t j = index % kBitsPerEntity; // size_t[][] bit index</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   // How many bytes process in the first group.</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       3152 :   size_t c = kBitsPerEntity - j;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   if (c &gt; len)</a>
+<a name="103"><span class="lineNum">     103 </span>            :     c = len;</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Offset.</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       3152 :   buf += i;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       3152 :   *buf++ |= ((~(size_t)0) &gt;&gt; (kBitsPerEntity - c)) &lt;&lt; j;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       3152 :   len -= c;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       3152 :   while (len &gt;= kBitsPerEntity) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     *buf++ = ~(size_t)0;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :     len -= kBitsPerEntity;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       3152 :   if (len)</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     *buf |= ((~(size_t)0) &gt;&gt; (kBitsPerEntity - len));</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : // ============================================================================</a>
+<a name="121"><span class="lineNum">     121 </span>            : // [asmjit::VMemMgr::TypeDefs]</a>
+<a name="122"><span class="lineNum">     122 </span>            : // ============================================================================</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : typedef VMemMgr::RbNode RbNode;</a>
+<a name="125"><span class="lineNum">     125 </span>            : typedef VMemMgr::MemNode MemNode;</a>
+<a name="126"><span class="lineNum">     126 </span>            : typedef VMemMgr::PermanentNode PermanentNode;</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : // ============================================================================</a>
+<a name="129"><span class="lineNum">     129 </span>            : // [asmjit::VMemMgr::RbNode]</a>
+<a name="130"><span class="lineNum">     130 </span>            : // ============================================================================</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : //! \internal</a>
+<a name="133"><span class="lineNum">     133 </span>            : //!</a>
+<a name="134"><span class="lineNum">     134 </span>            : //! Base red-black tree node.</a>
+<a name="135"><span class="lineNum">     135 </span>            : struct VMemMgr::RbNode {</a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Implementation is based on article by Julienne Walker (Public Domain),</a>
+<a name="137"><span class="lineNum">     137 </span>            :   // including C code and original comments. Thanks for the excellent article.</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   RbNode* node[2];                       //!&lt; Left[0] and right[1] nodes.</a>
+<a name="140"><span class="lineNum">     140 </span>            :   uint8_t* mem;                          //!&lt; Virtual memory address.</a>
+<a name="141"><span class="lineNum">     141 </span>            :   uint32_t red;                          //!&lt; Node color (red vs. black).</a>
+<a name="142"><span class="lineNum">     142 </span>            : };</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : //! \internal</a>
+<a name="145"><span class="lineNum">     145 </span>            : //!</a>
+<a name="146"><span class="lineNum">     146 </span>            : //! Get if the node is red (nullptr or node with red flag).</a>
+<a name="147"><span class="lineNum">     147 </span>            : static ASMJIT_INLINE bool rbIsRed(RbNode* node) noexcept {</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   return node &amp;&amp; node-&gt;red;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : //! \internal</a>
+<a name="152"><span class="lineNum">     152 </span>            : //!</a>
+<a name="153"><span class="lineNum">     153 </span>            : //! Check whether the RB tree is valid.</a>
+<a name="154"><span class="lineNum">     154 </span>            : static int rbAssert(RbNode* root) noexcept {</a>
+<a name="155"><span class="lineNum">     155 </span>            :   if (!root) return 1;</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   RbNode* ln = root-&gt;node[0];</a>
+<a name="158"><span class="lineNum">     158 </span>            :   RbNode* rn = root-&gt;node[1];</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   // Red violation.</a>
+<a name="161"><span class="lineNum">     161 </span>            :   ASMJIT_ASSERT(!(rbIsRed(root) &amp;&amp; (rbIsRed(ln) || rbIsRed(rn))));</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   int lh = rbAssert(ln);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   int rh = rbAssert(rn);</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   // Invalid btree.</a>
+<a name="167"><span class="lineNum">     167 </span>            :   ASMJIT_ASSERT(ln == nullptr || ln-&gt;mem &lt; root-&gt;mem);</a>
+<a name="168"><span class="lineNum">     168 </span>            :   ASMJIT_ASSERT(rn == nullptr || rn-&gt;mem &gt; root-&gt;mem);</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            :   // Black violation.</a>
+<a name="171"><span class="lineNum">     171 </span>            :   ASMJIT_ASSERT(!(lh != 0 &amp;&amp; rh != 0 &amp;&amp; lh != rh));</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :   // Only count black links.</a>
+<a name="174"><span class="lineNum">     174 </span>            :   if (lh != 0 &amp;&amp; rh != 0)</a>
+<a name="175"><span class="lineNum">     175 </span>            :     return rbIsRed(root) ? lh : lh + 1;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   else</a>
+<a name="177"><span class="lineNum">     177 </span>            :     return 0;</a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : //! \internal</a>
+<a name="181"><span class="lineNum">     181 </span>            : //!</a>
+<a name="182"><span class="lineNum">     182 </span>            : //! Single rotation.</a>
+<a name="183"><span class="lineNum">     183 </span>            : static ASMJIT_INLINE RbNode* rbRotateSingle(RbNode* root, int dir) noexcept {</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :   RbNode* save = root-&gt;node[!dir];</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   root-&gt;node[!dir] = save-&gt;node[dir];</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   save-&gt;node[dir] = root;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   root-&gt;red = 1;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   save-&gt;red = 0;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   return save;</a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : //! \internal</a>
+<a name="196"><span class="lineNum">     196 </span>            : //!</a>
+<a name="197"><span class="lineNum">     197 </span>            : //! Double rotation.</a>
+<a name="198"><span class="lineNum">     198 </span>            : static ASMJIT_INLINE RbNode* rbRotateDouble(RbNode* root, int dir) noexcept {</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   root-&gt;node[!dir] = rbRotateSingle(root-&gt;node[!dir], !dir);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   return rbRotateSingle(root, dir);</a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : // ============================================================================</a>
+<a name="204"><span class="lineNum">     204 </span>            : // [asmjit::VMemMgr::MemNode]</a>
+<a name="205"><span class="lineNum">     205 </span>            : // ============================================================================</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : struct VMemMgr::MemNode : public RbNode {</a>
+<a name="208"><span class="lineNum">     208 </span>            :   ASMJIT_INLINE void init(MemNode* other) noexcept {</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :     mem = other-&gt;mem;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :     size = other-&gt;size;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :     used = other-&gt;used;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :     blocks = other-&gt;blocks;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     density = other-&gt;density;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     largestBlock = other-&gt;largestBlock;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :     baUsed = other-&gt;baUsed;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :     baCont = other-&gt;baCont;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   // Get available space.</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE size_t getAvailable() const noexcept { return size - used; }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   MemNode* prev;         // Prev node in list.</a>
+<a name="225"><span class="lineNum">     225 </span>            :   MemNode* next;         // Next node in list.</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :   size_t size;           // How many bytes contain this node.</a>
+<a name="228"><span class="lineNum">     228 </span>            :   size_t used;           // How many bytes are used in this node.</a>
+<a name="229"><span class="lineNum">     229 </span>            :   size_t blocks;         // How many blocks are here.</a>
+<a name="230"><span class="lineNum">     230 </span>            :   size_t density;        // Minimum count of allocated bytes in this node (also alignment).</a>
+<a name="231"><span class="lineNum">     231 </span>            :   size_t largestBlock;   // Contains largest block that can be allocated.</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :   size_t* baUsed;        // Contains bits about used blocks       (0 = unused, 1 = used).</a>
+<a name="234"><span class="lineNum">     234 </span>            :   size_t* baCont;        // Contains bits about continuous blocks (0 = stop  , 1 = continue).</a>
+<a name="235"><span class="lineNum">     235 </span>            : };</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : // ============================================================================</a>
+<a name="238"><span class="lineNum">     238 </span>            : // [asmjit::VMemMgr::PermanentNode]</a>
+<a name="239"><span class="lineNum">     239 </span>            : // ============================================================================</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : //! \internal</a>
+<a name="242"><span class="lineNum">     242 </span>            : //!</a>
+<a name="243"><span class="lineNum">     243 </span>            : //! Permanent node.</a>
+<a name="244"><span class="lineNum">     244 </span>            : struct VMemMgr::PermanentNode {</a>
+<a name="245"><span class="lineNum">     245 </span>            :   //! Get available space.</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE size_t getAvailable() const noexcept { return size - used; }</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   PermanentNode* prev;   // Pointer to prev chunk or nullptr.</a>
+<a name="249"><span class="lineNum">     249 </span>            :   uint8_t* mem;          // Base pointer (virtual memory address).</a>
+<a name="250"><span class="lineNum">     250 </span>            :   size_t size;           // Count of bytes allocated.</a>
+<a name="251"><span class="lineNum">     251 </span>            :   size_t used;           // Count of bytes used.</a>
+<a name="252"><span class="lineNum">     252 </span>            : };</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : // ============================================================================</a>
+<a name="255"><span class="lineNum">     255 </span>            : // [asmjit::VMemMgr - Private]</a>
+<a name="256"><span class="lineNum">     256 </span>            : // ============================================================================</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : //! \internal</a>
+<a name="259"><span class="lineNum">     259 </span>            : //!</a>
+<a name="260"><span class="lineNum">     260 </span>            : //! Helper to avoid `#ifdef`s in the code.</a>
+<a name="261"><span class="lineNum">     261 </span>            : ASMJIT_INLINE uint8_t* vMemMgrAllocVMem(VMemMgr* self, size_t size, size_t* vSize) noexcept {</a>
+<a name="262"><span class="lineNum">     262 </span>            :   uint32_t flags = OSUtils::kVMWritable | OSUtils::kVMExecutable;</a>
+<a name="263"><span class="lineNum">     263 </span>            : #if !ASMJIT_OS_WINDOWS</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       1948 :   return static_cast&lt;uint8_t*&gt;(OSUtils::allocVirtualMemory(size, vSize, flags));</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : #else</a>
+<a name="266"><span class="lineNum">     266 </span>            :   return static_cast&lt;uint8_t*&gt;(OSUtils::allocProcessMemory(self-&gt;_hProcess, size, vSize, flags));</a>
+<a name="267"><span class="lineNum">     267 </span>            : #endif</a>
+<a name="268"><span class="lineNum">     268 </span>            : }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            : //! \internal</a>
+<a name="271"><span class="lineNum">     271 </span>            : //!</a>
+<a name="272"><span class="lineNum">     272 </span>            : //! Helper to avoid `#ifdef`s in the code.</a>
+<a name="273"><span class="lineNum">     273 </span>            : ASMJIT_INLINE Error vMemMgrReleaseVMem(VMemMgr* self, void* p, size_t vSize) noexcept {</a>
+<a name="274"><span class="lineNum">     274 </span>            : #if !ASMJIT_OS_WINDOWS</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   return OSUtils::releaseVirtualMemory(p, vSize);</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : #else</a>
+<a name="277"><span class="lineNum">     277 </span>            :   return OSUtils::releaseProcessMemory(self-&gt;_hProcess, p, vSize);</a>
+<a name="278"><span class="lineNum">     278 </span>            : #endif</a>
+<a name="279"><span class="lineNum">     279 </span>            : }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : //! \internal</a>
+<a name="282"><span class="lineNum">     282 </span>            : //!</a>
+<a name="283"><span class="lineNum">     283 </span>            : //! Check whether the Red-Black tree is valid.</a>
+<a name="284"><span class="lineNum">     284 </span>            : static bool vMemMgrCheckTree(VMemMgr* self) noexcept {</a>
+<a name="285"><span class="lineNum">     285 </span>            :   return rbAssert(self-&gt;_root) &gt; 0;</a>
+<a name="286"><span class="lineNum">     286 </span>            : }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : //! \internal</a>
+<a name="289"><span class="lineNum">     289 </span>            : //!</a>
+<a name="290"><span class="lineNum">     290 </span>            : //! Alloc virtual memory including a heap memory needed for `MemNode` data.</a>
+<a name="291"><span class="lineNum">     291 </span>            : //!</a>
+<a name="292"><span class="lineNum">     292 </span>            : //! Returns set-up `MemNode*` or nullptr if allocation failed.</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1948 : static MemNode* vMemMgrCreateNode(VMemMgr* self, size_t size, size_t density) noexcept {</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   size_t vSize;</a>
+<a name="295"><span class="lineNum">     295 </span>            :   uint8_t* vmem = vMemMgrAllocVMem(self, size, &amp;vSize);</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       1948 :   if (!vmem) return nullptr;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1948 :   size_t blocks = (vSize / density);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       1948 :   size_t bsize = (((blocks + 7) &gt;&gt; 3) + sizeof(size_t) - 1) &amp; ~(size_t)(sizeof(size_t) - 1);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   MemNode* node = static_cast&lt;MemNode*&gt;(Internal::allocMemory(sizeof(MemNode)));</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       1948 :   uint8_t* data = static_cast&lt;uint8_t*&gt;(Internal::allocMemory(bsize * 2));</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   // Out of memory.</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1948 :   if (!node || !data) {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     vMemMgrReleaseVMem(self, vmem, vSize);</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :     if (node) Internal::releaseMemory(node);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :     if (data) Internal::releaseMemory(data);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :     return nullptr;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   }</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            :   // Initialize RbNode data.</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       1948 :   node-&gt;node[0] = nullptr;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       1948 :   node-&gt;node[1] = nullptr;</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       1948 :   node-&gt;mem = vmem;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       1948 :   node-&gt;red = 1;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :   // Initialize MemNode data.</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       1948 :   node-&gt;prev = nullptr;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       1948 :   node-&gt;next = nullptr;</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       1948 :   node-&gt;size = vSize;</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       1948 :   node-&gt;used = 0;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">       1948 :   node-&gt;blocks = blocks;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       1948 :   node-&gt;density = density;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       1948 :   node-&gt;largestBlock = vSize;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            :   ::memset(data, 0, bsize * 2);</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       1948 :   node-&gt;baUsed = reinterpret_cast&lt;size_t*&gt;(data);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       1948 :   node-&gt;baCont = reinterpret_cast&lt;size_t*&gt;(data + bsize);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       1948 :   return node;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">       1948 : static void vMemMgrInsertNode(VMemMgr* self, MemNode* node) noexcept {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       1948 :   if (!self-&gt;_root) {</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     // Empty tree case.</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">       1948 :     self-&gt;_root = node;</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span>            :   else {</a>
+<a name="341"><span class="lineNum">     341 </span>            :     // False tree root.</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :     RbNode head = { { nullptr, nullptr }, 0, 0 };</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :     // Grandparent &amp; parent.</a>
+<a name="345"><span class="lineNum">     345 </span>            :     RbNode* g = nullptr;</a>
+<a name="346"><span class="lineNum">     346 </span>            :     RbNode* t = &amp;head;</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            :     // Iterator &amp; parent.</a>
+<a name="349"><span class="lineNum">     349 </span>            :     RbNode* p = nullptr;</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :     RbNode* q = t-&gt;node[1] = self-&gt;_root;</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            :     int dir = 0;</a>
+<a name="353"><span class="lineNum">     353 </span>            :     int last = 0; // Not needed to initialize, but makes some tools happy.</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :     // Search down the tree.</a>
+<a name="356"><span class="lineNum">     356 </span>            :     for (;;) {</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :       if (!q) {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :         // Insert new node at the bottom.</a>
+<a name="359"><span class="lineNum">     359 </span>            :         q = node;</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :         p-&gt;node[dir] = node;</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :       }</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :       else if (rbIsRed(q-&gt;node[0]) &amp;&amp; rbIsRed(q-&gt;node[1])) {</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :         // Color flip.</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :         q-&gt;red = 1;</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :         q-&gt;node[0]-&gt;red = 0;</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :         q-&gt;node[1]-&gt;red = 0;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :       }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            :       // Fix red violation.</a>
+<a name="370"><span class="lineNum">     370 </span>            :       if (rbIsRed(q) &amp;&amp; rbIsRed(p)) {</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :         int dir2 = t-&gt;node[1] == g;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :         t-&gt;node[dir2] = q == p-&gt;node[last] ? rbRotateSingle(g, !last) : rbRotateDouble(g, !last);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :       }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            :       // Stop if found.</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :       if (q == node)</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :         break;</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :       last = dir;</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :       dir = q-&gt;mem &lt; node-&gt;mem;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :       // Update helpers.</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :       if (g) t = g;</span></a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            :       g = p;</a>
+<a name="386"><span class="lineNum">     386 </span>            :       p = q;</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :       q = q-&gt;node[dir];</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :     // Update root.</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :     self-&gt;_root = static_cast&lt;MemNode*&gt;(head.node[1]);</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   }</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            :   // Make root black.</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       1948 :   self-&gt;_root-&gt;red = 0;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :   // Link with others.</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       1948 :   node-&gt;prev = self-&gt;_last;</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       1948 :   if (!self-&gt;_first) {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       1948 :     self-&gt;_first = node;</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">       1948 :     self-&gt;_last = node;</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       1948 :     self-&gt;_optimal = node;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :   }</a>
+<a name="405"><span class="lineNum">     405 </span>            :   else {</a>
+<a name="406"><span class="lineNum">     406 </span>            :     node-&gt;prev = self-&gt;_last;</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :     self-&gt;_last-&gt;next = node;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :     self-&gt;_last = node;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :   }</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">       1948 : }</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            : //! \internal</a>
+<a name="413"><span class="lineNum">     413 </span>            : //!</a>
+<a name="414"><span class="lineNum">     414 </span>            : //! Remove node from Red-Black tree.</a>
+<a name="415"><span class="lineNum">     415 </span>            : //!</a>
+<a name="416"><span class="lineNum">     416 </span>            : //! Returns node that should be freed, but it doesn't have to be necessarily</a>
+<a name="417"><span class="lineNum">     417 </span>            : //! the `node` passed.</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 : static MemNode* vMemMgrRemoveNode(VMemMgr* self, MemNode* node) noexcept {</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :   // False tree root.</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :   RbNode head = { { nullptr, nullptr }, 0, 0 };</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            :   // Helpers.</a>
+<a name="423"><span class="lineNum">     423 </span>            :   RbNode* q = &amp;head;</a>
+<a name="424"><span class="lineNum">     424 </span>            :   RbNode* p = nullptr;</a>
+<a name="425"><span class="lineNum">     425 </span>            :   RbNode* g = nullptr;</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :   // Found item.</a>
+<a name="428"><span class="lineNum">     428 </span>            :   RbNode* f = nullptr;</a>
+<a name="429"><span class="lineNum">     429 </span>            :   int dir = 1;</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            :   // Set up.</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :   q-&gt;node[1] = self-&gt;_root;</span></a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span>            :   // Search and push a red down.</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :   while (q-&gt;node[dir]) {</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :     int last = dir;</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            :     // Update helpers.</a>
+<a name="439"><span class="lineNum">     439 </span>            :     g = p;</a>
+<a name="440"><span class="lineNum">     440 </span>            :     p = q;</a>
+<a name="441"><span class="lineNum">     441 </span>            :     q = q-&gt;node[dir];</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :     dir = q-&gt;mem &lt; node-&gt;mem;</span></a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            :     // Save found node.</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :     if (q == node)</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :       f = q;</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            :     // Push the red node down.</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 :     if (!rbIsRed(q) &amp;&amp; !rbIsRed(q-&gt;node[dir])) {</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :       if (rbIsRed(q-&gt;node[!dir])) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :         p = p-&gt;node[last] = rbRotateSingle(q, dir);</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :       }</a>
+<a name="453"><span class="lineNum">     453 </span>            :       else if (!rbIsRed(q-&gt;node[!dir])) {</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :         RbNode* s = p-&gt;node[!last];</span></a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :         if (s) {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :           if (!rbIsRed(s-&gt;node[!last]) &amp;&amp; !rbIsRed(s-&gt;node[last])) {</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :             // Color flip.</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineNoCov">          0 :             p-&gt;red = 0;</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :             s-&gt;red = 1;</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :             q-&gt;red = 1;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :           }</a>
+<a name="463"><span class="lineNum">     463 </span>            :           else {</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :             int dir2 = g-&gt;node[1] == p;</span></a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :             if (rbIsRed(s-&gt;node[last]))</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :               g-&gt;node[dir2] = rbRotateDouble(p, last);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :             else if (rbIsRed(s-&gt;node[!last]))</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :               g-&gt;node[dir2] = rbRotateSingle(p, last);</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            :             // Ensure correct coloring.</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :             q-&gt;red = g-&gt;node[dir2]-&gt;red = 1;</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :             g-&gt;node[dir2]-&gt;node[0]-&gt;red = 0;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :             g-&gt;node[dir2]-&gt;node[1]-&gt;red = 0;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :           }</a>
+<a name="476"><span class="lineNum">     476 </span>            :         }</a>
+<a name="477"><span class="lineNum">     477 </span>            :       }</a>
+<a name="478"><span class="lineNum">     478 </span>            :     }</a>
+<a name="479"><span class="lineNum">     479 </span>            :   }</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            :   // Replace and remove.</a>
+<a name="482"><span class="lineNum">     482 </span>            :   ASMJIT_ASSERT(f != nullptr);</a>
+<a name="483"><span class="lineNum">     483 </span>            :   ASMJIT_ASSERT(f != &amp;head);</a>
+<a name="484"><span class="lineNum">     484 </span>            :   ASMJIT_ASSERT(q != &amp;head);</a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :   if (f != q) {</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     ASMJIT_ASSERT(f != &amp;head);</a>
+<a name="488"><span class="lineNum">     488 </span>            :     static_cast&lt;MemNode*&gt;(f)-&gt;init(static_cast&lt;MemNode*&gt;(q));</a>
+<a name="489"><span class="lineNum">     489 </span>            :   }</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineNoCov">          0 :   p-&gt;node[p-&gt;node[1] == q] = q-&gt;node[q-&gt;node[0] == nullptr];</span></a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            :   // Update root and make it black.</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :   self-&gt;_root = static_cast&lt;MemNode*&gt;(head.node[1]);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineNoCov">          0 :   if (self-&gt;_root) self-&gt;_root-&gt;red = 0;</span></a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span>            :   // Unlink.</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :   MemNode* next = static_cast&lt;MemNode*&gt;(q)-&gt;next;</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :   MemNode* prev = static_cast&lt;MemNode*&gt;(q)-&gt;prev;</span></a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineNoCov">          0 :   if (prev)</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 :     prev-&gt;next = next;</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   else</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :     self-&gt;_first = next;</span></a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :   if (next)</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :     next-&gt;prev = prev;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   else</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :     self-&gt;_last  = prev;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :   if (self-&gt;_optimal == q)</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :     self-&gt;_optimal = prev ? prev : next;</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :   return static_cast&lt;MemNode*&gt;(q);</span></a>
+<a name="515"><span class="lineNum">     515 </span>            : }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 : static MemNode* vMemMgrFindNodeByPtr(VMemMgr* self, uint8_t* mem) noexcept {</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :   MemNode* node = self-&gt;_root;</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :   while (node) {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :     uint8_t* nodeMem = node-&gt;mem;</span></a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            :     // Go left.</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :     if (mem &lt; nodeMem) {</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :       node = static_cast&lt;MemNode*&gt;(node-&gt;node[0]);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :     }</a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span>            :     // Go right.</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :     uint8_t* nodeEnd = nodeMem + node-&gt;size;</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :     if (mem &gt;= nodeEnd) {</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :       node = static_cast&lt;MemNode*&gt;(node-&gt;node[1]);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :     }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            :     // Match.</a>
+<a name="536"><span class="lineNum">     536 </span>            :     break;</a>
+<a name="537"><span class="lineNum">     537 </span>            :   }</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :   return node;</span></a>
+<a name="539"><span class="lineNum">     539 </span>            : }</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 : static void* vMemMgrAllocPermanent(VMemMgr* self, size_t vSize) noexcept {</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :   static const size_t permanentAlignment = 32;</a>
+<a name="543"><span class="lineNum">     543 </span>            :   static const size_t permanentNodeSize  = 32768;</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span>            :   vSize = Utils::alignTo&lt;size_t&gt;(vSize, permanentAlignment);</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :   AutoLock locked(self-&gt;_lock);</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineNoCov">          0 :   PermanentNode* node = self-&gt;_permanent;</span></a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            :   // Try to find space in allocated chunks.</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :   while (node &amp;&amp; vSize &gt; node-&gt;getAvailable())</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :     node = node-&gt;prev;</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            :   // Or allocate new node.</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineNoCov">          0 :   if (!node) {</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :     size_t nodeSize = permanentNodeSize;</a>
+<a name="557"><span class="lineNum">     557 </span>            :     if (nodeSize &lt; vSize) nodeSize = vSize;</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span>            :     node = static_cast&lt;PermanentNode*&gt;(Internal::allocMemory(sizeof(PermanentNode)));</a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineNoCov">          0 :     if (!node) return nullptr;</span></a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :     node-&gt;mem = vMemMgrAllocVMem(self, nodeSize, &amp;node-&gt;size);</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineNoCov">          0 :     if (!node-&gt;mem) {</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :       Internal::releaseMemory(node);</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :       return nullptr;</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :     }</a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineNoCov">          0 :     node-&gt;used = 0;</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :     node-&gt;prev = self-&gt;_permanent;</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :     self-&gt;_permanent = node;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :   }</a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span>            :   // Finally, copy function code to our space we reserved for.</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineNoCov">          0 :   uint8_t* result = node-&gt;mem + node-&gt;used;</span></a>
+<a name="575"><span class="lineNum">     575 </span>            : </a>
+<a name="576"><span class="lineNum">     576 </span>            :   // Update Statistics.</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :   node-&gt;used += vSize;</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :   self-&gt;_usedBytes += vSize;</span></a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span>            :   // Code can be null to only reserve space for code.</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :   return static_cast&lt;void*&gt;(result);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : }</a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">       1948 : static void* vMemMgrAllocFreeable(VMemMgr* self, size_t vSize) noexcept {</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :   // Current index.</a>
+<a name="586"><span class="lineNum">     586 </span>            :   size_t i;</a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span>            :   // How many we need to be freed.</a>
+<a name="589"><span class="lineNum">     589 </span>            :   size_t need;</a>
+<a name="590"><span class="lineNum">     590 </span>            :   size_t minVSize;</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            :   // Align to 32 bytes by default.</a>
+<a name="593"><span class="lineNum">     593 </span>            :   vSize = Utils::alignTo&lt;size_t&gt;(vSize, 32);</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">       1948 :   if (vSize == 0)</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :     return nullptr;</a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            :   AutoLock locked(self-&gt;_lock);</a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">       1948 :   MemNode* node = self-&gt;_optimal;</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">       1948 :   minVSize = self-&gt;_blockSize;</span></a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span>            :   // Try to find memory block in existing nodes.</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">       1948 :   while (node) {</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :     // Skip this node?</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :     if ((node-&gt;getAvailable() &lt; vSize) || (node-&gt;largestBlock &lt; vSize &amp;&amp; node-&gt;largestBlock != 0)) {</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 :       MemNode* next = node-&gt;next;</span></a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :       if (node-&gt;getAvailable() &lt; minVSize &amp;&amp; node == self-&gt;_optimal &amp;&amp; next)</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :         self-&gt;_optimal = next;</span></a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            :       node = next;</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineNoCov">          0 :     size_t* up = node-&gt;baUsed;     // Current ubits address.</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :     size_t ubits;                  // Current ubits[0] value.</a>
+<a name="616"><span class="lineNum">     616 </span>            :     size_t bit;                    // Current bit mask.</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :     size_t blocks = node-&gt;blocks;  // Count of blocks in node.</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :     size_t cont = 0;               // How many bits are currently freed in find loop.</a>
+<a name="619"><span class="lineNum">     619 </span>            :     size_t maxCont = 0;            // Largest continuous block (bits count).</a>
+<a name="620"><span class="lineNum">     620 </span>            :     size_t j;</a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :     need = M_DIV((vSize + node-&gt;density - 1), node-&gt;density);</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :     i = 0;</a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span>            :     // Try to find node that is large enough.</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :     while (i &lt; blocks) {</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :       ubits = *up++;</span></a>
+<a name="628"><span class="lineNum">     628 </span>            : </a>
+<a name="629"><span class="lineNum">     629 </span>            :       // Fast skip used blocks.</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :       if (ubits == ~(size_t)0) {</span></a>
+<a name="631"><span class="lineNum">     631 </span>            :         if (cont &gt; maxCont)</a>
+<a name="632"><span class="lineNum">     632 </span>            :           maxCont = cont;</a>
+<a name="633"><span class="lineNum">     633 </span>            :         cont = 0;</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineNoCov">          0 :         i += kBitsPerEntity;</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :       }</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            :       size_t max = kBitsPerEntity;</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :       if (i + max &gt; blocks)</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 :         max = blocks - i;</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :       for (j = 0, bit = 1; j &lt; max; bit &lt;&lt;= 1) {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :         j++;</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :         if ((ubits &amp; bit) == 0) {</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 :           if (++cont == need) {</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineNoCov">          0 :             i += j;</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineNoCov">          0 :             i -= cont;</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :             goto L_Found;</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :           }</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="653"><span class="lineNum">     653 </span>            :         }</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :         if (cont &gt; maxCont) maxCont = cont;</a>
+<a name="656"><span class="lineNum">     656 </span>            :         cont = 0;</a>
+<a name="657"><span class="lineNum">     657 </span>            :       }</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            :       i += kBitsPerEntity;</a>
+<a name="660"><span class="lineNum">     660 </span>            :     }</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span>            :     // Because we traversed the entire node, we can set largest node size that</a>
+<a name="663"><span class="lineNum">     663 </span>            :     // will be used to cache next traversing.</a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :     node-&gt;largestBlock = maxCont * node-&gt;density;</span></a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :     node = node-&gt;next;</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :   }</a>
+<a name="668"><span class="lineNum">     668 </span>            : </a>
+<a name="669"><span class="lineNum">     669 </span>            :   // If we are here, we failed to find existing memory block and we must</a>
+<a name="670"><span class="lineNum">     670 </span>            :   // allocate a new one.</a>
+<a name="671"><span class="lineNum">     671 </span>            :   {</a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">       1948 :     size_t blockSize = self-&gt;_blockSize;</span></a>
+<a name="673"><span class="lineNum">     673 </span>            :     if (blockSize &lt; vSize) blockSize = vSize;</a>
+<a name="674"><span class="lineNum">     674 </span>            : </a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">       1948 :     node = vMemMgrCreateNode(self, blockSize, self-&gt;_blockDensity);</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">       1948 :     if (!node) return nullptr;</span></a>
+<a name="677"><span class="lineNum">     677 </span>            : </a>
+<a name="678"><span class="lineNum">     678 </span>            :     // Update binary tree.</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">       1948 :     vMemMgrInsertNode(self, node);</span></a>
+<a name="680"><span class="lineNum">     680 </span>            :     ASMJIT_ASSERT(vMemMgrCheckTree(self));</a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span>            :     // Alloc first node at start.</a>
+<a name="683"><span class="lineNum">     683 </span>            :     i = 0;</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">       1948 :     need = (vSize + node-&gt;density - 1) / node-&gt;density;</span></a>
+<a name="685"><span class="lineNum">     685 </span>            : </a>
+<a name="686"><span class="lineNum">     686 </span>            :     // Update statistics.</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">       1948 :     self-&gt;_allocatedBytes += node-&gt;size;</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :   }</a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">       1948 : L_Found:</span></a>
+<a name="691"><span class="lineNum">     691 </span>            :   // Update bits.</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">       1948 :   _SetBits(node-&gt;baUsed, i, need);</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">       1948 :   _SetBits(node-&gt;baCont, i, need - 1);</span></a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span>            :   // Update statistics.</a>
+<a name="696"><span class="lineNum">     696 </span>            :   {</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">       1948 :     size_t u = need * node-&gt;density;</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">       1948 :     node-&gt;used += u;</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">       1948 :     node-&gt;largestBlock = 0;</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">       1948 :     self-&gt;_usedBytes += u;</span></a>
+<a name="701"><span class="lineNum">     701 </span>            :   }</a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span>            :   // And return pointer to allocated memory.</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">       1948 :   uint8_t* result = node-&gt;mem + i * node-&gt;density;</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :   ASMJIT_ASSERT(result &gt;= node-&gt;mem &amp;&amp; result &lt;= node-&gt;mem + node-&gt;size - vSize);</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">       1948 :   return result;</span></a>
+<a name="707"><span class="lineNum">     707 </span>            : }</a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span>            : //! \internal</a>
+<a name="710"><span class="lineNum">     710 </span>            : //!</a>
+<a name="711"><span class="lineNum">     711 </span>            : //! Reset the whole `VMemMgr` instance, freeing all heap memory allocated an</a>
+<a name="712"><span class="lineNum">     712 </span>            : //! virtual memory allocated unless `keepVirtualMemory` is true (and this is</a>
+<a name="713"><span class="lineNum">     713 </span>            : //! only used when writing data to a remote process).</a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">       1976 : static void vMemMgrReset(VMemMgr* self, bool keepVirtualMemory) noexcept {</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">       1976 :   MemNode* node = self-&gt;_first;</span></a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">       3924 :   while (node) {</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">       1948 :     MemNode* next = node-&gt;next;</span></a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">       1948 :     if (!keepVirtualMemory)</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">       1948 :       vMemMgrReleaseVMem(self, node-&gt;mem, node-&gt;size);</span></a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">       1948 :     Internal::releaseMemory(node-&gt;baUsed);</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :     Internal::releaseMemory(node);</a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            :     node = next;</a>
+<a name="727"><span class="lineNum">     727 </span>            :   }</a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">       1976 :   self-&gt;_allocatedBytes = 0;</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">       1976 :   self-&gt;_usedBytes = 0;</span></a>
+<a name="731"><span class="lineNum">     731 </span>            : </a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">       1976 :   self-&gt;_root = nullptr;</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">       1976 :   self-&gt;_first = nullptr;</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">       1976 :   self-&gt;_last = nullptr;</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">       1976 :   self-&gt;_optimal = nullptr;</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">       1976 : }</span></a>
+<a name="737"><span class="lineNum">     737 </span>            : </a>
+<a name="738"><span class="lineNum">     738 </span>            : // ============================================================================</a>
+<a name="739"><span class="lineNum">     739 </span>            : // [asmjit::VMemMgr - Construction / Destruction]</a>
+<a name="740"><span class="lineNum">     740 </span>            : // ============================================================================</a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span>            : #if !ASMJIT_OS_WINDOWS</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">       1976 : VMemMgr::VMemMgr() noexcept {</span></a>
+<a name="744"><span class="lineNum">     744 </span>            : #else</a>
+<a name="745"><span class="lineNum">     745 </span>            : VMemMgr::VMemMgr(HANDLE hProcess) noexcept {</a>
+<a name="746"><span class="lineNum">     746 </span>            : #endif</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">       1976 :   VMemInfo vm = OSUtils::getVirtualMemoryInfo();</span></a>
+<a name="749"><span class="lineNum">     749 </span>            : </a>
+<a name="750"><span class="lineNum">     750 </span>            : #if ASMJIT_OS_WINDOWS</a>
+<a name="751"><span class="lineNum">     751 </span>            :   _hProcess = hProcess ? hProcess : vm.hCurrentProcess;</a>
+<a name="752"><span class="lineNum">     752 </span>            : #endif // ASMJIT_OS_WINDOWS</a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">       1976 :   _blockSize = vm.pageGranularity;</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">       1976 :   _blockDensity = 64;</span></a>
+<a name="756"><span class="lineNum">     756 </span>            : </a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">       1976 :   _allocatedBytes = 0;</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">       1976 :   _usedBytes = 0;</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">       1976 :   _root = nullptr;</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">       1976 :   _first = nullptr;</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">       1976 :   _last = nullptr;</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">       1976 :   _optimal = nullptr;</span></a>
+<a name="764"><span class="lineNum">     764 </span>            : </a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">       1976 :   _permanent = nullptr;</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">       1976 :   _keepVirtualMemory = false;</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       1976 : }</span></a>
+<a name="768"><span class="lineNum">     768 </span>            : </a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">       1976 : VMemMgr::~VMemMgr() noexcept {</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :   // Freeable memory cleanup - Also frees the virtual memory if configured to.</a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">       1976 :   vMemMgrReset(this, _keepVirtualMemory);</span></a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            :   // Permanent memory cleanup - Never frees the virtual memory.</a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">       1976 :   PermanentNode* node = _permanent;</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">       1976 :   while (node) {</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineNoCov">          0 :     PermanentNode* prev = node-&gt;prev;</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :     Internal::releaseMemory(node);</a>
+<a name="778"><span class="lineNum">     778 </span>            :     node = prev;</a>
+<a name="779"><span class="lineNum">     779 </span>            :   }</a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">       1976 : }</span></a>
+<a name="781"><span class="lineNum">     781 </span>            : </a>
+<a name="782"><span class="lineNum">     782 </span>            : // ============================================================================</a>
+<a name="783"><span class="lineNum">     783 </span>            : // [asmjit::VMemMgr - Reset]</a>
+<a name="784"><span class="lineNum">     784 </span>            : // ============================================================================</a>
+<a name="785"><span class="lineNum">     785 </span>            : </a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineNoCov">          0 : void VMemMgr::reset() noexcept {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineNoCov">          0 :   vMemMgrReset(this, false);</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="789"><span class="lineNum">     789 </span>            : </a>
+<a name="790"><span class="lineNum">     790 </span>            : // ============================================================================</a>
+<a name="791"><span class="lineNum">     791 </span>            : // [asmjit::VMemMgr - Alloc / Release]</a>
+<a name="792"><span class="lineNum">     792 </span>            : // ============================================================================</a>
+<a name="793"><span class="lineNum">     793 </span>            : </a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">       1948 : void* VMemMgr::alloc(size_t size, uint32_t type) noexcept {</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">       1948 :   if (type == kAllocPermanent)</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineNoCov">          0 :     return vMemMgrAllocPermanent(this, size);</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :   else</a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">       1948 :     return vMemMgrAllocFreeable(this, size);</span></a>
+<a name="799"><span class="lineNum">     799 </span>            : }</a>
+<a name="800"><span class="lineNum">     800 </span>            : </a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineNoCov">          0 : Error VMemMgr::release(void* p) noexcept {</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineNoCov">          0 :   if (!p) return kErrorOk;</span></a>
+<a name="803"><span class="lineNum">     803 </span>            : </a>
+<a name="804"><span class="lineNum">     804 </span>            :   AutoLock locked(_lock);</a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineNoCov">          0 :   MemNode* node = vMemMgrFindNodeByPtr(this, static_cast&lt;uint8_t*&gt;(p));</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineNoCov">          0 :   if (!node) return DebugUtils::errored(kErrorInvalidArgument);</span></a>
+<a name="807"><span class="lineNum">     807 </span>            : </a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineNoCov">          0 :   size_t offset = (size_t)((uint8_t*)p - (uint8_t*)node-&gt;mem);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineNoCov">          0 :   size_t bitpos = M_DIV(offset, node-&gt;density);</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineNoCov">          0 :   size_t i = (bitpos / kBitsPerEntity);</span></a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineNoCov">          0 :   size_t* up = node-&gt;baUsed + i;  // Current ubits address.</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineNoCov">          0 :   size_t* cp = node-&gt;baCont + i;  // Current cbits address.</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineNoCov">          0 :   size_t ubits = *up;             // Current ubits[0] value.</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineNoCov">          0 :   size_t cbits = *cp;             // Current cbits[0] value.</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineNoCov">          0 :   size_t bit = (size_t)1 &lt;&lt; (bitpos % kBitsPerEntity);</span></a>
+<a name="817"><span class="lineNum">     817 </span>            : </a>
+<a name="818"><span class="lineNum">     818 </span>            :   size_t cont = 0;</a>
+<a name="819"><span class="lineNum">     819 </span>            :   bool stop;</a>
+<a name="820"><span class="lineNum">     820 </span>            : </a>
+<a name="821"><span class="lineNum">     821 </span>            :   for (;;) {</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineNoCov">          0 :     stop = (cbits &amp; bit) == 0;</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 :     ubits &amp;= ~bit;</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineNoCov">          0 :     cbits &amp;= ~bit;</span></a>
+<a name="825"><span class="lineNum">     825 </span>            : </a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineNoCov">          0 :     bit &lt;&lt;= 1;</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineNoCov">          0 :     cont++;</span></a>
+<a name="828"><span class="lineNum">     828 </span>            : </a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineNoCov">          0 :     if (stop || bit == 0) {</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineNoCov">          0 :       *up = ubits;</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineNoCov">          0 :       *cp = cbits;</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineNoCov">          0 :       if (stop)</span></a>
+<a name="833"><span class="lineNum">     833 </span>            :         break;</a>
+<a name="834"><span class="lineNum">     834 </span>            : </a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineNoCov">          0 :       ubits = *++up;</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineNoCov">          0 :       cbits = *++cp;</span></a>
+<a name="837"><span class="lineNum">     837 </span>            :       bit = 1;</a>
+<a name="838"><span class="lineNum">     838 </span>            :     }</a>
+<a name="839"><span class="lineNum">     839 </span>            :   }</a>
+<a name="840"><span class="lineNum">     840 </span>            : </a>
+<a name="841"><span class="lineNum">     841 </span>            :   // If the freed block is fully allocated node then it's needed to</a>
+<a name="842"><span class="lineNum">     842 </span>            :   // update 'optimal' pointer in memory manager.</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineNoCov">          0 :   if (node-&gt;used == node-&gt;size) {</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineNoCov">          0 :     MemNode* cur = _optimal;</span></a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span>            :     do {</a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineNoCov">          0 :       cur = cur-&gt;prev;</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineNoCov">          0 :       if (cur == node) {</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :         _optimal = node;</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="851"><span class="lineNum">     851 </span>            :       }</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineNoCov">          0 :     } while (cur);</span></a>
+<a name="853"><span class="lineNum">     853 </span>            :   }</a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span>            :   // Statistics.</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :   cont *= node-&gt;density;</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineNoCov">          0 :   if (node-&gt;largestBlock &lt; cont)</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 :     node-&gt;largestBlock = cont;</span></a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineNoCov">          0 :   node-&gt;used -= cont;</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineNoCov">          0 :   _usedBytes -= cont;</span></a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span>            :   // If page is empty, we can free it.</a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineNoCov">          0 :   if (node-&gt;used == 0) {</span></a>
+<a name="865"><span class="lineNum">     865 </span>            :     // Free memory associated with node (this memory is not accessed</a>
+<a name="866"><span class="lineNum">     866 </span>            :     // anymore so it's safe).</a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineNoCov">          0 :     vMemMgrReleaseVMem(this, node-&gt;mem, node-&gt;size);</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineNoCov">          0 :     Internal::releaseMemory(node-&gt;baUsed);</span></a>
+<a name="869"><span class="lineNum">     869 </span>            : </a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineNoCov">          0 :     node-&gt;baUsed = nullptr;</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :     node-&gt;baCont = nullptr;</span></a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            :     // Statistics.</a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineNoCov">          0 :     _allocatedBytes -= node-&gt;size;</span></a>
+<a name="875"><span class="lineNum">     875 </span>            : </a>
+<a name="876"><span class="lineNum">     876 </span>            :     // Remove node. This function can return different node than</a>
+<a name="877"><span class="lineNum">     877 </span>            :     // passed into, but data is copied into previous node if needed.</a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineNoCov">          0 :     Internal::releaseMemory(vMemMgrRemoveNode(this, node));</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :     ASMJIT_ASSERT(vMemMgrCheckTree(this));</a>
+<a name="880"><span class="lineNum">     880 </span>            :   }</a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span>            :   return kErrorOk;</a>
+<a name="883"><span class="lineNum">     883 </span>            : }</a>
+<a name="884"><span class="lineNum">     884 </span>            : </a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineNoCov">          0 : Error VMemMgr::shrink(void* p, size_t used) noexcept {</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineNoCov">          0 :   if (!p) return kErrorOk;</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :   if (used == 0)</span></a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineNoCov">          0 :     return release(p);</span></a>
+<a name="889"><span class="lineNum">     889 </span>            : </a>
+<a name="890"><span class="lineNum">     890 </span>            :   AutoLock locked(_lock);</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineNoCov">          0 :   MemNode* node = vMemMgrFindNodeByPtr(this, (uint8_t*)p);</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineNoCov">          0 :   if (!node) return DebugUtils::errored(kErrorInvalidArgument);</span></a>
+<a name="893"><span class="lineNum">     893 </span>            : </a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineNoCov">          0 :   size_t offset = (size_t)((uint8_t*)p - (uint8_t*)node-&gt;mem);</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineNoCov">          0 :   size_t bitpos = M_DIV(offset, node-&gt;density);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineNoCov">          0 :   size_t i = (bitpos / kBitsPerEntity);</span></a>
+<a name="897"><span class="lineNum">     897 </span>            : </a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineNoCov">          0 :   size_t* up = node-&gt;baUsed + i;  // Current ubits address.</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineNoCov">          0 :   size_t* cp = node-&gt;baCont + i;  // Current cbits address.</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :   size_t ubits = *up;             // Current ubits[0] value.</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineNoCov">          0 :   size_t cbits = *cp;             // Current cbits[0] value.</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineNoCov">          0 :   size_t bit = (size_t)1 &lt;&lt; (bitpos % kBitsPerEntity);</span></a>
+<a name="903"><span class="lineNum">     903 </span>            : </a>
+<a name="904"><span class="lineNum">     904 </span>            :   size_t cont = 0;</a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineNoCov">          0 :   size_t usedBlocks = (used + node-&gt;density - 1) / node-&gt;density;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            : </a>
+<a name="907"><span class="lineNum">     907 </span>            :   bool stop;</a>
+<a name="908"><span class="lineNum">     908 </span>            : </a>
+<a name="909"><span class="lineNum">     909 </span>            :   // Find the first block we can mark as free.</a>
+<a name="910"><span class="lineNum">     910 </span>            :   for (;;) {</a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineNoCov">          0 :     stop = (cbits &amp; bit) == 0;</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineNoCov">          0 :     if (stop)</span></a>
+<a name="913"><span class="lineNum">     913 </span>            :       return kErrorOk;</a>
+<a name="914"><span class="lineNum">     914 </span>            : </a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineNoCov">          0 :     if (++cont == usedBlocks)</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :       break;</a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineNoCov">          0 :     bit &lt;&lt;= 1;</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :     if (bit == 0) {</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :       ubits = *++up;</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineNoCov">          0 :       cbits = *++cp;</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :       bit = 1;</a>
+<a name="923"><span class="lineNum">     923 </span>            :     }</a>
+<a name="924"><span class="lineNum">     924 </span>            :   }</a>
+<a name="925"><span class="lineNum">     925 </span>            : </a>
+<a name="926"><span class="lineNum">     926 </span>            :   // Free the tail blocks.</a>
+<a name="927"><span class="lineNum">     927 </span>            :   cont = ~(size_t)0;</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineNoCov">          0 :   goto _EnterFreeLoop;</span></a>
+<a name="929"><span class="lineNum">     929 </span>            : </a>
+<a name="930"><span class="lineNum">     930 </span>            :   for (;;) {</a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineNoCov">          0 :     stop = (cbits &amp; bit) == 0;</span></a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineNoCov">          0 :     ubits &amp;= ~bit;</span></a>
+<a name="933"><span class="lineNum">     933 </span>            : </a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 : _EnterFreeLoop:</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineNoCov">          0 :     cbits &amp;= ~bit;</span></a>
+<a name="936"><span class="lineNum">     936 </span>            : </a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineNoCov">          0 :     bit &lt;&lt;= 1;</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 :     cont++;</span></a>
+<a name="939"><span class="lineNum">     939 </span>            : </a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineNoCov">          0 :     if (stop || bit == 0) {</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineNoCov">          0 :       *up = ubits;</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :       *cp = cbits;</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineNoCov">          0 :       if (stop)</span></a>
+<a name="944"><span class="lineNum">     944 </span>            :         break;</a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineNoCov">          0 :       ubits = *++up;</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineNoCov">          0 :       cbits = *++cp;</span></a>
+<a name="948"><span class="lineNum">     948 </span>            :       bit = 1;</a>
+<a name="949"><span class="lineNum">     949 </span>            :     }</a>
+<a name="950"><span class="lineNum">     950 </span>            :   }</a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span>            :   // Statistics.</a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineNoCov">          0 :   cont *= node-&gt;density;</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineNoCov">          0 :   if (node-&gt;largestBlock &lt; cont)</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineNoCov">          0 :     node-&gt;largestBlock = cont;</span></a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineNoCov">          0 :   node-&gt;used -= cont;</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineNoCov">          0 :   _usedBytes -= cont;</span></a>
+<a name="959"><span class="lineNum">     959 </span>            : </a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="961"><span class="lineNum">     961 </span>            : }</a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span>            : // ============================================================================</a>
+<a name="964"><span class="lineNum">     964 </span>            : // [asmjit::VMem - Test]</a>
+<a name="965"><span class="lineNum">     965 </span>            : // ============================================================================</a>
+<a name="966"><span class="lineNum">     966 </span>            : </a>
+<a name="967"><span class="lineNum">     967 </span>            : #if defined(ASMJIT_TEST)</a>
+<a name="968"><span class="lineNum">     968 </span>            : static void VMemTest_fill(void* a, void* b, int i) noexcept {</a>
+<a name="969"><span class="lineNum">     969 </span>            :   int pattern = rand() % 256;</a>
+<a name="970"><span class="lineNum">     970 </span>            :   *(int *)a = i;</a>
+<a name="971"><span class="lineNum">     971 </span>            :   *(int *)b = i;</a>
+<a name="972"><span class="lineNum">     972 </span>            :   ::memset((char*)a + sizeof(int), pattern, i - sizeof(int));</a>
+<a name="973"><span class="lineNum">     973 </span>            :   ::memset((char*)b + sizeof(int), pattern, i - sizeof(int));</a>
+<a name="974"><span class="lineNum">     974 </span>            : }</a>
+<a name="975"><span class="lineNum">     975 </span>            : </a>
+<a name="976"><span class="lineNum">     976 </span>            : static void VMemTest_verify(void* a, void* b) noexcept {</a>
+<a name="977"><span class="lineNum">     977 </span>            :   int ai = *(int*)a;</a>
+<a name="978"><span class="lineNum">     978 </span>            :   int bi = *(int*)b;</a>
+<a name="979"><span class="lineNum">     979 </span>            : </a>
+<a name="980"><span class="lineNum">     980 </span>            :   EXPECT(ai == bi,</a>
+<a name="981"><span class="lineNum">     981 </span>            :     &quot;The length of 'a' (%d) and 'b' (%d) should be same&quot;, ai, bi);</a>
+<a name="982"><span class="lineNum">     982 </span>            : </a>
+<a name="983"><span class="lineNum">     983 </span>            :   EXPECT(::memcmp(a, b, ai) == 0,</a>
+<a name="984"><span class="lineNum">     984 </span>            :     &quot;Pattern (%p) doesn't match&quot;, a);</a>
+<a name="985"><span class="lineNum">     985 </span>            : }</a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span>            : static void VMemTest_stats(VMemMgr&amp; memmgr) noexcept {</a>
+<a name="988"><span class="lineNum">     988 </span>            :   INFO(&quot;Used     : %u&quot;, static_cast&lt;unsigned int&gt;(memmgr.getUsedBytes()));</a>
+<a name="989"><span class="lineNum">     989 </span>            :   INFO(&quot;Allocated: %u&quot;, static_cast&lt;unsigned int&gt;(memmgr.getAllocatedBytes()));</a>
+<a name="990"><span class="lineNum">     990 </span>            : }</a>
+<a name="991"><span class="lineNum">     991 </span>            : </a>
+<a name="992"><span class="lineNum">     992 </span>            : static void VMemTest_shuffle(void** a, void** b, size_t count) noexcept {</a>
+<a name="993"><span class="lineNum">     993 </span>            :   for (size_t i = 0; i &lt; count; ++i) {</a>
+<a name="994"><span class="lineNum">     994 </span>            :     size_t si = (size_t)rand() % count;</a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span>            :     void* ta = a[i];</a>
+<a name="997"><span class="lineNum">     997 </span>            :     void* tb = b[i];</a>
+<a name="998"><span class="lineNum">     998 </span>            : </a>
+<a name="999"><span class="lineNum">     999 </span>            :     a[i] = a[si];</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :     b[i] = b[si];</a>
+<a name="1001"><span class="lineNum">    1001 </span>            : </a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     a[si] = ta;</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :     b[si] = tb;</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :   }</a>
+<a name="1005"><span class="lineNum">    1005 </span>            : }</a>
+<a name="1006"><span class="lineNum">    1006 </span>            : </a>
+<a name="1007"><span class="lineNum">    1007 </span>            : UNIT(base_vmem) {</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   VMemMgr memmgr;</a>
+<a name="1009"><span class="lineNum">    1009 </span>            : </a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   // Should be predictible.</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :   srand(100);</a>
+<a name="1012"><span class="lineNum">    1012 </span>            : </a>
+<a name="1013"><span class="lineNum">    1013 </span>            :   int i;</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   int kCount = 200000;</a>
+<a name="1015"><span class="lineNum">    1015 </span>            : </a>
+<a name="1016"><span class="lineNum">    1016 </span>            :   INFO(&quot;Memory alloc/free test - %d allocations&quot;, static_cast&lt;int&gt;(kCount));</a>
+<a name="1017"><span class="lineNum">    1017 </span>            : </a>
+<a name="1018"><span class="lineNum">    1018 </span>            :   void** a = (void**)Internal::allocMemory(sizeof(void*) * kCount);</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   void** b = (void**)Internal::allocMemory(sizeof(void*) * kCount);</a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span>            :   EXPECT(a != nullptr &amp;&amp; b != nullptr,</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :     &quot;Couldn't allocate %u bytes on heap&quot;, kCount * 2);</a>
+<a name="1023"><span class="lineNum">    1023 </span>            : </a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   INFO(&quot;Allocating virtual memory...&quot;);</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   for (i = 0; i &lt; kCount; i++) {</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :     int r = (rand() % 1000) + 4;</a>
+<a name="1027"><span class="lineNum">    1027 </span>            : </a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     a[i] = memmgr.alloc(r);</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     EXPECT(a[i] != nullptr,</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :       &quot;Couldn't allocate %d bytes of virtual memory&quot;, r);</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :     ::memset(a[i], 0, r);</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :   }</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   VMemTest_stats(memmgr);</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : </a>
+<a name="1035"><span class="lineNum">    1035 </span>            :   INFO(&quot;Freeing virtual memory...&quot;);</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   for (i = 0; i &lt; kCount; i++) {</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     EXPECT(memmgr.release(a[i]) == kErrorOk,</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :       &quot;Failed to free %p&quot;, b[i]);</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :   }</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   VMemTest_stats(memmgr);</a>
+<a name="1041"><span class="lineNum">    1041 </span>            : </a>
+<a name="1042"><span class="lineNum">    1042 </span>            :   INFO(&quot;Verified alloc/free test - %d allocations&quot;, static_cast&lt;int&gt;(kCount));</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :   for (i = 0; i &lt; kCount; i++) {</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     int r = (rand() % 1000) + 4;</a>
+<a name="1045"><span class="lineNum">    1045 </span>            : </a>
+<a name="1046"><span class="lineNum">    1046 </span>            :     a[i] = memmgr.alloc(r);</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :     EXPECT(a[i] != nullptr,</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :       &quot;Couldn't allocate %d bytes of virtual memory&quot;, r);</a>
+<a name="1049"><span class="lineNum">    1049 </span>            : </a>
+<a name="1050"><span class="lineNum">    1050 </span>            :     b[i] = Internal::allocMemory(r);</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     EXPECT(b[i] != nullptr,</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :       &quot;Couldn't allocate %d bytes on heap&quot;, r);</a>
+<a name="1053"><span class="lineNum">    1053 </span>            : </a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     VMemTest_fill(a[i], b[i], r);</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   }</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :   VMemTest_stats(memmgr);</a>
+<a name="1057"><span class="lineNum">    1057 </span>            : </a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   INFO(&quot;Shuffling...&quot;);</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   VMemTest_shuffle(a, b, kCount);</a>
+<a name="1060"><span class="lineNum">    1060 </span>            : </a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   INFO(&quot;Verify and free...&quot;);</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   for (i = 0; i &lt; kCount / 2; i++) {</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :     VMemTest_verify(a[i], b[i]);</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     EXPECT(memmgr.release(a[i]) == kErrorOk,</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :       &quot;Failed to free %p&quot;, a[i]);</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :     Internal::releaseMemory(b[i]);</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   }</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   VMemTest_stats(memmgr);</a>
+<a name="1069"><span class="lineNum">    1069 </span>            : </a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   INFO(&quot;Alloc again&quot;);</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   for (i = 0; i &lt; kCount / 2; i++) {</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     int r = (rand() % 1000) + 4;</a>
+<a name="1073"><span class="lineNum">    1073 </span>            : </a>
+<a name="1074"><span class="lineNum">    1074 </span>            :     a[i] = memmgr.alloc(r);</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     EXPECT(a[i] != nullptr,</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :       &quot;Couldn't allocate %d bytes of virtual memory&quot;, r);</a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     b[i] = Internal::allocMemory(r);</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     EXPECT(b[i] != nullptr,</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :       &quot;Couldn't allocate %d bytes on heap&quot;);</a>
+<a name="1081"><span class="lineNum">    1081 </span>            : </a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     VMemTest_fill(a[i], b[i], r);</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   }</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :   VMemTest_stats(memmgr);</a>
+<a name="1085"><span class="lineNum">    1085 </span>            : </a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   INFO(&quot;Verify and free...&quot;);</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :   for (i = 0; i &lt; kCount; i++) {</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     VMemTest_verify(a[i], b[i]);</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :     EXPECT(memmgr.release(a[i]) == kErrorOk,</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :       &quot;Failed to free %p&quot;, a[i]);</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :     Internal::releaseMemory(b[i]);</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   }</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   VMemTest_stats(memmgr);</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   Internal::releaseMemory(a);</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   Internal::releaseMemory(b);</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : }</a>
+<a name="1098"><span class="lineNum">    1098 </span>            : #endif // ASMJIT_TEST</a>
+<a name="1099"><span class="lineNum">    1099 </span>            : </a>
+<a name="1100"><span class="lineNum">    1100 </span>            : } // asmjit namespace</a>
+<a name="1101"><span class="lineNum">    1101 </span>            : } // namespace PLMD</a>
+<a name="1102"><span class="lineNum">    1102 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86assembler.cpp.func-sort-c.html b/coverage-libs/asmjit/x86assembler.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f7d7361b2f
--- /dev/null
+++ b/coverage-libs/asmjit/x86assembler.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86assembler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86assembler.cpp<span style="font-size: 80%;"> (<a href="x86assembler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">183</td>
+            <td class="headerCovTableEntry">1705</td>
+            <td class="headerCovTableEntryLo">10.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86assembler.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#4556">_ZN4PLMD6asmjit12X86Assembler5alignEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#412">_ZN4PLMD6asmjit12X86Assembler8onDetachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#383">_ZN4PLMD6asmjit12X86AssemblerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#389">_ZN4PLMD6asmjit12X86Assembler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#379">_ZN4PLMD6asmjit12X86AssemblerC2EPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#383">_ZN4PLMD6asmjit12X86AssemblerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#526">_ZN4PLMD6asmjit12X86Assembler5_emitEjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnHi">48362</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86assembler.cpp.func.html b/coverage-libs/asmjit/x86assembler.cpp.func.html
new file mode 100644
index 0000000000..969c6f88c3
--- /dev/null
+++ b/coverage-libs/asmjit/x86assembler.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86assembler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86assembler.cpp<span style="font-size: 80%;"> (<a href="x86assembler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">183</td>
+            <td class="headerCovTableEntry">1705</td>
+            <td class="headerCovTableEntryLo">10.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86assembler.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#526">_ZN4PLMD6asmjit12X86Assembler5_emitEjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnHi">48362</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#4556">_ZN4PLMD6asmjit12X86Assembler5alignEjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#389">_ZN4PLMD6asmjit12X86Assembler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#412">_ZN4PLMD6asmjit12X86Assembler8onDetachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#379">_ZN4PLMD6asmjit12X86AssemblerC2EPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#383">_ZN4PLMD6asmjit12X86AssemblerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86assembler.cpp.gcov.html#383">_ZN4PLMD6asmjit12X86AssemblerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86assembler.cpp.gcov.html b/coverage-libs/asmjit/x86assembler.cpp.gcov.html
new file mode 100644
index 0000000000..c244db8edf
--- /dev/null
+++ b/coverage-libs/asmjit/x86assembler.cpp.gcov.html
@@ -0,0 +1,4721 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86assembler.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86assembler.cpp<span style="font-size: 80%;"> (source / <a href="x86assembler.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">183</td>
+            <td class="headerCovTableEntry">1705</td>
+            <td class="headerCovTableEntryLo">10.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./logging.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./misc_p.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./x86assembler.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./x86logging_p.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // [Api-Begin]</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : namespace PLMD {</a>
+<a name="48"><span class="lineNum">      48 </span>            : namespace asmjit {</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : // [FastUInt8]</a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : #if ASMJIT_ARCH_X86 || ASMJIT_ARCH_X64</a>
+<a name="55"><span class="lineNum">      55 </span>            : typedef unsigned char FastUInt8;</a>
+<a name="56"><span class="lineNum">      56 </span>            : #else</a>
+<a name="57"><span class="lineNum">      57 </span>            : typedef unsigned int FastUInt8;</a>
+<a name="58"><span class="lineNum">      58 </span>            : #endif</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : // ============================================================================</a>
+<a name="61"><span class="lineNum">      61 </span>            : // [Constants]</a>
+<a name="62"><span class="lineNum">      62 </span>            : // ============================================================================</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : //! \internal</a>
+<a name="65"><span class="lineNum">      65 </span>            : //!</a>
+<a name="66"><span class="lineNum">      66 </span>            : //! X86/X64 bytes used to encode important prefixes.</a>
+<a name="67"><span class="lineNum">      67 </span>            : enum X86Byte {</a>
+<a name="68"><span class="lineNum">      68 </span>            :   //! 1-byte REX prefix mask.</a>
+<a name="69"><span class="lineNum">      69 </span>            :   kX86ByteRex = 0x40,</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   //! 1-byte REX.W component.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   kX86ByteRexW = 0x08,</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   //! 2-byte VEX prefix:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   //!   - `[0]` - `0xC5`.</a>
+<a name="76"><span class="lineNum">      76 </span>            :   //!   - `[1]` - `RvvvvLpp`.</a>
+<a name="77"><span class="lineNum">      77 </span>            :   kX86ByteVex2 = 0xC5,</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   //! 3-byte VEX prefix.</a>
+<a name="80"><span class="lineNum">      80 </span>            :   //!   - `[0]` - `0xC4`.</a>
+<a name="81"><span class="lineNum">      81 </span>            :   //!   - `[1]` - `RXBmmmmm`.</a>
+<a name="82"><span class="lineNum">      82 </span>            :   //!   - `[2]` - `WvvvvLpp`.</a>
+<a name="83"><span class="lineNum">      83 </span>            :   kX86ByteVex3 = 0xC4,</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   //! 3-byte XOP prefix.</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //!   - `[0]` - `0x8F`.</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //!   - `[1]` - `RXBmmmmm`.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   //!   - `[2]` - `WvvvvLpp`.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   kX86ByteXop3 = 0x8F,</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   //! 4-byte EVEX prefix.</a>
+<a name="92"><span class="lineNum">      92 </span>            :   //!   - `[0]` - `0x62`.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   //!   - `[1]` - Payload0 or `P[ 7: 0]` - `[R  X  B  R' 0  0  m  m]`.</a>
+<a name="94"><span class="lineNum">      94 </span>            :   //!   - `[2]` - Payload1 or `P[15: 8]` - `[W  v  v  v  v  1  p  p]`.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   //!   - `[3]` - Payload2 or `P[23:16]` - `[z  L' L  b  V' a  a  a]`.</a>
+<a name="96"><span class="lineNum">      96 </span>            :   //!</a>
+<a name="97"><span class="lineNum">      97 </span>            :   //! Groups:</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //!   - `P[ 1: 0]` - OPCODE: EVEX.mmmmm, only lowest 2 bits [1:0] used.</a>
+<a name="99"><span class="lineNum">      99 </span>            :   //!   - `P[ 3: 2]` - ______: Must be 0.</a>
+<a name="100"><span class="lineNum">     100 </span>            :   //!   - `P[    4]` - REG-ID: EVEX.R' - 5th bit of 'RRRRR'.</a>
+<a name="101"><span class="lineNum">     101 </span>            :   //!   - `P[    5]` - REG-ID: EVEX.B  - 4th bit of 'BBBBB'.</a>
+<a name="102"><span class="lineNum">     102 </span>            :   //!   - `P[    6]` - REG-ID: EVEX.X  - 5th bit of 'BBBBB' or 4th bit of 'XXXX' (with SIB).</a>
+<a name="103"><span class="lineNum">     103 </span>            :   //!   - `P[    7]` - REG-ID: EVEX.R  - 4th bit of 'RRRRR'.</a>
+<a name="104"><span class="lineNum">     104 </span>            :   //!   - `P[ 9: 8]` - OPCODE: EVEX.pp.</a>
+<a name="105"><span class="lineNum">     105 </span>            :   //!   - `P[   10]` - ______: Must be 1.</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //!   - `P[14:11]` - REG-ID: 4 bits of 'VVVV'.</a>
+<a name="107"><span class="lineNum">     107 </span>            :   //!   - `P[   15]` - OPCODE: EVEX.W.</a>
+<a name="108"><span class="lineNum">     108 </span>            :   //!   - `P[18:16]` - REG-ID: K register k0...k7 (Merging/Zeroing Vector Ops).</a>
+<a name="109"><span class="lineNum">     109 </span>            :   //!   - `P[   19]` - REG-ID: 5th bit of 'VVVVV'.</a>
+<a name="110"><span class="lineNum">     110 </span>            :   //!   - `P[   20]` - OPCODE: Broadcast/Rounding Control/SAE bit.</a>
+<a name="111"><span class="lineNum">     111 </span>            :   //!   - `P[22.21]` - OPCODE: Vector Length (L' and  L) / Rounding Control.</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //!   - `P[   23]` - OPCODE: Zeroing/Merging.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   kX86ByteEvex = 0x62</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : // AsmJit specific (used to encode VVVVV field in XOP/VEX/EVEX).</a>
+<a name="117"><span class="lineNum">     117 </span>            : enum VexVVVVV {</a>
+<a name="118"><span class="lineNum">     118 </span>            :   kVexVVVVVShift = 7,</a>
+<a name="119"><span class="lineNum">     119 </span>            :   kVexVVVVVMask = 0x1F &lt;&lt; kVexVVVVVShift</a>
+<a name="120"><span class="lineNum">     120 </span>            : };</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : //! \internal</a>
+<a name="123"><span class="lineNum">     123 </span>            : //!</a>
+<a name="124"><span class="lineNum">     124 </span>            : //! Instruction 2-byte/3-byte opcode prefix definition.</a>
+<a name="125"><span class="lineNum">     125 </span>            : struct X86OpCodeMM {</a>
+<a name="126"><span class="lineNum">     126 </span>            :   uint8_t len;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   uint8_t data[3];</a>
+<a name="128"><span class="lineNum">     128 </span>            : };</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : //! \internal</a>
+<a name="131"><span class="lineNum">     131 </span>            : //!</a>
+<a name="132"><span class="lineNum">     132 </span>            : //! Mandatory prefixes used to encode legacy [66, F3, F2] or [9B] byte.</a>
+<a name="133"><span class="lineNum">     133 </span>            : static const uint8_t x86OpCodePP[8] = { 0x00, 0x66, 0xF3, 0xF2, 0x00, 0x00, 0x00, 0x9B };</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : //! \internal</a>
+<a name="136"><span class="lineNum">     136 </span>            : //!</a>
+<a name="137"><span class="lineNum">     137 </span>            : //! Instruction 2-byte/3-byte opcode prefix data.</a>
+<a name="138"><span class="lineNum">     138 </span>            : static const X86OpCodeMM x86OpCodeMM[] = {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #00 (0b0000).</a>
+<a name="140"><span class="lineNum">     140 </span>            :   { 1, { 0x0F, 0x00, 0 } }, // #01 (0b0001).</a>
+<a name="141"><span class="lineNum">     141 </span>            :   { 2, { 0x0F, 0x38, 0 } }, // #02 (0b0010).</a>
+<a name="142"><span class="lineNum">     142 </span>            :   { 2, { 0x0F, 0x3A, 0 } }, // #03 (0b0011).</a>
+<a name="143"><span class="lineNum">     143 </span>            :   { 2, { 0x0F, 0x01, 0 } }, // #04 (0b0100).</a>
+<a name="144"><span class="lineNum">     144 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #05 (0b0101).</a>
+<a name="145"><span class="lineNum">     145 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #06 (0b0110).</a>
+<a name="146"><span class="lineNum">     146 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #07 (0b0111).</a>
+<a name="147"><span class="lineNum">     147 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #08 (0b1000).</a>
+<a name="148"><span class="lineNum">     148 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #09 (0b1001).</a>
+<a name="149"><span class="lineNum">     149 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #0A (0b1010).</a>
+<a name="150"><span class="lineNum">     150 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #0B (0b1011).</a>
+<a name="151"><span class="lineNum">     151 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #0C (0b1100).</a>
+<a name="152"><span class="lineNum">     152 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #0D (0b1101).</a>
+<a name="153"><span class="lineNum">     153 </span>            :   { 0, { 0x00, 0x00, 0 } }, // #0E (0b1110).</a>
+<a name="154"><span class="lineNum">     154 </span>            :   { 0, { 0x00, 0x00, 0 } }  // #0F (0b1111).</a>
+<a name="155"><span class="lineNum">     155 </span>            : };</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : static const uint8_t x86SegmentPrefix[8] = { 0x00, 0x26, 0x2E, 0x36, 0x3E, 0x64, 0x65, 0x00 };</a>
+<a name="158"><span class="lineNum">     158 </span>            : static const uint8_t x86OpCodePushSeg[8] = { 0x00, 0x06, 0x0E, 0x16, 0x1E, 0xA0, 0xA8, 0x00 };</a>
+<a name="159"><span class="lineNum">     159 </span>            : static const uint8_t x86OpCodePopSeg[8]  = { 0x00, 0x07, 0x00, 0x17, 0x1F, 0xA1, 0xA9, 0x00 };</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : // ============================================================================</a>
+<a name="162"><span class="lineNum">     162 </span>            : // [asmjit::X86MemInfo | X86VEXPrefix | X86LLByRegType | X86CDisp8Table]</a>
+<a name="163"><span class="lineNum">     163 </span>            : // ============================================================================</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : //! \internal</a>
+<a name="166"><span class="lineNum">     166 </span>            : //!</a>
+<a name="167"><span class="lineNum">     167 </span>            : //! Memory operand's info bits.</a>
+<a name="168"><span class="lineNum">     168 </span>            : //!</a>
+<a name="169"><span class="lineNum">     169 </span>            : //! A lookup table that contains various information based on the BASE and INDEX</a>
+<a name="170"><span class="lineNum">     170 </span>            : //! information of a memory operand. This is much better and safer than playing</a>
+<a name="171"><span class="lineNum">     171 </span>            : //! with IFs in the code and can check for errors must faster and better.</a>
+<a name="172"><span class="lineNum">     172 </span>            : enum X86MemInfo_Enum {</a>
+<a name="173"><span class="lineNum">     173 </span>            :   kX86MemInfo_0         = 0x00,</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   kX86MemInfo_BaseGp    = 0x01, //!&lt; Has BASE reg, REX.B can be 1, compatible with REX.B byte.</a>
+<a name="176"><span class="lineNum">     176 </span>            :   kX86MemInfo_Index     = 0x02, //!&lt; Has INDEX reg, REX.X can be 1, compatible with REX.X byte.</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   kX86MemInfo_BaseLabel = 0x10, //!&lt; Base is Label.</a>
+<a name="179"><span class="lineNum">     179 </span>            :   kX86MemInfo_BaseRip   = 0x20, //!&lt; Base is RIP.</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   kX86MemInfo_67H_X86   = 0x40, //!&lt; Address-size override in 32-bit mode.</a>
+<a name="182"><span class="lineNum">     182 </span>            :   kX86MemInfo_67H_X64   = 0x80, //!&lt; Address-size override in 64-bit mode.</a>
+<a name="183"><span class="lineNum">     183 </span>            :   kX86MemInfo_67H_Mask  = 0xC0  //!&lt; Contains all address-size override bits.</a>
+<a name="184"><span class="lineNum">     184 </span>            : };</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="187"><span class="lineNum">     187 </span>            : struct X86MemInfo_T {</a>
+<a name="188"><span class="lineNum">     188 </span>            :   enum {</a>
+<a name="189"><span class="lineNum">     189 </span>            :     B = (X     ) &amp; 0x1F,</a>
+<a name="190"><span class="lineNum">     190 </span>            :     I = (X &gt;&gt; 5) &amp; 0x1F,</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :     kBase  = ((B &gt;= X86Reg::kRegGpw  &amp;&amp; B &lt;= X86Reg::kRegGpq ) ? kX86MemInfo_BaseGp    :</a>
+<a name="193"><span class="lineNum">     193 </span>            :               (B == X86Reg::kRegRip                          ) ? kX86MemInfo_BaseRip   :</a>
+<a name="194"><span class="lineNum">     194 </span>            :               (B == Label::kLabelTag                         ) ? kX86MemInfo_BaseLabel : 0),</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :     kIndex = ((I &gt;= X86Reg::kRegGpw  &amp;&amp; I &lt;= X86Reg::kRegGpq ) ? kX86MemInfo_Index     :</a>
+<a name="197"><span class="lineNum">     197 </span>            :               (I &gt;= X86Reg::kRegXmm  &amp;&amp; I &lt;= X86Reg::kRegZmm ) ? kX86MemInfo_Index     : 0),</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :     k67H   = ((B == X86Reg::kRegGpw  &amp;&amp; I == X86Reg::kRegNone) ? kX86MemInfo_67H_X86   :</a>
+<a name="200"><span class="lineNum">     200 </span>            :               (B == X86Reg::kRegGpd  &amp;&amp; I == X86Reg::kRegNone) ? kX86MemInfo_67H_X64   :</a>
+<a name="201"><span class="lineNum">     201 </span>            :               (B == X86Reg::kRegNone &amp;&amp; I == X86Reg::kRegGpw ) ? kX86MemInfo_67H_X86   :</a>
+<a name="202"><span class="lineNum">     202 </span>            :               (B == X86Reg::kRegNone &amp;&amp; I == X86Reg::kRegGpd ) ? kX86MemInfo_67H_X64   :</a>
+<a name="203"><span class="lineNum">     203 </span>            :               (B == X86Reg::kRegGpw  &amp;&amp; I == X86Reg::kRegGpw ) ? kX86MemInfo_67H_X86   :</a>
+<a name="204"><span class="lineNum">     204 </span>            :               (B == X86Reg::kRegGpd  &amp;&amp; I == X86Reg::kRegGpd ) ? kX86MemInfo_67H_X64   :</a>
+<a name="205"><span class="lineNum">     205 </span>            :               (B == X86Reg::kRegGpw  &amp;&amp; I == X86Reg::kRegXmm ) ? kX86MemInfo_67H_X86   :</a>
+<a name="206"><span class="lineNum">     206 </span>            :               (B == X86Reg::kRegGpd  &amp;&amp; I == X86Reg::kRegXmm ) ? kX86MemInfo_67H_X64   :</a>
+<a name="207"><span class="lineNum">     207 </span>            :               (B == X86Reg::kRegGpw  &amp;&amp; I == X86Reg::kRegYmm ) ? kX86MemInfo_67H_X86   :</a>
+<a name="208"><span class="lineNum">     208 </span>            :               (B == X86Reg::kRegGpd  &amp;&amp; I == X86Reg::kRegYmm ) ? kX86MemInfo_67H_X64   :</a>
+<a name="209"><span class="lineNum">     209 </span>            :               (B == X86Reg::kRegGpw  &amp;&amp; I == X86Reg::kRegZmm ) ? kX86MemInfo_67H_X86   :</a>
+<a name="210"><span class="lineNum">     210 </span>            :               (B == X86Reg::kRegGpd  &amp;&amp; I == X86Reg::kRegZmm ) ? kX86MemInfo_67H_X64   :</a>
+<a name="211"><span class="lineNum">     211 </span>            :               (B == Label::kLabelTag &amp;&amp; I == X86Reg::kRegGpw ) ? kX86MemInfo_67H_X86   :</a>
+<a name="212"><span class="lineNum">     212 </span>            :               (B == Label::kLabelTag &amp;&amp; I == X86Reg::kRegGpd ) ? kX86MemInfo_67H_X64   : 0),</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :     kValue = kBase | kIndex | k67H | 0x04 | 0x08</a>
+<a name="215"><span class="lineNum">     215 </span>            :   };</a>
+<a name="216"><span class="lineNum">     216 </span>            : };</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : // The result stored in the LUT is a combination of</a>
+<a name="219"><span class="lineNum">     219 </span>            : //   - 67H - Address override prefix - depends on BASE+INDEX register types and</a>
+<a name="220"><span class="lineNum">     220 </span>            : //           the target architecture.</a>
+<a name="221"><span class="lineNum">     221 </span>            : //   - REX - A possible combination of REX.[B|X|R|W] bits in REX prefix where</a>
+<a name="222"><span class="lineNum">     222 </span>            : //           REX.B and REX.X are possibly masked out, but REX.R and REX.W are</a>
+<a name="223"><span class="lineNum">     223 </span>            : //           kept as is.</a>
+<a name="224"><span class="lineNum">     224 </span>            : static const uint8_t x86MemInfo[] = { ASMJIT_TABLE_T_1024(X86MemInfo_T, kValue, 0) };</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : // VEX3 or XOP xor bits applied to the opcode before emitted. The index to this</a>
+<a name="227"><span class="lineNum">     227 </span>            : // table is 'mmmmm' value, which contains all we need. This is only used by a</a>
+<a name="228"><span class="lineNum">     228 </span>            : // 3 BYTE VEX and XOP prefixes, 2 BYTE VEX prefix is handled differently. The</a>
+<a name="229"><span class="lineNum">     229 </span>            : // idea is to minimize the difference between VEX3 vs XOP when encoding VEX</a>
+<a name="230"><span class="lineNum">     230 </span>            : // or XOP instruction. This should minimize the code required to emit such</a>
+<a name="231"><span class="lineNum">     231 </span>            : // instructions and should also make it faster as we don't need any branch to</a>
+<a name="232"><span class="lineNum">     232 </span>            : // decide between VEX3 vs XOP.</a>
+<a name="233"><span class="lineNum">     233 </span>            : //            ____    ___</a>
+<a name="234"><span class="lineNum">     234 </span>            : // [_OPCODE_|WvvvvLpp|RXBmmmmm|VEX3_XOP]</a>
+<a name="235"><span class="lineNum">     235 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="236"><span class="lineNum">     236 </span>            : struct X86VEXPrefix_T {</a>
+<a name="237"><span class="lineNum">     237 </span>            :   enum { kValue = ((X &amp; 0x08) ? kX86ByteXop3 : kX86ByteVex3) | (0xF &lt;&lt; 19) | (0x7 &lt;&lt; 13) };</a>
+<a name="238"><span class="lineNum">     238 </span>            : };</a>
+<a name="239"><span class="lineNum">     239 </span>            : static const uint32_t x86VEXPrefix[] = { ASMJIT_TABLE_T_16(X86VEXPrefix_T, kValue, 0) };</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : // Table that contains LL opcode field addressed by a register size / 16. It's</a>
+<a name="242"><span class="lineNum">     242 </span>            : // used to propagate L.256 or L.512 when YMM or ZMM registers are used,</a>
+<a name="243"><span class="lineNum">     243 </span>            : // respectively.</a>
+<a name="244"><span class="lineNum">     244 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="245"><span class="lineNum">     245 </span>            : struct X86LLBySizeDiv16_T {</a>
+<a name="246"><span class="lineNum">     246 </span>            :   enum {</a>
+<a name="247"><span class="lineNum">     247 </span>            :     kValue = (X &amp; (64 &gt;&gt; 4)) ? X86Inst::kOpCode_LL_512 :</a>
+<a name="248"><span class="lineNum">     248 </span>            :              (X &amp; (32 &gt;&gt; 4)) ? X86Inst::kOpCode_LL_256 : 0</a>
+<a name="249"><span class="lineNum">     249 </span>            :   };</a>
+<a name="250"><span class="lineNum">     250 </span>            : };</a>
+<a name="251"><span class="lineNum">     251 </span>            : static const uint32_t x86LLBySizeDiv16[] = { ASMJIT_TABLE_T_16(X86LLBySizeDiv16_T, kValue, 0) };</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : // Table that contains LL opcode field addressed by a register size / 16. It's</a>
+<a name="254"><span class="lineNum">     254 </span>            : // used to propagate L.256 or L.512 when YMM or ZMM registers are used,</a>
+<a name="255"><span class="lineNum">     255 </span>            : // respectively.</a>
+<a name="256"><span class="lineNum">     256 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="257"><span class="lineNum">     257 </span>            : struct X86LLByRegType_T {</a>
+<a name="258"><span class="lineNum">     258 </span>            :   enum {</a>
+<a name="259"><span class="lineNum">     259 </span>            :     kValue = X == X86Reg::kRegZmm ? X86Inst::kOpCode_LL_512 :</a>
+<a name="260"><span class="lineNum">     260 </span>            :              X == X86Reg::kRegYmm ? X86Inst::kOpCode_LL_256 : 0</a>
+<a name="261"><span class="lineNum">     261 </span>            :   };</a>
+<a name="262"><span class="lineNum">     262 </span>            : };</a>
+<a name="263"><span class="lineNum">     263 </span>            : static const uint32_t x86LLByRegType[] = { ASMJIT_TABLE_T_16(X86LLByRegType_T, kValue, 0) };</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : // Table that contains a scale (shift left) based on 'TTWLL' field and</a>
+<a name="266"><span class="lineNum">     266 </span>            : // the instruction's tuple-type (TT) field. The scale is then applied to</a>
+<a name="267"><span class="lineNum">     267 </span>            : // the BASE-N stored in each opcode to calculate the final compressed</a>
+<a name="268"><span class="lineNum">     268 </span>            : // displacement used by all EVEX encoded instructions.</a>
+<a name="269"><span class="lineNum">     269 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="270"><span class="lineNum">     270 </span>            : struct X86CDisp8SHL_T {</a>
+<a name="271"><span class="lineNum">     271 </span>            :   enum {</a>
+<a name="272"><span class="lineNum">     272 </span>            :     TT = (((X) &gt;&gt; 3) &lt;&lt; X86Inst::kOpCode_CDTT_Shift),</a>
+<a name="273"><span class="lineNum">     273 </span>            :     LL = (((X) &gt;&gt; 0) &amp; 0x3),</a>
+<a name="274"><span class="lineNum">     274 </span>            :     W  = (((X) &gt;&gt; 2) &amp; 0x1),</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :     kValue = (TT == X86Inst::kOpCode_CDTT_None ? ((LL==0) ? 0 : (LL==1) ? 0   : 0  ) :</a>
+<a name="277"><span class="lineNum">     277 </span>            :               TT == X86Inst::kOpCode_CDTT_ByLL ? ((LL==0) ? 0 : (LL==1) ? 1   : 2  ) :</a>
+<a name="278"><span class="lineNum">     278 </span>            :               TT == X86Inst::kOpCode_CDTT_T1W  ? ((LL==0) ? W : (LL==1) ? 1+W : 2+W) :</a>
+<a name="279"><span class="lineNum">     279 </span>            :               TT == X86Inst::kOpCode_CDTT_DUP  ? ((LL==0) ? 0 : (LL==1) ? 2   : 3  ) : 0 ) &lt;&lt; X86Inst::kOpCode_CDSHL_Shift</a>
+<a name="280"><span class="lineNum">     280 </span>            :   };</a>
+<a name="281"><span class="lineNum">     281 </span>            : };</a>
+<a name="282"><span class="lineNum">     282 </span>            : static const uint32_t x86CDisp8SHL[] = { ASMJIT_TABLE_T_32(X86CDisp8SHL_T, kValue, 0) };</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : // Table that contains MOD byte of a 16-bit [BASE + disp] address.</a>
+<a name="285"><span class="lineNum">     285 </span>            : //   0xFF == Invalid.</a>
+<a name="286"><span class="lineNum">     286 </span>            : static const uint8_t x86Mod16BaseTable[8] = {</a>
+<a name="287"><span class="lineNum">     287 </span>            :   0xFF, // AX -&gt; N/A.</a>
+<a name="288"><span class="lineNum">     288 </span>            :   0xFF, // CX -&gt; N/A.</a>
+<a name="289"><span class="lineNum">     289 </span>            :   0xFF, // DX -&gt; N/A.</a>
+<a name="290"><span class="lineNum">     290 </span>            :   0x07, // BX -&gt; 111.</a>
+<a name="291"><span class="lineNum">     291 </span>            :   0xFF, // SP -&gt; N/A.</a>
+<a name="292"><span class="lineNum">     292 </span>            :   0x06, // BP -&gt; 110.</a>
+<a name="293"><span class="lineNum">     293 </span>            :   0x04, // SI -&gt; 100.</a>
+<a name="294"><span class="lineNum">     294 </span>            :   0x05  // DI -&gt; 101.</a>
+<a name="295"><span class="lineNum">     295 </span>            : };</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : // Table that contains MOD byte of a 16-bit [BASE + INDEX + disp] combination.</a>
+<a name="298"><span class="lineNum">     298 </span>            : //   0xFF == Invalid.</a>
+<a name="299"><span class="lineNum">     299 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="300"><span class="lineNum">     300 </span>            : struct X86Mod16BaseIndexTable_T {</a>
+<a name="301"><span class="lineNum">     301 </span>            :   enum {</a>
+<a name="302"><span class="lineNum">     302 </span>            :     B = X &gt;&gt; 3,</a>
+<a name="303"><span class="lineNum">     303 </span>            :     I = X &amp; 0x7,</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            :     kValue = ((B == X86Gp::kIdBx &amp;&amp; I == X86Gp::kIdSi) || (B == X86Gp::kIdSi &amp;&amp; I == X86Gp::kIdBx)) ? 0x00 :</a>
+<a name="306"><span class="lineNum">     306 </span>            :              ((B == X86Gp::kIdBx &amp;&amp; I == X86Gp::kIdDi) || (B == X86Gp::kIdDi &amp;&amp; I == X86Gp::kIdBx)) ? 0x01 :</a>
+<a name="307"><span class="lineNum">     307 </span>            :              ((B == X86Gp::kIdBp &amp;&amp; I == X86Gp::kIdSi) || (B == X86Gp::kIdSi &amp;&amp; I == X86Gp::kIdBp)) ? 0x02 :</a>
+<a name="308"><span class="lineNum">     308 </span>            :              ((B == X86Gp::kIdBp &amp;&amp; I == X86Gp::kIdDi) || (B == X86Gp::kIdDi &amp;&amp; I == X86Gp::kIdBp)) ? 0x03 : 0xFF</a>
+<a name="309"><span class="lineNum">     309 </span>            :   };</a>
+<a name="310"><span class="lineNum">     310 </span>            : };</a>
+<a name="311"><span class="lineNum">     311 </span>            : static const uint8_t x86Mod16BaseIndexTable[] = { ASMJIT_TABLE_T_64(X86Mod16BaseIndexTable_T, kValue, 0) };</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : // ============================================================================</a>
+<a name="314"><span class="lineNum">     314 </span>            : // [asmjit::X86Assembler - Helpers]</a>
+<a name="315"><span class="lineNum">     315 </span>            : // ============================================================================</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : static ASMJIT_INLINE bool x86IsJmpOrCall(uint32_t instId) noexcept {</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :   return instId == X86Inst::kIdJmp ||</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :          instId == X86Inst::kIdCall;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : }</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : static ASMJIT_INLINE bool x86IsImplicitMem(const Operand_&amp; op, uint32_t base) noexcept {</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :   return op.isMem() &amp;&amp; op.as&lt;X86Mem&gt;().getBaseId() == base;</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : static ASMJIT_INLINE int64_t x86SignExtend32To64(int64_t imm) noexcept {</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :   return static_cast&lt;int64_t&gt;(static_cast&lt;int32_t&gt;(imm &amp; 0xFFFFFFFF));</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            : //! Get `O` field of `opCode`.</a>
+<a name="331"><span class="lineNum">     331 </span>            : static ASMJIT_INLINE uint32_t x86ExtractO(uint32_t opCode) noexcept {</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      48362 :   return (opCode &gt;&gt; X86Inst::kOpCode_O_Shift) &amp; 0x07;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            : static ASMJIT_INLINE uint32_t x86ExtractREX(uint32_t opCode, uint32_t options) noexcept {</a>
+<a name="336"><span class="lineNum">     336 </span>            :   // kOpCode_REX was designed in a way that when shifted there will be no bytes</a>
+<a name="337"><span class="lineNum">     337 </span>            :   // set except REX.[B|X|R|W]. The returned value forms a real REX prefix byte.</a>
+<a name="338"><span class="lineNum">     338 </span>            :   // This case is tested by `X86Inst.cpp`.</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      48362 :   return (opCode | options) &gt;&gt; X86Inst::kOpCode_REX_Shift;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : }</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            : //! Combine `regId` and `vvvvvId` into a single value (used by AVX and AVX-512).</a>
+<a name="343"><span class="lineNum">     343 </span>            : static ASMJIT_INLINE uint32_t x86PackRegAndVvvvv(uint32_t regId, uint32_t vvvvvId) noexcept {</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :   return regId + (vvvvvId &lt;&lt; kVexVVVVVShift);</span></a>
+<a name="345"><span class="lineNum">     345 </span>            : }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            : static ASMJIT_INLINE uint32_t x86OpCodeLByVMem(const Operand_&amp; op) noexcept {</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :   return x86LLByRegType[op.as&lt;X86Mem&gt;().getIndexType()];</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            : static ASMJIT_INLINE uint32_t x86OpCodeLBySize(uint32_t size) noexcept {</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :   return x86LLBySizeDiv16[size / 16];</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : static ASMJIT_INLINE uint32_t x86ExtractLLMM(uint32_t opCode, uint32_t options) noexcept {</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :   uint32_t x = opCode &amp; (X86Inst::kOpCode_LL_Mask | X86Inst::kOpCode_MM_Mask);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :   uint32_t y = options &amp; X86Inst::kOptionVex3;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   return (x | y) &gt;&gt; X86Inst::kOpCode_MM_Shift;</span></a>
+<a name="359"><span class="lineNum">     359 </span>            : }</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : //! Encode MOD byte.</a>
+<a name="362"><span class="lineNum">     362 </span>            : static ASMJIT_INLINE uint32_t x86EncodeMod(uint32_t m, uint32_t o, uint32_t rm) noexcept {</a>
+<a name="363"><span class="lineNum">     363 </span>            :   ASMJIT_ASSERT(m &lt;= 3);</a>
+<a name="364"><span class="lineNum">     364 </span>            :   ASMJIT_ASSERT(o &lt;= 7);</a>
+<a name="365"><span class="lineNum">     365 </span>            :   ASMJIT_ASSERT(rm &lt;= 7);</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :   return (m &lt;&lt; 6) + (o &lt;&lt; 3) + rm;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : //! Encode SIB byte.</a>
+<a name="370"><span class="lineNum">     370 </span>            : static ASMJIT_INLINE uint32_t x86EncodeSib(uint32_t s, uint32_t i, uint32_t b) noexcept {</a>
+<a name="371"><span class="lineNum">     371 </span>            :   ASMJIT_ASSERT(s &lt;= 3);</a>
+<a name="372"><span class="lineNum">     372 </span>            :   ASMJIT_ASSERT(i &lt;= 7);</a>
+<a name="373"><span class="lineNum">     373 </span>            :   ASMJIT_ASSERT(b &lt;= 7);</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :   return (s &lt;&lt; 6) + (i &lt;&lt; 3) + b;</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : }</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : // ============================================================================</a>
+<a name="378"><span class="lineNum">     378 </span>            : // [asmjit::X86Assembler - Construction / Destruction]</a>
+<a name="379"><span class="lineNum">     379 </span>            : // ============================================================================</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       1948 : X86Assembler::X86Assembler(CodeHolder* code) noexcept : Assembler() {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       1948 :   if (code)</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       1948 :     code-&gt;attach(this);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       1948 : }</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       1948 : X86Assembler::~X86Assembler() noexcept {}</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            : // ============================================================================</a>
+<a name="388"><span class="lineNum">     388 </span>            : // [asmjit::X86Assembler - Events]</a>
+<a name="389"><span class="lineNum">     389 </span>            : // ============================================================================</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">       1948 : Error X86Assembler::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   uint32_t archType = code-&gt;getArchType();</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       1948 :   if (!ArchInfo::isX86Family(archType))</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :     return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       1948 :   ASMJIT_PROPAGATE(Base::onAttach(code));</span></a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       1948 :   if (archType == ArchInfo::kTypeX86) {</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :     // 32 bit architecture - X86.</a>
+<a name="400"><span class="lineNum">     400 </span>            :     _setAddressOverrideMask(kX86MemInfo_67H_X86);</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :     _globalOptions |= X86Inst::_kOptionInvalidRex;</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :     _nativeGpArray = x86OpData.gpd;</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span>            :   else {</a>
+<a name="405"><span class="lineNum">     405 </span>            :     // 64 bit architecture - X64 or X32.</a>
+<a name="406"><span class="lineNum">     406 </span>            :     _setAddressOverrideMask(kX86MemInfo_67H_X64);</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">       1948 :     _nativeGpArray = x86OpData.gpq;</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :   }</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">       1948 :   _nativeGpReg = _nativeGpArray[0];</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 : Error X86Assembler::onDetach(CodeHolder* code) noexcept {</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :   return Base::onDetach(code);</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : }</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            : // ============================================================================</a>
+<a name="419"><span class="lineNum">     419 </span>            : // [asmjit::X86Assembler - Helpers]</a>
+<a name="420"><span class="lineNum">     420 </span>            : // ============================================================================</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            : #define EMIT_BYTE(VAL)                               \</a>
+<a name="423"><span class="lineNum">     423 </span>            :   do {                                               \</a>
+<a name="424"><span class="lineNum">     424 </span>            :     cursor[0] = static_cast&lt;uint8_t&gt;((VAL) &amp; 0xFFU); \</a>
+<a name="425"><span class="lineNum">     425 </span>            :     cursor += 1;                                     \</a>
+<a name="426"><span class="lineNum">     426 </span>            :   } while (0)</a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span>            : #define EMIT_16(VAL)                                 \</a>
+<a name="429"><span class="lineNum">     429 </span>            :   do {                                               \</a>
+<a name="430"><span class="lineNum">     430 </span>            :     Utils::writeU16uLE(cursor,                       \</a>
+<a name="431"><span class="lineNum">     431 </span>            :       static_cast&lt;uint32_t&gt;((VAL) &amp; 0xFFFFU));       \</a>
+<a name="432"><span class="lineNum">     432 </span>            :     cursor += 2;                                     \</a>
+<a name="433"><span class="lineNum">     433 </span>            :   } while (0)</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            : #define EMIT_32(VAL)                                 \</a>
+<a name="436"><span class="lineNum">     436 </span>            :   do {                                               \</a>
+<a name="437"><span class="lineNum">     437 </span>            :     Utils::writeU32uLE(cursor,                       \</a>
+<a name="438"><span class="lineNum">     438 </span>            :       static_cast&lt;uint32_t&gt;((VAL) &amp; 0xFFFFFFFFU));   \</a>
+<a name="439"><span class="lineNum">     439 </span>            :     cursor += 4;                                     \</a>
+<a name="440"><span class="lineNum">     440 </span>            :   } while (0)</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            : #define ADD_66H_P(EXP)                                                   \</a>
+<a name="443"><span class="lineNum">     443 </span>            :   do {                                                                   \</a>
+<a name="444"><span class="lineNum">     444 </span>            :     opCode |= (static_cast&lt;uint32_t&gt;(EXP) &lt;&lt; X86Inst::kOpCode_PP_Shift); \</a>
+<a name="445"><span class="lineNum">     445 </span>            :   } while (0)</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span>            : #define ADD_66H_P_BY_SIZE(SIZE)                                          \</a>
+<a name="448"><span class="lineNum">     448 </span>            :   do {                                                                   \</a>
+<a name="449"><span class="lineNum">     449 </span>            :     opCode |= (static_cast&lt;uint32_t&gt;((SIZE) &amp; 0x02))                     \</a>
+<a name="450"><span class="lineNum">     450 </span>            :            &lt;&lt; (X86Inst::kOpCode_PP_Shift - 1);                           \</a>
+<a name="451"><span class="lineNum">     451 </span>            :   } while (0)</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            : #define ADD_REX_W(EXP)                                                   \</a>
+<a name="454"><span class="lineNum">     454 </span>            :   do {                                                                   \</a>
+<a name="455"><span class="lineNum">     455 </span>            :     if (EXP)                                                             \</a>
+<a name="456"><span class="lineNum">     456 </span>            :       opCode |= X86Inst::kOpCode_W;                                      \</a>
+<a name="457"><span class="lineNum">     457 </span>            :   } while (0)</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            : #define ADD_REX_W_BY_SIZE(SIZE)                                          \</a>
+<a name="460"><span class="lineNum">     460 </span>            :   do {                                                                   \</a>
+<a name="461"><span class="lineNum">     461 </span>            :     if ((SIZE) == 8)                                                     \</a>
+<a name="462"><span class="lineNum">     462 </span>            :       opCode |= X86Inst::kOpCode_W;                                      \</a>
+<a name="463"><span class="lineNum">     463 </span>            :   } while (0)</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span>            : #define ADD_PREFIX_BY_SIZE(SIZE)                                         \</a>
+<a name="466"><span class="lineNum">     466 </span>            :   do {                                                                   \</a>
+<a name="467"><span class="lineNum">     467 </span>            :     ADD_66H_P_BY_SIZE(SIZE);                                             \</a>
+<a name="468"><span class="lineNum">     468 </span>            :     ADD_REX_W_BY_SIZE(SIZE);                                             \</a>
+<a name="469"><span class="lineNum">     469 </span>            :   } while (0)</a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            : #define ADD_VEX_W(EXP)                                                   \</a>
+<a name="472"><span class="lineNum">     472 </span>            :   do {                                                                   \</a>
+<a name="473"><span class="lineNum">     473 </span>            :     opCode |= static_cast&lt;uint32_t&gt;(EXP) &lt;&lt; X86Inst::kOpCode_W_Shift;    \</a>
+<a name="474"><span class="lineNum">     474 </span>            :   } while (0)</a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            : #define EMIT_PP(OPCODE)                                                  \</a>
+<a name="477"><span class="lineNum">     477 </span>            :   do {                                                                   \</a>
+<a name="478"><span class="lineNum">     478 </span>            :     uint32_t ppIndex =                                                   \</a>
+<a name="479"><span class="lineNum">     479 </span>            :       ((OPCODE                   ) &gt;&gt; X86Inst::kOpCode_PP_Shift) &amp;       \</a>
+<a name="480"><span class="lineNum">     480 </span>            :       (X86Inst::kOpCode_PP_FPUMask &gt;&gt; X86Inst::kOpCode_PP_Shift) ;       \</a>
+<a name="481"><span class="lineNum">     481 </span>            :     uint8_t ppCode = x86OpCodePP[ppIndex];                               \</a>
+<a name="482"><span class="lineNum">     482 </span>            :                                                                          \</a>
+<a name="483"><span class="lineNum">     483 </span>            :     cursor[0] = ppCode;                                                  \</a>
+<a name="484"><span class="lineNum">     484 </span>            :     cursor   += ppIndex != 0;                                            \</a>
+<a name="485"><span class="lineNum">     485 </span>            :   } while (0)</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span>            : #define EMIT_MM_OP(OPCODE)                                               \</a>
+<a name="488"><span class="lineNum">     488 </span>            :   do {                                                                   \</a>
+<a name="489"><span class="lineNum">     489 </span>            :     uint32_t op = OPCODE &amp; (0x00FF | X86Inst::kOpCode_MM_Mask);          \</a>
+<a name="490"><span class="lineNum">     490 </span>            :                                                                          \</a>
+<a name="491"><span class="lineNum">     491 </span>            :     uint32_t mmIndex = op &gt;&gt; X86Inst::kOpCode_MM_Shift;                  \</a>
+<a name="492"><span class="lineNum">     492 </span>            :     const X86OpCodeMM&amp; mmCode = x86OpCodeMM[mmIndex];                    \</a>
+<a name="493"><span class="lineNum">     493 </span>            :                                                                          \</a>
+<a name="494"><span class="lineNum">     494 </span>            :     if (mmIndex) {                                                       \</a>
+<a name="495"><span class="lineNum">     495 </span>            :       cursor[0] = mmCode.data[0];                                        \</a>
+<a name="496"><span class="lineNum">     496 </span>            :       cursor[1] = mmCode.data[1];                                        \</a>
+<a name="497"><span class="lineNum">     497 </span>            :       cursor   += mmCode.len;                                            \</a>
+<a name="498"><span class="lineNum">     498 </span>            :     }                                                                    \</a>
+<a name="499"><span class="lineNum">     499 </span>            :                                                                          \</a>
+<a name="500"><span class="lineNum">     500 </span>            :     EMIT_BYTE(op);                                                       \</a>
+<a name="501"><span class="lineNum">     501 </span>            :   } while (0)</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            : // If the operand is BPL|SPL|SIL|DIL|R8B-15B</a>
+<a name="504"><span class="lineNum">     504 </span>            : //   - Force REX prefix</a>
+<a name="505"><span class="lineNum">     505 </span>            : // If the operand is AH|BH|CH|DH</a>
+<a name="506"><span class="lineNum">     506 </span>            : //   - patch its index from 0..3 to 4..7 as encoded by X86.</a>
+<a name="507"><span class="lineNum">     507 </span>            : //   - Disallow REX prefix.</a>
+<a name="508"><span class="lineNum">     508 </span>            : #define FIXUP_GPB(REG_OP, REG_ID)                                   \</a>
+<a name="509"><span class="lineNum">     509 </span>            :   do {                                                                   \</a>
+<a name="510"><span class="lineNum">     510 </span>            :     if (!static_cast&lt;const X86Gp&amp;&gt;(REG_OP).isGpbHi()) {                  \</a>
+<a name="511"><span class="lineNum">     511 </span>            :       options |= (REG_ID &gt;= 4) ? X86Inst::kOptionRex : 0;                \</a>
+<a name="512"><span class="lineNum">     512 </span>            :     }                                                                    \</a>
+<a name="513"><span class="lineNum">     513 </span>            :     else {                                                               \</a>
+<a name="514"><span class="lineNum">     514 </span>            :       options |= X86Inst::_kOptionInvalidRex;                            \</a>
+<a name="515"><span class="lineNum">     515 </span>            :       REG_ID += 4;                                                       \</a>
+<a name="516"><span class="lineNum">     516 </span>            :     }                                                                    \</a>
+<a name="517"><span class="lineNum">     517 </span>            :   } while (0)</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span>            : #define ENC_OPS1(OP0)                     ((Operand::kOp##OP0))</a>
+<a name="520"><span class="lineNum">     520 </span>            : #define ENC_OPS2(OP0, OP1)                ((Operand::kOp##OP0) + ((Operand::kOp##OP1) &lt;&lt; 3))</a>
+<a name="521"><span class="lineNum">     521 </span>            : #define ENC_OPS3(OP0, OP1, OP2)           ((Operand::kOp##OP0) + ((Operand::kOp##OP1) &lt;&lt; 3) + ((Operand::kOp##OP2) &lt;&lt; 6))</a>
+<a name="522"><span class="lineNum">     522 </span>            : #define ENC_OPS4(OP0, OP1, OP2, OP3)      ((Operand::kOp##OP0) + ((Operand::kOp##OP1) &lt;&lt; 3) + ((Operand::kOp##OP2) &lt;&lt; 6) + ((Operand::kOp##OP3) &lt;&lt; 9))</a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            : // ============================================================================</a>
+<a name="525"><span class="lineNum">     525 </span>            : // [asmjit::X86Assembler - Emit]</a>
+<a name="526"><span class="lineNum">     526 </span>            : // ============================================================================</a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">      48362 : Error X86Assembler::_emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) {</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :   Error err;</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   const Operand_* rmRel;         // Memory operand or operand that holds Label|Imm.</a>
+<a name="532"><span class="lineNum">     532 </span>            :   uint32_t rmInfo;               // Memory operand's info based on x86MemInfo.</a>
+<a name="533"><span class="lineNum">     533 </span>            :   uint32_t rbReg;                // Memory base or modRM register.</a>
+<a name="534"><span class="lineNum">     534 </span>            :   uint32_t rxReg;                // Memory index register.</a>
+<a name="535"><span class="lineNum">     535 </span>            :   uint32_t opReg;                // ModR/M opcode or register id.</a>
+<a name="536"><span class="lineNum">     536 </span>            :   uint32_t opCode;               // Instruction opcode.</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            :   LabelEntry* label;             // Label entry.</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">      48362 :   RelocEntry* re = nullptr;      // Relocation entry.</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :   int32_t relOffset;             // Relative offset</a>
+<a name="541"><span class="lineNum">     541 </span>            :   FastUInt8 relSize = 0;         // Relative size.</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            :   int64_t imVal = 0;             // Immediate value (must be 64-bit).</a>
+<a name="544"><span class="lineNum">     544 </span>            :   FastUInt8 imLen = 0;           // Immediate length.</a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span>            :   const uint32_t kSHR_W_PP = X86Inst::kOpCode_PP_Shift - 16;</a>
+<a name="547"><span class="lineNum">     547 </span>            :   const uint32_t kSHR_W_EW = X86Inst::kOpCode_EW_Shift - 23;</a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">      48362 :   uint8_t* cursor = _bufferPtr;</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">      48362 :   uint32_t options = static_cast&lt;uint32_t&gt;(instId &gt;= X86Inst::_kIdCount)       |</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">      48362 :                      static_cast&lt;uint32_t&gt;((size_t)(_bufferEnd - cursor) &lt; 16) |</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">      48362 :                      getGlobalOptions() | getOptions();</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">      48362 :   const X86Inst* instData = X86InstDB::instData + instId;</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :   const X86Inst::CommonData* commonData;</a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span>            :   // Handle failure and rare cases first.</a>
+<a name="558"><span class="lineNum">     558 </span>            :   const uint32_t kErrorsAndSpecialCases =</a>
+<a name="559"><span class="lineNum">     559 </span>            :     CodeEmitter::kOptionMaybeFailureCase | // Error and buffer check.</a>
+<a name="560"><span class="lineNum">     560 </span>            :     CodeEmitter::kOptionStrictValidation | // Strict validation.</a>
+<a name="561"><span class="lineNum">     561 </span>            :     X86Inst::kOptionRep                  | // REP/REPZ prefix.</a>
+<a name="562"><span class="lineNum">     562 </span>            :     X86Inst::kOptionRepnz                | // REPNZ prefix.</a>
+<a name="563"><span class="lineNum">     563 </span>            :     X86Inst::kOptionLock                 | // LOCK prefix.</a>
+<a name="564"><span class="lineNum">     564 </span>            :     X86Inst::kOptionXAcquire             | // XACQUIRE prefix.</a>
+<a name="565"><span class="lineNum">     565 </span>            :     X86Inst::kOptionXRelease             ; // XRELEASE prefix.</a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            :   // Signature of the first 3 operands.</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">      48362 :   uint32_t isign3 = o0.getOp() + (o1.getOp() &lt;&lt; 3) + (o2.getOp() &lt;&lt; 6);</span></a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">      48362 :   if (ASMJIT_UNLIKELY(options &amp; kErrorsAndSpecialCases)) {</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :     // Don't do anything if we are in error state.</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">       1948 :     if (_lastError) return _lastError;</span></a>
+<a name="573"><span class="lineNum">     573 </span>            : </a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">       1948 :     if (options &amp; CodeEmitter::kOptionMaybeFailureCase) {</span></a>
+<a name="575"><span class="lineNum">     575 </span>            :       // Unknown instruction.</a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">       1948 :       if (ASMJIT_UNLIKELY(instId &gt;= X86Inst::_kIdCount))</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :         goto InvalidArgument;</span></a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span>            :       // Grow request, happens rarely.</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">       1948 :       if ((size_t)(_bufferEnd - cursor) &lt; 16) {</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">       1948 :         err = _code-&gt;growBuffer(&amp;_section-&gt;_buffer, 16);</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">       1948 :         if (ASMJIT_UNLIKELY(err)) goto Failed;</span></a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">       1948 :         cursor = _bufferPtr;</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">       1948 :         options &amp;= ~1;</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :       }</a>
+<a name="587"><span class="lineNum">     587 </span>            :     }</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span>            :     // Strict validation.</a>
+<a name="590"><span class="lineNum">     590 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">       1948 :     if (options &amp; CodeEmitter::kOptionStrictValidation) {</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :       Operand_ opArray[6];</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span>            :       opArray[0].copyFrom(o0);</a>
+<a name="595"><span class="lineNum">     595 </span>            :       opArray[1].copyFrom(o1);</a>
+<a name="596"><span class="lineNum">     596 </span>            :       opArray[2].copyFrom(o2);</a>
+<a name="597"><span class="lineNum">     597 </span>            :       opArray[3].copyFrom(o3);</a>
+<a name="598"><span class="lineNum">     598 </span>            : </a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 :       if (options &amp; kOptionOp4Op5Used) {</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :         opArray[4].copyFrom(_op4);</a>
+<a name="601"><span class="lineNum">     601 </span>            :         opArray[5].copyFrom(_op5);</a>
+<a name="602"><span class="lineNum">     602 </span>            :       }</a>
+<a name="603"><span class="lineNum">     603 </span>            :       else {</a>
+<a name="604"><span class="lineNum">     604 </span>            :         opArray[4].reset();</a>
+<a name="605"><span class="lineNum">     605 </span>            :         opArray[5].reset();</a>
+<a name="606"><span class="lineNum">     606 </span>            :       }</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :       err = Inst::validate(getArchType(), Inst::Detail(instId, options, _extraReg), opArray, 6);</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(err)) goto Failed;</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :     }</a>
+<a name="611"><span class="lineNum">     611 </span>            : #endif // !ASMJIT_DISABLE_VALIDATION</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span>            :     uint32_t iFlags = instData-&gt;getFlags();</a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span>            :     // LOCK, XACQUIRE, and XRELEASE prefixes.</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">       1948 :     if (options &amp; X86Inst::kOptionLock) {</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :       bool xAcqRel = (options &amp; (X86Inst::kOptionXAcquire | X86Inst::kOptionXRelease)) != 0;</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!(iFlags &amp; (X86Inst::kFlagLock)) &amp;&amp; !xAcqRel))</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :         goto InvalidLockPrefix;</span></a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :       if (xAcqRel) {</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionXAcquire) &amp;&amp; !(iFlags &amp; X86Inst::kFlagXAcquire)))</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineNoCov">          0 :           goto InvalidXAcquirePrefix;</span></a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionXRelease) &amp;&amp; !(iFlags &amp; X86Inst::kFlagXRelease)))</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :           goto InvalidXReleasePrefix;</span></a>
+<a name="628"><span class="lineNum">     628 </span>            : </a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :         EMIT_BYTE((options &amp; X86Inst::kOptionXAcquire) ? 0xF2 : 0xF3);</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :       }</a>
+<a name="631"><span class="lineNum">     631 </span>            : </a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :       EMIT_BYTE(0xF0);</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :     }</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            :     // REP and REPNZ prefixes.</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       1948 :     if (options &amp; (X86Inst::kOptionRep | X86Inst::kOptionRepnz)) {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!(iFlags &amp; (X86Inst::kFlagRep | X86Inst::kFlagRepnz))))</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineNoCov">          0 :         goto InvalidRepPrefix;</span></a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :       if (_extraReg.isValid() &amp;&amp; ASMJIT_UNLIKELY(_extraReg.getKind() != X86Reg::kKindGp || _extraReg.getId() != X86Gp::kIdCx))</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 :         goto InvalidRepPrefix;</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :       EMIT_BYTE((options &amp; X86Inst::kOptionRepnz) ? 0xF2 : 0xF3);</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :     }</a>
+<a name="645"><span class="lineNum">     645 </span>            :   }</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="648"><span class="lineNum">     648 </span>            :   // [Encoding Scope]</a>
+<a name="649"><span class="lineNum">     649 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="650"><span class="lineNum">     650 </span>            : </a>
+<a name="651"><span class="lineNum">     651 </span>            :   opCode = instData-&gt;getMainOpCode();</a>
+<a name="652"><span class="lineNum">     652 </span>            :   opReg = x86ExtractO(opCode);</a>
+<a name="653"><span class="lineNum">     653 </span>            :   commonData = &amp;instData-&gt;getCommonData();</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">      48362 :   switch (instData-&gt;getEncodingType()) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingNone:</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="660"><span class="lineNum">     660 </span>            :     // [X86]</a>
+<a name="661"><span class="lineNum">     661 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Op:</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :       goto EmitX86Op;</span></a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Op_O_I8:</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(isign3 != ENC_OPS1(Imm)))</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :       imVal = o0.as&lt;Imm&gt;().getUInt8();</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :       imLen = 1;</a>
+<a name="672"><span class="lineNum">     672 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Op_O:</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :       rbReg = 0;</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :       goto EmitX86R;</span></a>
+<a name="677"><span class="lineNum">     677 </span>            : </a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Op_xAX:</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :       if (isign3 == 0)</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg) &amp;&amp; o0.getId() == X86Gp::kIdAx)</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :       break;</a>
+<a name="685"><span class="lineNum">     685 </span>            : </a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Op_xDX_xAX:</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :       if (isign3 == 0)</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg) &amp;&amp; o0.getId() == X86Gp::kIdDx &amp;&amp;</span></a>
+<a name="691"><span class="lineNum">     691 </span>            :                                           o1.getId() == X86Gp::kIdAx)</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :       break;</a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Op_ZAX:</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :       if (isign3 == 0)</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="698"><span class="lineNum">     698 </span>            : </a>
+<a name="699"><span class="lineNum">     699 </span>            :       rmRel = &amp;o0;</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem) &amp;&amp; x86IsImplicitMem(o0, X86Gp::kIdAx))</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :         goto EmitX86OpImplicitMem;</span></a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span>            :       break;</a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86I_xAX:</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :       // Implicit form.</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Imm)) {</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :         imVal = o0.as&lt;Imm&gt;().getUInt8();</span></a>
+<a name="709"><span class="lineNum">     709 </span>            :         imLen = 1;</a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="711"><span class="lineNum">     711 </span>            :       }</a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span>            :       // Explicit form.</a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm) &amp;&amp; o0.getId() == X86Gp::kIdAx) {</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :         imVal = o1.as&lt;Imm&gt;().getUInt8();</span></a>
+<a name="716"><span class="lineNum">     716 </span>            :         imLen = 1;</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="718"><span class="lineNum">     718 </span>            :       }</a>
+<a name="719"><span class="lineNum">     719 </span>            :       break;</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span>            :     case X86Inst::kEncodingX86M:</a>
+<a name="722"><span class="lineNum">     722 </span>            :       rbReg = o0.getId();</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :       ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="724"><span class="lineNum">     724 </span>            : </a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg))</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="727"><span class="lineNum">     727 </span>            : </a>
+<a name="728"><span class="lineNum">     728 </span>            :       rmRel = &amp;o0;</a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem))</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="731"><span class="lineNum">     731 </span>            :       break;</a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span>            :     case X86Inst::kEncodingX86M_GPB_MulDiv:</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineNoCov">          0 : CaseX86M_GPB_MulDiv:</span></a>
+<a name="735"><span class="lineNum">     735 </span>            :       // Explicit form?</a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :       if (isign3 &gt; 0x7) {</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :         // [AX] &lt;- [AX] div|mul r8.</a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(!X86Reg::isGpw(o0, X86Gp::kIdAx) || !X86Reg::isGpb(o1)))</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span>            :           rbReg = o1.getId();</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, rbReg);</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="745"><span class="lineNum">     745 </span>            :         }</a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span>            :         // [AX] &lt;- [AX] div|mul m8.</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(!X86Reg::isGpw(o0, X86Gp::kIdAx)))</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span>            :           rmRel = &amp;o1;</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :         }</a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span>            :         // [?DX:?AX] &lt;- [?DX:?AX] div|mul r16|r32|r64</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(o0.getSize() != o1.getSize()))</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="760"><span class="lineNum">     760 </span>            :           rbReg = o2.getId();</a>
+<a name="761"><span class="lineNum">     761 </span>            : </a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :         }</a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            :         // [?DX:?AX] &lt;- [?DX:?AX] div|mul m16|m32|m64</a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(o0.getSize() != o1.getSize()))</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="771"><span class="lineNum">     771 </span>            :           rmRel = &amp;o2;</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="776"><span class="lineNum">     776 </span>            :         }</a>
+<a name="777"><span class="lineNum">     777 </span>            : </a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="779"><span class="lineNum">     779 </span>            :       }</a>
+<a name="780"><span class="lineNum">     780 </span>            : </a>
+<a name="781"><span class="lineNum">     781 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            :     case X86Inst::kEncodingX86M_GPB:</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="785"><span class="lineNum">     785 </span>            :         rbReg = o0.getId();</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :         }</a>
+<a name="790"><span class="lineNum">     790 </span>            :         else {</a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :         }</a>
+<a name="795"><span class="lineNum">     795 </span>            :       }</a>
+<a name="796"><span class="lineNum">     796 </span>            : </a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() == 0))</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="800"><span class="lineNum">     800 </span>            :         rmRel = &amp;o0;</a>
+<a name="801"><span class="lineNum">     801 </span>            : </a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineNoCov">          0 :         opCode += o0.getSize() != 1;</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="805"><span class="lineNum">     805 </span>            :       }</a>
+<a name="806"><span class="lineNum">     806 </span>            :       break;</a>
+<a name="807"><span class="lineNum">     807 </span>            : </a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86M_Only:</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="810"><span class="lineNum">     810 </span>            :         rmRel = &amp;o0;</a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="812"><span class="lineNum">     812 </span>            :       }</a>
+<a name="813"><span class="lineNum">     813 </span>            :       break;</a>
+<a name="814"><span class="lineNum">     814 </span>            : </a>
+<a name="815"><span class="lineNum">     815 </span>            :     case X86Inst::kEncodingX86Rm:</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineNoCov">          0 :       ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="817"><span class="lineNum">     817 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="818"><span class="lineNum">     818 </span>            : </a>
+<a name="819"><span class="lineNum">     819 </span>            :     case X86Inst::kEncodingX86Rm_NoRexW:</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :         opReg = o0.getId();</a>
+<a name="822"><span class="lineNum">     822 </span>            :         rbReg = o1.getId();</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="824"><span class="lineNum">     824 </span>            :       }</a>
+<a name="825"><span class="lineNum">     825 </span>            : </a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="827"><span class="lineNum">     827 </span>            :         opReg = o0.getId();</a>
+<a name="828"><span class="lineNum">     828 </span>            :         rmRel = &amp;o1;</a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="830"><span class="lineNum">     830 </span>            :       }</a>
+<a name="831"><span class="lineNum">     831 </span>            :       break;</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Rm_Raw66H:</span></a>
+<a name="834"><span class="lineNum">     834 </span>            :       // We normally emit either [66|F2|F3], this instruction requires 66+[F2|F3].</a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :         opReg = o0.getId();</a>
+<a name="837"><span class="lineNum">     837 </span>            :         rbReg = o1.getId();</a>
+<a name="838"><span class="lineNum">     838 </span>            : </a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 2)</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineNoCov">          0 :           EMIT_BYTE(0x66);</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :         else</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineNoCov">          0 :           ADD_REX_W_BY_SIZE(o0.getSize());</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="844"><span class="lineNum">     844 </span>            :       }</a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :         opReg = o0.getId();</a>
+<a name="848"><span class="lineNum">     848 </span>            :         rmRel = &amp;o1;</a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 2)</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineNoCov">          0 :           EMIT_BYTE(0x66);</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :         else</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :           ADD_REX_W_BY_SIZE(o0.getSize());</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="855"><span class="lineNum">     855 </span>            :       }</a>
+<a name="856"><span class="lineNum">     856 </span>            :       break;</a>
+<a name="857"><span class="lineNum">     857 </span>            : </a>
+<a name="858"><span class="lineNum">     858 </span>            :     case X86Inst::kEncodingX86Mr:</a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineNoCov">          0 :       ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="861"><span class="lineNum">     861 </span>            : </a>
+<a name="862"><span class="lineNum">     862 </span>            :     case X86Inst::kEncodingX86Mr_NoSize:</a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="864"><span class="lineNum">     864 </span>            :         rbReg = o0.getId();</a>
+<a name="865"><span class="lineNum">     865 </span>            :         opReg = o1.getId();</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="867"><span class="lineNum">     867 </span>            :       }</a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="870"><span class="lineNum">     870 </span>            :         rmRel = &amp;o0;</a>
+<a name="871"><span class="lineNum">     871 </span>            :         opReg = o1.getId();</a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="873"><span class="lineNum">     873 </span>            :       }</a>
+<a name="874"><span class="lineNum">     874 </span>            :       break;</a>
+<a name="875"><span class="lineNum">     875 </span>            : </a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">       1864 :     case X86Inst::kEncodingX86Arith:</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">       1864 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineNoCov">          0 :         if (o0.getSize() != o1.getSize())</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="880"><span class="lineNum">     880 </span>            : </a>
+<a name="881"><span class="lineNum">     881 </span>            :         opReg = o0.getId();</a>
+<a name="882"><span class="lineNum">     882 </span>            :         rbReg = o1.getId();</a>
+<a name="883"><span class="lineNum">     883 </span>            : </a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineNoCov">          0 :           opCode += 2;</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, opReg);</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, rbReg);</span></a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineNoCov">          0 :           if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="891"><span class="lineNum">     891 </span>            : </a>
+<a name="892"><span class="lineNum">     892 </span>            :           opCode -= 2;</a>
+<a name="893"><span class="lineNum">     893 </span>            :           Utils::swap(opReg, rbReg);</a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="895"><span class="lineNum">     895 </span>            :         }</a>
+<a name="896"><span class="lineNum">     896 </span>            :         else {</a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineNoCov">          0 :           opCode += 3;</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="899"><span class="lineNum">     899 </span>            : </a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :           if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="902"><span class="lineNum">     902 </span>            : </a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineNoCov">          0 :           opCode -= 2;</span></a>
+<a name="904"><span class="lineNum">     904 </span>            :           Utils::swap(opReg, rbReg);</a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :         }</a>
+<a name="907"><span class="lineNum">     907 </span>            :       }</a>
+<a name="908"><span class="lineNum">     908 </span>            : </a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">       1864 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="910"><span class="lineNum">     910 </span>            :         opReg = o0.getId();</a>
+<a name="911"><span class="lineNum">     911 </span>            :         rmRel = &amp;o1;</a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, opReg);</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineNoCov">          0 :           opCode += 2;</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="917"><span class="lineNum">     917 </span>            :         }</a>
+<a name="918"><span class="lineNum">     918 </span>            :         else {</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :           opCode += 3;</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :         }</a>
+<a name="923"><span class="lineNum">     923 </span>            :       }</a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">       1864 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="926"><span class="lineNum">     926 </span>            :         opReg = o1.getId();</a>
+<a name="927"><span class="lineNum">     927 </span>            :         rmRel = &amp;o0;</a>
+<a name="928"><span class="lineNum">     928 </span>            : </a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1) {</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, opReg);</span></a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="932"><span class="lineNum">     932 </span>            :         }</a>
+<a name="933"><span class="lineNum">     933 </span>            :         else {</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="937"><span class="lineNum">     937 </span>            :         }</a>
+<a name="938"><span class="lineNum">     938 </span>            :       }</a>
+<a name="939"><span class="lineNum">     939 </span>            : </a>
+<a name="940"><span class="lineNum">     940 </span>            :       // The remaining instructions use 0x80 opcode.</a>
+<a name="941"><span class="lineNum">     941 </span>            :       opCode = 0x80;</a>
+<a name="942"><span class="lineNum">     942 </span>            : </a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">       1864 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">       1864 :         uint32_t size = o0.getSize();</span></a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span>            :         rbReg = o0.getId();</a>
+<a name="947"><span class="lineNum">     947 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">       1864 :         if (size == 1) {</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :           imLen = 1;</a>
+<a name="952"><span class="lineNum">     952 </span>            :         }</a>
+<a name="953"><span class="lineNum">     953 </span>            :         else {</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">       1864 :           if (size == 2) {</span></a>
+<a name="955"><span class="lineNum">     955 </span>            :             ADD_66H_P(1);</a>
+<a name="956"><span class="lineNum">     956 </span>            :           }</a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">       1864 :           else if (size == 4) {</span></a>
+<a name="958"><span class="lineNum">     958 </span>            :             // Sign extend so isInt8 returns the right result.</a>
+<a name="959"><span class="lineNum">     959 </span>            :             imVal = x86SignExtend32To64(imVal);</a>
+<a name="960"><span class="lineNum">     960 </span>            :           }</a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">       1864 :           else if (size == 8) {</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :             // In 64-bit mode it's not possible to use 64-bit immediate.</a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">       1864 :             if (Utils::isUInt32(imVal)) {</span></a>
+<a name="964"><span class="lineNum">     964 </span>            :               // Zero-extend `and` by using a 32-bit GPD destination instead of a 64-bit GPQ.</a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">       1864 :               if (instId == X86Inst::kIdAnd)</span></a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineNoCov">          0 :                 size = 4;</span></a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">       1864 :               else if (!Utils::isInt32(imVal))</span></a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineNoCov">          0 :                 goto InvalidImmediate;</span></a>
+<a name="969"><span class="lineNum">     969 </span>            :             }</a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">       1864 :             ADD_REX_W_BY_SIZE(size);</span></a>
+<a name="971"><span class="lineNum">     971 </span>            :           }</a>
+<a name="972"><span class="lineNum">     972 </span>            : </a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">       3728 :           imLen = std::min&lt;uint32_t&gt;(size, 4);</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">       1864 :           if (Utils::isInt8(imVal) &amp;&amp; !(options &amp; X86Inst::kOptionLongForm))</span></a>
+<a name="975"><span class="lineNum">     975 </span>            :             imLen = 1;</a>
+<a name="976"><span class="lineNum">     976 </span>            :         }</a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span>            :         // Alternate Form - AL, AX, EAX, RAX.</a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">       1864 :         if (rbReg == 0 &amp;&amp; (size == 1 || imLen != 1) &amp;&amp; !(options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :           opCode &amp;= X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_W;</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 :           opCode |= ((opReg &lt;&lt; 3) | (0x04 + (size != 1)));</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineNoCov">          0 :           imLen = std::min&lt;uint32_t&gt;(size, 4);</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineNoCov">          0 :           goto EmitX86Op;</span></a>
+<a name="984"><span class="lineNum">     984 </span>            :         }</a>
+<a name="985"><span class="lineNum">     985 </span>            : </a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">       1864 :         opCode += size != 1 ? (imLen != 1 ? 1 : 3) : 0;</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">       1864 :         goto EmitX86R;</span></a>
+<a name="988"><span class="lineNum">     988 </span>            :       }</a>
+<a name="989"><span class="lineNum">     989 </span>            : </a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Imm)) {</span></a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineNoCov">          0 :         uint32_t memSize = o0.getSize();</span></a>
+<a name="992"><span class="lineNum">     992 </span>            : </a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(memSize == 0))</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineNoCov">          0 :         imLen = std::min&lt;uint32_t&gt;(memSize, 4);</span></a>
+<a name="998"><span class="lineNum">     998 </span>            : </a>
+<a name="999"><span class="lineNum">     999 </span>            :         // Sign extend so isInt8 returns the right result.</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineNoCov">          0 :         if (memSize == 4)</span></a>
+<a name="1001"><span class="lineNum">    1001 </span>            :           imVal = x86SignExtend32To64(imVal);</a>
+<a name="1002"><span class="lineNum">    1002 </span>            : </a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineNoCov">          0 :         if (Utils::isInt8(imVal) &amp;&amp; !(options &amp; X86Inst::kOptionLongForm))</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :           imLen = 1;</a>
+<a name="1005"><span class="lineNum">    1005 </span>            : </a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineNoCov">          0 :         opCode += memSize != 1 ? (imLen != 1 ? 1 : 3) : 0;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(memSize);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            : </a>
+<a name="1009"><span class="lineNum">    1009 </span>            :         rmRel = &amp;o0;</a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            :       }</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :       break;</a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Bswap:</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() &lt; 4))</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1018"><span class="lineNum">    1018 </span>            : </a>
+<a name="1019"><span class="lineNum">    1019 </span>            :         opReg = o0.getId();</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineNoCov">          0 :         ADD_REX_W_BY_SIZE(o0.getSize());</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineNoCov">          0 :         goto EmitX86OpReg;</span></a>
+<a name="1022"><span class="lineNum">    1022 </span>            :       }</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :       break;</a>
+<a name="1024"><span class="lineNum">    1024 </span>            : </a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Bt:</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1028"><span class="lineNum">    1028 </span>            :         opReg = o1.getId();</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :         rbReg = o0.getId();</a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :       }</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : </a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            :         opReg = o1.getId();</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :         rmRel = &amp;o0;</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1038"><span class="lineNum">    1038 </span>            :       }</a>
+<a name="1039"><span class="lineNum">    1039 </span>            : </a>
+<a name="1040"><span class="lineNum">    1040 </span>            :       // The remaining instructions use the secondary opcode/r.</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :       imLen = 1;</a>
+<a name="1043"><span class="lineNum">    1043 </span>            : </a>
+<a name="1044"><span class="lineNum">    1044 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :       opReg = x86ExtractO(opCode);</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineNoCov">          0 :       ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1047"><span class="lineNum">    1047 </span>            : </a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="1049"><span class="lineNum">    1049 </span>            :         rbReg = o0.getId();</a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1051"><span class="lineNum">    1051 </span>            :       }</a>
+<a name="1052"><span class="lineNum">    1052 </span>            : </a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Imm)) {</span></a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() == 0))</span></a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            : </a>
+<a name="1057"><span class="lineNum">    1057 </span>            :         rmRel = &amp;o0;</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :       }</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :       break;</a>
+<a name="1061"><span class="lineNum">    1061 </span>            : </a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">       1648 :     case X86Inst::kEncodingX86Call:</span></a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">       1648 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1064"><span class="lineNum">    1064 </span>            :         rbReg = o0.getId();</a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">       1648 :         goto EmitX86R;</span></a>
+<a name="1066"><span class="lineNum">    1066 </span>            :       }</a>
+<a name="1067"><span class="lineNum">    1067 </span>            : </a>
+<a name="1068"><span class="lineNum">    1068 </span>            :       rmRel = &amp;o0;</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem))</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1071"><span class="lineNum">    1071 </span>            : </a>
+<a name="1072"><span class="lineNum">    1072 </span>            :       // Call with 32-bit displacement use 0xE8 opcode. Call with 8-bit</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :       // displacement is not encodable so the alternative opcode field</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :       // in X86DB must be zero.</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :       opCode = 0xE8;</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :       opReg = 0;</a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineNoCov">          0 :       goto EmitJmpCall;</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            : </a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Cmpxchg: {</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :       // Convert explicit to implicit.</a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineNoCov">          0 :       if (isign3 &amp; (0x7 &lt;&lt; 6)) {</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineNoCov">          0 :         if (!X86Reg::isGp(o2) || o2.getId() != X86Gp::kIdAx)</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineNoCov">          0 :         isign3 &amp;= 0x3F;</span></a>
+<a name="1085"><span class="lineNum">    1085 </span>            :       }</a>
+<a name="1086"><span class="lineNum">    1086 </span>            : </a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineNoCov">          0 :         if (o0.getSize() != o1.getSize())</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            : </a>
+<a name="1091"><span class="lineNum">    1091 </span>            :         rbReg = o0.getId();</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :         opReg = o1.getId();</a>
+<a name="1093"><span class="lineNum">    1093 </span>            : </a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, opReg);</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1098"><span class="lineNum">    1098 </span>            :         }</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :         else {</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1103"><span class="lineNum">    1103 </span>            :         }</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :       }</a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            :         opReg = o1.getId();</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :         rmRel = &amp;o0;</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, opReg);</span></a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1113"><span class="lineNum">    1113 </span>            :         }</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :         else {</a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1118"><span class="lineNum">    1118 </span>            :         }</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :       }</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :       break;</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     }</a>
+<a name="1122"><span class="lineNum">    1122 </span>            : </a>
+<a name="1123"><span class="lineNum">    1123 </span>            :     case X86Inst::kEncodingX86Crc:</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :       opReg = o0.getId();</a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineNoCov">          0 :       ADD_REX_W_BY_SIZE(o0.getSize());</span></a>
+<a name="1126"><span class="lineNum">    1126 </span>            : </a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1128"><span class="lineNum">    1128 </span>            :         rbReg = o1.getId();</a>
+<a name="1129"><span class="lineNum">    1129 </span>            : </a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1) {</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, rbReg);</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1133"><span class="lineNum">    1133 </span>            :         }</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :         else {</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :           // This seems to be the only exception of encoding 66F2 PP prefix.</a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineNoCov">          0 :           if (o1.getSize() == 2) EMIT_BYTE(0x66);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span>            : </a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            :         }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :       }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            : </a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            :         rmRel = &amp;o1;</a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 0)</span></a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1147"><span class="lineNum">    1147 </span>            : </a>
+<a name="1148"><span class="lineNum">    1148 </span>            :         // This seems to be the only exception of encoding 66F2 PP prefix.</a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 2) EMIT_BYTE(0x66);</span></a>
+<a name="1150"><span class="lineNum">    1150 </span>            : </a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineNoCov">          0 :         opCode += o1.getSize() != 1;</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1153"><span class="lineNum">    1153 </span>            :       }</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :       break;</a>
+<a name="1155"><span class="lineNum">    1155 </span>            : </a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Enter:</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Imm, Imm)) {</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :         uint32_t iw = static_cast&lt;const Imm&amp;&gt;(o0).getUInt16();</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :         uint32_t ib = static_cast&lt;const Imm&amp;&gt;(o1).getUInt8();</a>
+<a name="1160"><span class="lineNum">    1160 </span>            : </a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineNoCov">          0 :         imVal = iw | (ib &lt;&lt; 16);</span></a>
+<a name="1162"><span class="lineNum">    1162 </span>            :         imLen = 3;</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :       }</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :       break;</a>
+<a name="1166"><span class="lineNum">    1166 </span>            : </a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Imul:</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :       // First process all forms distinct of `kEncodingX86M_OptB_MulDiv`.</a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="1170"><span class="lineNum">    1170 </span>            :         opCode = 0x6B;</a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1172"><span class="lineNum">    1172 </span>            : </a>
+<a name="1173"><span class="lineNum">    1173 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :         imLen = 1;</a>
+<a name="1175"><span class="lineNum">    1175 </span>            : </a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineNoCov">          0 :         if (!Utils::isInt8(imVal) || (options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 :           opCode -= 2;</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineNoCov">          0 :           imLen = o0.getSize() == 2 ? 2 : 4;</span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            :         }</a>
+<a name="1180"><span class="lineNum">    1180 </span>            : </a>
+<a name="1181"><span class="lineNum">    1181 </span>            :         opReg = o0.getId();</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :         rbReg = o1.getId();</a>
+<a name="1183"><span class="lineNum">    1183 </span>            : </a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span>            :       }</a>
+<a name="1186"><span class="lineNum">    1186 </span>            : </a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :         opCode = 0x6B;</a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            : </a>
+<a name="1191"><span class="lineNum">    1191 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :         imLen = 1;</a>
+<a name="1193"><span class="lineNum">    1193 </span>            : </a>
+<a name="1194"><span class="lineNum">    1194 </span>            :         // Sign extend so isInt8 returns the right result.</a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 4)</span></a>
+<a name="1196"><span class="lineNum">    1196 </span>            :           imVal = x86SignExtend32To64(imVal);</a>
+<a name="1197"><span class="lineNum">    1197 </span>            : </a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineNoCov">          0 :         if (!Utils::isInt8(imVal) || (options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :           opCode -= 2;</span></a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineNoCov">          0 :           imLen = o0.getSize() == 2 ? 2 : 4;</span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            :         }</a>
+<a name="1202"><span class="lineNum">    1202 </span>            : </a>
+<a name="1203"><span class="lineNum">    1203 </span>            :         opReg = o0.getId();</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :         rmRel = &amp;o1;</a>
+<a name="1205"><span class="lineNum">    1205 </span>            : </a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            :       }</a>
+<a name="1208"><span class="lineNum">    1208 </span>            : </a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1210"><span class="lineNum">    1210 </span>            :         // Must be explicit 'ax, r8' form.</a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1)</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineNoCov">          0 :           goto CaseX86M_GPB_MulDiv;</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            : </a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineNoCov">          0 :         if (o0.getSize() != o1.getSize())</span></a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span>            :         opReg = o0.getId();</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :         rbReg = o1.getId();</a>
+<a name="1219"><span class="lineNum">    1219 </span>            : </a>
+<a name="1220"><span class="lineNum">    1220 </span>            :         opCode = X86Inst::kOpCode_MM_0F | 0xAF;</a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1223"><span class="lineNum">    1223 </span>            :       }</a>
+<a name="1224"><span class="lineNum">    1224 </span>            : </a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1226"><span class="lineNum">    1226 </span>            :         // Must be explicit 'ax, m8' form.</a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1)</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineNoCov">          0 :           goto CaseX86M_GPB_MulDiv;</span></a>
+<a name="1229"><span class="lineNum">    1229 </span>            : </a>
+<a name="1230"><span class="lineNum">    1230 </span>            :         opReg = o0.getId();</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :         rmRel = &amp;o1;</a>
+<a name="1232"><span class="lineNum">    1232 </span>            : </a>
+<a name="1233"><span class="lineNum">    1233 </span>            :         opCode = X86Inst::kOpCode_MM_0F | 0xAF;</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1236"><span class="lineNum">    1236 </span>            :       }</a>
+<a name="1237"><span class="lineNum">    1237 </span>            : </a>
+<a name="1238"><span class="lineNum">    1238 </span>            :       // Shorthand to imul 'reg, reg, imm'.</a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            :         opCode = 0x6B;</a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1242"><span class="lineNum">    1242 </span>            : </a>
+<a name="1243"><span class="lineNum">    1243 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :         imLen = 1;</a>
+<a name="1245"><span class="lineNum">    1245 </span>            : </a>
+<a name="1246"><span class="lineNum">    1246 </span>            :         // Sign extend so isInt8 returns the right result.</a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 4)</span></a>
+<a name="1248"><span class="lineNum">    1248 </span>            :           imVal = x86SignExtend32To64(imVal);</a>
+<a name="1249"><span class="lineNum">    1249 </span>            : </a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineNoCov">          0 :         if (!Utils::isInt8(imVal) || (options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineNoCov">          0 :           opCode -= 2;</span></a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineNoCov">          0 :           imLen = o0.getSize() == 2 ? 2 : 4;</span></a>
+<a name="1253"><span class="lineNum">    1253 </span>            :         }</a>
+<a name="1254"><span class="lineNum">    1254 </span>            : </a>
+<a name="1255"><span class="lineNum">    1255 </span>            :         opReg = rbReg = o0.getId();</a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1257"><span class="lineNum">    1257 </span>            :       }</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : </a>
+<a name="1259"><span class="lineNum">    1259 </span>            :       // Try implicit form.</a>
+<a name="1260"><span class="lineNum">    1260 </span><span class="lineNoCov">          0 :       goto CaseX86M_GPB_MulDiv;</span></a>
+<a name="1261"><span class="lineNum">    1261 </span>            : </a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86In:</span></a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getId() != X86Gp::kIdAx))</span></a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1266"><span class="lineNum">    1266 </span>            : </a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineNoCov">          0 :         imVal = o1.as&lt;Imm&gt;().getUInt8();</span></a>
+<a name="1268"><span class="lineNum">    1268 </span>            :         imLen = 1;</a>
+<a name="1269"><span class="lineNum">    1269 </span>            : </a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineNoCov">          0 :         opCode = commonData-&gt;getAltOpCode() + (o0.getSize() != 1);</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(o0.getSize());</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :       }</a>
+<a name="1274"><span class="lineNum">    1274 </span>            : </a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getId() != X86Gp::kIdAx || o1.getId() != X86Gp::kIdDx))</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1278"><span class="lineNum">    1278 </span>            : </a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineNoCov">          0 :         opCode += o0.getSize() != 1;</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(o0.getSize());</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1282"><span class="lineNum">    1282 </span>            :       }</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :       break;</a>
+<a name="1284"><span class="lineNum">    1284 </span>            : </a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Ins:</span></a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(!x86IsImplicitMem(o0, X86Gp::kIdDi) || o1.getId() != X86Gp::kIdDx))</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1289"><span class="lineNum">    1289 </span>            : </a>
+<a name="1290"><span class="lineNum">    1290 </span>            :         uint32_t size = o0.getSize();</a>
+<a name="1291"><span class="lineNum">    1291 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(size == 0))</span></a>
+<a name="1292"><span class="lineNum">    1292 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1293"><span class="lineNum">    1293 </span>            : </a>
+<a name="1294"><span class="lineNum">    1294 </span>            :         rmRel = &amp;o0;</a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineNoCov">          0 :         opCode += (size != 1);</span></a>
+<a name="1296"><span class="lineNum">    1296 </span>            : </a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(size);</span></a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineNoCov">          0 :         goto EmitX86OpImplicitMem;</span></a>
+<a name="1299"><span class="lineNum">    1299 </span>            :       }</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :       break;</a>
+<a name="1301"><span class="lineNum">    1301 </span>            : </a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86IncDec:</span></a>
+<a name="1303"><span class="lineNum">    1303 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1304"><span class="lineNum">    1304 </span>            :         rbReg = o0.getId();</a>
+<a name="1305"><span class="lineNum">    1305 </span>            : </a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="1307"><span class="lineNum">    1307 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1309"><span class="lineNum">    1309 </span>            :         }</a>
+<a name="1310"><span class="lineNum">    1310 </span>            : </a>
+<a name="1311"><span class="lineNum">    1311 </span><span class="lineNoCov">          0 :         if (is32Bit()) {</span></a>
+<a name="1312"><span class="lineNum">    1312 </span>            :           // INC r16|r32 is only encodable in 32-bit mode (collides with REX).</a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineNoCov">          0 :           opCode = commonData-&gt;getAltOpCode() + (rbReg &amp; 0x07);</span></a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineNoCov">          0 :           ADD_66H_P_BY_SIZE(o0.getSize());</span></a>
+<a name="1315"><span class="lineNum">    1315 </span><span class="lineNoCov">          0 :           goto EmitX86Op;</span></a>
+<a name="1316"><span class="lineNum">    1316 </span>            :         }</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :         else {</a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1321"><span class="lineNum">    1321 </span>            :         }</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :       }</a>
+<a name="1323"><span class="lineNum">    1323 </span>            : </a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="1325"><span class="lineNum">    1325 </span>            :         rmRel = &amp;o0;</a>
+<a name="1326"><span class="lineNum">    1326 </span><span class="lineNoCov">          0 :         opCode += o0.getSize() != 1;</span></a>
+<a name="1327"><span class="lineNum">    1327 </span>            : </a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1330"><span class="lineNum">    1330 </span>            :       }</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :       break;</a>
+<a name="1332"><span class="lineNum">    1332 </span>            : </a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Int:</span></a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Imm)) {</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o0).getInt64();</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :         imLen = 1;</a>
+<a name="1337"><span class="lineNum">    1337 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1338"><span class="lineNum">    1338 </span>            :       }</a>
+<a name="1339"><span class="lineNum">    1339 </span>            :       break;</a>
+<a name="1340"><span class="lineNum">    1340 </span>            : </a>
+<a name="1341"><span class="lineNum">    1341 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Jcc:</span></a>
+<a name="1342"><span class="lineNum">    1342 </span><span class="lineNoCov">          0 :       if (_globalHints &amp; CodeEmitter::kHintPredictedJumps) {</span></a>
+<a name="1343"><span class="lineNum">    1343 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionTaken)</span></a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineNoCov">          0 :           EMIT_BYTE(0x3E);</span></a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionNotTaken)</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineNoCov">          0 :           EMIT_BYTE(0x2E);</span></a>
+<a name="1347"><span class="lineNum">    1347 </span>            :       }</a>
+<a name="1348"><span class="lineNum">    1348 </span>            : </a>
+<a name="1349"><span class="lineNum">    1349 </span>            :       rmRel = &amp;o0;</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :       opReg = 0;</a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineNoCov">          0 :       goto EmitJmpCall;</span></a>
+<a name="1352"><span class="lineNum">    1352 </span>            : </a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86JecxzLoop:</span></a>
+<a name="1354"><span class="lineNum">    1354 </span>            :       rmRel = &amp;o0;</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :       // Explicit jecxz|loop [r|e]cx, dst</a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineNoCov">          0 :       if (o0.isReg()) {</span></a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(!X86Reg::isGp(o0, X86Gp::kIdCx)))</span></a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1359"><span class="lineNum">    1359 </span>            : </a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineNoCov">          0 :         if ((is32Bit() &amp;&amp; o0.getSize() == 2) || (is64Bit() &amp;&amp; o0.getSize() == 4))</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineNoCov">          0 :           EMIT_BYTE(0x67);</span></a>
+<a name="1362"><span class="lineNum">    1362 </span>            : </a>
+<a name="1363"><span class="lineNum">    1363 </span>            :         rmRel = &amp;o1;</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :       }</a>
+<a name="1365"><span class="lineNum">    1365 </span>            : </a>
+<a name="1366"><span class="lineNum">    1366 </span>            :       opReg = 0;</a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineNoCov">          0 :       goto EmitJmpCall;</span></a>
+<a name="1368"><span class="lineNum">    1368 </span>            : </a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Jmp:</span></a>
+<a name="1370"><span class="lineNum">    1370 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1371"><span class="lineNum">    1371 </span>            :         rbReg = o0.getId();</a>
+<a name="1372"><span class="lineNum">    1372 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1373"><span class="lineNum">    1373 </span>            :       }</a>
+<a name="1374"><span class="lineNum">    1374 </span>            : </a>
+<a name="1375"><span class="lineNum">    1375 </span>            :       rmRel = &amp;o0;</a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem))</span></a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1378"><span class="lineNum">    1378 </span>            : </a>
+<a name="1379"><span class="lineNum">    1379 </span>            :       // Jump encoded with 32-bit displacement use 0xE9 opcode. Jump encoded</a>
+<a name="1380"><span class="lineNum">    1380 </span>            :       // with 8-bit displacement's opcode is stored as an alternative opcode.</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :       opCode = 0xE9;</a>
+<a name="1382"><span class="lineNum">    1382 </span>            :       opReg = 0;</a>
+<a name="1383"><span class="lineNum">    1383 </span><span class="lineNoCov">          0 :       goto EmitJmpCall;</span></a>
+<a name="1384"><span class="lineNum">    1384 </span>            : </a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86JmpRel:</span></a>
+<a name="1386"><span class="lineNum">    1386 </span>            :       rmRel = &amp;o0;</a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineNoCov">          0 :       goto EmitJmpCall;</span></a>
+<a name="1388"><span class="lineNum">    1388 </span>            : </a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Lea:</span></a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1392"><span class="lineNum">    1392 </span>            :         opReg = o0.getId();</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :         rmRel = &amp;o1;</a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1395"><span class="lineNum">    1395 </span>            :       }</a>
+<a name="1396"><span class="lineNum">    1396 </span>            :       break;</a>
+<a name="1397"><span class="lineNum">    1397 </span>            : </a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineCov">       7688 :     case X86Inst::kEncodingX86Mov:</span></a>
+<a name="1399"><span class="lineNum">    1399 </span>            :       // Reg &lt;- Reg</a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineCov">       7688 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1401"><span class="lineNum">    1401 </span>            :         opReg = o0.getId();</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :         rbReg = o1.getId();</a>
+<a name="1403"><span class="lineNum">    1403 </span>            : </a>
+<a name="1404"><span class="lineNum">    1404 </span>            :         // Asmjit uses segment registers indexed from 1 to 6, leaving zero as</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :         // &quot;no segment register used&quot;. We have to fix this (decrement the index</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :         // of the register) when emitting MOV instructions which move to/from</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :         // a segment register. The segment register is always `opReg`, because</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :         // the MOV instruction uses either RM or MR encoding.</a>
+<a name="1409"><span class="lineNum">    1409 </span>            : </a>
+<a name="1410"><span class="lineNum">    1410 </span>            :         // GP &lt;- ??</a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineNoCov">          0 :         if (X86Reg::isGp(o0)) {</span></a>
+<a name="1412"><span class="lineNum">    1412 </span>            :           // GP &lt;- GP</a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineNoCov">          0 :           if (X86Reg::isGp(o1)) {</span></a>
+<a name="1414"><span class="lineNum">    1414 </span>            :             uint32_t size0 = o0.getSize();</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :             uint32_t size1 = o1.getSize();</a>
+<a name="1416"><span class="lineNum">    1416 </span>            : </a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineNoCov">          0 :             if (size0 != size1) {</span></a>
+<a name="1418"><span class="lineNum">    1418 </span>            :               // We allow 'mov r64, r32' as it's basically zero-extend.</a>
+<a name="1419"><span class="lineNum">    1419 </span><span class="lineNoCov">          0 :               if (size0 == 8 &amp;&amp; size1 == 4)</span></a>
+<a name="1420"><span class="lineNum">    1420 </span>            :                 size0 = 4; // Zero extend, don't promote to 64-bit.</a>
+<a name="1421"><span class="lineNum">    1421 </span>            :               else</a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineNoCov">          0 :                 goto InvalidInstruction;</span></a>
+<a name="1423"><span class="lineNum">    1423 </span>            :             }</a>
+<a name="1424"><span class="lineNum">    1424 </span>            : </a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineNoCov">          0 :             if (size0 == 1) {</span></a>
+<a name="1426"><span class="lineNum">    1426 </span><span class="lineNoCov">          0 :               FIXUP_GPB(o0, opReg);</span></a>
+<a name="1427"><span class="lineNum">    1427 </span><span class="lineNoCov">          0 :               FIXUP_GPB(o1, rbReg);</span></a>
+<a name="1428"><span class="lineNum">    1428 </span>            :               opCode = 0x8A;</a>
+<a name="1429"><span class="lineNum">    1429 </span>            : </a>
+<a name="1430"><span class="lineNum">    1430 </span><span class="lineNoCov">          0 :               if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="1431"><span class="lineNum">    1431 </span><span class="lineNoCov">          0 :                 goto EmitX86R;</span></a>
+<a name="1432"><span class="lineNum">    1432 </span>            : </a>
+<a name="1433"><span class="lineNum">    1433 </span>            :               opCode -= 2;</a>
+<a name="1434"><span class="lineNum">    1434 </span>            :               Utils::swap(opReg, rbReg);</a>
+<a name="1435"><span class="lineNum">    1435 </span><span class="lineNoCov">          0 :               goto EmitX86R;</span></a>
+<a name="1436"><span class="lineNum">    1436 </span>            :             }</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :             else {</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :               opCode = 0x8B;</a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineNoCov">          0 :               ADD_PREFIX_BY_SIZE(size0);</span></a>
+<a name="1440"><span class="lineNum">    1440 </span>            : </a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineNoCov">          0 :               if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineNoCov">          0 :                 goto EmitX86R;</span></a>
+<a name="1443"><span class="lineNum">    1443 </span>            : </a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineNoCov">          0 :               opCode -= 2;</span></a>
+<a name="1445"><span class="lineNum">    1445 </span>            :               Utils::swap(opReg, rbReg);</a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineNoCov">          0 :               goto EmitX86R;</span></a>
+<a name="1447"><span class="lineNum">    1447 </span>            :             }</a>
+<a name="1448"><span class="lineNum">    1448 </span>            :           }</a>
+<a name="1449"><span class="lineNum">    1449 </span>            : </a>
+<a name="1450"><span class="lineNum">    1450 </span>            :           opReg = rbReg;</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :           rbReg = o0.getId();</a>
+<a name="1452"><span class="lineNum">    1452 </span>            : </a>
+<a name="1453"><span class="lineNum">    1453 </span>            :           // GP &lt;- SEG</a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineNoCov">          0 :           if (X86Reg::isSeg(o1)) {</span></a>
+<a name="1455"><span class="lineNum">    1455 </span>            :             opCode = 0x8C;</a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineNoCov">          0 :             opReg--;</span></a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineNoCov">          0 :             ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1459"><span class="lineNum">    1459 </span>            :           }</a>
+<a name="1460"><span class="lineNum">    1460 </span>            : </a>
+<a name="1461"><span class="lineNum">    1461 </span>            :           // GP &lt;- CR</a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineNoCov">          0 :           if (X86Reg::isCr(o1)) {</span></a>
+<a name="1463"><span class="lineNum">    1463 </span>            :             opCode = 0x20 | X86Inst::kOpCode_MM_0F;</a>
+<a name="1464"><span class="lineNum">    1464 </span>            : </a>
+<a name="1465"><span class="lineNum">    1465 </span>            :             // Use `LOCK MOV` in 32-bit mode if CR8+ register is accessed (AMD extension).</a>
+<a name="1466"><span class="lineNum">    1466 </span><span class="lineNoCov">          0 :             if ((opReg &amp; 0x8) &amp;&amp; is32Bit()) {</span></a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineNoCov">          0 :               EMIT_BYTE(0xF0);</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineNoCov">          0 :               opReg &amp;= 0x7;</span></a>
+<a name="1469"><span class="lineNum">    1469 </span>            :             }</a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1471"><span class="lineNum">    1471 </span>            :           }</a>
+<a name="1472"><span class="lineNum">    1472 </span>            : </a>
+<a name="1473"><span class="lineNum">    1473 </span>            :           // GP &lt;- DR</a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineNoCov">          0 :           if (X86Reg::isDr(o1)) {</span></a>
+<a name="1475"><span class="lineNum">    1475 </span>            :             opCode = 0x21 | X86Inst::kOpCode_MM_0F;</a>
+<a name="1476"><span class="lineNum">    1476 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1477"><span class="lineNum">    1477 </span>            :           }</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :         }</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :         else {</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :           // ?? &lt;- GP</a>
+<a name="1481"><span class="lineNum">    1481 </span><span class="lineNoCov">          0 :           if (!X86Reg::isGp(o1))</span></a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="1483"><span class="lineNum">    1483 </span>            : </a>
+<a name="1484"><span class="lineNum">    1484 </span>            :           // SEG &lt;- GP</a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineNoCov">          0 :           if (X86Reg::isSeg(o0)) {</span></a>
+<a name="1486"><span class="lineNum">    1486 </span>            :             opCode = 0x8E;</a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineNoCov">          0 :             opReg--;</span></a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineNoCov">          0 :             ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1490"><span class="lineNum">    1490 </span>            :           }</a>
+<a name="1491"><span class="lineNum">    1491 </span>            : </a>
+<a name="1492"><span class="lineNum">    1492 </span>            :           // CR &lt;- GP</a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineNoCov">          0 :           if (X86Reg::isCr(o0)) {</span></a>
+<a name="1494"><span class="lineNum">    1494 </span>            :             opCode = 0x22 | X86Inst::kOpCode_MM_0F;</a>
+<a name="1495"><span class="lineNum">    1495 </span>            : </a>
+<a name="1496"><span class="lineNum">    1496 </span>            :             // Use `LOCK MOV` in 32-bit mode if CR8+ register is accessed (AMD extension).</a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineNoCov">          0 :             if ((opReg &amp; 0x8) &amp;&amp; is32Bit()) {</span></a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineNoCov">          0 :               EMIT_BYTE(0xF0);</span></a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineNoCov">          0 :               opReg &amp;= 0x7;</span></a>
+<a name="1500"><span class="lineNum">    1500 </span>            :             }</a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1502"><span class="lineNum">    1502 </span>            :           }</a>
+<a name="1503"><span class="lineNum">    1503 </span>            : </a>
+<a name="1504"><span class="lineNum">    1504 </span>            :           // DR &lt;- GP</a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineNoCov">          0 :           if (X86Reg::isDr(o0)) {</span></a>
+<a name="1506"><span class="lineNum">    1506 </span>            :             opCode = 0x23 | X86Inst::kOpCode_MM_0F;</a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1508"><span class="lineNum">    1508 </span>            :           }</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :         }</a>
+<a name="1510"><span class="lineNum">    1510 </span>            : </a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="1512"><span class="lineNum">    1512 </span>            :       }</a>
+<a name="1513"><span class="lineNum">    1513 </span>            : </a>
+<a name="1514"><span class="lineNum">    1514 </span><span class="lineCov">       7688 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1515"><span class="lineNum">    1515 </span>            :         opReg = o0.getId();</a>
+<a name="1516"><span class="lineNum">    1516 </span>            :         rmRel = &amp;o1;</a>
+<a name="1517"><span class="lineNum">    1517 </span>            : </a>
+<a name="1518"><span class="lineNum">    1518 </span>            :         // SEG &lt;- Mem</a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineNoCov">          0 :         if (X86Reg::isSeg(o0)) {</span></a>
+<a name="1520"><span class="lineNum">    1520 </span>            :           opCode = 0x8E;</a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineNoCov">          0 :           opReg--;</span></a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1523"><span class="lineNum">    1523 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1524"><span class="lineNum">    1524 </span>            :         }</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :         // Reg &lt;- Mem</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :         else {</a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineNoCov">          0 :           if (o0.getSize() == 1) {</span></a>
+<a name="1528"><span class="lineNum">    1528 </span>            :             opCode = 0;</a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineNoCov">          0 :             FIXUP_GPB(o0, opReg);</span></a>
+<a name="1530"><span class="lineNum">    1530 </span>            :           }</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :           else {</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :             opCode = 1;</a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineNoCov">          0 :             ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1534"><span class="lineNum">    1534 </span>            :           }</a>
+<a name="1535"><span class="lineNum">    1535 </span>            : </a>
+<a name="1536"><span class="lineNum">    1536 </span>            :           // Handle a special form `mov al|ax|eax|rax, [ptr64]` that doesn't use MOD.</a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineNoCov">          0 :           if (o0.getId() == X86Gp::kIdAx &amp;&amp; !rmRel-&gt;as&lt;X86Mem&gt;().hasBaseOrIndex()) {</span></a>
+<a name="1538"><span class="lineNum">    1538 </span>            :             imVal = rmRel-&gt;as&lt;X86Mem&gt;().getOffset();</a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineNoCov">          0 :             if (!is64Bit() || (is64Bit() &amp;&amp; ((options &amp; X86Inst::kOptionLongForm) || !Utils::isInt32(imVal)))) {</span></a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineNoCov">          0 :               opCode += 0xA0;</span></a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineNoCov">          0 :               goto EmitX86OpMovAbs;</span></a>
+<a name="1542"><span class="lineNum">    1542 </span>            :             }</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :           }</a>
+<a name="1544"><span class="lineNum">    1544 </span>            : </a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineNoCov">          0 :           opCode += 0x8A;</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1547"><span class="lineNum">    1547 </span>            :         }</a>
+<a name="1548"><span class="lineNum">    1548 </span>            :       }</a>
+<a name="1549"><span class="lineNum">    1549 </span>            : </a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">       7688 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="1551"><span class="lineNum">    1551 </span>            :         opReg = o1.getId();</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :         rmRel = &amp;o0;</a>
+<a name="1553"><span class="lineNum">    1553 </span>            : </a>
+<a name="1554"><span class="lineNum">    1554 </span>            :         // Mem &lt;- SEG</a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineNoCov">          0 :         if (X86Reg::isSeg(o1)) {</span></a>
+<a name="1556"><span class="lineNum">    1556 </span>            :           opCode = 0x8C;</a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineNoCov">          0 :           opReg--;</span></a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1560"><span class="lineNum">    1560 </span>            :         }</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :         // Mem &lt;- Reg</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :         else {</a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineNoCov">          0 :           if (o1.getSize() == 1) {</span></a>
+<a name="1564"><span class="lineNum">    1564 </span>            :             opCode = 0;</a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineNoCov">          0 :             FIXUP_GPB(o1, opReg);</span></a>
+<a name="1566"><span class="lineNum">    1566 </span>            :           }</a>
+<a name="1567"><span class="lineNum">    1567 </span>            :           else {</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :             opCode = 1;</a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineNoCov">          0 :             ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1570"><span class="lineNum">    1570 </span>            :           }</a>
+<a name="1571"><span class="lineNum">    1571 </span>            : </a>
+<a name="1572"><span class="lineNum">    1572 </span>            :           // Handle a special form `mov [ptr64], al|ax|eax|rax` that doesn't use MOD.</a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineNoCov">          0 :           if (o1.getId() == X86Gp::kIdAx &amp;&amp; !rmRel-&gt;as&lt;X86Mem&gt;().hasBaseOrIndex()) {</span></a>
+<a name="1574"><span class="lineNum">    1574 </span>            :             imVal = rmRel-&gt;as&lt;X86Mem&gt;().getOffset();</a>
+<a name="1575"><span class="lineNum">    1575 </span><span class="lineNoCov">          0 :             if (!is64Bit() || (is64Bit() &amp;&amp; ((options &amp; X86Inst::kOptionLongForm) || !Utils::isInt32(imVal)))) {</span></a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineNoCov">          0 :               opCode += 0xA2;</span></a>
+<a name="1577"><span class="lineNum">    1577 </span><span class="lineNoCov">          0 :               goto EmitX86OpMovAbs;</span></a>
+<a name="1578"><span class="lineNum">    1578 </span>            :             }</a>
+<a name="1579"><span class="lineNum">    1579 </span>            :           }</a>
+<a name="1580"><span class="lineNum">    1580 </span>            : </a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineNoCov">          0 :           opCode += 0x88;</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1583"><span class="lineNum">    1583 </span>            :         }</a>
+<a name="1584"><span class="lineNum">    1584 </span>            :       }</a>
+<a name="1585"><span class="lineNum">    1585 </span>            : </a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineCov">       7688 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="1587"><span class="lineNum">    1587 </span>            :         opReg = o0.getId();</a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineCov">       7688 :         imLen = o0.getSize();</span></a>
+<a name="1589"><span class="lineNum">    1589 </span>            : </a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineCov">       7688 :         if (imLen == 1) {</span></a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, opReg);</span></a>
+<a name="1592"><span class="lineNum">    1592 </span>            : </a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineNoCov">          0 :           imVal = static_cast&lt;const Imm&amp;&gt;(o1).getUInt8();</span></a>
+<a name="1594"><span class="lineNum">    1594 </span>            :           opCode = 0xB0;</a>
+<a name="1595"><span class="lineNum">    1595 </span><span class="lineNoCov">          0 :           goto EmitX86OpReg;</span></a>
+<a name="1596"><span class="lineNum">    1596 </span>            :         }</a>
+<a name="1597"><span class="lineNum">    1597 </span>            :         else {</a>
+<a name="1598"><span class="lineNum">    1598 </span>            :           // 64-bit immediate in 64-bit mode is allowed.</a>
+<a name="1599"><span class="lineNum">    1599 </span>            :           imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="1600"><span class="lineNum">    1600 </span>            : </a>
+<a name="1601"><span class="lineNum">    1601 </span>            :           // Optimize the instruction size by using a 32-bit immediate if possible.</a>
+<a name="1602"><span class="lineNum">    1602 </span><span class="lineCov">       7688 :           if (imLen == 8 &amp;&amp; !(options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineCov">       7688 :             if (Utils::isUInt32(imVal)) {</span></a>
+<a name="1604"><span class="lineNum">    1604 </span>            :               // Zero-extend by using a 32-bit GPD destination instead of a 64-bit GPQ.</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :               imLen = 4;</a>
+<a name="1606"><span class="lineNum">    1606 </span>            :             }</a>
+<a name="1607"><span class="lineNum">    1607 </span><span class="lineCov">       7688 :             else if (Utils::isInt32(imVal)) {</span></a>
+<a name="1608"><span class="lineNum">    1608 </span>            :               // Sign-extend, uses 'C7 /0' opcode.</a>
+<a name="1609"><span class="lineNum">    1609 </span>            :               rbReg = opReg;</a>
+<a name="1610"><span class="lineNum">    1610 </span>            : </a>
+<a name="1611"><span class="lineNum">    1611 </span>            :               opCode = 0xC7 | X86Inst::kOpCode_W;</a>
+<a name="1612"><span class="lineNum">    1612 </span>            :               opReg = 0;</a>
+<a name="1613"><span class="lineNum">    1613 </span>            : </a>
+<a name="1614"><span class="lineNum">    1614 </span>            :               imLen = 4;</a>
+<a name="1615"><span class="lineNum">    1615 </span><span class="lineNoCov">          0 :               goto EmitX86R;</span></a>
+<a name="1616"><span class="lineNum">    1616 </span>            :             }</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :           }</a>
+<a name="1618"><span class="lineNum">    1618 </span>            : </a>
+<a name="1619"><span class="lineNum">    1619 </span>            :           opCode = 0xB8;</a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineCov">       7688 :           ADD_PREFIX_BY_SIZE(imLen);</span></a>
+<a name="1621"><span class="lineNum">    1621 </span><span class="lineCov">       7688 :           goto EmitX86OpReg;</span></a>
+<a name="1622"><span class="lineNum">    1622 </span>            :         }</a>
+<a name="1623"><span class="lineNum">    1623 </span>            :       }</a>
+<a name="1624"><span class="lineNum">    1624 </span>            : </a>
+<a name="1625"><span class="lineNum">    1625 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Imm)) {</span></a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineNoCov">          0 :         uint32_t memSize = o0.getSize();</span></a>
+<a name="1627"><span class="lineNum">    1627 </span>            : </a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(memSize == 0))</span></a>
+<a name="1629"><span class="lineNum">    1629 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1630"><span class="lineNum">    1630 </span>            : </a>
+<a name="1631"><span class="lineNum">    1631 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineNoCov">          0 :         imLen = std::min&lt;uint32_t&gt;(memSize, 4);</span></a>
+<a name="1633"><span class="lineNum">    1633 </span>            : </a>
+<a name="1634"><span class="lineNum">    1634 </span><span class="lineNoCov">          0 :         opCode = 0xC6 + (memSize != 1);</span></a>
+<a name="1635"><span class="lineNum">    1635 </span>            :         opReg = 0;</a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(memSize);</span></a>
+<a name="1637"><span class="lineNum">    1637 </span>            : </a>
+<a name="1638"><span class="lineNum">    1638 </span>            :         rmRel = &amp;o0;</a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1640"><span class="lineNum">    1640 </span>            :       }</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :       break;</a>
+<a name="1642"><span class="lineNum">    1642 </span>            : </a>
+<a name="1643"><span class="lineNum">    1643 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86MovsxMovzx:</span></a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1645"><span class="lineNum">    1645 </span>            :         opReg = o0.getId();</a>
+<a name="1646"><span class="lineNum">    1646 </span>            :         rbReg = o1.getId();</a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1648"><span class="lineNum">    1648 </span>            : </a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1) {</span></a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, rbReg);</span></a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1652"><span class="lineNum">    1652 </span>            :         }</a>
+<a name="1653"><span class="lineNum">    1653 </span>            :         else {</a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1656"><span class="lineNum">    1656 </span>            :         }</a>
+<a name="1657"><span class="lineNum">    1657 </span>            :       }</a>
+<a name="1658"><span class="lineNum">    1658 </span>            : </a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineNoCov">          0 :         opCode += o1.getSize() != 1;</span></a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1662"><span class="lineNum">    1662 </span>            : </a>
+<a name="1663"><span class="lineNum">    1663 </span>            :         opReg = o0.getId();</a>
+<a name="1664"><span class="lineNum">    1664 </span>            :         rmRel = &amp;o1;</a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1666"><span class="lineNum">    1666 </span>            :       }</a>
+<a name="1667"><span class="lineNum">    1667 </span>            :       break;</a>
+<a name="1668"><span class="lineNum">    1668 </span>            : </a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Out:</span></a>
+<a name="1670"><span class="lineNum">    1670 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Imm, Reg)) {</span></a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o1.getId() != X86Gp::kIdAx))</span></a>
+<a name="1672"><span class="lineNum">    1672 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1673"><span class="lineNum">    1673 </span>            : </a>
+<a name="1674"><span class="lineNum">    1674 </span><span class="lineNoCov">          0 :         imVal = o0.as&lt;Imm&gt;().getUInt8();</span></a>
+<a name="1675"><span class="lineNum">    1675 </span>            :         imLen = 1;</a>
+<a name="1676"><span class="lineNum">    1676 </span>            : </a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineNoCov">          0 :         opCode = commonData-&gt;getAltOpCode() + (o1.getSize() != 1);</span></a>
+<a name="1678"><span class="lineNum">    1678 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(o1.getSize());</span></a>
+<a name="1679"><span class="lineNum">    1679 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1680"><span class="lineNum">    1680 </span>            :       }</a>
+<a name="1681"><span class="lineNum">    1681 </span>            : </a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getId() != X86Gp::kIdDx || o1.getId() != X86Gp::kIdAx))</span></a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1685"><span class="lineNum">    1685 </span>            : </a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineNoCov">          0 :         opCode += o1.getSize() != 1;</span></a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(o1.getSize());</span></a>
+<a name="1688"><span class="lineNum">    1688 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1689"><span class="lineNum">    1689 </span>            :       }</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :       break;</a>
+<a name="1691"><span class="lineNum">    1691 </span>            : </a>
+<a name="1692"><span class="lineNum">    1692 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Outs:</span></a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1694"><span class="lineNum">    1694 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getId() != X86Gp::kIdDx || !x86IsImplicitMem(o1, X86Gp::kIdSi)))</span></a>
+<a name="1695"><span class="lineNum">    1695 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1696"><span class="lineNum">    1696 </span>            : </a>
+<a name="1697"><span class="lineNum">    1697 </span>            :         uint32_t size = o1.getSize();</a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(size == 0))</span></a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1700"><span class="lineNum">    1700 </span>            : </a>
+<a name="1701"><span class="lineNum">    1701 </span>            :         rmRel = &amp;o1;</a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineNoCov">          0 :         opCode += (size != 1);</span></a>
+<a name="1703"><span class="lineNum">    1703 </span>            : </a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(size);</span></a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineNoCov">          0 :         goto EmitX86OpImplicitMem;</span></a>
+<a name="1706"><span class="lineNum">    1706 </span>            :       }</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :       break;</a>
+<a name="1708"><span class="lineNum">    1708 </span>            : </a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineCov">       1120 :     case X86Inst::kEncodingX86Push:</span></a>
+<a name="1710"><span class="lineNum">    1710 </span><span class="lineCov">       1120 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1711"><span class="lineNum">    1711 </span><span class="lineCov">       1120 :         if (X86Reg::isSeg(o0)) {</span></a>
+<a name="1712"><span class="lineNum">    1712 </span>            :           uint32_t segment = o0.getId();</a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(segment &gt;= X86Seg::kIdCount))</span></a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineNoCov">          0 :             goto InvalidSegment;</span></a>
+<a name="1715"><span class="lineNum">    1715 </span>            : </a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineNoCov">          0 :           if (segment &gt;= X86Seg::kIdFs)</span></a>
+<a name="1717"><span class="lineNum">    1717 </span><span class="lineNoCov">          0 :             EMIT_BYTE(0x0F);</span></a>
+<a name="1718"><span class="lineNum">    1718 </span>            : </a>
+<a name="1719"><span class="lineNum">    1719 </span><span class="lineNoCov">          0 :           EMIT_BYTE(x86OpCodePushSeg[segment]);</span></a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineNoCov">          0 :           goto EmitDone;</span></a>
+<a name="1721"><span class="lineNum">    1721 </span>            :         }</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :         else {</a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineCov">       1120 :           goto CaseX86Pop_Gp;</span></a>
+<a name="1724"><span class="lineNum">    1724 </span>            :         }</a>
+<a name="1725"><span class="lineNum">    1725 </span>            :       }</a>
+<a name="1726"><span class="lineNum">    1726 </span>            : </a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Imm)) {</span></a>
+<a name="1728"><span class="lineNum">    1728 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o0).getInt64();</a>
+<a name="1729"><span class="lineNum">    1729 </span>            :         imLen = 4;</a>
+<a name="1730"><span class="lineNum">    1730 </span>            : </a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineNoCov">          0 :         if (Utils::isInt8(imVal) &amp;&amp; !(options &amp; X86Inst::kOptionLongForm))</span></a>
+<a name="1732"><span class="lineNum">    1732 </span>            :           imLen = 1;</a>
+<a name="1733"><span class="lineNum">    1733 </span>            : </a>
+<a name="1734"><span class="lineNum">    1734 </span>            :         opCode = imLen == 1 ? 0x6A : 0x68;</a>
+<a name="1735"><span class="lineNum">    1735 </span><span class="lineNoCov">          0 :         goto EmitX86Op;</span></a>
+<a name="1736"><span class="lineNum">    1736 </span>            :       }</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="1738"><span class="lineNum">    1738 </span>            : </a>
+<a name="1739"><span class="lineNum">    1739 </span>            :     case X86Inst::kEncodingX86Pop:</a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">       1120 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineCov">       1120 :         if (X86Reg::isSeg(o0)) {</span></a>
+<a name="1742"><span class="lineNum">    1742 </span>            :           uint32_t segment = o0.getId();</a>
+<a name="1743"><span class="lineNum">    1743 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(segment == X86Seg::kIdCs || segment &gt;= X86Seg::kIdCount))</span></a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineNoCov">          0 :             goto InvalidSegment;</span></a>
+<a name="1745"><span class="lineNum">    1745 </span>            : </a>
+<a name="1746"><span class="lineNum">    1746 </span><span class="lineNoCov">          0 :           if (segment &gt;= X86Seg::kIdFs)</span></a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineNoCov">          0 :             EMIT_BYTE(0x0F);</span></a>
+<a name="1748"><span class="lineNum">    1748 </span>            : </a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineNoCov">          0 :           EMIT_BYTE(x86OpCodePopSeg[segment]);</span></a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineNoCov">          0 :           goto EmitDone;</span></a>
+<a name="1751"><span class="lineNum">    1751 </span>            :         }</a>
+<a name="1752"><span class="lineNum">    1752 </span>            :         else {</a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineCov">       2240 : CaseX86Pop_Gp:</span></a>
+<a name="1754"><span class="lineNum">    1754 </span>            :           // We allow 2 byte, 4 byte, and 8 byte register sizes, although PUSH</a>
+<a name="1755"><span class="lineNum">    1755 </span>            :           // and POP only allow 2 bytes or native size. On 64-bit we simply</a>
+<a name="1756"><span class="lineNum">    1756 </span>            :           // PUSH/POP 64-bit register even if 32-bit register was given.</a>
+<a name="1757"><span class="lineNum">    1757 </span><span class="lineCov">       2240 :           if (ASMJIT_UNLIKELY(o0.getSize() &lt; 2))</span></a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="1759"><span class="lineNum">    1759 </span>            : </a>
+<a name="1760"><span class="lineNum">    1760 </span>            :           opCode = commonData-&gt;getAltOpCode();</a>
+<a name="1761"><span class="lineNum">    1761 </span>            :           opReg = o0.getId();</a>
+<a name="1762"><span class="lineNum">    1762 </span>            : </a>
+<a name="1763"><span class="lineNum">    1763 </span><span class="lineCov">       2240 :           ADD_66H_P_BY_SIZE(o0.getSize());</span></a>
+<a name="1764"><span class="lineNum">    1764 </span><span class="lineCov">       2240 :           goto EmitX86OpReg;</span></a>
+<a name="1765"><span class="lineNum">    1765 </span>            :         }</a>
+<a name="1766"><span class="lineNum">    1766 </span>            :       }</a>
+<a name="1767"><span class="lineNum">    1767 </span>            : </a>
+<a name="1768"><span class="lineNum">    1768 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="1769"><span class="lineNum">    1769 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() == 0))</span></a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1771"><span class="lineNum">    1771 </span>            : </a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() != 2 &amp;&amp; o0.getSize() != getGpSize()))</span></a>
+<a name="1773"><span class="lineNum">    1773 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1774"><span class="lineNum">    1774 </span>            : </a>
+<a name="1775"><span class="lineNum">    1775 </span><span class="lineNoCov">          0 :         ADD_66H_P_BY_SIZE(o0.getSize());</span></a>
+<a name="1776"><span class="lineNum">    1776 </span>            :         rmRel = &amp;o0;</a>
+<a name="1777"><span class="lineNum">    1777 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1778"><span class="lineNum">    1778 </span>            :       }</a>
+<a name="1779"><span class="lineNum">    1779 </span>            :       break;</a>
+<a name="1780"><span class="lineNum">    1780 </span>            : </a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineCov">       1948 :     case X86Inst::kEncodingX86Ret:</span></a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineCov">       1948 :       if (isign3 == 0) {</span></a>
+<a name="1783"><span class="lineNum">    1783 </span>            :         // 'ret' without immediate, change C2 to C3.</a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineCov">       1948 :         opCode++;</span></a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineCov">       1948 :         goto EmitX86Op;</span></a>
+<a name="1786"><span class="lineNum">    1786 </span>            :       }</a>
+<a name="1787"><span class="lineNum">    1787 </span>            : </a>
+<a name="1788"><span class="lineNum">    1788 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Imm)) {</span></a>
+<a name="1789"><span class="lineNum">    1789 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o0).getInt64();</a>
+<a name="1790"><span class="lineNum">    1790 </span><span class="lineNoCov">          0 :         if (imVal == 0 &amp;&amp; !(options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="1791"><span class="lineNum">    1791 </span>            :           // 'ret' without immediate, change C2 to C3.</a>
+<a name="1792"><span class="lineNum">    1792 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1793"><span class="lineNum">    1793 </span><span class="lineNoCov">          0 :           goto EmitX86Op;</span></a>
+<a name="1794"><span class="lineNum">    1794 </span>            :         }</a>
+<a name="1795"><span class="lineNum">    1795 </span>            :         else {</a>
+<a name="1796"><span class="lineNum">    1796 </span>            :           imLen = 2;</a>
+<a name="1797"><span class="lineNum">    1797 </span><span class="lineNoCov">          0 :           goto EmitX86Op;</span></a>
+<a name="1798"><span class="lineNum">    1798 </span>            :         }</a>
+<a name="1799"><span class="lineNum">    1799 </span>            :       }</a>
+<a name="1800"><span class="lineNum">    1800 </span>            :       break;</a>
+<a name="1801"><span class="lineNum">    1801 </span>            : </a>
+<a name="1802"><span class="lineNum">    1802 </span>            :     case X86Inst::kEncodingX86Rot:</a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineNoCov">          0 :       if (o0.isReg()) {</span></a>
+<a name="1804"><span class="lineNum">    1804 </span>            :         rbReg = o0.getId();</a>
+<a name="1805"><span class="lineNum">    1805 </span>            : </a>
+<a name="1806"><span class="lineNum">    1806 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="1808"><span class="lineNum">    1808 </span>            :         }</a>
+<a name="1809"><span class="lineNum">    1809 </span>            :         else {</a>
+<a name="1810"><span class="lineNum">    1810 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1811"><span class="lineNum">    1811 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1812"><span class="lineNum">    1812 </span>            :         }</a>
+<a name="1813"><span class="lineNum">    1813 </span>            : </a>
+<a name="1814"><span class="lineNum">    1814 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1815"><span class="lineNum">    1815 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(o1.getId() != X86Gp::kIdCx))</span></a>
+<a name="1816"><span class="lineNum">    1816 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="1817"><span class="lineNum">    1817 </span>            : </a>
+<a name="1818"><span class="lineNum">    1818 </span><span class="lineNoCov">          0 :           opCode += 2;</span></a>
+<a name="1819"><span class="lineNum">    1819 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1820"><span class="lineNum">    1820 </span>            :         }</a>
+<a name="1821"><span class="lineNum">    1821 </span>            : </a>
+<a name="1822"><span class="lineNum">    1822 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="1823"><span class="lineNum">    1823 </span><span class="lineNoCov">          0 :           imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64() &amp; 0xFF;</span></a>
+<a name="1824"><span class="lineNum">    1824 </span>            :           imLen = 0;</a>
+<a name="1825"><span class="lineNum">    1825 </span>            : </a>
+<a name="1826"><span class="lineNum">    1826 </span><span class="lineNoCov">          0 :           if (imVal == 1 &amp;&amp; !(options &amp; X86Inst::kOptionLongForm))</span></a>
+<a name="1827"><span class="lineNum">    1827 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="1828"><span class="lineNum">    1828 </span>            : </a>
+<a name="1829"><span class="lineNum">    1829 </span>            :           imLen = 1;</a>
+<a name="1830"><span class="lineNum">    1830 </span><span class="lineNoCov">          0 :           opCode -= 0x10;</span></a>
+<a name="1831"><span class="lineNum">    1831 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1832"><span class="lineNum">    1832 </span>            :         }</a>
+<a name="1833"><span class="lineNum">    1833 </span>            :       }</a>
+<a name="1834"><span class="lineNum">    1834 </span>            :       else {</a>
+<a name="1835"><span class="lineNum">    1835 </span><span class="lineNoCov">          0 :         opCode += o0.getSize() != 1;</span></a>
+<a name="1836"><span class="lineNum">    1836 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1837"><span class="lineNum">    1837 </span>            : </a>
+<a name="1838"><span class="lineNum">    1838 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="1839"><span class="lineNum">    1839 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(o1.getId() != X86Gp::kIdCx))</span></a>
+<a name="1840"><span class="lineNum">    1840 </span><span class="lineNoCov">          0 :             goto InvalidInstruction;</span></a>
+<a name="1841"><span class="lineNum">    1841 </span>            : </a>
+<a name="1842"><span class="lineNum">    1842 </span><span class="lineNoCov">          0 :           opCode += 2;</span></a>
+<a name="1843"><span class="lineNum">    1843 </span>            :           rmRel = &amp;o0;</a>
+<a name="1844"><span class="lineNum">    1844 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1845"><span class="lineNum">    1845 </span>            :         }</a>
+<a name="1846"><span class="lineNum">    1846 </span>            : </a>
+<a name="1847"><span class="lineNum">    1847 </span><span class="lineNoCov">          0 :         if (isign3 == ENC_OPS2(Mem, Imm)) {</span></a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(o0.getSize() == 0))</span></a>
+<a name="1849"><span class="lineNum">    1849 </span><span class="lineNoCov">          0 :             goto AmbiguousOperandSize;</span></a>
+<a name="1850"><span class="lineNum">    1850 </span>            : </a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineNoCov">          0 :           imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64() &amp; 0xFF;</span></a>
+<a name="1852"><span class="lineNum">    1852 </span>            :           imLen = 0;</a>
+<a name="1853"><span class="lineNum">    1853 </span>            :           rmRel = &amp;o0;</a>
+<a name="1854"><span class="lineNum">    1854 </span>            : </a>
+<a name="1855"><span class="lineNum">    1855 </span><span class="lineNoCov">          0 :           if (imVal == 1 &amp;&amp; !(options &amp; X86Inst::kOptionLongForm))</span></a>
+<a name="1856"><span class="lineNum">    1856 </span><span class="lineNoCov">          0 :             goto EmitX86M;</span></a>
+<a name="1857"><span class="lineNum">    1857 </span>            : </a>
+<a name="1858"><span class="lineNum">    1858 </span>            :           imLen = 1;</a>
+<a name="1859"><span class="lineNum">    1859 </span><span class="lineNoCov">          0 :           opCode -= 0x10;</span></a>
+<a name="1860"><span class="lineNum">    1860 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="1861"><span class="lineNum">    1861 </span>            :         }</a>
+<a name="1862"><span class="lineNum">    1862 </span>            :       }</a>
+<a name="1863"><span class="lineNum">    1863 </span>            :       break;</a>
+<a name="1864"><span class="lineNum">    1864 </span>            : </a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Set:</span></a>
+<a name="1866"><span class="lineNum">    1866 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="1867"><span class="lineNum">    1867 </span>            :         rbReg = o0.getId();</a>
+<a name="1868"><span class="lineNum">    1868 </span><span class="lineNoCov">          0 :         FIXUP_GPB(o0, rbReg);</span></a>
+<a name="1869"><span class="lineNum">    1869 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1870"><span class="lineNum">    1870 </span>            :       }</a>
+<a name="1871"><span class="lineNum">    1871 </span>            : </a>
+<a name="1872"><span class="lineNum">    1872 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="1873"><span class="lineNum">    1873 </span>            :         rmRel = &amp;o0;</a>
+<a name="1874"><span class="lineNum">    1874 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1875"><span class="lineNum">    1875 </span>            :       }</a>
+<a name="1876"><span class="lineNum">    1876 </span>            :       break;</a>
+<a name="1877"><span class="lineNum">    1877 </span>            : </a>
+<a name="1878"><span class="lineNum">    1878 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86ShldShrd:</span></a>
+<a name="1879"><span class="lineNum">    1879 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="1880"><span class="lineNum">    1880 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1881"><span class="lineNum">    1881 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="1882"><span class="lineNum">    1882 </span>            :         imLen = 1;</a>
+<a name="1883"><span class="lineNum">    1883 </span>            : </a>
+<a name="1884"><span class="lineNum">    1884 </span>            :         opReg = o1.getId();</a>
+<a name="1885"><span class="lineNum">    1885 </span>            :         rbReg = o0.getId();</a>
+<a name="1886"><span class="lineNum">    1886 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1887"><span class="lineNum">    1887 </span>            :       }</a>
+<a name="1888"><span class="lineNum">    1888 </span>            : </a>
+<a name="1889"><span class="lineNum">    1889 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Mem, Reg, Imm)) {</span></a>
+<a name="1890"><span class="lineNum">    1890 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1891"><span class="lineNum">    1891 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="1892"><span class="lineNum">    1892 </span>            :         imLen = 1;</a>
+<a name="1893"><span class="lineNum">    1893 </span>            : </a>
+<a name="1894"><span class="lineNum">    1894 </span>            :         opReg = o1.getId();</a>
+<a name="1895"><span class="lineNum">    1895 </span>            :         rmRel = &amp;o0;</a>
+<a name="1896"><span class="lineNum">    1896 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1897"><span class="lineNum">    1897 </span>            :       }</a>
+<a name="1898"><span class="lineNum">    1898 </span>            : </a>
+<a name="1899"><span class="lineNum">    1899 </span>            :       // The following instructions use opCode + 1.</a>
+<a name="1900"><span class="lineNum">    1900 </span><span class="lineNoCov">          0 :       opCode++;</span></a>
+<a name="1901"><span class="lineNum">    1901 </span>            : </a>
+<a name="1902"><span class="lineNum">    1902 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="1903"><span class="lineNum">    1903 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o2.getId() != X86Gp::kIdCx))</span></a>
+<a name="1904"><span class="lineNum">    1904 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1905"><span class="lineNum">    1905 </span>            : </a>
+<a name="1906"><span class="lineNum">    1906 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1907"><span class="lineNum">    1907 </span>            :         opReg = o1.getId();</a>
+<a name="1908"><span class="lineNum">    1908 </span>            :         rbReg = o0.getId();</a>
+<a name="1909"><span class="lineNum">    1909 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="1910"><span class="lineNum">    1910 </span>            :       }</a>
+<a name="1911"><span class="lineNum">    1911 </span>            : </a>
+<a name="1912"><span class="lineNum">    1912 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Mem, Reg, Reg)) {</span></a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o2.getId() != X86Gp::kIdCx))</span></a>
+<a name="1914"><span class="lineNum">    1914 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1915"><span class="lineNum">    1915 </span>            : </a>
+<a name="1916"><span class="lineNum">    1916 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="1917"><span class="lineNum">    1917 </span>            :         opReg = o1.getId();</a>
+<a name="1918"><span class="lineNum">    1918 </span>            :         rmRel = &amp;o0;</a>
+<a name="1919"><span class="lineNum">    1919 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="1920"><span class="lineNum">    1920 </span>            :       }</a>
+<a name="1921"><span class="lineNum">    1921 </span>            :       break;</a>
+<a name="1922"><span class="lineNum">    1922 </span>            : </a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86StrRm:</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="1925"><span class="lineNum">    1925 </span>            :         rmRel = &amp;o1;</a>
+<a name="1926"><span class="lineNum">    1926 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32() || !X86Reg::isGp(o0.as&lt;X86Reg&gt;(), X86Gp::kIdAx)))</span></a>
+<a name="1927"><span class="lineNum">    1927 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1928"><span class="lineNum">    1928 </span>            : </a>
+<a name="1929"><span class="lineNum">    1929 </span>            :         uint32_t size = o0.getSize();</a>
+<a name="1930"><span class="lineNum">    1930 </span><span class="lineNoCov">          0 :         if (o1.hasSize() &amp;&amp; ASMJIT_UNLIKELY(o1.getSize() != size))</span></a>
+<a name="1931"><span class="lineNum">    1931 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="1932"><span class="lineNum">    1932 </span>            : </a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(size);</span></a>
+<a name="1934"><span class="lineNum">    1934 </span><span class="lineNoCov">          0 :         opCode += static_cast&lt;uint32_t&gt;(size != 1);</span></a>
+<a name="1935"><span class="lineNum">    1935 </span>            : </a>
+<a name="1936"><span class="lineNum">    1936 </span><span class="lineNoCov">          0 :         goto EmitX86OpImplicitMem;</span></a>
+<a name="1937"><span class="lineNum">    1937 </span>            :       }</a>
+<a name="1938"><span class="lineNum">    1938 </span>            :       break;</a>
+<a name="1939"><span class="lineNum">    1939 </span>            : </a>
+<a name="1940"><span class="lineNum">    1940 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86StrMr:</span></a>
+<a name="1941"><span class="lineNum">    1941 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="1942"><span class="lineNum">    1942 </span>            :         rmRel = &amp;o0;</a>
+<a name="1943"><span class="lineNum">    1943 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32() || !X86Reg::isGp(o1.as&lt;X86Reg&gt;(), X86Gp::kIdAx)))</span></a>
+<a name="1944"><span class="lineNum">    1944 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1945"><span class="lineNum">    1945 </span>            : </a>
+<a name="1946"><span class="lineNum">    1946 </span>            :         uint32_t size = o1.getSize();</a>
+<a name="1947"><span class="lineNum">    1947 </span><span class="lineNoCov">          0 :         if (o0.hasSize() &amp;&amp; ASMJIT_UNLIKELY(o0.getSize() != size))</span></a>
+<a name="1948"><span class="lineNum">    1948 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="1949"><span class="lineNum">    1949 </span>            : </a>
+<a name="1950"><span class="lineNum">    1950 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(size);</span></a>
+<a name="1951"><span class="lineNum">    1951 </span><span class="lineNoCov">          0 :         opCode += static_cast&lt;uint32_t&gt;(size != 1);</span></a>
+<a name="1952"><span class="lineNum">    1952 </span>            : </a>
+<a name="1953"><span class="lineNum">    1953 </span><span class="lineNoCov">          0 :         goto EmitX86OpImplicitMem;</span></a>
+<a name="1954"><span class="lineNum">    1954 </span>            :       }</a>
+<a name="1955"><span class="lineNum">    1955 </span>            :       break;</a>
+<a name="1956"><span class="lineNum">    1956 </span>            : </a>
+<a name="1957"><span class="lineNum">    1957 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86StrMm:</span></a>
+<a name="1958"><span class="lineNum">    1958 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Mem)) {</span></a>
+<a name="1959"><span class="lineNum">    1959 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.as&lt;X86Mem&gt;().getBaseIndexType() !=</span></a>
+<a name="1960"><span class="lineNum">    1960 </span>            :                             o1.as&lt;X86Mem&gt;().getBaseIndexType()))</a>
+<a name="1961"><span class="lineNum">    1961 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1962"><span class="lineNum">    1962 </span>            : </a>
+<a name="1963"><span class="lineNum">    1963 </span>            :         rmRel = &amp;o1;</a>
+<a name="1964"><span class="lineNum">    1964 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.as&lt;X86Mem&gt;().hasOffset()))</span></a>
+<a name="1965"><span class="lineNum">    1965 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="1966"><span class="lineNum">    1966 </span>            : </a>
+<a name="1967"><span class="lineNum">    1967 </span>            :         uint32_t size = o1.getSize();</a>
+<a name="1968"><span class="lineNum">    1968 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(size == 0))</span></a>
+<a name="1969"><span class="lineNum">    1969 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="1970"><span class="lineNum">    1970 </span>            : </a>
+<a name="1971"><span class="lineNum">    1971 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() != size))</span></a>
+<a name="1972"><span class="lineNum">    1972 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="1973"><span class="lineNum">    1973 </span>            : </a>
+<a name="1974"><span class="lineNum">    1974 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(size);</span></a>
+<a name="1975"><span class="lineNum">    1975 </span><span class="lineNoCov">          0 :         opCode += static_cast&lt;uint32_t&gt;(size != 1);</span></a>
+<a name="1976"><span class="lineNum">    1976 </span>            : </a>
+<a name="1977"><span class="lineNum">    1977 </span><span class="lineNoCov">          0 :         goto EmitX86OpImplicitMem;</span></a>
+<a name="1978"><span class="lineNum">    1978 </span>            :       }</a>
+<a name="1979"><span class="lineNum">    1979 </span>            :       break;</a>
+<a name="1980"><span class="lineNum">    1980 </span>            : </a>
+<a name="1981"><span class="lineNum">    1981 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Test:</span></a>
+<a name="1982"><span class="lineNum">    1982 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="1983"><span class="lineNum">    1983 </span><span class="lineNoCov">          0 :         if (o0.getSize() != o1.getSize())</span></a>
+<a name="1984"><span class="lineNum">    1984 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="1985"><span class="lineNum">    1985 </span>            : </a>
+<a name="1986"><span class="lineNum">    1986 </span>            :         rbReg = o0.getId();</a>
+<a name="1987"><span class="lineNum">    1987 </span>            :         opReg = o1.getId();</a>
+<a name="1988"><span class="lineNum">    1988 </span>            : </a>
+<a name="1989"><span class="lineNum">    1989 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="1990"><span class="lineNum">    1990 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="1991"><span class="lineNum">    1991 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, opReg);</span></a>
+<a name="1992"><span class="lineNum">    1992 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1993"><span class="lineNum">    1993 </span>            :         }</a>
+<a name="1994"><span class="lineNum">    1994 </span>            :         else {</a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="1996"><span class="lineNum">    1996 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="1997"><span class="lineNum">    1997 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="1998"><span class="lineNum">    1998 </span>            :         }</a>
+<a name="1999"><span class="lineNum">    1999 </span>            :       }</a>
+<a name="2000"><span class="lineNum">    2000 </span>            : </a>
+<a name="2001"><span class="lineNum">    2001 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2002"><span class="lineNum">    2002 </span>            :         opReg = o1.getId();</a>
+<a name="2003"><span class="lineNum">    2003 </span>            :         rmRel = &amp;o0;</a>
+<a name="2004"><span class="lineNum">    2004 </span>            : </a>
+<a name="2005"><span class="lineNum">    2005 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1) {</span></a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, opReg);</span></a>
+<a name="2007"><span class="lineNum">    2007 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2008"><span class="lineNum">    2008 </span>            :         }</a>
+<a name="2009"><span class="lineNum">    2009 </span>            :         else {</a>
+<a name="2010"><span class="lineNum">    2010 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="2011"><span class="lineNum">    2011 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="2012"><span class="lineNum">    2012 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2013"><span class="lineNum">    2013 </span>            :         }</a>
+<a name="2014"><span class="lineNum">    2014 </span>            :       }</a>
+<a name="2015"><span class="lineNum">    2015 </span>            : </a>
+<a name="2016"><span class="lineNum">    2016 </span>            :       // The following instructions use the secondary opcode.</a>
+<a name="2017"><span class="lineNum">    2017 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2018"><span class="lineNum">    2018 </span>            :       opReg = x86ExtractO(opCode);</a>
+<a name="2019"><span class="lineNum">    2019 </span>            : </a>
+<a name="2020"><span class="lineNum">    2020 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="2021"><span class="lineNum">    2021 </span>            :         rbReg = o0.getId();</a>
+<a name="2022"><span class="lineNum">    2022 </span>            : </a>
+<a name="2023"><span class="lineNum">    2023 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="2024"><span class="lineNum">    2024 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="2025"><span class="lineNum">    2025 </span>            : </a>
+<a name="2026"><span class="lineNum">    2026 </span><span class="lineNoCov">          0 :           imVal = static_cast&lt;const Imm&amp;&gt;(o1).getUInt8();</span></a>
+<a name="2027"><span class="lineNum">    2027 </span>            :           imLen = 1;</a>
+<a name="2028"><span class="lineNum">    2028 </span>            :         }</a>
+<a name="2029"><span class="lineNum">    2029 </span>            :         else {</a>
+<a name="2030"><span class="lineNum">    2030 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="2031"><span class="lineNum">    2031 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="2032"><span class="lineNum">    2032 </span>            : </a>
+<a name="2033"><span class="lineNum">    2033 </span>            :           imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="2034"><span class="lineNum">    2034 </span><span class="lineNoCov">          0 :           imLen = std::min&lt;uint32_t&gt;(o0.getSize(), 4);</span></a>
+<a name="2035"><span class="lineNum">    2035 </span>            :         }</a>
+<a name="2036"><span class="lineNum">    2036 </span>            : </a>
+<a name="2037"><span class="lineNum">    2037 </span>            :         // Alternate Form - AL, AX, EAX, RAX.</a>
+<a name="2038"><span class="lineNum">    2038 </span><span class="lineNoCov">          0 :         if (o0.getId() == 0 &amp;&amp; !(options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="2039"><span class="lineNum">    2039 </span><span class="lineNoCov">          0 :           opCode &amp;= X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_W;</span></a>
+<a name="2040"><span class="lineNum">    2040 </span><span class="lineNoCov">          0 :           opCode |= 0xA8 + (o0.getSize() != 1);</span></a>
+<a name="2041"><span class="lineNum">    2041 </span><span class="lineNoCov">          0 :           goto EmitX86Op;</span></a>
+<a name="2042"><span class="lineNum">    2042 </span>            :         }</a>
+<a name="2043"><span class="lineNum">    2043 </span>            : </a>
+<a name="2044"><span class="lineNum">    2044 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2045"><span class="lineNum">    2045 </span>            :       }</a>
+<a name="2046"><span class="lineNum">    2046 </span>            : </a>
+<a name="2047"><span class="lineNum">    2047 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Imm)) {</span></a>
+<a name="2048"><span class="lineNum">    2048 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getSize() == 0))</span></a>
+<a name="2049"><span class="lineNum">    2049 </span><span class="lineNoCov">          0 :           goto AmbiguousOperandSize;</span></a>
+<a name="2050"><span class="lineNum">    2050 </span>            : </a>
+<a name="2051"><span class="lineNum">    2051 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="2052"><span class="lineNum">    2052 </span><span class="lineNoCov">          0 :         imLen = std::min&lt;uint32_t&gt;(o0.getSize(), 4);</span></a>
+<a name="2053"><span class="lineNum">    2053 </span>            : </a>
+<a name="2054"><span class="lineNum">    2054 </span><span class="lineNoCov">          0 :         opCode += (o0.getSize() != 1);</span></a>
+<a name="2055"><span class="lineNum">    2055 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="2056"><span class="lineNum">    2056 </span>            : </a>
+<a name="2057"><span class="lineNum">    2057 </span>            :         rmRel = &amp;o0;</a>
+<a name="2058"><span class="lineNum">    2058 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2059"><span class="lineNum">    2059 </span>            :       }</a>
+<a name="2060"><span class="lineNum">    2060 </span>            :       break;</a>
+<a name="2061"><span class="lineNum">    2061 </span>            : </a>
+<a name="2062"><span class="lineNum">    2062 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Xchg:</span></a>
+<a name="2063"><span class="lineNum">    2063 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2064"><span class="lineNum">    2064 </span>            :         opReg = o0.getId();</a>
+<a name="2065"><span class="lineNum">    2065 </span>            :         rmRel = &amp;o1;</a>
+<a name="2066"><span class="lineNum">    2066 </span>            : </a>
+<a name="2067"><span class="lineNum">    2067 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="2068"><span class="lineNum">    2068 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, opReg);</span></a>
+<a name="2069"><span class="lineNum">    2069 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2070"><span class="lineNum">    2070 </span>            :         }</a>
+<a name="2071"><span class="lineNum">    2071 </span>            :         else {</a>
+<a name="2072"><span class="lineNum">    2072 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="2073"><span class="lineNum">    2073 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="2074"><span class="lineNum">    2074 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2075"><span class="lineNum">    2075 </span>            :         }</a>
+<a name="2076"><span class="lineNum">    2076 </span>            :       }</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2078"><span class="lineNum">    2078 </span>            : </a>
+<a name="2079"><span class="lineNum">    2079 </span>            :     case X86Inst::kEncodingX86Xadd:</a>
+<a name="2080"><span class="lineNum">    2080 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2081"><span class="lineNum">    2081 </span>            :         rbReg = o0.getId();</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :         opReg = o1.getId();</a>
+<a name="2083"><span class="lineNum">    2083 </span>            : </a>
+<a name="2084"><span class="lineNum">    2084 </span><span class="lineNoCov">          0 :         if (o0.getSize() != o1.getSize())</span></a>
+<a name="2085"><span class="lineNum">    2085 </span><span class="lineNoCov">          0 :           goto OperandSizeMismatch;</span></a>
+<a name="2086"><span class="lineNum">    2086 </span>            : </a>
+<a name="2087"><span class="lineNum">    2087 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1) {</span></a>
+<a name="2088"><span class="lineNum">    2088 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o0, rbReg);</span></a>
+<a name="2089"><span class="lineNum">    2089 </span><span class="lineNoCov">          0 :           FIXUP_GPB(o1, opReg);</span></a>
+<a name="2090"><span class="lineNum">    2090 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="2091"><span class="lineNum">    2091 </span>            :         }</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :         else {</a>
+<a name="2093"><span class="lineNum">    2093 </span><span class="lineNoCov">          0 :           opCode++;</span></a>
+<a name="2094"><span class="lineNum">    2094 </span><span class="lineNoCov">          0 :           ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="2095"><span class="lineNum">    2095 </span>            : </a>
+<a name="2096"><span class="lineNum">    2096 </span>            :           // Special opcode for 'xchg ?ax, reg'.</a>
+<a name="2097"><span class="lineNum">    2097 </span><span class="lineNoCov">          0 :           if (instId == X86Inst::kIdXchg &amp;&amp; (opReg == 0 || rbReg == 0)) {</span></a>
+<a name="2098"><span class="lineNum">    2098 </span><span class="lineNoCov">          0 :             opCode &amp;= X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_W;</span></a>
+<a name="2099"><span class="lineNum">    2099 </span><span class="lineNoCov">          0 :             opCode |= 0x90;</span></a>
+<a name="2100"><span class="lineNum">    2100 </span>            :             // One of `xchg a, b` or `xchg b, a` is AX/EAX/RAX.</a>
+<a name="2101"><span class="lineNum">    2101 </span><span class="lineNoCov">          0 :             opReg += rbReg;</span></a>
+<a name="2102"><span class="lineNum">    2102 </span><span class="lineNoCov">          0 :             goto EmitX86OpReg;</span></a>
+<a name="2103"><span class="lineNum">    2103 </span>            :           }</a>
+<a name="2104"><span class="lineNum">    2104 </span>            :           else {</a>
+<a name="2105"><span class="lineNum">    2105 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="2106"><span class="lineNum">    2106 </span>            :           }</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :         }</a>
+<a name="2108"><span class="lineNum">    2108 </span>            :       }</a>
+<a name="2109"><span class="lineNum">    2109 </span>            : </a>
+<a name="2110"><span class="lineNum">    2110 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2111"><span class="lineNum">    2111 </span><span class="lineNoCov">          0 :         opCode += o1.getSize() != 1;</span></a>
+<a name="2112"><span class="lineNum">    2112 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="2113"><span class="lineNum">    2113 </span>            : </a>
+<a name="2114"><span class="lineNum">    2114 </span>            :         opReg = o1.getId();</a>
+<a name="2115"><span class="lineNum">    2115 </span>            :         rmRel = &amp;o0;</a>
+<a name="2116"><span class="lineNum">    2116 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2117"><span class="lineNum">    2117 </span>            :       }</a>
+<a name="2118"><span class="lineNum">    2118 </span>            :       break;</a>
+<a name="2119"><span class="lineNum">    2119 </span>            : </a>
+<a name="2120"><span class="lineNum">    2120 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Fence:</span></a>
+<a name="2121"><span class="lineNum">    2121 </span>            :       rbReg = 0;</a>
+<a name="2122"><span class="lineNum">    2122 </span><span class="lineNoCov">          0 :       goto EmitX86R;</span></a>
+<a name="2123"><span class="lineNum">    2123 </span>            : </a>
+<a name="2124"><span class="lineNum">    2124 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingX86Bndmov:</span></a>
+<a name="2125"><span class="lineNum">    2125 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2126"><span class="lineNum">    2126 </span>            :         opReg = o0.getId();</a>
+<a name="2127"><span class="lineNum">    2127 </span>            :         rbReg = o1.getId();</a>
+<a name="2128"><span class="lineNum">    2128 </span>            : </a>
+<a name="2129"><span class="lineNum">    2129 </span>            :         // ModRM encoding:</a>
+<a name="2130"><span class="lineNum">    2130 </span><span class="lineNoCov">          0 :         if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="2131"><span class="lineNum">    2131 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="2132"><span class="lineNum">    2132 </span>            : </a>
+<a name="2133"><span class="lineNum">    2133 </span>            :         // ModMR encoding:</a>
+<a name="2134"><span class="lineNum">    2134 </span>            :         opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2135"><span class="lineNum">    2135 </span>            :         std::swap(opReg, rbReg);</a>
+<a name="2136"><span class="lineNum">    2136 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2137"><span class="lineNum">    2137 </span>            :       }</a>
+<a name="2138"><span class="lineNum">    2138 </span>            : </a>
+<a name="2139"><span class="lineNum">    2139 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2140"><span class="lineNum">    2140 </span>            :         opReg = o0.getId();</a>
+<a name="2141"><span class="lineNum">    2141 </span>            :         rmRel = &amp;o1;</a>
+<a name="2142"><span class="lineNum">    2142 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2143"><span class="lineNum">    2143 </span>            :       }</a>
+<a name="2144"><span class="lineNum">    2144 </span>            : </a>
+<a name="2145"><span class="lineNum">    2145 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2146"><span class="lineNum">    2146 </span>            :         opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2147"><span class="lineNum">    2147 </span>            : </a>
+<a name="2148"><span class="lineNum">    2148 </span>            :         rmRel = &amp;o0;</a>
+<a name="2149"><span class="lineNum">    2149 </span>            :         opReg = o1.getId();</a>
+<a name="2150"><span class="lineNum">    2150 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2151"><span class="lineNum">    2151 </span>            :       }</a>
+<a name="2152"><span class="lineNum">    2152 </span>            :       break;</a>
+<a name="2153"><span class="lineNum">    2153 </span>            : </a>
+<a name="2154"><span class="lineNum">    2154 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2155"><span class="lineNum">    2155 </span>            :     // [FPU]</a>
+<a name="2156"><span class="lineNum">    2156 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2157"><span class="lineNum">    2157 </span>            : </a>
+<a name="2158"><span class="lineNum">    2158 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuOp:</span></a>
+<a name="2159"><span class="lineNum">    2159 </span><span class="lineNoCov">          0 :       goto EmitFpuOp;</span></a>
+<a name="2160"><span class="lineNum">    2160 </span>            : </a>
+<a name="2161"><span class="lineNum">    2161 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuArith:</span></a>
+<a name="2162"><span class="lineNum">    2162 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2163"><span class="lineNum">    2163 </span>            :         opReg = o0.getId();</a>
+<a name="2164"><span class="lineNum">    2164 </span>            :         rbReg = o1.getId();</a>
+<a name="2165"><span class="lineNum">    2165 </span>            : </a>
+<a name="2166"><span class="lineNum">    2166 </span>            :         // We switch to the alternative opcode if the first operand is zero.</a>
+<a name="2167"><span class="lineNum">    2167 </span><span class="lineNoCov">          0 :         if (opReg == 0) {</span></a>
+<a name="2168"><span class="lineNum">    2168 </span><span class="lineNoCov">          0 : CaseFpuArith_Reg:</span></a>
+<a name="2169"><span class="lineNum">    2169 </span><span class="lineNoCov">          0 :           opCode = ((0xD8   &lt;&lt; X86Inst::kOpCode_FPU_2B_Shift)       ) +</span></a>
+<a name="2170"><span class="lineNum">    2170 </span><span class="lineNoCov">          0 :                    ((opCode &gt;&gt; X86Inst::kOpCode_FPU_2B_Shift) &amp; 0xFF) + rbReg;</span></a>
+<a name="2171"><span class="lineNum">    2171 </span><span class="lineNoCov">          0 :           goto EmitFpuOp;</span></a>
+<a name="2172"><span class="lineNum">    2172 </span>            :         }</a>
+<a name="2173"><span class="lineNum">    2173 </span><span class="lineNoCov">          0 :         else if (rbReg == 0) {</span></a>
+<a name="2174"><span class="lineNum">    2174 </span>            :           rbReg = opReg;</a>
+<a name="2175"><span class="lineNum">    2175 </span><span class="lineNoCov">          0 :           opCode = ((0xDC   &lt;&lt; X86Inst::kOpCode_FPU_2B_Shift)       ) +</span></a>
+<a name="2176"><span class="lineNum">    2176 </span><span class="lineNoCov">          0 :                    ((opCode                                 ) &amp; 0xFF) + rbReg;</span></a>
+<a name="2177"><span class="lineNum">    2177 </span><span class="lineNoCov">          0 :           goto EmitFpuOp;</span></a>
+<a name="2178"><span class="lineNum">    2178 </span>            :         }</a>
+<a name="2179"><span class="lineNum">    2179 </span>            :         else {</a>
+<a name="2180"><span class="lineNum">    2180 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="2181"><span class="lineNum">    2181 </span>            :         }</a>
+<a name="2182"><span class="lineNum">    2182 </span>            :       }</a>
+<a name="2183"><span class="lineNum">    2183 </span>            : </a>
+<a name="2184"><span class="lineNum">    2184 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2185"><span class="lineNum">    2185 </span><span class="lineNoCov">          0 : CaseFpuArith_Mem:</span></a>
+<a name="2186"><span class="lineNum">    2186 </span>            :         // 0xD8/0xDC, depends on the size of the memory operand; opReg is valid.</a>
+<a name="2187"><span class="lineNum">    2187 </span><span class="lineNoCov">          0 :         opCode = (o0.getSize() == 4) ? 0xD8 : 0xDC;</span></a>
+<a name="2188"><span class="lineNum">    2188 </span>            :         // Clear compressed displacement before going to EmitX86M.</a>
+<a name="2189"><span class="lineNum">    2189 </span><span class="lineNoCov">          0 :         opCode &amp;= ~static_cast&lt;uint32_t&gt;(X86Inst::kOpCode_CDSHL_Mask);</span></a>
+<a name="2190"><span class="lineNum">    2190 </span>            : </a>
+<a name="2191"><span class="lineNum">    2191 </span>            :         rmRel = &amp;o0;</a>
+<a name="2192"><span class="lineNum">    2192 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2193"><span class="lineNum">    2193 </span>            :       }</a>
+<a name="2194"><span class="lineNum">    2194 </span>            :       break;</a>
+<a name="2195"><span class="lineNum">    2195 </span>            : </a>
+<a name="2196"><span class="lineNum">    2196 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuCom:</span></a>
+<a name="2197"><span class="lineNum">    2197 </span><span class="lineNoCov">          0 :       if (isign3 == 0) {</span></a>
+<a name="2198"><span class="lineNum">    2198 </span>            :         rbReg = 1;</a>
+<a name="2199"><span class="lineNum">    2199 </span><span class="lineNoCov">          0 :         goto CaseFpuArith_Reg;</span></a>
+<a name="2200"><span class="lineNum">    2200 </span>            :       }</a>
+<a name="2201"><span class="lineNum">    2201 </span>            : </a>
+<a name="2202"><span class="lineNum">    2202 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="2203"><span class="lineNum">    2203 </span>            :         rbReg = o0.getId();</a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineNoCov">          0 :         goto CaseFpuArith_Reg;</span></a>
+<a name="2205"><span class="lineNum">    2205 </span>            :       }</a>
+<a name="2206"><span class="lineNum">    2206 </span>            : </a>
+<a name="2207"><span class="lineNum">    2207 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2208"><span class="lineNum">    2208 </span><span class="lineNoCov">          0 :         goto CaseFpuArith_Mem;</span></a>
+<a name="2209"><span class="lineNum">    2209 </span>            :       }</a>
+<a name="2210"><span class="lineNum">    2210 </span>            :       break;</a>
+<a name="2211"><span class="lineNum">    2211 </span>            : </a>
+<a name="2212"><span class="lineNum">    2212 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuFldFst:</span></a>
+<a name="2213"><span class="lineNum">    2213 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2214"><span class="lineNum">    2214 </span>            :         rmRel = &amp;o0;</a>
+<a name="2215"><span class="lineNum">    2215 </span>            : </a>
+<a name="2216"><span class="lineNum">    2216 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 4 &amp;&amp; commonData-&gt;hasFlag(X86Inst::kFlagFpuM32)) {</span></a>
+<a name="2217"><span class="lineNum">    2217 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2218"><span class="lineNum">    2218 </span>            :         }</a>
+<a name="2219"><span class="lineNum">    2219 </span>            : </a>
+<a name="2220"><span class="lineNum">    2220 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 8 &amp;&amp; commonData-&gt;hasFlag(X86Inst::kFlagFpuM64)) {</span></a>
+<a name="2221"><span class="lineNum">    2221 </span><span class="lineNoCov">          0 :           opCode += 4;</span></a>
+<a name="2222"><span class="lineNum">    2222 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2223"><span class="lineNum">    2223 </span>            :         }</a>
+<a name="2224"><span class="lineNum">    2224 </span>            : </a>
+<a name="2225"><span class="lineNum">    2225 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 10 &amp;&amp; commonData-&gt;hasFlag(X86Inst::kFlagFpuM80)) {</span></a>
+<a name="2226"><span class="lineNum">    2226 </span>            :           opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2227"><span class="lineNum">    2227 </span>            :           opReg  = x86ExtractO(opCode);</a>
+<a name="2228"><span class="lineNum">    2228 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2229"><span class="lineNum">    2229 </span>            :         }</a>
+<a name="2230"><span class="lineNum">    2230 </span>            :       }</a>
+<a name="2231"><span class="lineNum">    2231 </span>            : </a>
+<a name="2232"><span class="lineNum">    2232 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="2233"><span class="lineNum">    2233 </span><span class="lineNoCov">          0 :         if (instId == X86Inst::kIdFld ) { opCode = (0xD9 &lt;&lt; X86Inst::kOpCode_FPU_2B_Shift) + 0xC0 + o0.getId(); goto EmitFpuOp; }</span></a>
+<a name="2234"><span class="lineNum">    2234 </span><span class="lineNoCov">          0 :         if (instId == X86Inst::kIdFst ) { opCode = (0xDD &lt;&lt; X86Inst::kOpCode_FPU_2B_Shift) + 0xD0 + o0.getId(); goto EmitFpuOp; }</span></a>
+<a name="2235"><span class="lineNum">    2235 </span><span class="lineNoCov">          0 :         if (instId == X86Inst::kIdFstp) { opCode = (0xDD &lt;&lt; X86Inst::kOpCode_FPU_2B_Shift) + 0xD8 + o0.getId(); goto EmitFpuOp; }</span></a>
+<a name="2236"><span class="lineNum">    2236 </span>            :       }</a>
+<a name="2237"><span class="lineNum">    2237 </span>            :       break;</a>
+<a name="2238"><span class="lineNum">    2238 </span>            : </a>
+<a name="2239"><span class="lineNum">    2239 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuM:</span></a>
+<a name="2240"><span class="lineNum">    2240 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2241"><span class="lineNum">    2241 </span>            :         // Clear compressed displacement before going to EmitX86M.</a>
+<a name="2242"><span class="lineNum">    2242 </span><span class="lineNoCov">          0 :         opCode &amp;= ~static_cast&lt;uint32_t&gt;(X86Inst::kOpCode_CDSHL_Mask);</span></a>
+<a name="2243"><span class="lineNum">    2243 </span>            : </a>
+<a name="2244"><span class="lineNum">    2244 </span>            :         rmRel = &amp;o0;</a>
+<a name="2245"><span class="lineNum">    2245 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 2 &amp;&amp; commonData-&gt;hasFlag(X86Inst::kFlagFpuM16)) {</span></a>
+<a name="2246"><span class="lineNum">    2246 </span><span class="lineNoCov">          0 :           opCode += 4;</span></a>
+<a name="2247"><span class="lineNum">    2247 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2248"><span class="lineNum">    2248 </span>            :         }</a>
+<a name="2249"><span class="lineNum">    2249 </span>            : </a>
+<a name="2250"><span class="lineNum">    2250 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 4 &amp;&amp; commonData-&gt;hasFlag(X86Inst::kFlagFpuM32)) {</span></a>
+<a name="2251"><span class="lineNum">    2251 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2252"><span class="lineNum">    2252 </span>            :         }</a>
+<a name="2253"><span class="lineNum">    2253 </span>            : </a>
+<a name="2254"><span class="lineNum">    2254 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 8 &amp;&amp; commonData-&gt;hasFlag(X86Inst::kFlagFpuM64)) {</span></a>
+<a name="2255"><span class="lineNum">    2255 </span><span class="lineNoCov">          0 :           opCode = commonData-&gt;getAltOpCode() &amp; ~static_cast&lt;uint32_t&gt;(X86Inst::kOpCode_CDSHL_Mask);</span></a>
+<a name="2256"><span class="lineNum">    2256 </span>            :           opReg  = x86ExtractO(opCode);</a>
+<a name="2257"><span class="lineNum">    2257 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2258"><span class="lineNum">    2258 </span>            :         }</a>
+<a name="2259"><span class="lineNum">    2259 </span>            :       }</a>
+<a name="2260"><span class="lineNum">    2260 </span>            :       break;</a>
+<a name="2261"><span class="lineNum">    2261 </span>            : </a>
+<a name="2262"><span class="lineNum">    2262 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuRDef:</span></a>
+<a name="2263"><span class="lineNum">    2263 </span><span class="lineNoCov">          0 :       if (isign3 == 0) {</span></a>
+<a name="2264"><span class="lineNum">    2264 </span><span class="lineNoCov">          0 :         opCode += 1;</span></a>
+<a name="2265"><span class="lineNum">    2265 </span><span class="lineNoCov">          0 :         goto EmitFpuOp;</span></a>
+<a name="2266"><span class="lineNum">    2266 </span>            :       }</a>
+<a name="2267"><span class="lineNum">    2267 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2268"><span class="lineNum">    2268 </span>            : </a>
+<a name="2269"><span class="lineNum">    2269 </span>            :     case X86Inst::kEncodingFpuR:</a>
+<a name="2270"><span class="lineNum">    2270 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="2271"><span class="lineNum">    2271 </span><span class="lineNoCov">          0 :         opCode += o0.getId();</span></a>
+<a name="2272"><span class="lineNum">    2272 </span><span class="lineNoCov">          0 :         goto EmitFpuOp;</span></a>
+<a name="2273"><span class="lineNum">    2273 </span>            :       }</a>
+<a name="2274"><span class="lineNum">    2274 </span>            :       break;</a>
+<a name="2275"><span class="lineNum">    2275 </span>            : </a>
+<a name="2276"><span class="lineNum">    2276 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFpuStsw:</span></a>
+<a name="2277"><span class="lineNum">    2277 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Reg)) {</span></a>
+<a name="2278"><span class="lineNum">    2278 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(o0.getId() != X86Gp::kIdAx))</span></a>
+<a name="2279"><span class="lineNum">    2279 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="2280"><span class="lineNum">    2280 </span>            : </a>
+<a name="2281"><span class="lineNum">    2281 </span>            :         opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2282"><span class="lineNum">    2282 </span><span class="lineNoCov">          0 :         goto EmitFpuOp;</span></a>
+<a name="2283"><span class="lineNum">    2283 </span>            :       }</a>
+<a name="2284"><span class="lineNum">    2284 </span>            : </a>
+<a name="2285"><span class="lineNum">    2285 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2286"><span class="lineNum">    2286 </span>            :         // Clear compressed displacement before going to EmitX86M.</a>
+<a name="2287"><span class="lineNum">    2287 </span><span class="lineNoCov">          0 :         opCode &amp;= ~static_cast&lt;uint32_t&gt;(X86Inst::kOpCode_CDSHL_Mask);</span></a>
+<a name="2288"><span class="lineNum">    2288 </span>            : </a>
+<a name="2289"><span class="lineNum">    2289 </span>            :         rmRel = &amp;o0;</a>
+<a name="2290"><span class="lineNum">    2290 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2291"><span class="lineNum">    2291 </span>            :       }</a>
+<a name="2292"><span class="lineNum">    2292 </span>            :       break;</a>
+<a name="2293"><span class="lineNum">    2293 </span>            : </a>
+<a name="2294"><span class="lineNum">    2294 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2295"><span class="lineNum">    2295 </span>            :     // [Ext]</a>
+<a name="2296"><span class="lineNum">    2296 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2297"><span class="lineNum">    2297 </span>            : </a>
+<a name="2298"><span class="lineNum">    2298 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtPextrw:</span></a>
+<a name="2299"><span class="lineNum">    2299 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="2300"><span class="lineNum">    2300 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o1));</span></a>
+<a name="2301"><span class="lineNum">    2301 </span>            : </a>
+<a name="2302"><span class="lineNum">    2302 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2303"><span class="lineNum">    2303 </span>            :         imLen = 1;</a>
+<a name="2304"><span class="lineNum">    2304 </span>            : </a>
+<a name="2305"><span class="lineNum">    2305 </span>            :         opReg = o0.getId();</a>
+<a name="2306"><span class="lineNum">    2306 </span>            :         rbReg = o1.getId();</a>
+<a name="2307"><span class="lineNum">    2307 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2308"><span class="lineNum">    2308 </span>            :       }</a>
+<a name="2309"><span class="lineNum">    2309 </span>            : </a>
+<a name="2310"><span class="lineNum">    2310 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Mem, Reg, Imm)) {</span></a>
+<a name="2311"><span class="lineNum">    2311 </span>            :         // Secondary opcode of 'pextrw' instruction (SSE4.1).</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :         opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2313"><span class="lineNum">    2313 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o1));</span></a>
+<a name="2314"><span class="lineNum">    2314 </span>            : </a>
+<a name="2315"><span class="lineNum">    2315 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2316"><span class="lineNum">    2316 </span>            :         imLen = 1;</a>
+<a name="2317"><span class="lineNum">    2317 </span>            : </a>
+<a name="2318"><span class="lineNum">    2318 </span>            :         opReg = o1.getId();</a>
+<a name="2319"><span class="lineNum">    2319 </span>            :         rmRel = &amp;o0;</a>
+<a name="2320"><span class="lineNum">    2320 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2321"><span class="lineNum">    2321 </span>            :       }</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :       break;</a>
+<a name="2323"><span class="lineNum">    2323 </span>            : </a>
+<a name="2324"><span class="lineNum">    2324 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtExtract:</span></a>
+<a name="2325"><span class="lineNum">    2325 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="2326"><span class="lineNum">    2326 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o1));</span></a>
+<a name="2327"><span class="lineNum">    2327 </span>            : </a>
+<a name="2328"><span class="lineNum">    2328 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2329"><span class="lineNum">    2329 </span>            :         imLen = 1;</a>
+<a name="2330"><span class="lineNum">    2330 </span>            : </a>
+<a name="2331"><span class="lineNum">    2331 </span>            :         opReg = o1.getId();</a>
+<a name="2332"><span class="lineNum">    2332 </span>            :         rbReg = o0.getId();</a>
+<a name="2333"><span class="lineNum">    2333 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2334"><span class="lineNum">    2334 </span>            :       }</a>
+<a name="2335"><span class="lineNum">    2335 </span>            : </a>
+<a name="2336"><span class="lineNum">    2336 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Mem, Reg, Imm)) {</span></a>
+<a name="2337"><span class="lineNum">    2337 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o1));</span></a>
+<a name="2338"><span class="lineNum">    2338 </span>            : </a>
+<a name="2339"><span class="lineNum">    2339 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2340"><span class="lineNum">    2340 </span>            :         imLen = 1;</a>
+<a name="2341"><span class="lineNum">    2341 </span>            : </a>
+<a name="2342"><span class="lineNum">    2342 </span>            :         opReg = o1.getId();</a>
+<a name="2343"><span class="lineNum">    2343 </span>            :         rmRel = &amp;o0;</a>
+<a name="2344"><span class="lineNum">    2344 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2345"><span class="lineNum">    2345 </span>            :       }</a>
+<a name="2346"><span class="lineNum">    2346 </span>            :       break;</a>
+<a name="2347"><span class="lineNum">    2347 </span>            : </a>
+<a name="2348"><span class="lineNum">    2348 </span><span class="lineCov">      23848 :     case X86Inst::kEncodingExtMov:</span></a>
+<a name="2349"><span class="lineNum">    2349 </span>            :       // GP|MMX|XMM &lt;- GP|MMX|XMM</a>
+<a name="2350"><span class="lineNum">    2350 </span><span class="lineCov">      23848 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2351"><span class="lineNum">    2351 </span>            :         opReg = o0.getId();</a>
+<a name="2352"><span class="lineNum">    2352 </span>            :         rbReg = o1.getId();</a>
+<a name="2353"><span class="lineNum">    2353 </span>            : </a>
+<a name="2354"><span class="lineNum">    2354 </span><span class="lineCov">       9320 :         if (!(options &amp; X86Inst::kOptionModMR) || !commonData-&gt;hasAltOpCode())</span></a>
+<a name="2355"><span class="lineNum">    2355 </span><span class="lineCov">       9320 :           goto EmitX86R;</span></a>
+<a name="2356"><span class="lineNum">    2356 </span>            : </a>
+<a name="2357"><span class="lineNum">    2357 </span>            :         opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2358"><span class="lineNum">    2358 </span>            :         Utils::swap(opReg, rbReg);</a>
+<a name="2359"><span class="lineNum">    2359 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2360"><span class="lineNum">    2360 </span>            :       }</a>
+<a name="2361"><span class="lineNum">    2361 </span>            : </a>
+<a name="2362"><span class="lineNum">    2362 </span>            :       // GP|MMX|XMM &lt;- Mem</a>
+<a name="2363"><span class="lineNum">    2363 </span><span class="lineCov">      14528 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2364"><span class="lineNum">    2364 </span>            :         opReg = o0.getId();</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :         rmRel = &amp;o1;</a>
+<a name="2366"><span class="lineNum">    2366 </span><span class="lineCov">      10258 :         goto EmitX86M;</span></a>
+<a name="2367"><span class="lineNum">    2367 </span>            :       }</a>
+<a name="2368"><span class="lineNum">    2368 </span>            : </a>
+<a name="2369"><span class="lineNum">    2369 </span>            :       // The following instruction uses opCode[1].</a>
+<a name="2370"><span class="lineNum">    2370 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2371"><span class="lineNum">    2371 </span>            : </a>
+<a name="2372"><span class="lineNum">    2372 </span>            :       // Mem &lt;- GP|MMX|XMM</a>
+<a name="2373"><span class="lineNum">    2373 </span><span class="lineCov">       4270 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2374"><span class="lineNum">    2374 </span>            :         opReg = o1.getId();</a>
+<a name="2375"><span class="lineNum">    2375 </span>            :         rmRel = &amp;o0;</a>
+<a name="2376"><span class="lineNum">    2376 </span><span class="lineCov">       4270 :         goto EmitX86M;</span></a>
+<a name="2377"><span class="lineNum">    2377 </span>            :       }</a>
+<a name="2378"><span class="lineNum">    2378 </span>            :       break;</a>
+<a name="2379"><span class="lineNum">    2379 </span>            : </a>
+<a name="2380"><span class="lineNum">    2380 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtMovnti:</span></a>
+<a name="2381"><span class="lineNum">    2381 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2382"><span class="lineNum">    2382 </span><span class="lineNoCov">          0 :         ADD_REX_W(X86Reg::isGpq(o1));</span></a>
+<a name="2383"><span class="lineNum">    2383 </span>            : </a>
+<a name="2384"><span class="lineNum">    2384 </span>            :         opReg = o1.getId();</a>
+<a name="2385"><span class="lineNum">    2385 </span>            :         rmRel = &amp;o0;</a>
+<a name="2386"><span class="lineNum">    2386 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2387"><span class="lineNum">    2387 </span>            :       }</a>
+<a name="2388"><span class="lineNum">    2388 </span>            :       break;</a>
+<a name="2389"><span class="lineNum">    2389 </span>            : </a>
+<a name="2390"><span class="lineNum">    2390 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtMovbe:</span></a>
+<a name="2391"><span class="lineNum">    2391 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2392"><span class="lineNum">    2392 </span><span class="lineNoCov">          0 :         if (o0.getSize() == 1)</span></a>
+<a name="2393"><span class="lineNum">    2393 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="2394"><span class="lineNum">    2394 </span>            : </a>
+<a name="2395"><span class="lineNum">    2395 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o0.getSize());</span></a>
+<a name="2396"><span class="lineNum">    2396 </span>            :         opReg = o0.getId();</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :         rmRel = &amp;o1;</a>
+<a name="2398"><span class="lineNum">    2398 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2399"><span class="lineNum">    2399 </span>            :       }</a>
+<a name="2400"><span class="lineNum">    2400 </span>            : </a>
+<a name="2401"><span class="lineNum">    2401 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="2402"><span class="lineNum">    2402 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2403"><span class="lineNum">    2403 </span>            : </a>
+<a name="2404"><span class="lineNum">    2404 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2405"><span class="lineNum">    2405 </span><span class="lineNoCov">          0 :         if (o1.getSize() == 1)</span></a>
+<a name="2406"><span class="lineNum">    2406 </span><span class="lineNoCov">          0 :           goto InvalidInstruction;</span></a>
+<a name="2407"><span class="lineNum">    2407 </span>            : </a>
+<a name="2408"><span class="lineNum">    2408 </span><span class="lineNoCov">          0 :         ADD_PREFIX_BY_SIZE(o1.getSize());</span></a>
+<a name="2409"><span class="lineNum">    2409 </span>            :         opReg = o1.getId();</a>
+<a name="2410"><span class="lineNum">    2410 </span>            :         rmRel = &amp;o0;</a>
+<a name="2411"><span class="lineNum">    2411 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2412"><span class="lineNum">    2412 </span>            :       }</a>
+<a name="2413"><span class="lineNum">    2413 </span>            :       break;</a>
+<a name="2414"><span class="lineNum">    2414 </span>            : </a>
+<a name="2415"><span class="lineNum">    2415 </span>            :     case X86Inst::kEncodingExtMovd:</a>
+<a name="2416"><span class="lineNum">    2416 </span><span class="lineNoCov">          0 : CaseExtMovd:</span></a>
+<a name="2417"><span class="lineNum">    2417 </span>            :       opReg = o0.getId();</a>
+<a name="2418"><span class="lineNum">    2418 </span><span class="lineNoCov">          0 :       ADD_66H_P(X86Reg::isXmm(o0));</span></a>
+<a name="2419"><span class="lineNum">    2419 </span>            : </a>
+<a name="2420"><span class="lineNum">    2420 </span>            :       // MMX/XMM &lt;- Gp</a>
+<a name="2421"><span class="lineNum">    2421 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg) &amp;&amp; X86Reg::isGp(o1)) {</span></a>
+<a name="2422"><span class="lineNum">    2422 </span>            :         rbReg = o1.getId();</a>
+<a name="2423"><span class="lineNum">    2423 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2424"><span class="lineNum">    2424 </span>            :       }</a>
+<a name="2425"><span class="lineNum">    2425 </span>            : </a>
+<a name="2426"><span class="lineNum">    2426 </span>            :       // MMX/XMM &lt;- Mem</a>
+<a name="2427"><span class="lineNum">    2427 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2428"><span class="lineNum">    2428 </span>            :         rmRel = &amp;o1;</a>
+<a name="2429"><span class="lineNum">    2429 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2430"><span class="lineNum">    2430 </span>            :       }</a>
+<a name="2431"><span class="lineNum">    2431 </span>            : </a>
+<a name="2432"><span class="lineNum">    2432 </span>            :       // The following instructions use the secondary opcode.</a>
+<a name="2433"><span class="lineNum">    2433 </span><span class="lineNoCov">          0 :       opCode &amp;= X86Inst::kOpCode_W;</span></a>
+<a name="2434"><span class="lineNum">    2434 </span><span class="lineNoCov">          0 :       opCode |= commonData-&gt;getAltOpCode();</span></a>
+<a name="2435"><span class="lineNum">    2435 </span>            :       opReg = o1.getId();</a>
+<a name="2436"><span class="lineNum">    2436 </span><span class="lineNoCov">          0 :       ADD_66H_P(X86Reg::isXmm(o1));</span></a>
+<a name="2437"><span class="lineNum">    2437 </span>            : </a>
+<a name="2438"><span class="lineNum">    2438 </span>            :       // GP &lt;- MMX/XMM</a>
+<a name="2439"><span class="lineNum">    2439 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg) &amp;&amp; X86Reg::isGp(o0)) {</span></a>
+<a name="2440"><span class="lineNum">    2440 </span>            :         rbReg = o0.getId();</a>
+<a name="2441"><span class="lineNum">    2441 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2442"><span class="lineNum">    2442 </span>            :       }</a>
+<a name="2443"><span class="lineNum">    2443 </span>            : </a>
+<a name="2444"><span class="lineNum">    2444 </span>            :       // Mem &lt;- MMX/XMM</a>
+<a name="2445"><span class="lineNum">    2445 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2446"><span class="lineNum">    2446 </span>            :         rmRel = &amp;o0;</a>
+<a name="2447"><span class="lineNum">    2447 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2448"><span class="lineNum">    2448 </span>            :       }</a>
+<a name="2449"><span class="lineNum">    2449 </span>            :       break;</a>
+<a name="2450"><span class="lineNum">    2450 </span>            : </a>
+<a name="2451"><span class="lineNum">    2451 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtMovq:</span></a>
+<a name="2452"><span class="lineNum">    2452 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2453"><span class="lineNum">    2453 </span>            :         opReg = o0.getId();</a>
+<a name="2454"><span class="lineNum">    2454 </span>            :         rbReg = o1.getId();</a>
+<a name="2455"><span class="lineNum">    2455 </span>            : </a>
+<a name="2456"><span class="lineNum">    2456 </span>            :         // MMX &lt;- MMX</a>
+<a name="2457"><span class="lineNum">    2457 </span><span class="lineNoCov">          0 :         if (X86Reg::isMm(o0) &amp;&amp; X86Reg::isMm(o1)) {</span></a>
+<a name="2458"><span class="lineNum">    2458 </span>            :           opCode = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F | 0x6F;</a>
+<a name="2459"><span class="lineNum">    2459 </span>            : </a>
+<a name="2460"><span class="lineNum">    2460 </span><span class="lineNoCov">          0 :           if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="2461"><span class="lineNum">    2461 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="2462"><span class="lineNum">    2462 </span>            : </a>
+<a name="2463"><span class="lineNum">    2463 </span>            :           opCode += 0x10;</a>
+<a name="2464"><span class="lineNum">    2464 </span>            :           Utils::swap(opReg, rbReg);</a>
+<a name="2465"><span class="lineNum">    2465 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="2466"><span class="lineNum">    2466 </span>            :         }</a>
+<a name="2467"><span class="lineNum">    2467 </span>            : </a>
+<a name="2468"><span class="lineNum">    2468 </span>            :         // XMM &lt;- XMM</a>
+<a name="2469"><span class="lineNum">    2469 </span><span class="lineNoCov">          0 :         if (X86Reg::isXmm(o0) &amp;&amp; X86Reg::isXmm(o1)) {</span></a>
+<a name="2470"><span class="lineNum">    2470 </span>            :           opCode = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_0F | 0x7E;</a>
+<a name="2471"><span class="lineNum">    2471 </span>            : </a>
+<a name="2472"><span class="lineNum">    2472 </span><span class="lineNoCov">          0 :           if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="2473"><span class="lineNum">    2473 </span><span class="lineNoCov">          0 :             goto EmitX86R;</span></a>
+<a name="2474"><span class="lineNum">    2474 </span>            : </a>
+<a name="2475"><span class="lineNum">    2475 </span>            :           opCode = X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_MM_0F | 0xD6;</a>
+<a name="2476"><span class="lineNum">    2476 </span>            :           Utils::swap(opReg, rbReg);</a>
+<a name="2477"><span class="lineNum">    2477 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="2478"><span class="lineNum">    2478 </span>            :         }</a>
+<a name="2479"><span class="lineNum">    2479 </span>            : </a>
+<a name="2480"><span class="lineNum">    2480 </span>            :         // MMX &lt;- XMM (MOVDQ2Q)</a>
+<a name="2481"><span class="lineNum">    2481 </span><span class="lineNoCov">          0 :         if (X86Reg::isMm(o0) &amp;&amp; X86Reg::isXmm(o1)) {</span></a>
+<a name="2482"><span class="lineNum">    2482 </span>            :           opCode = X86Inst::kOpCode_PP_F2 | X86Inst::kOpCode_MM_0F | 0xD6;</a>
+<a name="2483"><span class="lineNum">    2483 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="2484"><span class="lineNum">    2484 </span>            :         }</a>
+<a name="2485"><span class="lineNum">    2485 </span>            : </a>
+<a name="2486"><span class="lineNum">    2486 </span>            :         // XMM &lt;- MMX (MOVQ2DQ)</a>
+<a name="2487"><span class="lineNum">    2487 </span><span class="lineNoCov">          0 :         if (X86Reg::isXmm(o0) &amp;&amp; X86Reg::isMm(o1)) {</span></a>
+<a name="2488"><span class="lineNum">    2488 </span>            :           opCode = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_0F | 0xD6;</a>
+<a name="2489"><span class="lineNum">    2489 </span><span class="lineNoCov">          0 :           goto EmitX86R;</span></a>
+<a name="2490"><span class="lineNum">    2490 </span>            :         }</a>
+<a name="2491"><span class="lineNum">    2491 </span>            :       }</a>
+<a name="2492"><span class="lineNum">    2492 </span>            : </a>
+<a name="2493"><span class="lineNum">    2493 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2494"><span class="lineNum">    2494 </span>            :         opReg = o0.getId();</a>
+<a name="2495"><span class="lineNum">    2495 </span>            :         rmRel = &amp;o1;</a>
+<a name="2496"><span class="lineNum">    2496 </span>            : </a>
+<a name="2497"><span class="lineNum">    2497 </span>            :         // MMX &lt;- Mem</a>
+<a name="2498"><span class="lineNum">    2498 </span><span class="lineNoCov">          0 :         if (X86Reg::isMm(o0)) {</span></a>
+<a name="2499"><span class="lineNum">    2499 </span>            :           opCode = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F | 0x6F;</a>
+<a name="2500"><span class="lineNum">    2500 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2501"><span class="lineNum">    2501 </span>            :         }</a>
+<a name="2502"><span class="lineNum">    2502 </span>            : </a>
+<a name="2503"><span class="lineNum">    2503 </span>            :         // XMM &lt;- Mem</a>
+<a name="2504"><span class="lineNum">    2504 </span><span class="lineNoCov">          0 :         if (X86Reg::isXmm(o0)) {</span></a>
+<a name="2505"><span class="lineNum">    2505 </span>            :           opCode = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_0F | 0x7E;</a>
+<a name="2506"><span class="lineNum">    2506 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2507"><span class="lineNum">    2507 </span>            :         }</a>
+<a name="2508"><span class="lineNum">    2508 </span>            :       }</a>
+<a name="2509"><span class="lineNum">    2509 </span>            : </a>
+<a name="2510"><span class="lineNum">    2510 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2511"><span class="lineNum">    2511 </span>            :         opReg = o1.getId();</a>
+<a name="2512"><span class="lineNum">    2512 </span>            :         rmRel = &amp;o0;</a>
+<a name="2513"><span class="lineNum">    2513 </span>            : </a>
+<a name="2514"><span class="lineNum">    2514 </span>            :         // Mem &lt;- MMX</a>
+<a name="2515"><span class="lineNum">    2515 </span><span class="lineNoCov">          0 :         if (X86Reg::isMm(o1)) {</span></a>
+<a name="2516"><span class="lineNum">    2516 </span>            :           opCode = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F | 0x7F;</a>
+<a name="2517"><span class="lineNum">    2517 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2518"><span class="lineNum">    2518 </span>            :         }</a>
+<a name="2519"><span class="lineNum">    2519 </span>            : </a>
+<a name="2520"><span class="lineNum">    2520 </span>            :         // Mem &lt;- XMM</a>
+<a name="2521"><span class="lineNum">    2521 </span><span class="lineNoCov">          0 :         if (X86Reg::isXmm(o1)) {</span></a>
+<a name="2522"><span class="lineNum">    2522 </span>            :           opCode = X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_MM_0F | 0xD6;</a>
+<a name="2523"><span class="lineNum">    2523 </span><span class="lineNoCov">          0 :           goto EmitX86M;</span></a>
+<a name="2524"><span class="lineNum">    2524 </span>            :         }</a>
+<a name="2525"><span class="lineNum">    2525 </span>            :       }</a>
+<a name="2526"><span class="lineNum">    2526 </span>            : </a>
+<a name="2527"><span class="lineNum">    2527 </span>            :       // MOVQ in other case is simply a MOVD instruction promoted to 64-bit.</a>
+<a name="2528"><span class="lineNum">    2528 </span><span class="lineNoCov">          0 :       opCode |= X86Inst::kOpCode_W;</span></a>
+<a name="2529"><span class="lineNum">    2529 </span><span class="lineNoCov">          0 :       goto CaseExtMovd;</span></a>
+<a name="2530"><span class="lineNum">    2530 </span>            : </a>
+<a name="2531"><span class="lineNum">    2531 </span>            :     case X86Inst::kEncodingExtRm_XMM0:</a>
+<a name="2532"><span class="lineNum">    2532 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!o2.isNone() &amp;&amp; !X86Reg::isXmm(o2, 0)))</span></a>
+<a name="2533"><span class="lineNum">    2533 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="2534"><span class="lineNum">    2534 </span>            : </a>
+<a name="2535"><span class="lineNum">    2535 </span><span class="lineNoCov">          0 :       isign3 &amp;= 0x3F;</span></a>
+<a name="2536"><span class="lineNum">    2536 </span><span class="lineNoCov">          0 :       goto CaseExtRm;</span></a>
+<a name="2537"><span class="lineNum">    2537 </span>            : </a>
+<a name="2538"><span class="lineNum">    2538 </span>            :     case X86Inst::kEncodingExtRm_ZDI:</a>
+<a name="2539"><span class="lineNum">    2539 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!o2.isNone() &amp;&amp; !x86IsImplicitMem(o2, X86Gp::kIdDi)))</span></a>
+<a name="2540"><span class="lineNum">    2540 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="2541"><span class="lineNum">    2541 </span>            : </a>
+<a name="2542"><span class="lineNum">    2542 </span><span class="lineNoCov">          0 :       isign3 &amp;= 0x3F;</span></a>
+<a name="2543"><span class="lineNum">    2543 </span><span class="lineNoCov">          0 :       goto CaseExtRm;</span></a>
+<a name="2544"><span class="lineNum">    2544 </span>            : </a>
+<a name="2545"><span class="lineNum">    2545 </span>            :     case X86Inst::kEncodingExtRm_Wx:</a>
+<a name="2546"><span class="lineNum">    2546 </span><span class="lineNoCov">          0 :       ADD_REX_W(X86Reg::isGpq(o0) || o1.getSize() == 8);</span></a>
+<a name="2547"><span class="lineNum">    2547 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2548"><span class="lineNum">    2548 </span>            : </a>
+<a name="2549"><span class="lineNum">    2549 </span>            :     case X86Inst::kEncodingExtRm:</a>
+<a name="2550"><span class="lineNum">    2550 </span><span class="lineCov">       9006 : CaseExtRm:</span></a>
+<a name="2551"><span class="lineNum">    2551 </span><span class="lineCov">       9006 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2552"><span class="lineNum">    2552 </span>            :         opReg = o0.getId();</a>
+<a name="2553"><span class="lineNum">    2553 </span>            :         rbReg = o1.getId();</a>
+<a name="2554"><span class="lineNum">    2554 </span><span class="lineCov">       9006 :         goto EmitX86R;</span></a>
+<a name="2555"><span class="lineNum">    2555 </span>            :       }</a>
+<a name="2556"><span class="lineNum">    2556 </span>            : </a>
+<a name="2557"><span class="lineNum">    2557 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2558"><span class="lineNum">    2558 </span>            :         opReg = o0.getId();</a>
+<a name="2559"><span class="lineNum">    2559 </span>            :         rmRel = &amp;o1;</a>
+<a name="2560"><span class="lineNum">    2560 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2561"><span class="lineNum">    2561 </span>            :       }</a>
+<a name="2562"><span class="lineNum">    2562 </span>            :       break;</a>
+<a name="2563"><span class="lineNum">    2563 </span>            : </a>
+<a name="2564"><span class="lineNum">    2564 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtRm_P:</span></a>
+<a name="2565"><span class="lineNum">    2565 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2566"><span class="lineNum">    2566 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0) | X86Reg::isXmm(o1));</span></a>
+<a name="2567"><span class="lineNum">    2567 </span>            : </a>
+<a name="2568"><span class="lineNum">    2568 </span>            :         opReg = o0.getId();</a>
+<a name="2569"><span class="lineNum">    2569 </span>            :         rbReg = o1.getId();</a>
+<a name="2570"><span class="lineNum">    2570 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2571"><span class="lineNum">    2571 </span>            :       }</a>
+<a name="2572"><span class="lineNum">    2572 </span>            : </a>
+<a name="2573"><span class="lineNum">    2573 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2574"><span class="lineNum">    2574 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0));</span></a>
+<a name="2575"><span class="lineNum">    2575 </span>            : </a>
+<a name="2576"><span class="lineNum">    2576 </span>            :         opReg = o0.getId();</a>
+<a name="2577"><span class="lineNum">    2577 </span>            :         rmRel = &amp;o1;</a>
+<a name="2578"><span class="lineNum">    2578 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2579"><span class="lineNum">    2579 </span>            :       }</a>
+<a name="2580"><span class="lineNum">    2580 </span>            :       break;</a>
+<a name="2581"><span class="lineNum">    2581 </span>            : </a>
+<a name="2582"><span class="lineNum">    2582 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtRmRi:</span></a>
+<a name="2583"><span class="lineNum">    2583 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2584"><span class="lineNum">    2584 </span>            :         opReg = o0.getId();</a>
+<a name="2585"><span class="lineNum">    2585 </span>            :         rbReg = o1.getId();</a>
+<a name="2586"><span class="lineNum">    2586 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2587"><span class="lineNum">    2587 </span>            :       }</a>
+<a name="2588"><span class="lineNum">    2588 </span>            : </a>
+<a name="2589"><span class="lineNum">    2589 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2590"><span class="lineNum">    2590 </span>            :         opReg = o0.getId();</a>
+<a name="2591"><span class="lineNum">    2591 </span>            :         rmRel = &amp;o1;</a>
+<a name="2592"><span class="lineNum">    2592 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2593"><span class="lineNum">    2593 </span>            :       }</a>
+<a name="2594"><span class="lineNum">    2594 </span>            : </a>
+<a name="2595"><span class="lineNum">    2595 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="2596"><span class="lineNum">    2596 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2597"><span class="lineNum">    2597 </span>            :       opReg  = x86ExtractO(opCode);</a>
+<a name="2598"><span class="lineNum">    2598 </span>            : </a>
+<a name="2599"><span class="lineNum">    2599 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="2600"><span class="lineNum">    2600 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="2601"><span class="lineNum">    2601 </span>            :         imLen = 1;</a>
+<a name="2602"><span class="lineNum">    2602 </span>            : </a>
+<a name="2603"><span class="lineNum">    2603 </span>            :         rbReg = o0.getId();</a>
+<a name="2604"><span class="lineNum">    2604 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2605"><span class="lineNum">    2605 </span>            :       }</a>
+<a name="2606"><span class="lineNum">    2606 </span>            :       break;</a>
+<a name="2607"><span class="lineNum">    2607 </span>            : </a>
+<a name="2608"><span class="lineNum">    2608 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExtRmRi_P:</span></a>
+<a name="2609"><span class="lineNum">    2609 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2610"><span class="lineNum">    2610 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0) | X86Reg::isXmm(o1));</span></a>
+<a name="2611"><span class="lineNum">    2611 </span>            : </a>
+<a name="2612"><span class="lineNum">    2612 </span>            :         opReg = o0.getId();</a>
+<a name="2613"><span class="lineNum">    2613 </span>            :         rbReg = o1.getId();</a>
+<a name="2614"><span class="lineNum">    2614 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2615"><span class="lineNum">    2615 </span>            :       }</a>
+<a name="2616"><span class="lineNum">    2616 </span>            : </a>
+<a name="2617"><span class="lineNum">    2617 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2618"><span class="lineNum">    2618 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0));</span></a>
+<a name="2619"><span class="lineNum">    2619 </span>            : </a>
+<a name="2620"><span class="lineNum">    2620 </span>            :         opReg = o0.getId();</a>
+<a name="2621"><span class="lineNum">    2621 </span>            :         rmRel = &amp;o1;</a>
+<a name="2622"><span class="lineNum">    2622 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2623"><span class="lineNum">    2623 </span>            :       }</a>
+<a name="2624"><span class="lineNum">    2624 </span>            : </a>
+<a name="2625"><span class="lineNum">    2625 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="2626"><span class="lineNum">    2626 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2627"><span class="lineNum">    2627 </span>            :       opReg  = x86ExtractO(opCode);</a>
+<a name="2628"><span class="lineNum">    2628 </span>            : </a>
+<a name="2629"><span class="lineNum">    2629 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Imm)) {</span></a>
+<a name="2630"><span class="lineNum">    2630 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0));</span></a>
+<a name="2631"><span class="lineNum">    2631 </span>            : </a>
+<a name="2632"><span class="lineNum">    2632 </span>            :         imVal = static_cast&lt;const Imm&amp;&gt;(o1).getInt64();</a>
+<a name="2633"><span class="lineNum">    2633 </span>            :         imLen = 1;</a>
+<a name="2634"><span class="lineNum">    2634 </span>            : </a>
+<a name="2635"><span class="lineNum">    2635 </span>            :         rbReg = o0.getId();</a>
+<a name="2636"><span class="lineNum">    2636 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2637"><span class="lineNum">    2637 </span>            :       }</a>
+<a name="2638"><span class="lineNum">    2638 </span>            :       break;</a>
+<a name="2639"><span class="lineNum">    2639 </span>            : </a>
+<a name="2640"><span class="lineNum">    2640 </span>            :     case X86Inst::kEncodingExtRmi:</a>
+<a name="2641"><span class="lineNum">    2641 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2642"><span class="lineNum">    2642 </span>            :       imLen = 1;</a>
+<a name="2643"><span class="lineNum">    2643 </span>            : </a>
+<a name="2644"><span class="lineNum">    2644 </span><span class="lineCov">        120 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="2645"><span class="lineNum">    2645 </span>            :         opReg = o0.getId();</a>
+<a name="2646"><span class="lineNum">    2646 </span>            :         rbReg = o1.getId();</a>
+<a name="2647"><span class="lineNum">    2647 </span><span class="lineCov">        120 :         goto EmitX86R;</span></a>
+<a name="2648"><span class="lineNum">    2648 </span>            :       }</a>
+<a name="2649"><span class="lineNum">    2649 </span>            : </a>
+<a name="2650"><span class="lineNum">    2650 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="2651"><span class="lineNum">    2651 </span>            :         opReg = o0.getId();</a>
+<a name="2652"><span class="lineNum">    2652 </span>            :         rmRel = &amp;o1;</a>
+<a name="2653"><span class="lineNum">    2653 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2654"><span class="lineNum">    2654 </span>            :       }</a>
+<a name="2655"><span class="lineNum">    2655 </span>            :       break;</a>
+<a name="2656"><span class="lineNum">    2656 </span>            : </a>
+<a name="2657"><span class="lineNum">    2657 </span>            :     case X86Inst::kEncodingExtRmi_P:</a>
+<a name="2658"><span class="lineNum">    2658 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2659"><span class="lineNum">    2659 </span>            :       imLen = 1;</a>
+<a name="2660"><span class="lineNum">    2660 </span>            : </a>
+<a name="2661"><span class="lineNum">    2661 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="2662"><span class="lineNum">    2662 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0) | X86Reg::isXmm(o1));</span></a>
+<a name="2663"><span class="lineNum">    2663 </span>            : </a>
+<a name="2664"><span class="lineNum">    2664 </span>            :         opReg = o0.getId();</a>
+<a name="2665"><span class="lineNum">    2665 </span>            :         rbReg = o1.getId();</a>
+<a name="2666"><span class="lineNum">    2666 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2667"><span class="lineNum">    2667 </span>            :       }</a>
+<a name="2668"><span class="lineNum">    2668 </span>            : </a>
+<a name="2669"><span class="lineNum">    2669 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="2670"><span class="lineNum">    2670 </span><span class="lineNoCov">          0 :         ADD_66H_P(X86Reg::isXmm(o0));</span></a>
+<a name="2671"><span class="lineNum">    2671 </span>            : </a>
+<a name="2672"><span class="lineNum">    2672 </span>            :         opReg = o0.getId();</a>
+<a name="2673"><span class="lineNum">    2673 </span>            :         rmRel = &amp;o1;</a>
+<a name="2674"><span class="lineNum">    2674 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2675"><span class="lineNum">    2675 </span>            :       }</a>
+<a name="2676"><span class="lineNum">    2676 </span>            :       break;</a>
+<a name="2677"><span class="lineNum">    2677 </span>            : </a>
+<a name="2678"><span class="lineNum">    2678 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2679"><span class="lineNum">    2679 </span>            :     // [Extrq / Insertq (SSE4A)]</a>
+<a name="2680"><span class="lineNum">    2680 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2681"><span class="lineNum">    2681 </span>            : </a>
+<a name="2682"><span class="lineNum">    2682 </span>            :     case X86Inst::kEncodingExtExtrq:</a>
+<a name="2683"><span class="lineNum">    2683 </span>            :       opReg = o0.getId();</a>
+<a name="2684"><span class="lineNum">    2684 </span>            :       rbReg = o1.getId();</a>
+<a name="2685"><span class="lineNum">    2685 </span>            : </a>
+<a name="2686"><span class="lineNum">    2686 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg))</span></a>
+<a name="2687"><span class="lineNum">    2687 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2688"><span class="lineNum">    2688 </span>            : </a>
+<a name="2689"><span class="lineNum">    2689 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="2690"><span class="lineNum">    2690 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2691"><span class="lineNum">    2691 </span>            : </a>
+<a name="2692"><span class="lineNum">    2692 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Imm, Imm)) {</span></a>
+<a name="2693"><span class="lineNum">    2693 </span><span class="lineNoCov">          0 :         imVal = (static_cast&lt;const Imm&amp;&gt;(o1).getUInt32()     ) +</span></a>
+<a name="2694"><span class="lineNum">    2694 </span><span class="lineNoCov">          0 :                 (static_cast&lt;const Imm&amp;&gt;(o2).getUInt32() &lt;&lt; 8) ;</span></a>
+<a name="2695"><span class="lineNum">    2695 </span>            :         imLen = 2;</a>
+<a name="2696"><span class="lineNum">    2696 </span>            : </a>
+<a name="2697"><span class="lineNum">    2697 </span>            :         rbReg = x86ExtractO(opCode);</a>
+<a name="2698"><span class="lineNum">    2698 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2699"><span class="lineNum">    2699 </span>            :       }</a>
+<a name="2700"><span class="lineNum">    2700 </span>            :       break;</a>
+<a name="2701"><span class="lineNum">    2701 </span>            : </a>
+<a name="2702"><span class="lineNum">    2702 </span>            :     case X86Inst::kEncodingExtInsertq: {</a>
+<a name="2703"><span class="lineNum">    2703 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="2704"><span class="lineNum">    2704 </span>            :       opReg = o0.getId();</a>
+<a name="2705"><span class="lineNum">    2705 </span>            :       rbReg = o1.getId();</a>
+<a name="2706"><span class="lineNum">    2706 </span>            : </a>
+<a name="2707"><span class="lineNum">    2707 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS2(Reg, Reg))</span></a>
+<a name="2708"><span class="lineNum">    2708 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2709"><span class="lineNum">    2709 </span>            : </a>
+<a name="2710"><span class="lineNum">    2710 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="2711"><span class="lineNum">    2711 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2712"><span class="lineNum">    2712 </span>            : </a>
+<a name="2713"><span class="lineNum">    2713 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Imm, Imm)) {</span></a>
+<a name="2714"><span class="lineNum">    2714 </span><span class="lineNoCov">          0 :         imVal = (static_cast&lt;const Imm&amp;&gt;(o2).getUInt32()     ) +</span></a>
+<a name="2715"><span class="lineNum">    2715 </span><span class="lineNoCov">          0 :                 (static_cast&lt;const Imm&amp;&gt;(o3).getUInt32() &lt;&lt; 8) ;</span></a>
+<a name="2716"><span class="lineNum">    2716 </span>            :         imLen = 2;</a>
+<a name="2717"><span class="lineNum">    2717 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2718"><span class="lineNum">    2718 </span>            :       }</a>
+<a name="2719"><span class="lineNum">    2719 </span>            :       break;</a>
+<a name="2720"><span class="lineNum">    2720 </span>            :     }</a>
+<a name="2721"><span class="lineNum">    2721 </span>            : </a>
+<a name="2722"><span class="lineNum">    2722 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2723"><span class="lineNum">    2723 </span>            :     // [3dNow]</a>
+<a name="2724"><span class="lineNum">    2724 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2725"><span class="lineNum">    2725 </span>            : </a>
+<a name="2726"><span class="lineNum">    2726 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingExt3dNow:</span></a>
+<a name="2727"><span class="lineNum">    2727 </span>            :       // Every 3dNow instruction starts with 0x0F0F and the actual opcode is</a>
+<a name="2728"><span class="lineNum">    2728 </span>            :       // stored as 8-bit immediate.</a>
+<a name="2729"><span class="lineNum">    2729 </span><span class="lineNoCov">          0 :       imVal = opCode &amp; 0xFF;</span></a>
+<a name="2730"><span class="lineNum">    2730 </span>            :       imLen = 1;</a>
+<a name="2731"><span class="lineNum">    2731 </span>            : </a>
+<a name="2732"><span class="lineNum">    2732 </span>            :       opCode = X86Inst::kOpCode_MM_0F | 0x0F;</a>
+<a name="2733"><span class="lineNum">    2733 </span>            :       opReg = o0.getId();</a>
+<a name="2734"><span class="lineNum">    2734 </span>            : </a>
+<a name="2735"><span class="lineNum">    2735 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2736"><span class="lineNum">    2736 </span>            :         rbReg = o1.getId();</a>
+<a name="2737"><span class="lineNum">    2737 </span><span class="lineNoCov">          0 :         goto EmitX86R;</span></a>
+<a name="2738"><span class="lineNum">    2738 </span>            :       }</a>
+<a name="2739"><span class="lineNum">    2739 </span>            : </a>
+<a name="2740"><span class="lineNum">    2740 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2741"><span class="lineNum">    2741 </span>            :         rmRel = &amp;o1;</a>
+<a name="2742"><span class="lineNum">    2742 </span><span class="lineNoCov">          0 :         goto EmitX86M;</span></a>
+<a name="2743"><span class="lineNum">    2743 </span>            :       }</a>
+<a name="2744"><span class="lineNum">    2744 </span>            :       break;</a>
+<a name="2745"><span class="lineNum">    2745 </span>            : </a>
+<a name="2746"><span class="lineNum">    2746 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2747"><span class="lineNum">    2747 </span>            :     // [VEX/EVEX]</a>
+<a name="2748"><span class="lineNum">    2748 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="2749"><span class="lineNum">    2749 </span>            : </a>
+<a name="2750"><span class="lineNum">    2750 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexOp:</span></a>
+<a name="2751"><span class="lineNum">    2751 </span><span class="lineNoCov">          0 :       goto EmitVexEvexOp;</span></a>
+<a name="2752"><span class="lineNum">    2752 </span>            : </a>
+<a name="2753"><span class="lineNum">    2753 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexKmov:</span></a>
+<a name="2754"><span class="lineNum">    2754 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2755"><span class="lineNum">    2755 </span>            :         opReg = o0.getId();</a>
+<a name="2756"><span class="lineNum">    2756 </span>            :         rbReg = o1.getId();</a>
+<a name="2757"><span class="lineNum">    2757 </span>            : </a>
+<a name="2758"><span class="lineNum">    2758 </span>            :         // Form 'k, reg'.</a>
+<a name="2759"><span class="lineNum">    2759 </span><span class="lineNoCov">          0 :         if (X86Reg::isGp(o1)) {</span></a>
+<a name="2760"><span class="lineNum">    2760 </span>            :           opCode = commonData-&gt;getAltOpCode();</a>
+<a name="2761"><span class="lineNum">    2761 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="2762"><span class="lineNum">    2762 </span>            :         }</a>
+<a name="2763"><span class="lineNum">    2763 </span>            : </a>
+<a name="2764"><span class="lineNum">    2764 </span>            :         // Form 'reg, k'.</a>
+<a name="2765"><span class="lineNum">    2765 </span><span class="lineNoCov">          0 :         if (X86Reg::isGp(o0)) {</span></a>
+<a name="2766"><span class="lineNum">    2766 </span><span class="lineNoCov">          0 :           opCode = commonData-&gt;getAltOpCode() + 1;</span></a>
+<a name="2767"><span class="lineNum">    2767 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="2768"><span class="lineNum">    2768 </span>            :         }</a>
+<a name="2769"><span class="lineNum">    2769 </span>            : </a>
+<a name="2770"><span class="lineNum">    2770 </span>            :         // Form 'k, k'.</a>
+<a name="2771"><span class="lineNum">    2771 </span><span class="lineNoCov">          0 :         if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="2772"><span class="lineNum">    2772 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="2773"><span class="lineNum">    2773 </span>            : </a>
+<a name="2774"><span class="lineNum">    2774 </span><span class="lineNoCov">          0 :         opCode++;</span></a>
+<a name="2775"><span class="lineNum">    2775 </span>            :         Utils::swap(opReg, rbReg);</a>
+<a name="2776"><span class="lineNum">    2776 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2777"><span class="lineNum">    2777 </span>            :       }</a>
+<a name="2778"><span class="lineNum">    2778 </span>            : </a>
+<a name="2779"><span class="lineNum">    2779 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2780"><span class="lineNum">    2780 </span>            :         opReg = o0.getId();</a>
+<a name="2781"><span class="lineNum">    2781 </span>            :         rmRel = &amp;o1;</a>
+<a name="2782"><span class="lineNum">    2782 </span>            : </a>
+<a name="2783"><span class="lineNum">    2783 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2784"><span class="lineNum">    2784 </span>            :       }</a>
+<a name="2785"><span class="lineNum">    2785 </span>            : </a>
+<a name="2786"><span class="lineNum">    2786 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2787"><span class="lineNum">    2787 </span>            :         opReg = o1.getId();</a>
+<a name="2788"><span class="lineNum">    2788 </span>            :         rmRel = &amp;o0;</a>
+<a name="2789"><span class="lineNum">    2789 </span>            : </a>
+<a name="2790"><span class="lineNum">    2790 </span><span class="lineNoCov">          0 :         opCode++;</span></a>
+<a name="2791"><span class="lineNum">    2791 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2792"><span class="lineNum">    2792 </span>            :       }</a>
+<a name="2793"><span class="lineNum">    2793 </span>            :       break;</a>
+<a name="2794"><span class="lineNum">    2794 </span>            : </a>
+<a name="2795"><span class="lineNum">    2795 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexM:</span></a>
+<a name="2796"><span class="lineNum">    2796 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2797"><span class="lineNum">    2797 </span>            :         rmRel = &amp;o0;</a>
+<a name="2798"><span class="lineNum">    2798 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2799"><span class="lineNum">    2799 </span>            :       }</a>
+<a name="2800"><span class="lineNum">    2800 </span>            :       break;</a>
+<a name="2801"><span class="lineNum">    2801 </span>            : </a>
+<a name="2802"><span class="lineNum">    2802 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexM_VM:</span></a>
+<a name="2803"><span class="lineNum">    2803 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS1(Mem)) {</span></a>
+<a name="2804"><span class="lineNum">    2804 </span><span class="lineNoCov">          0 :         opCode |= x86OpCodeLByVMem(o0);</span></a>
+<a name="2805"><span class="lineNum">    2805 </span>            :         rmRel = &amp;o0;</a>
+<a name="2806"><span class="lineNum">    2806 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2807"><span class="lineNum">    2807 </span>            :       }</a>
+<a name="2808"><span class="lineNum">    2808 </span>            :       break;</a>
+<a name="2809"><span class="lineNum">    2809 </span>            : </a>
+<a name="2810"><span class="lineNum">    2810 </span>            :     case X86Inst::kEncodingVexMr_Lx:</a>
+<a name="2811"><span class="lineNum">    2811 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="2812"><span class="lineNum">    2812 </span>            : </a>
+<a name="2813"><span class="lineNum">    2813 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2814"><span class="lineNum">    2814 </span>            :         opReg = o1.getId();</a>
+<a name="2815"><span class="lineNum">    2815 </span>            :         rbReg = o0.getId();</a>
+<a name="2816"><span class="lineNum">    2816 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2817"><span class="lineNum">    2817 </span>            :       }</a>
+<a name="2818"><span class="lineNum">    2818 </span>            : </a>
+<a name="2819"><span class="lineNum">    2819 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2820"><span class="lineNum">    2820 </span>            :         opReg = o1.getId();</a>
+<a name="2821"><span class="lineNum">    2821 </span>            :         rmRel = &amp;o0;</a>
+<a name="2822"><span class="lineNum">    2822 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2823"><span class="lineNum">    2823 </span>            :       }</a>
+<a name="2824"><span class="lineNum">    2824 </span>            :       break;</a>
+<a name="2825"><span class="lineNum">    2825 </span>            : </a>
+<a name="2826"><span class="lineNum">    2826 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexMr_VM:</span></a>
+<a name="2827"><span class="lineNum">    2827 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="2828"><span class="lineNum">    2828 </span><span class="lineNoCov">          0 :         opCode |= std::max(x86OpCodeLByVMem(o0), x86OpCodeLBySize(o1.getSize()));</span></a>
+<a name="2829"><span class="lineNum">    2829 </span>            : </a>
+<a name="2830"><span class="lineNum">    2830 </span>            :         opReg = o1.getId();</a>
+<a name="2831"><span class="lineNum">    2831 </span>            :         rmRel = &amp;o0;</a>
+<a name="2832"><span class="lineNum">    2832 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2833"><span class="lineNum">    2833 </span>            :       }</a>
+<a name="2834"><span class="lineNum">    2834 </span>            :       break;</a>
+<a name="2835"><span class="lineNum">    2835 </span>            : </a>
+<a name="2836"><span class="lineNum">    2836 </span>            :     case X86Inst::kEncodingVexMri_Lx:</a>
+<a name="2837"><span class="lineNum">    2837 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="2838"><span class="lineNum">    2838 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2839"><span class="lineNum">    2839 </span>            : </a>
+<a name="2840"><span class="lineNum">    2840 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexMri:</span></a>
+<a name="2841"><span class="lineNum">    2841 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2842"><span class="lineNum">    2842 </span>            :       imLen = 1;</a>
+<a name="2843"><span class="lineNum">    2843 </span>            : </a>
+<a name="2844"><span class="lineNum">    2844 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="2845"><span class="lineNum">    2845 </span>            :         opReg = o1.getId();</a>
+<a name="2846"><span class="lineNum">    2846 </span>            :         rbReg = o0.getId();</a>
+<a name="2847"><span class="lineNum">    2847 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2848"><span class="lineNum">    2848 </span>            :       }</a>
+<a name="2849"><span class="lineNum">    2849 </span>            : </a>
+<a name="2850"><span class="lineNum">    2850 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Mem, Reg, Imm)) {</span></a>
+<a name="2851"><span class="lineNum">    2851 </span>            :         opReg = o1.getId();</a>
+<a name="2852"><span class="lineNum">    2852 </span>            :         rmRel = &amp;o0;</a>
+<a name="2853"><span class="lineNum">    2853 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2854"><span class="lineNum">    2854 </span>            :       }</a>
+<a name="2855"><span class="lineNum">    2855 </span>            :       break;</a>
+<a name="2856"><span class="lineNum">    2856 </span>            : </a>
+<a name="2857"><span class="lineNum">    2857 </span>            :     case X86Inst::kEncodingVexRm_ZDI:</a>
+<a name="2858"><span class="lineNum">    2858 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!o2.isNone() &amp;&amp; !x86IsImplicitMem(o2, X86Gp::kIdDi)))</span></a>
+<a name="2859"><span class="lineNum">    2859 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="2860"><span class="lineNum">    2860 </span>            : </a>
+<a name="2861"><span class="lineNum">    2861 </span><span class="lineNoCov">          0 :       isign3 &amp;= 0x3F;</span></a>
+<a name="2862"><span class="lineNum">    2862 </span><span class="lineNoCov">          0 :       goto CaseVexRm;</span></a>
+<a name="2863"><span class="lineNum">    2863 </span>            : </a>
+<a name="2864"><span class="lineNum">    2864 </span>            :     case X86Inst::kEncodingVexRm_Wx:</a>
+<a name="2865"><span class="lineNum">    2865 </span><span class="lineNoCov">          0 :       ADD_REX_W(X86Reg::isGpq(o0) | X86Reg::isGpq(o1));</span></a>
+<a name="2866"><span class="lineNum">    2866 </span><span class="lineNoCov">          0 :       goto CaseVexRm;</span></a>
+<a name="2867"><span class="lineNum">    2867 </span>            : </a>
+<a name="2868"><span class="lineNum">    2868 </span>            :     case X86Inst::kEncodingVexRm_Lx:</a>
+<a name="2869"><span class="lineNum">    2869 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="2870"><span class="lineNum">    2870 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2871"><span class="lineNum">    2871 </span>            : </a>
+<a name="2872"><span class="lineNum">    2872 </span>            :     case X86Inst::kEncodingVexRm:</a>
+<a name="2873"><span class="lineNum">    2873 </span><span class="lineNoCov">          0 : CaseVexRm:</span></a>
+<a name="2874"><span class="lineNum">    2874 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="2875"><span class="lineNum">    2875 </span>            :         opReg = o0.getId();</a>
+<a name="2876"><span class="lineNum">    2876 </span>            :         rbReg = o1.getId();</a>
+<a name="2877"><span class="lineNum">    2877 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2878"><span class="lineNum">    2878 </span>            :       }</a>
+<a name="2879"><span class="lineNum">    2879 </span>            : </a>
+<a name="2880"><span class="lineNum">    2880 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2881"><span class="lineNum">    2881 </span>            :         opReg = o0.getId();</a>
+<a name="2882"><span class="lineNum">    2882 </span>            :         rmRel = &amp;o1;</a>
+<a name="2883"><span class="lineNum">    2883 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2884"><span class="lineNum">    2884 </span>            :       }</a>
+<a name="2885"><span class="lineNum">    2885 </span>            :       break;</a>
+<a name="2886"><span class="lineNum">    2886 </span>            : </a>
+<a name="2887"><span class="lineNum">    2887 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRm_VM:</span></a>
+<a name="2888"><span class="lineNum">    2888 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="2889"><span class="lineNum">    2889 </span><span class="lineNoCov">          0 :         opCode |= std::max(x86OpCodeLByVMem(o1), x86OpCodeLBySize(o0.getSize()));</span></a>
+<a name="2890"><span class="lineNum">    2890 </span>            :         opReg = o0.getId();</a>
+<a name="2891"><span class="lineNum">    2891 </span>            :         rmRel = &amp;o1;</a>
+<a name="2892"><span class="lineNum">    2892 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2893"><span class="lineNum">    2893 </span>            :       }</a>
+<a name="2894"><span class="lineNum">    2894 </span>            :       break;</a>
+<a name="2895"><span class="lineNum">    2895 </span>            : </a>
+<a name="2896"><span class="lineNum">    2896 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRm_T1_4X: {</span></a>
+<a name="2897"><span class="lineNum">    2897 </span><span class="lineNoCov">          0 :       if (!(options &amp; kOptionOp4Op5Used))</span></a>
+<a name="2898"><span class="lineNum">    2898 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="2899"><span class="lineNum">    2899 </span>            : </a>
+<a name="2900"><span class="lineNum">    2900 </span><span class="lineNoCov">          0 :       if (X86Reg::isZmm(o0  ) &amp;&amp; X86Reg::isZmm(o1) &amp;&amp;</span></a>
+<a name="2901"><span class="lineNum">    2901 </span><span class="lineNoCov">          0 :           X86Reg::isZmm(o2  ) &amp;&amp; X86Reg::isZmm(o3) &amp;&amp;</span></a>
+<a name="2902"><span class="lineNum">    2902 </span><span class="lineNoCov">          0 :           X86Reg::isZmm(_op4) &amp;&amp; _op5.isMem()) {</span></a>
+<a name="2903"><span class="lineNum">    2903 </span>            : </a>
+<a name="2904"><span class="lineNum">    2904 </span>            :         // Registers [o1, o2, o3, _op4] must start aligned and must be consecutive.</a>
+<a name="2905"><span class="lineNum">    2905 </span>            :         uint32_t i1 = o1.getId();</a>
+<a name="2906"><span class="lineNum">    2906 </span>            :         uint32_t i2 = o2.getId();</a>
+<a name="2907"><span class="lineNum">    2907 </span>            :         uint32_t i3 = o3.getId();</a>
+<a name="2908"><span class="lineNum">    2908 </span>            :         uint32_t i4 = _op4.getId();</a>
+<a name="2909"><span class="lineNum">    2909 </span>            : </a>
+<a name="2910"><span class="lineNum">    2910 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY((i1 &amp; 0x3) != 0 || i2 != i1 + 1 || i3 != i1 + 2 || i4 != i1 + 3))</span></a>
+<a name="2911"><span class="lineNum">    2911 </span><span class="lineNoCov">          0 :           goto NotConsecutiveRegs;</span></a>
+<a name="2912"><span class="lineNum">    2912 </span>            : </a>
+<a name="2913"><span class="lineNum">    2913 </span>            :         opReg = o0.getId();</a>
+<a name="2914"><span class="lineNum">    2914 </span><span class="lineNoCov">          0 :         rmRel = &amp;_op5;</span></a>
+<a name="2915"><span class="lineNum">    2915 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2916"><span class="lineNum">    2916 </span>            :       }</a>
+<a name="2917"><span class="lineNum">    2917 </span>            :       break;</a>
+<a name="2918"><span class="lineNum">    2918 </span>            :     }</a>
+<a name="2919"><span class="lineNum">    2919 </span>            : </a>
+<a name="2920"><span class="lineNum">    2920 </span>            :     case X86Inst::kEncodingVexRmi_Wx:</a>
+<a name="2921"><span class="lineNum">    2921 </span><span class="lineNoCov">          0 :       ADD_REX_W(X86Reg::isGpq(o0) | X86Reg::isGpq(o1));</span></a>
+<a name="2922"><span class="lineNum">    2922 </span><span class="lineNoCov">          0 :       goto CaseVexRmi;</span></a>
+<a name="2923"><span class="lineNum">    2923 </span>            : </a>
+<a name="2924"><span class="lineNum">    2924 </span>            :     case X86Inst::kEncodingVexRmi_Lx:</a>
+<a name="2925"><span class="lineNum">    2925 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="2926"><span class="lineNum">    2926 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2927"><span class="lineNum">    2927 </span>            : </a>
+<a name="2928"><span class="lineNum">    2928 </span>            :     case X86Inst::kEncodingVexRmi:</a>
+<a name="2929"><span class="lineNum">    2929 </span><span class="lineNoCov">          0 : CaseVexRmi:</span></a>
+<a name="2930"><span class="lineNum">    2930 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="2931"><span class="lineNum">    2931 </span>            :       imLen = 1;</a>
+<a name="2932"><span class="lineNum">    2932 </span>            : </a>
+<a name="2933"><span class="lineNum">    2933 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="2934"><span class="lineNum">    2934 </span>            :         opReg = o0.getId();</a>
+<a name="2935"><span class="lineNum">    2935 </span>            :         rbReg = o1.getId();</a>
+<a name="2936"><span class="lineNum">    2936 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2937"><span class="lineNum">    2937 </span>            :       }</a>
+<a name="2938"><span class="lineNum">    2938 </span>            : </a>
+<a name="2939"><span class="lineNum">    2939 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="2940"><span class="lineNum">    2940 </span>            :         opReg = o0.getId();</a>
+<a name="2941"><span class="lineNum">    2941 </span>            :         rmRel = &amp;o1;</a>
+<a name="2942"><span class="lineNum">    2942 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2943"><span class="lineNum">    2943 </span>            :       }</a>
+<a name="2944"><span class="lineNum">    2944 </span>            :       break;</a>
+<a name="2945"><span class="lineNum">    2945 </span>            : </a>
+<a name="2946"><span class="lineNum">    2946 </span>            :     case X86Inst::kEncodingVexRvm:</a>
+<a name="2947"><span class="lineNum">    2947 </span><span class="lineNoCov">          0 : CaseVexRvm:</span></a>
+<a name="2948"><span class="lineNum">    2948 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="2949"><span class="lineNum">    2949 </span><span class="lineNoCov">          0 : CaseVexRvm_R:</span></a>
+<a name="2950"><span class="lineNum">    2950 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="2951"><span class="lineNum">    2951 </span>            :         rbReg = o2.getId();</a>
+<a name="2952"><span class="lineNum">    2952 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2953"><span class="lineNum">    2953 </span>            :       }</a>
+<a name="2954"><span class="lineNum">    2954 </span>            : </a>
+<a name="2955"><span class="lineNum">    2955 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="2956"><span class="lineNum">    2956 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="2957"><span class="lineNum">    2957 </span>            :         rmRel = &amp;o2;</a>
+<a name="2958"><span class="lineNum">    2958 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2959"><span class="lineNum">    2959 </span>            :       }</a>
+<a name="2960"><span class="lineNum">    2960 </span>            :       break;</a>
+<a name="2961"><span class="lineNum">    2961 </span>            : </a>
+<a name="2962"><span class="lineNum">    2962 </span>            :     case X86Inst::kEncodingVexRvm_ZDX_Wx:</a>
+<a name="2963"><span class="lineNum">    2963 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!o3.isNone() &amp;&amp; !X86Reg::isGp(o3, X86Gp::kIdDx)))</span></a>
+<a name="2964"><span class="lineNum">    2964 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="2965"><span class="lineNum">    2965 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2966"><span class="lineNum">    2966 </span>            : </a>
+<a name="2967"><span class="lineNum">    2967 </span>            :     case X86Inst::kEncodingVexRvm_Wx:</a>
+<a name="2968"><span class="lineNum">    2968 </span><span class="lineNoCov">          0 :       ADD_REX_W(X86Reg::isGpq(o0) | (o2.getSize() == 8));</span></a>
+<a name="2969"><span class="lineNum">    2969 </span><span class="lineNoCov">          0 :       goto CaseVexRvm;</span></a>
+<a name="2970"><span class="lineNum">    2970 </span>            : </a>
+<a name="2971"><span class="lineNum">    2971 </span>            :     case X86Inst::kEncodingVexRvm_Lx:</a>
+<a name="2972"><span class="lineNum">    2972 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="2973"><span class="lineNum">    2973 </span><span class="lineNoCov">          0 :       goto CaseVexRvm;</span></a>
+<a name="2974"><span class="lineNum">    2974 </span>            : </a>
+<a name="2975"><span class="lineNum">    2975 </span>            :     case X86Inst::kEncodingVexRvmr_Lx:</a>
+<a name="2976"><span class="lineNum">    2976 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="2977"><span class="lineNum">    2977 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="2978"><span class="lineNum">    2978 </span>            : </a>
+<a name="2979"><span class="lineNum">    2979 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmr: {</span></a>
+<a name="2980"><span class="lineNum">    2980 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="2981"><span class="lineNum">    2981 </span><span class="lineNoCov">          0 :       imVal = o3.getId() &lt;&lt; 4;</span></a>
+<a name="2982"><span class="lineNum">    2982 </span>            :       imLen = 1;</a>
+<a name="2983"><span class="lineNum">    2983 </span>            : </a>
+<a name="2984"><span class="lineNum">    2984 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Reg)) {</span></a>
+<a name="2985"><span class="lineNum">    2985 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="2986"><span class="lineNum">    2986 </span>            :         rbReg = o2.getId();</a>
+<a name="2987"><span class="lineNum">    2987 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="2988"><span class="lineNum">    2988 </span>            :       }</a>
+<a name="2989"><span class="lineNum">    2989 </span>            : </a>
+<a name="2990"><span class="lineNum">    2990 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Mem, Reg)) {</span></a>
+<a name="2991"><span class="lineNum">    2991 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="2992"><span class="lineNum">    2992 </span>            :         rmRel = &amp;o2;</a>
+<a name="2993"><span class="lineNum">    2993 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="2994"><span class="lineNum">    2994 </span>            :       }</a>
+<a name="2995"><span class="lineNum">    2995 </span>            :       break;</a>
+<a name="2996"><span class="lineNum">    2996 </span>            :     }</a>
+<a name="2997"><span class="lineNum">    2997 </span>            : </a>
+<a name="2998"><span class="lineNum">    2998 </span>            :     case X86Inst::kEncodingVexRvmi_Lx:</a>
+<a name="2999"><span class="lineNum">    2999 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3000"><span class="lineNum">    3000 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3001"><span class="lineNum">    3001 </span>            : </a>
+<a name="3002"><span class="lineNum">    3002 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmi: {</span></a>
+<a name="3003"><span class="lineNum">    3003 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="3004"><span class="lineNum">    3004 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o3).getInt64();</a>
+<a name="3005"><span class="lineNum">    3005 </span>            :       imLen = 1;</a>
+<a name="3006"><span class="lineNum">    3006 </span>            : </a>
+<a name="3007"><span class="lineNum">    3007 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Imm)) {</span></a>
+<a name="3008"><span class="lineNum">    3008 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3009"><span class="lineNum">    3009 </span>            :         rbReg = o2.getId();</a>
+<a name="3010"><span class="lineNum">    3010 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3011"><span class="lineNum">    3011 </span>            :       }</a>
+<a name="3012"><span class="lineNum">    3012 </span>            : </a>
+<a name="3013"><span class="lineNum">    3013 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Mem, Imm)) {</span></a>
+<a name="3014"><span class="lineNum">    3014 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3015"><span class="lineNum">    3015 </span>            :         rmRel = &amp;o2;</a>
+<a name="3016"><span class="lineNum">    3016 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3017"><span class="lineNum">    3017 </span>            :       }</a>
+<a name="3018"><span class="lineNum">    3018 </span>            :       break;</a>
+<a name="3019"><span class="lineNum">    3019 </span>            :     }</a>
+<a name="3020"><span class="lineNum">    3020 </span>            : </a>
+<a name="3021"><span class="lineNum">    3021 </span>            :     case X86Inst::kEncodingVexRmv_Wx:</a>
+<a name="3022"><span class="lineNum">    3022 </span><span class="lineNoCov">          0 :       ADD_REX_W(X86Reg::isGpq(o0) | X86Reg::isGpq(o2));</span></a>
+<a name="3023"><span class="lineNum">    3023 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3024"><span class="lineNum">    3024 </span>            : </a>
+<a name="3025"><span class="lineNum">    3025 </span>            :     case X86Inst::kEncodingVexRmv:</a>
+<a name="3026"><span class="lineNum">    3026 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3027"><span class="lineNum">    3027 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3028"><span class="lineNum">    3028 </span>            :         rbReg = o1.getId();</a>
+<a name="3029"><span class="lineNum">    3029 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3030"><span class="lineNum">    3030 </span>            :       }</a>
+<a name="3031"><span class="lineNum">    3031 </span>            : </a>
+<a name="3032"><span class="lineNum">    3032 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Reg)) {</span></a>
+<a name="3033"><span class="lineNum">    3033 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3034"><span class="lineNum">    3034 </span>            :         rmRel = &amp;o1;</a>
+<a name="3035"><span class="lineNum">    3035 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3036"><span class="lineNum">    3036 </span>            :       }</a>
+<a name="3037"><span class="lineNum">    3037 </span>            :       break;</a>
+<a name="3038"><span class="lineNum">    3038 </span>            : </a>
+<a name="3039"><span class="lineNum">    3039 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRmvRm_VM:</span></a>
+<a name="3040"><span class="lineNum">    3040 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="3041"><span class="lineNum">    3041 </span>            :         opCode  = commonData-&gt;getAltOpCode();</a>
+<a name="3042"><span class="lineNum">    3042 </span><span class="lineNoCov">          0 :         opCode |= std::max(x86OpCodeLByVMem(o1), x86OpCodeLBySize(o0.getSize()));</span></a>
+<a name="3043"><span class="lineNum">    3043 </span>            : </a>
+<a name="3044"><span class="lineNum">    3044 </span>            :         opReg = o0.getId();</a>
+<a name="3045"><span class="lineNum">    3045 </span>            :         rmRel = &amp;o1;</a>
+<a name="3046"><span class="lineNum">    3046 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3047"><span class="lineNum">    3047 </span>            :       }</a>
+<a name="3048"><span class="lineNum">    3048 </span>            : </a>
+<a name="3049"><span class="lineNum">    3049 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3050"><span class="lineNum">    3050 </span>            : </a>
+<a name="3051"><span class="lineNum">    3051 </span>            :     case X86Inst::kEncodingVexRmv_VM:</a>
+<a name="3052"><span class="lineNum">    3052 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Reg)) {</span></a>
+<a name="3053"><span class="lineNum">    3053 </span><span class="lineNoCov">          0 :         opCode |= std::max(x86OpCodeLByVMem(o1), x86OpCodeLBySize(o0.getSize() | o2.getSize()));</span></a>
+<a name="3054"><span class="lineNum">    3054 </span>            : </a>
+<a name="3055"><span class="lineNum">    3055 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3056"><span class="lineNum">    3056 </span>            :         rmRel = &amp;o1;</a>
+<a name="3057"><span class="lineNum">    3057 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3058"><span class="lineNum">    3058 </span>            :       }</a>
+<a name="3059"><span class="lineNum">    3059 </span>            :       break;</a>
+<a name="3060"><span class="lineNum">    3060 </span>            : </a>
+<a name="3061"><span class="lineNum">    3061 </span>            : </a>
+<a name="3062"><span class="lineNum">    3062 </span>            :     case X86Inst::kEncodingVexRmvi: {</a>
+<a name="3063"><span class="lineNum">    3063 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="3064"><span class="lineNum">    3064 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o3).getInt64();</a>
+<a name="3065"><span class="lineNum">    3065 </span>            :       imLen = 1;</a>
+<a name="3066"><span class="lineNum">    3066 </span>            : </a>
+<a name="3067"><span class="lineNum">    3067 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Imm)) {</span></a>
+<a name="3068"><span class="lineNum">    3068 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3069"><span class="lineNum">    3069 </span>            :         rbReg = o1.getId();</a>
+<a name="3070"><span class="lineNum">    3070 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3071"><span class="lineNum">    3071 </span>            :       }</a>
+<a name="3072"><span class="lineNum">    3072 </span>            : </a>
+<a name="3073"><span class="lineNum">    3073 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Mem, Reg, Imm)) {</span></a>
+<a name="3074"><span class="lineNum">    3074 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3075"><span class="lineNum">    3075 </span>            :         rmRel = &amp;o1;</a>
+<a name="3076"><span class="lineNum">    3076 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3077"><span class="lineNum">    3077 </span>            :       }</a>
+<a name="3078"><span class="lineNum">    3078 </span>            :       break;</a>
+<a name="3079"><span class="lineNum">    3079 </span>            :     }</a>
+<a name="3080"><span class="lineNum">    3080 </span>            : </a>
+<a name="3081"><span class="lineNum">    3081 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexMovdMovq:</span></a>
+<a name="3082"><span class="lineNum">    3082 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="3083"><span class="lineNum">    3083 </span><span class="lineNoCov">          0 :         if (X86Reg::isGp(o0)) {</span></a>
+<a name="3084"><span class="lineNum">    3084 </span>            :           opCode = commonData-&gt;getAltOpCode();</a>
+<a name="3085"><span class="lineNum">    3085 </span><span class="lineNoCov">          0 :           ADD_REX_W_BY_SIZE(o0.getSize());</span></a>
+<a name="3086"><span class="lineNum">    3086 </span>            :           opReg = o1.getId();</a>
+<a name="3087"><span class="lineNum">    3087 </span>            :           rbReg = o0.getId();</a>
+<a name="3088"><span class="lineNum">    3088 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="3089"><span class="lineNum">    3089 </span>            :         }</a>
+<a name="3090"><span class="lineNum">    3090 </span>            : </a>
+<a name="3091"><span class="lineNum">    3091 </span><span class="lineNoCov">          0 :         if (X86Reg::isGp(o1)) {</span></a>
+<a name="3092"><span class="lineNum">    3092 </span><span class="lineNoCov">          0 :           ADD_REX_W_BY_SIZE(o1.getSize());</span></a>
+<a name="3093"><span class="lineNum">    3093 </span>            :           opReg = o0.getId();</a>
+<a name="3094"><span class="lineNum">    3094 </span>            :           rbReg = o1.getId();</a>
+<a name="3095"><span class="lineNum">    3095 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="3096"><span class="lineNum">    3096 </span>            :         }</a>
+<a name="3097"><span class="lineNum">    3097 </span>            : </a>
+<a name="3098"><span class="lineNum">    3098 </span>            :         // If this is a 'W' version (movq) then allow also vmovq 'xmm|xmm' form.</a>
+<a name="3099"><span class="lineNum">    3099 </span><span class="lineNoCov">          0 :         if (opCode &amp; X86Inst::kOpCode_EW) {</span></a>
+<a name="3100"><span class="lineNum">    3100 </span><span class="lineNoCov">          0 :           opCode &amp;= ~(X86Inst::kOpCode_PP_VEXMask | X86Inst::kOpCode_MM_Mask | 0xFF);</span></a>
+<a name="3101"><span class="lineNum">    3101 </span><span class="lineNoCov">          0 :           opCode |=  (X86Inst::kOpCode_PP_F3      | X86Inst::kOpCode_MM_0F   | 0x7E);</span></a>
+<a name="3102"><span class="lineNum">    3102 </span>            : </a>
+<a name="3103"><span class="lineNum">    3103 </span>            :           opReg = o0.getId();</a>
+<a name="3104"><span class="lineNum">    3104 </span>            :           rbReg = o1.getId();</a>
+<a name="3105"><span class="lineNum">    3105 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="3106"><span class="lineNum">    3106 </span>            :         }</a>
+<a name="3107"><span class="lineNum">    3107 </span>            :       }</a>
+<a name="3108"><span class="lineNum">    3108 </span>            : </a>
+<a name="3109"><span class="lineNum">    3109 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="3110"><span class="lineNum">    3110 </span><span class="lineNoCov">          0 :         if (opCode &amp; X86Inst::kOpCode_EW) {</span></a>
+<a name="3111"><span class="lineNum">    3111 </span><span class="lineNoCov">          0 :           opCode &amp;= ~(X86Inst::kOpCode_PP_VEXMask | X86Inst::kOpCode_MM_Mask | 0xFF);</span></a>
+<a name="3112"><span class="lineNum">    3112 </span><span class="lineNoCov">          0 :           opCode |=  (X86Inst::kOpCode_PP_F3      | X86Inst::kOpCode_MM_0F   | 0x7E);</span></a>
+<a name="3113"><span class="lineNum">    3113 </span>            :         }</a>
+<a name="3114"><span class="lineNum">    3114 </span>            : </a>
+<a name="3115"><span class="lineNum">    3115 </span>            :         opReg = o0.getId();</a>
+<a name="3116"><span class="lineNum">    3116 </span>            :         rmRel = &amp;o1;</a>
+<a name="3117"><span class="lineNum">    3117 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3118"><span class="lineNum">    3118 </span>            :       }</a>
+<a name="3119"><span class="lineNum">    3119 </span>            : </a>
+<a name="3120"><span class="lineNum">    3120 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="3121"><span class="lineNum">    3121 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="3122"><span class="lineNum">    3122 </span>            : </a>
+<a name="3123"><span class="lineNum">    3123 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="3124"><span class="lineNum">    3124 </span><span class="lineNoCov">          0 :         if (opCode &amp; X86Inst::kOpCode_EW) {</span></a>
+<a name="3125"><span class="lineNum">    3125 </span><span class="lineNoCov">          0 :           opCode &amp;= ~(X86Inst::kOpCode_PP_VEXMask | X86Inst::kOpCode_MM_Mask | 0xFF);</span></a>
+<a name="3126"><span class="lineNum">    3126 </span><span class="lineNoCov">          0 :           opCode |=  (X86Inst::kOpCode_PP_66      | X86Inst::kOpCode_MM_0F   | 0xD6);</span></a>
+<a name="3127"><span class="lineNum">    3127 </span>            :         }</a>
+<a name="3128"><span class="lineNum">    3128 </span>            : </a>
+<a name="3129"><span class="lineNum">    3129 </span>            :         opReg = o1.getId();</a>
+<a name="3130"><span class="lineNum">    3130 </span>            :         rmRel = &amp;o0;</a>
+<a name="3131"><span class="lineNum">    3131 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3132"><span class="lineNum">    3132 </span>            :       }</a>
+<a name="3133"><span class="lineNum">    3133 </span>            :       break;</a>
+<a name="3134"><span class="lineNum">    3134 </span>            : </a>
+<a name="3135"><span class="lineNum">    3135 </span>            :     case X86Inst::kEncodingVexRmMr_Lx:</a>
+<a name="3136"><span class="lineNum">    3136 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3137"><span class="lineNum">    3137 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3138"><span class="lineNum">    3138 </span>            : </a>
+<a name="3139"><span class="lineNum">    3139 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRmMr:</span></a>
+<a name="3140"><span class="lineNum">    3140 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="3141"><span class="lineNum">    3141 </span>            :         opReg = o0.getId();</a>
+<a name="3142"><span class="lineNum">    3142 </span>            :         rbReg = o1.getId();</a>
+<a name="3143"><span class="lineNum">    3143 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3144"><span class="lineNum">    3144 </span>            :       }</a>
+<a name="3145"><span class="lineNum">    3145 </span>            : </a>
+<a name="3146"><span class="lineNum">    3146 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="3147"><span class="lineNum">    3147 </span>            :         opReg = o0.getId();</a>
+<a name="3148"><span class="lineNum">    3148 </span>            :         rmRel = &amp;o1;</a>
+<a name="3149"><span class="lineNum">    3149 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3150"><span class="lineNum">    3150 </span>            :       }</a>
+<a name="3151"><span class="lineNum">    3151 </span>            : </a>
+<a name="3152"><span class="lineNum">    3152 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="3153"><span class="lineNum">    3153 </span><span class="lineNoCov">          0 :       opCode &amp;= X86Inst::kOpCode_LL_Mask;</span></a>
+<a name="3154"><span class="lineNum">    3154 </span><span class="lineNoCov">          0 :       opCode |= commonData-&gt;getAltOpCode();</span></a>
+<a name="3155"><span class="lineNum">    3155 </span>            : </a>
+<a name="3156"><span class="lineNum">    3156 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="3157"><span class="lineNum">    3157 </span>            :         opReg = o1.getId();</a>
+<a name="3158"><span class="lineNum">    3158 </span>            :         rmRel = &amp;o0;</a>
+<a name="3159"><span class="lineNum">    3159 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3160"><span class="lineNum">    3160 </span>            :       }</a>
+<a name="3161"><span class="lineNum">    3161 </span>            :       break;</a>
+<a name="3162"><span class="lineNum">    3162 </span>            : </a>
+<a name="3163"><span class="lineNum">    3163 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmRmv:</span></a>
+<a name="3164"><span class="lineNum">    3164 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3165"><span class="lineNum">    3165 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3166"><span class="lineNum">    3166 </span>            :         rbReg = o1.getId();</a>
+<a name="3167"><span class="lineNum">    3167 </span>            : </a>
+<a name="3168"><span class="lineNum">    3168 </span><span class="lineNoCov">          0 :         if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="3169"><span class="lineNum">    3169 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="3170"><span class="lineNum">    3170 </span>            : </a>
+<a name="3171"><span class="lineNum">    3171 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3172"><span class="lineNum">    3172 </span>            :         rbReg = o2.getId();</a>
+<a name="3173"><span class="lineNum">    3173 </span>            : </a>
+<a name="3174"><span class="lineNum">    3174 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3175"><span class="lineNum">    3175 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3176"><span class="lineNum">    3176 </span>            :       }</a>
+<a name="3177"><span class="lineNum">    3177 </span>            : </a>
+<a name="3178"><span class="lineNum">    3178 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Reg)) {</span></a>
+<a name="3179"><span class="lineNum">    3179 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3180"><span class="lineNum">    3180 </span>            :         rmRel = &amp;o1;</a>
+<a name="3181"><span class="lineNum">    3181 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3182"><span class="lineNum">    3182 </span>            :       }</a>
+<a name="3183"><span class="lineNum">    3183 </span>            : </a>
+<a name="3184"><span class="lineNum">    3184 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="3185"><span class="lineNum">    3185 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3186"><span class="lineNum">    3186 </span>            :         rmRel = &amp;o2;</a>
+<a name="3187"><span class="lineNum">    3187 </span>            : </a>
+<a name="3188"><span class="lineNum">    3188 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3189"><span class="lineNum">    3189 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3190"><span class="lineNum">    3190 </span>            :       }</a>
+<a name="3191"><span class="lineNum">    3191 </span>            :       break;</a>
+<a name="3192"><span class="lineNum">    3192 </span>            : </a>
+<a name="3193"><span class="lineNum">    3193 </span>            :     case X86Inst::kEncodingVexRvmRmi_Lx:</a>
+<a name="3194"><span class="lineNum">    3194 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3195"><span class="lineNum">    3195 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3196"><span class="lineNum">    3196 </span>            : </a>
+<a name="3197"><span class="lineNum">    3197 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmRmi:</span></a>
+<a name="3198"><span class="lineNum">    3198 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3199"><span class="lineNum">    3199 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3200"><span class="lineNum">    3200 </span>            :         rbReg = o2.getId();</a>
+<a name="3201"><span class="lineNum">    3201 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3202"><span class="lineNum">    3202 </span>            :       }</a>
+<a name="3203"><span class="lineNum">    3203 </span>            : </a>
+<a name="3204"><span class="lineNum">    3204 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="3205"><span class="lineNum">    3205 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3206"><span class="lineNum">    3206 </span>            :         rmRel = &amp;o2;</a>
+<a name="3207"><span class="lineNum">    3207 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3208"><span class="lineNum">    3208 </span>            :       }</a>
+<a name="3209"><span class="lineNum">    3209 </span>            : </a>
+<a name="3210"><span class="lineNum">    3210 </span>            :       // The following instructions use the secondary opcode.</a>
+<a name="3211"><span class="lineNum">    3211 </span><span class="lineNoCov">          0 :       opCode &amp;= X86Inst::kOpCode_LL_Mask;</span></a>
+<a name="3212"><span class="lineNum">    3212 </span><span class="lineNoCov">          0 :       opCode |= commonData-&gt;getAltOpCode();</span></a>
+<a name="3213"><span class="lineNum">    3213 </span>            : </a>
+<a name="3214"><span class="lineNum">    3214 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="3215"><span class="lineNum">    3215 </span>            :       imLen = 1;</a>
+<a name="3216"><span class="lineNum">    3216 </span>            : </a>
+<a name="3217"><span class="lineNum">    3217 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="3218"><span class="lineNum">    3218 </span>            :         opReg = o0.getId();</a>
+<a name="3219"><span class="lineNum">    3219 </span>            :         rbReg = o1.getId();</a>
+<a name="3220"><span class="lineNum">    3220 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3221"><span class="lineNum">    3221 </span>            :       }</a>
+<a name="3222"><span class="lineNum">    3222 </span>            : </a>
+<a name="3223"><span class="lineNum">    3223 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="3224"><span class="lineNum">    3224 </span>            :         opReg = o0.getId();</a>
+<a name="3225"><span class="lineNum">    3225 </span>            :         rmRel = &amp;o1;</a>
+<a name="3226"><span class="lineNum">    3226 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3227"><span class="lineNum">    3227 </span>            :       }</a>
+<a name="3228"><span class="lineNum">    3228 </span>            :       break;</a>
+<a name="3229"><span class="lineNum">    3229 </span>            : </a>
+<a name="3230"><span class="lineNum">    3230 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmRmvRmi:</span></a>
+<a name="3231"><span class="lineNum">    3231 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3232"><span class="lineNum">    3232 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3233"><span class="lineNum">    3233 </span>            :         rbReg = o1.getId();</a>
+<a name="3234"><span class="lineNum">    3234 </span>            : </a>
+<a name="3235"><span class="lineNum">    3235 </span><span class="lineNoCov">          0 :         if (!(options &amp; X86Inst::kOptionModMR))</span></a>
+<a name="3236"><span class="lineNum">    3236 </span><span class="lineNoCov">          0 :           goto EmitVexEvexR;</span></a>
+<a name="3237"><span class="lineNum">    3237 </span>            : </a>
+<a name="3238"><span class="lineNum">    3238 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3239"><span class="lineNum">    3239 </span>            :         rbReg = o2.getId();</a>
+<a name="3240"><span class="lineNum">    3240 </span>            : </a>
+<a name="3241"><span class="lineNum">    3241 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3242"><span class="lineNum">    3242 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3243"><span class="lineNum">    3243 </span>            :       }</a>
+<a name="3244"><span class="lineNum">    3244 </span>            : </a>
+<a name="3245"><span class="lineNum">    3245 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Reg)) {</span></a>
+<a name="3246"><span class="lineNum">    3246 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o2.getId());</a>
+<a name="3247"><span class="lineNum">    3247 </span>            :         rmRel = &amp;o1;</a>
+<a name="3248"><span class="lineNum">    3248 </span>            : </a>
+<a name="3249"><span class="lineNum">    3249 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3250"><span class="lineNum">    3250 </span>            :       }</a>
+<a name="3251"><span class="lineNum">    3251 </span>            : </a>
+<a name="3252"><span class="lineNum">    3252 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="3253"><span class="lineNum">    3253 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3254"><span class="lineNum">    3254 </span>            :         rmRel = &amp;o2;</a>
+<a name="3255"><span class="lineNum">    3255 </span>            : </a>
+<a name="3256"><span class="lineNum">    3256 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3257"><span class="lineNum">    3257 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3258"><span class="lineNum">    3258 </span>            :       }</a>
+<a name="3259"><span class="lineNum">    3259 </span>            : </a>
+<a name="3260"><span class="lineNum">    3260 </span>            :       // The following instructions use the secondary opcode.</a>
+<a name="3261"><span class="lineNum">    3261 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="3262"><span class="lineNum">    3262 </span>            : </a>
+<a name="3263"><span class="lineNum">    3263 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="3264"><span class="lineNum">    3264 </span>            :       imLen = 1;</a>
+<a name="3265"><span class="lineNum">    3265 </span>            : </a>
+<a name="3266"><span class="lineNum">    3266 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="3267"><span class="lineNum">    3267 </span>            :         opReg = o0.getId();</a>
+<a name="3268"><span class="lineNum">    3268 </span>            :         rbReg = o1.getId();</a>
+<a name="3269"><span class="lineNum">    3269 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3270"><span class="lineNum">    3270 </span>            :       }</a>
+<a name="3271"><span class="lineNum">    3271 </span>            : </a>
+<a name="3272"><span class="lineNum">    3272 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="3273"><span class="lineNum">    3273 </span>            :         opReg = o0.getId();</a>
+<a name="3274"><span class="lineNum">    3274 </span>            :         rmRel = &amp;o1;</a>
+<a name="3275"><span class="lineNum">    3275 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3276"><span class="lineNum">    3276 </span>            :       }</a>
+<a name="3277"><span class="lineNum">    3277 </span>            :       break;</a>
+<a name="3278"><span class="lineNum">    3278 </span>            : </a>
+<a name="3279"><span class="lineNum">    3279 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmMr:</span></a>
+<a name="3280"><span class="lineNum">    3280 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3281"><span class="lineNum">    3281 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3282"><span class="lineNum">    3282 </span>            :         rbReg = o2.getId();</a>
+<a name="3283"><span class="lineNum">    3283 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3284"><span class="lineNum">    3284 </span>            :       }</a>
+<a name="3285"><span class="lineNum">    3285 </span>            : </a>
+<a name="3286"><span class="lineNum">    3286 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="3287"><span class="lineNum">    3287 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3288"><span class="lineNum">    3288 </span>            :         rmRel = &amp;o2;</a>
+<a name="3289"><span class="lineNum">    3289 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3290"><span class="lineNum">    3290 </span>            :       }</a>
+<a name="3291"><span class="lineNum">    3291 </span>            : </a>
+<a name="3292"><span class="lineNum">    3292 </span>            :       // The following instructions use the secondary opcode.</a>
+<a name="3293"><span class="lineNum">    3293 </span>            :       opCode = commonData-&gt;getAltOpCode();</a>
+<a name="3294"><span class="lineNum">    3294 </span>            : </a>
+<a name="3295"><span class="lineNum">    3295 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="3296"><span class="lineNum">    3296 </span>            :         opReg = o1.getId();</a>
+<a name="3297"><span class="lineNum">    3297 </span>            :         rbReg = o0.getId();</a>
+<a name="3298"><span class="lineNum">    3298 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3299"><span class="lineNum">    3299 </span>            :       }</a>
+<a name="3300"><span class="lineNum">    3300 </span>            : </a>
+<a name="3301"><span class="lineNum">    3301 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="3302"><span class="lineNum">    3302 </span>            :         opReg = o1.getId();</a>
+<a name="3303"><span class="lineNum">    3303 </span>            :         rmRel = &amp;o0;</a>
+<a name="3304"><span class="lineNum">    3304 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3305"><span class="lineNum">    3305 </span>            :       }</a>
+<a name="3306"><span class="lineNum">    3306 </span>            :       break;</a>
+<a name="3307"><span class="lineNum">    3307 </span>            : </a>
+<a name="3308"><span class="lineNum">    3308 </span>            :     case X86Inst::kEncodingVexRvmMvr_Lx:</a>
+<a name="3309"><span class="lineNum">    3309 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3310"><span class="lineNum">    3310 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3311"><span class="lineNum">    3311 </span>            : </a>
+<a name="3312"><span class="lineNum">    3312 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmMvr:</span></a>
+<a name="3313"><span class="lineNum">    3313 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3314"><span class="lineNum">    3314 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3315"><span class="lineNum">    3315 </span>            :         rbReg = o2.getId();</a>
+<a name="3316"><span class="lineNum">    3316 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3317"><span class="lineNum">    3317 </span>            :       }</a>
+<a name="3318"><span class="lineNum">    3318 </span>            : </a>
+<a name="3319"><span class="lineNum">    3319 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="3320"><span class="lineNum">    3320 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3321"><span class="lineNum">    3321 </span>            :         rmRel = &amp;o2;</a>
+<a name="3322"><span class="lineNum">    3322 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3323"><span class="lineNum">    3323 </span>            :       }</a>
+<a name="3324"><span class="lineNum">    3324 </span>            : </a>
+<a name="3325"><span class="lineNum">    3325 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="3326"><span class="lineNum">    3326 </span><span class="lineNoCov">          0 :       opCode &amp;= X86Inst::kOpCode_LL_Mask;</span></a>
+<a name="3327"><span class="lineNum">    3327 </span><span class="lineNoCov">          0 :       opCode |= commonData-&gt;getAltOpCode();</span></a>
+<a name="3328"><span class="lineNum">    3328 </span>            : </a>
+<a name="3329"><span class="lineNum">    3329 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Mem, Reg, Reg)) {</span></a>
+<a name="3330"><span class="lineNum">    3330 </span>            :         opReg = x86PackRegAndVvvvv(o2.getId(), o1.getId());</a>
+<a name="3331"><span class="lineNum">    3331 </span>            :         rmRel = &amp;o0;</a>
+<a name="3332"><span class="lineNum">    3332 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3333"><span class="lineNum">    3333 </span>            :       }</a>
+<a name="3334"><span class="lineNum">    3334 </span>            :       break;</a>
+<a name="3335"><span class="lineNum">    3335 </span>            : </a>
+<a name="3336"><span class="lineNum">    3336 </span>            :     case X86Inst::kEncodingVexRvmVmi_Lx:</a>
+<a name="3337"><span class="lineNum">    3337 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3338"><span class="lineNum">    3338 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3339"><span class="lineNum">    3339 </span>            : </a>
+<a name="3340"><span class="lineNum">    3340 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvmVmi:</span></a>
+<a name="3341"><span class="lineNum">    3341 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3342"><span class="lineNum">    3342 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3343"><span class="lineNum">    3343 </span>            :         rbReg = o2.getId();</a>
+<a name="3344"><span class="lineNum">    3344 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3345"><span class="lineNum">    3345 </span>            :       }</a>
+<a name="3346"><span class="lineNum">    3346 </span>            : </a>
+<a name="3347"><span class="lineNum">    3347 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Mem)) {</span></a>
+<a name="3348"><span class="lineNum">    3348 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3349"><span class="lineNum">    3349 </span>            :         rmRel = &amp;o2;</a>
+<a name="3350"><span class="lineNum">    3350 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3351"><span class="lineNum">    3351 </span>            :       }</a>
+<a name="3352"><span class="lineNum">    3352 </span>            : </a>
+<a name="3353"><span class="lineNum">    3353 </span>            :       // The following instruction uses the secondary opcode.</a>
+<a name="3354"><span class="lineNum">    3354 </span><span class="lineNoCov">          0 :       opCode &amp;= X86Inst::kOpCode_LL_Mask;</span></a>
+<a name="3355"><span class="lineNum">    3355 </span><span class="lineNoCov">          0 :       opCode |= commonData-&gt;getAltOpCode();</span></a>
+<a name="3356"><span class="lineNum">    3356 </span>            :       opReg = x86ExtractO(opCode);</a>
+<a name="3357"><span class="lineNum">    3357 </span>            : </a>
+<a name="3358"><span class="lineNum">    3358 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="3359"><span class="lineNum">    3359 </span>            :       imLen = 1;</a>
+<a name="3360"><span class="lineNum">    3360 </span>            : </a>
+<a name="3361"><span class="lineNum">    3361 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="3362"><span class="lineNum">    3362 </span>            :         opReg = x86PackRegAndVvvvv(opReg, o0.getId());</a>
+<a name="3363"><span class="lineNum">    3363 </span>            :         rbReg = o1.getId();</a>
+<a name="3364"><span class="lineNum">    3364 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3365"><span class="lineNum">    3365 </span>            :       }</a>
+<a name="3366"><span class="lineNum">    3366 </span>            : </a>
+<a name="3367"><span class="lineNum">    3367 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="3368"><span class="lineNum">    3368 </span>            :         opReg = x86PackRegAndVvvvv(opReg, o0.getId());</a>
+<a name="3369"><span class="lineNum">    3369 </span>            :         rmRel = &amp;o1;</a>
+<a name="3370"><span class="lineNum">    3370 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3371"><span class="lineNum">    3371 </span>            :       }</a>
+<a name="3372"><span class="lineNum">    3372 </span>            :       break;</a>
+<a name="3373"><span class="lineNum">    3373 </span>            : </a>
+<a name="3374"><span class="lineNum">    3374 </span>            :     case X86Inst::kEncodingVexVm_Wx:</a>
+<a name="3375"><span class="lineNum">    3375 </span><span class="lineNoCov">          0 :       ADD_REX_W(X86Reg::isGpq(o0) | X86Reg::isGpq(o1));</span></a>
+<a name="3376"><span class="lineNum">    3376 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3377"><span class="lineNum">    3377 </span>            : </a>
+<a name="3378"><span class="lineNum">    3378 </span>            :     case X86Inst::kEncodingVexVm:</a>
+<a name="3379"><span class="lineNum">    3379 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Reg)) {</span></a>
+<a name="3380"><span class="lineNum">    3380 </span>            :         opReg = x86PackRegAndVvvvv(opReg, o0.getId());</a>
+<a name="3381"><span class="lineNum">    3381 </span>            :         rbReg = o1.getId();</a>
+<a name="3382"><span class="lineNum">    3382 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3383"><span class="lineNum">    3383 </span>            :       }</a>
+<a name="3384"><span class="lineNum">    3384 </span>            : </a>
+<a name="3385"><span class="lineNum">    3385 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="3386"><span class="lineNum">    3386 </span>            :         opReg = x86PackRegAndVvvvv(opReg, o0.getId());</a>
+<a name="3387"><span class="lineNum">    3387 </span>            :         rmRel = &amp;o1;</a>
+<a name="3388"><span class="lineNum">    3388 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3389"><span class="lineNum">    3389 </span>            :       }</a>
+<a name="3390"><span class="lineNum">    3390 </span>            :       break;</a>
+<a name="3391"><span class="lineNum">    3391 </span>            : </a>
+<a name="3392"><span class="lineNum">    3392 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexEvexVmi_Lx:</span></a>
+<a name="3393"><span class="lineNum">    3393 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm))</span></a>
+<a name="3394"><span class="lineNum">    3394 </span><span class="lineNoCov">          0 :         opCode |= X86Inst::kOpCode_MM_ForceEvex;</span></a>
+<a name="3395"><span class="lineNum">    3395 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3396"><span class="lineNum">    3396 </span>            : </a>
+<a name="3397"><span class="lineNum">    3397 </span>            :     case X86Inst::kEncodingVexVmi_Lx:</a>
+<a name="3398"><span class="lineNum">    3398 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3399"><span class="lineNum">    3399 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3400"><span class="lineNum">    3400 </span>            : </a>
+<a name="3401"><span class="lineNum">    3401 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexVmi:</span></a>
+<a name="3402"><span class="lineNum">    3402 </span>            :       imVal = static_cast&lt;const Imm&amp;&gt;(o2).getInt64();</a>
+<a name="3403"><span class="lineNum">    3403 </span>            :       imLen = 1;</a>
+<a name="3404"><span class="lineNum">    3404 </span>            : </a>
+<a name="3405"><span class="lineNum">    3405 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Imm)) {</span></a>
+<a name="3406"><span class="lineNum">    3406 </span>            :         opReg = x86PackRegAndVvvvv(opReg, o0.getId());</a>
+<a name="3407"><span class="lineNum">    3407 </span>            :         rbReg = o1.getId();</a>
+<a name="3408"><span class="lineNum">    3408 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3409"><span class="lineNum">    3409 </span>            :       }</a>
+<a name="3410"><span class="lineNum">    3410 </span>            : </a>
+<a name="3411"><span class="lineNum">    3411 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Mem, Imm)) {</span></a>
+<a name="3412"><span class="lineNum">    3412 </span>            :         opReg = x86PackRegAndVvvvv(opReg, o0.getId());</a>
+<a name="3413"><span class="lineNum">    3413 </span>            :         rmRel = &amp;o1;</a>
+<a name="3414"><span class="lineNum">    3414 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3415"><span class="lineNum">    3415 </span>            :       }</a>
+<a name="3416"><span class="lineNum">    3416 </span>            :       break;</a>
+<a name="3417"><span class="lineNum">    3417 </span>            : </a>
+<a name="3418"><span class="lineNum">    3418 </span>            :     case X86Inst::kEncodingVexRvrmRvmr_Lx:</a>
+<a name="3419"><span class="lineNum">    3419 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3420"><span class="lineNum">    3420 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3421"><span class="lineNum">    3421 </span>            : </a>
+<a name="3422"><span class="lineNum">    3422 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvrmRvmr: {</span></a>
+<a name="3423"><span class="lineNum">    3423 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="3424"><span class="lineNum">    3424 </span>            : </a>
+<a name="3425"><span class="lineNum">    3425 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Reg)) {</span></a>
+<a name="3426"><span class="lineNum">    3426 </span><span class="lineNoCov">          0 :         imVal = o3.getId() &lt;&lt; 4;</span></a>
+<a name="3427"><span class="lineNum">    3427 </span>            :         imLen = 1;</a>
+<a name="3428"><span class="lineNum">    3428 </span>            : </a>
+<a name="3429"><span class="lineNum">    3429 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3430"><span class="lineNum">    3430 </span>            :         rbReg = o2.getId();</a>
+<a name="3431"><span class="lineNum">    3431 </span>            : </a>
+<a name="3432"><span class="lineNum">    3432 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3433"><span class="lineNum">    3433 </span>            :       }</a>
+<a name="3434"><span class="lineNum">    3434 </span>            : </a>
+<a name="3435"><span class="lineNum">    3435 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Mem)) {</span></a>
+<a name="3436"><span class="lineNum">    3436 </span><span class="lineNoCov">          0 :         imVal = o2.getId() &lt;&lt; 4;</span></a>
+<a name="3437"><span class="lineNum">    3437 </span>            :         imLen = 1;</a>
+<a name="3438"><span class="lineNum">    3438 </span>            : </a>
+<a name="3439"><span class="lineNum">    3439 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3440"><span class="lineNum">    3440 </span>            :         rmRel = &amp;o3;</a>
+<a name="3441"><span class="lineNum">    3441 </span>            : </a>
+<a name="3442"><span class="lineNum">    3442 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3443"><span class="lineNum">    3443 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3444"><span class="lineNum">    3444 </span>            :       }</a>
+<a name="3445"><span class="lineNum">    3445 </span>            : </a>
+<a name="3446"><span class="lineNum">    3446 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Mem, Reg)) {</span></a>
+<a name="3447"><span class="lineNum">    3447 </span><span class="lineNoCov">          0 :         imVal = o3.getId() &lt;&lt; 4;</span></a>
+<a name="3448"><span class="lineNum">    3448 </span>            :         imLen = 1;</a>
+<a name="3449"><span class="lineNum">    3449 </span>            : </a>
+<a name="3450"><span class="lineNum">    3450 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3451"><span class="lineNum">    3451 </span>            :         rmRel = &amp;o2;</a>
+<a name="3452"><span class="lineNum">    3452 </span>            : </a>
+<a name="3453"><span class="lineNum">    3453 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3454"><span class="lineNum">    3454 </span>            :       }</a>
+<a name="3455"><span class="lineNum">    3455 </span>            :       break;</a>
+<a name="3456"><span class="lineNum">    3456 </span>            :     }</a>
+<a name="3457"><span class="lineNum">    3457 </span>            : </a>
+<a name="3458"><span class="lineNum">    3458 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexRvrmiRvmri_Lx: {</span></a>
+<a name="3459"><span class="lineNum">    3459 </span><span class="lineNoCov">          0 :       if (!(options &amp; CodeEmitter::kOptionOp4Op5Used) || !_op4.isImm())</span></a>
+<a name="3460"><span class="lineNum">    3460 </span><span class="lineNoCov">          0 :         goto InvalidInstruction;</span></a>
+<a name="3461"><span class="lineNum">    3461 </span>            : </a>
+<a name="3462"><span class="lineNum">    3462 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="3463"><span class="lineNum">    3463 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize() | o2.getSize() | o3.getSize());</span></a>
+<a name="3464"><span class="lineNum">    3464 </span>            : </a>
+<a name="3465"><span class="lineNum">    3465 </span><span class="lineNoCov">          0 :       imVal = static_cast&lt;const Imm&amp;&gt;(_op4).getUInt8() &amp; 0x0F;</span></a>
+<a name="3466"><span class="lineNum">    3466 </span>            :       imLen = 1;</a>
+<a name="3467"><span class="lineNum">    3467 </span>            : </a>
+<a name="3468"><span class="lineNum">    3468 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Reg)) {</span></a>
+<a name="3469"><span class="lineNum">    3469 </span><span class="lineNoCov">          0 :         imVal |= o3.getId() &lt;&lt; 4;</span></a>
+<a name="3470"><span class="lineNum">    3470 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3471"><span class="lineNum">    3471 </span>            :         rbReg = o2.getId();</a>
+<a name="3472"><span class="lineNum">    3472 </span>            : </a>
+<a name="3473"><span class="lineNum">    3473 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3474"><span class="lineNum">    3474 </span>            :       }</a>
+<a name="3475"><span class="lineNum">    3475 </span>            : </a>
+<a name="3476"><span class="lineNum">    3476 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Mem)) {</span></a>
+<a name="3477"><span class="lineNum">    3477 </span><span class="lineNoCov">          0 :         imVal |= o2.getId() &lt;&lt; 4;</span></a>
+<a name="3478"><span class="lineNum">    3478 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3479"><span class="lineNum">    3479 </span>            :         rmRel = &amp;o3;</a>
+<a name="3480"><span class="lineNum">    3480 </span>            : </a>
+<a name="3481"><span class="lineNum">    3481 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3482"><span class="lineNum">    3482 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3483"><span class="lineNum">    3483 </span>            :       }</a>
+<a name="3484"><span class="lineNum">    3484 </span>            : </a>
+<a name="3485"><span class="lineNum">    3485 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Mem, Reg)) {</span></a>
+<a name="3486"><span class="lineNum">    3486 </span><span class="lineNoCov">          0 :         imVal |= o3.getId() &lt;&lt; 4;</span></a>
+<a name="3487"><span class="lineNum">    3487 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3488"><span class="lineNum">    3488 </span>            :         rmRel = &amp;o2;</a>
+<a name="3489"><span class="lineNum">    3489 </span>            : </a>
+<a name="3490"><span class="lineNum">    3490 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3491"><span class="lineNum">    3491 </span>            :       }</a>
+<a name="3492"><span class="lineNum">    3492 </span>            :       break;</a>
+<a name="3493"><span class="lineNum">    3493 </span>            :     }</a>
+<a name="3494"><span class="lineNum">    3494 </span>            : </a>
+<a name="3495"><span class="lineNum">    3495 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingVexMovssMovsd:</span></a>
+<a name="3496"><span class="lineNum">    3496 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS3(Reg, Reg, Reg)) {</span></a>
+<a name="3497"><span class="lineNum">    3497 </span><span class="lineNoCov">          0 :         goto CaseVexRvm_R;</span></a>
+<a name="3498"><span class="lineNum">    3498 </span>            :       }</a>
+<a name="3499"><span class="lineNum">    3499 </span>            : </a>
+<a name="3500"><span class="lineNum">    3500 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Reg, Mem)) {</span></a>
+<a name="3501"><span class="lineNum">    3501 </span>            :         opReg = o0.getId();</a>
+<a name="3502"><span class="lineNum">    3502 </span>            :         rmRel = &amp;o1;</a>
+<a name="3503"><span class="lineNum">    3503 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3504"><span class="lineNum">    3504 </span>            :       }</a>
+<a name="3505"><span class="lineNum">    3505 </span>            : </a>
+<a name="3506"><span class="lineNum">    3506 </span><span class="lineNoCov">          0 :       if (isign3 == ENC_OPS2(Mem, Reg)) {</span></a>
+<a name="3507"><span class="lineNum">    3507 </span>            :         opCode = commonData-&gt;getAltOpCode();</a>
+<a name="3508"><span class="lineNum">    3508 </span>            :         opReg = o1.getId();</a>
+<a name="3509"><span class="lineNum">    3509 </span>            :         rmRel = &amp;o0;</a>
+<a name="3510"><span class="lineNum">    3510 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3511"><span class="lineNum">    3511 </span>            :       }</a>
+<a name="3512"><span class="lineNum">    3512 </span>            :       break;</a>
+<a name="3513"><span class="lineNum">    3513 </span>            : </a>
+<a name="3514"><span class="lineNum">    3514 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="3515"><span class="lineNum">    3515 </span>            :     // [FMA4]</a>
+<a name="3516"><span class="lineNum">    3516 </span>            :     // ------------------------------------------------------------------------</a>
+<a name="3517"><span class="lineNum">    3517 </span>            : </a>
+<a name="3518"><span class="lineNum">    3518 </span>            :     case X86Inst::kEncodingFma4_Lx:</a>
+<a name="3519"><span class="lineNum">    3519 </span>            :       // It's fine to just check the first operand, second is just for sanity.</a>
+<a name="3520"><span class="lineNum">    3520 </span><span class="lineNoCov">          0 :       opCode |= x86OpCodeLBySize(o0.getSize() | o1.getSize());</span></a>
+<a name="3521"><span class="lineNum">    3521 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="3522"><span class="lineNum">    3522 </span>            : </a>
+<a name="3523"><span class="lineNum">    3523 </span><span class="lineNoCov">          0 :     case X86Inst::kEncodingFma4: {</span></a>
+<a name="3524"><span class="lineNum">    3524 </span><span class="lineNoCov">          0 :       const uint32_t isign4 = isign3 + (o3.getOp() &lt;&lt; 9);</span></a>
+<a name="3525"><span class="lineNum">    3525 </span>            : </a>
+<a name="3526"><span class="lineNum">    3526 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Reg)) {</span></a>
+<a name="3527"><span class="lineNum">    3527 </span><span class="lineNoCov">          0 :         imVal = o3.getId() &lt;&lt; 4;</span></a>
+<a name="3528"><span class="lineNum">    3528 </span>            :         imLen = 1;</a>
+<a name="3529"><span class="lineNum">    3529 </span>            : </a>
+<a name="3530"><span class="lineNum">    3530 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3531"><span class="lineNum">    3531 </span>            :         rbReg = o2.getId();</a>
+<a name="3532"><span class="lineNum">    3532 </span>            : </a>
+<a name="3533"><span class="lineNum">    3533 </span><span class="lineNoCov">          0 :         goto EmitVexEvexR;</span></a>
+<a name="3534"><span class="lineNum">    3534 </span>            :       }</a>
+<a name="3535"><span class="lineNum">    3535 </span>            : </a>
+<a name="3536"><span class="lineNum">    3536 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Reg, Mem)) {</span></a>
+<a name="3537"><span class="lineNum">    3537 </span><span class="lineNoCov">          0 :         imVal = o2.getId() &lt;&lt; 4;</span></a>
+<a name="3538"><span class="lineNum">    3538 </span>            :         imLen = 1;</a>
+<a name="3539"><span class="lineNum">    3539 </span>            : </a>
+<a name="3540"><span class="lineNum">    3540 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3541"><span class="lineNum">    3541 </span>            :         rmRel = &amp;o3;</a>
+<a name="3542"><span class="lineNum">    3542 </span>            : </a>
+<a name="3543"><span class="lineNum">    3543 </span><span class="lineNoCov">          0 :         ADD_VEX_W(true);</span></a>
+<a name="3544"><span class="lineNum">    3544 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3545"><span class="lineNum">    3545 </span>            :       }</a>
+<a name="3546"><span class="lineNum">    3546 </span>            : </a>
+<a name="3547"><span class="lineNum">    3547 </span><span class="lineNoCov">          0 :       if (isign4 == ENC_OPS4(Reg, Reg, Mem, Reg)) {</span></a>
+<a name="3548"><span class="lineNum">    3548 </span><span class="lineNoCov">          0 :         imVal = o3.getId() &lt;&lt; 4;</span></a>
+<a name="3549"><span class="lineNum">    3549 </span>            :         imLen = 1;</a>
+<a name="3550"><span class="lineNum">    3550 </span>            : </a>
+<a name="3551"><span class="lineNum">    3551 </span>            :         opReg = x86PackRegAndVvvvv(o0.getId(), o1.getId());</a>
+<a name="3552"><span class="lineNum">    3552 </span>            :         rmRel = &amp;o2;</a>
+<a name="3553"><span class="lineNum">    3553 </span>            : </a>
+<a name="3554"><span class="lineNum">    3554 </span><span class="lineNoCov">          0 :         goto EmitVexEvexM;</span></a>
+<a name="3555"><span class="lineNum">    3555 </span>            :       }</a>
+<a name="3556"><span class="lineNum">    3556 </span>            :       break;</a>
+<a name="3557"><span class="lineNum">    3557 </span>            :     }</a>
+<a name="3558"><span class="lineNum">    3558 </span>            :   }</a>
+<a name="3559"><span class="lineNum">    3559 </span><span class="lineNoCov">          0 :   goto InvalidInstruction;</span></a>
+<a name="3560"><span class="lineNum">    3560 </span>            : </a>
+<a name="3561"><span class="lineNum">    3561 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3562"><span class="lineNum">    3562 </span>            :   // [Emit - X86]</a>
+<a name="3563"><span class="lineNum">    3563 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3564"><span class="lineNum">    3564 </span>            : </a>
+<a name="3565"><span class="lineNum">    3565 </span><span class="lineNoCov">          0 : EmitX86OpMovAbs:</span></a>
+<a name="3566"><span class="lineNum">    3566 </span>            :   imLen = getGpSize();</a>
+<a name="3567"><span class="lineNum">    3567 </span>            : </a>
+<a name="3568"><span class="lineNum">    3568 </span>            :   // Segment-override prefix.</a>
+<a name="3569"><span class="lineNum">    3569 </span><span class="lineNoCov">          0 :   if (rmRel-&gt;as&lt;X86Mem&gt;().hasSegment())</span></a>
+<a name="3570"><span class="lineNum">    3570 </span><span class="lineNoCov">          0 :     EMIT_BYTE(x86SegmentPrefix[rmRel-&gt;as&lt;X86Mem&gt;().getSegmentId()]);</span></a>
+<a name="3571"><span class="lineNum">    3571 </span>            : </a>
+<a name="3572"><span class="lineNum">    3572 </span><span class="lineNoCov">          0 : EmitX86Op:</span></a>
+<a name="3573"><span class="lineNum">    3573 </span>            :   // Emit mandatory instruction prefix.</a>
+<a name="3574"><span class="lineNum">    3574 </span><span class="lineCov">       1948 :   EMIT_PP(opCode);</span></a>
+<a name="3575"><span class="lineNum">    3575 </span>            : </a>
+<a name="3576"><span class="lineNum">    3576 </span>            :   // Emit REX prefix (64-bit only).</a>
+<a name="3577"><span class="lineNum">    3577 </span>            :   {</a>
+<a name="3578"><span class="lineNum">    3578 </span>            :     uint32_t rex = x86ExtractREX(opCode, options);</a>
+<a name="3579"><span class="lineNum">    3579 </span><span class="lineCov">       1948 :     if (rex) {</span></a>
+<a name="3580"><span class="lineNum">    3580 </span><span class="lineNoCov">          0 :       if (options &amp; X86Inst::_kOptionInvalidRex)</span></a>
+<a name="3581"><span class="lineNum">    3581 </span><span class="lineNoCov">          0 :         goto InvalidRexPrefix;</span></a>
+<a name="3582"><span class="lineNum">    3582 </span><span class="lineNoCov">          0 :       EMIT_BYTE(rex | kX86ByteRex);</span></a>
+<a name="3583"><span class="lineNum">    3583 </span>            :     }</a>
+<a name="3584"><span class="lineNum">    3584 </span>            :   }</a>
+<a name="3585"><span class="lineNum">    3585 </span>            : </a>
+<a name="3586"><span class="lineNum">    3586 </span>            :   // Emit instruction opcodes.</a>
+<a name="3587"><span class="lineNum">    3587 </span><span class="lineCov">       1948 :   EMIT_MM_OP(opCode);</span></a>
+<a name="3588"><span class="lineNum">    3588 </span>            : </a>
+<a name="3589"><span class="lineNum">    3589 </span><span class="lineCov">       1948 :   if (imLen != 0)</span></a>
+<a name="3590"><span class="lineNum">    3590 </span><span class="lineNoCov">          0 :     goto EmitImm;</span></a>
+<a name="3591"><span class="lineNum">    3591 </span>            :   else</a>
+<a name="3592"><span class="lineNum">    3592 </span><span class="lineCov">       1948 :     goto EmitDone;</span></a>
+<a name="3593"><span class="lineNum">    3593 </span>            : </a>
+<a name="3594"><span class="lineNum">    3594 </span><span class="lineCov">       9928 : EmitX86OpReg:</span></a>
+<a name="3595"><span class="lineNum">    3595 </span>            :   // Emit mandatory instruction prefix.</a>
+<a name="3596"><span class="lineNum">    3596 </span><span class="lineCov">       9928 :   EMIT_PP(opCode);</span></a>
+<a name="3597"><span class="lineNum">    3597 </span>            : </a>
+<a name="3598"><span class="lineNum">    3598 </span>            :   // Emit REX prefix (64-bit only).</a>
+<a name="3599"><span class="lineNum">    3599 </span>            :   {</a>
+<a name="3600"><span class="lineNum">    3600 </span>            :     uint32_t rex = x86ExtractREX(opCode, options) |</a>
+<a name="3601"><span class="lineNum">    3601 </span><span class="lineCov">       9928 :                    (opReg &gt;&gt; 3); // Rex.B (0x01).</span></a>
+<a name="3602"><span class="lineNum">    3602 </span><span class="lineCov">       9928 :     if (rex) {</span></a>
+<a name="3603"><span class="lineNum">    3603 </span><span class="lineCov">       7688 :       EMIT_BYTE(rex | kX86ByteRex);</span></a>
+<a name="3604"><span class="lineNum">    3604 </span><span class="lineCov">       7688 :       if (options &amp; X86Inst::_kOptionInvalidRex)</span></a>
+<a name="3605"><span class="lineNum">    3605 </span><span class="lineNoCov">          0 :         goto InvalidRexPrefix;</span></a>
+<a name="3606"><span class="lineNum">    3606 </span><span class="lineCov">       7688 :       opReg &amp;= 0x7;</span></a>
+<a name="3607"><span class="lineNum">    3607 </span>            :     }</a>
+<a name="3608"><span class="lineNum">    3608 </span>            :   }</a>
+<a name="3609"><span class="lineNum">    3609 </span>            : </a>
+<a name="3610"><span class="lineNum">    3610 </span>            :   // Emit instruction opcodes.</a>
+<a name="3611"><span class="lineNum">    3611 </span><span class="lineCov">       9928 :   opCode += opReg;</span></a>
+<a name="3612"><span class="lineNum">    3612 </span><span class="lineCov">       9928 :   EMIT_MM_OP(opCode);</span></a>
+<a name="3613"><span class="lineNum">    3613 </span>            : </a>
+<a name="3614"><span class="lineNum">    3614 </span><span class="lineCov">       9928 :   if (imLen != 0)</span></a>
+<a name="3615"><span class="lineNum">    3615 </span><span class="lineCov">       7688 :     goto EmitImm;</span></a>
+<a name="3616"><span class="lineNum">    3616 </span>            :   else</a>
+<a name="3617"><span class="lineNum">    3617 </span><span class="lineCov">       2240 :     goto EmitDone;</span></a>
+<a name="3618"><span class="lineNum">    3618 </span>            : </a>
+<a name="3619"><span class="lineNum">    3619 </span><span class="lineNoCov">          0 : EmitX86OpImplicitMem:</span></a>
+<a name="3620"><span class="lineNum">    3620 </span>            :   // NOTE: Don't change the emit order here, it's compatible with KeyStone/LLVM.</a>
+<a name="3621"><span class="lineNum">    3621 </span><span class="lineNoCov">          0 :   rmInfo = x86MemInfo[rmRel-&gt;as&lt;X86Mem&gt;().getBaseIndexType()];</span></a>
+<a name="3622"><span class="lineNum">    3622 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(rmRel-&gt;as&lt;X86Mem&gt;().hasOffset() || (rmInfo &amp; kX86MemInfo_Index)))</span></a>
+<a name="3623"><span class="lineNum">    3623 </span><span class="lineNoCov">          0 :     goto InvalidInstruction;</span></a>
+<a name="3624"><span class="lineNum">    3624 </span>            : </a>
+<a name="3625"><span class="lineNum">    3625 </span>            :   // Emit mandatory instruction prefix.</a>
+<a name="3626"><span class="lineNum">    3626 </span><span class="lineNoCov">          0 :   EMIT_PP(opCode);</span></a>
+<a name="3627"><span class="lineNum">    3627 </span>            : </a>
+<a name="3628"><span class="lineNum">    3628 </span>            :   // Emit REX prefix (64-bit only).</a>
+<a name="3629"><span class="lineNum">    3629 </span>            :   {</a>
+<a name="3630"><span class="lineNum">    3630 </span>            :     uint32_t rex = x86ExtractREX(opCode, options);</a>
+<a name="3631"><span class="lineNum">    3631 </span><span class="lineNoCov">          0 :     if (rex) {</span></a>
+<a name="3632"><span class="lineNum">    3632 </span><span class="lineNoCov">          0 :       if (options &amp; X86Inst::_kOptionInvalidRex)</span></a>
+<a name="3633"><span class="lineNum">    3633 </span><span class="lineNoCov">          0 :         goto InvalidRexPrefix;</span></a>
+<a name="3634"><span class="lineNum">    3634 </span><span class="lineNoCov">          0 :       EMIT_BYTE(rex | kX86ByteRex);</span></a>
+<a name="3635"><span class="lineNum">    3635 </span>            :     }</a>
+<a name="3636"><span class="lineNum">    3636 </span>            :   }</a>
+<a name="3637"><span class="lineNum">    3637 </span>            : </a>
+<a name="3638"><span class="lineNum">    3638 </span>            :   // Segment-override prefix.</a>
+<a name="3639"><span class="lineNum">    3639 </span><span class="lineNoCov">          0 :   if (rmRel-&gt;as&lt;X86Mem&gt;().hasSegment())</span></a>
+<a name="3640"><span class="lineNum">    3640 </span><span class="lineNoCov">          0 :     EMIT_BYTE(x86SegmentPrefix[rmRel-&gt;as&lt;X86Mem&gt;().getSegmentId()]);</span></a>
+<a name="3641"><span class="lineNum">    3641 </span>            : </a>
+<a name="3642"><span class="lineNum">    3642 </span>            :   // Address-override prefix.</a>
+<a name="3643"><span class="lineNum">    3643 </span><span class="lineNoCov">          0 :   if (rmInfo &amp; _getAddressOverrideMask())</span></a>
+<a name="3644"><span class="lineNum">    3644 </span><span class="lineNoCov">          0 :     EMIT_BYTE(0x67);</span></a>
+<a name="3645"><span class="lineNum">    3645 </span>            : </a>
+<a name="3646"><span class="lineNum">    3646 </span>            :   // Emit instruction opcodes.</a>
+<a name="3647"><span class="lineNum">    3647 </span><span class="lineNoCov">          0 :   EMIT_MM_OP(opCode);</span></a>
+<a name="3648"><span class="lineNum">    3648 </span>            : </a>
+<a name="3649"><span class="lineNum">    3649 </span>            :   if (imLen != 0)</a>
+<a name="3650"><span class="lineNum">    3650 </span>            :     goto EmitImm;</a>
+<a name="3651"><span class="lineNum">    3651 </span>            :   else</a>
+<a name="3652"><span class="lineNum">    3652 </span><span class="lineNoCov">          0 :     goto EmitDone;</span></a>
+<a name="3653"><span class="lineNum">    3653 </span>            : </a>
+<a name="3654"><span class="lineNum">    3654 </span><span class="lineCov">      21958 : EmitX86R:</span></a>
+<a name="3655"><span class="lineNum">    3655 </span>            :   // Mandatory instruction prefix.</a>
+<a name="3656"><span class="lineNum">    3656 </span><span class="lineCov">      21958 :   EMIT_PP(opCode);</span></a>
+<a name="3657"><span class="lineNum">    3657 </span>            : </a>
+<a name="3658"><span class="lineNum">    3658 </span>            :   // Rex prefix (64-bit only).</a>
+<a name="3659"><span class="lineNum">    3659 </span>            :   {</a>
+<a name="3660"><span class="lineNum">    3660 </span><span class="lineCov">      21958 :     uint32_t rex = x86ExtractREX(opCode, options) |</span></a>
+<a name="3661"><span class="lineNum">    3661 </span><span class="lineCov">      21958 :                    ((opReg &amp; 0x08) &gt;&gt; 1) | // REX.R (0x04).</span></a>
+<a name="3662"><span class="lineNum">    3662 </span><span class="lineCov">      21958 :                    ((rbReg       ) &gt;&gt; 3) ; // REX.B (0x01).</span></a>
+<a name="3663"><span class="lineNum">    3663 </span><span class="lineCov">      21958 :     if (rex) {</span></a>
+<a name="3664"><span class="lineNum">    3664 </span><span class="lineCov">       2198 :       if (options &amp; X86Inst::_kOptionInvalidRex)</span></a>
+<a name="3665"><span class="lineNum">    3665 </span><span class="lineNoCov">          0 :         goto InvalidRexPrefix;</span></a>
+<a name="3666"><span class="lineNum">    3666 </span><span class="lineCov">       2198 :       EMIT_BYTE(rex | kX86ByteRex);</span></a>
+<a name="3667"><span class="lineNum">    3667 </span><span class="lineCov">       2198 :       opReg &amp;= 0x07;</span></a>
+<a name="3668"><span class="lineNum">    3668 </span><span class="lineCov">       2198 :       rbReg &amp;= 0x07;</span></a>
+<a name="3669"><span class="lineNum">    3669 </span>            :     }</a>
+<a name="3670"><span class="lineNum">    3670 </span>            :   }</a>
+<a name="3671"><span class="lineNum">    3671 </span>            : </a>
+<a name="3672"><span class="lineNum">    3672 </span>            :   // Instruction opcodes.</a>
+<a name="3673"><span class="lineNum">    3673 </span><span class="lineCov">      21958 :   EMIT_MM_OP(opCode);</span></a>
+<a name="3674"><span class="lineNum">    3674 </span>            :   // ModR.</a>
+<a name="3675"><span class="lineNum">    3675 </span><span class="lineCov">      21958 :   EMIT_BYTE(x86EncodeMod(3, opReg, rbReg));</span></a>
+<a name="3676"><span class="lineNum">    3676 </span>            : </a>
+<a name="3677"><span class="lineNum">    3677 </span><span class="lineCov">      21958 :   if (imLen != 0)</span></a>
+<a name="3678"><span class="lineNum">    3678 </span><span class="lineCov">       1984 :     goto EmitImm;</span></a>
+<a name="3679"><span class="lineNum">    3679 </span>            :   else</a>
+<a name="3680"><span class="lineNum">    3680 </span><span class="lineCov">      19974 :     goto EmitDone;</span></a>
+<a name="3681"><span class="lineNum">    3681 </span>            : </a>
+<a name="3682"><span class="lineNum">    3682 </span><span class="lineCov">      14528 : EmitX86M:</span></a>
+<a name="3683"><span class="lineNum">    3683 </span>            :   ASMJIT_ASSERT(rmRel != nullptr);</a>
+<a name="3684"><span class="lineNum">    3684 </span>            :   ASMJIT_ASSERT(rmRel-&gt;getOp() == Operand::kOpMem);</a>
+<a name="3685"><span class="lineNum">    3685 </span><span class="lineCov">      14528 :   rmInfo = x86MemInfo[rmRel-&gt;as&lt;X86Mem&gt;().getBaseIndexType()];</span></a>
+<a name="3686"><span class="lineNum">    3686 </span>            : </a>
+<a name="3687"><span class="lineNum">    3687 </span>            :   // GP instructions have never compressed displacement specified.</a>
+<a name="3688"><span class="lineNum">    3688 </span>            :   ASMJIT_ASSERT((opCode &amp; X86Inst::kOpCode_CDSHL_Mask) == 0);</a>
+<a name="3689"><span class="lineNum">    3689 </span>            : </a>
+<a name="3690"><span class="lineNum">    3690 </span>            :   // Segment-override prefix.</a>
+<a name="3691"><span class="lineNum">    3691 </span><span class="lineCov">      14528 :   if (rmRel-&gt;as&lt;X86Mem&gt;().hasSegment())</span></a>
+<a name="3692"><span class="lineNum">    3692 </span><span class="lineNoCov">          0 :     EMIT_BYTE(x86SegmentPrefix[rmRel-&gt;as&lt;X86Mem&gt;().getSegmentId()]);</span></a>
+<a name="3693"><span class="lineNum">    3693 </span>            : </a>
+<a name="3694"><span class="lineNum">    3694 </span>            :   // Address-override prefix.</a>
+<a name="3695"><span class="lineNum">    3695 </span><span class="lineCov">      14528 :   if (rmInfo &amp; _getAddressOverrideMask())</span></a>
+<a name="3696"><span class="lineNum">    3696 </span><span class="lineNoCov">          0 :     EMIT_BYTE(0x67);</span></a>
+<a name="3697"><span class="lineNum">    3697 </span>            : </a>
+<a name="3698"><span class="lineNum">    3698 </span>            :   // Mandatory instruction prefix.</a>
+<a name="3699"><span class="lineNum">    3699 </span><span class="lineCov">      14528 :   EMIT_PP(opCode);</span></a>
+<a name="3700"><span class="lineNum">    3700 </span>            : </a>
+<a name="3701"><span class="lineNum">    3701 </span>            :   rbReg = rmRel-&gt;as&lt;X86Mem&gt;().getBaseId();</a>
+<a name="3702"><span class="lineNum">    3702 </span>            :   rxReg = rmRel-&gt;as&lt;X86Mem&gt;().getIndexId();</a>
+<a name="3703"><span class="lineNum">    3703 </span>            : </a>
+<a name="3704"><span class="lineNum">    3704 </span>            :   // REX prefix (64-bit only).</a>
+<a name="3705"><span class="lineNum">    3705 </span>            :   {</a>
+<a name="3706"><span class="lineNum">    3706 </span>            :     uint32_t rex;</a>
+<a name="3707"><span class="lineNum">    3707 </span>            : </a>
+<a name="3708"><span class="lineNum">    3708 </span><span class="lineCov">      14528 :     rex  = (rbReg &gt;&gt; 3) &amp; 0x01; // REX.B (0x01).</span></a>
+<a name="3709"><span class="lineNum">    3709 </span><span class="lineCov">      14528 :     rex |= (rxReg &gt;&gt; 2) &amp; 0x02; // REX.X (0x02).</span></a>
+<a name="3710"><span class="lineNum">    3710 </span><span class="lineCov">      14528 :     rex |= (opReg &gt;&gt; 1) &amp; 0x04; // REX.R (0x04).</span></a>
+<a name="3711"><span class="lineNum">    3711 </span>            : </a>
+<a name="3712"><span class="lineNum">    3712 </span><span class="lineCov">      14528 :     rex &amp;= rmInfo;</span></a>
+<a name="3713"><span class="lineNum">    3713 </span><span class="lineCov">      14528 :     rex |= x86ExtractREX(opCode, options);</span></a>
+<a name="3714"><span class="lineNum">    3714 </span>            : </a>
+<a name="3715"><span class="lineNum">    3715 </span><span class="lineCov">      14528 :     if (rex) {</span></a>
+<a name="3716"><span class="lineNum">    3716 </span><span class="lineCov">         82 :       if (options &amp; X86Inst::_kOptionInvalidRex)</span></a>
+<a name="3717"><span class="lineNum">    3717 </span><span class="lineNoCov">          0 :         goto InvalidRexPrefix;</span></a>
+<a name="3718"><span class="lineNum">    3718 </span><span class="lineCov">         82 :       EMIT_BYTE(rex | kX86ByteRex);</span></a>
+<a name="3719"><span class="lineNum">    3719 </span><span class="lineCov">         82 :       opReg &amp;= 0x07;</span></a>
+<a name="3720"><span class="lineNum">    3720 </span>            :     }</a>
+<a name="3721"><span class="lineNum">    3721 </span>            :   }</a>
+<a name="3722"><span class="lineNum">    3722 </span>            : </a>
+<a name="3723"><span class="lineNum">    3723 </span>            :   // Instruction opcodes.</a>
+<a name="3724"><span class="lineNum">    3724 </span><span class="lineCov">      14528 :   EMIT_MM_OP(opCode);</span></a>
+<a name="3725"><span class="lineNum">    3725 </span>            :   // ... Fall through ...</a>
+<a name="3726"><span class="lineNum">    3726 </span>            : </a>
+<a name="3727"><span class="lineNum">    3727 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3728"><span class="lineNum">    3728 </span>            :   // [Emit - MOD/SIB]</a>
+<a name="3729"><span class="lineNum">    3729 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3730"><span class="lineNum">    3730 </span>            : </a>
+<a name="3731"><span class="lineNum">    3731 </span><span class="lineCov">      14528 : EmitModSib:</span></a>
+<a name="3732"><span class="lineNum">    3732 </span><span class="lineCov">      14528 :   if (!(rmInfo &amp; (kX86MemInfo_Index | kX86MemInfo_67H_X86))) {</span></a>
+<a name="3733"><span class="lineNum">    3733 </span>            :     // ==========|&gt; [BASE + DISP8|DISP32].</a>
+<a name="3734"><span class="lineNum">    3734 </span><span class="lineCov">      14528 :     if (rmInfo &amp; kX86MemInfo_BaseGp) {</span></a>
+<a name="3735"><span class="lineNum">    3735 </span><span class="lineCov">      14528 :       rbReg &amp;= 0x7;</span></a>
+<a name="3736"><span class="lineNum">    3736 </span>            :       relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3737"><span class="lineNum">    3737 </span>            : </a>
+<a name="3738"><span class="lineNum">    3738 </span>            :       uint32_t mod = x86EncodeMod(0, opReg, rbReg);</a>
+<a name="3739"><span class="lineNum">    3739 </span><span class="lineCov">      14528 :       if (rbReg == X86Gp::kIdSp) {</span></a>
+<a name="3740"><span class="lineNum">    3740 </span>            :         // [XSP|R12].</a>
+<a name="3741"><span class="lineNum">    3741 </span><span class="lineCov">       8428 :         if (relOffset == 0) {</span></a>
+<a name="3742"><span class="lineNum">    3742 </span><span class="lineCov">       1864 :           EMIT_BYTE(mod);</span></a>
+<a name="3743"><span class="lineNum">    3743 </span><span class="lineCov">       1864 :           EMIT_BYTE(x86EncodeSib(0, 4, 4));</span></a>
+<a name="3744"><span class="lineNum">    3744 </span>            :         }</a>
+<a name="3745"><span class="lineNum">    3745 </span>            :         // [XSP|R12 + DISP8|DISP32].</a>
+<a name="3746"><span class="lineNum">    3746 </span>            :         else {</a>
+<a name="3747"><span class="lineNum">    3747 </span><span class="lineCov">       6564 :           uint32_t cdShift = (opCode &amp; X86Inst::kOpCode_CDSHL_Mask) &gt;&gt; X86Inst::kOpCode_CDSHL_Shift;</span></a>
+<a name="3748"><span class="lineNum">    3748 </span><span class="lineCov">       6564 :           int32_t cdOffset = relOffset &gt;&gt; cdShift;</span></a>
+<a name="3749"><span class="lineNum">    3749 </span>            : </a>
+<a name="3750"><span class="lineNum">    3750 </span><span class="lineCov">       6564 :           if (Utils::isInt8(cdOffset) &amp;&amp; relOffset == (cdOffset &lt;&lt; cdShift)) {</span></a>
+<a name="3751"><span class="lineNum">    3751 </span><span class="lineCov">       6564 :             EMIT_BYTE(mod + 0x40); // &lt;- MOD(1, opReg, rbReg).</span></a>
+<a name="3752"><span class="lineNum">    3752 </span><span class="lineCov">       6564 :             EMIT_BYTE(x86EncodeSib(0, 4, 4));</span></a>
+<a name="3753"><span class="lineNum">    3753 </span><span class="lineCov">       6564 :             EMIT_BYTE(cdOffset &amp; 0xFF);</span></a>
+<a name="3754"><span class="lineNum">    3754 </span>            :           }</a>
+<a name="3755"><span class="lineNum">    3755 </span>            :           else {</a>
+<a name="3756"><span class="lineNum">    3756 </span><span class="lineNoCov">          0 :             EMIT_BYTE(mod + 0x80); // &lt;- MOD(2, opReg, rbReg).</span></a>
+<a name="3757"><span class="lineNum">    3757 </span><span class="lineNoCov">          0 :             EMIT_BYTE(x86EncodeSib(0, 4, 4));</span></a>
+<a name="3758"><span class="lineNum">    3758 </span><span class="lineNoCov">          0 :             EMIT_32(relOffset);</span></a>
+<a name="3759"><span class="lineNum">    3759 </span>            :           }</a>
+<a name="3760"><span class="lineNum">    3760 </span>            :         }</a>
+<a name="3761"><span class="lineNum">    3761 </span>            :       }</a>
+<a name="3762"><span class="lineNum">    3762 </span><span class="lineCov">       6100 :       else if (rbReg != X86Gp::kIdBp &amp;&amp; relOffset == 0) {</span></a>
+<a name="3763"><span class="lineNum">    3763 </span>            :         // [BASE].</a>
+<a name="3764"><span class="lineNum">    3764 </span><span class="lineCov">       3882 :         EMIT_BYTE(mod);</span></a>
+<a name="3765"><span class="lineNum">    3765 </span>            :       }</a>
+<a name="3766"><span class="lineNum">    3766 </span>            :       else {</a>
+<a name="3767"><span class="lineNum">    3767 </span>            :         // [BASE + DISP8|DISP32].</a>
+<a name="3768"><span class="lineNum">    3768 </span><span class="lineCov">       2218 :         uint32_t cdShift = (opCode &amp; X86Inst::kOpCode_CDSHL_Mask) &gt;&gt; X86Inst::kOpCode_CDSHL_Shift;</span></a>
+<a name="3769"><span class="lineNum">    3769 </span><span class="lineCov">       2218 :         int32_t cdOffset = relOffset &gt;&gt; cdShift;</span></a>
+<a name="3770"><span class="lineNum">    3770 </span>            : </a>
+<a name="3771"><span class="lineNum">    3771 </span><span class="lineCov">       2218 :         if (Utils::isInt8(cdOffset) &amp;&amp; relOffset == (cdOffset &lt;&lt; cdShift)) {</span></a>
+<a name="3772"><span class="lineNum">    3772 </span><span class="lineCov">       2206 :           EMIT_BYTE(mod + 0x40);</span></a>
+<a name="3773"><span class="lineNum">    3773 </span><span class="lineCov">       2206 :           EMIT_BYTE(cdOffset &amp; 0xFF);</span></a>
+<a name="3774"><span class="lineNum">    3774 </span>            :         }</a>
+<a name="3775"><span class="lineNum">    3775 </span>            :         else {</a>
+<a name="3776"><span class="lineNum">    3776 </span><span class="lineCov">         12 :           EMIT_BYTE(mod + 0x80);</span></a>
+<a name="3777"><span class="lineNum">    3777 </span><span class="lineCov">         12 :           EMIT_32(relOffset);</span></a>
+<a name="3778"><span class="lineNum">    3778 </span>            :         }</a>
+<a name="3779"><span class="lineNum">    3779 </span>            :       }</a>
+<a name="3780"><span class="lineNum">    3780 </span>            :     }</a>
+<a name="3781"><span class="lineNum">    3781 </span>            :     // ==========|&gt; [ABSOLUTE | DISP32].</a>
+<a name="3782"><span class="lineNum">    3782 </span><span class="lineNoCov">          0 :     else if (!(rmInfo &amp; (kX86MemInfo_BaseLabel | kX86MemInfo_BaseRip))) {</span></a>
+<a name="3783"><span class="lineNum">    3783 </span><span class="lineNoCov">          0 :       if (is32Bit()) {</span></a>
+<a name="3784"><span class="lineNum">    3784 </span>            :         relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3785"><span class="lineNum">    3785 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x86EncodeMod(0, opReg, 5));</span></a>
+<a name="3786"><span class="lineNum">    3786 </span><span class="lineNoCov">          0 :         EMIT_32(relOffset);</span></a>
+<a name="3787"><span class="lineNum">    3787 </span>            :       }</a>
+<a name="3788"><span class="lineNum">    3788 </span>            :       else {</a>
+<a name="3789"><span class="lineNum">    3789 </span>            :         uint64_t baseAddress = getCodeInfo().getBaseAddress();</a>
+<a name="3790"><span class="lineNum">    3790 </span>            :         relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3791"><span class="lineNum">    3791 </span>            : </a>
+<a name="3792"><span class="lineNum">    3792 </span>            :         // Prefer absolute addressing mode if FS|GS segment override is present.</a>
+<a name="3793"><span class="lineNum">    3793 </span><span class="lineNoCov">          0 :         bool absoluteValid = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetHi32() == (relOffset &gt;&gt; 31);</span></a>
+<a name="3794"><span class="lineNum">    3794 </span><span class="lineNoCov">          0 :         bool preferAbsolute = (rmRel-&gt;as&lt;X86Mem&gt;().getSegmentId() &gt;= X86Seg::kIdFs) || rmRel-&gt;as&lt;X86Mem&gt;().isAbs();</span></a>
+<a name="3795"><span class="lineNum">    3795 </span>            : </a>
+<a name="3796"><span class="lineNum">    3796 </span>            :         // If we know the base address and the memory operand points to an</a>
+<a name="3797"><span class="lineNum">    3797 </span>            :         // absolute address it's possible to calculate REL32 that can be</a>
+<a name="3798"><span class="lineNum">    3798 </span>            :         // be used as [RIP+REL32] in 64-bit mode.</a>
+<a name="3799"><span class="lineNum">    3799 </span><span class="lineNoCov">          0 :         if (baseAddress != Globals::kNoBaseAddress &amp;&amp; !preferAbsolute) {</span></a>
+<a name="3800"><span class="lineNum">    3800 </span>            :           const uint32_t kModRel32Size = 5;</a>
+<a name="3801"><span class="lineNum">    3801 </span><span class="lineNoCov">          0 :           uint64_t rip64 = baseAddress +</span></a>
+<a name="3802"><span class="lineNum">    3802 </span><span class="lineNoCov">          0 :             static_cast&lt;uint64_t&gt;((uintptr_t)(cursor - _bufferData)) + imLen + kModRel32Size;</span></a>
+<a name="3803"><span class="lineNum">    3803 </span>            : </a>
+<a name="3804"><span class="lineNum">    3804 </span><span class="lineNoCov">          0 :           uint64_t rel64 = static_cast&lt;uint64_t&gt;(rmRel-&gt;as&lt;X86Mem&gt;().getOffset()) - rip64;</span></a>
+<a name="3805"><span class="lineNum">    3805 </span><span class="lineNoCov">          0 :           if (Utils::isInt32(static_cast&lt;int64_t&gt;(rel64))) {</span></a>
+<a name="3806"><span class="lineNum">    3806 </span><span class="lineNoCov">          0 :             EMIT_BYTE(x86EncodeMod(0, opReg, 5));</span></a>
+<a name="3807"><span class="lineNum">    3807 </span><span class="lineNoCov">          0 :             EMIT_32(static_cast&lt;uint32_t&gt;(rel64 &amp; 0xFFFFFFFFU));</span></a>
+<a name="3808"><span class="lineNum">    3808 </span><span class="lineNoCov">          0 :             if (imLen != 0)</span></a>
+<a name="3809"><span class="lineNum">    3809 </span><span class="lineNoCov">          0 :               goto EmitImm;</span></a>
+<a name="3810"><span class="lineNum">    3810 </span>            :             else</a>
+<a name="3811"><span class="lineNum">    3811 </span><span class="lineNoCov">          0 :               goto EmitDone;</span></a>
+<a name="3812"><span class="lineNum">    3812 </span>            :           }</a>
+<a name="3813"><span class="lineNum">    3813 </span>            :         }</a>
+<a name="3814"><span class="lineNum">    3814 </span>            : </a>
+<a name="3815"><span class="lineNum">    3815 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(!absoluteValid))</span></a>
+<a name="3816"><span class="lineNum">    3816 </span><span class="lineNoCov">          0 :           goto InvalidAddress64Bit;</span></a>
+<a name="3817"><span class="lineNum">    3817 </span>            : </a>
+<a name="3818"><span class="lineNum">    3818 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x86EncodeMod(0, opReg, 4));</span></a>
+<a name="3819"><span class="lineNum">    3819 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x86EncodeSib(0, 4, 5));</span></a>
+<a name="3820"><span class="lineNum">    3820 </span><span class="lineNoCov">          0 :         EMIT_32(relOffset);</span></a>
+<a name="3821"><span class="lineNum">    3821 </span>            :       }</a>
+<a name="3822"><span class="lineNum">    3822 </span>            :     }</a>
+<a name="3823"><span class="lineNum">    3823 </span>            :     // ==========|&gt; [LABEL|RIP + DISP32]</a>
+<a name="3824"><span class="lineNum">    3824 </span>            :     else {</a>
+<a name="3825"><span class="lineNum">    3825 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x86EncodeMod(0, opReg, 5));</span></a>
+<a name="3826"><span class="lineNum">    3826 </span>            : </a>
+<a name="3827"><span class="lineNum">    3827 </span><span class="lineNoCov">          0 :       if (is32Bit()) {</span></a>
+<a name="3828"><span class="lineNum">    3828 </span><span class="lineNoCov">          0 : EmitModSib_LabelRip_X86:</span></a>
+<a name="3829"><span class="lineNum">    3829 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(_code-&gt;_relocations.willGrow(&amp;_code-&gt;_baseHeap) != kErrorOk))</span></a>
+<a name="3830"><span class="lineNum">    3830 </span><span class="lineNoCov">          0 :           goto NoHeapMemory;</span></a>
+<a name="3831"><span class="lineNum">    3831 </span>            : </a>
+<a name="3832"><span class="lineNum">    3832 </span>            :         relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3833"><span class="lineNum">    3833 </span><span class="lineNoCov">          0 :         if (rmInfo &amp; kX86MemInfo_BaseLabel) {</span></a>
+<a name="3834"><span class="lineNum">    3834 </span>            :           // [LABEL-&gt;ABS].</a>
+<a name="3835"><span class="lineNum">    3835 </span><span class="lineNoCov">          0 :           label = _code-&gt;getLabelEntry(rmRel-&gt;as&lt;X86Mem&gt;().getBaseId());</span></a>
+<a name="3836"><span class="lineNum">    3836 </span><span class="lineNoCov">          0 :           if (!label) goto InvalidLabel;</span></a>
+<a name="3837"><span class="lineNum">    3837 </span>            : </a>
+<a name="3838"><span class="lineNum">    3838 </span><span class="lineNoCov">          0 :           err = _code-&gt;newRelocEntry(&amp;re, RelocEntry::kTypeRelToAbs, 4);</span></a>
+<a name="3839"><span class="lineNum">    3839 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(err)) goto Failed;</span></a>
+<a name="3840"><span class="lineNum">    3840 </span>            : </a>
+<a name="3841"><span class="lineNum">    3841 </span><span class="lineNoCov">          0 :           re-&gt;_sourceSectionId = _section-&gt;getId();</span></a>
+<a name="3842"><span class="lineNum">    3842 </span><span class="lineNoCov">          0 :           re-&gt;_sourceOffset = static_cast&lt;uint64_t&gt;((uintptr_t)(cursor - _bufferData));</span></a>
+<a name="3843"><span class="lineNum">    3843 </span><span class="lineNoCov">          0 :           re-&gt;_data = static_cast&lt;int64_t&gt;(relOffset);</span></a>
+<a name="3844"><span class="lineNum">    3844 </span>            : </a>
+<a name="3845"><span class="lineNum">    3845 </span><span class="lineNoCov">          0 :           if (label-&gt;isBound()) {</span></a>
+<a name="3846"><span class="lineNum">    3846 </span>            :             // Bound label.</a>
+<a name="3847"><span class="lineNum">    3847 </span><span class="lineNoCov">          0 :             re-&gt;_data += static_cast&lt;uint64_t&gt;(label-&gt;getOffset());</span></a>
+<a name="3848"><span class="lineNum">    3848 </span><span class="lineNoCov">          0 :             EMIT_32(0);</span></a>
+<a name="3849"><span class="lineNum">    3849 </span>            :           }</a>
+<a name="3850"><span class="lineNum">    3850 </span>            :           else {</a>
+<a name="3851"><span class="lineNum">    3851 </span>            :             // Non-bound label.</a>
+<a name="3852"><span class="lineNum">    3852 </span><span class="lineNoCov">          0 :             relOffset = -4 - imLen;</span></a>
+<a name="3853"><span class="lineNum">    3853 </span>            :             relSize = 4;</a>
+<a name="3854"><span class="lineNum">    3854 </span><span class="lineNoCov">          0 :             goto EmitRel;</span></a>
+<a name="3855"><span class="lineNum">    3855 </span>            :           }</a>
+<a name="3856"><span class="lineNum">    3856 </span>            :         }</a>
+<a name="3857"><span class="lineNum">    3857 </span>            :         else {</a>
+<a name="3858"><span class="lineNum">    3858 </span>            :           // [RIP-&gt;ABS].</a>
+<a name="3859"><span class="lineNum">    3859 </span><span class="lineNoCov">          0 :           err = _code-&gt;newRelocEntry(&amp;re, RelocEntry::kTypeRelToAbs, 4);</span></a>
+<a name="3860"><span class="lineNum">    3860 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(err)) goto Failed;</span></a>
+<a name="3861"><span class="lineNum">    3861 </span>            : </a>
+<a name="3862"><span class="lineNum">    3862 </span><span class="lineNoCov">          0 :           re-&gt;_sourceSectionId = _section-&gt;getId();</span></a>
+<a name="3863"><span class="lineNum">    3863 </span><span class="lineNoCov">          0 :           re-&gt;_sourceOffset = static_cast&lt;uint64_t&gt;((uintptr_t)(cursor - _bufferData));</span></a>
+<a name="3864"><span class="lineNum">    3864 </span><span class="lineNoCov">          0 :           re-&gt;_data = re-&gt;_sourceOffset + static_cast&lt;uint64_t&gt;(static_cast&lt;int64_t&gt;(relOffset));</span></a>
+<a name="3865"><span class="lineNum">    3865 </span><span class="lineNoCov">          0 :           EMIT_32(0);</span></a>
+<a name="3866"><span class="lineNum">    3866 </span>            :         }</a>
+<a name="3867"><span class="lineNum">    3867 </span>            :       }</a>
+<a name="3868"><span class="lineNum">    3868 </span>            :       else {</a>
+<a name="3869"><span class="lineNum">    3869 </span>            :         relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3870"><span class="lineNum">    3870 </span><span class="lineNoCov">          0 :         if (rmInfo &amp; kX86MemInfo_BaseLabel) {</span></a>
+<a name="3871"><span class="lineNum">    3871 </span>            :           // [RIP].</a>
+<a name="3872"><span class="lineNum">    3872 </span><span class="lineNoCov">          0 :           label = _code-&gt;getLabelEntry(rmRel-&gt;as&lt;X86Mem&gt;().getBaseId());</span></a>
+<a name="3873"><span class="lineNum">    3873 </span><span class="lineNoCov">          0 :           if (!label) goto InvalidLabel;</span></a>
+<a name="3874"><span class="lineNum">    3874 </span>            : </a>
+<a name="3875"><span class="lineNum">    3875 </span><span class="lineNoCov">          0 :           relOffset -= (4 + imLen);</span></a>
+<a name="3876"><span class="lineNum">    3876 </span><span class="lineNoCov">          0 :           if (label-&gt;isBound()) {</span></a>
+<a name="3877"><span class="lineNum">    3877 </span>            :             // Bound label.</a>
+<a name="3878"><span class="lineNum">    3878 </span><span class="lineNoCov">          0 :             relOffset += label-&gt;getOffset() - static_cast&lt;int32_t&gt;((intptr_t)(cursor - _bufferData));</span></a>
+<a name="3879"><span class="lineNum">    3879 </span><span class="lineNoCov">          0 :             EMIT_32(static_cast&lt;int32_t&gt;(relOffset));</span></a>
+<a name="3880"><span class="lineNum">    3880 </span>            :           }</a>
+<a name="3881"><span class="lineNum">    3881 </span>            :           else {</a>
+<a name="3882"><span class="lineNum">    3882 </span>            :             // Non-bound label.</a>
+<a name="3883"><span class="lineNum">    3883 </span>            :             relSize = 4;</a>
+<a name="3884"><span class="lineNum">    3884 </span><span class="lineNoCov">          0 :             goto EmitRel;</span></a>
+<a name="3885"><span class="lineNum">    3885 </span>            :           }</a>
+<a name="3886"><span class="lineNum">    3886 </span>            :         }</a>
+<a name="3887"><span class="lineNum">    3887 </span>            :         else {</a>
+<a name="3888"><span class="lineNum">    3888 </span>            :           // [RIP].</a>
+<a name="3889"><span class="lineNum">    3889 </span><span class="lineNoCov">          0 :           EMIT_32(static_cast&lt;int32_t&gt;(relOffset));</span></a>
+<a name="3890"><span class="lineNum">    3890 </span>            :         }</a>
+<a name="3891"><span class="lineNum">    3891 </span>            :       }</a>
+<a name="3892"><span class="lineNum">    3892 </span>            :     }</a>
+<a name="3893"><span class="lineNum">    3893 </span>            :   }</a>
+<a name="3894"><span class="lineNum">    3894 </span><span class="lineNoCov">          0 :   else if (!(rmInfo &amp; kX86MemInfo_67H_X86)) {</span></a>
+<a name="3895"><span class="lineNum">    3895 </span>            :     // ESP|RSP can't be used as INDEX in pure SIB mode, however, VSIB mode</a>
+<a name="3896"><span class="lineNum">    3896 </span>            :     // allows XMM4|YMM4|ZMM4 (that's why the check is before the label).</a>
+<a name="3897"><span class="lineNum">    3897 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(rxReg == X86Gp::kIdSp))</span></a>
+<a name="3898"><span class="lineNum">    3898 </span><span class="lineNoCov">          0 :       goto InvalidAddressIndex;</span></a>
+<a name="3899"><span class="lineNum">    3899 </span>            : </a>
+<a name="3900"><span class="lineNum">    3900 </span><span class="lineNoCov">          0 : EmitModVSib:</span></a>
+<a name="3901"><span class="lineNum">    3901 </span><span class="lineNoCov">          0 :     rxReg &amp;= 0x7;</span></a>
+<a name="3902"><span class="lineNum">    3902 </span>            : </a>
+<a name="3903"><span class="lineNum">    3903 </span>            :     // ==========|&gt; [BASE + INDEX + DISP8|DISP32].</a>
+<a name="3904"><span class="lineNum">    3904 </span><span class="lineNoCov">          0 :     if (rmInfo &amp; kX86MemInfo_BaseGp) {</span></a>
+<a name="3905"><span class="lineNum">    3905 </span><span class="lineNoCov">          0 :       rbReg &amp;= 0x7;</span></a>
+<a name="3906"><span class="lineNum">    3906 </span>            :       relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3907"><span class="lineNum">    3907 </span>            : </a>
+<a name="3908"><span class="lineNum">    3908 </span>            :       uint32_t mod = x86EncodeMod(0, opReg, 4);</a>
+<a name="3909"><span class="lineNum">    3909 </span>            :       uint32_t sib = x86EncodeSib(rmRel-&gt;as&lt;X86Mem&gt;().getShift(), rxReg, rbReg);</a>
+<a name="3910"><span class="lineNum">    3910 </span>            : </a>
+<a name="3911"><span class="lineNum">    3911 </span><span class="lineNoCov">          0 :       if (relOffset == 0 &amp;&amp; rbReg != X86Gp::kIdBp) {</span></a>
+<a name="3912"><span class="lineNum">    3912 </span>            :         // [BASE + INDEX &lt;&lt; SHIFT].</a>
+<a name="3913"><span class="lineNum">    3913 </span><span class="lineNoCov">          0 :         EMIT_BYTE(mod);</span></a>
+<a name="3914"><span class="lineNum">    3914 </span><span class="lineNoCov">          0 :         EMIT_BYTE(sib);</span></a>
+<a name="3915"><span class="lineNum">    3915 </span>            :       }</a>
+<a name="3916"><span class="lineNum">    3916 </span>            :       else {</a>
+<a name="3917"><span class="lineNum">    3917 </span><span class="lineNoCov">          0 :         uint32_t cdShift = (opCode &amp; X86Inst::kOpCode_CDSHL_Mask) &gt;&gt; X86Inst::kOpCode_CDSHL_Shift;</span></a>
+<a name="3918"><span class="lineNum">    3918 </span><span class="lineNoCov">          0 :         int32_t cdOffset = relOffset &gt;&gt; cdShift;</span></a>
+<a name="3919"><span class="lineNum">    3919 </span>            : </a>
+<a name="3920"><span class="lineNum">    3920 </span><span class="lineNoCov">          0 :         if (Utils::isInt8(cdOffset) &amp;&amp; relOffset == (cdOffset &lt;&lt; cdShift)) {</span></a>
+<a name="3921"><span class="lineNum">    3921 </span>            :           // [BASE + INDEX &lt;&lt; SHIFT + DISP8].</a>
+<a name="3922"><span class="lineNum">    3922 </span><span class="lineNoCov">          0 :           EMIT_BYTE(mod + 0x40); // &lt;- MOD(1, opReg, 4).</span></a>
+<a name="3923"><span class="lineNum">    3923 </span><span class="lineNoCov">          0 :           EMIT_BYTE(sib);</span></a>
+<a name="3924"><span class="lineNum">    3924 </span><span class="lineNoCov">          0 :           EMIT_BYTE(cdOffset);</span></a>
+<a name="3925"><span class="lineNum">    3925 </span>            :         }</a>
+<a name="3926"><span class="lineNum">    3926 </span>            :         else {</a>
+<a name="3927"><span class="lineNum">    3927 </span>            :           // [BASE + INDEX &lt;&lt; SHIFT + DISP32].</a>
+<a name="3928"><span class="lineNum">    3928 </span><span class="lineNoCov">          0 :           EMIT_BYTE(mod + 0x80); // &lt;- MOD(2, opReg, 4).</span></a>
+<a name="3929"><span class="lineNum">    3929 </span><span class="lineNoCov">          0 :           EMIT_BYTE(sib);</span></a>
+<a name="3930"><span class="lineNum">    3930 </span><span class="lineNoCov">          0 :           EMIT_32(relOffset);</span></a>
+<a name="3931"><span class="lineNum">    3931 </span>            :         }</a>
+<a name="3932"><span class="lineNum">    3932 </span>            :       }</a>
+<a name="3933"><span class="lineNum">    3933 </span>            :     }</a>
+<a name="3934"><span class="lineNum">    3934 </span>            :     // ==========|&gt; [INDEX + DISP32].</a>
+<a name="3935"><span class="lineNum">    3935 </span><span class="lineNoCov">          0 :     else if (!(rmInfo &amp; (kX86MemInfo_BaseLabel | kX86MemInfo_BaseRip))) {</span></a>
+<a name="3936"><span class="lineNum">    3936 </span>            :       // [INDEX &lt;&lt; SHIFT + DISP32].</a>
+<a name="3937"><span class="lineNum">    3937 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x86EncodeMod(0, opReg, 4));</span></a>
+<a name="3938"><span class="lineNum">    3938 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x86EncodeSib(rmRel-&gt;as&lt;X86Mem&gt;().getShift(), rxReg, 5));</span></a>
+<a name="3939"><span class="lineNum">    3939 </span>            : </a>
+<a name="3940"><span class="lineNum">    3940 </span>            :       relOffset = rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32();</a>
+<a name="3941"><span class="lineNum">    3941 </span><span class="lineNoCov">          0 :       EMIT_32(relOffset);</span></a>
+<a name="3942"><span class="lineNum">    3942 </span>            :     }</a>
+<a name="3943"><span class="lineNum">    3943 </span>            :     // ==========|&gt; [LABEL|RIP + INDEX + DISP32].</a>
+<a name="3944"><span class="lineNum">    3944 </span>            :     else {</a>
+<a name="3945"><span class="lineNum">    3945 </span><span class="lineNoCov">          0 :       if (is32Bit()) {</span></a>
+<a name="3946"><span class="lineNum">    3946 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x86EncodeMod(0, opReg, 4));</span></a>
+<a name="3947"><span class="lineNum">    3947 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x86EncodeSib(rmRel-&gt;as&lt;X86Mem&gt;().getShift(), rxReg, 5));</span></a>
+<a name="3948"><span class="lineNum">    3948 </span><span class="lineNoCov">          0 :         goto EmitModSib_LabelRip_X86;</span></a>
+<a name="3949"><span class="lineNum">    3949 </span>            :       }</a>
+<a name="3950"><span class="lineNum">    3950 </span>            :       else {</a>
+<a name="3951"><span class="lineNum">    3951 </span>            :         // NOTE: This also handles VSIB+RIP, which is not allowed in 64-bit mode.</a>
+<a name="3952"><span class="lineNum">    3952 </span><span class="lineNoCov">          0 :         goto InvalidAddress;</span></a>
+<a name="3953"><span class="lineNum">    3953 </span>            :       }</a>
+<a name="3954"><span class="lineNum">    3954 </span>            :     }</a>
+<a name="3955"><span class="lineNum">    3955 </span>            :   }</a>
+<a name="3956"><span class="lineNum">    3956 </span>            :   else {</a>
+<a name="3957"><span class="lineNum">    3957 </span>            :     // 16-bit address mode (32-bit mode with 67 override prefix).</a>
+<a name="3958"><span class="lineNum">    3958 </span><span class="lineNoCov">          0 :     relOffset = (static_cast&lt;int32_t&gt;(rmRel-&gt;as&lt;X86Mem&gt;().getOffsetLo32()) &lt;&lt; 16) &gt;&gt; 16;</span></a>
+<a name="3959"><span class="lineNum">    3959 </span>            : </a>
+<a name="3960"><span class="lineNum">    3960 </span>            :     // NOTE: 16-bit addresses don't use SIB byte and their encoding differs. We</a>
+<a name="3961"><span class="lineNum">    3961 </span>            :     // use a table-based approach to calculate the proper MOD byte as it's easier.</a>
+<a name="3962"><span class="lineNum">    3962 </span>            :     // Also, not all BASE [+ INDEX] combinations are supported in 16-bit mode, so</a>
+<a name="3963"><span class="lineNum">    3963 </span>            :     // this may fail.</a>
+<a name="3964"><span class="lineNum">    3964 </span>            :     const uint32_t kBaseGpIdx = (kX86MemInfo_BaseGp | kX86MemInfo_Index);</a>
+<a name="3965"><span class="lineNum">    3965 </span>            : </a>
+<a name="3966"><span class="lineNum">    3966 </span><span class="lineNoCov">          0 :     if (rmInfo &amp; kBaseGpIdx) {</span></a>
+<a name="3967"><span class="lineNum">    3967 </span>            :       // ==========|&gt; [BASE + INDEX + DISP16].</a>
+<a name="3968"><span class="lineNum">    3968 </span>            :       uint32_t mod;</a>
+<a name="3969"><span class="lineNum">    3969 </span>            : </a>
+<a name="3970"><span class="lineNum">    3970 </span><span class="lineNoCov">          0 :       rbReg &amp;= 0x7;</span></a>
+<a name="3971"><span class="lineNum">    3971 </span><span class="lineNoCov">          0 :       rxReg &amp;= 0x7;</span></a>
+<a name="3972"><span class="lineNum">    3972 </span>            : </a>
+<a name="3973"><span class="lineNum">    3973 </span><span class="lineNoCov">          0 :       if ((rmInfo &amp; kBaseGpIdx) == kBaseGpIdx) {</span></a>
+<a name="3974"><span class="lineNum">    3974 </span>            :         uint32_t shf = rmRel-&gt;as&lt;X86Mem&gt;().getShift();</a>
+<a name="3975"><span class="lineNum">    3975 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(shf != 0))</span></a>
+<a name="3976"><span class="lineNum">    3976 </span><span class="lineNoCov">          0 :           goto InvalidAddress;</span></a>
+<a name="3977"><span class="lineNum">    3977 </span><span class="lineNoCov">          0 :         mod = x86Mod16BaseIndexTable[(rbReg &lt;&lt; 3) + rxReg];</span></a>
+<a name="3978"><span class="lineNum">    3978 </span>            :       }</a>
+<a name="3979"><span class="lineNum">    3979 </span>            :       else {</a>
+<a name="3980"><span class="lineNum">    3980 </span><span class="lineNoCov">          0 :         if (rmInfo &amp; kX86MemInfo_Index)</span></a>
+<a name="3981"><span class="lineNum">    3981 </span>            :           rbReg = rxReg;</a>
+<a name="3982"><span class="lineNum">    3982 </span><span class="lineNoCov">          0 :         mod = x86Mod16BaseTable[rbReg];</span></a>
+<a name="3983"><span class="lineNum">    3983 </span>            :       }</a>
+<a name="3984"><span class="lineNum">    3984 </span>            : </a>
+<a name="3985"><span class="lineNum">    3985 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(mod == 0xFF))</span></a>
+<a name="3986"><span class="lineNum">    3986 </span><span class="lineNoCov">          0 :         goto InvalidAddress;</span></a>
+<a name="3987"><span class="lineNum">    3987 </span>            : </a>
+<a name="3988"><span class="lineNum">    3988 </span><span class="lineNoCov">          0 :       mod += opReg &lt;&lt; 3;</span></a>
+<a name="3989"><span class="lineNum">    3989 </span><span class="lineNoCov">          0 :       if (relOffset == 0 &amp;&amp; mod != 0x06) {</span></a>
+<a name="3990"><span class="lineNum">    3990 </span><span class="lineNoCov">          0 :         EMIT_BYTE(mod);</span></a>
+<a name="3991"><span class="lineNum">    3991 </span>            :       }</a>
+<a name="3992"><span class="lineNum">    3992 </span><span class="lineNoCov">          0 :       else if (Utils::isInt8(relOffset)) {</span></a>
+<a name="3993"><span class="lineNum">    3993 </span><span class="lineNoCov">          0 :         EMIT_BYTE(mod + 0x40);</span></a>
+<a name="3994"><span class="lineNum">    3994 </span><span class="lineNoCov">          0 :         EMIT_BYTE(relOffset);</span></a>
+<a name="3995"><span class="lineNum">    3995 </span>            :       }</a>
+<a name="3996"><span class="lineNum">    3996 </span>            :       else {</a>
+<a name="3997"><span class="lineNum">    3997 </span><span class="lineNoCov">          0 :         EMIT_BYTE(mod + 0x80);</span></a>
+<a name="3998"><span class="lineNum">    3998 </span><span class="lineNoCov">          0 :         EMIT_16(relOffset);</span></a>
+<a name="3999"><span class="lineNum">    3999 </span>            :       }</a>
+<a name="4000"><span class="lineNum">    4000 </span>            :     }</a>
+<a name="4001"><span class="lineNum">    4001 </span>            :     else {</a>
+<a name="4002"><span class="lineNum">    4002 </span>            :       // Not supported in 16-bit addresses.</a>
+<a name="4003"><span class="lineNum">    4003 </span><span class="lineNoCov">          0 :       if (rmInfo &amp; (kX86MemInfo_BaseRip | kX86MemInfo_BaseLabel))</span></a>
+<a name="4004"><span class="lineNum">    4004 </span><span class="lineNoCov">          0 :         goto InvalidAddress;</span></a>
+<a name="4005"><span class="lineNum">    4005 </span>            : </a>
+<a name="4006"><span class="lineNum">    4006 </span>            :       // ==========|&gt; [DISP16].</a>
+<a name="4007"><span class="lineNum">    4007 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opReg | 0x06);</span></a>
+<a name="4008"><span class="lineNum">    4008 </span><span class="lineNoCov">          0 :       EMIT_16(relOffset);</span></a>
+<a name="4009"><span class="lineNum">    4009 </span>            :     }</a>
+<a name="4010"><span class="lineNum">    4010 </span>            :   }</a>
+<a name="4011"><span class="lineNum">    4011 </span>            : </a>
+<a name="4012"><span class="lineNum">    4012 </span><span class="lineCov">      14528 :   if (imLen != 0)</span></a>
+<a name="4013"><span class="lineNum">    4013 </span><span class="lineNoCov">          0 :     goto EmitImm;</span></a>
+<a name="4014"><span class="lineNum">    4014 </span>            :   else</a>
+<a name="4015"><span class="lineNum">    4015 </span><span class="lineCov">      14528 :     goto EmitDone;</span></a>
+<a name="4016"><span class="lineNum">    4016 </span>            : </a>
+<a name="4017"><span class="lineNum">    4017 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4018"><span class="lineNum">    4018 </span>            :   // [Emit - FPU]</a>
+<a name="4019"><span class="lineNum">    4019 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4020"><span class="lineNum">    4020 </span>            : </a>
+<a name="4021"><span class="lineNum">    4021 </span><span class="lineNoCov">          0 : EmitFpuOp:</span></a>
+<a name="4022"><span class="lineNum">    4022 </span>            :   // Mandatory instruction prefix.</a>
+<a name="4023"><span class="lineNum">    4023 </span><span class="lineNoCov">          0 :   EMIT_PP(opCode);</span></a>
+<a name="4024"><span class="lineNum">    4024 </span>            : </a>
+<a name="4025"><span class="lineNum">    4025 </span>            :   // FPU instructions consist of two opcodes.</a>
+<a name="4026"><span class="lineNum">    4026 </span><span class="lineNoCov">          0 :   EMIT_BYTE(opCode &gt;&gt; X86Inst::kOpCode_FPU_2B_Shift);</span></a>
+<a name="4027"><span class="lineNum">    4027 </span><span class="lineNoCov">          0 :   EMIT_BYTE(opCode);</span></a>
+<a name="4028"><span class="lineNum">    4028 </span><span class="lineNoCov">          0 :   goto EmitDone;</span></a>
+<a name="4029"><span class="lineNum">    4029 </span>            : </a>
+<a name="4030"><span class="lineNum">    4030 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4031"><span class="lineNum">    4031 </span>            :   // [Emit - VEX / EVEX]</a>
+<a name="4032"><span class="lineNum">    4032 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4033"><span class="lineNum">    4033 </span>            : </a>
+<a name="4034"><span class="lineNum">    4034 </span>            : EmitVexEvexOp:</a>
+<a name="4035"><span class="lineNum">    4035 </span>            :   {</a>
+<a name="4036"><span class="lineNum">    4036 </span>            :     // These don't use immediate.</a>
+<a name="4037"><span class="lineNum">    4037 </span>            :     ASMJIT_ASSERT(imLen == 0);</a>
+<a name="4038"><span class="lineNum">    4038 </span>            : </a>
+<a name="4039"><span class="lineNum">    4039 </span>            :     // Only 'vzeroall' and 'vzeroupper' instructions use this encoding, they</a>
+<a name="4040"><span class="lineNum">    4040 </span>            :     // don't define 'W' to be '1' so we can just check the 'mmmmm' field. Both</a>
+<a name="4041"><span class="lineNum">    4041 </span>            :     // functions can encode by using VEV2 prefix so VEV3 is basically only used</a>
+<a name="4042"><span class="lineNum">    4042 </span>            :     // when forced from outside.</a>
+<a name="4043"><span class="lineNum">    4043 </span>            :     ASMJIT_ASSERT((opCode &amp; X86Inst::kOpCode_W) == 0);</a>
+<a name="4044"><span class="lineNum">    4044 </span>            : </a>
+<a name="4045"><span class="lineNum">    4045 </span><span class="lineNoCov">          0 :     uint32_t x = ((opCode &amp; X86Inst::kOpCode_MM_Mask   ) &gt;&gt; (X86Inst::kOpCode_MM_Shift     )) |</span></a>
+<a name="4046"><span class="lineNum">    4046 </span><span class="lineNoCov">          0 :                  ((opCode &amp; X86Inst::kOpCode_LL_Mask   ) &gt;&gt; (X86Inst::kOpCode_LL_Shift - 10)) |</span></a>
+<a name="4047"><span class="lineNum">    4047 </span><span class="lineNoCov">          0 :                  ((opCode &amp; X86Inst::kOpCode_PP_VEXMask) &gt;&gt; (X86Inst::kOpCode_PP_Shift -  8)) |</span></a>
+<a name="4048"><span class="lineNum">    4048 </span><span class="lineNoCov">          0 :                  ((options &amp; X86Inst::kOptionVex3      ) &gt;&gt; (X86Inst::kOpCode_MM_Shift     )) ;</span></a>
+<a name="4049"><span class="lineNum">    4049 </span><span class="lineNoCov">          0 :     if (x &amp; 0x04U) {</span></a>
+<a name="4050"><span class="lineNum">    4050 </span><span class="lineNoCov">          0 :       x  = (x &amp; (0x4 ^ 0xFFFF)) &lt;&lt; 8;                    // [00000000|00000Lpp|0000m0mm|00000000].</span></a>
+<a name="4051"><span class="lineNum">    4051 </span><span class="lineNoCov">          0 :       x ^= (kX86ByteVex3) |                              // [........|00000Lpp|0000m0mm|__VEX3__].</span></a>
+<a name="4052"><span class="lineNum">    4052 </span>            :            (0x07U  &lt;&lt; 13) |                              // [........|00000Lpp|1110m0mm|__VEX3__].</a>
+<a name="4053"><span class="lineNum">    4053 </span><span class="lineNoCov">          0 :            (0x0FU  &lt;&lt; 19) |                              // [........|01111Lpp|1110m0mm|__VEX3__].</span></a>
+<a name="4054"><span class="lineNum">    4054 </span><span class="lineNoCov">          0 :            (opCode &lt;&lt; 24) ;                              // [_OPCODE_|01111Lpp|1110m0mm|__VEX3__].</span></a>
+<a name="4055"><span class="lineNum">    4055 </span>            : </a>
+<a name="4056"><span class="lineNum">    4056 </span><span class="lineNoCov">          0 :       EMIT_32(x);</span></a>
+<a name="4057"><span class="lineNum">    4057 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4058"><span class="lineNum">    4058 </span>            :     }</a>
+<a name="4059"><span class="lineNum">    4059 </span>            :     else {</a>
+<a name="4060"><span class="lineNum">    4060 </span><span class="lineNoCov">          0 :       x = ((x &gt;&gt; 8) ^ x) ^ 0xF9;</span></a>
+<a name="4061"><span class="lineNum">    4061 </span><span class="lineNoCov">          0 :       EMIT_BYTE(kX86ByteVex2);</span></a>
+<a name="4062"><span class="lineNum">    4062 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x);</span></a>
+<a name="4063"><span class="lineNum">    4063 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opCode);</span></a>
+<a name="4064"><span class="lineNum">    4064 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4065"><span class="lineNum">    4065 </span>            :     }</a>
+<a name="4066"><span class="lineNum">    4066 </span>            :   }</a>
+<a name="4067"><span class="lineNum">    4067 </span>            : </a>
+<a name="4068"><span class="lineNum">    4068 </span><span class="lineNoCov">          0 : EmitVexEvexR:</span></a>
+<a name="4069"><span class="lineNum">    4069 </span>            :   {</a>
+<a name="4070"><span class="lineNum">    4070 </span>            :     // VEX instructions use only 0-1 BYTE immediate.</a>
+<a name="4071"><span class="lineNum">    4071 </span>            :     ASMJIT_ASSERT(imLen &lt;= 1);</a>
+<a name="4072"><span class="lineNum">    4072 </span>            : </a>
+<a name="4073"><span class="lineNum">    4073 </span>            :     // Construct `x` - a complete EVEX|VEX prefix.</a>
+<a name="4074"><span class="lineNum">    4074 </span><span class="lineNoCov">          0 :     uint32_t x = ((opReg &lt;&lt; 4) &amp; 0xF980U) |              // [........|........|Vvvvv..R|R.......].</span></a>
+<a name="4075"><span class="lineNum">    4075 </span><span class="lineNoCov">          0 :                  ((rbReg &lt;&lt; 2) &amp; 0x0060U) |              // [........|........|........|.BB.....].</span></a>
+<a name="4076"><span class="lineNum">    4076 </span>            :                  (x86ExtractLLMM(opCode, options)) |     // [........|.LL.....|Vvvvv..R|RBBmmmmm].</a>
+<a name="4077"><span class="lineNum">    4077 </span><span class="lineNoCov">          0 :                  (_extraReg.getId() &lt;&lt; 16);              // [........|.LL..aaa|Vvvvv..R|RBBmmmmm].</span></a>
+<a name="4078"><span class="lineNum">    4078 </span><span class="lineNoCov">          0 :     opReg &amp;= 0x7;</span></a>
+<a name="4079"><span class="lineNum">    4079 </span>            : </a>
+<a name="4080"><span class="lineNum">    4080 </span>            :     // Mark invalid VEX (force EVEX) case:               // [@.......|.LL..aaa|Vvvvv..R|RBBmmmmm].</a>
+<a name="4081"><span class="lineNum">    4081 </span><span class="lineNoCov">          0 :     x |= (~commonData-&gt;getFlags() &amp; X86Inst::kFlagVex) &lt;&lt; (31 - Utils::firstBitOfT&lt;X86Inst::kFlagVex&gt;());</span></a>
+<a name="4082"><span class="lineNum">    4082 </span>            : </a>
+<a name="4083"><span class="lineNum">    4083 </span>            :     // Handle AVX512 options by a single branch.</a>
+<a name="4084"><span class="lineNum">    4084 </span>            :     const uint32_t kAvx512Options = X86Inst::kOptionZMask   |</a>
+<a name="4085"><span class="lineNum">    4085 </span>            :                                     X86Inst::kOption1ToX    |</a>
+<a name="4086"><span class="lineNum">    4086 </span>            :                                     X86Inst::kOptionSAE     |</a>
+<a name="4087"><span class="lineNum">    4087 </span>            :                                     X86Inst::kOptionER      ;</a>
+<a name="4088"><span class="lineNum">    4088 </span><span class="lineNoCov">          0 :     if (options &amp; kAvx512Options) {</span></a>
+<a name="4089"><span class="lineNum">    4089 </span>            :       // Memory broadcast without a memory operand is invalid.</a>
+<a name="4090"><span class="lineNum">    4090 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(options &amp; X86Inst::kOption1ToX))</span></a>
+<a name="4091"><span class="lineNum">    4091 </span><span class="lineNoCov">          0 :         goto InvalidBroadcast;</span></a>
+<a name="4092"><span class="lineNum">    4092 </span>            : </a>
+<a name="4093"><span class="lineNum">    4093 </span>            :       // TODO: {sae} and {er}</a>
+<a name="4094"><span class="lineNum">    4094 </span><span class="lineNoCov">          0 :       x |= options &amp; X86Inst::kOptionZMask;              // [@.......|zLL..aaa|Vvvvv..R|RBBmmmmm].</span></a>
+<a name="4095"><span class="lineNum">    4095 </span>            :     }</a>
+<a name="4096"><span class="lineNum">    4096 </span>            : </a>
+<a name="4097"><span class="lineNum">    4097 </span>            :     // Check if EVEX is required by checking bits in `x` :  [@.......|xx...xxx|x......x|.x.x....].</a>
+<a name="4098"><span class="lineNum">    4098 </span><span class="lineNoCov">          0 :     if (x &amp; 0x80C78150U) {</span></a>
+<a name="4099"><span class="lineNum">    4099 </span><span class="lineNoCov">          0 :       uint32_t y = ((x &lt;&lt; 4) &amp; 0x00080000U) |            // [@.......|....V...|........|........].</span></a>
+<a name="4100"><span class="lineNum">    4100 </span><span class="lineNoCov">          0 :                    ((x &gt;&gt; 4) &amp; 0x00000010U) ;            // [@.......|....V...|........|...R....].</span></a>
+<a name="4101"><span class="lineNum">    4101 </span><span class="lineNoCov">          0 :       x  = (x &amp; 0x00FF78E3U) | y;                        // [........|zLL.Vaaa|0vvvv000|RBBR00mm].</span></a>
+<a name="4102"><span class="lineNum">    4102 </span><span class="lineNoCov">          0 :       x  = (x &lt;&lt; 8) |                                    // [zLL.Vaaa|0vvvv000|RBBR00mm|00000000].</span></a>
+<a name="4103"><span class="lineNum">    4103 </span><span class="lineNoCov">          0 :            ((opCode &gt;&gt; kSHR_W_PP) &amp; 0x00830000U) |       // [zLL.Vaaa|Wvvvv0pp|RBBR00mm|00000000].</span></a>
+<a name="4104"><span class="lineNum">    4104 </span><span class="lineNoCov">          0 :            ((opCode &gt;&gt; kSHR_W_EW) &amp; 0x00800000U) ;       // [zLL.Vaaa|Wvvvv0pp|RBBR00mm|00000000] (added EVEX.W).</span></a>
+<a name="4105"><span class="lineNum">    4105 </span>            :                                                          //      _     ____    ____</a>
+<a name="4106"><span class="lineNum">    4106 </span><span class="lineNoCov">          0 :       x ^= 0x087CF000U | kX86ByteEvex;                   // [zLL.Vaaa|Wvvvv1pp|RBBR00mm|01100010].</span></a>
+<a name="4107"><span class="lineNum">    4107 </span>            : </a>
+<a name="4108"><span class="lineNum">    4108 </span>            :       EMIT_32(x);</a>
+<a name="4109"><span class="lineNum">    4109 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opCode);</span></a>
+<a name="4110"><span class="lineNum">    4110 </span>            : </a>
+<a name="4111"><span class="lineNum">    4111 </span><span class="lineNoCov">          0 :       rbReg &amp;= 0x7;</span></a>
+<a name="4112"><span class="lineNum">    4112 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x86EncodeMod(3, opReg, rbReg));</span></a>
+<a name="4113"><span class="lineNum">    4113 </span>            : </a>
+<a name="4114"><span class="lineNum">    4114 </span><span class="lineNoCov">          0 :       if (imLen == 0) goto EmitDone;</span></a>
+<a name="4115"><span class="lineNum">    4115 </span><span class="lineNoCov">          0 :       EMIT_BYTE(imVal &amp; 0xFF);</span></a>
+<a name="4116"><span class="lineNum">    4116 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4117"><span class="lineNum">    4117 </span>            :     }</a>
+<a name="4118"><span class="lineNum">    4118 </span>            : </a>
+<a name="4119"><span class="lineNum">    4119 </span>            :     // Not EVEX, prepare `x` for VEX2 or VEX3:          x = [........|00L00000|0vvvv000|R0B0mmmm].</a>
+<a name="4120"><span class="lineNum">    4120 </span><span class="lineNoCov">          0 :     x |= ((opCode &gt;&gt; (kSHR_W_PP + 8)) &amp; 0x8300U) |       // [00000000|00L00000|Wvvvv0pp|R0B0mmmm].</span></a>
+<a name="4121"><span class="lineNum">    4121 </span><span class="lineNoCov">          0 :          ((x      &gt;&gt; 11             ) &amp; 0x0400U) ;       // [00000000|00L00000|WvvvvLpp|R0B0mmmm].</span></a>
+<a name="4122"><span class="lineNum">    4122 </span>            : </a>
+<a name="4123"><span class="lineNum">    4123 </span>            :     // Check if VEX3 is required / forced:                  [........|........|x.......|..x..x..].</a>
+<a name="4124"><span class="lineNum">    4124 </span><span class="lineNoCov">          0 :     if (x &amp; 0x0008024U) {</span></a>
+<a name="4125"><span class="lineNum">    4125 </span><span class="lineNoCov">          0 :       uint32_t xorMsk = x86VEXPrefix[x &amp; 0xF] | (opCode &lt;&lt; 24);</span></a>
+<a name="4126"><span class="lineNum">    4126 </span>            : </a>
+<a name="4127"><span class="lineNum">    4127 </span>            :       // Clear 'FORCE-VEX3' bit and all high bits.</a>
+<a name="4128"><span class="lineNum">    4128 </span><span class="lineNoCov">          0 :       x  = (x &amp; (0x4 ^ 0xFFFF)) &lt;&lt; 8;                    // [00000000|WvvvvLpp|R0B0m0mm|00000000].</span></a>
+<a name="4129"><span class="lineNum">    4129 </span>            :                                                          //            ____    _ _</a>
+<a name="4130"><span class="lineNum">    4130 </span><span class="lineNoCov">          0 :       x ^= xorMsk;                                       // [_OPCODE_|WvvvvLpp|R1Bmmmmm|VEX3|XOP].</span></a>
+<a name="4131"><span class="lineNum">    4131 </span>            :       EMIT_32(x);</a>
+<a name="4132"><span class="lineNum">    4132 </span>            : </a>
+<a name="4133"><span class="lineNum">    4133 </span><span class="lineNoCov">          0 :       rbReg &amp;= 0x7;</span></a>
+<a name="4134"><span class="lineNum">    4134 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x86EncodeMod(3, opReg, rbReg));</span></a>
+<a name="4135"><span class="lineNum">    4135 </span>            : </a>
+<a name="4136"><span class="lineNum">    4136 </span><span class="lineNoCov">          0 :       if (imLen == 0) goto EmitDone;</span></a>
+<a name="4137"><span class="lineNum">    4137 </span><span class="lineNoCov">          0 :       EMIT_BYTE(imVal &amp; 0xFF);</span></a>
+<a name="4138"><span class="lineNum">    4138 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4139"><span class="lineNum">    4139 </span>            :     }</a>
+<a name="4140"><span class="lineNum">    4140 </span>            :     else {</a>
+<a name="4141"><span class="lineNum">    4141 </span>            :       // 'mmmmm' must be '00001'.</a>
+<a name="4142"><span class="lineNum">    4142 </span>            :       ASMJIT_ASSERT((x &amp; 0x1F) == 0x01);</a>
+<a name="4143"><span class="lineNum">    4143 </span>            : </a>
+<a name="4144"><span class="lineNum">    4144 </span><span class="lineNoCov">          0 :       x = ((x &gt;&gt; 8) ^ x) ^ 0xF9;</span></a>
+<a name="4145"><span class="lineNum">    4145 </span><span class="lineNoCov">          0 :       EMIT_BYTE(kX86ByteVex2);</span></a>
+<a name="4146"><span class="lineNum">    4146 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x);</span></a>
+<a name="4147"><span class="lineNum">    4147 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opCode);</span></a>
+<a name="4148"><span class="lineNum">    4148 </span>            : </a>
+<a name="4149"><span class="lineNum">    4149 </span><span class="lineNoCov">          0 :       rbReg &amp;= 0x7;</span></a>
+<a name="4150"><span class="lineNum">    4150 </span><span class="lineNoCov">          0 :       EMIT_BYTE(x86EncodeMod(3, opReg, rbReg));</span></a>
+<a name="4151"><span class="lineNum">    4151 </span>            : </a>
+<a name="4152"><span class="lineNum">    4152 </span><span class="lineNoCov">          0 :       if (imLen == 0) goto EmitDone;</span></a>
+<a name="4153"><span class="lineNum">    4153 </span><span class="lineNoCov">          0 :       EMIT_BYTE(imVal &amp; 0xFF);</span></a>
+<a name="4154"><span class="lineNum">    4154 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4155"><span class="lineNum">    4155 </span>            :     }</a>
+<a name="4156"><span class="lineNum">    4156 </span>            :   }</a>
+<a name="4157"><span class="lineNum">    4157 </span>            : </a>
+<a name="4158"><span class="lineNum">    4158 </span><span class="lineNoCov">          0 : EmitVexEvexM:</span></a>
+<a name="4159"><span class="lineNum">    4159 </span>            :   ASMJIT_ASSERT(rmRel != nullptr);</a>
+<a name="4160"><span class="lineNum">    4160 </span>            :   ASMJIT_ASSERT(rmRel-&gt;getOp() == Operand::kOpMem);</a>
+<a name="4161"><span class="lineNum">    4161 </span><span class="lineNoCov">          0 :   rmInfo = x86MemInfo[rmRel-&gt;as&lt;X86Mem&gt;().getBaseIndexType()];</span></a>
+<a name="4162"><span class="lineNum">    4162 </span>            : </a>
+<a name="4163"><span class="lineNum">    4163 </span>            :   // Segment-override prefix.</a>
+<a name="4164"><span class="lineNum">    4164 </span><span class="lineNoCov">          0 :   if (rmRel-&gt;as&lt;X86Mem&gt;().hasSegment())</span></a>
+<a name="4165"><span class="lineNum">    4165 </span><span class="lineNoCov">          0 :     EMIT_BYTE(x86SegmentPrefix[rmRel-&gt;as&lt;X86Mem&gt;().getSegmentId()]);</span></a>
+<a name="4166"><span class="lineNum">    4166 </span>            : </a>
+<a name="4167"><span class="lineNum">    4167 </span>            :   // Address-override prefix.</a>
+<a name="4168"><span class="lineNum">    4168 </span><span class="lineNoCov">          0 :   if (rmInfo &amp; _getAddressOverrideMask())</span></a>
+<a name="4169"><span class="lineNum">    4169 </span><span class="lineNoCov">          0 :     EMIT_BYTE(0x67);</span></a>
+<a name="4170"><span class="lineNum">    4170 </span>            : </a>
+<a name="4171"><span class="lineNum">    4171 </span><span class="lineNoCov">          0 :   rbReg = rmRel-&gt;as&lt;X86Mem&gt;().hasBaseReg()  ? rmRel-&gt;as&lt;X86Mem&gt;().getBaseId()  : uint32_t(0);</span></a>
+<a name="4172"><span class="lineNum">    4172 </span><span class="lineNoCov">          0 :   rxReg = rmRel-&gt;as&lt;X86Mem&gt;().hasIndexReg() ? rmRel-&gt;as&lt;X86Mem&gt;().getIndexId() : uint32_t(0);</span></a>
+<a name="4173"><span class="lineNum">    4173 </span>            : </a>
+<a name="4174"><span class="lineNum">    4174 </span>            :   {</a>
+<a name="4175"><span class="lineNum">    4175 </span>            :     // VEX instructions use only 0-1 BYTE immediate.</a>
+<a name="4176"><span class="lineNum">    4176 </span>            :     ASMJIT_ASSERT(imLen &lt;= 1);</a>
+<a name="4177"><span class="lineNum">    4177 </span>            : </a>
+<a name="4178"><span class="lineNum">    4178 </span>            :     // Construct `x` - a complete EVEX|VEX prefix.</a>
+<a name="4179"><span class="lineNum">    4179 </span><span class="lineNoCov">          0 :     uint32_t x = ((opReg &lt;&lt; 4 ) &amp; 0x0000F980U) |         // [........|........|Vvvvv..R|R.......].</span></a>
+<a name="4180"><span class="lineNum">    4180 </span><span class="lineNoCov">          0 :                  ((rxReg &lt;&lt; 3 ) &amp; 0x00000040U) |         // [........|........|........|.X......].</span></a>
+<a name="4181"><span class="lineNum">    4181 </span><span class="lineNoCov">          0 :                  ((rxReg &lt;&lt; 15) &amp; 0x00080000U) |         // [........|....X...|........|........].</span></a>
+<a name="4182"><span class="lineNum">    4182 </span><span class="lineNoCov">          0 :                  ((rbReg &lt;&lt; 2 ) &amp; 0x00000020U) |         // [........|........|........|..B.....].</span></a>
+<a name="4183"><span class="lineNum">    4183 </span>            :                  (x86ExtractLLMM(opCode, options)) |     // [........|.LL.X...|Vvvvv..R|RXBmmmmm].</a>
+<a name="4184"><span class="lineNum">    4184 </span><span class="lineNoCov">          0 :                  (_extraReg.getId() &lt;&lt; 16)         ;     // [........|.LL.Xaaa|Vvvvv..R|RXBmmmmm].</span></a>
+<a name="4185"><span class="lineNum">    4185 </span><span class="lineNoCov">          0 :     opReg &amp;= 0x07U;</span></a>
+<a name="4186"><span class="lineNum">    4186 </span>            : </a>
+<a name="4187"><span class="lineNum">    4187 </span>            :     // Mark invalid VEX (force EVEX) case:               // [@.......|.LL.Xaaa|Vvvvv..R|RXBmmmmm].</a>
+<a name="4188"><span class="lineNum">    4188 </span><span class="lineNoCov">          0 :     x |= (~commonData-&gt;getFlags() &amp; X86Inst::kFlagVex) &lt;&lt; (31 - Utils::firstBitOfT&lt;X86Inst::kFlagVex&gt;());</span></a>
+<a name="4189"><span class="lineNum">    4189 </span>            : </a>
+<a name="4190"><span class="lineNum">    4190 </span>            :     // Handle AVX512 options by a single branch.</a>
+<a name="4191"><span class="lineNum">    4191 </span>            :     const uint32_t kAvx512Options = X86Inst::kOption1ToX    |</a>
+<a name="4192"><span class="lineNum">    4192 </span>            :                                     X86Inst::kOptionZMask   |</a>
+<a name="4193"><span class="lineNum">    4193 </span>            :                                     X86Inst::kOptionSAE     |</a>
+<a name="4194"><span class="lineNum">    4194 </span>            :                                     X86Inst::kOptionER      ;</a>
+<a name="4195"><span class="lineNum">    4195 </span><span class="lineNoCov">          0 :     if (options &amp; kAvx512Options) {</span></a>
+<a name="4196"><span class="lineNum">    4196 </span>            :       // {er} and {sae} are both invalid if memory operand is used.</a>
+<a name="4197"><span class="lineNum">    4197 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(options &amp; (X86Inst::kOptionSAE | X86Inst::kOptionER)))</span></a>
+<a name="4198"><span class="lineNum">    4198 </span><span class="lineNoCov">          0 :         goto InvalidEROrSAE;</span></a>
+<a name="4199"><span class="lineNum">    4199 </span>            : </a>
+<a name="4200"><span class="lineNum">    4200 </span><span class="lineNoCov">          0 :       x |= options &amp; (X86Inst::kOption1ToX |             // [@.......|.LLbXaaa|Vvvvv..R|RXBmmmmm].</span></a>
+<a name="4201"><span class="lineNum">    4201 </span>            :                       X86Inst::kOptionZMask);            // [@.......|zLLbXaaa|Vvvvv..R|RXBmmmmm].</a>
+<a name="4202"><span class="lineNum">    4202 </span>            :     }</a>
+<a name="4203"><span class="lineNum">    4203 </span>            : </a>
+<a name="4204"><span class="lineNum">    4204 </span>            :     // Check if EVEX is required by checking bits in `x` :  [@.......|xx.xxxxx|x......x|...x....].</a>
+<a name="4205"><span class="lineNum">    4205 </span><span class="lineNoCov">          0 :     if (x &amp; 0x80DF8110U) {</span></a>
+<a name="4206"><span class="lineNum">    4206 </span><span class="lineNoCov">          0 :       uint32_t y = ((x &lt;&lt; 4) &amp; 0x00080000U) |            // [@.......|....V...|........|........].</span></a>
+<a name="4207"><span class="lineNum">    4207 </span><span class="lineNoCov">          0 :                    ((x &gt;&gt; 4) &amp; 0x00000010U) ;            // [@.......|....V...|........|...R....].</span></a>
+<a name="4208"><span class="lineNum">    4208 </span><span class="lineNoCov">          0 :       x  = (x &amp; 0x00FF78E3U) | y;                        // [........|zLLbVaaa|0vvvv000|RXBR00mm].</span></a>
+<a name="4209"><span class="lineNum">    4209 </span><span class="lineNoCov">          0 :       x  = (x &lt;&lt; 8) |                                    // [zLLbVaaa|0vvvv000|RBBR00mm|00000000].</span></a>
+<a name="4210"><span class="lineNum">    4210 </span><span class="lineNoCov">          0 :            ((opCode &gt;&gt; kSHR_W_PP) &amp; 0x00830000U) |       // [zLLbVaaa|Wvvvv0pp|RBBR00mm|00000000].</span></a>
+<a name="4211"><span class="lineNum">    4211 </span><span class="lineNoCov">          0 :            ((opCode &gt;&gt; kSHR_W_EW) &amp; 0x00800000U) ;       // [zLLbVaaa|Wvvvv0pp|RBBR00mm|00000000] (added EVEX.W).</span></a>
+<a name="4212"><span class="lineNum">    4212 </span>            :                                                          //      _     ____    ____</a>
+<a name="4213"><span class="lineNum">    4213 </span><span class="lineNoCov">          0 :       x ^= 0x087CF000U | kX86ByteEvex;                   // [zLLbVaaa|Wvvvv1pp|RBBR00mm|01100010].</span></a>
+<a name="4214"><span class="lineNum">    4214 </span>            : </a>
+<a name="4215"><span class="lineNum">    4215 </span>            :       EMIT_32(x);</a>
+<a name="4216"><span class="lineNum">    4216 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opCode);</span></a>
+<a name="4217"><span class="lineNum">    4217 </span>            : </a>
+<a name="4218"><span class="lineNum">    4218 </span><span class="lineNoCov">          0 :       if (opCode &amp; 0x10000000U) {</span></a>
+<a name="4219"><span class="lineNum">    4219 </span>            :         // Broadcast, change the compressed displacement scale to either x4 (SHL 2) or x8 (SHL 3)</a>
+<a name="4220"><span class="lineNum">    4220 </span>            :         // depending on instruction's W. If 'W' is 1 'SHL' must be 3, otherwise it must be 2.</a>
+<a name="4221"><span class="lineNum">    4221 </span><span class="lineNoCov">          0 :         opCode &amp;=~static_cast&lt;uint32_t&gt;(X86Inst::kOpCode_CDSHL_Mask);</span></a>
+<a name="4222"><span class="lineNum">    4222 </span><span class="lineNoCov">          0 :         opCode |= ((x &amp; 0x00800000U) ? 3 : 2) &lt;&lt; X86Inst::kOpCode_CDSHL_Shift;</span></a>
+<a name="4223"><span class="lineNum">    4223 </span>            :       }</a>
+<a name="4224"><span class="lineNum">    4224 </span>            :       else {</a>
+<a name="4225"><span class="lineNum">    4225 </span>            :         // Add the compressed displacement 'SHF' to the opcode based on 'TTWLL'.</a>
+<a name="4226"><span class="lineNum">    4226 </span><span class="lineNoCov">          0 :         uint32_t TTWLL = ((opCode &gt;&gt; (X86Inst::kOpCode_CDTT_Shift - 3)) &amp; 0x18) +</span></a>
+<a name="4227"><span class="lineNum">    4227 </span><span class="lineNoCov">          0 :                          ((opCode &gt;&gt; (X86Inst::kOpCode_W_Shift    - 2)) &amp; 0x04) +</span></a>
+<a name="4228"><span class="lineNum">    4228 </span><span class="lineNoCov">          0 :                          ((x &gt;&gt; 29) &amp; 0x3);</span></a>
+<a name="4229"><span class="lineNum">    4229 </span><span class="lineNoCov">          0 :         opCode += x86CDisp8SHL[TTWLL];</span></a>
+<a name="4230"><span class="lineNum">    4230 </span>            :       }</a>
+<a name="4231"><span class="lineNum">    4231 </span>            :     }</a>
+<a name="4232"><span class="lineNum">    4232 </span>            :     else {</a>
+<a name="4233"><span class="lineNum">    4233 </span>            :       // Not EVEX, prepare `x` for VEX2 or VEX3:        x = [........|00L00000|0vvvv000|RXB0mmmm].</a>
+<a name="4234"><span class="lineNum">    4234 </span><span class="lineNoCov">          0 :       x |= ((opCode &gt;&gt; (kSHR_W_PP + 8)) &amp; 0x8300U) |     // [00000000|00L00000|Wvvvv0pp|RXB0mmmm].</span></a>
+<a name="4235"><span class="lineNum">    4235 </span><span class="lineNoCov">          0 :            ((x      &gt;&gt; 11             ) &amp; 0x0400U) ;     // [00000000|00L00000|WvvvvLpp|RXB0mmmm].</span></a>
+<a name="4236"><span class="lineNum">    4236 </span>            : </a>
+<a name="4237"><span class="lineNum">    4237 </span>            :       // Clear a possible CDisp specified by EVEX.</a>
+<a name="4238"><span class="lineNum">    4238 </span><span class="lineNoCov">          0 :       opCode &amp;= ~X86Inst::kOpCode_CDSHL_Mask;</span></a>
+<a name="4239"><span class="lineNum">    4239 </span>            : </a>
+<a name="4240"><span class="lineNum">    4240 </span>            :       // Check if VEX3 is required / forced:                [........|........|x.......|.xx..x..].</a>
+<a name="4241"><span class="lineNum">    4241 </span><span class="lineNoCov">          0 :       if (x &amp; 0x0008064U) {</span></a>
+<a name="4242"><span class="lineNum">    4242 </span><span class="lineNoCov">          0 :         uint32_t xorMsk = x86VEXPrefix[x &amp; 0xF] | (opCode &lt;&lt; 24);</span></a>
+<a name="4243"><span class="lineNum">    4243 </span>            : </a>
+<a name="4244"><span class="lineNum">    4244 </span>            :         // Clear 'FORCE-VEX3' bit and all high bits.</a>
+<a name="4245"><span class="lineNum">    4245 </span><span class="lineNoCov">          0 :         x  = (x &amp; (0x4 ^ 0xFFFF)) &lt;&lt; 8;                  // [00000000|WvvvvLpp|RXB0m0mm|00000000].</span></a>
+<a name="4246"><span class="lineNum">    4246 </span>            :                                                          //            ____    ___</a>
+<a name="4247"><span class="lineNum">    4247 </span><span class="lineNoCov">          0 :         x ^= xorMsk;                                     // [_OPCODE_|WvvvvLpp|RXBmmmmm|VEX3_XOP].</span></a>
+<a name="4248"><span class="lineNum">    4248 </span><span class="lineNoCov">          0 :         EMIT_32(x);</span></a>
+<a name="4249"><span class="lineNum">    4249 </span>            :       }</a>
+<a name="4250"><span class="lineNum">    4250 </span>            :       else {</a>
+<a name="4251"><span class="lineNum">    4251 </span>            :         // 'mmmmm' must be '00001'.</a>
+<a name="4252"><span class="lineNum">    4252 </span>            :         ASMJIT_ASSERT((x &amp; 0x1F) == 0x01);</a>
+<a name="4253"><span class="lineNum">    4253 </span>            : </a>
+<a name="4254"><span class="lineNum">    4254 </span><span class="lineNoCov">          0 :         x = ((x &gt;&gt; 8) ^ x) ^ 0xF9;</span></a>
+<a name="4255"><span class="lineNum">    4255 </span><span class="lineNoCov">          0 :         EMIT_BYTE(kX86ByteVex2);</span></a>
+<a name="4256"><span class="lineNum">    4256 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x);</span></a>
+<a name="4257"><span class="lineNum">    4257 </span><span class="lineNoCov">          0 :         EMIT_BYTE(opCode);</span></a>
+<a name="4258"><span class="lineNum">    4258 </span>            :       }</a>
+<a name="4259"><span class="lineNum">    4259 </span>            :     }</a>
+<a name="4260"><span class="lineNum">    4260 </span>            :   }</a>
+<a name="4261"><span class="lineNum">    4261 </span>            : </a>
+<a name="4262"><span class="lineNum">    4262 </span>            :   // MOD|SIB address.</a>
+<a name="4263"><span class="lineNum">    4263 </span><span class="lineNoCov">          0 :   if (!commonData-&gt;hasFlag(X86Inst::kFlagVsib))</span></a>
+<a name="4264"><span class="lineNum">    4264 </span><span class="lineNoCov">          0 :     goto EmitModSib;</span></a>
+<a name="4265"><span class="lineNum">    4265 </span>            : </a>
+<a name="4266"><span class="lineNum">    4266 </span>            :   // MOD|VSIB address without INDEX is invalid.</a>
+<a name="4267"><span class="lineNum">    4267 </span><span class="lineNoCov">          0 :   if (rmInfo &amp; kX86MemInfo_Index)</span></a>
+<a name="4268"><span class="lineNum">    4268 </span><span class="lineNoCov">          0 :     goto EmitModVSib;</span></a>
+<a name="4269"><span class="lineNum">    4269 </span><span class="lineNoCov">          0 :   goto InvalidInstruction;</span></a>
+<a name="4270"><span class="lineNum">    4270 </span>            : </a>
+<a name="4271"><span class="lineNum">    4271 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4272"><span class="lineNum">    4272 </span>            :   // [Emit - Jmp/Jcc/Call]</a>
+<a name="4273"><span class="lineNum">    4273 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4274"><span class="lineNum">    4274 </span>            : </a>
+<a name="4275"><span class="lineNum">    4275 </span>            :   // TODO: Should be adjusted after the support for multiple sections feature is added.</a>
+<a name="4276"><span class="lineNum">    4276 </span><span class="lineNoCov">          0 : EmitJmpCall:</span></a>
+<a name="4277"><span class="lineNum">    4277 </span>            :   {</a>
+<a name="4278"><span class="lineNum">    4278 </span>            :     // Emit REX prefix if asked for (64-bit only).</a>
+<a name="4279"><span class="lineNum">    4279 </span>            :     uint32_t rex = x86ExtractREX(opCode, options);</a>
+<a name="4280"><span class="lineNum">    4280 </span><span class="lineNoCov">          0 :     if (rex) {</span></a>
+<a name="4281"><span class="lineNum">    4281 </span><span class="lineNoCov">          0 :       if (options &amp; X86Inst::_kOptionInvalidRex)</span></a>
+<a name="4282"><span class="lineNum">    4282 </span><span class="lineNoCov">          0 :         goto InvalidRexPrefix;</span></a>
+<a name="4283"><span class="lineNum">    4283 </span><span class="lineNoCov">          0 :       EMIT_BYTE(rex | kX86ByteRex);</span></a>
+<a name="4284"><span class="lineNum">    4284 </span>            :     }</a>
+<a name="4285"><span class="lineNum">    4285 </span>            : </a>
+<a name="4286"><span class="lineNum">    4286 </span><span class="lineNoCov">          0 :     uint64_t ip = static_cast&lt;uint64_t&gt;((intptr_t)(cursor - _bufferData));</span></a>
+<a name="4287"><span class="lineNum">    4287 </span>            :     uint32_t rel32 = 0;</a>
+<a name="4288"><span class="lineNum">    4288 </span>            :     uint32_t opCode8 = commonData-&gt;getAltOpCode();</a>
+<a name="4289"><span class="lineNum">    4289 </span>            : </a>
+<a name="4290"><span class="lineNum">    4290 </span>            :     uint32_t inst8Size  = 1 + 1; //          OPCODE + REL8 .</a>
+<a name="4291"><span class="lineNum">    4291 </span>            :     uint32_t inst32Size = 1 + 4; // [PREFIX] OPCODE + REL32.</a>
+<a name="4292"><span class="lineNum">    4292 </span>            : </a>
+<a name="4293"><span class="lineNum">    4293 </span>            :     // Jcc instructions with 32-bit displacement use 0x0F prefix,</a>
+<a name="4294"><span class="lineNum">    4294 </span>            :     // other instructions don't. No other prefixes are used by X86.</a>
+<a name="4295"><span class="lineNum">    4295 </span>            :     ASMJIT_ASSERT((opCode8 &amp; X86Inst::kOpCode_MM_Mask) == 0);</a>
+<a name="4296"><span class="lineNum">    4296 </span>            :     ASMJIT_ASSERT((opCode  &amp; X86Inst::kOpCode_MM_Mask) == 0 ||</a>
+<a name="4297"><span class="lineNum">    4297 </span>            :                   (opCode  &amp; X86Inst::kOpCode_MM_Mask) == X86Inst::kOpCode_MM_0F);</a>
+<a name="4298"><span class="lineNum">    4298 </span>            : </a>
+<a name="4299"><span class="lineNum">    4299 </span>            :     // Only one of these should be used at the same time.</a>
+<a name="4300"><span class="lineNum">    4300 </span><span class="lineNoCov">          0 :     inst32Size += static_cast&lt;uint32_t&gt;(opReg != 0);</span></a>
+<a name="4301"><span class="lineNum">    4301 </span><span class="lineNoCov">          0 :     inst32Size += static_cast&lt;uint32_t&gt;((opCode &amp; X86Inst::kOpCode_MM_Mask) == X86Inst::kOpCode_MM_0F);</span></a>
+<a name="4302"><span class="lineNum">    4302 </span>            : </a>
+<a name="4303"><span class="lineNum">    4303 </span><span class="lineNoCov">          0 :     if (rmRel-&gt;isLabel()) {</span></a>
+<a name="4304"><span class="lineNum">    4304 </span><span class="lineNoCov">          0 :       label = _code-&gt;getLabelEntry(rmRel-&gt;as&lt;Label&gt;());</span></a>
+<a name="4305"><span class="lineNum">    4305 </span><span class="lineNoCov">          0 :       if (!label) goto InvalidLabel;</span></a>
+<a name="4306"><span class="lineNum">    4306 </span>            : </a>
+<a name="4307"><span class="lineNum">    4307 </span><span class="lineNoCov">          0 :       if (label-&gt;isBound()) {</span></a>
+<a name="4308"><span class="lineNum">    4308 </span>            :         // Bound label.</a>
+<a name="4309"><span class="lineNum">    4309 </span><span class="lineNoCov">          0 :         rel32 = static_cast&lt;uint32_t&gt;((static_cast&lt;uint64_t&gt;(label-&gt;getOffset()) - ip - inst32Size) &amp; 0xFFFFFFFFU);</span></a>
+<a name="4310"><span class="lineNum">    4310 </span><span class="lineNoCov">          0 :         goto EmitJmpCallRel;</span></a>
+<a name="4311"><span class="lineNum">    4311 </span>            :       }</a>
+<a name="4312"><span class="lineNum">    4312 </span>            :       else {</a>
+<a name="4313"><span class="lineNum">    4313 </span>            :         // Non-bound label.</a>
+<a name="4314"><span class="lineNum">    4314 </span><span class="lineNoCov">          0 :         if (opCode8 &amp;&amp; (!opCode || (options &amp; X86Inst::kOptionShortForm))) {</span></a>
+<a name="4315"><span class="lineNum">    4315 </span><span class="lineNoCov">          0 :           EMIT_BYTE(opCode8);</span></a>
+<a name="4316"><span class="lineNum">    4316 </span>            :           relOffset = -1;</a>
+<a name="4317"><span class="lineNum">    4317 </span>            :           relSize = 1;</a>
+<a name="4318"><span class="lineNum">    4318 </span><span class="lineNoCov">          0 :           goto EmitRel;</span></a>
+<a name="4319"><span class="lineNum">    4319 </span>            :         }</a>
+<a name="4320"><span class="lineNum">    4320 </span>            :         else {</a>
+<a name="4321"><span class="lineNum">    4321 </span>            :           // Refuse also 'short' prefix, if specified.</a>
+<a name="4322"><span class="lineNum">    4322 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(!opCode || (options &amp; X86Inst::kOptionShortForm) != 0))</span></a>
+<a name="4323"><span class="lineNum">    4323 </span><span class="lineNoCov">          0 :             goto InvalidDisplacement;</span></a>
+<a name="4324"><span class="lineNum">    4324 </span>            : </a>
+<a name="4325"><span class="lineNum">    4325 </span>            :           // Emit [PREFIX] OPCODE [/X] &lt;DISP32&gt;.</a>
+<a name="4326"><span class="lineNum">    4326 </span><span class="lineNoCov">          0 :           if (opCode &amp; X86Inst::kOpCode_MM_Mask)</span></a>
+<a name="4327"><span class="lineNum">    4327 </span><span class="lineNoCov">          0 :             EMIT_BYTE(0x0F);</span></a>
+<a name="4328"><span class="lineNum">    4328 </span>            : </a>
+<a name="4329"><span class="lineNum">    4329 </span><span class="lineNoCov">          0 :           EMIT_BYTE(opCode);</span></a>
+<a name="4330"><span class="lineNum">    4330 </span><span class="lineNoCov">          0 :           if (opReg)</span></a>
+<a name="4331"><span class="lineNum">    4331 </span><span class="lineNoCov">          0 :             EMIT_BYTE(x86EncodeMod(3, opReg, 0));</span></a>
+<a name="4332"><span class="lineNum">    4332 </span>            : </a>
+<a name="4333"><span class="lineNum">    4333 </span>            :           relOffset = -4;</a>
+<a name="4334"><span class="lineNum">    4334 </span>            :           relSize = 4;</a>
+<a name="4335"><span class="lineNum">    4335 </span><span class="lineNoCov">          0 :           goto EmitRel;</span></a>
+<a name="4336"><span class="lineNum">    4336 </span>            :         }</a>
+<a name="4337"><span class="lineNum">    4337 </span>            :       }</a>
+<a name="4338"><span class="lineNum">    4338 </span>            :     }</a>
+<a name="4339"><span class="lineNum">    4339 </span>            : </a>
+<a name="4340"><span class="lineNum">    4340 </span><span class="lineNoCov">          0 :     if (rmRel-&gt;isImm()) {</span></a>
+<a name="4341"><span class="lineNum">    4341 </span>            :       uint64_t baseAddress = getCodeInfo().getBaseAddress();</a>
+<a name="4342"><span class="lineNum">    4342 </span>            :       uint64_t jumpAddress = rmRel-&gt;as&lt;Imm&gt;().getUInt64();</a>
+<a name="4343"><span class="lineNum">    4343 </span>            : </a>
+<a name="4344"><span class="lineNum">    4344 </span>            :       // If the base-address is known calculate a relative displacement and</a>
+<a name="4345"><span class="lineNum">    4345 </span>            :       // check if it fits in 32 bits (which is always true in 32-bit mode).</a>
+<a name="4346"><span class="lineNum">    4346 </span>            :       // Emit relative displacement as it was a bound label if all checks ok.</a>
+<a name="4347"><span class="lineNum">    4347 </span><span class="lineNoCov">          0 :       if (baseAddress != Globals::kNoBaseAddress) {</span></a>
+<a name="4348"><span class="lineNum">    4348 </span><span class="lineNoCov">          0 :         uint64_t rel64 = jumpAddress - (ip + baseAddress) - inst32Size;</span></a>
+<a name="4349"><span class="lineNum">    4349 </span><span class="lineNoCov">          0 :         if (getArchType() == ArchInfo::kTypeX86 || Utils::isInt32(static_cast&lt;int64_t&gt;(rel64))) {</span></a>
+<a name="4350"><span class="lineNum">    4350 </span><span class="lineNoCov">          0 :           rel32 = static_cast&lt;uint32_t&gt;(rel64 &amp; 0xFFFFFFFFU);</span></a>
+<a name="4351"><span class="lineNum">    4351 </span><span class="lineNoCov">          0 :           goto EmitJmpCallRel;</span></a>
+<a name="4352"><span class="lineNum">    4352 </span>            :         }</a>
+<a name="4353"><span class="lineNum">    4353 </span>            :         else {</a>
+<a name="4354"><span class="lineNum">    4354 </span>            :           // Relative displacement exceeds 32-bits - relocator can only</a>
+<a name="4355"><span class="lineNum">    4355 </span>            :           // insert trampoline for jmp/call, but not for jcc/jecxz.</a>
+<a name="4356"><span class="lineNum">    4356 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(!x86IsJmpOrCall(instId)))</span></a>
+<a name="4357"><span class="lineNum">    4357 </span><span class="lineNoCov">          0 :             goto InvalidDisplacement;</span></a>
+<a name="4358"><span class="lineNum">    4358 </span>            :         }</a>
+<a name="4359"><span class="lineNum">    4359 </span>            :       }</a>
+<a name="4360"><span class="lineNum">    4360 </span>            : </a>
+<a name="4361"><span class="lineNum">    4361 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(_code-&gt;_relocations.willGrow(&amp;_code-&gt;_baseHeap) != kErrorOk))</span></a>
+<a name="4362"><span class="lineNum">    4362 </span><span class="lineNoCov">          0 :         goto NoHeapMemory;</span></a>
+<a name="4363"><span class="lineNum">    4363 </span>            : </a>
+<a name="4364"><span class="lineNum">    4364 </span><span class="lineNoCov">          0 :       err = _code-&gt;newRelocEntry(&amp;re, RelocEntry::kTypeAbsToRel, 0);</span></a>
+<a name="4365"><span class="lineNum">    4365 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(err)) goto Failed;</span></a>
+<a name="4366"><span class="lineNum">    4366 </span>            : </a>
+<a name="4367"><span class="lineNum">    4367 </span><span class="lineNoCov">          0 :       re-&gt;_sourceSectionId = _section-&gt;getId();</span></a>
+<a name="4368"><span class="lineNum">    4368 </span><span class="lineNoCov">          0 :       re-&gt;_data = static_cast&lt;int64_t&gt;(jumpAddress);</span></a>
+<a name="4369"><span class="lineNum">    4369 </span>            : </a>
+<a name="4370"><span class="lineNum">    4370 </span><span class="lineNoCov">          0 :       if (ASMJIT_LIKELY(opCode)) {</span></a>
+<a name="4371"><span class="lineNum">    4371 </span>            :         // 64-bit: Emit REX prefix so the instruction can be patched later.</a>
+<a name="4372"><span class="lineNum">    4372 </span>            :         // REX prefix does nothing if not patched, but allows to patch the</a>
+<a name="4373"><span class="lineNum">    4373 </span>            :         // instruction to use MOD/M and to point to a memory where the final</a>
+<a name="4374"><span class="lineNum">    4374 </span>            :         // 64-bit address is stored.</a>
+<a name="4375"><span class="lineNum">    4375 </span><span class="lineNoCov">          0 :         re-&gt;_size = 4;</span></a>
+<a name="4376"><span class="lineNum">    4376 </span><span class="lineNoCov">          0 :         re-&gt;_sourceOffset = ip + inst32Size - 4;</span></a>
+<a name="4377"><span class="lineNum">    4377 </span>            : </a>
+<a name="4378"><span class="lineNum">    4378 </span><span class="lineNoCov">          0 :         if (getArchType() != ArchInfo::kTypeX86 &amp;&amp; x86IsJmpOrCall(instId)) {</span></a>
+<a name="4379"><span class="lineNum">    4379 </span><span class="lineNoCov">          0 :           if (!rex) {</span></a>
+<a name="4380"><span class="lineNum">    4380 </span><span class="lineNoCov">          0 :             re-&gt;_sourceOffset++;</span></a>
+<a name="4381"><span class="lineNum">    4381 </span><span class="lineNoCov">          0 :             EMIT_BYTE(kX86ByteRex);</span></a>
+<a name="4382"><span class="lineNum">    4382 </span>            :           }</a>
+<a name="4383"><span class="lineNum">    4383 </span>            : </a>
+<a name="4384"><span class="lineNum">    4384 </span><span class="lineNoCov">          0 :           re-&gt;_type = RelocEntry::kTypeTrampoline;</span></a>
+<a name="4385"><span class="lineNum">    4385 </span><span class="lineNoCov">          0 :           _code-&gt;_trampolinesSize += 8;</span></a>
+<a name="4386"><span class="lineNum">    4386 </span>            :         }</a>
+<a name="4387"><span class="lineNum">    4387 </span>            : </a>
+<a name="4388"><span class="lineNum">    4388 </span>            :         // Emit [PREFIX] OPCODE [/X] DISP32.</a>
+<a name="4389"><span class="lineNum">    4389 </span><span class="lineNoCov">          0 :         if (opCode &amp; X86Inst::kOpCode_MM_Mask)</span></a>
+<a name="4390"><span class="lineNum">    4390 </span><span class="lineNoCov">          0 :           EMIT_BYTE(0x0F);</span></a>
+<a name="4391"><span class="lineNum">    4391 </span>            : </a>
+<a name="4392"><span class="lineNum">    4392 </span><span class="lineNoCov">          0 :         EMIT_BYTE(opCode);</span></a>
+<a name="4393"><span class="lineNum">    4393 </span><span class="lineNoCov">          0 :         if (opReg)</span></a>
+<a name="4394"><span class="lineNum">    4394 </span><span class="lineNoCov">          0 :           EMIT_BYTE(x86EncodeMod(3, opReg, 0));</span></a>
+<a name="4395"><span class="lineNum">    4395 </span>            : </a>
+<a name="4396"><span class="lineNum">    4396 </span><span class="lineNoCov">          0 :         EMIT_32(0);</span></a>
+<a name="4397"><span class="lineNum">    4397 </span>            :       }</a>
+<a name="4398"><span class="lineNum">    4398 </span>            :       else {</a>
+<a name="4399"><span class="lineNum">    4399 </span><span class="lineNoCov">          0 :         re-&gt;_size = 1;</span></a>
+<a name="4400"><span class="lineNum">    4400 </span><span class="lineNoCov">          0 :         re-&gt;_sourceOffset = ip + inst8Size - 1;</span></a>
+<a name="4401"><span class="lineNum">    4401 </span>            : </a>
+<a name="4402"><span class="lineNum">    4402 </span>            :         // Emit OPCODE + DISP8.</a>
+<a name="4403"><span class="lineNum">    4403 </span><span class="lineNoCov">          0 :         EMIT_BYTE(opCode8);</span></a>
+<a name="4404"><span class="lineNum">    4404 </span><span class="lineNoCov">          0 :         EMIT_BYTE(0);</span></a>
+<a name="4405"><span class="lineNum">    4405 </span>            :       }</a>
+<a name="4406"><span class="lineNum">    4406 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4407"><span class="lineNum">    4407 </span>            :     }</a>
+<a name="4408"><span class="lineNum">    4408 </span>            : </a>
+<a name="4409"><span class="lineNum">    4409 </span>            :     // Not Label|Imm -&gt; Invalid.</a>
+<a name="4410"><span class="lineNum">    4410 </span><span class="lineNoCov">          0 :     goto InvalidInstruction;</span></a>
+<a name="4411"><span class="lineNum">    4411 </span>            : </a>
+<a name="4412"><span class="lineNum">    4412 </span>            :     // Emit jmp/call with relative displacement known at assembly-time. Decide</a>
+<a name="4413"><span class="lineNum">    4413 </span>            :     // between 8-bit and 32-bit displacement encoding. Some instructions only</a>
+<a name="4414"><span class="lineNum">    4414 </span>            :     // allow either 8-bit or 32-bit encoding, others allow both encodings.</a>
+<a name="4415"><span class="lineNum">    4415 </span><span class="lineNoCov">          0 : EmitJmpCallRel:</span></a>
+<a name="4416"><span class="lineNum">    4416 </span><span class="lineNoCov">          0 :     if (Utils::isInt8(static_cast&lt;int32_t&gt;(rel32 + inst32Size - inst8Size)) &amp;&amp; opCode8 &amp;&amp; !(options &amp; X86Inst::kOptionLongForm)) {</span></a>
+<a name="4417"><span class="lineNum">    4417 </span><span class="lineNoCov">          0 :       options |= X86Inst::kOptionShortForm;</span></a>
+<a name="4418"><span class="lineNum">    4418 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opCode8);</span></a>
+<a name="4419"><span class="lineNum">    4419 </span><span class="lineNoCov">          0 :       EMIT_BYTE(rel32 + inst32Size - inst8Size);</span></a>
+<a name="4420"><span class="lineNum">    4420 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4421"><span class="lineNum">    4421 </span>            :     }</a>
+<a name="4422"><span class="lineNum">    4422 </span>            :     else {</a>
+<a name="4423"><span class="lineNum">    4423 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!opCode || (options &amp; X86Inst::kOptionShortForm) != 0))</span></a>
+<a name="4424"><span class="lineNum">    4424 </span><span class="lineNoCov">          0 :         goto InvalidDisplacement;</span></a>
+<a name="4425"><span class="lineNum">    4425 </span>            : </a>
+<a name="4426"><span class="lineNum">    4426 </span><span class="lineNoCov">          0 :       options &amp;= ~X86Inst::kOptionShortForm;</span></a>
+<a name="4427"><span class="lineNum">    4427 </span><span class="lineNoCov">          0 :       if (opCode &amp; X86Inst::kOpCode_MM_Mask)</span></a>
+<a name="4428"><span class="lineNum">    4428 </span><span class="lineNoCov">          0 :         EMIT_BYTE(0x0F);</span></a>
+<a name="4429"><span class="lineNum">    4429 </span>            : </a>
+<a name="4430"><span class="lineNum">    4430 </span><span class="lineNoCov">          0 :       EMIT_BYTE(opCode);</span></a>
+<a name="4431"><span class="lineNum">    4431 </span><span class="lineNoCov">          0 :       if (opReg)</span></a>
+<a name="4432"><span class="lineNum">    4432 </span><span class="lineNoCov">          0 :         EMIT_BYTE(x86EncodeMod(3, opReg, 0));</span></a>
+<a name="4433"><span class="lineNum">    4433 </span>            : </a>
+<a name="4434"><span class="lineNum">    4434 </span><span class="lineNoCov">          0 :       EMIT_32(rel32);</span></a>
+<a name="4435"><span class="lineNum">    4435 </span><span class="lineNoCov">          0 :       goto EmitDone;</span></a>
+<a name="4436"><span class="lineNum">    4436 </span>            :     }</a>
+<a name="4437"><span class="lineNum">    4437 </span>            :   }</a>
+<a name="4438"><span class="lineNum">    4438 </span>            : </a>
+<a name="4439"><span class="lineNum">    4439 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4440"><span class="lineNum">    4440 </span>            :   // [Emit - Relative]</a>
+<a name="4441"><span class="lineNum">    4441 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4442"><span class="lineNum">    4442 </span>            : </a>
+<a name="4443"><span class="lineNum">    4443 </span><span class="lineNoCov">          0 : EmitRel:</span></a>
+<a name="4444"><span class="lineNum">    4444 </span>            :   {</a>
+<a name="4445"><span class="lineNum">    4445 </span>            :     ASMJIT_ASSERT(!label-&gt;isBound());</a>
+<a name="4446"><span class="lineNum">    4446 </span>            :     ASMJIT_ASSERT(relSize == 1 || relSize == 4);</a>
+<a name="4447"><span class="lineNum">    4447 </span>            : </a>
+<a name="4448"><span class="lineNum">    4448 </span>            :     // Chain with label.</a>
+<a name="4449"><span class="lineNum">    4449 </span><span class="lineNoCov">          0 :     size_t offset = (size_t)(cursor - _bufferData);</span></a>
+<a name="4450"><span class="lineNum">    4450 </span><span class="lineNoCov">          0 :     LabelLink* link = _code-&gt;newLabelLink(label, _section-&gt;getId(), offset, relOffset);</span></a>
+<a name="4451"><span class="lineNum">    4451 </span>            : </a>
+<a name="4452"><span class="lineNum">    4452 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!link))</span></a>
+<a name="4453"><span class="lineNum">    4453 </span><span class="lineNoCov">          0 :       goto NoHeapMemory;</span></a>
+<a name="4454"><span class="lineNum">    4454 </span>            : </a>
+<a name="4455"><span class="lineNum">    4455 </span><span class="lineNoCov">          0 :     if (re)</span></a>
+<a name="4456"><span class="lineNum">    4456 </span><span class="lineNoCov">          0 :       link-&gt;relocId = re-&gt;getId();</span></a>
+<a name="4457"><span class="lineNum">    4457 </span>            : </a>
+<a name="4458"><span class="lineNum">    4458 </span>            :     // Emit label size as dummy data.</a>
+<a name="4459"><span class="lineNum">    4459 </span><span class="lineNoCov">          0 :     if (relSize == 1)</span></a>
+<a name="4460"><span class="lineNum">    4460 </span><span class="lineNoCov">          0 :       EMIT_BYTE(0x01);</span></a>
+<a name="4461"><span class="lineNum">    4461 </span>            :     else // if (relSize == 4)</a>
+<a name="4462"><span class="lineNum">    4462 </span><span class="lineNoCov">          0 :       EMIT_32(0x04040404);</span></a>
+<a name="4463"><span class="lineNum">    4463 </span>            :   }</a>
+<a name="4464"><span class="lineNum">    4464 </span>            : </a>
+<a name="4465"><span class="lineNum">    4465 </span><span class="lineNoCov">          0 :   if (imLen == 0)</span></a>
+<a name="4466"><span class="lineNum">    4466 </span><span class="lineNoCov">          0 :     goto EmitDone;</span></a>
+<a name="4467"><span class="lineNum">    4467 </span>            : </a>
+<a name="4468"><span class="lineNum">    4468 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4469"><span class="lineNum">    4469 </span>            :   // [Emit - Immediate]</a>
+<a name="4470"><span class="lineNum">    4470 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4471"><span class="lineNum">    4471 </span>            : </a>
+<a name="4472"><span class="lineNum">    4472 </span><span class="lineNoCov">          0 : EmitImm:</span></a>
+<a name="4473"><span class="lineNum">    4473 </span>            :   {</a>
+<a name="4474"><span class="lineNum">    4474 </span>            : #if ASMJIT_ARCH_64BIT</a>
+<a name="4475"><span class="lineNum">    4475 </span><span class="lineCov">       9672 :     uint32_t i = imLen;</span></a>
+<a name="4476"><span class="lineNum">    4476 </span><span class="lineCov">       9672 :     uint64_t imm = static_cast&lt;uint64_t&gt;(imVal);</span></a>
+<a name="4477"><span class="lineNum">    4477 </span>            : #else</a>
+<a name="4478"><span class="lineNum">    4478 </span>            :     uint32_t i = imLen;</a>
+<a name="4479"><span class="lineNum">    4479 </span>            :     uint32_t imm = static_cast&lt;uint32_t&gt;(imVal &amp; 0xFFFFFFFFU);</a>
+<a name="4480"><span class="lineNum">    4480 </span>            : #endif</a>
+<a name="4481"><span class="lineNum">    4481 </span>            : </a>
+<a name="4482"><span class="lineNum">    4482 </span>            :     // Many instructions just use a single byte immediate, so make it fast.</a>
+<a name="4483"><span class="lineNum">    4483 </span><span class="lineCov">       9672 :     EMIT_BYTE(imm &amp; 0xFFU); if (--i == 0) goto EmitDone;</span></a>
+<a name="4484"><span class="lineNum">    4484 </span><span class="lineCov">       7688 :     imm &gt;&gt;= 8;</span></a>
+<a name="4485"><span class="lineNum">    4485 </span><span class="lineCov">       7688 :     EMIT_BYTE(imm &amp; 0xFFU); if (--i == 0) goto EmitDone;</span></a>
+<a name="4486"><span class="lineNum">    4486 </span><span class="lineCov">       7688 :     imm &gt;&gt;= 8;</span></a>
+<a name="4487"><span class="lineNum">    4487 </span><span class="lineCov">       7688 :     EMIT_BYTE(imm &amp; 0xFFU); if (--i == 0) goto EmitDone;</span></a>
+<a name="4488"><span class="lineNum">    4488 </span><span class="lineCov">       7688 :     imm &gt;&gt;= 8;</span></a>
+<a name="4489"><span class="lineNum">    4489 </span><span class="lineCov">       7688 :     EMIT_BYTE(imm &amp; 0xFFU); if (--i == 0) goto EmitDone;</span></a>
+<a name="4490"><span class="lineNum">    4490 </span>            : </a>
+<a name="4491"><span class="lineNum">    4491 </span>            :     // Can be 1-4 or 8 bytes, this handles the remaining high DWORD of an 8-byte immediate.</a>
+<a name="4492"><span class="lineNum">    4492 </span>            :     ASMJIT_ASSERT(i == 4);</a>
+<a name="4493"><span class="lineNum">    4493 </span>            : </a>
+<a name="4494"><span class="lineNum">    4494 </span>            : #if ASMJIT_ARCH_64BIT</a>
+<a name="4495"><span class="lineNum">    4495 </span><span class="lineCov">       7688 :     imm &gt;&gt;= 8;</span></a>
+<a name="4496"><span class="lineNum">    4496 </span><span class="lineCov">       7688 :     EMIT_32(static_cast&lt;uint32_t&gt;(imm));</span></a>
+<a name="4497"><span class="lineNum">    4497 </span>            : #else</a>
+<a name="4498"><span class="lineNum">    4498 </span>            :     EMIT_32(static_cast&lt;uint32_t&gt;((static_cast&lt;uint64_t&gt;(imVal) &gt;&gt; 32) &amp; 0xFFFFFFFFU));</a>
+<a name="4499"><span class="lineNum">    4499 </span>            : #endif</a>
+<a name="4500"><span class="lineNum">    4500 </span>            :   }</a>
+<a name="4501"><span class="lineNum">    4501 </span>            : </a>
+<a name="4502"><span class="lineNum">    4502 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4503"><span class="lineNum">    4503 </span>            :   // [Done]</a>
+<a name="4504"><span class="lineNum">    4504 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4505"><span class="lineNum">    4505 </span>            : </a>
+<a name="4506"><span class="lineNum">    4506 </span><span class="lineCov">      48362 : EmitDone:</span></a>
+<a name="4507"><span class="lineNum">    4507 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="4508"><span class="lineNum">    4508 </span>            :   // Logging is a performance hit anyway, so make it the unlikely case.</a>
+<a name="4509"><span class="lineNum">    4509 </span><span class="lineCov">      48362 :   if (ASMJIT_UNLIKELY(options &amp; CodeEmitter::kOptionLoggingEnabled))</span></a>
+<a name="4510"><span class="lineNum">    4510 </span><span class="lineNoCov">          0 :     _emitLog(instId, options, o0, o1, o2, o3, relSize, imLen, cursor);</span></a>
+<a name="4511"><span class="lineNum">    4511 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="4512"><span class="lineNum">    4512 </span>            : </a>
+<a name="4513"><span class="lineNum">    4513 </span>            :   resetOptions();</a>
+<a name="4514"><span class="lineNum">    4514 </span>            :   resetExtraReg();</a>
+<a name="4515"><span class="lineNum">    4515 </span>            :   resetInlineComment();</a>
+<a name="4516"><span class="lineNum">    4516 </span>            : </a>
+<a name="4517"><span class="lineNum">    4517 </span><span class="lineCov">      48362 :   _bufferPtr = cursor;</span></a>
+<a name="4518"><span class="lineNum">    4518 </span><span class="lineCov">      48362 :   return kErrorOk;</span></a>
+<a name="4519"><span class="lineNum">    4519 </span>            : </a>
+<a name="4520"><span class="lineNum">    4520 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4521"><span class="lineNum">    4521 </span>            :   // [Error Cases]</a>
+<a name="4522"><span class="lineNum">    4522 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4523"><span class="lineNum">    4523 </span>            : </a>
+<a name="4524"><span class="lineNum">    4524 </span>            : #define ERROR_HANDLER(ERROR)                \</a>
+<a name="4525"><span class="lineNum">    4525 </span>            : ERROR:                                      \</a>
+<a name="4526"><span class="lineNum">    4526 </span>            :   err = DebugUtils::errored(kError##ERROR); \</a>
+<a name="4527"><span class="lineNum">    4527 </span>            :   goto Failed;</a>
+<a name="4528"><span class="lineNum">    4528 </span>            : </a>
+<a name="4529"><span class="lineNum">    4529 </span><span class="lineNoCov">          0 : ERROR_HANDLER(NoHeapMemory)</span></a>
+<a name="4530"><span class="lineNum">    4530 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidArgument)</span></a>
+<a name="4531"><span class="lineNum">    4531 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidLabel)</span></a>
+<a name="4532"><span class="lineNum">    4532 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidInstruction)</span></a>
+<a name="4533"><span class="lineNum">    4533 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidLockPrefix)</span></a>
+<a name="4534"><span class="lineNum">    4534 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidXAcquirePrefix)</span></a>
+<a name="4535"><span class="lineNum">    4535 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidXReleasePrefix)</span></a>
+<a name="4536"><span class="lineNum">    4536 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidRepPrefix)</span></a>
+<a name="4537"><span class="lineNum">    4537 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidRexPrefix)</span></a>
+<a name="4538"><span class="lineNum">    4538 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidBroadcast)</span></a>
+<a name="4539"><span class="lineNum">    4539 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidEROrSAE)</span></a>
+<a name="4540"><span class="lineNum">    4540 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidAddress)</span></a>
+<a name="4541"><span class="lineNum">    4541 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidAddressIndex)</span></a>
+<a name="4542"><span class="lineNum">    4542 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidAddress64Bit)</span></a>
+<a name="4543"><span class="lineNum">    4543 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidDisplacement)</span></a>
+<a name="4544"><span class="lineNum">    4544 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidSegment)</span></a>
+<a name="4545"><span class="lineNum">    4545 </span><span class="lineNoCov">          0 : ERROR_HANDLER(InvalidImmediate)</span></a>
+<a name="4546"><span class="lineNum">    4546 </span><span class="lineNoCov">          0 : ERROR_HANDLER(OperandSizeMismatch)</span></a>
+<a name="4547"><span class="lineNum">    4547 </span><span class="lineNoCov">          0 : ERROR_HANDLER(AmbiguousOperandSize)</span></a>
+<a name="4548"><span class="lineNum">    4548 </span><span class="lineNoCov">          0 : ERROR_HANDLER(NotConsecutiveRegs)</span></a>
+<a name="4549"><span class="lineNum">    4549 </span>            : </a>
+<a name="4550"><span class="lineNum">    4550 </span><span class="lineNoCov">          0 : Failed:</span></a>
+<a name="4551"><span class="lineNum">    4551 </span><span class="lineNoCov">          0 :   return _emitFailed(err, instId, options, o0, o1, o2, o3);</span></a>
+<a name="4552"><span class="lineNum">    4552 </span>            : }</a>
+<a name="4553"><span class="lineNum">    4553 </span>            : </a>
+<a name="4554"><span class="lineNum">    4554 </span>            : // ============================================================================</a>
+<a name="4555"><span class="lineNum">    4555 </span>            : // [asmjit::X86Assembler - Align]</a>
+<a name="4556"><span class="lineNum">    4556 </span>            : // ============================================================================</a>
+<a name="4557"><span class="lineNum">    4557 </span>            : </a>
+<a name="4558"><span class="lineNum">    4558 </span><span class="lineNoCov">          0 : Error X86Assembler::align(uint32_t mode, uint32_t alignment) {</span></a>
+<a name="4559"><span class="lineNum">    4559 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="4560"><span class="lineNum">    4560 </span><span class="lineNoCov">          0 :   if (_globalOptions &amp; kOptionLoggingEnabled)</span></a>
+<a name="4561"><span class="lineNum">    4561 </span><span class="lineNoCov">          0 :     _code-&gt;_logger-&gt;logf(&quot;%s.align %u\n&quot;, _code-&gt;_logger-&gt;getIndentation(), alignment);</span></a>
+<a name="4562"><span class="lineNum">    4562 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="4563"><span class="lineNum">    4563 </span>            : </a>
+<a name="4564"><span class="lineNum">    4564 </span><span class="lineNoCov">          0 :   if (mode &gt;= kAlignCount)</span></a>
+<a name="4565"><span class="lineNum">    4565 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidArgument));</span></a>
+<a name="4566"><span class="lineNum">    4566 </span>            : </a>
+<a name="4567"><span class="lineNum">    4567 </span><span class="lineNoCov">          0 :   if (alignment &lt;= 1)</span></a>
+<a name="4568"><span class="lineNum">    4568 </span>            :     return kErrorOk;</a>
+<a name="4569"><span class="lineNum">    4569 </span>            : </a>
+<a name="4570"><span class="lineNum">    4570 </span><span class="lineNoCov">          0 :   if (!Utils::isPowerOf2(alignment) || alignment &gt; Globals::kMaxAlignment)</span></a>
+<a name="4571"><span class="lineNum">    4571 </span><span class="lineNoCov">          0 :     return setLastError(DebugUtils::errored(kErrorInvalidArgument));</span></a>
+<a name="4572"><span class="lineNum">    4572 </span>            : </a>
+<a name="4573"><span class="lineNum">    4573 </span><span class="lineNoCov">          0 :   uint32_t i = static_cast&lt;uint32_t&gt;(Utils::alignDiff&lt;size_t&gt;(getOffset(), alignment));</span></a>
+<a name="4574"><span class="lineNum">    4574 </span><span class="lineNoCov">          0 :   if (i == 0)</span></a>
+<a name="4575"><span class="lineNum">    4575 </span>            :     return kErrorOk;</a>
+<a name="4576"><span class="lineNum">    4576 </span>            : </a>
+<a name="4577"><span class="lineNum">    4577 </span><span class="lineNoCov">          0 :   if (getRemainingSpace() &lt; i) {</span></a>
+<a name="4578"><span class="lineNum">    4578 </span><span class="lineNoCov">          0 :     Error err = _code-&gt;growBuffer(&amp;_section-&gt;_buffer, i);</span></a>
+<a name="4579"><span class="lineNum">    4579 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="4580"><span class="lineNum">    4580 </span>            :   }</a>
+<a name="4581"><span class="lineNum">    4581 </span>            : </a>
+<a name="4582"><span class="lineNum">    4582 </span><span class="lineNoCov">          0 :   uint8_t* cursor = _bufferPtr;</span></a>
+<a name="4583"><span class="lineNum">    4583 </span>            :   uint8_t pattern = 0x00;</a>
+<a name="4584"><span class="lineNum">    4584 </span>            : </a>
+<a name="4585"><span class="lineNum">    4585 </span><span class="lineNoCov">          0 :   switch (mode) {</span></a>
+<a name="4586"><span class="lineNum">    4586 </span><span class="lineNoCov">          0 :     case kAlignCode: {</span></a>
+<a name="4587"><span class="lineNum">    4587 </span><span class="lineNoCov">          0 :       if (_globalHints &amp; kHintOptimizedAlign) {</span></a>
+<a name="4588"><span class="lineNum">    4588 </span>            :         // Intel 64 and IA-32 Architectures Software Developer's Manual - Volume 2B (NOP).</a>
+<a name="4589"><span class="lineNum">    4589 </span>            :         enum { kMaxNopSize = 9 };</a>
+<a name="4590"><span class="lineNum">    4590 </span>            : </a>
+<a name="4591"><span class="lineNum">    4591 </span>            :         static const uint8_t nopData[kMaxNopSize][kMaxNopSize] = {</a>
+<a name="4592"><span class="lineNum">    4592 </span>            :           { 0x90 },</a>
+<a name="4593"><span class="lineNum">    4593 </span>            :           { 0x66, 0x90 },</a>
+<a name="4594"><span class="lineNum">    4594 </span>            :           { 0x0F, 0x1F, 0x00 },</a>
+<a name="4595"><span class="lineNum">    4595 </span>            :           { 0x0F, 0x1F, 0x40, 0x00 },</a>
+<a name="4596"><span class="lineNum">    4596 </span>            :           { 0x0F, 0x1F, 0x44, 0x00, 0x00 },</a>
+<a name="4597"><span class="lineNum">    4597 </span>            :           { 0x66, 0x0F, 0x1F, 0x44, 0x00, 0x00 },</a>
+<a name="4598"><span class="lineNum">    4598 </span>            :           { 0x0F, 0x1F, 0x80, 0x00, 0x00, 0x00, 0x00 },</a>
+<a name="4599"><span class="lineNum">    4599 </span>            :           { 0x0F, 0x1F, 0x84, 0x00, 0x00, 0x00, 0x00, 0x00 },</a>
+<a name="4600"><span class="lineNum">    4600 </span>            :           { 0x66, 0x0F, 0x1F, 0x84, 0x00, 0x00, 0x00, 0x00, 0x00 }</a>
+<a name="4601"><span class="lineNum">    4601 </span>            :         };</a>
+<a name="4602"><span class="lineNum">    4602 </span>            : </a>
+<a name="4603"><span class="lineNum">    4603 </span>            :         do {</a>
+<a name="4604"><span class="lineNum">    4604 </span><span class="lineNoCov">          0 :           uint32_t n = std::min&lt;uint32_t&gt;(i, kMaxNopSize);</span></a>
+<a name="4605"><span class="lineNum">    4605 </span><span class="lineNoCov">          0 :           const uint8_t* src = nopData[n - 1];</span></a>
+<a name="4606"><span class="lineNum">    4606 </span>            : </a>
+<a name="4607"><span class="lineNum">    4607 </span><span class="lineNoCov">          0 :           i -= n;</span></a>
+<a name="4608"><span class="lineNum">    4608 </span>            :           do {</a>
+<a name="4609"><span class="lineNum">    4609 </span><span class="lineNoCov">          0 :             EMIT_BYTE(*src++);</span></a>
+<a name="4610"><span class="lineNum">    4610 </span><span class="lineNoCov">          0 :           } while (--n);</span></a>
+<a name="4611"><span class="lineNum">    4611 </span><span class="lineNoCov">          0 :         } while (i);</span></a>
+<a name="4612"><span class="lineNum">    4612 </span>            :       }</a>
+<a name="4613"><span class="lineNum">    4613 </span>            : </a>
+<a name="4614"><span class="lineNum">    4614 </span>            :       pattern = 0x90;</a>
+<a name="4615"><span class="lineNum">    4615 </span>            :       break;</a>
+<a name="4616"><span class="lineNum">    4616 </span>            :     }</a>
+<a name="4617"><span class="lineNum">    4617 </span>            : </a>
+<a name="4618"><span class="lineNum">    4618 </span><span class="lineNoCov">          0 :     case kAlignData:</span></a>
+<a name="4619"><span class="lineNum">    4619 </span>            :       pattern = 0xCC;</a>
+<a name="4620"><span class="lineNum">    4620 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="4621"><span class="lineNum">    4621 </span>            : </a>
+<a name="4622"><span class="lineNum">    4622 </span>            :     case kAlignZero:</a>
+<a name="4623"><span class="lineNum">    4623 </span>            :       // Pattern already set to zero.</a>
+<a name="4624"><span class="lineNum">    4624 </span>            :       break;</a>
+<a name="4625"><span class="lineNum">    4625 </span>            :   }</a>
+<a name="4626"><span class="lineNum">    4626 </span>            : </a>
+<a name="4627"><span class="lineNum">    4627 </span><span class="lineNoCov">          0 :   while (i) {</span></a>
+<a name="4628"><span class="lineNum">    4628 </span><span class="lineNoCov">          0 :     EMIT_BYTE(pattern);</span></a>
+<a name="4629"><span class="lineNum">    4629 </span><span class="lineNoCov">          0 :     i--;</span></a>
+<a name="4630"><span class="lineNum">    4630 </span>            :   }</a>
+<a name="4631"><span class="lineNum">    4631 </span>            : </a>
+<a name="4632"><span class="lineNum">    4632 </span><span class="lineNoCov">          0 :   _bufferPtr = cursor;</span></a>
+<a name="4633"><span class="lineNum">    4633 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="4634"><span class="lineNum">    4634 </span>            : }</a>
+<a name="4635"><span class="lineNum">    4635 </span>            : </a>
+<a name="4636"><span class="lineNum">    4636 </span>            : } // asmjit namespace</a>
+<a name="4637"><span class="lineNum">    4637 </span>            : } // namespace PLMD</a>
+<a name="4638"><span class="lineNum">    4638 </span>            : </a>
+<a name="4639"><span class="lineNum">    4639 </span>            : // [Api-End]</a>
+<a name="4640"><span class="lineNum">    4640 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="4641"><span class="lineNum">    4641 </span>            : </a>
+<a name="4642"><span class="lineNum">    4642 </span>            : // [Guard]</a>
+<a name="4643"><span class="lineNum">    4643 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="4644"><span class="lineNum">    4644 </span>            : #pragma GCC diagnostic pop</a>
+<a name="4645"><span class="lineNum">    4645 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86assembler.h.func-sort-c.html b/coverage-libs/asmjit/x86assembler.h.func-sort-c.html
new file mode 100644
index 0000000000..8ba2570666
--- /dev/null
+++ b/coverage-libs/asmjit/x86assembler.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86assembler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86assembler.h<span style="font-size: 80%;"> (<a href="x86assembler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86assembler.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86assembler.h.func.html b/coverage-libs/asmjit/x86assembler.h.func.html
new file mode 100644
index 0000000000..23720b6896
--- /dev/null
+++ b/coverage-libs/asmjit/x86assembler.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86assembler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86assembler.h<span style="font-size: 80%;"> (<a href="x86assembler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86assembler.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86assembler.h.gcov.html b/coverage-libs/asmjit/x86assembler.h.gcov.html
new file mode 100644
index 0000000000..d0f22321f9
--- /dev/null
+++ b/coverage-libs/asmjit/x86assembler.h.gcov.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86assembler.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86assembler.h<span style="font-size: 80%;"> (source / <a href="x86assembler.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86assembler_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86assembler_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86ASSEMBLER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86ASSEMBLER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./assembler.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./x86emitter.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : // [Api-Begin]</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace asmjit {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="48"><span class="lineNum">      48 </span>            : //! \{</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : // [asmjit::X86Assembler]</a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : //! X86/X64 assembler.</a>
+<a name="55"><span class="lineNum">      55 </span>            : //!</a>
+<a name="56"><span class="lineNum">      56 </span>            : //! X86/X64 assembler emits machine-code into buffers managed by \ref CodeHolder.</a>
+<a name="57"><span class="lineNum">      57 </span>            : class ASMJIT_VIRTAPI X86Assembler</a>
+<a name="58"><span class="lineNum">      58 </span>            :   : public Assembler,</a>
+<a name="59"><span class="lineNum">      59 </span>            :     public X86EmitterImplicitT&lt;X86Assembler&gt; {</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : public:</a>
+<a name="62"><span class="lineNum">      62 </span>            :   typedef Assembler Base;</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="65"><span class="lineNum">      65 </span>            :   // [Construction / Destruction]</a>
+<a name="66"><span class="lineNum">      66 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   ASMJIT_API X86Assembler(CodeHolder* code = nullptr) noexcept;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   ASMJIT_API virtual ~X86Assembler() noexcept;</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="72"><span class="lineNum">      72 </span>            :   // [Compatibility]</a>
+<a name="73"><span class="lineNum">      73 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   //! Explicit cast to `X86Emitter`.</a>
+<a name="76"><span class="lineNum">      76 </span>            :   ASMJIT_INLINE X86Emitter* asEmitter() noexcept { return reinterpret_cast&lt;X86Emitter*&gt;(this); }</a>
+<a name="77"><span class="lineNum">      77 </span>            :   //! Explicit cast to `X86Emitter` (const).</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ASMJIT_INLINE const X86Emitter* asEmitter() const noexcept { return reinterpret_cast&lt;const X86Emitter*&gt;(this); }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   //! Implicit cast to `X86Emitter`.</a>
+<a name="81"><span class="lineNum">      81 </span>            :   ASMJIT_INLINE operator X86Emitter&amp;() noexcept { return *asEmitter(); }</a>
+<a name="82"><span class="lineNum">      82 </span>            :   //! Implicit cast to `X86Emitter` (const).</a>
+<a name="83"><span class="lineNum">      83 </span>            :   ASMJIT_INLINE operator const X86Emitter&amp;() const noexcept { return *asEmitter(); }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="86"><span class="lineNum">      86 </span>            :   // [Accessors]</a>
+<a name="87"><span class="lineNum">      87 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   // NOTE: X86Assembler uses _privateData to store 'address-override' bit that</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // is used to decide whether to emit address-override (67H) prefix based on</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // the memory BASE+INDEX registers. It's either `kX86MemInfo_67H_X86` or</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // `kX86MemInfo_67H_X64`.</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      14528 :   ASMJIT_INLINE uint32_t _getAddressOverrideMask() const noexcept { return _privateData; }</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1948 :   ASMJIT_INLINE void _setAddressOverrideMask(uint32_t m) noexcept { _privateData = m; }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // [Events]</a>
+<a name="98"><span class="lineNum">      98 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   ASMJIT_API Error onAttach(CodeHolder* code) noexcept override;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   ASMJIT_API Error onDetach(CodeHolder* code) noexcept override;</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="104"><span class="lineNum">     104 </span>            :   // [Code-Generation]</a>
+<a name="105"><span class="lineNum">     105 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   using CodeEmitter::_emit;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   ASMJIT_API Error _emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) override;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   ASMJIT_API Error align(uint32_t mode, uint32_t alignment) override;</a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : //! \}</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : } // asmjit namespace</a>
+<a name="116"><span class="lineNum">     116 </span>            : } // namespace PLMD</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : // [Api-End]</a>
+<a name="119"><span class="lineNum">     119 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : // [Guard]</a>
+<a name="122"><span class="lineNum">     122 </span>            : #endif // _ASMJIT_X86_X86ASSEMBLER_H</a>
+<a name="123"><span class="lineNum">     123 </span>            : #pragma GCC diagnostic pop</a>
+<a name="124"><span class="lineNum">     124 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="125"><span class="lineNum">     125 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86builder.cpp.func-sort-c.html b/coverage-libs/asmjit/x86builder.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c5ca9a3fe1
--- /dev/null
+++ b/coverage-libs/asmjit/x86builder.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86builder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86builder.cpp<span style="font-size: 80%;"> (<a href="x86builder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86builder.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#76">_ZN4PLMD6asmjit10X86Builder5_emitEjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#57">_ZN4PLMD6asmjit10X86Builder8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#47">_ZN4PLMD6asmjit10X86BuilderC2EPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#51">_ZN4PLMD6asmjit10X86BuilderD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#51">_ZN4PLMD6asmjit10X86BuilderD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86builder.cpp.func.html b/coverage-libs/asmjit/x86builder.cpp.func.html
new file mode 100644
index 0000000000..16f6bed63d
--- /dev/null
+++ b/coverage-libs/asmjit/x86builder.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86builder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86builder.cpp<span style="font-size: 80%;"> (<a href="x86builder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86builder.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#76">_ZN4PLMD6asmjit10X86Builder5_emitEjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#57">_ZN4PLMD6asmjit10X86Builder8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#47">_ZN4PLMD6asmjit10X86BuilderC2EPNS0_10CodeHolderE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#51">_ZN4PLMD6asmjit10X86BuilderD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86builder.cpp.gcov.html#51">_ZN4PLMD6asmjit10X86BuilderD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86builder.cpp.gcov.html b/coverage-libs/asmjit/x86builder.cpp.gcov.html
new file mode 100644
index 0000000000..8ea974e853
--- /dev/null
+++ b/coverage-libs/asmjit/x86builder.cpp.gcov.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86builder.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86builder.cpp<span style="font-size: 80%;"> (source / <a href="x86builder.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if defined(ASMJIT_BUILD_X86) &amp;&amp; !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./x86builder.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // ============================================================================</a>
+<a name="46"><span class="lineNum">      46 </span>            : // [asmjit::X86Builder - Construction / Destruction]</a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 : X86Builder::X86Builder(CodeHolder* code) noexcept : CodeBuilder() {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :   if (code)</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :     code-&gt;attach(this);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 : X86Builder::~X86Builder() noexcept {}</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : // [asmjit::X86Builder - Events]</a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 : Error X86Builder::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   uint32_t archType = code-&gt;getArchType();</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   if (!ArchInfo::isX86Family(archType))</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :     return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(Base::onAttach(code));</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   if (archType == ArchInfo::kTypeX86)</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :     _nativeGpArray = x86OpData.gpd;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   else</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :     _nativeGpArray = x86OpData.gpq;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :   _nativeGpReg = _nativeGpArray[0];</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : // ============================================================================</a>
+<a name="75"><span class="lineNum">      75 </span>            : // [asmjit::X86Builder - Inst]</a>
+<a name="76"><span class="lineNum">      76 </span>            : // ============================================================================</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 : Error X86Builder::_emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   // TODO:</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : } // asmjit namespace</a>
+<a name="84"><span class="lineNum">      84 </span>            : } // namespace PLMD</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : // [Api-End]</a>
+<a name="87"><span class="lineNum">      87 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : // [Guard]</a>
+<a name="90"><span class="lineNum">      90 </span>            : #endif // ASMJIT_BUILD_X86 &amp;&amp; !ASMJIT_DISABLE_COMPILER</a>
+<a name="91"><span class="lineNum">      91 </span>            : #pragma GCC diagnostic pop</a>
+<a name="92"><span class="lineNum">      92 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86compiler.cpp.func-sort-c.html b/coverage-libs/asmjit/x86compiler.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8d8ff1485d
--- /dev/null
+++ b/coverage-libs/asmjit/x86compiler.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86compiler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86compiler.cpp<span style="font-size: 80%;"> (<a href="x86compiler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryLo">31.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86compiler.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#251">_ZN4PLMD6asmjit11X86Compiler5_emitEjRKNS0_8Operand_ES4_S4_S4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#53">_ZN4PLMD6asmjit11X86CompilerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#80">_ZN4PLMD6asmjit11X86Compiler8finalizeEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#59">_ZN4PLMD6asmjit11X86Compiler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#49">_ZN4PLMD6asmjit11X86CompilerC2EPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#53">_ZN4PLMD6asmjit11X86CompilerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#121">_ZN4PLMD6asmjit11X86Compiler5_emitEjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnHi">46714</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86compiler.cpp.func.html b/coverage-libs/asmjit/x86compiler.cpp.func.html
new file mode 100644
index 0000000000..3529ddd037
--- /dev/null
+++ b/coverage-libs/asmjit/x86compiler.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86compiler.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86compiler.cpp<span style="font-size: 80%;"> (<a href="x86compiler.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryLo">31.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86compiler.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#121">_ZN4PLMD6asmjit11X86Compiler5_emitEjRKNS0_8Operand_ES4_S4_S4_</a></td>
+              <td class="coverFnHi">46714</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#251">_ZN4PLMD6asmjit11X86Compiler5_emitEjRKNS0_8Operand_ES4_S4_S4_S4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#80">_ZN4PLMD6asmjit11X86Compiler8finalizeEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#59">_ZN4PLMD6asmjit11X86Compiler8onAttachEPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#49">_ZN4PLMD6asmjit11X86CompilerC2EPNS0_10CodeHolderE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#53">_ZN4PLMD6asmjit11X86CompilerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.cpp.gcov.html#53">_ZN4PLMD6asmjit11X86CompilerD2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86compiler.cpp.gcov.html b/coverage-libs/asmjit/x86compiler.cpp.gcov.html
new file mode 100644
index 0000000000..afc5bcc0f7
--- /dev/null
+++ b/coverage-libs/asmjit/x86compiler.cpp.gcov.html
@@ -0,0 +1,478 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86compiler.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86compiler.cpp<span style="font-size: 80%;"> (source / <a href="x86compiler.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryLo">31.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if defined(ASMJIT_BUILD_X86) &amp;&amp; !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./x86compiler.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./x86regalloc_p.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : // [Api-Begin]</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace asmjit {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::X86Compiler - Construction / Destruction]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1948 : X86Compiler::X86Compiler(CodeHolder* code) noexcept : CodeCompiler() {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       1948 :   if (code)</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       1948 :     code-&gt;attach(this);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1948 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1948 : X86Compiler::~X86Compiler() noexcept {}</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : // [asmjit::X86Compiler - Events]</a>
+<a name="59"><span class="lineNum">      59 </span>            : // ============================================================================</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1948 : Error X86Compiler::onAttach(CodeHolder* code) noexcept {</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   uint32_t archType = code-&gt;getArchType();</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       1948 :   if (!ArchInfo::isX86Family(archType))</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :     return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       3896 :   ASMJIT_PROPAGATE(_cbPasses.willGrow(&amp;_cbHeap, 1));</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       1948 :   ASMJIT_PROPAGATE(Base::onAttach(code));</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1948 :   if (archType == ArchInfo::kTypeX86)</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     _nativeGpArray = x86OpData.gpd;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   else</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       1948 :     _nativeGpArray = x86OpData.gpq;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       1948 :   _nativeGpReg = _nativeGpArray[0];</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       3896 :   return addPassT&lt;X86RAPass&gt;();</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : // ============================================================================</a>
+<a name="79"><span class="lineNum">      79 </span>            : // [asmjit::X86Compiler - Finalize]</a>
+<a name="80"><span class="lineNum">      80 </span>            : // ============================================================================</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       1948 : Error X86Compiler::finalize() {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1948 :   if (_lastError) return _lastError;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   // Flush the global constant pool.</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1948 :   if (_globalConstPool) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     addNode(_globalConstPool);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     _globalConstPool = nullptr;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   Error err = kErrorOk;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ZoneVector&lt;CBPass*&gt;&amp; passes = _cbPasses;</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       3896 :   for (size_t i = 0, len = passes.getLength(); i &lt; len; i++) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1948 :     CBPass* pass = passes[i];</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1948 :     err = pass-&gt;process(&amp;_cbPassZone);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1948 :     _cbPassZone.reset();</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1948 :     if (err) break;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1948 :   _cbPassZone.reset();</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       1948 :   if (ASMJIT_UNLIKELY(err)) return setLastError(err);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   // TODO: There must be possibility to attach more assemblers, this is not so nice.</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1948 :   if (_code-&gt;_cgAsm) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     return serialize(_code-&gt;_cgAsm);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span>            :   else {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1948 :     X86Assembler a(_code);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       1948 :     return serialize(&amp;a);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1948 :   }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : // ============================================================================</a>
+<a name="115"><span class="lineNum">     115 </span>            : // [asmjit::X86Compiler - Inst]</a>
+<a name="116"><span class="lineNum">     116 </span>            : // ============================================================================</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : static ASMJIT_INLINE bool isJumpInst(uint32_t instId) noexcept {</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      46714 :   return (instId &gt;= X86Inst::kIdJa   &amp;&amp; instId &lt;= X86Inst::kIdJz    ) ||</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      46714 :          (instId &gt;= X86Inst::kIdLoop &amp;&amp; instId &lt;= X86Inst::kIdLoopne) ;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      46714 : Error X86Compiler::_emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      46714 :   uint32_t options = getOptions() | getGlobalOptions();</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   const char* inlineComment = getInlineComment();</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      46714 :   uint32_t opCount = static_cast&lt;uint32_t&gt;(!o0.isNone()) +</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      46714 :                      static_cast&lt;uint32_t&gt;(!o1.isNone()) +</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      46714 :                      static_cast&lt;uint32_t&gt;(!o2.isNone()) +</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      46714 :                      static_cast&lt;uint32_t&gt;(!o3.isNone()) ;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   // Handle failure and rare cases first.</a>
+<a name="133"><span class="lineNum">     133 </span>            :   const uint32_t kErrorsAndSpecialCases = kOptionMaybeFailureCase | // CodeEmitter is in error state.</a>
+<a name="134"><span class="lineNum">     134 </span>            :                                           kOptionStrictValidation ; // Strict validation.</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      46714 :   if (ASMJIT_UNLIKELY(options &amp; kErrorsAndSpecialCases)) {</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     // Don't do anything if we are in error state.</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     if (_lastError) return _lastError;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="141"><span class="lineNum">     141 </span>            :     // Strict validation.</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     if (options &amp; kOptionStrictValidation) {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :       Operand opArray[] = {</a>
+<a name="144"><span class="lineNum">     144 </span>            :         Operand(o0),</a>
+<a name="145"><span class="lineNum">     145 </span>            :         Operand(o1),</a>
+<a name="146"><span class="lineNum">     146 </span>            :         Operand(o2),</a>
+<a name="147"><span class="lineNum">     147 </span>            :         Operand(o3)</a>
+<a name="148"><span class="lineNum">     148 </span>            :       };</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :       Inst::Detail instDetail(instId, options, _extraReg);</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :       Error err = Inst::validate(getArchType(), instDetail, opArray, opCount);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :       if (err) {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="155"><span class="lineNum">     155 </span>            :         StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :         sb.appendString(DebugUtils::errorAsString(err));</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :         sb.appendString(&quot;: &quot;);</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :         Logging::formatInstruction(sb, 0, this, getArchType(), instDetail, opArray, opCount);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :         return setLastError(err, sb.getData());</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : #else</a>
+<a name="161"><span class="lineNum">     161 </span>            :         return setLastError(err);</a>
+<a name="162"><span class="lineNum">     162 </span>            : #endif</a>
+<a name="163"><span class="lineNum">     163 </span>            :       }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            :       // Clear it as it must be enabled explicitly on assembler side.</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :       options &amp;= ~kOptionStrictValidation;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :     }</a>
+<a name="168"><span class="lineNum">     168 </span>            : #endif // ASMJIT_DISABLE_VALIDATION</a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   resetOptions();</a>
+<a name="172"><span class="lineNum">     172 </span>            :   resetInlineComment();</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // decide between `CBInst` and `CBJump`.</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      46714 :   if (isJumpInst(instId)) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     CBJump* node = _cbHeap.allocT&lt;CBJump&gt;(sizeof(CBJump) + opCount * sizeof(Operand));</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     Operand* opArray = reinterpret_cast&lt;Operand*&gt;(reinterpret_cast&lt;uint8_t*&gt;(node) + sizeof(CBJump));</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :       return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     if (opCount &gt; 0) opArray[0].copyFrom(o0);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     if (opCount &gt; 1) opArray[1].copyFrom(o1);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :     if (opCount &gt; 2) opArray[2].copyFrom(o2);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     if (opCount &gt; 3) opArray[3].copyFrom(o3);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :     new(node) CBJump(this, instId, options, opArray, opCount);</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     node-&gt;_instDetail.extraReg = _extraReg;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     _extraReg.reset();</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     CBLabel* jTarget = nullptr;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     if (!(options &amp; kOptionUnfollow)) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :       if (opArray[0].isLabel()) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :         Error err = getCBLabel(&amp;jTarget, static_cast&lt;Label&amp;&gt;(opArray[0]));</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :         if (err) return setLastError(err);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       }</a>
+<a name="197"><span class="lineNum">     197 </span>            :       else {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :         options |= kOptionUnfollow;</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :       }</a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span>            :     node-&gt;setOptions(options);</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     node-&gt;orFlags(instId == X86Inst::kIdJmp ? CBNode::kFlagIsJmp | CBNode::kFlagIsTaken : CBNode::kFlagIsJcc);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     node-&gt;_target = jTarget;</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :     node-&gt;_jumpNext = nullptr;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :     if (jTarget) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :       node-&gt;_jumpNext = static_cast&lt;CBJump*&gt;(jTarget-&gt;_from);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       jTarget-&gt;_from = node;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :       jTarget-&gt;addNumRefs();</a>
+<a name="211"><span class="lineNum">     211 </span>            :     }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            :     // The 'jmp' is always taken, conditional jump can contain hint, we detect it.</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     if (instId == X86Inst::kIdJmp)</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :       node-&gt;orFlags(CBNode::kFlagIsTaken);</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :     else if (options &amp; X86Inst::kOptionTaken)</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :       node-&gt;orFlags(CBNode::kFlagIsTaken);</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :     if (inlineComment) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :       inlineComment = static_cast&lt;char*&gt;(_cbDataZone.dup(inlineComment, ::strlen(inlineComment), true));</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :       node-&gt;setInlineComment(inlineComment);</a>
+<a name="222"><span class="lineNum">     222 </span>            :     }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :     addNode(node);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span>            :   else {</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      46714 :     CBInst* node = _cbHeap.allocT&lt;CBInst&gt;(sizeof(CBInst) + opCount * sizeof(Operand));</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      46714 :     Operand* opArray = reinterpret_cast&lt;Operand*&gt;(reinterpret_cast&lt;uint8_t*&gt;(node) + sizeof(CBInst));</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      46714 :     if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :       return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      46714 :     if (opCount &gt; 0) opArray[0].copyFrom(o0);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      46714 :     if (opCount &gt; 1) opArray[1].copyFrom(o1);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      46714 :     if (opCount &gt; 2) opArray[2].copyFrom(o2);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      46714 :     if (opCount &gt; 3) opArray[3].copyFrom(o3);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            :     node = new(node) CBInst(this, instId, options, opArray, opCount);</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      46714 :     node-&gt;_instDetail.extraReg = _extraReg;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :     _extraReg.reset();</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      46714 :     if (inlineComment) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :       inlineComment = static_cast&lt;char*&gt;(_cbDataZone.dup(inlineComment, ::strlen(inlineComment), true));</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :       node-&gt;setInlineComment(inlineComment);</a>
+<a name="246"><span class="lineNum">     246 </span>            :     }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">      46714 :     addNode(node);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      46714 :     return kErrorOk;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   }</a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 : Error X86Compiler::_emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, const Operand_&amp; o5) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   uint32_t options = getOptions() | getGlobalOptions();</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :   const char* inlineComment = getInlineComment();</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   uint32_t opCount = static_cast&lt;uint32_t&gt;(!o0.isNone()) +</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :                      static_cast&lt;uint32_t&gt;(!o1.isNone()) +</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :                      static_cast&lt;uint32_t&gt;(!o2.isNone()) +</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :                      static_cast&lt;uint32_t&gt;(!o3.isNone()) ;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :   // Count 5th and 6th operands.</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :   if (!o4.isNone()) opCount = 5;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   if (!o5.isNone()) opCount = 6;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :   // Handle failure and rare cases first.</a>
+<a name="267"><span class="lineNum">     267 </span>            :   const uint32_t kErrorsAndSpecialCases = kOptionMaybeFailureCase | // CodeEmitter in error state.</a>
+<a name="268"><span class="lineNum">     268 </span>            :                                           kOptionStrictValidation ; // Strict validation.</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(options &amp; kErrorsAndSpecialCases)) {</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :     // Don't do anything if we are in error state.</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     if (_lastError) return _lastError;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="275"><span class="lineNum">     275 </span>            :     // Strict validation.</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     if (options &amp; kOptionStrictValidation) {</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :       Operand opArray[] = {</a>
+<a name="278"><span class="lineNum">     278 </span>            :         Operand(o0),</a>
+<a name="279"><span class="lineNum">     279 </span>            :         Operand(o1),</a>
+<a name="280"><span class="lineNum">     280 </span>            :         Operand(o2),</a>
+<a name="281"><span class="lineNum">     281 </span>            :         Operand(o3),</a>
+<a name="282"><span class="lineNum">     282 </span>            :         Operand(o4),</a>
+<a name="283"><span class="lineNum">     283 </span>            :         Operand(o5)</a>
+<a name="284"><span class="lineNum">     284 </span>            :       };</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :       Inst::Detail instDetail(instId, options, _extraReg);</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :       Error err = Inst::validate(getArchType(), instDetail, opArray, opCount);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :       if (err) {</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="291"><span class="lineNum">     291 </span>            :         StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :         sb.appendString(DebugUtils::errorAsString(err));</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :         sb.appendString(&quot;: &quot;);</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :         Logging::formatInstruction(sb, 0, this, getArchType(), instDetail, opArray, opCount);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :         return setLastError(err, sb.getData());</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : #else</a>
+<a name="297"><span class="lineNum">     297 </span>            :         return setLastError(err);</a>
+<a name="298"><span class="lineNum">     298 </span>            : #endif</a>
+<a name="299"><span class="lineNum">     299 </span>            :       }</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :       // Clear it as it must be enabled explicitly on assembler side.</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :       options &amp;= ~kOptionStrictValidation;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     }</a>
+<a name="304"><span class="lineNum">     304 </span>            : #endif // ASMJIT_DISABLE_VALIDATION</a>
+<a name="305"><span class="lineNum">     305 </span>            :   }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   resetOptions();</a>
+<a name="308"><span class="lineNum">     308 </span>            :   resetInlineComment();</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            :   // decide between `CBInst` and `CBJump`.</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :   if (isJumpInst(instId)) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :     CBJump* node = _cbHeap.allocT&lt;CBJump&gt;(sizeof(CBJump) + opCount * sizeof(Operand));</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     Operand* opArray = reinterpret_cast&lt;Operand*&gt;(reinterpret_cast&lt;uint8_t*&gt;(node) + sizeof(CBJump));</span></a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :       return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :     if (opCount &gt; 0) opArray[0].copyFrom(o0);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :     if (opCount &gt; 1) opArray[1].copyFrom(o1);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :     if (opCount &gt; 2) opArray[2].copyFrom(o2);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :     if (opCount &gt; 3) opArray[3].copyFrom(o3);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :     if (opCount &gt; 4) opArray[4].copyFrom(o4);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     if (opCount &gt; 5) opArray[5].copyFrom(o5);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :     new(node) CBJump(this, instId, options, opArray, opCount);</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :     node-&gt;_instDetail.extraReg = _extraReg;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     _extraReg.reset();</a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :     CBLabel* jTarget = nullptr;</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :     if (!(options &amp; kOptionUnfollow)) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :       if (opArray[0].isLabel()) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :         Error err = getCBLabel(&amp;jTarget, static_cast&lt;Label&amp;&gt;(opArray[0]));</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :         if (err) return setLastError(err);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :       }</a>
+<a name="335"><span class="lineNum">     335 </span>            :       else {</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :         options |= kOptionUnfollow;</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :       }</a>
+<a name="338"><span class="lineNum">     338 </span>            :     }</a>
+<a name="339"><span class="lineNum">     339 </span>            :     node-&gt;setOptions(options);</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :     node-&gt;orFlags(instId == X86Inst::kIdJmp ? CBNode::kFlagIsJmp | CBNode::kFlagIsTaken : CBNode::kFlagIsJcc);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :     node-&gt;_target = jTarget;</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :     node-&gt;_jumpNext = nullptr;</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :     if (jTarget) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :       node-&gt;_jumpNext = static_cast&lt;CBJump*&gt;(jTarget-&gt;_from);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :       jTarget-&gt;_from = node;</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :       jTarget-&gt;addNumRefs();</a>
+<a name="349"><span class="lineNum">     349 </span>            :     }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :     // The 'jmp' is always taken, conditional jump can contain hint, we detect it.</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :     if (instId == X86Inst::kIdJmp)</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :       node-&gt;orFlags(CBNode::kFlagIsTaken);</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :     else if (options &amp; X86Inst::kOptionTaken)</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :       node-&gt;orFlags(CBNode::kFlagIsTaken);</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :     if (inlineComment) {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :       inlineComment = static_cast&lt;char*&gt;(_cbDataZone.dup(inlineComment, ::strlen(inlineComment), true));</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :       node-&gt;setInlineComment(inlineComment);</a>
+<a name="360"><span class="lineNum">     360 </span>            :     }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :     addNode(node);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   }</a>
+<a name="365"><span class="lineNum">     365 </span>            :   else {</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :     CBInst* node = _cbHeap.allocT&lt;CBInst&gt;(sizeof(CBInst) + opCount * sizeof(Operand));</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :     Operand* opArray = reinterpret_cast&lt;Operand*&gt;(reinterpret_cast&lt;uint8_t*&gt;(node) + sizeof(CBInst));</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!node))</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :       return setLastError(DebugUtils::errored(kErrorNoHeapMemory));</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     if (opCount &gt; 0) opArray[0].copyFrom(o0);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :     if (opCount &gt; 1) opArray[1].copyFrom(o1);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :     if (opCount &gt; 2) opArray[2].copyFrom(o2);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :     if (opCount &gt; 3) opArray[3].copyFrom(o3);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :     if (opCount &gt; 4) opArray[4].copyFrom(o4);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :     if (opCount &gt; 5) opArray[5].copyFrom(o5);</span></a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :     node = new(node) CBInst(this, instId, options, opArray, opCount);</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     node-&gt;_instDetail.extraReg = _extraReg;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :     _extraReg.reset();</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :     if (inlineComment) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :       inlineComment = static_cast&lt;char*&gt;(_cbDataZone.dup(inlineComment, ::strlen(inlineComment), true));</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :       node-&gt;setInlineComment(inlineComment);</a>
+<a name="386"><span class="lineNum">     386 </span>            :     }</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :     addNode(node);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :   }</a>
+<a name="391"><span class="lineNum">     391 </span>            : }</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span>            : } // asmjit namespace</a>
+<a name="394"><span class="lineNum">     394 </span>            : } // namespace PLMD</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            : // [Api-End]</a>
+<a name="397"><span class="lineNum">     397 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : // [Guard]</a>
+<a name="400"><span class="lineNum">     400 </span>            : #endif // ASMJIT_BUILD_X86 &amp;&amp; !ASMJIT_DISABLE_COMPILER</a>
+<a name="401"><span class="lineNum">     401 </span>            : #pragma GCC diagnostic pop</a>
+<a name="402"><span class="lineNum">     402 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86compiler.h.func-sort-c.html b/coverage-libs/asmjit/x86compiler.h.func-sort-c.html
new file mode 100644
index 0000000000..5567397b9b
--- /dev/null
+++ b/coverage-libs/asmjit/x86compiler.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86compiler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86compiler.h<span style="font-size: 80%;"> (<a href="x86compiler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86compiler.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.h.gcov.html#193">_ZN4PLMD6asmjit11X86Compiler6newGpzEPKcz</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.h.gcov.html#162">_ZN4PLMD6asmjit11X86Compiler6newRegEjPKcz</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86compiler.h.func.html b/coverage-libs/asmjit/x86compiler.h.func.html
new file mode 100644
index 0000000000..bf7c48f7a8
--- /dev/null
+++ b/coverage-libs/asmjit/x86compiler.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86compiler.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86compiler.h<span style="font-size: 80%;"> (<a href="x86compiler.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86compiler.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.h.gcov.html#193">_ZN4PLMD6asmjit11X86Compiler6newGpzEPKcz</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86compiler.h.gcov.html#162">_ZN4PLMD6asmjit11X86Compiler6newRegEjPKcz</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86compiler.h.gcov.html b/coverage-libs/asmjit/x86compiler.h.gcov.html
new file mode 100644
index 0000000000..cfac0311f1
--- /dev/null
+++ b/coverage-libs/asmjit/x86compiler.h.gcov.html
@@ -0,0 +1,398 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86compiler.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86compiler.h<span style="font-size: 80%;"> (source / <a href="x86compiler.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86compiler_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86compiler_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86COMPILER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86COMPILER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Dependencies]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./codecompiler.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./simdtypes.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./x86emitter.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./x86misc.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // [Api-Begin]</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : namespace PLMD {</a>
+<a name="48"><span class="lineNum">      48 </span>            : namespace asmjit {</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="51"><span class="lineNum">      51 </span>            : //! \{</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : // [asmjit::X86Compiler]</a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : //! Architecture-dependent \ref CodeCompiler targeting X86 and X64.</a>
+<a name="58"><span class="lineNum">      58 </span>            : class ASMJIT_VIRTAPI X86Compiler</a>
+<a name="59"><span class="lineNum">      59 </span>            :   : public CodeCompiler,</a>
+<a name="60"><span class="lineNum">      60 </span>            :     public X86EmitterExplicitT&lt;X86Compiler&gt; {</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : public:</a>
+<a name="63"><span class="lineNum">      63 </span>            :   ASMJIT_NONCOPYABLE(X86Compiler)</a>
+<a name="64"><span class="lineNum">      64 </span>            :   typedef CodeCompiler Base;</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="67"><span class="lineNum">      67 </span>            :   // [Construction / Destruction]</a>
+<a name="68"><span class="lineNum">      68 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   //! Create a `X86Compiler` instance.</a>
+<a name="71"><span class="lineNum">      71 </span>            :   ASMJIT_API X86Compiler(CodeHolder* code = nullptr) noexcept;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   //! Destroy the `X86Compiler` instance.</a>
+<a name="73"><span class="lineNum">      73 </span>            :   ASMJIT_API ~X86Compiler() noexcept;</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="76"><span class="lineNum">      76 </span>            :   // [Compatibility]</a>
+<a name="77"><span class="lineNum">      77 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   //! Explicit cast to `X86Emitter`.</a>
+<a name="80"><span class="lineNum">      80 </span>            :   ASMJIT_INLINE X86Emitter* asEmitter() noexcept { return reinterpret_cast&lt;X86Emitter*&gt;(this); }</a>
+<a name="81"><span class="lineNum">      81 </span>            :   //! Explicit cast to `X86Emitter` (const).</a>
+<a name="82"><span class="lineNum">      82 </span>            :   ASMJIT_INLINE const X86Emitter* asEmitter() const noexcept { return reinterpret_cast&lt;const X86Emitter*&gt;(this); }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! Implicit cast to `X86Emitter`.</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ASMJIT_INLINE operator X86Emitter&amp;() noexcept { return *asEmitter(); }</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //! Implicit cast to `X86Emitter` (const).</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ASMJIT_INLINE operator const X86Emitter&amp;() const noexcept { return *asEmitter(); }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // [Events]</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   ASMJIT_API virtual Error onAttach(CodeHolder* code) noexcept override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // [Code-Generation]</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   ASMJIT_API virtual Error _emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3) override;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   ASMJIT_API virtual Error _emit(uint32_t instId, const Operand_&amp; o0, const Operand_&amp; o1, const Operand_&amp; o2, const Operand_&amp; o3, const Operand_&amp; o4, const Operand_&amp; o5) override;</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="103"><span class="lineNum">     103 </span>            :   // [Finalize]</a>
+<a name="104"><span class="lineNum">     104 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :   ASMJIT_API virtual Error finalize() override;</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="109"><span class="lineNum">     109 </span>            :   // [VirtReg]</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="113"><span class="lineNum">     113 </span>            : #define ASMJIT_NEW_REG(OUT, PARAM, NAME_FMT)            \</a>
+<a name="114"><span class="lineNum">     114 </span>            :   va_list ap;                                           \</a>
+<a name="115"><span class="lineNum">     115 </span>            :   va_start(ap, NAME_FMT);                               \</a>
+<a name="116"><span class="lineNum">     116 </span>            :   _newReg(OUT, PARAM, NAME_FMT, ap);                    \</a>
+<a name="117"><span class="lineNum">     117 </span>            :   va_end(ap)</a>
+<a name="118"><span class="lineNum">     118 </span>            : #else</a>
+<a name="119"><span class="lineNum">     119 </span>            : #define ASMJIT_NEW_REG(OUT, PARAM, NAME_FMT)            \</a>
+<a name="120"><span class="lineNum">     120 </span>            :   ASMJIT_UNUSED(NAME_FMT);                              \</a>
+<a name="121"><span class="lineNum">     121 </span>            :   _newReg(OUT, PARAM, nullptr)</a>
+<a name="122"><span class="lineNum">     122 </span>            : #endif</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : #define ASMJIT_NEW_REG_USER(FUNC, REG)                  \</a>
+<a name="125"><span class="lineNum">     125 </span>            :   ASMJIT_INLINE REG FUNC(uint32_t typeId) {             \</a>
+<a name="126"><span class="lineNum">     126 </span>            :     REG reg(NoInit);                                    \</a>
+<a name="127"><span class="lineNum">     127 </span>            :     _newReg(reg, typeId, nullptr);                      \</a>
+<a name="128"><span class="lineNum">     128 </span>            :     return reg;                                         \</a>
+<a name="129"><span class="lineNum">     129 </span>            :   }                                                     \</a>
+<a name="130"><span class="lineNum">     130 </span>            :                                                         \</a>
+<a name="131"><span class="lineNum">     131 </span>            :   REG FUNC(uint32_t typeId, const char* nameFmt, ...) { \</a>
+<a name="132"><span class="lineNum">     132 </span>            :     REG reg(NoInit);                                    \</a>
+<a name="133"><span class="lineNum">     133 </span>            :     ASMJIT_NEW_REG(reg, typeId, nameFmt);               \</a>
+<a name="134"><span class="lineNum">     134 </span>            :     return reg;                                         \</a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : #define ASMJIT_NEW_REG_AUTO(FUNC, REG, TYPE_ID)         \</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ASMJIT_INLINE REG FUNC() {                            \</a>
+<a name="139"><span class="lineNum">     139 </span>            :     REG reg(NoInit);                                    \</a>
+<a name="140"><span class="lineNum">     140 </span>            :     _newReg(reg, TYPE_ID, nullptr);                     \</a>
+<a name="141"><span class="lineNum">     141 </span>            :     return reg;                                         \</a>
+<a name="142"><span class="lineNum">     142 </span>            :   }                                                     \</a>
+<a name="143"><span class="lineNum">     143 </span>            :                                                         \</a>
+<a name="144"><span class="lineNum">     144 </span>            :   REG FUNC(const char* nameFmt, ...) {                  \</a>
+<a name="145"><span class="lineNum">     145 </span>            :     REG reg(NoInit);                                    \</a>
+<a name="146"><span class="lineNum">     146 </span>            :     ASMJIT_NEW_REG(reg, TYPE_ID, nameFmt);              \</a>
+<a name="147"><span class="lineNum">     147 </span>            :     return reg;                                         \</a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   template&lt;typename RegT&gt;</a>
+<a name="151"><span class="lineNum">     151 </span>            :   ASMJIT_INLINE RegT newSimilarReg(const RegT&amp; ref) {</a>
+<a name="152"><span class="lineNum">     152 </span>            :     RegT reg(NoInit);</a>
+<a name="153"><span class="lineNum">     153 </span>            :     _newReg(reg, ref, nullptr);</a>
+<a name="154"><span class="lineNum">     154 </span>            :     return reg;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   template&lt;typename RegT&gt;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   RegT newSimilarReg(const RegT&amp; ref, const char* nameFmt, ...) {</a>
+<a name="159"><span class="lineNum">     159 </span>            :     RegT reg(NoInit);</a>
+<a name="160"><span class="lineNum">     160 </span>            :     ASMJIT_NEW_REG(reg, ref, nameFmt);</a>
+<a name="161"><span class="lineNum">     161 </span>            :     return reg;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   ASMJIT_NEW_REG_USER(newReg    , X86Reg )</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   ASMJIT_NEW_REG_USER(newGpReg  , X86Gp  )</a>
+<a name="166"><span class="lineNum">     166 </span>            :   ASMJIT_NEW_REG_USER(newMmReg  , X86Mm  )</a>
+<a name="167"><span class="lineNum">     167 </span>            :   ASMJIT_NEW_REG_USER(newKReg   , X86KReg)</a>
+<a name="168"><span class="lineNum">     168 </span>            :   ASMJIT_NEW_REG_USER(newXmmReg , X86Xmm )</a>
+<a name="169"><span class="lineNum">     169 </span>            :   ASMJIT_NEW_REG_USER(newYmmReg , X86Ymm )</a>
+<a name="170"><span class="lineNum">     170 </span>            :   ASMJIT_NEW_REG_USER(newZmmReg , X86Zmm )</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   ASMJIT_NEW_REG_AUTO(newI8     , X86Gp  , TypeId::kI8     )</a>
+<a name="173"><span class="lineNum">     173 </span>            :   ASMJIT_NEW_REG_AUTO(newU8     , X86Gp  , TypeId::kU8     )</a>
+<a name="174"><span class="lineNum">     174 </span>            :   ASMJIT_NEW_REG_AUTO(newI16    , X86Gp  , TypeId::kI16    )</a>
+<a name="175"><span class="lineNum">     175 </span>            :   ASMJIT_NEW_REG_AUTO(newU16    , X86Gp  , TypeId::kU16    )</a>
+<a name="176"><span class="lineNum">     176 </span>            :   ASMJIT_NEW_REG_AUTO(newI32    , X86Gp  , TypeId::kI32    )</a>
+<a name="177"><span class="lineNum">     177 </span>            :   ASMJIT_NEW_REG_AUTO(newU32    , X86Gp  , TypeId::kU32    )</a>
+<a name="178"><span class="lineNum">     178 </span>            :   ASMJIT_NEW_REG_AUTO(newI64    , X86Gp  , TypeId::kI64    )</a>
+<a name="179"><span class="lineNum">     179 </span>            :   ASMJIT_NEW_REG_AUTO(newU64    , X86Gp  , TypeId::kU64    )</a>
+<a name="180"><span class="lineNum">     180 </span>            :   ASMJIT_NEW_REG_AUTO(newInt8   , X86Gp  , TypeId::kI8     )</a>
+<a name="181"><span class="lineNum">     181 </span>            :   ASMJIT_NEW_REG_AUTO(newUInt8  , X86Gp  , TypeId::kU8     )</a>
+<a name="182"><span class="lineNum">     182 </span>            :   ASMJIT_NEW_REG_AUTO(newInt16  , X86Gp  , TypeId::kI16    )</a>
+<a name="183"><span class="lineNum">     183 </span>            :   ASMJIT_NEW_REG_AUTO(newUInt16 , X86Gp  , TypeId::kU16    )</a>
+<a name="184"><span class="lineNum">     184 </span>            :   ASMJIT_NEW_REG_AUTO(newInt32  , X86Gp  , TypeId::kI32    )</a>
+<a name="185"><span class="lineNum">     185 </span>            :   ASMJIT_NEW_REG_AUTO(newUInt32 , X86Gp  , TypeId::kU32    )</a>
+<a name="186"><span class="lineNum">     186 </span>            :   ASMJIT_NEW_REG_AUTO(newInt64  , X86Gp  , TypeId::kI64    )</a>
+<a name="187"><span class="lineNum">     187 </span>            :   ASMJIT_NEW_REG_AUTO(newUInt64 , X86Gp  , TypeId::kU64    )</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       7268 :   ASMJIT_NEW_REG_AUTO(newIntPtr , X86Gp  , TypeId::kIntPtr )</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   ASMJIT_NEW_REG_AUTO(newUIntPtr, X86Gp  , TypeId::kUIntPtr)</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   ASMJIT_NEW_REG_AUTO(newGpb    , X86Gp  , TypeId::kU8     )</a>
+<a name="192"><span class="lineNum">     192 </span>            :   ASMJIT_NEW_REG_AUTO(newGpw    , X86Gp  , TypeId::kU16    )</a>
+<a name="193"><span class="lineNum">     193 </span>            :   ASMJIT_NEW_REG_AUTO(newGpd    , X86Gp  , TypeId::kU32    )</a>
+<a name="194"><span class="lineNum">     194 </span>            :   ASMJIT_NEW_REG_AUTO(newGpq    , X86Gp  , TypeId::kU64    )</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   ASMJIT_NEW_REG_AUTO(newGpz    , X86Gp  , TypeId::kUIntPtr)</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   ASMJIT_NEW_REG_AUTO(newKb     , X86KReg, TypeId::kMask8  )</a>
+<a name="197"><span class="lineNum">     197 </span>            :   ASMJIT_NEW_REG_AUTO(newKw     , X86KReg, TypeId::kMask16 )</a>
+<a name="198"><span class="lineNum">     198 </span>            :   ASMJIT_NEW_REG_AUTO(newKd     , X86KReg, TypeId::kMask32 )</a>
+<a name="199"><span class="lineNum">     199 </span>            :   ASMJIT_NEW_REG_AUTO(newKq     , X86KReg, TypeId::kMask64 )</a>
+<a name="200"><span class="lineNum">     200 </span>            :   ASMJIT_NEW_REG_AUTO(newMm     , X86Mm  , TypeId::kMmx64  )</a>
+<a name="201"><span class="lineNum">     201 </span>            :   ASMJIT_NEW_REG_AUTO(newXmm    , X86Xmm , TypeId::kI32x4  )</a>
+<a name="202"><span class="lineNum">     202 </span>            :   ASMJIT_NEW_REG_AUTO(newXmmSs  , X86Xmm , TypeId::kF32x1  )</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      16520 :   ASMJIT_NEW_REG_AUTO(newXmmSd  , X86Xmm , TypeId::kF64x1  )</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   ASMJIT_NEW_REG_AUTO(newXmmPs  , X86Xmm , TypeId::kF32x4  )</a>
+<a name="205"><span class="lineNum">     205 </span>            :   ASMJIT_NEW_REG_AUTO(newXmmPd  , X86Xmm , TypeId::kF64x2  )</a>
+<a name="206"><span class="lineNum">     206 </span>            :   ASMJIT_NEW_REG_AUTO(newYmm    , X86Ymm , TypeId::kI32x8  )</a>
+<a name="207"><span class="lineNum">     207 </span>            :   ASMJIT_NEW_REG_AUTO(newYmmPs  , X86Ymm , TypeId::kF32x8  )</a>
+<a name="208"><span class="lineNum">     208 </span>            :   ASMJIT_NEW_REG_AUTO(newYmmPd  , X86Ymm , TypeId::kF64x4  )</a>
+<a name="209"><span class="lineNum">     209 </span>            :   ASMJIT_NEW_REG_AUTO(newZmm    , X86Zmm , TypeId::kI32x16 )</a>
+<a name="210"><span class="lineNum">     210 </span>            :   ASMJIT_NEW_REG_AUTO(newZmmPs  , X86Zmm , TypeId::kF32x16 )</a>
+<a name="211"><span class="lineNum">     211 </span>            :   ASMJIT_NEW_REG_AUTO(newZmmPd  , X86Zmm , TypeId::kF64x8  )</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : #undef ASMJIT_NEW_REG_AUTO</a>
+<a name="214"><span class="lineNum">     214 </span>            : #undef ASMJIT_NEW_REG_USER</a>
+<a name="215"><span class="lineNum">     215 </span>            : #undef ASMJIT_NEW_REG</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="218"><span class="lineNum">     218 </span>            :   // [Stack]</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   //! Create a new memory chunk allocated on the current function's stack.</a>
+<a name="222"><span class="lineNum">     222 </span>            :   ASMJIT_INLINE X86Mem newStack(uint32_t size, uint32_t alignment, const char* name = nullptr) {</a>
+<a name="223"><span class="lineNum">     223 </span>            :     X86Mem m(NoInit);</a>
+<a name="224"><span class="lineNum">     224 </span>            :     _newStack(m, size, alignment, name);</a>
+<a name="225"><span class="lineNum">     225 </span>            :     return m;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="229"><span class="lineNum">     229 </span>            :   // [Const]</a>
+<a name="230"><span class="lineNum">     230 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :   //! Put data to a constant-pool and get a memory reference to it.</a>
+<a name="233"><span class="lineNum">     233 </span>            :   ASMJIT_INLINE X86Mem newConst(uint32_t scope, const void* data, size_t size) {</a>
+<a name="234"><span class="lineNum">     234 </span>            :     X86Mem m(NoInit);</a>
+<a name="235"><span class="lineNum">     235 </span>            :     _newConst(m, scope, data, size);</a>
+<a name="236"><span class="lineNum">     236 </span>            :     return m;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            :   //! Put a BYTE `val` to a constant-pool.</a>
+<a name="240"><span class="lineNum">     240 </span>            :   ASMJIT_INLINE X86Mem newByteConst(uint32_t scope, uint8_t val) noexcept { return newConst(scope, &amp;val, 1); }</a>
+<a name="241"><span class="lineNum">     241 </span>            :   //! Put a WORD `val` to a constant-pool.</a>
+<a name="242"><span class="lineNum">     242 </span>            :   ASMJIT_INLINE X86Mem newWordConst(uint32_t scope, uint16_t val) noexcept { return newConst(scope, &amp;val, 2); }</a>
+<a name="243"><span class="lineNum">     243 </span>            :   //! Put a DWORD `val` to a constant-pool.</a>
+<a name="244"><span class="lineNum">     244 </span>            :   ASMJIT_INLINE X86Mem newDWordConst(uint32_t scope, uint32_t val) noexcept { return newConst(scope, &amp;val, 4); }</a>
+<a name="245"><span class="lineNum">     245 </span>            :   //! Put a QWORD `val` to a constant-pool.</a>
+<a name="246"><span class="lineNum">     246 </span>            :   ASMJIT_INLINE X86Mem newQWordConst(uint32_t scope, uint64_t val) noexcept { return newConst(scope, &amp;val, 8); }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   //! Put a WORD `val` to a constant-pool.</a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_INLINE X86Mem newInt16Const(uint32_t scope, int16_t val) noexcept { return newConst(scope, &amp;val, 2); }</a>
+<a name="250"><span class="lineNum">     250 </span>            :   //! Put a WORD `val` to a constant-pool.</a>
+<a name="251"><span class="lineNum">     251 </span>            :   ASMJIT_INLINE X86Mem newUInt16Const(uint32_t scope, uint16_t val) noexcept { return newConst(scope, &amp;val, 2); }</a>
+<a name="252"><span class="lineNum">     252 </span>            :   //! Put a DWORD `val` to a constant-pool.</a>
+<a name="253"><span class="lineNum">     253 </span>            :   ASMJIT_INLINE X86Mem newInt32Const(uint32_t scope, int32_t val) noexcept { return newConst(scope, &amp;val, 4); }</a>
+<a name="254"><span class="lineNum">     254 </span>            :   //! Put a DWORD `val` to a constant-pool.</a>
+<a name="255"><span class="lineNum">     255 </span>            :   ASMJIT_INLINE X86Mem newUInt32Const(uint32_t scope, uint32_t val) noexcept { return newConst(scope, &amp;val, 4); }</a>
+<a name="256"><span class="lineNum">     256 </span>            :   //! Put a QWORD `val` to a constant-pool.</a>
+<a name="257"><span class="lineNum">     257 </span>            :   ASMJIT_INLINE X86Mem newInt64Const(uint32_t scope, int64_t val) noexcept { return newConst(scope, &amp;val, 8); }</a>
+<a name="258"><span class="lineNum">     258 </span>            :   //! Put a QWORD `val` to a constant-pool.</a>
+<a name="259"><span class="lineNum">     259 </span>            :   ASMJIT_INLINE X86Mem newUInt64Const(uint32_t scope, uint64_t val) noexcept { return newConst(scope, &amp;val, 8); }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   //! Put a SP-FP `val` to a constant-pool.</a>
+<a name="262"><span class="lineNum">     262 </span>            :   ASMJIT_INLINE X86Mem newFloatConst(uint32_t scope, float val) noexcept { return newConst(scope, &amp;val, 4); }</a>
+<a name="263"><span class="lineNum">     263 </span>            :   //! Put a DP-FP `val` to a constant-pool.</a>
+<a name="264"><span class="lineNum">     264 </span>            :   ASMJIT_INLINE X86Mem newDoubleConst(uint32_t scope, double val) noexcept { return newConst(scope, &amp;val, 8); }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :   //! Put a MMX `val` to a constant-pool.</a>
+<a name="267"><span class="lineNum">     267 </span>            :   ASMJIT_INLINE X86Mem newMmConst(uint32_t scope, const Data64&amp; val) noexcept { return newConst(scope, &amp;val, 8); }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   //! Put a XMM `val` to a constant-pool.</a>
+<a name="269"><span class="lineNum">     269 </span>            :   ASMJIT_INLINE X86Mem newXmmConst(uint32_t scope, const Data128&amp; val) noexcept { return newConst(scope, &amp;val, 16); }</a>
+<a name="270"><span class="lineNum">     270 </span>            :   //! Put a YMM `val` to a constant-pool.</a>
+<a name="271"><span class="lineNum">     271 </span>            :   ASMJIT_INLINE X86Mem newYmmConst(uint32_t scope, const Data256&amp; val) noexcept { return newConst(scope, &amp;val, 32); }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="274"><span class="lineNum">     274 </span>            :   // [Instruction Options]</a>
+<a name="275"><span class="lineNum">     275 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :   //! Force the compiler to not follow the conditional or unconditional jump.</a>
+<a name="278"><span class="lineNum">     278 </span>            :   ASMJIT_INLINE X86Compiler&amp; unfollow() noexcept { _options |= kOptionUnfollow; return *this; }</a>
+<a name="279"><span class="lineNum">     279 </span>            :   //! Tell the compiler that the destination variable will be overwritten.</a>
+<a name="280"><span class="lineNum">     280 </span>            :   ASMJIT_INLINE X86Compiler&amp; overwrite() noexcept { _options |= kOptionOverwrite; return *this; }</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="283"><span class="lineNum">     283 </span>            :   // [Emit]</a>
+<a name="284"><span class="lineNum">     284 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :   //! Call a function.</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       1648 :   ASMJIT_INLINE CCFuncCall* call(const X86Gp&amp; dst, const FuncSignature&amp; sign) { return addCall(X86Inst::kIdCall, dst, sign); }</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   //! \overload</a>
+<a name="289"><span class="lineNum">     289 </span>            :   ASMJIT_INLINE CCFuncCall* call(const X86Mem&amp; dst, const FuncSignature&amp; sign) { return addCall(X86Inst::kIdCall, dst, sign); }</a>
+<a name="290"><span class="lineNum">     290 </span>            :   //! \overload</a>
+<a name="291"><span class="lineNum">     291 </span>            :   ASMJIT_INLINE CCFuncCall* call(const Label&amp; label, const FuncSignature&amp; sign) { return addCall(X86Inst::kIdCall, label, sign); }</a>
+<a name="292"><span class="lineNum">     292 </span>            :   //! \overload</a>
+<a name="293"><span class="lineNum">     293 </span>            :   ASMJIT_INLINE CCFuncCall* call(const Imm&amp; dst, const FuncSignature&amp; sign) { return addCall(X86Inst::kIdCall, dst, sign); }</a>
+<a name="294"><span class="lineNum">     294 </span>            :   //! \overload</a>
+<a name="295"><span class="lineNum">     295 </span>            :   ASMJIT_INLINE CCFuncCall* call(uint64_t dst, const FuncSignature&amp; sign) { return addCall(X86Inst::kIdCall, Imm(dst), sign); }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   //! Return.</a>
+<a name="298"><span class="lineNum">     298 </span>            :   ASMJIT_INLINE CCFuncRet* ret() { return addRet(Operand(), Operand()); }</a>
+<a name="299"><span class="lineNum">     299 </span>            :   //! \overload</a>
+<a name="300"><span class="lineNum">     300 </span>            :   ASMJIT_INLINE CCFuncRet* ret(const X86Gp&amp; o0) { return addRet(o0, Operand()); }</a>
+<a name="301"><span class="lineNum">     301 </span>            :   //! \overload</a>
+<a name="302"><span class="lineNum">     302 </span>            :   ASMJIT_INLINE CCFuncRet* ret(const X86Gp&amp; o0, const X86Gp&amp; o1) { return addRet(o0, o1); }</a>
+<a name="303"><span class="lineNum">     303 </span>            :   //! \overload</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       1948 :   ASMJIT_INLINE CCFuncRet* ret(const X86Xmm&amp; o0) { return addRet(o0, Operand()); }</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! \overload</a>
+<a name="306"><span class="lineNum">     306 </span>            :   ASMJIT_INLINE CCFuncRet* ret(const X86Xmm&amp; o0, const X86Xmm&amp; o1) { return addRet(o0, o1); }</a>
+<a name="307"><span class="lineNum">     307 </span>            : };</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : //! \}</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            : } // asmjit namespace</a>
+<a name="312"><span class="lineNum">     312 </span>            : } // namespace PLMD</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : // [Api-End]</a>
+<a name="315"><span class="lineNum">     315 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : // [Guard]</a>
+<a name="318"><span class="lineNum">     318 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="319"><span class="lineNum">     319 </span>            : #endif // _ASMJIT_X86_X86COMPILER_H</a>
+<a name="320"><span class="lineNum">     320 </span>            : #pragma GCC diagnostic pop</a>
+<a name="321"><span class="lineNum">     321 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="322"><span class="lineNum">     322 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86emitter.h.func-sort-c.html b/coverage-libs/asmjit/x86emitter.h.func-sort-c.html
new file mode 100644
index 0000000000..949ab2fb03
--- /dev/null
+++ b/coverage-libs/asmjit/x86emitter.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86emitter.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86emitter.h<span style="font-size: 80%;"> (<a href="x86emitter.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">63.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86emitter.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86emitter.h.func.html b/coverage-libs/asmjit/x86emitter.h.func.html
new file mode 100644
index 0000000000..5944aaa725
--- /dev/null
+++ b/coverage-libs/asmjit/x86emitter.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86emitter.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86emitter.h<span style="font-size: 80%;"> (<a href="x86emitter.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">63.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86emitter.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86emitter.h.gcov.html b/coverage-libs/asmjit/x86emitter.h.gcov.html
new file mode 100644
index 0000000000..7de707dd38
--- /dev/null
+++ b/coverage-libs/asmjit/x86emitter.h.gcov.html
@@ -0,0 +1,5225 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86emitter.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86emitter.h<span style="font-size: 80%;"> (source / <a href="x86emitter.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">63.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86emitter_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86emitter_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86EMITTER_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86EMITTER_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./codeemitter.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./x86inst.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : // [Api-Begin]</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace PLMD {</a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace asmjit {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="47"><span class="lineNum">      47 </span>            : //! \{</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : // [asmjit::X86EmitterExplicitT]</a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : #define ASMJIT_EMIT static_cast&lt;This*&gt;(this)-&gt;emit</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : #define ASMJIT_INST_0x(NAME, ID) \</a>
+<a name="56"><span class="lineNum">      56 </span>            :   ASMJIT_INLINE Error NAME() { return ASMJIT_EMIT(X86Inst::kId##ID); }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : #define ASMJIT_INST_1x(NAME, ID, T0) \</a>
+<a name="59"><span class="lineNum">      59 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID, o0); }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : #define ASMJIT_INST_1i(NAME, ID, T0) \</a>
+<a name="62"><span class="lineNum">      62 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID, o0); } \</a>
+<a name="63"><span class="lineNum">      63 </span>            :   ASMJIT_INLINE Error NAME(int o0) { return ASMJIT_EMIT(X86Inst::kId##ID, Utils::asInt(o0)); } \</a>
+<a name="64"><span class="lineNum">      64 </span>            :   ASMJIT_INLINE Error NAME(unsigned int o0) { return ASMJIT_EMIT(X86Inst::kId##ID, Utils::asInt(o0)); } \</a>
+<a name="65"><span class="lineNum">      65 </span>            :   ASMJIT_INLINE Error NAME(int64_t o0) { return ASMJIT_EMIT(X86Inst::kId##ID, Utils::asInt(o0)); } \</a>
+<a name="66"><span class="lineNum">      66 </span>            :   ASMJIT_INLINE Error NAME(uint64_t o0) { return ASMJIT_EMIT(X86Inst::kId##ID, Utils::asInt(o0)); }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : #define ASMJIT_INST_1c(NAME, ID, CONV, T0) \</a>
+<a name="69"><span class="lineNum">      69 </span>            :   ASMJIT_INLINE Error NAME(uint32_t cc, const T0&amp; o0) { return ASMJIT_EMIT(CONV(cc), o0); } \</a>
+<a name="70"><span class="lineNum">      70 </span>            :   ASMJIT_INLINE Error NAME##a(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##a, o0); } \</a>
+<a name="71"><span class="lineNum">      71 </span>            :   ASMJIT_INLINE Error NAME##ae(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##ae, o0); } \</a>
+<a name="72"><span class="lineNum">      72 </span>            :   ASMJIT_INLINE Error NAME##b(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##b, o0); } \</a>
+<a name="73"><span class="lineNum">      73 </span>            :   ASMJIT_INLINE Error NAME##be(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##be, o0); } \</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ASMJIT_INLINE Error NAME##c(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##c, o0); } \</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ASMJIT_INLINE Error NAME##e(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##e, o0); } \</a>
+<a name="76"><span class="lineNum">      76 </span>            :   ASMJIT_INLINE Error NAME##g(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##g, o0); } \</a>
+<a name="77"><span class="lineNum">      77 </span>            :   ASMJIT_INLINE Error NAME##ge(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##ge, o0); } \</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ASMJIT_INLINE Error NAME##l(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##l, o0); } \</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ASMJIT_INLINE Error NAME##le(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##le, o0); } \</a>
+<a name="80"><span class="lineNum">      80 </span>            :   ASMJIT_INLINE Error NAME##na(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##na, o0); } \</a>
+<a name="81"><span class="lineNum">      81 </span>            :   ASMJIT_INLINE Error NAME##nae(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nae, o0); } \</a>
+<a name="82"><span class="lineNum">      82 </span>            :   ASMJIT_INLINE Error NAME##nb(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nb, o0); } \</a>
+<a name="83"><span class="lineNum">      83 </span>            :   ASMJIT_INLINE Error NAME##nbe(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nbe, o0); } \</a>
+<a name="84"><span class="lineNum">      84 </span>            :   ASMJIT_INLINE Error NAME##nc(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nc, o0); } \</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ASMJIT_INLINE Error NAME##ne(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##ne, o0); } \</a>
+<a name="86"><span class="lineNum">      86 </span>            :   ASMJIT_INLINE Error NAME##ng(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##ng, o0); } \</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ASMJIT_INLINE Error NAME##nge(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nge, o0); } \</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ASMJIT_INLINE Error NAME##nl(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nl, o0); } \</a>
+<a name="89"><span class="lineNum">      89 </span>            :   ASMJIT_INLINE Error NAME##nle(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nle, o0); } \</a>
+<a name="90"><span class="lineNum">      90 </span>            :   ASMJIT_INLINE Error NAME##no(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##no, o0); } \</a>
+<a name="91"><span class="lineNum">      91 </span>            :   ASMJIT_INLINE Error NAME##np(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##np, o0); } \</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ASMJIT_INLINE Error NAME##ns(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##ns, o0); } \</a>
+<a name="93"><span class="lineNum">      93 </span>            :   ASMJIT_INLINE Error NAME##nz(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##nz, o0); } \</a>
+<a name="94"><span class="lineNum">      94 </span>            :   ASMJIT_INLINE Error NAME##o(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##o, o0); } \</a>
+<a name="95"><span class="lineNum">      95 </span>            :   ASMJIT_INLINE Error NAME##p(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##p, o0); } \</a>
+<a name="96"><span class="lineNum">      96 </span>            :   ASMJIT_INLINE Error NAME##pe(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##pe, o0); } \</a>
+<a name="97"><span class="lineNum">      97 </span>            :   ASMJIT_INLINE Error NAME##po(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##po, o0); } \</a>
+<a name="98"><span class="lineNum">      98 </span>            :   ASMJIT_INLINE Error NAME##s(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##s, o0); } \</a>
+<a name="99"><span class="lineNum">      99 </span>            :   ASMJIT_INLINE Error NAME##z(const T0&amp; o0) { return ASMJIT_EMIT(X86Inst::kId##ID##z, o0); }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : #define ASMJIT_INST_2x(NAME, ID, T0, T1) \</a>
+<a name="102"><span class="lineNum">     102 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1) { \</a>
+<a name="103"><span class="lineNum">     103 </span>            :     return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1); \</a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : #define ASMJIT_INST_2i(NAME, ID, T0, T1) \</a>
+<a name="107"><span class="lineNum">     107 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1); } \</a>
+<a name="108"><span class="lineNum">     108 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, int o1) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, Utils::asInt(o1)); } \</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, unsigned int o1) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, Utils::asInt(o1)); } \</a>
+<a name="110"><span class="lineNum">     110 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, int64_t o1) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, Utils::asInt(o1)); } \</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, uint64_t o1) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, Utils::asInt(o1)); }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : #define ASMJIT_INST_2c(NAME, ID, CONV, T0, T1) \</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_INLINE Error NAME(uint32_t cc, const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(CONV(cc), o0, o1); } \</a>
+<a name="115"><span class="lineNum">     115 </span>            :   ASMJIT_INLINE Error NAME##a(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##a, o0, o1); } \</a>
+<a name="116"><span class="lineNum">     116 </span>            :   ASMJIT_INLINE Error NAME##ae(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##ae, o0, o1); } \</a>
+<a name="117"><span class="lineNum">     117 </span>            :   ASMJIT_INLINE Error NAME##b(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##b, o0, o1); } \</a>
+<a name="118"><span class="lineNum">     118 </span>            :   ASMJIT_INLINE Error NAME##be(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##be, o0, o1); } \</a>
+<a name="119"><span class="lineNum">     119 </span>            :   ASMJIT_INLINE Error NAME##c(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##c, o0, o1); } \</a>
+<a name="120"><span class="lineNum">     120 </span>            :   ASMJIT_INLINE Error NAME##e(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##e, o0, o1); } \</a>
+<a name="121"><span class="lineNum">     121 </span>            :   ASMJIT_INLINE Error NAME##g(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##g, o0, o1); } \</a>
+<a name="122"><span class="lineNum">     122 </span>            :   ASMJIT_INLINE Error NAME##ge(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##ge, o0, o1); } \</a>
+<a name="123"><span class="lineNum">     123 </span>            :   ASMJIT_INLINE Error NAME##l(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##l, o0, o1); } \</a>
+<a name="124"><span class="lineNum">     124 </span>            :   ASMJIT_INLINE Error NAME##le(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##le, o0, o1); } \</a>
+<a name="125"><span class="lineNum">     125 </span>            :   ASMJIT_INLINE Error NAME##na(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##na, o0, o1); } \</a>
+<a name="126"><span class="lineNum">     126 </span>            :   ASMJIT_INLINE Error NAME##nae(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nae, o0, o1); } \</a>
+<a name="127"><span class="lineNum">     127 </span>            :   ASMJIT_INLINE Error NAME##nb(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nb, o0, o1); } \</a>
+<a name="128"><span class="lineNum">     128 </span>            :   ASMJIT_INLINE Error NAME##nbe(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nbe, o0, o1); } \</a>
+<a name="129"><span class="lineNum">     129 </span>            :   ASMJIT_INLINE Error NAME##nc(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nc, o0, o1); } \</a>
+<a name="130"><span class="lineNum">     130 </span>            :   ASMJIT_INLINE Error NAME##ne(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##ne, o0, o1); } \</a>
+<a name="131"><span class="lineNum">     131 </span>            :   ASMJIT_INLINE Error NAME##ng(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##ng, o0, o1); } \</a>
+<a name="132"><span class="lineNum">     132 </span>            :   ASMJIT_INLINE Error NAME##nge(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nge, o0, o1); } \</a>
+<a name="133"><span class="lineNum">     133 </span>            :   ASMJIT_INLINE Error NAME##nl(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nl, o0, o1); } \</a>
+<a name="134"><span class="lineNum">     134 </span>            :   ASMJIT_INLINE Error NAME##nle(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nle, o0, o1); } \</a>
+<a name="135"><span class="lineNum">     135 </span>            :   ASMJIT_INLINE Error NAME##no(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##no, o0, o1); } \</a>
+<a name="136"><span class="lineNum">     136 </span>            :   ASMJIT_INLINE Error NAME##np(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##np, o0, o1); } \</a>
+<a name="137"><span class="lineNum">     137 </span>            :   ASMJIT_INLINE Error NAME##ns(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##ns, o0, o1); } \</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ASMJIT_INLINE Error NAME##nz(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##nz, o0, o1); } \</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ASMJIT_INLINE Error NAME##o(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##o, o0, o1); } \</a>
+<a name="140"><span class="lineNum">     140 </span>            :   ASMJIT_INLINE Error NAME##p(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##p, o0, o1); } \</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ASMJIT_INLINE Error NAME##pe(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##pe, o0, o1); } \</a>
+<a name="142"><span class="lineNum">     142 </span>            :   ASMJIT_INLINE Error NAME##po(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##po, o0, o1); } \</a>
+<a name="143"><span class="lineNum">     143 </span>            :   ASMJIT_INLINE Error NAME##s(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##s, o0, o1); } \</a>
+<a name="144"><span class="lineNum">     144 </span>            :   ASMJIT_INLINE Error NAME##z(const T0&amp; o0, const T1&amp; o1) { return ASMJIT_EMIT(X86Inst::kId##ID##z, o0, o1); }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : #define ASMJIT_INST_3x(NAME, ID, T0, T1, T2) \</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2); }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : #define ASMJIT_INST_3i(NAME, ID, T0, T1, T2) \</a>
+<a name="150"><span class="lineNum">     150 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2); } \</a>
+<a name="151"><span class="lineNum">     151 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, int o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, Utils::asInt(o2)); } \</a>
+<a name="152"><span class="lineNum">     152 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, unsigned int o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, Utils::asInt(o2)); } \</a>
+<a name="153"><span class="lineNum">     153 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, int64_t o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, Utils::asInt(o2)); } \</a>
+<a name="154"><span class="lineNum">     154 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, uint64_t o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, Utils::asInt(o2)); }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : #define ASMJIT_INST_3ii(NAME, ID, T0, T1, T2) \</a>
+<a name="157"><span class="lineNum">     157 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2); } \</a>
+<a name="158"><span class="lineNum">     158 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, int o1, int o2) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, Imm(o1), Utils::asInt(o2)); }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : #define ASMJIT_INST_4x(NAME, ID, T0, T1, T2, T3) \</a>
+<a name="161"><span class="lineNum">     161 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3); }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : #define ASMJIT_INST_4i(NAME, ID, T0, T1, T2, T3) \</a>
+<a name="164"><span class="lineNum">     164 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3); } \</a>
+<a name="165"><span class="lineNum">     165 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, int o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, Utils::asInt(o3)); } \</a>
+<a name="166"><span class="lineNum">     166 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, unsigned int o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, Utils::asInt(o3)); } \</a>
+<a name="167"><span class="lineNum">     167 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, int64_t o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, Utils::asInt(o3)); } \</a>
+<a name="168"><span class="lineNum">     168 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, uint64_t o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, Utils::asInt(o3)); }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : #define ASMJIT_INST_4ii(NAME, ID, T0, T1, T2, T3) \</a>
+<a name="171"><span class="lineNum">     171 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3); } \</a>
+<a name="172"><span class="lineNum">     172 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, int o2, int o3) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, Imm(o2), Utils::asInt(o3)); }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : #define ASMJIT_INST_5x(NAME, ID, T0, T1, T2, T3, T4) \</a>
+<a name="175"><span class="lineNum">     175 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, const T4&amp; o4) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, o4); }</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : #define ASMJIT_INST_5i(NAME, ID, T0, T1, T2, T3, T4) \</a>
+<a name="178"><span class="lineNum">     178 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, const T4&amp; o4) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, o4); } \</a>
+<a name="179"><span class="lineNum">     179 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, int o4) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, Utils::asInt(o4)); } \</a>
+<a name="180"><span class="lineNum">     180 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, unsigned int o4) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, Utils::asInt(o4)); } \</a>
+<a name="181"><span class="lineNum">     181 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, int64_t o4) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, Utils::asInt(o4)); } \</a>
+<a name="182"><span class="lineNum">     182 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, uint64_t o4) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, Utils::asInt(o4)); }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : #define ASMJIT_INST_6x(NAME, ID, T0, T1, T2, T3, T4, T5) \</a>
+<a name="185"><span class="lineNum">     185 </span>            :   ASMJIT_INLINE Error NAME(const T0&amp; o0, const T1&amp; o1, const T2&amp; o2, const T3&amp; o3, const T4&amp; o4, const T5&amp; o5) { return ASMJIT_EMIT(X86Inst::kId##ID, o0, o1, o2, o3, o4, o5); }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : template&lt;typename This&gt;</a>
+<a name="188"><span class="lineNum">     188 </span>            : struct X86EmitterExplicitT {</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // These typedefs are used to describe implicit operands passed explicitly.</a>
+<a name="190"><span class="lineNum">     190 </span>            :   typedef X86Gp AL;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   typedef X86Gp AH;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   typedef X86Gp CL;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   typedef X86Gp AX;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   typedef X86Gp DX;</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   typedef X86Gp EAX;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   typedef X86Gp EBX;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   typedef X86Gp ECX;</a>
+<a name="199"><span class="lineNum">     199 </span>            :   typedef X86Gp EDX;</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :   typedef X86Gp RAX;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   typedef X86Gp RBX;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   typedef X86Gp RCX;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   typedef X86Gp RDX;</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   typedef X86Gp ZAX;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   typedef X86Gp ZBX;</a>
+<a name="208"><span class="lineNum">     208 </span>            :   typedef X86Gp ZCX;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   typedef X86Gp ZDX;</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   typedef X86Mem DS_ZAX; // ds:[zax]</a>
+<a name="212"><span class="lineNum">     212 </span>            :   typedef X86Mem DS_ZDI; // ds:[zdi]</a>
+<a name="213"><span class="lineNum">     213 </span>            :   typedef X86Mem ES_ZDI; // es:[zdi]</a>
+<a name="214"><span class="lineNum">     214 </span>            :   typedef X86Mem DS_ZSI; // ds:[zsi]</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :   typedef X86Xmm XMM0;</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // [Accessors]</a>
+<a name="220"><span class="lineNum">     220 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   //! Get GPD or GPQ register at index `id` depending on the current architecture.</a>
+<a name="223"><span class="lineNum">     223 </span>            :   ASMJIT_INLINE X86Gp gpz(uint32_t id) const noexcept {</a>
+<a name="224"><span class="lineNum">     224 </span>            :     return X86Gp(Init, static_cast&lt;const This*&gt;(this)-&gt;_nativeGpReg.getSignature(), id);</a>
+<a name="225"><span class="lineNum">     225 </span>            :   }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :   ASMJIT_INLINE const X86Gp&amp; gpzRef(uint32_t id) const noexcept {</a>
+<a name="228"><span class="lineNum">     228 </span>            :     ASMJIT_ASSERT(id &lt; 16);</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       5844 :     return static_cast&lt;const X86Gp&amp;&gt;(static_cast&lt;const This*&gt;(this)-&gt;_nativeGpArray[id]);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :   ASMJIT_INLINE const X86Gp&amp; zax() const noexcept { return gpzRef(X86Gp::kIdAx); }</a>
+<a name="233"><span class="lineNum">     233 </span>            :   ASMJIT_INLINE const X86Gp&amp; zcx() const noexcept { return gpzRef(X86Gp::kIdCx); }</a>
+<a name="234"><span class="lineNum">     234 </span>            :   ASMJIT_INLINE const X86Gp&amp; zdx() const noexcept { return gpzRef(X86Gp::kIdDx); }</a>
+<a name="235"><span class="lineNum">     235 </span>            :   ASMJIT_INLINE const X86Gp&amp; zbx() const noexcept { return gpzRef(X86Gp::kIdBx); }</a>
+<a name="236"><span class="lineNum">     236 </span>            :   ASMJIT_INLINE const X86Gp&amp; zsp() const noexcept { return gpzRef(X86Gp::kIdSp); }</a>
+<a name="237"><span class="lineNum">     237 </span>            :   ASMJIT_INLINE const X86Gp&amp; zbp() const noexcept { return gpzRef(X86Gp::kIdBp); }</a>
+<a name="238"><span class="lineNum">     238 </span>            :   ASMJIT_INLINE const X86Gp&amp; zsi() const noexcept { return gpzRef(X86Gp::kIdSi); }</a>
+<a name="239"><span class="lineNum">     239 </span>            :   ASMJIT_INLINE const X86Gp&amp; zdi() const noexcept { return gpzRef(X86Gp::kIdDi); }</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   //! Create a target dependent pointer of which base register's id is `baseId`.</a>
+<a name="242"><span class="lineNum">     242 </span>            :   ASMJIT_INLINE X86Mem ptr_base(uint32_t baseId, int32_t off = 0, uint32_t size = 0) const noexcept {</a>
+<a name="243"><span class="lineNum">     243 </span>            :     uint32_t baseType = static_cast&lt;const This*&gt;(this)-&gt;_nativeGpReg.getType();</a>
+<a name="244"><span class="lineNum">     244 </span>            :     uint32_t flags = 0;</a>
+<a name="245"><span class="lineNum">     245 </span>            :     return X86Mem(Init, baseType, baseId, 0, 0, off, size, flags);</a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   ASMJIT_INLINE X86Mem ptr_zax(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdAx, off, size); }</a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_INLINE X86Mem ptr_zcx(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdCx, off, size); }</a>
+<a name="250"><span class="lineNum">     250 </span>            :   ASMJIT_INLINE X86Mem ptr_zdx(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdDx, off, size); }</a>
+<a name="251"><span class="lineNum">     251 </span>            :   ASMJIT_INLINE X86Mem ptr_zbx(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdBx, off, size); }</a>
+<a name="252"><span class="lineNum">     252 </span>            :   ASMJIT_INLINE X86Mem ptr_zsp(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdSp, off, size); }</a>
+<a name="253"><span class="lineNum">     253 </span>            :   ASMJIT_INLINE X86Mem ptr_zbp(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdBp, off, size); }</a>
+<a name="254"><span class="lineNum">     254 </span>            :   ASMJIT_INLINE X86Mem ptr_zsi(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdSi, off, size); }</a>
+<a name="255"><span class="lineNum">     255 </span>            :   ASMJIT_INLINE X86Mem ptr_zdi(int32_t off = 0, uint32_t size = 0) const noexcept { return ptr_base(X86Gp::kIdDi, off, size); }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :   //! Create an `intptr_t` memory operand depending on the current architecture.</a>
+<a name="258"><span class="lineNum">     258 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const X86Gp&amp; base, int32_t offset = 0) const noexcept {</a>
+<a name="259"><span class="lineNum">     259 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="260"><span class="lineNum">     260 </span>            :     return X86Mem(base, offset, nativeGpSize);</a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            :   //! \overload</a>
+<a name="263"><span class="lineNum">     263 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const X86Gp&amp; base, const X86Gp&amp; index, uint32_t shift = 0, int32_t offset = 0) const noexcept {</a>
+<a name="264"><span class="lineNum">     264 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="265"><span class="lineNum">     265 </span>            :     return X86Mem(base, index, shift, offset, nativeGpSize);</a>
+<a name="266"><span class="lineNum">     266 </span>            :   }</a>
+<a name="267"><span class="lineNum">     267 </span>            :   //! \overload</a>
+<a name="268"><span class="lineNum">     268 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const X86Gp&amp; base, const X86Vec&amp; index, uint32_t shift = 0, int32_t offset = 0) const noexcept {</a>
+<a name="269"><span class="lineNum">     269 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="270"><span class="lineNum">     270 </span>            :     return X86Mem(base, index, shift, offset, nativeGpSize);</a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span>            :   //! \overload</a>
+<a name="273"><span class="lineNum">     273 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const Label&amp; base, int32_t offset = 0) const noexcept {</a>
+<a name="274"><span class="lineNum">     274 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="275"><span class="lineNum">     275 </span>            :     return X86Mem(base, offset, nativeGpSize);</a>
+<a name="276"><span class="lineNum">     276 </span>            :   }</a>
+<a name="277"><span class="lineNum">     277 </span>            :   //! \overload</a>
+<a name="278"><span class="lineNum">     278 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const Label&amp; base, const X86Gp&amp; index, uint32_t shift, int32_t offset = 0) const noexcept {</a>
+<a name="279"><span class="lineNum">     279 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="280"><span class="lineNum">     280 </span>            :     return X86Mem(base, index, shift, offset, nativeGpSize);</a>
+<a name="281"><span class="lineNum">     281 </span>            :   }</a>
+<a name="282"><span class="lineNum">     282 </span>            :   //! \overload</a>
+<a name="283"><span class="lineNum">     283 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const Label&amp; base, const X86Vec&amp; index, uint32_t shift, int32_t offset = 0) const noexcept {</a>
+<a name="284"><span class="lineNum">     284 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="285"><span class="lineNum">     285 </span>            :     return X86Mem(base, index, shift, offset, nativeGpSize);</a>
+<a name="286"><span class="lineNum">     286 </span>            :   }</a>
+<a name="287"><span class="lineNum">     287 </span>            :   //! \overload</a>
+<a name="288"><span class="lineNum">     288 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(const X86Rip&amp; rip, int32_t offset = 0) const noexcept {</a>
+<a name="289"><span class="lineNum">     289 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="290"><span class="lineNum">     290 </span>            :     return X86Mem(rip, offset, nativeGpSize);</a>
+<a name="291"><span class="lineNum">     291 </span>            :   }</a>
+<a name="292"><span class="lineNum">     292 </span>            :   //! \overload</a>
+<a name="293"><span class="lineNum">     293 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(uint64_t base) const noexcept {</a>
+<a name="294"><span class="lineNum">     294 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="295"><span class="lineNum">     295 </span>            :     return X86Mem(base, nativeGpSize);</a>
+<a name="296"><span class="lineNum">     296 </span>            :   }</a>
+<a name="297"><span class="lineNum">     297 </span>            :   //! \overload</a>
+<a name="298"><span class="lineNum">     298 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr(uint64_t base, const X86Gp&amp; index, uint32_t shift = 0) const noexcept {</a>
+<a name="299"><span class="lineNum">     299 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="300"><span class="lineNum">     300 </span>            :     return X86Mem(base, index, shift, nativeGpSize);</a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span>            :   //! \overload</a>
+<a name="303"><span class="lineNum">     303 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr_abs(uint64_t base) const noexcept {</a>
+<a name="304"><span class="lineNum">     304 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="305"><span class="lineNum">     305 </span>            :     return X86Mem(base, nativeGpSize, Mem::kSignatureMemAbs);</a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span>            :   //! \overload</a>
+<a name="308"><span class="lineNum">     308 </span>            :   ASMJIT_INLINE X86Mem intptr_ptr_abs(uint64_t base, const X86Gp&amp; index, uint32_t shift = 0) const noexcept {</a>
+<a name="309"><span class="lineNum">     309 </span>            :     uint32_t nativeGpSize = static_cast&lt;const This*&gt;(this)-&gt;getGpSize();</a>
+<a name="310"><span class="lineNum">     310 </span>            :     return X86Mem(base, index, shift, nativeGpSize, Mem::kSignatureMemAbs);</a>
+<a name="311"><span class="lineNum">     311 </span>            :   }</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="314"><span class="lineNum">     314 </span>            :   // [Embed]</a>
+<a name="315"><span class="lineNum">     315 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :   //! Add 8-bit integer data to the instruction stream.</a>
+<a name="318"><span class="lineNum">     318 </span>            :   ASMJIT_INLINE Error db(uint8_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, 1); }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   //! Add 16-bit integer data to the instruction stream.</a>
+<a name="320"><span class="lineNum">     320 </span>            :   ASMJIT_INLINE Error dw(uint16_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, 2); }</a>
+<a name="321"><span class="lineNum">     321 </span>            :   //! Add 32-bit integer data to the instruction stream.</a>
+<a name="322"><span class="lineNum">     322 </span>            :   ASMJIT_INLINE Error dd(uint32_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, 4); }</a>
+<a name="323"><span class="lineNum">     323 </span>            :   //! Add 64-bit integer data to the instruction stream.</a>
+<a name="324"><span class="lineNum">     324 </span>            :   ASMJIT_INLINE Error dq(uint64_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, 8); }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   //! Add 8-bit integer data to the instruction stream.</a>
+<a name="327"><span class="lineNum">     327 </span>            :   ASMJIT_INLINE Error dint8(int8_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(int8_t)); }</a>
+<a name="328"><span class="lineNum">     328 </span>            :   //! Add 8-bit integer data to the instruction stream.</a>
+<a name="329"><span class="lineNum">     329 </span>            :   ASMJIT_INLINE Error duint8(uint8_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(uint8_t)); }</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            :   //! Add 16-bit integer data to the instruction stream.</a>
+<a name="332"><span class="lineNum">     332 </span>            :   ASMJIT_INLINE Error dint16(int16_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(int16_t)); }</a>
+<a name="333"><span class="lineNum">     333 </span>            :   //! Add 16-bit integer data to the instruction stream.</a>
+<a name="334"><span class="lineNum">     334 </span>            :   ASMJIT_INLINE Error duint16(uint16_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(uint16_t)); }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :   //! Add 32-bit integer data to the instruction stream.</a>
+<a name="337"><span class="lineNum">     337 </span>            :   ASMJIT_INLINE Error dint32(int32_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(int32_t)); }</a>
+<a name="338"><span class="lineNum">     338 </span>            :   //! Add 32-bit integer data to the instruction stream.</a>
+<a name="339"><span class="lineNum">     339 </span>            :   ASMJIT_INLINE Error duint32(uint32_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(uint32_t)); }</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   //! Add 64-bit integer data to the instruction stream.</a>
+<a name="342"><span class="lineNum">     342 </span>            :   ASMJIT_INLINE Error dint64(int64_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(int64_t)); }</a>
+<a name="343"><span class="lineNum">     343 </span>            :   //! Add 64-bit integer data to the instruction stream.</a>
+<a name="344"><span class="lineNum">     344 </span>            :   ASMJIT_INLINE Error duint64(uint64_t x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(uint64_t)); }</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            :   //! Add float data to the instruction stream.</a>
+<a name="347"><span class="lineNum">     347 </span>            :   ASMJIT_INLINE Error dfloat(float x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(float)); }</a>
+<a name="348"><span class="lineNum">     348 </span>            :   //! Add double data to the instruction stream.</a>
+<a name="349"><span class="lineNum">     349 </span>            :   ASMJIT_INLINE Error ddouble(double x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(double)); }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :   //! Add MMX data to the instruction stream.</a>
+<a name="352"><span class="lineNum">     352 </span>            :   ASMJIT_INLINE Error dmm(const Data64&amp; x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(Data64)); }</a>
+<a name="353"><span class="lineNum">     353 </span>            :   //! Add XMM data to the instruction stream.</a>
+<a name="354"><span class="lineNum">     354 </span>            :   ASMJIT_INLINE Error dxmm(const Data128&amp; x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(Data128)); }</a>
+<a name="355"><span class="lineNum">     355 </span>            :   //! Add YMM data to the instruction stream.</a>
+<a name="356"><span class="lineNum">     356 </span>            :   ASMJIT_INLINE Error dymm(const Data256&amp; x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, sizeof(Data256)); }</a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            :   //! Add data in a given structure instance to the instruction stream.</a>
+<a name="359"><span class="lineNum">     359 </span>            :   template&lt;typename T&gt;</a>
+<a name="360"><span class="lineNum">     360 </span>            :   ASMJIT_INLINE Error dstruct(const T&amp; x) { return static_cast&lt;This*&gt;(this)-&gt;embed(&amp;x, static_cast&lt;uint32_t&gt;(sizeof(T))); }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="363"><span class="lineNum">     363 </span>            :   // [Options]</a>
+<a name="364"><span class="lineNum">     364 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            : protected:</a>
+<a name="367"><span class="lineNum">     367 </span>            :   ASMJIT_INLINE This&amp; _addOptions(uint32_t options) noexcept {</a>
+<a name="368"><span class="lineNum">     368 </span>            :     static_cast&lt;This*&gt;(this)-&gt;addOptions(options);</a>
+<a name="369"><span class="lineNum">     369 </span>            :     return *static_cast&lt;This*&gt;(this);</a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : public:</a>
+<a name="373"><span class="lineNum">     373 </span>            :   //! Force short form of jmp/jcc instruction.</a>
+<a name="374"><span class="lineNum">     374 </span>            :   ASMJIT_INLINE This&amp; short_() noexcept { return _addOptions(X86Inst::kOptionShortForm); }</a>
+<a name="375"><span class="lineNum">     375 </span>            :   //! Force long form of jmp/jcc instruction.</a>
+<a name="376"><span class="lineNum">     376 </span>            :   ASMJIT_INLINE This&amp; long_() noexcept { return _addOptions(X86Inst::kOptionLongForm); }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :   //! Condition is likely to be taken (has only benefit on P4).</a>
+<a name="379"><span class="lineNum">     379 </span>            :   ASMJIT_INLINE This&amp; taken() noexcept { return _addOptions(X86Inst::kOptionTaken); }</a>
+<a name="380"><span class="lineNum">     380 </span>            :   //! Condition is unlikely to be taken (has only benefit on P4).</a>
+<a name="381"><span class="lineNum">     381 </span>            :   ASMJIT_INLINE This&amp; notTaken() noexcept { return _addOptions(X86Inst::kOptionNotTaken); }</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            :   //! Use LOCK prefix.</a>
+<a name="384"><span class="lineNum">     384 </span>            :   ASMJIT_INLINE This&amp; lock() noexcept { return _addOptions(X86Inst::kOptionLock); }</a>
+<a name="385"><span class="lineNum">     385 </span>            :   //! Use XACQUIRE prefix.</a>
+<a name="386"><span class="lineNum">     386 </span>            :   ASMJIT_INLINE This&amp; xacquire() noexcept { return _addOptions(X86Inst::kOptionXAcquire); }</a>
+<a name="387"><span class="lineNum">     387 </span>            :   //! Use XRELEASE prefix.</a>
+<a name="388"><span class="lineNum">     388 </span>            :   ASMJIT_INLINE This&amp; xrelease() noexcept { return _addOptions(X86Inst::kOptionXRelease); }</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :   //! Use REP/REPZ prefix.</a>
+<a name="391"><span class="lineNum">     391 </span>            :   ASMJIT_INLINE This&amp; rep(const X86Gp&amp; zcx) noexcept {</a>
+<a name="392"><span class="lineNum">     392 </span>            :     static_cast&lt;This*&gt;(this)-&gt;_extraReg.init(zcx);</a>
+<a name="393"><span class="lineNum">     393 </span>            :     return _addOptions(X86Inst::kOptionRep);</a>
+<a name="394"><span class="lineNum">     394 </span>            :   }</a>
+<a name="395"><span class="lineNum">     395 </span>            :   //! Use REPNZ prefix.</a>
+<a name="396"><span class="lineNum">     396 </span>            :   ASMJIT_INLINE This&amp; repnz(const X86Gp&amp; zcx) noexcept {</a>
+<a name="397"><span class="lineNum">     397 </span>            :     static_cast&lt;This*&gt;(this)-&gt;_extraReg.init(zcx);</a>
+<a name="398"><span class="lineNum">     398 </span>            :     return _addOptions(X86Inst::kOptionRepnz);</a>
+<a name="399"><span class="lineNum">     399 </span>            :   }</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :   //! Use REP/REPZ prefix.</a>
+<a name="402"><span class="lineNum">     402 </span>            :   ASMJIT_INLINE This&amp; repe(const X86Gp&amp; zcx) noexcept { return rep(zcx); }</a>
+<a name="403"><span class="lineNum">     403 </span>            :   //! Use REP/REPZ prefix.</a>
+<a name="404"><span class="lineNum">     404 </span>            :   ASMJIT_INLINE This&amp; repz(const X86Gp&amp; zcx) noexcept { return rep(zcx); }</a>
+<a name="405"><span class="lineNum">     405 </span>            :   //! Use REPNZ prefix.</a>
+<a name="406"><span class="lineNum">     406 </span>            :   ASMJIT_INLINE This&amp; repne(const X86Gp&amp; zcx) noexcept { return repnz(zcx); }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :   //! Prefer MOD_MR encoding over MOD_RM (the default) when encoding instruction</a>
+<a name="409"><span class="lineNum">     409 </span>            :   //! that allows both. This option is only applicable to legacy instructions</a>
+<a name="410"><span class="lineNum">     410 </span>            :   //! where both operands are registers.</a>
+<a name="411"><span class="lineNum">     411 </span>            :   ASMJIT_INLINE This&amp; mod_mr() noexcept { return _addOptions(X86Inst::kOptionModMR); }</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span>            :   //! Force REX prefix to be emitted even when it's not needed (X64).</a>
+<a name="414"><span class="lineNum">     414 </span>            :   //!</a>
+<a name="415"><span class="lineNum">     415 </span>            :   //! NOTE: Don't use when using high 8-bit registers as REX prefix makes them</a>
+<a name="416"><span class="lineNum">     416 </span>            :   //! inaccessible and \ref X86Assembler refuses to encode such instructions.</a>
+<a name="417"><span class="lineNum">     417 </span>            :   ASMJIT_INLINE This&amp; rex() noexcept { return _addOptions(X86Inst::kOptionRex);}</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span>            :   //! Force REX.B prefix (X64) [It exists for special purposes only].</a>
+<a name="420"><span class="lineNum">     420 </span>            :   ASMJIT_INLINE This&amp; rex_b() noexcept { return _addOptions(X86Inst::kOptionOpCodeB); }</a>
+<a name="421"><span class="lineNum">     421 </span>            :   //! Force REX.X prefix (X64) [It exists for special purposes only].</a>
+<a name="422"><span class="lineNum">     422 </span>            :   ASMJIT_INLINE This&amp; rex_x() noexcept { return _addOptions(X86Inst::kOptionOpCodeX); }</a>
+<a name="423"><span class="lineNum">     423 </span>            :   //! Force REX.R prefix (X64) [It exists for special purposes only].</a>
+<a name="424"><span class="lineNum">     424 </span>            :   ASMJIT_INLINE This&amp; rex_r() noexcept { return _addOptions(X86Inst::kOptionOpCodeR); }</a>
+<a name="425"><span class="lineNum">     425 </span>            :   //! Force REX.W prefix (X64) [It exists for special purposes only].</a>
+<a name="426"><span class="lineNum">     426 </span>            :   ASMJIT_INLINE This&amp; rex_w() noexcept { return _addOptions(X86Inst::kOptionOpCodeW); }</a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span>            :   //! Force 3-byte VEX prefix (AVX+).</a>
+<a name="429"><span class="lineNum">     429 </span>            :   ASMJIT_INLINE This&amp; vex3() noexcept { return _addOptions(X86Inst::kOptionVex3); }</a>
+<a name="430"><span class="lineNum">     430 </span>            :   //! Force 4-byte EVEX prefix (AVX512+).</a>
+<a name="431"><span class="lineNum">     431 </span>            :   ASMJIT_INLINE This&amp; evex() noexcept { return _addOptions(X86Inst::kOptionEvex); }</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :   //! Use masking {k} (AVX512+).</a>
+<a name="434"><span class="lineNum">     434 </span>            :   ASMJIT_INLINE This&amp; k(const X86KReg&amp; kreg) noexcept {</a>
+<a name="435"><span class="lineNum">     435 </span>            :     static_cast&lt;This*&gt;(this)-&gt;_extraReg.init(kreg);</a>
+<a name="436"><span class="lineNum">     436 </span>            :     return *static_cast&lt;This*&gt;(this);</a>
+<a name="437"><span class="lineNum">     437 </span>            :   }</a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span>            :   //! Use zeroing instead of merging (AVX512+).</a>
+<a name="440"><span class="lineNum">     440 </span>            :   ASMJIT_INLINE This&amp; z() noexcept { return _addOptions(X86Inst::kOptionZMask); }</a>
+<a name="441"><span class="lineNum">     441 </span>            :   //! Broadcast one element to all other elements (AVX512+).</a>
+<a name="442"><span class="lineNum">     442 </span>            :   ASMJIT_INLINE This&amp; _1tox() noexcept { return _addOptions(X86Inst::kOption1ToX); }</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            :   //! Suppress all exceptions (AVX512+).</a>
+<a name="445"><span class="lineNum">     445 </span>            :   ASMJIT_INLINE This&amp; sae() noexcept { return _addOptions(X86Inst::kOptionSAE); }</a>
+<a name="446"><span class="lineNum">     446 </span>            :   //! Static rounding mode {rn} (round-to-nearest even) and {sae} (AVX512+).</a>
+<a name="447"><span class="lineNum">     447 </span>            :   ASMJIT_INLINE This&amp; rn_sae() noexcept { return _addOptions(X86Inst::kOptionER | X86Inst::kOptionRN_SAE); }</a>
+<a name="448"><span class="lineNum">     448 </span>            :   //! Static rounding mode {rd} (round-down, toward -inf) and {sae} (AVX512+).</a>
+<a name="449"><span class="lineNum">     449 </span>            :   ASMJIT_INLINE This&amp; rd_sae() noexcept { return _addOptions(X86Inst::kOptionER | X86Inst::kOptionRD_SAE); }</a>
+<a name="450"><span class="lineNum">     450 </span>            :   //! Static rounding mode {ru} (round-up, toward +inf) and {sae} (AVX512+).</a>
+<a name="451"><span class="lineNum">     451 </span>            :   ASMJIT_INLINE This&amp; ru_sae() noexcept { return _addOptions(X86Inst::kOptionER | X86Inst::kOptionRU_SAE); }</a>
+<a name="452"><span class="lineNum">     452 </span>            :   //! Static rounding mode {rz} (round-toward-zero, truncate) and {sae} (AVX512+).</a>
+<a name="453"><span class="lineNum">     453 </span>            :   ASMJIT_INLINE This&amp; rz_sae() noexcept { return _addOptions(X86Inst::kOptionER | X86Inst::kOptionRZ_SAE); }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="456"><span class="lineNum">     456 </span>            :   // [General Purpose and Non-SIMD Instructions]</a>
+<a name="457"><span class="lineNum">     457 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            :   ASMJIT_INST_2x(adc, Adc, X86Gp, X86Gp)                                      // ANY</a>
+<a name="460"><span class="lineNum">     460 </span>            :   ASMJIT_INST_2x(adc, Adc, X86Gp, X86Mem)                                     // ANY</a>
+<a name="461"><span class="lineNum">     461 </span>            :   ASMJIT_INST_2i(adc, Adc, X86Gp, Imm)                                        // ANY</a>
+<a name="462"><span class="lineNum">     462 </span>            :   ASMJIT_INST_2x(adc, Adc, X86Mem, X86Gp)                                     // ANY</a>
+<a name="463"><span class="lineNum">     463 </span>            :   ASMJIT_INST_2i(adc, Adc, X86Mem, Imm)                                       // ANY</a>
+<a name="464"><span class="lineNum">     464 </span>            :   ASMJIT_INST_2x(adcx, Adcx, X86Gp, X86Gp)                                    // ADX</a>
+<a name="465"><span class="lineNum">     465 </span>            :   ASMJIT_INST_2x(adcx, Adcx, X86Gp, X86Mem)                                   // ADX</a>
+<a name="466"><span class="lineNum">     466 </span>            :   ASMJIT_INST_2x(add, Add, X86Gp, X86Gp)                                      // ANY</a>
+<a name="467"><span class="lineNum">     467 </span>            :   ASMJIT_INST_2x(add, Add, X86Gp, X86Mem)                                     // ANY</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">        932 :   ASMJIT_INST_2i(add, Add, X86Gp, Imm)                                        // ANY</span></a>
+<a name="469"><span class="lineNum">     469 </span>            :   ASMJIT_INST_2x(add, Add, X86Mem, X86Gp)                                     // ANY</a>
+<a name="470"><span class="lineNum">     470 </span>            :   ASMJIT_INST_2i(add, Add, X86Mem, Imm)                                       // ANY</a>
+<a name="471"><span class="lineNum">     471 </span>            :   ASMJIT_INST_2x(adox, Adox, X86Gp, X86Gp)                                    // ADX</a>
+<a name="472"><span class="lineNum">     472 </span>            :   ASMJIT_INST_2x(adox, Adox, X86Gp, X86Mem)                                   // ADX</a>
+<a name="473"><span class="lineNum">     473 </span>            :   ASMJIT_INST_2x(and_, And, X86Gp, X86Gp)                                     // ANY</a>
+<a name="474"><span class="lineNum">     474 </span>            :   ASMJIT_INST_2x(and_, And, X86Gp, X86Mem)                                    // ANY</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :   ASMJIT_INST_2i(and_, And, X86Gp, Imm)                                       // ANY</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :   ASMJIT_INST_2x(and_, And, X86Mem, X86Gp)                                    // ANY</a>
+<a name="477"><span class="lineNum">     477 </span>            :   ASMJIT_INST_2i(and_, And, X86Mem, Imm)                                      // ANY</a>
+<a name="478"><span class="lineNum">     478 </span>            :   ASMJIT_INST_3x(andn, Andn, X86Gp, X86Gp, X86Gp)                             // BMI</a>
+<a name="479"><span class="lineNum">     479 </span>            :   ASMJIT_INST_3x(andn, Andn, X86Gp, X86Gp, X86Mem)                            // BMI</a>
+<a name="480"><span class="lineNum">     480 </span>            :   ASMJIT_INST_2x(arpl, Arpl, X86Gp, X86Gp)                                    // X86</a>
+<a name="481"><span class="lineNum">     481 </span>            :   ASMJIT_INST_2x(arpl, Arpl, X86Mem, X86Gp)                                   // X86</a>
+<a name="482"><span class="lineNum">     482 </span>            :   ASMJIT_INST_3x(bextr, Bextr, X86Gp, X86Gp, X86Gp)                           // BMI</a>
+<a name="483"><span class="lineNum">     483 </span>            :   ASMJIT_INST_3x(bextr, Bextr, X86Gp, X86Mem, X86Gp)                          // BMI</a>
+<a name="484"><span class="lineNum">     484 </span>            :   ASMJIT_INST_2x(blcfill, Blcfill, X86Gp, X86Gp)                              // TBM</a>
+<a name="485"><span class="lineNum">     485 </span>            :   ASMJIT_INST_2x(blcfill, Blcfill, X86Gp, X86Mem)                             // TBM</a>
+<a name="486"><span class="lineNum">     486 </span>            :   ASMJIT_INST_2x(blci, Blci, X86Gp, X86Gp)                                    // TBM</a>
+<a name="487"><span class="lineNum">     487 </span>            :   ASMJIT_INST_2x(blci, Blci, X86Gp, X86Mem)                                   // TBM</a>
+<a name="488"><span class="lineNum">     488 </span>            :   ASMJIT_INST_2x(blcic, Blcic, X86Gp, X86Gp)                                  // TBM</a>
+<a name="489"><span class="lineNum">     489 </span>            :   ASMJIT_INST_2x(blcic, Blcic, X86Gp, X86Mem)                                 // TBM</a>
+<a name="490"><span class="lineNum">     490 </span>            :   ASMJIT_INST_2x(blcmsk, Blcmsk, X86Gp, X86Gp)                                // TBM</a>
+<a name="491"><span class="lineNum">     491 </span>            :   ASMJIT_INST_2x(blcmsk, Blcmsk, X86Gp, X86Mem)                               // TBM</a>
+<a name="492"><span class="lineNum">     492 </span>            :   ASMJIT_INST_2x(blcs, Blcs, X86Gp, X86Gp)                                    // TBM</a>
+<a name="493"><span class="lineNum">     493 </span>            :   ASMJIT_INST_2x(blcs, Blcs, X86Gp, X86Mem)                                   // TBM</a>
+<a name="494"><span class="lineNum">     494 </span>            :   ASMJIT_INST_2x(blsfill, Blsfill, X86Gp, X86Gp)                              // TBM</a>
+<a name="495"><span class="lineNum">     495 </span>            :   ASMJIT_INST_2x(blsfill, Blsfill, X86Gp, X86Mem)                             // TBM</a>
+<a name="496"><span class="lineNum">     496 </span>            :   ASMJIT_INST_2x(blsi, Blsi, X86Gp, X86Gp)                                    // BMI</a>
+<a name="497"><span class="lineNum">     497 </span>            :   ASMJIT_INST_2x(blsi, Blsi, X86Gp, X86Mem)                                   // BMI</a>
+<a name="498"><span class="lineNum">     498 </span>            :   ASMJIT_INST_2x(blsic, Blsic, X86Gp, X86Gp)                                  // TBM</a>
+<a name="499"><span class="lineNum">     499 </span>            :   ASMJIT_INST_2x(blsic, Blsic, X86Gp, X86Mem)                                 // TBM</a>
+<a name="500"><span class="lineNum">     500 </span>            :   ASMJIT_INST_2x(blsmsk, Blsmsk, X86Gp, X86Gp)                                // BMI</a>
+<a name="501"><span class="lineNum">     501 </span>            :   ASMJIT_INST_2x(blsmsk, Blsmsk, X86Gp, X86Mem)                               // BMI</a>
+<a name="502"><span class="lineNum">     502 </span>            :   ASMJIT_INST_2x(blsr, Blsr, X86Gp, X86Gp)                                    // BMI</a>
+<a name="503"><span class="lineNum">     503 </span>            :   ASMJIT_INST_2x(blsr, Blsr, X86Gp, X86Mem)                                   // BMI</a>
+<a name="504"><span class="lineNum">     504 </span>            :   ASMJIT_INST_2x(bndcl, Bndcl, X86Bnd, X86Gp)                                 // MPX</a>
+<a name="505"><span class="lineNum">     505 </span>            :   ASMJIT_INST_2x(bndcl, Bndcl, X86Bnd, X86Mem)                                // MPX</a>
+<a name="506"><span class="lineNum">     506 </span>            :   ASMJIT_INST_2x(bndcn, Bndcn, X86Bnd, X86Gp)                                 // MPX</a>
+<a name="507"><span class="lineNum">     507 </span>            :   ASMJIT_INST_2x(bndcn, Bndcn, X86Bnd, X86Mem)                                // MPX</a>
+<a name="508"><span class="lineNum">     508 </span>            :   ASMJIT_INST_2x(bndcu, Bndcu, X86Bnd, X86Gp)                                 // MPX</a>
+<a name="509"><span class="lineNum">     509 </span>            :   ASMJIT_INST_2x(bndcu, Bndcu, X86Bnd, X86Mem)                                // MPX</a>
+<a name="510"><span class="lineNum">     510 </span>            :   ASMJIT_INST_2x(bndldx, Bndldx, X86Bnd, X86Mem)                              // MPX</a>
+<a name="511"><span class="lineNum">     511 </span>            :   ASMJIT_INST_2x(bndmk, Bndmk, X86Bnd, X86Mem)                                // MPX</a>
+<a name="512"><span class="lineNum">     512 </span>            :   ASMJIT_INST_2x(bndmov, Bndmov, X86Bnd, X86Bnd)                              // MPX</a>
+<a name="513"><span class="lineNum">     513 </span>            :   ASMJIT_INST_2x(bndmov, Bndmov, X86Bnd, X86Mem)                              // MPX</a>
+<a name="514"><span class="lineNum">     514 </span>            :   ASMJIT_INST_2x(bndmov, Bndmov, X86Mem, X86Bnd)                              // MPX</a>
+<a name="515"><span class="lineNum">     515 </span>            :   ASMJIT_INST_2x(bndstx, Bndstx, X86Mem, X86Bnd)                              // MPX</a>
+<a name="516"><span class="lineNum">     516 </span>            :   ASMJIT_INST_2x(bound, Bound, X86Gp, X86Mem)                                 // X86</a>
+<a name="517"><span class="lineNum">     517 </span>            :   ASMJIT_INST_2x(bsf, Bsf, X86Gp, X86Gp)                                      // ANY</a>
+<a name="518"><span class="lineNum">     518 </span>            :   ASMJIT_INST_2x(bsf, Bsf, X86Gp, X86Mem)                                     // ANY</a>
+<a name="519"><span class="lineNum">     519 </span>            :   ASMJIT_INST_2x(bsr, Bsr, X86Gp, X86Gp)                                      // ANY</a>
+<a name="520"><span class="lineNum">     520 </span>            :   ASMJIT_INST_2x(bsr, Bsr, X86Gp, X86Mem)                                     // ANY</a>
+<a name="521"><span class="lineNum">     521 </span>            :   ASMJIT_INST_1x(bswap, Bswap, X86Gp)                                         // ANY</a>
+<a name="522"><span class="lineNum">     522 </span>            :   ASMJIT_INST_2x(bt, Bt, X86Gp, X86Gp)                                        // ANY</a>
+<a name="523"><span class="lineNum">     523 </span>            :   ASMJIT_INST_2i(bt, Bt, X86Gp, Imm)                                          // ANY</a>
+<a name="524"><span class="lineNum">     524 </span>            :   ASMJIT_INST_2x(bt, Bt, X86Mem, X86Gp)                                       // ANY</a>
+<a name="525"><span class="lineNum">     525 </span>            :   ASMJIT_INST_2i(bt, Bt, X86Mem, Imm)                                         // ANY</a>
+<a name="526"><span class="lineNum">     526 </span>            :   ASMJIT_INST_2x(btc, Btc, X86Gp, X86Gp)                                      // ANY</a>
+<a name="527"><span class="lineNum">     527 </span>            :   ASMJIT_INST_2i(btc, Btc, X86Gp, Imm)                                        // ANY</a>
+<a name="528"><span class="lineNum">     528 </span>            :   ASMJIT_INST_2x(btc, Btc, X86Mem, X86Gp)                                     // ANY</a>
+<a name="529"><span class="lineNum">     529 </span>            :   ASMJIT_INST_2i(btc, Btc, X86Mem, Imm)                                       // ANY</a>
+<a name="530"><span class="lineNum">     530 </span>            :   ASMJIT_INST_2x(btr, Btr, X86Gp, X86Gp)                                      // ANY</a>
+<a name="531"><span class="lineNum">     531 </span>            :   ASMJIT_INST_2i(btr, Btr, X86Gp, Imm)                                        // ANY</a>
+<a name="532"><span class="lineNum">     532 </span>            :   ASMJIT_INST_2x(btr, Btr, X86Mem, X86Gp)                                     // ANY</a>
+<a name="533"><span class="lineNum">     533 </span>            :   ASMJIT_INST_2i(btr, Btr, X86Mem, Imm)                                       // ANY</a>
+<a name="534"><span class="lineNum">     534 </span>            :   ASMJIT_INST_2x(bts, Bts, X86Gp, X86Gp)                                      // ANY</a>
+<a name="535"><span class="lineNum">     535 </span>            :   ASMJIT_INST_2i(bts, Bts, X86Gp, Imm)                                        // ANY</a>
+<a name="536"><span class="lineNum">     536 </span>            :   ASMJIT_INST_2x(bts, Bts, X86Mem, X86Gp)                                     // ANY</a>
+<a name="537"><span class="lineNum">     537 </span>            :   ASMJIT_INST_2i(bts, Bts, X86Mem, Imm)                                       // ANY</a>
+<a name="538"><span class="lineNum">     538 </span>            :   ASMJIT_INST_3x(bzhi, Bzhi, X86Gp, X86Gp, X86Gp)                             // BMI2</a>
+<a name="539"><span class="lineNum">     539 </span>            :   ASMJIT_INST_3x(bzhi, Bzhi, X86Gp, X86Mem, X86Gp)                            // BMI2</a>
+<a name="540"><span class="lineNum">     540 </span>            :   ASMJIT_INST_1x(cbw, Cbw, AX)                                                // ANY       [EXPLICIT] AX      &lt;- Sign Extend AL</a>
+<a name="541"><span class="lineNum">     541 </span>            :   ASMJIT_INST_2x(cdq, Cdq, EDX, EAX)                                          // ANY       [EXPLICIT] EDX:EAX &lt;- Sign Extend EAX</a>
+<a name="542"><span class="lineNum">     542 </span>            :   ASMJIT_INST_1x(cdqe, Cdqe, EAX)                                             // X64       [EXPLICIT] RAX     &lt;- Sign Extend EAX</a>
+<a name="543"><span class="lineNum">     543 </span>            :   ASMJIT_INST_2x(cqo, Cqo, RDX, RAX)                                          // X64       [EXPLICIT] RDX:RAX &lt;- Sign Extend RAX</a>
+<a name="544"><span class="lineNum">     544 </span>            :   ASMJIT_INST_2x(cwd, Cwd, DX, AX)                                            // ANY       [EXPLICIT] DX:AX   &lt;- Sign Extend AX</a>
+<a name="545"><span class="lineNum">     545 </span>            :   ASMJIT_INST_1x(cwde, Cwde, EAX)                                             // ANY       [EXPLICIT] EAX     &lt;- Sign Extend AX</a>
+<a name="546"><span class="lineNum">     546 </span>            :   ASMJIT_INST_1x(call, Call, X86Gp)                                           // ANY</a>
+<a name="547"><span class="lineNum">     547 </span>            :   ASMJIT_INST_1x(call, Call, X86Mem)                                          // ANY</a>
+<a name="548"><span class="lineNum">     548 </span>            :   ASMJIT_INST_1x(call, Call, Label)                                           // ANY</a>
+<a name="549"><span class="lineNum">     549 </span>            :   ASMJIT_INST_1i(call, Call, Imm)                                             // ANY</a>
+<a name="550"><span class="lineNum">     550 </span>            :   ASMJIT_INST_0x(clac, Clac)                                                  // SMAP</a>
+<a name="551"><span class="lineNum">     551 </span>            :   ASMJIT_INST_0x(clc, Clc)                                                    // ANY</a>
+<a name="552"><span class="lineNum">     552 </span>            :   ASMJIT_INST_0x(cld, Cld)                                                    // ANY</a>
+<a name="553"><span class="lineNum">     553 </span>            :   ASMJIT_INST_1x(clflush, Clflush, X86Mem)                                    // CLFLUSH</a>
+<a name="554"><span class="lineNum">     554 </span>            :   ASMJIT_INST_1x(clflushopt, Clflushopt, X86Mem)                              // CLFLUSH_OPT</a>
+<a name="555"><span class="lineNum">     555 </span>            :   ASMJIT_INST_0x(cli, Cli)                                                    // ANY</a>
+<a name="556"><span class="lineNum">     556 </span>            :   ASMJIT_INST_0x(clts, Clts)                                                  // ANY</a>
+<a name="557"><span class="lineNum">     557 </span>            :   ASMJIT_INST_1x(clwb, Clwb, X86Mem)                                          // CLWB</a>
+<a name="558"><span class="lineNum">     558 </span>            :   ASMJIT_INST_1x(clzero, Clzero, DS_ZAX)                                      // CLZERO    [EXPLICIT]</a>
+<a name="559"><span class="lineNum">     559 </span>            :   ASMJIT_INST_0x(cmc, Cmc)                                                    // ANY</a>
+<a name="560"><span class="lineNum">     560 </span>            :   ASMJIT_INST_2c(cmov, Cmov, X86Inst::condToCmovcc, X86Gp, X86Gp)             // CMOV</a>
+<a name="561"><span class="lineNum">     561 </span>            :   ASMJIT_INST_2c(cmov, Cmov, X86Inst::condToCmovcc, X86Gp, X86Mem)            // CMOV</a>
+<a name="562"><span class="lineNum">     562 </span>            :   ASMJIT_INST_2x(cmp, Cmp, X86Gp, X86Gp)                                      // ANY</a>
+<a name="563"><span class="lineNum">     563 </span>            :   ASMJIT_INST_2x(cmp, Cmp, X86Gp, X86Mem)                                     // ANY</a>
+<a name="564"><span class="lineNum">     564 </span>            :   ASMJIT_INST_2i(cmp, Cmp, X86Gp, Imm)                                        // ANY</a>
+<a name="565"><span class="lineNum">     565 </span>            :   ASMJIT_INST_2x(cmp, Cmp, X86Mem, X86Gp)                                     // ANY</a>
+<a name="566"><span class="lineNum">     566 </span>            :   ASMJIT_INST_2i(cmp, Cmp, X86Mem, Imm)                                       // ANY</a>
+<a name="567"><span class="lineNum">     567 </span>            :   ASMJIT_INST_2x(cmps, Cmps, DS_ZSI, ES_ZDI)                                  // ANY       [EXPLICIT]</a>
+<a name="568"><span class="lineNum">     568 </span>            :   ASMJIT_INST_3x(cmpxchg, Cmpxchg, X86Gp, X86Gp, ZAX)                         // I486      [EXPLICIT]</a>
+<a name="569"><span class="lineNum">     569 </span>            :   ASMJIT_INST_3x(cmpxchg, Cmpxchg, X86Mem, X86Gp, ZAX)                        // I486      [EXPLICIT]</a>
+<a name="570"><span class="lineNum">     570 </span>            :   ASMJIT_INST_5x(cmpxchg16b, Cmpxchg16b, X86Mem, RDX, RAX, RCX, RBX);         // CMPXCHG16B[EXPLICIT] m == EDX:EAX ? m &lt;- ECX:EBX</a>
+<a name="571"><span class="lineNum">     571 </span>            :   ASMJIT_INST_5x(cmpxchg8b, Cmpxchg8b, X86Mem, EDX, EAX, ECX, EBX);           // CMPXCHG8B [EXPLICIT] m == RDX:RAX ? m &lt;- RCX:RBX</a>
+<a name="572"><span class="lineNum">     572 </span>            :   ASMJIT_INST_4x(cpuid, Cpuid, EAX, EBX, ECX, EDX)                            // I486      [EXPLICIT] EAX:EBX:ECX:EDX  &lt;- CPUID[EAX:ECX]</a>
+<a name="573"><span class="lineNum">     573 </span>            :   ASMJIT_INST_2x(crc32, Crc32, X86Gp, X86Gp)                                  // SSE4_2</a>
+<a name="574"><span class="lineNum">     574 </span>            :   ASMJIT_INST_2x(crc32, Crc32, X86Gp, X86Mem)                                 // SSE4_2</a>
+<a name="575"><span class="lineNum">     575 </span>            :   ASMJIT_INST_1x(daa, Daa, X86Gp)                                             // X86       [EXPLICIT]</a>
+<a name="576"><span class="lineNum">     576 </span>            :   ASMJIT_INST_1x(das, Das, X86Gp)                                             // X86       [EXPLICIT]</a>
+<a name="577"><span class="lineNum">     577 </span>            :   ASMJIT_INST_1x(dec, Dec, X86Gp)                                             // ANY</a>
+<a name="578"><span class="lineNum">     578 </span>            :   ASMJIT_INST_1x(dec, Dec, X86Mem)                                            // ANY</a>
+<a name="579"><span class="lineNum">     579 </span>            :   ASMJIT_INST_2x(div, Div, X86Gp, X86Gp)                                      // ANY       [EXPLICIT]  AH[Rem]: AL[Quot] &lt;- AX / r8</a>
+<a name="580"><span class="lineNum">     580 </span>            :   ASMJIT_INST_2x(div, Div, X86Gp, X86Mem)                                     // ANY       [EXPLICIT]  AH[Rem]: AL[Quot] &lt;- AX / m8</a>
+<a name="581"><span class="lineNum">     581 </span>            :   ASMJIT_INST_3x(div, Div, X86Gp, X86Gp, X86Gp)                               // ANY       [EXPLICIT] xDX[Rem]:xAX[Quot] &lt;- xDX:xAX / r16|r32|r64</a>
+<a name="582"><span class="lineNum">     582 </span>            :   ASMJIT_INST_3x(div, Div, X86Gp, X86Gp, X86Mem)                              // ANY       [EXPLICIT] xDX[Rem]:xAX[Quot] &lt;- xDX:xAX / m16|m32|m64</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :   ASMJIT_INST_0x(emms, Emms)                                                  // MMX</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :   ASMJIT_INST_2x(enter, Enter, Imm, Imm)                                      // ANY</a>
+<a name="585"><span class="lineNum">     585 </span>            :   ASMJIT_INST_1x(fxrstor, Fxrstor, X86Mem)                                    // FXSR</a>
+<a name="586"><span class="lineNum">     586 </span>            :   ASMJIT_INST_1x(fxrstor64, Fxrstor64, X86Mem)                                // FXSR</a>
+<a name="587"><span class="lineNum">     587 </span>            :   ASMJIT_INST_1x(fxsave, Fxsave, X86Mem)                                      // FXSR</a>
+<a name="588"><span class="lineNum">     588 </span>            :   ASMJIT_INST_1x(fxsave64, Fxsave64, X86Mem)                                  // FXSR</a>
+<a name="589"><span class="lineNum">     589 </span>            :   ASMJIT_INST_0x(hlt, Hlt)                                                    // ANY</a>
+<a name="590"><span class="lineNum">     590 </span>            :   ASMJIT_INST_2x(idiv, Idiv, X86Gp, X86Gp)                                    // ANY       [EXPLICIT]  AH[Rem]: AL[Quot] &lt;- AX / r8</a>
+<a name="591"><span class="lineNum">     591 </span>            :   ASMJIT_INST_2x(idiv, Idiv, X86Gp, X86Mem)                                   // ANY       [EXPLICIT]  AH[Rem]: AL[Quot] &lt;- AX / m8</a>
+<a name="592"><span class="lineNum">     592 </span>            :   ASMJIT_INST_3x(idiv, Idiv, X86Gp, X86Gp, X86Gp)                             // ANY       [EXPLICIT] xDX[Rem]:xAX[Quot] &lt;- xDX:xAX / r16|r32|r64</a>
+<a name="593"><span class="lineNum">     593 </span>            :   ASMJIT_INST_3x(idiv, Idiv, X86Gp, X86Gp, X86Mem)                            // ANY       [EXPLICIT] xDX[Rem]:xAX[Quot] &lt;- xDX:xAX / m16|m32|m64</a>
+<a name="594"><span class="lineNum">     594 </span>            :   ASMJIT_INST_2x(imul, Imul, X86Gp, X86Gp)                                    // ANY       [EXPLICIT] AX &lt;- AL * r8 | ra &lt;- ra * rb</a>
+<a name="595"><span class="lineNum">     595 </span>            :   ASMJIT_INST_2x(imul, Imul, X86Gp, X86Mem)                                   // ANY       [EXPLICIT] AX &lt;- AL * m8 | ra &lt;- ra * m16|m32|m64</a>
+<a name="596"><span class="lineNum">     596 </span>            :   ASMJIT_INST_2i(imul, Imul, X86Gp, Imm)                                      // ANY</a>
+<a name="597"><span class="lineNum">     597 </span>            :   ASMJIT_INST_3i(imul, Imul, X86Gp, X86Gp, Imm)                               // ANY</a>
+<a name="598"><span class="lineNum">     598 </span>            :   ASMJIT_INST_3i(imul, Imul, X86Gp, X86Mem, Imm)                              // ANY</a>
+<a name="599"><span class="lineNum">     599 </span>            :   ASMJIT_INST_3x(imul, Imul, X86Gp, X86Gp, X86Gp)                             // ANY       [EXPLICIT] xDX:xAX &lt;- xAX * r16|r32|r64</a>
+<a name="600"><span class="lineNum">     600 </span>            :   ASMJIT_INST_3x(imul, Imul, X86Gp, X86Gp, X86Mem)                            // ANY       [EXPLICIT] xDX:xAX &lt;- xAX * m16|m32|m64</a>
+<a name="601"><span class="lineNum">     601 </span>            :   ASMJIT_INST_2i(in, In, ZAX, Imm)                                            // ANY</a>
+<a name="602"><span class="lineNum">     602 </span>            :   ASMJIT_INST_2x(in, In, ZAX, DX)                                             // ANY</a>
+<a name="603"><span class="lineNum">     603 </span>            :   ASMJIT_INST_1x(inc, Inc, X86Gp)                                             // ANY</a>
+<a name="604"><span class="lineNum">     604 </span>            :   ASMJIT_INST_1x(inc, Inc, X86Mem)                                            // ANY</a>
+<a name="605"><span class="lineNum">     605 </span>            :   ASMJIT_INST_2x(ins, Ins, ES_ZDI, DX)                                        // ANY</a>
+<a name="606"><span class="lineNum">     606 </span>            :   ASMJIT_INST_1i(int_, Int, Imm)                                              // ANY</a>
+<a name="607"><span class="lineNum">     607 </span>            :   ASMJIT_INST_0x(int3, Int3)                                                  // ANY</a>
+<a name="608"><span class="lineNum">     608 </span>            :   ASMJIT_INST_0x(into, Into)                                                  // ANY</a>
+<a name="609"><span class="lineNum">     609 </span>            :   ASMJIT_INST_0x(invd, Invd)                                                  // ANY</a>
+<a name="610"><span class="lineNum">     610 </span>            :   ASMJIT_INST_1x(invlpg, Invlpg, X86Mem)                                      // ANY</a>
+<a name="611"><span class="lineNum">     611 </span>            :   ASMJIT_INST_2x(invpcid, Invpcid, X86Gp, X86Mem)                             // ANY</a>
+<a name="612"><span class="lineNum">     612 </span>            :   ASMJIT_INST_1c(j, J, X86Inst::condToJcc, Label)                             // ANY</a>
+<a name="613"><span class="lineNum">     613 </span>            :   ASMJIT_INST_1c(j, J, X86Inst::condToJcc, Imm)                               // ANY</a>
+<a name="614"><span class="lineNum">     614 </span>            :   ASMJIT_INST_1c(j, J, X86Inst::condToJcc, uint64_t)                          // ANY</a>
+<a name="615"><span class="lineNum">     615 </span>            :   ASMJIT_INST_2x(jecxz, Jecxz, X86Gp, Label)                                  // ANY       [EXPLICIT] Short jump if CX/ECX/RCX is zero.</a>
+<a name="616"><span class="lineNum">     616 </span>            :   ASMJIT_INST_2x(jecxz, Jecxz, X86Gp, Imm)                                    // ANY       [EXPLICIT] Short jump if CX/ECX/RCX is zero.</a>
+<a name="617"><span class="lineNum">     617 </span>            :   ASMJIT_INST_2x(jecxz, Jecxz, X86Gp, uint64_t)                               // ANY       [EXPLICIT] Short jump if CX/ECX/RCX is zero.</a>
+<a name="618"><span class="lineNum">     618 </span>            :   ASMJIT_INST_1x(jmp, Jmp, X86Gp)                                             // ANY</a>
+<a name="619"><span class="lineNum">     619 </span>            :   ASMJIT_INST_1x(jmp, Jmp, X86Mem)                                            // ANY</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :   ASMJIT_INST_1x(jmp, Jmp, Label)                                             // ANY</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :   ASMJIT_INST_1x(jmp, Jmp, Imm)                                               // ANY</a>
+<a name="622"><span class="lineNum">     622 </span>            :   ASMJIT_INST_1x(jmp, Jmp, uint64_t)                                          // ANY</a>
+<a name="623"><span class="lineNum">     623 </span>            :   ASMJIT_INST_1x(lahf, Lahf, AH)                                              // LAHFSAHF  [EXPLICIT] AH &lt;- EFL</a>
+<a name="624"><span class="lineNum">     624 </span>            :   ASMJIT_INST_2x(lar, Lar, X86Gp, X86Gp)                                      // ANY</a>
+<a name="625"><span class="lineNum">     625 </span>            :   ASMJIT_INST_2x(lar, Lar, X86Gp, X86Mem)                                     // ANY</a>
+<a name="626"><span class="lineNum">     626 </span>            :   ASMJIT_INST_1x(ldmxcsr, Ldmxcsr, X86Mem)                                    // SSE</a>
+<a name="627"><span class="lineNum">     627 </span>            :   ASMJIT_INST_2x(lds, Lds, X86Gp, X86Mem)                                     // X86</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :   ASMJIT_INST_2x(lea, Lea, X86Gp, X86Mem)                                     // ANY</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :   ASMJIT_INST_0x(leave, Leave)                                                // ANY</a>
+<a name="630"><span class="lineNum">     630 </span>            :   ASMJIT_INST_2x(les, Les, X86Gp, X86Mem)                                     // X86</a>
+<a name="631"><span class="lineNum">     631 </span>            :   ASMJIT_INST_0x(lfence, Lfence)                                              // SSE2</a>
+<a name="632"><span class="lineNum">     632 </span>            :   ASMJIT_INST_2x(lfs, Lfs, X86Gp, X86Mem)                                     // ANY</a>
+<a name="633"><span class="lineNum">     633 </span>            :   ASMJIT_INST_1x(lgdt, Lgdt, X86Mem)                                          // ANY</a>
+<a name="634"><span class="lineNum">     634 </span>            :   ASMJIT_INST_2x(lgs, Lgs, X86Gp, X86Mem)                                     // ANY</a>
+<a name="635"><span class="lineNum">     635 </span>            :   ASMJIT_INST_1x(lidt, Lidt, X86Mem)                                          // ANY</a>
+<a name="636"><span class="lineNum">     636 </span>            :   ASMJIT_INST_1x(lldt, Lldt, X86Gp)                                           // ANY</a>
+<a name="637"><span class="lineNum">     637 </span>            :   ASMJIT_INST_1x(lldt, Lldt, X86Mem)                                          // ANY</a>
+<a name="638"><span class="lineNum">     638 </span>            :   ASMJIT_INST_1x(lmsw, Lmsw, X86Gp)                                           // ANY</a>
+<a name="639"><span class="lineNum">     639 </span>            :   ASMJIT_INST_1x(lmsw, Lmsw, X86Mem)                                          // ANY</a>
+<a name="640"><span class="lineNum">     640 </span>            :   ASMJIT_INST_2x(lods, Lods, ZAX, DS_ZSI)                                     // ANY       [EXPLICIT]</a>
+<a name="641"><span class="lineNum">     641 </span>            :   ASMJIT_INST_2x(loop, Loop, ZCX, Label)                                      // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0.</a>
+<a name="642"><span class="lineNum">     642 </span>            :   ASMJIT_INST_2x(loop, Loop, ZCX, Imm)                                        // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0.</a>
+<a name="643"><span class="lineNum">     643 </span>            :   ASMJIT_INST_2x(loop, Loop, ZCX, uint64_t)                                   // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0.</a>
+<a name="644"><span class="lineNum">     644 </span>            :   ASMJIT_INST_2x(loope, Loope, ZCX, Label)                                    // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 1.</a>
+<a name="645"><span class="lineNum">     645 </span>            :   ASMJIT_INST_2x(loope, Loope, ZCX, Imm)                                      // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 1.</a>
+<a name="646"><span class="lineNum">     646 </span>            :   ASMJIT_INST_2x(loope, Loope, ZCX, uint64_t)                                 // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 1.</a>
+<a name="647"><span class="lineNum">     647 </span>            :   ASMJIT_INST_2x(loopne, Loopne, ZCX, Label)                                  // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 0.</a>
+<a name="648"><span class="lineNum">     648 </span>            :   ASMJIT_INST_2x(loopne, Loopne, ZCX, Imm)                                    // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 0.</a>
+<a name="649"><span class="lineNum">     649 </span>            :   ASMJIT_INST_2x(loopne, Loopne, ZCX, uint64_t)                               // ANY       [EXPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 0.</a>
+<a name="650"><span class="lineNum">     650 </span>            :   ASMJIT_INST_2x(lsl, Lsl, X86Gp, X86Gp)                                      // ANY</a>
+<a name="651"><span class="lineNum">     651 </span>            :   ASMJIT_INST_2x(lsl, Lsl, X86Gp, X86Mem)                                     // ANY</a>
+<a name="652"><span class="lineNum">     652 </span>            :   ASMJIT_INST_2x(lss, Lss, X86Gp, X86Mem)                                     // ANY</a>
+<a name="653"><span class="lineNum">     653 </span>            :   ASMJIT_INST_1x(ltr, Ltr, X86Gp)                                             // ANY</a>
+<a name="654"><span class="lineNum">     654 </span>            :   ASMJIT_INST_1x(ltr, Ltr, X86Mem)                                            // ANY</a>
+<a name="655"><span class="lineNum">     655 </span>            :   ASMJIT_INST_2x(lzcnt, Lzcnt, X86Gp, X86Gp)                                  // LZCNT</a>
+<a name="656"><span class="lineNum">     656 </span>            :   ASMJIT_INST_2x(lzcnt, Lzcnt, X86Gp, X86Mem)                                 // LZCNT</a>
+<a name="657"><span class="lineNum">     657 </span>            :   ASMJIT_INST_0x(mfence, Mfence)                                              // SSE2</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 :   ASMJIT_INST_2x(mov, Mov, X86Gp, X86Gp)                                      // ANY</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineNoCov">          0 :   ASMJIT_INST_2x(mov, Mov, X86Gp, X86Mem)                                     // ANY</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">       7268 :   ASMJIT_INST_2i(mov, Mov, X86Gp, Imm)                                        // ANY</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :   ASMJIT_INST_2x(mov, Mov, X86Mem, X86Gp)                                     // ANY</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :   ASMJIT_INST_2i(mov, Mov, X86Mem, Imm)                                       // ANY</a>
+<a name="663"><span class="lineNum">     663 </span>            :   ASMJIT_INST_2x(mov, Mov, X86Gp, X86CReg)                                    // ANY</a>
+<a name="664"><span class="lineNum">     664 </span>            :   ASMJIT_INST_2x(mov, Mov, X86CReg, X86Gp)                                    // ANY</a>
+<a name="665"><span class="lineNum">     665 </span>            :   ASMJIT_INST_2x(mov, Mov, X86Gp, X86DReg)                                    // ANY</a>
+<a name="666"><span class="lineNum">     666 </span>            :   ASMJIT_INST_2x(mov, Mov, X86DReg, X86Gp)                                    // ANY</a>
+<a name="667"><span class="lineNum">     667 </span>            :   ASMJIT_INST_2x(mov, Mov, X86Gp, X86Seg)                                     // ANY</a>
+<a name="668"><span class="lineNum">     668 </span>            :   ASMJIT_INST_2x(mov, Mov, X86Mem, X86Seg)                                    // ANY</a>
+<a name="669"><span class="lineNum">     669 </span>            :   ASMJIT_INST_2x(mov, Mov, X86Seg, X86Gp)                                     // ANY</a>
+<a name="670"><span class="lineNum">     670 </span>            :   ASMJIT_INST_2x(mov, Mov, X86Seg, X86Mem)                                    // ANY</a>
+<a name="671"><span class="lineNum">     671 </span>            :   ASMJIT_INST_2x(movbe, Movbe, X86Gp, X86Mem)                                 // MOVBE</a>
+<a name="672"><span class="lineNum">     672 </span>            :   ASMJIT_INST_2x(movbe, Movbe, X86Mem, X86Gp)                                 // MOVBE</a>
+<a name="673"><span class="lineNum">     673 </span>            :   ASMJIT_INST_2x(movnti, Movnti, X86Mem, X86Gp)                               // SSE2</a>
+<a name="674"><span class="lineNum">     674 </span>            :   ASMJIT_INST_2x(movs, Movs, ES_ZDI, DS_ZSI)                                  // ANY       [EXPLICIT]</a>
+<a name="675"><span class="lineNum">     675 </span>            :   ASMJIT_INST_2x(movsx, Movsx, X86Gp, X86Gp)                                  // ANY</a>
+<a name="676"><span class="lineNum">     676 </span>            :   ASMJIT_INST_2x(movsx, Movsx, X86Gp, X86Mem)                                 // ANY</a>
+<a name="677"><span class="lineNum">     677 </span>            :   ASMJIT_INST_2x(movsxd, Movsxd, X86Gp, X86Gp)                                // X64</a>
+<a name="678"><span class="lineNum">     678 </span>            :   ASMJIT_INST_2x(movsxd, Movsxd, X86Gp, X86Mem)                               // X64</a>
+<a name="679"><span class="lineNum">     679 </span>            :   ASMJIT_INST_2x(movzx, Movzx, X86Gp, X86Gp)                                  // ANY</a>
+<a name="680"><span class="lineNum">     680 </span>            :   ASMJIT_INST_2x(movzx, Movzx, X86Gp, X86Mem)                                 // ANY</a>
+<a name="681"><span class="lineNum">     681 </span>            :   ASMJIT_INST_2x(mul, Mul, AX, X86Gp)                                         // ANY       [EXPLICIT] AX      &lt;-  AL * r8</a>
+<a name="682"><span class="lineNum">     682 </span>            :   ASMJIT_INST_2x(mul, Mul, AX, X86Mem)                                        // ANY       [EXPLICIT] AX      &lt;-  AL * m8</a>
+<a name="683"><span class="lineNum">     683 </span>            :   ASMJIT_INST_3x(mul, Mul, ZDX, ZAX, X86Gp)                                   // ANY       [EXPLICIT] xDX:xAX &lt;- xAX * r16|r32|r64</a>
+<a name="684"><span class="lineNum">     684 </span>            :   ASMJIT_INST_3x(mul, Mul, ZDX, ZAX, X86Mem)                                  // ANY       [EXPLICIT] xDX:xAX &lt;- xAX * m16|m32|m64</a>
+<a name="685"><span class="lineNum">     685 </span>            :   ASMJIT_INST_4x(mulx, Mulx, X86Gp, X86Gp, X86Gp, ZDX)                        // BMI2      [EXPLICIT]</a>
+<a name="686"><span class="lineNum">     686 </span>            :   ASMJIT_INST_4x(mulx, Mulx, X86Gp, X86Gp, X86Mem, ZDX)                       // BMI2      [EXPLICIT]</a>
+<a name="687"><span class="lineNum">     687 </span>            :   ASMJIT_INST_1x(neg, Neg, X86Gp)                                             // ANY</a>
+<a name="688"><span class="lineNum">     688 </span>            :   ASMJIT_INST_1x(neg, Neg, X86Mem)                                            // ANY</a>
+<a name="689"><span class="lineNum">     689 </span>            :   ASMJIT_INST_0x(nop, Nop)                                                    // ANY</a>
+<a name="690"><span class="lineNum">     690 </span>            :   ASMJIT_INST_1x(not_, Not, X86Gp)                                            // ANY</a>
+<a name="691"><span class="lineNum">     691 </span>            :   ASMJIT_INST_1x(not_, Not, X86Mem)                                           // ANY</a>
+<a name="692"><span class="lineNum">     692 </span>            :   ASMJIT_INST_2x(or_, Or, X86Gp, X86Gp)                                       // ANY</a>
+<a name="693"><span class="lineNum">     693 </span>            :   ASMJIT_INST_2x(or_, Or, X86Gp, X86Mem)                                      // ANY</a>
+<a name="694"><span class="lineNum">     694 </span>            :   ASMJIT_INST_2i(or_, Or, X86Gp, Imm)                                         // ANY</a>
+<a name="695"><span class="lineNum">     695 </span>            :   ASMJIT_INST_2x(or_, Or, X86Mem, X86Gp)                                      // ANY</a>
+<a name="696"><span class="lineNum">     696 </span>            :   ASMJIT_INST_2i(or_, Or, X86Mem, Imm)                                        // ANY</a>
+<a name="697"><span class="lineNum">     697 </span>            :   ASMJIT_INST_2x(out, Out, Imm, ZAX)                                          // ANY</a>
+<a name="698"><span class="lineNum">     698 </span>            :   ASMJIT_INST_2i(out, Out, DX, ZAX)                                           // ANY</a>
+<a name="699"><span class="lineNum">     699 </span>            :   ASMJIT_INST_2i(outs, Outs, DX, DS_ZSI)                                      // ANY</a>
+<a name="700"><span class="lineNum">     700 </span>            :   ASMJIT_INST_0x(pause, Pause)                                                // SSE2</a>
+<a name="701"><span class="lineNum">     701 </span>            :   ASMJIT_INST_3x(pdep, Pdep, X86Gp, X86Gp, X86Gp)                             // BMI2</a>
+<a name="702"><span class="lineNum">     702 </span>            :   ASMJIT_INST_3x(pdep, Pdep, X86Gp, X86Gp, X86Mem)                            // BMI2</a>
+<a name="703"><span class="lineNum">     703 </span>            :   ASMJIT_INST_3x(pext, Pext, X86Gp, X86Gp, X86Gp)                             // BMI2</a>
+<a name="704"><span class="lineNum">     704 </span>            :   ASMJIT_INST_3x(pext, Pext, X86Gp, X86Gp, X86Mem)                            // BMI2</a>
+<a name="705"><span class="lineNum">     705 </span>            :   ASMJIT_INST_0x(pcommit, Pcommit)                                            // PCOMMIT</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">       1120 :   ASMJIT_INST_1x(pop, Pop, X86Gp)                                             // ANY</span></a>
+<a name="707"><span class="lineNum">     707 </span>            :   ASMJIT_INST_1x(pop, Pop, X86Mem)                                            // ANY</a>
+<a name="708"><span class="lineNum">     708 </span>            :   ASMJIT_INST_1x(pop, Pop, X86Seg);                                           // ANY</a>
+<a name="709"><span class="lineNum">     709 </span>            :   ASMJIT_INST_0x(popa, Popa)                                                  // X86</a>
+<a name="710"><span class="lineNum">     710 </span>            :   ASMJIT_INST_0x(popad, Popad)                                                // X86</a>
+<a name="711"><span class="lineNum">     711 </span>            :   ASMJIT_INST_2x(popcnt, Popcnt, X86Gp, X86Gp)                                // POPCNT</a>
+<a name="712"><span class="lineNum">     712 </span>            :   ASMJIT_INST_2x(popcnt, Popcnt, X86Gp, X86Mem)                               // POPCNT</a>
+<a name="713"><span class="lineNum">     713 </span>            :   ASMJIT_INST_0x(popf, Popf)                                                  // ANY</a>
+<a name="714"><span class="lineNum">     714 </span>            :   ASMJIT_INST_0x(popfd, Popfd)                                                // X86</a>
+<a name="715"><span class="lineNum">     715 </span>            :   ASMJIT_INST_0x(popfq, Popfq)                                                // X64</a>
+<a name="716"><span class="lineNum">     716 </span>            :   ASMJIT_INST_1x(prefetch, Prefetch, X86Mem)                                  // 3DNOW</a>
+<a name="717"><span class="lineNum">     717 </span>            :   ASMJIT_INST_1x(prefetchnta, Prefetchnta, X86Mem)                            // SSE</a>
+<a name="718"><span class="lineNum">     718 </span>            :   ASMJIT_INST_1x(prefetcht0, Prefetcht0, X86Mem)                              // SSE</a>
+<a name="719"><span class="lineNum">     719 </span>            :   ASMJIT_INST_1x(prefetcht1, Prefetcht1, X86Mem)                              // SSE</a>
+<a name="720"><span class="lineNum">     720 </span>            :   ASMJIT_INST_1x(prefetcht2, Prefetcht2, X86Mem)                              // SSE</a>
+<a name="721"><span class="lineNum">     721 </span>            :   ASMJIT_INST_1x(prefetchw, Prefetchw, X86Mem)                                // PREFETCHW</a>
+<a name="722"><span class="lineNum">     722 </span>            :   ASMJIT_INST_1x(prefetchwt1, Prefetchwt1, X86Mem)                            // PREFETCHW1</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">       1120 :   ASMJIT_INST_1x(push, Push, X86Gp)                                           // ANY</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :   ASMJIT_INST_1x(push, Push, X86Mem)                                          // ANY</a>
+<a name="725"><span class="lineNum">     725 </span>            :   ASMJIT_INST_1x(push, Push, X86Seg)                                          // ANY</a>
+<a name="726"><span class="lineNum">     726 </span>            :   ASMJIT_INST_1i(push, Push, Imm)                                             // ANY</a>
+<a name="727"><span class="lineNum">     727 </span>            :   ASMJIT_INST_0x(pusha, Pusha)                                                // X86</a>
+<a name="728"><span class="lineNum">     728 </span>            :   ASMJIT_INST_0x(pushad, Pushad)                                              // X86</a>
+<a name="729"><span class="lineNum">     729 </span>            :   ASMJIT_INST_0x(pushf, Pushf)                                                // ANY</a>
+<a name="730"><span class="lineNum">     730 </span>            :   ASMJIT_INST_0x(pushfd, Pushfd)                                              // X86</a>
+<a name="731"><span class="lineNum">     731 </span>            :   ASMJIT_INST_0x(pushfq, Pushfq)                                              // X64</a>
+<a name="732"><span class="lineNum">     732 </span>            :   ASMJIT_INST_2x(rcl, Rcl, X86Gp, CL)                                         // ANY</a>
+<a name="733"><span class="lineNum">     733 </span>            :   ASMJIT_INST_2x(rcl, Rcl, X86Mem, CL)                                        // ANY</a>
+<a name="734"><span class="lineNum">     734 </span>            :   ASMJIT_INST_2i(rcl, Rcl, X86Gp, Imm)                                        // ANY</a>
+<a name="735"><span class="lineNum">     735 </span>            :   ASMJIT_INST_2i(rcl, Rcl, X86Mem, Imm)                                       // ANY</a>
+<a name="736"><span class="lineNum">     736 </span>            :   ASMJIT_INST_2x(rcr, Rcr, X86Gp, CL)                                         // ANY</a>
+<a name="737"><span class="lineNum">     737 </span>            :   ASMJIT_INST_2x(rcr, Rcr, X86Mem, CL)                                        // ANY</a>
+<a name="738"><span class="lineNum">     738 </span>            :   ASMJIT_INST_2i(rcr, Rcr, X86Gp, Imm)                                        // ANY</a>
+<a name="739"><span class="lineNum">     739 </span>            :   ASMJIT_INST_2i(rcr, Rcr, X86Mem, Imm)                                       // ANY</a>
+<a name="740"><span class="lineNum">     740 </span>            :   ASMJIT_INST_1x(rdfsbase, Rdfsbase, X86Gp)                                   // FSGSBASE</a>
+<a name="741"><span class="lineNum">     741 </span>            :   ASMJIT_INST_1x(rdgsbase, Rdgsbase, X86Gp)                                   // FSGSBASE</a>
+<a name="742"><span class="lineNum">     742 </span>            :   ASMJIT_INST_1x(rdrand, Rdrand, X86Gp)                                       // RDRAND</a>
+<a name="743"><span class="lineNum">     743 </span>            :   ASMJIT_INST_1x(rdseed, Rdseed, X86Gp)                                       // RDSEED</a>
+<a name="744"><span class="lineNum">     744 </span>            :   ASMJIT_INST_3x(rdmsr, Rdmsr, EDX, EAX, ECX)                                 // MSR       [EXPLICIT] RDX:EAX     &lt;- MSR[ECX]</a>
+<a name="745"><span class="lineNum">     745 </span>            :   ASMJIT_INST_3x(rdpmc, Rdpmc, EDX, EAX, ECX)                                 // ANY       [EXPLICIT] RDX:EAX     &lt;- PMC[ECX]</a>
+<a name="746"><span class="lineNum">     746 </span>            :   ASMJIT_INST_2x(rdtsc, Rdtsc, EDX, EAX)                                      // RDTSC     [EXPLICIT] EDX:EAX     &lt;- Counter</a>
+<a name="747"><span class="lineNum">     747 </span>            :   ASMJIT_INST_3x(rdtscp, Rdtscp, EDX, EAX, ECX)                               // RDTSCP    [EXPLICIT] EDX:EAX:EXC &lt;- Counter</a>
+<a name="748"><span class="lineNum">     748 </span>            :   ASMJIT_INST_2x(rol, Rol, X86Gp, CL)                                         // ANY</a>
+<a name="749"><span class="lineNum">     749 </span>            :   ASMJIT_INST_2x(rol, Rol, X86Mem, CL)                                        // ANY</a>
+<a name="750"><span class="lineNum">     750 </span>            :   ASMJIT_INST_2i(rol, Rol, X86Gp, Imm)                                        // ANY</a>
+<a name="751"><span class="lineNum">     751 </span>            :   ASMJIT_INST_2i(rol, Rol, X86Mem, Imm)                                       // ANY</a>
+<a name="752"><span class="lineNum">     752 </span>            :   ASMJIT_INST_2x(ror, Ror, X86Gp, CL)                                         // ANY</a>
+<a name="753"><span class="lineNum">     753 </span>            :   ASMJIT_INST_2x(ror, Ror, X86Mem, CL)                                        // ANY</a>
+<a name="754"><span class="lineNum">     754 </span>            :   ASMJIT_INST_2i(ror, Ror, X86Gp, Imm)                                        // ANY</a>
+<a name="755"><span class="lineNum">     755 </span>            :   ASMJIT_INST_2i(ror, Ror, X86Mem, Imm)                                       // ANY</a>
+<a name="756"><span class="lineNum">     756 </span>            :   ASMJIT_INST_3i(rorx, Rorx, X86Gp, X86Gp, Imm)                               // BMI2</a>
+<a name="757"><span class="lineNum">     757 </span>            :   ASMJIT_INST_3i(rorx, Rorx, X86Gp, X86Mem, Imm)                              // BMI2</a>
+<a name="758"><span class="lineNum">     758 </span>            :   ASMJIT_INST_0x(rsm, Rsm)                                                    // X86</a>
+<a name="759"><span class="lineNum">     759 </span>            :   ASMJIT_INST_2x(sbb, Sbb, X86Gp, X86Gp)                                      // ANY</a>
+<a name="760"><span class="lineNum">     760 </span>            :   ASMJIT_INST_2x(sbb, Sbb, X86Gp, X86Mem)                                     // ANY</a>
+<a name="761"><span class="lineNum">     761 </span>            :   ASMJIT_INST_2i(sbb, Sbb, X86Gp, Imm)                                        // ANY</a>
+<a name="762"><span class="lineNum">     762 </span>            :   ASMJIT_INST_2x(sbb, Sbb, X86Mem, X86Gp)                                     // ANY</a>
+<a name="763"><span class="lineNum">     763 </span>            :   ASMJIT_INST_2i(sbb, Sbb, X86Mem, Imm)                                       // ANY</a>
+<a name="764"><span class="lineNum">     764 </span>            :   ASMJIT_INST_1x(sahf, Sahf, AH)                                              // LAHFSAHF  [EXPLICIT] EFL &lt;- AH</a>
+<a name="765"><span class="lineNum">     765 </span>            :   ASMJIT_INST_2x(sal, Sal, X86Gp, CL)                                         // ANY</a>
+<a name="766"><span class="lineNum">     766 </span>            :   ASMJIT_INST_2x(sal, Sal, X86Mem, CL)                                        // ANY</a>
+<a name="767"><span class="lineNum">     767 </span>            :   ASMJIT_INST_2i(sal, Sal, X86Gp, Imm)                                        // ANY</a>
+<a name="768"><span class="lineNum">     768 </span>            :   ASMJIT_INST_2i(sal, Sal, X86Mem, Imm)                                       // ANY</a>
+<a name="769"><span class="lineNum">     769 </span>            :   ASMJIT_INST_2x(sar, Sar, X86Gp, CL)                                         // ANY</a>
+<a name="770"><span class="lineNum">     770 </span>            :   ASMJIT_INST_2x(sar, Sar, X86Mem, CL)                                        // ANY</a>
+<a name="771"><span class="lineNum">     771 </span>            :   ASMJIT_INST_2i(sar, Sar, X86Gp, Imm)                                        // ANY</a>
+<a name="772"><span class="lineNum">     772 </span>            :   ASMJIT_INST_2i(sar, Sar, X86Mem, Imm)                                       // ANY</a>
+<a name="773"><span class="lineNum">     773 </span>            :   ASMJIT_INST_3x(sarx, Sarx, X86Gp, X86Gp, X86Gp)                             // BMI2</a>
+<a name="774"><span class="lineNum">     774 </span>            :   ASMJIT_INST_3x(sarx, Sarx, X86Gp, X86Mem, X86Gp)                            // BMI2</a>
+<a name="775"><span class="lineNum">     775 </span>            :   ASMJIT_INST_2x(scas, Scas, ZAX, ES_ZDI)                                     // ANY       [EXPLICIT]</a>
+<a name="776"><span class="lineNum">     776 </span>            :   ASMJIT_INST_1c(set, Set, X86Inst::condToSetcc, X86Gp)                       // ANY</a>
+<a name="777"><span class="lineNum">     777 </span>            :   ASMJIT_INST_1c(set, Set, X86Inst::condToSetcc, X86Mem)                      // ANY</a>
+<a name="778"><span class="lineNum">     778 </span>            :   ASMJIT_INST_0x(sfence, Sfence)                                              // SSE</a>
+<a name="779"><span class="lineNum">     779 </span>            :   ASMJIT_INST_1x(sgdt, Sgdt, X86Mem)                                          // ANY</a>
+<a name="780"><span class="lineNum">     780 </span>            :   ASMJIT_INST_2x(shl, Shl, X86Gp, CL)                                         // ANY</a>
+<a name="781"><span class="lineNum">     781 </span>            :   ASMJIT_INST_2x(shl, Shl, X86Mem, CL)                                        // ANY</a>
+<a name="782"><span class="lineNum">     782 </span>            :   ASMJIT_INST_2i(shl, Shl, X86Gp, Imm)                                        // ANY</a>
+<a name="783"><span class="lineNum">     783 </span>            :   ASMJIT_INST_2i(shl, Shl, X86Mem, Imm)                                       // ANY</a>
+<a name="784"><span class="lineNum">     784 </span>            :   ASMJIT_INST_3x(shlx, Shlx, X86Gp, X86Gp, X86Gp)                             // BMI2</a>
+<a name="785"><span class="lineNum">     785 </span>            :   ASMJIT_INST_3x(shlx, Shlx, X86Gp, X86Mem, X86Gp)                            // BMI2</a>
+<a name="786"><span class="lineNum">     786 </span>            :   ASMJIT_INST_2x(shr, Shr, X86Gp, CL)                                         // ANY</a>
+<a name="787"><span class="lineNum">     787 </span>            :   ASMJIT_INST_2x(shr, Shr, X86Mem, CL)                                        // ANY</a>
+<a name="788"><span class="lineNum">     788 </span>            :   ASMJIT_INST_2i(shr, Shr, X86Gp, Imm)                                        // ANY</a>
+<a name="789"><span class="lineNum">     789 </span>            :   ASMJIT_INST_2i(shr, Shr, X86Mem, Imm)                                       // ANY</a>
+<a name="790"><span class="lineNum">     790 </span>            :   ASMJIT_INST_3x(shrx, Shrx, X86Gp, X86Gp, X86Gp)                             // BMI2</a>
+<a name="791"><span class="lineNum">     791 </span>            :   ASMJIT_INST_3x(shrx, Shrx, X86Gp, X86Mem, X86Gp)                            // BMI2</a>
+<a name="792"><span class="lineNum">     792 </span>            :   ASMJIT_INST_3x(shld, Shld, X86Gp, X86Gp, CL)                                // ANY</a>
+<a name="793"><span class="lineNum">     793 </span>            :   ASMJIT_INST_3x(shld, Shld, X86Mem, X86Gp, CL)                               // ANY</a>
+<a name="794"><span class="lineNum">     794 </span>            :   ASMJIT_INST_3i(shld, Shld, X86Gp, X86Gp, Imm)                               // ANY</a>
+<a name="795"><span class="lineNum">     795 </span>            :   ASMJIT_INST_3i(shld, Shld, X86Mem, X86Gp, Imm)                              // ANY</a>
+<a name="796"><span class="lineNum">     796 </span>            :   ASMJIT_INST_3x(shrd, Shrd, X86Gp, X86Gp, CL)                                // ANY</a>
+<a name="797"><span class="lineNum">     797 </span>            :   ASMJIT_INST_3x(shrd, Shrd, X86Mem, X86Gp, CL)                               // ANY</a>
+<a name="798"><span class="lineNum">     798 </span>            :   ASMJIT_INST_3i(shrd, Shrd, X86Gp, X86Gp, Imm)                               // ANY</a>
+<a name="799"><span class="lineNum">     799 </span>            :   ASMJIT_INST_3i(shrd, Shrd, X86Mem, X86Gp, Imm)                              // ANY</a>
+<a name="800"><span class="lineNum">     800 </span>            :   ASMJIT_INST_1x(sidt, Sidt, X86Mem)                                          // ANY</a>
+<a name="801"><span class="lineNum">     801 </span>            :   ASMJIT_INST_1x(sldt, Sldt, X86Gp)                                           // ANY</a>
+<a name="802"><span class="lineNum">     802 </span>            :   ASMJIT_INST_1x(sldt, Sldt, X86Mem)                                          // ANY</a>
+<a name="803"><span class="lineNum">     803 </span>            :   ASMJIT_INST_1x(smsw, Smsw, X86Gp)                                           // ANY</a>
+<a name="804"><span class="lineNum">     804 </span>            :   ASMJIT_INST_1x(smsw, Smsw, X86Mem)                                          // ANY</a>
+<a name="805"><span class="lineNum">     805 </span>            :   ASMJIT_INST_0x(stac, Stac)                                                  // SMAP</a>
+<a name="806"><span class="lineNum">     806 </span>            :   ASMJIT_INST_0x(stc, Stc)                                                    // ANY</a>
+<a name="807"><span class="lineNum">     807 </span>            :   ASMJIT_INST_0x(std, Std)                                                    // ANY</a>
+<a name="808"><span class="lineNum">     808 </span>            :   ASMJIT_INST_0x(sti, Sti)                                                    // ANY</a>
+<a name="809"><span class="lineNum">     809 </span>            :   ASMJIT_INST_1x(stmxcsr, Stmxcsr, X86Mem)                                    // SSE</a>
+<a name="810"><span class="lineNum">     810 </span>            :   ASMJIT_INST_2x(stos, Stos, ES_ZDI, ZAX)                                     // ANY       [EXPLICIT]</a>
+<a name="811"><span class="lineNum">     811 </span>            :   ASMJIT_INST_1x(str, Str, X86Gp)                                             // ANY</a>
+<a name="812"><span class="lineNum">     812 </span>            :   ASMJIT_INST_1x(str, Str, X86Mem)                                            // ANY</a>
+<a name="813"><span class="lineNum">     813 </span>            :   ASMJIT_INST_2x(sub, Sub, X86Gp, X86Gp)                                      // ANY</a>
+<a name="814"><span class="lineNum">     814 </span>            :   ASMJIT_INST_2x(sub, Sub, X86Gp, X86Mem)                                     // ANY</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">        932 :   ASMJIT_INST_2i(sub, Sub, X86Gp, Imm)                                        // ANY</span></a>
+<a name="816"><span class="lineNum">     816 </span>            :   ASMJIT_INST_2x(sub, Sub, X86Mem, X86Gp)                                     // ANY</a>
+<a name="817"><span class="lineNum">     817 </span>            :   ASMJIT_INST_2i(sub, Sub, X86Mem, Imm)                                       // ANY</a>
+<a name="818"><span class="lineNum">     818 </span>            :   ASMJIT_INST_0x(swapgs, Swapgs)                                              // X64</a>
+<a name="819"><span class="lineNum">     819 </span>            :   ASMJIT_INST_2x(t1mskc, T1mskc, X86Gp, X86Gp)                                // TBM</a>
+<a name="820"><span class="lineNum">     820 </span>            :   ASMJIT_INST_2x(t1mskc, T1mskc, X86Gp, X86Mem)                               // TBM</a>
+<a name="821"><span class="lineNum">     821 </span>            :   ASMJIT_INST_2x(test, Test, X86Gp, X86Gp)                                    // ANY</a>
+<a name="822"><span class="lineNum">     822 </span>            :   ASMJIT_INST_2i(test, Test, X86Gp, Imm)                                      // ANY</a>
+<a name="823"><span class="lineNum">     823 </span>            :   ASMJIT_INST_2x(test, Test, X86Mem, X86Gp)                                   // ANY</a>
+<a name="824"><span class="lineNum">     824 </span>            :   ASMJIT_INST_2i(test, Test, X86Mem, Imm)                                     // ANY</a>
+<a name="825"><span class="lineNum">     825 </span>            :   ASMJIT_INST_2x(tzcnt, Tzcnt, X86Gp, X86Gp)                                  // BMI</a>
+<a name="826"><span class="lineNum">     826 </span>            :   ASMJIT_INST_2x(tzcnt, Tzcnt, X86Gp, X86Mem)                                 // BMI</a>
+<a name="827"><span class="lineNum">     827 </span>            :   ASMJIT_INST_2x(tzmsk, Tzmsk, X86Gp, X86Gp)                                  // TBM</a>
+<a name="828"><span class="lineNum">     828 </span>            :   ASMJIT_INST_2x(tzmsk, Tzmsk, X86Gp, X86Mem)                                 // TBM</a>
+<a name="829"><span class="lineNum">     829 </span>            :   ASMJIT_INST_0x(ud2, Ud2)                                                    // ANY</a>
+<a name="830"><span class="lineNum">     830 </span>            :   ASMJIT_INST_1x(verr, Verr, X86Gp)                                           // ANY</a>
+<a name="831"><span class="lineNum">     831 </span>            :   ASMJIT_INST_1x(verr, Verr, X86Mem)                                          // ANY</a>
+<a name="832"><span class="lineNum">     832 </span>            :   ASMJIT_INST_1x(verw, Verw, X86Gp)                                           // ANY</a>
+<a name="833"><span class="lineNum">     833 </span>            :   ASMJIT_INST_1x(verw, Verw, X86Mem)                                          // ANY</a>
+<a name="834"><span class="lineNum">     834 </span>            :   ASMJIT_INST_1x(wrfsbase, Wrfsbase, X86Gp)                                   // FSGSBASE</a>
+<a name="835"><span class="lineNum">     835 </span>            :   ASMJIT_INST_1x(wrgsbase, Wrgsbase, X86Gp)                                   // FSGSBASE</a>
+<a name="836"><span class="lineNum">     836 </span>            :   ASMJIT_INST_3x(wrmsr, Wrmsr, EDX, EAX, ECX)                                 // MSR       [EXPLICIT] RDX:EAX     -&gt; MSR[ECX]</a>
+<a name="837"><span class="lineNum">     837 </span>            :   ASMJIT_INST_0x(xabort, Xabort)                                              // RTM</a>
+<a name="838"><span class="lineNum">     838 </span>            :   ASMJIT_INST_2x(xadd, Xadd, X86Gp, X86Gp)                                    // ANY</a>
+<a name="839"><span class="lineNum">     839 </span>            :   ASMJIT_INST_2x(xadd, Xadd, X86Mem, X86Gp)                                   // ANY</a>
+<a name="840"><span class="lineNum">     840 </span>            :   ASMJIT_INST_1x(xbegin, Xbegin, Label)                                       // RTM</a>
+<a name="841"><span class="lineNum">     841 </span>            :   ASMJIT_INST_1x(xbegin, Xbegin, Imm)                                         // RTM</a>
+<a name="842"><span class="lineNum">     842 </span>            :   ASMJIT_INST_1x(xbegin, Xbegin, uint64_t)                                    // RTM</a>
+<a name="843"><span class="lineNum">     843 </span>            :   ASMJIT_INST_2x(xchg, Xchg, X86Gp, X86Gp)                                    // ANY</a>
+<a name="844"><span class="lineNum">     844 </span>            :   ASMJIT_INST_2x(xchg, Xchg, X86Mem, X86Gp)                                   // ANY</a>
+<a name="845"><span class="lineNum">     845 </span>            :   ASMJIT_INST_2x(xchg, Xchg, X86Gp, X86Mem)                                   // ANY</a>
+<a name="846"><span class="lineNum">     846 </span>            :   ASMJIT_INST_0x(xend, Xend)                                                  // RTM</a>
+<a name="847"><span class="lineNum">     847 </span>            :   ASMJIT_INST_3x(xgetbv, Xgetbv, EDX, EAX, ECX)                               // XSAVE     [EXPLICIT] EDX:EAX &lt;- XCR[ECX]</a>
+<a name="848"><span class="lineNum">     848 </span>            :   ASMJIT_INST_2x(xor_, Xor, X86Gp, X86Gp)                                     // ANY</a>
+<a name="849"><span class="lineNum">     849 </span>            :   ASMJIT_INST_2x(xor_, Xor, X86Gp, X86Mem)                                    // ANY</a>
+<a name="850"><span class="lineNum">     850 </span>            :   ASMJIT_INST_2i(xor_, Xor, X86Gp, Imm)                                       // ANY</a>
+<a name="851"><span class="lineNum">     851 </span>            :   ASMJIT_INST_2x(xor_, Xor, X86Mem, X86Gp)                                    // ANY</a>
+<a name="852"><span class="lineNum">     852 </span>            :   ASMJIT_INST_2i(xor_, Xor, X86Mem, Imm)                                      // ANY</a>
+<a name="853"><span class="lineNum">     853 </span>            :   ASMJIT_INST_3x(xsetbv, Xsetbv, EDX, EAX, ECX)                               // XSAVE     [EXPLICIT] XCR[ECX] &lt;- EDX:EAX</a>
+<a name="854"><span class="lineNum">     854 </span>            :   ASMJIT_INST_0x(xtest, Xtest)                                                // TSX</a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="857"><span class="lineNum">     857 </span>            :   // [FPU Instructions]</a>
+<a name="858"><span class="lineNum">     858 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :   ASMJIT_INST_0x(f2xm1, F2xm1)                                                // FPU</a>
+<a name="861"><span class="lineNum">     861 </span>            :   ASMJIT_INST_0x(fabs, Fabs)                                                  // FPU</a>
+<a name="862"><span class="lineNum">     862 </span>            :   ASMJIT_INST_2x(fadd, Fadd, X86Fp, X86Fp)                                    // FPU</a>
+<a name="863"><span class="lineNum">     863 </span>            :   ASMJIT_INST_1x(fadd, Fadd, X86Mem)                                          // FPU</a>
+<a name="864"><span class="lineNum">     864 </span>            :   ASMJIT_INST_1x(faddp, Faddp, X86Fp)                                         // FPU</a>
+<a name="865"><span class="lineNum">     865 </span>            :   ASMJIT_INST_0x(faddp, Faddp)                                                // FPU</a>
+<a name="866"><span class="lineNum">     866 </span>            :   ASMJIT_INST_1x(fbld, Fbld, X86Mem)                                          // FPU</a>
+<a name="867"><span class="lineNum">     867 </span>            :   ASMJIT_INST_1x(fbstp, Fbstp, X86Mem)                                        // FPU</a>
+<a name="868"><span class="lineNum">     868 </span>            :   ASMJIT_INST_0x(fchs, Fchs)                                                  // FPU</a>
+<a name="869"><span class="lineNum">     869 </span>            :   ASMJIT_INST_0x(fclex, Fclex)                                                // FPU</a>
+<a name="870"><span class="lineNum">     870 </span>            :   ASMJIT_INST_1x(fcmovb, Fcmovb, X86Fp)                                       // FPU</a>
+<a name="871"><span class="lineNum">     871 </span>            :   ASMJIT_INST_1x(fcmovbe, Fcmovbe, X86Fp)                                     // FPU</a>
+<a name="872"><span class="lineNum">     872 </span>            :   ASMJIT_INST_1x(fcmove, Fcmove, X86Fp)                                       // FPU</a>
+<a name="873"><span class="lineNum">     873 </span>            :   ASMJIT_INST_1x(fcmovnb, Fcmovnb, X86Fp)                                     // FPU</a>
+<a name="874"><span class="lineNum">     874 </span>            :   ASMJIT_INST_1x(fcmovnbe, Fcmovnbe, X86Fp)                                   // FPU</a>
+<a name="875"><span class="lineNum">     875 </span>            :   ASMJIT_INST_1x(fcmovne, Fcmovne, X86Fp)                                     // FPU</a>
+<a name="876"><span class="lineNum">     876 </span>            :   ASMJIT_INST_1x(fcmovnu, Fcmovnu, X86Fp)                                     // FPU</a>
+<a name="877"><span class="lineNum">     877 </span>            :   ASMJIT_INST_1x(fcmovu, Fcmovu, X86Fp)                                       // FPU</a>
+<a name="878"><span class="lineNum">     878 </span>            :   ASMJIT_INST_1x(fcom, Fcom, X86Fp)                                           // FPU</a>
+<a name="879"><span class="lineNum">     879 </span>            :   ASMJIT_INST_0x(fcom, Fcom)                                                  // FPU</a>
+<a name="880"><span class="lineNum">     880 </span>            :   ASMJIT_INST_1x(fcom, Fcom, X86Mem)                                          // FPU</a>
+<a name="881"><span class="lineNum">     881 </span>            :   ASMJIT_INST_1x(fcomp, Fcomp, X86Fp)                                         // FPU</a>
+<a name="882"><span class="lineNum">     882 </span>            :   ASMJIT_INST_0x(fcomp, Fcomp)                                                // FPU</a>
+<a name="883"><span class="lineNum">     883 </span>            :   ASMJIT_INST_1x(fcomp, Fcomp, X86Mem)                                        // FPU</a>
+<a name="884"><span class="lineNum">     884 </span>            :   ASMJIT_INST_0x(fcompp, Fcompp)                                              // FPU</a>
+<a name="885"><span class="lineNum">     885 </span>            :   ASMJIT_INST_1x(fcomi, Fcomi, X86Fp)                                         // FPU</a>
+<a name="886"><span class="lineNum">     886 </span>            :   ASMJIT_INST_1x(fcomip, Fcomip, X86Fp)                                       // FPU</a>
+<a name="887"><span class="lineNum">     887 </span>            :   ASMJIT_INST_0x(fcos, Fcos)                                                  // FPU</a>
+<a name="888"><span class="lineNum">     888 </span>            :   ASMJIT_INST_0x(fdecstp, Fdecstp)                                            // FPU</a>
+<a name="889"><span class="lineNum">     889 </span>            :   ASMJIT_INST_2x(fdiv, Fdiv, X86Fp, X86Fp)                                    // FPU</a>
+<a name="890"><span class="lineNum">     890 </span>            :   ASMJIT_INST_1x(fdiv, Fdiv, X86Mem)                                          // FPU</a>
+<a name="891"><span class="lineNum">     891 </span>            :   ASMJIT_INST_1x(fdivp, Fdivp, X86Fp)                                         // FPU</a>
+<a name="892"><span class="lineNum">     892 </span>            :   ASMJIT_INST_0x(fdivp, Fdivp)                                                // FPU</a>
+<a name="893"><span class="lineNum">     893 </span>            :   ASMJIT_INST_2x(fdivr, Fdivr, X86Fp, X86Fp)                                  // FPU</a>
+<a name="894"><span class="lineNum">     894 </span>            :   ASMJIT_INST_1x(fdivr, Fdivr, X86Mem)                                        // FPU</a>
+<a name="895"><span class="lineNum">     895 </span>            :   ASMJIT_INST_1x(fdivrp, Fdivrp, X86Fp)                                       // FPU</a>
+<a name="896"><span class="lineNum">     896 </span>            :   ASMJIT_INST_0x(fdivrp, Fdivrp)                                              // FPU</a>
+<a name="897"><span class="lineNum">     897 </span>            :   ASMJIT_INST_1x(ffree, Ffree, X86Fp)                                         // FPU</a>
+<a name="898"><span class="lineNum">     898 </span>            :   ASMJIT_INST_1x(fiadd, Fiadd, X86Mem)                                        // FPU</a>
+<a name="899"><span class="lineNum">     899 </span>            :   ASMJIT_INST_1x(ficom, Ficom, X86Mem)                                        // FPU</a>
+<a name="900"><span class="lineNum">     900 </span>            :   ASMJIT_INST_1x(ficomp, Ficomp, X86Mem)                                      // FPU</a>
+<a name="901"><span class="lineNum">     901 </span>            :   ASMJIT_INST_1x(fidiv, Fidiv, X86Mem)                                        // FPU</a>
+<a name="902"><span class="lineNum">     902 </span>            :   ASMJIT_INST_1x(fidivr, Fidivr, X86Mem)                                      // FPU</a>
+<a name="903"><span class="lineNum">     903 </span>            :   ASMJIT_INST_1x(fild, Fild, X86Mem)                                          // FPU</a>
+<a name="904"><span class="lineNum">     904 </span>            :   ASMJIT_INST_1x(fimul, Fimul, X86Mem)                                        // FPU</a>
+<a name="905"><span class="lineNum">     905 </span>            :   ASMJIT_INST_0x(fincstp, Fincstp)                                            // FPU</a>
+<a name="906"><span class="lineNum">     906 </span>            :   ASMJIT_INST_0x(finit, Finit)                                                // FPU</a>
+<a name="907"><span class="lineNum">     907 </span>            :   ASMJIT_INST_1x(fisub, Fisub, X86Mem)                                        // FPU</a>
+<a name="908"><span class="lineNum">     908 </span>            :   ASMJIT_INST_1x(fisubr, Fisubr, X86Mem)                                      // FPU</a>
+<a name="909"><span class="lineNum">     909 </span>            :   ASMJIT_INST_0x(fninit, Fninit)                                              // FPU</a>
+<a name="910"><span class="lineNum">     910 </span>            :   ASMJIT_INST_1x(fist, Fist, X86Mem)                                          // FPU</a>
+<a name="911"><span class="lineNum">     911 </span>            :   ASMJIT_INST_1x(fistp, Fistp, X86Mem)                                        // FPU</a>
+<a name="912"><span class="lineNum">     912 </span>            :   ASMJIT_INST_1x(fisttp, Fisttp, X86Mem)                                      // FPU+SSE3</a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineNoCov">          0 :   ASMJIT_INST_1x(fld, Fld, X86Mem)                                            // FPU</span></a>
+<a name="914"><span class="lineNum">     914 </span>            :   ASMJIT_INST_1x(fld, Fld, X86Fp)                                             // FPU</a>
+<a name="915"><span class="lineNum">     915 </span>            :   ASMJIT_INST_0x(fld1, Fld1)                                                  // FPU</a>
+<a name="916"><span class="lineNum">     916 </span>            :   ASMJIT_INST_0x(fldl2t, Fldl2t)                                              // FPU</a>
+<a name="917"><span class="lineNum">     917 </span>            :   ASMJIT_INST_0x(fldl2e, Fldl2e)                                              // FPU</a>
+<a name="918"><span class="lineNum">     918 </span>            :   ASMJIT_INST_0x(fldpi, Fldpi)                                                // FPU</a>
+<a name="919"><span class="lineNum">     919 </span>            :   ASMJIT_INST_0x(fldlg2, Fldlg2)                                              // FPU</a>
+<a name="920"><span class="lineNum">     920 </span>            :   ASMJIT_INST_0x(fldln2, Fldln2)                                              // FPU</a>
+<a name="921"><span class="lineNum">     921 </span>            :   ASMJIT_INST_0x(fldz, Fldz)                                                  // FPU</a>
+<a name="922"><span class="lineNum">     922 </span>            :   ASMJIT_INST_1x(fldcw, Fldcw, X86Mem)                                        // FPU</a>
+<a name="923"><span class="lineNum">     923 </span>            :   ASMJIT_INST_1x(fldenv, Fldenv, X86Mem)                                      // FPU</a>
+<a name="924"><span class="lineNum">     924 </span>            :   ASMJIT_INST_2x(fmul, Fmul, X86Fp, X86Fp)                                    // FPU</a>
+<a name="925"><span class="lineNum">     925 </span>            :   ASMJIT_INST_1x(fmul, Fmul, X86Mem)                                          // FPU</a>
+<a name="926"><span class="lineNum">     926 </span>            :   ASMJIT_INST_1x(fmulp, Fmulp, X86Fp)                                         // FPU</a>
+<a name="927"><span class="lineNum">     927 </span>            :   ASMJIT_INST_0x(fmulp, Fmulp)                                                // FPU</a>
+<a name="928"><span class="lineNum">     928 </span>            :   ASMJIT_INST_0x(fnclex, Fnclex)                                              // FPU</a>
+<a name="929"><span class="lineNum">     929 </span>            :   ASMJIT_INST_0x(fnop, Fnop)                                                  // FPU</a>
+<a name="930"><span class="lineNum">     930 </span>            :   ASMJIT_INST_1x(fnsave, Fnsave, X86Mem)                                      // FPU</a>
+<a name="931"><span class="lineNum">     931 </span>            :   ASMJIT_INST_1x(fnstenv, Fnstenv, X86Mem)                                    // FPU</a>
+<a name="932"><span class="lineNum">     932 </span>            :   ASMJIT_INST_1x(fnstcw, Fnstcw, X86Mem)                                      // FPU</a>
+<a name="933"><span class="lineNum">     933 </span>            :   ASMJIT_INST_0x(fpatan, Fpatan)                                              // FPU</a>
+<a name="934"><span class="lineNum">     934 </span>            :   ASMJIT_INST_0x(fprem, Fprem)                                                // FPU</a>
+<a name="935"><span class="lineNum">     935 </span>            :   ASMJIT_INST_0x(fprem1, Fprem1)                                              // FPU</a>
+<a name="936"><span class="lineNum">     936 </span>            :   ASMJIT_INST_0x(fptan, Fptan)                                                // FPU</a>
+<a name="937"><span class="lineNum">     937 </span>            :   ASMJIT_INST_0x(frndint, Frndint)                                            // FPU</a>
+<a name="938"><span class="lineNum">     938 </span>            :   ASMJIT_INST_1x(frstor, Frstor, X86Mem)                                      // FPU</a>
+<a name="939"><span class="lineNum">     939 </span>            :   ASMJIT_INST_1x(fsave, Fsave, X86Mem)                                        // FPU</a>
+<a name="940"><span class="lineNum">     940 </span>            :   ASMJIT_INST_0x(fscale, Fscale)                                              // FPU</a>
+<a name="941"><span class="lineNum">     941 </span>            :   ASMJIT_INST_0x(fsin, Fsin)                                                  // FPU</a>
+<a name="942"><span class="lineNum">     942 </span>            :   ASMJIT_INST_0x(fsincos, Fsincos)                                            // FPU</a>
+<a name="943"><span class="lineNum">     943 </span>            :   ASMJIT_INST_0x(fsqrt, Fsqrt)                                                // FPU</a>
+<a name="944"><span class="lineNum">     944 </span>            :   ASMJIT_INST_1x(fst, Fst, X86Mem)                                            // FPU</a>
+<a name="945"><span class="lineNum">     945 </span>            :   ASMJIT_INST_1x(fst, Fst, X86Fp)                                             // FPU</a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineNoCov">          0 :   ASMJIT_INST_1x(fstp, Fstp, X86Mem)                                          // FPU</span></a>
+<a name="947"><span class="lineNum">     947 </span>            :   ASMJIT_INST_1x(fstp, Fstp, X86Fp)                                           // FPU</a>
+<a name="948"><span class="lineNum">     948 </span>            :   ASMJIT_INST_1x(fstcw, Fstcw, X86Mem)                                        // FPU</a>
+<a name="949"><span class="lineNum">     949 </span>            :   ASMJIT_INST_1x(fstenv, Fstenv, X86Mem)                                      // FPU</a>
+<a name="950"><span class="lineNum">     950 </span>            :   ASMJIT_INST_2x(fsub, Fsub, X86Fp, X86Fp)                                    // FPU</a>
+<a name="951"><span class="lineNum">     951 </span>            :   ASMJIT_INST_1x(fsub, Fsub, X86Mem)                                          // FPU</a>
+<a name="952"><span class="lineNum">     952 </span>            :   ASMJIT_INST_1x(fsubp, Fsubp, X86Fp)                                         // FPU</a>
+<a name="953"><span class="lineNum">     953 </span>            :   ASMJIT_INST_0x(fsubp, Fsubp)                                                // FPU</a>
+<a name="954"><span class="lineNum">     954 </span>            :   ASMJIT_INST_2x(fsubr, Fsubr, X86Fp, X86Fp)                                  // FPU</a>
+<a name="955"><span class="lineNum">     955 </span>            :   ASMJIT_INST_1x(fsubr, Fsubr, X86Mem)                                        // FPU</a>
+<a name="956"><span class="lineNum">     956 </span>            :   ASMJIT_INST_1x(fsubrp, Fsubrp, X86Fp)                                       // FPU</a>
+<a name="957"><span class="lineNum">     957 </span>            :   ASMJIT_INST_0x(fsubrp, Fsubrp)                                              // FPU</a>
+<a name="958"><span class="lineNum">     958 </span>            :   ASMJIT_INST_0x(ftst, Ftst)                                                  // FPU</a>
+<a name="959"><span class="lineNum">     959 </span>            :   ASMJIT_INST_1x(fucom, Fucom, X86Fp)                                         // FPU</a>
+<a name="960"><span class="lineNum">     960 </span>            :   ASMJIT_INST_0x(fucom, Fucom)                                                // FPU</a>
+<a name="961"><span class="lineNum">     961 </span>            :   ASMJIT_INST_1x(fucomi, Fucomi, X86Fp)                                       // FPU</a>
+<a name="962"><span class="lineNum">     962 </span>            :   ASMJIT_INST_1x(fucomip, Fucomip, X86Fp)                                     // FPU</a>
+<a name="963"><span class="lineNum">     963 </span>            :   ASMJIT_INST_1x(fucomp, Fucomp, X86Fp)                                       // FPU</a>
+<a name="964"><span class="lineNum">     964 </span>            :   ASMJIT_INST_0x(fucomp, Fucomp)                                              // FPU</a>
+<a name="965"><span class="lineNum">     965 </span>            :   ASMJIT_INST_0x(fucompp, Fucompp)                                            // FPU</a>
+<a name="966"><span class="lineNum">     966 </span>            :   ASMJIT_INST_0x(fwait, Fwait)                                                // FPU</a>
+<a name="967"><span class="lineNum">     967 </span>            :   ASMJIT_INST_0x(fxam, Fxam)                                                  // FPU</a>
+<a name="968"><span class="lineNum">     968 </span>            :   ASMJIT_INST_1x(fxch, Fxch, X86Fp)                                           // FPU</a>
+<a name="969"><span class="lineNum">     969 </span>            :   ASMJIT_INST_0x(fxtract, Fxtract)                                            // FPU</a>
+<a name="970"><span class="lineNum">     970 </span>            :   ASMJIT_INST_0x(fyl2x, Fyl2x)                                                // FPU</a>
+<a name="971"><span class="lineNum">     971 </span>            :   ASMJIT_INST_0x(fyl2xp1, Fyl2xp1)                                            // FPU</a>
+<a name="972"><span class="lineNum">     972 </span>            :   ASMJIT_INST_1x(fstsw, Fstsw, X86Gp)                                         // FPU</a>
+<a name="973"><span class="lineNum">     973 </span>            :   ASMJIT_INST_1x(fstsw, Fstsw, X86Mem)                                        // FPU</a>
+<a name="974"><span class="lineNum">     974 </span>            :   ASMJIT_INST_1x(fnstsw, Fnstsw, X86Gp)                                       // FPU</a>
+<a name="975"><span class="lineNum">     975 </span>            :   ASMJIT_INST_1x(fnstsw, Fnstsw, X86Mem)                                      // FPU</a>
+<a name="976"><span class="lineNum">     976 </span>            : </a>
+<a name="977"><span class="lineNum">     977 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="978"><span class="lineNum">     978 </span>            :   // [MMX &amp; SSE Instructions]</a>
+<a name="979"><span class="lineNum">     979 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="980"><span class="lineNum">     980 </span>            : </a>
+<a name="981"><span class="lineNum">     981 </span>            :   ASMJIT_INST_2x(addpd, Addpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="982"><span class="lineNum">     982 </span>            :   ASMJIT_INST_2x(addpd, Addpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="983"><span class="lineNum">     983 </span>            :   ASMJIT_INST_2x(addps, Addps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="984"><span class="lineNum">     984 </span>            :   ASMJIT_INST_2x(addps, Addps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">       1986 :   ASMJIT_INST_2x(addsd, Addsd, X86Xmm, X86Xmm)                                // SSE2</span></a>
+<a name="986"><span class="lineNum">     986 </span>            :   ASMJIT_INST_2x(addsd, Addsd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="987"><span class="lineNum">     987 </span>            :   ASMJIT_INST_2x(addss, Addss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="988"><span class="lineNum">     988 </span>            :   ASMJIT_INST_2x(addss, Addss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="989"><span class="lineNum">     989 </span>            :   ASMJIT_INST_2x(addsubpd, Addsubpd, X86Xmm, X86Xmm)                          // SSE3</a>
+<a name="990"><span class="lineNum">     990 </span>            :   ASMJIT_INST_2x(addsubpd, Addsubpd, X86Xmm, X86Mem)                          // SSE3</a>
+<a name="991"><span class="lineNum">     991 </span>            :   ASMJIT_INST_2x(addsubps, Addsubps, X86Xmm, X86Xmm)                          // SSE3</a>
+<a name="992"><span class="lineNum">     992 </span>            :   ASMJIT_INST_2x(addsubps, Addsubps, X86Xmm, X86Mem)                          // SSE3</a>
+<a name="993"><span class="lineNum">     993 </span>            :   ASMJIT_INST_2x(andnpd, Andnpd, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="994"><span class="lineNum">     994 </span>            :   ASMJIT_INST_2x(andnpd, Andnpd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="995"><span class="lineNum">     995 </span>            :   ASMJIT_INST_2x(andnps, Andnps, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="996"><span class="lineNum">     996 </span>            :   ASMJIT_INST_2x(andnps, Andnps, X86Xmm, X86Mem)                              // SSE</a>
+<a name="997"><span class="lineNum">     997 </span>            :   ASMJIT_INST_2x(andpd, Andpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="998"><span class="lineNum">     998 </span>            :   ASMJIT_INST_2x(andpd, Andpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">        120 :   ASMJIT_INST_2x(andps, Andps, X86Xmm, X86Xmm)                                // SSE</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            :   ASMJIT_INST_2x(andps, Andps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   ASMJIT_INST_3i(blendpd, Blendpd, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :   ASMJIT_INST_3i(blendpd, Blendpd, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   ASMJIT_INST_3i(blendps, Blendps, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :   ASMJIT_INST_3i(blendps, Blendps, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :   ASMJIT_INST_3x(blendvpd, Blendvpd, X86Xmm, X86Xmm, XMM0)                    // SSE4_1 [EXPLICIT]</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   ASMJIT_INST_3x(blendvpd, Blendvpd, X86Xmm, X86Mem, XMM0)                    // SSE4_1 [EXPLICIT]</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :   ASMJIT_INST_3x(blendvps, Blendvps, X86Xmm, X86Xmm, XMM0)                    // SSE4_1 [EXPLICIT]</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   ASMJIT_INST_3x(blendvps, Blendvps, X86Xmm, X86Mem, XMM0)                    // SSE4_1 [EXPLICIT]</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   ASMJIT_INST_3i(cmppd, Cmppd, X86Xmm, X86Xmm, Imm)                           // SSE2</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   ASMJIT_INST_3i(cmppd, Cmppd, X86Xmm, X86Mem, Imm)                           // SSE2</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :   ASMJIT_INST_3i(cmpps, Cmpps, X86Xmm, X86Xmm, Imm)                           // SSE</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :   ASMJIT_INST_3i(cmpps, Cmpps, X86Xmm, X86Mem, Imm)                           // SSE</a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">        120 :   ASMJIT_INST_3i(cmpsd, Cmpsd, X86Xmm, X86Xmm, Imm)                           // SSE2</span></a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   ASMJIT_INST_3i(cmpsd, Cmpsd, X86Xmm, X86Mem, Imm)                           // SSE2</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   ASMJIT_INST_3i(cmpss, Cmpss, X86Xmm, X86Xmm, Imm)                           // SSE</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :   ASMJIT_INST_3i(cmpss, Cmpss, X86Xmm, X86Mem, Imm)                           // SSE</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   ASMJIT_INST_2x(comisd, Comisd, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :   ASMJIT_INST_2x(comisd, Comisd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   ASMJIT_INST_2x(comiss, Comiss, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="1020"><span class="lineNum">    1020 </span>            :   ASMJIT_INST_2x(comiss, Comiss, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :   ASMJIT_INST_2x(cvtdq2pd, Cvtdq2pd, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :   ASMJIT_INST_2x(cvtdq2pd, Cvtdq2pd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :   ASMJIT_INST_2x(cvtdq2ps, Cvtdq2ps, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   ASMJIT_INST_2x(cvtdq2ps, Cvtdq2ps, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   ASMJIT_INST_2x(cvtpd2dq, Cvtpd2dq, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :   ASMJIT_INST_2x(cvtpd2dq, Cvtpd2dq, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :   ASMJIT_INST_2x(cvtpd2pi, Cvtpd2pi, X86Mm, X86Xmm)                           // SSE2</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :   ASMJIT_INST_2x(cvtpd2pi, Cvtpd2pi, X86Mm, X86Mem)                           // SSE2</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :   ASMJIT_INST_2x(cvtpd2ps, Cvtpd2ps, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :   ASMJIT_INST_2x(cvtpd2ps, Cvtpd2ps, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   ASMJIT_INST_2x(cvtpi2pd, Cvtpi2pd, X86Xmm, X86Mm)                           // SSE2</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :   ASMJIT_INST_2x(cvtpi2pd, Cvtpi2pd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   ASMJIT_INST_2x(cvtpi2ps, Cvtpi2ps, X86Xmm, X86Mm)                           // SSE</a>
+<a name="1034"><span class="lineNum">    1034 </span>            :   ASMJIT_INST_2x(cvtpi2ps, Cvtpi2ps, X86Xmm, X86Mem)                          // SSE</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :   ASMJIT_INST_2x(cvtps2dq, Cvtps2dq, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   ASMJIT_INST_2x(cvtps2dq, Cvtps2dq, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :   ASMJIT_INST_2x(cvtps2pd, Cvtps2pd, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :   ASMJIT_INST_2x(cvtps2pd, Cvtps2pd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :   ASMJIT_INST_2x(cvtps2pi, Cvtps2pi, X86Mm, X86Xmm)                           // SSE</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   ASMJIT_INST_2x(cvtps2pi, Cvtps2pi, X86Mm, X86Mem)                           // SSE</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   ASMJIT_INST_2x(cvtsd2si, Cvtsd2si, X86Gp, X86Xmm)                           // SSE2</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :   ASMJIT_INST_2x(cvtsd2si, Cvtsd2si, X86Gp, X86Mem)                           // SSE2</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :   ASMJIT_INST_2x(cvtsd2ss, Cvtsd2ss, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :   ASMJIT_INST_2x(cvtsd2ss, Cvtsd2ss, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :   ASMJIT_INST_2x(cvtsi2sd, Cvtsi2sd, X86Xmm, X86Gp)                           // SSE2</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :   ASMJIT_INST_2x(cvtsi2sd, Cvtsi2sd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   ASMJIT_INST_2x(cvtsi2ss, Cvtsi2ss, X86Xmm, X86Gp)                           // SSE</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :   ASMJIT_INST_2x(cvtsi2ss, Cvtsi2ss, X86Xmm, X86Mem)                          // SSE</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :   ASMJIT_INST_2x(cvtss2sd, Cvtss2sd, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   ASMJIT_INST_2x(cvtss2sd, Cvtss2sd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   ASMJIT_INST_2x(cvtss2si, Cvtss2si, X86Gp, X86Xmm)                           // SSE</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   ASMJIT_INST_2x(cvtss2si, Cvtss2si, X86Gp, X86Mem)                           // SSE</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   ASMJIT_INST_2x(cvttpd2pi, Cvttpd2pi, X86Mm, X86Xmm)                         // SSE2</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   ASMJIT_INST_2x(cvttpd2pi, Cvttpd2pi, X86Mm, X86Mem)                         // SSE2</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   ASMJIT_INST_2x(cvttpd2dq, Cvttpd2dq, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :   ASMJIT_INST_2x(cvttpd2dq, Cvttpd2dq, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   ASMJIT_INST_2x(cvttps2dq, Cvttps2dq, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   ASMJIT_INST_2x(cvttps2dq, Cvttps2dq, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   ASMJIT_INST_2x(cvttps2pi, Cvttps2pi, X86Mm, X86Xmm)                         // SSE</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :   ASMJIT_INST_2x(cvttps2pi, Cvttps2pi, X86Mm, X86Mem)                         // SSE</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   ASMJIT_INST_2x(cvttsd2si, Cvttsd2si, X86Gp, X86Xmm)                         // SSE2</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   ASMJIT_INST_2x(cvttsd2si, Cvttsd2si, X86Gp, X86Mem)                         // SSE2</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   ASMJIT_INST_2x(cvttss2si, Cvttss2si, X86Gp, X86Xmm)                         // SSE</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   ASMJIT_INST_2x(cvttss2si, Cvttss2si, X86Gp, X86Mem)                         // SSE</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   ASMJIT_INST_2x(divpd, Divpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :   ASMJIT_INST_2x(divpd, Divpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   ASMJIT_INST_2x(divps, Divps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   ASMJIT_INST_2x(divps, Divps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">        270 :   ASMJIT_INST_2x(divsd, Divsd, X86Xmm, X86Xmm)                                // SSE2</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   ASMJIT_INST_2x(divsd, Divsd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   ASMJIT_INST_2x(divss, Divss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :   ASMJIT_INST_2x(divss, Divss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   ASMJIT_INST_3i(dppd, Dppd, X86Xmm, X86Xmm, Imm)                             // SSE4_1</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   ASMJIT_INST_3i(dppd, Dppd, X86Xmm, X86Mem, Imm)                             // SSE4_1</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   ASMJIT_INST_3i(dpps, Dpps, X86Xmm, X86Xmm, Imm)                             // SSE4_1</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :   ASMJIT_INST_3i(dpps, Dpps, X86Xmm, X86Mem, Imm)                             // SSE4_1</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   ASMJIT_INST_3i(extractps, Extractps, X86Gp, X86Xmm, Imm)                    // SSE4_1</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :   ASMJIT_INST_3i(extractps, Extractps, X86Mem, X86Xmm, Imm)                   // SSE4_1</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   ASMJIT_INST_2x(extrq, Extrq, X86Xmm, X86Xmm)                                // SSE4A</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :   ASMJIT_INST_3ii(extrq, Extrq, X86Xmm, Imm, Imm)                             // SSE4A</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   ASMJIT_INST_2x(haddpd, Haddpd, X86Xmm, X86Xmm)                              // SSE3</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   ASMJIT_INST_2x(haddpd, Haddpd, X86Xmm, X86Mem)                              // SSE3</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   ASMJIT_INST_2x(haddps, Haddps, X86Xmm, X86Xmm)                              // SSE3</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :   ASMJIT_INST_2x(haddps, Haddps, X86Xmm, X86Mem)                              // SSE3</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   ASMJIT_INST_2x(hsubpd, Hsubpd, X86Xmm, X86Xmm)                              // SSE3</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   ASMJIT_INST_2x(hsubpd, Hsubpd, X86Xmm, X86Mem)                              // SSE3</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :   ASMJIT_INST_2x(hsubps, Hsubps, X86Xmm, X86Xmm)                              // SSE3</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :   ASMJIT_INST_2x(hsubps, Hsubps, X86Xmm, X86Mem)                              // SSE3</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :   ASMJIT_INST_3i(insertps, Insertps, X86Xmm, X86Xmm, Imm)                     // SSE4_1</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   ASMJIT_INST_3i(insertps, Insertps, X86Xmm, X86Mem, Imm)                     // SSE4_1</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   ASMJIT_INST_2x(insertq, Insertq, X86Xmm, X86Xmm)                            // SSE4A</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   ASMJIT_INST_4ii(insertq, Insertq, X86Xmm, X86Xmm, Imm, Imm)                 // SSE4A</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   ASMJIT_INST_2x(lddqu, Lddqu, X86Xmm, X86Mem)                                // SSE3</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   ASMJIT_INST_3x(maskmovq, Maskmovq, X86Mm, X86Mm, DS_ZDI)                    // SSE  [EXPLICIT]</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   ASMJIT_INST_3x(maskmovdqu, Maskmovdqu, X86Xmm, X86Xmm, DS_ZDI)              // SSE2 [EXPLICIT]</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   ASMJIT_INST_2x(maxpd, Maxpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   ASMJIT_INST_2x(maxpd, Maxpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   ASMJIT_INST_2x(maxps, Maxps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :   ASMJIT_INST_2x(maxps, Maxps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :   ASMJIT_INST_2x(maxsd, Maxsd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   ASMJIT_INST_2x(maxsd, Maxsd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   ASMJIT_INST_2x(maxss, Maxss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   ASMJIT_INST_2x(maxss, Maxss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :   ASMJIT_INST_2x(minpd, Minpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :   ASMJIT_INST_2x(minpd, Minpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   ASMJIT_INST_2x(minps, Minps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   ASMJIT_INST_2x(minps, Minps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   ASMJIT_INST_2x(minsd, Minsd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1109"><span class="lineNum">    1109 </span>            :   ASMJIT_INST_2x(minsd, Minsd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   ASMJIT_INST_2x(minss, Minss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   ASMJIT_INST_2x(minss, Minss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   ASMJIT_INST_2x(movapd, Movapd, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :   ASMJIT_INST_2x(movapd, Movapd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :   ASMJIT_INST_2x(movapd, Movapd, X86Mem, X86Xmm)                              // SSE2</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   ASMJIT_INST_2x(movaps, Movaps, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :   ASMJIT_INST_2x(movaps, Movaps, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   ASMJIT_INST_2x(movaps, Movaps, X86Mem, X86Xmm)                              // SSE</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Mem, X86Mm)                                   // MMX</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Mem, X86Xmm)                                  // SSE</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Gp, X86Mm)                                    // MMX</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Gp, X86Xmm)                                   // SSE</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Mm, X86Mem)                                   // MMX</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Xmm, X86Mem)                                  // SSE</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Mm, X86Gp)                                    // MMX</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   ASMJIT_INST_2x(movd, Movd, X86Xmm, X86Gp)                                   // SSE</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :   ASMJIT_INST_2x(movddup, Movddup, X86Xmm, X86Xmm)                            // SSE3</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   ASMJIT_INST_2x(movddup, Movddup, X86Xmm, X86Mem)                            // SSE3</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   ASMJIT_INST_2x(movdq2q, Movdq2q, X86Mm, X86Xmm)                             // SSE2</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   ASMJIT_INST_2x(movdqa, Movdqa, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   ASMJIT_INST_2x(movdqa, Movdqa, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   ASMJIT_INST_2x(movdqa, Movdqa, X86Mem, X86Xmm)                              // SSE2</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   ASMJIT_INST_2x(movdqu, Movdqu, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :   ASMJIT_INST_2x(movdqu, Movdqu, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   ASMJIT_INST_2x(movdqu, Movdqu, X86Mem, X86Xmm)                              // SSE2</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   ASMJIT_INST_2x(movhlps, Movhlps, X86Xmm, X86Xmm)                            // SSE</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :   ASMJIT_INST_2x(movhpd, Movhpd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :   ASMJIT_INST_2x(movhpd, Movhpd, X86Mem, X86Xmm)                              // SSE2</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   ASMJIT_INST_2x(movhps, Movhps, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :   ASMJIT_INST_2x(movhps, Movhps, X86Mem, X86Xmm)                              // SSE</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   ASMJIT_INST_2x(movlhps, Movlhps, X86Xmm, X86Xmm)                            // SSE</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   ASMJIT_INST_2x(movlpd, Movlpd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :   ASMJIT_INST_2x(movlpd, Movlpd, X86Mem, X86Xmm)                              // SSE2</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :   ASMJIT_INST_2x(movlps, Movlps, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   ASMJIT_INST_2x(movlps, Movlps, X86Mem, X86Xmm)                              // SSE</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   ASMJIT_INST_2x(movmskps, Movmskps, X86Gp, X86Xmm)                           // SSE2</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   ASMJIT_INST_2x(movmskpd, Movmskpd, X86Gp, X86Xmm)                           // SSE2</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   ASMJIT_INST_2x(movntdq, Movntdq, X86Mem, X86Xmm)                            // SSE2</a>
+<a name="1148"><span class="lineNum">    1148 </span>            :   ASMJIT_INST_2x(movntdqa, Movntdqa, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   ASMJIT_INST_2x(movntpd, Movntpd, X86Mem, X86Xmm)                            // SSE2</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :   ASMJIT_INST_2x(movntps, Movntps, X86Mem, X86Xmm)                            // SSE</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   ASMJIT_INST_2x(movntsd, Movntsd, X86Mem, X86Xmm)                            // SSE4A</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :   ASMJIT_INST_2x(movntss, Movntss, X86Mem, X86Xmm)                            // SSE4A</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   ASMJIT_INST_2x(movntq, Movntq, X86Mem, X86Mm)                               // SSE</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Mm, X86Mm)                                    // MMX</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Xmm, X86Xmm)                                  // SSE</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Mem, X86Mm)                                   // MMX</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Mem, X86Xmm)                                  // SSE</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Mm, X86Mem)                                   // MMX</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Xmm, X86Mem)                                  // SSE</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Gp, X86Mm)                                    // MMX</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Gp, X86Xmm)                                   // SSE+X64.</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Mm, X86Gp)                                    // MMX</a>
+<a name="1163"><span class="lineNum">    1163 </span>            :   ASMJIT_INST_2x(movq, Movq, X86Xmm, X86Gp)                                   // SSE+X64.</a>
+<a name="1164"><span class="lineNum">    1164 </span>            :   ASMJIT_INST_2x(movq2dq, Movq2dq, X86Xmm, X86Mm)                             // SSE2</a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">       8664 :   ASMJIT_INST_2x(movsd, Movsd, X86Xmm, X86Xmm)                                // SSE2</span></a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">       5834 :   ASMJIT_INST_2x(movsd, Movsd, X86Xmm, X86Mem)                                // SSE2</span></a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">        266 :   ASMJIT_INST_2x(movsd, Movsd, X86Mem, X86Xmm)                                // SSE2</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :   ASMJIT_INST_2x(movshdup, Movshdup, X86Xmm, X86Xmm)                          // SSE3</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :   ASMJIT_INST_2x(movshdup, Movshdup, X86Xmm, X86Mem)                          // SSE3</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :   ASMJIT_INST_2x(movsldup, Movsldup, X86Xmm, X86Xmm)                          // SSE3</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :   ASMJIT_INST_2x(movsldup, Movsldup, X86Xmm, X86Mem)                          // SSE3</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :   ASMJIT_INST_2x(movss, Movss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :   ASMJIT_INST_2x(movss, Movss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :   ASMJIT_INST_2x(movss, Movss, X86Mem, X86Xmm)                                // SSE</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :   ASMJIT_INST_2x(movupd, Movupd, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :   ASMJIT_INST_2x(movupd, Movupd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :   ASMJIT_INST_2x(movupd, Movupd, X86Mem, X86Xmm)                              // SSE2</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :   ASMJIT_INST_2x(movups, Movups, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :   ASMJIT_INST_2x(movups, Movups, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1180"><span class="lineNum">    1180 </span>            :   ASMJIT_INST_2x(movups, Movups, X86Mem, X86Xmm)                              // SSE</a>
+<a name="1181"><span class="lineNum">    1181 </span>            :   ASMJIT_INST_3i(mpsadbw, Mpsadbw, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :   ASMJIT_INST_3i(mpsadbw, Mpsadbw, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :   ASMJIT_INST_2x(mulpd, Mulpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :   ASMJIT_INST_2x(mulpd, Mulpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :   ASMJIT_INST_2x(mulps, Mulps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   ASMJIT_INST_2x(mulps, Mulps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">       5200 :   ASMJIT_INST_2x(mulsd, Mulsd, X86Xmm, X86Xmm)                                // SSE2</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :   ASMJIT_INST_2x(mulsd, Mulsd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1189"><span class="lineNum">    1189 </span>            :   ASMJIT_INST_2x(mulss, Mulss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :   ASMJIT_INST_2x(mulss, Mulss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :   ASMJIT_INST_2x(orpd, Orpd, X86Xmm, X86Xmm)                                  // SSE2</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :   ASMJIT_INST_2x(orpd, Orpd, X86Xmm, X86Mem)                                  // SSE2</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :   ASMJIT_INST_2x(orps, Orps, X86Xmm, X86Xmm)                                  // SSE</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :   ASMJIT_INST_2x(orps, Orps, X86Xmm, X86Mem)                                  // SSE</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :   ASMJIT_INST_2x(packssdw, Packssdw, X86Mm, X86Mm)                            // MMX</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :   ASMJIT_INST_2x(packssdw, Packssdw, X86Mm, X86Mem)                           // MMX</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :   ASMJIT_INST_2x(packssdw, Packssdw, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1198"><span class="lineNum">    1198 </span>            :   ASMJIT_INST_2x(packssdw, Packssdw, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1199"><span class="lineNum">    1199 </span>            :   ASMJIT_INST_2x(packsswb, Packsswb, X86Mm, X86Mm)                            // MMX</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :   ASMJIT_INST_2x(packsswb, Packsswb, X86Mm, X86Mem)                           // MMX</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :   ASMJIT_INST_2x(packsswb, Packsswb, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :   ASMJIT_INST_2x(packsswb, Packsswb, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :   ASMJIT_INST_2x(packusdw, Packusdw, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :   ASMJIT_INST_2x(packusdw, Packusdw, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :   ASMJIT_INST_2x(packuswb, Packuswb, X86Mm, X86Mm)                            // MMX</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :   ASMJIT_INST_2x(packuswb, Packuswb, X86Mm, X86Mem)                           // MMX</a>
+<a name="1207"><span class="lineNum">    1207 </span>            :   ASMJIT_INST_2x(packuswb, Packuswb, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   ASMJIT_INST_2x(packuswb, Packuswb, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :   ASMJIT_INST_2x(pabsb, Pabsb, X86Mm, X86Mm)                                  // SSSE3</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :   ASMJIT_INST_2x(pabsb, Pabsb, X86Mm, X86Mem)                                 // SSSE3</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :   ASMJIT_INST_2x(pabsb, Pabsb, X86Xmm, X86Xmm)                                // SSSE3</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :   ASMJIT_INST_2x(pabsb, Pabsb, X86Xmm, X86Mem)                                // SSSE3</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :   ASMJIT_INST_2x(pabsd, Pabsd, X86Mm, X86Mm)                                  // SSSE3</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :   ASMJIT_INST_2x(pabsd, Pabsd, X86Mm, X86Mem)                                 // SSSE3</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :   ASMJIT_INST_2x(pabsd, Pabsd, X86Xmm, X86Xmm)                                // SSSE3</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :   ASMJIT_INST_2x(pabsd, Pabsd, X86Xmm, X86Mem)                                // SSSE3</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   ASMJIT_INST_2x(pabsw, Pabsw, X86Mm, X86Mm)                                  // SSSE3</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   ASMJIT_INST_2x(pabsw, Pabsw, X86Mm, X86Mem)                                 // SSSE3</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   ASMJIT_INST_2x(pabsw, Pabsw, X86Xmm, X86Xmm)                                // SSSE3</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :   ASMJIT_INST_2x(pabsw, Pabsw, X86Xmm, X86Mem)                                // SSSE3</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :   ASMJIT_INST_2x(paddb, Paddb, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   ASMJIT_INST_2x(paddb, Paddb, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   ASMJIT_INST_2x(paddb, Paddb, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :   ASMJIT_INST_2x(paddb, Paddb, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :   ASMJIT_INST_2x(paddd, Paddd, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :   ASMJIT_INST_2x(paddd, Paddd, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1227"><span class="lineNum">    1227 </span>            :   ASMJIT_INST_2x(paddd, Paddd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :   ASMJIT_INST_2x(paddd, Paddd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   ASMJIT_INST_2x(paddq, Paddq, X86Mm, X86Mm)                                  // SSE2</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   ASMJIT_INST_2x(paddq, Paddq, X86Mm, X86Mem)                                 // SSE2</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :   ASMJIT_INST_2x(paddq, Paddq, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   ASMJIT_INST_2x(paddq, Paddq, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :   ASMJIT_INST_2x(paddsb, Paddsb, X86Mm, X86Mm)                                // MMX</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :   ASMJIT_INST_2x(paddsb, Paddsb, X86Mm, X86Mem)                               // MMX</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :   ASMJIT_INST_2x(paddsb, Paddsb, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :   ASMJIT_INST_2x(paddsb, Paddsb, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :   ASMJIT_INST_2x(paddsw, Paddsw, X86Mm, X86Mm)                                // MMX</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :   ASMJIT_INST_2x(paddsw, Paddsw, X86Mm, X86Mem)                               // MMX</a>
+<a name="1239"><span class="lineNum">    1239 </span>            :   ASMJIT_INST_2x(paddsw, Paddsw, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :   ASMJIT_INST_2x(paddsw, Paddsw, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :   ASMJIT_INST_2x(paddusb, Paddusb, X86Mm, X86Mm)                              // MMX</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :   ASMJIT_INST_2x(paddusb, Paddusb, X86Mm, X86Mem)                             // MMX</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :   ASMJIT_INST_2x(paddusb, Paddusb, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :   ASMJIT_INST_2x(paddusb, Paddusb, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :   ASMJIT_INST_2x(paddusw, Paddusw, X86Mm, X86Mm)                              // MMX</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :   ASMJIT_INST_2x(paddusw, Paddusw, X86Mm, X86Mem)                             // MMX</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :   ASMJIT_INST_2x(paddusw, Paddusw, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :   ASMJIT_INST_2x(paddusw, Paddusw, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :   ASMJIT_INST_2x(paddw, Paddw, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1250"><span class="lineNum">    1250 </span>            :   ASMJIT_INST_2x(paddw, Paddw, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :   ASMJIT_INST_2x(paddw, Paddw, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :   ASMJIT_INST_2x(paddw, Paddw, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :   ASMJIT_INST_3i(palignr, Palignr, X86Mm, X86Mm, Imm)                         // SSSE3</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   ASMJIT_INST_3i(palignr, Palignr, X86Mm, X86Mem, Imm)                        // SSSE3</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :   ASMJIT_INST_3i(palignr, Palignr, X86Xmm, X86Xmm, Imm)                       // SSSE3</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :   ASMJIT_INST_3i(palignr, Palignr, X86Xmm, X86Mem, Imm)                       // SSSE3</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :   ASMJIT_INST_2x(pand, Pand, X86Mm, X86Mm)                                    // MMX</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :   ASMJIT_INST_2x(pand, Pand, X86Mm, X86Mem)                                   // MMX</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :   ASMJIT_INST_2x(pand, Pand, X86Xmm, X86Xmm)                                  // SSE2</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   ASMJIT_INST_2x(pand, Pand, X86Xmm, X86Mem)                                  // SSE2</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :   ASMJIT_INST_2x(pandn, Pandn, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   ASMJIT_INST_2x(pandn, Pandn, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1263"><span class="lineNum">    1263 </span>            :   ASMJIT_INST_2x(pandn, Pandn, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :   ASMJIT_INST_2x(pandn, Pandn, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :   ASMJIT_INST_2x(pavgb, Pavgb, X86Mm, X86Mm)                                  // SSE</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   ASMJIT_INST_2x(pavgb, Pavgb, X86Mm, X86Mem)                                 // SSE</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :   ASMJIT_INST_2x(pavgb, Pavgb, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :   ASMJIT_INST_2x(pavgb, Pavgb, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :   ASMJIT_INST_2x(pavgw, Pavgw, X86Mm, X86Mm)                                  // SSE</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :   ASMJIT_INST_2x(pavgw, Pavgw, X86Mm, X86Mem)                                 // SSE</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :   ASMJIT_INST_2x(pavgw, Pavgw, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :   ASMJIT_INST_2x(pavgw, Pavgw, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   ASMJIT_INST_3x(pblendvb, Pblendvb, X86Xmm, X86Xmm, XMM0)                    // SSE4_1 [EXPLICIT]</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :   ASMJIT_INST_3x(pblendvb, Pblendvb, X86Xmm, X86Mem, XMM0)                    // SSE4_1 [EXPLICIT]</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :   ASMJIT_INST_3i(pblendw, Pblendw, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :   ASMJIT_INST_3i(pblendw, Pblendw, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :   ASMJIT_INST_3i(pclmulqdq, Pclmulqdq, X86Xmm, X86Xmm, Imm)                   // PCLMULQDQ.</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :   ASMJIT_INST_3i(pclmulqdq, Pclmulqdq, X86Xmm, X86Mem, Imm)                   // PCLMULQDQ.</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :   ASMJIT_INST_6x(pcmpestri, Pcmpestri, X86Xmm, X86Xmm, Imm, ECX, EAX, EDX)    // SSE4_2 [EXPLICIT]</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :   ASMJIT_INST_6x(pcmpestri, Pcmpestri, X86Xmm, X86Mem, Imm, ECX, EAX, EDX)    // SSE4_2 [EXPLICIT]</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :   ASMJIT_INST_6x(pcmpestrm, Pcmpestrm, X86Xmm, X86Xmm, Imm, XMM0, EAX, EDX)   // SSE4_2 [EXPLICIT]</a>
+<a name="1282"><span class="lineNum">    1282 </span>            :   ASMJIT_INST_6x(pcmpestrm, Pcmpestrm, X86Xmm, X86Mem, Imm, XMM0, EAX, EDX)   // SSE4_2 [EXPLICIT]</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   ASMJIT_INST_2x(pcmpeqb, Pcmpeqb, X86Mm, X86Mm)                              // MMX</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :   ASMJIT_INST_2x(pcmpeqb, Pcmpeqb, X86Mm, X86Mem)                             // MMX</a>
+<a name="1285"><span class="lineNum">    1285 </span>            :   ASMJIT_INST_2x(pcmpeqb, Pcmpeqb, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1286"><span class="lineNum">    1286 </span>            :   ASMJIT_INST_2x(pcmpeqb, Pcmpeqb, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :   ASMJIT_INST_2x(pcmpeqd, Pcmpeqd, X86Mm, X86Mm)                              // MMX</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :   ASMJIT_INST_2x(pcmpeqd, Pcmpeqd, X86Mm, X86Mem)                             // MMX</a>
+<a name="1289"><span class="lineNum">    1289 </span>            :   ASMJIT_INST_2x(pcmpeqd, Pcmpeqd, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :   ASMJIT_INST_2x(pcmpeqd, Pcmpeqd, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :   ASMJIT_INST_2x(pcmpeqq, Pcmpeqq, X86Xmm, X86Xmm)                            // SSE4_1</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :   ASMJIT_INST_2x(pcmpeqq, Pcmpeqq, X86Xmm, X86Mem)                            // SSE4_1</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :   ASMJIT_INST_2x(pcmpeqw, Pcmpeqw, X86Mm, X86Mm)                              // MMX</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :   ASMJIT_INST_2x(pcmpeqw, Pcmpeqw, X86Mm, X86Mem)                             // MMX</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :   ASMJIT_INST_2x(pcmpeqw, Pcmpeqw, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1296"><span class="lineNum">    1296 </span>            :   ASMJIT_INST_2x(pcmpeqw, Pcmpeqw, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1297"><span class="lineNum">    1297 </span>            :   ASMJIT_INST_2x(pcmpgtb, Pcmpgtb, X86Mm, X86Mm)                              // MMX</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :   ASMJIT_INST_2x(pcmpgtb, Pcmpgtb, X86Mm, X86Mem)                             // MMX</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :   ASMJIT_INST_2x(pcmpgtb, Pcmpgtb, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :   ASMJIT_INST_2x(pcmpgtb, Pcmpgtb, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :   ASMJIT_INST_2x(pcmpgtd, Pcmpgtd, X86Mm, X86Mm)                              // MMX</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :   ASMJIT_INST_2x(pcmpgtd, Pcmpgtd, X86Mm, X86Mem)                             // MMX</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :   ASMJIT_INST_2x(pcmpgtd, Pcmpgtd, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :   ASMJIT_INST_2x(pcmpgtd, Pcmpgtd, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :   ASMJIT_INST_2x(pcmpgtq, Pcmpgtq, X86Xmm, X86Xmm)                            // SSE4_2.</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :   ASMJIT_INST_2x(pcmpgtq, Pcmpgtq, X86Xmm, X86Mem)                            // SSE4_2.</a>
+<a name="1307"><span class="lineNum">    1307 </span>            :   ASMJIT_INST_2x(pcmpgtw, Pcmpgtw, X86Mm, X86Mm)                              // MMX</a>
+<a name="1308"><span class="lineNum">    1308 </span>            :   ASMJIT_INST_2x(pcmpgtw, Pcmpgtw, X86Mm, X86Mem)                             // MMX</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :   ASMJIT_INST_2x(pcmpgtw, Pcmpgtw, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   ASMJIT_INST_2x(pcmpgtw, Pcmpgtw, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :   ASMJIT_INST_4x(pcmpistri, Pcmpistri, X86Xmm, X86Xmm, Imm, ECX)              // SSE4_2 [EXPLICIT]</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :   ASMJIT_INST_4x(pcmpistri, Pcmpistri, X86Xmm, X86Mem, Imm, ECX)              // SSE4_2 [EXPLICIT]</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :   ASMJIT_INST_4x(pcmpistrm, Pcmpistrm, X86Xmm, X86Xmm, Imm, XMM0)             // SSE4_2 [EXPLICIT]</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :   ASMJIT_INST_4x(pcmpistrm, Pcmpistrm, X86Xmm, X86Mem, Imm, XMM0)             // SSE4_2 [EXPLICIT]</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :   ASMJIT_INST_3i(pextrb, Pextrb, X86Gp, X86Xmm, Imm)                          // SSE4_1</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :   ASMJIT_INST_3i(pextrb, Pextrb, X86Mem, X86Xmm, Imm)                         // SSE4_1</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :   ASMJIT_INST_3i(pextrd, Pextrd, X86Gp, X86Xmm, Imm)                          // SSE4_1</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :   ASMJIT_INST_3i(pextrd, Pextrd, X86Mem, X86Xmm, Imm)                         // SSE4_1</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :   ASMJIT_INST_3i(pextrq, Pextrq, X86Gp, X86Xmm, Imm)                          // SSE4_1</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :   ASMJIT_INST_3i(pextrq, Pextrq, X86Mem, X86Xmm, Imm)                         // SSE4_1</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :   ASMJIT_INST_3i(pextrw, Pextrw, X86Gp, X86Mm, Imm)                           // SSE</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :   ASMJIT_INST_3i(pextrw, Pextrw, X86Gp, X86Xmm, Imm)                          // SSE2</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :   ASMJIT_INST_3i(pextrw, Pextrw, X86Mem, X86Xmm, Imm)                         // SSE4_1</a>
+<a name="1324"><span class="lineNum">    1324 </span>            :   ASMJIT_INST_2x(phaddd, Phaddd, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :   ASMJIT_INST_2x(phaddd, Phaddd, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :   ASMJIT_INST_2x(phaddd, Phaddd, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   ASMJIT_INST_2x(phaddd, Phaddd, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :   ASMJIT_INST_2x(phaddsw, Phaddsw, X86Mm, X86Mm)                              // SSSE3</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :   ASMJIT_INST_2x(phaddsw, Phaddsw, X86Mm, X86Mem)                             // SSSE3</a>
+<a name="1330"><span class="lineNum">    1330 </span>            :   ASMJIT_INST_2x(phaddsw, Phaddsw, X86Xmm, X86Xmm)                            // SSSE3</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :   ASMJIT_INST_2x(phaddsw, Phaddsw, X86Xmm, X86Mem)                            // SSSE3</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   ASMJIT_INST_2x(phaddw, Phaddw, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :   ASMJIT_INST_2x(phaddw, Phaddw, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1334"><span class="lineNum">    1334 </span>            :   ASMJIT_INST_2x(phaddw, Phaddw, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1335"><span class="lineNum">    1335 </span>            :   ASMJIT_INST_2x(phaddw, Phaddw, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :   ASMJIT_INST_2x(phminposuw, Phminposuw, X86Xmm, X86Xmm)                      // SSE4_1</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   ASMJIT_INST_2x(phminposuw, Phminposuw, X86Xmm, X86Mem)                      // SSE4_1</a>
+<a name="1338"><span class="lineNum">    1338 </span>            :   ASMJIT_INST_2x(phsubd, Phsubd, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1339"><span class="lineNum">    1339 </span>            :   ASMJIT_INST_2x(phsubd, Phsubd, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :   ASMJIT_INST_2x(phsubd, Phsubd, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :   ASMJIT_INST_2x(phsubd, Phsubd, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1342"><span class="lineNum">    1342 </span>            :   ASMJIT_INST_2x(phsubsw, Phsubsw, X86Mm, X86Mm)                              // SSSE3</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :   ASMJIT_INST_2x(phsubsw, Phsubsw, X86Mm, X86Mem)                             // SSSE3</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :   ASMJIT_INST_2x(phsubsw, Phsubsw, X86Xmm, X86Xmm)                            // SSSE3</a>
+<a name="1345"><span class="lineNum">    1345 </span>            :   ASMJIT_INST_2x(phsubsw, Phsubsw, X86Xmm, X86Mem)                            // SSSE3</a>
+<a name="1346"><span class="lineNum">    1346 </span>            :   ASMJIT_INST_2x(phsubw, Phsubw, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :   ASMJIT_INST_2x(phsubw, Phsubw, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :   ASMJIT_INST_2x(phsubw, Phsubw, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :   ASMJIT_INST_2x(phsubw, Phsubw, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :   ASMJIT_INST_3i(pinsrb, Pinsrb, X86Xmm, X86Gp, Imm)                          // SSE4_1</a>
+<a name="1351"><span class="lineNum">    1351 </span>            :   ASMJIT_INST_3i(pinsrb, Pinsrb, X86Xmm, X86Mem, Imm)                         // SSE4_1</a>
+<a name="1352"><span class="lineNum">    1352 </span>            :   ASMJIT_INST_3i(pinsrd, Pinsrd, X86Xmm, X86Gp, Imm)                          // SSE4_1</a>
+<a name="1353"><span class="lineNum">    1353 </span>            :   ASMJIT_INST_3i(pinsrd, Pinsrd, X86Xmm, X86Mem, Imm)                         // SSE4_1</a>
+<a name="1354"><span class="lineNum">    1354 </span>            :   ASMJIT_INST_3i(pinsrq, Pinsrq, X86Xmm, X86Gp, Imm)                          // SSE4_1</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :   ASMJIT_INST_3i(pinsrq, Pinsrq, X86Xmm, X86Mem, Imm)                         // SSE4_1</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :   ASMJIT_INST_3i(pinsrw, Pinsrw, X86Mm, X86Gp, Imm)                           // SSE</a>
+<a name="1357"><span class="lineNum">    1357 </span>            :   ASMJIT_INST_3i(pinsrw, Pinsrw, X86Mm, X86Mem, Imm)                          // SSE</a>
+<a name="1358"><span class="lineNum">    1358 </span>            :   ASMJIT_INST_3i(pinsrw, Pinsrw, X86Xmm, X86Gp, Imm)                          // SSE2</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :   ASMJIT_INST_3i(pinsrw, Pinsrw, X86Xmm, X86Mem, Imm)                         // SSE2</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :   ASMJIT_INST_2x(pmaddubsw, Pmaddubsw, X86Mm, X86Mm)                          // SSSE3</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :   ASMJIT_INST_2x(pmaddubsw, Pmaddubsw, X86Mm, X86Mem)                         // SSSE3</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :   ASMJIT_INST_2x(pmaddubsw, Pmaddubsw, X86Xmm, X86Xmm)                        // SSSE3</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :   ASMJIT_INST_2x(pmaddubsw, Pmaddubsw, X86Xmm, X86Mem)                        // SSSE3</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :   ASMJIT_INST_2x(pmaddwd, Pmaddwd, X86Mm, X86Mm)                              // MMX</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :   ASMJIT_INST_2x(pmaddwd, Pmaddwd, X86Mm, X86Mem)                             // MMX</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :   ASMJIT_INST_2x(pmaddwd, Pmaddwd, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :   ASMJIT_INST_2x(pmaddwd, Pmaddwd, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1368"><span class="lineNum">    1368 </span>            :   ASMJIT_INST_2x(pmaxsb, Pmaxsb, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :   ASMJIT_INST_2x(pmaxsb, Pmaxsb, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :   ASMJIT_INST_2x(pmaxsd, Pmaxsd, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :   ASMJIT_INST_2x(pmaxsd, Pmaxsd, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :   ASMJIT_INST_2x(pmaxsw, Pmaxsw, X86Mm, X86Mm)                                // SSE</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :   ASMJIT_INST_2x(pmaxsw, Pmaxsw, X86Mm, X86Mem)                               // SSE</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :   ASMJIT_INST_2x(pmaxsw, Pmaxsw, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   ASMJIT_INST_2x(pmaxsw, Pmaxsw, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1376"><span class="lineNum">    1376 </span>            :   ASMJIT_INST_2x(pmaxub, Pmaxub, X86Mm, X86Mm)                                // SSE</a>
+<a name="1377"><span class="lineNum">    1377 </span>            :   ASMJIT_INST_2x(pmaxub, Pmaxub, X86Mm, X86Mem)                               // SSE</a>
+<a name="1378"><span class="lineNum">    1378 </span>            :   ASMJIT_INST_2x(pmaxub, Pmaxub, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1379"><span class="lineNum">    1379 </span>            :   ASMJIT_INST_2x(pmaxub, Pmaxub, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1380"><span class="lineNum">    1380 </span>            :   ASMJIT_INST_2x(pmaxud, Pmaxud, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :   ASMJIT_INST_2x(pmaxud, Pmaxud, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1382"><span class="lineNum">    1382 </span>            :   ASMJIT_INST_2x(pmaxuw, Pmaxuw, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1383"><span class="lineNum">    1383 </span>            :   ASMJIT_INST_2x(pmaxuw, Pmaxuw, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :   ASMJIT_INST_2x(pminsb, Pminsb, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1385"><span class="lineNum">    1385 </span>            :   ASMJIT_INST_2x(pminsb, Pminsb, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1386"><span class="lineNum">    1386 </span>            :   ASMJIT_INST_2x(pminsd, Pminsd, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :   ASMJIT_INST_2x(pminsd, Pminsd, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :   ASMJIT_INST_2x(pminsw, Pminsw, X86Mm, X86Mm)                                // SSE</a>
+<a name="1389"><span class="lineNum">    1389 </span>            :   ASMJIT_INST_2x(pminsw, Pminsw, X86Mm, X86Mem)                               // SSE</a>
+<a name="1390"><span class="lineNum">    1390 </span>            :   ASMJIT_INST_2x(pminsw, Pminsw, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1391"><span class="lineNum">    1391 </span>            :   ASMJIT_INST_2x(pminsw, Pminsw, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :   ASMJIT_INST_2x(pminub, Pminub, X86Mm, X86Mm)                                // SSE</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :   ASMJIT_INST_2x(pminub, Pminub, X86Mm, X86Mem)                               // SSE</a>
+<a name="1394"><span class="lineNum">    1394 </span>            :   ASMJIT_INST_2x(pminub, Pminub, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1395"><span class="lineNum">    1395 </span>            :   ASMJIT_INST_2x(pminub, Pminub, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1396"><span class="lineNum">    1396 </span>            :   ASMJIT_INST_2x(pminud, Pminud, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1397"><span class="lineNum">    1397 </span>            :   ASMJIT_INST_2x(pminud, Pminud, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1398"><span class="lineNum">    1398 </span>            :   ASMJIT_INST_2x(pminuw, Pminuw, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1399"><span class="lineNum">    1399 </span>            :   ASMJIT_INST_2x(pminuw, Pminuw, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1400"><span class="lineNum">    1400 </span>            :   ASMJIT_INST_2x(pmovmskb, Pmovmskb, X86Gp, X86Mm)                            // SSE</a>
+<a name="1401"><span class="lineNum">    1401 </span>            :   ASMJIT_INST_2x(pmovmskb, Pmovmskb, X86Gp, X86Xmm)                           // SSE2</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :   ASMJIT_INST_2x(pmovsxbd, Pmovsxbd, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :   ASMJIT_INST_2x(pmovsxbd, Pmovsxbd, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :   ASMJIT_INST_2x(pmovsxbq, Pmovsxbq, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :   ASMJIT_INST_2x(pmovsxbq, Pmovsxbq, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :   ASMJIT_INST_2x(pmovsxbw, Pmovsxbw, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :   ASMJIT_INST_2x(pmovsxbw, Pmovsxbw, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :   ASMJIT_INST_2x(pmovsxdq, Pmovsxdq, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :   ASMJIT_INST_2x(pmovsxdq, Pmovsxdq, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :   ASMJIT_INST_2x(pmovsxwd, Pmovsxwd, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1411"><span class="lineNum">    1411 </span>            :   ASMJIT_INST_2x(pmovsxwd, Pmovsxwd, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1412"><span class="lineNum">    1412 </span>            :   ASMJIT_INST_2x(pmovsxwq, Pmovsxwq, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1413"><span class="lineNum">    1413 </span>            :   ASMJIT_INST_2x(pmovsxwq, Pmovsxwq, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :   ASMJIT_INST_2x(pmovzxbd, Pmovzxbd, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :   ASMJIT_INST_2x(pmovzxbd, Pmovzxbd, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :   ASMJIT_INST_2x(pmovzxbq, Pmovzxbq, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :   ASMJIT_INST_2x(pmovzxbq, Pmovzxbq, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :   ASMJIT_INST_2x(pmovzxbw, Pmovzxbw, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :   ASMJIT_INST_2x(pmovzxbw, Pmovzxbw, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :   ASMJIT_INST_2x(pmovzxdq, Pmovzxdq, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1421"><span class="lineNum">    1421 </span>            :   ASMJIT_INST_2x(pmovzxdq, Pmovzxdq, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :   ASMJIT_INST_2x(pmovzxwd, Pmovzxwd, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1423"><span class="lineNum">    1423 </span>            :   ASMJIT_INST_2x(pmovzxwd, Pmovzxwd, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1424"><span class="lineNum">    1424 </span>            :   ASMJIT_INST_2x(pmovzxwq, Pmovzxwq, X86Xmm, X86Xmm)                          // SSE4_1</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :   ASMJIT_INST_2x(pmovzxwq, Pmovzxwq, X86Xmm, X86Mem)                          // SSE4_1</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :   ASMJIT_INST_2x(pmuldq, Pmuldq, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :   ASMJIT_INST_2x(pmuldq, Pmuldq, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :   ASMJIT_INST_2x(pmulhrsw, Pmulhrsw, X86Mm, X86Mm)                            // SSSE3</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :   ASMJIT_INST_2x(pmulhrsw, Pmulhrsw, X86Mm, X86Mem)                           // SSSE3</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :   ASMJIT_INST_2x(pmulhrsw, Pmulhrsw, X86Xmm, X86Xmm)                          // SSSE3</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :   ASMJIT_INST_2x(pmulhrsw, Pmulhrsw, X86Xmm, X86Mem)                          // SSSE3</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :   ASMJIT_INST_2x(pmulhw, Pmulhw, X86Mm, X86Mm)                                // MMX</a>
+<a name="1433"><span class="lineNum">    1433 </span>            :   ASMJIT_INST_2x(pmulhw, Pmulhw, X86Mm, X86Mem)                               // MMX</a>
+<a name="1434"><span class="lineNum">    1434 </span>            :   ASMJIT_INST_2x(pmulhw, Pmulhw, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :   ASMJIT_INST_2x(pmulhw, Pmulhw, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :   ASMJIT_INST_2x(pmulhuw, Pmulhuw, X86Mm, X86Mm)                              // SSE</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :   ASMJIT_INST_2x(pmulhuw, Pmulhuw, X86Mm, X86Mem)                             // SSE</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :   ASMJIT_INST_2x(pmulhuw, Pmulhuw, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :   ASMJIT_INST_2x(pmulhuw, Pmulhuw, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1440"><span class="lineNum">    1440 </span>            :   ASMJIT_INST_2x(pmulld, Pmulld, X86Xmm, X86Xmm)                              // SSE4_1</a>
+<a name="1441"><span class="lineNum">    1441 </span>            :   ASMJIT_INST_2x(pmulld, Pmulld, X86Xmm, X86Mem)                              // SSE4_1</a>
+<a name="1442"><span class="lineNum">    1442 </span>            :   ASMJIT_INST_2x(pmullw, Pmullw, X86Mm, X86Mm)                                // MMX</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :   ASMJIT_INST_2x(pmullw, Pmullw, X86Mm, X86Mem)                               // MMX</a>
+<a name="1444"><span class="lineNum">    1444 </span>            :   ASMJIT_INST_2x(pmullw, Pmullw, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1445"><span class="lineNum">    1445 </span>            :   ASMJIT_INST_2x(pmullw, Pmullw, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :   ASMJIT_INST_2x(pmuludq, Pmuludq, X86Mm, X86Mm)                              // SSE2</a>
+<a name="1447"><span class="lineNum">    1447 </span>            :   ASMJIT_INST_2x(pmuludq, Pmuludq, X86Mm, X86Mem)                             // SSE2</a>
+<a name="1448"><span class="lineNum">    1448 </span>            :   ASMJIT_INST_2x(pmuludq, Pmuludq, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :   ASMJIT_INST_2x(pmuludq, Pmuludq, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :   ASMJIT_INST_2x(por, Por, X86Mm, X86Mm)                                      // MMX</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :   ASMJIT_INST_2x(por, Por, X86Mm, X86Mem)                                     // MMX</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :   ASMJIT_INST_2x(por, Por, X86Xmm, X86Xmm)                                    // SSE2</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :   ASMJIT_INST_2x(por, Por, X86Xmm, X86Mem)                                    // SSE2</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :   ASMJIT_INST_2x(psadbw, Psadbw, X86Mm, X86Mm)                                // SSE</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :   ASMJIT_INST_2x(psadbw, Psadbw, X86Mm, X86Mem)                               // SSE</a>
+<a name="1456"><span class="lineNum">    1456 </span>            :   ASMJIT_INST_2x(psadbw, Psadbw, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :   ASMJIT_INST_2x(psadbw, Psadbw, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :   ASMJIT_INST_2x(pslld, Pslld, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1459"><span class="lineNum">    1459 </span>            :   ASMJIT_INST_2x(pslld, Pslld, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1460"><span class="lineNum">    1460 </span>            :   ASMJIT_INST_2i(pslld, Pslld, X86Mm, Imm)                                    // MMX</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :   ASMJIT_INST_2x(pslld, Pslld, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :   ASMJIT_INST_2x(pslld, Pslld, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :   ASMJIT_INST_2i(pslld, Pslld, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1464"><span class="lineNum">    1464 </span>            :   ASMJIT_INST_2i(pslldq, Pslldq, X86Xmm, Imm)                                 // SSE2</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :   ASMJIT_INST_2x(psllq, Psllq, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :   ASMJIT_INST_2x(psllq, Psllq, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1467"><span class="lineNum">    1467 </span>            :   ASMJIT_INST_2i(psllq, Psllq, X86Mm, Imm)                                    // MMX</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :   ASMJIT_INST_2x(psllq, Psllq, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1469"><span class="lineNum">    1469 </span>            :   ASMJIT_INST_2x(psllq, Psllq, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :   ASMJIT_INST_2i(psllq, Psllq, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :   ASMJIT_INST_2x(psllw, Psllw, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1472"><span class="lineNum">    1472 </span>            :   ASMJIT_INST_2x(psllw, Psllw, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1473"><span class="lineNum">    1473 </span>            :   ASMJIT_INST_2i(psllw, Psllw, X86Mm, Imm)                                    // MMX</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :   ASMJIT_INST_2x(psllw, Psllw, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :   ASMJIT_INST_2x(psllw, Psllw, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :   ASMJIT_INST_2i(psllw, Psllw, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1477"><span class="lineNum">    1477 </span>            :   ASMJIT_INST_2x(psrad, Psrad, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :   ASMJIT_INST_2x(psrad, Psrad, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :   ASMJIT_INST_2i(psrad, Psrad, X86Mm, Imm)                                    // MMX</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :   ASMJIT_INST_2x(psrad, Psrad, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1481"><span class="lineNum">    1481 </span>            :   ASMJIT_INST_2x(psrad, Psrad, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1482"><span class="lineNum">    1482 </span>            :   ASMJIT_INST_2i(psrad, Psrad, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1483"><span class="lineNum">    1483 </span>            :   ASMJIT_INST_2x(psraw, Psraw, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :   ASMJIT_INST_2x(psraw, Psraw, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :   ASMJIT_INST_2i(psraw, Psraw, X86Mm, Imm)                                    // MMX</a>
+<a name="1486"><span class="lineNum">    1486 </span>            :   ASMJIT_INST_2x(psraw, Psraw, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1487"><span class="lineNum">    1487 </span>            :   ASMJIT_INST_2x(psraw, Psraw, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :   ASMJIT_INST_2i(psraw, Psraw, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :   ASMJIT_INST_2x(pshufb, Pshufb, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :   ASMJIT_INST_2x(pshufb, Pshufb, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1491"><span class="lineNum">    1491 </span>            :   ASMJIT_INST_2x(pshufb, Pshufb, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1492"><span class="lineNum">    1492 </span>            :   ASMJIT_INST_2x(pshufb, Pshufb, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1493"><span class="lineNum">    1493 </span>            :   ASMJIT_INST_3i(pshufd, Pshufd, X86Xmm, X86Xmm, Imm)                         // SSE2</a>
+<a name="1494"><span class="lineNum">    1494 </span>            :   ASMJIT_INST_3i(pshufd, Pshufd, X86Xmm, X86Mem, Imm)                         // SSE2</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :   ASMJIT_INST_3i(pshufhw, Pshufhw, X86Xmm, X86Xmm, Imm)                       // SSE2</a>
+<a name="1496"><span class="lineNum">    1496 </span>            :   ASMJIT_INST_3i(pshufhw, Pshufhw, X86Xmm, X86Mem, Imm)                       // SSE2</a>
+<a name="1497"><span class="lineNum">    1497 </span>            :   ASMJIT_INST_3i(pshuflw, Pshuflw, X86Xmm, X86Xmm, Imm)                       // SSE2</a>
+<a name="1498"><span class="lineNum">    1498 </span>            :   ASMJIT_INST_3i(pshuflw, Pshuflw, X86Xmm, X86Mem, Imm)                       // SSE2</a>
+<a name="1499"><span class="lineNum">    1499 </span>            :   ASMJIT_INST_3i(pshufw, Pshufw, X86Mm, X86Mm, Imm)                           // SSE</a>
+<a name="1500"><span class="lineNum">    1500 </span>            :   ASMJIT_INST_3i(pshufw, Pshufw, X86Mm, X86Mem, Imm)                          // SSE</a>
+<a name="1501"><span class="lineNum">    1501 </span>            :   ASMJIT_INST_2x(psignb, Psignb, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1502"><span class="lineNum">    1502 </span>            :   ASMJIT_INST_2x(psignb, Psignb, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1503"><span class="lineNum">    1503 </span>            :   ASMJIT_INST_2x(psignb, Psignb, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1504"><span class="lineNum">    1504 </span>            :   ASMJIT_INST_2x(psignb, Psignb, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1505"><span class="lineNum">    1505 </span>            :   ASMJIT_INST_2x(psignd, Psignd, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1506"><span class="lineNum">    1506 </span>            :   ASMJIT_INST_2x(psignd, Psignd, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1507"><span class="lineNum">    1507 </span>            :   ASMJIT_INST_2x(psignd, Psignd, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :   ASMJIT_INST_2x(psignd, Psignd, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :   ASMJIT_INST_2x(psignw, Psignw, X86Mm, X86Mm)                                // SSSE3</a>
+<a name="1510"><span class="lineNum">    1510 </span>            :   ASMJIT_INST_2x(psignw, Psignw, X86Mm, X86Mem)                               // SSSE3</a>
+<a name="1511"><span class="lineNum">    1511 </span>            :   ASMJIT_INST_2x(psignw, Psignw, X86Xmm, X86Xmm)                              // SSSE3</a>
+<a name="1512"><span class="lineNum">    1512 </span>            :   ASMJIT_INST_2x(psignw, Psignw, X86Xmm, X86Mem)                              // SSSE3</a>
+<a name="1513"><span class="lineNum">    1513 </span>            :   ASMJIT_INST_2x(psrld, Psrld, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :   ASMJIT_INST_2x(psrld, Psrld, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1515"><span class="lineNum">    1515 </span>            :   ASMJIT_INST_2i(psrld, Psrld, X86Mm, Imm)                                    // MMX</a>
+<a name="1516"><span class="lineNum">    1516 </span>            :   ASMJIT_INST_2x(psrld, Psrld, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1517"><span class="lineNum">    1517 </span>            :   ASMJIT_INST_2x(psrld, Psrld, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :   ASMJIT_INST_2i(psrld, Psrld, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :   ASMJIT_INST_2i(psrldq, Psrldq, X86Xmm, Imm)                                 // SSE2</a>
+<a name="1520"><span class="lineNum">    1520 </span>            :   ASMJIT_INST_2x(psrlq, Psrlq, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :   ASMJIT_INST_2x(psrlq, Psrlq, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1522"><span class="lineNum">    1522 </span>            :   ASMJIT_INST_2i(psrlq, Psrlq, X86Mm, Imm)                                    // MMX</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :   ASMJIT_INST_2x(psrlq, Psrlq, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :   ASMJIT_INST_2x(psrlq, Psrlq, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :   ASMJIT_INST_2i(psrlq, Psrlq, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :   ASMJIT_INST_2x(psrlw, Psrlw, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :   ASMJIT_INST_2x(psrlw, Psrlw, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1528"><span class="lineNum">    1528 </span>            :   ASMJIT_INST_2i(psrlw, Psrlw, X86Mm, Imm)                                    // MMX</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :   ASMJIT_INST_2x(psrlw, Psrlw, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :   ASMJIT_INST_2x(psrlw, Psrlw, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :   ASMJIT_INST_2i(psrlw, Psrlw, X86Xmm, Imm)                                   // SSE2</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :   ASMJIT_INST_2x(psubb, Psubb, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1533"><span class="lineNum">    1533 </span>            :   ASMJIT_INST_2x(psubb, Psubb, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :   ASMJIT_INST_2x(psubb, Psubb, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :   ASMJIT_INST_2x(psubb, Psubb, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1536"><span class="lineNum">    1536 </span>            :   ASMJIT_INST_2x(psubd, Psubd, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1537"><span class="lineNum">    1537 </span>            :   ASMJIT_INST_2x(psubd, Psubd, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1538"><span class="lineNum">    1538 </span>            :   ASMJIT_INST_2x(psubd, Psubd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1539"><span class="lineNum">    1539 </span>            :   ASMJIT_INST_2x(psubd, Psubd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1540"><span class="lineNum">    1540 </span>            :   ASMJIT_INST_2x(psubq, Psubq, X86Mm, X86Mm)                                  // SSE2</a>
+<a name="1541"><span class="lineNum">    1541 </span>            :   ASMJIT_INST_2x(psubq, Psubq, X86Mm, X86Mem)                                 // SSE2</a>
+<a name="1542"><span class="lineNum">    1542 </span>            :   ASMJIT_INST_2x(psubq, Psubq, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :   ASMJIT_INST_2x(psubq, Psubq, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1544"><span class="lineNum">    1544 </span>            :   ASMJIT_INST_2x(psubsb, Psubsb, X86Mm, X86Mm)                                // MMX</a>
+<a name="1545"><span class="lineNum">    1545 </span>            :   ASMJIT_INST_2x(psubsb, Psubsb, X86Mm, X86Mem)                               // MMX</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :   ASMJIT_INST_2x(psubsb, Psubsb, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1547"><span class="lineNum">    1547 </span>            :   ASMJIT_INST_2x(psubsb, Psubsb, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1548"><span class="lineNum">    1548 </span>            :   ASMJIT_INST_2x(psubsw, Psubsw, X86Mm, X86Mm)                                // MMX</a>
+<a name="1549"><span class="lineNum">    1549 </span>            :   ASMJIT_INST_2x(psubsw, Psubsw, X86Mm, X86Mem)                               // MMX</a>
+<a name="1550"><span class="lineNum">    1550 </span>            :   ASMJIT_INST_2x(psubsw, Psubsw, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1551"><span class="lineNum">    1551 </span>            :   ASMJIT_INST_2x(psubsw, Psubsw, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :   ASMJIT_INST_2x(psubusb, Psubusb, X86Mm, X86Mm)                              // MMX</a>
+<a name="1553"><span class="lineNum">    1553 </span>            :   ASMJIT_INST_2x(psubusb, Psubusb, X86Mm, X86Mem)                             // MMX</a>
+<a name="1554"><span class="lineNum">    1554 </span>            :   ASMJIT_INST_2x(psubusb, Psubusb, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1555"><span class="lineNum">    1555 </span>            :   ASMJIT_INST_2x(psubusb, Psubusb, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1556"><span class="lineNum">    1556 </span>            :   ASMJIT_INST_2x(psubusw, Psubusw, X86Mm, X86Mm)                              // MMX</a>
+<a name="1557"><span class="lineNum">    1557 </span>            :   ASMJIT_INST_2x(psubusw, Psubusw, X86Mm, X86Mem)                             // MMX</a>
+<a name="1558"><span class="lineNum">    1558 </span>            :   ASMJIT_INST_2x(psubusw, Psubusw, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1559"><span class="lineNum">    1559 </span>            :   ASMJIT_INST_2x(psubusw, Psubusw, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1560"><span class="lineNum">    1560 </span>            :   ASMJIT_INST_2x(psubw, Psubw, X86Mm, X86Mm)                                  // MMX</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :   ASMJIT_INST_2x(psubw, Psubw, X86Mm, X86Mem)                                 // MMX</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :   ASMJIT_INST_2x(psubw, Psubw, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1563"><span class="lineNum">    1563 </span>            :   ASMJIT_INST_2x(psubw, Psubw, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1564"><span class="lineNum">    1564 </span>            :   ASMJIT_INST_2x(ptest, Ptest, X86Xmm, X86Xmm)                                // SSE4_1</a>
+<a name="1565"><span class="lineNum">    1565 </span>            :   ASMJIT_INST_2x(ptest, Ptest, X86Xmm, X86Mem)                                // SSE4_1</a>
+<a name="1566"><span class="lineNum">    1566 </span>            :   ASMJIT_INST_2x(punpckhbw, Punpckhbw, X86Mm, X86Mm)                          // MMX</a>
+<a name="1567"><span class="lineNum">    1567 </span>            :   ASMJIT_INST_2x(punpckhbw, Punpckhbw, X86Mm, X86Mem)                         // MMX</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :   ASMJIT_INST_2x(punpckhbw, Punpckhbw, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1569"><span class="lineNum">    1569 </span>            :   ASMJIT_INST_2x(punpckhbw, Punpckhbw, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1570"><span class="lineNum">    1570 </span>            :   ASMJIT_INST_2x(punpckhdq, Punpckhdq, X86Mm, X86Mm)                          // MMX</a>
+<a name="1571"><span class="lineNum">    1571 </span>            :   ASMJIT_INST_2x(punpckhdq, Punpckhdq, X86Mm, X86Mem)                         // MMX</a>
+<a name="1572"><span class="lineNum">    1572 </span>            :   ASMJIT_INST_2x(punpckhdq, Punpckhdq, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1573"><span class="lineNum">    1573 </span>            :   ASMJIT_INST_2x(punpckhdq, Punpckhdq, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1574"><span class="lineNum">    1574 </span>            :   ASMJIT_INST_2x(punpckhqdq, Punpckhqdq, X86Xmm, X86Xmm)                      // SSE2</a>
+<a name="1575"><span class="lineNum">    1575 </span>            :   ASMJIT_INST_2x(punpckhqdq, Punpckhqdq, X86Xmm, X86Mem)                      // SSE2</a>
+<a name="1576"><span class="lineNum">    1576 </span>            :   ASMJIT_INST_2x(punpckhwd, Punpckhwd, X86Mm, X86Mm)                          // MMX</a>
+<a name="1577"><span class="lineNum">    1577 </span>            :   ASMJIT_INST_2x(punpckhwd, Punpckhwd, X86Mm, X86Mem)                         // MMX</a>
+<a name="1578"><span class="lineNum">    1578 </span>            :   ASMJIT_INST_2x(punpckhwd, Punpckhwd, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1579"><span class="lineNum">    1579 </span>            :   ASMJIT_INST_2x(punpckhwd, Punpckhwd, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1580"><span class="lineNum">    1580 </span>            :   ASMJIT_INST_2x(punpcklbw, Punpcklbw, X86Mm, X86Mm)                          // MMX</a>
+<a name="1581"><span class="lineNum">    1581 </span>            :   ASMJIT_INST_2x(punpcklbw, Punpcklbw, X86Mm, X86Mem)                         // MMX</a>
+<a name="1582"><span class="lineNum">    1582 </span>            :   ASMJIT_INST_2x(punpcklbw, Punpcklbw, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1583"><span class="lineNum">    1583 </span>            :   ASMJIT_INST_2x(punpcklbw, Punpcklbw, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1584"><span class="lineNum">    1584 </span>            :   ASMJIT_INST_2x(punpckldq, Punpckldq, X86Mm, X86Mm)                          // MMX</a>
+<a name="1585"><span class="lineNum">    1585 </span>            :   ASMJIT_INST_2x(punpckldq, Punpckldq, X86Mm, X86Mem)                         // MMX</a>
+<a name="1586"><span class="lineNum">    1586 </span>            :   ASMJIT_INST_2x(punpckldq, Punpckldq, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1587"><span class="lineNum">    1587 </span>            :   ASMJIT_INST_2x(punpckldq, Punpckldq, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1588"><span class="lineNum">    1588 </span>            :   ASMJIT_INST_2x(punpcklqdq, Punpcklqdq, X86Xmm, X86Xmm)                      // SSE2</a>
+<a name="1589"><span class="lineNum">    1589 </span>            :   ASMJIT_INST_2x(punpcklqdq, Punpcklqdq, X86Xmm, X86Mem)                      // SSE2</a>
+<a name="1590"><span class="lineNum">    1590 </span>            :   ASMJIT_INST_2x(punpcklwd, Punpcklwd, X86Mm, X86Mm)                          // MMX</a>
+<a name="1591"><span class="lineNum">    1591 </span>            :   ASMJIT_INST_2x(punpcklwd, Punpcklwd, X86Mm, X86Mem)                         // MMX</a>
+<a name="1592"><span class="lineNum">    1592 </span>            :   ASMJIT_INST_2x(punpcklwd, Punpcklwd, X86Xmm, X86Xmm)                        // SSE2</a>
+<a name="1593"><span class="lineNum">    1593 </span>            :   ASMJIT_INST_2x(punpcklwd, Punpcklwd, X86Xmm, X86Mem)                        // SSE2</a>
+<a name="1594"><span class="lineNum">    1594 </span>            :   ASMJIT_INST_2x(pxor, Pxor, X86Mm, X86Mm)                                    // MMX</a>
+<a name="1595"><span class="lineNum">    1595 </span>            :   ASMJIT_INST_2x(pxor, Pxor, X86Mm, X86Mem)                                   // MMX</a>
+<a name="1596"><span class="lineNum">    1596 </span>            :   ASMJIT_INST_2x(pxor, Pxor, X86Xmm, X86Xmm)                                  // SSE2</a>
+<a name="1597"><span class="lineNum">    1597 </span>            :   ASMJIT_INST_2x(pxor, Pxor, X86Xmm, X86Mem)                                  // SSE2</a>
+<a name="1598"><span class="lineNum">    1598 </span>            :   ASMJIT_INST_2x(rcpps, Rcpps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1599"><span class="lineNum">    1599 </span>            :   ASMJIT_INST_2x(rcpps, Rcpps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1600"><span class="lineNum">    1600 </span>            :   ASMJIT_INST_2x(rcpss, Rcpss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1601"><span class="lineNum">    1601 </span>            :   ASMJIT_INST_2x(rcpss, Rcpss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1602"><span class="lineNum">    1602 </span>            :   ASMJIT_INST_3i(roundpd, Roundpd, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1603"><span class="lineNum">    1603 </span>            :   ASMJIT_INST_3i(roundpd, Roundpd, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1604"><span class="lineNum">    1604 </span>            :   ASMJIT_INST_3i(roundps, Roundps, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :   ASMJIT_INST_3i(roundps, Roundps, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1606"><span class="lineNum">    1606 </span>            :   ASMJIT_INST_3i(roundsd, Roundsd, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1607"><span class="lineNum">    1607 </span>            :   ASMJIT_INST_3i(roundsd, Roundsd, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1608"><span class="lineNum">    1608 </span>            :   ASMJIT_INST_3i(roundss, Roundss, X86Xmm, X86Xmm, Imm)                       // SSE4_1</a>
+<a name="1609"><span class="lineNum">    1609 </span>            :   ASMJIT_INST_3i(roundss, Roundss, X86Xmm, X86Mem, Imm)                       // SSE4_1</a>
+<a name="1610"><span class="lineNum">    1610 </span>            :   ASMJIT_INST_2x(rsqrtps, Rsqrtps, X86Xmm, X86Xmm)                            // SSE</a>
+<a name="1611"><span class="lineNum">    1611 </span>            :   ASMJIT_INST_2x(rsqrtps, Rsqrtps, X86Xmm, X86Mem)                            // SSE</a>
+<a name="1612"><span class="lineNum">    1612 </span>            :   ASMJIT_INST_2x(rsqrtss, Rsqrtss, X86Xmm, X86Xmm)                            // SSE</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :   ASMJIT_INST_2x(rsqrtss, Rsqrtss, X86Xmm, X86Mem)                            // SSE</a>
+<a name="1614"><span class="lineNum">    1614 </span>            :   ASMJIT_INST_3i(shufpd, Shufpd, X86Xmm, X86Xmm, Imm)                         // SSE2</a>
+<a name="1615"><span class="lineNum">    1615 </span>            :   ASMJIT_INST_3i(shufpd, Shufpd, X86Xmm, X86Mem, Imm)                         // SSE2</a>
+<a name="1616"><span class="lineNum">    1616 </span>            :   ASMJIT_INST_3i(shufps, Shufps, X86Xmm, X86Xmm, Imm)                         // SSE</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :   ASMJIT_INST_3i(shufps, Shufps, X86Xmm, X86Mem, Imm)                         // SSE</a>
+<a name="1618"><span class="lineNum">    1618 </span>            :   ASMJIT_INST_2x(sqrtpd, Sqrtpd, X86Xmm, X86Xmm)                              // SSE2</a>
+<a name="1619"><span class="lineNum">    1619 </span>            :   ASMJIT_INST_2x(sqrtpd, Sqrtpd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1620"><span class="lineNum">    1620 </span>            :   ASMJIT_INST_2x(sqrtps, Sqrtps, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="1621"><span class="lineNum">    1621 </span>            :   ASMJIT_INST_2x(sqrtps, Sqrtps, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1622"><span class="lineNum">    1622 </span><span class="lineCov">        126 :   ASMJIT_INST_2x(sqrtsd, Sqrtsd, X86Xmm, X86Xmm)                              // SSE2</span></a>
+<a name="1623"><span class="lineNum">    1623 </span>            :   ASMJIT_INST_2x(sqrtsd, Sqrtsd, X86Xmm, X86Mem)                              // SSE2</a>
+<a name="1624"><span class="lineNum">    1624 </span>            :   ASMJIT_INST_2x(sqrtss, Sqrtss, X86Xmm, X86Xmm)                              // SSE</a>
+<a name="1625"><span class="lineNum">    1625 </span>            :   ASMJIT_INST_2x(sqrtss, Sqrtss, X86Xmm, X86Mem)                              // SSE</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :   ASMJIT_INST_2x(subpd, Subpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1627"><span class="lineNum">    1627 </span>            :   ASMJIT_INST_2x(subpd, Subpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :   ASMJIT_INST_2x(subps, Subps, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :   ASMJIT_INST_2x(subps, Subps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineCov">        990 :   ASMJIT_INST_2x(subsd, Subsd, X86Xmm, X86Xmm)                                // SSE2</span></a>
+<a name="1631"><span class="lineNum">    1631 </span>            :   ASMJIT_INST_2x(subsd, Subsd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1632"><span class="lineNum">    1632 </span>            :   ASMJIT_INST_2x(subss, Subss, X86Xmm, X86Xmm)                                // SSE</a>
+<a name="1633"><span class="lineNum">    1633 </span>            :   ASMJIT_INST_2x(subss, Subss, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1634"><span class="lineNum">    1634 </span>            :   ASMJIT_INST_2x(ucomisd, Ucomisd, X86Xmm, X86Xmm)                            // SSE2</a>
+<a name="1635"><span class="lineNum">    1635 </span>            :   ASMJIT_INST_2x(ucomisd, Ucomisd, X86Xmm, X86Mem)                            // SSE2</a>
+<a name="1636"><span class="lineNum">    1636 </span>            :   ASMJIT_INST_2x(ucomiss, Ucomiss, X86Xmm, X86Xmm)                            // SSE</a>
+<a name="1637"><span class="lineNum">    1637 </span>            :   ASMJIT_INST_2x(ucomiss, Ucomiss, X86Xmm, X86Mem)                            // SSE</a>
+<a name="1638"><span class="lineNum">    1638 </span>            :   ASMJIT_INST_2x(unpckhpd, Unpckhpd, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1639"><span class="lineNum">    1639 </span>            :   ASMJIT_INST_2x(unpckhpd, Unpckhpd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1640"><span class="lineNum">    1640 </span>            :   ASMJIT_INST_2x(unpckhps, Unpckhps, X86Xmm, X86Xmm)                          // SSE</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :   ASMJIT_INST_2x(unpckhps, Unpckhps, X86Xmm, X86Mem)                          // SSE</a>
+<a name="1642"><span class="lineNum">    1642 </span>            :   ASMJIT_INST_2x(unpcklpd, Unpcklpd, X86Xmm, X86Xmm)                          // SSE2</a>
+<a name="1643"><span class="lineNum">    1643 </span>            :   ASMJIT_INST_2x(unpcklpd, Unpcklpd, X86Xmm, X86Mem)                          // SSE2</a>
+<a name="1644"><span class="lineNum">    1644 </span>            :   ASMJIT_INST_2x(unpcklps, Unpcklps, X86Xmm, X86Xmm)                          // SSE</a>
+<a name="1645"><span class="lineNum">    1645 </span>            :   ASMJIT_INST_2x(unpcklps, Unpcklps, X86Xmm, X86Mem)                          // SSE</a>
+<a name="1646"><span class="lineNum">    1646 </span>            :   ASMJIT_INST_2x(xorpd, Xorpd, X86Xmm, X86Xmm)                                // SSE2</a>
+<a name="1647"><span class="lineNum">    1647 </span>            :   ASMJIT_INST_2x(xorpd, Xorpd, X86Xmm, X86Mem)                                // SSE2</a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">        248 :   ASMJIT_INST_2x(xorps, Xorps, X86Xmm, X86Xmm)                                // SSE</span></a>
+<a name="1649"><span class="lineNum">    1649 </span>            :   ASMJIT_INST_2x(xorps, Xorps, X86Xmm, X86Mem)                                // SSE</a>
+<a name="1650"><span class="lineNum">    1650 </span>            : </a>
+<a name="1651"><span class="lineNum">    1651 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="1652"><span class="lineNum">    1652 </span>            :   // [3DNOW &amp; GEODE]</a>
+<a name="1653"><span class="lineNum">    1653 </span>            :   // -------------------------------------------------------------------------</a>
+<a name="1654"><span class="lineNum">    1654 </span>            : </a>
+<a name="1655"><span class="lineNum">    1655 </span>            :   ASMJIT_INST_2x(pavgusb, Pavgusb, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1656"><span class="lineNum">    1656 </span>            :   ASMJIT_INST_2x(pavgusb, Pavgusb, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1657"><span class="lineNum">    1657 </span>            :   ASMJIT_INST_2x(pf2id, Pf2id, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1658"><span class="lineNum">    1658 </span>            :   ASMJIT_INST_2x(pf2id, Pf2id, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1659"><span class="lineNum">    1659 </span>            :   ASMJIT_INST_2x(pf2iw, Pf2iw, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1660"><span class="lineNum">    1660 </span>            :   ASMJIT_INST_2x(pf2iw, Pf2iw, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1661"><span class="lineNum">    1661 </span>            :   ASMJIT_INST_2x(pfacc, Pfacc, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1662"><span class="lineNum">    1662 </span>            :   ASMJIT_INST_2x(pfacc, Pfacc, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1663"><span class="lineNum">    1663 </span>            :   ASMJIT_INST_2x(pfadd, Pfadd, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1664"><span class="lineNum">    1664 </span>            :   ASMJIT_INST_2x(pfadd, Pfadd, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1665"><span class="lineNum">    1665 </span>            :   ASMJIT_INST_2x(pfcmpeq, Pfcmpeq, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1666"><span class="lineNum">    1666 </span>            :   ASMJIT_INST_2x(pfcmpeq, Pfcmpeq, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1667"><span class="lineNum">    1667 </span>            :   ASMJIT_INST_2x(pfcmpge, Pfcmpge, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1668"><span class="lineNum">    1668 </span>            :   ASMJIT_INST_2x(pfcmpge, Pfcmpge, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1669"><span class="lineNum">    1669 </span>            :   ASMJIT_INST_2x(pfcmpgt, Pfcmpgt, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1670"><span class="lineNum">    1670 </span>            :   ASMJIT_INST_2x(pfcmpgt, Pfcmpgt, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1671"><span class="lineNum">    1671 </span>            :   ASMJIT_INST_2x(pfmax, Pfmax, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1672"><span class="lineNum">    1672 </span>            :   ASMJIT_INST_2x(pfmax, Pfmax, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1673"><span class="lineNum">    1673 </span>            :   ASMJIT_INST_2x(pfmin, Pfmin, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1674"><span class="lineNum">    1674 </span>            :   ASMJIT_INST_2x(pfmin, Pfmin, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1675"><span class="lineNum">    1675 </span>            :   ASMJIT_INST_2x(pfmul, Pfmul, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1676"><span class="lineNum">    1676 </span>            :   ASMJIT_INST_2x(pfmul, Pfmul, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1677"><span class="lineNum">    1677 </span>            :   ASMJIT_INST_2x(pfnacc, Pfnacc, X86Mm, X86Mm)                                // 3DNOW</a>
+<a name="1678"><span class="lineNum">    1678 </span>            :   ASMJIT_INST_2x(pfnacc, Pfnacc, X86Mm, X86Mem)                               // 3DNOW</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :   ASMJIT_INST_2x(pfpnacc, Pfpnacc, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :   ASMJIT_INST_2x(pfpnacc, Pfpnacc, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1681"><span class="lineNum">    1681 </span>            :   ASMJIT_INST_2x(pfrcp, Pfrcp, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1682"><span class="lineNum">    1682 </span>            :   ASMJIT_INST_2x(pfrcp, Pfrcp, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1683"><span class="lineNum">    1683 </span>            :   ASMJIT_INST_2x(pfrcpit1, Pfrcpit1, X86Mm, X86Mm)                            // 3DNOW</a>
+<a name="1684"><span class="lineNum">    1684 </span>            :   ASMJIT_INST_2x(pfrcpit1, Pfrcpit1, X86Mm, X86Mem)                           // 3DNOW</a>
+<a name="1685"><span class="lineNum">    1685 </span>            :   ASMJIT_INST_2x(pfrcpit2, Pfrcpit2, X86Mm, X86Mm)                            // 3DNOW</a>
+<a name="1686"><span class="lineNum">    1686 </span>            :   ASMJIT_INST_2x(pfrcpit2, Pfrcpit2, X86Mm, X86Mem)                           // 3DNOW</a>
+<a name="1687"><span class="lineNum">    1687 </span>            :   ASMJIT_INST_2x(pfrcpv, Pfrcpv, X86Mm, X86Mm)                                // GEODE</a>
+<a name="1688"><span class="lineNum">    1688 </span>            :   ASMJIT_INST_2x(pfrcpv, Pfrcpv, X86Mm, X86Mem)                               // GEODE</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :   ASMJIT_INST_2x(pfrsqit1, Pfrsqit1, X86Mm, X86Mm)                            // 3DNOW</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :   ASMJIT_INST_2x(pfrsqit1, Pfrsqit1, X86Mm, X86Mem)                           // 3DNOW</a>
+<a name="1691"><span class="lineNum">    1691 </span>            :   ASMJIT_INST_2x(pfrsqrt, Pfrsqrt, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1692"><span class="lineNum">    1692 </span>            :   ASMJIT_INST_2x(pfrsqrt, Pfrsqrt, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :   ASMJIT_INST_2x(pfrsqrtv, Pfrsqrtv, X86Mm, X86Mm)                            // GEODE</a>
+<a name="1694"><span class="lineNum">    1694 </span>            :   ASMJIT_INST_2x(pfrsqrtv, Pfrsqrtv, X86Mm, X86Mem)                           // GEODE</a>
+<a name="1695"><span class="lineNum">    1695 </span>            :   ASMJIT_INST_2x(pfsub, Pfsub, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1696"><span class="lineNum">    1696 </span>            :   ASMJIT_INST_2x(pfsub, Pfsub, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1697"><span class="lineNum">    1697 </span>            :   ASMJIT_INST_2x(pfsubr, Pfsubr, X86Mm, X86Mm)                                // 3DNOW</a>
+<a name="1698"><span class="lineNum">    1698 </span>            :   ASMJIT_INST_2x(pfsubr, Pfsubr, X86Mm, X86Mem)                               // 3DNOW</a>
+<a name="1699"><span class="lineNum">    1699 </span>            :   ASMJIT_INST_2x(pi2fd, Pi2fd, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1700"><span class="lineNum">    1700 </span>            :   ASMJIT_INST_2x(pi2fd, Pi2fd, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1701"><span class="lineNum">    1701 </span>            :   ASMJIT_INST_2x(pi2fw, Pi2fw, X86Mm, X86Mm)                                  // 3DNOW</a>
+<a name="1702"><span class="lineNum">    1702 </span>            :   ASMJIT_INST_2x(pi2fw, Pi2fw, X86Mm, X86Mem)                                 // 3DNOW</a>
+<a name="1703"><span class="lineNum">    1703 </span>            :   ASMJIT_INST_2x(pmulhrw, Pmulhrw, X86Mm, X86Mm)                              // 3DNOW</a>
+<a name="1704"><span class="lineNum">    1704 </span>            :   ASMJIT_INST_2x(pmulhrw, Pmulhrw, X86Mm, X86Mem)                             // 3DNOW</a>
+<a name="1705"><span class="lineNum">    1705 </span>            :   ASMJIT_INST_2x(pswapd, Pswapd, X86Mm, X86Mm)                                // 3DNOW</a>
+<a name="1706"><span class="lineNum">    1706 </span>            :   ASMJIT_INST_2x(pswapd, Pswapd, X86Mm, X86Mem)                               // 3DNOW</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :   ASMJIT_INST_0x(femms, Femms)                                                // 3DNOW</a>
+<a name="1708"><span class="lineNum">    1708 </span>            : </a>
+<a name="1709"><span class="lineNum">    1709 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1710"><span class="lineNum">    1710 </span>            :   // [AESNI]</a>
+<a name="1711"><span class="lineNum">    1711 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1712"><span class="lineNum">    1712 </span>            : </a>
+<a name="1713"><span class="lineNum">    1713 </span>            :   ASMJIT_INST_2x(aesdec, Aesdec, X86Xmm, X86Xmm)                              // AESNI</a>
+<a name="1714"><span class="lineNum">    1714 </span>            :   ASMJIT_INST_2x(aesdec, Aesdec, X86Xmm, X86Mem)                              // AESNI</a>
+<a name="1715"><span class="lineNum">    1715 </span>            :   ASMJIT_INST_2x(aesdeclast, Aesdeclast, X86Xmm, X86Xmm)                      // AESNI</a>
+<a name="1716"><span class="lineNum">    1716 </span>            :   ASMJIT_INST_2x(aesdeclast, Aesdeclast, X86Xmm, X86Mem)                      // AESNI</a>
+<a name="1717"><span class="lineNum">    1717 </span>            :   ASMJIT_INST_2x(aesenc, Aesenc, X86Xmm, X86Xmm)                              // AESNI</a>
+<a name="1718"><span class="lineNum">    1718 </span>            :   ASMJIT_INST_2x(aesenc, Aesenc, X86Xmm, X86Mem)                              // AESNI</a>
+<a name="1719"><span class="lineNum">    1719 </span>            :   ASMJIT_INST_2x(aesenclast, Aesenclast, X86Xmm, X86Xmm)                      // AESNI</a>
+<a name="1720"><span class="lineNum">    1720 </span>            :   ASMJIT_INST_2x(aesenclast, Aesenclast, X86Xmm, X86Mem)                      // AESNI</a>
+<a name="1721"><span class="lineNum">    1721 </span>            :   ASMJIT_INST_2x(aesimc, Aesimc, X86Xmm, X86Xmm)                              // AESNI</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :   ASMJIT_INST_2x(aesimc, Aesimc, X86Xmm, X86Mem)                              // AESNI</a>
+<a name="1723"><span class="lineNum">    1723 </span>            :   ASMJIT_INST_3i(aeskeygenassist, Aeskeygenassist, X86Xmm, X86Xmm, Imm)       // AESNI</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :   ASMJIT_INST_3i(aeskeygenassist, Aeskeygenassist, X86Xmm, X86Mem, Imm)       // AESNI</a>
+<a name="1725"><span class="lineNum">    1725 </span>            : </a>
+<a name="1726"><span class="lineNum">    1726 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1727"><span class="lineNum">    1727 </span>            :   // [SHA]</a>
+<a name="1728"><span class="lineNum">    1728 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1729"><span class="lineNum">    1729 </span>            : </a>
+<a name="1730"><span class="lineNum">    1730 </span>            :   ASMJIT_INST_2x(sha1msg1, Sha1msg1, X86Xmm, X86Xmm)                          // SHA</a>
+<a name="1731"><span class="lineNum">    1731 </span>            :   ASMJIT_INST_2x(sha1msg1, Sha1msg1, X86Xmm, X86Mem)                          // SHA</a>
+<a name="1732"><span class="lineNum">    1732 </span>            :   ASMJIT_INST_2x(sha1msg2, Sha1msg2, X86Xmm, X86Xmm)                          // SHA</a>
+<a name="1733"><span class="lineNum">    1733 </span>            :   ASMJIT_INST_2x(sha1msg2, Sha1msg2, X86Xmm, X86Mem)                          // SHA</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :   ASMJIT_INST_2x(sha1nexte, Sha1nexte, X86Xmm, X86Xmm)                        // SHA</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :   ASMJIT_INST_2x(sha1nexte, Sha1nexte, X86Xmm, X86Mem)                        // SHA</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :   ASMJIT_INST_3i(sha1rnds4, Sha1rnds4, X86Xmm, X86Xmm, Imm)                   // SHA</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :   ASMJIT_INST_3i(sha1rnds4, Sha1rnds4, X86Xmm, X86Mem, Imm)                   // SHA</a>
+<a name="1738"><span class="lineNum">    1738 </span>            :   ASMJIT_INST_2x(sha256msg1, Sha256msg1, X86Xmm, X86Xmm)                      // SHA</a>
+<a name="1739"><span class="lineNum">    1739 </span>            :   ASMJIT_INST_2x(sha256msg1, Sha256msg1, X86Xmm, X86Mem)                      // SHA</a>
+<a name="1740"><span class="lineNum">    1740 </span>            :   ASMJIT_INST_2x(sha256msg2, Sha256msg2, X86Xmm, X86Xmm)                      // SHA</a>
+<a name="1741"><span class="lineNum">    1741 </span>            :   ASMJIT_INST_2x(sha256msg2, Sha256msg2, X86Xmm, X86Mem)                      // SHA</a>
+<a name="1742"><span class="lineNum">    1742 </span>            :   ASMJIT_INST_3x(sha256rnds2, Sha256rnds2, X86Xmm, X86Xmm, XMM0)              // SHA [EXPLICIT]</a>
+<a name="1743"><span class="lineNum">    1743 </span>            :   ASMJIT_INST_3x(sha256rnds2, Sha256rnds2, X86Xmm, X86Mem, XMM0)              // SHA [EXPLICIT]</a>
+<a name="1744"><span class="lineNum">    1744 </span>            : </a>
+<a name="1745"><span class="lineNum">    1745 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1746"><span class="lineNum">    1746 </span>            :   // [AVX...AVX512]</a>
+<a name="1747"><span class="lineNum">    1747 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1748"><span class="lineNum">    1748 </span>            : </a>
+<a name="1749"><span class="lineNum">    1749 </span>            :   ASMJIT_INST_3x(kaddb, Kaddb, X86KReg, X86KReg, X86KReg)                     // AVX512_DQ</a>
+<a name="1750"><span class="lineNum">    1750 </span>            :   ASMJIT_INST_3x(kaddd, Kaddd, X86KReg, X86KReg, X86KReg)                     // AVX512_BW</a>
+<a name="1751"><span class="lineNum">    1751 </span>            :   ASMJIT_INST_3x(kaddq, Kaddq, X86KReg, X86KReg, X86KReg)                     // AVX512_BW</a>
+<a name="1752"><span class="lineNum">    1752 </span>            :   ASMJIT_INST_3x(kaddw, Kaddw, X86KReg, X86KReg, X86KReg)                     // AVX512_DQ</a>
+<a name="1753"><span class="lineNum">    1753 </span>            :   ASMJIT_INST_3x(kandb, Kandb, X86KReg, X86KReg, X86KReg)                     // AVX512_DQ</a>
+<a name="1754"><span class="lineNum">    1754 </span>            :   ASMJIT_INST_3x(kandd, Kandd, X86KReg, X86KReg, X86KReg)                     // AVX512_BW</a>
+<a name="1755"><span class="lineNum">    1755 </span>            :   ASMJIT_INST_3x(kandnb, Kandnb, X86KReg, X86KReg, X86KReg)                   // AVX512_DQ</a>
+<a name="1756"><span class="lineNum">    1756 </span>            :   ASMJIT_INST_3x(kandnd, Kandnd, X86KReg, X86KReg, X86KReg)                   // AVX512_BW</a>
+<a name="1757"><span class="lineNum">    1757 </span>            :   ASMJIT_INST_3x(kandnq, Kandnq, X86KReg, X86KReg, X86KReg)                   // AVX512_BW</a>
+<a name="1758"><span class="lineNum">    1758 </span>            :   ASMJIT_INST_3x(kandnw, Kandnw, X86KReg, X86KReg, X86KReg)                   // AVX512_F</a>
+<a name="1759"><span class="lineNum">    1759 </span>            :   ASMJIT_INST_3x(kandq, Kandq, X86KReg, X86KReg, X86KReg)                     // AVX512_BW</a>
+<a name="1760"><span class="lineNum">    1760 </span>            :   ASMJIT_INST_3x(kandw, Kandw, X86KReg, X86KReg, X86KReg)                     // AVX512_F</a>
+<a name="1761"><span class="lineNum">    1761 </span>            :   ASMJIT_INST_2x(kmovb, Kmovb, X86KReg, X86KReg)                              // AVX512_DQ</a>
+<a name="1762"><span class="lineNum">    1762 </span>            :   ASMJIT_INST_2x(kmovb, Kmovb, X86KReg, X86Mem)                               // AVX512_DQ</a>
+<a name="1763"><span class="lineNum">    1763 </span>            :   ASMJIT_INST_2x(kmovb, Kmovb, X86KReg, X86Gp)                                // AVX512_DQ</a>
+<a name="1764"><span class="lineNum">    1764 </span>            :   ASMJIT_INST_2x(kmovb, Kmovb, X86Mem, X86KReg)                               // AVX512_DQ</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :   ASMJIT_INST_2x(kmovb, Kmovb, X86Gp, X86KReg)                                // AVX512_DQ</a>
+<a name="1766"><span class="lineNum">    1766 </span>            :   ASMJIT_INST_2x(kmovd, Kmovd, X86KReg, X86KReg)                              // AVX512_BW</a>
+<a name="1767"><span class="lineNum">    1767 </span>            :   ASMJIT_INST_2x(kmovd, Kmovd, X86KReg, X86Mem)                               // AVX512_BW</a>
+<a name="1768"><span class="lineNum">    1768 </span>            :   ASMJIT_INST_2x(kmovd, Kmovd, X86KReg, X86Gp)                                // AVX512_BW</a>
+<a name="1769"><span class="lineNum">    1769 </span>            :   ASMJIT_INST_2x(kmovd, Kmovd, X86Mem, X86KReg)                               // AVX512_BW</a>
+<a name="1770"><span class="lineNum">    1770 </span>            :   ASMJIT_INST_2x(kmovd, Kmovd, X86Gp, X86KReg)                                // AVX512_BW</a>
+<a name="1771"><span class="lineNum">    1771 </span>            :   ASMJIT_INST_2x(kmovq, Kmovq, X86KReg, X86KReg)                              // AVX512_BW</a>
+<a name="1772"><span class="lineNum">    1772 </span>            :   ASMJIT_INST_2x(kmovq, Kmovq, X86KReg, X86Mem)                               // AVX512_BW</a>
+<a name="1773"><span class="lineNum">    1773 </span>            :   ASMJIT_INST_2x(kmovq, Kmovq, X86KReg, X86Gp)                                // AVX512_BW</a>
+<a name="1774"><span class="lineNum">    1774 </span>            :   ASMJIT_INST_2x(kmovq, Kmovq, X86Mem, X86KReg)                               // AVX512_BW</a>
+<a name="1775"><span class="lineNum">    1775 </span>            :   ASMJIT_INST_2x(kmovq, Kmovq, X86Gp, X86KReg)                                // AVX512_BW</a>
+<a name="1776"><span class="lineNum">    1776 </span>            :   ASMJIT_INST_2x(kmovw, Kmovw, X86KReg, X86KReg)                              // AVX512_F</a>
+<a name="1777"><span class="lineNum">    1777 </span>            :   ASMJIT_INST_2x(kmovw, Kmovw, X86KReg, X86Mem)                               // AVX512_F</a>
+<a name="1778"><span class="lineNum">    1778 </span>            :   ASMJIT_INST_2x(kmovw, Kmovw, X86KReg, X86Gp)                                // AVX512_F</a>
+<a name="1779"><span class="lineNum">    1779 </span>            :   ASMJIT_INST_2x(kmovw, Kmovw, X86Mem, X86KReg)                               // AVX512_F</a>
+<a name="1780"><span class="lineNum">    1780 </span>            :   ASMJIT_INST_2x(kmovw, Kmovw, X86Gp, X86KReg)                                // AVX512_F</a>
+<a name="1781"><span class="lineNum">    1781 </span>            :   ASMJIT_INST_2x(knotb, Knotb, X86KReg, X86KReg)                              // AVX512_DQ</a>
+<a name="1782"><span class="lineNum">    1782 </span>            :   ASMJIT_INST_2x(knotd, Knotd, X86KReg, X86KReg)                              // AVX512_BW</a>
+<a name="1783"><span class="lineNum">    1783 </span>            :   ASMJIT_INST_2x(knotq, Knotq, X86KReg, X86KReg)                              // AVX512_BW</a>
+<a name="1784"><span class="lineNum">    1784 </span>            :   ASMJIT_INST_2x(knotw, Knotw, X86KReg, X86KReg)                              // AVX512_F</a>
+<a name="1785"><span class="lineNum">    1785 </span>            :   ASMJIT_INST_3x(korb, Korb, X86KReg, X86KReg, X86KReg)                       // AVX512_DQ</a>
+<a name="1786"><span class="lineNum">    1786 </span>            :   ASMJIT_INST_3x(kord, Kord, X86KReg, X86KReg, X86KReg)                       // AVX512_BW</a>
+<a name="1787"><span class="lineNum">    1787 </span>            :   ASMJIT_INST_3x(korq, Korq, X86KReg, X86KReg, X86KReg)                       // AVX512_BW</a>
+<a name="1788"><span class="lineNum">    1788 </span>            :   ASMJIT_INST_2x(kortestb, Kortestb, X86KReg, X86KReg)                        // AVX512_DQ</a>
+<a name="1789"><span class="lineNum">    1789 </span>            :   ASMJIT_INST_2x(kortestd, Kortestd, X86KReg, X86KReg)                        // AVX512_BW</a>
+<a name="1790"><span class="lineNum">    1790 </span>            :   ASMJIT_INST_2x(kortestq, Kortestq, X86KReg, X86KReg)                        // AVX512_BW</a>
+<a name="1791"><span class="lineNum">    1791 </span>            :   ASMJIT_INST_2x(kortestw, Kortestw, X86KReg, X86KReg)                        // AVX512_F</a>
+<a name="1792"><span class="lineNum">    1792 </span>            :   ASMJIT_INST_3x(korw, Korw, X86KReg, X86KReg, X86KReg)                       // AVX512_F</a>
+<a name="1793"><span class="lineNum">    1793 </span>            :   ASMJIT_INST_3i(kshiftlb, Kshiftlb, X86KReg, X86KReg, Imm)                   // AVX512_DQ</a>
+<a name="1794"><span class="lineNum">    1794 </span>            :   ASMJIT_INST_3i(kshiftld, Kshiftld, X86KReg, X86KReg, Imm)                   // AVX512_BW</a>
+<a name="1795"><span class="lineNum">    1795 </span>            :   ASMJIT_INST_3i(kshiftlq, Kshiftlq, X86KReg, X86KReg, Imm)                   // AVX512_BW</a>
+<a name="1796"><span class="lineNum">    1796 </span>            :   ASMJIT_INST_3i(kshiftlw, Kshiftlw, X86KReg, X86KReg, Imm)                   // AVX512_F</a>
+<a name="1797"><span class="lineNum">    1797 </span>            :   ASMJIT_INST_3i(kshiftrb, Kshiftrb, X86KReg, X86KReg, Imm)                   // AVX512_DQ</a>
+<a name="1798"><span class="lineNum">    1798 </span>            :   ASMJIT_INST_3i(kshiftrd, Kshiftrd, X86KReg, X86KReg, Imm)                   // AVX512_BW</a>
+<a name="1799"><span class="lineNum">    1799 </span>            :   ASMJIT_INST_3i(kshiftrq, Kshiftrq, X86KReg, X86KReg, Imm)                   // AVX512_BW</a>
+<a name="1800"><span class="lineNum">    1800 </span>            :   ASMJIT_INST_3i(kshiftrw, Kshiftrw, X86KReg, X86KReg, Imm)                   // AVX512_F</a>
+<a name="1801"><span class="lineNum">    1801 </span>            :   ASMJIT_INST_2x(ktestb, Ktestb, X86KReg, X86KReg)                            // AVX512_DQ</a>
+<a name="1802"><span class="lineNum">    1802 </span>            :   ASMJIT_INST_2x(ktestd, Ktestd, X86KReg, X86KReg)                            // AVX512_BW</a>
+<a name="1803"><span class="lineNum">    1803 </span>            :   ASMJIT_INST_2x(ktestq, Ktestq, X86KReg, X86KReg)                            // AVX512_BW</a>
+<a name="1804"><span class="lineNum">    1804 </span>            :   ASMJIT_INST_2x(ktestw, Ktestw, X86KReg, X86KReg)                            // AVX512_DQ</a>
+<a name="1805"><span class="lineNum">    1805 </span>            :   ASMJIT_INST_3x(kunpckbw, Kunpckbw, X86KReg, X86KReg, X86KReg)               // AVX512_F</a>
+<a name="1806"><span class="lineNum">    1806 </span>            :   ASMJIT_INST_3x(kunpckdq, Kunpckdq, X86KReg, X86KReg, X86KReg)               // AVX512_BW</a>
+<a name="1807"><span class="lineNum">    1807 </span>            :   ASMJIT_INST_3x(kunpckwd, Kunpckwd, X86KReg, X86KReg, X86KReg)               // AVX512_BW</a>
+<a name="1808"><span class="lineNum">    1808 </span>            :   ASMJIT_INST_3x(kxnorb, Kxnorb, X86KReg, X86KReg, X86KReg)                   // AVX512_DQ</a>
+<a name="1809"><span class="lineNum">    1809 </span>            :   ASMJIT_INST_3x(kxnord, Kxnord, X86KReg, X86KReg, X86KReg)                   // AVX512_BW</a>
+<a name="1810"><span class="lineNum">    1810 </span>            :   ASMJIT_INST_3x(kxnorq, Kxnorq, X86KReg, X86KReg, X86KReg)                   // AVX512_BW</a>
+<a name="1811"><span class="lineNum">    1811 </span>            :   ASMJIT_INST_3x(kxnorw, Kxnorw, X86KReg, X86KReg, X86KReg)                   // AVX512_F</a>
+<a name="1812"><span class="lineNum">    1812 </span>            :   ASMJIT_INST_3x(kxorb, Kxorb, X86KReg, X86KReg, X86KReg)                     // AVX512_DQ</a>
+<a name="1813"><span class="lineNum">    1813 </span>            :   ASMJIT_INST_3x(kxord, Kxord, X86KReg, X86KReg, X86KReg)                     // AVX512_BW</a>
+<a name="1814"><span class="lineNum">    1814 </span>            :   ASMJIT_INST_3x(kxorq, Kxorq, X86KReg, X86KReg, X86KReg)                     // AVX512_BW</a>
+<a name="1815"><span class="lineNum">    1815 </span>            :   ASMJIT_INST_3x(kxorw, Kxorw, X86KReg, X86KReg, X86KReg)                     // AVX512_F</a>
+<a name="1816"><span class="lineNum">    1816 </span>            :   ASMJIT_INST_6x(v4fmaddps, V4fmaddps, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Mem)   // AVX512_4FMAPS{kz}</a>
+<a name="1817"><span class="lineNum">    1817 </span>            :   ASMJIT_INST_6x(v4fnmaddps, V4fnmaddps, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Mem) // AVX512_4FMAPS{kz}</a>
+<a name="1818"><span class="lineNum">    1818 </span>            :   ASMJIT_INST_3x(vaddpd, Vaddpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="1819"><span class="lineNum">    1819 </span>            :   ASMJIT_INST_3x(vaddpd, Vaddpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="1820"><span class="lineNum">    1820 </span>            :   ASMJIT_INST_3x(vaddpd, Vaddpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="1821"><span class="lineNum">    1821 </span>            :   ASMJIT_INST_3x(vaddpd, Vaddpd, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="1822"><span class="lineNum">    1822 </span>            :   ASMJIT_INST_3x(vaddpd, Vaddpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b64}</a>
+<a name="1823"><span class="lineNum">    1823 </span>            :   ASMJIT_INST_3x(vaddpd, Vaddpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b64}</a>
+<a name="1824"><span class="lineNum">    1824 </span>            :   ASMJIT_INST_3x(vaddps, Vaddps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="1825"><span class="lineNum">    1825 </span>            :   ASMJIT_INST_3x(vaddps, Vaddps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="1826"><span class="lineNum">    1826 </span>            :   ASMJIT_INST_3x(vaddps, Vaddps, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="1827"><span class="lineNum">    1827 </span>            :   ASMJIT_INST_3x(vaddps, Vaddps, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="1828"><span class="lineNum">    1828 </span>            :   ASMJIT_INST_3x(vaddps, Vaddps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b32}</a>
+<a name="1829"><span class="lineNum">    1829 </span>            :   ASMJIT_INST_3x(vaddps, Vaddps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b32}</a>
+<a name="1830"><span class="lineNum">    1830 </span>            :   ASMJIT_INST_3x(vaddsd, Vaddsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="1831"><span class="lineNum">    1831 </span>            :   ASMJIT_INST_3x(vaddsd, Vaddsd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="1832"><span class="lineNum">    1832 </span>            :   ASMJIT_INST_3x(vaddss, Vaddss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="1833"><span class="lineNum">    1833 </span>            :   ASMJIT_INST_3x(vaddss, Vaddss, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="1834"><span class="lineNum">    1834 </span>            :   ASMJIT_INST_3x(vaddsubpd, Vaddsubpd, X86Xmm, X86Xmm, X86Xmm)                // AVX</a>
+<a name="1835"><span class="lineNum">    1835 </span>            :   ASMJIT_INST_3x(vaddsubpd, Vaddsubpd, X86Xmm, X86Xmm, X86Mem)                // AVX</a>
+<a name="1836"><span class="lineNum">    1836 </span>            :   ASMJIT_INST_3x(vaddsubpd, Vaddsubpd, X86Ymm, X86Ymm, X86Ymm)                // AVX</a>
+<a name="1837"><span class="lineNum">    1837 </span>            :   ASMJIT_INST_3x(vaddsubpd, Vaddsubpd, X86Ymm, X86Ymm, X86Mem)                // AVX</a>
+<a name="1838"><span class="lineNum">    1838 </span>            :   ASMJIT_INST_3x(vaddsubps, Vaddsubps, X86Xmm, X86Xmm, X86Xmm)                // AVX</a>
+<a name="1839"><span class="lineNum">    1839 </span>            :   ASMJIT_INST_3x(vaddsubps, Vaddsubps, X86Xmm, X86Xmm, X86Mem)                // AVX</a>
+<a name="1840"><span class="lineNum">    1840 </span>            :   ASMJIT_INST_3x(vaddsubps, Vaddsubps, X86Ymm, X86Ymm, X86Ymm)                // AVX</a>
+<a name="1841"><span class="lineNum">    1841 </span>            :   ASMJIT_INST_3x(vaddsubps, Vaddsubps, X86Ymm, X86Ymm, X86Mem)                // AVX</a>
+<a name="1842"><span class="lineNum">    1842 </span>            :   ASMJIT_INST_3x(vaesdec, Vaesdec, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="1843"><span class="lineNum">    1843 </span>            :   ASMJIT_INST_3x(vaesdec, Vaesdec, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="1844"><span class="lineNum">    1844 </span>            :   ASMJIT_INST_3x(vaesdeclast, Vaesdeclast, X86Xmm, X86Xmm, X86Xmm)            // AVX</a>
+<a name="1845"><span class="lineNum">    1845 </span>            :   ASMJIT_INST_3x(vaesdeclast, Vaesdeclast, X86Xmm, X86Xmm, X86Mem)            // AVX</a>
+<a name="1846"><span class="lineNum">    1846 </span>            :   ASMJIT_INST_3x(vaesenc, Vaesenc, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="1847"><span class="lineNum">    1847 </span>            :   ASMJIT_INST_3x(vaesenc, Vaesenc, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="1848"><span class="lineNum">    1848 </span>            :   ASMJIT_INST_3x(vaesenclast, Vaesenclast, X86Xmm, X86Xmm, X86Xmm)            // AVX</a>
+<a name="1849"><span class="lineNum">    1849 </span>            :   ASMJIT_INST_3x(vaesenclast, Vaesenclast, X86Xmm, X86Xmm, X86Mem)            // AVX</a>
+<a name="1850"><span class="lineNum">    1850 </span>            :   ASMJIT_INST_2x(vaesimc, Vaesimc, X86Xmm, X86Xmm)                            // AVX</a>
+<a name="1851"><span class="lineNum">    1851 </span>            :   ASMJIT_INST_2x(vaesimc, Vaesimc, X86Xmm, X86Mem)                            // AVX</a>
+<a name="1852"><span class="lineNum">    1852 </span>            :   ASMJIT_INST_3i(vaeskeygenassist, Vaeskeygenassist, X86Xmm, X86Xmm, Imm)     // AVX</a>
+<a name="1853"><span class="lineNum">    1853 </span>            :   ASMJIT_INST_3i(vaeskeygenassist, Vaeskeygenassist, X86Xmm, X86Mem, Imm)     // AVX</a>
+<a name="1854"><span class="lineNum">    1854 </span>            :   ASMJIT_INST_4i(valignd, Valignd, X86Xmm, X86Xmm, X86Xmm, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="1855"><span class="lineNum">    1855 </span>            :   ASMJIT_INST_4i(valignd, Valignd, X86Xmm, X86Xmm, X86Mem, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="1856"><span class="lineNum">    1856 </span>            :   ASMJIT_INST_4i(valignd, Valignd, X86Ymm, X86Ymm, X86Ymm, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="1857"><span class="lineNum">    1857 </span>            :   ASMJIT_INST_4i(valignd, Valignd, X86Ymm, X86Ymm, X86Mem, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="1858"><span class="lineNum">    1858 </span>            :   ASMJIT_INST_4i(valignd, Valignd, X86Zmm, X86Zmm, X86Zmm, Imm)               //      AVX512_F{kz|b32}</a>
+<a name="1859"><span class="lineNum">    1859 </span>            :   ASMJIT_INST_4i(valignd, Valignd, X86Zmm, X86Zmm, X86Mem, Imm)               //      AVX512_F{kz|b32}</a>
+<a name="1860"><span class="lineNum">    1860 </span>            :   ASMJIT_INST_4i(valignq, Valignq, X86Xmm, X86Xmm, X86Xmm, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="1861"><span class="lineNum">    1861 </span>            :   ASMJIT_INST_4i(valignq, Valignq, X86Xmm, X86Xmm, X86Mem, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="1862"><span class="lineNum">    1862 </span>            :   ASMJIT_INST_4i(valignq, Valignq, X86Ymm, X86Ymm, X86Ymm, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="1863"><span class="lineNum">    1863 </span>            :   ASMJIT_INST_4i(valignq, Valignq, X86Ymm, X86Ymm, X86Mem, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="1864"><span class="lineNum">    1864 </span>            :   ASMJIT_INST_4i(valignq, Valignq, X86Zmm, X86Zmm, X86Zmm, Imm)               //      AVX512_F{kz|b64}</a>
+<a name="1865"><span class="lineNum">    1865 </span>            :   ASMJIT_INST_4i(valignq, Valignq, X86Zmm, X86Zmm, X86Mem, Imm)               //      AVX512_F{kz|b64}</a>
+<a name="1866"><span class="lineNum">    1866 </span>            :   ASMJIT_INST_3x(vandnpd, Vandnpd, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1867"><span class="lineNum">    1867 </span>            :   ASMJIT_INST_3x(vandnpd, Vandnpd, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1868"><span class="lineNum">    1868 </span>            :   ASMJIT_INST_3x(vandnpd, Vandnpd, X86Ymm, X86Ymm, X86Ymm)                    // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1869"><span class="lineNum">    1869 </span>            :   ASMJIT_INST_3x(vandnpd, Vandnpd, X86Ymm, X86Ymm, X86Mem)                    // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1870"><span class="lineNum">    1870 </span>            :   ASMJIT_INST_3x(vandnpd, Vandnpd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_DQ{kz|b64}</a>
+<a name="1871"><span class="lineNum">    1871 </span>            :   ASMJIT_INST_3x(vandnpd, Vandnpd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_DQ{kz|b64}</a>
+<a name="1872"><span class="lineNum">    1872 </span>            :   ASMJIT_INST_3x(vandnps, Vandnps, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1873"><span class="lineNum">    1873 </span>            :   ASMJIT_INST_3x(vandnps, Vandnps, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1874"><span class="lineNum">    1874 </span>            :   ASMJIT_INST_3x(vandnps, Vandnps, X86Ymm, X86Ymm, X86Ymm)                    // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1875"><span class="lineNum">    1875 </span>            :   ASMJIT_INST_3x(vandnps, Vandnps, X86Ymm, X86Ymm, X86Mem)                    // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1876"><span class="lineNum">    1876 </span>            :   ASMJIT_INST_3x(vandnps, Vandnps, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_DQ{kz|b32}</a>
+<a name="1877"><span class="lineNum">    1877 </span>            :   ASMJIT_INST_3x(vandnps, Vandnps, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_DQ{kz|b32}</a>
+<a name="1878"><span class="lineNum">    1878 </span>            :   ASMJIT_INST_3x(vandpd, Vandpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1879"><span class="lineNum">    1879 </span>            :   ASMJIT_INST_3x(vandpd, Vandpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1880"><span class="lineNum">    1880 </span>            :   ASMJIT_INST_3x(vandpd, Vandpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1881"><span class="lineNum">    1881 </span>            :   ASMJIT_INST_3x(vandpd, Vandpd, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="1882"><span class="lineNum">    1882 </span>            :   ASMJIT_INST_3x(vandpd, Vandpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_DQ{kz|b64}</a>
+<a name="1883"><span class="lineNum">    1883 </span>            :   ASMJIT_INST_3x(vandpd, Vandpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|b64}</a>
+<a name="1884"><span class="lineNum">    1884 </span>            :   ASMJIT_INST_3x(vandps, Vandps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1885"><span class="lineNum">    1885 </span>            :   ASMJIT_INST_3x(vandps, Vandps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1886"><span class="lineNum">    1886 </span>            :   ASMJIT_INST_3x(vandps, Vandps, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1887"><span class="lineNum">    1887 </span>            :   ASMJIT_INST_3x(vandps, Vandps, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="1888"><span class="lineNum">    1888 </span>            :   ASMJIT_INST_3x(vandps, Vandps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_DQ{kz|b32}</a>
+<a name="1889"><span class="lineNum">    1889 </span>            :   ASMJIT_INST_3x(vandps, Vandps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|b32}</a>
+<a name="1890"><span class="lineNum">    1890 </span>            :   ASMJIT_INST_3x(vblendmb, Vblendmb, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_BW{kz}-VL</a>
+<a name="1891"><span class="lineNum">    1891 </span>            :   ASMJIT_INST_3x(vblendmb, Vblendmb, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="1892"><span class="lineNum">    1892 </span>            :   ASMJIT_INST_3x(vblendmb, Vblendmb, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_BW{kz}-VL</a>
+<a name="1893"><span class="lineNum">    1893 </span>            :   ASMJIT_INST_3x(vblendmb, Vblendmb, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="1894"><span class="lineNum">    1894 </span>            :   ASMJIT_INST_3x(vblendmb, Vblendmb, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="1895"><span class="lineNum">    1895 </span>            :   ASMJIT_INST_3x(vblendmb, Vblendmb, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="1896"><span class="lineNum">    1896 </span>            :   ASMJIT_INST_3x(vblendmd, Vblendmd, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="1897"><span class="lineNum">    1897 </span>            :   ASMJIT_INST_3x(vblendmd, Vblendmd, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="1898"><span class="lineNum">    1898 </span>            :   ASMJIT_INST_3x(vblendmd, Vblendmd, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="1899"><span class="lineNum">    1899 </span>            :   ASMJIT_INST_3x(vblendmd, Vblendmd, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="1900"><span class="lineNum">    1900 </span>            :   ASMJIT_INST_3x(vblendmd, Vblendmd, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b32}</a>
+<a name="1901"><span class="lineNum">    1901 </span>            :   ASMJIT_INST_3x(vblendmd, Vblendmd, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b32}</a>
+<a name="1902"><span class="lineNum">    1902 </span>            :   ASMJIT_INST_3x(vblendmpd, Vblendmpd, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1903"><span class="lineNum">    1903 </span>            :   ASMJIT_INST_3x(vblendmpd, Vblendmpd, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1904"><span class="lineNum">    1904 </span>            :   ASMJIT_INST_3x(vblendmpd, Vblendmpd, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1905"><span class="lineNum">    1905 </span>            :   ASMJIT_INST_3x(vblendmpd, Vblendmpd, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1906"><span class="lineNum">    1906 </span>            :   ASMJIT_INST_3x(vblendmpd, Vblendmpd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="1907"><span class="lineNum">    1907 </span>            :   ASMJIT_INST_3x(vblendmpd, Vblendmpd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="1908"><span class="lineNum">    1908 </span>            :   ASMJIT_INST_3x(vblendmps, Vblendmps, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1909"><span class="lineNum">    1909 </span>            :   ASMJIT_INST_3x(vblendmps, Vblendmps, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1910"><span class="lineNum">    1910 </span>            :   ASMJIT_INST_3x(vblendmps, Vblendmps, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1911"><span class="lineNum">    1911 </span>            :   ASMJIT_INST_3x(vblendmps, Vblendmps, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1912"><span class="lineNum">    1912 </span>            :   ASMJIT_INST_3x(vblendmps, Vblendmps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b32}</a>
+<a name="1913"><span class="lineNum">    1913 </span>            :   ASMJIT_INST_3x(vblendmps, Vblendmps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b32}</a>
+<a name="1914"><span class="lineNum">    1914 </span>            :   ASMJIT_INST_3x(vblendmq, Vblendmq, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="1915"><span class="lineNum">    1915 </span>            :   ASMJIT_INST_3x(vblendmq, Vblendmq, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="1916"><span class="lineNum">    1916 </span>            :   ASMJIT_INST_3x(vblendmq, Vblendmq, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="1917"><span class="lineNum">    1917 </span>            :   ASMJIT_INST_3x(vblendmq, Vblendmq, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="1918"><span class="lineNum">    1918 </span>            :   ASMJIT_INST_3x(vblendmq, Vblendmq, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b64}</a>
+<a name="1919"><span class="lineNum">    1919 </span>            :   ASMJIT_INST_3x(vblendmq, Vblendmq, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b64}</a>
+<a name="1920"><span class="lineNum">    1920 </span>            :   ASMJIT_INST_3x(vblendmw, Vblendmw, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_BW{kz}-VL</a>
+<a name="1921"><span class="lineNum">    1921 </span>            :   ASMJIT_INST_3x(vblendmw, Vblendmw, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="1922"><span class="lineNum">    1922 </span>            :   ASMJIT_INST_3x(vblendmw, Vblendmw, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_BW{kz}-VL</a>
+<a name="1923"><span class="lineNum">    1923 </span>            :   ASMJIT_INST_3x(vblendmw, Vblendmw, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="1924"><span class="lineNum">    1924 </span>            :   ASMJIT_INST_3x(vblendmw, Vblendmw, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="1925"><span class="lineNum">    1925 </span>            :   ASMJIT_INST_3x(vblendmw, Vblendmw, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="1926"><span class="lineNum">    1926 </span>            :   ASMJIT_INST_4i(vblendpd, Vblendpd, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX</a>
+<a name="1927"><span class="lineNum">    1927 </span>            :   ASMJIT_INST_4i(vblendpd, Vblendpd, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX</a>
+<a name="1928"><span class="lineNum">    1928 </span>            :   ASMJIT_INST_4i(vblendpd, Vblendpd, X86Ymm, X86Ymm, X86Ymm, Imm)             // AVX</a>
+<a name="1929"><span class="lineNum">    1929 </span>            :   ASMJIT_INST_4i(vblendpd, Vblendpd, X86Ymm, X86Ymm, X86Mem, Imm)             // AVX</a>
+<a name="1930"><span class="lineNum">    1930 </span>            :   ASMJIT_INST_4i(vblendps, Vblendps, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX</a>
+<a name="1931"><span class="lineNum">    1931 </span>            :   ASMJIT_INST_4i(vblendps, Vblendps, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX</a>
+<a name="1932"><span class="lineNum">    1932 </span>            :   ASMJIT_INST_4i(vblendps, Vblendps, X86Ymm, X86Ymm, X86Ymm, Imm)             // AVX</a>
+<a name="1933"><span class="lineNum">    1933 </span>            :   ASMJIT_INST_4i(vblendps, Vblendps, X86Ymm, X86Ymm, X86Mem, Imm)             // AVX</a>
+<a name="1934"><span class="lineNum">    1934 </span>            :   ASMJIT_INST_4x(vblendvpd, Vblendvpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // AVX</a>
+<a name="1935"><span class="lineNum">    1935 </span>            :   ASMJIT_INST_4x(vblendvpd, Vblendvpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // AVX</a>
+<a name="1936"><span class="lineNum">    1936 </span>            :   ASMJIT_INST_4x(vblendvpd, Vblendvpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // AVX</a>
+<a name="1937"><span class="lineNum">    1937 </span>            :   ASMJIT_INST_4x(vblendvpd, Vblendvpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // AVX</a>
+<a name="1938"><span class="lineNum">    1938 </span>            :   ASMJIT_INST_4x(vblendvps, Vblendvps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // AVX</a>
+<a name="1939"><span class="lineNum">    1939 </span>            :   ASMJIT_INST_4x(vblendvps, Vblendvps, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // AVX</a>
+<a name="1940"><span class="lineNum">    1940 </span>            :   ASMJIT_INST_4x(vblendvps, Vblendvps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // AVX</a>
+<a name="1941"><span class="lineNum">    1941 </span>            :   ASMJIT_INST_4x(vblendvps, Vblendvps, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // AVX</a>
+<a name="1942"><span class="lineNum">    1942 </span>            :   ASMJIT_INST_2x(vbroadcastf128, Vbroadcastf128, X86Ymm, X86Mem)              // AVX</a>
+<a name="1943"><span class="lineNum">    1943 </span>            :   ASMJIT_INST_2x(vbroadcastf32x2, Vbroadcastf32x2, X86Ymm, X86Xmm)            //      AVX512_DQ{kz}-VL</a>
+<a name="1944"><span class="lineNum">    1944 </span>            :   ASMJIT_INST_2x(vbroadcastf32x2, Vbroadcastf32x2, X86Ymm, X86Mem)            //      AVX512_DQ{kz}-VL</a>
+<a name="1945"><span class="lineNum">    1945 </span>            :   ASMJIT_INST_2x(vbroadcastf32x2, Vbroadcastf32x2, X86Zmm, X86Xmm)            //      AVX512_DQ{kz}</a>
+<a name="1946"><span class="lineNum">    1946 </span>            :   ASMJIT_INST_2x(vbroadcastf32x2, Vbroadcastf32x2, X86Zmm, X86Mem)            //      AVX512_DQ{kz}</a>
+<a name="1947"><span class="lineNum">    1947 </span>            :   ASMJIT_INST_2x(vbroadcastf32x4, Vbroadcastf32x4, X86Ymm, X86Mem)            //      AVX512_F{kz}</a>
+<a name="1948"><span class="lineNum">    1948 </span>            :   ASMJIT_INST_2x(vbroadcastf32x4, Vbroadcastf32x4, X86Zmm, X86Mem)            //      AVX512_F{kz}</a>
+<a name="1949"><span class="lineNum">    1949 </span>            :   ASMJIT_INST_2x(vbroadcastf32x8, Vbroadcastf32x8, X86Zmm, X86Mem)            //      AVX512_DQ{kz}</a>
+<a name="1950"><span class="lineNum">    1950 </span>            :   ASMJIT_INST_2x(vbroadcastf64x2, Vbroadcastf64x2, X86Ymm, X86Mem)            //      AVX512_DQ{kz}-VL</a>
+<a name="1951"><span class="lineNum">    1951 </span>            :   ASMJIT_INST_2x(vbroadcastf64x2, Vbroadcastf64x2, X86Zmm, X86Mem)            //      AVX512_DQ{kz}</a>
+<a name="1952"><span class="lineNum">    1952 </span>            :   ASMJIT_INST_2x(vbroadcastf64x4, Vbroadcastf64x4, X86Zmm, X86Mem)            //      AVX512_F{kz}</a>
+<a name="1953"><span class="lineNum">    1953 </span>            :   ASMJIT_INST_2x(vbroadcasti128, Vbroadcasti128, X86Ymm, X86Mem)              // AVX2</a>
+<a name="1954"><span class="lineNum">    1954 </span>            :   ASMJIT_INST_2x(vbroadcasti32x2, Vbroadcasti32x2, X86Xmm, X86Xmm)            //      AVX512_DQ{kz}-VL</a>
+<a name="1955"><span class="lineNum">    1955 </span>            :   ASMJIT_INST_2x(vbroadcasti32x2, Vbroadcasti32x2, X86Xmm, X86Mem)            //      AVX512_DQ{kz}-VL</a>
+<a name="1956"><span class="lineNum">    1956 </span>            :   ASMJIT_INST_2x(vbroadcasti32x2, Vbroadcasti32x2, X86Ymm, X86Xmm)            //      AVX512_DQ{kz}-VL</a>
+<a name="1957"><span class="lineNum">    1957 </span>            :   ASMJIT_INST_2x(vbroadcasti32x2, Vbroadcasti32x2, X86Ymm, X86Mem)            //      AVX512_DQ{kz}-VL</a>
+<a name="1958"><span class="lineNum">    1958 </span>            :   ASMJIT_INST_2x(vbroadcasti32x2, Vbroadcasti32x2, X86Zmm, X86Xmm)            //      AVX512_DQ{kz}</a>
+<a name="1959"><span class="lineNum">    1959 </span>            :   ASMJIT_INST_2x(vbroadcasti32x2, Vbroadcasti32x2, X86Zmm, X86Mem)            //      AVX512_DQ{kz}</a>
+<a name="1960"><span class="lineNum">    1960 </span>            :   ASMJIT_INST_2x(vbroadcasti32x4, Vbroadcasti32x4, X86Ymm, X86Xmm)            //      AVX512_F{kz}-VL</a>
+<a name="1961"><span class="lineNum">    1961 </span>            :   ASMJIT_INST_2x(vbroadcasti32x4, Vbroadcasti32x4, X86Ymm, X86Mem)            //      AVX512_F{kz}-VL</a>
+<a name="1962"><span class="lineNum">    1962 </span>            :   ASMJIT_INST_2x(vbroadcasti32x4, Vbroadcasti32x4, X86Zmm, X86Xmm)            //      AVX512_F{kz}</a>
+<a name="1963"><span class="lineNum">    1963 </span>            :   ASMJIT_INST_2x(vbroadcasti32x4, Vbroadcasti32x4, X86Zmm, X86Mem)            //      AVX512_F{kz}</a>
+<a name="1964"><span class="lineNum">    1964 </span>            :   ASMJIT_INST_2x(vbroadcasti32x8, Vbroadcasti32x8, X86Zmm, X86Xmm)            //      AVX512_DQ{kz}</a>
+<a name="1965"><span class="lineNum">    1965 </span>            :   ASMJIT_INST_2x(vbroadcasti32x8, Vbroadcasti32x8, X86Zmm, X86Mem)            //      AVX512_DQ{kz}</a>
+<a name="1966"><span class="lineNum">    1966 </span>            :   ASMJIT_INST_2x(vbroadcasti64x2, Vbroadcasti64x2, X86Ymm, X86Xmm)            //      AVX512_DQ{kz}-VL</a>
+<a name="1967"><span class="lineNum">    1967 </span>            :   ASMJIT_INST_2x(vbroadcasti64x2, Vbroadcasti64x2, X86Ymm, X86Mem)            //      AVX512_DQ{kz}-VL</a>
+<a name="1968"><span class="lineNum">    1968 </span>            :   ASMJIT_INST_2x(vbroadcasti64x2, Vbroadcasti64x2, X86Zmm, X86Xmm)            //      AVX512_DQ{kz}</a>
+<a name="1969"><span class="lineNum">    1969 </span>            :   ASMJIT_INST_2x(vbroadcasti64x2, Vbroadcasti64x2, X86Zmm, X86Mem)            //      AVX512_DQ{kz}</a>
+<a name="1970"><span class="lineNum">    1970 </span>            :   ASMJIT_INST_2x(vbroadcasti64x4, Vbroadcasti64x4, X86Zmm, X86Xmm)            //      AVX512_F{kz}</a>
+<a name="1971"><span class="lineNum">    1971 </span>            :   ASMJIT_INST_2x(vbroadcasti64x4, Vbroadcasti64x4, X86Zmm, X86Mem)            //      AVX512_F{kz}</a>
+<a name="1972"><span class="lineNum">    1972 </span>            :   ASMJIT_INST_2x(vbroadcastsd, Vbroadcastsd, X86Ymm, X86Mem)                  // AVX  AVX512_F{kz}-VL</a>
+<a name="1973"><span class="lineNum">    1973 </span>            :   ASMJIT_INST_2x(vbroadcastsd, Vbroadcastsd, X86Ymm, X86Xmm)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="1974"><span class="lineNum">    1974 </span>            :   ASMJIT_INST_2x(vbroadcastsd, Vbroadcastsd, X86Zmm, X86Xmm)                  //      AVX512_F{kz}</a>
+<a name="1975"><span class="lineNum">    1975 </span>            :   ASMJIT_INST_2x(vbroadcastsd, Vbroadcastsd, X86Zmm, X86Mem)                  //      AVX512_F{kz}</a>
+<a name="1976"><span class="lineNum">    1976 </span>            :   ASMJIT_INST_2x(vbroadcastss, Vbroadcastss, X86Xmm, X86Mem)                  // AVX  AVX512_F{kz}-VL</a>
+<a name="1977"><span class="lineNum">    1977 </span>            :   ASMJIT_INST_2x(vbroadcastss, Vbroadcastss, X86Xmm, X86Xmm)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="1978"><span class="lineNum">    1978 </span>            :   ASMJIT_INST_2x(vbroadcastss, Vbroadcastss, X86Ymm, X86Mem)                  // AVX  AVX512_F{kz}</a>
+<a name="1979"><span class="lineNum">    1979 </span>            :   ASMJIT_INST_2x(vbroadcastss, Vbroadcastss, X86Ymm, X86Xmm)                  // AVX2 AVX512_F{kz}</a>
+<a name="1980"><span class="lineNum">    1980 </span>            :   ASMJIT_INST_2x(vbroadcastss, Vbroadcastss, X86Zmm, X86Xmm)                  //      AVX512_F{kz}-VL</a>
+<a name="1981"><span class="lineNum">    1981 </span>            :   ASMJIT_INST_2x(vbroadcastss, Vbroadcastss, X86Zmm, X86Mem)                  //      AVX512_F{kz}-VL</a>
+<a name="1982"><span class="lineNum">    1982 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86Xmm, X86Xmm, X86Xmm, Imm)                 // AVX</a>
+<a name="1983"><span class="lineNum">    1983 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86Xmm, X86Xmm, X86Mem, Imm)                 // AVX</a>
+<a name="1984"><span class="lineNum">    1984 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86Ymm, X86Ymm, X86Ymm, Imm)                 // AVX</a>
+<a name="1985"><span class="lineNum">    1985 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86Ymm, X86Ymm, X86Mem, Imm)                 // AVX</a>
+<a name="1986"><span class="lineNum">    1986 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1987"><span class="lineNum">    1987 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1988"><span class="lineNum">    1988 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86KReg, X86Ymm, X86Ymm, Imm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1989"><span class="lineNum">    1989 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86KReg, X86Ymm, X86Mem, Imm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="1990"><span class="lineNum">    1990 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86KReg, X86Zmm, X86Zmm, Imm)                //      AVX512_F{kz|sae|b64}</a>
+<a name="1991"><span class="lineNum">    1991 </span>            :   ASMJIT_INST_4i(vcmppd, Vcmppd, X86KReg, X86Zmm, X86Mem, Imm)                //      AVX512_F{kz|sae|b64}</a>
+<a name="1992"><span class="lineNum">    1992 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86Xmm, X86Xmm, X86Xmm, Imm)                 // AVX</a>
+<a name="1993"><span class="lineNum">    1993 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86Xmm, X86Xmm, X86Mem, Imm)                 // AVX</a>
+<a name="1994"><span class="lineNum">    1994 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86Ymm, X86Ymm, X86Ymm, Imm)                 // AVX</a>
+<a name="1995"><span class="lineNum">    1995 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86Ymm, X86Ymm, X86Mem, Imm)                 // AVX</a>
+<a name="1996"><span class="lineNum">    1996 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1997"><span class="lineNum">    1997 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1998"><span class="lineNum">    1998 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86KReg, X86Ymm, X86Ymm, Imm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="1999"><span class="lineNum">    1999 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86KReg, X86Ymm, X86Mem, Imm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="2000"><span class="lineNum">    2000 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86KReg, X86Zmm, X86Zmm, Imm)                //      AVX512_F{kz|sae|b32}</a>
+<a name="2001"><span class="lineNum">    2001 </span>            :   ASMJIT_INST_4i(vcmpps, Vcmpps, X86KReg, X86Zmm, X86Mem, Imm)                //      AVX512_F{kz|sae|b32}</a>
+<a name="2002"><span class="lineNum">    2002 </span>            :   ASMJIT_INST_4i(vcmpsd, Vcmpsd, X86Xmm, X86Xmm, X86Xmm, Imm)                 // AVX</a>
+<a name="2003"><span class="lineNum">    2003 </span>            :   ASMJIT_INST_4i(vcmpsd, Vcmpsd, X86Xmm, X86Xmm, X86Mem, Imm)                 // AVX</a>
+<a name="2004"><span class="lineNum">    2004 </span>            :   ASMJIT_INST_4i(vcmpsd, Vcmpsd, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_F{kz|sae}</a>
+<a name="2005"><span class="lineNum">    2005 </span>            :   ASMJIT_INST_4i(vcmpsd, Vcmpsd, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_F{kz|sae}</a>
+<a name="2006"><span class="lineNum">    2006 </span>            :   ASMJIT_INST_4i(vcmpss, Vcmpss, X86Xmm, X86Xmm, X86Xmm, Imm)                 // AVX</a>
+<a name="2007"><span class="lineNum">    2007 </span>            :   ASMJIT_INST_4i(vcmpss, Vcmpss, X86Xmm, X86Xmm, X86Mem, Imm)                 // AVX</a>
+<a name="2008"><span class="lineNum">    2008 </span>            :   ASMJIT_INST_4i(vcmpss, Vcmpss, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_F{kz|sae}</a>
+<a name="2009"><span class="lineNum">    2009 </span>            :   ASMJIT_INST_4i(vcmpss, Vcmpss, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_F{kz|sae}</a>
+<a name="2010"><span class="lineNum">    2010 </span>            :   ASMJIT_INST_2x(vcomisd, Vcomisd, X86Xmm, X86Xmm)                            // AVX  AVX512_F{sae}</a>
+<a name="2011"><span class="lineNum">    2011 </span>            :   ASMJIT_INST_2x(vcomisd, Vcomisd, X86Xmm, X86Mem)                            // AVX  AVX512_F{sae}</a>
+<a name="2012"><span class="lineNum">    2012 </span>            :   ASMJIT_INST_2x(vcomiss, Vcomiss, X86Xmm, X86Xmm)                            // AVX  AVX512_F{sae}</a>
+<a name="2013"><span class="lineNum">    2013 </span>            :   ASMJIT_INST_2x(vcomiss, Vcomiss, X86Xmm, X86Mem)                            // AVX  AVX512_F{sae}</a>
+<a name="2014"><span class="lineNum">    2014 </span>            :   ASMJIT_INST_2x(vcompresspd, Vcompresspd, X86Xmm, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="2015"><span class="lineNum">    2015 </span>            :   ASMJIT_INST_2x(vcompresspd, Vcompresspd, X86Mem, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="2016"><span class="lineNum">    2016 </span>            :   ASMJIT_INST_2x(vcompresspd, Vcompresspd, X86Ymm, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="2017"><span class="lineNum">    2017 </span>            :   ASMJIT_INST_2x(vcompresspd, Vcompresspd, X86Mem, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="2018"><span class="lineNum">    2018 </span>            :   ASMJIT_INST_2x(vcompresspd, Vcompresspd, X86Zmm, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="2019"><span class="lineNum">    2019 </span>            :   ASMJIT_INST_2x(vcompresspd, Vcompresspd, X86Mem, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="2020"><span class="lineNum">    2020 </span>            :   ASMJIT_INST_2x(vcompressps, Vcompressps, X86Xmm, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="2021"><span class="lineNum">    2021 </span>            :   ASMJIT_INST_2x(vcompressps, Vcompressps, X86Mem, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="2022"><span class="lineNum">    2022 </span>            :   ASMJIT_INST_2x(vcompressps, Vcompressps, X86Ymm, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="2023"><span class="lineNum">    2023 </span>            :   ASMJIT_INST_2x(vcompressps, Vcompressps, X86Mem, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="2024"><span class="lineNum">    2024 </span>            :   ASMJIT_INST_2x(vcompressps, Vcompressps, X86Zmm, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="2025"><span class="lineNum">    2025 </span>            :   ASMJIT_INST_2x(vcompressps, Vcompressps, X86Mem, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="2026"><span class="lineNum">    2026 </span>            :   ASMJIT_INST_2x(vcvtdq2pd, Vcvtdq2pd, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :   ASMJIT_INST_2x(vcvtdq2pd, Vcvtdq2pd, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2028"><span class="lineNum">    2028 </span>            :   ASMJIT_INST_2x(vcvtdq2pd, Vcvtdq2pd, X86Ymm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2029"><span class="lineNum">    2029 </span>            :   ASMJIT_INST_2x(vcvtdq2pd, Vcvtdq2pd, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2030"><span class="lineNum">    2030 </span>            :   ASMJIT_INST_2x(vcvtdq2pd, Vcvtdq2pd, X86Zmm, X86Ymm)                        //      AVX512_F{kz|b32}</a>
+<a name="2031"><span class="lineNum">    2031 </span>            :   ASMJIT_INST_2x(vcvtdq2pd, Vcvtdq2pd, X86Zmm, X86Mem)                        //      AVX512_F{kz|b32}</a>
+<a name="2032"><span class="lineNum">    2032 </span>            :   ASMJIT_INST_2x(vcvtdq2ps, Vcvtdq2ps, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2033"><span class="lineNum">    2033 </span>            :   ASMJIT_INST_2x(vcvtdq2ps, Vcvtdq2ps, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2034"><span class="lineNum">    2034 </span>            :   ASMJIT_INST_2x(vcvtdq2ps, Vcvtdq2ps, X86Ymm, X86Ymm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2035"><span class="lineNum">    2035 </span>            :   ASMJIT_INST_2x(vcvtdq2ps, Vcvtdq2ps, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2036"><span class="lineNum">    2036 </span>            :   ASMJIT_INST_2x(vcvtdq2ps, Vcvtdq2ps, X86Zmm, X86Zmm)                        //      AVX512_F{kz|er|b32}</a>
+<a name="2037"><span class="lineNum">    2037 </span>            :   ASMJIT_INST_2x(vcvtdq2ps, Vcvtdq2ps, X86Zmm, X86Mem)                        //      AVX512_F{kz|er|b32}</a>
+<a name="2038"><span class="lineNum">    2038 </span>            :   ASMJIT_INST_2x(vcvtpd2dq, Vcvtpd2dq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2039"><span class="lineNum">    2039 </span>            :   ASMJIT_INST_2x(vcvtpd2dq, Vcvtpd2dq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2040"><span class="lineNum">    2040 </span>            :   ASMJIT_INST_2x(vcvtpd2dq, Vcvtpd2dq, X86Xmm, X86Ymm)                        // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2041"><span class="lineNum">    2041 </span>            :   ASMJIT_INST_2x(vcvtpd2dq, Vcvtpd2dq, X86Ymm, X86Zmm)                        //      AVX512_F{kz|er|b64}</a>
+<a name="2042"><span class="lineNum">    2042 </span>            :   ASMJIT_INST_2x(vcvtpd2dq, Vcvtpd2dq, X86Ymm, X86Mem)                        //      AVX512_F{kz|er|b64}</a>
+<a name="2043"><span class="lineNum">    2043 </span>            :   ASMJIT_INST_2x(vcvtpd2ps, Vcvtpd2ps, X86Xmm, X86Xmm)                        // AVX</a>
+<a name="2044"><span class="lineNum">    2044 </span>            :   ASMJIT_INST_2x(vcvtpd2ps, Vcvtpd2ps, X86Xmm, X86Mem)                        // AVX</a>
+<a name="2045"><span class="lineNum">    2045 </span>            :   ASMJIT_INST_2x(vcvtpd2ps, Vcvtpd2ps, X86Xmm, X86Ymm)                        // AVX</a>
+<a name="2046"><span class="lineNum">    2046 </span>            :   ASMJIT_INST_2x(vcvtpd2qq, Vcvtpd2qq, X86Xmm, X86Xmm)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2047"><span class="lineNum">    2047 </span>            :   ASMJIT_INST_2x(vcvtpd2qq, Vcvtpd2qq, X86Xmm, X86Mem)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2048"><span class="lineNum">    2048 </span>            :   ASMJIT_INST_2x(vcvtpd2qq, Vcvtpd2qq, X86Ymm, X86Ymm)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2049"><span class="lineNum">    2049 </span>            :   ASMJIT_INST_2x(vcvtpd2qq, Vcvtpd2qq, X86Ymm, X86Mem)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2050"><span class="lineNum">    2050 </span>            :   ASMJIT_INST_2x(vcvtpd2qq, Vcvtpd2qq, X86Zmm, X86Zmm)                        //      AVX512_DQ{kz|er|b64}</a>
+<a name="2051"><span class="lineNum">    2051 </span>            :   ASMJIT_INST_2x(vcvtpd2qq, Vcvtpd2qq, X86Zmm, X86Mem)                        //      AVX512_DQ{kz|er|b64}</a>
+<a name="2052"><span class="lineNum">    2052 </span>            :   ASMJIT_INST_2x(vcvtpd2udq, Vcvtpd2udq, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2053"><span class="lineNum">    2053 </span>            :   ASMJIT_INST_2x(vcvtpd2udq, Vcvtpd2udq, X86Xmm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2054"><span class="lineNum">    2054 </span>            :   ASMJIT_INST_2x(vcvtpd2udq, Vcvtpd2udq, X86Xmm, X86Ymm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :   ASMJIT_INST_2x(vcvtpd2udq, Vcvtpd2udq, X86Ymm, X86Zmm)                      //      AVX512_F{kz|er|b64}</a>
+<a name="2056"><span class="lineNum">    2056 </span>            :   ASMJIT_INST_2x(vcvtpd2udq, Vcvtpd2udq, X86Ymm, X86Mem)                      //      AVX512_F{kz|er|b64}</a>
+<a name="2057"><span class="lineNum">    2057 </span>            :   ASMJIT_INST_2x(vcvtpd2uqq, Vcvtpd2uqq, X86Xmm, X86Xmm)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2058"><span class="lineNum">    2058 </span>            :   ASMJIT_INST_2x(vcvtpd2uqq, Vcvtpd2uqq, X86Xmm, X86Mem)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2059"><span class="lineNum">    2059 </span>            :   ASMJIT_INST_2x(vcvtpd2uqq, Vcvtpd2uqq, X86Ymm, X86Ymm)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2060"><span class="lineNum">    2060 </span>            :   ASMJIT_INST_2x(vcvtpd2uqq, Vcvtpd2uqq, X86Ymm, X86Mem)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2061"><span class="lineNum">    2061 </span>            :   ASMJIT_INST_2x(vcvtpd2uqq, Vcvtpd2uqq, X86Zmm, X86Zmm)                      //      AVX512_DQ{kz|er|b64}</a>
+<a name="2062"><span class="lineNum">    2062 </span>            :   ASMJIT_INST_2x(vcvtpd2uqq, Vcvtpd2uqq, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|er|b64}</a>
+<a name="2063"><span class="lineNum">    2063 </span>            :   ASMJIT_INST_2x(vcvtph2ps, Vcvtph2ps, X86Xmm, X86Xmm)                        // F16C AVX512_F{kz}-VL</a>
+<a name="2064"><span class="lineNum">    2064 </span>            :   ASMJIT_INST_2x(vcvtph2ps, Vcvtph2ps, X86Xmm, X86Mem)                        // F16C AVX512_F{kz}-VL</a>
+<a name="2065"><span class="lineNum">    2065 </span>            :   ASMJIT_INST_2x(vcvtph2ps, Vcvtph2ps, X86Ymm, X86Xmm)                        // F16C AVX512_F{kz}-VL</a>
+<a name="2066"><span class="lineNum">    2066 </span>            :   ASMJIT_INST_2x(vcvtph2ps, Vcvtph2ps, X86Ymm, X86Mem)                        // F16C AVX512_F{kz}-VL</a>
+<a name="2067"><span class="lineNum">    2067 </span>            :   ASMJIT_INST_2x(vcvtph2ps, Vcvtph2ps, X86Zmm, X86Ymm)                        //      AVX512_F{kz|sae}</a>
+<a name="2068"><span class="lineNum">    2068 </span>            :   ASMJIT_INST_2x(vcvtph2ps, Vcvtph2ps, X86Zmm, X86Mem)                        //      AVX512_F{kz|sae}</a>
+<a name="2069"><span class="lineNum">    2069 </span>            :   ASMJIT_INST_2x(vcvtps2dq, Vcvtps2dq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2070"><span class="lineNum">    2070 </span>            :   ASMJIT_INST_2x(vcvtps2dq, Vcvtps2dq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2071"><span class="lineNum">    2071 </span>            :   ASMJIT_INST_2x(vcvtps2dq, Vcvtps2dq, X86Ymm, X86Ymm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2072"><span class="lineNum">    2072 </span>            :   ASMJIT_INST_2x(vcvtps2dq, Vcvtps2dq, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2073"><span class="lineNum">    2073 </span>            :   ASMJIT_INST_2x(vcvtps2dq, Vcvtps2dq, X86Zmm, X86Zmm)                        //      AVX512_F{kz|er|b32}</a>
+<a name="2074"><span class="lineNum">    2074 </span>            :   ASMJIT_INST_2x(vcvtps2dq, Vcvtps2dq, X86Zmm, X86Mem)                        //      AVX512_F{kz|er|b32}</a>
+<a name="2075"><span class="lineNum">    2075 </span>            :   ASMJIT_INST_2x(vcvtps2pd, Vcvtps2pd, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2076"><span class="lineNum">    2076 </span>            :   ASMJIT_INST_2x(vcvtps2pd, Vcvtps2pd, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :   ASMJIT_INST_2x(vcvtps2pd, Vcvtps2pd, X86Ymm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2078"><span class="lineNum">    2078 </span>            :   ASMJIT_INST_2x(vcvtps2pd, Vcvtps2pd, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2079"><span class="lineNum">    2079 </span>            :   ASMJIT_INST_2x(vcvtps2pd, Vcvtps2pd, X86Zmm, X86Ymm)                        //      AVX512_F{kz|er|b32}</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :   ASMJIT_INST_2x(vcvtps2pd, Vcvtps2pd, X86Zmm, X86Mem)                        //      AVX512_F{kz|er|b32}</a>
+<a name="2081"><span class="lineNum">    2081 </span>            :   ASMJIT_INST_3i(vcvtps2ph, Vcvtps2ph, X86Xmm, X86Xmm, Imm)                   // F16C AVX512_F{kz}-VL</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :   ASMJIT_INST_3i(vcvtps2ph, Vcvtps2ph, X86Mem, X86Xmm, Imm)                   // F16C AVX512_F{kz}-VL</a>
+<a name="2083"><span class="lineNum">    2083 </span>            :   ASMJIT_INST_3i(vcvtps2ph, Vcvtps2ph, X86Xmm, X86Ymm, Imm)                   // F16C AVX512_F{kz}-VL</a>
+<a name="2084"><span class="lineNum">    2084 </span>            :   ASMJIT_INST_3i(vcvtps2ph, Vcvtps2ph, X86Mem, X86Ymm, Imm)                   // F16C AVX512_F{kz}-VL</a>
+<a name="2085"><span class="lineNum">    2085 </span>            :   ASMJIT_INST_3i(vcvtps2ph, Vcvtps2ph, X86Ymm, X86Zmm, Imm)                   //      AVX512_F{kz|sae}</a>
+<a name="2086"><span class="lineNum">    2086 </span>            :   ASMJIT_INST_3i(vcvtps2ph, Vcvtps2ph, X86Mem, X86Zmm, Imm)                   //      AVX512_F{kz|sae}</a>
+<a name="2087"><span class="lineNum">    2087 </span>            :   ASMJIT_INST_2x(vcvtps2qq, Vcvtps2qq, X86Xmm, X86Xmm)                        //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2088"><span class="lineNum">    2088 </span>            :   ASMJIT_INST_2x(vcvtps2qq, Vcvtps2qq, X86Xmm, X86Mem)                        //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2089"><span class="lineNum">    2089 </span>            :   ASMJIT_INST_2x(vcvtps2qq, Vcvtps2qq, X86Ymm, X86Xmm)                        //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2090"><span class="lineNum">    2090 </span>            :   ASMJIT_INST_2x(vcvtps2qq, Vcvtps2qq, X86Ymm, X86Mem)                        //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2091"><span class="lineNum">    2091 </span>            :   ASMJIT_INST_2x(vcvtps2qq, Vcvtps2qq, X86Zmm, X86Ymm)                        //      AVX512_DQ{kz|er|b32}</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :   ASMJIT_INST_2x(vcvtps2qq, Vcvtps2qq, X86Zmm, X86Mem)                        //      AVX512_DQ{kz|er|b32}</a>
+<a name="2093"><span class="lineNum">    2093 </span>            :   ASMJIT_INST_2x(vcvtps2udq, Vcvtps2udq, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2094"><span class="lineNum">    2094 </span>            :   ASMJIT_INST_2x(vcvtps2udq, Vcvtps2udq, X86Xmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2095"><span class="lineNum">    2095 </span>            :   ASMJIT_INST_2x(vcvtps2udq, Vcvtps2udq, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2096"><span class="lineNum">    2096 </span>            :   ASMJIT_INST_2x(vcvtps2udq, Vcvtps2udq, X86Ymm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2097"><span class="lineNum">    2097 </span>            :   ASMJIT_INST_2x(vcvtps2udq, Vcvtps2udq, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2098"><span class="lineNum">    2098 </span>            :   ASMJIT_INST_2x(vcvtps2udq, Vcvtps2udq, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2099"><span class="lineNum">    2099 </span>            :   ASMJIT_INST_2x(vcvtps2uqq, Vcvtps2uqq, X86Xmm, X86Xmm)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2100"><span class="lineNum">    2100 </span>            :   ASMJIT_INST_2x(vcvtps2uqq, Vcvtps2uqq, X86Xmm, X86Mem)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2101"><span class="lineNum">    2101 </span>            :   ASMJIT_INST_2x(vcvtps2uqq, Vcvtps2uqq, X86Ymm, X86Xmm)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2102"><span class="lineNum">    2102 </span>            :   ASMJIT_INST_2x(vcvtps2uqq, Vcvtps2uqq, X86Ymm, X86Mem)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2103"><span class="lineNum">    2103 </span>            :   ASMJIT_INST_2x(vcvtps2uqq, Vcvtps2uqq, X86Zmm, X86Ymm)                      //      AVX512_DQ{kz|er|b32}</a>
+<a name="2104"><span class="lineNum">    2104 </span>            :   ASMJIT_INST_2x(vcvtps2uqq, Vcvtps2uqq, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|er|b32}</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :   ASMJIT_INST_2x(vcvtqq2pd, Vcvtqq2pd, X86Xmm, X86Xmm)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2106"><span class="lineNum">    2106 </span>            :   ASMJIT_INST_2x(vcvtqq2pd, Vcvtqq2pd, X86Xmm, X86Mem)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :   ASMJIT_INST_2x(vcvtqq2pd, Vcvtqq2pd, X86Ymm, X86Ymm)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2108"><span class="lineNum">    2108 </span>            :   ASMJIT_INST_2x(vcvtqq2pd, Vcvtqq2pd, X86Ymm, X86Mem)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2109"><span class="lineNum">    2109 </span>            :   ASMJIT_INST_2x(vcvtqq2pd, Vcvtqq2pd, X86Zmm, X86Zmm)                        //      AVX512_DQ{kz|er|b64}</a>
+<a name="2110"><span class="lineNum">    2110 </span>            :   ASMJIT_INST_2x(vcvtqq2pd, Vcvtqq2pd, X86Zmm, X86Mem)                        //      AVX512_DQ{kz|er|b64}</a>
+<a name="2111"><span class="lineNum">    2111 </span>            :   ASMJIT_INST_2x(vcvtqq2ps, Vcvtqq2ps, X86Xmm, X86Xmm)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2112"><span class="lineNum">    2112 </span>            :   ASMJIT_INST_2x(vcvtqq2ps, Vcvtqq2ps, X86Xmm, X86Mem)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2113"><span class="lineNum">    2113 </span>            :   ASMJIT_INST_2x(vcvtqq2ps, Vcvtqq2ps, X86Xmm, X86Ymm)                        //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2114"><span class="lineNum">    2114 </span>            :   ASMJIT_INST_2x(vcvtqq2ps, Vcvtqq2ps, X86Ymm, X86Zmm)                        //      AVX512_DQ{kz|er|b64}</a>
+<a name="2115"><span class="lineNum">    2115 </span>            :   ASMJIT_INST_2x(vcvtqq2ps, Vcvtqq2ps, X86Ymm, X86Mem)                        //      AVX512_DQ{kz|er|b64}</a>
+<a name="2116"><span class="lineNum">    2116 </span>            :   ASMJIT_INST_2x(vcvtsd2si, Vcvtsd2si, X86Gp, X86Xmm)                         // AVX  AVX512_F{er}</a>
+<a name="2117"><span class="lineNum">    2117 </span>            :   ASMJIT_INST_2x(vcvtsd2si, Vcvtsd2si, X86Gp, X86Mem)                         // AVX  AVX512_F{er}</a>
+<a name="2118"><span class="lineNum">    2118 </span>            :   ASMJIT_INST_3x(vcvtsd2ss, Vcvtsd2ss, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|er}</a>
+<a name="2119"><span class="lineNum">    2119 </span>            :   ASMJIT_INST_3x(vcvtsd2ss, Vcvtsd2ss, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|er}</a>
+<a name="2120"><span class="lineNum">    2120 </span>            :   ASMJIT_INST_2x(vcvtsd2usi, Vcvtsd2usi, X86Gp, X86Xmm)                       //      AVX512_F{er}</a>
+<a name="2121"><span class="lineNum">    2121 </span>            :   ASMJIT_INST_2x(vcvtsd2usi, Vcvtsd2usi, X86Gp, X86Mem)                       //      AVX512_F{er}</a>
+<a name="2122"><span class="lineNum">    2122 </span>            :   ASMJIT_INST_3x(vcvtsi2sd, Vcvtsi2sd, X86Xmm, X86Xmm, X86Gp)                 // AVX  AVX512_F{er}</a>
+<a name="2123"><span class="lineNum">    2123 </span>            :   ASMJIT_INST_3x(vcvtsi2sd, Vcvtsi2sd, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{er}</a>
+<a name="2124"><span class="lineNum">    2124 </span>            :   ASMJIT_INST_3x(vcvtsi2ss, Vcvtsi2ss, X86Xmm, X86Xmm, X86Gp)                 // AVX  AVX512_F{er}</a>
+<a name="2125"><span class="lineNum">    2125 </span>            :   ASMJIT_INST_3x(vcvtsi2ss, Vcvtsi2ss, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{er}</a>
+<a name="2126"><span class="lineNum">    2126 </span>            :   ASMJIT_INST_3x(vcvtss2sd, Vcvtss2sd, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|sae}</a>
+<a name="2127"><span class="lineNum">    2127 </span>            :   ASMJIT_INST_3x(vcvtss2sd, Vcvtss2sd, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|sae}</a>
+<a name="2128"><span class="lineNum">    2128 </span>            :   ASMJIT_INST_2x(vcvtss2si, Vcvtss2si, X86Gp, X86Xmm)                         // AVX  AVX512_F{er}</a>
+<a name="2129"><span class="lineNum">    2129 </span>            :   ASMJIT_INST_2x(vcvtss2si, Vcvtss2si, X86Gp, X86Mem)                         // AVX  AVX512_F{er}</a>
+<a name="2130"><span class="lineNum">    2130 </span>            :   ASMJIT_INST_2x(vcvtss2usi, Vcvtss2usi, X86Gp, X86Xmm)                       //      AVX512_F{er}</a>
+<a name="2131"><span class="lineNum">    2131 </span>            :   ASMJIT_INST_2x(vcvtss2usi, Vcvtss2usi, X86Gp, X86Mem)                       //      AVX512_F{er}</a>
+<a name="2132"><span class="lineNum">    2132 </span>            :   ASMJIT_INST_2x(vcvttpd2dq, Vcvttpd2dq, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2133"><span class="lineNum">    2133 </span>            :   ASMJIT_INST_2x(vcvttpd2dq, Vcvttpd2dq, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2134"><span class="lineNum">    2134 </span>            :   ASMJIT_INST_2x(vcvttpd2dq, Vcvttpd2dq, X86Xmm, X86Ymm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2135"><span class="lineNum">    2135 </span>            :   ASMJIT_INST_2x(vcvttpd2dq, Vcvttpd2dq, X86Ymm, X86Zmm)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2136"><span class="lineNum">    2136 </span>            :   ASMJIT_INST_2x(vcvttpd2dq, Vcvttpd2dq, X86Ymm, X86Mem)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2137"><span class="lineNum">    2137 </span>            :   ASMJIT_INST_2x(vcvttpd2qq, Vcvttpd2qq, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2138"><span class="lineNum">    2138 </span>            :   ASMJIT_INST_2x(vcvttpd2qq, Vcvttpd2qq, X86Xmm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2139"><span class="lineNum">    2139 </span>            :   ASMJIT_INST_2x(vcvttpd2qq, Vcvttpd2qq, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2140"><span class="lineNum">    2140 </span>            :   ASMJIT_INST_2x(vcvttpd2qq, Vcvttpd2qq, X86Ymm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="2141"><span class="lineNum">    2141 </span>            :   ASMJIT_INST_2x(vcvttpd2qq, Vcvttpd2qq, X86Zmm, X86Zmm)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2142"><span class="lineNum">    2142 </span>            :   ASMJIT_INST_2x(vcvttpd2qq, Vcvttpd2qq, X86Zmm, X86Mem)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2143"><span class="lineNum">    2143 </span>            :   ASMJIT_INST_2x(vcvttpd2udq, Vcvttpd2udq, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="2144"><span class="lineNum">    2144 </span>            :   ASMJIT_INST_2x(vcvttpd2udq, Vcvttpd2udq, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :   ASMJIT_INST_2x(vcvttpd2udq, Vcvttpd2udq, X86Xmm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="2146"><span class="lineNum">    2146 </span>            :   ASMJIT_INST_2x(vcvttpd2udq, Vcvttpd2udq, X86Ymm, X86Zmm)                    //      AVX512_F{kz|sae|b64}</a>
+<a name="2147"><span class="lineNum">    2147 </span>            :   ASMJIT_INST_2x(vcvttpd2udq, Vcvttpd2udq, X86Ymm, X86Mem)                    //      AVX512_F{kz|sae|b64}</a>
+<a name="2148"><span class="lineNum">    2148 </span>            :   ASMJIT_INST_2x(vcvttpd2uqq, Vcvttpd2uqq, X86Xmm, X86Xmm)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2149"><span class="lineNum">    2149 </span>            :   ASMJIT_INST_2x(vcvttpd2uqq, Vcvttpd2uqq, X86Xmm, X86Mem)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2150"><span class="lineNum">    2150 </span>            :   ASMJIT_INST_2x(vcvttpd2uqq, Vcvttpd2uqq, X86Ymm, X86Ymm)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2151"><span class="lineNum">    2151 </span>            :   ASMJIT_INST_2x(vcvttpd2uqq, Vcvttpd2uqq, X86Ymm, X86Mem)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2152"><span class="lineNum">    2152 </span>            :   ASMJIT_INST_2x(vcvttpd2uqq, Vcvttpd2uqq, X86Zmm, X86Zmm)                    //      AVX512_DQ{kz|sae|b64}</a>
+<a name="2153"><span class="lineNum">    2153 </span>            :   ASMJIT_INST_2x(vcvttpd2uqq, Vcvttpd2uqq, X86Zmm, X86Mem)                    //      AVX512_DQ{kz|sae|b64}</a>
+<a name="2154"><span class="lineNum">    2154 </span>            :   ASMJIT_INST_2x(vcvttps2dq, Vcvttps2dq, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2155"><span class="lineNum">    2155 </span>            :   ASMJIT_INST_2x(vcvttps2dq, Vcvttps2dq, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2156"><span class="lineNum">    2156 </span>            :   ASMJIT_INST_2x(vcvttps2dq, Vcvttps2dq, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2157"><span class="lineNum">    2157 </span>            :   ASMJIT_INST_2x(vcvttps2dq, Vcvttps2dq, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2158"><span class="lineNum">    2158 </span>            :   ASMJIT_INST_2x(vcvttps2dq, Vcvttps2dq, X86Zmm, X86Zmm)                      //      AVX512_F{kz|sae|b32}</a>
+<a name="2159"><span class="lineNum">    2159 </span>            :   ASMJIT_INST_2x(vcvttps2dq, Vcvttps2dq, X86Zmm, X86Mem)                      //      AVX512_F{kz|sae|b32}</a>
+<a name="2160"><span class="lineNum">    2160 </span>            :   ASMJIT_INST_2x(vcvttps2qq, Vcvttps2qq, X86Xmm, X86Xmm)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2161"><span class="lineNum">    2161 </span>            :   ASMJIT_INST_2x(vcvttps2qq, Vcvttps2qq, X86Xmm, X86Mem)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2162"><span class="lineNum">    2162 </span>            :   ASMJIT_INST_2x(vcvttps2qq, Vcvttps2qq, X86Ymm, X86Xmm)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2163"><span class="lineNum">    2163 </span>            :   ASMJIT_INST_2x(vcvttps2qq, Vcvttps2qq, X86Ymm, X86Mem)                      //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2164"><span class="lineNum">    2164 </span>            :   ASMJIT_INST_2x(vcvttps2qq, Vcvttps2qq, X86Zmm, X86Ymm)                      //      AVX512_DQ{kz|sae|b32}</a>
+<a name="2165"><span class="lineNum">    2165 </span>            :   ASMJIT_INST_2x(vcvttps2qq, Vcvttps2qq, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|sae|b32}</a>
+<a name="2166"><span class="lineNum">    2166 </span>            :   ASMJIT_INST_2x(vcvttps2udq, Vcvttps2udq, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="2167"><span class="lineNum">    2167 </span>            :   ASMJIT_INST_2x(vcvttps2udq, Vcvttps2udq, X86Xmm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="2168"><span class="lineNum">    2168 </span>            :   ASMJIT_INST_2x(vcvttps2udq, Vcvttps2udq, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="2169"><span class="lineNum">    2169 </span>            :   ASMJIT_INST_2x(vcvttps2udq, Vcvttps2udq, X86Ymm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="2170"><span class="lineNum">    2170 </span>            :   ASMJIT_INST_2x(vcvttps2udq, Vcvttps2udq, X86Zmm, X86Zmm)                    //      AVX512_F{kz|sae|b32}</a>
+<a name="2171"><span class="lineNum">    2171 </span>            :   ASMJIT_INST_2x(vcvttps2udq, Vcvttps2udq, X86Zmm, X86Mem)                    //      AVX512_F{kz|sae|b32}</a>
+<a name="2172"><span class="lineNum">    2172 </span>            :   ASMJIT_INST_2x(vcvttps2uqq, Vcvttps2uqq, X86Xmm, X86Xmm)                    //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2173"><span class="lineNum">    2173 </span>            :   ASMJIT_INST_2x(vcvttps2uqq, Vcvttps2uqq, X86Xmm, X86Mem)                    //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2174"><span class="lineNum">    2174 </span>            :   ASMJIT_INST_2x(vcvttps2uqq, Vcvttps2uqq, X86Ymm, X86Xmm)                    //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :   ASMJIT_INST_2x(vcvttps2uqq, Vcvttps2uqq, X86Ymm, X86Mem)                    //      AVX512_DQ{kz|b32}-VL</a>
+<a name="2176"><span class="lineNum">    2176 </span>            :   ASMJIT_INST_2x(vcvttps2uqq, Vcvttps2uqq, X86Zmm, X86Ymm)                    //      AVX512_DQ{kz|sae|b32}</a>
+<a name="2177"><span class="lineNum">    2177 </span>            :   ASMJIT_INST_2x(vcvttps2uqq, Vcvttps2uqq, X86Zmm, X86Mem)                    //      AVX512_DQ{kz|sae|b32}</a>
+<a name="2178"><span class="lineNum">    2178 </span>            :   ASMJIT_INST_2x(vcvttsd2si, Vcvttsd2si, X86Gp, X86Xmm)                       // AVX  AVX512_F{sae}</a>
+<a name="2179"><span class="lineNum">    2179 </span>            :   ASMJIT_INST_2x(vcvttsd2si, Vcvttsd2si, X86Gp, X86Mem)                       // AVX  AVX512_F{sae}</a>
+<a name="2180"><span class="lineNum">    2180 </span>            :   ASMJIT_INST_2x(vcvttsd2usi, Vcvttsd2usi, X86Gp, X86Xmm)                     //      AVX512_F{sae}</a>
+<a name="2181"><span class="lineNum">    2181 </span>            :   ASMJIT_INST_2x(vcvttsd2usi, Vcvttsd2usi, X86Gp, X86Mem)                     //      AVX512_F{sae}</a>
+<a name="2182"><span class="lineNum">    2182 </span>            :   ASMJIT_INST_2x(vcvttss2si, Vcvttss2si, X86Gp, X86Xmm)                       // AVX  AVX512_F{sae}</a>
+<a name="2183"><span class="lineNum">    2183 </span>            :   ASMJIT_INST_2x(vcvttss2si, Vcvttss2si, X86Gp, X86Mem)                       // AVX  AVX512_F{sae}</a>
+<a name="2184"><span class="lineNum">    2184 </span>            :   ASMJIT_INST_2x(vcvttss2usi, Vcvttss2usi, X86Gp, X86Xmm)                     //      AVX512_F{sae}</a>
+<a name="2185"><span class="lineNum">    2185 </span>            :   ASMJIT_INST_2x(vcvttss2usi, Vcvttss2usi, X86Gp, X86Mem)                     //      AVX512_F{sae}</a>
+<a name="2186"><span class="lineNum">    2186 </span>            :   ASMJIT_INST_2x(vcvtudq2pd, Vcvtudq2pd, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2187"><span class="lineNum">    2187 </span>            :   ASMJIT_INST_2x(vcvtudq2pd, Vcvtudq2pd, X86Xmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2188"><span class="lineNum">    2188 </span>            :   ASMJIT_INST_2x(vcvtudq2pd, Vcvtudq2pd, X86Ymm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2189"><span class="lineNum">    2189 </span>            :   ASMJIT_INST_2x(vcvtudq2pd, Vcvtudq2pd, X86Ymm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2190"><span class="lineNum">    2190 </span>            :   ASMJIT_INST_2x(vcvtudq2pd, Vcvtudq2pd, X86Zmm, X86Ymm)                      //      AVX512_F{kz|b32}</a>
+<a name="2191"><span class="lineNum">    2191 </span>            :   ASMJIT_INST_2x(vcvtudq2pd, Vcvtudq2pd, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}</a>
+<a name="2192"><span class="lineNum">    2192 </span>            :   ASMJIT_INST_2x(vcvtudq2ps, Vcvtudq2ps, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2193"><span class="lineNum">    2193 </span>            :   ASMJIT_INST_2x(vcvtudq2ps, Vcvtudq2ps, X86Xmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2194"><span class="lineNum">    2194 </span>            :   ASMJIT_INST_2x(vcvtudq2ps, Vcvtudq2ps, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2195"><span class="lineNum">    2195 </span>            :   ASMJIT_INST_2x(vcvtudq2ps, Vcvtudq2ps, X86Ymm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="2196"><span class="lineNum">    2196 </span>            :   ASMJIT_INST_2x(vcvtudq2ps, Vcvtudq2ps, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2197"><span class="lineNum">    2197 </span>            :   ASMJIT_INST_2x(vcvtudq2ps, Vcvtudq2ps, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2198"><span class="lineNum">    2198 </span>            :   ASMJIT_INST_2x(vcvtuqq2pd, Vcvtuqq2pd, X86Xmm, X86Xmm)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :   ASMJIT_INST_2x(vcvtuqq2pd, Vcvtuqq2pd, X86Xmm, X86Mem)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2200"><span class="lineNum">    2200 </span>            :   ASMJIT_INST_2x(vcvtuqq2pd, Vcvtuqq2pd, X86Ymm, X86Ymm)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2201"><span class="lineNum">    2201 </span>            :   ASMJIT_INST_2x(vcvtuqq2pd, Vcvtuqq2pd, X86Ymm, X86Mem)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2202"><span class="lineNum">    2202 </span>            :   ASMJIT_INST_2x(vcvtuqq2pd, Vcvtuqq2pd, X86Zmm, X86Zmm)                      //      AVX512_DQ{kz|er|b64}</a>
+<a name="2203"><span class="lineNum">    2203 </span>            :   ASMJIT_INST_2x(vcvtuqq2pd, Vcvtuqq2pd, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|er|b64}</a>
+<a name="2204"><span class="lineNum">    2204 </span>            :   ASMJIT_INST_2x(vcvtuqq2ps, Vcvtuqq2ps, X86Xmm, X86Xmm)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2205"><span class="lineNum">    2205 </span>            :   ASMJIT_INST_2x(vcvtuqq2ps, Vcvtuqq2ps, X86Xmm, X86Mem)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2206"><span class="lineNum">    2206 </span>            :   ASMJIT_INST_2x(vcvtuqq2ps, Vcvtuqq2ps, X86Xmm, X86Ymm)                      //      AVX512_DQ{kz|b64}-VL</a>
+<a name="2207"><span class="lineNum">    2207 </span>            :   ASMJIT_INST_2x(vcvtuqq2ps, Vcvtuqq2ps, X86Ymm, X86Zmm)                      //      AVX512_DQ{kz|er|b64}</a>
+<a name="2208"><span class="lineNum">    2208 </span>            :   ASMJIT_INST_2x(vcvtuqq2ps, Vcvtuqq2ps, X86Ymm, X86Mem)                      //      AVX512_DQ{kz|er|b64}</a>
+<a name="2209"><span class="lineNum">    2209 </span>            :   ASMJIT_INST_3x(vcvtusi2sd, Vcvtusi2sd, X86Xmm, X86Xmm, X86Gp)               //      AVX512_F{er}</a>
+<a name="2210"><span class="lineNum">    2210 </span>            :   ASMJIT_INST_3x(vcvtusi2sd, Vcvtusi2sd, X86Xmm, X86Xmm, X86Mem)              //      AVX512_F{er}</a>
+<a name="2211"><span class="lineNum">    2211 </span>            :   ASMJIT_INST_3x(vcvtusi2ss, Vcvtusi2ss, X86Xmm, X86Xmm, X86Gp)               //      AVX512_F{er}</a>
+<a name="2212"><span class="lineNum">    2212 </span>            :   ASMJIT_INST_3x(vcvtusi2ss, Vcvtusi2ss, X86Xmm, X86Xmm, X86Mem)              //      AVX512_F{er}</a>
+<a name="2213"><span class="lineNum">    2213 </span>            :   ASMJIT_INST_4i(vdbpsadbw, Vdbpsadbw, X86Xmm, X86Xmm, X86Xmm, Imm)           //      AVX512_BW{kz}-VL</a>
+<a name="2214"><span class="lineNum">    2214 </span>            :   ASMJIT_INST_4i(vdbpsadbw, Vdbpsadbw, X86Xmm, X86Xmm, X86Mem, Imm)           //      AVX512_BW{kz}-VL</a>
+<a name="2215"><span class="lineNum">    2215 </span>            :   ASMJIT_INST_4i(vdbpsadbw, Vdbpsadbw, X86Ymm, X86Ymm, X86Ymm, Imm)           //      AVX512_BW{kz}-VL</a>
+<a name="2216"><span class="lineNum">    2216 </span>            :   ASMJIT_INST_4i(vdbpsadbw, Vdbpsadbw, X86Ymm, X86Ymm, X86Mem, Imm)           //      AVX512_BW{kz}-VL</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :   ASMJIT_INST_4i(vdbpsadbw, Vdbpsadbw, X86Zmm, X86Zmm, X86Zmm, Imm)           //      AVX512_BW{kz}</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :   ASMJIT_INST_4i(vdbpsadbw, Vdbpsadbw, X86Zmm, X86Zmm, X86Mem, Imm)           //      AVX512_BW{kz}</a>
+<a name="2219"><span class="lineNum">    2219 </span>            :   ASMJIT_INST_3x(vdivpd, Vdivpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2220"><span class="lineNum">    2220 </span>            :   ASMJIT_INST_3x(vdivpd, Vdivpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2221"><span class="lineNum">    2221 </span>            :   ASMJIT_INST_3x(vdivpd, Vdivpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2222"><span class="lineNum">    2222 </span>            :   ASMJIT_INST_3x(vdivpd, Vdivpd, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2223"><span class="lineNum">    2223 </span>            :   ASMJIT_INST_3x(vdivpd, Vdivpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b64}</a>
+<a name="2224"><span class="lineNum">    2224 </span>            :   ASMJIT_INST_3x(vdivpd, Vdivpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b64}</a>
+<a name="2225"><span class="lineNum">    2225 </span>            :   ASMJIT_INST_3x(vdivps, Vdivps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2226"><span class="lineNum">    2226 </span>            :   ASMJIT_INST_3x(vdivps, Vdivps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2227"><span class="lineNum">    2227 </span>            :   ASMJIT_INST_3x(vdivps, Vdivps, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2228"><span class="lineNum">    2228 </span>            :   ASMJIT_INST_3x(vdivps, Vdivps, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2229"><span class="lineNum">    2229 </span>            :   ASMJIT_INST_3x(vdivps, Vdivps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2230"><span class="lineNum">    2230 </span>            :   ASMJIT_INST_3x(vdivps, Vdivps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2231"><span class="lineNum">    2231 </span>            :   ASMJIT_INST_3x(vdivsd, Vdivsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2232"><span class="lineNum">    2232 </span>            :   ASMJIT_INST_3x(vdivsd, Vdivsd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2233"><span class="lineNum">    2233 </span>            :   ASMJIT_INST_3x(vdivss, Vdivss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2234"><span class="lineNum">    2234 </span>            :   ASMJIT_INST_3x(vdivss, Vdivss, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2235"><span class="lineNum">    2235 </span>            :   ASMJIT_INST_4i(vdppd, Vdppd, X86Xmm, X86Xmm, X86Xmm, Imm)                   // AVX</a>
+<a name="2236"><span class="lineNum">    2236 </span>            :   ASMJIT_INST_4i(vdppd, Vdppd, X86Xmm, X86Xmm, X86Mem, Imm)                   // AVX</a>
+<a name="2237"><span class="lineNum">    2237 </span>            :   ASMJIT_INST_4i(vdpps, Vdpps, X86Xmm, X86Xmm, X86Xmm, Imm)                   // AVX</a>
+<a name="2238"><span class="lineNum">    2238 </span>            :   ASMJIT_INST_4i(vdpps, Vdpps, X86Xmm, X86Xmm, X86Mem, Imm)                   // AVX</a>
+<a name="2239"><span class="lineNum">    2239 </span>            :   ASMJIT_INST_4i(vdpps, Vdpps, X86Ymm, X86Ymm, X86Ymm, Imm)                   // AVX</a>
+<a name="2240"><span class="lineNum">    2240 </span>            :   ASMJIT_INST_4i(vdpps, Vdpps, X86Ymm, X86Ymm, X86Mem, Imm)                   // AVX</a>
+<a name="2241"><span class="lineNum">    2241 </span>            :   ASMJIT_INST_2x(vexp2pd, Vexp2pd, X86Zmm, X86Zmm)                            //      AVX512_ER{kz|sae|b64}</a>
+<a name="2242"><span class="lineNum">    2242 </span>            :   ASMJIT_INST_2x(vexp2pd, Vexp2pd, X86Zmm, X86Mem)                            //      AVX512_ER{kz|sae|b64}</a>
+<a name="2243"><span class="lineNum">    2243 </span>            :   ASMJIT_INST_2x(vexp2ps, Vexp2ps, X86Zmm, X86Zmm)                            //      AVX512_ER{kz|sae|b32}</a>
+<a name="2244"><span class="lineNum">    2244 </span>            :   ASMJIT_INST_2x(vexp2ps, Vexp2ps, X86Zmm, X86Mem)                            //      AVX512_ER{kz|sae|b32}</a>
+<a name="2245"><span class="lineNum">    2245 </span>            :   ASMJIT_INST_2x(vexpandpd, Vexpandpd, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2246"><span class="lineNum">    2246 </span>            :   ASMJIT_INST_2x(vexpandpd, Vexpandpd, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2247"><span class="lineNum">    2247 </span>            :   ASMJIT_INST_2x(vexpandpd, Vexpandpd, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2248"><span class="lineNum">    2248 </span>            :   ASMJIT_INST_2x(vexpandpd, Vexpandpd, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2249"><span class="lineNum">    2249 </span>            :   ASMJIT_INST_2x(vexpandpd, Vexpandpd, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2250"><span class="lineNum">    2250 </span>            :   ASMJIT_INST_2x(vexpandpd, Vexpandpd, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2251"><span class="lineNum">    2251 </span>            :   ASMJIT_INST_2x(vexpandps, Vexpandps, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2252"><span class="lineNum">    2252 </span>            :   ASMJIT_INST_2x(vexpandps, Vexpandps, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2253"><span class="lineNum">    2253 </span>            :   ASMJIT_INST_2x(vexpandps, Vexpandps, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2254"><span class="lineNum">    2254 </span>            :   ASMJIT_INST_2x(vexpandps, Vexpandps, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2255"><span class="lineNum">    2255 </span>            :   ASMJIT_INST_2x(vexpandps, Vexpandps, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2256"><span class="lineNum">    2256 </span>            :   ASMJIT_INST_2x(vexpandps, Vexpandps, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2257"><span class="lineNum">    2257 </span>            :   ASMJIT_INST_3i(vextractf128, Vextractf128, X86Xmm, X86Ymm, Imm)             // AVX</a>
+<a name="2258"><span class="lineNum">    2258 </span>            :   ASMJIT_INST_3i(vextractf128, Vextractf128, X86Mem, X86Ymm, Imm)             // AVX</a>
+<a name="2259"><span class="lineNum">    2259 </span>            :   ASMJIT_INST_3i(vextractf32x4, Vextractf32x4, X86Xmm, X86Ymm, Imm)           //      AVX512_F{kz}-VL</a>
+<a name="2260"><span class="lineNum">    2260 </span>            :   ASMJIT_INST_3i(vextractf32x4, Vextractf32x4, X86Mem, X86Ymm, Imm)           //      AVX512_F{kz}-VL</a>
+<a name="2261"><span class="lineNum">    2261 </span>            :   ASMJIT_INST_3i(vextractf32x4, Vextractf32x4, X86Xmm, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2262"><span class="lineNum">    2262 </span>            :   ASMJIT_INST_3i(vextractf32x4, Vextractf32x4, X86Mem, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2263"><span class="lineNum">    2263 </span>            :   ASMJIT_INST_3i(vextractf32x8, Vextractf32x8, X86Ymm, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2264"><span class="lineNum">    2264 </span>            :   ASMJIT_INST_3i(vextractf32x8, Vextractf32x8, X86Mem, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2265"><span class="lineNum">    2265 </span>            :   ASMJIT_INST_3i(vextractf64x2, Vextractf64x2, X86Xmm, X86Ymm, Imm)           //      AVX512_DQ{kz}-VL</a>
+<a name="2266"><span class="lineNum">    2266 </span>            :   ASMJIT_INST_3i(vextractf64x2, Vextractf64x2, X86Mem, X86Ymm, Imm)           //      AVX512_DQ{kz}-VL</a>
+<a name="2267"><span class="lineNum">    2267 </span>            :   ASMJIT_INST_3i(vextractf64x2, Vextractf64x2, X86Xmm, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2268"><span class="lineNum">    2268 </span>            :   ASMJIT_INST_3i(vextractf64x2, Vextractf64x2, X86Mem, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2269"><span class="lineNum">    2269 </span>            :   ASMJIT_INST_3i(vextractf64x4, Vextractf64x4, X86Ymm, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2270"><span class="lineNum">    2270 </span>            :   ASMJIT_INST_3i(vextractf64x4, Vextractf64x4, X86Mem, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :   ASMJIT_INST_3i(vextracti128, Vextracti128, X86Xmm, X86Ymm, Imm)             // AVX2</a>
+<a name="2272"><span class="lineNum">    2272 </span>            :   ASMJIT_INST_3i(vextracti128, Vextracti128, X86Mem, X86Ymm, Imm)             // AVX2</a>
+<a name="2273"><span class="lineNum">    2273 </span>            :   ASMJIT_INST_3i(vextracti32x4, Vextracti32x4, X86Xmm, X86Ymm, Imm)           //      AVX512_F{kz}-VL</a>
+<a name="2274"><span class="lineNum">    2274 </span>            :   ASMJIT_INST_3i(vextracti32x4, Vextracti32x4, X86Mem, X86Ymm, Imm)           //      AVX512_F{kz}-VL</a>
+<a name="2275"><span class="lineNum">    2275 </span>            :   ASMJIT_INST_3i(vextracti32x4, Vextracti32x4, X86Xmm, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2276"><span class="lineNum">    2276 </span>            :   ASMJIT_INST_3i(vextracti32x4, Vextracti32x4, X86Mem, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2277"><span class="lineNum">    2277 </span>            :   ASMJIT_INST_3i(vextracti32x8, Vextracti32x8, X86Ymm, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2278"><span class="lineNum">    2278 </span>            :   ASMJIT_INST_3i(vextracti32x8, Vextracti32x8, X86Mem, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2279"><span class="lineNum">    2279 </span>            :   ASMJIT_INST_3i(vextracti64x2, Vextracti64x2, X86Xmm, X86Ymm, Imm)           //      AVX512_DQ{kz}-VL</a>
+<a name="2280"><span class="lineNum">    2280 </span>            :   ASMJIT_INST_3i(vextracti64x2, Vextracti64x2, X86Mem, X86Ymm, Imm)           //      AVX512_DQ{kz}-VL</a>
+<a name="2281"><span class="lineNum">    2281 </span>            :   ASMJIT_INST_3i(vextracti64x2, Vextracti64x2, X86Xmm, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2282"><span class="lineNum">    2282 </span>            :   ASMJIT_INST_3i(vextracti64x2, Vextracti64x2, X86Mem, X86Zmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="2283"><span class="lineNum">    2283 </span>            :   ASMJIT_INST_3i(vextracti64x4, Vextracti64x4, X86Ymm, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2284"><span class="lineNum">    2284 </span>            :   ASMJIT_INST_3i(vextracti64x4, Vextracti64x4, X86Mem, X86Zmm, Imm)           //      AVX512_F{kz}</a>
+<a name="2285"><span class="lineNum">    2285 </span>            :   ASMJIT_INST_3i(vextractps, Vextractps, X86Gp, X86Xmm, Imm)                  // AVX  AVX512_F</a>
+<a name="2286"><span class="lineNum">    2286 </span>            :   ASMJIT_INST_3i(vextractps, Vextractps, X86Mem, X86Xmm, Imm)                 // AVX  AVX512_F</a>
+<a name="2287"><span class="lineNum">    2287 </span>            :   ASMJIT_INST_4i(vfixupimmpd, Vfixupimmpd, X86Xmm, X86Xmm, X86Xmm, Imm)       //      AVX512_F{kz|b64}-VL</a>
+<a name="2288"><span class="lineNum">    2288 </span>            :   ASMJIT_INST_4i(vfixupimmpd, Vfixupimmpd, X86Xmm, X86Xmm, X86Mem, Imm)       //      AVX512_F{kz|b64}-VL</a>
+<a name="2289"><span class="lineNum">    2289 </span>            :   ASMJIT_INST_4i(vfixupimmpd, Vfixupimmpd, X86Ymm, X86Ymm, X86Ymm, Imm)       //      AVX512_F{kz|b64}-VL</a>
+<a name="2290"><span class="lineNum">    2290 </span>            :   ASMJIT_INST_4i(vfixupimmpd, Vfixupimmpd, X86Ymm, X86Ymm, X86Mem, Imm)       //      AVX512_F{kz|b64}-VL</a>
+<a name="2291"><span class="lineNum">    2291 </span>            :   ASMJIT_INST_4i(vfixupimmpd, Vfixupimmpd, X86Zmm, X86Zmm, X86Zmm, Imm)       //      AVX512_F{kz|sae|b64}</a>
+<a name="2292"><span class="lineNum">    2292 </span>            :   ASMJIT_INST_4i(vfixupimmpd, Vfixupimmpd, X86Zmm, X86Zmm, X86Mem, Imm)       //      AVX512_F{kz|sae|b64}</a>
+<a name="2293"><span class="lineNum">    2293 </span>            :   ASMJIT_INST_4i(vfixupimmps, Vfixupimmps, X86Xmm, X86Xmm, X86Xmm, Imm)       //      AVX512_F{kz|b32}-VL</a>
+<a name="2294"><span class="lineNum">    2294 </span>            :   ASMJIT_INST_4i(vfixupimmps, Vfixupimmps, X86Xmm, X86Xmm, X86Mem, Imm)       //      AVX512_F{kz|b32}-VL</a>
+<a name="2295"><span class="lineNum">    2295 </span>            :   ASMJIT_INST_4i(vfixupimmps, Vfixupimmps, X86Ymm, X86Ymm, X86Ymm, Imm)       //      AVX512_F{kz|b32}-VL</a>
+<a name="2296"><span class="lineNum">    2296 </span>            :   ASMJIT_INST_4i(vfixupimmps, Vfixupimmps, X86Ymm, X86Ymm, X86Mem, Imm)       //      AVX512_F{kz|b32}-VL</a>
+<a name="2297"><span class="lineNum">    2297 </span>            :   ASMJIT_INST_4i(vfixupimmps, Vfixupimmps, X86Zmm, X86Zmm, X86Zmm, Imm)       //      AVX512_F{kz|sae|b32}</a>
+<a name="2298"><span class="lineNum">    2298 </span>            :   ASMJIT_INST_4i(vfixupimmps, Vfixupimmps, X86Zmm, X86Zmm, X86Mem, Imm)       //      AVX512_F{kz|sae|b32}</a>
+<a name="2299"><span class="lineNum">    2299 </span>            :   ASMJIT_INST_4i(vfixupimmsd, Vfixupimmsd, X86Xmm, X86Xmm, X86Xmm, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="2300"><span class="lineNum">    2300 </span>            :   ASMJIT_INST_4i(vfixupimmsd, Vfixupimmsd, X86Xmm, X86Xmm, X86Mem, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="2301"><span class="lineNum">    2301 </span>            :   ASMJIT_INST_4i(vfixupimmss, Vfixupimmss, X86Xmm, X86Xmm, X86Xmm, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="2302"><span class="lineNum">    2302 </span>            :   ASMJIT_INST_4i(vfixupimmss, Vfixupimmss, X86Xmm, X86Xmm, X86Mem, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="2303"><span class="lineNum">    2303 </span>            :   ASMJIT_INST_3x(vfmadd132pd, Vfmadd132pd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2304"><span class="lineNum">    2304 </span>            :   ASMJIT_INST_3x(vfmadd132pd, Vfmadd132pd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2305"><span class="lineNum">    2305 </span>            :   ASMJIT_INST_3x(vfmadd132pd, Vfmadd132pd, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2306"><span class="lineNum">    2306 </span>            :   ASMJIT_INST_3x(vfmadd132pd, Vfmadd132pd, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2307"><span class="lineNum">    2307 </span>            :   ASMJIT_INST_3x(vfmadd132pd, Vfmadd132pd, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2308"><span class="lineNum">    2308 </span>            :   ASMJIT_INST_3x(vfmadd132pd, Vfmadd132pd, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2309"><span class="lineNum">    2309 </span>            :   ASMJIT_INST_3x(vfmadd132ps, Vfmadd132ps, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2310"><span class="lineNum">    2310 </span>            :   ASMJIT_INST_3x(vfmadd132ps, Vfmadd132ps, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2311"><span class="lineNum">    2311 </span>            :   ASMJIT_INST_3x(vfmadd132ps, Vfmadd132ps, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :   ASMJIT_INST_3x(vfmadd132ps, Vfmadd132ps, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2313"><span class="lineNum">    2313 </span>            :   ASMJIT_INST_3x(vfmadd132ps, Vfmadd132ps, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2314"><span class="lineNum">    2314 </span>            :   ASMJIT_INST_3x(vfmadd132ps, Vfmadd132ps, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2315"><span class="lineNum">    2315 </span>            :   ASMJIT_INST_3x(vfmadd132sd, Vfmadd132sd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2316"><span class="lineNum">    2316 </span>            :   ASMJIT_INST_3x(vfmadd132sd, Vfmadd132sd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2317"><span class="lineNum">    2317 </span>            :   ASMJIT_INST_3x(vfmadd132ss, Vfmadd132ss, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2318"><span class="lineNum">    2318 </span>            :   ASMJIT_INST_3x(vfmadd132ss, Vfmadd132ss, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2319"><span class="lineNum">    2319 </span>            :   ASMJIT_INST_3x(vfmadd213pd, Vfmadd213pd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2320"><span class="lineNum">    2320 </span>            :   ASMJIT_INST_3x(vfmadd213pd, Vfmadd213pd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2321"><span class="lineNum">    2321 </span>            :   ASMJIT_INST_3x(vfmadd213pd, Vfmadd213pd, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :   ASMJIT_INST_3x(vfmadd213pd, Vfmadd213pd, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2323"><span class="lineNum">    2323 </span>            :   ASMJIT_INST_3x(vfmadd213pd, Vfmadd213pd, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2324"><span class="lineNum">    2324 </span>            :   ASMJIT_INST_3x(vfmadd213pd, Vfmadd213pd, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2325"><span class="lineNum">    2325 </span>            :   ASMJIT_INST_3x(vfmadd213ps, Vfmadd213ps, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2326"><span class="lineNum">    2326 </span>            :   ASMJIT_INST_3x(vfmadd213ps, Vfmadd213ps, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2327"><span class="lineNum">    2327 </span>            :   ASMJIT_INST_3x(vfmadd213ps, Vfmadd213ps, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2328"><span class="lineNum">    2328 </span>            :   ASMJIT_INST_3x(vfmadd213ps, Vfmadd213ps, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2329"><span class="lineNum">    2329 </span>            :   ASMJIT_INST_3x(vfmadd213ps, Vfmadd213ps, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2330"><span class="lineNum">    2330 </span>            :   ASMJIT_INST_3x(vfmadd213ps, Vfmadd213ps, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2331"><span class="lineNum">    2331 </span>            :   ASMJIT_INST_3x(vfmadd213sd, Vfmadd213sd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2332"><span class="lineNum">    2332 </span>            :   ASMJIT_INST_3x(vfmadd213sd, Vfmadd213sd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2333"><span class="lineNum">    2333 </span>            :   ASMJIT_INST_3x(vfmadd213ss, Vfmadd213ss, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2334"><span class="lineNum">    2334 </span>            :   ASMJIT_INST_3x(vfmadd213ss, Vfmadd213ss, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2335"><span class="lineNum">    2335 </span>            :   ASMJIT_INST_3x(vfmadd231pd, Vfmadd231pd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2336"><span class="lineNum">    2336 </span>            :   ASMJIT_INST_3x(vfmadd231pd, Vfmadd231pd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2337"><span class="lineNum">    2337 </span>            :   ASMJIT_INST_3x(vfmadd231pd, Vfmadd231pd, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2338"><span class="lineNum">    2338 </span>            :   ASMJIT_INST_3x(vfmadd231pd, Vfmadd231pd, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2339"><span class="lineNum">    2339 </span>            :   ASMJIT_INST_3x(vfmadd231pd, Vfmadd231pd, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2340"><span class="lineNum">    2340 </span>            :   ASMJIT_INST_3x(vfmadd231pd, Vfmadd231pd, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2341"><span class="lineNum">    2341 </span>            :   ASMJIT_INST_3x(vfmadd231ps, Vfmadd231ps, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2342"><span class="lineNum">    2342 </span>            :   ASMJIT_INST_3x(vfmadd231ps, Vfmadd231ps, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2343"><span class="lineNum">    2343 </span>            :   ASMJIT_INST_3x(vfmadd231ps, Vfmadd231ps, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2344"><span class="lineNum">    2344 </span>            :   ASMJIT_INST_3x(vfmadd231ps, Vfmadd231ps, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2345"><span class="lineNum">    2345 </span>            :   ASMJIT_INST_3x(vfmadd231ps, Vfmadd231ps, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2346"><span class="lineNum">    2346 </span>            :   ASMJIT_INST_3x(vfmadd231ps, Vfmadd231ps, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2347"><span class="lineNum">    2347 </span>            :   ASMJIT_INST_3x(vfmadd231sd, Vfmadd231sd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2348"><span class="lineNum">    2348 </span>            :   ASMJIT_INST_3x(vfmadd231sd, Vfmadd231sd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2349"><span class="lineNum">    2349 </span>            :   ASMJIT_INST_3x(vfmadd231ss, Vfmadd231ss, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2350"><span class="lineNum">    2350 </span>            :   ASMJIT_INST_3x(vfmadd231ss, Vfmadd231ss, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2351"><span class="lineNum">    2351 </span>            :   ASMJIT_INST_3x(vfmaddsub132pd, Vfmaddsub132pd, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2352"><span class="lineNum">    2352 </span>            :   ASMJIT_INST_3x(vfmaddsub132pd, Vfmaddsub132pd, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2353"><span class="lineNum">    2353 </span>            :   ASMJIT_INST_3x(vfmaddsub132pd, Vfmaddsub132pd, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2354"><span class="lineNum">    2354 </span>            :   ASMJIT_INST_3x(vfmaddsub132pd, Vfmaddsub132pd, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2355"><span class="lineNum">    2355 </span>            :   ASMJIT_INST_3x(vfmaddsub132pd, Vfmaddsub132pd, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2356"><span class="lineNum">    2356 </span>            :   ASMJIT_INST_3x(vfmaddsub132pd, Vfmaddsub132pd, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2357"><span class="lineNum">    2357 </span>            :   ASMJIT_INST_3x(vfmaddsub132ps, Vfmaddsub132ps, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2358"><span class="lineNum">    2358 </span>            :   ASMJIT_INST_3x(vfmaddsub132ps, Vfmaddsub132ps, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2359"><span class="lineNum">    2359 </span>            :   ASMJIT_INST_3x(vfmaddsub132ps, Vfmaddsub132ps, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2360"><span class="lineNum">    2360 </span>            :   ASMJIT_INST_3x(vfmaddsub132ps, Vfmaddsub132ps, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2361"><span class="lineNum">    2361 </span>            :   ASMJIT_INST_3x(vfmaddsub132ps, Vfmaddsub132ps, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2362"><span class="lineNum">    2362 </span>            :   ASMJIT_INST_3x(vfmaddsub132ps, Vfmaddsub132ps, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2363"><span class="lineNum">    2363 </span>            :   ASMJIT_INST_3x(vfmaddsub213pd, Vfmaddsub213pd, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2364"><span class="lineNum">    2364 </span>            :   ASMJIT_INST_3x(vfmaddsub213pd, Vfmaddsub213pd, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :   ASMJIT_INST_3x(vfmaddsub213pd, Vfmaddsub213pd, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2366"><span class="lineNum">    2366 </span>            :   ASMJIT_INST_3x(vfmaddsub213pd, Vfmaddsub213pd, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2367"><span class="lineNum">    2367 </span>            :   ASMJIT_INST_3x(vfmaddsub213pd, Vfmaddsub213pd, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :   ASMJIT_INST_3x(vfmaddsub213pd, Vfmaddsub213pd, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2369"><span class="lineNum">    2369 </span>            :   ASMJIT_INST_3x(vfmaddsub213ps, Vfmaddsub213ps, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2370"><span class="lineNum">    2370 </span>            :   ASMJIT_INST_3x(vfmaddsub213ps, Vfmaddsub213ps, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2371"><span class="lineNum">    2371 </span>            :   ASMJIT_INST_3x(vfmaddsub213ps, Vfmaddsub213ps, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2372"><span class="lineNum">    2372 </span>            :   ASMJIT_INST_3x(vfmaddsub213ps, Vfmaddsub213ps, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2373"><span class="lineNum">    2373 </span>            :   ASMJIT_INST_3x(vfmaddsub213ps, Vfmaddsub213ps, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :   ASMJIT_INST_3x(vfmaddsub213ps, Vfmaddsub213ps, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2375"><span class="lineNum">    2375 </span>            :   ASMJIT_INST_3x(vfmaddsub231pd, Vfmaddsub231pd, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2376"><span class="lineNum">    2376 </span>            :   ASMJIT_INST_3x(vfmaddsub231pd, Vfmaddsub231pd, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2377"><span class="lineNum">    2377 </span>            :   ASMJIT_INST_3x(vfmaddsub231pd, Vfmaddsub231pd, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2378"><span class="lineNum">    2378 </span>            :   ASMJIT_INST_3x(vfmaddsub231pd, Vfmaddsub231pd, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2379"><span class="lineNum">    2379 </span>            :   ASMJIT_INST_3x(vfmaddsub231pd, Vfmaddsub231pd, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2380"><span class="lineNum">    2380 </span>            :   ASMJIT_INST_3x(vfmaddsub231pd, Vfmaddsub231pd, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2381"><span class="lineNum">    2381 </span>            :   ASMJIT_INST_3x(vfmaddsub231ps, Vfmaddsub231ps, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2382"><span class="lineNum">    2382 </span>            :   ASMJIT_INST_3x(vfmaddsub231ps, Vfmaddsub231ps, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2383"><span class="lineNum">    2383 </span>            :   ASMJIT_INST_3x(vfmaddsub231ps, Vfmaddsub231ps, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2384"><span class="lineNum">    2384 </span>            :   ASMJIT_INST_3x(vfmaddsub231ps, Vfmaddsub231ps, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2385"><span class="lineNum">    2385 </span>            :   ASMJIT_INST_3x(vfmaddsub231ps, Vfmaddsub231ps, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2386"><span class="lineNum">    2386 </span>            :   ASMJIT_INST_3x(vfmaddsub231ps, Vfmaddsub231ps, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2387"><span class="lineNum">    2387 </span>            :   ASMJIT_INST_3x(vfmsub132pd, Vfmsub132pd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2388"><span class="lineNum">    2388 </span>            :   ASMJIT_INST_3x(vfmsub132pd, Vfmsub132pd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2389"><span class="lineNum">    2389 </span>            :   ASMJIT_INST_3x(vfmsub132pd, Vfmsub132pd, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2390"><span class="lineNum">    2390 </span>            :   ASMJIT_INST_3x(vfmsub132pd, Vfmsub132pd, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :   ASMJIT_INST_3x(vfmsub132pd, Vfmsub132pd, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2392"><span class="lineNum">    2392 </span>            :   ASMJIT_INST_3x(vfmsub132pd, Vfmsub132pd, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2393"><span class="lineNum">    2393 </span>            :   ASMJIT_INST_3x(vfmsub132ps, Vfmsub132ps, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2394"><span class="lineNum">    2394 </span>            :   ASMJIT_INST_3x(vfmsub132ps, Vfmsub132ps, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2395"><span class="lineNum">    2395 </span>            :   ASMJIT_INST_3x(vfmsub132ps, Vfmsub132ps, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2396"><span class="lineNum">    2396 </span>            :   ASMJIT_INST_3x(vfmsub132ps, Vfmsub132ps, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :   ASMJIT_INST_3x(vfmsub132ps, Vfmsub132ps, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2398"><span class="lineNum">    2398 </span>            :   ASMJIT_INST_3x(vfmsub132ps, Vfmsub132ps, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2399"><span class="lineNum">    2399 </span>            :   ASMJIT_INST_3x(vfmsub132sd, Vfmsub132sd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2400"><span class="lineNum">    2400 </span>            :   ASMJIT_INST_3x(vfmsub132sd, Vfmsub132sd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2401"><span class="lineNum">    2401 </span>            :   ASMJIT_INST_3x(vfmsub132ss, Vfmsub132ss, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2402"><span class="lineNum">    2402 </span>            :   ASMJIT_INST_3x(vfmsub132ss, Vfmsub132ss, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2403"><span class="lineNum">    2403 </span>            :   ASMJIT_INST_3x(vfmsub213pd, Vfmsub213pd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2404"><span class="lineNum">    2404 </span>            :   ASMJIT_INST_3x(vfmsub213pd, Vfmsub213pd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2405"><span class="lineNum">    2405 </span>            :   ASMJIT_INST_3x(vfmsub213pd, Vfmsub213pd, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2406"><span class="lineNum">    2406 </span>            :   ASMJIT_INST_3x(vfmsub213pd, Vfmsub213pd, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2407"><span class="lineNum">    2407 </span>            :   ASMJIT_INST_3x(vfmsub213pd, Vfmsub213pd, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2408"><span class="lineNum">    2408 </span>            :   ASMJIT_INST_3x(vfmsub213pd, Vfmsub213pd, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2409"><span class="lineNum">    2409 </span>            :   ASMJIT_INST_3x(vfmsub213ps, Vfmsub213ps, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2410"><span class="lineNum">    2410 </span>            :   ASMJIT_INST_3x(vfmsub213ps, Vfmsub213ps, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2411"><span class="lineNum">    2411 </span>            :   ASMJIT_INST_3x(vfmsub213ps, Vfmsub213ps, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2412"><span class="lineNum">    2412 </span>            :   ASMJIT_INST_3x(vfmsub213ps, Vfmsub213ps, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2413"><span class="lineNum">    2413 </span>            :   ASMJIT_INST_3x(vfmsub213ps, Vfmsub213ps, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2414"><span class="lineNum">    2414 </span>            :   ASMJIT_INST_3x(vfmsub213ps, Vfmsub213ps, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2415"><span class="lineNum">    2415 </span>            :   ASMJIT_INST_3x(vfmsub213sd, Vfmsub213sd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2416"><span class="lineNum">    2416 </span>            :   ASMJIT_INST_3x(vfmsub213sd, Vfmsub213sd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2417"><span class="lineNum">    2417 </span>            :   ASMJIT_INST_3x(vfmsub213ss, Vfmsub213ss, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2418"><span class="lineNum">    2418 </span>            :   ASMJIT_INST_3x(vfmsub213ss, Vfmsub213ss, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2419"><span class="lineNum">    2419 </span>            :   ASMJIT_INST_3x(vfmsub231pd, Vfmsub231pd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2420"><span class="lineNum">    2420 </span>            :   ASMJIT_INST_3x(vfmsub231pd, Vfmsub231pd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2421"><span class="lineNum">    2421 </span>            :   ASMJIT_INST_3x(vfmsub231pd, Vfmsub231pd, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2422"><span class="lineNum">    2422 </span>            :   ASMJIT_INST_3x(vfmsub231pd, Vfmsub231pd, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2423"><span class="lineNum">    2423 </span>            :   ASMJIT_INST_3x(vfmsub231pd, Vfmsub231pd, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2424"><span class="lineNum">    2424 </span>            :   ASMJIT_INST_3x(vfmsub231pd, Vfmsub231pd, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2425"><span class="lineNum">    2425 </span>            :   ASMJIT_INST_3x(vfmsub231ps, Vfmsub231ps, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2426"><span class="lineNum">    2426 </span>            :   ASMJIT_INST_3x(vfmsub231ps, Vfmsub231ps, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2427"><span class="lineNum">    2427 </span>            :   ASMJIT_INST_3x(vfmsub231ps, Vfmsub231ps, X86Ymm, X86Ymm, X86Ymm)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2428"><span class="lineNum">    2428 </span>            :   ASMJIT_INST_3x(vfmsub231ps, Vfmsub231ps, X86Ymm, X86Ymm, X86Mem)            // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2429"><span class="lineNum">    2429 </span>            :   ASMJIT_INST_3x(vfmsub231ps, Vfmsub231ps, X86Zmm, X86Zmm, X86Zmm)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2430"><span class="lineNum">    2430 </span>            :   ASMJIT_INST_3x(vfmsub231ps, Vfmsub231ps, X86Zmm, X86Zmm, X86Mem)            // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2431"><span class="lineNum">    2431 </span>            :   ASMJIT_INST_3x(vfmsub231sd, Vfmsub231sd, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2432"><span class="lineNum">    2432 </span>            :   ASMJIT_INST_3x(vfmsub231sd, Vfmsub231sd, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2433"><span class="lineNum">    2433 </span>            :   ASMJIT_INST_3x(vfmsub231ss, Vfmsub231ss, X86Xmm, X86Xmm, X86Xmm)            // FMA  AVX512_F{kz|er}</a>
+<a name="2434"><span class="lineNum">    2434 </span>            :   ASMJIT_INST_3x(vfmsub231ss, Vfmsub231ss, X86Xmm, X86Xmm, X86Mem)            // FMA  AVX512_F{kz|er}</a>
+<a name="2435"><span class="lineNum">    2435 </span>            :   ASMJIT_INST_3x(vfmsubadd132pd, Vfmsubadd132pd, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2436"><span class="lineNum">    2436 </span>            :   ASMJIT_INST_3x(vfmsubadd132pd, Vfmsubadd132pd, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2437"><span class="lineNum">    2437 </span>            :   ASMJIT_INST_3x(vfmsubadd132pd, Vfmsubadd132pd, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2438"><span class="lineNum">    2438 </span>            :   ASMJIT_INST_3x(vfmsubadd132pd, Vfmsubadd132pd, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :   ASMJIT_INST_3x(vfmsubadd132pd, Vfmsubadd132pd, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2440"><span class="lineNum">    2440 </span>            :   ASMJIT_INST_3x(vfmsubadd132pd, Vfmsubadd132pd, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2441"><span class="lineNum">    2441 </span>            :   ASMJIT_INST_3x(vfmsubadd132ps, Vfmsubadd132ps, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2442"><span class="lineNum">    2442 </span>            :   ASMJIT_INST_3x(vfmsubadd132ps, Vfmsubadd132ps, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2443"><span class="lineNum">    2443 </span>            :   ASMJIT_INST_3x(vfmsubadd132ps, Vfmsubadd132ps, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2444"><span class="lineNum">    2444 </span>            :   ASMJIT_INST_3x(vfmsubadd132ps, Vfmsubadd132ps, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2445"><span class="lineNum">    2445 </span>            :   ASMJIT_INST_3x(vfmsubadd132ps, Vfmsubadd132ps, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2446"><span class="lineNum">    2446 </span>            :   ASMJIT_INST_3x(vfmsubadd132ps, Vfmsubadd132ps, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2447"><span class="lineNum">    2447 </span>            :   ASMJIT_INST_3x(vfmsubadd213pd, Vfmsubadd213pd, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2448"><span class="lineNum">    2448 </span>            :   ASMJIT_INST_3x(vfmsubadd213pd, Vfmsubadd213pd, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2449"><span class="lineNum">    2449 </span>            :   ASMJIT_INST_3x(vfmsubadd213pd, Vfmsubadd213pd, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2450"><span class="lineNum">    2450 </span>            :   ASMJIT_INST_3x(vfmsubadd213pd, Vfmsubadd213pd, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2451"><span class="lineNum">    2451 </span>            :   ASMJIT_INST_3x(vfmsubadd213pd, Vfmsubadd213pd, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2452"><span class="lineNum">    2452 </span>            :   ASMJIT_INST_3x(vfmsubadd213pd, Vfmsubadd213pd, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2453"><span class="lineNum">    2453 </span>            :   ASMJIT_INST_3x(vfmsubadd213ps, Vfmsubadd213ps, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2454"><span class="lineNum">    2454 </span>            :   ASMJIT_INST_3x(vfmsubadd213ps, Vfmsubadd213ps, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2455"><span class="lineNum">    2455 </span>            :   ASMJIT_INST_3x(vfmsubadd213ps, Vfmsubadd213ps, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2456"><span class="lineNum">    2456 </span>            :   ASMJIT_INST_3x(vfmsubadd213ps, Vfmsubadd213ps, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :   ASMJIT_INST_3x(vfmsubadd213ps, Vfmsubadd213ps, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2458"><span class="lineNum">    2458 </span>            :   ASMJIT_INST_3x(vfmsubadd213ps, Vfmsubadd213ps, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2459"><span class="lineNum">    2459 </span>            :   ASMJIT_INST_3x(vfmsubadd231pd, Vfmsubadd231pd, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2460"><span class="lineNum">    2460 </span>            :   ASMJIT_INST_3x(vfmsubadd231pd, Vfmsubadd231pd, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2461"><span class="lineNum">    2461 </span>            :   ASMJIT_INST_3x(vfmsubadd231pd, Vfmsubadd231pd, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2462"><span class="lineNum">    2462 </span>            :   ASMJIT_INST_3x(vfmsubadd231pd, Vfmsubadd231pd, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2463"><span class="lineNum">    2463 </span>            :   ASMJIT_INST_3x(vfmsubadd231pd, Vfmsubadd231pd, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2464"><span class="lineNum">    2464 </span>            :   ASMJIT_INST_3x(vfmsubadd231pd, Vfmsubadd231pd, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2465"><span class="lineNum">    2465 </span>            :   ASMJIT_INST_3x(vfmsubadd231ps, Vfmsubadd231ps, X86Xmm, X86Xmm, X86Xmm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2466"><span class="lineNum">    2466 </span>            :   ASMJIT_INST_3x(vfmsubadd231ps, Vfmsubadd231ps, X86Xmm, X86Xmm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2467"><span class="lineNum">    2467 </span>            :   ASMJIT_INST_3x(vfmsubadd231ps, Vfmsubadd231ps, X86Ymm, X86Ymm, X86Ymm)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2468"><span class="lineNum">    2468 </span>            :   ASMJIT_INST_3x(vfmsubadd231ps, Vfmsubadd231ps, X86Ymm, X86Ymm, X86Mem)      // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2469"><span class="lineNum">    2469 </span>            :   ASMJIT_INST_3x(vfmsubadd231ps, Vfmsubadd231ps, X86Zmm, X86Zmm, X86Zmm)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2470"><span class="lineNum">    2470 </span>            :   ASMJIT_INST_3x(vfmsubadd231ps, Vfmsubadd231ps, X86Zmm, X86Zmm, X86Mem)      // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2471"><span class="lineNum">    2471 </span>            :   ASMJIT_INST_3x(vfnmadd132pd, Vfnmadd132pd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2472"><span class="lineNum">    2472 </span>            :   ASMJIT_INST_3x(vfnmadd132pd, Vfnmadd132pd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2473"><span class="lineNum">    2473 </span>            :   ASMJIT_INST_3x(vfnmadd132pd, Vfnmadd132pd, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2474"><span class="lineNum">    2474 </span>            :   ASMJIT_INST_3x(vfnmadd132pd, Vfnmadd132pd, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2475"><span class="lineNum">    2475 </span>            :   ASMJIT_INST_3x(vfnmadd132pd, Vfnmadd132pd, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2476"><span class="lineNum">    2476 </span>            :   ASMJIT_INST_3x(vfnmadd132pd, Vfnmadd132pd, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2477"><span class="lineNum">    2477 </span>            :   ASMJIT_INST_3x(vfnmadd132ps, Vfnmadd132ps, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2478"><span class="lineNum">    2478 </span>            :   ASMJIT_INST_3x(vfnmadd132ps, Vfnmadd132ps, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2479"><span class="lineNum">    2479 </span>            :   ASMJIT_INST_3x(vfnmadd132ps, Vfnmadd132ps, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2480"><span class="lineNum">    2480 </span>            :   ASMJIT_INST_3x(vfnmadd132ps, Vfnmadd132ps, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2481"><span class="lineNum">    2481 </span>            :   ASMJIT_INST_3x(vfnmadd132ps, Vfnmadd132ps, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2482"><span class="lineNum">    2482 </span>            :   ASMJIT_INST_3x(vfnmadd132ps, Vfnmadd132ps, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2483"><span class="lineNum">    2483 </span>            :   ASMJIT_INST_3x(vfnmadd132sd, Vfnmadd132sd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2484"><span class="lineNum">    2484 </span>            :   ASMJIT_INST_3x(vfnmadd132sd, Vfnmadd132sd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2485"><span class="lineNum">    2485 </span>            :   ASMJIT_INST_3x(vfnmadd132ss, Vfnmadd132ss, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2486"><span class="lineNum">    2486 </span>            :   ASMJIT_INST_3x(vfnmadd132ss, Vfnmadd132ss, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2487"><span class="lineNum">    2487 </span>            :   ASMJIT_INST_3x(vfnmadd213pd, Vfnmadd213pd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2488"><span class="lineNum">    2488 </span>            :   ASMJIT_INST_3x(vfnmadd213pd, Vfnmadd213pd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2489"><span class="lineNum">    2489 </span>            :   ASMJIT_INST_3x(vfnmadd213pd, Vfnmadd213pd, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2490"><span class="lineNum">    2490 </span>            :   ASMJIT_INST_3x(vfnmadd213pd, Vfnmadd213pd, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2491"><span class="lineNum">    2491 </span>            :   ASMJIT_INST_3x(vfnmadd213pd, Vfnmadd213pd, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2492"><span class="lineNum">    2492 </span>            :   ASMJIT_INST_3x(vfnmadd213pd, Vfnmadd213pd, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2493"><span class="lineNum">    2493 </span>            :   ASMJIT_INST_3x(vfnmadd213ps, Vfnmadd213ps, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2494"><span class="lineNum">    2494 </span>            :   ASMJIT_INST_3x(vfnmadd213ps, Vfnmadd213ps, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2495"><span class="lineNum">    2495 </span>            :   ASMJIT_INST_3x(vfnmadd213ps, Vfnmadd213ps, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2496"><span class="lineNum">    2496 </span>            :   ASMJIT_INST_3x(vfnmadd213ps, Vfnmadd213ps, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2497"><span class="lineNum">    2497 </span>            :   ASMJIT_INST_3x(vfnmadd213ps, Vfnmadd213ps, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2498"><span class="lineNum">    2498 </span>            :   ASMJIT_INST_3x(vfnmadd213ps, Vfnmadd213ps, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2499"><span class="lineNum">    2499 </span>            :   ASMJIT_INST_3x(vfnmadd213sd, Vfnmadd213sd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2500"><span class="lineNum">    2500 </span>            :   ASMJIT_INST_3x(vfnmadd213sd, Vfnmadd213sd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2501"><span class="lineNum">    2501 </span>            :   ASMJIT_INST_3x(vfnmadd213ss, Vfnmadd213ss, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2502"><span class="lineNum">    2502 </span>            :   ASMJIT_INST_3x(vfnmadd213ss, Vfnmadd213ss, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2503"><span class="lineNum">    2503 </span>            :   ASMJIT_INST_3x(vfnmadd231pd, Vfnmadd231pd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2504"><span class="lineNum">    2504 </span>            :   ASMJIT_INST_3x(vfnmadd231pd, Vfnmadd231pd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2505"><span class="lineNum">    2505 </span>            :   ASMJIT_INST_3x(vfnmadd231pd, Vfnmadd231pd, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2506"><span class="lineNum">    2506 </span>            :   ASMJIT_INST_3x(vfnmadd231pd, Vfnmadd231pd, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2507"><span class="lineNum">    2507 </span>            :   ASMJIT_INST_3x(vfnmadd231pd, Vfnmadd231pd, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2508"><span class="lineNum">    2508 </span>            :   ASMJIT_INST_3x(vfnmadd231pd, Vfnmadd231pd, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2509"><span class="lineNum">    2509 </span>            :   ASMJIT_INST_3x(vfnmadd231ps, Vfnmadd231ps, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2510"><span class="lineNum">    2510 </span>            :   ASMJIT_INST_3x(vfnmadd231ps, Vfnmadd231ps, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2511"><span class="lineNum">    2511 </span>            :   ASMJIT_INST_3x(vfnmadd231ps, Vfnmadd231ps, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2512"><span class="lineNum">    2512 </span>            :   ASMJIT_INST_3x(vfnmadd231ps, Vfnmadd231ps, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :   ASMJIT_INST_3x(vfnmadd231ps, Vfnmadd231ps, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2514"><span class="lineNum">    2514 </span>            :   ASMJIT_INST_3x(vfnmadd231ps, Vfnmadd231ps, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2515"><span class="lineNum">    2515 </span>            :   ASMJIT_INST_3x(vfnmadd231sd, Vfnmadd231sd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2516"><span class="lineNum">    2516 </span>            :   ASMJIT_INST_3x(vfnmadd231sd, Vfnmadd231sd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2517"><span class="lineNum">    2517 </span>            :   ASMJIT_INST_3x(vfnmadd231ss, Vfnmadd231ss, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2518"><span class="lineNum">    2518 </span>            :   ASMJIT_INST_3x(vfnmadd231ss, Vfnmadd231ss, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2519"><span class="lineNum">    2519 </span>            :   ASMJIT_INST_3x(vfnmsub132pd, Vfnmsub132pd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2520"><span class="lineNum">    2520 </span>            :   ASMJIT_INST_3x(vfnmsub132pd, Vfnmsub132pd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2521"><span class="lineNum">    2521 </span>            :   ASMJIT_INST_3x(vfnmsub132pd, Vfnmsub132pd, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2522"><span class="lineNum">    2522 </span>            :   ASMJIT_INST_3x(vfnmsub132pd, Vfnmsub132pd, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2523"><span class="lineNum">    2523 </span>            :   ASMJIT_INST_3x(vfnmsub132pd, Vfnmsub132pd, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2524"><span class="lineNum">    2524 </span>            :   ASMJIT_INST_3x(vfnmsub132pd, Vfnmsub132pd, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2525"><span class="lineNum">    2525 </span>            :   ASMJIT_INST_3x(vfnmsub132ps, Vfnmsub132ps, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2526"><span class="lineNum">    2526 </span>            :   ASMJIT_INST_3x(vfnmsub132ps, Vfnmsub132ps, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2527"><span class="lineNum">    2527 </span>            :   ASMJIT_INST_3x(vfnmsub132ps, Vfnmsub132ps, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2528"><span class="lineNum">    2528 </span>            :   ASMJIT_INST_3x(vfnmsub132ps, Vfnmsub132ps, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2529"><span class="lineNum">    2529 </span>            :   ASMJIT_INST_3x(vfnmsub132ps, Vfnmsub132ps, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2530"><span class="lineNum">    2530 </span>            :   ASMJIT_INST_3x(vfnmsub132ps, Vfnmsub132ps, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2531"><span class="lineNum">    2531 </span>            :   ASMJIT_INST_3x(vfnmsub132sd, Vfnmsub132sd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2532"><span class="lineNum">    2532 </span>            :   ASMJIT_INST_3x(vfnmsub132sd, Vfnmsub132sd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2533"><span class="lineNum">    2533 </span>            :   ASMJIT_INST_3x(vfnmsub132ss, Vfnmsub132ss, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2534"><span class="lineNum">    2534 </span>            :   ASMJIT_INST_3x(vfnmsub132ss, Vfnmsub132ss, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2535"><span class="lineNum">    2535 </span>            :   ASMJIT_INST_3x(vfnmsub213pd, Vfnmsub213pd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2536"><span class="lineNum">    2536 </span>            :   ASMJIT_INST_3x(vfnmsub213pd, Vfnmsub213pd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2537"><span class="lineNum">    2537 </span>            :   ASMJIT_INST_3x(vfnmsub213pd, Vfnmsub213pd, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2538"><span class="lineNum">    2538 </span>            :   ASMJIT_INST_3x(vfnmsub213pd, Vfnmsub213pd, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2539"><span class="lineNum">    2539 </span>            :   ASMJIT_INST_3x(vfnmsub213pd, Vfnmsub213pd, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2540"><span class="lineNum">    2540 </span>            :   ASMJIT_INST_3x(vfnmsub213pd, Vfnmsub213pd, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2541"><span class="lineNum">    2541 </span>            :   ASMJIT_INST_3x(vfnmsub213ps, Vfnmsub213ps, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2542"><span class="lineNum">    2542 </span>            :   ASMJIT_INST_3x(vfnmsub213ps, Vfnmsub213ps, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2543"><span class="lineNum">    2543 </span>            :   ASMJIT_INST_3x(vfnmsub213ps, Vfnmsub213ps, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2544"><span class="lineNum">    2544 </span>            :   ASMJIT_INST_3x(vfnmsub213ps, Vfnmsub213ps, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2545"><span class="lineNum">    2545 </span>            :   ASMJIT_INST_3x(vfnmsub213ps, Vfnmsub213ps, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2546"><span class="lineNum">    2546 </span>            :   ASMJIT_INST_3x(vfnmsub213ps, Vfnmsub213ps, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2547"><span class="lineNum">    2547 </span>            :   ASMJIT_INST_3x(vfnmsub213sd, Vfnmsub213sd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2548"><span class="lineNum">    2548 </span>            :   ASMJIT_INST_3x(vfnmsub213sd, Vfnmsub213sd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2549"><span class="lineNum">    2549 </span>            :   ASMJIT_INST_3x(vfnmsub213ss, Vfnmsub213ss, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2550"><span class="lineNum">    2550 </span>            :   ASMJIT_INST_3x(vfnmsub213ss, Vfnmsub213ss, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2551"><span class="lineNum">    2551 </span>            :   ASMJIT_INST_3x(vfnmsub231pd, Vfnmsub231pd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2552"><span class="lineNum">    2552 </span>            :   ASMJIT_INST_3x(vfnmsub231pd, Vfnmsub231pd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2553"><span class="lineNum">    2553 </span>            :   ASMJIT_INST_3x(vfnmsub231pd, Vfnmsub231pd, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2554"><span class="lineNum">    2554 </span>            :   ASMJIT_INST_3x(vfnmsub231pd, Vfnmsub231pd, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b64}-VL</a>
+<a name="2555"><span class="lineNum">    2555 </span>            :   ASMJIT_INST_3x(vfnmsub231pd, Vfnmsub231pd, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2556"><span class="lineNum">    2556 </span>            :   ASMJIT_INST_3x(vfnmsub231pd, Vfnmsub231pd, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b64}</a>
+<a name="2557"><span class="lineNum">    2557 </span>            :   ASMJIT_INST_3x(vfnmsub231ps, Vfnmsub231ps, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2558"><span class="lineNum">    2558 </span>            :   ASMJIT_INST_3x(vfnmsub231ps, Vfnmsub231ps, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2559"><span class="lineNum">    2559 </span>            :   ASMJIT_INST_3x(vfnmsub231ps, Vfnmsub231ps, X86Ymm, X86Ymm, X86Ymm)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2560"><span class="lineNum">    2560 </span>            :   ASMJIT_INST_3x(vfnmsub231ps, Vfnmsub231ps, X86Ymm, X86Ymm, X86Mem)          // FMA  AVX512_F{kz|b32}-VL</a>
+<a name="2561"><span class="lineNum">    2561 </span>            :   ASMJIT_INST_3x(vfnmsub231ps, Vfnmsub231ps, X86Zmm, X86Zmm, X86Zmm)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2562"><span class="lineNum">    2562 </span>            :   ASMJIT_INST_3x(vfnmsub231ps, Vfnmsub231ps, X86Zmm, X86Zmm, X86Mem)          // FMA  AVX512_F{kz|er|b32}</a>
+<a name="2563"><span class="lineNum">    2563 </span>            :   ASMJIT_INST_3x(vfnmsub231sd, Vfnmsub231sd, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2564"><span class="lineNum">    2564 </span>            :   ASMJIT_INST_3x(vfnmsub231sd, Vfnmsub231sd, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2565"><span class="lineNum">    2565 </span>            :   ASMJIT_INST_3x(vfnmsub231ss, Vfnmsub231ss, X86Xmm, X86Xmm, X86Xmm)          // FMA  AVX512_F{kz|er}</a>
+<a name="2566"><span class="lineNum">    2566 </span>            :   ASMJIT_INST_3x(vfnmsub231ss, Vfnmsub231ss, X86Xmm, X86Xmm, X86Mem)          // FMA  AVX512_F{kz|er}</a>
+<a name="2567"><span class="lineNum">    2567 </span>            :   ASMJIT_INST_3i(vfpclasspd, Vfpclasspd, X86KReg, X86Xmm, Imm)                //      AVX512_DQ{k|b64}-VL</a>
+<a name="2568"><span class="lineNum">    2568 </span>            :   ASMJIT_INST_3i(vfpclasspd, Vfpclasspd, X86KReg, X86Mem, Imm)                //      AVX512_DQ{k|b64} AVX512_DQ{k|b64}-VL</a>
+<a name="2569"><span class="lineNum">    2569 </span>            :   ASMJIT_INST_3i(vfpclasspd, Vfpclasspd, X86KReg, X86Ymm, Imm)                //      AVX512_DQ{k|b64}-VL</a>
+<a name="2570"><span class="lineNum">    2570 </span>            :   ASMJIT_INST_3i(vfpclasspd, Vfpclasspd, X86KReg, X86Zmm, Imm)                //      AVX512_DQ{k|b64}</a>
+<a name="2571"><span class="lineNum">    2571 </span>            :   ASMJIT_INST_3i(vfpclassps, Vfpclassps, X86KReg, X86Xmm, Imm)                //      AVX512_DQ{k|b32}-VL</a>
+<a name="2572"><span class="lineNum">    2572 </span>            :   ASMJIT_INST_3i(vfpclassps, Vfpclassps, X86KReg, X86Mem, Imm)                //      AVX512_DQ{k|b32} AVX512_DQ{k|b32}-VL</a>
+<a name="2573"><span class="lineNum">    2573 </span>            :   ASMJIT_INST_3i(vfpclassps, Vfpclassps, X86KReg, X86Ymm, Imm)                //      AVX512_DQ{k|b32}-VL</a>
+<a name="2574"><span class="lineNum">    2574 </span>            :   ASMJIT_INST_3i(vfpclassps, Vfpclassps, X86KReg, X86Zmm, Imm)                //      AVX512_DQ{k|b32}</a>
+<a name="2575"><span class="lineNum">    2575 </span>            :   ASMJIT_INST_3i(vfpclasssd, Vfpclasssd, X86KReg, X86Xmm, Imm)                //      AVX512_DQ{k}</a>
+<a name="2576"><span class="lineNum">    2576 </span>            :   ASMJIT_INST_3i(vfpclasssd, Vfpclasssd, X86KReg, X86Mem, Imm)                //      AVX512_DQ{k}</a>
+<a name="2577"><span class="lineNum">    2577 </span>            :   ASMJIT_INST_3i(vfpclassss, Vfpclassss, X86KReg, X86Xmm, Imm)                //      AVX512_DQ{k}</a>
+<a name="2578"><span class="lineNum">    2578 </span>            :   ASMJIT_INST_3i(vfpclassss, Vfpclassss, X86KReg, X86Mem, Imm)                //      AVX512_DQ{k}</a>
+<a name="2579"><span class="lineNum">    2579 </span>            :   ASMJIT_INST_3x(vgatherdpd, Vgatherdpd, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="2580"><span class="lineNum">    2580 </span>            :   ASMJIT_INST_3x(vgatherdpd, Vgatherdpd, X86Ymm, X86Mem, X86Ymm)              // AVX2</a>
+<a name="2581"><span class="lineNum">    2581 </span>            :   ASMJIT_INST_2x(vgatherdpd, Vgatherdpd, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2582"><span class="lineNum">    2582 </span>            :   ASMJIT_INST_2x(vgatherdpd, Vgatherdpd, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2583"><span class="lineNum">    2583 </span>            :   ASMJIT_INST_2x(vgatherdpd, Vgatherdpd, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="2584"><span class="lineNum">    2584 </span>            :   ASMJIT_INST_3x(vgatherdps, Vgatherdps, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="2585"><span class="lineNum">    2585 </span>            :   ASMJIT_INST_3x(vgatherdps, Vgatherdps, X86Ymm, X86Mem, X86Ymm)              // AVX2</a>
+<a name="2586"><span class="lineNum">    2586 </span>            :   ASMJIT_INST_2x(vgatherdps, Vgatherdps, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2587"><span class="lineNum">    2587 </span>            :   ASMJIT_INST_2x(vgatherdps, Vgatherdps, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2588"><span class="lineNum">    2588 </span>            :   ASMJIT_INST_2x(vgatherdps, Vgatherdps, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="2589"><span class="lineNum">    2589 </span>            :   ASMJIT_INST_1x(vgatherpf0dpd, Vgatherpf0dpd, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2590"><span class="lineNum">    2590 </span>            :   ASMJIT_INST_1x(vgatherpf0dps, Vgatherpf0dps, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2591"><span class="lineNum">    2591 </span>            :   ASMJIT_INST_1x(vgatherpf0qpd, Vgatherpf0qpd, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2592"><span class="lineNum">    2592 </span>            :   ASMJIT_INST_1x(vgatherpf0qps, Vgatherpf0qps, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2593"><span class="lineNum">    2593 </span>            :   ASMJIT_INST_1x(vgatherpf1dpd, Vgatherpf1dpd, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2594"><span class="lineNum">    2594 </span>            :   ASMJIT_INST_1x(vgatherpf1dps, Vgatherpf1dps, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2595"><span class="lineNum">    2595 </span>            :   ASMJIT_INST_1x(vgatherpf1qpd, Vgatherpf1qpd, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2596"><span class="lineNum">    2596 </span>            :   ASMJIT_INST_1x(vgatherpf1qps, Vgatherpf1qps, X86Mem)                        //      AVX512_PF{k}</a>
+<a name="2597"><span class="lineNum">    2597 </span>            :   ASMJIT_INST_3x(vgatherqpd, Vgatherqpd, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="2598"><span class="lineNum">    2598 </span>            :   ASMJIT_INST_3x(vgatherqpd, Vgatherqpd, X86Ymm, X86Mem, X86Ymm)              // AVX2</a>
+<a name="2599"><span class="lineNum">    2599 </span>            :   ASMJIT_INST_2x(vgatherqpd, Vgatherqpd, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2600"><span class="lineNum">    2600 </span>            :   ASMJIT_INST_2x(vgatherqpd, Vgatherqpd, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2601"><span class="lineNum">    2601 </span>            :   ASMJIT_INST_2x(vgatherqpd, Vgatherqpd, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="2602"><span class="lineNum">    2602 </span>            :   ASMJIT_INST_3x(vgatherqps, Vgatherqps, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="2603"><span class="lineNum">    2603 </span>            :   ASMJIT_INST_2x(vgatherqps, Vgatherqps, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2604"><span class="lineNum">    2604 </span>            :   ASMJIT_INST_2x(vgatherqps, Vgatherqps, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="2605"><span class="lineNum">    2605 </span>            :   ASMJIT_INST_2x(vgatherqps, Vgatherqps, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="2606"><span class="lineNum">    2606 </span>            :   ASMJIT_INST_2x(vgetexppd, Vgetexppd, X86Xmm, X86Xmm)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="2607"><span class="lineNum">    2607 </span>            :   ASMJIT_INST_2x(vgetexppd, Vgetexppd, X86Xmm, X86Mem)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="2608"><span class="lineNum">    2608 </span>            :   ASMJIT_INST_2x(vgetexppd, Vgetexppd, X86Ymm, X86Ymm)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="2609"><span class="lineNum">    2609 </span>            :   ASMJIT_INST_2x(vgetexppd, Vgetexppd, X86Ymm, X86Mem)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="2610"><span class="lineNum">    2610 </span>            :   ASMJIT_INST_2x(vgetexppd, Vgetexppd, X86Zmm, X86Zmm)                        //      AVX512_F{kz|sae|b64}</a>
+<a name="2611"><span class="lineNum">    2611 </span>            :   ASMJIT_INST_2x(vgetexppd, Vgetexppd, X86Zmm, X86Mem)                        //      AVX512_F{kz|sae|b64}</a>
+<a name="2612"><span class="lineNum">    2612 </span>            :   ASMJIT_INST_2x(vgetexpps, Vgetexpps, X86Xmm, X86Xmm)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="2613"><span class="lineNum">    2613 </span>            :   ASMJIT_INST_2x(vgetexpps, Vgetexpps, X86Xmm, X86Mem)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="2614"><span class="lineNum">    2614 </span>            :   ASMJIT_INST_2x(vgetexpps, Vgetexpps, X86Ymm, X86Ymm)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="2615"><span class="lineNum">    2615 </span>            :   ASMJIT_INST_2x(vgetexpps, Vgetexpps, X86Ymm, X86Mem)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="2616"><span class="lineNum">    2616 </span>            :   ASMJIT_INST_2x(vgetexpps, Vgetexpps, X86Zmm, X86Zmm)                        //      AVX512_F{kz|sae|b32}</a>
+<a name="2617"><span class="lineNum">    2617 </span>            :   ASMJIT_INST_2x(vgetexpps, Vgetexpps, X86Zmm, X86Mem)                        //      AVX512_F{kz|sae|b32}</a>
+<a name="2618"><span class="lineNum">    2618 </span>            :   ASMJIT_INST_2x(vgetexpsd, Vgetexpsd, X86Xmm, X86Xmm)                        //      AVX512_F{kz|sae}</a>
+<a name="2619"><span class="lineNum">    2619 </span>            :   ASMJIT_INST_2x(vgetexpsd, Vgetexpsd, X86Xmm, X86Mem)                        //      AVX512_F{kz|sae}</a>
+<a name="2620"><span class="lineNum">    2620 </span>            :   ASMJIT_INST_2x(vgetexpss, Vgetexpss, X86Xmm, X86Xmm)                        //      AVX512_F{kz|sae}</a>
+<a name="2621"><span class="lineNum">    2621 </span>            :   ASMJIT_INST_2x(vgetexpss, Vgetexpss, X86Xmm, X86Mem)                        //      AVX512_F{kz|sae}</a>
+<a name="2622"><span class="lineNum">    2622 </span>            :   ASMJIT_INST_3i(vgetmantpd, Vgetmantpd, X86Xmm, X86Xmm, Imm)                 //      AVX512_F{kz|b64}-VL</a>
+<a name="2623"><span class="lineNum">    2623 </span>            :   ASMJIT_INST_3i(vgetmantpd, Vgetmantpd, X86Xmm, X86Mem, Imm)                 //      AVX512_F{kz|b64}-VL</a>
+<a name="2624"><span class="lineNum">    2624 </span>            :   ASMJIT_INST_3i(vgetmantpd, Vgetmantpd, X86Ymm, X86Ymm, Imm)                 //      AVX512_F{kz|b64}-VL</a>
+<a name="2625"><span class="lineNum">    2625 </span>            :   ASMJIT_INST_3i(vgetmantpd, Vgetmantpd, X86Ymm, X86Mem, Imm)                 //      AVX512_F{kz|b64}-VL</a>
+<a name="2626"><span class="lineNum">    2626 </span>            :   ASMJIT_INST_3i(vgetmantpd, Vgetmantpd, X86Zmm, X86Zmm, Imm)                 //      AVX512_F{kz|sae|b64}</a>
+<a name="2627"><span class="lineNum">    2627 </span>            :   ASMJIT_INST_3i(vgetmantpd, Vgetmantpd, X86Zmm, X86Mem, Imm)                 //      AVX512_F{kz|sae|b64}</a>
+<a name="2628"><span class="lineNum">    2628 </span>            :   ASMJIT_INST_3i(vgetmantps, Vgetmantps, X86Xmm, X86Xmm, Imm)                 //      AVX512_F{kz|b32}-VL</a>
+<a name="2629"><span class="lineNum">    2629 </span>            :   ASMJIT_INST_3i(vgetmantps, Vgetmantps, X86Xmm, X86Mem, Imm)                 //      AVX512_F{kz|b32}-VL</a>
+<a name="2630"><span class="lineNum">    2630 </span>            :   ASMJIT_INST_3i(vgetmantps, Vgetmantps, X86Ymm, X86Ymm, Imm)                 //      AVX512_F{kz|b32}-VL</a>
+<a name="2631"><span class="lineNum">    2631 </span>            :   ASMJIT_INST_3i(vgetmantps, Vgetmantps, X86Ymm, X86Mem, Imm)                 //      AVX512_F{kz|b32}-VL</a>
+<a name="2632"><span class="lineNum">    2632 </span>            :   ASMJIT_INST_3i(vgetmantps, Vgetmantps, X86Zmm, X86Zmm, Imm)                 //      AVX512_F{kz|sae|b32}</a>
+<a name="2633"><span class="lineNum">    2633 </span>            :   ASMJIT_INST_3i(vgetmantps, Vgetmantps, X86Zmm, X86Mem, Imm)                 //      AVX512_F{kz|sae|b32}</a>
+<a name="2634"><span class="lineNum">    2634 </span>            :   ASMJIT_INST_3i(vgetmantsd, Vgetmantsd, X86Xmm, X86Xmm, Imm)                 //      AVX512_F{kz|sae}</a>
+<a name="2635"><span class="lineNum">    2635 </span>            :   ASMJIT_INST_3i(vgetmantsd, Vgetmantsd, X86Xmm, X86Mem, Imm)                 //      AVX512_F{kz|sae}</a>
+<a name="2636"><span class="lineNum">    2636 </span>            :   ASMJIT_INST_3i(vgetmantss, Vgetmantss, X86Xmm, X86Xmm, Imm)                 //      AVX512_F{kz|sae}</a>
+<a name="2637"><span class="lineNum">    2637 </span>            :   ASMJIT_INST_3i(vgetmantss, Vgetmantss, X86Xmm, X86Mem, Imm)                 //      AVX512_F{kz|sae}</a>
+<a name="2638"><span class="lineNum">    2638 </span>            :   ASMJIT_INST_3x(vhaddpd, Vhaddpd, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="2639"><span class="lineNum">    2639 </span>            :   ASMJIT_INST_3x(vhaddpd, Vhaddpd, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="2640"><span class="lineNum">    2640 </span>            :   ASMJIT_INST_3x(vhaddpd, Vhaddpd, X86Ymm, X86Ymm, X86Ymm)                    // AVX</a>
+<a name="2641"><span class="lineNum">    2641 </span>            :   ASMJIT_INST_3x(vhaddpd, Vhaddpd, X86Ymm, X86Ymm, X86Mem)                    // AVX</a>
+<a name="2642"><span class="lineNum">    2642 </span>            :   ASMJIT_INST_3x(vhaddps, Vhaddps, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="2643"><span class="lineNum">    2643 </span>            :   ASMJIT_INST_3x(vhaddps, Vhaddps, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="2644"><span class="lineNum">    2644 </span>            :   ASMJIT_INST_3x(vhaddps, Vhaddps, X86Ymm, X86Ymm, X86Ymm)                    // AVX</a>
+<a name="2645"><span class="lineNum">    2645 </span>            :   ASMJIT_INST_3x(vhaddps, Vhaddps, X86Ymm, X86Ymm, X86Mem)                    // AVX</a>
+<a name="2646"><span class="lineNum">    2646 </span>            :   ASMJIT_INST_3x(vhsubpd, Vhsubpd, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="2647"><span class="lineNum">    2647 </span>            :   ASMJIT_INST_3x(vhsubpd, Vhsubpd, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="2648"><span class="lineNum">    2648 </span>            :   ASMJIT_INST_3x(vhsubpd, Vhsubpd, X86Ymm, X86Ymm, X86Ymm)                    // AVX</a>
+<a name="2649"><span class="lineNum">    2649 </span>            :   ASMJIT_INST_3x(vhsubpd, Vhsubpd, X86Ymm, X86Ymm, X86Mem)                    // AVX</a>
+<a name="2650"><span class="lineNum">    2650 </span>            :   ASMJIT_INST_3x(vhsubps, Vhsubps, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="2651"><span class="lineNum">    2651 </span>            :   ASMJIT_INST_3x(vhsubps, Vhsubps, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="2652"><span class="lineNum">    2652 </span>            :   ASMJIT_INST_3x(vhsubps, Vhsubps, X86Ymm, X86Ymm, X86Ymm)                    // AVX</a>
+<a name="2653"><span class="lineNum">    2653 </span>            :   ASMJIT_INST_3x(vhsubps, Vhsubps, X86Ymm, X86Ymm, X86Mem)                    // AVX</a>
+<a name="2654"><span class="lineNum">    2654 </span>            :   ASMJIT_INST_4i(vinsertf128, Vinsertf128, X86Ymm, X86Ymm, X86Xmm, Imm)       // AVX</a>
+<a name="2655"><span class="lineNum">    2655 </span>            :   ASMJIT_INST_4i(vinsertf128, Vinsertf128, X86Ymm, X86Ymm, X86Mem, Imm)       // AVX</a>
+<a name="2656"><span class="lineNum">    2656 </span>            :   ASMJIT_INST_4i(vinsertf32x4, Vinsertf32x4, X86Ymm, X86Ymm, X86Xmm, Imm)     //      AVX512_F{kz}-VL</a>
+<a name="2657"><span class="lineNum">    2657 </span>            :   ASMJIT_INST_4i(vinsertf32x4, Vinsertf32x4, X86Ymm, X86Ymm, X86Mem, Imm)     //      AVX512_F{kz}-VL</a>
+<a name="2658"><span class="lineNum">    2658 </span>            :   ASMJIT_INST_4i(vinsertf32x4, Vinsertf32x4, X86Zmm, X86Zmm, X86Xmm, Imm)     //      AVX512_F{kz}</a>
+<a name="2659"><span class="lineNum">    2659 </span>            :   ASMJIT_INST_4i(vinsertf32x4, Vinsertf32x4, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_F{kz}</a>
+<a name="2660"><span class="lineNum">    2660 </span>            :   ASMJIT_INST_4i(vinsertf32x8, Vinsertf32x8, X86Zmm, X86Zmm, X86Ymm, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2661"><span class="lineNum">    2661 </span>            :   ASMJIT_INST_4i(vinsertf32x8, Vinsertf32x8, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2662"><span class="lineNum">    2662 </span>            :   ASMJIT_INST_4i(vinsertf64x2, Vinsertf64x2, X86Ymm, X86Ymm, X86Xmm, Imm)     //      AVX512_DQ{kz}-VL</a>
+<a name="2663"><span class="lineNum">    2663 </span>            :   ASMJIT_INST_4i(vinsertf64x2, Vinsertf64x2, X86Ymm, X86Ymm, X86Mem, Imm)     //      AVX512_DQ{kz}-VL</a>
+<a name="2664"><span class="lineNum">    2664 </span>            :   ASMJIT_INST_4i(vinsertf64x2, Vinsertf64x2, X86Zmm, X86Zmm, X86Xmm, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2665"><span class="lineNum">    2665 </span>            :   ASMJIT_INST_4i(vinsertf64x2, Vinsertf64x2, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2666"><span class="lineNum">    2666 </span>            :   ASMJIT_INST_4i(vinsertf64x4, Vinsertf64x4, X86Zmm, X86Zmm, X86Ymm, Imm)     //      AVX512_F{kz}</a>
+<a name="2667"><span class="lineNum">    2667 </span>            :   ASMJIT_INST_4i(vinsertf64x4, Vinsertf64x4, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_F{kz}</a>
+<a name="2668"><span class="lineNum">    2668 </span>            :   ASMJIT_INST_4i(vinserti128, Vinserti128, X86Ymm, X86Ymm, X86Xmm, Imm)       // AVX2</a>
+<a name="2669"><span class="lineNum">    2669 </span>            :   ASMJIT_INST_4i(vinserti128, Vinserti128, X86Ymm, X86Ymm, X86Mem, Imm)       // AVX2</a>
+<a name="2670"><span class="lineNum">    2670 </span>            :   ASMJIT_INST_4i(vinserti32x4, Vinserti32x4, X86Ymm, X86Ymm, X86Xmm, Imm)     //      AVX512_F{kz}-VL</a>
+<a name="2671"><span class="lineNum">    2671 </span>            :   ASMJIT_INST_4i(vinserti32x4, Vinserti32x4, X86Ymm, X86Ymm, X86Mem, Imm)     //      AVX512_F{kz}-VL</a>
+<a name="2672"><span class="lineNum">    2672 </span>            :   ASMJIT_INST_4i(vinserti32x4, Vinserti32x4, X86Zmm, X86Zmm, X86Xmm, Imm)     //      AVX512_F{kz}</a>
+<a name="2673"><span class="lineNum">    2673 </span>            :   ASMJIT_INST_4i(vinserti32x4, Vinserti32x4, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_F{kz}</a>
+<a name="2674"><span class="lineNum">    2674 </span>            :   ASMJIT_INST_4i(vinserti32x8, Vinserti32x8, X86Zmm, X86Zmm, X86Ymm, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2675"><span class="lineNum">    2675 </span>            :   ASMJIT_INST_4i(vinserti32x8, Vinserti32x8, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2676"><span class="lineNum">    2676 </span>            :   ASMJIT_INST_4i(vinserti64x2, Vinserti64x2, X86Ymm, X86Ymm, X86Xmm, Imm)     //      AVX512_DQ{kz}-VL</a>
+<a name="2677"><span class="lineNum">    2677 </span>            :   ASMJIT_INST_4i(vinserti64x2, Vinserti64x2, X86Ymm, X86Ymm, X86Mem, Imm)     //      AVX512_DQ{kz}-VL</a>
+<a name="2678"><span class="lineNum">    2678 </span>            :   ASMJIT_INST_4i(vinserti64x2, Vinserti64x2, X86Zmm, X86Zmm, X86Xmm, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2679"><span class="lineNum">    2679 </span>            :   ASMJIT_INST_4i(vinserti64x2, Vinserti64x2, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_DQ{kz}</a>
+<a name="2680"><span class="lineNum">    2680 </span>            :   ASMJIT_INST_4i(vinserti64x4, Vinserti64x4, X86Zmm, X86Zmm, X86Ymm, Imm)     //      AVX512_F{kz}</a>
+<a name="2681"><span class="lineNum">    2681 </span>            :   ASMJIT_INST_4i(vinserti64x4, Vinserti64x4, X86Zmm, X86Zmm, X86Mem, Imm)     //      AVX512_F{kz}</a>
+<a name="2682"><span class="lineNum">    2682 </span>            :   ASMJIT_INST_4i(vinsertps, Vinsertps, X86Xmm, X86Xmm, X86Xmm, Imm)           // AVX  AVX512_F</a>
+<a name="2683"><span class="lineNum">    2683 </span>            :   ASMJIT_INST_4i(vinsertps, Vinsertps, X86Xmm, X86Xmm, X86Mem, Imm)           // AVX  AVX512_F</a>
+<a name="2684"><span class="lineNum">    2684 </span>            :   ASMJIT_INST_2x(vlddqu, Vlddqu, X86Xmm, X86Mem)                              // AVX</a>
+<a name="2685"><span class="lineNum">    2685 </span>            :   ASMJIT_INST_2x(vlddqu, Vlddqu, X86Ymm, X86Mem)                              // AVX</a>
+<a name="2686"><span class="lineNum">    2686 </span>            :   ASMJIT_INST_1x(vldmxcsr, Vldmxcsr, X86Mem)                                  // AVX</a>
+<a name="2687"><span class="lineNum">    2687 </span>            :   ASMJIT_INST_3x(vmaskmovdqu, Vmaskmovdqu, X86Xmm, X86Xmm, DS_ZDI)            // AVX  [EXPLICIT]</a>
+<a name="2688"><span class="lineNum">    2688 </span>            :   ASMJIT_INST_3x(vmaskmovpd, Vmaskmovpd, X86Mem, X86Xmm, X86Xmm)              // AVX</a>
+<a name="2689"><span class="lineNum">    2689 </span>            :   ASMJIT_INST_3x(vmaskmovpd, Vmaskmovpd, X86Mem, X86Ymm, X86Ymm)              // AVX</a>
+<a name="2690"><span class="lineNum">    2690 </span>            :   ASMJIT_INST_3x(vmaskmovpd, Vmaskmovpd, X86Xmm, X86Xmm, X86Mem)              // AVX</a>
+<a name="2691"><span class="lineNum">    2691 </span>            :   ASMJIT_INST_3x(vmaskmovpd, Vmaskmovpd, X86Ymm, X86Ymm, X86Mem)              // AVX</a>
+<a name="2692"><span class="lineNum">    2692 </span>            :   ASMJIT_INST_3x(vmaskmovps, Vmaskmovps, X86Mem, X86Xmm, X86Xmm)              // AVX</a>
+<a name="2693"><span class="lineNum">    2693 </span>            :   ASMJIT_INST_3x(vmaskmovps, Vmaskmovps, X86Mem, X86Ymm, X86Ymm)              // AVX</a>
+<a name="2694"><span class="lineNum">    2694 </span>            :   ASMJIT_INST_3x(vmaskmovps, Vmaskmovps, X86Xmm, X86Xmm, X86Mem)              // AVX</a>
+<a name="2695"><span class="lineNum">    2695 </span>            :   ASMJIT_INST_3x(vmaskmovps, Vmaskmovps, X86Ymm, X86Ymm, X86Mem)              // AVX</a>
+<a name="2696"><span class="lineNum">    2696 </span>            :   ASMJIT_INST_3x(vmaxpd, Vmaxpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2697"><span class="lineNum">    2697 </span>            :   ASMJIT_INST_3x(vmaxpd, Vmaxpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2698"><span class="lineNum">    2698 </span>            :   ASMJIT_INST_3x(vmaxpd, Vmaxpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2699"><span class="lineNum">    2699 </span>            :   ASMJIT_INST_3x(vmaxpd, Vmaxpd, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2700"><span class="lineNum">    2700 </span>            :   ASMJIT_INST_3x(vmaxpd, Vmaxpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2701"><span class="lineNum">    2701 </span>            :   ASMJIT_INST_3x(vmaxpd, Vmaxpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2702"><span class="lineNum">    2702 </span>            :   ASMJIT_INST_3x(vmaxps, Vmaxps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2703"><span class="lineNum">    2703 </span>            :   ASMJIT_INST_3x(vmaxps, Vmaxps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2704"><span class="lineNum">    2704 </span>            :   ASMJIT_INST_3x(vmaxps, Vmaxps, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2705"><span class="lineNum">    2705 </span>            :   ASMJIT_INST_3x(vmaxps, Vmaxps, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2706"><span class="lineNum">    2706 </span>            :   ASMJIT_INST_3x(vmaxps, Vmaxps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|sae|b32}</a>
+<a name="2707"><span class="lineNum">    2707 </span>            :   ASMJIT_INST_3x(vmaxps, Vmaxps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|sae|b32}</a>
+<a name="2708"><span class="lineNum">    2708 </span>            :   ASMJIT_INST_3x(vmaxsd, Vmaxsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2709"><span class="lineNum">    2709 </span>            :   ASMJIT_INST_3x(vmaxsd, Vmaxsd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2710"><span class="lineNum">    2710 </span>            :   ASMJIT_INST_3x(vmaxss, Vmaxss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2711"><span class="lineNum">    2711 </span>            :   ASMJIT_INST_3x(vmaxss, Vmaxss, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2712"><span class="lineNum">    2712 </span>            :   ASMJIT_INST_3x(vminpd, Vminpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2713"><span class="lineNum">    2713 </span>            :   ASMJIT_INST_3x(vminpd, Vminpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2714"><span class="lineNum">    2714 </span>            :   ASMJIT_INST_3x(vminpd, Vminpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2715"><span class="lineNum">    2715 </span>            :   ASMJIT_INST_3x(vminpd, Vminpd, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2716"><span class="lineNum">    2716 </span>            :   ASMJIT_INST_3x(vminpd, Vminpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2717"><span class="lineNum">    2717 </span>            :   ASMJIT_INST_3x(vminpd, Vminpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|sae|b64}</a>
+<a name="2718"><span class="lineNum">    2718 </span>            :   ASMJIT_INST_3x(vminps, Vminps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2719"><span class="lineNum">    2719 </span>            :   ASMJIT_INST_3x(vminps, Vminps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2720"><span class="lineNum">    2720 </span>            :   ASMJIT_INST_3x(vminps, Vminps, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2721"><span class="lineNum">    2721 </span>            :   ASMJIT_INST_3x(vminps, Vminps, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2722"><span class="lineNum">    2722 </span>            :   ASMJIT_INST_3x(vminps, Vminps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|sae|b32}</a>
+<a name="2723"><span class="lineNum">    2723 </span>            :   ASMJIT_INST_3x(vminps, Vminps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|sae|b32}</a>
+<a name="2724"><span class="lineNum">    2724 </span>            :   ASMJIT_INST_3x(vminsd, Vminsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2725"><span class="lineNum">    2725 </span>            :   ASMJIT_INST_3x(vminsd, Vminsd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2726"><span class="lineNum">    2726 </span>            :   ASMJIT_INST_3x(vminss, Vminss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2727"><span class="lineNum">    2727 </span>            :   ASMJIT_INST_3x(vminss, Vminss, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|sae}-VL</a>
+<a name="2728"><span class="lineNum">    2728 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Xmm, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2729"><span class="lineNum">    2729 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Xmm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2730"><span class="lineNum">    2730 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Mem, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2731"><span class="lineNum">    2731 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Ymm, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2732"><span class="lineNum">    2732 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Ymm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2733"><span class="lineNum">    2733 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Mem, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2734"><span class="lineNum">    2734 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Zmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2735"><span class="lineNum">    2735 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Zmm, X86Mem)                            //      AVX512_F{kz}</a>
+<a name="2736"><span class="lineNum">    2736 </span>            :   ASMJIT_INST_2x(vmovapd, Vmovapd, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2737"><span class="lineNum">    2737 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Xmm, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2738"><span class="lineNum">    2738 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Xmm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2739"><span class="lineNum">    2739 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Mem, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2740"><span class="lineNum">    2740 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Ymm, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2741"><span class="lineNum">    2741 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Ymm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2742"><span class="lineNum">    2742 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Mem, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2743"><span class="lineNum">    2743 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Zmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2744"><span class="lineNum">    2744 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Zmm, X86Mem)                            //      AVX512_F{kz}</a>
+<a name="2745"><span class="lineNum">    2745 </span>            :   ASMJIT_INST_2x(vmovaps, Vmovaps, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2746"><span class="lineNum">    2746 </span>            :   ASMJIT_INST_2x(vmovd, Vmovd, X86Gp, X86Xmm)                                 // AVX  AVX512_F</a>
+<a name="2747"><span class="lineNum">    2747 </span>            :   ASMJIT_INST_2x(vmovd, Vmovd, X86Mem, X86Xmm)                                // AVX  AVX512_F</a>
+<a name="2748"><span class="lineNum">    2748 </span>            :   ASMJIT_INST_2x(vmovd, Vmovd, X86Xmm, X86Gp)                                 // AVX  AVX512_F</a>
+<a name="2749"><span class="lineNum">    2749 </span>            :   ASMJIT_INST_2x(vmovd, Vmovd, X86Xmm, X86Mem)                                // AVX  AVX512_F</a>
+<a name="2750"><span class="lineNum">    2750 </span>            :   ASMJIT_INST_2x(vmovddup, Vmovddup, X86Xmm, X86Xmm)                          // AVX  AVX512_F{kz}-VL</a>
+<a name="2751"><span class="lineNum">    2751 </span>            :   ASMJIT_INST_2x(vmovddup, Vmovddup, X86Xmm, X86Mem)                          // AVX  AVX512_F{kz}-VL</a>
+<a name="2752"><span class="lineNum">    2752 </span>            :   ASMJIT_INST_2x(vmovddup, Vmovddup, X86Ymm, X86Ymm)                          // AVX  AVX512_F{kz}-VL</a>
+<a name="2753"><span class="lineNum">    2753 </span>            :   ASMJIT_INST_2x(vmovddup, Vmovddup, X86Ymm, X86Mem)                          // AVX  AVX512_F{kz}-VL</a>
+<a name="2754"><span class="lineNum">    2754 </span>            :   ASMJIT_INST_2x(vmovddup, Vmovddup, X86Zmm, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="2755"><span class="lineNum">    2755 </span>            :   ASMJIT_INST_2x(vmovddup, Vmovddup, X86Zmm, X86Mem)                          //      AVX512_F{kz}</a>
+<a name="2756"><span class="lineNum">    2756 </span>            :   ASMJIT_INST_2x(vmovdqa, Vmovdqa, X86Xmm, X86Xmm)                            // AVX</a>
+<a name="2757"><span class="lineNum">    2757 </span>            :   ASMJIT_INST_2x(vmovdqa, Vmovdqa, X86Xmm, X86Mem)                            // AVX</a>
+<a name="2758"><span class="lineNum">    2758 </span>            :   ASMJIT_INST_2x(vmovdqa, Vmovdqa, X86Mem, X86Xmm)                            // AVX</a>
+<a name="2759"><span class="lineNum">    2759 </span>            :   ASMJIT_INST_2x(vmovdqa, Vmovdqa, X86Ymm, X86Ymm)                            // AVX</a>
+<a name="2760"><span class="lineNum">    2760 </span>            :   ASMJIT_INST_2x(vmovdqa, Vmovdqa, X86Ymm, X86Mem)                            // AVX</a>
+<a name="2761"><span class="lineNum">    2761 </span>            :   ASMJIT_INST_2x(vmovdqa, Vmovdqa, X86Mem, X86Ymm)                            // AVX</a>
+<a name="2762"><span class="lineNum">    2762 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2763"><span class="lineNum">    2763 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2764"><span class="lineNum">    2764 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2765"><span class="lineNum">    2765 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2766"><span class="lineNum">    2766 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2767"><span class="lineNum">    2767 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2768"><span class="lineNum">    2768 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2769"><span class="lineNum">    2769 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2770"><span class="lineNum">    2770 </span>            :   ASMJIT_INST_2x(vmovdqa32, Vmovdqa32, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2771"><span class="lineNum">    2771 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2772"><span class="lineNum">    2772 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2773"><span class="lineNum">    2773 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2774"><span class="lineNum">    2774 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2775"><span class="lineNum">    2775 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2776"><span class="lineNum">    2776 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2777"><span class="lineNum">    2777 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2778"><span class="lineNum">    2778 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2779"><span class="lineNum">    2779 </span>            :   ASMJIT_INST_2x(vmovdqa64, Vmovdqa64, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2780"><span class="lineNum">    2780 </span>            :   ASMJIT_INST_2x(vmovdqu, Vmovdqu, X86Xmm, X86Xmm)                            // AVX</a>
+<a name="2781"><span class="lineNum">    2781 </span>            :   ASMJIT_INST_2x(vmovdqu, Vmovdqu, X86Xmm, X86Mem)                            // AVX</a>
+<a name="2782"><span class="lineNum">    2782 </span>            :   ASMJIT_INST_2x(vmovdqu, Vmovdqu, X86Mem, X86Xmm)                            // AVX</a>
+<a name="2783"><span class="lineNum">    2783 </span>            :   ASMJIT_INST_2x(vmovdqu, Vmovdqu, X86Ymm, X86Ymm)                            // AVX</a>
+<a name="2784"><span class="lineNum">    2784 </span>            :   ASMJIT_INST_2x(vmovdqu, Vmovdqu, X86Ymm, X86Mem)                            // AVX</a>
+<a name="2785"><span class="lineNum">    2785 </span>            :   ASMJIT_INST_2x(vmovdqu, Vmovdqu, X86Mem, X86Ymm)                            // AVX</a>
+<a name="2786"><span class="lineNum">    2786 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Xmm, X86Xmm)                        //      AVX512_BW{kz}-VL</a>
+<a name="2787"><span class="lineNum">    2787 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Xmm, X86Mem)                        //      AVX512_BW{kz}-VL</a>
+<a name="2788"><span class="lineNum">    2788 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Mem, X86Xmm)                        //      AVX512_BW{kz}-VL</a>
+<a name="2789"><span class="lineNum">    2789 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Ymm, X86Ymm)                        //      AVX512_BW{kz}-VL</a>
+<a name="2790"><span class="lineNum">    2790 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Ymm, X86Mem)                        //      AVX512_BW{kz}-VL</a>
+<a name="2791"><span class="lineNum">    2791 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Mem, X86Ymm)                        //      AVX512_BW{kz}-VL</a>
+<a name="2792"><span class="lineNum">    2792 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Zmm, X86Zmm)                        //      AVX512_BW{kz}</a>
+<a name="2793"><span class="lineNum">    2793 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Zmm, X86Mem)                        //      AVX512_BW{kz}</a>
+<a name="2794"><span class="lineNum">    2794 </span>            :   ASMJIT_INST_2x(vmovdqu16, Vmovdqu16, X86Mem, X86Zmm)                        //      AVX512_BW{kz}</a>
+<a name="2795"><span class="lineNum">    2795 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2796"><span class="lineNum">    2796 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2797"><span class="lineNum">    2797 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2798"><span class="lineNum">    2798 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2799"><span class="lineNum">    2799 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2800"><span class="lineNum">    2800 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2801"><span class="lineNum">    2801 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2802"><span class="lineNum">    2802 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2803"><span class="lineNum">    2803 </span>            :   ASMJIT_INST_2x(vmovdqu32, Vmovdqu32, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2804"><span class="lineNum">    2804 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2805"><span class="lineNum">    2805 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2806"><span class="lineNum">    2806 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="2807"><span class="lineNum">    2807 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2808"><span class="lineNum">    2808 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="2809"><span class="lineNum">    2809 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="2810"><span class="lineNum">    2810 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2811"><span class="lineNum">    2811 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2812"><span class="lineNum">    2812 </span>            :   ASMJIT_INST_2x(vmovdqu64, Vmovdqu64, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2813"><span class="lineNum">    2813 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Xmm, X86Xmm)                          //      AVX512_BW{kz}-VL</a>
+<a name="2814"><span class="lineNum">    2814 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Xmm, X86Mem)                          //      AVX512_BW{kz}-VL</a>
+<a name="2815"><span class="lineNum">    2815 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Mem, X86Xmm)                          //      AVX512_BW{kz}-VL</a>
+<a name="2816"><span class="lineNum">    2816 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Ymm, X86Ymm)                          //      AVX512_BW{kz}-VL</a>
+<a name="2817"><span class="lineNum">    2817 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Ymm, X86Mem)                          //      AVX512_BW{kz}-VL</a>
+<a name="2818"><span class="lineNum">    2818 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Mem, X86Ymm)                          //      AVX512_BW{kz}-VL</a>
+<a name="2819"><span class="lineNum">    2819 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Zmm, X86Zmm)                          //      AVX512_BW{kz}</a>
+<a name="2820"><span class="lineNum">    2820 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Zmm, X86Mem)                          //      AVX512_BW{kz}</a>
+<a name="2821"><span class="lineNum">    2821 </span>            :   ASMJIT_INST_2x(vmovdqu8, Vmovdqu8, X86Mem, X86Zmm)                          //      AVX512_BW{kz}</a>
+<a name="2822"><span class="lineNum">    2822 </span>            :   ASMJIT_INST_3x(vmovhlps, Vmovhlps, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_F</a>
+<a name="2823"><span class="lineNum">    2823 </span>            :   ASMJIT_INST_2x(vmovhpd, Vmovhpd, X86Mem, X86Xmm)                            // AVX  AVX512_F</a>
+<a name="2824"><span class="lineNum">    2824 </span>            :   ASMJIT_INST_3x(vmovhpd, Vmovhpd, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F</a>
+<a name="2825"><span class="lineNum">    2825 </span>            :   ASMJIT_INST_2x(vmovhps, Vmovhps, X86Mem, X86Xmm)                            // AVX  AVX512_F</a>
+<a name="2826"><span class="lineNum">    2826 </span>            :   ASMJIT_INST_3x(vmovhps, Vmovhps, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F</a>
+<a name="2827"><span class="lineNum">    2827 </span>            :   ASMJIT_INST_3x(vmovlhps, Vmovlhps, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_F</a>
+<a name="2828"><span class="lineNum">    2828 </span>            :   ASMJIT_INST_2x(vmovlpd, Vmovlpd, X86Mem, X86Xmm)                            // AVX  AVX512_F</a>
+<a name="2829"><span class="lineNum">    2829 </span>            :   ASMJIT_INST_3x(vmovlpd, Vmovlpd, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F</a>
+<a name="2830"><span class="lineNum">    2830 </span>            :   ASMJIT_INST_2x(vmovlps, Vmovlps, X86Mem, X86Xmm)                            // AVX  AVX512_F</a>
+<a name="2831"><span class="lineNum">    2831 </span>            :   ASMJIT_INST_3x(vmovlps, Vmovlps, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F</a>
+<a name="2832"><span class="lineNum">    2832 </span>            :   ASMJIT_INST_2x(vmovmskpd, Vmovmskpd, X86Gp, X86Xmm)                         // AVX</a>
+<a name="2833"><span class="lineNum">    2833 </span>            :   ASMJIT_INST_2x(vmovmskpd, Vmovmskpd, X86Gp, X86Ymm)                         // AVX</a>
+<a name="2834"><span class="lineNum">    2834 </span>            :   ASMJIT_INST_2x(vmovmskps, Vmovmskps, X86Gp, X86Xmm)                         // AVX</a>
+<a name="2835"><span class="lineNum">    2835 </span>            :   ASMJIT_INST_2x(vmovmskps, Vmovmskps, X86Gp, X86Ymm)                         // AVX</a>
+<a name="2836"><span class="lineNum">    2836 </span>            :   ASMJIT_INST_2x(vmovntdq, Vmovntdq, X86Mem, X86Xmm)                          // AVX  AVX512_F-VL</a>
+<a name="2837"><span class="lineNum">    2837 </span>            :   ASMJIT_INST_2x(vmovntdq, Vmovntdq, X86Mem, X86Ymm)                          // AVX  AVX512_F-VL</a>
+<a name="2838"><span class="lineNum">    2838 </span>            :   ASMJIT_INST_2x(vmovntdq, Vmovntdq, X86Mem, X86Zmm)                          //      AVX512_F</a>
+<a name="2839"><span class="lineNum">    2839 </span>            :   ASMJIT_INST_2x(vmovntdqa, Vmovntdqa, X86Xmm, X86Mem)                        // AVX  AVX512_F-VL</a>
+<a name="2840"><span class="lineNum">    2840 </span>            :   ASMJIT_INST_2x(vmovntdqa, Vmovntdqa, X86Ymm, X86Mem)                        // AVX2 AVX512_F-VL</a>
+<a name="2841"><span class="lineNum">    2841 </span>            :   ASMJIT_INST_2x(vmovntdqa, Vmovntdqa, X86Zmm, X86Mem)                        //      AVX512_F</a>
+<a name="2842"><span class="lineNum">    2842 </span>            :   ASMJIT_INST_2x(vmovntpd, Vmovntpd, X86Mem, X86Xmm)                          // AVX  AVX512_F-VL</a>
+<a name="2843"><span class="lineNum">    2843 </span>            :   ASMJIT_INST_2x(vmovntpd, Vmovntpd, X86Mem, X86Ymm)                          // AVX  AVX512_F-VL</a>
+<a name="2844"><span class="lineNum">    2844 </span>            :   ASMJIT_INST_2x(vmovntpd, Vmovntpd, X86Mem, X86Zmm)                          //      AVX512_F</a>
+<a name="2845"><span class="lineNum">    2845 </span>            :   ASMJIT_INST_2x(vmovntps, Vmovntps, X86Mem, X86Xmm)                          // AVX  AVX512_F-VL</a>
+<a name="2846"><span class="lineNum">    2846 </span>            :   ASMJIT_INST_2x(vmovntps, Vmovntps, X86Mem, X86Ymm)                          // AVX  AVX512_F-VL</a>
+<a name="2847"><span class="lineNum">    2847 </span>            :   ASMJIT_INST_2x(vmovntps, Vmovntps, X86Mem, X86Zmm)                          //      AVX512_F</a>
+<a name="2848"><span class="lineNum">    2848 </span>            :   ASMJIT_INST_2x(vmovq, Vmovq, X86Gp, X86Xmm)                                 // AVX  AVX512_F</a>
+<a name="2849"><span class="lineNum">    2849 </span>            :   ASMJIT_INST_2x(vmovq, Vmovq, X86Mem, X86Xmm)                                // AVX  AVX512_F</a>
+<a name="2850"><span class="lineNum">    2850 </span>            :   ASMJIT_INST_2x(vmovq, Vmovq, X86Xmm, X86Mem)                                // AVX  AVX512_F</a>
+<a name="2851"><span class="lineNum">    2851 </span>            :   ASMJIT_INST_2x(vmovq, Vmovq, X86Xmm, X86Gp)                                 // AVX  AVX512_F</a>
+<a name="2852"><span class="lineNum">    2852 </span>            :   ASMJIT_INST_2x(vmovq, Vmovq, X86Xmm, X86Xmm)                                // AVX  AVX512_F</a>
+<a name="2853"><span class="lineNum">    2853 </span>            :   ASMJIT_INST_2x(vmovsd, Vmovsd, X86Mem, X86Xmm)                              // AVX  AVX512_F</a>
+<a name="2854"><span class="lineNum">    2854 </span>            :   ASMJIT_INST_2x(vmovsd, Vmovsd, X86Xmm, X86Mem)                              // AVX  AVX512_F{kz}</a>
+<a name="2855"><span class="lineNum">    2855 </span>            :   ASMJIT_INST_3x(vmovsd, Vmovsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}</a>
+<a name="2856"><span class="lineNum">    2856 </span>            :   ASMJIT_INST_2x(vmovshdup, Vmovshdup, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2857"><span class="lineNum">    2857 </span>            :   ASMJIT_INST_2x(vmovshdup, Vmovshdup, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2858"><span class="lineNum">    2858 </span>            :   ASMJIT_INST_2x(vmovshdup, Vmovshdup, X86Ymm, X86Ymm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2859"><span class="lineNum">    2859 </span>            :   ASMJIT_INST_2x(vmovshdup, Vmovshdup, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2860"><span class="lineNum">    2860 </span>            :   ASMJIT_INST_2x(vmovshdup, Vmovshdup, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2861"><span class="lineNum">    2861 </span>            :   ASMJIT_INST_2x(vmovshdup, Vmovshdup, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2862"><span class="lineNum">    2862 </span>            :   ASMJIT_INST_2x(vmovsldup, Vmovsldup, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2863"><span class="lineNum">    2863 </span>            :   ASMJIT_INST_2x(vmovsldup, Vmovsldup, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2864"><span class="lineNum">    2864 </span>            :   ASMJIT_INST_2x(vmovsldup, Vmovsldup, X86Ymm, X86Ymm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2865"><span class="lineNum">    2865 </span>            :   ASMJIT_INST_2x(vmovsldup, Vmovsldup, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="2866"><span class="lineNum">    2866 </span>            :   ASMJIT_INST_2x(vmovsldup, Vmovsldup, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="2867"><span class="lineNum">    2867 </span>            :   ASMJIT_INST_2x(vmovsldup, Vmovsldup, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="2868"><span class="lineNum">    2868 </span>            :   ASMJIT_INST_2x(vmovss, Vmovss, X86Mem, X86Xmm)                              // AVX  AVX512_F</a>
+<a name="2869"><span class="lineNum">    2869 </span>            :   ASMJIT_INST_2x(vmovss, Vmovss, X86Xmm, X86Mem)                              // AVX  AVX512_F{kz}</a>
+<a name="2870"><span class="lineNum">    2870 </span>            :   ASMJIT_INST_3x(vmovss, Vmovss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}</a>
+<a name="2871"><span class="lineNum">    2871 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Xmm, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2872"><span class="lineNum">    2872 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Xmm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2873"><span class="lineNum">    2873 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Mem, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2874"><span class="lineNum">    2874 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Ymm, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2875"><span class="lineNum">    2875 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Ymm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2876"><span class="lineNum">    2876 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Mem, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2877"><span class="lineNum">    2877 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Zmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2878"><span class="lineNum">    2878 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Zmm, X86Mem)                            //      AVX512_F{kz}</a>
+<a name="2879"><span class="lineNum">    2879 </span>            :   ASMJIT_INST_2x(vmovupd, Vmovupd, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2880"><span class="lineNum">    2880 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Xmm, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2881"><span class="lineNum">    2881 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Xmm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2882"><span class="lineNum">    2882 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Mem, X86Xmm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2883"><span class="lineNum">    2883 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Ymm, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2884"><span class="lineNum">    2884 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Ymm, X86Mem)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2885"><span class="lineNum">    2885 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Mem, X86Ymm)                            // AVX  AVX512_F{kz}-VL</a>
+<a name="2886"><span class="lineNum">    2886 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Zmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2887"><span class="lineNum">    2887 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Zmm, X86Mem)                            //      AVX512_F{kz}</a>
+<a name="2888"><span class="lineNum">    2888 </span>            :   ASMJIT_INST_2x(vmovups, Vmovups, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="2889"><span class="lineNum">    2889 </span>            :   ASMJIT_INST_4i(vmpsadbw, Vmpsadbw, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX</a>
+<a name="2890"><span class="lineNum">    2890 </span>            :   ASMJIT_INST_4i(vmpsadbw, Vmpsadbw, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX</a>
+<a name="2891"><span class="lineNum">    2891 </span>            :   ASMJIT_INST_4i(vmpsadbw, Vmpsadbw, X86Ymm, X86Ymm, X86Ymm, Imm)             // AVX2</a>
+<a name="2892"><span class="lineNum">    2892 </span>            :   ASMJIT_INST_4i(vmpsadbw, Vmpsadbw, X86Ymm, X86Ymm, X86Mem, Imm)             // AVX2</a>
+<a name="2893"><span class="lineNum">    2893 </span>            :   ASMJIT_INST_3x(vmulpd, Vmulpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2894"><span class="lineNum">    2894 </span>            :   ASMJIT_INST_3x(vmulpd, Vmulpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2895"><span class="lineNum">    2895 </span>            :   ASMJIT_INST_3x(vmulpd, Vmulpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="2896"><span class="lineNum">    2896 </span>            :   ASMJIT_INST_3x(vmulpd, Vmulpd, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="2897"><span class="lineNum">    2897 </span>            :   ASMJIT_INST_3x(vmulpd, Vmulpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b64}</a>
+<a name="2898"><span class="lineNum">    2898 </span>            :   ASMJIT_INST_3x(vmulpd, Vmulpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b64}</a>
+<a name="2899"><span class="lineNum">    2899 </span>            :   ASMJIT_INST_3x(vmulps, Vmulps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2900"><span class="lineNum">    2900 </span>            :   ASMJIT_INST_3x(vmulps, Vmulps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2901"><span class="lineNum">    2901 </span>            :   ASMJIT_INST_3x(vmulps, Vmulps, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="2902"><span class="lineNum">    2902 </span>            :   ASMJIT_INST_3x(vmulps, Vmulps, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="2903"><span class="lineNum">    2903 </span>            :   ASMJIT_INST_3x(vmulps, Vmulps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2904"><span class="lineNum">    2904 </span>            :   ASMJIT_INST_3x(vmulps, Vmulps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b32}</a>
+<a name="2905"><span class="lineNum">    2905 </span>            :   ASMJIT_INST_3x(vmulsd, Vmulsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2906"><span class="lineNum">    2906 </span>            :   ASMJIT_INST_3x(vmulsd, Vmulsd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2907"><span class="lineNum">    2907 </span>            :   ASMJIT_INST_3x(vmulss, Vmulss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2908"><span class="lineNum">    2908 </span>            :   ASMJIT_INST_3x(vmulss, Vmulss, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="2909"><span class="lineNum">    2909 </span>            :   ASMJIT_INST_3x(vorpd, Vorpd, X86Xmm, X86Xmm, X86Xmm)                        // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="2910"><span class="lineNum">    2910 </span>            :   ASMJIT_INST_3x(vorpd, Vorpd, X86Xmm, X86Xmm, X86Mem)                        // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="2911"><span class="lineNum">    2911 </span>            :   ASMJIT_INST_3x(vorpd, Vorpd, X86Ymm, X86Ymm, X86Ymm)                        // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="2912"><span class="lineNum">    2912 </span>            :   ASMJIT_INST_3x(vorpd, Vorpd, X86Ymm, X86Ymm, X86Mem)                        // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="2913"><span class="lineNum">    2913 </span>            :   ASMJIT_INST_3x(vorpd, Vorpd, X86Zmm, X86Zmm, X86Zmm)                        //      AVX512_DQ{kz|b64}</a>
+<a name="2914"><span class="lineNum">    2914 </span>            :   ASMJIT_INST_3x(vorpd, Vorpd, X86Zmm, X86Zmm, X86Mem)                        //      AVX512_DQ{kz|b64}</a>
+<a name="2915"><span class="lineNum">    2915 </span>            :   ASMJIT_INST_3x(vorps, Vorps, X86Xmm, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2916"><span class="lineNum">    2916 </span>            :   ASMJIT_INST_3x(vorps, Vorps, X86Xmm, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2917"><span class="lineNum">    2917 </span>            :   ASMJIT_INST_3x(vorps, Vorps, X86Ymm, X86Ymm, X86Ymm)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2918"><span class="lineNum">    2918 </span>            :   ASMJIT_INST_3x(vorps, Vorps, X86Ymm, X86Ymm, X86Mem)                        // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2919"><span class="lineNum">    2919 </span>            :   ASMJIT_INST_3x(vorps, Vorps, X86Zmm, X86Zmm, X86Zmm)                        //      AVX512_F{kz|b32}</a>
+<a name="2920"><span class="lineNum">    2920 </span>            :   ASMJIT_INST_3x(vorps, Vorps, X86Zmm, X86Zmm, X86Mem)                        //      AVX512_F{kz|b32}</a>
+<a name="2921"><span class="lineNum">    2921 </span>            :   ASMJIT_INST_6x(vp4dpwssd, Vp4dpwssd, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Mem)   // AVX512_4FMAPS{kz}</a>
+<a name="2922"><span class="lineNum">    2922 </span>            :   ASMJIT_INST_6x(vp4dpwssds, Vp4dpwssds, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Zmm, X86Mem) // AVX512_4FMAPS{kz}</a>
+<a name="2923"><span class="lineNum">    2923 </span>            :   ASMJIT_INST_2x(vpabsb, Vpabsb, X86Xmm, X86Xmm)                              // AVX  AVX512_BW{kz}-VL</a>
+<a name="2924"><span class="lineNum">    2924 </span>            :   ASMJIT_INST_2x(vpabsb, Vpabsb, X86Xmm, X86Mem)                              // AVX  AVX512_BW{kz}-VL</a>
+<a name="2925"><span class="lineNum">    2925 </span>            :   ASMJIT_INST_2x(vpabsb, Vpabsb, X86Ymm, X86Ymm)                              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2926"><span class="lineNum">    2926 </span>            :   ASMJIT_INST_2x(vpabsb, Vpabsb, X86Ymm, X86Mem)                              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2927"><span class="lineNum">    2927 </span>            :   ASMJIT_INST_2x(vpabsb, Vpabsb, X86Zmm, X86Zmm)                              //      AVX512_BW{kz}</a>
+<a name="2928"><span class="lineNum">    2928 </span>            :   ASMJIT_INST_2x(vpabsb, Vpabsb, X86Zmm, X86Mem)                              //      AVX512_BW{kz}</a>
+<a name="2929"><span class="lineNum">    2929 </span>            :   ASMJIT_INST_2x(vpabsd, Vpabsd, X86Xmm, X86Xmm)                              // AVX  AVX512_F{kz}-VL</a>
+<a name="2930"><span class="lineNum">    2930 </span>            :   ASMJIT_INST_2x(vpabsd, Vpabsd, X86Xmm, X86Mem)                              // AVX  AVX512_F{kz}-VL</a>
+<a name="2931"><span class="lineNum">    2931 </span>            :   ASMJIT_INST_2x(vpabsd, Vpabsd, X86Ymm, X86Ymm)                              // AVX2 AVX512_F{kz}-VL</a>
+<a name="2932"><span class="lineNum">    2932 </span>            :   ASMJIT_INST_2x(vpabsd, Vpabsd, X86Ymm, X86Mem)                              // AVX2 AVX512_F{kz}-VL</a>
+<a name="2933"><span class="lineNum">    2933 </span>            :   ASMJIT_INST_2x(vpabsd, Vpabsd, X86Zmm, X86Zmm)                              //      AVX512_F{kz}</a>
+<a name="2934"><span class="lineNum">    2934 </span>            :   ASMJIT_INST_2x(vpabsd, Vpabsd, X86Zmm, X86Mem)                              //      AVX512_F{kz}</a>
+<a name="2935"><span class="lineNum">    2935 </span>            :   ASMJIT_INST_2x(vpabsq, Vpabsq, X86Xmm, X86Xmm)                              //      AVX512_F{kz}-VL</a>
+<a name="2936"><span class="lineNum">    2936 </span>            :   ASMJIT_INST_2x(vpabsq, Vpabsq, X86Xmm, X86Mem)                              //      AVX512_F{kz}-VL</a>
+<a name="2937"><span class="lineNum">    2937 </span>            :   ASMJIT_INST_2x(vpabsq, Vpabsq, X86Ymm, X86Ymm)                              //      AVX512_F{kz}-VL</a>
+<a name="2938"><span class="lineNum">    2938 </span>            :   ASMJIT_INST_2x(vpabsq, Vpabsq, X86Ymm, X86Mem)                              //      AVX512_F{kz}-VL</a>
+<a name="2939"><span class="lineNum">    2939 </span>            :   ASMJIT_INST_2x(vpabsq, Vpabsq, X86Zmm, X86Zmm)                              //      AVX512_F{kz}</a>
+<a name="2940"><span class="lineNum">    2940 </span>            :   ASMJIT_INST_2x(vpabsq, Vpabsq, X86Zmm, X86Mem)                              //      AVX512_F{kz}</a>
+<a name="2941"><span class="lineNum">    2941 </span>            :   ASMJIT_INST_2x(vpabsw, Vpabsw, X86Xmm, X86Xmm)                              // AVX  AVX512_BW{kz}-VL</a>
+<a name="2942"><span class="lineNum">    2942 </span>            :   ASMJIT_INST_2x(vpabsw, Vpabsw, X86Xmm, X86Mem)                              // AVX  AVX512_BW{kz}-VL</a>
+<a name="2943"><span class="lineNum">    2943 </span>            :   ASMJIT_INST_2x(vpabsw, Vpabsw, X86Ymm, X86Ymm)                              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2944"><span class="lineNum">    2944 </span>            :   ASMJIT_INST_2x(vpabsw, Vpabsw, X86Ymm, X86Mem)                              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2945"><span class="lineNum">    2945 </span>            :   ASMJIT_INST_2x(vpabsw, Vpabsw, X86Zmm, X86Zmm)                              //      AVX512_BW{kz}</a>
+<a name="2946"><span class="lineNum">    2946 </span>            :   ASMJIT_INST_2x(vpabsw, Vpabsw, X86Zmm, X86Mem)                              //      AVX512_BW{kz}</a>
+<a name="2947"><span class="lineNum">    2947 </span>            :   ASMJIT_INST_3x(vpackssdw, Vpackssdw, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_BW{kz|b32}-VL</a>
+<a name="2948"><span class="lineNum">    2948 </span>            :   ASMJIT_INST_3x(vpackssdw, Vpackssdw, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_BW{kz|b32}-VL</a>
+<a name="2949"><span class="lineNum">    2949 </span>            :   ASMJIT_INST_3x(vpackssdw, Vpackssdw, X86Ymm, X86Ymm, X86Ymm)                // AVX2 AVX512_BW{kz|b32}-VL</a>
+<a name="2950"><span class="lineNum">    2950 </span>            :   ASMJIT_INST_3x(vpackssdw, Vpackssdw, X86Ymm, X86Ymm, X86Mem)                // AVX2 AVX512_BW{kz|b32}-VL</a>
+<a name="2951"><span class="lineNum">    2951 </span>            :   ASMJIT_INST_3x(vpackssdw, Vpackssdw, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_BW{kz|b32}</a>
+<a name="2952"><span class="lineNum">    2952 </span>            :   ASMJIT_INST_3x(vpackssdw, Vpackssdw, X86Zmm, X86Zmm, X86Mem)                //      AVX512_BW{kz|b32}</a>
+<a name="2953"><span class="lineNum">    2953 </span>            :   ASMJIT_INST_3x(vpacksswb, Vpacksswb, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_BW{kz}-VL</a>
+<a name="2954"><span class="lineNum">    2954 </span>            :   ASMJIT_INST_3x(vpacksswb, Vpacksswb, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_BW{kz}-VL</a>
+<a name="2955"><span class="lineNum">    2955 </span>            :   ASMJIT_INST_3x(vpacksswb, Vpacksswb, X86Ymm, X86Ymm, X86Ymm)                // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2956"><span class="lineNum">    2956 </span>            :   ASMJIT_INST_3x(vpacksswb, Vpacksswb, X86Ymm, X86Ymm, X86Mem)                // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2957"><span class="lineNum">    2957 </span>            :   ASMJIT_INST_3x(vpacksswb, Vpacksswb, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_BW{kz}</a>
+<a name="2958"><span class="lineNum">    2958 </span>            :   ASMJIT_INST_3x(vpacksswb, Vpacksswb, X86Zmm, X86Zmm, X86Mem)                //      AVX512_BW{kz}</a>
+<a name="2959"><span class="lineNum">    2959 </span>            :   ASMJIT_INST_3x(vpackusdw, Vpackusdw, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_BW{kz|b32}-VL</a>
+<a name="2960"><span class="lineNum">    2960 </span>            :   ASMJIT_INST_3x(vpackusdw, Vpackusdw, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_BW{kz|b32}-VL</a>
+<a name="2961"><span class="lineNum">    2961 </span>            :   ASMJIT_INST_3x(vpackusdw, Vpackusdw, X86Ymm, X86Ymm, X86Ymm)                // AVX2 AVX512_BW{kz|b32}-VL</a>
+<a name="2962"><span class="lineNum">    2962 </span>            :   ASMJIT_INST_3x(vpackusdw, Vpackusdw, X86Ymm, X86Ymm, X86Mem)                // AVX2 AVX512_BW{kz|b32}-VL</a>
+<a name="2963"><span class="lineNum">    2963 </span>            :   ASMJIT_INST_3x(vpackusdw, Vpackusdw, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_BW{kz|b32}</a>
+<a name="2964"><span class="lineNum">    2964 </span>            :   ASMJIT_INST_3x(vpackusdw, Vpackusdw, X86Zmm, X86Zmm, X86Mem)                //      AVX512_BW{kz|b32}</a>
+<a name="2965"><span class="lineNum">    2965 </span>            :   ASMJIT_INST_3x(vpackuswb, Vpackuswb, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_BW{kz}-VL</a>
+<a name="2966"><span class="lineNum">    2966 </span>            :   ASMJIT_INST_3x(vpackuswb, Vpackuswb, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_BW{kz}-VL</a>
+<a name="2967"><span class="lineNum">    2967 </span>            :   ASMJIT_INST_3x(vpackuswb, Vpackuswb, X86Ymm, X86Ymm, X86Ymm)                // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2968"><span class="lineNum">    2968 </span>            :   ASMJIT_INST_3x(vpackuswb, Vpackuswb, X86Ymm, X86Ymm, X86Mem)                // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2969"><span class="lineNum">    2969 </span>            :   ASMJIT_INST_3x(vpackuswb, Vpackuswb, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_BW{kz}</a>
+<a name="2970"><span class="lineNum">    2970 </span>            :   ASMJIT_INST_3x(vpackuswb, Vpackuswb, X86Zmm, X86Zmm, X86Mem)                //      AVX512_BW{kz}</a>
+<a name="2971"><span class="lineNum">    2971 </span>            :   ASMJIT_INST_3x(vpaddb, Vpaddb, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="2972"><span class="lineNum">    2972 </span>            :   ASMJIT_INST_3x(vpaddb, Vpaddb, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="2973"><span class="lineNum">    2973 </span>            :   ASMJIT_INST_3x(vpaddb, Vpaddb, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2974"><span class="lineNum">    2974 </span>            :   ASMJIT_INST_3x(vpaddb, Vpaddb, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2975"><span class="lineNum">    2975 </span>            :   ASMJIT_INST_3x(vpaddb, Vpaddb, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="2976"><span class="lineNum">    2976 </span>            :   ASMJIT_INST_3x(vpaddb, Vpaddb, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="2977"><span class="lineNum">    2977 </span>            :   ASMJIT_INST_3x(vpaddd, Vpaddd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2978"><span class="lineNum">    2978 </span>            :   ASMJIT_INST_3x(vpaddd, Vpaddd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="2979"><span class="lineNum">    2979 </span>            :   ASMJIT_INST_3x(vpaddd, Vpaddd, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="2980"><span class="lineNum">    2980 </span>            :   ASMJIT_INST_3x(vpaddd, Vpaddd, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="2981"><span class="lineNum">    2981 </span>            :   ASMJIT_INST_3x(vpaddd, Vpaddd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b32}</a>
+<a name="2982"><span class="lineNum">    2982 </span>            :   ASMJIT_INST_3x(vpaddd, Vpaddd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}</a>
+<a name="2983"><span class="lineNum">    2983 </span>            :   ASMJIT_INST_3x(vpaddq, Vpaddq, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2984"><span class="lineNum">    2984 </span>            :   ASMJIT_INST_3x(vpaddq, Vpaddq, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="2985"><span class="lineNum">    2985 </span>            :   ASMJIT_INST_3x(vpaddq, Vpaddq, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="2986"><span class="lineNum">    2986 </span>            :   ASMJIT_INST_3x(vpaddq, Vpaddq, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="2987"><span class="lineNum">    2987 </span>            :   ASMJIT_INST_3x(vpaddq, Vpaddq, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b64}</a>
+<a name="2988"><span class="lineNum">    2988 </span>            :   ASMJIT_INST_3x(vpaddq, Vpaddq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b64}</a>
+<a name="2989"><span class="lineNum">    2989 </span>            :   ASMJIT_INST_3x(vpaddsb, Vpaddsb, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="2990"><span class="lineNum">    2990 </span>            :   ASMJIT_INST_3x(vpaddsb, Vpaddsb, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="2991"><span class="lineNum">    2991 </span>            :   ASMJIT_INST_3x(vpaddsb, Vpaddsb, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2992"><span class="lineNum">    2992 </span>            :   ASMJIT_INST_3x(vpaddsb, Vpaddsb, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2993"><span class="lineNum">    2993 </span>            :   ASMJIT_INST_3x(vpaddsb, Vpaddsb, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="2994"><span class="lineNum">    2994 </span>            :   ASMJIT_INST_3x(vpaddsb, Vpaddsb, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="2995"><span class="lineNum">    2995 </span>            :   ASMJIT_INST_3x(vpaddsw, Vpaddsw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="2996"><span class="lineNum">    2996 </span>            :   ASMJIT_INST_3x(vpaddsw, Vpaddsw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="2997"><span class="lineNum">    2997 </span>            :   ASMJIT_INST_3x(vpaddsw, Vpaddsw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2998"><span class="lineNum">    2998 </span>            :   ASMJIT_INST_3x(vpaddsw, Vpaddsw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="2999"><span class="lineNum">    2999 </span>            :   ASMJIT_INST_3x(vpaddsw, Vpaddsw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3000"><span class="lineNum">    3000 </span>            :   ASMJIT_INST_3x(vpaddsw, Vpaddsw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3001"><span class="lineNum">    3001 </span>            :   ASMJIT_INST_3x(vpaddusb, Vpaddusb, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3002"><span class="lineNum">    3002 </span>            :   ASMJIT_INST_3x(vpaddusb, Vpaddusb, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3003"><span class="lineNum">    3003 </span>            :   ASMJIT_INST_3x(vpaddusb, Vpaddusb, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3004"><span class="lineNum">    3004 </span>            :   ASMJIT_INST_3x(vpaddusb, Vpaddusb, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3005"><span class="lineNum">    3005 </span>            :   ASMJIT_INST_3x(vpaddusb, Vpaddusb, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="3006"><span class="lineNum">    3006 </span>            :   ASMJIT_INST_3x(vpaddusb, Vpaddusb, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3007"><span class="lineNum">    3007 </span>            :   ASMJIT_INST_3x(vpaddusw, Vpaddusw, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3008"><span class="lineNum">    3008 </span>            :   ASMJIT_INST_3x(vpaddusw, Vpaddusw, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3009"><span class="lineNum">    3009 </span>            :   ASMJIT_INST_3x(vpaddusw, Vpaddusw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3010"><span class="lineNum">    3010 </span>            :   ASMJIT_INST_3x(vpaddusw, Vpaddusw, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3011"><span class="lineNum">    3011 </span>            :   ASMJIT_INST_3x(vpaddusw, Vpaddusw, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="3012"><span class="lineNum">    3012 </span>            :   ASMJIT_INST_3x(vpaddusw, Vpaddusw, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3013"><span class="lineNum">    3013 </span>            :   ASMJIT_INST_3x(vpaddw, Vpaddw, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="3014"><span class="lineNum">    3014 </span>            :   ASMJIT_INST_3x(vpaddw, Vpaddw, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="3015"><span class="lineNum">    3015 </span>            :   ASMJIT_INST_3x(vpaddw, Vpaddw, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3016"><span class="lineNum">    3016 </span>            :   ASMJIT_INST_3x(vpaddw, Vpaddw, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3017"><span class="lineNum">    3017 </span>            :   ASMJIT_INST_3x(vpaddw, Vpaddw, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="3018"><span class="lineNum">    3018 </span>            :   ASMJIT_INST_3x(vpaddw, Vpaddw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="3019"><span class="lineNum">    3019 </span>            :   ASMJIT_INST_4i(vpalignr, Vpalignr, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX  AVX512_BW{kz}-VL</a>
+<a name="3020"><span class="lineNum">    3020 </span>            :   ASMJIT_INST_4i(vpalignr, Vpalignr, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX  AVX512_BW{kz}-VL</a>
+<a name="3021"><span class="lineNum">    3021 </span>            :   ASMJIT_INST_4i(vpalignr, Vpalignr, X86Ymm, X86Ymm, X86Ymm, Imm)             // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3022"><span class="lineNum">    3022 </span>            :   ASMJIT_INST_4i(vpalignr, Vpalignr, X86Ymm, X86Ymm, X86Mem, Imm)             // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3023"><span class="lineNum">    3023 </span>            :   ASMJIT_INST_4i(vpalignr, Vpalignr, X86Zmm, X86Zmm, X86Zmm, Imm)             //      AVX512_BW{kz}</a>
+<a name="3024"><span class="lineNum">    3024 </span>            :   ASMJIT_INST_4i(vpalignr, Vpalignr, X86Zmm, X86Zmm, X86Mem, Imm)             //      AVX512_BW{kz}</a>
+<a name="3025"><span class="lineNum">    3025 </span>            :   ASMJIT_INST_3x(vpand, Vpand, X86Xmm, X86Xmm, X86Xmm)                        // AVX</a>
+<a name="3026"><span class="lineNum">    3026 </span>            :   ASMJIT_INST_3x(vpand, Vpand, X86Xmm, X86Xmm, X86Mem)                        // AVX</a>
+<a name="3027"><span class="lineNum">    3027 </span>            :   ASMJIT_INST_3x(vpand, Vpand, X86Ymm, X86Ymm, X86Ymm)                        // AVX2</a>
+<a name="3028"><span class="lineNum">    3028 </span>            :   ASMJIT_INST_3x(vpand, Vpand, X86Ymm, X86Ymm, X86Mem)                        // AVX2</a>
+<a name="3029"><span class="lineNum">    3029 </span>            :   ASMJIT_INST_3x(vpandd, Vpandd, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="3030"><span class="lineNum">    3030 </span>            :   ASMJIT_INST_3x(vpandd, Vpandd, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="3031"><span class="lineNum">    3031 </span>            :   ASMJIT_INST_3x(vpandd, Vpandd, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="3032"><span class="lineNum">    3032 </span>            :   ASMJIT_INST_3x(vpandd, Vpandd, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="3033"><span class="lineNum">    3033 </span>            :   ASMJIT_INST_3x(vpandd, Vpandd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b32}</a>
+<a name="3034"><span class="lineNum">    3034 </span>            :   ASMJIT_INST_3x(vpandd, Vpandd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}</a>
+<a name="3035"><span class="lineNum">    3035 </span>            :   ASMJIT_INST_3x(vpandn, Vpandn, X86Xmm, X86Xmm, X86Xmm)                      // AVX</a>
+<a name="3036"><span class="lineNum">    3036 </span>            :   ASMJIT_INST_3x(vpandn, Vpandn, X86Xmm, X86Xmm, X86Mem)                      // AVX</a>
+<a name="3037"><span class="lineNum">    3037 </span>            :   ASMJIT_INST_3x(vpandn, Vpandn, X86Ymm, X86Ymm, X86Ymm)                      // AVX2</a>
+<a name="3038"><span class="lineNum">    3038 </span>            :   ASMJIT_INST_3x(vpandn, Vpandn, X86Ymm, X86Ymm, X86Mem)                      // AVX2</a>
+<a name="3039"><span class="lineNum">    3039 </span>            :   ASMJIT_INST_3x(vpandnd, Vpandnd, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3040"><span class="lineNum">    3040 </span>            :   ASMJIT_INST_3x(vpandnd, Vpandnd, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3041"><span class="lineNum">    3041 </span>            :   ASMJIT_INST_3x(vpandnd, Vpandnd, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3042"><span class="lineNum">    3042 </span>            :   ASMJIT_INST_3x(vpandnd, Vpandnd, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3043"><span class="lineNum">    3043 </span>            :   ASMJIT_INST_3x(vpandnd, Vpandnd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3044"><span class="lineNum">    3044 </span>            :   ASMJIT_INST_3x(vpandnd, Vpandnd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3045"><span class="lineNum">    3045 </span>            :   ASMJIT_INST_3x(vpandnq, Vpandnq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3046"><span class="lineNum">    3046 </span>            :   ASMJIT_INST_3x(vpandnq, Vpandnq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3047"><span class="lineNum">    3047 </span>            :   ASMJIT_INST_3x(vpandnq, Vpandnq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3048"><span class="lineNum">    3048 </span>            :   ASMJIT_INST_3x(vpandnq, Vpandnq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3049"><span class="lineNum">    3049 </span>            :   ASMJIT_INST_3x(vpandnq, Vpandnq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3050"><span class="lineNum">    3050 </span>            :   ASMJIT_INST_3x(vpandnq, Vpandnq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3051"><span class="lineNum">    3051 </span>            :   ASMJIT_INST_3x(vpandq, Vpandq, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3052"><span class="lineNum">    3052 </span>            :   ASMJIT_INST_3x(vpandq, Vpandq, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3053"><span class="lineNum">    3053 </span>            :   ASMJIT_INST_3x(vpandq, Vpandq, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3054"><span class="lineNum">    3054 </span>            :   ASMJIT_INST_3x(vpandq, Vpandq, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3055"><span class="lineNum">    3055 </span>            :   ASMJIT_INST_3x(vpandq, Vpandq, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b64}</a>
+<a name="3056"><span class="lineNum">    3056 </span>            :   ASMJIT_INST_3x(vpandq, Vpandq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b64}</a>
+<a name="3057"><span class="lineNum">    3057 </span>            :   ASMJIT_INST_3x(vpavgb, Vpavgb, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="3058"><span class="lineNum">    3058 </span>            :   ASMJIT_INST_3x(vpavgb, Vpavgb, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="3059"><span class="lineNum">    3059 </span>            :   ASMJIT_INST_3x(vpavgb, Vpavgb, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="3060"><span class="lineNum">    3060 </span>            :   ASMJIT_INST_3x(vpavgb, Vpavgb, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="3061"><span class="lineNum">    3061 </span>            :   ASMJIT_INST_3x(vpavgb, Vpavgb, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="3062"><span class="lineNum">    3062 </span>            :   ASMJIT_INST_3x(vpavgb, Vpavgb, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="3063"><span class="lineNum">    3063 </span>            :   ASMJIT_INST_3x(vpavgw, Vpavgw, X86Xmm, X86Xmm, X86Xmm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3064"><span class="lineNum">    3064 </span>            :   ASMJIT_INST_3x(vpavgw, Vpavgw, X86Xmm, X86Xmm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3065"><span class="lineNum">    3065 </span>            :   ASMJIT_INST_3x(vpavgw, Vpavgw, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3066"><span class="lineNum">    3066 </span>            :   ASMJIT_INST_3x(vpavgw, Vpavgw, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3067"><span class="lineNum">    3067 </span>            :   ASMJIT_INST_3x(vpavgw, Vpavgw, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="3068"><span class="lineNum">    3068 </span>            :   ASMJIT_INST_3x(vpavgw, Vpavgw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="3069"><span class="lineNum">    3069 </span>            :   ASMJIT_INST_4i(vpblendd, Vpblendd, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX2</a>
+<a name="3070"><span class="lineNum">    3070 </span>            :   ASMJIT_INST_4i(vpblendd, Vpblendd, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX2</a>
+<a name="3071"><span class="lineNum">    3071 </span>            :   ASMJIT_INST_4i(vpblendd, Vpblendd, X86Ymm, X86Ymm, X86Ymm, Imm)             // AVX2</a>
+<a name="3072"><span class="lineNum">    3072 </span>            :   ASMJIT_INST_4i(vpblendd, Vpblendd, X86Ymm, X86Ymm, X86Mem, Imm)             // AVX2</a>
+<a name="3073"><span class="lineNum">    3073 </span>            :   ASMJIT_INST_4x(vpblendvb, Vpblendvb, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // AVX</a>
+<a name="3074"><span class="lineNum">    3074 </span>            :   ASMJIT_INST_4x(vpblendvb, Vpblendvb, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // AVX</a>
+<a name="3075"><span class="lineNum">    3075 </span>            :   ASMJIT_INST_4x(vpblendvb, Vpblendvb, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // AVX2</a>
+<a name="3076"><span class="lineNum">    3076 </span>            :   ASMJIT_INST_4x(vpblendvb, Vpblendvb, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // AVX2</a>
+<a name="3077"><span class="lineNum">    3077 </span>            :   ASMJIT_INST_4i(vpblendw, Vpblendw, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX</a>
+<a name="3078"><span class="lineNum">    3078 </span>            :   ASMJIT_INST_4i(vpblendw, Vpblendw, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX</a>
+<a name="3079"><span class="lineNum">    3079 </span>            :   ASMJIT_INST_4i(vpblendw, Vpblendw, X86Ymm, X86Ymm, X86Ymm, Imm)             // AVX2</a>
+<a name="3080"><span class="lineNum">    3080 </span>            :   ASMJIT_INST_4i(vpblendw, Vpblendw, X86Ymm, X86Ymm, X86Mem, Imm)             // AVX2</a>
+<a name="3081"><span class="lineNum">    3081 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Xmm, X86Xmm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3082"><span class="lineNum">    3082 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Xmm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3083"><span class="lineNum">    3083 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Ymm, X86Xmm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3084"><span class="lineNum">    3084 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3085"><span class="lineNum">    3085 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Xmm, X86Gp)                   //      AVX512_BW{kz}-VL</a>
+<a name="3086"><span class="lineNum">    3086 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Ymm, X86Gp)                   //      AVX512_BW{kz}-VL</a>
+<a name="3087"><span class="lineNum">    3087 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Zmm, X86Gp)                   //      AVX512_BW{kz}</a>
+<a name="3088"><span class="lineNum">    3088 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Zmm, X86Xmm)                  //      AVX512_BW{kz}</a>
+<a name="3089"><span class="lineNum">    3089 </span>            :   ASMJIT_INST_2x(vpbroadcastb, Vpbroadcastb, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3090"><span class="lineNum">    3090 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Xmm, X86Xmm)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3091"><span class="lineNum">    3091 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Xmm, X86Mem)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3092"><span class="lineNum">    3092 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Ymm, X86Xmm)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3093"><span class="lineNum">    3093 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Ymm, X86Mem)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3094"><span class="lineNum">    3094 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Xmm, X86Gp)                   //      AVX512_F{kz}-VL</a>
+<a name="3095"><span class="lineNum">    3095 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Ymm, X86Gp)                   //      AVX512_F{kz}-VL</a>
+<a name="3096"><span class="lineNum">    3096 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Zmm, X86Gp)                   //      AVX512_F{kz}</a>
+<a name="3097"><span class="lineNum">    3097 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Zmm, X86Xmm)                  //      AVX512_F{kz}</a>
+<a name="3098"><span class="lineNum">    3098 </span>            :   ASMJIT_INST_2x(vpbroadcastd, Vpbroadcastd, X86Zmm, X86Mem)                  //      AVX512_F{kz}</a>
+<a name="3099"><span class="lineNum">    3099 </span>            :   ASMJIT_INST_2x(vpbroadcastmb2d, Vpbroadcastmb2d, X86Xmm, X86KReg)           //      AVX512_CD-VL</a>
+<a name="3100"><span class="lineNum">    3100 </span>            :   ASMJIT_INST_2x(vpbroadcastmb2d, Vpbroadcastmb2d, X86Ymm, X86KReg)           //      AVX512_CD-VL</a>
+<a name="3101"><span class="lineNum">    3101 </span>            :   ASMJIT_INST_2x(vpbroadcastmb2d, Vpbroadcastmb2d, X86Zmm, X86KReg)           //      AVX512_CD</a>
+<a name="3102"><span class="lineNum">    3102 </span>            :   ASMJIT_INST_2x(vpbroadcastmb2q, Vpbroadcastmb2q, X86Xmm, X86KReg)           //      AVX512_CD-VL</a>
+<a name="3103"><span class="lineNum">    3103 </span>            :   ASMJIT_INST_2x(vpbroadcastmb2q, Vpbroadcastmb2q, X86Ymm, X86KReg)           //      AVX512_CD-VL</a>
+<a name="3104"><span class="lineNum">    3104 </span>            :   ASMJIT_INST_2x(vpbroadcastmb2q, Vpbroadcastmb2q, X86Zmm, X86KReg)           //      AVX512_CD</a>
+<a name="3105"><span class="lineNum">    3105 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Xmm, X86Xmm)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3106"><span class="lineNum">    3106 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Xmm, X86Mem)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3107"><span class="lineNum">    3107 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Ymm, X86Xmm)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3108"><span class="lineNum">    3108 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Ymm, X86Mem)                  // AVX2 AVX512_F{kz}-VL</a>
+<a name="3109"><span class="lineNum">    3109 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Xmm, X86Gp)                   //      AVX512_F{kz}-VL</a>
+<a name="3110"><span class="lineNum">    3110 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Ymm, X86Gp)                   //      AVX512_F{kz}-VL</a>
+<a name="3111"><span class="lineNum">    3111 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Zmm, X86Gp)                   //      AVX512_F{kz}</a>
+<a name="3112"><span class="lineNum">    3112 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Zmm, X86Xmm)                  //      AVX512_F{kz}</a>
+<a name="3113"><span class="lineNum">    3113 </span>            :   ASMJIT_INST_2x(vpbroadcastq, Vpbroadcastq, X86Zmm, X86Mem)                  //      AVX512_F{kz}</a>
+<a name="3114"><span class="lineNum">    3114 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Xmm, X86Xmm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3115"><span class="lineNum">    3115 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Xmm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3116"><span class="lineNum">    3116 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Ymm, X86Xmm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3117"><span class="lineNum">    3117 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3118"><span class="lineNum">    3118 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Xmm, X86Gp)                   //      AVX512_BW{kz}-VL</a>
+<a name="3119"><span class="lineNum">    3119 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Ymm, X86Gp)                   //      AVX512_BW{kz}-VL</a>
+<a name="3120"><span class="lineNum">    3120 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Zmm, X86Gp)                   //      AVX512_BW{kz}</a>
+<a name="3121"><span class="lineNum">    3121 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Zmm, X86Xmm)                  //      AVX512_BW{kz}</a>
+<a name="3122"><span class="lineNum">    3122 </span>            :   ASMJIT_INST_2x(vpbroadcastw, Vpbroadcastw, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3123"><span class="lineNum">    3123 </span>            :   ASMJIT_INST_4i(vpclmulqdq, Vpclmulqdq, X86Xmm, X86Xmm, X86Xmm, Imm)         // AVX</a>
+<a name="3124"><span class="lineNum">    3124 </span>            :   ASMJIT_INST_4i(vpclmulqdq, Vpclmulqdq, X86Xmm, X86Xmm, X86Mem, Imm)         // AVX</a>
+<a name="3125"><span class="lineNum">    3125 </span>            :   ASMJIT_INST_4i(vpcmpb, Vpcmpb, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_BW{k}-VL</a>
+<a name="3126"><span class="lineNum">    3126 </span>            :   ASMJIT_INST_4i(vpcmpb, Vpcmpb, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_BW{k}-VL</a>
+<a name="3127"><span class="lineNum">    3127 </span>            :   ASMJIT_INST_4i(vpcmpb, Vpcmpb, X86KReg, X86Ymm, X86Ymm, Imm)                //      AVX512_BW{k}-VL</a>
+<a name="3128"><span class="lineNum">    3128 </span>            :   ASMJIT_INST_4i(vpcmpb, Vpcmpb, X86KReg, X86Ymm, X86Mem, Imm)                //      AVX512_BW{k}-VL</a>
+<a name="3129"><span class="lineNum">    3129 </span>            :   ASMJIT_INST_4i(vpcmpb, Vpcmpb, X86KReg, X86Zmm, X86Zmm, Imm)                //      AVX512_BW{k}</a>
+<a name="3130"><span class="lineNum">    3130 </span>            :   ASMJIT_INST_4i(vpcmpb, Vpcmpb, X86KReg, X86Zmm, X86Mem, Imm)                //      AVX512_BW{k}</a>
+<a name="3131"><span class="lineNum">    3131 </span>            :   ASMJIT_INST_4i(vpcmpd, Vpcmpd, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_F{k|b32}-VL</a>
+<a name="3132"><span class="lineNum">    3132 </span>            :   ASMJIT_INST_4i(vpcmpd, Vpcmpd, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_F{k|b32}-VL</a>
+<a name="3133"><span class="lineNum">    3133 </span>            :   ASMJIT_INST_4i(vpcmpd, Vpcmpd, X86KReg, X86Ymm, X86Ymm, Imm)                //      AVX512_F{k|b32}-VL</a>
+<a name="3134"><span class="lineNum">    3134 </span>            :   ASMJIT_INST_4i(vpcmpd, Vpcmpd, X86KReg, X86Ymm, X86Mem, Imm)                //      AVX512_F{k|b32}-VL</a>
+<a name="3135"><span class="lineNum">    3135 </span>            :   ASMJIT_INST_4i(vpcmpd, Vpcmpd, X86KReg, X86Zmm, X86Zmm, Imm)                //      AVX512_F{k|b32}</a>
+<a name="3136"><span class="lineNum">    3136 </span>            :   ASMJIT_INST_4i(vpcmpd, Vpcmpd, X86KReg, X86Zmm, X86Mem, Imm)                //      AVX512_F{k|b32}</a>
+<a name="3137"><span class="lineNum">    3137 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3138"><span class="lineNum">    3138 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3139"><span class="lineNum">    3139 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3140"><span class="lineNum">    3140 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3141"><span class="lineNum">    3141 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_BW{k}-VL</a>
+<a name="3142"><span class="lineNum">    3142 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86KReg, X86Xmm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3143"><span class="lineNum">    3143 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_BW{k}-VL</a>
+<a name="3144"><span class="lineNum">    3144 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86KReg, X86Ymm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3145"><span class="lineNum">    3145 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_BW{k}</a>
+<a name="3146"><span class="lineNum">    3146 </span>            :   ASMJIT_INST_3x(vpcmpeqb, Vpcmpeqb, X86KReg, X86Zmm, X86Mem)                 //      AVX512_BW{k}</a>
+<a name="3147"><span class="lineNum">    3147 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3148"><span class="lineNum">    3148 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3149"><span class="lineNum">    3149 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3150"><span class="lineNum">    3150 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3151"><span class="lineNum">    3151 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3152"><span class="lineNum">    3152 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86KReg, X86Xmm, X86Mem)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3153"><span class="lineNum">    3153 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3154"><span class="lineNum">    3154 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86KReg, X86Ymm, X86Mem)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3155"><span class="lineNum">    3155 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_F{k|b32}</a>
+<a name="3156"><span class="lineNum">    3156 </span>            :   ASMJIT_INST_3x(vpcmpeqd, Vpcmpeqd, X86KReg, X86Zmm, X86Mem)                 //      AVX512_F{k|b32}</a>
+<a name="3157"><span class="lineNum">    3157 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3158"><span class="lineNum">    3158 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3159"><span class="lineNum">    3159 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3160"><span class="lineNum">    3160 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3161"><span class="lineNum">    3161 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3162"><span class="lineNum">    3162 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86KReg, X86Xmm, X86Mem)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3163"><span class="lineNum">    3163 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3164"><span class="lineNum">    3164 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86KReg, X86Ymm, X86Mem)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3165"><span class="lineNum">    3165 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_F{k|b64}</a>
+<a name="3166"><span class="lineNum">    3166 </span>            :   ASMJIT_INST_3x(vpcmpeqq, Vpcmpeqq, X86KReg, X86Zmm, X86Mem)                 //      AVX512_F{k|b64}</a>
+<a name="3167"><span class="lineNum">    3167 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3168"><span class="lineNum">    3168 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3169"><span class="lineNum">    3169 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3170"><span class="lineNum">    3170 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3171"><span class="lineNum">    3171 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_BW{k}-VL</a>
+<a name="3172"><span class="lineNum">    3172 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86KReg, X86Xmm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3173"><span class="lineNum">    3173 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_BW{k}-VL</a>
+<a name="3174"><span class="lineNum">    3174 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86KReg, X86Ymm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3175"><span class="lineNum">    3175 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_BW{k}</a>
+<a name="3176"><span class="lineNum">    3176 </span>            :   ASMJIT_INST_3x(vpcmpeqw, Vpcmpeqw, X86KReg, X86Zmm, X86Mem)                 //      AVX512_BW{k}</a>
+<a name="3177"><span class="lineNum">    3177 </span>            :   ASMJIT_INST_6x(vpcmpestri, Vpcmpestri, X86Xmm, X86Xmm, Imm, ECX, EAX, EDX)  // AVX  [EXPLICIT]</a>
+<a name="3178"><span class="lineNum">    3178 </span>            :   ASMJIT_INST_6x(vpcmpestri, Vpcmpestri, X86Xmm, X86Mem, Imm, ECX, EAX, EDX)  // AVX  [EXPLICIT]</a>
+<a name="3179"><span class="lineNum">    3179 </span>            :   ASMJIT_INST_6x(vpcmpestrm, Vpcmpestrm, X86Xmm, X86Xmm, Imm, XMM0, EAX, EDX) // AVX  [EXPLICIT]</a>
+<a name="3180"><span class="lineNum">    3180 </span>            :   ASMJIT_INST_6x(vpcmpestrm, Vpcmpestrm, X86Xmm, X86Mem, Imm, XMM0, EAX, EDX) // AVX  [EXPLICIT]</a>
+<a name="3181"><span class="lineNum">    3181 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3182"><span class="lineNum">    3182 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3183"><span class="lineNum">    3183 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3184"><span class="lineNum">    3184 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3185"><span class="lineNum">    3185 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_BW{k}-VL</a>
+<a name="3186"><span class="lineNum">    3186 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86KReg, X86Xmm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3187"><span class="lineNum">    3187 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_BW{k}-VL</a>
+<a name="3188"><span class="lineNum">    3188 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86KReg, X86Ymm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3189"><span class="lineNum">    3189 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_BW{k}</a>
+<a name="3190"><span class="lineNum">    3190 </span>            :   ASMJIT_INST_3x(vpcmpgtb, Vpcmpgtb, X86KReg, X86Zmm, X86Mem)                 //      AVX512_BW{k}</a>
+<a name="3191"><span class="lineNum">    3191 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3192"><span class="lineNum">    3192 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3193"><span class="lineNum">    3193 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3194"><span class="lineNum">    3194 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3195"><span class="lineNum">    3195 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3196"><span class="lineNum">    3196 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86KReg, X86Xmm, X86Mem)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3197"><span class="lineNum">    3197 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3198"><span class="lineNum">    3198 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86KReg, X86Ymm, X86Mem)                 //      AVX512_F{k|b32}-VL</a>
+<a name="3199"><span class="lineNum">    3199 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_F{k|b32}</a>
+<a name="3200"><span class="lineNum">    3200 </span>            :   ASMJIT_INST_3x(vpcmpgtd, Vpcmpgtd, X86KReg, X86Zmm, X86Mem)                 //      AVX512_F{k|b32}</a>
+<a name="3201"><span class="lineNum">    3201 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3202"><span class="lineNum">    3202 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3203"><span class="lineNum">    3203 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3204"><span class="lineNum">    3204 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3205"><span class="lineNum">    3205 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3206"><span class="lineNum">    3206 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86KReg, X86Xmm, X86Mem)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3207"><span class="lineNum">    3207 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3208"><span class="lineNum">    3208 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86KReg, X86Ymm, X86Mem)                 //      AVX512_F{k|b64}-VL</a>
+<a name="3209"><span class="lineNum">    3209 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_F{k|b64}</a>
+<a name="3210"><span class="lineNum">    3210 </span>            :   ASMJIT_INST_3x(vpcmpgtq, Vpcmpgtq, X86KReg, X86Zmm, X86Mem)                 //      AVX512_F{k|b64}</a>
+<a name="3211"><span class="lineNum">    3211 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3212"><span class="lineNum">    3212 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3213"><span class="lineNum">    3213 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3214"><span class="lineNum">    3214 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3215"><span class="lineNum">    3215 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_BW{k}-VL</a>
+<a name="3216"><span class="lineNum">    3216 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86KReg, X86Xmm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3217"><span class="lineNum">    3217 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_BW{k}-VL</a>
+<a name="3218"><span class="lineNum">    3218 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86KReg, X86Ymm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="3219"><span class="lineNum">    3219 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_BW{k}</a>
+<a name="3220"><span class="lineNum">    3220 </span>            :   ASMJIT_INST_3x(vpcmpgtw, Vpcmpgtw, X86KReg, X86Zmm, X86Mem)                 //      AVX512_BW{k}</a>
+<a name="3221"><span class="lineNum">    3221 </span>            :   ASMJIT_INST_4x(vpcmpistri, Vpcmpistri, X86Xmm, X86Xmm, Imm, ECX)            // AVX  [EXPLICIT]</a>
+<a name="3222"><span class="lineNum">    3222 </span>            :   ASMJIT_INST_4x(vpcmpistri, Vpcmpistri, X86Xmm, X86Mem, Imm, ECX)            // AVX  [EXPLICIT]</a>
+<a name="3223"><span class="lineNum">    3223 </span>            :   ASMJIT_INST_4x(vpcmpistrm, Vpcmpistrm, X86Xmm, X86Xmm, Imm, XMM0)           // AVX  [EXPLICIT]</a>
+<a name="3224"><span class="lineNum">    3224 </span>            :   ASMJIT_INST_4x(vpcmpistrm, Vpcmpistrm, X86Xmm, X86Mem, Imm, XMM0)           // AVX  [EXPLICIT]</a>
+<a name="3225"><span class="lineNum">    3225 </span>            :   ASMJIT_INST_4i(vpcmpq, Vpcmpq, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_F{k|b64}-VL</a>
+<a name="3226"><span class="lineNum">    3226 </span>            :   ASMJIT_INST_4i(vpcmpq, Vpcmpq, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_F{k|b64}-VL</a>
+<a name="3227"><span class="lineNum">    3227 </span>            :   ASMJIT_INST_4i(vpcmpq, Vpcmpq, X86KReg, X86Ymm, X86Ymm, Imm)                //      AVX512_F{k|b64}-VL</a>
+<a name="3228"><span class="lineNum">    3228 </span>            :   ASMJIT_INST_4i(vpcmpq, Vpcmpq, X86KReg, X86Ymm, X86Mem, Imm)                //      AVX512_F{k|b64}-VL</a>
+<a name="3229"><span class="lineNum">    3229 </span>            :   ASMJIT_INST_4i(vpcmpq, Vpcmpq, X86KReg, X86Zmm, X86Zmm, Imm)                //      AVX512_F{k|b64}</a>
+<a name="3230"><span class="lineNum">    3230 </span>            :   ASMJIT_INST_4i(vpcmpq, Vpcmpq, X86KReg, X86Zmm, X86Mem, Imm)                //      AVX512_F{k|b64}</a>
+<a name="3231"><span class="lineNum">    3231 </span>            :   ASMJIT_INST_4i(vpcmpub, Vpcmpub, X86KReg, X86Xmm, X86Xmm, Imm)              //      AVX512_BW{k}-VL</a>
+<a name="3232"><span class="lineNum">    3232 </span>            :   ASMJIT_INST_4i(vpcmpub, Vpcmpub, X86KReg, X86Xmm, X86Mem, Imm)              //      AVX512_BW{k}-VL</a>
+<a name="3233"><span class="lineNum">    3233 </span>            :   ASMJIT_INST_4i(vpcmpub, Vpcmpub, X86KReg, X86Ymm, X86Ymm, Imm)              //      AVX512_BW{k}-VL</a>
+<a name="3234"><span class="lineNum">    3234 </span>            :   ASMJIT_INST_4i(vpcmpub, Vpcmpub, X86KReg, X86Ymm, X86Mem, Imm)              //      AVX512_BW{k}-VL</a>
+<a name="3235"><span class="lineNum">    3235 </span>            :   ASMJIT_INST_4i(vpcmpub, Vpcmpub, X86KReg, X86Zmm, X86Zmm, Imm)              //      AVX512_BW{k}</a>
+<a name="3236"><span class="lineNum">    3236 </span>            :   ASMJIT_INST_4i(vpcmpub, Vpcmpub, X86KReg, X86Zmm, X86Mem, Imm)              //      AVX512_BW{k}</a>
+<a name="3237"><span class="lineNum">    3237 </span>            :   ASMJIT_INST_4i(vpcmpud, Vpcmpud, X86KReg, X86Xmm, X86Xmm, Imm)              //      AVX512_F{k|b32}-VL</a>
+<a name="3238"><span class="lineNum">    3238 </span>            :   ASMJIT_INST_4i(vpcmpud, Vpcmpud, X86KReg, X86Xmm, X86Mem, Imm)              //      AVX512_F{k|b32}-VL</a>
+<a name="3239"><span class="lineNum">    3239 </span>            :   ASMJIT_INST_4i(vpcmpud, Vpcmpud, X86KReg, X86Ymm, X86Ymm, Imm)              //      AVX512_F{k|b32}-VL</a>
+<a name="3240"><span class="lineNum">    3240 </span>            :   ASMJIT_INST_4i(vpcmpud, Vpcmpud, X86KReg, X86Ymm, X86Mem, Imm)              //      AVX512_F{k|b32}-VL</a>
+<a name="3241"><span class="lineNum">    3241 </span>            :   ASMJIT_INST_4i(vpcmpud, Vpcmpud, X86KReg, X86Zmm, X86Zmm, Imm)              //      AVX512_F{k|b32}</a>
+<a name="3242"><span class="lineNum">    3242 </span>            :   ASMJIT_INST_4i(vpcmpud, Vpcmpud, X86KReg, X86Zmm, X86Mem, Imm)              //      AVX512_F{k|b32}</a>
+<a name="3243"><span class="lineNum">    3243 </span>            :   ASMJIT_INST_4i(vpcmpuq, Vpcmpuq, X86KReg, X86Xmm, X86Xmm, Imm)              //      AVX512_F{k|b64}-VL</a>
+<a name="3244"><span class="lineNum">    3244 </span>            :   ASMJIT_INST_4i(vpcmpuq, Vpcmpuq, X86KReg, X86Xmm, X86Mem, Imm)              //      AVX512_F{k|b64}-VL</a>
+<a name="3245"><span class="lineNum">    3245 </span>            :   ASMJIT_INST_4i(vpcmpuq, Vpcmpuq, X86KReg, X86Ymm, X86Ymm, Imm)              //      AVX512_F{k|b64}-VL</a>
+<a name="3246"><span class="lineNum">    3246 </span>            :   ASMJIT_INST_4i(vpcmpuq, Vpcmpuq, X86KReg, X86Ymm, X86Mem, Imm)              //      AVX512_F{k|b64}-VL</a>
+<a name="3247"><span class="lineNum">    3247 </span>            :   ASMJIT_INST_4i(vpcmpuq, Vpcmpuq, X86KReg, X86Zmm, X86Zmm, Imm)              //      AVX512_F{k|b64}</a>
+<a name="3248"><span class="lineNum">    3248 </span>            :   ASMJIT_INST_4i(vpcmpuq, Vpcmpuq, X86KReg, X86Zmm, X86Mem, Imm)              //      AVX512_F{k|b64}</a>
+<a name="3249"><span class="lineNum">    3249 </span>            :   ASMJIT_INST_4i(vpcmpuw, Vpcmpuw, X86KReg, X86Xmm, X86Xmm, Imm)              //      AVX512_BW{k|b64}-VL</a>
+<a name="3250"><span class="lineNum">    3250 </span>            :   ASMJIT_INST_4i(vpcmpuw, Vpcmpuw, X86KReg, X86Xmm, X86Mem, Imm)              //      AVX512_BW{k|b64}-VL</a>
+<a name="3251"><span class="lineNum">    3251 </span>            :   ASMJIT_INST_4i(vpcmpuw, Vpcmpuw, X86KReg, X86Ymm, X86Ymm, Imm)              //      AVX512_BW{k|b64}-VL</a>
+<a name="3252"><span class="lineNum">    3252 </span>            :   ASMJIT_INST_4i(vpcmpuw, Vpcmpuw, X86KReg, X86Ymm, X86Mem, Imm)              //      AVX512_BW{k|b64}-VL</a>
+<a name="3253"><span class="lineNum">    3253 </span>            :   ASMJIT_INST_4i(vpcmpuw, Vpcmpuw, X86KReg, X86Zmm, X86Zmm, Imm)              //      AVX512_BW{k|b64}</a>
+<a name="3254"><span class="lineNum">    3254 </span>            :   ASMJIT_INST_4i(vpcmpuw, Vpcmpuw, X86KReg, X86Zmm, X86Mem, Imm)              //      AVX512_BW{k|b64}</a>
+<a name="3255"><span class="lineNum">    3255 </span>            :   ASMJIT_INST_4i(vpcmpw, Vpcmpw, X86KReg, X86Xmm, X86Xmm, Imm)                //      AVX512_BW{k|b64}-VL</a>
+<a name="3256"><span class="lineNum">    3256 </span>            :   ASMJIT_INST_4i(vpcmpw, Vpcmpw, X86KReg, X86Xmm, X86Mem, Imm)                //      AVX512_BW{k|b64}-VL</a>
+<a name="3257"><span class="lineNum">    3257 </span>            :   ASMJIT_INST_4i(vpcmpw, Vpcmpw, X86KReg, X86Ymm, X86Ymm, Imm)                //      AVX512_BW{k|b64}-VL</a>
+<a name="3258"><span class="lineNum">    3258 </span>            :   ASMJIT_INST_4i(vpcmpw, Vpcmpw, X86KReg, X86Ymm, X86Mem, Imm)                //      AVX512_BW{k|b64}-VL</a>
+<a name="3259"><span class="lineNum">    3259 </span>            :   ASMJIT_INST_4i(vpcmpw, Vpcmpw, X86KReg, X86Zmm, X86Zmm, Imm)                //      AVX512_BW{k|b64}</a>
+<a name="3260"><span class="lineNum">    3260 </span>            :   ASMJIT_INST_4i(vpcmpw, Vpcmpw, X86KReg, X86Zmm, X86Mem, Imm)                //      AVX512_BW{k|b64}</a>
+<a name="3261"><span class="lineNum">    3261 </span>            :   ASMJIT_INST_2x(vpcompressd, Vpcompressd, X86Xmm, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="3262"><span class="lineNum">    3262 </span>            :   ASMJIT_INST_2x(vpcompressd, Vpcompressd, X86Mem, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="3263"><span class="lineNum">    3263 </span>            :   ASMJIT_INST_2x(vpcompressd, Vpcompressd, X86Ymm, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="3264"><span class="lineNum">    3264 </span>            :   ASMJIT_INST_2x(vpcompressd, Vpcompressd, X86Mem, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="3265"><span class="lineNum">    3265 </span>            :   ASMJIT_INST_2x(vpcompressd, Vpcompressd, X86Zmm, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="3266"><span class="lineNum">    3266 </span>            :   ASMJIT_INST_2x(vpcompressd, Vpcompressd, X86Mem, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="3267"><span class="lineNum">    3267 </span>            :   ASMJIT_INST_2x(vpcompressq, Vpcompressq, X86Xmm, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="3268"><span class="lineNum">    3268 </span>            :   ASMJIT_INST_2x(vpcompressq, Vpcompressq, X86Mem, X86Xmm)                    //      AVX512_F{kz}-VL</a>
+<a name="3269"><span class="lineNum">    3269 </span>            :   ASMJIT_INST_2x(vpcompressq, Vpcompressq, X86Ymm, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="3270"><span class="lineNum">    3270 </span>            :   ASMJIT_INST_2x(vpcompressq, Vpcompressq, X86Mem, X86Ymm)                    //      AVX512_F{kz}-VL</a>
+<a name="3271"><span class="lineNum">    3271 </span>            :   ASMJIT_INST_2x(vpcompressq, Vpcompressq, X86Zmm, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="3272"><span class="lineNum">    3272 </span>            :   ASMJIT_INST_2x(vpcompressq, Vpcompressq, X86Mem, X86Zmm)                    //      AVX512_F{kz}</a>
+<a name="3273"><span class="lineNum">    3273 </span>            :   ASMJIT_INST_2x(vpconflictd, Vpconflictd, X86Xmm, X86Xmm)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3274"><span class="lineNum">    3274 </span>            :   ASMJIT_INST_2x(vpconflictd, Vpconflictd, X86Xmm, X86Mem)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3275"><span class="lineNum">    3275 </span>            :   ASMJIT_INST_2x(vpconflictd, Vpconflictd, X86Ymm, X86Ymm)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3276"><span class="lineNum">    3276 </span>            :   ASMJIT_INST_2x(vpconflictd, Vpconflictd, X86Ymm, X86Mem)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3277"><span class="lineNum">    3277 </span>            :   ASMJIT_INST_2x(vpconflictd, Vpconflictd, X86Zmm, X86Zmm)                    //      AVX512_CD{kz|b32}</a>
+<a name="3278"><span class="lineNum">    3278 </span>            :   ASMJIT_INST_2x(vpconflictd, Vpconflictd, X86Zmm, X86Mem)                    //      AVX512_CD{kz|b32}</a>
+<a name="3279"><span class="lineNum">    3279 </span>            :   ASMJIT_INST_2x(vpconflictq, Vpconflictq, X86Xmm, X86Xmm)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3280"><span class="lineNum">    3280 </span>            :   ASMJIT_INST_2x(vpconflictq, Vpconflictq, X86Xmm, X86Mem)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3281"><span class="lineNum">    3281 </span>            :   ASMJIT_INST_2x(vpconflictq, Vpconflictq, X86Ymm, X86Ymm)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3282"><span class="lineNum">    3282 </span>            :   ASMJIT_INST_2x(vpconflictq, Vpconflictq, X86Ymm, X86Mem)                    //      AVX512_CD{kz|b32}-VL</a>
+<a name="3283"><span class="lineNum">    3283 </span>            :   ASMJIT_INST_2x(vpconflictq, Vpconflictq, X86Zmm, X86Zmm)                    //      AVX512_CD{kz|b32}</a>
+<a name="3284"><span class="lineNum">    3284 </span>            :   ASMJIT_INST_2x(vpconflictq, Vpconflictq, X86Zmm, X86Mem)                    //      AVX512_CD{kz|b32}</a>
+<a name="3285"><span class="lineNum">    3285 </span>            :   ASMJIT_INST_4i(vperm2f128, Vperm2f128, X86Ymm, X86Ymm, X86Ymm, Imm)         // AVX</a>
+<a name="3286"><span class="lineNum">    3286 </span>            :   ASMJIT_INST_4i(vperm2f128, Vperm2f128, X86Ymm, X86Ymm, X86Mem, Imm)         // AVX</a>
+<a name="3287"><span class="lineNum">    3287 </span>            :   ASMJIT_INST_4i(vperm2i128, Vperm2i128, X86Ymm, X86Ymm, X86Ymm, Imm)         // AVX2</a>
+<a name="3288"><span class="lineNum">    3288 </span>            :   ASMJIT_INST_4i(vperm2i128, Vperm2i128, X86Ymm, X86Ymm, X86Mem, Imm)         // AVX2</a>
+<a name="3289"><span class="lineNum">    3289 </span>            :   ASMJIT_INST_3x(vpermb, Vpermb, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_VBMI{kz}-VL</a>
+<a name="3290"><span class="lineNum">    3290 </span>            :   ASMJIT_INST_3x(vpermb, Vpermb, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_VBMI{kz}-VL</a>
+<a name="3291"><span class="lineNum">    3291 </span>            :   ASMJIT_INST_3x(vpermb, Vpermb, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_VBMI{kz}-VL</a>
+<a name="3292"><span class="lineNum">    3292 </span>            :   ASMJIT_INST_3x(vpermb, Vpermb, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_VBMI{kz}-VL</a>
+<a name="3293"><span class="lineNum">    3293 </span>            :   ASMJIT_INST_3x(vpermb, Vpermb, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_VBMI{kz}</a>
+<a name="3294"><span class="lineNum">    3294 </span>            :   ASMJIT_INST_3x(vpermb, Vpermb, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_VBMI{kz}</a>
+<a name="3295"><span class="lineNum">    3295 </span>            :   ASMJIT_INST_3x(vpermd, Vpermd, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3296"><span class="lineNum">    3296 </span>            :   ASMJIT_INST_3x(vpermd, Vpermd, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3297"><span class="lineNum">    3297 </span>            :   ASMJIT_INST_3x(vpermd, Vpermd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="3298"><span class="lineNum">    3298 </span>            :   ASMJIT_INST_3x(vpermd, Vpermd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="3299"><span class="lineNum">    3299 </span>            :   ASMJIT_INST_3x(vpermi2b, Vpermi2b, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3300"><span class="lineNum">    3300 </span>            :   ASMJIT_INST_3x(vpermi2b, Vpermi2b, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3301"><span class="lineNum">    3301 </span>            :   ASMJIT_INST_3x(vpermi2b, Vpermi2b, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3302"><span class="lineNum">    3302 </span>            :   ASMJIT_INST_3x(vpermi2b, Vpermi2b, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3303"><span class="lineNum">    3303 </span>            :   ASMJIT_INST_3x(vpermi2b, Vpermi2b, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_VBMI{kz}</a>
+<a name="3304"><span class="lineNum">    3304 </span>            :   ASMJIT_INST_3x(vpermi2b, Vpermi2b, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_VBMI{kz}</a>
+<a name="3305"><span class="lineNum">    3305 </span>            :   ASMJIT_INST_3x(vpermi2d, Vpermi2d, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3306"><span class="lineNum">    3306 </span>            :   ASMJIT_INST_3x(vpermi2d, Vpermi2d, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3307"><span class="lineNum">    3307 </span>            :   ASMJIT_INST_3x(vpermi2d, Vpermi2d, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3308"><span class="lineNum">    3308 </span>            :   ASMJIT_INST_3x(vpermi2d, Vpermi2d, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3309"><span class="lineNum">    3309 </span>            :   ASMJIT_INST_3x(vpermi2d, Vpermi2d, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b32}</a>
+<a name="3310"><span class="lineNum">    3310 </span>            :   ASMJIT_INST_3x(vpermi2d, Vpermi2d, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b32}</a>
+<a name="3311"><span class="lineNum">    3311 </span>            :   ASMJIT_INST_3x(vpermi2pd, Vpermi2pd, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3312"><span class="lineNum">    3312 </span>            :   ASMJIT_INST_3x(vpermi2pd, Vpermi2pd, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3313"><span class="lineNum">    3313 </span>            :   ASMJIT_INST_3x(vpermi2pd, Vpermi2pd, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3314"><span class="lineNum">    3314 </span>            :   ASMJIT_INST_3x(vpermi2pd, Vpermi2pd, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3315"><span class="lineNum">    3315 </span>            :   ASMJIT_INST_3x(vpermi2pd, Vpermi2pd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="3316"><span class="lineNum">    3316 </span>            :   ASMJIT_INST_3x(vpermi2pd, Vpermi2pd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="3317"><span class="lineNum">    3317 </span>            :   ASMJIT_INST_3x(vpermi2ps, Vpermi2ps, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3318"><span class="lineNum">    3318 </span>            :   ASMJIT_INST_3x(vpermi2ps, Vpermi2ps, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3319"><span class="lineNum">    3319 </span>            :   ASMJIT_INST_3x(vpermi2ps, Vpermi2ps, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3320"><span class="lineNum">    3320 </span>            :   ASMJIT_INST_3x(vpermi2ps, Vpermi2ps, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3321"><span class="lineNum">    3321 </span>            :   ASMJIT_INST_3x(vpermi2ps, Vpermi2ps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b32}</a>
+<a name="3322"><span class="lineNum">    3322 </span>            :   ASMJIT_INST_3x(vpermi2ps, Vpermi2ps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b32}</a>
+<a name="3323"><span class="lineNum">    3323 </span>            :   ASMJIT_INST_3x(vpermi2q, Vpermi2q, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3324"><span class="lineNum">    3324 </span>            :   ASMJIT_INST_3x(vpermi2q, Vpermi2q, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3325"><span class="lineNum">    3325 </span>            :   ASMJIT_INST_3x(vpermi2q, Vpermi2q, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3326"><span class="lineNum">    3326 </span>            :   ASMJIT_INST_3x(vpermi2q, Vpermi2q, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3327"><span class="lineNum">    3327 </span>            :   ASMJIT_INST_3x(vpermi2q, Vpermi2q, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b64}</a>
+<a name="3328"><span class="lineNum">    3328 </span>            :   ASMJIT_INST_3x(vpermi2q, Vpermi2q, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b64}</a>
+<a name="3329"><span class="lineNum">    3329 </span>            :   ASMJIT_INST_3x(vpermi2w, Vpermi2w, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_BW{kz}-VL</a>
+<a name="3330"><span class="lineNum">    3330 </span>            :   ASMJIT_INST_3x(vpermi2w, Vpermi2w, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="3331"><span class="lineNum">    3331 </span>            :   ASMJIT_INST_3x(vpermi2w, Vpermi2w, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_BW{kz}-VL</a>
+<a name="3332"><span class="lineNum">    3332 </span>            :   ASMJIT_INST_3x(vpermi2w, Vpermi2w, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="3333"><span class="lineNum">    3333 </span>            :   ASMJIT_INST_3x(vpermi2w, Vpermi2w, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="3334"><span class="lineNum">    3334 </span>            :   ASMJIT_INST_3x(vpermi2w, Vpermi2w, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3335"><span class="lineNum">    3335 </span>            :   ASMJIT_INST_3x(vpermilpd, Vpermilpd, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3336"><span class="lineNum">    3336 </span>            :   ASMJIT_INST_3x(vpermilpd, Vpermilpd, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3337"><span class="lineNum">    3337 </span>            :   ASMJIT_INST_3i(vpermilpd, Vpermilpd, X86Xmm, X86Xmm, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3338"><span class="lineNum">    3338 </span>            :   ASMJIT_INST_3i(vpermilpd, Vpermilpd, X86Xmm, X86Mem, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3339"><span class="lineNum">    3339 </span>            :   ASMJIT_INST_3x(vpermilpd, Vpermilpd, X86Ymm, X86Ymm, X86Ymm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3340"><span class="lineNum">    3340 </span>            :   ASMJIT_INST_3x(vpermilpd, Vpermilpd, X86Ymm, X86Ymm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3341"><span class="lineNum">    3341 </span>            :   ASMJIT_INST_3i(vpermilpd, Vpermilpd, X86Ymm, X86Ymm, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3342"><span class="lineNum">    3342 </span>            :   ASMJIT_INST_3i(vpermilpd, Vpermilpd, X86Ymm, X86Mem, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3343"><span class="lineNum">    3343 </span>            :   ASMJIT_INST_3x(vpermilpd, Vpermilpd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="3344"><span class="lineNum">    3344 </span>            :   ASMJIT_INST_3x(vpermilpd, Vpermilpd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="3345"><span class="lineNum">    3345 </span>            :   ASMJIT_INST_3i(vpermilpd, Vpermilpd, X86Zmm, X86Zmm, Imm)                   //      AVX512_F{kz|b64}</a>
+<a name="3346"><span class="lineNum">    3346 </span>            :   ASMJIT_INST_3i(vpermilpd, Vpermilpd, X86Zmm, X86Mem, Imm)                   //      AVX512_F{kz|b64}</a>
+<a name="3347"><span class="lineNum">    3347 </span>            :   ASMJIT_INST_3x(vpermilps, Vpermilps, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3348"><span class="lineNum">    3348 </span>            :   ASMJIT_INST_3x(vpermilps, Vpermilps, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3349"><span class="lineNum">    3349 </span>            :   ASMJIT_INST_3i(vpermilps, Vpermilps, X86Xmm, X86Xmm, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3350"><span class="lineNum">    3350 </span>            :   ASMJIT_INST_3i(vpermilps, Vpermilps, X86Xmm, X86Mem, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3351"><span class="lineNum">    3351 </span>            :   ASMJIT_INST_3x(vpermilps, Vpermilps, X86Ymm, X86Ymm, X86Ymm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3352"><span class="lineNum">    3352 </span>            :   ASMJIT_INST_3x(vpermilps, Vpermilps, X86Ymm, X86Ymm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3353"><span class="lineNum">    3353 </span>            :   ASMJIT_INST_3i(vpermilps, Vpermilps, X86Ymm, X86Ymm, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3354"><span class="lineNum">    3354 </span>            :   ASMJIT_INST_3i(vpermilps, Vpermilps, X86Ymm, X86Mem, Imm)                   // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3355"><span class="lineNum">    3355 </span>            :   ASMJIT_INST_3x(vpermilps, Vpermilps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="3356"><span class="lineNum">    3356 </span>            :   ASMJIT_INST_3x(vpermilps, Vpermilps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="3357"><span class="lineNum">    3357 </span>            :   ASMJIT_INST_3i(vpermilps, Vpermilps, X86Zmm, X86Zmm, Imm)                   //      AVX512_F{kz|b64}</a>
+<a name="3358"><span class="lineNum">    3358 </span>            :   ASMJIT_INST_3i(vpermilps, Vpermilps, X86Zmm, X86Mem, Imm)                   //      AVX512_F{kz|b64}</a>
+<a name="3359"><span class="lineNum">    3359 </span>            :   ASMJIT_INST_3i(vpermpd, Vpermpd, X86Ymm, X86Ymm, Imm)                       // AVX2</a>
+<a name="3360"><span class="lineNum">    3360 </span>            :   ASMJIT_INST_3i(vpermpd, Vpermpd, X86Ymm, X86Mem, Imm)                       // AVX2</a>
+<a name="3361"><span class="lineNum">    3361 </span>            :   ASMJIT_INST_3x(vpermps, Vpermps, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="3362"><span class="lineNum">    3362 </span>            :   ASMJIT_INST_3x(vpermps, Vpermps, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="3363"><span class="lineNum">    3363 </span>            :   ASMJIT_INST_3i(vpermq, Vpermq, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="3364"><span class="lineNum">    3364 </span>            :   ASMJIT_INST_3i(vpermq, Vpermq, X86Ymm, X86Mem, Imm)                         // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="3365"><span class="lineNum">    3365 </span>            :   ASMJIT_INST_3x(vpermq, Vpermq, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3366"><span class="lineNum">    3366 </span>            :   ASMJIT_INST_3x(vpermq, Vpermq, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3367"><span class="lineNum">    3367 </span>            :   ASMJIT_INST_3x(vpermq, Vpermq, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3368"><span class="lineNum">    3368 </span>            :   ASMJIT_INST_3x(vpermq, Vpermq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="3369"><span class="lineNum">    3369 </span>            :   ASMJIT_INST_3i(vpermq, Vpermq, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3370"><span class="lineNum">    3370 </span>            :   ASMJIT_INST_3i(vpermq, Vpermq, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3371"><span class="lineNum">    3371 </span>            :   ASMJIT_INST_3x(vpermt2b, Vpermt2b, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3372"><span class="lineNum">    3372 </span>            :   ASMJIT_INST_3x(vpermt2b, Vpermt2b, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3373"><span class="lineNum">    3373 </span>            :   ASMJIT_INST_3x(vpermt2b, Vpermt2b, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3374"><span class="lineNum">    3374 </span>            :   ASMJIT_INST_3x(vpermt2b, Vpermt2b, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_VBMI{kz}-VL</a>
+<a name="3375"><span class="lineNum">    3375 </span>            :   ASMJIT_INST_3x(vpermt2b, Vpermt2b, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_VBMI{kz}</a>
+<a name="3376"><span class="lineNum">    3376 </span>            :   ASMJIT_INST_3x(vpermt2b, Vpermt2b, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_VBMI{kz}</a>
+<a name="3377"><span class="lineNum">    3377 </span>            :   ASMJIT_INST_3x(vpermt2d, Vpermt2d, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3378"><span class="lineNum">    3378 </span>            :   ASMJIT_INST_3x(vpermt2d, Vpermt2d, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3379"><span class="lineNum">    3379 </span>            :   ASMJIT_INST_3x(vpermt2d, Vpermt2d, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3380"><span class="lineNum">    3380 </span>            :   ASMJIT_INST_3x(vpermt2d, Vpermt2d, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_F{kz|b32}-VL</a>
+<a name="3381"><span class="lineNum">    3381 </span>            :   ASMJIT_INST_3x(vpermt2d, Vpermt2d, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b32}</a>
+<a name="3382"><span class="lineNum">    3382 </span>            :   ASMJIT_INST_3x(vpermt2d, Vpermt2d, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b32}</a>
+<a name="3383"><span class="lineNum">    3383 </span>            :   ASMJIT_INST_3x(vpermt2pd, Vpermt2pd, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3384"><span class="lineNum">    3384 </span>            :   ASMJIT_INST_3x(vpermt2pd, Vpermt2pd, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3385"><span class="lineNum">    3385 </span>            :   ASMJIT_INST_3x(vpermt2pd, Vpermt2pd, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3386"><span class="lineNum">    3386 </span>            :   ASMJIT_INST_3x(vpermt2pd, Vpermt2pd, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="3387"><span class="lineNum">    3387 </span>            :   ASMJIT_INST_3x(vpermt2pd, Vpermt2pd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="3388"><span class="lineNum">    3388 </span>            :   ASMJIT_INST_3x(vpermt2pd, Vpermt2pd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="3389"><span class="lineNum">    3389 </span>            :   ASMJIT_INST_3x(vpermt2ps, Vpermt2ps, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3390"><span class="lineNum">    3390 </span>            :   ASMJIT_INST_3x(vpermt2ps, Vpermt2ps, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3391"><span class="lineNum">    3391 </span>            :   ASMJIT_INST_3x(vpermt2ps, Vpermt2ps, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3392"><span class="lineNum">    3392 </span>            :   ASMJIT_INST_3x(vpermt2ps, Vpermt2ps, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="3393"><span class="lineNum">    3393 </span>            :   ASMJIT_INST_3x(vpermt2ps, Vpermt2ps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b32}</a>
+<a name="3394"><span class="lineNum">    3394 </span>            :   ASMJIT_INST_3x(vpermt2ps, Vpermt2ps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b32}</a>
+<a name="3395"><span class="lineNum">    3395 </span>            :   ASMJIT_INST_3x(vpermt2q, Vpermt2q, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3396"><span class="lineNum">    3396 </span>            :   ASMJIT_INST_3x(vpermt2q, Vpermt2q, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3397"><span class="lineNum">    3397 </span>            :   ASMJIT_INST_3x(vpermt2q, Vpermt2q, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3398"><span class="lineNum">    3398 </span>            :   ASMJIT_INST_3x(vpermt2q, Vpermt2q, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_F{kz|b64}-VL</a>
+<a name="3399"><span class="lineNum">    3399 </span>            :   ASMJIT_INST_3x(vpermt2q, Vpermt2q, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b64}</a>
+<a name="3400"><span class="lineNum">    3400 </span>            :   ASMJIT_INST_3x(vpermt2q, Vpermt2q, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b64}</a>
+<a name="3401"><span class="lineNum">    3401 </span>            :   ASMJIT_INST_3x(vpermt2w, Vpermt2w, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_BW{kz}-VL</a>
+<a name="3402"><span class="lineNum">    3402 </span>            :   ASMJIT_INST_3x(vpermt2w, Vpermt2w, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="3403"><span class="lineNum">    3403 </span>            :   ASMJIT_INST_3x(vpermt2w, Vpermt2w, X86Ymm, X86Ymm, X86Ymm)                  //      AVX512_BW{kz}-VL</a>
+<a name="3404"><span class="lineNum">    3404 </span>            :   ASMJIT_INST_3x(vpermt2w, Vpermt2w, X86Ymm, X86Ymm, X86Mem)                  //      AVX512_BW{kz}-VL</a>
+<a name="3405"><span class="lineNum">    3405 </span>            :   ASMJIT_INST_3x(vpermt2w, Vpermt2w, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="3406"><span class="lineNum">    3406 </span>            :   ASMJIT_INST_3x(vpermt2w, Vpermt2w, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3407"><span class="lineNum">    3407 </span>            :   ASMJIT_INST_3x(vpermw, Vpermw, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_BW{kz}-VL</a>
+<a name="3408"><span class="lineNum">    3408 </span>            :   ASMJIT_INST_3x(vpermw, Vpermw, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_BW{kz}-VL</a>
+<a name="3409"><span class="lineNum">    3409 </span>            :   ASMJIT_INST_3x(vpermw, Vpermw, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_BW{kz}-VL</a>
+<a name="3410"><span class="lineNum">    3410 </span>            :   ASMJIT_INST_3x(vpermw, Vpermw, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_BW{kz}-VL</a>
+<a name="3411"><span class="lineNum">    3411 </span>            :   ASMJIT_INST_3x(vpermw, Vpermw, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="3412"><span class="lineNum">    3412 </span>            :   ASMJIT_INST_3x(vpermw, Vpermw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="3413"><span class="lineNum">    3413 </span>            :   ASMJIT_INST_2x(vpexpandd, Vpexpandd, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3414"><span class="lineNum">    3414 </span>            :   ASMJIT_INST_2x(vpexpandd, Vpexpandd, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="3415"><span class="lineNum">    3415 </span>            :   ASMJIT_INST_2x(vpexpandd, Vpexpandd, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3416"><span class="lineNum">    3416 </span>            :   ASMJIT_INST_2x(vpexpandd, Vpexpandd, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="3417"><span class="lineNum">    3417 </span>            :   ASMJIT_INST_2x(vpexpandd, Vpexpandd, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3418"><span class="lineNum">    3418 </span>            :   ASMJIT_INST_2x(vpexpandd, Vpexpandd, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3419"><span class="lineNum">    3419 </span>            :   ASMJIT_INST_2x(vpexpandq, Vpexpandq, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3420"><span class="lineNum">    3420 </span>            :   ASMJIT_INST_2x(vpexpandq, Vpexpandq, X86Xmm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="3421"><span class="lineNum">    3421 </span>            :   ASMJIT_INST_2x(vpexpandq, Vpexpandq, X86Ymm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3422"><span class="lineNum">    3422 </span>            :   ASMJIT_INST_2x(vpexpandq, Vpexpandq, X86Ymm, X86Mem)                        //      AVX512_F{kz}-VL</a>
+<a name="3423"><span class="lineNum">    3423 </span>            :   ASMJIT_INST_2x(vpexpandq, Vpexpandq, X86Zmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3424"><span class="lineNum">    3424 </span>            :   ASMJIT_INST_2x(vpexpandq, Vpexpandq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3425"><span class="lineNum">    3425 </span>            :   ASMJIT_INST_3i(vpextrb, Vpextrb, X86Gp, X86Xmm, Imm)                        // AVX  AVX512_BW</a>
+<a name="3426"><span class="lineNum">    3426 </span>            :   ASMJIT_INST_3i(vpextrb, Vpextrb, X86Mem, X86Xmm, Imm)                       // AVX  AVX512_BW</a>
+<a name="3427"><span class="lineNum">    3427 </span>            :   ASMJIT_INST_3i(vpextrd, Vpextrd, X86Gp, X86Xmm, Imm)                        // AVX  AVX512_DQ</a>
+<a name="3428"><span class="lineNum">    3428 </span>            :   ASMJIT_INST_3i(vpextrd, Vpextrd, X86Mem, X86Xmm, Imm)                       // AVX  AVX512_DQ</a>
+<a name="3429"><span class="lineNum">    3429 </span>            :   ASMJIT_INST_3i(vpextrq, Vpextrq, X86Gp, X86Xmm, Imm)                        // AVX  AVX512_DQ</a>
+<a name="3430"><span class="lineNum">    3430 </span>            :   ASMJIT_INST_3i(vpextrq, Vpextrq, X86Mem, X86Xmm, Imm)                       // AVX  AVX512_DQ</a>
+<a name="3431"><span class="lineNum">    3431 </span>            :   ASMJIT_INST_3i(vpextrw, Vpextrw, X86Gp, X86Xmm, Imm)                        // AVX  AVX512_BW</a>
+<a name="3432"><span class="lineNum">    3432 </span>            :   ASMJIT_INST_3i(vpextrw, Vpextrw, X86Mem, X86Xmm, Imm)                       // AVX  AVX512_BW</a>
+<a name="3433"><span class="lineNum">    3433 </span>            :   ASMJIT_INST_3x(vpgatherdd, Vpgatherdd, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="3434"><span class="lineNum">    3434 </span>            :   ASMJIT_INST_3x(vpgatherdd, Vpgatherdd, X86Ymm, X86Mem, X86Ymm)              // AVX2</a>
+<a name="3435"><span class="lineNum">    3435 </span>            :   ASMJIT_INST_2x(vpgatherdd, Vpgatherdd, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3436"><span class="lineNum">    3436 </span>            :   ASMJIT_INST_2x(vpgatherdd, Vpgatherdd, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3437"><span class="lineNum">    3437 </span>            :   ASMJIT_INST_2x(vpgatherdd, Vpgatherdd, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="3438"><span class="lineNum">    3438 </span>            :   ASMJIT_INST_3x(vpgatherdq, Vpgatherdq, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="3439"><span class="lineNum">    3439 </span>            :   ASMJIT_INST_3x(vpgatherdq, Vpgatherdq, X86Ymm, X86Mem, X86Ymm)              // AVX2</a>
+<a name="3440"><span class="lineNum">    3440 </span>            :   ASMJIT_INST_2x(vpgatherdq, Vpgatherdq, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3441"><span class="lineNum">    3441 </span>            :   ASMJIT_INST_2x(vpgatherdq, Vpgatherdq, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3442"><span class="lineNum">    3442 </span>            :   ASMJIT_INST_2x(vpgatherdq, Vpgatherdq, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="3443"><span class="lineNum">    3443 </span>            :   ASMJIT_INST_3x(vpgatherqd, Vpgatherqd, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="3444"><span class="lineNum">    3444 </span>            :   ASMJIT_INST_2x(vpgatherqd, Vpgatherqd, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3445"><span class="lineNum">    3445 </span>            :   ASMJIT_INST_2x(vpgatherqd, Vpgatherqd, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3446"><span class="lineNum">    3446 </span>            :   ASMJIT_INST_2x(vpgatherqd, Vpgatherqd, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="3447"><span class="lineNum">    3447 </span>            :   ASMJIT_INST_3x(vpgatherqq, Vpgatherqq, X86Xmm, X86Mem, X86Xmm)              // AVX2</a>
+<a name="3448"><span class="lineNum">    3448 </span>            :   ASMJIT_INST_3x(vpgatherqq, Vpgatherqq, X86Ymm, X86Mem, X86Ymm)              // AVX2</a>
+<a name="3449"><span class="lineNum">    3449 </span>            :   ASMJIT_INST_2x(vpgatherqq, Vpgatherqq, X86Xmm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3450"><span class="lineNum">    3450 </span>            :   ASMJIT_INST_2x(vpgatherqq, Vpgatherqq, X86Ymm, X86Mem)                      //      AVX512_F{k}-VL</a>
+<a name="3451"><span class="lineNum">    3451 </span>            :   ASMJIT_INST_2x(vpgatherqq, Vpgatherqq, X86Zmm, X86Mem)                      //      AVX512_F{k}</a>
+<a name="3452"><span class="lineNum">    3452 </span>            :   ASMJIT_INST_3x(vphaddd, Vphaddd, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="3453"><span class="lineNum">    3453 </span>            :   ASMJIT_INST_3x(vphaddd, Vphaddd, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="3454"><span class="lineNum">    3454 </span>            :   ASMJIT_INST_3x(vphaddd, Vphaddd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="3455"><span class="lineNum">    3455 </span>            :   ASMJIT_INST_3x(vphaddd, Vphaddd, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="3456"><span class="lineNum">    3456 </span>            :   ASMJIT_INST_3x(vphaddsw, Vphaddsw, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3457"><span class="lineNum">    3457 </span>            :   ASMJIT_INST_3x(vphaddsw, Vphaddsw, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3458"><span class="lineNum">    3458 </span>            :   ASMJIT_INST_3x(vphaddsw, Vphaddsw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3459"><span class="lineNum">    3459 </span>            :   ASMJIT_INST_3x(vphaddsw, Vphaddsw, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3460"><span class="lineNum">    3460 </span>            :   ASMJIT_INST_3x(vphaddw, Vphaddw, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="3461"><span class="lineNum">    3461 </span>            :   ASMJIT_INST_3x(vphaddw, Vphaddw, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="3462"><span class="lineNum">    3462 </span>            :   ASMJIT_INST_3x(vphaddw, Vphaddw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="3463"><span class="lineNum">    3463 </span>            :   ASMJIT_INST_3x(vphaddw, Vphaddw, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="3464"><span class="lineNum">    3464 </span>            :   ASMJIT_INST_2x(vphminposuw, Vphminposuw, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="3465"><span class="lineNum">    3465 </span>            :   ASMJIT_INST_2x(vphminposuw, Vphminposuw, X86Xmm, X86Mem)                    // AVX</a>
+<a name="3466"><span class="lineNum">    3466 </span>            :   ASMJIT_INST_3x(vphsubd, Vphsubd, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="3467"><span class="lineNum">    3467 </span>            :   ASMJIT_INST_3x(vphsubd, Vphsubd, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="3468"><span class="lineNum">    3468 </span>            :   ASMJIT_INST_3x(vphsubd, Vphsubd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="3469"><span class="lineNum">    3469 </span>            :   ASMJIT_INST_3x(vphsubd, Vphsubd, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="3470"><span class="lineNum">    3470 </span>            :   ASMJIT_INST_3x(vphsubsw, Vphsubsw, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="3471"><span class="lineNum">    3471 </span>            :   ASMJIT_INST_3x(vphsubsw, Vphsubsw, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="3472"><span class="lineNum">    3472 </span>            :   ASMJIT_INST_3x(vphsubsw, Vphsubsw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2</a>
+<a name="3473"><span class="lineNum">    3473 </span>            :   ASMJIT_INST_3x(vphsubsw, Vphsubsw, X86Ymm, X86Ymm, X86Mem)                  // AVX2</a>
+<a name="3474"><span class="lineNum">    3474 </span>            :   ASMJIT_INST_3x(vphsubw, Vphsubw, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="3475"><span class="lineNum">    3475 </span>            :   ASMJIT_INST_3x(vphsubw, Vphsubw, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="3476"><span class="lineNum">    3476 </span>            :   ASMJIT_INST_3x(vphsubw, Vphsubw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="3477"><span class="lineNum">    3477 </span>            :   ASMJIT_INST_3x(vphsubw, Vphsubw, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="3478"><span class="lineNum">    3478 </span>            :   ASMJIT_INST_3i(vpinsrb, Vpinsrb, X86Xmm, X86Gp, Imm)                        // AVX</a>
+<a name="3479"><span class="lineNum">    3479 </span>            :   ASMJIT_INST_3i(vpinsrb, Vpinsrb, X86Xmm, X86Mem, Imm)                       // AVX</a>
+<a name="3480"><span class="lineNum">    3480 </span>            :   ASMJIT_INST_4i(vpinsrb, Vpinsrb, X86Xmm, X86Xmm, X86Gp, Imm)                //      AVX512_BW{kz}</a>
+<a name="3481"><span class="lineNum">    3481 </span>            :   ASMJIT_INST_4i(vpinsrb, Vpinsrb, X86Xmm, X86Xmm, X86Mem, Imm)               //      AVX512_BW{kz}</a>
+<a name="3482"><span class="lineNum">    3482 </span>            :   ASMJIT_INST_3i(vpinsrd, Vpinsrd, X86Xmm, X86Gp, Imm)                        // AVX</a>
+<a name="3483"><span class="lineNum">    3483 </span>            :   ASMJIT_INST_3i(vpinsrd, Vpinsrd, X86Xmm, X86Mem, Imm)                       // AVX</a>
+<a name="3484"><span class="lineNum">    3484 </span>            :   ASMJIT_INST_4i(vpinsrd, Vpinsrd, X86Xmm, X86Xmm, X86Gp, Imm)                //      AVX512_DQ{kz}</a>
+<a name="3485"><span class="lineNum">    3485 </span>            :   ASMJIT_INST_4i(vpinsrd, Vpinsrd, X86Xmm, X86Xmm, X86Mem, Imm)               //      AVX512_DQ{kz}</a>
+<a name="3486"><span class="lineNum">    3486 </span>            :   ASMJIT_INST_3i(vpinsrq, Vpinsrq, X86Xmm, X86Gp, Imm)                        // AVX</a>
+<a name="3487"><span class="lineNum">    3487 </span>            :   ASMJIT_INST_3i(vpinsrq, Vpinsrq, X86Xmm, X86Mem, Imm)                       // AVX</a>
+<a name="3488"><span class="lineNum">    3488 </span>            :   ASMJIT_INST_4i(vpinsrq, Vpinsrq, X86Xmm, X86Xmm, X86Gp, Imm)                //      AVX512_DQ{kz}</a>
+<a name="3489"><span class="lineNum">    3489 </span>            :   ASMJIT_INST_4i(vpinsrq, Vpinsrq, X86Xmm, X86Xmm, X86Mem, Imm)               //      AVX512_DQ{kz}</a>
+<a name="3490"><span class="lineNum">    3490 </span>            :   ASMJIT_INST_4i(vpinsrw, Vpinsrw, X86Xmm, X86Xmm, X86Gp, Imm)                // AVX  AVX512_BW{kz}</a>
+<a name="3491"><span class="lineNum">    3491 </span>            :   ASMJIT_INST_4i(vpinsrw, Vpinsrw, X86Xmm, X86Xmm, X86Mem, Imm)               // AVX  AVX512_BW{kz}</a>
+<a name="3492"><span class="lineNum">    3492 </span>            :   ASMJIT_INST_2x(vplzcntd, Vplzcntd, X86Xmm, X86Xmm)                          //      AVX512_CD{kz|b32}-VL</a>
+<a name="3493"><span class="lineNum">    3493 </span>            :   ASMJIT_INST_2x(vplzcntd, Vplzcntd, X86Xmm, X86Mem)                          //      AVX512_CD{kz|b32}-VL</a>
+<a name="3494"><span class="lineNum">    3494 </span>            :   ASMJIT_INST_2x(vplzcntd, Vplzcntd, X86Ymm, X86Ymm)                          //      AVX512_CD{kz|b32}-VL</a>
+<a name="3495"><span class="lineNum">    3495 </span>            :   ASMJIT_INST_2x(vplzcntd, Vplzcntd, X86Ymm, X86Mem)                          //      AVX512_CD{kz|b32}-VL</a>
+<a name="3496"><span class="lineNum">    3496 </span>            :   ASMJIT_INST_2x(vplzcntd, Vplzcntd, X86Zmm, X86Zmm)                          //      AVX512_CD{kz|b32}</a>
+<a name="3497"><span class="lineNum">    3497 </span>            :   ASMJIT_INST_2x(vplzcntd, Vplzcntd, X86Zmm, X86Mem)                          //      AVX512_CD{kz|b32}</a>
+<a name="3498"><span class="lineNum">    3498 </span>            :   ASMJIT_INST_2x(vplzcntq, Vplzcntq, X86Xmm, X86Xmm)                          //      AVX512_CD{kz|b64}-VL</a>
+<a name="3499"><span class="lineNum">    3499 </span>            :   ASMJIT_INST_2x(vplzcntq, Vplzcntq, X86Xmm, X86Mem)                          //      AVX512_CD{kz|b64}-VL</a>
+<a name="3500"><span class="lineNum">    3500 </span>            :   ASMJIT_INST_2x(vplzcntq, Vplzcntq, X86Ymm, X86Ymm)                          //      AVX512_CD{kz|b64}-VL</a>
+<a name="3501"><span class="lineNum">    3501 </span>            :   ASMJIT_INST_2x(vplzcntq, Vplzcntq, X86Ymm, X86Mem)                          //      AVX512_CD{kz|b64}-VL</a>
+<a name="3502"><span class="lineNum">    3502 </span>            :   ASMJIT_INST_2x(vplzcntq, Vplzcntq, X86Zmm, X86Zmm)                          //      AVX512_CD{kz|b64}</a>
+<a name="3503"><span class="lineNum">    3503 </span>            :   ASMJIT_INST_2x(vplzcntq, Vplzcntq, X86Zmm, X86Mem)                          //      AVX512_CD{kz|b64}</a>
+<a name="3504"><span class="lineNum">    3504 </span>            :   ASMJIT_INST_3x(vpmadd52huq, Vpmadd52huq, X86Xmm, X86Xmm, X86Xmm)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3505"><span class="lineNum">    3505 </span>            :   ASMJIT_INST_3x(vpmadd52huq, Vpmadd52huq, X86Xmm, X86Xmm, X86Mem)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3506"><span class="lineNum">    3506 </span>            :   ASMJIT_INST_3x(vpmadd52huq, Vpmadd52huq, X86Ymm, X86Ymm, X86Ymm)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3507"><span class="lineNum">    3507 </span>            :   ASMJIT_INST_3x(vpmadd52huq, Vpmadd52huq, X86Ymm, X86Ymm, X86Mem)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3508"><span class="lineNum">    3508 </span>            :   ASMJIT_INST_3x(vpmadd52huq, Vpmadd52huq, X86Zmm, X86Zmm, X86Zmm)            //      AVX512_IFMA{kz|b64}</a>
+<a name="3509"><span class="lineNum">    3509 </span>            :   ASMJIT_INST_3x(vpmadd52huq, Vpmadd52huq, X86Zmm, X86Zmm, X86Mem)            //      AVX512_IFMA{kz|b64}</a>
+<a name="3510"><span class="lineNum">    3510 </span>            :   ASMJIT_INST_3x(vpmadd52luq, Vpmadd52luq, X86Xmm, X86Xmm, X86Xmm)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3511"><span class="lineNum">    3511 </span>            :   ASMJIT_INST_3x(vpmadd52luq, Vpmadd52luq, X86Xmm, X86Xmm, X86Mem)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3512"><span class="lineNum">    3512 </span>            :   ASMJIT_INST_3x(vpmadd52luq, Vpmadd52luq, X86Ymm, X86Ymm, X86Ymm)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3513"><span class="lineNum">    3513 </span>            :   ASMJIT_INST_3x(vpmadd52luq, Vpmadd52luq, X86Ymm, X86Ymm, X86Mem)            //      AVX512_IFMA{kz|b64}-VL</a>
+<a name="3514"><span class="lineNum">    3514 </span>            :   ASMJIT_INST_3x(vpmadd52luq, Vpmadd52luq, X86Zmm, X86Zmm, X86Zmm)            //      AVX512_IFMA{kz|b64}</a>
+<a name="3515"><span class="lineNum">    3515 </span>            :   ASMJIT_INST_3x(vpmadd52luq, Vpmadd52luq, X86Zmm, X86Zmm, X86Mem)            //      AVX512_IFMA{kz|b64}</a>
+<a name="3516"><span class="lineNum">    3516 </span>            :   ASMJIT_INST_3x(vpmaddubsw, Vpmaddubsw, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="3517"><span class="lineNum">    3517 </span>            :   ASMJIT_INST_3x(vpmaddubsw, Vpmaddubsw, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="3518"><span class="lineNum">    3518 </span>            :   ASMJIT_INST_3x(vpmaddubsw, Vpmaddubsw, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3519"><span class="lineNum">    3519 </span>            :   ASMJIT_INST_3x(vpmaddubsw, Vpmaddubsw, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3520"><span class="lineNum">    3520 </span>            :   ASMJIT_INST_3x(vpmaddubsw, Vpmaddubsw, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_BW{kz}</a>
+<a name="3521"><span class="lineNum">    3521 </span>            :   ASMJIT_INST_3x(vpmaddubsw, Vpmaddubsw, X86Zmm, X86Zmm, X86Mem)              //      AVX512_BW{kz}</a>
+<a name="3522"><span class="lineNum">    3522 </span>            :   ASMJIT_INST_3x(vpmaddwd, Vpmaddwd, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3523"><span class="lineNum">    3523 </span>            :   ASMJIT_INST_3x(vpmaddwd, Vpmaddwd, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3524"><span class="lineNum">    3524 </span>            :   ASMJIT_INST_3x(vpmaddwd, Vpmaddwd, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3525"><span class="lineNum">    3525 </span>            :   ASMJIT_INST_3x(vpmaddwd, Vpmaddwd, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3526"><span class="lineNum">    3526 </span>            :   ASMJIT_INST_3x(vpmaddwd, Vpmaddwd, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="3527"><span class="lineNum">    3527 </span>            :   ASMJIT_INST_3x(vpmaddwd, Vpmaddwd, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3528"><span class="lineNum">    3528 </span>            :   ASMJIT_INST_3x(vpmaskmovd, Vpmaskmovd, X86Mem, X86Xmm, X86Xmm)              // AVX2</a>
+<a name="3529"><span class="lineNum">    3529 </span>            :   ASMJIT_INST_3x(vpmaskmovd, Vpmaskmovd, X86Mem, X86Ymm, X86Ymm)              // AVX2</a>
+<a name="3530"><span class="lineNum">    3530 </span>            :   ASMJIT_INST_3x(vpmaskmovd, Vpmaskmovd, X86Xmm, X86Xmm, X86Mem)              // AVX2</a>
+<a name="3531"><span class="lineNum">    3531 </span>            :   ASMJIT_INST_3x(vpmaskmovd, Vpmaskmovd, X86Ymm, X86Ymm, X86Mem)              // AVX2</a>
+<a name="3532"><span class="lineNum">    3532 </span>            :   ASMJIT_INST_3x(vpmaskmovq, Vpmaskmovq, X86Mem, X86Xmm, X86Xmm)              // AVX2</a>
+<a name="3533"><span class="lineNum">    3533 </span>            :   ASMJIT_INST_3x(vpmaskmovq, Vpmaskmovq, X86Mem, X86Ymm, X86Ymm)              // AVX2</a>
+<a name="3534"><span class="lineNum">    3534 </span>            :   ASMJIT_INST_3x(vpmaskmovq, Vpmaskmovq, X86Xmm, X86Xmm, X86Mem)              // AVX2</a>
+<a name="3535"><span class="lineNum">    3535 </span>            :   ASMJIT_INST_3x(vpmaskmovq, Vpmaskmovq, X86Ymm, X86Ymm, X86Mem)              // AVX2</a>
+<a name="3536"><span class="lineNum">    3536 </span>            :   ASMJIT_INST_3x(vpmaxsb, Vpmaxsb, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3537"><span class="lineNum">    3537 </span>            :   ASMJIT_INST_3x(vpmaxsb, Vpmaxsb, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3538"><span class="lineNum">    3538 </span>            :   ASMJIT_INST_3x(vpmaxsb, Vpmaxsb, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3539"><span class="lineNum">    3539 </span>            :   ASMJIT_INST_3x(vpmaxsb, Vpmaxsb, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3540"><span class="lineNum">    3540 </span>            :   ASMJIT_INST_3x(vpmaxsb, Vpmaxsb, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3541"><span class="lineNum">    3541 </span>            :   ASMJIT_INST_3x(vpmaxsb, Vpmaxsb, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3542"><span class="lineNum">    3542 </span>            :   ASMJIT_INST_3x(vpmaxsd, Vpmaxsd, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3543"><span class="lineNum">    3543 </span>            :   ASMJIT_INST_3x(vpmaxsd, Vpmaxsd, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3544"><span class="lineNum">    3544 </span>            :   ASMJIT_INST_3x(vpmaxsd, Vpmaxsd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3545"><span class="lineNum">    3545 </span>            :   ASMJIT_INST_3x(vpmaxsd, Vpmaxsd, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3546"><span class="lineNum">    3546 </span>            :   ASMJIT_INST_3x(vpmaxsd, Vpmaxsd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3547"><span class="lineNum">    3547 </span>            :   ASMJIT_INST_3x(vpmaxsd, Vpmaxsd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3548"><span class="lineNum">    3548 </span>            :   ASMJIT_INST_3x(vpmaxsq, Vpmaxsq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3549"><span class="lineNum">    3549 </span>            :   ASMJIT_INST_3x(vpmaxsq, Vpmaxsq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3550"><span class="lineNum">    3550 </span>            :   ASMJIT_INST_3x(vpmaxsq, Vpmaxsq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3551"><span class="lineNum">    3551 </span>            :   ASMJIT_INST_3x(vpmaxsq, Vpmaxsq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3552"><span class="lineNum">    3552 </span>            :   ASMJIT_INST_3x(vpmaxsq, Vpmaxsq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3553"><span class="lineNum">    3553 </span>            :   ASMJIT_INST_3x(vpmaxsq, Vpmaxsq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3554"><span class="lineNum">    3554 </span>            :   ASMJIT_INST_3x(vpmaxsw, Vpmaxsw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3555"><span class="lineNum">    3555 </span>            :   ASMJIT_INST_3x(vpmaxsw, Vpmaxsw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3556"><span class="lineNum">    3556 </span>            :   ASMJIT_INST_3x(vpmaxsw, Vpmaxsw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3557"><span class="lineNum">    3557 </span>            :   ASMJIT_INST_3x(vpmaxsw, Vpmaxsw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3558"><span class="lineNum">    3558 </span>            :   ASMJIT_INST_3x(vpmaxsw, Vpmaxsw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3559"><span class="lineNum">    3559 </span>            :   ASMJIT_INST_3x(vpmaxsw, Vpmaxsw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3560"><span class="lineNum">    3560 </span>            :   ASMJIT_INST_3x(vpmaxub, Vpmaxub, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3561"><span class="lineNum">    3561 </span>            :   ASMJIT_INST_3x(vpmaxub, Vpmaxub, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3562"><span class="lineNum">    3562 </span>            :   ASMJIT_INST_3x(vpmaxub, Vpmaxub, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3563"><span class="lineNum">    3563 </span>            :   ASMJIT_INST_3x(vpmaxub, Vpmaxub, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3564"><span class="lineNum">    3564 </span>            :   ASMJIT_INST_3x(vpmaxub, Vpmaxub, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3565"><span class="lineNum">    3565 </span>            :   ASMJIT_INST_3x(vpmaxub, Vpmaxub, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3566"><span class="lineNum">    3566 </span>            :   ASMJIT_INST_3x(vpmaxud, Vpmaxud, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3567"><span class="lineNum">    3567 </span>            :   ASMJIT_INST_3x(vpmaxud, Vpmaxud, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3568"><span class="lineNum">    3568 </span>            :   ASMJIT_INST_3x(vpmaxud, Vpmaxud, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3569"><span class="lineNum">    3569 </span>            :   ASMJIT_INST_3x(vpmaxud, Vpmaxud, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3570"><span class="lineNum">    3570 </span>            :   ASMJIT_INST_3x(vpmaxud, Vpmaxud, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3571"><span class="lineNum">    3571 </span>            :   ASMJIT_INST_3x(vpmaxud, Vpmaxud, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3572"><span class="lineNum">    3572 </span>            :   ASMJIT_INST_3x(vpmaxuq, Vpmaxuq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3573"><span class="lineNum">    3573 </span>            :   ASMJIT_INST_3x(vpmaxuq, Vpmaxuq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3574"><span class="lineNum">    3574 </span>            :   ASMJIT_INST_3x(vpmaxuq, Vpmaxuq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3575"><span class="lineNum">    3575 </span>            :   ASMJIT_INST_3x(vpmaxuq, Vpmaxuq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3576"><span class="lineNum">    3576 </span>            :   ASMJIT_INST_3x(vpmaxuq, Vpmaxuq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3577"><span class="lineNum">    3577 </span>            :   ASMJIT_INST_3x(vpmaxuq, Vpmaxuq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3578"><span class="lineNum">    3578 </span>            :   ASMJIT_INST_3x(vpmaxuw, Vpmaxuw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3579"><span class="lineNum">    3579 </span>            :   ASMJIT_INST_3x(vpmaxuw, Vpmaxuw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3580"><span class="lineNum">    3580 </span>            :   ASMJIT_INST_3x(vpmaxuw, Vpmaxuw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3581"><span class="lineNum">    3581 </span>            :   ASMJIT_INST_3x(vpmaxuw, Vpmaxuw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3582"><span class="lineNum">    3582 </span>            :   ASMJIT_INST_3x(vpmaxuw, Vpmaxuw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3583"><span class="lineNum">    3583 </span>            :   ASMJIT_INST_3x(vpmaxuw, Vpmaxuw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3584"><span class="lineNum">    3584 </span>            :   ASMJIT_INST_3x(vpminsb, Vpminsb, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3585"><span class="lineNum">    3585 </span>            :   ASMJIT_INST_3x(vpminsb, Vpminsb, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3586"><span class="lineNum">    3586 </span>            :   ASMJIT_INST_3x(vpminsb, Vpminsb, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3587"><span class="lineNum">    3587 </span>            :   ASMJIT_INST_3x(vpminsb, Vpminsb, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3588"><span class="lineNum">    3588 </span>            :   ASMJIT_INST_3x(vpminsb, Vpminsb, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3589"><span class="lineNum">    3589 </span>            :   ASMJIT_INST_3x(vpminsb, Vpminsb, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3590"><span class="lineNum">    3590 </span>            :   ASMJIT_INST_3x(vpminsd, Vpminsd, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3591"><span class="lineNum">    3591 </span>            :   ASMJIT_INST_3x(vpminsd, Vpminsd, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3592"><span class="lineNum">    3592 </span>            :   ASMJIT_INST_3x(vpminsd, Vpminsd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3593"><span class="lineNum">    3593 </span>            :   ASMJIT_INST_3x(vpminsd, Vpminsd, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3594"><span class="lineNum">    3594 </span>            :   ASMJIT_INST_3x(vpminsd, Vpminsd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3595"><span class="lineNum">    3595 </span>            :   ASMJIT_INST_3x(vpminsd, Vpminsd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3596"><span class="lineNum">    3596 </span>            :   ASMJIT_INST_3x(vpminsq, Vpminsq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3597"><span class="lineNum">    3597 </span>            :   ASMJIT_INST_3x(vpminsq, Vpminsq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3598"><span class="lineNum">    3598 </span>            :   ASMJIT_INST_3x(vpminsq, Vpminsq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3599"><span class="lineNum">    3599 </span>            :   ASMJIT_INST_3x(vpminsq, Vpminsq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3600"><span class="lineNum">    3600 </span>            :   ASMJIT_INST_3x(vpminsq, Vpminsq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3601"><span class="lineNum">    3601 </span>            :   ASMJIT_INST_3x(vpminsq, Vpminsq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3602"><span class="lineNum">    3602 </span>            :   ASMJIT_INST_3x(vpminsw, Vpminsw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3603"><span class="lineNum">    3603 </span>            :   ASMJIT_INST_3x(vpminsw, Vpminsw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3604"><span class="lineNum">    3604 </span>            :   ASMJIT_INST_3x(vpminsw, Vpminsw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3605"><span class="lineNum">    3605 </span>            :   ASMJIT_INST_3x(vpminsw, Vpminsw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3606"><span class="lineNum">    3606 </span>            :   ASMJIT_INST_3x(vpminsw, Vpminsw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3607"><span class="lineNum">    3607 </span>            :   ASMJIT_INST_3x(vpminsw, Vpminsw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3608"><span class="lineNum">    3608 </span>            :   ASMJIT_INST_3x(vpminub, Vpminub, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3609"><span class="lineNum">    3609 </span>            :   ASMJIT_INST_3x(vpminub, Vpminub, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3610"><span class="lineNum">    3610 </span>            :   ASMJIT_INST_3x(vpminub, Vpminub, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3611"><span class="lineNum">    3611 </span>            :   ASMJIT_INST_3x(vpminub, Vpminub, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3612"><span class="lineNum">    3612 </span>            :   ASMJIT_INST_3x(vpminub, Vpminub, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3613"><span class="lineNum">    3613 </span>            :   ASMJIT_INST_3x(vpminub, Vpminub, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3614"><span class="lineNum">    3614 </span>            :   ASMJIT_INST_3x(vpminud, Vpminud, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3615"><span class="lineNum">    3615 </span>            :   ASMJIT_INST_3x(vpminud, Vpminud, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3616"><span class="lineNum">    3616 </span>            :   ASMJIT_INST_3x(vpminud, Vpminud, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3617"><span class="lineNum">    3617 </span>            :   ASMJIT_INST_3x(vpminud, Vpminud, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3618"><span class="lineNum">    3618 </span>            :   ASMJIT_INST_3x(vpminud, Vpminud, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3619"><span class="lineNum">    3619 </span>            :   ASMJIT_INST_3x(vpminud, Vpminud, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3620"><span class="lineNum">    3620 </span>            :   ASMJIT_INST_3x(vpminuq, Vpminuq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3621"><span class="lineNum">    3621 </span>            :   ASMJIT_INST_3x(vpminuq, Vpminuq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3622"><span class="lineNum">    3622 </span>            :   ASMJIT_INST_3x(vpminuq, Vpminuq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3623"><span class="lineNum">    3623 </span>            :   ASMJIT_INST_3x(vpminuq, Vpminuq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3624"><span class="lineNum">    3624 </span>            :   ASMJIT_INST_3x(vpminuq, Vpminuq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3625"><span class="lineNum">    3625 </span>            :   ASMJIT_INST_3x(vpminuq, Vpminuq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3626"><span class="lineNum">    3626 </span>            :   ASMJIT_INST_3x(vpminuw, Vpminuw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3627"><span class="lineNum">    3627 </span>            :   ASMJIT_INST_3x(vpminuw, Vpminuw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3628"><span class="lineNum">    3628 </span>            :   ASMJIT_INST_3x(vpminuw, Vpminuw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3629"><span class="lineNum">    3629 </span>            :   ASMJIT_INST_3x(vpminuw, Vpminuw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3630"><span class="lineNum">    3630 </span>            :   ASMJIT_INST_3x(vpminuw, Vpminuw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3631"><span class="lineNum">    3631 </span>            :   ASMJIT_INST_3x(vpminuw, Vpminuw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3632"><span class="lineNum">    3632 </span>            :   ASMJIT_INST_2x(vpmovb2m, Vpmovb2m, X86KReg, X86Xmm)                         //      AVX512_BW-VL</a>
+<a name="3633"><span class="lineNum">    3633 </span>            :   ASMJIT_INST_2x(vpmovb2m, Vpmovb2m, X86KReg, X86Ymm)                         //      AVX512_BW-VL</a>
+<a name="3634"><span class="lineNum">    3634 </span>            :   ASMJIT_INST_2x(vpmovb2m, Vpmovb2m, X86KReg, X86Zmm)                         //      AVX512_BW</a>
+<a name="3635"><span class="lineNum">    3635 </span>            :   ASMJIT_INST_2x(vpmovd2m, Vpmovd2m, X86KReg, X86Xmm)                         //      AVX512_DQ-VL</a>
+<a name="3636"><span class="lineNum">    3636 </span>            :   ASMJIT_INST_2x(vpmovd2m, Vpmovd2m, X86KReg, X86Ymm)                         //      AVX512_DQ-VL</a>
+<a name="3637"><span class="lineNum">    3637 </span>            :   ASMJIT_INST_2x(vpmovd2m, Vpmovd2m, X86KReg, X86Zmm)                         //      AVX512_DQ</a>
+<a name="3638"><span class="lineNum">    3638 </span>            :   ASMJIT_INST_2x(vpmovdb, Vpmovdb, X86Xmm, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3639"><span class="lineNum">    3639 </span>            :   ASMJIT_INST_2x(vpmovdb, Vpmovdb, X86Mem, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3640"><span class="lineNum">    3640 </span>            :   ASMJIT_INST_2x(vpmovdb, Vpmovdb, X86Xmm, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3641"><span class="lineNum">    3641 </span>            :   ASMJIT_INST_2x(vpmovdb, Vpmovdb, X86Mem, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3642"><span class="lineNum">    3642 </span>            :   ASMJIT_INST_2x(vpmovdb, Vpmovdb, X86Xmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3643"><span class="lineNum">    3643 </span>            :   ASMJIT_INST_2x(vpmovdb, Vpmovdb, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3644"><span class="lineNum">    3644 </span>            :   ASMJIT_INST_2x(vpmovdw, Vpmovdw, X86Xmm, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3645"><span class="lineNum">    3645 </span>            :   ASMJIT_INST_2x(vpmovdw, Vpmovdw, X86Mem, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3646"><span class="lineNum">    3646 </span>            :   ASMJIT_INST_2x(vpmovdw, Vpmovdw, X86Xmm, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3647"><span class="lineNum">    3647 </span>            :   ASMJIT_INST_2x(vpmovdw, Vpmovdw, X86Mem, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3648"><span class="lineNum">    3648 </span>            :   ASMJIT_INST_2x(vpmovdw, Vpmovdw, X86Ymm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3649"><span class="lineNum">    3649 </span>            :   ASMJIT_INST_2x(vpmovdw, Vpmovdw, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3650"><span class="lineNum">    3650 </span>            :   ASMJIT_INST_2x(vpmovm2b, Vpmovm2b, X86Xmm, X86KReg)                         //      AVX512_BW-VL</a>
+<a name="3651"><span class="lineNum">    3651 </span>            :   ASMJIT_INST_2x(vpmovm2b, Vpmovm2b, X86Ymm, X86KReg)                         //      AVX512_BW-VL</a>
+<a name="3652"><span class="lineNum">    3652 </span>            :   ASMJIT_INST_2x(vpmovm2b, Vpmovm2b, X86Zmm, X86KReg)                         //      AVX512_BW</a>
+<a name="3653"><span class="lineNum">    3653 </span>            :   ASMJIT_INST_2x(vpmovm2d, Vpmovm2d, X86Xmm, X86KReg)                         //      AVX512_DQ-VL</a>
+<a name="3654"><span class="lineNum">    3654 </span>            :   ASMJIT_INST_2x(vpmovm2d, Vpmovm2d, X86Ymm, X86KReg)                         //      AVX512_DQ-VL</a>
+<a name="3655"><span class="lineNum">    3655 </span>            :   ASMJIT_INST_2x(vpmovm2d, Vpmovm2d, X86Zmm, X86KReg)                         //      AVX512_DQ</a>
+<a name="3656"><span class="lineNum">    3656 </span>            :   ASMJIT_INST_2x(vpmovm2q, Vpmovm2q, X86Xmm, X86KReg)                         //      AVX512_DQ-VL</a>
+<a name="3657"><span class="lineNum">    3657 </span>            :   ASMJIT_INST_2x(vpmovm2q, Vpmovm2q, X86Ymm, X86KReg)                         //      AVX512_DQ-VL</a>
+<a name="3658"><span class="lineNum">    3658 </span>            :   ASMJIT_INST_2x(vpmovm2q, Vpmovm2q, X86Zmm, X86KReg)                         //      AVX512_DQ</a>
+<a name="3659"><span class="lineNum">    3659 </span>            :   ASMJIT_INST_2x(vpmovm2w, Vpmovm2w, X86Xmm, X86KReg)                         //      AVX512_BW-VL</a>
+<a name="3660"><span class="lineNum">    3660 </span>            :   ASMJIT_INST_2x(vpmovm2w, Vpmovm2w, X86Ymm, X86KReg)                         //      AVX512_BW-VL</a>
+<a name="3661"><span class="lineNum">    3661 </span>            :   ASMJIT_INST_2x(vpmovm2w, Vpmovm2w, X86Zmm, X86KReg)                         //      AVX512_BW</a>
+<a name="3662"><span class="lineNum">    3662 </span>            :   ASMJIT_INST_2x(vpmovmskb, Vpmovmskb, X86Gp, X86Xmm)                         // AVX</a>
+<a name="3663"><span class="lineNum">    3663 </span>            :   ASMJIT_INST_2x(vpmovmskb, Vpmovmskb, X86Gp, X86Ymm)                         // AVX2</a>
+<a name="3664"><span class="lineNum">    3664 </span>            :   ASMJIT_INST_2x(vpmovq2m, Vpmovq2m, X86KReg, X86Xmm)                         //      AVX512_DQ-VL</a>
+<a name="3665"><span class="lineNum">    3665 </span>            :   ASMJIT_INST_2x(vpmovq2m, Vpmovq2m, X86KReg, X86Ymm)                         //      AVX512_DQ-VL</a>
+<a name="3666"><span class="lineNum">    3666 </span>            :   ASMJIT_INST_2x(vpmovq2m, Vpmovq2m, X86KReg, X86Zmm)                         //      AVX512_DQ</a>
+<a name="3667"><span class="lineNum">    3667 </span>            :   ASMJIT_INST_2x(vpmovqb, Vpmovqb, X86Xmm, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3668"><span class="lineNum">    3668 </span>            :   ASMJIT_INST_2x(vpmovqb, Vpmovqb, X86Mem, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3669"><span class="lineNum">    3669 </span>            :   ASMJIT_INST_2x(vpmovqb, Vpmovqb, X86Xmm, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3670"><span class="lineNum">    3670 </span>            :   ASMJIT_INST_2x(vpmovqb, Vpmovqb, X86Mem, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3671"><span class="lineNum">    3671 </span>            :   ASMJIT_INST_2x(vpmovqb, Vpmovqb, X86Xmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3672"><span class="lineNum">    3672 </span>            :   ASMJIT_INST_2x(vpmovqb, Vpmovqb, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3673"><span class="lineNum">    3673 </span>            :   ASMJIT_INST_2x(vpmovqd, Vpmovqd, X86Xmm, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3674"><span class="lineNum">    3674 </span>            :   ASMJIT_INST_2x(vpmovqd, Vpmovqd, X86Mem, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3675"><span class="lineNum">    3675 </span>            :   ASMJIT_INST_2x(vpmovqd, Vpmovqd, X86Xmm, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3676"><span class="lineNum">    3676 </span>            :   ASMJIT_INST_2x(vpmovqd, Vpmovqd, X86Mem, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3677"><span class="lineNum">    3677 </span>            :   ASMJIT_INST_2x(vpmovqd, Vpmovqd, X86Ymm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3678"><span class="lineNum">    3678 </span>            :   ASMJIT_INST_2x(vpmovqd, Vpmovqd, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3679"><span class="lineNum">    3679 </span>            :   ASMJIT_INST_2x(vpmovqw, Vpmovqw, X86Xmm, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3680"><span class="lineNum">    3680 </span>            :   ASMJIT_INST_2x(vpmovqw, Vpmovqw, X86Mem, X86Xmm)                            //      AVX512_F{kz}-VL</a>
+<a name="3681"><span class="lineNum">    3681 </span>            :   ASMJIT_INST_2x(vpmovqw, Vpmovqw, X86Xmm, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3682"><span class="lineNum">    3682 </span>            :   ASMJIT_INST_2x(vpmovqw, Vpmovqw, X86Mem, X86Ymm)                            //      AVX512_F{kz}-VL</a>
+<a name="3683"><span class="lineNum">    3683 </span>            :   ASMJIT_INST_2x(vpmovqw, Vpmovqw, X86Xmm, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3684"><span class="lineNum">    3684 </span>            :   ASMJIT_INST_2x(vpmovqw, Vpmovqw, X86Mem, X86Zmm)                            //      AVX512_F{kz}</a>
+<a name="3685"><span class="lineNum">    3685 </span>            :   ASMJIT_INST_2x(vpmovsdb, Vpmovsdb, X86Xmm, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3686"><span class="lineNum">    3686 </span>            :   ASMJIT_INST_2x(vpmovsdb, Vpmovsdb, X86Mem, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3687"><span class="lineNum">    3687 </span>            :   ASMJIT_INST_2x(vpmovsdb, Vpmovsdb, X86Xmm, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3688"><span class="lineNum">    3688 </span>            :   ASMJIT_INST_2x(vpmovsdb, Vpmovsdb, X86Mem, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3689"><span class="lineNum">    3689 </span>            :   ASMJIT_INST_2x(vpmovsdb, Vpmovsdb, X86Xmm, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3690"><span class="lineNum">    3690 </span>            :   ASMJIT_INST_2x(vpmovsdb, Vpmovsdb, X86Mem, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3691"><span class="lineNum">    3691 </span>            :   ASMJIT_INST_2x(vpmovsdw, Vpmovsdw, X86Xmm, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3692"><span class="lineNum">    3692 </span>            :   ASMJIT_INST_2x(vpmovsdw, Vpmovsdw, X86Mem, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3693"><span class="lineNum">    3693 </span>            :   ASMJIT_INST_2x(vpmovsdw, Vpmovsdw, X86Xmm, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3694"><span class="lineNum">    3694 </span>            :   ASMJIT_INST_2x(vpmovsdw, Vpmovsdw, X86Mem, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3695"><span class="lineNum">    3695 </span>            :   ASMJIT_INST_2x(vpmovsdw, Vpmovsdw, X86Ymm, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3696"><span class="lineNum">    3696 </span>            :   ASMJIT_INST_2x(vpmovsdw, Vpmovsdw, X86Mem, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3697"><span class="lineNum">    3697 </span>            :   ASMJIT_INST_2x(vpmovsqb, Vpmovsqb, X86Xmm, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3698"><span class="lineNum">    3698 </span>            :   ASMJIT_INST_2x(vpmovsqb, Vpmovsqb, X86Mem, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3699"><span class="lineNum">    3699 </span>            :   ASMJIT_INST_2x(vpmovsqb, Vpmovsqb, X86Xmm, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3700"><span class="lineNum">    3700 </span>            :   ASMJIT_INST_2x(vpmovsqb, Vpmovsqb, X86Mem, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3701"><span class="lineNum">    3701 </span>            :   ASMJIT_INST_2x(vpmovsqb, Vpmovsqb, X86Xmm, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3702"><span class="lineNum">    3702 </span>            :   ASMJIT_INST_2x(vpmovsqb, Vpmovsqb, X86Mem, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3703"><span class="lineNum">    3703 </span>            :   ASMJIT_INST_2x(vpmovsqd, Vpmovsqd, X86Xmm, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3704"><span class="lineNum">    3704 </span>            :   ASMJIT_INST_2x(vpmovsqd, Vpmovsqd, X86Mem, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3705"><span class="lineNum">    3705 </span>            :   ASMJIT_INST_2x(vpmovsqd, Vpmovsqd, X86Xmm, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3706"><span class="lineNum">    3706 </span>            :   ASMJIT_INST_2x(vpmovsqd, Vpmovsqd, X86Mem, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3707"><span class="lineNum">    3707 </span>            :   ASMJIT_INST_2x(vpmovsqd, Vpmovsqd, X86Ymm, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3708"><span class="lineNum">    3708 </span>            :   ASMJIT_INST_2x(vpmovsqd, Vpmovsqd, X86Mem, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3709"><span class="lineNum">    3709 </span>            :   ASMJIT_INST_2x(vpmovsqw, Vpmovsqw, X86Xmm, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3710"><span class="lineNum">    3710 </span>            :   ASMJIT_INST_2x(vpmovsqw, Vpmovsqw, X86Mem, X86Xmm)                          //      AVX512_F{kz}-VL</a>
+<a name="3711"><span class="lineNum">    3711 </span>            :   ASMJIT_INST_2x(vpmovsqw, Vpmovsqw, X86Xmm, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3712"><span class="lineNum">    3712 </span>            :   ASMJIT_INST_2x(vpmovsqw, Vpmovsqw, X86Mem, X86Ymm)                          //      AVX512_F{kz}-VL</a>
+<a name="3713"><span class="lineNum">    3713 </span>            :   ASMJIT_INST_2x(vpmovsqw, Vpmovsqw, X86Xmm, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3714"><span class="lineNum">    3714 </span>            :   ASMJIT_INST_2x(vpmovsqw, Vpmovsqw, X86Mem, X86Zmm)                          //      AVX512_F{kz}</a>
+<a name="3715"><span class="lineNum">    3715 </span>            :   ASMJIT_INST_2x(vpmovswb, Vpmovswb, X86Xmm, X86Xmm)                          //      AVX512_BW{kz}-VL</a>
+<a name="3716"><span class="lineNum">    3716 </span>            :   ASMJIT_INST_2x(vpmovswb, Vpmovswb, X86Mem, X86Xmm)                          //      AVX512_BW{kz}-VL</a>
+<a name="3717"><span class="lineNum">    3717 </span>            :   ASMJIT_INST_2x(vpmovswb, Vpmovswb, X86Xmm, X86Ymm)                          //      AVX512_BW{kz}-VL</a>
+<a name="3718"><span class="lineNum">    3718 </span>            :   ASMJIT_INST_2x(vpmovswb, Vpmovswb, X86Mem, X86Ymm)                          //      AVX512_BW{kz}-VL</a>
+<a name="3719"><span class="lineNum">    3719 </span>            :   ASMJIT_INST_2x(vpmovswb, Vpmovswb, X86Ymm, X86Zmm)                          //      AVX512_BW{kz}</a>
+<a name="3720"><span class="lineNum">    3720 </span>            :   ASMJIT_INST_2x(vpmovswb, Vpmovswb, X86Mem, X86Zmm)                          //      AVX512_BW{kz}</a>
+<a name="3721"><span class="lineNum">    3721 </span>            :   ASMJIT_INST_2x(vpmovsxbd, Vpmovsxbd, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3722"><span class="lineNum">    3722 </span>            :   ASMJIT_INST_2x(vpmovsxbd, Vpmovsxbd, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3723"><span class="lineNum">    3723 </span>            :   ASMJIT_INST_2x(vpmovsxbd, Vpmovsxbd, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3724"><span class="lineNum">    3724 </span>            :   ASMJIT_INST_2x(vpmovsxbd, Vpmovsxbd, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3725"><span class="lineNum">    3725 </span>            :   ASMJIT_INST_2x(vpmovsxbd, Vpmovsxbd, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3726"><span class="lineNum">    3726 </span>            :   ASMJIT_INST_2x(vpmovsxbd, Vpmovsxbd, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3727"><span class="lineNum">    3727 </span>            :   ASMJIT_INST_2x(vpmovsxbq, Vpmovsxbq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3728"><span class="lineNum">    3728 </span>            :   ASMJIT_INST_2x(vpmovsxbq, Vpmovsxbq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3729"><span class="lineNum">    3729 </span>            :   ASMJIT_INST_2x(vpmovsxbq, Vpmovsxbq, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3730"><span class="lineNum">    3730 </span>            :   ASMJIT_INST_2x(vpmovsxbq, Vpmovsxbq, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3731"><span class="lineNum">    3731 </span>            :   ASMJIT_INST_2x(vpmovsxbq, Vpmovsxbq, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3732"><span class="lineNum">    3732 </span>            :   ASMJIT_INST_2x(vpmovsxbq, Vpmovsxbq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3733"><span class="lineNum">    3733 </span>            :   ASMJIT_INST_2x(vpmovsxbw, Vpmovsxbw, X86Xmm, X86Xmm)                        // AVX  AVX512_BW{kz}-VL</a>
+<a name="3734"><span class="lineNum">    3734 </span>            :   ASMJIT_INST_2x(vpmovsxbw, Vpmovsxbw, X86Xmm, X86Mem)                        // AVX  AVX512_BW{kz}-VL</a>
+<a name="3735"><span class="lineNum">    3735 </span>            :   ASMJIT_INST_2x(vpmovsxbw, Vpmovsxbw, X86Ymm, X86Xmm)                        // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3736"><span class="lineNum">    3736 </span>            :   ASMJIT_INST_2x(vpmovsxbw, Vpmovsxbw, X86Ymm, X86Mem)                        // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3737"><span class="lineNum">    3737 </span>            :   ASMJIT_INST_2x(vpmovsxbw, Vpmovsxbw, X86Zmm, X86Ymm)                        //      AVX512_BW{kz}</a>
+<a name="3738"><span class="lineNum">    3738 </span>            :   ASMJIT_INST_2x(vpmovsxbw, Vpmovsxbw, X86Zmm, X86Mem)                        //      AVX512_BW{kz}</a>
+<a name="3739"><span class="lineNum">    3739 </span>            :   ASMJIT_INST_2x(vpmovsxdq, Vpmovsxdq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3740"><span class="lineNum">    3740 </span>            :   ASMJIT_INST_2x(vpmovsxdq, Vpmovsxdq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3741"><span class="lineNum">    3741 </span>            :   ASMJIT_INST_2x(vpmovsxdq, Vpmovsxdq, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3742"><span class="lineNum">    3742 </span>            :   ASMJIT_INST_2x(vpmovsxdq, Vpmovsxdq, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3743"><span class="lineNum">    3743 </span>            :   ASMJIT_INST_2x(vpmovsxdq, Vpmovsxdq, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3744"><span class="lineNum">    3744 </span>            :   ASMJIT_INST_2x(vpmovsxdq, Vpmovsxdq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3745"><span class="lineNum">    3745 </span>            :   ASMJIT_INST_2x(vpmovsxwd, Vpmovsxwd, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3746"><span class="lineNum">    3746 </span>            :   ASMJIT_INST_2x(vpmovsxwd, Vpmovsxwd, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3747"><span class="lineNum">    3747 </span>            :   ASMJIT_INST_2x(vpmovsxwd, Vpmovsxwd, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3748"><span class="lineNum">    3748 </span>            :   ASMJIT_INST_2x(vpmovsxwd, Vpmovsxwd, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3749"><span class="lineNum">    3749 </span>            :   ASMJIT_INST_2x(vpmovsxwd, Vpmovsxwd, X86Zmm, X86Ymm)                        //      AVX512_F{kz}</a>
+<a name="3750"><span class="lineNum">    3750 </span>            :   ASMJIT_INST_2x(vpmovsxwd, Vpmovsxwd, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3751"><span class="lineNum">    3751 </span>            :   ASMJIT_INST_2x(vpmovsxwq, Vpmovsxwq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3752"><span class="lineNum">    3752 </span>            :   ASMJIT_INST_2x(vpmovsxwq, Vpmovsxwq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3753"><span class="lineNum">    3753 </span>            :   ASMJIT_INST_2x(vpmovsxwq, Vpmovsxwq, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3754"><span class="lineNum">    3754 </span>            :   ASMJIT_INST_2x(vpmovsxwq, Vpmovsxwq, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3755"><span class="lineNum">    3755 </span>            :   ASMJIT_INST_2x(vpmovsxwq, Vpmovsxwq, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3756"><span class="lineNum">    3756 </span>            :   ASMJIT_INST_2x(vpmovsxwq, Vpmovsxwq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3757"><span class="lineNum">    3757 </span>            :   ASMJIT_INST_2x(vpmovusdb, Vpmovusdb, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3758"><span class="lineNum">    3758 </span>            :   ASMJIT_INST_2x(vpmovusdb, Vpmovusdb, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3759"><span class="lineNum">    3759 </span>            :   ASMJIT_INST_2x(vpmovusdb, Vpmovusdb, X86Xmm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3760"><span class="lineNum">    3760 </span>            :   ASMJIT_INST_2x(vpmovusdb, Vpmovusdb, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3761"><span class="lineNum">    3761 </span>            :   ASMJIT_INST_2x(vpmovusdb, Vpmovusdb, X86Xmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3762"><span class="lineNum">    3762 </span>            :   ASMJIT_INST_2x(vpmovusdb, Vpmovusdb, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3763"><span class="lineNum">    3763 </span>            :   ASMJIT_INST_2x(vpmovusdw, Vpmovusdw, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3764"><span class="lineNum">    3764 </span>            :   ASMJIT_INST_2x(vpmovusdw, Vpmovusdw, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3765"><span class="lineNum">    3765 </span>            :   ASMJIT_INST_2x(vpmovusdw, Vpmovusdw, X86Xmm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3766"><span class="lineNum">    3766 </span>            :   ASMJIT_INST_2x(vpmovusdw, Vpmovusdw, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3767"><span class="lineNum">    3767 </span>            :   ASMJIT_INST_2x(vpmovusdw, Vpmovusdw, X86Ymm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3768"><span class="lineNum">    3768 </span>            :   ASMJIT_INST_2x(vpmovusdw, Vpmovusdw, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3769"><span class="lineNum">    3769 </span>            :   ASMJIT_INST_2x(vpmovusqb, Vpmovusqb, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3770"><span class="lineNum">    3770 </span>            :   ASMJIT_INST_2x(vpmovusqb, Vpmovusqb, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3771"><span class="lineNum">    3771 </span>            :   ASMJIT_INST_2x(vpmovusqb, Vpmovusqb, X86Xmm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3772"><span class="lineNum">    3772 </span>            :   ASMJIT_INST_2x(vpmovusqb, Vpmovusqb, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3773"><span class="lineNum">    3773 </span>            :   ASMJIT_INST_2x(vpmovusqb, Vpmovusqb, X86Xmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3774"><span class="lineNum">    3774 </span>            :   ASMJIT_INST_2x(vpmovusqb, Vpmovusqb, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3775"><span class="lineNum">    3775 </span>            :   ASMJIT_INST_2x(vpmovusqd, Vpmovusqd, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3776"><span class="lineNum">    3776 </span>            :   ASMJIT_INST_2x(vpmovusqd, Vpmovusqd, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3777"><span class="lineNum">    3777 </span>            :   ASMJIT_INST_2x(vpmovusqd, Vpmovusqd, X86Xmm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3778"><span class="lineNum">    3778 </span>            :   ASMJIT_INST_2x(vpmovusqd, Vpmovusqd, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3779"><span class="lineNum">    3779 </span>            :   ASMJIT_INST_2x(vpmovusqd, Vpmovusqd, X86Ymm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3780"><span class="lineNum">    3780 </span>            :   ASMJIT_INST_2x(vpmovusqd, Vpmovusqd, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3781"><span class="lineNum">    3781 </span>            :   ASMJIT_INST_2x(vpmovusqw, Vpmovusqw, X86Xmm, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3782"><span class="lineNum">    3782 </span>            :   ASMJIT_INST_2x(vpmovusqw, Vpmovusqw, X86Mem, X86Xmm)                        //      AVX512_F{kz}-VL</a>
+<a name="3783"><span class="lineNum">    3783 </span>            :   ASMJIT_INST_2x(vpmovusqw, Vpmovusqw, X86Xmm, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3784"><span class="lineNum">    3784 </span>            :   ASMJIT_INST_2x(vpmovusqw, Vpmovusqw, X86Mem, X86Ymm)                        //      AVX512_F{kz}-VL</a>
+<a name="3785"><span class="lineNum">    3785 </span>            :   ASMJIT_INST_2x(vpmovusqw, Vpmovusqw, X86Xmm, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3786"><span class="lineNum">    3786 </span>            :   ASMJIT_INST_2x(vpmovusqw, Vpmovusqw, X86Mem, X86Zmm)                        //      AVX512_F{kz}</a>
+<a name="3787"><span class="lineNum">    3787 </span>            :   ASMJIT_INST_2x(vpmovuswb, Vpmovuswb, X86Xmm, X86Xmm)                        //      AVX512_BW{kz}-VL</a>
+<a name="3788"><span class="lineNum">    3788 </span>            :   ASMJIT_INST_2x(vpmovuswb, Vpmovuswb, X86Mem, X86Xmm)                        //      AVX512_BW{kz}-VL</a>
+<a name="3789"><span class="lineNum">    3789 </span>            :   ASMJIT_INST_2x(vpmovuswb, Vpmovuswb, X86Xmm, X86Ymm)                        //      AVX512_BW{kz}-VL</a>
+<a name="3790"><span class="lineNum">    3790 </span>            :   ASMJIT_INST_2x(vpmovuswb, Vpmovuswb, X86Mem, X86Ymm)                        //      AVX512_BW{kz}-VL</a>
+<a name="3791"><span class="lineNum">    3791 </span>            :   ASMJIT_INST_2x(vpmovuswb, Vpmovuswb, X86Ymm, X86Zmm)                        //      AVX512_BW{kz}</a>
+<a name="3792"><span class="lineNum">    3792 </span>            :   ASMJIT_INST_2x(vpmovuswb, Vpmovuswb, X86Mem, X86Zmm)                        //      AVX512_BW{kz}</a>
+<a name="3793"><span class="lineNum">    3793 </span>            :   ASMJIT_INST_2x(vpmovw2m, Vpmovw2m, X86KReg, X86Xmm)                         //      AVX512_BW-VL</a>
+<a name="3794"><span class="lineNum">    3794 </span>            :   ASMJIT_INST_2x(vpmovw2m, Vpmovw2m, X86KReg, X86Ymm)                         //      AVX512_BW-VL</a>
+<a name="3795"><span class="lineNum">    3795 </span>            :   ASMJIT_INST_2x(vpmovw2m, Vpmovw2m, X86KReg, X86Zmm)                         //      AVX512_BW</a>
+<a name="3796"><span class="lineNum">    3796 </span>            :   ASMJIT_INST_2x(vpmovwb, Vpmovwb, X86Xmm, X86Xmm)                            //      AVX512_BW{kz}-VL</a>
+<a name="3797"><span class="lineNum">    3797 </span>            :   ASMJIT_INST_2x(vpmovwb, Vpmovwb, X86Mem, X86Xmm)                            //      AVX512_BW{kz}-VL</a>
+<a name="3798"><span class="lineNum">    3798 </span>            :   ASMJIT_INST_2x(vpmovwb, Vpmovwb, X86Xmm, X86Ymm)                            //      AVX512_BW{kz}-VL</a>
+<a name="3799"><span class="lineNum">    3799 </span>            :   ASMJIT_INST_2x(vpmovwb, Vpmovwb, X86Mem, X86Ymm)                            //      AVX512_BW{kz}-VL</a>
+<a name="3800"><span class="lineNum">    3800 </span>            :   ASMJIT_INST_2x(vpmovwb, Vpmovwb, X86Ymm, X86Zmm)                            //      AVX512_BW{kz}</a>
+<a name="3801"><span class="lineNum">    3801 </span>            :   ASMJIT_INST_2x(vpmovwb, Vpmovwb, X86Mem, X86Zmm)                            //      AVX512_BW{kz}</a>
+<a name="3802"><span class="lineNum">    3802 </span>            :   ASMJIT_INST_2x(vpmovzxbd, Vpmovzxbd, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3803"><span class="lineNum">    3803 </span>            :   ASMJIT_INST_2x(vpmovzxbd, Vpmovzxbd, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3804"><span class="lineNum">    3804 </span>            :   ASMJIT_INST_2x(vpmovzxbd, Vpmovzxbd, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3805"><span class="lineNum">    3805 </span>            :   ASMJIT_INST_2x(vpmovzxbd, Vpmovzxbd, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3806"><span class="lineNum">    3806 </span>            :   ASMJIT_INST_2x(vpmovzxbd, Vpmovzxbd, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3807"><span class="lineNum">    3807 </span>            :   ASMJIT_INST_2x(vpmovzxbd, Vpmovzxbd, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3808"><span class="lineNum">    3808 </span>            :   ASMJIT_INST_2x(vpmovzxbq, Vpmovzxbq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3809"><span class="lineNum">    3809 </span>            :   ASMJIT_INST_2x(vpmovzxbq, Vpmovzxbq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3810"><span class="lineNum">    3810 </span>            :   ASMJIT_INST_2x(vpmovzxbq, Vpmovzxbq, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3811"><span class="lineNum">    3811 </span>            :   ASMJIT_INST_2x(vpmovzxbq, Vpmovzxbq, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3812"><span class="lineNum">    3812 </span>            :   ASMJIT_INST_2x(vpmovzxbq, Vpmovzxbq, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3813"><span class="lineNum">    3813 </span>            :   ASMJIT_INST_2x(vpmovzxbq, Vpmovzxbq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3814"><span class="lineNum">    3814 </span>            :   ASMJIT_INST_2x(vpmovzxbw, Vpmovzxbw, X86Xmm, X86Xmm)                        // AVX  AVX512_BW{kz}-VL</a>
+<a name="3815"><span class="lineNum">    3815 </span>            :   ASMJIT_INST_2x(vpmovzxbw, Vpmovzxbw, X86Xmm, X86Mem)                        // AVX  AVX512_BW{kz}-VL</a>
+<a name="3816"><span class="lineNum">    3816 </span>            :   ASMJIT_INST_2x(vpmovzxbw, Vpmovzxbw, X86Ymm, X86Xmm)                        // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3817"><span class="lineNum">    3817 </span>            :   ASMJIT_INST_2x(vpmovzxbw, Vpmovzxbw, X86Ymm, X86Mem)                        // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3818"><span class="lineNum">    3818 </span>            :   ASMJIT_INST_2x(vpmovzxbw, Vpmovzxbw, X86Zmm, X86Ymm)                        //      AVX512_BW{kz}</a>
+<a name="3819"><span class="lineNum">    3819 </span>            :   ASMJIT_INST_2x(vpmovzxbw, Vpmovzxbw, X86Zmm, X86Mem)                        //      AVX512_BW{kz}</a>
+<a name="3820"><span class="lineNum">    3820 </span>            :   ASMJIT_INST_2x(vpmovzxdq, Vpmovzxdq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3821"><span class="lineNum">    3821 </span>            :   ASMJIT_INST_2x(vpmovzxdq, Vpmovzxdq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3822"><span class="lineNum">    3822 </span>            :   ASMJIT_INST_2x(vpmovzxdq, Vpmovzxdq, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3823"><span class="lineNum">    3823 </span>            :   ASMJIT_INST_2x(vpmovzxdq, Vpmovzxdq, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3824"><span class="lineNum">    3824 </span>            :   ASMJIT_INST_2x(vpmovzxdq, Vpmovzxdq, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3825"><span class="lineNum">    3825 </span>            :   ASMJIT_INST_2x(vpmovzxdq, Vpmovzxdq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3826"><span class="lineNum">    3826 </span>            :   ASMJIT_INST_2x(vpmovzxwd, Vpmovzxwd, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3827"><span class="lineNum">    3827 </span>            :   ASMJIT_INST_2x(vpmovzxwd, Vpmovzxwd, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3828"><span class="lineNum">    3828 </span>            :   ASMJIT_INST_2x(vpmovzxwd, Vpmovzxwd, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3829"><span class="lineNum">    3829 </span>            :   ASMJIT_INST_2x(vpmovzxwd, Vpmovzxwd, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3830"><span class="lineNum">    3830 </span>            :   ASMJIT_INST_2x(vpmovzxwd, Vpmovzxwd, X86Zmm, X86Ymm)                        //      AVX512_F{kz}</a>
+<a name="3831"><span class="lineNum">    3831 </span>            :   ASMJIT_INST_2x(vpmovzxwd, Vpmovzxwd, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3832"><span class="lineNum">    3832 </span>            :   ASMJIT_INST_2x(vpmovzxwq, Vpmovzxwq, X86Xmm, X86Xmm)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3833"><span class="lineNum">    3833 </span>            :   ASMJIT_INST_2x(vpmovzxwq, Vpmovzxwq, X86Xmm, X86Mem)                        // AVX  AVX512_F{kz}-VL</a>
+<a name="3834"><span class="lineNum">    3834 </span>            :   ASMJIT_INST_2x(vpmovzxwq, Vpmovzxwq, X86Ymm, X86Xmm)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3835"><span class="lineNum">    3835 </span>            :   ASMJIT_INST_2x(vpmovzxwq, Vpmovzxwq, X86Ymm, X86Mem)                        // AVX2 AVX512_F{kz}-VL</a>
+<a name="3836"><span class="lineNum">    3836 </span>            :   ASMJIT_INST_2x(vpmovzxwq, Vpmovzxwq, X86Zmm, X86Xmm)                        //      AVX512_F{kz}</a>
+<a name="3837"><span class="lineNum">    3837 </span>            :   ASMJIT_INST_2x(vpmovzxwq, Vpmovzxwq, X86Zmm, X86Mem)                        //      AVX512_F{kz}</a>
+<a name="3838"><span class="lineNum">    3838 </span>            :   ASMJIT_INST_3x(vpmuldq, Vpmuldq, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3839"><span class="lineNum">    3839 </span>            :   ASMJIT_INST_3x(vpmuldq, Vpmuldq, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3840"><span class="lineNum">    3840 </span>            :   ASMJIT_INST_3x(vpmuldq, Vpmuldq, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="3841"><span class="lineNum">    3841 </span>            :   ASMJIT_INST_3x(vpmuldq, Vpmuldq, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="3842"><span class="lineNum">    3842 </span>            :   ASMJIT_INST_3x(vpmuldq, Vpmuldq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3843"><span class="lineNum">    3843 </span>            :   ASMJIT_INST_3x(vpmuldq, Vpmuldq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3844"><span class="lineNum">    3844 </span>            :   ASMJIT_INST_3x(vpmulhrsw, Vpmulhrsw, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_BW{kz}-VL</a>
+<a name="3845"><span class="lineNum">    3845 </span>            :   ASMJIT_INST_3x(vpmulhrsw, Vpmulhrsw, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_BW{kz}-VL</a>
+<a name="3846"><span class="lineNum">    3846 </span>            :   ASMJIT_INST_3x(vpmulhrsw, Vpmulhrsw, X86Ymm, X86Ymm, X86Ymm)                // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3847"><span class="lineNum">    3847 </span>            :   ASMJIT_INST_3x(vpmulhrsw, Vpmulhrsw, X86Ymm, X86Ymm, X86Mem)                // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3848"><span class="lineNum">    3848 </span>            :   ASMJIT_INST_3x(vpmulhrsw, Vpmulhrsw, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_BW{kz}</a>
+<a name="3849"><span class="lineNum">    3849 </span>            :   ASMJIT_INST_3x(vpmulhrsw, Vpmulhrsw, X86Zmm, X86Zmm, X86Mem)                //      AVX512_BW{kz}</a>
+<a name="3850"><span class="lineNum">    3850 </span>            :   ASMJIT_INST_3x(vpmulhuw, Vpmulhuw, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3851"><span class="lineNum">    3851 </span>            :   ASMJIT_INST_3x(vpmulhuw, Vpmulhuw, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="3852"><span class="lineNum">    3852 </span>            :   ASMJIT_INST_3x(vpmulhuw, Vpmulhuw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3853"><span class="lineNum">    3853 </span>            :   ASMJIT_INST_3x(vpmulhuw, Vpmulhuw, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3854"><span class="lineNum">    3854 </span>            :   ASMJIT_INST_3x(vpmulhuw, Vpmulhuw, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="3855"><span class="lineNum">    3855 </span>            :   ASMJIT_INST_3x(vpmulhuw, Vpmulhuw, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="3856"><span class="lineNum">    3856 </span>            :   ASMJIT_INST_3x(vpmulhw, Vpmulhw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3857"><span class="lineNum">    3857 </span>            :   ASMJIT_INST_3x(vpmulhw, Vpmulhw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3858"><span class="lineNum">    3858 </span>            :   ASMJIT_INST_3x(vpmulhw, Vpmulhw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3859"><span class="lineNum">    3859 </span>            :   ASMJIT_INST_3x(vpmulhw, Vpmulhw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3860"><span class="lineNum">    3860 </span>            :   ASMJIT_INST_3x(vpmulhw, Vpmulhw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3861"><span class="lineNum">    3861 </span>            :   ASMJIT_INST_3x(vpmulhw, Vpmulhw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3862"><span class="lineNum">    3862 </span>            :   ASMJIT_INST_3x(vpmulld, Vpmulld, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3863"><span class="lineNum">    3863 </span>            :   ASMJIT_INST_3x(vpmulld, Vpmulld, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3864"><span class="lineNum">    3864 </span>            :   ASMJIT_INST_3x(vpmulld, Vpmulld, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3865"><span class="lineNum">    3865 </span>            :   ASMJIT_INST_3x(vpmulld, Vpmulld, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3866"><span class="lineNum">    3866 </span>            :   ASMJIT_INST_3x(vpmulld, Vpmulld, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3867"><span class="lineNum">    3867 </span>            :   ASMJIT_INST_3x(vpmulld, Vpmulld, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3868"><span class="lineNum">    3868 </span>            :   ASMJIT_INST_3x(vpmullq, Vpmullq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="3869"><span class="lineNum">    3869 </span>            :   ASMJIT_INST_3x(vpmullq, Vpmullq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="3870"><span class="lineNum">    3870 </span>            :   ASMJIT_INST_3x(vpmullq, Vpmullq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="3871"><span class="lineNum">    3871 </span>            :   ASMJIT_INST_3x(vpmullq, Vpmullq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_DQ{kz|b64}-VL</a>
+<a name="3872"><span class="lineNum">    3872 </span>            :   ASMJIT_INST_3x(vpmullq, Vpmullq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_DQ{kz|b64}</a>
+<a name="3873"><span class="lineNum">    3873 </span>            :   ASMJIT_INST_3x(vpmullq, Vpmullq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_DQ{kz|b64}</a>
+<a name="3874"><span class="lineNum">    3874 </span>            :   ASMJIT_INST_3x(vpmullw, Vpmullw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3875"><span class="lineNum">    3875 </span>            :   ASMJIT_INST_3x(vpmullw, Vpmullw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3876"><span class="lineNum">    3876 </span>            :   ASMJIT_INST_3x(vpmullw, Vpmullw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3877"><span class="lineNum">    3877 </span>            :   ASMJIT_INST_3x(vpmullw, Vpmullw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3878"><span class="lineNum">    3878 </span>            :   ASMJIT_INST_3x(vpmullw, Vpmullw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3879"><span class="lineNum">    3879 </span>            :   ASMJIT_INST_3x(vpmullw, Vpmullw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3880"><span class="lineNum">    3880 </span>            :   ASMJIT_INST_3x(vpmultishiftqb, Vpmultishiftqb, X86Xmm, X86Xmm, X86Xmm)      //      AVX512_VBMI{kz|b64}-VL</a>
+<a name="3881"><span class="lineNum">    3881 </span>            :   ASMJIT_INST_3x(vpmultishiftqb, Vpmultishiftqb, X86Xmm, X86Xmm, X86Mem)      //      AVX512_VBMI{kz|b64}-VL</a>
+<a name="3882"><span class="lineNum">    3882 </span>            :   ASMJIT_INST_3x(vpmultishiftqb, Vpmultishiftqb, X86Ymm, X86Ymm, X86Ymm)      //      AVX512_VBMI{kz|b64}-VL</a>
+<a name="3883"><span class="lineNum">    3883 </span>            :   ASMJIT_INST_3x(vpmultishiftqb, Vpmultishiftqb, X86Ymm, X86Ymm, X86Mem)      //      AVX512_VBMI{kz|b64}-VL</a>
+<a name="3884"><span class="lineNum">    3884 </span>            :   ASMJIT_INST_3x(vpmultishiftqb, Vpmultishiftqb, X86Zmm, X86Zmm, X86Zmm)      //      AVX512_VBMI{kz|b64}</a>
+<a name="3885"><span class="lineNum">    3885 </span>            :   ASMJIT_INST_3x(vpmultishiftqb, Vpmultishiftqb, X86Zmm, X86Zmm, X86Mem)      //      AVX512_VBMI{kz|b64}</a>
+<a name="3886"><span class="lineNum">    3886 </span>            :   ASMJIT_INST_3x(vpmuludq, Vpmuludq, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3887"><span class="lineNum">    3887 </span>            :   ASMJIT_INST_3x(vpmuludq, Vpmuludq, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="3888"><span class="lineNum">    3888 </span>            :   ASMJIT_INST_3x(vpmuludq, Vpmuludq, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="3889"><span class="lineNum">    3889 </span>            :   ASMJIT_INST_3x(vpmuludq, Vpmuludq, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="3890"><span class="lineNum">    3890 </span>            :   ASMJIT_INST_3x(vpmuludq, Vpmuludq, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_F{kz|b64}</a>
+<a name="3891"><span class="lineNum">    3891 </span>            :   ASMJIT_INST_3x(vpmuludq, Vpmuludq, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_F{kz|b64}</a>
+<a name="3892"><span class="lineNum">    3892 </span>            :   ASMJIT_INST_2x(vpopcntd, Vpopcntd, X86Zmm, X86Zmm)                          //      AVX512_VPOPCNTDQ{kz|b32}</a>
+<a name="3893"><span class="lineNum">    3893 </span>            :   ASMJIT_INST_2x(vpopcntd, Vpopcntd, X86Zmm, X86Mem)                          //      AVX512_VPOPCNTDQ{kz|b32}</a>
+<a name="3894"><span class="lineNum">    3894 </span>            :   ASMJIT_INST_2x(vpopcntq, Vpopcntq, X86Zmm, X86Zmm)                          //      AVX512_VPOPCNTDQ{kz|b64}</a>
+<a name="3895"><span class="lineNum">    3895 </span>            :   ASMJIT_INST_2x(vpopcntq, Vpopcntq, X86Zmm, X86Mem)                          //      AVX512_VPOPCNTDQ{kz|b64}</a>
+<a name="3896"><span class="lineNum">    3896 </span>            :   ASMJIT_INST_3x(vpor, Vpor, X86Xmm, X86Xmm, X86Xmm)                          // AVX</a>
+<a name="3897"><span class="lineNum">    3897 </span>            :   ASMJIT_INST_3x(vpor, Vpor, X86Xmm, X86Xmm, X86Mem)                          // AVX</a>
+<a name="3898"><span class="lineNum">    3898 </span>            :   ASMJIT_INST_3x(vpor, Vpor, X86Ymm, X86Ymm, X86Ymm)                          // AVX2</a>
+<a name="3899"><span class="lineNum">    3899 </span>            :   ASMJIT_INST_3x(vpor, Vpor, X86Ymm, X86Ymm, X86Mem)                          // AVX2</a>
+<a name="3900"><span class="lineNum">    3900 </span>            :   ASMJIT_INST_3x(vpord, Vpord, X86Xmm, X86Xmm, X86Xmm)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="3901"><span class="lineNum">    3901 </span>            :   ASMJIT_INST_3x(vpord, Vpord, X86Xmm, X86Xmm, X86Mem)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="3902"><span class="lineNum">    3902 </span>            :   ASMJIT_INST_3x(vpord, Vpord, X86Ymm, X86Ymm, X86Ymm)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="3903"><span class="lineNum">    3903 </span>            :   ASMJIT_INST_3x(vpord, Vpord, X86Ymm, X86Ymm, X86Mem)                        //      AVX512_F{kz|b32}-VL</a>
+<a name="3904"><span class="lineNum">    3904 </span>            :   ASMJIT_INST_3x(vpord, Vpord, X86Zmm, X86Zmm, X86Zmm)                        //      AVX512_F{kz|b32}</a>
+<a name="3905"><span class="lineNum">    3905 </span>            :   ASMJIT_INST_3x(vpord, Vpord, X86Zmm, X86Zmm, X86Mem)                        //      AVX512_F{kz|b32}</a>
+<a name="3906"><span class="lineNum">    3906 </span>            :   ASMJIT_INST_3x(vporq, Vporq, X86Xmm, X86Xmm, X86Xmm)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="3907"><span class="lineNum">    3907 </span>            :   ASMJIT_INST_3x(vporq, Vporq, X86Xmm, X86Xmm, X86Mem)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="3908"><span class="lineNum">    3908 </span>            :   ASMJIT_INST_3x(vporq, Vporq, X86Ymm, X86Ymm, X86Ymm)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="3909"><span class="lineNum">    3909 </span>            :   ASMJIT_INST_3x(vporq, Vporq, X86Ymm, X86Ymm, X86Mem)                        //      AVX512_F{kz|b64}-VL</a>
+<a name="3910"><span class="lineNum">    3910 </span>            :   ASMJIT_INST_3x(vporq, Vporq, X86Zmm, X86Zmm, X86Zmm)                        //      AVX512_F{kz|b64}</a>
+<a name="3911"><span class="lineNum">    3911 </span>            :   ASMJIT_INST_3x(vporq, Vporq, X86Zmm, X86Zmm, X86Mem)                        //      AVX512_F{kz|b64}</a>
+<a name="3912"><span class="lineNum">    3912 </span>            :   ASMJIT_INST_3i(vprold, Vprold, X86Xmm, X86Xmm, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3913"><span class="lineNum">    3913 </span>            :   ASMJIT_INST_3i(vprold, Vprold, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3914"><span class="lineNum">    3914 </span>            :   ASMJIT_INST_3i(vprold, Vprold, X86Ymm, X86Ymm, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3915"><span class="lineNum">    3915 </span>            :   ASMJIT_INST_3i(vprold, Vprold, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3916"><span class="lineNum">    3916 </span>            :   ASMJIT_INST_3i(vprold, Vprold, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="3917"><span class="lineNum">    3917 </span>            :   ASMJIT_INST_3i(vprold, Vprold, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="3918"><span class="lineNum">    3918 </span>            :   ASMJIT_INST_3i(vprolq, Vprolq, X86Xmm, X86Xmm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3919"><span class="lineNum">    3919 </span>            :   ASMJIT_INST_3i(vprolq, Vprolq, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3920"><span class="lineNum">    3920 </span>            :   ASMJIT_INST_3i(vprolq, Vprolq, X86Ymm, X86Ymm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3921"><span class="lineNum">    3921 </span>            :   ASMJIT_INST_3i(vprolq, Vprolq, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3922"><span class="lineNum">    3922 </span>            :   ASMJIT_INST_3i(vprolq, Vprolq, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="3923"><span class="lineNum">    3923 </span>            :   ASMJIT_INST_3i(vprolq, Vprolq, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="3924"><span class="lineNum">    3924 </span>            :   ASMJIT_INST_3x(vprolvd, Vprolvd, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3925"><span class="lineNum">    3925 </span>            :   ASMJIT_INST_3x(vprolvd, Vprolvd, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3926"><span class="lineNum">    3926 </span>            :   ASMJIT_INST_3x(vprolvd, Vprolvd, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3927"><span class="lineNum">    3927 </span>            :   ASMJIT_INST_3x(vprolvd, Vprolvd, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3928"><span class="lineNum">    3928 </span>            :   ASMJIT_INST_3x(vprolvd, Vprolvd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3929"><span class="lineNum">    3929 </span>            :   ASMJIT_INST_3x(vprolvd, Vprolvd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3930"><span class="lineNum">    3930 </span>            :   ASMJIT_INST_3x(vprolvq, Vprolvq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3931"><span class="lineNum">    3931 </span>            :   ASMJIT_INST_3x(vprolvq, Vprolvq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3932"><span class="lineNum">    3932 </span>            :   ASMJIT_INST_3x(vprolvq, Vprolvq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3933"><span class="lineNum">    3933 </span>            :   ASMJIT_INST_3x(vprolvq, Vprolvq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3934"><span class="lineNum">    3934 </span>            :   ASMJIT_INST_3x(vprolvq, Vprolvq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3935"><span class="lineNum">    3935 </span>            :   ASMJIT_INST_3x(vprolvq, Vprolvq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3936"><span class="lineNum">    3936 </span>            :   ASMJIT_INST_3i(vprord, Vprord, X86Xmm, X86Xmm, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3937"><span class="lineNum">    3937 </span>            :   ASMJIT_INST_3i(vprord, Vprord, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3938"><span class="lineNum">    3938 </span>            :   ASMJIT_INST_3i(vprord, Vprord, X86Ymm, X86Ymm, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3939"><span class="lineNum">    3939 </span>            :   ASMJIT_INST_3i(vprord, Vprord, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="3940"><span class="lineNum">    3940 </span>            :   ASMJIT_INST_3i(vprord, Vprord, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="3941"><span class="lineNum">    3941 </span>            :   ASMJIT_INST_3i(vprord, Vprord, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="3942"><span class="lineNum">    3942 </span>            :   ASMJIT_INST_3i(vprorq, Vprorq, X86Xmm, X86Xmm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3943"><span class="lineNum">    3943 </span>            :   ASMJIT_INST_3i(vprorq, Vprorq, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3944"><span class="lineNum">    3944 </span>            :   ASMJIT_INST_3i(vprorq, Vprorq, X86Ymm, X86Ymm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3945"><span class="lineNum">    3945 </span>            :   ASMJIT_INST_3i(vprorq, Vprorq, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="3946"><span class="lineNum">    3946 </span>            :   ASMJIT_INST_3i(vprorq, Vprorq, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="3947"><span class="lineNum">    3947 </span>            :   ASMJIT_INST_3i(vprorq, Vprorq, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="3948"><span class="lineNum">    3948 </span>            :   ASMJIT_INST_3x(vprorvd, Vprorvd, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3949"><span class="lineNum">    3949 </span>            :   ASMJIT_INST_3x(vprorvd, Vprorvd, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3950"><span class="lineNum">    3950 </span>            :   ASMJIT_INST_3x(vprorvd, Vprorvd, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3951"><span class="lineNum">    3951 </span>            :   ASMJIT_INST_3x(vprorvd, Vprorvd, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b32}-VL</a>
+<a name="3952"><span class="lineNum">    3952 </span>            :   ASMJIT_INST_3x(vprorvd, Vprorvd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="3953"><span class="lineNum">    3953 </span>            :   ASMJIT_INST_3x(vprorvd, Vprorvd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="3954"><span class="lineNum">    3954 </span>            :   ASMJIT_INST_3x(vprorvq, Vprorvq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3955"><span class="lineNum">    3955 </span>            :   ASMJIT_INST_3x(vprorvq, Vprorvq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3956"><span class="lineNum">    3956 </span>            :   ASMJIT_INST_3x(vprorvq, Vprorvq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3957"><span class="lineNum">    3957 </span>            :   ASMJIT_INST_3x(vprorvq, Vprorvq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="3958"><span class="lineNum">    3958 </span>            :   ASMJIT_INST_3x(vprorvq, Vprorvq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="3959"><span class="lineNum">    3959 </span>            :   ASMJIT_INST_3x(vprorvq, Vprorvq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="3960"><span class="lineNum">    3960 </span>            :   ASMJIT_INST_3x(vpsadbw, Vpsadbw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW-VL</a>
+<a name="3961"><span class="lineNum">    3961 </span>            :   ASMJIT_INST_3x(vpsadbw, Vpsadbw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW-VL</a>
+<a name="3962"><span class="lineNum">    3962 </span>            :   ASMJIT_INST_3x(vpsadbw, Vpsadbw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW-VL</a>
+<a name="3963"><span class="lineNum">    3963 </span>            :   ASMJIT_INST_3x(vpsadbw, Vpsadbw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW-VL</a>
+<a name="3964"><span class="lineNum">    3964 </span>            :   ASMJIT_INST_3x(vpsadbw, Vpsadbw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW</a>
+<a name="3965"><span class="lineNum">    3965 </span>            :   ASMJIT_INST_3x(vpsadbw, Vpsadbw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW</a>
+<a name="3966"><span class="lineNum">    3966 </span>            :   ASMJIT_INST_2x(vpscatterdd, Vpscatterdd, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="3967"><span class="lineNum">    3967 </span>            :   ASMJIT_INST_2x(vpscatterdd, Vpscatterdd, X86Mem, X86Ymm)                    //      AVX512_F{k}-VL</a>
+<a name="3968"><span class="lineNum">    3968 </span>            :   ASMJIT_INST_2x(vpscatterdd, Vpscatterdd, X86Mem, X86Zmm)                    //      AVX512_F{k}</a>
+<a name="3969"><span class="lineNum">    3969 </span>            :   ASMJIT_INST_2x(vpscatterdq, Vpscatterdq, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="3970"><span class="lineNum">    3970 </span>            :   ASMJIT_INST_2x(vpscatterdq, Vpscatterdq, X86Mem, X86Ymm)                    //      AVX512_F{k}-VL</a>
+<a name="3971"><span class="lineNum">    3971 </span>            :   ASMJIT_INST_2x(vpscatterdq, Vpscatterdq, X86Mem, X86Zmm)                    //      AVX512_F{k}</a>
+<a name="3972"><span class="lineNum">    3972 </span>            :   ASMJIT_INST_2x(vpscatterqd, Vpscatterqd, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="3973"><span class="lineNum">    3973 </span>            :   ASMJIT_INST_2x(vpscatterqd, Vpscatterqd, X86Mem, X86Ymm)                    //      AVX512_F{k}</a>
+<a name="3974"><span class="lineNum">    3974 </span>            :   ASMJIT_INST_2x(vpscatterqq, Vpscatterqq, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="3975"><span class="lineNum">    3975 </span>            :   ASMJIT_INST_2x(vpscatterqq, Vpscatterqq, X86Mem, X86Ymm)                    //      AVX512_F{k}-VL</a>
+<a name="3976"><span class="lineNum">    3976 </span>            :   ASMJIT_INST_2x(vpscatterqq, Vpscatterqq, X86Mem, X86Zmm)                    //      AVX512_F{k}</a>
+<a name="3977"><span class="lineNum">    3977 </span>            :   ASMJIT_INST_3x(vpshufb, Vpshufb, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3978"><span class="lineNum">    3978 </span>            :   ASMJIT_INST_3x(vpshufb, Vpshufb, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="3979"><span class="lineNum">    3979 </span>            :   ASMJIT_INST_3x(vpshufb, Vpshufb, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3980"><span class="lineNum">    3980 </span>            :   ASMJIT_INST_3x(vpshufb, Vpshufb, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3981"><span class="lineNum">    3981 </span>            :   ASMJIT_INST_3x(vpshufb, Vpshufb, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="3982"><span class="lineNum">    3982 </span>            :   ASMJIT_INST_3x(vpshufb, Vpshufb, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="3983"><span class="lineNum">    3983 </span>            :   ASMJIT_INST_3i(vpshufd, Vpshufd, X86Xmm, X86Xmm, Imm)                       // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3984"><span class="lineNum">    3984 </span>            :   ASMJIT_INST_3i(vpshufd, Vpshufd, X86Xmm, X86Mem, Imm)                       // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="3985"><span class="lineNum">    3985 </span>            :   ASMJIT_INST_3i(vpshufd, Vpshufd, X86Ymm, X86Ymm, Imm)                       // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3986"><span class="lineNum">    3986 </span>            :   ASMJIT_INST_3i(vpshufd, Vpshufd, X86Ymm, X86Mem, Imm)                       // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="3987"><span class="lineNum">    3987 </span>            :   ASMJIT_INST_3i(vpshufd, Vpshufd, X86Zmm, X86Zmm, Imm)                       //      AVX512_F{kz|b32}</a>
+<a name="3988"><span class="lineNum">    3988 </span>            :   ASMJIT_INST_3i(vpshufd, Vpshufd, X86Zmm, X86Mem, Imm)                       //      AVX512_F{kz|b32}</a>
+<a name="3989"><span class="lineNum">    3989 </span>            :   ASMJIT_INST_3i(vpshufhw, Vpshufhw, X86Xmm, X86Xmm, Imm)                     // AVX  AVX512_BW{kz}-VL</a>
+<a name="3990"><span class="lineNum">    3990 </span>            :   ASMJIT_INST_3i(vpshufhw, Vpshufhw, X86Xmm, X86Mem, Imm)                     // AVX  AVX512_BW{kz}-VL</a>
+<a name="3991"><span class="lineNum">    3991 </span>            :   ASMJIT_INST_3i(vpshufhw, Vpshufhw, X86Ymm, X86Ymm, Imm)                     // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3992"><span class="lineNum">    3992 </span>            :   ASMJIT_INST_3i(vpshufhw, Vpshufhw, X86Ymm, X86Mem, Imm)                     // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3993"><span class="lineNum">    3993 </span>            :   ASMJIT_INST_3i(vpshufhw, Vpshufhw, X86Zmm, X86Zmm, Imm)                     //      AVX512_BW{kz}</a>
+<a name="3994"><span class="lineNum">    3994 </span>            :   ASMJIT_INST_3i(vpshufhw, Vpshufhw, X86Zmm, X86Mem, Imm)                     //      AVX512_BW{kz}</a>
+<a name="3995"><span class="lineNum">    3995 </span>            :   ASMJIT_INST_3i(vpshuflw, Vpshuflw, X86Xmm, X86Xmm, Imm)                     // AVX  AVX512_BW{kz}-VL</a>
+<a name="3996"><span class="lineNum">    3996 </span>            :   ASMJIT_INST_3i(vpshuflw, Vpshuflw, X86Xmm, X86Mem, Imm)                     // AVX  AVX512_BW{kz}-VL</a>
+<a name="3997"><span class="lineNum">    3997 </span>            :   ASMJIT_INST_3i(vpshuflw, Vpshuflw, X86Ymm, X86Ymm, Imm)                     // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3998"><span class="lineNum">    3998 </span>            :   ASMJIT_INST_3i(vpshuflw, Vpshuflw, X86Ymm, X86Mem, Imm)                     // AVX2 AVX512_BW{kz}-VL</a>
+<a name="3999"><span class="lineNum">    3999 </span>            :   ASMJIT_INST_3i(vpshuflw, Vpshuflw, X86Zmm, X86Zmm, Imm)                     //      AVX512_BW{kz}</a>
+<a name="4000"><span class="lineNum">    4000 </span>            :   ASMJIT_INST_3i(vpshuflw, Vpshuflw, X86Zmm, X86Mem, Imm)                     //      AVX512_BW{kz}</a>
+<a name="4001"><span class="lineNum">    4001 </span>            :   ASMJIT_INST_3x(vpsignb, Vpsignb, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="4002"><span class="lineNum">    4002 </span>            :   ASMJIT_INST_3x(vpsignb, Vpsignb, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="4003"><span class="lineNum">    4003 </span>            :   ASMJIT_INST_3x(vpsignb, Vpsignb, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="4004"><span class="lineNum">    4004 </span>            :   ASMJIT_INST_3x(vpsignb, Vpsignb, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="4005"><span class="lineNum">    4005 </span>            :   ASMJIT_INST_3x(vpsignd, Vpsignd, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="4006"><span class="lineNum">    4006 </span>            :   ASMJIT_INST_3x(vpsignd, Vpsignd, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="4007"><span class="lineNum">    4007 </span>            :   ASMJIT_INST_3x(vpsignd, Vpsignd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="4008"><span class="lineNum">    4008 </span>            :   ASMJIT_INST_3x(vpsignd, Vpsignd, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="4009"><span class="lineNum">    4009 </span>            :   ASMJIT_INST_3x(vpsignw, Vpsignw, X86Xmm, X86Xmm, X86Xmm)                    // AVX</a>
+<a name="4010"><span class="lineNum">    4010 </span>            :   ASMJIT_INST_3x(vpsignw, Vpsignw, X86Xmm, X86Xmm, X86Mem)                    // AVX</a>
+<a name="4011"><span class="lineNum">    4011 </span>            :   ASMJIT_INST_3x(vpsignw, Vpsignw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2</a>
+<a name="4012"><span class="lineNum">    4012 </span>            :   ASMJIT_INST_3x(vpsignw, Vpsignw, X86Ymm, X86Ymm, X86Mem)                    // AVX2</a>
+<a name="4013"><span class="lineNum">    4013 </span>            :   ASMJIT_INST_3i(vpslld, Vpslld, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4014"><span class="lineNum">    4014 </span>            :   ASMJIT_INST_3x(vpslld, Vpslld, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4015"><span class="lineNum">    4015 </span>            :   ASMJIT_INST_3x(vpslld, Vpslld, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4016"><span class="lineNum">    4016 </span>            :   ASMJIT_INST_3i(vpslld, Vpslld, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4017"><span class="lineNum">    4017 </span>            :   ASMJIT_INST_3x(vpslld, Vpslld, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4018"><span class="lineNum">    4018 </span>            :   ASMJIT_INST_3x(vpslld, Vpslld, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4019"><span class="lineNum">    4019 </span>            :   ASMJIT_INST_3i(vpslld, Vpslld, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="4020"><span class="lineNum">    4020 </span>            :   ASMJIT_INST_3i(vpslld, Vpslld, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="4021"><span class="lineNum">    4021 </span>            :   ASMJIT_INST_3x(vpslld, Vpslld, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_F{kz}</a>
+<a name="4022"><span class="lineNum">    4022 </span>            :   ASMJIT_INST_3x(vpslld, Vpslld, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz}</a>
+<a name="4023"><span class="lineNum">    4023 </span>            :   ASMJIT_INST_3i(vpslld, Vpslld, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="4024"><span class="lineNum">    4024 </span>            :   ASMJIT_INST_3i(vpslld, Vpslld, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="4025"><span class="lineNum">    4025 </span>            :   ASMJIT_INST_3i(vpslldq, Vpslldq, X86Xmm, X86Xmm, Imm)                       // AVX  AVX512_BW-VL</a>
+<a name="4026"><span class="lineNum">    4026 </span>            :   ASMJIT_INST_3i(vpslldq, Vpslldq, X86Ymm, X86Ymm, Imm)                       // AVX2 AVX512_BW-VL</a>
+<a name="4027"><span class="lineNum">    4027 </span>            :   ASMJIT_INST_3i(vpslldq, Vpslldq, X86Xmm, X86Mem, Imm)                       //      AVX512_BW-VL</a>
+<a name="4028"><span class="lineNum">    4028 </span>            :   ASMJIT_INST_3i(vpslldq, Vpslldq, X86Ymm, X86Mem, Imm)                       //      AVX512_BW-VL</a>
+<a name="4029"><span class="lineNum">    4029 </span>            :   ASMJIT_INST_3i(vpslldq, Vpslldq, X86Zmm, X86Zmm, Imm)                       //      AVX512_BW</a>
+<a name="4030"><span class="lineNum">    4030 </span>            :   ASMJIT_INST_3i(vpslldq, Vpslldq, X86Zmm, X86Mem, Imm)                       //      AVX512_BW</a>
+<a name="4031"><span class="lineNum">    4031 </span>            :   ASMJIT_INST_3i(vpsllq, Vpsllq, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4032"><span class="lineNum">    4032 </span>            :   ASMJIT_INST_3x(vpsllq, Vpsllq, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4033"><span class="lineNum">    4033 </span>            :   ASMJIT_INST_3x(vpsllq, Vpsllq, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4034"><span class="lineNum">    4034 </span>            :   ASMJIT_INST_3i(vpsllq, Vpsllq, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4035"><span class="lineNum">    4035 </span>            :   ASMJIT_INST_3x(vpsllq, Vpsllq, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4036"><span class="lineNum">    4036 </span>            :   ASMJIT_INST_3x(vpsllq, Vpsllq, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4037"><span class="lineNum">    4037 </span>            :   ASMJIT_INST_3i(vpsllq, Vpsllq, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4038"><span class="lineNum">    4038 </span>            :   ASMJIT_INST_3i(vpsllq, Vpsllq, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4039"><span class="lineNum">    4039 </span>            :   ASMJIT_INST_3x(vpsllq, Vpsllq, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_F{kz}</a>
+<a name="4040"><span class="lineNum">    4040 </span>            :   ASMJIT_INST_3x(vpsllq, Vpsllq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz}</a>
+<a name="4041"><span class="lineNum">    4041 </span>            :   ASMJIT_INST_3i(vpsllq, Vpsllq, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="4042"><span class="lineNum">    4042 </span>            :   ASMJIT_INST_3i(vpsllq, Vpsllq, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="4043"><span class="lineNum">    4043 </span>            :   ASMJIT_INST_3x(vpsllvd, Vpsllvd, X86Xmm, X86Xmm, X86Xmm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4044"><span class="lineNum">    4044 </span>            :   ASMJIT_INST_3x(vpsllvd, Vpsllvd, X86Xmm, X86Xmm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4045"><span class="lineNum">    4045 </span>            :   ASMJIT_INST_3x(vpsllvd, Vpsllvd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4046"><span class="lineNum">    4046 </span>            :   ASMJIT_INST_3x(vpsllvd, Vpsllvd, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4047"><span class="lineNum">    4047 </span>            :   ASMJIT_INST_3x(vpsllvd, Vpsllvd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="4048"><span class="lineNum">    4048 </span>            :   ASMJIT_INST_3x(vpsllvd, Vpsllvd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="4049"><span class="lineNum">    4049 </span>            :   ASMJIT_INST_3x(vpsllvq, Vpsllvq, X86Xmm, X86Xmm, X86Xmm)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4050"><span class="lineNum">    4050 </span>            :   ASMJIT_INST_3x(vpsllvq, Vpsllvq, X86Xmm, X86Xmm, X86Mem)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4051"><span class="lineNum">    4051 </span>            :   ASMJIT_INST_3x(vpsllvq, Vpsllvq, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4052"><span class="lineNum">    4052 </span>            :   ASMJIT_INST_3x(vpsllvq, Vpsllvq, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4053"><span class="lineNum">    4053 </span>            :   ASMJIT_INST_3x(vpsllvq, Vpsllvq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="4054"><span class="lineNum">    4054 </span>            :   ASMJIT_INST_3x(vpsllvq, Vpsllvq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="4055"><span class="lineNum">    4055 </span>            :   ASMJIT_INST_3x(vpsllvw, Vpsllvw, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_BW{kz}-VL</a>
+<a name="4056"><span class="lineNum">    4056 </span>            :   ASMJIT_INST_3x(vpsllvw, Vpsllvw, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_BW{kz}-VL</a>
+<a name="4057"><span class="lineNum">    4057 </span>            :   ASMJIT_INST_3x(vpsllvw, Vpsllvw, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_BW{kz}-VL</a>
+<a name="4058"><span class="lineNum">    4058 </span>            :   ASMJIT_INST_3x(vpsllvw, Vpsllvw, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_BW{kz}-VL</a>
+<a name="4059"><span class="lineNum">    4059 </span>            :   ASMJIT_INST_3x(vpsllvw, Vpsllvw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="4060"><span class="lineNum">    4060 </span>            :   ASMJIT_INST_3x(vpsllvw, Vpsllvw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="4061"><span class="lineNum">    4061 </span>            :   ASMJIT_INST_3i(vpsllw, Vpsllw, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_BW{kz}-VL</a>
+<a name="4062"><span class="lineNum">    4062 </span>            :   ASMJIT_INST_3x(vpsllw, Vpsllw, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4063"><span class="lineNum">    4063 </span>            :   ASMJIT_INST_3x(vpsllw, Vpsllw, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4064"><span class="lineNum">    4064 </span>            :   ASMJIT_INST_3i(vpsllw, Vpsllw, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4065"><span class="lineNum">    4065 </span>            :   ASMJIT_INST_3x(vpsllw, Vpsllw, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4066"><span class="lineNum">    4066 </span>            :   ASMJIT_INST_3x(vpsllw, Vpsllw, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4067"><span class="lineNum">    4067 </span>            :   ASMJIT_INST_3i(vpsllw, Vpsllw, X86Xmm, X86Mem, Imm)                         //      AVX512_BW{kz}-VL</a>
+<a name="4068"><span class="lineNum">    4068 </span>            :   ASMJIT_INST_3i(vpsllw, Vpsllw, X86Ymm, X86Mem, Imm)                         //      AVX512_BW{kz}-VL</a>
+<a name="4069"><span class="lineNum">    4069 </span>            :   ASMJIT_INST_3x(vpsllw, Vpsllw, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_BW{kz}</a>
+<a name="4070"><span class="lineNum">    4070 </span>            :   ASMJIT_INST_3x(vpsllw, Vpsllw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="4071"><span class="lineNum">    4071 </span>            :   ASMJIT_INST_3i(vpsllw, Vpsllw, X86Zmm, X86Zmm, Imm)                         //      AVX512_BW{kz}</a>
+<a name="4072"><span class="lineNum">    4072 </span>            :   ASMJIT_INST_3i(vpsllw, Vpsllw, X86Zmm, X86Mem, Imm)                         //      AVX512_BW{kz}</a>
+<a name="4073"><span class="lineNum">    4073 </span>            :   ASMJIT_INST_3i(vpsrad, Vpsrad, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4074"><span class="lineNum">    4074 </span>            :   ASMJIT_INST_3x(vpsrad, Vpsrad, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4075"><span class="lineNum">    4075 </span>            :   ASMJIT_INST_3x(vpsrad, Vpsrad, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4076"><span class="lineNum">    4076 </span>            :   ASMJIT_INST_3i(vpsrad, Vpsrad, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4077"><span class="lineNum">    4077 </span>            :   ASMJIT_INST_3x(vpsrad, Vpsrad, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4078"><span class="lineNum">    4078 </span>            :   ASMJIT_INST_3x(vpsrad, Vpsrad, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4079"><span class="lineNum">    4079 </span>            :   ASMJIT_INST_3i(vpsrad, Vpsrad, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="4080"><span class="lineNum">    4080 </span>            :   ASMJIT_INST_3i(vpsrad, Vpsrad, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="4081"><span class="lineNum">    4081 </span>            :   ASMJIT_INST_3x(vpsrad, Vpsrad, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_F{kz}</a>
+<a name="4082"><span class="lineNum">    4082 </span>            :   ASMJIT_INST_3x(vpsrad, Vpsrad, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz}</a>
+<a name="4083"><span class="lineNum">    4083 </span>            :   ASMJIT_INST_3i(vpsrad, Vpsrad, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="4084"><span class="lineNum">    4084 </span>            :   ASMJIT_INST_3i(vpsrad, Vpsrad, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="4085"><span class="lineNum">    4085 </span>            :   ASMJIT_INST_3x(vpsraq, Vpsraq, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_F{kz}-VL</a>
+<a name="4086"><span class="lineNum">    4086 </span>            :   ASMJIT_INST_3x(vpsraq, Vpsraq, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_F{kz}-VL</a>
+<a name="4087"><span class="lineNum">    4087 </span>            :   ASMJIT_INST_3i(vpsraq, Vpsraq, X86Xmm, X86Xmm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4088"><span class="lineNum">    4088 </span>            :   ASMJIT_INST_3i(vpsraq, Vpsraq, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4089"><span class="lineNum">    4089 </span>            :   ASMJIT_INST_3x(vpsraq, Vpsraq, X86Ymm, X86Ymm, X86Xmm)                      //      AVX512_F{kz}-VL</a>
+<a name="4090"><span class="lineNum">    4090 </span>            :   ASMJIT_INST_3x(vpsraq, Vpsraq, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_F{kz}-VL</a>
+<a name="4091"><span class="lineNum">    4091 </span>            :   ASMJIT_INST_3i(vpsraq, Vpsraq, X86Ymm, X86Ymm, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4092"><span class="lineNum">    4092 </span>            :   ASMJIT_INST_3i(vpsraq, Vpsraq, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4093"><span class="lineNum">    4093 </span>            :   ASMJIT_INST_3x(vpsraq, Vpsraq, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_F{kz}</a>
+<a name="4094"><span class="lineNum">    4094 </span>            :   ASMJIT_INST_3x(vpsraq, Vpsraq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz}</a>
+<a name="4095"><span class="lineNum">    4095 </span>            :   ASMJIT_INST_3i(vpsraq, Vpsraq, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="4096"><span class="lineNum">    4096 </span>            :   ASMJIT_INST_3i(vpsraq, Vpsraq, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="4097"><span class="lineNum">    4097 </span>            :   ASMJIT_INST_3x(vpsravd, Vpsravd, X86Xmm, X86Xmm, X86Xmm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4098"><span class="lineNum">    4098 </span>            :   ASMJIT_INST_3x(vpsravd, Vpsravd, X86Xmm, X86Xmm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4099"><span class="lineNum">    4099 </span>            :   ASMJIT_INST_3x(vpsravd, Vpsravd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4100"><span class="lineNum">    4100 </span>            :   ASMJIT_INST_3x(vpsravd, Vpsravd, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4101"><span class="lineNum">    4101 </span>            :   ASMJIT_INST_3x(vpsravd, Vpsravd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="4102"><span class="lineNum">    4102 </span>            :   ASMJIT_INST_3x(vpsravd, Vpsravd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="4103"><span class="lineNum">    4103 </span>            :   ASMJIT_INST_3x(vpsravq, Vpsravq, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="4104"><span class="lineNum">    4104 </span>            :   ASMJIT_INST_3x(vpsravq, Vpsravq, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="4105"><span class="lineNum">    4105 </span>            :   ASMJIT_INST_3x(vpsravq, Vpsravq, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="4106"><span class="lineNum">    4106 </span>            :   ASMJIT_INST_3x(vpsravq, Vpsravq, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_F{kz|b64}-VL</a>
+<a name="4107"><span class="lineNum">    4107 </span>            :   ASMJIT_INST_3x(vpsravq, Vpsravq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="4108"><span class="lineNum">    4108 </span>            :   ASMJIT_INST_3x(vpsravq, Vpsravq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="4109"><span class="lineNum">    4109 </span>            :   ASMJIT_INST_3x(vpsravw, Vpsravw, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_BW{kz}-VL</a>
+<a name="4110"><span class="lineNum">    4110 </span>            :   ASMJIT_INST_3x(vpsravw, Vpsravw, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_BW{kz}-VL</a>
+<a name="4111"><span class="lineNum">    4111 </span>            :   ASMJIT_INST_3x(vpsravw, Vpsravw, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_BW{kz}-VL</a>
+<a name="4112"><span class="lineNum">    4112 </span>            :   ASMJIT_INST_3x(vpsravw, Vpsravw, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_BW{kz}-VL</a>
+<a name="4113"><span class="lineNum">    4113 </span>            :   ASMJIT_INST_3x(vpsravw, Vpsravw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="4114"><span class="lineNum">    4114 </span>            :   ASMJIT_INST_3x(vpsravw, Vpsravw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="4115"><span class="lineNum">    4115 </span>            :   ASMJIT_INST_3i(vpsraw, Vpsraw, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_BW{kz}-VL</a>
+<a name="4116"><span class="lineNum">    4116 </span>            :   ASMJIT_INST_3x(vpsraw, Vpsraw, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4117"><span class="lineNum">    4117 </span>            :   ASMJIT_INST_3x(vpsraw, Vpsraw, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4118"><span class="lineNum">    4118 </span>            :   ASMJIT_INST_3i(vpsraw, Vpsraw, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4119"><span class="lineNum">    4119 </span>            :   ASMJIT_INST_3x(vpsraw, Vpsraw, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4120"><span class="lineNum">    4120 </span>            :   ASMJIT_INST_3x(vpsraw, Vpsraw, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4121"><span class="lineNum">    4121 </span>            :   ASMJIT_INST_3i(vpsraw, Vpsraw, X86Xmm, X86Mem, Imm)                         //      AVX512_BW{kz}-VL</a>
+<a name="4122"><span class="lineNum">    4122 </span>            :   ASMJIT_INST_3i(vpsraw, Vpsraw, X86Ymm, X86Mem, Imm)                         //      AVX512_BW{kz}-VL</a>
+<a name="4123"><span class="lineNum">    4123 </span>            :   ASMJIT_INST_3x(vpsraw, Vpsraw, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_BW{kz}</a>
+<a name="4124"><span class="lineNum">    4124 </span>            :   ASMJIT_INST_3x(vpsraw, Vpsraw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="4125"><span class="lineNum">    4125 </span>            :   ASMJIT_INST_3i(vpsraw, Vpsraw, X86Zmm, X86Zmm, Imm)                         //      AVX512_BW{kz}</a>
+<a name="4126"><span class="lineNum">    4126 </span>            :   ASMJIT_INST_3i(vpsraw, Vpsraw, X86Zmm, X86Mem, Imm)                         //      AVX512_BW{kz}</a>
+<a name="4127"><span class="lineNum">    4127 </span>            :   ASMJIT_INST_3i(vpsrld, Vpsrld, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4128"><span class="lineNum">    4128 </span>            :   ASMJIT_INST_3x(vpsrld, Vpsrld, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4129"><span class="lineNum">    4129 </span>            :   ASMJIT_INST_3x(vpsrld, Vpsrld, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4130"><span class="lineNum">    4130 </span>            :   ASMJIT_INST_3i(vpsrld, Vpsrld, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4131"><span class="lineNum">    4131 </span>            :   ASMJIT_INST_3x(vpsrld, Vpsrld, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4132"><span class="lineNum">    4132 </span>            :   ASMJIT_INST_3x(vpsrld, Vpsrld, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4133"><span class="lineNum">    4133 </span>            :   ASMJIT_INST_3i(vpsrld, Vpsrld, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="4134"><span class="lineNum">    4134 </span>            :   ASMJIT_INST_3i(vpsrld, Vpsrld, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b32}-VL</a>
+<a name="4135"><span class="lineNum">    4135 </span>            :   ASMJIT_INST_3x(vpsrld, Vpsrld, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_F{kz}</a>
+<a name="4136"><span class="lineNum">    4136 </span>            :   ASMJIT_INST_3x(vpsrld, Vpsrld, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz}</a>
+<a name="4137"><span class="lineNum">    4137 </span>            :   ASMJIT_INST_3i(vpsrld, Vpsrld, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="4138"><span class="lineNum">    4138 </span>            :   ASMJIT_INST_3i(vpsrld, Vpsrld, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b32}</a>
+<a name="4139"><span class="lineNum">    4139 </span>            :   ASMJIT_INST_3i(vpsrldq, Vpsrldq, X86Xmm, X86Xmm, Imm)                       // AVX  AVX512_BW-VL</a>
+<a name="4140"><span class="lineNum">    4140 </span>            :   ASMJIT_INST_3i(vpsrldq, Vpsrldq, X86Ymm, X86Ymm, Imm)                       // AVX2 AVX512_BW-VL</a>
+<a name="4141"><span class="lineNum">    4141 </span>            :   ASMJIT_INST_3i(vpsrldq, Vpsrldq, X86Xmm, X86Mem, Imm)                       //      AVX512_BW-VL</a>
+<a name="4142"><span class="lineNum">    4142 </span>            :   ASMJIT_INST_3i(vpsrldq, Vpsrldq, X86Ymm, X86Mem, Imm)                       //      AVX512_BW-VL</a>
+<a name="4143"><span class="lineNum">    4143 </span>            :   ASMJIT_INST_3i(vpsrldq, Vpsrldq, X86Zmm, X86Zmm, Imm)                       //      AVX512_BW</a>
+<a name="4144"><span class="lineNum">    4144 </span>            :   ASMJIT_INST_3i(vpsrldq, Vpsrldq, X86Zmm, X86Mem, Imm)                       //      AVX512_BW</a>
+<a name="4145"><span class="lineNum">    4145 </span>            :   ASMJIT_INST_3i(vpsrlq, Vpsrlq, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4146"><span class="lineNum">    4146 </span>            :   ASMJIT_INST_3x(vpsrlq, Vpsrlq, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4147"><span class="lineNum">    4147 </span>            :   ASMJIT_INST_3x(vpsrlq, Vpsrlq, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz}-VL</a>
+<a name="4148"><span class="lineNum">    4148 </span>            :   ASMJIT_INST_3i(vpsrlq, Vpsrlq, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4149"><span class="lineNum">    4149 </span>            :   ASMJIT_INST_3x(vpsrlq, Vpsrlq, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4150"><span class="lineNum">    4150 </span>            :   ASMJIT_INST_3x(vpsrlq, Vpsrlq, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz}-VL</a>
+<a name="4151"><span class="lineNum">    4151 </span>            :   ASMJIT_INST_3i(vpsrlq, Vpsrlq, X86Xmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4152"><span class="lineNum">    4152 </span>            :   ASMJIT_INST_3i(vpsrlq, Vpsrlq, X86Ymm, X86Mem, Imm)                         //      AVX512_F{kz|b64}-VL</a>
+<a name="4153"><span class="lineNum">    4153 </span>            :   ASMJIT_INST_3x(vpsrlq, Vpsrlq, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_F{kz}</a>
+<a name="4154"><span class="lineNum">    4154 </span>            :   ASMJIT_INST_3x(vpsrlq, Vpsrlq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz}</a>
+<a name="4155"><span class="lineNum">    4155 </span>            :   ASMJIT_INST_3i(vpsrlq, Vpsrlq, X86Zmm, X86Zmm, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="4156"><span class="lineNum">    4156 </span>            :   ASMJIT_INST_3i(vpsrlq, Vpsrlq, X86Zmm, X86Mem, Imm)                         //      AVX512_F{kz|b64}</a>
+<a name="4157"><span class="lineNum">    4157 </span>            :   ASMJIT_INST_3x(vpsrlvd, Vpsrlvd, X86Xmm, X86Xmm, X86Xmm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4158"><span class="lineNum">    4158 </span>            :   ASMJIT_INST_3x(vpsrlvd, Vpsrlvd, X86Xmm, X86Xmm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4159"><span class="lineNum">    4159 </span>            :   ASMJIT_INST_3x(vpsrlvd, Vpsrlvd, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4160"><span class="lineNum">    4160 </span>            :   ASMJIT_INST_3x(vpsrlvd, Vpsrlvd, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4161"><span class="lineNum">    4161 </span>            :   ASMJIT_INST_3x(vpsrlvd, Vpsrlvd, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b32}</a>
+<a name="4162"><span class="lineNum">    4162 </span>            :   ASMJIT_INST_3x(vpsrlvd, Vpsrlvd, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b32}</a>
+<a name="4163"><span class="lineNum">    4163 </span>            :   ASMJIT_INST_3x(vpsrlvq, Vpsrlvq, X86Xmm, X86Xmm, X86Xmm)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4164"><span class="lineNum">    4164 </span>            :   ASMJIT_INST_3x(vpsrlvq, Vpsrlvq, X86Xmm, X86Xmm, X86Mem)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4165"><span class="lineNum">    4165 </span>            :   ASMJIT_INST_3x(vpsrlvq, Vpsrlvq, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4166"><span class="lineNum">    4166 </span>            :   ASMJIT_INST_3x(vpsrlvq, Vpsrlvq, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4167"><span class="lineNum">    4167 </span>            :   ASMJIT_INST_3x(vpsrlvq, Vpsrlvq, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_F{kz|b64}</a>
+<a name="4168"><span class="lineNum">    4168 </span>            :   ASMJIT_INST_3x(vpsrlvq, Vpsrlvq, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_F{kz|b64}</a>
+<a name="4169"><span class="lineNum">    4169 </span>            :   ASMJIT_INST_3x(vpsrlvw, Vpsrlvw, X86Xmm, X86Xmm, X86Xmm)                    //      AVX512_BW{kz}-VL</a>
+<a name="4170"><span class="lineNum">    4170 </span>            :   ASMJIT_INST_3x(vpsrlvw, Vpsrlvw, X86Xmm, X86Xmm, X86Mem)                    //      AVX512_BW{kz}-VL</a>
+<a name="4171"><span class="lineNum">    4171 </span>            :   ASMJIT_INST_3x(vpsrlvw, Vpsrlvw, X86Ymm, X86Ymm, X86Ymm)                    //      AVX512_BW{kz}-VL</a>
+<a name="4172"><span class="lineNum">    4172 </span>            :   ASMJIT_INST_3x(vpsrlvw, Vpsrlvw, X86Ymm, X86Ymm, X86Mem)                    //      AVX512_BW{kz}-VL</a>
+<a name="4173"><span class="lineNum">    4173 </span>            :   ASMJIT_INST_3x(vpsrlvw, Vpsrlvw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="4174"><span class="lineNum">    4174 </span>            :   ASMJIT_INST_3x(vpsrlvw, Vpsrlvw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="4175"><span class="lineNum">    4175 </span>            :   ASMJIT_INST_3i(vpsrlw, Vpsrlw, X86Xmm, X86Xmm, Imm)                         // AVX  AVX512_BW{kz}-VL</a>
+<a name="4176"><span class="lineNum">    4176 </span>            :   ASMJIT_INST_3x(vpsrlw, Vpsrlw, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4177"><span class="lineNum">    4177 </span>            :   ASMJIT_INST_3x(vpsrlw, Vpsrlw, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4178"><span class="lineNum">    4178 </span>            :   ASMJIT_INST_3i(vpsrlw, Vpsrlw, X86Ymm, X86Ymm, Imm)                         // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4179"><span class="lineNum">    4179 </span>            :   ASMJIT_INST_3x(vpsrlw, Vpsrlw, X86Ymm, X86Ymm, X86Xmm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4180"><span class="lineNum">    4180 </span>            :   ASMJIT_INST_3x(vpsrlw, Vpsrlw, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4181"><span class="lineNum">    4181 </span>            :   ASMJIT_INST_3i(vpsrlw, Vpsrlw, X86Xmm, X86Mem, Imm)                         //      AVX512_BW{kz}-VL</a>
+<a name="4182"><span class="lineNum">    4182 </span>            :   ASMJIT_INST_3i(vpsrlw, Vpsrlw, X86Ymm, X86Mem, Imm)                         //      AVX512_BW{kz}-VL</a>
+<a name="4183"><span class="lineNum">    4183 </span>            :   ASMJIT_INST_3x(vpsrlw, Vpsrlw, X86Zmm, X86Zmm, X86Xmm)                      //      AVX512_BW{kz}</a>
+<a name="4184"><span class="lineNum">    4184 </span>            :   ASMJIT_INST_3x(vpsrlw, Vpsrlw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="4185"><span class="lineNum">    4185 </span>            :   ASMJIT_INST_3i(vpsrlw, Vpsrlw, X86Zmm, X86Zmm, Imm)                         //      AVX512_BW{kz}</a>
+<a name="4186"><span class="lineNum">    4186 </span>            :   ASMJIT_INST_3i(vpsrlw, Vpsrlw, X86Zmm, X86Mem, Imm)                         //      AVX512_BW{kz}</a>
+<a name="4187"><span class="lineNum">    4187 </span>            :   ASMJIT_INST_3x(vpsubb, Vpsubb, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4188"><span class="lineNum">    4188 </span>            :   ASMJIT_INST_3x(vpsubb, Vpsubb, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4189"><span class="lineNum">    4189 </span>            :   ASMJIT_INST_3x(vpsubb, Vpsubb, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4190"><span class="lineNum">    4190 </span>            :   ASMJIT_INST_3x(vpsubb, Vpsubb, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4191"><span class="lineNum">    4191 </span>            :   ASMJIT_INST_3x(vpsubb, Vpsubb, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="4192"><span class="lineNum">    4192 </span>            :   ASMJIT_INST_3x(vpsubb, Vpsubb, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="4193"><span class="lineNum">    4193 </span>            :   ASMJIT_INST_3x(vpsubd, Vpsubd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4194"><span class="lineNum">    4194 </span>            :   ASMJIT_INST_3x(vpsubd, Vpsubd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4195"><span class="lineNum">    4195 </span>            :   ASMJIT_INST_3x(vpsubd, Vpsubd, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4196"><span class="lineNum">    4196 </span>            :   ASMJIT_INST_3x(vpsubd, Vpsubd, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4197"><span class="lineNum">    4197 </span>            :   ASMJIT_INST_3x(vpsubd, Vpsubd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b32}</a>
+<a name="4198"><span class="lineNum">    4198 </span>            :   ASMJIT_INST_3x(vpsubd, Vpsubd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}</a>
+<a name="4199"><span class="lineNum">    4199 </span>            :   ASMJIT_INST_3x(vpsubq, Vpsubq, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4200"><span class="lineNum">    4200 </span>            :   ASMJIT_INST_3x(vpsubq, Vpsubq, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4201"><span class="lineNum">    4201 </span>            :   ASMJIT_INST_3x(vpsubq, Vpsubq, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4202"><span class="lineNum">    4202 </span>            :   ASMJIT_INST_3x(vpsubq, Vpsubq, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4203"><span class="lineNum">    4203 </span>            :   ASMJIT_INST_3x(vpsubq, Vpsubq, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b64}</a>
+<a name="4204"><span class="lineNum">    4204 </span>            :   ASMJIT_INST_3x(vpsubq, Vpsubq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b64}</a>
+<a name="4205"><span class="lineNum">    4205 </span>            :   ASMJIT_INST_3x(vpsubsb, Vpsubsb, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="4206"><span class="lineNum">    4206 </span>            :   ASMJIT_INST_3x(vpsubsb, Vpsubsb, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="4207"><span class="lineNum">    4207 </span>            :   ASMJIT_INST_3x(vpsubsb, Vpsubsb, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4208"><span class="lineNum">    4208 </span>            :   ASMJIT_INST_3x(vpsubsb, Vpsubsb, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4209"><span class="lineNum">    4209 </span>            :   ASMJIT_INST_3x(vpsubsb, Vpsubsb, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="4210"><span class="lineNum">    4210 </span>            :   ASMJIT_INST_3x(vpsubsb, Vpsubsb, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="4211"><span class="lineNum">    4211 </span>            :   ASMJIT_INST_3x(vpsubsw, Vpsubsw, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="4212"><span class="lineNum">    4212 </span>            :   ASMJIT_INST_3x(vpsubsw, Vpsubsw, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_BW{kz}-VL</a>
+<a name="4213"><span class="lineNum">    4213 </span>            :   ASMJIT_INST_3x(vpsubsw, Vpsubsw, X86Ymm, X86Ymm, X86Ymm)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4214"><span class="lineNum">    4214 </span>            :   ASMJIT_INST_3x(vpsubsw, Vpsubsw, X86Ymm, X86Ymm, X86Mem)                    // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4215"><span class="lineNum">    4215 </span>            :   ASMJIT_INST_3x(vpsubsw, Vpsubsw, X86Zmm, X86Zmm, X86Zmm)                    //      AVX512_BW{kz}</a>
+<a name="4216"><span class="lineNum">    4216 </span>            :   ASMJIT_INST_3x(vpsubsw, Vpsubsw, X86Zmm, X86Zmm, X86Mem)                    //      AVX512_BW{kz}</a>
+<a name="4217"><span class="lineNum">    4217 </span>            :   ASMJIT_INST_3x(vpsubusb, Vpsubusb, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="4218"><span class="lineNum">    4218 </span>            :   ASMJIT_INST_3x(vpsubusb, Vpsubusb, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="4219"><span class="lineNum">    4219 </span>            :   ASMJIT_INST_3x(vpsubusb, Vpsubusb, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4220"><span class="lineNum">    4220 </span>            :   ASMJIT_INST_3x(vpsubusb, Vpsubusb, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4221"><span class="lineNum">    4221 </span>            :   ASMJIT_INST_3x(vpsubusb, Vpsubusb, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="4222"><span class="lineNum">    4222 </span>            :   ASMJIT_INST_3x(vpsubusb, Vpsubusb, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="4223"><span class="lineNum">    4223 </span>            :   ASMJIT_INST_3x(vpsubusw, Vpsubusw, X86Xmm, X86Xmm, X86Xmm)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="4224"><span class="lineNum">    4224 </span>            :   ASMJIT_INST_3x(vpsubusw, Vpsubusw, X86Xmm, X86Xmm, X86Mem)                  // AVX  AVX512_BW{kz}-VL</a>
+<a name="4225"><span class="lineNum">    4225 </span>            :   ASMJIT_INST_3x(vpsubusw, Vpsubusw, X86Ymm, X86Ymm, X86Ymm)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4226"><span class="lineNum">    4226 </span>            :   ASMJIT_INST_3x(vpsubusw, Vpsubusw, X86Ymm, X86Ymm, X86Mem)                  // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4227"><span class="lineNum">    4227 </span>            :   ASMJIT_INST_3x(vpsubusw, Vpsubusw, X86Zmm, X86Zmm, X86Zmm)                  //      AVX512_BW{kz}</a>
+<a name="4228"><span class="lineNum">    4228 </span>            :   ASMJIT_INST_3x(vpsubusw, Vpsubusw, X86Zmm, X86Zmm, X86Mem)                  //      AVX512_BW{kz}</a>
+<a name="4229"><span class="lineNum">    4229 </span>            :   ASMJIT_INST_3x(vpsubw, Vpsubw, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4230"><span class="lineNum">    4230 </span>            :   ASMJIT_INST_3x(vpsubw, Vpsubw, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_BW{kz}-VL</a>
+<a name="4231"><span class="lineNum">    4231 </span>            :   ASMJIT_INST_3x(vpsubw, Vpsubw, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4232"><span class="lineNum">    4232 </span>            :   ASMJIT_INST_3x(vpsubw, Vpsubw, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4233"><span class="lineNum">    4233 </span>            :   ASMJIT_INST_3x(vpsubw, Vpsubw, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_BW{kz}</a>
+<a name="4234"><span class="lineNum">    4234 </span>            :   ASMJIT_INST_3x(vpsubw, Vpsubw, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_BW{kz}</a>
+<a name="4235"><span class="lineNum">    4235 </span>            :   ASMJIT_INST_4i(vpternlogd, Vpternlogd, X86Xmm, X86Xmm, X86Xmm, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4236"><span class="lineNum">    4236 </span>            :   ASMJIT_INST_4i(vpternlogd, Vpternlogd, X86Xmm, X86Xmm, X86Mem, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4237"><span class="lineNum">    4237 </span>            :   ASMJIT_INST_4i(vpternlogd, Vpternlogd, X86Ymm, X86Ymm, X86Ymm, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4238"><span class="lineNum">    4238 </span>            :   ASMJIT_INST_4i(vpternlogd, Vpternlogd, X86Ymm, X86Ymm, X86Mem, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4239"><span class="lineNum">    4239 </span>            :   ASMJIT_INST_4i(vpternlogd, Vpternlogd, X86Zmm, X86Zmm, X86Zmm, Imm)         //      AVX512_F{kz|b32}</a>
+<a name="4240"><span class="lineNum">    4240 </span>            :   ASMJIT_INST_4i(vpternlogd, Vpternlogd, X86Zmm, X86Zmm, X86Mem, Imm)         //      AVX512_F{kz|b32}</a>
+<a name="4241"><span class="lineNum">    4241 </span>            :   ASMJIT_INST_4i(vpternlogq, Vpternlogq, X86Xmm, X86Xmm, X86Xmm, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4242"><span class="lineNum">    4242 </span>            :   ASMJIT_INST_4i(vpternlogq, Vpternlogq, X86Xmm, X86Xmm, X86Mem, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4243"><span class="lineNum">    4243 </span>            :   ASMJIT_INST_4i(vpternlogq, Vpternlogq, X86Ymm, X86Ymm, X86Ymm, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4244"><span class="lineNum">    4244 </span>            :   ASMJIT_INST_4i(vpternlogq, Vpternlogq, X86Ymm, X86Ymm, X86Mem, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4245"><span class="lineNum">    4245 </span>            :   ASMJIT_INST_4i(vpternlogq, Vpternlogq, X86Zmm, X86Zmm, X86Zmm, Imm)         //      AVX512_F{kz|b64}</a>
+<a name="4246"><span class="lineNum">    4246 </span>            :   ASMJIT_INST_4i(vpternlogq, Vpternlogq, X86Zmm, X86Zmm, X86Mem, Imm)         //      AVX512_F{kz|b64}</a>
+<a name="4247"><span class="lineNum">    4247 </span>            :   ASMJIT_INST_2x(vptest, Vptest, X86Xmm, X86Xmm)                              // AVX</a>
+<a name="4248"><span class="lineNum">    4248 </span>            :   ASMJIT_INST_2x(vptest, Vptest, X86Xmm, X86Mem)                              // AVX</a>
+<a name="4249"><span class="lineNum">    4249 </span>            :   ASMJIT_INST_2x(vptest, Vptest, X86Ymm, X86Ymm)                              // AVX</a>
+<a name="4250"><span class="lineNum">    4250 </span>            :   ASMJIT_INST_2x(vptest, Vptest, X86Ymm, X86Mem)                              // AVX</a>
+<a name="4251"><span class="lineNum">    4251 </span>            :   ASMJIT_INST_3x(vptestmb, Vptestmb, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_BW{k}-VL</a>
+<a name="4252"><span class="lineNum">    4252 </span>            :   ASMJIT_INST_3x(vptestmb, Vptestmb, X86KReg, X86Xmm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="4253"><span class="lineNum">    4253 </span>            :   ASMJIT_INST_3x(vptestmb, Vptestmb, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_BW{k}-VL</a>
+<a name="4254"><span class="lineNum">    4254 </span>            :   ASMJIT_INST_3x(vptestmb, Vptestmb, X86KReg, X86Ymm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="4255"><span class="lineNum">    4255 </span>            :   ASMJIT_INST_3x(vptestmb, Vptestmb, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_BW{k}</a>
+<a name="4256"><span class="lineNum">    4256 </span>            :   ASMJIT_INST_3x(vptestmb, Vptestmb, X86KReg, X86Zmm, X86Mem)                 //      AVX512_BW{k}</a>
+<a name="4257"><span class="lineNum">    4257 </span>            :   ASMJIT_INST_3x(vptestmd, Vptestmd, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_F{k|b32}-VL</a>
+<a name="4258"><span class="lineNum">    4258 </span>            :   ASMJIT_INST_3x(vptestmd, Vptestmd, X86KReg, X86Xmm, X86Mem)                 //      AVX512_F{k|b32}-VL</a>
+<a name="4259"><span class="lineNum">    4259 </span>            :   ASMJIT_INST_3x(vptestmd, Vptestmd, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_F{k|b32}-VL</a>
+<a name="4260"><span class="lineNum">    4260 </span>            :   ASMJIT_INST_3x(vptestmd, Vptestmd, X86KReg, X86Ymm, X86Mem)                 //      AVX512_F{k|b32}-VL</a>
+<a name="4261"><span class="lineNum">    4261 </span>            :   ASMJIT_INST_3x(vptestmd, Vptestmd, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_F{k|b32}</a>
+<a name="4262"><span class="lineNum">    4262 </span>            :   ASMJIT_INST_3x(vptestmd, Vptestmd, X86KReg, X86Zmm, X86Mem)                 //      AVX512_F{k|b32}</a>
+<a name="4263"><span class="lineNum">    4263 </span>            :   ASMJIT_INST_3x(vptestmq, Vptestmq, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_F{k|b64}-VL</a>
+<a name="4264"><span class="lineNum">    4264 </span>            :   ASMJIT_INST_3x(vptestmq, Vptestmq, X86KReg, X86Xmm, X86Mem)                 //      AVX512_F{k|b64}-VL</a>
+<a name="4265"><span class="lineNum">    4265 </span>            :   ASMJIT_INST_3x(vptestmq, Vptestmq, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_F{k|b64}-VL</a>
+<a name="4266"><span class="lineNum">    4266 </span>            :   ASMJIT_INST_3x(vptestmq, Vptestmq, X86KReg, X86Ymm, X86Mem)                 //      AVX512_F{k|b64}-VL</a>
+<a name="4267"><span class="lineNum">    4267 </span>            :   ASMJIT_INST_3x(vptestmq, Vptestmq, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_F{k|b64}</a>
+<a name="4268"><span class="lineNum">    4268 </span>            :   ASMJIT_INST_3x(vptestmq, Vptestmq, X86KReg, X86Zmm, X86Mem)                 //      AVX512_F{k|b64}</a>
+<a name="4269"><span class="lineNum">    4269 </span>            :   ASMJIT_INST_3x(vptestmw, Vptestmw, X86KReg, X86Xmm, X86Xmm)                 //      AVX512_BW{k}-VL</a>
+<a name="4270"><span class="lineNum">    4270 </span>            :   ASMJIT_INST_3x(vptestmw, Vptestmw, X86KReg, X86Xmm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="4271"><span class="lineNum">    4271 </span>            :   ASMJIT_INST_3x(vptestmw, Vptestmw, X86KReg, X86Ymm, X86Ymm)                 //      AVX512_BW{k}-VL</a>
+<a name="4272"><span class="lineNum">    4272 </span>            :   ASMJIT_INST_3x(vptestmw, Vptestmw, X86KReg, X86Ymm, X86Mem)                 //      AVX512_BW{k}-VL</a>
+<a name="4273"><span class="lineNum">    4273 </span>            :   ASMJIT_INST_3x(vptestmw, Vptestmw, X86KReg, X86Zmm, X86Zmm)                 //      AVX512_BW{k}</a>
+<a name="4274"><span class="lineNum">    4274 </span>            :   ASMJIT_INST_3x(vptestmw, Vptestmw, X86KReg, X86Zmm, X86Mem)                 //      AVX512_BW{k}</a>
+<a name="4275"><span class="lineNum">    4275 </span>            :   ASMJIT_INST_3x(vptestnmb, Vptestnmb, X86KReg, X86Xmm, X86Xmm)               //      AVX512_BW{k}-VL</a>
+<a name="4276"><span class="lineNum">    4276 </span>            :   ASMJIT_INST_3x(vptestnmb, Vptestnmb, X86KReg, X86Xmm, X86Mem)               //      AVX512_BW{k}-VL</a>
+<a name="4277"><span class="lineNum">    4277 </span>            :   ASMJIT_INST_3x(vptestnmb, Vptestnmb, X86KReg, X86Ymm, X86Ymm)               //      AVX512_BW{k}-VL</a>
+<a name="4278"><span class="lineNum">    4278 </span>            :   ASMJIT_INST_3x(vptestnmb, Vptestnmb, X86KReg, X86Ymm, X86Mem)               //      AVX512_BW{k}-VL</a>
+<a name="4279"><span class="lineNum">    4279 </span>            :   ASMJIT_INST_3x(vptestnmb, Vptestnmb, X86KReg, X86Zmm, X86Zmm)               //      AVX512_BW{k}</a>
+<a name="4280"><span class="lineNum">    4280 </span>            :   ASMJIT_INST_3x(vptestnmb, Vptestnmb, X86KReg, X86Zmm, X86Mem)               //      AVX512_BW{k}</a>
+<a name="4281"><span class="lineNum">    4281 </span>            :   ASMJIT_INST_3x(vptestnmd, Vptestnmd, X86KReg, X86Xmm, X86Xmm)               //      AVX512_F{k|b32}-VL</a>
+<a name="4282"><span class="lineNum">    4282 </span>            :   ASMJIT_INST_3x(vptestnmd, Vptestnmd, X86KReg, X86Xmm, X86Mem)               //      AVX512_F{k|b32}-VL</a>
+<a name="4283"><span class="lineNum">    4283 </span>            :   ASMJIT_INST_3x(vptestnmd, Vptestnmd, X86KReg, X86Ymm, X86Ymm)               //      AVX512_F{k|b32}-VL</a>
+<a name="4284"><span class="lineNum">    4284 </span>            :   ASMJIT_INST_3x(vptestnmd, Vptestnmd, X86KReg, X86Ymm, X86Mem)               //      AVX512_F{k|b32}-VL</a>
+<a name="4285"><span class="lineNum">    4285 </span>            :   ASMJIT_INST_3x(vptestnmd, Vptestnmd, X86KReg, X86Zmm, X86Zmm)               //      AVX512_F{k|b32}</a>
+<a name="4286"><span class="lineNum">    4286 </span>            :   ASMJIT_INST_3x(vptestnmd, Vptestnmd, X86KReg, X86Zmm, X86Mem)               //      AVX512_F{k|b32}</a>
+<a name="4287"><span class="lineNum">    4287 </span>            :   ASMJIT_INST_3x(vptestnmq, Vptestnmq, X86KReg, X86Xmm, X86Xmm)               //      AVX512_F{k|b64}-VL</a>
+<a name="4288"><span class="lineNum">    4288 </span>            :   ASMJIT_INST_3x(vptestnmq, Vptestnmq, X86KReg, X86Xmm, X86Mem)               //      AVX512_F{k|b64}-VL</a>
+<a name="4289"><span class="lineNum">    4289 </span>            :   ASMJIT_INST_3x(vptestnmq, Vptestnmq, X86KReg, X86Ymm, X86Ymm)               //      AVX512_F{k|b64}-VL</a>
+<a name="4290"><span class="lineNum">    4290 </span>            :   ASMJIT_INST_3x(vptestnmq, Vptestnmq, X86KReg, X86Ymm, X86Mem)               //      AVX512_F{k|b64}-VL</a>
+<a name="4291"><span class="lineNum">    4291 </span>            :   ASMJIT_INST_3x(vptestnmq, Vptestnmq, X86KReg, X86Zmm, X86Zmm)               //      AVX512_F{k|b64}</a>
+<a name="4292"><span class="lineNum">    4292 </span>            :   ASMJIT_INST_3x(vptestnmq, Vptestnmq, X86KReg, X86Zmm, X86Mem)               //      AVX512_F{k|b64}</a>
+<a name="4293"><span class="lineNum">    4293 </span>            :   ASMJIT_INST_3x(vptestnmw, Vptestnmw, X86KReg, X86Xmm, X86Xmm)               //      AVX512_BW{k}-VL</a>
+<a name="4294"><span class="lineNum">    4294 </span>            :   ASMJIT_INST_3x(vptestnmw, Vptestnmw, X86KReg, X86Xmm, X86Mem)               //      AVX512_BW{k}-VL</a>
+<a name="4295"><span class="lineNum">    4295 </span>            :   ASMJIT_INST_3x(vptestnmw, Vptestnmw, X86KReg, X86Ymm, X86Ymm)               //      AVX512_BW{k}-VL</a>
+<a name="4296"><span class="lineNum">    4296 </span>            :   ASMJIT_INST_3x(vptestnmw, Vptestnmw, X86KReg, X86Ymm, X86Mem)               //      AVX512_BW{k}-VL</a>
+<a name="4297"><span class="lineNum">    4297 </span>            :   ASMJIT_INST_3x(vptestnmw, Vptestnmw, X86KReg, X86Zmm, X86Zmm)               //      AVX512_BW{k}</a>
+<a name="4298"><span class="lineNum">    4298 </span>            :   ASMJIT_INST_3x(vptestnmw, Vptestnmw, X86KReg, X86Zmm, X86Mem)               //      AVX512_BW{k}</a>
+<a name="4299"><span class="lineNum">    4299 </span>            :   ASMJIT_INST_3x(vpunpckhbw, Vpunpckhbw, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4300"><span class="lineNum">    4300 </span>            :   ASMJIT_INST_3x(vpunpckhbw, Vpunpckhbw, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4301"><span class="lineNum">    4301 </span>            :   ASMJIT_INST_3x(vpunpckhbw, Vpunpckhbw, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4302"><span class="lineNum">    4302 </span>            :   ASMJIT_INST_3x(vpunpckhbw, Vpunpckhbw, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4303"><span class="lineNum">    4303 </span>            :   ASMJIT_INST_3x(vpunpckhbw, Vpunpckhbw, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_BW{kz}</a>
+<a name="4304"><span class="lineNum">    4304 </span>            :   ASMJIT_INST_3x(vpunpckhbw, Vpunpckhbw, X86Zmm, X86Zmm, X86Mem)              //      AVX512_BW{kz}</a>
+<a name="4305"><span class="lineNum">    4305 </span>            :   ASMJIT_INST_3x(vpunpckhdq, Vpunpckhdq, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4306"><span class="lineNum">    4306 </span>            :   ASMJIT_INST_3x(vpunpckhdq, Vpunpckhdq, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4307"><span class="lineNum">    4307 </span>            :   ASMJIT_INST_3x(vpunpckhdq, Vpunpckhdq, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4308"><span class="lineNum">    4308 </span>            :   ASMJIT_INST_3x(vpunpckhdq, Vpunpckhdq, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4309"><span class="lineNum">    4309 </span>            :   ASMJIT_INST_3x(vpunpckhdq, Vpunpckhdq, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_F{kz|b32}</a>
+<a name="4310"><span class="lineNum">    4310 </span>            :   ASMJIT_INST_3x(vpunpckhdq, Vpunpckhdq, X86Zmm, X86Zmm, X86Mem)              //      AVX512_F{kz|b32}</a>
+<a name="4311"><span class="lineNum">    4311 </span>            :   ASMJIT_INST_3x(vpunpckhqdq, Vpunpckhqdq, X86Xmm, X86Xmm, X86Xmm)            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4312"><span class="lineNum">    4312 </span>            :   ASMJIT_INST_3x(vpunpckhqdq, Vpunpckhqdq, X86Xmm, X86Xmm, X86Mem)            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4313"><span class="lineNum">    4313 </span>            :   ASMJIT_INST_3x(vpunpckhqdq, Vpunpckhqdq, X86Ymm, X86Ymm, X86Ymm)            // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4314"><span class="lineNum">    4314 </span>            :   ASMJIT_INST_3x(vpunpckhqdq, Vpunpckhqdq, X86Ymm, X86Ymm, X86Mem)            // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4315"><span class="lineNum">    4315 </span>            :   ASMJIT_INST_3x(vpunpckhqdq, Vpunpckhqdq, X86Zmm, X86Zmm, X86Zmm)            //      AVX512_F{kz|b64}</a>
+<a name="4316"><span class="lineNum">    4316 </span>            :   ASMJIT_INST_3x(vpunpckhqdq, Vpunpckhqdq, X86Zmm, X86Zmm, X86Mem)            //      AVX512_F{kz|b64}</a>
+<a name="4317"><span class="lineNum">    4317 </span>            :   ASMJIT_INST_3x(vpunpckhwd, Vpunpckhwd, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4318"><span class="lineNum">    4318 </span>            :   ASMJIT_INST_3x(vpunpckhwd, Vpunpckhwd, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4319"><span class="lineNum">    4319 </span>            :   ASMJIT_INST_3x(vpunpckhwd, Vpunpckhwd, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4320"><span class="lineNum">    4320 </span>            :   ASMJIT_INST_3x(vpunpckhwd, Vpunpckhwd, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4321"><span class="lineNum">    4321 </span>            :   ASMJIT_INST_3x(vpunpckhwd, Vpunpckhwd, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_BW{kz}</a>
+<a name="4322"><span class="lineNum">    4322 </span>            :   ASMJIT_INST_3x(vpunpckhwd, Vpunpckhwd, X86Zmm, X86Zmm, X86Mem)              //      AVX512_BW{kz}</a>
+<a name="4323"><span class="lineNum">    4323 </span>            :   ASMJIT_INST_3x(vpunpcklbw, Vpunpcklbw, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4324"><span class="lineNum">    4324 </span>            :   ASMJIT_INST_3x(vpunpcklbw, Vpunpcklbw, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4325"><span class="lineNum">    4325 </span>            :   ASMJIT_INST_3x(vpunpcklbw, Vpunpcklbw, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4326"><span class="lineNum">    4326 </span>            :   ASMJIT_INST_3x(vpunpcklbw, Vpunpcklbw, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4327"><span class="lineNum">    4327 </span>            :   ASMJIT_INST_3x(vpunpcklbw, Vpunpcklbw, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_BW{kz}</a>
+<a name="4328"><span class="lineNum">    4328 </span>            :   ASMJIT_INST_3x(vpunpcklbw, Vpunpcklbw, X86Zmm, X86Zmm, X86Mem)              //      AVX512_BW{kz}</a>
+<a name="4329"><span class="lineNum">    4329 </span>            :   ASMJIT_INST_3x(vpunpckldq, Vpunpckldq, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4330"><span class="lineNum">    4330 </span>            :   ASMJIT_INST_3x(vpunpckldq, Vpunpckldq, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4331"><span class="lineNum">    4331 </span>            :   ASMJIT_INST_3x(vpunpckldq, Vpunpckldq, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4332"><span class="lineNum">    4332 </span>            :   ASMJIT_INST_3x(vpunpckldq, Vpunpckldq, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4333"><span class="lineNum">    4333 </span>            :   ASMJIT_INST_3x(vpunpckldq, Vpunpckldq, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_F{kz|b32}</a>
+<a name="4334"><span class="lineNum">    4334 </span>            :   ASMJIT_INST_3x(vpunpckldq, Vpunpckldq, X86Zmm, X86Zmm, X86Mem)              //      AVX512_F{kz|b32}</a>
+<a name="4335"><span class="lineNum">    4335 </span>            :   ASMJIT_INST_3x(vpunpcklqdq, Vpunpcklqdq, X86Xmm, X86Xmm, X86Xmm)            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4336"><span class="lineNum">    4336 </span>            :   ASMJIT_INST_3x(vpunpcklqdq, Vpunpcklqdq, X86Xmm, X86Xmm, X86Mem)            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4337"><span class="lineNum">    4337 </span>            :   ASMJIT_INST_3x(vpunpcklqdq, Vpunpcklqdq, X86Ymm, X86Ymm, X86Ymm)            // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4338"><span class="lineNum">    4338 </span>            :   ASMJIT_INST_3x(vpunpcklqdq, Vpunpcklqdq, X86Ymm, X86Ymm, X86Mem)            // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4339"><span class="lineNum">    4339 </span>            :   ASMJIT_INST_3x(vpunpcklqdq, Vpunpcklqdq, X86Zmm, X86Zmm, X86Zmm)            //      AVX512_F{kz|b64}</a>
+<a name="4340"><span class="lineNum">    4340 </span>            :   ASMJIT_INST_3x(vpunpcklqdq, Vpunpcklqdq, X86Zmm, X86Zmm, X86Mem)            //      AVX512_F{kz|b64}</a>
+<a name="4341"><span class="lineNum">    4341 </span>            :   ASMJIT_INST_3x(vpunpcklwd, Vpunpcklwd, X86Xmm, X86Xmm, X86Xmm)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4342"><span class="lineNum">    4342 </span>            :   ASMJIT_INST_3x(vpunpcklwd, Vpunpcklwd, X86Xmm, X86Xmm, X86Mem)              // AVX  AVX512_BW{kz}-VL</a>
+<a name="4343"><span class="lineNum">    4343 </span>            :   ASMJIT_INST_3x(vpunpcklwd, Vpunpcklwd, X86Ymm, X86Ymm, X86Ymm)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4344"><span class="lineNum">    4344 </span>            :   ASMJIT_INST_3x(vpunpcklwd, Vpunpcklwd, X86Ymm, X86Ymm, X86Mem)              // AVX2 AVX512_BW{kz}-VL</a>
+<a name="4345"><span class="lineNum">    4345 </span>            :   ASMJIT_INST_3x(vpunpcklwd, Vpunpcklwd, X86Zmm, X86Zmm, X86Zmm)              //      AVX512_BW{kz}</a>
+<a name="4346"><span class="lineNum">    4346 </span>            :   ASMJIT_INST_3x(vpunpcklwd, Vpunpcklwd, X86Zmm, X86Zmm, X86Mem)              //      AVX512_BW{kz}</a>
+<a name="4347"><span class="lineNum">    4347 </span>            :   ASMJIT_INST_3x(vpxor, Vpxor, X86Xmm, X86Xmm, X86Xmm)                        // AVX</a>
+<a name="4348"><span class="lineNum">    4348 </span>            :   ASMJIT_INST_3x(vpxor, Vpxor, X86Xmm, X86Xmm, X86Mem)                        // AVX</a>
+<a name="4349"><span class="lineNum">    4349 </span>            :   ASMJIT_INST_3x(vpxor, Vpxor, X86Ymm, X86Ymm, X86Ymm)                        // AVX2</a>
+<a name="4350"><span class="lineNum">    4350 </span>            :   ASMJIT_INST_3x(vpxor, Vpxor, X86Ymm, X86Ymm, X86Mem)                        // AVX2</a>
+<a name="4351"><span class="lineNum">    4351 </span>            :   ASMJIT_INST_3x(vpxord, Vpxord, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4352"><span class="lineNum">    4352 </span>            :   ASMJIT_INST_3x(vpxord, Vpxord, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4353"><span class="lineNum">    4353 </span>            :   ASMJIT_INST_3x(vpxord, Vpxord, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4354"><span class="lineNum">    4354 </span>            :   ASMJIT_INST_3x(vpxord, Vpxord, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4355"><span class="lineNum">    4355 </span>            :   ASMJIT_INST_3x(vpxord, Vpxord, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b32}</a>
+<a name="4356"><span class="lineNum">    4356 </span>            :   ASMJIT_INST_3x(vpxord, Vpxord, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}</a>
+<a name="4357"><span class="lineNum">    4357 </span>            :   ASMJIT_INST_3x(vpxorq, Vpxorq, X86Xmm, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4358"><span class="lineNum">    4358 </span>            :   ASMJIT_INST_3x(vpxorq, Vpxorq, X86Xmm, X86Xmm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4359"><span class="lineNum">    4359 </span>            :   ASMJIT_INST_3x(vpxorq, Vpxorq, X86Ymm, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4360"><span class="lineNum">    4360 </span>            :   ASMJIT_INST_3x(vpxorq, Vpxorq, X86Ymm, X86Ymm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4361"><span class="lineNum">    4361 </span>            :   ASMJIT_INST_3x(vpxorq, Vpxorq, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b64}</a>
+<a name="4362"><span class="lineNum">    4362 </span>            :   ASMJIT_INST_3x(vpxorq, Vpxorq, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|b64}</a>
+<a name="4363"><span class="lineNum">    4363 </span>            :   ASMJIT_INST_4i(vrangepd, Vrangepd, X86Xmm, X86Xmm, X86Xmm, Imm)             //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4364"><span class="lineNum">    4364 </span>            :   ASMJIT_INST_4i(vrangepd, Vrangepd, X86Xmm, X86Xmm, X86Mem, Imm)             //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4365"><span class="lineNum">    4365 </span>            :   ASMJIT_INST_4i(vrangepd, Vrangepd, X86Ymm, X86Ymm, X86Ymm, Imm)             //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4366"><span class="lineNum">    4366 </span>            :   ASMJIT_INST_4i(vrangepd, Vrangepd, X86Ymm, X86Ymm, X86Mem, Imm)             //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4367"><span class="lineNum">    4367 </span>            :   ASMJIT_INST_4i(vrangepd, Vrangepd, X86Zmm, X86Zmm, X86Zmm, Imm)             //      AVX512_DQ{kz|sae|b64}</a>
+<a name="4368"><span class="lineNum">    4368 </span>            :   ASMJIT_INST_4i(vrangepd, Vrangepd, X86Zmm, X86Zmm, X86Mem, Imm)             //      AVX512_DQ{kz|sae|b64}</a>
+<a name="4369"><span class="lineNum">    4369 </span>            :   ASMJIT_INST_4i(vrangeps, Vrangeps, X86Xmm, X86Xmm, X86Xmm, Imm)             //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4370"><span class="lineNum">    4370 </span>            :   ASMJIT_INST_4i(vrangeps, Vrangeps, X86Xmm, X86Xmm, X86Mem, Imm)             //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4371"><span class="lineNum">    4371 </span>            :   ASMJIT_INST_4i(vrangeps, Vrangeps, X86Ymm, X86Ymm, X86Ymm, Imm)             //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4372"><span class="lineNum">    4372 </span>            :   ASMJIT_INST_4i(vrangeps, Vrangeps, X86Ymm, X86Ymm, X86Mem, Imm)             //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4373"><span class="lineNum">    4373 </span>            :   ASMJIT_INST_4i(vrangeps, Vrangeps, X86Zmm, X86Zmm, X86Zmm, Imm)             //      AVX512_DQ{kz|sae|b32}</a>
+<a name="4374"><span class="lineNum">    4374 </span>            :   ASMJIT_INST_4i(vrangeps, Vrangeps, X86Zmm, X86Zmm, X86Mem, Imm)             //      AVX512_DQ{kz|sae|b32}</a>
+<a name="4375"><span class="lineNum">    4375 </span>            :   ASMJIT_INST_4i(vrangesd, Vrangesd, X86Xmm, X86Xmm, X86Xmm, Imm)             //      AVX512_DQ{kz|sae}</a>
+<a name="4376"><span class="lineNum">    4376 </span>            :   ASMJIT_INST_4i(vrangesd, Vrangesd, X86Xmm, X86Xmm, X86Mem, Imm)             //      AVX512_DQ{kz|sae}</a>
+<a name="4377"><span class="lineNum">    4377 </span>            :   ASMJIT_INST_4i(vrangess, Vrangess, X86Xmm, X86Xmm, X86Xmm, Imm)             //      AVX512_DQ{kz|sae}</a>
+<a name="4378"><span class="lineNum">    4378 </span>            :   ASMJIT_INST_4i(vrangess, Vrangess, X86Xmm, X86Xmm, X86Mem, Imm)             //      AVX512_DQ{kz|sae}</a>
+<a name="4379"><span class="lineNum">    4379 </span>            :   ASMJIT_INST_2x(vrcp14pd, Vrcp14pd, X86Xmm, X86Xmm)                          //      AVX512_F{kz|b64}-VL</a>
+<a name="4380"><span class="lineNum">    4380 </span>            :   ASMJIT_INST_2x(vrcp14pd, Vrcp14pd, X86Xmm, X86Mem)                          //      AVX512_F{kz|b64}-VL</a>
+<a name="4381"><span class="lineNum">    4381 </span>            :   ASMJIT_INST_2x(vrcp14pd, Vrcp14pd, X86Ymm, X86Ymm)                          //      AVX512_F{kz|b64}-VL</a>
+<a name="4382"><span class="lineNum">    4382 </span>            :   ASMJIT_INST_2x(vrcp14pd, Vrcp14pd, X86Ymm, X86Mem)                          //      AVX512_F{kz|b64}-VL</a>
+<a name="4383"><span class="lineNum">    4383 </span>            :   ASMJIT_INST_2x(vrcp14pd, Vrcp14pd, X86Zmm, X86Zmm)                          //      AVX512_F{kz|b64}</a>
+<a name="4384"><span class="lineNum">    4384 </span>            :   ASMJIT_INST_2x(vrcp14pd, Vrcp14pd, X86Zmm, X86Mem)                          //      AVX512_F{kz|b64}</a>
+<a name="4385"><span class="lineNum">    4385 </span>            :   ASMJIT_INST_2x(vrcp14ps, Vrcp14ps, X86Xmm, X86Xmm)                          //      AVX512_F{kz|b32}-VL</a>
+<a name="4386"><span class="lineNum">    4386 </span>            :   ASMJIT_INST_2x(vrcp14ps, Vrcp14ps, X86Xmm, X86Mem)                          //      AVX512_F{kz|b32}-VL</a>
+<a name="4387"><span class="lineNum">    4387 </span>            :   ASMJIT_INST_2x(vrcp14ps, Vrcp14ps, X86Ymm, X86Ymm)                          //      AVX512_F{kz|b32}-VL</a>
+<a name="4388"><span class="lineNum">    4388 </span>            :   ASMJIT_INST_2x(vrcp14ps, Vrcp14ps, X86Ymm, X86Mem)                          //      AVX512_F{kz|b32}-VL</a>
+<a name="4389"><span class="lineNum">    4389 </span>            :   ASMJIT_INST_2x(vrcp14ps, Vrcp14ps, X86Zmm, X86Zmm)                          //      AVX512_F{kz|b32}</a>
+<a name="4390"><span class="lineNum">    4390 </span>            :   ASMJIT_INST_2x(vrcp14ps, Vrcp14ps, X86Zmm, X86Mem)                          //      AVX512_F{kz|b32}</a>
+<a name="4391"><span class="lineNum">    4391 </span>            :   ASMJIT_INST_3x(vrcp14sd, Vrcp14sd, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz}</a>
+<a name="4392"><span class="lineNum">    4392 </span>            :   ASMJIT_INST_3x(vrcp14sd, Vrcp14sd, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz}</a>
+<a name="4393"><span class="lineNum">    4393 </span>            :   ASMJIT_INST_3x(vrcp14ss, Vrcp14ss, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_F{kz}</a>
+<a name="4394"><span class="lineNum">    4394 </span>            :   ASMJIT_INST_3x(vrcp14ss, Vrcp14ss, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_F{kz}</a>
+<a name="4395"><span class="lineNum">    4395 </span>            :   ASMJIT_INST_2x(vrcp28pd, Vrcp28pd, X86Zmm, X86Zmm)                          //      AVX512_ER{kz|sae|b64}</a>
+<a name="4396"><span class="lineNum">    4396 </span>            :   ASMJIT_INST_2x(vrcp28pd, Vrcp28pd, X86Zmm, X86Mem)                          //      AVX512_ER{kz|sae|b64}</a>
+<a name="4397"><span class="lineNum">    4397 </span>            :   ASMJIT_INST_2x(vrcp28ps, Vrcp28ps, X86Zmm, X86Zmm)                          //      AVX512_ER{kz|sae|b32}</a>
+<a name="4398"><span class="lineNum">    4398 </span>            :   ASMJIT_INST_2x(vrcp28ps, Vrcp28ps, X86Zmm, X86Mem)                          //      AVX512_ER{kz|sae|b32}</a>
+<a name="4399"><span class="lineNum">    4399 </span>            :   ASMJIT_INST_3x(vrcp28sd, Vrcp28sd, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_ER{kz|sae}</a>
+<a name="4400"><span class="lineNum">    4400 </span>            :   ASMJIT_INST_3x(vrcp28sd, Vrcp28sd, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_ER{kz|sae}</a>
+<a name="4401"><span class="lineNum">    4401 </span>            :   ASMJIT_INST_3x(vrcp28ss, Vrcp28ss, X86Xmm, X86Xmm, X86Xmm)                  //      AVX512_ER{kz|sae}</a>
+<a name="4402"><span class="lineNum">    4402 </span>            :   ASMJIT_INST_3x(vrcp28ss, Vrcp28ss, X86Xmm, X86Xmm, X86Mem)                  //      AVX512_ER{kz|sae}</a>
+<a name="4403"><span class="lineNum">    4403 </span>            :   ASMJIT_INST_2x(vrcpps, Vrcpps, X86Xmm, X86Xmm)                              // AVX</a>
+<a name="4404"><span class="lineNum">    4404 </span>            :   ASMJIT_INST_2x(vrcpps, Vrcpps, X86Xmm, X86Mem)                              // AVX</a>
+<a name="4405"><span class="lineNum">    4405 </span>            :   ASMJIT_INST_2x(vrcpps, Vrcpps, X86Ymm, X86Ymm)                              // AVX</a>
+<a name="4406"><span class="lineNum">    4406 </span>            :   ASMJIT_INST_2x(vrcpps, Vrcpps, X86Ymm, X86Mem)                              // AVX</a>
+<a name="4407"><span class="lineNum">    4407 </span>            :   ASMJIT_INST_3x(vrcpss, Vrcpss, X86Xmm, X86Xmm, X86Xmm)                      // AVX</a>
+<a name="4408"><span class="lineNum">    4408 </span>            :   ASMJIT_INST_3x(vrcpss, Vrcpss, X86Xmm, X86Xmm, X86Mem)                      // AVX</a>
+<a name="4409"><span class="lineNum">    4409 </span>            :   ASMJIT_INST_3i(vreducepd, Vreducepd, X86Xmm, X86Xmm, Imm)                   //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4410"><span class="lineNum">    4410 </span>            :   ASMJIT_INST_3i(vreducepd, Vreducepd, X86Xmm, X86Mem, Imm)                   //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4411"><span class="lineNum">    4411 </span>            :   ASMJIT_INST_3i(vreducepd, Vreducepd, X86Ymm, X86Ymm, Imm)                   //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4412"><span class="lineNum">    4412 </span>            :   ASMJIT_INST_3i(vreducepd, Vreducepd, X86Ymm, X86Mem, Imm)                   //      AVX512_DQ{kz|b64}-VL</a>
+<a name="4413"><span class="lineNum">    4413 </span>            :   ASMJIT_INST_3i(vreducepd, Vreducepd, X86Zmm, X86Zmm, Imm)                   //      AVX512_DQ{kz|b64}</a>
+<a name="4414"><span class="lineNum">    4414 </span>            :   ASMJIT_INST_3i(vreducepd, Vreducepd, X86Zmm, X86Mem, Imm)                   //      AVX512_DQ{kz|b64}</a>
+<a name="4415"><span class="lineNum">    4415 </span>            :   ASMJIT_INST_3i(vreduceps, Vreduceps, X86Xmm, X86Xmm, Imm)                   //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4416"><span class="lineNum">    4416 </span>            :   ASMJIT_INST_3i(vreduceps, Vreduceps, X86Xmm, X86Mem, Imm)                   //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4417"><span class="lineNum">    4417 </span>            :   ASMJIT_INST_3i(vreduceps, Vreduceps, X86Ymm, X86Ymm, Imm)                   //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4418"><span class="lineNum">    4418 </span>            :   ASMJIT_INST_3i(vreduceps, Vreduceps, X86Ymm, X86Mem, Imm)                   //      AVX512_DQ{kz|b32}-VL</a>
+<a name="4419"><span class="lineNum">    4419 </span>            :   ASMJIT_INST_3i(vreduceps, Vreduceps, X86Zmm, X86Zmm, Imm)                   //      AVX512_DQ{kz|b32}</a>
+<a name="4420"><span class="lineNum">    4420 </span>            :   ASMJIT_INST_3i(vreduceps, Vreduceps, X86Zmm, X86Mem, Imm)                   //      AVX512_DQ{kz|b32}</a>
+<a name="4421"><span class="lineNum">    4421 </span>            :   ASMJIT_INST_4i(vreducesd, Vreducesd, X86Xmm, X86Xmm, X86Xmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="4422"><span class="lineNum">    4422 </span>            :   ASMJIT_INST_4i(vreducesd, Vreducesd, X86Xmm, X86Xmm, X86Mem, Imm)           //      AVX512_DQ{kz}</a>
+<a name="4423"><span class="lineNum">    4423 </span>            :   ASMJIT_INST_4i(vreducess, Vreducess, X86Xmm, X86Xmm, X86Xmm, Imm)           //      AVX512_DQ{kz}</a>
+<a name="4424"><span class="lineNum">    4424 </span>            :   ASMJIT_INST_4i(vreducess, Vreducess, X86Xmm, X86Xmm, X86Mem, Imm)           //      AVX512_DQ{kz}</a>
+<a name="4425"><span class="lineNum">    4425 </span>            :   ASMJIT_INST_3i(vrndscalepd, Vrndscalepd, X86Xmm, X86Xmm, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="4426"><span class="lineNum">    4426 </span>            :   ASMJIT_INST_3i(vrndscalepd, Vrndscalepd, X86Xmm, X86Mem, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="4427"><span class="lineNum">    4427 </span>            :   ASMJIT_INST_3i(vrndscalepd, Vrndscalepd, X86Ymm, X86Ymm, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="4428"><span class="lineNum">    4428 </span>            :   ASMJIT_INST_3i(vrndscalepd, Vrndscalepd, X86Ymm, X86Mem, Imm)               //      AVX512_F{kz|b64}-VL</a>
+<a name="4429"><span class="lineNum">    4429 </span>            :   ASMJIT_INST_3i(vrndscalepd, Vrndscalepd, X86Zmm, X86Zmm, Imm)               //      AVX512_F{kz|sae|b64}</a>
+<a name="4430"><span class="lineNum">    4430 </span>            :   ASMJIT_INST_3i(vrndscalepd, Vrndscalepd, X86Zmm, X86Mem, Imm)               //      AVX512_F{kz|sae|b64}</a>
+<a name="4431"><span class="lineNum">    4431 </span>            :   ASMJIT_INST_3i(vrndscaleps, Vrndscaleps, X86Xmm, X86Xmm, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="4432"><span class="lineNum">    4432 </span>            :   ASMJIT_INST_3i(vrndscaleps, Vrndscaleps, X86Xmm, X86Mem, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="4433"><span class="lineNum">    4433 </span>            :   ASMJIT_INST_3i(vrndscaleps, Vrndscaleps, X86Ymm, X86Ymm, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="4434"><span class="lineNum">    4434 </span>            :   ASMJIT_INST_3i(vrndscaleps, Vrndscaleps, X86Ymm, X86Mem, Imm)               //      AVX512_F{kz|b32}-VL</a>
+<a name="4435"><span class="lineNum">    4435 </span>            :   ASMJIT_INST_3i(vrndscaleps, Vrndscaleps, X86Zmm, X86Zmm, Imm)               //      AVX512_F{kz|sae|b32}</a>
+<a name="4436"><span class="lineNum">    4436 </span>            :   ASMJIT_INST_3i(vrndscaleps, Vrndscaleps, X86Zmm, X86Mem, Imm)               //      AVX512_F{kz|sae|b32}</a>
+<a name="4437"><span class="lineNum">    4437 </span>            :   ASMJIT_INST_4i(vrndscalesd, Vrndscalesd, X86Xmm, X86Xmm, X86Xmm, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="4438"><span class="lineNum">    4438 </span>            :   ASMJIT_INST_4i(vrndscalesd, Vrndscalesd, X86Xmm, X86Xmm, X86Mem, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="4439"><span class="lineNum">    4439 </span>            :   ASMJIT_INST_4i(vrndscaless, Vrndscaless, X86Xmm, X86Xmm, X86Xmm, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="4440"><span class="lineNum">    4440 </span>            :   ASMJIT_INST_4i(vrndscaless, Vrndscaless, X86Xmm, X86Xmm, X86Mem, Imm)       //      AVX512_F{kz|sae}</a>
+<a name="4441"><span class="lineNum">    4441 </span>            :   ASMJIT_INST_3i(vroundpd, Vroundpd, X86Xmm, X86Xmm, Imm)                     // AVX</a>
+<a name="4442"><span class="lineNum">    4442 </span>            :   ASMJIT_INST_3i(vroundpd, Vroundpd, X86Xmm, X86Mem, Imm)                     // AVX</a>
+<a name="4443"><span class="lineNum">    4443 </span>            :   ASMJIT_INST_3i(vroundpd, Vroundpd, X86Ymm, X86Ymm, Imm)                     // AVX</a>
+<a name="4444"><span class="lineNum">    4444 </span>            :   ASMJIT_INST_3i(vroundpd, Vroundpd, X86Ymm, X86Mem, Imm)                     // AVX</a>
+<a name="4445"><span class="lineNum">    4445 </span>            :   ASMJIT_INST_3i(vroundps, Vroundps, X86Xmm, X86Xmm, Imm)                     // AVX</a>
+<a name="4446"><span class="lineNum">    4446 </span>            :   ASMJIT_INST_3i(vroundps, Vroundps, X86Xmm, X86Mem, Imm)                     // AVX</a>
+<a name="4447"><span class="lineNum">    4447 </span>            :   ASMJIT_INST_3i(vroundps, Vroundps, X86Ymm, X86Ymm, Imm)                     // AVX</a>
+<a name="4448"><span class="lineNum">    4448 </span>            :   ASMJIT_INST_3i(vroundps, Vroundps, X86Ymm, X86Mem, Imm)                     // AVX</a>
+<a name="4449"><span class="lineNum">    4449 </span>            :   ASMJIT_INST_4i(vroundsd, Vroundsd, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX</a>
+<a name="4450"><span class="lineNum">    4450 </span>            :   ASMJIT_INST_4i(vroundsd, Vroundsd, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX</a>
+<a name="4451"><span class="lineNum">    4451 </span>            :   ASMJIT_INST_4i(vroundss, Vroundss, X86Xmm, X86Xmm, X86Xmm, Imm)             // AVX</a>
+<a name="4452"><span class="lineNum">    4452 </span>            :   ASMJIT_INST_4i(vroundss, Vroundss, X86Xmm, X86Xmm, X86Mem, Imm)             // AVX</a>
+<a name="4453"><span class="lineNum">    4453 </span>            :   ASMJIT_INST_2x(vrsqrt14pd, Vrsqrt14pd, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4454"><span class="lineNum">    4454 </span>            :   ASMJIT_INST_2x(vrsqrt14pd, Vrsqrt14pd, X86Xmm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4455"><span class="lineNum">    4455 </span>            :   ASMJIT_INST_2x(vrsqrt14pd, Vrsqrt14pd, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4456"><span class="lineNum">    4456 </span>            :   ASMJIT_INST_2x(vrsqrt14pd, Vrsqrt14pd, X86Ymm, X86Mem)                      //      AVX512_F{kz|b64}-VL</a>
+<a name="4457"><span class="lineNum">    4457 </span>            :   ASMJIT_INST_2x(vrsqrt14pd, Vrsqrt14pd, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b64}</a>
+<a name="4458"><span class="lineNum">    4458 </span>            :   ASMJIT_INST_2x(vrsqrt14pd, Vrsqrt14pd, X86Zmm, X86Mem)                      //      AVX512_F{kz|b64}</a>
+<a name="4459"><span class="lineNum">    4459 </span>            :   ASMJIT_INST_2x(vrsqrt14ps, Vrsqrt14ps, X86Xmm, X86Xmm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4460"><span class="lineNum">    4460 </span>            :   ASMJIT_INST_2x(vrsqrt14ps, Vrsqrt14ps, X86Xmm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4461"><span class="lineNum">    4461 </span>            :   ASMJIT_INST_2x(vrsqrt14ps, Vrsqrt14ps, X86Ymm, X86Ymm)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4462"><span class="lineNum">    4462 </span>            :   ASMJIT_INST_2x(vrsqrt14ps, Vrsqrt14ps, X86Ymm, X86Mem)                      //      AVX512_F{kz|b32}-VL</a>
+<a name="4463"><span class="lineNum">    4463 </span>            :   ASMJIT_INST_2x(vrsqrt14ps, Vrsqrt14ps, X86Zmm, X86Zmm)                      //      AVX512_F{kz|b32}</a>
+<a name="4464"><span class="lineNum">    4464 </span>            :   ASMJIT_INST_2x(vrsqrt14ps, Vrsqrt14ps, X86Zmm, X86Mem)                      //      AVX512_F{kz|b32}</a>
+<a name="4465"><span class="lineNum">    4465 </span>            :   ASMJIT_INST_3x(vrsqrt14sd, Vrsqrt14sd, X86Xmm, X86Xmm, X86Xmm)              //      AVX512_F{kz}</a>
+<a name="4466"><span class="lineNum">    4466 </span>            :   ASMJIT_INST_3x(vrsqrt14sd, Vrsqrt14sd, X86Xmm, X86Xmm, X86Mem)              //      AVX512_F{kz}</a>
+<a name="4467"><span class="lineNum">    4467 </span>            :   ASMJIT_INST_3x(vrsqrt14ss, Vrsqrt14ss, X86Xmm, X86Xmm, X86Xmm)              //      AVX512_F{kz}</a>
+<a name="4468"><span class="lineNum">    4468 </span>            :   ASMJIT_INST_3x(vrsqrt14ss, Vrsqrt14ss, X86Xmm, X86Xmm, X86Mem)              //      AVX512_F{kz}</a>
+<a name="4469"><span class="lineNum">    4469 </span>            :   ASMJIT_INST_2x(vrsqrt28pd, Vrsqrt28pd, X86Zmm, X86Zmm)                      //      AVX512_ER{kz|sae|b64}</a>
+<a name="4470"><span class="lineNum">    4470 </span>            :   ASMJIT_INST_2x(vrsqrt28pd, Vrsqrt28pd, X86Zmm, X86Mem)                      //      AVX512_ER{kz|sae|b64}</a>
+<a name="4471"><span class="lineNum">    4471 </span>            :   ASMJIT_INST_2x(vrsqrt28ps, Vrsqrt28ps, X86Zmm, X86Zmm)                      //      AVX512_ER{kz|sae|b32}</a>
+<a name="4472"><span class="lineNum">    4472 </span>            :   ASMJIT_INST_2x(vrsqrt28ps, Vrsqrt28ps, X86Zmm, X86Mem)                      //      AVX512_ER{kz|sae|b32}</a>
+<a name="4473"><span class="lineNum">    4473 </span>            :   ASMJIT_INST_3x(vrsqrt28sd, Vrsqrt28sd, X86Xmm, X86Xmm, X86Xmm)              //      AVX512_ER{kz|sae}</a>
+<a name="4474"><span class="lineNum">    4474 </span>            :   ASMJIT_INST_3x(vrsqrt28sd, Vrsqrt28sd, X86Xmm, X86Xmm, X86Mem)              //      AVX512_ER{kz|sae}</a>
+<a name="4475"><span class="lineNum">    4475 </span>            :   ASMJIT_INST_3x(vrsqrt28ss, Vrsqrt28ss, X86Xmm, X86Xmm, X86Xmm)              //      AVX512_ER{kz|sae}</a>
+<a name="4476"><span class="lineNum">    4476 </span>            :   ASMJIT_INST_3x(vrsqrt28ss, Vrsqrt28ss, X86Xmm, X86Xmm, X86Mem)              //      AVX512_ER{kz|sae}</a>
+<a name="4477"><span class="lineNum">    4477 </span>            :   ASMJIT_INST_2x(vrsqrtps, Vrsqrtps, X86Xmm, X86Xmm)                          // AVX</a>
+<a name="4478"><span class="lineNum">    4478 </span>            :   ASMJIT_INST_2x(vrsqrtps, Vrsqrtps, X86Xmm, X86Mem)                          // AVX</a>
+<a name="4479"><span class="lineNum">    4479 </span>            :   ASMJIT_INST_2x(vrsqrtps, Vrsqrtps, X86Ymm, X86Ymm)                          // AVX</a>
+<a name="4480"><span class="lineNum">    4480 </span>            :   ASMJIT_INST_2x(vrsqrtps, Vrsqrtps, X86Ymm, X86Mem)                          // AVX</a>
+<a name="4481"><span class="lineNum">    4481 </span>            :   ASMJIT_INST_3x(vrsqrtss, Vrsqrtss, X86Xmm, X86Xmm, X86Xmm)                  // AVX</a>
+<a name="4482"><span class="lineNum">    4482 </span>            :   ASMJIT_INST_3x(vrsqrtss, Vrsqrtss, X86Xmm, X86Xmm, X86Mem)                  // AVX</a>
+<a name="4483"><span class="lineNum">    4483 </span>            :   ASMJIT_INST_3x(vscalefpd, Vscalefpd, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="4484"><span class="lineNum">    4484 </span>            :   ASMJIT_INST_3x(vscalefpd, Vscalefpd, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="4485"><span class="lineNum">    4485 </span>            :   ASMJIT_INST_3x(vscalefpd, Vscalefpd, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b64}-VL</a>
+<a name="4486"><span class="lineNum">    4486 </span>            :   ASMJIT_INST_3x(vscalefpd, Vscalefpd, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b64}-VL</a>
+<a name="4487"><span class="lineNum">    4487 </span>            :   ASMJIT_INST_3x(vscalefpd, Vscalefpd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|er|b64}</a>
+<a name="4488"><span class="lineNum">    4488 </span>            :   ASMJIT_INST_3x(vscalefpd, Vscalefpd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|er|b64}</a>
+<a name="4489"><span class="lineNum">    4489 </span>            :   ASMJIT_INST_3x(vscalefps, Vscalefps, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="4490"><span class="lineNum">    4490 </span>            :   ASMJIT_INST_3x(vscalefps, Vscalefps, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="4491"><span class="lineNum">    4491 </span>            :   ASMJIT_INST_3x(vscalefps, Vscalefps, X86Ymm, X86Ymm, X86Ymm)                //      AVX512_F{kz|b32}-VL</a>
+<a name="4492"><span class="lineNum">    4492 </span>            :   ASMJIT_INST_3x(vscalefps, Vscalefps, X86Ymm, X86Ymm, X86Mem)                //      AVX512_F{kz|b32}-VL</a>
+<a name="4493"><span class="lineNum">    4493 </span>            :   ASMJIT_INST_3x(vscalefps, Vscalefps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|er|b32}</a>
+<a name="4494"><span class="lineNum">    4494 </span>            :   ASMJIT_INST_3x(vscalefps, Vscalefps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|er|b32}</a>
+<a name="4495"><span class="lineNum">    4495 </span>            :   ASMJIT_INST_3x(vscalefsd, Vscalefsd, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|er}</a>
+<a name="4496"><span class="lineNum">    4496 </span>            :   ASMJIT_INST_3x(vscalefsd, Vscalefsd, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|er}</a>
+<a name="4497"><span class="lineNum">    4497 </span>            :   ASMJIT_INST_3x(vscalefss, Vscalefss, X86Xmm, X86Xmm, X86Xmm)                //      AVX512_F{kz|er}</a>
+<a name="4498"><span class="lineNum">    4498 </span>            :   ASMJIT_INST_3x(vscalefss, Vscalefss, X86Xmm, X86Xmm, X86Mem)                //      AVX512_F{kz|er}</a>
+<a name="4499"><span class="lineNum">    4499 </span>            :   ASMJIT_INST_2x(vscatterdpd, Vscatterdpd, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="4500"><span class="lineNum">    4500 </span>            :   ASMJIT_INST_2x(vscatterdpd, Vscatterdpd, X86Mem, X86Ymm)                    //      AVX512_F{k}-VL</a>
+<a name="4501"><span class="lineNum">    4501 </span>            :   ASMJIT_INST_2x(vscatterdpd, Vscatterdpd, X86Mem, X86Zmm)                    //      AVX512_F{k}</a>
+<a name="4502"><span class="lineNum">    4502 </span>            :   ASMJIT_INST_2x(vscatterdps, Vscatterdps, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="4503"><span class="lineNum">    4503 </span>            :   ASMJIT_INST_2x(vscatterdps, Vscatterdps, X86Mem, X86Ymm)                    //      AVX512_F{k}-VL</a>
+<a name="4504"><span class="lineNum">    4504 </span>            :   ASMJIT_INST_2x(vscatterdps, Vscatterdps, X86Mem, X86Zmm)                    //      AVX512_F{k}</a>
+<a name="4505"><span class="lineNum">    4505 </span>            :   ASMJIT_INST_1x(vscatterpf0dpd, Vscatterpf0dpd, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4506"><span class="lineNum">    4506 </span>            :   ASMJIT_INST_1x(vscatterpf0dps, Vscatterpf0dps, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4507"><span class="lineNum">    4507 </span>            :   ASMJIT_INST_1x(vscatterpf0qpd, Vscatterpf0qpd, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4508"><span class="lineNum">    4508 </span>            :   ASMJIT_INST_1x(vscatterpf0qps, Vscatterpf0qps, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4509"><span class="lineNum">    4509 </span>            :   ASMJIT_INST_1x(vscatterpf1dpd, Vscatterpf1dpd, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4510"><span class="lineNum">    4510 </span>            :   ASMJIT_INST_1x(vscatterpf1dps, Vscatterpf1dps, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4511"><span class="lineNum">    4511 </span>            :   ASMJIT_INST_1x(vscatterpf1qpd, Vscatterpf1qpd, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4512"><span class="lineNum">    4512 </span>            :   ASMJIT_INST_1x(vscatterpf1qps, Vscatterpf1qps, X86Mem)                      //      AVX512_PF{k}</a>
+<a name="4513"><span class="lineNum">    4513 </span>            :   ASMJIT_INST_2x(vscatterqpd, Vscatterqpd, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="4514"><span class="lineNum">    4514 </span>            :   ASMJIT_INST_2x(vscatterqpd, Vscatterqpd, X86Mem, X86Ymm)                    //      AVX512_F{k}-VL</a>
+<a name="4515"><span class="lineNum">    4515 </span>            :   ASMJIT_INST_2x(vscatterqpd, Vscatterqpd, X86Mem, X86Zmm)                    //      AVX512_F{k}</a>
+<a name="4516"><span class="lineNum">    4516 </span>            :   ASMJIT_INST_2x(vscatterqps, Vscatterqps, X86Mem, X86Xmm)                    //      AVX512_F{k}-VL</a>
+<a name="4517"><span class="lineNum">    4517 </span>            :   ASMJIT_INST_2x(vscatterqps, Vscatterqps, X86Mem, X86Ymm)                    //      AVX512_F{k}</a>
+<a name="4518"><span class="lineNum">    4518 </span>            :   ASMJIT_INST_4i(vshuff32x4, Vshuff32x4, X86Ymm, X86Ymm, X86Ymm, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4519"><span class="lineNum">    4519 </span>            :   ASMJIT_INST_4i(vshuff32x4, Vshuff32x4, X86Ymm, X86Ymm, X86Mem, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4520"><span class="lineNum">    4520 </span>            :   ASMJIT_INST_4i(vshuff32x4, Vshuff32x4, X86Zmm, X86Zmm, X86Zmm, Imm)         //      AVX512_F{kz|b32}</a>
+<a name="4521"><span class="lineNum">    4521 </span>            :   ASMJIT_INST_4i(vshuff32x4, Vshuff32x4, X86Zmm, X86Zmm, X86Mem, Imm)         //      AVX512_F{kz|b32}</a>
+<a name="4522"><span class="lineNum">    4522 </span>            :   ASMJIT_INST_4i(vshuff64x2, Vshuff64x2, X86Ymm, X86Ymm, X86Ymm, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4523"><span class="lineNum">    4523 </span>            :   ASMJIT_INST_4i(vshuff64x2, Vshuff64x2, X86Ymm, X86Ymm, X86Mem, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4524"><span class="lineNum">    4524 </span>            :   ASMJIT_INST_4i(vshuff64x2, Vshuff64x2, X86Zmm, X86Zmm, X86Zmm, Imm)         //      AVX512_F{kz|b64}</a>
+<a name="4525"><span class="lineNum">    4525 </span>            :   ASMJIT_INST_4i(vshuff64x2, Vshuff64x2, X86Zmm, X86Zmm, X86Mem, Imm)         //      AVX512_F{kz|b64}</a>
+<a name="4526"><span class="lineNum">    4526 </span>            :   ASMJIT_INST_4i(vshufi32x4, Vshufi32x4, X86Ymm, X86Ymm, X86Ymm, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4527"><span class="lineNum">    4527 </span>            :   ASMJIT_INST_4i(vshufi32x4, Vshufi32x4, X86Ymm, X86Ymm, X86Mem, Imm)         //      AVX512_F{kz|b32}-VL</a>
+<a name="4528"><span class="lineNum">    4528 </span>            :   ASMJIT_INST_4i(vshufi32x4, Vshufi32x4, X86Zmm, X86Zmm, X86Zmm, Imm)         //      AVX512_F{kz|b32}</a>
+<a name="4529"><span class="lineNum">    4529 </span>            :   ASMJIT_INST_4i(vshufi32x4, Vshufi32x4, X86Zmm, X86Zmm, X86Mem, Imm)         //      AVX512_F{kz|b32}</a>
+<a name="4530"><span class="lineNum">    4530 </span>            :   ASMJIT_INST_4i(vshufi64x2, Vshufi64x2, X86Ymm, X86Ymm, X86Ymm, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4531"><span class="lineNum">    4531 </span>            :   ASMJIT_INST_4i(vshufi64x2, Vshufi64x2, X86Ymm, X86Ymm, X86Mem, Imm)         //      AVX512_F{kz|b64}-VL</a>
+<a name="4532"><span class="lineNum">    4532 </span>            :   ASMJIT_INST_4i(vshufi64x2, Vshufi64x2, X86Zmm, X86Zmm, X86Zmm, Imm)         //      AVX512_F{kz|b64}</a>
+<a name="4533"><span class="lineNum">    4533 </span>            :   ASMJIT_INST_4i(vshufi64x2, Vshufi64x2, X86Zmm, X86Zmm, X86Mem, Imm)         //      AVX512_F{kz|b64}</a>
+<a name="4534"><span class="lineNum">    4534 </span>            :   ASMJIT_INST_4i(vshufpd, Vshufpd, X86Xmm, X86Xmm, X86Xmm, Imm)               // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4535"><span class="lineNum">    4535 </span>            :   ASMJIT_INST_4i(vshufpd, Vshufpd, X86Xmm, X86Xmm, X86Mem, Imm)               // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4536"><span class="lineNum">    4536 </span>            :   ASMJIT_INST_4i(vshufpd, Vshufpd, X86Ymm, X86Ymm, X86Ymm, Imm)               // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4537"><span class="lineNum">    4537 </span>            :   ASMJIT_INST_4i(vshufpd, Vshufpd, X86Ymm, X86Ymm, X86Mem, Imm)               // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4538"><span class="lineNum">    4538 </span>            :   ASMJIT_INST_4i(vshufpd, Vshufpd, X86Zmm, X86Zmm, X86Zmm, Imm)               //      AVX512_F{kz|b32}</a>
+<a name="4539"><span class="lineNum">    4539 </span>            :   ASMJIT_INST_4i(vshufpd, Vshufpd, X86Zmm, X86Zmm, X86Mem, Imm)               //      AVX512_F{kz|b32}</a>
+<a name="4540"><span class="lineNum">    4540 </span>            :   ASMJIT_INST_4i(vshufps, Vshufps, X86Xmm, X86Xmm, X86Xmm, Imm)               // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4541"><span class="lineNum">    4541 </span>            :   ASMJIT_INST_4i(vshufps, Vshufps, X86Xmm, X86Xmm, X86Mem, Imm)               // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4542"><span class="lineNum">    4542 </span>            :   ASMJIT_INST_4i(vshufps, Vshufps, X86Ymm, X86Ymm, X86Ymm, Imm)               // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4543"><span class="lineNum">    4543 </span>            :   ASMJIT_INST_4i(vshufps, Vshufps, X86Ymm, X86Ymm, X86Mem, Imm)               // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4544"><span class="lineNum">    4544 </span>            :   ASMJIT_INST_4i(vshufps, Vshufps, X86Zmm, X86Zmm, X86Zmm, Imm)               //      AVX512_F{kz|b64}</a>
+<a name="4545"><span class="lineNum">    4545 </span>            :   ASMJIT_INST_4i(vshufps, Vshufps, X86Zmm, X86Zmm, X86Mem, Imm)               //      AVX512_F{kz|b64}</a>
+<a name="4546"><span class="lineNum">    4546 </span>            :   ASMJIT_INST_2x(vsqrtpd, Vsqrtpd, X86Xmm, X86Xmm)                            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4547"><span class="lineNum">    4547 </span>            :   ASMJIT_INST_2x(vsqrtpd, Vsqrtpd, X86Xmm, X86Mem)                            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4548"><span class="lineNum">    4548 </span>            :   ASMJIT_INST_2x(vsqrtpd, Vsqrtpd, X86Ymm, X86Ymm)                            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4549"><span class="lineNum">    4549 </span>            :   ASMJIT_INST_2x(vsqrtpd, Vsqrtpd, X86Ymm, X86Mem)                            // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4550"><span class="lineNum">    4550 </span>            :   ASMJIT_INST_2x(vsqrtpd, Vsqrtpd, X86Zmm, X86Zmm)                            //      AVX512_F{kz|er|b64}</a>
+<a name="4551"><span class="lineNum">    4551 </span>            :   ASMJIT_INST_2x(vsqrtpd, Vsqrtpd, X86Zmm, X86Mem)                            //      AVX512_F{kz|er|b64}</a>
+<a name="4552"><span class="lineNum">    4552 </span>            :   ASMJIT_INST_2x(vsqrtps, Vsqrtps, X86Xmm, X86Xmm)                            // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4553"><span class="lineNum">    4553 </span>            :   ASMJIT_INST_2x(vsqrtps, Vsqrtps, X86Xmm, X86Mem)                            // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4554"><span class="lineNum">    4554 </span>            :   ASMJIT_INST_2x(vsqrtps, Vsqrtps, X86Ymm, X86Ymm)                            // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4555"><span class="lineNum">    4555 </span>            :   ASMJIT_INST_2x(vsqrtps, Vsqrtps, X86Ymm, X86Mem)                            // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4556"><span class="lineNum">    4556 </span>            :   ASMJIT_INST_2x(vsqrtps, Vsqrtps, X86Zmm, X86Zmm)                            //      AVX512_F{kz|er|b32}</a>
+<a name="4557"><span class="lineNum">    4557 </span>            :   ASMJIT_INST_2x(vsqrtps, Vsqrtps, X86Zmm, X86Mem)                            //      AVX512_F{kz|er|b32}</a>
+<a name="4558"><span class="lineNum">    4558 </span>            :   ASMJIT_INST_3x(vsqrtsd, Vsqrtsd, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|er}</a>
+<a name="4559"><span class="lineNum">    4559 </span>            :   ASMJIT_INST_3x(vsqrtsd, Vsqrtsd, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|er}</a>
+<a name="4560"><span class="lineNum">    4560 </span>            :   ASMJIT_INST_3x(vsqrtss, Vsqrtss, X86Xmm, X86Xmm, X86Xmm)                    // AVX  AVX512_F{kz|er}</a>
+<a name="4561"><span class="lineNum">    4561 </span>            :   ASMJIT_INST_3x(vsqrtss, Vsqrtss, X86Xmm, X86Xmm, X86Mem)                    // AVX  AVX512_F{kz|er}</a>
+<a name="4562"><span class="lineNum">    4562 </span>            :   ASMJIT_INST_1x(vstmxcsr, Vstmxcsr, X86Mem)                                  // AVX</a>
+<a name="4563"><span class="lineNum">    4563 </span>            :   ASMJIT_INST_3x(vsubpd, Vsubpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4564"><span class="lineNum">    4564 </span>            :   ASMJIT_INST_3x(vsubpd, Vsubpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4565"><span class="lineNum">    4565 </span>            :   ASMJIT_INST_3x(vsubpd, Vsubpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4566"><span class="lineNum">    4566 </span>            :   ASMJIT_INST_3x(vsubpd, Vsubpd, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b64}-VL</a>
+<a name="4567"><span class="lineNum">    4567 </span>            :   ASMJIT_INST_3x(vsubpd, Vsubpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b64}</a>
+<a name="4568"><span class="lineNum">    4568 </span>            :   ASMJIT_INST_3x(vsubpd, Vsubpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b64}</a>
+<a name="4569"><span class="lineNum">    4569 </span>            :   ASMJIT_INST_3x(vsubps, Vsubps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4570"><span class="lineNum">    4570 </span>            :   ASMJIT_INST_3x(vsubps, Vsubps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4571"><span class="lineNum">    4571 </span>            :   ASMJIT_INST_3x(vsubps, Vsubps, X86Ymm, X86Ymm, X86Ymm)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4572"><span class="lineNum">    4572 </span>            :   ASMJIT_INST_3x(vsubps, Vsubps, X86Ymm, X86Ymm, X86Mem)                      // AVX2 AVX512_F{kz|b32}-VL</a>
+<a name="4573"><span class="lineNum">    4573 </span>            :   ASMJIT_INST_3x(vsubps, Vsubps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_F{kz|er|b32}</a>
+<a name="4574"><span class="lineNum">    4574 </span>            :   ASMJIT_INST_3x(vsubps, Vsubps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_F{kz|er|b32}</a>
+<a name="4575"><span class="lineNum">    4575 </span>            :   ASMJIT_INST_3x(vsubsd, Vsubsd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="4576"><span class="lineNum">    4576 </span>            :   ASMJIT_INST_3x(vsubsd, Vsubsd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="4577"><span class="lineNum">    4577 </span>            :   ASMJIT_INST_3x(vsubss, Vsubss, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_F{kz|er}</a>
+<a name="4578"><span class="lineNum">    4578 </span>            :   ASMJIT_INST_3x(vsubss, Vsubss, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_F{kz|er}</a>
+<a name="4579"><span class="lineNum">    4579 </span>            :   ASMJIT_INST_2x(vtestpd, Vtestpd, X86Xmm, X86Xmm)                            // AVX</a>
+<a name="4580"><span class="lineNum">    4580 </span>            :   ASMJIT_INST_2x(vtestpd, Vtestpd, X86Xmm, X86Mem)                            // AVX</a>
+<a name="4581"><span class="lineNum">    4581 </span>            :   ASMJIT_INST_2x(vtestpd, Vtestpd, X86Ymm, X86Ymm)                            // AVX</a>
+<a name="4582"><span class="lineNum">    4582 </span>            :   ASMJIT_INST_2x(vtestpd, Vtestpd, X86Ymm, X86Mem)                            // AVX</a>
+<a name="4583"><span class="lineNum">    4583 </span>            :   ASMJIT_INST_2x(vtestps, Vtestps, X86Xmm, X86Xmm)                            // AVX</a>
+<a name="4584"><span class="lineNum">    4584 </span>            :   ASMJIT_INST_2x(vtestps, Vtestps, X86Xmm, X86Mem)                            // AVX</a>
+<a name="4585"><span class="lineNum">    4585 </span>            :   ASMJIT_INST_2x(vtestps, Vtestps, X86Ymm, X86Ymm)                            // AVX</a>
+<a name="4586"><span class="lineNum">    4586 </span>            :   ASMJIT_INST_2x(vtestps, Vtestps, X86Ymm, X86Mem)                            // AVX</a>
+<a name="4587"><span class="lineNum">    4587 </span>            :   ASMJIT_INST_2x(vucomisd, Vucomisd, X86Xmm, X86Xmm)                          // AVX  AVX512_F{sae}</a>
+<a name="4588"><span class="lineNum">    4588 </span>            :   ASMJIT_INST_2x(vucomisd, Vucomisd, X86Xmm, X86Mem)                          // AVX  AVX512_F{sae}</a>
+<a name="4589"><span class="lineNum">    4589 </span>            :   ASMJIT_INST_2x(vucomiss, Vucomiss, X86Xmm, X86Xmm)                          // AVX  AVX512_F{sae}</a>
+<a name="4590"><span class="lineNum">    4590 </span>            :   ASMJIT_INST_2x(vucomiss, Vucomiss, X86Xmm, X86Mem)                          // AVX  AVX512_F{sae}</a>
+<a name="4591"><span class="lineNum">    4591 </span>            :   ASMJIT_INST_3x(vunpckhpd, Vunpckhpd, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4592"><span class="lineNum">    4592 </span>            :   ASMJIT_INST_3x(vunpckhpd, Vunpckhpd, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4593"><span class="lineNum">    4593 </span>            :   ASMJIT_INST_3x(vunpckhpd, Vunpckhpd, X86Ymm, X86Ymm, X86Ymm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4594"><span class="lineNum">    4594 </span>            :   ASMJIT_INST_3x(vunpckhpd, Vunpckhpd, X86Ymm, X86Ymm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4595"><span class="lineNum">    4595 </span>            :   ASMJIT_INST_3x(vunpckhpd, Vunpckhpd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="4596"><span class="lineNum">    4596 </span>            :   ASMJIT_INST_3x(vunpckhpd, Vunpckhpd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="4597"><span class="lineNum">    4597 </span>            :   ASMJIT_INST_3x(vunpckhps, Vunpckhps, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4598"><span class="lineNum">    4598 </span>            :   ASMJIT_INST_3x(vunpckhps, Vunpckhps, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4599"><span class="lineNum">    4599 </span>            :   ASMJIT_INST_3x(vunpckhps, Vunpckhps, X86Ymm, X86Ymm, X86Ymm)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4600"><span class="lineNum">    4600 </span>            :   ASMJIT_INST_3x(vunpckhps, Vunpckhps, X86Ymm, X86Ymm, X86Mem)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4601"><span class="lineNum">    4601 </span>            :   ASMJIT_INST_3x(vunpckhps, Vunpckhps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b32}</a>
+<a name="4602"><span class="lineNum">    4602 </span>            :   ASMJIT_INST_3x(vunpckhps, Vunpckhps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b32}</a>
+<a name="4603"><span class="lineNum">    4603 </span>            :   ASMJIT_INST_3x(vunpcklpd, Vunpcklpd, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4604"><span class="lineNum">    4604 </span>            :   ASMJIT_INST_3x(vunpcklpd, Vunpcklpd, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4605"><span class="lineNum">    4605 </span>            :   ASMJIT_INST_3x(vunpcklpd, Vunpcklpd, X86Ymm, X86Ymm, X86Ymm)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4606"><span class="lineNum">    4606 </span>            :   ASMJIT_INST_3x(vunpcklpd, Vunpcklpd, X86Ymm, X86Ymm, X86Mem)                // AVX  AVX512_F{kz|b64}-VL</a>
+<a name="4607"><span class="lineNum">    4607 </span>            :   ASMJIT_INST_3x(vunpcklpd, Vunpcklpd, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b64}</a>
+<a name="4608"><span class="lineNum">    4608 </span>            :   ASMJIT_INST_3x(vunpcklpd, Vunpcklpd, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b64}</a>
+<a name="4609"><span class="lineNum">    4609 </span>            :   ASMJIT_INST_3x(vunpcklps, Vunpcklps, X86Xmm, X86Xmm, X86Xmm)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4610"><span class="lineNum">    4610 </span>            :   ASMJIT_INST_3x(vunpcklps, Vunpcklps, X86Xmm, X86Xmm, X86Mem)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4611"><span class="lineNum">    4611 </span>            :   ASMJIT_INST_3x(vunpcklps, Vunpcklps, X86Ymm, X86Ymm, X86Ymm)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4612"><span class="lineNum">    4612 </span>            :   ASMJIT_INST_3x(vunpcklps, Vunpcklps, X86Ymm, X86Ymm, X86Mem)                // AVX  AVX512_F{kz|b32}-VL</a>
+<a name="4613"><span class="lineNum">    4613 </span>            :   ASMJIT_INST_3x(vunpcklps, Vunpcklps, X86Zmm, X86Zmm, X86Zmm)                //      AVX512_F{kz|b32}</a>
+<a name="4614"><span class="lineNum">    4614 </span>            :   ASMJIT_INST_3x(vunpcklps, Vunpcklps, X86Zmm, X86Zmm, X86Mem)                //      AVX512_F{kz|b32}</a>
+<a name="4615"><span class="lineNum">    4615 </span>            :   ASMJIT_INST_3x(vxorpd, Vxorpd, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="4616"><span class="lineNum">    4616 </span>            :   ASMJIT_INST_3x(vxorpd, Vxorpd, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="4617"><span class="lineNum">    4617 </span>            :   ASMJIT_INST_3x(vxorpd, Vxorpd, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="4618"><span class="lineNum">    4618 </span>            :   ASMJIT_INST_3x(vxorpd, Vxorpd, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_DQ{kz|b64}-VL</a>
+<a name="4619"><span class="lineNum">    4619 </span>            :   ASMJIT_INST_3x(vxorpd, Vxorpd, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_DQ{kz|b64}</a>
+<a name="4620"><span class="lineNum">    4620 </span>            :   ASMJIT_INST_3x(vxorpd, Vxorpd, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|b64}</a>
+<a name="4621"><span class="lineNum">    4621 </span>            :   ASMJIT_INST_3x(vxorps, Vxorps, X86Xmm, X86Xmm, X86Xmm)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="4622"><span class="lineNum">    4622 </span>            :   ASMJIT_INST_3x(vxorps, Vxorps, X86Xmm, X86Xmm, X86Mem)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="4623"><span class="lineNum">    4623 </span>            :   ASMJIT_INST_3x(vxorps, Vxorps, X86Ymm, X86Ymm, X86Ymm)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="4624"><span class="lineNum">    4624 </span>            :   ASMJIT_INST_3x(vxorps, Vxorps, X86Ymm, X86Ymm, X86Mem)                      // AVX  AVX512_DQ{kz|b32}-VL</a>
+<a name="4625"><span class="lineNum">    4625 </span>            :   ASMJIT_INST_3x(vxorps, Vxorps, X86Zmm, X86Zmm, X86Zmm)                      //      AVX512_DQ{kz|b32}</a>
+<a name="4626"><span class="lineNum">    4626 </span>            :   ASMJIT_INST_3x(vxorps, Vxorps, X86Zmm, X86Zmm, X86Mem)                      //      AVX512_DQ{kz|b32}</a>
+<a name="4627"><span class="lineNum">    4627 </span>            :   ASMJIT_INST_0x(vzeroall, Vzeroall)                                          // AVX</a>
+<a name="4628"><span class="lineNum">    4628 </span><span class="lineNoCov">          0 :   ASMJIT_INST_0x(vzeroupper, Vzeroupper)                                      // AVX</span></a>
+<a name="4629"><span class="lineNum">    4629 </span>            : </a>
+<a name="4630"><span class="lineNum">    4630 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4631"><span class="lineNum">    4631 </span>            :   // [FMA4]</a>
+<a name="4632"><span class="lineNum">    4632 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4633"><span class="lineNum">    4633 </span>            : </a>
+<a name="4634"><span class="lineNum">    4634 </span>            :   ASMJIT_INST_4x(vfmaddpd, Vfmaddpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4635"><span class="lineNum">    4635 </span>            :   ASMJIT_INST_4x(vfmaddpd, Vfmaddpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4636"><span class="lineNum">    4636 </span>            :   ASMJIT_INST_4x(vfmaddpd, Vfmaddpd, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4637"><span class="lineNum">    4637 </span>            :   ASMJIT_INST_4x(vfmaddpd, Vfmaddpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)          // FMA4</a>
+<a name="4638"><span class="lineNum">    4638 </span>            :   ASMJIT_INST_4x(vfmaddpd, Vfmaddpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)          // FMA4</a>
+<a name="4639"><span class="lineNum">    4639 </span>            :   ASMJIT_INST_4x(vfmaddpd, Vfmaddpd, X86Ymm, X86Ymm, X86Ymm, X86Mem)          // FMA4</a>
+<a name="4640"><span class="lineNum">    4640 </span>            :   ASMJIT_INST_4x(vfmaddps, Vfmaddps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4641"><span class="lineNum">    4641 </span>            :   ASMJIT_INST_4x(vfmaddps, Vfmaddps, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4642"><span class="lineNum">    4642 </span>            :   ASMJIT_INST_4x(vfmaddps, Vfmaddps, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4643"><span class="lineNum">    4643 </span>            :   ASMJIT_INST_4x(vfmaddps, Vfmaddps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)          // FMA4</a>
+<a name="4644"><span class="lineNum">    4644 </span>            :   ASMJIT_INST_4x(vfmaddps, Vfmaddps, X86Ymm, X86Ymm, X86Mem, X86Ymm)          // FMA4</a>
+<a name="4645"><span class="lineNum">    4645 </span>            :   ASMJIT_INST_4x(vfmaddps, Vfmaddps, X86Ymm, X86Ymm, X86Ymm, X86Mem)          // FMA4</a>
+<a name="4646"><span class="lineNum">    4646 </span>            :   ASMJIT_INST_4x(vfmaddsd, Vfmaddsd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4647"><span class="lineNum">    4647 </span>            :   ASMJIT_INST_4x(vfmaddsd, Vfmaddsd, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4648"><span class="lineNum">    4648 </span>            :   ASMJIT_INST_4x(vfmaddsd, Vfmaddsd, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4649"><span class="lineNum">    4649 </span>            :   ASMJIT_INST_4x(vfmaddss, Vfmaddss, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4650"><span class="lineNum">    4650 </span>            :   ASMJIT_INST_4x(vfmaddss, Vfmaddss, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4651"><span class="lineNum">    4651 </span>            :   ASMJIT_INST_4x(vfmaddss, Vfmaddss, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4652"><span class="lineNum">    4652 </span>            :   ASMJIT_INST_4x(vfmaddsubpd, Vfmaddsubpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)    // FMA4</a>
+<a name="4653"><span class="lineNum">    4653 </span>            :   ASMJIT_INST_4x(vfmaddsubpd, Vfmaddsubpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)    // FMA4</a>
+<a name="4654"><span class="lineNum">    4654 </span>            :   ASMJIT_INST_4x(vfmaddsubpd, Vfmaddsubpd, X86Xmm, X86Xmm, X86Xmm, X86Mem)    // FMA4</a>
+<a name="4655"><span class="lineNum">    4655 </span>            :   ASMJIT_INST_4x(vfmaddsubpd, Vfmaddsubpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)    // FMA4</a>
+<a name="4656"><span class="lineNum">    4656 </span>            :   ASMJIT_INST_4x(vfmaddsubpd, Vfmaddsubpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)    // FMA4</a>
+<a name="4657"><span class="lineNum">    4657 </span>            :   ASMJIT_INST_4x(vfmaddsubpd, Vfmaddsubpd, X86Ymm, X86Ymm, X86Ymm, X86Mem)    // FMA4</a>
+<a name="4658"><span class="lineNum">    4658 </span>            :   ASMJIT_INST_4x(vfmaddsubps, Vfmaddsubps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)    // FMA4</a>
+<a name="4659"><span class="lineNum">    4659 </span>            :   ASMJIT_INST_4x(vfmaddsubps, Vfmaddsubps, X86Xmm, X86Xmm, X86Mem, X86Xmm)    // FMA4</a>
+<a name="4660"><span class="lineNum">    4660 </span>            :   ASMJIT_INST_4x(vfmaddsubps, Vfmaddsubps, X86Xmm, X86Xmm, X86Xmm, X86Mem)    // FMA4</a>
+<a name="4661"><span class="lineNum">    4661 </span>            :   ASMJIT_INST_4x(vfmaddsubps, Vfmaddsubps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)    // FMA4</a>
+<a name="4662"><span class="lineNum">    4662 </span>            :   ASMJIT_INST_4x(vfmaddsubps, Vfmaddsubps, X86Ymm, X86Ymm, X86Mem, X86Ymm)    // FMA4</a>
+<a name="4663"><span class="lineNum">    4663 </span>            :   ASMJIT_INST_4x(vfmaddsubps, Vfmaddsubps, X86Ymm, X86Ymm, X86Ymm, X86Mem)    // FMA4</a>
+<a name="4664"><span class="lineNum">    4664 </span>            :   ASMJIT_INST_4x(vfmsubaddpd, Vfmsubaddpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)    // FMA4</a>
+<a name="4665"><span class="lineNum">    4665 </span>            :   ASMJIT_INST_4x(vfmsubaddpd, Vfmsubaddpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)    // FMA4</a>
+<a name="4666"><span class="lineNum">    4666 </span>            :   ASMJIT_INST_4x(vfmsubaddpd, Vfmsubaddpd, X86Xmm, X86Xmm, X86Xmm, X86Mem)    // FMA4</a>
+<a name="4667"><span class="lineNum">    4667 </span>            :   ASMJIT_INST_4x(vfmsubaddpd, Vfmsubaddpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)    // FMA4</a>
+<a name="4668"><span class="lineNum">    4668 </span>            :   ASMJIT_INST_4x(vfmsubaddpd, Vfmsubaddpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)    // FMA4</a>
+<a name="4669"><span class="lineNum">    4669 </span>            :   ASMJIT_INST_4x(vfmsubaddpd, Vfmsubaddpd, X86Ymm, X86Ymm, X86Ymm, X86Mem)    // FMA4</a>
+<a name="4670"><span class="lineNum">    4670 </span>            :   ASMJIT_INST_4x(vfmsubaddps, Vfmsubaddps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)    // FMA4</a>
+<a name="4671"><span class="lineNum">    4671 </span>            :   ASMJIT_INST_4x(vfmsubaddps, Vfmsubaddps, X86Xmm, X86Xmm, X86Mem, X86Xmm)    // FMA4</a>
+<a name="4672"><span class="lineNum">    4672 </span>            :   ASMJIT_INST_4x(vfmsubaddps, Vfmsubaddps, X86Xmm, X86Xmm, X86Xmm, X86Mem)    // FMA4</a>
+<a name="4673"><span class="lineNum">    4673 </span>            :   ASMJIT_INST_4x(vfmsubaddps, Vfmsubaddps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)    // FMA4</a>
+<a name="4674"><span class="lineNum">    4674 </span>            :   ASMJIT_INST_4x(vfmsubaddps, Vfmsubaddps, X86Ymm, X86Ymm, X86Mem, X86Ymm)    // FMA4</a>
+<a name="4675"><span class="lineNum">    4675 </span>            :   ASMJIT_INST_4x(vfmsubaddps, Vfmsubaddps, X86Ymm, X86Ymm, X86Ymm, X86Mem)    // FMA4</a>
+<a name="4676"><span class="lineNum">    4676 </span>            :   ASMJIT_INST_4x(vfmsubpd, Vfmsubpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4677"><span class="lineNum">    4677 </span>            :   ASMJIT_INST_4x(vfmsubpd, Vfmsubpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4678"><span class="lineNum">    4678 </span>            :   ASMJIT_INST_4x(vfmsubpd, Vfmsubpd, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4679"><span class="lineNum">    4679 </span>            :   ASMJIT_INST_4x(vfmsubpd, Vfmsubpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)          // FMA4</a>
+<a name="4680"><span class="lineNum">    4680 </span>            :   ASMJIT_INST_4x(vfmsubpd, Vfmsubpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)          // FMA4</a>
+<a name="4681"><span class="lineNum">    4681 </span>            :   ASMJIT_INST_4x(vfmsubpd, Vfmsubpd, X86Ymm, X86Ymm, X86Ymm, X86Mem)          // FMA4</a>
+<a name="4682"><span class="lineNum">    4682 </span>            :   ASMJIT_INST_4x(vfmsubps, Vfmsubps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4683"><span class="lineNum">    4683 </span>            :   ASMJIT_INST_4x(vfmsubps, Vfmsubps, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4684"><span class="lineNum">    4684 </span>            :   ASMJIT_INST_4x(vfmsubps, Vfmsubps, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4685"><span class="lineNum">    4685 </span>            :   ASMJIT_INST_4x(vfmsubps, Vfmsubps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)          // FMA4</a>
+<a name="4686"><span class="lineNum">    4686 </span>            :   ASMJIT_INST_4x(vfmsubps, Vfmsubps, X86Ymm, X86Ymm, X86Mem, X86Ymm)          // FMA4</a>
+<a name="4687"><span class="lineNum">    4687 </span>            :   ASMJIT_INST_4x(vfmsubps, Vfmsubps, X86Ymm, X86Ymm, X86Ymm, X86Mem)          // FMA4</a>
+<a name="4688"><span class="lineNum">    4688 </span>            :   ASMJIT_INST_4x(vfmsubsd, Vfmsubsd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4689"><span class="lineNum">    4689 </span>            :   ASMJIT_INST_4x(vfmsubsd, Vfmsubsd, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4690"><span class="lineNum">    4690 </span>            :   ASMJIT_INST_4x(vfmsubsd, Vfmsubsd, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4691"><span class="lineNum">    4691 </span>            :   ASMJIT_INST_4x(vfmsubss, Vfmsubss, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // FMA4</a>
+<a name="4692"><span class="lineNum">    4692 </span>            :   ASMJIT_INST_4x(vfmsubss, Vfmsubss, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // FMA4</a>
+<a name="4693"><span class="lineNum">    4693 </span>            :   ASMJIT_INST_4x(vfmsubss, Vfmsubss, X86Xmm, X86Xmm, X86Xmm, X86Mem)          // FMA4</a>
+<a name="4694"><span class="lineNum">    4694 </span>            :   ASMJIT_INST_4x(vfnmaddpd, Vfnmaddpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4695"><span class="lineNum">    4695 </span>            :   ASMJIT_INST_4x(vfnmaddpd, Vfnmaddpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4696"><span class="lineNum">    4696 </span>            :   ASMJIT_INST_4x(vfnmaddpd, Vfnmaddpd, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4697"><span class="lineNum">    4697 </span>            :   ASMJIT_INST_4x(vfnmaddpd, Vfnmaddpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // FMA4</a>
+<a name="4698"><span class="lineNum">    4698 </span>            :   ASMJIT_INST_4x(vfnmaddpd, Vfnmaddpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // FMA4</a>
+<a name="4699"><span class="lineNum">    4699 </span>            :   ASMJIT_INST_4x(vfnmaddpd, Vfnmaddpd, X86Ymm, X86Ymm, X86Ymm, X86Mem)        // FMA4</a>
+<a name="4700"><span class="lineNum">    4700 </span>            :   ASMJIT_INST_4x(vfnmaddps, Vfnmaddps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4701"><span class="lineNum">    4701 </span>            :   ASMJIT_INST_4x(vfnmaddps, Vfnmaddps, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4702"><span class="lineNum">    4702 </span>            :   ASMJIT_INST_4x(vfnmaddps, Vfnmaddps, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4703"><span class="lineNum">    4703 </span>            :   ASMJIT_INST_4x(vfnmaddps, Vfnmaddps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // FMA4</a>
+<a name="4704"><span class="lineNum">    4704 </span>            :   ASMJIT_INST_4x(vfnmaddps, Vfnmaddps, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // FMA4</a>
+<a name="4705"><span class="lineNum">    4705 </span>            :   ASMJIT_INST_4x(vfnmaddps, Vfnmaddps, X86Ymm, X86Ymm, X86Ymm, X86Mem)        // FMA4</a>
+<a name="4706"><span class="lineNum">    4706 </span>            :   ASMJIT_INST_4x(vfnmaddsd, Vfnmaddsd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4707"><span class="lineNum">    4707 </span>            :   ASMJIT_INST_4x(vfnmaddsd, Vfnmaddsd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4708"><span class="lineNum">    4708 </span>            :   ASMJIT_INST_4x(vfnmaddsd, Vfnmaddsd, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4709"><span class="lineNum">    4709 </span>            :   ASMJIT_INST_4x(vfnmaddss, Vfnmaddss, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4710"><span class="lineNum">    4710 </span>            :   ASMJIT_INST_4x(vfnmaddss, Vfnmaddss, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4711"><span class="lineNum">    4711 </span>            :   ASMJIT_INST_4x(vfnmaddss, Vfnmaddss, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4712"><span class="lineNum">    4712 </span>            :   ASMJIT_INST_4x(vfnmsubpd, Vfnmsubpd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4713"><span class="lineNum">    4713 </span>            :   ASMJIT_INST_4x(vfnmsubpd, Vfnmsubpd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4714"><span class="lineNum">    4714 </span>            :   ASMJIT_INST_4x(vfnmsubpd, Vfnmsubpd, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4715"><span class="lineNum">    4715 </span>            :   ASMJIT_INST_4x(vfnmsubpd, Vfnmsubpd, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // FMA4</a>
+<a name="4716"><span class="lineNum">    4716 </span>            :   ASMJIT_INST_4x(vfnmsubpd, Vfnmsubpd, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // FMA4</a>
+<a name="4717"><span class="lineNum">    4717 </span>            :   ASMJIT_INST_4x(vfnmsubpd, Vfnmsubpd, X86Ymm, X86Ymm, X86Ymm, X86Mem)        // FMA4</a>
+<a name="4718"><span class="lineNum">    4718 </span>            :   ASMJIT_INST_4x(vfnmsubps, Vfnmsubps, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4719"><span class="lineNum">    4719 </span>            :   ASMJIT_INST_4x(vfnmsubps, Vfnmsubps, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4720"><span class="lineNum">    4720 </span>            :   ASMJIT_INST_4x(vfnmsubps, Vfnmsubps, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4721"><span class="lineNum">    4721 </span>            :   ASMJIT_INST_4x(vfnmsubps, Vfnmsubps, X86Ymm, X86Ymm, X86Ymm, X86Ymm)        // FMA4</a>
+<a name="4722"><span class="lineNum">    4722 </span>            :   ASMJIT_INST_4x(vfnmsubps, Vfnmsubps, X86Ymm, X86Ymm, X86Mem, X86Ymm)        // FMA4</a>
+<a name="4723"><span class="lineNum">    4723 </span>            :   ASMJIT_INST_4x(vfnmsubps, Vfnmsubps, X86Ymm, X86Ymm, X86Ymm, X86Mem)        // FMA4</a>
+<a name="4724"><span class="lineNum">    4724 </span>            :   ASMJIT_INST_4x(vfnmsubsd, Vfnmsubsd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4725"><span class="lineNum">    4725 </span>            :   ASMJIT_INST_4x(vfnmsubsd, Vfnmsubsd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4726"><span class="lineNum">    4726 </span>            :   ASMJIT_INST_4x(vfnmsubsd, Vfnmsubsd, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4727"><span class="lineNum">    4727 </span>            :   ASMJIT_INST_4x(vfnmsubss, Vfnmsubss, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // FMA4</a>
+<a name="4728"><span class="lineNum">    4728 </span>            :   ASMJIT_INST_4x(vfnmsubss, Vfnmsubss, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // FMA4</a>
+<a name="4729"><span class="lineNum">    4729 </span>            :   ASMJIT_INST_4x(vfnmsubss, Vfnmsubss, X86Xmm, X86Xmm, X86Xmm, X86Mem)        // FMA4</a>
+<a name="4730"><span class="lineNum">    4730 </span>            : </a>
+<a name="4731"><span class="lineNum">    4731 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4732"><span class="lineNum">    4732 </span>            :   // [XOP]</a>
+<a name="4733"><span class="lineNum">    4733 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4734"><span class="lineNum">    4734 </span>            : </a>
+<a name="4735"><span class="lineNum">    4735 </span>            :   ASMJIT_INST_2x(vfrczpd, Vfrczpd, X86Xmm, X86Xmm)                            // XOP</a>
+<a name="4736"><span class="lineNum">    4736 </span>            :   ASMJIT_INST_2x(vfrczpd, Vfrczpd, X86Xmm, X86Mem)                            // XOP</a>
+<a name="4737"><span class="lineNum">    4737 </span>            :   ASMJIT_INST_2x(vfrczpd, Vfrczpd, X86Ymm, X86Ymm)                            // XOP</a>
+<a name="4738"><span class="lineNum">    4738 </span>            :   ASMJIT_INST_2x(vfrczpd, Vfrczpd, X86Ymm, X86Mem)                            // XOP</a>
+<a name="4739"><span class="lineNum">    4739 </span>            :   ASMJIT_INST_2x(vfrczps, Vfrczps, X86Xmm, X86Xmm)                            // XOP</a>
+<a name="4740"><span class="lineNum">    4740 </span>            :   ASMJIT_INST_2x(vfrczps, Vfrczps, X86Xmm, X86Mem)                            // XOP</a>
+<a name="4741"><span class="lineNum">    4741 </span>            :   ASMJIT_INST_2x(vfrczps, Vfrczps, X86Ymm, X86Ymm)                            // XOP</a>
+<a name="4742"><span class="lineNum">    4742 </span>            :   ASMJIT_INST_2x(vfrczps, Vfrczps, X86Ymm, X86Mem)                            // XOP</a>
+<a name="4743"><span class="lineNum">    4743 </span>            :   ASMJIT_INST_2x(vfrczsd, Vfrczsd, X86Xmm, X86Xmm)                            // XOP</a>
+<a name="4744"><span class="lineNum">    4744 </span>            :   ASMJIT_INST_2x(vfrczsd, Vfrczsd, X86Xmm, X86Mem)                            // XOP</a>
+<a name="4745"><span class="lineNum">    4745 </span>            :   ASMJIT_INST_2x(vfrczss, Vfrczss, X86Xmm, X86Xmm)                            // XOP</a>
+<a name="4746"><span class="lineNum">    4746 </span>            :   ASMJIT_INST_2x(vfrczss, Vfrczss, X86Xmm, X86Mem)                            // XOP</a>
+<a name="4747"><span class="lineNum">    4747 </span>            :   ASMJIT_INST_4x(vpcmov, Vpcmov, X86Xmm, X86Xmm, X86Xmm, X86Xmm)              // XOP</a>
+<a name="4748"><span class="lineNum">    4748 </span>            :   ASMJIT_INST_4x(vpcmov, Vpcmov, X86Xmm, X86Xmm, X86Mem, X86Xmm)              // XOP</a>
+<a name="4749"><span class="lineNum">    4749 </span>            :   ASMJIT_INST_4x(vpcmov, Vpcmov, X86Xmm, X86Xmm, X86Xmm, X86Mem)              // XOP</a>
+<a name="4750"><span class="lineNum">    4750 </span>            :   ASMJIT_INST_4x(vpcmov, Vpcmov, X86Ymm, X86Ymm, X86Ymm, X86Ymm)              // XOP</a>
+<a name="4751"><span class="lineNum">    4751 </span>            :   ASMJIT_INST_4x(vpcmov, Vpcmov, X86Ymm, X86Ymm, X86Mem, X86Ymm)              // XOP</a>
+<a name="4752"><span class="lineNum">    4752 </span>            :   ASMJIT_INST_4x(vpcmov, Vpcmov, X86Ymm, X86Ymm, X86Ymm, X86Mem)              // XOP</a>
+<a name="4753"><span class="lineNum">    4753 </span>            :   ASMJIT_INST_4i(vpcomb, Vpcomb, X86Xmm, X86Xmm, X86Xmm, Imm)                 // XOP</a>
+<a name="4754"><span class="lineNum">    4754 </span>            :   ASMJIT_INST_4i(vpcomb, Vpcomb, X86Xmm, X86Xmm, X86Mem, Imm)                 // XOP</a>
+<a name="4755"><span class="lineNum">    4755 </span>            :   ASMJIT_INST_4i(vpcomd, Vpcomd, X86Xmm, X86Xmm, X86Xmm, Imm)                 // XOP</a>
+<a name="4756"><span class="lineNum">    4756 </span>            :   ASMJIT_INST_4i(vpcomd, Vpcomd, X86Xmm, X86Xmm, X86Mem, Imm)                 // XOP</a>
+<a name="4757"><span class="lineNum">    4757 </span>            :   ASMJIT_INST_4i(vpcomq, Vpcomq, X86Xmm, X86Xmm, X86Xmm, Imm)                 // XOP</a>
+<a name="4758"><span class="lineNum">    4758 </span>            :   ASMJIT_INST_4i(vpcomq, Vpcomq, X86Xmm, X86Xmm, X86Mem, Imm)                 // XOP</a>
+<a name="4759"><span class="lineNum">    4759 </span>            :   ASMJIT_INST_4i(vpcomw, Vpcomw, X86Xmm, X86Xmm, X86Xmm, Imm)                 // XOP</a>
+<a name="4760"><span class="lineNum">    4760 </span>            :   ASMJIT_INST_4i(vpcomw, Vpcomw, X86Xmm, X86Xmm, X86Mem, Imm)                 // XOP</a>
+<a name="4761"><span class="lineNum">    4761 </span>            :   ASMJIT_INST_4i(vpcomub, Vpcomub, X86Xmm, X86Xmm, X86Xmm, Imm)               // XOP</a>
+<a name="4762"><span class="lineNum">    4762 </span>            :   ASMJIT_INST_4i(vpcomub, Vpcomub, X86Xmm, X86Xmm, X86Mem, Imm)               // XOP</a>
+<a name="4763"><span class="lineNum">    4763 </span>            :   ASMJIT_INST_4i(vpcomud, Vpcomud, X86Xmm, X86Xmm, X86Xmm, Imm)               // XOP</a>
+<a name="4764"><span class="lineNum">    4764 </span>            :   ASMJIT_INST_4i(vpcomud, Vpcomud, X86Xmm, X86Xmm, X86Mem, Imm)               // XOP</a>
+<a name="4765"><span class="lineNum">    4765 </span>            :   ASMJIT_INST_4i(vpcomuq, Vpcomuq, X86Xmm, X86Xmm, X86Xmm, Imm)               // XOP</a>
+<a name="4766"><span class="lineNum">    4766 </span>            :   ASMJIT_INST_4i(vpcomuq, Vpcomuq, X86Xmm, X86Xmm, X86Mem, Imm)               // XOP</a>
+<a name="4767"><span class="lineNum">    4767 </span>            :   ASMJIT_INST_4i(vpcomuw, Vpcomuw, X86Xmm, X86Xmm, X86Xmm, Imm)               // XOP</a>
+<a name="4768"><span class="lineNum">    4768 </span>            :   ASMJIT_INST_4i(vpcomuw, Vpcomuw, X86Xmm, X86Xmm, X86Mem, Imm)               // XOP</a>
+<a name="4769"><span class="lineNum">    4769 </span>            :   ASMJIT_INST_5i(vpermil2pd, Vpermil2pd, X86Xmm, X86Xmm, X86Xmm, X86Xmm, Imm) // XOP</a>
+<a name="4770"><span class="lineNum">    4770 </span>            :   ASMJIT_INST_5i(vpermil2pd, Vpermil2pd, X86Xmm, X86Xmm, X86Mem, X86Xmm, Imm) // XOP</a>
+<a name="4771"><span class="lineNum">    4771 </span>            :   ASMJIT_INST_5i(vpermil2pd, Vpermil2pd, X86Xmm, X86Xmm, X86Xmm, X86Mem, Imm) // XOP</a>
+<a name="4772"><span class="lineNum">    4772 </span>            :   ASMJIT_INST_5i(vpermil2pd, Vpermil2pd, X86Ymm, X86Ymm, X86Ymm, X86Ymm, Imm) // XOP</a>
+<a name="4773"><span class="lineNum">    4773 </span>            :   ASMJIT_INST_5i(vpermil2pd, Vpermil2pd, X86Ymm, X86Ymm, X86Mem, X86Ymm, Imm) // XOP</a>
+<a name="4774"><span class="lineNum">    4774 </span>            :   ASMJIT_INST_5i(vpermil2pd, Vpermil2pd, X86Ymm, X86Ymm, X86Ymm, X86Mem, Imm) // XOP</a>
+<a name="4775"><span class="lineNum">    4775 </span>            :   ASMJIT_INST_5i(vpermil2ps, Vpermil2ps, X86Xmm, X86Xmm, X86Xmm, X86Xmm, Imm) // XOP</a>
+<a name="4776"><span class="lineNum">    4776 </span>            :   ASMJIT_INST_5i(vpermil2ps, Vpermil2ps, X86Xmm, X86Xmm, X86Mem, X86Xmm, Imm) // XOP</a>
+<a name="4777"><span class="lineNum">    4777 </span>            :   ASMJIT_INST_5i(vpermil2ps, Vpermil2ps, X86Xmm, X86Xmm, X86Xmm, X86Mem, Imm) // XOP</a>
+<a name="4778"><span class="lineNum">    4778 </span>            :   ASMJIT_INST_5i(vpermil2ps, Vpermil2ps, X86Ymm, X86Ymm, X86Ymm, X86Ymm, Imm) // XOP</a>
+<a name="4779"><span class="lineNum">    4779 </span>            :   ASMJIT_INST_5i(vpermil2ps, Vpermil2ps, X86Ymm, X86Ymm, X86Mem, X86Ymm, Imm) // XOP</a>
+<a name="4780"><span class="lineNum">    4780 </span>            :   ASMJIT_INST_5i(vpermil2ps, Vpermil2ps, X86Ymm, X86Ymm, X86Ymm, X86Mem, Imm) // XOP</a>
+<a name="4781"><span class="lineNum">    4781 </span>            :   ASMJIT_INST_2x(vphaddbd, Vphaddbd, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4782"><span class="lineNum">    4782 </span>            :   ASMJIT_INST_2x(vphaddbd, Vphaddbd, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4783"><span class="lineNum">    4783 </span>            :   ASMJIT_INST_2x(vphaddbq, Vphaddbq, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4784"><span class="lineNum">    4784 </span>            :   ASMJIT_INST_2x(vphaddbq, Vphaddbq, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4785"><span class="lineNum">    4785 </span>            :   ASMJIT_INST_2x(vphaddbw, Vphaddbw, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4786"><span class="lineNum">    4786 </span>            :   ASMJIT_INST_2x(vphaddbw, Vphaddbw, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4787"><span class="lineNum">    4787 </span>            :   ASMJIT_INST_2x(vphadddq, Vphadddq, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4788"><span class="lineNum">    4788 </span>            :   ASMJIT_INST_2x(vphadddq, Vphadddq, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4789"><span class="lineNum">    4789 </span>            :   ASMJIT_INST_2x(vphaddwd, Vphaddwd, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4790"><span class="lineNum">    4790 </span>            :   ASMJIT_INST_2x(vphaddwd, Vphaddwd, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4791"><span class="lineNum">    4791 </span>            :   ASMJIT_INST_2x(vphaddwq, Vphaddwq, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4792"><span class="lineNum">    4792 </span>            :   ASMJIT_INST_2x(vphaddwq, Vphaddwq, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4793"><span class="lineNum">    4793 </span>            :   ASMJIT_INST_2x(vphaddubd, Vphaddubd, X86Xmm, X86Xmm)                        // XOP</a>
+<a name="4794"><span class="lineNum">    4794 </span>            :   ASMJIT_INST_2x(vphaddubd, Vphaddubd, X86Xmm, X86Mem)                        // XOP</a>
+<a name="4795"><span class="lineNum">    4795 </span>            :   ASMJIT_INST_2x(vphaddubq, Vphaddubq, X86Xmm, X86Xmm)                        // XOP</a>
+<a name="4796"><span class="lineNum">    4796 </span>            :   ASMJIT_INST_2x(vphaddubq, Vphaddubq, X86Xmm, X86Mem)                        // XOP</a>
+<a name="4797"><span class="lineNum">    4797 </span>            :   ASMJIT_INST_2x(vphaddubw, Vphaddubw, X86Xmm, X86Xmm)                        // XOP</a>
+<a name="4798"><span class="lineNum">    4798 </span>            :   ASMJIT_INST_2x(vphaddubw, Vphaddubw, X86Xmm, X86Mem)                        // XOP</a>
+<a name="4799"><span class="lineNum">    4799 </span>            :   ASMJIT_INST_2x(vphaddudq, Vphaddudq, X86Xmm, X86Xmm)                        // XOP</a>
+<a name="4800"><span class="lineNum">    4800 </span>            :   ASMJIT_INST_2x(vphaddudq, Vphaddudq, X86Xmm, X86Mem)                        // XOP</a>
+<a name="4801"><span class="lineNum">    4801 </span>            :   ASMJIT_INST_2x(vphadduwd, Vphadduwd, X86Xmm, X86Xmm)                        // XOP</a>
+<a name="4802"><span class="lineNum">    4802 </span>            :   ASMJIT_INST_2x(vphadduwd, Vphadduwd, X86Xmm, X86Mem)                        // XOP</a>
+<a name="4803"><span class="lineNum">    4803 </span>            :   ASMJIT_INST_2x(vphadduwq, Vphadduwq, X86Xmm, X86Xmm)                        // XOP</a>
+<a name="4804"><span class="lineNum">    4804 </span>            :   ASMJIT_INST_2x(vphadduwq, Vphadduwq, X86Xmm, X86Mem)                        // XOP</a>
+<a name="4805"><span class="lineNum">    4805 </span>            :   ASMJIT_INST_2x(vphsubbw, Vphsubbw, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4806"><span class="lineNum">    4806 </span>            :   ASMJIT_INST_2x(vphsubbw, Vphsubbw, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4807"><span class="lineNum">    4807 </span>            :   ASMJIT_INST_2x(vphsubdq, Vphsubdq, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4808"><span class="lineNum">    4808 </span>            :   ASMJIT_INST_2x(vphsubdq, Vphsubdq, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4809"><span class="lineNum">    4809 </span>            :   ASMJIT_INST_2x(vphsubwd, Vphsubwd, X86Xmm, X86Xmm)                          // XOP</a>
+<a name="4810"><span class="lineNum">    4810 </span>            :   ASMJIT_INST_2x(vphsubwd, Vphsubwd, X86Xmm, X86Mem)                          // XOP</a>
+<a name="4811"><span class="lineNum">    4811 </span>            :   ASMJIT_INST_4x(vpmacsdd, Vpmacsdd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // XOP</a>
+<a name="4812"><span class="lineNum">    4812 </span>            :   ASMJIT_INST_4x(vpmacsdd, Vpmacsdd, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // XOP</a>
+<a name="4813"><span class="lineNum">    4813 </span>            :   ASMJIT_INST_4x(vpmacsdqh, Vpmacsdqh, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // XOP</a>
+<a name="4814"><span class="lineNum">    4814 </span>            :   ASMJIT_INST_4x(vpmacsdqh, Vpmacsdqh, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // XOP</a>
+<a name="4815"><span class="lineNum">    4815 </span>            :   ASMJIT_INST_4x(vpmacsdql, Vpmacsdql, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // XOP</a>
+<a name="4816"><span class="lineNum">    4816 </span>            :   ASMJIT_INST_4x(vpmacsdql, Vpmacsdql, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // XOP</a>
+<a name="4817"><span class="lineNum">    4817 </span>            :   ASMJIT_INST_4x(vpmacswd, Vpmacswd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // XOP</a>
+<a name="4818"><span class="lineNum">    4818 </span>            :   ASMJIT_INST_4x(vpmacswd, Vpmacswd, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // XOP</a>
+<a name="4819"><span class="lineNum">    4819 </span>            :   ASMJIT_INST_4x(vpmacsww, Vpmacsww, X86Xmm, X86Xmm, X86Xmm, X86Xmm)          // XOP</a>
+<a name="4820"><span class="lineNum">    4820 </span>            :   ASMJIT_INST_4x(vpmacsww, Vpmacsww, X86Xmm, X86Xmm, X86Mem, X86Xmm)          // XOP</a>
+<a name="4821"><span class="lineNum">    4821 </span>            :   ASMJIT_INST_4x(vpmacssdd, Vpmacssdd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // XOP</a>
+<a name="4822"><span class="lineNum">    4822 </span>            :   ASMJIT_INST_4x(vpmacssdd, Vpmacssdd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // XOP</a>
+<a name="4823"><span class="lineNum">    4823 </span>            :   ASMJIT_INST_4x(vpmacssdqh, Vpmacssdqh, X86Xmm, X86Xmm, X86Xmm, X86Xmm)      // XOP</a>
+<a name="4824"><span class="lineNum">    4824 </span>            :   ASMJIT_INST_4x(vpmacssdqh, Vpmacssdqh, X86Xmm, X86Xmm, X86Mem, X86Xmm)      // XOP</a>
+<a name="4825"><span class="lineNum">    4825 </span>            :   ASMJIT_INST_4x(vpmacssdql, Vpmacssdql, X86Xmm, X86Xmm, X86Xmm, X86Xmm)      // XOP</a>
+<a name="4826"><span class="lineNum">    4826 </span>            :   ASMJIT_INST_4x(vpmacssdql, Vpmacssdql, X86Xmm, X86Xmm, X86Mem, X86Xmm)      // XOP</a>
+<a name="4827"><span class="lineNum">    4827 </span>            :   ASMJIT_INST_4x(vpmacsswd, Vpmacsswd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // XOP</a>
+<a name="4828"><span class="lineNum">    4828 </span>            :   ASMJIT_INST_4x(vpmacsswd, Vpmacsswd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // XOP</a>
+<a name="4829"><span class="lineNum">    4829 </span>            :   ASMJIT_INST_4x(vpmacssww, Vpmacssww, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // XOP</a>
+<a name="4830"><span class="lineNum">    4830 </span>            :   ASMJIT_INST_4x(vpmacssww, Vpmacssww, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // XOP</a>
+<a name="4831"><span class="lineNum">    4831 </span>            :   ASMJIT_INST_4x(vpmadcsswd, Vpmadcsswd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)      // XOP</a>
+<a name="4832"><span class="lineNum">    4832 </span>            :   ASMJIT_INST_4x(vpmadcsswd, Vpmadcsswd, X86Xmm, X86Xmm, X86Mem, X86Xmm)      // XOP</a>
+<a name="4833"><span class="lineNum">    4833 </span>            :   ASMJIT_INST_4x(vpmadcswd, Vpmadcswd, X86Xmm, X86Xmm, X86Xmm, X86Xmm)        // XOP</a>
+<a name="4834"><span class="lineNum">    4834 </span>            :   ASMJIT_INST_4x(vpmadcswd, Vpmadcswd, X86Xmm, X86Xmm, X86Mem, X86Xmm)        // XOP</a>
+<a name="4835"><span class="lineNum">    4835 </span>            :   ASMJIT_INST_4x(vpperm, Vpperm, X86Xmm, X86Xmm, X86Xmm, X86Xmm)              // XOP</a>
+<a name="4836"><span class="lineNum">    4836 </span>            :   ASMJIT_INST_4x(vpperm, Vpperm, X86Xmm, X86Xmm, X86Mem, X86Xmm)              // XOP</a>
+<a name="4837"><span class="lineNum">    4837 </span>            :   ASMJIT_INST_4x(vpperm, Vpperm, X86Xmm, X86Xmm, X86Xmm, X86Mem)              // XOP</a>
+<a name="4838"><span class="lineNum">    4838 </span>            :   ASMJIT_INST_3x(vprotb, Vprotb, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4839"><span class="lineNum">    4839 </span>            :   ASMJIT_INST_3x(vprotb, Vprotb, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4840"><span class="lineNum">    4840 </span>            :   ASMJIT_INST_3x(vprotb, Vprotb, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4841"><span class="lineNum">    4841 </span>            :   ASMJIT_INST_3i(vprotb, Vprotb, X86Xmm, X86Xmm, Imm)                         // XOP</a>
+<a name="4842"><span class="lineNum">    4842 </span>            :   ASMJIT_INST_3i(vprotb, Vprotb, X86Xmm, X86Mem, Imm)                         // XOP</a>
+<a name="4843"><span class="lineNum">    4843 </span>            :   ASMJIT_INST_3x(vprotd, Vprotd, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4844"><span class="lineNum">    4844 </span>            :   ASMJIT_INST_3x(vprotd, Vprotd, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4845"><span class="lineNum">    4845 </span>            :   ASMJIT_INST_3x(vprotd, Vprotd, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4846"><span class="lineNum">    4846 </span>            :   ASMJIT_INST_3i(vprotd, Vprotd, X86Xmm, X86Xmm, Imm)                         // XOP</a>
+<a name="4847"><span class="lineNum">    4847 </span>            :   ASMJIT_INST_3i(vprotd, Vprotd, X86Xmm, X86Mem, Imm)                         // XOP</a>
+<a name="4848"><span class="lineNum">    4848 </span>            :   ASMJIT_INST_3x(vprotq, Vprotq, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4849"><span class="lineNum">    4849 </span>            :   ASMJIT_INST_3x(vprotq, Vprotq, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4850"><span class="lineNum">    4850 </span>            :   ASMJIT_INST_3x(vprotq, Vprotq, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4851"><span class="lineNum">    4851 </span>            :   ASMJIT_INST_3i(vprotq, Vprotq, X86Xmm, X86Xmm, Imm)                         // XOP</a>
+<a name="4852"><span class="lineNum">    4852 </span>            :   ASMJIT_INST_3i(vprotq, Vprotq, X86Xmm, X86Mem, Imm)                         // XOP</a>
+<a name="4853"><span class="lineNum">    4853 </span>            :   ASMJIT_INST_3x(vprotw, Vprotw, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4854"><span class="lineNum">    4854 </span>            :   ASMJIT_INST_3x(vprotw, Vprotw, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4855"><span class="lineNum">    4855 </span>            :   ASMJIT_INST_3x(vprotw, Vprotw, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4856"><span class="lineNum">    4856 </span>            :   ASMJIT_INST_3i(vprotw, Vprotw, X86Xmm, X86Xmm, Imm)                         // XOP</a>
+<a name="4857"><span class="lineNum">    4857 </span>            :   ASMJIT_INST_3i(vprotw, Vprotw, X86Xmm, X86Mem, Imm)                         // XOP</a>
+<a name="4858"><span class="lineNum">    4858 </span>            :   ASMJIT_INST_3x(vpshab, Vpshab, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4859"><span class="lineNum">    4859 </span>            :   ASMJIT_INST_3x(vpshab, Vpshab, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4860"><span class="lineNum">    4860 </span>            :   ASMJIT_INST_3x(vpshab, Vpshab, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4861"><span class="lineNum">    4861 </span>            :   ASMJIT_INST_3x(vpshad, Vpshad, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4862"><span class="lineNum">    4862 </span>            :   ASMJIT_INST_3x(vpshad, Vpshad, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4863"><span class="lineNum">    4863 </span>            :   ASMJIT_INST_3x(vpshad, Vpshad, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4864"><span class="lineNum">    4864 </span>            :   ASMJIT_INST_3x(vpshaq, Vpshaq, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4865"><span class="lineNum">    4865 </span>            :   ASMJIT_INST_3x(vpshaq, Vpshaq, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4866"><span class="lineNum">    4866 </span>            :   ASMJIT_INST_3x(vpshaq, Vpshaq, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4867"><span class="lineNum">    4867 </span>            :   ASMJIT_INST_3x(vpshaw, Vpshaw, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4868"><span class="lineNum">    4868 </span>            :   ASMJIT_INST_3x(vpshaw, Vpshaw, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4869"><span class="lineNum">    4869 </span>            :   ASMJIT_INST_3x(vpshaw, Vpshaw, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4870"><span class="lineNum">    4870 </span>            :   ASMJIT_INST_3x(vpshlb, Vpshlb, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4871"><span class="lineNum">    4871 </span>            :   ASMJIT_INST_3x(vpshlb, Vpshlb, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4872"><span class="lineNum">    4872 </span>            :   ASMJIT_INST_3x(vpshlb, Vpshlb, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4873"><span class="lineNum">    4873 </span>            :   ASMJIT_INST_3x(vpshld, Vpshld, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4874"><span class="lineNum">    4874 </span>            :   ASMJIT_INST_3x(vpshld, Vpshld, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4875"><span class="lineNum">    4875 </span>            :   ASMJIT_INST_3x(vpshld, Vpshld, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4876"><span class="lineNum">    4876 </span>            :   ASMJIT_INST_3x(vpshlq, Vpshlq, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4877"><span class="lineNum">    4877 </span>            :   ASMJIT_INST_3x(vpshlq, Vpshlq, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4878"><span class="lineNum">    4878 </span>            :   ASMJIT_INST_3x(vpshlq, Vpshlq, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4879"><span class="lineNum">    4879 </span>            :   ASMJIT_INST_3x(vpshlw, Vpshlw, X86Xmm, X86Xmm, X86Xmm)                      // XOP</a>
+<a name="4880"><span class="lineNum">    4880 </span>            :   ASMJIT_INST_3x(vpshlw, Vpshlw, X86Xmm, X86Mem, X86Xmm)                      // XOP</a>
+<a name="4881"><span class="lineNum">    4881 </span>            :   ASMJIT_INST_3x(vpshlw, Vpshlw, X86Xmm, X86Xmm, X86Mem)                      // XOP</a>
+<a name="4882"><span class="lineNum">    4882 </span>            : };</a>
+<a name="4883"><span class="lineNum">    4883 </span>            : </a>
+<a name="4884"><span class="lineNum">    4884 </span>            : // ============================================================================</a>
+<a name="4885"><span class="lineNum">    4885 </span>            : // [asmjit::X86EmitterImplicitT]</a>
+<a name="4886"><span class="lineNum">    4886 </span>            : // ============================================================================</a>
+<a name="4887"><span class="lineNum">    4887 </span>            : </a>
+<a name="4888"><span class="lineNum">    4888 </span>            : template&lt;typename This&gt;</a>
+<a name="4889"><span class="lineNum">    4889 </span>            : struct X86EmitterImplicitT : public X86EmitterExplicitT&lt;This&gt; {</a>
+<a name="4890"><span class="lineNum">    4890 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4891"><span class="lineNum">    4891 </span>            :   // [Options]</a>
+<a name="4892"><span class="lineNum">    4892 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4893"><span class="lineNum">    4893 </span>            : </a>
+<a name="4894"><span class="lineNum">    4894 </span>            :   //! Use REP/REPZ prefix.</a>
+<a name="4895"><span class="lineNum">    4895 </span>            :   ASMJIT_INLINE This&amp; rep() noexcept { return X86EmitterExplicitT&lt;This&gt;::_addOptions(X86Inst::kOptionRep); }</a>
+<a name="4896"><span class="lineNum">    4896 </span>            :   //! Use REPNZ prefix.</a>
+<a name="4897"><span class="lineNum">    4897 </span>            :   ASMJIT_INLINE This&amp; repnz() noexcept { return X86EmitterExplicitT&lt;This&gt;::_addOptions(X86Inst::kOptionRepnz); }</a>
+<a name="4898"><span class="lineNum">    4898 </span>            : </a>
+<a name="4899"><span class="lineNum">    4899 </span>            :   //! Use REP/REPZ prefix.</a>
+<a name="4900"><span class="lineNum">    4900 </span>            :   ASMJIT_INLINE This&amp; repe() noexcept { return rep(); }</a>
+<a name="4901"><span class="lineNum">    4901 </span>            :   //! Use REP/REPZ prefix.</a>
+<a name="4902"><span class="lineNum">    4902 </span>            :   ASMJIT_INLINE This&amp; repz() noexcept { return rep(); }</a>
+<a name="4903"><span class="lineNum">    4903 </span>            :   //! Use REPNZ prefix.</a>
+<a name="4904"><span class="lineNum">    4904 </span>            :   ASMJIT_INLINE This&amp; repne() noexcept { return repnz(); }</a>
+<a name="4905"><span class="lineNum">    4905 </span>            : </a>
+<a name="4906"><span class="lineNum">    4906 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4907"><span class="lineNum">    4907 </span>            :   // [General Purpose and Non-SIMD Instructions]</a>
+<a name="4908"><span class="lineNum">    4908 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="4909"><span class="lineNum">    4909 </span>            : </a>
+<a name="4910"><span class="lineNum">    4910 </span>            :   // TODO: xrstor and xsave don't have explicit variants yet.</a>
+<a name="4911"><span class="lineNum">    4911 </span>            : </a>
+<a name="4912"><span class="lineNum">    4912 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cbw;</a>
+<a name="4913"><span class="lineNum">    4913 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cdq;</a>
+<a name="4914"><span class="lineNum">    4914 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cdqe;</a>
+<a name="4915"><span class="lineNum">    4915 </span>            :   using X86EmitterExplicitT&lt;This&gt;::clzero;</a>
+<a name="4916"><span class="lineNum">    4916 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cqo;</a>
+<a name="4917"><span class="lineNum">    4917 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cwd;</a>
+<a name="4918"><span class="lineNum">    4918 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cwde;</a>
+<a name="4919"><span class="lineNum">    4919 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cmpsd;</a>
+<a name="4920"><span class="lineNum">    4920 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cmpxchg;</a>
+<a name="4921"><span class="lineNum">    4921 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cmpxchg8b;</a>
+<a name="4922"><span class="lineNum">    4922 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cmpxchg16b;</a>
+<a name="4923"><span class="lineNum">    4923 </span>            :   using X86EmitterExplicitT&lt;This&gt;::cpuid;</a>
+<a name="4924"><span class="lineNum">    4924 </span>            :   using X86EmitterExplicitT&lt;This&gt;::div;</a>
+<a name="4925"><span class="lineNum">    4925 </span>            :   using X86EmitterExplicitT&lt;This&gt;::idiv;</a>
+<a name="4926"><span class="lineNum">    4926 </span>            :   using X86EmitterExplicitT&lt;This&gt;::imul;</a>
+<a name="4927"><span class="lineNum">    4927 </span>            :   using X86EmitterExplicitT&lt;This&gt;::jecxz;</a>
+<a name="4928"><span class="lineNum">    4928 </span>            :   using X86EmitterExplicitT&lt;This&gt;::lahf;</a>
+<a name="4929"><span class="lineNum">    4929 </span>            :   using X86EmitterExplicitT&lt;This&gt;::mulx;</a>
+<a name="4930"><span class="lineNum">    4930 </span>            :   using X86EmitterExplicitT&lt;This&gt;::movsd;</a>
+<a name="4931"><span class="lineNum">    4931 </span>            :   using X86EmitterExplicitT&lt;This&gt;::mul;</a>
+<a name="4932"><span class="lineNum">    4932 </span>            :   using X86EmitterExplicitT&lt;This&gt;::rdmsr;</a>
+<a name="4933"><span class="lineNum">    4933 </span>            :   using X86EmitterExplicitT&lt;This&gt;::rdpmc;</a>
+<a name="4934"><span class="lineNum">    4934 </span>            :   using X86EmitterExplicitT&lt;This&gt;::rdtsc;</a>
+<a name="4935"><span class="lineNum">    4935 </span>            :   using X86EmitterExplicitT&lt;This&gt;::rdtscp;</a>
+<a name="4936"><span class="lineNum">    4936 </span>            :   using X86EmitterExplicitT&lt;This&gt;::sahf;</a>
+<a name="4937"><span class="lineNum">    4937 </span>            :   using X86EmitterExplicitT&lt;This&gt;::wrmsr;</a>
+<a name="4938"><span class="lineNum">    4938 </span>            :   using X86EmitterExplicitT&lt;This&gt;::xgetbv;</a>
+<a name="4939"><span class="lineNum">    4939 </span>            :   using X86EmitterExplicitT&lt;This&gt;::xsetbv;</a>
+<a name="4940"><span class="lineNum">    4940 </span>            : </a>
+<a name="4941"><span class="lineNum">    4941 </span>            :   ASMJIT_INST_0x(cbw, Cbw)                                                    // ANY       [IMPLICIT] AX      &lt;- Sign Extend AL</a>
+<a name="4942"><span class="lineNum">    4942 </span>            :   ASMJIT_INST_0x(cdq, Cdq)                                                    // ANY       [IMPLICIT] EDX:EAX &lt;- Sign Extend EAX</a>
+<a name="4943"><span class="lineNum">    4943 </span>            :   ASMJIT_INST_0x(cdqe, Cdqe)                                                  // X64       [IMPLICIT] RAX     &lt;- Sign Extend EAX</a>
+<a name="4944"><span class="lineNum">    4944 </span>            :   ASMJIT_INST_0x(clzero, Clzero)                                              // CLZERO    [IMPLICIT]</a>
+<a name="4945"><span class="lineNum">    4945 </span>            :   ASMJIT_INST_2x(cmpxchg, Cmpxchg, X86Gp, X86Gp)                              // I486      [IMPLICIT]</a>
+<a name="4946"><span class="lineNum">    4946 </span>            :   ASMJIT_INST_2x(cmpxchg, Cmpxchg, X86Mem, X86Gp)                             // I486      [IMPLICIT]</a>
+<a name="4947"><span class="lineNum">    4947 </span>            :   ASMJIT_INST_1x(cmpxchg16b, Cmpxchg16b, X86Mem)                              // CMPXCHG8B [IMPLICIT] m == RDX:RAX ? m &lt;- RCX:RBX</a>
+<a name="4948"><span class="lineNum">    4948 </span>            :   ASMJIT_INST_1x(cmpxchg8b, Cmpxchg8b, X86Mem)                                // CMPXCHG16B[IMPLICIT] m == EDX:EAX ? m &lt;- ECX:EBX</a>
+<a name="4949"><span class="lineNum">    4949 </span>            :   ASMJIT_INST_0x(cpuid, Cpuid)                                                // I486      [IMPLICIT] EAX:EBX:ECX:EDX  &lt;- CPUID[EAX:ECX]</a>
+<a name="4950"><span class="lineNum">    4950 </span>            :   ASMJIT_INST_0x(cqo, Cqo)                                                    // X64       [IMPLICIT] RDX:RAX &lt;- Sign Extend RAX</a>
+<a name="4951"><span class="lineNum">    4951 </span>            :   ASMJIT_INST_0x(cwd, Cwd)                                                    // ANY       [IMPLICIT] DX:AX   &lt;- Sign Extend AX</a>
+<a name="4952"><span class="lineNum">    4952 </span>            :   ASMJIT_INST_0x(cwde, Cwde)                                                  // ANY       [IMPLICIT] EAX     &lt;- Sign Extend AX</a>
+<a name="4953"><span class="lineNum">    4953 </span>            :   ASMJIT_INST_0x(daa, Daa)</a>
+<a name="4954"><span class="lineNum">    4954 </span>            :   ASMJIT_INST_0x(das, Das)</a>
+<a name="4955"><span class="lineNum">    4955 </span>            :   ASMJIT_INST_1x(div, Div, X86Gp)                                             // ANY       [IMPLICIT] {AH[Rem]: AL[Quot] &lt;- AX / r8} {xDX[Rem]:xAX[Quot] &lt;- DX:AX / r16|r32|r64}</a>
+<a name="4956"><span class="lineNum">    4956 </span>            :   ASMJIT_INST_1x(div, Div, X86Mem)                                            // ANY       [IMPLICIT] {AH[Rem]: AL[Quot] &lt;- AX / m8} {xDX[Rem]:xAX[Quot] &lt;- DX:AX / m16|m32|m64}</a>
+<a name="4957"><span class="lineNum">    4957 </span>            :   ASMJIT_INST_1x(idiv, Idiv, X86Gp)                                           // ANY       [IMPLICIT] {AH[Rem]: AL[Quot] &lt;- AX / r8} {xDX[Rem]:xAX[Quot] &lt;- DX:AX / r16|r32|r64}</a>
+<a name="4958"><span class="lineNum">    4958 </span>            :   ASMJIT_INST_1x(idiv, Idiv, X86Mem)                                          // ANY       [IMPLICIT] {AH[Rem]: AL[Quot] &lt;- AX / m8} {xDX[Rem]:xAX[Quot] &lt;- DX:AX / m16|m32|m64}</a>
+<a name="4959"><span class="lineNum">    4959 </span>            :   ASMJIT_INST_1x(imul, Imul, X86Gp)                                           // ANY       [IMPLICIT] {AX &lt;- AL * r8} {xAX:xDX &lt;- xAX * r16|r32|r64}</a>
+<a name="4960"><span class="lineNum">    4960 </span>            :   ASMJIT_INST_1x(imul, Imul, X86Mem)                                          // ANY       [IMPLICIT] {AX &lt;- AL * m8} {xAX:xDX &lt;- xAX * m16|m32|m64}</a>
+<a name="4961"><span class="lineNum">    4961 </span>            :   ASMJIT_INST_0x(iret, Iret)                                                  // ANY       [IMPLICIT]</a>
+<a name="4962"><span class="lineNum">    4962 </span>            :   ASMJIT_INST_0x(iretd, Iretd)                                                // ANY       [IMPLICIT]</a>
+<a name="4963"><span class="lineNum">    4963 </span>            :   ASMJIT_INST_0x(iretq, Iretq)                                                // X64       [IMPLICIT]</a>
+<a name="4964"><span class="lineNum">    4964 </span>            :   ASMJIT_INST_0x(iretw, Iretw)                                                // ANY       [IMPLICIT]</a>
+<a name="4965"><span class="lineNum">    4965 </span>            :   ASMJIT_INST_1x(jecxz, Jecxz, Label)                                         // ANY       [IMPLICIT] Short jump if CX/ECX/RCX is zero.</a>
+<a name="4966"><span class="lineNum">    4966 </span>            :   ASMJIT_INST_1x(jecxz, Jecxz, Imm)                                           // ANY       [IMPLICIT] Short jump if CX/ECX/RCX is zero.</a>
+<a name="4967"><span class="lineNum">    4967 </span>            :   ASMJIT_INST_1x(jecxz, Jecxz, uint64_t)                                      // ANY       [IMPLICIT] Short jump if CX/ECX/RCX is zero.</a>
+<a name="4968"><span class="lineNum">    4968 </span>            :   ASMJIT_INST_0x(lahf, Lahf)                                                  // LAHFSAHF  [IMPLICIT] AH &lt;- EFL</a>
+<a name="4969"><span class="lineNum">    4969 </span>            :   ASMJIT_INST_1x(loop, Loop, Label)                                           // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0.</a>
+<a name="4970"><span class="lineNum">    4970 </span>            :   ASMJIT_INST_1x(loop, Loop, Imm)                                             // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0.</a>
+<a name="4971"><span class="lineNum">    4971 </span>            :   ASMJIT_INST_1x(loop, Loop, uint64_t)                                        // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0.</a>
+<a name="4972"><span class="lineNum">    4972 </span>            :   ASMJIT_INST_1x(loope, Loope, Label)                                         // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 1.</a>
+<a name="4973"><span class="lineNum">    4973 </span>            :   ASMJIT_INST_1x(loope, Loope, Imm)                                           // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 1.</a>
+<a name="4974"><span class="lineNum">    4974 </span>            :   ASMJIT_INST_1x(loope, Loope, uint64_t)                                      // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 1.</a>
+<a name="4975"><span class="lineNum">    4975 </span>            :   ASMJIT_INST_1x(loopne, Loopne, Label)                                       // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 0.</a>
+<a name="4976"><span class="lineNum">    4976 </span>            :   ASMJIT_INST_1x(loopne, Loopne, Imm)                                         // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 0.</a>
+<a name="4977"><span class="lineNum">    4977 </span>            :   ASMJIT_INST_1x(loopne, Loopne, uint64_t)                                    // ANY       [IMPLICIT] Decrement xCX; short jump if xCX != 0 &amp;&amp; ZF == 0.</a>
+<a name="4978"><span class="lineNum">    4978 </span>            :   ASMJIT_INST_1x(mul, Mul, X86Gp)                                             // ANY       [IMPLICIT] {AX &lt;- AL * r8} {xDX:xAX &lt;- xAX * r16|r32|r64}</a>
+<a name="4979"><span class="lineNum">    4979 </span>            :   ASMJIT_INST_1x(mul, Mul, X86Mem)                                            // ANY       [IMPLICIT] {AX &lt;- AL * m8} {xDX:xAX &lt;- xAX * m16|m32|m64}</a>
+<a name="4980"><span class="lineNum">    4980 </span>            :   ASMJIT_INST_3x(mulx, Mulx, X86Gp, X86Gp, X86Gp)                             // BMI2      [IMPLICIT]</a>
+<a name="4981"><span class="lineNum">    4981 </span>            :   ASMJIT_INST_3x(mulx, Mulx, X86Gp, X86Gp, X86Mem)                            // BMI2      [IMPLICIT]</a>
+<a name="4982"><span class="lineNum">    4982 </span>            :   ASMJIT_INST_0x(rdmsr, Rdmsr)                                                // ANY       [IMPLICIT]</a>
+<a name="4983"><span class="lineNum">    4983 </span>            :   ASMJIT_INST_0x(rdpmc, Rdpmc)                                                // ANY       [IMPLICIT]</a>
+<a name="4984"><span class="lineNum">    4984 </span>            :   ASMJIT_INST_0x(rdtsc, Rdtsc)                                                // RDTSC     [IMPLICIT] EDX:EAX &lt;- CNT</a>
+<a name="4985"><span class="lineNum">    4985 </span>            :   ASMJIT_INST_0x(rdtscp, Rdtscp)                                              // RDTSCP    [IMPLICIT] EDX:EAX:EXC &lt;- CNT</a>
+<a name="4986"><span class="lineNum">    4986 </span>            :   ASMJIT_INST_0x(ret, Ret)</a>
+<a name="4987"><span class="lineNum">    4987 </span>            :   ASMJIT_INST_1i(ret, Ret, Imm)</a>
+<a name="4988"><span class="lineNum">    4988 </span>            :   ASMJIT_INST_0x(sahf, Sahf)                                                  // LAHFSAHF  [IMPLICIT] EFL &lt;- AH</a>
+<a name="4989"><span class="lineNum">    4989 </span>            :   ASMJIT_INST_0x(syscall, Syscall)                                            // X64       [IMPLICIT]</a>
+<a name="4990"><span class="lineNum">    4990 </span>            :   ASMJIT_INST_0x(sysenter, Sysenter)                                          // X64       [IMPLICIT]</a>
+<a name="4991"><span class="lineNum">    4991 </span>            :   ASMJIT_INST_0x(sysexit, Sysexit)                                            // X64       [IMPLICIT]</a>
+<a name="4992"><span class="lineNum">    4992 </span>            :   ASMJIT_INST_0x(sysexit64, Sysexit64)                                        // X64       [IMPLICIT]</a>
+<a name="4993"><span class="lineNum">    4993 </span>            :   ASMJIT_INST_0x(sysret, Sysret)                                              // X64       [IMPLICIT]</a>
+<a name="4994"><span class="lineNum">    4994 </span>            :   ASMJIT_INST_0x(sysret64, Sysret64)                                          // X64       [IMPLICIT]</a>
+<a name="4995"><span class="lineNum">    4995 </span>            :   ASMJIT_INST_0x(wrmsr, Wrmsr)                                                // ANY       [IMPLICIT]</a>
+<a name="4996"><span class="lineNum">    4996 </span>            :   ASMJIT_INST_0x(xgetbv, Xgetbv)                                              // XSAVE     [IMPLICIT] EDX:EAX &lt;- XCR[ECX]</a>
+<a name="4997"><span class="lineNum">    4997 </span>            :   ASMJIT_INST_0x(xlatb, Xlatb)                                                // ANY       [IMPLICIT]</a>
+<a name="4998"><span class="lineNum">    4998 </span>            :   ASMJIT_INST_1x(xrstor, Xrstor, X86Mem)                                      // XSAVE     [IMPLICIT]</a>
+<a name="4999"><span class="lineNum">    4999 </span>            :   ASMJIT_INST_1x(xrstor64, Xrstor64, X86Mem)                                  // XSAVE+X64 [IMPLICIT]</a>
+<a name="5000"><span class="lineNum">    5000 </span>            :   ASMJIT_INST_1x(xrstors, Xrstors, X86Mem)                                    // XSAVE     [IMPLICIT]</a>
+<a name="5001"><span class="lineNum">    5001 </span>            :   ASMJIT_INST_1x(xrstors64, Xrstors64, X86Mem)                                // XSAVE+X64 [IMPLICIT]</a>
+<a name="5002"><span class="lineNum">    5002 </span>            :   ASMJIT_INST_1x(xsave, Xsave, X86Mem)                                        // XSAVE     [IMPLICIT]</a>
+<a name="5003"><span class="lineNum">    5003 </span>            :   ASMJIT_INST_1x(xsave64, Xsave64, X86Mem)                                    // XSAVE+X64 [IMPLICIT]</a>
+<a name="5004"><span class="lineNum">    5004 </span>            :   ASMJIT_INST_1x(xsavec, Xsavec, X86Mem)                                      // XSAVE     [IMPLICIT]</a>
+<a name="5005"><span class="lineNum">    5005 </span>            :   ASMJIT_INST_1x(xsavec64, Xsavec64, X86Mem)                                  // XSAVE+X64 [IMPLICIT]</a>
+<a name="5006"><span class="lineNum">    5006 </span>            :   ASMJIT_INST_1x(xsaveopt, Xsaveopt, X86Mem)                                  // XSAVE     [IMPLICIT]</a>
+<a name="5007"><span class="lineNum">    5007 </span>            :   ASMJIT_INST_1x(xsaveopt64, Xsaveopt64, X86Mem)                              // XSAVE+X64 [IMPLICIT]</a>
+<a name="5008"><span class="lineNum">    5008 </span>            :   ASMJIT_INST_1x(xsaves, Xsaves, X86Mem)                                      // XSAVE     [IMPLICIT]</a>
+<a name="5009"><span class="lineNum">    5009 </span>            :   ASMJIT_INST_1x(xsaves64, Xsaves64, X86Mem)                                  // XSAVE+X64 [IMPLICIT]</a>
+<a name="5010"><span class="lineNum">    5010 </span>            :   ASMJIT_INST_0x(xsetbv, Xsetbv)                                              // XSAVE     [IMPLICIT] XCR[ECX] &lt;- EDX:EAX</a>
+<a name="5011"><span class="lineNum">    5011 </span>            : </a>
+<a name="5012"><span class="lineNum">    5012 </span>            :   // String instructions aliases.</a>
+<a name="5013"><span class="lineNum">    5013 </span>            :   ASMJIT_INLINE Error cmpsb() { return ASMJIT_EMIT(X86Inst::kIdCmps, X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 1), X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 1)); }</a>
+<a name="5014"><span class="lineNum">    5014 </span>            :   ASMJIT_INLINE Error cmpsd() { return ASMJIT_EMIT(X86Inst::kIdCmps, X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 4), X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 4)); }</a>
+<a name="5015"><span class="lineNum">    5015 </span>            :   ASMJIT_INLINE Error cmpsq() { return ASMJIT_EMIT(X86Inst::kIdCmps, X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 8), X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 8)); }</a>
+<a name="5016"><span class="lineNum">    5016 </span>            :   ASMJIT_INLINE Error cmpsw() { return ASMJIT_EMIT(X86Inst::kIdCmps, X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 2), X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 2)); }</a>
+<a name="5017"><span class="lineNum">    5017 </span>            : </a>
+<a name="5018"><span class="lineNum">    5018 </span>            :   ASMJIT_INLINE Error lodsb() { return ASMJIT_EMIT(X86Inst::kIdLods, x86::al , X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 1)); }</a>
+<a name="5019"><span class="lineNum">    5019 </span>            :   ASMJIT_INLINE Error lodsd() { return ASMJIT_EMIT(X86Inst::kIdLods, x86::eax, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 4)); }</a>
+<a name="5020"><span class="lineNum">    5020 </span>            :   ASMJIT_INLINE Error lodsq() { return ASMJIT_EMIT(X86Inst::kIdLods, x86::rax, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 8)); }</a>
+<a name="5021"><span class="lineNum">    5021 </span>            :   ASMJIT_INLINE Error lodsw() { return ASMJIT_EMIT(X86Inst::kIdLods, x86::ax , X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 2)); }</a>
+<a name="5022"><span class="lineNum">    5022 </span>            : </a>
+<a name="5023"><span class="lineNum">    5023 </span>            :   ASMJIT_INLINE Error movsb() { return ASMJIT_EMIT(X86Inst::kIdMovs, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 1), X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 1)); }</a>
+<a name="5024"><span class="lineNum">    5024 </span>            :   ASMJIT_INLINE Error movsd() { return ASMJIT_EMIT(X86Inst::kIdMovs, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 4), X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 4)); }</a>
+<a name="5025"><span class="lineNum">    5025 </span>            :   ASMJIT_INLINE Error movsq() { return ASMJIT_EMIT(X86Inst::kIdMovs, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 8), X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 8)); }</a>
+<a name="5026"><span class="lineNum">    5026 </span>            :   ASMJIT_INLINE Error movsw() { return ASMJIT_EMIT(X86Inst::kIdMovs, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 2), X86EmitterExplicitT&lt;This&gt;::ptr_zsi(0, 2)); }</a>
+<a name="5027"><span class="lineNum">    5027 </span>            : </a>
+<a name="5028"><span class="lineNum">    5028 </span>            :   ASMJIT_INLINE Error scasb() { return ASMJIT_EMIT(X86Inst::kIdScas, x86::al , X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 1)); }</a>
+<a name="5029"><span class="lineNum">    5029 </span>            :   ASMJIT_INLINE Error scasd() { return ASMJIT_EMIT(X86Inst::kIdScas, x86::eax, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 4)); }</a>
+<a name="5030"><span class="lineNum">    5030 </span>            :   ASMJIT_INLINE Error scasq() { return ASMJIT_EMIT(X86Inst::kIdScas, x86::rax, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 8)); }</a>
+<a name="5031"><span class="lineNum">    5031 </span>            :   ASMJIT_INLINE Error scasw() { return ASMJIT_EMIT(X86Inst::kIdScas, x86::ax , X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 2)); }</a>
+<a name="5032"><span class="lineNum">    5032 </span>            : </a>
+<a name="5033"><span class="lineNum">    5033 </span>            :   ASMJIT_INLINE Error stosb() { return ASMJIT_EMIT(X86Inst::kIdStos, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 1), x86::al ); }</a>
+<a name="5034"><span class="lineNum">    5034 </span>            :   ASMJIT_INLINE Error stosd() { return ASMJIT_EMIT(X86Inst::kIdStos, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 4), x86::eax); }</a>
+<a name="5035"><span class="lineNum">    5035 </span>            :   ASMJIT_INLINE Error stosq() { return ASMJIT_EMIT(X86Inst::kIdStos, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 8), x86::rax); }</a>
+<a name="5036"><span class="lineNum">    5036 </span>            :   ASMJIT_INLINE Error stosw() { return ASMJIT_EMIT(X86Inst::kIdStos, X86EmitterExplicitT&lt;This&gt;::ptr_zdi(0, 2), x86::ax ); }</a>
+<a name="5037"><span class="lineNum">    5037 </span>            : </a>
+<a name="5038"><span class="lineNum">    5038 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5039"><span class="lineNum">    5039 </span>            :   // [MONITOR|MWAIT]</a>
+<a name="5040"><span class="lineNum">    5040 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5041"><span class="lineNum">    5041 </span>            : </a>
+<a name="5042"><span class="lineNum">    5042 </span>            :   ASMJIT_INST_0x(monitor, Monitor)</a>
+<a name="5043"><span class="lineNum">    5043 </span>            :   ASMJIT_INST_0x(mwait, Mwait)</a>
+<a name="5044"><span class="lineNum">    5044 </span>            : </a>
+<a name="5045"><span class="lineNum">    5045 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5046"><span class="lineNum">    5046 </span>            :   // [MMX &amp; SSE Instructions]</a>
+<a name="5047"><span class="lineNum">    5047 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5048"><span class="lineNum">    5048 </span>            : </a>
+<a name="5049"><span class="lineNum">    5049 </span>            :   using X86EmitterExplicitT&lt;This&gt;::blendvpd;</a>
+<a name="5050"><span class="lineNum">    5050 </span>            :   using X86EmitterExplicitT&lt;This&gt;::blendvps;</a>
+<a name="5051"><span class="lineNum">    5051 </span>            :   using X86EmitterExplicitT&lt;This&gt;::maskmovq;</a>
+<a name="5052"><span class="lineNum">    5052 </span>            :   using X86EmitterExplicitT&lt;This&gt;::maskmovdqu;</a>
+<a name="5053"><span class="lineNum">    5053 </span>            :   using X86EmitterExplicitT&lt;This&gt;::pblendvb;</a>
+<a name="5054"><span class="lineNum">    5054 </span>            :   using X86EmitterExplicitT&lt;This&gt;::pcmpestri;</a>
+<a name="5055"><span class="lineNum">    5055 </span>            :   using X86EmitterExplicitT&lt;This&gt;::pcmpestrm;</a>
+<a name="5056"><span class="lineNum">    5056 </span>            :   using X86EmitterExplicitT&lt;This&gt;::pcmpistri;</a>
+<a name="5057"><span class="lineNum">    5057 </span>            :   using X86EmitterExplicitT&lt;This&gt;::pcmpistrm;</a>
+<a name="5058"><span class="lineNum">    5058 </span>            : </a>
+<a name="5059"><span class="lineNum">    5059 </span>            :   ASMJIT_INST_2x(blendvpd, Blendvpd, X86Xmm, X86Xmm)                          // SSE4_1 [IMPLICIT]</a>
+<a name="5060"><span class="lineNum">    5060 </span>            :   ASMJIT_INST_2x(blendvpd, Blendvpd, X86Xmm, X86Mem)                          // SSE4_1 [IMPLICIT]</a>
+<a name="5061"><span class="lineNum">    5061 </span>            :   ASMJIT_INST_2x(blendvps, Blendvps, X86Xmm, X86Xmm)                          // SSE4_1 [IMPLICIT]</a>
+<a name="5062"><span class="lineNum">    5062 </span>            :   ASMJIT_INST_2x(blendvps, Blendvps, X86Xmm, X86Mem)                          // SSE4_1 [IMPLICIT]</a>
+<a name="5063"><span class="lineNum">    5063 </span>            :   ASMJIT_INST_2x(pblendvb, Pblendvb, X86Xmm, X86Xmm)                          // SSE4_1 [IMPLICIT]</a>
+<a name="5064"><span class="lineNum">    5064 </span>            :   ASMJIT_INST_2x(pblendvb, Pblendvb, X86Xmm, X86Mem)                          // SSE4_1 [IMPLICIT]</a>
+<a name="5065"><span class="lineNum">    5065 </span>            :   ASMJIT_INST_2x(maskmovq, Maskmovq, X86Mm, X86Mm)                            // SSE    [IMPLICIT]</a>
+<a name="5066"><span class="lineNum">    5066 </span>            :   ASMJIT_INST_2x(maskmovdqu, Maskmovdqu, X86Xmm, X86Xmm)                      // SSE2   [IMPLICIT]</a>
+<a name="5067"><span class="lineNum">    5067 </span>            :   ASMJIT_INST_3i(pcmpestri, Pcmpestri, X86Xmm, X86Xmm, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5068"><span class="lineNum">    5068 </span>            :   ASMJIT_INST_3i(pcmpestri, Pcmpestri, X86Xmm, X86Mem, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5069"><span class="lineNum">    5069 </span>            :   ASMJIT_INST_3i(pcmpestrm, Pcmpestrm, X86Xmm, X86Xmm, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5070"><span class="lineNum">    5070 </span>            :   ASMJIT_INST_3i(pcmpestrm, Pcmpestrm, X86Xmm, X86Mem, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5071"><span class="lineNum">    5071 </span>            :   ASMJIT_INST_3i(pcmpistri, Pcmpistri, X86Xmm, X86Xmm, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5072"><span class="lineNum">    5072 </span>            :   ASMJIT_INST_3i(pcmpistri, Pcmpistri, X86Xmm, X86Mem, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5073"><span class="lineNum">    5073 </span>            :   ASMJIT_INST_3i(pcmpistrm, Pcmpistrm, X86Xmm, X86Xmm, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5074"><span class="lineNum">    5074 </span>            :   ASMJIT_INST_3i(pcmpistrm, Pcmpistrm, X86Xmm, X86Mem, Imm)                   // SSE4_1 [IMPLICIT]</a>
+<a name="5075"><span class="lineNum">    5075 </span>            : </a>
+<a name="5076"><span class="lineNum">    5076 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5077"><span class="lineNum">    5077 </span>            :   // [SHA]</a>
+<a name="5078"><span class="lineNum">    5078 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5079"><span class="lineNum">    5079 </span>            : </a>
+<a name="5080"><span class="lineNum">    5080 </span>            :   using X86EmitterExplicitT&lt;This&gt;::sha256rnds2;</a>
+<a name="5081"><span class="lineNum">    5081 </span>            : </a>
+<a name="5082"><span class="lineNum">    5082 </span>            :   ASMJIT_INST_2x(sha256rnds2, Sha256rnds2, X86Xmm, X86Xmm)                    // SHA [IMPLICIT]</a>
+<a name="5083"><span class="lineNum">    5083 </span>            :   ASMJIT_INST_2x(sha256rnds2, Sha256rnds2, X86Xmm, X86Mem)                    // SHA [IMPLICIT]</a>
+<a name="5084"><span class="lineNum">    5084 </span>            : </a>
+<a name="5085"><span class="lineNum">    5085 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5086"><span class="lineNum">    5086 </span>            :   // [AVX...AVX512]</a>
+<a name="5087"><span class="lineNum">    5087 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="5088"><span class="lineNum">    5088 </span>            : </a>
+<a name="5089"><span class="lineNum">    5089 </span>            :   using X86EmitterExplicitT&lt;This&gt;::vmaskmovdqu;</a>
+<a name="5090"><span class="lineNum">    5090 </span>            :   using X86EmitterExplicitT&lt;This&gt;::vpcmpestri;</a>
+<a name="5091"><span class="lineNum">    5091 </span>            :   using X86EmitterExplicitT&lt;This&gt;::vpcmpestrm;</a>
+<a name="5092"><span class="lineNum">    5092 </span>            :   using X86EmitterExplicitT&lt;This&gt;::vpcmpistri;</a>
+<a name="5093"><span class="lineNum">    5093 </span>            :   using X86EmitterExplicitT&lt;This&gt;::vpcmpistrm;</a>
+<a name="5094"><span class="lineNum">    5094 </span>            : </a>
+<a name="5095"><span class="lineNum">    5095 </span>            :   ASMJIT_INST_2x(vmaskmovdqu, Vmaskmovdqu, X86Xmm, X86Xmm)                    // AVX  [IMPLICIT]</a>
+<a name="5096"><span class="lineNum">    5096 </span>            :   ASMJIT_INST_3i(vpcmpestri, Vpcmpestri, X86Xmm, X86Xmm, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5097"><span class="lineNum">    5097 </span>            :   ASMJIT_INST_3i(vpcmpestri, Vpcmpestri, X86Xmm, X86Mem, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5098"><span class="lineNum">    5098 </span>            :   ASMJIT_INST_3i(vpcmpestrm, Vpcmpestrm, X86Xmm, X86Xmm, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5099"><span class="lineNum">    5099 </span>            :   ASMJIT_INST_3i(vpcmpestrm, Vpcmpestrm, X86Xmm, X86Mem, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5100"><span class="lineNum">    5100 </span>            :   ASMJIT_INST_3i(vpcmpistri, Vpcmpistri, X86Xmm, X86Xmm, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5101"><span class="lineNum">    5101 </span>            :   ASMJIT_INST_3i(vpcmpistri, Vpcmpistri, X86Xmm, X86Mem, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5102"><span class="lineNum">    5102 </span>            :   ASMJIT_INST_3i(vpcmpistrm, Vpcmpistrm, X86Xmm, X86Xmm, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5103"><span class="lineNum">    5103 </span>            :   ASMJIT_INST_3i(vpcmpistrm, Vpcmpistrm, X86Xmm, X86Mem, Imm)                 // AVX  [IMPLICIT]</a>
+<a name="5104"><span class="lineNum">    5104 </span>            : };</a>
+<a name="5105"><span class="lineNum">    5105 </span>            : </a>
+<a name="5106"><span class="lineNum">    5106 </span>            : #undef ASMJIT_INST_0x</a>
+<a name="5107"><span class="lineNum">    5107 </span>            : #undef ASMJIT_INST_1x</a>
+<a name="5108"><span class="lineNum">    5108 </span>            : #undef ASMJIT_INST_1i</a>
+<a name="5109"><span class="lineNum">    5109 </span>            : #undef ASMJIT_INST_1c</a>
+<a name="5110"><span class="lineNum">    5110 </span>            : #undef ASMJIT_INST_2x</a>
+<a name="5111"><span class="lineNum">    5111 </span>            : #undef ASMJIT_INST_2i</a>
+<a name="5112"><span class="lineNum">    5112 </span>            : #undef ASMJIT_INST_2c</a>
+<a name="5113"><span class="lineNum">    5113 </span>            : #undef ASMJIT_INST_3x</a>
+<a name="5114"><span class="lineNum">    5114 </span>            : #undef ASMJIT_INST_3i</a>
+<a name="5115"><span class="lineNum">    5115 </span>            : #undef ASMJIT_INST_3ii</a>
+<a name="5116"><span class="lineNum">    5116 </span>            : #undef ASMJIT_INST_4x</a>
+<a name="5117"><span class="lineNum">    5117 </span>            : #undef ASMJIT_INST_4i</a>
+<a name="5118"><span class="lineNum">    5118 </span>            : #undef ASMJIT_INST_4ii</a>
+<a name="5119"><span class="lineNum">    5119 </span>            : #undef ASMJIT_INST_5x</a>
+<a name="5120"><span class="lineNum">    5120 </span>            : #undef ASMJIT_INST_5i</a>
+<a name="5121"><span class="lineNum">    5121 </span>            : #undef ASMJIT_INST_6x</a>
+<a name="5122"><span class="lineNum">    5122 </span>            : #undef ASMJIT_EMIT</a>
+<a name="5123"><span class="lineNum">    5123 </span>            : </a>
+<a name="5124"><span class="lineNum">    5124 </span>            : // ============================================================================</a>
+<a name="5125"><span class="lineNum">    5125 </span>            : // [asmjit::X86Emitter]</a>
+<a name="5126"><span class="lineNum">    5126 </span>            : // ============================================================================</a>
+<a name="5127"><span class="lineNum">    5127 </span>            : </a>
+<a name="5128"><span class="lineNum">    5128 </span>            : //! X86/X64 emitter.</a>
+<a name="5129"><span class="lineNum">    5129 </span>            : //!</a>
+<a name="5130"><span class="lineNum">    5130 </span>            : //! NOTE: This class cannot be created, you can only cast to it and use it as</a>
+<a name="5131"><span class="lineNum">    5131 </span>            : //! emitter that emits to either X86Assembler, X86Builder, or X86Compiler (use</a>
+<a name="5132"><span class="lineNum">    5132 </span>            : //! with caution with X86Compiler as it expects virtual registers to be used).</a>
+<a name="5133"><span class="lineNum">    5133 </span>            : class X86Emitter : public CodeEmitter, public X86EmitterImplicitT&lt;X86Emitter&gt; {</a>
+<a name="5134"><span class="lineNum">    5134 </span>            :   ASMJIT_NONCONSTRUCTIBLE(X86Emitter)</a>
+<a name="5135"><span class="lineNum">    5135 </span>            : };</a>
+<a name="5136"><span class="lineNum">    5136 </span>            : </a>
+<a name="5137"><span class="lineNum">    5137 </span>            : //! \}</a>
+<a name="5138"><span class="lineNum">    5138 </span>            : </a>
+<a name="5139"><span class="lineNum">    5139 </span>            : } // asmjit namespace</a>
+<a name="5140"><span class="lineNum">    5140 </span>            : } // namespace PLMD</a>
+<a name="5141"><span class="lineNum">    5141 </span>            : </a>
+<a name="5142"><span class="lineNum">    5142 </span>            : // [Api-End]</a>
+<a name="5143"><span class="lineNum">    5143 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="5144"><span class="lineNum">    5144 </span>            : </a>
+<a name="5145"><span class="lineNum">    5145 </span>            : // [Guard]</a>
+<a name="5146"><span class="lineNum">    5146 </span>            : #endif // _ASMJIT_X86_X86EMITTER_H</a>
+<a name="5147"><span class="lineNum">    5147 </span>            : #pragma GCC diagnostic pop</a>
+<a name="5148"><span class="lineNum">    5148 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="5149"><span class="lineNum">    5149 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86inst.cpp.func-sort-c.html b/coverage-libs/asmjit/x86inst.cpp.func-sort-c.html
new file mode 100644
index 0000000000..38657d7b77
--- /dev/null
+++ b/coverage-libs/asmjit/x86inst.cpp.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86inst.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86inst.cpp<span style="font-size: 80%;"> (<a href="x86inst.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86inst.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86inst.cpp.gcov.html#2814">_ZN4PLMD6asmjit7X86Inst11getIdByNameEPKcm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86inst.cpp.gcov.html#2857">_ZN4PLMD6asmjit7X86Inst11getNameByIdEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86inst.cpp.func.html b/coverage-libs/asmjit/x86inst.cpp.func.html
new file mode 100644
index 0000000000..92e30ac221
--- /dev/null
+++ b/coverage-libs/asmjit/x86inst.cpp.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86inst.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86inst.cpp<span style="font-size: 80%;"> (<a href="x86inst.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86inst.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86inst.cpp.gcov.html#2814">_ZN4PLMD6asmjit7X86Inst11getIdByNameEPKcm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86inst.cpp.gcov.html#2857">_ZN4PLMD6asmjit7X86Inst11getNameByIdEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86inst.cpp.gcov.html b/coverage-libs/asmjit/x86inst.cpp.gcov.html
new file mode 100644
index 0000000000..ffa2048d46
--- /dev/null
+++ b/coverage-libs/asmjit/x86inst.cpp.gcov.html
@@ -0,0 +1,3829 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86inst.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86inst.cpp<span style="font-size: 80%;"> (source / <a href="x86inst.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="30"><span class="lineNum">      30 </span>            : // IMPORTANT: AsmJit now uses an external instruction database to populate</a>
+<a name="31"><span class="lineNum">      31 </span>            : // static tables within this file. Perform the following steps to regenerate</a>
+<a name="32"><span class="lineNum">      32 </span>            : // all tables enclosed by ${...}:</a>
+<a name="33"><span class="lineNum">      33 </span>            : //</a>
+<a name="34"><span class="lineNum">      34 </span>            : //   1. Install node.js environment &lt;https://nodejs.org&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : //   2. Go to asmjit/tools directory</a>
+<a name="36"><span class="lineNum">      36 </span>            : //   3. Install either asmdb package by executing `npm install asmdb` or get</a>
+<a name="37"><span class="lineNum">      37 </span>            : //      the latest asmdb from &lt;https://github.com/asmjit/asmdb&gt; and copy/link</a>
+<a name="38"><span class="lineNum">      38 </span>            : //      the `asmdb` directory to `asmjit/tools/asmdb`.</a>
+<a name="39"><span class="lineNum">      39 </span>            : //   4. Execute `node generate-x86.js`</a>
+<a name="40"><span class="lineNum">      40 </span>            : //</a>
+<a name="41"><span class="lineNum">      41 </span>            : // Instruction encoding and opcodes were added to the `x86inst.cpp` database</a>
+<a name="42"><span class="lineNum">      42 </span>            : // manually in the past and they are not updated by the script as they seem</a>
+<a name="43"><span class="lineNum">      43 </span>            : // consistent. However, everything else is updated including instruction</a>
+<a name="44"><span class="lineNum">      44 </span>            : // operands and tables required to validate them, instruction read/write</a>
+<a name="45"><span class="lineNum">      45 </span>            : // information (including registers and flags), and all indexes to all tables.</a>
+<a name="46"><span class="lineNum">      46 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // [Export]</a>
+<a name="49"><span class="lineNum">      49 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // [Guard]</a>
+<a name="52"><span class="lineNum">      52 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="53"><span class="lineNum">      53 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // [Dependencies]</a>
+<a name="56"><span class="lineNum">      56 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            : #include &quot;./x86inst.h&quot;</a>
+<a name="59"><span class="lineNum">      59 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // [Api-Begin]</a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : namespace PLMD {</a>
+<a name="65"><span class="lineNum">      65 </span>            : namespace asmjit {</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : // ============================================================================</a>
+<a name="68"><span class="lineNum">      68 </span>            : // [Enums (Internal)]</a>
+<a name="69"><span class="lineNum">      69 </span>            : // ============================================================================</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : //! \internal</a>
+<a name="72"><span class="lineNum">      72 </span>            : enum ODATA_ {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   // PREFIX.</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ODATA_000000  = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_00,</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ODATA_000F00  = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F,</a>
+<a name="76"><span class="lineNum">      76 </span>            :   ODATA_000F01  = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F01,</a>
+<a name="77"><span class="lineNum">      77 </span>            :   ODATA_000F38  = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F38,</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ODATA_000F3A  = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F3A,</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ODATA_660000  = X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_MM_00,</a>
+<a name="80"><span class="lineNum">      80 </span>            :   ODATA_660F00  = X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_MM_0F,</a>
+<a name="81"><span class="lineNum">      81 </span>            :   ODATA_660F38  = X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_MM_0F38,</a>
+<a name="82"><span class="lineNum">      82 </span>            :   ODATA_660F3A  = X86Inst::kOpCode_PP_66 | X86Inst::kOpCode_MM_0F3A,</a>
+<a name="83"><span class="lineNum">      83 </span>            :   ODATA_F20000  = X86Inst::kOpCode_PP_F2 | X86Inst::kOpCode_MM_00,</a>
+<a name="84"><span class="lineNum">      84 </span>            :   ODATA_F20F00  = X86Inst::kOpCode_PP_F2 | X86Inst::kOpCode_MM_0F,</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ODATA_F20F38  = X86Inst::kOpCode_PP_F2 | X86Inst::kOpCode_MM_0F38,</a>
+<a name="86"><span class="lineNum">      86 </span>            :   ODATA_F20F3A  = X86Inst::kOpCode_PP_F2 | X86Inst::kOpCode_MM_0F3A,</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ODATA_F30000  = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_00,</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ODATA_F30F00  = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_0F,</a>
+<a name="89"><span class="lineNum">      89 </span>            :   ODATA_F30F38  = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_0F38,</a>
+<a name="90"><span class="lineNum">      90 </span>            :   ODATA_F30F3A  = X86Inst::kOpCode_PP_F3 | X86Inst::kOpCode_MM_0F3A,</a>
+<a name="91"><span class="lineNum">      91 </span>            :   ODATA_000F0F  = X86Inst::kOpCode_PP_00 | X86Inst::kOpCode_MM_0F, // 3DNOW, special case.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   ODATA_FPU_00  = X86Inst::kOpCode_PP_00,</a>
+<a name="94"><span class="lineNum">      94 </span>            :   ODATA_FPU_9B  = X86Inst::kOpCode_PP_9B,</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   ODATA_XOP_M8  = X86Inst::kOpCode_MM_XOP08,</a>
+<a name="97"><span class="lineNum">      97 </span>            :   ODATA_XOP_M9  = X86Inst::kOpCode_MM_XOP09,</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   ODATA_O__     = 0,</a>
+<a name="100"><span class="lineNum">     100 </span>            :   ODATA_O_0     = 0 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="101"><span class="lineNum">     101 </span>            :   ODATA_O_1     = 1 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="102"><span class="lineNum">     102 </span>            :   ODATA_O_2     = 2 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="103"><span class="lineNum">     103 </span>            :   ODATA_O_3     = 3 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="104"><span class="lineNum">     104 </span>            :   ODATA_O_4     = 4 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="105"><span class="lineNum">     105 </span>            :   ODATA_O_5     = 5 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="106"><span class="lineNum">     106 </span>            :   ODATA_O_6     = 6 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="107"><span class="lineNum">     107 </span>            :   ODATA_O_7     = 7 &lt;&lt; X86Inst::kOpCode_O_Shift,</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // REX/VEX.</a>
+<a name="110"><span class="lineNum">     110 </span>            :   ODATA_LL__    = 0,                                  // L is unspecified.</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ODATA_LL_x    = 0,                                  // L is based on operand(s).</a>
+<a name="112"><span class="lineNum">     112 </span>            :   ODATA_LL_I    = 0,                                  // L is ignored (LIG).</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ODATA_LL_0    = 0,                                  // L has to be zero (L.128).</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ODATA_LL_1    = X86Inst::kOpCode_LL_256,            // L has to be one (L.256).</a>
+<a name="115"><span class="lineNum">     115 </span>            :   ODATA_LL_2    = X86Inst::kOpCode_LL_512,            // L has to be two (L.512).</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   ODATA_W__     = 0,                                  // W is unspecified.</a>
+<a name="118"><span class="lineNum">     118 </span>            :   ODATA_W_x     = 0,                                  // W is based on operand(s).</a>
+<a name="119"><span class="lineNum">     119 </span>            :   ODATA_W_I     = 0,                                  // W is ignored (WIG).</a>
+<a name="120"><span class="lineNum">     120 </span>            :   ODATA_W_0     = 0,                                  // W has to be zero (W0).</a>
+<a name="121"><span class="lineNum">     121 </span>            :   ODATA_W_1     = X86Inst::kOpCode_W,                 // W has to be one (W1).</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   // EVEX.</a>
+<a name="124"><span class="lineNum">     124 </span>            :   ODATA_EvexW__ = 0,                                  // Not EVEX instruction.</a>
+<a name="125"><span class="lineNum">     125 </span>            :   ODATA_EvexW_x = 0,                                  // EVEX.W is based on operand(s).</a>
+<a name="126"><span class="lineNum">     126 </span>            :   ODATA_EvexW_I = 0,                                  // EVEX.W is ignored     (EVEX.WIG).</a>
+<a name="127"><span class="lineNum">     127 </span>            :   ODATA_EvexW_0 = 0,                                  // EVEX.W has to be zero (EVEX.W0).</a>
+<a name="128"><span class="lineNum">     128 </span>            :   ODATA_EvexW_1 = X86Inst::kOpCode_EW,                // EVEX.W has to be one  (EVEX.W1).</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :   ODATA_N__      = 0,                                 // Base element size not used.</a>
+<a name="131"><span class="lineNum">     131 </span>            :   ODATA_N_0      = 0 &lt;&lt; X86Inst::kOpCode_CDSHL_Shift, // N &lt;&lt; 0 (BYTE).</a>
+<a name="132"><span class="lineNum">     132 </span>            :   ODATA_N_1      = 1 &lt;&lt; X86Inst::kOpCode_CDSHL_Shift, // N &lt;&lt; 1 (WORD).</a>
+<a name="133"><span class="lineNum">     133 </span>            :   ODATA_N_2      = 2 &lt;&lt; X86Inst::kOpCode_CDSHL_Shift, // N &lt;&lt; 2 (DWORD).</a>
+<a name="134"><span class="lineNum">     134 </span>            :   ODATA_N_3      = 3 &lt;&lt; X86Inst::kOpCode_CDSHL_Shift, // N &lt;&lt; 3 (QWORD).</a>
+<a name="135"><span class="lineNum">     135 </span>            :   ODATA_N_4      = 4 &lt;&lt; X86Inst::kOpCode_CDSHL_Shift, // N &lt;&lt; 4 (OWORD).</a>
+<a name="136"><span class="lineNum">     136 </span>            :   ODATA_N_5      = 5 &lt;&lt; X86Inst::kOpCode_CDSHL_Shift, // N &lt;&lt; 5 (YWORD).</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   ODATA_TT__     = 0,</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ODATA_TT_FV    = X86Inst::kOpCode_CDTT_FV,</a>
+<a name="140"><span class="lineNum">     140 </span>            :   ODATA_TT_HV    = X86Inst::kOpCode_CDTT_HV,</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ODATA_TT_FVM   = X86Inst::kOpCode_CDTT_FVM,</a>
+<a name="142"><span class="lineNum">     142 </span>            :   ODATA_TT_T1S   = X86Inst::kOpCode_CDTT_T1S,</a>
+<a name="143"><span class="lineNum">     143 </span>            :   ODATA_TT_T1F   = X86Inst::kOpCode_CDTT_T1F,</a>
+<a name="144"><span class="lineNum">     144 </span>            :   ODATA_TT_T1W   = X86Inst::kOpCode_CDTT_T1W,</a>
+<a name="145"><span class="lineNum">     145 </span>            :   ODATA_TT_T2    = X86Inst::kOpCode_CDTT_T2,</a>
+<a name="146"><span class="lineNum">     146 </span>            :   ODATA_TT_T4    = X86Inst::kOpCode_CDTT_T4,</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ODATA_TT_T8    = X86Inst::kOpCode_CDTT_T8,</a>
+<a name="148"><span class="lineNum">     148 </span>            :   ODATA_TT_HVM   = X86Inst::kOpCode_CDTT_HVM,</a>
+<a name="149"><span class="lineNum">     149 </span>            :   ODATA_TT_OVM   = X86Inst::kOpCode_CDTT_OVM,</a>
+<a name="150"><span class="lineNum">     150 </span>            :   ODATA_TT_QVM   = X86Inst::kOpCode_CDTT_QVM,</a>
+<a name="151"><span class="lineNum">     151 </span>            :   ODATA_TT_128   = X86Inst::kOpCode_CDTT_128,</a>
+<a name="152"><span class="lineNum">     152 </span>            :   ODATA_TT_DUP   = X86Inst::kOpCode_CDTT_DUP,</a>
+<a name="153"><span class="lineNum">     153 </span>            :   ODATA_TT_T4X   = X86Inst::kOpCode_CDTT_T1_4X</a>
+<a name="154"><span class="lineNum">     154 </span>            : };</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : // ============================================================================</a>
+<a name="157"><span class="lineNum">     157 </span>            : // [asmjit::X86Inst]</a>
+<a name="158"><span class="lineNum">     158 </span>            : // ============================================================================</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : // Instruction opcode definitions:</a>
+<a name="161"><span class="lineNum">     161 </span>            : //   - `O` encodes X86|MMX|SSE instructions.</a>
+<a name="162"><span class="lineNum">     162 </span>            : //   - `V` encodes VEX|XOP|EVEX instructions.</a>
+<a name="163"><span class="lineNum">     163 </span>            : #define O_ENCODE(VEX, PREFIX, OPCODE, O, L, W, EvexW, N, TT) \</a>
+<a name="164"><span class="lineNum">     164 </span>            :   ((PREFIX) | (OPCODE) | (O) | (L) | (W) | (EvexW) | (N) | (TT) | \</a>
+<a name="165"><span class="lineNum">     165 </span>            :    (VEX &amp;&amp; ((PREFIX) &amp; X86Inst::kOpCode_MM_Mask) != X86Inst::kOpCode_MM_0F ? int(X86Inst::kOpCode_MM_ForceVex3) : 0))</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : #define O(PREFIX, OPCODE, O, LL, W, EvexW, N, TT) (O_ENCODE(0, ODATA_##PREFIX, 0x##OPCODE, ODATA_O_##O, ODATA_LL_##LL, ODATA_W_##W, ODATA_EvexW_##EvexW, ODATA_N_##N, ODATA_TT_##TT))</a>
+<a name="168"><span class="lineNum">     168 </span>            : #define V(PREFIX, OPCODE, O, LL, W, EvexW, N, TT) (O_ENCODE(1, ODATA_##PREFIX, 0x##OPCODE, ODATA_O_##O, ODATA_LL_##LL, ODATA_W_##W, ODATA_EvexW_##EvexW, ODATA_N_##N, ODATA_TT_##TT))</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : #define O_FPU(PREFIX, OPCODE, O) (ODATA_FPU_##PREFIX | (0x##OPCODE &amp; 0xFFU) | ((0x##OPCODE &gt;&gt; 8) &lt;&lt; X86Inst::kOpCode_FPU_2B_Shift) | ODATA_O_##O)</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : // Don't store `_nameDataIndex` if instruction names are disabled. Since some</a>
+<a name="173"><span class="lineNum">     173 </span>            : // APIs can use `_nameDataIndex` it's much safer if it's zero if it's not used.</a>
+<a name="174"><span class="lineNum">     174 </span>            : #if defined(ASMJIT_DISABLE_TEXT)</a>
+<a name="175"><span class="lineNum">     175 </span>            : # define NAME_DATA_INDEX(X) 0</a>
+<a name="176"><span class="lineNum">     176 </span>            : #else</a>
+<a name="177"><span class="lineNum">     177 </span>            : # define NAME_DATA_INDEX(X) X</a>
+<a name="178"><span class="lineNum">     178 </span>            : #endif</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : // Defines an X86/X64 instruction.</a>
+<a name="181"><span class="lineNum">     181 </span>            : #define INST(id, encoding, opcode0, opcode1, writeIndex, writeSize, nameDataIndex, commonDataIndex, operationDataIndex, seeToAvxDataIndex) { \</a>
+<a name="182"><span class="lineNum">     182 </span>            :   uint32_t(X86Inst::kEncoding##encoding),   \</a>
+<a name="183"><span class="lineNum">     183 </span>            :   uint32_t(NAME_DATA_INDEX(nameDataIndex)), \</a>
+<a name="184"><span class="lineNum">     184 </span>            :   uint32_t(commonDataIndex),                \</a>
+<a name="185"><span class="lineNum">     185 </span>            :   uint32_t(operationDataIndex),             \</a>
+<a name="186"><span class="lineNum">     186 </span>            :   uint32_t(seeToAvxDataIndex),              \</a>
+<a name="187"><span class="lineNum">     187 </span>            :   0,                                        \</a>
+<a name="188"><span class="lineNum">     188 </span>            :   opcode0                                   \</a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : const X86Inst X86InstDB::instData[] = {</a>
+<a name="191"><span class="lineNum">     191 </span>            :   // &lt;-----------------+--------------------+------------------+--------+------------------+--------+-------+-----+----+----+---+</a>
+<a name="192"><span class="lineNum">     192 </span>            :   //                   |                    |    Main OpCode   |#0 EVEX |Alternative OpCode|#1 EVEX | Write |     |    |    |Sse|</a>
+<a name="193"><span class="lineNum">     193 </span>            :   //    Instruction    |   Inst. Encoding   |                  +--------+                  +--------+---+---+NameX|ComX|OpnX|&lt;-&gt;|</a>
+<a name="194"><span class="lineNum">     194 </span>            :   //                   |                    |#0:PP-MMM OP/O L|W|W|N|TT. |#1:PP-MMM OP/O L|W|W|N|TT. |Idx|Cnt|     |    |    |Avx|</a>
+<a name="195"><span class="lineNum">     195 </span>            :   // &lt;-----------------+--------------------+------------------+--------+------------------+--------+---+---+-----+----+----+---+</a>
+<a name="196"><span class="lineNum">     196 </span>            :   // ${instData:Begin}</a>
+<a name="197"><span class="lineNum">     197 </span>            :   INST(None            , None               , 0                         , 0                         , 0 , 0 , 0   , 0  , 0  , 0 ),</a>
+<a name="198"><span class="lineNum">     198 </span>            :   INST(Aaa             , X86Op_xAX          , O(000000,37,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1   , 1  , 1  , 0 ),</a>
+<a name="199"><span class="lineNum">     199 </span>            :   INST(Aad             , X86I_xAX           , O(000000,D5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5   , 2  , 1  , 0 ),</a>
+<a name="200"><span class="lineNum">     200 </span>            :   INST(Aam             , X86I_xAX           , O(000000,D4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9   , 2  , 1  , 0 ),</a>
+<a name="201"><span class="lineNum">     201 </span>            :   INST(Aas             , X86Op_xAX          , O(000000,3F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 13  , 1  , 1  , 0 ),</a>
+<a name="202"><span class="lineNum">     202 </span>            :   INST(Adc             , X86Arith           , O(000000,10,2,_,x,_,_,_  ), 0                         , 0 , 0 , 17  , 3  , 2  , 0 ),</a>
+<a name="203"><span class="lineNum">     203 </span>            :   INST(Adcx            , X86Rm              , O(660F38,F6,_,_,x,_,_,_  ), 0                         , 0 , 0 , 21  , 4  , 3  , 0 ),</a>
+<a name="204"><span class="lineNum">     204 </span>            :   INST(Add             , X86Arith           , O(000000,00,0,_,x,_,_,_  ), 0                         , 0 , 0 , 732 , 3  , 1  , 0 ),</a>
+<a name="205"><span class="lineNum">     205 </span>            :   INST(Addpd           , ExtRm              , O(660F00,58,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4619, 5  , 4  , 1 ),</a>
+<a name="206"><span class="lineNum">     206 </span>            :   INST(Addps           , ExtRm              , O(000F00,58,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4631, 5  , 5  , 1 ),</a>
+<a name="207"><span class="lineNum">     207 </span>            :   INST(Addsd           , ExtRm              , O(F20F00,58,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4853, 6  , 4  , 1 ),</a>
+<a name="208"><span class="lineNum">     208 </span>            :   INST(Addss           , ExtRm              , O(F30F00,58,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4863, 7  , 5  , 1 ),</a>
+<a name="209"><span class="lineNum">     209 </span>            :   INST(Addsubpd        , ExtRm              , O(660F00,D0,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4358, 5  , 6  , 1 ),</a>
+<a name="210"><span class="lineNum">     210 </span>            :   INST(Addsubps        , ExtRm              , O(F20F00,D0,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4370, 5  , 6  , 1 ),</a>
+<a name="211"><span class="lineNum">     211 </span>            :   INST(Adox            , X86Rm              , O(F30F38,F6,_,_,x,_,_,_  ), 0                         , 0 , 0 , 26  , 4  , 7  , 0 ),</a>
+<a name="212"><span class="lineNum">     212 </span>            :   INST(Aesdec          , ExtRm              , O(660F38,DE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2854, 5  , 8  , 2 ),</a>
+<a name="213"><span class="lineNum">     213 </span>            :   INST(Aesdeclast      , ExtRm              , O(660F38,DF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2862, 5  , 8  , 2 ),</a>
+<a name="214"><span class="lineNum">     214 </span>            :   INST(Aesenc          , ExtRm              , O(660F38,DC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2874, 5  , 8  , 2 ),</a>
+<a name="215"><span class="lineNum">     215 </span>            :   INST(Aesenclast      , ExtRm              , O(660F38,DD,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2882, 5  , 8  , 2 ),</a>
+<a name="216"><span class="lineNum">     216 </span>            :   INST(Aesimc          , ExtRm              , O(660F38,DB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2894, 8  , 8  , 3 ),</a>
+<a name="217"><span class="lineNum">     217 </span>            :   INST(Aeskeygenassist , ExtRmi             , O(660F3A,DF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2902, 9  , 8  , 3 ),</a>
+<a name="218"><span class="lineNum">     218 </span>            :   INST(And             , X86Arith           , O(000000,20,4,_,x,_,_,_  ), 0                         , 0 , 0 , 2317, 10 , 1  , 0 ),</a>
+<a name="219"><span class="lineNum">     219 </span>            :   INST(Andn            , VexRvm_Wx          , V(000F38,F2,_,0,x,_,_,_  ), 0                         , 0 , 0 , 6150, 11 , 9  , 0 ),</a>
+<a name="220"><span class="lineNum">     220 </span>            :   INST(Andnpd          , ExtRm              , O(660F00,55,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2935, 5  , 4  , 2 ),</a>
+<a name="221"><span class="lineNum">     221 </span>            :   INST(Andnps          , ExtRm              , O(000F00,55,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2943, 5  , 5  , 2 ),</a>
+<a name="222"><span class="lineNum">     222 </span>            :   INST(Andpd           , ExtRm              , O(660F00,54,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3872, 12 , 4  , 2 ),</a>
+<a name="223"><span class="lineNum">     223 </span>            :   INST(Andps           , ExtRm              , O(000F00,54,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3882, 12 , 5  , 2 ),</a>
+<a name="224"><span class="lineNum">     224 </span>            :   INST(Arpl            , X86Mr_NoSize       , O(000000,63,_,_,_,_,_,_  ), 0                         , 0 , 0 , 31  , 13 , 10 , 0 ),</a>
+<a name="225"><span class="lineNum">     225 </span>            :   INST(Bextr           , VexRmv_Wx          , V(000F38,F7,_,0,x,_,_,_  ), 0                         , 0 , 0 , 36  , 14 , 9  , 0 ),</a>
+<a name="226"><span class="lineNum">     226 </span>            :   INST(Blcfill         , VexVm_Wx           , V(XOP_M9,01,1,0,x,_,_,_  ), 0                         , 0 , 0 , 42  , 15 , 11 , 0 ),</a>
+<a name="227"><span class="lineNum">     227 </span>            :   INST(Blci            , VexVm_Wx           , V(XOP_M9,02,6,0,x,_,_,_  ), 0                         , 0 , 0 , 50  , 15 , 11 , 0 ),</a>
+<a name="228"><span class="lineNum">     228 </span>            :   INST(Blcic           , VexVm_Wx           , V(XOP_M9,01,5,0,x,_,_,_  ), 0                         , 0 , 0 , 55  , 15 , 11 , 0 ),</a>
+<a name="229"><span class="lineNum">     229 </span>            :   INST(Blcmsk          , VexVm_Wx           , V(XOP_M9,02,1,0,x,_,_,_  ), 0                         , 0 , 0 , 61  , 15 , 11 , 0 ),</a>
+<a name="230"><span class="lineNum">     230 </span>            :   INST(Blcs            , VexVm_Wx           , V(XOP_M9,01,3,0,x,_,_,_  ), 0                         , 0 , 0 , 68  , 15 , 11 , 0 ),</a>
+<a name="231"><span class="lineNum">     231 </span>            :   INST(Blendpd         , ExtRmi             , O(660F3A,0D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3021, 16 , 12 , 4 ),</a>
+<a name="232"><span class="lineNum">     232 </span>            :   INST(Blendps         , ExtRmi             , O(660F3A,0C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3030, 16 , 12 , 4 ),</a>
+<a name="233"><span class="lineNum">     233 </span>            :   INST(Blendvpd        , ExtRm_XMM0         , O(660F38,15,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3039, 17 , 12 , 5 ),</a>
+<a name="234"><span class="lineNum">     234 </span>            :   INST(Blendvps        , ExtRm_XMM0         , O(660F38,14,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3049, 17 , 12 , 5 ),</a>
+<a name="235"><span class="lineNum">     235 </span>            :   INST(Blsfill         , VexVm_Wx           , V(XOP_M9,01,2,0,x,_,_,_  ), 0                         , 0 , 0 , 73  , 15 , 11 , 0 ),</a>
+<a name="236"><span class="lineNum">     236 </span>            :   INST(Blsi            , VexVm_Wx           , V(000F38,F3,3,0,x,_,_,_  ), 0                         , 0 , 0 , 81  , 15 , 9  , 0 ),</a>
+<a name="237"><span class="lineNum">     237 </span>            :   INST(Blsic           , VexVm_Wx           , V(XOP_M9,01,6,0,x,_,_,_  ), 0                         , 0 , 0 , 86  , 15 , 11 , 0 ),</a>
+<a name="238"><span class="lineNum">     238 </span>            :   INST(Blsmsk          , VexVm_Wx           , V(000F38,F3,2,0,x,_,_,_  ), 0                         , 0 , 0 , 92  , 15 , 9  , 0 ),</a>
+<a name="239"><span class="lineNum">     239 </span>            :   INST(Blsr            , VexVm_Wx           , V(000F38,F3,1,0,x,_,_,_  ), 0                         , 0 , 0 , 99  , 15 , 9  , 0 ),</a>
+<a name="240"><span class="lineNum">     240 </span>            :   INST(Bndcl           , X86Rm              , O(F30F00,1A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 104 , 18 , 13 , 0 ),</a>
+<a name="241"><span class="lineNum">     241 </span>            :   INST(Bndcn           , X86Rm              , O(F20F00,1B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 110 , 18 , 13 , 0 ),</a>
+<a name="242"><span class="lineNum">     242 </span>            :   INST(Bndcu           , X86Rm              , O(F20F00,1A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 116 , 18 , 13 , 0 ),</a>
+<a name="243"><span class="lineNum">     243 </span>            :   INST(Bndldx          , X86Rm              , O(000F00,1A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 122 , 19 , 13 , 0 ),</a>
+<a name="244"><span class="lineNum">     244 </span>            :   INST(Bndmk           , X86Rm              , O(F30F00,1B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 129 , 20 , 13 , 0 ),</a>
+<a name="245"><span class="lineNum">     245 </span>            :   INST(Bndmov          , X86Bndmov          , O(660F00,1A,_,_,_,_,_,_  ), O(660F00,1B,_,_,_,_,_,_  ), 0 , 0 , 135 , 21 , 13 , 0 ),</a>
+<a name="246"><span class="lineNum">     246 </span>            :   INST(Bndstx          , X86Mr              , O(000F00,1B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 142 , 22 , 13 , 0 ),</a>
+<a name="247"><span class="lineNum">     247 </span>            :   INST(Bound           , X86Rm              , O(000000,62,_,_,_,_,_,_  ), 0                         , 0 , 0 , 149 , 23 , 0  , 0 ),</a>
+<a name="248"><span class="lineNum">     248 </span>            :   INST(Bsf             , X86Rm              , O(000F00,BC,_,_,x,_,_,_  ), 0                         , 0 , 0 , 155 , 24 , 1  , 0 ),</a>
+<a name="249"><span class="lineNum">     249 </span>            :   INST(Bsr             , X86Rm              , O(000F00,BD,_,_,x,_,_,_  ), 0                         , 0 , 0 , 159 , 24 , 1  , 0 ),</a>
+<a name="250"><span class="lineNum">     250 </span>            :   INST(Bswap           , X86Bswap           , O(000F00,C8,_,_,x,_,_,_  ), 0                         , 0 , 0 , 163 , 25 , 0  , 0 ),</a>
+<a name="251"><span class="lineNum">     251 </span>            :   INST(Bt              , X86Bt              , O(000F00,A3,_,_,x,_,_,_  ), O(000F00,BA,4,_,x,_,_,_  ), 0 , 0 , 169 , 26 , 14 , 0 ),</a>
+<a name="252"><span class="lineNum">     252 </span>            :   INST(Btc             , X86Bt              , O(000F00,BB,_,_,x,_,_,_  ), O(000F00,BA,7,_,x,_,_,_  ), 0 , 0 , 172 , 27 , 14 , 0 ),</a>
+<a name="253"><span class="lineNum">     253 </span>            :   INST(Btr             , X86Bt              , O(000F00,B3,_,_,x,_,_,_  ), O(000F00,BA,6,_,x,_,_,_  ), 0 , 0 , 176 , 28 , 14 , 0 ),</a>
+<a name="254"><span class="lineNum">     254 </span>            :   INST(Bts             , X86Bt              , O(000F00,AB,_,_,x,_,_,_  ), O(000F00,BA,5,_,x,_,_,_  ), 0 , 0 , 180 , 29 , 14 , 0 ),</a>
+<a name="255"><span class="lineNum">     255 </span>            :   INST(Bzhi            , VexRmv_Wx          , V(000F38,F5,_,0,x,_,_,_  ), 0                         , 0 , 0 , 184 , 14 , 15 , 0 ),</a>
+<a name="256"><span class="lineNum">     256 </span>            :   INST(Call            , X86Call            , O(000000,FF,2,_,_,_,_,_  ), 0                         , 0 , 0 , 2713, 30 , 16 , 0 ),</a>
+<a name="257"><span class="lineNum">     257 </span>            :   INST(Cbw             , X86Op_xAX          , O(660000,98,_,_,_,_,_,_  ), 0                         , 0 , 0 , 189 , 31 , 0  , 0 ),</a>
+<a name="258"><span class="lineNum">     258 </span>            :   INST(Cdq             , X86Op_xDX_xAX      , O(000000,99,_,_,_,_,_,_  ), 0                         , 0 , 0 , 193 , 32 , 0  , 0 ),</a>
+<a name="259"><span class="lineNum">     259 </span>            :   INST(Cdqe            , X86Op_xAX          , O(000000,98,_,_,1,_,_,_  ), 0                         , 0 , 0 , 197 , 33 , 0  , 0 ),</a>
+<a name="260"><span class="lineNum">     260 </span>            :   INST(Clac            , X86Op              , O(000F01,CA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 202 , 34 , 17 , 0 ),</a>
+<a name="261"><span class="lineNum">     261 </span>            :   INST(Clc             , X86Op              , O(000000,F8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 207 , 34 , 18 , 0 ),</a>
+<a name="262"><span class="lineNum">     262 </span>            :   INST(Cld             , X86Op              , O(000000,FC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 211 , 34 , 19 , 0 ),</a>
+<a name="263"><span class="lineNum">     263 </span>            :   INST(Clflush         , X86M_Only          , O(000F00,AE,7,_,_,_,_,_  ), 0                         , 0 , 0 , 215 , 35 , 20 , 0 ),</a>
+<a name="264"><span class="lineNum">     264 </span>            :   INST(Clflushopt      , X86M_Only          , O(660F00,AE,7,_,_,_,_,_  ), 0                         , 0 , 0 , 223 , 35 , 21 , 0 ),</a>
+<a name="265"><span class="lineNum">     265 </span>            :   INST(Cli             , X86Op              , O(000000,FA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 234 , 34 , 22 , 0 ),</a>
+<a name="266"><span class="lineNum">     266 </span>            :   INST(Clts            , X86Op              , O(000F00,06,_,_,_,_,_,_  ), 0                         , 0 , 0 , 238 , 34 , 23 , 0 ),</a>
+<a name="267"><span class="lineNum">     267 </span>            :   INST(Clwb            , X86M_Only          , O(660F00,AE,6,_,_,_,_,_  ), 0                         , 0 , 0 , 243 , 35 , 24 , 0 ),</a>
+<a name="268"><span class="lineNum">     268 </span>            :   INST(Clzero          , X86Op_ZAX          , O(000F01,FC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 248 , 36 , 25 , 0 ),</a>
+<a name="269"><span class="lineNum">     269 </span>            :   INST(Cmc             , X86Op              , O(000000,F5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 255 , 34 , 26 , 0 ),</a>
+<a name="270"><span class="lineNum">     270 </span>            :   INST(Cmova           , X86Rm              , O(000F00,47,_,_,x,_,_,_  ), 0                         , 0 , 0 , 259 , 24 , 27 , 0 ),</a>
+<a name="271"><span class="lineNum">     271 </span>            :   INST(Cmovae          , X86Rm              , O(000F00,43,_,_,x,_,_,_  ), 0                         , 0 , 0 , 265 , 24 , 28 , 0 ),</a>
+<a name="272"><span class="lineNum">     272 </span>            :   INST(Cmovb           , X86Rm              , O(000F00,42,_,_,x,_,_,_  ), 0                         , 0 , 0 , 589 , 24 , 28 , 0 ),</a>
+<a name="273"><span class="lineNum">     273 </span>            :   INST(Cmovbe          , X86Rm              , O(000F00,46,_,_,x,_,_,_  ), 0                         , 0 , 0 , 596 , 24 , 27 , 0 ),</a>
+<a name="274"><span class="lineNum">     274 </span>            :   INST(Cmovc           , X86Rm              , O(000F00,42,_,_,x,_,_,_  ), 0                         , 0 , 0 , 272 , 24 , 28 , 0 ),</a>
+<a name="275"><span class="lineNum">     275 </span>            :   INST(Cmove           , X86Rm              , O(000F00,44,_,_,x,_,_,_  ), 0                         , 0 , 0 , 604 , 24 , 29 , 0 ),</a>
+<a name="276"><span class="lineNum">     276 </span>            :   INST(Cmovg           , X86Rm              , O(000F00,4F,_,_,x,_,_,_  ), 0                         , 0 , 0 , 278 , 24 , 30 , 0 ),</a>
+<a name="277"><span class="lineNum">     277 </span>            :   INST(Cmovge          , X86Rm              , O(000F00,4D,_,_,x,_,_,_  ), 0                         , 0 , 0 , 284 , 24 , 31 , 0 ),</a>
+<a name="278"><span class="lineNum">     278 </span>            :   INST(Cmovl           , X86Rm              , O(000F00,4C,_,_,x,_,_,_  ), 0                         , 0 , 0 , 291 , 24 , 31 , 0 ),</a>
+<a name="279"><span class="lineNum">     279 </span>            :   INST(Cmovle          , X86Rm              , O(000F00,4E,_,_,x,_,_,_  ), 0                         , 0 , 0 , 297 , 24 , 30 , 0 ),</a>
+<a name="280"><span class="lineNum">     280 </span>            :   INST(Cmovna          , X86Rm              , O(000F00,46,_,_,x,_,_,_  ), 0                         , 0 , 0 , 304 , 24 , 27 , 0 ),</a>
+<a name="281"><span class="lineNum">     281 </span>            :   INST(Cmovnae         , X86Rm              , O(000F00,42,_,_,x,_,_,_  ), 0                         , 0 , 0 , 311 , 24 , 28 , 0 ),</a>
+<a name="282"><span class="lineNum">     282 </span>            :   INST(Cmovnb          , X86Rm              , O(000F00,43,_,_,x,_,_,_  ), 0                         , 0 , 0 , 611 , 24 , 28 , 0 ),</a>
+<a name="283"><span class="lineNum">     283 </span>            :   INST(Cmovnbe         , X86Rm              , O(000F00,47,_,_,x,_,_,_  ), 0                         , 0 , 0 , 619 , 24 , 27 , 0 ),</a>
+<a name="284"><span class="lineNum">     284 </span>            :   INST(Cmovnc          , X86Rm              , O(000F00,43,_,_,x,_,_,_  ), 0                         , 0 , 0 , 319 , 24 , 28 , 0 ),</a>
+<a name="285"><span class="lineNum">     285 </span>            :   INST(Cmovne          , X86Rm              , O(000F00,45,_,_,x,_,_,_  ), 0                         , 0 , 0 , 628 , 24 , 29 , 0 ),</a>
+<a name="286"><span class="lineNum">     286 </span>            :   INST(Cmovng          , X86Rm              , O(000F00,4E,_,_,x,_,_,_  ), 0                         , 0 , 0 , 326 , 24 , 30 , 0 ),</a>
+<a name="287"><span class="lineNum">     287 </span>            :   INST(Cmovnge         , X86Rm              , O(000F00,4C,_,_,x,_,_,_  ), 0                         , 0 , 0 , 333 , 24 , 31 , 0 ),</a>
+<a name="288"><span class="lineNum">     288 </span>            :   INST(Cmovnl          , X86Rm              , O(000F00,4D,_,_,x,_,_,_  ), 0                         , 0 , 0 , 341 , 24 , 31 , 0 ),</a>
+<a name="289"><span class="lineNum">     289 </span>            :   INST(Cmovnle         , X86Rm              , O(000F00,4F,_,_,x,_,_,_  ), 0                         , 0 , 0 , 348 , 24 , 30 , 0 ),</a>
+<a name="290"><span class="lineNum">     290 </span>            :   INST(Cmovno          , X86Rm              , O(000F00,41,_,_,x,_,_,_  ), 0                         , 0 , 0 , 356 , 24 , 32 , 0 ),</a>
+<a name="291"><span class="lineNum">     291 </span>            :   INST(Cmovnp          , X86Rm              , O(000F00,4B,_,_,x,_,_,_  ), 0                         , 0 , 0 , 363 , 24 , 33 , 0 ),</a>
+<a name="292"><span class="lineNum">     292 </span>            :   INST(Cmovns          , X86Rm              , O(000F00,49,_,_,x,_,_,_  ), 0                         , 0 , 0 , 370 , 24 , 34 , 0 ),</a>
+<a name="293"><span class="lineNum">     293 </span>            :   INST(Cmovnz          , X86Rm              , O(000F00,45,_,_,x,_,_,_  ), 0                         , 0 , 0 , 377 , 24 , 29 , 0 ),</a>
+<a name="294"><span class="lineNum">     294 </span>            :   INST(Cmovo           , X86Rm              , O(000F00,40,_,_,x,_,_,_  ), 0                         , 0 , 0 , 384 , 24 , 32 , 0 ),</a>
+<a name="295"><span class="lineNum">     295 </span>            :   INST(Cmovp           , X86Rm              , O(000F00,4A,_,_,x,_,_,_  ), 0                         , 0 , 0 , 390 , 24 , 33 , 0 ),</a>
+<a name="296"><span class="lineNum">     296 </span>            :   INST(Cmovpe          , X86Rm              , O(000F00,4A,_,_,x,_,_,_  ), 0                         , 0 , 0 , 396 , 24 , 33 , 0 ),</a>
+<a name="297"><span class="lineNum">     297 </span>            :   INST(Cmovpo          , X86Rm              , O(000F00,4B,_,_,x,_,_,_  ), 0                         , 0 , 0 , 403 , 24 , 33 , 0 ),</a>
+<a name="298"><span class="lineNum">     298 </span>            :   INST(Cmovs           , X86Rm              , O(000F00,48,_,_,x,_,_,_  ), 0                         , 0 , 0 , 410 , 24 , 34 , 0 ),</a>
+<a name="299"><span class="lineNum">     299 </span>            :   INST(Cmovz           , X86Rm              , O(000F00,44,_,_,x,_,_,_  ), 0                         , 0 , 0 , 416 , 24 , 29 , 0 ),</a>
+<a name="300"><span class="lineNum">     300 </span>            :   INST(Cmp             , X86Arith           , O(000000,38,7,_,x,_,_,_  ), 0                         , 0 , 0 , 422 , 37 , 1  , 0 ),</a>
+<a name="301"><span class="lineNum">     301 </span>            :   INST(Cmppd           , ExtRmi             , O(660F00,C2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3275, 16 , 4  , 6 ),</a>
+<a name="302"><span class="lineNum">     302 </span>            :   INST(Cmpps           , ExtRmi             , O(000F00,C2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3282, 16 , 5  , 6 ),</a>
+<a name="303"><span class="lineNum">     303 </span>            :   INST(Cmps            , X86StrMm           , O(000000,A6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 426 , 38 , 35 , 0 ),</a>
+<a name="304"><span class="lineNum">     304 </span>            :   INST(Cmpsd           , ExtRmi             , O(F20F00,C2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3289, 39 , 4  , 7 ),</a>
+<a name="305"><span class="lineNum">     305 </span>            :   INST(Cmpss           , ExtRmi             , O(F30F00,C2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3296, 40 , 5  , 7 ),</a>
+<a name="306"><span class="lineNum">     306 </span>            :   INST(Cmpxchg         , X86Cmpxchg         , O(000F00,B0,_,_,x,_,_,_  ), 0                         , 0 , 0 , 431 , 41 , 36 , 0 ),</a>
+<a name="307"><span class="lineNum">     307 </span>            :   INST(Cmpxchg16b      , X86M_Only          , O(000F00,C7,1,_,1,_,_,_  ), 0                         , 0 , 0 , 439 , 42 , 37 , 0 ),</a>
+<a name="308"><span class="lineNum">     308 </span>            :   INST(Cmpxchg8b       , X86M_Only          , O(000F00,C7,1,_,_,_,_,_  ), 0                         , 0 , 0 , 450 , 43 , 38 , 0 ),</a>
+<a name="309"><span class="lineNum">     309 </span>            :   INST(Comisd          , ExtRm              , O(660F00,2F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9371, 44 , 39 , 8 ),</a>
+<a name="310"><span class="lineNum">     310 </span>            :   INST(Comiss          , ExtRm              , O(000F00,2F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9380, 45 , 40 , 8 ),</a>
+<a name="311"><span class="lineNum">     311 </span>            :   INST(Cpuid           , X86Op              , O(000F00,A2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 460 , 46 , 41 , 0 ),</a>
+<a name="312"><span class="lineNum">     312 </span>            :   INST(Cqo             , X86Op_xDX_xAX      , O(000000,99,_,_,1,_,_,_  ), 0                         , 0 , 0 , 466 , 47 , 0  , 0 ),</a>
+<a name="313"><span class="lineNum">     313 </span>            :   INST(Crc32           , X86Crc             , O(F20F38,F0,_,_,x,_,_,_  ), 0                         , 0 , 0 , 470 , 48 , 42 , 0 ),</a>
+<a name="314"><span class="lineNum">     314 </span>            :   INST(Cvtdq2pd        , ExtRm              , O(F30F00,E6,_,_,_,_,_,_  ), 0                         , 0 , 16, 3343, 49 , 4  , 9 ),</a>
+<a name="315"><span class="lineNum">     315 </span>            :   INST(Cvtdq2ps        , ExtRm              , O(000F00,5B,_,_,_,_,_,_  ), 0                         , 0 , 16, 3353, 50 , 4  , 9 ),</a>
+<a name="316"><span class="lineNum">     316 </span>            :   INST(Cvtpd2dq        , ExtRm              , O(F20F00,E6,_,_,_,_,_,_  ), 0                         , 0 , 16, 3363, 50 , 4  , 9 ),</a>
+<a name="317"><span class="lineNum">     317 </span>            :   INST(Cvtpd2pi        , ExtRm              , O(660F00,2D,_,_,_,_,_,_  ), 0                         , 0 , 8 , 476 , 51 , 4  , 0 ),</a>
+<a name="318"><span class="lineNum">     318 </span>            :   INST(Cvtpd2ps        , ExtRm              , O(660F00,5A,_,_,_,_,_,_  ), 0                         , 0 , 16, 3373, 50 , 4  , 10),</a>
+<a name="319"><span class="lineNum">     319 </span>            :   INST(Cvtpi2pd        , ExtRm              , O(660F00,2A,_,_,_,_,_,_  ), 0                         , 0 , 16, 485 , 52 , 4  , 0 ),</a>
+<a name="320"><span class="lineNum">     320 </span>            :   INST(Cvtpi2ps        , ExtRm              , O(000F00,2A,_,_,_,_,_,_  ), 0                         , 0 , 8 , 494 , 53 , 5  , 0 ),</a>
+<a name="321"><span class="lineNum">     321 </span>            :   INST(Cvtps2dq        , ExtRm              , O(660F00,5B,_,_,_,_,_,_  ), 0                         , 0 , 16, 3425, 50 , 4  , 8 ),</a>
+<a name="322"><span class="lineNum">     322 </span>            :   INST(Cvtps2pd        , ExtRm              , O(000F00,5A,_,_,_,_,_,_  ), 0                         , 0 , 16, 3435, 49 , 4  , 8 ),</a>
+<a name="323"><span class="lineNum">     323 </span>            :   INST(Cvtps2pi        , ExtRm              , O(000F00,2D,_,_,_,_,_,_  ), 0                         , 0 , 8 , 503 , 54 , 5  , 0 ),</a>
+<a name="324"><span class="lineNum">     324 </span>            :   INST(Cvtsd2si        , ExtRm_Wx           , O(F20F00,2D,_,_,x,_,_,_  ), 0                         , 0 , 8 , 3507, 55 , 4  , 11),</a>
+<a name="325"><span class="lineNum">     325 </span>            :   INST(Cvtsd2ss        , ExtRm              , O(F20F00,5A,_,_,_,_,_,_  ), 0                         , 0 , 4 , 3517, 56 , 4  , 12),</a>
+<a name="326"><span class="lineNum">     326 </span>            :   INST(Cvtsi2sd        , ExtRm_Wx           , O(F20F00,2A,_,_,x,_,_,_  ), 0                         , 0 , 8 , 3538, 57 , 4  , 13),</a>
+<a name="327"><span class="lineNum">     327 </span>            :   INST(Cvtsi2ss        , ExtRm_Wx           , O(F30F00,2A,_,_,x,_,_,_  ), 0                         , 0 , 4 , 3548, 58 , 5  , 13),</a>
+<a name="328"><span class="lineNum">     328 </span>            :   INST(Cvtss2sd        , ExtRm              , O(F30F00,5A,_,_,_,_,_,_  ), 0                         , 0 , 8 , 3558, 59 , 4  , 13),</a>
+<a name="329"><span class="lineNum">     329 </span>            :   INST(Cvtss2si        , ExtRm_Wx           , O(F30F00,2D,_,_,x,_,_,_  ), 0                         , 0 , 8 , 3568, 60 , 5  , 14),</a>
+<a name="330"><span class="lineNum">     330 </span>            :   INST(Cvttpd2dq       , ExtRm              , O(660F00,E6,_,_,_,_,_,_  ), 0                         , 0 , 16, 3589, 50 , 4  , 15),</a>
+<a name="331"><span class="lineNum">     331 </span>            :   INST(Cvttpd2pi       , ExtRm              , O(660F00,2C,_,_,_,_,_,_  ), 0                         , 0 , 8 , 512 , 51 , 4  , 0 ),</a>
+<a name="332"><span class="lineNum">     332 </span>            :   INST(Cvttps2dq       , ExtRm              , O(F30F00,5B,_,_,_,_,_,_  ), 0                         , 0 , 16, 3635, 50 , 4  , 16),</a>
+<a name="333"><span class="lineNum">     333 </span>            :   INST(Cvttps2pi       , ExtRm              , O(000F00,2C,_,_,_,_,_,_  ), 0                         , 0 , 8 , 522 , 54 , 5  , 0 ),</a>
+<a name="334"><span class="lineNum">     334 </span>            :   INST(Cvttsd2si       , ExtRm_Wx           , O(F20F00,2C,_,_,x,_,_,_  ), 0                         , 0 , 8 , 3681, 55 , 4  , 17),</a>
+<a name="335"><span class="lineNum">     335 </span>            :   INST(Cvttss2si       , ExtRm_Wx           , O(F30F00,2C,_,_,x,_,_,_  ), 0                         , 0 , 8 , 3704, 60 , 5  , 18),</a>
+<a name="336"><span class="lineNum">     336 </span>            :   INST(Cwd             , X86Op_xDX_xAX      , O(660000,99,_,_,_,_,_,_  ), 0                         , 0 , 0 , 532 , 61 , 0  , 0 ),</a>
+<a name="337"><span class="lineNum">     337 </span>            :   INST(Cwde            , X86Op_xAX          , O(000000,98,_,_,_,_,_,_  ), 0                         , 0 , 0 , 536 , 62 , 0  , 0 ),</a>
+<a name="338"><span class="lineNum">     338 </span>            :   INST(Daa             , X86Op              , O(000000,27,_,_,_,_,_,_  ), 0                         , 0 , 0 , 541 , 1  , 1  , 0 ),</a>
+<a name="339"><span class="lineNum">     339 </span>            :   INST(Das             , X86Op              , O(000000,2F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 545 , 1  , 1  , 0 ),</a>
+<a name="340"><span class="lineNum">     340 </span>            :   INST(Dec             , X86IncDec          , O(000000,FE,1,_,x,_,_,_  ), O(000000,48,_,_,x,_,_,_  ), 0 , 0 , 2857, 63 , 43 , 0 ),</a>
+<a name="341"><span class="lineNum">     341 </span>            :   INST(Div             , X86M_GPB_MulDiv    , O(000000,F6,6,_,x,_,_,_  ), 0                         , 0 , 0 , 751 , 64 , 1  , 0 ),</a>
+<a name="342"><span class="lineNum">     342 </span>            :   INST(Divpd           , ExtRm              , O(660F00,5E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3803, 5  , 4  , 19),</a>
+<a name="343"><span class="lineNum">     343 </span>            :   INST(Divps           , ExtRm              , O(000F00,5E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3810, 5  , 5  , 19),</a>
+<a name="344"><span class="lineNum">     344 </span>            :   INST(Divsd           , ExtRm              , O(F20F00,5E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3817, 6  , 4  , 19),</a>
+<a name="345"><span class="lineNum">     345 </span>            :   INST(Divss           , ExtRm              , O(F30F00,5E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3824, 7  , 5  , 19),</a>
+<a name="346"><span class="lineNum">     346 </span>            :   INST(Dppd            , ExtRmi             , O(660F3A,41,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3831, 16 , 12 , 19),</a>
+<a name="347"><span class="lineNum">     347 </span>            :   INST(Dpps            , ExtRmi             , O(660F3A,40,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3837, 16 , 12 , 19),</a>
+<a name="348"><span class="lineNum">     348 </span>            :   INST(Emms            , X86Op              , O(000F00,77,_,_,_,_,_,_  ), 0                         , 0 , 0 , 719 , 65 , 44 , 0 ),</a>
+<a name="349"><span class="lineNum">     349 </span>            :   INST(Enter           , X86Enter           , O(000000,C8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2721, 66 , 45 , 0 ),</a>
+<a name="350"><span class="lineNum">     350 </span>            :   INST(Extractps       , ExtExtract         , O(660F3A,17,_,_,_,_,_,_  ), 0                         , 0 , 8 , 4027, 67 , 12 , 20),</a>
+<a name="351"><span class="lineNum">     351 </span>            :   INST(Extrq           , ExtExtrq           , O(660F00,79,_,_,_,_,_,_  ), O(660F00,78,0,_,_,_,_,_  ), 0 , 0 , 6864, 68 , 46 , 0 ),</a>
+<a name="352"><span class="lineNum">     352 </span>            :   INST(F2xm1           , FpuOp              , O_FPU(00,D9F0,_)          , 0                         , 0 , 0 , 549 , 34 , 47 , 0 ),</a>
+<a name="353"><span class="lineNum">     353 </span>            :   INST(Fabs            , FpuOp              , O_FPU(00,D9E1,_)          , 0                         , 0 , 0 , 555 , 34 , 47 , 0 ),</a>
+<a name="354"><span class="lineNum">     354 </span>            :   INST(Fadd            , FpuArith           , O_FPU(00,C0C0,0)          , 0                         , 0 , 0 , 1957, 69 , 47 , 0 ),</a>
+<a name="355"><span class="lineNum">     355 </span>            :   INST(Faddp           , FpuRDef            , O_FPU(00,DEC0,_)          , 0                         , 0 , 0 , 560 , 70 , 47 , 0 ),</a>
+<a name="356"><span class="lineNum">     356 </span>            :   INST(Fbld            , X86M_Only          , O_FPU(00,00DF,4)          , 0                         , 0 , 0 , 566 , 71 , 47 , 0 ),</a>
+<a name="357"><span class="lineNum">     357 </span>            :   INST(Fbstp           , X86M_Only          , O_FPU(00,00DF,6)          , 0                         , 0 , 0 , 571 , 72 , 47 , 0 ),</a>
+<a name="358"><span class="lineNum">     358 </span>            :   INST(Fchs            , FpuOp              , O_FPU(00,D9E0,_)          , 0                         , 0 , 0 , 577 , 34 , 47 , 0 ),</a>
+<a name="359"><span class="lineNum">     359 </span>            :   INST(Fclex           , FpuOp              , O_FPU(9B,DBE2,_)          , 0                         , 0 , 0 , 582 , 34 , 47 , 0 ),</a>
+<a name="360"><span class="lineNum">     360 </span>            :   INST(Fcmovb          , FpuR               , O_FPU(00,DAC0,_)          , 0                         , 0 , 0 , 588 , 73 , 48 , 0 ),</a>
+<a name="361"><span class="lineNum">     361 </span>            :   INST(Fcmovbe         , FpuR               , O_FPU(00,DAD0,_)          , 0                         , 0 , 0 , 595 , 73 , 48 , 0 ),</a>
+<a name="362"><span class="lineNum">     362 </span>            :   INST(Fcmove          , FpuR               , O_FPU(00,DAC8,_)          , 0                         , 0 , 0 , 603 , 73 , 48 , 0 ),</a>
+<a name="363"><span class="lineNum">     363 </span>            :   INST(Fcmovnb         , FpuR               , O_FPU(00,DBC0,_)          , 0                         , 0 , 0 , 610 , 73 , 48 , 0 ),</a>
+<a name="364"><span class="lineNum">     364 </span>            :   INST(Fcmovnbe        , FpuR               , O_FPU(00,DBD0,_)          , 0                         , 0 , 0 , 618 , 73 , 48 , 0 ),</a>
+<a name="365"><span class="lineNum">     365 </span>            :   INST(Fcmovne         , FpuR               , O_FPU(00,DBC8,_)          , 0                         , 0 , 0 , 627 , 73 , 48 , 0 ),</a>
+<a name="366"><span class="lineNum">     366 </span>            :   INST(Fcmovnu         , FpuR               , O_FPU(00,DBD8,_)          , 0                         , 0 , 0 , 635 , 73 , 48 , 0 ),</a>
+<a name="367"><span class="lineNum">     367 </span>            :   INST(Fcmovu          , FpuR               , O_FPU(00,DAD8,_)          , 0                         , 0 , 0 , 643 , 73 , 48 , 0 ),</a>
+<a name="368"><span class="lineNum">     368 </span>            :   INST(Fcom            , FpuCom             , O_FPU(00,D0D0,2)          , 0                         , 0 , 0 , 650 , 74 , 47 , 0 ),</a>
+<a name="369"><span class="lineNum">     369 </span>            :   INST(Fcomi           , FpuR               , O_FPU(00,DBF0,_)          , 0                         , 0 , 0 , 655 , 75 , 49 , 0 ),</a>
+<a name="370"><span class="lineNum">     370 </span>            :   INST(Fcomip          , FpuR               , O_FPU(00,DFF0,_)          , 0                         , 0 , 0 , 661 , 75 , 49 , 0 ),</a>
+<a name="371"><span class="lineNum">     371 </span>            :   INST(Fcomp           , FpuCom             , O_FPU(00,D8D8,3)          , 0                         , 0 , 0 , 668 , 74 , 47 , 0 ),</a>
+<a name="372"><span class="lineNum">     372 </span>            :   INST(Fcompp          , FpuOp              , O_FPU(00,DED9,_)          , 0                         , 0 , 0 , 674 , 34 , 47 , 0 ),</a>
+<a name="373"><span class="lineNum">     373 </span>            :   INST(Fcos            , FpuOp              , O_FPU(00,D9FF,_)          , 0                         , 0 , 0 , 681 , 34 , 47 , 0 ),</a>
+<a name="374"><span class="lineNum">     374 </span>            :   INST(Fdecstp         , FpuOp              , O_FPU(00,D9F6,_)          , 0                         , 0 , 0 , 686 , 34 , 47 , 0 ),</a>
+<a name="375"><span class="lineNum">     375 </span>            :   INST(Fdiv            , FpuArith           , O_FPU(00,F0F8,6)          , 0                         , 0 , 0 , 694 , 69 , 47 , 0 ),</a>
+<a name="376"><span class="lineNum">     376 </span>            :   INST(Fdivp           , FpuRDef            , O_FPU(00,DEF8,_)          , 0                         , 0 , 0 , 699 , 70 , 47 , 0 ),</a>
+<a name="377"><span class="lineNum">     377 </span>            :   INST(Fdivr           , FpuArith           , O_FPU(00,F8F0,7)          , 0                         , 0 , 0 , 705 , 69 , 47 , 0 ),</a>
+<a name="378"><span class="lineNum">     378 </span>            :   INST(Fdivrp          , FpuRDef            , O_FPU(00,DEF0,_)          , 0                         , 0 , 0 , 711 , 70 , 47 , 0 ),</a>
+<a name="379"><span class="lineNum">     379 </span>            :   INST(Femms           , X86Op              , O(000F00,0E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 718 , 34 , 50 , 0 ),</a>
+<a name="380"><span class="lineNum">     380 </span>            :   INST(Ffree           , FpuR               , O_FPU(00,DDC0,_)          , 0                         , 0 , 0 , 724 , 73 , 47 , 0 ),</a>
+<a name="381"><span class="lineNum">     381 </span>            :   INST(Fiadd           , FpuM               , O_FPU(00,00DA,0)          , 0                         , 0 , 0 , 730 , 76 , 47 , 0 ),</a>
+<a name="382"><span class="lineNum">     382 </span>            :   INST(Ficom           , FpuM               , O_FPU(00,00DA,2)          , 0                         , 0 , 0 , 736 , 76 , 47 , 0 ),</a>
+<a name="383"><span class="lineNum">     383 </span>            :   INST(Ficomp          , FpuM               , O_FPU(00,00DA,3)          , 0                         , 0 , 0 , 742 , 76 , 47 , 0 ),</a>
+<a name="384"><span class="lineNum">     384 </span>            :   INST(Fidiv           , FpuM               , O_FPU(00,00DA,6)          , 0                         , 0 , 0 , 749 , 76 , 47 , 0 ),</a>
+<a name="385"><span class="lineNum">     385 </span>            :   INST(Fidivr          , FpuM               , O_FPU(00,00DA,7)          , 0                         , 0 , 0 , 755 , 76 , 47 , 0 ),</a>
+<a name="386"><span class="lineNum">     386 </span>            :   INST(Fild            , FpuM               , O_FPU(00,00DB,0)          , O_FPU(00,00DF,5)          , 0 , 0 , 762 , 77 , 47 , 0 ),</a>
+<a name="387"><span class="lineNum">     387 </span>            :   INST(Fimul           , FpuM               , O_FPU(00,00DA,1)          , 0                         , 0 , 0 , 767 , 76 , 47 , 0 ),</a>
+<a name="388"><span class="lineNum">     388 </span>            :   INST(Fincstp         , FpuOp              , O_FPU(00,D9F7,_)          , 0                         , 0 , 0 , 773 , 34 , 47 , 0 ),</a>
+<a name="389"><span class="lineNum">     389 </span>            :   INST(Finit           , FpuOp              , O_FPU(9B,DBE3,_)          , 0                         , 0 , 0 , 781 , 34 , 47 , 0 ),</a>
+<a name="390"><span class="lineNum">     390 </span>            :   INST(Fist            , FpuM               , O_FPU(00,00DB,2)          , 0                         , 0 , 0 , 787 , 78 , 47 , 0 ),</a>
+<a name="391"><span class="lineNum">     391 </span>            :   INST(Fistp           , FpuM               , O_FPU(00,00DB,3)          , O_FPU(00,00DF,7)          , 0 , 0 , 792 , 79 , 47 , 0 ),</a>
+<a name="392"><span class="lineNum">     392 </span>            :   INST(Fisttp          , FpuM               , O_FPU(00,00DB,1)          , O_FPU(00,00DD,1)          , 0 , 0 , 798 , 80 , 51 , 0 ),</a>
+<a name="393"><span class="lineNum">     393 </span>            :   INST(Fisub           , FpuM               , O_FPU(00,00DA,4)          , 0                         , 0 , 0 , 805 , 76 , 47 , 0 ),</a>
+<a name="394"><span class="lineNum">     394 </span>            :   INST(Fisubr          , FpuM               , O_FPU(00,00DA,5)          , 0                         , 0 , 0 , 811 , 76 , 47 , 0 ),</a>
+<a name="395"><span class="lineNum">     395 </span>            :   INST(Fld             , FpuFldFst          , O_FPU(00,00D9,0)          , O_FPU(00,00DB,5)          , 0 , 0 , 818 , 81 , 47 , 0 ),</a>
+<a name="396"><span class="lineNum">     396 </span>            :   INST(Fld1            , FpuOp              , O_FPU(00,D9E8,_)          , 0                         , 0 , 0 , 822 , 34 , 47 , 0 ),</a>
+<a name="397"><span class="lineNum">     397 </span>            :   INST(Fldcw           , X86M_Only          , O_FPU(00,00D9,5)          , 0                         , 0 , 0 , 827 , 82 , 47 , 0 ),</a>
+<a name="398"><span class="lineNum">     398 </span>            :   INST(Fldenv          , X86M_Only          , O_FPU(00,00D9,4)          , 0                         , 0 , 0 , 833 , 35 , 47 , 0 ),</a>
+<a name="399"><span class="lineNum">     399 </span>            :   INST(Fldl2e          , FpuOp              , O_FPU(00,D9EA,_)          , 0                         , 0 , 0 , 840 , 34 , 47 , 0 ),</a>
+<a name="400"><span class="lineNum">     400 </span>            :   INST(Fldl2t          , FpuOp              , O_FPU(00,D9E9,_)          , 0                         , 0 , 0 , 847 , 34 , 47 , 0 ),</a>
+<a name="401"><span class="lineNum">     401 </span>            :   INST(Fldlg2          , FpuOp              , O_FPU(00,D9EC,_)          , 0                         , 0 , 0 , 854 , 34 , 47 , 0 ),</a>
+<a name="402"><span class="lineNum">     402 </span>            :   INST(Fldln2          , FpuOp              , O_FPU(00,D9ED,_)          , 0                         , 0 , 0 , 861 , 34 , 47 , 0 ),</a>
+<a name="403"><span class="lineNum">     403 </span>            :   INST(Fldpi           , FpuOp              , O_FPU(00,D9EB,_)          , 0                         , 0 , 0 , 868 , 34 , 47 , 0 ),</a>
+<a name="404"><span class="lineNum">     404 </span>            :   INST(Fldz            , FpuOp              , O_FPU(00,D9EE,_)          , 0                         , 0 , 0 , 874 , 34 , 47 , 0 ),</a>
+<a name="405"><span class="lineNum">     405 </span>            :   INST(Fmul            , FpuArith           , O_FPU(00,C8C8,1)          , 0                         , 0 , 0 , 1999, 83 , 47 , 0 ),</a>
+<a name="406"><span class="lineNum">     406 </span>            :   INST(Fmulp           , FpuRDef            , O_FPU(00,DEC8,_)          , 0                         , 0 , 0 , 879 , 70 , 47 , 0 ),</a>
+<a name="407"><span class="lineNum">     407 </span>            :   INST(Fnclex          , FpuOp              , O_FPU(00,DBE2,_)          , 0                         , 0 , 0 , 885 , 34 , 47 , 0 ),</a>
+<a name="408"><span class="lineNum">     408 </span>            :   INST(Fninit          , FpuOp              , O_FPU(00,DBE3,_)          , 0                         , 0 , 0 , 892 , 34 , 47 , 0 ),</a>
+<a name="409"><span class="lineNum">     409 </span>            :   INST(Fnop            , FpuOp              , O_FPU(00,D9D0,_)          , 0                         , 0 , 0 , 899 , 34 , 47 , 0 ),</a>
+<a name="410"><span class="lineNum">     410 </span>            :   INST(Fnsave          , X86M_Only          , O_FPU(00,00DD,6)          , 0                         , 0 , 0 , 904 , 84 , 47 , 0 ),</a>
+<a name="411"><span class="lineNum">     411 </span>            :   INST(Fnstcw          , X86M_Only          , O_FPU(00,00D9,7)          , 0                         , 0 , 0 , 911 , 85 , 47 , 0 ),</a>
+<a name="412"><span class="lineNum">     412 </span>            :   INST(Fnstenv         , X86M_Only          , O_FPU(00,00D9,6)          , 0                         , 0 , 0 , 918 , 84 , 47 , 0 ),</a>
+<a name="413"><span class="lineNum">     413 </span>            :   INST(Fnstsw          , FpuStsw            , O_FPU(00,00DD,7)          , O_FPU(00,DFE0,_)          , 0 , 0 , 926 , 86 , 47 , 0 ),</a>
+<a name="414"><span class="lineNum">     414 </span>            :   INST(Fpatan          , FpuOp              , O_FPU(00,D9F3,_)          , 0                         , 0 , 0 , 933 , 34 , 47 , 0 ),</a>
+<a name="415"><span class="lineNum">     415 </span>            :   INST(Fprem           , FpuOp              , O_FPU(00,D9F8,_)          , 0                         , 0 , 0 , 940 , 34 , 47 , 0 ),</a>
+<a name="416"><span class="lineNum">     416 </span>            :   INST(Fprem1          , FpuOp              , O_FPU(00,D9F5,_)          , 0                         , 0 , 0 , 946 , 34 , 47 , 0 ),</a>
+<a name="417"><span class="lineNum">     417 </span>            :   INST(Fptan           , FpuOp              , O_FPU(00,D9F2,_)          , 0                         , 0 , 0 , 953 , 34 , 47 , 0 ),</a>
+<a name="418"><span class="lineNum">     418 </span>            :   INST(Frndint         , FpuOp              , O_FPU(00,D9FC,_)          , 0                         , 0 , 0 , 959 , 34 , 47 , 0 ),</a>
+<a name="419"><span class="lineNum">     419 </span>            :   INST(Frstor          , X86M_Only          , O_FPU(00,00DD,4)          , 0                         , 0 , 0 , 967 , 35 , 47 , 0 ),</a>
+<a name="420"><span class="lineNum">     420 </span>            :   INST(Fsave           , X86M_Only          , O_FPU(9B,00DD,6)          , 0                         , 0 , 0 , 974 , 84 , 47 , 0 ),</a>
+<a name="421"><span class="lineNum">     421 </span>            :   INST(Fscale          , FpuOp              , O_FPU(00,D9FD,_)          , 0                         , 0 , 0 , 980 , 34 , 47 , 0 ),</a>
+<a name="422"><span class="lineNum">     422 </span>            :   INST(Fsin            , FpuOp              , O_FPU(00,D9FE,_)          , 0                         , 0 , 0 , 987 , 34 , 47 , 0 ),</a>
+<a name="423"><span class="lineNum">     423 </span>            :   INST(Fsincos         , FpuOp              , O_FPU(00,D9FB,_)          , 0                         , 0 , 0 , 992 , 34 , 47 , 0 ),</a>
+<a name="424"><span class="lineNum">     424 </span>            :   INST(Fsqrt           , FpuOp              , O_FPU(00,D9FA,_)          , 0                         , 0 , 0 , 1000, 34 , 47 , 0 ),</a>
+<a name="425"><span class="lineNum">     425 </span>            :   INST(Fst             , FpuFldFst          , O_FPU(00,00D9,2)          , 0                         , 0 , 0 , 1006, 87 , 47 , 0 ),</a>
+<a name="426"><span class="lineNum">     426 </span>            :   INST(Fstcw           , X86M_Only          , O_FPU(9B,00D9,7)          , 0                         , 0 , 0 , 1010, 85 , 47 , 0 ),</a>
+<a name="427"><span class="lineNum">     427 </span>            :   INST(Fstenv          , X86M_Only          , O_FPU(9B,00D9,6)          , 0                         , 0 , 0 , 1016, 84 , 47 , 0 ),</a>
+<a name="428"><span class="lineNum">     428 </span>            :   INST(Fstp            , FpuFldFst          , O_FPU(00,00D9,3)          , O(000000,DB,7,_,_,_,_,_  ), 0 , 0 , 1023, 88 , 47 , 0 ),</a>
+<a name="429"><span class="lineNum">     429 </span>            :   INST(Fstsw           , FpuStsw            , O_FPU(9B,00DD,7)          , O_FPU(9B,DFE0,_)          , 0 , 0 , 1028, 89 , 47 , 0 ),</a>
+<a name="430"><span class="lineNum">     430 </span>            :   INST(Fsub            , FpuArith           , O_FPU(00,E0E8,4)          , 0                         , 0 , 0 , 2077, 69 , 47 , 0 ),</a>
+<a name="431"><span class="lineNum">     431 </span>            :   INST(Fsubp           , FpuRDef            , O_FPU(00,DEE8,_)          , 0                         , 0 , 0 , 1034, 70 , 47 , 0 ),</a>
+<a name="432"><span class="lineNum">     432 </span>            :   INST(Fsubr           , FpuArith           , O_FPU(00,E8E0,5)          , 0                         , 0 , 0 , 2083, 69 , 47 , 0 ),</a>
+<a name="433"><span class="lineNum">     433 </span>            :   INST(Fsubrp          , FpuRDef            , O_FPU(00,DEE0,_)          , 0                         , 0 , 0 , 1040, 70 , 47 , 0 ),</a>
+<a name="434"><span class="lineNum">     434 </span>            :   INST(Ftst            , FpuOp              , O_FPU(00,D9E4,_)          , 0                         , 0 , 0 , 1047, 34 , 47 , 0 ),</a>
+<a name="435"><span class="lineNum">     435 </span>            :   INST(Fucom           , FpuRDef            , O_FPU(00,DDE0,_)          , 0                         , 0 , 0 , 1052, 90 , 47 , 0 ),</a>
+<a name="436"><span class="lineNum">     436 </span>            :   INST(Fucomi          , FpuR               , O_FPU(00,DBE8,_)          , 0                         , 0 , 0 , 1058, 75 , 49 , 0 ),</a>
+<a name="437"><span class="lineNum">     437 </span>            :   INST(Fucomip         , FpuR               , O_FPU(00,DFE8,_)          , 0                         , 0 , 0 , 1065, 75 , 49 , 0 ),</a>
+<a name="438"><span class="lineNum">     438 </span>            :   INST(Fucomp          , FpuRDef            , O_FPU(00,DDE8,_)          , 0                         , 0 , 0 , 1073, 90 , 47 , 0 ),</a>
+<a name="439"><span class="lineNum">     439 </span>            :   INST(Fucompp         , FpuOp              , O_FPU(00,DAE9,_)          , 0                         , 0 , 0 , 1080, 34 , 47 , 0 ),</a>
+<a name="440"><span class="lineNum">     440 </span>            :   INST(Fwait           , X86Op              , O_FPU(00,00DB,_)          , 0                         , 0 , 0 , 1088, 34 , 47 , 0 ),</a>
+<a name="441"><span class="lineNum">     441 </span>            :   INST(Fxam            , FpuOp              , O_FPU(00,D9E5,_)          , 0                         , 0 , 0 , 1094, 34 , 47 , 0 ),</a>
+<a name="442"><span class="lineNum">     442 </span>            :   INST(Fxch            , FpuR               , O_FPU(00,D9C8,_)          , 0                         , 0 , 0 , 1099, 70 , 47 , 0 ),</a>
+<a name="443"><span class="lineNum">     443 </span>            :   INST(Fxrstor         , X86M_Only          , O(000F00,AE,1,_,_,_,_,_  ), 0                         , 0 , 0 , 1104, 35 , 52 , 0 ),</a>
+<a name="444"><span class="lineNum">     444 </span>            :   INST(Fxrstor64       , X86M_Only          , O(000F00,AE,1,_,1,_,_,_  ), 0                         , 0 , 0 , 1112, 91 , 52 , 0 ),</a>
+<a name="445"><span class="lineNum">     445 </span>            :   INST(Fxsave          , X86M_Only          , O(000F00,AE,0,_,_,_,_,_  ), 0                         , 0 , 0 , 1122, 84 , 53 , 0 ),</a>
+<a name="446"><span class="lineNum">     446 </span>            :   INST(Fxsave64        , X86M_Only          , O(000F00,AE,0,_,1,_,_,_  ), 0                         , 0 , 0 , 1129, 92 , 53 , 0 ),</a>
+<a name="447"><span class="lineNum">     447 </span>            :   INST(Fxtract         , FpuOp              , O_FPU(00,D9F4,_)          , 0                         , 0 , 0 , 1138, 34 , 47 , 0 ),</a>
+<a name="448"><span class="lineNum">     448 </span>            :   INST(Fyl2x           , FpuOp              , O_FPU(00,D9F1,_)          , 0                         , 0 , 0 , 1146, 34 , 47 , 0 ),</a>
+<a name="449"><span class="lineNum">     449 </span>            :   INST(Fyl2xp1         , FpuOp              , O_FPU(00,D9F9,_)          , 0                         , 0 , 0 , 1152, 34 , 47 , 0 ),</a>
+<a name="450"><span class="lineNum">     450 </span>            :   INST(Haddpd          , ExtRm              , O(660F00,7C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5382, 5  , 6  , 21),</a>
+<a name="451"><span class="lineNum">     451 </span>            :   INST(Haddps          , ExtRm              , O(F20F00,7C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5390, 5  , 6  , 21),</a>
+<a name="452"><span class="lineNum">     452 </span>            :   INST(Hlt             , X86Op              , O(000000,F4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1160, 34 , 23 , 0 ),</a>
+<a name="453"><span class="lineNum">     453 </span>            :   INST(Hsubpd          , ExtRm              , O(660F00,7D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5398, 5  , 6  , 22),</a>
+<a name="454"><span class="lineNum">     454 </span>            :   INST(Hsubps          , ExtRm              , O(F20F00,7D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5406, 5  , 6  , 22),</a>
+<a name="455"><span class="lineNum">     455 </span>            :   INST(Idiv            , X86M_GPB_MulDiv    , O(000000,F6,7,_,x,_,_,_  ), 0                         , 0 , 0 , 750 , 64 , 1  , 0 ),</a>
+<a name="456"><span class="lineNum">     456 </span>            :   INST(Imul            , X86Imul            , O(000000,F6,5,_,x,_,_,_  ), 0                         , 0 , 0 , 768 , 93 , 1  , 0 ),</a>
+<a name="457"><span class="lineNum">     457 </span>            :   INST(In              , X86In              , O(000000,EC,_,_,_,_,_,_  ), O(000000,E4,_,_,_,_,_,_  ), 0 , 0 , 9508, 94 , 45 , 0 ),</a>
+<a name="458"><span class="lineNum">     458 </span>            :   INST(Inc             , X86IncDec          , O(000000,FE,0,_,x,_,_,_  ), O(000000,40,_,_,x,_,_,_  ), 0 , 0 , 1164, 95 , 43 , 0 ),</a>
+<a name="459"><span class="lineNum">     459 </span>            :   INST(Ins             , X86Ins             , O(000000,6C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1168, 96 , 45 , 0 ),</a>
+<a name="460"><span class="lineNum">     460 </span>            :   INST(Insertps        , ExtRmi             , O(660F3A,21,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5542, 40 , 12 , 23),</a>
+<a name="461"><span class="lineNum">     461 </span>            :   INST(Insertq         , ExtInsertq         , O(F20F00,79,_,_,_,_,_,_  ), O(F20F00,78,_,_,_,_,_,_  ), 0 , 0 , 1172, 97 , 46 , 0 ),</a>
+<a name="462"><span class="lineNum">     462 </span>            :   INST(Int             , X86Int             , O(000000,CD,_,_,_,_,_,_  ), 0                         , 0 , 0 , 963 , 98 , 45 , 0 ),</a>
+<a name="463"><span class="lineNum">     463 </span>            :   INST(Int3            , X86Op              , O(000000,CC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1180, 34 , 45 , 0 ),</a>
+<a name="464"><span class="lineNum">     464 </span>            :   INST(Into            , X86Op              , O(000000,CE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1185, 99 , 54 , 0 ),</a>
+<a name="465"><span class="lineNum">     465 </span>            :   INST(Invd            , X86Op              , O(000F00,08,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9463, 34 , 55 , 0 ),</a>
+<a name="466"><span class="lineNum">     466 </span>            :   INST(Invlpg          , X86M_Only          , O(000F00,01,7,_,_,_,_,_  ), 0                         , 0 , 0 , 1190, 35 , 55 , 0 ),</a>
+<a name="467"><span class="lineNum">     467 </span>            :   INST(Invpcid         , X86Rm_NoRexW       , O(660F38,82,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1197, 100, 55 , 0 ),</a>
+<a name="468"><span class="lineNum">     468 </span>            :   INST(Iret            , X86Op              , O(000000,CF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1205, 34 , 16 , 0 ),</a>
+<a name="469"><span class="lineNum">     469 </span>            :   INST(Iretd           , X86Op              , O(000000,CF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1210, 34 , 16 , 0 ),</a>
+<a name="470"><span class="lineNum">     470 </span>            :   INST(Iretq           , X86Op              , O(000000,CF,_,_,1,_,_,_  ), 0                         , 0 , 0 , 1216, 101, 16 , 0 ),</a>
+<a name="471"><span class="lineNum">     471 </span>            :   INST(Iretw           , X86Op              , O(660000,CF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1222, 34 , 16 , 0 ),</a>
+<a name="472"><span class="lineNum">     472 </span>            :   INST(Ja              , X86Jcc             , O(000F00,87,_,_,_,_,_,_  ), O(000000,77,_,_,_,_,_,_  ), 0 , 0 , 1228, 102, 56 , 0 ),</a>
+<a name="473"><span class="lineNum">     473 </span>            :   INST(Jae             , X86Jcc             , O(000F00,83,_,_,_,_,_,_  ), O(000000,73,_,_,_,_,_,_  ), 0 , 0 , 1231, 103, 57 , 0 ),</a>
+<a name="474"><span class="lineNum">     474 </span>            :   INST(Jb              , X86Jcc             , O(000F00,82,_,_,_,_,_,_  ), O(000000,72,_,_,_,_,_,_  ), 0 , 0 , 1235, 104, 57 , 0 ),</a>
+<a name="475"><span class="lineNum">     475 </span>            :   INST(Jbe             , X86Jcc             , O(000F00,86,_,_,_,_,_,_  ), O(000000,76,_,_,_,_,_,_  ), 0 , 0 , 1238, 105, 56 , 0 ),</a>
+<a name="476"><span class="lineNum">     476 </span>            :   INST(Jc              , X86Jcc             , O(000F00,82,_,_,_,_,_,_  ), O(000000,72,_,_,_,_,_,_  ), 0 , 0 , 1242, 106, 57 , 0 ),</a>
+<a name="477"><span class="lineNum">     477 </span>            :   INST(Je              , X86Jcc             , O(000F00,84,_,_,_,_,_,_  ), O(000000,74,_,_,_,_,_,_  ), 0 , 0 , 1245, 107, 58 , 0 ),</a>
+<a name="478"><span class="lineNum">     478 </span>            :   INST(Jecxz           , X86JecxzLoop       , 0                         , O(000000,E3,_,_,_,_,_,_  ), 0 , 0 , 1248, 108, 45 , 0 ),</a>
+<a name="479"><span class="lineNum">     479 </span>            :   INST(Jg              , X86Jcc             , O(000F00,8F,_,_,_,_,_,_  ), O(000000,7F,_,_,_,_,_,_  ), 0 , 0 , 1254, 109, 59 , 0 ),</a>
+<a name="480"><span class="lineNum">     480 </span>            :   INST(Jge             , X86Jcc             , O(000F00,8D,_,_,_,_,_,_  ), O(000000,7D,_,_,_,_,_,_  ), 0 , 0 , 1257, 110, 60 , 0 ),</a>
+<a name="481"><span class="lineNum">     481 </span>            :   INST(Jl              , X86Jcc             , O(000F00,8C,_,_,_,_,_,_  ), O(000000,7C,_,_,_,_,_,_  ), 0 , 0 , 1261, 111, 60 , 0 ),</a>
+<a name="482"><span class="lineNum">     482 </span>            :   INST(Jle             , X86Jcc             , O(000F00,8E,_,_,_,_,_,_  ), O(000000,7E,_,_,_,_,_,_  ), 0 , 0 , 1264, 112, 59 , 0 ),</a>
+<a name="483"><span class="lineNum">     483 </span>            :   INST(Jmp             , X86Jmp             , O(000000,FF,4,_,_,_,_,_  ), O(000000,EB,_,_,_,_,_,_  ), 0 , 0 , 1268, 113, 45 , 0 ),</a>
+<a name="484"><span class="lineNum">     484 </span>            :   INST(Jna             , X86Jcc             , O(000F00,86,_,_,_,_,_,_  ), O(000000,76,_,_,_,_,_,_  ), 0 , 0 , 1272, 105, 56 , 0 ),</a>
+<a name="485"><span class="lineNum">     485 </span>            :   INST(Jnae            , X86Jcc             , O(000F00,82,_,_,_,_,_,_  ), O(000000,72,_,_,_,_,_,_  ), 0 , 0 , 1276, 104, 57 , 0 ),</a>
+<a name="486"><span class="lineNum">     486 </span>            :   INST(Jnb             , X86Jcc             , O(000F00,83,_,_,_,_,_,_  ), O(000000,73,_,_,_,_,_,_  ), 0 , 0 , 1281, 103, 57 , 0 ),</a>
+<a name="487"><span class="lineNum">     487 </span>            :   INST(Jnbe            , X86Jcc             , O(000F00,87,_,_,_,_,_,_  ), O(000000,77,_,_,_,_,_,_  ), 0 , 0 , 1285, 102, 56 , 0 ),</a>
+<a name="488"><span class="lineNum">     488 </span>            :   INST(Jnc             , X86Jcc             , O(000F00,83,_,_,_,_,_,_  ), O(000000,73,_,_,_,_,_,_  ), 0 , 0 , 1290, 114, 57 , 0 ),</a>
+<a name="489"><span class="lineNum">     489 </span>            :   INST(Jne             , X86Jcc             , O(000F00,85,_,_,_,_,_,_  ), O(000000,75,_,_,_,_,_,_  ), 0 , 0 , 1294, 115, 58 , 0 ),</a>
+<a name="490"><span class="lineNum">     490 </span>            :   INST(Jng             , X86Jcc             , O(000F00,8E,_,_,_,_,_,_  ), O(000000,7E,_,_,_,_,_,_  ), 0 , 0 , 1298, 112, 59 , 0 ),</a>
+<a name="491"><span class="lineNum">     491 </span>            :   INST(Jnge            , X86Jcc             , O(000F00,8C,_,_,_,_,_,_  ), O(000000,7C,_,_,_,_,_,_  ), 0 , 0 , 1302, 111, 60 , 0 ),</a>
+<a name="492"><span class="lineNum">     492 </span>            :   INST(Jnl             , X86Jcc             , O(000F00,8D,_,_,_,_,_,_  ), O(000000,7D,_,_,_,_,_,_  ), 0 , 0 , 1307, 110, 60 , 0 ),</a>
+<a name="493"><span class="lineNum">     493 </span>            :   INST(Jnle            , X86Jcc             , O(000F00,8F,_,_,_,_,_,_  ), O(000000,7F,_,_,_,_,_,_  ), 0 , 0 , 1311, 109, 59 , 0 ),</a>
+<a name="494"><span class="lineNum">     494 </span>            :   INST(Jno             , X86Jcc             , O(000F00,81,_,_,_,_,_,_  ), O(000000,71,_,_,_,_,_,_  ), 0 , 0 , 1316, 116, 54 , 0 ),</a>
+<a name="495"><span class="lineNum">     495 </span>            :   INST(Jnp             , X86Jcc             , O(000F00,8B,_,_,_,_,_,_  ), O(000000,7B,_,_,_,_,_,_  ), 0 , 0 , 1320, 117, 61 , 0 ),</a>
+<a name="496"><span class="lineNum">     496 </span>            :   INST(Jns             , X86Jcc             , O(000F00,89,_,_,_,_,_,_  ), O(000000,79,_,_,_,_,_,_  ), 0 , 0 , 1324, 118, 62 , 0 ),</a>
+<a name="497"><span class="lineNum">     497 </span>            :   INST(Jnz             , X86Jcc             , O(000F00,85,_,_,_,_,_,_  ), O(000000,75,_,_,_,_,_,_  ), 0 , 0 , 1328, 115, 58 , 0 ),</a>
+<a name="498"><span class="lineNum">     498 </span>            :   INST(Jo              , X86Jcc             , O(000F00,80,_,_,_,_,_,_  ), O(000000,70,_,_,_,_,_,_  ), 0 , 0 , 1332, 119, 54 , 0 ),</a>
+<a name="499"><span class="lineNum">     499 </span>            :   INST(Jp              , X86Jcc             , O(000F00,8A,_,_,_,_,_,_  ), O(000000,7A,_,_,_,_,_,_  ), 0 , 0 , 1335, 120, 61 , 0 ),</a>
+<a name="500"><span class="lineNum">     500 </span>            :   INST(Jpe             , X86Jcc             , O(000F00,8A,_,_,_,_,_,_  ), O(000000,7A,_,_,_,_,_,_  ), 0 , 0 , 1338, 120, 61 , 0 ),</a>
+<a name="501"><span class="lineNum">     501 </span>            :   INST(Jpo             , X86Jcc             , O(000F00,8B,_,_,_,_,_,_  ), O(000000,7B,_,_,_,_,_,_  ), 0 , 0 , 1342, 117, 61 , 0 ),</a>
+<a name="502"><span class="lineNum">     502 </span>            :   INST(Js              , X86Jcc             , O(000F00,88,_,_,_,_,_,_  ), O(000000,78,_,_,_,_,_,_  ), 0 , 0 , 1346, 121, 62 , 0 ),</a>
+<a name="503"><span class="lineNum">     503 </span>            :   INST(Jz              , X86Jcc             , O(000F00,84,_,_,_,_,_,_  ), O(000000,74,_,_,_,_,_,_  ), 0 , 0 , 1349, 107, 58 , 0 ),</a>
+<a name="504"><span class="lineNum">     504 </span>            :   INST(Kaddb           , VexRvm             , V(660F00,4A,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1352, 122, 63 , 0 ),</a>
+<a name="505"><span class="lineNum">     505 </span>            :   INST(Kaddd           , VexRvm             , V(660F00,4A,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1358, 122, 64 , 0 ),</a>
+<a name="506"><span class="lineNum">     506 </span>            :   INST(Kaddq           , VexRvm             , V(000F00,4A,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1364, 122, 64 , 0 ),</a>
+<a name="507"><span class="lineNum">     507 </span>            :   INST(Kaddw           , VexRvm             , V(000F00,4A,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1370, 122, 63 , 0 ),</a>
+<a name="508"><span class="lineNum">     508 </span>            :   INST(Kandb           , VexRvm             , V(660F00,41,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1376, 122, 63 , 0 ),</a>
+<a name="509"><span class="lineNum">     509 </span>            :   INST(Kandd           , VexRvm             , V(660F00,41,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1382, 122, 64 , 0 ),</a>
+<a name="510"><span class="lineNum">     510 </span>            :   INST(Kandnb          , VexRvm             , V(660F00,42,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1388, 122, 63 , 0 ),</a>
+<a name="511"><span class="lineNum">     511 </span>            :   INST(Kandnd          , VexRvm             , V(660F00,42,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1395, 122, 64 , 0 ),</a>
+<a name="512"><span class="lineNum">     512 </span>            :   INST(Kandnq          , VexRvm             , V(000F00,42,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1402, 122, 64 , 0 ),</a>
+<a name="513"><span class="lineNum">     513 </span>            :   INST(Kandnw          , VexRvm             , V(000F00,42,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1409, 122, 65 , 0 ),</a>
+<a name="514"><span class="lineNum">     514 </span>            :   INST(Kandq           , VexRvm             , V(000F00,41,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1416, 122, 64 , 0 ),</a>
+<a name="515"><span class="lineNum">     515 </span>            :   INST(Kandw           , VexRvm             , V(000F00,41,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1422, 122, 65 , 0 ),</a>
+<a name="516"><span class="lineNum">     516 </span>            :   INST(Kmovb           , VexKmov            , V(660F00,90,_,0,0,_,_,_  ), V(660F00,92,_,0,0,_,_,_  ), 0 , 0 , 1428, 123, 63 , 0 ),</a>
+<a name="517"><span class="lineNum">     517 </span>            :   INST(Kmovd           , VexKmov            , V(660F00,90,_,0,1,_,_,_  ), V(F20F00,92,_,0,0,_,_,_  ), 0 , 0 , 7344, 124, 64 , 0 ),</a>
+<a name="518"><span class="lineNum">     518 </span>            :   INST(Kmovq           , VexKmov            , V(000F00,90,_,0,1,_,_,_  ), V(F20F00,92,_,0,1,_,_,_  ), 0 , 0 , 7355, 125, 64 , 0 ),</a>
+<a name="519"><span class="lineNum">     519 </span>            :   INST(Kmovw           , VexKmov            , V(000F00,90,_,0,0,_,_,_  ), V(000F00,92,_,0,0,_,_,_  ), 0 , 0 , 1434, 126, 65 , 0 ),</a>
+<a name="520"><span class="lineNum">     520 </span>            :   INST(Knotb           , VexRm              , V(660F00,44,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1440, 127, 63 , 0 ),</a>
+<a name="521"><span class="lineNum">     521 </span>            :   INST(Knotd           , VexRm              , V(660F00,44,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1446, 127, 64 , 0 ),</a>
+<a name="522"><span class="lineNum">     522 </span>            :   INST(Knotq           , VexRm              , V(000F00,44,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1452, 127, 64 , 0 ),</a>
+<a name="523"><span class="lineNum">     523 </span>            :   INST(Knotw           , VexRm              , V(000F00,44,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1458, 127, 65 , 0 ),</a>
+<a name="524"><span class="lineNum">     524 </span>            :   INST(Korb            , VexRvm             , V(660F00,45,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1464, 122, 63 , 0 ),</a>
+<a name="525"><span class="lineNum">     525 </span>            :   INST(Kord            , VexRvm             , V(660F00,45,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1469, 122, 64 , 0 ),</a>
+<a name="526"><span class="lineNum">     526 </span>            :   INST(Korq            , VexRvm             , V(000F00,45,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1474, 122, 64 , 0 ),</a>
+<a name="527"><span class="lineNum">     527 </span>            :   INST(Kortestb        , VexRm              , V(660F00,98,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1479, 128, 66 , 0 ),</a>
+<a name="528"><span class="lineNum">     528 </span>            :   INST(Kortestd        , VexRm              , V(660F00,98,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1488, 128, 67 , 0 ),</a>
+<a name="529"><span class="lineNum">     529 </span>            :   INST(Kortestq        , VexRm              , V(000F00,98,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1497, 128, 67 , 0 ),</a>
+<a name="530"><span class="lineNum">     530 </span>            :   INST(Kortestw        , VexRm              , V(000F00,98,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1506, 128, 68 , 0 ),</a>
+<a name="531"><span class="lineNum">     531 </span>            :   INST(Korw            , VexRvm             , V(000F00,45,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1515, 122, 65 , 0 ),</a>
+<a name="532"><span class="lineNum">     532 </span>            :   INST(Kshiftlb        , VexRmi             , V(660F3A,32,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1520, 129, 63 , 0 ),</a>
+<a name="533"><span class="lineNum">     533 </span>            :   INST(Kshiftld        , VexRmi             , V(660F3A,33,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1529, 129, 64 , 0 ),</a>
+<a name="534"><span class="lineNum">     534 </span>            :   INST(Kshiftlq        , VexRmi             , V(660F3A,33,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1538, 129, 64 , 0 ),</a>
+<a name="535"><span class="lineNum">     535 </span>            :   INST(Kshiftlw        , VexRmi             , V(660F3A,32,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1547, 129, 65 , 0 ),</a>
+<a name="536"><span class="lineNum">     536 </span>            :   INST(Kshiftrb        , VexRmi             , V(660F3A,30,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1556, 129, 63 , 0 ),</a>
+<a name="537"><span class="lineNum">     537 </span>            :   INST(Kshiftrd        , VexRmi             , V(660F3A,31,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1565, 129, 64 , 0 ),</a>
+<a name="538"><span class="lineNum">     538 </span>            :   INST(Kshiftrq        , VexRmi             , V(660F3A,31,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1574, 129, 64 , 0 ),</a>
+<a name="539"><span class="lineNum">     539 </span>            :   INST(Kshiftrw        , VexRmi             , V(660F3A,30,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1583, 129, 65 , 0 ),</a>
+<a name="540"><span class="lineNum">     540 </span>            :   INST(Ktestb          , VexRm              , V(660F00,99,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1592, 128, 66 , 0 ),</a>
+<a name="541"><span class="lineNum">     541 </span>            :   INST(Ktestd          , VexRm              , V(660F00,99,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1599, 128, 67 , 0 ),</a>
+<a name="542"><span class="lineNum">     542 </span>            :   INST(Ktestq          , VexRm              , V(000F00,99,_,0,1,_,_,_  ), 0                         , 0 , 0 , 1606, 128, 67 , 0 ),</a>
+<a name="543"><span class="lineNum">     543 </span>            :   INST(Ktestw          , VexRm              , V(000F00,99,_,0,0,_,_,_  ), 0                         , 0 , 0 , 1613, 128, 66 , 0 ),</a>
+<a name="544"><span class="lineNum">     544 </span>            :   INST(Kunpckbw        , VexRvm             , V(660F00,4B,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1620, 122, 65 , 0 ),</a>
+<a name="545"><span class="lineNum">     545 </span>            :   INST(Kunpckdq        , VexRvm             , V(000F00,4B,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1629, 122, 64 , 0 ),</a>
+<a name="546"><span class="lineNum">     546 </span>            :   INST(Kunpckwd        , VexRvm             , V(000F00,4B,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1638, 122, 64 , 0 ),</a>
+<a name="547"><span class="lineNum">     547 </span>            :   INST(Kxnorb          , VexRvm             , V(660F00,46,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1647, 122, 63 , 0 ),</a>
+<a name="548"><span class="lineNum">     548 </span>            :   INST(Kxnord          , VexRvm             , V(660F00,46,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1654, 122, 64 , 0 ),</a>
+<a name="549"><span class="lineNum">     549 </span>            :   INST(Kxnorq          , VexRvm             , V(000F00,46,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1661, 122, 64 , 0 ),</a>
+<a name="550"><span class="lineNum">     550 </span>            :   INST(Kxnorw          , VexRvm             , V(000F00,46,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1668, 122, 65 , 0 ),</a>
+<a name="551"><span class="lineNum">     551 </span>            :   INST(Kxorb           , VexRvm             , V(660F00,47,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1675, 122, 63 , 0 ),</a>
+<a name="552"><span class="lineNum">     552 </span>            :   INST(Kxord           , VexRvm             , V(660F00,47,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1681, 122, 64 , 0 ),</a>
+<a name="553"><span class="lineNum">     553 </span>            :   INST(Kxorq           , VexRvm             , V(000F00,47,_,1,1,_,_,_  ), 0                         , 0 , 0 , 1687, 122, 64 , 0 ),</a>
+<a name="554"><span class="lineNum">     554 </span>            :   INST(Kxorw           , VexRvm             , V(000F00,47,_,1,0,_,_,_  ), 0                         , 0 , 0 , 1693, 122, 65 , 0 ),</a>
+<a name="555"><span class="lineNum">     555 </span>            :   INST(Lahf            , X86Op              , O(000000,9F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1699, 130, 69 , 0 ),</a>
+<a name="556"><span class="lineNum">     556 </span>            :   INST(Lar             , X86Rm              , O(000F00,02,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1704, 131, 70 , 0 ),</a>
+<a name="557"><span class="lineNum">     557 </span>            :   INST(Lddqu           , ExtRm              , O(F20F00,F0,_,_,_,_,_,_  ), 0                         , 0 , 16, 5552, 132, 6  , 24),</a>
+<a name="558"><span class="lineNum">     558 </span>            :   INST(Ldmxcsr         , X86M_Only          , O(000F00,AE,2,_,_,_,_,_  ), 0                         , 0 , 0 , 5559, 133, 5  , 0 ),</a>
+<a name="559"><span class="lineNum">     559 </span>            :   INST(Lds             , X86Rm              , O(000000,C5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1708, 134, 45 , 0 ),</a>
+<a name="560"><span class="lineNum">     560 </span>            :   INST(Lea             , X86Lea             , O(000000,8D,_,_,x,_,_,_  ), 0                         , 0 , 0 , 1712, 135, 0  , 0 ),</a>
+<a name="561"><span class="lineNum">     561 </span>            :   INST(Leave           , X86Op              , O(000000,C9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1716, 34 , 45 , 0 ),</a>
+<a name="562"><span class="lineNum">     562 </span>            :   INST(Les             , X86Rm              , O(000000,C4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1722, 134, 45 , 0 ),</a>
+<a name="563"><span class="lineNum">     563 </span>            :   INST(Lfence          , X86Fence           , O(000F00,AE,5,_,_,_,_,_  ), 0                         , 0 , 0 , 1726, 34 , 71 , 0 ),</a>
+<a name="564"><span class="lineNum">     564 </span>            :   INST(Lfs             , X86Rm              , O(000F00,B4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1733, 136, 45 , 0 ),</a>
+<a name="565"><span class="lineNum">     565 </span>            :   INST(Lgdt            , X86M_Only          , O(000F00,01,2,_,_,_,_,_  ), 0                         , 0 , 0 , 1737, 35 , 23 , 0 ),</a>
+<a name="566"><span class="lineNum">     566 </span>            :   INST(Lgs             , X86Rm              , O(000F00,B5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1742, 136, 45 , 0 ),</a>
+<a name="567"><span class="lineNum">     567 </span>            :   INST(Lidt            , X86M_Only          , O(000F00,01,3,_,_,_,_,_  ), 0                         , 0 , 0 , 1746, 35 , 23 , 0 ),</a>
+<a name="568"><span class="lineNum">     568 </span>            :   INST(Lldt            , X86M               , O(000F00,00,2,_,_,_,_,_  ), 0                         , 0 , 0 , 1751, 137, 23 , 0 ),</a>
+<a name="569"><span class="lineNum">     569 </span>            :   INST(Lmsw            , X86M               , O(000F00,01,6,_,_,_,_,_  ), 0                         , 0 , 0 , 1756, 137, 23 , 0 ),</a>
+<a name="570"><span class="lineNum">     570 </span>            :   INST(Lods            , X86StrRm           , O(000000,AC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1761, 138, 72 , 0 ),</a>
+<a name="571"><span class="lineNum">     571 </span>            :   INST(Loop            , X86JecxzLoop       , 0                         , O(000000,E2,_,_,_,_,_,_  ), 0 , 0 , 1766, 139, 45 , 0 ),</a>
+<a name="572"><span class="lineNum">     572 </span>            :   INST(Loope           , X86JecxzLoop       , 0                         , O(000000,E1,_,_,_,_,_,_  ), 0 , 0 , 1771, 140, 58 , 0 ),</a>
+<a name="573"><span class="lineNum">     573 </span>            :   INST(Loopne          , X86JecxzLoop       , 0                         , O(000000,E0,_,_,_,_,_,_  ), 0 , 0 , 1777, 141, 58 , 0 ),</a>
+<a name="574"><span class="lineNum">     574 </span>            :   INST(Lsl             , X86Rm              , O(000F00,03,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1784, 142, 70 , 0 ),</a>
+<a name="575"><span class="lineNum">     575 </span>            :   INST(Lss             , X86Rm              , O(000F00,B2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5959, 136, 45 , 0 ),</a>
+<a name="576"><span class="lineNum">     576 </span>            :   INST(Ltr             , X86M               , O(000F00,00,3,_,_,_,_,_  ), 0                         , 0 , 0 , 1788, 137, 23 , 0 ),</a>
+<a name="577"><span class="lineNum">     577 </span>            :   INST(Lzcnt           , X86Rm_Raw66H       , O(F30F00,BD,_,_,x,_,_,_  ), 0                         , 0 , 0 , 1792, 143, 73 , 0 ),</a>
+<a name="578"><span class="lineNum">     578 </span>            :   INST(Maskmovdqu      , ExtRm_ZDI          , O(660F00,57,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5568, 144, 4  , 25),</a>
+<a name="579"><span class="lineNum">     579 </span>            :   INST(Maskmovq        , ExtRm_ZDI          , O(000F00,F7,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7352, 145, 74 , 0 ),</a>
+<a name="580"><span class="lineNum">     580 </span>            :   INST(Maxpd           , ExtRm              , O(660F00,5F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5602, 5  , 4  , 26),</a>
+<a name="581"><span class="lineNum">     581 </span>            :   INST(Maxps           , ExtRm              , O(000F00,5F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5609, 5  , 5  , 26),</a>
+<a name="582"><span class="lineNum">     582 </span>            :   INST(Maxsd           , ExtRm              , O(F20F00,5F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7371, 6  , 4  , 26),</a>
+<a name="583"><span class="lineNum">     583 </span>            :   INST(Maxss           , ExtRm              , O(F30F00,5F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5623, 7  , 5  , 26),</a>
+<a name="584"><span class="lineNum">     584 </span>            :   INST(Mfence          , X86Fence           , O(000F00,AE,6,_,_,_,_,_  ), 0                         , 0 , 0 , 1798, 34 , 71 , 0 ),</a>
+<a name="585"><span class="lineNum">     585 </span>            :   INST(Minpd           , ExtRm              , O(660F00,5D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5630, 5  , 4  , 27),</a>
+<a name="586"><span class="lineNum">     586 </span>            :   INST(Minps           , ExtRm              , O(000F00,5D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5637, 5  , 5  , 27),</a>
+<a name="587"><span class="lineNum">     587 </span>            :   INST(Minsd           , ExtRm              , O(F20F00,5D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7435, 6  , 4  , 27),</a>
+<a name="588"><span class="lineNum">     588 </span>            :   INST(Minss           , ExtRm              , O(F30F00,5D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5651, 7  , 5  , 27),</a>
+<a name="589"><span class="lineNum">     589 </span>            :   INST(Monitor         , X86Op              , O(000F01,C8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1805, 146, 75 , 0 ),</a>
+<a name="590"><span class="lineNum">     590 </span>            :   INST(Mov             , X86Mov             , 0                         , 0                         , 0 , 0 , 138 , 147, 76 , 0 ),</a>
+<a name="591"><span class="lineNum">     591 </span>            :   INST(Movapd          , ExtMov             , O(660F00,28,_,_,_,_,_,_  ), O(660F00,29,_,_,_,_,_,_  ), 0 , 16, 5658, 148, 4  , 28),</a>
+<a name="592"><span class="lineNum">     592 </span>            :   INST(Movaps          , ExtMov             , O(000F00,28,_,_,_,_,_,_  ), O(000F00,29,_,_,_,_,_,_  ), 0 , 16, 5666, 149, 5  , 28),</a>
+<a name="593"><span class="lineNum">     593 </span>            :   INST(Movbe           , ExtMovbe           , O(000F38,F0,_,_,x,_,_,_  ), O(000F38,F1,_,_,x,_,_,_  ), 0 , 0 , 597 , 150, 77 , 0 ),</a>
+<a name="594"><span class="lineNum">     594 </span>            :   INST(Movd            , ExtMovd            , O(000F00,6E,_,_,_,_,_,_  ), O(000F00,7E,_,_,_,_,_,_  ), 0 , 16, 7345, 151, 78 , 29),</a>
+<a name="595"><span class="lineNum">     595 </span>            :   INST(Movddup         , ExtMov             , O(F20F00,12,_,_,_,_,_,_  ), 0                         , 0 , 16, 5680, 49 , 6  , 29),</a>
+<a name="596"><span class="lineNum">     596 </span>            :   INST(Movdq2q         , ExtMov             , O(F20F00,D6,_,_,_,_,_,_  ), 0                         , 0 , 8 , 1813, 152, 4  , 0 ),</a>
+<a name="597"><span class="lineNum">     597 </span>            :   INST(Movdqa          , ExtMov             , O(660F00,6F,_,_,_,_,_,_  ), O(660F00,7F,_,_,_,_,_,_  ), 0 , 16, 5689, 153, 4  , 30),</a>
+<a name="598"><span class="lineNum">     598 </span>            :   INST(Movdqu          , ExtMov             , O(F30F00,6F,_,_,_,_,_,_  ), O(F30F00,7F,_,_,_,_,_,_  ), 0 , 16, 5572, 154, 4  , 28),</a>
+<a name="599"><span class="lineNum">     599 </span>            :   INST(Movhlps         , ExtMov             , O(000F00,12,_,_,_,_,_,_  ), 0                         , 0 , 8 , 5764, 155, 5  , 31),</a>
+<a name="600"><span class="lineNum">     600 </span>            :   INST(Movhpd          , ExtMov             , O(660F00,16,_,_,_,_,_,_  ), O(660F00,17,_,_,_,_,_,_  ), 8 , 8 , 5773, 156, 4  , 32),</a>
+<a name="601"><span class="lineNum">     601 </span>            :   INST(Movhps          , ExtMov             , O(000F00,16,_,_,_,_,_,_  ), O(000F00,17,_,_,_,_,_,_  ), 8 , 8 , 5781, 157, 5  , 32),</a>
+<a name="602"><span class="lineNum">     602 </span>            :   INST(Movlhps         , ExtMov             , O(000F00,16,_,_,_,_,_,_  ), 0                         , 8 , 8 , 5789, 158, 5  , 31),</a>
+<a name="603"><span class="lineNum">     603 </span>            :   INST(Movlpd          , ExtMov             , O(660F00,12,_,_,_,_,_,_  ), O(660F00,13,_,_,_,_,_,_  ), 0 , 8 , 5798, 159, 4  , 32),</a>
+<a name="604"><span class="lineNum">     604 </span>            :   INST(Movlps          , ExtMov             , O(000F00,12,_,_,_,_,_,_  ), O(000F00,13,_,_,_,_,_,_  ), 0 , 8 , 5806, 160, 5  , 32),</a>
+<a name="605"><span class="lineNum">     605 </span>            :   INST(Movmskpd        , ExtMov             , O(660F00,50,_,_,_,_,_,_  ), 0                         , 0 , 8 , 5814, 161, 4  , 33),</a>
+<a name="606"><span class="lineNum">     606 </span>            :   INST(Movmskps        , ExtMov             , O(000F00,50,_,_,_,_,_,_  ), 0                         , 0 , 8 , 5824, 161, 5  , 33),</a>
+<a name="607"><span class="lineNum">     607 </span>            :   INST(Movntdq         , ExtMov             , 0                         , O(660F00,E7,_,_,_,_,_,_  ), 0 , 16, 5834, 162, 4  , 33),</a>
+<a name="608"><span class="lineNum">     608 </span>            :   INST(Movntdqa        , ExtMov             , O(660F38,2A,_,_,_,_,_,_  ), 0                         , 0 , 16, 5843, 132, 12 , 33),</a>
+<a name="609"><span class="lineNum">     609 </span>            :   INST(Movnti          , ExtMovnti          , O(000F00,C3,_,_,x,_,_,_  ), 0                         , 0 , 8 , 1821, 163, 4  , 0 ),</a>
+<a name="610"><span class="lineNum">     610 </span>            :   INST(Movntpd         , ExtMov             , 0                         , O(660F00,2B,_,_,_,_,_,_  ), 0 , 16, 5853, 164, 4  , 34),</a>
+<a name="611"><span class="lineNum">     611 </span>            :   INST(Movntps         , ExtMov             , 0                         , O(000F00,2B,_,_,_,_,_,_  ), 0 , 16, 5862, 165, 5  , 34),</a>
+<a name="612"><span class="lineNum">     612 </span>            :   INST(Movntq          , ExtMov             , 0                         , O(000F00,E7,_,_,_,_,_,_  ), 0 , 8 , 1828, 166, 74 , 0 ),</a>
+<a name="613"><span class="lineNum">     613 </span>            :   INST(Movntsd         , ExtMov             , 0                         , O(F20F00,2B,_,_,_,_,_,_  ), 0 , 8 , 1835, 167, 46 , 0 ),</a>
+<a name="614"><span class="lineNum">     614 </span>            :   INST(Movntss         , ExtMov             , 0                         , O(F30F00,2B,_,_,_,_,_,_  ), 0 , 4 , 1843, 168, 46 , 0 ),</a>
+<a name="615"><span class="lineNum">     615 </span>            :   INST(Movq            , ExtMovq            , O(000F00,6E,_,_,x,_,_,_  ), O(000F00,7E,_,_,x,_,_,_  ), 0 , 16, 7356, 169, 78 , 28),</a>
+<a name="616"><span class="lineNum">     616 </span>            :   INST(Movq2dq         , ExtRm              , O(F30F00,D6,_,_,_,_,_,_  ), 0                         , 0 , 16, 1851, 170, 4  , 0 ),</a>
+<a name="617"><span class="lineNum">     617 </span>            :   INST(Movs            , X86StrMm           , O(000000,A4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 411 , 171, 72 , 0 ),</a>
+<a name="618"><span class="lineNum">     618 </span>            :   INST(Movsd           , ExtMov             , O(F20F00,10,_,_,_,_,_,_  ), O(F20F00,11,_,_,_,_,_,_  ), 0 , 8 , 5877, 172, 79 , 35),</a>
+<a name="619"><span class="lineNum">     619 </span>            :   INST(Movshdup        , ExtRm              , O(F30F00,16,_,_,_,_,_,_  ), 0                         , 0 , 16, 5884, 50 , 6  , 30),</a>
+<a name="620"><span class="lineNum">     620 </span>            :   INST(Movsldup        , ExtRm              , O(F30F00,12,_,_,_,_,_,_  ), 0                         , 0 , 16, 5894, 50 , 6  , 30),</a>
+<a name="621"><span class="lineNum">     621 </span>            :   INST(Movss           , ExtMov             , O(F30F00,10,_,_,_,_,_,_  ), O(F30F00,11,_,_,_,_,_,_  ), 0 , 4 , 5904, 173, 80 , 35),</a>
+<a name="622"><span class="lineNum">     622 </span>            :   INST(Movsx           , X86MovsxMovzx      , O(000F00,BE,_,_,x,_,_,_  ), 0                         , 0 , 0 , 1859, 174, 0  , 0 ),</a>
+<a name="623"><span class="lineNum">     623 </span>            :   INST(Movsxd          , X86Rm              , O(000000,63,_,_,1,_,_,_  ), 0                         , 0 , 0 , 1865, 175, 0  , 0 ),</a>
+<a name="624"><span class="lineNum">     624 </span>            :   INST(Movupd          , ExtMov             , O(660F00,10,_,_,_,_,_,_  ), O(660F00,11,_,_,_,_,_,_  ), 0 , 16, 5911, 176, 4  , 36),</a>
+<a name="625"><span class="lineNum">     625 </span>            :   INST(Movups          , ExtMov             , O(000F00,10,_,_,_,_,_,_  ), O(000F00,11,_,_,_,_,_,_  ), 0 , 16, 5919, 177, 5  , 36),</a>
+<a name="626"><span class="lineNum">     626 </span>            :   INST(Movzx           , X86MovsxMovzx      , O(000F00,B6,_,_,x,_,_,_  ), 0                         , 0 , 0 , 1872, 174, 0  , 0 ),</a>
+<a name="627"><span class="lineNum">     627 </span>            :   INST(Mpsadbw         , ExtRmi             , O(660F3A,42,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5927, 16 , 12 , 37),</a>
+<a name="628"><span class="lineNum">     628 </span>            :   INST(Mul             , X86M_GPB_MulDiv    , O(000000,F6,4,_,x,_,_,_  ), 0                         , 0 , 0 , 769 , 178, 1  , 0 ),</a>
+<a name="629"><span class="lineNum">     629 </span>            :   INST(Mulpd           , ExtRm              , O(660F00,59,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5936, 5  , 4  , 38),</a>
+<a name="630"><span class="lineNum">     630 </span>            :   INST(Mulps           , ExtRm              , O(000F00,59,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5943, 5  , 5  , 38),</a>
+<a name="631"><span class="lineNum">     631 </span>            :   INST(Mulsd           , ExtRm              , O(F20F00,59,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5950, 6  , 4  , 38),</a>
+<a name="632"><span class="lineNum">     632 </span>            :   INST(Mulss           , ExtRm              , O(F30F00,59,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5957, 7  , 5  , 38),</a>
+<a name="633"><span class="lineNum">     633 </span>            :   INST(Mulx            , VexRvm_ZDX_Wx      , V(F20F38,F6,_,0,x,_,_,_  ), 0                         , 0 , 0 , 1878, 179, 81 , 0 ),</a>
+<a name="634"><span class="lineNum">     634 </span>            :   INST(Mwait           , X86Op              , O(000F01,C9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1883, 180, 75 , 0 ),</a>
+<a name="635"><span class="lineNum">     635 </span>            :   INST(Neg             , X86M_GPB           , O(000000,F6,3,_,x,_,_,_  ), 0                         , 0 , 0 , 1889, 181, 1  , 0 ),</a>
+<a name="636"><span class="lineNum">     636 </span>            :   INST(Nop             , X86Op              , O(000000,90,_,_,_,_,_,_  ), 0                         , 0 , 0 , 900 , 182, 0  , 0 ),</a>
+<a name="637"><span class="lineNum">     637 </span>            :   INST(Not             , X86M_GPB           , O(000000,F6,2,_,x,_,_,_  ), 0                         , 0 , 0 , 1893, 181, 0  , 0 ),</a>
+<a name="638"><span class="lineNum">     638 </span>            :   INST(Or              , X86Arith           , O(000000,08,1,_,x,_,_,_  ), 0                         , 0 , 0 , 1109, 183, 1  , 0 ),</a>
+<a name="639"><span class="lineNum">     639 </span>            :   INST(Orpd            , ExtRm              , O(660F00,56,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9429, 12 , 4  , 39),</a>
+<a name="640"><span class="lineNum">     640 </span>            :   INST(Orps            , ExtRm              , O(000F00,56,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9436, 12 , 5  , 39),</a>
+<a name="641"><span class="lineNum">     641 </span>            :   INST(Out             , X86Out             , O(000000,EE,_,_,_,_,_,_  ), O(000000,E6,_,_,_,_,_,_  ), 0 , 0 , 1897, 184, 45 , 0 ),</a>
+<a name="642"><span class="lineNum">     642 </span>            :   INST(Outs            , X86Outs            , O(000000,6E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1901, 185, 45 , 0 ),</a>
+<a name="643"><span class="lineNum">     643 </span>            :   INST(Pabsb           , ExtRm_P            , O(000F38,1C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5997, 186, 82 , 40),</a>
+<a name="644"><span class="lineNum">     644 </span>            :   INST(Pabsd           , ExtRm_P            , O(000F38,1E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6004, 186, 82 , 40),</a>
+<a name="645"><span class="lineNum">     645 </span>            :   INST(Pabsw           , ExtRm_P            , O(000F38,1D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6018, 186, 82 , 41),</a>
+<a name="646"><span class="lineNum">     646 </span>            :   INST(Packssdw        , ExtRm_P            , O(000F00,6B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6025, 187, 78 , 42),</a>
+<a name="647"><span class="lineNum">     647 </span>            :   INST(Packsswb        , ExtRm_P            , O(000F00,63,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6035, 187, 78 , 42),</a>
+<a name="648"><span class="lineNum">     648 </span>            :   INST(Packusdw        , ExtRm              , O(660F38,2B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6045, 5  , 12 , 42),</a>
+<a name="649"><span class="lineNum">     649 </span>            :   INST(Packuswb        , ExtRm_P            , O(000F00,67,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6055, 187, 78 , 42),</a>
+<a name="650"><span class="lineNum">     650 </span>            :   INST(Paddb           , ExtRm_P            , O(000F00,FC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6065, 187, 78 , 42),</a>
+<a name="651"><span class="lineNum">     651 </span>            :   INST(Paddd           , ExtRm_P            , O(000F00,FE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6072, 187, 78 , 42),</a>
+<a name="652"><span class="lineNum">     652 </span>            :   INST(Paddq           , ExtRm_P            , O(000F00,D4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6079, 187, 4  , 42),</a>
+<a name="653"><span class="lineNum">     653 </span>            :   INST(Paddsb          , ExtRm_P            , O(000F00,EC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6086, 187, 78 , 42),</a>
+<a name="654"><span class="lineNum">     654 </span>            :   INST(Paddsw          , ExtRm_P            , O(000F00,ED,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6094, 187, 78 , 42),</a>
+<a name="655"><span class="lineNum">     655 </span>            :   INST(Paddusb         , ExtRm_P            , O(000F00,DC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6102, 187, 78 , 42),</a>
+<a name="656"><span class="lineNum">     656 </span>            :   INST(Paddusw         , ExtRm_P            , O(000F00,DD,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6111, 187, 78 , 42),</a>
+<a name="657"><span class="lineNum">     657 </span>            :   INST(Paddw           , ExtRm_P            , O(000F00,FD,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6120, 187, 78 , 42),</a>
+<a name="658"><span class="lineNum">     658 </span>            :   INST(Palignr         , ExtRmi_P           , O(000F3A,0F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6127, 188, 6  , 42),</a>
+<a name="659"><span class="lineNum">     659 </span>            :   INST(Pand            , ExtRm_P            , O(000F00,DB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6136, 189, 78 , 42),</a>
+<a name="660"><span class="lineNum">     660 </span>            :   INST(Pandn           , ExtRm_P            , O(000F00,DF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6149, 190, 78 , 43),</a>
+<a name="661"><span class="lineNum">     661 </span>            :   INST(Pause           , X86Op              , O(F30000,90,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1906, 34 , 45 , 0 ),</a>
+<a name="662"><span class="lineNum">     662 </span>            :   INST(Pavgb           , ExtRm_P            , O(000F00,E0,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6179, 187, 83 , 44),</a>
+<a name="663"><span class="lineNum">     663 </span>            :   INST(Pavgusb         , Ext3dNow           , O(000F0F,BF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1912, 191, 84 , 0 ),</a>
+<a name="664"><span class="lineNum">     664 </span>            :   INST(Pavgw           , ExtRm_P            , O(000F00,E3,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6186, 187, 83 , 45),</a>
+<a name="665"><span class="lineNum">     665 </span>            :   INST(Pblendvb        , ExtRm_XMM0         , O(660F38,10,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6202, 17 , 12 , 46),</a>
+<a name="666"><span class="lineNum">     666 </span>            :   INST(Pblendw         , ExtRmi             , O(660F3A,0E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6212, 16 , 12 , 44),</a>
+<a name="667"><span class="lineNum">     667 </span>            :   INST(Pclmulqdq       , ExtRmi             , O(660F3A,44,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6305, 16 , 85 , 47),</a>
+<a name="668"><span class="lineNum">     668 </span>            :   INST(Pcmpeqb         , ExtRm_P            , O(000F00,74,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6337, 190, 78 , 48),</a>
+<a name="669"><span class="lineNum">     669 </span>            :   INST(Pcmpeqd         , ExtRm_P            , O(000F00,76,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6346, 190, 78 , 48),</a>
+<a name="670"><span class="lineNum">     670 </span>            :   INST(Pcmpeqq         , ExtRm              , O(660F38,29,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6355, 192, 12 , 48),</a>
+<a name="671"><span class="lineNum">     671 </span>            :   INST(Pcmpeqw         , ExtRm_P            , O(000F00,75,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6364, 190, 78 , 48),</a>
+<a name="672"><span class="lineNum">     672 </span>            :   INST(Pcmpestri       , ExtRmi             , O(660F3A,61,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6373, 193, 86 , 49),</a>
+<a name="673"><span class="lineNum">     673 </span>            :   INST(Pcmpestrm       , ExtRmi             , O(660F3A,60,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6384, 194, 86 , 49),</a>
+<a name="674"><span class="lineNum">     674 </span>            :   INST(Pcmpgtb         , ExtRm_P            , O(000F00,64,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6395, 190, 78 , 48),</a>
+<a name="675"><span class="lineNum">     675 </span>            :   INST(Pcmpgtd         , ExtRm_P            , O(000F00,66,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6404, 190, 78 , 48),</a>
+<a name="676"><span class="lineNum">     676 </span>            :   INST(Pcmpgtq         , ExtRm              , O(660F38,37,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6413, 192, 42 , 48),</a>
+<a name="677"><span class="lineNum">     677 </span>            :   INST(Pcmpgtw         , ExtRm_P            , O(000F00,65,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6422, 190, 78 , 48),</a>
+<a name="678"><span class="lineNum">     678 </span>            :   INST(Pcmpistri       , ExtRmi             , O(660F3A,63,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6431, 195, 86 , 49),</a>
+<a name="679"><span class="lineNum">     679 </span>            :   INST(Pcmpistrm       , ExtRmi             , O(660F3A,62,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6442, 196, 86 , 49),</a>
+<a name="680"><span class="lineNum">     680 </span>            :   INST(Pcommit         , X86Op_O            , O(660F00,AE,7,_,_,_,_,_  ), 0                         , 0 , 0 , 1920, 34 , 87 , 0 ),</a>
+<a name="681"><span class="lineNum">     681 </span>            :   INST(Pdep            , VexRvm_Wx          , V(F20F38,F5,_,0,x,_,_,_  ), 0                         , 0 , 0 , 1928, 11 , 81 , 0 ),</a>
+<a name="682"><span class="lineNum">     682 </span>            :   INST(Pext            , VexRvm_Wx          , V(F30F38,F5,_,0,x,_,_,_  ), 0                         , 0 , 0 , 1933, 11 , 81 , 0 ),</a>
+<a name="683"><span class="lineNum">     683 </span>            :   INST(Pextrb          , ExtExtract         , O(000F3A,14,_,_,_,_,_,_  ), 0                         , 0 , 8 , 6847, 197, 12 , 50),</a>
+<a name="684"><span class="lineNum">     684 </span>            :   INST(Pextrd          , ExtExtract         , O(000F3A,16,_,_,_,_,_,_  ), 0                         , 0 , 8 , 6855, 67 , 12 , 50),</a>
+<a name="685"><span class="lineNum">     685 </span>            :   INST(Pextrq          , ExtExtract         , O(000F3A,16,_,_,1,_,_,_  ), 0                         , 0 , 8 , 6863, 198, 12 , 50),</a>
+<a name="686"><span class="lineNum">     686 </span>            :   INST(Pextrw          , ExtPextrw          , O(000F00,C5,_,_,_,_,_,_  ), O(000F3A,15,_,_,_,_,_,_  ), 0 , 8 , 6871, 199, 88 , 50),</a>
+<a name="687"><span class="lineNum">     687 </span>            :   INST(Pf2id           , Ext3dNow           , O(000F0F,1D,_,_,_,_,_,_  ), 0                         , 0 , 8 , 1938, 200, 84 , 0 ),</a>
+<a name="688"><span class="lineNum">     688 </span>            :   INST(Pf2iw           , Ext3dNow           , O(000F0F,1C,_,_,_,_,_,_  ), 0                         , 0 , 8 , 1944, 200, 89 , 0 ),</a>
+<a name="689"><span class="lineNum">     689 </span>            :   INST(Pfacc           , Ext3dNow           , O(000F0F,AE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1950, 191, 84 , 0 ),</a>
+<a name="690"><span class="lineNum">     690 </span>            :   INST(Pfadd           , Ext3dNow           , O(000F0F,9E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1956, 191, 84 , 0 ),</a>
+<a name="691"><span class="lineNum">     691 </span>            :   INST(Pfcmpeq         , Ext3dNow           , O(000F0F,B0,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1962, 191, 84 , 0 ),</a>
+<a name="692"><span class="lineNum">     692 </span>            :   INST(Pfcmpge         , Ext3dNow           , O(000F0F,90,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1970, 191, 84 , 0 ),</a>
+<a name="693"><span class="lineNum">     693 </span>            :   INST(Pfcmpgt         , Ext3dNow           , O(000F0F,A0,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1978, 191, 84 , 0 ),</a>
+<a name="694"><span class="lineNum">     694 </span>            :   INST(Pfmax           , Ext3dNow           , O(000F0F,A4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1986, 191, 84 , 0 ),</a>
+<a name="695"><span class="lineNum">     695 </span>            :   INST(Pfmin           , Ext3dNow           , O(000F0F,94,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1992, 191, 84 , 0 ),</a>
+<a name="696"><span class="lineNum">     696 </span>            :   INST(Pfmul           , Ext3dNow           , O(000F0F,B4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 1998, 191, 84 , 0 ),</a>
+<a name="697"><span class="lineNum">     697 </span>            :   INST(Pfnacc          , Ext3dNow           , O(000F0F,8A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2004, 191, 89 , 0 ),</a>
+<a name="698"><span class="lineNum">     698 </span>            :   INST(Pfpnacc         , Ext3dNow           , O(000F0F,8E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2011, 191, 89 , 0 ),</a>
+<a name="699"><span class="lineNum">     699 </span>            :   INST(Pfrcp           , Ext3dNow           , O(000F0F,96,_,_,_,_,_,_  ), 0                         , 0 , 8 , 2019, 200, 84 , 0 ),</a>
+<a name="700"><span class="lineNum">     700 </span>            :   INST(Pfrcpit1        , Ext3dNow           , O(000F0F,A6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2025, 191, 84 , 0 ),</a>
+<a name="701"><span class="lineNum">     701 </span>            :   INST(Pfrcpit2        , Ext3dNow           , O(000F0F,B6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2034, 191, 84 , 0 ),</a>
+<a name="702"><span class="lineNum">     702 </span>            :   INST(Pfrcpv          , Ext3dNow           , O(000F0F,86,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2043, 191, 90 , 0 ),</a>
+<a name="703"><span class="lineNum">     703 </span>            :   INST(Pfrsqit1        , Ext3dNow           , O(000F0F,A7,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2050, 201, 84 , 0 ),</a>
+<a name="704"><span class="lineNum">     704 </span>            :   INST(Pfrsqrt         , Ext3dNow           , O(000F0F,97,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2059, 201, 84 , 0 ),</a>
+<a name="705"><span class="lineNum">     705 </span>            :   INST(Pfrsqrtv        , Ext3dNow           , O(000F0F,87,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2067, 191, 90 , 0 ),</a>
+<a name="706"><span class="lineNum">     706 </span>            :   INST(Pfsub           , Ext3dNow           , O(000F0F,9A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2076, 191, 84 , 0 ),</a>
+<a name="707"><span class="lineNum">     707 </span>            :   INST(Pfsubr          , Ext3dNow           , O(000F0F,AA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2082, 191, 84 , 0 ),</a>
+<a name="708"><span class="lineNum">     708 </span>            :   INST(Phaddd          , ExtRm_P            , O(000F38,02,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6950, 187, 82 , 51),</a>
+<a name="709"><span class="lineNum">     709 </span>            :   INST(Phaddsw         , ExtRm_P            , O(000F38,03,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6967, 187, 82 , 52),</a>
+<a name="710"><span class="lineNum">     710 </span>            :   INST(Phaddw          , ExtRm_P            , O(000F38,01,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7036, 187, 82 , 53),</a>
+<a name="711"><span class="lineNum">     711 </span>            :   INST(Phminposuw      , ExtRm              , O(660F38,41,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7062, 5  , 12 , 54),</a>
+<a name="712"><span class="lineNum">     712 </span>            :   INST(Phsubd          , ExtRm_P            , O(000F38,06,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7083, 187, 82 , 55),</a>
+<a name="713"><span class="lineNum">     713 </span>            :   INST(Phsubsw         , ExtRm_P            , O(000F38,07,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7100, 187, 82 , 56),</a>
+<a name="714"><span class="lineNum">     714 </span>            :   INST(Phsubw          , ExtRm_P            , O(000F38,05,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7109, 187, 82 , 56),</a>
+<a name="715"><span class="lineNum">     715 </span>            :   INST(Pi2fd           , Ext3dNow           , O(000F0F,0D,_,_,_,_,_,_  ), 0                         , 0 , 8 , 2089, 200, 84 , 0 ),</a>
+<a name="716"><span class="lineNum">     716 </span>            :   INST(Pi2fw           , Ext3dNow           , O(000F0F,0C,_,_,_,_,_,_  ), 0                         , 0 , 8 , 2095, 200, 89 , 0 ),</a>
+<a name="717"><span class="lineNum">     717 </span>            :   INST(Pinsrb          , ExtRmi             , O(660F3A,20,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7126, 202, 12 , 57),</a>
+<a name="718"><span class="lineNum">     718 </span>            :   INST(Pinsrd          , ExtRmi             , O(660F3A,22,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7134, 203, 12 , 57),</a>
+<a name="719"><span class="lineNum">     719 </span>            :   INST(Pinsrq          , ExtRmi             , O(660F3A,22,_,_,1,_,_,_  ), 0                         , 0 , 0 , 7142, 204, 12 , 57),</a>
+<a name="720"><span class="lineNum">     720 </span>            :   INST(Pinsrw          , ExtRmi_P           , O(000F00,C4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7150, 205, 83 , 55),</a>
+<a name="721"><span class="lineNum">     721 </span>            :   INST(Pmaddubsw       , ExtRm_P            , O(000F38,04,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7320, 187, 82 , 58),</a>
+<a name="722"><span class="lineNum">     722 </span>            :   INST(Pmaddwd         , ExtRm_P            , O(000F00,F5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7331, 187, 78 , 58),</a>
+<a name="723"><span class="lineNum">     723 </span>            :   INST(Pmaxsb          , ExtRm              , O(660F38,3C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7362, 12 , 12 , 59),</a>
+<a name="724"><span class="lineNum">     724 </span>            :   INST(Pmaxsd          , ExtRm              , O(660F38,3D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7370, 12 , 12 , 59),</a>
+<a name="725"><span class="lineNum">     725 </span>            :   INST(Pmaxsw          , ExtRm_P            , O(000F00,EE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7386, 189, 83 , 60),</a>
+<a name="726"><span class="lineNum">     726 </span>            :   INST(Pmaxub          , ExtRm_P            , O(000F00,DE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7394, 189, 83 , 60),</a>
+<a name="727"><span class="lineNum">     727 </span>            :   INST(Pmaxud          , ExtRm              , O(660F38,3F,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7402, 12 , 12 , 60),</a>
+<a name="728"><span class="lineNum">     728 </span>            :   INST(Pmaxuw          , ExtRm              , O(660F38,3E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7418, 12 , 12 , 61),</a>
+<a name="729"><span class="lineNum">     729 </span>            :   INST(Pminsb          , ExtRm              , O(660F38,38,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7426, 12 , 12 , 61),</a>
+<a name="730"><span class="lineNum">     730 </span>            :   INST(Pminsd          , ExtRm              , O(660F38,39,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7434, 12 , 12 , 61),</a>
+<a name="731"><span class="lineNum">     731 </span>            :   INST(Pminsw          , ExtRm_P            , O(000F00,EA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7450, 189, 83 , 62),</a>
+<a name="732"><span class="lineNum">     732 </span>            :   INST(Pminub          , ExtRm_P            , O(000F00,DA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7458, 189, 83 , 62),</a>
+<a name="733"><span class="lineNum">     733 </span>            :   INST(Pminud          , ExtRm              , O(660F38,3B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7466, 12 , 12 , 62),</a>
+<a name="734"><span class="lineNum">     734 </span>            :   INST(Pminuw          , ExtRm              , O(660F38,3A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7482, 12 , 12 , 63),</a>
+<a name="735"><span class="lineNum">     735 </span>            :   INST(Pmovmskb        , ExtRm_P            , O(000F00,D7,_,_,_,_,_,_  ), 0                         , 0 , 8 , 7560, 206, 83 , 64),</a>
+<a name="736"><span class="lineNum">     736 </span>            :   INST(Pmovsxbd        , ExtRm              , O(660F38,21,_,_,_,_,_,_  ), 0                         , 0 , 16, 7657, 207, 12 , 14),</a>
+<a name="737"><span class="lineNum">     737 </span>            :   INST(Pmovsxbq        , ExtRm              , O(660F38,22,_,_,_,_,_,_  ), 0                         , 0 , 16, 7667, 208, 12 , 14),</a>
+<a name="738"><span class="lineNum">     738 </span>            :   INST(Pmovsxbw        , ExtRm              , O(660F38,20,_,_,_,_,_,_  ), 0                         , 0 , 16, 7677, 49 , 12 , 14),</a>
+<a name="739"><span class="lineNum">     739 </span>            :   INST(Pmovsxdq        , ExtRm              , O(660F38,25,_,_,_,_,_,_  ), 0                         , 0 , 16, 7687, 49 , 12 , 14),</a>
+<a name="740"><span class="lineNum">     740 </span>            :   INST(Pmovsxwd        , ExtRm              , O(660F38,23,_,_,_,_,_,_  ), 0                         , 0 , 16, 7697, 49 , 12 , 14),</a>
+<a name="741"><span class="lineNum">     741 </span>            :   INST(Pmovsxwq        , ExtRm              , O(660F38,24,_,_,_,_,_,_  ), 0                         , 0 , 16, 7707, 207, 12 , 14),</a>
+<a name="742"><span class="lineNum">     742 </span>            :   INST(Pmovzxbd        , ExtRm              , O(660F38,31,_,_,_,_,_,_  ), 0                         , 0 , 16, 7794, 207, 12 , 65),</a>
+<a name="743"><span class="lineNum">     743 </span>            :   INST(Pmovzxbq        , ExtRm              , O(660F38,32,_,_,_,_,_,_  ), 0                         , 0 , 16, 7804, 208, 12 , 65),</a>
+<a name="744"><span class="lineNum">     744 </span>            :   INST(Pmovzxbw        , ExtRm              , O(660F38,30,_,_,_,_,_,_  ), 0                         , 0 , 16, 7814, 49 , 12 , 65),</a>
+<a name="745"><span class="lineNum">     745 </span>            :   INST(Pmovzxdq        , ExtRm              , O(660F38,35,_,_,_,_,_,_  ), 0                         , 0 , 16, 7824, 49 , 12 , 65),</a>
+<a name="746"><span class="lineNum">     746 </span>            :   INST(Pmovzxwd        , ExtRm              , O(660F38,33,_,_,_,_,_,_  ), 0                         , 0 , 16, 7834, 49 , 12 , 65),</a>
+<a name="747"><span class="lineNum">     747 </span>            :   INST(Pmovzxwq        , ExtRm              , O(660F38,34,_,_,_,_,_,_  ), 0                         , 0 , 16, 7844, 207, 12 , 65),</a>
+<a name="748"><span class="lineNum">     748 </span>            :   INST(Pmuldq          , ExtRm              , O(660F38,28,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7854, 5  , 12 , 19),</a>
+<a name="749"><span class="lineNum">     749 </span>            :   INST(Pmulhrsw        , ExtRm_P            , O(000F38,0B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7862, 187, 82 , 19),</a>
+<a name="750"><span class="lineNum">     750 </span>            :   INST(Pmulhrw         , Ext3dNow           , O(000F0F,B7,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2101, 191, 84 , 0 ),</a>
+<a name="751"><span class="lineNum">     751 </span>            :   INST(Pmulhuw         , ExtRm_P            , O(000F00,E4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7872, 187, 83 , 66),</a>
+<a name="752"><span class="lineNum">     752 </span>            :   INST(Pmulhw          , ExtRm_P            , O(000F00,E5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7881, 187, 78 , 66),</a>
+<a name="753"><span class="lineNum">     753 </span>            :   INST(Pmulld          , ExtRm              , O(660F38,40,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7889, 5  , 12 , 66),</a>
+<a name="754"><span class="lineNum">     754 </span>            :   INST(Pmullw          , ExtRm_P            , O(000F00,D5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7905, 187, 78 , 19),</a>
+<a name="755"><span class="lineNum">     755 </span>            :   INST(Pmuludq         , ExtRm_P            , O(000F00,F4,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7928, 187, 4  , 67),</a>
+<a name="756"><span class="lineNum">     756 </span>            :   INST(Pop             , X86Pop             , O(000000,8F,0,_,_,_,_,_  ), O(000000,58,_,_,_,_,_,_  ), 0 , 0 , 2109, 209, 45 , 0 ),</a>
+<a name="757"><span class="lineNum">     757 </span>            :   INST(Popa            , X86Op              , O(660000,61,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2113, 99 , 45 , 0 ),</a>
+<a name="758"><span class="lineNum">     758 </span>            :   INST(Popad           , X86Op              , O(000000,61,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2118, 99 , 45 , 0 ),</a>
+<a name="759"><span class="lineNum">     759 </span>            :   INST(Popcnt          , X86Rm_Raw66H       , O(F30F00,B8,_,_,x,_,_,_  ), 0                         , 0 , 0 , 2124, 143, 91 , 0 ),</a>
+<a name="760"><span class="lineNum">     760 </span>            :   INST(Popf            , X86Op              , O(660000,9D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2131, 34 , 16 , 0 ),</a>
+<a name="761"><span class="lineNum">     761 </span>            :   INST(Popfd           , X86Op              , O(000000,9D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2136, 99 , 16 , 0 ),</a>
+<a name="762"><span class="lineNum">     762 </span>            :   INST(Popfq           , X86Op              , O(000000,9D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2142, 101, 16 , 0 ),</a>
+<a name="763"><span class="lineNum">     763 </span>            :   INST(Por             , ExtRm_P            , O(000F00,EB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 7955, 189, 78 , 68),</a>
+<a name="764"><span class="lineNum">     764 </span>            :   INST(Prefetch        , X86M_Only          , O(000F00,0D,0,_,_,_,_,_  ), 0                         , 0 , 0 , 2148, 35 , 92 , 0 ),</a>
+<a name="765"><span class="lineNum">     765 </span>            :   INST(Prefetchnta     , X86M_Only          , O(000F00,18,0,_,_,_,_,_  ), 0                         , 0 , 0 , 2157, 35 , 93 , 0 ),</a>
+<a name="766"><span class="lineNum">     766 </span>            :   INST(Prefetcht0      , X86M_Only          , O(000F00,18,1,_,_,_,_,_  ), 0                         , 0 , 0 , 2169, 35 , 93 , 0 ),</a>
+<a name="767"><span class="lineNum">     767 </span>            :   INST(Prefetcht1      , X86M_Only          , O(000F00,18,2,_,_,_,_,_  ), 0                         , 0 , 0 , 2180, 35 , 93 , 0 ),</a>
+<a name="768"><span class="lineNum">     768 </span>            :   INST(Prefetcht2      , X86M_Only          , O(000F00,18,3,_,_,_,_,_  ), 0                         , 0 , 0 , 2191, 35 , 93 , 0 ),</a>
+<a name="769"><span class="lineNum">     769 </span>            :   INST(Prefetchw       , X86M_Only          , O(000F00,0D,1,_,_,_,_,_  ), 0                         , 0 , 0 , 2202, 35 , 94 , 0 ),</a>
+<a name="770"><span class="lineNum">     770 </span>            :   INST(Prefetchwt1     , X86M_Only          , O(000F00,0D,2,_,_,_,_,_  ), 0                         , 0 , 0 , 2212, 35 , 95 , 0 ),</a>
+<a name="771"><span class="lineNum">     771 </span>            :   INST(Psadbw          , ExtRm_P            , O(000F00,F6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 3795, 187, 83 , 69),</a>
+<a name="772"><span class="lineNum">     772 </span>            :   INST(Pshufb          , ExtRm_P            , O(000F38,00,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8179, 187, 82 , 70),</a>
+<a name="773"><span class="lineNum">     773 </span>            :   INST(Pshufd          , ExtRmi             , O(660F00,70,_,_,_,_,_,_  ), 0                         , 0 , 16, 8187, 210, 4  , 71),</a>
+<a name="774"><span class="lineNum">     774 </span>            :   INST(Pshufhw         , ExtRmi             , O(F30F00,70,_,_,_,_,_,_  ), 0                         , 0 , 16, 8195, 210, 4  , 71),</a>
+<a name="775"><span class="lineNum">     775 </span>            :   INST(Pshuflw         , ExtRmi             , O(F20F00,70,_,_,_,_,_,_  ), 0                         , 0 , 16, 8204, 210, 4  , 71),</a>
+<a name="776"><span class="lineNum">     776 </span>            :   INST(Pshufw          , ExtRmi_P           , O(000F00,70,_,_,_,_,_,_  ), 0                         , 0 , 8 , 2224, 211, 74 , 0 ),</a>
+<a name="777"><span class="lineNum">     777 </span>            :   INST(Psignb          , ExtRm_P            , O(000F38,08,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8213, 187, 82 , 72),</a>
+<a name="778"><span class="lineNum">     778 </span>            :   INST(Psignd          , ExtRm_P            , O(000F38,0A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8221, 187, 82 , 72),</a>
+<a name="779"><span class="lineNum">     779 </span>            :   INST(Psignw          , ExtRm_P            , O(000F38,09,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8229, 187, 82 , 72),</a>
+<a name="780"><span class="lineNum">     780 </span>            :   INST(Pslld           , ExtRmRi_P          , O(000F00,F2,_,_,_,_,_,_  ), O(000F00,72,6,_,_,_,_,_  ), 0 , 0 , 8237, 212, 78 , 72),</a>
+<a name="781"><span class="lineNum">     781 </span>            :   INST(Pslldq          , ExtRmRi            , 0                         , O(660F00,73,7,_,_,_,_,_  ), 0 , 0 , 8244, 213, 4  , 72),</a>
+<a name="782"><span class="lineNum">     782 </span>            :   INST(Psllq           , ExtRmRi_P          , O(000F00,F3,_,_,_,_,_,_  ), O(000F00,73,6,_,_,_,_,_  ), 0 , 0 , 8252, 214, 78 , 72),</a>
+<a name="783"><span class="lineNum">     783 </span>            :   INST(Psllw           , ExtRmRi_P          , O(000F00,F1,_,_,_,_,_,_  ), O(000F00,71,6,_,_,_,_,_  ), 0 , 0 , 8283, 215, 78 , 73),</a>
+<a name="784"><span class="lineNum">     784 </span>            :   INST(Psrad           , ExtRmRi_P          , O(000F00,E2,_,_,_,_,_,_  ), O(000F00,72,4,_,_,_,_,_  ), 0 , 0 , 8290, 216, 78 , 73),</a>
+<a name="785"><span class="lineNum">     785 </span>            :   INST(Psraw           , ExtRmRi_P          , O(000F00,E1,_,_,_,_,_,_  ), O(000F00,71,4,_,_,_,_,_  ), 0 , 0 , 8328, 217, 78 , 74),</a>
+<a name="786"><span class="lineNum">     786 </span>            :   INST(Psrld           , ExtRmRi_P          , O(000F00,D2,_,_,_,_,_,_  ), O(000F00,72,2,_,_,_,_,_  ), 0 , 0 , 8335, 218, 78 , 74),</a>
+<a name="787"><span class="lineNum">     787 </span>            :   INST(Psrldq          , ExtRmRi            , 0                         , O(660F00,73,3,_,_,_,_,_  ), 0 , 0 , 8342, 219, 4  , 74),</a>
+<a name="788"><span class="lineNum">     788 </span>            :   INST(Psrlq           , ExtRmRi_P          , O(000F00,D3,_,_,_,_,_,_  ), O(000F00,73,2,_,_,_,_,_  ), 0 , 0 , 8350, 220, 78 , 74),</a>
+<a name="789"><span class="lineNum">     789 </span>            :   INST(Psrlw           , ExtRmRi_P          , O(000F00,D1,_,_,_,_,_,_  ), O(000F00,71,2,_,_,_,_,_  ), 0 , 0 , 8381, 221, 78 , 75),</a>
+<a name="790"><span class="lineNum">     790 </span>            :   INST(Psubb           , ExtRm_P            , O(000F00,F8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8388, 190, 78 , 75),</a>
+<a name="791"><span class="lineNum">     791 </span>            :   INST(Psubd           , ExtRm_P            , O(000F00,FA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8395, 190, 78 , 75),</a>
+<a name="792"><span class="lineNum">     792 </span>            :   INST(Psubq           , ExtRm_P            , O(000F00,FB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8402, 190, 4  , 75),</a>
+<a name="793"><span class="lineNum">     793 </span>            :   INST(Psubsb          , ExtRm_P            , O(000F00,E8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8409, 190, 78 , 75),</a>
+<a name="794"><span class="lineNum">     794 </span>            :   INST(Psubsw          , ExtRm_P            , O(000F00,E9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8417, 190, 78 , 75),</a>
+<a name="795"><span class="lineNum">     795 </span>            :   INST(Psubusb         , ExtRm_P            , O(000F00,D8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8425, 190, 78 , 75),</a>
+<a name="796"><span class="lineNum">     796 </span>            :   INST(Psubusw         , ExtRm_P            , O(000F00,D9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8434, 190, 78 , 75),</a>
+<a name="797"><span class="lineNum">     797 </span>            :   INST(Psubw           , ExtRm_P            , O(000F00,F9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8443, 190, 78 , 75),</a>
+<a name="798"><span class="lineNum">     798 </span>            :   INST(Pswapd          , Ext3dNow           , O(000F0F,BB,_,_,_,_,_,_  ), 0                         , 0 , 8 , 2231, 200, 89 , 0 ),</a>
+<a name="799"><span class="lineNum">     799 </span>            :   INST(Ptest           , ExtRm              , O(660F38,17,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8472, 222, 96 , 76),</a>
+<a name="800"><span class="lineNum">     800 </span>            :   INST(Punpckhbw       , ExtRm_P            , O(000F00,68,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8555, 187, 78 , 77),</a>
+<a name="801"><span class="lineNum">     801 </span>            :   INST(Punpckhdq       , ExtRm_P            , O(000F00,6A,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8566, 187, 78 , 77),</a>
+<a name="802"><span class="lineNum">     802 </span>            :   INST(Punpckhqdq      , ExtRm              , O(660F00,6D,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8577, 5  , 4  , 77),</a>
+<a name="803"><span class="lineNum">     803 </span>            :   INST(Punpckhwd       , ExtRm_P            , O(000F00,69,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8589, 187, 78 , 77),</a>
+<a name="804"><span class="lineNum">     804 </span>            :   INST(Punpcklbw       , ExtRm_P            , O(000F00,60,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8600, 187, 78 , 77),</a>
+<a name="805"><span class="lineNum">     805 </span>            :   INST(Punpckldq       , ExtRm_P            , O(000F00,62,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8611, 187, 78 , 77),</a>
+<a name="806"><span class="lineNum">     806 </span>            :   INST(Punpcklqdq      , ExtRm              , O(660F00,6C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8622, 5  , 4  , 77),</a>
+<a name="807"><span class="lineNum">     807 </span>            :   INST(Punpcklwd       , ExtRm_P            , O(000F00,61,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8634, 187, 78 , 77),</a>
+<a name="808"><span class="lineNum">     808 </span>            :   INST(Push            , X86Push            , O(000000,FF,6,_,_,_,_,_  ), O(000000,50,_,_,_,_,_,_  ), 0 , 0 , 2238, 223, 45 , 0 ),</a>
+<a name="809"><span class="lineNum">     809 </span>            :   INST(Pusha           , X86Op              , O(660000,60,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2243, 99 , 45 , 0 ),</a>
+<a name="810"><span class="lineNum">     810 </span>            :   INST(Pushad          , X86Op              , O(000000,60,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2249, 99 , 45 , 0 ),</a>
+<a name="811"><span class="lineNum">     811 </span>            :   INST(Pushf           , X86Op              , O(660000,9C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2256, 34 , 45 , 0 ),</a>
+<a name="812"><span class="lineNum">     812 </span>            :   INST(Pushfd          , X86Op              , O(000000,9C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2262, 99 , 45 , 0 ),</a>
+<a name="813"><span class="lineNum">     813 </span>            :   INST(Pushfq          , X86Op              , O(000000,9C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2269, 101, 45 , 0 ),</a>
+<a name="814"><span class="lineNum">     814 </span>            :   INST(Pxor            , ExtRm_P            , O(000F00,EF,_,_,_,_,_,_  ), 0                         , 0 , 0 , 8645, 190, 78 , 78),</a>
+<a name="815"><span class="lineNum">     815 </span>            :   INST(Rcl             , X86Rot             , O(000000,D0,2,_,x,_,_,_  ), 0                         , 0 , 0 , 2276, 224, 97 , 0 ),</a>
+<a name="816"><span class="lineNum">     816 </span>            :   INST(Rcpps           , ExtRm              , O(000F00,53,_,_,_,_,_,_  ), 0                         , 0 , 16, 8773, 50 , 5  , 79),</a>
+<a name="817"><span class="lineNum">     817 </span>            :   INST(Rcpss           , ExtRm              , O(F30F00,53,_,_,_,_,_,_  ), 0                         , 0 , 4 , 8780, 225, 5  , 80),</a>
+<a name="818"><span class="lineNum">     818 </span>            :   INST(Rcr             , X86Rot             , O(000000,D0,3,_,x,_,_,_  ), 0                         , 0 , 0 , 2280, 224, 97 , 0 ),</a>
+<a name="819"><span class="lineNum">     819 </span>            :   INST(Rdfsbase        , X86M               , O(F30F00,AE,0,_,x,_,_,_  ), 0                         , 0 , 8 , 2284, 226, 98 , 0 ),</a>
+<a name="820"><span class="lineNum">     820 </span>            :   INST(Rdgsbase        , X86M               , O(F30F00,AE,1,_,x,_,_,_  ), 0                         , 0 , 8 , 2293, 226, 98 , 0 ),</a>
+<a name="821"><span class="lineNum">     821 </span>            :   INST(Rdmsr           , X86Op              , O(000F00,32,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2302, 227, 99 , 0 ),</a>
+<a name="822"><span class="lineNum">     822 </span>            :   INST(Rdpmc           , X86Op              , O(000F00,33,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2308, 227, 23 , 0 ),</a>
+<a name="823"><span class="lineNum">     823 </span>            :   INST(Rdrand          , X86M               , O(000F00,C7,6,_,x,_,_,_  ), 0                         , 0 , 8 , 2314, 228, 100, 0 ),</a>
+<a name="824"><span class="lineNum">     824 </span>            :   INST(Rdseed          , X86M               , O(000F00,C7,7,_,x,_,_,_  ), 0                         , 0 , 8 , 2321, 228, 101, 0 ),</a>
+<a name="825"><span class="lineNum">     825 </span>            :   INST(Rdtsc           , X86Op              , O(000F00,31,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2328, 229, 102, 0 ),</a>
+<a name="826"><span class="lineNum">     826 </span>            :   INST(Rdtscp          , X86Op              , O(000F01,F9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2334, 230, 103, 0 ),</a>
+<a name="827"><span class="lineNum">     827 </span>            :   INST(Ret             , X86Ret             , O(000000,C2,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2748, 231, 45 , 0 ),</a>
+<a name="828"><span class="lineNum">     828 </span>            :   INST(Rol             , X86Rot             , O(000000,D0,0,_,x,_,_,_  ), 0                         , 0 , 0 , 2341, 224, 97 , 0 ),</a>
+<a name="829"><span class="lineNum">     829 </span>            :   INST(Ror             , X86Rot             , O(000000,D0,1,_,x,_,_,_  ), 0                         , 0 , 0 , 2345, 224, 97 , 0 ),</a>
+<a name="830"><span class="lineNum">     830 </span>            :   INST(Rorx            , VexRmi_Wx          , V(F20F3A,F0,_,0,x,_,_,_  ), 0                         , 0 , 0 , 2349, 232, 81 , 0 ),</a>
+<a name="831"><span class="lineNum">     831 </span>            :   INST(Roundpd         , ExtRmi             , O(660F3A,09,_,_,_,_,_,_  ), 0                         , 0 , 16, 8875, 210, 12 , 81),</a>
+<a name="832"><span class="lineNum">     832 </span>            :   INST(Roundps         , ExtRmi             , O(660F3A,08,_,_,_,_,_,_  ), 0                         , 0 , 16, 8884, 210, 12 , 81),</a>
+<a name="833"><span class="lineNum">     833 </span>            :   INST(Roundsd         , ExtRmi             , O(660F3A,0B,_,_,_,_,_,_  ), 0                         , 0 , 8 , 8893, 233, 12 , 82),</a>
+<a name="834"><span class="lineNum">     834 </span>            :   INST(Roundss         , ExtRmi             , O(660F3A,0A,_,_,_,_,_,_  ), 0                         , 0 , 4 , 8902, 234, 12 , 82),</a>
+<a name="835"><span class="lineNum">     835 </span>            :   INST(Rsm             , X86Op              , O(000F00,AA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2354, 99 , 16 , 0 ),</a>
+<a name="836"><span class="lineNum">     836 </span>            :   INST(Rsqrtps         , ExtRm              , O(000F00,52,_,_,_,_,_,_  ), 0                         , 0 , 16, 8999, 50 , 5  , 3 ),</a>
+<a name="837"><span class="lineNum">     837 </span>            :   INST(Rsqrtss         , ExtRm              , O(F30F00,52,_,_,_,_,_,_  ), 0                         , 0 , 4 , 9008, 225, 5  , 2 ),</a>
+<a name="838"><span class="lineNum">     838 </span>            :   INST(Sahf            , X86Op              , O(000000,9E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2358, 235, 104, 0 ),</a>
+<a name="839"><span class="lineNum">     839 </span>            :   INST(Sal             , X86Rot             , O(000000,D0,4,_,x,_,_,_  ), 0                         , 0 , 0 , 2363, 224, 1  , 0 ),</a>
+<a name="840"><span class="lineNum">     840 </span>            :   INST(Sar             , X86Rot             , O(000000,D0,7,_,x,_,_,_  ), 0                         , 0 , 0 , 2367, 224, 1  , 0 ),</a>
+<a name="841"><span class="lineNum">     841 </span>            :   INST(Sarx            , VexRmv_Wx          , V(F30F38,F7,_,0,x,_,_,_  ), 0                         , 0 , 0 , 2371, 14 , 81 , 0 ),</a>
+<a name="842"><span class="lineNum">     842 </span>            :   INST(Sbb             , X86Arith           , O(000000,18,3,_,x,_,_,_  ), 0                         , 0 , 0 , 2376, 3  , 2  , 0 ),</a>
+<a name="843"><span class="lineNum">     843 </span>            :   INST(Scas            , X86StrRm           , O(000000,AE,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2380, 236, 35 , 0 ),</a>
+<a name="844"><span class="lineNum">     844 </span>            :   INST(Seta            , X86Set             , O(000F00,97,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2385, 237, 105, 0 ),</a>
+<a name="845"><span class="lineNum">     845 </span>            :   INST(Setae           , X86Set             , O(000F00,93,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2390, 237, 106, 0 ),</a>
+<a name="846"><span class="lineNum">     846 </span>            :   INST(Setb            , X86Set             , O(000F00,92,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2396, 237, 106, 0 ),</a>
+<a name="847"><span class="lineNum">     847 </span>            :   INST(Setbe           , X86Set             , O(000F00,96,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2401, 237, 105, 0 ),</a>
+<a name="848"><span class="lineNum">     848 </span>            :   INST(Setc            , X86Set             , O(000F00,92,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2407, 237, 106, 0 ),</a>
+<a name="849"><span class="lineNum">     849 </span>            :   INST(Sete            , X86Set             , O(000F00,94,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2412, 237, 107, 0 ),</a>
+<a name="850"><span class="lineNum">     850 </span>            :   INST(Setg            , X86Set             , O(000F00,9F,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2417, 237, 108, 0 ),</a>
+<a name="851"><span class="lineNum">     851 </span>            :   INST(Setge           , X86Set             , O(000F00,9D,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2422, 237, 109, 0 ),</a>
+<a name="852"><span class="lineNum">     852 </span>            :   INST(Setl            , X86Set             , O(000F00,9C,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2428, 237, 109, 0 ),</a>
+<a name="853"><span class="lineNum">     853 </span>            :   INST(Setle           , X86Set             , O(000F00,9E,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2433, 237, 108, 0 ),</a>
+<a name="854"><span class="lineNum">     854 </span>            :   INST(Setna           , X86Set             , O(000F00,96,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2439, 237, 105, 0 ),</a>
+<a name="855"><span class="lineNum">     855 </span>            :   INST(Setnae          , X86Set             , O(000F00,92,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2445, 237, 106, 0 ),</a>
+<a name="856"><span class="lineNum">     856 </span>            :   INST(Setnb           , X86Set             , O(000F00,93,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2452, 237, 106, 0 ),</a>
+<a name="857"><span class="lineNum">     857 </span>            :   INST(Setnbe          , X86Set             , O(000F00,97,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2458, 237, 105, 0 ),</a>
+<a name="858"><span class="lineNum">     858 </span>            :   INST(Setnc           , X86Set             , O(000F00,93,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2465, 237, 106, 0 ),</a>
+<a name="859"><span class="lineNum">     859 </span>            :   INST(Setne           , X86Set             , O(000F00,95,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2471, 237, 107, 0 ),</a>
+<a name="860"><span class="lineNum">     860 </span>            :   INST(Setng           , X86Set             , O(000F00,9E,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2477, 237, 108, 0 ),</a>
+<a name="861"><span class="lineNum">     861 </span>            :   INST(Setnge          , X86Set             , O(000F00,9C,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2483, 237, 109, 0 ),</a>
+<a name="862"><span class="lineNum">     862 </span>            :   INST(Setnl           , X86Set             , O(000F00,9D,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2490, 237, 109, 0 ),</a>
+<a name="863"><span class="lineNum">     863 </span>            :   INST(Setnle          , X86Set             , O(000F00,9F,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2496, 237, 108, 0 ),</a>
+<a name="864"><span class="lineNum">     864 </span>            :   INST(Setno           , X86Set             , O(000F00,91,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2503, 237, 110, 0 ),</a>
+<a name="865"><span class="lineNum">     865 </span>            :   INST(Setnp           , X86Set             , O(000F00,9B,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2509, 237, 111, 0 ),</a>
+<a name="866"><span class="lineNum">     866 </span>            :   INST(Setns           , X86Set             , O(000F00,99,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2515, 237, 112, 0 ),</a>
+<a name="867"><span class="lineNum">     867 </span>            :   INST(Setnz           , X86Set             , O(000F00,95,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2521, 237, 107, 0 ),</a>
+<a name="868"><span class="lineNum">     868 </span>            :   INST(Seto            , X86Set             , O(000F00,90,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2527, 237, 110, 0 ),</a>
+<a name="869"><span class="lineNum">     869 </span>            :   INST(Setp            , X86Set             , O(000F00,9A,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2532, 237, 111, 0 ),</a>
+<a name="870"><span class="lineNum">     870 </span>            :   INST(Setpe           , X86Set             , O(000F00,9A,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2537, 237, 111, 0 ),</a>
+<a name="871"><span class="lineNum">     871 </span>            :   INST(Setpo           , X86Set             , O(000F00,9B,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2543, 237, 111, 0 ),</a>
+<a name="872"><span class="lineNum">     872 </span>            :   INST(Sets            , X86Set             , O(000F00,98,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2549, 237, 112, 0 ),</a>
+<a name="873"><span class="lineNum">     873 </span>            :   INST(Setz            , X86Set             , O(000F00,94,_,_,_,_,_,_  ), 0                         , 0 , 1 , 2554, 237, 107, 0 ),</a>
+<a name="874"><span class="lineNum">     874 </span>            :   INST(Sfence          , X86Fence           , O(000F00,AE,7,_,_,_,_,_  ), 0                         , 0 , 0 , 2559, 34 , 113, 0 ),</a>
+<a name="875"><span class="lineNum">     875 </span>            :   INST(Sgdt            , X86M_Only          , O(000F00,01,0,_,_,_,_,_  ), 0                         , 0 , 0 , 2566, 84 , 45 , 0 ),</a>
+<a name="876"><span class="lineNum">     876 </span>            :   INST(Sha1msg1        , ExtRm              , O(000F38,C9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2571, 5  , 114, 0 ),</a>
+<a name="877"><span class="lineNum">     877 </span>            :   INST(Sha1msg2        , ExtRm              , O(000F38,CA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2580, 5  , 114, 0 ),</a>
+<a name="878"><span class="lineNum">     878 </span>            :   INST(Sha1nexte       , ExtRm              , O(000F38,C8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2589, 5  , 114, 0 ),</a>
+<a name="879"><span class="lineNum">     879 </span>            :   INST(Sha1rnds4       , ExtRmi             , O(000F3A,CC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2599, 16 , 114, 0 ),</a>
+<a name="880"><span class="lineNum">     880 </span>            :   INST(Sha256msg1      , ExtRm              , O(000F38,CC,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2609, 5  , 114, 0 ),</a>
+<a name="881"><span class="lineNum">     881 </span>            :   INST(Sha256msg2      , ExtRm              , O(000F38,CD,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2620, 5  , 114, 0 ),</a>
+<a name="882"><span class="lineNum">     882 </span>            :   INST(Sha256rnds2     , ExtRm_XMM0         , O(000F38,CB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2631, 17 , 114, 0 ),</a>
+<a name="883"><span class="lineNum">     883 </span>            :   INST(Shl             , X86Rot             , O(000000,D0,4,_,x,_,_,_  ), 0                         , 0 , 0 , 2643, 224, 1  , 0 ),</a>
+<a name="884"><span class="lineNum">     884 </span>            :   INST(Shld            , X86ShldShrd        , O(000F00,A4,_,_,x,_,_,_  ), 0                         , 0 , 0 , 8159, 238, 1  , 0 ),</a>
+<a name="885"><span class="lineNum">     885 </span>            :   INST(Shlx            , VexRmv_Wx          , V(660F38,F7,_,0,x,_,_,_  ), 0                         , 0 , 0 , 2647, 14 , 81 , 0 ),</a>
+<a name="886"><span class="lineNum">     886 </span>            :   INST(Shr             , X86Rot             , O(000000,D0,5,_,x,_,_,_  ), 0                         , 0 , 0 , 2652, 224, 1  , 0 ),</a>
+<a name="887"><span class="lineNum">     887 </span>            :   INST(Shrd            , X86ShldShrd        , O(000F00,AC,_,_,x,_,_,_  ), 0                         , 0 , 0 , 2656, 238, 1  , 0 ),</a>
+<a name="888"><span class="lineNum">     888 </span>            :   INST(Shrx            , VexRmv_Wx          , V(F20F38,F7,_,0,x,_,_,_  ), 0                         , 0 , 0 , 2661, 14 , 81 , 0 ),</a>
+<a name="889"><span class="lineNum">     889 </span>            :   INST(Shufpd          , ExtRmi             , O(660F00,C6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9269, 16 , 4  , 83),</a>
+<a name="890"><span class="lineNum">     890 </span>            :   INST(Shufps          , ExtRmi             , O(000F00,C6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9277, 16 , 5  , 83),</a>
+<a name="891"><span class="lineNum">     891 </span>            :   INST(Sidt            , X86M_Only          , O(000F00,01,1,_,_,_,_,_  ), 0                         , 0 , 0 , 2666, 84 , 45 , 0 ),</a>
+<a name="892"><span class="lineNum">     892 </span>            :   INST(Sldt            , X86M               , O(000F00,00,0,_,_,_,_,_  ), 0                         , 0 , 0 , 2671, 239, 45 , 0 ),</a>
+<a name="893"><span class="lineNum">     893 </span>            :   INST(Smsw            , X86M               , O(000F00,01,4,_,_,_,_,_  ), 0                         , 0 , 0 , 2676, 239, 45 , 0 ),</a>
+<a name="894"><span class="lineNum">     894 </span>            :   INST(Sqrtpd          , ExtRm              , O(660F00,51,_,_,_,_,_,_  ), 0                         , 0 , 16, 9285, 50 , 4  , 84),</a>
+<a name="895"><span class="lineNum">     895 </span>            :   INST(Sqrtps          , ExtRm              , O(000F00,51,_,_,_,_,_,_  ), 0                         , 0 , 16, 9000, 50 , 5  , 84),</a>
+<a name="896"><span class="lineNum">     896 </span>            :   INST(Sqrtsd          , ExtRm              , O(F20F00,51,_,_,_,_,_,_  ), 0                         , 0 , 8 , 9301, 240, 4  , 85),</a>
+<a name="897"><span class="lineNum">     897 </span>            :   INST(Sqrtss          , ExtRm              , O(F30F00,51,_,_,_,_,_,_  ), 0                         , 0 , 4 , 9009, 225, 5  , 85),</a>
+<a name="898"><span class="lineNum">     898 </span>            :   INST(Stac            , X86Op              , O(000F01,CB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2681, 34 , 17 , 0 ),</a>
+<a name="899"><span class="lineNum">     899 </span>            :   INST(Stc             , X86Op              , O(000000,F9,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2686, 34 , 18 , 0 ),</a>
+<a name="900"><span class="lineNum">     900 </span>            :   INST(Std             , X86Op              , O(000000,FD,_,_,_,_,_,_  ), 0                         , 0 , 0 , 6242, 34 , 19 , 0 ),</a>
+<a name="901"><span class="lineNum">     901 </span>            :   INST(Sti             , X86Op              , O(000000,FB,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2690, 34 , 22 , 0 ),</a>
+<a name="902"><span class="lineNum">     902 </span>            :   INST(Stmxcsr         , X86M_Only          , O(000F00,AE,3,_,_,_,_,_  ), 0                         , 0 , 0 , 9317, 241, 5  , 0 ),</a>
+<a name="903"><span class="lineNum">     903 </span>            :   INST(Stos            , X86StrMr           , O(000000,AA,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2694, 242, 72 , 0 ),</a>
+<a name="904"><span class="lineNum">     904 </span>            :   INST(Str             , X86M               , O(000F00,00,1,_,_,_,_,_  ), 0                         , 0 , 0 , 2699, 239, 45 , 0 ),</a>
+<a name="905"><span class="lineNum">     905 </span>            :   INST(Sub             , X86Arith           , O(000000,28,5,_,x,_,_,_  ), 0                         , 0 , 0 , 807 , 243, 1  , 0 ),</a>
+<a name="906"><span class="lineNum">     906 </span>            :   INST(Subpd           , ExtRm              , O(660F00,5C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4361, 5  , 4  , 86),</a>
+<a name="907"><span class="lineNum">     907 </span>            :   INST(Subps           , ExtRm              , O(000F00,5C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 4373, 5  , 5  , 86),</a>
+<a name="908"><span class="lineNum">     908 </span>            :   INST(Subsd           , ExtRm              , O(F20F00,5C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5049, 6  , 4  , 86),</a>
+<a name="909"><span class="lineNum">     909 </span>            :   INST(Subss           , ExtRm              , O(F30F00,5C,_,_,_,_,_,_  ), 0                         , 0 , 0 , 5059, 7  , 5  , 86),</a>
+<a name="910"><span class="lineNum">     910 </span>            :   INST(Swapgs          , X86Op              , O(000F01,F8,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2703, 101, 23 , 0 ),</a>
+<a name="911"><span class="lineNum">     911 </span>            :   INST(Syscall         , X86Op              , O(000F00,05,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2710, 101, 45 , 0 ),</a>
+<a name="912"><span class="lineNum">     912 </span>            :   INST(Sysenter        , X86Op              , O(000F00,34,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2718, 34 , 45 , 0 ),</a>
+<a name="913"><span class="lineNum">     913 </span>            :   INST(Sysexit         , X86Op              , O(000F00,35,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2727, 34 , 23 , 0 ),</a>
+<a name="914"><span class="lineNum">     914 </span>            :   INST(Sysexit64       , X86Op              , O(000F00,35,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2735, 34 , 23 , 0 ),</a>
+<a name="915"><span class="lineNum">     915 </span>            :   INST(Sysret          , X86Op              , O(000F00,07,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2745, 101, 23 , 0 ),</a>
+<a name="916"><span class="lineNum">     916 </span>            :   INST(Sysret64        , X86Op              , O(000F00,07,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2752, 101, 23 , 0 ),</a>
+<a name="917"><span class="lineNum">     917 </span>            :   INST(T1mskc          , VexVm_Wx           , V(XOP_M9,01,7,0,x,_,_,_  ), 0                         , 0 , 0 , 2761, 15 , 11 , 0 ),</a>
+<a name="918"><span class="lineNum">     918 </span>            :   INST(Test            , X86Test            , O(000000,84,_,_,x,_,_,_  ), O(000000,F6,_,_,x,_,_,_  ), 0 , 0 , 8473, 244, 1  , 0 ),</a>
+<a name="919"><span class="lineNum">     919 </span>            :   INST(Tzcnt           , X86Rm_Raw66H       , O(F30F00,BC,_,_,x,_,_,_  ), 0                         , 0 , 0 , 2768, 143, 9  , 0 ),</a>
+<a name="920"><span class="lineNum">     920 </span>            :   INST(Tzmsk           , VexVm_Wx           , V(XOP_M9,01,4,0,x,_,_,_  ), 0                         , 0 , 0 , 2774, 15 , 11 , 0 ),</a>
+<a name="921"><span class="lineNum">     921 </span>            :   INST(Ucomisd         , ExtRm              , O(660F00,2E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9370, 44 , 39 , 15),</a>
+<a name="922"><span class="lineNum">     922 </span>            :   INST(Ucomiss         , ExtRm              , O(000F00,2E,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9379, 45 , 40 , 15),</a>
+<a name="923"><span class="lineNum">     923 </span>            :   INST(Ud2             , X86Op              , O(000F00,0B,_,_,_,_,_,_  ), 0                         , 0 , 0 , 2780, 34 , 0  , 0 ),</a>
+<a name="924"><span class="lineNum">     924 </span>            :   INST(Unpckhpd        , ExtRm              , O(660F00,15,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9388, 5  , 4  , 13),</a>
+<a name="925"><span class="lineNum">     925 </span>            :   INST(Unpckhps        , ExtRm              , O(000F00,15,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9398, 5  , 5  , 13),</a>
+<a name="926"><span class="lineNum">     926 </span>            :   INST(Unpcklpd        , ExtRm              , O(660F00,14,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9408, 5  , 4  , 13),</a>
+<a name="927"><span class="lineNum">     927 </span>            :   INST(Unpcklps        , ExtRm              , O(000F00,14,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9418, 5  , 5  , 13),</a>
+<a name="928"><span class="lineNum">     928 </span>            :   INST(V4fmaddps       , VexRm_T1_4X        , V(F20F38,9A,_,2,_,0,2,T4X), 0                         , 0 , 0 , 2784, 245, 115, 0 ),</a>
+<a name="929"><span class="lineNum">     929 </span>            :   INST(V4fnmaddps      , VexRm_T1_4X        , V(F20F38,AA,_,2,_,0,2,T4X), 0                         , 0 , 0 , 2794, 245, 115, 0 ),</a>
+<a name="930"><span class="lineNum">     930 </span>            :   INST(Vaddpd          , VexRvm_Lx          , V(660F00,58,_,x,I,1,4,FV ), 0                         , 0 , 0 , 2805, 246, 116, 1 ),</a>
+<a name="931"><span class="lineNum">     931 </span>            :   INST(Vaddps          , VexRvm_Lx          , V(000F00,58,_,x,I,0,4,FV ), 0                         , 0 , 0 , 2812, 247, 116, 1 ),</a>
+<a name="932"><span class="lineNum">     932 </span>            :   INST(Vaddsd          , VexRvm             , V(F20F00,58,_,I,I,1,3,T1S), 0                         , 0 , 0 , 2819, 248, 117, 1 ),</a>
+<a name="933"><span class="lineNum">     933 </span>            :   INST(Vaddss          , VexRvm             , V(F30F00,58,_,I,I,0,2,T1S), 0                         , 0 , 0 , 2826, 249, 117, 1 ),</a>
+<a name="934"><span class="lineNum">     934 </span>            :   INST(Vaddsubpd       , VexRvm_Lx          , V(660F00,D0,_,x,I,_,_,_  ), 0                         , 0 , 0 , 2833, 250, 118, 1 ),</a>
+<a name="935"><span class="lineNum">     935 </span>            :   INST(Vaddsubps       , VexRvm_Lx          , V(F20F00,D0,_,x,I,_,_,_  ), 0                         , 0 , 0 , 2843, 250, 118, 1 ),</a>
+<a name="936"><span class="lineNum">     936 </span>            :   INST(Vaesdec         , VexRvm             , V(660F38,DE,_,0,I,_,_,_  ), 0                         , 0 , 0 , 2853, 251, 119, 2 ),</a>
+<a name="937"><span class="lineNum">     937 </span>            :   INST(Vaesdeclast     , VexRvm             , V(660F38,DF,_,0,I,_,_,_  ), 0                         , 0 , 0 , 2861, 251, 119, 2 ),</a>
+<a name="938"><span class="lineNum">     938 </span>            :   INST(Vaesenc         , VexRvm             , V(660F38,DC,_,0,I,_,_,_  ), 0                         , 0 , 0 , 2873, 251, 119, 2 ),</a>
+<a name="939"><span class="lineNum">     939 </span>            :   INST(Vaesenclast     , VexRvm             , V(660F38,DD,_,0,I,_,_,_  ), 0                         , 0 , 0 , 2881, 251, 119, 2 ),</a>
+<a name="940"><span class="lineNum">     940 </span>            :   INST(Vaesimc         , VexRm              , V(660F38,DB,_,0,I,_,_,_  ), 0                         , 0 , 0 , 2893, 252, 119, 3 ),</a>
+<a name="941"><span class="lineNum">     941 </span>            :   INST(Vaeskeygenassist, VexRmi             , V(660F3A,DF,_,0,I,_,_,_  ), 0                         , 0 , 0 , 2901, 253, 119, 3 ),</a>
+<a name="942"><span class="lineNum">     942 </span>            :   INST(Valignd         , VexRvmi_Lx         , V(660F3A,03,_,x,_,0,4,FV ), 0                         , 0 , 0 , 2918, 254, 120, 0 ),</a>
+<a name="943"><span class="lineNum">     943 </span>            :   INST(Valignq         , VexRvmi_Lx         , V(660F3A,03,_,x,_,1,4,FV ), 0                         , 0 , 0 , 2926, 255, 120, 0 ),</a>
+<a name="944"><span class="lineNum">     944 </span>            :   INST(Vandnpd         , VexRvm_Lx          , V(660F00,55,_,x,I,1,4,FV ), 0                         , 0 , 0 , 2934, 256, 121, 2 ),</a>
+<a name="945"><span class="lineNum">     945 </span>            :   INST(Vandnps         , VexRvm_Lx          , V(000F00,55,_,x,I,0,4,FV ), 0                         , 0 , 0 , 2942, 257, 121, 2 ),</a>
+<a name="946"><span class="lineNum">     946 </span>            :   INST(Vandpd          , VexRvm_Lx          , V(660F00,54,_,x,I,1,4,FV ), 0                         , 0 , 0 , 2950, 258, 121, 2 ),</a>
+<a name="947"><span class="lineNum">     947 </span>            :   INST(Vandps          , VexRvm_Lx          , V(000F00,54,_,x,I,0,4,FV ), 0                         , 0 , 0 , 2957, 259, 121, 2 ),</a>
+<a name="948"><span class="lineNum">     948 </span>            :   INST(Vblendmb        , VexRvm_Lx          , V(660F38,66,_,x,_,0,4,FVM), 0                         , 0 , 0 , 2964, 260, 122, 0 ),</a>
+<a name="949"><span class="lineNum">     949 </span>            :   INST(Vblendmd        , VexRvm_Lx          , V(660F38,64,_,x,_,0,4,FV ), 0                         , 0 , 0 , 2973, 261, 120, 0 ),</a>
+<a name="950"><span class="lineNum">     950 </span>            :   INST(Vblendmpd       , VexRvm_Lx          , V(660F38,65,_,x,_,1,4,FV ), 0                         , 0 , 0 , 2982, 262, 120, 0 ),</a>
+<a name="951"><span class="lineNum">     951 </span>            :   INST(Vblendmps       , VexRvm_Lx          , V(660F38,65,_,x,_,0,4,FV ), 0                         , 0 , 0 , 2992, 261, 120, 0 ),</a>
+<a name="952"><span class="lineNum">     952 </span>            :   INST(Vblendmq        , VexRvm_Lx          , V(660F38,64,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3002, 262, 120, 0 ),</a>
+<a name="953"><span class="lineNum">     953 </span>            :   INST(Vblendmw        , VexRvm_Lx          , V(660F38,66,_,x,_,1,4,FVM), 0                         , 0 , 0 , 3011, 260, 122, 0 ),</a>
+<a name="954"><span class="lineNum">     954 </span>            :   INST(Vblendpd        , VexRvmi_Lx         , V(660F3A,0D,_,x,I,_,_,_  ), 0                         , 0 , 0 , 3020, 263, 118, 4 ),</a>
+<a name="955"><span class="lineNum">     955 </span>            :   INST(Vblendps        , VexRvmi_Lx         , V(660F3A,0C,_,x,I,_,_,_  ), 0                         , 0 , 0 , 3029, 263, 118, 4 ),</a>
+<a name="956"><span class="lineNum">     956 </span>            :   INST(Vblendvpd       , VexRvmr_Lx         , V(660F3A,4B,_,x,0,_,_,_  ), 0                         , 0 , 0 , 3038, 264, 118, 5 ),</a>
+<a name="957"><span class="lineNum">     957 </span>            :   INST(Vblendvps       , VexRvmr_Lx         , V(660F3A,4A,_,x,0,_,_,_  ), 0                         , 0 , 0 , 3048, 264, 118, 5 ),</a>
+<a name="958"><span class="lineNum">     958 </span>            :   INST(Vbroadcastf128  , VexRm              , V(660F38,1A,_,1,0,_,_,_  ), 0                         , 0 , 0 , 3058, 265, 118, 0 ),</a>
+<a name="959"><span class="lineNum">     959 </span>            :   INST(Vbroadcastf32x2 , VexRm_Lx           , V(660F38,19,_,x,_,0,3,T2 ), 0                         , 0 , 0 , 3073, 266, 123, 0 ),</a>
+<a name="960"><span class="lineNum">     960 </span>            :   INST(Vbroadcastf32x4 , VexRm_Lx           , V(660F38,1A,_,x,_,0,4,T4 ), 0                         , 0 , 0 , 3089, 267, 65 , 0 ),</a>
+<a name="961"><span class="lineNum">     961 </span>            :   INST(Vbroadcastf32x8 , VexRm              , V(660F38,1B,_,2,_,0,5,T8 ), 0                         , 0 , 0 , 3105, 268, 63 , 0 ),</a>
+<a name="962"><span class="lineNum">     962 </span>            :   INST(Vbroadcastf64x2 , VexRm_Lx           , V(660F38,1A,_,x,_,1,4,T2 ), 0                         , 0 , 0 , 3121, 267, 123, 0 ),</a>
+<a name="963"><span class="lineNum">     963 </span>            :   INST(Vbroadcastf64x4 , VexRm              , V(660F38,1B,_,2,_,1,5,T4 ), 0                         , 0 , 0 , 3137, 268, 65 , 0 ),</a>
+<a name="964"><span class="lineNum">     964 </span>            :   INST(Vbroadcasti128  , VexRm              , V(660F38,5A,_,1,0,_,_,_  ), 0                         , 0 , 0 , 3153, 265, 124, 0 ),</a>
+<a name="965"><span class="lineNum">     965 </span>            :   INST(Vbroadcasti32x2 , VexRm_Lx           , V(660F38,59,_,x,_,0,3,T2 ), 0                         , 0 , 0 , 3168, 269, 123, 0 ),</a>
+<a name="966"><span class="lineNum">     966 </span>            :   INST(Vbroadcasti32x4 , VexRm_Lx           , V(660F38,5A,_,x,_,0,4,T4 ), 0                         , 0 , 0 , 3184, 266, 120, 0 ),</a>
+<a name="967"><span class="lineNum">     967 </span>            :   INST(Vbroadcasti32x8 , VexRm              , V(660F38,5B,_,2,_,0,5,T8 ), 0                         , 0 , 0 , 3200, 270, 63 , 0 ),</a>
+<a name="968"><span class="lineNum">     968 </span>            :   INST(Vbroadcasti64x2 , VexRm_Lx           , V(660F38,5A,_,x,_,1,4,T2 ), 0                         , 0 , 0 , 3216, 266, 123, 0 ),</a>
+<a name="969"><span class="lineNum">     969 </span>            :   INST(Vbroadcasti64x4 , VexRm              , V(660F38,5B,_,2,_,1,5,T4 ), 0                         , 0 , 0 , 3232, 270, 65 , 0 ),</a>
+<a name="970"><span class="lineNum">     970 </span>            :   INST(Vbroadcastsd    , VexRm_Lx           , V(660F38,19,_,x,0,1,3,T1S), 0                         , 0 , 0 , 3248, 271, 125, 0 ),</a>
+<a name="971"><span class="lineNum">     971 </span>            :   INST(Vbroadcastss    , VexRm_Lx           , V(660F38,18,_,x,0,0,2,T1S), 0                         , 0 , 0 , 3261, 272, 125, 0 ),</a>
+<a name="972"><span class="lineNum">     972 </span>            :   INST(Vcmppd          , VexRvmi_Lx         , V(660F00,C2,_,x,I,1,4,FV ), 0                         , 0 , 0 , 3274, 273, 116, 6 ),</a>
+<a name="973"><span class="lineNum">     973 </span>            :   INST(Vcmpps          , VexRvmi_Lx         , V(000F00,C2,_,x,I,0,4,FV ), 0                         , 0 , 0 , 3281, 274, 116, 6 ),</a>
+<a name="974"><span class="lineNum">     974 </span>            :   INST(Vcmpsd          , VexRvmi            , V(F20F00,C2,_,I,I,1,3,T1S), 0                         , 0 , 0 , 3288, 275, 117, 7 ),</a>
+<a name="975"><span class="lineNum">     975 </span>            :   INST(Vcmpss          , VexRvmi            , V(F30F00,C2,_,I,I,0,2,T1S), 0                         , 0 , 0 , 3295, 276, 117, 7 ),</a>
+<a name="976"><span class="lineNum">     976 </span>            :   INST(Vcomisd         , VexRm              , V(660F00,2F,_,I,I,1,3,T1S), 0                         , 0 , 0 , 3302, 277, 126, 8 ),</a>
+<a name="977"><span class="lineNum">     977 </span>            :   INST(Vcomiss         , VexRm              , V(000F00,2F,_,I,I,0,2,T1S), 0                         , 0 , 0 , 3310, 278, 126, 8 ),</a>
+<a name="978"><span class="lineNum">     978 </span>            :   INST(Vcompresspd     , VexMr_Lx           , V(660F38,8A,_,x,_,1,3,T1S), 0                         , 0 , 0 , 3318, 279, 120, 0 ),</a>
+<a name="979"><span class="lineNum">     979 </span>            :   INST(Vcompressps     , VexMr_Lx           , V(660F38,8A,_,x,_,0,2,T1S), 0                         , 0 , 0 , 3330, 279, 120, 0 ),</a>
+<a name="980"><span class="lineNum">     980 </span>            :   INST(Vcvtdq2pd       , VexRm_Lx           , V(F30F00,E6,_,x,I,0,3,HV ), 0                         , 0 , 0 , 3342, 280, 116, 9 ),</a>
+<a name="981"><span class="lineNum">     981 </span>            :   INST(Vcvtdq2ps       , VexRm_Lx           , V(000F00,5B,_,x,I,0,4,FV ), 0                         , 0 , 0 , 3352, 281, 116, 9 ),</a>
+<a name="982"><span class="lineNum">     982 </span>            :   INST(Vcvtpd2dq       , VexRm_Lx           , V(F20F00,E6,_,x,I,1,4,FV ), 0                         , 0 , 0 , 3362, 282, 116, 9 ),</a>
+<a name="983"><span class="lineNum">     983 </span>            :   INST(Vcvtpd2ps       , VexRm_Lx           , V(660F00,5A,_,x,I,1,4,FV ), 0                         , 0 , 0 , 3372, 283, 116, 10),</a>
+<a name="984"><span class="lineNum">     984 </span>            :   INST(Vcvtpd2qq       , VexRm_Lx           , V(660F00,7B,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3382, 284, 123, 0 ),</a>
+<a name="985"><span class="lineNum">     985 </span>            :   INST(Vcvtpd2udq      , VexRm_Lx           , V(000F00,79,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3392, 285, 120, 0 ),</a>
+<a name="986"><span class="lineNum">     986 </span>            :   INST(Vcvtpd2uqq      , VexRm_Lx           , V(660F00,79,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3403, 284, 123, 0 ),</a>
+<a name="987"><span class="lineNum">     987 </span>            :   INST(Vcvtph2ps       , VexRm_Lx           , V(660F38,13,_,x,0,0,3,HVM), 0                         , 0 , 0 , 3414, 286, 127, 0 ),</a>
+<a name="988"><span class="lineNum">     988 </span>            :   INST(Vcvtps2dq       , VexRm_Lx           , V(660F00,5B,_,x,I,0,4,FV ), 0                         , 0 , 0 , 3424, 281, 116, 8 ),</a>
+<a name="989"><span class="lineNum">     989 </span>            :   INST(Vcvtps2pd       , VexRm_Lx           , V(000F00,5A,_,x,I,0,4,HV ), 0                         , 0 , 0 , 3434, 287, 116, 8 ),</a>
+<a name="990"><span class="lineNum">     990 </span>            :   INST(Vcvtps2ph       , VexMri_Lx          , V(660F3A,1D,_,x,0,0,3,HVM), 0                         , 0 , 0 , 3444, 288, 127, 0 ),</a>
+<a name="991"><span class="lineNum">     991 </span>            :   INST(Vcvtps2qq       , VexRm_Lx           , V(660F00,7B,_,x,_,0,3,HV ), 0                         , 0 , 0 , 3454, 289, 123, 0 ),</a>
+<a name="992"><span class="lineNum">     992 </span>            :   INST(Vcvtps2udq      , VexRm_Lx           , V(000F00,79,_,x,_,0,4,FV ), 0                         , 0 , 0 , 3464, 290, 120, 0 ),</a>
+<a name="993"><span class="lineNum">     993 </span>            :   INST(Vcvtps2uqq      , VexRm_Lx           , V(660F00,79,_,x,_,0,3,HV ), 0                         , 0 , 0 , 3475, 289, 123, 0 ),</a>
+<a name="994"><span class="lineNum">     994 </span>            :   INST(Vcvtqq2pd       , VexRm_Lx           , V(F30F00,E6,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3486, 284, 123, 0 ),</a>
+<a name="995"><span class="lineNum">     995 </span>            :   INST(Vcvtqq2ps       , VexRm_Lx           , V(000F00,5B,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3496, 285, 123, 0 ),</a>
+<a name="996"><span class="lineNum">     996 </span>            :   INST(Vcvtsd2si       , VexRm_Wx           , V(F20F00,2D,_,I,x,x,3,T1F), 0                         , 0 , 0 , 3506, 291, 117, 11),</a>
+<a name="997"><span class="lineNum">     997 </span>            :   INST(Vcvtsd2ss       , VexRvm             , V(F20F00,5A,_,I,I,1,3,T1S), 0                         , 0 , 0 , 3516, 248, 117, 12),</a>
+<a name="998"><span class="lineNum">     998 </span>            :   INST(Vcvtsd2usi      , VexRm_Wx           , V(F20F00,79,_,I,_,x,3,T1F), 0                         , 0 , 0 , 3526, 292, 65 , 0 ),</a>
+<a name="999"><span class="lineNum">     999 </span>            :   INST(Vcvtsi2sd       , VexRvm_Wx          , V(F20F00,2A,_,I,x,x,2,T1W), 0                         , 0 , 0 , 3537, 293, 117, 13),</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :   INST(Vcvtsi2ss       , VexRvm_Wx          , V(F30F00,2A,_,I,x,x,2,T1W), 0                         , 0 , 0 , 3547, 293, 117, 13),</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   INST(Vcvtss2sd       , VexRvm             , V(F30F00,5A,_,I,I,0,2,T1S), 0                         , 0 , 0 , 3557, 294, 117, 13),</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :   INST(Vcvtss2si       , VexRm_Wx           , V(F30F00,2D,_,I,x,x,2,T1F), 0                         , 0 , 0 , 3567, 295, 117, 14),</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   INST(Vcvtss2usi      , VexRm_Wx           , V(F30F00,79,_,I,_,x,2,T1F), 0                         , 0 , 0 , 3577, 296, 65 , 0 ),</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :   INST(Vcvttpd2dq      , VexRm_Lx           , V(660F00,E6,_,x,I,1,4,FV ), 0                         , 0 , 0 , 3588, 297, 116, 15),</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :   INST(Vcvttpd2qq      , VexRm_Lx           , V(660F00,7A,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3599, 298, 120, 0 ),</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   INST(Vcvttpd2udq     , VexRm_Lx           , V(000F00,78,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3610, 299, 120, 0 ),</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :   INST(Vcvttpd2uqq     , VexRm_Lx           , V(660F00,78,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3622, 298, 123, 0 ),</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   INST(Vcvttps2dq      , VexRm_Lx           , V(F30F00,5B,_,x,I,0,4,FV ), 0                         , 0 , 0 , 3634, 300, 116, 16),</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   INST(Vcvttps2qq      , VexRm_Lx           , V(660F00,7A,_,x,_,0,3,HV ), 0                         , 0 , 0 , 3645, 301, 123, 0 ),</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   INST(Vcvttps2udq     , VexRm_Lx           , V(000F00,78,_,x,_,0,4,FV ), 0                         , 0 , 0 , 3656, 302, 120, 0 ),</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :   INST(Vcvttps2uqq     , VexRm_Lx           , V(660F00,78,_,x,_,0,3,HV ), 0                         , 0 , 0 , 3668, 301, 123, 0 ),</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :   INST(Vcvttsd2si      , VexRm_Wx           , V(F20F00,2C,_,I,x,x,3,T1F), 0                         , 0 , 0 , 3680, 303, 117, 17),</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :   INST(Vcvttsd2usi     , VexRm_Wx           , V(F20F00,78,_,I,_,x,3,T1F), 0                         , 0 , 0 , 3691, 304, 65 , 0 ),</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   INST(Vcvttss2si      , VexRm_Wx           , V(F30F00,2C,_,I,x,x,2,T1F), 0                         , 0 , 0 , 3703, 305, 117, 18),</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   INST(Vcvttss2usi     , VexRm_Wx           , V(F30F00,78,_,I,_,x,2,T1F), 0                         , 0 , 0 , 3714, 306, 65 , 0 ),</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :   INST(Vcvtudq2pd      , VexRm_Lx           , V(F30F00,7A,_,x,_,0,3,HV ), 0                         , 0 , 0 , 3726, 307, 120, 0 ),</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   INST(Vcvtudq2ps      , VexRm_Lx           , V(F20F00,7A,_,x,_,0,4,FV ), 0                         , 0 , 0 , 3737, 290, 120, 0 ),</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :   INST(Vcvtuqq2pd      , VexRm_Lx           , V(F30F00,7A,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3748, 284, 123, 0 ),</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   INST(Vcvtuqq2ps      , VexRm_Lx           , V(F20F00,7A,_,x,_,1,4,FV ), 0                         , 0 , 0 , 3759, 285, 123, 0 ),</a>
+<a name="1020"><span class="lineNum">    1020 </span>            :   INST(Vcvtusi2sd      , VexRvm_Wx          , V(F20F00,7B,_,I,_,x,2,T1W), 0                         , 0 , 0 , 3770, 308, 65 , 0 ),</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :   INST(Vcvtusi2ss      , VexRvm_Wx          , V(F30F00,7B,_,I,_,x,2,T1W), 0                         , 0 , 0 , 3781, 308, 65 , 0 ),</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :   INST(Vdbpsadbw       , VexRvmi_Lx         , V(660F3A,42,_,x,_,0,4,FVM), 0                         , 0 , 0 , 3792, 309, 122, 0 ),</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :   INST(Vdivpd          , VexRvm_Lx          , V(660F00,5E,_,x,I,1,4,FV ), 0                         , 0 , 0 , 3802, 246, 116, 19),</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   INST(Vdivps          , VexRvm_Lx          , V(000F00,5E,_,x,I,0,4,FV ), 0                         , 0 , 0 , 3809, 247, 116, 19),</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   INST(Vdivsd          , VexRvm             , V(F20F00,5E,_,I,I,1,3,T1S), 0                         , 0 , 0 , 3816, 248, 117, 19),</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :   INST(Vdivss          , VexRvm             , V(F30F00,5E,_,I,I,0,2,T1S), 0                         , 0 , 0 , 3823, 249, 117, 19),</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :   INST(Vdppd           , VexRvmi_Lx         , V(660F3A,41,_,x,I,_,_,_  ), 0                         , 0 , 0 , 3830, 310, 118, 19),</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :   INST(Vdpps           , VexRvmi_Lx         , V(660F3A,40,_,x,I,_,_,_  ), 0                         , 0 , 0 , 3836, 263, 118, 19),</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :   INST(Verr            , X86M               , O(000F00,00,4,_,_,_,_,_  ), 0                         , 0 , 0 , 3842, 137, 70 , 0 ),</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :   INST(Verw            , X86M               , O(000F00,00,5,_,_,_,_,_  ), 0                         , 0 , 0 , 3847, 137, 70 , 0 ),</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   INST(Vexp2pd         , VexRm              , V(660F38,C8,_,2,_,1,4,FV ), 0                         , 0 , 0 , 3852, 311, 128, 0 ),</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :   INST(Vexp2ps         , VexRm              , V(660F38,C8,_,2,_,0,4,FV ), 0                         , 0 , 0 , 3860, 312, 128, 0 ),</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   INST(Vexpandpd       , VexRm_Lx           , V(660F38,88,_,x,_,1,3,T1S), 0                         , 0 , 0 , 3868, 313, 120, 0 ),</a>
+<a name="1034"><span class="lineNum">    1034 </span>            :   INST(Vexpandps       , VexRm_Lx           , V(660F38,88,_,x,_,0,2,T1S), 0                         , 0 , 0 , 3878, 313, 120, 0 ),</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :   INST(Vextractf128    , VexMri             , V(660F3A,19,_,1,0,_,_,_  ), 0                         , 0 , 0 , 3888, 314, 118, 0 ),</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   INST(Vextractf32x4   , VexMri_Lx          , V(660F3A,19,_,x,_,0,4,T4 ), 0                         , 0 , 0 , 3901, 315, 120, 0 ),</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :   INST(Vextractf32x8   , VexMri             , V(660F3A,1B,_,2,_,0,5,T8 ), 0                         , 0 , 0 , 3915, 316, 63 , 0 ),</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :   INST(Vextractf64x2   , VexMri_Lx          , V(660F3A,19,_,x,_,1,4,T2 ), 0                         , 0 , 0 , 3929, 315, 123, 0 ),</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :   INST(Vextractf64x4   , VexMri             , V(660F3A,1B,_,2,_,1,5,T4 ), 0                         , 0 , 0 , 3943, 316, 65 , 0 ),</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   INST(Vextracti128    , VexMri             , V(660F3A,39,_,1,0,_,_,_  ), 0                         , 0 , 0 , 3957, 314, 124, 0 ),</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   INST(Vextracti32x4   , VexMri_Lx          , V(660F3A,39,_,x,_,0,4,T4 ), 0                         , 0 , 0 , 3970, 315, 120, 0 ),</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :   INST(Vextracti32x8   , VexMri             , V(660F3A,3B,_,2,_,0,5,T8 ), 0                         , 0 , 0 , 3984, 316, 63 , 0 ),</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :   INST(Vextracti64x2   , VexMri_Lx          , V(660F3A,39,_,x,_,1,4,T2 ), 0                         , 0 , 0 , 3998, 315, 123, 0 ),</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :   INST(Vextracti64x4   , VexMri             , V(660F3A,3B,_,2,_,1,5,T4 ), 0                         , 0 , 0 , 4012, 316, 65 , 0 ),</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :   INST(Vextractps      , VexMri             , V(660F3A,17,_,0,I,I,2,T1S), 0                         , 0 , 0 , 4026, 317, 117, 20),</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :   INST(Vfixupimmpd     , VexRvmi_Lx         , V(660F3A,54,_,x,_,1,4,FV ), 0                         , 0 , 0 , 4037, 318, 120, 0 ),</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   INST(Vfixupimmps     , VexRvmi_Lx         , V(660F3A,54,_,x,_,0,4,FV ), 0                         , 0 , 0 , 4049, 319, 120, 0 ),</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :   INST(Vfixupimmsd     , VexRvmi            , V(660F3A,55,_,I,_,1,3,T1S), 0                         , 0 , 0 , 4061, 320, 65 , 0 ),</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :   INST(Vfixupimmss     , VexRvmi            , V(660F3A,55,_,I,_,0,2,T1S), 0                         , 0 , 0 , 4073, 321, 65 , 0 ),</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   INST(Vfmadd132pd     , VexRvm_Lx          , V(660F38,98,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4085, 322, 129, 0 ),</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   INST(Vfmadd132ps     , VexRvm_Lx          , V(660F38,98,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4097, 323, 129, 0 ),</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   INST(Vfmadd132sd     , VexRvm             , V(660F38,99,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4109, 324, 130, 0 ),</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   INST(Vfmadd132ss     , VexRvm             , V(660F38,99,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4121, 325, 130, 0 ),</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   INST(Vfmadd213pd     , VexRvm_Lx          , V(660F38,A8,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4133, 322, 129, 0 ),</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   INST(Vfmadd213ps     , VexRvm_Lx          , V(660F38,A8,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4145, 323, 129, 0 ),</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :   INST(Vfmadd213sd     , VexRvm             , V(660F38,A9,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4157, 324, 130, 0 ),</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   INST(Vfmadd213ss     , VexRvm             , V(660F38,A9,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4169, 325, 130, 0 ),</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   INST(Vfmadd231pd     , VexRvm_Lx          , V(660F38,B8,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4181, 322, 129, 0 ),</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   INST(Vfmadd231ps     , VexRvm_Lx          , V(660F38,B8,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4193, 323, 129, 0 ),</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :   INST(Vfmadd231sd     , VexRvm             , V(660F38,B9,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4205, 324, 130, 0 ),</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   INST(Vfmadd231ss     , VexRvm             , V(660F38,B9,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4217, 325, 130, 0 ),</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   INST(Vfmaddpd        , Fma4_Lx            , V(660F3A,69,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4229, 326, 131, 0 ),</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   INST(Vfmaddps        , Fma4_Lx            , V(660F3A,68,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4238, 326, 131, 0 ),</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   INST(Vfmaddsd        , Fma4               , V(660F3A,6B,_,0,x,_,_,_  ), 0                         , 0 , 0 , 4247, 327, 131, 0 ),</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   INST(Vfmaddss        , Fma4               , V(660F3A,6A,_,0,x,_,_,_  ), 0                         , 0 , 0 , 4256, 328, 131, 0 ),</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :   INST(Vfmaddsub132pd  , VexRvm_Lx          , V(660F38,96,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4265, 322, 129, 0 ),</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   INST(Vfmaddsub132ps  , VexRvm_Lx          , V(660F38,96,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4280, 323, 129, 0 ),</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   INST(Vfmaddsub213pd  , VexRvm_Lx          , V(660F38,A6,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4295, 322, 129, 0 ),</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :   INST(Vfmaddsub213ps  , VexRvm_Lx          , V(660F38,A6,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4310, 323, 129, 0 ),</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   INST(Vfmaddsub231pd  , VexRvm_Lx          , V(660F38,B6,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4325, 322, 129, 0 ),</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   INST(Vfmaddsub231ps  , VexRvm_Lx          , V(660F38,B6,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4340, 323, 129, 0 ),</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :   INST(Vfmaddsubpd     , Fma4_Lx            , V(660F3A,5D,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4355, 326, 131, 0 ),</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   INST(Vfmaddsubps     , Fma4_Lx            , V(660F3A,5C,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4367, 326, 131, 0 ),</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   INST(Vfmsub132pd     , VexRvm_Lx          , V(660F38,9A,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4379, 322, 129, 0 ),</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   INST(Vfmsub132ps     , VexRvm_Lx          , V(660F38,9A,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4391, 323, 129, 0 ),</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :   INST(Vfmsub132sd     , VexRvm             , V(660F38,9B,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4403, 324, 130, 0 ),</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   INST(Vfmsub132ss     , VexRvm             , V(660F38,9B,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4415, 325, 130, 0 ),</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :   INST(Vfmsub213pd     , VexRvm_Lx          , V(660F38,AA,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4427, 322, 129, 0 ),</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   INST(Vfmsub213ps     , VexRvm_Lx          , V(660F38,AA,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4439, 323, 129, 0 ),</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :   INST(Vfmsub213sd     , VexRvm             , V(660F38,AB,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4451, 324, 130, 0 ),</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   INST(Vfmsub213ss     , VexRvm             , V(660F38,AB,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4463, 325, 130, 0 ),</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   INST(Vfmsub231pd     , VexRvm_Lx          , V(660F38,BA,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4475, 322, 129, 0 ),</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   INST(Vfmsub231ps     , VexRvm_Lx          , V(660F38,BA,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4487, 323, 129, 0 ),</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :   INST(Vfmsub231sd     , VexRvm             , V(660F38,BB,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4499, 324, 130, 0 ),</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   INST(Vfmsub231ss     , VexRvm             , V(660F38,BB,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4511, 325, 130, 0 ),</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   INST(Vfmsubadd132pd  , VexRvm_Lx          , V(660F38,97,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4523, 322, 129, 0 ),</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :   INST(Vfmsubadd132ps  , VexRvm_Lx          , V(660F38,97,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4538, 323, 129, 0 ),</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :   INST(Vfmsubadd213pd  , VexRvm_Lx          , V(660F38,A7,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4553, 322, 129, 0 ),</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :   INST(Vfmsubadd213ps  , VexRvm_Lx          , V(660F38,A7,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4568, 323, 129, 0 ),</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   INST(Vfmsubadd231pd  , VexRvm_Lx          , V(660F38,B7,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4583, 322, 129, 0 ),</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   INST(Vfmsubadd231ps  , VexRvm_Lx          , V(660F38,B7,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4598, 323, 129, 0 ),</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   INST(Vfmsubaddpd     , Fma4_Lx            , V(660F3A,5F,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4613, 326, 131, 0 ),</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   INST(Vfmsubaddps     , Fma4_Lx            , V(660F3A,5E,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4625, 326, 131, 0 ),</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   INST(Vfmsubpd        , Fma4_Lx            , V(660F3A,6D,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4637, 326, 131, 0 ),</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   INST(Vfmsubps        , Fma4_Lx            , V(660F3A,6C,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4646, 326, 131, 0 ),</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   INST(Vfmsubsd        , Fma4               , V(660F3A,6F,_,0,x,_,_,_  ), 0                         , 0 , 0 , 4655, 327, 131, 0 ),</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   INST(Vfmsubss        , Fma4               , V(660F3A,6E,_,0,x,_,_,_  ), 0                         , 0 , 0 , 4664, 328, 131, 0 ),</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   INST(Vfnmadd132pd    , VexRvm_Lx          , V(660F38,9C,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4673, 322, 129, 0 ),</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :   INST(Vfnmadd132ps    , VexRvm_Lx          , V(660F38,9C,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4686, 323, 129, 0 ),</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :   INST(Vfnmadd132sd    , VexRvm             , V(660F38,9D,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4699, 324, 130, 0 ),</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   INST(Vfnmadd132ss    , VexRvm             , V(660F38,9D,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4712, 325, 130, 0 ),</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   INST(Vfnmadd213pd    , VexRvm_Lx          , V(660F38,AC,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4725, 322, 129, 0 ),</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   INST(Vfnmadd213ps    , VexRvm_Lx          , V(660F38,AC,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4738, 323, 129, 0 ),</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :   INST(Vfnmadd213sd    , VexRvm             , V(660F38,AD,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4751, 324, 130, 0 ),</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :   INST(Vfnmadd213ss    , VexRvm             , V(660F38,AD,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4764, 325, 130, 0 ),</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   INST(Vfnmadd231pd    , VexRvm_Lx          , V(660F38,BC,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4777, 322, 129, 0 ),</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   INST(Vfnmadd231ps    , VexRvm_Lx          , V(660F38,BC,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4790, 323, 129, 0 ),</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   INST(Vfnmadd231sd    , VexRvm             , V(660F38,BC,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4803, 324, 130, 0 ),</a>
+<a name="1109"><span class="lineNum">    1109 </span>            :   INST(Vfnmadd231ss    , VexRvm             , V(660F38,BC,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4816, 325, 130, 0 ),</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   INST(Vfnmaddpd       , Fma4_Lx            , V(660F3A,79,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4829, 326, 131, 0 ),</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   INST(Vfnmaddps       , Fma4_Lx            , V(660F3A,78,_,x,x,_,_,_  ), 0                         , 0 , 0 , 4839, 326, 131, 0 ),</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   INST(Vfnmaddsd       , Fma4               , V(660F3A,7B,_,0,x,_,_,_  ), 0                         , 0 , 0 , 4849, 327, 131, 0 ),</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :   INST(Vfnmaddss       , Fma4               , V(660F3A,7A,_,0,x,_,_,_  ), 0                         , 0 , 0 , 4859, 328, 131, 0 ),</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :   INST(Vfnmsub132pd    , VexRvm_Lx          , V(660F38,9E,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4869, 322, 129, 0 ),</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   INST(Vfnmsub132ps    , VexRvm_Lx          , V(660F38,9E,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4882, 323, 129, 0 ),</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :   INST(Vfnmsub132sd    , VexRvm             , V(660F38,9F,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4895, 324, 130, 0 ),</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   INST(Vfnmsub132ss    , VexRvm             , V(660F38,9F,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4908, 325, 130, 0 ),</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   INST(Vfnmsub213pd    , VexRvm_Lx          , V(660F38,AE,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4921, 322, 129, 0 ),</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :   INST(Vfnmsub213ps    , VexRvm_Lx          , V(660F38,AE,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4934, 323, 129, 0 ),</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :   INST(Vfnmsub213sd    , VexRvm             , V(660F38,AF,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4947, 324, 130, 0 ),</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :   INST(Vfnmsub213ss    , VexRvm             , V(660F38,AF,_,I,0,0,2,T1S), 0                         , 0 , 0 , 4960, 325, 130, 0 ),</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   INST(Vfnmsub231pd    , VexRvm_Lx          , V(660F38,BE,_,x,1,1,4,FV ), 0                         , 0 , 0 , 4973, 322, 129, 0 ),</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   INST(Vfnmsub231ps    , VexRvm_Lx          , V(660F38,BE,_,x,0,0,4,FV ), 0                         , 0 , 0 , 4986, 323, 129, 0 ),</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   INST(Vfnmsub231sd    , VexRvm             , V(660F38,BF,_,I,1,1,3,T1S), 0                         , 0 , 0 , 4999, 324, 130, 0 ),</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   INST(Vfnmsub231ss    , VexRvm             , V(660F38,BF,_,I,0,0,2,T1S), 0                         , 0 , 0 , 5012, 325, 130, 0 ),</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :   INST(Vfnmsubpd       , Fma4_Lx            , V(660F3A,7D,_,x,x,_,_,_  ), 0                         , 0 , 0 , 5025, 326, 131, 0 ),</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   INST(Vfnmsubps       , Fma4_Lx            , V(660F3A,7C,_,x,x,_,_,_  ), 0                         , 0 , 0 , 5035, 326, 131, 0 ),</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   INST(Vfnmsubsd       , Fma4               , V(660F3A,7F,_,0,x,_,_,_  ), 0                         , 0 , 0 , 5045, 327, 131, 0 ),</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   INST(Vfnmsubss       , Fma4               , V(660F3A,7E,_,0,x,_,_,_  ), 0                         , 0 , 0 , 5055, 328, 131, 0 ),</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   INST(Vfpclasspd      , VexRmi_Lx          , V(660F3A,66,_,x,_,1,4,FV ), 0                         , 0 , 0 , 5065, 329, 123, 0 ),</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   INST(Vfpclassps      , VexRmi_Lx          , V(660F3A,66,_,x,_,0,4,FV ), 0                         , 0 , 0 , 5076, 330, 123, 0 ),</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   INST(Vfpclasssd      , VexRmi_Lx          , V(660F3A,67,_,I,_,1,3,T1S), 0                         , 0 , 0 , 5087, 331, 63 , 0 ),</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :   INST(Vfpclassss      , VexRmi_Lx          , V(660F3A,67,_,I,_,0,2,T1S), 0                         , 0 , 0 , 5098, 332, 63 , 0 ),</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   INST(Vfrczpd         , VexRm_Lx           , V(XOP_M9,81,_,x,0,_,_,_  ), 0                         , 0 , 0 , 5109, 333, 132, 0 ),</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   INST(Vfrczps         , VexRm_Lx           , V(XOP_M9,80,_,x,0,_,_,_  ), 0                         , 0 , 0 , 5117, 333, 132, 0 ),</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :   INST(Vfrczsd         , VexRm              , V(XOP_M9,83,_,0,0,_,_,_  ), 0                         , 0 , 0 , 5125, 334, 132, 0 ),</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :   INST(Vfrczss         , VexRm              , V(XOP_M9,82,_,0,0,_,_,_  ), 0                         , 0 , 0 , 5133, 335, 132, 0 ),</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   INST(Vgatherdpd      , VexRmvRm_VM        , V(660F38,92,_,x,1,_,_,_  ), V(660F38,92,_,x,_,1,3,T1S), 0 , 0 , 5141, 336, 133, 0 ),</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :   INST(Vgatherdps      , VexRmvRm_VM        , V(660F38,92,_,x,0,_,_,_  ), V(660F38,92,_,x,_,0,2,T1S), 0 , 0 , 5152, 337, 133, 0 ),</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   INST(Vgatherpf0dpd   , VexM_VM            , V(660F38,C6,1,2,_,1,3,T1S), 0                         , 0 , 0 , 5163, 338, 134, 0 ),</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   INST(Vgatherpf0dps   , VexM_VM            , V(660F38,C6,1,2,_,0,2,T1S), 0                         , 0 , 0 , 5177, 339, 134, 0 ),</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :   INST(Vgatherpf0qpd   , VexM_VM            , V(660F38,C7,1,2,_,1,3,T1S), 0                         , 0 , 0 , 5191, 340, 134, 0 ),</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :   INST(Vgatherpf0qps   , VexM_VM            , V(660F38,C7,1,2,_,0,2,T1S), 0                         , 0 , 0 , 5205, 340, 134, 0 ),</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   INST(Vgatherpf1dpd   , VexM_VM            , V(660F38,C6,2,2,_,1,3,T1S), 0                         , 0 , 0 , 5219, 338, 134, 0 ),</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   INST(Vgatherpf1dps   , VexM_VM            , V(660F38,C6,2,2,_,0,2,T1S), 0                         , 0 , 0 , 5233, 339, 134, 0 ),</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   INST(Vgatherpf1qpd   , VexM_VM            , V(660F38,C7,2,2,_,1,3,T1S), 0                         , 0 , 0 , 5247, 340, 134, 0 ),</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   INST(Vgatherpf1qps   , VexM_VM            , V(660F38,C7,2,2,_,0,2,T1S), 0                         , 0 , 0 , 5261, 340, 134, 0 ),</a>
+<a name="1148"><span class="lineNum">    1148 </span>            :   INST(Vgatherqpd      , VexRmvRm_VM        , V(660F38,93,_,x,1,_,_,_  ), V(660F38,93,_,x,_,1,3,T1S), 0 , 0 , 5275, 341, 133, 0 ),</a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   INST(Vgatherqps      , VexRmvRm_VM        , V(660F38,93,_,x,0,_,_,_  ), V(660F38,93,_,x,_,0,2,T1S), 0 , 0 , 5286, 342, 133, 0 ),</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :   INST(Vgetexppd       , VexRm_Lx           , V(660F38,42,_,x,_,1,4,FV ), 0                         , 0 , 0 , 5297, 298, 120, 0 ),</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   INST(Vgetexpps       , VexRm_Lx           , V(660F38,42,_,x,_,0,4,FV ), 0                         , 0 , 0 , 5307, 302, 120, 0 ),</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :   INST(Vgetexpsd       , VexRm              , V(660F38,43,_,I,_,1,3,T1S), 0                         , 0 , 0 , 5317, 343, 65 , 0 ),</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   INST(Vgetexpss       , VexRm              , V(660F38,43,_,I,_,0,2,T1S), 0                         , 0 , 0 , 5327, 344, 65 , 0 ),</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :   INST(Vgetmantpd      , VexRmi_Lx          , V(660F3A,26,_,x,_,1,4,FV ), 0                         , 0 , 0 , 5337, 345, 120, 0 ),</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :   INST(Vgetmantps      , VexRmi_Lx          , V(660F3A,26,_,x,_,0,4,FV ), 0                         , 0 , 0 , 5348, 346, 120, 0 ),</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :   INST(Vgetmantsd      , VexRmi             , V(660F3A,27,_,I,_,1,3,T1S), 0                         , 0 , 0 , 5359, 347, 65 , 0 ),</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :   INST(Vgetmantss      , VexRmi             , V(660F3A,27,_,I,_,0,2,T1S), 0                         , 0 , 0 , 5370, 348, 65 , 0 ),</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   INST(Vhaddpd         , VexRvm_Lx          , V(660F00,7C,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5381, 250, 118, 21),</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :   INST(Vhaddps         , VexRvm_Lx          , V(F20F00,7C,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5389, 250, 118, 21),</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   INST(Vhsubpd         , VexRvm_Lx          , V(660F00,7D,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5397, 250, 118, 22),</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :   INST(Vhsubps         , VexRvm_Lx          , V(F20F00,7D,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5405, 250, 118, 22),</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :   INST(Vinsertf128     , VexRvmi            , V(660F3A,18,_,1,0,_,_,_  ), 0                         , 0 , 0 , 5413, 349, 118, 0 ),</a>
+<a name="1163"><span class="lineNum">    1163 </span>            :   INST(Vinsertf32x4    , VexRvmi_Lx         , V(660F3A,18,_,x,_,0,4,T4 ), 0                         , 0 , 0 , 5425, 350, 120, 0 ),</a>
+<a name="1164"><span class="lineNum">    1164 </span>            :   INST(Vinsertf32x8    , VexRvmi            , V(660F3A,1A,_,2,_,0,5,T8 ), 0                         , 0 , 0 , 5438, 351, 63 , 0 ),</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :   INST(Vinsertf64x2    , VexRvmi_Lx         , V(660F3A,18,_,x,_,1,4,T2 ), 0                         , 0 , 0 , 5451, 350, 123, 0 ),</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :   INST(Vinsertf64x4    , VexRvmi            , V(660F3A,1A,_,2,_,1,5,T4 ), 0                         , 0 , 0 , 5464, 351, 65 , 0 ),</a>
+<a name="1167"><span class="lineNum">    1167 </span>            :   INST(Vinserti128     , VexRvmi            , V(660F3A,38,_,1,0,_,_,_  ), 0                         , 0 , 0 , 5477, 349, 124, 0 ),</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :   INST(Vinserti32x4    , VexRvmi_Lx         , V(660F3A,38,_,x,_,0,4,T4 ), 0                         , 0 , 0 , 5489, 350, 120, 0 ),</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :   INST(Vinserti32x8    , VexRvmi            , V(660F3A,3A,_,2,_,0,5,T8 ), 0                         , 0 , 0 , 5502, 351, 63 , 0 ),</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :   INST(Vinserti64x2    , VexRvmi_Lx         , V(660F3A,38,_,x,_,1,4,T2 ), 0                         , 0 , 0 , 5515, 350, 123, 0 ),</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :   INST(Vinserti64x4    , VexRvmi            , V(660F3A,3A,_,2,_,1,5,T4 ), 0                         , 0 , 0 , 5528, 351, 65 , 0 ),</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :   INST(Vinsertps       , VexRvmi            , V(660F3A,21,_,0,I,0,2,T1S), 0                         , 0 , 0 , 5541, 352, 117, 23),</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :   INST(Vlddqu          , VexRm_Lx           , V(F20F00,F0,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5551, 353, 118, 24),</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :   INST(Vldmxcsr        , VexM               , V(000F00,AE,2,0,I,_,_,_  ), 0                         , 0 , 0 , 5558, 354, 118, 0 ),</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :   INST(Vmaskmovdqu     , VexRm_ZDI          , V(660F00,F7,_,0,I,_,_,_  ), 0                         , 0 , 0 , 5567, 355, 118, 25),</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :   INST(Vmaskmovpd      , VexRvmMvr_Lx       , V(660F38,2D,_,x,0,_,_,_  ), V(660F38,2F,_,x,0,_,_,_  ), 0 , 0 , 5579, 356, 118, 0 ),</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :   INST(Vmaskmovps      , VexRvmMvr_Lx       , V(660F38,2C,_,x,0,_,_,_  ), V(660F38,2E,_,x,0,_,_,_  ), 0 , 0 , 5590, 357, 118, 0 ),</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :   INST(Vmaxpd          , VexRvm_Lx          , V(660F00,5F,_,x,I,1,4,FV ), 0                         , 0 , 0 , 5601, 358, 116, 26),</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :   INST(Vmaxps          , VexRvm_Lx          , V(000F00,5F,_,x,I,0,4,FV ), 0                         , 0 , 0 , 5608, 359, 116, 26),</a>
+<a name="1180"><span class="lineNum">    1180 </span>            :   INST(Vmaxsd          , VexRvm             , V(F20F00,5F,_,I,I,1,3,T1S), 0                         , 0 , 0 , 5615, 360, 116, 26),</a>
+<a name="1181"><span class="lineNum">    1181 </span>            :   INST(Vmaxss          , VexRvm             , V(F30F00,5F,_,I,I,0,2,T1S), 0                         , 0 , 0 , 5622, 294, 116, 26),</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :   INST(Vminpd          , VexRvm_Lx          , V(660F00,5D,_,x,I,1,4,FV ), 0                         , 0 , 0 , 5629, 358, 116, 27),</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :   INST(Vminps          , VexRvm_Lx          , V(000F00,5D,_,x,I,0,4,FV ), 0                         , 0 , 0 , 5636, 359, 116, 27),</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :   INST(Vminsd          , VexRvm             , V(F20F00,5D,_,I,I,1,3,T1S), 0                         , 0 , 0 , 5643, 360, 116, 27),</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :   INST(Vminss          , VexRvm             , V(F30F00,5D,_,I,I,0,2,T1S), 0                         , 0 , 0 , 5650, 294, 116, 27),</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   INST(Vmovapd         , VexRmMr_Lx         , V(660F00,28,_,x,I,1,4,FVM), V(660F00,29,_,x,I,1,4,FVM), 0 , 0 , 5657, 361, 116, 28),</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :   INST(Vmovaps         , VexRmMr_Lx         , V(000F00,28,_,x,I,0,4,FVM), V(000F00,29,_,x,I,0,4,FVM), 0 , 0 , 5665, 362, 116, 28),</a>
+<a name="1188"><span class="lineNum">    1188 </span>            :   INST(Vmovd           , VexMovdMovq        , V(660F00,6E,_,0,0,0,2,T1S), V(660F00,7E,_,0,0,0,2,T1S), 0 , 0 , 5673, 363, 117, 29),</a>
+<a name="1189"><span class="lineNum">    1189 </span>            :   INST(Vmovddup        , VexRm_Lx           , V(F20F00,12,_,x,I,1,3,DUP), 0                         , 0 , 0 , 5679, 364, 116, 29),</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :   INST(Vmovdqa         , VexRmMr_Lx         , V(660F00,6F,_,x,I,_,_,_  ), V(660F00,7F,_,x,I,_,_,_  ), 0 , 0 , 5688, 365, 118, 30),</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :   INST(Vmovdqa32       , VexRmMr_Lx         , V(660F00,6F,_,x,_,0,4,FVM), V(660F00,7F,_,x,_,0,4,FVM), 0 , 0 , 5696, 366, 120, 0 ),</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :   INST(Vmovdqa64       , VexRmMr_Lx         , V(660F00,6F,_,x,_,1,4,FVM), V(660F00,7F,_,x,_,1,4,FVM), 0 , 0 , 5706, 367, 120, 0 ),</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :   INST(Vmovdqu         , VexRmMr_Lx         , V(F30F00,6F,_,x,I,_,_,_  ), V(F30F00,7F,_,x,I,_,_,_  ), 0 , 0 , 5716, 368, 118, 28),</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :   INST(Vmovdqu16       , VexRmMr_Lx         , V(F20F00,6F,_,x,_,1,4,FVM), V(F20F00,7F,_,x,_,1,4,FVM), 0 , 0 , 5724, 369, 122, 0 ),</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :   INST(Vmovdqu32       , VexRmMr_Lx         , V(F30F00,6F,_,x,_,0,4,FVM), V(F30F00,7F,_,x,_,0,4,FVM), 0 , 0 , 5734, 370, 120, 0 ),</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :   INST(Vmovdqu64       , VexRmMr_Lx         , V(F30F00,6F,_,x,_,1,4,FVM), V(F30F00,7F,_,x,_,1,4,FVM), 0 , 0 , 5744, 371, 120, 0 ),</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :   INST(Vmovdqu8        , VexRmMr_Lx         , V(F20F00,6F,_,x,_,0,4,FVM), V(F20F00,7F,_,x,_,0,4,FVM), 0 , 0 , 5754, 372, 122, 0 ),</a>
+<a name="1198"><span class="lineNum">    1198 </span>            :   INST(Vmovhlps        , VexRvm             , V(000F00,12,_,0,I,0,_,_  ), 0                         , 0 , 0 , 5763, 373, 117, 31),</a>
+<a name="1199"><span class="lineNum">    1199 </span>            :   INST(Vmovhpd         , VexRvmMr           , V(660F00,16,_,0,I,1,3,T1S), V(660F00,17,_,0,I,1,3,T1S), 0 , 0 , 5772, 374, 117, 32),</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :   INST(Vmovhps         , VexRvmMr           , V(000F00,16,_,0,I,0,3,T2 ), V(000F00,17,_,0,I,0,3,T2 ), 0 , 0 , 5780, 375, 117, 32),</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :   INST(Vmovlhps        , VexRvm             , V(000F00,16,_,0,I,0,_,_  ), 0                         , 0 , 0 , 5788, 373, 117, 31),</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :   INST(Vmovlpd         , VexRvmMr           , V(660F00,12,_,0,I,1,3,T1S), V(660F00,13,_,0,I,1,3,T1S), 0 , 0 , 5797, 376, 117, 32),</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :   INST(Vmovlps         , VexRvmMr           , V(000F00,12,_,0,I,0,3,T2 ), V(000F00,13,_,0,I,0,3,T2 ), 0 , 0 , 5805, 377, 117, 32),</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :   INST(Vmovmskpd       , VexRm_Lx           , V(660F00,50,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5813, 378, 118, 33),</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :   INST(Vmovmskps       , VexRm_Lx           , V(000F00,50,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5823, 378, 118, 33),</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :   INST(Vmovntdq        , VexMr_Lx           , V(660F00,E7,_,x,I,0,4,FVM), 0                         , 0 , 0 , 5833, 379, 116, 33),</a>
+<a name="1207"><span class="lineNum">    1207 </span>            :   INST(Vmovntdqa       , VexRm_Lx           , V(660F38,2A,_,x,I,0,4,FVM), 0                         , 0 , 0 , 5842, 380, 125, 33),</a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   INST(Vmovntpd        , VexMr_Lx           , V(660F00,2B,_,x,I,1,4,FVM), 0                         , 0 , 0 , 5852, 379, 116, 34),</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :   INST(Vmovntps        , VexMr_Lx           , V(000F00,2B,_,x,I,0,4,FVM), 0                         , 0 , 0 , 5861, 379, 116, 34),</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :   INST(Vmovq           , VexMovdMovq        , V(660F00,6E,_,0,I,1,3,T1S), V(660F00,7E,_,0,I,1,3,T1S), 0 , 0 , 5870, 381, 117, 28),</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :   INST(Vmovsd          , VexMovssMovsd      , V(F20F00,10,_,I,I,1,3,T1S), V(F20F00,11,_,I,I,1,3,T1S), 0 , 0 , 5876, 382, 117, 35),</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :   INST(Vmovshdup       , VexRm_Lx           , V(F30F00,16,_,x,I,0,4,FVM), 0                         , 0 , 0 , 5883, 383, 116, 30),</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :   INST(Vmovsldup       , VexRm_Lx           , V(F30F00,12,_,x,I,0,4,FVM), 0                         , 0 , 0 , 5893, 383, 116, 30),</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :   INST(Vmovss          , VexMovssMovsd      , V(F30F00,10,_,I,I,0,2,T1S), V(F30F00,11,_,I,I,0,2,T1S), 0 , 0 , 5903, 384, 117, 35),</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :   INST(Vmovupd         , VexRmMr_Lx         , V(660F00,10,_,x,I,1,4,FVM), V(660F00,11,_,x,I,1,4,FVM), 0 , 0 , 5910, 385, 116, 36),</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :   INST(Vmovups         , VexRmMr_Lx         , V(000F00,10,_,x,I,0,4,FVM), V(000F00,11,_,x,I,0,4,FVM), 0 , 0 , 5918, 386, 116, 36),</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   INST(Vmpsadbw        , VexRvmi_Lx         , V(660F3A,42,_,x,I,_,_,_  ), 0                         , 0 , 0 , 5926, 263, 135, 37),</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   INST(Vmulpd          , VexRvm_Lx          , V(660F00,59,_,x,I,1,4,FV ), 0                         , 0 , 0 , 5935, 246, 116, 38),</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   INST(Vmulps          , VexRvm_Lx          , V(000F00,59,_,x,I,0,4,FV ), 0                         , 0 , 0 , 5942, 247, 116, 38),</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :   INST(Vmulsd          , VexRvm_Lx          , V(F20F00,59,_,I,I,1,3,T1S), 0                         , 0 , 0 , 5949, 248, 117, 38),</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :   INST(Vmulss          , VexRvm_Lx          , V(F30F00,59,_,I,I,0,2,T1S), 0                         , 0 , 0 , 5956, 249, 117, 38),</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   INST(Vorpd           , VexRvm_Lx          , V(660F00,56,_,x,I,1,4,FV ), 0                         , 0 , 0 , 5963, 258, 121, 39),</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   INST(Vorps           , VexRvm_Lx          , V(000F00,56,_,x,I,0,4,FV ), 0                         , 0 , 0 , 5969, 259, 116, 39),</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :   INST(Vp4dpwssd       , VexRm_T1_4X        , V(F20F38,52,_,2,_,0,2,T4X), 0                         , 0 , 0 , 5975, 387, 136, 0 ),</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :   INST(Vp4dpwssds      , VexRm_T1_4X        , V(F20F38,53,_,2,_,0,2,T4X), 0                         , 0 , 0 , 5985, 387, 136, 0 ),</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :   INST(Vpabsb          , VexRm_Lx           , V(660F38,1C,_,x,I,_,4,FVM), 0                         , 0 , 0 , 5996, 383, 137, 40),</a>
+<a name="1227"><span class="lineNum">    1227 </span>            :   INST(Vpabsd          , VexRm_Lx           , V(660F38,1E,_,x,I,0,4,FV ), 0                         , 0 , 0 , 6003, 383, 125, 40),</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :   INST(Vpabsq          , VexRm_Lx           , V(660F38,1F,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6010, 313, 120, 0 ),</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   INST(Vpabsw          , VexRm_Lx           , V(660F38,1D,_,x,I,_,4,FVM), 0                         , 0 , 0 , 6017, 383, 137, 41),</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   INST(Vpackssdw       , VexRvm_Lx          , V(660F00,6B,_,x,I,0,4,FV ), 0                         , 0 , 0 , 6024, 257, 137, 42),</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :   INST(Vpacksswb       , VexRvm_Lx          , V(660F00,63,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6034, 388, 137, 42),</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   INST(Vpackusdw       , VexRvm_Lx          , V(660F38,2B,_,x,I,0,4,FV ), 0                         , 0 , 0 , 6044, 257, 137, 42),</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :   INST(Vpackuswb       , VexRvm_Lx          , V(660F00,67,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6054, 388, 137, 42),</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :   INST(Vpaddb          , VexRvm_Lx          , V(660F00,FC,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6064, 388, 137, 42),</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :   INST(Vpaddd          , VexRvm_Lx          , V(660F00,FE,_,x,I,0,4,FV ), 0                         , 0 , 0 , 6071, 257, 125, 42),</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :   INST(Vpaddq          , VexRvm_Lx          , V(660F00,D4,_,x,I,1,4,FV ), 0                         , 0 , 0 , 6078, 256, 125, 42),</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :   INST(Vpaddsb         , VexRvm_Lx          , V(660F00,EC,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6085, 388, 137, 42),</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :   INST(Vpaddsw         , VexRvm_Lx          , V(660F00,ED,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6093, 388, 137, 42),</a>
+<a name="1239"><span class="lineNum">    1239 </span>            :   INST(Vpaddusb        , VexRvm_Lx          , V(660F00,DC,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6101, 388, 137, 42),</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :   INST(Vpaddusw        , VexRvm_Lx          , V(660F00,DD,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6110, 388, 137, 42),</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :   INST(Vpaddw          , VexRvm_Lx          , V(660F00,FD,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6119, 388, 137, 42),</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :   INST(Vpalignr        , VexRvmi_Lx         , V(660F3A,0F,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6126, 389, 137, 42),</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :   INST(Vpand           , VexRvm_Lx          , V(660F00,DB,_,x,I,_,_,_  ), 0                         , 0 , 0 , 6135, 390, 135, 42),</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :   INST(Vpandd          , VexRvm_Lx          , V(660F00,DB,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6141, 391, 120, 0 ),</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :   INST(Vpandn          , VexRvm_Lx          , V(660F00,DF,_,x,I,_,_,_  ), 0                         , 0 , 0 , 6148, 392, 135, 43),</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :   INST(Vpandnd         , VexRvm_Lx          , V(660F00,DF,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6155, 393, 120, 0 ),</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :   INST(Vpandnq         , VexRvm_Lx          , V(660F00,DF,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6163, 394, 120, 0 ),</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :   INST(Vpandq          , VexRvm_Lx          , V(660F00,DB,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6171, 395, 120, 0 ),</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :   INST(Vpavgb          , VexRvm_Lx          , V(660F00,E0,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6178, 388, 137, 44),</a>
+<a name="1250"><span class="lineNum">    1250 </span>            :   INST(Vpavgw          , VexRvm_Lx          , V(660F00,E3,_,x,I,I,4,FVM), 0                         , 0 , 0 , 6185, 388, 137, 45),</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :   INST(Vpblendd        , VexRvmi_Lx         , V(660F3A,02,_,x,0,_,_,_  ), 0                         , 0 , 0 , 6192, 263, 124, 0 ),</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :   INST(Vpblendvb       , VexRvmr            , V(660F3A,4C,_,x,0,_,_,_  ), 0                         , 0 , 0 , 6201, 264, 135, 46),</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :   INST(Vpblendw        , VexRvmi_Lx         , V(660F3A,0E,_,x,I,_,_,_  ), 0                         , 0 , 0 , 6211, 263, 135, 44),</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   INST(Vpbroadcastb    , VexRm_Lx           , V(660F38,78,_,x,0,0,0,T1S), 0                         , 0 , 0 , 6220, 396, 138, 0 ),</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :   INST(Vpbroadcastd    , VexRm_Lx           , V(660F38,58,_,x,0,0,2,T1S), 0                         , 0 , 0 , 6233, 397, 133, 0 ),</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :   INST(Vpbroadcastmb2d , VexRm_Lx           , V(F30F38,3A,_,x,_,0,_,_  ), 0                         , 0 , 0 , 6246, 398, 139, 0 ),</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :   INST(Vpbroadcastmb2q , VexRm_Lx           , V(F30F38,2A,_,x,_,1,_,_  ), 0                         , 0 , 0 , 6262, 398, 139, 0 ),</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :   INST(Vpbroadcastq    , VexRm_Lx           , V(660F38,59,_,x,0,1,3,T1S), 0                         , 0 , 0 , 6278, 399, 133, 0 ),</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :   INST(Vpbroadcastw    , VexRm_Lx           , V(660F38,79,_,x,0,0,1,T1S), 0                         , 0 , 0 , 6291, 400, 138, 0 ),</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   INST(Vpclmulqdq      , VexRvmi            , V(660F3A,44,_,0,I,_,_,_  ), 0                         , 0 , 0 , 6304, 310, 140, 47),</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :   INST(Vpcmov          , VexRvrmRvmr_Lx     , V(XOP_M8,A2,_,x,x,_,_,_  ), 0                         , 0 , 0 , 6315, 326, 132, 0 ),</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   INST(Vpcmpb          , VexRvmi_Lx         , V(660F3A,3F,_,x,_,0,4,FVM), 0                         , 0 , 0 , 6322, 401, 122, 0 ),</a>
+<a name="1263"><span class="lineNum">    1263 </span>            :   INST(Vpcmpd          , VexRvmi_Lx         , V(660F3A,1F,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6329, 402, 120, 0 ),</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :   INST(Vpcmpeqb        , VexRvm_Lx          , V(660F00,74,_,x,I,I,4,FV ), 0                         , 0 , 0 , 6336, 403, 137, 48),</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :   INST(Vpcmpeqd        , VexRvm_Lx          , V(660F00,76,_,x,I,0,4,FVM), 0                         , 0 , 0 , 6345, 404, 125, 48),</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   INST(Vpcmpeqq        , VexRvm_Lx          , V(660F38,29,_,x,I,1,4,FVM), 0                         , 0 , 0 , 6354, 405, 125, 48),</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :   INST(Vpcmpeqw        , VexRvm_Lx          , V(660F00,75,_,x,I,I,4,FV ), 0                         , 0 , 0 , 6363, 403, 137, 48),</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :   INST(Vpcmpestri      , VexRmi             , V(660F3A,61,_,0,I,_,_,_  ), 0                         , 0 , 0 , 6372, 406, 141, 49),</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :   INST(Vpcmpestrm      , VexRmi             , V(660F3A,60,_,0,I,_,_,_  ), 0                         , 0 , 0 , 6383, 407, 141, 49),</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :   INST(Vpcmpgtb        , VexRvm_Lx          , V(660F00,64,_,x,I,I,4,FV ), 0                         , 0 , 0 , 6394, 403, 137, 48),</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :   INST(Vpcmpgtd        , VexRvm_Lx          , V(660F00,66,_,x,I,0,4,FVM), 0                         , 0 , 0 , 6403, 404, 125, 48),</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :   INST(Vpcmpgtq        , VexRvm_Lx          , V(660F38,37,_,x,I,1,4,FVM), 0                         , 0 , 0 , 6412, 405, 125, 48),</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   INST(Vpcmpgtw        , VexRvm_Lx          , V(660F00,65,_,x,I,I,4,FV ), 0                         , 0 , 0 , 6421, 403, 137, 48),</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :   INST(Vpcmpistri      , VexRmi             , V(660F3A,63,_,0,I,_,_,_  ), 0                         , 0 , 0 , 6430, 408, 141, 49),</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :   INST(Vpcmpistrm      , VexRmi             , V(660F3A,62,_,0,I,_,_,_  ), 0                         , 0 , 0 , 6441, 409, 141, 49),</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :   INST(Vpcmpq          , VexRvmi_Lx         , V(660F3A,1F,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6452, 410, 120, 0 ),</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :   INST(Vpcmpub         , VexRvmi_Lx         , V(660F3A,3E,_,x,_,0,4,FVM), 0                         , 0 , 0 , 6459, 401, 122, 0 ),</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :   INST(Vpcmpud         , VexRvmi_Lx         , V(660F3A,1E,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6467, 402, 120, 0 ),</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :   INST(Vpcmpuq         , VexRvmi_Lx         , V(660F3A,1E,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6475, 410, 120, 0 ),</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :   INST(Vpcmpuw         , VexRvmi_Lx         , V(660F3A,3E,_,x,_,1,4,FVM), 0                         , 0 , 0 , 6483, 410, 122, 0 ),</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :   INST(Vpcmpw          , VexRvmi_Lx         , V(660F3A,3F,_,x,_,1,4,FVM), 0                         , 0 , 0 , 6491, 410, 122, 0 ),</a>
+<a name="1282"><span class="lineNum">    1282 </span>            :   INST(Vpcomb          , VexRvmi            , V(XOP_M8,CC,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6498, 310, 132, 0 ),</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   INST(Vpcomd          , VexRvmi            , V(XOP_M8,CE,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6505, 310, 132, 0 ),</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :   INST(Vpcompressd     , VexMr_Lx           , V(660F38,8B,_,x,_,0,2,T1S), 0                         , 0 , 0 , 6512, 279, 120, 0 ),</a>
+<a name="1285"><span class="lineNum">    1285 </span>            :   INST(Vpcompressq     , VexMr_Lx           , V(660F38,8B,_,x,_,1,3,T1S), 0                         , 0 , 0 , 6524, 279, 120, 0 ),</a>
+<a name="1286"><span class="lineNum">    1286 </span>            :   INST(Vpcomq          , VexRvmi            , V(XOP_M8,CF,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6536, 310, 132, 0 ),</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :   INST(Vpcomub         , VexRvmi            , V(XOP_M8,EC,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6543, 310, 132, 0 ),</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :   INST(Vpcomud         , VexRvmi            , V(XOP_M8,EE,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6551, 310, 132, 0 ),</a>
+<a name="1289"><span class="lineNum">    1289 </span>            :   INST(Vpcomuq         , VexRvmi            , V(XOP_M8,EF,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6559, 310, 132, 0 ),</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :   INST(Vpcomuw         , VexRvmi            , V(XOP_M8,ED,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6567, 310, 132, 0 ),</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :   INST(Vpcomw          , VexRvmi            , V(XOP_M8,CD,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6575, 310, 132, 0 ),</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :   INST(Vpconflictd     , VexRm_Lx           , V(660F38,C4,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6582, 411, 139, 0 ),</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :   INST(Vpconflictq     , VexRm_Lx           , V(660F38,C4,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6594, 411, 139, 0 ),</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :   INST(Vperm2f128      , VexRvmi            , V(660F3A,06,_,1,0,_,_,_  ), 0                         , 0 , 0 , 6606, 412, 118, 0 ),</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :   INST(Vperm2i128      , VexRvmi            , V(660F3A,46,_,1,0,_,_,_  ), 0                         , 0 , 0 , 6617, 412, 124, 0 ),</a>
+<a name="1296"><span class="lineNum">    1296 </span>            :   INST(Vpermb          , VexRvm_Lx          , V(660F38,8D,_,x,_,0,4,FVM), 0                         , 0 , 0 , 6628, 260, 142, 0 ),</a>
+<a name="1297"><span class="lineNum">    1297 </span>            :   INST(Vpermd          , VexRvm_Lx          , V(660F38,36,_,x,0,0,4,FV ), 0                         , 0 , 0 , 6635, 413, 133, 0 ),</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :   INST(Vpermi2b        , VexRvm_Lx          , V(660F38,75,_,x,_,0,4,FVM), 0                         , 0 , 0 , 6642, 260, 142, 0 ),</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :   INST(Vpermi2d        , VexRvm_Lx          , V(660F38,76,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6651, 414, 120, 0 ),</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :   INST(Vpermi2pd       , VexRvm_Lx          , V(660F38,77,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6660, 262, 120, 0 ),</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :   INST(Vpermi2ps       , VexRvm_Lx          , V(660F38,77,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6670, 261, 120, 0 ),</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :   INST(Vpermi2q        , VexRvm_Lx          , V(660F38,76,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6680, 415, 120, 0 ),</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :   INST(Vpermi2w        , VexRvm_Lx          , V(660F38,75,_,x,_,1,4,FVM), 0                         , 0 , 0 , 6689, 416, 122, 0 ),</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :   INST(Vpermil2pd      , VexRvrmiRvmri_Lx   , V(660F3A,49,_,x,x,_,_,_  ), 0                         , 0 , 0 , 6698, 417, 132, 0 ),</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :   INST(Vpermil2ps      , VexRvrmiRvmri_Lx   , V(660F3A,48,_,x,x,_,_,_  ), 0                         , 0 , 0 , 6709, 417, 132, 0 ),</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :   INST(Vpermilpd       , VexRvmRmi_Lx       , V(660F38,0D,_,x,0,1,4,FV ), V(660F3A,05,_,x,0,1,4,FV ), 0 , 0 , 6720, 418, 116, 0 ),</a>
+<a name="1307"><span class="lineNum">    1307 </span>            :   INST(Vpermilps       , VexRvmRmi_Lx       , V(660F38,0C,_,x,0,0,4,FV ), V(660F3A,04,_,x,0,0,4,FV ), 0 , 0 , 6730, 419, 116, 0 ),</a>
+<a name="1308"><span class="lineNum">    1308 </span>            :   INST(Vpermpd         , VexRmi             , V(660F3A,01,_,1,1,_,_,_  ), 0                         , 0 , 0 , 6740, 420, 124, 0 ),</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :   INST(Vpermps         , VexRvm             , V(660F38,16,_,1,0,_,_,_  ), 0                         , 0 , 0 , 6748, 421, 124, 0 ),</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   INST(Vpermq          , VexRvmRmi_Lx       , V(660F38,36,_,x,_,1,4,FV ), V(660F3A,00,_,x,1,1,4,FV ), 0 , 0 , 6756, 422, 133, 0 ),</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :   INST(Vpermt2b        , VexRvm_Lx          , V(660F38,7D,_,x,_,0,4,FVM), 0                         , 0 , 0 , 6763, 260, 142, 0 ),</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :   INST(Vpermt2d        , VexRvm_Lx          , V(660F38,7E,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6772, 414, 120, 0 ),</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :   INST(Vpermt2pd       , VexRvm_Lx          , V(660F38,7F,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6781, 415, 120, 0 ),</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :   INST(Vpermt2ps       , VexRvm_Lx          , V(660F38,7F,_,x,_,0,4,FV ), 0                         , 0 , 0 , 6791, 414, 120, 0 ),</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :   INST(Vpermt2q        , VexRvm_Lx          , V(660F38,7E,_,x,_,1,4,FV ), 0                         , 0 , 0 , 6801, 415, 120, 0 ),</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :   INST(Vpermt2w        , VexRvm_Lx          , V(660F38,7D,_,x,_,1,4,FVM), 0                         , 0 , 0 , 6810, 416, 122, 0 ),</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :   INST(Vpermw          , VexRvm_Lx          , V(660F38,8D,_,x,_,1,4,FVM), 0                         , 0 , 0 , 6819, 260, 122, 0 ),</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :   INST(Vpexpandd       , VexRm_Lx           , V(660F38,89,_,x,_,0,2,T1S), 0                         , 0 , 0 , 6826, 313, 120, 0 ),</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :   INST(Vpexpandq       , VexRm_Lx           , V(660F38,89,_,x,_,1,3,T1S), 0                         , 0 , 0 , 6836, 313, 120, 0 ),</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :   INST(Vpextrb         , VexMri             , V(660F3A,14,_,0,0,I,0,T1S), 0                         , 0 , 0 , 6846, 423, 143, 50),</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :   INST(Vpextrd         , VexMri             , V(660F3A,16,_,0,0,0,2,T1S), 0                         , 0 , 0 , 6854, 317, 144, 50),</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :   INST(Vpextrq         , VexMri             , V(660F3A,16,_,0,1,1,3,T1S), 0                         , 0 , 0 , 6862, 424, 144, 50),</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :   INST(Vpextrw         , VexMri             , V(660F3A,15,_,0,0,I,1,T1S), 0                         , 0 , 0 , 6870, 425, 143, 50),</a>
+<a name="1324"><span class="lineNum">    1324 </span>            :   INST(Vpgatherdd      , VexRmvRm_VM        , V(660F38,90,_,x,0,_,_,_  ), V(660F38,90,_,x,_,0,2,T1S), 0 , 0 , 6878, 426, 133, 0 ),</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :   INST(Vpgatherdq      , VexRmvRm_VM        , V(660F38,90,_,x,1,_,_,_  ), V(660F38,90,_,x,_,1,3,T1S), 0 , 0 , 6889, 427, 133, 0 ),</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :   INST(Vpgatherqd      , VexRmvRm_VM        , V(660F38,91,_,x,0,_,_,_  ), V(660F38,91,_,x,_,0,2,T1S), 0 , 0 , 6900, 428, 133, 0 ),</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   INST(Vpgatherqq      , VexRmvRm_VM        , V(660F38,91,_,x,1,_,_,_  ), V(660F38,91,_,x,_,1,3,T1S), 0 , 0 , 6911, 429, 133, 0 ),</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :   INST(Vphaddbd        , VexRm              , V(XOP_M9,C2,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6922, 252, 132, 0 ),</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :   INST(Vphaddbq        , VexRm              , V(XOP_M9,C3,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6931, 252, 132, 0 ),</a>
+<a name="1330"><span class="lineNum">    1330 </span>            :   INST(Vphaddbw        , VexRm              , V(XOP_M9,C1,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6940, 252, 132, 0 ),</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :   INST(Vphaddd         , VexRvm_Lx          , V(660F38,02,_,x,I,_,_,_  ), 0                         , 0 , 0 , 6949, 250, 135, 51),</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   INST(Vphadddq        , VexRm              , V(XOP_M9,CB,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6957, 252, 132, 0 ),</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :   INST(Vphaddsw        , VexRvm_Lx          , V(660F38,03,_,x,I,_,_,_  ), 0                         , 0 , 0 , 6966, 250, 135, 52),</a>
+<a name="1334"><span class="lineNum">    1334 </span>            :   INST(Vphaddubd       , VexRm              , V(XOP_M9,D2,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6975, 252, 132, 0 ),</a>
+<a name="1335"><span class="lineNum">    1335 </span>            :   INST(Vphaddubq       , VexRm              , V(XOP_M9,D3,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6985, 252, 132, 0 ),</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :   INST(Vphaddubw       , VexRm              , V(XOP_M9,D1,_,0,0,_,_,_  ), 0                         , 0 , 0 , 6995, 252, 132, 0 ),</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   INST(Vphaddudq       , VexRm              , V(XOP_M9,DB,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7005, 252, 132, 0 ),</a>
+<a name="1338"><span class="lineNum">    1338 </span>            :   INST(Vphadduwd       , VexRm              , V(XOP_M9,D6,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7015, 252, 132, 0 ),</a>
+<a name="1339"><span class="lineNum">    1339 </span>            :   INST(Vphadduwq       , VexRm              , V(XOP_M9,D7,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7025, 252, 132, 0 ),</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :   INST(Vphaddw         , VexRvm_Lx          , V(660F38,01,_,x,I,_,_,_  ), 0                         , 0 , 0 , 7035, 250, 135, 53),</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :   INST(Vphaddwd        , VexRm              , V(XOP_M9,C6,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7043, 252, 132, 0 ),</a>
+<a name="1342"><span class="lineNum">    1342 </span>            :   INST(Vphaddwq        , VexRm              , V(XOP_M9,C7,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7052, 252, 132, 0 ),</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :   INST(Vphminposuw     , VexRm              , V(660F38,41,_,0,I,_,_,_  ), 0                         , 0 , 0 , 7061, 252, 118, 54),</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :   INST(Vphsubbw        , VexRm              , V(XOP_M9,E1,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7073, 252, 132, 0 ),</a>
+<a name="1345"><span class="lineNum">    1345 </span>            :   INST(Vphsubd         , VexRvm_Lx          , V(660F38,06,_,x,I,_,_,_  ), 0                         , 0 , 0 , 7082, 250, 135, 55),</a>
+<a name="1346"><span class="lineNum">    1346 </span>            :   INST(Vphsubdq        , VexRm              , V(XOP_M9,E3,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7090, 252, 132, 0 ),</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :   INST(Vphsubsw        , VexRvm_Lx          , V(660F38,07,_,x,I,_,_,_  ), 0                         , 0 , 0 , 7099, 250, 135, 56),</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :   INST(Vphsubw         , VexRvm_Lx          , V(660F38,05,_,x,I,_,_,_  ), 0                         , 0 , 0 , 7108, 250, 135, 56),</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :   INST(Vphsubwd        , VexRm              , V(XOP_M9,E2,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7116, 252, 132, 0 ),</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :   INST(Vpinsrb         , VexRvmi            , V(660F3A,20,_,0,0,I,0,T1S), 0                         , 0 , 0 , 7125, 430, 143, 57),</a>
+<a name="1351"><span class="lineNum">    1351 </span>            :   INST(Vpinsrd         , VexRvmi            , V(660F3A,22,_,0,0,0,2,T1S), 0                         , 0 , 0 , 7133, 431, 144, 57),</a>
+<a name="1352"><span class="lineNum">    1352 </span>            :   INST(Vpinsrq         , VexRvmi            , V(660F3A,22,_,0,1,1,3,T1S), 0                         , 0 , 0 , 7141, 432, 144, 57),</a>
+<a name="1353"><span class="lineNum">    1353 </span>            :   INST(Vpinsrw         , VexRvmi            , V(660F00,C4,_,0,0,I,1,T1S), 0                         , 0 , 0 , 7149, 433, 143, 55),</a>
+<a name="1354"><span class="lineNum">    1354 </span>            :   INST(Vplzcntd        , VexRm_Lx           , V(660F38,44,_,x,_,0,4,FV ), 0                         , 0 , 0 , 7157, 411, 139, 0 ),</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :   INST(Vplzcntq        , VexRm_Lx           , V(660F38,44,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7166, 434, 139, 0 ),</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :   INST(Vpmacsdd        , VexRvmr            , V(XOP_M8,9E,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7175, 435, 132, 0 ),</a>
+<a name="1357"><span class="lineNum">    1357 </span>            :   INST(Vpmacsdqh       , VexRvmr            , V(XOP_M8,9F,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7184, 435, 132, 0 ),</a>
+<a name="1358"><span class="lineNum">    1358 </span>            :   INST(Vpmacsdql       , VexRvmr            , V(XOP_M8,97,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7194, 435, 132, 0 ),</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :   INST(Vpmacssdd       , VexRvmr            , V(XOP_M8,8E,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7204, 435, 132, 0 ),</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :   INST(Vpmacssdqh      , VexRvmr            , V(XOP_M8,8F,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7214, 435, 132, 0 ),</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :   INST(Vpmacssdql      , VexRvmr            , V(XOP_M8,87,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7225, 435, 132, 0 ),</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :   INST(Vpmacsswd       , VexRvmr            , V(XOP_M8,86,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7236, 435, 132, 0 ),</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :   INST(Vpmacssww       , VexRvmr            , V(XOP_M8,85,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7246, 435, 132, 0 ),</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :   INST(Vpmacswd        , VexRvmr            , V(XOP_M8,96,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7256, 435, 132, 0 ),</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :   INST(Vpmacsww        , VexRvmr            , V(XOP_M8,95,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7265, 435, 132, 0 ),</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :   INST(Vpmadcsswd      , VexRvmr            , V(XOP_M8,A6,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7274, 435, 132, 0 ),</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :   INST(Vpmadcswd       , VexRvmr            , V(XOP_M8,B6,_,0,0,_,_,_  ), 0                         , 0 , 0 , 7285, 435, 132, 0 ),</a>
+<a name="1368"><span class="lineNum">    1368 </span>            :   INST(Vpmadd52huq     , VexRvm_Lx          , V(660F38,B5,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7295, 262, 145, 0 ),</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :   INST(Vpmadd52luq     , VexRvm_Lx          , V(660F38,B4,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7307, 262, 145, 0 ),</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :   INST(Vpmaddubsw      , VexRvm_Lx          , V(660F38,04,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7319, 388, 137, 58),</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :   INST(Vpmaddwd        , VexRvm_Lx          , V(660F00,F5,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7330, 388, 137, 58),</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :   INST(Vpmaskmovd      , VexRvmMvr_Lx       , V(660F38,8C,_,x,0,_,_,_  ), V(660F38,8E,_,x,0,_,_,_  ), 0 , 0 , 7339, 436, 124, 0 ),</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :   INST(Vpmaskmovq      , VexRvmMvr_Lx       , V(660F38,8C,_,x,1,_,_,_  ), V(660F38,8E,_,x,1,_,_,_  ), 0 , 0 , 7350, 437, 124, 0 ),</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :   INST(Vpmaxsb         , VexRvm_Lx          , V(660F38,3C,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7361, 438, 137, 59),</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   INST(Vpmaxsd         , VexRvm_Lx          , V(660F38,3D,_,x,I,0,4,FV ), 0                         , 0 , 0 , 7369, 259, 125, 59),</a>
+<a name="1376"><span class="lineNum">    1376 </span>            :   INST(Vpmaxsq         , VexRvm_Lx          , V(660F38,3D,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7377, 262, 120, 0 ),</a>
+<a name="1377"><span class="lineNum">    1377 </span>            :   INST(Vpmaxsw         , VexRvm_Lx          , V(660F00,EE,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7385, 438, 137, 60),</a>
+<a name="1378"><span class="lineNum">    1378 </span>            :   INST(Vpmaxub         , VexRvm_Lx          , V(660F00,DE,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7393, 438, 137, 60),</a>
+<a name="1379"><span class="lineNum">    1379 </span>            :   INST(Vpmaxud         , VexRvm_Lx          , V(660F38,3F,_,x,I,0,4,FV ), 0                         , 0 , 0 , 7401, 259, 125, 60),</a>
+<a name="1380"><span class="lineNum">    1380 </span>            :   INST(Vpmaxuq         , VexRvm_Lx          , V(660F38,3F,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7409, 262, 120, 0 ),</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :   INST(Vpmaxuw         , VexRvm_Lx          , V(660F38,3E,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7417, 438, 137, 61),</a>
+<a name="1382"><span class="lineNum">    1382 </span>            :   INST(Vpminsb         , VexRvm_Lx          , V(660F38,38,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7425, 438, 137, 61),</a>
+<a name="1383"><span class="lineNum">    1383 </span>            :   INST(Vpminsd         , VexRvm_Lx          , V(660F38,39,_,x,I,0,4,FV ), 0                         , 0 , 0 , 7433, 259, 125, 61),</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :   INST(Vpminsq         , VexRvm_Lx          , V(660F38,39,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7441, 262, 120, 0 ),</a>
+<a name="1385"><span class="lineNum">    1385 </span>            :   INST(Vpminsw         , VexRvm_Lx          , V(660F00,EA,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7449, 438, 137, 62),</a>
+<a name="1386"><span class="lineNum">    1386 </span>            :   INST(Vpminub         , VexRvm_Lx          , V(660F00,DA,_,x,I,_,4,FVM), 0                         , 0 , 0 , 7457, 438, 137, 62),</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :   INST(Vpminud         , VexRvm_Lx          , V(660F38,3B,_,x,I,0,4,FV ), 0                         , 0 , 0 , 7465, 259, 125, 62),</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :   INST(Vpminuq         , VexRvm_Lx          , V(660F38,3B,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7473, 262, 120, 0 ),</a>
+<a name="1389"><span class="lineNum">    1389 </span>            :   INST(Vpminuw         , VexRvm_Lx          , V(660F38,3A,_,x,I,_,4,FVM), 0                         , 0 , 0 , 7481, 438, 137, 63),</a>
+<a name="1390"><span class="lineNum">    1390 </span>            :   INST(Vpmovb2m        , VexRm_Lx           , V(F30F38,29,_,x,_,0,_,_  ), 0                         , 0 , 0 , 7489, 439, 122, 0 ),</a>
+<a name="1391"><span class="lineNum">    1391 </span>            :   INST(Vpmovd2m        , VexRm_Lx           , V(F30F38,39,_,x,_,0,_,_  ), 0                         , 0 , 0 , 7498, 439, 123, 0 ),</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :   INST(Vpmovdb         , VexMr_Lx           , V(F30F38,31,_,x,_,0,2,QVM), 0                         , 0 , 0 , 7507, 440, 120, 0 ),</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :   INST(Vpmovdw         , VexMr_Lx           , V(F30F38,33,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7515, 441, 120, 0 ),</a>
+<a name="1394"><span class="lineNum">    1394 </span>            :   INST(Vpmovm2b        , VexRm_Lx           , V(F30F38,28,_,x,_,0,_,_  ), 0                         , 0 , 0 , 7523, 398, 122, 0 ),</a>
+<a name="1395"><span class="lineNum">    1395 </span>            :   INST(Vpmovm2d        , VexRm_Lx           , V(F30F38,38,_,x,_,0,_,_  ), 0                         , 0 , 0 , 7532, 398, 123, 0 ),</a>
+<a name="1396"><span class="lineNum">    1396 </span>            :   INST(Vpmovm2q        , VexRm_Lx           , V(F30F38,38,_,x,_,1,_,_  ), 0                         , 0 , 0 , 7541, 398, 123, 0 ),</a>
+<a name="1397"><span class="lineNum">    1397 </span>            :   INST(Vpmovm2w        , VexRm_Lx           , V(F30F38,28,_,x,_,1,_,_  ), 0                         , 0 , 0 , 7550, 398, 122, 0 ),</a>
+<a name="1398"><span class="lineNum">    1398 </span>            :   INST(Vpmovmskb       , VexRm_Lx           , V(660F00,D7,_,x,I,_,_,_  ), 0                         , 0 , 0 , 7559, 378, 135, 64),</a>
+<a name="1399"><span class="lineNum">    1399 </span>            :   INST(Vpmovq2m        , VexRm_Lx           , V(F30F38,39,_,x,_,1,_,_  ), 0                         , 0 , 0 , 7569, 439, 123, 0 ),</a>
+<a name="1400"><span class="lineNum">    1400 </span>            :   INST(Vpmovqb         , VexMr_Lx           , V(F30F38,32,_,x,_,0,1,OVM), 0                         , 0 , 0 , 7578, 442, 120, 0 ),</a>
+<a name="1401"><span class="lineNum">    1401 </span>            :   INST(Vpmovqd         , VexMr_Lx           , V(F30F38,35,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7586, 441, 120, 0 ),</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :   INST(Vpmovqw         , VexMr_Lx           , V(F30F38,34,_,x,_,0,2,QVM), 0                         , 0 , 0 , 7594, 440, 120, 0 ),</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :   INST(Vpmovsdb        , VexMr_Lx           , V(F30F38,21,_,x,_,0,2,QVM), 0                         , 0 , 0 , 7602, 440, 120, 0 ),</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :   INST(Vpmovsdw        , VexMr_Lx           , V(F30F38,23,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7611, 441, 120, 0 ),</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :   INST(Vpmovsqb        , VexMr_Lx           , V(F30F38,22,_,x,_,0,1,OVM), 0                         , 0 , 0 , 7620, 442, 120, 0 ),</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :   INST(Vpmovsqd        , VexMr_Lx           , V(F30F38,25,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7629, 441, 120, 0 ),</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :   INST(Vpmovsqw        , VexMr_Lx           , V(F30F38,24,_,x,_,0,2,QVM), 0                         , 0 , 0 , 7638, 440, 120, 0 ),</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :   INST(Vpmovswb        , VexMr_Lx           , V(F30F38,20,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7647, 441, 122, 0 ),</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :   INST(Vpmovsxbd       , VexRm_Lx           , V(660F38,21,_,x,I,I,2,QVM), 0                         , 0 , 0 , 7656, 443, 125, 14),</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :   INST(Vpmovsxbq       , VexRm_Lx           , V(660F38,22,_,x,I,I,1,OVM), 0                         , 0 , 0 , 7666, 444, 125, 14),</a>
+<a name="1411"><span class="lineNum">    1411 </span>            :   INST(Vpmovsxbw       , VexRm_Lx           , V(660F38,20,_,x,I,I,3,HVM), 0                         , 0 , 0 , 7676, 445, 137, 14),</a>
+<a name="1412"><span class="lineNum">    1412 </span>            :   INST(Vpmovsxdq       , VexRm_Lx           , V(660F38,25,_,x,I,0,3,HVM), 0                         , 0 , 0 , 7686, 446, 125, 14),</a>
+<a name="1413"><span class="lineNum">    1413 </span>            :   INST(Vpmovsxwd       , VexRm_Lx           , V(660F38,23,_,x,I,I,3,HVM), 0                         , 0 , 0 , 7696, 445, 125, 14),</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :   INST(Vpmovsxwq       , VexRm_Lx           , V(660F38,24,_,x,I,I,2,QVM), 0                         , 0 , 0 , 7706, 443, 125, 14),</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :   INST(Vpmovusdb       , VexMr_Lx           , V(F30F38,11,_,x,_,0,2,QVM), 0                         , 0 , 0 , 7716, 440, 120, 0 ),</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :   INST(Vpmovusdw       , VexMr_Lx           , V(F30F38,13,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7726, 441, 120, 0 ),</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :   INST(Vpmovusqb       , VexMr_Lx           , V(F30F38,12,_,x,_,0,1,OVM), 0                         , 0 , 0 , 7736, 442, 120, 0 ),</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :   INST(Vpmovusqd       , VexMr_Lx           , V(F30F38,15,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7746, 441, 120, 0 ),</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :   INST(Vpmovusqw       , VexMr_Lx           , V(F30F38,14,_,x,_,0,2,QVM), 0                         , 0 , 0 , 7756, 440, 120, 0 ),</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :   INST(Vpmovuswb       , VexMr_Lx           , V(F30F38,10,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7766, 441, 122, 0 ),</a>
+<a name="1421"><span class="lineNum">    1421 </span>            :   INST(Vpmovw2m        , VexRm_Lx           , V(F30F38,29,_,x,_,1,_,_  ), 0                         , 0 , 0 , 7776, 439, 122, 0 ),</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :   INST(Vpmovwb         , VexMr_Lx           , V(F30F38,30,_,x,_,0,3,HVM), 0                         , 0 , 0 , 7785, 441, 122, 0 ),</a>
+<a name="1423"><span class="lineNum">    1423 </span>            :   INST(Vpmovzxbd       , VexRm_Lx           , V(660F38,31,_,x,I,I,2,QVM), 0                         , 0 , 0 , 7793, 443, 125, 65),</a>
+<a name="1424"><span class="lineNum">    1424 </span>            :   INST(Vpmovzxbq       , VexRm_Lx           , V(660F38,32,_,x,I,I,1,OVM), 0                         , 0 , 0 , 7803, 444, 125, 65),</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :   INST(Vpmovzxbw       , VexRm_Lx           , V(660F38,30,_,x,I,I,3,HVM), 0                         , 0 , 0 , 7813, 445, 137, 65),</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :   INST(Vpmovzxdq       , VexRm_Lx           , V(660F38,35,_,x,I,0,3,HVM), 0                         , 0 , 0 , 7823, 446, 125, 65),</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :   INST(Vpmovzxwd       , VexRm_Lx           , V(660F38,33,_,x,I,I,3,HVM), 0                         , 0 , 0 , 7833, 445, 125, 65),</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :   INST(Vpmovzxwq       , VexRm_Lx           , V(660F38,34,_,x,I,I,2,QVM), 0                         , 0 , 0 , 7843, 443, 125, 65),</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :   INST(Vpmuldq         , VexRvm_Lx          , V(660F38,28,_,x,I,1,4,FV ), 0                         , 0 , 0 , 7853, 256, 125, 19),</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :   INST(Vpmulhrsw       , VexRvm_Lx          , V(660F38,0B,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7861, 388, 137, 19),</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :   INST(Vpmulhuw        , VexRvm_Lx          , V(660F00,E4,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7871, 388, 137, 66),</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :   INST(Vpmulhw         , VexRvm_Lx          , V(660F00,E5,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7880, 388, 137, 66),</a>
+<a name="1433"><span class="lineNum">    1433 </span>            :   INST(Vpmulld         , VexRvm_Lx          , V(660F38,40,_,x,I,0,4,FV ), 0                         , 0 , 0 , 7888, 257, 125, 66),</a>
+<a name="1434"><span class="lineNum">    1434 </span>            :   INST(Vpmullq         , VexRvm_Lx          , V(660F38,40,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7896, 262, 123, 0 ),</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :   INST(Vpmullw         , VexRvm_Lx          , V(660F00,D5,_,x,I,I,4,FVM), 0                         , 0 , 0 , 7904, 388, 137, 19),</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :   INST(Vpmultishiftqb  , VexRvm_Lx          , V(660F38,83,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7912, 262, 142, 0 ),</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :   INST(Vpmuludq        , VexRvm_Lx          , V(660F00,F4,_,x,I,1,4,FV ), 0                         , 0 , 0 , 7927, 256, 125, 67),</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :   INST(Vpopcntd        , VexRm              , V(660F38,55,_,2,_,0,4,FVM), 0                         , 0 , 0 , 7936, 447, 146, 0 ),</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :   INST(Vpopcntq        , VexRm              , V(660F38,55,_,2,_,1,4,FVM), 0                         , 0 , 0 , 7945, 448, 146, 0 ),</a>
+<a name="1440"><span class="lineNum">    1440 </span>            :   INST(Vpor            , VexRvm_Lx          , V(660F00,EB,_,x,I,_,_,_  ), 0                         , 0 , 0 , 7954, 390, 135, 68),</a>
+<a name="1441"><span class="lineNum">    1441 </span>            :   INST(Vpord           , VexRvm_Lx          , V(660F00,EB,_,x,_,0,4,FV ), 0                         , 0 , 0 , 7959, 391, 120, 0 ),</a>
+<a name="1442"><span class="lineNum">    1442 </span>            :   INST(Vporq           , VexRvm_Lx          , V(660F00,EB,_,x,_,1,4,FV ), 0                         , 0 , 0 , 7965, 395, 120, 0 ),</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :   INST(Vpperm          , VexRvrmRvmr        , V(XOP_M8,A3,_,0,x,_,_,_  ), 0                         , 0 , 0 , 7971, 449, 132, 0 ),</a>
+<a name="1444"><span class="lineNum">    1444 </span>            :   INST(Vprold          , VexVmi_Lx          , V(660F00,72,1,x,_,0,4,FV ), 0                         , 0 , 0 , 7978, 450, 120, 0 ),</a>
+<a name="1445"><span class="lineNum">    1445 </span>            :   INST(Vprolq          , VexVmi_Lx          , V(660F00,72,1,x,_,1,4,FV ), 0                         , 0 , 0 , 7985, 451, 120, 0 ),</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :   INST(Vprolvd         , VexRvm_Lx          , V(660F38,15,_,x,_,0,4,FV ), 0                         , 0 , 0 , 7992, 261, 120, 0 ),</a>
+<a name="1447"><span class="lineNum">    1447 </span>            :   INST(Vprolvq         , VexRvm_Lx          , V(660F38,15,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8000, 262, 120, 0 ),</a>
+<a name="1448"><span class="lineNum">    1448 </span>            :   INST(Vprord          , VexVmi_Lx          , V(660F00,72,0,x,_,0,4,FV ), 0                         , 0 , 0 , 8008, 450, 120, 0 ),</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :   INST(Vprorq          , VexVmi_Lx          , V(660F00,72,0,x,_,1,4,FV ), 0                         , 0 , 0 , 8015, 451, 120, 0 ),</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :   INST(Vprorvd         , VexRvm_Lx          , V(660F38,14,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8022, 261, 120, 0 ),</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :   INST(Vprorvq         , VexRvm_Lx          , V(660F38,14,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8030, 262, 120, 0 ),</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :   INST(Vprotb          , VexRvmRmvRmi       , V(XOP_M9,90,_,0,x,_,_,_  ), V(XOP_M8,C0,_,0,x,_,_,_  ), 0 , 0 , 8038, 452, 132, 0 ),</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :   INST(Vprotd          , VexRvmRmvRmi       , V(XOP_M9,92,_,0,x,_,_,_  ), V(XOP_M8,C2,_,0,x,_,_,_  ), 0 , 0 , 8045, 453, 132, 0 ),</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :   INST(Vprotq          , VexRvmRmvRmi       , V(XOP_M9,93,_,0,x,_,_,_  ), V(XOP_M8,C3,_,0,x,_,_,_  ), 0 , 0 , 8052, 454, 132, 0 ),</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :   INST(Vprotw          , VexRvmRmvRmi       , V(XOP_M9,91,_,0,x,_,_,_  ), V(XOP_M8,C1,_,0,x,_,_,_  ), 0 , 0 , 8059, 455, 132, 0 ),</a>
+<a name="1456"><span class="lineNum">    1456 </span>            :   INST(Vpsadbw         , VexRvm_Lx          , V(660F00,F6,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8066, 456, 137, 69),</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :   INST(Vpscatterdd     , VexMr_VM           , V(660F38,A0,_,x,_,0,2,T1S), 0                         , 0 , 0 , 8074, 457, 120, 0 ),</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :   INST(Vpscatterdq     , VexMr_VM           , V(660F38,A0,_,x,_,1,3,T1S), 0                         , 0 , 0 , 8086, 457, 120, 0 ),</a>
+<a name="1459"><span class="lineNum">    1459 </span>            :   INST(Vpscatterqd     , VexMr_VM           , V(660F38,A1,_,x,_,0,2,T1S), 0                         , 0 , 0 , 8098, 458, 120, 0 ),</a>
+<a name="1460"><span class="lineNum">    1460 </span>            :   INST(Vpscatterqq     , VexMr_VM           , V(660F38,A1,_,x,_,1,3,T1S), 0                         , 0 , 0 , 8110, 459, 120, 0 ),</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :   INST(Vpshab          , VexRvmRmv          , V(XOP_M9,98,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8122, 460, 132, 0 ),</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :   INST(Vpshad          , VexRvmRmv          , V(XOP_M9,9A,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8129, 460, 132, 0 ),</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :   INST(Vpshaq          , VexRvmRmv          , V(XOP_M9,9B,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8136, 460, 132, 0 ),</a>
+<a name="1464"><span class="lineNum">    1464 </span>            :   INST(Vpshaw          , VexRvmRmv          , V(XOP_M9,99,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8143, 460, 132, 0 ),</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :   INST(Vpshlb          , VexRvmRmv          , V(XOP_M9,94,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8150, 460, 132, 0 ),</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :   INST(Vpshld          , VexRvmRmv          , V(XOP_M9,96,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8157, 460, 132, 0 ),</a>
+<a name="1467"><span class="lineNum">    1467 </span>            :   INST(Vpshlq          , VexRvmRmv          , V(XOP_M9,97,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8164, 460, 132, 0 ),</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :   INST(Vpshlw          , VexRvmRmv          , V(XOP_M9,95,_,0,x,_,_,_  ), 0                         , 0 , 0 , 8171, 460, 132, 0 ),</a>
+<a name="1469"><span class="lineNum">    1469 </span>            :   INST(Vpshufb         , VexRvm_Lx          , V(660F38,00,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8178, 388, 137, 70),</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :   INST(Vpshufd         , VexRmi_Lx          , V(660F00,70,_,x,I,0,4,FV ), 0                         , 0 , 0 , 8186, 461, 125, 71),</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :   INST(Vpshufhw        , VexRmi_Lx          , V(F30F00,70,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8194, 462, 137, 71),</a>
+<a name="1472"><span class="lineNum">    1472 </span>            :   INST(Vpshuflw        , VexRmi_Lx          , V(F20F00,70,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8203, 462, 137, 71),</a>
+<a name="1473"><span class="lineNum">    1473 </span>            :   INST(Vpsignb         , VexRvm_Lx          , V(660F38,08,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8212, 250, 135, 72),</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :   INST(Vpsignd         , VexRvm_Lx          , V(660F38,0A,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8220, 250, 135, 72),</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :   INST(Vpsignw         , VexRvm_Lx          , V(660F38,09,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8228, 250, 135, 72),</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :   INST(Vpslld          , VexRvmVmi_Lx       , V(660F00,F2,_,x,I,0,4,128), V(660F00,72,6,x,I,0,4,FV ), 0 , 0 , 8236, 463, 125, 72),</a>
+<a name="1477"><span class="lineNum">    1477 </span>            :   INST(Vpslldq         , VexEvexVmi_Lx      , V(660F00,73,7,x,I,I,4,FVM), 0                         , 0 , 0 , 8243, 464, 137, 72),</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :   INST(Vpsllq          , VexRvmVmi_Lx       , V(660F00,F3,_,x,I,1,4,128), V(660F00,73,6,x,I,1,4,FV ), 0 , 0 , 8251, 465, 125, 72),</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :   INST(Vpsllvd         , VexRvm_Lx          , V(660F38,47,_,x,0,0,4,FV ), 0                         , 0 , 0 , 8258, 257, 133, 0 ),</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :   INST(Vpsllvq         , VexRvm_Lx          , V(660F38,47,_,x,1,1,4,FV ), 0                         , 0 , 0 , 8266, 256, 133, 0 ),</a>
+<a name="1481"><span class="lineNum">    1481 </span>            :   INST(Vpsllvw         , VexRvm_Lx          , V(660F38,12,_,x,_,1,4,FVM), 0                         , 0 , 0 , 8274, 260, 122, 0 ),</a>
+<a name="1482"><span class="lineNum">    1482 </span>            :   INST(Vpsllw          , VexRvmVmi_Lx       , V(660F00,F1,_,x,I,I,4,FVM), V(660F00,71,6,x,I,I,4,FVM), 0 , 0 , 8282, 466, 137, 73),</a>
+<a name="1483"><span class="lineNum">    1483 </span>            :   INST(Vpsrad          , VexRvmVmi_Lx       , V(660F00,E2,_,x,I,0,4,128), V(660F00,72,4,x,I,0,4,FV ), 0 , 0 , 8289, 467, 125, 73),</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :   INST(Vpsraq          , VexRvmVmi_Lx       , V(660F00,E2,_,x,_,1,4,128), V(660F00,72,4,x,_,1,4,FV ), 0 , 0 , 8296, 468, 120, 0 ),</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :   INST(Vpsravd         , VexRvm_Lx          , V(660F38,46,_,x,0,0,4,FV ), 0                         , 0 , 0 , 8303, 257, 133, 0 ),</a>
+<a name="1486"><span class="lineNum">    1486 </span>            :   INST(Vpsravq         , VexRvm_Lx          , V(660F38,46,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8311, 262, 120, 0 ),</a>
+<a name="1487"><span class="lineNum">    1487 </span>            :   INST(Vpsravw         , VexRvm_Lx          , V(660F38,11,_,x,_,1,4,FVM), 0                         , 0 , 0 , 8319, 260, 122, 0 ),</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :   INST(Vpsraw          , VexRvmVmi_Lx       , V(660F00,E1,_,x,I,I,4,128), V(660F00,71,4,x,I,I,4,FVM), 0 , 0 , 8327, 469, 137, 74),</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :   INST(Vpsrld          , VexRvmVmi_Lx       , V(660F00,D2,_,x,I,0,4,128), V(660F00,72,2,x,I,0,4,FV ), 0 , 0 , 8334, 470, 125, 74),</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :   INST(Vpsrldq         , VexEvexVmi_Lx      , V(660F00,73,3,x,I,I,4,FVM), 0                         , 0 , 0 , 8341, 464, 137, 74),</a>
+<a name="1491"><span class="lineNum">    1491 </span>            :   INST(Vpsrlq          , VexRvmVmi_Lx       , V(660F00,D3,_,x,I,1,4,128), V(660F00,73,2,x,I,1,4,FV ), 0 , 0 , 8349, 471, 125, 74),</a>
+<a name="1492"><span class="lineNum">    1492 </span>            :   INST(Vpsrlvd         , VexRvm_Lx          , V(660F38,45,_,x,0,0,4,FV ), 0                         , 0 , 0 , 8356, 257, 133, 0 ),</a>
+<a name="1493"><span class="lineNum">    1493 </span>            :   INST(Vpsrlvq         , VexRvm_Lx          , V(660F38,45,_,x,1,1,4,FV ), 0                         , 0 , 0 , 8364, 256, 133, 0 ),</a>
+<a name="1494"><span class="lineNum">    1494 </span>            :   INST(Vpsrlvw         , VexRvm_Lx          , V(660F38,10,_,x,_,1,4,FVM), 0                         , 0 , 0 , 8372, 260, 122, 0 ),</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :   INST(Vpsrlw          , VexRvmVmi_Lx       , V(660F00,D1,_,x,I,I,4,128), V(660F00,71,2,x,I,I,4,FVM), 0 , 0 , 8380, 472, 137, 75),</a>
+<a name="1496"><span class="lineNum">    1496 </span>            :   INST(Vpsubb          , VexRvm_Lx          , V(660F00,F8,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8387, 473, 137, 75),</a>
+<a name="1497"><span class="lineNum">    1497 </span>            :   INST(Vpsubd          , VexRvm_Lx          , V(660F00,FA,_,x,I,0,4,FV ), 0                         , 0 , 0 , 8394, 474, 125, 75),</a>
+<a name="1498"><span class="lineNum">    1498 </span>            :   INST(Vpsubq          , VexRvm_Lx          , V(660F00,FB,_,x,I,1,4,FV ), 0                         , 0 , 0 , 8401, 475, 125, 75),</a>
+<a name="1499"><span class="lineNum">    1499 </span>            :   INST(Vpsubsb         , VexRvm_Lx          , V(660F00,E8,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8408, 473, 137, 75),</a>
+<a name="1500"><span class="lineNum">    1500 </span>            :   INST(Vpsubsw         , VexRvm_Lx          , V(660F00,E9,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8416, 473, 137, 75),</a>
+<a name="1501"><span class="lineNum">    1501 </span>            :   INST(Vpsubusb        , VexRvm_Lx          , V(660F00,D8,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8424, 473, 137, 75),</a>
+<a name="1502"><span class="lineNum">    1502 </span>            :   INST(Vpsubusw        , VexRvm_Lx          , V(660F00,D9,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8433, 473, 137, 75),</a>
+<a name="1503"><span class="lineNum">    1503 </span>            :   INST(Vpsubw          , VexRvm_Lx          , V(660F00,F9,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8442, 473, 137, 75),</a>
+<a name="1504"><span class="lineNum">    1504 </span>            :   INST(Vpternlogd      , VexRvmi_Lx         , V(660F3A,25,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8449, 476, 120, 0 ),</a>
+<a name="1505"><span class="lineNum">    1505 </span>            :   INST(Vpternlogq      , VexRvmi_Lx         , V(660F3A,25,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8460, 477, 120, 0 ),</a>
+<a name="1506"><span class="lineNum">    1506 </span>            :   INST(Vptest          , VexRm_Lx           , V(660F38,17,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8471, 478, 141, 76),</a>
+<a name="1507"><span class="lineNum">    1507 </span>            :   INST(Vptestmb        , VexRvm_Lx          , V(660F38,26,_,x,_,0,4,FVM), 0                         , 0 , 0 , 8478, 479, 122, 0 ),</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :   INST(Vptestmd        , VexRvm_Lx          , V(660F38,27,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8487, 480, 120, 0 ),</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :   INST(Vptestmq        , VexRvm_Lx          , V(660F38,27,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8496, 481, 120, 0 ),</a>
+<a name="1510"><span class="lineNum">    1510 </span>            :   INST(Vptestmw        , VexRvm_Lx          , V(660F38,26,_,x,_,1,4,FVM), 0                         , 0 , 0 , 8505, 479, 122, 0 ),</a>
+<a name="1511"><span class="lineNum">    1511 </span>            :   INST(Vptestnmb       , VexRvm_Lx          , V(F30F38,26,_,x,_,0,4,FVM), 0                         , 0 , 0 , 8514, 479, 122, 0 ),</a>
+<a name="1512"><span class="lineNum">    1512 </span>            :   INST(Vptestnmd       , VexRvm_Lx          , V(F30F38,27,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8524, 480, 120, 0 ),</a>
+<a name="1513"><span class="lineNum">    1513 </span>            :   INST(Vptestnmq       , VexRvm_Lx          , V(F30F38,27,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8534, 481, 120, 0 ),</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :   INST(Vptestnmw       , VexRvm_Lx          , V(F30F38,26,_,x,_,1,4,FVM), 0                         , 0 , 0 , 8544, 479, 122, 0 ),</a>
+<a name="1515"><span class="lineNum">    1515 </span>            :   INST(Vpunpckhbw      , VexRvm_Lx          , V(660F00,68,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8554, 388, 137, 77),</a>
+<a name="1516"><span class="lineNum">    1516 </span>            :   INST(Vpunpckhdq      , VexRvm_Lx          , V(660F00,6A,_,x,I,0,4,FV ), 0                         , 0 , 0 , 8565, 257, 125, 77),</a>
+<a name="1517"><span class="lineNum">    1517 </span>            :   INST(Vpunpckhqdq     , VexRvm_Lx          , V(660F00,6D,_,x,I,1,4,FV ), 0                         , 0 , 0 , 8576, 256, 125, 77),</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :   INST(Vpunpckhwd      , VexRvm_Lx          , V(660F00,69,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8588, 388, 137, 77),</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :   INST(Vpunpcklbw      , VexRvm_Lx          , V(660F00,60,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8599, 388, 137, 77),</a>
+<a name="1520"><span class="lineNum">    1520 </span>            :   INST(Vpunpckldq      , VexRvm_Lx          , V(660F00,62,_,x,I,0,4,FV ), 0                         , 0 , 0 , 8610, 257, 125, 77),</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :   INST(Vpunpcklqdq     , VexRvm_Lx          , V(660F00,6C,_,x,I,1,4,FV ), 0                         , 0 , 0 , 8621, 256, 125, 77),</a>
+<a name="1522"><span class="lineNum">    1522 </span>            :   INST(Vpunpcklwd      , VexRvm_Lx          , V(660F00,61,_,x,I,I,4,FVM), 0                         , 0 , 0 , 8633, 388, 137, 77),</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :   INST(Vpxor           , VexRvm_Lx          , V(660F00,EF,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8644, 392, 135, 78),</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :   INST(Vpxord          , VexRvm_Lx          , V(660F00,EF,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8650, 393, 120, 0 ),</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :   INST(Vpxorq          , VexRvm_Lx          , V(660F00,EF,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8657, 394, 120, 0 ),</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :   INST(Vrangepd        , VexRvmi_Lx         , V(660F3A,50,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8664, 482, 123, 0 ),</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :   INST(Vrangeps        , VexRvmi_Lx         , V(660F3A,50,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8673, 483, 123, 0 ),</a>
+<a name="1528"><span class="lineNum">    1528 </span>            :   INST(Vrangesd        , VexRvmi            , V(660F3A,51,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8682, 484, 63 , 0 ),</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :   INST(Vrangess        , VexRvmi            , V(660F3A,51,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8691, 485, 63 , 0 ),</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :   INST(Vrcp14pd        , VexRm_Lx           , V(660F38,4C,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8700, 434, 120, 0 ),</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :   INST(Vrcp14ps        , VexRm_Lx           , V(660F38,4C,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8709, 411, 120, 0 ),</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :   INST(Vrcp14sd        , VexRvm             , V(660F38,4D,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8718, 486, 65 , 0 ),</a>
+<a name="1533"><span class="lineNum">    1533 </span>            :   INST(Vrcp14ss        , VexRvm             , V(660F38,4D,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8727, 487, 65 , 0 ),</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :   INST(Vrcp28pd        , VexRm              , V(660F38,CA,_,2,_,1,4,FV ), 0                         , 0 , 0 , 8736, 311, 128, 0 ),</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :   INST(Vrcp28ps        , VexRm              , V(660F38,CA,_,2,_,0,4,FV ), 0                         , 0 , 0 , 8745, 312, 128, 0 ),</a>
+<a name="1536"><span class="lineNum">    1536 </span>            :   INST(Vrcp28sd        , VexRvm             , V(660F38,CB,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8754, 488, 128, 0 ),</a>
+<a name="1537"><span class="lineNum">    1537 </span>            :   INST(Vrcp28ss        , VexRvm             , V(660F38,CB,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8763, 489, 128, 0 ),</a>
+<a name="1538"><span class="lineNum">    1538 </span>            :   INST(Vrcpps          , VexRm_Lx           , V(000F00,53,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8772, 333, 118, 79),</a>
+<a name="1539"><span class="lineNum">    1539 </span>            :   INST(Vrcpss          , VexRvm             , V(F30F00,53,_,I,I,_,_,_  ), 0                         , 0 , 0 , 8779, 490, 118, 80),</a>
+<a name="1540"><span class="lineNum">    1540 </span>            :   INST(Vreducepd       , VexRmi_Lx          , V(660F3A,56,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8786, 451, 123, 0 ),</a>
+<a name="1541"><span class="lineNum">    1541 </span>            :   INST(Vreduceps       , VexRmi_Lx          , V(660F3A,56,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8796, 450, 123, 0 ),</a>
+<a name="1542"><span class="lineNum">    1542 </span>            :   INST(Vreducesd       , VexRvmi            , V(660F3A,57,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8806, 491, 63 , 0 ),</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :   INST(Vreducess       , VexRvmi            , V(660F3A,57,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8816, 492, 63 , 0 ),</a>
+<a name="1544"><span class="lineNum">    1544 </span>            :   INST(Vrndscalepd     , VexRmi_Lx          , V(660F3A,09,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8826, 345, 120, 0 ),</a>
+<a name="1545"><span class="lineNum">    1545 </span>            :   INST(Vrndscaleps     , VexRmi_Lx          , V(660F3A,08,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8838, 346, 120, 0 ),</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :   INST(Vrndscalesd     , VexRvmi            , V(660F3A,0B,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8850, 484, 65 , 0 ),</a>
+<a name="1547"><span class="lineNum">    1547 </span>            :   INST(Vrndscaless     , VexRvmi            , V(660F3A,0A,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8862, 485, 65 , 0 ),</a>
+<a name="1548"><span class="lineNum">    1548 </span>            :   INST(Vroundpd        , VexRmi_Lx          , V(660F3A,09,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8874, 493, 118, 81),</a>
+<a name="1549"><span class="lineNum">    1549 </span>            :   INST(Vroundps        , VexRmi_Lx          , V(660F3A,08,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8883, 493, 118, 81),</a>
+<a name="1550"><span class="lineNum">    1550 </span>            :   INST(Vroundsd        , VexRvmi            , V(660F3A,0B,_,I,I,_,_,_  ), 0                         , 0 , 0 , 8892, 494, 118, 82),</a>
+<a name="1551"><span class="lineNum">    1551 </span>            :   INST(Vroundss        , VexRvmi            , V(660F3A,0A,_,I,I,_,_,_  ), 0                         , 0 , 0 , 8901, 495, 118, 82),</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :   INST(Vrsqrt14pd      , VexRm_Lx           , V(660F38,4E,_,x,_,1,4,FV ), 0                         , 0 , 0 , 8910, 434, 120, 0 ),</a>
+<a name="1553"><span class="lineNum">    1553 </span>            :   INST(Vrsqrt14ps      , VexRm_Lx           , V(660F38,4E,_,x,_,0,4,FV ), 0                         , 0 , 0 , 8921, 411, 120, 0 ),</a>
+<a name="1554"><span class="lineNum">    1554 </span>            :   INST(Vrsqrt14sd      , VexRvm             , V(660F38,4F,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8932, 486, 65 , 0 ),</a>
+<a name="1555"><span class="lineNum">    1555 </span>            :   INST(Vrsqrt14ss      , VexRvm             , V(660F38,4F,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8943, 487, 65 , 0 ),</a>
+<a name="1556"><span class="lineNum">    1556 </span>            :   INST(Vrsqrt28pd      , VexRm              , V(660F38,CC,_,2,_,1,4,FV ), 0                         , 0 , 0 , 8954, 311, 128, 0 ),</a>
+<a name="1557"><span class="lineNum">    1557 </span>            :   INST(Vrsqrt28ps      , VexRm              , V(660F38,CC,_,2,_,0,4,FV ), 0                         , 0 , 0 , 8965, 312, 128, 0 ),</a>
+<a name="1558"><span class="lineNum">    1558 </span>            :   INST(Vrsqrt28sd      , VexRvm             , V(660F38,CD,_,I,_,1,3,T1S), 0                         , 0 , 0 , 8976, 488, 128, 0 ),</a>
+<a name="1559"><span class="lineNum">    1559 </span>            :   INST(Vrsqrt28ss      , VexRvm             , V(660F38,CD,_,I,_,0,2,T1S), 0                         , 0 , 0 , 8987, 489, 128, 0 ),</a>
+<a name="1560"><span class="lineNum">    1560 </span>            :   INST(Vrsqrtps        , VexRm_Lx           , V(000F00,52,_,x,I,_,_,_  ), 0                         , 0 , 0 , 8998, 333, 118, 3 ),</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :   INST(Vrsqrtss        , VexRvm             , V(F30F00,52,_,I,I,_,_,_  ), 0                         , 0 , 0 , 9007, 490, 118, 2 ),</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :   INST(Vscalefpd       , VexRvm_Lx          , V(660F38,2C,_,x,_,1,4,FV ), 0                         , 0 , 0 , 9016, 496, 120, 0 ),</a>
+<a name="1563"><span class="lineNum">    1563 </span>            :   INST(Vscalefps       , VexRvm_Lx          , V(660F38,2C,_,x,_,0,4,FV ), 0                         , 0 , 0 , 9026, 497, 120, 0 ),</a>
+<a name="1564"><span class="lineNum">    1564 </span>            :   INST(Vscalefsd       , VexRvm             , V(660F38,2D,_,I,_,1,3,T1S), 0                         , 0 , 0 , 9036, 498, 65 , 0 ),</a>
+<a name="1565"><span class="lineNum">    1565 </span>            :   INST(Vscalefss       , VexRvm             , V(660F38,2D,_,I,_,0,2,T1S), 0                         , 0 , 0 , 9046, 499, 65 , 0 ),</a>
+<a name="1566"><span class="lineNum">    1566 </span>            :   INST(Vscatterdpd     , VexMr_Lx           , V(660F38,A2,_,x,_,1,3,T1S), 0                         , 0 , 0 , 9056, 500, 120, 0 ),</a>
+<a name="1567"><span class="lineNum">    1567 </span>            :   INST(Vscatterdps     , VexMr_Lx           , V(660F38,A2,_,x,_,0,2,T1S), 0                         , 0 , 0 , 9068, 457, 120, 0 ),</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :   INST(Vscatterpf0dpd  , VexM_VM            , V(660F38,C6,5,2,_,1,3,T1S), 0                         , 0 , 0 , 9080, 338, 134, 0 ),</a>
+<a name="1569"><span class="lineNum">    1569 </span>            :   INST(Vscatterpf0dps  , VexM_VM            , V(660F38,C6,5,2,_,0,2,T1S), 0                         , 0 , 0 , 9095, 339, 134, 0 ),</a>
+<a name="1570"><span class="lineNum">    1570 </span>            :   INST(Vscatterpf0qpd  , VexM_VM            , V(660F38,C7,5,2,_,1,3,T1S), 0                         , 0 , 0 , 9110, 340, 134, 0 ),</a>
+<a name="1571"><span class="lineNum">    1571 </span>            :   INST(Vscatterpf0qps  , VexM_VM            , V(660F38,C7,5,2,_,0,2,T1S), 0                         , 0 , 0 , 9125, 340, 134, 0 ),</a>
+<a name="1572"><span class="lineNum">    1572 </span>            :   INST(Vscatterpf1dpd  , VexM_VM            , V(660F38,C6,6,2,_,1,3,T1S), 0                         , 0 , 0 , 9140, 338, 134, 0 ),</a>
+<a name="1573"><span class="lineNum">    1573 </span>            :   INST(Vscatterpf1dps  , VexM_VM            , V(660F38,C6,6,2,_,0,2,T1S), 0                         , 0 , 0 , 9155, 339, 134, 0 ),</a>
+<a name="1574"><span class="lineNum">    1574 </span>            :   INST(Vscatterpf1qpd  , VexM_VM            , V(660F38,C7,6,2,_,1,3,T1S), 0                         , 0 , 0 , 9170, 340, 134, 0 ),</a>
+<a name="1575"><span class="lineNum">    1575 </span>            :   INST(Vscatterpf1qps  , VexM_VM            , V(660F38,C7,6,2,_,0,2,T1S), 0                         , 0 , 0 , 9185, 340, 134, 0 ),</a>
+<a name="1576"><span class="lineNum">    1576 </span>            :   INST(Vscatterqpd     , VexMr_Lx           , V(660F38,A3,_,x,_,1,3,T1S), 0                         , 0 , 0 , 9200, 459, 120, 0 ),</a>
+<a name="1577"><span class="lineNum">    1577 </span>            :   INST(Vscatterqps     , VexMr_Lx           , V(660F38,A3,_,x,_,0,2,T1S), 0                         , 0 , 0 , 9212, 458, 120, 0 ),</a>
+<a name="1578"><span class="lineNum">    1578 </span>            :   INST(Vshuff32x4      , VexRvmi_Lx         , V(660F3A,23,_,x,_,0,4,FV ), 0                         , 0 , 0 , 9224, 501, 120, 0 ),</a>
+<a name="1579"><span class="lineNum">    1579 </span>            :   INST(Vshuff64x2      , VexRvmi_Lx         , V(660F3A,23,_,x,_,1,4,FV ), 0                         , 0 , 0 , 9235, 502, 120, 0 ),</a>
+<a name="1580"><span class="lineNum">    1580 </span>            :   INST(Vshufi32x4      , VexRvmi_Lx         , V(660F3A,43,_,x,_,0,4,FV ), 0                         , 0 , 0 , 9246, 501, 120, 0 ),</a>
+<a name="1581"><span class="lineNum">    1581 </span>            :   INST(Vshufi64x2      , VexRvmi_Lx         , V(660F3A,43,_,x,_,1,4,FV ), 0                         , 0 , 0 , 9257, 502, 120, 0 ),</a>
+<a name="1582"><span class="lineNum">    1582 </span>            :   INST(Vshufpd         , VexRvmi_Lx         , V(660F00,C6,_,x,I,1,4,FV ), 0                         , 0 , 0 , 9268, 503, 116, 83),</a>
+<a name="1583"><span class="lineNum">    1583 </span>            :   INST(Vshufps         , VexRvmi_Lx         , V(000F00,C6,_,x,I,0,4,FV ), 0                         , 0 , 0 , 9276, 504, 116, 83),</a>
+<a name="1584"><span class="lineNum">    1584 </span>            :   INST(Vsqrtpd         , VexRm_Lx           , V(660F00,51,_,x,I,1,4,FV ), 0                         , 0 , 0 , 9284, 505, 116, 84),</a>
+<a name="1585"><span class="lineNum">    1585 </span>            :   INST(Vsqrtps         , VexRm_Lx           , V(000F00,51,_,x,I,0,4,FV ), 0                         , 0 , 0 , 9292, 281, 116, 84),</a>
+<a name="1586"><span class="lineNum">    1586 </span>            :   INST(Vsqrtsd         , VexRvm             , V(F20F00,51,_,I,I,1,3,T1S), 0                         , 0 , 0 , 9300, 248, 117, 85),</a>
+<a name="1587"><span class="lineNum">    1587 </span>            :   INST(Vsqrtss         , VexRvm             , V(F30F00,51,_,I,I,0,2,T1S), 0                         , 0 , 0 , 9308, 249, 117, 85),</a>
+<a name="1588"><span class="lineNum">    1588 </span>            :   INST(Vstmxcsr        , VexM               , V(000F00,AE,3,0,I,_,_,_  ), 0                         , 0 , 0 , 9316, 506, 118, 0 ),</a>
+<a name="1589"><span class="lineNum">    1589 </span>            :   INST(Vsubpd          , VexRvm_Lx          , V(660F00,5C,_,x,I,1,4,FV ), 0                         , 0 , 0 , 9325, 246, 116, 86),</a>
+<a name="1590"><span class="lineNum">    1590 </span>            :   INST(Vsubps          , VexRvm_Lx          , V(000F00,5C,_,x,I,0,4,FV ), 0                         , 0 , 0 , 9332, 247, 116, 86),</a>
+<a name="1591"><span class="lineNum">    1591 </span>            :   INST(Vsubsd          , VexRvm             , V(F20F00,5C,_,I,I,1,3,T1S), 0                         , 0 , 0 , 9339, 248, 117, 86),</a>
+<a name="1592"><span class="lineNum">    1592 </span>            :   INST(Vsubss          , VexRvm             , V(F30F00,5C,_,I,I,0,2,T1S), 0                         , 0 , 0 , 9346, 249, 117, 86),</a>
+<a name="1593"><span class="lineNum">    1593 </span>            :   INST(Vtestpd         , VexRm_Lx           , V(660F38,0F,_,x,0,_,_,_  ), 0                         , 0 , 0 , 9353, 478, 141, 0 ),</a>
+<a name="1594"><span class="lineNum">    1594 </span>            :   INST(Vtestps         , VexRm_Lx           , V(660F38,0E,_,x,0,_,_,_  ), 0                         , 0 , 0 , 9361, 478, 141, 0 ),</a>
+<a name="1595"><span class="lineNum">    1595 </span>            :   INST(Vucomisd        , VexRm              , V(660F00,2E,_,I,I,1,3,T1S), 0                         , 0 , 0 , 9369, 277, 126, 15),</a>
+<a name="1596"><span class="lineNum">    1596 </span>            :   INST(Vucomiss        , VexRm              , V(000F00,2E,_,I,I,0,2,T1S), 0                         , 0 , 0 , 9378, 278, 126, 15),</a>
+<a name="1597"><span class="lineNum">    1597 </span>            :   INST(Vunpckhpd       , VexRvm_Lx          , V(660F00,15,_,x,I,1,4,FV ), 0                         , 0 , 0 , 9387, 256, 116, 13),</a>
+<a name="1598"><span class="lineNum">    1598 </span>            :   INST(Vunpckhps       , VexRvm_Lx          , V(000F00,15,_,x,I,0,4,FV ), 0                         , 0 , 0 , 9397, 257, 116, 13),</a>
+<a name="1599"><span class="lineNum">    1599 </span>            :   INST(Vunpcklpd       , VexRvm_Lx          , V(660F00,14,_,x,I,1,4,FV ), 0                         , 0 , 0 , 9407, 256, 116, 13),</a>
+<a name="1600"><span class="lineNum">    1600 </span>            :   INST(Vunpcklps       , VexRvm_Lx          , V(000F00,14,_,x,I,0,4,FV ), 0                         , 0 , 0 , 9417, 257, 116, 13),</a>
+<a name="1601"><span class="lineNum">    1601 </span>            :   INST(Vxorpd          , VexRvm_Lx          , V(660F00,57,_,x,I,1,4,FV ), 0                         , 0 , 0 , 9427, 475, 121, 87),</a>
+<a name="1602"><span class="lineNum">    1602 </span>            :   INST(Vxorps          , VexRvm_Lx          , V(000F00,57,_,x,I,0,4,FV ), 0                         , 0 , 0 , 9434, 474, 121, 87),</a>
+<a name="1603"><span class="lineNum">    1603 </span>            :   INST(Vzeroall        , VexOp              , V(000F00,77,_,1,I,_,_,_  ), 0                         , 0 , 0 , 9441, 507, 118, 0 ),</a>
+<a name="1604"><span class="lineNum">    1604 </span>            :   INST(Vzeroupper      , VexOp              , V(000F00,77,_,0,I,_,_,_  ), 0                         , 0 , 0 , 9450, 507, 118, 0 ),</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :   INST(Wbinvd          , X86Op              , O(000F00,09,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9461, 34 , 23 , 0 ),</a>
+<a name="1606"><span class="lineNum">    1606 </span>            :   INST(Wrfsbase        , X86M               , O(F30F00,AE,2,_,x,_,_,_  ), 0                         , 0 , 0 , 9468, 508, 98 , 0 ),</a>
+<a name="1607"><span class="lineNum">    1607 </span>            :   INST(Wrgsbase        , X86M               , O(F30F00,AE,3,_,x,_,_,_  ), 0                         , 0 , 0 , 9477, 508, 98 , 0 ),</a>
+<a name="1608"><span class="lineNum">    1608 </span>            :   INST(Wrmsr           , X86Op              , O(000F00,30,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9486, 509, 147, 0 ),</a>
+<a name="1609"><span class="lineNum">    1609 </span>            :   INST(Xabort          , X86Op_O_I8         , O(000000,C6,7,_,_,_,_,_  ), 0                         , 0 , 0 , 9492, 98 , 148, 0 ),</a>
+<a name="1610"><span class="lineNum">    1610 </span>            :   INST(Xadd            , X86Xadd            , O(000F00,C0,_,_,x,_,_,_  ), 0                         , 0 , 0 , 9499, 510, 36 , 0 ),</a>
+<a name="1611"><span class="lineNum">    1611 </span>            :   INST(Xbegin          , X86JmpRel          , O(000000,C7,7,_,_,_,_,_  ), 0                         , 0 , 0 , 9504, 511, 148, 0 ),</a>
+<a name="1612"><span class="lineNum">    1612 </span>            :   INST(Xchg            , X86Xchg            , O(000000,86,_,_,x,_,_,_  ), 0                         , 0 , 0 , 434 , 512, 0  , 0 ),</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :   INST(Xend            , X86Op              , O(000F01,D5,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9511, 34 , 148, 0 ),</a>
+<a name="1614"><span class="lineNum">    1614 </span>            :   INST(Xgetbv          , X86Op              , O(000F01,D0,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9516, 227, 149, 0 ),</a>
+<a name="1615"><span class="lineNum">    1615 </span>            :   INST(Xlatb           , X86Op              , O(000000,D7,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9523, 34 , 45 , 0 ),</a>
+<a name="1616"><span class="lineNum">    1616 </span>            :   INST(Xor             , X86Arith           , O(000000,30,6,_,x,_,_,_  ), 0                         , 0 , 0 , 8646, 243, 1  , 0 ),</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :   INST(Xorpd           , ExtRm              , O(660F00,57,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9428, 192, 4  , 87),</a>
+<a name="1618"><span class="lineNum">    1618 </span>            :   INST(Xorps           , ExtRm              , O(000F00,57,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9435, 192, 5  , 87),</a>
+<a name="1619"><span class="lineNum">    1619 </span>            :   INST(Xrstor          , X86M_Only          , O(000F00,AE,5,_,_,_,_,_  ), 0                         , 0 , 0 , 1105, 513, 149, 0 ),</a>
+<a name="1620"><span class="lineNum">    1620 </span>            :   INST(Xrstor64        , X86M_Only          , O(000F00,AE,5,_,1,_,_,_  ), 0                         , 0 , 0 , 1113, 514, 149, 0 ),</a>
+<a name="1621"><span class="lineNum">    1621 </span>            :   INST(Xrstors         , X86M_Only          , O(000F00,C7,3,_,_,_,_,_  ), 0                         , 0 , 0 , 9529, 513, 150, 0 ),</a>
+<a name="1622"><span class="lineNum">    1622 </span>            :   INST(Xrstors64       , X86M_Only          , O(000F00,C7,3,_,1,_,_,_  ), 0                         , 0 , 0 , 9537, 514, 150, 0 ),</a>
+<a name="1623"><span class="lineNum">    1623 </span>            :   INST(Xsave           , X86M_Only          , O(000F00,AE,4,_,_,_,_,_  ), 0                         , 0 , 0 , 1123, 515, 149, 0 ),</a>
+<a name="1624"><span class="lineNum">    1624 </span>            :   INST(Xsave64         , X86M_Only          , O(000F00,AE,4,_,1,_,_,_  ), 0                         , 0 , 0 , 1130, 516, 149, 0 ),</a>
+<a name="1625"><span class="lineNum">    1625 </span>            :   INST(Xsavec          , X86M_Only          , O(000F00,C7,4,_,_,_,_,_  ), 0                         , 0 , 0 , 9547, 515, 151, 0 ),</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :   INST(Xsavec64        , X86M_Only          , O(000F00,C7,4,_,1,_,_,_  ), 0                         , 0 , 0 , 9554, 516, 151, 0 ),</a>
+<a name="1627"><span class="lineNum">    1627 </span>            :   INST(Xsaveopt        , X86M_Only          , O(000F00,AE,6,_,_,_,_,_  ), 0                         , 0 , 0 , 9563, 515, 152, 0 ),</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :   INST(Xsaveopt64      , X86M_Only          , O(000F00,AE,6,_,1,_,_,_  ), 0                         , 0 , 0 , 9572, 516, 152, 0 ),</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :   INST(Xsaves          , X86M_Only          , O(000F00,C7,5,_,_,_,_,_  ), 0                         , 0 , 0 , 9583, 515, 150, 0 ),</a>
+<a name="1630"><span class="lineNum">    1630 </span>            :   INST(Xsaves64        , X86M_Only          , O(000F00,C7,5,_,1,_,_,_  ), 0                         , 0 , 0 , 9590, 516, 150, 0 ),</a>
+<a name="1631"><span class="lineNum">    1631 </span>            :   INST(Xsetbv          , X86Op              , O(000F01,D1,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9599, 509, 153, 0 ),</a>
+<a name="1632"><span class="lineNum">    1632 </span>            :   INST(Xtest           , X86Op              , O(000F01,D6,_,_,_,_,_,_  ), 0                         , 0 , 0 , 9606, 34 , 154, 0 )</a>
+<a name="1633"><span class="lineNum">    1633 </span>            :   // ${instData:End}</a>
+<a name="1634"><span class="lineNum">    1634 </span>            : };</a>
+<a name="1635"><span class="lineNum">    1635 </span>            : #undef NAME_DATA_INDEX</a>
+<a name="1636"><span class="lineNum">    1636 </span>            : #undef INST</a>
+<a name="1637"><span class="lineNum">    1637 </span>            : </a>
+<a name="1638"><span class="lineNum">    1638 </span>            : // ${altOpCodeData:Begin}</a>
+<a name="1639"><span class="lineNum">    1639 </span>            : // ------------------- Automatically generated, do not edit -------------------</a>
+<a name="1640"><span class="lineNum">    1640 </span>            : const uint32_t X86InstDB::altOpCodeData[] = {</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :   0                         , // #0</a>
+<a name="1642"><span class="lineNum">    1642 </span>            :   O(660F00,1B,_,_,_,_,_,_  ), // #1</a>
+<a name="1643"><span class="lineNum">    1643 </span>            :   O(000F00,BA,4,_,x,_,_,_  ), // #2</a>
+<a name="1644"><span class="lineNum">    1644 </span>            :   O(000F00,BA,7,_,x,_,_,_  ), // #3</a>
+<a name="1645"><span class="lineNum">    1645 </span>            :   O(000F00,BA,6,_,x,_,_,_  ), // #4</a>
+<a name="1646"><span class="lineNum">    1646 </span>            :   O(000F00,BA,5,_,x,_,_,_  ), // #5</a>
+<a name="1647"><span class="lineNum">    1647 </span>            :   O(000000,48,_,_,x,_,_,_  ), // #6</a>
+<a name="1648"><span class="lineNum">    1648 </span>            :   O(660F00,78,0,_,_,_,_,_  ), // #7</a>
+<a name="1649"><span class="lineNum">    1649 </span>            :   O_FPU(00,00DF,5)          , // #8</a>
+<a name="1650"><span class="lineNum">    1650 </span>            :   O_FPU(00,00DF,7)          , // #9</a>
+<a name="1651"><span class="lineNum">    1651 </span>            :   O_FPU(00,00DD,1)          , // #10</a>
+<a name="1652"><span class="lineNum">    1652 </span>            :   O_FPU(00,00DB,5)          , // #11</a>
+<a name="1653"><span class="lineNum">    1653 </span>            :   O_FPU(00,DFE0,_)          , // #12</a>
+<a name="1654"><span class="lineNum">    1654 </span>            :   O(000000,DB,7,_,_,_,_,_  ), // #13</a>
+<a name="1655"><span class="lineNum">    1655 </span>            :   O_FPU(9B,DFE0,_)          , // #14</a>
+<a name="1656"><span class="lineNum">    1656 </span>            :   O(000000,E4,_,_,_,_,_,_  ), // #15</a>
+<a name="1657"><span class="lineNum">    1657 </span>            :   O(000000,40,_,_,x,_,_,_  ), // #16</a>
+<a name="1658"><span class="lineNum">    1658 </span>            :   O(F20F00,78,_,_,_,_,_,_  ), // #17</a>
+<a name="1659"><span class="lineNum">    1659 </span>            :   O(000000,77,_,_,_,_,_,_  ), // #18</a>
+<a name="1660"><span class="lineNum">    1660 </span>            :   O(000000,73,_,_,_,_,_,_  ), // #19</a>
+<a name="1661"><span class="lineNum">    1661 </span>            :   O(000000,72,_,_,_,_,_,_  ), // #20</a>
+<a name="1662"><span class="lineNum">    1662 </span>            :   O(000000,76,_,_,_,_,_,_  ), // #21</a>
+<a name="1663"><span class="lineNum">    1663 </span>            :   O(000000,74,_,_,_,_,_,_  ), // #22</a>
+<a name="1664"><span class="lineNum">    1664 </span>            :   O(000000,E3,_,_,_,_,_,_  ), // #23</a>
+<a name="1665"><span class="lineNum">    1665 </span>            :   O(000000,7F,_,_,_,_,_,_  ), // #24</a>
+<a name="1666"><span class="lineNum">    1666 </span>            :   O(000000,7D,_,_,_,_,_,_  ), // #25</a>
+<a name="1667"><span class="lineNum">    1667 </span>            :   O(000000,7C,_,_,_,_,_,_  ), // #26</a>
+<a name="1668"><span class="lineNum">    1668 </span>            :   O(000000,7E,_,_,_,_,_,_  ), // #27</a>
+<a name="1669"><span class="lineNum">    1669 </span>            :   O(000000,EB,_,_,_,_,_,_  ), // #28</a>
+<a name="1670"><span class="lineNum">    1670 </span>            :   O(000000,75,_,_,_,_,_,_  ), // #29</a>
+<a name="1671"><span class="lineNum">    1671 </span>            :   O(000000,71,_,_,_,_,_,_  ), // #30</a>
+<a name="1672"><span class="lineNum">    1672 </span>            :   O(000000,7B,_,_,_,_,_,_  ), // #31</a>
+<a name="1673"><span class="lineNum">    1673 </span>            :   O(000000,79,_,_,_,_,_,_  ), // #32</a>
+<a name="1674"><span class="lineNum">    1674 </span>            :   O(000000,70,_,_,_,_,_,_  ), // #33</a>
+<a name="1675"><span class="lineNum">    1675 </span>            :   O(000000,7A,_,_,_,_,_,_  ), // #34</a>
+<a name="1676"><span class="lineNum">    1676 </span>            :   O(000000,78,_,_,_,_,_,_  ), // #35</a>
+<a name="1677"><span class="lineNum">    1677 </span>            :   V(660F00,92,_,0,0,_,_,_  ), // #36</a>
+<a name="1678"><span class="lineNum">    1678 </span>            :   V(F20F00,92,_,0,0,_,_,_  ), // #37</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :   V(F20F00,92,_,0,1,_,_,_  ), // #38</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :   V(000F00,92,_,0,0,_,_,_  ), // #39</a>
+<a name="1681"><span class="lineNum">    1681 </span>            :   O(000000,E2,_,_,_,_,_,_  ), // #40</a>
+<a name="1682"><span class="lineNum">    1682 </span>            :   O(000000,E1,_,_,_,_,_,_  ), // #41</a>
+<a name="1683"><span class="lineNum">    1683 </span>            :   O(000000,E0,_,_,_,_,_,_  ), // #42</a>
+<a name="1684"><span class="lineNum">    1684 </span>            :   O(660F00,29,_,_,_,_,_,_  ), // #43</a>
+<a name="1685"><span class="lineNum">    1685 </span>            :   O(000F00,29,_,_,_,_,_,_  ), // #44</a>
+<a name="1686"><span class="lineNum">    1686 </span>            :   O(000F38,F1,_,_,x,_,_,_  ), // #45</a>
+<a name="1687"><span class="lineNum">    1687 </span>            :   O(000F00,7E,_,_,_,_,_,_  ), // #46</a>
+<a name="1688"><span class="lineNum">    1688 </span>            :   O(660F00,7F,_,_,_,_,_,_  ), // #47</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :   O(F30F00,7F,_,_,_,_,_,_  ), // #48</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :   O(660F00,17,_,_,_,_,_,_  ), // #49</a>
+<a name="1691"><span class="lineNum">    1691 </span>            :   O(000F00,17,_,_,_,_,_,_  ), // #50</a>
+<a name="1692"><span class="lineNum">    1692 </span>            :   O(660F00,13,_,_,_,_,_,_  ), // #51</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :   O(000F00,13,_,_,_,_,_,_  ), // #52</a>
+<a name="1694"><span class="lineNum">    1694 </span>            :   O(660F00,E7,_,_,_,_,_,_  ), // #53</a>
+<a name="1695"><span class="lineNum">    1695 </span>            :   O(660F00,2B,_,_,_,_,_,_  ), // #54</a>
+<a name="1696"><span class="lineNum">    1696 </span>            :   O(000F00,2B,_,_,_,_,_,_  ), // #55</a>
+<a name="1697"><span class="lineNum">    1697 </span>            :   O(000F00,E7,_,_,_,_,_,_  ), // #56</a>
+<a name="1698"><span class="lineNum">    1698 </span>            :   O(F20F00,2B,_,_,_,_,_,_  ), // #57</a>
+<a name="1699"><span class="lineNum">    1699 </span>            :   O(F30F00,2B,_,_,_,_,_,_  ), // #58</a>
+<a name="1700"><span class="lineNum">    1700 </span>            :   O(000F00,7E,_,_,x,_,_,_  ), // #59</a>
+<a name="1701"><span class="lineNum">    1701 </span>            :   O(F20F00,11,_,_,_,_,_,_  ), // #60</a>
+<a name="1702"><span class="lineNum">    1702 </span>            :   O(F30F00,11,_,_,_,_,_,_  ), // #61</a>
+<a name="1703"><span class="lineNum">    1703 </span>            :   O(660F00,11,_,_,_,_,_,_  ), // #62</a>
+<a name="1704"><span class="lineNum">    1704 </span>            :   O(000F00,11,_,_,_,_,_,_  ), // #63</a>
+<a name="1705"><span class="lineNum">    1705 </span>            :   O(000000,E6,_,_,_,_,_,_  ), // #64</a>
+<a name="1706"><span class="lineNum">    1706 </span>            :   O(000F3A,15,_,_,_,_,_,_  ), // #65</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :   O(000000,58,_,_,_,_,_,_  ), // #66</a>
+<a name="1708"><span class="lineNum">    1708 </span>            :   O(000F00,72,6,_,_,_,_,_  ), // #67</a>
+<a name="1709"><span class="lineNum">    1709 </span>            :   O(660F00,73,7,_,_,_,_,_  ), // #68</a>
+<a name="1710"><span class="lineNum">    1710 </span>            :   O(000F00,73,6,_,_,_,_,_  ), // #69</a>
+<a name="1711"><span class="lineNum">    1711 </span>            :   O(000F00,71,6,_,_,_,_,_  ), // #70</a>
+<a name="1712"><span class="lineNum">    1712 </span>            :   O(000F00,72,4,_,_,_,_,_  ), // #71</a>
+<a name="1713"><span class="lineNum">    1713 </span>            :   O(000F00,71,4,_,_,_,_,_  ), // #72</a>
+<a name="1714"><span class="lineNum">    1714 </span>            :   O(000F00,72,2,_,_,_,_,_  ), // #73</a>
+<a name="1715"><span class="lineNum">    1715 </span>            :   O(660F00,73,3,_,_,_,_,_  ), // #74</a>
+<a name="1716"><span class="lineNum">    1716 </span>            :   O(000F00,73,2,_,_,_,_,_  ), // #75</a>
+<a name="1717"><span class="lineNum">    1717 </span>            :   O(000F00,71,2,_,_,_,_,_  ), // #76</a>
+<a name="1718"><span class="lineNum">    1718 </span>            :   O(000000,50,_,_,_,_,_,_  ), // #77</a>
+<a name="1719"><span class="lineNum">    1719 </span>            :   O(000000,F6,_,_,x,_,_,_  ), // #78</a>
+<a name="1720"><span class="lineNum">    1720 </span>            :   V(660F38,92,_,x,_,1,3,T1S), // #79</a>
+<a name="1721"><span class="lineNum">    1721 </span>            :   V(660F38,92,_,x,_,0,2,T1S), // #80</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :   V(660F38,93,_,x,_,1,3,T1S), // #81</a>
+<a name="1723"><span class="lineNum">    1723 </span>            :   V(660F38,93,_,x,_,0,2,T1S), // #82</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :   V(660F38,2F,_,x,0,_,_,_  ), // #83</a>
+<a name="1725"><span class="lineNum">    1725 </span>            :   V(660F38,2E,_,x,0,_,_,_  ), // #84</a>
+<a name="1726"><span class="lineNum">    1726 </span>            :   V(660F00,29,_,x,I,1,4,FVM), // #85</a>
+<a name="1727"><span class="lineNum">    1727 </span>            :   V(000F00,29,_,x,I,0,4,FVM), // #86</a>
+<a name="1728"><span class="lineNum">    1728 </span>            :   V(660F00,7E,_,0,0,0,2,T1S), // #87</a>
+<a name="1729"><span class="lineNum">    1729 </span>            :   V(660F00,7F,_,x,I,_,_,_  ), // #88</a>
+<a name="1730"><span class="lineNum">    1730 </span>            :   V(660F00,7F,_,x,_,0,4,FVM), // #89</a>
+<a name="1731"><span class="lineNum">    1731 </span>            :   V(660F00,7F,_,x,_,1,4,FVM), // #90</a>
+<a name="1732"><span class="lineNum">    1732 </span>            :   V(F30F00,7F,_,x,I,_,_,_  ), // #91</a>
+<a name="1733"><span class="lineNum">    1733 </span>            :   V(F20F00,7F,_,x,_,1,4,FVM), // #92</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :   V(F30F00,7F,_,x,_,0,4,FVM), // #93</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :   V(F30F00,7F,_,x,_,1,4,FVM), // #94</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :   V(F20F00,7F,_,x,_,0,4,FVM), // #95</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :   V(660F00,17,_,0,I,1,3,T1S), // #96</a>
+<a name="1738"><span class="lineNum">    1738 </span>            :   V(000F00,17,_,0,I,0,3,T2 ), // #97</a>
+<a name="1739"><span class="lineNum">    1739 </span>            :   V(660F00,13,_,0,I,1,3,T1S), // #98</a>
+<a name="1740"><span class="lineNum">    1740 </span>            :   V(000F00,13,_,0,I,0,3,T2 ), // #99</a>
+<a name="1741"><span class="lineNum">    1741 </span>            :   V(660F00,7E,_,0,I,1,3,T1S), // #100</a>
+<a name="1742"><span class="lineNum">    1742 </span>            :   V(F20F00,11,_,I,I,1,3,T1S), // #101</a>
+<a name="1743"><span class="lineNum">    1743 </span>            :   V(F30F00,11,_,I,I,0,2,T1S), // #102</a>
+<a name="1744"><span class="lineNum">    1744 </span>            :   V(660F00,11,_,x,I,1,4,FVM), // #103</a>
+<a name="1745"><span class="lineNum">    1745 </span>            :   V(000F00,11,_,x,I,0,4,FVM), // #104</a>
+<a name="1746"><span class="lineNum">    1746 </span>            :   V(660F3A,05,_,x,0,1,4,FV ), // #105</a>
+<a name="1747"><span class="lineNum">    1747 </span>            :   V(660F3A,04,_,x,0,0,4,FV ), // #106</a>
+<a name="1748"><span class="lineNum">    1748 </span>            :   V(660F3A,00,_,x,1,1,4,FV ), // #107</a>
+<a name="1749"><span class="lineNum">    1749 </span>            :   V(660F38,90,_,x,_,0,2,T1S), // #108</a>
+<a name="1750"><span class="lineNum">    1750 </span>            :   V(660F38,90,_,x,_,1,3,T1S), // #109</a>
+<a name="1751"><span class="lineNum">    1751 </span>            :   V(660F38,91,_,x,_,0,2,T1S), // #110</a>
+<a name="1752"><span class="lineNum">    1752 </span>            :   V(660F38,91,_,x,_,1,3,T1S), // #111</a>
+<a name="1753"><span class="lineNum">    1753 </span>            :   V(660F38,8E,_,x,0,_,_,_  ), // #112</a>
+<a name="1754"><span class="lineNum">    1754 </span>            :   V(660F38,8E,_,x,1,_,_,_  ), // #113</a>
+<a name="1755"><span class="lineNum">    1755 </span>            :   V(XOP_M8,C0,_,0,x,_,_,_  ), // #114</a>
+<a name="1756"><span class="lineNum">    1756 </span>            :   V(XOP_M8,C2,_,0,x,_,_,_  ), // #115</a>
+<a name="1757"><span class="lineNum">    1757 </span>            :   V(XOP_M8,C3,_,0,x,_,_,_  ), // #116</a>
+<a name="1758"><span class="lineNum">    1758 </span>            :   V(XOP_M8,C1,_,0,x,_,_,_  ), // #117</a>
+<a name="1759"><span class="lineNum">    1759 </span>            :   V(660F00,72,6,x,I,0,4,FV ), // #118</a>
+<a name="1760"><span class="lineNum">    1760 </span>            :   V(660F00,73,6,x,I,1,4,FV ), // #119</a>
+<a name="1761"><span class="lineNum">    1761 </span>            :   V(660F00,71,6,x,I,I,4,FVM), // #120</a>
+<a name="1762"><span class="lineNum">    1762 </span>            :   V(660F00,72,4,x,I,0,4,FV ), // #121</a>
+<a name="1763"><span class="lineNum">    1763 </span>            :   V(660F00,72,4,x,_,1,4,FV ), // #122</a>
+<a name="1764"><span class="lineNum">    1764 </span>            :   V(660F00,71,4,x,I,I,4,FVM), // #123</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :   V(660F00,72,2,x,I,0,4,FV ), // #124</a>
+<a name="1766"><span class="lineNum">    1766 </span>            :   V(660F00,73,2,x,I,1,4,FV ), // #125</a>
+<a name="1767"><span class="lineNum">    1767 </span>            :   V(660F00,71,2,x,I,I,4,FVM)  // #126</a>
+<a name="1768"><span class="lineNum">    1768 </span>            : };</a>
+<a name="1769"><span class="lineNum">    1769 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="1770"><span class="lineNum">    1770 </span>            : // ${altOpCodeData:End}</a>
+<a name="1771"><span class="lineNum">    1771 </span>            : </a>
+<a name="1772"><span class="lineNum">    1772 </span>            : #undef O_FPU</a>
+<a name="1773"><span class="lineNum">    1773 </span>            : #undef O</a>
+<a name="1774"><span class="lineNum">    1774 </span>            : #undef V</a>
+<a name="1775"><span class="lineNum">    1775 </span>            : </a>
+<a name="1776"><span class="lineNum">    1776 </span>            : // ${commonData:Begin}</a>
+<a name="1777"><span class="lineNum">    1777 </span>            : // ------------------- Automatically generated, do not edit -------------------</a>
+<a name="1778"><span class="lineNum">    1778 </span>            : #define F(VAL) X86Inst::kFlag##VAL</a>
+<a name="1779"><span class="lineNum">    1779 </span>            : #define JUMP_TYPE(VAL) Inst::kJumpType##VAL</a>
+<a name="1780"><span class="lineNum">    1780 </span>            : #define SINGLE_REG(VAL) X86Inst::kSingleReg##VAL</a>
+<a name="1781"><span class="lineNum">    1781 </span>            : const X86Inst::CommonData X86InstDB::commonData[] = {</a>
+<a name="1782"><span class="lineNum">    1782 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 0  , 0 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #0</a>
+<a name="1783"><span class="lineNum">    1783 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 383, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #1</a>
+<a name="1784"><span class="lineNum">    1784 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 384, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #2</a>
+<a name="1785"><span class="lineNum">    1785 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 0  , 15 , 12, JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #3</a>
+<a name="1786"><span class="lineNum">    1786 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 25 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #4</a>
+<a name="1787"><span class="lineNum">    1787 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 336, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #5</a>
+<a name="1788"><span class="lineNum">    1788 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 385, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #6</a>
+<a name="1789"><span class="lineNum">    1789 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 386, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #7</a>
+<a name="1790"><span class="lineNum">    1790 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 0  , 0  , 87 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #8</a>
+<a name="1791"><span class="lineNum">    1791 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 0  , 0  , 94 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #9</a>
+<a name="1792"><span class="lineNum">    1792 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 0  , 39 , 11, JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #10</a>
+<a name="1793"><span class="lineNum">    1793 </span>            :   { F(UseW)|F(Vex)                                        , 0  , 0  , 0  , 273, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #11</a>
+<a name="1794"><span class="lineNum">    1794 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 336, 1 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #12</a>
+<a name="1795"><span class="lineNum">    1795 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 387, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #13</a>
+<a name="1796"><span class="lineNum">    1796 </span>            :   { F(UseW)|F(Vex)                                        , 0  , 0  , 0  , 275, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #14</a>
+<a name="1797"><span class="lineNum">    1797 </span>            :   { F(UseW)|F(Vex)                                        , 0  , 0  , 0  , 184, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #15</a>
+<a name="1798"><span class="lineNum">    1798 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 338, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #16</a>
+<a name="1799"><span class="lineNum">    1799 </span>            :   { F(UseX)|F(FixedReg)|F(Vec)                            , 0  , 0  , 0  , 388, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #17</a>
+<a name="1800"><span class="lineNum">    1800 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 277, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #18</a>
+<a name="1801"><span class="lineNum">    1801 </span>            :   { F(UseW)|F(Mib)                                        , 0  , 0  , 0  , 389, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #19</a>
+<a name="1802"><span class="lineNum">    1802 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 390, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #20</a>
+<a name="1803"><span class="lineNum">    1803 </span>            :   { F(UseW)                                               , 0  , 0  , 1  , 279, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #21</a>
+<a name="1804"><span class="lineNum">    1804 </span>            :   { F(UseW)|F(Mib)                                        , 0  , 0  , 0  , 391, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #22</a>
+<a name="1805"><span class="lineNum">    1805 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 281, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #23</a>
+<a name="1806"><span class="lineNum">    1806 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 24 , 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #24</a>
+<a name="1807"><span class="lineNum">    1807 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 392, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #25</a>
+<a name="1808"><span class="lineNum">    1808 </span>            :   { F(UseR)                                               , 0  , 0  , 2  , 126, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #26</a>
+<a name="1809"><span class="lineNum">    1809 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 3  , 130, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #27</a>
+<a name="1810"><span class="lineNum">    1810 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 4  , 130, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #28</a>
+<a name="1811"><span class="lineNum">    1811 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 5  , 130, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #29</a>
+<a name="1812"><span class="lineNum">    1812 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 283, 2 , JUMP_TYPE(Call)       , SINGLE_REG(None), 0 }, // #30</a>
+<a name="1813"><span class="lineNum">    1813 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 393, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #31</a>
+<a name="1814"><span class="lineNum">    1814 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 394, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #32</a>
+<a name="1815"><span class="lineNum">    1815 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 395, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #33</a>
+<a name="1816"><span class="lineNum">    1816 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 291, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #34</a>
+<a name="1817"><span class="lineNum">    1817 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 396, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #35</a>
+<a name="1818"><span class="lineNum">    1818 </span>            :   { F(UseR)|F(FixedRM)                                    , 0  , 0  , 0  , 397, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #36</a>
+<a name="1819"><span class="lineNum">    1819 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 27 , 12, JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #37</a>
+<a name="1820"><span class="lineNum">    1820 </span>            :   { F(UseX)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 398, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #38</a>
+<a name="1821"><span class="lineNum">    1821 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 399, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #39</a>
+<a name="1822"><span class="lineNum">    1822 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 400, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #40</a>
+<a name="1823"><span class="lineNum">    1823 </span>            :   { F(UseX)|F(FixedReg)|F(Lock)|F(XAcquire)|F(XRelease)   , 0  , 0  , 0  , 134, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #41</a>
+<a name="1824"><span class="lineNum">    1824 </span>            :   { F(UseX)|F(FixedReg)|F(Lock)|F(XAcquire)|F(XRelease)   , 0  , 0  , 0  , 401, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #42</a>
+<a name="1825"><span class="lineNum">    1825 </span>            :   { F(UseX)|F(FixedReg)|F(Lock)|F(XAcquire)|F(XRelease)   , 0  , 0  , 0  , 402, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #43</a>
+<a name="1826"><span class="lineNum">    1826 </span>            :   { F(UseR)|F(Vec)                                        , 0  , 0  , 0  , 403, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #44</a>
+<a name="1827"><span class="lineNum">    1827 </span>            :   { F(UseR)|F(Vec)                                        , 0  , 0  , 0  , 404, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #45</a>
+<a name="1828"><span class="lineNum">    1828 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 405, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #46</a>
+<a name="1829"><span class="lineNum">    1829 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 406, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #47</a>
+<a name="1830"><span class="lineNum">    1830 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 285, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #48</a>
+<a name="1831"><span class="lineNum">    1831 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 0  , 85 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #49</a>
+<a name="1832"><span class="lineNum">    1832 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 0  , 87 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #50</a>
+<a name="1833"><span class="lineNum">    1833 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 8  , 0  , 407, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #51</a>
+<a name="1834"><span class="lineNum">    1834 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 16 , 0  , 408, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #52</a>
+<a name="1835"><span class="lineNum">    1835 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 8  , 0  , 408, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #53</a>
+<a name="1836"><span class="lineNum">    1836 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 8  , 0  , 409, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #54</a>
+<a name="1837"><span class="lineNum">    1837 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 410, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #55</a>
+<a name="1838"><span class="lineNum">    1838 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 4  , 0  , 85 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #56</a>
+<a name="1839"><span class="lineNum">    1839 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 411, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #57</a>
+<a name="1840"><span class="lineNum">    1840 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 4  , 0  , 411, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #58</a>
+<a name="1841"><span class="lineNum">    1841 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 255, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #59</a>
+<a name="1842"><span class="lineNum">    1842 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 412, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #60</a>
+<a name="1843"><span class="lineNum">    1843 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 413, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #61</a>
+<a name="1844"><span class="lineNum">    1844 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 414, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #62</a>
+<a name="1845"><span class="lineNum">    1845 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 6  , 287, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #63</a>
+<a name="1846"><span class="lineNum">    1846 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 138, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #64</a>
+<a name="1847"><span class="lineNum">    1847 </span>            :   { F(UseR)|F(Mmx)                                        , 0  , 0  , 0  , 291, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #65</a>
+<a name="1848"><span class="lineNum">    1848 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 415, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #66</a>
+<a name="1849"><span class="lineNum">    1849 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 416, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #67</a>
+<a name="1850"><span class="lineNum">    1850 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 7  , 289, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #68</a>
+<a name="1851"><span class="lineNum">    1851 </span>            :   { F(UseA)|F(FixedReg)|F(FpuM32)|F(FpuM64)               , 0  , 0  , 0  , 174, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #69</a>
+<a name="1852"><span class="lineNum">    1852 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 291, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #70</a>
+<a name="1853"><span class="lineNum">    1853 </span>            :   { F(UseR)|F(FpuM80)                                     , 0  , 0  , 0  , 417, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #71</a>
+<a name="1854"><span class="lineNum">    1854 </span>            :   { F(UseW)|F(FpuM80)                                     , 0  , 0  , 0  , 418, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #72</a>
+<a name="1855"><span class="lineNum">    1855 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 292, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #73</a>
+<a name="1856"><span class="lineNum">    1856 </span>            :   { F(UseR)|F(FpuM32)|F(FpuM64)                           , 0  , 0  , 0  , 293, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #74</a>
+<a name="1857"><span class="lineNum">    1857 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 296, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #75</a>
+<a name="1858"><span class="lineNum">    1858 </span>            :   { F(UseR)|F(FpuM16)|F(FpuM32)                           , 0  , 0  , 0  , 419, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #76</a>
+<a name="1859"><span class="lineNum">    1859 </span>            :   { F(UseR)|F(FpuM16)|F(FpuM32)|F(FpuM64)                 , 0  , 0  , 8  , 420, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #77</a>
+<a name="1860"><span class="lineNum">    1860 </span>            :   { F(UseW)|F(FpuM16)|F(FpuM32)                           , 0  , 0  , 0  , 421, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #78</a>
+<a name="1861"><span class="lineNum">    1861 </span>            :   { F(UseW)|F(FpuM16)|F(FpuM32)|F(FpuM64)                 , 0  , 0  , 9  , 422, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #79</a>
+<a name="1862"><span class="lineNum">    1862 </span>            :   { F(UseW)|F(FpuM16)|F(FpuM32)|F(FpuM64)                 , 0  , 0  , 10 , 422, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #80</a>
+<a name="1863"><span class="lineNum">    1863 </span>            :   { F(UseR)|F(FpuM32)|F(FpuM64)|F(FpuM80)                 , 0  , 0  , 11 , 423, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #81</a>
+<a name="1864"><span class="lineNum">    1864 </span>            :   { F(UseR)|F(FpuM16)                                     , 0  , 0  , 0  , 424, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #82</a>
+<a name="1865"><span class="lineNum">    1865 </span>            :   { F(UseX)|F(FixedReg)|F(FpuM32)|F(FpuM64)               , 0  , 0  , 0  , 177, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #83</a>
+<a name="1866"><span class="lineNum">    1866 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 425, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #84</a>
+<a name="1867"><span class="lineNum">    1867 </span>            :   { F(UseW)|F(FpuM16)                                     , 0  , 0  , 0  , 426, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #85</a>
+<a name="1868"><span class="lineNum">    1868 </span>            :   { F(UseW)|F(FixedReg)|F(FpuM16)                         , 0  , 0  , 12 , 427, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #86</a>
+<a name="1869"><span class="lineNum">    1869 </span>            :   { F(UseW)|F(FpuM32)|F(FpuM64)                           , 0  , 0  , 0  , 428, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #87</a>
+<a name="1870"><span class="lineNum">    1870 </span>            :   { F(UseW)|F(FpuM32)|F(FpuM64)|F(FpuM80)                 , 0  , 0  , 13 , 429, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #88</a>
+<a name="1871"><span class="lineNum">    1871 </span>            :   { F(UseW)|F(FixedReg)|F(FpuM16)                         , 0  , 0  , 14 , 427, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #89</a>
+<a name="1872"><span class="lineNum">    1872 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 295, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #90</a>
+<a name="1873"><span class="lineNum">    1873 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 430, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #91</a>
+<a name="1874"><span class="lineNum">    1874 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 431, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #92</a>
+<a name="1875"><span class="lineNum">    1875 </span>            :   { F(UseA)|F(FixedReg)                                   , 0  , 0  , 0  , 50 , 10, JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #93</a>
+<a name="1876"><span class="lineNum">    1876 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 15 , 432, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #94</a>
+<a name="1877"><span class="lineNum">    1877 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 16 , 287, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #95</a>
+<a name="1878"><span class="lineNum">    1878 </span>            :   { F(UseW)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 433, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #96</a>
+<a name="1879"><span class="lineNum">    1879 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 17 , 297, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #97</a>
+<a name="1880"><span class="lineNum">    1880 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 434, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #98</a>
+<a name="1881"><span class="lineNum">    1881 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 435, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #99</a>
+<a name="1882"><span class="lineNum">    1882 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 299, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #100</a>
+<a name="1883"><span class="lineNum">    1883 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 436, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #101</a>
+<a name="1884"><span class="lineNum">    1884 </span>            :   { F(UseR)                                               , 0  , 0  , 18 , 437, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #102</a>
+<a name="1885"><span class="lineNum">    1885 </span>            :   { F(UseR)                                               , 0  , 0  , 19 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #103</a>
+<a name="1886"><span class="lineNum">    1886 </span>            :   { F(UseR)                                               , 0  , 0  , 20 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #104</a>
+<a name="1887"><span class="lineNum">    1887 </span>            :   { F(UseR)                                               , 0  , 0  , 21 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #105</a>
+<a name="1888"><span class="lineNum">    1888 </span>            :   { F(UseR)                                               , 0  , 0  , 20 , 438, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #106</a>
+<a name="1889"><span class="lineNum">    1889 </span>            :   { F(UseR)                                               , 0  , 0  , 22 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #107</a>
+<a name="1890"><span class="lineNum">    1890 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 23 , 301, 2 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #108</a>
+<a name="1891"><span class="lineNum">    1891 </span>            :   { F(UseR)                                               , 0  , 0  , 24 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #109</a>
+<a name="1892"><span class="lineNum">    1892 </span>            :   { F(UseR)                                               , 0  , 0  , 25 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #110</a>
+<a name="1893"><span class="lineNum">    1893 </span>            :   { F(UseR)                                               , 0  , 0  , 26 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #111</a>
+<a name="1894"><span class="lineNum">    1894 </span>            :   { F(UseR)                                               , 0  , 0  , 27 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #112</a>
+<a name="1895"><span class="lineNum">    1895 </span>            :   { F(UseR)                                               , 0  , 0  , 28 , 303, 2 , JUMP_TYPE(Direct)     , SINGLE_REG(None), 0 }, // #113</a>
+<a name="1896"><span class="lineNum">    1896 </span>            :   { F(UseR)                                               , 0  , 0  , 19 , 438, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #114</a>
+<a name="1897"><span class="lineNum">    1897 </span>            :   { F(UseR)                                               , 0  , 0  , 29 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #115</a>
+<a name="1898"><span class="lineNum">    1898 </span>            :   { F(UseR)                                               , 0  , 0  , 30 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #116</a>
+<a name="1899"><span class="lineNum">    1899 </span>            :   { F(UseR)                                               , 0  , 0  , 31 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #117</a>
+<a name="1900"><span class="lineNum">    1900 </span>            :   { F(UseR)                                               , 0  , 0  , 32 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #118</a>
+<a name="1901"><span class="lineNum">    1901 </span>            :   { F(UseR)                                               , 0  , 0  , 33 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #119</a>
+<a name="1902"><span class="lineNum">    1902 </span>            :   { F(UseR)                                               , 0  , 0  , 34 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #120</a>
+<a name="1903"><span class="lineNum">    1903 </span>            :   { F(UseR)                                               , 0  , 0  , 35 , 437, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #121</a>
+<a name="1904"><span class="lineNum">    1904 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 439, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #122</a>
+<a name="1905"><span class="lineNum">    1905 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 36 , 305, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #123</a>
+<a name="1906"><span class="lineNum">    1906 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 37 , 307, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #124</a>
+<a name="1907"><span class="lineNum">    1907 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 38 , 309, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #125</a>
+<a name="1908"><span class="lineNum">    1908 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 39 , 311, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #126</a>
+<a name="1909"><span class="lineNum">    1909 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 440, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #127</a>
+<a name="1910"><span class="lineNum">    1910 </span>            :   { F(UseR)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 441, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #128</a>
+<a name="1911"><span class="lineNum">    1911 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 442, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #129</a>
+<a name="1912"><span class="lineNum">    1912 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 443, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #130</a>
+<a name="1913"><span class="lineNum">    1913 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 313, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #131</a>
+<a name="1914"><span class="lineNum">    1914 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 0  , 228, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #132</a>
+<a name="1915"><span class="lineNum">    1915 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 444, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #133</a>
+<a name="1916"><span class="lineNum">    1916 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 315, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #134</a>
+<a name="1917"><span class="lineNum">    1917 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 445, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #135</a>
+<a name="1918"><span class="lineNum">    1918 </span>            :   { F(UseX)                                               , 0  , 0  , 0  , 180, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #136</a>
+<a name="1919"><span class="lineNum">    1919 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 446, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #137</a>
+<a name="1920"><span class="lineNum">    1920 </span>            :   { F(UseW)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 447, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #138</a>
+<a name="1921"><span class="lineNum">    1921 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 40 , 317, 2 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #139</a>
+<a name="1922"><span class="lineNum">    1922 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 41 , 317, 2 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #140</a>
+<a name="1923"><span class="lineNum">    1923 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 42 , 317, 2 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #141</a>
+<a name="1924"><span class="lineNum">    1924 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 319, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #142</a>
+<a name="1925"><span class="lineNum">    1925 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 183, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #143</a>
+<a name="1926"><span class="lineNum">    1926 </span>            :   { F(UseX)|F(FixedRM)|F(Vec)                             , 0  , 0  , 0  , 448, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #144</a>
+<a name="1927"><span class="lineNum">    1927 </span>            :   { F(UseX)|F(FixedRM)|F(Mmx)                             , 0  , 0  , 0  , 449, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #145</a>
+<a name="1928"><span class="lineNum">    1928 </span>            :   { F(UseR)|F(FixedRM)                                    , 0  , 0  , 0  , 450, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #146</a>
+<a name="1929"><span class="lineNum">    1929 </span>            :   { F(UseW)|F(XRelease)                                   , 0  , 0  , 0  , 0  , 15, JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #147</a>
+<a name="1930"><span class="lineNum">    1930 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 43 , 87 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #148</a>
+<a name="1931"><span class="lineNum">    1931 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 44 , 87 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #149</a>
+<a name="1932"><span class="lineNum">    1932 </span>            :   { F(UseW)                                               , 0  , 0  , 45 , 75 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #150</a>
+<a name="1933"><span class="lineNum">    1933 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 16 , 46 , 321, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #151</a>
+<a name="1934"><span class="lineNum">    1934 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 8  , 0  , 451, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #152</a>
+<a name="1935"><span class="lineNum">    1935 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 47 , 87 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #153</a>
+<a name="1936"><span class="lineNum">    1936 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 48 , 87 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #154</a>
+<a name="1937"><span class="lineNum">    1937 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 452, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #155</a>
+<a name="1938"><span class="lineNum">    1938 </span>            :   { F(UseW)|F(Vec)                                        , 8  , 8  , 49 , 234, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #156</a>
+<a name="1939"><span class="lineNum">    1939 </span>            :   { F(UseW)|F(Vec)                                        , 8  , 8  , 50 , 234, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #157</a>
+<a name="1940"><span class="lineNum">    1940 </span>            :   { F(UseW)|F(Vec)                                        , 8  , 8  , 0  , 452, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #158</a>
+<a name="1941"><span class="lineNum">    1941 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 51 , 234, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #159</a>
+<a name="1942"><span class="lineNum">    1942 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 52 , 234, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #160</a>
+<a name="1943"><span class="lineNum">    1943 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 453, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #161</a>
+<a name="1944"><span class="lineNum">    1944 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 53 , 225, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #162</a>
+<a name="1945"><span class="lineNum">    1945 </span>            :   { F(UseW)                                               , 0  , 8  , 0  , 79 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #163</a>
+<a name="1946"><span class="lineNum">    1946 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 54 , 225, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #164</a>
+<a name="1947"><span class="lineNum">    1947 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 55 , 225, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #165</a>
+<a name="1948"><span class="lineNum">    1948 </span>            :   { F(UseW)|F(Mmx)                                        , 0  , 8  , 56 , 454, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #166</a>
+<a name="1949"><span class="lineNum">    1949 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 57 , 234, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #167</a>
+<a name="1950"><span class="lineNum">    1950 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 4  , 58 , 237, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #168</a>
+<a name="1951"><span class="lineNum">    1951 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 16 , 59 , 81 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #169</a>
+<a name="1952"><span class="lineNum">    1952 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 16 , 0  , 455, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #170</a>
+<a name="1953"><span class="lineNum">    1953 </span>            :   { F(UseX)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 456, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #171</a>
+<a name="1954"><span class="lineNum">    1954 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 60 , 323, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #172</a>
+<a name="1955"><span class="lineNum">    1955 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 4  , 61 , 325, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #173</a>
+<a name="1956"><span class="lineNum">    1956 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 327, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #174</a>
+<a name="1957"><span class="lineNum">    1957 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 457, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #175</a>
+<a name="1958"><span class="lineNum">    1958 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 62 , 87 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #176</a>
+<a name="1959"><span class="lineNum">    1959 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 63 , 87 , 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #177</a>
+<a name="1960"><span class="lineNum">    1960 </span>            :   { F(UseA)|F(FixedReg)                                   , 0  , 0  , 0  , 50 , 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #178</a>
+<a name="1961"><span class="lineNum">    1961 </span>            :   { F(UseW)|F(FixedReg)|F(Vex)                            , 0  , 0  , 0  , 329, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #179</a>
+<a name="1962"><span class="lineNum">    1962 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 0  , 458, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #180</a>
+<a name="1963"><span class="lineNum">    1963 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 0  , 288, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #181</a>
+<a name="1964"><span class="lineNum">    1964 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 331, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #182</a>
+<a name="1965"><span class="lineNum">    1965 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 0  , 15 , 12, JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #183</a>
+<a name="1966"><span class="lineNum">    1966 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 64 , 459, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #184</a>
+<a name="1967"><span class="lineNum">    1967 </span>            :   { F(UseR)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 460, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #185</a>
+<a name="1968"><span class="lineNum">    1968 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 0  , 0  , 333, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #186</a>
+<a name="1969"><span class="lineNum">    1969 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 0  , 335, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #187</a>
+<a name="1970"><span class="lineNum">    1970 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 0  , 337, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #188</a>
+<a name="1971"><span class="lineNum">    1971 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 0  , 335, 2 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #189</a>
+<a name="1972"><span class="lineNum">    1972 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 0  , 335, 2 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #190</a>
+<a name="1973"><span class="lineNum">    1973 </span>            :   { F(UseX)|F(Mmx)                                        , 0  , 0  , 0  , 335, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #191</a>
+<a name="1974"><span class="lineNum">    1974 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 336, 1 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #192</a>
+<a name="1975"><span class="lineNum">    1975 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)                            , 0  , 0  , 0  , 461, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #193</a>
+<a name="1976"><span class="lineNum">    1976 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)                            , 0  , 0  , 0  , 462, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #194</a>
+<a name="1977"><span class="lineNum">    1977 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)                            , 0  , 0  , 0  , 463, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #195</a>
+<a name="1978"><span class="lineNum">    1978 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)                            , 0  , 0  , 0  , 464, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #196</a>
+<a name="1979"><span class="lineNum">    1979 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 465, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #197</a>
+<a name="1980"><span class="lineNum">    1980 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 466, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #198</a>
+<a name="1981"><span class="lineNum">    1981 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 8  , 65 , 339, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #199</a>
+<a name="1982"><span class="lineNum">    1982 </span>            :   { F(UseW)|F(Mmx)                                        , 0  , 8  , 0  , 333, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #200</a>
+<a name="1983"><span class="lineNum">    1983 </span>            :   { F(UseW)|F(Mmx)                                        , 0  , 0  , 0  , 333, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #201</a>
+<a name="1984"><span class="lineNum">    1984 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 467, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #202</a>
+<a name="1985"><span class="lineNum">    1985 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 468, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #203</a>
+<a name="1986"><span class="lineNum">    1986 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 0  , 469, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #204</a>
+<a name="1987"><span class="lineNum">    1987 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 0  , 470, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #205</a>
+<a name="1988"><span class="lineNum">    1988 </span>            :   { F(UseW)|F(Mmx)|F(Vec)                                 , 0  , 8  , 0  , 471, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #206</a>
+<a name="1989"><span class="lineNum">    1989 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 0  , 255, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #207</a>
+<a name="1990"><span class="lineNum">    1990 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 0  , 258, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #208</a>
+<a name="1991"><span class="lineNum">    1991 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 66 , 142, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #209</a>
+<a name="1992"><span class="lineNum">    1992 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 16 , 0  , 94 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #210</a>
+<a name="1993"><span class="lineNum">    1993 </span>            :   { F(UseW)|F(Mmx)                                        , 0  , 8  , 0  , 472, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #211</a>
+<a name="1994"><span class="lineNum">    1994 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 67 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #212</a>
+<a name="1995"><span class="lineNum">    1995 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 68 , 473, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #213</a>
+<a name="1996"><span class="lineNum">    1996 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 69 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #214</a>
+<a name="1997"><span class="lineNum">    1997 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 70 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #215</a>
+<a name="1998"><span class="lineNum">    1998 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 71 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #216</a>
+<a name="1999"><span class="lineNum">    1999 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 72 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #217</a>
+<a name="2000"><span class="lineNum">    2000 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 73 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #218</a>
+<a name="2001"><span class="lineNum">    2001 </span>            :   { F(UseX)|F(Vec)                                        , 0  , 0  , 74 , 473, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #219</a>
+<a name="2002"><span class="lineNum">    2002 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 75 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #220</a>
+<a name="2003"><span class="lineNum">    2003 </span>            :   { F(UseX)|F(Mmx)|F(Vec)                                 , 0  , 0  , 76 , 341, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #221</a>
+<a name="2004"><span class="lineNum">    2004 </span>            :   { F(UseR)|F(Vec)                                        , 0  , 0  , 0  , 379, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #222</a>
+<a name="2005"><span class="lineNum">    2005 </span>            :   { F(UseA)|F(FixedReg)                                   , 0  , 0  , 77 , 146, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #223</a>
+<a name="2006"><span class="lineNum">    2006 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 474, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #224</a>
+<a name="2007"><span class="lineNum">    2007 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 4  , 0  , 255, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #225</a>
+<a name="2008"><span class="lineNum">    2008 </span>            :   { F(UseW)                                               , 0  , 8  , 0  , 475, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #226</a>
+<a name="2009"><span class="lineNum">    2009 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 476, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #227</a>
+<a name="2010"><span class="lineNum">    2010 </span>            :   { F(UseW)                                               , 0  , 8  , 0  , 477, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #228</a>
+<a name="2011"><span class="lineNum">    2011 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 478, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #229</a>
+<a name="2012"><span class="lineNum">    2012 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 479, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #230</a>
+<a name="2013"><span class="lineNum">    2013 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 343, 2 , JUMP_TYPE(Return)     , SINGLE_REG(None), 0 }, // #231</a>
+<a name="2014"><span class="lineNum">    2014 </span>            :   { F(UseW)|F(Vex)                                        , 0  , 0  , 0  , 345, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #232</a>
+<a name="2015"><span class="lineNum">    2015 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 480, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #233</a>
+<a name="2016"><span class="lineNum">    2016 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 4  , 0  , 481, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #234</a>
+<a name="2017"><span class="lineNum">    2017 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 0  , 482, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #235</a>
+<a name="2018"><span class="lineNum">    2018 </span>            :   { F(UseR)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 483, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #236</a>
+<a name="2019"><span class="lineNum">    2019 </span>            :   { F(UseW)                                               , 0  , 1  , 0  , 484, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #237</a>
+<a name="2020"><span class="lineNum">    2020 </span>            :   { F(UseX)|F(FixedReg)                                   , 0  , 0  , 0  , 186, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #238</a>
+<a name="2021"><span class="lineNum">    2021 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 485, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #239</a>
+<a name="2022"><span class="lineNum">    2022 </span>            :   { F(UseW)|F(Vec)                                        , 0  , 8  , 0  , 85 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #240</a>
+<a name="2023"><span class="lineNum">    2023 </span>            :   { F(UseW)                                               , 0  , 0  , 0  , 486, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #241</a>
+<a name="2024"><span class="lineNum">    2024 </span>            :   { F(UseX)|F(FixedRM)|F(Rep)|F(Repnz)                    , 0  , 0  , 0  , 487, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #242</a>
+<a name="2025"><span class="lineNum">    2025 </span>            :   { F(UseX)|F(Lock)|F(XAcquire)|F(XRelease)               , 0  , 0  , 0  , 15 , 12, JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #243</a>
+<a name="2026"><span class="lineNum">    2026 </span>            :   { F(UseR)                                               , 0  , 0  , 78 , 68 , 7 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #244</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512T4X)|F(Avx512KZ)       , 0  , 0  , 0  , 488, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #245</a>
+<a name="2028"><span class="lineNum">    2028 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B64)  , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #246</a>
+<a name="2029"><span class="lineNum">    2029 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B32)  , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #247</a>
+<a name="2030"><span class="lineNum">    2030 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE)      , 0  , 0  , 0  , 489, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #248</a>
+<a name="2031"><span class="lineNum">    2031 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE)      , 0  , 0  , 0  , 490, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #249</a>
+<a name="2032"><span class="lineNum">    2032 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 189, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #250</a>
+<a name="2033"><span class="lineNum">    2033 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 93 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #251</a>
+<a name="2034"><span class="lineNum">    2034 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 87 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #252</a>
+<a name="2035"><span class="lineNum">    2035 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 94 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #253</a>
+<a name="2036"><span class="lineNum">    2036 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #254</a>
+<a name="2037"><span class="lineNum">    2037 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #255</a>
+<a name="2038"><span class="lineNum">    2038 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #256</a>
+<a name="2039"><span class="lineNum">    2039 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #257</a>
+<a name="2040"><span class="lineNum">    2040 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #258</a>
+<a name="2041"><span class="lineNum">    2041 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #259</a>
+<a name="2042"><span class="lineNum">    2042 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #260</a>
+<a name="2043"><span class="lineNum">    2043 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #261</a>
+<a name="2044"><span class="lineNum">    2044 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #262</a>
+<a name="2045"><span class="lineNum">    2045 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 192, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #263</a>
+<a name="2046"><span class="lineNum">    2046 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 347, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #264</a>
+<a name="2047"><span class="lineNum">    2047 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 491, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #265</a>
+<a name="2048"><span class="lineNum">    2048 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 492, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #266</a>
+<a name="2049"><span class="lineNum">    2049 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 493, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #267</a>
+<a name="2050"><span class="lineNum">    2050 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 494, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #268</a>
+<a name="2051"><span class="lineNum">    2051 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 495, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #269</a>
+<a name="2052"><span class="lineNum">    2052 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 260, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #270</a>
+<a name="2053"><span class="lineNum">    2053 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 492, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #271</a>
+<a name="2054"><span class="lineNum">    2054 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 363, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #272</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE_B64)     , 0  , 0  , 0  , 195, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #273</a>
+<a name="2056"><span class="lineNum">    2056 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE_B32)     , 0  , 0  , 0  , 195, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #274</a>
+<a name="2057"><span class="lineNum">    2057 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE)         , 0  , 0  , 0  , 496, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #275</a>
+<a name="2058"><span class="lineNum">    2058 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE)         , 0  , 0  , 0  , 497, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #276</a>
+<a name="2059"><span class="lineNum">    2059 </span>            :   { F(UseR)|F(Vec)|F(Vex)|F(Evex)|F(Avx512SAE)            , 0  , 0  , 0  , 403, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #277</a>
+<a name="2060"><span class="lineNum">    2060 </span>            :   { F(UseR)|F(Vec)|F(Vex)|F(Evex)|F(Avx512SAE)            , 0  , 0  , 0  , 404, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #278</a>
+<a name="2061"><span class="lineNum">    2061 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 198, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #279</a>
+<a name="2062"><span class="lineNum">    2062 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #280</a>
+<a name="2063"><span class="lineNum">    2063 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B32)  , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #281</a>
+<a name="2064"><span class="lineNum">    2064 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B64)  , 0  , 0  , 0  , 349, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #282</a>
+<a name="2065"><span class="lineNum">    2065 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B64)  , 0  , 0  , 0  , 207, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #283</a>
+<a name="2066"><span class="lineNum">    2066 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE_B64)         , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #284</a>
+<a name="2067"><span class="lineNum">    2067 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE_B64)         , 0  , 0  , 0  , 349, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #285</a>
+<a name="2068"><span class="lineNum">    2068 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE)         , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #286</a>
+<a name="2069"><span class="lineNum">    2069 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B32)  , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #287</a>
+<a name="2070"><span class="lineNum">    2070 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE)         , 0  , 0  , 0  , 210, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #288</a>
+<a name="2071"><span class="lineNum">    2071 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE_B32)         , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #289</a>
+<a name="2072"><span class="lineNum">    2072 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE_B32)         , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #290</a>
+<a name="2073"><span class="lineNum">    2073 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512ER_SAE)         , 0  , 0  , 0  , 410, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #291</a>
+<a name="2074"><span class="lineNum">    2074 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512ER_SAE)                , 0  , 0  , 0  , 410, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #292</a>
+<a name="2075"><span class="lineNum">    2075 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512ER_SAE)         , 0  , 0  , 0  , 498, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #293</a>
+<a name="2076"><span class="lineNum">    2076 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE)         , 0  , 0  , 0  , 490, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #294</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512ER_SAE)         , 0  , 0  , 0  , 412, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #295</a>
+<a name="2078"><span class="lineNum">    2078 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512ER_SAE)                , 0  , 0  , 0  , 412, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #296</a>
+<a name="2079"><span class="lineNum">    2079 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE_B64)     , 0  , 0  , 0  , 349, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #297</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B64)            , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #298</a>
+<a name="2081"><span class="lineNum">    2081 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B64)            , 0  , 0  , 0  , 349, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #299</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE_B32)     , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #300</a>
+<a name="2083"><span class="lineNum">    2083 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B32)            , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #301</a>
+<a name="2084"><span class="lineNum">    2084 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B32)            , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #302</a>
+<a name="2085"><span class="lineNum">    2085 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512SAE)            , 0  , 0  , 0  , 410, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #303</a>
+<a name="2086"><span class="lineNum">    2086 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512SAE)                   , 0  , 0  , 0  , 410, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #304</a>
+<a name="2087"><span class="lineNum">    2087 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512SAE)            , 0  , 0  , 0  , 412, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #305</a>
+<a name="2088"><span class="lineNum">    2088 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512SAE)                   , 0  , 0  , 0  , 412, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #306</a>
+<a name="2089"><span class="lineNum">    2089 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #307</a>
+<a name="2090"><span class="lineNum">    2090 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512ER_SAE)                , 0  , 0  , 0  , 498, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #308</a>
+<a name="2091"><span class="lineNum">    2091 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #309</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 192, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #310</a>
+<a name="2093"><span class="lineNum">    2093 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B64)            , 0  , 0  , 0  , 91 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #311</a>
+<a name="2094"><span class="lineNum">    2094 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B32)            , 0  , 0  , 0  , 91 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #312</a>
+<a name="2095"><span class="lineNum">    2095 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #313</a>
+<a name="2096"><span class="lineNum">    2096 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 211, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #314</a>
+<a name="2097"><span class="lineNum">    2097 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 499, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #315</a>
+<a name="2098"><span class="lineNum">    2098 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 212, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #316</a>
+<a name="2099"><span class="lineNum">    2099 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 416, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #317</a>
+<a name="2100"><span class="lineNum">    2100 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B64)            , 0  , 0  , 0  , 213, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #318</a>
+<a name="2101"><span class="lineNum">    2101 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B32)            , 0  , 0  , 0  , 213, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #319</a>
+<a name="2102"><span class="lineNum">    2102 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 500, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #320</a>
+<a name="2103"><span class="lineNum">    2103 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 501, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #321</a>
+<a name="2104"><span class="lineNum">    2104 </span>            :   { F(UseX)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B64)  , 0  , 0  , 0  , 216, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #322</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :   { F(UseX)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B32)  , 0  , 0  , 0  , 216, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #323</a>
+<a name="2106"><span class="lineNum">    2106 </span>            :   { F(UseX)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE)      , 0  , 0  , 0  , 502, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #324</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :   { F(UseX)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE)      , 0  , 0  , 0  , 503, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #325</a>
+<a name="2108"><span class="lineNum">    2108 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 150, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #326</a>
+<a name="2109"><span class="lineNum">    2109 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 351, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #327</a>
+<a name="2110"><span class="lineNum">    2110 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 353, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #328</a>
+<a name="2111"><span class="lineNum">    2111 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K_B64)                 , 0  , 0  , 0  , 504, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #329</a>
+<a name="2112"><span class="lineNum">    2112 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K_B32)                 , 0  , 0  , 0  , 504, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #330</a>
+<a name="2113"><span class="lineNum">    2113 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K)                     , 0  , 0  , 0  , 505, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #331</a>
+<a name="2114"><span class="lineNum">    2114 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K)                     , 0  , 0  , 0  , 506, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #332</a>
+<a name="2115"><span class="lineNum">    2115 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 204, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #333</a>
+<a name="2116"><span class="lineNum">    2116 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 85 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #334</a>
+<a name="2117"><span class="lineNum">    2117 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 255, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #335</a>
+<a name="2118"><span class="lineNum">    2118 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 79 , 111, 5 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #336</a>
+<a name="2119"><span class="lineNum">    2119 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 80 , 116, 5 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #337</a>
+<a name="2120"><span class="lineNum">    2120 </span>            :   { F(UseR)|F(Vsib)|F(Evex)|F(Avx512K)                    , 0  , 0  , 0  , 507, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #338</a>
+<a name="2121"><span class="lineNum">    2121 </span>            :   { F(UseR)|F(Vsib)|F(Evex)|F(Avx512K)                    , 0  , 0  , 0  , 508, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #339</a>
+<a name="2122"><span class="lineNum">    2122 </span>            :   { F(UseR)|F(Vsib)|F(Evex)|F(Avx512K)                    , 0  , 0  , 0  , 509, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #340</a>
+<a name="2123"><span class="lineNum">    2123 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 81 , 121, 5 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #341</a>
+<a name="2124"><span class="lineNum">    2124 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 82 , 154, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #342</a>
+<a name="2125"><span class="lineNum">    2125 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 85 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #343</a>
+<a name="2126"><span class="lineNum">    2126 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 255, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #344</a>
+<a name="2127"><span class="lineNum">    2127 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B64)            , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #345</a>
+<a name="2128"><span class="lineNum">    2128 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B32)            , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #346</a>
+<a name="2129"><span class="lineNum">    2129 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 480, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #347</a>
+<a name="2130"><span class="lineNum">    2130 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 481, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #348</a>
+<a name="2131"><span class="lineNum">    2131 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 355, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #349</a>
+<a name="2132"><span class="lineNum">    2132 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 355, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #350</a>
+<a name="2133"><span class="lineNum">    2133 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 510, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #351</a>
+<a name="2134"><span class="lineNum">    2134 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 511, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #352</a>
+<a name="2135"><span class="lineNum">    2135 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 228, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #353</a>
+<a name="2136"><span class="lineNum">    2136 </span>            :   { F(UseR)|F(Vex)                                        , 0  , 0  , 0  , 444, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #354</a>
+<a name="2137"><span class="lineNum">    2137 </span>            :   { F(UseR)|F(FixedRM)|F(Vec)|F(Vex)                      , 0  , 0  , 0  , 512, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #355</a>
+<a name="2138"><span class="lineNum">    2138 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 83 , 158, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #356</a>
+<a name="2139"><span class="lineNum">    2139 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 84 , 158, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #357</a>
+<a name="2140"><span class="lineNum">    2140 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE_B64)     , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #358</a>
+<a name="2141"><span class="lineNum">    2141 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE_B32)     , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #359</a>
+<a name="2142"><span class="lineNum">    2142 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_SAE)         , 0  , 0  , 0  , 489, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #360</a>
+<a name="2143"><span class="lineNum">    2143 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 85 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #361</a>
+<a name="2144"><span class="lineNum">    2144 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 86 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #362</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 87 , 357, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #363</a>
+<a name="2146"><span class="lineNum">    2146 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 222, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #364</a>
+<a name="2147"><span class="lineNum">    2147 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 88 , 87 , 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #365</a>
+<a name="2148"><span class="lineNum">    2148 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 89 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #366</a>
+<a name="2149"><span class="lineNum">    2149 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 90 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #367</a>
+<a name="2150"><span class="lineNum">    2150 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 91 , 87 , 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #368</a>
+<a name="2151"><span class="lineNum">    2151 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 92 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #369</a>
+<a name="2152"><span class="lineNum">    2152 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 93 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #370</a>
+<a name="2153"><span class="lineNum">    2153 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 94 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #371</a>
+<a name="2154"><span class="lineNum">    2154 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 95 , 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #372</a>
+<a name="2155"><span class="lineNum">    2155 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 236, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #373</a>
+<a name="2156"><span class="lineNum">    2156 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 96 , 359, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #374</a>
+<a name="2157"><span class="lineNum">    2157 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 97 , 359, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #375</a>
+<a name="2158"><span class="lineNum">    2158 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 98 , 359, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #376</a>
+<a name="2159"><span class="lineNum">    2159 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 99 , 359, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #377</a>
+<a name="2160"><span class="lineNum">    2160 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 513, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #378</a>
+<a name="2161"><span class="lineNum">    2161 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 225, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #379</a>
+<a name="2162"><span class="lineNum">    2162 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 228, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #380</a>
+<a name="2163"><span class="lineNum">    2163 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 100, 231, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #381</a>
+<a name="2164"><span class="lineNum">    2164 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 101, 234, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #382</a>
+<a name="2165"><span class="lineNum">    2165 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #383</a>
+<a name="2166"><span class="lineNum">    2166 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 102, 237, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #384</a>
+<a name="2167"><span class="lineNum">    2167 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 103, 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #385</a>
+<a name="2168"><span class="lineNum">    2168 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 104, 87 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #386</a>
+<a name="2169"><span class="lineNum">    2169 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512T4X)|F(Avx512KZ)       , 0  , 0  , 0  , 514, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #387</a>
+<a name="2170"><span class="lineNum">    2170 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #388</a>
+<a name="2171"><span class="lineNum">    2171 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #389</a>
+<a name="2172"><span class="lineNum">    2172 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 189, 2 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #390</a>
+<a name="2173"><span class="lineNum">    2173 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #391</a>
+<a name="2174"><span class="lineNum">    2174 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 189, 2 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #392</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #393</a>
+<a name="2176"><span class="lineNum">    2176 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #394</a>
+<a name="2177"><span class="lineNum">    2177 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #395</a>
+<a name="2178"><span class="lineNum">    2178 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 361, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #396</a>
+<a name="2179"><span class="lineNum">    2179 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 363, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #397</a>
+<a name="2180"><span class="lineNum">    2180 </span>            :   { F(UseW)|F(Vec)|F(Evex)                                , 0  , 0  , 0  , 515, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #398</a>
+<a name="2181"><span class="lineNum">    2181 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 516, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #399</a>
+<a name="2182"><span class="lineNum">    2182 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 365, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #400</a>
+<a name="2183"><span class="lineNum">    2183 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K)                     , 0  , 0  , 0  , 240, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #401</a>
+<a name="2184"><span class="lineNum">    2184 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K_B32)                 , 0  , 0  , 0  , 240, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #402</a>
+<a name="2185"><span class="lineNum">    2185 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512K)              , 0  , 0  , 0  , 243, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #403</a>
+<a name="2186"><span class="lineNum">    2186 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512K_B32)          , 0  , 0  , 0  , 243, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #404</a>
+<a name="2187"><span class="lineNum">    2187 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512K_B64)          , 0  , 0  , 0  , 243, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #405</a>
+<a name="2188"><span class="lineNum">    2188 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)|F(Vex)                     , 0  , 0  , 0  , 461, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #406</a>
+<a name="2189"><span class="lineNum">    2189 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)|F(Vex)                     , 0  , 0  , 0  , 462, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #407</a>
+<a name="2190"><span class="lineNum">    2190 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)|F(Vex)                     , 0  , 0  , 0  , 463, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #408</a>
+<a name="2191"><span class="lineNum">    2191 </span>            :   { F(UseR)|F(FixedReg)|F(Vec)|F(Vex)                     , 0  , 0  , 0  , 464, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #409</a>
+<a name="2192"><span class="lineNum">    2192 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K_B64)                 , 0  , 0  , 0  , 240, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #410</a>
+<a name="2193"><span class="lineNum">    2193 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #411</a>
+<a name="2194"><span class="lineNum">    2194 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 193, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #412</a>
+<a name="2195"><span class="lineNum">    2195 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 167, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #413</a>
+<a name="2196"><span class="lineNum">    2196 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 216, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #414</a>
+<a name="2197"><span class="lineNum">    2197 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 216, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #415</a>
+<a name="2198"><span class="lineNum">    2198 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 216, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #416</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 162, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #417</a>
+<a name="2200"><span class="lineNum">    2200 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 105, 93 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #418</a>
+<a name="2201"><span class="lineNum">    2201 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 106, 93 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #419</a>
+<a name="2202"><span class="lineNum">    2202 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 96 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #420</a>
+<a name="2203"><span class="lineNum">    2203 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 95 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #421</a>
+<a name="2204"><span class="lineNum">    2204 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 107, 166, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #422</a>
+<a name="2205"><span class="lineNum">    2205 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 465, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #423</a>
+<a name="2206"><span class="lineNum">    2206 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 466, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #424</a>
+<a name="2207"><span class="lineNum">    2207 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 340, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #425</a>
+<a name="2208"><span class="lineNum">    2208 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 108, 116, 5 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #426</a>
+<a name="2209"><span class="lineNum">    2209 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 109, 111, 5 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #427</a>
+<a name="2210"><span class="lineNum">    2210 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 110, 154, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #428</a>
+<a name="2211"><span class="lineNum">    2211 </span>            :   { F(UseX)|F(Vec)|F(Vsib)|F(Vex)|F(Evex)|F(Avx512K)      , 0  , 0  , 111, 121, 5 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #429</a>
+<a name="2212"><span class="lineNum">    2212 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 367, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #430</a>
+<a name="2213"><span class="lineNum">    2213 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 369, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #431</a>
+<a name="2214"><span class="lineNum">    2214 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 371, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #432</a>
+<a name="2215"><span class="lineNum">    2215 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 517, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #433</a>
+<a name="2216"><span class="lineNum">    2216 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #434</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 151, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #435</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 112, 158, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #436</a>
+<a name="2219"><span class="lineNum">    2219 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 113, 158, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #437</a>
+<a name="2220"><span class="lineNum">    2220 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #438</a>
+<a name="2221"><span class="lineNum">    2221 </span>            :   { F(UseW)|F(Vec)|F(Evex)                                , 0  , 0  , 0  , 518, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #439</a>
+<a name="2222"><span class="lineNum">    2222 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 246, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #440</a>
+<a name="2223"><span class="lineNum">    2223 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 249, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #441</a>
+<a name="2224"><span class="lineNum">    2224 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 252, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #442</a>
+<a name="2225"><span class="lineNum">    2225 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 255, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #443</a>
+<a name="2226"><span class="lineNum">    2226 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 258, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #444</a>
+<a name="2227"><span class="lineNum">    2227 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 201, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #445</a>
+<a name="2228"><span class="lineNum">    2228 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 261, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #446</a>
+<a name="2229"><span class="lineNum">    2229 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 91 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #447</a>
+<a name="2230"><span class="lineNum">    2230 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 91 , 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #448</a>
+<a name="2231"><span class="lineNum">    2231 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 150, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #449</a>
+<a name="2232"><span class="lineNum">    2232 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #450</a>
+<a name="2233"><span class="lineNum">    2233 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #451</a>
+<a name="2234"><span class="lineNum">    2234 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 114, 373, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #452</a>
+<a name="2235"><span class="lineNum">    2235 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 115, 373, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #453</a>
+<a name="2236"><span class="lineNum">    2236 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 116, 373, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #454</a>
+<a name="2237"><span class="lineNum">    2237 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 117, 373, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #455</a>
+<a name="2238"><span class="lineNum">    2238 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #456</a>
+<a name="2239"><span class="lineNum">    2239 </span>            :   { F(UseW)|F(Vec)|F(Vsib)|F(Evex)|F(Avx512K)             , 0  , 0  , 0  , 264, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #457</a>
+<a name="2240"><span class="lineNum">    2240 </span>            :   { F(UseW)|F(Vec)|F(Vsib)|F(Evex)|F(Avx512K)             , 0  , 0  , 0  , 375, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #458</a>
+<a name="2241"><span class="lineNum">    2241 </span>            :   { F(UseW)|F(Vec)|F(Vsib)|F(Evex)|F(Avx512K)             , 0  , 0  , 0  , 267, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #459</a>
+<a name="2242"><span class="lineNum">    2242 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 377, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #460</a>
+<a name="2243"><span class="lineNum">    2243 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #461</a>
+<a name="2244"><span class="lineNum">    2244 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #462</a>
+<a name="2245"><span class="lineNum">    2245 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 118, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #463</a>
+<a name="2246"><span class="lineNum">    2246 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)                         , 0  , 0  , 0  , 219, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #464</a>
+<a name="2247"><span class="lineNum">    2247 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 119, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #465</a>
+<a name="2248"><span class="lineNum">    2248 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 120, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #466</a>
+<a name="2249"><span class="lineNum">    2249 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 121, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #467</a>
+<a name="2250"><span class="lineNum">    2250 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 122, 105, 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #468</a>
+<a name="2251"><span class="lineNum">    2251 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 123, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #469</a>
+<a name="2252"><span class="lineNum">    2252 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 124, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #470</a>
+<a name="2253"><span class="lineNum">    2253 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 125, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #471</a>
+<a name="2254"><span class="lineNum">    2254 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 126, 99 , 6 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #472</a>
+<a name="2255"><span class="lineNum">    2255 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ)             , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #473</a>
+<a name="2256"><span class="lineNum">    2256 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #474</a>
+<a name="2257"><span class="lineNum">    2257 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(WO)  , 0 }, // #475</a>
+<a name="2258"><span class="lineNum">    2258 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 213, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #476</a>
+<a name="2259"><span class="lineNum">    2259 </span>            :   { F(UseX)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 213, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #477</a>
+<a name="2260"><span class="lineNum">    2260 </span>            :   { F(UseR)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 379, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #478</a>
+<a name="2261"><span class="lineNum">    2261 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K)                     , 0  , 0  , 0  , 270, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #479</a>
+<a name="2262"><span class="lineNum">    2262 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K_B32)                 , 0  , 0  , 0  , 270, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #480</a>
+<a name="2263"><span class="lineNum">    2263 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512K_B64)                 , 0  , 0  , 0  , 270, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #481</a>
+<a name="2264"><span class="lineNum">    2264 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B64)            , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #482</a>
+<a name="2265"><span class="lineNum">    2265 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE_B32)            , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #483</a>
+<a name="2266"><span class="lineNum">    2266 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 519, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #484</a>
+<a name="2267"><span class="lineNum">    2267 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 511, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #485</a>
+<a name="2268"><span class="lineNum">    2268 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 489, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #486</a>
+<a name="2269"><span class="lineNum">    2269 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 490, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #487</a>
+<a name="2270"><span class="lineNum">    2270 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 489, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #488</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_SAE)                , 0  , 0  , 0  , 490, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #489</a>
+<a name="2272"><span class="lineNum">    2272 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 490, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #490</a>
+<a name="2273"><span class="lineNum">    2273 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 519, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #491</a>
+<a name="2274"><span class="lineNum">    2274 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ)                    , 0  , 0  , 0  , 511, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #492</a>
+<a name="2275"><span class="lineNum">    2275 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 101, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #493</a>
+<a name="2276"><span class="lineNum">    2276 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 519, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #494</a>
+<a name="2277"><span class="lineNum">    2277 </span>            :   { F(UseW)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 511, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #495</a>
+<a name="2278"><span class="lineNum">    2278 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE_B64)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #496</a>
+<a name="2279"><span class="lineNum">    2279 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE_B32)         , 0  , 0  , 0  , 189, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #497</a>
+<a name="2280"><span class="lineNum">    2280 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE)             , 0  , 0  , 0  , 489, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #498</a>
+<a name="2281"><span class="lineNum">    2281 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_ER_SAE)             , 0  , 0  , 0  , 490, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #499</a>
+<a name="2282"><span class="lineNum">    2282 </span>            :   { F(UseW)|F(Vec)|F(Vsib)|F(Evex)|F(Avx512K)             , 0  , 0  , 0  , 381, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #500</a>
+<a name="2283"><span class="lineNum">    2283 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B32)                , 0  , 0  , 0  , 193, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #501</a>
+<a name="2284"><span class="lineNum">    2284 </span>            :   { F(UseW)|F(Vec)|F(Evex)|F(Avx512KZ_B64)                , 0  , 0  , 0  , 193, 2 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #502</a>
+<a name="2285"><span class="lineNum">    2285 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B32)         , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #503</a>
+<a name="2286"><span class="lineNum">    2286 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_B64)         , 0  , 0  , 0  , 192, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #504</a>
+<a name="2287"><span class="lineNum">    2287 </span>            :   { F(UseW)|F(Vec)|F(Vex)|F(Evex)|F(Avx512KZ_ER_SAE_B64)  , 0  , 0  , 0  , 204, 3 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #505</a>
+<a name="2288"><span class="lineNum">    2288 </span>            :   { F(UseW)|F(Vex)                                        , 0  , 0  , 0  , 486, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #506</a>
+<a name="2289"><span class="lineNum">    2289 </span>            :   { F(UseR)|F(Vec)|F(Vex)                                 , 0  , 0  , 0  , 291, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #507</a>
+<a name="2290"><span class="lineNum">    2290 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 520, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #508</a>
+<a name="2291"><span class="lineNum">    2291 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 0  , 521, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #509</a>
+<a name="2292"><span class="lineNum">    2292 </span>            :   { F(UseX)|F(UseXX)|F(Lock)|F(XAcquire)|F(XRelease)      , 0  , 0  , 0  , 170, 4 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #510</a>
+<a name="2293"><span class="lineNum">    2293 </span>            :   { F(UseR)                                               , 0  , 0  , 0  , 522, 1 , JUMP_TYPE(Conditional), SINGLE_REG(None), 0 }, // #511</a>
+<a name="2294"><span class="lineNum">    2294 </span>            :   { F(UseX)|F(UseXX)|F(Lock)|F(XAcquire)                  , 0  , 0  , 0  , 60 , 8 , JUMP_TYPE(None)       , SINGLE_REG(RO)  , 0 }, // #512</a>
+<a name="2295"><span class="lineNum">    2295 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 0  , 523, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #513</a>
+<a name="2296"><span class="lineNum">    2296 </span>            :   { F(UseR)|F(FixedReg)                                   , 0  , 0  , 0  , 524, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #514</a>
+<a name="2297"><span class="lineNum">    2297 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 525, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }, // #515</a>
+<a name="2298"><span class="lineNum">    2298 </span>            :   { F(UseW)|F(FixedReg)                                   , 0  , 0  , 0  , 526, 1 , JUMP_TYPE(None)       , SINGLE_REG(None), 0 }  // #516</a>
+<a name="2299"><span class="lineNum">    2299 </span>            : };</a>
+<a name="2300"><span class="lineNum">    2300 </span>            : #undef SINGLE_REG</a>
+<a name="2301"><span class="lineNum">    2301 </span>            : #undef JUMP_TYPE</a>
+<a name="2302"><span class="lineNum">    2302 </span>            : #undef F</a>
+<a name="2303"><span class="lineNum">    2303 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="2304"><span class="lineNum">    2304 </span>            : // ${commonData:End}</a>
+<a name="2305"><span class="lineNum">    2305 </span>            : </a>
+<a name="2306"><span class="lineNum">    2306 </span>            : // ${operationData:Begin}</a>
+<a name="2307"><span class="lineNum">    2307 </span>            : // ------------------- Automatically generated, do not edit -------------------</a>
+<a name="2308"><span class="lineNum">    2308 </span>            : #define OP_FLAG(F) X86Inst::kOperation##F</a>
+<a name="2309"><span class="lineNum">    2309 </span>            : #define FEATURE(F) CpuInfo::kX86Feature##F</a>
+<a name="2310"><span class="lineNum">    2310 </span>            : #define SPECIAL(F) x86::kSpecialReg_##F</a>
+<a name="2311"><span class="lineNum">    2311 </span>            : const X86Inst::OperationData X86InstDB::operationData[] = {</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :   { 0, { 0 }, 0, 0 }, // #0</a>
+<a name="2313"><span class="lineNum">    2313 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #1</a>
+<a name="2314"><span class="lineNum">    2314 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_CF), SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #2</a>
+<a name="2315"><span class="lineNum">    2315 </span>            :   { 0, { FEATURE(ADX) }, SPECIAL(FLAGS_CF), SPECIAL(FLAGS_CF) }, // #3</a>
+<a name="2316"><span class="lineNum">    2316 </span>            :   { 0, { FEATURE(SSE2) }, 0, 0 }, // #4</a>
+<a name="2317"><span class="lineNum">    2317 </span>            :   { 0, { FEATURE(SSE) }, 0, 0 }, // #5</a>
+<a name="2318"><span class="lineNum">    2318 </span>            :   { 0, { FEATURE(SSE3) }, 0, 0 }, // #6</a>
+<a name="2319"><span class="lineNum">    2319 </span>            :   { 0, { FEATURE(ADX) }, SPECIAL(FLAGS_OF), SPECIAL(FLAGS_OF) }, // #7</a>
+<a name="2320"><span class="lineNum">    2320 </span>            :   { 0, { FEATURE(AESNI) }, 0, 0 }, // #8</a>
+<a name="2321"><span class="lineNum">    2321 </span>            :   { 0, { FEATURE(BMI) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #9</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_ZF) }, // #10</a>
+<a name="2323"><span class="lineNum">    2323 </span>            :   { 0, { FEATURE(TBM) }, 0, 0 }, // #11</a>
+<a name="2324"><span class="lineNum">    2324 </span>            :   { 0, { FEATURE(SSE4_1) }, 0, 0 }, // #12</a>
+<a name="2325"><span class="lineNum">    2325 </span>            :   { 0, { FEATURE(MPX) }, 0, 0 }, // #13</a>
+<a name="2326"><span class="lineNum">    2326 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) }, // #14</a>
+<a name="2327"><span class="lineNum">    2327 </span>            :   { 0, { FEATURE(BMI2) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #15</a>
+<a name="2328"><span class="lineNum">    2328 </span>            :   { OP_FLAG(Volatile), { 0 }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #16</a>
+<a name="2329"><span class="lineNum">    2329 </span>            :   { OP_FLAG(Volatile), { FEATURE(SMAP) }, 0, SPECIAL(FLAGS_AC) }, // #17</a>
+<a name="2330"><span class="lineNum">    2330 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_CF) }, // #18</a>
+<a name="2331"><span class="lineNum">    2331 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_DF) }, // #19</a>
+<a name="2332"><span class="lineNum">    2332 </span>            :   { OP_FLAG(Volatile), { FEATURE(CLFLUSH) }, 0, 0 }, // #20</a>
+<a name="2333"><span class="lineNum">    2333 </span>            :   { OP_FLAG(Volatile), { FEATURE(CLFLUSHOPT) }, 0, 0 }, // #21</a>
+<a name="2334"><span class="lineNum">    2334 </span>            :   { OP_FLAG(Volatile), { 0 }, 0, SPECIAL(FLAGS_IF) }, // #22</a>
+<a name="2335"><span class="lineNum">    2335 </span>            :   { OP_FLAG(Volatile) | OP_FLAG(Privileged), { 0 }, 0, 0 }, // #23</a>
+<a name="2336"><span class="lineNum">    2336 </span>            :   { OP_FLAG(Volatile), { FEATURE(CLWB) }, 0, 0 }, // #24</a>
+<a name="2337"><span class="lineNum">    2337 </span>            :   { OP_FLAG(Volatile), { FEATURE(CLZERO) }, 0, 0 }, // #25</a>
+<a name="2338"><span class="lineNum">    2338 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_CF), SPECIAL(FLAGS_CF) }, // #26</a>
+<a name="2339"><span class="lineNum">    2339 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_ZF), 0 }, // #27</a>
+<a name="2340"><span class="lineNum">    2340 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_CF), 0 }, // #28</a>
+<a name="2341"><span class="lineNum">    2341 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_ZF), 0 }, // #29</a>
+<a name="2342"><span class="lineNum">    2342 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF), 0 }, // #30</a>
+<a name="2343"><span class="lineNum">    2343 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_SF), 0 }, // #31</a>
+<a name="2344"><span class="lineNum">    2344 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_OF), 0 }, // #32</a>
+<a name="2345"><span class="lineNum">    2345 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_PF), 0 }, // #33</a>
+<a name="2346"><span class="lineNum">    2346 </span>            :   { 0, { FEATURE(CMOV) }, SPECIAL(FLAGS_SF), 0 }, // #34</a>
+<a name="2347"><span class="lineNum">    2347 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_DF), SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #35</a>
+<a name="2348"><span class="lineNum">    2348 </span>            :   { 0, { FEATURE(I486) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #36</a>
+<a name="2349"><span class="lineNum">    2349 </span>            :   { OP_FLAG(Volatile), { FEATURE(CMPXCHG16B) }, 0, SPECIAL(FLAGS_ZF) }, // #37</a>
+<a name="2350"><span class="lineNum">    2350 </span>            :   { OP_FLAG(Volatile), { FEATURE(CMPXCHG8B) }, 0, SPECIAL(FLAGS_ZF) }, // #38</a>
+<a name="2351"><span class="lineNum">    2351 </span>            :   { 0, { FEATURE(SSE2) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #39</a>
+<a name="2352"><span class="lineNum">    2352 </span>            :   { 0, { FEATURE(SSE) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #40</a>
+<a name="2353"><span class="lineNum">    2353 </span>            :   { OP_FLAG(Volatile), { FEATURE(I486) }, 0, 0 }, // #41</a>
+<a name="2354"><span class="lineNum">    2354 </span>            :   { 0, { FEATURE(SSE4_2) }, 0, 0 }, // #42</a>
+<a name="2355"><span class="lineNum">    2355 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #43</a>
+<a name="2356"><span class="lineNum">    2356 </span>            :   { OP_FLAG(Volatile), { FEATURE(MMX) }, 0, 0 }, // #44</a>
+<a name="2357"><span class="lineNum">    2357 </span>            :   { OP_FLAG(Volatile), { 0 }, 0, 0 }, // #45</a>
+<a name="2358"><span class="lineNum">    2358 </span>            :   { 0, { FEATURE(SSE4A) }, 0, 0 }, // #46</a>
+<a name="2359"><span class="lineNum">    2359 </span>            :   { 0, { 0 }, 0, SPECIAL(X87SW_C0) | SPECIAL(X87SW_C1) | SPECIAL(X87SW_C2) | SPECIAL(X87SW_C3) }, // #47</a>
+<a name="2360"><span class="lineNum">    2360 </span>            :   { 0, { FEATURE(CMOV) }, 0, SPECIAL(X87SW_C0) | SPECIAL(X87SW_C1) | SPECIAL(X87SW_C2) | SPECIAL(X87SW_C3) }, // #48</a>
+<a name="2361"><span class="lineNum">    2361 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_ZF) | SPECIAL(X87SW_C1) }, // #49</a>
+<a name="2362"><span class="lineNum">    2362 </span>            :   { OP_FLAG(Volatile), { FEATURE(3DNOW) }, 0, 0 }, // #50</a>
+<a name="2363"><span class="lineNum">    2363 </span>            :   { 0, { FEATURE(SSE3) }, 0, SPECIAL(X87SW_C0) | SPECIAL(X87SW_C1) | SPECIAL(X87SW_C2) | SPECIAL(X87SW_C3) }, // #51</a>
+<a name="2364"><span class="lineNum">    2364 </span>            :   { OP_FLAG(Volatile), { FEATURE(FXSR) }, 0, SPECIAL(X87SW_C0) | SPECIAL(X87SW_C1) | SPECIAL(X87SW_C2) | SPECIAL(X87SW_C3) }, // #52</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :   { OP_FLAG(Volatile), { FEATURE(FXSR) }, 0, 0 }, // #53</a>
+<a name="2366"><span class="lineNum">    2366 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_OF), 0 }, // #54</a>
+<a name="2367"><span class="lineNum">    2367 </span>            :   { OP_FLAG(Volatile) | OP_FLAG(Privileged), { FEATURE(I486) }, 0, 0 }, // #55</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_ZF), 0 }, // #56</a>
+<a name="2369"><span class="lineNum">    2369 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_CF), 0 }, // #57</a>
+<a name="2370"><span class="lineNum">    2370 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_ZF), 0 }, // #58</a>
+<a name="2371"><span class="lineNum">    2371 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF), 0 }, // #59</a>
+<a name="2372"><span class="lineNum">    2372 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_SF), 0 }, // #60</a>
+<a name="2373"><span class="lineNum">    2373 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_PF), 0 }, // #61</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :   { OP_FLAG(Volatile), { 0 }, SPECIAL(FLAGS_SF), 0 }, // #62</a>
+<a name="2375"><span class="lineNum">    2375 </span>            :   { 0, { FEATURE(AVX512_DQ) }, 0, 0 }, // #63</a>
+<a name="2376"><span class="lineNum">    2376 </span>            :   { 0, { FEATURE(AVX512_BW) }, 0, 0 }, // #64</a>
+<a name="2377"><span class="lineNum">    2377 </span>            :   { 0, { FEATURE(AVX512_F) }, 0, 0 }, // #65</a>
+<a name="2378"><span class="lineNum">    2378 </span>            :   { 0, { FEATURE(AVX512_DQ) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #66</a>
+<a name="2379"><span class="lineNum">    2379 </span>            :   { 0, { FEATURE(AVX512_BW) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #67</a>
+<a name="2380"><span class="lineNum">    2380 </span>            :   { 0, { FEATURE(AVX512_F) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #68</a>
+<a name="2381"><span class="lineNum">    2381 </span>            :   { OP_FLAG(Volatile), { FEATURE(LAHFSAHF) }, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF), 0 }, // #69</a>
+<a name="2382"><span class="lineNum">    2382 </span>            :   { OP_FLAG(Volatile), { 0 }, 0, SPECIAL(FLAGS_ZF) }, // #70</a>
+<a name="2383"><span class="lineNum">    2383 </span>            :   { OP_FLAG(Barrier) | OP_FLAG(Volatile), { FEATURE(SSE2) }, 0, 0 }, // #71</a>
+<a name="2384"><span class="lineNum">    2384 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_DF), 0 }, // #72</a>
+<a name="2385"><span class="lineNum">    2385 </span>            :   { 0, { FEATURE(LZCNT) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #73</a>
+<a name="2386"><span class="lineNum">    2386 </span>            :   { 0, { FEATURE(MMX2) }, 0, 0 }, // #74</a>
+<a name="2387"><span class="lineNum">    2387 </span>            :   { OP_FLAG(Volatile) | OP_FLAG(Privileged), { FEATURE(MONITOR) }, 0, 0 }, // #75</a>
+<a name="2388"><span class="lineNum">    2388 </span>            :   { OP_FLAG(MovCrDr), { 0 }, 0, 0 }, // #76</a>
+<a name="2389"><span class="lineNum">    2389 </span>            :   { 0, { FEATURE(MOVBE) }, 0, 0 }, // #77</a>
+<a name="2390"><span class="lineNum">    2390 </span>            :   { 0, { FEATURE(MMX), FEATURE(SSE2) }, 0, 0 }, // #78</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :   { OP_FLAG(MovSsSd), { FEATURE(SSE2) }, 0, 0 }, // #79</a>
+<a name="2392"><span class="lineNum">    2392 </span>            :   { OP_FLAG(MovSsSd), { FEATURE(SSE) }, 0, 0 }, // #80</a>
+<a name="2393"><span class="lineNum">    2393 </span>            :   { 0, { FEATURE(BMI2) }, 0, 0 }, // #81</a>
+<a name="2394"><span class="lineNum">    2394 </span>            :   { 0, { FEATURE(SSSE3) }, 0, 0 }, // #82</a>
+<a name="2395"><span class="lineNum">    2395 </span>            :   { 0, { FEATURE(MMX2), FEATURE(SSE2) }, 0, 0 }, // #83</a>
+<a name="2396"><span class="lineNum">    2396 </span>            :   { 0, { FEATURE(3DNOW) }, 0, 0 }, // #84</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :   { 0, { FEATURE(PCLMULQDQ) }, 0, 0 }, // #85</a>
+<a name="2398"><span class="lineNum">    2398 </span>            :   { 0, { FEATURE(SSE4_2) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #86</a>
+<a name="2399"><span class="lineNum">    2399 </span>            :   { OP_FLAG(Volatile), { FEATURE(PCOMMIT) }, 0, 0 }, // #87</a>
+<a name="2400"><span class="lineNum">    2400 </span>            :   { 0, { FEATURE(MMX2), FEATURE(SSE2), FEATURE(SSE4_1) }, 0, 0 }, // #88</a>
+<a name="2401"><span class="lineNum">    2401 </span>            :   { 0, { FEATURE(3DNOW2) }, 0, 0 }, // #89</a>
+<a name="2402"><span class="lineNum">    2402 </span>            :   { 0, { FEATURE(GEODE) }, 0, 0 }, // #90</a>
+<a name="2403"><span class="lineNum">    2403 </span>            :   { 0, { FEATURE(POPCNT) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #91</a>
+<a name="2404"><span class="lineNum">    2404 </span>            :   { OP_FLAG(Prefetch), { FEATURE(3DNOW) }, 0, 0 }, // #92</a>
+<a name="2405"><span class="lineNum">    2405 </span>            :   { OP_FLAG(Prefetch), { FEATURE(MMX2) }, 0, 0 }, // #93</a>
+<a name="2406"><span class="lineNum">    2406 </span>            :   { OP_FLAG(Prefetch), { FEATURE(PREFETCHW) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #94</a>
+<a name="2407"><span class="lineNum">    2407 </span>            :   { OP_FLAG(Prefetch), { FEATURE(PREFETCHWT1) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #95</a>
+<a name="2408"><span class="lineNum">    2408 </span>            :   { 0, { FEATURE(SSE4_1) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #96</a>
+<a name="2409"><span class="lineNum">    2409 </span>            :   { 0, { 0 }, 0, SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) }, // #97</a>
+<a name="2410"><span class="lineNum">    2410 </span>            :   { OP_FLAG(Volatile), { FEATURE(FSGSBASE) }, 0, 0 }, // #98</a>
+<a name="2411"><span class="lineNum">    2411 </span>            :   { OP_FLAG(Volatile) | OP_FLAG(Privileged), { FEATURE(MSR) }, SPECIAL(MSR), 0 }, // #99</a>
+<a name="2412"><span class="lineNum">    2412 </span>            :   { OP_FLAG(Volatile), { FEATURE(RDRAND) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #100</a>
+<a name="2413"><span class="lineNum">    2413 </span>            :   { OP_FLAG(Volatile), { FEATURE(RDSEED) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #101</a>
+<a name="2414"><span class="lineNum">    2414 </span>            :   { OP_FLAG(Volatile), { FEATURE(RDTSC) }, 0, 0 }, // #102</a>
+<a name="2415"><span class="lineNum">    2415 </span>            :   { OP_FLAG(Volatile), { FEATURE(RDTSCP) }, 0, 0 }, // #103</a>
+<a name="2416"><span class="lineNum">    2416 </span>            :   { OP_FLAG(Volatile), { FEATURE(LAHFSAHF) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #104</a>
+<a name="2417"><span class="lineNum">    2417 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_ZF), 0 }, // #105</a>
+<a name="2418"><span class="lineNum">    2418 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_CF), 0 }, // #106</a>
+<a name="2419"><span class="lineNum">    2419 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_ZF), 0 }, // #107</a>
+<a name="2420"><span class="lineNum">    2420 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF), 0 }, // #108</a>
+<a name="2421"><span class="lineNum">    2421 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_SF), 0 }, // #109</a>
+<a name="2422"><span class="lineNum">    2422 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_OF), 0 }, // #110</a>
+<a name="2423"><span class="lineNum">    2423 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_PF), 0 }, // #111</a>
+<a name="2424"><span class="lineNum">    2424 </span>            :   { 0, { 0 }, SPECIAL(FLAGS_SF), 0 }, // #112</a>
+<a name="2425"><span class="lineNum">    2425 </span>            :   { OP_FLAG(Barrier) | OP_FLAG(Volatile), { FEATURE(MMX2) }, 0, 0 }, // #113</a>
+<a name="2426"><span class="lineNum">    2426 </span>            :   { 0, { FEATURE(SHA) }, 0, 0 }, // #114</a>
+<a name="2427"><span class="lineNum">    2427 </span>            :   { 0, { FEATURE(AVX512_4FMAPS) }, 0, 0 }, // #115</a>
+<a name="2428"><span class="lineNum">    2428 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX512_F), FEATURE(AVX512_VL) }, 0, 0 }, // #116</a>
+<a name="2429"><span class="lineNum">    2429 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX512_F) }, 0, 0 }, // #117</a>
+<a name="2430"><span class="lineNum">    2430 </span>            :   { 0, { FEATURE(AVX) }, 0, 0 }, // #118</a>
+<a name="2431"><span class="lineNum">    2431 </span>            :   { 0, { FEATURE(AESNI), FEATURE(AVX) }, 0, 0 }, // #119</a>
+<a name="2432"><span class="lineNum">    2432 </span>            :   { 0, { FEATURE(AVX512_F), FEATURE(AVX512_VL) }, 0, 0 }, // #120</a>
+<a name="2433"><span class="lineNum">    2433 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX512_DQ), FEATURE(AVX512_VL) }, 0, 0 }, // #121</a>
+<a name="2434"><span class="lineNum">    2434 </span>            :   { 0, { FEATURE(AVX512_BW), FEATURE(AVX512_VL) }, 0, 0 }, // #122</a>
+<a name="2435"><span class="lineNum">    2435 </span>            :   { 0, { FEATURE(AVX512_DQ), FEATURE(AVX512_VL) }, 0, 0 }, // #123</a>
+<a name="2436"><span class="lineNum">    2436 </span>            :   { 0, { FEATURE(AVX2) }, 0, 0 }, // #124</a>
+<a name="2437"><span class="lineNum">    2437 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX2), FEATURE(AVX512_F), FEATURE(AVX512_VL) }, 0, 0 }, // #125</a>
+<a name="2438"><span class="lineNum">    2438 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX512_F) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #126</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :   { 0, { FEATURE(AVX512_F), FEATURE(AVX512_VL), FEATURE(F16C) }, 0, 0 }, // #127</a>
+<a name="2440"><span class="lineNum">    2440 </span>            :   { 0, { FEATURE(AVX512_ERI) }, 0, 0 }, // #128</a>
+<a name="2441"><span class="lineNum">    2441 </span>            :   { 0, { FEATURE(AVX512_F), FEATURE(AVX512_VL), FEATURE(FMA) }, 0, 0 }, // #129</a>
+<a name="2442"><span class="lineNum">    2442 </span>            :   { 0, { FEATURE(AVX512_F), FEATURE(FMA) }, 0, 0 }, // #130</a>
+<a name="2443"><span class="lineNum">    2443 </span>            :   { 0, { FEATURE(FMA4) }, 0, 0 }, // #131</a>
+<a name="2444"><span class="lineNum">    2444 </span>            :   { 0, { FEATURE(XOP) }, 0, 0 }, // #132</a>
+<a name="2445"><span class="lineNum">    2445 </span>            :   { 0, { FEATURE(AVX2), FEATURE(AVX512_F), FEATURE(AVX512_VL) }, 0, 0 }, // #133</a>
+<a name="2446"><span class="lineNum">    2446 </span>            :   { 0, { FEATURE(AVX512_PFI) }, 0, 0 }, // #134</a>
+<a name="2447"><span class="lineNum">    2447 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX2) }, 0, 0 }, // #135</a>
+<a name="2448"><span class="lineNum">    2448 </span>            :   { 0, { FEATURE(AVX512_4VNNIW) }, 0, 0 }, // #136</a>
+<a name="2449"><span class="lineNum">    2449 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX2), FEATURE(AVX512_BW), FEATURE(AVX512_VL) }, 0, 0 }, // #137</a>
+<a name="2450"><span class="lineNum">    2450 </span>            :   { 0, { FEATURE(AVX2), FEATURE(AVX512_BW), FEATURE(AVX512_VL) }, 0, 0 }, // #138</a>
+<a name="2451"><span class="lineNum">    2451 </span>            :   { 0, { FEATURE(AVX512_CDI), FEATURE(AVX512_VL) }, 0, 0 }, // #139</a>
+<a name="2452"><span class="lineNum">    2452 </span>            :   { 0, { FEATURE(AVX), FEATURE(PCLMULQDQ) }, 0, 0 }, // #140</a>
+<a name="2453"><span class="lineNum">    2453 </span>            :   { 0, { FEATURE(AVX) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }, // #141</a>
+<a name="2454"><span class="lineNum">    2454 </span>            :   { 0, { FEATURE(AVX512_VBMI), FEATURE(AVX512_VL) }, 0, 0 }, // #142</a>
+<a name="2455"><span class="lineNum">    2455 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX512_BW) }, 0, 0 }, // #143</a>
+<a name="2456"><span class="lineNum">    2456 </span>            :   { 0, { FEATURE(AVX), FEATURE(AVX512_DQ) }, 0, 0 }, // #144</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :   { 0, { FEATURE(AVX512_IFMA), FEATURE(AVX512_VL) }, 0, 0 }, // #145</a>
+<a name="2458"><span class="lineNum">    2458 </span>            :   { 0, { FEATURE(AVX512_VPOPCNTDQ) }, 0, 0 }, // #146</a>
+<a name="2459"><span class="lineNum">    2459 </span>            :   { OP_FLAG(Volatile) | OP_FLAG(Privileged), { FEATURE(MSR) }, 0, SPECIAL(MSR) }, // #147</a>
+<a name="2460"><span class="lineNum">    2460 </span>            :   { OP_FLAG(Volatile), { FEATURE(RTM) }, 0, 0 }, // #148</a>
+<a name="2461"><span class="lineNum">    2461 </span>            :   { OP_FLAG(Volatile), { FEATURE(XSAVE) }, SPECIAL(XCR), 0 }, // #149</a>
+<a name="2462"><span class="lineNum">    2462 </span>            :   { OP_FLAG(Volatile), { FEATURE(XSAVES) }, SPECIAL(XCR), 0 }, // #150</a>
+<a name="2463"><span class="lineNum">    2463 </span>            :   { OP_FLAG(Volatile), { FEATURE(XSAVEC) }, SPECIAL(XCR), 0 }, // #151</a>
+<a name="2464"><span class="lineNum">    2464 </span>            :   { OP_FLAG(Volatile), { FEATURE(XSAVEOPT) }, SPECIAL(XCR), 0 }, // #152</a>
+<a name="2465"><span class="lineNum">    2465 </span>            :   { OP_FLAG(Volatile) | OP_FLAG(Privileged), { FEATURE(XSAVE) }, 0, SPECIAL(XCR) }, // #153</a>
+<a name="2466"><span class="lineNum">    2466 </span>            :   { OP_FLAG(Volatile), { FEATURE(TSX) }, 0, SPECIAL(FLAGS_AF) | SPECIAL(FLAGS_CF) | SPECIAL(FLAGS_OF) | SPECIAL(FLAGS_PF) | SPECIAL(FLAGS_SF) | SPECIAL(FLAGS_ZF) }  // #154</a>
+<a name="2467"><span class="lineNum">    2467 </span>            : };</a>
+<a name="2468"><span class="lineNum">    2468 </span>            : #undef SPECIAL</a>
+<a name="2469"><span class="lineNum">    2469 </span>            : #undef FEATURE</a>
+<a name="2470"><span class="lineNum">    2470 </span>            : #undef OP_FLAG</a>
+<a name="2471"><span class="lineNum">    2471 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="2472"><span class="lineNum">    2472 </span>            : // ${operationData:End}</a>
+<a name="2473"><span class="lineNum">    2473 </span>            : </a>
+<a name="2474"><span class="lineNum">    2474 </span>            : // ${sseToAvxData:Begin}</a>
+<a name="2475"><span class="lineNum">    2475 </span>            : // ------------------- Automatically generated, do not edit -------------------</a>
+<a name="2476"><span class="lineNum">    2476 </span>            : const X86Inst::SseToAvxData X86InstDB::sseToAvxData[] = {</a>
+<a name="2477"><span class="lineNum">    2477 </span>            :   { X86Inst::kSseToAvxNone     , 0    }, // #0</a>
+<a name="2478"><span class="lineNum">    2478 </span>            :   { X86Inst::kSseToAvxExtend   , 725  }, // #1</a>
+<a name="2479"><span class="lineNum">    2479 </span>            :   { X86Inst::kSseToAvxExtend   , 724  }, // #2</a>
+<a name="2480"><span class="lineNum">    2480 </span>            :   { X86Inst::kSseToAvxMove     , 724  }, // #3</a>
+<a name="2481"><span class="lineNum">    2481 </span>            :   { X86Inst::kSseToAvxExtend   , 723  }, // #4</a>
+<a name="2482"><span class="lineNum">    2482 </span>            :   { X86Inst::kSseToAvxBlend    , 723  }, // #5</a>
+<a name="2483"><span class="lineNum">    2483 </span>            :   { X86Inst::kSseToAvxExtend   , 671  }, // #6</a>
+<a name="2484"><span class="lineNum">    2484 </span>            :   { X86Inst::kSseToAvxExtend   , 670  }, // #7</a>
+<a name="2485"><span class="lineNum">    2485 </span>            :   { X86Inst::kSseToAvxMove     , 667  }, // #8</a>
+<a name="2486"><span class="lineNum">    2486 </span>            :   { X86Inst::kSseToAvxMove     , 666  }, // #9</a>
+<a name="2487"><span class="lineNum">    2487 </span>            :   { X86Inst::kSseToAvxMove     , 665  }, // #10</a>
+<a name="2488"><span class="lineNum">    2488 </span>            :   { X86Inst::kSseToAvxMove     , 672  }, // #11</a>
+<a name="2489"><span class="lineNum">    2489 </span>            :   { X86Inst::kSseToAvxExtend   , 672  }, // #12</a>
+<a name="2490"><span class="lineNum">    2490 </span>            :   { X86Inst::kSseToAvxExtend   , 673  }, // #13</a>
+<a name="2491"><span class="lineNum">    2491 </span>            :   { X86Inst::kSseToAvxMove     , 673  }, // #14</a>
+<a name="2492"><span class="lineNum">    2492 </span>            :   { X86Inst::kSseToAvxMove     , 674  }, // #15</a>
+<a name="2493"><span class="lineNum">    2493 </span>            :   { X86Inst::kSseToAvxMove     , 676  }, // #16</a>
+<a name="2494"><span class="lineNum">    2494 </span>            :   { X86Inst::kSseToAvxMove     , 678  }, // #17</a>
+<a name="2495"><span class="lineNum">    2495 </span>            :   { X86Inst::kSseToAvxMove     , 679  }, // #18</a>
+<a name="2496"><span class="lineNum">    2496 </span>            :   { X86Inst::kSseToAvxExtend   , 681  }, // #19</a>
+<a name="2497"><span class="lineNum">    2497 </span>            :   { X86Inst::kSseToAvxMove     , 695  }, // #20</a>
+<a name="2498"><span class="lineNum">    2498 </span>            :   { X86Inst::kSseToAvxExtend   , 708  }, // #21</a>
+<a name="2499"><span class="lineNum">    2499 </span>            :   { X86Inst::kSseToAvxExtend   , 707  }, // #22</a>
+<a name="2500"><span class="lineNum">    2500 </span>            :   { X86Inst::kSseToAvxExtend   , 712  }, // #23</a>
+<a name="2501"><span class="lineNum">    2501 </span>            :   { X86Inst::kSseToAvxMove     , 616  }, // #24</a>
+<a name="2502"><span class="lineNum">    2502 </span>            :   { X86Inst::kSseToAvxMove     , 597  }, // #25</a>
+<a name="2503"><span class="lineNum">    2503 </span>            :   { X86Inst::kSseToAvxExtend   , 598  }, // #26</a>
+<a name="2504"><span class="lineNum">    2504 </span>            :   { X86Inst::kSseToAvxExtend   , 597  }, // #27</a>
+<a name="2505"><span class="lineNum">    2505 </span>            :   { X86Inst::kSseToAvxMove     , 595  }, // #28</a>
+<a name="2506"><span class="lineNum">    2506 </span>            :   { X86Inst::kSseToAvxMove     , 594  }, // #29</a>
+<a name="2507"><span class="lineNum">    2507 </span>            :   { X86Inst::kSseToAvxMove     , 593  }, // #30</a>
+<a name="2508"><span class="lineNum">    2508 </span>            :   { X86Inst::kSseToAvxExtend   , 599  }, // #31</a>
+<a name="2509"><span class="lineNum">    2509 </span>            :   { X86Inst::kSseToAvxMoveIfMem, 599  }, // #32</a>
+<a name="2510"><span class="lineNum">    2510 </span>            :   { X86Inst::kSseToAvxMove     , 599  }, // #33</a>
+<a name="2511"><span class="lineNum">    2511 </span>            :   { X86Inst::kSseToAvxMove     , 598  }, // #34</a>
+<a name="2512"><span class="lineNum">    2512 </span>            :   { X86Inst::kSseToAvxMoveIfMem, 593  }, // #35</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :   { X86Inst::kSseToAvxMove     , 591  }, // #36</a>
+<a name="2514"><span class="lineNum">    2514 </span>            :   { X86Inst::kSseToAvxExtend   , 590  }, // #37</a>
+<a name="2515"><span class="lineNum">    2515 </span>            :   { X86Inst::kSseToAvxExtend   , 589  }, // #38</a>
+<a name="2516"><span class="lineNum">    2516 </span>            :   { X86Inst::kSseToAvxExtend   , 583  }, // #39</a>
+<a name="2517"><span class="lineNum">    2517 </span>            :   { X86Inst::kSseToAvxMove     , 583  }, // #40</a>
+<a name="2518"><span class="lineNum">    2518 </span>            :   { X86Inst::kSseToAvxMove     , 584  }, // #41</a>
+<a name="2519"><span class="lineNum">    2519 </span>            :   { X86Inst::kSseToAvxExtend   , 584  }, // #42</a>
+<a name="2520"><span class="lineNum">    2520 </span>            :   { X86Inst::kSseToAvxExtend   , 585  }, // #43</a>
+<a name="2521"><span class="lineNum">    2521 </span>            :   { X86Inst::kSseToAvxExtend   , 587  }, // #44</a>
+<a name="2522"><span class="lineNum">    2522 </span>            :   { X86Inst::kSseToAvxExtend   , 586  }, // #45</a>
+<a name="2523"><span class="lineNum">    2523 </span>            :   { X86Inst::kSseToAvxBlend    , 587  }, // #46</a>
+<a name="2524"><span class="lineNum">    2524 </span>            :   { X86Inst::kSseToAvxExtend   , 593  }, // #47</a>
+<a name="2525"><span class="lineNum">    2525 </span>            :   { X86Inst::kSseToAvxExtend   , 596  }, // #48</a>
+<a name="2526"><span class="lineNum">    2526 </span>            :   { X86Inst::kSseToAvxMove     , 596  }, // #49</a>
+<a name="2527"><span class="lineNum">    2527 </span>            :   { X86Inst::kSseToAvxMove     , 637  }, // #50</a>
+<a name="2528"><span class="lineNum">    2528 </span>            :   { X86Inst::kSseToAvxExtend   , 623  }, // #51</a>
+<a name="2529"><span class="lineNum">    2529 </span>            :   { X86Inst::kSseToAvxExtend   , 624  }, // #52</a>
+<a name="2530"><span class="lineNum">    2530 </span>            :   { X86Inst::kSseToAvxExtend   , 630  }, // #53</a>
+<a name="2531"><span class="lineNum">    2531 </span>            :   { X86Inst::kSseToAvxMove     , 632  }, // #54</a>
+<a name="2532"><span class="lineNum">    2532 </span>            :   { X86Inst::kSseToAvxExtend   , 633  }, // #55</a>
+<a name="2533"><span class="lineNum">    2533 </span>            :   { X86Inst::kSseToAvxExtend   , 634  }, // #56</a>
+<a name="2534"><span class="lineNum">    2534 </span>            :   { X86Inst::kSseToAvxMove     , 633  }, // #57</a>
+<a name="2535"><span class="lineNum">    2535 </span>            :   { X86Inst::kSseToAvxExtend   , 649  }, // #58</a>
+<a name="2536"><span class="lineNum">    2536 </span>            :   { X86Inst::kSseToAvxExtend   , 651  }, // #59</a>
+<a name="2537"><span class="lineNum">    2537 </span>            :   { X86Inst::kSseToAvxExtend   , 652  }, // #60</a>
+<a name="2538"><span class="lineNum">    2538 </span>            :   { X86Inst::kSseToAvxExtend   , 653  }, // #61</a>
+<a name="2539"><span class="lineNum">    2539 </span>            :   { X86Inst::kSseToAvxExtend   , 654  }, // #62</a>
+<a name="2540"><span class="lineNum">    2540 </span>            :   { X86Inst::kSseToAvxExtend   , 655  }, // #63</a>
+<a name="2541"><span class="lineNum">    2541 </span>            :   { X86Inst::kSseToAvxMove     , 663  }, // #64</a>
+<a name="2542"><span class="lineNum">    2542 </span>            :   { X86Inst::kSseToAvxMove     , 681  }, // #65</a>
+<a name="2543"><span class="lineNum">    2543 </span>            :   { X86Inst::kSseToAvxExtend   , 680  }, // #66</a>
+<a name="2544"><span class="lineNum">    2544 </span>            :   { X86Inst::kSseToAvxExtend   , 682  }, // #67</a>
+<a name="2545"><span class="lineNum">    2545 </span>            :   { X86Inst::kSseToAvxExtend   , 677  }, // #68</a>
+<a name="2546"><span class="lineNum">    2546 </span>            :   { X86Inst::kSseToAvxExtend   , 685  }, // #69</a>
+<a name="2547"><span class="lineNum">    2547 </span>            :   { X86Inst::kSseToAvxExtend   , 697  }, // #70</a>
+<a name="2548"><span class="lineNum">    2548 </span>            :   { X86Inst::kSseToAvxMove     , 697  }, // #71</a>
+<a name="2549"><span class="lineNum">    2549 </span>            :   { X86Inst::kSseToAvxExtend   , 696  }, // #72</a>
+<a name="2550"><span class="lineNum">    2550 </span>            :   { X86Inst::kSseToAvxExtend   , 699  }, // #73</a>
+<a name="2551"><span class="lineNum">    2551 </span>            :   { X86Inst::kSseToAvxExtend   , 703  }, // #74</a>
+<a name="2552"><span class="lineNum">    2552 </span>            :   { X86Inst::kSseToAvxExtend   , 706  }, // #75</a>
+<a name="2553"><span class="lineNum">    2553 </span>            :   { X86Inst::kSseToAvxMove     , 707  }, // #76</a>
+<a name="2554"><span class="lineNum">    2554 </span>            :   { X86Inst::kSseToAvxExtend   , 715  }, // #77</a>
+<a name="2555"><span class="lineNum">    2555 </span>            :   { X86Inst::kSseToAvxExtend   , 709  }, // #78</a>
+<a name="2556"><span class="lineNum">    2556 </span>            :   { X86Inst::kSseToAvxMove     , 722  }, // #79</a>
+<a name="2557"><span class="lineNum">    2557 </span>            :   { X86Inst::kSseToAvxExtend   , 722  }, // #80</a>
+<a name="2558"><span class="lineNum">    2558 </span>            :   { X86Inst::kSseToAvxMove     , 717  }, // #81</a>
+<a name="2559"><span class="lineNum">    2559 </span>            :   { X86Inst::kSseToAvxExtend   , 717  }, // #82</a>
+<a name="2560"><span class="lineNum">    2560 </span>            :   { X86Inst::kSseToAvxExtend   , 693  }, // #83</a>
+<a name="2561"><span class="lineNum">    2561 </span>            :   { X86Inst::kSseToAvxMove     , 690  }, // #84</a>
+<a name="2562"><span class="lineNum">    2562 </span>            :   { X86Inst::kSseToAvxExtend   , 690  }, // #85</a>
+<a name="2563"><span class="lineNum">    2563 </span>            :   { X86Inst::kSseToAvxExtend   , 683  }, // #86</a>
+<a name="2564"><span class="lineNum">    2564 </span>            :   { X86Inst::kSseToAvxExtend   , -16  }  // #87</a>
+<a name="2565"><span class="lineNum">    2565 </span>            : };</a>
+<a name="2566"><span class="lineNum">    2566 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="2567"><span class="lineNum">    2567 </span>            : // ${sseToAvxData:End}</a>
+<a name="2568"><span class="lineNum">    2568 </span>            : </a>
+<a name="2569"><span class="lineNum">    2569 </span>            : // ============================================================================</a>
+<a name="2570"><span class="lineNum">    2570 </span>            : // [asmjit::X86Inst - Id &lt;-&gt; Name]</a>
+<a name="2571"><span class="lineNum">    2571 </span>            : // ============================================================================</a>
+<a name="2572"><span class="lineNum">    2572 </span>            : </a>
+<a name="2573"><span class="lineNum">    2573 </span>            : #if !defined(ASMJIT_DISABLE_TEXT)</a>
+<a name="2574"><span class="lineNum">    2574 </span>            : // ${nameData:Begin}</a>
+<a name="2575"><span class="lineNum">    2575 </span>            : // ------------------- Automatically generated, do not edit -------------------</a>
+<a name="2576"><span class="lineNum">    2576 </span>            : const char X86InstDB::nameData[] =</a>
+<a name="2577"><span class="lineNum">    2577 </span>            :   &quot;\0&quot; &quot;aaa\0&quot; &quot;aad\0&quot; &quot;aam\0&quot; &quot;aas\0&quot; &quot;adc\0&quot; &quot;adcx\0&quot; &quot;adox\0&quot; &quot;arpl\0&quot;</a>
+<a name="2578"><span class="lineNum">    2578 </span>            :   &quot;bextr\0&quot; &quot;blcfill\0&quot; &quot;blci\0&quot; &quot;blcic\0&quot; &quot;blcmsk\0&quot; &quot;blcs\0&quot; &quot;blsfill\0&quot;</a>
+<a name="2579"><span class="lineNum">    2579 </span>            :   &quot;blsi\0&quot; &quot;blsic\0&quot; &quot;blsmsk\0&quot; &quot;blsr\0&quot; &quot;bndcl\0&quot; &quot;bndcn\0&quot; &quot;bndcu\0&quot;</a>
+<a name="2580"><span class="lineNum">    2580 </span>            :   &quot;bndldx\0&quot; &quot;bndmk\0&quot; &quot;bndmov\0&quot; &quot;bndstx\0&quot; &quot;bound\0&quot; &quot;bsf\0&quot; &quot;bsr\0&quot;</a>
+<a name="2581"><span class="lineNum">    2581 </span>            :   &quot;bswap\0&quot; &quot;bt\0&quot; &quot;btc\0&quot; &quot;btr\0&quot; &quot;bts\0&quot; &quot;bzhi\0&quot; &quot;cbw\0&quot; &quot;cdq\0&quot; &quot;cdqe\0&quot;</a>
+<a name="2582"><span class="lineNum">    2582 </span>            :   &quot;clac\0&quot; &quot;clc\0&quot; &quot;cld\0&quot; &quot;clflush\0&quot; &quot;clflushopt\0&quot; &quot;cli\0&quot; &quot;clts\0&quot; &quot;clwb\0&quot;</a>
+<a name="2583"><span class="lineNum">    2583 </span>            :   &quot;clzero\0&quot; &quot;cmc\0&quot; &quot;cmova\0&quot; &quot;cmovae\0&quot; &quot;cmovc\0&quot; &quot;cmovg\0&quot; &quot;cmovge\0&quot;</a>
+<a name="2584"><span class="lineNum">    2584 </span>            :   &quot;cmovl\0&quot; &quot;cmovle\0&quot; &quot;cmovna\0&quot; &quot;cmovnae\0&quot; &quot;cmovnc\0&quot; &quot;cmovng\0&quot; &quot;cmovnge\0&quot;</a>
+<a name="2585"><span class="lineNum">    2585 </span>            :   &quot;cmovnl\0&quot; &quot;cmovnle\0&quot; &quot;cmovno\0&quot; &quot;cmovnp\0&quot; &quot;cmovns\0&quot; &quot;cmovnz\0&quot; &quot;cmovo\0&quot;</a>
+<a name="2586"><span class="lineNum">    2586 </span>            :   &quot;cmovp\0&quot; &quot;cmovpe\0&quot; &quot;cmovpo\0&quot; &quot;cmovs\0&quot; &quot;cmovz\0&quot; &quot;cmp\0&quot; &quot;cmps\0&quot;</a>
+<a name="2587"><span class="lineNum">    2587 </span>            :   &quot;cmpxchg\0&quot; &quot;cmpxchg16b\0&quot; &quot;cmpxchg8b\0&quot; &quot;cpuid\0&quot; &quot;cqo\0&quot; &quot;crc32\0&quot;</a>
+<a name="2588"><span class="lineNum">    2588 </span>            :   &quot;cvtpd2pi\0&quot; &quot;cvtpi2pd\0&quot; &quot;cvtpi2ps\0&quot; &quot;cvtps2pi\0&quot; &quot;cvttpd2pi\0&quot;</a>
+<a name="2589"><span class="lineNum">    2589 </span>            :   &quot;cvttps2pi\0&quot; &quot;cwd\0&quot; &quot;cwde\0&quot; &quot;daa\0&quot; &quot;das\0&quot; &quot;f2xm1\0&quot; &quot;fabs\0&quot; &quot;faddp\0&quot;</a>
+<a name="2590"><span class="lineNum">    2590 </span>            :   &quot;fbld\0&quot; &quot;fbstp\0&quot; &quot;fchs\0&quot; &quot;fclex\0&quot; &quot;fcmovb\0&quot; &quot;fcmovbe\0&quot; &quot;fcmove\0&quot;</a>
+<a name="2591"><span class="lineNum">    2591 </span>            :   &quot;fcmovnb\0&quot; &quot;fcmovnbe\0&quot; &quot;fcmovne\0&quot; &quot;fcmovnu\0&quot; &quot;fcmovu\0&quot; &quot;fcom\0&quot;</a>
+<a name="2592"><span class="lineNum">    2592 </span>            :   &quot;fcomi\0&quot; &quot;fcomip\0&quot; &quot;fcomp\0&quot; &quot;fcompp\0&quot; &quot;fcos\0&quot; &quot;fdecstp\0&quot; &quot;fdiv\0&quot;</a>
+<a name="2593"><span class="lineNum">    2593 </span>            :   &quot;fdivp\0&quot; &quot;fdivr\0&quot; &quot;fdivrp\0&quot; &quot;femms\0&quot; &quot;ffree\0&quot; &quot;fiadd\0&quot; &quot;ficom\0&quot;</a>
+<a name="2594"><span class="lineNum">    2594 </span>            :   &quot;ficomp\0&quot; &quot;fidiv\0&quot; &quot;fidivr\0&quot; &quot;fild\0&quot; &quot;fimul\0&quot; &quot;fincstp\0&quot; &quot;finit\0&quot;</a>
+<a name="2595"><span class="lineNum">    2595 </span>            :   &quot;fist\0&quot; &quot;fistp\0&quot; &quot;fisttp\0&quot; &quot;fisub\0&quot; &quot;fisubr\0&quot; &quot;fld\0&quot; &quot;fld1\0&quot; &quot;fldcw\0&quot;</a>
+<a name="2596"><span class="lineNum">    2596 </span>            :   &quot;fldenv\0&quot; &quot;fldl2e\0&quot; &quot;fldl2t\0&quot; &quot;fldlg2\0&quot; &quot;fldln2\0&quot; &quot;fldpi\0&quot; &quot;fldz\0&quot;</a>
+<a name="2597"><span class="lineNum">    2597 </span>            :   &quot;fmulp\0&quot; &quot;fnclex\0&quot; &quot;fninit\0&quot; &quot;fnop\0&quot; &quot;fnsave\0&quot; &quot;fnstcw\0&quot; &quot;fnstenv\0&quot;</a>
+<a name="2598"><span class="lineNum">    2598 </span>            :   &quot;fnstsw\0&quot; &quot;fpatan\0&quot; &quot;fprem\0&quot; &quot;fprem1\0&quot; &quot;fptan\0&quot; &quot;frndint\0&quot; &quot;frstor\0&quot;</a>
+<a name="2599"><span class="lineNum">    2599 </span>            :   &quot;fsave\0&quot; &quot;fscale\0&quot; &quot;fsin\0&quot; &quot;fsincos\0&quot; &quot;fsqrt\0&quot; &quot;fst\0&quot; &quot;fstcw\0&quot;</a>
+<a name="2600"><span class="lineNum">    2600 </span>            :   &quot;fstenv\0&quot; &quot;fstp\0&quot; &quot;fstsw\0&quot; &quot;fsubp\0&quot; &quot;fsubrp\0&quot; &quot;ftst\0&quot; &quot;fucom\0&quot;</a>
+<a name="2601"><span class="lineNum">    2601 </span>            :   &quot;fucomi\0&quot; &quot;fucomip\0&quot; &quot;fucomp\0&quot; &quot;fucompp\0&quot; &quot;fwait\0&quot; &quot;fxam\0&quot; &quot;fxch\0&quot;</a>
+<a name="2602"><span class="lineNum">    2602 </span>            :   &quot;fxrstor\0&quot; &quot;fxrstor64\0&quot; &quot;fxsave\0&quot; &quot;fxsave64\0&quot; &quot;fxtract\0&quot; &quot;fyl2x\0&quot;</a>
+<a name="2603"><span class="lineNum">    2603 </span>            :   &quot;fyl2xp1\0&quot; &quot;hlt\0&quot; &quot;inc\0&quot; &quot;ins\0&quot; &quot;insertq\0&quot; &quot;int3\0&quot; &quot;into\0&quot; &quot;invlpg\0&quot;</a>
+<a name="2604"><span class="lineNum">    2604 </span>            :   &quot;invpcid\0&quot; &quot;iret\0&quot; &quot;iretd\0&quot; &quot;iretq\0&quot; &quot;iretw\0&quot; &quot;ja\0&quot; &quot;jae\0&quot; &quot;jb\0&quot;</a>
+<a name="2605"><span class="lineNum">    2605 </span>            :   &quot;jbe\0&quot; &quot;jc\0&quot; &quot;je\0&quot; &quot;jecxz\0&quot; &quot;jg\0&quot; &quot;jge\0&quot; &quot;jl\0&quot; &quot;jle\0&quot; &quot;jmp\0&quot; &quot;jna\0&quot;</a>
+<a name="2606"><span class="lineNum">    2606 </span>            :   &quot;jnae\0&quot; &quot;jnb\0&quot; &quot;jnbe\0&quot; &quot;jnc\0&quot; &quot;jne\0&quot; &quot;jng\0&quot; &quot;jnge\0&quot; &quot;jnl\0&quot; &quot;jnle\0&quot;</a>
+<a name="2607"><span class="lineNum">    2607 </span>            :   &quot;jno\0&quot; &quot;jnp\0&quot; &quot;jns\0&quot; &quot;jnz\0&quot; &quot;jo\0&quot; &quot;jp\0&quot; &quot;jpe\0&quot; &quot;jpo\0&quot; &quot;js\0&quot; &quot;jz\0&quot;</a>
+<a name="2608"><span class="lineNum">    2608 </span>            :   &quot;kaddb\0&quot; &quot;kaddd\0&quot; &quot;kaddq\0&quot; &quot;kaddw\0&quot; &quot;kandb\0&quot; &quot;kandd\0&quot; &quot;kandnb\0&quot;</a>
+<a name="2609"><span class="lineNum">    2609 </span>            :   &quot;kandnd\0&quot; &quot;kandnq\0&quot; &quot;kandnw\0&quot; &quot;kandq\0&quot; &quot;kandw\0&quot; &quot;kmovb\0&quot; &quot;kmovw\0&quot;</a>
+<a name="2610"><span class="lineNum">    2610 </span>            :   &quot;knotb\0&quot; &quot;knotd\0&quot; &quot;knotq\0&quot; &quot;knotw\0&quot; &quot;korb\0&quot; &quot;kord\0&quot; &quot;korq\0&quot;</a>
+<a name="2611"><span class="lineNum">    2611 </span>            :   &quot;kortestb\0&quot; &quot;kortestd\0&quot; &quot;kortestq\0&quot; &quot;kortestw\0&quot; &quot;korw\0&quot; &quot;kshiftlb\0&quot;</a>
+<a name="2612"><span class="lineNum">    2612 </span>            :   &quot;kshiftld\0&quot; &quot;kshiftlq\0&quot; &quot;kshiftlw\0&quot; &quot;kshiftrb\0&quot; &quot;kshiftrd\0&quot; &quot;kshiftrq\0&quot;</a>
+<a name="2613"><span class="lineNum">    2613 </span>            :   &quot;kshiftrw\0&quot; &quot;ktestb\0&quot; &quot;ktestd\0&quot; &quot;ktestq\0&quot; &quot;ktestw\0&quot; &quot;kunpckbw\0&quot;</a>
+<a name="2614"><span class="lineNum">    2614 </span>            :   &quot;kunpckdq\0&quot; &quot;kunpckwd\0&quot; &quot;kxnorb\0&quot; &quot;kxnord\0&quot; &quot;kxnorq\0&quot; &quot;kxnorw\0&quot;</a>
+<a name="2615"><span class="lineNum">    2615 </span>            :   &quot;kxorb\0&quot; &quot;kxord\0&quot; &quot;kxorq\0&quot; &quot;kxorw\0&quot; &quot;lahf\0&quot; &quot;lar\0&quot; &quot;lds\0&quot; &quot;lea\0&quot;</a>
+<a name="2616"><span class="lineNum">    2616 </span>            :   &quot;leave\0&quot; &quot;les\0&quot; &quot;lfence\0&quot; &quot;lfs\0&quot; &quot;lgdt\0&quot; &quot;lgs\0&quot; &quot;lidt\0&quot; &quot;lldt\0&quot;</a>
+<a name="2617"><span class="lineNum">    2617 </span>            :   &quot;lmsw\0&quot; &quot;lods\0&quot; &quot;loop\0&quot; &quot;loope\0&quot; &quot;loopne\0&quot; &quot;lsl\0&quot; &quot;ltr\0&quot; &quot;lzcnt\0&quot;</a>
+<a name="2618"><span class="lineNum">    2618 </span>            :   &quot;mfence\0&quot; &quot;monitor\0&quot; &quot;movdq2q\0&quot; &quot;movnti\0&quot; &quot;movntq\0&quot; &quot;movntsd\0&quot;</a>
+<a name="2619"><span class="lineNum">    2619 </span>            :   &quot;movntss\0&quot; &quot;movq2dq\0&quot; &quot;movsx\0&quot; &quot;movsxd\0&quot; &quot;movzx\0&quot; &quot;mulx\0&quot; &quot;mwait\0&quot;</a>
+<a name="2620"><span class="lineNum">    2620 </span>            :   &quot;neg\0&quot; &quot;not\0&quot; &quot;out\0&quot; &quot;outs\0&quot; &quot;pause\0&quot; &quot;pavgusb\0&quot; &quot;pcommit\0&quot; &quot;pdep\0&quot;</a>
+<a name="2621"><span class="lineNum">    2621 </span>            :   &quot;pext\0&quot; &quot;pf2id\0&quot; &quot;pf2iw\0&quot; &quot;pfacc\0&quot; &quot;pfadd\0&quot; &quot;pfcmpeq\0&quot; &quot;pfcmpge\0&quot;</a>
+<a name="2622"><span class="lineNum">    2622 </span>            :   &quot;pfcmpgt\0&quot; &quot;pfmax\0&quot; &quot;pfmin\0&quot; &quot;pfmul\0&quot; &quot;pfnacc\0&quot; &quot;pfpnacc\0&quot; &quot;pfrcp\0&quot;</a>
+<a name="2623"><span class="lineNum">    2623 </span>            :   &quot;pfrcpit1\0&quot; &quot;pfrcpit2\0&quot; &quot;pfrcpv\0&quot; &quot;pfrsqit1\0&quot; &quot;pfrsqrt\0&quot; &quot;pfrsqrtv\0&quot;</a>
+<a name="2624"><span class="lineNum">    2624 </span>            :   &quot;pfsub\0&quot; &quot;pfsubr\0&quot; &quot;pi2fd\0&quot; &quot;pi2fw\0&quot; &quot;pmulhrw\0&quot; &quot;pop\0&quot; &quot;popa\0&quot;</a>
+<a name="2625"><span class="lineNum">    2625 </span>            :   &quot;popad\0&quot; &quot;popcnt\0&quot; &quot;popf\0&quot; &quot;popfd\0&quot; &quot;popfq\0&quot; &quot;prefetch\0&quot;</a>
+<a name="2626"><span class="lineNum">    2626 </span>            :   &quot;prefetchnta\0&quot; &quot;prefetcht0\0&quot; &quot;prefetcht1\0&quot; &quot;prefetcht2\0&quot; &quot;prefetchw\0&quot;</a>
+<a name="2627"><span class="lineNum">    2627 </span>            :   &quot;prefetchwt1\0&quot; &quot;pshufw\0&quot; &quot;pswapd\0&quot; &quot;push\0&quot; &quot;pusha\0&quot; &quot;pushad\0&quot; &quot;pushf\0&quot;</a>
+<a name="2628"><span class="lineNum">    2628 </span>            :   &quot;pushfd\0&quot; &quot;pushfq\0&quot; &quot;rcl\0&quot; &quot;rcr\0&quot; &quot;rdfsbase\0&quot; &quot;rdgsbase\0&quot; &quot;rdmsr\0&quot;</a>
+<a name="2629"><span class="lineNum">    2629 </span>            :   &quot;rdpmc\0&quot; &quot;rdrand\0&quot; &quot;rdseed\0&quot; &quot;rdtsc\0&quot; &quot;rdtscp\0&quot; &quot;rol\0&quot; &quot;ror\0&quot; &quot;rorx\0&quot;</a>
+<a name="2630"><span class="lineNum">    2630 </span>            :   &quot;rsm\0&quot; &quot;sahf\0&quot; &quot;sal\0&quot; &quot;sar\0&quot; &quot;sarx\0&quot; &quot;sbb\0&quot; &quot;scas\0&quot; &quot;seta\0&quot; &quot;setae\0&quot;</a>
+<a name="2631"><span class="lineNum">    2631 </span>            :   &quot;setb\0&quot; &quot;setbe\0&quot; &quot;setc\0&quot; &quot;sete\0&quot; &quot;setg\0&quot; &quot;setge\0&quot; &quot;setl\0&quot; &quot;setle\0&quot;</a>
+<a name="2632"><span class="lineNum">    2632 </span>            :   &quot;setna\0&quot; &quot;setnae\0&quot; &quot;setnb\0&quot; &quot;setnbe\0&quot; &quot;setnc\0&quot; &quot;setne\0&quot; &quot;setng\0&quot;</a>
+<a name="2633"><span class="lineNum">    2633 </span>            :   &quot;setnge\0&quot; &quot;setnl\0&quot; &quot;setnle\0&quot; &quot;setno\0&quot; &quot;setnp\0&quot; &quot;setns\0&quot; &quot;setnz\0&quot;</a>
+<a name="2634"><span class="lineNum">    2634 </span>            :   &quot;seto\0&quot; &quot;setp\0&quot; &quot;setpe\0&quot; &quot;setpo\0&quot; &quot;sets\0&quot; &quot;setz\0&quot; &quot;sfence\0&quot; &quot;sgdt\0&quot;</a>
+<a name="2635"><span class="lineNum">    2635 </span>            :   &quot;sha1msg1\0&quot; &quot;sha1msg2\0&quot; &quot;sha1nexte\0&quot; &quot;sha1rnds4\0&quot; &quot;sha256msg1\0&quot;</a>
+<a name="2636"><span class="lineNum">    2636 </span>            :   &quot;sha256msg2\0&quot; &quot;sha256rnds2\0&quot; &quot;shl\0&quot; &quot;shlx\0&quot; &quot;shr\0&quot; &quot;shrd\0&quot; &quot;shrx\0&quot;</a>
+<a name="2637"><span class="lineNum">    2637 </span>            :   &quot;sidt\0&quot; &quot;sldt\0&quot; &quot;smsw\0&quot; &quot;stac\0&quot; &quot;stc\0&quot; &quot;sti\0&quot; &quot;stos\0&quot; &quot;str\0&quot;</a>
+<a name="2638"><span class="lineNum">    2638 </span>            :   &quot;swapgs\0&quot; &quot;syscall\0&quot; &quot;sysenter\0&quot; &quot;sysexit\0&quot; &quot;sysexit64\0&quot; &quot;sysret\0&quot;</a>
+<a name="2639"><span class="lineNum">    2639 </span>            :   &quot;sysret64\0&quot; &quot;t1mskc\0&quot; &quot;tzcnt\0&quot; &quot;tzmsk\0&quot; &quot;ud2\0&quot; &quot;v4fmaddps\0&quot;</a>
+<a name="2640"><span class="lineNum">    2640 </span>            :   &quot;v4fnmaddps\0&quot; &quot;vaddpd\0&quot; &quot;vaddps\0&quot; &quot;vaddsd\0&quot; &quot;vaddss\0&quot; &quot;vaddsubpd\0&quot;</a>
+<a name="2641"><span class="lineNum">    2641 </span>            :   &quot;vaddsubps\0&quot; &quot;vaesdec\0&quot; &quot;vaesdeclast\0&quot; &quot;vaesenc\0&quot; &quot;vaesenclast\0&quot;</a>
+<a name="2642"><span class="lineNum">    2642 </span>            :   &quot;vaesimc\0&quot; &quot;vaeskeygenassist\0&quot; &quot;valignd\0&quot; &quot;valignq\0&quot; &quot;vandnpd\0&quot;</a>
+<a name="2643"><span class="lineNum">    2643 </span>            :   &quot;vandnps\0&quot; &quot;vandpd\0&quot; &quot;vandps\0&quot; &quot;vblendmb\0&quot; &quot;vblendmd\0&quot; &quot;vblendmpd\0&quot;</a>
+<a name="2644"><span class="lineNum">    2644 </span>            :   &quot;vblendmps\0&quot; &quot;vblendmq\0&quot; &quot;vblendmw\0&quot; &quot;vblendpd\0&quot; &quot;vblendps\0&quot;</a>
+<a name="2645"><span class="lineNum">    2645 </span>            :   &quot;vblendvpd\0&quot; &quot;vblendvps\0&quot; &quot;vbroadcastf128\0&quot; &quot;vbroadcastf32x2\0&quot;</a>
+<a name="2646"><span class="lineNum">    2646 </span>            :   &quot;vbroadcastf32x4\0&quot; &quot;vbroadcastf32x8\0&quot; &quot;vbroadcastf64x2\0&quot;</a>
+<a name="2647"><span class="lineNum">    2647 </span>            :   &quot;vbroadcastf64x4\0&quot; &quot;vbroadcasti128\0&quot; &quot;vbroadcasti32x2\0&quot;</a>
+<a name="2648"><span class="lineNum">    2648 </span>            :   &quot;vbroadcasti32x4\0&quot; &quot;vbroadcasti32x8\0&quot; &quot;vbroadcasti64x2\0&quot;</a>
+<a name="2649"><span class="lineNum">    2649 </span>            :   &quot;vbroadcasti64x4\0&quot; &quot;vbroadcastsd\0&quot; &quot;vbroadcastss\0&quot; &quot;vcmppd\0&quot; &quot;vcmpps\0&quot;</a>
+<a name="2650"><span class="lineNum">    2650 </span>            :   &quot;vcmpsd\0&quot; &quot;vcmpss\0&quot; &quot;vcomisd\0&quot; &quot;vcomiss\0&quot; &quot;vcompresspd\0&quot; &quot;vcompressps\0&quot;</a>
+<a name="2651"><span class="lineNum">    2651 </span>            :   &quot;vcvtdq2pd\0&quot; &quot;vcvtdq2ps\0&quot; &quot;vcvtpd2dq\0&quot; &quot;vcvtpd2ps\0&quot; &quot;vcvtpd2qq\0&quot;</a>
+<a name="2652"><span class="lineNum">    2652 </span>            :   &quot;vcvtpd2udq\0&quot; &quot;vcvtpd2uqq\0&quot; &quot;vcvtph2ps\0&quot; &quot;vcvtps2dq\0&quot; &quot;vcvtps2pd\0&quot;</a>
+<a name="2653"><span class="lineNum">    2653 </span>            :   &quot;vcvtps2ph\0&quot; &quot;vcvtps2qq\0&quot; &quot;vcvtps2udq\0&quot; &quot;vcvtps2uqq\0&quot; &quot;vcvtqq2pd\0&quot;</a>
+<a name="2654"><span class="lineNum">    2654 </span>            :   &quot;vcvtqq2ps\0&quot; &quot;vcvtsd2si\0&quot; &quot;vcvtsd2ss\0&quot; &quot;vcvtsd2usi\0&quot; &quot;vcvtsi2sd\0&quot;</a>
+<a name="2655"><span class="lineNum">    2655 </span>            :   &quot;vcvtsi2ss\0&quot; &quot;vcvtss2sd\0&quot; &quot;vcvtss2si\0&quot; &quot;vcvtss2usi\0&quot; &quot;vcvttpd2dq\0&quot;</a>
+<a name="2656"><span class="lineNum">    2656 </span>            :   &quot;vcvttpd2qq\0&quot; &quot;vcvttpd2udq\0&quot; &quot;vcvttpd2uqq\0&quot; &quot;vcvttps2dq\0&quot; &quot;vcvttps2qq\0&quot;</a>
+<a name="2657"><span class="lineNum">    2657 </span>            :   &quot;vcvttps2udq\0&quot; &quot;vcvttps2uqq\0&quot; &quot;vcvttsd2si\0&quot; &quot;vcvttsd2usi\0&quot; &quot;vcvttss2si\0&quot;</a>
+<a name="2658"><span class="lineNum">    2658 </span>            :   &quot;vcvttss2usi\0&quot; &quot;vcvtudq2pd\0&quot; &quot;vcvtudq2ps\0&quot; &quot;vcvtuqq2pd\0&quot; &quot;vcvtuqq2ps\0&quot;</a>
+<a name="2659"><span class="lineNum">    2659 </span>            :   &quot;vcvtusi2sd\0&quot; &quot;vcvtusi2ss\0&quot; &quot;vdbpsadbw\0&quot; &quot;vdivpd\0&quot; &quot;vdivps\0&quot; &quot;vdivsd\0&quot;</a>
+<a name="2660"><span class="lineNum">    2660 </span>            :   &quot;vdivss\0&quot; &quot;vdppd\0&quot; &quot;vdpps\0&quot; &quot;verr\0&quot; &quot;verw\0&quot; &quot;vexp2pd\0&quot; &quot;vexp2ps\0&quot;</a>
+<a name="2661"><span class="lineNum">    2661 </span>            :   &quot;vexpandpd\0&quot; &quot;vexpandps\0&quot; &quot;vextractf128\0&quot; &quot;vextractf32x4\0&quot;</a>
+<a name="2662"><span class="lineNum">    2662 </span>            :   &quot;vextractf32x8\0&quot; &quot;vextractf64x2\0&quot; &quot;vextractf64x4\0&quot; &quot;vextracti128\0&quot;</a>
+<a name="2663"><span class="lineNum">    2663 </span>            :   &quot;vextracti32x4\0&quot; &quot;vextracti32x8\0&quot; &quot;vextracti64x2\0&quot; &quot;vextracti64x4\0&quot;</a>
+<a name="2664"><span class="lineNum">    2664 </span>            :   &quot;vextractps\0&quot; &quot;vfixupimmpd\0&quot; &quot;vfixupimmps\0&quot; &quot;vfixupimmsd\0&quot;</a>
+<a name="2665"><span class="lineNum">    2665 </span>            :   &quot;vfixupimmss\0&quot; &quot;vfmadd132pd\0&quot; &quot;vfmadd132ps\0&quot; &quot;vfmadd132sd\0&quot;</a>
+<a name="2666"><span class="lineNum">    2666 </span>            :   &quot;vfmadd132ss\0&quot; &quot;vfmadd213pd\0&quot; &quot;vfmadd213ps\0&quot; &quot;vfmadd213sd\0&quot;</a>
+<a name="2667"><span class="lineNum">    2667 </span>            :   &quot;vfmadd213ss\0&quot; &quot;vfmadd231pd\0&quot; &quot;vfmadd231ps\0&quot; &quot;vfmadd231sd\0&quot;</a>
+<a name="2668"><span class="lineNum">    2668 </span>            :   &quot;vfmadd231ss\0&quot; &quot;vfmaddpd\0&quot; &quot;vfmaddps\0&quot; &quot;vfmaddsd\0&quot; &quot;vfmaddss\0&quot;</a>
+<a name="2669"><span class="lineNum">    2669 </span>            :   &quot;vfmaddsub132pd\0&quot; &quot;vfmaddsub132ps\0&quot; &quot;vfmaddsub213pd\0&quot; &quot;vfmaddsub213ps\0&quot;</a>
+<a name="2670"><span class="lineNum">    2670 </span>            :   &quot;vfmaddsub231pd\0&quot; &quot;vfmaddsub231ps\0&quot; &quot;vfmaddsubpd\0&quot; &quot;vfmaddsubps\0&quot;</a>
+<a name="2671"><span class="lineNum">    2671 </span>            :   &quot;vfmsub132pd\0&quot; &quot;vfmsub132ps\0&quot; &quot;vfmsub132sd\0&quot; &quot;vfmsub132ss\0&quot;</a>
+<a name="2672"><span class="lineNum">    2672 </span>            :   &quot;vfmsub213pd\0&quot; &quot;vfmsub213ps\0&quot; &quot;vfmsub213sd\0&quot; &quot;vfmsub213ss\0&quot;</a>
+<a name="2673"><span class="lineNum">    2673 </span>            :   &quot;vfmsub231pd\0&quot; &quot;vfmsub231ps\0&quot; &quot;vfmsub231sd\0&quot; &quot;vfmsub231ss\0&quot;</a>
+<a name="2674"><span class="lineNum">    2674 </span>            :   &quot;vfmsubadd132pd\0&quot; &quot;vfmsubadd132ps\0&quot; &quot;vfmsubadd213pd\0&quot; &quot;vfmsubadd213ps\0&quot;</a>
+<a name="2675"><span class="lineNum">    2675 </span>            :   &quot;vfmsubadd231pd\0&quot; &quot;vfmsubadd231ps\0&quot; &quot;vfmsubaddpd\0&quot; &quot;vfmsubaddps\0&quot;</a>
+<a name="2676"><span class="lineNum">    2676 </span>            :   &quot;vfmsubpd\0&quot; &quot;vfmsubps\0&quot; &quot;vfmsubsd\0&quot; &quot;vfmsubss\0&quot; &quot;vfnmadd132pd\0&quot;</a>
+<a name="2677"><span class="lineNum">    2677 </span>            :   &quot;vfnmadd132ps\0&quot; &quot;vfnmadd132sd\0&quot; &quot;vfnmadd132ss\0&quot; &quot;vfnmadd213pd\0&quot;</a>
+<a name="2678"><span class="lineNum">    2678 </span>            :   &quot;vfnmadd213ps\0&quot; &quot;vfnmadd213sd\0&quot; &quot;vfnmadd213ss\0&quot; &quot;vfnmadd231pd\0&quot;</a>
+<a name="2679"><span class="lineNum">    2679 </span>            :   &quot;vfnmadd231ps\0&quot; &quot;vfnmadd231sd\0&quot; &quot;vfnmadd231ss\0&quot; &quot;vfnmaddpd\0&quot;</a>
+<a name="2680"><span class="lineNum">    2680 </span>            :   &quot;vfnmaddps\0&quot; &quot;vfnmaddsd\0&quot; &quot;vfnmaddss\0&quot; &quot;vfnmsub132pd\0&quot; &quot;vfnmsub132ps\0&quot;</a>
+<a name="2681"><span class="lineNum">    2681 </span>            :   &quot;vfnmsub132sd\0&quot; &quot;vfnmsub132ss\0&quot; &quot;vfnmsub213pd\0&quot; &quot;vfnmsub213ps\0&quot;</a>
+<a name="2682"><span class="lineNum">    2682 </span>            :   &quot;vfnmsub213sd\0&quot; &quot;vfnmsub213ss\0&quot; &quot;vfnmsub231pd\0&quot; &quot;vfnmsub231ps\0&quot;</a>
+<a name="2683"><span class="lineNum">    2683 </span>            :   &quot;vfnmsub231sd\0&quot; &quot;vfnmsub231ss\0&quot; &quot;vfnmsubpd\0&quot; &quot;vfnmsubps\0&quot; &quot;vfnmsubsd\0&quot;</a>
+<a name="2684"><span class="lineNum">    2684 </span>            :   &quot;vfnmsubss\0&quot; &quot;vfpclasspd\0&quot; &quot;vfpclassps\0&quot; &quot;vfpclasssd\0&quot; &quot;vfpclassss\0&quot;</a>
+<a name="2685"><span class="lineNum">    2685 </span>            :   &quot;vfrczpd\0&quot; &quot;vfrczps\0&quot; &quot;vfrczsd\0&quot; &quot;vfrczss\0&quot; &quot;vgatherdpd\0&quot; &quot;vgatherdps\0&quot;</a>
+<a name="2686"><span class="lineNum">    2686 </span>            :   &quot;vgatherpf0dpd\0&quot; &quot;vgatherpf0dps\0&quot; &quot;vgatherpf0qpd\0&quot; &quot;vgatherpf0qps\0&quot;</a>
+<a name="2687"><span class="lineNum">    2687 </span>            :   &quot;vgatherpf1dpd\0&quot; &quot;vgatherpf1dps\0&quot; &quot;vgatherpf1qpd\0&quot; &quot;vgatherpf1qps\0&quot;</a>
+<a name="2688"><span class="lineNum">    2688 </span>            :   &quot;vgatherqpd\0&quot; &quot;vgatherqps\0&quot; &quot;vgetexppd\0&quot; &quot;vgetexpps\0&quot; &quot;vgetexpsd\0&quot;</a>
+<a name="2689"><span class="lineNum">    2689 </span>            :   &quot;vgetexpss\0&quot; &quot;vgetmantpd\0&quot; &quot;vgetmantps\0&quot; &quot;vgetmantsd\0&quot; &quot;vgetmantss\0&quot;</a>
+<a name="2690"><span class="lineNum">    2690 </span>            :   &quot;vhaddpd\0&quot; &quot;vhaddps\0&quot; &quot;vhsubpd\0&quot; &quot;vhsubps\0&quot; &quot;vinsertf128\0&quot;</a>
+<a name="2691"><span class="lineNum">    2691 </span>            :   &quot;vinsertf32x4\0&quot; &quot;vinsertf32x8\0&quot; &quot;vinsertf64x2\0&quot; &quot;vinsertf64x4\0&quot;</a>
+<a name="2692"><span class="lineNum">    2692 </span>            :   &quot;vinserti128\0&quot; &quot;vinserti32x4\0&quot; &quot;vinserti32x8\0&quot; &quot;vinserti64x2\0&quot;</a>
+<a name="2693"><span class="lineNum">    2693 </span>            :   &quot;vinserti64x4\0&quot; &quot;vinsertps\0&quot; &quot;vlddqu\0&quot; &quot;vldmxcsr\0&quot; &quot;vmaskmovdqu\0&quot;</a>
+<a name="2694"><span class="lineNum">    2694 </span>            :   &quot;vmaskmovpd\0&quot; &quot;vmaskmovps\0&quot; &quot;vmaxpd\0&quot; &quot;vmaxps\0&quot; &quot;vmaxsd\0&quot; &quot;vmaxss\0&quot;</a>
+<a name="2695"><span class="lineNum">    2695 </span>            :   &quot;vminpd\0&quot; &quot;vminps\0&quot; &quot;vminsd\0&quot; &quot;vminss\0&quot; &quot;vmovapd\0&quot; &quot;vmovaps\0&quot; &quot;vmovd\0&quot;</a>
+<a name="2696"><span class="lineNum">    2696 </span>            :   &quot;vmovddup\0&quot; &quot;vmovdqa\0&quot; &quot;vmovdqa32\0&quot; &quot;vmovdqa64\0&quot; &quot;vmovdqu\0&quot;</a>
+<a name="2697"><span class="lineNum">    2697 </span>            :   &quot;vmovdqu16\0&quot; &quot;vmovdqu32\0&quot; &quot;vmovdqu64\0&quot; &quot;vmovdqu8\0&quot; &quot;vmovhlps\0&quot;</a>
+<a name="2698"><span class="lineNum">    2698 </span>            :   &quot;vmovhpd\0&quot; &quot;vmovhps\0&quot; &quot;vmovlhps\0&quot; &quot;vmovlpd\0&quot; &quot;vmovlps\0&quot; &quot;vmovmskpd\0&quot;</a>
+<a name="2699"><span class="lineNum">    2699 </span>            :   &quot;vmovmskps\0&quot; &quot;vmovntdq\0&quot; &quot;vmovntdqa\0&quot; &quot;vmovntpd\0&quot; &quot;vmovntps\0&quot; &quot;vmovq\0&quot;</a>
+<a name="2700"><span class="lineNum">    2700 </span>            :   &quot;vmovsd\0&quot; &quot;vmovshdup\0&quot; &quot;vmovsldup\0&quot; &quot;vmovss\0&quot; &quot;vmovupd\0&quot; &quot;vmovups\0&quot;</a>
+<a name="2701"><span class="lineNum">    2701 </span>            :   &quot;vmpsadbw\0&quot; &quot;vmulpd\0&quot; &quot;vmulps\0&quot; &quot;vmulsd\0&quot; &quot;vmulss\0&quot; &quot;vorpd\0&quot; &quot;vorps\0&quot;</a>
+<a name="2702"><span class="lineNum">    2702 </span>            :   &quot;vp4dpwssd\0&quot; &quot;vp4dpwssds\0&quot; &quot;vpabsb\0&quot; &quot;vpabsd\0&quot; &quot;vpabsq\0&quot; &quot;vpabsw\0&quot;</a>
+<a name="2703"><span class="lineNum">    2703 </span>            :   &quot;vpackssdw\0&quot; &quot;vpacksswb\0&quot; &quot;vpackusdw\0&quot; &quot;vpackuswb\0&quot; &quot;vpaddb\0&quot; &quot;vpaddd\0&quot;</a>
+<a name="2704"><span class="lineNum">    2704 </span>            :   &quot;vpaddq\0&quot; &quot;vpaddsb\0&quot; &quot;vpaddsw\0&quot; &quot;vpaddusb\0&quot; &quot;vpaddusw\0&quot; &quot;vpaddw\0&quot;</a>
+<a name="2705"><span class="lineNum">    2705 </span>            :   &quot;vpalignr\0&quot; &quot;vpand\0&quot; &quot;vpandd\0&quot; &quot;vpandn\0&quot; &quot;vpandnd\0&quot; &quot;vpandnq\0&quot;</a>
+<a name="2706"><span class="lineNum">    2706 </span>            :   &quot;vpandq\0&quot; &quot;vpavgb\0&quot; &quot;vpavgw\0&quot; &quot;vpblendd\0&quot; &quot;vpblendvb\0&quot; &quot;vpblendw\0&quot;</a>
+<a name="2707"><span class="lineNum">    2707 </span>            :   &quot;vpbroadcastb\0&quot; &quot;vpbroadcastd\0&quot; &quot;vpbroadcastmb2d\0&quot; &quot;vpbroadcastmb2q\0&quot;</a>
+<a name="2708"><span class="lineNum">    2708 </span>            :   &quot;vpbroadcastq\0&quot; &quot;vpbroadcastw\0&quot; &quot;vpclmulqdq\0&quot; &quot;vpcmov\0&quot; &quot;vpcmpb\0&quot;</a>
+<a name="2709"><span class="lineNum">    2709 </span>            :   &quot;vpcmpd\0&quot; &quot;vpcmpeqb\0&quot; &quot;vpcmpeqd\0&quot; &quot;vpcmpeqq\0&quot; &quot;vpcmpeqw\0&quot; &quot;vpcmpestri\0&quot;</a>
+<a name="2710"><span class="lineNum">    2710 </span>            :   &quot;vpcmpestrm\0&quot; &quot;vpcmpgtb\0&quot; &quot;vpcmpgtd\0&quot; &quot;vpcmpgtq\0&quot; &quot;vpcmpgtw\0&quot;</a>
+<a name="2711"><span class="lineNum">    2711 </span>            :   &quot;vpcmpistri\0&quot; &quot;vpcmpistrm\0&quot; &quot;vpcmpq\0&quot; &quot;vpcmpub\0&quot; &quot;vpcmpud\0&quot; &quot;vpcmpuq\0&quot;</a>
+<a name="2712"><span class="lineNum">    2712 </span>            :   &quot;vpcmpuw\0&quot; &quot;vpcmpw\0&quot; &quot;vpcomb\0&quot; &quot;vpcomd\0&quot; &quot;vpcompressd\0&quot; &quot;vpcompressq\0&quot;</a>
+<a name="2713"><span class="lineNum">    2713 </span>            :   &quot;vpcomq\0&quot; &quot;vpcomub\0&quot; &quot;vpcomud\0&quot; &quot;vpcomuq\0&quot; &quot;vpcomuw\0&quot; &quot;vpcomw\0&quot;</a>
+<a name="2714"><span class="lineNum">    2714 </span>            :   &quot;vpconflictd\0&quot; &quot;vpconflictq\0&quot; &quot;vperm2f128\0&quot; &quot;vperm2i128\0&quot; &quot;vpermb\0&quot;</a>
+<a name="2715"><span class="lineNum">    2715 </span>            :   &quot;vpermd\0&quot; &quot;vpermi2b\0&quot; &quot;vpermi2d\0&quot; &quot;vpermi2pd\0&quot; &quot;vpermi2ps\0&quot; &quot;vpermi2q\0&quot;</a>
+<a name="2716"><span class="lineNum">    2716 </span>            :   &quot;vpermi2w\0&quot; &quot;vpermil2pd\0&quot; &quot;vpermil2ps\0&quot; &quot;vpermilpd\0&quot; &quot;vpermilps\0&quot;</a>
+<a name="2717"><span class="lineNum">    2717 </span>            :   &quot;vpermpd\0&quot; &quot;vpermps\0&quot; &quot;vpermq\0&quot; &quot;vpermt2b\0&quot; &quot;vpermt2d\0&quot; &quot;vpermt2pd\0&quot;</a>
+<a name="2718"><span class="lineNum">    2718 </span>            :   &quot;vpermt2ps\0&quot; &quot;vpermt2q\0&quot; &quot;vpermt2w\0&quot; &quot;vpermw\0&quot; &quot;vpexpandd\0&quot;</a>
+<a name="2719"><span class="lineNum">    2719 </span>            :   &quot;vpexpandq\0&quot; &quot;vpextrb\0&quot; &quot;vpextrd\0&quot; &quot;vpextrq\0&quot; &quot;vpextrw\0&quot; &quot;vpgatherdd\0&quot;</a>
+<a name="2720"><span class="lineNum">    2720 </span>            :   &quot;vpgatherdq\0&quot; &quot;vpgatherqd\0&quot; &quot;vpgatherqq\0&quot; &quot;vphaddbd\0&quot; &quot;vphaddbq\0&quot;</a>
+<a name="2721"><span class="lineNum">    2721 </span>            :   &quot;vphaddbw\0&quot; &quot;vphaddd\0&quot; &quot;vphadddq\0&quot; &quot;vphaddsw\0&quot; &quot;vphaddubd\0&quot;</a>
+<a name="2722"><span class="lineNum">    2722 </span>            :   &quot;vphaddubq\0&quot; &quot;vphaddubw\0&quot; &quot;vphaddudq\0&quot; &quot;vphadduwd\0&quot; &quot;vphadduwq\0&quot;</a>
+<a name="2723"><span class="lineNum">    2723 </span>            :   &quot;vphaddw\0&quot; &quot;vphaddwd\0&quot; &quot;vphaddwq\0&quot; &quot;vphminposuw\0&quot; &quot;vphsubbw\0&quot;</a>
+<a name="2724"><span class="lineNum">    2724 </span>            :   &quot;vphsubd\0&quot; &quot;vphsubdq\0&quot; &quot;vphsubsw\0&quot; &quot;vphsubw\0&quot; &quot;vphsubwd\0&quot; &quot;vpinsrb\0&quot;</a>
+<a name="2725"><span class="lineNum">    2725 </span>            :   &quot;vpinsrd\0&quot; &quot;vpinsrq\0&quot; &quot;vpinsrw\0&quot; &quot;vplzcntd\0&quot; &quot;vplzcntq\0&quot; &quot;vpmacsdd\0&quot;</a>
+<a name="2726"><span class="lineNum">    2726 </span>            :   &quot;vpmacsdqh\0&quot; &quot;vpmacsdql\0&quot; &quot;vpmacssdd\0&quot; &quot;vpmacssdqh\0&quot; &quot;vpmacssdql\0&quot;</a>
+<a name="2727"><span class="lineNum">    2727 </span>            :   &quot;vpmacsswd\0&quot; &quot;vpmacssww\0&quot; &quot;vpmacswd\0&quot; &quot;vpmacsww\0&quot; &quot;vpmadcsswd\0&quot;</a>
+<a name="2728"><span class="lineNum">    2728 </span>            :   &quot;vpmadcswd\0&quot; &quot;vpmadd52huq\0&quot; &quot;vpmadd52luq\0&quot; &quot;vpmaddubsw\0&quot; &quot;vpmaddwd\0&quot;</a>
+<a name="2729"><span class="lineNum">    2729 </span>            :   &quot;vpmaskmovd\0&quot; &quot;vpmaskmovq\0&quot; &quot;vpmaxsb\0&quot; &quot;vpmaxsd\0&quot; &quot;vpmaxsq\0&quot; &quot;vpmaxsw\0&quot;</a>
+<a name="2730"><span class="lineNum">    2730 </span>            :   &quot;vpmaxub\0&quot; &quot;vpmaxud\0&quot; &quot;vpmaxuq\0&quot; &quot;vpmaxuw\0&quot; &quot;vpminsb\0&quot; &quot;vpminsd\0&quot;</a>
+<a name="2731"><span class="lineNum">    2731 </span>            :   &quot;vpminsq\0&quot; &quot;vpminsw\0&quot; &quot;vpminub\0&quot; &quot;vpminud\0&quot; &quot;vpminuq\0&quot; &quot;vpminuw\0&quot;</a>
+<a name="2732"><span class="lineNum">    2732 </span>            :   &quot;vpmovb2m\0&quot; &quot;vpmovd2m\0&quot; &quot;vpmovdb\0&quot; &quot;vpmovdw\0&quot; &quot;vpmovm2b\0&quot; &quot;vpmovm2d\0&quot;</a>
+<a name="2733"><span class="lineNum">    2733 </span>            :   &quot;vpmovm2q\0&quot; &quot;vpmovm2w\0&quot; &quot;vpmovmskb\0&quot; &quot;vpmovq2m\0&quot; &quot;vpmovqb\0&quot; &quot;vpmovqd\0&quot;</a>
+<a name="2734"><span class="lineNum">    2734 </span>            :   &quot;vpmovqw\0&quot; &quot;vpmovsdb\0&quot; &quot;vpmovsdw\0&quot; &quot;vpmovsqb\0&quot; &quot;vpmovsqd\0&quot; &quot;vpmovsqw\0&quot;</a>
+<a name="2735"><span class="lineNum">    2735 </span>            :   &quot;vpmovswb\0&quot; &quot;vpmovsxbd\0&quot; &quot;vpmovsxbq\0&quot; &quot;vpmovsxbw\0&quot; &quot;vpmovsxdq\0&quot;</a>
+<a name="2736"><span class="lineNum">    2736 </span>            :   &quot;vpmovsxwd\0&quot; &quot;vpmovsxwq\0&quot; &quot;vpmovusdb\0&quot; &quot;vpmovusdw\0&quot; &quot;vpmovusqb\0&quot;</a>
+<a name="2737"><span class="lineNum">    2737 </span>            :   &quot;vpmovusqd\0&quot; &quot;vpmovusqw\0&quot; &quot;vpmovuswb\0&quot; &quot;vpmovw2m\0&quot; &quot;vpmovwb\0&quot;</a>
+<a name="2738"><span class="lineNum">    2738 </span>            :   &quot;vpmovzxbd\0&quot; &quot;vpmovzxbq\0&quot; &quot;vpmovzxbw\0&quot; &quot;vpmovzxdq\0&quot; &quot;vpmovzxwd\0&quot;</a>
+<a name="2739"><span class="lineNum">    2739 </span>            :   &quot;vpmovzxwq\0&quot; &quot;vpmuldq\0&quot; &quot;vpmulhrsw\0&quot; &quot;vpmulhuw\0&quot; &quot;vpmulhw\0&quot; &quot;vpmulld\0&quot;</a>
+<a name="2740"><span class="lineNum">    2740 </span>            :   &quot;vpmullq\0&quot; &quot;vpmullw\0&quot; &quot;vpmultishiftqb\0&quot; &quot;vpmuludq\0&quot; &quot;vpopcntd\0&quot;</a>
+<a name="2741"><span class="lineNum">    2741 </span>            :   &quot;vpopcntq\0&quot; &quot;vpor\0&quot; &quot;vpord\0&quot; &quot;vporq\0&quot; &quot;vpperm\0&quot; &quot;vprold\0&quot; &quot;vprolq\0&quot;</a>
+<a name="2742"><span class="lineNum">    2742 </span>            :   &quot;vprolvd\0&quot; &quot;vprolvq\0&quot; &quot;vprord\0&quot; &quot;vprorq\0&quot; &quot;vprorvd\0&quot; &quot;vprorvq\0&quot;</a>
+<a name="2743"><span class="lineNum">    2743 </span>            :   &quot;vprotb\0&quot; &quot;vprotd\0&quot; &quot;vprotq\0&quot; &quot;vprotw\0&quot; &quot;vpsadbw\0&quot; &quot;vpscatterdd\0&quot;</a>
+<a name="2744"><span class="lineNum">    2744 </span>            :   &quot;vpscatterdq\0&quot; &quot;vpscatterqd\0&quot; &quot;vpscatterqq\0&quot; &quot;vpshab\0&quot; &quot;vpshad\0&quot;</a>
+<a name="2745"><span class="lineNum">    2745 </span>            :   &quot;vpshaq\0&quot; &quot;vpshaw\0&quot; &quot;vpshlb\0&quot; &quot;vpshld\0&quot; &quot;vpshlq\0&quot; &quot;vpshlw\0&quot; &quot;vpshufb\0&quot;</a>
+<a name="2746"><span class="lineNum">    2746 </span>            :   &quot;vpshufd\0&quot; &quot;vpshufhw\0&quot; &quot;vpshuflw\0&quot; &quot;vpsignb\0&quot; &quot;vpsignd\0&quot; &quot;vpsignw\0&quot;</a>
+<a name="2747"><span class="lineNum">    2747 </span>            :   &quot;vpslld\0&quot; &quot;vpslldq\0&quot; &quot;vpsllq\0&quot; &quot;vpsllvd\0&quot; &quot;vpsllvq\0&quot; &quot;vpsllvw\0&quot;</a>
+<a name="2748"><span class="lineNum">    2748 </span>            :   &quot;vpsllw\0&quot; &quot;vpsrad\0&quot; &quot;vpsraq\0&quot; &quot;vpsravd\0&quot; &quot;vpsravq\0&quot; &quot;vpsravw\0&quot;</a>
+<a name="2749"><span class="lineNum">    2749 </span>            :   &quot;vpsraw\0&quot; &quot;vpsrld\0&quot; &quot;vpsrldq\0&quot; &quot;vpsrlq\0&quot; &quot;vpsrlvd\0&quot; &quot;vpsrlvq\0&quot;</a>
+<a name="2750"><span class="lineNum">    2750 </span>            :   &quot;vpsrlvw\0&quot; &quot;vpsrlw\0&quot; &quot;vpsubb\0&quot; &quot;vpsubd\0&quot; &quot;vpsubq\0&quot; &quot;vpsubsb\0&quot;</a>
+<a name="2751"><span class="lineNum">    2751 </span>            :   &quot;vpsubsw\0&quot; &quot;vpsubusb\0&quot; &quot;vpsubusw\0&quot; &quot;vpsubw\0&quot; &quot;vpternlogd\0&quot;</a>
+<a name="2752"><span class="lineNum">    2752 </span>            :   &quot;vpternlogq\0&quot; &quot;vptest\0&quot; &quot;vptestmb\0&quot; &quot;vptestmd\0&quot; &quot;vptestmq\0&quot; &quot;vptestmw\0&quot;</a>
+<a name="2753"><span class="lineNum">    2753 </span>            :   &quot;vptestnmb\0&quot; &quot;vptestnmd\0&quot; &quot;vptestnmq\0&quot; &quot;vptestnmw\0&quot; &quot;vpunpckhbw\0&quot;</a>
+<a name="2754"><span class="lineNum">    2754 </span>            :   &quot;vpunpckhdq\0&quot; &quot;vpunpckhqdq\0&quot; &quot;vpunpckhwd\0&quot; &quot;vpunpcklbw\0&quot; &quot;vpunpckldq\0&quot;</a>
+<a name="2755"><span class="lineNum">    2755 </span>            :   &quot;vpunpcklqdq\0&quot; &quot;vpunpcklwd\0&quot; &quot;vpxor\0&quot; &quot;vpxord\0&quot; &quot;vpxorq\0&quot; &quot;vrangepd\0&quot;</a>
+<a name="2756"><span class="lineNum">    2756 </span>            :   &quot;vrangeps\0&quot; &quot;vrangesd\0&quot; &quot;vrangess\0&quot; &quot;vrcp14pd\0&quot; &quot;vrcp14ps\0&quot; &quot;vrcp14sd\0&quot;</a>
+<a name="2757"><span class="lineNum">    2757 </span>            :   &quot;vrcp14ss\0&quot; &quot;vrcp28pd\0&quot; &quot;vrcp28ps\0&quot; &quot;vrcp28sd\0&quot; &quot;vrcp28ss\0&quot; &quot;vrcpps\0&quot;</a>
+<a name="2758"><span class="lineNum">    2758 </span>            :   &quot;vrcpss\0&quot; &quot;vreducepd\0&quot; &quot;vreduceps\0&quot; &quot;vreducesd\0&quot; &quot;vreducess\0&quot;</a>
+<a name="2759"><span class="lineNum">    2759 </span>            :   &quot;vrndscalepd\0&quot; &quot;vrndscaleps\0&quot; &quot;vrndscalesd\0&quot; &quot;vrndscaless\0&quot; &quot;vroundpd\0&quot;</a>
+<a name="2760"><span class="lineNum">    2760 </span>            :   &quot;vroundps\0&quot; &quot;vroundsd\0&quot; &quot;vroundss\0&quot; &quot;vrsqrt14pd\0&quot; &quot;vrsqrt14ps\0&quot;</a>
+<a name="2761"><span class="lineNum">    2761 </span>            :   &quot;vrsqrt14sd\0&quot; &quot;vrsqrt14ss\0&quot; &quot;vrsqrt28pd\0&quot; &quot;vrsqrt28ps\0&quot; &quot;vrsqrt28sd\0&quot;</a>
+<a name="2762"><span class="lineNum">    2762 </span>            :   &quot;vrsqrt28ss\0&quot; &quot;vrsqrtps\0&quot; &quot;vrsqrtss\0&quot; &quot;vscalefpd\0&quot; &quot;vscalefps\0&quot;</a>
+<a name="2763"><span class="lineNum">    2763 </span>            :   &quot;vscalefsd\0&quot; &quot;vscalefss\0&quot; &quot;vscatterdpd\0&quot; &quot;vscatterdps\0&quot;</a>
+<a name="2764"><span class="lineNum">    2764 </span>            :   &quot;vscatterpf0dpd\0&quot; &quot;vscatterpf0dps\0&quot; &quot;vscatterpf0qpd\0&quot; &quot;vscatterpf0qps\0&quot;</a>
+<a name="2765"><span class="lineNum">    2765 </span>            :   &quot;vscatterpf1dpd\0&quot; &quot;vscatterpf1dps\0&quot; &quot;vscatterpf1qpd\0&quot; &quot;vscatterpf1qps\0&quot;</a>
+<a name="2766"><span class="lineNum">    2766 </span>            :   &quot;vscatterqpd\0&quot; &quot;vscatterqps\0&quot; &quot;vshuff32x4\0&quot; &quot;vshuff64x2\0&quot; &quot;vshufi32x4\0&quot;</a>
+<a name="2767"><span class="lineNum">    2767 </span>            :   &quot;vshufi64x2\0&quot; &quot;vshufpd\0&quot; &quot;vshufps\0&quot; &quot;vsqrtpd\0&quot; &quot;vsqrtps\0&quot; &quot;vsqrtsd\0&quot;</a>
+<a name="2768"><span class="lineNum">    2768 </span>            :   &quot;vsqrtss\0&quot; &quot;vstmxcsr\0&quot; &quot;vsubpd\0&quot; &quot;vsubps\0&quot; &quot;vsubsd\0&quot; &quot;vsubss\0&quot;</a>
+<a name="2769"><span class="lineNum">    2769 </span>            :   &quot;vtestpd\0&quot; &quot;vtestps\0&quot; &quot;vucomisd\0&quot; &quot;vucomiss\0&quot; &quot;vunpckhpd\0&quot; &quot;vunpckhps\0&quot;</a>
+<a name="2770"><span class="lineNum">    2770 </span>            :   &quot;vunpcklpd\0&quot; &quot;vunpcklps\0&quot; &quot;vxorpd\0&quot; &quot;vxorps\0&quot; &quot;vzeroall\0&quot; &quot;vzeroupper\0&quot;</a>
+<a name="2771"><span class="lineNum">    2771 </span>            :   &quot;wbinvd\0&quot; &quot;wrfsbase\0&quot; &quot;wrgsbase\0&quot; &quot;wrmsr\0&quot; &quot;xabort\0&quot; &quot;xadd\0&quot; &quot;xbegin\0&quot;</a>
+<a name="2772"><span class="lineNum">    2772 </span>            :   &quot;xend\0&quot; &quot;xgetbv\0&quot; &quot;xlatb\0&quot; &quot;xrstors\0&quot; &quot;xrstors64\0&quot; &quot;xsavec\0&quot;</a>
+<a name="2773"><span class="lineNum">    2773 </span>            :   &quot;xsavec64\0&quot; &quot;xsaveopt\0&quot; &quot;xsaveopt64\0&quot; &quot;xsaves\0&quot; &quot;xsaves64\0&quot; &quot;xsetbv\0&quot;</a>
+<a name="2774"><span class="lineNum">    2774 </span>            :   &quot;xtest&quot;;</a>
+<a name="2775"><span class="lineNum">    2775 </span>            : </a>
+<a name="2776"><span class="lineNum">    2776 </span>            : enum {</a>
+<a name="2777"><span class="lineNum">    2777 </span>            :   kX86InstMaxLength = 16</a>
+<a name="2778"><span class="lineNum">    2778 </span>            : };</a>
+<a name="2779"><span class="lineNum">    2779 </span>            : </a>
+<a name="2780"><span class="lineNum">    2780 </span>            : struct InstNameAZ {</a>
+<a name="2781"><span class="lineNum">    2781 </span>            :   uint16_t start;</a>
+<a name="2782"><span class="lineNum">    2782 </span>            :   uint16_t end;</a>
+<a name="2783"><span class="lineNum">    2783 </span>            : };</a>
+<a name="2784"><span class="lineNum">    2784 </span>            : </a>
+<a name="2785"><span class="lineNum">    2785 </span>            : static const InstNameAZ X86InstNameAZ[26] = {</a>
+<a name="2786"><span class="lineNum">    2786 </span>            :   { X86Inst::kIdAaa       , X86Inst::kIdArpl       + 1 },</a>
+<a name="2787"><span class="lineNum">    2787 </span>            :   { X86Inst::kIdBextr     , X86Inst::kIdBzhi       + 1 },</a>
+<a name="2788"><span class="lineNum">    2788 </span>            :   { X86Inst::kIdCall      , X86Inst::kIdCwde       + 1 },</a>
+<a name="2789"><span class="lineNum">    2789 </span>            :   { X86Inst::kIdDaa       , X86Inst::kIdDpps       + 1 },</a>
+<a name="2790"><span class="lineNum">    2790 </span>            :   { X86Inst::kIdEmms      , X86Inst::kIdExtrq      + 1 },</a>
+<a name="2791"><span class="lineNum">    2791 </span>            :   { X86Inst::kIdF2xm1     , X86Inst::kIdFyl2xp1    + 1 },</a>
+<a name="2792"><span class="lineNum">    2792 </span>            :   { X86Inst::kIdNone      , X86Inst::kIdNone       + 1 },</a>
+<a name="2793"><span class="lineNum">    2793 </span>            :   { X86Inst::kIdHaddpd    , X86Inst::kIdHsubps     + 1 },</a>
+<a name="2794"><span class="lineNum">    2794 </span>            :   { X86Inst::kIdIdiv      , X86Inst::kIdIretw      + 1 },</a>
+<a name="2795"><span class="lineNum">    2795 </span>            :   { X86Inst::kIdJa        , X86Inst::kIdJz         + 1 },</a>
+<a name="2796"><span class="lineNum">    2796 </span>            :   { X86Inst::kIdKaddb     , X86Inst::kIdKxorw      + 1 },</a>
+<a name="2797"><span class="lineNum">    2797 </span>            :   { X86Inst::kIdLahf      , X86Inst::kIdLzcnt      + 1 },</a>
+<a name="2798"><span class="lineNum">    2798 </span>            :   { X86Inst::kIdMaskmovdqu, X86Inst::kIdMwait      + 1 },</a>
+<a name="2799"><span class="lineNum">    2799 </span>            :   { X86Inst::kIdNeg       , X86Inst::kIdNot        + 1 },</a>
+<a name="2800"><span class="lineNum">    2800 </span>            :   { X86Inst::kIdOr        , X86Inst::kIdOuts       + 1 },</a>
+<a name="2801"><span class="lineNum">    2801 </span>            :   { X86Inst::kIdPabsb     , X86Inst::kIdPxor       + 1 },</a>
+<a name="2802"><span class="lineNum">    2802 </span>            :   { X86Inst::kIdNone      , X86Inst::kIdNone       + 1 },</a>
+<a name="2803"><span class="lineNum">    2803 </span>            :   { X86Inst::kIdRcl       , X86Inst::kIdRsqrtss    + 1 },</a>
+<a name="2804"><span class="lineNum">    2804 </span>            :   { X86Inst::kIdSahf      , X86Inst::kIdSysret64   + 1 },</a>
+<a name="2805"><span class="lineNum">    2805 </span>            :   { X86Inst::kIdT1mskc    , X86Inst::kIdTzmsk      + 1 },</a>
+<a name="2806"><span class="lineNum">    2806 </span>            :   { X86Inst::kIdUcomisd   , X86Inst::kIdUnpcklps   + 1 },</a>
+<a name="2807"><span class="lineNum">    2807 </span>            :   { X86Inst::kIdV4fmaddps , X86Inst::kIdVzeroupper + 1 },</a>
+<a name="2808"><span class="lineNum">    2808 </span>            :   { X86Inst::kIdWbinvd    , X86Inst::kIdWrmsr      + 1 },</a>
+<a name="2809"><span class="lineNum">    2809 </span>            :   { X86Inst::kIdXabort    , X86Inst::kIdXtest      + 1 },</a>
+<a name="2810"><span class="lineNum">    2810 </span>            :   { X86Inst::kIdNone      , X86Inst::kIdNone       + 1 },</a>
+<a name="2811"><span class="lineNum">    2811 </span>            :   { X86Inst::kIdNone      , X86Inst::kIdNone       + 1 }</a>
+<a name="2812"><span class="lineNum">    2812 </span>            : };</a>
+<a name="2813"><span class="lineNum">    2813 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="2814"><span class="lineNum">    2814 </span>            : // ${nameData:End}</a>
+<a name="2815"><span class="lineNum">    2815 </span>            : </a>
+<a name="2816"><span class="lineNum">    2816 </span><span class="lineNoCov">          0 : uint32_t X86Inst::getIdByName(const char* name, size_t len) noexcept {</span></a>
+<a name="2817"><span class="lineNum">    2817 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!name))</span></a>
+<a name="2818"><span class="lineNum">    2818 </span>            :     return Inst::kIdNone;</a>
+<a name="2819"><span class="lineNum">    2819 </span>            : </a>
+<a name="2820"><span class="lineNum">    2820 </span><span class="lineNoCov">          0 :   if (len == Globals::kInvalidIndex)</span></a>
+<a name="2821"><span class="lineNum">    2821 </span><span class="lineNoCov">          0 :     len = ::strlen(name);</span></a>
+<a name="2822"><span class="lineNum">    2822 </span>            : </a>
+<a name="2823"><span class="lineNum">    2823 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(len == 0 || len &gt; kX86InstMaxLength))</span></a>
+<a name="2824"><span class="lineNum">    2824 </span>            :     return Inst::kIdNone;</a>
+<a name="2825"><span class="lineNum">    2825 </span>            : </a>
+<a name="2826"><span class="lineNum">    2826 </span><span class="lineNoCov">          0 :   uint32_t prefix = static_cast&lt;uint32_t&gt;(name[0]) - 'a';</span></a>
+<a name="2827"><span class="lineNum">    2827 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(prefix &gt; 'z' - 'a'))</span></a>
+<a name="2828"><span class="lineNum">    2828 </span>            :     return Inst::kIdNone;</a>
+<a name="2829"><span class="lineNum">    2829 </span>            : </a>
+<a name="2830"><span class="lineNum">    2830 </span><span class="lineNoCov">          0 :   uint32_t index = X86InstNameAZ[prefix].start;</span></a>
+<a name="2831"><span class="lineNum">    2831 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!index))</span></a>
+<a name="2832"><span class="lineNum">    2832 </span>            :     return Inst::kIdNone;</a>
+<a name="2833"><span class="lineNum">    2833 </span>            : </a>
+<a name="2834"><span class="lineNum">    2834 </span>            :   const char* nameData = X86InstDB::nameData;</a>
+<a name="2835"><span class="lineNum">    2835 </span>            :   const X86Inst* instData = X86InstDB::instData;</a>
+<a name="2836"><span class="lineNum">    2836 </span>            : </a>
+<a name="2837"><span class="lineNum">    2837 </span><span class="lineNoCov">          0 :   const X86Inst* base = instData + index;</span></a>
+<a name="2838"><span class="lineNum">    2838 </span><span class="lineNoCov">          0 :   const X86Inst* end  = instData + X86InstNameAZ[prefix].end;</span></a>
+<a name="2839"><span class="lineNum">    2839 </span>            : </a>
+<a name="2840"><span class="lineNum">    2840 </span><span class="lineNoCov">          0 :   for (size_t lim = (size_t)(end - base); lim != 0; lim &gt;&gt;= 1) {</span></a>
+<a name="2841"><span class="lineNum">    2841 </span><span class="lineNoCov">          0 :     const X86Inst* cur = base + (lim &gt;&gt; 1);</span></a>
+<a name="2842"><span class="lineNum">    2842 </span><span class="lineNoCov">          0 :     int result = Utils::cmpInstName(nameData + cur[0].getNameDataIndex(), name, len);</span></a>
+<a name="2843"><span class="lineNum">    2843 </span>            : </a>
+<a name="2844"><span class="lineNum">    2844 </span><span class="lineNoCov">          0 :     if (result &lt; 0) {</span></a>
+<a name="2845"><span class="lineNum">    2845 </span><span class="lineNoCov">          0 :       base = cur + 1;</span></a>
+<a name="2846"><span class="lineNum">    2846 </span><span class="lineNoCov">          0 :       lim--;</span></a>
+<a name="2847"><span class="lineNum">    2847 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="2848"><span class="lineNum">    2848 </span>            :     }</a>
+<a name="2849"><span class="lineNum">    2849 </span>            : </a>
+<a name="2850"><span class="lineNum">    2850 </span><span class="lineNoCov">          0 :     if (result &gt; 0)</span></a>
+<a name="2851"><span class="lineNum">    2851 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="2852"><span class="lineNum">    2852 </span>            : </a>
+<a name="2853"><span class="lineNum">    2853 </span><span class="lineNoCov">          0 :     return static_cast&lt;uint32_t&gt;((size_t)(cur - instData));</span></a>
+<a name="2854"><span class="lineNum">    2854 </span>            :   }</a>
+<a name="2855"><span class="lineNum">    2855 </span>            : </a>
+<a name="2856"><span class="lineNum">    2856 </span>            :   return Inst::kIdNone;</a>
+<a name="2857"><span class="lineNum">    2857 </span>            : }</a>
+<a name="2858"><span class="lineNum">    2858 </span>            : </a>
+<a name="2859"><span class="lineNum">    2859 </span><span class="lineNoCov">          0 : const char* X86Inst::getNameById(uint32_t id) noexcept {</span></a>
+<a name="2860"><span class="lineNum">    2860 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(id &gt;= X86Inst::_kIdCount))</span></a>
+<a name="2861"><span class="lineNum">    2861 </span>            :     return nullptr;</a>
+<a name="2862"><span class="lineNum">    2862 </span><span class="lineNoCov">          0 :   return X86Inst::getInst(id).getName();</span></a>
+<a name="2863"><span class="lineNum">    2863 </span>            : }</a>
+<a name="2864"><span class="lineNum">    2864 </span>            : #else</a>
+<a name="2865"><span class="lineNum">    2865 </span>            : const char X86InstDB::nameData[] = &quot;&quot;;</a>
+<a name="2866"><span class="lineNum">    2866 </span>            : #endif // !ASMJIT_DISABLE_TEXT</a>
+<a name="2867"><span class="lineNum">    2867 </span>            : </a>
+<a name="2868"><span class="lineNum">    2868 </span>            : // ============================================================================</a>
+<a name="2869"><span class="lineNum">    2869 </span>            : // [asmjit::X86Inst - Validation]</a>
+<a name="2870"><span class="lineNum">    2870 </span>            : // ============================================================================</a>
+<a name="2871"><span class="lineNum">    2871 </span>            : </a>
+<a name="2872"><span class="lineNum">    2872 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="2873"><span class="lineNum">    2873 </span>            : // ${signatureData:Begin}</a>
+<a name="2874"><span class="lineNum">    2874 </span>            : // ------------------- Automatically generated, do not edit -------------------</a>
+<a name="2875"><span class="lineNum">    2875 </span>            : #define FLAG(flag) X86Inst::kOp##flag</a>
+<a name="2876"><span class="lineNum">    2876 </span>            : #define MEM(mem) X86Inst::kMemOp##mem</a>
+<a name="2877"><span class="lineNum">    2877 </span>            : #define OSIGNATURE(flags, memFlags, extFlags, regId) \</a>
+<a name="2878"><span class="lineNum">    2878 </span>            :   { uint32_t(flags), uint16_t(memFlags), uint8_t(extFlags), uint8_t(regId) }</a>
+<a name="2879"><span class="lineNum">    2879 </span>            : const X86Inst::OSignature X86InstDB::oSignatureData[] = {</a>
+<a name="2880"><span class="lineNum">    2880 </span>            :   OSIGNATURE(0, 0, 0, 0xFF),</a>
+<a name="2881"><span class="lineNum">    2881 </span>            :   OSIGNATURE(FLAG(W) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="2882"><span class="lineNum">    2882 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi), 0, 0, 0x00),</a>
+<a name="2883"><span class="lineNum">    2883 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="2884"><span class="lineNum">    2884 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Seg), 0, 0, 0x00),</a>
+<a name="2885"><span class="lineNum">    2885 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpd) | FLAG(Seg) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2886"><span class="lineNum">    2886 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd), 0, 0, 0x00),</a>
+<a name="2887"><span class="lineNum">    2887 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2888"><span class="lineNum">    2888 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Seg) | FLAG(I32), 0, 0, 0x00),</a>
+<a name="2889"><span class="lineNum">    2889 </span>            :   OSIGNATURE(FLAG(W) | FLAG(GpbLo) | FLAG(GpbHi), 0, 0, 0x00),</a>
+<a name="2890"><span class="lineNum">    2890 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem) | FLAG(I8) | FLAG(U8), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="2891"><span class="lineNum">    2891 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Seg), 0, 0, 0x00),</a>
+<a name="2892"><span class="lineNum">    2892 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="2893"><span class="lineNum">    2893 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpd), 0, 0, 0x00),</a>
+<a name="2894"><span class="lineNum">    2894 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Seg) | FLAG(Mem) | FLAG(I32) | FLAG(U32), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2895"><span class="lineNum">    2895 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpq) | FLAG(Seg), 0, 0, 0x00),</a>
+<a name="2896"><span class="lineNum">    2896 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2897"><span class="lineNum">    2897 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Mem), MEM(M16), 0, 0x00),</a>
+<a name="2898"><span class="lineNum">    2898 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I16) | FLAG(U16), 0, 0, 0x00),</a>
+<a name="2899"><span class="lineNum">    2899 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="2900"><span class="lineNum">    2900 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Cr) | FLAG(Dr) | FLAG(I64) | FLAG(U64), 0, 0, 0x00),</a>
+<a name="2901"><span class="lineNum">    2901 </span>            :   OSIGNATURE(FLAG(W) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem), MEM(M8), 0, 0x00),</a>
+<a name="2902"><span class="lineNum">    2902 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I8) | FLAG(U8), 0, 0, 0x00),</a>
+<a name="2903"><span class="lineNum">    2903 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpd) | FLAG(Mem), MEM(M32), 0, 0x00),</a>
+<a name="2904"><span class="lineNum">    2904 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I32) | FLAG(U32), 0, 0, 0x00),</a>
+<a name="2905"><span class="lineNum">    2905 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Cr) | FLAG(Dr), 0, 0, 0x00),</a>
+<a name="2906"><span class="lineNum">    2906 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Cr) | FLAG(Dr), 0, 0, 0x00),</a>
+<a name="2907"><span class="lineNum">    2907 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="2908"><span class="lineNum">    2908 </span>            :   OSIGNATURE(FLAG(X) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem), MEM(M8), 0, 0x00),</a>
+<a name="2909"><span class="lineNum">    2909 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpw) | FLAG(Mem), MEM(M16), 0, 0x00),</a>
+<a name="2910"><span class="lineNum">    2910 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpd) | FLAG(Mem), MEM(M32), 0, 0x00),</a>
+<a name="2911"><span class="lineNum">    2911 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2912"><span class="lineNum">    2912 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(I32), 0, 0, 0x00),</a>
+<a name="2913"><span class="lineNum">    2913 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M16) | MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="2914"><span class="lineNum">    2914 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I8), 0, 0, 0x00),</a>
+<a name="2915"><span class="lineNum">    2915 </span>            :   OSIGNATURE(FLAG(X) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="2916"><span class="lineNum">    2916 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpw) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="2917"><span class="lineNum">    2917 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw), 0, 0, 0x00),</a>
+<a name="2918"><span class="lineNum">    2918 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpd) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2919"><span class="lineNum">    2919 </span>            :   OSIGNATURE(FLAG(X) | FLAG(GpbLo) | FLAG(GpbHi), 0, 0, 0x00),</a>
+<a name="2920"><span class="lineNum">    2920 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="2921"><span class="lineNum">    2921 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpw), 0, 0, 0x00),</a>
+<a name="2922"><span class="lineNum">    2922 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpd), 0, 0, 0x00),</a>
+<a name="2923"><span class="lineNum">    2923 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2924"><span class="lineNum">    2924 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="2925"><span class="lineNum">    2925 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Mem), MEM(M8), 0, 0x00),</a>
+<a name="2926"><span class="lineNum">    2926 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Mem), MEM(M16), 0, 0x00),</a>
+<a name="2927"><span class="lineNum">    2927 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Mem), MEM(M32), 0, 0x00),</a>
+<a name="2928"><span class="lineNum">    2928 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M16) | MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="2929"><span class="lineNum">    2929 </span>            :   OSIGNATURE(FLAG(X) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M8) | MEM(M16) | MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="2930"><span class="lineNum">    2930 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpw), 0, 0, 0x01),</a>
+<a name="2931"><span class="lineNum">    2931 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Gpw), 0, 0, 0x04),</a>
+<a name="2932"><span class="lineNum">    2932 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x04),</a>
+<a name="2933"><span class="lineNum">    2933 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x01),</a>
+<a name="2934"><span class="lineNum">    2934 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x04),</a>
+<a name="2935"><span class="lineNum">    2935 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x01),</a>
+<a name="2936"><span class="lineNum">    2936 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Mem) | FLAG(I8) | FLAG(I16), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="2937"><span class="lineNum">    2937 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Mem) | FLAG(I8) | FLAG(I32), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2938"><span class="lineNum">    2938 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Mem) | FLAG(I8) | FLAG(I32), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2939"><span class="lineNum">    2939 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw), 0, 0, 0x00),</a>
+<a name="2940"><span class="lineNum">    2940 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I8) | FLAG(I16) | FLAG(U16), 0, 0, 0x00),</a>
+<a name="2941"><span class="lineNum">    2941 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I8) | FLAG(I32) | FLAG(U32), 0, 0, 0x00),</a>
+<a name="2942"><span class="lineNum">    2942 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I8) | FLAG(I32), 0, 0, 0x00),</a>
+<a name="2943"><span class="lineNum">    2943 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="2944"><span class="lineNum">    2944 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2945"><span class="lineNum">    2945 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2946"><span class="lineNum">    2946 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="2947"><span class="lineNum">    2947 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="2948"><span class="lineNum">    2948 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2949"><span class="lineNum">    2949 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mm), 0, 0, 0x00),</a>
+<a name="2950"><span class="lineNum">    2950 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Mm) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2951"><span class="lineNum">    2951 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpq) | FLAG(Mm) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2952"><span class="lineNum">    2952 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mm), 0, 0, 0x00),</a>
+<a name="2953"><span class="lineNum">    2953 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="2954"><span class="lineNum">    2954 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="2955"><span class="lineNum">    2955 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2956"><span class="lineNum">    2956 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="2957"><span class="lineNum">    2957 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M128), 0, 0x00),</a>
+<a name="2958"><span class="lineNum">    2958 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M128), 0, 0x00),</a>
+<a name="2959"><span class="lineNum">    2959 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Ymm), 0, 0, 0x00),</a>
+<a name="2960"><span class="lineNum">    2960 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Ymm) | FLAG(Mem), MEM(Any) | MEM(M256), 0, 0x00),</a>
+<a name="2961"><span class="lineNum">    2961 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Ymm) | FLAG(Mem), MEM(Any) | MEM(M256), 0, 0x00),</a>
+<a name="2962"><span class="lineNum">    2962 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Ymm), 0, 0, 0x00),</a>
+<a name="2963"><span class="lineNum">    2963 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="2964"><span class="lineNum">    2964 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Zmm) | FLAG(Mem), MEM(Any) | MEM(M512), 0, 0x00),</a>
+<a name="2965"><span class="lineNum">    2965 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Zmm) | FLAG(Mem), MEM(Any) | MEM(M512), 0, 0x00),</a>
+<a name="2966"><span class="lineNum">    2966 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="2967"><span class="lineNum">    2967 </span>            :   OSIGNATURE(FLAG(R) | FLAG(U8), 0, 0, 0x00),</a>
+<a name="2968"><span class="lineNum">    2968 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem) | FLAG(U8), MEM(Any) | MEM(M128), 0, 0x00),</a>
+<a name="2969"><span class="lineNum">    2969 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="2970"><span class="lineNum">    2970 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm32x), 0, 0x00),</a>
+<a name="2971"><span class="lineNum">    2971 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Ymm), 0, 0, 0x00),</a>
+<a name="2972"><span class="lineNum">    2972 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm32y), 0, 0x00),</a>
+<a name="2973"><span class="lineNum">    2973 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="2974"><span class="lineNum">    2974 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm32z), 0, 0x00),</a>
+<a name="2975"><span class="lineNum">    2975 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm64x), 0, 0x00),</a>
+<a name="2976"><span class="lineNum">    2976 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm64y), 0, 0x00),</a>
+<a name="2977"><span class="lineNum">    2977 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm64z), 0, 0x00),</a>
+<a name="2978"><span class="lineNum">    2978 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(U8), 0, 0, 0x00),</a>
+<a name="2979"><span class="lineNum">    2979 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Mem), MEM(M16) | MEM(M32), 0, 0x00),</a>
+<a name="2980"><span class="lineNum">    2980 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Mem), MEM(M16) | MEM(M32), 0, 0x00),</a>
+<a name="2981"><span class="lineNum">    2981 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(GpbLo), 0, 0, 0x01),</a>
+<a name="2982"><span class="lineNum">    2982 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpw), 0, 0, 0x01),</a>
+<a name="2983"><span class="lineNum">    2983 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x01),</a>
+<a name="2984"><span class="lineNum">    2984 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x01),</a>
+<a name="2985"><span class="lineNum">    2985 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpw), 0, 0, 0x04),</a>
+<a name="2986"><span class="lineNum">    2986 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x04),</a>
+<a name="2987"><span class="lineNum">    2987 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x04),</a>
+<a name="2988"><span class="lineNum">    2988 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M16) | MEM(M64), 0, 0x00),</a>
+<a name="2989"><span class="lineNum">    2989 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Seg), 0, 0, 0x1A),</a>
+<a name="2990"><span class="lineNum">    2990 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Seg), 0, 0, 0x60),</a>
+<a name="2991"><span class="lineNum">    2991 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Gpq) | FLAG(Mem) | FLAG(I8) | FLAG(I16) | FLAG(I32), MEM(Any) | MEM(M16) | MEM(M64), 0, 0x00),</a>
+<a name="2992"><span class="lineNum">    2992 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Seg), 0, 0, 0x1E),</a>
+<a name="2993"><span class="lineNum">    2993 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Seg), 0, 0, 0x60),</a>
+<a name="2994"><span class="lineNum">    2994 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Vm), MEM(Vm64x) | MEM(Vm64y), 0, 0x00),</a>
+<a name="2995"><span class="lineNum">    2995 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M128), 0, 0x00),</a>
+<a name="2996"><span class="lineNum">    2996 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M256), 0, 0x00),</a>
+<a name="2997"><span class="lineNum">    2997 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M128), 0, 0x00),</a>
+<a name="2998"><span class="lineNum">    2998 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M256), 0, 0x00),</a>
+<a name="2999"><span class="lineNum">    2999 </span>            :   OSIGNATURE(FLAG(R) | FLAG(U4), 0, 0, 0x00),</a>
+<a name="3000"><span class="lineNum">    3000 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3001"><span class="lineNum">    3001 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Fp), 0, 0, 0x01),</a>
+<a name="3002"><span class="lineNum">    3002 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Fp), 0, 0, 0x00),</a>
+<a name="3003"><span class="lineNum">    3003 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Fp), 0, 0, 0x00),</a>
+<a name="3004"><span class="lineNum">    3004 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Fp), 0, 0, 0x01),</a>
+<a name="3005"><span class="lineNum">    3005 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Mem), MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3006"><span class="lineNum">    3006 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M48), 0, 0x00),</a>
+<a name="3007"><span class="lineNum">    3007 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M80), 0, 0x00),</a>
+<a name="3008"><span class="lineNum">    3008 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(U8), 0, 0, 0x02),</a>
+<a name="3009"><span class="lineNum">    3009 </span>            :   OSIGNATURE(FLAG(W) | FLAG(K) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="3010"><span class="lineNum">    3010 </span>            :   OSIGNATURE(FLAG(W) | FLAG(K) | FLAG(Ymm), 0, 0, 0x00),</a>
+<a name="3011"><span class="lineNum">    3011 </span>            :   OSIGNATURE(FLAG(W) | FLAG(K), 0, 0, 0x00),</a>
+<a name="3012"><span class="lineNum">    3012 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Ymm) | FLAG(Mem), MEM(M64) | MEM(M128) | MEM(M256), 0, 0x00),</a>
+<a name="3013"><span class="lineNum">    3013 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(M128), 0, 0x00),</a>
+<a name="3014"><span class="lineNum">    3014 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Ymm) | FLAG(Mem), MEM(M256), 0, 0x00),</a>
+<a name="3015"><span class="lineNum">    3015 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M512), 0, 0x00),</a>
+<a name="3016"><span class="lineNum">    3016 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M512), 0, 0x00),</a>
+<a name="3017"><span class="lineNum">    3017 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3018"><span class="lineNum">    3018 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="3019"><span class="lineNum">    3019 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="3020"><span class="lineNum">    3020 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="3021"><span class="lineNum">    3021 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="3022"><span class="lineNum">    3022 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M256), 0, 0x00),</a>
+<a name="3023"><span class="lineNum">    3023 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm32x), 0, 0x00),</a>
+<a name="3024"><span class="lineNum">    3024 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm32y), 0, 0x00),</a>
+<a name="3025"><span class="lineNum">    3025 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm32z), 0, 0x00),</a>
+<a name="3026"><span class="lineNum">    3026 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm64x), 0, 0x00),</a>
+<a name="3027"><span class="lineNum">    3027 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm64y), 0, 0x00),</a>
+<a name="3028"><span class="lineNum">    3028 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm64z), 0, 0x00),</a>
+<a name="3029"><span class="lineNum">    3029 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Bnd), 0, 0, 0x00),</a>
+<a name="3030"><span class="lineNum">    3030 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Bnd), 0, 0, 0x00),</a>
+<a name="3031"><span class="lineNum">    3031 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Bnd) | FLAG(Mem), MEM(Any), 0, 0x00),</a>
+<a name="3032"><span class="lineNum">    3032 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Bnd) | FLAG(Mem), MEM(Any), 0, 0x00),</a>
+<a name="3033"><span class="lineNum">    3033 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Mem) | FLAG(I32) | FLAG(I64) | FLAG(Rel32), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3034"><span class="lineNum">    3034 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Mem), MEM(M8) | MEM(M16) | MEM(M32), 0, 0x00),</a>
+<a name="3035"><span class="lineNum">    3035 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Gpq) | FLAG(Mem), MEM(M8) | MEM(M64), 0, 0x00),</a>
+<a name="3036"><span class="lineNum">    3036 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpw) | FLAG(Gpd), 0, 0, 0x00),</a>
+<a name="3037"><span class="lineNum">    3037 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Fp) | FLAG(Mem), MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3038"><span class="lineNum">    3038 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpw) | FLAG(Gpd), 0, 0, 0x02),</a>
+<a name="3039"><span class="lineNum">    3039 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I32) | FLAG(I64) | FLAG(Rel8), 0, 0, 0x00),</a>
+<a name="3040"><span class="lineNum">    3040 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x02),</a>
+<a name="3041"><span class="lineNum">    3041 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(Mem) | FLAG(I32) | FLAG(I64) | FLAG(Rel8) | FLAG(Rel32), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3042"><span class="lineNum">    3042 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(K) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="3043"><span class="lineNum">    3043 </span>            :   OSIGNATURE(FLAG(W) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="3044"><span class="lineNum">    3044 </span>            :   OSIGNATURE(FLAG(R) | FLAG(K), 0, 0, 0x00),</a>
+<a name="3045"><span class="lineNum">    3045 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Gpq) | FLAG(K) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="3046"><span class="lineNum">    3046 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="3047"><span class="lineNum">    3047 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpq) | FLAG(K) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3048"><span class="lineNum">    3048 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(K) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="3049"><span class="lineNum">    3049 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="3050"><span class="lineNum">    3050 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="3051"><span class="lineNum">    3051 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpw) | FLAG(Gpd), 0, 0, 0x02),</a>
+<a name="3052"><span class="lineNum">    3052 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x02),</a>
+<a name="3053"><span class="lineNum">    3053 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="3054"><span class="lineNum">    3054 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mm) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="3055"><span class="lineNum">    3055 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M32), 0, 0x00),</a>
+<a name="3056"><span class="lineNum">    3056 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mm) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="3057"><span class="lineNum">    3057 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="3058"><span class="lineNum">    3058 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x04),</a>
+<a name="3059"><span class="lineNum">    3059 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x04),</a>
+<a name="3060"><span class="lineNum">    3060 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mm) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3061"><span class="lineNum">    3061 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Mm), 0, 0, 0x00),</a>
+<a name="3062"><span class="lineNum">    3062 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mm) | FLAG(Mem) | FLAG(U8), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3063"><span class="lineNum">    3063 </span>            :   OSIGNATURE(FLAG(R) | FLAG(U16), 0, 0, 0x00),</a>
+<a name="3064"><span class="lineNum">    3064 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Ymm) | FLAG(Mem), MEM(M128) | MEM(M256), 0, 0x00),</a>
+<a name="3065"><span class="lineNum">    3065 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Xmm) | FLAG(Ymm) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="3066"><span class="lineNum">    3066 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="3067"><span class="lineNum">    3067 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="3068"><span class="lineNum">    3068 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(GpbHi) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M8), 0, 0x00),</a>
+<a name="3069"><span class="lineNum">    3069 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(U8), 0, 0, 0x00),</a>
+<a name="3070"><span class="lineNum">    3070 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Vm), MEM(Vm64x) | MEM(Vm64y), 0, 0x00),</a>
+<a name="3071"><span class="lineNum">    3071 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Ymm), 0, 0, 0x00),</a>
+<a name="3072"><span class="lineNum">    3072 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Xmm), 0, 0, 0x01),</a>
+<a name="3073"><span class="lineNum">    3073 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Mib), 0, 0x00),</a>
+<a name="3074"><span class="lineNum">    3074 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any), 0, 0x00),</a>
+<a name="3075"><span class="lineNum">    3075 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Mib), 0, 0x00),</a>
+<a name="3076"><span class="lineNum">    3076 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x00),</a>
+<a name="3077"><span class="lineNum">    3077 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Mem), MEM(BaseOnly) | MEM(Ds), 0, 0x01),</a>
+<a name="3078"><span class="lineNum">    3078 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Mem), MEM(BaseOnly) | MEM(Ds), 0, 0x40),</a>
+<a name="3079"><span class="lineNum">    3079 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Mem), MEM(BaseOnly) | MEM(Es), 0, 0x80),</a>
+<a name="3080"><span class="lineNum">    3080 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Mem), MEM(Any) | MEM(M128), 0, 0x00),</a>
+<a name="3081"><span class="lineNum">    3081 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x02),</a>
+<a name="3082"><span class="lineNum">    3082 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpq), 0, 0, 0x08),</a>
+<a name="3083"><span class="lineNum">    3083 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Mem), MEM(Any) | MEM(M64), 0, 0x00),</a>
+<a name="3084"><span class="lineNum">    3084 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x02),</a>
+<a name="3085"><span class="lineNum">    3085 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x08),</a>
+<a name="3086"><span class="lineNum">    3086 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x08),</a>
+<a name="3087"><span class="lineNum">    3087 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x02),</a>
+<a name="3088"><span class="lineNum">    3088 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3089"><span class="lineNum">    3089 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any) | MEM(M80), 0, 0x00),</a>
+<a name="3090"><span class="lineNum">    3090 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(M16) | MEM(M32), 0, 0x00),</a>
+<a name="3091"><span class="lineNum">    3091 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(M16) | MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3092"><span class="lineNum">    3092 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(M16) | MEM(M32), 0, 0x00),</a>
+<a name="3093"><span class="lineNum">    3093 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(M16) | MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3094"><span class="lineNum">    3094 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Fp) | FLAG(Mem), MEM(M32) | MEM(M64) | MEM(M80), 0, 0x00),</a>
+<a name="3095"><span class="lineNum">    3095 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(Any), 0, 0x00),</a>
+<a name="3096"><span class="lineNum">    3096 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Gpw) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x01),</a>
+<a name="3097"><span class="lineNum">    3097 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Fp) | FLAG(Mem), MEM(M32) | MEM(M64), 0, 0x00),</a>
+<a name="3098"><span class="lineNum">    3098 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Fp) | FLAG(Mem), MEM(M32) | MEM(M64) | MEM(M80), 0, 0x00),</a>
+<a name="3099"><span class="lineNum">    3099 </span>            :   OSIGNATURE(FLAG(W) | FLAG(GpbLo) | FLAG(Gpw) | FLAG(Gpd), 0, 0, 0x01),</a>
+<a name="3100"><span class="lineNum">    3100 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(U8), 0, 0, 0x04),</a>
+<a name="3101"><span class="lineNum">    3101 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Mem), MEM(BaseOnly) | MEM(Es), 0, 0x80),</a>
+<a name="3102"><span class="lineNum">    3102 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw), 0, 0, 0x04),</a>
+<a name="3103"><span class="lineNum">    3103 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I32) | FLAG(I64) | FLAG(Rel8) | FLAG(Rel32), 0, 0, 0x00),</a>
+<a name="3104"><span class="lineNum">    3104 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(GpbHi), 0, 0, 0x01),</a>
+<a name="3105"><span class="lineNum">    3105 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(Any) | MEM(M8) | MEM(M16) | MEM(M32) | MEM(M48) | MEM(M64) | MEM(M80) | MEM(M128) | MEM(M256) | MEM(M512) | MEM(M1024), 0, 0x00),</a>
+<a name="3106"><span class="lineNum">    3106 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq) | FLAG(Mem), MEM(Any) | MEM(M16), 0, 0x00),</a>
+<a name="3107"><span class="lineNum">    3107 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(GpbLo) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x01),</a>
+<a name="3108"><span class="lineNum">    3108 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(Mem), MEM(BaseOnly) | MEM(Ds), 0, 0x80),</a>
+<a name="3109"><span class="lineNum">    3109 </span>            :   OSIGNATURE(FLAG(R) | FLAG(GpbLo) | FLAG(Gpw) | FLAG(Gpd), 0, 0, 0x01),</a>
+<a name="3110"><span class="lineNum">    3110 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Mem), MEM(BaseOnly) | MEM(Ds), 0, 0x40),</a>
+<a name="3111"><span class="lineNum">    3111 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x02),</a>
+<a name="3112"><span class="lineNum">    3112 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Xmm), 0, 0, 0x01),</a>
+<a name="3113"><span class="lineNum">    3113 </span>            :   OSIGNATURE(FLAG(X) | FLAG(Mm) | FLAG(Xmm), 0, 0, 0x00),</a>
+<a name="3114"><span class="lineNum">    3114 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Implicit) | FLAG(Gpd), 0, 0, 0x01),</a>
+<a name="3115"><span class="lineNum">    3115 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(GpbHi), 0, 0, 0x01),</a>
+<a name="3116"><span class="lineNum">    3116 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Implicit) | FLAG(GpbLo) | FLAG(Gpw) | FLAG(Gpd) | FLAG(Gpq), 0, 0, 0x01),</a>
+<a name="3117"><span class="lineNum">    3117 </span>            :   OSIGNATURE(FLAG(W) | FLAG(Ymm) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="3118"><span class="lineNum">    3118 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Ymm) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="3119"><span class="lineNum">    3119 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Ymm) | FLAG(Zmm) | FLAG(Mem), MEM(M128) | MEM(M256) | MEM(M512), 0, 0x00),</a>
+<a name="3120"><span class="lineNum">    3120 </span>            :   OSIGNATURE(FLAG(R) | FLAG(Xmm) | FLAG(Ymm) | FLAG(Zmm), 0, 0, 0x00),</a>
+<a name="3121"><span class="lineNum">    3121 </span>            :   OSIGNATURE(FLAG(R) | FLAG(I32) | FLAG(I64) | FLAG(Rel32), 0, 0, 0x00)</a>
+<a name="3122"><span class="lineNum">    3122 </span>            : };</a>
+<a name="3123"><span class="lineNum">    3123 </span>            : #undef OSIGNATURE</a>
+<a name="3124"><span class="lineNum">    3124 </span>            : #undef MEM</a>
+<a name="3125"><span class="lineNum">    3125 </span>            : #undef FLAG</a>
+<a name="3126"><span class="lineNum">    3126 </span>            : </a>
+<a name="3127"><span class="lineNum">    3127 </span>            : #define ISIGNATURE(count, x86, x64, implicit, o0, o1, o2, o3, o4, o5) \</a>
+<a name="3128"><span class="lineNum">    3128 </span>            :   { count, (x86 ? uint8_t(X86Inst::kArchMaskX86) : uint8_t(0)) |      \</a>
+<a name="3129"><span class="lineNum">    3129 </span>            :            (x64 ? uint8_t(X86Inst::kArchMaskX64) : uint8_t(0)) ,      \</a>
+<a name="3130"><span class="lineNum">    3130 </span>            :     implicit,                                                         \</a>
+<a name="3131"><span class="lineNum">    3131 </span>            :     0,                                                                \</a>
+<a name="3132"><span class="lineNum">    3132 </span>            :     { o0, o1, o2, o3, o4, o5 }                                        \</a>
+<a name="3133"><span class="lineNum">    3133 </span>            :   }</a>
+<a name="3134"><span class="lineNum">    3134 </span>            : const X86Inst::ISignature X86InstDB::iSignatureData[] = {</a>
+<a name="3135"><span class="lineNum">    3135 </span>            :   ISIGNATURE(2, 1, 1, 0, 1  , 2  , 0  , 0  , 0  , 0  ), // #0   {W:r8lo|r8hi|m8|mem, R:r8lo|r8hi}</a>
+<a name="3136"><span class="lineNum">    3136 </span>            :   ISIGNATURE(2, 1, 1, 0, 3  , 4  , 0  , 0  , 0  , 0  ), //      {W:r16|m16|mem, R:r16|sreg}</a>
+<a name="3137"><span class="lineNum">    3137 </span>            :   ISIGNATURE(2, 1, 1, 0, 5  , 6  , 0  , 0  , 0  , 0  ), //      {W:r32|m32|mem|sreg, R:r32}</a>
+<a name="3138"><span class="lineNum">    3138 </span>            :   ISIGNATURE(2, 0, 1, 0, 7  , 8  , 0  , 0  , 0  , 0  ), //      {W:r64|m64|mem, R:r64|sreg|i32}</a>
+<a name="3139"><span class="lineNum">    3139 </span>            :   ISIGNATURE(2, 1, 1, 0, 9  , 10 , 0  , 0  , 0  , 0  ), //      {W:r8lo|r8hi, R:r8lo|r8hi|m8|mem|i8|u8}</a>
+<a name="3140"><span class="lineNum">    3140 </span>            :   ISIGNATURE(2, 1, 1, 0, 11 , 12 , 0  , 0  , 0  , 0  ), //      {W:r16|sreg, R:r16|m16|mem}</a>
+<a name="3141"><span class="lineNum">    3141 </span>            :   ISIGNATURE(2, 1, 1, 0, 13 , 14 , 0  , 0  , 0  , 0  ), //      {W:r32, R:r32|m32|mem|sreg|i32|u32}</a>
+<a name="3142"><span class="lineNum">    3142 </span>            :   ISIGNATURE(2, 0, 1, 0, 15 , 16 , 0  , 0  , 0  , 0  ), //      {W:r64|sreg, R:r64|m64|mem}</a>
+<a name="3143"><span class="lineNum">    3143 </span>            :   ISIGNATURE(2, 1, 1, 0, 17 , 18 , 0  , 0  , 0  , 0  ), //      {W:r16|m16, R:i16|u16}</a>
+<a name="3144"><span class="lineNum">    3144 </span>            :   ISIGNATURE(2, 0, 1, 0, 19 , 20 , 0  , 0  , 0  , 0  ), //      {W:r64, R:i64|u64|creg|dreg}</a>
+<a name="3145"><span class="lineNum">    3145 </span>            :   ISIGNATURE(2, 1, 1, 0, 21 , 22 , 0  , 0  , 0  , 0  ), //      {W:r8lo|r8hi|m8, R:i8|u8}</a>
+<a name="3146"><span class="lineNum">    3146 </span>            :   ISIGNATURE(2, 1, 1, 0, 23 , 24 , 0  , 0  , 0  , 0  ), //      {W:r32|m32, R:i32|u32}</a>
+<a name="3147"><span class="lineNum">    3147 </span>            :   ISIGNATURE(2, 1, 0, 0, 13 , 25 , 0  , 0  , 0  , 0  ), //      {W:r32, R:creg|dreg}</a>
+<a name="3148"><span class="lineNum">    3148 </span>            :   ISIGNATURE(2, 1, 0, 0, 26 , 6  , 0  , 0  , 0  , 0  ), //      {W:creg|dreg, R:r32}</a>
+<a name="3149"><span class="lineNum">    3149 </span>            :   ISIGNATURE(2, 0, 1, 0, 26 , 27 , 0  , 0  , 0  , 0  ), //      {W:creg|dreg, R:r64}</a>
+<a name="3150"><span class="lineNum">    3150 </span>            :   ISIGNATURE(2, 1, 1, 0, 28 , 22 , 0  , 0  , 0  , 0  ), // #15  {X:r8lo|r8hi|m8, R:i8|u8}</a>
+<a name="3151"><span class="lineNum">    3151 </span>            :   ISIGNATURE(2, 1, 1, 0, 29 , 18 , 0  , 0  , 0  , 0  ), //      {X:r16|m16, R:i16|u16}</a>
+<a name="3152"><span class="lineNum">    3152 </span>            :   ISIGNATURE(2, 1, 1, 0, 30 , 24 , 0  , 0  , 0  , 0  ), //      {X:r32|m32, R:i32|u32}</a>
+<a name="3153"><span class="lineNum">    3153 </span>            :   ISIGNATURE(2, 0, 1, 0, 31 , 32 , 0  , 0  , 0  , 0  ), //      {X:r64|m64|mem, R:i32|r64}</a>
+<a name="3154"><span class="lineNum">    3154 </span>            :   ISIGNATURE(2, 1, 1, 0, 33 , 34 , 0  , 0  , 0  , 0  ), //      {X:r16|m16|r32|m32|r64|m64|mem, R:i8}</a>
+<a name="3155"><span class="lineNum">    3155 </span>            :   ISIGNATURE(2, 1, 1, 0, 35 , 2  , 0  , 0  , 0  , 0  ), //      {X:r8lo|r8hi|m8|mem, R:r8lo|r8hi}</a>
+<a name="3156"><span class="lineNum">    3156 </span>            :   ISIGNATURE(2, 1, 1, 0, 36 , 37 , 0  , 0  , 0  , 0  ), //      {X:r16|m16|mem, R:r16}</a>
+<a name="3157"><span class="lineNum">    3157 </span>            :   ISIGNATURE(2, 1, 1, 0, 38 , 6  , 0  , 0  , 0  , 0  ), //      {X:r32|m32|mem, R:r32}</a>
+<a name="3158"><span class="lineNum">    3158 </span>            :   ISIGNATURE(2, 1, 1, 0, 39 , 40 , 0  , 0  , 0  , 0  ), //      {X:r8lo|r8hi, R:r8lo|r8hi|m8|mem}</a>
+<a name="3159"><span class="lineNum">    3159 </span>            :   ISIGNATURE(2, 1, 1, 0, 41 , 12 , 0  , 0  , 0  , 0  ), // #24  {X:r16, R:r16|m16|mem}</a>
+<a name="3160"><span class="lineNum">    3160 </span>            :   ISIGNATURE(2, 1, 1, 0, 42 , 43 , 0  , 0  , 0  , 0  ), // #25  {X:r32, R:r32|m32|mem}</a>
+<a name="3161"><span class="lineNum">    3161 </span>            :   ISIGNATURE(2, 0, 1, 0, 44 , 16 , 0  , 0  , 0  , 0  ), //      {X:r64, R:r64|m64|mem}</a>
+<a name="3162"><span class="lineNum">    3162 </span>            :   ISIGNATURE(2, 1, 1, 0, 45 , 22 , 0  , 0  , 0  , 0  ), // #27  {R:r8lo|r8hi|m8, R:i8|u8}</a>
+<a name="3163"><span class="lineNum">    3163 </span>            :   ISIGNATURE(2, 1, 1, 0, 46 , 18 , 0  , 0  , 0  , 0  ), //      {R:r16|m16, R:i16|u16}</a>
+<a name="3164"><span class="lineNum">    3164 </span>            :   ISIGNATURE(2, 1, 1, 0, 47 , 24 , 0  , 0  , 0  , 0  ), //      {R:r32|m32, R:i32|u32}</a>
+<a name="3165"><span class="lineNum">    3165 </span>            :   ISIGNATURE(2, 0, 1, 0, 16 , 32 , 0  , 0  , 0  , 0  ), //      {R:r64|m64|mem, R:i32|r64}</a>
+<a name="3166"><span class="lineNum">    3166 </span>            :   ISIGNATURE(2, 1, 1, 0, 48 , 34 , 0  , 0  , 0  , 0  ), //      {R:r16|m16|r32|m32|r64|m64|mem, R:i8}</a>
+<a name="3167"><span class="lineNum">    3167 </span>            :   ISIGNATURE(2, 1, 1, 0, 40 , 2  , 0  , 0  , 0  , 0  ), //      {R:r8lo|r8hi|m8|mem, R:r8lo|r8hi}</a>
+<a name="3168"><span class="lineNum">    3168 </span>            :   ISIGNATURE(2, 1, 1, 0, 12 , 37 , 0  , 0  , 0  , 0  ), //      {R:r16|m16|mem, R:r16}</a>
+<a name="3169"><span class="lineNum">    3169 </span>            :   ISIGNATURE(2, 1, 1, 0, 43 , 6  , 0  , 0  , 0  , 0  ), //      {R:r32|m32|mem, R:r32}</a>
+<a name="3170"><span class="lineNum">    3170 </span>            :   ISIGNATURE(2, 1, 1, 0, 2  , 40 , 0  , 0  , 0  , 0  ), //      {R:r8lo|r8hi, R:r8lo|r8hi|m8|mem}</a>
+<a name="3171"><span class="lineNum">    3171 </span>            :   ISIGNATURE(2, 1, 1, 0, 37 , 12 , 0  , 0  , 0  , 0  ), //      {R:r16, R:r16|m16|mem}</a>
+<a name="3172"><span class="lineNum">    3172 </span>            :   ISIGNATURE(2, 1, 1, 0, 6  , 43 , 0  , 0  , 0  , 0  ), //      {R:r32, R:r32|m32|mem}</a>
+<a name="3173"><span class="lineNum">    3173 </span>            :   ISIGNATURE(2, 0, 1, 0, 27 , 16 , 0  , 0  , 0  , 0  ), //      {R:r64, R:r64|m64|mem}</a>
+<a name="3174"><span class="lineNum">    3174 </span>            :   ISIGNATURE(2, 1, 1, 0, 49 , 22 , 0  , 0  , 0  , 0  ), // #39  {X:r8lo|r8hi|m8|r16|m16|r32|m32|r64|m64|mem, R:i8|u8}</a>
+<a name="3175"><span class="lineNum">    3175 </span>            :   ISIGNATURE(2, 1, 1, 0, 29 , 18 , 0  , 0  , 0  , 0  ), //      {X:r16|m16, R:i16|u16}</a>
+<a name="3176"><span class="lineNum">    3176 </span>            :   ISIGNATURE(2, 1, 1, 0, 30 , 24 , 0  , 0  , 0  , 0  ), //      {X:r32|m32, R:i32|u32}</a>
+<a name="3177"><span class="lineNum">    3177 </span>            :   ISIGNATURE(2, 0, 1, 0, 31 , 32 , 0  , 0  , 0  , 0  ), //      {X:r64|m64|mem, R:i32|r64}</a>
+<a name="3178"><span class="lineNum">    3178 </span>            :   ISIGNATURE(2, 1, 1, 0, 35 , 2  , 0  , 0  , 0  , 0  ), //      {X:r8lo|r8hi|m8|mem, R:r8lo|r8hi}</a>
+<a name="3179"><span class="lineNum">    3179 </span>            :   ISIGNATURE(2, 1, 1, 0, 36 , 37 , 0  , 0  , 0  , 0  ), //      {X:r16|m16|mem, R:r16}</a>
+<a name="3180"><span class="lineNum">    3180 </span>            :   ISIGNATURE(2, 1, 1, 0, 38 , 6  , 0  , 0  , 0  , 0  ), //      {X:r32|m32|mem, R:r32}</a>
+<a name="3181"><span class="lineNum">    3181 </span>            :   ISIGNATURE(2, 1, 1, 0, 39 , 40 , 0  , 0  , 0  , 0  ), //      {X:r8lo|r8hi, R:r8lo|r8hi|m8|mem}</a>
+<a name="3182"><span class="lineNum">    3182 </span>            :   ISIGNATURE(2, 1, 1, 0, 41 , 12 , 0  , 0  , 0  , 0  ), //      {X:r16, R:r16|m16|mem}</a>
+<a name="3183"><span class="lineNum">    3183 </span>            :   ISIGNATURE(2, 1, 1, 0, 42 , 43 , 0  , 0  , 0  , 0  ), //      {X:r32, R:r32|m32|mem}</a>
+<a name="3184"><span class="lineNum">    3184 </span>            :   ISIGNATURE(2, 0, 1, 0, 44 , 16 , 0  , 0  , 0  , 0  ), //      {X:r64, R:r64|m64|mem}</a>
+<a name="3185"><span class="lineNum">    3185 </span>            :   ISIGNATURE(2, 1, 1, 1, 50 , 40 , 0  , 0  , 0  , 0  ), // #50  {X:&lt;ax&gt;, R:r8lo|r8hi|m8|mem}</a>
+<a name="3186"><span class="lineNum">    3186 </span>            :   ISIGNATURE(3, 1, 1, 2, 51 , 50 , 12 , 0  , 0  , 0  ), //      {W:&lt;dx&gt;, X:&lt;ax&gt;, R:r16|m16|mem}</a>
+<a name="3187"><span class="lineNum">    3187 </span>            :   ISIGNATURE(3, 1, 1, 2, 52 , 53 , 43 , 0  , 0  , 0  ), //      {W:&lt;edx&gt;, X:&lt;eax&gt;, R:r32|m32|mem}</a>
+<a name="3188"><span class="lineNum">    3188 </span>            :   ISIGNATURE(3, 0, 1, 2, 54 , 55 , 16 , 0  , 0  , 0  ), //      {W:&lt;rdx&gt;, X:&lt;rax&gt;, R:r64|m64|mem}</a>
+<a name="3189"><span class="lineNum">    3189 </span>            :   ISIGNATURE(2, 1, 1, 0, 41 , 56 , 0  , 0  , 0  , 0  ), //      {X:r16, R:r16|m16|mem|i8|i16}</a>
+<a name="3190"><span class="lineNum">    3190 </span>            :   ISIGNATURE(2, 1, 1, 0, 42 , 57 , 0  , 0  , 0  , 0  ), //      {X:r32, R:r32|m32|mem|i8|i32}</a>
+<a name="3191"><span class="lineNum">    3191 </span>            :   ISIGNATURE(2, 0, 1, 0, 44 , 58 , 0  , 0  , 0  , 0  ), //      {X:r64, R:r64|m64|mem|i8|i32}</a>
+<a name="3192"><span class="lineNum">    3192 </span>            :   ISIGNATURE(3, 1, 1, 0, 59 , 12 , 60 , 0  , 0  , 0  ), //      {W:r16, R:r16|m16|mem, R:i8|i16|u16}</a>
+<a name="3193"><span class="lineNum">    3193 </span>            :   ISIGNATURE(3, 1, 1, 0, 13 , 43 , 61 , 0  , 0  , 0  ), //      {W:r32, R:r32|m32|mem, R:i8|i32|u32}</a>
+<a name="3194"><span class="lineNum">    3194 </span>            :   ISIGNATURE(3, 0, 1, 0, 19 , 16 , 62 , 0  , 0  , 0  ), //      {W:r64, R:r64|m64|mem, R:i8|i32}</a>
+<a name="3195"><span class="lineNum">    3195 </span>            :   ISIGNATURE(2, 1, 1, 0, 36 , 41 , 0  , 0  , 0  , 0  ), // #60  {X:r16|m16|mem, X:r16}</a>
+<a name="3196"><span class="lineNum">    3196 </span>            :   ISIGNATURE(2, 1, 1, 0, 38 , 42 , 0  , 0  , 0  , 0  ), //      {X:r32|m32|mem, X:r32}</a>
+<a name="3197"><span class="lineNum">    3197 </span>            :   ISIGNATURE(2, 0, 1, 0, 31 , 44 , 0  , 0  , 0  , 0  ), //      {X:r64|m64|mem, X:r64}</a>
+<a name="3198"><span class="lineNum">    3198 </span>            :   ISIGNATURE(2, 1, 1, 0, 41 , 36 , 0  , 0  , 0  , 0  ), //      {X:r16, X:r16|m16|mem}</a>
+<a name="3199"><span class="lineNum">    3199 </span>            :   ISIGNATURE(2, 1, 1, 0, 42 , 38 , 0  , 0  , 0  , 0  ), //      {X:r32, X:r32|m32|mem}</a>
+<a name="3200"><span class="lineNum">    3200 </span>            :   ISIGNATURE(2, 0, 1, 0, 44 , 31 , 0  , 0  , 0  , 0  ), //      {X:r64, X:r64|m64|mem}</a>
+<a name="3201"><span class="lineNum">    3201 </span>            :   ISIGNATURE(2, 1, 1, 0, 35 , 39 , 0  , 0  , 0  , 0  ), //      {X:r8lo|r8hi|m8|mem, X:r8lo|r8hi}</a>
+<a name="3202"><span class="lineNum">    3202 </span>            :   ISIGNATURE(2, 1, 1, 0, 39 , 35 , 0  , 0  , 0  , 0  ), //      {X:r8lo|r8hi, X:r8lo|r8hi|m8|mem}</a>
+<a name="3203"><span class="lineNum">    3203 </span>            :   ISIGNATURE(2, 1, 1, 0, 45 , 22 , 0  , 0  , 0  , 0  ), // #68  {R:r8lo|r8hi|m8, R:i8|u8}</a>
+<a name="3204"><span class="lineNum">    3204 </span>            :   ISIGNATURE(2, 1, 1, 0, 46 , 18 , 0  , 0  , 0  , 0  ), //      {R:r16|m16, R:i16|u16}</a>
+<a name="3205"><span class="lineNum">    3205 </span>            :   ISIGNATURE(2, 1, 1, 0, 47 , 24 , 0  , 0  , 0  , 0  ), //      {R:r32|m32, R:i32|u32}</a>
+<a name="3206"><span class="lineNum">    3206 </span>            :   ISIGNATURE(2, 0, 1, 0, 16 , 32 , 0  , 0  , 0  , 0  ), //      {R:r64|m64|mem, R:i32|r64}</a>
+<a name="3207"><span class="lineNum">    3207 </span>            :   ISIGNATURE(2, 1, 1, 0, 40 , 2  , 0  , 0  , 0  , 0  ), //      {R:r8lo|r8hi|m8|mem, R:r8lo|r8hi}</a>
+<a name="3208"><span class="lineNum">    3208 </span>            :   ISIGNATURE(2, 1, 1, 0, 12 , 37 , 0  , 0  , 0  , 0  ), //      {R:r16|m16|mem, R:r16}</a>
+<a name="3209"><span class="lineNum">    3209 </span>            :   ISIGNATURE(2, 1, 1, 0, 43 , 6  , 0  , 0  , 0  , 0  ), //      {R:r32|m32|mem, R:r32}</a>
+<a name="3210"><span class="lineNum">    3210 </span>            :   ISIGNATURE(2, 1, 1, 0, 59 , 63 , 0  , 0  , 0  , 0  ), // #75  {W:r16, R:m16|mem}</a>
+<a name="3211"><span class="lineNum">    3211 </span>            :   ISIGNATURE(2, 1, 1, 0, 13 , 64 , 0  , 0  , 0  , 0  ), //      {W:r32, R:m32|mem}</a>
+<a name="3212"><span class="lineNum">    3212 </span>            :   ISIGNATURE(2, 0, 1, 0, 19 , 65 , 0  , 0  , 0  , 0  ), //      {W:r64, R:m64|mem}</a>
+<a name="3213"><span class="lineNum">    3213 </span>            :   ISIGNATURE(2, 1, 1, 0, 66 , 37 , 0  , 0  , 0  , 0  ), //      {W:m16|mem, R:r16}</a>
+<a name="3214"><span class="lineNum">    3214 </span>            :   ISIGNATURE(2, 1, 1, 0, 67 , 6  , 0  , 0  , 0  , 0  ), // #79  {W:m32|mem, R:r32}</a>
+<a name="3215"><span class="lineNum">    3215 </span>            :   ISIGNATURE(2, 0, 1, 0, 68 , 27 , 0  , 0  , 0  , 0  ), //      {W:m64|mem, R:r64}</a>
+<a name="3216"><span class="lineNum">    3216 </span>            :   ISIGNATURE(2, 1, 1, 0, 69 , 70 , 0  , 0  , 0  , 0  ), // #81  {W:mm, R:mm|m64|mem|r64|xmm}</a>
+<a name="3217"><span class="lineNum">    3217 </span>            :   ISIGNATURE(2, 1, 1, 0, 71 , 72 , 0  , 0  , 0  , 0  ), //      {W:mm|m64|mem|r64|xmm, R:mm}</a>
+<a name="3218"><span class="lineNum">    3218 </span>            :   ISIGNATURE(2, 0, 1, 0, 7  , 73 , 0  , 0  , 0  , 0  ), //      {W:r64|m64|mem, R:xmm}</a>
+<a name="3219"><span class="lineNum">    3219 </span>            :   ISIGNATURE(2, 0, 1, 0, 74 , 16 , 0  , 0  , 0  , 0  ), //      {W:xmm, R:r64|m64|mem}</a>
+<a name="3220"><span class="lineNum">    3220 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 75 , 0  , 0  , 0  , 0  ), // #85  {W:xmm, R:xmm|m64|mem}</a>
+<a name="3221"><span class="lineNum">    3221 </span>            :   ISIGNATURE(2, 1, 1, 0, 76 , 73 , 0  , 0  , 0  , 0  ), //      {W:xmm|m64|mem, R:xmm}</a>
+<a name="3222"><span class="lineNum">    3222 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 77 , 0  , 0  , 0  , 0  ), // #87  {W:xmm, R:xmm|m128|mem}</a>
+<a name="3223"><span class="lineNum">    3223 </span>            :   ISIGNATURE(2, 1, 1, 0, 78 , 73 , 0  , 0  , 0  , 0  ), //      {W:xmm|m128|mem, R:xmm}</a>
+<a name="3224"><span class="lineNum">    3224 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 80 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:ymm|m256|mem}</a>
+<a name="3225"><span class="lineNum">    3225 </span>            :   ISIGNATURE(2, 1, 1, 0, 81 , 82 , 0  , 0  , 0  , 0  ), //      {W:ymm|m256|mem, R:ymm}</a>
+<a name="3226"><span class="lineNum">    3226 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 84 , 0  , 0  , 0  , 0  ), // #91  {W:zmm, R:zmm|m512|mem}</a>
+<a name="3227"><span class="lineNum">    3227 </span>            :   ISIGNATURE(2, 1, 1, 0, 85 , 86 , 0  , 0  , 0  , 0  ), //      {W:zmm|m512|mem, R:zmm}</a>
+<a name="3228"><span class="lineNum">    3228 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 77 , 0  , 0  , 0  ), // #93  {W:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3229"><span class="lineNum">    3229 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 77 , 87 , 0  , 0  , 0  ), // #94  {W:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3230"><span class="lineNum">    3230 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 82 , 80 , 0  , 0  , 0  ), // #95  {W:ymm, R:ymm, R:ymm|m256|mem}</a>
+<a name="3231"><span class="lineNum">    3231 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 80 , 87 , 0  , 0  , 0  ), // #96  {W:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3232"><span class="lineNum">    3232 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 86 , 84 , 0  , 0  , 0  ), //      {W:zmm, R:zmm, R:zmm|m512|mem}</a>
+<a name="3233"><span class="lineNum">    3233 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 84 , 87 , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3234"><span class="lineNum">    3234 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 88 , 0  , 0  , 0  ), // #99  {W:xmm, R:xmm, R:u8|xmm|m128|mem}</a>
+<a name="3235"><span class="lineNum">    3235 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 82 , 88 , 0  , 0  , 0  ), //      {W:ymm, R:ymm, R:u8|xmm|m128|mem}</a>
+<a name="3236"><span class="lineNum">    3236 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 77 , 87 , 0  , 0  , 0  ), // #101 {W:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3237"><span class="lineNum">    3237 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 80 , 87 , 0  , 0  , 0  ), //      {W:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3238"><span class="lineNum">    3238 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 86 , 77 , 0  , 0  , 0  ), //      {W:zmm, R:zmm, R:xmm|m128|mem}</a>
+<a name="3239"><span class="lineNum">    3239 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 84 , 87 , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3240"><span class="lineNum">    3240 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 77 , 0  , 0  , 0  ), // #105 {W:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3241"><span class="lineNum">    3241 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 77 , 87 , 0  , 0  , 0  ), //      {W:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3242"><span class="lineNum">    3242 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 82 , 77 , 0  , 0  , 0  ), //      {W:ymm, R:ymm, R:xmm|m128|mem}</a>
+<a name="3243"><span class="lineNum">    3243 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 80 , 87 , 0  , 0  , 0  ), //      {W:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3244"><span class="lineNum">    3244 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 86 , 77 , 0  , 0  , 0  ), //      {W:zmm, R:zmm, R:xmm|m128|mem}</a>
+<a name="3245"><span class="lineNum">    3245 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 84 , 87 , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3246"><span class="lineNum">    3246 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 90 , 89 , 0  , 0  , 0  ), // #111 {X:xmm, R:vm32x, X:xmm}</a>
+<a name="3247"><span class="lineNum">    3247 </span>            :   ISIGNATURE(3, 1, 1, 0, 91 , 90 , 91 , 0  , 0  , 0  ), //      {X:ymm, R:vm32x, X:ymm}</a>
+<a name="3248"><span class="lineNum">    3248 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 90 , 0  , 0  , 0  , 0  ), //      {X:xmm, R:vm32x}</a>
+<a name="3249"><span class="lineNum">    3249 </span>            :   ISIGNATURE(2, 1, 1, 0, 91 , 92 , 0  , 0  , 0  , 0  ), //      {X:ymm, R:vm32y}</a>
+<a name="3250"><span class="lineNum">    3250 </span>            :   ISIGNATURE(2, 1, 1, 0, 93 , 94 , 0  , 0  , 0  , 0  ), //      {X:zmm, R:vm32z}</a>
+<a name="3251"><span class="lineNum">    3251 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 90 , 89 , 0  , 0  , 0  ), // #116 {X:xmm, R:vm32x, X:xmm}</a>
+<a name="3252"><span class="lineNum">    3252 </span>            :   ISIGNATURE(3, 1, 1, 0, 91 , 92 , 91 , 0  , 0  , 0  ), //      {X:ymm, R:vm32y, X:ymm}</a>
+<a name="3253"><span class="lineNum">    3253 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 90 , 0  , 0  , 0  , 0  ), //      {X:xmm, R:vm32x}</a>
+<a name="3254"><span class="lineNum">    3254 </span>            :   ISIGNATURE(2, 1, 1, 0, 91 , 92 , 0  , 0  , 0  , 0  ), //      {X:ymm, R:vm32y}</a>
+<a name="3255"><span class="lineNum">    3255 </span>            :   ISIGNATURE(2, 1, 1, 0, 93 , 94 , 0  , 0  , 0  , 0  ), //      {X:zmm, R:vm32z}</a>
+<a name="3256"><span class="lineNum">    3256 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 95 , 89 , 0  , 0  , 0  ), // #121 {X:xmm, R:vm64x, X:xmm}</a>
+<a name="3257"><span class="lineNum">    3257 </span>            :   ISIGNATURE(3, 1, 1, 0, 91 , 96 , 91 , 0  , 0  , 0  ), //      {X:ymm, R:vm64y, X:ymm}</a>
+<a name="3258"><span class="lineNum">    3258 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 95 , 0  , 0  , 0  , 0  ), //      {X:xmm, R:vm64x}</a>
+<a name="3259"><span class="lineNum">    3259 </span>            :   ISIGNATURE(2, 1, 1, 0, 91 , 96 , 0  , 0  , 0  , 0  ), //      {X:ymm, R:vm64y}</a>
+<a name="3260"><span class="lineNum">    3260 </span>            :   ISIGNATURE(2, 1, 1, 0, 93 , 97 , 0  , 0  , 0  , 0  ), //      {X:zmm, R:vm64z}</a>
+<a name="3261"><span class="lineNum">    3261 </span>            :   ISIGNATURE(2, 1, 1, 0, 12 , 37 , 0  , 0  , 0  , 0  ), // #126 {R:r16|m16|mem, R:r16}</a>
+<a name="3262"><span class="lineNum">    3262 </span>            :   ISIGNATURE(2, 1, 1, 0, 43 , 6  , 0  , 0  , 0  , 0  ), //      {R:r32|m32|mem, R:r32}</a>
+<a name="3263"><span class="lineNum">    3263 </span>            :   ISIGNATURE(2, 0, 1, 0, 16 , 98 , 0  , 0  , 0  , 0  ), //      {R:r64|m64|mem, R:r64|u8}</a>
+<a name="3264"><span class="lineNum">    3264 </span>            :   ISIGNATURE(2, 1, 1, 0, 99 , 87 , 0  , 0  , 0  , 0  ), //      {R:r16|m16|r32|m32, R:u8}</a>
+<a name="3265"><span class="lineNum">    3265 </span>            :   ISIGNATURE(2, 1, 1, 0, 36 , 37 , 0  , 0  , 0  , 0  ), // #130 {X:r16|m16|mem, R:r16}</a>
+<a name="3266"><span class="lineNum">    3266 </span>            :   ISIGNATURE(2, 1, 1, 0, 38 , 6  , 0  , 0  , 0  , 0  ), //      {X:r32|m32|mem, R:r32}</a>
+<a name="3267"><span class="lineNum">    3267 </span>            :   ISIGNATURE(2, 0, 1, 0, 31 , 98 , 0  , 0  , 0  , 0  ), //      {X:r64|m64|mem, R:r64|u8}</a>
+<a name="3268"><span class="lineNum">    3268 </span>            :   ISIGNATURE(2, 1, 1, 0, 100, 87 , 0  , 0  , 0  , 0  ), //      {X:r16|m16|r32|m32, R:u8}</a>
+<a name="3269"><span class="lineNum">    3269 </span>            :   ISIGNATURE(3, 1, 1, 1, 35 , 2  , 101, 0  , 0  , 0  ), // #134 {X:r8lo|r8hi|m8|mem, R:r8lo|r8hi, R:&lt;al&gt;}</a>
+<a name="3270"><span class="lineNum">    3270 </span>            :   ISIGNATURE(3, 1, 1, 1, 36 , 37 , 102, 0  , 0  , 0  ), //      {X:r16|m16|mem, R:r16, R:&lt;ax&gt;}</a>
+<a name="3271"><span class="lineNum">    3271 </span>            :   ISIGNATURE(3, 1, 1, 1, 38 , 6  , 103, 0  , 0  , 0  ), //      {X:r32|m32|mem, R:r32, R:&lt;eax&gt;}</a>
+<a name="3272"><span class="lineNum">    3272 </span>            :   ISIGNATURE(3, 0, 1, 1, 31 , 27 , 104, 0  , 0  , 0  ), //      {X:r64|m64|mem, R:r64, R:&lt;rax&gt;}</a>
+<a name="3273"><span class="lineNum">    3273 </span>            :   ISIGNATURE(2, 1, 1, 1, 50 , 40 , 0  , 0  , 0  , 0  ), // #138 {X:&lt;ax&gt;, R:r8lo|r8hi|m8|mem}</a>
+<a name="3274"><span class="lineNum">    3274 </span>            :   ISIGNATURE(3, 1, 1, 2, 105, 50 , 12 , 0  , 0  , 0  ), //      {X:&lt;dx&gt;, X:&lt;ax&gt;, R:r16|m16|mem}</a>
+<a name="3275"><span class="lineNum">    3275 </span>            :   ISIGNATURE(3, 1, 1, 2, 106, 53 , 43 , 0  , 0  , 0  ), //      {X:&lt;edx&gt;, X:&lt;eax&gt;, R:r32|m32|mem}</a>
+<a name="3276"><span class="lineNum">    3276 </span>            :   ISIGNATURE(3, 0, 1, 2, 107, 55 , 16 , 0  , 0  , 0  ), //      {X:&lt;rdx&gt;, X:&lt;rax&gt;, R:r64|m64|mem}</a>
+<a name="3277"><span class="lineNum">    3277 </span>            :   ISIGNATURE(1, 1, 1, 0, 108, 0  , 0  , 0  , 0  , 0  ), // #142 {W:r16|m16|r64|m64|mem}</a>
+<a name="3278"><span class="lineNum">    3278 </span>            :   ISIGNATURE(1, 1, 0, 0, 23 , 0  , 0  , 0  , 0  , 0  ), //      {W:r32|m32}</a>
+<a name="3279"><span class="lineNum">    3279 </span>            :   ISIGNATURE(1, 1, 0, 0, 109, 0  , 0  , 0  , 0  , 0  ), //      {W:ds|es|ss}</a>
+<a name="3280"><span class="lineNum">    3280 </span>            :   ISIGNATURE(1, 1, 1, 0, 110, 0  , 0  , 0  , 0  , 0  ), //      {W:fs|gs}</a>
+<a name="3281"><span class="lineNum">    3281 </span>            :   ISIGNATURE(1, 1, 1, 0, 111, 0  , 0  , 0  , 0  , 0  ), // #146 {R:r16|m16|r64|m64|mem|i8|i16|i32}</a>
+<a name="3282"><span class="lineNum">    3282 </span>            :   ISIGNATURE(1, 1, 0, 0, 47 , 0  , 0  , 0  , 0  , 0  ), //      {R:r32|m32}</a>
+<a name="3283"><span class="lineNum">    3283 </span>            :   ISIGNATURE(1, 1, 0, 0, 112, 0  , 0  , 0  , 0  , 0  ), //      {R:cs|ss|ds|es}</a>
+<a name="3284"><span class="lineNum">    3284 </span>            :   ISIGNATURE(1, 1, 1, 0, 113, 0  , 0  , 0  , 0  , 0  ), //      {R:fs|gs}</a>
+<a name="3285"><span class="lineNum">    3285 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 73 , 77 , 0  , 0  ), // #150 {W:xmm, R:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3286"><span class="lineNum">    3286 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 77 , 73 , 0  , 0  ), // #151 {W:xmm, R:xmm, R:xmm|m128|mem, R:xmm}</a>
+<a name="3287"><span class="lineNum">    3287 </span>            :   ISIGNATURE(4, 1, 1, 0, 79 , 82 , 82 , 80 , 0  , 0  ), //      {W:ymm, R:ymm, R:ymm, R:ymm|m256|mem}</a>
+<a name="3288"><span class="lineNum">    3288 </span>            :   ISIGNATURE(4, 1, 1, 0, 79 , 82 , 80 , 82 , 0  , 0  ), //      {W:ymm, R:ymm, R:ymm|m256|mem, R:ymm}</a>
+<a name="3289"><span class="lineNum">    3289 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 114, 89 , 0  , 0  , 0  ), // #154 {X:xmm, R:vm64x|vm64y, X:xmm}</a>
+<a name="3290"><span class="lineNum">    3290 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 95 , 0  , 0  , 0  , 0  ), //      {X:xmm, R:vm64x}</a>
+<a name="3291"><span class="lineNum">    3291 </span>            :   ISIGNATURE(2, 1, 1, 0, 91 , 96 , 0  , 0  , 0  , 0  ), //      {X:ymm, R:vm64y}</a>
+<a name="3292"><span class="lineNum">    3292 </span>            :   ISIGNATURE(2, 1, 1, 0, 93 , 97 , 0  , 0  , 0  , 0  ), //      {X:zmm, R:vm64z}</a>
+<a name="3293"><span class="lineNum">    3293 </span>            :   ISIGNATURE(3, 1, 1, 0, 115, 73 , 73 , 0  , 0  , 0  ), // #158 {W:m128|mem, R:xmm, R:xmm}</a>
+<a name="3294"><span class="lineNum">    3294 </span>            :   ISIGNATURE(3, 1, 1, 0, 116, 82 , 82 , 0  , 0  , 0  ), //      {W:m256|mem, R:ymm, R:ymm}</a>
+<a name="3295"><span class="lineNum">    3295 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 117, 0  , 0  , 0  ), //      {W:xmm, R:xmm, R:m128|mem}</a>
+<a name="3296"><span class="lineNum">    3296 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 82 , 118, 0  , 0  , 0  ), //      {W:ymm, R:ymm, R:m256|mem}</a>
+<a name="3297"><span class="lineNum">    3297 </span>            :   ISIGNATURE(5, 1, 1, 0, 74 , 73 , 77 , 73 , 119, 0  ), // #162 {W:xmm, R:xmm, R:xmm|m128|mem, R:xmm, R:u4}</a>
+<a name="3298"><span class="lineNum">    3298 </span>            :   ISIGNATURE(5, 1, 1, 0, 74 , 73 , 73 , 77 , 119, 0  ), //      {W:xmm, R:xmm, R:xmm, R:xmm|m128|mem, R:u4}</a>
+<a name="3299"><span class="lineNum">    3299 </span>            :   ISIGNATURE(5, 1, 1, 0, 79 , 82 , 80 , 82 , 119, 0  ), //      {W:ymm, R:ymm, R:ymm|m256|mem, R:ymm, R:u4}</a>
+<a name="3300"><span class="lineNum">    3300 </span>            :   ISIGNATURE(5, 1, 1, 0, 79 , 82 , 82 , 80 , 119, 0  ), //      {W:ymm, R:ymm, R:ymm, R:ymm|m256|mem, R:u4}</a>
+<a name="3301"><span class="lineNum">    3301 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 80 , 87 , 0  , 0  , 0  ), // #166 {W:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3302"><span class="lineNum">    3302 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 82 , 80 , 0  , 0  , 0  ), // #167 {W:ymm, R:ymm, R:ymm|m256|mem}</a>
+<a name="3303"><span class="lineNum">    3303 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 86 , 84 , 0  , 0  , 0  ), //      {W:zmm, R:zmm, R:zmm|m512|mem}</a>
+<a name="3304"><span class="lineNum">    3304 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 84 , 87 , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3305"><span class="lineNum">    3305 </span>            :   ISIGNATURE(2, 1, 1, 0, 35 , 39 , 0  , 0  , 0  , 0  ), // #170 {X:r8lo|r8hi|m8|mem, X:r8lo|r8hi}</a>
+<a name="3306"><span class="lineNum">    3306 </span>            :   ISIGNATURE(2, 1, 1, 0, 36 , 41 , 0  , 0  , 0  , 0  ), //      {X:r16|m16|mem, X:r16}</a>
+<a name="3307"><span class="lineNum">    3307 </span>            :   ISIGNATURE(2, 1, 1, 0, 38 , 42 , 0  , 0  , 0  , 0  ), //      {X:r32|m32|mem, X:r32}</a>
+<a name="3308"><span class="lineNum">    3308 </span>            :   ISIGNATURE(2, 0, 1, 0, 31 , 44 , 0  , 0  , 0  , 0  ), //      {X:r64|m64|mem, X:r64}</a>
+<a name="3309"><span class="lineNum">    3309 </span>            :   ISIGNATURE(1, 1, 1, 0, 120, 0  , 0  , 0  , 0  , 0  ), // #174 {R:m32|m64}</a>
+<a name="3310"><span class="lineNum">    3310 </span>            :   ISIGNATURE(2, 1, 1, 0, 121, 122, 0  , 0  , 0  , 0  ), //      {X:fp0, R:fp}</a>
+<a name="3311"><span class="lineNum">    3311 </span>            :   ISIGNATURE(2, 1, 1, 0, 123, 124, 0  , 0  , 0  , 0  ), //      {X:fp, R:fp0}</a>
+<a name="3312"><span class="lineNum">    3312 </span>            :   ISIGNATURE(1, 1, 1, 0, 125, 0  , 0  , 0  , 0  , 0  ), // #177 {X:m32|m64}</a>
+<a name="3313"><span class="lineNum">    3313 </span>            :   ISIGNATURE(2, 1, 1, 0, 121, 122, 0  , 0  , 0  , 0  ), //      {X:fp0, R:fp}</a>
+<a name="3314"><span class="lineNum">    3314 </span>            :   ISIGNATURE(2, 1, 1, 0, 123, 124, 0  , 0  , 0  , 0  ), //      {X:fp, R:fp0}</a>
+<a name="3315"><span class="lineNum">    3315 </span>            :   ISIGNATURE(2, 1, 1, 0, 41 , 64 , 0  , 0  , 0  , 0  ), // #180 {X:r16, R:m32|mem}</a>
+<a name="3316"><span class="lineNum">    3316 </span>            :   ISIGNATURE(2, 1, 1, 0, 42 , 126, 0  , 0  , 0  , 0  ), //      {X:r32, R:m48|mem}</a>
+<a name="3317"><span class="lineNum">    3317 </span>            :   ISIGNATURE(2, 0, 1, 0, 44 , 127, 0  , 0  , 0  , 0  ), //      {X:r64, R:m80|mem}</a>
+<a name="3318"><span class="lineNum">    3318 </span>            :   ISIGNATURE(2, 1, 1, 0, 59 , 12 , 0  , 0  , 0  , 0  ), // #183 {W:r16, R:r16|m16|mem}</a>
+<a name="3319"><span class="lineNum">    3319 </span>            :   ISIGNATURE(2, 1, 1, 0, 13 , 43 , 0  , 0  , 0  , 0  ), // #184 {W:r32, R:r32|m32|mem}</a>
+<a name="3320"><span class="lineNum">    3320 </span>            :   ISIGNATURE(2, 0, 1, 0, 19 , 16 , 0  , 0  , 0  , 0  ), //      {W:r64, R:r64|m64|mem}</a>
+<a name="3321"><span class="lineNum">    3321 </span>            :   ISIGNATURE(3, 1, 1, 0, 36 , 37 , 128, 0  , 0  , 0  ), // #186 {X:r16|m16|mem, R:r16, R:u8|cl}</a>
+<a name="3322"><span class="lineNum">    3322 </span>            :   ISIGNATURE(3, 1, 1, 0, 38 , 6  , 128, 0  , 0  , 0  ), //      {X:r32|m32|mem, R:r32, R:u8|cl}</a>
+<a name="3323"><span class="lineNum">    3323 </span>            :   ISIGNATURE(3, 0, 1, 0, 31 , 27 , 128, 0  , 0  , 0  ), //      {X:r64|m64|mem, R:r64, R:u8|cl}</a>
+<a name="3324"><span class="lineNum">    3324 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 77 , 0  , 0  , 0  ), // #189 {W:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3325"><span class="lineNum">    3325 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 82 , 80 , 0  , 0  , 0  ), //      {W:ymm, R:ymm, R:ymm|m256|mem}</a>
+<a name="3326"><span class="lineNum">    3326 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 86 , 84 , 0  , 0  , 0  ), //      {W:zmm, R:zmm, R:zmm|m512|mem}</a>
+<a name="3327"><span class="lineNum">    3327 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 77 , 87 , 0  , 0  ), // #192 {W:xmm, R:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3328"><span class="lineNum">    3328 </span>            :   ISIGNATURE(4, 1, 1, 0, 79 , 82 , 80 , 87 , 0  , 0  ), // #193 {W:ymm, R:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3329"><span class="lineNum">    3329 </span>            :   ISIGNATURE(4, 1, 1, 0, 83 , 86 , 84 , 87 , 0  , 0  ), //      {W:zmm, R:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3330"><span class="lineNum">    3330 </span>            :   ISIGNATURE(4, 1, 1, 0, 129, 73 , 77 , 87 , 0  , 0  ), // #195 {W:xmm|k, R:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3331"><span class="lineNum">    3331 </span>            :   ISIGNATURE(4, 1, 1, 0, 130, 82 , 80 , 87 , 0  , 0  ), //      {W:ymm|k, R:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3332"><span class="lineNum">    3332 </span>            :   ISIGNATURE(4, 1, 1, 0, 131, 86 , 84 , 87 , 0  , 0  ), //      {W:k, R:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3333"><span class="lineNum">    3333 </span>            :   ISIGNATURE(2, 1, 1, 0, 78 , 73 , 0  , 0  , 0  , 0  ), // #198 {W:xmm|m128|mem, R:xmm}</a>
+<a name="3334"><span class="lineNum">    3334 </span>            :   ISIGNATURE(2, 1, 1, 0, 81 , 82 , 0  , 0  , 0  , 0  ), //      {W:ymm|m256|mem, R:ymm}</a>
+<a name="3335"><span class="lineNum">    3335 </span>            :   ISIGNATURE(2, 1, 1, 0, 85 , 86 , 0  , 0  , 0  , 0  ), //      {W:zmm|m512|mem, R:zmm}</a>
+<a name="3336"><span class="lineNum">    3336 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 75 , 0  , 0  , 0  , 0  ), // #201 {W:xmm, R:xmm|m64|mem}</a>
+<a name="3337"><span class="lineNum">    3337 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 77 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:xmm|m128|mem}</a>
+<a name="3338"><span class="lineNum">    3338 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 80 , 0  , 0  , 0  , 0  ), //      {W:zmm, R:ymm|m256|mem}</a>
+<a name="3339"><span class="lineNum">    3339 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 77 , 0  , 0  , 0  , 0  ), // #204 {W:xmm, R:xmm|m128|mem}</a>
+<a name="3340"><span class="lineNum">    3340 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 80 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:ymm|m256|mem}</a>
+<a name="3341"><span class="lineNum">    3341 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 84 , 0  , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem}</a>
+<a name="3342"><span class="lineNum">    3342 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 132, 0  , 0  , 0  , 0  ), // #207 {W:xmm, R:xmm|m128|ymm|m256|m64}</a>
+<a name="3343"><span class="lineNum">    3343 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 133, 0  , 0  , 0  , 0  ), //      {W:ymm, R:xmm|m128}</a>
+<a name="3344"><span class="lineNum">    3344 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 134, 0  , 0  , 0  , 0  ), //      {W:zmm, R:ymm|m256}</a>
+<a name="3345"><span class="lineNum">    3345 </span>            :   ISIGNATURE(3, 1, 1, 0, 76 , 73 , 87 , 0  , 0  , 0  ), // #210 {W:xmm|m64|mem, R:xmm, R:u8}</a>
+<a name="3346"><span class="lineNum">    3346 </span>            :   ISIGNATURE(3, 1, 1, 0, 78 , 82 , 87 , 0  , 0  , 0  ), // #211 {W:xmm|m128|mem, R:ymm, R:u8}</a>
+<a name="3347"><span class="lineNum">    3347 </span>            :   ISIGNATURE(3, 1, 1, 0, 81 , 86 , 87 , 0  , 0  , 0  ), // #212 {W:ymm|m256|mem, R:zmm, R:u8}</a>
+<a name="3348"><span class="lineNum">    3348 </span>            :   ISIGNATURE(4, 1, 1, 0, 89 , 73 , 77 , 87 , 0  , 0  ), // #213 {X:xmm, R:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3349"><span class="lineNum">    3349 </span>            :   ISIGNATURE(4, 1, 1, 0, 91 , 82 , 80 , 87 , 0  , 0  ), //      {X:ymm, R:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3350"><span class="lineNum">    3350 </span>            :   ISIGNATURE(4, 1, 1, 0, 93 , 86 , 84 , 87 , 0  , 0  ), //      {X:zmm, R:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3351"><span class="lineNum">    3351 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 73 , 77 , 0  , 0  , 0  ), // #216 {X:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3352"><span class="lineNum">    3352 </span>            :   ISIGNATURE(3, 1, 1, 0, 91 , 82 , 80 , 0  , 0  , 0  ), //      {X:ymm, R:ymm, R:ymm|m256|mem}</a>
+<a name="3353"><span class="lineNum">    3353 </span>            :   ISIGNATURE(3, 1, 1, 0, 93 , 86 , 84 , 0  , 0  , 0  ), //      {X:zmm, R:zmm, R:zmm|m512|mem}</a>
+<a name="3354"><span class="lineNum">    3354 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 77 , 87 , 0  , 0  , 0  ), // #219 {W:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3355"><span class="lineNum">    3355 </span>            :   ISIGNATURE(3, 1, 1, 0, 79 , 80 , 87 , 0  , 0  , 0  ), //      {W:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3356"><span class="lineNum">    3356 </span>            :   ISIGNATURE(3, 1, 1, 0, 83 , 84 , 87 , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3357"><span class="lineNum">    3357 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 75 , 0  , 0  , 0  , 0  ), // #222 {W:xmm, R:xmm|m64|mem}</a>
+<a name="3358"><span class="lineNum">    3358 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 80 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:ymm|m256|mem}</a>
+<a name="3359"><span class="lineNum">    3359 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 84 , 0  , 0  , 0  , 0  ), //      {W:zmm, R:zmm|m512|mem}</a>
+<a name="3360"><span class="lineNum">    3360 </span>            :   ISIGNATURE(2, 1, 1, 0, 115, 73 , 0  , 0  , 0  , 0  ), // #225 {W:m128|mem, R:xmm}</a>
+<a name="3361"><span class="lineNum">    3361 </span>            :   ISIGNATURE(2, 1, 1, 0, 116, 82 , 0  , 0  , 0  , 0  ), //      {W:m256|mem, R:ymm}</a>
+<a name="3362"><span class="lineNum">    3362 </span>            :   ISIGNATURE(2, 1, 1, 0, 135, 86 , 0  , 0  , 0  , 0  ), //      {W:m512|mem, R:zmm}</a>
+<a name="3363"><span class="lineNum">    3363 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 117, 0  , 0  , 0  , 0  ), // #228 {W:xmm, R:m128|mem}</a>
+<a name="3364"><span class="lineNum">    3364 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 118, 0  , 0  , 0  , 0  ), //      {W:ymm, R:m256|mem}</a>
+<a name="3365"><span class="lineNum">    3365 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 136, 0  , 0  , 0  , 0  ), //      {W:zmm, R:m512|mem}</a>
+<a name="3366"><span class="lineNum">    3366 </span>            :   ISIGNATURE(2, 0, 1, 0, 7  , 73 , 0  , 0  , 0  , 0  ), // #231 {W:r64|m64|mem, R:xmm}</a>
+<a name="3367"><span class="lineNum">    3367 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 137, 0  , 0  , 0  , 0  ), //      {W:xmm, R:xmm|m64|mem|r64}</a>
+<a name="3368"><span class="lineNum">    3368 </span>            :   ISIGNATURE(2, 1, 1, 0, 76 , 73 , 0  , 0  , 0  , 0  ), //      {W:xmm|m64|mem, R:xmm}</a>
+<a name="3369"><span class="lineNum">    3369 </span>            :   ISIGNATURE(2, 1, 1, 0, 68 , 73 , 0  , 0  , 0  , 0  ), // #234 {W:m64|mem, R:xmm}</a>
+<a name="3370"><span class="lineNum">    3370 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 65 , 0  , 0  , 0  , 0  ), //      {W:xmm, R:m64|mem}</a>
+<a name="3371"><span class="lineNum">    3371 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 73 , 0  , 0  , 0  ), // #236 {W:xmm, R:xmm, R:xmm}</a>
+<a name="3372"><span class="lineNum">    3372 </span>            :   ISIGNATURE(2, 1, 1, 0, 67 , 73 , 0  , 0  , 0  , 0  ), // #237 {W:m32|mem, R:xmm}</a>
+<a name="3373"><span class="lineNum">    3373 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 64 , 0  , 0  , 0  , 0  ), //      {W:xmm, R:m32|mem}</a>
+<a name="3374"><span class="lineNum">    3374 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 73 , 0  , 0  , 0  ), //      {W:xmm, R:xmm, R:xmm}</a>
+<a name="3375"><span class="lineNum">    3375 </span>            :   ISIGNATURE(4, 1, 1, 0, 131, 73 , 77 , 87 , 0  , 0  ), // #240 {W:k, R:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3376"><span class="lineNum">    3376 </span>            :   ISIGNATURE(4, 1, 1, 0, 131, 82 , 80 , 87 , 0  , 0  ), //      {W:k, R:ymm, R:ymm|m256|mem, R:u8}</a>
+<a name="3377"><span class="lineNum">    3377 </span>            :   ISIGNATURE(4, 1, 1, 0, 131, 86 , 84 , 87 , 0  , 0  ), //      {W:k, R:zmm, R:zmm|m512|mem, R:u8}</a>
+<a name="3378"><span class="lineNum">    3378 </span>            :   ISIGNATURE(3, 1, 1, 0, 129, 73 , 77 , 0  , 0  , 0  ), // #243 {W:xmm|k, R:xmm, R:xmm|m128|mem}</a>
+<a name="3379"><span class="lineNum">    3379 </span>            :   ISIGNATURE(3, 1, 1, 0, 130, 82 , 80 , 0  , 0  , 0  ), //      {W:ymm|k, R:ymm, R:ymm|m256|mem}</a>
+<a name="3380"><span class="lineNum">    3380 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 86 , 84 , 0  , 0  , 0  ), //      {W:k, R:zmm, R:zmm|m512|mem}</a>
+<a name="3381"><span class="lineNum">    3381 </span>            :   ISIGNATURE(2, 1, 1, 0, 138, 73 , 0  , 0  , 0  , 0  ), // #246 {W:xmm|m32|mem, R:xmm}</a>
+<a name="3382"><span class="lineNum">    3382 </span>            :   ISIGNATURE(2, 1, 1, 0, 76 , 82 , 0  , 0  , 0  , 0  ), //      {W:xmm|m64|mem, R:ymm}</a>
+<a name="3383"><span class="lineNum">    3383 </span>            :   ISIGNATURE(2, 1, 1, 0, 78 , 86 , 0  , 0  , 0  , 0  ), //      {W:xmm|m128|mem, R:zmm}</a>
+<a name="3384"><span class="lineNum">    3384 </span>            :   ISIGNATURE(2, 1, 1, 0, 76 , 73 , 0  , 0  , 0  , 0  ), // #249 {W:xmm|m64|mem, R:xmm}</a>
+<a name="3385"><span class="lineNum">    3385 </span>            :   ISIGNATURE(2, 1, 1, 0, 78 , 82 , 0  , 0  , 0  , 0  ), //      {W:xmm|m128|mem, R:ymm}</a>
+<a name="3386"><span class="lineNum">    3386 </span>            :   ISIGNATURE(2, 1, 1, 0, 81 , 86 , 0  , 0  , 0  , 0  ), //      {W:ymm|m256|mem, R:zmm}</a>
+<a name="3387"><span class="lineNum">    3387 </span>            :   ISIGNATURE(2, 1, 1, 0, 139, 73 , 0  , 0  , 0  , 0  ), // #252 {W:xmm|m16|mem, R:xmm}</a>
+<a name="3388"><span class="lineNum">    3388 </span>            :   ISIGNATURE(2, 1, 1, 0, 138, 82 , 0  , 0  , 0  , 0  ), //      {W:xmm|m32|mem, R:ymm}</a>
+<a name="3389"><span class="lineNum">    3389 </span>            :   ISIGNATURE(2, 1, 1, 0, 76 , 86 , 0  , 0  , 0  , 0  ), //      {W:xmm|m64|mem, R:zmm}</a>
+<a name="3390"><span class="lineNum">    3390 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 140, 0  , 0  , 0  , 0  ), // #255 {W:xmm, R:xmm|m32|mem}</a>
+<a name="3391"><span class="lineNum">    3391 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 75 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:xmm|m64|mem}</a>
+<a name="3392"><span class="lineNum">    3392 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 77 , 0  , 0  , 0  , 0  ), //      {W:zmm, R:xmm|m128|mem}</a>
+<a name="3393"><span class="lineNum">    3393 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 141, 0  , 0  , 0  , 0  ), // #258 {W:xmm, R:xmm|m16|mem}</a>
+<a name="3394"><span class="lineNum">    3394 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 140, 0  , 0  , 0  , 0  ), //      {W:ymm, R:xmm|m32|mem}</a>
+<a name="3395"><span class="lineNum">    3395 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 75 , 0  , 0  , 0  , 0  ), // #260 {W:zmm, R:xmm|m64|mem}</a>
+<a name="3396"><span class="lineNum">    3396 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 75 , 0  , 0  , 0  , 0  ), // #261 {W:xmm, R:xmm|m64|mem}</a>
+<a name="3397"><span class="lineNum">    3397 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 77 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:xmm|m128|mem}</a>
+<a name="3398"><span class="lineNum">    3398 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 142, 0  , 0  , 0  , 0  ), //      {W:zmm, R:xmm|m256|mem}</a>
+<a name="3399"><span class="lineNum">    3399 </span>            :   ISIGNATURE(2, 1, 1, 0, 143, 73 , 0  , 0  , 0  , 0  ), // #264 {W:vm32x, R:xmm}</a>
+<a name="3400"><span class="lineNum">    3400 </span>            :   ISIGNATURE(2, 1, 1, 0, 144, 82 , 0  , 0  , 0  , 0  ), //      {W:vm32y, R:ymm}</a>
+<a name="3401"><span class="lineNum">    3401 </span>            :   ISIGNATURE(2, 1, 1, 0, 145, 86 , 0  , 0  , 0  , 0  ), //      {W:vm32z, R:zmm}</a>
+<a name="3402"><span class="lineNum">    3402 </span>            :   ISIGNATURE(2, 1, 1, 0, 146, 73 , 0  , 0  , 0  , 0  ), // #267 {W:vm64x, R:xmm}</a>
+<a name="3403"><span class="lineNum">    3403 </span>            :   ISIGNATURE(2, 1, 1, 0, 147, 82 , 0  , 0  , 0  , 0  ), //      {W:vm64y, R:ymm}</a>
+<a name="3404"><span class="lineNum">    3404 </span>            :   ISIGNATURE(2, 1, 1, 0, 148, 86 , 0  , 0  , 0  , 0  ), //      {W:vm64z, R:zmm}</a>
+<a name="3405"><span class="lineNum">    3405 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 73 , 77 , 0  , 0  , 0  ), // #270 {W:k, R:xmm, R:xmm|m128|mem}</a>
+<a name="3406"><span class="lineNum">    3406 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 82 , 80 , 0  , 0  , 0  ), //      {W:k, R:ymm, R:ymm|m256|mem}</a>
+<a name="3407"><span class="lineNum">    3407 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 86 , 84 , 0  , 0  , 0  ), //      {W:k, R:zmm, R:zmm|m512|mem}</a>
+<a name="3408"><span class="lineNum">    3408 </span>            :   ISIGNATURE(3, 1, 1, 0, 13 , 6  , 43 , 0  , 0  , 0  ), // #273 {W:r32, R:r32, R:r32|m32|mem}</a>
+<a name="3409"><span class="lineNum">    3409 </span>            :   ISIGNATURE(3, 0, 1, 0, 19 , 27 , 16 , 0  , 0  , 0  ), //      {W:r64, R:r64, R:r64|m64|mem}</a>
+<a name="3410"><span class="lineNum">    3410 </span>            :   ISIGNATURE(3, 1, 1, 0, 13 , 43 , 6  , 0  , 0  , 0  ), // #275 {W:r32, R:r32|m32|mem, R:r32}</a>
+<a name="3411"><span class="lineNum">    3411 </span>            :   ISIGNATURE(3, 0, 1, 0, 19 , 16 , 27 , 0  , 0  , 0  ), //      {W:r64, R:r64|m64|mem, R:r64}</a>
+<a name="3412"><span class="lineNum">    3412 </span>            :   ISIGNATURE(2, 1, 0, 0, 149, 43 , 0  , 0  , 0  , 0  ), // #277 {R:bnd, R:r32|m32|mem}</a>
+<a name="3413"><span class="lineNum">    3413 </span>            :   ISIGNATURE(2, 0, 1, 0, 149, 16 , 0  , 0  , 0  , 0  ), //      {R:bnd, R:r64|m64|mem}</a>
+<a name="3414"><span class="lineNum">    3414 </span>            :   ISIGNATURE(2, 1, 1, 0, 150, 151, 0  , 0  , 0  , 0  ), // #279 {W:bnd, R:bnd|mem}</a>
+<a name="3415"><span class="lineNum">    3415 </span>            :   ISIGNATURE(2, 1, 1, 0, 152, 149, 0  , 0  , 0  , 0  ), //      {W:bnd|mem, R:bnd}</a>
+<a name="3416"><span class="lineNum">    3416 </span>            :   ISIGNATURE(2, 1, 0, 0, 37 , 64 , 0  , 0  , 0  , 0  ), // #281 {R:r16, R:m32|mem}</a>
+<a name="3417"><span class="lineNum">    3417 </span>            :   ISIGNATURE(2, 1, 0, 0, 6  , 65 , 0  , 0  , 0  , 0  ), //      {R:r32, R:m64|mem}</a>
+<a name="3418"><span class="lineNum">    3418 </span>            :   ISIGNATURE(1, 1, 1, 0, 153, 0  , 0  , 0  , 0  , 0  ), // #283 {R:rel32|r64|m64|mem}</a>
+<a name="3419"><span class="lineNum">    3419 </span>            :   ISIGNATURE(1, 1, 0, 0, 43 , 0  , 0  , 0  , 0  , 0  ), //      {R:r32|m32|mem}</a>
+<a name="3420"><span class="lineNum">    3420 </span>            :   ISIGNATURE(2, 1, 1, 0, 42 , 154, 0  , 0  , 0  , 0  ), // #285 {X:r32, R:r8lo|r8hi|m8|r16|m16|r32|m32}</a>
+<a name="3421"><span class="lineNum">    3421 </span>            :   ISIGNATURE(2, 0, 1, 0, 44 , 155, 0  , 0  , 0  , 0  ), //      {X:r64, R:r8lo|r8hi|m8|r64|m64}</a>
+<a name="3422"><span class="lineNum">    3422 </span>            :   ISIGNATURE(1, 1, 0, 0, 156, 0  , 0  , 0  , 0  , 0  ), // #287 {X:r16|r32}</a>
+<a name="3423"><span class="lineNum">    3423 </span>            :   ISIGNATURE(1, 1, 1, 0, 49 , 0  , 0  , 0  , 0  , 0  ), // #288 {X:r8lo|r8hi|m8|r16|m16|r32|m32|r64|m64|mem}</a>
+<a name="3424"><span class="lineNum">    3424 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 87 , 87 , 0  , 0  , 0  ), // #289 {X:xmm, R:u8, R:u8}</a>
+<a name="3425"><span class="lineNum">    3425 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 73 , 0  , 0  , 0  , 0  ), //      {X:xmm, R:xmm}</a>
+<a name="3426"><span class="lineNum">    3426 </span>            :   ISIGNATURE(0, 1, 1, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #291 {}</a>
+<a name="3427"><span class="lineNum">    3427 </span>            :   ISIGNATURE(1, 1, 1, 0, 123, 0  , 0  , 0  , 0  , 0  ), // #292 {X:fp}</a>
+<a name="3428"><span class="lineNum">    3428 </span>            :   ISIGNATURE(0, 1, 1, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #293 {}</a>
+<a name="3429"><span class="lineNum">    3429 </span>            :   ISIGNATURE(1, 1, 1, 0, 157, 0  , 0  , 0  , 0  , 0  ), //      {R:m32|m64|fp}</a>
+<a name="3430"><span class="lineNum">    3430 </span>            :   ISIGNATURE(0, 1, 1, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #295 {}</a>
+<a name="3431"><span class="lineNum">    3431 </span>            :   ISIGNATURE(1, 1, 1, 0, 122, 0  , 0  , 0  , 0  , 0  ), // #296 {R:fp}</a>
+<a name="3432"><span class="lineNum">    3432 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 73 , 0  , 0  , 0  , 0  ), // #297 {X:xmm, R:xmm}</a>
+<a name="3433"><span class="lineNum">    3433 </span>            :   ISIGNATURE(4, 1, 1, 0, 89 , 73 , 87 , 87 , 0  , 0  ), //      {X:xmm, R:xmm, R:u8, R:u8}</a>
+<a name="3434"><span class="lineNum">    3434 </span>            :   ISIGNATURE(2, 1, 0, 0, 6  , 117, 0  , 0  , 0  , 0  ), // #299 {R:r32, R:m128|mem}</a>
+<a name="3435"><span class="lineNum">    3435 </span>            :   ISIGNATURE(2, 0, 1, 0, 27 , 117, 0  , 0  , 0  , 0  ), //      {R:r64, R:m128|mem}</a>
+<a name="3436"><span class="lineNum">    3436 </span>            :   ISIGNATURE(2, 1, 0, 1, 158, 159, 0  , 0  , 0  , 0  ), // #301 {R:&lt;cx|ecx&gt;, R:rel8}</a>
+<a name="3437"><span class="lineNum">    3437 </span>            :   ISIGNATURE(2, 0, 1, 1, 160, 159, 0  , 0  , 0  , 0  ), //      {R:&lt;ecx|rcx&gt;, R:rel8}</a>
+<a name="3438"><span class="lineNum">    3438 </span>            :   ISIGNATURE(1, 1, 1, 0, 161, 0  , 0  , 0  , 0  , 0  ), // #303 {R:rel8|rel32|r64|m64|mem}</a>
+<a name="3439"><span class="lineNum">    3439 </span>            :   ISIGNATURE(1, 1, 0, 0, 43 , 0  , 0  , 0  , 0  , 0  ), //      {R:r32|m32|mem}</a>
+<a name="3440"><span class="lineNum">    3440 </span>            :   ISIGNATURE(2, 1, 1, 0, 131, 162, 0  , 0  , 0  , 0  ), // #305 {W:k, R:k|m8|mem|r32|r64|r8lo|r8hi|r16}</a>
+<a name="3441"><span class="lineNum">    3441 </span>            :   ISIGNATURE(2, 1, 1, 0, 163, 164, 0  , 0  , 0  , 0  ), //      {W:m8|mem|r32|r64|r8lo|r8hi|r16, R:k}</a>
+<a name="3442"><span class="lineNum">    3442 </span>            :   ISIGNATURE(2, 1, 1, 0, 131, 165, 0  , 0  , 0  , 0  ), // #307 {W:k, R:k|m32|mem|r32|r64}</a>
+<a name="3443"><span class="lineNum">    3443 </span>            :   ISIGNATURE(2, 1, 1, 0, 166, 164, 0  , 0  , 0  , 0  ), //      {W:m32|mem|r32|r64, R:k}</a>
+<a name="3444"><span class="lineNum">    3444 </span>            :   ISIGNATURE(2, 1, 1, 0, 131, 167, 0  , 0  , 0  , 0  ), // #309 {W:k, R:k|m64|mem|r64}</a>
+<a name="3445"><span class="lineNum">    3445 </span>            :   ISIGNATURE(2, 1, 1, 0, 7  , 164, 0  , 0  , 0  , 0  ), //      {W:m64|mem|r64, R:k}</a>
+<a name="3446"><span class="lineNum">    3446 </span>            :   ISIGNATURE(2, 1, 1, 0, 131, 168, 0  , 0  , 0  , 0  ), // #311 {W:k, R:k|m16|mem|r32|r64|r16}</a>
+<a name="3447"><span class="lineNum">    3447 </span>            :   ISIGNATURE(2, 1, 1, 0, 169, 164, 0  , 0  , 0  , 0  ), //      {W:m16|mem|r32|r64|r16, R:k}</a>
+<a name="3448"><span class="lineNum">    3448 </span>            :   ISIGNATURE(2, 1, 1, 0, 59 , 12 , 0  , 0  , 0  , 0  ), // #313 {W:r16, R:r16|m16|mem}</a>
+<a name="3449"><span class="lineNum">    3449 </span>            :   ISIGNATURE(2, 1, 1, 0, 13 , 170, 0  , 0  , 0  , 0  ), //      {W:r32, R:r32|m16|mem|r16}</a>
+<a name="3450"><span class="lineNum">    3450 </span>            :   ISIGNATURE(2, 1, 0, 0, 41 , 64 , 0  , 0  , 0  , 0  ), // #315 {X:r16, R:m32|mem}</a>
+<a name="3451"><span class="lineNum">    3451 </span>            :   ISIGNATURE(2, 1, 0, 0, 42 , 126, 0  , 0  , 0  , 0  ), //      {X:r32, R:m48|mem}</a>
+<a name="3452"><span class="lineNum">    3452 </span>            :   ISIGNATURE(2, 1, 0, 1, 171, 159, 0  , 0  , 0  , 0  ), // #317 {X:&lt;cx|ecx&gt;, R:rel8}</a>
+<a name="3453"><span class="lineNum">    3453 </span>            :   ISIGNATURE(2, 0, 1, 1, 172, 159, 0  , 0  , 0  , 0  ), //      {X:&lt;ecx|rcx&gt;, R:rel8}</a>
+<a name="3454"><span class="lineNum">    3454 </span>            :   ISIGNATURE(2, 1, 1, 0, 59 , 12 , 0  , 0  , 0  , 0  ), // #319 {W:r16, R:r16|m16|mem}</a>
+<a name="3455"><span class="lineNum">    3455 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 170, 0  , 0  , 0  , 0  ), //      {W:r32|r64, R:r32|m16|mem|r16}</a>
+<a name="3456"><span class="lineNum">    3456 </span>            :   ISIGNATURE(2, 1, 1, 0, 174, 175, 0  , 0  , 0  , 0  ), // #321 {W:mm|xmm, R:r32|m32|mem|r64}</a>
+<a name="3457"><span class="lineNum">    3457 </span>            :   ISIGNATURE(2, 1, 1, 0, 166, 176, 0  , 0  , 0  , 0  ), //      {W:r32|m32|mem|r64, R:mm|xmm}</a>
+<a name="3458"><span class="lineNum">    3458 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 75 , 0  , 0  , 0  , 0  ), // #323 {W:xmm, R:xmm|m64|mem}</a>
+<a name="3459"><span class="lineNum">    3459 </span>            :   ISIGNATURE(2, 1, 1, 0, 68 , 73 , 0  , 0  , 0  , 0  ), //      {W:m64|mem, R:xmm}</a>
+<a name="3460"><span class="lineNum">    3460 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 140, 0  , 0  , 0  , 0  ), // #325 {W:xmm, R:xmm|m32|mem}</a>
+<a name="3461"><span class="lineNum">    3461 </span>            :   ISIGNATURE(2, 1, 1, 0, 67 , 73 , 0  , 0  , 0  , 0  ), //      {W:m32|mem, R:xmm}</a>
+<a name="3462"><span class="lineNum">    3462 </span>            :   ISIGNATURE(2, 1, 1, 0, 177, 45 , 0  , 0  , 0  , 0  ), // #327 {W:r16|r32|r64, R:r8lo|r8hi|m8}</a>
+<a name="3463"><span class="lineNum">    3463 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 46 , 0  , 0  , 0  , 0  ), //      {W:r32|r64, R:r16|m16}</a>
+<a name="3464"><span class="lineNum">    3464 </span>            :   ISIGNATURE(4, 1, 1, 1, 13 , 13 , 43 , 178, 0  , 0  ), // #329 {W:r32, W:r32, R:r32|m32|mem, R:&lt;edx&gt;}</a>
+<a name="3465"><span class="lineNum">    3465 </span>            :   ISIGNATURE(4, 0, 1, 1, 19 , 19 , 16 , 179, 0  , 0  ), //      {W:r64, W:r64, R:r64|m64|mem, R:&lt;rdx&gt;}</a>
+<a name="3466"><span class="lineNum">    3466 </span>            :   ISIGNATURE(0, 1, 1, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #331 {}</a>
+<a name="3467"><span class="lineNum">    3467 </span>            :   ISIGNATURE(1, 1, 1, 0, 99 , 0  , 0  , 0  , 0  , 0  ), //      {R:r16|m16|r32|m32}</a>
+<a name="3468"><span class="lineNum">    3468 </span>            :   ISIGNATURE(2, 1, 1, 0, 69 , 180, 0  , 0  , 0  , 0  ), // #333 {W:mm, R:mm|m64|mem}</a>
+<a name="3469"><span class="lineNum">    3469 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 77 , 0  , 0  , 0  , 0  ), //      {W:xmm, R:xmm|m128|mem}</a>
+<a name="3470"><span class="lineNum">    3470 </span>            :   ISIGNATURE(2, 1, 1, 0, 181, 180, 0  , 0  , 0  , 0  ), // #335 {X:mm, R:mm|m64|mem}</a>
+<a name="3471"><span class="lineNum">    3471 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 77 , 0  , 0  , 0  , 0  ), // #336 {X:xmm, R:xmm|m128|mem}</a>
+<a name="3472"><span class="lineNum">    3472 </span>            :   ISIGNATURE(3, 1, 1, 0, 181, 180, 87 , 0  , 0  , 0  ), // #337 {X:mm, R:mm|m64|mem, R:u8}</a>
+<a name="3473"><span class="lineNum">    3473 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 77 , 87 , 0  , 0  , 0  ), // #338 {X:xmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3474"><span class="lineNum">    3474 </span>            :   ISIGNATURE(3, 1, 1, 0, 173, 72 , 87 , 0  , 0  , 0  ), // #339 {W:r32|r64, R:mm, R:u8}</a>
+<a name="3475"><span class="lineNum">    3475 </span>            :   ISIGNATURE(3, 1, 1, 0, 169, 73 , 87 , 0  , 0  , 0  ), // #340 {W:r32|r64|m16|mem|r16, R:xmm, R:u8}</a>
+<a name="3476"><span class="lineNum">    3476 </span>            :   ISIGNATURE(2, 1, 1, 0, 181, 182, 0  , 0  , 0  , 0  ), // #341 {X:mm, R:u8|mm|m64|mem}</a>
+<a name="3477"><span class="lineNum">    3477 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 88 , 0  , 0  , 0  , 0  ), //      {X:xmm, R:u8|xmm|m128|mem}</a>
+<a name="3478"><span class="lineNum">    3478 </span>            :   ISIGNATURE(0, 1, 1, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #343 {}</a>
+<a name="3479"><span class="lineNum">    3479 </span>            :   ISIGNATURE(1, 1, 1, 0, 183, 0  , 0  , 0  , 0  , 0  ), //      {R:u16}</a>
+<a name="3480"><span class="lineNum">    3480 </span>            :   ISIGNATURE(3, 1, 1, 0, 13 , 43 , 87 , 0  , 0  , 0  ), // #345 {W:r32, R:r32|m32|mem, R:u8}</a>
+<a name="3481"><span class="lineNum">    3481 </span>            :   ISIGNATURE(3, 0, 1, 0, 19 , 16 , 87 , 0  , 0  , 0  ), //      {W:r64, R:r64|m64|mem, R:u8}</a>
+<a name="3482"><span class="lineNum">    3482 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 77 , 73 , 0  , 0  ), // #347 {W:xmm, R:xmm, R:xmm|m128|mem, R:xmm}</a>
+<a name="3483"><span class="lineNum">    3483 </span>            :   ISIGNATURE(4, 1, 1, 0, 79 , 82 , 80 , 82 , 0  , 0  ), //      {W:ymm, R:ymm, R:ymm|m256|mem, R:ymm}</a>
+<a name="3484"><span class="lineNum">    3484 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 184, 0  , 0  , 0  , 0  ), // #349 {W:xmm, R:xmm|m128|ymm|m256}</a>
+<a name="3485"><span class="lineNum">    3485 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 84 , 0  , 0  , 0  , 0  ), //      {W:ymm, R:zmm|m512|mem}</a>
+<a name="3486"><span class="lineNum">    3486 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 73 , 75 , 0  , 0  ), // #351 {W:xmm, R:xmm, R:xmm, R:xmm|m64|mem}</a>
+<a name="3487"><span class="lineNum">    3487 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 75 , 73 , 0  , 0  ), //      {W:xmm, R:xmm, R:xmm|m64|mem, R:xmm}</a>
+<a name="3488"><span class="lineNum">    3488 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 73 , 140, 0  , 0  ), // #353 {W:xmm, R:xmm, R:xmm, R:xmm|m32|mem}</a>
+<a name="3489"><span class="lineNum">    3489 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 140, 73 , 0  , 0  ), //      {W:xmm, R:xmm, R:xmm|m32|mem, R:xmm}</a>
+<a name="3490"><span class="lineNum">    3490 </span>            :   ISIGNATURE(4, 1, 1, 0, 79 , 82 , 77 , 87 , 0  , 0  ), // #355 {W:ymm, R:ymm, R:xmm|m128|mem, R:u8}</a>
+<a name="3491"><span class="lineNum">    3491 </span>            :   ISIGNATURE(4, 1, 1, 0, 83 , 86 , 77 , 87 , 0  , 0  ), //      {W:zmm, R:zmm, R:xmm|m128|mem, R:u8}</a>
+<a name="3492"><span class="lineNum">    3492 </span>            :   ISIGNATURE(2, 1, 1, 0, 166, 73 , 0  , 0  , 0  , 0  ), // #357 {W:r32|m32|mem|r64, R:xmm}</a>
+<a name="3493"><span class="lineNum">    3493 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 175, 0  , 0  , 0  , 0  ), //      {W:xmm, R:r32|m32|mem|r64}</a>
+<a name="3494"><span class="lineNum">    3494 </span>            :   ISIGNATURE(2, 1, 1, 0, 68 , 73 , 0  , 0  , 0  , 0  ), // #359 {W:m64|mem, R:xmm}</a>
+<a name="3495"><span class="lineNum">    3495 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 65 , 0  , 0  , 0  ), //      {W:xmm, R:xmm, R:m64|mem}</a>
+<a name="3496"><span class="lineNum">    3496 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 186, 0  , 0  , 0  , 0  ), // #361 {W:xmm|ymm|zmm, R:xmm|m8|mem}</a>
+<a name="3497"><span class="lineNum">    3497 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 187, 0  , 0  , 0  , 0  ), //      {W:xmm|ymm|zmm, R:r32|r64}</a>
+<a name="3498"><span class="lineNum">    3498 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 140, 0  , 0  , 0  , 0  ), // #363 {W:xmm|ymm|zmm, R:xmm|m32|mem}</a>
+<a name="3499"><span class="lineNum">    3499 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 187, 0  , 0  , 0  , 0  ), //      {W:xmm|ymm|zmm, R:r32|r64}</a>
+<a name="3500"><span class="lineNum">    3500 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 141, 0  , 0  , 0  , 0  ), // #365 {W:xmm|ymm|zmm, R:xmm|m16|mem}</a>
+<a name="3501"><span class="lineNum">    3501 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 187, 0  , 0  , 0  , 0  ), //      {W:xmm|ymm|zmm, R:r32|r64}</a>
+<a name="3502"><span class="lineNum">    3502 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 188, 87 , 0  , 0  , 0  ), // #367 {W:xmm, R:r32|m8|mem|r8lo|r8hi|r16|r64, R:u8}</a>
+<a name="3503"><span class="lineNum">    3503 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 188, 87 , 0  , 0  ), //      {W:xmm, R:xmm, R:r32|m8|mem|r8lo|r8hi|r16|r64, R:u8}</a>
+<a name="3504"><span class="lineNum">    3504 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 175, 87 , 0  , 0  , 0  ), // #369 {W:xmm, R:r32|m32|mem|r64, R:u8}</a>
+<a name="3505"><span class="lineNum">    3505 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 175, 87 , 0  , 0  ), //      {W:xmm, R:xmm, R:r32|m32|mem|r64, R:u8}</a>
+<a name="3506"><span class="lineNum">    3506 </span>            :   ISIGNATURE(3, 0, 1, 0, 74 , 16 , 87 , 0  , 0  , 0  ), // #371 {W:xmm, R:r64|m64|mem, R:u8}</a>
+<a name="3507"><span class="lineNum">    3507 </span>            :   ISIGNATURE(4, 0, 1, 0, 74 , 73 , 16 , 87 , 0  , 0  ), //      {W:xmm, R:xmm, R:r64|m64|mem, R:u8}</a>
+<a name="3508"><span class="lineNum">    3508 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 77 , 0  , 0  , 0  ), // #373 {W:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3509"><span class="lineNum">    3509 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 77 , 189, 0  , 0  , 0  ), //      {W:xmm, R:xmm|m128|mem, R:u8|xmm}</a>
+<a name="3510"><span class="lineNum">    3510 </span>            :   ISIGNATURE(2, 1, 1, 0, 190, 73 , 0  , 0  , 0  , 0  ), // #375 {W:vm64x|vm64y, R:xmm}</a>
+<a name="3511"><span class="lineNum">    3511 </span>            :   ISIGNATURE(2, 1, 1, 0, 148, 82 , 0  , 0  , 0  , 0  ), //      {W:vm64z, R:ymm}</a>
+<a name="3512"><span class="lineNum">    3512 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 77 , 0  , 0  , 0  ), // #377 {W:xmm, R:xmm, R:xmm|m128|mem}</a>
+<a name="3513"><span class="lineNum">    3513 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 77 , 73 , 0  , 0  , 0  ), //      {W:xmm, R:xmm|m128|mem, R:xmm}</a>
+<a name="3514"><span class="lineNum">    3514 </span>            :   ISIGNATURE(2, 1, 1, 0, 73 , 77 , 0  , 0  , 0  , 0  ), // #379 {R:xmm, R:xmm|m128|mem}</a>
+<a name="3515"><span class="lineNum">    3515 </span>            :   ISIGNATURE(2, 1, 1, 0, 82 , 80 , 0  , 0  , 0  , 0  ), //      {R:ymm, R:ymm|m256|mem}</a>
+<a name="3516"><span class="lineNum">    3516 </span>            :   ISIGNATURE(2, 1, 1, 0, 143, 191, 0  , 0  , 0  , 0  ), // #381 {W:vm32x, R:xmm|ymm}</a>
+<a name="3517"><span class="lineNum">    3517 </span>            :   ISIGNATURE(2, 1, 1, 0, 144, 86 , 0  , 0  , 0  , 0  ), //      {W:vm32y, R:zmm}</a>
+<a name="3518"><span class="lineNum">    3518 </span>            :   ISIGNATURE(1, 1, 0, 1, 50 , 0  , 0  , 0  , 0  , 0  ), // #383 {X:&lt;ax&gt;}</a>
+<a name="3519"><span class="lineNum">    3519 </span>            :   ISIGNATURE(2, 1, 0, 1, 50 , 87 , 0  , 0  , 0  , 0  ), // #384 {X:&lt;ax&gt;, R:u8}</a>
+<a name="3520"><span class="lineNum">    3520 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 75 , 0  , 0  , 0  , 0  ), // #385 {X:xmm, R:xmm|m64|mem}</a>
+<a name="3521"><span class="lineNum">    3521 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 140, 0  , 0  , 0  , 0  ), // #386 {X:xmm, R:xmm|m32|mem}</a>
+<a name="3522"><span class="lineNum">    3522 </span>            :   ISIGNATURE(2, 1, 0, 0, 36 , 37 , 0  , 0  , 0  , 0  ), // #387 {X:r16|m16|mem, R:r16}</a>
+<a name="3523"><span class="lineNum">    3523 </span>            :   ISIGNATURE(3, 1, 1, 1, 89 , 77 , 192, 0  , 0  , 0  ), // #388 {X:xmm, R:xmm|m128|mem, R:&lt;xmm0&gt;}</a>
+<a name="3524"><span class="lineNum">    3524 </span>            :   ISIGNATURE(2, 1, 1, 0, 150, 193, 0  , 0  , 0  , 0  ), // #389 {W:bnd, R:mib}</a>
+<a name="3525"><span class="lineNum">    3525 </span>            :   ISIGNATURE(2, 1, 1, 0, 150, 194, 0  , 0  , 0  , 0  ), // #390 {W:bnd, R:mem}</a>
+<a name="3526"><span class="lineNum">    3526 </span>            :   ISIGNATURE(2, 1, 1, 0, 195, 149, 0  , 0  , 0  , 0  ), // #391 {W:mib, R:bnd}</a>
+<a name="3527"><span class="lineNum">    3527 </span>            :   ISIGNATURE(1, 1, 1, 0, 196, 0  , 0  , 0  , 0  , 0  ), // #392 {X:r32|r64}</a>
+<a name="3528"><span class="lineNum">    3528 </span>            :   ISIGNATURE(1, 1, 1, 1, 50 , 0  , 0  , 0  , 0  , 0  ), // #393 {X:&lt;ax&gt;}</a>
+<a name="3529"><span class="lineNum">    3529 </span>            :   ISIGNATURE(2, 1, 1, 2, 52 , 103, 0  , 0  , 0  , 0  ), // #394 {W:&lt;edx&gt;, R:&lt;eax&gt;}</a>
+<a name="3530"><span class="lineNum">    3530 </span>            :   ISIGNATURE(1, 0, 1, 1, 55 , 0  , 0  , 0  , 0  , 0  ), // #395 {X:&lt;rax&gt;}</a>
+<a name="3531"><span class="lineNum">    3531 </span>            :   ISIGNATURE(1, 1, 1, 0, 194, 0  , 0  , 0  , 0  , 0  ), // #396 {R:mem}</a>
+<a name="3532"><span class="lineNum">    3532 </span>            :   ISIGNATURE(1, 1, 1, 1, 197, 0  , 0  , 0  , 0  , 0  ), // #397 {R:&lt;ds:[zax]&gt;}</a>
+<a name="3533"><span class="lineNum">    3533 </span>            :   ISIGNATURE(2, 1, 1, 2, 198, 199, 0  , 0  , 0  , 0  ), // #398 {X:&lt;ds:[zsi]&gt;, X:&lt;es:[zdi]&gt;}</a>
+<a name="3534"><span class="lineNum">    3534 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 75 , 87 , 0  , 0  , 0  ), // #399 {X:xmm, R:xmm|m64|mem, R:u8}</a>
+<a name="3535"><span class="lineNum">    3535 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 140, 87 , 0  , 0  , 0  ), // #400 {X:xmm, R:xmm|m32|mem, R:u8}</a>
+<a name="3536"><span class="lineNum">    3536 </span>            :   ISIGNATURE(5, 0, 1, 4, 200, 107, 55 , 201, 202, 0  ), // #401 {X:m128|mem, X:&lt;rdx&gt;, X:&lt;rax&gt;, R:&lt;rcx&gt;, R:&lt;rbx&gt;}</a>
+<a name="3537"><span class="lineNum">    3537 </span>            :   ISIGNATURE(5, 1, 1, 4, 203, 106, 53 , 204, 205, 0  ), // #402 {X:m64|mem, X:&lt;edx&gt;, X:&lt;eax&gt;, R:&lt;ecx&gt;, R:&lt;ebx&gt;}</a>
+<a name="3538"><span class="lineNum">    3538 </span>            :   ISIGNATURE(2, 1, 1, 0, 73 , 75 , 0  , 0  , 0  , 0  ), // #403 {R:xmm, R:xmm|m64|mem}</a>
+<a name="3539"><span class="lineNum">    3539 </span>            :   ISIGNATURE(2, 1, 1, 0, 73 , 140, 0  , 0  , 0  , 0  ), // #404 {R:xmm, R:xmm|m32|mem}</a>
+<a name="3540"><span class="lineNum">    3540 </span>            :   ISIGNATURE(4, 1, 1, 4, 53 , 206, 207, 52 , 0  , 0  ), // #405 {X:&lt;eax&gt;, W:&lt;ebx&gt;, X:&lt;ecx&gt;, W:&lt;edx&gt;}</a>
+<a name="3541"><span class="lineNum">    3541 </span>            :   ISIGNATURE(2, 0, 1, 2, 54 , 104, 0  , 0  , 0  , 0  ), // #406 {W:&lt;rdx&gt;, R:&lt;rax&gt;}</a>
+<a name="3542"><span class="lineNum">    3542 </span>            :   ISIGNATURE(2, 1, 1, 0, 69 , 77 , 0  , 0  , 0  , 0  ), // #407 {W:mm, R:xmm|m128|mem}</a>
+<a name="3543"><span class="lineNum">    3543 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 180, 0  , 0  , 0  , 0  ), // #408 {W:xmm, R:mm|m64|mem}</a>
+<a name="3544"><span class="lineNum">    3544 </span>            :   ISIGNATURE(2, 1, 1, 0, 69 , 75 , 0  , 0  , 0  , 0  ), // #409 {W:mm, R:xmm|m64|mem}</a>
+<a name="3545"><span class="lineNum">    3545 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 75 , 0  , 0  , 0  , 0  ), // #410 {W:r32|r64, R:xmm|m64|mem}</a>
+<a name="3546"><span class="lineNum">    3546 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 208, 0  , 0  , 0  , 0  ), // #411 {W:xmm, R:r32|m32|mem|r64|m64}</a>
+<a name="3547"><span class="lineNum">    3547 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 140, 0  , 0  , 0  , 0  ), // #412 {W:r32|r64, R:xmm|m32|mem}</a>
+<a name="3548"><span class="lineNum">    3548 </span>            :   ISIGNATURE(2, 1, 1, 2, 51 , 102, 0  , 0  , 0  , 0  ), // #413 {W:&lt;dx&gt;, R:&lt;ax&gt;}</a>
+<a name="3549"><span class="lineNum">    3549 </span>            :   ISIGNATURE(1, 1, 1, 1, 53 , 0  , 0  , 0  , 0  , 0  ), // #414 {X:&lt;eax&gt;}</a>
+<a name="3550"><span class="lineNum">    3550 </span>            :   ISIGNATURE(2, 1, 1, 0, 183, 87 , 0  , 0  , 0  , 0  ), // #415 {R:u16, R:u8}</a>
+<a name="3551"><span class="lineNum">    3551 </span>            :   ISIGNATURE(3, 1, 1, 0, 166, 73 , 87 , 0  , 0  , 0  ), // #416 {W:r32|m32|mem|r64, R:xmm, R:u8}</a>
+<a name="3552"><span class="lineNum">    3552 </span>            :   ISIGNATURE(1, 1, 1, 0, 127, 0  , 0  , 0  , 0  , 0  ), // #417 {R:m80|mem}</a>
+<a name="3553"><span class="lineNum">    3553 </span>            :   ISIGNATURE(1, 1, 1, 0, 209, 0  , 0  , 0  , 0  , 0  ), // #418 {W:m80|mem}</a>
+<a name="3554"><span class="lineNum">    3554 </span>            :   ISIGNATURE(1, 1, 1, 0, 210, 0  , 0  , 0  , 0  , 0  ), // #419 {R:m16|m32}</a>
+<a name="3555"><span class="lineNum">    3555 </span>            :   ISIGNATURE(1, 1, 1, 0, 211, 0  , 0  , 0  , 0  , 0  ), // #420 {R:m16|m32|m64}</a>
+<a name="3556"><span class="lineNum">    3556 </span>            :   ISIGNATURE(1, 1, 1, 0, 212, 0  , 0  , 0  , 0  , 0  ), // #421 {W:m16|m32}</a>
+<a name="3557"><span class="lineNum">    3557 </span>            :   ISIGNATURE(1, 1, 1, 0, 213, 0  , 0  , 0  , 0  , 0  ), // #422 {W:m16|m32|m64}</a>
+<a name="3558"><span class="lineNum">    3558 </span>            :   ISIGNATURE(1, 1, 1, 0, 214, 0  , 0  , 0  , 0  , 0  ), // #423 {R:m32|m64|m80|fp}</a>
+<a name="3559"><span class="lineNum">    3559 </span>            :   ISIGNATURE(1, 1, 1, 0, 63 , 0  , 0  , 0  , 0  , 0  ), // #424 {R:m16|mem}</a>
+<a name="3560"><span class="lineNum">    3560 </span>            :   ISIGNATURE(1, 1, 1, 0, 215, 0  , 0  , 0  , 0  , 0  ), // #425 {W:mem}</a>
+<a name="3561"><span class="lineNum">    3561 </span>            :   ISIGNATURE(1, 1, 1, 0, 66 , 0  , 0  , 0  , 0  , 0  ), // #426 {W:m16|mem}</a>
+<a name="3562"><span class="lineNum">    3562 </span>            :   ISIGNATURE(1, 1, 1, 0, 216, 0  , 0  , 0  , 0  , 0  ), // #427 {W:ax|m16|mem}</a>
+<a name="3563"><span class="lineNum">    3563 </span>            :   ISIGNATURE(1, 1, 1, 0, 217, 0  , 0  , 0  , 0  , 0  ), // #428 {W:m32|m64|fp}</a>
+<a name="3564"><span class="lineNum">    3564 </span>            :   ISIGNATURE(1, 1, 1, 0, 218, 0  , 0  , 0  , 0  , 0  ), // #429 {W:m32|m64|m80|fp}</a>
+<a name="3565"><span class="lineNum">    3565 </span>            :   ISIGNATURE(1, 0, 1, 0, 194, 0  , 0  , 0  , 0  , 0  ), // #430 {R:mem}</a>
+<a name="3566"><span class="lineNum">    3566 </span>            :   ISIGNATURE(1, 0, 1, 0, 215, 0  , 0  , 0  , 0  , 0  ), // #431 {W:mem}</a>
+<a name="3567"><span class="lineNum">    3567 </span>            :   ISIGNATURE(2, 1, 1, 0, 219, 220, 0  , 0  , 0  , 0  ), // #432 {W:al|ax|eax, R:u8|dx}</a>
+<a name="3568"><span class="lineNum">    3568 </span>            :   ISIGNATURE(2, 1, 1, 0, 221, 222, 0  , 0  , 0  , 0  ), // #433 {W:es:[zdi], R:dx}</a>
+<a name="3569"><span class="lineNum">    3569 </span>            :   ISIGNATURE(1, 1, 1, 0, 87 , 0  , 0  , 0  , 0  , 0  ), // #434 {R:u8}</a>
+<a name="3570"><span class="lineNum">    3570 </span>            :   ISIGNATURE(0, 1, 0, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #435 {}</a>
+<a name="3571"><span class="lineNum">    3571 </span>            :   ISIGNATURE(0, 0, 1, 0, 0  , 0  , 0  , 0  , 0  , 0  ), // #436 {}</a>
+<a name="3572"><span class="lineNum">    3572 </span>            :   ISIGNATURE(1, 1, 1, 0, 223, 0  , 0  , 0  , 0  , 0  ), // #437 {R:rel8|rel32}</a>
+<a name="3573"><span class="lineNum">    3573 </span>            :   ISIGNATURE(1, 1, 1, 0, 159, 0  , 0  , 0  , 0  , 0  ), // #438 {R:rel8}</a>
+<a name="3574"><span class="lineNum">    3574 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 164, 164, 0  , 0  , 0  ), // #439 {W:k, R:k, R:k}</a>
+<a name="3575"><span class="lineNum">    3575 </span>            :   ISIGNATURE(2, 1, 1, 0, 131, 164, 0  , 0  , 0  , 0  ), // #440 {W:k, R:k}</a>
+<a name="3576"><span class="lineNum">    3576 </span>            :   ISIGNATURE(2, 1, 1, 0, 164, 164, 0  , 0  , 0  , 0  ), // #441 {R:k, R:k}</a>
+<a name="3577"><span class="lineNum">    3577 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 164, 87 , 0  , 0  , 0  ), // #442 {W:k, R:k, R:u8}</a>
+<a name="3578"><span class="lineNum">    3578 </span>            :   ISIGNATURE(1, 1, 1, 1, 224, 0  , 0  , 0  , 0  , 0  ), // #443 {W:&lt;ah&gt;}</a>
+<a name="3579"><span class="lineNum">    3579 </span>            :   ISIGNATURE(1, 1, 1, 0, 64 , 0  , 0  , 0  , 0  , 0  ), // #444 {R:m32|mem}</a>
+<a name="3580"><span class="lineNum">    3580 </span>            :   ISIGNATURE(2, 1, 1, 0, 177, 225, 0  , 0  , 0  , 0  ), // #445 {W:r16|r32|r64, R:mem|m8|m16|m32|m48|m64|m80|m128|m256|m512|m1024}</a>
+<a name="3581"><span class="lineNum">    3581 </span>            :   ISIGNATURE(1, 1, 1, 0, 226, 0  , 0  , 0  , 0  , 0  ), // #446 {R:r16|m16|mem|r32|r64}</a>
+<a name="3582"><span class="lineNum">    3582 </span>            :   ISIGNATURE(2, 1, 1, 2, 227, 198, 0  , 0  , 0  , 0  ), // #447 {W:&lt;al|ax|eax|rax&gt;, X:&lt;ds:[zsi]&gt;}</a>
+<a name="3583"><span class="lineNum">    3583 </span>            :   ISIGNATURE(3, 1, 1, 1, 89 , 73 , 228, 0  , 0  , 0  ), // #448 {X:xmm, R:xmm, R:&lt;ds:[zdi]&gt;}</a>
+<a name="3584"><span class="lineNum">    3584 </span>            :   ISIGNATURE(3, 1, 1, 1, 181, 72 , 228, 0  , 0  , 0  ), // #449 {X:mm, R:mm, R:&lt;ds:[zdi]&gt;}</a>
+<a name="3585"><span class="lineNum">    3585 </span>            :   ISIGNATURE(3, 1, 1, 3, 197, 204, 178, 0  , 0  , 0  ), // #450 {R:&lt;ds:[zax]&gt;, R:&lt;ecx&gt;, R:&lt;edx&gt;}</a>
+<a name="3586"><span class="lineNum">    3586 </span>            :   ISIGNATURE(2, 1, 1, 0, 69 , 73 , 0  , 0  , 0  , 0  ), // #451 {W:mm, R:xmm}</a>
+<a name="3587"><span class="lineNum">    3587 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 73 , 0  , 0  , 0  , 0  ), // #452 {W:xmm, R:xmm}</a>
+<a name="3588"><span class="lineNum">    3588 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 73 , 0  , 0  , 0  , 0  ), // #453 {W:r32|r64, R:xmm}</a>
+<a name="3589"><span class="lineNum">    3589 </span>            :   ISIGNATURE(2, 1, 1, 0, 68 , 72 , 0  , 0  , 0  , 0  ), // #454 {W:m64|mem, R:mm}</a>
+<a name="3590"><span class="lineNum">    3590 </span>            :   ISIGNATURE(2, 1, 1, 0, 74 , 72 , 0  , 0  , 0  , 0  ), // #455 {W:xmm, R:mm}</a>
+<a name="3591"><span class="lineNum">    3591 </span>            :   ISIGNATURE(2, 1, 1, 2, 199, 198, 0  , 0  , 0  , 0  ), // #456 {X:&lt;es:[zdi]&gt;, X:&lt;ds:[zsi]&gt;}</a>
+<a name="3592"><span class="lineNum">    3592 </span>            :   ISIGNATURE(2, 0, 1, 0, 19 , 43 , 0  , 0  , 0  , 0  ), // #457 {W:r64, R:r32|m32|mem}</a>
+<a name="3593"><span class="lineNum">    3593 </span>            :   ISIGNATURE(2, 1, 1, 2, 103, 204, 0  , 0  , 0  , 0  ), // #458 {R:&lt;eax&gt;, R:&lt;ecx&gt;}</a>
+<a name="3594"><span class="lineNum">    3594 </span>            :   ISIGNATURE(2, 1, 1, 0, 220, 229, 0  , 0  , 0  , 0  ), // #459 {R:u8|dx, R:al|ax|eax}</a>
+<a name="3595"><span class="lineNum">    3595 </span>            :   ISIGNATURE(2, 1, 1, 0, 222, 230, 0  , 0  , 0  , 0  ), // #460 {R:dx, R:ds:[zsi]}</a>
+<a name="3596"><span class="lineNum">    3596 </span>            :   ISIGNATURE(6, 1, 1, 3, 73 , 77 , 87 , 231, 103, 178), // #461 {R:xmm, R:xmm|m128|mem, R:u8, W:&lt;ecx&gt;, R:&lt;eax&gt;, R:&lt;edx&gt;}</a>
+<a name="3597"><span class="lineNum">    3597 </span>            :   ISIGNATURE(6, 1, 1, 3, 73 , 77 , 87 , 232, 103, 178), // #462 {R:xmm, R:xmm|m128|mem, R:u8, W:&lt;xmm0&gt;, R:&lt;eax&gt;, R:&lt;edx&gt;}</a>
+<a name="3598"><span class="lineNum">    3598 </span>            :   ISIGNATURE(4, 1, 1, 1, 73 , 77 , 87 , 231, 0  , 0  ), // #463 {R:xmm, R:xmm|m128|mem, R:u8, W:&lt;ecx&gt;}</a>
+<a name="3599"><span class="lineNum">    3599 </span>            :   ISIGNATURE(4, 1, 1, 1, 73 , 77 , 87 , 232, 0  , 0  ), // #464 {R:xmm, R:xmm|m128|mem, R:u8, W:&lt;xmm0&gt;}</a>
+<a name="3600"><span class="lineNum">    3600 </span>            :   ISIGNATURE(3, 1, 1, 0, 163, 73 , 87 , 0  , 0  , 0  ), // #465 {W:r32|m8|mem|r8lo|r8hi|r16|r64, R:xmm, R:u8}</a>
+<a name="3601"><span class="lineNum">    3601 </span>            :   ISIGNATURE(3, 0, 1, 0, 7  , 73 , 87 , 0  , 0  , 0  ), // #466 {W:r64|m64|mem, R:xmm, R:u8}</a>
+<a name="3602"><span class="lineNum">    3602 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 188, 87 , 0  , 0  , 0  ), // #467 {X:xmm, R:r32|m8|mem|r8lo|r8hi|r16|r64, R:u8}</a>
+<a name="3603"><span class="lineNum">    3603 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 175, 87 , 0  , 0  , 0  ), // #468 {X:xmm, R:r32|m32|mem|r64, R:u8}</a>
+<a name="3604"><span class="lineNum">    3604 </span>            :   ISIGNATURE(3, 0, 1, 0, 89 , 16 , 87 , 0  , 0  , 0  ), // #469 {X:xmm, R:r64|m64|mem, R:u8}</a>
+<a name="3605"><span class="lineNum">    3605 </span>            :   ISIGNATURE(3, 1, 1, 0, 233, 226, 87 , 0  , 0  , 0  ), // #470 {X:mm|xmm, R:r32|m16|mem|r16|r64, R:u8}</a>
+<a name="3606"><span class="lineNum">    3606 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 176, 0  , 0  , 0  , 0  ), // #471 {W:r32|r64, R:mm|xmm}</a>
+<a name="3607"><span class="lineNum">    3607 </span>            :   ISIGNATURE(3, 1, 1, 0, 69 , 180, 87 , 0  , 0  , 0  ), // #472 {W:mm, R:mm|m64|mem, R:u8}</a>
+<a name="3608"><span class="lineNum">    3608 </span>            :   ISIGNATURE(2, 1, 1, 0, 89 , 87 , 0  , 0  , 0  , 0  ), // #473 {X:xmm, R:u8}</a>
+<a name="3609"><span class="lineNum">    3609 </span>            :   ISIGNATURE(2, 1, 1, 0, 49 , 128, 0  , 0  , 0  , 0  ), // #474 {X:r8lo|r8hi|m8|r16|m16|r32|m32|r64|m64|mem, R:cl|u8}</a>
+<a name="3610"><span class="lineNum">    3610 </span>            :   ISIGNATURE(1, 0, 1, 0, 173, 0  , 0  , 0  , 0  , 0  ), // #475 {W:r32|r64}</a>
+<a name="3611"><span class="lineNum">    3611 </span>            :   ISIGNATURE(3, 1, 1, 3, 52 , 234, 204, 0  , 0  , 0  ), // #476 {W:&lt;edx&gt;, W:&lt;eax&gt;, R:&lt;ecx&gt;}</a>
+<a name="3612"><span class="lineNum">    3612 </span>            :   ISIGNATURE(1, 1, 1, 0, 177, 0  , 0  , 0  , 0  , 0  ), // #477 {W:r16|r32|r64}</a>
+<a name="3613"><span class="lineNum">    3613 </span>            :   ISIGNATURE(2, 1, 1, 2, 52 , 234, 0  , 0  , 0  , 0  ), // #478 {W:&lt;edx&gt;, W:&lt;eax&gt;}</a>
+<a name="3614"><span class="lineNum">    3614 </span>            :   ISIGNATURE(3, 1, 1, 3, 52 , 234, 231, 0  , 0  , 0  ), // #479 {W:&lt;edx&gt;, W:&lt;eax&gt;, W:&lt;ecx&gt;}</a>
+<a name="3615"><span class="lineNum">    3615 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 75 , 87 , 0  , 0  , 0  ), // #480 {W:xmm, R:xmm|m64|mem, R:u8}</a>
+<a name="3616"><span class="lineNum">    3616 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 140, 87 , 0  , 0  , 0  ), // #481 {W:xmm, R:xmm|m32|mem, R:u8}</a>
+<a name="3617"><span class="lineNum">    3617 </span>            :   ISIGNATURE(1, 1, 1, 1, 235, 0  , 0  , 0  , 0  , 0  ), // #482 {R:&lt;ah&gt;}</a>
+<a name="3618"><span class="lineNum">    3618 </span>            :   ISIGNATURE(2, 1, 1, 2, 236, 199, 0  , 0  , 0  , 0  ), // #483 {R:&lt;al|ax|eax|rax&gt;, X:&lt;es:[zdi]&gt;}</a>
+<a name="3619"><span class="lineNum">    3619 </span>            :   ISIGNATURE(1, 1, 1, 0, 1  , 0  , 0  , 0  , 0  , 0  ), // #484 {W:r8lo|r8hi|m8|mem}</a>
+<a name="3620"><span class="lineNum">    3620 </span>            :   ISIGNATURE(1, 1, 1, 0, 169, 0  , 0  , 0  , 0  , 0  ), // #485 {W:r16|m16|mem|r32|r64}</a>
+<a name="3621"><span class="lineNum">    3621 </span>            :   ISIGNATURE(1, 1, 1, 0, 67 , 0  , 0  , 0  , 0  , 0  ), // #486 {W:m32|mem}</a>
+<a name="3622"><span class="lineNum">    3622 </span>            :   ISIGNATURE(2, 1, 1, 2, 199, 236, 0  , 0  , 0  , 0  ), // #487 {X:&lt;es:[zdi]&gt;, R:&lt;al|ax|eax|rax&gt;}</a>
+<a name="3623"><span class="lineNum">    3623 </span>            :   ISIGNATURE(6, 1, 1, 0, 93 , 86 , 86 , 86 , 86 , 117), // #488 {X:zmm, R:zmm, R:zmm, R:zmm, R:zmm, R:m128|mem}</a>
+<a name="3624"><span class="lineNum">    3624 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 75 , 0  , 0  , 0  ), // #489 {W:xmm, R:xmm, R:xmm|m64|mem}</a>
+<a name="3625"><span class="lineNum">    3625 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 140, 0  , 0  , 0  ), // #490 {W:xmm, R:xmm, R:xmm|m32|mem}</a>
+<a name="3626"><span class="lineNum">    3626 </span>            :   ISIGNATURE(2, 1, 1, 0, 79 , 117, 0  , 0  , 0  , 0  ), // #491 {W:ymm, R:m128|mem}</a>
+<a name="3627"><span class="lineNum">    3627 </span>            :   ISIGNATURE(2, 1, 1, 0, 237, 75 , 0  , 0  , 0  , 0  ), // #492 {W:ymm|zmm, R:xmm|m64|mem}</a>
+<a name="3628"><span class="lineNum">    3628 </span>            :   ISIGNATURE(2, 1, 1, 0, 237, 117, 0  , 0  , 0  , 0  ), // #493 {W:ymm|zmm, R:m128|mem}</a>
+<a name="3629"><span class="lineNum">    3629 </span>            :   ISIGNATURE(2, 1, 1, 0, 83 , 118, 0  , 0  , 0  , 0  ), // #494 {W:zmm, R:m256|mem}</a>
+<a name="3630"><span class="lineNum">    3630 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 75 , 0  , 0  , 0  , 0  ), // #495 {W:xmm|ymm|zmm, R:xmm|m64|mem}</a>
+<a name="3631"><span class="lineNum">    3631 </span>            :   ISIGNATURE(4, 1, 1, 0, 129, 73 , 75 , 87 , 0  , 0  ), // #496 {W:xmm|k, R:xmm, R:xmm|m64|mem, R:u8}</a>
+<a name="3632"><span class="lineNum">    3632 </span>            :   ISIGNATURE(4, 1, 1, 0, 129, 73 , 140, 87 , 0  , 0  ), // #497 {W:xmm|k, R:xmm, R:xmm|m32|mem, R:u8}</a>
+<a name="3633"><span class="lineNum">    3633 </span>            :   ISIGNATURE(3, 1, 1, 0, 74 , 73 , 208, 0  , 0  , 0  ), // #498 {W:xmm, R:xmm, R:r32|m32|mem|r64|m64}</a>
+<a name="3634"><span class="lineNum">    3634 </span>            :   ISIGNATURE(3, 1, 1, 0, 78 , 238, 87 , 0  , 0  , 0  ), // #499 {W:xmm|m128|mem, R:ymm|zmm, R:u8}</a>
+<a name="3635"><span class="lineNum">    3635 </span>            :   ISIGNATURE(4, 1, 1, 0, 89 , 73 , 75 , 87 , 0  , 0  ), // #500 {X:xmm, R:xmm, R:xmm|m64|mem, R:u8}</a>
+<a name="3636"><span class="lineNum">    3636 </span>            :   ISIGNATURE(4, 1, 1, 0, 89 , 73 , 140, 87 , 0  , 0  ), // #501 {X:xmm, R:xmm, R:xmm|m32|mem, R:u8}</a>
+<a name="3637"><span class="lineNum">    3637 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 73 , 75 , 0  , 0  , 0  ), // #502 {X:xmm, R:xmm, R:xmm|m64|mem}</a>
+<a name="3638"><span class="lineNum">    3638 </span>            :   ISIGNATURE(3, 1, 1, 0, 89 , 73 , 140, 0  , 0  , 0  ), // #503 {X:xmm, R:xmm, R:xmm|m32|mem}</a>
+<a name="3639"><span class="lineNum">    3639 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 239, 87 , 0  , 0  , 0  ), // #504 {W:k, R:xmm|m128|ymm|m256|zmm|m512, R:u8}</a>
+<a name="3640"><span class="lineNum">    3640 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 75 , 87 , 0  , 0  , 0  ), // #505 {W:k, R:xmm|m64|mem, R:u8}</a>
+<a name="3641"><span class="lineNum">    3641 </span>            :   ISIGNATURE(3, 1, 1, 0, 131, 140, 87 , 0  , 0  , 0  ), // #506 {W:k, R:xmm|m32|mem, R:u8}</a>
+<a name="3642"><span class="lineNum">    3642 </span>            :   ISIGNATURE(1, 1, 1, 0, 92 , 0  , 0  , 0  , 0  , 0  ), // #507 {R:vm32y}</a>
+<a name="3643"><span class="lineNum">    3643 </span>            :   ISIGNATURE(1, 1, 1, 0, 94 , 0  , 0  , 0  , 0  , 0  ), // #508 {R:vm32z}</a>
+<a name="3644"><span class="lineNum">    3644 </span>            :   ISIGNATURE(1, 1, 1, 0, 97 , 0  , 0  , 0  , 0  , 0  ), // #509 {R:vm64z}</a>
+<a name="3645"><span class="lineNum">    3645 </span>            :   ISIGNATURE(4, 1, 1, 0, 83 , 86 , 80 , 87 , 0  , 0  ), // #510 {W:zmm, R:zmm, R:ymm|m256|mem, R:u8}</a>
+<a name="3646"><span class="lineNum">    3646 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 140, 87 , 0  , 0  ), // #511 {W:xmm, R:xmm, R:xmm|m32|mem, R:u8}</a>
+<a name="3647"><span class="lineNum">    3647 </span>            :   ISIGNATURE(3, 1, 1, 1, 73 , 73 , 228, 0  , 0  , 0  ), // #512 {R:xmm, R:xmm, R:&lt;ds:[zdi]&gt;}</a>
+<a name="3648"><span class="lineNum">    3648 </span>            :   ISIGNATURE(2, 1, 1, 0, 173, 191, 0  , 0  , 0  , 0  ), // #513 {W:r32|r64, R:xmm|ymm}</a>
+<a name="3649"><span class="lineNum">    3649 </span>            :   ISIGNATURE(6, 1, 1, 0, 83 , 86 , 86 , 86 , 86 , 117), // #514 {W:zmm, R:zmm, R:zmm, R:zmm, R:zmm, R:m128|mem}</a>
+<a name="3650"><span class="lineNum">    3650 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 164, 0  , 0  , 0  , 0  ), // #515 {W:xmm|ymm|zmm, R:k}</a>
+<a name="3651"><span class="lineNum">    3651 </span>            :   ISIGNATURE(2, 1, 1, 0, 185, 137, 0  , 0  , 0  , 0  ), // #516 {W:xmm|ymm|zmm, R:xmm|m64|mem|r64}</a>
+<a name="3652"><span class="lineNum">    3652 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 226, 87 , 0  , 0  ), // #517 {W:xmm, R:xmm, R:r32|m16|mem|r16|r64, R:u8}</a>
+<a name="3653"><span class="lineNum">    3653 </span>            :   ISIGNATURE(2, 1, 1, 0, 131, 240, 0  , 0  , 0  , 0  ), // #518 {W:k, R:xmm|ymm|zmm}</a>
+<a name="3654"><span class="lineNum">    3654 </span>            :   ISIGNATURE(4, 1, 1, 0, 74 , 73 , 75 , 87 , 0  , 0  ), // #519 {W:xmm, R:xmm, R:xmm|m64|mem, R:u8}</a>
+<a name="3655"><span class="lineNum">    3655 </span>            :   ISIGNATURE(1, 0, 1, 0, 187, 0  , 0  , 0  , 0  , 0  ), // #520 {R:r32|r64}</a>
+<a name="3656"><span class="lineNum">    3656 </span>            :   ISIGNATURE(3, 1, 1, 3, 178, 103, 204, 0  , 0  , 0  ), // #521 {R:&lt;edx&gt;, R:&lt;eax&gt;, R:&lt;ecx&gt;}</a>
+<a name="3657"><span class="lineNum">    3657 </span>            :   ISIGNATURE(1, 1, 1, 0, 241, 0  , 0  , 0  , 0  , 0  ), // #522 {R:rel16|rel32}</a>
+<a name="3658"><span class="lineNum">    3658 </span>            :   ISIGNATURE(3, 1, 1, 2, 194, 178, 103, 0  , 0  , 0  ), // #523 {R:mem, R:&lt;edx&gt;, R:&lt;eax&gt;}</a>
+<a name="3659"><span class="lineNum">    3659 </span>            :   ISIGNATURE(3, 0, 1, 2, 194, 178, 103, 0  , 0  , 0  ), // #524 {R:mem, R:&lt;edx&gt;, R:&lt;eax&gt;}</a>
+<a name="3660"><span class="lineNum">    3660 </span>            :   ISIGNATURE(3, 1, 1, 2, 215, 178, 103, 0  , 0  , 0  ), // #525 {W:mem, R:&lt;edx&gt;, R:&lt;eax&gt;}</a>
+<a name="3661"><span class="lineNum">    3661 </span>            :   ISIGNATURE(3, 0, 1, 2, 215, 178, 103, 0  , 0  , 0  )  // #526 {W:mem, R:&lt;edx&gt;, R:&lt;eax&gt;}</a>
+<a name="3662"><span class="lineNum">    3662 </span>            : };</a>
+<a name="3663"><span class="lineNum">    3663 </span>            : #undef ISIGNATURE</a>
+<a name="3664"><span class="lineNum">    3664 </span>            : // ----------------------------------------------------------------------------</a>
+<a name="3665"><span class="lineNum">    3665 </span>            : // ${signatureData:End}</a>
+<a name="3666"><span class="lineNum">    3666 </span>            : #endif // !ASMJIT_DISABLE_VALIDATION</a>
+<a name="3667"><span class="lineNum">    3667 </span>            : </a>
+<a name="3668"><span class="lineNum">    3668 </span>            : // ============================================================================</a>
+<a name="3669"><span class="lineNum">    3669 </span>            : // [asmjit::X86Inst - MiscData]</a>
+<a name="3670"><span class="lineNum">    3670 </span>            : // ============================================================================</a>
+<a name="3671"><span class="lineNum">    3671 </span>            : </a>
+<a name="3672"><span class="lineNum">    3672 </span>            : #define CC_TO_INST(inst) {               \</a>
+<a name="3673"><span class="lineNum">    3673 </span>            :   inst##o, inst##no, inst##b , inst##ae, \</a>
+<a name="3674"><span class="lineNum">    3674 </span>            :   inst##e, inst##ne, inst##be, inst##a , \</a>
+<a name="3675"><span class="lineNum">    3675 </span>            :   inst##s, inst##ns, inst##pe, inst##po, \</a>
+<a name="3676"><span class="lineNum">    3676 </span>            :   inst##l, inst##ge, inst##le, inst##g   \</a>
+<a name="3677"><span class="lineNum">    3677 </span>            : }</a>
+<a name="3678"><span class="lineNum">    3678 </span>            : </a>
+<a name="3679"><span class="lineNum">    3679 </span>            : const X86Inst::MiscData X86InstDB::miscData = {</a>
+<a name="3680"><span class="lineNum">    3680 </span>            :   CC_TO_INST(X86Inst::kIdJ),</a>
+<a name="3681"><span class="lineNum">    3681 </span>            :   CC_TO_INST(X86Inst::kIdSet),</a>
+<a name="3682"><span class="lineNum">    3682 </span>            :   CC_TO_INST(X86Inst::kIdCmov),</a>
+<a name="3683"><span class="lineNum">    3683 </span>            : </a>
+<a name="3684"><span class="lineNum">    3684 </span>            :   // ReversedCond[]:</a>
+<a name="3685"><span class="lineNum">    3685 </span>            :   {</a>
+<a name="3686"><span class="lineNum">    3686 </span>            :     x86::kCondO, x86::kCondNO, x86::kCondA , x86::kCondBE, // O|NO|B |AE</a>
+<a name="3687"><span class="lineNum">    3687 </span>            :     x86::kCondE, x86::kCondNE, x86::kCondAE, x86::kCondB , // E|NE|BE|A</a>
+<a name="3688"><span class="lineNum">    3688 </span>            :     x86::kCondS, x86::kCondNS, x86::kCondPE, x86::kCondPO, // S|NS|PE|PO</a>
+<a name="3689"><span class="lineNum">    3689 </span>            :     x86::kCondG, x86::kCondLE, x86::kCondGE, x86::kCondL   // L|GE|LE|G</a>
+<a name="3690"><span class="lineNum">    3690 </span>            :   }</a>
+<a name="3691"><span class="lineNum">    3691 </span>            : };</a>
+<a name="3692"><span class="lineNum">    3692 </span>            : </a>
+<a name="3693"><span class="lineNum">    3693 </span>            : #undef CC_TO_INST</a>
+<a name="3694"><span class="lineNum">    3694 </span>            : </a>
+<a name="3695"><span class="lineNum">    3695 </span>            : // ============================================================================</a>
+<a name="3696"><span class="lineNum">    3696 </span>            : // [asmjit::X86Inst - Test]</a>
+<a name="3697"><span class="lineNum">    3697 </span>            : // ============================================================================</a>
+<a name="3698"><span class="lineNum">    3698 </span>            : </a>
+<a name="3699"><span class="lineNum">    3699 </span>            : #if defined(ASMJIT_TEST)</a>
+<a name="3700"><span class="lineNum">    3700 </span>            : UNIT(x86_inst_bits) {</a>
+<a name="3701"><span class="lineNum">    3701 </span>            :   INFO(&quot;Checking validity of X86Inst enums&quot;);</a>
+<a name="3702"><span class="lineNum">    3702 </span>            : </a>
+<a name="3703"><span class="lineNum">    3703 </span>            :   // Cross-validate prefixes.</a>
+<a name="3704"><span class="lineNum">    3704 </span>            :   EXPECT(X86Inst::kOptionRex  == 0x80000000U, &quot;REX prefix must be at 0x80000000&quot;);</a>
+<a name="3705"><span class="lineNum">    3705 </span>            :   EXPECT(X86Inst::kOptionVex3 == 0x00000400U, &quot;VEX3 prefix must be at 0x00000400&quot;);</a>
+<a name="3706"><span class="lineNum">    3706 </span>            :   EXPECT(X86Inst::kOptionEvex == 0x00001000U, &quot;EVEX prefix must be at 0x00001000&quot;);</a>
+<a name="3707"><span class="lineNum">    3707 </span>            : </a>
+<a name="3708"><span class="lineNum">    3708 </span>            :   // These could be combined together to form a valid REX prefix, they must match.</a>
+<a name="3709"><span class="lineNum">    3709 </span>            :   EXPECT(int(X86Inst::kOptionOpCodeB) == int(X86Inst::kOpCode_B));</a>
+<a name="3710"><span class="lineNum">    3710 </span>            :   EXPECT(int(X86Inst::kOptionOpCodeX) == int(X86Inst::kOpCode_X));</a>
+<a name="3711"><span class="lineNum">    3711 </span>            :   EXPECT(int(X86Inst::kOptionOpCodeR) == int(X86Inst::kOpCode_R));</a>
+<a name="3712"><span class="lineNum">    3712 </span>            :   EXPECT(int(X86Inst::kOptionOpCodeW) == int(X86Inst::kOpCode_W));</a>
+<a name="3713"><span class="lineNum">    3713 </span>            : </a>
+<a name="3714"><span class="lineNum">    3714 </span>            :   uint32_t rex_rb = (X86Inst::kOpCode_R &gt;&gt; X86Inst::kOpCode_REX_Shift) |</a>
+<a name="3715"><span class="lineNum">    3715 </span>            :                     (X86Inst::kOpCode_B &gt;&gt; X86Inst::kOpCode_REX_Shift) | 0x40;</a>
+<a name="3716"><span class="lineNum">    3716 </span>            :   uint32_t rex_rw = (X86Inst::kOpCode_R &gt;&gt; X86Inst::kOpCode_REX_Shift) |</a>
+<a name="3717"><span class="lineNum">    3717 </span>            :                     (X86Inst::kOpCode_W &gt;&gt; X86Inst::kOpCode_REX_Shift) | 0x40;</a>
+<a name="3718"><span class="lineNum">    3718 </span>            :   EXPECT(rex_rb == 0x45, &quot;kOpCode_R|B must form a valid REX prefix 0x45 if combined with 0x40&quot;);</a>
+<a name="3719"><span class="lineNum">    3719 </span>            :   EXPECT(rex_rw == 0x4C, &quot;kOpCode_R|W must form a valid REX prefix 0x4C if combined with 0x40&quot;);</a>
+<a name="3720"><span class="lineNum">    3720 </span>            : }</a>
+<a name="3721"><span class="lineNum">    3721 </span>            : #endif // ASMJIT_TEST</a>
+<a name="3722"><span class="lineNum">    3722 </span>            : </a>
+<a name="3723"><span class="lineNum">    3723 </span>            : #if defined(ASMJIT_TEST) &amp;&amp; !defined(ASMJIT_DISABLE_TEXT)</a>
+<a name="3724"><span class="lineNum">    3724 </span>            : UNIT(x86_inst_names) {</a>
+<a name="3725"><span class="lineNum">    3725 </span>            :   // All known instructions should be matched.</a>
+<a name="3726"><span class="lineNum">    3726 </span>            :   INFO(&quot;Matching all X86/X64 instructions&quot;);</a>
+<a name="3727"><span class="lineNum">    3727 </span>            :   for (uint32_t a = 0; a &lt; X86Inst::_kIdCount; a++) {</a>
+<a name="3728"><span class="lineNum">    3728 </span>            :     uint32_t b = X86Inst::getIdByName(X86Inst::getInst(a).getName());</a>
+<a name="3729"><span class="lineNum">    3729 </span>            :     EXPECT(a == b,</a>
+<a name="3730"><span class="lineNum">    3730 </span>            :       &quot;Should match existing instruction \&quot;%s\&quot; {id:%u} != \&quot;%s\&quot; {id:%u}&quot;,</a>
+<a name="3731"><span class="lineNum">    3731 </span>            :         X86Inst::getInst(a).getName(), a,</a>
+<a name="3732"><span class="lineNum">    3732 </span>            :         X86Inst::getInst(b).getName(), b);</a>
+<a name="3733"><span class="lineNum">    3733 </span>            :   }</a>
+<a name="3734"><span class="lineNum">    3734 </span>            : </a>
+<a name="3735"><span class="lineNum">    3735 </span>            :   // Everything else should return `Inst::kIdNone`.</a>
+<a name="3736"><span class="lineNum">    3736 </span>            :   INFO(&quot;Trying to look-up instructions that don't exist&quot;);</a>
+<a name="3737"><span class="lineNum">    3737 </span>            :   EXPECT(X86Inst::getIdByName(nullptr)  == Inst::kIdNone, &quot;Should return Inst::kIdNone for null input&quot;);</a>
+<a name="3738"><span class="lineNum">    3738 </span>            :   EXPECT(X86Inst::getIdByName(&quot;&quot;)       == Inst::kIdNone, &quot;Should return Inst::kIdNone for empty string&quot;);</a>
+<a name="3739"><span class="lineNum">    3739 </span>            :   EXPECT(X86Inst::getIdByName(&quot;_&quot;)      == Inst::kIdNone, &quot;Should return Inst::kIdNone for unknown instruction&quot;);</a>
+<a name="3740"><span class="lineNum">    3740 </span>            :   EXPECT(X86Inst::getIdByName(&quot;123xyz&quot;) == Inst::kIdNone, &quot;Should return Inst::kIdNone for unknown instruction&quot;);</a>
+<a name="3741"><span class="lineNum">    3741 </span>            : }</a>
+<a name="3742"><span class="lineNum">    3742 </span>            : #endif // ASMJIT_TEST &amp;&amp; !ASMJIT_DISABLE_TEXT</a>
+<a name="3743"><span class="lineNum">    3743 </span>            : </a>
+<a name="3744"><span class="lineNum">    3744 </span>            : } // asmjit namespace</a>
+<a name="3745"><span class="lineNum">    3745 </span>            : } // namespace PLMD</a>
+<a name="3746"><span class="lineNum">    3746 </span>            : </a>
+<a name="3747"><span class="lineNum">    3747 </span>            : // [Api-End]</a>
+<a name="3748"><span class="lineNum">    3748 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="3749"><span class="lineNum">    3749 </span>            : </a>
+<a name="3750"><span class="lineNum">    3750 </span>            : // [Guard]</a>
+<a name="3751"><span class="lineNum">    3751 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="3752"><span class="lineNum">    3752 </span>            : #pragma GCC diagnostic pop</a>
+<a name="3753"><span class="lineNum">    3753 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86inst.h.func-sort-c.html b/coverage-libs/asmjit/x86inst.h.func-sort-c.html
new file mode 100644
index 0000000000..2df8065e4e
--- /dev/null
+++ b/coverage-libs/asmjit/x86inst.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86inst.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86inst.h<span style="font-size: 80%;"> (<a href="x86inst.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86inst.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86inst.h.func.html b/coverage-libs/asmjit/x86inst.h.func.html
new file mode 100644
index 0000000000..96e08327fb
--- /dev/null
+++ b/coverage-libs/asmjit/x86inst.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86inst.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86inst.h<span style="font-size: 80%;"> (<a href="x86inst.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86inst.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86inst.h.gcov.html b/coverage-libs/asmjit/x86inst.h.gcov.html
new file mode 100644
index 0000000000..06dadd9e20
--- /dev/null
+++ b/coverage-libs/asmjit/x86inst.h.gcov.html
@@ -0,0 +1,2623 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86inst.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86inst.h<span style="font-size: 80%;"> (source / <a href="x86inst.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86inst_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86inst_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86INST_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86INST_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./assembler.h&quot; // TODO: Is that necessary?</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./inst.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./x86globals.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // [Api-Begin]</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace PLMD {</a>
+<a name="46"><span class="lineNum">      46 </span>            : namespace asmjit {</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="49"><span class="lineNum">      49 </span>            : //! \{</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : // ============================================================================</a>
+<a name="52"><span class="lineNum">      52 </span>            : // [asmjit::X86Inst]</a>
+<a name="53"><span class="lineNum">      53 </span>            : // ============================================================================</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : //! X86/X64 instruction data.</a>
+<a name="56"><span class="lineNum">      56 </span>            : struct X86Inst {</a>
+<a name="57"><span class="lineNum">      57 </span>            :   //! Instruction id (AsmJit specific).</a>
+<a name="58"><span class="lineNum">      58 </span>            :   //!</a>
+<a name="59"><span class="lineNum">      59 </span>            :   //! Each instruction has a unique ID that is used as an index to AsmJit's</a>
+<a name="60"><span class="lineNum">      60 </span>            :   //! instruction table. Instructions are sorted alphabetically.</a>
+<a name="61"><span class="lineNum">      61 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="62"><span class="lineNum">      62 </span>            :     // ${idData:Begin}</a>
+<a name="63"><span class="lineNum">      63 </span>            :     kIdNone = 0,</a>
+<a name="64"><span class="lineNum">      64 </span>            :     kIdAaa,                              // [X86]</a>
+<a name="65"><span class="lineNum">      65 </span>            :     kIdAad,                              // [X86]</a>
+<a name="66"><span class="lineNum">      66 </span>            :     kIdAam,                              // [X86]</a>
+<a name="67"><span class="lineNum">      67 </span>            :     kIdAas,                              // [X86]</a>
+<a name="68"><span class="lineNum">      68 </span>            :     kIdAdc,                              // [ANY]</a>
+<a name="69"><span class="lineNum">      69 </span>            :     kIdAdcx,                             // [ANY] {ADX}</a>
+<a name="70"><span class="lineNum">      70 </span>            :     kIdAdd,                              // [ANY]</a>
+<a name="71"><span class="lineNum">      71 </span>            :     kIdAddpd,                            // [ANY] {SSE2}</a>
+<a name="72"><span class="lineNum">      72 </span>            :     kIdAddps,                            // [ANY] {SSE}</a>
+<a name="73"><span class="lineNum">      73 </span>            :     kIdAddsd,                            // [ANY] {SSE2}</a>
+<a name="74"><span class="lineNum">      74 </span>            :     kIdAddss,                            // [ANY] {SSE}</a>
+<a name="75"><span class="lineNum">      75 </span>            :     kIdAddsubpd,                         // [ANY] {SSE3}</a>
+<a name="76"><span class="lineNum">      76 </span>            :     kIdAddsubps,                         // [ANY] {SSE3}</a>
+<a name="77"><span class="lineNum">      77 </span>            :     kIdAdox,                             // [ANY] {ADX}</a>
+<a name="78"><span class="lineNum">      78 </span>            :     kIdAesdec,                           // [ANY] {AESNI}</a>
+<a name="79"><span class="lineNum">      79 </span>            :     kIdAesdeclast,                       // [ANY] {AESNI}</a>
+<a name="80"><span class="lineNum">      80 </span>            :     kIdAesenc,                           // [ANY] {AESNI}</a>
+<a name="81"><span class="lineNum">      81 </span>            :     kIdAesenclast,                       // [ANY] {AESNI}</a>
+<a name="82"><span class="lineNum">      82 </span>            :     kIdAesimc,                           // [ANY] {AESNI}</a>
+<a name="83"><span class="lineNum">      83 </span>            :     kIdAeskeygenassist,                  // [ANY] {AESNI}</a>
+<a name="84"><span class="lineNum">      84 </span>            :     kIdAnd,                              // [ANY]</a>
+<a name="85"><span class="lineNum">      85 </span>            :     kIdAndn,                             // [ANY] {BMI}</a>
+<a name="86"><span class="lineNum">      86 </span>            :     kIdAndnpd,                           // [ANY] {SSE2}</a>
+<a name="87"><span class="lineNum">      87 </span>            :     kIdAndnps,                           // [ANY] {SSE}</a>
+<a name="88"><span class="lineNum">      88 </span>            :     kIdAndpd,                            // [ANY] {SSE2}</a>
+<a name="89"><span class="lineNum">      89 </span>            :     kIdAndps,                            // [ANY] {SSE}</a>
+<a name="90"><span class="lineNum">      90 </span>            :     kIdArpl,                             // [X86]</a>
+<a name="91"><span class="lineNum">      91 </span>            :     kIdBextr,                            // [ANY] {BMI}</a>
+<a name="92"><span class="lineNum">      92 </span>            :     kIdBlcfill,                          // [ANY] {TBM}</a>
+<a name="93"><span class="lineNum">      93 </span>            :     kIdBlci,                             // [ANY] {TBM}</a>
+<a name="94"><span class="lineNum">      94 </span>            :     kIdBlcic,                            // [ANY] {TBM}</a>
+<a name="95"><span class="lineNum">      95 </span>            :     kIdBlcmsk,                           // [ANY] {TBM}</a>
+<a name="96"><span class="lineNum">      96 </span>            :     kIdBlcs,                             // [ANY] {TBM}</a>
+<a name="97"><span class="lineNum">      97 </span>            :     kIdBlendpd,                          // [ANY] {SSE4_1}</a>
+<a name="98"><span class="lineNum">      98 </span>            :     kIdBlendps,                          // [ANY] {SSE4_1}</a>
+<a name="99"><span class="lineNum">      99 </span>            :     kIdBlendvpd,                         // [ANY] {SSE4_1}</a>
+<a name="100"><span class="lineNum">     100 </span>            :     kIdBlendvps,                         // [ANY] {SSE4_1}</a>
+<a name="101"><span class="lineNum">     101 </span>            :     kIdBlsfill,                          // [ANY] {TBM}</a>
+<a name="102"><span class="lineNum">     102 </span>            :     kIdBlsi,                             // [ANY] {BMI}</a>
+<a name="103"><span class="lineNum">     103 </span>            :     kIdBlsic,                            // [ANY] {TBM}</a>
+<a name="104"><span class="lineNum">     104 </span>            :     kIdBlsmsk,                           // [ANY] {BMI}</a>
+<a name="105"><span class="lineNum">     105 </span>            :     kIdBlsr,                             // [ANY] {BMI}</a>
+<a name="106"><span class="lineNum">     106 </span>            :     kIdBndcl,                            // [ANY] {MPX}</a>
+<a name="107"><span class="lineNum">     107 </span>            :     kIdBndcn,                            // [ANY] {MPX}</a>
+<a name="108"><span class="lineNum">     108 </span>            :     kIdBndcu,                            // [ANY] {MPX}</a>
+<a name="109"><span class="lineNum">     109 </span>            :     kIdBndldx,                           // [ANY] {MPX}</a>
+<a name="110"><span class="lineNum">     110 </span>            :     kIdBndmk,                            // [ANY] {MPX}</a>
+<a name="111"><span class="lineNum">     111 </span>            :     kIdBndmov,                           // [ANY] {MPX}</a>
+<a name="112"><span class="lineNum">     112 </span>            :     kIdBndstx,                           // [ANY] {MPX}</a>
+<a name="113"><span class="lineNum">     113 </span>            :     kIdBound,                            // [X86]</a>
+<a name="114"><span class="lineNum">     114 </span>            :     kIdBsf,                              // [ANY]</a>
+<a name="115"><span class="lineNum">     115 </span>            :     kIdBsr,                              // [ANY]</a>
+<a name="116"><span class="lineNum">     116 </span>            :     kIdBswap,                            // [ANY]</a>
+<a name="117"><span class="lineNum">     117 </span>            :     kIdBt,                               // [ANY]</a>
+<a name="118"><span class="lineNum">     118 </span>            :     kIdBtc,                              // [ANY]</a>
+<a name="119"><span class="lineNum">     119 </span>            :     kIdBtr,                              // [ANY]</a>
+<a name="120"><span class="lineNum">     120 </span>            :     kIdBts,                              // [ANY]</a>
+<a name="121"><span class="lineNum">     121 </span>            :     kIdBzhi,                             // [ANY] {BMI2}</a>
+<a name="122"><span class="lineNum">     122 </span>            :     kIdCall,                             // [ANY]</a>
+<a name="123"><span class="lineNum">     123 </span>            :     kIdCbw,                              // [ANY]</a>
+<a name="124"><span class="lineNum">     124 </span>            :     kIdCdq,                              // [ANY]</a>
+<a name="125"><span class="lineNum">     125 </span>            :     kIdCdqe,                             // [X64]</a>
+<a name="126"><span class="lineNum">     126 </span>            :     kIdClac,                             // [ANY] {SMAP}</a>
+<a name="127"><span class="lineNum">     127 </span>            :     kIdClc,                              // [ANY]</a>
+<a name="128"><span class="lineNum">     128 </span>            :     kIdCld,                              // [ANY]</a>
+<a name="129"><span class="lineNum">     129 </span>            :     kIdClflush,                          // [ANY] {CLFLUSH}</a>
+<a name="130"><span class="lineNum">     130 </span>            :     kIdClflushopt,                       // [ANY] {CLFLUSHOPT}</a>
+<a name="131"><span class="lineNum">     131 </span>            :     kIdCli,                              // [ANY]</a>
+<a name="132"><span class="lineNum">     132 </span>            :     kIdClts,                             // [ANY]</a>
+<a name="133"><span class="lineNum">     133 </span>            :     kIdClwb,                             // [ANY] {CLWB}</a>
+<a name="134"><span class="lineNum">     134 </span>            :     kIdClzero,                           // [ANY] {CLZERO}</a>
+<a name="135"><span class="lineNum">     135 </span>            :     kIdCmc,                              // [ANY]</a>
+<a name="136"><span class="lineNum">     136 </span>            :     kIdCmova,                            // [ANY] {CMOV}</a>
+<a name="137"><span class="lineNum">     137 </span>            :     kIdCmovae,                           // [ANY] {CMOV}</a>
+<a name="138"><span class="lineNum">     138 </span>            :     kIdCmovb,                            // [ANY] {CMOV}</a>
+<a name="139"><span class="lineNum">     139 </span>            :     kIdCmovbe,                           // [ANY] {CMOV}</a>
+<a name="140"><span class="lineNum">     140 </span>            :     kIdCmovc,                            // [ANY] {CMOV}</a>
+<a name="141"><span class="lineNum">     141 </span>            :     kIdCmove,                            // [ANY] {CMOV}</a>
+<a name="142"><span class="lineNum">     142 </span>            :     kIdCmovg,                            // [ANY] {CMOV}</a>
+<a name="143"><span class="lineNum">     143 </span>            :     kIdCmovge,                           // [ANY] {CMOV}</a>
+<a name="144"><span class="lineNum">     144 </span>            :     kIdCmovl,                            // [ANY] {CMOV}</a>
+<a name="145"><span class="lineNum">     145 </span>            :     kIdCmovle,                           // [ANY] {CMOV}</a>
+<a name="146"><span class="lineNum">     146 </span>            :     kIdCmovna,                           // [ANY] {CMOV}</a>
+<a name="147"><span class="lineNum">     147 </span>            :     kIdCmovnae,                          // [ANY] {CMOV}</a>
+<a name="148"><span class="lineNum">     148 </span>            :     kIdCmovnb,                           // [ANY] {CMOV}</a>
+<a name="149"><span class="lineNum">     149 </span>            :     kIdCmovnbe,                          // [ANY] {CMOV}</a>
+<a name="150"><span class="lineNum">     150 </span>            :     kIdCmovnc,                           // [ANY] {CMOV}</a>
+<a name="151"><span class="lineNum">     151 </span>            :     kIdCmovne,                           // [ANY] {CMOV}</a>
+<a name="152"><span class="lineNum">     152 </span>            :     kIdCmovng,                           // [ANY] {CMOV}</a>
+<a name="153"><span class="lineNum">     153 </span>            :     kIdCmovnge,                          // [ANY] {CMOV}</a>
+<a name="154"><span class="lineNum">     154 </span>            :     kIdCmovnl,                           // [ANY] {CMOV}</a>
+<a name="155"><span class="lineNum">     155 </span>            :     kIdCmovnle,                          // [ANY] {CMOV}</a>
+<a name="156"><span class="lineNum">     156 </span>            :     kIdCmovno,                           // [ANY] {CMOV}</a>
+<a name="157"><span class="lineNum">     157 </span>            :     kIdCmovnp,                           // [ANY] {CMOV}</a>
+<a name="158"><span class="lineNum">     158 </span>            :     kIdCmovns,                           // [ANY] {CMOV}</a>
+<a name="159"><span class="lineNum">     159 </span>            :     kIdCmovnz,                           // [ANY] {CMOV}</a>
+<a name="160"><span class="lineNum">     160 </span>            :     kIdCmovo,                            // [ANY] {CMOV}</a>
+<a name="161"><span class="lineNum">     161 </span>            :     kIdCmovp,                            // [ANY] {CMOV}</a>
+<a name="162"><span class="lineNum">     162 </span>            :     kIdCmovpe,                           // [ANY] {CMOV}</a>
+<a name="163"><span class="lineNum">     163 </span>            :     kIdCmovpo,                           // [ANY] {CMOV}</a>
+<a name="164"><span class="lineNum">     164 </span>            :     kIdCmovs,                            // [ANY] {CMOV}</a>
+<a name="165"><span class="lineNum">     165 </span>            :     kIdCmovz,                            // [ANY] {CMOV}</a>
+<a name="166"><span class="lineNum">     166 </span>            :     kIdCmp,                              // [ANY]</a>
+<a name="167"><span class="lineNum">     167 </span>            :     kIdCmppd,                            // [ANY] {SSE2}</a>
+<a name="168"><span class="lineNum">     168 </span>            :     kIdCmpps,                            // [ANY] {SSE}</a>
+<a name="169"><span class="lineNum">     169 </span>            :     kIdCmps,                             // [ANY]</a>
+<a name="170"><span class="lineNum">     170 </span>            :     kIdCmpsd,                            // [ANY] {SSE2}</a>
+<a name="171"><span class="lineNum">     171 </span>            :     kIdCmpss,                            // [ANY] {SSE}</a>
+<a name="172"><span class="lineNum">     172 </span>            :     kIdCmpxchg,                          // [ANY] {I486}</a>
+<a name="173"><span class="lineNum">     173 </span>            :     kIdCmpxchg16b,                       // [X64] {CMPXCHG16B}</a>
+<a name="174"><span class="lineNum">     174 </span>            :     kIdCmpxchg8b,                        // [ANY] {CMPXCHG8B}</a>
+<a name="175"><span class="lineNum">     175 </span>            :     kIdComisd,                           // [ANY] {SSE2}</a>
+<a name="176"><span class="lineNum">     176 </span>            :     kIdComiss,                           // [ANY] {SSE}</a>
+<a name="177"><span class="lineNum">     177 </span>            :     kIdCpuid,                            // [ANY] {I486}</a>
+<a name="178"><span class="lineNum">     178 </span>            :     kIdCqo,                              // [X64]</a>
+<a name="179"><span class="lineNum">     179 </span>            :     kIdCrc32,                            // [ANY] {SSE4_2}</a>
+<a name="180"><span class="lineNum">     180 </span>            :     kIdCvtdq2pd,                         // [ANY] {SSE2}</a>
+<a name="181"><span class="lineNum">     181 </span>            :     kIdCvtdq2ps,                         // [ANY] {SSE2}</a>
+<a name="182"><span class="lineNum">     182 </span>            :     kIdCvtpd2dq,                         // [ANY] {SSE2}</a>
+<a name="183"><span class="lineNum">     183 </span>            :     kIdCvtpd2pi,                         // [ANY] {SSE2}</a>
+<a name="184"><span class="lineNum">     184 </span>            :     kIdCvtpd2ps,                         // [ANY] {SSE2}</a>
+<a name="185"><span class="lineNum">     185 </span>            :     kIdCvtpi2pd,                         // [ANY] {SSE2}</a>
+<a name="186"><span class="lineNum">     186 </span>            :     kIdCvtpi2ps,                         // [ANY] {SSE}</a>
+<a name="187"><span class="lineNum">     187 </span>            :     kIdCvtps2dq,                         // [ANY] {SSE2}</a>
+<a name="188"><span class="lineNum">     188 </span>            :     kIdCvtps2pd,                         // [ANY] {SSE2}</a>
+<a name="189"><span class="lineNum">     189 </span>            :     kIdCvtps2pi,                         // [ANY] {SSE}</a>
+<a name="190"><span class="lineNum">     190 </span>            :     kIdCvtsd2si,                         // [ANY] {SSE2}</a>
+<a name="191"><span class="lineNum">     191 </span>            :     kIdCvtsd2ss,                         // [ANY] {SSE2}</a>
+<a name="192"><span class="lineNum">     192 </span>            :     kIdCvtsi2sd,                         // [ANY] {SSE2}</a>
+<a name="193"><span class="lineNum">     193 </span>            :     kIdCvtsi2ss,                         // [ANY] {SSE}</a>
+<a name="194"><span class="lineNum">     194 </span>            :     kIdCvtss2sd,                         // [ANY] {SSE2}</a>
+<a name="195"><span class="lineNum">     195 </span>            :     kIdCvtss2si,                         // [ANY] {SSE}</a>
+<a name="196"><span class="lineNum">     196 </span>            :     kIdCvttpd2dq,                        // [ANY] {SSE2}</a>
+<a name="197"><span class="lineNum">     197 </span>            :     kIdCvttpd2pi,                        // [ANY] {SSE2}</a>
+<a name="198"><span class="lineNum">     198 </span>            :     kIdCvttps2dq,                        // [ANY] {SSE2}</a>
+<a name="199"><span class="lineNum">     199 </span>            :     kIdCvttps2pi,                        // [ANY] {SSE}</a>
+<a name="200"><span class="lineNum">     200 </span>            :     kIdCvttsd2si,                        // [ANY] {SSE2}</a>
+<a name="201"><span class="lineNum">     201 </span>            :     kIdCvttss2si,                        // [ANY] {SSE}</a>
+<a name="202"><span class="lineNum">     202 </span>            :     kIdCwd,                              // [ANY]</a>
+<a name="203"><span class="lineNum">     203 </span>            :     kIdCwde,                             // [ANY]</a>
+<a name="204"><span class="lineNum">     204 </span>            :     kIdDaa,                              // [X86]</a>
+<a name="205"><span class="lineNum">     205 </span>            :     kIdDas,                              // [X86]</a>
+<a name="206"><span class="lineNum">     206 </span>            :     kIdDec,                              // [ANY]</a>
+<a name="207"><span class="lineNum">     207 </span>            :     kIdDiv,                              // [ANY]</a>
+<a name="208"><span class="lineNum">     208 </span>            :     kIdDivpd,                            // [ANY] {SSE2}</a>
+<a name="209"><span class="lineNum">     209 </span>            :     kIdDivps,                            // [ANY] {SSE}</a>
+<a name="210"><span class="lineNum">     210 </span>            :     kIdDivsd,                            // [ANY] {SSE2}</a>
+<a name="211"><span class="lineNum">     211 </span>            :     kIdDivss,                            // [ANY] {SSE}</a>
+<a name="212"><span class="lineNum">     212 </span>            :     kIdDppd,                             // [ANY] {SSE4_1}</a>
+<a name="213"><span class="lineNum">     213 </span>            :     kIdDpps,                             // [ANY] {SSE4_1}</a>
+<a name="214"><span class="lineNum">     214 </span>            :     kIdEmms,                             // [ANY] {MMX}</a>
+<a name="215"><span class="lineNum">     215 </span>            :     kIdEnter,                            // [ANY]</a>
+<a name="216"><span class="lineNum">     216 </span>            :     kIdExtractps,                        // [ANY] {SSE4_1}</a>
+<a name="217"><span class="lineNum">     217 </span>            :     kIdExtrq,                            // [ANY] {SSE4A}</a>
+<a name="218"><span class="lineNum">     218 </span>            :     kIdF2xm1,                            // [ANY]</a>
+<a name="219"><span class="lineNum">     219 </span>            :     kIdFabs,                             // [ANY]</a>
+<a name="220"><span class="lineNum">     220 </span>            :     kIdFadd,                             // [ANY]</a>
+<a name="221"><span class="lineNum">     221 </span>            :     kIdFaddp,                            // [ANY]</a>
+<a name="222"><span class="lineNum">     222 </span>            :     kIdFbld,                             // [ANY]</a>
+<a name="223"><span class="lineNum">     223 </span>            :     kIdFbstp,                            // [ANY]</a>
+<a name="224"><span class="lineNum">     224 </span>            :     kIdFchs,                             // [ANY]</a>
+<a name="225"><span class="lineNum">     225 </span>            :     kIdFclex,                            // [ANY]</a>
+<a name="226"><span class="lineNum">     226 </span>            :     kIdFcmovb,                           // [ANY] {CMOV}</a>
+<a name="227"><span class="lineNum">     227 </span>            :     kIdFcmovbe,                          // [ANY] {CMOV}</a>
+<a name="228"><span class="lineNum">     228 </span>            :     kIdFcmove,                           // [ANY] {CMOV}</a>
+<a name="229"><span class="lineNum">     229 </span>            :     kIdFcmovnb,                          // [ANY] {CMOV}</a>
+<a name="230"><span class="lineNum">     230 </span>            :     kIdFcmovnbe,                         // [ANY] {CMOV}</a>
+<a name="231"><span class="lineNum">     231 </span>            :     kIdFcmovne,                          // [ANY] {CMOV}</a>
+<a name="232"><span class="lineNum">     232 </span>            :     kIdFcmovnu,                          // [ANY] {CMOV}</a>
+<a name="233"><span class="lineNum">     233 </span>            :     kIdFcmovu,                           // [ANY] {CMOV}</a>
+<a name="234"><span class="lineNum">     234 </span>            :     kIdFcom,                             // [ANY]</a>
+<a name="235"><span class="lineNum">     235 </span>            :     kIdFcomi,                            // [ANY]</a>
+<a name="236"><span class="lineNum">     236 </span>            :     kIdFcomip,                           // [ANY]</a>
+<a name="237"><span class="lineNum">     237 </span>            :     kIdFcomp,                            // [ANY]</a>
+<a name="238"><span class="lineNum">     238 </span>            :     kIdFcompp,                           // [ANY]</a>
+<a name="239"><span class="lineNum">     239 </span>            :     kIdFcos,                             // [ANY]</a>
+<a name="240"><span class="lineNum">     240 </span>            :     kIdFdecstp,                          // [ANY]</a>
+<a name="241"><span class="lineNum">     241 </span>            :     kIdFdiv,                             // [ANY]</a>
+<a name="242"><span class="lineNum">     242 </span>            :     kIdFdivp,                            // [ANY]</a>
+<a name="243"><span class="lineNum">     243 </span>            :     kIdFdivr,                            // [ANY]</a>
+<a name="244"><span class="lineNum">     244 </span>            :     kIdFdivrp,                           // [ANY]</a>
+<a name="245"><span class="lineNum">     245 </span>            :     kIdFemms,                            // [ANY] {3DNOW}</a>
+<a name="246"><span class="lineNum">     246 </span>            :     kIdFfree,                            // [ANY]</a>
+<a name="247"><span class="lineNum">     247 </span>            :     kIdFiadd,                            // [ANY]</a>
+<a name="248"><span class="lineNum">     248 </span>            :     kIdFicom,                            // [ANY]</a>
+<a name="249"><span class="lineNum">     249 </span>            :     kIdFicomp,                           // [ANY]</a>
+<a name="250"><span class="lineNum">     250 </span>            :     kIdFidiv,                            // [ANY]</a>
+<a name="251"><span class="lineNum">     251 </span>            :     kIdFidivr,                           // [ANY]</a>
+<a name="252"><span class="lineNum">     252 </span>            :     kIdFild,                             // [ANY]</a>
+<a name="253"><span class="lineNum">     253 </span>            :     kIdFimul,                            // [ANY]</a>
+<a name="254"><span class="lineNum">     254 </span>            :     kIdFincstp,                          // [ANY]</a>
+<a name="255"><span class="lineNum">     255 </span>            :     kIdFinit,                            // [ANY]</a>
+<a name="256"><span class="lineNum">     256 </span>            :     kIdFist,                             // [ANY]</a>
+<a name="257"><span class="lineNum">     257 </span>            :     kIdFistp,                            // [ANY]</a>
+<a name="258"><span class="lineNum">     258 </span>            :     kIdFisttp,                           // [ANY] {SSE3}</a>
+<a name="259"><span class="lineNum">     259 </span>            :     kIdFisub,                            // [ANY]</a>
+<a name="260"><span class="lineNum">     260 </span>            :     kIdFisubr,                           // [ANY]</a>
+<a name="261"><span class="lineNum">     261 </span>            :     kIdFld,                              // [ANY]</a>
+<a name="262"><span class="lineNum">     262 </span>            :     kIdFld1,                             // [ANY]</a>
+<a name="263"><span class="lineNum">     263 </span>            :     kIdFldcw,                            // [ANY]</a>
+<a name="264"><span class="lineNum">     264 </span>            :     kIdFldenv,                           // [ANY]</a>
+<a name="265"><span class="lineNum">     265 </span>            :     kIdFldl2e,                           // [ANY]</a>
+<a name="266"><span class="lineNum">     266 </span>            :     kIdFldl2t,                           // [ANY]</a>
+<a name="267"><span class="lineNum">     267 </span>            :     kIdFldlg2,                           // [ANY]</a>
+<a name="268"><span class="lineNum">     268 </span>            :     kIdFldln2,                           // [ANY]</a>
+<a name="269"><span class="lineNum">     269 </span>            :     kIdFldpi,                            // [ANY]</a>
+<a name="270"><span class="lineNum">     270 </span>            :     kIdFldz,                             // [ANY]</a>
+<a name="271"><span class="lineNum">     271 </span>            :     kIdFmul,                             // [ANY]</a>
+<a name="272"><span class="lineNum">     272 </span>            :     kIdFmulp,                            // [ANY]</a>
+<a name="273"><span class="lineNum">     273 </span>            :     kIdFnclex,                           // [ANY]</a>
+<a name="274"><span class="lineNum">     274 </span>            :     kIdFninit,                           // [ANY]</a>
+<a name="275"><span class="lineNum">     275 </span>            :     kIdFnop,                             // [ANY]</a>
+<a name="276"><span class="lineNum">     276 </span>            :     kIdFnsave,                           // [ANY]</a>
+<a name="277"><span class="lineNum">     277 </span>            :     kIdFnstcw,                           // [ANY]</a>
+<a name="278"><span class="lineNum">     278 </span>            :     kIdFnstenv,                          // [ANY]</a>
+<a name="279"><span class="lineNum">     279 </span>            :     kIdFnstsw,                           // [ANY]</a>
+<a name="280"><span class="lineNum">     280 </span>            :     kIdFpatan,                           // [ANY]</a>
+<a name="281"><span class="lineNum">     281 </span>            :     kIdFprem,                            // [ANY]</a>
+<a name="282"><span class="lineNum">     282 </span>            :     kIdFprem1,                           // [ANY]</a>
+<a name="283"><span class="lineNum">     283 </span>            :     kIdFptan,                            // [ANY]</a>
+<a name="284"><span class="lineNum">     284 </span>            :     kIdFrndint,                          // [ANY]</a>
+<a name="285"><span class="lineNum">     285 </span>            :     kIdFrstor,                           // [ANY]</a>
+<a name="286"><span class="lineNum">     286 </span>            :     kIdFsave,                            // [ANY]</a>
+<a name="287"><span class="lineNum">     287 </span>            :     kIdFscale,                           // [ANY]</a>
+<a name="288"><span class="lineNum">     288 </span>            :     kIdFsin,                             // [ANY]</a>
+<a name="289"><span class="lineNum">     289 </span>            :     kIdFsincos,                          // [ANY]</a>
+<a name="290"><span class="lineNum">     290 </span>            :     kIdFsqrt,                            // [ANY]</a>
+<a name="291"><span class="lineNum">     291 </span>            :     kIdFst,                              // [ANY]</a>
+<a name="292"><span class="lineNum">     292 </span>            :     kIdFstcw,                            // [ANY]</a>
+<a name="293"><span class="lineNum">     293 </span>            :     kIdFstenv,                           // [ANY]</a>
+<a name="294"><span class="lineNum">     294 </span>            :     kIdFstp,                             // [ANY]</a>
+<a name="295"><span class="lineNum">     295 </span>            :     kIdFstsw,                            // [ANY]</a>
+<a name="296"><span class="lineNum">     296 </span>            :     kIdFsub,                             // [ANY]</a>
+<a name="297"><span class="lineNum">     297 </span>            :     kIdFsubp,                            // [ANY]</a>
+<a name="298"><span class="lineNum">     298 </span>            :     kIdFsubr,                            // [ANY]</a>
+<a name="299"><span class="lineNum">     299 </span>            :     kIdFsubrp,                           // [ANY]</a>
+<a name="300"><span class="lineNum">     300 </span>            :     kIdFtst,                             // [ANY]</a>
+<a name="301"><span class="lineNum">     301 </span>            :     kIdFucom,                            // [ANY]</a>
+<a name="302"><span class="lineNum">     302 </span>            :     kIdFucomi,                           // [ANY]</a>
+<a name="303"><span class="lineNum">     303 </span>            :     kIdFucomip,                          // [ANY]</a>
+<a name="304"><span class="lineNum">     304 </span>            :     kIdFucomp,                           // [ANY]</a>
+<a name="305"><span class="lineNum">     305 </span>            :     kIdFucompp,                          // [ANY]</a>
+<a name="306"><span class="lineNum">     306 </span>            :     kIdFwait,                            // [ANY]</a>
+<a name="307"><span class="lineNum">     307 </span>            :     kIdFxam,                             // [ANY]</a>
+<a name="308"><span class="lineNum">     308 </span>            :     kIdFxch,                             // [ANY]</a>
+<a name="309"><span class="lineNum">     309 </span>            :     kIdFxrstor,                          // [ANY] {FXSR}</a>
+<a name="310"><span class="lineNum">     310 </span>            :     kIdFxrstor64,                        // [X64] {FXSR}</a>
+<a name="311"><span class="lineNum">     311 </span>            :     kIdFxsave,                           // [ANY] {FXSR}</a>
+<a name="312"><span class="lineNum">     312 </span>            :     kIdFxsave64,                         // [X64] {FXSR}</a>
+<a name="313"><span class="lineNum">     313 </span>            :     kIdFxtract,                          // [ANY]</a>
+<a name="314"><span class="lineNum">     314 </span>            :     kIdFyl2x,                            // [ANY]</a>
+<a name="315"><span class="lineNum">     315 </span>            :     kIdFyl2xp1,                          // [ANY]</a>
+<a name="316"><span class="lineNum">     316 </span>            :     kIdHaddpd,                           // [ANY] {SSE3}</a>
+<a name="317"><span class="lineNum">     317 </span>            :     kIdHaddps,                           // [ANY] {SSE3}</a>
+<a name="318"><span class="lineNum">     318 </span>            :     kIdHlt,                              // [ANY]</a>
+<a name="319"><span class="lineNum">     319 </span>            :     kIdHsubpd,                           // [ANY] {SSE3}</a>
+<a name="320"><span class="lineNum">     320 </span>            :     kIdHsubps,                           // [ANY] {SSE3}</a>
+<a name="321"><span class="lineNum">     321 </span>            :     kIdIdiv,                             // [ANY]</a>
+<a name="322"><span class="lineNum">     322 </span>            :     kIdImul,                             // [ANY]</a>
+<a name="323"><span class="lineNum">     323 </span>            :     kIdIn,                               // [ANY]</a>
+<a name="324"><span class="lineNum">     324 </span>            :     kIdInc,                              // [ANY]</a>
+<a name="325"><span class="lineNum">     325 </span>            :     kIdIns,                              // [ANY]</a>
+<a name="326"><span class="lineNum">     326 </span>            :     kIdInsertps,                         // [ANY] {SSE4_1}</a>
+<a name="327"><span class="lineNum">     327 </span>            :     kIdInsertq,                          // [ANY] {SSE4A}</a>
+<a name="328"><span class="lineNum">     328 </span>            :     kIdInt,                              // [ANY]</a>
+<a name="329"><span class="lineNum">     329 </span>            :     kIdInt3,                             // [ANY]</a>
+<a name="330"><span class="lineNum">     330 </span>            :     kIdInto,                             // [X86]</a>
+<a name="331"><span class="lineNum">     331 </span>            :     kIdInvd,                             // [ANY] {I486}</a>
+<a name="332"><span class="lineNum">     332 </span>            :     kIdInvlpg,                           // [ANY] {I486}</a>
+<a name="333"><span class="lineNum">     333 </span>            :     kIdInvpcid,                          // [ANY] {I486}</a>
+<a name="334"><span class="lineNum">     334 </span>            :     kIdIret,                             // [ANY]</a>
+<a name="335"><span class="lineNum">     335 </span>            :     kIdIretd,                            // [ANY]</a>
+<a name="336"><span class="lineNum">     336 </span>            :     kIdIretq,                            // [X64]</a>
+<a name="337"><span class="lineNum">     337 </span>            :     kIdIretw,                            // [ANY]</a>
+<a name="338"><span class="lineNum">     338 </span>            :     kIdJa,                               // [ANY]</a>
+<a name="339"><span class="lineNum">     339 </span>            :     kIdJae,                              // [ANY]</a>
+<a name="340"><span class="lineNum">     340 </span>            :     kIdJb,                               // [ANY]</a>
+<a name="341"><span class="lineNum">     341 </span>            :     kIdJbe,                              // [ANY]</a>
+<a name="342"><span class="lineNum">     342 </span>            :     kIdJc,                               // [ANY]</a>
+<a name="343"><span class="lineNum">     343 </span>            :     kIdJe,                               // [ANY]</a>
+<a name="344"><span class="lineNum">     344 </span>            :     kIdJecxz,                            // [ANY]</a>
+<a name="345"><span class="lineNum">     345 </span>            :     kIdJg,                               // [ANY]</a>
+<a name="346"><span class="lineNum">     346 </span>            :     kIdJge,                              // [ANY]</a>
+<a name="347"><span class="lineNum">     347 </span>            :     kIdJl,                               // [ANY]</a>
+<a name="348"><span class="lineNum">     348 </span>            :     kIdJle,                              // [ANY]</a>
+<a name="349"><span class="lineNum">     349 </span>            :     kIdJmp,                              // [ANY]</a>
+<a name="350"><span class="lineNum">     350 </span>            :     kIdJna,                              // [ANY]</a>
+<a name="351"><span class="lineNum">     351 </span>            :     kIdJnae,                             // [ANY]</a>
+<a name="352"><span class="lineNum">     352 </span>            :     kIdJnb,                              // [ANY]</a>
+<a name="353"><span class="lineNum">     353 </span>            :     kIdJnbe,                             // [ANY]</a>
+<a name="354"><span class="lineNum">     354 </span>            :     kIdJnc,                              // [ANY]</a>
+<a name="355"><span class="lineNum">     355 </span>            :     kIdJne,                              // [ANY]</a>
+<a name="356"><span class="lineNum">     356 </span>            :     kIdJng,                              // [ANY]</a>
+<a name="357"><span class="lineNum">     357 </span>            :     kIdJnge,                             // [ANY]</a>
+<a name="358"><span class="lineNum">     358 </span>            :     kIdJnl,                              // [ANY]</a>
+<a name="359"><span class="lineNum">     359 </span>            :     kIdJnle,                             // [ANY]</a>
+<a name="360"><span class="lineNum">     360 </span>            :     kIdJno,                              // [ANY]</a>
+<a name="361"><span class="lineNum">     361 </span>            :     kIdJnp,                              // [ANY]</a>
+<a name="362"><span class="lineNum">     362 </span>            :     kIdJns,                              // [ANY]</a>
+<a name="363"><span class="lineNum">     363 </span>            :     kIdJnz,                              // [ANY]</a>
+<a name="364"><span class="lineNum">     364 </span>            :     kIdJo,                               // [ANY]</a>
+<a name="365"><span class="lineNum">     365 </span>            :     kIdJp,                               // [ANY]</a>
+<a name="366"><span class="lineNum">     366 </span>            :     kIdJpe,                              // [ANY]</a>
+<a name="367"><span class="lineNum">     367 </span>            :     kIdJpo,                              // [ANY]</a>
+<a name="368"><span class="lineNum">     368 </span>            :     kIdJs,                               // [ANY]</a>
+<a name="369"><span class="lineNum">     369 </span>            :     kIdJz,                               // [ANY]</a>
+<a name="370"><span class="lineNum">     370 </span>            :     kIdKaddb,                            // [ANY] {AVX512_DQ}</a>
+<a name="371"><span class="lineNum">     371 </span>            :     kIdKaddd,                            // [ANY] {AVX512_BW}</a>
+<a name="372"><span class="lineNum">     372 </span>            :     kIdKaddq,                            // [ANY] {AVX512_BW}</a>
+<a name="373"><span class="lineNum">     373 </span>            :     kIdKaddw,                            // [ANY] {AVX512_DQ}</a>
+<a name="374"><span class="lineNum">     374 </span>            :     kIdKandb,                            // [ANY] {AVX512_DQ}</a>
+<a name="375"><span class="lineNum">     375 </span>            :     kIdKandd,                            // [ANY] {AVX512_BW}</a>
+<a name="376"><span class="lineNum">     376 </span>            :     kIdKandnb,                           // [ANY] {AVX512_DQ}</a>
+<a name="377"><span class="lineNum">     377 </span>            :     kIdKandnd,                           // [ANY] {AVX512_BW}</a>
+<a name="378"><span class="lineNum">     378 </span>            :     kIdKandnq,                           // [ANY] {AVX512_BW}</a>
+<a name="379"><span class="lineNum">     379 </span>            :     kIdKandnw,                           // [ANY] {AVX512_F}</a>
+<a name="380"><span class="lineNum">     380 </span>            :     kIdKandq,                            // [ANY] {AVX512_BW}</a>
+<a name="381"><span class="lineNum">     381 </span>            :     kIdKandw,                            // [ANY] {AVX512_F}</a>
+<a name="382"><span class="lineNum">     382 </span>            :     kIdKmovb,                            // [ANY] {AVX512_DQ}</a>
+<a name="383"><span class="lineNum">     383 </span>            :     kIdKmovd,                            // [ANY] {AVX512_BW}</a>
+<a name="384"><span class="lineNum">     384 </span>            :     kIdKmovq,                            // [ANY] {AVX512_BW}</a>
+<a name="385"><span class="lineNum">     385 </span>            :     kIdKmovw,                            // [ANY] {AVX512_F}</a>
+<a name="386"><span class="lineNum">     386 </span>            :     kIdKnotb,                            // [ANY] {AVX512_DQ}</a>
+<a name="387"><span class="lineNum">     387 </span>            :     kIdKnotd,                            // [ANY] {AVX512_BW}</a>
+<a name="388"><span class="lineNum">     388 </span>            :     kIdKnotq,                            // [ANY] {AVX512_BW}</a>
+<a name="389"><span class="lineNum">     389 </span>            :     kIdKnotw,                            // [ANY] {AVX512_F}</a>
+<a name="390"><span class="lineNum">     390 </span>            :     kIdKorb,                             // [ANY] {AVX512_DQ}</a>
+<a name="391"><span class="lineNum">     391 </span>            :     kIdKord,                             // [ANY] {AVX512_BW}</a>
+<a name="392"><span class="lineNum">     392 </span>            :     kIdKorq,                             // [ANY] {AVX512_BW}</a>
+<a name="393"><span class="lineNum">     393 </span>            :     kIdKortestb,                         // [ANY] {AVX512_DQ}</a>
+<a name="394"><span class="lineNum">     394 </span>            :     kIdKortestd,                         // [ANY] {AVX512_BW}</a>
+<a name="395"><span class="lineNum">     395 </span>            :     kIdKortestq,                         // [ANY] {AVX512_BW}</a>
+<a name="396"><span class="lineNum">     396 </span>            :     kIdKortestw,                         // [ANY] {AVX512_F}</a>
+<a name="397"><span class="lineNum">     397 </span>            :     kIdKorw,                             // [ANY] {AVX512_F}</a>
+<a name="398"><span class="lineNum">     398 </span>            :     kIdKshiftlb,                         // [ANY] {AVX512_DQ}</a>
+<a name="399"><span class="lineNum">     399 </span>            :     kIdKshiftld,                         // [ANY] {AVX512_BW}</a>
+<a name="400"><span class="lineNum">     400 </span>            :     kIdKshiftlq,                         // [ANY] {AVX512_BW}</a>
+<a name="401"><span class="lineNum">     401 </span>            :     kIdKshiftlw,                         // [ANY] {AVX512_F}</a>
+<a name="402"><span class="lineNum">     402 </span>            :     kIdKshiftrb,                         // [ANY] {AVX512_DQ}</a>
+<a name="403"><span class="lineNum">     403 </span>            :     kIdKshiftrd,                         // [ANY] {AVX512_BW}</a>
+<a name="404"><span class="lineNum">     404 </span>            :     kIdKshiftrq,                         // [ANY] {AVX512_BW}</a>
+<a name="405"><span class="lineNum">     405 </span>            :     kIdKshiftrw,                         // [ANY] {AVX512_F}</a>
+<a name="406"><span class="lineNum">     406 </span>            :     kIdKtestb,                           // [ANY] {AVX512_DQ}</a>
+<a name="407"><span class="lineNum">     407 </span>            :     kIdKtestd,                           // [ANY] {AVX512_BW}</a>
+<a name="408"><span class="lineNum">     408 </span>            :     kIdKtestq,                           // [ANY] {AVX512_BW}</a>
+<a name="409"><span class="lineNum">     409 </span>            :     kIdKtestw,                           // [ANY] {AVX512_DQ}</a>
+<a name="410"><span class="lineNum">     410 </span>            :     kIdKunpckbw,                         // [ANY] {AVX512_F}</a>
+<a name="411"><span class="lineNum">     411 </span>            :     kIdKunpckdq,                         // [ANY] {AVX512_BW}</a>
+<a name="412"><span class="lineNum">     412 </span>            :     kIdKunpckwd,                         // [ANY] {AVX512_BW}</a>
+<a name="413"><span class="lineNum">     413 </span>            :     kIdKxnorb,                           // [ANY] {AVX512_DQ}</a>
+<a name="414"><span class="lineNum">     414 </span>            :     kIdKxnord,                           // [ANY] {AVX512_BW}</a>
+<a name="415"><span class="lineNum">     415 </span>            :     kIdKxnorq,                           // [ANY] {AVX512_BW}</a>
+<a name="416"><span class="lineNum">     416 </span>            :     kIdKxnorw,                           // [ANY] {AVX512_F}</a>
+<a name="417"><span class="lineNum">     417 </span>            :     kIdKxorb,                            // [ANY] {AVX512_DQ}</a>
+<a name="418"><span class="lineNum">     418 </span>            :     kIdKxord,                            // [ANY] {AVX512_BW}</a>
+<a name="419"><span class="lineNum">     419 </span>            :     kIdKxorq,                            // [ANY] {AVX512_BW}</a>
+<a name="420"><span class="lineNum">     420 </span>            :     kIdKxorw,                            // [ANY] {AVX512_F}</a>
+<a name="421"><span class="lineNum">     421 </span>            :     kIdLahf,                             // [ANY] {LAHFSAHF}</a>
+<a name="422"><span class="lineNum">     422 </span>            :     kIdLar,                              // [ANY]</a>
+<a name="423"><span class="lineNum">     423 </span>            :     kIdLddqu,                            // [ANY] {SSE3}</a>
+<a name="424"><span class="lineNum">     424 </span>            :     kIdLdmxcsr,                          // [ANY] {SSE}</a>
+<a name="425"><span class="lineNum">     425 </span>            :     kIdLds,                              // [X86]</a>
+<a name="426"><span class="lineNum">     426 </span>            :     kIdLea,                              // [ANY]</a>
+<a name="427"><span class="lineNum">     427 </span>            :     kIdLeave,                            // [ANY]</a>
+<a name="428"><span class="lineNum">     428 </span>            :     kIdLes,                              // [X86]</a>
+<a name="429"><span class="lineNum">     429 </span>            :     kIdLfence,                           // [ANY] {SSE2}</a>
+<a name="430"><span class="lineNum">     430 </span>            :     kIdLfs,                              // [ANY]</a>
+<a name="431"><span class="lineNum">     431 </span>            :     kIdLgdt,                             // [ANY]</a>
+<a name="432"><span class="lineNum">     432 </span>            :     kIdLgs,                              // [ANY]</a>
+<a name="433"><span class="lineNum">     433 </span>            :     kIdLidt,                             // [ANY]</a>
+<a name="434"><span class="lineNum">     434 </span>            :     kIdLldt,                             // [ANY]</a>
+<a name="435"><span class="lineNum">     435 </span>            :     kIdLmsw,                             // [ANY]</a>
+<a name="436"><span class="lineNum">     436 </span>            :     kIdLods,                             // [ANY]</a>
+<a name="437"><span class="lineNum">     437 </span>            :     kIdLoop,                             // [ANY]</a>
+<a name="438"><span class="lineNum">     438 </span>            :     kIdLoope,                            // [ANY]</a>
+<a name="439"><span class="lineNum">     439 </span>            :     kIdLoopne,                           // [ANY]</a>
+<a name="440"><span class="lineNum">     440 </span>            :     kIdLsl,                              // [ANY]</a>
+<a name="441"><span class="lineNum">     441 </span>            :     kIdLss,                              // [ANY]</a>
+<a name="442"><span class="lineNum">     442 </span>            :     kIdLtr,                              // [ANY]</a>
+<a name="443"><span class="lineNum">     443 </span>            :     kIdLzcnt,                            // [ANY] {LZCNT}</a>
+<a name="444"><span class="lineNum">     444 </span>            :     kIdMaskmovdqu,                       // [ANY] {SSE2}</a>
+<a name="445"><span class="lineNum">     445 </span>            :     kIdMaskmovq,                         // [ANY] {MMX2}</a>
+<a name="446"><span class="lineNum">     446 </span>            :     kIdMaxpd,                            // [ANY] {SSE2}</a>
+<a name="447"><span class="lineNum">     447 </span>            :     kIdMaxps,                            // [ANY] {SSE}</a>
+<a name="448"><span class="lineNum">     448 </span>            :     kIdMaxsd,                            // [ANY] {SSE2}</a>
+<a name="449"><span class="lineNum">     449 </span>            :     kIdMaxss,                            // [ANY] {SSE}</a>
+<a name="450"><span class="lineNum">     450 </span>            :     kIdMfence,                           // [ANY] {SSE2}</a>
+<a name="451"><span class="lineNum">     451 </span>            :     kIdMinpd,                            // [ANY] {SSE2}</a>
+<a name="452"><span class="lineNum">     452 </span>            :     kIdMinps,                            // [ANY] {SSE}</a>
+<a name="453"><span class="lineNum">     453 </span>            :     kIdMinsd,                            // [ANY] {SSE2}</a>
+<a name="454"><span class="lineNum">     454 </span>            :     kIdMinss,                            // [ANY] {SSE}</a>
+<a name="455"><span class="lineNum">     455 </span>            :     kIdMonitor,                          // [ANY] {MONITOR}</a>
+<a name="456"><span class="lineNum">     456 </span>            :     kIdMov,                              // [ANY]</a>
+<a name="457"><span class="lineNum">     457 </span>            :     kIdMovapd,                           // [ANY] {SSE2}</a>
+<a name="458"><span class="lineNum">     458 </span>            :     kIdMovaps,                           // [ANY] {SSE}</a>
+<a name="459"><span class="lineNum">     459 </span>            :     kIdMovbe,                            // [ANY] {MOVBE}</a>
+<a name="460"><span class="lineNum">     460 </span>            :     kIdMovd,                             // [ANY] {MMX|SSE2}</a>
+<a name="461"><span class="lineNum">     461 </span>            :     kIdMovddup,                          // [ANY] {SSE3}</a>
+<a name="462"><span class="lineNum">     462 </span>            :     kIdMovdq2q,                          // [ANY] {SSE2}</a>
+<a name="463"><span class="lineNum">     463 </span>            :     kIdMovdqa,                           // [ANY] {SSE2}</a>
+<a name="464"><span class="lineNum">     464 </span>            :     kIdMovdqu,                           // [ANY] {SSE2}</a>
+<a name="465"><span class="lineNum">     465 </span>            :     kIdMovhlps,                          // [ANY] {SSE}</a>
+<a name="466"><span class="lineNum">     466 </span>            :     kIdMovhpd,                           // [ANY] {SSE2}</a>
+<a name="467"><span class="lineNum">     467 </span>            :     kIdMovhps,                           // [ANY] {SSE}</a>
+<a name="468"><span class="lineNum">     468 </span>            :     kIdMovlhps,                          // [ANY] {SSE}</a>
+<a name="469"><span class="lineNum">     469 </span>            :     kIdMovlpd,                           // [ANY] {SSE2}</a>
+<a name="470"><span class="lineNum">     470 </span>            :     kIdMovlps,                           // [ANY] {SSE}</a>
+<a name="471"><span class="lineNum">     471 </span>            :     kIdMovmskpd,                         // [ANY] {SSE2}</a>
+<a name="472"><span class="lineNum">     472 </span>            :     kIdMovmskps,                         // [ANY] {SSE}</a>
+<a name="473"><span class="lineNum">     473 </span>            :     kIdMovntdq,                          // [ANY] {SSE2}</a>
+<a name="474"><span class="lineNum">     474 </span>            :     kIdMovntdqa,                         // [ANY] {SSE4_1}</a>
+<a name="475"><span class="lineNum">     475 </span>            :     kIdMovnti,                           // [ANY] {SSE2}</a>
+<a name="476"><span class="lineNum">     476 </span>            :     kIdMovntpd,                          // [ANY] {SSE2}</a>
+<a name="477"><span class="lineNum">     477 </span>            :     kIdMovntps,                          // [ANY] {SSE}</a>
+<a name="478"><span class="lineNum">     478 </span>            :     kIdMovntq,                           // [ANY] {MMX2}</a>
+<a name="479"><span class="lineNum">     479 </span>            :     kIdMovntsd,                          // [ANY] {SSE4A}</a>
+<a name="480"><span class="lineNum">     480 </span>            :     kIdMovntss,                          // [ANY] {SSE4A}</a>
+<a name="481"><span class="lineNum">     481 </span>            :     kIdMovq,                             // [ANY] {MMX|SSE2}</a>
+<a name="482"><span class="lineNum">     482 </span>            :     kIdMovq2dq,                          // [ANY] {SSE2}</a>
+<a name="483"><span class="lineNum">     483 </span>            :     kIdMovs,                             // [ANY]</a>
+<a name="484"><span class="lineNum">     484 </span>            :     kIdMovsd,                            // [ANY] {SSE2}</a>
+<a name="485"><span class="lineNum">     485 </span>            :     kIdMovshdup,                         // [ANY] {SSE3}</a>
+<a name="486"><span class="lineNum">     486 </span>            :     kIdMovsldup,                         // [ANY] {SSE3}</a>
+<a name="487"><span class="lineNum">     487 </span>            :     kIdMovss,                            // [ANY] {SSE}</a>
+<a name="488"><span class="lineNum">     488 </span>            :     kIdMovsx,                            // [ANY]</a>
+<a name="489"><span class="lineNum">     489 </span>            :     kIdMovsxd,                           // [X64]</a>
+<a name="490"><span class="lineNum">     490 </span>            :     kIdMovupd,                           // [ANY] {SSE2}</a>
+<a name="491"><span class="lineNum">     491 </span>            :     kIdMovups,                           // [ANY] {SSE}</a>
+<a name="492"><span class="lineNum">     492 </span>            :     kIdMovzx,                            // [ANY]</a>
+<a name="493"><span class="lineNum">     493 </span>            :     kIdMpsadbw,                          // [ANY] {SSE4_1}</a>
+<a name="494"><span class="lineNum">     494 </span>            :     kIdMul,                              // [ANY]</a>
+<a name="495"><span class="lineNum">     495 </span>            :     kIdMulpd,                            // [ANY] {SSE2}</a>
+<a name="496"><span class="lineNum">     496 </span>            :     kIdMulps,                            // [ANY] {SSE}</a>
+<a name="497"><span class="lineNum">     497 </span>            :     kIdMulsd,                            // [ANY] {SSE2}</a>
+<a name="498"><span class="lineNum">     498 </span>            :     kIdMulss,                            // [ANY] {SSE}</a>
+<a name="499"><span class="lineNum">     499 </span>            :     kIdMulx,                             // [ANY] {BMI2}</a>
+<a name="500"><span class="lineNum">     500 </span>            :     kIdMwait,                            // [ANY] {MONITOR}</a>
+<a name="501"><span class="lineNum">     501 </span>            :     kIdNeg,                              // [ANY]</a>
+<a name="502"><span class="lineNum">     502 </span>            :     kIdNop,                              // [ANY]</a>
+<a name="503"><span class="lineNum">     503 </span>            :     kIdNot,                              // [ANY]</a>
+<a name="504"><span class="lineNum">     504 </span>            :     kIdOr,                               // [ANY]</a>
+<a name="505"><span class="lineNum">     505 </span>            :     kIdOrpd,                             // [ANY] {SSE2}</a>
+<a name="506"><span class="lineNum">     506 </span>            :     kIdOrps,                             // [ANY] {SSE}</a>
+<a name="507"><span class="lineNum">     507 </span>            :     kIdOut,                              // [ANY]</a>
+<a name="508"><span class="lineNum">     508 </span>            :     kIdOuts,                             // [ANY]</a>
+<a name="509"><span class="lineNum">     509 </span>            :     kIdPabsb,                            // [ANY] {SSSE3}</a>
+<a name="510"><span class="lineNum">     510 </span>            :     kIdPabsd,                            // [ANY] {SSSE3}</a>
+<a name="511"><span class="lineNum">     511 </span>            :     kIdPabsw,                            // [ANY] {SSSE3}</a>
+<a name="512"><span class="lineNum">     512 </span>            :     kIdPackssdw,                         // [ANY] {MMX|SSE2}</a>
+<a name="513"><span class="lineNum">     513 </span>            :     kIdPacksswb,                         // [ANY] {MMX|SSE2}</a>
+<a name="514"><span class="lineNum">     514 </span>            :     kIdPackusdw,                         // [ANY] {SSE4_1}</a>
+<a name="515"><span class="lineNum">     515 </span>            :     kIdPackuswb,                         // [ANY] {MMX|SSE2}</a>
+<a name="516"><span class="lineNum">     516 </span>            :     kIdPaddb,                            // [ANY] {MMX|SSE2}</a>
+<a name="517"><span class="lineNum">     517 </span>            :     kIdPaddd,                            // [ANY] {MMX|SSE2}</a>
+<a name="518"><span class="lineNum">     518 </span>            :     kIdPaddq,                            // [ANY] {SSE2}</a>
+<a name="519"><span class="lineNum">     519 </span>            :     kIdPaddsb,                           // [ANY] {MMX|SSE2}</a>
+<a name="520"><span class="lineNum">     520 </span>            :     kIdPaddsw,                           // [ANY] {MMX|SSE2}</a>
+<a name="521"><span class="lineNum">     521 </span>            :     kIdPaddusb,                          // [ANY] {MMX|SSE2}</a>
+<a name="522"><span class="lineNum">     522 </span>            :     kIdPaddusw,                          // [ANY] {MMX|SSE2}</a>
+<a name="523"><span class="lineNum">     523 </span>            :     kIdPaddw,                            // [ANY] {MMX|SSE2}</a>
+<a name="524"><span class="lineNum">     524 </span>            :     kIdPalignr,                          // [ANY] {SSE3}</a>
+<a name="525"><span class="lineNum">     525 </span>            :     kIdPand,                             // [ANY] {MMX|SSE2}</a>
+<a name="526"><span class="lineNum">     526 </span>            :     kIdPandn,                            // [ANY] {MMX|SSE2}</a>
+<a name="527"><span class="lineNum">     527 </span>            :     kIdPause,                            // [ANY]</a>
+<a name="528"><span class="lineNum">     528 </span>            :     kIdPavgb,                            // [ANY] {MMX2|SSE2}</a>
+<a name="529"><span class="lineNum">     529 </span>            :     kIdPavgusb,                          // [ANY] {3DNOW}</a>
+<a name="530"><span class="lineNum">     530 </span>            :     kIdPavgw,                            // [ANY] {MMX2|SSE2}</a>
+<a name="531"><span class="lineNum">     531 </span>            :     kIdPblendvb,                         // [ANY] {SSE4_1}</a>
+<a name="532"><span class="lineNum">     532 </span>            :     kIdPblendw,                          // [ANY] {SSE4_1}</a>
+<a name="533"><span class="lineNum">     533 </span>            :     kIdPclmulqdq,                        // [ANY] {PCLMULQDQ}</a>
+<a name="534"><span class="lineNum">     534 </span>            :     kIdPcmpeqb,                          // [ANY] {MMX|SSE2}</a>
+<a name="535"><span class="lineNum">     535 </span>            :     kIdPcmpeqd,                          // [ANY] {MMX|SSE2}</a>
+<a name="536"><span class="lineNum">     536 </span>            :     kIdPcmpeqq,                          // [ANY] {SSE4_1}</a>
+<a name="537"><span class="lineNum">     537 </span>            :     kIdPcmpeqw,                          // [ANY] {MMX|SSE2}</a>
+<a name="538"><span class="lineNum">     538 </span>            :     kIdPcmpestri,                        // [ANY] {SSE4_2}</a>
+<a name="539"><span class="lineNum">     539 </span>            :     kIdPcmpestrm,                        // [ANY] {SSE4_2}</a>
+<a name="540"><span class="lineNum">     540 </span>            :     kIdPcmpgtb,                          // [ANY] {MMX|SSE2}</a>
+<a name="541"><span class="lineNum">     541 </span>            :     kIdPcmpgtd,                          // [ANY] {MMX|SSE2}</a>
+<a name="542"><span class="lineNum">     542 </span>            :     kIdPcmpgtq,                          // [ANY] {SSE4_2}</a>
+<a name="543"><span class="lineNum">     543 </span>            :     kIdPcmpgtw,                          // [ANY] {MMX|SSE2}</a>
+<a name="544"><span class="lineNum">     544 </span>            :     kIdPcmpistri,                        // [ANY] {SSE4_2}</a>
+<a name="545"><span class="lineNum">     545 </span>            :     kIdPcmpistrm,                        // [ANY] {SSE4_2}</a>
+<a name="546"><span class="lineNum">     546 </span>            :     kIdPcommit,                          // [ANY] {PCOMMIT}</a>
+<a name="547"><span class="lineNum">     547 </span>            :     kIdPdep,                             // [ANY] {BMI2}</a>
+<a name="548"><span class="lineNum">     548 </span>            :     kIdPext,                             // [ANY] {BMI2}</a>
+<a name="549"><span class="lineNum">     549 </span>            :     kIdPextrb,                           // [ANY] {SSE4_1}</a>
+<a name="550"><span class="lineNum">     550 </span>            :     kIdPextrd,                           // [ANY] {SSE4_1}</a>
+<a name="551"><span class="lineNum">     551 </span>            :     kIdPextrq,                           // [X64] {SSE4_1}</a>
+<a name="552"><span class="lineNum">     552 </span>            :     kIdPextrw,                           // [ANY] {MMX2|SSE2|SSE4_1}</a>
+<a name="553"><span class="lineNum">     553 </span>            :     kIdPf2id,                            // [ANY] {3DNOW}</a>
+<a name="554"><span class="lineNum">     554 </span>            :     kIdPf2iw,                            // [ANY] {3DNOW2}</a>
+<a name="555"><span class="lineNum">     555 </span>            :     kIdPfacc,                            // [ANY] {3DNOW}</a>
+<a name="556"><span class="lineNum">     556 </span>            :     kIdPfadd,                            // [ANY] {3DNOW}</a>
+<a name="557"><span class="lineNum">     557 </span>            :     kIdPfcmpeq,                          // [ANY] {3DNOW}</a>
+<a name="558"><span class="lineNum">     558 </span>            :     kIdPfcmpge,                          // [ANY] {3DNOW}</a>
+<a name="559"><span class="lineNum">     559 </span>            :     kIdPfcmpgt,                          // [ANY] {3DNOW}</a>
+<a name="560"><span class="lineNum">     560 </span>            :     kIdPfmax,                            // [ANY] {3DNOW}</a>
+<a name="561"><span class="lineNum">     561 </span>            :     kIdPfmin,                            // [ANY] {3DNOW}</a>
+<a name="562"><span class="lineNum">     562 </span>            :     kIdPfmul,                            // [ANY] {3DNOW}</a>
+<a name="563"><span class="lineNum">     563 </span>            :     kIdPfnacc,                           // [ANY] {3DNOW2}</a>
+<a name="564"><span class="lineNum">     564 </span>            :     kIdPfpnacc,                          // [ANY] {3DNOW2}</a>
+<a name="565"><span class="lineNum">     565 </span>            :     kIdPfrcp,                            // [ANY] {3DNOW}</a>
+<a name="566"><span class="lineNum">     566 </span>            :     kIdPfrcpit1,                         // [ANY] {3DNOW}</a>
+<a name="567"><span class="lineNum">     567 </span>            :     kIdPfrcpit2,                         // [ANY] {3DNOW}</a>
+<a name="568"><span class="lineNum">     568 </span>            :     kIdPfrcpv,                           // [ANY] {GEODE}</a>
+<a name="569"><span class="lineNum">     569 </span>            :     kIdPfrsqit1,                         // [ANY] {3DNOW}</a>
+<a name="570"><span class="lineNum">     570 </span>            :     kIdPfrsqrt,                          // [ANY] {3DNOW}</a>
+<a name="571"><span class="lineNum">     571 </span>            :     kIdPfrsqrtv,                         // [ANY] {GEODE}</a>
+<a name="572"><span class="lineNum">     572 </span>            :     kIdPfsub,                            // [ANY] {3DNOW}</a>
+<a name="573"><span class="lineNum">     573 </span>            :     kIdPfsubr,                           // [ANY] {3DNOW}</a>
+<a name="574"><span class="lineNum">     574 </span>            :     kIdPhaddd,                           // [ANY] {SSSE3}</a>
+<a name="575"><span class="lineNum">     575 </span>            :     kIdPhaddsw,                          // [ANY] {SSSE3}</a>
+<a name="576"><span class="lineNum">     576 </span>            :     kIdPhaddw,                           // [ANY] {SSSE3}</a>
+<a name="577"><span class="lineNum">     577 </span>            :     kIdPhminposuw,                       // [ANY] {SSE4_1}</a>
+<a name="578"><span class="lineNum">     578 </span>            :     kIdPhsubd,                           // [ANY] {SSSE3}</a>
+<a name="579"><span class="lineNum">     579 </span>            :     kIdPhsubsw,                          // [ANY] {SSSE3}</a>
+<a name="580"><span class="lineNum">     580 </span>            :     kIdPhsubw,                           // [ANY] {SSSE3}</a>
+<a name="581"><span class="lineNum">     581 </span>            :     kIdPi2fd,                            // [ANY] {3DNOW}</a>
+<a name="582"><span class="lineNum">     582 </span>            :     kIdPi2fw,                            // [ANY] {3DNOW2}</a>
+<a name="583"><span class="lineNum">     583 </span>            :     kIdPinsrb,                           // [ANY] {SSE4_1}</a>
+<a name="584"><span class="lineNum">     584 </span>            :     kIdPinsrd,                           // [ANY] {SSE4_1}</a>
+<a name="585"><span class="lineNum">     585 </span>            :     kIdPinsrq,                           // [X64] {SSE4_1}</a>
+<a name="586"><span class="lineNum">     586 </span>            :     kIdPinsrw,                           // [ANY] {MMX2|SSE2}</a>
+<a name="587"><span class="lineNum">     587 </span>            :     kIdPmaddubsw,                        // [ANY] {SSSE3}</a>
+<a name="588"><span class="lineNum">     588 </span>            :     kIdPmaddwd,                          // [ANY] {MMX|SSE2}</a>
+<a name="589"><span class="lineNum">     589 </span>            :     kIdPmaxsb,                           // [ANY] {SSE4_1}</a>
+<a name="590"><span class="lineNum">     590 </span>            :     kIdPmaxsd,                           // [ANY] {SSE4_1}</a>
+<a name="591"><span class="lineNum">     591 </span>            :     kIdPmaxsw,                           // [ANY] {MMX2|SSE2}</a>
+<a name="592"><span class="lineNum">     592 </span>            :     kIdPmaxub,                           // [ANY] {MMX2|SSE2}</a>
+<a name="593"><span class="lineNum">     593 </span>            :     kIdPmaxud,                           // [ANY] {SSE4_1}</a>
+<a name="594"><span class="lineNum">     594 </span>            :     kIdPmaxuw,                           // [ANY] {SSE4_1}</a>
+<a name="595"><span class="lineNum">     595 </span>            :     kIdPminsb,                           // [ANY] {SSE4_1}</a>
+<a name="596"><span class="lineNum">     596 </span>            :     kIdPminsd,                           // [ANY] {SSE4_1}</a>
+<a name="597"><span class="lineNum">     597 </span>            :     kIdPminsw,                           // [ANY] {MMX2|SSE2}</a>
+<a name="598"><span class="lineNum">     598 </span>            :     kIdPminub,                           // [ANY] {MMX2|SSE2}</a>
+<a name="599"><span class="lineNum">     599 </span>            :     kIdPminud,                           // [ANY] {SSE4_1}</a>
+<a name="600"><span class="lineNum">     600 </span>            :     kIdPminuw,                           // [ANY] {SSE4_1}</a>
+<a name="601"><span class="lineNum">     601 </span>            :     kIdPmovmskb,                         // [ANY] {MMX2|SSE2}</a>
+<a name="602"><span class="lineNum">     602 </span>            :     kIdPmovsxbd,                         // [ANY] {SSE4_1}</a>
+<a name="603"><span class="lineNum">     603 </span>            :     kIdPmovsxbq,                         // [ANY] {SSE4_1}</a>
+<a name="604"><span class="lineNum">     604 </span>            :     kIdPmovsxbw,                         // [ANY] {SSE4_1}</a>
+<a name="605"><span class="lineNum">     605 </span>            :     kIdPmovsxdq,                         // [ANY] {SSE4_1}</a>
+<a name="606"><span class="lineNum">     606 </span>            :     kIdPmovsxwd,                         // [ANY] {SSE4_1}</a>
+<a name="607"><span class="lineNum">     607 </span>            :     kIdPmovsxwq,                         // [ANY] {SSE4_1}</a>
+<a name="608"><span class="lineNum">     608 </span>            :     kIdPmovzxbd,                         // [ANY] {SSE4_1}</a>
+<a name="609"><span class="lineNum">     609 </span>            :     kIdPmovzxbq,                         // [ANY] {SSE4_1}</a>
+<a name="610"><span class="lineNum">     610 </span>            :     kIdPmovzxbw,                         // [ANY] {SSE4_1}</a>
+<a name="611"><span class="lineNum">     611 </span>            :     kIdPmovzxdq,                         // [ANY] {SSE4_1}</a>
+<a name="612"><span class="lineNum">     612 </span>            :     kIdPmovzxwd,                         // [ANY] {SSE4_1}</a>
+<a name="613"><span class="lineNum">     613 </span>            :     kIdPmovzxwq,                         // [ANY] {SSE4_1}</a>
+<a name="614"><span class="lineNum">     614 </span>            :     kIdPmuldq,                           // [ANY] {SSE4_1}</a>
+<a name="615"><span class="lineNum">     615 </span>            :     kIdPmulhrsw,                         // [ANY] {SSSE3}</a>
+<a name="616"><span class="lineNum">     616 </span>            :     kIdPmulhrw,                          // [ANY] {3DNOW}</a>
+<a name="617"><span class="lineNum">     617 </span>            :     kIdPmulhuw,                          // [ANY] {MMX2|SSE2}</a>
+<a name="618"><span class="lineNum">     618 </span>            :     kIdPmulhw,                           // [ANY] {MMX|SSE2}</a>
+<a name="619"><span class="lineNum">     619 </span>            :     kIdPmulld,                           // [ANY] {SSE4_1}</a>
+<a name="620"><span class="lineNum">     620 </span>            :     kIdPmullw,                           // [ANY] {MMX|SSE2}</a>
+<a name="621"><span class="lineNum">     621 </span>            :     kIdPmuludq,                          // [ANY] {SSE2}</a>
+<a name="622"><span class="lineNum">     622 </span>            :     kIdPop,                              // [ANY]</a>
+<a name="623"><span class="lineNum">     623 </span>            :     kIdPopa,                             // [X86]</a>
+<a name="624"><span class="lineNum">     624 </span>            :     kIdPopad,                            // [X86]</a>
+<a name="625"><span class="lineNum">     625 </span>            :     kIdPopcnt,                           // [ANY] {POPCNT}</a>
+<a name="626"><span class="lineNum">     626 </span>            :     kIdPopf,                             // [ANY]</a>
+<a name="627"><span class="lineNum">     627 </span>            :     kIdPopfd,                            // [X86]</a>
+<a name="628"><span class="lineNum">     628 </span>            :     kIdPopfq,                            // [X64]</a>
+<a name="629"><span class="lineNum">     629 </span>            :     kIdPor,                              // [ANY] {MMX|SSE2}</a>
+<a name="630"><span class="lineNum">     630 </span>            :     kIdPrefetch,                         // [ANY] {3DNOW}</a>
+<a name="631"><span class="lineNum">     631 </span>            :     kIdPrefetchnta,                      // [ANY] {MMX2}</a>
+<a name="632"><span class="lineNum">     632 </span>            :     kIdPrefetcht0,                       // [ANY] {MMX2}</a>
+<a name="633"><span class="lineNum">     633 </span>            :     kIdPrefetcht1,                       // [ANY] {MMX2}</a>
+<a name="634"><span class="lineNum">     634 </span>            :     kIdPrefetcht2,                       // [ANY] {MMX2}</a>
+<a name="635"><span class="lineNum">     635 </span>            :     kIdPrefetchw,                        // [ANY] {PREFETCHW}</a>
+<a name="636"><span class="lineNum">     636 </span>            :     kIdPrefetchwt1,                      // [ANY] {PREFETCHWT1}</a>
+<a name="637"><span class="lineNum">     637 </span>            :     kIdPsadbw,                           // [ANY] {MMX2|SSE2}</a>
+<a name="638"><span class="lineNum">     638 </span>            :     kIdPshufb,                           // [ANY] {SSSE3}</a>
+<a name="639"><span class="lineNum">     639 </span>            :     kIdPshufd,                           // [ANY] {SSE2}</a>
+<a name="640"><span class="lineNum">     640 </span>            :     kIdPshufhw,                          // [ANY] {SSE2}</a>
+<a name="641"><span class="lineNum">     641 </span>            :     kIdPshuflw,                          // [ANY] {SSE2}</a>
+<a name="642"><span class="lineNum">     642 </span>            :     kIdPshufw,                           // [ANY] {MMX2}</a>
+<a name="643"><span class="lineNum">     643 </span>            :     kIdPsignb,                           // [ANY] {SSSE3}</a>
+<a name="644"><span class="lineNum">     644 </span>            :     kIdPsignd,                           // [ANY] {SSSE3}</a>
+<a name="645"><span class="lineNum">     645 </span>            :     kIdPsignw,                           // [ANY] {SSSE3}</a>
+<a name="646"><span class="lineNum">     646 </span>            :     kIdPslld,                            // [ANY] {MMX|SSE2}</a>
+<a name="647"><span class="lineNum">     647 </span>            :     kIdPslldq,                           // [ANY] {SSE2}</a>
+<a name="648"><span class="lineNum">     648 </span>            :     kIdPsllq,                            // [ANY] {MMX|SSE2}</a>
+<a name="649"><span class="lineNum">     649 </span>            :     kIdPsllw,                            // [ANY] {MMX|SSE2}</a>
+<a name="650"><span class="lineNum">     650 </span>            :     kIdPsrad,                            // [ANY] {MMX|SSE2}</a>
+<a name="651"><span class="lineNum">     651 </span>            :     kIdPsraw,                            // [ANY] {MMX|SSE2}</a>
+<a name="652"><span class="lineNum">     652 </span>            :     kIdPsrld,                            // [ANY] {MMX|SSE2}</a>
+<a name="653"><span class="lineNum">     653 </span>            :     kIdPsrldq,                           // [ANY] {SSE2}</a>
+<a name="654"><span class="lineNum">     654 </span>            :     kIdPsrlq,                            // [ANY] {MMX|SSE2}</a>
+<a name="655"><span class="lineNum">     655 </span>            :     kIdPsrlw,                            // [ANY] {MMX|SSE2}</a>
+<a name="656"><span class="lineNum">     656 </span>            :     kIdPsubb,                            // [ANY] {MMX|SSE2}</a>
+<a name="657"><span class="lineNum">     657 </span>            :     kIdPsubd,                            // [ANY] {MMX|SSE2}</a>
+<a name="658"><span class="lineNum">     658 </span>            :     kIdPsubq,                            // [ANY] {SSE2}</a>
+<a name="659"><span class="lineNum">     659 </span>            :     kIdPsubsb,                           // [ANY] {MMX|SSE2}</a>
+<a name="660"><span class="lineNum">     660 </span>            :     kIdPsubsw,                           // [ANY] {MMX|SSE2}</a>
+<a name="661"><span class="lineNum">     661 </span>            :     kIdPsubusb,                          // [ANY] {MMX|SSE2}</a>
+<a name="662"><span class="lineNum">     662 </span>            :     kIdPsubusw,                          // [ANY] {MMX|SSE2}</a>
+<a name="663"><span class="lineNum">     663 </span>            :     kIdPsubw,                            // [ANY] {MMX|SSE2}</a>
+<a name="664"><span class="lineNum">     664 </span>            :     kIdPswapd,                           // [ANY] {3DNOW2}</a>
+<a name="665"><span class="lineNum">     665 </span>            :     kIdPtest,                            // [ANY] {SSE4_1}</a>
+<a name="666"><span class="lineNum">     666 </span>            :     kIdPunpckhbw,                        // [ANY] {MMX|SSE2}</a>
+<a name="667"><span class="lineNum">     667 </span>            :     kIdPunpckhdq,                        // [ANY] {MMX|SSE2}</a>
+<a name="668"><span class="lineNum">     668 </span>            :     kIdPunpckhqdq,                       // [ANY] {SSE2}</a>
+<a name="669"><span class="lineNum">     669 </span>            :     kIdPunpckhwd,                        // [ANY] {MMX|SSE2}</a>
+<a name="670"><span class="lineNum">     670 </span>            :     kIdPunpcklbw,                        // [ANY] {MMX|SSE2}</a>
+<a name="671"><span class="lineNum">     671 </span>            :     kIdPunpckldq,                        // [ANY] {MMX|SSE2}</a>
+<a name="672"><span class="lineNum">     672 </span>            :     kIdPunpcklqdq,                       // [ANY] {SSE2}</a>
+<a name="673"><span class="lineNum">     673 </span>            :     kIdPunpcklwd,                        // [ANY] {MMX|SSE2}</a>
+<a name="674"><span class="lineNum">     674 </span>            :     kIdPush,                             // [ANY]</a>
+<a name="675"><span class="lineNum">     675 </span>            :     kIdPusha,                            // [X86]</a>
+<a name="676"><span class="lineNum">     676 </span>            :     kIdPushad,                           // [X86]</a>
+<a name="677"><span class="lineNum">     677 </span>            :     kIdPushf,                            // [ANY]</a>
+<a name="678"><span class="lineNum">     678 </span>            :     kIdPushfd,                           // [X86]</a>
+<a name="679"><span class="lineNum">     679 </span>            :     kIdPushfq,                           // [X64]</a>
+<a name="680"><span class="lineNum">     680 </span>            :     kIdPxor,                             // [ANY] {MMX|SSE2}</a>
+<a name="681"><span class="lineNum">     681 </span>            :     kIdRcl,                              // [ANY]</a>
+<a name="682"><span class="lineNum">     682 </span>            :     kIdRcpps,                            // [ANY] {SSE}</a>
+<a name="683"><span class="lineNum">     683 </span>            :     kIdRcpss,                            // [ANY] {SSE}</a>
+<a name="684"><span class="lineNum">     684 </span>            :     kIdRcr,                              // [ANY]</a>
+<a name="685"><span class="lineNum">     685 </span>            :     kIdRdfsbase,                         // [X64] {FSGSBASE}</a>
+<a name="686"><span class="lineNum">     686 </span>            :     kIdRdgsbase,                         // [X64] {FSGSBASE}</a>
+<a name="687"><span class="lineNum">     687 </span>            :     kIdRdmsr,                            // [ANY] {MSR}</a>
+<a name="688"><span class="lineNum">     688 </span>            :     kIdRdpmc,                            // [ANY]</a>
+<a name="689"><span class="lineNum">     689 </span>            :     kIdRdrand,                           // [ANY] {RDRAND}</a>
+<a name="690"><span class="lineNum">     690 </span>            :     kIdRdseed,                           // [ANY] {RDSEED}</a>
+<a name="691"><span class="lineNum">     691 </span>            :     kIdRdtsc,                            // [ANY] {RDTSC}</a>
+<a name="692"><span class="lineNum">     692 </span>            :     kIdRdtscp,                           // [ANY] {RDTSCP}</a>
+<a name="693"><span class="lineNum">     693 </span>            :     kIdRet,                              // [ANY]</a>
+<a name="694"><span class="lineNum">     694 </span>            :     kIdRol,                              // [ANY]</a>
+<a name="695"><span class="lineNum">     695 </span>            :     kIdRor,                              // [ANY]</a>
+<a name="696"><span class="lineNum">     696 </span>            :     kIdRorx,                             // [ANY] {BMI2}</a>
+<a name="697"><span class="lineNum">     697 </span>            :     kIdRoundpd,                          // [ANY] {SSE4_1}</a>
+<a name="698"><span class="lineNum">     698 </span>            :     kIdRoundps,                          // [ANY] {SSE4_1}</a>
+<a name="699"><span class="lineNum">     699 </span>            :     kIdRoundsd,                          // [ANY] {SSE4_1}</a>
+<a name="700"><span class="lineNum">     700 </span>            :     kIdRoundss,                          // [ANY] {SSE4_1}</a>
+<a name="701"><span class="lineNum">     701 </span>            :     kIdRsm,                              // [X86]</a>
+<a name="702"><span class="lineNum">     702 </span>            :     kIdRsqrtps,                          // [ANY] {SSE}</a>
+<a name="703"><span class="lineNum">     703 </span>            :     kIdRsqrtss,                          // [ANY] {SSE}</a>
+<a name="704"><span class="lineNum">     704 </span>            :     kIdSahf,                             // [ANY] {LAHFSAHF}</a>
+<a name="705"><span class="lineNum">     705 </span>            :     kIdSal,                              // [ANY]</a>
+<a name="706"><span class="lineNum">     706 </span>            :     kIdSar,                              // [ANY]</a>
+<a name="707"><span class="lineNum">     707 </span>            :     kIdSarx,                             // [ANY] {BMI2}</a>
+<a name="708"><span class="lineNum">     708 </span>            :     kIdSbb,                              // [ANY]</a>
+<a name="709"><span class="lineNum">     709 </span>            :     kIdScas,                             // [ANY]</a>
+<a name="710"><span class="lineNum">     710 </span>            :     kIdSeta,                             // [ANY]</a>
+<a name="711"><span class="lineNum">     711 </span>            :     kIdSetae,                            // [ANY]</a>
+<a name="712"><span class="lineNum">     712 </span>            :     kIdSetb,                             // [ANY]</a>
+<a name="713"><span class="lineNum">     713 </span>            :     kIdSetbe,                            // [ANY]</a>
+<a name="714"><span class="lineNum">     714 </span>            :     kIdSetc,                             // [ANY]</a>
+<a name="715"><span class="lineNum">     715 </span>            :     kIdSete,                             // [ANY]</a>
+<a name="716"><span class="lineNum">     716 </span>            :     kIdSetg,                             // [ANY]</a>
+<a name="717"><span class="lineNum">     717 </span>            :     kIdSetge,                            // [ANY]</a>
+<a name="718"><span class="lineNum">     718 </span>            :     kIdSetl,                             // [ANY]</a>
+<a name="719"><span class="lineNum">     719 </span>            :     kIdSetle,                            // [ANY]</a>
+<a name="720"><span class="lineNum">     720 </span>            :     kIdSetna,                            // [ANY]</a>
+<a name="721"><span class="lineNum">     721 </span>            :     kIdSetnae,                           // [ANY]</a>
+<a name="722"><span class="lineNum">     722 </span>            :     kIdSetnb,                            // [ANY]</a>
+<a name="723"><span class="lineNum">     723 </span>            :     kIdSetnbe,                           // [ANY]</a>
+<a name="724"><span class="lineNum">     724 </span>            :     kIdSetnc,                            // [ANY]</a>
+<a name="725"><span class="lineNum">     725 </span>            :     kIdSetne,                            // [ANY]</a>
+<a name="726"><span class="lineNum">     726 </span>            :     kIdSetng,                            // [ANY]</a>
+<a name="727"><span class="lineNum">     727 </span>            :     kIdSetnge,                           // [ANY]</a>
+<a name="728"><span class="lineNum">     728 </span>            :     kIdSetnl,                            // [ANY]</a>
+<a name="729"><span class="lineNum">     729 </span>            :     kIdSetnle,                           // [ANY]</a>
+<a name="730"><span class="lineNum">     730 </span>            :     kIdSetno,                            // [ANY]</a>
+<a name="731"><span class="lineNum">     731 </span>            :     kIdSetnp,                            // [ANY]</a>
+<a name="732"><span class="lineNum">     732 </span>            :     kIdSetns,                            // [ANY]</a>
+<a name="733"><span class="lineNum">     733 </span>            :     kIdSetnz,                            // [ANY]</a>
+<a name="734"><span class="lineNum">     734 </span>            :     kIdSeto,                             // [ANY]</a>
+<a name="735"><span class="lineNum">     735 </span>            :     kIdSetp,                             // [ANY]</a>
+<a name="736"><span class="lineNum">     736 </span>            :     kIdSetpe,                            // [ANY]</a>
+<a name="737"><span class="lineNum">     737 </span>            :     kIdSetpo,                            // [ANY]</a>
+<a name="738"><span class="lineNum">     738 </span>            :     kIdSets,                             // [ANY]</a>
+<a name="739"><span class="lineNum">     739 </span>            :     kIdSetz,                             // [ANY]</a>
+<a name="740"><span class="lineNum">     740 </span>            :     kIdSfence,                           // [ANY] {MMX2}</a>
+<a name="741"><span class="lineNum">     741 </span>            :     kIdSgdt,                             // [ANY]</a>
+<a name="742"><span class="lineNum">     742 </span>            :     kIdSha1msg1,                         // [ANY] {SHA}</a>
+<a name="743"><span class="lineNum">     743 </span>            :     kIdSha1msg2,                         // [ANY] {SHA}</a>
+<a name="744"><span class="lineNum">     744 </span>            :     kIdSha1nexte,                        // [ANY] {SHA}</a>
+<a name="745"><span class="lineNum">     745 </span>            :     kIdSha1rnds4,                        // [ANY] {SHA}</a>
+<a name="746"><span class="lineNum">     746 </span>            :     kIdSha256msg1,                       // [ANY] {SHA}</a>
+<a name="747"><span class="lineNum">     747 </span>            :     kIdSha256msg2,                       // [ANY] {SHA}</a>
+<a name="748"><span class="lineNum">     748 </span>            :     kIdSha256rnds2,                      // [ANY] {SHA}</a>
+<a name="749"><span class="lineNum">     749 </span>            :     kIdShl,                              // [ANY]</a>
+<a name="750"><span class="lineNum">     750 </span>            :     kIdShld,                             // [ANY]</a>
+<a name="751"><span class="lineNum">     751 </span>            :     kIdShlx,                             // [ANY] {BMI2}</a>
+<a name="752"><span class="lineNum">     752 </span>            :     kIdShr,                              // [ANY]</a>
+<a name="753"><span class="lineNum">     753 </span>            :     kIdShrd,                             // [ANY]</a>
+<a name="754"><span class="lineNum">     754 </span>            :     kIdShrx,                             // [ANY] {BMI2}</a>
+<a name="755"><span class="lineNum">     755 </span>            :     kIdShufpd,                           // [ANY] {SSE2}</a>
+<a name="756"><span class="lineNum">     756 </span>            :     kIdShufps,                           // [ANY] {SSE}</a>
+<a name="757"><span class="lineNum">     757 </span>            :     kIdSidt,                             // [ANY]</a>
+<a name="758"><span class="lineNum">     758 </span>            :     kIdSldt,                             // [ANY]</a>
+<a name="759"><span class="lineNum">     759 </span>            :     kIdSmsw,                             // [ANY]</a>
+<a name="760"><span class="lineNum">     760 </span>            :     kIdSqrtpd,                           // [ANY] {SSE2}</a>
+<a name="761"><span class="lineNum">     761 </span>            :     kIdSqrtps,                           // [ANY] {SSE}</a>
+<a name="762"><span class="lineNum">     762 </span>            :     kIdSqrtsd,                           // [ANY] {SSE2}</a>
+<a name="763"><span class="lineNum">     763 </span>            :     kIdSqrtss,                           // [ANY] {SSE}</a>
+<a name="764"><span class="lineNum">     764 </span>            :     kIdStac,                             // [ANY] {SMAP}</a>
+<a name="765"><span class="lineNum">     765 </span>            :     kIdStc,                              // [ANY]</a>
+<a name="766"><span class="lineNum">     766 </span>            :     kIdStd,                              // [ANY]</a>
+<a name="767"><span class="lineNum">     767 </span>            :     kIdSti,                              // [ANY]</a>
+<a name="768"><span class="lineNum">     768 </span>            :     kIdStmxcsr,                          // [ANY] {SSE}</a>
+<a name="769"><span class="lineNum">     769 </span>            :     kIdStos,                             // [ANY]</a>
+<a name="770"><span class="lineNum">     770 </span>            :     kIdStr,                              // [ANY]</a>
+<a name="771"><span class="lineNum">     771 </span>            :     kIdSub,                              // [ANY]</a>
+<a name="772"><span class="lineNum">     772 </span>            :     kIdSubpd,                            // [ANY] {SSE2}</a>
+<a name="773"><span class="lineNum">     773 </span>            :     kIdSubps,                            // [ANY] {SSE}</a>
+<a name="774"><span class="lineNum">     774 </span>            :     kIdSubsd,                            // [ANY] {SSE2}</a>
+<a name="775"><span class="lineNum">     775 </span>            :     kIdSubss,                            // [ANY] {SSE}</a>
+<a name="776"><span class="lineNum">     776 </span>            :     kIdSwapgs,                           // [X64]</a>
+<a name="777"><span class="lineNum">     777 </span>            :     kIdSyscall,                          // [X64]</a>
+<a name="778"><span class="lineNum">     778 </span>            :     kIdSysenter,                         // [ANY]</a>
+<a name="779"><span class="lineNum">     779 </span>            :     kIdSysexit,                          // [ANY]</a>
+<a name="780"><span class="lineNum">     780 </span>            :     kIdSysexit64,                        // [ANY]</a>
+<a name="781"><span class="lineNum">     781 </span>            :     kIdSysret,                           // [X64]</a>
+<a name="782"><span class="lineNum">     782 </span>            :     kIdSysret64,                         // [X64]</a>
+<a name="783"><span class="lineNum">     783 </span>            :     kIdT1mskc,                           // [ANY] {TBM}</a>
+<a name="784"><span class="lineNum">     784 </span>            :     kIdTest,                             // [ANY]</a>
+<a name="785"><span class="lineNum">     785 </span>            :     kIdTzcnt,                            // [ANY] {BMI}</a>
+<a name="786"><span class="lineNum">     786 </span>            :     kIdTzmsk,                            // [ANY] {TBM}</a>
+<a name="787"><span class="lineNum">     787 </span>            :     kIdUcomisd,                          // [ANY] {SSE2}</a>
+<a name="788"><span class="lineNum">     788 </span>            :     kIdUcomiss,                          // [ANY] {SSE}</a>
+<a name="789"><span class="lineNum">     789 </span>            :     kIdUd2,                              // [ANY]</a>
+<a name="790"><span class="lineNum">     790 </span>            :     kIdUnpckhpd,                         // [ANY] {SSE2}</a>
+<a name="791"><span class="lineNum">     791 </span>            :     kIdUnpckhps,                         // [ANY] {SSE}</a>
+<a name="792"><span class="lineNum">     792 </span>            :     kIdUnpcklpd,                         // [ANY] {SSE2}</a>
+<a name="793"><span class="lineNum">     793 </span>            :     kIdUnpcklps,                         // [ANY] {SSE}</a>
+<a name="794"><span class="lineNum">     794 </span>            :     kIdV4fmaddps,                        // [ANY] {AVX512_4FMAPS}</a>
+<a name="795"><span class="lineNum">     795 </span>            :     kIdV4fnmaddps,                       // [ANY] {AVX512_4FMAPS}</a>
+<a name="796"><span class="lineNum">     796 </span>            :     kIdVaddpd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="797"><span class="lineNum">     797 </span>            :     kIdVaddps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="798"><span class="lineNum">     798 </span>            :     kIdVaddsd,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="799"><span class="lineNum">     799 </span>            :     kIdVaddss,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="800"><span class="lineNum">     800 </span>            :     kIdVaddsubpd,                        // [ANY] {AVX}</a>
+<a name="801"><span class="lineNum">     801 </span>            :     kIdVaddsubps,                        // [ANY] {AVX}</a>
+<a name="802"><span class="lineNum">     802 </span>            :     kIdVaesdec,                          // [ANY] {AESNI|AVX}</a>
+<a name="803"><span class="lineNum">     803 </span>            :     kIdVaesdeclast,                      // [ANY] {AESNI|AVX}</a>
+<a name="804"><span class="lineNum">     804 </span>            :     kIdVaesenc,                          // [ANY] {AESNI|AVX}</a>
+<a name="805"><span class="lineNum">     805 </span>            :     kIdVaesenclast,                      // [ANY] {AESNI|AVX}</a>
+<a name="806"><span class="lineNum">     806 </span>            :     kIdVaesimc,                          // [ANY] {AESNI|AVX}</a>
+<a name="807"><span class="lineNum">     807 </span>            :     kIdVaeskeygenassist,                 // [ANY] {AESNI|AVX}</a>
+<a name="808"><span class="lineNum">     808 </span>            :     kIdValignd,                          // [ANY] {AVX512_F+VL}</a>
+<a name="809"><span class="lineNum">     809 </span>            :     kIdValignq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="810"><span class="lineNum">     810 </span>            :     kIdVandnpd,                          // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="811"><span class="lineNum">     811 </span>            :     kIdVandnps,                          // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="812"><span class="lineNum">     812 </span>            :     kIdVandpd,                           // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="813"><span class="lineNum">     813 </span>            :     kIdVandps,                           // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="814"><span class="lineNum">     814 </span>            :     kIdVblendmb,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="815"><span class="lineNum">     815 </span>            :     kIdVblendmd,                         // [ANY] {AVX512_F+VL}</a>
+<a name="816"><span class="lineNum">     816 </span>            :     kIdVblendmpd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="817"><span class="lineNum">     817 </span>            :     kIdVblendmps,                        // [ANY] {AVX512_F+VL}</a>
+<a name="818"><span class="lineNum">     818 </span>            :     kIdVblendmq,                         // [ANY] {AVX512_F+VL}</a>
+<a name="819"><span class="lineNum">     819 </span>            :     kIdVblendmw,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="820"><span class="lineNum">     820 </span>            :     kIdVblendpd,                         // [ANY] {AVX}</a>
+<a name="821"><span class="lineNum">     821 </span>            :     kIdVblendps,                         // [ANY] {AVX}</a>
+<a name="822"><span class="lineNum">     822 </span>            :     kIdVblendvpd,                        // [ANY] {AVX}</a>
+<a name="823"><span class="lineNum">     823 </span>            :     kIdVblendvps,                        // [ANY] {AVX}</a>
+<a name="824"><span class="lineNum">     824 </span>            :     kIdVbroadcastf128,                   // [ANY] {AVX}</a>
+<a name="825"><span class="lineNum">     825 </span>            :     kIdVbroadcastf32x2,                  // [ANY] {AVX512_DQ+VL}</a>
+<a name="826"><span class="lineNum">     826 </span>            :     kIdVbroadcastf32x4,                  // [ANY] {AVX512_F}</a>
+<a name="827"><span class="lineNum">     827 </span>            :     kIdVbroadcastf32x8,                  // [ANY] {AVX512_DQ}</a>
+<a name="828"><span class="lineNum">     828 </span>            :     kIdVbroadcastf64x2,                  // [ANY] {AVX512_DQ+VL}</a>
+<a name="829"><span class="lineNum">     829 </span>            :     kIdVbroadcastf64x4,                  // [ANY] {AVX512_F}</a>
+<a name="830"><span class="lineNum">     830 </span>            :     kIdVbroadcasti128,                   // [ANY] {AVX2}</a>
+<a name="831"><span class="lineNum">     831 </span>            :     kIdVbroadcasti32x2,                  // [ANY] {AVX512_DQ+VL}</a>
+<a name="832"><span class="lineNum">     832 </span>            :     kIdVbroadcasti32x4,                  // [ANY] {AVX512_F+VL}</a>
+<a name="833"><span class="lineNum">     833 </span>            :     kIdVbroadcasti32x8,                  // [ANY] {AVX512_DQ}</a>
+<a name="834"><span class="lineNum">     834 </span>            :     kIdVbroadcasti64x2,                  // [ANY] {AVX512_DQ+VL}</a>
+<a name="835"><span class="lineNum">     835 </span>            :     kIdVbroadcasti64x4,                  // [ANY] {AVX512_F}</a>
+<a name="836"><span class="lineNum">     836 </span>            :     kIdVbroadcastsd,                     // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="837"><span class="lineNum">     837 </span>            :     kIdVbroadcastss,                     // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="838"><span class="lineNum">     838 </span>            :     kIdVcmppd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="839"><span class="lineNum">     839 </span>            :     kIdVcmpps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="840"><span class="lineNum">     840 </span>            :     kIdVcmpsd,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="841"><span class="lineNum">     841 </span>            :     kIdVcmpss,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="842"><span class="lineNum">     842 </span>            :     kIdVcomisd,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="843"><span class="lineNum">     843 </span>            :     kIdVcomiss,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="844"><span class="lineNum">     844 </span>            :     kIdVcompresspd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="845"><span class="lineNum">     845 </span>            :     kIdVcompressps,                      // [ANY] {AVX512_F+VL}</a>
+<a name="846"><span class="lineNum">     846 </span>            :     kIdVcvtdq2pd,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="847"><span class="lineNum">     847 </span>            :     kIdVcvtdq2ps,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="848"><span class="lineNum">     848 </span>            :     kIdVcvtpd2dq,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="849"><span class="lineNum">     849 </span>            :     kIdVcvtpd2ps,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="850"><span class="lineNum">     850 </span>            :     kIdVcvtpd2qq,                        // [ANY] {AVX512_DQ+VL}</a>
+<a name="851"><span class="lineNum">     851 </span>            :     kIdVcvtpd2udq,                       // [ANY] {AVX512_F+VL}</a>
+<a name="852"><span class="lineNum">     852 </span>            :     kIdVcvtpd2uqq,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="853"><span class="lineNum">     853 </span>            :     kIdVcvtph2ps,                        // [ANY] {AVX512_F|F16C+VL}</a>
+<a name="854"><span class="lineNum">     854 </span>            :     kIdVcvtps2dq,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="855"><span class="lineNum">     855 </span>            :     kIdVcvtps2pd,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="856"><span class="lineNum">     856 </span>            :     kIdVcvtps2ph,                        // [ANY] {AVX512_F|F16C+VL}</a>
+<a name="857"><span class="lineNum">     857 </span>            :     kIdVcvtps2qq,                        // [ANY] {AVX512_DQ+VL}</a>
+<a name="858"><span class="lineNum">     858 </span>            :     kIdVcvtps2udq,                       // [ANY] {AVX512_F+VL}</a>
+<a name="859"><span class="lineNum">     859 </span>            :     kIdVcvtps2uqq,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="860"><span class="lineNum">     860 </span>            :     kIdVcvtqq2pd,                        // [ANY] {AVX512_DQ+VL}</a>
+<a name="861"><span class="lineNum">     861 </span>            :     kIdVcvtqq2ps,                        // [ANY] {AVX512_DQ+VL}</a>
+<a name="862"><span class="lineNum">     862 </span>            :     kIdVcvtsd2si,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="863"><span class="lineNum">     863 </span>            :     kIdVcvtsd2ss,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="864"><span class="lineNum">     864 </span>            :     kIdVcvtsd2usi,                       // [ANY] {AVX512_F}</a>
+<a name="865"><span class="lineNum">     865 </span>            :     kIdVcvtsi2sd,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="866"><span class="lineNum">     866 </span>            :     kIdVcvtsi2ss,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="867"><span class="lineNum">     867 </span>            :     kIdVcvtss2sd,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="868"><span class="lineNum">     868 </span>            :     kIdVcvtss2si,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="869"><span class="lineNum">     869 </span>            :     kIdVcvtss2usi,                       // [ANY] {AVX512_F}</a>
+<a name="870"><span class="lineNum">     870 </span>            :     kIdVcvttpd2dq,                       // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="871"><span class="lineNum">     871 </span>            :     kIdVcvttpd2qq,                       // [ANY] {AVX512_F+VL}</a>
+<a name="872"><span class="lineNum">     872 </span>            :     kIdVcvttpd2udq,                      // [ANY] {AVX512_F+VL}</a>
+<a name="873"><span class="lineNum">     873 </span>            :     kIdVcvttpd2uqq,                      // [ANY] {AVX512_DQ+VL}</a>
+<a name="874"><span class="lineNum">     874 </span>            :     kIdVcvttps2dq,                       // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="875"><span class="lineNum">     875 </span>            :     kIdVcvttps2qq,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="876"><span class="lineNum">     876 </span>            :     kIdVcvttps2udq,                      // [ANY] {AVX512_F+VL}</a>
+<a name="877"><span class="lineNum">     877 </span>            :     kIdVcvttps2uqq,                      // [ANY] {AVX512_DQ+VL}</a>
+<a name="878"><span class="lineNum">     878 </span>            :     kIdVcvttsd2si,                       // [ANY] {AVX|AVX512_F}</a>
+<a name="879"><span class="lineNum">     879 </span>            :     kIdVcvttsd2usi,                      // [ANY] {AVX512_F}</a>
+<a name="880"><span class="lineNum">     880 </span>            :     kIdVcvttss2si,                       // [ANY] {AVX|AVX512_F}</a>
+<a name="881"><span class="lineNum">     881 </span>            :     kIdVcvttss2usi,                      // [ANY] {AVX512_F}</a>
+<a name="882"><span class="lineNum">     882 </span>            :     kIdVcvtudq2pd,                       // [ANY] {AVX512_F+VL}</a>
+<a name="883"><span class="lineNum">     883 </span>            :     kIdVcvtudq2ps,                       // [ANY] {AVX512_F+VL}</a>
+<a name="884"><span class="lineNum">     884 </span>            :     kIdVcvtuqq2pd,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="885"><span class="lineNum">     885 </span>            :     kIdVcvtuqq2ps,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="886"><span class="lineNum">     886 </span>            :     kIdVcvtusi2sd,                       // [ANY] {AVX512_F}</a>
+<a name="887"><span class="lineNum">     887 </span>            :     kIdVcvtusi2ss,                       // [ANY] {AVX512_F}</a>
+<a name="888"><span class="lineNum">     888 </span>            :     kIdVdbpsadbw,                        // [ANY] {AVX512_BW+VL}</a>
+<a name="889"><span class="lineNum">     889 </span>            :     kIdVdivpd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="890"><span class="lineNum">     890 </span>            :     kIdVdivps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="891"><span class="lineNum">     891 </span>            :     kIdVdivsd,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="892"><span class="lineNum">     892 </span>            :     kIdVdivss,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="893"><span class="lineNum">     893 </span>            :     kIdVdppd,                            // [ANY] {AVX}</a>
+<a name="894"><span class="lineNum">     894 </span>            :     kIdVdpps,                            // [ANY] {AVX}</a>
+<a name="895"><span class="lineNum">     895 </span>            :     kIdVerr,                             // [ANY]</a>
+<a name="896"><span class="lineNum">     896 </span>            :     kIdVerw,                             // [ANY]</a>
+<a name="897"><span class="lineNum">     897 </span>            :     kIdVexp2pd,                          // [ANY] {AVX512_ERI}</a>
+<a name="898"><span class="lineNum">     898 </span>            :     kIdVexp2ps,                          // [ANY] {AVX512_ERI}</a>
+<a name="899"><span class="lineNum">     899 </span>            :     kIdVexpandpd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="900"><span class="lineNum">     900 </span>            :     kIdVexpandps,                        // [ANY] {AVX512_F+VL}</a>
+<a name="901"><span class="lineNum">     901 </span>            :     kIdVextractf128,                     // [ANY] {AVX}</a>
+<a name="902"><span class="lineNum">     902 </span>            :     kIdVextractf32x4,                    // [ANY] {AVX512_F+VL}</a>
+<a name="903"><span class="lineNum">     903 </span>            :     kIdVextractf32x8,                    // [ANY] {AVX512_DQ}</a>
+<a name="904"><span class="lineNum">     904 </span>            :     kIdVextractf64x2,                    // [ANY] {AVX512_DQ+VL}</a>
+<a name="905"><span class="lineNum">     905 </span>            :     kIdVextractf64x4,                    // [ANY] {AVX512_F}</a>
+<a name="906"><span class="lineNum">     906 </span>            :     kIdVextracti128,                     // [ANY] {AVX2}</a>
+<a name="907"><span class="lineNum">     907 </span>            :     kIdVextracti32x4,                    // [ANY] {AVX512_F+VL}</a>
+<a name="908"><span class="lineNum">     908 </span>            :     kIdVextracti32x8,                    // [ANY] {AVX512_DQ}</a>
+<a name="909"><span class="lineNum">     909 </span>            :     kIdVextracti64x2,                    // [ANY] {AVX512_DQ+VL}</a>
+<a name="910"><span class="lineNum">     910 </span>            :     kIdVextracti64x4,                    // [ANY] {AVX512_F}</a>
+<a name="911"><span class="lineNum">     911 </span>            :     kIdVextractps,                       // [ANY] {AVX|AVX512_F}</a>
+<a name="912"><span class="lineNum">     912 </span>            :     kIdVfixupimmpd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="913"><span class="lineNum">     913 </span>            :     kIdVfixupimmps,                      // [ANY] {AVX512_F+VL}</a>
+<a name="914"><span class="lineNum">     914 </span>            :     kIdVfixupimmsd,                      // [ANY] {AVX512_F}</a>
+<a name="915"><span class="lineNum">     915 </span>            :     kIdVfixupimmss,                      // [ANY] {AVX512_F}</a>
+<a name="916"><span class="lineNum">     916 </span>            :     kIdVfmadd132pd,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="917"><span class="lineNum">     917 </span>            :     kIdVfmadd132ps,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="918"><span class="lineNum">     918 </span>            :     kIdVfmadd132sd,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="919"><span class="lineNum">     919 </span>            :     kIdVfmadd132ss,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="920"><span class="lineNum">     920 </span>            :     kIdVfmadd213pd,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="921"><span class="lineNum">     921 </span>            :     kIdVfmadd213ps,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="922"><span class="lineNum">     922 </span>            :     kIdVfmadd213sd,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="923"><span class="lineNum">     923 </span>            :     kIdVfmadd213ss,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="924"><span class="lineNum">     924 </span>            :     kIdVfmadd231pd,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="925"><span class="lineNum">     925 </span>            :     kIdVfmadd231ps,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="926"><span class="lineNum">     926 </span>            :     kIdVfmadd231sd,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="927"><span class="lineNum">     927 </span>            :     kIdVfmadd231ss,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="928"><span class="lineNum">     928 </span>            :     kIdVfmaddpd,                         // [ANY] {FMA4}</a>
+<a name="929"><span class="lineNum">     929 </span>            :     kIdVfmaddps,                         // [ANY] {FMA4}</a>
+<a name="930"><span class="lineNum">     930 </span>            :     kIdVfmaddsd,                         // [ANY] {FMA4}</a>
+<a name="931"><span class="lineNum">     931 </span>            :     kIdVfmaddss,                         // [ANY] {FMA4}</a>
+<a name="932"><span class="lineNum">     932 </span>            :     kIdVfmaddsub132pd,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="933"><span class="lineNum">     933 </span>            :     kIdVfmaddsub132ps,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="934"><span class="lineNum">     934 </span>            :     kIdVfmaddsub213pd,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="935"><span class="lineNum">     935 </span>            :     kIdVfmaddsub213ps,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="936"><span class="lineNum">     936 </span>            :     kIdVfmaddsub231pd,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="937"><span class="lineNum">     937 </span>            :     kIdVfmaddsub231ps,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="938"><span class="lineNum">     938 </span>            :     kIdVfmaddsubpd,                      // [ANY] {FMA4}</a>
+<a name="939"><span class="lineNum">     939 </span>            :     kIdVfmaddsubps,                      // [ANY] {FMA4}</a>
+<a name="940"><span class="lineNum">     940 </span>            :     kIdVfmsub132pd,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="941"><span class="lineNum">     941 </span>            :     kIdVfmsub132ps,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="942"><span class="lineNum">     942 </span>            :     kIdVfmsub132sd,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="943"><span class="lineNum">     943 </span>            :     kIdVfmsub132ss,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="944"><span class="lineNum">     944 </span>            :     kIdVfmsub213pd,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="945"><span class="lineNum">     945 </span>            :     kIdVfmsub213ps,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="946"><span class="lineNum">     946 </span>            :     kIdVfmsub213sd,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="947"><span class="lineNum">     947 </span>            :     kIdVfmsub213ss,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="948"><span class="lineNum">     948 </span>            :     kIdVfmsub231pd,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="949"><span class="lineNum">     949 </span>            :     kIdVfmsub231ps,                      // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="950"><span class="lineNum">     950 </span>            :     kIdVfmsub231sd,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="951"><span class="lineNum">     951 </span>            :     kIdVfmsub231ss,                      // [ANY] {AVX512_F|FMA}</a>
+<a name="952"><span class="lineNum">     952 </span>            :     kIdVfmsubadd132pd,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="953"><span class="lineNum">     953 </span>            :     kIdVfmsubadd132ps,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="954"><span class="lineNum">     954 </span>            :     kIdVfmsubadd213pd,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="955"><span class="lineNum">     955 </span>            :     kIdVfmsubadd213ps,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="956"><span class="lineNum">     956 </span>            :     kIdVfmsubadd231pd,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="957"><span class="lineNum">     957 </span>            :     kIdVfmsubadd231ps,                   // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="958"><span class="lineNum">     958 </span>            :     kIdVfmsubaddpd,                      // [ANY] {FMA4}</a>
+<a name="959"><span class="lineNum">     959 </span>            :     kIdVfmsubaddps,                      // [ANY] {FMA4}</a>
+<a name="960"><span class="lineNum">     960 </span>            :     kIdVfmsubpd,                         // [ANY] {FMA4}</a>
+<a name="961"><span class="lineNum">     961 </span>            :     kIdVfmsubps,                         // [ANY] {FMA4}</a>
+<a name="962"><span class="lineNum">     962 </span>            :     kIdVfmsubsd,                         // [ANY] {FMA4}</a>
+<a name="963"><span class="lineNum">     963 </span>            :     kIdVfmsubss,                         // [ANY] {FMA4}</a>
+<a name="964"><span class="lineNum">     964 </span>            :     kIdVfnmadd132pd,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="965"><span class="lineNum">     965 </span>            :     kIdVfnmadd132ps,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="966"><span class="lineNum">     966 </span>            :     kIdVfnmadd132sd,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="967"><span class="lineNum">     967 </span>            :     kIdVfnmadd132ss,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="968"><span class="lineNum">     968 </span>            :     kIdVfnmadd213pd,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="969"><span class="lineNum">     969 </span>            :     kIdVfnmadd213ps,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="970"><span class="lineNum">     970 </span>            :     kIdVfnmadd213sd,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="971"><span class="lineNum">     971 </span>            :     kIdVfnmadd213ss,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="972"><span class="lineNum">     972 </span>            :     kIdVfnmadd231pd,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="973"><span class="lineNum">     973 </span>            :     kIdVfnmadd231ps,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="974"><span class="lineNum">     974 </span>            :     kIdVfnmadd231sd,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="975"><span class="lineNum">     975 </span>            :     kIdVfnmadd231ss,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="976"><span class="lineNum">     976 </span>            :     kIdVfnmaddpd,                        // [ANY] {FMA4}</a>
+<a name="977"><span class="lineNum">     977 </span>            :     kIdVfnmaddps,                        // [ANY] {FMA4}</a>
+<a name="978"><span class="lineNum">     978 </span>            :     kIdVfnmaddsd,                        // [ANY] {FMA4}</a>
+<a name="979"><span class="lineNum">     979 </span>            :     kIdVfnmaddss,                        // [ANY] {FMA4}</a>
+<a name="980"><span class="lineNum">     980 </span>            :     kIdVfnmsub132pd,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="981"><span class="lineNum">     981 </span>            :     kIdVfnmsub132ps,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="982"><span class="lineNum">     982 </span>            :     kIdVfnmsub132sd,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="983"><span class="lineNum">     983 </span>            :     kIdVfnmsub132ss,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="984"><span class="lineNum">     984 </span>            :     kIdVfnmsub213pd,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="985"><span class="lineNum">     985 </span>            :     kIdVfnmsub213ps,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="986"><span class="lineNum">     986 </span>            :     kIdVfnmsub213sd,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="987"><span class="lineNum">     987 </span>            :     kIdVfnmsub213ss,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="988"><span class="lineNum">     988 </span>            :     kIdVfnmsub231pd,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="989"><span class="lineNum">     989 </span>            :     kIdVfnmsub231ps,                     // [ANY] {AVX512_F|FMA+VL}</a>
+<a name="990"><span class="lineNum">     990 </span>            :     kIdVfnmsub231sd,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="991"><span class="lineNum">     991 </span>            :     kIdVfnmsub231ss,                     // [ANY] {AVX512_F|FMA}</a>
+<a name="992"><span class="lineNum">     992 </span>            :     kIdVfnmsubpd,                        // [ANY] {FMA4}</a>
+<a name="993"><span class="lineNum">     993 </span>            :     kIdVfnmsubps,                        // [ANY] {FMA4}</a>
+<a name="994"><span class="lineNum">     994 </span>            :     kIdVfnmsubsd,                        // [ANY] {FMA4}</a>
+<a name="995"><span class="lineNum">     995 </span>            :     kIdVfnmsubss,                        // [ANY] {FMA4}</a>
+<a name="996"><span class="lineNum">     996 </span>            :     kIdVfpclasspd,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="997"><span class="lineNum">     997 </span>            :     kIdVfpclassps,                       // [ANY] {AVX512_DQ+VL}</a>
+<a name="998"><span class="lineNum">     998 </span>            :     kIdVfpclasssd,                       // [ANY] {AVX512_DQ}</a>
+<a name="999"><span class="lineNum">     999 </span>            :     kIdVfpclassss,                       // [ANY] {AVX512_DQ}</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :     kIdVfrczpd,                          // [ANY] {XOP}</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :     kIdVfrczps,                          // [ANY] {XOP}</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     kIdVfrczsd,                          // [ANY] {XOP}</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :     kIdVfrczss,                          // [ANY] {XOP}</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :     kIdVgatherdpd,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :     kIdVgatherdps,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :     kIdVgatherpf0dpd,                    // [ANY] {AVX512_PFI}</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :     kIdVgatherpf0dps,                    // [ANY] {AVX512_PFI}</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :     kIdVgatherpf0qpd,                    // [ANY] {AVX512_PFI}</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :     kIdVgatherpf0qps,                    // [ANY] {AVX512_PFI}</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :     kIdVgatherpf1dpd,                    // [ANY] {AVX512_PFI}</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :     kIdVgatherpf1dps,                    // [ANY] {AVX512_PFI}</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :     kIdVgatherpf1qpd,                    // [ANY] {AVX512_PFI}</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :     kIdVgatherpf1qps,                    // [ANY] {AVX512_PFI}</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :     kIdVgatherqpd,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :     kIdVgatherqps,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :     kIdVgetexppd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :     kIdVgetexpps,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :     kIdVgetexpsd,                        // [ANY] {AVX512_F}</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :     kIdVgetexpss,                        // [ANY] {AVX512_F}</a>
+<a name="1020"><span class="lineNum">    1020 </span>            :     kIdVgetmantpd,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :     kIdVgetmantps,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :     kIdVgetmantsd,                       // [ANY] {AVX512_F}</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :     kIdVgetmantss,                       // [ANY] {AVX512_F}</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :     kIdVhaddpd,                          // [ANY] {AVX}</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :     kIdVhaddps,                          // [ANY] {AVX}</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :     kIdVhsubpd,                          // [ANY] {AVX}</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :     kIdVhsubps,                          // [ANY] {AVX}</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     kIdVinsertf128,                      // [ANY] {AVX}</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     kIdVinsertf32x4,                     // [ANY] {AVX512_F+VL}</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     kIdVinsertf32x8,                     // [ANY] {AVX512_DQ}</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :     kIdVinsertf64x2,                     // [ANY] {AVX512_DQ+VL}</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :     kIdVinsertf64x4,                     // [ANY] {AVX512_F}</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :     kIdVinserti128,                      // [ANY] {AVX2}</a>
+<a name="1034"><span class="lineNum">    1034 </span>            :     kIdVinserti32x4,                     // [ANY] {AVX512_F+VL}</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     kIdVinserti32x8,                     // [ANY] {AVX512_DQ}</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :     kIdVinserti64x2,                     // [ANY] {AVX512_DQ+VL}</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     kIdVinserti64x4,                     // [ANY] {AVX512_F}</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :     kIdVinsertps,                        // [ANY] {AVX|AVX512_F}</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :     kIdVlddqu,                           // [ANY] {AVX}</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :     kIdVldmxcsr,                         // [ANY] {AVX}</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     kIdVmaskmovdqu,                      // [ANY] {AVX}</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     kIdVmaskmovpd,                       // [ANY] {AVX}</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :     kIdVmaskmovps,                       // [ANY] {AVX}</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     kIdVmaxpd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     kIdVmaxps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :     kIdVmaxsd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :     kIdVmaxss,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     kIdVminpd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :     kIdVminps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :     kIdVminsd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     kIdVminss,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :     kIdVmovapd,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :     kIdVmovaps,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     kIdVmovd,                            // [ANY] {AVX|AVX512_F}</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :     kIdVmovddup,                         // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :     kIdVmovdqa,                          // [ANY] {AVX}</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :     kIdVmovdqa32,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :     kIdVmovdqa64,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :     kIdVmovdqu,                          // [ANY] {AVX}</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     kIdVmovdqu16,                        // [ANY] {AVX512_BW+VL}</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :     kIdVmovdqu32,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     kIdVmovdqu64,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :     kIdVmovdqu8,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     kIdVmovhlps,                         // [ANY] {AVX|AVX512_F}</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :     kIdVmovhpd,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :     kIdVmovhps,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :     kIdVmovlhps,                         // [ANY] {AVX|AVX512_F}</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     kIdVmovlpd,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :     kIdVmovlps,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :     kIdVmovmskpd,                        // [ANY] {AVX}</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :     kIdVmovmskps,                        // [ANY] {AVX}</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     kIdVmovntdq,                         // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :     kIdVmovntdqa,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :     kIdVmovntpd,                         // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     kIdVmovntps,                         // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :     kIdVmovq,                            // [ANY] {AVX|AVX512_F}</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :     kIdVmovsd,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     kIdVmovshdup,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     kIdVmovsldup,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     kIdVmovss,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     kIdVmovupd,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     kIdVmovups,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :     kIdVmpsadbw,                         // [ANY] {AVX|AVX2}</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :     kIdVmulpd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     kIdVmulps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :     kIdVmulsd,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :     kIdVmulss,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     kIdVorpd,                            // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :     kIdVorps,                            // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :     kIdVp4dpwssd,                        // [ANY] {AVX512_4VNNIW}</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :     kIdVp4dpwssds,                       // [ANY] {AVX512_4VNNIW}</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :     kIdVpabsb,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :     kIdVpabsd,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :     kIdVpabsq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :     kIdVpabsw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :     kIdVpackssdw,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :     kIdVpacksswb,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :     kIdVpackusdw,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :     kIdVpackuswb,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :     kIdVpaddb,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :     kIdVpaddd,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     kIdVpaddq,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :     kIdVpaddsb,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :     kIdVpaddsw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :     kIdVpaddusb,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :     kIdVpaddusw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :     kIdVpaddw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :     kIdVpalignr,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1109"><span class="lineNum">    1109 </span>            :     kIdVpand,                            // [ANY] {AVX|AVX2}</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :     kIdVpandd,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :     kIdVpandn,                           // [ANY] {AVX|AVX2}</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :     kIdVpandnd,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :     kIdVpandnq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :     kIdVpandq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :     kIdVpavgb,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :     kIdVpavgw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     kIdVpblendd,                         // [ANY] {AVX2}</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :     kIdVpblendvb,                        // [ANY] {AVX|AVX2}</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :     kIdVpblendw,                         // [ANY] {AVX|AVX2}</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :     kIdVpbroadcastb,                     // [ANY] {AVX2|AVX512_BW+VL}</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     kIdVpbroadcastd,                     // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     kIdVpbroadcastmb2d,                  // [ANY] {AVX512_CDI+VL}</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :     kIdVpbroadcastmb2q,                  // [ANY] {AVX512_CDI+VL}</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :     kIdVpbroadcastq,                     // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :     kIdVpbroadcastw,                     // [ANY] {AVX2|AVX512_BW+VL}</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :     kIdVpclmulqdq,                       // [ANY] {AVX|PCLMULQDQ}</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :     kIdVpcmov,                           // [ANY] {XOP}</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :     kIdVpcmpb,                           // [ANY] {AVX512_BW+VL}</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :     kIdVpcmpd,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :     kIdVpcmpeqb,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :     kIdVpcmpeqd,                         // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :     kIdVpcmpeqq,                         // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     kIdVpcmpeqw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     kIdVpcmpestri,                       // [ANY] {AVX}</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :     kIdVpcmpestrm,                       // [ANY] {AVX}</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :     kIdVpcmpgtb,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :     kIdVpcmpgtd,                         // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     kIdVpcmpgtq,                         // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :     kIdVpcmpgtw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :     kIdVpcmpistri,                       // [ANY] {AVX}</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     kIdVpcmpistrm,                       // [ANY] {AVX}</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :     kIdVpcmpq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :     kIdVpcmpub,                          // [ANY] {AVX512_BW+VL}</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :     kIdVpcmpud,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :     kIdVpcmpuq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :     kIdVpcmpuw,                          // [ANY] {AVX512_BW+VL}</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :     kIdVpcmpw,                           // [ANY] {AVX512_BW+VL}</a>
+<a name="1148"><span class="lineNum">    1148 </span>            :     kIdVpcomb,                           // [ANY] {XOP}</a>
+<a name="1149"><span class="lineNum">    1149 </span>            :     kIdVpcomd,                           // [ANY] {XOP}</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :     kIdVpcompressd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :     kIdVpcompressq,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :     kIdVpcomq,                           // [ANY] {XOP}</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :     kIdVpcomub,                          // [ANY] {XOP}</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :     kIdVpcomud,                          // [ANY] {XOP}</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :     kIdVpcomuq,                          // [ANY] {XOP}</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     kIdVpcomuw,                          // [ANY] {XOP}</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :     kIdVpcomw,                           // [ANY] {XOP}</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :     kIdVpconflictd,                      // [ANY] {AVX512_CDI+VL}</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :     kIdVpconflictq,                      // [ANY] {AVX512_CDI+VL}</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :     kIdVperm2f128,                       // [ANY] {AVX}</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :     kIdVperm2i128,                       // [ANY] {AVX2}</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :     kIdVpermb,                           // [ANY] {AVX512_VBMI+VL}</a>
+<a name="1163"><span class="lineNum">    1163 </span>            :     kIdVpermd,                           // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     kIdVpermi2b,                         // [ANY] {AVX512_VBMI+VL}</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :     kIdVpermi2d,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :     kIdVpermi2pd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1167"><span class="lineNum">    1167 </span>            :     kIdVpermi2ps,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :     kIdVpermi2q,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :     kIdVpermi2w,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :     kIdVpermil2pd,                       // [ANY] {XOP}</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :     kIdVpermil2ps,                       // [ANY] {XOP}</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :     kIdVpermilpd,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :     kIdVpermilps,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :     kIdVpermpd,                          // [ANY] {AVX2}</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :     kIdVpermps,                          // [ANY] {AVX2}</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     kIdVpermq,                           // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :     kIdVpermt2b,                         // [ANY] {AVX512_VBMI+VL}</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :     kIdVpermt2d,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :     kIdVpermt2pd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1180"><span class="lineNum">    1180 </span>            :     kIdVpermt2ps,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1181"><span class="lineNum">    1181 </span>            :     kIdVpermt2q,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :     kIdVpermt2w,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :     kIdVpermw,                           // [ANY] {AVX512_BW+VL}</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :     kIdVpexpandd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     kIdVpexpandq,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :     kIdVpextrb,                          // [ANY] {AVX|AVX512_BW}</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :     kIdVpextrd,                          // [ANY] {AVX|AVX512_DQ}</a>
+<a name="1188"><span class="lineNum">    1188 </span>            :     kIdVpextrq,                          // [X64] {AVX|AVX512_DQ}</a>
+<a name="1189"><span class="lineNum">    1189 </span>            :     kIdVpextrw,                          // [ANY] {AVX|AVX512_BW}</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     kIdVpgatherdd,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :     kIdVpgatherdq,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :     kIdVpgatherqd,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :     kIdVpgatherqq,                       // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :     kIdVphaddbd,                         // [ANY] {XOP}</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :     kIdVphaddbq,                         // [ANY] {XOP}</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :     kIdVphaddbw,                         // [ANY] {XOP}</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :     kIdVphaddd,                          // [ANY] {AVX|AVX2}</a>
+<a name="1198"><span class="lineNum">    1198 </span>            :     kIdVphadddq,                         // [ANY] {XOP}</a>
+<a name="1199"><span class="lineNum">    1199 </span>            :     kIdVphaddsw,                         // [ANY] {AVX|AVX2}</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :     kIdVphaddubd,                        // [ANY] {XOP}</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :     kIdVphaddubq,                        // [ANY] {XOP}</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :     kIdVphaddubw,                        // [ANY] {XOP}</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :     kIdVphaddudq,                        // [ANY] {XOP}</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     kIdVphadduwd,                        // [ANY] {XOP}</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :     kIdVphadduwq,                        // [ANY] {XOP}</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :     kIdVphaddw,                          // [ANY] {AVX|AVX2}</a>
+<a name="1207"><span class="lineNum">    1207 </span>            :     kIdVphaddwd,                         // [ANY] {XOP}</a>
+<a name="1208"><span class="lineNum">    1208 </span>            :     kIdVphaddwq,                         // [ANY] {XOP}</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :     kIdVphminposuw,                      // [ANY] {AVX}</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :     kIdVphsubbw,                         // [ANY] {XOP}</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :     kIdVphsubd,                          // [ANY] {AVX|AVX2}</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :     kIdVphsubdq,                         // [ANY] {XOP}</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :     kIdVphsubsw,                         // [ANY] {AVX|AVX2}</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :     kIdVphsubw,                          // [ANY] {AVX|AVX2}</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :     kIdVphsubwd,                         // [ANY] {XOP}</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :     kIdVpinsrb,                          // [ANY] {AVX|AVX512_BW}</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :     kIdVpinsrd,                          // [ANY] {AVX|AVX512_DQ}</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :     kIdVpinsrq,                          // [X64] {AVX|AVX512_DQ}</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :     kIdVpinsrw,                          // [ANY] {AVX|AVX512_BW}</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :     kIdVplzcntd,                         // [ANY] {AVX512_CDI+VL}</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :     kIdVplzcntq,                         // [ANY] {AVX512_CDI+VL}</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :     kIdVpmacsdd,                         // [ANY] {XOP}</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :     kIdVpmacsdqh,                        // [ANY] {XOP}</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :     kIdVpmacsdql,                        // [ANY] {XOP}</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :     kIdVpmacssdd,                        // [ANY] {XOP}</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :     kIdVpmacssdqh,                       // [ANY] {XOP}</a>
+<a name="1227"><span class="lineNum">    1227 </span>            :     kIdVpmacssdql,                       // [ANY] {XOP}</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :     kIdVpmacsswd,                        // [ANY] {XOP}</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :     kIdVpmacssww,                        // [ANY] {XOP}</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :     kIdVpmacswd,                         // [ANY] {XOP}</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :     kIdVpmacsww,                         // [ANY] {XOP}</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :     kIdVpmadcsswd,                       // [ANY] {XOP}</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     kIdVpmadcswd,                        // [ANY] {XOP}</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :     kIdVpmadd52huq,                      // [ANY] {AVX512_IFMA+VL}</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :     kIdVpmadd52luq,                      // [ANY] {AVX512_IFMA+VL}</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     kIdVpmaddubsw,                       // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :     kIdVpmaddwd,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :     kIdVpmaskmovd,                       // [ANY] {AVX2}</a>
+<a name="1239"><span class="lineNum">    1239 </span>            :     kIdVpmaskmovq,                       // [ANY] {AVX2}</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :     kIdVpmaxsb,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :     kIdVpmaxsd,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :     kIdVpmaxsq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :     kIdVpmaxsw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :     kIdVpmaxub,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :     kIdVpmaxud,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :     kIdVpmaxuq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :     kIdVpmaxuw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :     kIdVpminsb,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :     kIdVpminsd,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1250"><span class="lineNum">    1250 </span>            :     kIdVpminsq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :     kIdVpminsw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :     kIdVpminub,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :     kIdVpminud,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :     kIdVpminuq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :     kIdVpminuw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :     kIdVpmovb2m,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :     kIdVpmovd2m,                         // [ANY] {AVX512_DQ+VL}</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :     kIdVpmovdb,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :     kIdVpmovdw,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :     kIdVpmovm2b,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :     kIdVpmovm2d,                         // [ANY] {AVX512_DQ+VL}</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :     kIdVpmovm2q,                         // [ANY] {AVX512_DQ+VL}</a>
+<a name="1263"><span class="lineNum">    1263 </span>            :     kIdVpmovm2w,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :     kIdVpmovmskb,                        // [ANY] {AVX|AVX2}</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :     kIdVpmovq2m,                         // [ANY] {AVX512_DQ+VL}</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :     kIdVpmovqb,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :     kIdVpmovqd,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :     kIdVpmovqw,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :     kIdVpmovsdb,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :     kIdVpmovsdw,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :     kIdVpmovsqb,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :     kIdVpmovsqd,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :     kIdVpmovsqw,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :     kIdVpmovswb,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :     kIdVpmovsxbd,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :     kIdVpmovsxbq,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :     kIdVpmovsxbw,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :     kIdVpmovsxdq,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :     kIdVpmovsxwd,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :     kIdVpmovsxwq,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :     kIdVpmovusdb,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1282"><span class="lineNum">    1282 </span>            :     kIdVpmovusdw,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :     kIdVpmovusqb,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :     kIdVpmovusqd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1285"><span class="lineNum">    1285 </span>            :     kIdVpmovusqw,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1286"><span class="lineNum">    1286 </span>            :     kIdVpmovuswb,                        // [ANY] {AVX512_BW+VL}</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :     kIdVpmovw2m,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :     kIdVpmovwb,                          // [ANY] {AVX512_BW+VL}</a>
+<a name="1289"><span class="lineNum">    1289 </span>            :     kIdVpmovzxbd,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :     kIdVpmovzxbq,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     kIdVpmovzxbw,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :     kIdVpmovzxdq,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :     kIdVpmovzxwd,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :     kIdVpmovzxwq,                        // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :     kIdVpmuldq,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1296"><span class="lineNum">    1296 </span>            :     kIdVpmulhrsw,                        // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1297"><span class="lineNum">    1297 </span>            :     kIdVpmulhuw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :     kIdVpmulhw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :     kIdVpmulld,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :     kIdVpmullq,                          // [ANY] {AVX512_DQ+VL}</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :     kIdVpmullw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :     kIdVpmultishiftqb,                   // [ANY] {AVX512_VBMI+VL}</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :     kIdVpmuludq,                         // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :     kIdVpopcntd,                         // [ANY] {AVX512_VPOPCNTDQ}</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :     kIdVpopcntq,                         // [ANY] {AVX512_VPOPCNTDQ}</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :     kIdVpor,                             // [ANY] {AVX|AVX2}</a>
+<a name="1307"><span class="lineNum">    1307 </span>            :     kIdVpord,                            // [ANY] {AVX512_F+VL}</a>
+<a name="1308"><span class="lineNum">    1308 </span>            :     kIdVporq,                            // [ANY] {AVX512_F+VL}</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :     kIdVpperm,                           // [ANY] {XOP}</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :     kIdVprold,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :     kIdVprolq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :     kIdVprolvd,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :     kIdVprolvq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :     kIdVprord,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :     kIdVprorq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :     kIdVprorvd,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :     kIdVprorvq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :     kIdVprotb,                           // [ANY] {XOP}</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :     kIdVprotd,                           // [ANY] {XOP}</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :     kIdVprotq,                           // [ANY] {XOP}</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :     kIdVprotw,                           // [ANY] {XOP}</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :     kIdVpsadbw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :     kIdVpscatterdd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1324"><span class="lineNum">    1324 </span>            :     kIdVpscatterdq,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :     kIdVpscatterqd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :     kIdVpscatterqq,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :     kIdVpshab,                           // [ANY] {XOP}</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :     kIdVpshad,                           // [ANY] {XOP}</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :     kIdVpshaq,                           // [ANY] {XOP}</a>
+<a name="1330"><span class="lineNum">    1330 </span>            :     kIdVpshaw,                           // [ANY] {XOP}</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :     kIdVpshlb,                           // [ANY] {XOP}</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :     kIdVpshld,                           // [ANY] {XOP}</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :     kIdVpshlq,                           // [ANY] {XOP}</a>
+<a name="1334"><span class="lineNum">    1334 </span>            :     kIdVpshlw,                           // [ANY] {XOP}</a>
+<a name="1335"><span class="lineNum">    1335 </span>            :     kIdVpshufb,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :     kIdVpshufd,                          // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :     kIdVpshufhw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1338"><span class="lineNum">    1338 </span>            :     kIdVpshuflw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1339"><span class="lineNum">    1339 </span>            :     kIdVpsignb,                          // [ANY] {AVX|AVX2}</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :     kIdVpsignd,                          // [ANY] {AVX|AVX2}</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :     kIdVpsignw,                          // [ANY] {AVX|AVX2}</a>
+<a name="1342"><span class="lineNum">    1342 </span>            :     kIdVpslld,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :     kIdVpslldq,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :     kIdVpsllq,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1345"><span class="lineNum">    1345 </span>            :     kIdVpsllvd,                          // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1346"><span class="lineNum">    1346 </span>            :     kIdVpsllvq,                          // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :     kIdVpsllvw,                          // [ANY] {AVX512_BW+VL}</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :     kIdVpsllw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :     kIdVpsrad,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :     kIdVpsraq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1351"><span class="lineNum">    1351 </span>            :     kIdVpsravd,                          // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1352"><span class="lineNum">    1352 </span>            :     kIdVpsravq,                          // [ANY] {AVX512_F+VL}</a>
+<a name="1353"><span class="lineNum">    1353 </span>            :     kIdVpsravw,                          // [ANY] {AVX512_BW+VL}</a>
+<a name="1354"><span class="lineNum">    1354 </span>            :     kIdVpsraw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :     kIdVpsrld,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :     kIdVpsrldq,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1357"><span class="lineNum">    1357 </span>            :     kIdVpsrlq,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1358"><span class="lineNum">    1358 </span>            :     kIdVpsrlvd,                          // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :     kIdVpsrlvq,                          // [ANY] {AVX2|AVX512_F+VL}</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :     kIdVpsrlvw,                          // [ANY] {AVX512_BW+VL}</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :     kIdVpsrlw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :     kIdVpsubb,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :     kIdVpsubd,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :     kIdVpsubq,                           // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :     kIdVpsubsb,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :     kIdVpsubsw,                          // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :     kIdVpsubusb,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1368"><span class="lineNum">    1368 </span>            :     kIdVpsubusw,                         // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :     kIdVpsubw,                           // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :     kIdVpternlogd,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :     kIdVpternlogq,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :     kIdVptest,                           // [ANY] {AVX}</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :     kIdVptestmb,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :     kIdVptestmd,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :     kIdVptestmq,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1376"><span class="lineNum">    1376 </span>            :     kIdVptestmw,                         // [ANY] {AVX512_BW+VL}</a>
+<a name="1377"><span class="lineNum">    1377 </span>            :     kIdVptestnmb,                        // [ANY] {AVX512_BW+VL}</a>
+<a name="1378"><span class="lineNum">    1378 </span>            :     kIdVptestnmd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1379"><span class="lineNum">    1379 </span>            :     kIdVptestnmq,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1380"><span class="lineNum">    1380 </span>            :     kIdVptestnmw,                        // [ANY] {AVX512_BW+VL}</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :     kIdVpunpckhbw,                       // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1382"><span class="lineNum">    1382 </span>            :     kIdVpunpckhdq,                       // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1383"><span class="lineNum">    1383 </span>            :     kIdVpunpckhqdq,                      // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :     kIdVpunpckhwd,                       // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1385"><span class="lineNum">    1385 </span>            :     kIdVpunpcklbw,                       // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1386"><span class="lineNum">    1386 </span>            :     kIdVpunpckldq,                       // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :     kIdVpunpcklqdq,                      // [ANY] {AVX|AVX2|AVX512_F+VL}</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :     kIdVpunpcklwd,                       // [ANY] {AVX|AVX2|AVX512_BW+VL}</a>
+<a name="1389"><span class="lineNum">    1389 </span>            :     kIdVpxor,                            // [ANY] {AVX|AVX2}</a>
+<a name="1390"><span class="lineNum">    1390 </span>            :     kIdVpxord,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1391"><span class="lineNum">    1391 </span>            :     kIdVpxorq,                           // [ANY] {AVX512_F+VL}</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :     kIdVrangepd,                         // [ANY] {AVX512_DQ+VL}</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :     kIdVrangeps,                         // [ANY] {AVX512_DQ+VL}</a>
+<a name="1394"><span class="lineNum">    1394 </span>            :     kIdVrangesd,                         // [ANY] {AVX512_DQ}</a>
+<a name="1395"><span class="lineNum">    1395 </span>            :     kIdVrangess,                         // [ANY] {AVX512_DQ}</a>
+<a name="1396"><span class="lineNum">    1396 </span>            :     kIdVrcp14pd,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1397"><span class="lineNum">    1397 </span>            :     kIdVrcp14ps,                         // [ANY] {AVX512_F+VL}</a>
+<a name="1398"><span class="lineNum">    1398 </span>            :     kIdVrcp14sd,                         // [ANY] {AVX512_F}</a>
+<a name="1399"><span class="lineNum">    1399 </span>            :     kIdVrcp14ss,                         // [ANY] {AVX512_F}</a>
+<a name="1400"><span class="lineNum">    1400 </span>            :     kIdVrcp28pd,                         // [ANY] {AVX512_ERI}</a>
+<a name="1401"><span class="lineNum">    1401 </span>            :     kIdVrcp28ps,                         // [ANY] {AVX512_ERI}</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :     kIdVrcp28sd,                         // [ANY] {AVX512_ERI}</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :     kIdVrcp28ss,                         // [ANY] {AVX512_ERI}</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :     kIdVrcpps,                           // [ANY] {AVX}</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :     kIdVrcpss,                           // [ANY] {AVX}</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :     kIdVreducepd,                        // [ANY] {AVX512_DQ+VL}</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :     kIdVreduceps,                        // [ANY] {AVX512_DQ+VL}</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :     kIdVreducesd,                        // [ANY] {AVX512_DQ}</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :     kIdVreducess,                        // [ANY] {AVX512_DQ}</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :     kIdVrndscalepd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1411"><span class="lineNum">    1411 </span>            :     kIdVrndscaleps,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1412"><span class="lineNum">    1412 </span>            :     kIdVrndscalesd,                      // [ANY] {AVX512_F}</a>
+<a name="1413"><span class="lineNum">    1413 </span>            :     kIdVrndscaless,                      // [ANY] {AVX512_F}</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :     kIdVroundpd,                         // [ANY] {AVX}</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :     kIdVroundps,                         // [ANY] {AVX}</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :     kIdVroundsd,                         // [ANY] {AVX}</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :     kIdVroundss,                         // [ANY] {AVX}</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :     kIdVrsqrt14pd,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     kIdVrsqrt14ps,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :     kIdVrsqrt14sd,                       // [ANY] {AVX512_F}</a>
+<a name="1421"><span class="lineNum">    1421 </span>            :     kIdVrsqrt14ss,                       // [ANY] {AVX512_F}</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     kIdVrsqrt28pd,                       // [ANY] {AVX512_ERI}</a>
+<a name="1423"><span class="lineNum">    1423 </span>            :     kIdVrsqrt28ps,                       // [ANY] {AVX512_ERI}</a>
+<a name="1424"><span class="lineNum">    1424 </span>            :     kIdVrsqrt28sd,                       // [ANY] {AVX512_ERI}</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :     kIdVrsqrt28ss,                       // [ANY] {AVX512_ERI}</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :     kIdVrsqrtps,                         // [ANY] {AVX}</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :     kIdVrsqrtss,                         // [ANY] {AVX}</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :     kIdVscalefpd,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :     kIdVscalefps,                        // [ANY] {AVX512_F+VL}</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :     kIdVscalefsd,                        // [ANY] {AVX512_F}</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :     kIdVscalefss,                        // [ANY] {AVX512_F}</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :     kIdVscatterdpd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1433"><span class="lineNum">    1433 </span>            :     kIdVscatterdps,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1434"><span class="lineNum">    1434 </span>            :     kIdVscatterpf0dpd,                   // [ANY] {AVX512_PFI}</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :     kIdVscatterpf0dps,                   // [ANY] {AVX512_PFI}</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :     kIdVscatterpf0qpd,                   // [ANY] {AVX512_PFI}</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :     kIdVscatterpf0qps,                   // [ANY] {AVX512_PFI}</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :     kIdVscatterpf1dpd,                   // [ANY] {AVX512_PFI}</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :     kIdVscatterpf1dps,                   // [ANY] {AVX512_PFI}</a>
+<a name="1440"><span class="lineNum">    1440 </span>            :     kIdVscatterpf1qpd,                   // [ANY] {AVX512_PFI}</a>
+<a name="1441"><span class="lineNum">    1441 </span>            :     kIdVscatterpf1qps,                   // [ANY] {AVX512_PFI}</a>
+<a name="1442"><span class="lineNum">    1442 </span>            :     kIdVscatterqpd,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :     kIdVscatterqps,                      // [ANY] {AVX512_F+VL}</a>
+<a name="1444"><span class="lineNum">    1444 </span>            :     kIdVshuff32x4,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1445"><span class="lineNum">    1445 </span>            :     kIdVshuff64x2,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :     kIdVshufi32x4,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1447"><span class="lineNum">    1447 </span>            :     kIdVshufi64x2,                       // [ANY] {AVX512_F+VL}</a>
+<a name="1448"><span class="lineNum">    1448 </span>            :     kIdVshufpd,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :     kIdVshufps,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :     kIdVsqrtpd,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :     kIdVsqrtps,                          // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :     kIdVsqrtsd,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :     kIdVsqrtss,                          // [ANY] {AVX|AVX512_F}</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :     kIdVstmxcsr,                         // [ANY] {AVX}</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :     kIdVsubpd,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1456"><span class="lineNum">    1456 </span>            :     kIdVsubps,                           // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :     kIdVsubsd,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :     kIdVsubss,                           // [ANY] {AVX|AVX512_F}</a>
+<a name="1459"><span class="lineNum">    1459 </span>            :     kIdVtestpd,                          // [ANY] {AVX}</a>
+<a name="1460"><span class="lineNum">    1460 </span>            :     kIdVtestps,                          // [ANY] {AVX}</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :     kIdVucomisd,                         // [ANY] {AVX|AVX512_F}</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :     kIdVucomiss,                         // [ANY] {AVX|AVX512_F}</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :     kIdVunpckhpd,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1464"><span class="lineNum">    1464 </span>            :     kIdVunpckhps,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :     kIdVunpcklpd,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :     kIdVunpcklps,                        // [ANY] {AVX|AVX512_F+VL}</a>
+<a name="1467"><span class="lineNum">    1467 </span>            :     kIdVxorpd,                           // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :     kIdVxorps,                           // [ANY] {AVX|AVX512_DQ+VL}</a>
+<a name="1469"><span class="lineNum">    1469 </span>            :     kIdVzeroall,                         // [ANY] {AVX}</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :     kIdVzeroupper,                       // [ANY] {AVX}</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :     kIdWbinvd,                           // [ANY]</a>
+<a name="1472"><span class="lineNum">    1472 </span>            :     kIdWrfsbase,                         // [X64] {FSGSBASE}</a>
+<a name="1473"><span class="lineNum">    1473 </span>            :     kIdWrgsbase,                         // [X64] {FSGSBASE}</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :     kIdWrmsr,                            // [ANY] {MSR}</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :     kIdXabort,                           // [ANY] {RTM}</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :     kIdXadd,                             // [ANY] {I486}</a>
+<a name="1477"><span class="lineNum">    1477 </span>            :     kIdXbegin,                           // [ANY] {RTM}</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :     kIdXchg,                             // [ANY]</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :     kIdXend,                             // [ANY] {RTM}</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :     kIdXgetbv,                           // [ANY] {XSAVE}</a>
+<a name="1481"><span class="lineNum">    1481 </span>            :     kIdXlatb,                            // [ANY]</a>
+<a name="1482"><span class="lineNum">    1482 </span>            :     kIdXor,                              // [ANY]</a>
+<a name="1483"><span class="lineNum">    1483 </span>            :     kIdXorpd,                            // [ANY] {SSE2}</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :     kIdXorps,                            // [ANY] {SSE}</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :     kIdXrstor,                           // [ANY] {XSAVE}</a>
+<a name="1486"><span class="lineNum">    1486 </span>            :     kIdXrstor64,                         // [X64] {XSAVE}</a>
+<a name="1487"><span class="lineNum">    1487 </span>            :     kIdXrstors,                          // [ANY] {XSAVES}</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :     kIdXrstors64,                        // [X64] {XSAVES}</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :     kIdXsave,                            // [ANY] {XSAVE}</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :     kIdXsave64,                          // [X64] {XSAVE}</a>
+<a name="1491"><span class="lineNum">    1491 </span>            :     kIdXsavec,                           // [ANY] {XSAVEC}</a>
+<a name="1492"><span class="lineNum">    1492 </span>            :     kIdXsavec64,                         // [X64] {XSAVEC}</a>
+<a name="1493"><span class="lineNum">    1493 </span>            :     kIdXsaveopt,                         // [ANY] {XSAVEOPT}</a>
+<a name="1494"><span class="lineNum">    1494 </span>            :     kIdXsaveopt64,                       // [X64] {XSAVEOPT}</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :     kIdXsaves,                           // [ANY] {XSAVES}</a>
+<a name="1496"><span class="lineNum">    1496 </span>            :     kIdXsaves64,                         // [X64] {XSAVES}</a>
+<a name="1497"><span class="lineNum">    1497 </span>            :     kIdXsetbv,                           // [ANY] {XSAVE}</a>
+<a name="1498"><span class="lineNum">    1498 </span>            :     kIdXtest,                            // [ANY] {TSX}</a>
+<a name="1499"><span class="lineNum">    1499 </span>            :     _kIdCount</a>
+<a name="1500"><span class="lineNum">    1500 </span>            :     // ${idData:End}</a>
+<a name="1501"><span class="lineNum">    1501 </span>            :   };</a>
+<a name="1502"><span class="lineNum">    1502 </span>            : </a>
+<a name="1503"><span class="lineNum">    1503 </span>            :   //! Instruction encodings, used by \ref X86Assembler (AsmJit specific).</a>
+<a name="1504"><span class="lineNum">    1504 </span>            :   ASMJIT_ENUM(EncodingType) {</a>
+<a name="1505"><span class="lineNum">    1505 </span>            :     kEncodingNone = 0,                   //!&lt; Never used.</a>
+<a name="1506"><span class="lineNum">    1506 </span>            :     kEncodingX86Op,                      //!&lt; X86 [OP].</a>
+<a name="1507"><span class="lineNum">    1507 </span>            :     kEncodingX86Op_O,                    //!&lt; X86 [OP] (opcode and /0-7).</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :     kEncodingX86Op_O_I8,                 //!&lt; X86 [OP] (opcode and /0-7 + 8-bit immediate).</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :     kEncodingX86Op_xAX,                  //!&lt; X86 [OP] (implicit or explicit '?AX' form).</a>
+<a name="1510"><span class="lineNum">    1510 </span>            :     kEncodingX86Op_xDX_xAX,              //!&lt; X86 [OP] (implicit or explicit '?DX, ?AX' form).</a>
+<a name="1511"><span class="lineNum">    1511 </span>            :     kEncodingX86Op_ZAX,                  //!&lt; X86 [OP] (implicit or explicit '[EAX|RDX]' form).</a>
+<a name="1512"><span class="lineNum">    1512 </span>            :     kEncodingX86I_xAX,                   //!&lt; X86 [I] (implicit or explicit '?AX' form).</a>
+<a name="1513"><span class="lineNum">    1513 </span>            :     kEncodingX86M,                       //!&lt; X86 [M] (handles 2|4|8-bytes size).</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :     kEncodingX86M_GPB,                   //!&lt; X86 [M] (handles single-byte size).</a>
+<a name="1515"><span class="lineNum">    1515 </span>            :     kEncodingX86M_GPB_MulDiv,            //!&lt; X86 [M] (like GPB, handles implicit|explicit MUL|DIV|IDIV).</a>
+<a name="1516"><span class="lineNum">    1516 </span>            :     kEncodingX86M_Only,                  //!&lt; X86 [M] (restricted to memory operand of any size).</a>
+<a name="1517"><span class="lineNum">    1517 </span>            :     kEncodingX86Rm,                      //!&lt; X86 [RM] (doesn't handle single-byte size).</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :     kEncodingX86Rm_Raw66H,               //!&lt; X86 [RM] (used by LZCNT, POPCNT, and TZCNT).</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :     kEncodingX86Rm_NoRexW,               //!&lt; X86 [RM] (doesn't add REX.W prefix if 64-bit reg is used).</a>
+<a name="1520"><span class="lineNum">    1520 </span>            :     kEncodingX86Mr,                      //!&lt; X86 [MR] (doesn't handle single-byte size).</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :     kEncodingX86Mr_NoSize,               //!&lt; X86 [MR] (doesn't handle any size).</a>
+<a name="1522"><span class="lineNum">    1522 </span>            :     kEncodingX86Arith,                   //!&lt; X86 adc, add, and, cmp, or, sbb, sub, xor.</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :     kEncodingX86Bswap,                   //!&lt; X86 bswap.</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :     kEncodingX86Bt,                      //!&lt; X86 bt, btc, btr, bts.</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :     kEncodingX86Call,                    //!&lt; X86 call.</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :     kEncodingX86Cmpxchg,                 //!&lt; X86 [MR] cmpxchg.</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :     kEncodingX86Crc,                     //!&lt; X86 crc32.</a>
+<a name="1528"><span class="lineNum">    1528 </span>            :     kEncodingX86Enter,                   //!&lt; X86 enter.</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :     kEncodingX86Imul,                    //!&lt; X86 imul.</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :     kEncodingX86In,                      //!&lt; X86 in.</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :     kEncodingX86Ins,                     //!&lt; X86 ins[b|q|d].</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :     kEncodingX86IncDec,                  //!&lt; X86 inc, dec.</a>
+<a name="1533"><span class="lineNum">    1533 </span>            :     kEncodingX86Int,                     //!&lt; X86 int (interrupt).</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :     kEncodingX86Jcc,                     //!&lt; X86 jcc.</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :     kEncodingX86JecxzLoop,               //!&lt; X86 jcxz, jecxz, jrcxz, loop, loope, loopne.</a>
+<a name="1536"><span class="lineNum">    1536 </span>            :     kEncodingX86Jmp,                     //!&lt; X86 jmp.</a>
+<a name="1537"><span class="lineNum">    1537 </span>            :     kEncodingX86JmpRel,                  //!&lt; X86 xbegin.</a>
+<a name="1538"><span class="lineNum">    1538 </span>            :     kEncodingX86Lea,                     //!&lt; X86 lea.</a>
+<a name="1539"><span class="lineNum">    1539 </span>            :     kEncodingX86Mov,                     //!&lt; X86 mov (all possible cases).</a>
+<a name="1540"><span class="lineNum">    1540 </span>            :     kEncodingX86MovsxMovzx,              //!&lt; X86 movsx, movzx.</a>
+<a name="1541"><span class="lineNum">    1541 </span>            :     kEncodingX86Out,                     //!&lt; X86 out.</a>
+<a name="1542"><span class="lineNum">    1542 </span>            :     kEncodingX86Outs,                    //!&lt; X86 out[b|q|d].</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :     kEncodingX86Push,                    //!&lt; X86 push.</a>
+<a name="1544"><span class="lineNum">    1544 </span>            :     kEncodingX86Pop,                     //!&lt; X86 pop.</a>
+<a name="1545"><span class="lineNum">    1545 </span>            :     kEncodingX86Ret,                     //!&lt; X86 ret.</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :     kEncodingX86Rot,                     //!&lt; X86 rcl, rcr, rol, ror, sal, sar, shl, shr.</a>
+<a name="1547"><span class="lineNum">    1547 </span>            :     kEncodingX86Set,                     //!&lt; X86 setcc.</a>
+<a name="1548"><span class="lineNum">    1548 </span>            :     kEncodingX86ShldShrd,                //!&lt; X86 shld, shrd.</a>
+<a name="1549"><span class="lineNum">    1549 </span>            :     kEncodingX86StrRm,                   //!&lt; X86 lods.</a>
+<a name="1550"><span class="lineNum">    1550 </span>            :     kEncodingX86StrMr,                   //!&lt; X86 scas, stos.</a>
+<a name="1551"><span class="lineNum">    1551 </span>            :     kEncodingX86StrMm,                   //!&lt; X86 cmps, movs.</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :     kEncodingX86Test,                    //!&lt; X86 test.</a>
+<a name="1553"><span class="lineNum">    1553 </span>            :     kEncodingX86Xadd,                    //!&lt; X86 xadd.</a>
+<a name="1554"><span class="lineNum">    1554 </span>            :     kEncodingX86Xchg,                    //!&lt; X86 xchg.</a>
+<a name="1555"><span class="lineNum">    1555 </span>            :     kEncodingX86Fence,                   //!&lt; X86 lfence, mfence, sfence.</a>
+<a name="1556"><span class="lineNum">    1556 </span>            :     kEncodingX86Bndmov,                  //!&lt; X86 [RM|MR] (used by BNDMOV).</a>
+<a name="1557"><span class="lineNum">    1557 </span>            :     kEncodingFpuOp,                      //!&lt; FPU [OP].</a>
+<a name="1558"><span class="lineNum">    1558 </span>            :     kEncodingFpuArith,                   //!&lt; FPU fadd, fdiv, fdivr, fmul, fsub, fsubr.</a>
+<a name="1559"><span class="lineNum">    1559 </span>            :     kEncodingFpuCom,                     //!&lt; FPU fcom, fcomp.</a>
+<a name="1560"><span class="lineNum">    1560 </span>            :     kEncodingFpuFldFst,                  //!&lt; FPU fld, fst, fstp.</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :     kEncodingFpuM,                       //!&lt; FPU fiadd, ficom, ficomp, fidiv, fidivr, fild, fimul, fist, fistp, fisttp, fisub, fisubr.</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :     kEncodingFpuR,                       //!&lt; FPU fcmov, fcomi, fcomip, ffree, fucom, fucomi, fucomip, fucomp, fxch.</a>
+<a name="1563"><span class="lineNum">    1563 </span>            :     kEncodingFpuRDef,                    //!&lt; FPU faddp, fdivp, fdivrp, fmulp, fsubp, fsubrp.</a>
+<a name="1564"><span class="lineNum">    1564 </span>            :     kEncodingFpuStsw,                    //!&lt; FPU fnstsw, Fstsw.</a>
+<a name="1565"><span class="lineNum">    1565 </span>            :     kEncodingExtRm,                      //!&lt; EXT [RM].</a>
+<a name="1566"><span class="lineNum">    1566 </span>            :     kEncodingExtRm_XMM0,                 //!&lt; EXT [RM&lt;XMM0&gt;].</a>
+<a name="1567"><span class="lineNum">    1567 </span>            :     kEncodingExtRm_ZDI,                  //!&lt; EXT [RM&lt;ZDI&gt;].</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :     kEncodingExtRm_P,                    //!&lt; EXT [RM] (propagates 66H if the instruction uses XMM register).</a>
+<a name="1569"><span class="lineNum">    1569 </span>            :     kEncodingExtRm_Wx,                   //!&lt; EXT [RM] (propagates REX.W if GPQ is used).</a>
+<a name="1570"><span class="lineNum">    1570 </span>            :     kEncodingExtRmRi,                    //!&lt; EXT [RM|RI].</a>
+<a name="1571"><span class="lineNum">    1571 </span>            :     kEncodingExtRmRi_P,                  //!&lt; EXT [RM|RI] (propagates 66H if the instruction uses XMM register).</a>
+<a name="1572"><span class="lineNum">    1572 </span>            :     kEncodingExtRmi,                     //!&lt; EXT [RMI].</a>
+<a name="1573"><span class="lineNum">    1573 </span>            :     kEncodingExtRmi_P,                   //!&lt; EXT [RMI] (propagates 66H if the instruction uses XMM register).</a>
+<a name="1574"><span class="lineNum">    1574 </span>            :     kEncodingExtPextrw,                  //!&lt; EXT pextrw.</a>
+<a name="1575"><span class="lineNum">    1575 </span>            :     kEncodingExtExtract,                 //!&lt; EXT pextrb, pextrd, pextrq, extractps.</a>
+<a name="1576"><span class="lineNum">    1576 </span>            :     kEncodingExtMov,                     //!&lt; EXT mov?? - #1:[MM|XMM, MM|XMM|Mem] #2:[MM|XMM|Mem, MM|XMM].</a>
+<a name="1577"><span class="lineNum">    1577 </span>            :     kEncodingExtMovnti,                  //!&lt; EXT movnti.</a>
+<a name="1578"><span class="lineNum">    1578 </span>            :     kEncodingExtMovbe,                   //!&lt; EXT movbe.</a>
+<a name="1579"><span class="lineNum">    1579 </span>            :     kEncodingExtMovd,                    //!&lt; EXT movd.</a>
+<a name="1580"><span class="lineNum">    1580 </span>            :     kEncodingExtMovq,                    //!&lt; EXT movq.</a>
+<a name="1581"><span class="lineNum">    1581 </span>            :     kEncodingExtExtrq,                   //!&lt; EXT extrq (SSE4A).</a>
+<a name="1582"><span class="lineNum">    1582 </span>            :     kEncodingExtInsertq,                 //!&lt; EXT insrq (SSE4A).</a>
+<a name="1583"><span class="lineNum">    1583 </span>            :     kEncodingExt3dNow,                   //!&lt; EXT [RMI] (3DNOW specific).</a>
+<a name="1584"><span class="lineNum">    1584 </span>            :     kEncodingVexOp,                      //!&lt; VEX [OP].</a>
+<a name="1585"><span class="lineNum">    1585 </span>            :     kEncodingVexKmov,                    //!&lt; VEX [RM|MR] (used by kmov[b|w|d|q]).</a>
+<a name="1586"><span class="lineNum">    1586 </span>            :     kEncodingVexM,                       //!&lt; VEX|EVEX [M].</a>
+<a name="1587"><span class="lineNum">    1587 </span>            :     kEncodingVexM_VM,                    //!&lt; VEX|EVEX [M] (propagates VEX|EVEX.L, VSIB support).</a>
+<a name="1588"><span class="lineNum">    1588 </span>            :     kEncodingVexMr_Lx,                   //!&lt; VEX|EVEX [MR] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1589"><span class="lineNum">    1589 </span>            :     kEncodingVexMr_VM,                   //!&lt; VEX|EVEX [MR] (propagates VEX|EVEX.L, VSIB support).</a>
+<a name="1590"><span class="lineNum">    1590 </span>            :     kEncodingVexMri,                     //!&lt; VEX|EVEX [MRI].</a>
+<a name="1591"><span class="lineNum">    1591 </span>            :     kEncodingVexMri_Lx,                  //!&lt; VEX|EVEX [MRI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1592"><span class="lineNum">    1592 </span>            :     kEncodingVexRm,                      //!&lt; VEX|EVEX [RM].</a>
+<a name="1593"><span class="lineNum">    1593 </span>            :     kEncodingVexRm_ZDI,                  //!&lt; VEX|EVEX [RM&lt;ZDI&gt;].</a>
+<a name="1594"><span class="lineNum">    1594 </span>            :     kEncodingVexRm_Wx,                   //!&lt; VEX|EVEX [RM] (propagates VEX|EVEX.W if GPQ used).</a>
+<a name="1595"><span class="lineNum">    1595 </span>            :     kEncodingVexRm_Lx,                   //!&lt; VEX|EVEX [RM] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1596"><span class="lineNum">    1596 </span>            :     kEncodingVexRm_VM,                   //!&lt; VEX|EVEX [RM] (propagates VEX|EVEX.L, VSIB support).</a>
+<a name="1597"><span class="lineNum">    1597 </span>            :     kEncodingVexRm_T1_4X,                //!&lt;     EVEX [RM] (used by NN instructions that use RM-T1_4X encoding).</a>
+<a name="1598"><span class="lineNum">    1598 </span>            :     kEncodingVexRmi,                     //!&lt; VEX|EVEX [RMI].</a>
+<a name="1599"><span class="lineNum">    1599 </span>            :     kEncodingVexRmi_Wx,                  //!&lt; VEX|EVEX [RMI] (propagates VEX|EVEX.W if GPQ used).</a>
+<a name="1600"><span class="lineNum">    1600 </span>            :     kEncodingVexRmi_Lx,                  //!&lt; VEX|EVEX [RMI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1601"><span class="lineNum">    1601 </span>            :     kEncodingVexRvm,                     //!&lt; VEX|EVEX [RVM].</a>
+<a name="1602"><span class="lineNum">    1602 </span>            :     kEncodingVexRvm_Wx,                  //!&lt; VEX|EVEX [RVM] (propagates VEX|EVEX.W if GPQ used).</a>
+<a name="1603"><span class="lineNum">    1603 </span>            :     kEncodingVexRvm_ZDX_Wx,              //!&lt; VEX|EVEX [RVM&lt;ZDX&gt;] (propagates VEX|EVEX.W if GPQ used).</a>
+<a name="1604"><span class="lineNum">    1604 </span>            :     kEncodingVexRvm_Lx,                  //!&lt; VEX|EVEX [RVM] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :     kEncodingVexRvmr,                    //!&lt; VEX|EVEX [RVMR].</a>
+<a name="1606"><span class="lineNum">    1606 </span>            :     kEncodingVexRvmr_Lx,                 //!&lt; VEX|EVEX [RVMR] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1607"><span class="lineNum">    1607 </span>            :     kEncodingVexRvmi,                    //!&lt; VEX|EVEX [RVMI].</a>
+<a name="1608"><span class="lineNum">    1608 </span>            :     kEncodingVexRvmi_Lx,                 //!&lt; VEX|EVEX [RVMI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1609"><span class="lineNum">    1609 </span>            :     kEncodingVexRmv,                     //!&lt; VEX|EVEX [RMV].</a>
+<a name="1610"><span class="lineNum">    1610 </span>            :     kEncodingVexRmv_Wx,                  //!&lt; VEX|EVEX [RMV] (propagates VEX|EVEX.W if GPQ used).</a>
+<a name="1611"><span class="lineNum">    1611 </span>            :     kEncodingVexRmv_VM,                  //!&lt; VEX|EVEX [RMV] (propagates VEX|EVEX.L, VSIB support).</a>
+<a name="1612"><span class="lineNum">    1612 </span>            :     kEncodingVexRmvRm_VM,                //!&lt; VEX|EVEX [RMV|RM] (propagates VEX|EVEX.L, VSIB support).</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :     kEncodingVexRmvi,                    //!&lt; VEX|EVEX [RMVI].</a>
+<a name="1614"><span class="lineNum">    1614 </span>            :     kEncodingVexRmMr,                    //!&lt; VEX|EVEX [RM|MR].</a>
+<a name="1615"><span class="lineNum">    1615 </span>            :     kEncodingVexRmMr_Lx,                 //!&lt; VEX|EVEX [RM|MR] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1616"><span class="lineNum">    1616 </span>            :     kEncodingVexRvmRmv,                  //!&lt; VEX|EVEX [RVM|RMV].</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :     kEncodingVexRvmRmi,                  //!&lt; VEX|EVEX [RVM|RMI].</a>
+<a name="1618"><span class="lineNum">    1618 </span>            :     kEncodingVexRvmRmi_Lx,               //!&lt; VEX|EVEX [RVM|RMI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1619"><span class="lineNum">    1619 </span>            :     kEncodingVexRvmRmvRmi,               //!&lt; VEX|EVEX [RVM|RMV|RMI].</a>
+<a name="1620"><span class="lineNum">    1620 </span>            :     kEncodingVexRvmMr,                   //!&lt; VEX|EVEX [RVM|MR].</a>
+<a name="1621"><span class="lineNum">    1621 </span>            :     kEncodingVexRvmMvr,                  //!&lt; VEX|EVEX [RVM|MVR].</a>
+<a name="1622"><span class="lineNum">    1622 </span>            :     kEncodingVexRvmMvr_Lx,               //!&lt; VEX|EVEX [RVM|MVR] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1623"><span class="lineNum">    1623 </span>            :     kEncodingVexRvmVmi,                  //!&lt; VEX|EVEX [RVM|VMI].</a>
+<a name="1624"><span class="lineNum">    1624 </span>            :     kEncodingVexRvmVmi_Lx,               //!&lt; VEX|EVEX [RVM|VMI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1625"><span class="lineNum">    1625 </span>            :     kEncodingVexVm,                      //!&lt; VEX|EVEX [VM].</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :     kEncodingVexVm_Wx,                   //!&lt; VEX|EVEX [VM] (propagates VEX|EVEX.W if GPQ used).</a>
+<a name="1627"><span class="lineNum">    1627 </span>            :     kEncodingVexVmi,                     //!&lt; VEX|EVEX [VMI].</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :     kEncodingVexVmi_Lx,                  //!&lt; VEX|EVEX [VMI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :     kEncodingVexEvexVmi_Lx,              //!&lt; VEX|EVEX [VMI] (special, used by vpsrldq and vpslldq)</a>
+<a name="1630"><span class="lineNum">    1630 </span>            :     kEncodingVexRvrmRvmr,                //!&lt; VEX|EVEX [RVRM|RVMR].</a>
+<a name="1631"><span class="lineNum">    1631 </span>            :     kEncodingVexRvrmRvmr_Lx,             //!&lt; VEX|EVEX [RVRM|RVMR] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1632"><span class="lineNum">    1632 </span>            :     kEncodingVexRvrmiRvmri_Lx,           //!&lt; VEX|EVEX [RVRMI|RVMRI] (propagates VEX|EVEX.L if YMM used).</a>
+<a name="1633"><span class="lineNum">    1633 </span>            :     kEncodingVexMovdMovq,                //!&lt; VEX|EVEX vmovd, vmovq.</a>
+<a name="1634"><span class="lineNum">    1634 </span>            :     kEncodingVexMovssMovsd,              //!&lt; VEX|EVEX vmovss, vmovsd.</a>
+<a name="1635"><span class="lineNum">    1635 </span>            :     kEncodingFma4,                       //!&lt; FMA4 [R, R, R/M, R/M].</a>
+<a name="1636"><span class="lineNum">    1636 </span>            :     kEncodingFma4_Lx,                    //!&lt; FMA4 [R, R, R/M, R/M] (propagates AVX.L if YMM used).</a>
+<a name="1637"><span class="lineNum">    1637 </span>            :     _kEncodingCount                      //!&lt; Count of instruction encodings.</a>
+<a name="1638"><span class="lineNum">    1638 </span>            :   };</a>
+<a name="1639"><span class="lineNum">    1639 </span>            : </a>
+<a name="1640"><span class="lineNum">    1640 </span>            :   //! Describes a meaning of all bits of AsmJit's 32-bit opcode (AsmJit specific).</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :   //!</a>
+<a name="1642"><span class="lineNum">    1642 </span>            :   //! This schema is AsmJit specific and has been designed to allow encoding of</a>
+<a name="1643"><span class="lineNum">    1643 </span>            :   //! all X86 instructions available. X86, MMX, and SSE+ instructions always use</a>
+<a name="1644"><span class="lineNum">    1644 </span>            :   //! `MM` and `PP` fields, which are encoded to corresponding prefixes needed</a>
+<a name="1645"><span class="lineNum">    1645 </span>            :   //! by X86 or SIMD instructions. AVX+ instructions embed `MMMMM` and `PP` fields</a>
+<a name="1646"><span class="lineNum">    1646 </span>            :   //! in a VEX prefix, and AVX-512 instructions embed `MM` and `PP` in EVEX prefix.</a>
+<a name="1647"><span class="lineNum">    1647 </span>            :   //!</a>
+<a name="1648"><span class="lineNum">    1648 </span>            :   //! The instruction opcode definition uses 1 or 2 bytes as an opcode value. 1</a>
+<a name="1649"><span class="lineNum">    1649 </span>            :   //! byte is needed by most of the instructions, 2 bytes are only used by legacy</a>
+<a name="1650"><span class="lineNum">    1650 </span>            :   //! X87-FPU instructions. This means that a second byte is free to by used by</a>
+<a name="1651"><span class="lineNum">    1651 </span>            :   //! instructions encoded by using VEX and/or EVEX prefix.</a>
+<a name="1652"><span class="lineNum">    1652 </span>            :   //!</a>
+<a name="1653"><span class="lineNum">    1653 </span>            :   //! The fields description:</a>
+<a name="1654"><span class="lineNum">    1654 </span>            :   //!</a>
+<a name="1655"><span class="lineNum">    1655 </span>            :   //! - `MM` field is used to encode prefixes needed by the instruction or as</a>
+<a name="1656"><span class="lineNum">    1656 </span>            :   //!   a part of VEX/EVEX prefix. Described as `mm` and `mmmmm` in instruction</a>
+<a name="1657"><span class="lineNum">    1657 </span>            :   //!   manuals.</a>
+<a name="1658"><span class="lineNum">    1658 </span>            :   //!</a>
+<a name="1659"><span class="lineNum">    1659 </span>            :   //!   NOTE: Since `MM` field is defined as `mmmmm` (5 bits), but only 2 least</a>
+<a name="1660"><span class="lineNum">    1660 </span>            :   //!   significant bits are used by VEX and EVEX prefixes, and additional 4th</a>
+<a name="1661"><span class="lineNum">    1661 </span>            :   //!   bit is used by XOP prefix, AsmJit uses the 3rd and 5th bit for it's own</a>
+<a name="1662"><span class="lineNum">    1662 </span>            :   //!   purposes. These bits will probably never be used in future encodings as</a>
+<a name="1663"><span class="lineNum">    1663 </span>            :   //!   AVX512 uses only `000mm` from `mmmmm`.</a>
+<a name="1664"><span class="lineNum">    1664 </span>            :   //!</a>
+<a name="1665"><span class="lineNum">    1665 </span>            :   //! - `PP` field is used to encode prefixes needed by the instruction or as a</a>
+<a name="1666"><span class="lineNum">    1666 </span>            :   //!   part of VEX/EVEX prefix. Described as `pp` in instruction manuals.</a>
+<a name="1667"><span class="lineNum">    1667 </span>            :   //!</a>
+<a name="1668"><span class="lineNum">    1668 </span>            :   //! - `LL` field is used exclusively by AVX+ and AVX512+ instruction sets. It</a>
+<a name="1669"><span class="lineNum">    1669 </span>            :   //!   describes vector size, which is `L.128` for XMM register, `L.256` for</a>
+<a name="1670"><span class="lineNum">    1670 </span>            :   //!   for YMM register, and `L.512` for ZMM register. The `LL` field is omitted</a>
+<a name="1671"><span class="lineNum">    1671 </span>            :   //!   in case that instruction supports multiple vector lengths, however, if the</a>
+<a name="1672"><span class="lineNum">    1672 </span>            :   //!   instruction requires specific `L` value it must be specified as a part of</a>
+<a name="1673"><span class="lineNum">    1673 </span>            :   //!   the opcode.</a>
+<a name="1674"><span class="lineNum">    1674 </span>            :   //!</a>
+<a name="1675"><span class="lineNum">    1675 </span>            :   //!   NOTE: `LL` having value `11` is not defined yet.</a>
+<a name="1676"><span class="lineNum">    1676 </span>            :   //!</a>
+<a name="1677"><span class="lineNum">    1677 </span>            :   //! - `W` field is the most complicated. It was added by 64-bit architecture</a>
+<a name="1678"><span class="lineNum">    1678 </span>            :   //!   to promote default operation width (instructions that perform 32-bit</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :   //!   operation by default require to override the width to 64-bit explicitly).</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :   //!   There is nothing wrong on this, however, some instructions introduced</a>
+<a name="1681"><span class="lineNum">    1681 </span>            :   //!   implicit `W` override, for example a `cdqe` instruction is basically a</a>
+<a name="1682"><span class="lineNum">    1682 </span>            :   //!   `cwde` instruction with overridden `W` (set to 1). There are some others</a>
+<a name="1683"><span class="lineNum">    1683 </span>            :   //!   in the base X86 instruction set. More recent instruction sets started</a>
+<a name="1684"><span class="lineNum">    1684 </span>            :   //!   using `W` field more often:</a>
+<a name="1685"><span class="lineNum">    1685 </span>            :   //!</a>
+<a name="1686"><span class="lineNum">    1686 </span>            :   //!   - AVX instructions started using `W` field as an extended opcode for FMA,</a>
+<a name="1687"><span class="lineNum">    1687 </span>            :   //!     GATHER, PERM, and other instructions. It also uses `W` field to override</a>
+<a name="1688"><span class="lineNum">    1688 </span>            :   //!     the default operation width in instructions like `vmovq`.</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :   //!</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :   //!   - AVX-512 instructions started using `W` field as an extended opcode for</a>
+<a name="1691"><span class="lineNum">    1691 </span>            :   //!     all new instructions. This wouldn't have been an issue if the `W` field</a>
+<a name="1692"><span class="lineNum">    1692 </span>            :   //!     of AVX-512 have matched AVX, but this is not always the case.</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :   //!</a>
+<a name="1694"><span class="lineNum">    1694 </span>            :   //! - `O` field is an extended opcode field (3 bits) embedded in ModR/M BYTE.</a>
+<a name="1695"><span class="lineNum">    1695 </span>            :   //!</a>
+<a name="1696"><span class="lineNum">    1696 </span>            :   //! - `CDSHL` and `CDTT` fields describe 'compressed-displacement'. `CDSHL` is</a>
+<a name="1697"><span class="lineNum">    1697 </span>            :   //!   defined for each instruction that is AVX-512 encodable (EVEX) and contains</a>
+<a name="1698"><span class="lineNum">    1698 </span>            :   //!   a base N shift (base shift to perform the calculation). The `CDTT` field</a>
+<a name="1699"><span class="lineNum">    1699 </span>            :   //!   is derived from instruction specification and describes additional shift</a>
+<a name="1700"><span class="lineNum">    1700 </span>            :   //!   to calculate the final `CDSHL` that will be used in SIB byte.</a>
+<a name="1701"><span class="lineNum">    1701 </span>            :   //!</a>
+<a name="1702"><span class="lineNum">    1702 </span>            :   //! NOTE: Don't reorder any fields here, the shifts and masks were defined</a>
+<a name="1703"><span class="lineNum">    1703 </span>            :   //! carefully to make encoding of X86|X64 instructions fast, especially to</a>
+<a name="1704"><span class="lineNum">    1704 </span>            :   //! construct REX, VEX, and EVEX prefixes in the most efficient way. Changing</a>
+<a name="1705"><span class="lineNum">    1705 </span>            :   //! values defined by these enums many cause AsmJit to emit invalid binary</a>
+<a name="1706"><span class="lineNum">    1706 </span>            :   //! representations of instructions passed to `X86Assembler::_emit`.</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :   ASMJIT_ENUM(OpCodeBits) {</a>
+<a name="1708"><span class="lineNum">    1708 </span>            :     // MM &amp; VEX &amp; EVEX &amp; XOP</a>
+<a name="1709"><span class="lineNum">    1709 </span>            :     // ---------------------</a>
+<a name="1710"><span class="lineNum">    1710 </span>            :     //</a>
+<a name="1711"><span class="lineNum">    1711 </span>            :     // Two meanings:</a>
+<a name="1712"><span class="lineNum">    1712 </span>            :     //  * `MMMMM` field in AVX/XOP/AVX-512 instruction.</a>
+<a name="1713"><span class="lineNum">    1713 </span>            :     //  * Part of the opcode in legacy encoding (bytes emitted before the main</a>
+<a name="1714"><span class="lineNum">    1714 </span>            :     //    opcode byte).</a>
+<a name="1715"><span class="lineNum">    1715 </span>            :     //</a>
+<a name="1716"><span class="lineNum">    1716 </span>            :     // AVX reserves 5 bits for `MMMMM` field, however AVX instructions only use</a>
+<a name="1717"><span class="lineNum">    1717 </span>            :     // 2 bits and XOP 3 bits. AVX-512 shrinks `MMMMM` field into `MM` so it's</a>
+<a name="1718"><span class="lineNum">    1718 </span>            :     // safe to assume that bits [4:2] of `MM` field won't be used in future</a>
+<a name="1719"><span class="lineNum">    1719 </span>            :     // extensions, which will most probably use EVEX encoding. AsmJit divides</a>
+<a name="1720"><span class="lineNum">    1720 </span>            :     // MM field into this layout:</a>
+<a name="1721"><span class="lineNum">    1721 </span>            :     //</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :     // [1:0] - Used to describe 0F, 0F38 and 0F3A legacy prefix bytes and</a>
+<a name="1723"><span class="lineNum">    1723 </span>            :     //         2 bits of MM field.</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :     // [2]   - Used to force 3-BYTE VEX prefix, but then cleared to zero before</a>
+<a name="1725"><span class="lineNum">    1725 </span>            :     //         the prefix is emitted. This bit is not used by any instruction</a>
+<a name="1726"><span class="lineNum">    1726 </span>            :     //         so it can be used for any purpose by AsmJit. Also, this bit is</a>
+<a name="1727"><span class="lineNum">    1727 </span>            :     //         used as an extension to `MM` field describing 0F|0F38|0F3A to also</a>
+<a name="1728"><span class="lineNum">    1728 </span>            :     //         describe 0F01 as used by some legacy instructions (instructions</a>
+<a name="1729"><span class="lineNum">    1729 </span>            :     //         not using VEX/EVEX prefix).</a>
+<a name="1730"><span class="lineNum">    1730 </span>            :     // [3]   - Required by XOP instructions, so we use this bit also to indicate</a>
+<a name="1731"><span class="lineNum">    1731 </span>            :     //         that this is a XOP opcode.</a>
+<a name="1732"><span class="lineNum">    1732 </span>            :     kOpCode_MM_Shift      = 8,</a>
+<a name="1733"><span class="lineNum">    1733 </span>            :     kOpCode_MM_Mask       = 0x1FU &lt;&lt; kOpCode_MM_Shift,</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :     kOpCode_MM_00         = 0x00U &lt;&lt; kOpCode_MM_Shift,</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :     kOpCode_MM_0F         = 0x01U &lt;&lt; kOpCode_MM_Shift,</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :     kOpCode_MM_0F38       = 0x02U &lt;&lt; kOpCode_MM_Shift,</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :     kOpCode_MM_0F3A       = 0x03U &lt;&lt; kOpCode_MM_Shift, // Described also as XOP.M3 in AMD manuals.</a>
+<a name="1738"><span class="lineNum">    1738 </span>            :     kOpCode_MM_0F01       = 0x04U &lt;&lt; kOpCode_MM_Shift, // AsmJit way to describe 0F01 (never VEX/EVEX).</a>
+<a name="1739"><span class="lineNum">    1739 </span>            : </a>
+<a name="1740"><span class="lineNum">    1740 </span>            :     // `XOP` field is only used to force XOP prefix instead of VEX3 prefix. We</a>
+<a name="1741"><span class="lineNum">    1741 </span>            :     // know that only XOP encoding uses bit 0b1000 of MM field and that no VEX</a>
+<a name="1742"><span class="lineNum">    1742 </span>            :     // and EVEX instruction uses such bit, so we can use this bit to force XOP</a>
+<a name="1743"><span class="lineNum">    1743 </span>            :     // prefix to be emitted instead of VEX3 prefix. See `x86VEXPrefix` defined</a>
+<a name="1744"><span class="lineNum">    1744 </span>            :     // in `x86assembler.cpp`.</a>
+<a name="1745"><span class="lineNum">    1745 </span>            :     kOpCode_MM_XOP08      = 0x08U &lt;&lt; kOpCode_MM_Shift, // XOP.M8.</a>
+<a name="1746"><span class="lineNum">    1746 </span>            :     kOpCode_MM_XOP09      = 0x09U &lt;&lt; kOpCode_MM_Shift, // XOP.M9.</a>
+<a name="1747"><span class="lineNum">    1747 </span>            : </a>
+<a name="1748"><span class="lineNum">    1748 </span>            :     kOpCode_MM_IsXOP_Shift= kOpCode_MM_Shift + 3,</a>
+<a name="1749"><span class="lineNum">    1749 </span>            :     kOpCode_MM_IsXOP      = kOpCode_MM_XOP08,</a>
+<a name="1750"><span class="lineNum">    1750 </span>            : </a>
+<a name="1751"><span class="lineNum">    1751 </span>            :     // NOTE: Force VEX3 allows to force to emit VEX3 instead of VEX2 in some</a>
+<a name="1752"><span class="lineNum">    1752 </span>            :     // cases (similar to forcing REX prefix). Force EVEX will force emitting</a>
+<a name="1753"><span class="lineNum">    1753 </span>            :     // EVEX prefix instead of VEX2|VEX3. EVEX-only instructions will have</a>
+<a name="1754"><span class="lineNum">    1754 </span>            :     // ForceEvex always set, however. instructions that can be encoded by</a>
+<a name="1755"><span class="lineNum">    1755 </span>            :     // either VEX or EVEX prefix shall not have ForceEvex set.</a>
+<a name="1756"><span class="lineNum">    1756 </span>            : </a>
+<a name="1757"><span class="lineNum">    1757 </span>            :     kOpCode_MM_ForceVex3  = 0x04U &lt;&lt; kOpCode_MM_Shift, // Force 3-BYTE VEX prefix.</a>
+<a name="1758"><span class="lineNum">    1758 </span>            :     kOpCode_MM_ForceEvex  = 0x10U &lt;&lt; kOpCode_MM_Shift, // Force 4-BYTE EVEX prefix.</a>
+<a name="1759"><span class="lineNum">    1759 </span>            : </a>
+<a name="1760"><span class="lineNum">    1760 </span>            :     // FPU_2B - Second-Byte of OpCode used by FPU</a>
+<a name="1761"><span class="lineNum">    1761 </span>            :     // ------------------------------------------</a>
+<a name="1762"><span class="lineNum">    1762 </span>            :     //</a>
+<a name="1763"><span class="lineNum">    1763 </span>            :     // Second byte opcode. This BYTE is ONLY used by FPU instructions and</a>
+<a name="1764"><span class="lineNum">    1764 </span>            :     // collides with 3 bits from `MM` and 5 bits from 'CDSHL' and 'CDTT'.</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :     // It's fine as FPU and AVX512 flags are never used at the same time.</a>
+<a name="1766"><span class="lineNum">    1766 </span>            :     kOpCode_FPU_2B_Shift  = 10,</a>
+<a name="1767"><span class="lineNum">    1767 </span>            :     kOpCode_FPU_2B_Mask   = 0xFF &lt;&lt; kOpCode_FPU_2B_Shift,</a>
+<a name="1768"><span class="lineNum">    1768 </span>            : </a>
+<a name="1769"><span class="lineNum">    1769 </span>            :     // CDSHL &amp; CDTT</a>
+<a name="1770"><span class="lineNum">    1770 </span>            :     // ------------</a>
+<a name="1771"><span class="lineNum">    1771 </span>            :     //</a>
+<a name="1772"><span class="lineNum">    1772 </span>            :     // Compressed displacement bits.</a>
+<a name="1773"><span class="lineNum">    1773 </span>            :     //</a>
+<a name="1774"><span class="lineNum">    1774 </span>            :     // Each opcode defines the base size (N) shift:</a>
+<a name="1775"><span class="lineNum">    1775 </span>            :     //   [0]: BYTE  (1 byte).</a>
+<a name="1776"><span class="lineNum">    1776 </span>            :     //   [1]: WORD  (2 bytes).</a>
+<a name="1777"><span class="lineNum">    1777 </span>            :     //   [2]: DWORD (4 bytes - float/int32).</a>
+<a name="1778"><span class="lineNum">    1778 </span>            :     //   [3]: QWORD (8 bytes - double/int64).</a>
+<a name="1779"><span class="lineNum">    1779 </span>            :     //   [4]: OWORD (16 bytes - used by FV|FVM|M128).</a>
+<a name="1780"><span class="lineNum">    1780 </span>            :     //</a>
+<a name="1781"><span class="lineNum">    1781 </span>            :     // Which is then scaled by the instruction's TT (TupleType) into possible:</a>
+<a name="1782"><span class="lineNum">    1782 </span>            :     //   [5]: YWORD (32 bytes)</a>
+<a name="1783"><span class="lineNum">    1783 </span>            :     //   [6]: ZWORD (64 bytes)</a>
+<a name="1784"><span class="lineNum">    1784 </span>            :     //</a>
+<a name="1785"><span class="lineNum">    1785 </span>            :     // These bits are then adjusted before calling EmitModSib or EmitModVSib.</a>
+<a name="1786"><span class="lineNum">    1786 </span>            :     kOpCode_CDSHL_Shift   = 13,</a>
+<a name="1787"><span class="lineNum">    1787 </span>            :     kOpCode_CDSHL_Mask    = 0x7 &lt;&lt; kOpCode_CDSHL_Shift,</a>
+<a name="1788"><span class="lineNum">    1788 </span>            : </a>
+<a name="1789"><span class="lineNum">    1789 </span>            :     // Compressed displacement tuple-type (specific to AsmJit).</a>
+<a name="1790"><span class="lineNum">    1790 </span>            :     //</a>
+<a name="1791"><span class="lineNum">    1791 </span>            :     // Since we store the base offset independently of CDTT we can simplify the</a>
+<a name="1792"><span class="lineNum">    1792 </span>            :     // number of 'TUPLE_TYPE' kinds significantly and just handle special cases.</a>
+<a name="1793"><span class="lineNum">    1793 </span>            :     kOpCode_CDTT_Shift    = 16,</a>
+<a name="1794"><span class="lineNum">    1794 </span>            :     kOpCode_CDTT_Mask     = 0x3 &lt;&lt; kOpCode_CDTT_Shift,</a>
+<a name="1795"><span class="lineNum">    1795 </span>            :     kOpCode_CDTT_None     = 0x0 &lt;&lt; kOpCode_CDTT_Shift, // Does nothing.</a>
+<a name="1796"><span class="lineNum">    1796 </span>            :     kOpCode_CDTT_ByLL     = 0x1 &lt;&lt; kOpCode_CDTT_Shift, // Scales by LL (1x 2x 4x).</a>
+<a name="1797"><span class="lineNum">    1797 </span>            :     kOpCode_CDTT_T1W      = 0x2 &lt;&lt; kOpCode_CDTT_Shift, // Used to add 'W' to the shift.</a>
+<a name="1798"><span class="lineNum">    1798 </span>            :     kOpCode_CDTT_DUP      = 0x3 &lt;&lt; kOpCode_CDTT_Shift, // Special 'VMOVDDUP' case.</a>
+<a name="1799"><span class="lineNum">    1799 </span>            : </a>
+<a name="1800"><span class="lineNum">    1800 </span>            :     // Aliases that match names used in instruction manuals.</a>
+<a name="1801"><span class="lineNum">    1801 </span>            :     kOpCode_CDTT_FV       = kOpCode_CDTT_ByLL,</a>
+<a name="1802"><span class="lineNum">    1802 </span>            :     kOpCode_CDTT_HV       = kOpCode_CDTT_ByLL,</a>
+<a name="1803"><span class="lineNum">    1803 </span>            :     kOpCode_CDTT_FVM      = kOpCode_CDTT_ByLL,</a>
+<a name="1804"><span class="lineNum">    1804 </span>            :     kOpCode_CDTT_T1S      = kOpCode_CDTT_None,</a>
+<a name="1805"><span class="lineNum">    1805 </span>            :     kOpCode_CDTT_T1F      = kOpCode_CDTT_None,</a>
+<a name="1806"><span class="lineNum">    1806 </span>            :     kOpCode_CDTT_T1_4X    = kOpCode_CDTT_None,</a>
+<a name="1807"><span class="lineNum">    1807 </span>            :     kOpCode_CDTT_T2       = kOpCode_CDTT_None,</a>
+<a name="1808"><span class="lineNum">    1808 </span>            :     kOpCode_CDTT_T4       = kOpCode_CDTT_None,</a>
+<a name="1809"><span class="lineNum">    1809 </span>            :     kOpCode_CDTT_T8       = kOpCode_CDTT_None,</a>
+<a name="1810"><span class="lineNum">    1810 </span>            :     kOpCode_CDTT_HVM      = kOpCode_CDTT_ByLL,</a>
+<a name="1811"><span class="lineNum">    1811 </span>            :     kOpCode_CDTT_QVM      = kOpCode_CDTT_ByLL,</a>
+<a name="1812"><span class="lineNum">    1812 </span>            :     kOpCode_CDTT_OVM      = kOpCode_CDTT_ByLL,</a>
+<a name="1813"><span class="lineNum">    1813 </span>            :     kOpCode_CDTT_128      = kOpCode_CDTT_None,</a>
+<a name="1814"><span class="lineNum">    1814 </span>            : </a>
+<a name="1815"><span class="lineNum">    1815 </span>            :     // `O` Field in MorR/M</a>
+<a name="1816"><span class="lineNum">    1816 </span>            :     // -------------------</a>
+<a name="1817"><span class="lineNum">    1817 </span>            : </a>
+<a name="1818"><span class="lineNum">    1818 </span>            :     kOpCode_O_Shift       = 18,</a>
+<a name="1819"><span class="lineNum">    1819 </span>            :     kOpCode_O_Mask        = 0x07U &lt;&lt; kOpCode_O_Shift,</a>
+<a name="1820"><span class="lineNum">    1820 </span>            : </a>
+<a name="1821"><span class="lineNum">    1821 </span>            :     // `PP` and `L` Fields</a>
+<a name="1822"><span class="lineNum">    1822 </span>            :     // -------------------</a>
+<a name="1823"><span class="lineNum">    1823 </span>            :     //</a>
+<a name="1824"><span class="lineNum">    1824 </span>            :     // These fields are stored deliberately right after each other as it makes</a>
+<a name="1825"><span class="lineNum">    1825 </span>            :     // it easier to construct VEX prefix from the opcode value stored in the</a>
+<a name="1826"><span class="lineNum">    1826 </span>            :     // instruction database.</a>
+<a name="1827"><span class="lineNum">    1827 </span>            :     //</a>
+<a name="1828"><span class="lineNum">    1828 </span>            :     // Two meanings:</a>
+<a name="1829"><span class="lineNum">    1829 </span>            :     //   * &quot;PP&quot; field in AVX/XOP/AVX-512 instruction.</a>
+<a name="1830"><span class="lineNum">    1830 </span>            :     //   * Mandatory Prefix in legacy encoding.</a>
+<a name="1831"><span class="lineNum">    1831 </span>            :     //</a>
+<a name="1832"><span class="lineNum">    1832 </span>            :     // AVX reserves 2 bits for `PP` field, but AsmJit extends the storage by 1</a>
+<a name="1833"><span class="lineNum">    1833 </span>            :     // more bit that is used to emit 9B prefix for some X87-FPU instructions.</a>
+<a name="1834"><span class="lineNum">    1834 </span>            : </a>
+<a name="1835"><span class="lineNum">    1835 </span>            :     kOpCode_PP_Shift      = 21,</a>
+<a name="1836"><span class="lineNum">    1836 </span>            :     kOpCode_PP_VEXMask    = 0x03U &lt;&lt; kOpCode_PP_Shift, // PP field mask used by VEX/EVEX.</a>
+<a name="1837"><span class="lineNum">    1837 </span>            :     kOpCode_PP_FPUMask    = 0x07U &lt;&lt; kOpCode_PP_Shift, // Mask used by EMIT_PP, also includes 0x9B.</a>
+<a name="1838"><span class="lineNum">    1838 </span>            :     kOpCode_PP_00         = 0x00U &lt;&lt; kOpCode_PP_Shift,</a>
+<a name="1839"><span class="lineNum">    1839 </span>            :     kOpCode_PP_66         = 0x01U &lt;&lt; kOpCode_PP_Shift,</a>
+<a name="1840"><span class="lineNum">    1840 </span>            :     kOpCode_PP_F3         = 0x02U &lt;&lt; kOpCode_PP_Shift,</a>
+<a name="1841"><span class="lineNum">    1841 </span>            :     kOpCode_PP_F2         = 0x03U &lt;&lt; kOpCode_PP_Shift,</a>
+<a name="1842"><span class="lineNum">    1842 </span>            : </a>
+<a name="1843"><span class="lineNum">    1843 </span>            :     // AsmJit specific to emit FPU's 9B byte.</a>
+<a name="1844"><span class="lineNum">    1844 </span>            :     kOpCode_PP_9B         = 0x07U &lt;&lt; kOpCode_PP_Shift,</a>
+<a name="1845"><span class="lineNum">    1845 </span>            : </a>
+<a name="1846"><span class="lineNum">    1846 </span>            :     // EVEX.W Field</a>
+<a name="1847"><span class="lineNum">    1847 </span>            :     // ------------</a>
+<a name="1848"><span class="lineNum">    1848 </span>            :     //</a>
+<a name="1849"><span class="lineNum">    1849 </span>            :     // `W` field used by EVEX instruction encoding.</a>
+<a name="1850"><span class="lineNum">    1850 </span>            : </a>
+<a name="1851"><span class="lineNum">    1851 </span>            :     kOpCode_EW_Shift      = 24,</a>
+<a name="1852"><span class="lineNum">    1852 </span>            :     kOpCode_EW            = 0x01U &lt;&lt; kOpCode_EW_Shift,</a>
+<a name="1853"><span class="lineNum">    1853 </span>            : </a>
+<a name="1854"><span class="lineNum">    1854 </span>            :     // REX B|X|R|W Bits</a>
+<a name="1855"><span class="lineNum">    1855 </span>            :     // ----------------</a>
+<a name="1856"><span class="lineNum">    1856 </span>            :     //</a>
+<a name="1857"><span class="lineNum">    1857 </span>            :     // NOTE: REX.[B|X|R] are never stored within the opcode itself, they are</a>
+<a name="1858"><span class="lineNum">    1858 </span>            :     // reserved by AsmJit are are added dynamically to the opcode to represent</a>
+<a name="1859"><span class="lineNum">    1859 </span>            :     // [REX|VEX|EVEX].[B|X|R] bits. REX.W can be stored in DB as it's sometimes</a>
+<a name="1860"><span class="lineNum">    1860 </span>            :     // part of the opcode itself.</a>
+<a name="1861"><span class="lineNum">    1861 </span>            : </a>
+<a name="1862"><span class="lineNum">    1862 </span>            :     // These must be binary compatible with instruction options.</a>
+<a name="1863"><span class="lineNum">    1863 </span>            :     kOpCode_REX_Shift     = 25,</a>
+<a name="1864"><span class="lineNum">    1864 </span>            :     kOpCode_REX_Mask      = 0x0FU &lt;&lt; kOpCode_REX_Shift,</a>
+<a name="1865"><span class="lineNum">    1865 </span>            :     kOpCode_B             = 0x01U &lt;&lt; kOpCode_REX_Shift, // Never stored in DB.</a>
+<a name="1866"><span class="lineNum">    1866 </span>            :     kOpCode_X             = 0x02U &lt;&lt; kOpCode_REX_Shift, // Never stored in DB.</a>
+<a name="1867"><span class="lineNum">    1867 </span>            :     kOpCode_R             = 0x04U &lt;&lt; kOpCode_REX_Shift, // Never stored in DB.</a>
+<a name="1868"><span class="lineNum">    1868 </span>            :     kOpCode_W             = 0x08U &lt;&lt; kOpCode_REX_Shift,</a>
+<a name="1869"><span class="lineNum">    1869 </span>            :     kOpCode_W_Shift       = kOpCode_REX_Shift + 3,</a>
+<a name="1870"><span class="lineNum">    1870 </span>            : </a>
+<a name="1871"><span class="lineNum">    1871 </span>            :     // `L` field in AVX/XOP/AVX-512</a>
+<a name="1872"><span class="lineNum">    1872 </span>            :     // ----------------------------</a>
+<a name="1873"><span class="lineNum">    1873 </span>            :     //</a>
+<a name="1874"><span class="lineNum">    1874 </span>            :     // VEX/XOP prefix can only use the first bit `L.128` or `L.256`. EVEX prefix</a>
+<a name="1875"><span class="lineNum">    1875 </span>            :     // prefix makes it possible to use also `L.512`.</a>
+<a name="1876"><span class="lineNum">    1876 </span>            :     //</a>
+<a name="1877"><span class="lineNum">    1877 </span>            :     // If the instruction set manual describes an instruction by `LIG` it means</a>
+<a name="1878"><span class="lineNum">    1878 </span>            :     // that the `L` field is ignored and AsmJit defaults to `0` in such case.</a>
+<a name="1879"><span class="lineNum">    1879 </span>            :     kOpCode_LL_Shift      = 29,</a>
+<a name="1880"><span class="lineNum">    1880 </span>            :     kOpCode_LL_Mask       = 0x03U &lt;&lt; kOpCode_LL_Shift,</a>
+<a name="1881"><span class="lineNum">    1881 </span>            :     kOpCode_LL_128        = 0x00U &lt;&lt; kOpCode_LL_Shift,</a>
+<a name="1882"><span class="lineNum">    1882 </span>            :     kOpCode_LL_256        = 0x01U &lt;&lt; kOpCode_LL_Shift,</a>
+<a name="1883"><span class="lineNum">    1883 </span>            :     kOpCode_LL_512        = 0x02U &lt;&lt; kOpCode_LL_Shift</a>
+<a name="1884"><span class="lineNum">    1884 </span>            :   };</a>
+<a name="1885"><span class="lineNum">    1885 </span>            : </a>
+<a name="1886"><span class="lineNum">    1886 </span>            :   //! Instruction flags.</a>
+<a name="1887"><span class="lineNum">    1887 </span>            :   //!</a>
+<a name="1888"><span class="lineNum">    1888 </span>            :   //! Details about instruction encoding, operation, features, and some limitations.</a>
+<a name="1889"><span class="lineNum">    1889 </span>            :   ASMJIT_ENUM(Flags) {</a>
+<a name="1890"><span class="lineNum">    1890 </span>            :     kFlagNone             = 0x00000000U, //!&lt; No flags.</a>
+<a name="1891"><span class="lineNum">    1891 </span>            : </a>
+<a name="1892"><span class="lineNum">    1892 </span>            :     // Operand's Use</a>
+<a name="1893"><span class="lineNum">    1893 </span>            :     // -------------</a>
+<a name="1894"><span class="lineNum">    1894 </span>            :     //</a>
+<a name="1895"><span class="lineNum">    1895 </span>            :     // These flags describe the use of 1st and/or 1st+2nd operands. This allows</a>
+<a name="1896"><span class="lineNum">    1896 </span>            :     // to fast calculate which operands are read, written, or read and written.</a>
+<a name="1897"><span class="lineNum">    1897 </span>            :     //</a>
+<a name="1898"><span class="lineNum">    1898 </span>            :     // In some cases this information is not reliable, because AsmJit uses data</a>
+<a name="1899"><span class="lineNum">    1899 </span>            :     // generated by a script that merges usually more than one instruction into</a>
+<a name="1900"><span class="lineNum">    1900 </span>            :     // one AsmJit instruction as some X86 instructions uses more encodings to</a>
+<a name="1901"><span class="lineNum">    1901 </span>            :     // describe the same operation. In such case `kFlagUseComplex` is set and</a>
+<a name="1902"><span class="lineNum">    1902 </span>            :     // AsmJit will use different approach to calculate operand's use flags.</a>
+<a name="1903"><span class="lineNum">    1903 </span>            : </a>
+<a name="1904"><span class="lineNum">    1904 </span>            :     kFlagUseA             = 0x00000001U, //!&lt; Use flags are 'A'mbiguous as USE information couldn't be flattened.</a>
+<a name="1905"><span class="lineNum">    1905 </span>            :     kFlagUseR             = 0x00000002U, //!&lt; 1st operand is R (read), read-only if `kFlagOpW` isn't set.</a>
+<a name="1906"><span class="lineNum">    1906 </span>            :     kFlagUseW             = 0x00000004U, //!&lt; 1st operand is W (written), write-only if `kFlagOpR` isn't set.</a>
+<a name="1907"><span class="lineNum">    1907 </span>            :     kFlagUseX             = 0x00000006U, //!&lt; 1st operand is X (read-write).</a>
+<a name="1908"><span class="lineNum">    1908 </span>            :     kFlagUseXX            = 0x00000008U, //!&lt; 1st and 2nd operands are XX (read &amp; written) (XCHG, XADD).</a>
+<a name="1909"><span class="lineNum">    1909 </span>            : </a>
+<a name="1910"><span class="lineNum">    1910 </span>            :     kFlagFixedReg         = 0x00000010U, //!&lt; Some operand uses fixed register.</a>
+<a name="1911"><span class="lineNum">    1911 </span>            :     kFlagFixedMem         = 0x00000020U, //!&lt; Some operand uses fixed register to access memory (EAX|RAX, EDI|RDI, ESI|RSI).</a>
+<a name="1912"><span class="lineNum">    1912 </span>            :     kFlagFixedRM          = 0x00000030U, //!&lt; Combination of `kFlagUseFixedReg` and `kFlagUseFixedMem`.</a>
+<a name="1913"><span class="lineNum">    1913 </span>            : </a>
+<a name="1914"><span class="lineNum">    1914 </span>            :     // Instruction Family</a>
+<a name="1915"><span class="lineNum">    1915 </span>            :     // ------------------</a>
+<a name="1916"><span class="lineNum">    1916 </span>            :     //</a>
+<a name="1917"><span class="lineNum">    1917 </span>            :     // Instruction family information.</a>
+<a name="1918"><span class="lineNum">    1918 </span>            : </a>
+<a name="1919"><span class="lineNum">    1919 </span>            :     kFlagFpu              = 0x00000100U, //!&lt; Instruction that accesses FPU registers.</a>
+<a name="1920"><span class="lineNum">    1920 </span>            :     kFlagMmx              = 0x00000200U, //!&lt; Instruction that accesses MMX registers (including 3DNOW and GEODE) and EMMS.</a>
+<a name="1921"><span class="lineNum">    1921 </span>            :     kFlagVec              = 0x00000400U, //!&lt; Instruction that accesses XMM registers (SSE, AVX, AVX512).</a>
+<a name="1922"><span class="lineNum">    1922 </span>            : </a>
+<a name="1923"><span class="lineNum">    1923 </span>            :     // Prefixes and Encoding Flags</a>
+<a name="1924"><span class="lineNum">    1924 </span>            :     // ---------------------------</a>
+<a name="1925"><span class="lineNum">    1925 </span>            :     //</a>
+<a name="1926"><span class="lineNum">    1926 </span>            :     // These describe optional X86 prefixes that can be used to change the instruction's operation.</a>
+<a name="1927"><span class="lineNum">    1927 </span>            : </a>
+<a name="1928"><span class="lineNum">    1928 </span>            :     kFlagRep              = 0x00001000U, //!&lt; Instruction can be prefixed by using the REP/REPZ/REPE prefix.</a>
+<a name="1929"><span class="lineNum">    1929 </span>            :     kFlagRepnz            = 0x00002000U, //!&lt; Instruction can be prefixed by using the REPNZ/REPNE prefix.</a>
+<a name="1930"><span class="lineNum">    1930 </span>            :     kFlagLock             = 0x00004000U, //!&lt; Instruction can be prefixed by using the LOCK prefix.</a>
+<a name="1931"><span class="lineNum">    1931 </span>            :     kFlagXAcquire         = 0x00008000U, //!&lt; Instruction can be prefixed by using the XACQUIRE prefix.</a>
+<a name="1932"><span class="lineNum">    1932 </span>            :     kFlagXRelease         = 0x00010000U, //!&lt; Instruction can be prefixed by using the XRELEASE prefix.</a>
+<a name="1933"><span class="lineNum">    1933 </span>            :     kFlagMib              = 0x00020000U, //!&lt; Instruction uses MIB (BNDLDX|BNDSTX) to encode two registers.</a>
+<a name="1934"><span class="lineNum">    1934 </span>            :     kFlagVsib             = 0x00040000U, //!&lt; Instruction uses VSIB instead of legacy SIB.</a>
+<a name="1935"><span class="lineNum">    1935 </span>            :     kFlagVex              = 0x00080000U, //!&lt; Instruction can be encoded by VEX|XOP (AVX|AVX2|BMI|XOP|...).</a>
+<a name="1936"><span class="lineNum">    1936 </span>            :     kFlagEvex             = 0x00100000U, //!&lt; Instruction can be encoded by EVEX (AVX512).</a>
+<a name="1937"><span class="lineNum">    1937 </span>            : </a>
+<a name="1938"><span class="lineNum">    1938 </span>            :     // FPU Flags</a>
+<a name="1939"><span class="lineNum">    1939 </span>            :     // ---------</a>
+<a name="1940"><span class="lineNum">    1940 </span>            :     //</a>
+<a name="1941"><span class="lineNum">    1941 </span>            :     // Used to tell the encoder which memory operand sizes are encodable.</a>
+<a name="1942"><span class="lineNum">    1942 </span>            : </a>
+<a name="1943"><span class="lineNum">    1943 </span>            :     kFlagFpuM16           = 0x00200000U, //!&lt; FPU instruction can address `word_ptr` (shared with M10).</a>
+<a name="1944"><span class="lineNum">    1944 </span>            :     kFlagFpuM32           = 0x00400000U, //!&lt; FPU instruction can address `dword_ptr`.</a>
+<a name="1945"><span class="lineNum">    1945 </span>            :     kFlagFpuM64           = 0x00800000U, //!&lt; FPU instruction can address `qword_ptr`.</a>
+<a name="1946"><span class="lineNum">    1946 </span>            :     kFlagFpuM80           = 0x00200000U, //!&lt; FPU instruction can address `tword_ptr` (shared with M2).</a>
+<a name="1947"><span class="lineNum">    1947 </span>            : </a>
+<a name="1948"><span class="lineNum">    1948 </span>            :     // AVX and AVX515 Flags</a>
+<a name="1949"><span class="lineNum">    1949 </span>            :     // --------------------</a>
+<a name="1950"><span class="lineNum">    1950 </span>            :     //</a>
+<a name="1951"><span class="lineNum">    1951 </span>            :     // If both `kFlagPrefixVex` and `kFlagPrefixEvex` flags are specified it</a>
+<a name="1952"><span class="lineNum">    1952 </span>            :     // means that the instructions can be encoded by either VEX or EVEX prefix.</a>
+<a name="1953"><span class="lineNum">    1953 </span>            :     // In that case AsmJit checks global options and also instruction options</a>
+<a name="1954"><span class="lineNum">    1954 </span>            :     // to decide whether to emit VEX or EVEX prefix.</a>
+<a name="1955"><span class="lineNum">    1955 </span>            : </a>
+<a name="1956"><span class="lineNum">    1956 </span>            :     kFlagAvx512_          = 0x00000000U, //!&lt; Internally used in tables, has no meaning.</a>
+<a name="1957"><span class="lineNum">    1957 </span>            :     kFlagAvx512K          = 0x01000000U, //!&lt; Supports masking {k0..k7}.</a>
+<a name="1958"><span class="lineNum">    1958 </span>            :     kFlagAvx512Z          = 0x02000000U, //!&lt; Supports zeroing {z}, must be used together with `kAvx512k`.</a>
+<a name="1959"><span class="lineNum">    1959 </span>            :     kFlagAvx512ER         = 0x04000000U, //!&lt; Supports 'embedded-rounding' {er} with implicit {sae},</a>
+<a name="1960"><span class="lineNum">    1960 </span>            :     kFlagAvx512SAE        = 0x08000000U, //!&lt; Supports 'suppress-all-exceptions' {sae}.</a>
+<a name="1961"><span class="lineNum">    1961 </span>            :     kFlagAvx512B32        = 0x10000000U, //!&lt; Supports 32-bit broadcast 'b32'.</a>
+<a name="1962"><span class="lineNum">    1962 </span>            :     kFlagAvx512B64        = 0x20000000U, //!&lt; Supports 64-bit broadcast 'b64'.</a>
+<a name="1963"><span class="lineNum">    1963 </span>            :     kFlagAvx512T4X        = 0x80000000U, //!&lt; Operates on a vector of consecutive registers (AVX512_4FMAPS and AVX512_4VNNIW).</a>
+<a name="1964"><span class="lineNum">    1964 </span>            : </a>
+<a name="1965"><span class="lineNum">    1965 </span>            :     // Combinations used by instruction tables to make AVX512 definitions more compact.</a>
+<a name="1966"><span class="lineNum">    1966 </span>            :     kFlagAvx512KZ            = kFlagAvx512K         | kFlagAvx512Z,</a>
+<a name="1967"><span class="lineNum">    1967 </span>            :     kFlagAvx512ER_SAE        = kFlagAvx512ER        | kFlagAvx512SAE,</a>
+<a name="1968"><span class="lineNum">    1968 </span>            :     kFlagAvx512KZ_SAE        = kFlagAvx512KZ        | kFlagAvx512SAE,</a>
+<a name="1969"><span class="lineNum">    1969 </span>            :     kFlagAvx512KZ_SAE_B32    = kFlagAvx512KZ_SAE    | kFlagAvx512B32,</a>
+<a name="1970"><span class="lineNum">    1970 </span>            :     kFlagAvx512KZ_SAE_B64    = kFlagAvx512KZ_SAE    | kFlagAvx512B64,</a>
+<a name="1971"><span class="lineNum">    1971 </span>            : </a>
+<a name="1972"><span class="lineNum">    1972 </span>            :     kFlagAvx512KZ_ER_SAE     = kFlagAvx512KZ        | kFlagAvx512ER_SAE,</a>
+<a name="1973"><span class="lineNum">    1973 </span>            :     kFlagAvx512KZ_ER_SAE_B32 = kFlagAvx512KZ_ER_SAE | kFlagAvx512B32,</a>
+<a name="1974"><span class="lineNum">    1974 </span>            :     kFlagAvx512KZ_ER_SAE_B64 = kFlagAvx512KZ_ER_SAE | kFlagAvx512B64,</a>
+<a name="1975"><span class="lineNum">    1975 </span>            : </a>
+<a name="1976"><span class="lineNum">    1976 </span>            :     kFlagAvx512K_B32         = kFlagAvx512K         | kFlagAvx512B32,</a>
+<a name="1977"><span class="lineNum">    1977 </span>            :     kFlagAvx512K_B64         = kFlagAvx512K         | kFlagAvx512B64,</a>
+<a name="1978"><span class="lineNum">    1978 </span>            :     kFlagAvx512KZ_B32        = kFlagAvx512KZ        | kFlagAvx512B32,</a>
+<a name="1979"><span class="lineNum">    1979 </span>            :     kFlagAvx512KZ_B64        = kFlagAvx512KZ        | kFlagAvx512B64</a>
+<a name="1980"><span class="lineNum">    1980 </span>            :   };</a>
+<a name="1981"><span class="lineNum">    1981 </span>            : </a>
+<a name="1982"><span class="lineNum">    1982 </span>            :   //! Used to describe what the instruction does and some of its quirks.</a>
+<a name="1983"><span class="lineNum">    1983 </span>            :   enum OperationFlags {</a>
+<a name="1984"><span class="lineNum">    1984 </span>            :     kOperationMovCrDr      = 0x00000001U, //!&lt; `MOV REG &lt;-&gt; CREG|DREG` - OS|SF|ZF|AF|PF|CF flags are undefined.</a>
+<a name="1985"><span class="lineNum">    1985 </span>            :     kOperationMovSsSd      = 0x00000002U, //!&lt; `MOVSS|MOVSD XMM, [MEM]` - Sestination operand is completely overwritten.</a>
+<a name="1986"><span class="lineNum">    1986 </span>            : </a>
+<a name="1987"><span class="lineNum">    1987 </span>            :     kOperationPrefetch     = 0x10000000U, //!&lt; Instruction does hardware prefetch.</a>
+<a name="1988"><span class="lineNum">    1988 </span>            :     kOperationBarrier      = 0x20000000U, //!&lt; Instruction acts as a barrier / fence.</a>
+<a name="1989"><span class="lineNum">    1989 </span>            :     kOperationVolatile     = 0x40000000U, //!&lt; Hint for instruction schedulers to never reorder this instruction (side effects, memory barrier, etc).</a>
+<a name="1990"><span class="lineNum">    1990 </span>            :     kOperationPrivileged   = 0x80000000U  //!&lt; This is a privileged operation that cannot run in user mode (system instruction).</a>
+<a name="1991"><span class="lineNum">    1991 </span>            :   };</a>
+<a name="1992"><span class="lineNum">    1992 </span>            : </a>
+<a name="1993"><span class="lineNum">    1993 </span>            :   //! SSE to AVX conversion mode.</a>
+<a name="1994"><span class="lineNum">    1994 </span>            :   enum SseToAvxMode {</a>
+<a name="1995"><span class="lineNum">    1995 </span>            :     kSseToAvxNone         = 0,           //!&lt; No conversion possible.</a>
+<a name="1996"><span class="lineNum">    1996 </span>            :     kSseToAvxMove         = 1,           //!&lt; No change (no operands changed).</a>
+<a name="1997"><span class="lineNum">    1997 </span>            :     kSseToAvxMoveIfMem    = 2,           //!&lt; No change if the second operand is mem, extend otherwise.</a>
+<a name="1998"><span class="lineNum">    1998 </span>            :     kSseToAvxExtend       = 3,           //!&lt; The first SSE operand becomes first and second AVX operand.</a>
+<a name="1999"><span class="lineNum">    1999 </span>            :     kSseToAvxBlend        = 4            //!&lt; Special case for 'vblendvpd', 'vblendvps', and 'vpblendvb'.</a>
+<a name="2000"><span class="lineNum">    2000 </span>            :   };</a>
+<a name="2001"><span class="lineNum">    2001 </span>            : </a>
+<a name="2002"><span class="lineNum">    2002 </span>            :   //! Instruction options (AsmJit specific).</a>
+<a name="2003"><span class="lineNum">    2003 </span>            :   ASMJIT_ENUM(Options) {</a>
+<a name="2004"><span class="lineNum">    2004 </span>            :     // NOTE: Don't collide with reserved bits used by CodeEmitter (0x0000003F).</a>
+<a name="2005"><span class="lineNum">    2005 </span>            :     kOptionOp4Op5Used     = CodeEmitter::kOptionOp4Op5Used,</a>
+<a name="2006"><span class="lineNum">    2006 </span>            : </a>
+<a name="2007"><span class="lineNum">    2007 </span>            :     kOptionShortForm      = 0x00000040U, //!&lt; Emit short-form of the instruction.</a>
+<a name="2008"><span class="lineNum">    2008 </span>            :     kOptionLongForm       = 0x00000080U, //!&lt; Emit long-form of the instruction.</a>
+<a name="2009"><span class="lineNum">    2009 </span>            : </a>
+<a name="2010"><span class="lineNum">    2010 </span>            :     kOptionTaken          = 0x00000100U, //!&lt; Conditional jump is likely to be taken.</a>
+<a name="2011"><span class="lineNum">    2011 </span>            :     kOptionNotTaken       = 0x00000200U, //!&lt; Conditional jump is unlikely to be taken.</a>
+<a name="2012"><span class="lineNum">    2012 </span>            : </a>
+<a name="2013"><span class="lineNum">    2013 </span>            :     kOptionVex3           = 0x00000400U, //!&lt; Use 3-byte VEX prefix if possible (AVX) (must be 0x00000400).</a>
+<a name="2014"><span class="lineNum">    2014 </span>            :     kOptionModMR          = 0x00000800U, //!&lt; Use ModMR instead of ModRM when it's available.</a>
+<a name="2015"><span class="lineNum">    2015 </span>            :     kOptionEvex           = 0x00001000U, //!&lt; Use 4-byte EVEX prefix if possible (AVX-512) (must be 0x00001000).</a>
+<a name="2016"><span class="lineNum">    2016 </span>            : </a>
+<a name="2017"><span class="lineNum">    2017 </span>            :     kOptionLock           = 0x00002000U, //!&lt; LOCK prefix (lock-enabled instructions only).</a>
+<a name="2018"><span class="lineNum">    2018 </span>            :     kOptionRep            = 0x00004000U, //!&lt; REP/REPZ prefix (string instructions only).</a>
+<a name="2019"><span class="lineNum">    2019 </span>            :     kOptionRepnz          = 0x00008000U, //!&lt; REPNZ prefix (string instructions only).</a>
+<a name="2020"><span class="lineNum">    2020 </span>            : </a>
+<a name="2021"><span class="lineNum">    2021 </span>            :     kOptionXAcquire       = 0x00010000U, //!&lt; XACQUIRE prefix (only allowed instructions).</a>
+<a name="2022"><span class="lineNum">    2022 </span>            :     kOptionXRelease       = 0x00020000U, //!&lt; XRELEASE prefix (only allowed instructions).</a>
+<a name="2023"><span class="lineNum">    2023 </span>            : </a>
+<a name="2024"><span class="lineNum">    2024 </span>            :     kOptionER             = 0x00040000U, //!&lt; AVX-512: 'embedded-rounding' {er} and {sae}.</a>
+<a name="2025"><span class="lineNum">    2025 </span>            :     kOptionSAE            = 0x00080000U, //!&lt; AVX-512: 'suppress-all-exceptions' {sae}.</a>
+<a name="2026"><span class="lineNum">    2026 </span>            :     kOption1ToX           = 0x00100000U, //!&lt; AVX-512: broadcast the first element to all {1tox}.</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :     kOptionRN_SAE         = 0x00000000U, //!&lt; AVX-512: round-to-nearest (even)      {rn-sae} (bits 00).</a>
+<a name="2028"><span class="lineNum">    2028 </span>            :     kOptionRD_SAE         = 0x00200000U, //!&lt; AVX-512: round-down (toward -inf)     {rd-sae} (bits 01).</a>
+<a name="2029"><span class="lineNum">    2029 </span>            :     kOptionRU_SAE         = 0x00400000U, //!&lt; AVX-512: round-up (toward +inf)       {ru-sae} (bits 10).</a>
+<a name="2030"><span class="lineNum">    2030 </span>            :     kOptionRZ_SAE         = 0x00600000U, //!&lt; AVX-512: round-toward-zero (truncate) {rz-sae} (bits 11).</a>
+<a name="2031"><span class="lineNum">    2031 </span>            :     kOptionZMask          = 0x00800000U, //!&lt; AVX-512: Use zeroing {k}{z} instead of merging {k}.</a>
+<a name="2032"><span class="lineNum">    2032 </span>            :     _kOptionAvx512Mask    = 0x00FC0000U, //!&lt; AVX-512: Mask of all possible AVX-512 options except EVEX prefix flag.</a>
+<a name="2033"><span class="lineNum">    2033 </span>            : </a>
+<a name="2034"><span class="lineNum">    2034 </span>            :     _kOptionInvalidRex    = 0x01000000U, //!&lt; REX prefix can't be emitted (internal).</a>
+<a name="2035"><span class="lineNum">    2035 </span>            :     kOptionOpCodeB        = 0x02000000U, //!&lt; REX.B and/or VEX.B field (X64).</a>
+<a name="2036"><span class="lineNum">    2036 </span>            :     kOptionOpCodeX        = 0x04000000U, //!&lt; REX.X and/or VEX.X field (X64).</a>
+<a name="2037"><span class="lineNum">    2037 </span>            :     kOptionOpCodeR        = 0x08000000U, //!&lt; REX.R and/or VEX.R field (X64).</a>
+<a name="2038"><span class="lineNum">    2038 </span>            :     kOptionOpCodeW        = 0x10000000U, //!&lt; REX.W and/or VEX.W field (X64).</a>
+<a name="2039"><span class="lineNum">    2039 </span>            :     kOptionRex            = 0x80000000U  //!&lt; Use REX prefix (X64) (must be 0x80000000).</a>
+<a name="2040"><span class="lineNum">    2040 </span>            :   };</a>
+<a name="2041"><span class="lineNum">    2041 </span>            : </a>
+<a name="2042"><span class="lineNum">    2042 </span>            :   //! Supported architectures.</a>
+<a name="2043"><span class="lineNum">    2043 </span>            :   ASMJIT_ENUM(ArchMask) {</a>
+<a name="2044"><span class="lineNum">    2044 </span>            :     kArchMaskX86          = 0x01,        //!&lt; X86 mode supported.</a>
+<a name="2045"><span class="lineNum">    2045 </span>            :     kArchMaskX64          = 0x02         //!&lt; X64 mode supported.</a>
+<a name="2046"><span class="lineNum">    2046 </span>            :   };</a>
+<a name="2047"><span class="lineNum">    2047 </span>            : </a>
+<a name="2048"><span class="lineNum">    2048 </span>            :   ASMJIT_ENUM(SingleRegCase) {</a>
+<a name="2049"><span class="lineNum">    2049 </span>            :     kSingleRegNone        = 0,           //!&lt; No special handling.</a>
+<a name="2050"><span class="lineNum">    2050 </span>            :     kSingleRegRO          = 1,           //!&lt; Operands become read-only  - `REG &amp; REG` and similar.</a>
+<a name="2051"><span class="lineNum">    2051 </span>            :     kSingleRegWO          = 2            //!&lt; Operands become write-only - `REG ^ REG` and similar.</a>
+<a name="2052"><span class="lineNum">    2052 </span>            :   };</a>
+<a name="2053"><span class="lineNum">    2053 </span>            : </a>
+<a name="2054"><span class="lineNum">    2054 </span>            :   //! Instruction's operand flags.</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :   ASMJIT_ENUM(OpFlags) {</a>
+<a name="2056"><span class="lineNum">    2056 </span>            :     kOpNone               = 0x00000000U, //!&lt; No operand.</a>
+<a name="2057"><span class="lineNum">    2057 </span>            : </a>
+<a name="2058"><span class="lineNum">    2058 </span>            :     kOpGpbLo              = 0x00000001U, //!&lt; Operand can be a low 8-bit GPB register.</a>
+<a name="2059"><span class="lineNum">    2059 </span>            :     kOpGpbHi              = 0x00000002U, //!&lt; Operand can be a high 8-bit GPB register.</a>
+<a name="2060"><span class="lineNum">    2060 </span>            :     kOpGpw                = 0x00000004U, //!&lt; Operand can be a 16-bit GPW register.</a>
+<a name="2061"><span class="lineNum">    2061 </span>            :     kOpGpd                = 0x00000008U, //!&lt; Operand can be a 32-bit GPD register.</a>
+<a name="2062"><span class="lineNum">    2062 </span>            :     kOpGpq                = 0x00000010U, //!&lt; Operand can be a 64-bit GPQ register.</a>
+<a name="2063"><span class="lineNum">    2063 </span>            :     kOpFp                 = 0x00000020U, //!&lt; Operand can be an FPU register.</a>
+<a name="2064"><span class="lineNum">    2064 </span>            :     kOpMm                 = 0x00000040U, //!&lt; Operand can be a 64-bit MM register.</a>
+<a name="2065"><span class="lineNum">    2065 </span>            :     kOpK                  = 0x00000080U, //!&lt; Operand can be a 64-bit K register.</a>
+<a name="2066"><span class="lineNum">    2066 </span>            :     kOpCr                 = 0x00000100U, //!&lt; Operand can be a control register.</a>
+<a name="2067"><span class="lineNum">    2067 </span>            :     kOpDr                 = 0x00000200U, //!&lt; Operand can be a debug register.</a>
+<a name="2068"><span class="lineNum">    2068 </span>            :     kOpBnd                = 0x00000400U, //!&lt; Operand can be a BND register.</a>
+<a name="2069"><span class="lineNum">    2069 </span>            :     kOpSeg                = 0x00000800U, //!&lt; Operand can be a segment register.</a>
+<a name="2070"><span class="lineNum">    2070 </span>            :     kOpXmm                = 0x00001000U, //!&lt; Operand can be a 128-bit XMM register.</a>
+<a name="2071"><span class="lineNum">    2071 </span>            :     kOpYmm                = 0x00002000U, //!&lt; Operand can be a 256-bit YMM register.</a>
+<a name="2072"><span class="lineNum">    2072 </span>            :     kOpZmm                = 0x00004000U, //!&lt; Operand can be a 512-bit ZMM register.</a>
+<a name="2073"><span class="lineNum">    2073 </span>            : </a>
+<a name="2074"><span class="lineNum">    2074 </span>            :     kOpAllRegs            = 0x00007FFFU, //!&lt; Combination of all possible registers.</a>
+<a name="2075"><span class="lineNum">    2075 </span>            : </a>
+<a name="2076"><span class="lineNum">    2076 </span>            :     kOpMem                = 0x00010000U, //!&lt; Operand can be a scalar memory pointer.</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :     kOpVm                 = 0x00020000U, //!&lt; Operand can be a vector memory pointer.</a>
+<a name="2078"><span class="lineNum">    2078 </span>            : </a>
+<a name="2079"><span class="lineNum">    2079 </span>            :     kOpU4                 = 0x00040000U, //!&lt; Operand can be unsigned 4-bit  immediate.</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :     kOpI8                 = 0x00080000U, //!&lt; Operand can be signed   8-bit  immediate.</a>
+<a name="2081"><span class="lineNum">    2081 </span>            :     kOpU8                 = 0x00100000U, //!&lt; Operand can be unsigned 8-bit  immediate.</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :     kOpI16                = 0x00200000U, //!&lt; Operand can be signed   16-bit immediate.</a>
+<a name="2083"><span class="lineNum">    2083 </span>            :     kOpU16                = 0x00400000U, //!&lt; Operand can be unsigned 16-bit immediate.</a>
+<a name="2084"><span class="lineNum">    2084 </span>            :     kOpI32                = 0x00800000U, //!&lt; Operand can be signed   32-bit immediate.</a>
+<a name="2085"><span class="lineNum">    2085 </span>            :     kOpU32                = 0x01000000U, //!&lt; Operand can be unsigned 32-bit immediate.</a>
+<a name="2086"><span class="lineNum">    2086 </span>            :     kOpI64                = 0x02000000U, //!&lt; Operand can be signed   64-bit immediate.</a>
+<a name="2087"><span class="lineNum">    2087 </span>            :     kOpU64                = 0x04000000U, //!&lt; Operand can be unsigned 64-bit immediate.</a>
+<a name="2088"><span class="lineNum">    2088 </span>            :     kOpAllImm             = 0x07FC0000U, //!&lt; Operand can be any immediate.</a>
+<a name="2089"><span class="lineNum">    2089 </span>            : </a>
+<a name="2090"><span class="lineNum">    2090 </span>            :     kOpRel8               = 0x08000000U, //!&lt; Operand can be relative 8-bit  displacement.</a>
+<a name="2091"><span class="lineNum">    2091 </span>            :     kOpRel32              = 0x10000000U, //!&lt; Operand can be relative 32-bit displacement.</a>
+<a name="2092"><span class="lineNum">    2092 </span>            : </a>
+<a name="2093"><span class="lineNum">    2093 </span>            :     kOpR                  = 0x20000000U, //!&lt; Operand is read.</a>
+<a name="2094"><span class="lineNum">    2094 </span>            :     kOpW                  = 0x40000000U, //!&lt; Operand is written.</a>
+<a name="2095"><span class="lineNum">    2095 </span>            :     kOpX                  = 0x60000000U, //!&lt; Operand is read &amp; written.</a>
+<a name="2096"><span class="lineNum">    2096 </span>            :     kOpImplicit           = 0x80000000U  //!&lt; Operand is implicit.</a>
+<a name="2097"><span class="lineNum">    2097 </span>            :   };</a>
+<a name="2098"><span class="lineNum">    2098 </span>            : </a>
+<a name="2099"><span class="lineNum">    2099 </span>            :   //! Instruction's memory operand flags.</a>
+<a name="2100"><span class="lineNum">    2100 </span>            :   ASMJIT_ENUM(MemOpFlags) {</a>
+<a name="2101"><span class="lineNum">    2101 </span>            :     // NOTE: Instruction uses either scalar or vector memory operands, they</a>
+<a name="2102"><span class="lineNum">    2102 </span>            :     // never collide, this is the reason &quot;M&quot; and &quot;Vm&quot; can share bits here.</a>
+<a name="2103"><span class="lineNum">    2103 </span>            : </a>
+<a name="2104"><span class="lineNum">    2104 </span>            :     kMemOpM8              = 0x0001U,     //!&lt; Operand can be an 8-bit memory pointer.</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :     kMemOpM16             = 0x0002U,     //!&lt; Operand can be a 16-bit memory pointer.</a>
+<a name="2106"><span class="lineNum">    2106 </span>            :     kMemOpM32             = 0x0004U,     //!&lt; Operand can be a 32-bit memory pointer.</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :     kMemOpM48             = 0x0008U,     //!&lt; Operand can be a 32-bit memory pointer.</a>
+<a name="2108"><span class="lineNum">    2108 </span>            :     kMemOpM64             = 0x0010U,     //!&lt; Operand can be a 64-bit memory pointer.</a>
+<a name="2109"><span class="lineNum">    2109 </span>            :     kMemOpM80             = 0x0020U,     //!&lt; Operand can be an 80-bit memory pointer.</a>
+<a name="2110"><span class="lineNum">    2110 </span>            :     kMemOpM128            = 0x0040U,     //!&lt; Operand can be a 128-bit memory pointer.</a>
+<a name="2111"><span class="lineNum">    2111 </span>            :     kMemOpM256            = 0x0080U,     //!&lt; Operand can be a 256-bit memory pointer.</a>
+<a name="2112"><span class="lineNum">    2112 </span>            :     kMemOpM512            = 0x0100U,     //!&lt; Operand can be a 512-bit memory pointer.</a>
+<a name="2113"><span class="lineNum">    2113 </span>            :     kMemOpM1024           = 0x0200U,     //!&lt; Operand can be a 1024-bit memory pointer.</a>
+<a name="2114"><span class="lineNum">    2114 </span>            : </a>
+<a name="2115"><span class="lineNum">    2115 </span>            :     kMemOpVm32x           = 0x0001U,     //!&lt; Operand can be a vm32x (vector) pointer.</a>
+<a name="2116"><span class="lineNum">    2116 </span>            :     kMemOpVm32y           = 0x0002U,     //!&lt; Operand can be a vm32y (vector) pointer.</a>
+<a name="2117"><span class="lineNum">    2117 </span>            :     kMemOpVm32z           = 0x0004U,     //!&lt; Operand can be a vm32z (vector) pointer.</a>
+<a name="2118"><span class="lineNum">    2118 </span>            :     kMemOpVm64x           = 0x0010U,     //!&lt; Operand can be a vm64x (vector) pointer.</a>
+<a name="2119"><span class="lineNum">    2119 </span>            :     kMemOpVm64y           = 0x0020U,     //!&lt; Operand can be a vm64y (vector) pointer.</a>
+<a name="2120"><span class="lineNum">    2120 </span>            :     kMemOpVm64z           = 0x0040U,     //!&lt; Operand can be a vm64z (vector) pointer.</a>
+<a name="2121"><span class="lineNum">    2121 </span>            : </a>
+<a name="2122"><span class="lineNum">    2122 </span>            :     kMemOpBaseOnly        = 0x0800U,     //!&lt; Only memory base is allowed (no index, no offset).</a>
+<a name="2123"><span class="lineNum">    2123 </span>            :     kMemOpDs              = 0x1000U,     //!&lt; Implicit memory operand's DS segment.</a>
+<a name="2124"><span class="lineNum">    2124 </span>            :     kMemOpEs              = 0x2000U,     //!&lt; Implicit memory operand's ES segment.</a>
+<a name="2125"><span class="lineNum">    2125 </span>            : </a>
+<a name="2126"><span class="lineNum">    2126 </span>            :     kMemOpMib             = 0x4000U,     //!&lt; Operand must be MIB (base+index) pointer.</a>
+<a name="2127"><span class="lineNum">    2127 </span>            :     kMemOpAny             = 0x8000U      //!&lt; Operand can be any scalar memory pointer.</a>
+<a name="2128"><span class="lineNum">    2128 </span>            :   };</a>
+<a name="2129"><span class="lineNum">    2129 </span>            : </a>
+<a name="2130"><span class="lineNum">    2130 </span>            :   //! Instruction signature.</a>
+<a name="2131"><span class="lineNum">    2131 </span>            :   //!</a>
+<a name="2132"><span class="lineNum">    2132 </span>            :   //! Contains a sequence of operands' combinations and other metadata that defines</a>
+<a name="2133"><span class="lineNum">    2133 </span>            :   //! a single instruction. This data is used by instruction validator.</a>
+<a name="2134"><span class="lineNum">    2134 </span>            :   struct ISignature {</a>
+<a name="2135"><span class="lineNum">    2135 </span>            :     uint8_t opCount  : 3;                //!&lt; Count of operands in `opIndex` (0..6).</a>
+<a name="2136"><span class="lineNum">    2136 </span>            :     uint8_t archMask : 2;                //!&lt; Architecture mask of this record.</a>
+<a name="2137"><span class="lineNum">    2137 </span>            :     uint8_t implicit : 3;                //!&lt; Number of implicit operands.</a>
+<a name="2138"><span class="lineNum">    2138 </span>            :     uint8_t reserved;                    //!&lt; Reserved for future use.</a>
+<a name="2139"><span class="lineNum">    2139 </span>            :     uint8_t operands[6];                 //!&lt; Indexes to `OSignature` table.</a>
+<a name="2140"><span class="lineNum">    2140 </span>            :   };</a>
+<a name="2141"><span class="lineNum">    2141 </span>            : </a>
+<a name="2142"><span class="lineNum">    2142 </span>            :   //! Operand signature, used by \ref ISignature.</a>
+<a name="2143"><span class="lineNum">    2143 </span>            :   //!</a>
+<a name="2144"><span class="lineNum">    2144 </span>            :   //! Contains all possible operand combinations, memory size information,</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :   //! and register index (or \ref Globals::kInvalidRegId if not mandatory).</a>
+<a name="2146"><span class="lineNum">    2146 </span>            :   struct OSignature {</a>
+<a name="2147"><span class="lineNum">    2147 </span>            :     uint32_t flags;                      //!&lt; Operand flags.</a>
+<a name="2148"><span class="lineNum">    2148 </span>            :     uint16_t memFlags;                   //!&lt; Memory flags.</a>
+<a name="2149"><span class="lineNum">    2149 </span>            :     uint8_t extFlags;                    //!&lt; Extra flags.</a>
+<a name="2150"><span class="lineNum">    2150 </span>            :     uint8_t regMask;                     //!&lt; Mask of possible register IDs.</a>
+<a name="2151"><span class="lineNum">    2151 </span>            :   };</a>
+<a name="2152"><span class="lineNum">    2152 </span>            : </a>
+<a name="2153"><span class="lineNum">    2153 </span>            :   //! Common data - aggregated data that is shared across many instructions.</a>
+<a name="2154"><span class="lineNum">    2154 </span>            :   struct CommonData {</a>
+<a name="2155"><span class="lineNum">    2155 </span>            :     //! Get all instruction flags, see \ref X86Inst::Flags.</a>
+<a name="2156"><span class="lineNum">    2156 </span><span class="lineCov">      30892 :     ASMJIT_INLINE uint32_t getFlags() const noexcept { return _flags; }</span></a>
+<a name="2157"><span class="lineNum">    2157 </span>            :     //! Get if the instruction has a `flag`, see \ref X86Inst::Flags.</a>
+<a name="2158"><span class="lineNum">    2158 </span><span class="lineCov">      73104 :     ASMJIT_INLINE bool hasFlag(uint32_t flag) const noexcept { return (_flags &amp; flag) != 0; }</span></a>
+<a name="2159"><span class="lineNum">    2159 </span>            : </a>
+<a name="2160"><span class="lineNum">    2160 </span>            :     //! Get if 1st operand is read-only.</a>
+<a name="2161"><span class="lineNum">    2161 </span>            :     ASMJIT_INLINE bool isUseR() const noexcept { return (getFlags() &amp; kFlagUseX) == kFlagUseR; }</a>
+<a name="2162"><span class="lineNum">    2162 </span>            :     //! Get if 1st operand is write-only.</a>
+<a name="2163"><span class="lineNum">    2163 </span><span class="lineCov">      30892 :     ASMJIT_INLINE bool isUseW() const noexcept { return (getFlags() &amp; kFlagUseX) == kFlagUseW; }</span></a>
+<a name="2164"><span class="lineNum">    2164 </span>            :     //! Get if 1st operand is read-write.</a>
+<a name="2165"><span class="lineNum">    2165 </span>            :     ASMJIT_INLINE bool isUseX() const noexcept { return (getFlags() &amp; kFlagUseX) == kFlagUseX; }</a>
+<a name="2166"><span class="lineNum">    2166 </span>            :     //! Get if 1st and 2nd operands are read-write.</a>
+<a name="2167"><span class="lineNum">    2167 </span>            :     ASMJIT_INLINE bool isUseXX() const noexcept { return hasFlag(kFlagUseXX); }</a>
+<a name="2168"><span class="lineNum">    2168 </span>            : </a>
+<a name="2169"><span class="lineNum">    2169 </span>            :     ASMJIT_INLINE bool hasFixedReg() const noexcept { return hasFlag(kFlagFixedReg); }</a>
+<a name="2170"><span class="lineNum">    2170 </span>            :     ASMJIT_INLINE bool hasFixedMem() const noexcept { return hasFlag(kFlagFixedMem); }</a>
+<a name="2171"><span class="lineNum">    2171 </span>            :     ASMJIT_INLINE bool hasFixedRM() const noexcept { return hasFlag(kFlagFixedRM); }</a>
+<a name="2172"><span class="lineNum">    2172 </span>            : </a>
+<a name="2173"><span class="lineNum">    2173 </span>            :     //! Get if the instruction is FPU instruction.</a>
+<a name="2174"><span class="lineNum">    2174 </span>            :     ASMJIT_INLINE bool isFpu() const noexcept { return hasFlag(kFlagFpu); }</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :     //! Get if the instruction is MMX|3DNOW instruction that accesses MMX registers (includes EMMS).</a>
+<a name="2176"><span class="lineNum">    2176 </span>            :     ASMJIT_INLINE bool isMmx() const noexcept { return hasFlag(kFlagMmx); }</a>
+<a name="2177"><span class="lineNum">    2177 </span>            : </a>
+<a name="2178"><span class="lineNum">    2178 </span>            :     //! Get if the instruction is SSE|AVX|AVX512 instruction that accesses XMM|YMM|ZMM registers (includes VZEROALL|VZEROUPPER).</a>
+<a name="2179"><span class="lineNum">    2179 </span>            :     ASMJIT_INLINE bool isVec() const noexcept { return hasFlag(kFlagVec); }</a>
+<a name="2180"><span class="lineNum">    2180 </span>            :     //! Get if the instruction is SSE+ (SSE4.2, AES, SHA included) instruction that accesses XMM registers.</a>
+<a name="2181"><span class="lineNum">    2181 </span>            :     ASMJIT_INLINE bool isSse() const noexcept { return (getFlags() &amp; (kFlagVec | kFlagVex | kFlagEvex)) == kFlagVec; }</a>
+<a name="2182"><span class="lineNum">    2182 </span>            :     //! Get if the instruction is AVX+ (FMA included) instruction that accesses XMM|YMM|ZMM registers.</a>
+<a name="2183"><span class="lineNum">    2183 </span>            :     ASMJIT_INLINE bool isAvx() const noexcept { return isVec() &amp;&amp; isVexOrEvex(); }</a>
+<a name="2184"><span class="lineNum">    2184 </span>            : </a>
+<a name="2185"><span class="lineNum">    2185 </span>            :     //! Get if the instruction can be prefixed by LOCK prefix.</a>
+<a name="2186"><span class="lineNum">    2186 </span>            :     ASMJIT_INLINE bool isLockEnabled() const noexcept { return hasFlag(kFlagLock); }</a>
+<a name="2187"><span class="lineNum">    2187 </span>            :     //! Get if the instruction can be prefixed by REP prefix.</a>
+<a name="2188"><span class="lineNum">    2188 </span>            :     ASMJIT_INLINE bool isRepEnabled() const noexcept { return hasFlag(kFlagRep); }</a>
+<a name="2189"><span class="lineNum">    2189 </span>            :     //! Get if the instruction can be prefixed by REPZ prefix.</a>
+<a name="2190"><span class="lineNum">    2190 </span>            :     ASMJIT_INLINE bool isRepzEnabled() const noexcept { return hasFlag(kFlagRep); }</a>
+<a name="2191"><span class="lineNum">    2191 </span>            :     //! Get if the instruction can be prefixed by REPNZ prefix.</a>
+<a name="2192"><span class="lineNum">    2192 </span>            :     ASMJIT_INLINE bool isRepnzEnabled() const noexcept { return hasFlag(kFlagRepnz); }</a>
+<a name="2193"><span class="lineNum">    2193 </span>            : </a>
+<a name="2194"><span class="lineNum">    2194 </span>            :     //! Get if the instruction uses MIB.</a>
+<a name="2195"><span class="lineNum">    2195 </span>            :     ASMJIT_INLINE bool isMibOp() const noexcept { return hasFlag(kFlagMib); }</a>
+<a name="2196"><span class="lineNum">    2196 </span>            :     //! Get if the instruction uses VSIB.</a>
+<a name="2197"><span class="lineNum">    2197 </span>            :     ASMJIT_INLINE bool isVsibOp() const noexcept { return hasFlag(kFlagVsib); }</a>
+<a name="2198"><span class="lineNum">    2198 </span>            :     //! Get if the instruction uses VEX (can be set together with EVEX if both are encodable).</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :     ASMJIT_INLINE bool isVex() const noexcept { return hasFlag(kFlagVex); }</a>
+<a name="2200"><span class="lineNum">    2200 </span>            :     //! Get if the instruction uses EVEX (can be set together with VEX if both are encodable).</a>
+<a name="2201"><span class="lineNum">    2201 </span>            :     ASMJIT_INLINE bool isEvex() const noexcept { return hasFlag(kFlagEvex); }</a>
+<a name="2202"><span class="lineNum">    2202 </span>            :     //! Get if the instruction uses VEX and/or EVEX.</a>
+<a name="2203"><span class="lineNum">    2203 </span>            :     ASMJIT_INLINE bool isVexOrEvex() const noexcept { return hasFlag(kFlagVex | kFlagEvex); }</a>
+<a name="2204"><span class="lineNum">    2204 </span>            : </a>
+<a name="2205"><span class="lineNum">    2205 </span>            :     //! Get if the instruction supports AVX512 masking {k}.</a>
+<a name="2206"><span class="lineNum">    2206 </span>            :     ASMJIT_INLINE bool hasAvx512K() const noexcept { return hasFlag(kFlagAvx512K); }</a>
+<a name="2207"><span class="lineNum">    2207 </span>            :     //! Get if the instruction supports AVX512 zeroing {k}{z}.</a>
+<a name="2208"><span class="lineNum">    2208 </span>            :     ASMJIT_INLINE bool hasAvx512Z() const noexcept { return hasFlag(kFlagAvx512Z); }</a>
+<a name="2209"><span class="lineNum">    2209 </span>            :     //! Get if the instruction supports AVX512 embedded-rounding {er}.</a>
+<a name="2210"><span class="lineNum">    2210 </span>            :     ASMJIT_INLINE bool hasAvx512ER() const noexcept { return hasFlag(kFlagAvx512ER); }</a>
+<a name="2211"><span class="lineNum">    2211 </span>            :     //! Get if the instruction supports AVX512 suppress-all-exceptions {sae}.</a>
+<a name="2212"><span class="lineNum">    2212 </span>            :     ASMJIT_INLINE bool hasAvx512SAE() const noexcept { return hasFlag(kFlagAvx512SAE); }</a>
+<a name="2213"><span class="lineNum">    2213 </span>            :     //! Get if the instruction supports AVX512 broadcast (either 32-bit or 64-bit).</a>
+<a name="2214"><span class="lineNum">    2214 </span>            :     ASMJIT_INLINE bool hasAvx512B() const noexcept { return hasFlag(kFlagAvx512B32 | kFlagAvx512B64); }</a>
+<a name="2215"><span class="lineNum">    2215 </span>            :     //! Get if the instruction supports AVX512 broadcast (32-bit).</a>
+<a name="2216"><span class="lineNum">    2216 </span>            :     ASMJIT_INLINE bool hasAvx512B32() const noexcept { return hasFlag(kFlagAvx512B32); }</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :     //! Get if the instruction supports AVX512 broadcast (64-bit).</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :     ASMJIT_INLINE bool hasAvx512B64() const noexcept { return hasFlag(kFlagAvx512B64); }</a>
+<a name="2219"><span class="lineNum">    2219 </span>            : </a>
+<a name="2220"><span class="lineNum">    2220 </span>            :     //! Get if the instruction may or will jump (returns true also for calls and returns).</a>
+<a name="2221"><span class="lineNum">    2221 </span>            :     ASMJIT_INLINE bool doesJump() const noexcept { return _jumpType != Inst::kJumpTypeNone; }</a>
+<a name="2222"><span class="lineNum">    2222 </span>            : </a>
+<a name="2223"><span class="lineNum">    2223 </span>            :     //! Get the destination index of WRITE operation.</a>
+<a name="2224"><span class="lineNum">    2224 </span>            :     ASMJIT_INLINE uint32_t getWriteIndex() const noexcept { return _writeIndex; }</a>
+<a name="2225"><span class="lineNum">    2225 </span>            :     //! Get the number of bytes that will be written by a WRITE operation.</a>
+<a name="2226"><span class="lineNum">    2226 </span>            :     //!</a>
+<a name="2227"><span class="lineNum">    2227 </span>            :     //! This information is required by a liveness analysis to mark virtual</a>
+<a name="2228"><span class="lineNum">    2228 </span>            :     //! registers dead even if the instruction doesn't completely overwrite</a>
+<a name="2229"><span class="lineNum">    2229 </span>            :     //! the whole register. If the analysis keeps which bytes are completely</a>
+<a name="2230"><span class="lineNum">    2230 </span>            :     //! overwritten by the instruction it can find the where a register becomes</a>
+<a name="2231"><span class="lineNum">    2231 </span>            :     //! dead by simply checking if the instruction overwrites all remaining</a>
+<a name="2232"><span class="lineNum">    2232 </span>            :     //! bytes.</a>
+<a name="2233"><span class="lineNum">    2233 </span><span class="lineCov">      21892 :     ASMJIT_INLINE uint32_t getWriteSize() const noexcept { return _writeSize; }</span></a>
+<a name="2234"><span class="lineNum">    2234 </span>            : </a>
+<a name="2235"><span class="lineNum">    2235 </span>            :     //! Get if the instruction has alternative opcode.</a>
+<a name="2236"><span class="lineNum">    2236 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE bool hasAltOpCode() const noexcept { return _altOpCodeIndex != 0; }</span></a>
+<a name="2237"><span class="lineNum">    2237 </span>            :     //! Get alternative opcode, see \ref OpCodeBits.</a>
+<a name="2238"><span class="lineNum">    2238 </span>            :     ASMJIT_INLINE uint32_t getAltOpCode() const noexcept;</a>
+<a name="2239"><span class="lineNum">    2239 </span>            : </a>
+<a name="2240"><span class="lineNum">    2240 </span>            :     ASMJIT_INLINE uint32_t getISignatureIndex() const noexcept { return _iSignatureIndex; }</a>
+<a name="2241"><span class="lineNum">    2241 </span>            :     ASMJIT_INLINE uint32_t getISignatureCount() const noexcept { return _iSignatureCount; }</a>
+<a name="2242"><span class="lineNum">    2242 </span>            : </a>
+<a name="2243"><span class="lineNum">    2243 </span>            :     ASMJIT_INLINE const ISignature* getISignatureData() const noexcept;</a>
+<a name="2244"><span class="lineNum">    2244 </span>            :     ASMJIT_INLINE const ISignature* getISignatureEnd() const noexcept;</a>
+<a name="2245"><span class="lineNum">    2245 </span>            : </a>
+<a name="2246"><span class="lineNum">    2246 </span>            :     ASMJIT_INLINE uint32_t getJumpType() const noexcept { return _jumpType; }</a>
+<a name="2247"><span class="lineNum">    2247 </span>            :     ASMJIT_INLINE uint32_t getSingleRegCase() const noexcept { return _singleRegCase; }</a>
+<a name="2248"><span class="lineNum">    2248 </span>            : </a>
+<a name="2249"><span class="lineNum">    2249 </span>            :     uint32_t _flags;                     //!&lt; Instruction flags.</a>
+<a name="2250"><span class="lineNum">    2250 </span>            :     uint32_t _writeIndex         : 8;    //!&lt; First DST byte of a WRITE operation (default 0).</a>
+<a name="2251"><span class="lineNum">    2251 </span>            :     uint32_t _writeSize          :24;    //!&lt; Number of bytes to be written in DST.</a>
+<a name="2252"><span class="lineNum">    2252 </span>            : </a>
+<a name="2253"><span class="lineNum">    2253 </span>            :     uint32_t _altOpCodeIndex     : 8;    //!&lt; Index to table with alternative opcodes.</a>
+<a name="2254"><span class="lineNum">    2254 </span>            :     uint32_t _iSignatureIndex    :10;    //!&lt; First `ISignature` entry in the database.</a>
+<a name="2255"><span class="lineNum">    2255 </span>            :     uint32_t _iSignatureCount    : 4;    //!&lt; Number of relevant `ISignature` entries.</a>
+<a name="2256"><span class="lineNum">    2256 </span>            :     uint32_t _jumpType           : 3;    //!&lt; Jump type, see `Inst::JumpType`.</a>
+<a name="2257"><span class="lineNum">    2257 </span>            :     uint32_t _singleRegCase      : 2;    //!&lt; Specifies what happens if all source operands share the same register.</a>
+<a name="2258"><span class="lineNum">    2258 </span>            :     uint32_t _reserved           : 5;    //!&lt; \internal</a>
+<a name="2259"><span class="lineNum">    2259 </span>            :   };</a>
+<a name="2260"><span class="lineNum">    2260 </span>            : </a>
+<a name="2261"><span class="lineNum">    2261 </span>            :   //! Detailed data about instruction's operation, requirements, and side-effects.</a>
+<a name="2262"><span class="lineNum">    2262 </span>            :   struct OperationData {</a>
+<a name="2263"><span class="lineNum">    2263 </span>            :     ASMJIT_INLINE uint32_t getOperationFlags() const noexcept { return _flags; }</a>
+<a name="2264"><span class="lineNum">    2264 </span><span class="lineCov">       5834 :     ASMJIT_INLINE bool hasOperationFlag(uint32_t flag) const noexcept { return (_flags &amp; flag) != 0; }</span></a>
+<a name="2265"><span class="lineNum">    2265 </span>            : </a>
+<a name="2266"><span class="lineNum">    2266 </span>            :     ASMJIT_INLINE bool isMovCrDr() const noexcept { return hasOperationFlag(kOperationMovCrDr); }</a>
+<a name="2267"><span class="lineNum">    2267 </span>            :     ASMJIT_INLINE bool isMovSsSd() const noexcept { return hasOperationFlag(kOperationMovSsSd); }</a>
+<a name="2268"><span class="lineNum">    2268 </span>            : </a>
+<a name="2269"><span class="lineNum">    2269 </span>            :     ASMJIT_INLINE bool isPrefetch() const noexcept { return hasOperationFlag(kOperationPrefetch); }</a>
+<a name="2270"><span class="lineNum">    2270 </span>            :     ASMJIT_INLINE bool isBarrier() const noexcept { return hasOperationFlag(kOperationBarrier); }</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :     ASMJIT_INLINE bool isVolatile() const noexcept { return hasOperationFlag(kOperationVolatile); }</a>
+<a name="2272"><span class="lineNum">    2272 </span>            :     ASMJIT_INLINE bool isPrivileged() const noexcept { return hasOperationFlag(kOperationPrivileged); }</a>
+<a name="2273"><span class="lineNum">    2273 </span>            : </a>
+<a name="2274"><span class="lineNum">    2274 </span>            :     ASMJIT_INLINE bool hasFeature(uint32_t feature) const noexcept {</a>
+<a name="2275"><span class="lineNum">    2275 </span>            :       for (uint32_t i = 0; i &lt; ASMJIT_ARRAY_SIZE(_features); i++)</a>
+<a name="2276"><span class="lineNum">    2276 </span>            :         if (feature == _features[i])</a>
+<a name="2277"><span class="lineNum">    2277 </span>            :           return true;</a>
+<a name="2278"><span class="lineNum">    2278 </span>            :       return false;</a>
+<a name="2279"><span class="lineNum">    2279 </span>            :     }</a>
+<a name="2280"><span class="lineNum">    2280 </span>            : </a>
+<a name="2281"><span class="lineNum">    2281 </span>            :     ASMJIT_INLINE uint32_t getSpecialRegsR() const noexcept { return _specialRegsR; }</a>
+<a name="2282"><span class="lineNum">    2282 </span>            :     ASMJIT_INLINE uint32_t getSpecialRegsW() const noexcept { return _specialRegsW; }</a>
+<a name="2283"><span class="lineNum">    2283 </span>            : </a>
+<a name="2284"><span class="lineNum">    2284 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE const uint8_t* getFeaturesData() const noexcept { return _features; }</span></a>
+<a name="2285"><span class="lineNum">    2285 </span><span class="lineNoCov">          0 :     ASMJIT_INLINE const uint8_t* getFeaturesEnd() const noexcept { return _features + ASMJIT_ARRAY_SIZE(_features); }</span></a>
+<a name="2286"><span class="lineNum">    2286 </span>            : </a>
+<a name="2287"><span class="lineNum">    2287 </span>            :     uint32_t _flags;                     //!&lt; Operation flags.</a>
+<a name="2288"><span class="lineNum">    2288 </span>            :     uint8_t _features[4];                //!&lt; Features vector (max 4 features).</a>
+<a name="2289"><span class="lineNum">    2289 </span>            :     uint32_t _specialRegsR;              //!&lt; Special registers read.</a>
+<a name="2290"><span class="lineNum">    2290 </span>            :     uint32_t _specialRegsW;              //!&lt; Special registers written.</a>
+<a name="2291"><span class="lineNum">    2291 </span>            :   };</a>
+<a name="2292"><span class="lineNum">    2292 </span>            : </a>
+<a name="2293"><span class="lineNum">    2293 </span>            :   //! Contains data that can be used to convert SSE to AVX (or back).</a>
+<a name="2294"><span class="lineNum">    2294 </span>            :   struct SseToAvxData {</a>
+<a name="2295"><span class="lineNum">    2295 </span>            :     ASMJIT_INLINE uint32_t getMode() const noexcept { return _mode; }</a>
+<a name="2296"><span class="lineNum">    2296 </span>            :     ASMJIT_INLINE int32_t getDelta() const noexcept { return _delta; }</a>
+<a name="2297"><span class="lineNum">    2297 </span>            : </a>
+<a name="2298"><span class="lineNum">    2298 </span>            :     uint16_t _mode :  3;                 //!&lt; SSE to AVX conversion mode, see \ref AvxConvMode.</a>
+<a name="2299"><span class="lineNum">    2299 </span>            :     int16_t _delta : 13;                 //!&lt; Delta to get a corresponding AVX instruction.</a>
+<a name="2300"><span class="lineNum">    2300 </span>            :   };</a>
+<a name="2301"><span class="lineNum">    2301 </span>            : </a>
+<a name="2302"><span class="lineNum">    2302 </span>            :   //! Data that is not related to a specific X86 instruction (not referenced by</a>
+<a name="2303"><span class="lineNum">    2303 </span>            :   //! any tables).</a>
+<a name="2304"><span class="lineNum">    2304 </span>            :   struct MiscData {</a>
+<a name="2305"><span class="lineNum">    2305 </span>            :     uint32_t condToJcc[x86::kCondCount];</a>
+<a name="2306"><span class="lineNum">    2306 </span>            :     uint32_t condToSetcc[x86::kCondCount];</a>
+<a name="2307"><span class="lineNum">    2307 </span>            :     uint32_t condToCmovcc[x86::kCondCount];</a>
+<a name="2308"><span class="lineNum">    2308 </span>            :     uint32_t reversedCond[x86::kCondCount];</a>
+<a name="2309"><span class="lineNum">    2309 </span>            :   };</a>
+<a name="2310"><span class="lineNum">    2310 </span>            : </a>
+<a name="2311"><span class="lineNum">    2311 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :   // [Accessors]</a>
+<a name="2313"><span class="lineNum">    2313 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2314"><span class="lineNum">    2314 </span>            : </a>
+<a name="2315"><span class="lineNum">    2315 </span>            :   //! Get instruction name (null terminated).</a>
+<a name="2316"><span class="lineNum">    2316 </span>            :   //!</a>
+<a name="2317"><span class="lineNum">    2317 </span>            :   //! NOTE: If AsmJit was compiled with `ASMJIT_DISABLE_TEXT` then this will</a>
+<a name="2318"><span class="lineNum">    2318 </span>            :   //! return an empty string (null terminated string of zero length).</a>
+<a name="2319"><span class="lineNum">    2319 </span>            :   ASMJIT_INLINE const char* getName() const noexcept;</a>
+<a name="2320"><span class="lineNum">    2320 </span>            :   //! Get index to `X86InstDB::nameData` of this instruction.</a>
+<a name="2321"><span class="lineNum">    2321 </span>            :   //!</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :   //! NOTE: If AsmJit was compiled with `ASMJIT_DISABLE_TEXT` then this will</a>
+<a name="2323"><span class="lineNum">    2323 </span>            :   //! always return zero.</a>
+<a name="2324"><span class="lineNum">    2324 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getNameDataIndex() const noexcept { return _nameDataIndex; }</span></a>
+<a name="2325"><span class="lineNum">    2325 </span>            : </a>
+<a name="2326"><span class="lineNum">    2326 </span>            :   //! Get \ref CommonData of the instruction.</a>
+<a name="2327"><span class="lineNum">    2327 </span>            :   ASMJIT_INLINE const CommonData&amp; getCommonData() const noexcept;</a>
+<a name="2328"><span class="lineNum">    2328 </span>            :   //! Get index to `X86InstDB::commonData` of this instruction.</a>
+<a name="2329"><span class="lineNum">    2329 </span>            :   ASMJIT_INLINE uint32_t getCommonDataIndex() const noexcept { return _commonDataIndex; }</a>
+<a name="2330"><span class="lineNum">    2330 </span>            : </a>
+<a name="2331"><span class="lineNum">    2331 </span>            :   //! Get \ref OperationData of the instruction.</a>
+<a name="2332"><span class="lineNum">    2332 </span>            :   ASMJIT_INLINE const OperationData&amp; getOperationData() const noexcept;</a>
+<a name="2333"><span class="lineNum">    2333 </span>            :   //! Get index to `X86InstDB::operationData` of this instruction.</a>
+<a name="2334"><span class="lineNum">    2334 </span>            :   ASMJIT_INLINE uint32_t getOperationDataIndex() const noexcept { return _operationDataIndex; }</a>
+<a name="2335"><span class="lineNum">    2335 </span>            : </a>
+<a name="2336"><span class="lineNum">    2336 </span>            :   //! Get data that can be used to convert SSE instruction to AVX (or back).</a>
+<a name="2337"><span class="lineNum">    2337 </span>            :   ASMJIT_INLINE const SseToAvxData&amp; getSseToAvxData() const noexcept;</a>
+<a name="2338"><span class="lineNum">    2338 </span>            :   //! Get index to `X86InstDB::sseToAvxData` of this instruction.</a>
+<a name="2339"><span class="lineNum">    2339 </span>            :   ASMJIT_INLINE uint32_t getSseToAvxDataIndex() const noexcept { return _sseToAvxDataIndex; }</a>
+<a name="2340"><span class="lineNum">    2340 </span>            : </a>
+<a name="2341"><span class="lineNum">    2341 </span>            :   //! Get instruction encoding, see \ref EncodingType.</a>
+<a name="2342"><span class="lineNum">    2342 </span><span class="lineCov">      48362 :   ASMJIT_INLINE uint32_t getEncodingType() const noexcept { return _encodingType; }</span></a>
+<a name="2343"><span class="lineNum">    2343 </span>            : </a>
+<a name="2344"><span class="lineNum">    2344 </span>            :   //! Get if the instruction has main opcode (rare, but it's possible it doesn't have).</a>
+<a name="2345"><span class="lineNum">    2345 </span>            :   ASMJIT_INLINE bool hasMainOpCode() const noexcept { return _mainOpCode != 0; }</a>
+<a name="2346"><span class="lineNum">    2346 </span>            :   //! Get main opcode, see \ref OpCodeBits.</a>
+<a name="2347"><span class="lineNum">    2347 </span><span class="lineCov">      48362 :   ASMJIT_INLINE uint32_t getMainOpCode() const noexcept { return _mainOpCode; }</span></a>
+<a name="2348"><span class="lineNum">    2348 </span>            : </a>
+<a name="2349"><span class="lineNum">    2349 </span>            :   //! Get if the instruction has alternative opcode.</a>
+<a name="2350"><span class="lineNum">    2350 </span>            :   ASMJIT_INLINE bool hasAltOpCode() const noexcept { return getCommonData().hasAltOpCode(); }</a>
+<a name="2351"><span class="lineNum">    2351 </span>            :   //! Get alternative opcode, see \ref OpCodeBits.</a>
+<a name="2352"><span class="lineNum">    2352 </span>            :   ASMJIT_INLINE uint32_t getAltOpCode() const noexcept { return getCommonData().getAltOpCode(); }</a>
+<a name="2353"><span class="lineNum">    2353 </span>            : </a>
+<a name="2354"><span class="lineNum">    2354 </span>            :   //! Get if the instruction has flag `flag`, see \ref Flags.</a>
+<a name="2355"><span class="lineNum">    2355 </span>            :   ASMJIT_INLINE bool hasFlag(uint32_t flag) const noexcept { return getCommonData().hasFlag(flag); }</a>
+<a name="2356"><span class="lineNum">    2356 </span>            :   //! Get instruction flags, see \ref Flags.</a>
+<a name="2357"><span class="lineNum">    2357 </span>            :   ASMJIT_INLINE uint32_t getFlags() const noexcept { return getCommonData().getFlags(); }</a>
+<a name="2358"><span class="lineNum">    2358 </span>            : </a>
+<a name="2359"><span class="lineNum">    2359 </span>            :   //! Get if the instruction is FPU instruction.</a>
+<a name="2360"><span class="lineNum">    2360 </span>            :   ASMJIT_INLINE bool isFpu() const noexcept { return getCommonData().isFpu(); }</a>
+<a name="2361"><span class="lineNum">    2361 </span>            :   //! Get if the instruction is MMX instruction that accesses MMX registersm, including EMMS.</a>
+<a name="2362"><span class="lineNum">    2362 </span>            :   ASMJIT_INLINE bool isMmx() const noexcept { return getCommonData().isMmx(); }</a>
+<a name="2363"><span class="lineNum">    2363 </span>            : </a>
+<a name="2364"><span class="lineNum">    2364 </span>            :   //! Get if the instruction is SSE|AVX|AVX512 instruction that accesses XMM|YMM|ZMM registers.</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :   ASMJIT_INLINE bool isVec() const noexcept { return getCommonData().isVec(); }</a>
+<a name="2366"><span class="lineNum">    2366 </span>            :   //! Get if the instruction is SSE+ (SSE4.2, AES, SHA included) instruction that accesses XMM registers.</a>
+<a name="2367"><span class="lineNum">    2367 </span>            :   ASMJIT_INLINE bool isSse() const noexcept { return getCommonData().isSse(); }</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :   //! Get if the instruction is AVX+ (FMA included) instruction that accesses XMM|YMM|ZMM registers.</a>
+<a name="2369"><span class="lineNum">    2369 </span>            :   ASMJIT_INLINE bool isAvx() const noexcept { return getCommonData().isAvx(); }</a>
+<a name="2370"><span class="lineNum">    2370 </span>            : </a>
+<a name="2371"><span class="lineNum">    2371 </span>            :   //! Get if the instruction can be prefixed by LOCK prefix.</a>
+<a name="2372"><span class="lineNum">    2372 </span>            :   ASMJIT_INLINE bool isLockEnabled() const noexcept { return getCommonData().isLockEnabled(); }</a>
+<a name="2373"><span class="lineNum">    2373 </span>            :   //! Get if the instruction can be prefixed by REP prefix.</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :   ASMJIT_INLINE bool isRepEnabled() const noexcept { return getCommonData().isRepEnabled(); }</a>
+<a name="2375"><span class="lineNum">    2375 </span>            :   //! Get if the instruction can be prefixed by REPZ prefix.</a>
+<a name="2376"><span class="lineNum">    2376 </span>            :   ASMJIT_INLINE bool isRepzEnabled() const noexcept { return getCommonData().isRepzEnabled(); }</a>
+<a name="2377"><span class="lineNum">    2377 </span>            :   //! Get if the instruction can be prefixed by REPNZ prefix.</a>
+<a name="2378"><span class="lineNum">    2378 </span>            :   ASMJIT_INLINE bool isRepnzEnabled() const noexcept { return getCommonData().isRepnzEnabled(); }</a>
+<a name="2379"><span class="lineNum">    2379 </span>            : </a>
+<a name="2380"><span class="lineNum">    2380 </span>            :   //! Get if the instruction uses MIB.</a>
+<a name="2381"><span class="lineNum">    2381 </span>            :   ASMJIT_INLINE bool isMibOp() const noexcept { return getCommonData().isMibOp(); }</a>
+<a name="2382"><span class="lineNum">    2382 </span>            :   //! Get if the instruction uses VSIB.</a>
+<a name="2383"><span class="lineNum">    2383 </span>            :   ASMJIT_INLINE bool isVsibOp() const noexcept { return getCommonData().isVsibOp(); }</a>
+<a name="2384"><span class="lineNum">    2384 </span>            :   //! Get if the instruction uses VEX (can be set together with EVEX if both are encodable).</a>
+<a name="2385"><span class="lineNum">    2385 </span>            :   ASMJIT_INLINE bool isVex() const noexcept { return getCommonData().isVex(); }</a>
+<a name="2386"><span class="lineNum">    2386 </span>            :   //! Get if the instruction uses EVEX (can be set together with VEX if both are encodable).</a>
+<a name="2387"><span class="lineNum">    2387 </span>            :   ASMJIT_INLINE bool isEvex() const noexcept { return getCommonData().isEvex(); }</a>
+<a name="2388"><span class="lineNum">    2388 </span>            : </a>
+<a name="2389"><span class="lineNum">    2389 </span>            :   //! Get if the instruction supports AVX512 masking {k}.</a>
+<a name="2390"><span class="lineNum">    2390 </span>            :   ASMJIT_INLINE bool hasAvx512K() const noexcept { return getCommonData().hasAvx512K(); }</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :   //! Get if the instruction supports AVX512 zeroing {k}{z}.</a>
+<a name="2392"><span class="lineNum">    2392 </span>            :   ASMJIT_INLINE bool hasAvx512Z() const noexcept { return getCommonData().hasAvx512Z(); }</a>
+<a name="2393"><span class="lineNum">    2393 </span>            :   //! Get if the instruction supports AVX512 embedded-rounding {er}.</a>
+<a name="2394"><span class="lineNum">    2394 </span>            :   ASMJIT_INLINE bool hasAvx512ER() const noexcept { return getCommonData().hasAvx512ER(); }</a>
+<a name="2395"><span class="lineNum">    2395 </span>            :   //! Get if the instruction supports AVX512 suppress-all-exceptions {sae}.</a>
+<a name="2396"><span class="lineNum">    2396 </span>            :   ASMJIT_INLINE bool hasAvx512SAE() const noexcept { return getCommonData().hasAvx512SAE(); }</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :   //! Get if the instruction supports AVX512 broadcast (either 32-bit or 64-bit).</a>
+<a name="2398"><span class="lineNum">    2398 </span>            :   ASMJIT_INLINE bool hasAvx512B() const noexcept { return getCommonData().hasAvx512B(); }</a>
+<a name="2399"><span class="lineNum">    2399 </span>            :   //! Get if the instruction supports AVX512 broadcast (32-bit).</a>
+<a name="2400"><span class="lineNum">    2400 </span>            :   ASMJIT_INLINE bool hasAvx512B32() const noexcept { return getCommonData().hasAvx512B32(); }</a>
+<a name="2401"><span class="lineNum">    2401 </span>            :   //! Get if the instruction supports AVX512 broadcast (64-bit).</a>
+<a name="2402"><span class="lineNum">    2402 </span>            :   ASMJIT_INLINE bool hasAvx512B64() const noexcept { return getCommonData().hasAvx512B64(); }</a>
+<a name="2403"><span class="lineNum">    2403 </span>            : </a>
+<a name="2404"><span class="lineNum">    2404 </span>            :   ASMJIT_INLINE uint32_t getISignatureIndex() const noexcept { return getCommonData().getISignatureIndex(); }</a>
+<a name="2405"><span class="lineNum">    2405 </span>            :   ASMJIT_INLINE uint32_t getISignatureCount() const noexcept { return getCommonData().getISignatureCount(); }</a>
+<a name="2406"><span class="lineNum">    2406 </span>            : </a>
+<a name="2407"><span class="lineNum">    2407 </span>            :   ASMJIT_INLINE const ISignature* getISignatureData() const noexcept { return getCommonData().getISignatureData(); }</a>
+<a name="2408"><span class="lineNum">    2408 </span>            :   ASMJIT_INLINE const ISignature* getISignatureEnd() const noexcept { return getCommonData().getISignatureEnd(); }</a>
+<a name="2409"><span class="lineNum">    2409 </span>            : </a>
+<a name="2410"><span class="lineNum">    2410 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2411"><span class="lineNum">    2411 </span>            :   // [Get]</a>
+<a name="2412"><span class="lineNum">    2412 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2413"><span class="lineNum">    2413 </span>            : </a>
+<a name="2414"><span class="lineNum">    2414 </span>            :   //! Get if the `instId` is defined (counts also Inst::kIdNone, which must be zero).</a>
+<a name="2415"><span class="lineNum">    2415 </span>            :   static ASMJIT_INLINE bool isDefinedId(uint32_t instId) noexcept { return instId &lt; _kIdCount; }</a>
+<a name="2416"><span class="lineNum">    2416 </span>            : </a>
+<a name="2417"><span class="lineNum">    2417 </span>            :   //! Get instruction information based on the instruction `instId`.</a>
+<a name="2418"><span class="lineNum">    2418 </span>            :   //!</a>
+<a name="2419"><span class="lineNum">    2419 </span>            :   //! NOTE: `instId` has to be a valid instruction ID, it can't be greater than</a>
+<a name="2420"><span class="lineNum">    2420 </span>            :   //! or equal to `X86Inst::_kIdCount`. It asserts in debug mode.</a>
+<a name="2421"><span class="lineNum">    2421 </span>            :   static ASMJIT_INLINE const X86Inst&amp; getInst(uint32_t instId) noexcept;</a>
+<a name="2422"><span class="lineNum">    2422 </span>            : </a>
+<a name="2423"><span class="lineNum">    2423 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2424"><span class="lineNum">    2424 </span>            :   // [Utilities]</a>
+<a name="2425"><span class="lineNum">    2425 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2426"><span class="lineNum">    2426 </span>            : </a>
+<a name="2427"><span class="lineNum">    2427 </span>            :   static ASMJIT_INLINE const MiscData&amp; getMiscData() noexcept;</a>
+<a name="2428"><span class="lineNum">    2428 </span>            : </a>
+<a name="2429"><span class="lineNum">    2429 </span>            :   //! Get the equivalent of a negated condition code.</a>
+<a name="2430"><span class="lineNum">    2430 </span>            :   static ASMJIT_INLINE uint32_t negateCond(uint32_t cond) noexcept {</a>
+<a name="2431"><span class="lineNum">    2431 </span>            :     ASMJIT_ASSERT(cond &lt; x86::kCondCount);</a>
+<a name="2432"><span class="lineNum">    2432 </span>            :     return cond ^ 1;</a>
+<a name="2433"><span class="lineNum">    2433 </span>            :   }</a>
+<a name="2434"><span class="lineNum">    2434 </span>            : </a>
+<a name="2435"><span class="lineNum">    2435 </span>            :   //! Convert a condition code into a condition code that reverses the</a>
+<a name="2436"><span class="lineNum">    2436 </span>            :   //! corresponding operands of a comparison.</a>
+<a name="2437"><span class="lineNum">    2437 </span>            :   static ASMJIT_INLINE uint32_t reverseCond(uint32_t cond) noexcept {</a>
+<a name="2438"><span class="lineNum">    2438 </span>            :     ASMJIT_ASSERT(cond &lt; x86::kCondCount);</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :     return getMiscData().reversedCond[cond];</a>
+<a name="2440"><span class="lineNum">    2440 </span>            :   }</a>
+<a name="2441"><span class="lineNum">    2441 </span>            : </a>
+<a name="2442"><span class="lineNum">    2442 </span>            :   //! Translate a condition code `cc` to a &quot;cmovcc&quot; instruction id.</a>
+<a name="2443"><span class="lineNum">    2443 </span>            :   static ASMJIT_INLINE uint32_t condToCmovcc(uint32_t cond) noexcept {</a>
+<a name="2444"><span class="lineNum">    2444 </span>            :     ASMJIT_ASSERT(cond &lt; x86::kCondCount);</a>
+<a name="2445"><span class="lineNum">    2445 </span>            :     return getMiscData().condToCmovcc[cond];</a>
+<a name="2446"><span class="lineNum">    2446 </span>            :   }</a>
+<a name="2447"><span class="lineNum">    2447 </span>            : </a>
+<a name="2448"><span class="lineNum">    2448 </span>            :   //! Translate a condition code `cc` to a &quot;jcc&quot; instruction id.</a>
+<a name="2449"><span class="lineNum">    2449 </span>            :   static ASMJIT_INLINE uint32_t condToJcc(uint32_t cond) noexcept {</a>
+<a name="2450"><span class="lineNum">    2450 </span>            :     ASMJIT_ASSERT(cond &lt; x86::kCondCount);</a>
+<a name="2451"><span class="lineNum">    2451 </span>            :     return getMiscData().condToJcc[cond];</a>
+<a name="2452"><span class="lineNum">    2452 </span>            :   }</a>
+<a name="2453"><span class="lineNum">    2453 </span>            : </a>
+<a name="2454"><span class="lineNum">    2454 </span>            :   //! Translate a condition code `cc` to a &quot;setcc&quot; instruction id.</a>
+<a name="2455"><span class="lineNum">    2455 </span>            :   static ASMJIT_INLINE uint32_t condToSetcc(uint32_t cond) noexcept {</a>
+<a name="2456"><span class="lineNum">    2456 </span>            :     ASMJIT_ASSERT(cond &lt; x86::kCondCount);</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :     return getMiscData().condToSetcc[cond];</a>
+<a name="2458"><span class="lineNum">    2458 </span>            :   }</a>
+<a name="2459"><span class="lineNum">    2459 </span>            : </a>
+<a name="2460"><span class="lineNum">    2460 </span>            :   //! Get a 'kmov?' instruction by register `size`.</a>
+<a name="2461"><span class="lineNum">    2461 </span>            :   static ASMJIT_INLINE uint32_t kmovIdFromSize(uint32_t size) noexcept {</a>
+<a name="2462"><span class="lineNum">    2462 </span>            :     return size == 1 ? X86Inst::kIdKmovb :</a>
+<a name="2463"><span class="lineNum">    2463 </span>            :            size == 2 ? X86Inst::kIdKmovw :</a>
+<a name="2464"><span class="lineNum">    2464 </span>            :            size == 4 ? X86Inst::kIdKmovd : X86Inst::kIdKmovq;</a>
+<a name="2465"><span class="lineNum">    2465 </span>            :   }</a>
+<a name="2466"><span class="lineNum">    2466 </span>            : </a>
+<a name="2467"><span class="lineNum">    2467 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2468"><span class="lineNum">    2468 </span>            :   // [Id &lt;-&gt; Name]</a>
+<a name="2469"><span class="lineNum">    2469 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2470"><span class="lineNum">    2470 </span>            : </a>
+<a name="2471"><span class="lineNum">    2471 </span>            : #if !defined(ASMJIT_DISABLE_TEXT)</a>
+<a name="2472"><span class="lineNum">    2472 </span>            :   //! Get an instruction ID from a given instruction `name`.</a>
+<a name="2473"><span class="lineNum">    2473 </span>            :   //!</a>
+<a name="2474"><span class="lineNum">    2474 </span>            :   //! NOTE: Instruction name MUST BE in lowercase, otherwise there will be no</a>
+<a name="2475"><span class="lineNum">    2475 </span>            :   //! match. If there is an exact match the instruction id is returned, otherwise</a>
+<a name="2476"><span class="lineNum">    2476 </span>            :   //! `kInvalidInstId` (zero) is returned instead. The given `name` doesn't have</a>
+<a name="2477"><span class="lineNum">    2477 </span>            :   //! to be null-terminated if `len` is provided.</a>
+<a name="2478"><span class="lineNum">    2478 </span>            :   ASMJIT_API static uint32_t getIdByName(const char* name, size_t len = Globals::kInvalidIndex) noexcept;</a>
+<a name="2479"><span class="lineNum">    2479 </span>            : </a>
+<a name="2480"><span class="lineNum">    2480 </span>            :   //! Get an instruction name from a given instruction id `instId`.</a>
+<a name="2481"><span class="lineNum">    2481 </span>            :   ASMJIT_API static const char* getNameById(uint32_t instId) noexcept;</a>
+<a name="2482"><span class="lineNum">    2482 </span>            : #endif // !ASMJIT_DISABLE_TEXT</a>
+<a name="2483"><span class="lineNum">    2483 </span>            : </a>
+<a name="2484"><span class="lineNum">    2484 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2485"><span class="lineNum">    2485 </span>            :   // [Members]</a>
+<a name="2486"><span class="lineNum">    2486 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2487"><span class="lineNum">    2487 </span>            : </a>
+<a name="2488"><span class="lineNum">    2488 </span>            :   uint32_t _encodingType       : 8;      //!&lt; Encoding type.</a>
+<a name="2489"><span class="lineNum">    2489 </span>            :   uint32_t _nameDataIndex      : 14;     //!&lt; Index to `X86InstDB::nameData` table.</a>
+<a name="2490"><span class="lineNum">    2490 </span>            :   uint32_t _commonDataIndex    : 10;     //!&lt; Index to `X86InstDB::commonData` table.</a>
+<a name="2491"><span class="lineNum">    2491 </span>            :   uint32_t _operationDataIndex : 8;      //!&lt; Index to `X86InstDB::operationData` table.</a>
+<a name="2492"><span class="lineNum">    2492 </span>            :   uint32_t _sseToAvxDataIndex  : 7;      //!&lt; Index to `X86InstDB::sseToAvxData` table.</a>
+<a name="2493"><span class="lineNum">    2493 </span>            :   uint32_t _reserved           : 17;     //!&lt; \internal</a>
+<a name="2494"><span class="lineNum">    2494 </span>            :   uint32_t _mainOpCode;                  //!&lt; Instruction's primary opcode.</a>
+<a name="2495"><span class="lineNum">    2495 </span>            : };</a>
+<a name="2496"><span class="lineNum">    2496 </span>            : </a>
+<a name="2497"><span class="lineNum">    2497 </span>            : //! X86 instruction data under a single namespace.</a>
+<a name="2498"><span class="lineNum">    2498 </span>            : struct X86InstDB {</a>
+<a name="2499"><span class="lineNum">    2499 </span>            :   ASMJIT_API static const X86Inst instData[];</a>
+<a name="2500"><span class="lineNum">    2500 </span>            :   ASMJIT_API static const uint32_t altOpCodeData[];</a>
+<a name="2501"><span class="lineNum">    2501 </span>            : </a>
+<a name="2502"><span class="lineNum">    2502 </span>            :   ASMJIT_API static const X86Inst::CommonData commonData[];</a>
+<a name="2503"><span class="lineNum">    2503 </span>            :   ASMJIT_API static const X86Inst::OperationData operationData[];</a>
+<a name="2504"><span class="lineNum">    2504 </span>            :   ASMJIT_API static const X86Inst::SseToAvxData sseToAvxData[];</a>
+<a name="2505"><span class="lineNum">    2505 </span>            : </a>
+<a name="2506"><span class="lineNum">    2506 </span>            :   ASMJIT_API static const char nameData[];</a>
+<a name="2507"><span class="lineNum">    2507 </span>            :   ASMJIT_API static const X86Inst::MiscData miscData;</a>
+<a name="2508"><span class="lineNum">    2508 </span>            : </a>
+<a name="2509"><span class="lineNum">    2509 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="2510"><span class="lineNum">    2510 </span>            :   ASMJIT_API static const X86Inst::ISignature iSignatureData[];</a>
+<a name="2511"><span class="lineNum">    2511 </span>            :   ASMJIT_API static const X86Inst::OSignature oSignatureData[];</a>
+<a name="2512"><span class="lineNum">    2512 </span>            : #endif // ASMJIT_DISABLE_VALIDATION</a>
+<a name="2513"><span class="lineNum">    2513 </span>            : };</a>
+<a name="2514"><span class="lineNum">    2514 </span>            : </a>
+<a name="2515"><span class="lineNum">    2515 </span>            : ASMJIT_INLINE const X86Inst&amp; X86Inst::getInst(uint32_t instId) noexcept {</a>
+<a name="2516"><span class="lineNum">    2516 </span>            :   ASMJIT_ASSERT(instId &lt; X86Inst::_kIdCount);</a>
+<a name="2517"><span class="lineNum">    2517 </span>            :   return X86InstDB::instData[instId];</a>
+<a name="2518"><span class="lineNum">    2518 </span>            : }</a>
+<a name="2519"><span class="lineNum">    2519 </span>            : </a>
+<a name="2520"><span class="lineNum">    2520 </span><span class="lineNoCov">          0 : ASMJIT_INLINE const char* X86Inst::getName() const noexcept { return &amp;X86InstDB::nameData[_nameDataIndex]; }</span></a>
+<a name="2521"><span class="lineNum">    2521 </span><span class="lineCov">      81468 : ASMJIT_INLINE const X86Inst::CommonData&amp; X86Inst::getCommonData() const noexcept { return X86InstDB::commonData[_commonDataIndex]; }</span></a>
+<a name="2522"><span class="lineNum">    2522 </span><span class="lineCov">       5834 : ASMJIT_INLINE const X86Inst::OperationData&amp; X86Inst::getOperationData() const noexcept { return X86InstDB::operationData[_operationDataIndex]; }</span></a>
+<a name="2523"><span class="lineNum">    2523 </span>            : ASMJIT_INLINE const X86Inst::SseToAvxData&amp; X86Inst::getSseToAvxData() const noexcept { return X86InstDB::sseToAvxData[_sseToAvxDataIndex]; }</a>
+<a name="2524"><span class="lineNum">    2524 </span><span class="lineCov">       6510 : ASMJIT_INLINE uint32_t X86Inst::CommonData::getAltOpCode() const noexcept { return X86InstDB::altOpCodeData[_altOpCodeIndex]; }</span></a>
+<a name="2525"><span class="lineNum">    2525 </span>            : ASMJIT_INLINE const X86Inst::MiscData&amp; X86Inst::getMiscData() noexcept { return X86InstDB::miscData; }</a>
+<a name="2526"><span class="lineNum">    2526 </span>            : </a>
+<a name="2527"><span class="lineNum">    2527 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="2528"><span class="lineNum">    2528 </span>            : ASMJIT_INLINE const X86Inst::ISignature* X86Inst::CommonData::getISignatureData() const noexcept { return X86InstDB::iSignatureData + _iSignatureIndex; }</a>
+<a name="2529"><span class="lineNum">    2529 </span>            : ASMJIT_INLINE const X86Inst::ISignature* X86Inst::CommonData::getISignatureEnd() const noexcept { return X86InstDB::iSignatureData + _iSignatureIndex + _iSignatureCount; }</a>
+<a name="2530"><span class="lineNum">    2530 </span>            : #else</a>
+<a name="2531"><span class="lineNum">    2531 </span>            : ASMJIT_INLINE const X86Inst::ISignature* X86Inst::CommonData::getISignatureData() const noexcept { return static_cast&lt;const X86Inst::ISignature*&gt;(nullptr); }</a>
+<a name="2532"><span class="lineNum">    2532 </span>            : ASMJIT_INLINE const X86Inst::ISignature* X86Inst::CommonData::getISignatureEnd() const noexcept { return static_cast&lt;const X86Inst::ISignature*&gt;(nullptr); }</a>
+<a name="2533"><span class="lineNum">    2533 </span>            : #endif // ASMJIT_DISABLE_VALIDATION</a>
+<a name="2534"><span class="lineNum">    2534 </span>            : </a>
+<a name="2535"><span class="lineNum">    2535 </span>            : //! \}</a>
+<a name="2536"><span class="lineNum">    2536 </span>            : </a>
+<a name="2537"><span class="lineNum">    2537 </span>            : } // asmjit namespace</a>
+<a name="2538"><span class="lineNum">    2538 </span>            : } // namespace PLMD</a>
+<a name="2539"><span class="lineNum">    2539 </span>            : </a>
+<a name="2540"><span class="lineNum">    2540 </span>            : // [Api-End]</a>
+<a name="2541"><span class="lineNum">    2541 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="2542"><span class="lineNum">    2542 </span>            : </a>
+<a name="2543"><span class="lineNum">    2543 </span>            : // [Guard]</a>
+<a name="2544"><span class="lineNum">    2544 </span>            : #endif // _ASMJIT_X86_X86INST_H</a>
+<a name="2545"><span class="lineNum">    2545 </span>            : #pragma GCC diagnostic pop</a>
+<a name="2546"><span class="lineNum">    2546 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="2547"><span class="lineNum">    2547 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86instimpl.cpp.func-sort-c.html b/coverage-libs/asmjit/x86instimpl.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e701acb14c
--- /dev/null
+++ b/coverage-libs/asmjit/x86instimpl.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86instimpl.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86instimpl.cpp<span style="font-size: 80%;"> (<a href="x86instimpl.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86instimpl.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86instimpl.cpp.gcov.html#641">_ZN4PLMD6asmjit11X86InstImpl13checkFeaturesEjRKNS0_4Inst6DetailEPKNS0_8Operand_EjRNS0_11CpuFeaturesE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86instimpl.cpp.gcov.html#170">_ZN4PLMD6asmjit11X86InstImpl8validateEjRKNS0_4Inst6DetailEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86instimpl.cpp.gcov.html#624">_ZN4PLMD6asmjitL18x86GetRegTypesMaskEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86instimpl.cpp.func.html b/coverage-libs/asmjit/x86instimpl.cpp.func.html
new file mode 100644
index 0000000000..bfc4606f39
--- /dev/null
+++ b/coverage-libs/asmjit/x86instimpl.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86instimpl.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86instimpl.cpp<span style="font-size: 80%;"> (<a href="x86instimpl.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86instimpl.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86instimpl.cpp.gcov.html#641">_ZN4PLMD6asmjit11X86InstImpl13checkFeaturesEjRKNS0_4Inst6DetailEPKNS0_8Operand_EjRNS0_11CpuFeaturesE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86instimpl.cpp.gcov.html#170">_ZN4PLMD6asmjit11X86InstImpl8validateEjRKNS0_4Inst6DetailEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86instimpl.cpp.gcov.html#624">_ZN4PLMD6asmjitL18x86GetRegTypesMaskEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86instimpl.cpp.gcov.html b/coverage-libs/asmjit/x86instimpl.cpp.gcov.html
new file mode 100644
index 0000000000..70f50f226b
--- /dev/null
+++ b/coverage-libs/asmjit/x86instimpl.cpp.gcov.html
@@ -0,0 +1,833 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86instimpl.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86instimpl.cpp<span style="font-size: 80%;"> (source / <a href="x86instimpl.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./misc_p.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./x86instimpl_p.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // ============================================================================</a>
+<a name="45"><span class="lineNum">      45 </span>            : // [asmjit::X86InstImpl - Validate]</a>
+<a name="46"><span class="lineNum">      46 </span>            : // ============================================================================</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : #if !defined(ASMJIT_DISABLE_VALIDATION)</a>
+<a name="49"><span class="lineNum">      49 </span>            : template&lt;uint32_t RegType&gt;</a>
+<a name="50"><span class="lineNum">      50 </span>            : struct X86OpTypeFromRegTypeT {</a>
+<a name="51"><span class="lineNum">      51 </span>            :   enum {</a>
+<a name="52"><span class="lineNum">      52 </span>            :     kValue = (RegType == X86Reg::kRegGpbLo) ? X86Inst::kOpGpbLo :</a>
+<a name="53"><span class="lineNum">      53 </span>            :              (RegType == X86Reg::kRegGpbHi) ? X86Inst::kOpGpbHi :</a>
+<a name="54"><span class="lineNum">      54 </span>            :              (RegType == X86Reg::kRegGpw  ) ? X86Inst::kOpGpw   :</a>
+<a name="55"><span class="lineNum">      55 </span>            :              (RegType == X86Reg::kRegGpd  ) ? X86Inst::kOpGpd   :</a>
+<a name="56"><span class="lineNum">      56 </span>            :              (RegType == X86Reg::kRegGpq  ) ? X86Inst::kOpGpq   :</a>
+<a name="57"><span class="lineNum">      57 </span>            :              (RegType == X86Reg::kRegXmm  ) ? X86Inst::kOpXmm   :</a>
+<a name="58"><span class="lineNum">      58 </span>            :              (RegType == X86Reg::kRegYmm  ) ? X86Inst::kOpYmm   :</a>
+<a name="59"><span class="lineNum">      59 </span>            :              (RegType == X86Reg::kRegZmm  ) ? X86Inst::kOpZmm   :</a>
+<a name="60"><span class="lineNum">      60 </span>            :              (RegType == X86Reg::kRegRip  ) ? X86Inst::kOpNone  :</a>
+<a name="61"><span class="lineNum">      61 </span>            :              (RegType == X86Reg::kRegSeg  ) ? X86Inst::kOpSeg   :</a>
+<a name="62"><span class="lineNum">      62 </span>            :              (RegType == X86Reg::kRegFp   ) ? X86Inst::kOpFp    :</a>
+<a name="63"><span class="lineNum">      63 </span>            :              (RegType == X86Reg::kRegMm   ) ? X86Inst::kOpMm    :</a>
+<a name="64"><span class="lineNum">      64 </span>            :              (RegType == X86Reg::kRegK    ) ? X86Inst::kOpK     :</a>
+<a name="65"><span class="lineNum">      65 </span>            :              (RegType == X86Reg::kRegBnd  ) ? X86Inst::kOpBnd   :</a>
+<a name="66"><span class="lineNum">      66 </span>            :              (RegType == X86Reg::kRegCr   ) ? X86Inst::kOpCr    :</a>
+<a name="67"><span class="lineNum">      67 </span>            :              (RegType == X86Reg::kRegDr   ) ? X86Inst::kOpDr    : X86Inst::kOpNone</a>
+<a name="68"><span class="lineNum">      68 </span>            :   };</a>
+<a name="69"><span class="lineNum">      69 </span>            : };</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : template&lt;uint32_t RegType&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : struct X86RegMaskFromRegTypeT {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   enum {</a>
+<a name="74"><span class="lineNum">      74 </span>            :     kMask = (RegType == X86Reg::kRegGpbLo) ? 0x0000000FU :</a>
+<a name="75"><span class="lineNum">      75 </span>            :             (RegType == X86Reg::kRegGpbHi) ? 0x0000000FU :</a>
+<a name="76"><span class="lineNum">      76 </span>            :             (RegType == X86Reg::kRegGpw  ) ? 0x000000FFU :</a>
+<a name="77"><span class="lineNum">      77 </span>            :             (RegType == X86Reg::kRegGpd  ) ? 0x000000FFU :</a>
+<a name="78"><span class="lineNum">      78 </span>            :             (RegType == X86Reg::kRegGpq  ) ? 0x000000FFU :</a>
+<a name="79"><span class="lineNum">      79 </span>            :             (RegType == X86Reg::kRegXmm  ) ? 0x000000FFU :</a>
+<a name="80"><span class="lineNum">      80 </span>            :             (RegType == X86Reg::kRegYmm  ) ? 0x000000FFU :</a>
+<a name="81"><span class="lineNum">      81 </span>            :             (RegType == X86Reg::kRegZmm  ) ? 0x000000FFU :</a>
+<a name="82"><span class="lineNum">      82 </span>            :             (RegType == X86Reg::kRegRip  ) ? 0x00000001U :</a>
+<a name="83"><span class="lineNum">      83 </span>            :             (RegType == X86Reg::kRegSeg  ) ? 0x0000007EU : // [ES|CS|SS|DS|FS|GS]</a>
+<a name="84"><span class="lineNum">      84 </span>            :             (RegType == X86Reg::kRegFp   ) ? 0x000000FFU :</a>
+<a name="85"><span class="lineNum">      85 </span>            :             (RegType == X86Reg::kRegMm   ) ? 0x000000FFU :</a>
+<a name="86"><span class="lineNum">      86 </span>            :             (RegType == X86Reg::kRegK    ) ? 0x000000FFU :</a>
+<a name="87"><span class="lineNum">      87 </span>            :             (RegType == X86Reg::kRegBnd  ) ? 0x0000000FU :</a>
+<a name="88"><span class="lineNum">      88 </span>            :             (RegType == X86Reg::kRegCr   ) ? 0x0000FFFFU :</a>
+<a name="89"><span class="lineNum">      89 </span>            :             (RegType == X86Reg::kRegDr   ) ? 0x000000FFU : X86Inst::kOpNone</a>
+<a name="90"><span class="lineNum">      90 </span>            :   };</a>
+<a name="91"><span class="lineNum">      91 </span>            : };</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : template&lt;uint32_t RegType&gt;</a>
+<a name="94"><span class="lineNum">      94 </span>            : struct X64RegMaskFromRegTypeT {</a>
+<a name="95"><span class="lineNum">      95 </span>            :   enum {</a>
+<a name="96"><span class="lineNum">      96 </span>            :     kMask = (RegType == X86Reg::kRegGpbLo) ? 0x0000FFFFU :</a>
+<a name="97"><span class="lineNum">      97 </span>            :             (RegType == X86Reg::kRegGpbHi) ? 0x0000000FU :</a>
+<a name="98"><span class="lineNum">      98 </span>            :             (RegType == X86Reg::kRegGpw  ) ? 0x0000FFFFU :</a>
+<a name="99"><span class="lineNum">      99 </span>            :             (RegType == X86Reg::kRegGpd  ) ? 0x0000FFFFU :</a>
+<a name="100"><span class="lineNum">     100 </span>            :             (RegType == X86Reg::kRegGpq  ) ? 0x0000FFFFU :</a>
+<a name="101"><span class="lineNum">     101 </span>            :             (RegType == X86Reg::kRegXmm  ) ? 0xFFFFFFFFU :</a>
+<a name="102"><span class="lineNum">     102 </span>            :             (RegType == X86Reg::kRegYmm  ) ? 0xFFFFFFFFU :</a>
+<a name="103"><span class="lineNum">     103 </span>            :             (RegType == X86Reg::kRegZmm  ) ? 0xFFFFFFFFU :</a>
+<a name="104"><span class="lineNum">     104 </span>            :             (RegType == X86Reg::kRegRip  ) ? 0x00000001U :</a>
+<a name="105"><span class="lineNum">     105 </span>            :             (RegType == X86Reg::kRegSeg  ) ? 0x0000007EU : // [ES|CS|SS|DS|FS|GS]</a>
+<a name="106"><span class="lineNum">     106 </span>            :             (RegType == X86Reg::kRegFp   ) ? 0x000000FFU :</a>
+<a name="107"><span class="lineNum">     107 </span>            :             (RegType == X86Reg::kRegMm   ) ? 0x000000FFU :</a>
+<a name="108"><span class="lineNum">     108 </span>            :             (RegType == X86Reg::kRegK    ) ? 0x000000FFU :</a>
+<a name="109"><span class="lineNum">     109 </span>            :             (RegType == X86Reg::kRegBnd  ) ? 0x0000000FU :</a>
+<a name="110"><span class="lineNum">     110 </span>            :             (RegType == X86Reg::kRegCr   ) ? 0x0000FFFFU :</a>
+<a name="111"><span class="lineNum">     111 </span>            :             (RegType == X86Reg::kRegDr   ) ? 0x0000FFFFU : X86Inst::kOpNone</a>
+<a name="112"><span class="lineNum">     112 </span>            :   };</a>
+<a name="113"><span class="lineNum">     113 </span>            : };</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : struct X86ValidationData {</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //! Allowed registers by reg-type (X86::kReg...).</a>
+<a name="117"><span class="lineNum">     117 </span>            :   uint32_t allowedRegMask[X86Reg::kRegMax + 1];</a>
+<a name="118"><span class="lineNum">     118 </span>            :   uint32_t allowedMemBaseRegs;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   uint32_t allowedMemIndexRegs;</a>
+<a name="120"><span class="lineNum">     120 </span>            : };</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : static const uint32_t _x86OpFlagFromRegType[X86Reg::kRegMax + 1] = {</a>
+<a name="123"><span class="lineNum">     123 </span>            :   ASMJIT_TABLE_T_32(X86OpTypeFromRegTypeT, kValue, 0)</a>
+<a name="124"><span class="lineNum">     124 </span>            : };</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : static const X86ValidationData _x86ValidationData = {</a>
+<a name="127"><span class="lineNum">     127 </span>            :   { ASMJIT_TABLE_T_32(X86RegMaskFromRegTypeT, kMask, 0) },</a>
+<a name="128"><span class="lineNum">     128 </span>            :   (1U &lt;&lt; X86Reg::kRegGpw) | (1U &lt;&lt; X86Reg::kRegGpd) | (1U &lt;&lt; X86Reg::kRegRip) | (1U &lt;&lt; Label::kLabelTag),</a>
+<a name="129"><span class="lineNum">     129 </span>            :   (1U &lt;&lt; X86Reg::kRegGpw) | (1U &lt;&lt; X86Reg::kRegGpd) | (1U &lt;&lt; X86Reg::kRegXmm) | (1U &lt;&lt; X86Reg::kRegYmm) | (1U &lt;&lt; X86Reg::kRegZmm)</a>
+<a name="130"><span class="lineNum">     130 </span>            : };</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : static const X86ValidationData _x64ValidationData = {</a>
+<a name="133"><span class="lineNum">     133 </span>            :   { ASMJIT_TABLE_T_32(X64RegMaskFromRegTypeT, kMask, 0) },</a>
+<a name="134"><span class="lineNum">     134 </span>            :   (1U &lt;&lt; X86Reg::kRegGpd) | (1U &lt;&lt; X86Reg::kRegGpq) | (1U &lt;&lt; X86Reg::kRegRip) | (1U &lt;&lt; Label::kLabelTag),</a>
+<a name="135"><span class="lineNum">     135 </span>            :   (1U &lt;&lt; X86Reg::kRegGpd) | (1U &lt;&lt; X86Reg::kRegGpq) | (1U &lt;&lt; X86Reg::kRegXmm) | (1U &lt;&lt; X86Reg::kRegYmm) | (1U &lt;&lt; X86Reg::kRegZmm)</a>
+<a name="136"><span class="lineNum">     136 </span>            : };</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : static ASMJIT_INLINE bool x86CheckOSig(const X86Inst::OSignature&amp; op, const X86Inst::OSignature&amp; ref, bool&amp; immOutOfRange) noexcept {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   // Fail if operand types are incompatible.</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   uint32_t opFlags = op.flags;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   if ((opFlags &amp; ref.flags) == 0) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     // Mark temporarily `immOutOfRange` so we can return a more descriptive error.</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     if ((opFlags &amp; X86Inst::kOpAllImm) &amp;&amp; (ref.flags &amp; X86Inst::kOpAllImm)) {</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :       immOutOfRange = true;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :       return true;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :     return false;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Fail if memory specific flags and sizes are incompatibles.</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   uint32_t opMemFlags = op.memFlags;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   if (opMemFlags != 0) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :     uint32_t refMemFlags = ref.memFlags;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     if ((refMemFlags &amp; opMemFlags) == 0)</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :       return false;</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     if ((refMemFlags &amp; X86Inst::kMemOpBaseOnly) &amp;&amp; !(opMemFlags &amp; X86Inst::kMemOpBaseOnly))</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :       return false;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Specific register index.</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   if (opFlags &amp; X86Inst::kOpAllRegs) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     uint32_t refRegMask = ref.regMask;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     if (refRegMask &amp;&amp; !(op.regMask &amp; refRegMask))</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :       return false;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   return true;</a>
+<a name="170"><span class="lineNum">     170 </span>            : }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86InstImpl::validate(uint32_t archType, const Inst::Detail&amp; detail, const Operand_* operands, uint32_t count) noexcept {</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   uint32_t i;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   uint32_t archMask;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   const X86ValidationData* vd;</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   if (!ArchInfo::isX86Family(archType))</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   if (archType == ArchInfo::kTypeX86) {</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     vd = &amp;_x86ValidationData;</a>
+<a name="182"><span class="lineNum">     182 </span>            :     archMask = X86Inst::kArchMaskX86;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   else {</a>
+<a name="185"><span class="lineNum">     185 </span>            :     vd = &amp;_x64ValidationData;</a>
+<a name="186"><span class="lineNum">     186 </span>            :     archMask = X86Inst::kArchMaskX64;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   // Get the instruction data.</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   uint32_t instId = detail.instId;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :   uint32_t options = detail.options;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(instId &gt;= X86Inst::_kIdCount))</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   const X86Inst* iData = &amp;X86InstDB::instData[instId];</a>
+<a name="197"><span class="lineNum">     197 </span>            :   uint32_t iFlags = iData-&gt;getFlags();</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Validate LOCK, XACQUIRE, and XRELEASE prefixes.</a>
+<a name="200"><span class="lineNum">     200 </span>            :   const uint32_t kLockXAcqRel = X86Inst::kOptionXAcquire | X86Inst::kOptionXRelease;</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   if (options &amp; (X86Inst::kOptionLock | kLockXAcqRel)) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionLock) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!(iFlags &amp; X86Inst::kFlagLock) &amp;&amp; !(options &amp; kLockXAcqRel)))</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :         return DebugUtils::errored(kErrorInvalidLockPrefix);</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(count &lt; 1 || !operands[0].isMem()))</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :         return DebugUtils::errored(kErrorInvalidLockPrefix);</a>
+<a name="208"><span class="lineNum">     208 </span>            :     }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :     if (options &amp; kLockXAcqRel) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!(options &amp; X86Inst::kOptionLock) || (options &amp; kLockXAcqRel) == kLockXAcqRel))</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :         return DebugUtils::errored(kErrorInvalidPrefixCombination);</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionXAcquire) &amp;&amp; !(iFlags &amp; X86Inst::kFlagXAcquire)))</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :         return DebugUtils::errored(kErrorInvalidXAcquirePrefix);</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionXRelease) &amp;&amp; !(iFlags &amp; X86Inst::kFlagXRelease)))</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :         return DebugUtils::errored(kErrorInvalidXReleasePrefix);</a>
+<a name="219"><span class="lineNum">     219 </span>            :     }</a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   // Validate REP and REPNZ prefixes.</a>
+<a name="223"><span class="lineNum">     223 </span>            :   const uint32_t kRepRepRepnz = X86Inst::kOptionRep | X86Inst::kOptionRepnz;</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :   if (options &amp; kRepRepRepnz) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY((options &amp; kRepRepRepnz) == kRepRepRepnz))</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :       return DebugUtils::errored(kErrorInvalidPrefixCombination);</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionRep) &amp;&amp; !(iFlags &amp; X86Inst::kFlagRep)))</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :       return DebugUtils::errored(kErrorInvalidRepPrefix);</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionRepnz) &amp;&amp; !(iFlags &amp; X86Inst::kFlagRepnz)))</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :       return DebugUtils::errored(kErrorInvalidRepPrefix);</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            :     // TODO: Validate extraReg {cx|ecx|rcx}.</a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   // Translate the given operands to `X86Inst::OSignature`.</a>
+<a name="238"><span class="lineNum">     238 </span>            :   X86Inst::OSignature oSigTranslated[6];</a>
+<a name="239"><span class="lineNum">     239 </span>            :   uint32_t combinedOpFlags = 0;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   uint32_t combinedRegMask = 0;</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :   const X86Mem* memOp = nullptr;</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; count; i++) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :     const Operand_&amp; op = operands[i];</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :     if (op.getOp() == Operand::kOpNone) break;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :     uint32_t opFlags = 0;</a>
+<a name="249"><span class="lineNum">     249 </span>            :     uint32_t memFlags = 0;</a>
+<a name="250"><span class="lineNum">     250 </span>            :     uint32_t regMask = 0;</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :     switch (op.getOp()) {</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :       case Operand::kOpReg: {</a>
+<a name="254"><span class="lineNum">     254 </span>            :         uint32_t regType = op.as&lt;Reg&gt;().getType();</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(regType &gt;= X86Reg::kRegCount))</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :           return DebugUtils::errored(kErrorInvalidRegType);</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :         opFlags = _x86OpFlagFromRegType[regType];</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(opFlags == 0))</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :           return DebugUtils::errored(kErrorInvalidRegType);</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :         // If `regId` is equal or greater than Operand::kPackedIdMin it means</a>
+<a name="263"><span class="lineNum">     263 </span>            :         // that the register is virtual and its index will be assigned later</a>
+<a name="264"><span class="lineNum">     264 </span>            :         // by the register allocator. We must pass unless asked to disallow</a>
+<a name="265"><span class="lineNum">     265 </span>            :         // virtual registers.</a>
+<a name="266"><span class="lineNum">     266 </span>            :         // TODO: We need an option to refuse virtual regs here.</a>
+<a name="267"><span class="lineNum">     267 </span>            :         uint32_t regId = op.getId();</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :         if (regId &lt; Operand::kPackedIdMin) {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(regId &gt;= 32))</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :             return DebugUtils::errored(kErrorInvalidPhysId);</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :           regMask = Utils::mask(regId);</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY((vd-&gt;allowedRegMask[regType] &amp; regMask) == 0))</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :             return DebugUtils::errored(kErrorInvalidPhysId);</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :           combinedRegMask |= regMask;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :         }</a>
+<a name="278"><span class="lineNum">     278 </span>            :         else {</a>
+<a name="279"><span class="lineNum">     279 </span>            :           regMask = 0xFFFFFFFFU;</a>
+<a name="280"><span class="lineNum">     280 </span>            :         }</a>
+<a name="281"><span class="lineNum">     281 </span>            :         break;</a>
+<a name="282"><span class="lineNum">     282 </span>            :       }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :       // TODO: Validate base and index and combine with `combinedRegMask`.</a>
+<a name="285"><span class="lineNum">     285 </span>            :       case Operand::kOpMem: {</a>
+<a name="286"><span class="lineNum">     286 </span>            :         const X86Mem&amp; m = op.as&lt;X86Mem&gt;();</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :         uint32_t baseType = m.getBaseType();</a>
+<a name="289"><span class="lineNum">     289 </span>            :         uint32_t indexType = m.getIndexType();</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :         memOp = &amp;m;</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :         if (m.getSegmentId() &gt; 6)</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :           return DebugUtils::errored(kErrorInvalidSegment);</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :         if (baseType) {</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :           uint32_t baseId = m.getBaseId();</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :           if (m.isRegHome()) {</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :             // Home address of virtual register. In such case we don't want to</a>
+<a name="301"><span class="lineNum">     301 </span>            :             // validate the type of the base register as it will always be patched</a>
+<a name="302"><span class="lineNum">     302 </span>            :             // to ESP|RSP.</a>
+<a name="303"><span class="lineNum">     303 </span>            :           }</a>
+<a name="304"><span class="lineNum">     304 </span>            :           else {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :             if (ASMJIT_UNLIKELY((vd-&gt;allowedMemBaseRegs &amp; (1U &lt;&lt; baseType)) == 0))</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :               return DebugUtils::errored(kErrorInvalidAddress);</a>
+<a name="307"><span class="lineNum">     307 </span>            :           }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :           // Create information that will be validated only if this is an implicit</a>
+<a name="310"><span class="lineNum">     310 </span>            :           // memory operand. Basically only usable for string instructions and other</a>
+<a name="311"><span class="lineNum">     311 </span>            :           // instructions where memory operand is implicit and has 'seg:[reg]' form.</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :           if (baseId &lt; Operand::kPackedIdMin) {</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :             // Physical base id.</a>
+<a name="314"><span class="lineNum">     314 </span>            :             regMask = Utils::mask(baseId);</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :             combinedRegMask |= regMask;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :           }</a>
+<a name="317"><span class="lineNum">     317 </span>            :           else {</a>
+<a name="318"><span class="lineNum">     318 </span>            :             // Virtual base id - will the whole mask for implicit mem validation.</a>
+<a name="319"><span class="lineNum">     319 </span>            :             // The register is not assigned yet, so we cannot predict the phys id.</a>
+<a name="320"><span class="lineNum">     320 </span>            :             regMask = 0xFFFFFFFFU;</a>
+<a name="321"><span class="lineNum">     321 </span>            :           }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :           if (!indexType &amp;&amp; !m.getOffsetLo32())</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :             memFlags |= X86Inst::kMemOpBaseOnly;</a>
+<a name="325"><span class="lineNum">     325 </span>            :         }</a>
+<a name="326"><span class="lineNum">     326 </span>            :         else {</a>
+<a name="327"><span class="lineNum">     327 </span>            :           // Base is an address, make sure that the address doesn't overflow 32-bit</a>
+<a name="328"><span class="lineNum">     328 </span>            :           // integer (either int32_t or uint32_t) in 32-bit targets.</a>
+<a name="329"><span class="lineNum">     329 </span>            :           int64_t offset = m.getOffset();</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :           if (archMask == X86Inst::kArchMaskX86 &amp;&amp; !Utils::isInt32(offset) &amp;&amp; !Utils::isUInt32(offset))</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :             return DebugUtils::errored(kErrorInvalidAddress);</a>
+<a name="332"><span class="lineNum">     332 </span>            :         }</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :         if (indexType) {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY((vd-&gt;allowedMemIndexRegs &amp; (1U &lt;&lt; indexType)) == 0))</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :             return DebugUtils::errored(kErrorInvalidAddress);</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :           if (indexType == X86Reg::kRegXmm) {</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :             opFlags |= X86Inst::kOpVm;</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :             memFlags |= X86Inst::kMemOpVm32x | X86Inst::kMemOpVm64x;</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :           }</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :           else if (indexType == X86Reg::kRegYmm) {</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :             opFlags |= X86Inst::kOpVm;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :             memFlags |= X86Inst::kMemOpVm32y | X86Inst::kMemOpVm64y;</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :           }</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :           else if (indexType == X86Reg::kRegZmm) {</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :             opFlags |= X86Inst::kOpVm;</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :             memFlags |= X86Inst::kMemOpVm32z | X86Inst::kMemOpVm64z;</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :           }</a>
+<a name="350"><span class="lineNum">     350 </span>            :           else {</a>
+<a name="351"><span class="lineNum">     351 </span>            :             opFlags |= X86Inst::kOpMem;</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :             if (baseType)</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :               memFlags |= X86Inst::kMemOpMib;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :           }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            :           // [RIP + {XMM|YMM|ZMM}] is not allowed.</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :           if (baseType == X86Reg::kRegRip &amp;&amp; (opFlags &amp; X86Inst::kOpVm))</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :             return DebugUtils::errored(kErrorInvalidAddress);</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            :           uint32_t indexId = m.getIndexId();</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :           if (indexId &lt; Operand::kPackedIdMin)</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :             combinedRegMask |= Utils::mask(indexId);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :           // Only used for implicit memory operands having 'seg:[reg]' form, so clear it.</a>
+<a name="365"><span class="lineNum">     365 </span>            :           regMask = 0;</a>
+<a name="366"><span class="lineNum">     366 </span>            :         }</a>
+<a name="367"><span class="lineNum">     367 </span>            :         else {</a>
+<a name="368"><span class="lineNum">     368 </span>            :           opFlags |= X86Inst::kOpMem;</a>
+<a name="369"><span class="lineNum">     369 </span>            :         }</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span>            :         switch (m.getSize()) {</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :           case  0: memFlags |= X86Inst::kMemOpAny ; break;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :           case  1: memFlags |= X86Inst::kMemOpM8  ; break;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :           case  2: memFlags |= X86Inst::kMemOpM16 ; break;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :           case  4: memFlags |= X86Inst::kMemOpM32 ; break;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :           case  6: memFlags |= X86Inst::kMemOpM48 ; break;</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :           case  8: memFlags |= X86Inst::kMemOpM64 ; break;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :           case 10: memFlags |= X86Inst::kMemOpM80 ; break;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :           case 16: memFlags |= X86Inst::kMemOpM128; break;</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :           case 32: memFlags |= X86Inst::kMemOpM256; break;</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :           case 64: memFlags |= X86Inst::kMemOpM512; break;</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :           default:</a>
+<a name="383"><span class="lineNum">     383 </span>            :             return DebugUtils::errored(kErrorInvalidOperandSize);</a>
+<a name="384"><span class="lineNum">     384 </span>            :         }</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            :         break;</a>
+<a name="387"><span class="lineNum">     387 </span>            :       }</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            :       case Operand::kOpImm: {</a>
+<a name="390"><span class="lineNum">     390 </span>            :         uint64_t immValue = op.as&lt;Imm&gt;().getUInt64();</a>
+<a name="391"><span class="lineNum">     391 </span>            :         uint32_t immFlags = 0;</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :         if (static_cast&lt;int64_t&gt;(immValue) &gt;= 0) {</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :           const uint32_t k32AndMore = X86Inst::kOpI32 | X86Inst::kOpU32 |</a>
+<a name="395"><span class="lineNum">     395 </span>            :                                       X86Inst::kOpI64 | X86Inst::kOpU64 ;</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :           if (immValue &lt;= 0xFU)</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :             immFlags = X86Inst::kOpU4 | X86Inst::kOpI8 | X86Inst::kOpU8 | X86Inst::kOpI16 | X86Inst::kOpU16 | k32AndMore;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0x7FU)</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :             immFlags = X86Inst::kOpI8 | X86Inst::kOpU8 | X86Inst::kOpI16 | X86Inst::kOpU16 | k32AndMore;</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0xFFU)</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :             immFlags = X86Inst::kOpU8 | X86Inst::kOpI16 | X86Inst::kOpU16 | k32AndMore;</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0x7FFFU)</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :             immFlags = X86Inst::kOpI16 | X86Inst::kOpU16 | k32AndMore;</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0xFFFFU)</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :             immFlags = X86Inst::kOpU16 | k32AndMore;</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0x7FFFFFFFU)</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :             immFlags = k32AndMore;</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0xFFFFFFFFU)</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :             immFlags = X86Inst::kOpU32 | X86Inst::kOpI64 | X86Inst::kOpU64;</a>
+<a name="411"><span class="lineNum">     411 </span>            :           else if (immValue &lt;= ASMJIT_UINT64_C(0x7FFFFFFFFFFFFFFF))</a>
+<a name="412"><span class="lineNum">     412 </span>            :             immFlags = X86Inst::kOpI64 | X86Inst::kOpU64;</a>
+<a name="413"><span class="lineNum">     413 </span>            :           else</a>
+<a name="414"><span class="lineNum">     414 </span>            :             immFlags = X86Inst::kOpU64;</a>
+<a name="415"><span class="lineNum">     415 </span>            :         }</a>
+<a name="416"><span class="lineNum">     416 </span>            :         else {</a>
+<a name="417"><span class="lineNum">     417 </span>            :           // 2s complement negation, as our number is unsigned...</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :           immValue = (~immValue + 1);</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :           if (immValue &lt;= 0x80U)</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :             immFlags = X86Inst::kOpI8 | X86Inst::kOpI16 | X86Inst::kOpI32 | X86Inst::kOpI64;</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0x8000U)</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :             immFlags = X86Inst::kOpI16 | X86Inst::kOpI32 | X86Inst::kOpI64;</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :           else if (immValue &lt;= 0x80000000U)</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :             immFlags = X86Inst::kOpI32 | X86Inst::kOpI64;</a>
+<a name="426"><span class="lineNum">     426 </span>            :           else</a>
+<a name="427"><span class="lineNum">     427 </span>            :             immFlags = X86Inst::kOpI64;</a>
+<a name="428"><span class="lineNum">     428 </span>            :         }</a>
+<a name="429"><span class="lineNum">     429 </span>            :         opFlags |= immFlags;</a>
+<a name="430"><span class="lineNum">     430 </span>            :         break;</a>
+<a name="431"><span class="lineNum">     431 </span>            :       }</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :       case Operand::kOpLabel: {</a>
+<a name="434"><span class="lineNum">     434 </span>            :         opFlags |= X86Inst::kOpRel8 | X86Inst::kOpRel32;</a>
+<a name="435"><span class="lineNum">     435 </span>            :         break;</a>
+<a name="436"><span class="lineNum">     436 </span>            :       }</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            :       default:</a>
+<a name="439"><span class="lineNum">     439 </span>            :         return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="440"><span class="lineNum">     440 </span>            :     }</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :     X86Inst::OSignature&amp; tod = oSigTranslated[i];</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :     tod.flags = opFlags;</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :     tod.memFlags = static_cast&lt;uint16_t&gt;(memFlags);</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :     tod.regMask = static_cast&lt;uint8_t&gt;(regMask &amp; 0xFFU);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     combinedOpFlags |= opFlags;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   }</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            :   // Decrease the number of operands of those that are none. This is important</a>
+<a name="450"><span class="lineNum">     450 </span>            :   // as Assembler and CodeCompiler may just pass more operands where some of</a>
+<a name="451"><span class="lineNum">     451 </span>            :   // them are none (it means that no operand is given at that index). However,</a>
+<a name="452"><span class="lineNum">     452 </span>            :   // validate that there are no gaps (like [reg, none, reg] or [none, reg]).</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :   if (i &lt; count) {</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :     while (--count &gt; i)</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!operands[count].isNone()))</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :         return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="457"><span class="lineNum">     457 </span>            :   }</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            :   // Validate X86 and X64 specific cases.</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :   if (archMask == X86Inst::kArchMaskX86) {</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :     // Illegal use of 64-bit register in 32-bit mode.</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY((combinedOpFlags &amp; X86Inst::kOpGpq) != 0))</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :       return DebugUtils::errored(kErrorInvalidUseOfGpq);</a>
+<a name="464"><span class="lineNum">     464 </span>            :   }</a>
+<a name="465"><span class="lineNum">     465 </span>            :   else {</a>
+<a name="466"><span class="lineNum">     466 </span>            :     // Illegal use of a high 8-bit register with REX prefix.</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY((combinedOpFlags &amp; X86Inst::kOpGpbHi) != 0 &amp;&amp; (combinedRegMask &amp; 0xFFFFFF00U) != 0))</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :       return DebugUtils::errored(kErrorInvalidUseOfGpbHi);</a>
+<a name="469"><span class="lineNum">     469 </span>            :   }</a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            :   // Validate instruction operands.</a>
+<a name="472"><span class="lineNum">     472 </span>            :   const X86Inst::CommonData* commonData = &amp;iData-&gt;getCommonData();</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :   const X86Inst::ISignature* iSig = X86InstDB::iSignatureData + commonData-&gt;_iSignatureIndex;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :   const X86Inst::ISignature* iEnd = iSig                      + commonData-&gt;_iSignatureCount;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :   if (iSig != iEnd) {</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :     const X86Inst::OSignature* oSigData = X86InstDB::oSignatureData;</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            :     // If set it means that we matched a signature where only immediate value</a>
+<a name="480"><span class="lineNum">     480 </span>            :     // was out of bounds. We can return a more descriptive error if we know this.</a>
+<a name="481"><span class="lineNum">     481 </span>            :     bool globalImmOutOfRange = false;</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            :     do {</a>
+<a name="484"><span class="lineNum">     484 </span>            :       // Check if the architecture is compatible.</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :       if ((iSig-&gt;archMask &amp; archMask) == 0) continue;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span>            :       // Compare the operands table with reference operands.</a>
+<a name="488"><span class="lineNum">     488 </span>            :       uint32_t j = 0;</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :       uint32_t iSigCount = iSig-&gt;opCount;</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :       bool localImmOutOfRange = false;</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :       if (iSigCount == count) {</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :         for (j = 0; j &lt; count; j++)</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :           if (!x86CheckOSig(oSigTranslated[j], oSigData[iSig-&gt;operands[j]], localImmOutOfRange))</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :             break;</a>
+<a name="496"><span class="lineNum">     496 </span>            :       }</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :       else if (iSigCount - iSig-&gt;implicit == count) {</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :         uint32_t r = 0;</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :         for (j = 0; j &lt; count &amp;&amp; r &lt; iSigCount; j++, r++) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :           const X86Inst::OSignature* oChk = oSigTranslated + j;</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :           const X86Inst::OSignature* oRef;</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 : Next:</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :           oRef = oSigData + iSig-&gt;operands[r];</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :           // Skip implicit.</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :           if ((oRef-&gt;flags &amp; X86Inst::kOpImplicit) != 0) {</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :             if (++r &gt;= iSigCount)</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :               break;</a>
+<a name="508"><span class="lineNum">     508 </span>            :             else</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :               goto Next;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :           }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :           if (!x86CheckOSig(*oChk, *oRef, localImmOutOfRange))</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :             break;</a>
+<a name="514"><span class="lineNum">     514 </span>            :         }</a>
+<a name="515"><span class="lineNum">     515 </span>            :       }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :       if (j == count) {</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :         if (!localImmOutOfRange) {</span></a>
+<a name="519"><span class="lineNum">     519 </span>            :           // Match, must clear possible `globalImmOutOfRange`.</a>
+<a name="520"><span class="lineNum">     520 </span>            :           globalImmOutOfRange = false;</a>
+<a name="521"><span class="lineNum">     521 </span>            :           break;</a>
+<a name="522"><span class="lineNum">     522 </span>            :         }</a>
+<a name="523"><span class="lineNum">     523 </span>            :         globalImmOutOfRange = localImmOutOfRange;</a>
+<a name="524"><span class="lineNum">     524 </span>            :       }</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :     } while (++iSig != iEnd);</span></a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :     if (iSig == iEnd) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 :       if (globalImmOutOfRange)</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :         return DebugUtils::errored(kErrorInvalidImmediate);</a>
+<a name="530"><span class="lineNum">     530 </span>            :       else</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :         return DebugUtils::errored(kErrorInvalidInstruction);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :     }</a>
+<a name="533"><span class="lineNum">     533 </span>            :   }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            :   // Validate AVX-512 options:</a>
+<a name="536"><span class="lineNum">     536 </span>            :   const RegOnly&amp; extraReg = detail.extraReg;</a>
+<a name="537"><span class="lineNum">     537 </span>            :   const uint32_t kAvx512Options = X86Inst::kOptionZMask   |</a>
+<a name="538"><span class="lineNum">     538 </span>            :                                   X86Inst::kOption1ToX    |</a>
+<a name="539"><span class="lineNum">     539 </span>            :                                   X86Inst::kOptionER      |</a>
+<a name="540"><span class="lineNum">     540 </span>            :                                   X86Inst::kOptionSAE     ;</a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :   if (!extraReg.isNone() || (options &amp; kAvx512Options)) {</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     if (commonData-&gt;hasFlag(X86Inst::kFlagEvex)) {</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :       // Validate AVX-512 {k} and {k}{z}.</a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :       if (!extraReg.isNone()) {</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :         // Mask can only be specified by a 'k' register.</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(extraReg.getType() != X86Reg::kRegK))</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :           return DebugUtils::errored(kErrorInvalidKMaskReg);</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(!commonData-&gt;hasAvx512K()))</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :           return DebugUtils::errored(kErrorInvalidKMaskUse);</a>
+<a name="552"><span class="lineNum">     552 </span>            :       }</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :       if ((options &amp; X86Inst::kOptionZMask)) {</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY((options &amp; X86Inst::kOptionZMask) != 0 &amp;&amp; !commonData-&gt;hasAvx512Z()))</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :           return DebugUtils::errored(kErrorInvalidKZeroUse);</a>
+<a name="557"><span class="lineNum">     557 </span>            :       }</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span>            :       // Validate AVX-512 broadcast {1tox}.</a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineNoCov">          0 :       if (options &amp; X86Inst::kOption1ToX) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(!memOp))</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :           return DebugUtils::errored(kErrorInvalidBroadcast);</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :         uint32_t size = memOp-&gt;getSize();</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :         if (size != 0) {</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :           // The the size is specified it has to match the broadcast size.</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(commonData-&gt;hasAvx512B32() &amp;&amp; size != 4))</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :             return DebugUtils::errored(kErrorInvalidBroadcast);</a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(commonData-&gt;hasAvx512B64() &amp;&amp; size != 8))</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :             return DebugUtils::errored(kErrorInvalidBroadcast);</a>
+<a name="572"><span class="lineNum">     572 </span>            :         }</a>
+<a name="573"><span class="lineNum">     573 </span>            :       }</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span>            :       // Validate AVX-512 {sae} and {er}.</a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :       if (options &amp; (X86Inst::kOptionSAE | X86Inst::kOptionER)) {</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :         // Rounding control is impossible if the instruction is not reg-to-reg.</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(memOp))</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :           return DebugUtils::errored(kErrorInvalidEROrSAE);</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            :         // Check if {sae} or {er} is supported by the instruction.</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionER) {</span></a>
+<a name="583"><span class="lineNum">     583 </span>            :           // NOTE: if both {sae} and {er} are set, we don't care, as {sae} is implied.</a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(!commonData-&gt;hasAvx512ER()))</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :             return DebugUtils::errored(kErrorInvalidEROrSAE);</a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span>            :           // {er} is defined for scalar ops or vector ops using zmm (LL = 10). We</a>
+<a name="588"><span class="lineNum">     588 </span>            :           // don't need any more bits in the instruction database to be able to</a>
+<a name="589"><span class="lineNum">     589 </span>            :           // validate this, as each AVX512 instruction that has broadcast is vector</a>
+<a name="590"><span class="lineNum">     590 </span>            :           // instruction (in this case we require zmm registers), otherwise it's a</a>
+<a name="591"><span class="lineNum">     591 </span>            :           // scalar instruction, which is valid.</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineNoCov">          0 :           if (commonData-&gt;hasAvx512B()) {</span></a>
+<a name="593"><span class="lineNum">     593 </span>            :             // Supports broadcast, thus we require LL to be '10', which means there</a>
+<a name="594"><span class="lineNum">     594 </span>            :             // have to be zmm registers used. We don't calculate LL here, but we know</a>
+<a name="595"><span class="lineNum">     595 </span>            :             // that it would be '10' if there is at least one ZMM register used.</a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            :             // There is no 'ER' enabled instruction with less than two operands.</a>
+<a name="598"><span class="lineNum">     598 </span>            :             ASMJIT_ASSERT(count &gt;= 2);</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 :             if (ASMJIT_UNLIKELY(!X86Reg::isZmm(operands[0]) &amp;&amp; !X86Reg::isZmm(operands[1])))</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :               return DebugUtils::errored(kErrorInvalidEROrSAE);</a>
+<a name="601"><span class="lineNum">     601 </span>            :           }</a>
+<a name="602"><span class="lineNum">     602 </span>            :         }</a>
+<a name="603"><span class="lineNum">     603 </span>            :         else {</a>
+<a name="604"><span class="lineNum">     604 </span>            :           // {sae} doesn't have the same limitations as {er}, this is enough.</a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 :           if (ASMJIT_UNLIKELY(!commonData-&gt;hasAvx512SAE()))</span></a>
+<a name="606"><span class="lineNum">     606 </span>            :             return DebugUtils::errored(kErrorInvalidEROrSAE);</a>
+<a name="607"><span class="lineNum">     607 </span>            :         }</a>
+<a name="608"><span class="lineNum">     608 </span>            :       }</a>
+<a name="609"><span class="lineNum">     609 </span>            :     }</a>
+<a name="610"><span class="lineNum">     610 </span>            :     else {</a>
+<a name="611"><span class="lineNum">     611 </span>            :       // Not AVX512 instruction - maybe OpExtra is xCX register used by REP/REPNZ prefix. Otherwise the instruction is invalid.</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :       if ((options &amp; kAvx512Options) || (options &amp; (X86Inst::kOptionRep | X86Inst::kOptionRepnz)) == 0)</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :         return DebugUtils::errored(kErrorInvalidInstruction);</a>
+<a name="614"><span class="lineNum">     614 </span>            :     }</a>
+<a name="615"><span class="lineNum">     615 </span>            :   }</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            :   return kErrorOk;</a>
+<a name="618"><span class="lineNum">     618 </span>            : }</a>
+<a name="619"><span class="lineNum">     619 </span>            : #endif</a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span>            : // ============================================================================</a>
+<a name="622"><span class="lineNum">     622 </span>            : // [asmjit::X86InstImpl - CheckFeatures]</a>
+<a name="623"><span class="lineNum">     623 </span>            : // ============================================================================</a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span>            : #if !defined(ASMJIT_DISABLE_EXTENSIONS)</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE static uint32_t x86GetRegTypesMask(const Operand_* operands, uint32_t count) noexcept {</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :   uint32_t mask = 0;</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++) {</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :     const Operand_&amp; op = operands[i];</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :     if (op.isReg()) {</span></a>
+<a name="631"><span class="lineNum">     631 </span>            :       const Reg&amp; reg = op.as&lt;Reg&gt;();</a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :       mask |= Utils::mask(reg.getType());</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :     }</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :     else if (op.isMem()) {</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :       const Mem&amp; mem = op.as&lt;Mem&gt;();</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :       if (mem.hasBaseReg()) mask |= Utils::mask(mem.getBaseType());</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :       if (mem.hasIndexReg()) mask |= Utils::mask(mem.getIndexType());</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :     }</a>
+<a name="639"><span class="lineNum">     639 </span>            :   }</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :   return mask;</span></a>
+<a name="641"><span class="lineNum">     641 </span>            : }</a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86InstImpl::checkFeatures(uint32_t archType, const Inst::Detail&amp; detail, const Operand_* operands, uint32_t count, CpuFeatures&amp; out) noexcept {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :   if (!ArchInfo::isX86Family(archType))</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :     return DebugUtils::errored(kErrorInvalidArch);</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            :   // Get the instruction data.</a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineNoCov">          0 :   uint32_t instId = detail.instId;</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(instId &gt;= X86Inst::_kIdCount))</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :     return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :   const X86Inst* iData = &amp;X86InstDB::instData[instId];</a>
+<a name="653"><span class="lineNum">     653 </span>            :   const X86Inst::OperationData&amp; od = iData-&gt;getOperationData();</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :   const uint8_t* fData = od.getFeaturesData();</a>
+<a name="656"><span class="lineNum">     656 </span>            :   const uint8_t* fEnd = od.getFeaturesEnd();</a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span>            :   // Copy all features to `out`.</a>
+<a name="659"><span class="lineNum">     659 </span>            :   out.reset();</a>
+<a name="660"><span class="lineNum">     660 </span>            :   do {</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :     uint32_t feature = fData[0];</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :     if (!feature)</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :       break;</a>
+<a name="664"><span class="lineNum">     664 </span>            :     out.add(feature);</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineNoCov">          0 :   } while (++fData != fEnd);</span></a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span>            :   // Since AsmJit merges all instructions that share the same name we have to</a>
+<a name="668"><span class="lineNum">     668 </span>            :   // deal with some special cases and also with MMX/SSE and AVX/AVX2 overlaps.</a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span>            :   // Only proceed if there were some CPU flags set.</a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :   if (fData != od.getFeaturesData()) {</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :     uint32_t mask = x86GetRegTypesMask(operands, count);</span></a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :     // Check for MMX vs SSE overlap.</a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :     if (out.has(CpuInfo::kX86FeatureMMX) || out.has(CpuInfo::kX86FeatureMMX2)) {</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :       // Only instructions defined by SSE and SSE2 overlap. Instructions introduced</a>
+<a name="677"><span class="lineNum">     677 </span>            :       // by newer instruction sets like SSE3+ don't state MMX as they require SSE3+.</a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :       if (out.has(CpuInfo::kX86FeatureSSE) || out.has(CpuInfo::kX86FeatureSSE2)) {</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :         if (!(mask &amp; Utils::mask(X86Reg::kRegXmm))) {</span></a>
+<a name="680"><span class="lineNum">     680 </span>            :           // The instruction doesn't use XMM register(s), thus it's MMX/MMX2 only.</a>
+<a name="681"><span class="lineNum">     681 </span>            :           out.remove(CpuInfo::kX86FeatureSSE);</a>
+<a name="682"><span class="lineNum">     682 </span>            :           out.remove(CpuInfo::kX86FeatureSSE2);</a>
+<a name="683"><span class="lineNum">     683 </span>            :         }</a>
+<a name="684"><span class="lineNum">     684 </span>            :         else {</a>
+<a name="685"><span class="lineNum">     685 </span>            :           out.remove(CpuInfo::kX86FeatureMMX);</a>
+<a name="686"><span class="lineNum">     686 </span>            :           out.remove(CpuInfo::kX86FeatureMMX2);</a>
+<a name="687"><span class="lineNum">     687 </span>            :         }</a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span>            :         // Special case: PEXTRW instruction is MMX/SSE2 instruction. However, this</a>
+<a name="690"><span class="lineNum">     690 </span>            :         // instruction couldn't access memory (only register to register extract) so</a>
+<a name="691"><span class="lineNum">     691 </span>            :         // when SSE4.1 introduced the whole family of PEXTR/PINSR instructions they</a>
+<a name="692"><span class="lineNum">     692 </span>            :         // also introduced PEXTRW with a new opcode 0x15 that can extract directly to</a>
+<a name="693"><span class="lineNum">     693 </span>            :         // memory. This instruction is, of course, not compatible with MMX/SSE2 one.</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :         if (instId == X86Inst::kIdPextrw &amp;&amp; count &gt; 0 &amp;&amp; !operands[0].isMem()) {</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :           out.remove(CpuInfo::kX86FeatureSSE4_1);</a>
+<a name="696"><span class="lineNum">     696 </span>            :         }</a>
+<a name="697"><span class="lineNum">     697 </span>            :       }</a>
+<a name="698"><span class="lineNum">     698 </span>            :     }</a>
+<a name="699"><span class="lineNum">     699 </span>            : </a>
+<a name="700"><span class="lineNum">     700 </span>            :     // Check for AVX vs AVX2 overlap.</a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :     if (out.has(CpuInfo::kX86FeatureAVX) &amp;&amp; out.has(CpuInfo::kX86FeatureAVX2)) {</span></a>
+<a name="702"><span class="lineNum">     702 </span>            :       bool isAVX2 = true;</a>
+<a name="703"><span class="lineNum">     703 </span>            :       // Special case: VBROADCASTSS and VBROADCASTSD were introduced in AVX, but</a>
+<a name="704"><span class="lineNum">     704 </span>            :       // only version that uses memory as a source operand. AVX2 then added support</a>
+<a name="705"><span class="lineNum">     705 </span>            :       // for register source operand.</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineNoCov">          0 :       if (instId == X86Inst::kIdVbroadcastss || instId == X86Inst::kIdVbroadcastsd) {</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineNoCov">          0 :         if (count &gt; 1 &amp;&amp; operands[0].isMem())</span></a>
+<a name="708"><span class="lineNum">     708 </span>            :           isAVX2 = false;</a>
+<a name="709"><span class="lineNum">     709 </span>            :       }</a>
+<a name="710"><span class="lineNum">     710 </span>            :       else {</a>
+<a name="711"><span class="lineNum">     711 </span>            :         // AVX instruction set doesn't support integer operations on YMM registers</a>
+<a name="712"><span class="lineNum">     712 </span>            :         // as these were later introcuced by AVX2. In our case we have to check if</a>
+<a name="713"><span class="lineNum">     713 </span>            :         // YMM register(s) are in use and if that is the case this is an AVX2 instruction.</a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :         if (!(mask &amp; Utils::mask(X86Reg::kRegYmm, X86Reg::kRegZmm)))</span></a>
+<a name="715"><span class="lineNum">     715 </span>            :           isAVX2 = false;</a>
+<a name="716"><span class="lineNum">     716 </span>            :       }</a>
+<a name="717"><span class="lineNum">     717 </span>            : </a>
+<a name="718"><span class="lineNum">     718 </span>            :       if (isAVX2)</a>
+<a name="719"><span class="lineNum">     719 </span>            :         out.remove(CpuInfo::kX86FeatureAVX);</a>
+<a name="720"><span class="lineNum">     720 </span>            :       else</a>
+<a name="721"><span class="lineNum">     721 </span>            :         out.remove(CpuInfo::kX86FeatureAVX2);</a>
+<a name="722"><span class="lineNum">     722 </span>            :     }</a>
+<a name="723"><span class="lineNum">     723 </span>            : </a>
+<a name="724"><span class="lineNum">     724 </span>            :     // Check for AVX|AVX2|FMA|F16C vs AVX512 overlap.</a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineNoCov">          0 :     if (out.has(CpuInfo::kX86FeatureAVX) || out.has(CpuInfo::kX86FeatureAVX2) || out.has(CpuInfo::kX86FeatureFMA) || out.has(CpuInfo::kX86FeatureF16C)) {</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :       // Only AVX512-F|BW|DQ allow to encode AVX/AVX2 instructions</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :       if (out.has(CpuInfo::kX86FeatureAVX512_F) || out.has(CpuInfo::kX86FeatureAVX512_BW) || out.has(CpuInfo::kX86FeatureAVX512_DQ)) {</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :         uint32_t options = detail.options;</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :         uint32_t kAvx512Options = X86Inst::kOptionEvex | X86Inst::_kOptionAvx512Mask;</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :         if (!(mask &amp; Utils::mask(X86Reg::kRegZmm, X86Reg::kRegK)) &amp;&amp; !(options &amp; (kAvx512Options)) &amp;&amp; detail.extraReg.getType() != X86Reg::kRegK) {</span></a>
+<a name="732"><span class="lineNum">     732 </span>            :           out.remove(CpuInfo::kX86FeatureAVX512_F)</a>
+<a name="733"><span class="lineNum">     733 </span>            :              .remove(CpuInfo::kX86FeatureAVX512_BW)</a>
+<a name="734"><span class="lineNum">     734 </span>            :              .remove(CpuInfo::kX86FeatureAVX512_DQ)</a>
+<a name="735"><span class="lineNum">     735 </span>            :              .remove(CpuInfo::kX86FeatureAVX512_VL);</a>
+<a name="736"><span class="lineNum">     736 </span>            :         }</a>
+<a name="737"><span class="lineNum">     737 </span>            :       }</a>
+<a name="738"><span class="lineNum">     738 </span>            :     }</a>
+<a name="739"><span class="lineNum">     739 </span>            : </a>
+<a name="740"><span class="lineNum">     740 </span>            :     // Remove or keep AVX512_VL feature.</a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 :     if (out.has(CpuInfo::kX86FeatureAVX512_VL)) {</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineNoCov">          0 :       if (!(mask &amp; Utils::mask(X86Reg::kRegZmm)))</span></a>
+<a name="743"><span class="lineNum">     743 </span>            :         out.remove(CpuInfo::kX86FeatureAVX512_VL);</a>
+<a name="744"><span class="lineNum">     744 </span>            :     }</a>
+<a name="745"><span class="lineNum">     745 </span>            :   }</a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span>            :   return kErrorOk;</a>
+<a name="748"><span class="lineNum">     748 </span>            : }</a>
+<a name="749"><span class="lineNum">     749 </span>            : #endif</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            : } // asmjit namespace</a>
+<a name="752"><span class="lineNum">     752 </span>            : } // namespace PLMD</a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span>            : // [Api-End]</a>
+<a name="755"><span class="lineNum">     755 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="756"><span class="lineNum">     756 </span>            : #pragma GCC diagnostic pop</a>
+<a name="757"><span class="lineNum">     757 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86internal.cpp.func-sort-c.html b/coverage-libs/asmjit/x86internal.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6c6078d168
--- /dev/null
+++ b/coverage-libs/asmjit/x86internal.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86internal.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86internal.cpp<span style="font-size: 80%;"> (<a href="x86internal.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">113</td>
+            <td class="headerCovTableEntry">394</td>
+            <td class="headerCovTableEntryLo">28.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86internal.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#838">_ZN4PLMD6asmjit11X86Internal11emitArgMoveEPNS0_10X86EmitterERKNS0_6X86RegEjRKNS0_8Operand_EjbPKc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#725">_ZN4PLMD6asmjit11X86Internal15argsToFrameInfoERKNS0_14FuncArgsMapperERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#1200">_ZN4PLMD6asmjit11X86Internal9allocArgsEPNS0_10X86EmitterERKNS0_15FuncFrameLayoutERKNS0_14FuncArgsMapperE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#108">_ZN4PLMD6asmjit18X86FuncArgsContext12initWorkDataERKNS0_14FuncArgsMapperEPKjb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#199">_ZN4PLMD6asmjit18X86FuncArgsContext16markDstRegsDirtyERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#211">_ZN4PLMD6asmjit18X86FuncArgsContext16markRegsForSwapsERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#249">_ZN4PLMD6asmjit18X86FuncArgsContext16markStackArgsRegERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#102">_ZN4PLMD6asmjit18X86FuncArgsContextC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#1114">_ZN4PLMD6asmjit11X86Internal10emitEpilogEPNS0_10X86EmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#1047">_ZN4PLMD6asmjit11X86Internal10emitPrologEPNS0_10X86EmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#588">_ZN4PLMD6asmjit11X86Internal15initFrameLayoutERNS0_15FuncFrameLayoutERKNS0_10FuncDetailERKNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#296">_ZN4PLMD6asmjit11X86Internal12initCallConvERNS0_8CallConvEj</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#418">_ZN4PLMD6asmjit11X86Internal14initFuncDetailERNS0_10FuncDetailERKNS0_13FuncSignatureEj</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#739">_ZN4PLMD6asmjit11X86Internal11emitRegMoveEPNS0_10X86EmitterERKNS0_8Operand_ES6_jbPKc</a></td>
+              <td class="coverFnHi">9084</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86internal.cpp.func.html b/coverage-libs/asmjit/x86internal.cpp.func.html
new file mode 100644
index 0000000000..3439277375
--- /dev/null
+++ b/coverage-libs/asmjit/x86internal.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86internal.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86internal.cpp<span style="font-size: 80%;"> (<a href="x86internal.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">113</td>
+            <td class="headerCovTableEntry">394</td>
+            <td class="headerCovTableEntryLo">28.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86internal.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#1114">_ZN4PLMD6asmjit11X86Internal10emitEpilogEPNS0_10X86EmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#1047">_ZN4PLMD6asmjit11X86Internal10emitPrologEPNS0_10X86EmitterERKNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#838">_ZN4PLMD6asmjit11X86Internal11emitArgMoveEPNS0_10X86EmitterERKNS0_6X86RegEjRKNS0_8Operand_EjbPKc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#739">_ZN4PLMD6asmjit11X86Internal11emitRegMoveEPNS0_10X86EmitterERKNS0_8Operand_ES6_jbPKc</a></td>
+              <td class="coverFnHi">9084</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#296">_ZN4PLMD6asmjit11X86Internal12initCallConvERNS0_8CallConvEj</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#418">_ZN4PLMD6asmjit11X86Internal14initFuncDetailERNS0_10FuncDetailERKNS0_13FuncSignatureEj</a></td>
+              <td class="coverFnHi">3596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#725">_ZN4PLMD6asmjit11X86Internal15argsToFrameInfoERKNS0_14FuncArgsMapperERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#588">_ZN4PLMD6asmjit11X86Internal15initFrameLayoutERNS0_15FuncFrameLayoutERKNS0_10FuncDetailERKNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#1200">_ZN4PLMD6asmjit11X86Internal9allocArgsEPNS0_10X86EmitterERKNS0_15FuncFrameLayoutERKNS0_14FuncArgsMapperE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#108">_ZN4PLMD6asmjit18X86FuncArgsContext12initWorkDataERKNS0_14FuncArgsMapperEPKjb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#199">_ZN4PLMD6asmjit18X86FuncArgsContext16markDstRegsDirtyERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#211">_ZN4PLMD6asmjit18X86FuncArgsContext16markRegsForSwapsERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#249">_ZN4PLMD6asmjit18X86FuncArgsContext16markStackArgsRegERNS0_13FuncFrameInfoE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86internal.cpp.gcov.html#102">_ZN4PLMD6asmjit18X86FuncArgsContextC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86internal.cpp.gcov.html b/coverage-libs/asmjit/x86internal.cpp.gcov.html
new file mode 100644
index 0000000000..554f701659
--- /dev/null
+++ b/coverage-libs/asmjit/x86internal.cpp.gcov.html
@@ -0,0 +1,1458 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86internal.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86internal.cpp<span style="font-size: 80%;"> (source / <a href="x86internal.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">113</td>
+            <td class="headerCovTableEntry">394</td>
+            <td class="headerCovTableEntryLo">28.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if defined(ASMJIT_BUILD_X86)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./x86internal_p.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : // [Api-Begin]</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace asmjit {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // ============================================================================</a>
+<a name="46"><span class="lineNum">      46 </span>            : // [asmjit::X86Internal - Helpers]</a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : static ASMJIT_INLINE uint32_t x86GetXmmMovInst(const FuncFrameLayout&amp; layout) {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   bool avx = layout.isAvxEnabled();</a>
+<a name="51"><span class="lineNum">      51 </span>            :   bool aligned = layout.hasAlignedVecSR();</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   return aligned ? (avx ? X86Inst::kIdVmovaps : X86Inst::kIdMovaps)</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :                  : (avx ? X86Inst::kIdVmovups : X86Inst::kIdMovups);</a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : static ASMJIT_INLINE uint32_t x86VecTypeIdToRegType(uint32_t typeId) noexcept {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       1450 :   return typeId &lt;= TypeId::_kVec128End ? X86Reg::kRegXmm :</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :          typeId &lt;= TypeId::_kVec256End ? X86Reg::kRegYmm :</a>
+<a name="60"><span class="lineNum">      60 </span>            :                                          X86Reg::kRegZmm ;</a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : // ============================================================================</a>
+<a name="64"><span class="lineNum">      64 </span>            : // [asmjit::X86FuncArgsContext]</a>
+<a name="65"><span class="lineNum">      65 </span>            : // ============================================================================</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : // Used by both, `Utils::argsToFrameInfo()` and `Utils::allocArgs()`.</a>
+<a name="68"><span class="lineNum">      68 </span>            : class X86FuncArgsContext {</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   typedef FuncDetail::Value SrcArg;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   typedef FuncArgsMapper::Value DstArg;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   enum { kMaxVRegKinds = Globals::kMaxVRegKinds };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   struct WorkData {</a>
+<a name="76"><span class="lineNum">      76 </span>            :     uint32_t archRegs;                   //!&lt; Architecture provided and allocable regs.</a>
+<a name="77"><span class="lineNum">      77 </span>            :     uint32_t workRegs;                   //!&lt; Registers that can be used by shuffler.</a>
+<a name="78"><span class="lineNum">      78 </span>            :     uint32_t usedRegs;                   //!&lt; Only registers used to pass arguments.</a>
+<a name="79"><span class="lineNum">      79 </span>            :     uint32_t srcRegs;                    //!&lt; Source registers that need shuffling.</a>
+<a name="80"><span class="lineNum">      80 </span>            :     uint32_t dstRegs;                    //!&lt; Destination registers that need shuffling.</a>
+<a name="81"><span class="lineNum">      81 </span>            :     uint8_t numOps;                      //!&lt; Number of operations to finish.</a>
+<a name="82"><span class="lineNum">      82 </span>            :     uint8_t numSwaps;                    //!&lt; Number of register swaps.</a>
+<a name="83"><span class="lineNum">      83 </span>            :     uint8_t numStackArgs;                //!&lt; Number of stack loads.</a>
+<a name="84"><span class="lineNum">      84 </span>            :     uint8_t reserved[9];                 //!&lt; Reserved (only used as padding).</a>
+<a name="85"><span class="lineNum">      85 </span>            :     uint8_t argIndex[32];                //!&lt; Only valid if a corresponding bit in `userRegs` is true.</a>
+<a name="86"><span class="lineNum">      86 </span>            :   };</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :   X86FuncArgsContext() noexcept;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   Error initWorkData(const FuncArgsMapper&amp; args, const uint32_t* dirtyRegs, bool preservedFP) noexcept;</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   Error markRegsForSwaps(FuncFrameInfo&amp; ffi) noexcept;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   Error markDstRegsDirty(FuncFrameInfo&amp; ffi) noexcept;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   Error markStackArgsReg(FuncFrameInfo&amp; ffi) noexcept;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // [Members]</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   WorkData _workData[kMaxVRegKinds];</a>
+<a name="100"><span class="lineNum">     100 </span>            :   bool _hasStackArgs;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   bool _hasRegSwaps;</a>
+<a name="102"><span class="lineNum">     102 </span>            : };</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 : X86FuncArgsContext::X86FuncArgsContext() noexcept {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   ::memset(_workData, 0, sizeof(_workData));</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   _hasStackArgs = false;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   _hasRegSwaps = false;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86FuncArgsContext::initWorkData(const FuncArgsMapper&amp; args, const uint32_t* dirtyRegs, bool preservedFP) noexcept {</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   // This code has to be updated if this changes.</a>
+<a name="112"><span class="lineNum">     112 </span>            :   ASMJIT_ASSERT(kMaxVRegKinds == 4);</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   uint32_t i;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   const FuncDetail&amp; func = *args.getFuncDetail();</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   uint32_t archType = func.getCallConv().getArchType();</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   uint32_t count = (archType == ArchInfo::kTypeX86) ? 8 : 16;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   // Initialize WorkData::archRegs.</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :   _workData[X86Reg::kKindGp ].archRegs = Utils::bits(count) &amp; ~Utils::mask(X86Gp::kIdSp);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :   _workData[X86Reg::kKindMm ].archRegs = Utils::bits(8);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :   _workData[X86Reg::kKindK  ].archRegs = Utils::bits(8);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :   _workData[X86Reg::kKindVec].archRegs = Utils::bits(count);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :   if (preservedFP)</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     _workData[X86Reg::kKindGp].archRegs &amp;= ~Utils::mask(X86Gp::kIdBp);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :   // Initialize WorkData::workRegs.</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; kMaxVRegKinds; i++)</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     _workData[i].workRegs = _workData[i].archRegs &amp; (dirtyRegs[i] | ~func.getCallConv().getPreservedRegs(i));</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   // Build WorkData.</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; kFuncArgCountLoHi; i++) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     const DstArg&amp; dstArg = args.getArg(i);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     if (!dstArg.isAssigned()) continue;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :     const SrcArg&amp; srcArg = func.getArg(i);</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!srcArg.isAssigned()))</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :       return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :     uint32_t dstRegType = dstArg.getRegType();</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(dstRegType &gt;= X86Reg::kRegCount))</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :       return DebugUtils::errored(kErrorInvalidRegType);</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :     uint32_t dstRegKind = X86Reg::kindOf(dstRegType);</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(dstRegKind &gt;= kMaxVRegKinds))</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :       return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :     WorkData&amp; dstData = _workData[dstRegKind];</a>
+<a name="151"><span class="lineNum">     151 </span>            :     uint32_t dstRegId = dstArg.getRegId();</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(dstRegId &gt;= 32 || !(dstData.archRegs &amp; Utils::mask(dstRegId))))</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       return DebugUtils::errored(kErrorInvalidPhysId);</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :     uint32_t dstRegMask = Utils::mask(dstRegId);</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(dstData.usedRegs &amp; dstRegMask))</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       return DebugUtils::errored(kErrorOverlappedRegs);</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     dstData.usedRegs |= dstRegMask;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     dstData.argIndex[dstRegId] = static_cast&lt;uint8_t&gt;(i);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     if (srcArg.byReg()) {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :       uint32_t srcRegKind = X86Reg::kindOf(srcArg.getRegType());</a>
+<a name="164"><span class="lineNum">     164 </span>            :       uint32_t srcRegId = srcArg.getRegId();</a>
+<a name="165"><span class="lineNum">     165 </span>            :       uint32_t srcRegMask = Utils::mask(srcRegId);</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       if (dstRegKind == srcRegKind) {</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :         // The best case, register is allocated where it is expected to be.</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :         if (dstRegId == srcRegId) continue;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :         // Detect a register swap.</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :         if (dstData.usedRegs &amp; srcRegMask) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :           const SrcArg&amp; ref = func.getArg(dstData.argIndex[srcRegId]);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :           if (ref.byReg() &amp;&amp; X86Reg::kindOf(ref.getRegType()) == dstRegKind &amp;&amp; ref.getRegId() == dstRegId) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :             dstData.numSwaps++;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :             _hasRegSwaps = true;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :           }</a>
+<a name="178"><span class="lineNum">     178 </span>            :         }</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :         dstData.srcRegs |= srcRegMask;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :       }</a>
+<a name="181"><span class="lineNum">     181 </span>            :       else {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :         if (ASMJIT_UNLIKELY(srcRegKind &gt;= kMaxVRegKinds))</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :           return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :         WorkData&amp; srcData = _workData[srcRegKind];</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :         srcData.srcRegs |= srcRegMask;</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :       }</a>
+<a name="188"><span class="lineNum">     188 </span>            :     }</a>
+<a name="189"><span class="lineNum">     189 </span>            :     else {</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :       dstData.numStackArgs++;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :       _hasStackArgs = true;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     dstData.numOps++;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     dstData.dstRegs |= dstRegMask;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :   return kErrorOk;</a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86FuncArgsContext::markDstRegsDirty(FuncFrameInfo&amp; ffi) noexcept {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; kMaxVRegKinds; i++) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     WorkData&amp; wd = _workData[i];</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     uint32_t regs = wd.usedRegs | wd.dstRegs;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :     wd.workRegs |= regs;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     ffi.addDirtyRegs(i, regs);</a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86FuncArgsContext::markRegsForSwaps(FuncFrameInfo&amp; ffi) noexcept {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :   if (!_hasRegSwaps)</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :     return kErrorOk;</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // If some registers require swapping then select one dirty register that</a>
+<a name="218"><span class="lineNum">     218 </span>            :   // can be used as a temporary. We can do it also without it (by using xors),</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // but using temporary is always safer and also faster approach.</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; kMaxVRegKinds; i++) {</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     // Skip all register kinds where swapping is natively supported (GP regs).</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :     if (i == X86Reg::kKindGp) continue;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :     // Skip all register kinds that don't require swapping.</a>
+<a name="225"><span class="lineNum">     225 </span>            :     WorkData&amp; wd = _workData[i];</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     if (!wd.numSwaps) continue;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :     // Initially, pick some clobbered or dirty register.</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     uint32_t workRegs = wd.workRegs;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :     uint32_t regs = workRegs &amp; ~(wd.usedRegs | wd.dstRegs);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :     // If that didn't work out pick some register which is not in 'used'.</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :     if (!regs) regs = workRegs &amp; ~wd.usedRegs;</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :     // If that didn't work out pick any other register that is allocable.</a>
+<a name="236"><span class="lineNum">     236 </span>            :     // This last resort case will, however, result in marking one more</a>
+<a name="237"><span class="lineNum">     237 </span>            :     // register dirty.</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :     if (!regs) regs = wd.archRegs &amp; ~workRegs;</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :     // If that didn't work out we will have to use xors instead of moves.</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :     if (!regs) continue;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :     uint32_t regMask = Utils::mask(Utils::findFirstBit(regs));</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :     wd.workRegs |= regMask;</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :     ffi.addDirtyRegs(i, regMask);</a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   return kErrorOk;</a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86FuncArgsContext::markStackArgsReg(FuncFrameInfo&amp; ffi) noexcept {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :   if (!_hasStackArgs)</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     return kErrorOk;</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   // Decide which register to use to hold the stack base address.</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   if (!ffi.hasPreservedFP()) {</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :     WorkData&amp; wd = _workData[X86Reg::kKindGp];</a>
+<a name="258"><span class="lineNum">     258 </span>            :     uint32_t saRegId = ffi.getStackArgsRegId();</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     uint32_t usedRegs = wd.usedRegs;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :     if (saRegId != Globals::kInvalidRegId) {</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :       // Check if the user chosen SA register doesn't overlap with others.</a>
+<a name="263"><span class="lineNum">     263 </span>            :       // However, it's fine if it overlaps with some 'dstMove' register.</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :       if (usedRegs &amp; Utils::mask(saRegId))</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :         return DebugUtils::errored(kErrorOverlappingStackRegWithRegArg);</a>
+<a name="266"><span class="lineNum">     266 </span>            :     }</a>
+<a name="267"><span class="lineNum">     267 </span>            :     else {</a>
+<a name="268"><span class="lineNum">     268 </span>            :       // Initially, pick some clobbered or dirty register that is neither</a>
+<a name="269"><span class="lineNum">     269 </span>            :       // in 'used' and neither in 'dstMove'. That's the safest bet as the</a>
+<a name="270"><span class="lineNum">     270 </span>            :       // register won't collide with anything right now.</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :       uint32_t regs = wd.workRegs &amp; ~(usedRegs | wd.dstRegs);</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :       // If that didn't work out pick some register which is not in 'used'.</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :       if (!regs) regs = wd.workRegs &amp; ~usedRegs;</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :       // If that didn't work out then we have to make one more register dirty.</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :       if (!regs) regs = wd.archRegs &amp; ~wd.workRegs;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :       // If that didn't work out we can't continue.</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :       if (ASMJIT_UNLIKELY(!regs))</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :         return DebugUtils::errored(kErrorNoMorePhysRegs);</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            :       saRegId = Utils::findFirstBit(regs);</a>
+<a name="284"><span class="lineNum">     284 </span>            :       ffi.setStackArgsRegId(saRegId);</a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span>            :   }</a>
+<a name="287"><span class="lineNum">     287 </span>            :   else {</a>
+<a name="288"><span class="lineNum">     288 </span>            :     ffi.setStackArgsRegId(X86Gp::kIdBp);</a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :   return kErrorOk;</a>
+<a name="292"><span class="lineNum">     292 </span>            : }</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : // ============================================================================</a>
+<a name="295"><span class="lineNum">     295 </span>            : // [asmjit::X86Internal - CallConv]</a>
+<a name="296"><span class="lineNum">     296 </span>            : // ============================================================================</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       3596 : ASMJIT_FAVOR_SIZE Error X86Internal::initCallConv(CallConv&amp; cc, uint32_t ccId) noexcept {</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   const uint32_t kKindGp  = X86Reg::kKindGp;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   const uint32_t kKindVec = X86Reg::kKindVec;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   const uint32_t kKindMm  = X86Reg::kKindMm;</a>
+<a name="302"><span class="lineNum">     302 </span>            :   const uint32_t kKindK   = X86Reg::kKindK;</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   const uint32_t kZax = X86Gp::kIdAx;</a>
+<a name="305"><span class="lineNum">     305 </span>            :   const uint32_t kZbx = X86Gp::kIdBx;</a>
+<a name="306"><span class="lineNum">     306 </span>            :   const uint32_t kZcx = X86Gp::kIdCx;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   const uint32_t kZdx = X86Gp::kIdDx;</a>
+<a name="308"><span class="lineNum">     308 </span>            :   const uint32_t kZsp = X86Gp::kIdSp;</a>
+<a name="309"><span class="lineNum">     309 </span>            :   const uint32_t kZbp = X86Gp::kIdBp;</a>
+<a name="310"><span class="lineNum">     310 </span>            :   const uint32_t kZsi = X86Gp::kIdSi;</a>
+<a name="311"><span class="lineNum">     311 </span>            :   const uint32_t kZdi = X86Gp::kIdDi;</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       3596 :   switch (ccId) {</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :     case CallConv::kIdX86StdCall:</a>
+<a name="315"><span class="lineNum">     315 </span>            :       cc.setFlags(CallConv::kFlagCalleePopsStack);</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :       goto X86CallConv;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :     case CallConv::kIdX86MsThisCall:</a>
+<a name="319"><span class="lineNum">     319 </span>            :       cc.setFlags(CallConv::kFlagCalleePopsStack);</a>
+<a name="320"><span class="lineNum">     320 </span>            :       cc.setPassedOrder(kKindGp, kZcx);</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :       goto X86CallConv;</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :     case CallConv::kIdX86MsFastCall:</a>
+<a name="324"><span class="lineNum">     324 </span>            :     case CallConv::kIdX86GccFastCall:</a>
+<a name="325"><span class="lineNum">     325 </span>            :       cc.setFlags(CallConv::kFlagCalleePopsStack);</a>
+<a name="326"><span class="lineNum">     326 </span>            :       cc.setPassedOrder(kKindGp, kZcx, kZdx);</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :       goto X86CallConv;</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            :     case CallConv::kIdX86GccRegParm1:</a>
+<a name="330"><span class="lineNum">     330 </span>            :       cc.setPassedOrder(kKindGp, kZax);</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :       goto X86CallConv;</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :     case CallConv::kIdX86GccRegParm2:</a>
+<a name="334"><span class="lineNum">     334 </span>            :       cc.setPassedOrder(kKindGp, kZax, kZdx);</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :       goto X86CallConv;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            :     case CallConv::kIdX86GccRegParm3:</a>
+<a name="338"><span class="lineNum">     338 </span>            :       cc.setPassedOrder(kKindGp, kZax, kZdx, kZcx);</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :       goto X86CallConv;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :     case CallConv::kIdX86CDecl:</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 : X86CallConv:</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :       cc.setNaturalStackAlignment(4);</a>
+<a name="344"><span class="lineNum">     344 </span>            :       cc.setArchType(ArchInfo::kTypeX86);</a>
+<a name="345"><span class="lineNum">     345 </span>            :       cc.setPreservedRegs(kKindGp, Utils::mask(kZbx, kZsp, kZbp, kZsi, kZdi));</a>
+<a name="346"><span class="lineNum">     346 </span>            :       break;</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            :     case CallConv::kIdX86Win64:</a>
+<a name="349"><span class="lineNum">     349 </span>            :       cc.setArchType(ArchInfo::kTypeX64);</a>
+<a name="350"><span class="lineNum">     350 </span>            :       cc.setAlgorithm(CallConv::kAlgorithmWin64);</a>
+<a name="351"><span class="lineNum">     351 </span>            :       cc.setFlags(CallConv::kFlagPassFloatsByVec | CallConv::kFlagIndirectVecArgs);</a>
+<a name="352"><span class="lineNum">     352 </span>            :       cc.setNaturalStackAlignment(16);</a>
+<a name="353"><span class="lineNum">     353 </span>            :       cc.setSpillZoneSize(32);</a>
+<a name="354"><span class="lineNum">     354 </span>            :       cc.setPassedOrder(kKindGp, kZcx, kZdx, 8, 9);</a>
+<a name="355"><span class="lineNum">     355 </span>            :       cc.setPassedOrder(kKindVec, 0, 1, 2, 3);</a>
+<a name="356"><span class="lineNum">     356 </span>            :       cc.setPreservedRegs(kKindGp, Utils::mask(kZbx, kZsp, kZbp, kZsi, kZdi, 12, 13, 14, 15));</a>
+<a name="357"><span class="lineNum">     357 </span>            :       cc.setPreservedRegs(kKindVec, Utils::mask(6, 7, 8, 9, 10, 11, 12, 13, 14, 15));</a>
+<a name="358"><span class="lineNum">     358 </span>            :       break;</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            :     case CallConv::kIdX86SysV64:</a>
+<a name="361"><span class="lineNum">     361 </span>            :       cc.setArchType(ArchInfo::kTypeX64);</a>
+<a name="362"><span class="lineNum">     362 </span>            :       cc.setFlags(CallConv::kFlagPassFloatsByVec);</a>
+<a name="363"><span class="lineNum">     363 </span>            :       cc.setNaturalStackAlignment(16);</a>
+<a name="364"><span class="lineNum">     364 </span>            :       cc.setRedZoneSize(128);</a>
+<a name="365"><span class="lineNum">     365 </span>            :       cc.setPassedOrder(kKindGp, kZdi, kZsi, kZdx, kZcx, 8, 9);</a>
+<a name="366"><span class="lineNum">     366 </span>            :       cc.setPassedOrder(kKindVec, 0, 1, 2, 3, 4, 5, 6, 7);</a>
+<a name="367"><span class="lineNum">     367 </span>            :       cc.setPreservedRegs(kKindGp, Utils::mask(kZbx, kZsp, kZbp, 12, 13, 14, 15));</a>
+<a name="368"><span class="lineNum">     368 </span>            :       break;</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :     case CallConv::kIdX86FastEval2:</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :     case CallConv::kIdX86FastEval3:</a>
+<a name="372"><span class="lineNum">     372 </span>            :     case CallConv::kIdX86FastEval4: {</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :       uint32_t n = ccId - CallConv::kIdX86FastEval2;</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            :       cc.setArchType(ArchInfo::kTypeX86);</a>
+<a name="376"><span class="lineNum">     376 </span>            :       cc.setFlags(CallConv::kFlagPassFloatsByVec);</a>
+<a name="377"><span class="lineNum">     377 </span>            :       cc.setNaturalStackAlignment(16);</a>
+<a name="378"><span class="lineNum">     378 </span>            :       cc.setPassedOrder(kKindGp, kZax, kZdx, kZcx, kZsi, kZdi);</a>
+<a name="379"><span class="lineNum">     379 </span>            :       cc.setPassedOrder(kKindMm, 0, 1, 2, 3, 4, 5, 6, 7);</a>
+<a name="380"><span class="lineNum">     380 </span>            :       cc.setPassedOrder(kKindVec, 0, 1, 2, 3, 4, 5, 6, 7);</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :       cc.setPreservedRegs(kKindGp , Utils::bits(8));</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :       cc.setPreservedRegs(kKindVec, Utils::bits(8) &amp; ~Utils::bits(n));</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :       cc.setPreservedRegs(kKindMm , Utils::bits(8));</a>
+<a name="385"><span class="lineNum">     385 </span>            :       cc.setPreservedRegs(kKindK  , Utils::bits(8));</a>
+<a name="386"><span class="lineNum">     386 </span>            :       break;</a>
+<a name="387"><span class="lineNum">     387 </span>            :     }</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :     case CallConv::kIdX64FastEval2:</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :     case CallConv::kIdX64FastEval3:</a>
+<a name="391"><span class="lineNum">     391 </span>            :     case CallConv::kIdX64FastEval4: {</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :       uint32_t n = ccId - CallConv::kIdX64FastEval2;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            :       cc.setArchType(ArchInfo::kTypeX64);</a>
+<a name="395"><span class="lineNum">     395 </span>            :       cc.setFlags(CallConv::kFlagPassFloatsByVec);</a>
+<a name="396"><span class="lineNum">     396 </span>            :       cc.setNaturalStackAlignment(16);</a>
+<a name="397"><span class="lineNum">     397 </span>            :       cc.setPassedOrder(kKindGp, kZax, kZdx, kZcx, kZsi, kZdi);</a>
+<a name="398"><span class="lineNum">     398 </span>            :       cc.setPassedOrder(kKindMm, 0, 1, 2, 3, 4, 5, 6, 7);</a>
+<a name="399"><span class="lineNum">     399 </span>            :       cc.setPassedOrder(kKindVec, 0, 1, 2, 3, 4, 5, 6, 7);</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :       cc.setPreservedRegs(kKindGp , Utils::bits(16));</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :       cc.setPreservedRegs(kKindVec,~Utils::bits(n));</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :       cc.setPreservedRegs(kKindMm , Utils::bits(8));</a>
+<a name="404"><span class="lineNum">     404 </span>            :       cc.setPreservedRegs(kKindK  , Utils::bits(8));</a>
+<a name="405"><span class="lineNum">     405 </span>            :       break;</a>
+<a name="406"><span class="lineNum">     406 </span>            :     }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :     default:</a>
+<a name="409"><span class="lineNum">     409 </span>            :       return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            :   cc.setId(ccId);</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">       3596 :   return kErrorOk;</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : }</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            : // ============================================================================</a>
+<a name="417"><span class="lineNum">     417 </span>            : // [asmjit::X86Internal - FuncDetail]</a>
+<a name="418"><span class="lineNum">     418 </span>            : // ============================================================================</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">       3596 : ASMJIT_FAVOR_SIZE Error X86Internal::initFuncDetail(FuncDetail&amp; func, const FuncSignature&amp; sign, uint32_t gpSize) noexcept {</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :   const CallConv&amp; cc = func.getCallConv();</a>
+<a name="422"><span class="lineNum">     422 </span>            :   uint32_t archType = cc.getArchType();</a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span>            :   uint32_t i;</a>
+<a name="425"><span class="lineNum">     425 </span>            :   uint32_t argCount = func.getArgCount();</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">       3596 :   if (func.getRetCount() != 0) {</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :     uint32_t typeId = func._rets[0].getTypeId();</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       3596 :     switch (typeId) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :       case TypeId::kI64:</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :       case TypeId::kU64: {</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :         if (archType == ArchInfo::kTypeX86) {</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :           // Convert a 64-bit return to two 32-bit returns.</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :           func._retCount = 2;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :           typeId -= 2;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            :           // 64-bit value is returned in EDX:EAX on X86.</a>
+<a name="438"><span class="lineNum">     438 </span>            :           func._rets[0].initReg(typeId, X86Gp::kRegGpd, X86Gp::kIdAx);</a>
+<a name="439"><span class="lineNum">     439 </span>            :           func._rets[1].initReg(typeId, X86Gp::kRegGpd, X86Gp::kIdDx);</a>
+<a name="440"><span class="lineNum">     440 </span>            :           break;</a>
+<a name="441"><span class="lineNum">     441 </span>            :         }</a>
+<a name="442"><span class="lineNum">     442 </span>            :         else {</a>
+<a name="443"><span class="lineNum">     443 </span>            :           func._rets[0].initReg(typeId, X86Gp::kRegGpq, X86Gp::kIdAx);</a>
+<a name="444"><span class="lineNum">     444 </span>            :         }</a>
+<a name="445"><span class="lineNum">     445 </span>            :         break;</a>
+<a name="446"><span class="lineNum">     446 </span>            :       }</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :       case TypeId::kI8:</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :       case TypeId::kU8:</a>
+<a name="450"><span class="lineNum">     450 </span>            :       case TypeId::kI16:</a>
+<a name="451"><span class="lineNum">     451 </span>            :       case TypeId::kU16:</a>
+<a name="452"><span class="lineNum">     452 </span>            :       case TypeId::kI32:</a>
+<a name="453"><span class="lineNum">     453 </span>            :       case TypeId::kU32: {</a>
+<a name="454"><span class="lineNum">     454 </span>            :         func._rets[0].assignToReg(X86Gp::kRegGpd, X86Gp::kIdAx);</a>
+<a name="455"><span class="lineNum">     455 </span>            :         break;</a>
+<a name="456"><span class="lineNum">     456 </span>            :       }</a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">       3596 :       case TypeId::kF32:</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :       case TypeId::kF64: {</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">       3596 :         uint32_t regType = (archType == ArchInfo::kTypeX86) ? X86Reg::kRegFp : X86Reg::kRegXmm;</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :         func._rets[0].assignToReg(regType, 0);</a>
+<a name="462"><span class="lineNum">     462 </span>            :         break;</a>
+<a name="463"><span class="lineNum">     463 </span>            :       }</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 :       case TypeId::kF80: {</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :         // 80-bit floats are always returned by FP0.</a>
+<a name="467"><span class="lineNum">     467 </span>            :         func._rets[0].assignToReg(X86Reg::kRegFp, 0);</a>
+<a name="468"><span class="lineNum">     468 </span>            :         break;</a>
+<a name="469"><span class="lineNum">     469 </span>            :       }</a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :       case TypeId::kMmx32:</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :       case TypeId::kMmx64: {</a>
+<a name="473"><span class="lineNum">     473 </span>            :         // On X64 MM register(s) are returned through XMM or GPQ (Win64).</a>
+<a name="474"><span class="lineNum">     474 </span>            :         uint32_t regType = X86Reg::kRegMm;</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :         if (archType != ArchInfo::kTypeX86)</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :           regType = cc.getAlgorithm() == CallConv::kAlgorithmDefault ? X86Reg::kRegXmm : X86Reg::kRegGpq;</span></a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span>            :         func._rets[0].assignToReg(regType, 0);</a>
+<a name="479"><span class="lineNum">     479 </span>            :         break;</a>
+<a name="480"><span class="lineNum">     480 </span>            :       }</a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :       default: {</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :         func._rets[0].assignToReg(x86VecTypeIdToRegType(typeId), 0);</a>
+<a name="484"><span class="lineNum">     484 </span>            :         break;</a>
+<a name="485"><span class="lineNum">     485 </span>            :       }</a>
+<a name="486"><span class="lineNum">     486 </span>            :     }</a>
+<a name="487"><span class="lineNum">     487 </span>            :   }</a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">       3596 :   uint32_t stackBase = gpSize;</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">       3596 :   uint32_t stackOffset = stackBase + cc._spillZoneSize;</span></a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">       3596 :   if (cc.getAlgorithm() == CallConv::kAlgorithmDefault) {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :     uint32_t gpzPos = 0;</a>
+<a name="494"><span class="lineNum">     494 </span>            :     uint32_t vecPos = 0;</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">       5466 :     for (i = 0; i &lt; argCount; i++) {</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :       FuncDetail::Value&amp; arg = func._args[i];</a>
+<a name="498"><span class="lineNum">     498 </span>            :       uint32_t typeId = arg.getTypeId();</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">       1870 :       if (TypeId::isInt(typeId)) {</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        420 :         uint32_t regId = gpzPos &lt; CallConv::kNumRegArgsPerKind ? cc._passedOrder[X86Reg::kKindGp].id[gpzPos] : Globals::kInvalidRegId;</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        420 :         if (regId != Globals::kInvalidRegId) {</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :           uint32_t regType = (typeId &lt;= TypeId::kU32)</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        420 :             ? X86Reg::kRegGpd</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :             : X86Reg::kRegGpq;</a>
+<a name="506"><span class="lineNum">     506 </span>            :           arg.assignToReg(regType, regId);</a>
+<a name="507"><span class="lineNum">     507 </span>            :           func.addUsedRegs(X86Reg::kKindGp, Utils::mask(regId));</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">        420 :           gpzPos++;</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :         }</a>
+<a name="510"><span class="lineNum">     510 </span>            :         else {</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :           uint32_t size = std::max&lt;uint32_t&gt;(TypeId::sizeOf(typeId), gpSize);</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :           arg.assignToStack(stackOffset);</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :           stackOffset += size;</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :         }</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        420 :         continue;</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        420 :       }</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">       1450 :       if (TypeId::isFloat(typeId) || TypeId::isVec(typeId)) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">       1450 :         uint32_t regId = vecPos &lt; CallConv::kNumRegArgsPerKind ? cc._passedOrder[X86Reg::kKindVec].id[vecPos] : Globals::kInvalidRegId;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            :         // If this is a float, but `floatByVec` is false, we have to pass by stack.</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">       1450 :         if (TypeId::isFloat(typeId) &amp;&amp; !cc.hasFlag(CallConv::kFlagPassFloatsByVec))</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :           regId = Globals::kInvalidRegId;</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">       1450 :         if (regId != Globals::kInvalidRegId) {</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :           arg.initReg(typeId, x86VecTypeIdToRegType(typeId), regId);</a>
+<a name="527"><span class="lineNum">     527 </span>            :           func.addUsedRegs(X86Reg::kKindVec, Utils::mask(regId));</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">       1450 :           vecPos++;</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :         }</a>
+<a name="530"><span class="lineNum">     530 </span>            :         else {</a>
+<a name="531"><span class="lineNum">     531 </span>            :           int32_t size = TypeId::sizeOf(typeId);</a>
+<a name="532"><span class="lineNum">     532 </span>            :           arg.assignToStack(stackOffset);</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :           stackOffset += size;</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :         }</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">       1450 :         continue;</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">       1450 :       }</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :     }</a>
+<a name="538"><span class="lineNum">     538 </span>            :   }</a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">       3596 :   if (cc.getAlgorithm() == CallConv::kAlgorithmWin64) {</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; argCount; i++) {</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :       FuncDetail::Value&amp; arg = func._args[i];</a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span>            :       uint32_t typeId = arg.getTypeId();</a>
+<a name="545"><span class="lineNum">     545 </span>            :       uint32_t size = TypeId::sizeOf(typeId);</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(typeId) || TypeId::isMmx(typeId)) {</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineNoCov">          0 :         uint32_t regId = i &lt; CallConv::kNumRegArgsPerKind ? cc._passedOrder[X86Reg::kKindGp].id[i] : Globals::kInvalidRegId;</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :         if (regId != Globals::kInvalidRegId) {</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :           uint32_t regType = (size &lt;= 4 &amp;&amp; !TypeId::isMmx(typeId))</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :             ? X86Reg::kRegGpd</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :             : X86Reg::kRegGpq;</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            :           arg.assignToReg(regType, regId);</a>
+<a name="555"><span class="lineNum">     555 </span>            :           func.addUsedRegs(X86Reg::kKindGp, Utils::mask(regId));</a>
+<a name="556"><span class="lineNum">     556 </span>            :         }</a>
+<a name="557"><span class="lineNum">     557 </span>            :         else {</a>
+<a name="558"><span class="lineNum">     558 </span>            :           arg.assignToStack(stackOffset);</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :           stackOffset += gpSize;</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :         }</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :       if (TypeId::isFloat(typeId) || TypeId::isVec(typeId)) {</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :         uint32_t regId = i &lt; CallConv::kNumRegArgsPerKind ? cc._passedOrder[X86Reg::kKindVec].id[i] : Globals::kInvalidRegId;</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineNoCov">          0 :         if (regId != Globals::kInvalidRegId &amp;&amp; (TypeId::isFloat(typeId) || cc.hasFlag(CallConv::kFlagVectorCall))) {</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :           uint32_t regType = x86VecTypeIdToRegType(typeId);</a>
+<a name="568"><span class="lineNum">     568 </span>            :           uint32_t regId = cc._passedOrder[X86Reg::kKindVec].id[i];</a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span>            :           arg.assignToReg(regType, regId);</a>
+<a name="571"><span class="lineNum">     571 </span>            :           func.addUsedRegs(X86Reg::kKindVec, Utils::mask(regId));</a>
+<a name="572"><span class="lineNum">     572 </span>            :         }</a>
+<a name="573"><span class="lineNum">     573 </span>            :         else {</a>
+<a name="574"><span class="lineNum">     574 </span>            :           arg.assignToStack(stackOffset);</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :           stackOffset += 8; // Always 8 bytes (float/double).</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :         }</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :     }</a>
+<a name="580"><span class="lineNum">     580 </span>            :   }</a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">       3596 :   func._argStackSize = stackOffset - stackBase;</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">       3596 :   return kErrorOk;</span></a>
+<a name="584"><span class="lineNum">     584 </span>            : }</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span>            : // ============================================================================</a>
+<a name="587"><span class="lineNum">     587 </span>            : // [asmjit::X86Internal - FrameLayout]</a>
+<a name="588"><span class="lineNum">     588 </span>            : // ============================================================================</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error X86Internal::initFrameLayout(FuncFrameLayout&amp; layout, const FuncDetail&amp; func, const FuncFrameInfo&amp; ffi) noexcept {</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :   layout.reset();</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span>            :   uint32_t kind;</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">       1948 :   uint32_t gpSize = (func.getCallConv().getArchType() == ArchInfo::kTypeX86) ? 4 : 8;</span></a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            :   // Calculate a bit-mask of all registers that must be saved &amp; restored.</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">       9740 :   for (kind = 0; kind &lt; Globals::kMaxVRegKinds; kind++)</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">       7792 :     layout._savedRegs[kind] = (ffi.getDirtyRegs(kind) &amp; ~func.getPassedRegs(kind)) &amp; func.getPreservedRegs(kind);</span></a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span>            :   // Include EBP|RBP if the function preserves the frame-pointer.</a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">       1948 :   if (ffi.hasPreservedFP()) {</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :     layout._preservedFP = true;</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :     layout._savedRegs[X86Reg::kKindGp] |= Utils::mask(X86Gp::kIdBp);</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :   }</a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            :   // Exclude ESP/RSP - this register is never included in saved-regs.</a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">       1948 :   layout._savedRegs[X86Reg::kKindGp] &amp;= ~Utils::mask(X86Gp::kIdSp);</span></a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            :   // Calculate the final stack alignment.</a>
+<a name="610"><span class="lineNum">     610 </span>            :   uint32_t stackAlignment =</a>
+<a name="611"><span class="lineNum">     611 </span>            :     std::max&lt;uint32_t&gt;(</a>
+<a name="612"><span class="lineNum">     612 </span>            :       std::max&lt;uint32_t&gt;(</a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       1948 :         ffi.getStackFrameAlignment(),</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">       1948 :         ffi.getCallFrameAlignment()),</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">       1948 :       func.getCallConv().getNaturalStackAlignment());</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">       1948 :   layout._stackAlignment = static_cast&lt;uint8_t&gt;(stackAlignment);</span></a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span>            :   // Calculate if dynamic stack alignment is required. If true the function has</a>
+<a name="619"><span class="lineNum">     619 </span>            :   // to align stack dynamically to match `_stackAlignment` and would require to</a>
+<a name="620"><span class="lineNum">     620 </span>            :   // access its stack-based arguments through `_stackArgsRegId`.</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">       1948 :   bool dsa = stackAlignment &gt; func.getCallConv().getNaturalStackAlignment() &amp;&amp; stackAlignment &gt;= 16;</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :   layout._dynamicAlignment = dsa;</span></a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            :   // This flag describes if the prolog inserter must store the previous ESP|RSP</a>
+<a name="625"><span class="lineNum">     625 </span>            :   // to stack so the epilog inserter can load the stack from it before returning.</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :   bool dsaSlotUsed = dsa &amp;&amp; !ffi.hasPreservedFP();</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">       1948 :   layout._dsaSlotUsed = dsaSlotUsed;</span></a>
+<a name="628"><span class="lineNum">     628 </span>            : </a>
+<a name="629"><span class="lineNum">     629 </span>            :   // These two are identical if the function doesn't align its stack dynamically.</a>
+<a name="630"><span class="lineNum">     630 </span>            :   uint32_t stackArgsRegId = ffi.getStackArgsRegId();</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">       1948 :   if (stackArgsRegId == Globals::kInvalidRegId)</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :     stackArgsRegId = X86Gp::kIdSp;</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :   // Fix stack arguments base-register from ESP|RSP to EBP|RBP in case it was</a>
+<a name="635"><span class="lineNum">     635 </span>            :   // not picked before and the function performs dynamic stack alignment.</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       1948 :   if (dsa &amp;&amp; stackArgsRegId == X86Gp::kIdSp)</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :     stackArgsRegId = X86Gp::kIdBp;</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">       1948 :   if (stackArgsRegId != X86Gp::kIdSp)</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :     layout._savedRegs[X86Reg::kKindGp] |= Utils::mask(stackArgsRegId) &amp; func.getPreservedRegs(X86Gp::kKindGp);</span></a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">       1948 :   layout._stackBaseRegId = X86Gp::kIdSp;</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">       1948 :   layout._stackArgsRegId = static_cast&lt;uint8_t&gt;(stackArgsRegId);</span></a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span>            :   // Setup stack size used to save preserved registers.</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">       1948 :   layout._gpStackSize  = Utils::bitCount(layout.getSavedRegs(X86Reg::kKindGp )) * gpSize;</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">       1948 :   layout._vecStackSize = Utils::bitCount(layout.getSavedRegs(X86Reg::kKindVec)) * 16 +</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :                          Utils::bitCount(layout.getSavedRegs(X86Reg::kKindMm )) *  8 ;</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span>            :   uint32_t v = 0;                        // The beginning of the stack frame, aligned to CallFrame alignment.</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">       1948 :   v += ffi._callFrameSize;               // Count '_callFrameSize'  &lt;- This is used to call functions.</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :   v  = Utils::alignTo(v, stackAlignment);// Align to function's SA</a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">       1948 :   layout._stackBaseOffset = v;           // Store '_stackBaseOffset'&lt;- Function's own stack starts here..</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">       1948 :   v += ffi._stackFrameSize;              // Count '_stackFrameSize' &lt;- Function's own stack ends here.</span></a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            :   // If the function is aligned, calculate the alignment necessary to store</a>
+<a name="658"><span class="lineNum">     658 </span>            :   // vector registers, and set `FuncFrameInfo::kX86FlagAlignedVecSR` to inform</a>
+<a name="659"><span class="lineNum">     659 </span>            :   // PrologEpilog inserter that it can use instructions to perform aligned</a>
+<a name="660"><span class="lineNum">     660 </span>            :   // stores/loads to save/restore VEC registers.</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">       1948 :   if (stackAlignment &gt;= 16 &amp;&amp; layout._vecStackSize) {</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :     v = Utils::alignTo(v, 16);           // Align '_vecStackOffset'.</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :     layout._alignedVecSR = true;</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :   }</a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">       1948 :   layout._vecStackOffset = v;            // Store '_vecStackOffset' &lt;- Functions VEC Save|Restore starts here.</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">       1948 :   v += layout._vecStackSize;             // Count '_vecStackSize'   &lt;- Functions VEC Save|Restore ends here.</span></a>
+<a name="668"><span class="lineNum">     668 </span>            : </a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">       1948 :   if (dsaSlotUsed) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :     layout._dsaSlot = v;                 // Store '_dsaSlot'        &lt;- Old stack pointer is stored here.</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :     v += gpSize;</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :   }</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :   // The return address should be stored after GP save/restore regs. It has</a>
+<a name="675"><span class="lineNum">     675 </span>            :   // the same size as `gpSize` (basically the native register/pointer size).</a>
+<a name="676"><span class="lineNum">     676 </span>            :   // We don't adjust it now as `v` now contains the exact size that the</a>
+<a name="677"><span class="lineNum">     677 </span>            :   // function requires to adjust (call frame + stack frame, vec stack size).</a>
+<a name="678"><span class="lineNum">     678 </span>            :   // The stack (if we consider this size) is misaligned now, as it's always</a>
+<a name="679"><span class="lineNum">     679 </span>            :   // aligned before the function call - when `call()` is executed it pushes</a>
+<a name="680"><span class="lineNum">     680 </span>            :   // the current EIP|RIP onto the stack, and misaligns it by 12 or 8 bytes</a>
+<a name="681"><span class="lineNum">     681 </span>            :   // (depending on the architecture). So count number of bytes needed to align</a>
+<a name="682"><span class="lineNum">     682 </span>            :   // it up to the function's CallFrame (the beginning).</a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">       1948 :   if (v || ffi.hasCalls())</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">       1092 :     v += Utils::alignDiff(v + layout._gpStackSize + gpSize, stackAlignment);</span></a>
+<a name="685"><span class="lineNum">     685 </span>            : </a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">       1948 :   layout._stackAdjustment = v;           // Store '_stackAdjustment'&lt;- SA used by 'add zsp, SA' and 'sub zsp, SA'.</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">       1948 :   layout._gpStackOffset = v;             // Store '_gpStackOffset'  &lt;- Functions GP Save|Restore starts here.</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">       1948 :   v += layout._gpStackSize;              // Count '_gpStackSize'    &lt;- Functions GP Save|Restore ends here.</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">       1948 :   v += gpSize;                           // Count 'ReturnAddress'.</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">       1948 :   v += func.getSpillZoneSize();          // Count 'SpillZoneSize'.</span></a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :   // Calculate where function arguments start, relative to the stackArgsRegId.</a>
+<a name="694"><span class="lineNum">     694 </span>            :   // If the register that will be used to access arguments passed by stack is</a>
+<a name="695"><span class="lineNum">     695 </span>            :   // ESP|RSP then it's exactly where we are now, otherwise we must calculate</a>
+<a name="696"><span class="lineNum">     696 </span>            :   // how many 'push regs' we did and adjust it based on that.</a>
+<a name="697"><span class="lineNum">     697 </span>            :   uint32_t stackArgsOffset = v;</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">       1948 :   if (stackArgsRegId != X86Gp::kIdSp) {</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :     if (ffi.hasPreservedFP())</span></a>
+<a name="700"><span class="lineNum">     700 </span>            :       stackArgsOffset = gpSize;</a>
+<a name="701"><span class="lineNum">     701 </span>            :     else</a>
+<a name="702"><span class="lineNum">     702 </span>            :       stackArgsOffset = layout._gpStackSize;</a>
+<a name="703"><span class="lineNum">     703 </span>            :   }</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">       1948 :   layout._stackArgsOffset = stackArgsOffset;</span></a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            :   // If the function does dynamic stack adjustment then the stack-adjustment</a>
+<a name="707"><span class="lineNum">     707 </span>            :   // must be aligned.</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">       1948 :   if (dsa)</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :     layout._stackAdjustment = Utils::alignTo(layout._stackAdjustment, stackAlignment);</span></a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            :   // Initialize variables based on CallConv flags.</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">       1948 :   if (func.hasFlag(CallConv::kFlagCalleePopsStack))</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :     layout._calleeStackCleanup = static_cast&lt;uint16_t&gt;(func.getArgStackSize());</span></a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            :   // Initialize variables based on FFI flags.</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">       1948 :   layout._mmxCleanup = ffi.hasMmxCleanup();</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">       1948 :   layout._avxEnabled = ffi.isAvxEnabled();</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">       1948 :   layout._avxCleanup = ffi.hasAvxCleanup();</span></a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="721"><span class="lineNum">     721 </span>            : }</a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            : // ============================================================================</a>
+<a name="724"><span class="lineNum">     724 </span>            : // [asmjit::X86Internal - ArgsToFrameInfo]</a>
+<a name="725"><span class="lineNum">     725 </span>            : // ============================================================================</a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86Internal::argsToFrameInfo(const FuncArgsMapper&amp; args, FuncFrameInfo&amp; ffi) noexcept {</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :   X86FuncArgsContext ctx;</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(ctx.initWorkData(args, ffi._dirtyRegs, ffi.hasPreservedFP()));</span></a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(ctx.markDstRegsDirty(ffi));</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(ctx.markRegsForSwaps(ffi));</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(ctx.markStackArgsReg(ffi));</span></a>
+<a name="734"><span class="lineNum">     734 </span>            :   return kErrorOk;</a>
+<a name="735"><span class="lineNum">     735 </span>            : }</a>
+<a name="736"><span class="lineNum">     736 </span>            : </a>
+<a name="737"><span class="lineNum">     737 </span>            : // ============================================================================</a>
+<a name="738"><span class="lineNum">     738 </span>            : // [asmjit::X86Internal - Emit Helpers]</a>
+<a name="739"><span class="lineNum">     739 </span>            : // ============================================================================</a>
+<a name="740"><span class="lineNum">     740 </span>            : </a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">       9084 : ASMJIT_FAVOR_SIZE Error X86Internal::emitRegMove(X86Emitter* emitter,</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :   const Operand_&amp; dst_,</a>
+<a name="743"><span class="lineNum">     743 </span>            :   const Operand_&amp; src_, uint32_t typeId, bool avxEnabled, const char* comment) {</a>
+<a name="744"><span class="lineNum">     744 </span>            : </a>
+<a name="745"><span class="lineNum">     745 </span>            :   // Invalid or abstract TypeIds are not allowed.</a>
+<a name="746"><span class="lineNum">     746 </span>            :   ASMJIT_ASSERT(TypeId::isValid(typeId) &amp;&amp; !TypeId::isAbstract(typeId));</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span>            :   Operand dst(dst_);</a>
+<a name="749"><span class="lineNum">     749 </span>            :   Operand src(src_);</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            :   uint32_t instId = Inst::kIdNone;</a>
+<a name="752"><span class="lineNum">     752 </span>            :   uint32_t memFlags = 0;</a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span>            :   enum MemFlags {</a>
+<a name="755"><span class="lineNum">     755 </span>            :     kDstMem = 0x1,</a>
+<a name="756"><span class="lineNum">     756 </span>            :     kSrcMem = 0x2</a>
+<a name="757"><span class="lineNum">     757 </span>            :   };</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            :   // Detect memory operands and patch them to have the same size as the register.</a>
+<a name="760"><span class="lineNum">     760 </span>            :   // CodeCompiler always sets memory size of allocs and spills, so it shouldn't</a>
+<a name="761"><span class="lineNum">     761 </span>            :   // be really necessary, however, after this function was separated from Compiler</a>
+<a name="762"><span class="lineNum">     762 </span>            :   // it's better to make sure that the size is always specified, as we can use</a>
+<a name="763"><span class="lineNum">     763 </span>            :   // 'movzx' and 'movsx' that rely on it.</a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">       9084 :   if (dst.isMem()) { memFlags |= kDstMem; dst.as&lt;X86Mem&gt;().setSize(src.getSize()); }</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">       9084 :   if (src.isMem()) { memFlags |= kSrcMem; src.as&lt;X86Mem&gt;().setSize(dst.getSize()); }</span></a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       9084 :   switch (typeId) {</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineNoCov">          0 :     case TypeId::kI8:</span></a>
+<a name="769"><span class="lineNum">     769 </span>            :     case TypeId::kU8:</a>
+<a name="770"><span class="lineNum">     770 </span>            :     case TypeId::kI16:</a>
+<a name="771"><span class="lineNum">     771 </span>            :     case TypeId::kU16:</a>
+<a name="772"><span class="lineNum">     772 </span>            :       // Special case - 'movzx' load.</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineNoCov">          0 :       if (memFlags &amp; kSrcMem) {</span></a>
+<a name="774"><span class="lineNum">     774 </span>            :         instId = X86Inst::kIdMovzx;</a>
+<a name="775"><span class="lineNum">     775 </span>            :         dst.setSignature(X86RegTraits&lt;X86Reg::kRegGpd&gt;::kSignature);</a>
+<a name="776"><span class="lineNum">     776 </span>            :       }</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineNoCov">          0 :       else if (!memFlags) {</span></a>
+<a name="778"><span class="lineNum">     778 </span>            :         // Change both destination and source registers to GPD (safer, no dependencies).</a>
+<a name="779"><span class="lineNum">     779 </span>            :         dst.setSignature(X86RegTraits&lt;X86Reg::kRegGpd&gt;::kSignature);</a>
+<a name="780"><span class="lineNum">     780 </span>            :         src.setSignature(X86RegTraits&lt;X86Reg::kRegGpd&gt;::kSignature);</a>
+<a name="781"><span class="lineNum">     781 </span>            :       }</a>
+<a name="782"><span class="lineNum">     782 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span>            :     case TypeId::kI32:</a>
+<a name="785"><span class="lineNum">     785 </span>            :     case TypeId::kU32:</a>
+<a name="786"><span class="lineNum">     786 </span>            :     case TypeId::kI64:</a>
+<a name="787"><span class="lineNum">     787 </span>            :     case TypeId::kU64:</a>
+<a name="788"><span class="lineNum">     788 </span>            :       instId = X86Inst::kIdMov;</a>
+<a name="789"><span class="lineNum">     789 </span>            :       break;</a>
+<a name="790"><span class="lineNum">     790 </span>            : </a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineNoCov">          0 :     case TypeId::kMmx32:</span></a>
+<a name="792"><span class="lineNum">     792 </span>            :       instId = X86Inst::kIdMovd;</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineNoCov">          0 :       if (memFlags) break;</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineNoCov">          0 :     case TypeId::kMmx64 : instId = X86Inst::kIdMovq ; break;</span></a>
+<a name="796"><span class="lineNum">     796 </span>            :     case TypeId::kMask8 : instId = X86Inst::kIdKmovb; break;</a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineNoCov">          0 :     case TypeId::kMask16: instId = X86Inst::kIdKmovw; break;</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 :     case TypeId::kMask32: instId = X86Inst::kIdKmovd; break;</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineNoCov">          0 :     case TypeId::kMask64: instId = X86Inst::kIdKmovq; break;</span></a>
+<a name="800"><span class="lineNum">     800 </span>            : </a>
+<a name="801"><span class="lineNum">     801 </span>            :     default: {</a>
+<a name="802"><span class="lineNum">     802 </span>            :       uint32_t elementTypeId = TypeId::elementOf(typeId);</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">       9084 :       if (TypeId::isVec32(typeId) &amp;&amp; memFlags) {</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineNoCov">          0 :         if (elementTypeId == TypeId::kF32)</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVmovss : X86Inst::kIdMovss;</span></a>
+<a name="806"><span class="lineNum">     806 </span>            :         else</a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVmovd : X86Inst::kIdMovd;</span></a>
+<a name="808"><span class="lineNum">     808 </span>            :         break;</a>
+<a name="809"><span class="lineNum">     809 </span>            :       }</a>
+<a name="810"><span class="lineNum">     810 </span>            : </a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">       9084 :       if (TypeId::isVec64(typeId) &amp;&amp; memFlags) {</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">       8428 :         if (elementTypeId == TypeId::kF64)</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">       8428 :           instId = avxEnabled ? X86Inst::kIdVmovsd : X86Inst::kIdMovsd;</span></a>
+<a name="814"><span class="lineNum">     814 </span>            :         else</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVmovq : X86Inst::kIdMovq;</span></a>
+<a name="816"><span class="lineNum">     816 </span>            :         break;</a>
+<a name="817"><span class="lineNum">     817 </span>            :       }</a>
+<a name="818"><span class="lineNum">     818 </span>            : </a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">        656 :       if (elementTypeId == TypeId::kF32)</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineNoCov">          0 :         instId = avxEnabled ? X86Inst::kIdVmovaps : X86Inst::kIdMovaps;</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">        656 :       else if (elementTypeId == TypeId::kF64)</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">        656 :         instId = avxEnabled ? X86Inst::kIdVmovapd : X86Inst::kIdMovapd;</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 :       else if (typeId &lt;= TypeId::_kVec256End)</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineNoCov">          0 :         instId = avxEnabled ? X86Inst::kIdVmovdqa : X86Inst::kIdMovdqa;</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineNoCov">          0 :       else if (elementTypeId &lt;= TypeId::kU32)</span></a>
+<a name="826"><span class="lineNum">     826 </span>            :         instId = X86Inst::kIdVmovdqa32;</a>
+<a name="827"><span class="lineNum">     827 </span>            :       else</a>
+<a name="828"><span class="lineNum">     828 </span>            :         instId = X86Inst::kIdVmovdqa64;</a>
+<a name="829"><span class="lineNum">     829 </span>            :       break;</a>
+<a name="830"><span class="lineNum">     830 </span>            :     }</a>
+<a name="831"><span class="lineNum">     831 </span>            :   }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            :   if (!instId)</a>
+<a name="834"><span class="lineNum">     834 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="835"><span class="lineNum">     835 </span>            : </a>
+<a name="836"><span class="lineNum">     836 </span>            :   emitter-&gt;setInlineComment(comment);</a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">       9084 :   return emitter-&gt;emit(instId, dst, src);</span></a>
+<a name="838"><span class="lineNum">     838 </span>            : }</a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86Internal::emitArgMove(X86Emitter* emitter,</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :   const X86Reg&amp; dst_, uint32_t dstTypeId,</a>
+<a name="842"><span class="lineNum">     842 </span>            :   const Operand_&amp; src_, uint32_t srcTypeId, bool avxEnabled, const char* comment) {</a>
+<a name="843"><span class="lineNum">     843 </span>            : </a>
+<a name="844"><span class="lineNum">     844 </span>            :   // Deduce optional `dstTypeId`, which may be `TypeId::kVoid` in some cases.</a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineNoCov">          0 :   if (!dstTypeId) dstTypeId = x86OpData.archRegs.regTypeToTypeId[dst_.getType()];</span></a>
+<a name="846"><span class="lineNum">     846 </span>            : </a>
+<a name="847"><span class="lineNum">     847 </span>            :   // Invalid or abstract TypeIds are not allowed.</a>
+<a name="848"><span class="lineNum">     848 </span>            :   ASMJIT_ASSERT(TypeId::isValid(dstTypeId) &amp;&amp; !TypeId::isAbstract(dstTypeId));</a>
+<a name="849"><span class="lineNum">     849 </span>            :   ASMJIT_ASSERT(TypeId::isValid(srcTypeId) &amp;&amp; !TypeId::isAbstract(srcTypeId));</a>
+<a name="850"><span class="lineNum">     850 </span>            : </a>
+<a name="851"><span class="lineNum">     851 </span>            :   X86Reg dst(dst_);</a>
+<a name="852"><span class="lineNum">     852 </span>            :   Operand src(src_);</a>
+<a name="853"><span class="lineNum">     853 </span>            : </a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :   uint32_t dstSize = TypeId::sizeOf(dstTypeId);</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineNoCov">          0 :   uint32_t srcSize = TypeId::sizeOf(srcTypeId);</span></a>
+<a name="856"><span class="lineNum">     856 </span>            : </a>
+<a name="857"><span class="lineNum">     857 </span>            :   int32_t instId = Inst::kIdNone;</a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span>            :   // Not a real loop, just 'break' is nicer than 'goto'.</a>
+<a name="860"><span class="lineNum">     860 </span>            :   for (;;) {</a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineNoCov">          0 :     if (TypeId::isInt(dstTypeId)) {</span></a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(srcTypeId)) {</span></a>
+<a name="863"><span class="lineNum">     863 </span>            :         instId = X86Inst::kIdMovsx;</a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineNoCov">          0 :         uint32_t typeOp = (dstTypeId &lt;&lt; 8) | srcTypeId;</span></a>
+<a name="865"><span class="lineNum">     865 </span>            : </a>
+<a name="866"><span class="lineNum">     866 </span>            :         // Sign extend by using 'movsx'.</a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineNoCov">          0 :         if (typeOp == ((TypeId::kI16 &lt;&lt; 8) | TypeId::kI8 ) ||</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineNoCov">          0 :             typeOp == ((TypeId::kI32 &lt;&lt; 8) | TypeId::kI8 ) ||</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineNoCov">          0 :             typeOp == ((TypeId::kI32 &lt;&lt; 8) | TypeId::kI16) ||</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineNoCov">          0 :             typeOp == ((TypeId::kI64 &lt;&lt; 8) | TypeId::kI8 ) ||</span></a>
+<a name="871"><span class="lineNum">     871 </span>            :             typeOp == ((TypeId::kI64 &lt;&lt; 8) | TypeId::kI16)) break;</a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            :         // Sign extend by using 'movsxd'.</a>
+<a name="874"><span class="lineNum">     874 </span>            :         instId = X86Inst::kIdMovsxd;</a>
+<a name="875"><span class="lineNum">     875 </span>            :         if (typeOp == ((TypeId::kI64 &lt;&lt; 8) | TypeId::kI32)) break;</a>
+<a name="876"><span class="lineNum">     876 </span>            :       }</a>
+<a name="877"><span class="lineNum">     877 </span>            : </a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(srcTypeId) || src_.isMem()) {</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :         // Zero extend by using 'movzx' or 'mov'.</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :         if (dstSize &lt;= 4 &amp;&amp; srcSize &lt; 4) {</span></a>
+<a name="881"><span class="lineNum">     881 </span>            :           instId = X86Inst::kIdMovzx;</a>
+<a name="882"><span class="lineNum">     882 </span>            :           dst.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;());</a>
+<a name="883"><span class="lineNum">     883 </span>            :         }</a>
+<a name="884"><span class="lineNum">     884 </span>            :         else {</a>
+<a name="885"><span class="lineNum">     885 </span>            :           // We should have caught all possibilities where `srcSize` is less</a>
+<a name="886"><span class="lineNum">     886 </span>            :           // than 4, so we don't have to worry about 'movzx' anymore. Minimum</a>
+<a name="887"><span class="lineNum">     887 </span>            :           // size is enough to determine if we want 32-bit or 64-bit move.</a>
+<a name="888"><span class="lineNum">     888 </span>            :           instId = X86Inst::kIdMov;</a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineNoCov">          0 :           srcSize = std::min(srcSize, dstSize);</span></a>
+<a name="890"><span class="lineNum">     890 </span>            : </a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineNoCov">          0 :           dst.setSignature(srcSize == 4 ? X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;()</span></a>
+<a name="892"><span class="lineNum">     892 </span>            :                                         : X86Reg::signatureOfT&lt;X86Reg::kRegGpq&gt;());</a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineNoCov">          0 :           if (src.isReg()) src.setSignature(dst.getSignature());</span></a>
+<a name="894"><span class="lineNum">     894 </span>            :         }</a>
+<a name="895"><span class="lineNum">     895 </span>            :         break;</a>
+<a name="896"><span class="lineNum">     896 </span>            :       }</a>
+<a name="897"><span class="lineNum">     897 </span>            : </a>
+<a name="898"><span class="lineNum">     898 </span>            :       // NOTE: The previous branch caught all memory sources, from here it's</a>
+<a name="899"><span class="lineNum">     899 </span>            :       // always register to register conversion, so catch the remaining cases.</a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :       srcSize = std::min(srcSize, dstSize);</span></a>
+<a name="901"><span class="lineNum">     901 </span>            : </a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineNoCov">          0 :       if (TypeId::isMmx(srcTypeId)) {</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :         // 64-bit move.</a>
+<a name="904"><span class="lineNum">     904 </span>            :         instId = X86Inst::kIdMovq;</a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineNoCov">          0 :         if (srcSize == 8) break;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            : </a>
+<a name="907"><span class="lineNum">     907 </span>            :         // 32-bit move.</a>
+<a name="908"><span class="lineNum">     908 </span>            :         instId = X86Inst::kIdMovd;</a>
+<a name="909"><span class="lineNum">     909 </span>            :         dst.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;());</a>
+<a name="910"><span class="lineNum">     910 </span>            :         break;</a>
+<a name="911"><span class="lineNum">     911 </span>            :       }</a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineNoCov">          0 :       if (TypeId::isMask(srcTypeId)) {</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineNoCov">          0 :         instId = X86Inst::kmovIdFromSize(srcSize);</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineNoCov">          0 :         dst.setSignature(srcSize &lt;= 4 ? X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;()</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :                                       : X86Reg::signatureOfT&lt;X86Reg::kRegGpq&gt;());</a>
+<a name="917"><span class="lineNum">     917 </span>            :         break;</a>
+<a name="918"><span class="lineNum">     918 </span>            :       }</a>
+<a name="919"><span class="lineNum">     919 </span>            : </a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) {</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :         // 64-bit move.</a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineNoCov">          0 :         instId = avxEnabled ? X86Inst::kIdVmovq : X86Inst::kIdMovq;</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineNoCov">          0 :         if (srcSize == 8) break;</span></a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span>            :         // 32-bit move.</a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineNoCov">          0 :         instId = avxEnabled ? X86Inst::kIdVmovd : X86Inst::kIdMovd;</span></a>
+<a name="927"><span class="lineNum">     927 </span>            :         dst.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;());</a>
+<a name="928"><span class="lineNum">     928 </span>            :         break;</a>
+<a name="929"><span class="lineNum">     929 </span>            :       }</a>
+<a name="930"><span class="lineNum">     930 </span>            :     }</a>
+<a name="931"><span class="lineNum">     931 </span>            : </a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineNoCov">          0 :     if (TypeId::isMmx(dstTypeId)) {</span></a>
+<a name="933"><span class="lineNum">     933 </span>            :       instId = X86Inst::kIdMovq;</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :       srcSize = std::min(srcSize, dstSize);</span></a>
+<a name="935"><span class="lineNum">     935 </span>            : </a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(srcTypeId) || src.isMem()) {</span></a>
+<a name="937"><span class="lineNum">     937 </span>            :         // 64-bit move.</a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 :         if (srcSize == 8) break;</span></a>
+<a name="939"><span class="lineNum">     939 </span>            : </a>
+<a name="940"><span class="lineNum">     940 </span>            :         // 32-bit move.</a>
+<a name="941"><span class="lineNum">     941 </span>            :         instId = X86Inst::kIdMovd;</a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :         if (src.isReg()) src.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;());</span></a>
+<a name="943"><span class="lineNum">     943 </span>            :         break;</a>
+<a name="944"><span class="lineNum">     944 </span>            :       }</a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineNoCov">          0 :       if (TypeId::isMmx(srcTypeId)) break;</span></a>
+<a name="947"><span class="lineNum">     947 </span>            : </a>
+<a name="948"><span class="lineNum">     948 </span>            :       // NOTE: This will hurt if `avxEnabled`.</a>
+<a name="949"><span class="lineNum">     949 </span>            :       instId = X86Inst::kIdMovdq2q;</a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) break;</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :     }</a>
+<a name="952"><span class="lineNum">     952 </span>            : </a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineNoCov">          0 :     if (TypeId::isMask(dstTypeId)) {</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineNoCov">          0 :       srcSize = std::min(srcSize, dstSize);</span></a>
+<a name="955"><span class="lineNum">     955 </span>            : </a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(srcTypeId) || TypeId::isMask(srcTypeId) || src.isMem()) {</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineNoCov">          0 :         instId = X86Inst::kmovIdFromSize(srcSize);</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineNoCov">          0 :         if (X86Reg::isGp(src) &amp;&amp; srcSize &lt;= 4) src.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;());</span></a>
+<a name="959"><span class="lineNum">     959 </span>            :         break;</a>
+<a name="960"><span class="lineNum">     960 </span>            :       }</a>
+<a name="961"><span class="lineNum">     961 </span>            :     }</a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineNoCov">          0 :     if (TypeId::isVec(dstTypeId)) {</span></a>
+<a name="964"><span class="lineNum">     964 </span>            :       // By default set destination to XMM, will be set to YMM|ZMM if needed.</a>
+<a name="965"><span class="lineNum">     965 </span>            :       dst.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegXmm&gt;());</a>
+<a name="966"><span class="lineNum">     966 </span>            : </a>
+<a name="967"><span class="lineNum">     967 </span>            :       // NOTE: This will hurt if `avxEnabled`.</a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineNoCov">          0 :       if (X86Reg::isMm(src)) {</span></a>
+<a name="969"><span class="lineNum">     969 </span>            :         // 64-bit move.</a>
+<a name="970"><span class="lineNum">     970 </span>            :         instId = X86Inst::kIdMovq2dq;</a>
+<a name="971"><span class="lineNum">     971 </span>            :         break;</a>
+<a name="972"><span class="lineNum">     972 </span>            :       }</a>
+<a name="973"><span class="lineNum">     973 </span>            : </a>
+<a name="974"><span class="lineNum">     974 </span>            :       // Argument conversion.</a>
+<a name="975"><span class="lineNum">     975 </span>            :       uint32_t dstElement = TypeId::elementOf(dstTypeId);</a>
+<a name="976"><span class="lineNum">     976 </span>            :       uint32_t srcElement = TypeId::elementOf(srcTypeId);</a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineNoCov">          0 :       if (dstElement == TypeId::kF32 &amp;&amp; srcElement == TypeId::kF64) {</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineNoCov">          0 :         srcSize = std::min(dstSize * 2, srcSize);</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :         dstSize = srcSize / 2;</span></a>
+<a name="981"><span class="lineNum">     981 </span>            : </a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineNoCov">          0 :         if (srcSize &lt;= 8)</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVcvtss2sd : X86Inst::kIdCvtss2sd;</span></a>
+<a name="984"><span class="lineNum">     984 </span>            :         else</a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVcvtps2pd : X86Inst::kIdCvtps2pd;</span></a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineNoCov">          0 :         if (dstSize == 32)</span></a>
+<a name="988"><span class="lineNum">     988 </span>            :           dst.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegYmm&gt;());</a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineNoCov">          0 :         if (src.isReg())</span></a>
+<a name="990"><span class="lineNum">     990 </span>            :           src.setSignature(X86Reg::signatureOfVecBySize(srcSize));</a>
+<a name="991"><span class="lineNum">     991 </span>            :         break;</a>
+<a name="992"><span class="lineNum">     992 </span>            :       }</a>
+<a name="993"><span class="lineNum">     993 </span>            : </a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineNoCov">          0 :       if (dstElement == TypeId::kF64 &amp;&amp; srcElement == TypeId::kF32) {</span></a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineNoCov">          0 :         srcSize = std::min(dstSize, srcSize * 2) / 2;</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineNoCov">          0 :         dstSize = srcSize * 2;</span></a>
+<a name="997"><span class="lineNum">     997 </span>            : </a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineNoCov">          0 :         if (srcSize &lt;= 4)</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVcvtsd2ss : X86Inst::kIdCvtsd2ss;</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            :         else</a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVcvtpd2ps : X86Inst::kIdCvtpd2ps;</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            : </a>
+<a name="1003"><span class="lineNum">    1003 </span>            :         dst.setSignature(X86Reg::signatureOfVecBySize(dstSize));</a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineNoCov">          0 :         if (src.isReg() &amp;&amp; srcSize &gt;= 32)</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            :           src.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegYmm&gt;());</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :         break;</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :       }</a>
+<a name="1008"><span class="lineNum">    1008 </span>            : </a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineNoCov">          0 :       srcSize = std::min(srcSize, dstSize);</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineNoCov">          0 :       if (X86Reg::isGp(src) || src.isMem()) {</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            :         // 32-bit move.</a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineNoCov">          0 :         if (srcSize &lt;= 4) {</span></a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVmovd : X86Inst::kIdMovd;</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineNoCov">          0 :           if (src.isReg()) src.setSignature(X86Reg::signatureOfT&lt;X86Reg::kRegGpd&gt;());</span></a>
+<a name="1015"><span class="lineNum">    1015 </span>            :           break;</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :         }</a>
+<a name="1017"><span class="lineNum">    1017 </span>            : </a>
+<a name="1018"><span class="lineNum">    1018 </span>            :         // 64-bit move.</a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineNoCov">          0 :         if (srcSize == 8) {</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineNoCov">          0 :           instId = avxEnabled ? X86Inst::kIdVmovq : X86Inst::kIdMovq;</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            :           break;</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :         }</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :       }</a>
+<a name="1024"><span class="lineNum">    1024 </span>            : </a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineNoCov">          0 :       if (X86Reg::isVec(src) || src.isMem()) {</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineNoCov">          0 :         instId = avxEnabled ? X86Inst::kIdVmovaps : X86Inst::kIdMovaps;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span>            :         uint32_t sign = X86Reg::signatureOfVecBySize(srcSize);</a>
+<a name="1028"><span class="lineNum">    1028 </span>            : </a>
+<a name="1029"><span class="lineNum">    1029 </span>            :         dst.setSignature(sign);</a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineNoCov">          0 :         if (src.isReg()) src.setSignature(sign);</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :         break;</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :       }</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :     }</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : </a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   }</a>
+<a name="1037"><span class="lineNum">    1037 </span>            : </a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineNoCov">          0 :   if (src.isMem())</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineNoCov">          0 :     src.as&lt;X86Mem&gt;().setSize(srcSize);</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            : </a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   emitter-&gt;setInlineComment(comment);</a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineNoCov">          0 :   return emitter-&gt;emit(instId, dst, src);</span></a>
+<a name="1043"><span class="lineNum">    1043 </span>            : }</a>
+<a name="1044"><span class="lineNum">    1044 </span>            : </a>
+<a name="1045"><span class="lineNum">    1045 </span>            : // ============================================================================</a>
+<a name="1046"><span class="lineNum">    1046 </span>            : // [asmjit::X86Internal - Emit Prolog &amp; Epilog]</a>
+<a name="1047"><span class="lineNum">    1047 </span>            : // ============================================================================</a>
+<a name="1048"><span class="lineNum">    1048 </span>            : </a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error X86Internal::emitProlog(X86Emitter* emitter, const FuncFrameLayout&amp; layout) {</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   uint32_t gpSaved = layout.getSavedRegs(X86Reg::kKindGp);</a>
+<a name="1051"><span class="lineNum">    1051 </span>            : </a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   X86Gp zsp = emitter-&gt;zsp();   // ESP|RSP register.</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   X86Gp zbp = emitter-&gt;zbp();   // EBP|RBP register.</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   X86Gp gpReg = emitter-&gt;zsp(); // General purpose register (temporary).</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   X86Gp saReg = emitter-&gt;zsp(); // Stack-arguments base register.</a>
+<a name="1056"><span class="lineNum">    1056 </span>            : </a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   // Emit: 'push zbp'</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   //       'mov  zbp, zsp'.</a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">       1948 :   if (layout.hasPreservedFP()) {</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineNoCov">          0 :     gpSaved &amp;= ~Utils::mask(X86Gp::kIdBp);</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(emitter-&gt;push(zbp));</span></a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(emitter-&gt;mov(zbp, zsp));</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   }</a>
+<a name="1064"><span class="lineNum">    1064 </span>            : </a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   // Emit: 'push gp' sequence.</a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">       1948 :   if (gpSaved) {</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">       5468 :     for (uint32_t i = gpSaved, regId = 0; i; i &gt;&gt;= 1, regId++) {</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">       4392 :       if (!(i &amp; 0x1)) continue;</span></a>
+<a name="1069"><span class="lineNum">    1069 </span>            :       gpReg.setId(regId);</a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">       1120 :       ASMJIT_PROPAGATE(emitter-&gt;push(gpReg));</span></a>
+<a name="1071"><span class="lineNum">    1071 </span>            :     }</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :   }</a>
+<a name="1073"><span class="lineNum">    1073 </span>            : </a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   // Emit: 'mov saReg, zsp'.</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   uint32_t stackArgsRegId = layout.getStackArgsRegId();</a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">       1948 :   if (stackArgsRegId != Globals::kInvalidRegId &amp;&amp; stackArgsRegId != X86Gp::kIdSp) {</span></a>
+<a name="1077"><span class="lineNum">    1077 </span>            :     saReg.setId(stackArgsRegId);</a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineNoCov">          0 :     if (!(layout.hasPreservedFP() &amp;&amp; stackArgsRegId == X86Gp::kIdBp))</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(emitter-&gt;mov(saReg, zsp));</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :   }</a>
+<a name="1081"><span class="lineNum">    1081 </span>            : </a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   // Emit: 'and zsp, StackAlignment'.</a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">       1948 :   if (layout.hasDynamicAlignment())</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(emitter-&gt;and_(zsp, -static_cast&lt;int32_t&gt;(layout.getStackAlignment())));</span></a>
+<a name="1085"><span class="lineNum">    1085 </span>            : </a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   // Emit: 'sub zsp, StackAdjustment'.</a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">       1948 :   if (layout.hasStackAdjustment())</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">        932 :     ASMJIT_PROPAGATE(emitter-&gt;sub(zsp, layout.getStackAdjustment()));</span></a>
+<a name="1089"><span class="lineNum">    1089 </span>            : </a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   // Emit: 'mov [zsp + dsaSlot], saReg'.</a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">       1948 :   if (layout.hasDynamicAlignment() &amp;&amp; layout.hasDsaSlotUsed()) {</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineNoCov">          0 :     X86Mem saMem = x86::ptr(zsp, layout._dsaSlot);</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(emitter-&gt;mov(saMem, saReg));</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   }</a>
+<a name="1095"><span class="lineNum">    1095 </span>            : </a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   // Emit 'movaps|movups [zsp + X], xmm0..15'.</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   uint32_t xmmSaved = layout.getSavedRegs(X86Reg::kKindVec);</a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">       1948 :   if (xmmSaved) {</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            :     X86Mem vecBase = x86::ptr(zsp, layout.getVecStackOffset());</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :     X86Reg vecReg = x86::xmm(0);</a>
+<a name="1101"><span class="lineNum">    1101 </span>            : </a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     uint32_t vecInst = x86GetXmmMovInst(layout);</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :     uint32_t vecSize = 16;</a>
+<a name="1104"><span class="lineNum">    1104 </span>            : </a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineNoCov">          0 :     for (uint32_t i = xmmSaved, regId = 0; i; i &gt;&gt;= 1, regId++) {</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineNoCov">          0 :       if (!(i &amp; 0x1)) continue;</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            :       vecReg.setId(regId);</a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(emitter-&gt;emit(vecInst, vecBase, vecReg));</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            :       vecBase.addOffsetLo32(static_cast&lt;int32_t&gt;(vecSize));</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :     }</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   }</a>
+<a name="1112"><span class="lineNum">    1112 </span>            : </a>
+<a name="1113"><span class="lineNum">    1113 </span>            :   return kErrorOk;</a>
+<a name="1114"><span class="lineNum">    1114 </span>            : }</a>
+<a name="1115"><span class="lineNum">    1115 </span>            : </a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">       1948 : ASMJIT_FAVOR_SIZE Error X86Internal::emitEpilog(X86Emitter* emitter, const FuncFrameLayout&amp; layout) {</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   uint32_t i;</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   uint32_t regId;</a>
+<a name="1119"><span class="lineNum">    1119 </span>            : </a>
+<a name="1120"><span class="lineNum">    1120 </span>            :   uint32_t gpSize = emitter-&gt;getGpSize();</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :   uint32_t gpSaved = layout.getSavedRegs(X86Reg::kKindGp);</a>
+<a name="1122"><span class="lineNum">    1122 </span>            : </a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   X86Gp zsp = emitter-&gt;zsp();   // ESP|RSP register.</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   X86Gp zbp = emitter-&gt;zbp();   // EBP|RBP register.</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   X86Gp gpReg = emitter-&gt;zsp(); // General purpose register (temporary).</a>
+<a name="1126"><span class="lineNum">    1126 </span>            : </a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   // Don't emit 'pop zbp' in the pop sequence, this case is handled separately.</a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">       1948 :   if (layout.hasPreservedFP()) gpSaved &amp;= ~Utils::mask(X86Gp::kIdBp);</span></a>
+<a name="1129"><span class="lineNum">    1129 </span>            : </a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   // Emit 'movaps|movups xmm0..15, [zsp + X]'.</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   uint32_t xmmSaved = layout.getSavedRegs(X86Reg::kKindVec);</a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">       1948 :   if (xmmSaved) {</span></a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     X86Mem vecBase = x86::ptr(zsp, layout.getVecStackOffset());</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     X86Reg vecReg = x86::xmm(0);</a>
+<a name="1135"><span class="lineNum">    1135 </span>            : </a>
+<a name="1136"><span class="lineNum">    1136 </span>            :     uint32_t vecInst = x86GetXmmMovInst(layout);</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :     uint32_t vecSize = 16;</a>
+<a name="1138"><span class="lineNum">    1138 </span>            : </a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineNoCov">          0 :     for (i = xmmSaved, regId = 0; i; i &gt;&gt;= 1, regId++) {</span></a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineNoCov">          0 :       if (!(i &amp; 0x1)) continue;</span></a>
+<a name="1141"><span class="lineNum">    1141 </span>            :       vecReg.setId(regId);</a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(emitter-&gt;emit(vecInst, vecReg, vecBase));</span></a>
+<a name="1143"><span class="lineNum">    1143 </span>            :       vecBase.addOffsetLo32(static_cast&lt;int32_t&gt;(vecSize));</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :     }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   }</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : </a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   // Emit 'emms' and 'vzeroupper'.</a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">       1948 :   if (layout.hasMmxCleanup()) ASMJIT_PROPAGATE(emitter-&gt;emms());</span></a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">       1948 :   if (layout.hasAvxCleanup()) ASMJIT_PROPAGATE(emitter-&gt;vzeroupper());</span></a>
+<a name="1150"><span class="lineNum">    1150 </span>            : </a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">       1948 :   if (layout.hasPreservedFP()) {</span></a>
+<a name="1152"><span class="lineNum">    1152 </span>            :     // Emit 'mov zsp, zbp' or 'lea zsp, [zbp - x]'</a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineNoCov">          0 :     int32_t count = static_cast&lt;int32_t&gt;(layout.getGpStackSize() - gpSize);</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineNoCov">          0 :     if (!count)</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(emitter-&gt;mov(zsp, zbp));</span></a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     else</a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(emitter-&gt;lea(zsp, x86::ptr(zbp, -count)));</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   }</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :   else {</a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">       1948 :     if (layout.hasDynamicAlignment() &amp;&amp; layout.hasDsaSlotUsed()) {</span></a>
+<a name="1161"><span class="lineNum">    1161 </span>            :       // Emit 'mov zsp, [zsp + DsaSlot]'.</a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineNoCov">          0 :       X86Mem saMem = x86::ptr(zsp, layout._dsaSlot);</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(emitter-&gt;mov(zsp, saMem));</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     }</a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">       1948 :     else if (layout.hasStackAdjustment()) {</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            :       // Emit 'add zsp, StackAdjustment'.</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">        932 :       ASMJIT_PROPAGATE(emitter-&gt;add(zsp, static_cast&lt;int32_t&gt;(layout.getStackAdjustment())));</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :     }</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :   }</a>
+<a name="1170"><span class="lineNum">    1170 </span>            : </a>
+<a name="1171"><span class="lineNum">    1171 </span>            :   // Emit 'pop gp' sequence.</a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineCov">       1948 :   if (gpSaved) {</span></a>
+<a name="1173"><span class="lineNum">    1173 </span>            :     i = gpSaved;</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :     regId = 16;</a>
+<a name="1175"><span class="lineNum">    1175 </span>            : </a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     do {</a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">      17216 :       regId--;</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">      17216 :       if (i &amp; 0x8000) {</span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            :         gpReg.setId(regId);</a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineCov">       1120 :         ASMJIT_PROPAGATE(emitter-&gt;pop(gpReg));</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            :       }</a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">      17216 :       i &lt;&lt;= 1;</span></a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineCov">      17216 :     } while (regId != 0);</span></a>
+<a name="1184"><span class="lineNum">    1184 </span>            :   }</a>
+<a name="1185"><span class="lineNum">    1185 </span>            : </a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   // Emit 'pop zbp'.</a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">       1948 :   if (layout.hasPreservedFP()) ASMJIT_PROPAGATE(emitter-&gt;pop(zbp));</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            : </a>
+<a name="1189"><span class="lineNum">    1189 </span>            :   // Emit 'ret' or 'ret x'.</a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineCov">       1948 :   if (layout.hasCalleeStackCleanup())</span></a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(emitter-&gt;emit(X86Inst::kIdRet, static_cast&lt;int&gt;(layout.getCalleeStackCleanup())));</span></a>
+<a name="1192"><span class="lineNum">    1192 </span>            :   else</a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(emitter-&gt;emit(X86Inst::kIdRet));</span></a>
+<a name="1194"><span class="lineNum">    1194 </span>            : </a>
+<a name="1195"><span class="lineNum">    1195 </span>            :   return kErrorOk;</a>
+<a name="1196"><span class="lineNum">    1196 </span>            : }</a>
+<a name="1197"><span class="lineNum">    1197 </span>            : </a>
+<a name="1198"><span class="lineNum">    1198 </span>            : // ============================================================================</a>
+<a name="1199"><span class="lineNum">    1199 </span>            : // [asmjit::X86Internal - AllocArgs]</a>
+<a name="1200"><span class="lineNum">    1200 </span>            : // ============================================================================</a>
+<a name="1201"><span class="lineNum">    1201 </span>            : </a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86Internal::allocArgs(X86Emitter* emitter, const FuncFrameLayout&amp; layout, const FuncArgsMapper&amp; args) {</span></a>
+<a name="1203"><span class="lineNum">    1203 </span>            :   typedef X86FuncArgsContext::SrcArg SrcArg;</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :   typedef X86FuncArgsContext::DstArg DstArg;</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :   typedef X86FuncArgsContext::WorkData WorkData;</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :   enum { kMaxVRegKinds = Globals::kMaxVRegKinds };</a>
+<a name="1207"><span class="lineNum">    1207 </span>            : </a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   uint32_t i;</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :   const FuncDetail&amp; func = *args.getFuncDetail();</a>
+<a name="1210"><span class="lineNum">    1210 </span>            : </a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineNoCov">          0 :   X86FuncArgsContext ctx;</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(ctx.initWorkData(args, layout._savedRegs, layout.hasPreservedFP()));</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            : </a>
+<a name="1214"><span class="lineNum">    1214 </span>            :   // We must honor AVX if it's enabled.</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :   bool avxEnabled = layout.isAvxEnabled();</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   // Free registers that can be used as temporaries and during shuffling.</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   // We initialize them to match all workRegs (registers that can be used</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   // by the function) except source regs, which are used to pass arguments.</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :   // Free registers are changed during shuffling - when an argument is moved</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :   // to the final register then the register itself is removed from freeRegs</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   // (it can't be altered anymore during shuffling).</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   uint32_t freeRegs[kMaxVRegKinds];</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; kMaxVRegKinds; i++)</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineNoCov">          0 :     freeRegs[i] = ctx._workData[i].workRegs &amp; ~ctx._workData[i].srcRegs;</span></a>
+<a name="1226"><span class="lineNum">    1226 </span>            : </a>
+<a name="1227"><span class="lineNum">    1227 </span>            :   // This is an iterative process that runs until there is a work to do. When</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :   // one register is moved it can create space for another move. Such moves can</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   // depend on each other so the algorithm may run multiple times before all</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   // arguments are in place. This part does only register-to-register work,</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :   // arguments moved from stack-to-register area handled later.</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   for (;;) {</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     bool hasWork = false; // Do we have a work to do?</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :     bool didWork = false; // If we did something...</a>
+<a name="1235"><span class="lineNum">    1235 </span>            : </a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     uint32_t dstRegKind = kMaxVRegKinds;</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :     do {</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineNoCov">          0 :       WorkData&amp; wd = ctx._workData[--dstRegKind];</span></a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineNoCov">          0 :       if (wd.numOps &gt; wd.numStackArgs) {</span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            :         hasWork = true;</a>
+<a name="1241"><span class="lineNum">    1241 </span>            : </a>
+<a name="1242"><span class="lineNum">    1242 </span>            :         // Iterate over all destination regs and check if we can do something.</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :         // We always go from destination to source, never the opposite.</a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineNoCov">          0 :         uint32_t regsToDo = wd.dstRegs;</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :         do {</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :           // If there is a work to do there has to be at least one dstReg.</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :           ASMJIT_ASSERT(regsToDo != 0);</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :           uint32_t dstRegId = Utils::findFirstBit(regsToDo);</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :           uint32_t dstRegMask = Utils::mask(dstRegId);</a>
+<a name="1250"><span class="lineNum">    1250 </span>            : </a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineNoCov">          0 :           uint32_t argIndex = wd.argIndex[dstRegId];</span></a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineNoCov">          0 :           const DstArg&amp; dstArg = args.getArg(argIndex);</span></a>
+<a name="1253"><span class="lineNum">    1253 </span>            :           const SrcArg&amp; srcArg = func.getArg(argIndex);</a>
+<a name="1254"><span class="lineNum">    1254 </span>            : </a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineNoCov">          0 :           if (srcArg.byReg()) {</span></a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineNoCov">          0 :             uint32_t srcRegType = srcArg.getRegType();</span></a>
+<a name="1257"><span class="lineNum">    1257 </span>            :             uint32_t srcRegKind = X86Reg::kindOf(srcRegType);</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : </a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineNoCov">          0 :             if (freeRegs[dstRegKind] &amp; dstRegMask) {</span></a>
+<a name="1260"><span class="lineNum">    1260 </span>            :               X86Reg dstReg(X86Reg::fromTypeAndId(dstArg.getRegType(), dstRegId));</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :               X86Reg srcReg(X86Reg::fromTypeAndId(srcRegType, srcArg.getRegId()));</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineNoCov">          0 :               ASMJIT_PROPAGATE(</span></a>
+<a name="1264"><span class="lineNum">    1264 </span>            :                 emitArgMove(emitter,</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :                   dstReg, dstArg.getTypeId(),</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :                   srcReg, srcArg.getTypeId(), avxEnabled));</a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineNoCov">          0 :               freeRegs[dstRegKind] ^= dstRegMask;                     // Make the DST reg occupied.</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineNoCov">          0 :               freeRegs[srcRegKind] |= Utils::mask(srcArg.getRegId()); // Make the SRC reg free.</span></a>
+<a name="1269"><span class="lineNum">    1269 </span>            : </a>
+<a name="1270"><span class="lineNum">    1270 </span>            :               ASMJIT_ASSERT(wd.numOps &gt;= 1);</a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineNoCov">          0 :               wd.numOps--;</span></a>
+<a name="1272"><span class="lineNum">    1272 </span>            :               didWork = true;</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :             }</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :             else {</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :               // Check if this is a swap operation.</a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineNoCov">          0 :               if (dstRegKind == srcRegKind) {</span></a>
+<a name="1277"><span class="lineNum">    1277 </span>            :                 uint32_t srcRegId = srcArg.getRegId();</a>
+<a name="1278"><span class="lineNum">    1278 </span>            : </a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineNoCov">          0 :                 uint32_t otherIndex = wd.argIndex[srcRegId];</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineNoCov">          0 :                 const DstArg&amp; otherArg = args.getArg(otherIndex);</span></a>
+<a name="1281"><span class="lineNum">    1281 </span>            : </a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineNoCov">          0 :                 if (otherArg.getRegId() == srcRegId &amp;&amp; X86Reg::kindOf(otherArg.getRegType()) == dstRegKind) {</span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            :                   // If this is GP reg it can be handled by 'xchg'.</a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineNoCov">          0 :                   if (dstRegKind == X86Reg::kKindGp) {</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineNoCov">          0 :                     uint32_t highestType = std::max(dstArg.getRegType(), srcRegType);</span></a>
+<a name="1286"><span class="lineNum">    1286 </span>            : </a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineNoCov">          0 :                     X86Reg dstReg = x86::gpd(dstRegId);</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineNoCov">          0 :                     X86Reg srcReg = x86::gpd(srcRegId);</span></a>
+<a name="1289"><span class="lineNum">    1289 </span>            : </a>
+<a name="1290"><span class="lineNum">    1290 </span><span class="lineNoCov">          0 :                     if (highestType == X86Reg::kRegGpq) {</span></a>
+<a name="1291"><span class="lineNum">    1291 </span>            :                       dstReg.setSignature(X86RegTraits&lt;X86Reg::kRegGpq&gt;::kSignature);</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :                       srcReg.setSignature(X86RegTraits&lt;X86Reg::kRegGpq&gt;::kSignature);</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :                     }</a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineNoCov">          0 :                     ASMJIT_PROPAGATE(emitter-&gt;emit(X86Inst::kIdXchg, dstReg, srcReg));</span></a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineNoCov">          0 :                     regsToDo &amp;= ~Utils::mask(srcRegId);</span></a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineNoCov">          0 :                     freeRegs[dstRegKind] &amp;= ~(Utils::mask(srcRegId) | dstRegMask);</span></a>
+<a name="1297"><span class="lineNum">    1297 </span>            : </a>
+<a name="1298"><span class="lineNum">    1298 </span>            :                     ASMJIT_ASSERT(wd.numOps &gt;= 2);</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :                     ASMJIT_ASSERT(wd.numSwaps &gt;= 1);</a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineNoCov">          0 :                     wd.numOps-=2;</span></a>
+<a name="1301"><span class="lineNum">    1301 </span><span class="lineNoCov">          0 :                     wd.numSwaps--;</span></a>
+<a name="1302"><span class="lineNum">    1302 </span>            :                     didWork = true;</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :                   }</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :                 }</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :               }</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :             }</a>
+<a name="1307"><span class="lineNum">    1307 </span>            :           }</a>
+<a name="1308"><span class="lineNum">    1308 </span>            : </a>
+<a name="1309"><span class="lineNum">    1309 </span>            :           // Clear the reg in `regsToDo` and continue if there are more.</a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineNoCov">          0 :           regsToDo ^= dstRegMask;</span></a>
+<a name="1311"><span class="lineNum">    1311 </span><span class="lineNoCov">          0 :         } while (regsToDo);</span></a>
+<a name="1312"><span class="lineNum">    1312 </span>            :       }</a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineNoCov">          0 :     } while (dstRegKind);</span></a>
+<a name="1314"><span class="lineNum">    1314 </span>            : </a>
+<a name="1315"><span class="lineNum">    1315 </span><span class="lineNoCov">          0 :     if (!hasWork)</span></a>
+<a name="1316"><span class="lineNum">    1316 </span>            :       break;</a>
+<a name="1317"><span class="lineNum">    1317 </span>            : </a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineNoCov">          0 :     if (!didWork)</span></a>
+<a name="1319"><span class="lineNum">    1319 </span>            :       return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :   }</a>
+<a name="1321"><span class="lineNum">    1321 </span>            : </a>
+<a name="1322"><span class="lineNum">    1322 </span>            :   // Load arguments passed by stack into registers. This is pretty simple and</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :   // it never requires multiple iterations like the previous phase.</a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineNoCov">          0 :   if (ctx._hasStackArgs) {</span></a>
+<a name="1325"><span class="lineNum">    1325 </span>            :     // Base address of all arguments passed by stack.</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :     X86Mem saBase = x86::ptr(emitter-&gt;gpz(layout.getStackArgsRegId()), layout.getStackArgsOffset());</a>
+<a name="1327"><span class="lineNum">    1327 </span>            : </a>
+<a name="1328"><span class="lineNum">    1328 </span>            :     uint32_t dstRegKind = kMaxVRegKinds;</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :     do {</a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineNoCov">          0 :       WorkData&amp; wd = ctx._workData[--dstRegKind];</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineNoCov">          0 :       if (wd.numStackArgs) {</span></a>
+<a name="1332"><span class="lineNum">    1332 </span>            :         // Iterate over all destination regs and check if we can do something.</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :         // We always go from destination to source, never the opposite.</a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineNoCov">          0 :         uint32_t regsToDo = wd.dstRegs;</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            :         do {</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :           // If there is a work to do there has to be at least one dstReg.</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :           ASMJIT_ASSERT(regsToDo != 0);</a>
+<a name="1338"><span class="lineNum">    1338 </span>            :           ASMJIT_ASSERT(wd.numOps &gt; 0);</a>
+<a name="1339"><span class="lineNum">    1339 </span>            : </a>
+<a name="1340"><span class="lineNum">    1340 </span>            :           uint32_t dstRegId = Utils::findFirstBit(regsToDo);</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :           uint32_t dstRegMask = Utils::mask(dstRegId);</a>
+<a name="1342"><span class="lineNum">    1342 </span>            : </a>
+<a name="1343"><span class="lineNum">    1343 </span><span class="lineNoCov">          0 :           uint32_t argIndex = wd.argIndex[dstRegId];</span></a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineNoCov">          0 :           const DstArg&amp; dstArg = args.getArg(argIndex);</span></a>
+<a name="1345"><span class="lineNum">    1345 </span>            :           const SrcArg&amp; srcArg = func.getArg(argIndex);</a>
+<a name="1346"><span class="lineNum">    1346 </span>            : </a>
+<a name="1347"><span class="lineNum">    1347 </span>            :           // Only arguments passed by stack should remain, also the destination</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :           // registers must be free now (otherwise the first part of the algorithm</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :           // failed). Ideally this should be assert, but it's much safer to enforce</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :           // this in release as well.</a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineNoCov">          0 :           if (!srcArg.byStack() || !(freeRegs[dstRegKind] &amp; dstRegMask))</span></a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineNoCov">          0 :             return DebugUtils::errored(kErrorInvalidState);</span></a>
+<a name="1353"><span class="lineNum">    1353 </span>            : </a>
+<a name="1354"><span class="lineNum">    1354 </span>            :           X86Reg dstReg = X86Reg::fromTypeAndId(dstArg.getRegType(), dstRegId);</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :           X86Mem srcMem = saBase.adjusted(srcArg.getStackOffset());</a>
+<a name="1356"><span class="lineNum">    1356 </span>            : </a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineNoCov">          0 :           ASMJIT_PROPAGATE(</span></a>
+<a name="1358"><span class="lineNum">    1358 </span>            :             emitArgMove(emitter,</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :               dstReg, dstArg.getTypeId(),</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :               srcMem, srcArg.getTypeId(), avxEnabled));</a>
+<a name="1361"><span class="lineNum">    1361 </span>            : </a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineNoCov">          0 :           freeRegs[dstRegKind] ^= dstRegMask;</span></a>
+<a name="1363"><span class="lineNum">    1363 </span><span class="lineNoCov">          0 :           regsToDo ^= dstRegMask;</span></a>
+<a name="1364"><span class="lineNum">    1364 </span><span class="lineNoCov">          0 :           wd.numOps--;</span></a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineNoCov">          0 :         } while (regsToDo);</span></a>
+<a name="1366"><span class="lineNum">    1366 </span>            :       }</a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineNoCov">          0 :     } while (dstRegKind);</span></a>
+<a name="1368"><span class="lineNum">    1368 </span>            :   }</a>
+<a name="1369"><span class="lineNum">    1369 </span>            : </a>
+<a name="1370"><span class="lineNum">    1370 </span>            :   return kErrorOk;</a>
+<a name="1371"><span class="lineNum">    1371 </span>            : }</a>
+<a name="1372"><span class="lineNum">    1372 </span>            : </a>
+<a name="1373"><span class="lineNum">    1373 </span>            : } // asmjit namespace</a>
+<a name="1374"><span class="lineNum">    1374 </span>            : } // namespace PLMD</a>
+<a name="1375"><span class="lineNum">    1375 </span>            : </a>
+<a name="1376"><span class="lineNum">    1376 </span>            : // [Api-End]</a>
+<a name="1377"><span class="lineNum">    1377 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="1378"><span class="lineNum">    1378 </span>            : </a>
+<a name="1379"><span class="lineNum">    1379 </span>            : // [Guard]</a>
+<a name="1380"><span class="lineNum">    1380 </span>            : #endif // ASMJIT_BUILD_X86</a>
+<a name="1381"><span class="lineNum">    1381 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1382"><span class="lineNum">    1382 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86logging.cpp.func-sort-c.html b/coverage-libs/asmjit/x86logging.cpp.func-sort-c.html
new file mode 100644
index 0000000000..335144c05c
--- /dev/null
+++ b/coverage-libs/asmjit/x86logging.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86logging.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86logging.cpp<span style="font-size: 80%;"> (<a href="x86logging.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">203</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86logging.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#158">_ZN4PLMD6asmjit10X86Logging13formatOperandERNS0_13StringBuilderEjPKNS0_11CodeEmitterEjRKNS0_8Operand_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#549">_ZN4PLMD6asmjit10X86Logging14formatRegisterERNS0_13StringBuilderEjPKNS0_11CodeEmitterEjjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#599">_ZN4PLMD6asmjit10X86Logging17formatInstructionERNS0_13StringBuilderEjPKNS0_11CodeEmitterEjRKNS0_4Inst6DetailEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#139">_ZN4PLMD6asmjitL23x86GetAddressSizeStringEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#267">_ZN4PLMD6asmjitL24X86Logging_formatImmBitsERNS0_13StringBuilderEjPKNS0_7ImmBitsEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#253">_ZN4PLMD6asmjitL24X86Logging_formatImmShufERNS0_13StringBuilderEjjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#301">_ZN4PLMD6asmjitL24X86Logging_formatImmTextERNS0_13StringBuilderEjjjPKcj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#317">_ZN4PLMD6asmjitL28X86Logging_formatImmExtendedERNS0_13StringBuilderEjjjRKNS0_3ImmE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86logging.cpp.func.html b/coverage-libs/asmjit/x86logging.cpp.func.html
new file mode 100644
index 0000000000..53659eb27d
--- /dev/null
+++ b/coverage-libs/asmjit/x86logging.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86logging.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86logging.cpp<span style="font-size: 80%;"> (<a href="x86logging.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">203</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86logging.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#158">_ZN4PLMD6asmjit10X86Logging13formatOperandERNS0_13StringBuilderEjPKNS0_11CodeEmitterEjRKNS0_8Operand_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#549">_ZN4PLMD6asmjit10X86Logging14formatRegisterERNS0_13StringBuilderEjPKNS0_11CodeEmitterEjjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#599">_ZN4PLMD6asmjit10X86Logging17formatInstructionERNS0_13StringBuilderEjPKNS0_11CodeEmitterEjRKNS0_4Inst6DetailEPKNS0_8Operand_Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#139">_ZN4PLMD6asmjitL23x86GetAddressSizeStringEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#267">_ZN4PLMD6asmjitL24X86Logging_formatImmBitsERNS0_13StringBuilderEjPKNS0_7ImmBitsEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#253">_ZN4PLMD6asmjitL24X86Logging_formatImmShufERNS0_13StringBuilderEjjj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#301">_ZN4PLMD6asmjitL24X86Logging_formatImmTextERNS0_13StringBuilderEjjjPKcj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86logging.cpp.gcov.html#317">_ZN4PLMD6asmjitL28X86Logging_formatImmExtendedERNS0_13StringBuilderEjjjRKNS0_3ImmE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86logging.cpp.gcov.html b/coverage-libs/asmjit/x86logging.cpp.gcov.html
new file mode 100644
index 0000000000..d3a99d0b9b
--- /dev/null
+++ b/coverage-libs/asmjit/x86logging.cpp.gcov.html
@@ -0,0 +1,786 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86logging.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86logging.cpp<span style="font-size: 80%;"> (source / <a href="x86logging.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">203</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./misc_p.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./x86inst.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./x86logging_p.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./codecompiler.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : // [Api-Begin]</a>
+<a name="47"><span class="lineNum">      47 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : namespace PLMD {</a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace asmjit {</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : // [asmjit::X86Logging - Constants]</a>
+<a name="54"><span class="lineNum">      54 </span>            : // ============================================================================</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : struct X86RegFormatInfo {</a>
+<a name="57"><span class="lineNum">      57 </span>            :   uint8_t count;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   uint8_t formatIndex;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   uint8_t specialIndex;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   uint8_t specialCount;</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : static const char x86RegFormatStrings[] =</a>
+<a name="64"><span class="lineNum">      64 </span>            :   &quot;r%ub&quot;  &quot;\0&quot; // #0</a>
+<a name="65"><span class="lineNum">      65 </span>            :   &quot;r%uh&quot;  &quot;\0&quot; // #5</a>
+<a name="66"><span class="lineNum">      66 </span>            :   &quot;r%uw&quot;  &quot;\0&quot; // #10</a>
+<a name="67"><span class="lineNum">      67 </span>            :   &quot;r%ud&quot;  &quot;\0&quot; // #15</a>
+<a name="68"><span class="lineNum">      68 </span>            :   &quot;r%u&quot;   &quot;\0&quot; // #20</a>
+<a name="69"><span class="lineNum">      69 </span>            :   &quot;xmm%u&quot; &quot;\0&quot; // #24</a>
+<a name="70"><span class="lineNum">      70 </span>            :   &quot;ymm%u&quot; &quot;\0&quot; // #30</a>
+<a name="71"><span class="lineNum">      71 </span>            :   &quot;zmm%u&quot; &quot;\0&quot; // #36</a>
+<a name="72"><span class="lineNum">      72 </span>            :   &quot;rip%u&quot; &quot;\0&quot; // #42</a>
+<a name="73"><span class="lineNum">      73 </span>            :   &quot;seg%u&quot; &quot;\0&quot; // #48</a>
+<a name="74"><span class="lineNum">      74 </span>            :   &quot;fp%u&quot;  &quot;\0&quot; // #54</a>
+<a name="75"><span class="lineNum">      75 </span>            :   &quot;mm%u&quot;  &quot;\0&quot; // #59</a>
+<a name="76"><span class="lineNum">      76 </span>            :   &quot;k%u&quot;   &quot;\0&quot; // #64</a>
+<a name="77"><span class="lineNum">      77 </span>            :   &quot;bnd%u&quot; &quot;\0&quot; // #68</a>
+<a name="78"><span class="lineNum">      78 </span>            :   &quot;cr%u&quot;  &quot;\0&quot; // #74</a>
+<a name="79"><span class="lineNum">      79 </span>            :   &quot;dr%u&quot;  &quot;\0&quot; // #79</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   &quot;rip\0&quot;      // #84</a>
+<a name="82"><span class="lineNum">      82 </span>            :   &quot;\0\0\0\0&quot;   // #88</a>
+<a name="83"><span class="lineNum">      83 </span>            :   &quot;\0\0\0\0&quot;   // #92</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   &quot;al\0\0&quot; &quot;cl\0\0&quot; &quot;dl\0\0&quot; &quot;bl\0\0&quot; &quot;spl\0&quot;  &quot;bpl\0&quot;  &quot;sil\0&quot;  &quot;dil\0&quot;  // #96</a>
+<a name="86"><span class="lineNum">      86 </span>            :   &quot;ah\0\0&quot; &quot;ch\0\0&quot; &quot;dh\0\0&quot; &quot;bh\0\0&quot; &quot;n/a\0&quot;  &quot;n/a\0&quot;  &quot;n/a\0&quot;  &quot;n/a\0&quot;  // #128</a>
+<a name="87"><span class="lineNum">      87 </span>            :   &quot;eax\0&quot;  &quot;ecx\0&quot;  &quot;edx\0&quot;  &quot;ebx\0&quot;  &quot;esp\0&quot;  &quot;ebp\0&quot;  &quot;esi\0&quot;  &quot;edi\0&quot;  // #160</a>
+<a name="88"><span class="lineNum">      88 </span>            :   &quot;rax\0&quot;  &quot;rcx\0&quot;  &quot;rdx\0&quot;  &quot;rbx\0&quot;  &quot;rsp\0&quot;  &quot;rbp\0&quot;  &quot;rsi\0&quot;  &quot;rdi\0&quot;  // #192</a>
+<a name="89"><span class="lineNum">      89 </span>            :   &quot;n/a\0&quot;  &quot;es\0\0&quot; &quot;cs\0\0&quot; &quot;ss\0\0&quot; &quot;ds\0\0&quot; &quot;fs\0\0&quot; &quot;gs\0\0&quot; &quot;n/a\0&quot;; // #224</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : template&lt;uint32_t X&gt;</a>
+<a name="92"><span class="lineNum">      92 </span>            : struct X86RegFormatInfo_T {</a>
+<a name="93"><span class="lineNum">      93 </span>            :   enum {</a>
+<a name="94"><span class="lineNum">      94 </span>            :     kFormatIndex  = X == X86Reg::kRegGpbLo ? 0   :</a>
+<a name="95"><span class="lineNum">      95 </span>            :                     X == X86Reg::kRegGpbHi ? 5   :</a>
+<a name="96"><span class="lineNum">      96 </span>            :                     X == X86Reg::kRegGpw   ? 10  :</a>
+<a name="97"><span class="lineNum">      97 </span>            :                     X == X86Reg::kRegGpd   ? 15  :</a>
+<a name="98"><span class="lineNum">      98 </span>            :                     X == X86Reg::kRegGpq   ? 20  :</a>
+<a name="99"><span class="lineNum">      99 </span>            :                     X == X86Reg::kRegXmm   ? 24  :</a>
+<a name="100"><span class="lineNum">     100 </span>            :                     X == X86Reg::kRegYmm   ? 30  :</a>
+<a name="101"><span class="lineNum">     101 </span>            :                     X == X86Reg::kRegZmm   ? 36  :</a>
+<a name="102"><span class="lineNum">     102 </span>            :                     X == X86Reg::kRegRip   ? 42  :</a>
+<a name="103"><span class="lineNum">     103 </span>            :                     X == X86Reg::kRegSeg   ? 48  :</a>
+<a name="104"><span class="lineNum">     104 </span>            :                     X == X86Reg::kRegFp    ? 54  :</a>
+<a name="105"><span class="lineNum">     105 </span>            :                     X == X86Reg::kRegMm    ? 59  :</a>
+<a name="106"><span class="lineNum">     106 </span>            :                     X == X86Reg::kRegK     ? 64  :</a>
+<a name="107"><span class="lineNum">     107 </span>            :                     X == X86Reg::kRegBnd   ? 68  :</a>
+<a name="108"><span class="lineNum">     108 </span>            :                     X == X86Reg::kRegCr    ? 74  :</a>
+<a name="109"><span class="lineNum">     109 </span>            :                     X == X86Reg::kRegDr    ? 79  : 0,</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :     kSpecialIndex = X == X86Reg::kRegGpbLo ? 96  :</a>
+<a name="112"><span class="lineNum">     112 </span>            :                     X == X86Reg::kRegGpbHi ? 128 :</a>
+<a name="113"><span class="lineNum">     113 </span>            :                     X == X86Reg::kRegGpw   ? 161 :</a>
+<a name="114"><span class="lineNum">     114 </span>            :                     X == X86Reg::kRegGpd   ? 160 :</a>
+<a name="115"><span class="lineNum">     115 </span>            :                     X == X86Reg::kRegGpq   ? 192 :</a>
+<a name="116"><span class="lineNum">     116 </span>            :                     X == X86Reg::kRegRip   ? 84  :</a>
+<a name="117"><span class="lineNum">     117 </span>            :                     X == X86Reg::kRegSeg   ? 224 : 0,</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :     kSpecialCount = X == X86Reg::kRegGpbLo ? 8   :</a>
+<a name="120"><span class="lineNum">     120 </span>            :                     X == X86Reg::kRegGpbHi ? 4   :</a>
+<a name="121"><span class="lineNum">     121 </span>            :                     X == X86Reg::kRegGpw   ? 8   :</a>
+<a name="122"><span class="lineNum">     122 </span>            :                     X == X86Reg::kRegGpd   ? 8   :</a>
+<a name="123"><span class="lineNum">     123 </span>            :                     X == X86Reg::kRegGpq   ? 8   :</a>
+<a name="124"><span class="lineNum">     124 </span>            :                     X == X86Reg::kRegRip   ? 1   :</a>
+<a name="125"><span class="lineNum">     125 </span>            :                     X == X86Reg::kRegSeg   ? 7   : 0</a>
+<a name="126"><span class="lineNum">     126 </span>            :   };</a>
+<a name="127"><span class="lineNum">     127 </span>            : };</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : #define ASMJIT_X86_REG_FORMAT(TYPE) {      \</a>
+<a name="130"><span class="lineNum">     130 </span>            :   X86RegTraits&lt;TYPE&gt;::kCount,              \</a>
+<a name="131"><span class="lineNum">     131 </span>            :   X86RegFormatInfo_T&lt;TYPE&gt;::kFormatIndex,  \</a>
+<a name="132"><span class="lineNum">     132 </span>            :   X86RegFormatInfo_T&lt;TYPE&gt;::kSpecialIndex, \</a>
+<a name="133"><span class="lineNum">     133 </span>            :   X86RegFormatInfo_T&lt;TYPE&gt;::kSpecialCount  \</a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : static const X86RegFormatInfo x86RegFormatInfo[] = {</a>
+<a name="137"><span class="lineNum">     137 </span>            :   ASMJIT_TABLE_16(ASMJIT_X86_REG_FORMAT, 0 ),</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ASMJIT_TABLE_16(ASMJIT_X86_REG_FORMAT, 16)</a>
+<a name="139"><span class="lineNum">     139 </span>            : };</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : static const char* x86GetAddressSizeString(uint32_t size) noexcept {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   switch (size) {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     case 1 : return &quot;byte &quot;;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :     case 2 : return &quot;word &quot;;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     case 4 : return &quot;dword &quot;;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     case 6 : return &quot;fword &quot;;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     case 8 : return &quot;qword &quot;;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :     case 10: return &quot;tword &quot;;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     case 16: return &quot;oword &quot;;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :     case 32: return &quot;yword &quot;;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     case 64: return &quot;zword &quot;;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     default: return &quot;&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : // ============================================================================</a>
+<a name="157"><span class="lineNum">     157 </span>            : // [asmjit::X86Logging - Format Operand]</a>
+<a name="158"><span class="lineNum">     158 </span>            : // ============================================================================</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86Logging::formatOperand(</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   StringBuilder&amp; sb,</a>
+<a name="162"><span class="lineNum">     162 </span>            :   uint32_t logOptions,</a>
+<a name="163"><span class="lineNum">     163 </span>            :   const CodeEmitter* emitter,</a>
+<a name="164"><span class="lineNum">     164 </span>            :   uint32_t archType,</a>
+<a name="165"><span class="lineNum">     165 </span>            :   const Operand_&amp; op) noexcept {</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :   if (op.isReg())</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     return formatRegister(sb, logOptions, emitter, archType, op.as&lt;Reg&gt;().getType(), op.as&lt;Reg&gt;().getId());</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :   if (op.isMem()) {</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     const X86Mem&amp; m = op.as&lt;X86Mem&gt;();</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendString(x86GetAddressSizeString(m.getSize())));</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :     // Segment override prefix.</a>
+<a name="175"><span class="lineNum">     175 </span>            :     uint32_t seg = m.getSegmentId();</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     if (seg != X86Seg::kIdNone &amp;&amp; seg &lt; X86Seg::kIdCount)</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendFormat(&quot;%s:&quot;, x86RegFormatStrings + 224 + seg * 4));</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendChar('['));</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :     if (m.isAbs())</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot;abs &quot;));</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     if (m.hasBase()) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :       if (m.hasBaseLabel()) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(Logging::formatLabel(sb, logOptions, emitter, m.getBaseId()));</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :       }</a>
+<a name="187"><span class="lineNum">     187 </span>            :       else {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :         if (m.isArgHome()) ASMJIT_PROPAGATE(sb.appendString(&quot;$&quot;));</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :         if (m.isRegHome()) ASMJIT_PROPAGATE(sb.appendString(&quot;&amp;&quot;));</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(formatRegister(sb, logOptions, emitter, archType, m.getBaseType(), m.getBaseId()));</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       }</a>
+<a name="192"><span class="lineNum">     192 </span>            :     }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     if (m.hasIndex()) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendChar('+'));</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(formatRegister(sb, logOptions, emitter, archType, m.getIndexType(), m.getIndexId()));</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :       if (m.hasShift())</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendFormat(&quot;*%u&quot;, 1 &lt;&lt; m.getShift()));</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     uint64_t off = static_cast&lt;uint64_t&gt;(m.getOffset());</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     if (off) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       uint32_t base = 10;</a>
+<a name="204"><span class="lineNum">     204 </span>            :       char prefix = '+';</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       if (static_cast&lt;int64_t&gt;(off) &lt; 0) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :         off = ~off + 1;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :         prefix = '-';</a>
+<a name="209"><span class="lineNum">     209 </span>            :       }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendChar(prefix));</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       if ((logOptions &amp; Logger::kOptionHexDisplacement) != 0 &amp;&amp; off &gt; 9) {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(&quot;0x&quot;, 2));</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :         base = 16;</a>
+<a name="215"><span class="lineNum">     215 </span>            :       }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendUInt(off, base));</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :     return sb.appendChar(']');</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :   if (op.isImm()) {</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :     const Imm&amp; i = op.as&lt;Imm&gt;();</a>
+<a name="224"><span class="lineNum">     224 </span>            :     int64_t val = i.getInt64();</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     if ((logOptions &amp; Logger::kOptionHexImmediate) != 0 &amp;&amp; static_cast&lt;uint64_t&gt;(val) &gt; 9)</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       return sb.appendUInt(static_cast&lt;uint64_t&gt;(val), 16);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     else</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       return sb.appendInt(val, 10);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :   if (op.isLabel()) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :     return Logging::formatLabel(sb, logOptions, emitter, op.getId());</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   return sb.appendString(&quot;&lt;None&gt;&quot;);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : // ============================================================================</a>
+<a name="240"><span class="lineNum">     240 </span>            : // [asmjit::X86Logging - Format Immediate (Extension)]</a>
+<a name="241"><span class="lineNum">     241 </span>            : // ============================================================================</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : struct ImmBits {</a>
+<a name="244"><span class="lineNum">     244 </span>            :   enum Mode {</a>
+<a name="245"><span class="lineNum">     245 </span>            :     kModeLookup = 0x0,</a>
+<a name="246"><span class="lineNum">     246 </span>            :     kModeFormat = 0x1</a>
+<a name="247"><span class="lineNum">     247 </span>            :   };</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   uint8_t mask;</a>
+<a name="250"><span class="lineNum">     250 </span>            :   uint8_t shift;</a>
+<a name="251"><span class="lineNum">     251 </span>            :   uint8_t mode;</a>
+<a name="252"><span class="lineNum">     252 </span>            :   char text[45];</a>
+<a name="253"><span class="lineNum">     253 </span>            : };</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE static Error X86Logging_formatImmShuf(StringBuilder&amp; sb, uint32_t u8, uint32_t bits, uint32_t count) noexcept {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(sb.appendChar('&lt;'));</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   uint32_t mask = (1 &lt;&lt; bits) - 1;</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++, u8 &gt;&gt;= bits) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :     uint32_t value = u8 &amp; mask;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :     if (i != 0)</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendChar('|'));</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendUInt(value));</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :   return sb.appendChar('&gt;');</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE static Error X86Logging_formatImmBits(StringBuilder&amp; sb, uint32_t u8, const ImmBits* bits, uint32_t count) noexcept {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   uint32_t n = 0;</a>
+<a name="271"><span class="lineNum">     271 </span>            :   char buf[64];</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :     const ImmBits&amp; spec = bits[i];</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     uint32_t value = (u8 &amp; static_cast&lt;uint32_t&gt;(spec.mask)) &gt;&gt; spec.shift;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :     const char* str = nullptr;</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :     switch (spec.mode) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :       case ImmBits::kModeLookup:</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :         str = Utils::findPackedString(spec.text, value);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :         break;</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :       case ImmBits::kModeFormat:</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :         snprintf(buf, sizeof(buf), spec.text, static_cast&lt;unsigned int&gt;(value));</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :         str = buf;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :       default:</a>
+<a name="290"><span class="lineNum">     290 </span>            :         return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="291"><span class="lineNum">     291 </span>            :     }</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :     if (!str[0])</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendChar(++n == 1 ? '&lt;' : '|'));</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendString(str));</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :   }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   return n ? sb.appendChar('&gt;') : static_cast&lt;Error&gt;(kErrorOk);</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE static Error X86Logging_formatImmText(StringBuilder&amp; sb, uint32_t u8, uint32_t bits, uint32_t advance, const char* text, uint32_t count = 1) noexcept {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(sb.appendChar('&lt;'));</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 :   uint32_t mask = (1 &lt;&lt; bits) - 1;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   uint32_t pos = 0;</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++, u8 &gt;&gt;= bits, pos += advance) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :     uint32_t value = (u8 &amp; mask) + pos;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :     if (i != 0)</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendChar('|'));</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendString(Utils::findPackedString(text, value)));</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :   }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :   return sb.appendChar('&gt;');</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : }</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE static Error X86Logging_formatImmExtended(</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   StringBuilder&amp; sb,</a>
+<a name="321"><span class="lineNum">     321 </span>            :   uint32_t logOptions,</a>
+<a name="322"><span class="lineNum">     322 </span>            :   uint32_t instId,</a>
+<a name="323"><span class="lineNum">     323 </span>            :   uint32_t vecSize,</a>
+<a name="324"><span class="lineNum">     324 </span>            :   const Imm&amp; imm) noexcept {</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   static const char vcmpx[] =</a>
+<a name="327"><span class="lineNum">     327 </span>            :     &quot;eq_oq\0&quot; &quot;lt_os\0&quot;  &quot;le_os\0&quot;  &quot;unord_q\0&quot;  &quot;neq_uq\0&quot; &quot;nlt_us\0&quot; &quot;nle_us\0&quot; &quot;ord_q\0&quot;</a>
+<a name="328"><span class="lineNum">     328 </span>            :     &quot;eq_uq\0&quot; &quot;nge_us\0&quot; &quot;ngt_us\0&quot; &quot;false_oq\0&quot; &quot;neq_oq\0&quot; &quot;ge_os\0&quot;  &quot;gt_os\0&quot;  &quot;true_uq\0&quot;</a>
+<a name="329"><span class="lineNum">     329 </span>            :     &quot;eq_os\0&quot; &quot;lt_oq\0&quot;  &quot;le_oq\0&quot;  &quot;unord_s\0&quot;  &quot;neq_us\0&quot; &quot;nlt_uq\0&quot; &quot;nle_uq\0&quot; &quot;ord_s\0&quot;</a>
+<a name="330"><span class="lineNum">     330 </span>            :     &quot;eq_us\0&quot; &quot;nge_uq\0&quot; &quot;ngt_uq\0&quot; &quot;false_os\0&quot; &quot;neq_os\0&quot; &quot;ge_oq\0&quot;  &quot;gt_oq\0&quot;  &quot;true_us\0&quot;;</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            :   // Try to find 7 differences...</a>
+<a name="333"><span class="lineNum">     333 </span>            :   static const char vpcmpx[] = &quot;eq\0&quot; &quot;lt\0&quot; &quot;le\0&quot; &quot;false\0&quot; &quot;neq\0&quot; &quot;ge\0&quot;  &quot;gt\0&quot;    &quot;true\0&quot;;</a>
+<a name="334"><span class="lineNum">     334 </span>            :   static const char vpcomx[] = &quot;lt\0&quot; &quot;le\0&quot; &quot;gt\0&quot; &quot;ge\0&quot;    &quot;eq\0&quot;  &quot;neq\0&quot; &quot;false\0&quot; &quot;true\0&quot;;</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :   static const char vshufpd[] = &quot;a0\0a1\0b0\0b1\0a2\0a3\0b2\0b3\0a4\0a5\0b4\0b5\0a6\0a7\0b6\0b7\0&quot;;</a>
+<a name="337"><span class="lineNum">     337 </span>            :   static const char vshufps[] = &quot;a0\0a1\0a2\0a3\0a0\0a1\0a2\0a3\0b0\0b1\0b2\0b3\0b0\0b1\0b2\0b3\0&quot;;</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            :   static const ImmBits vfpclassxx[] = {</a>
+<a name="340"><span class="lineNum">     340 </span>            :     { 0x07, 0, ImmBits::kModeLookup, &quot;qnan\0&quot; &quot;+0\0&quot; &quot;-0\0&quot; &quot;+inf\0&quot; &quot;-inf\0&quot; &quot;denormal\0&quot; &quot;-finite\0&quot; &quot;snan\0&quot; }</a>
+<a name="341"><span class="lineNum">     341 </span>            :   };</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :   static const ImmBits vgetmantxx[] = {</a>
+<a name="344"><span class="lineNum">     344 </span>            :     { 0x03, 0, ImmBits::kModeLookup, &quot;[1, 2)\0&quot; &quot;[1/2, 2)\0&quot; &quot;1/2, 1)\0&quot; &quot;[3/4, 3/2)\0&quot; },</a>
+<a name="345"><span class="lineNum">     345 </span>            :     { 0x04, 2, ImmBits::kModeLookup, &quot;\0&quot; &quot;no-sign\0&quot; },</a>
+<a name="346"><span class="lineNum">     346 </span>            :     { 0x08, 3, ImmBits::kModeLookup, &quot;\0&quot; &quot;qnan-if-sign\0&quot; }</a>
+<a name="347"><span class="lineNum">     347 </span>            :   };</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   static const ImmBits vmpsadbw[] = {</a>
+<a name="350"><span class="lineNum">     350 </span>            :     { 0x04, 2, ImmBits::kModeLookup, &quot;blk1[0]\0&quot; &quot;blk1[1]\0&quot; },</a>
+<a name="351"><span class="lineNum">     351 </span>            :     { 0x03, 0, ImmBits::kModeLookup, &quot;blk2[0]\0&quot; &quot;blk2[1]\0&quot; &quot;blk2[2]\0&quot; &quot;blk2[3]\0&quot; },</a>
+<a name="352"><span class="lineNum">     352 </span>            :     { 0x40, 6, ImmBits::kModeLookup, &quot;blk1[4]\0&quot; &quot;blk1[5]\0&quot; },</a>
+<a name="353"><span class="lineNum">     353 </span>            :     { 0x30, 4, ImmBits::kModeLookup, &quot;blk2[4]\0&quot; &quot;blk2[5]\0&quot; &quot;blk2[6]\0&quot; &quot;blk2[7]\0&quot; }</a>
+<a name="354"><span class="lineNum">     354 </span>            :   };</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            :   static const ImmBits vpclmulqdq[] = {</a>
+<a name="357"><span class="lineNum">     357 </span>            :     { 0x01, 0, ImmBits::kModeLookup, &quot;lq\0&quot; &quot;hq\0&quot; },</a>
+<a name="358"><span class="lineNum">     358 </span>            :     { 0x10, 4, ImmBits::kModeLookup, &quot;lq\0&quot; &quot;hq\0&quot; }</a>
+<a name="359"><span class="lineNum">     359 </span>            :   };</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            :   static const ImmBits vperm2x128[] = {</a>
+<a name="362"><span class="lineNum">     362 </span>            :     { 0x0B, 0, ImmBits::kModeLookup, &quot;a0\0&quot; &quot;a1\0&quot; &quot;b0\0&quot; &quot;b1\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;0\0&quot; &quot;0\0&quot; &quot;0\0&quot; &quot;0\0&quot; },</a>
+<a name="363"><span class="lineNum">     363 </span>            :     { 0xB0, 4, ImmBits::kModeLookup, &quot;a0\0&quot; &quot;a1\0&quot; &quot;b0\0&quot; &quot;b1\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;0\0&quot; &quot;0\0&quot; &quot;0\0&quot; &quot;0\0&quot; }</a>
+<a name="364"><span class="lineNum">     364 </span>            :   };</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            :   static const ImmBits vrangexx[] = {</a>
+<a name="367"><span class="lineNum">     367 </span>            :     { 0x03, 0, ImmBits::kModeLookup, &quot;min\0&quot; &quot;max\0&quot; &quot;min-abs\0&quot; &quot;max-abs\0&quot; },</a>
+<a name="368"><span class="lineNum">     368 </span>            :     { 0x0C, 2, ImmBits::kModeLookup, &quot;sign=src1\0&quot; &quot;sign=src2\0&quot; &quot;sign=0\0&quot; &quot;sign=1\0&quot; }</a>
+<a name="369"><span class="lineNum">     369 </span>            :   };</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span>            :   static const ImmBits vreducexx_vrndscalexx[] = {</a>
+<a name="372"><span class="lineNum">     372 </span>            :     { 0x07, 0, ImmBits::kModeLookup, &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;round\0&quot; &quot;floor\0&quot; &quot;ceil\0&quot; &quot;truncate\0&quot; },</a>
+<a name="373"><span class="lineNum">     373 </span>            :     { 0x08, 3, ImmBits::kModeLookup, &quot;\0&quot; &quot;suppress\0&quot; },</a>
+<a name="374"><span class="lineNum">     374 </span>            :     { 0xF0, 4, ImmBits::kModeFormat, &quot;len=%d&quot; }</a>
+<a name="375"><span class="lineNum">     375 </span>            :   };</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            :   static const ImmBits vroundxx[] = {</a>
+<a name="378"><span class="lineNum">     378 </span>            :     { 0x07, 0, ImmBits::kModeLookup, &quot;round\0&quot; &quot;floor\0&quot; &quot;ceil\0&quot; &quot;truncate\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; &quot;\0&quot; },</a>
+<a name="379"><span class="lineNum">     379 </span>            :     { 0x08, 3, ImmBits::kModeLookup, &quot;\0&quot; &quot;inexact\0&quot; }</a>
+<a name="380"><span class="lineNum">     380 </span>            :   };</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :   uint32_t u8 = imm.getUInt8();</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :   switch (instId) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVblendpd:</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :     case X86Inst::kIdBlendpd:</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, vecSize / 8);</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVblendps:</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :     case X86Inst::kIdBlendps:</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, vecSize / 4);</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVcmppd:</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :     case X86Inst::kIdVcmpps:</a>
+<a name="394"><span class="lineNum">     394 </span>            :     case X86Inst::kIdVcmpsd:</a>
+<a name="395"><span class="lineNum">     395 </span>            :     case X86Inst::kIdVcmpss:</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmText(sb, u8, 5, 0, vcmpx);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCmppd:</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :     case X86Inst::kIdCmpps:</a>
+<a name="400"><span class="lineNum">     400 </span>            :     case X86Inst::kIdCmpsd:</a>
+<a name="401"><span class="lineNum">     401 </span>            :     case X86Inst::kIdCmpss:</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmText(sb, u8, 3, 0, vcmpx);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVdbpsadbw:</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 2, 4);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVdppd:</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :     case X86Inst::kIdVdpps:</a>
+<a name="409"><span class="lineNum">     409 </span>            :     case X86Inst::kIdDppd:</a>
+<a name="410"><span class="lineNum">     410 </span>            :     case X86Inst::kIdDpps:</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, 8);</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVmpsadbw:</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :     case X86Inst::kIdMpsadbw:</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vmpsadbw, std::min&lt;uint32_t&gt;(vecSize / 8, 4));</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpblendw:</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :     case X86Inst::kIdPblendw:</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, 8);</span></a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpblendd:</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, std::min&lt;uint32_t&gt;(vecSize / 4, 8));</span></a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpclmulqdq:</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :     case X86Inst::kIdPclmulqdq:</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vpclmulqdq, ASMJIT_ARRAY_SIZE(vpclmulqdq));</span></a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVroundpd:</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :     case X86Inst::kIdVroundps:</a>
+<a name="430"><span class="lineNum">     430 </span>            :     case X86Inst::kIdVroundsd:</a>
+<a name="431"><span class="lineNum">     431 </span>            :     case X86Inst::kIdVroundss:</a>
+<a name="432"><span class="lineNum">     432 </span>            :     case X86Inst::kIdRoundpd:</a>
+<a name="433"><span class="lineNum">     433 </span>            :     case X86Inst::kIdRoundps:</a>
+<a name="434"><span class="lineNum">     434 </span>            :     case X86Inst::kIdRoundsd:</a>
+<a name="435"><span class="lineNum">     435 </span>            :     case X86Inst::kIdRoundss:</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vroundxx, ASMJIT_ARRAY_SIZE(vroundxx));</span></a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVshufpd:</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     case X86Inst::kIdShufpd:</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmText(sb, u8, 1, 2, vshufpd, std::min&lt;uint32_t&gt;(vecSize / 8, 8));</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVshufps:</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     case X86Inst::kIdShufps:</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmText(sb, u8, 2, 4, vshufps, 4);</span></a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVcvtps2ph:</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vroundxx, 1);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVperm2f128:</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :     case X86Inst::kIdVperm2i128:</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vperm2x128, ASMJIT_ARRAY_SIZE(vperm2x128));</span></a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpermilpd:</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, vecSize / 8);</span></a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpermilps:</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 2, 4);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpshufd:</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :     case X86Inst::kIdPshufd:</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 2, 4);</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpshufhw:</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :     case X86Inst::kIdVpshuflw:</a>
+<a name="465"><span class="lineNum">     465 </span>            :     case X86Inst::kIdPshufhw:</a>
+<a name="466"><span class="lineNum">     466 </span>            :     case X86Inst::kIdPshuflw:</a>
+<a name="467"><span class="lineNum">     467 </span>            :     case X86Inst::kIdPshufw:</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 2, 4);</span></a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            :     // TODO: Maybe?</a>
+<a name="471"><span class="lineNum">     471 </span>            :     case X86Inst::kIdVfixupimmpd:</a>
+<a name="472"><span class="lineNum">     472 </span>            :     case X86Inst::kIdVfixupimmps:</a>
+<a name="473"><span class="lineNum">     473 </span>            :     case X86Inst::kIdVfixupimmsd:</a>
+<a name="474"><span class="lineNum">     474 </span>            :     case X86Inst::kIdVfixupimmss:</a>
+<a name="475"><span class="lineNum">     475 </span>            :       return kErrorOk;</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVfpclasspd:</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :     case X86Inst::kIdVfpclassps:</a>
+<a name="479"><span class="lineNum">     479 </span>            :     case X86Inst::kIdVfpclasssd:</a>
+<a name="480"><span class="lineNum">     480 </span>            :     case X86Inst::kIdVfpclassss:</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vfpclassxx, ASMJIT_ARRAY_SIZE(vfpclassxx));</span></a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVgetmantpd:</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :     case X86Inst::kIdVgetmantps:</a>
+<a name="485"><span class="lineNum">     485 </span>            :     case X86Inst::kIdVgetmantsd:</a>
+<a name="486"><span class="lineNum">     486 </span>            :     case X86Inst::kIdVgetmantss:</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vgetmantxx, ASMJIT_ARRAY_SIZE(vgetmantxx));</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpcmpb:</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :     case X86Inst::kIdVpcmpd:</a>
+<a name="491"><span class="lineNum">     491 </span>            :     case X86Inst::kIdVpcmpq:</a>
+<a name="492"><span class="lineNum">     492 </span>            :     case X86Inst::kIdVpcmpw:</a>
+<a name="493"><span class="lineNum">     493 </span>            :     case X86Inst::kIdVpcmpub:</a>
+<a name="494"><span class="lineNum">     494 </span>            :     case X86Inst::kIdVpcmpud:</a>
+<a name="495"><span class="lineNum">     495 </span>            :     case X86Inst::kIdVpcmpuq:</a>
+<a name="496"><span class="lineNum">     496 </span>            :     case X86Inst::kIdVpcmpuw:</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmText(sb, u8, 2, 4, vpcmpx, 4);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpcomb:</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :     case X86Inst::kIdVpcomd:</a>
+<a name="501"><span class="lineNum">     501 </span>            :     case X86Inst::kIdVpcomq:</a>
+<a name="502"><span class="lineNum">     502 </span>            :     case X86Inst::kIdVpcomw:</a>
+<a name="503"><span class="lineNum">     503 </span>            :     case X86Inst::kIdVpcomub:</a>
+<a name="504"><span class="lineNum">     504 </span>            :     case X86Inst::kIdVpcomud:</a>
+<a name="505"><span class="lineNum">     505 </span>            :     case X86Inst::kIdVpcomuq:</a>
+<a name="506"><span class="lineNum">     506 </span>            :     case X86Inst::kIdVpcomuw:</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmText(sb, u8, 2, 4, vpcomx, 4);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpermq:</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :     case X86Inst::kIdVpermpd:</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 2, 4);</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpternlogd:</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :     case X86Inst::kIdVpternlogq:</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, 1, 8);</span></a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVrangepd:</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :     case X86Inst::kIdVrangeps:</a>
+<a name="519"><span class="lineNum">     519 </span>            :     case X86Inst::kIdVrangesd:</a>
+<a name="520"><span class="lineNum">     520 </span>            :     case X86Inst::kIdVrangess:</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vrangexx, ASMJIT_ARRAY_SIZE(vrangexx));</span></a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVreducepd:</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :     case X86Inst::kIdVreduceps:</a>
+<a name="525"><span class="lineNum">     525 </span>            :     case X86Inst::kIdVreducesd:</a>
+<a name="526"><span class="lineNum">     526 </span>            :     case X86Inst::kIdVreducess:</a>
+<a name="527"><span class="lineNum">     527 </span>            :     case X86Inst::kIdVrndscalepd:</a>
+<a name="528"><span class="lineNum">     528 </span>            :     case X86Inst::kIdVrndscaleps:</a>
+<a name="529"><span class="lineNum">     529 </span>            :     case X86Inst::kIdVrndscalesd:</a>
+<a name="530"><span class="lineNum">     530 </span>            :     case X86Inst::kIdVrndscaless:</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmBits(sb, u8, vreducexx_vrndscalexx, ASMJIT_ARRAY_SIZE(vreducexx_vrndscalexx));</span></a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVshuff32x4:</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :     case X86Inst::kIdVshuff64x2:</a>
+<a name="535"><span class="lineNum">     535 </span>            :     case X86Inst::kIdVshufi32x4:</a>
+<a name="536"><span class="lineNum">     536 </span>            :     case X86Inst::kIdVshufi64x2: {</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :       uint32_t count = std::max&lt;uint32_t&gt;(vecSize / 16, 2);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :       uint32_t bits = count &lt;= 2 ? 1 : 2;</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :       return X86Logging_formatImmShuf(sb, u8, bits, count);</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :     }</a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span>            :     default:</a>
+<a name="543"><span class="lineNum">     543 </span>            :       return kErrorOk;</a>
+<a name="544"><span class="lineNum">     544 </span>            :   }</a>
+<a name="545"><span class="lineNum">     545 </span>            : }</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            : // ============================================================================</a>
+<a name="548"><span class="lineNum">     548 </span>            : // [asmjit::X86Logging - Format Register]</a>
+<a name="549"><span class="lineNum">     549 </span>            : // ============================================================================</a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86Logging::formatRegister(</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   StringBuilder&amp; sb,</a>
+<a name="553"><span class="lineNum">     553 </span>            :   uint32_t logOptions,</a>
+<a name="554"><span class="lineNum">     554 </span>            :   const CodeEmitter* emitter,</a>
+<a name="555"><span class="lineNum">     555 </span>            :   uint32_t archType,</a>
+<a name="556"><span class="lineNum">     556 </span>            :   uint32_t rType,</a>
+<a name="557"><span class="lineNum">     557 </span>            :   uint32_t rId) noexcept {</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span>            :   ASMJIT_UNUSED(logOptions);</a>
+<a name="560"><span class="lineNum">     560 </span>            :   ASMJIT_UNUSED(archType);</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :   if (Operand::isPackedId(rId)) {</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :     if (emitter &amp;&amp; emitter-&gt;getType() == CodeEmitter::kTypeCompiler) {</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :       const CodeCompiler* cc = static_cast&lt;const CodeCompiler*&gt;(emitter);</a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineNoCov">          0 :       if (cc-&gt;isVirtRegValid(rId)) {</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :         VirtReg* vReg = cc-&gt;getVirtRegById(rId);</a>
+<a name="569"><span class="lineNum">     569 </span>            :         ASMJIT_ASSERT(vReg != nullptr);</a>
+<a name="570"><span class="lineNum">     570 </span>            : </a>
+<a name="571"><span class="lineNum">     571 </span>            :         const char* name = vReg-&gt;getName();</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineNoCov">          0 :         if (name &amp;&amp; name[0] != '\0')</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :           return sb.appendString(name);</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :         else</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :           return sb.appendFormat(&quot;v%u&quot;, static_cast&lt;unsigned int&gt;(Operand::unpackId(rId)));</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :       }</a>
+<a name="577"><span class="lineNum">     577 </span>            :     }</a>
+<a name="578"><span class="lineNum">     578 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :     return sb.appendFormat(&quot;VirtReg&lt;Type=%u Id=%u&gt;&quot;, rType, rId);</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :   }</a>
+<a name="582"><span class="lineNum">     582 </span>            :   else {</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :     if (rType &lt; ASMJIT_ARRAY_SIZE(x86RegFormatInfo)) {</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :       const X86RegFormatInfo&amp; rfi = x86RegFormatInfo[rType];</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 :       if (rId &lt; rfi.specialCount)</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineNoCov">          0 :         return sb.appendString(x86RegFormatStrings + rfi.specialIndex + rId * 4);</span></a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :       if (rId &lt; rfi.count)</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :         return sb.appendFormat(x86RegFormatStrings + rfi.formatIndex, static_cast&lt;unsigned int&gt;(rId));</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :     }</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 :     return sb.appendFormat(&quot;PhysReg&lt;Type=%u Id=%u&gt;&quot;, rType, rId);</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :   }</a>
+<a name="595"><span class="lineNum">     595 </span>            : }</a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            : // ============================================================================</a>
+<a name="598"><span class="lineNum">     598 </span>            : // [asmjit::X86Logging - Format Instruction]</a>
+<a name="599"><span class="lineNum">     599 </span>            : // ============================================================================</a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 : ASMJIT_FAVOR_SIZE Error X86Logging::formatInstruction(</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :   StringBuilder&amp; sb,</a>
+<a name="603"><span class="lineNum">     603 </span>            :   uint32_t logOptions,</a>
+<a name="604"><span class="lineNum">     604 </span>            :   const CodeEmitter* emitter,</a>
+<a name="605"><span class="lineNum">     605 </span>            :   uint32_t archType,</a>
+<a name="606"><span class="lineNum">     606 </span>            :   const Inst::Detail&amp; detail, const Operand_* opArray, uint32_t opCount) noexcept {</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :   uint32_t instId = detail.instId;</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :   uint32_t options = detail.options;</span></a>
+<a name="610"><span class="lineNum">     610 </span>            : </a>
+<a name="611"><span class="lineNum">     611 </span>            :   // Format instruction options and instruction mnemonic.</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :   if (instId &lt; X86Inst::_kIdCount) {</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :     const X86Inst&amp; instInfo = X86Inst::getInst(instId);</a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span>            :     // SHORT|LONG options.</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionShortForm) ASMJIT_PROPAGATE(sb.appendString(&quot;short &quot;));</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionLongForm) ASMJIT_PROPAGATE(sb.appendString(&quot;long &quot;));</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span>            :     // LOCK|XACQUIRE|XRELEASE options.</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionXAcquire) ASMJIT_PROPAGATE(sb.appendString(&quot;xacquire &quot;));</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionXRelease) ASMJIT_PROPAGATE(sb.appendString(&quot;xrelease &quot;));</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionLock) ASMJIT_PROPAGATE(sb.appendString(&quot;lock &quot;));</span></a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            :     // REP|REPNZ options.</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineNoCov">          0 :     if (options &amp; (X86Inst::kOptionRep | X86Inst::kOptionRepnz)) {</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :       sb.appendString((options &amp; X86Inst::kOptionRep) ? &quot;rep &quot; : &quot;repnz &quot;);</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :       if (detail.hasExtraReg()) {</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendChar('{'));</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(formatOperand(sb, logOptions, emitter, archType, detail.extraReg.toReg&lt;Reg&gt;()));</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(&quot;} &quot;));</span></a>
+<a name="631"><span class="lineNum">     631 </span>            :       }</a>
+<a name="632"><span class="lineNum">     632 </span>            :     }</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :     // REX options.</a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionRex) {</span></a>
+<a name="636"><span class="lineNum">     636 </span>            :       const uint32_t kRXBWMask = X86Inst::kOptionOpCodeR |</a>
+<a name="637"><span class="lineNum">     637 </span>            :                                  X86Inst::kOptionOpCodeX |</a>
+<a name="638"><span class="lineNum">     638 </span>            :                                  X86Inst::kOptionOpCodeB |</a>
+<a name="639"><span class="lineNum">     639 </span>            :                                  X86Inst::kOptionOpCodeW ;</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :       if (options &amp; kRXBWMask) {</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :         sb.appendString(&quot;rex.&quot;);</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionOpCodeR) sb.appendChar('r');</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionOpCodeX) sb.appendChar('x');</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionOpCodeB) sb.appendChar('b');</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionOpCodeW) sb.appendChar('w');</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :         sb.appendChar(' ');</a>
+<a name="647"><span class="lineNum">     647 </span>            :       }</a>
+<a name="648"><span class="lineNum">     648 </span>            :       else {</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(&quot;rex &quot;));</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :       }</a>
+<a name="651"><span class="lineNum">     651 </span>            :     }</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            :     // VEX|EVEX options.</a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionVex3) ASMJIT_PROPAGATE(sb.appendString(&quot;vex3 &quot;));</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineNoCov">          0 :     if (options &amp; X86Inst::kOptionEvex) ASMJIT_PROPAGATE(sb.appendString(&quot;evex &quot;));</span></a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendString(instInfo.getName()));</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :   }</a>
+<a name="659"><span class="lineNum">     659 </span>            :   else {</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendFormat(&quot;&lt;unknown id=#%u&gt;&quot;, static_cast&lt;unsigned int&gt;(instId)));</span></a>
+<a name="661"><span class="lineNum">     661 </span>            :   }</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; opCount; i++) {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :     const Operand_&amp; op = opArray[i];</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineNoCov">          0 :     if (op.isNone()) break;</span></a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(sb.appendString(i == 0 ? &quot; &quot; : &quot;, &quot;));</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(formatOperand(sb, logOptions, emitter, archType, op));</span></a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :     if (op.isImm() &amp;&amp; (logOptions &amp; Logger::kOptionImmExtended)) {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :       uint32_t vecSize = 16;</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :       for (uint32_t j = 0; j &lt; opCount; j++)</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :         if (opArray[j].isReg())</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :           vecSize = std::max&lt;uint32_t&gt;(vecSize, opArray[j].getSize());</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(X86Logging_formatImmExtended(sb, logOptions, instId, vecSize, op.as&lt;Imm&gt;()));</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :     }</a>
+<a name="677"><span class="lineNum">     677 </span>            : </a>
+<a name="678"><span class="lineNum">     678 </span>            :     // Support AVX-512 {k}{z}.</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :     if (i == 0) {</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :       if (detail.extraReg.getKind() == X86Reg::kKindK) {</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(&quot; {&quot;));</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(formatOperand(sb, logOptions, emitter, archType, detail.extraReg.toReg&lt;Reg&gt;()));</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendChar('}'));</span></a>
+<a name="684"><span class="lineNum">     684 </span>            : </a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :         if (options &amp; X86Inst::kOptionZMask)</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :           ASMJIT_PROPAGATE(sb.appendString(&quot;{z}&quot;));</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :       }</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :       else if (options &amp; X86Inst::kOptionZMask) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(sb.appendString(&quot; {z}&quot;));</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :       }</a>
+<a name="691"><span class="lineNum">     691 </span>            :     }</a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :     // Support AVX-512 {1tox}.</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :     if (op.isMem() &amp;&amp; (options &amp; X86Inst::kOption1ToX))</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :       ASMJIT_PROPAGATE(sb.appendString(&quot; {1tox}&quot;));</span></a>
+<a name="696"><span class="lineNum">     696 </span>            :   }</a>
+<a name="697"><span class="lineNum">     697 </span>            : </a>
+<a name="698"><span class="lineNum">     698 </span>            :   return kErrorOk;</a>
+<a name="699"><span class="lineNum">     699 </span>            : }</a>
+<a name="700"><span class="lineNum">     700 </span>            : </a>
+<a name="701"><span class="lineNum">     701 </span>            : } // asmjit namespace</a>
+<a name="702"><span class="lineNum">     702 </span>            : } // namespace PLMD</a>
+<a name="703"><span class="lineNum">     703 </span>            : </a>
+<a name="704"><span class="lineNum">     704 </span>            : // [Api-End]</a>
+<a name="705"><span class="lineNum">     705 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="706"><span class="lineNum">     706 </span>            : </a>
+<a name="707"><span class="lineNum">     707 </span>            : // [Guard]</a>
+<a name="708"><span class="lineNum">     708 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="709"><span class="lineNum">     709 </span>            : #pragma GCC diagnostic pop</a>
+<a name="710"><span class="lineNum">     710 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86misc.h.func-sort-c.html b/coverage-libs/asmjit/x86misc.h.func-sort-c.html
new file mode 100644
index 0000000000..c9a81138ec
--- /dev/null
+++ b/coverage-libs/asmjit/x86misc.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86misc.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86misc.h<span style="font-size: 80%;"> (<a href="x86misc.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryLo">59.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86misc.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86misc.h.func.html b/coverage-libs/asmjit/x86misc.h.func.html
new file mode 100644
index 0000000000..016111c8df
--- /dev/null
+++ b/coverage-libs/asmjit/x86misc.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86misc.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86misc.h<span style="font-size: 80%;"> (<a href="x86misc.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryLo">59.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86misc.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86misc.h.gcov.html b/coverage-libs/asmjit/x86misc.h.gcov.html
new file mode 100644
index 0000000000..62141dc3c9
--- /dev/null
+++ b/coverage-libs/asmjit/x86misc.h.gcov.html
@@ -0,0 +1,493 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86misc.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86misc.h<span style="font-size: 80%;"> (source / <a href="x86misc.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryLo">59.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86misc_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86misc_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86MISC_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86MISC_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./x86operand.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::X86RegCount]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! \internal</a>
+<a name="52"><span class="lineNum">      52 </span>            : //!</a>
+<a name="53"><span class="lineNum">      53 </span>            : //! X86/X64 registers count.</a>
+<a name="54"><span class="lineNum">      54 </span>            : //!</a>
+<a name="55"><span class="lineNum">      55 </span>            : //! Since the number of registers changed across CPU generations `X86RegCount`</a>
+<a name="56"><span class="lineNum">      56 </span>            : //! class is used by `X86Assembler` and `X86Compiler` to provide a way to get</a>
+<a name="57"><span class="lineNum">      57 </span>            : //! number of available registers dynamically. 32-bit mode offers always only</a>
+<a name="58"><span class="lineNum">      58 </span>            : //! 8 registers of all classes, however, 64-bit mode offers 16 GP registers and</a>
+<a name="59"><span class="lineNum">      59 </span>            : //! 16 XMM/YMM/ZMM registers. AVX512 instruction set doubles the number of SIMD</a>
+<a name="60"><span class="lineNum">      60 </span>            : //! registers (XMM/YMM/ZMM) to 32, this mode has to be explicitly enabled to</a>
+<a name="61"><span class="lineNum">      61 </span>            : //! take effect as it changes some assumptions.</a>
+<a name="62"><span class="lineNum">      62 </span>            : //!</a>
+<a name="63"><span class="lineNum">      63 </span>            : //! `X86RegCount` is also used extensively by X86Compiler's register allocator</a>
+<a name="64"><span class="lineNum">      64 </span>            : //! and data structures. FP registers were omitted as they are never mapped to</a>
+<a name="65"><span class="lineNum">      65 </span>            : //! variables, thus, not needed to be managed.</a>
+<a name="66"><span class="lineNum">      66 </span>            : //!</a>
+<a name="67"><span class="lineNum">      67 </span>            : //! NOTE: At the moment `X86RegCount` can fit into 32-bits, having 8-bits for</a>
+<a name="68"><span class="lineNum">      68 </span>            : //! each register kind except FP. This can change in the future after a new</a>
+<a name="69"><span class="lineNum">      69 </span>            : //! instruction set, which adds more registers, is introduced.</a>
+<a name="70"><span class="lineNum">      70 </span>            : struct X86RegCount {</a>
+<a name="71"><span class="lineNum">      71 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="72"><span class="lineNum">      72 </span>            :   // [Zero]</a>
+<a name="73"><span class="lineNum">      73 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   //! Reset all counters to zero.</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     114002 :   ASMJIT_INLINE void reset() noexcept { _packed = 0; }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="79"><span class="lineNum">      79 </span>            :   // [Get]</a>
+<a name="80"><span class="lineNum">      80 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   //! Get register count by a register `kind`.</a>
+<a name="83"><span class="lineNum">      83 </span>            :   ASMJIT_INLINE uint32_t get(uint32_t kind) const noexcept {</a>
+<a name="84"><span class="lineNum">      84 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :     uint32_t shift = Utils::byteShiftOfDWordStruct(kind);</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     574028 :     return (_packed &gt;&gt; shift) &amp; static_cast&lt;uint32_t&gt;(0xFF);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   //! Get Gp count.</a>
+<a name="91"><span class="lineNum">      91 </span>            :   ASMJIT_INLINE uint32_t getGp() const noexcept { return get(X86Reg::kKindGp); }</a>
+<a name="92"><span class="lineNum">      92 </span>            :   //! Get Mm count.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   ASMJIT_INLINE uint32_t getMm() const noexcept { return get(X86Reg::kKindMm); }</a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Get K count.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   ASMJIT_INLINE uint32_t getK() const noexcept { return get(X86Reg::kKindK); }</a>
+<a name="96"><span class="lineNum">      96 </span>            :   //! Get XMM/YMM/ZMM count.</a>
+<a name="97"><span class="lineNum">      97 </span>            :   ASMJIT_INLINE uint32_t getVec() const noexcept { return get(X86Reg::kKindVec); }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="100"><span class="lineNum">     100 </span>            :   // [Set]</a>
+<a name="101"><span class="lineNum">     101 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   //! Set register count by a register `kind`.</a>
+<a name="104"><span class="lineNum">     104 </span>            :   ASMJIT_INLINE void set(uint32_t kind, uint32_t n) noexcept {</a>
+<a name="105"><span class="lineNum">     105 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="106"><span class="lineNum">     106 </span>            :     ASMJIT_ASSERT(n &lt;= 0xFF);</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :     uint32_t shift = Utils::byteShiftOfDWordStruct(kind);</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     _packed = (_packed &amp; ~static_cast&lt;uint32_t&gt;(0xFF &lt;&lt; shift)) + (n &lt;&lt; shift);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   //! Set Gp count.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ASMJIT_INLINE void setGp(uint32_t n) noexcept { set(X86Reg::kKindGp, n); }</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //! Set Mm count.</a>
+<a name="115"><span class="lineNum">     115 </span>            :   ASMJIT_INLINE void setMm(uint32_t n) noexcept { set(X86Reg::kKindMm, n); }</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //! Set K count.</a>
+<a name="117"><span class="lineNum">     117 </span>            :   ASMJIT_INLINE void setK(uint32_t n) noexcept { set(X86Reg::kKindK, n); }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   //! Set XMM/YMM/ZMM count.</a>
+<a name="119"><span class="lineNum">     119 </span>            :   ASMJIT_INLINE void setVec(uint32_t n) noexcept { set(X86Reg::kKindVec, n); }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="122"><span class="lineNum">     122 </span>            :   // [Add]</a>
+<a name="123"><span class="lineNum">     123 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   //! Add register count by a register `kind`.</a>
+<a name="126"><span class="lineNum">     126 </span>            :   ASMJIT_INLINE void add(uint32_t kind, uint32_t n = 1) noexcept {</a>
+<a name="127"><span class="lineNum">     127 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="128"><span class="lineNum">     128 </span>            :     ASMJIT_ASSERT(0xFF - static_cast&lt;uint32_t&gt;(_regs[kind]) &gt;= n);</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :     uint32_t shift = Utils::byteShiftOfDWordStruct(kind);</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     122988 :     _packed += n &lt;&lt; shift;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      61494 :   }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   //! Add GP count.</a>
+<a name="135"><span class="lineNum">     135 </span>            :   ASMJIT_INLINE void addGp(uint32_t n) noexcept { add(X86Reg::kKindGp, n); }</a>
+<a name="136"><span class="lineNum">     136 </span>            :   //! Add MMX count.</a>
+<a name="137"><span class="lineNum">     137 </span>            :   ASMJIT_INLINE void addMm(uint32_t n) noexcept { add(X86Reg::kKindMm, n); }</a>
+<a name="138"><span class="lineNum">     138 </span>            :   //! Add K count.</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ASMJIT_INLINE void addK(uint32_t n) noexcept { add(X86Reg::kKindK, n); }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   //! Add XMM/YMM/ZMM count.</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ASMJIT_INLINE void addVec(uint32_t n) noexcept { add(X86Reg::kKindVec, n); }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="144"><span class="lineNum">     144 </span>            :   // [Misc]</a>
+<a name="145"><span class="lineNum">     145 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   //! Build register indexes based on the given `count` of registers.</a>
+<a name="148"><span class="lineNum">     148 </span>            :   ASMJIT_INLINE void indexFromRegCount(const X86RegCount&amp; count) noexcept {</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      36702 :     uint32_t x = static_cast&lt;uint32_t&gt;(count._regs[0]);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      36702 :     uint32_t y = static_cast&lt;uint32_t&gt;(count._regs[1]) + x;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      36702 :     uint32_t z = static_cast&lt;uint32_t&gt;(count._regs[2]) + y;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :     ASMJIT_ASSERT(y &lt;= 0xFF);</a>
+<a name="154"><span class="lineNum">     154 </span>            :     ASMJIT_ASSERT(z &lt;= 0xFF);</a>
+<a name="155"><span class="lineNum">     155 </span>            :     _packed = Utils::pack32_4x8(0, x, y, z);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="159"><span class="lineNum">     159 </span>            :   // [Members]</a>
+<a name="160"><span class="lineNum">     160 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   union {</a>
+<a name="163"><span class="lineNum">     163 </span>            :     struct {</a>
+<a name="164"><span class="lineNum">     164 </span>            :       //! Count of GP registers.</a>
+<a name="165"><span class="lineNum">     165 </span>            :       uint8_t _gp;</a>
+<a name="166"><span class="lineNum">     166 </span>            :       //! Count of XMM|YMM|ZMM registers.</a>
+<a name="167"><span class="lineNum">     167 </span>            :       uint8_t _vec;</a>
+<a name="168"><span class="lineNum">     168 </span>            :       //! Count of MMX registers.</a>
+<a name="169"><span class="lineNum">     169 </span>            :       uint8_t _mm;</a>
+<a name="170"><span class="lineNum">     170 </span>            :       //! Count of K registers.</a>
+<a name="171"><span class="lineNum">     171 </span>            :       uint8_t _k;</a>
+<a name="172"><span class="lineNum">     172 </span>            :     };</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :     uint8_t _regs[4];</a>
+<a name="175"><span class="lineNum">     175 </span>            :     uint32_t _packed;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   };</a>
+<a name="177"><span class="lineNum">     177 </span>            : };</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : // ============================================================================</a>
+<a name="180"><span class="lineNum">     180 </span>            : // [asmjit::X86RegMask]</a>
+<a name="181"><span class="lineNum">     181 </span>            : // ============================================================================</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : //! \internal</a>
+<a name="184"><span class="lineNum">     184 </span>            : //!</a>
+<a name="185"><span class="lineNum">     185 </span>            : //! X86/X64 registers mask.</a>
+<a name="186"><span class="lineNum">     186 </span>            : struct X86RegMask {</a>
+<a name="187"><span class="lineNum">     187 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="188"><span class="lineNum">     188 </span>            :   // [Reset]</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   //! Reset all register masks to zero.</a>
+<a name="192"><span class="lineNum">     192 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="193"><span class="lineNum">     193 </span>            :     _packed.reset();</a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="197"><span class="lineNum">     197 </span>            :   // [IsEmpty / Has]</a>
+<a name="198"><span class="lineNum">     198 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   //! Get whether all register masks are zero (empty).</a>
+<a name="201"><span class="lineNum">     201 </span>            :   ASMJIT_INLINE bool isEmpty() const noexcept {</a>
+<a name="202"><span class="lineNum">     202 </span>            :     return _packed.isZero();</a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            :   ASMJIT_INLINE bool has(uint32_t kind, uint32_t mask = 0xFFFFFFFFU) const noexcept {</a>
+<a name="206"><span class="lineNum">     206 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     switch (kind) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       case X86Reg::kKindGp : return (static_cast&lt;uint32_t&gt;(_gp ) &amp; mask) != 0;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :       case X86Reg::kKindVec: return (static_cast&lt;uint32_t&gt;(_vec) &amp; mask) != 0;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       case X86Reg::kKindMm : return (static_cast&lt;uint32_t&gt;(_mm ) &amp; mask) != 0;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       case X86Reg::kKindK  : return (static_cast&lt;uint32_t&gt;(_k  ) &amp; mask) != 0;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :     return false;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   ASMJIT_INLINE bool hasGp(uint32_t mask = 0xFFFFFFFFU) const noexcept { return has(X86Reg::kKindGp, mask); }</a>
+<a name="219"><span class="lineNum">     219 </span>            :   ASMJIT_INLINE bool hasVec(uint32_t mask = 0xFFFFFFFFU) const noexcept { return has(X86Reg::kKindVec, mask); }</a>
+<a name="220"><span class="lineNum">     220 </span>            :   ASMJIT_INLINE bool hasMm(uint32_t mask = 0xFFFFFFFFU) const noexcept { return has(X86Reg::kKindMm, mask); }</a>
+<a name="221"><span class="lineNum">     221 </span>            :   ASMJIT_INLINE bool hasK(uint32_t mask = 0xFFFFFFFFU) const noexcept { return has(X86Reg::kKindK, mask); }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="224"><span class="lineNum">     224 </span>            :   // [Get]</a>
+<a name="225"><span class="lineNum">     225 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :   ASMJIT_INLINE uint32_t get(uint32_t kind) const noexcept {</a>
+<a name="228"><span class="lineNum">     228 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      54800 :     switch (kind) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      95866 :       case X86Reg::kKindGp : return _gp;</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     215126 :       case X86Reg::kKindVec: return _vec;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      41346 :       case X86Reg::kKindMm : return _mm;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :       case X86Reg::kKindK  : return _k;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :     return 0;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   ASMJIT_INLINE uint32_t getGp() const noexcept { return get(X86Reg::kKindGp); }</a>
+<a name="241"><span class="lineNum">     241 </span>            :   ASMJIT_INLINE uint32_t getVec() const noexcept { return get(X86Reg::kKindVec); }</a>
+<a name="242"><span class="lineNum">     242 </span>            :   ASMJIT_INLINE uint32_t getMm() const noexcept { return get(X86Reg::kKindMm); }</a>
+<a name="243"><span class="lineNum">     243 </span>            :   ASMJIT_INLINE uint32_t getK() const noexcept { return get(X86Reg::kKindK); }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="246"><span class="lineNum">     246 </span>            :   // [Zero]</a>
+<a name="247"><span class="lineNum">     247 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_INLINE void zero(uint32_t kind) noexcept {</a>
+<a name="250"><span class="lineNum">     250 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :     switch (kind) {</a>
+<a name="253"><span class="lineNum">     253 </span>            :       case X86Reg::kKindGp : _gp  = 0; break;</a>
+<a name="254"><span class="lineNum">     254 </span>            :       case X86Reg::kKindVec: _vec = 0; break;</a>
+<a name="255"><span class="lineNum">     255 </span>            :       case X86Reg::kKindMm : _mm  = 0; break;</a>
+<a name="256"><span class="lineNum">     256 </span>            :       case X86Reg::kKindK  : _k   = 0; break;</a>
+<a name="257"><span class="lineNum">     257 </span>            :     }</a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            :   ASMJIT_INLINE void zeroGp() noexcept { zero(X86Reg::kKindGp); }</a>
+<a name="261"><span class="lineNum">     261 </span>            :   ASMJIT_INLINE void zeroVec() noexcept { zero(X86Reg::kKindVec); }</a>
+<a name="262"><span class="lineNum">     262 </span>            :   ASMJIT_INLINE void zeroMm() noexcept { zero(X86Reg::kKindMm); }</a>
+<a name="263"><span class="lineNum">     263 </span>            :   ASMJIT_INLINE void zeroK() noexcept { zero(X86Reg::kKindK); }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="266"><span class="lineNum">     266 </span>            :   // [Set]</a>
+<a name="267"><span class="lineNum">     267 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :   ASMJIT_INLINE void set(const X86RegMask&amp; other) noexcept {</a>
+<a name="270"><span class="lineNum">     270 </span>            :     _packed = other._packed;</a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   ASMJIT_INLINE void set(uint32_t kind, uint32_t mask) noexcept {</a>
+<a name="274"><span class="lineNum">     274 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :     switch (kind) {</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">      16664 :       case X86Reg::kKindGp : _gp  = static_cast&lt;uint16_t&gt;(mask); break;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       3296 :       case X86Reg::kKindMm : _mm  = static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       1648 :       case X86Reg::kKindK  : _k   = static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      30782 :       case X86Reg::kKindVec: _vec = static_cast&lt;uint32_t&gt;(mask); break;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     }</a>
+<a name="282"><span class="lineNum">     282 </span>            :   }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   ASMJIT_INLINE void setGp(uint32_t mask) noexcept { return set(X86Reg::kKindGp, mask); }</a>
+<a name="285"><span class="lineNum">     285 </span>            :   ASMJIT_INLINE void setVec(uint32_t mask) noexcept { return set(X86Reg::kKindVec, mask); }</a>
+<a name="286"><span class="lineNum">     286 </span>            :   ASMJIT_INLINE void setMm(uint32_t mask) noexcept { return set(X86Reg::kKindMm, mask); }</a>
+<a name="287"><span class="lineNum">     287 </span>            :   ASMJIT_INLINE void setK(uint32_t mask) noexcept { return set(X86Reg::kKindK, mask); }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="290"><span class="lineNum">     290 </span>            :   // [And]</a>
+<a name="291"><span class="lineNum">     291 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            :   ASMJIT_INLINE void and_(const X86RegMask&amp; other) noexcept {</a>
+<a name="294"><span class="lineNum">     294 </span>            :     _packed.and_(other._packed);</a>
+<a name="295"><span class="lineNum">     295 </span>            :   }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   ASMJIT_INLINE void and_(uint32_t kind, uint32_t mask) noexcept {</a>
+<a name="298"><span class="lineNum">     298 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :     switch (kind) {</a>
+<a name="301"><span class="lineNum">     301 </span>            :       case X86Reg::kKindGp : _gp  &amp;= static_cast&lt;uint16_t&gt;(mask); break;</a>
+<a name="302"><span class="lineNum">     302 </span>            :       case X86Reg::kKindMm : _mm  &amp;= static_cast&lt;uint8_t &gt;(mask); break;</a>
+<a name="303"><span class="lineNum">     303 </span>            :       case X86Reg::kKindK  : _k   &amp;= static_cast&lt;uint8_t &gt;(mask); break;</a>
+<a name="304"><span class="lineNum">     304 </span>            :       case X86Reg::kKindVec: _vec &amp;= static_cast&lt;uint32_t&gt;(mask); break;</a>
+<a name="305"><span class="lineNum">     305 </span>            :     }</a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            :   ASMJIT_INLINE void andGp(uint32_t mask) noexcept { and_(X86Reg::kKindGp, mask); }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   ASMJIT_INLINE void andVec(uint32_t mask) noexcept { and_(X86Reg::kKindVec, mask); }</a>
+<a name="310"><span class="lineNum">     310 </span>            :   ASMJIT_INLINE void andMm(uint32_t mask) noexcept { and_(X86Reg::kKindMm, mask); }</a>
+<a name="311"><span class="lineNum">     311 </span>            :   ASMJIT_INLINE void andK(uint32_t mask) noexcept { and_(X86Reg::kKindK, mask); }</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="314"><span class="lineNum">     314 </span>            :   // [AndNot]</a>
+<a name="315"><span class="lineNum">     315 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :   ASMJIT_INLINE void andNot(const X86RegMask&amp; other) noexcept {</a>
+<a name="318"><span class="lineNum">     318 </span>            :     _packed.andNot(other._packed);</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :   ASMJIT_INLINE void andNot(uint32_t kind, uint32_t mask) noexcept {</a>
+<a name="322"><span class="lineNum">     322 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            :     switch (kind) {</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       7268 :       case X86Reg::kKindGp : _gp  &amp;= ~static_cast&lt;uint16_t&gt;(mask); break;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :       case X86Reg::kKindMm : _mm  &amp;= ~static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :       case X86Reg::kKindK  : _k   &amp;= ~static_cast&lt;uint8_t &gt;(mask); break;</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">      22464 :       case X86Reg::kKindVec: _vec &amp;= ~static_cast&lt;uint32_t&gt;(mask); break;</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :     }</a>
+<a name="330"><span class="lineNum">     330 </span>            :   }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            :   ASMJIT_INLINE void andNotGp(uint32_t mask) noexcept { andNot(X86Reg::kKindGp, mask); }</a>
+<a name="333"><span class="lineNum">     333 </span>            :   ASMJIT_INLINE void andNotVec(uint32_t mask) noexcept { andNot(X86Reg::kKindVec, mask); }</a>
+<a name="334"><span class="lineNum">     334 </span>            :   ASMJIT_INLINE void andNotMm(uint32_t mask) noexcept { andNot(X86Reg::kKindMm, mask); }</a>
+<a name="335"><span class="lineNum">     335 </span>            :   ASMJIT_INLINE void andNotK(uint32_t mask) noexcept { andNot(X86Reg::kKindK, mask); }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="338"><span class="lineNum">     338 </span>            :   // [Or]</a>
+<a name="339"><span class="lineNum">     339 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   ASMJIT_INLINE void or_(const X86RegMask&amp; other) noexcept {</a>
+<a name="342"><span class="lineNum">     342 </span>            :     _packed.or_(other._packed);</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">      33106 :   }</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            :   ASMJIT_INLINE void or_(uint32_t kind, uint32_t mask) noexcept {</a>
+<a name="346"><span class="lineNum">     346 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       1948 :     switch (kind) {</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      14536 :       case X86Reg::kKindGp : _gp  |= static_cast&lt;uint16_t&gt;(mask); break;</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :       case X86Reg::kKindMm : _mm  |= static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :       case X86Reg::kKindK  : _k   |= static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">      42900 :       case X86Reg::kKindVec: _vec |= static_cast&lt;uint32_t&gt;(mask); break;</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :     }</a>
+<a name="353"><span class="lineNum">     353 </span>            :   }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :   ASMJIT_INLINE void orGp(uint32_t mask) noexcept { return or_(X86Reg::kKindGp, mask); }</a>
+<a name="356"><span class="lineNum">     356 </span>            :   ASMJIT_INLINE void orVec(uint32_t mask) noexcept { return or_(X86Reg::kKindVec, mask); }</a>
+<a name="357"><span class="lineNum">     357 </span>            :   ASMJIT_INLINE void orMm(uint32_t mask) noexcept { return or_(X86Reg::kKindMm, mask); }</a>
+<a name="358"><span class="lineNum">     358 </span>            :   ASMJIT_INLINE void orK(uint32_t mask) noexcept { return or_(X86Reg::kKindK, mask); }</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="361"><span class="lineNum">     361 </span>            :   // [Xor]</a>
+<a name="362"><span class="lineNum">     362 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :   ASMJIT_INLINE void xor_(const X86RegMask&amp; other) noexcept {</a>
+<a name="365"><span class="lineNum">     365 </span>            :     _packed.xor_(other._packed);</a>
+<a name="366"><span class="lineNum">     366 </span>            :   }</a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span>            :   ASMJIT_INLINE void xor_(uint32_t kind, uint32_t mask) noexcept {</a>
+<a name="369"><span class="lineNum">     369 </span>            :     ASMJIT_ASSERT(kind &lt; Globals::kMaxVRegKinds);</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :     switch (kind) {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :       case X86Reg::kKindGp : _gp  ^= static_cast&lt;uint16_t&gt;(mask); break;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :       case X86Reg::kKindMm : _mm  ^= static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :       case X86Reg::kKindK  : _k   ^= static_cast&lt;uint8_t &gt;(mask); break;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">       5080 :       case X86Reg::kKindVec: _vec ^= static_cast&lt;uint32_t&gt;(mask); break;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     }</a>
+<a name="377"><span class="lineNum">     377 </span>            :   }</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :   ASMJIT_INLINE void xorGp(uint32_t mask) noexcept { xor_(X86Reg::kKindGp, mask); }</a>
+<a name="380"><span class="lineNum">     380 </span>            :   ASMJIT_INLINE void xorVec(uint32_t mask) noexcept { xor_(X86Reg::kKindVec, mask); }</a>
+<a name="381"><span class="lineNum">     381 </span>            :   ASMJIT_INLINE void xorMm(uint32_t mask) noexcept { xor_(X86Reg::kKindMm, mask); }</a>
+<a name="382"><span class="lineNum">     382 </span>            :   ASMJIT_INLINE void xorK(uint32_t mask) noexcept { xor_(X86Reg::kKindK, mask); }</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="385"><span class="lineNum">     385 </span>            :   // [Members]</a>
+<a name="386"><span class="lineNum">     386 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            :   union {</a>
+<a name="389"><span class="lineNum">     389 </span>            :     struct {</a>
+<a name="390"><span class="lineNum">     390 </span>            :       //! GP registers mask (16 bits).</a>
+<a name="391"><span class="lineNum">     391 </span>            :       uint16_t _gp;</a>
+<a name="392"><span class="lineNum">     392 </span>            :       //! MMX registers mask (8 bits).</a>
+<a name="393"><span class="lineNum">     393 </span>            :       uint8_t _mm;</a>
+<a name="394"><span class="lineNum">     394 </span>            :       //! K registers mask (8 bits).</a>
+<a name="395"><span class="lineNum">     395 </span>            :       uint8_t _k;</a>
+<a name="396"><span class="lineNum">     396 </span>            :       //! XMM|YMM|ZMM registers mask (32 bits).</a>
+<a name="397"><span class="lineNum">     397 </span>            :       uint32_t _vec;</a>
+<a name="398"><span class="lineNum">     398 </span>            :     };</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :     //! Packed masks.</a>
+<a name="401"><span class="lineNum">     401 </span>            :     UInt64 _packed;</a>
+<a name="402"><span class="lineNum">     402 </span>            :   };</a>
+<a name="403"><span class="lineNum">     403 </span>            : };</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            : //! \}</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            : } // asmjit namespace</a>
+<a name="408"><span class="lineNum">     408 </span>            : } // namespace PLMD</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            : // [Api-End]</a>
+<a name="411"><span class="lineNum">     411 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span>            : // [Guard]</a>
+<a name="414"><span class="lineNum">     414 </span>            : #endif // _ASMJIT_X86_X86MISC_H</a>
+<a name="415"><span class="lineNum">     415 </span>            : #pragma GCC diagnostic pop</a>
+<a name="416"><span class="lineNum">     416 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="417"><span class="lineNum">     417 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86operand.h.func-sort-c.html b/coverage-libs/asmjit/x86operand.h.func-sort-c.html
new file mode 100644
index 0000000000..146909e43e
--- /dev/null
+++ b/coverage-libs/asmjit/x86operand.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86operand.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86operand.h<span style="font-size: 80%;"> (<a href="x86operand.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">54.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86operand.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86operand.h.func.html b/coverage-libs/asmjit/x86operand.h.func.html
new file mode 100644
index 0000000000..df1c42abf8
--- /dev/null
+++ b/coverage-libs/asmjit/x86operand.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86operand.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86operand.h<span style="font-size: 80%;"> (<a href="x86operand.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">54.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86operand.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86operand.h.gcov.html b/coverage-libs/asmjit/x86operand.h.gcov.html
new file mode 100644
index 0000000000..050d6cdf7e
--- /dev/null
+++ b/coverage-libs/asmjit/x86operand.h.gcov.html
@@ -0,0 +1,1209 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86operand.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86operand.h<span style="font-size: 80%;"> (source / <a href="x86operand.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">54.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86operand_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86operand_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86OPERAND_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86OPERAND_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./arch.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./operand.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./x86globals.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : // [Api-Begin]</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace asmjit {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [Forward Declarations]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : class X86Mem;</a>
+<a name="52"><span class="lineNum">      52 </span>            : class X86Reg;</a>
+<a name="53"><span class="lineNum">      53 </span>            : class X86Vec;</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : class X86Gp;</a>
+<a name="56"><span class="lineNum">      56 </span>            : class X86Gpb;</a>
+<a name="57"><span class="lineNum">      57 </span>            : class X86GpbLo;</a>
+<a name="58"><span class="lineNum">      58 </span>            : class X86GpbHi;</a>
+<a name="59"><span class="lineNum">      59 </span>            : class X86Gpw;</a>
+<a name="60"><span class="lineNum">      60 </span>            : class X86Gpd;</a>
+<a name="61"><span class="lineNum">      61 </span>            : class X86Gpq;</a>
+<a name="62"><span class="lineNum">      62 </span>            : class X86Fp;</a>
+<a name="63"><span class="lineNum">      63 </span>            : class X86Mm;</a>
+<a name="64"><span class="lineNum">      64 </span>            : class X86KReg;</a>
+<a name="65"><span class="lineNum">      65 </span>            : class X86Xmm;</a>
+<a name="66"><span class="lineNum">      66 </span>            : class X86Ymm;</a>
+<a name="67"><span class="lineNum">      67 </span>            : class X86Zmm;</a>
+<a name="68"><span class="lineNum">      68 </span>            : class X86Bnd;</a>
+<a name="69"><span class="lineNum">      69 </span>            : class X86Seg;</a>
+<a name="70"><span class="lineNum">      70 </span>            : class X86Rip;</a>
+<a name="71"><span class="lineNum">      71 </span>            : class X86CReg;</a>
+<a name="72"><span class="lineNum">      72 </span>            : class X86DReg;</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="75"><span class="lineNum">      75 </span>            : //! \{</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : // ============================================================================</a>
+<a name="78"><span class="lineNum">      78 </span>            : // [asmjit::X86Mem]</a>
+<a name="79"><span class="lineNum">      79 </span>            : // ============================================================================</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : //! Memory operand (X86).</a>
+<a name="82"><span class="lineNum">      82 </span>            : class X86Mem : public Mem {</a>
+<a name="83"><span class="lineNum">      83 </span>            : public:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! Additional bits of operand's signature used by `X86Mem`.</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ASMJIT_ENUM(AdditionalBits) {</a>
+<a name="86"><span class="lineNum">      86 </span>            :     kSignatureMemShiftShift   = 19,</a>
+<a name="87"><span class="lineNum">      87 </span>            :     kSignatureMemShiftBits    = 0x03U,</a>
+<a name="88"><span class="lineNum">      88 </span>            :     kSignatureMemShiftMask    = kSignatureMemShiftBits &lt;&lt; kSignatureMemShiftShift,</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :     kSignatureMemSegmentShift = 21,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     kSignatureMemSegmentBits  = 0x07U,</a>
+<a name="92"><span class="lineNum">      92 </span>            :     kSignatureMemSegmentMask  = kSignatureMemSegmentBits &lt;&lt; kSignatureMemSegmentShift</a>
+<a name="93"><span class="lineNum">      93 </span>            :   };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // [Construction / Destruction]</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   //! Construct a default `X86Mem` operand, that points to [0].</a>
+<a name="100"><span class="lineNum">     100 </span>            :   ASMJIT_INLINE X86Mem() noexcept : Mem(NoInit) { reset(); }</a>
+<a name="101"><span class="lineNum">     101 </span>            :   ASMJIT_INLINE X86Mem(const X86Mem&amp; other) noexcept : Mem(other) {}</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   ASMJIT_INLINE X86Mem(const Label&amp; base, int32_t off, uint32_t size = 0, uint32_t flags = 0) noexcept : Mem(NoInit) {</a>
+<a name="104"><span class="lineNum">     104 </span>            :     uint32_t signature = (Label::kLabelTag &lt;&lt; kSignatureMemBaseTypeShift ) |</a>
+<a name="105"><span class="lineNum">     105 </span>            :                          (size             &lt;&lt; kSignatureSizeShift        ) ;</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :     _init_packed_d0_d1(kOpMem | signature | flags, 0);</a>
+<a name="108"><span class="lineNum">     108 </span>            :     _mem.base = base.getId();</a>
+<a name="109"><span class="lineNum">     109 </span>            :     _mem.offsetLo32 = static_cast&lt;uint32_t&gt;(off);</a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   ASMJIT_INLINE X86Mem(const Label&amp; base, const Reg&amp; index, uint32_t shift, int32_t off, uint32_t size = 0, uint32_t flags = 0) noexcept : Mem(NoInit) {</a>
+<a name="113"><span class="lineNum">     113 </span>            :     ASMJIT_ASSERT(shift &lt;= kSignatureMemShiftMask);</a>
+<a name="114"><span class="lineNum">     114 </span>            :     uint32_t signature = (Label::kLabelTag &lt;&lt; kSignatureMemBaseTypeShift ) |</a>
+<a name="115"><span class="lineNum">     115 </span>            :                          (index.getType()  &lt;&lt; kSignatureMemIndexTypeShift) |</a>
+<a name="116"><span class="lineNum">     116 </span>            :                          (shift            &lt;&lt; kSignatureMemShiftShift    ) |</a>
+<a name="117"><span class="lineNum">     117 </span>            :                          (size             &lt;&lt; kSignatureSizeShift        ) ;</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :     _init_packed_d0_d1(kOpMem | signature | flags, index.getId());</a>
+<a name="120"><span class="lineNum">     120 </span>            :     _mem.base = base.getId();</a>
+<a name="121"><span class="lineNum">     121 </span>            :     _mem.offsetLo32 = static_cast&lt;uint32_t&gt;(off);</a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   ASMJIT_INLINE X86Mem(const Reg&amp; base, int32_t off, uint32_t size = 0, uint32_t flags = 0) noexcept : Mem(NoInit) {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       6100 :     uint32_t signature = (base.getType()   &lt;&lt; kSignatureMemBaseTypeShift ) |</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :                          (size             &lt;&lt; kSignatureSizeShift        ) ;</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       6100 :     _init_packed_d0_d1(kOpMem | signature | flags, 0);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       6100 :     _mem.base = base.getId();</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       6100 :     _mem.offsetLo32 = static_cast&lt;uint32_t&gt;(off);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   ASMJIT_INLINE X86Mem(const Reg&amp; base, const Reg&amp; index, uint32_t shift, int32_t off, uint32_t size = 0, uint32_t flags = 0) noexcept : Mem(NoInit) {</a>
+<a name="134"><span class="lineNum">     134 </span>            :     ASMJIT_ASSERT(shift &lt;= kSignatureMemShiftMask);</a>
+<a name="135"><span class="lineNum">     135 </span>            :     uint32_t signature = (base.getType()   &lt;&lt; kSignatureMemBaseTypeShift ) |</a>
+<a name="136"><span class="lineNum">     136 </span>            :                          (index.getType()  &lt;&lt; kSignatureMemIndexTypeShift) |</a>
+<a name="137"><span class="lineNum">     137 </span>            :                          (shift            &lt;&lt; kSignatureMemShiftShift    ) |</a>
+<a name="138"><span class="lineNum">     138 </span>            :                          (size             &lt;&lt; kSignatureSizeShift        ) ;</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :     _init_packed_d0_d1(kOpMem | signature | flags, index.getId());</a>
+<a name="141"><span class="lineNum">     141 </span>            :     _mem.base = base.getId();</a>
+<a name="142"><span class="lineNum">     142 </span>            :     _mem.offsetLo32 = static_cast&lt;uint32_t&gt;(off);</a>
+<a name="143"><span class="lineNum">     143 </span>            :   }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   ASMJIT_INLINE X86Mem(uint64_t base, uint32_t size = 0, uint32_t flags = 0) noexcept : Mem(NoInit) {</a>
+<a name="146"><span class="lineNum">     146 </span>            :     _init_packed_d0_d1(kOpMem | flags | (size &lt;&lt; kSignatureSizeShift), 0);</a>
+<a name="147"><span class="lineNum">     147 </span>            :     _mem.offset64 = base;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   ASMJIT_INLINE X86Mem(uint64_t base, const Reg&amp; index, uint32_t shift = 0, uint32_t size = 0, uint32_t flags = 0) noexcept : Mem(NoInit) {</a>
+<a name="151"><span class="lineNum">     151 </span>            :     ASMJIT_ASSERT(shift &lt;= kSignatureMemShiftMask);</a>
+<a name="152"><span class="lineNum">     152 </span>            :     uint32_t signature = (index.getType()  &lt;&lt; kSignatureMemIndexTypeShift) |</a>
+<a name="153"><span class="lineNum">     153 </span>            :                          (shift            &lt;&lt; kSignatureMemShiftShift    ) |</a>
+<a name="154"><span class="lineNum">     154 </span>            :                          (size             &lt;&lt; kSignatureSizeShift        ) ;</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :     _init_packed_d0_d1(kOpMem | signature | flags, index.getId());</a>
+<a name="157"><span class="lineNum">     157 </span>            :     _mem.offset64 = base;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   ASMJIT_INLINE X86Mem(const _Init&amp; init,</a>
+<a name="161"><span class="lineNum">     161 </span>            :     uint32_t baseType, uint32_t baseId,</a>
+<a name="162"><span class="lineNum">     162 </span>            :     uint32_t indexType, uint32_t indexId,</a>
+<a name="163"><span class="lineNum">     163 </span>            :     int32_t off, uint32_t size, uint32_t flags) noexcept : Mem(init, baseType, baseId, indexType, indexId, off, size, flags) {}</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            :   explicit ASMJIT_INLINE X86Mem(const _NoInit&amp;) noexcept : Mem(NoInit) {}</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="168"><span class="lineNum">     168 </span>            :   // [X86Mem]</a>
+<a name="169"><span class="lineNum">     169 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   //! Clone the memory operand.</a>
+<a name="172"><span class="lineNum">     172 </span>            :   ASMJIT_INLINE X86Mem clone() const noexcept { return X86Mem(*this); }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   using Mem::setIndex;</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   ASMJIT_INLINE void setIndex(const Reg&amp; index, uint32_t shift) noexcept {</a>
+<a name="177"><span class="lineNum">     177 </span>            :     setIndex(index);</a>
+<a name="178"><span class="lineNum">     178 </span>            :     setShift(shift);</a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   //! Get if the memory operand has shift (aka scale) constant.</a>
+<a name="182"><span class="lineNum">     182 </span>            :   ASMJIT_INLINE bool hasShift() const noexcept { return _hasSignatureData(kSignatureMemShiftMask); }</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //! Get the memory operand's shift (aka scale) constant.</a>
+<a name="184"><span class="lineNum">     184 </span>            :   ASMJIT_INLINE uint32_t getShift() const noexcept { return _getSignatureData(kSignatureMemShiftBits, kSignatureMemShiftShift); }</a>
+<a name="185"><span class="lineNum">     185 </span>            :   //! Set the memory operand's shift (aka scale) constant.</a>
+<a name="186"><span class="lineNum">     186 </span>            :   ASMJIT_INLINE void setShift(uint32_t shift) noexcept { _setSignatureData(shift, kSignatureMemShiftBits, kSignatureMemShiftShift); }</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //! Reset the memory operand's shift (aka scale) constant to zero.</a>
+<a name="188"><span class="lineNum">     188 </span>            :   ASMJIT_INLINE void resetShift() noexcept { _signature &amp;= ~kSignatureMemShiftMask; }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   //! Get if the memory operand has a segment override.</a>
+<a name="191"><span class="lineNum">     191 </span>            :   ASMJIT_INLINE bool hasSegment() const noexcept { return _hasSignatureData(kSignatureMemSegmentMask); }</a>
+<a name="192"><span class="lineNum">     192 </span>            :   //! Get associated segment override as `X86Seg` operand.</a>
+<a name="193"><span class="lineNum">     193 </span>            :   ASMJIT_INLINE X86Seg getSegment() const noexcept;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   //! Set the segment override to `seg`.</a>
+<a name="195"><span class="lineNum">     195 </span>            :   ASMJIT_INLINE void setSegment(const X86Seg&amp; seg) noexcept;</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   //! Get segment override as id, see \ref X86Seg::Id.</a>
+<a name="198"><span class="lineNum">     198 </span>            :   ASMJIT_INLINE uint32_t getSegmentId() const noexcept { return _getSignatureData(kSignatureMemSegmentBits, kSignatureMemSegmentShift); }</a>
+<a name="199"><span class="lineNum">     199 </span>            :   //! Set the segment override to `id`.</a>
+<a name="200"><span class="lineNum">     200 </span>            :   ASMJIT_INLINE void setSegmentId(uint32_t sId) noexcept { _setSignatureData(sId, kSignatureMemSegmentBits, kSignatureMemSegmentShift); }</a>
+<a name="201"><span class="lineNum">     201 </span>            :   //! Reset the segment override.</a>
+<a name="202"><span class="lineNum">     202 </span>            :   ASMJIT_INLINE void resetSegment() noexcept { _signature &amp;= ~kSignatureMemSegmentMask; }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :   //! Get new memory operand adjusted by `off`.</a>
+<a name="205"><span class="lineNum">     205 </span>            :   ASMJIT_INLINE X86Mem adjusted(int64_t off) const noexcept {</a>
+<a name="206"><span class="lineNum">     206 </span>            :     X86Mem result(*this);</a>
+<a name="207"><span class="lineNum">     207 </span>            :     result.addOffset(off);</a>
+<a name="208"><span class="lineNum">     208 </span>            :     return result;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="212"><span class="lineNum">     212 </span>            :   // [Operator Overload]</a>
+<a name="213"><span class="lineNum">     213 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   ASMJIT_INLINE X86Mem&amp; operator=(const X86Mem&amp; other) noexcept { copyFrom(other); return *this; }</a>
+<a name="216"><span class="lineNum">     216 </span>            : };</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : // ============================================================================</a>
+<a name="219"><span class="lineNum">     219 </span>            : // [asmjit::X86Reg]</a>
+<a name="220"><span class="lineNum">     220 </span>            : // ============================================================================</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : //! Register traits (X86/X64).</a>
+<a name="223"><span class="lineNum">     223 </span>            : //!</a>
+<a name="224"><span class="lineNum">     224 </span>            : //! Register traits contains information about a particular register type. It's</a>
+<a name="225"><span class="lineNum">     225 </span>            : //! used by asmjit to setup register information on-the-fly and to populate</a>
+<a name="226"><span class="lineNum">     226 </span>            : //! tables that contain register information (this way it's possible to change</a>
+<a name="227"><span class="lineNum">     227 </span>            : //! register types and kinds without having to reorder these tables).</a>
+<a name="228"><span class="lineNum">     228 </span>            : template&lt;uint32_t RegType&gt;</a>
+<a name="229"><span class="lineNum">     229 </span>            : struct X86RegTraits {</a>
+<a name="230"><span class="lineNum">     230 </span>            :   enum {</a>
+<a name="231"><span class="lineNum">     231 </span>            :     kValid     = 0,                      //!&lt; RegType is not valid by default.</a>
+<a name="232"><span class="lineNum">     232 </span>            :     kCount     = 0,                      //!&lt; Count of registers (0 if none).</a>
+<a name="233"><span class="lineNum">     233 </span>            :     kTypeId    = TypeId::kVoid,          //!&lt; Everything is void by default.</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :     kType      = 0,                      //!&lt; Zero type by default.</a>
+<a name="236"><span class="lineNum">     236 </span>            :     kKind      = 0,                      //!&lt; Zero kind by default.</a>
+<a name="237"><span class="lineNum">     237 </span>            :     kSize      = 0,                      //!&lt; No size by default.</a>
+<a name="238"><span class="lineNum">     238 </span>            :     kSignature = 0                       //!&lt; No signature by default.</a>
+<a name="239"><span class="lineNum">     239 </span>            :   };</a>
+<a name="240"><span class="lineNum">     240 </span>            : };</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : //! Register (X86/X64).</a>
+<a name="243"><span class="lineNum">     243 </span>            : class X86Reg : public Reg {</a>
+<a name="244"><span class="lineNum">     244 </span>            : public:</a>
+<a name="245"><span class="lineNum">     245 </span>            :   //! Register type.</a>
+<a name="246"><span class="lineNum">     246 </span>            :   //!</a>
+<a name="247"><span class="lineNum">     247 </span>            :   //! Don't change these constants; they are essential to some built-in tables.</a>
+<a name="248"><span class="lineNum">     248 </span>            :   ASMJIT_ENUM(RegType) {</a>
+<a name="249"><span class="lineNum">     249 </span>            :     kRegNone      = Reg::kRegNone,       //!&lt; No register type or invalid register.</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :     kRegGpbLo     = Reg::kRegGp8Lo,      //!&lt; Low GPB register (AL, BL, CL, DL, ...).</a>
+<a name="252"><span class="lineNum">     252 </span>            :     kRegGpbHi     = Reg::kRegGp8Hi,      //!&lt; High GPB register (AH, BH, CH, DH only).</a>
+<a name="253"><span class="lineNum">     253 </span>            :     kRegGpw       = Reg::kRegGp16,       //!&lt; GPW register.</a>
+<a name="254"><span class="lineNum">     254 </span>            :     kRegGpd       = Reg::kRegGp32,       //!&lt; GPD register.</a>
+<a name="255"><span class="lineNum">     255 </span>            :     kRegGpq       = Reg::kRegGp64,       //!&lt; GPQ register (X64).</a>
+<a name="256"><span class="lineNum">     256 </span>            :     kRegXmm       = Reg::kRegVec128,     //!&lt; XMM register (SSE+).</a>
+<a name="257"><span class="lineNum">     257 </span>            :     kRegYmm       = Reg::kRegVec256,     //!&lt; YMM register (AVX+).</a>
+<a name="258"><span class="lineNum">     258 </span>            :     kRegZmm       = Reg::kRegVec512,     //!&lt; ZMM register (AVX512+).</a>
+<a name="259"><span class="lineNum">     259 </span>            :     kRegRip       = Reg::kRegIP,         //!&lt; Instruction pointer (EIP, RIP).</a>
+<a name="260"><span class="lineNum">     260 </span>            :     kRegSeg       = Reg::kRegCustom,     //!&lt; Segment register (None, ES, CS, SS, DS, FS, GS).</a>
+<a name="261"><span class="lineNum">     261 </span>            :     kRegFp        = Reg::kRegCustom + 1, //!&lt; FPU (x87) register.</a>
+<a name="262"><span class="lineNum">     262 </span>            :     kRegMm        = Reg::kRegCustom + 2, //!&lt; MMX register.</a>
+<a name="263"><span class="lineNum">     263 </span>            :     kRegK         = Reg::kRegCustom + 3, //!&lt; K register (AVX512+).</a>
+<a name="264"><span class="lineNum">     264 </span>            :     kRegBnd       = Reg::kRegCustom + 4, //!&lt; Bound register (BND).</a>
+<a name="265"><span class="lineNum">     265 </span>            :     kRegCr        = Reg::kRegCustom + 5, //!&lt; Control register (CR).</a>
+<a name="266"><span class="lineNum">     266 </span>            :     kRegDr        = Reg::kRegCustom + 6, //!&lt; Debug register (DR).</a>
+<a name="267"><span class="lineNum">     267 </span>            :     kRegCount                            //!&lt; Count of register types.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   };</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   //! Register kind.</a>
+<a name="271"><span class="lineNum">     271 </span>            :   ASMJIT_ENUM(Kind) {</a>
+<a name="272"><span class="lineNum">     272 </span>            :     kKindGp       = Reg::kKindGp,        //!&lt; GP register kind or none (universal).</a>
+<a name="273"><span class="lineNum">     273 </span>            :     kKindVec      = Reg::kKindVec,       //!&lt; XMM|YMM|ZMM register kind (universal).</a>
+<a name="274"><span class="lineNum">     274 </span>            :     kKindMm       = 2,                   //!&lt; MMX register kind (legacy).</a>
+<a name="275"><span class="lineNum">     275 </span>            :     kKindK        = 3,                   //!&lt; K register kind.</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :     // These are not managed by CodeCompiler nor used by Func-API:</a>
+<a name="278"><span class="lineNum">     278 </span>            :     kKindFp       = 4,                   //!&lt; FPU (x87) register kind.</a>
+<a name="279"><span class="lineNum">     279 </span>            :     kKindCr       = 5,                   //!&lt; Control register kind.</a>
+<a name="280"><span class="lineNum">     280 </span>            :     kKindDr       = 6,                   //!&lt; Debug register kind.</a>
+<a name="281"><span class="lineNum">     281 </span>            :     kKindBnd      = 7,                   //!&lt; Bound register kind.</a>
+<a name="282"><span class="lineNum">     282 </span>            :     kKindSeg      = 8,                   //!&lt; Segment register kind.</a>
+<a name="283"><span class="lineNum">     283 </span>            :     kKindRip      = 9,                   //!&lt; Instrucion pointer (IP).</a>
+<a name="284"><span class="lineNum">     284 </span>            :     kKindCount                           //!&lt; Count of all register kinds.</a>
+<a name="285"><span class="lineNum">     285 </span>            :   };</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :   ASMJIT_DEFINE_ABSTRACT_REG(X86Reg, Reg)</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   //! Get if the register is a GPB register (8-bit).</a>
+<a name="290"><span class="lineNum">     290 </span>            :   ASMJIT_INLINE bool isGpb() const noexcept { return getSize() == 1; }</a>
+<a name="291"><span class="lineNum">     291 </span>            :   //! Get if the register is RIP.</a>
+<a name="292"><span class="lineNum">     292 </span>            :   ASMJIT_INLINE bool isRip() const noexcept { return hasSignature(signatureOf(kRegRip)); }</a>
+<a name="293"><span class="lineNum">     293 </span>            :   //! Get if the register is a segment register.</a>
+<a name="294"><span class="lineNum">     294 </span>            :   ASMJIT_INLINE bool isSeg() const noexcept { return hasSignature(signatureOf(kRegSeg)); }</a>
+<a name="295"><span class="lineNum">     295 </span>            :   //! Get if the register is a low GPB register (8-bit).</a>
+<a name="296"><span class="lineNum">     296 </span>            :   ASMJIT_INLINE bool isGpbLo() const noexcept { return hasSignature(signatureOf(kRegGpbLo)); }</a>
+<a name="297"><span class="lineNum">     297 </span>            :   //! Get if the register is a high GPB register (8-bit).</a>
+<a name="298"><span class="lineNum">     298 </span>            :   ASMJIT_INLINE bool isGpbHi() const noexcept { return hasSignature(signatureOf(kRegGpbHi)); }</a>
+<a name="299"><span class="lineNum">     299 </span>            :   //! Get if the register is a GPW register (16-bit).</a>
+<a name="300"><span class="lineNum">     300 </span>            :   ASMJIT_INLINE bool isGpw() const noexcept { return hasSignature(signatureOf(kRegGpw)); }</a>
+<a name="301"><span class="lineNum">     301 </span>            :   //! Get if the register is a GPD register (32-bit).</a>
+<a name="302"><span class="lineNum">     302 </span>            :   ASMJIT_INLINE bool isGpd() const noexcept { return hasSignature(signatureOf(kRegGpd)); }</a>
+<a name="303"><span class="lineNum">     303 </span>            :   //! Get if the register is a GPQ register (64-bit).</a>
+<a name="304"><span class="lineNum">     304 </span>            :   ASMJIT_INLINE bool isGpq() const noexcept { return hasSignature(signatureOf(kRegGpq)); }</a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! Get if the register is an FPU register (80-bit).</a>
+<a name="306"><span class="lineNum">     306 </span>            :   ASMJIT_INLINE bool isFp() const noexcept { return hasSignature(signatureOf(kRegFp)); }</a>
+<a name="307"><span class="lineNum">     307 </span>            :   //! Get if the register is an MMX register (64-bit).</a>
+<a name="308"><span class="lineNum">     308 </span>            :   ASMJIT_INLINE bool isMm() const noexcept { return hasSignature(signatureOf(kRegMm)); }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   //! Get if the register is a K register (64-bit).</a>
+<a name="310"><span class="lineNum">     310 </span>            :   ASMJIT_INLINE bool isK() const noexcept { return hasSignature(signatureOf(kRegK)); }</a>
+<a name="311"><span class="lineNum">     311 </span>            :   //! Get if the register is an XMM register (128-bit).</a>
+<a name="312"><span class="lineNum">     312 </span>            :   ASMJIT_INLINE bool isXmm() const noexcept { return hasSignature(signatureOf(kRegXmm)); }</a>
+<a name="313"><span class="lineNum">     313 </span>            :   //! Get if the register is a YMM register (256-bit).</a>
+<a name="314"><span class="lineNum">     314 </span>            :   ASMJIT_INLINE bool isYmm() const noexcept { return hasSignature(signatureOf(kRegYmm)); }</a>
+<a name="315"><span class="lineNum">     315 </span>            :   //! Get if the register is a ZMM register (512-bit).</a>
+<a name="316"><span class="lineNum">     316 </span>            :   ASMJIT_INLINE bool isZmm() const noexcept { return hasSignature(signatureOf(kRegZmm)); }</a>
+<a name="317"><span class="lineNum">     317 </span>            :   //! Get if the register is a bound register.</a>
+<a name="318"><span class="lineNum">     318 </span>            :   ASMJIT_INLINE bool isBnd() const noexcept { return hasSignature(signatureOf(kRegBnd)); }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   //! Get if the register is a control register.</a>
+<a name="320"><span class="lineNum">     320 </span>            :   ASMJIT_INLINE bool isCr() const noexcept { return hasSignature(signatureOf(kRegCr)); }</a>
+<a name="321"><span class="lineNum">     321 </span>            :   //! Get if the register is a debug register.</a>
+<a name="322"><span class="lineNum">     322 </span>            :   ASMJIT_INLINE bool isDr() const noexcept { return hasSignature(signatureOf(kRegDr)); }</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            :   template&lt;uint32_t Type&gt;</a>
+<a name="325"><span class="lineNum">     325 </span>            :   ASMJIT_INLINE void setX86RegT(uint32_t rId) noexcept {</a>
+<a name="326"><span class="lineNum">     326 </span>            :     setSignature(X86RegTraits&lt;Type&gt;::kSignature);</a>
+<a name="327"><span class="lineNum">     327 </span>            :     setId(rId);</a>
+<a name="328"><span class="lineNum">     328 </span>            :   }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :   ASMJIT_INLINE void setTypeAndId(uint32_t rType, uint32_t rId) noexcept {</a>
+<a name="331"><span class="lineNum">     331 </span>            :     ASMJIT_ASSERT(rType &lt; kRegCount);</a>
+<a name="332"><span class="lineNum">     332 </span>            :     setSignature(signatureOf(rType));</a>
+<a name="333"><span class="lineNum">     333 </span>            :     setId(rId);</a>
+<a name="334"><span class="lineNum">     334 </span>            :   }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :   static ASMJIT_INLINE uint32_t kindOf(uint32_t rType) noexcept;</a>
+<a name="337"><span class="lineNum">     337 </span>            :   template&lt;uint32_t Type&gt;</a>
+<a name="338"><span class="lineNum">     338 </span>            :   static ASMJIT_INLINE uint32_t kindOfT() noexcept { return X86RegTraits&lt;Type&gt;::kKind; }</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            :   static ASMJIT_INLINE uint32_t signatureOf(uint32_t rType) noexcept;</a>
+<a name="341"><span class="lineNum">     341 </span>            :   template&lt;uint32_t Type&gt;</a>
+<a name="342"><span class="lineNum">     342 </span>            :   static ASMJIT_INLINE uint32_t signatureOfT() noexcept { return X86RegTraits&lt;Type&gt;::kSignature; }</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :   static ASMJIT_INLINE uint32_t signatureOfVecByType(uint32_t typeId) noexcept {</a>
+<a name="345"><span class="lineNum">     345 </span>            :     return typeId &lt;= TypeId::_kVec128End ? signatureOfT&lt;kRegXmm&gt;() :</a>
+<a name="346"><span class="lineNum">     346 </span>            :            typeId &lt;= TypeId::_kVec256End ? signatureOfT&lt;kRegYmm&gt;() : signatureOfT&lt;kRegZmm&gt;() ;</a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   static ASMJIT_INLINE uint32_t signatureOfVecBySize(uint32_t size) noexcept {</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :     return size &lt;= 16 ? signatureOfT&lt;kRegXmm&gt;() :</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :            size &lt;= 32 ? signatureOfT&lt;kRegYmm&gt;() : signatureOfT&lt;kRegZmm&gt;() ;</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   }</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            :   //! Get if the `op` operand is either a low or high 8-bit GPB register.</a>
+<a name="355"><span class="lineNum">     355 </span>            :   static ASMJIT_INLINE bool isGpb(const Operand_&amp; op) noexcept {</a>
+<a name="356"><span class="lineNum">     356 </span>            :     // Check operand type, register kind, and size. Not interested in register type.</a>
+<a name="357"><span class="lineNum">     357 </span>            :     const uint32_t kSgn = (Operand::kOpReg &lt;&lt; kSignatureOpShift  ) |</a>
+<a name="358"><span class="lineNum">     358 </span>            :                           (1               &lt;&lt; kSignatureSizeShift) ;</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :     return (op.getSignature() &amp; (kSignatureOpMask | kSignatureSizeMask)) == kSgn;</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :   }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   static ASMJIT_INLINE bool isRip(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isRip(); }</a>
+<a name="363"><span class="lineNum">     363 </span>            :   static ASMJIT_INLINE bool isSeg(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isSeg(); }</a>
+<a name="364"><span class="lineNum">     364 </span>            :   static ASMJIT_INLINE bool isGpbLo(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isGpbLo(); }</a>
+<a name="365"><span class="lineNum">     365 </span>            :   static ASMJIT_INLINE bool isGpbHi(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isGpbHi(); }</a>
+<a name="366"><span class="lineNum">     366 </span>            :   static ASMJIT_INLINE bool isGpw(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isGpw(); }</a>
+<a name="367"><span class="lineNum">     367 </span>            :   static ASMJIT_INLINE bool isGpd(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isGpd(); }</a>
+<a name="368"><span class="lineNum">     368 </span>            :   static ASMJIT_INLINE bool isGpq(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isGpq(); }</a>
+<a name="369"><span class="lineNum">     369 </span>            :   static ASMJIT_INLINE bool isFp(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isFp(); }</a>
+<a name="370"><span class="lineNum">     370 </span>            :   static ASMJIT_INLINE bool isMm(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isMm(); }</a>
+<a name="371"><span class="lineNum">     371 </span>            :   static ASMJIT_INLINE bool isK(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isK(); }</a>
+<a name="372"><span class="lineNum">     372 </span>            :   static ASMJIT_INLINE bool isXmm(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isXmm(); }</a>
+<a name="373"><span class="lineNum">     373 </span>            :   static ASMJIT_INLINE bool isYmm(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isYmm(); }</a>
+<a name="374"><span class="lineNum">     374 </span>            :   static ASMJIT_INLINE bool isZmm(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isZmm(); }</a>
+<a name="375"><span class="lineNum">     375 </span>            :   static ASMJIT_INLINE bool isBnd(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isBnd(); }</a>
+<a name="376"><span class="lineNum">     376 </span>            :   static ASMJIT_INLINE bool isCr(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isCr(); }</a>
+<a name="377"><span class="lineNum">     377 </span>            :   static ASMJIT_INLINE bool isDr(const Operand_&amp; op) noexcept { return op.as&lt;X86Reg&gt;().isDr(); }</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :   static ASMJIT_INLINE bool isGpb(const Operand_&amp; op, uint32_t rId) noexcept { return isGpb(op) &amp; (op.getId() == rId); }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            :   static ASMJIT_INLINE bool isRip(const Operand_&amp; op, uint32_t rId) noexcept { return isRip(op) &amp; (op.getId() == rId); }</a>
+<a name="382"><span class="lineNum">     382 </span>            :   static ASMJIT_INLINE bool isSeg(const Operand_&amp; op, uint32_t rId) noexcept { return isSeg(op) &amp; (op.getId() == rId); }</a>
+<a name="383"><span class="lineNum">     383 </span>            :   static ASMJIT_INLINE bool isGpbLo(const Operand_&amp; op, uint32_t rId) noexcept { return isGpbLo(op) &amp; (op.getId() == rId); }</a>
+<a name="384"><span class="lineNum">     384 </span>            :   static ASMJIT_INLINE bool isGpbHi(const Operand_&amp; op, uint32_t rId) noexcept { return isGpbHi(op) &amp; (op.getId() == rId); }</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isGpw(const Operand_&amp; op, uint32_t rId) noexcept { return isGpw(op) &amp; (op.getId() == rId); }</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :   static ASMJIT_INLINE bool isGpd(const Operand_&amp; op, uint32_t rId) noexcept { return isGpd(op) &amp; (op.getId() == rId); }</a>
+<a name="387"><span class="lineNum">     387 </span>            :   static ASMJIT_INLINE bool isGpq(const Operand_&amp; op, uint32_t rId) noexcept { return isGpq(op) &amp; (op.getId() == rId); }</a>
+<a name="388"><span class="lineNum">     388 </span>            :   static ASMJIT_INLINE bool isFp(const Operand_&amp; op, uint32_t rId) noexcept { return isFp(op) &amp; (op.getId() == rId); }</a>
+<a name="389"><span class="lineNum">     389 </span>            :   static ASMJIT_INLINE bool isMm(const Operand_&amp; op, uint32_t rId) noexcept { return isMm(op) &amp; (op.getId() == rId); }</a>
+<a name="390"><span class="lineNum">     390 </span>            :   static ASMJIT_INLINE bool isK(const Operand_&amp; op, uint32_t rId) noexcept { return isK(op) &amp; (op.getId() == rId); }</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :   static ASMJIT_INLINE bool isXmm(const Operand_&amp; op, uint32_t rId) noexcept { return isXmm(op) &amp; (op.getId() == rId); }</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   static ASMJIT_INLINE bool isYmm(const Operand_&amp; op, uint32_t rId) noexcept { return isYmm(op) &amp; (op.getId() == rId); }</a>
+<a name="393"><span class="lineNum">     393 </span>            :   static ASMJIT_INLINE bool isZmm(const Operand_&amp; op, uint32_t rId) noexcept { return isZmm(op) &amp; (op.getId() == rId); }</a>
+<a name="394"><span class="lineNum">     394 </span>            :   static ASMJIT_INLINE bool isBnd(const Operand_&amp; op, uint32_t rId) noexcept { return isBnd(op) &amp; (op.getId() == rId); }</a>
+<a name="395"><span class="lineNum">     395 </span>            :   static ASMJIT_INLINE bool isCr(const Operand_&amp; op, uint32_t rId) noexcept { return isCr(op) &amp; (op.getId() == rId); }</a>
+<a name="396"><span class="lineNum">     396 </span>            :   static ASMJIT_INLINE bool isDr(const Operand_&amp; op, uint32_t rId) noexcept { return isDr(op) &amp; (op.getId() == rId); }</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="399"><span class="lineNum">     399 </span>            :   // [Memory Cast]</a>
+<a name="400"><span class="lineNum">     400 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            :   // DEPRECATED in next-wip.</a>
+<a name="403"><span class="lineNum">     403 </span>            :   ASMJIT_INLINE X86Mem m(int32_t disp = 0) const noexcept {</a>
+<a name="404"><span class="lineNum">     404 </span>            :     return X86Mem(*this, disp, getSize(), Mem::kSignatureMemRegHomeFlag);</a>
+<a name="405"><span class="lineNum">     405 </span>            :   }</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   //! \overload</a>
+<a name="408"><span class="lineNum">     408 </span>            :   ASMJIT_INLINE X86Mem m(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="409"><span class="lineNum">     409 </span>            :     return X86Mem(*this, index, shift, disp, getSize(), Mem::kSignatureMemRegHomeFlag);</a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            :   //! Cast this variable to 8-bit memory operand.</a>
+<a name="413"><span class="lineNum">     413 </span>            :   ASMJIT_INLINE X86Mem m8(int32_t disp = 0) const noexcept {</a>
+<a name="414"><span class="lineNum">     414 </span>            :     return X86Mem(*this, disp, 1, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   //! \overload</a>
+<a name="418"><span class="lineNum">     418 </span>            :   ASMJIT_INLINE X86Mem m8(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="419"><span class="lineNum">     419 </span>            :     return X86Mem(*this, index, shift, disp, 1, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            :   //! Cast this variable to 16-bit memory operand.</a>
+<a name="423"><span class="lineNum">     423 </span>            :   ASMJIT_INLINE X86Mem m16(int32_t disp = 0) const noexcept {</a>
+<a name="424"><span class="lineNum">     424 </span>            :     return X86Mem(*this, disp, 2, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="425"><span class="lineNum">     425 </span>            :   }</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :   //! \overload</a>
+<a name="428"><span class="lineNum">     428 </span>            :   ASMJIT_INLINE X86Mem m16(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="429"><span class="lineNum">     429 </span>            :     return X86Mem(*this, index, shift, disp, 2, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="430"><span class="lineNum">     430 </span>            :   }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :   //! Cast this variable to 32-bit memory operand.</a>
+<a name="433"><span class="lineNum">     433 </span>            :   ASMJIT_INLINE X86Mem m32(int32_t disp = 0) const noexcept {</a>
+<a name="434"><span class="lineNum">     434 </span>            :     return X86Mem(*this, disp, 4, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="435"><span class="lineNum">     435 </span>            :   }</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            :   //! \overload</a>
+<a name="438"><span class="lineNum">     438 </span>            :   ASMJIT_INLINE X86Mem m32(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="439"><span class="lineNum">     439 </span>            :     return X86Mem(*this, index, shift, disp, 4, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="440"><span class="lineNum">     440 </span>            :   }</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :   //! Cast this variable to 64-bit memory operand.</a>
+<a name="443"><span class="lineNum">     443 </span>            :   ASMJIT_INLINE X86Mem m64(int32_t disp = 0) const noexcept {</a>
+<a name="444"><span class="lineNum">     444 </span>            :     return X86Mem(*this, disp, 8, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="445"><span class="lineNum">     445 </span>            :   }</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span>            :   //! \overload</a>
+<a name="448"><span class="lineNum">     448 </span>            :   ASMJIT_INLINE X86Mem m64(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="449"><span class="lineNum">     449 </span>            :     return X86Mem(*this, index, shift, disp, 8, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :   //! Cast this variable to 80-bit memory operand (long double).</a>
+<a name="453"><span class="lineNum">     453 </span>            :   ASMJIT_INLINE X86Mem m80(int32_t disp = 0) const noexcept {</a>
+<a name="454"><span class="lineNum">     454 </span>            :     return X86Mem(*this, disp, 10, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="455"><span class="lineNum">     455 </span>            :   }</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   //! \overload</a>
+<a name="458"><span class="lineNum">     458 </span>            :   ASMJIT_INLINE X86Mem m80(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="459"><span class="lineNum">     459 </span>            :     return X86Mem(*this, index, shift, disp, 10, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="460"><span class="lineNum">     460 </span>            :   }</a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            :   //! Cast this variable to 128-bit memory operand.</a>
+<a name="463"><span class="lineNum">     463 </span>            :   ASMJIT_INLINE X86Mem m128(int32_t disp = 0) const noexcept {</a>
+<a name="464"><span class="lineNum">     464 </span>            :     return X86Mem(*this, disp, 16, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="465"><span class="lineNum">     465 </span>            :   }</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span>            :   //! \overload</a>
+<a name="468"><span class="lineNum">     468 </span>            :   ASMJIT_INLINE X86Mem m128(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="469"><span class="lineNum">     469 </span>            :     return X86Mem(*this, index, shift, disp, 16, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="470"><span class="lineNum">     470 </span>            :   }</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :   //! Cast this variable to 256-bit memory operand.</a>
+<a name="473"><span class="lineNum">     473 </span>            :   ASMJIT_INLINE X86Mem m256(int32_t disp = 0) const noexcept {</a>
+<a name="474"><span class="lineNum">     474 </span>            :     return X86Mem(*this, disp, 32, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="475"><span class="lineNum">     475 </span>            :   }</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span>            :   //! \overload</a>
+<a name="478"><span class="lineNum">     478 </span>            :   ASMJIT_INLINE X86Mem m256(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="479"><span class="lineNum">     479 </span>            :     return X86Mem(*this, index, shift, disp, 32, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="480"><span class="lineNum">     480 </span>            :   }</a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span>            :   //! Cast this variable to 256-bit memory operand.</a>
+<a name="483"><span class="lineNum">     483 </span>            :   ASMJIT_INLINE X86Mem m512(int32_t disp = 0) const noexcept {</a>
+<a name="484"><span class="lineNum">     484 </span>            :     return X86Mem(*this, disp, 64, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="485"><span class="lineNum">     485 </span>            :   }</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span>            :   //! \overload</a>
+<a name="488"><span class="lineNum">     488 </span>            :   ASMJIT_INLINE X86Mem m512(const X86Reg&amp; index, uint32_t shift = 0, int32_t disp = 0) const noexcept {</a>
+<a name="489"><span class="lineNum">     489 </span>            :     return X86Mem(*this, index, shift, disp, 64, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="490"><span class="lineNum">     490 </span>            :   };</a>
+<a name="491"><span class="lineNum">     491 </span>            : };</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Gp  , X86Reg::kRegGpbLo, X86Reg::kKindGp , 1 , 16, TypeId::kI8    );</a>
+<a name="494"><span class="lineNum">     494 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Gp  , X86Reg::kRegGpbHi, X86Reg::kKindGp , 1 , 4 , TypeId::kI8    );</a>
+<a name="495"><span class="lineNum">     495 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Gp  , X86Reg::kRegGpw  , X86Reg::kKindGp , 2 , 16, TypeId::kI16   );</a>
+<a name="496"><span class="lineNum">     496 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Gp  , X86Reg::kRegGpd  , X86Reg::kKindGp , 4 , 16, TypeId::kI32   );</a>
+<a name="497"><span class="lineNum">     497 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Gp  , X86Reg::kRegGpq  , X86Reg::kKindGp , 8 , 16, TypeId::kI64   );</a>
+<a name="498"><span class="lineNum">     498 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Xmm , X86Reg::kRegXmm  , X86Reg::kKindVec, 16, 32, TypeId::kI32x4 );</a>
+<a name="499"><span class="lineNum">     499 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Ymm , X86Reg::kRegYmm  , X86Reg::kKindVec, 32, 32, TypeId::kI32x8 );</a>
+<a name="500"><span class="lineNum">     500 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Zmm , X86Reg::kRegZmm  , X86Reg::kKindVec, 64, 32, TypeId::kI32x16);</a>
+<a name="501"><span class="lineNum">     501 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Rip , X86Reg::kRegRip  , X86Reg::kKindRip, 0 , 1 , TypeId::kVoid  );</a>
+<a name="502"><span class="lineNum">     502 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Seg , X86Reg::kRegSeg  , X86Reg::kKindSeg, 2 , 7 , TypeId::kVoid  );</a>
+<a name="503"><span class="lineNum">     503 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Fp  , X86Reg::kRegFp   , X86Reg::kKindFp , 10, 8 , TypeId::kF80   );</a>
+<a name="504"><span class="lineNum">     504 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Mm  , X86Reg::kRegMm   , X86Reg::kKindMm , 8 , 8 , TypeId::kMmx64 );</a>
+<a name="505"><span class="lineNum">     505 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86KReg, X86Reg::kRegK    , X86Reg::kKindK  , 0 , 8 , TypeId::kVoid  );</a>
+<a name="506"><span class="lineNum">     506 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86Bnd , X86Reg::kRegBnd  , X86Reg::kKindBnd, 16, 4 , TypeId::kVoid  );</a>
+<a name="507"><span class="lineNum">     507 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86CReg, X86Reg::kRegCr   , X86Reg::kKindCr , 0 , 16, TypeId::kVoid  );</a>
+<a name="508"><span class="lineNum">     508 </span>            : ASMJIT_DEFINE_REG_TRAITS(X86RegTraits, X86DReg, X86Reg::kRegDr   , X86Reg::kKindDr , 0 , 16, TypeId::kVoid  );</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : //! General purpose register (X86/X64).</a>
+<a name="511"><span class="lineNum">     511 </span>            : class X86Gp : public X86Reg {</a>
+<a name="512"><span class="lineNum">     512 </span>            : public:</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">       1948 :   ASMJIT_DEFINE_ABSTRACT_REG(X86Gp, X86Reg)</span></a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :   //! X86/X64 physical id.</a>
+<a name="516"><span class="lineNum">     516 </span>            :   //!</a>
+<a name="517"><span class="lineNum">     517 </span>            :   //! NOTE: Register indexes have been reduced to only support general purpose</a>
+<a name="518"><span class="lineNum">     518 </span>            :   //! registers. There is no need to have enumerations with number suffix that</a>
+<a name="519"><span class="lineNum">     519 </span>            :   //! expands to the exactly same value as the suffix value itself.</a>
+<a name="520"><span class="lineNum">     520 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="521"><span class="lineNum">     521 </span>            :     kIdAx  = 0,  //!&lt; Physical id of AL|AH|AX|EAX|RAX registers.</a>
+<a name="522"><span class="lineNum">     522 </span>            :     kIdCx  = 1,  //!&lt; Physical id of CL|CH|CX|ECX|RCX registers.</a>
+<a name="523"><span class="lineNum">     523 </span>            :     kIdDx  = 2,  //!&lt; Physical id of DL|DH|DX|EDX|RDX registers.</a>
+<a name="524"><span class="lineNum">     524 </span>            :     kIdBx  = 3,  //!&lt; Physical id of BL|BH|BX|EBX|RBX registers.</a>
+<a name="525"><span class="lineNum">     525 </span>            :     kIdSp  = 4,  //!&lt; Physical id of SPL|SP|ESP|RSP registers.</a>
+<a name="526"><span class="lineNum">     526 </span>            :     kIdBp  = 5,  //!&lt; Physical id of BPL|BP|EBP|RBP registers.</a>
+<a name="527"><span class="lineNum">     527 </span>            :     kIdSi  = 6,  //!&lt; Physical id of SIL|SI|ESI|RSI registers.</a>
+<a name="528"><span class="lineNum">     528 </span>            :     kIdDi  = 7,  //!&lt; Physical id of DIL|DI|EDI|RDI registers.</a>
+<a name="529"><span class="lineNum">     529 </span>            :     kIdR8  = 8,  //!&lt; Physical id of R8B|R8W|R8D|R8 registers (64-bit only).</a>
+<a name="530"><span class="lineNum">     530 </span>            :     kIdR9  = 9,  //!&lt; Physical id of R9B|R9W|R9D|R9 registers (64-bit only).</a>
+<a name="531"><span class="lineNum">     531 </span>            :     kIdR10 = 10, //!&lt; Physical id of R10B|R10W|R10D|R10 registers (64-bit only).</a>
+<a name="532"><span class="lineNum">     532 </span>            :     kIdR11 = 11, //!&lt; Physical id of R11B|R11W|R11D|R11 registers (64-bit only).</a>
+<a name="533"><span class="lineNum">     533 </span>            :     kIdR12 = 12, //!&lt; Physical id of R12B|R12W|R12D|R12 registers (64-bit only).</a>
+<a name="534"><span class="lineNum">     534 </span>            :     kIdR13 = 13, //!&lt; Physical id of R13B|R13W|R13D|R13 registers (64-bit only).</a>
+<a name="535"><span class="lineNum">     535 </span>            :     kIdR14 = 14, //!&lt; Physical id of R14B|R14W|R14D|R14 registers (64-bit only).</a>
+<a name="536"><span class="lineNum">     536 </span>            :     kIdR15 = 15  //!&lt; Physical id of R15B|R15W|R15D|R15 registers (64-bit only).</a>
+<a name="537"><span class="lineNum">     537 </span>            :   };</a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span>            :   //! Cast this register to 8-bit (LO) part.</a>
+<a name="540"><span class="lineNum">     540 </span>            :   ASMJIT_INLINE X86GpbLo r8() const noexcept;</a>
+<a name="541"><span class="lineNum">     541 </span>            :   //! Cast this register to 8-bit (LO) part.</a>
+<a name="542"><span class="lineNum">     542 </span>            :   ASMJIT_INLINE X86GpbLo r8Lo() const noexcept;</a>
+<a name="543"><span class="lineNum">     543 </span>            :   //! Cast this register to 8-bit (HI) part.</a>
+<a name="544"><span class="lineNum">     544 </span>            :   ASMJIT_INLINE X86GpbHi r8Hi() const noexcept;</a>
+<a name="545"><span class="lineNum">     545 </span>            :   //! Cast this register to 16-bit.</a>
+<a name="546"><span class="lineNum">     546 </span>            :   ASMJIT_INLINE X86Gpw r16() const noexcept;</a>
+<a name="547"><span class="lineNum">     547 </span>            :   //! Cast this register to 32-bit.</a>
+<a name="548"><span class="lineNum">     548 </span>            :   ASMJIT_INLINE X86Gpd r32() const noexcept;</a>
+<a name="549"><span class="lineNum">     549 </span>            :   //! Cast this register to 64-bit.</a>
+<a name="550"><span class="lineNum">     550 </span>            :   ASMJIT_INLINE X86Gpq r64() const noexcept;</a>
+<a name="551"><span class="lineNum">     551 </span>            : };</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span>            : //! XMM|YMM|ZMM register (X86/X64).</a>
+<a name="554"><span class="lineNum">     554 </span>            : class X86Vec : public X86Reg {</a>
+<a name="555"><span class="lineNum">     555 </span>            :   ASMJIT_DEFINE_ABSTRACT_REG(X86Vec, X86Reg)</a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span>            :   //! Cast this register to XMM (clone).</a>
+<a name="558"><span class="lineNum">     558 </span>            :   ASMJIT_INLINE X86Xmm xmm() const noexcept;</a>
+<a name="559"><span class="lineNum">     559 </span>            :   //! Cast this register to YMM.</a>
+<a name="560"><span class="lineNum">     560 </span>            :   ASMJIT_INLINE X86Ymm ymm() const noexcept;</a>
+<a name="561"><span class="lineNum">     561 </span>            :   //! Cast this register to ZMM.</a>
+<a name="562"><span class="lineNum">     562 </span>            :   ASMJIT_INLINE X86Zmm zmm() const noexcept;</a>
+<a name="563"><span class="lineNum">     563 </span>            : };</a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span>            : //! Segment register (X86/X64).</a>
+<a name="566"><span class="lineNum">     566 </span>            : class X86Seg : public X86Reg {</a>
+<a name="567"><span class="lineNum">     567 </span>            :   ASMJIT_DEFINE_FINAL_REG(X86Seg, X86Reg, X86RegTraits&lt;kRegSeg&gt;)</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span>            :   //! X86/X64 segment id.</a>
+<a name="570"><span class="lineNum">     570 </span>            :   ASMJIT_ENUM(Id) {</a>
+<a name="571"><span class="lineNum">     571 </span>            :     kIdNone = 0, //!&lt; No segment (default).</a>
+<a name="572"><span class="lineNum">     572 </span>            :     kIdEs   = 1, //!&lt; ES segment.</a>
+<a name="573"><span class="lineNum">     573 </span>            :     kIdCs   = 2, //!&lt; CS segment.</a>
+<a name="574"><span class="lineNum">     574 </span>            :     kIdSs   = 3, //!&lt; SS segment.</a>
+<a name="575"><span class="lineNum">     575 </span>            :     kIdDs   = 4, //!&lt; DS segment.</a>
+<a name="576"><span class="lineNum">     576 </span>            :     kIdFs   = 5, //!&lt; FS segment.</a>
+<a name="577"><span class="lineNum">     577 </span>            :     kIdGs   = 6, //!&lt; GS segment.</a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span>            :     //! Count of X86 segment registers supported by AsmJit.</a>
+<a name="580"><span class="lineNum">     580 </span>            :     //!</a>
+<a name="581"><span class="lineNum">     581 </span>            :     //! NOTE: X86 architecture has 6 segment registers - ES, CS, SS, DS, FS, GS.</a>
+<a name="582"><span class="lineNum">     582 </span>            :     //! X64 architecture lowers them down to just FS and GS. AsmJit supports 7</a>
+<a name="583"><span class="lineNum">     583 </span>            :     //! segment registers - all addressable in both X86 and X64 modes and one</a>
+<a name="584"><span class="lineNum">     584 </span>            :     //! extra called `X86Seg::kIdNone`, which is AsmJit specific and means that</a>
+<a name="585"><span class="lineNum">     585 </span>            :     //! there is no segment register specified.</a>
+<a name="586"><span class="lineNum">     586 </span>            :     kIdCount = 7</a>
+<a name="587"><span class="lineNum">     587 </span>            :   };</a>
+<a name="588"><span class="lineNum">     588 </span>            : };</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span>            : //! GPB (low or high) register (X86/X64).</a>
+<a name="591"><span class="lineNum">     591 </span>            : class X86Gpb : public X86Gp { ASMJIT_DEFINE_ABSTRACT_REG(X86Gpb, X86Gp) };</a>
+<a name="592"><span class="lineNum">     592 </span>            : //! GPB low register (X86/X64).</a>
+<a name="593"><span class="lineNum">     593 </span>            : class X86GpbLo : public X86Gpb { ASMJIT_DEFINE_FINAL_REG(X86GpbLo, X86Gpb, X86RegTraits&lt;kRegGpbLo&gt;) };</a>
+<a name="594"><span class="lineNum">     594 </span>            : //! GPB high register (X86/X64).</a>
+<a name="595"><span class="lineNum">     595 </span>            : class X86GpbHi : public X86Gpb { ASMJIT_DEFINE_FINAL_REG(X86GpbHi, X86Gpb, X86RegTraits&lt;kRegGpbHi&gt;) };</a>
+<a name="596"><span class="lineNum">     596 </span>            : //! GPW register (X86/X64).</a>
+<a name="597"><span class="lineNum">     597 </span>            : class X86Gpw : public X86Gp { ASMJIT_DEFINE_FINAL_REG(X86Gpw, X86Gp, X86RegTraits&lt;kRegGpw&gt;) };</a>
+<a name="598"><span class="lineNum">     598 </span>            : //! GPD register (X86/X64).</a>
+<a name="599"><span class="lineNum">     599 </span>            : class X86Gpd : public X86Gp { ASMJIT_DEFINE_FINAL_REG(X86Gpd, X86Gp, X86RegTraits&lt;kRegGpd&gt;) };</a>
+<a name="600"><span class="lineNum">     600 </span>            : //! GPQ register (X64).</a>
+<a name="601"><span class="lineNum">     601 </span>            : class X86Gpq : public X86Gp { ASMJIT_DEFINE_FINAL_REG(X86Gpq, X86Gp, X86RegTraits&lt;kRegGpq&gt;) };</a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span>            : //! RIP register (X86/X64).</a>
+<a name="604"><span class="lineNum">     604 </span>            : class X86Rip : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86Rip, X86Reg, X86RegTraits&lt;kRegRip&gt;) };</a>
+<a name="605"><span class="lineNum">     605 </span>            : //! 80-bit FPU register (X86/X64).</a>
+<a name="606"><span class="lineNum">     606 </span>            : class X86Fp : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86Fp, X86Reg, X86RegTraits&lt;kRegFp&gt;) };</a>
+<a name="607"><span class="lineNum">     607 </span>            : //! 64-bit MMX register (MMX+).</a>
+<a name="608"><span class="lineNum">     608 </span>            : class X86Mm : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86Mm, X86Reg, X86RegTraits&lt;kRegMm&gt;) };</a>
+<a name="609"><span class="lineNum">     609 </span>            : //! 64-bit K register (AVX512+).</a>
+<a name="610"><span class="lineNum">     610 </span>            : class X86KReg : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86KReg, X86Reg, X86RegTraits&lt;kRegK&gt;) };</a>
+<a name="611"><span class="lineNum">     611 </span>            : //! 128-bit XMM register (SSE+).</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">      16520 : class X86Xmm : public X86Vec { ASMJIT_DEFINE_FINAL_REG(X86Xmm, X86Vec, X86RegTraits&lt;kRegXmm&gt;) };</span></a>
+<a name="613"><span class="lineNum">     613 </span>            : //! 256-bit YMM register (AVX+).</a>
+<a name="614"><span class="lineNum">     614 </span>            : class X86Ymm : public X86Vec { ASMJIT_DEFINE_FINAL_REG(X86Ymm, X86Vec, X86RegTraits&lt;kRegYmm&gt;) };</a>
+<a name="615"><span class="lineNum">     615 </span>            : //! 512-bit ZMM register (AVX512+).</a>
+<a name="616"><span class="lineNum">     616 </span>            : class X86Zmm : public X86Vec { ASMJIT_DEFINE_FINAL_REG(X86Zmm, X86Vec, X86RegTraits&lt;kRegZmm&gt;) };</a>
+<a name="617"><span class="lineNum">     617 </span>            : //! 128-bit BND register (BND+).</a>
+<a name="618"><span class="lineNum">     618 </span>            : class X86Bnd : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86Bnd, X86Reg, X86RegTraits&lt;kRegBnd&gt;) };</a>
+<a name="619"><span class="lineNum">     619 </span>            : //! 32-bit or 64-bit control register (X86/X64).</a>
+<a name="620"><span class="lineNum">     620 </span>            : class X86CReg : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86CReg, X86Reg, X86RegTraits&lt;kRegCr&gt;) };</a>
+<a name="621"><span class="lineNum">     621 </span>            : //! 32-bit or 64-bit debug register (X86/X64).</a>
+<a name="622"><span class="lineNum">     622 </span>            : class X86DReg : public X86Reg { ASMJIT_DEFINE_FINAL_REG(X86DReg, X86Reg, X86RegTraits&lt;kRegDr&gt;) };</a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            : ASMJIT_INLINE X86GpbLo X86Gp::r8() const noexcept { return X86GpbLo(getId()); }</a>
+<a name="625"><span class="lineNum">     625 </span>            : ASMJIT_INLINE X86GpbLo X86Gp::r8Lo() const noexcept { return X86GpbLo(getId()); }</a>
+<a name="626"><span class="lineNum">     626 </span>            : ASMJIT_INLINE X86GpbHi X86Gp::r8Hi() const noexcept { return X86GpbHi(getId()); }</a>
+<a name="627"><span class="lineNum">     627 </span>            : ASMJIT_INLINE X86Gpw X86Gp::r16() const noexcept { return X86Gpw(getId()); }</a>
+<a name="628"><span class="lineNum">     628 </span>            : ASMJIT_INLINE X86Gpd X86Gp::r32() const noexcept { return X86Gpd(getId()); }</a>
+<a name="629"><span class="lineNum">     629 </span>            : ASMJIT_INLINE X86Gpq X86Gp::r64() const noexcept { return X86Gpq(getId()); }</a>
+<a name="630"><span class="lineNum">     630 </span>            : ASMJIT_INLINE X86Xmm X86Vec::xmm() const noexcept { return X86Xmm(*this, getId()); }</a>
+<a name="631"><span class="lineNum">     631 </span>            : ASMJIT_INLINE X86Ymm X86Vec::ymm() const noexcept { return X86Ymm(*this, getId()); }</a>
+<a name="632"><span class="lineNum">     632 </span>            : ASMJIT_INLINE X86Zmm X86Vec::zmm() const noexcept { return X86Zmm(*this, getId()); }</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            : ASMJIT_INLINE X86Seg X86Mem::getSegment() const noexcept { return X86Seg(getSegmentId()); }</a>
+<a name="635"><span class="lineNum">     635 </span>            : ASMJIT_INLINE void X86Mem::setSegment(const X86Seg&amp; seg) noexcept { setSegmentId(seg.getId()); }</a>
+<a name="636"><span class="lineNum">     636 </span>            : </a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Gpb, TypeId::kI8);</a>
+<a name="639"><span class="lineNum">     639 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Gpw, TypeId::kI16);</a>
+<a name="640"><span class="lineNum">     640 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Gpd, TypeId::kI32);</a>
+<a name="641"><span class="lineNum">     641 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Gpq, TypeId::kI64);</a>
+<a name="642"><span class="lineNum">     642 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Mm , TypeId::kMmx64);</a>
+<a name="643"><span class="lineNum">     643 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Xmm, TypeId::kI32x4);</a>
+<a name="644"><span class="lineNum">     644 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Ymm, TypeId::kI32x8);</a>
+<a name="645"><span class="lineNum">     645 </span>            : ASMJIT_DEFINE_TYPE_ID(X86Zmm, TypeId::kI32x16);</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            : // ============================================================================</a>
+<a name="648"><span class="lineNum">     648 </span>            : // [asmjit::X86OpData]</a>
+<a name="649"><span class="lineNum">     649 </span>            : // ============================================================================</a>
+<a name="650"><span class="lineNum">     650 </span>            : </a>
+<a name="651"><span class="lineNum">     651 </span>            : struct X86OpData {</a>
+<a name="652"><span class="lineNum">     652 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="653"><span class="lineNum">     653 </span>            :   // [Signatures]</a>
+<a name="654"><span class="lineNum">     654 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="655"><span class="lineNum">     655 </span>            : </a>
+<a name="656"><span class="lineNum">     656 </span>            :   //! Information about all architecture registers.</a>
+<a name="657"><span class="lineNum">     657 </span>            :   ArchRegs archRegs;</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="660"><span class="lineNum">     660 </span>            :   // [Operands]</a>
+<a name="661"><span class="lineNum">     661 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span>            :   // Prevent calling constructors of these registers when exporting.</a>
+<a name="664"><span class="lineNum">     664 </span>            : #if defined(ASMJIT_EXPORTS_X86_OPERAND)</a>
+<a name="665"><span class="lineNum">     665 </span>            : # define ASMJIT_X86_REG_DATA(REG) Operand_</a>
+<a name="666"><span class="lineNum">     666 </span>            : #else</a>
+<a name="667"><span class="lineNum">     667 </span>            : # define ASMJIT_X86_REG_DATA(REG) REG</a>
+<a name="668"><span class="lineNum">     668 </span>            : #endif</a>
+<a name="669"><span class="lineNum">     669 </span>            :   ASMJIT_X86_REG_DATA(X86Rip ) rip[1];</a>
+<a name="670"><span class="lineNum">     670 </span>            :   ASMJIT_X86_REG_DATA(X86Seg ) seg[7];</a>
+<a name="671"><span class="lineNum">     671 </span>            :   ASMJIT_X86_REG_DATA(X86Gp  ) gpbLo[16];</a>
+<a name="672"><span class="lineNum">     672 </span>            :   ASMJIT_X86_REG_DATA(X86Gp  ) gpbHi[4];</a>
+<a name="673"><span class="lineNum">     673 </span>            :   ASMJIT_X86_REG_DATA(X86Gp  ) gpw[16];</a>
+<a name="674"><span class="lineNum">     674 </span>            :   ASMJIT_X86_REG_DATA(X86Gp  ) gpd[16];</a>
+<a name="675"><span class="lineNum">     675 </span>            :   ASMJIT_X86_REG_DATA(X86Gp  ) gpq[16];</a>
+<a name="676"><span class="lineNum">     676 </span>            :   ASMJIT_X86_REG_DATA(X86Fp  ) fp[8];</a>
+<a name="677"><span class="lineNum">     677 </span>            :   ASMJIT_X86_REG_DATA(X86Mm  ) mm[8];</a>
+<a name="678"><span class="lineNum">     678 </span>            :   ASMJIT_X86_REG_DATA(X86KReg) k[8];</a>
+<a name="679"><span class="lineNum">     679 </span>            :   ASMJIT_X86_REG_DATA(X86Xmm ) xmm[32];</a>
+<a name="680"><span class="lineNum">     680 </span>            :   ASMJIT_X86_REG_DATA(X86Ymm ) ymm[32];</a>
+<a name="681"><span class="lineNum">     681 </span>            :   ASMJIT_X86_REG_DATA(X86Zmm ) zmm[32];</a>
+<a name="682"><span class="lineNum">     682 </span>            :   ASMJIT_X86_REG_DATA(X86Bnd ) bnd[4];</a>
+<a name="683"><span class="lineNum">     683 </span>            :   ASMJIT_X86_REG_DATA(X86CReg) cr[16];</a>
+<a name="684"><span class="lineNum">     684 </span>            :   ASMJIT_X86_REG_DATA(X86DReg) dr[16];</a>
+<a name="685"><span class="lineNum">     685 </span>            : #undef ASMJIT_X86_REG_DATA</a>
+<a name="686"><span class="lineNum">     686 </span>            : };</a>
+<a name="687"><span class="lineNum">     687 </span>            : ASMJIT_VARAPI const X86OpData x86OpData;</a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span>            : // ... X86Reg methods that require `x86OpData`.</a>
+<a name="690"><span class="lineNum">     690 </span>            : ASMJIT_INLINE uint32_t X86Reg::signatureOf(uint32_t rType) noexcept {</a>
+<a name="691"><span class="lineNum">     691 </span>            :   ASMJIT_ASSERT(rType &lt;= Reg::kRegMax);</a>
+<a name="692"><span class="lineNum">     692 </span>            :   return x86OpData.archRegs.regInfo[rType].getSignature();</a>
+<a name="693"><span class="lineNum">     693 </span>            : }</a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span>            : ASMJIT_INLINE uint32_t X86Reg::kindOf(uint32_t rType) noexcept {</a>
+<a name="696"><span class="lineNum">     696 </span>            :   ASMJIT_ASSERT(rType &lt;= Reg::kRegMax);</a>
+<a name="697"><span class="lineNum">     697 </span>            :   return x86OpData.archRegs.regInfo[rType].getKind();</a>
+<a name="698"><span class="lineNum">     698 </span>            : }</a>
+<a name="699"><span class="lineNum">     699 </span>            : </a>
+<a name="700"><span class="lineNum">     700 </span>            : // ============================================================================</a>
+<a name="701"><span class="lineNum">     701 </span>            : // [asmjit::x86]</a>
+<a name="702"><span class="lineNum">     702 </span>            : // ============================================================================</a>
+<a name="703"><span class="lineNum">     703 </span>            : </a>
+<a name="704"><span class="lineNum">     704 </span>            : namespace x86 {</a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            : // ============================================================================</a>
+<a name="707"><span class="lineNum">     707 </span>            : // [asmjit::x86 - Reg]</a>
+<a name="708"><span class="lineNum">     708 </span>            : // ============================================================================</a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span>            : #if !defined(ASMJIT_EXPORTS_X86_OPERAND)</a>
+<a name="711"><span class="lineNum">     711 </span>            : namespace {</a>
+<a name="712"><span class="lineNum">     712 </span>            : #define ASMJIT_X86_PHYS_REG(TYPE, NAME, PROPERTY) \</a>
+<a name="713"><span class="lineNum">     713 </span>            :   static const TYPE&amp; NAME = x86OpData.PROPERTY</a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            : ASMJIT_X86_PHYS_REG(X86Rip , rip  , rip[0]);    //!&lt; RIP register.</a>
+<a name="716"><span class="lineNum">     716 </span>            : ASMJIT_X86_PHYS_REG(X86Seg , es   , seg[1]);    //!&lt; CS segment register.</a>
+<a name="717"><span class="lineNum">     717 </span>            : ASMJIT_X86_PHYS_REG(X86Seg , cs   , seg[2]);    //!&lt; SS segment register.</a>
+<a name="718"><span class="lineNum">     718 </span>            : ASMJIT_X86_PHYS_REG(X86Seg , ss   , seg[3]);    //!&lt; DS segment register.</a>
+<a name="719"><span class="lineNum">     719 </span>            : ASMJIT_X86_PHYS_REG(X86Seg , ds   , seg[4]);    //!&lt; ES segment register.</a>
+<a name="720"><span class="lineNum">     720 </span>            : ASMJIT_X86_PHYS_REG(X86Seg , fs   , seg[5]);    //!&lt; FS segment register.</a>
+<a name="721"><span class="lineNum">     721 </span>            : ASMJIT_X86_PHYS_REG(X86Seg , gs   , seg[6]);    //!&lt; GS segment register.</a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , al   , gpbLo[0]);  //!&lt; 8-bit low GPB register.</a>
+<a name="724"><span class="lineNum">     724 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , cl   , gpbLo[1]);  //!&lt; 8-bit low GPB register.</a>
+<a name="725"><span class="lineNum">     725 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , dl   , gpbLo[2]);  //!&lt; 8-bit low GPB register.</a>
+<a name="726"><span class="lineNum">     726 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , bl   , gpbLo[3]);  //!&lt; 8-bit low GPB register.</a>
+<a name="727"><span class="lineNum">     727 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , spl  , gpbLo[4]);  //!&lt; 8-bit low GPB register (X64).</a>
+<a name="728"><span class="lineNum">     728 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , bpl  , gpbLo[5]);  //!&lt; 8-bit low GPB register (X64).</a>
+<a name="729"><span class="lineNum">     729 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , sil  , gpbLo[6]);  //!&lt; 8-bit low GPB register (X64).</a>
+<a name="730"><span class="lineNum">     730 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , dil  , gpbLo[7]);  //!&lt; 8-bit low GPB register (X64).</a>
+<a name="731"><span class="lineNum">     731 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r8b  , gpbLo[8]);  //!&lt; 8-bit low GPB register (X64).</a>
+<a name="732"><span class="lineNum">     732 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r9b  , gpbLo[9]);  //!&lt; 8-bit low GPB register (X64).</a>
+<a name="733"><span class="lineNum">     733 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r10b , gpbLo[10]); //!&lt; 8-bit low GPB register (X64).</a>
+<a name="734"><span class="lineNum">     734 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r11b , gpbLo[11]); //!&lt; 8-bit low GPB register (X64).</a>
+<a name="735"><span class="lineNum">     735 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r12b , gpbLo[12]); //!&lt; 8-bit low GPB register (X64).</a>
+<a name="736"><span class="lineNum">     736 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r13b , gpbLo[13]); //!&lt; 8-bit low GPB register (X64).</a>
+<a name="737"><span class="lineNum">     737 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r14b , gpbLo[14]); //!&lt; 8-bit low GPB register (X64).</a>
+<a name="738"><span class="lineNum">     738 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r15b , gpbLo[15]); //!&lt; 8-bit low GPB register (X64).</a>
+<a name="739"><span class="lineNum">     739 </span>            : </a>
+<a name="740"><span class="lineNum">     740 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , ah   , gpbHi[0]);  //!&lt; 8-bit high GPB register.</a>
+<a name="741"><span class="lineNum">     741 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , ch   , gpbHi[1]);  //!&lt; 8-bit high GPB register.</a>
+<a name="742"><span class="lineNum">     742 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , dh   , gpbHi[2]);  //!&lt; 8-bit high GPB register.</a>
+<a name="743"><span class="lineNum">     743 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , bh   , gpbHi[3]);  //!&lt; 8-bit high GPB register.</a>
+<a name="744"><span class="lineNum">     744 </span>            : </a>
+<a name="745"><span class="lineNum">     745 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , ax   , gpw[0]);    //!&lt; 16-bit GPW register.</a>
+<a name="746"><span class="lineNum">     746 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , cx   , gpw[1]);    //!&lt; 16-bit GPW register.</a>
+<a name="747"><span class="lineNum">     747 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , dx   , gpw[2]);    //!&lt; 16-bit GPW register.</a>
+<a name="748"><span class="lineNum">     748 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , bx   , gpw[3]);    //!&lt; 16-bit GPW register.</a>
+<a name="749"><span class="lineNum">     749 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , sp   , gpw[4]);    //!&lt; 16-bit GPW register.</a>
+<a name="750"><span class="lineNum">     750 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , bp   , gpw[5]);    //!&lt; 16-bit GPW register.</a>
+<a name="751"><span class="lineNum">     751 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , si   , gpw[6]);    //!&lt; 16-bit GPW register.</a>
+<a name="752"><span class="lineNum">     752 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , di   , gpw[7]);    //!&lt; 16-bit GPW register.</a>
+<a name="753"><span class="lineNum">     753 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r8w  , gpw[8]);    //!&lt; 16-bit GPW register (X64).</a>
+<a name="754"><span class="lineNum">     754 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r9w  , gpw[9]);    //!&lt; 16-bit GPW register (X64).</a>
+<a name="755"><span class="lineNum">     755 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r10w , gpw[10]);   //!&lt; 16-bit GPW register (X64).</a>
+<a name="756"><span class="lineNum">     756 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r11w , gpw[11]);   //!&lt; 16-bit GPW register (X64).</a>
+<a name="757"><span class="lineNum">     757 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r12w , gpw[12]);   //!&lt; 16-bit GPW register (X64).</a>
+<a name="758"><span class="lineNum">     758 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r13w , gpw[13]);   //!&lt; 16-bit GPW register (X64).</a>
+<a name="759"><span class="lineNum">     759 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r14w , gpw[14]);   //!&lt; 16-bit GPW register (X64).</a>
+<a name="760"><span class="lineNum">     760 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r15w , gpw[15]);   //!&lt; 16-bit GPW register (X64).</a>
+<a name="761"><span class="lineNum">     761 </span>            : </a>
+<a name="762"><span class="lineNum">     762 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , eax  , gpd[0]);    //!&lt; 32-bit GPD register.</a>
+<a name="763"><span class="lineNum">     763 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , ecx  , gpd[1]);    //!&lt; 32-bit GPD register.</a>
+<a name="764"><span class="lineNum">     764 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , edx  , gpd[2]);    //!&lt; 32-bit GPD register.</a>
+<a name="765"><span class="lineNum">     765 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , ebx  , gpd[3]);    //!&lt; 32-bit GPD register.</a>
+<a name="766"><span class="lineNum">     766 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , esp  , gpd[4]);    //!&lt; 32-bit GPD register.</a>
+<a name="767"><span class="lineNum">     767 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , ebp  , gpd[5]);    //!&lt; 32-bit GPD register.</a>
+<a name="768"><span class="lineNum">     768 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , esi  , gpd[6]);    //!&lt; 32-bit GPD register.</a>
+<a name="769"><span class="lineNum">     769 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , edi  , gpd[7]);    //!&lt; 32-bit GPD register.</a>
+<a name="770"><span class="lineNum">     770 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r8d  , gpd[8]);    //!&lt; 32-bit GPD register (X64).</a>
+<a name="771"><span class="lineNum">     771 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r9d  , gpd[9]);    //!&lt; 32-bit GPD register (X64).</a>
+<a name="772"><span class="lineNum">     772 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r10d , gpd[10]);   //!&lt; 32-bit GPD register (X64).</a>
+<a name="773"><span class="lineNum">     773 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r11d , gpd[11]);   //!&lt; 32-bit GPD register (X64).</a>
+<a name="774"><span class="lineNum">     774 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r12d , gpd[12]);   //!&lt; 32-bit GPD register (X64).</a>
+<a name="775"><span class="lineNum">     775 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r13d , gpd[13]);   //!&lt; 32-bit GPD register (X64).</a>
+<a name="776"><span class="lineNum">     776 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r14d , gpd[14]);   //!&lt; 32-bit GPD register (X64).</a>
+<a name="777"><span class="lineNum">     777 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r15d , gpd[15]);   //!&lt; 32-bit GPD register (X64).</a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rax  , gpq[0]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="780"><span class="lineNum">     780 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rcx  , gpq[1]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="781"><span class="lineNum">     781 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rdx  , gpq[2]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="782"><span class="lineNum">     782 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rbx  , gpq[3]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="783"><span class="lineNum">     783 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rsp  , gpq[4]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="784"><span class="lineNum">     784 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rbp  , gpq[5]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="785"><span class="lineNum">     785 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rsi  , gpq[6]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="786"><span class="lineNum">     786 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , rdi  , gpq[7]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="787"><span class="lineNum">     787 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r8   , gpq[8]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="788"><span class="lineNum">     788 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r9   , gpq[9]);    //!&lt; 64-bit GPQ register (X64).</a>
+<a name="789"><span class="lineNum">     789 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r10  , gpq[10]);   //!&lt; 64-bit GPQ register (X64).</a>
+<a name="790"><span class="lineNum">     790 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r11  , gpq[11]);   //!&lt; 64-bit GPQ register (X64).</a>
+<a name="791"><span class="lineNum">     791 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r12  , gpq[12]);   //!&lt; 64-bit GPQ register (X64).</a>
+<a name="792"><span class="lineNum">     792 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r13  , gpq[13]);   //!&lt; 64-bit GPQ register (X64).</a>
+<a name="793"><span class="lineNum">     793 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r14  , gpq[14]);   //!&lt; 64-bit GPQ register (X64).</a>
+<a name="794"><span class="lineNum">     794 </span>            : ASMJIT_X86_PHYS_REG(X86Gp  , r15  , gpq[15]);   //!&lt; 64-bit GPQ register (X64).</a>
+<a name="795"><span class="lineNum">     795 </span>            : </a>
+<a name="796"><span class="lineNum">     796 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp0  , fp[0]);     //!&lt; 80-bit FPU register.</a>
+<a name="797"><span class="lineNum">     797 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp1  , fp[1]);     //!&lt; 80-bit FPU register.</a>
+<a name="798"><span class="lineNum">     798 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp2  , fp[2]);     //!&lt; 80-bit FPU register.</a>
+<a name="799"><span class="lineNum">     799 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp3  , fp[3]);     //!&lt; 80-bit FPU register.</a>
+<a name="800"><span class="lineNum">     800 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp4  , fp[4]);     //!&lt; 80-bit FPU register.</a>
+<a name="801"><span class="lineNum">     801 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp5  , fp[5]);     //!&lt; 80-bit FPU register.</a>
+<a name="802"><span class="lineNum">     802 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp6  , fp[6]);     //!&lt; 80-bit FPU register.</a>
+<a name="803"><span class="lineNum">     803 </span>            : ASMJIT_X86_PHYS_REG(X86Fp  , fp7  , fp[7]);     //!&lt; 80-bit FPU register.</a>
+<a name="804"><span class="lineNum">     804 </span>            : </a>
+<a name="805"><span class="lineNum">     805 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm0  , mm[0]);     //!&lt; 64-bit MMX register.</a>
+<a name="806"><span class="lineNum">     806 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm1  , mm[1]);     //!&lt; 64-bit MMX register.</a>
+<a name="807"><span class="lineNum">     807 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm2  , mm[2]);     //!&lt; 64-bit MMX register.</a>
+<a name="808"><span class="lineNum">     808 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm3  , mm[3]);     //!&lt; 64-bit MMX register.</a>
+<a name="809"><span class="lineNum">     809 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm4  , mm[4]);     //!&lt; 64-bit MMX register.</a>
+<a name="810"><span class="lineNum">     810 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm5  , mm[5]);     //!&lt; 64-bit MMX register.</a>
+<a name="811"><span class="lineNum">     811 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm6  , mm[6]);     //!&lt; 64-bit MMX register.</a>
+<a name="812"><span class="lineNum">     812 </span>            : ASMJIT_X86_PHYS_REG(X86Mm  , mm7  , mm[7]);     //!&lt; 64-bit MMX register.</a>
+<a name="813"><span class="lineNum">     813 </span>            : </a>
+<a name="814"><span class="lineNum">     814 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k0   , k[0]);      //!&lt; 64-bit K register.</a>
+<a name="815"><span class="lineNum">     815 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k1   , k[1]);      //!&lt; 64-bit K register.</a>
+<a name="816"><span class="lineNum">     816 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k2   , k[2]);      //!&lt; 64-bit K register.</a>
+<a name="817"><span class="lineNum">     817 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k3   , k[3]);      //!&lt; 64-bit K register.</a>
+<a name="818"><span class="lineNum">     818 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k4   , k[4]);      //!&lt; 64-bit K register.</a>
+<a name="819"><span class="lineNum">     819 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k5   , k[5]);      //!&lt; 64-bit K register.</a>
+<a name="820"><span class="lineNum">     820 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k6   , k[6]);      //!&lt; 64-bit K register.</a>
+<a name="821"><span class="lineNum">     821 </span>            : ASMJIT_X86_PHYS_REG(X86KReg, k7   , k[7]);      //!&lt; 64-bit K register.</a>
+<a name="822"><span class="lineNum">     822 </span>            : </a>
+<a name="823"><span class="lineNum">     823 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm0 , xmm[0]);    //!&lt; 128-bit XMM register.</a>
+<a name="824"><span class="lineNum">     824 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm1 , xmm[1]);    //!&lt; 128-bit XMM register.</a>
+<a name="825"><span class="lineNum">     825 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm2 , xmm[2]);    //!&lt; 128-bit XMM register.</a>
+<a name="826"><span class="lineNum">     826 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm3 , xmm[3]);    //!&lt; 128-bit XMM register.</a>
+<a name="827"><span class="lineNum">     827 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm4 , xmm[4]);    //!&lt; 128-bit XMM register.</a>
+<a name="828"><span class="lineNum">     828 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm5 , xmm[5]);    //!&lt; 128-bit XMM register.</a>
+<a name="829"><span class="lineNum">     829 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm6 , xmm[6]);    //!&lt; 128-bit XMM register.</a>
+<a name="830"><span class="lineNum">     830 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm7 , xmm[7]);    //!&lt; 128-bit XMM register.</a>
+<a name="831"><span class="lineNum">     831 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm8 , xmm[8]);    //!&lt; 128-bit XMM register (X64).</a>
+<a name="832"><span class="lineNum">     832 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm9 , xmm[9]);    //!&lt; 128-bit XMM register (X64).</a>
+<a name="833"><span class="lineNum">     833 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm10, xmm[10]);   //!&lt; 128-bit XMM register (X64).</a>
+<a name="834"><span class="lineNum">     834 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm11, xmm[11]);   //!&lt; 128-bit XMM register (X64).</a>
+<a name="835"><span class="lineNum">     835 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm12, xmm[12]);   //!&lt; 128-bit XMM register (X64).</a>
+<a name="836"><span class="lineNum">     836 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm13, xmm[13]);   //!&lt; 128-bit XMM register (X64).</a>
+<a name="837"><span class="lineNum">     837 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm14, xmm[14]);   //!&lt; 128-bit XMM register (X64).</a>
+<a name="838"><span class="lineNum">     838 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm15, xmm[15]);   //!&lt; 128-bit XMM register (X64).</a>
+<a name="839"><span class="lineNum">     839 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm16, xmm[16]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="840"><span class="lineNum">     840 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm17, xmm[17]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="841"><span class="lineNum">     841 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm18, xmm[18]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="842"><span class="lineNum">     842 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm19, xmm[19]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="843"><span class="lineNum">     843 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm20, xmm[20]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="844"><span class="lineNum">     844 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm21, xmm[21]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="845"><span class="lineNum">     845 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm22, xmm[22]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="846"><span class="lineNum">     846 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm23, xmm[23]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="847"><span class="lineNum">     847 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm24, xmm[24]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="848"><span class="lineNum">     848 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm25, xmm[25]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="849"><span class="lineNum">     849 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm26, xmm[26]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="850"><span class="lineNum">     850 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm27, xmm[27]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="851"><span class="lineNum">     851 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm28, xmm[28]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="852"><span class="lineNum">     852 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm29, xmm[29]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="853"><span class="lineNum">     853 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm30, xmm[30]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="854"><span class="lineNum">     854 </span>            : ASMJIT_X86_PHYS_REG(X86Xmm , xmm31, xmm[31]);   //!&lt; 128-bit XMM register (X64 &amp; AVX512_VL+).</a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm0 , ymm[0]);    //!&lt; 256-bit YMM register.</a>
+<a name="857"><span class="lineNum">     857 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm1 , ymm[1]);    //!&lt; 256-bit YMM register.</a>
+<a name="858"><span class="lineNum">     858 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm2 , ymm[2]);    //!&lt; 256-bit YMM register.</a>
+<a name="859"><span class="lineNum">     859 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm3 , ymm[3]);    //!&lt; 256-bit YMM register.</a>
+<a name="860"><span class="lineNum">     860 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm4 , ymm[4]);    //!&lt; 256-bit YMM register.</a>
+<a name="861"><span class="lineNum">     861 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm5 , ymm[5]);    //!&lt; 256-bit YMM register.</a>
+<a name="862"><span class="lineNum">     862 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm6 , ymm[6]);    //!&lt; 256-bit YMM register.</a>
+<a name="863"><span class="lineNum">     863 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm7 , ymm[7]);    //!&lt; 256-bit YMM register.</a>
+<a name="864"><span class="lineNum">     864 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm8 , ymm[8]);    //!&lt; 256-bit YMM register (X64).</a>
+<a name="865"><span class="lineNum">     865 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm9 , ymm[9]);    //!&lt; 256-bit YMM register (X64).</a>
+<a name="866"><span class="lineNum">     866 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm10, ymm[10]);   //!&lt; 256-bit YMM register (X64).</a>
+<a name="867"><span class="lineNum">     867 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm11, ymm[11]);   //!&lt; 256-bit YMM register (X64).</a>
+<a name="868"><span class="lineNum">     868 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm12, ymm[12]);   //!&lt; 256-bit YMM register (X64).</a>
+<a name="869"><span class="lineNum">     869 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm13, ymm[13]);   //!&lt; 256-bit YMM register (X64).</a>
+<a name="870"><span class="lineNum">     870 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm14, ymm[14]);   //!&lt; 256-bit YMM register (X64).</a>
+<a name="871"><span class="lineNum">     871 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm15, ymm[15]);   //!&lt; 256-bit YMM register (X64).</a>
+<a name="872"><span class="lineNum">     872 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm16, ymm[16]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="873"><span class="lineNum">     873 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm17, ymm[17]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="874"><span class="lineNum">     874 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm18, ymm[18]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="875"><span class="lineNum">     875 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm19, ymm[19]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="876"><span class="lineNum">     876 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm20, ymm[20]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="877"><span class="lineNum">     877 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm21, ymm[21]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="878"><span class="lineNum">     878 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm22, ymm[22]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="879"><span class="lineNum">     879 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm23, ymm[23]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="880"><span class="lineNum">     880 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm24, ymm[24]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="881"><span class="lineNum">     881 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm25, ymm[25]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="882"><span class="lineNum">     882 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm26, ymm[26]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="883"><span class="lineNum">     883 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm27, ymm[27]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="884"><span class="lineNum">     884 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm28, ymm[28]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="885"><span class="lineNum">     885 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm29, ymm[29]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="886"><span class="lineNum">     886 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm30, ymm[30]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="887"><span class="lineNum">     887 </span>            : ASMJIT_X86_PHYS_REG(X86Ymm , ymm31, ymm[31]);   //!&lt; 256-bit YMM register (X64 &amp; AVX512_VL+).</a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm0 , zmm[0]);    //!&lt; 512-bit ZMM register.</a>
+<a name="890"><span class="lineNum">     890 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm1 , zmm[1]);    //!&lt; 512-bit ZMM register.</a>
+<a name="891"><span class="lineNum">     891 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm2 , zmm[2]);    //!&lt; 512-bit ZMM register.</a>
+<a name="892"><span class="lineNum">     892 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm3 , zmm[3]);    //!&lt; 512-bit ZMM register.</a>
+<a name="893"><span class="lineNum">     893 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm4 , zmm[4]);    //!&lt; 512-bit ZMM register.</a>
+<a name="894"><span class="lineNum">     894 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm5 , zmm[5]);    //!&lt; 512-bit ZMM register.</a>
+<a name="895"><span class="lineNum">     895 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm6 , zmm[6]);    //!&lt; 512-bit ZMM register.</a>
+<a name="896"><span class="lineNum">     896 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm7 , zmm[7]);    //!&lt; 512-bit ZMM register.</a>
+<a name="897"><span class="lineNum">     897 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm8 , zmm[8]);    //!&lt; 512-bit ZMM register (X64).</a>
+<a name="898"><span class="lineNum">     898 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm9 , zmm[9]);    //!&lt; 512-bit ZMM register (X64).</a>
+<a name="899"><span class="lineNum">     899 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm10, zmm[10]);   //!&lt; 512-bit ZMM register (X64).</a>
+<a name="900"><span class="lineNum">     900 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm11, zmm[11]);   //!&lt; 512-bit ZMM register (X64).</a>
+<a name="901"><span class="lineNum">     901 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm12, zmm[12]);   //!&lt; 512-bit ZMM register (X64).</a>
+<a name="902"><span class="lineNum">     902 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm13, zmm[13]);   //!&lt; 512-bit ZMM register (X64).</a>
+<a name="903"><span class="lineNum">     903 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm14, zmm[14]);   //!&lt; 512-bit ZMM register (X64).</a>
+<a name="904"><span class="lineNum">     904 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm15, zmm[15]);   //!&lt; 512-bit ZMM register (X64).</a>
+<a name="905"><span class="lineNum">     905 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm16, zmm[16]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="906"><span class="lineNum">     906 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm17, zmm[17]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="907"><span class="lineNum">     907 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm18, zmm[18]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="908"><span class="lineNum">     908 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm19, zmm[19]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="909"><span class="lineNum">     909 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm20, zmm[20]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="910"><span class="lineNum">     910 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm21, zmm[21]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="911"><span class="lineNum">     911 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm22, zmm[22]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="912"><span class="lineNum">     912 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm23, zmm[23]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="913"><span class="lineNum">     913 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm24, zmm[24]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="914"><span class="lineNum">     914 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm25, zmm[25]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="915"><span class="lineNum">     915 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm26, zmm[26]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="916"><span class="lineNum">     916 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm27, zmm[27]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="917"><span class="lineNum">     917 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm28, zmm[28]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="918"><span class="lineNum">     918 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm29, zmm[29]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="919"><span class="lineNum">     919 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm30, zmm[30]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="920"><span class="lineNum">     920 </span>            : ASMJIT_X86_PHYS_REG(X86Zmm , zmm31, zmm[31]);   //!&lt; 512-bit ZMM register (X64 &amp; AVX512_F+).</a>
+<a name="921"><span class="lineNum">     921 </span>            : </a>
+<a name="922"><span class="lineNum">     922 </span>            : ASMJIT_X86_PHYS_REG(X86Bnd , bnd0 , bnd[0]);    //!&lt; 128-bit bound register.</a>
+<a name="923"><span class="lineNum">     923 </span>            : ASMJIT_X86_PHYS_REG(X86Bnd , bnd1 , bnd[1]);    //!&lt; 128-bit bound register.</a>
+<a name="924"><span class="lineNum">     924 </span>            : ASMJIT_X86_PHYS_REG(X86Bnd , bnd2 , bnd[2]);    //!&lt; 128-bit bound register.</a>
+<a name="925"><span class="lineNum">     925 </span>            : ASMJIT_X86_PHYS_REG(X86Bnd , bnd3 , bnd[3]);    //!&lt; 128-bit bound register.</a>
+<a name="926"><span class="lineNum">     926 </span>            : </a>
+<a name="927"><span class="lineNum">     927 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr0  , cr[0]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="928"><span class="lineNum">     928 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr1  , cr[1]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="929"><span class="lineNum">     929 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr2  , cr[2]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="930"><span class="lineNum">     930 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr3  , cr[3]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="931"><span class="lineNum">     931 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr4  , cr[4]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="932"><span class="lineNum">     932 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr5  , cr[5]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="933"><span class="lineNum">     933 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr6  , cr[6]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="934"><span class="lineNum">     934 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr7  , cr[7]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="935"><span class="lineNum">     935 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr8  , cr[8]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="936"><span class="lineNum">     936 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr9  , cr[9]);     //!&lt; 32-bit or 64-bit control register.</a>
+<a name="937"><span class="lineNum">     937 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr10 , cr[10]);    //!&lt; 32-bit or 64-bit control register.</a>
+<a name="938"><span class="lineNum">     938 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr11 , cr[11]);    //!&lt; 32-bit or 64-bit control register.</a>
+<a name="939"><span class="lineNum">     939 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr12 , cr[12]);    //!&lt; 32-bit or 64-bit control register.</a>
+<a name="940"><span class="lineNum">     940 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr13 , cr[13]);    //!&lt; 32-bit or 64-bit control register.</a>
+<a name="941"><span class="lineNum">     941 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr14 , cr[14]);    //!&lt; 32-bit or 64-bit control register.</a>
+<a name="942"><span class="lineNum">     942 </span>            : ASMJIT_X86_PHYS_REG(X86CReg, cr15 , cr[15]);    //!&lt; 32-bit or 64-bit control register.</a>
+<a name="943"><span class="lineNum">     943 </span>            : </a>
+<a name="944"><span class="lineNum">     944 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr0  , dr[0]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="945"><span class="lineNum">     945 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr1  , dr[1]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="946"><span class="lineNum">     946 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr2  , dr[2]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="947"><span class="lineNum">     947 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr3  , dr[3]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="948"><span class="lineNum">     948 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr4  , dr[4]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="949"><span class="lineNum">     949 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr5  , dr[5]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="950"><span class="lineNum">     950 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr6  , dr[6]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="951"><span class="lineNum">     951 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr7  , dr[7]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="952"><span class="lineNum">     952 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr8  , dr[8]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="953"><span class="lineNum">     953 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr9  , dr[9]);     //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="954"><span class="lineNum">     954 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr10 , dr[10]);    //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="955"><span class="lineNum">     955 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr11 , dr[11]);    //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="956"><span class="lineNum">     956 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr12 , dr[12]);    //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="957"><span class="lineNum">     957 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr13 , dr[13]);    //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="958"><span class="lineNum">     958 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr14 , dr[14]);    //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="959"><span class="lineNum">     959 </span>            : ASMJIT_X86_PHYS_REG(X86DReg, dr15 , dr[15]);    //!&lt; 32-bit or 64-bit debug register.</a>
+<a name="960"><span class="lineNum">     960 </span>            : </a>
+<a name="961"><span class="lineNum">     961 </span>            : #undef ASMJIT_X86_PHYS_REG</a>
+<a name="962"><span class="lineNum">     962 </span>            : } // anonymous namespace</a>
+<a name="963"><span class="lineNum">     963 </span>            : #endif // !ASMJIT_EXPORTS_X86_OPERAND</a>
+<a name="964"><span class="lineNum">     964 </span>            : </a>
+<a name="965"><span class="lineNum">     965 </span>            : //! Create an 8-bit low GPB register operand.</a>
+<a name="966"><span class="lineNum">     966 </span>            : static ASMJIT_INLINE X86GpbLo gpb(uint32_t rId) noexcept { return X86GpbLo(rId); }</a>
+<a name="967"><span class="lineNum">     967 </span>            : //! Create an 8-bit low GPB register operand.</a>
+<a name="968"><span class="lineNum">     968 </span>            : static ASMJIT_INLINE X86GpbLo gpb_lo(uint32_t rId) noexcept { return X86GpbLo(rId); }</a>
+<a name="969"><span class="lineNum">     969 </span>            : //! Create an 8-bit high GPB register operand.</a>
+<a name="970"><span class="lineNum">     970 </span>            : static ASMJIT_INLINE X86GpbHi gpb_hi(uint32_t rId) noexcept { return X86GpbHi(rId); }</a>
+<a name="971"><span class="lineNum">     971 </span>            : //! Create a 16-bit GPW register operand.</a>
+<a name="972"><span class="lineNum">     972 </span>            : static ASMJIT_INLINE X86Gpw gpw(uint32_t rId) noexcept { return X86Gpw(rId); }</a>
+<a name="973"><span class="lineNum">     973 </span>            : //! Create a 32-bit GPD register operand.</a>
+<a name="974"><span class="lineNum">     974 </span>            : static ASMJIT_INLINE X86Gpd gpd(uint32_t rId) noexcept { return X86Gpd(rId); }</a>
+<a name="975"><span class="lineNum">     975 </span>            : //! Create a 64-bit GPQ register operand (X64).</a>
+<a name="976"><span class="lineNum">     976 </span>            : static ASMJIT_INLINE X86Gpq gpq(uint32_t rId) noexcept { return X86Gpq(rId); }</a>
+<a name="977"><span class="lineNum">     977 </span>            : //! Create an 80-bit Fp register operand.</a>
+<a name="978"><span class="lineNum">     978 </span>            : static ASMJIT_INLINE X86Fp fp(uint32_t rId) noexcept { return X86Fp(rId); }</a>
+<a name="979"><span class="lineNum">     979 </span>            : //! Create a 64-bit Mm register operand.</a>
+<a name="980"><span class="lineNum">     980 </span>            : static ASMJIT_INLINE X86Mm mm(uint32_t rId) noexcept { return X86Mm(rId); }</a>
+<a name="981"><span class="lineNum">     981 </span>            : //! Create a 64-bit K register operand.</a>
+<a name="982"><span class="lineNum">     982 </span>            : static ASMJIT_INLINE X86KReg k(uint32_t rId) noexcept { return X86KReg(rId); }</a>
+<a name="983"><span class="lineNum">     983 </span>            : //! Create a 128-bit XMM register operand.</a>
+<a name="984"><span class="lineNum">     984 </span>            : static ASMJIT_INLINE X86Xmm xmm(uint32_t rId) noexcept { return X86Xmm(rId); }</a>
+<a name="985"><span class="lineNum">     985 </span>            : //! Create a 256-bit YMM register operand.</a>
+<a name="986"><span class="lineNum">     986 </span>            : static ASMJIT_INLINE X86Ymm ymm(uint32_t rId) noexcept { return X86Ymm(rId); }</a>
+<a name="987"><span class="lineNum">     987 </span>            : //! Create a 512-bit ZMM register operand.</a>
+<a name="988"><span class="lineNum">     988 </span>            : static ASMJIT_INLINE X86Zmm zmm(uint32_t rId) noexcept { return X86Zmm(rId); }</a>
+<a name="989"><span class="lineNum">     989 </span>            : //! Create a 128-bit bound register operand.</a>
+<a name="990"><span class="lineNum">     990 </span>            : static ASMJIT_INLINE X86Bnd bnd(uint32_t rId) noexcept { return X86Bnd(rId); }</a>
+<a name="991"><span class="lineNum">     991 </span>            : //! Create a 32-bit or 64-bit control register operand.</a>
+<a name="992"><span class="lineNum">     992 </span>            : static ASMJIT_INLINE X86CReg cr(uint32_t rId) noexcept { return X86CReg(rId); }</a>
+<a name="993"><span class="lineNum">     993 </span>            : //! Create a 32-bit or 64-bit debug register operand.</a>
+<a name="994"><span class="lineNum">     994 </span>            : static ASMJIT_INLINE X86DReg dr(uint32_t rId) noexcept { return X86DReg(rId); }</a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span>            : // ============================================================================</a>
+<a name="997"><span class="lineNum">     997 </span>            : // [asmjit::x86 - Ptr (Reg)]</a>
+<a name="998"><span class="lineNum">     998 </span>            : // ============================================================================</a>
+<a name="999"><span class="lineNum">     999 </span>            : </a>
+<a name="1000"><span class="lineNum">    1000 </span>            : //! Create a `[base.reg + offset]` memory operand.</a>
+<a name="1001"><span class="lineNum">    1001 </span>            : static ASMJIT_INLINE X86Mem ptr(const X86Gp&amp; base, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :   return X86Mem(base, offset, size);</a>
+<a name="1003"><span class="lineNum">    1003 </span>            : }</a>
+<a name="1004"><span class="lineNum">    1004 </span>            : //! Create a `[base.reg + (index &lt;&lt; shift) + offset]` memory operand (scalar index).</a>
+<a name="1005"><span class="lineNum">    1005 </span>            : static ASMJIT_INLINE X86Mem ptr(const X86Gp&amp; base, const X86Gp&amp; index, uint32_t shift = 0, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   return X86Mem(base, index, shift, offset, size);</a>
+<a name="1007"><span class="lineNum">    1007 </span>            : }</a>
+<a name="1008"><span class="lineNum">    1008 </span>            : //! Create a `[base.reg + (index &lt;&lt; shift) + offset]` memory operand (vector index).</a>
+<a name="1009"><span class="lineNum">    1009 </span>            : static ASMJIT_INLINE X86Mem ptr(const X86Gp&amp; base, const X86Vec&amp; index, uint32_t shift = 0, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   return X86Mem(base, index, shift, offset, size);</a>
+<a name="1011"><span class="lineNum">    1011 </span>            : }</a>
+<a name="1012"><span class="lineNum">    1012 </span>            : </a>
+<a name="1013"><span class="lineNum">    1013 </span>            : //! Create a `[base + offset]` memory operand.</a>
+<a name="1014"><span class="lineNum">    1014 </span>            : static ASMJIT_INLINE X86Mem ptr(const Label&amp; base, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   return X86Mem(base, offset, size);</a>
+<a name="1016"><span class="lineNum">    1016 </span>            : }</a>
+<a name="1017"><span class="lineNum">    1017 </span>            : //! Create a `[base + (index &lt;&lt; shift) + offset]` memory operand.</a>
+<a name="1018"><span class="lineNum">    1018 </span>            : static ASMJIT_INLINE X86Mem ptr(const Label&amp; base, const X86Gp&amp; index, uint32_t shift, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   return X86Mem(base, index, shift, offset, size);</a>
+<a name="1020"><span class="lineNum">    1020 </span>            : }</a>
+<a name="1021"><span class="lineNum">    1021 </span>            : //! Create a `[base + (index &lt;&lt; shift) + offset]` memory operand.</a>
+<a name="1022"><span class="lineNum">    1022 </span>            : static ASMJIT_INLINE X86Mem ptr(const Label&amp; base, const X86Vec&amp; index, uint32_t shift, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :   return X86Mem(base, index, shift, offset, size);</a>
+<a name="1024"><span class="lineNum">    1024 </span>            : }</a>
+<a name="1025"><span class="lineNum">    1025 </span>            : </a>
+<a name="1026"><span class="lineNum">    1026 </span>            : //! Create `[rip + offset]` memory operand.</a>
+<a name="1027"><span class="lineNum">    1027 </span>            : static ASMJIT_INLINE X86Mem ptr(const X86Rip&amp; rip_, int32_t offset = 0, uint32_t size = 0) noexcept {</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :   return X86Mem(rip_, offset, size);</a>
+<a name="1029"><span class="lineNum">    1029 </span>            : }</a>
+<a name="1030"><span class="lineNum">    1030 </span>            : </a>
+<a name="1031"><span class="lineNum">    1031 </span>            : //! Create an `[base]` absolute memory operand.</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : static ASMJIT_INLINE X86Mem ptr(uint64_t base, uint32_t size = 0) noexcept {</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   return X86Mem(base, size);</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : }</a>
+<a name="1035"><span class="lineNum">    1035 </span>            : //! Create an `[abs + (index.reg &lt;&lt; shift)]` absolute memory operand.</a>
+<a name="1036"><span class="lineNum">    1036 </span>            : static ASMJIT_INLINE X86Mem ptr(uint64_t base, const X86Reg&amp; index, uint32_t shift = 0, uint32_t size = 0) noexcept {</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :   return X86Mem(base, index, shift, size);</a>
+<a name="1038"><span class="lineNum">    1038 </span>            : }</a>
+<a name="1039"><span class="lineNum">    1039 </span>            : //! Create an `[abs + (index.reg &lt;&lt; shift)]` absolute memory operand.</a>
+<a name="1040"><span class="lineNum">    1040 </span>            : static ASMJIT_INLINE X86Mem ptr(uint64_t base, const X86Vec&amp; index, uint32_t shift = 0, uint32_t size = 0) noexcept {</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   return X86Mem(base, index, shift, size);</a>
+<a name="1042"><span class="lineNum">    1042 </span>            : }</a>
+<a name="1043"><span class="lineNum">    1043 </span>            : </a>
+<a name="1044"><span class="lineNum">    1044 </span>            : //! \internal</a>
+<a name="1045"><span class="lineNum">    1045 </span>            : #define ASMJIT_X86_PTR_FN(FUNC, SIZE)                                                 \</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :   /*! Create a `[base + offset]` memory operand. */                                   \</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   static ASMJIT_INLINE X86Mem FUNC(const X86Gp&amp; base, int32_t offset = 0) noexcept {  \</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     return X86Mem(base, offset, SIZE);                                                \</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :   }                                                                                   \</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   /*! Create a `[base + (index &lt;&lt; shift) + offset]` memory operand. */                \</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   static ASMJIT_INLINE X86Mem FUNC(const X86Gp&amp; base, const X86Gp&amp; index, uint32_t shift = 0, int32_t offset = 0) noexcept { \</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :     return X86Mem(base, index, shift, offset, SIZE);                                  \</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   }                                                                                   \</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   /*! Create a `[base + (vec_index &lt;&lt; shift) + offset]` memory operand. */            \</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   static ASMJIT_INLINE X86Mem FUNC(const X86Gp&amp; base, const X86Vec&amp; index, uint32_t shift = 0, int32_t offset = 0) noexcept { \</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :     return X86Mem(base, index, shift, offset, SIZE);                                  \</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   }                                                                                   \</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   /*! Create a `[base + offset]` memory operand. */                                   \</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   static ASMJIT_INLINE X86Mem FUNC(const Label&amp; base, int32_t offset = 0) noexcept {  \</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     return X86Mem(base, offset, SIZE);                                                \</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   }                                                                                   \</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   /*! Create a `[base + (index &lt;&lt; shift) + offset]` memory operand. */                \</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   static ASMJIT_INLINE X86Mem FUNC(const Label&amp; base, const X86Gp&amp; index, uint32_t shift, int32_t offset = 0) noexcept { \</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     return X86Mem(base, index, shift, offset, SIZE);                                  \</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   }                                                                                   \</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :   /*! Create a `[rip + offset]` memory operand. */                                    \</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   static ASMJIT_INLINE X86Mem FUNC(const X86Rip&amp; rip_, int32_t offset = 0) noexcept { \</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     return X86Mem(rip_, offset, SIZE);                                                \</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :   }                                                                                   \</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   /*! Create a `[base + offset]` memory operand. */                                   \</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   static ASMJIT_INLINE X86Mem FUNC(uint64_t base) noexcept {                          \</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     return X86Mem(base, SIZE);                                                        \</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   }                                                                                   \</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   /*! Create a `[base + (index &lt;&lt; shift) + offset]` memory operand. */                \</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   static ASMJIT_INLINE X86Mem FUNC(uint64_t base, const X86Gp&amp; index, uint32_t shift = 0) noexcept { \</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :     return X86Mem(base, index, shift, SIZE);                                          \</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   }                                                                                   \</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :   /*! Create a `[base + (vec_index &lt;&lt; shift) + offset]` memory operand. */            \</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   static ASMJIT_INLINE X86Mem FUNC(uint64_t base, const X86Vec&amp; index, uint32_t shift = 0) noexcept { \</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     return X86Mem(base, index, shift, SIZE, Mem::kSignatureMemAbs);                   \</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   }                                                                                   \</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   /*! Create a `[base + offset]` memory operand. */                                   \</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   static ASMJIT_INLINE X86Mem FUNC##_abs(uint64_t base) noexcept {                    \</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :     return X86Mem(base, SIZE);                                                        \</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   }                                                                                   \</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   /*! Create a `[base + (index &lt;&lt; shift) + offset]` memory operand. */                \</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :   static ASMJIT_INLINE X86Mem FUNC##_abs(uint64_t base, const X86Gp&amp; index, uint32_t shift = 0) noexcept { \</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     return X86Mem(base, index, shift, SIZE, Mem::kSignatureMemAbs);                   \</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :   }                                                                                   \</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   /*! Create a `[base + (vec_index &lt;&lt; shift) + offset]` memory operand. */            \</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   static ASMJIT_INLINE X86Mem FUNC##_abs(uint64_t base, const X86Vec&amp; index, uint32_t shift = 0) noexcept { \</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :     return X86Mem(base, index, shift, SIZE, Mem::kSignatureMemAbs);                   \</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   }</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            : // Define memory operand constructors that use platform independent naming.</a>
+<a name="1096"><span class="lineNum">    1096 </span>            : ASMJIT_X86_PTR_FN(ptr_8, 1)</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : ASMJIT_X86_PTR_FN(ptr_16, 2)</a>
+<a name="1098"><span class="lineNum">    1098 </span>            : ASMJIT_X86_PTR_FN(ptr_32, 4)</a>
+<a name="1099"><span class="lineNum">    1099 </span>            : ASMJIT_X86_PTR_FN(ptr_48, 6)</a>
+<a name="1100"><span class="lineNum">    1100 </span>            : ASMJIT_X86_PTR_FN(ptr_64, 8)</a>
+<a name="1101"><span class="lineNum">    1101 </span>            : ASMJIT_X86_PTR_FN(ptr_80, 10)</a>
+<a name="1102"><span class="lineNum">    1102 </span>            : ASMJIT_X86_PTR_FN(ptr_128, 16)</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : ASMJIT_X86_PTR_FN(ptr_256, 32)</a>
+<a name="1104"><span class="lineNum">    1104 </span>            : ASMJIT_X86_PTR_FN(ptr_512, 64)</a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span>            : // Define memory operand constructors that use X86/X64 specific naming.</a>
+<a name="1107"><span class="lineNum">    1107 </span>            : ASMJIT_X86_PTR_FN(byte_ptr, 1)</a>
+<a name="1108"><span class="lineNum">    1108 </span>            : ASMJIT_X86_PTR_FN(word_ptr, 2)</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : ASMJIT_X86_PTR_FN(dword_ptr, 4)</a>
+<a name="1110"><span class="lineNum">    1110 </span>            : ASMJIT_X86_PTR_FN(qword_ptr, 8)</a>
+<a name="1111"><span class="lineNum">    1111 </span>            : ASMJIT_X86_PTR_FN(tword_ptr, 10)</a>
+<a name="1112"><span class="lineNum">    1112 </span>            : ASMJIT_X86_PTR_FN(oword_ptr, 16)</a>
+<a name="1113"><span class="lineNum">    1113 </span>            : ASMJIT_X86_PTR_FN(dqword_ptr, 16)</a>
+<a name="1114"><span class="lineNum">    1114 </span>            : ASMJIT_X86_PTR_FN(yword_ptr, 32)</a>
+<a name="1115"><span class="lineNum">    1115 </span>            : ASMJIT_X86_PTR_FN(zword_ptr, 64)</a>
+<a name="1116"><span class="lineNum">    1116 </span>            : </a>
+<a name="1117"><span class="lineNum">    1117 </span>            : #undef ASMJIT_X86_PTR_FN</a>
+<a name="1118"><span class="lineNum">    1118 </span>            : </a>
+<a name="1119"><span class="lineNum">    1119 </span>            : } // x86 namespace</a>
+<a name="1120"><span class="lineNum">    1120 </span>            : </a>
+<a name="1121"><span class="lineNum">    1121 </span>            : //! \}</a>
+<a name="1122"><span class="lineNum">    1122 </span>            : </a>
+<a name="1123"><span class="lineNum">    1123 </span>            : } // asmjit namespace</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : } // namespace PLMD</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : </a>
+<a name="1126"><span class="lineNum">    1126 </span>            : // [Api-End]</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="1128"><span class="lineNum">    1128 </span>            : </a>
+<a name="1129"><span class="lineNum">    1129 </span>            : // [Guard]</a>
+<a name="1130"><span class="lineNum">    1130 </span>            : #endif // _ASMJIT_X86_X86OPERAND_H</a>
+<a name="1131"><span class="lineNum">    1131 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1132"><span class="lineNum">    1132 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="1133"><span class="lineNum">    1133 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86regalloc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86regalloc.cpp<span style="font-size: 80%;"> (<a href="x86regalloc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">466</td>
+            <td class="headerCovTableEntry">1055</td>
+            <td class="headerCovTableEntryLo">44.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">29</td>
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
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+              <td class="coverFnHi">1948</td>
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+              <td class="coverFnHi">1948</td>
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+              <td class="coverFnHi">1948</td>
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+              <td class="coverFnHi">32806</td>
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+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#2413">_ZN4PLMD6asmjit11X86VarAlloc3runEPNS0_6CBNodeE</a></td>
+              <td class="coverFnHi">35054</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86regalloc.cpp.func.html b/coverage-libs/asmjit/x86regalloc.cpp.func.html
new file mode 100644
index 0000000000..dc717e392e
--- /dev/null
+++ b/coverage-libs/asmjit/x86regalloc.cpp.func.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86regalloc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86regalloc.cpp<span style="font-size: 80%;"> (<a href="x86regalloc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">466</td>
+            <td class="headerCovTableEntry">1055</td>
+            <td class="headerCovTableEntryLo">44.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryLo">58.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86regalloc.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#2413">_ZN4PLMD6asmjit11X86VarAlloc3runEPNS0_6CBNodeE</a></td>
+              <td class="coverFnHi">35054</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3090">_ZN4PLMD6asmjit12X86CallAlloc3runEPNS0_10CCFuncCallE</a></td>
+              <td class="coverFnHi">1648</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#278">_ZN4PLMD6asmjit9X86RAPass10emitSwapGpEPNS0_7VirtRegES3_jjPKc</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#639">_ZN4PLMD6asmjit9X86RAPass11_checkStateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">420</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#350">_ZN4PLMD6asmjit9X86RAPass14emitImmToStackEjPKNS0_6X86MemEPKNS0_3ImmE</a></td>
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+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#1257">_ZN4PLMD6asmjit9X86RAPass5fetchEv</a></td>
+              <td class="coverFnHi">1948</td>
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+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#2121">_ZN4PLMD6asmjit9X86RAPass8annotateEv</a></td>
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+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#254">_ZN4PLMD6asmjit9X86RAPass8emitLoadEPNS0_7VirtRegEjPKc</a></td>
+              <td class="coverFnHi">4424</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#242">_ZN4PLMD6asmjit9X86RAPass8emitMoveEPNS0_7VirtRegEjjPKc</a></td>
+              <td class="coverFnHi">656</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#266">_ZN4PLMD6asmjit9X86RAPass8emitSaveEPNS0_7VirtRegEjPKc</a></td>
+              <td class="coverFnHi">4004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#668">_ZN4PLMD6asmjit9X86RAPass9loadStateEPNS0_7RAStateE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#703">_ZN4PLMD6asmjit9X86RAPass9saveStateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3856">_ZN4PLMD6asmjit9X86RAPass9translateEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#197">_ZN4PLMD6asmjit9X86RAPassC2Ev</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#201">_ZN4PLMD6asmjit9X86RAPassD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#201">_ZN4PLMD6asmjit9X86RAPassD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3706">_ZN4PLMD6asmjitL22X86RAPass_patchFuncMemEPNS0_9X86RAPassEPNS0_6CCFuncEPNS0_6CBNodeERNS0_15FuncFrameLayoutE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3783">_ZN4PLMD6asmjitL22X86RAPass_translateRetEPNS0_9X86RAPassEPNS0_9CCFuncRetEPNS0_7CBLabelE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3747">_ZN4PLMD6asmjitL23X86RAPass_translateJumpEPNS0_9X86RAPassEPNS0_6CBJumpEPNS0_7CBLabelE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3687">_ZN4PLMD6asmjitL26X86RAPass_prepareFuncFrameEPNS0_9X86RAPassEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#3645">_ZN4PLMD6asmjitL27X86RAPass_translateOperandsEPNS0_9X86RAPassEPNS0_8Operand_Ej</a></td>
+              <td class="coverFnHi">32806</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#1056">_ZN4PLMD6asmjitL30X86RAPass_assignStackArgsRegIdEPNS0_9X86RAPassEPNS0_6CCFuncE</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="x86regalloc.cpp.gcov.html#1024">_ZN4PLMD6asmjitL30X86RAPass_prepareSingleVarInstEjPNS0_7TiedRegE</a></td>
+              <td class="coverFnHi">248</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86regalloc.cpp.gcov.html b/coverage-libs/asmjit/x86regalloc.cpp.gcov.html
new file mode 100644
index 0000000000..f0962900cd
--- /dev/null
+++ b/coverage-libs/asmjit/x86regalloc.cpp.gcov.html
@@ -0,0 +1,4164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86regalloc.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86regalloc.cpp<span style="font-size: 80%;"> (source / <a href="x86regalloc.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">466</td>
+            <td class="headerCovTableEntry">1055</td>
+            <td class="headerCovTableEntryLo">44.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryLo">58.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Guard]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #if defined(ASMJIT_BUILD_X86) &amp;&amp; !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Dependencies]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./cpuinfo.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./x86assembler.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./x86compiler.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./x86internal_p.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./x86regalloc_p.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : // [Api-Begin]</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : namespace PLMD {</a>
+<a name="48"><span class="lineNum">      48 </span>            : namespace asmjit {</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : // ============================================================================</a>
+<a name="51"><span class="lineNum">      51 </span>            : // [Forward Declarations]</a>
+<a name="52"><span class="lineNum">      52 </span>            : // ============================================================================</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : enum { kCompilerDefaultLookAhead = 64 };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : static Error X86RAPass_translateOperands(X86RAPass* self, Operand_* opArray, uint32_t opCount);</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : // ============================================================================</a>
+<a name="59"><span class="lineNum">      59 </span>            : // [asmjit::X86RAPass - SpecialInst]</a>
+<a name="60"><span class="lineNum">      60 </span>            : // ============================================================================</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : struct X86SpecialInst {</a>
+<a name="63"><span class="lineNum">      63 </span>            :   uint8_t inReg;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   uint8_t outReg;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   uint16_t flags;</a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : static ASMJIT_INLINE const X86SpecialInst* X86SpecialInst_get(uint32_t instId, const Operand* opArray, uint32_t opCount) noexcept {</a>
+<a name="69"><span class="lineNum">      69 </span>            :   enum { kAny = Globals::kInvalidRegId };</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : #define R(ri) { uint8_t(ri)  , uint8_t(kAny), uint16_t(TiedReg::kRReg) }</a>
+<a name="72"><span class="lineNum">      72 </span>            : #define W(ri) { uint8_t(kAny), uint8_t(ri)  , uint16_t(TiedReg::kWReg) }</a>
+<a name="73"><span class="lineNum">      73 </span>            : #define X(ri) { uint8_t(ri)  , uint8_t(ri)  , uint16_t(TiedReg::kXReg) }</a>
+<a name="74"><span class="lineNum">      74 </span>            : #define NONE() { uint8_t(kAny), uint8_t(kAny), 0 }</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static const X86SpecialInst instCpuid[]        = { X(X86Gp::kIdAx), W(X86Gp::kIdBx), X(X86Gp::kIdCx), W(X86Gp::kIdDx) };</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static const X86SpecialInst instCbwCdqeCwde[]  = { X(X86Gp::kIdAx) };</a>
+<a name="77"><span class="lineNum">      77 </span>            :   static const X86SpecialInst instCdqCwdCqo[]    = { W(X86Gp::kIdDx), R(X86Gp::kIdAx) };</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static const X86SpecialInst instCmpxchg[]      = { X(kAny), R(kAny), X(X86Gp::kIdAx) };</a>
+<a name="79"><span class="lineNum">      79 </span>            :   static const X86SpecialInst instCmpxchg8b16b[] = { NONE(), X(X86Gp::kIdDx), X(X86Gp::kIdAx), R(X86Gp::kIdCx), R(X86Gp::kIdBx) };</a>
+<a name="80"><span class="lineNum">      80 </span>            :   static const X86SpecialInst instDaaDas[]       = { X(X86Gp::kIdAx) };</a>
+<a name="81"><span class="lineNum">      81 </span>            :   static const X86SpecialInst instDiv2[]         = { X(X86Gp::kIdAx), R(kAny) };</a>
+<a name="82"><span class="lineNum">      82 </span>            :   static const X86SpecialInst instDiv3[]         = { X(X86Gp::kIdDx), X(X86Gp::kIdAx), R(kAny) };</a>
+<a name="83"><span class="lineNum">      83 </span>            :   static const X86SpecialInst instJecxz[]        = { R(X86Gp::kIdCx) };</a>
+<a name="84"><span class="lineNum">      84 </span>            :   static const X86SpecialInst instMul2[]         = { X(X86Gp::kIdAx), R(kAny) };</a>
+<a name="85"><span class="lineNum">      85 </span>            :   static const X86SpecialInst instMul3[]         = { W(X86Gp::kIdDx), X(X86Gp::kIdAx), R(kAny) };</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static const X86SpecialInst instMulx[]         = { W(kAny), W(kAny), R(kAny), R(X86Gp::kIdDx) };</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static const X86SpecialInst instLahf[]         = { W(X86Gp::kIdAx) };</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static const X86SpecialInst instSahf[]         = { R(X86Gp::kIdAx) };</a>
+<a name="89"><span class="lineNum">      89 </span>            :   static const X86SpecialInst instMaskmovq[]     = { R(kAny), R(kAny), R(X86Gp::kIdDi) };</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static const X86SpecialInst instRdtscRdtscp[]  = { W(X86Gp::kIdDx), W(X86Gp::kIdAx), W(X86Gp::kIdCx) };</a>
+<a name="91"><span class="lineNum">      91 </span>            :   static const X86SpecialInst instRot[]          = { X(kAny), R(X86Gp::kIdCx) };</a>
+<a name="92"><span class="lineNum">      92 </span>            :   static const X86SpecialInst instShldShrd[]     = { X(kAny), R(kAny), R(X86Gp::kIdCx) };</a>
+<a name="93"><span class="lineNum">      93 </span>            :   static const X86SpecialInst instThirdXMM0[]    = { W(kAny), R(kAny), R(0) };</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static const X86SpecialInst instPcmpestri[]    = { R(kAny), R(kAny), NONE(), W(X86Gp::kIdCx) };</a>
+<a name="95"><span class="lineNum">      95 </span>            :   static const X86SpecialInst instPcmpestrm[]    = { R(kAny), R(kAny), NONE(), W(0) };</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static const X86SpecialInst instPcmpistri[]    = { R(kAny), R(kAny), NONE(), W(X86Gp::kIdCx), R(X86Gp::kIdAx), R(X86Gp::kIdDx) };</a>
+<a name="97"><span class="lineNum">      97 </span>            :   static const X86SpecialInst instPcmpistrm[]    = { R(kAny), R(kAny), NONE(), W(0)           , R(X86Gp::kIdAx), R(X86Gp::kIdDx) };</a>
+<a name="98"><span class="lineNum">      98 </span>            :   static const X86SpecialInst instXsaveXrstor[]  = { W(kAny), R(X86Gp::kIdDx), R(X86Gp::kIdAx) };</a>
+<a name="99"><span class="lineNum">      99 </span>            :   static const X86SpecialInst instReadMR[]       = { W(X86Gp::kIdDx), W(X86Gp::kIdAx), R(X86Gp::kIdCx) };</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static const X86SpecialInst instWriteMR[]      = { R(X86Gp::kIdDx), R(X86Gp::kIdAx), R(X86Gp::kIdCx) };</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   static const X86SpecialInst instCmps[]         = { X(X86Gp::kIdSi), X(X86Gp::kIdDi) };</a>
+<a name="103"><span class="lineNum">     103 </span>            :   static const X86SpecialInst instLods[]         = { W(X86Gp::kIdAx), X(X86Gp::kIdSi) };</a>
+<a name="104"><span class="lineNum">     104 </span>            :   static const X86SpecialInst instMovs[]         = { X(X86Gp::kIdDi), X(X86Gp::kIdSi) };</a>
+<a name="105"><span class="lineNum">     105 </span>            :   static const X86SpecialInst instScas[]         = { X(X86Gp::kIdDi), R(X86Gp::kIdAx) };</a>
+<a name="106"><span class="lineNum">     106 </span>            :   static const X86SpecialInst instStos[]         = { X(X86Gp::kIdDi), R(X86Gp::kIdAx) };</a>
+<a name="107"><span class="lineNum">     107 </span>            : #undef NONE</a>
+<a name="108"><span class="lineNum">     108 </span>            : #undef X</a>
+<a name="109"><span class="lineNum">     109 </span>            : #undef W</a>
+<a name="110"><span class="lineNum">     110 </span>            : #undef R</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   switch (instId) {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     case X86Inst::kIdCpuid      : return instCpuid;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCbw        :</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     case X86Inst::kIdCdqe       :</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCwde       : return instCbwCdqeCwde;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCdq        :</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :     case X86Inst::kIdCwd        :</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCqo        : return instCdqCwdCqo;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCmps       : return instCmps;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCmpxchg    : return instCmpxchg;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCmpxchg8b  :</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     case X86Inst::kIdCmpxchg16b : return instCmpxchg8b16b;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     case X86Inst::kIdDaa        :</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     case X86Inst::kIdDas        : return instDaaDas;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     case X86Inst::kIdDiv        : return (opCount == 2) ? instDiv2 : instDiv3;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     case X86Inst::kIdIdiv       : return (opCount == 2) ? instDiv2 : instDiv3;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :     case X86Inst::kIdImul       : if (opCount == 2) return nullptr;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :                                   if (opCount == 3 &amp;&amp; !(opArray[0].isReg() &amp;&amp; opArray[1].isReg() &amp;&amp; opArray[2].isRegOrMem())) return nullptr;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :                                   ASMJIT_FALLTHROUGH;</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     case X86Inst::kIdMul        : return (opCount == 2) ? instMul2 : instMul3;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     case X86Inst::kIdMulx       : return instMulx;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     case X86Inst::kIdJecxz      : return instJecxz;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     case X86Inst::kIdLods       : return instLods;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     case X86Inst::kIdMovs       : return instMovs;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     case X86Inst::kIdLahf       : return instLahf;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     case X86Inst::kIdSahf       : return instSahf;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     case X86Inst::kIdMaskmovq   :</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     case X86Inst::kIdMaskmovdqu :</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVmaskmovdqu: return instMaskmovq;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     case X86Inst::kIdEnter      : return nullptr; // Not supported.</a>
+<a name="142"><span class="lineNum">     142 </span>            :     case X86Inst::kIdLeave      : return nullptr; // Not supported.</a>
+<a name="143"><span class="lineNum">     143 </span>            :     case X86Inst::kIdRet        : return nullptr; // Not supported.</a>
+<a name="144"><span class="lineNum">     144 </span>            :     case X86Inst::kIdMonitor    : return nullptr; // TODO: [COMPILER] Monitor/MWait.</a>
+<a name="145"><span class="lineNum">     145 </span>            :     case X86Inst::kIdMwait      : return nullptr; // TODO: [COMPILER] Monitor/MWait.</a>
+<a name="146"><span class="lineNum">     146 </span>            :     case X86Inst::kIdPop        : return nullptr; // TODO: [COMPILER] Pop/Push.</a>
+<a name="147"><span class="lineNum">     147 </span>            :     case X86Inst::kIdPush       : return nullptr; // TODO: [COMPILER] Pop/Push.</a>
+<a name="148"><span class="lineNum">     148 </span>            :     case X86Inst::kIdPopa       : return nullptr; // Not supported.</a>
+<a name="149"><span class="lineNum">     149 </span>            :     case X86Inst::kIdPopf       : return nullptr; // Not supported.</a>
+<a name="150"><span class="lineNum">     150 </span>            :     case X86Inst::kIdPusha      : return nullptr; // Not supported.</a>
+<a name="151"><span class="lineNum">     151 </span>            :     case X86Inst::kIdPushf      : return nullptr; // Not supported.</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     case X86Inst::kIdRcl        :</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     case X86Inst::kIdRcr        :</a>
+<a name="154"><span class="lineNum">     154 </span>            :     case X86Inst::kIdRol        :</a>
+<a name="155"><span class="lineNum">     155 </span>            :     case X86Inst::kIdRor        :</a>
+<a name="156"><span class="lineNum">     156 </span>            :     case X86Inst::kIdSal        :</a>
+<a name="157"><span class="lineNum">     157 </span>            :     case X86Inst::kIdSar        :</a>
+<a name="158"><span class="lineNum">     158 </span>            :     case X86Inst::kIdShl        : // Rot instruction is special only if the last operand is a variable.</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     case X86Inst::kIdShr        : if (!opArray[1].isReg()) return nullptr;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :                                   return instRot;</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     case X86Inst::kIdShld       : // Shld/Shrd instruction is special only if the last operand is a variable.</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     case X86Inst::kIdShrd       : if (!opArray[2].isReg()) return nullptr;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :                                   return instShldShrd;</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     case X86Inst::kIdRdtsc      :</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     case X86Inst::kIdRdtscp     : return instRdtscRdtscp;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     case X86Inst::kIdScas       : return instScas;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     case X86Inst::kIdStos       : return instStos;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     case X86Inst::kIdBlendvpd   :</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     case X86Inst::kIdBlendvps   :</a>
+<a name="170"><span class="lineNum">     170 </span>            :     case X86Inst::kIdPblendvb   :</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :     case X86Inst::kIdSha256rnds2: return instThirdXMM0;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :     case X86Inst::kIdPcmpestri  :</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpcmpestri : return instPcmpestri;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :     case X86Inst::kIdPcmpistri  :</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpcmpistri : return instPcmpistri;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     case X86Inst::kIdPcmpestrm  :</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpcmpestrm : return instPcmpestrm;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     case X86Inst::kIdPcmpistrm  :</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     case X86Inst::kIdVpcmpistrm : return instPcmpistrm;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :     case X86Inst::kIdXrstor     :</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     case X86Inst::kIdXrstor64   :</a>
+<a name="182"><span class="lineNum">     182 </span>            :     case X86Inst::kIdXsave      :</a>
+<a name="183"><span class="lineNum">     183 </span>            :     case X86Inst::kIdXsave64    :</a>
+<a name="184"><span class="lineNum">     184 </span>            :     case X86Inst::kIdXsaveopt   :</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     case X86Inst::kIdXsaveopt64 : return instXsaveXrstor;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     case X86Inst::kIdRdmsr      :</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     case X86Inst::kIdRdpmc      :</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     case X86Inst::kIdXgetbv     : return instReadMR;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     case X86Inst::kIdWrmsr      :</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :     case X86Inst::kIdXsetbv     : return instWriteMR;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     default                     : return nullptr;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : // ============================================================================</a>
+<a name="196"><span class="lineNum">     196 </span>            : // [asmjit::X86RAPass - Construction / Destruction]</a>
+<a name="197"><span class="lineNum">     197 </span>            : // ============================================================================</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       1948 : X86RAPass::X86RAPass() noexcept : RAPass() {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1948 :   _state = &amp;_x86State;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1948 :   _varMapToVaListOffset = ASMJIT_OFFSET_OF(X86RAData, tiedArray);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       1948 : }</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 : X86RAPass::~X86RAPass() noexcept {}</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : // ============================================================================</a>
+<a name="206"><span class="lineNum">     206 </span>            : // [asmjit::X86RAPass - Interface]</a>
+<a name="207"><span class="lineNum">     207 </span>            : // ============================================================================</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1948 : Error X86RAPass::process(Zone* zone) noexcept {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       1948 :   return Base::process(zone);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1948 : Error X86RAPass::prepare(CCFunc* func) noexcept {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1948 :   ASMJIT_PROPAGATE(Base::prepare(func));</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :   uint32_t archType = cc()-&gt;getArchType();</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       1948 :   _regCount._gp  = archType == ArchInfo::kTypeX86 ? 8 : 16;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       1948 :   _regCount._mm  = 8;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1948 :   _regCount._k   = 8;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       1948 :   _regCount._vec = archType == ArchInfo::kTypeX86 ? 8 : 16;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   _zsp = cc()-&gt;zsp();</a>
+<a name="222"><span class="lineNum">     222 </span>            :   _zbp = cc()-&gt;zbp();</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       1948 :   _gaRegs[X86Reg::kKindGp ] = Utils::bits(_regCount.getGp()) &amp; ~Utils::mask(X86Gp::kIdSp);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       1948 :   _gaRegs[X86Reg::kKindMm ] = Utils::bits(_regCount.getMm());</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       1948 :   _gaRegs[X86Reg::kKindK  ] = Utils::bits(_regCount.getK());</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       1948 :   _gaRegs[X86Reg::kKindVec] = Utils::bits(_regCount.getVec());</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       1948 :   _x86State.reset(0);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   _clobberedRegs.reset();</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       1948 :   _avxEnabled = false;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       1948 :   _varBaseRegId = Globals::kInvalidRegId; // Used by patcher.</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       1948 :   _varBaseOffset = 0;                     // Used by patcher.</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : // ============================================================================</a>
+<a name="241"><span class="lineNum">     241 </span>            : // [asmjit::X86RAPass - Emit]</a>
+<a name="242"><span class="lineNum">     242 </span>            : // ============================================================================</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        656 : Error X86RAPass::emitMove(VirtReg* vReg, uint32_t dstId, uint32_t srcId, const char* reason) {</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   const char* comment = nullptr;</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        656 :   if (_emitComments) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :     _stringBuilder.setFormat(&quot;[%s] %s&quot;, reason, vReg-&gt;getName());</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :     comment = _stringBuilder.getData();</a>
+<a name="249"><span class="lineNum">     249 </span>            :   }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :   X86Reg dst(X86Reg::fromSignature(vReg-&gt;getSignature(), dstId));</a>
+<a name="252"><span class="lineNum">     252 </span>            :   X86Reg src(X86Reg::fromSignature(vReg-&gt;getSignature(), srcId));</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        656 :   return X86Internal::emitRegMove(reinterpret_cast&lt;X86Emitter*&gt;(cc()), dst, src, vReg-&gt;getTypeId(), _avxEnabled, comment);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       4424 : Error X86RAPass::emitLoad(VirtReg* vReg, uint32_t id, const char* reason) {</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   const char* comment = nullptr;</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       4424 :   if (_emitComments) {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     _stringBuilder.setFormat(&quot;[%s] %s&quot;, reason, vReg-&gt;getName());</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :     comment = _stringBuilder.getData();</a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   X86Reg dst(X86Reg::fromSignature(vReg-&gt;getSignature(), id));</a>
+<a name="264"><span class="lineNum">     264 </span>            :   X86Mem src(getVarMem(vReg));</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       4424 :   return X86Internal::emitRegMove(reinterpret_cast&lt;X86Emitter*&gt;(cc()), dst, src, vReg-&gt;getTypeId(), _avxEnabled, comment);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       4004 : Error X86RAPass::emitSave(VirtReg* vReg, uint32_t id, const char* reason) {</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   const char* comment = nullptr;</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       4004 :   if (_emitComments) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :     _stringBuilder.setFormat(&quot;[%s] %s&quot;, reason, vReg-&gt;getName());</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :     comment = _stringBuilder.getData();</a>
+<a name="273"><span class="lineNum">     273 </span>            :   }</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :   X86Mem dst(getVarMem(vReg));</a>
+<a name="276"><span class="lineNum">     276 </span>            :   X86Reg src(X86Reg::fromSignature(vReg-&gt;getSignature(), id));</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       4004 :   return X86Internal::emitRegMove(reinterpret_cast&lt;X86Emitter*&gt;(cc()), dst, src, vReg-&gt;getTypeId(), _avxEnabled, comment);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : }</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 : Error X86RAPass::emitSwapGp(VirtReg* dstReg, VirtReg* srcReg, uint32_t dstPhysId, uint32_t srcPhysId, const char* reason) noexcept {</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   ASMJIT_ASSERT(dstPhysId != Globals::kInvalidRegId);</a>
+<a name="282"><span class="lineNum">     282 </span>            :   ASMJIT_ASSERT(srcPhysId != Globals::kInvalidRegId);</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :   uint32_t is64 = std::max(dstReg-&gt;getTypeId(), srcReg-&gt;getTypeId()) &gt;= TypeId::kI64;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :   uint32_t sign = is64 ? uint32_t(X86RegTraits&lt;X86Reg::kRegGpq&gt;::kSignature)</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :                        : uint32_t(X86RegTraits&lt;X86Reg::kRegGpd&gt;::kSignature);</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   X86Reg a = X86Reg::fromSignature(sign, dstPhysId);</a>
+<a name="289"><span class="lineNum">     289 </span>            :   X86Reg b = X86Reg::fromSignature(sign, srcPhysId);</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   ASMJIT_PROPAGATE(cc()-&gt;emit(X86Inst::kIdXchg, a, b));</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   if (_emitComments)</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :     cc()-&gt;getCursor()-&gt;setInlineComment(cc()-&gt;_cbDataZone.sformat(&quot;[%s] %s, %s&quot;, reason, dstReg-&gt;getName(), srcReg-&gt;getName()));</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   return kErrorOk;</a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">        420 : Error X86RAPass::emitImmToReg(uint32_t dstTypeId, uint32_t dstPhysId, const Imm* src) noexcept {</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :   ASMJIT_ASSERT(dstPhysId != Globals::kInvalidRegId);</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :   X86Reg r0;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   Imm imm(*src);</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        420 :   switch (dstTypeId) {</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :     case TypeId::kI8:</a>
+<a name="305"><span class="lineNum">     305 </span>            :     case TypeId::kU8:</a>
+<a name="306"><span class="lineNum">     306 </span>            :       imm.truncateTo8Bits();</a>
+<a name="307"><span class="lineNum">     307 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :     case TypeId::kI16:</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     case TypeId::kU16:</a>
+<a name="311"><span class="lineNum">     311 </span>            :       imm.truncateTo16Bits();</a>
+<a name="312"><span class="lineNum">     312 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :     case TypeId::kI32:</a>
+<a name="315"><span class="lineNum">     315 </span>            :     case TypeId::kU32:</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 : Mov32Truncate:</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :       imm.truncateTo32Bits();</a>
+<a name="318"><span class="lineNum">     318 </span>            :       r0.setX86RegT&lt;X86Reg::kRegGpd&gt;(dstPhysId);</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :       cc()-&gt;emit(X86Inst::kIdMov, r0, imm);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            :     case TypeId::kI64:</a>
+<a name="323"><span class="lineNum">     323 </span>            :     case TypeId::kU64:</a>
+<a name="324"><span class="lineNum">     324 </span>            :       // Move to GPD register will also clear the high DWORD of GPQ</a>
+<a name="325"><span class="lineNum">     325 </span>            :       // register in 64-bit mode.</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">        420 :       if (imm.isUInt32())</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :         goto Mov32Truncate;</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            :       r0.setX86RegT&lt;X86Reg::kRegGpq&gt;(dstPhysId);</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        420 :       cc()-&gt;emit(X86Inst::kIdMov, r0, imm);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        420 :       break;</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :     case TypeId::kF32:</a>
+<a name="334"><span class="lineNum">     334 </span>            :     case TypeId::kF64:</a>
+<a name="335"><span class="lineNum">     335 </span>            :       // Compiler doesn't manage FPU stack.</a>
+<a name="336"><span class="lineNum">     336 </span>            :       ASMJIT_NOT_REACHED();</a>
+<a name="337"><span class="lineNum">     337 </span>            :       break;</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            :     case TypeId::kMmx32:</a>
+<a name="340"><span class="lineNum">     340 </span>            :     case TypeId::kMmx64:</a>
+<a name="341"><span class="lineNum">     341 </span>            :       // TODO: [COMPILER] EmitMoveImmToReg.</a>
+<a name="342"><span class="lineNum">     342 </span>            :       break;</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :     default:</a>
+<a name="345"><span class="lineNum">     345 </span>            :       // TODO: [COMPILER] EmitMoveImmToReg.</a>
+<a name="346"><span class="lineNum">     346 </span>            :       break;</a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        420 :   return kErrorOk;</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 : Error X86RAPass::emitImmToStack(uint32_t dstTypeId, const X86Mem* dst, const Imm* src) noexcept {</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :   X86Mem mem(*dst);</a>
+<a name="354"><span class="lineNum">     354 </span>            :   Imm imm(*src);</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            :   // One stack entry has the same size as the native register size. That means</a>
+<a name="357"><span class="lineNum">     357 </span>            :   // that if we want to move a 32-bit integer on the stack in 64-bit mode, we</a>
+<a name="358"><span class="lineNum">     358 </span>            :   // need to extend it to a 64-bit integer first. In 32-bit mode, pushing a</a>
+<a name="359"><span class="lineNum">     359 </span>            :   // 64-bit on stack is done in two steps by pushing low and high parts</a>
+<a name="360"><span class="lineNum">     360 </span>            :   // separately.</a>
+<a name="361"><span class="lineNum">     361 </span>            :   uint32_t gpSize = cc()-&gt;getGpSize();</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   switch (dstTypeId) {</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :     case TypeId::kI8:</a>
+<a name="365"><span class="lineNum">     365 </span>            :     case TypeId::kU8:</a>
+<a name="366"><span class="lineNum">     366 </span>            :       imm.truncateTo8Bits();</a>
+<a name="367"><span class="lineNum">     367 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     case TypeId::kI16:</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :     case TypeId::kU16:</a>
+<a name="371"><span class="lineNum">     371 </span>            :       imm.truncateTo16Bits();</a>
+<a name="372"><span class="lineNum">     372 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :     case TypeId::kI32:</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :     case TypeId::kU32:</a>
+<a name="376"><span class="lineNum">     376 </span>            :     case TypeId::kF32:</a>
+<a name="377"><span class="lineNum">     377 </span>            :       mem.setSize(4);</a>
+<a name="378"><span class="lineNum">     378 </span>            :       imm.truncateTo32Bits();</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :       cc()-&gt;emit(X86Inst::kIdMov, mem, imm);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :     case TypeId::kI64:</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     case TypeId::kU64:</a>
+<a name="384"><span class="lineNum">     384 </span>            :     case TypeId::kF64:</a>
+<a name="385"><span class="lineNum">     385 </span>            :     case TypeId::kMmx32:</a>
+<a name="386"><span class="lineNum">     386 </span>            :     case TypeId::kMmx64:</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :       if (gpSize == 4) {</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :         uint32_t hi = imm.getUInt32Hi();</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :         // Lo-Part.</a>
+<a name="391"><span class="lineNum">     391 </span>            :         mem.setSize(4);</a>
+<a name="392"><span class="lineNum">     392 </span>            :         imm.truncateTo32Bits();</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :         cc()-&gt;emit(X86Inst::kIdMov, mem, imm);</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :         mem.addOffsetLo32(gpSize);</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :         // Hi-Part.</a>
+<a name="398"><span class="lineNum">     398 </span>            :         imm.setUInt32(hi);</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :         cc()-&gt;emit(X86Inst::kIdMov, mem, imm);</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :       }</a>
+<a name="401"><span class="lineNum">     401 </span>            :       else {</a>
+<a name="402"><span class="lineNum">     402 </span>            :         mem.setSize(8);</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :         cc()-&gt;emit(X86Inst::kIdMov, mem, imm);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :       }</a>
+<a name="405"><span class="lineNum">     405 </span>            :       break;</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :     default:</a>
+<a name="408"><span class="lineNum">     408 </span>            :       return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="409"><span class="lineNum">     409 </span>            :   }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            :   return kErrorOk;</a>
+<a name="412"><span class="lineNum">     412 </span>            : }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 : Error X86RAPass::emitRegToStack(uint32_t dstTypeId, const X86Mem* dst, uint32_t srcTypeId, uint32_t srcPhysId) noexcept {</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   ASMJIT_ASSERT(srcPhysId != Globals::kInvalidRegId);</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   X86Mem m0(*dst);</a>
+<a name="418"><span class="lineNum">     418 </span>            :   X86Reg r0, r1;</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   uint32_t gpSize = cc()-&gt;getGpSize();</a>
+<a name="421"><span class="lineNum">     421 </span>            :   uint32_t instId = 0;</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :   switch (dstTypeId) {</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :     case TypeId::kI64:</a>
+<a name="425"><span class="lineNum">     425 </span>            :     case TypeId::kU64:</a>
+<a name="426"><span class="lineNum">     426 </span>            :       // Extend BYTE-&gt;QWORD (GP).</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :       if (TypeId::isGpb(srcTypeId)) {</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpbLo&gt;(srcPhysId);</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :         instId = (dstTypeId == TypeId::kI64 &amp;&amp; srcTypeId == TypeId::kI8) ? X86Inst::kIdMovsx : X86Inst::kIdMovzx;</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :         goto _ExtendMovGpXQ;</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :       }</a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span>            :       // Extend WORD-&gt;QWORD (GP).</a>
+<a name="435"><span class="lineNum">     435 </span>            :       if (TypeId::isGpw(srcTypeId)) {</a>
+<a name="436"><span class="lineNum">     436 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpw&gt;(srcPhysId);</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :         instId = (dstTypeId == TypeId::kI64 &amp;&amp; srcTypeId == TypeId::kI16) ? X86Inst::kIdMovsx : X86Inst::kIdMovzx;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :         goto _ExtendMovGpXQ;</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :       }</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :       // Extend DWORD-&gt;QWORD (GP).</a>
+<a name="443"><span class="lineNum">     443 </span>            :       if (TypeId::isGpd(srcTypeId)) {</a>
+<a name="444"><span class="lineNum">     444 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpd&gt;(srcPhysId);</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            :         instId = X86Inst::kIdMovsxd;</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineNoCov">          0 :         if (dstTypeId == TypeId::kI64 &amp;&amp; srcTypeId == TypeId::kI32)</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :           goto _ExtendMovGpXQ;</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :         else</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :           goto _ZeroExtendGpDQ;</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :       }</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            :       // Move QWORD (GP).</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :       if (TypeId::isGpq(srcTypeId)) goto MovGpQ;</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :       if (TypeId::isMmx(srcTypeId)) goto MovMmQ;</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) goto MovXmmQ;</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :       break;</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            :     case TypeId::kI32:</a>
+<a name="460"><span class="lineNum">     460 </span>            :     case TypeId::kU32:</a>
+<a name="461"><span class="lineNum">     461 </span>            :     case TypeId::kI16:</a>
+<a name="462"><span class="lineNum">     462 </span>            :     case TypeId::kU16:</a>
+<a name="463"><span class="lineNum">     463 </span>            :       // DWORD &lt;- WORD (Zero|Sign Extend).</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :       if (TypeId::isGpw(srcTypeId)) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 :         bool isDstSigned = dstTypeId == TypeId::kI16 || dstTypeId == TypeId::kI32;</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :         bool isSrcSigned = srcTypeId == TypeId::kI8  || srcTypeId == TypeId::kI16;</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpw&gt;(srcPhysId);</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :         instId = isDstSigned &amp;&amp; isSrcSigned ? X86Inst::kIdMovsx : X86Inst::kIdMovzx;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 :         goto _ExtendMovGpD;</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :       }</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            :       // DWORD &lt;- BYTE (Zero|Sign Extend).</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :       if (TypeId::isGpb(srcTypeId)) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :         bool isDstSigned = dstTypeId == TypeId::kI16 || dstTypeId == TypeId::kI32;</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :         bool isSrcSigned = srcTypeId == TypeId::kI8  || srcTypeId == TypeId::kI16;</span></a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpbLo&gt;(srcPhysId);</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :         instId = isDstSigned &amp;&amp; isSrcSigned ? X86Inst::kIdMovsx : X86Inst::kIdMovzx;</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 :         goto _ExtendMovGpD;</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :       }</a>
+<a name="482"><span class="lineNum">     482 </span>            :       ASMJIT_FALLTHROUGH;</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :     case TypeId::kI8:</a>
+<a name="485"><span class="lineNum">     485 </span>            :     case TypeId::kU8:</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :       if (TypeId::isInt(srcTypeId)) goto MovGpD;</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :       if (TypeId::isMmx(srcTypeId)) goto MovMmD;</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) goto MovXmmD;</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :       break;</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            :     case TypeId::kMmx32:</a>
+<a name="492"><span class="lineNum">     492 </span>            :     case TypeId::kMmx64:</a>
+<a name="493"><span class="lineNum">     493 </span>            :       // Extend BYTE-&gt;QWORD (GP).</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :       if (TypeId::isGpb(srcTypeId)) {</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpbLo&gt;(srcPhysId);</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span>            :         instId = X86Inst::kIdMovzx;</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :         goto _ExtendMovGpXQ;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :       }</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            :       // Extend WORD-&gt;QWORD (GP).</a>
+<a name="502"><span class="lineNum">     502 </span>            :       if (TypeId::isGpw(srcTypeId)) {</a>
+<a name="503"><span class="lineNum">     503 </span>            :         r1.setX86RegT&lt;X86Reg::kRegGpw&gt;(srcPhysId);</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            :         instId = X86Inst::kIdMovzx;</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :         goto _ExtendMovGpXQ;</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :       }</a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :       if (TypeId::isGpd(srcTypeId)) goto _ExtendMovGpDQ;</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :       if (TypeId::isGpq(srcTypeId)) goto MovGpQ;</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :       if (TypeId::isMmx(srcTypeId)) goto MovMmQ;</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) goto MovXmmQ;</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :       break;</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :     case TypeId::kF32:</a>
+<a name="516"><span class="lineNum">     516 </span>            :     case TypeId::kF32x1:</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) goto MovXmmD;</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :       break;</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            :     case TypeId::kF64:</a>
+<a name="521"><span class="lineNum">     521 </span>            :     case TypeId::kF64x1:</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 :       if (TypeId::isVec(srcTypeId)) goto MovXmmQ;</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :       break;</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            :     default:</a>
+<a name="526"><span class="lineNum">     526 </span>            :       // TODO: Vector types by stack.</a>
+<a name="527"><span class="lineNum">     527 </span>            :       break;</a>
+<a name="528"><span class="lineNum">     528 </span>            :   }</a>
+<a name="529"><span class="lineNum">     529 </span>            :   return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   // Extend+Move Gp.</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 : _ExtendMovGpD:</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   m0.setSize(4);</a>
+<a name="534"><span class="lineNum">     534 </span>            :   r0.setX86RegT&lt;X86Reg::kRegGpd&gt;(srcPhysId);</a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :   cc()-&gt;emit(instId, r0, r1);</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :   cc()-&gt;emit(X86Inst::kIdMov, m0, r0);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 : _ExtendMovGpXQ:</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :   if (gpSize == 8) {</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :     m0.setSize(8);</a>
+<a name="543"><span class="lineNum">     543 </span>            :     r0.setX86RegT&lt;X86Reg::kRegGpq&gt;(srcPhysId);</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :     cc()-&gt;emit(instId, r0, r1);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :     cc()-&gt;emit(X86Inst::kIdMov, m0, r0);</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :   }</a>
+<a name="548"><span class="lineNum">     548 </span>            :   else {</a>
+<a name="549"><span class="lineNum">     549 </span>            :     m0.setSize(4);</a>
+<a name="550"><span class="lineNum">     550 </span>            :     r0.setX86RegT&lt;X86Reg::kRegGpd&gt;(srcPhysId);</a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :     cc()-&gt;emit(instId, r0, r1);</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 : _ExtendMovGpDQ:</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineNoCov">          0 :     cc()-&gt;emit(X86Inst::kIdMov, m0, r0);</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :     m0.addOffsetLo32(4);</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :     cc()-&gt;emit(X86Inst::kIdAnd, m0, 0);</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span>            :   return kErrorOk;</a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            : _ZeroExtendGpDQ:</a>
+<a name="562"><span class="lineNum">     562 </span>            :   m0.setSize(4);</a>
+<a name="563"><span class="lineNum">     563 </span>            :   r0.setX86RegT&lt;X86Reg::kRegGpd&gt;(srcPhysId);</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :   goto _ExtendMovGpDQ;</span></a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span>            :   // Move Gp.</a>
+<a name="567"><span class="lineNum">     567 </span>            : MovGpD:</a>
+<a name="568"><span class="lineNum">     568 </span>            :   m0.setSize(4);</a>
+<a name="569"><span class="lineNum">     569 </span>            :   r0.setX86RegT&lt;X86Reg::kRegGpd&gt;(srcPhysId);</a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :   return cc()-&gt;emit(X86Inst::kIdMov, m0, r0);</span></a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineNoCov">          0 : MovGpQ:</span></a>
+<a name="573"><span class="lineNum">     573 </span>            :   m0.setSize(8);</a>
+<a name="574"><span class="lineNum">     574 </span>            :   r0.setX86RegT&lt;X86Reg::kRegGpq&gt;(srcPhysId);</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :   return cc()-&gt;emit(X86Inst::kIdMov, m0, r0);</span></a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span>            :   // Move Mm.</a>
+<a name="578"><span class="lineNum">     578 </span>            : MovMmD:</a>
+<a name="579"><span class="lineNum">     579 </span>            :   m0.setSize(4);</a>
+<a name="580"><span class="lineNum">     580 </span>            :   r0.setX86RegT&lt;X86Reg::kRegMm&gt;(srcPhysId);</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :   return cc()-&gt;emit(X86Inst::kIdMovd, m0, r0);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 : MovMmQ:</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :   m0.setSize(8);</a>
+<a name="585"><span class="lineNum">     585 </span>            :   r0.setX86RegT&lt;X86Reg::kRegMm&gt;(srcPhysId);</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 :   return cc()-&gt;emit(X86Inst::kIdMovq, m0, r0);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span>            :   // Move XMM.</a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 : MovXmmD:</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :   m0.setSize(4);</a>
+<a name="591"><span class="lineNum">     591 </span>            :   r0.setX86RegT&lt;X86Reg::kRegXmm&gt;(srcPhysId);</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineNoCov">          0 :   return cc()-&gt;emit(X86Inst::kIdMovss, m0, r0);</span></a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 : MovXmmQ:</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :   m0.setSize(8);</a>
+<a name="596"><span class="lineNum">     596 </span>            :   r0.setX86RegT&lt;X86Reg::kRegXmm&gt;(srcPhysId);</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :   return cc()-&gt;emit(X86Inst::kIdMovlps, m0, r0);</span></a>
+<a name="598"><span class="lineNum">     598 </span>            : }</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span>            : // ============================================================================</a>
+<a name="601"><span class="lineNum">     601 </span>            : // [asmjit::X86RAPass - Register Management]</a>
+<a name="602"><span class="lineNum">     602 </span>            : // ============================================================================</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span>            : #if defined(ASMJIT_DEBUG)</a>
+<a name="605"><span class="lineNum">     605 </span>            : template&lt;int C&gt;</a>
+<a name="606"><span class="lineNum">     606 </span>            : static ASMJIT_INLINE void X86RAPass_checkStateVars(X86RAPass* self) {</a>
+<a name="607"><span class="lineNum">     607 </span>            :   X86RAState* state = self-&gt;getState();</a>
+<a name="608"><span class="lineNum">     608 </span>            :   VirtReg** sVars = state-&gt;getListByKind(C);</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            :   uint32_t physId;</a>
+<a name="611"><span class="lineNum">     611 </span>            :   uint32_t regMask;</a>
+<a name="612"><span class="lineNum">     612 </span>            :   uint32_t regCount = self-&gt;_regCount.get(C);</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            :   uint32_t occupied = state-&gt;_occupied.get(C);</a>
+<a name="615"><span class="lineNum">     615 </span>            :   uint32_t modified = state-&gt;_modified.get(C);</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            :   for (physId = 0, regMask = 1; physId &lt; regCount; physId++, regMask &lt;&lt;= 1) {</a>
+<a name="618"><span class="lineNum">     618 </span>            :     VirtReg* vreg = sVars[physId];</a>
+<a name="619"><span class="lineNum">     619 </span>            : </a>
+<a name="620"><span class="lineNum">     620 </span>            :     if (!vreg) {</a>
+<a name="621"><span class="lineNum">     621 </span>            :       ASMJIT_ASSERT((occupied &amp; regMask) == 0);</a>
+<a name="622"><span class="lineNum">     622 </span>            :       ASMJIT_ASSERT((modified &amp; regMask) == 0);</a>
+<a name="623"><span class="lineNum">     623 </span>            :     }</a>
+<a name="624"><span class="lineNum">     624 </span>            :     else {</a>
+<a name="625"><span class="lineNum">     625 </span>            :       ASMJIT_ASSERT((occupied &amp; regMask) != 0);</a>
+<a name="626"><span class="lineNum">     626 </span>            :       ASMJIT_ASSERT((modified &amp; regMask) == (static_cast&lt;uint32_t&gt;(vreg-&gt;isModified()) &lt;&lt; physId));</a>
+<a name="627"><span class="lineNum">     627 </span>            : </a>
+<a name="628"><span class="lineNum">     628 </span>            :       ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="629"><span class="lineNum">     629 </span>            :       ASMJIT_ASSERT(vreg-&gt;getState() == VirtReg::kStateReg);</a>
+<a name="630"><span class="lineNum">     630 </span>            :       ASMJIT_ASSERT(vreg-&gt;getPhysId() == physId);</a>
+<a name="631"><span class="lineNum">     631 </span>            :     }</a>
+<a name="632"><span class="lineNum">     632 </span>            :   }</a>
+<a name="633"><span class="lineNum">     633 </span>            : }</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            : void X86RAPass::_checkState() {</a>
+<a name="636"><span class="lineNum">     636 </span>            :   X86RAPass_checkStateVars&lt;X86Reg::kKindGp &gt;(this);</a>
+<a name="637"><span class="lineNum">     637 </span>            :   X86RAPass_checkStateVars&lt;X86Reg::kKindMm &gt;(this);</a>
+<a name="638"><span class="lineNum">     638 </span>            :   X86RAPass_checkStateVars&lt;X86Reg::kKindVec&gt;(this);</a>
+<a name="639"><span class="lineNum">     639 </span>            : }</a>
+<a name="640"><span class="lineNum">     640 </span>            : #else</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 : void X86RAPass::_checkState() {}</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : #endif // ASMJIT_DEBUG</a>
+<a name="643"><span class="lineNum">     643 </span>            : </a>
+<a name="644"><span class="lineNum">     644 </span>            : // ============================================================================</a>
+<a name="645"><span class="lineNum">     645 </span>            : // [asmjit::X86RAPass - State - Load]</a>
+<a name="646"><span class="lineNum">     646 </span>            : // ============================================================================</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            : template&lt;int C&gt;</a>
+<a name="649"><span class="lineNum">     649 </span>            : static ASMJIT_INLINE void X86RAPass_loadStateVars(X86RAPass* self, X86RAState* src) {</a>
+<a name="650"><span class="lineNum">     650 </span>            :   X86RAState* cur = self-&gt;getState();</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :   VirtReg** cVars = cur-&gt;getListByKind(C);</a>
+<a name="653"><span class="lineNum">     653 </span>            :   VirtReg** sVars = src-&gt;getListByKind(C);</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :   uint32_t physId;</a>
+<a name="656"><span class="lineNum">     656 </span>            :   uint32_t modified = src-&gt;_modified.get(C);</a>
+<a name="657"><span class="lineNum">     657 </span>            :   uint32_t regCount = self-&gt;_regCount.get(C);</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineNoCov">          0 :   for (physId = 0; physId &lt; regCount; physId++, modified &gt;&gt;= 1) {</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineNoCov">          0 :     VirtReg* vreg = sVars[physId];</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :     cVars[physId] = vreg;</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :     if (!vreg) continue;</span></a>
+<a name="663"><span class="lineNum">     663 </span>            : </a>
+<a name="664"><span class="lineNum">     664 </span>            :     vreg-&gt;setState(VirtReg::kStateReg);</a>
+<a name="665"><span class="lineNum">     665 </span>            :     vreg-&gt;setPhysId(physId);</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :     vreg-&gt;setModified(modified &amp; 0x1);</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :   }</a>
+<a name="668"><span class="lineNum">     668 </span>            : }</a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 : void X86RAPass::loadState(RAState* src_) {</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :   X86RAState* cur = getState();</a>
+<a name="672"><span class="lineNum">     672 </span>            :   X86RAState* src = static_cast&lt;X86RAState*&gt;(src_);</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :   VirtReg** vregs = _contextVd.getData();</a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :   uint32_t count = static_cast&lt;uint32_t&gt;(_contextVd.getLength());</span></a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span>            :   // Load allocated variables.</a>
+<a name="678"><span class="lineNum">     678 </span>            :   X86RAPass_loadStateVars&lt;X86Reg::kKindGp &gt;(this, src);</a>
+<a name="679"><span class="lineNum">     679 </span>            :   X86RAPass_loadStateVars&lt;X86Reg::kKindMm &gt;(this, src);</a>
+<a name="680"><span class="lineNum">     680 </span>            :   X86RAPass_loadStateVars&lt;X86Reg::kKindVec&gt;(this, src);</a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span>            :   // Load masks.</a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :   cur-&gt;_occupied = src-&gt;_occupied;</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineNoCov">          0 :   cur-&gt;_modified = src-&gt;_modified;</span></a>
+<a name="685"><span class="lineNum">     685 </span>            : </a>
+<a name="686"><span class="lineNum">     686 </span>            :   // Load states of other variables and clear their 'Modified' flags.</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++) {</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :     uint32_t vState = src-&gt;_cells[i].getState();</a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :     if (vState == VirtReg::kStateReg)</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :     vregs[i]-&gt;setState(vState);</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :     vregs[i]-&gt;setPhysId(Globals::kInvalidRegId);</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :     vregs[i]-&gt;setModified(false);</span></a>
+<a name="696"><span class="lineNum">     696 </span>            :   }</a>
+<a name="697"><span class="lineNum">     697 </span>            : </a>
+<a name="698"><span class="lineNum">     698 </span>            :   ASMJIT_X86_CHECK_STATE</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="700"><span class="lineNum">     700 </span>            : </a>
+<a name="701"><span class="lineNum">     701 </span>            : // ============================================================================</a>
+<a name="702"><span class="lineNum">     702 </span>            : // [asmjit::X86RAPass - State - Save]</a>
+<a name="703"><span class="lineNum">     703 </span>            : // ============================================================================</a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineNoCov">          0 : RAState* X86RAPass::saveState() {</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :   VirtReg** vregs = _contextVd.getData();</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineNoCov">          0 :   uint32_t count = static_cast&lt;uint32_t&gt;(_contextVd.getLength());</span></a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span>            :   size_t size = Utils::alignTo&lt;size_t&gt;(</a>
+<a name="710"><span class="lineNum">     710 </span>            :     sizeof(X86RAState) + count * sizeof(X86StateCell), sizeof(void*));</a>
+<a name="711"><span class="lineNum">     711 </span>            : </a>
+<a name="712"><span class="lineNum">     712 </span>            :   X86RAState* cur = getState();</a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :   X86RAState* dst = _zone-&gt;allocT&lt;X86RAState&gt;(size);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :   if (!dst) return nullptr;</span></a>
+<a name="715"><span class="lineNum">     715 </span>            : </a>
+<a name="716"><span class="lineNum">     716 </span>            :   // Store links.</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :   ::memcpy(dst-&gt;_list, cur-&gt;_list, X86RAState::kAllCount * sizeof(VirtReg*));</span></a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            :   // Store masks.</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineNoCov">          0 :   dst-&gt;_occupied = cur-&gt;_occupied;</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineNoCov">          0 :   dst-&gt;_modified = cur-&gt;_modified;</span></a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            :   // Store cells.</a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++) {</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineNoCov">          0 :     VirtReg* vreg = static_cast&lt;VirtReg*&gt;(vregs[i]);</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :     X86StateCell&amp; cell = dst-&gt;_cells[i];</a>
+<a name="727"><span class="lineNum">     727 </span>            : </a>
+<a name="728"><span class="lineNum">     728 </span>            :     cell.reset();</a>
+<a name="729"><span class="lineNum">     729 </span>            :     cell.setState(vreg-&gt;getState());</a>
+<a name="730"><span class="lineNum">     730 </span>            :   }</a>
+<a name="731"><span class="lineNum">     731 </span>            : </a>
+<a name="732"><span class="lineNum">     732 </span>            :   return dst;</a>
+<a name="733"><span class="lineNum">     733 </span>            : }</a>
+<a name="734"><span class="lineNum">     734 </span>            : </a>
+<a name="735"><span class="lineNum">     735 </span>            : // ============================================================================</a>
+<a name="736"><span class="lineNum">     736 </span>            : // [asmjit::X86RAPass - State - Switch]</a>
+<a name="737"><span class="lineNum">     737 </span>            : // ============================================================================</a>
+<a name="738"><span class="lineNum">     738 </span>            : </a>
+<a name="739"><span class="lineNum">     739 </span>            : template&lt;int C&gt;</a>
+<a name="740"><span class="lineNum">     740 </span>            : static ASMJIT_INLINE void X86RAPass_switchStateVars(X86RAPass* self, X86RAState* src) {</a>
+<a name="741"><span class="lineNum">     741 </span>            :   X86RAState* dst = self-&gt;getState();</a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span>            :   VirtReg** dVars = dst-&gt;getListByKind(C);</a>
+<a name="744"><span class="lineNum">     744 </span>            :   VirtReg** sVars = src-&gt;getListByKind(C);</a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 :   X86StateCell* cells = src-&gt;_cells;</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :   uint32_t regCount = self-&gt;_regCount.get(C);</a>
+<a name="748"><span class="lineNum">     748 </span>            :   bool didWork;</a>
+<a name="749"><span class="lineNum">     749 </span>            : </a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :   do {</span></a>
+<a name="751"><span class="lineNum">     751 </span>            :     didWork = false;</a>
+<a name="752"><span class="lineNum">     752 </span>            : </a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :     for (uint32_t physId = 0, regMask = 0x1; physId &lt; regCount; physId++, regMask &lt;&lt;= 1) {</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineNoCov">          0 :       VirtReg* dVReg = dVars[physId];</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :       VirtReg* sVd = sVars[physId];</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineNoCov">          0 :       if (dVReg == sVd) continue;</span></a>
+<a name="757"><span class="lineNum">     757 </span>            : </a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :       if (dVReg) {</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineNoCov">          0 :         const X86StateCell&amp; cell = cells[dVReg-&gt;_raId];</span></a>
+<a name="760"><span class="lineNum">     760 </span>            : </a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineNoCov">          0 :         if (cell.getState() != VirtReg::kStateReg) {</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :           if (cell.getState() == VirtReg::kStateMem)</span></a>
+<a name="763"><span class="lineNum">     763 </span>            :             self-&gt;spill&lt;C&gt;(dVReg);</a>
+<a name="764"><span class="lineNum">     764 </span>            :           else</a>
+<a name="765"><span class="lineNum">     765 </span>            :             self-&gt;unuse&lt;C&gt;(dVReg);</a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            :           dVReg = nullptr;</a>
+<a name="768"><span class="lineNum">     768 </span>            :           didWork = true;</a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :           if (!sVd) continue;</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :         }</a>
+<a name="771"><span class="lineNum">     771 </span>            :       }</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineNoCov">          0 :       if (!dVReg &amp;&amp; sVd) {</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineNoCov">          0 : _MoveOrLoad:</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineNoCov">          0 :         if (sVd-&gt;getPhysId() != Globals::kInvalidRegId)</span></a>
+<a name="776"><span class="lineNum">     776 </span>            :           self-&gt;move&lt;C&gt;(sVd, physId);</a>
+<a name="777"><span class="lineNum">     777 </span>            :         else</a>
+<a name="778"><span class="lineNum">     778 </span>            :           self-&gt;load&lt;C&gt;(sVd, physId);</a>
+<a name="779"><span class="lineNum">     779 </span>            : </a>
+<a name="780"><span class="lineNum">     780 </span>            :         didWork = true;</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="782"><span class="lineNum">     782 </span>            :       }</a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineNoCov">          0 :       if (dVReg) {</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineNoCov">          0 :         const X86StateCell&amp; cell = cells[dVReg-&gt;_raId];</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineNoCov">          0 :         if (!sVd) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineNoCov">          0 :           if (cell.getState() == VirtReg::kStateReg)</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="789"><span class="lineNum">     789 </span>            : </a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineNoCov">          0 :           if (cell.getState() == VirtReg::kStateMem)</span></a>
+<a name="791"><span class="lineNum">     791 </span>            :             self-&gt;spill&lt;C&gt;(dVReg);</a>
+<a name="792"><span class="lineNum">     792 </span>            :           else</a>
+<a name="793"><span class="lineNum">     793 </span>            :             self-&gt;unuse&lt;C&gt;(dVReg);</a>
+<a name="794"><span class="lineNum">     794 </span>            : </a>
+<a name="795"><span class="lineNum">     795 </span>            :           didWork = true;</a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :         }</a>
+<a name="798"><span class="lineNum">     798 </span>            :         else {</a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineNoCov">          0 :           if (cell.getState() == VirtReg::kStateReg) {</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineNoCov">          0 :             if (dVReg-&gt;getPhysId() != Globals::kInvalidRegId &amp;&amp; sVd-&gt;getPhysId() != Globals::kInvalidRegId) {</span></a>
+<a name="801"><span class="lineNum">     801 </span>            :               if (C == X86Reg::kKindGp) {</a>
+<a name="802"><span class="lineNum">     802 </span>            :                 self-&gt;swapGp(dVReg, sVd);</a>
+<a name="803"><span class="lineNum">     803 </span>            :               }</a>
+<a name="804"><span class="lineNum">     804 </span>            :               else {</a>
+<a name="805"><span class="lineNum">     805 </span>            :                 self-&gt;spill&lt;C&gt;(dVReg);</a>
+<a name="806"><span class="lineNum">     806 </span>            :                 self-&gt;move&lt;C&gt;(sVd, physId);</a>
+<a name="807"><span class="lineNum">     807 </span>            :               }</a>
+<a name="808"><span class="lineNum">     808 </span>            : </a>
+<a name="809"><span class="lineNum">     809 </span>            :               didWork = true;</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineNoCov">          0 :               continue;</span></a>
+<a name="811"><span class="lineNum">     811 </span>            :             }</a>
+<a name="812"><span class="lineNum">     812 </span>            :             else {</a>
+<a name="813"><span class="lineNum">     813 </span>            :               didWork = true;</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineNoCov">          0 :               continue;</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :             }</a>
+<a name="816"><span class="lineNum">     816 </span>            :           }</a>
+<a name="817"><span class="lineNum">     817 </span>            : </a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineNoCov">          0 :           if (cell.getState() == VirtReg::kStateMem)</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :             self-&gt;spill&lt;C&gt;(dVReg);</a>
+<a name="820"><span class="lineNum">     820 </span>            :           else</a>
+<a name="821"><span class="lineNum">     821 </span>            :             self-&gt;unuse&lt;C&gt;(dVReg);</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineNoCov">          0 :           goto _MoveOrLoad;</span></a>
+<a name="823"><span class="lineNum">     823 </span>            :         }</a>
+<a name="824"><span class="lineNum">     824 </span>            :       }</a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span>            :   } while (didWork);</a>
+<a name="827"><span class="lineNum">     827 </span>            : </a>
+<a name="828"><span class="lineNum">     828 </span>            :   uint32_t dModified = dst-&gt;_modified.get(C);</a>
+<a name="829"><span class="lineNum">     829 </span>            :   uint32_t sModified = src-&gt;_modified.get(C);</a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineNoCov">          0 :   if (dModified != sModified) {</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineNoCov">          0 :     for (uint32_t physId = 0, regMask = 0x1; physId &lt; regCount; physId++, regMask &lt;&lt;= 1) {</span></a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineNoCov">          0 :       VirtReg* vreg = dVars[physId];</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineNoCov">          0 :       if (!vreg) continue;</span></a>
+<a name="835"><span class="lineNum">     835 </span>            : </a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineNoCov">          0 :       if ((dModified &amp; regMask) &amp;&amp; !(sModified &amp; regMask)) {</span></a>
+<a name="837"><span class="lineNum">     837 </span>            :         self-&gt;save&lt;C&gt;(vreg);</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="839"><span class="lineNum">     839 </span>            :       }</a>
+<a name="840"><span class="lineNum">     840 </span>            : </a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineNoCov">          0 :       if (!(dModified &amp; regMask) &amp;&amp; (sModified &amp; regMask)) {</span></a>
+<a name="842"><span class="lineNum">     842 </span>            :         self-&gt;modify&lt;C&gt;(vreg);</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="844"><span class="lineNum">     844 </span>            :       }</a>
+<a name="845"><span class="lineNum">     845 </span>            :     }</a>
+<a name="846"><span class="lineNum">     846 </span>            :   }</a>
+<a name="847"><span class="lineNum">     847 </span>            : }</a>
+<a name="848"><span class="lineNum">     848 </span>            : </a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 : void X86RAPass::switchState(RAState* src_) {</span></a>
+<a name="850"><span class="lineNum">     850 </span>            :   ASMJIT_ASSERT(src_ != nullptr);</a>
+<a name="851"><span class="lineNum">     851 </span>            : </a>
+<a name="852"><span class="lineNum">     852 </span>            :   X86RAState* cur = getState();</a>
+<a name="853"><span class="lineNum">     853 </span>            :   X86RAState* src = static_cast&lt;X86RAState*&gt;(src_);</a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span>            :   // Ignore if both states are equal.</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :   if (cur == src)</span></a>
+<a name="857"><span class="lineNum">     857 </span>            :     return;</a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span>            :   // Switch variables.</a>
+<a name="860"><span class="lineNum">     860 </span>            :   X86RAPass_switchStateVars&lt;X86Reg::kKindGp &gt;(this, src);</a>
+<a name="861"><span class="lineNum">     861 </span>            :   X86RAPass_switchStateVars&lt;X86Reg::kKindMm &gt;(this, src);</a>
+<a name="862"><span class="lineNum">     862 </span>            :   X86RAPass_switchStateVars&lt;X86Reg::kKindVec&gt;(this, src);</a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span>            :   // Calculate changed state.</a>
+<a name="865"><span class="lineNum">     865 </span>            :   VirtReg** vregs = _contextVd.getData();</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineNoCov">          0 :   uint32_t count = static_cast&lt;uint32_t&gt;(_contextVd.getLength());</span></a>
+<a name="867"><span class="lineNum">     867 </span>            : </a>
+<a name="868"><span class="lineNum">     868 </span>            :   X86StateCell* cells = src-&gt;_cells;</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineNoCov">          0 :   for (uint32_t i = 0; i &lt; count; i++) {</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineNoCov">          0 :     VirtReg* vreg = static_cast&lt;VirtReg*&gt;(vregs[i]);</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :     const X86StateCell&amp; cell = cells[i];</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :     uint32_t vState = cell.getState();</a>
+<a name="873"><span class="lineNum">     873 </span>            : </a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineNoCov">          0 :     if (vState != VirtReg::kStateReg) {</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :       vreg-&gt;setState(vState);</a>
+<a name="876"><span class="lineNum">     876 </span>            :       vreg-&gt;setModified(false);</a>
+<a name="877"><span class="lineNum">     877 </span>            :     }</a>
+<a name="878"><span class="lineNum">     878 </span>            :   }</a>
+<a name="879"><span class="lineNum">     879 </span>            : </a>
+<a name="880"><span class="lineNum">     880 </span>            :   ASMJIT_X86_CHECK_STATE</a>
+<a name="881"><span class="lineNum">     881 </span>            : }</a>
+<a name="882"><span class="lineNum">     882 </span>            : </a>
+<a name="883"><span class="lineNum">     883 </span>            : // ============================================================================</a>
+<a name="884"><span class="lineNum">     884 </span>            : // [asmjit::X86RAPass - State - Intersect]</a>
+<a name="885"><span class="lineNum">     885 </span>            : // ============================================================================</a>
+<a name="886"><span class="lineNum">     886 </span>            : </a>
+<a name="887"><span class="lineNum">     887 </span>            : // The algorithm is actually not so smart, but tries to find an intersection od</a>
+<a name="888"><span class="lineNum">     888 </span>            : // `a` and `b` and tries to move/alloc a variable into that location if it's</a>
+<a name="889"><span class="lineNum">     889 </span>            : // possible. It also finds out which variables will be spilled/unused  by `a`</a>
+<a name="890"><span class="lineNum">     890 </span>            : // and `b` and performs that action here. It may improve the switch state code</a>
+<a name="891"><span class="lineNum">     891 </span>            : // in certain cases, but doesn't necessarily do the best job possible.</a>
+<a name="892"><span class="lineNum">     892 </span>            : template&lt;int C&gt;</a>
+<a name="893"><span class="lineNum">     893 </span>            : static ASMJIT_INLINE void X86RAPass_intersectStateVars(X86RAPass* self, X86RAState* a, X86RAState* b) {</a>
+<a name="894"><span class="lineNum">     894 </span>            :   X86RAState* dst = self-&gt;getState();</a>
+<a name="895"><span class="lineNum">     895 </span>            : </a>
+<a name="896"><span class="lineNum">     896 </span>            :   VirtReg** dVars = dst-&gt;getListByKind(C);</a>
+<a name="897"><span class="lineNum">     897 </span>            :   VirtReg** aVars = a-&gt;getListByKind(C);</a>
+<a name="898"><span class="lineNum">     898 </span>            : </a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineNoCov">          0 :   X86StateCell* aCells = a-&gt;_cells;</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :   X86StateCell* bCells = b-&gt;_cells;</span></a>
+<a name="901"><span class="lineNum">     901 </span>            : </a>
+<a name="902"><span class="lineNum">     902 </span>            :   uint32_t regCount = self-&gt;_regCount.get(C);</a>
+<a name="903"><span class="lineNum">     903 </span>            :   bool didWork;</a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span>            :   // Similar to `switchStateVars()`, we iterate over and over until there is</a>
+<a name="906"><span class="lineNum">     906 </span>            :   // no work to be done.</a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineNoCov">          0 :   do {</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :     didWork = false;</a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineNoCov">          0 :     for (uint32_t physId = 0, regMask = 0x1; physId &lt; regCount; physId++, regMask &lt;&lt;= 1) {</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineNoCov">          0 :       VirtReg* dVReg = dVars[physId]; // Destination reg.</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineNoCov">          0 :       VirtReg* aVReg = aVars[physId]; // State-a reg.</span></a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineNoCov">          0 :       if (dVReg == aVReg) continue;</span></a>
+<a name="915"><span class="lineNum">     915 </span>            : </a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineNoCov">          0 :       if (dVReg) {</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineNoCov">          0 :         const X86StateCell&amp; aCell = aCells[dVReg-&gt;_raId];</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineNoCov">          0 :         const X86StateCell&amp; bCell = bCells[dVReg-&gt;_raId];</span></a>
+<a name="919"><span class="lineNum">     919 </span>            : </a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :         if (aCell.getState() != VirtReg::kStateReg &amp;&amp; bCell.getState() != VirtReg::kStateReg) {</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineNoCov">          0 :           if (aCell.getState() == VirtReg::kStateMem || bCell.getState() == VirtReg::kStateMem)</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :             self-&gt;spill&lt;C&gt;(dVReg);</a>
+<a name="923"><span class="lineNum">     923 </span>            :           else</a>
+<a name="924"><span class="lineNum">     924 </span>            :             self-&gt;unuse&lt;C&gt;(dVReg);</a>
+<a name="925"><span class="lineNum">     925 </span>            : </a>
+<a name="926"><span class="lineNum">     926 </span>            :           dVReg = nullptr;</a>
+<a name="927"><span class="lineNum">     927 </span>            :           didWork = true;</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineNoCov">          0 :           if (!aVReg) continue;</span></a>
+<a name="929"><span class="lineNum">     929 </span>            :         }</a>
+<a name="930"><span class="lineNum">     930 </span>            :       }</a>
+<a name="931"><span class="lineNum">     931 </span>            : </a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineNoCov">          0 :       if (!dVReg &amp;&amp; aVReg) {</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineNoCov">          0 :         if (aVReg-&gt;getPhysId() != Globals::kInvalidRegId)</span></a>
+<a name="934"><span class="lineNum">     934 </span>            :           self-&gt;move&lt;C&gt;(aVReg, physId);</a>
+<a name="935"><span class="lineNum">     935 </span>            :         else</a>
+<a name="936"><span class="lineNum">     936 </span>            :           self-&gt;load&lt;C&gt;(aVReg, physId);</a>
+<a name="937"><span class="lineNum">     937 </span>            : </a>
+<a name="938"><span class="lineNum">     938 </span>            :         didWork = true;</a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="940"><span class="lineNum">     940 </span>            :       }</a>
+<a name="941"><span class="lineNum">     941 </span>            : </a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :       if (dVReg) {</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineNoCov">          0 :         const X86StateCell&amp; aCell = aCells[dVReg-&gt;_raId];</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 :         const X86StateCell&amp; bCell = bCells[dVReg-&gt;_raId];</span></a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineNoCov">          0 :         if (!aVReg) {</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineNoCov">          0 :           if (aCell.getState() == VirtReg::kStateReg || bCell.getState() == VirtReg::kStateReg)</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="949"><span class="lineNum">     949 </span>            : </a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineNoCov">          0 :           if (aCell.getState() == VirtReg::kStateMem || bCell.getState() == VirtReg::kStateMem)</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :             self-&gt;spill&lt;C&gt;(dVReg);</a>
+<a name="952"><span class="lineNum">     952 </span>            :           else</a>
+<a name="953"><span class="lineNum">     953 </span>            :             self-&gt;unuse&lt;C&gt;(dVReg);</a>
+<a name="954"><span class="lineNum">     954 </span>            : </a>
+<a name="955"><span class="lineNum">     955 </span>            :           didWork = true;</a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="957"><span class="lineNum">     957 </span>            :         }</a>
+<a name="958"><span class="lineNum">     958 </span>            :         else if (C == X86Reg::kKindGp) {</a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineNoCov">          0 :           if (aCell.getState() == VirtReg::kStateReg) {</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineNoCov">          0 :             if (dVReg-&gt;getPhysId() != Globals::kInvalidRegId &amp;&amp; aVReg-&gt;getPhysId() != Globals::kInvalidRegId) {</span></a>
+<a name="961"><span class="lineNum">     961 </span>            :               self-&gt;swapGp(dVReg, aVReg);</a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span>            :               didWork = true;</a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineNoCov">          0 :               continue;</span></a>
+<a name="965"><span class="lineNum">     965 </span>            :             }</a>
+<a name="966"><span class="lineNum">     966 </span>            :           }</a>
+<a name="967"><span class="lineNum">     967 </span>            :         }</a>
+<a name="968"><span class="lineNum">     968 </span>            :       }</a>
+<a name="969"><span class="lineNum">     969 </span>            :     }</a>
+<a name="970"><span class="lineNum">     970 </span>            :   } while (didWork);</a>
+<a name="971"><span class="lineNum">     971 </span>            : </a>
+<a name="972"><span class="lineNum">     972 </span>            :   uint32_t dModified = dst-&gt;_modified.get(C);</a>
+<a name="973"><span class="lineNum">     973 </span>            :   uint32_t aModified = a-&gt;_modified.get(C);</a>
+<a name="974"><span class="lineNum">     974 </span>            : </a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineNoCov">          0 :   if (dModified != aModified) {</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineNoCov">          0 :     for (uint32_t physId = 0, regMask = 0x1; physId &lt; regCount; physId++, regMask &lt;&lt;= 1) {</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineNoCov">          0 :       VirtReg* vreg = dVars[physId];</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineNoCov">          0 :       if (!vreg) continue;</span></a>
+<a name="979"><span class="lineNum">     979 </span>            : </a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :       const X86StateCell&amp; aCell = aCells[vreg-&gt;_raId];</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 :       if ((dModified &amp; regMask) &amp;&amp; !(aModified &amp; regMask) &amp;&amp; aCell.getState() == VirtReg::kStateReg)</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :         self-&gt;save&lt;C&gt;(vreg);</a>
+<a name="983"><span class="lineNum">     983 </span>            :     }</a>
+<a name="984"><span class="lineNum">     984 </span>            :   }</a>
+<a name="985"><span class="lineNum">     985 </span>            : }</a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineNoCov">          0 : void X86RAPass::intersectStates(RAState* a_, RAState* b_) {</span></a>
+<a name="988"><span class="lineNum">     988 </span>            :   X86RAState* a = static_cast&lt;X86RAState*&gt;(a_);</a>
+<a name="989"><span class="lineNum">     989 </span>            :   X86RAState* b = static_cast&lt;X86RAState*&gt;(b_);</a>
+<a name="990"><span class="lineNum">     990 </span>            : </a>
+<a name="991"><span class="lineNum">     991 </span>            :   ASMJIT_ASSERT(a != nullptr);</a>
+<a name="992"><span class="lineNum">     992 </span>            :   ASMJIT_ASSERT(b != nullptr);</a>
+<a name="993"><span class="lineNum">     993 </span>            : </a>
+<a name="994"><span class="lineNum">     994 </span>            :   X86RAPass_intersectStateVars&lt;X86Reg::kKindGp &gt;(this, a, b);</a>
+<a name="995"><span class="lineNum">     995 </span>            :   X86RAPass_intersectStateVars&lt;X86Reg::kKindMm &gt;(this, a, b);</a>
+<a name="996"><span class="lineNum">     996 </span>            :   X86RAPass_intersectStateVars&lt;X86Reg::kKindVec&gt;(this, a, b);</a>
+<a name="997"><span class="lineNum">     997 </span>            : </a>
+<a name="998"><span class="lineNum">     998 </span>            :   ASMJIT_X86_CHECK_STATE</a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            : </a>
+<a name="1001"><span class="lineNum">    1001 </span>            : // ============================================================================</a>
+<a name="1002"><span class="lineNum">    1002 </span>            : // [asmjit::X86RAPass - GetJccFlow / GetOppositeJccFlow]</a>
+<a name="1003"><span class="lineNum">    1003 </span>            : // ============================================================================</a>
+<a name="1004"><span class="lineNum">    1004 </span>            : </a>
+<a name="1005"><span class="lineNum">    1005 </span>            : //! \internal</a>
+<a name="1006"><span class="lineNum">    1006 </span>            : static ASMJIT_INLINE CBNode* X86RAPass_getJccFlow(CBJump* jNode) {</a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :   if (jNode-&gt;isTaken())</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineNoCov">          0 :     return jNode-&gt;getTarget();</span></a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   else</a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineNoCov">          0 :     return jNode-&gt;getNext();</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            : }</a>
+<a name="1012"><span class="lineNum">    1012 </span>            : </a>
+<a name="1013"><span class="lineNum">    1013 </span>            : //! \internal</a>
+<a name="1014"><span class="lineNum">    1014 </span>            : static ASMJIT_INLINE CBNode* X86RAPass_getOppositeJccFlow(CBJump* jNode) {</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineNoCov">          0 :   if (jNode-&gt;isTaken())</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineNoCov">          0 :     return jNode-&gt;getNext();</span></a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   else</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineNoCov">          0 :     return jNode-&gt;getTarget();</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            : }</a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span>            : // ============================================================================</a>
+<a name="1022"><span class="lineNum">    1022 </span>            : // [asmjit::X86RAPass - SingleVarInst]</a>
+<a name="1023"><span class="lineNum">    1023 </span>            : // ============================================================================</a>
+<a name="1024"><span class="lineNum">    1024 </span>            : </a>
+<a name="1025"><span class="lineNum">    1025 </span>            : //! \internal</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">        248 : static void X86RAPass_prepareSingleVarInst(uint32_t instId, TiedReg* tr) {</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">        248 :   switch (instId) {</span></a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     // - andn     reg, reg ; Set all bits in reg to 0.</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     // - xor/pxor reg, reg ; Set all bits in reg to 0.</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     // - sub/psub reg, reg ; Set all bits in reg to 0.</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :     // - pcmpgt   reg, reg ; Set all bits in reg to 0.</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :     // - pcmpeq   reg, reg ; Set all bits in reg to 1.</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">        248 :     case X86Inst::kIdPandn     :</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :     case X86Inst::kIdXor       : case X86Inst::kIdXorpd     : case X86Inst::kIdXorps     : case X86Inst::kIdPxor      :</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     case X86Inst::kIdSub:</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :     case X86Inst::kIdPsubb     : case X86Inst::kIdPsubw     : case X86Inst::kIdPsubd     : case X86Inst::kIdPsubq     :</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     case X86Inst::kIdPsubsb    : case X86Inst::kIdPsubsw    : case X86Inst::kIdPsubusb   : case X86Inst::kIdPsubusw   :</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :     case X86Inst::kIdPcmpeqb   : case X86Inst::kIdPcmpeqw   : case X86Inst::kIdPcmpeqd   : case X86Inst::kIdPcmpeqq   :</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :     case X86Inst::kIdPcmpgtb   : case X86Inst::kIdPcmpgtw   : case X86Inst::kIdPcmpgtd   : case X86Inst::kIdPcmpgtq   :</a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">        248 :       tr-&gt;flags &amp;= ~TiedReg::kRReg;</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">        248 :       break;</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            : </a>
+<a name="1043"><span class="lineNum">    1043 </span>            :     // - and      reg, reg ; Nop.</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     // - or       reg, reg ; Nop.</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     // - xchg     reg, reg ; Nop.</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineNoCov">          0 :     case X86Inst::kIdAnd       : case X86Inst::kIdAndpd     : case X86Inst::kIdAndps     : case X86Inst::kIdPand      :</span></a>
+<a name="1047"><span class="lineNum">    1047 </span>            :     case X86Inst::kIdOr        : case X86Inst::kIdOrpd      : case X86Inst::kIdOrps      : case X86Inst::kIdPor       :</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     case X86Inst::kIdXchg      :</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineNoCov">          0 :       tr-&gt;flags &amp;= ~TiedReg::kWReg;</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   }</a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">        248 : }</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            : </a>
+<a name="1054"><span class="lineNum">    1054 </span>            : // ============================================================================</a>
+<a name="1055"><span class="lineNum">    1055 </span>            : // [asmjit::X86RAPass - Helpers]</a>
+<a name="1056"><span class="lineNum">    1056 </span>            : // ============================================================================</a>
+<a name="1057"><span class="lineNum">    1057 </span>            : </a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">       1948 : static void X86RAPass_assignStackArgsRegId(X86RAPass* self, CCFunc* func) {</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   const FuncDetail&amp; fd = func-&gt;getDetail();</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :   FuncFrameInfo&amp; ffi = func-&gt;getFrameInfo();</a>
+<a name="1061"><span class="lineNum">    1061 </span>            : </a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   // Select some register which will contain the base address of function</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   // arguments and return address. The algorithm tries to select registers</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   // which are saved or not preserved by default, if not successful it picks</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   // any other register and adds it to `_savedRegs`.</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :   uint32_t stackArgsRegId;</a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">       1948 :   if (ffi.hasPreservedFP()) {</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     stackArgsRegId = X86Gp::kIdBp;</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :   }</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   else {</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :     // Passed registers as defined by the calling convention.</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     uint32_t passed = fd.getPassedRegs(X86Reg::kKindGp);</a>
+<a name="1073"><span class="lineNum">    1073 </span>            : </a>
+<a name="1074"><span class="lineNum">    1074 </span>            :     // Registers actually used to pass function arguments (related to this</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     // function signature) with ESP|RSP included as this register can't be</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :     // used in general to hold anything bug stack pointer.</a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">       1948 :     uint32_t used = fd.getUsedRegs(X86Reg::kKindGp) | Utils::mask(X86Gp::kIdSp);</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            : </a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     // First try register that is defined to pass a function argument by the</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     // calling convention, but is not used by this function. This will most</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     // likely fail in 32-bit mode, but there is a high chance that it will</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     // pass in 64-bit mode if the function doesn't use so many arguments.</a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">       1948 :     uint32_t regs = passed &amp; ~used;</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            : </a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     // Pick any other register if that didn't work out.</a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">       1948 :     if (!regs) regs = ~passed &amp; ~used;</span></a>
+<a name="1087"><span class="lineNum">    1087 </span>            : </a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     stackArgsRegId = Utils::findFirstBit(regs);</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :     ASMJIT_ASSERT(stackArgsRegId &lt; self-&gt;cc()-&gt;getGpCount());</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   }</a>
+<a name="1091"><span class="lineNum">    1091 </span>            : </a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   ffi.setStackArgsRegId(stackArgsRegId);</a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">       1948 : }</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            : // ============================================================================</a>
+<a name="1096"><span class="lineNum">    1096 </span>            : // [asmjit::X86RAPass - SArg Insertion]</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : // ============================================================================</a>
+<a name="1098"><span class="lineNum">    1098 </span>            : </a>
+<a name="1099"><span class="lineNum">    1099 </span>            : struct SArgData {</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :   VirtReg* sVd;</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   VirtReg* cVd;</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   CCPushArg* sArg;</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   uint32_t aType;</a>
+<a name="1104"><span class="lineNum">    1104 </span>            : };</a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span>            : static ASMJIT_INLINE bool X86RAPass_mustConvertSArg(X86RAPass* self, uint32_t dstTypeId, uint32_t srcTypeId) noexcept{</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineNoCov">          0 :   uint32_t dstFloatSize = dstTypeId == TypeId::kF32   ? 4 :</span></a>
+<a name="1108"><span class="lineNum">    1108 </span>            :                           dstTypeId == TypeId::kF64   ? 8 : 0;</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineNoCov">          0 :   uint32_t srcFloatSize = srcTypeId == TypeId::kF32   ? 4 :</span></a>
+<a name="1111"><span class="lineNum">    1111 </span>            :                           srcTypeId == TypeId::kF32x1 ? 4 :</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :                           srcTypeId == TypeId::kF64   ? 8 :</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :                           srcTypeId == TypeId::kF64x1 ? 8 : 0;</a>
+<a name="1114"><span class="lineNum">    1114 </span>            : </a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineNoCov">          0 :   if (dstFloatSize &amp;&amp; srcFloatSize)</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            :     return dstFloatSize != srcFloatSize;</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   else</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :     return false;</a>
+<a name="1119"><span class="lineNum">    1119 </span>            : }</a>
+<a name="1120"><span class="lineNum">    1120 </span>            : </a>
+<a name="1121"><span class="lineNum">    1121 </span>            : static ASMJIT_INLINE uint32_t X86RAPass_typeOfConvertedSArg(X86RAPass* self, uint32_t dstTypeId, uint32_t srcTypeId) noexcept {</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   ASMJIT_ASSERT(X86RAPass_mustConvertSArg(self, dstTypeId, srcTypeId));</a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineNoCov">          0 :   return dstTypeId == TypeId::kF32 ? TypeId::kF32x1 : TypeId::kF64x1;</span></a>
+<a name="1124"><span class="lineNum">    1124 </span>            : }</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : </a>
+<a name="1126"><span class="lineNum">    1126 </span>            : static ASMJIT_INLINE Error X86RAPass_insertPushArg(</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   X86RAPass* self, CCFuncCall* call,</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   VirtReg* sReg, const uint32_t* gaRegs,</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   const FuncDetail::Value&amp; arg, uint32_t argIndex,</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   SArgData* sArgList, uint32_t&amp; sArgCount) {</a>
+<a name="1131"><span class="lineNum">    1131 </span>            : </a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   X86Compiler* cc = self-&gt;cc();</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :   uint32_t i;</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   uint32_t dstTypeId = arg.getTypeId();</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   uint32_t srcTypeId = sReg-&gt;getTypeId();</a>
+<a name="1136"><span class="lineNum">    1136 </span>            : </a>
+<a name="1137"><span class="lineNum">    1137 </span>            :   // First locate or create sArgBase.</a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; sArgCount; i++)</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineNoCov">          0 :     if (sArgList[i].sVd == sReg &amp;&amp; !sArgList[i].cVd)</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            :       break;</a>
+<a name="1141"><span class="lineNum">    1141 </span>            : </a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineNoCov">          0 :   SArgData* sArgData = &amp;sArgList[i];</span></a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineNoCov">          0 :   if (i == sArgCount) {</span></a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineNoCov">          0 :     sArgData-&gt;sVd = sReg;</span></a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineNoCov">          0 :     sArgData-&gt;cVd = nullptr;</span></a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineNoCov">          0 :     sArgData-&gt;sArg = nullptr;</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineNoCov">          0 :     sArgData-&gt;aType = 0xFF;</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineNoCov">          0 :     sArgCount++;</span></a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   }</a>
+<a name="1150"><span class="lineNum">    1150 </span>            : </a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   uint32_t srcRegKind = sReg-&gt;getKind();</a>
+<a name="1152"><span class="lineNum">    1152 </span>            : </a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   // Only handles float&lt;-&gt;double conversion.</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineNoCov">          0 :   if (X86RAPass_mustConvertSArg(self, dstTypeId, srcTypeId)) {</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :     uint32_t cvtTypeId = X86RAPass_typeOfConvertedSArg(self, dstTypeId, srcTypeId);</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     uint32_t cvtRegKind = X86Reg::kKindVec;</a>
+<a name="1157"><span class="lineNum">    1157 </span>            : </a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineNoCov">          0 :     while (++i &lt; sArgCount) {</span></a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineNoCov">          0 :       sArgData = &amp;sArgList[i];</span></a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineNoCov">          0 :       if (sArgData-&gt;sVd != sReg)</span></a>
+<a name="1161"><span class="lineNum">    1161 </span>            :         break;</a>
+<a name="1162"><span class="lineNum">    1162 </span>            : </a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineNoCov">          0 :       if (sArgData-&gt;cVd-&gt;getTypeId() != cvtTypeId || sArgData-&gt;aType != dstTypeId)</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            : </a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineNoCov">          0 :       sArgData-&gt;sArg-&gt;_args |= Utils::mask(argIndex);</span></a>
+<a name="1167"><span class="lineNum">    1167 </span>            :       return kErrorOk;</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :     }</a>
+<a name="1169"><span class="lineNum">    1169 </span>            : </a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineNoCov">          0 :     VirtReg* cReg = cc-&gt;newVirtReg(dstTypeId, x86OpData.archRegs.regInfo[X86Reg::kRegXmm].getSignature(), nullptr);</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :     if (!cReg) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="1172"><span class="lineNum">    1172 </span>            : </a>
+<a name="1173"><span class="lineNum">    1173 </span>            :     CCPushArg* sArg = cc-&gt;newNodeT&lt;CCPushArg&gt;(call, sReg, cReg);</a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineNoCov">          0 :     if (!sArg) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="1175"><span class="lineNum">    1175 </span>            : </a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     X86RAData* raData = self-&gt;newRAData(2);</a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 :     if (!raData) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="1178"><span class="lineNum">    1178 </span>            : </a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(self-&gt;assignRAId(cReg));</span></a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(self-&gt;assignRAId(sReg));</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            : </a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineNoCov">          0 :     raData-&gt;tiedTotal = 2;</span></a>
+<a name="1183"><span class="lineNum">    1183 </span>            :     raData-&gt;tiedCount.reset();</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :     raData-&gt;tiedCount.add(srcRegKind);</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     raData-&gt;tiedCount.add(cvtRegKind);</a>
+<a name="1186"><span class="lineNum">    1186 </span>            : </a>
+<a name="1187"><span class="lineNum">    1187 </span>            :     raData-&gt;tiedIndex.reset();</a>
+<a name="1188"><span class="lineNum">    1188 </span>            :     raData-&gt;inRegs.reset();</a>
+<a name="1189"><span class="lineNum">    1189 </span>            :     raData-&gt;outRegs.reset();</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     raData-&gt;clobberedRegs.reset();</a>
+<a name="1191"><span class="lineNum">    1191 </span>            : </a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :     if (srcRegKind &lt;= cvtRegKind) {</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineNoCov">          0 :       raData-&gt;tiedArray[0].init(sReg, TiedReg::kRReg, 0, gaRegs[srcRegKind]);</span></a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineNoCov">          0 :       raData-&gt;tiedArray[1].init(cReg, TiedReg::kWReg, 0, gaRegs[cvtRegKind]);</span></a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineNoCov">          0 :       raData-&gt;tiedIndex.set(cvtRegKind, srcRegKind != cvtRegKind);</span></a>
+<a name="1196"><span class="lineNum">    1196 </span>            :     }</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :     else {</a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineNoCov">          0 :       raData-&gt;tiedArray[0].init(cReg, TiedReg::kWReg, 0, gaRegs[cvtRegKind]);</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :       raData-&gt;tiedArray[1].init(sReg, TiedReg::kRReg, 0, gaRegs[srcRegKind]);</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            :       raData-&gt;tiedIndex.set(srcRegKind, 1);</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :     }</a>
+<a name="1202"><span class="lineNum">    1202 </span>            : </a>
+<a name="1203"><span class="lineNum">    1203 </span>            :     sArg-&gt;setPassData(raData);</a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineNoCov">          0 :     sArg-&gt;_args |= Utils::mask(argIndex);</span></a>
+<a name="1205"><span class="lineNum">    1205 </span>            : </a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :     cc-&gt;addBefore(sArg, call);</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineNoCov">          0 :     ::memmove(sArgData + 1, sArgData, (sArgCount - i) * sizeof(SArgData));</span></a>
+<a name="1208"><span class="lineNum">    1208 </span>            : </a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineNoCov">          0 :     sArgData-&gt;sVd = sReg;</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineNoCov">          0 :     sArgData-&gt;cVd = cReg;</span></a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineNoCov">          0 :     sArgData-&gt;sArg = sArg;</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineNoCov">          0 :     sArgData-&gt;aType = dstTypeId;</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            : </a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineNoCov">          0 :     sArgCount++;</span></a>
+<a name="1215"><span class="lineNum">    1215 </span>            :     return kErrorOk;</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :   }</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   else {</a>
+<a name="1218"><span class="lineNum">    1218 </span><span class="lineNoCov">          0 :     CCPushArg* sArg = sArgData-&gt;sArg;</span></a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineNoCov">          0 :     ASMJIT_PROPAGATE(self-&gt;assignRAId(sReg));</span></a>
+<a name="1220"><span class="lineNum">    1220 </span>            : </a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineNoCov">          0 :     if (!sArg) {</span></a>
+<a name="1222"><span class="lineNum">    1222 </span>            :       sArg = cc-&gt;newNodeT&lt;CCPushArg&gt;(call, sReg, (VirtReg*)nullptr);</a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineNoCov">          0 :       if (!sArg) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="1224"><span class="lineNum">    1224 </span>            : </a>
+<a name="1225"><span class="lineNum">    1225 </span>            :       X86RAData* raData = self-&gt;newRAData(1);</a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineNoCov">          0 :       if (!raData) return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="1227"><span class="lineNum">    1227 </span>            : </a>
+<a name="1228"><span class="lineNum">    1228 </span>            :       raData-&gt;tiedTotal = 1;</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :       raData-&gt;tiedIndex.reset();</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :       raData-&gt;tiedCount.reset();</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :       raData-&gt;tiedCount.add(srcRegKind);</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :       raData-&gt;inRegs.reset();</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :       raData-&gt;outRegs.reset();</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :       raData-&gt;clobberedRegs.reset();</a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineNoCov">          0 :       raData-&gt;tiedArray[0].init(sReg, TiedReg::kRReg, 0, gaRegs[srcRegKind]);</span></a>
+<a name="1236"><span class="lineNum">    1236 </span>            : </a>
+<a name="1237"><span class="lineNum">    1237 </span>            :       sArg-&gt;setPassData(raData);</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineNoCov">          0 :       sArgData-&gt;sArg = sArg;</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            : </a>
+<a name="1240"><span class="lineNum">    1240 </span><span class="lineNoCov">          0 :       cc-&gt;addBefore(sArg, call);</span></a>
+<a name="1241"><span class="lineNum">    1241 </span>            :     }</a>
+<a name="1242"><span class="lineNum">    1242 </span>            : </a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineNoCov">          0 :     sArg-&gt;_args |= Utils::mask(argIndex);</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            :     return kErrorOk;</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :   }</a>
+<a name="1246"><span class="lineNum">    1246 </span>            : }</a>
+<a name="1247"><span class="lineNum">    1247 </span>            : </a>
+<a name="1248"><span class="lineNum">    1248 </span>            : // ============================================================================</a>
+<a name="1249"><span class="lineNum">    1249 </span>            : // [asmjit::X86RAPass - Fetch]</a>
+<a name="1250"><span class="lineNum">    1250 </span>            : // ============================================================================</a>
+<a name="1251"><span class="lineNum">    1251 </span>            : </a>
+<a name="1252"><span class="lineNum">    1252 </span>            : //! \internal</a>
+<a name="1253"><span class="lineNum">    1253 </span>            : //!</a>
+<a name="1254"><span class="lineNum">    1254 </span>            : //! Prepare the given function `func`.</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : //!</a>
+<a name="1256"><span class="lineNum">    1256 </span>            : //! For each node:</a>
+<a name="1257"><span class="lineNum">    1257 </span>            : //! - Create and assign groupId and position.</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : //! - Collect all variables and merge them to vaList.</a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineCov">       1948 : Error X86RAPass::fetch() {</span></a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   uint32_t archType = cc()-&gt;getArchType();</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :   CCFunc* func = getFunc();</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span>            :   CBNode* node_ = func;</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :   CBNode* next = nullptr;</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :   CBNode* stop = getStop();</a>
+<a name="1266"><span class="lineNum">    1266 </span>            : </a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineCov">     157788 :   TiedReg agTmp[80];</span></a>
+<a name="1268"><span class="lineNum">    1268 </span>            :   SArgData sArgList[80];</a>
+<a name="1269"><span class="lineNum">    1269 </span>            : </a>
+<a name="1270"><span class="lineNum">    1270 </span>            :   uint32_t position = 0;</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :   ZoneList&lt;CBNode*&gt;::Link* jLink = nullptr;</a>
+<a name="1272"><span class="lineNum">    1272 </span>            : </a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   // Global allocable registers.</a>
+<a name="1274"><span class="lineNum">    1274 </span><span class="lineCov">       1948 :   uint32_t* gaRegs = _gaRegs;</span></a>
+<a name="1275"><span class="lineNum">    1275 </span>            : </a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">       1948 :   if (func-&gt;getFrameInfo().hasPreservedFP())</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineNoCov">          0 :     gaRegs[X86Reg::kKindGp] &amp;= ~Utils::mask(X86Gp::kIdBp);</span></a>
+<a name="1278"><span class="lineNum">    1278 </span>            : </a>
+<a name="1279"><span class="lineNum">    1279 </span>            :   // Allowed index registers (GP/XMM/YMM).</a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">       1948 :   const uint32_t indexMask = Utils::bits(_regCount.getGp()) &amp; ~(Utils::mask(4));</span></a>
+<a name="1281"><span class="lineNum">    1281 </span>            : </a>
+<a name="1282"><span class="lineNum">    1282 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   // [VI Macros]</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1285"><span class="lineNum">    1285 </span>            : </a>
+<a name="1286"><span class="lineNum">    1286 </span>            : #define RA_POPULATE(NODE) \</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :   do { \</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :     X86RAData* raData = newRAData(0); \</a>
+<a name="1289"><span class="lineNum">    1289 </span>            :     if (!raData) goto NoMem; \</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :     NODE-&gt;setPassData(raData); \</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :   } while (0)</a>
+<a name="1292"><span class="lineNum">    1292 </span>            : </a>
+<a name="1293"><span class="lineNum">    1293 </span>            : #define RA_DECLARE() \</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :   do { \</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :     X86RegCount tiedCount; \</a>
+<a name="1296"><span class="lineNum">    1296 </span>            :     X86RegCount tiedIndex; \</a>
+<a name="1297"><span class="lineNum">    1297 </span>            :     uint32_t tiedTotal = 0; \</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :     \</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :     X86RegMask inRegs; \</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :     X86RegMask outRegs; \</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :     X86RegMask clobberedRegs; \</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :     \</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :     tiedCount.reset(); \</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :     inRegs.reset(); \</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :     outRegs.reset(); \</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :     clobberedRegs.reset()</a>
+<a name="1307"><span class="lineNum">    1307 </span>            : </a>
+<a name="1308"><span class="lineNum">    1308 </span>            : #define RA_FINALIZE(NODE) \</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :     { \</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :       X86RAData* raData = newRAData(tiedTotal); \</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :       if (!raData) goto NoMem; \</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :       \</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :       tiedIndex.indexFromRegCount(tiedCount); \</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :       raData-&gt;tiedCount = tiedCount; \</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :       raData-&gt;tiedIndex = tiedIndex; \</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :       \</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :       raData-&gt;inRegs = inRegs; \</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :       raData-&gt;outRegs = outRegs; \</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :       raData-&gt;clobberedRegs = clobberedRegs; \</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :       \</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :       TiedReg* tied = agTmp; \</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :       while (tiedTotal) { \</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :         VirtReg* vreg = tied-&gt;vreg; \</a>
+<a name="1324"><span class="lineNum">    1324 </span>            :         \</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :         uint32_t _kind  = vreg-&gt;getKind(); \</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :         uint32_t _index = tiedIndex.get(_kind); \</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :         \</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :         tiedIndex.add(_kind); \</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :         if (tied-&gt;inRegs) \</a>
+<a name="1330"><span class="lineNum">    1330 </span>            :           tied-&gt;allocableRegs = tied-&gt;inRegs; \</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :         else if (tied-&gt;outPhysId != Globals::kInvalidRegId) \</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :           tied-&gt;allocableRegs = Utils::mask(tied-&gt;outPhysId); \</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :         else \</a>
+<a name="1334"><span class="lineNum">    1334 </span>            :           tied-&gt;allocableRegs &amp;= ~inRegs.get(_kind); \</a>
+<a name="1335"><span class="lineNum">    1335 </span>            :         \</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :         vreg-&gt;_tied = nullptr; \</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :         raData-&gt;setTiedAt(_index, *tied); \</a>
+<a name="1338"><span class="lineNum">    1338 </span>            :         \</a>
+<a name="1339"><span class="lineNum">    1339 </span>            :         tied++; \</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :         tiedTotal--; \</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :       } \</a>
+<a name="1342"><span class="lineNum">    1342 </span>            :       NODE-&gt;setPassData(raData); \</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :      } \</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :   } while (0)</a>
+<a name="1345"><span class="lineNum">    1345 </span>            : </a>
+<a name="1346"><span class="lineNum">    1346 </span>            : #define RA_INSERT(REG, TIED, FLAGS, NEW_ALLOCABLE) \</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :   do { \</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :     ASMJIT_ASSERT(REG-&gt;_tied == nullptr); \</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :     TIED = &amp;agTmp[tiedTotal++]; \</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :     TIED-&gt;init(REG, FLAGS, 0, NEW_ALLOCABLE); \</a>
+<a name="1351"><span class="lineNum">    1351 </span>            :     TIED-&gt;refCount++; \</a>
+<a name="1352"><span class="lineNum">    1352 </span>            :     REG-&gt;_tied = TIED; \</a>
+<a name="1353"><span class="lineNum">    1353 </span>            :     \</a>
+<a name="1354"><span class="lineNum">    1354 </span>            :     if (assignRAId(REG) != kErrorOk) goto NoMem; \</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :     tiedCount.add(REG-&gt;getKind()); \</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :   } while (0)</a>
+<a name="1357"><span class="lineNum">    1357 </span>            : </a>
+<a name="1358"><span class="lineNum">    1358 </span>            : #define RA_MERGE(REG, TIED, FLAGS, NEW_ALLOCABLE) \</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :   do { \</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :     TIED = REG-&gt;_tied; \</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :     \</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :     if (!TIED) { \</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :       TIED = &amp;agTmp[tiedTotal++]; \</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :       TIED-&gt;init(REG, 0, 0, NEW_ALLOCABLE); \</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :       REG-&gt;_tied = TIED; \</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :       \</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :       if (assignRAId(REG) != kErrorOk) goto NoMem; \</a>
+<a name="1368"><span class="lineNum">    1368 </span>            :       tiedCount.add(REG-&gt;getKind()); \</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :     } \</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :     \</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :     TIED-&gt;flags |= FLAGS; \</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :     TIED-&gt;refCount++; \</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :   } while (0)</a>
+<a name="1374"><span class="lineNum">    1374 </span>            : </a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1376"><span class="lineNum">    1376 </span>            :   // [Loop]</a>
+<a name="1377"><span class="lineNum">    1377 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1378"><span class="lineNum">    1378 </span>            : </a>
+<a name="1379"><span class="lineNum">    1379 </span>            :   do {</a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">      34754 : _Do:</span></a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineCov">      36702 :     while (node_-&gt;hasPassData()) {</span></a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineNoCov">          0 : _NextGroup:</span></a>
+<a name="1383"><span class="lineNum">    1383 </span><span class="lineCov">       1948 :       if (!jLink)</span></a>
+<a name="1384"><span class="lineNum">    1384 </span>            :         jLink = _jccList.getFirst();</a>
+<a name="1385"><span class="lineNum">    1385 </span>            :       else</a>
+<a name="1386"><span class="lineNum">    1386 </span>            :         jLink = jLink-&gt;getNext();</a>
+<a name="1387"><span class="lineNum">    1387 </span>            : </a>
+<a name="1388"><span class="lineNum">    1388 </span><span class="lineCov">       1948 :       if (!jLink) goto _Done;</span></a>
+<a name="1389"><span class="lineNum">    1389 </span>            :       node_ = X86RAPass_getOppositeJccFlow(static_cast&lt;CBJump*&gt;(jLink-&gt;getValue()));</a>
+<a name="1390"><span class="lineNum">    1390 </span>            :     }</a>
+<a name="1391"><span class="lineNum">    1391 </span>            : </a>
+<a name="1392"><span class="lineNum">    1392 </span><span class="lineCov">      36702 :     position++;</span></a>
+<a name="1393"><span class="lineNum">    1393 </span>            : </a>
+<a name="1394"><span class="lineNum">    1394 </span>            :     next = node_-&gt;getNext();</a>
+<a name="1395"><span class="lineNum">    1395 </span>            :     node_-&gt;setPosition(position);</a>
+<a name="1396"><span class="lineNum">    1396 </span>            : </a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">      36702 :     switch (node_-&gt;getType()) {</span></a>
+<a name="1398"><span class="lineNum">    1398 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1399"><span class="lineNum">    1399 </span>            :       // [Align/Embed]</a>
+<a name="1400"><span class="lineNum">    1400 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1401"><span class="lineNum">    1401 </span>            : </a>
+<a name="1402"><span class="lineNum">    1402 </span>            :       case CBNode::kNodeAlign:</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :       case CBNode::kNodeData:</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :       default:</a>
+<a name="1405"><span class="lineNum">    1405 </span><span class="lineNoCov">          0 :         RA_POPULATE(node_);</span></a>
+<a name="1406"><span class="lineNum">    1406 </span>            :         break;</a>
+<a name="1407"><span class="lineNum">    1407 </span>            : </a>
+<a name="1408"><span class="lineNum">    1408 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :       // [Hint]</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1411"><span class="lineNum">    1411 </span>            : </a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineNoCov">          0 :       case CBNode::kNodeHint: {</span></a>
+<a name="1413"><span class="lineNum">    1413 </span>            :         CCHint* node = static_cast&lt;CCHint*&gt;(node_);</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :         RA_DECLARE();</a>
+<a name="1415"><span class="lineNum">    1415 </span>            : </a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineNoCov">          0 :         if (node-&gt;getHint() == CCHint::kHintAlloc) {</span></a>
+<a name="1417"><span class="lineNum">    1417 </span>            :           uint32_t remain[Globals::kMaxVRegKinds];</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :           CCHint* cur = node;</a>
+<a name="1419"><span class="lineNum">    1419 </span>            : </a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineNoCov">          0 :           remain[X86Reg::kKindGp ] = _regCount.getGp() - 1 - func-&gt;getFrameInfo().hasPreservedFP();</span></a>
+<a name="1421"><span class="lineNum">    1421 </span><span class="lineNoCov">          0 :           remain[X86Reg::kKindMm ] = _regCount.getMm();</span></a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineNoCov">          0 :           remain[X86Reg::kKindK  ] = _regCount.getK();</span></a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineNoCov">          0 :           remain[X86Reg::kKindVec] = _regCount.getVec();</span></a>
+<a name="1424"><span class="lineNum">    1424 </span>            : </a>
+<a name="1425"><span class="lineNum">    1425 </span>            :           // Merge as many alloc-hints as possible.</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :           for (;;) {</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :             VirtReg* vreg = static_cast&lt;VirtReg*&gt;(cur-&gt;getVReg());</a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineNoCov">          0 :             TiedReg* tied = vreg-&gt;_tied;</span></a>
+<a name="1429"><span class="lineNum">    1429 </span>            : </a>
+<a name="1430"><span class="lineNum">    1430 </span>            :             uint32_t kind = vreg-&gt;getKind();</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :             uint32_t physId = cur-&gt;getValue();</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :             uint32_t regMask = 0;</a>
+<a name="1433"><span class="lineNum">    1433 </span>            : </a>
+<a name="1434"><span class="lineNum">    1434 </span>            :             // We handle both kInvalidReg and kInvalidValue.</a>
+<a name="1435"><span class="lineNum">    1435 </span><span class="lineNoCov">          0 :             if (physId &lt; Globals::kInvalidRegId)</span></a>
+<a name="1436"><span class="lineNum">    1436 </span>            :               regMask = Utils::mask(physId);</a>
+<a name="1437"><span class="lineNum">    1437 </span>            : </a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineNoCov">          0 :             if (!tied) {</span></a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineNoCov">          0 :               if (inRegs.has(kind, regMask) || remain[kind] == 0)</span></a>
+<a name="1440"><span class="lineNum">    1440 </span>            :                 break;</a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineNoCov">          0 :               RA_INSERT(vreg, tied, TiedReg::kRReg, gaRegs[kind]);</span></a>
+<a name="1442"><span class="lineNum">    1442 </span>            : </a>
+<a name="1443"><span class="lineNum">    1443 </span><span class="lineNoCov">          0 :               if (regMask != 0) {</span></a>
+<a name="1444"><span class="lineNum">    1444 </span>            :                 inRegs.xor_(kind, regMask);</a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineNoCov">          0 :                 tied-&gt;inRegs = regMask;</span></a>
+<a name="1446"><span class="lineNum">    1446 </span>            :                 tied-&gt;setInPhysId(physId);</a>
+<a name="1447"><span class="lineNum">    1447 </span>            :               }</a>
+<a name="1448"><span class="lineNum">    1448 </span><span class="lineNoCov">          0 :               remain[kind]--;</span></a>
+<a name="1449"><span class="lineNum">    1449 </span>            :             }</a>
+<a name="1450"><span class="lineNum">    1450 </span><span class="lineNoCov">          0 :             else if (regMask != 0) {</span></a>
+<a name="1451"><span class="lineNum">    1451 </span><span class="lineNoCov">          0 :               if (inRegs.has(kind, regMask) &amp;&amp; tied-&gt;inRegs != regMask)</span></a>
+<a name="1452"><span class="lineNum">    1452 </span>            :                 break;</a>
+<a name="1453"><span class="lineNum">    1453 </span>            : </a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineNoCov">          0 :               inRegs.xor_(kind, tied-&gt;inRegs | regMask);</span></a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineNoCov">          0 :               tied-&gt;inRegs = regMask;</span></a>
+<a name="1456"><span class="lineNum">    1456 </span>            :               tied-&gt;setInPhysId(physId);</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :             }</a>
+<a name="1458"><span class="lineNum">    1458 </span>            : </a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineNoCov">          0 :             if (cur != node)</span></a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineNoCov">          0 :               cc()-&gt;removeNode(cur);</span></a>
+<a name="1461"><span class="lineNum">    1461 </span>            : </a>
+<a name="1462"><span class="lineNum">    1462 </span>            :             cur = static_cast&lt;CCHint*&gt;(node-&gt;getNext());</a>
+<a name="1463"><span class="lineNum">    1463 </span><span class="lineNoCov">          0 :             if (!cur || cur-&gt;getType() != CBNode::kNodeHint || cur-&gt;getHint() != CCHint::kHintAlloc)</span></a>
+<a name="1464"><span class="lineNum">    1464 </span>            :               break;</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :           }</a>
+<a name="1466"><span class="lineNum">    1466 </span>            : </a>
+<a name="1467"><span class="lineNum">    1467 </span>            :           next = node-&gt;getNext();</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :         }</a>
+<a name="1469"><span class="lineNum">    1469 </span>            :         else  {</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :           VirtReg* vreg = static_cast&lt;VirtReg*&gt;(node-&gt;getVReg());</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :           TiedReg* tied;</a>
+<a name="1472"><span class="lineNum">    1472 </span>            : </a>
+<a name="1473"><span class="lineNum">    1473 </span>            :           uint32_t flags = 0;</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :           switch (node-&gt;getHint()) {</a>
+<a name="1475"><span class="lineNum">    1475 </span><span class="lineNoCov">          0 :             case CCHint::kHintSpill       : flags = TiedReg::kRMem | TiedReg::kSpill; break;</span></a>
+<a name="1476"><span class="lineNum">    1476 </span><span class="lineNoCov">          0 :             case CCHint::kHintSave        : flags = TiedReg::kRMem                  ; break;</span></a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineNoCov">          0 :             case CCHint::kHintSaveAndUnuse: flags = TiedReg::kRMem | TiedReg::kUnuse; break;</span></a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineNoCov">          0 :             case CCHint::kHintUnuse       : flags = TiedReg::kUnuse                 ; break;</span></a>
+<a name="1479"><span class="lineNum">    1479 </span>            :           }</a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineNoCov">          0 :           RA_INSERT(vreg, tied, flags, 0);</span></a>
+<a name="1481"><span class="lineNum">    1481 </span>            :         }</a>
+<a name="1482"><span class="lineNum">    1482 </span>            : </a>
+<a name="1483"><span class="lineNum">    1483 </span><span class="lineNoCov">          0 :         RA_FINALIZE(node_);</span></a>
+<a name="1484"><span class="lineNum">    1484 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="1485"><span class="lineNum">    1485 </span>            :       }</a>
+<a name="1486"><span class="lineNum">    1486 </span>            : </a>
+<a name="1487"><span class="lineNum">    1487 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :       // [Label]</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1490"><span class="lineNum">    1490 </span>            : </a>
+<a name="1491"><span class="lineNum">    1491 </span>            :       case CBNode::kNodeLabel: {</a>
+<a name="1492"><span class="lineNum">    1492 </span><span class="lineNoCov">          0 :         RA_POPULATE(node_);</span></a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineNoCov">          0 :         if (node_ == func-&gt;getExitNode()) {</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineNoCov">          0 :           ASMJIT_PROPAGATE(addReturningNode(node_));</span></a>
+<a name="1495"><span class="lineNum">    1495 </span><span class="lineNoCov">          0 :           goto _NextGroup;</span></a>
+<a name="1496"><span class="lineNum">    1496 </span>            :         }</a>
+<a name="1497"><span class="lineNum">    1497 </span>            :         break;</a>
+<a name="1498"><span class="lineNum">    1498 </span>            :       }</a>
+<a name="1499"><span class="lineNum">    1499 </span>            : </a>
+<a name="1500"><span class="lineNum">    1500 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1501"><span class="lineNum">    1501 </span>            :       // [Inst]</a>
+<a name="1502"><span class="lineNum">    1502 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1503"><span class="lineNum">    1503 </span>            : </a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineCov">      31158 :       case CBNode::kNodeInst: {</span></a>
+<a name="1505"><span class="lineNum">    1505 </span>            :         CBInst* node = static_cast&lt;CBInst*&gt;(node_);</a>
+<a name="1506"><span class="lineNum">    1506 </span>            : </a>
+<a name="1507"><span class="lineNum">    1507 </span>            :         uint32_t instId = node-&gt;getInstId();</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :         uint32_t flags = node-&gt;getFlags();</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :         uint32_t options = node-&gt;getOptions();</a>
+<a name="1510"><span class="lineNum">    1510 </span>            :         uint32_t gpAllowedMask = 0xFFFFFFFF;</a>
+<a name="1511"><span class="lineNum">    1511 </span>            : </a>
+<a name="1512"><span class="lineNum">    1512 </span>            :         Operand* opArray = node-&gt;getOpArray();</a>
+<a name="1513"><span class="lineNum">    1513 </span>            :         uint32_t opCount = node-&gt;getOpCount();</a>
+<a name="1514"><span class="lineNum">    1514 </span>            : </a>
+<a name="1515"><span class="lineNum">    1515 </span>            :         RA_DECLARE();</a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">      31158 :         if (opCount) {</span></a>
+<a name="1517"><span class="lineNum">    1517 </span>            :           const X86Inst&amp; inst = X86Inst::getInst(instId);</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :           const X86Inst::CommonData&amp; commonData = inst.getCommonData();</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :           const X86SpecialInst* special = nullptr;</a>
+<a name="1520"><span class="lineNum">    1520 </span>            : </a>
+<a name="1521"><span class="lineNum">    1521 </span>            :           // Collect instruction flags and merge all 'TiedReg's.</a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineCov">      31158 :           if (commonData.isFpu())</span></a>
+<a name="1523"><span class="lineNum">    1523 </span>            :             flags |= CBNode::kFlagIsFp;</a>
+<a name="1524"><span class="lineNum">    1524 </span>            : </a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineCov">      31158 :           if (commonData.hasFixedRM() &amp;&amp; (special = X86SpecialInst_get(instId, opArray, opCount)) != nullptr)</span></a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineNoCov">          0 :             flags |= CBNode::kFlagIsSpecial;</span></a>
+<a name="1527"><span class="lineNum">    1527 </span>            : </a>
+<a name="1528"><span class="lineNum">    1528 </span><span class="lineCov">      93594 :           for (uint32_t i = 0; i &lt; opCount; i++) {</span></a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">      62436 :             Operand* op = &amp;opArray[i];</span></a>
+<a name="1530"><span class="lineNum">    1530 </span>            :             VirtReg* vreg;</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :             TiedReg* tied;</a>
+<a name="1532"><span class="lineNum">    1532 </span>            : </a>
+<a name="1533"><span class="lineNum">    1533 </span>            :             if (op-&gt;isVirtReg()) {</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :               vreg = cc()-&gt;getVirtRegById(op-&gt;getId());</a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineCov">      48948 :               if (vreg-&gt;isFixed()) continue;</span></a>
+<a name="1536"><span class="lineNum">    1536 </span>            : </a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineCov">     119788 :               RA_MERGE(vreg, tied, 0, gaRegs[vreg-&gt;getKind()] &amp; gpAllowedMask);</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">      48948 :               if (static_cast&lt;X86Reg*&gt;(op)-&gt;isGpb()) {</span></a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineNoCov">          0 :                 tied-&gt;flags |= static_cast&lt;X86Gp*&gt;(op)-&gt;isGpbLo() ? TiedReg::kX86GpbLo : TiedReg::kX86GpbHi;</span></a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineNoCov">          0 :                 if (archType == ArchInfo::kTypeX86) {</span></a>
+<a name="1541"><span class="lineNum">    1541 </span>            :                   // If a byte register is accessed in 32-bit mode we have to limit</a>
+<a name="1542"><span class="lineNum">    1542 </span>            :                   // all allocable registers for that variable to eax/ebx/ecx/edx.</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :                   // Other variables are not affected.</a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineNoCov">          0 :                   tied-&gt;allocableRegs &amp;= 0x0F;</span></a>
+<a name="1545"><span class="lineNum">    1545 </span>            :                 }</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :                 else {</a>
+<a name="1547"><span class="lineNum">    1547 </span>            :                   // It's fine if lo-byte register is accessed in 64-bit mode;</a>
+<a name="1548"><span class="lineNum">    1548 </span>            :                   // however, hi-byte has to be checked and if it's used all</a>
+<a name="1549"><span class="lineNum">    1549 </span>            :                   // registers (GP/XMM) could be only allocated in the lower eight</a>
+<a name="1550"><span class="lineNum">    1550 </span>            :                   // half. To do that, we patch 'allocableRegs' of all variables</a>
+<a name="1551"><span class="lineNum">    1551 </span>            :                   // we collected until now and change the allocable restriction</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :                   // for variables that come after.</a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineNoCov">          0 :                   if (static_cast&lt;X86Gp*&gt;(op)-&gt;isGpbHi()) {</span></a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineNoCov">          0 :                     tied-&gt;allocableRegs &amp;= 0x0F;</span></a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineNoCov">          0 :                     if (gpAllowedMask != 0xFF) {</span></a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineNoCov">          0 :                       for (uint32_t j = 0; j &lt; i; j++)</span></a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineNoCov">          0 :                         agTmp[j].allocableRegs &amp;= (agTmp[j].flags &amp; TiedReg::kX86GpbHi) ? 0x0F : 0xFF;</span></a>
+<a name="1558"><span class="lineNum">    1558 </span>            :                       gpAllowedMask = 0xFF;</a>
+<a name="1559"><span class="lineNum">    1559 </span>            :                     }</a>
+<a name="1560"><span class="lineNum">    1560 </span>            :                   }</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :                 }</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :               }</a>
+<a name="1563"><span class="lineNum">    1563 </span>            : </a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineCov">      48948 :               if (special) {</span></a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineNoCov">          0 :                 uint32_t inReg = special[i].inReg;</span></a>
+<a name="1566"><span class="lineNum">    1566 </span><span class="lineNoCov">          0 :                 uint32_t outReg = special[i].outReg;</span></a>
+<a name="1567"><span class="lineNum">    1567 </span>            :                 uint32_t c;</a>
+<a name="1568"><span class="lineNum">    1568 </span>            : </a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineNoCov">          0 :                 if (static_cast&lt;const X86Reg*&gt;(op)-&gt;isGp())</span></a>
+<a name="1570"><span class="lineNum">    1570 </span>            :                   c = X86Reg::kKindGp;</a>
+<a name="1571"><span class="lineNum">    1571 </span>            :                 else</a>
+<a name="1572"><span class="lineNum">    1572 </span>            :                   c = X86Reg::kKindVec;</a>
+<a name="1573"><span class="lineNum">    1573 </span>            : </a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineNoCov">          0 :                 if (inReg != Globals::kInvalidRegId) {</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            :                   uint32_t mask = Utils::mask(inReg);</a>
+<a name="1576"><span class="lineNum">    1576 </span>            :                   inRegs.or_(c, mask);</a>
+<a name="1577"><span class="lineNum">    1577 </span><span class="lineNoCov">          0 :                   tied-&gt;inRegs |= mask;</span></a>
+<a name="1578"><span class="lineNum">    1578 </span>            :                 }</a>
+<a name="1579"><span class="lineNum">    1579 </span>            : </a>
+<a name="1580"><span class="lineNum">    1580 </span><span class="lineNoCov">          0 :                 if (outReg != Globals::kInvalidRegId) {</span></a>
+<a name="1581"><span class="lineNum">    1581 </span>            :                   uint32_t mask = Utils::mask(outReg);</a>
+<a name="1582"><span class="lineNum">    1582 </span>            :                   outRegs.or_(c, mask);</a>
+<a name="1583"><span class="lineNum">    1583 </span>            :                   tied-&gt;setOutPhysId(outReg);</a>
+<a name="1584"><span class="lineNum">    1584 </span>            :                 }</a>
+<a name="1585"><span class="lineNum">    1585 </span>            : </a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineNoCov">          0 :                 tied-&gt;flags |= special[i].flags;</span></a>
+<a name="1587"><span class="lineNum">    1587 </span>            :               }</a>
+<a name="1588"><span class="lineNum">    1588 </span>            :               else {</a>
+<a name="1589"><span class="lineNum">    1589 </span>            :                 uint32_t inFlags = TiedReg::kRReg;</a>
+<a name="1590"><span class="lineNum">    1590 </span>            :                 uint32_t outFlags = TiedReg::kWReg;</a>
+<a name="1591"><span class="lineNum">    1591 </span>            :                 uint32_t combinedFlags;</a>
+<a name="1592"><span class="lineNum">    1592 </span>            : </a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineCov">      48948 :                 if (i == 0) {</span></a>
+<a name="1594"><span class="lineNum">    1594 </span>            :                   // Read/Write is usually the combination of the first operand.</a>
+<a name="1595"><span class="lineNum">    1595 </span>            :                   combinedFlags = inFlags | outFlags;</a>
+<a name="1596"><span class="lineNum">    1596 </span>            : </a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineCov">      30892 :                   if (node-&gt;getOptions() &amp; CodeEmitter::kOptionOverwrite) {</span></a>
+<a name="1598"><span class="lineNum">    1598 </span>            :                     // Manually forcing write-only.</a>
+<a name="1599"><span class="lineNum">    1599 </span>            :                     combinedFlags = outFlags;</a>
+<a name="1600"><span class="lineNum">    1600 </span>            :                   }</a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineCov">      30892 :                   else if (commonData.isUseW()) {</span></a>
+<a name="1602"><span class="lineNum">    1602 </span>            :                     // Write-only instruction.</a>
+<a name="1603"><span class="lineNum">    1603 </span>            :                     uint32_t movSize = commonData.getWriteSize();</a>
+<a name="1604"><span class="lineNum">    1604 </span>            :                     uint32_t regSize = vreg-&gt;getSize();</a>
+<a name="1605"><span class="lineNum">    1605 </span>            : </a>
+<a name="1606"><span class="lineNum">    1606 </span>            :                     // Exception - If the source operand is a memory location</a>
+<a name="1607"><span class="lineNum">    1607 </span>            :                     // promote move size into 16 bytes.</a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineCov">      21892 :                     if (opArray[1].isMem() &amp;&amp; inst.getOperationData().isMovSsSd())</span></a>
+<a name="1609"><span class="lineNum">    1609 </span>            :                       movSize = 16;</a>
+<a name="1610"><span class="lineNum">    1610 </span>            : </a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineCov">      21892 :                     if (static_cast&lt;const X86Reg*&gt;(op)-&gt;isGp()) {</span></a>
+<a name="1612"><span class="lineNum">    1612 </span>            :                       uint32_t opSize = static_cast&lt;const X86Reg*&gt;(op)-&gt;getSize();</a>
+<a name="1613"><span class="lineNum">    1613 </span>            : </a>
+<a name="1614"><span class="lineNum">    1614 </span>            :                       // Move size is zero in case that it should be determined</a>
+<a name="1615"><span class="lineNum">    1615 </span>            :                       // from the destination register.</a>
+<a name="1616"><span class="lineNum">    1616 </span><span class="lineCov">       7268 :                       if (movSize == 0)</span></a>
+<a name="1617"><span class="lineNum">    1617 </span>            :                         movSize = opSize;</a>
+<a name="1618"><span class="lineNum">    1618 </span>            : </a>
+<a name="1619"><span class="lineNum">    1619 </span>            :                       // Handle the case that a 32-bit operation in 64-bit mode</a>
+<a name="1620"><span class="lineNum">    1620 </span>            :                       // always clears the rest of the destination register and</a>
+<a name="1621"><span class="lineNum">    1621 </span>            :                       // the case that move size is actually greater than or</a>
+<a name="1622"><span class="lineNum">    1622 </span>            :                       // equal to the size of the variable.</a>
+<a name="1623"><span class="lineNum">    1623 </span><span class="lineCov">       7268 :                       if (movSize &gt;= 4 || movSize &gt;= regSize)</span></a>
+<a name="1624"><span class="lineNum">    1624 </span>            :                         combinedFlags = outFlags;</a>
+<a name="1625"><span class="lineNum">    1625 </span>            :                     }</a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineCov">      14624 :                     else if (movSize == 0 || movSize &gt;= regSize) {</span></a>
+<a name="1627"><span class="lineNum">    1627 </span>            :                       // If move size is greater than or equal to the size of</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :                       // the variable there is nothing to do, because the move</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :                       // will overwrite the variable in all cases.</a>
+<a name="1630"><span class="lineNum">    1630 </span>            :                       combinedFlags = outFlags;</a>
+<a name="1631"><span class="lineNum">    1631 </span>            :                     }</a>
+<a name="1632"><span class="lineNum">    1632 </span>            :                   }</a>
+<a name="1633"><span class="lineNum">    1633 </span><span class="lineCov">       9000 :                   else if (commonData.isUseR()) {</span></a>
+<a name="1634"><span class="lineNum">    1634 </span>            :                     // Comparison/Test instructions don't modify any operand.</a>
+<a name="1635"><span class="lineNum">    1635 </span>            :                     combinedFlags = inFlags;</a>
+<a name="1636"><span class="lineNum">    1636 </span>            :                   }</a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineCov">       9000 :                   else if (instId == X86Inst::kIdImul &amp;&amp; opCount == 3) {</span></a>
+<a name="1638"><span class="lineNum">    1638 </span>            :                     // Imul.</a>
+<a name="1639"><span class="lineNum">    1639 </span>            :                     combinedFlags = outFlags;</a>
+<a name="1640"><span class="lineNum">    1640 </span>            :                   }</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :                 }</a>
+<a name="1642"><span class="lineNum">    1642 </span>            :                 else {</a>
+<a name="1643"><span class="lineNum">    1643 </span>            :                   // Read-Only is usually the combination of the second/third/fourth operands.</a>
+<a name="1644"><span class="lineNum">    1644 </span>            :                   combinedFlags = inFlags;</a>
+<a name="1645"><span class="lineNum">    1645 </span>            : </a>
+<a name="1646"><span class="lineNum">    1646 </span>            :                   // Idiv is a special instruction, never handled here.</a>
+<a name="1647"><span class="lineNum">    1647 </span>            :                   ASMJIT_ASSERT(instId != X86Inst::kIdIdiv);</a>
+<a name="1648"><span class="lineNum">    1648 </span>            : </a>
+<a name="1649"><span class="lineNum">    1649 </span>            :                   // Xchg/Xadd/Imul.</a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineCov">      18056 :                   if (commonData.isUseXX() || (instId == X86Inst::kIdImul &amp;&amp; opCount == 3 &amp;&amp; i == 1))</span></a>
+<a name="1651"><span class="lineNum">    1651 </span>            :                     combinedFlags = inFlags | outFlags;</a>
+<a name="1652"><span class="lineNum">    1652 </span>            :                 }</a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineCov">      48948 :                 tied-&gt;flags |= combinedFlags;</span></a>
+<a name="1654"><span class="lineNum">    1654 </span>            :               }</a>
+<a name="1655"><span class="lineNum">    1655 </span>            :             }</a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineCov">      13488 :             else if (op-&gt;isMem()) {</span></a>
+<a name="1657"><span class="lineNum">    1657 </span>            :               X86Mem* m = static_cast&lt;X86Mem*&gt;(op);</a>
+<a name="1658"><span class="lineNum">    1658 </span>            :               node-&gt;setMemOpIndex(i);</a>
+<a name="1659"><span class="lineNum">    1659 </span>            : </a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">       6100 :               uint32_t specBase = special ? uint32_t(special[i].inReg) : uint32_t(Globals::kInvalidRegId);</span></a>
+<a name="1661"><span class="lineNum">    1661 </span>            : </a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineCov">       6100 :               if (m-&gt;hasBaseReg()) {</span></a>
+<a name="1663"><span class="lineNum">    1663 </span>            :                 uint32_t id = m-&gt;getBaseId();</a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">       6100 :                 if (cc()-&gt;isVirtRegValid(id)) {</span></a>
+<a name="1665"><span class="lineNum">    1665 </span>            :                   vreg = cc()-&gt;getVirtRegById(id);</a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineCov">       6100 :                   if (!vreg-&gt;isStack() &amp;&amp; !vreg-&gt;isFixed()) {</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineCov">      12200 :                     RA_MERGE(vreg, tied, 0, gaRegs[vreg-&gt;getKind()] &amp; gpAllowedMask);</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">       6100 :                     if (m-&gt;isRegHome()) {</span></a>
+<a name="1669"><span class="lineNum">    1669 </span>            :                       uint32_t inFlags = TiedReg::kRMem;</a>
+<a name="1670"><span class="lineNum">    1670 </span>            :                       uint32_t outFlags = TiedReg::kWMem;</a>
+<a name="1671"><span class="lineNum">    1671 </span>            :                       uint32_t combinedFlags;</a>
+<a name="1672"><span class="lineNum">    1672 </span>            : </a>
+<a name="1673"><span class="lineNum">    1673 </span><span class="lineNoCov">          0 :                       if (i == 0) {</span></a>
+<a name="1674"><span class="lineNum">    1674 </span>            :                         // Default for the first operand.</a>
+<a name="1675"><span class="lineNum">    1675 </span>            :                         combinedFlags = inFlags | outFlags;</a>
+<a name="1676"><span class="lineNum">    1676 </span>            : </a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineNoCov">          0 :                         if (commonData.isUseW()) {</span></a>
+<a name="1678"><span class="lineNum">    1678 </span>            :                           // Move to memory - setting the right flags is important</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :                           // as if it's just move to the register. It's just a bit</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :                           // simpler as there are no special cases.</a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineNoCov">          0 :                           uint32_t movSize = std::max&lt;uint32_t&gt;(commonData.getWriteSize(), m-&gt;getSize());</span></a>
+<a name="1682"><span class="lineNum">    1682 </span>            :                           uint32_t regSize = vreg-&gt;getSize();</a>
+<a name="1683"><span class="lineNum">    1683 </span>            : </a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineNoCov">          0 :                           if (movSize &gt;= regSize)</span></a>
+<a name="1685"><span class="lineNum">    1685 </span>            :                             combinedFlags = outFlags;</a>
+<a name="1686"><span class="lineNum">    1686 </span>            :                         }</a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineNoCov">          0 :                         else if (commonData.isUseR()) {</span></a>
+<a name="1688"><span class="lineNum">    1688 </span>            :                           // Comparison/Test instructions don't modify any operand.</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :                           combinedFlags = inFlags;</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :                         }</a>
+<a name="1691"><span class="lineNum">    1691 </span>            :                       }</a>
+<a name="1692"><span class="lineNum">    1692 </span>            :                       else {</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :                         // Default for the second operand.</a>
+<a name="1694"><span class="lineNum">    1694 </span>            :                         combinedFlags = inFlags;</a>
+<a name="1695"><span class="lineNum">    1695 </span>            : </a>
+<a name="1696"><span class="lineNum">    1696 </span>            :                         // Handle Xchg instruction (modifies both operands).</a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineNoCov">          0 :                         if (commonData.isUseXX())</span></a>
+<a name="1698"><span class="lineNum">    1698 </span>            :                           combinedFlags = inFlags | outFlags;</a>
+<a name="1699"><span class="lineNum">    1699 </span>            :                       }</a>
+<a name="1700"><span class="lineNum">    1700 </span>            : </a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineNoCov">          0 :                       tied-&gt;flags |= combinedFlags;</span></a>
+<a name="1702"><span class="lineNum">    1702 </span>            :                     }</a>
+<a name="1703"><span class="lineNum">    1703 </span>            :                     else {</a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineCov">       6100 :                       if (specBase != Globals::kInvalidRegId) {</span></a>
+<a name="1705"><span class="lineNum">    1705 </span>            :                         uint32_t mask = Utils::mask(specBase);</a>
+<a name="1706"><span class="lineNum">    1706 </span>            :                         inRegs.or_(vreg-&gt;getKind(), mask);</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :                         outRegs.or_(vreg-&gt;getKind(), mask);</a>
+<a name="1708"><span class="lineNum">    1708 </span><span class="lineNoCov">          0 :                         tied-&gt;inRegs |= mask;</span></a>
+<a name="1709"><span class="lineNum">    1709 </span>            :                         tied-&gt;setOutPhysId(specBase);</a>
+<a name="1710"><span class="lineNum">    1710 </span><span class="lineNoCov">          0 :                         tied-&gt;flags |= special[i].flags;</span></a>
+<a name="1711"><span class="lineNum">    1711 </span>            :                       }</a>
+<a name="1712"><span class="lineNum">    1712 </span>            :                       else {</a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineCov">       6100 :                         tied-&gt;flags |= TiedReg::kRReg;</span></a>
+<a name="1714"><span class="lineNum">    1714 </span>            :                       }</a>
+<a name="1715"><span class="lineNum">    1715 </span>            :                     }</a>
+<a name="1716"><span class="lineNum">    1716 </span>            :                   }</a>
+<a name="1717"><span class="lineNum">    1717 </span>            :                 }</a>
+<a name="1718"><span class="lineNum">    1718 </span>            :               }</a>
+<a name="1719"><span class="lineNum">    1719 </span>            : </a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineCov">       6100 :               if (m-&gt;hasIndexReg()) {</span></a>
+<a name="1721"><span class="lineNum">    1721 </span>            :                 uint32_t id = m-&gt;getIndexId();</a>
+<a name="1722"><span class="lineNum">    1722 </span><span class="lineNoCov">          0 :                 if (cc()-&gt;isVirtRegValid(id)) {</span></a>
+<a name="1723"><span class="lineNum">    1723 </span>            :                   // Restrict allocation to all registers except ESP|RSP.</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :                   vreg = cc()-&gt;getVirtRegById(m-&gt;getIndexId());</a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineNoCov">          0 :                   if (!vreg-&gt;isFixed()) {</span></a>
+<a name="1726"><span class="lineNum">    1726 </span>            :                     // TODO: AVX vector operands support.</a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineNoCov">          0 :                     RA_MERGE(vreg, tied, 0, gaRegs[X86Reg::kKindGp] &amp; gpAllowedMask);</span></a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineNoCov">          0 :                     tied-&gt;allocableRegs &amp;= indexMask;</span></a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineNoCov">          0 :                     tied-&gt;flags |= TiedReg::kRReg;</span></a>
+<a name="1730"><span class="lineNum">    1730 </span>            :                   }</a>
+<a name="1731"><span class="lineNum">    1731 </span>            :                 }</a>
+<a name="1732"><span class="lineNum">    1732 </span>            :               }</a>
+<a name="1733"><span class="lineNum">    1733 </span>            :             }</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :           }</a>
+<a name="1735"><span class="lineNum">    1735 </span>            : </a>
+<a name="1736"><span class="lineNum">    1736 </span>            :           node-&gt;setFlags(flags);</a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineCov">      31158 :           if (tiedTotal) {</span></a>
+<a name="1738"><span class="lineNum">    1738 </span>            :             // Handle instructions which result in zeros/ones or nop if used with the</a>
+<a name="1739"><span class="lineNum">    1739 </span>            :             // same destination and source operand.</a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">      31406 :             if (tiedTotal == 1 &amp;&amp; opCount &gt;= 2 &amp;&amp; opArray[0].isVirtReg() &amp;&amp; opArray[1].isVirtReg() &amp;&amp; !node-&gt;hasMemOp())</span></a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineCov">        248 :               X86RAPass_prepareSingleVarInst(instId, &amp;agTmp[0]);</span></a>
+<a name="1742"><span class="lineNum">    1742 </span>            :           }</a>
+<a name="1743"><span class="lineNum">    1743 </span>            : </a>
+<a name="1744"><span class="lineNum">    1744 </span>            :           // Turn on AVX if the instruction operates on XMM|YMM|ZMM registers and uses VEX|EVEX prefix.</a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineCov">      31158 :           if (tiedCount.getVec() &amp;&amp; commonData.hasFlag(X86Inst::kFlagVex | X86Inst::kFlagEvex))</span></a>
+<a name="1746"><span class="lineNum">    1746 </span><span class="lineNoCov">          0 :             _avxEnabled = true;</span></a>
+<a name="1747"><span class="lineNum">    1747 </span>            :         }</a>
+<a name="1748"><span class="lineNum">    1748 </span>            : </a>
+<a name="1749"><span class="lineNum">    1749 </span>            :         const RegOnly&amp; extraReg = node-&gt;getExtraReg();</a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineCov">      31158 :         if (extraReg.isValid()) {</span></a>
+<a name="1751"><span class="lineNum">    1751 </span>            :           uint32_t id = extraReg.getId();</a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineNoCov">          0 :           if (cc()-&gt;isVirtRegValid(id)) {</span></a>
+<a name="1753"><span class="lineNum">    1753 </span>            :             VirtReg* vreg = cc()-&gt;getVirtRegById(id);</a>
+<a name="1754"><span class="lineNum">    1754 </span>            :             TiedReg* tied;</a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineNoCov">          0 :             RA_MERGE(vreg, tied, 0, gaRegs[vreg-&gt;getKind()] &amp; gpAllowedMask);</span></a>
+<a name="1756"><span class="lineNum">    1756 </span>            : </a>
+<a name="1757"><span class="lineNum">    1757 </span><span class="lineNoCov">          0 :             if (options &amp; (X86Inst::kOptionRep | X86Inst::kOptionRepnz)) {</span></a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineNoCov">          0 :               tied-&gt;allocableRegs = Utils::mask(X86Gp::kIdCx);</span></a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineNoCov">          0 :               tied-&gt;flags |= TiedReg::kXReg;</span></a>
+<a name="1760"><span class="lineNum">    1760 </span>            :             }</a>
+<a name="1761"><span class="lineNum">    1761 </span>            :             else {</a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineNoCov">          0 :               tied-&gt;flags |= TiedReg::kRReg;</span></a>
+<a name="1763"><span class="lineNum">    1763 </span>            :             }</a>
+<a name="1764"><span class="lineNum">    1764 </span>            :           }</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :         }</a>
+<a name="1766"><span class="lineNum">    1766 </span>            : </a>
+<a name="1767"><span class="lineNum">    1767 </span><span class="lineCov">      85958 :         RA_FINALIZE(node_);</span></a>
+<a name="1768"><span class="lineNum">    1768 </span>            : </a>
+<a name="1769"><span class="lineNum">    1769 </span>            :         // Handle conditional/unconditional jump.</a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineCov">      31158 :         if (node-&gt;isJmpOrJcc()) {</span></a>
+<a name="1771"><span class="lineNum">    1771 </span>            :           CBJump* jNode = static_cast&lt;CBJump*&gt;(node);</a>
+<a name="1772"><span class="lineNum">    1772 </span>            :           CBLabel* jTarget = jNode-&gt;getTarget();</a>
+<a name="1773"><span class="lineNum">    1773 </span>            : </a>
+<a name="1774"><span class="lineNum">    1774 </span>            :           // If this jump is unconditional we put next node to unreachable node</a>
+<a name="1775"><span class="lineNum">    1775 </span>            :           // list so we can eliminate possible dead code. We have to do this in</a>
+<a name="1776"><span class="lineNum">    1776 </span>            :           // all cases since we are unable to translate without fetch() step.</a>
+<a name="1777"><span class="lineNum">    1777 </span>            :           //</a>
+<a name="1778"><span class="lineNum">    1778 </span>            :           // We also advance our node pointer to the target node to simulate</a>
+<a name="1779"><span class="lineNum">    1779 </span>            :           // natural flow of the function.</a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineNoCov">          0 :           if (jNode-&gt;isJmp()) {</span></a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineNoCov">          0 :             if (next &amp;&amp; !next-&gt;hasPassData())</span></a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineNoCov">          0 :               ASMJIT_PROPAGATE(addUnreachableNode(next));</span></a>
+<a name="1783"><span class="lineNum">    1783 </span>            : </a>
+<a name="1784"><span class="lineNum">    1784 </span>            :             // Jump not followed.</a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineNoCov">          0 :             if (!jTarget) {</span></a>
+<a name="1786"><span class="lineNum">    1786 </span><span class="lineNoCov">          0 :               ASMJIT_PROPAGATE(addReturningNode(jNode));</span></a>
+<a name="1787"><span class="lineNum">    1787 </span><span class="lineNoCov">          0 :               goto _NextGroup;</span></a>
+<a name="1788"><span class="lineNum">    1788 </span>            :             }</a>
+<a name="1789"><span class="lineNum">    1789 </span>            : </a>
+<a name="1790"><span class="lineNum">    1790 </span>            :             node_ = jTarget;</a>
+<a name="1791"><span class="lineNum">    1791 </span><span class="lineNoCov">          0 :             goto _Do;</span></a>
+<a name="1792"><span class="lineNum">    1792 </span>            :           }</a>
+<a name="1793"><span class="lineNum">    1793 </span>            :           else {</a>
+<a name="1794"><span class="lineNum">    1794 </span>            :             // Jump not followed.</a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineNoCov">          0 :             if (!jTarget) break;</span></a>
+<a name="1796"><span class="lineNum">    1796 </span>            : </a>
+<a name="1797"><span class="lineNum">    1797 </span><span class="lineNoCov">          0 :             if (jTarget-&gt;hasPassData()) {</span></a>
+<a name="1798"><span class="lineNum">    1798 </span>            :               uint32_t jTargetPosition = jTarget-&gt;getPosition();</a>
+<a name="1799"><span class="lineNum">    1799 </span>            : </a>
+<a name="1800"><span class="lineNum">    1800 </span>            :               // Update CBNode::kFlagIsTaken to true if this is a conditional</a>
+<a name="1801"><span class="lineNum">    1801 </span>            :               // backward jump. This behavior can be overridden by using</a>
+<a name="1802"><span class="lineNum">    1802 </span>            :               // `X86Inst::kOptionTaken` when the instruction is created.</a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineNoCov">          0 :               if (!jNode-&gt;isTaken() &amp;&amp; opCount == 1 &amp;&amp; jTargetPosition &lt;= position) {</span></a>
+<a name="1804"><span class="lineNum">    1804 </span><span class="lineNoCov">          0 :                 jNode-&gt;_flags |= CBNode::kFlagIsTaken;</span></a>
+<a name="1805"><span class="lineNum">    1805 </span>            :               }</a>
+<a name="1806"><span class="lineNum">    1806 </span>            :             }</a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineNoCov">          0 :             else if (next-&gt;hasPassData()) {</span></a>
+<a name="1808"><span class="lineNum">    1808 </span>            :               node_ = jTarget;</a>
+<a name="1809"><span class="lineNum">    1809 </span><span class="lineNoCov">          0 :               goto _Do;</span></a>
+<a name="1810"><span class="lineNum">    1810 </span>            :             }</a>
+<a name="1811"><span class="lineNum">    1811 </span>            :             else {</a>
+<a name="1812"><span class="lineNum">    1812 </span><span class="lineNoCov">          0 :               ASMJIT_PROPAGATE(addJccNode(jNode));</span></a>
+<a name="1813"><span class="lineNum">    1813 </span>            :               node_ = X86RAPass_getJccFlow(jNode);</a>
+<a name="1814"><span class="lineNum">    1814 </span><span class="lineNoCov">          0 :               goto _Do;</span></a>
+<a name="1815"><span class="lineNum">    1815 </span>            :             }</a>
+<a name="1816"><span class="lineNum">    1816 </span>            :           }</a>
+<a name="1817"><span class="lineNum">    1817 </span>            :         }</a>
+<a name="1818"><span class="lineNum">    1818 </span>            :         break;</a>
+<a name="1819"><span class="lineNum">    1819 </span>            :       }</a>
+<a name="1820"><span class="lineNum">    1820 </span>            : </a>
+<a name="1821"><span class="lineNum">    1821 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1822"><span class="lineNum">    1822 </span>            :       // [Func-Entry]</a>
+<a name="1823"><span class="lineNum">    1823 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1824"><span class="lineNum">    1824 </span>            : </a>
+<a name="1825"><span class="lineNum">    1825 </span><span class="lineCov">       1948 :       case CBNode::kNodeFunc: {</span></a>
+<a name="1826"><span class="lineNum">    1826 </span>            :         ASMJIT_ASSERT(node_ == func);</a>
+<a name="1827"><span class="lineNum">    1827 </span><span class="lineCov">       1948 :         X86RAPass_assignStackArgsRegId(this, func);</span></a>
+<a name="1828"><span class="lineNum">    1828 </span>            : </a>
+<a name="1829"><span class="lineNum">    1829 </span>            :         FuncDetail&amp; fd = func-&gt;getDetail();</a>
+<a name="1830"><span class="lineNum">    1830 </span>            :         TiedReg* tied;</a>
+<a name="1831"><span class="lineNum">    1831 </span>            : </a>
+<a name="1832"><span class="lineNum">    1832 </span>            :         RA_DECLARE();</a>
+<a name="1833"><span class="lineNum">    1833 </span><span class="lineCov">       1948 :         cc()-&gt;setCursor(node_);</span></a>
+<a name="1834"><span class="lineNum">    1834 </span>            : </a>
+<a name="1835"><span class="lineNum">    1835 </span>            :         X86Gp saReg;</a>
+<a name="1836"><span class="lineNum">    1836 </span>            :         uint32_t argCount = fd.getArgCount();</a>
+<a name="1837"><span class="lineNum">    1837 </span>            : </a>
+<a name="1838"><span class="lineNum">    1838 </span><span class="lineCov">       1948 :         for (uint32_t i = 0; i &lt; argCount; i++) {</span></a>
+<a name="1839"><span class="lineNum">    1839 </span><span class="lineNoCov">          0 :           const FuncDetail::Value&amp; arg = fd.getArg(i);</span></a>
+<a name="1840"><span class="lineNum">    1840 </span>            : </a>
+<a name="1841"><span class="lineNum">    1841 </span>            :           VirtReg* vReg = func-&gt;getArg(i);</a>
+<a name="1842"><span class="lineNum">    1842 </span><span class="lineNoCov">          0 :           if (!vReg) continue;</span></a>
+<a name="1843"><span class="lineNum">    1843 </span>            : </a>
+<a name="1844"><span class="lineNum">    1844 </span>            :           // Overlapped function arguments.</a>
+<a name="1845"><span class="lineNum">    1845 </span><span class="lineNoCov">          0 :           if (vReg-&gt;_tied)</span></a>
+<a name="1846"><span class="lineNum">    1846 </span><span class="lineNoCov">          0 :             return DebugUtils::errored(kErrorOverlappedRegs);</span></a>
+<a name="1847"><span class="lineNum">    1847 </span>            : </a>
+<a name="1848"><span class="lineNum">    1848 </span>            :           uint32_t aKind = X86Reg::kindOf(arg.getRegType());</a>
+<a name="1849"><span class="lineNum">    1849 </span>            :           uint32_t vKind = vReg-&gt;getKind();</a>
+<a name="1850"><span class="lineNum">    1850 </span>            : </a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineNoCov">          0 :           if (arg.byReg()) {</span></a>
+<a name="1852"><span class="lineNum">    1852 </span><span class="lineNoCov">          0 :             if (aKind == vKind) {</span></a>
+<a name="1853"><span class="lineNum">    1853 </span><span class="lineNoCov">          0 :               RA_INSERT(vReg, tied, TiedReg::kWReg, 0);</span></a>
+<a name="1854"><span class="lineNum">    1854 </span>            :               tied-&gt;setOutPhysId(arg.getRegId());</a>
+<a name="1855"><span class="lineNum">    1855 </span>            :             }</a>
+<a name="1856"><span class="lineNum">    1856 </span>            :             else {</a>
+<a name="1857"><span class="lineNum">    1857 </span><span class="lineNoCov">          0 :               X86Reg rTmp = cc()-&gt;newReg(arg.getTypeId(), &quot;arg%u&quot;, i);</span></a>
+<a name="1858"><span class="lineNum">    1858 </span>            :               VirtReg* vTmp = cc()-&gt;getVirtReg(rTmp);</a>
+<a name="1859"><span class="lineNum">    1859 </span>            : </a>
+<a name="1860"><span class="lineNum">    1860 </span><span class="lineNoCov">          0 :               RA_INSERT(vTmp, tied, TiedReg::kWReg, 0);</span></a>
+<a name="1861"><span class="lineNum">    1861 </span>            :               tied-&gt;setOutPhysId(arg.getRegId());</a>
+<a name="1862"><span class="lineNum">    1862 </span>            : </a>
+<a name="1863"><span class="lineNum">    1863 </span>            :               X86Reg dstReg(X86Reg::fromSignature(vReg-&gt;getSignature(), vReg-&gt;getId()));</a>
+<a name="1864"><span class="lineNum">    1864 </span>            :               X86Reg srcReg(X86Reg::fromSignature(vTmp-&gt;getSignature(), vTmp-&gt;getId()));</a>
+<a name="1865"><span class="lineNum">    1865 </span>            : </a>
+<a name="1866"><span class="lineNum">    1866 </span>            :               // Emit conversion after the prolog.</a>
+<a name="1867"><span class="lineNum">    1867 </span><span class="lineNoCov">          0 :               return X86Internal::emitArgMove(reinterpret_cast&lt;X86Emitter*&gt;(cc()),</span></a>
+<a name="1868"><span class="lineNum">    1868 </span>            :                 dstReg, vReg-&gt;getTypeId(),</a>
+<a name="1869"><span class="lineNum">    1869 </span><span class="lineNoCov">          0 :                 srcReg, vTmp-&gt;getTypeId(), _avxEnabled);</span></a>
+<a name="1870"><span class="lineNum">    1870 </span>            :             }</a>
+<a name="1871"><span class="lineNum">    1871 </span>            :           }</a>
+<a name="1872"><span class="lineNum">    1872 </span>            :           else {</a>
+<a name="1873"><span class="lineNum">    1873 </span>            :             // Instead of complicating the prolog allocation we create a virtual</a>
+<a name="1874"><span class="lineNum">    1874 </span>            :             // register that holds the base address to all arguments passed by</a>
+<a name="1875"><span class="lineNum">    1875 </span>            :             // stack and then insert nodes that copy these arguments to registers.</a>
+<a name="1876"><span class="lineNum">    1876 </span><span class="lineNoCov">          0 :             if (!saReg.isValid()) {</span></a>
+<a name="1877"><span class="lineNum">    1877 </span><span class="lineNoCov">          0 :               saReg = cc()-&gt;newGpz(&quot;__args&quot;);</span></a>
+<a name="1878"><span class="lineNum">    1878 </span><span class="lineNoCov">          0 :               if (!saReg.isValid()) goto NoMem;</span></a>
+<a name="1879"><span class="lineNum">    1879 </span>            : </a>
+<a name="1880"><span class="lineNum">    1880 </span>            :               VirtReg* saBase = cc()-&gt;getVirtReg(saReg);</a>
+<a name="1881"><span class="lineNum">    1881 </span><span class="lineNoCov">          0 :               RA_INSERT(saBase, tied, TiedReg::kWReg, 0);</span></a>
+<a name="1882"><span class="lineNum">    1882 </span>            : </a>
+<a name="1883"><span class="lineNum">    1883 </span><span class="lineNoCov">          0 :               if (func-&gt;getFrameInfo().hasPreservedFP())</span></a>
+<a name="1884"><span class="lineNum">    1884 </span><span class="lineNoCov">          0 :                 saBase-&gt;_isFixed = true;</span></a>
+<a name="1885"><span class="lineNum">    1885 </span>            :               tied-&gt;setOutPhysId(func-&gt;getFrameInfo().getStackArgsRegId());</a>
+<a name="1886"><span class="lineNum">    1886 </span>            :             }</a>
+<a name="1887"><span class="lineNum">    1887 </span>            : </a>
+<a name="1888"><span class="lineNum">    1888 </span>            :             // Argument passed by stack is handled after the prolog.</a>
+<a name="1889"><span class="lineNum">    1889 </span>            :             X86Gp aReg = X86Gp::fromSignature(vReg-&gt;getSignature(), vReg-&gt;getId());</a>
+<a name="1890"><span class="lineNum">    1890 </span>            :             X86Mem aMem = x86::ptr(saReg, arg.getStackOffset());</a>
+<a name="1891"><span class="lineNum">    1891 </span>            :             aMem.setArgHome();</a>
+<a name="1892"><span class="lineNum">    1892 </span>            : </a>
+<a name="1893"><span class="lineNum">    1893 </span><span class="lineNoCov">          0 :             ASMJIT_PROPAGATE(</span></a>
+<a name="1894"><span class="lineNum">    1894 </span>            :               X86Internal::emitArgMove(reinterpret_cast&lt;X86Emitter*&gt;(cc()),</a>
+<a name="1895"><span class="lineNum">    1895 </span>            :                 aReg, vReg-&gt;getTypeId(), aMem, arg.getTypeId(), _avxEnabled));</a>
+<a name="1896"><span class="lineNum">    1896 </span>            :           }</a>
+<a name="1897"><span class="lineNum">    1897 </span>            :         }</a>
+<a name="1898"><span class="lineNum">    1898 </span>            : </a>
+<a name="1899"><span class="lineNum">    1899 </span>            :         // If saReg is not needed, clear it also from FuncFrameInfo.</a>
+<a name="1900"><span class="lineNum">    1900 </span><span class="lineCov">       1948 :         if (!saReg.isValid())</span></a>
+<a name="1901"><span class="lineNum">    1901 </span>            :           func-&gt;getFrameInfo().setStackArgsRegId(Globals::kInvalidRegId);</a>
+<a name="1902"><span class="lineNum">    1902 </span>            : </a>
+<a name="1903"><span class="lineNum">    1903 </span><span class="lineCov">       1948 :         RA_FINALIZE(node_);</span></a>
+<a name="1904"><span class="lineNum">    1904 </span>            :         next = node_-&gt;getNext();</a>
+<a name="1905"><span class="lineNum">    1905 </span><span class="lineCov">       1948 :         break;</span></a>
+<a name="1906"><span class="lineNum">    1906 </span>            :       }</a>
+<a name="1907"><span class="lineNum">    1907 </span>            : </a>
+<a name="1908"><span class="lineNum">    1908 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1909"><span class="lineNum">    1909 </span>            :       // [End]</a>
+<a name="1910"><span class="lineNum">    1910 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1911"><span class="lineNum">    1911 </span>            : </a>
+<a name="1912"><span class="lineNum">    1912 </span>            :       case CBNode::kNodeSentinel: {</a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineNoCov">          0 :         RA_POPULATE(node_);</span></a>
+<a name="1914"><span class="lineNum">    1914 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(addReturningNode(node_));</span></a>
+<a name="1915"><span class="lineNum">    1915 </span><span class="lineNoCov">          0 :         goto _NextGroup;</span></a>
+<a name="1916"><span class="lineNum">    1916 </span>            :       }</a>
+<a name="1917"><span class="lineNum">    1917 </span>            : </a>
+<a name="1918"><span class="lineNum">    1918 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1919"><span class="lineNum">    1919 </span>            :       // [Func-Exit]</a>
+<a name="1920"><span class="lineNum">    1920 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1921"><span class="lineNum">    1921 </span>            : </a>
+<a name="1922"><span class="lineNum">    1922 </span><span class="lineCov">       1948 :       case CBNode::kNodeFuncExit: {</span></a>
+<a name="1923"><span class="lineNum">    1923 </span>            :         CCFuncRet* node = static_cast&lt;CCFuncRet*&gt;(node_);</a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineCov">       1948 :         ASMJIT_PROPAGATE(addReturningNode(node));</span></a>
+<a name="1925"><span class="lineNum">    1925 </span>            : </a>
+<a name="1926"><span class="lineNum">    1926 </span>            :         FuncDetail&amp; fd = func-&gt;getDetail();</a>
+<a name="1927"><span class="lineNum">    1927 </span>            :         RA_DECLARE();</a>
+<a name="1928"><span class="lineNum">    1928 </span>            : </a>
+<a name="1929"><span class="lineNum">    1929 </span><span class="lineCov">       1948 :         if (fd.hasRet()) {</span></a>
+<a name="1930"><span class="lineNum">    1930 </span>            :           const FuncDetail::Value&amp; ret = fd.getRet(0);</a>
+<a name="1931"><span class="lineNum">    1931 </span>            :           uint32_t retKind = X86Reg::kindOf(ret.getRegType());</a>
+<a name="1932"><span class="lineNum">    1932 </span>            : </a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineCov">       5844 :           for (uint32_t i = 0; i &lt; 2; i++) {</span></a>
+<a name="1934"><span class="lineNum">    1934 </span>            :             Operand_* op = &amp;node-&gt;_ret[i];</a>
+<a name="1935"><span class="lineNum">    1935 </span>            :             if (op-&gt;isVirtReg()) {</a>
+<a name="1936"><span class="lineNum">    1936 </span>            :               VirtReg* vreg = cc()-&gt;getVirtRegById(op-&gt;getId());</a>
+<a name="1937"><span class="lineNum">    1937 </span>            :               TiedReg* tied;</a>
+<a name="1938"><span class="lineNum">    1938 </span><span class="lineCov">       3896 :               RA_MERGE(vreg, tied, 0, 0);</span></a>
+<a name="1939"><span class="lineNum">    1939 </span>            : </a>
+<a name="1940"><span class="lineNum">    1940 </span><span class="lineCov">       1948 :               if (retKind == vreg-&gt;getKind()) {</span></a>
+<a name="1941"><span class="lineNum">    1941 </span><span class="lineCov">       1948 :                 tied-&gt;flags |= TiedReg::kRReg;</span></a>
+<a name="1942"><span class="lineNum">    1942 </span><span class="lineCov">       1948 :                 tied-&gt;inRegs = Utils::mask(ret.getRegId());</span></a>
+<a name="1943"><span class="lineNum">    1943 </span>            :                 inRegs.or_(retKind, tied-&gt;inRegs);</a>
+<a name="1944"><span class="lineNum">    1944 </span>            :               }</a>
+<a name="1945"><span class="lineNum">    1945 </span><span class="lineNoCov">          0 :               else if (retKind == X86Reg::kKindFp) {</span></a>
+<a name="1946"><span class="lineNum">    1946 </span><span class="lineNoCov">          0 :                 uint32_t fldFlag = ret.getTypeId() == TypeId::kF32 ? TiedReg::kX86Fld4 : TiedReg::kX86Fld8;</span></a>
+<a name="1947"><span class="lineNum">    1947 </span><span class="lineNoCov">          0 :                 tied-&gt;flags |= TiedReg::kRMem | fldFlag;</span></a>
+<a name="1948"><span class="lineNum">    1948 </span>            :               }</a>
+<a name="1949"><span class="lineNum">    1949 </span>            :               else {</a>
+<a name="1950"><span class="lineNum">    1950 </span>            :                 // TODO: Fix possible other return type conversions.</a>
+<a name="1951"><span class="lineNum">    1951 </span><span class="lineNoCov">          0 :                 ASMJIT_NOT_REACHED();</span></a>
+<a name="1952"><span class="lineNum">    1952 </span>            :               }</a>
+<a name="1953"><span class="lineNum">    1953 </span>            :             }</a>
+<a name="1954"><span class="lineNum">    1954 </span>            :           }</a>
+<a name="1955"><span class="lineNum">    1955 </span>            :         }</a>
+<a name="1956"><span class="lineNum">    1956 </span><span class="lineCov">       3896 :         RA_FINALIZE(node_);</span></a>
+<a name="1957"><span class="lineNum">    1957 </span>            : </a>
+<a name="1958"><span class="lineNum">    1958 </span><span class="lineCov">       1948 :         if (!next-&gt;hasPassData())</span></a>
+<a name="1959"><span class="lineNum">    1959 </span><span class="lineCov">       1948 :           ASMJIT_PROPAGATE(addUnreachableNode(next));</span></a>
+<a name="1960"><span class="lineNum">    1960 </span><span class="lineCov">       1948 :         goto _NextGroup;</span></a>
+<a name="1961"><span class="lineNum">    1961 </span>            :       }</a>
+<a name="1962"><span class="lineNum">    1962 </span>            : </a>
+<a name="1963"><span class="lineNum">    1963 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1964"><span class="lineNum">    1964 </span>            :       // [Func-Call]</a>
+<a name="1965"><span class="lineNum">    1965 </span>            :       // ----------------------------------------------------------------------</a>
+<a name="1966"><span class="lineNum">    1966 </span>            : </a>
+<a name="1967"><span class="lineNum">    1967 </span><span class="lineCov">       1648 :       case CBNode::kNodeFuncCall: {</span></a>
+<a name="1968"><span class="lineNum">    1968 </span>            :         CCFuncCall* node = static_cast&lt;CCFuncCall*&gt;(node_);</a>
+<a name="1969"><span class="lineNum">    1969 </span>            :         FuncDetail&amp; fd = node-&gt;getDetail();</a>
+<a name="1970"><span class="lineNum">    1970 </span>            : </a>
+<a name="1971"><span class="lineNum">    1971 </span><span class="lineCov">       1648 :         Operand_* target = node-&gt;_opArray;</span></a>
+<a name="1972"><span class="lineNum">    1972 </span><span class="lineCov">       1648 :         Operand_* args = node-&gt;_args;</span></a>
+<a name="1973"><span class="lineNum">    1973 </span><span class="lineCov">       1648 :         Operand_* rets = node-&gt;_ret;</span></a>
+<a name="1974"><span class="lineNum">    1974 </span>            : </a>
+<a name="1975"><span class="lineNum">    1975 </span>            :         func-&gt;getFrameInfo().enableCalls();</a>
+<a name="1976"><span class="lineNum">    1976 </span><span class="lineCov">       1648 :         func-&gt;getFrameInfo().mergeCallFrameSize(fd.getArgStackSize());</span></a>
+<a name="1977"><span class="lineNum">    1977 </span>            :         // TODO: Each function frame should also define its stack arguments' alignment.</a>
+<a name="1978"><span class="lineNum">    1978 </span>            :         // func-&gt;getFrameInfo().mergeCallFrameAlignment();</a>
+<a name="1979"><span class="lineNum">    1979 </span>            : </a>
+<a name="1980"><span class="lineNum">    1980 </span>            :         uint32_t i;</a>
+<a name="1981"><span class="lineNum">    1981 </span>            :         uint32_t argCount = fd.getArgCount();</a>
+<a name="1982"><span class="lineNum">    1982 </span>            :         uint32_t sArgCount = 0;</a>
+<a name="1983"><span class="lineNum">    1983 </span><span class="lineCov">       1648 :         uint32_t gpAllocableMask = gaRegs[X86Reg::kKindGp] &amp; ~node-&gt;getDetail().getUsedRegs(X86Reg::kKindGp);</span></a>
+<a name="1984"><span class="lineNum">    1984 </span>            : </a>
+<a name="1985"><span class="lineNum">    1985 </span>            :         VirtReg* vreg;</a>
+<a name="1986"><span class="lineNum">    1986 </span>            :         TiedReg* tied;</a>
+<a name="1987"><span class="lineNum">    1987 </span>            : </a>
+<a name="1988"><span class="lineNum">    1988 </span>            :         RA_DECLARE();</a>
+<a name="1989"><span class="lineNum">    1989 </span>            : </a>
+<a name="1990"><span class="lineNum">    1990 </span>            :         // Function-call operand.</a>
+<a name="1991"><span class="lineNum">    1991 </span>            :         if (target-&gt;isVirtReg()) {</a>
+<a name="1992"><span class="lineNum">    1992 </span>            :           vreg = cc()-&gt;getVirtRegById(target-&gt;getId());</a>
+<a name="1993"><span class="lineNum">    1993 </span><span class="lineCov">       1648 :           RA_MERGE(vreg, tied, 0, 0);</span></a>
+<a name="1994"><span class="lineNum">    1994 </span>            : </a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineCov">       1648 :           tied-&gt;flags |= TiedReg::kRReg | TiedReg::kRCall;</span></a>
+<a name="1996"><span class="lineNum">    1996 </span><span class="lineCov">       1648 :           if (tied-&gt;inRegs == 0)</span></a>
+<a name="1997"><span class="lineNum">    1997 </span><span class="lineCov">       1648 :             tied-&gt;allocableRegs |= gpAllocableMask;</span></a>
+<a name="1998"><span class="lineNum">    1998 </span>            :         }</a>
+<a name="1999"><span class="lineNum">    1999 </span><span class="lineNoCov">          0 :         else if (target-&gt;isMem()) {</span></a>
+<a name="2000"><span class="lineNum">    2000 </span>            :           X86Mem* m = static_cast&lt;X86Mem*&gt;(target);</a>
+<a name="2001"><span class="lineNum">    2001 </span>            : </a>
+<a name="2002"><span class="lineNum">    2002 </span><span class="lineNoCov">          0 :           if (m-&gt;hasBaseReg() &amp;&amp;  Operand::isPackedId(m-&gt;getBaseId())) {</span></a>
+<a name="2003"><span class="lineNum">    2003 </span>            :             vreg = cc()-&gt;getVirtRegById(m-&gt;getBaseId());</a>
+<a name="2004"><span class="lineNum">    2004 </span><span class="lineNoCov">          0 :             if (!vreg-&gt;isStack()) {</span></a>
+<a name="2005"><span class="lineNum">    2005 </span><span class="lineNoCov">          0 :               RA_MERGE(vreg, tied, 0, 0);</span></a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineNoCov">          0 :               if (m-&gt;isRegHome()) {</span></a>
+<a name="2007"><span class="lineNum">    2007 </span><span class="lineNoCov">          0 :                 tied-&gt;flags |= TiedReg::kRMem | TiedReg::kRCall;</span></a>
+<a name="2008"><span class="lineNum">    2008 </span>            :               }</a>
+<a name="2009"><span class="lineNum">    2009 </span>            :               else {</a>
+<a name="2010"><span class="lineNum">    2010 </span><span class="lineNoCov">          0 :                 tied-&gt;flags |= TiedReg::kRReg | TiedReg::kRCall;</span></a>
+<a name="2011"><span class="lineNum">    2011 </span><span class="lineNoCov">          0 :                 if (tied-&gt;inRegs == 0)</span></a>
+<a name="2012"><span class="lineNum">    2012 </span><span class="lineNoCov">          0 :                   tied-&gt;allocableRegs |= gpAllocableMask;</span></a>
+<a name="2013"><span class="lineNum">    2013 </span>            :               }</a>
+<a name="2014"><span class="lineNum">    2014 </span>            :             }</a>
+<a name="2015"><span class="lineNum">    2015 </span>            :           }</a>
+<a name="2016"><span class="lineNum">    2016 </span>            : </a>
+<a name="2017"><span class="lineNum">    2017 </span><span class="lineNoCov">          0 :           if (m-&gt;hasIndexReg() &amp;&amp; Operand::isPackedId(m-&gt;getIndexId())) {</span></a>
+<a name="2018"><span class="lineNum">    2018 </span>            :             // Restrict allocation to all registers except ESP/RSP.</a>
+<a name="2019"><span class="lineNum">    2019 </span>            :             vreg = cc()-&gt;getVirtRegById(m-&gt;getIndexId());</a>
+<a name="2020"><span class="lineNum">    2020 </span><span class="lineNoCov">          0 :             RA_MERGE(vreg, tied, 0, 0);</span></a>
+<a name="2021"><span class="lineNum">    2021 </span>            : </a>
+<a name="2022"><span class="lineNum">    2022 </span><span class="lineNoCov">          0 :             tied-&gt;flags |= TiedReg::kRReg | TiedReg::kRCall;</span></a>
+<a name="2023"><span class="lineNum">    2023 </span><span class="lineNoCov">          0 :             if ((tied-&gt;inRegs &amp; ~indexMask) == 0)</span></a>
+<a name="2024"><span class="lineNum">    2024 </span><span class="lineNoCov">          0 :               tied-&gt;allocableRegs &amp;= gpAllocableMask &amp; indexMask;</span></a>
+<a name="2025"><span class="lineNum">    2025 </span>            :           }</a>
+<a name="2026"><span class="lineNum">    2026 </span>            :         }</a>
+<a name="2027"><span class="lineNum">    2027 </span>            : </a>
+<a name="2028"><span class="lineNum">    2028 </span>            :         // Function-call arguments.</a>
+<a name="2029"><span class="lineNum">    2029 </span><span class="lineCov">       3518 :         for (i = 0; i &lt; argCount; i++) {</span></a>
+<a name="2030"><span class="lineNum">    2030 </span><span class="lineCov">       1870 :           Operand_* op = &amp;args[i];</span></a>
+<a name="2031"><span class="lineNum">    2031 </span><span class="lineCov">        420 :           if (!op-&gt;isVirtReg()) continue;</span></a>
+<a name="2032"><span class="lineNum">    2032 </span>            : </a>
+<a name="2033"><span class="lineNum">    2033 </span>            :           vreg = cc()-&gt;getVirtRegById(op-&gt;getId());</a>
+<a name="2034"><span class="lineNum">    2034 </span>            :           const FuncDetail::Value&amp; arg = fd.getArg(i);</a>
+<a name="2035"><span class="lineNum">    2035 </span>            : </a>
+<a name="2036"><span class="lineNum">    2036 </span><span class="lineCov">       1450 :           if (arg.byReg()) {</span></a>
+<a name="2037"><span class="lineNum">    2037 </span><span class="lineCov">       2900 :             RA_MERGE(vreg, tied, 0, 0);</span></a>
+<a name="2038"><span class="lineNum">    2038 </span>            : </a>
+<a name="2039"><span class="lineNum">    2039 </span>            :             uint32_t argClass = X86Reg::kindOf(arg.getRegType());</a>
+<a name="2040"><span class="lineNum">    2040 </span>            : </a>
+<a name="2041"><span class="lineNum">    2041 </span><span class="lineCov">       1450 :             if (vreg-&gt;getKind() == argClass) {</span></a>
+<a name="2042"><span class="lineNum">    2042 </span><span class="lineCov">       1450 :               tied-&gt;inRegs |= Utils::mask(arg.getRegId());</span></a>
+<a name="2043"><span class="lineNum">    2043 </span><span class="lineCov">       1450 :               tied-&gt;flags |= TiedReg::kRReg | TiedReg::kRFunc;</span></a>
+<a name="2044"><span class="lineNum">    2044 </span>            :             }</a>
+<a name="2045"><span class="lineNum">    2045 </span>            :             else {</a>
+<a name="2046"><span class="lineNum">    2046 </span>            :               // TODO: Function-call argument conversion.</a>
+<a name="2047"><span class="lineNum">    2047 </span>            :             }</a>
+<a name="2048"><span class="lineNum">    2048 </span>            :           }</a>
+<a name="2049"><span class="lineNum">    2049 </span>            :           // If this is a stack-based argument we insert CCPushArg instead of</a>
+<a name="2050"><span class="lineNum">    2050 </span>            :           // using TiedReg. It improves the code, because the argument can be</a>
+<a name="2051"><span class="lineNum">    2051 </span>            :           // moved onto stack as soon as it is ready and the register used by</a>
+<a name="2052"><span class="lineNum">    2052 </span>            :           // the variable can be reused for something else. It is also much</a>
+<a name="2053"><span class="lineNum">    2053 </span>            :           // easier to handle argument conversions, because there will be at</a>
+<a name="2054"><span class="lineNum">    2054 </span>            :           // most only one node per conversion.</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :           else {</a>
+<a name="2056"><span class="lineNum">    2056 </span><span class="lineNoCov">          0 :             if (X86RAPass_insertPushArg(this, node, vreg, gaRegs, arg, i, sArgList, sArgCount) != kErrorOk)</span></a>
+<a name="2057"><span class="lineNum">    2057 </span><span class="lineNoCov">          0 :               goto NoMem;</span></a>
+<a name="2058"><span class="lineNum">    2058 </span>            :           }</a>
+<a name="2059"><span class="lineNum">    2059 </span>            :         }</a>
+<a name="2060"><span class="lineNum">    2060 </span>            : </a>
+<a name="2061"><span class="lineNum">    2061 </span>            :         // Function-call returns.</a>
+<a name="2062"><span class="lineNum">    2062 </span><span class="lineCov">       4944 :         for (i = 0; i &lt; 2; i++) {</span></a>
+<a name="2063"><span class="lineNum">    2063 </span><span class="lineCov">       3296 :           Operand_* op = &amp;rets[i];</span></a>
+<a name="2064"><span class="lineNum">    2064 </span><span class="lineCov">       1648 :           if (!op-&gt;isVirtReg()) continue;</span></a>
+<a name="2065"><span class="lineNum">    2065 </span>            : </a>
+<a name="2066"><span class="lineNum">    2066 </span>            :           const FuncDetail::Value&amp; ret = fd.getRet(i);</a>
+<a name="2067"><span class="lineNum">    2067 </span><span class="lineCov">       1648 :           if (ret.byReg()) {</span></a>
+<a name="2068"><span class="lineNum">    2068 </span>            :             uint32_t retKind = X86Reg::kindOf(ret.getRegType());</a>
+<a name="2069"><span class="lineNum">    2069 </span>            : </a>
+<a name="2070"><span class="lineNum">    2070 </span>            :             vreg = cc()-&gt;getVirtRegById(op-&gt;getId());</a>
+<a name="2071"><span class="lineNum">    2071 </span><span class="lineCov">       4944 :             RA_MERGE(vreg, tied, 0, 0);</span></a>
+<a name="2072"><span class="lineNum">    2072 </span>            : </a>
+<a name="2073"><span class="lineNum">    2073 </span><span class="lineCov">       1648 :             if (vreg-&gt;getKind() == retKind) {</span></a>
+<a name="2074"><span class="lineNum">    2074 </span>            :               tied-&gt;setOutPhysId(ret.getRegId());</a>
+<a name="2075"><span class="lineNum">    2075 </span><span class="lineCov">       1648 :               tied-&gt;flags |= TiedReg::kWReg | TiedReg::kWFunc;</span></a>
+<a name="2076"><span class="lineNum">    2076 </span>            :             }</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :             else {</a>
+<a name="2078"><span class="lineNum">    2078 </span>            :               // TODO: Function-call return value conversion.</a>
+<a name="2079"><span class="lineNum">    2079 </span>            :             }</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :           }</a>
+<a name="2081"><span class="lineNum">    2081 </span>            :         }</a>
+<a name="2082"><span class="lineNum">    2082 </span>            : </a>
+<a name="2083"><span class="lineNum">    2083 </span>            :         // Init clobbered.</a>
+<a name="2084"><span class="lineNum">    2084 </span><span class="lineCov">       1648 :         clobberedRegs.set(X86Reg::kKindGp , Utils::bits(_regCount.getGp())  &amp; (fd.getPassedRegs(X86Reg::kKindGp ) | ~fd.getPreservedRegs(X86Reg::kKindGp )));</span></a>
+<a name="2085"><span class="lineNum">    2085 </span><span class="lineCov">       1648 :         clobberedRegs.set(X86Reg::kKindMm , Utils::bits(_regCount.getMm())  &amp; (fd.getPassedRegs(X86Reg::kKindMm ) | ~fd.getPreservedRegs(X86Reg::kKindMm )));</span></a>
+<a name="2086"><span class="lineNum">    2086 </span><span class="lineCov">       1648 :         clobberedRegs.set(X86Reg::kKindK  , Utils::bits(_regCount.getK())   &amp; (fd.getPassedRegs(X86Reg::kKindK  ) | ~fd.getPreservedRegs(X86Reg::kKindK  )));</span></a>
+<a name="2087"><span class="lineNum">    2087 </span><span class="lineCov">       1648 :         clobberedRegs.set(X86Reg::kKindVec, Utils::bits(_regCount.getVec()) &amp; (fd.getPassedRegs(X86Reg::kKindVec) | ~fd.getPreservedRegs(X86Reg::kKindVec)));</span></a>
+<a name="2088"><span class="lineNum">    2088 </span>            : </a>
+<a name="2089"><span class="lineNum">    2089 </span><span class="lineCov">       6394 :         RA_FINALIZE(node_);</span></a>
+<a name="2090"><span class="lineNum">    2090 </span>            :         break;</a>
+<a name="2091"><span class="lineNum">    2091 </span>            :       }</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :     }</a>
+<a name="2093"><span class="lineNum">    2093 </span>            : </a>
+<a name="2094"><span class="lineNum">    2094 </span>            :     node_ = next;</a>
+<a name="2095"><span class="lineNum">    2095 </span><span class="lineCov">      34754 :   } while (node_ != stop);</span></a>
+<a name="2096"><span class="lineNum">    2096 </span>            : </a>
+<a name="2097"><span class="lineNum">    2097 </span><span class="lineCov">       1948 : _Done:</span></a>
+<a name="2098"><span class="lineNum">    2098 </span>            :   // Mark exit label and end node as fetched, otherwise they can be removed by</a>
+<a name="2099"><span class="lineNum">    2099 </span>            :   // `removeUnreachableCode()`, which could lead to a crash in some later step.</a>
+<a name="2100"><span class="lineNum">    2100 </span>            :   node_ = func-&gt;getEnd();</a>
+<a name="2101"><span class="lineNum">    2101 </span><span class="lineCov">       1948 :   if (!node_-&gt;hasPassData()) {</span></a>
+<a name="2102"><span class="lineNum">    2102 </span>            :     CBLabel* fExit = func-&gt;getExitNode();</a>
+<a name="2103"><span class="lineNum">    2103 </span><span class="lineCov">       1948 :     RA_POPULATE(fExit);</span></a>
+<a name="2104"><span class="lineNum">    2104 </span><span class="lineCov">       1948 :     fExit-&gt;setPosition(++position);</span></a>
+<a name="2105"><span class="lineNum">    2105 </span>            : </a>
+<a name="2106"><span class="lineNum">    2106 </span><span class="lineCov">       1948 :     RA_POPULATE(node_);</span></a>
+<a name="2107"><span class="lineNum">    2107 </span><span class="lineCov">       1948 :     node_-&gt;setPosition(++position);</span></a>
+<a name="2108"><span class="lineNum">    2108 </span>            :   }</a>
+<a name="2109"><span class="lineNum">    2109 </span>            :   return kErrorOk;</a>
+<a name="2110"><span class="lineNum">    2110 </span>            : </a>
+<a name="2111"><span class="lineNum">    2111 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2112"><span class="lineNum">    2112 </span>            :   // [Failure]</a>
+<a name="2113"><span class="lineNum">    2113 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2114"><span class="lineNum">    2114 </span>            : </a>
+<a name="2115"><span class="lineNum">    2115 </span>            : NoMem:</a>
+<a name="2116"><span class="lineNum">    2116 </span>            :   return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="2117"><span class="lineNum">    2117 </span>            : }</a>
+<a name="2118"><span class="lineNum">    2118 </span>            : </a>
+<a name="2119"><span class="lineNum">    2119 </span>            : // ============================================================================</a>
+<a name="2120"><span class="lineNum">    2120 </span>            : // [asmjit::X86RAPass - Annotate]</a>
+<a name="2121"><span class="lineNum">    2121 </span>            : // ============================================================================</a>
+<a name="2122"><span class="lineNum">    2122 </span>            : </a>
+<a name="2123"><span class="lineNum">    2123 </span><span class="lineNoCov">          0 : Error X86RAPass::annotate() {</span></a>
+<a name="2124"><span class="lineNum">    2124 </span>            : #if !defined(ASMJIT_DISABLE_LOGGING)</a>
+<a name="2125"><span class="lineNum">    2125 </span>            :   CCFunc* func = getFunc();</a>
+<a name="2126"><span class="lineNum">    2126 </span>            : </a>
+<a name="2127"><span class="lineNum">    2127 </span>            :   CBNode* node_ = func;</a>
+<a name="2128"><span class="lineNum">    2128 </span>            :   CBNode* end = func-&gt;getEnd();</a>
+<a name="2129"><span class="lineNum">    2129 </span>            : </a>
+<a name="2130"><span class="lineNum">    2130 </span><span class="lineNoCov">          0 :   Zone&amp; dataZone = cc()-&gt;_cbDataZone;</span></a>
+<a name="2131"><span class="lineNum">    2131 </span>            :   StringBuilderTmp&lt;256&gt; sb;</a>
+<a name="2132"><span class="lineNum">    2132 </span>            : </a>
+<a name="2133"><span class="lineNum">    2133 </span><span class="lineNoCov">          0 :   uint32_t maxLen = 0;</span></a>
+<a name="2134"><span class="lineNum">    2134 </span><span class="lineNoCov">          0 :   while (node_ &amp;&amp; node_ != end) {</span></a>
+<a name="2135"><span class="lineNum">    2135 </span><span class="lineNoCov">          0 :     if (!node_-&gt;hasInlineComment()) {</span></a>
+<a name="2136"><span class="lineNum">    2136 </span><span class="lineNoCov">          0 :       if (node_-&gt;getType() == CBNode::kNodeInst) {</span></a>
+<a name="2137"><span class="lineNum">    2137 </span>            :         CBInst* node = static_cast&lt;CBInst*&gt;(node_);</a>
+<a name="2138"><span class="lineNum">    2138 </span><span class="lineNoCov">          0 :         Logging::formatInstruction(</span></a>
+<a name="2139"><span class="lineNum">    2139 </span>            :           sb,</a>
+<a name="2140"><span class="lineNum">    2140 </span>            :           0,</a>
+<a name="2141"><span class="lineNum">    2141 </span>            :           cc(),</a>
+<a name="2142"><span class="lineNum">    2142 </span>            :           cc()-&gt;getArchType(),</a>
+<a name="2143"><span class="lineNum">    2143 </span>            :           node-&gt;getInstDetail(), node-&gt;getOpArray(), node-&gt;getOpCount());</a>
+<a name="2144"><span class="lineNum">    2144 </span>            : </a>
+<a name="2145"><span class="lineNum">    2145 </span>            :         node_-&gt;setInlineComment(</a>
+<a name="2146"><span class="lineNum">    2146 </span><span class="lineNoCov">          0 :           static_cast&lt;char*&gt;(dataZone.dup(sb.getData(), sb.getLength(), true)));</span></a>
+<a name="2147"><span class="lineNum">    2147 </span><span class="lineNoCov">          0 :         maxLen = std::max&lt;uint32_t&gt;(maxLen, static_cast&lt;uint32_t&gt;(sb.getLength()));</span></a>
+<a name="2148"><span class="lineNum">    2148 </span>            : </a>
+<a name="2149"><span class="lineNum">    2149 </span><span class="lineNoCov">          0 :         sb.clear();</span></a>
+<a name="2150"><span class="lineNum">    2150 </span>            :       }</a>
+<a name="2151"><span class="lineNum">    2151 </span>            :     }</a>
+<a name="2152"><span class="lineNum">    2152 </span>            : </a>
+<a name="2153"><span class="lineNum">    2153 </span>            :     node_ = node_-&gt;getNext();</a>
+<a name="2154"><span class="lineNum">    2154 </span>            :   }</a>
+<a name="2155"><span class="lineNum">    2155 </span><span class="lineNoCov">          0 :   _annotationLength = maxLen + 1;</span></a>
+<a name="2156"><span class="lineNum">    2156 </span>            : #endif // !ASMJIT_DISABLE_LOGGING</a>
+<a name="2157"><span class="lineNum">    2157 </span>            : </a>
+<a name="2158"><span class="lineNum">    2158 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="2159"><span class="lineNum">    2159 </span>            : }</a>
+<a name="2160"><span class="lineNum">    2160 </span>            : </a>
+<a name="2161"><span class="lineNum">    2161 </span>            : // ============================================================================</a>
+<a name="2162"><span class="lineNum">    2162 </span>            : // [asmjit::X86BaseAlloc]</a>
+<a name="2163"><span class="lineNum">    2163 </span>            : // ============================================================================</a>
+<a name="2164"><span class="lineNum">    2164 </span>            : </a>
+<a name="2165"><span class="lineNum">    2165 </span>            : struct X86BaseAlloc {</a>
+<a name="2166"><span class="lineNum">    2166 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2167"><span class="lineNum">    2167 </span>            :   // [Construction / Destruction]</a>
+<a name="2168"><span class="lineNum">    2168 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2169"><span class="lineNum">    2169 </span>            : </a>
+<a name="2170"><span class="lineNum">    2170 </span><span class="lineCov">       1948 :   ASMJIT_INLINE X86BaseAlloc(X86RAPass* context) {</span></a>
+<a name="2171"><span class="lineNum">    2171 </span><span class="lineCov">       1948 :     _context = context;</span></a>
+<a name="2172"><span class="lineNum">    2172 </span><span class="lineCov">       1948 :     _cc = context-&gt;cc();</span></a>
+<a name="2173"><span class="lineNum">    2173 </span>            :   }</a>
+<a name="2174"><span class="lineNum">    2174 </span>            :   ASMJIT_INLINE ~X86BaseAlloc() {}</a>
+<a name="2175"><span class="lineNum">    2175 </span>            : </a>
+<a name="2176"><span class="lineNum">    2176 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2177"><span class="lineNum">    2177 </span>            :   // [Accessors]</a>
+<a name="2178"><span class="lineNum">    2178 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2179"><span class="lineNum">    2179 </span>            : </a>
+<a name="2180"><span class="lineNum">    2180 </span>            :   //! Get the context.</a>
+<a name="2181"><span class="lineNum">    2181 </span>            :   ASMJIT_INLINE X86RAPass* getContext() const { return _context; }</a>
+<a name="2182"><span class="lineNum">    2182 </span>            :   //! Get the current state (always the same instance as X86RAPass::_x86State).</a>
+<a name="2183"><span class="lineNum">    2183 </span><span class="lineCov">      10432 :   ASMJIT_INLINE X86RAState* getState() const { return _context-&gt;getState(); }</span></a>
+<a name="2184"><span class="lineNum">    2184 </span>            : </a>
+<a name="2185"><span class="lineNum">    2185 </span>            :   //! Get the node.</a>
+<a name="2186"><span class="lineNum">    2186 </span>            :   ASMJIT_INLINE CBNode* getNode() const { return _node; }</a>
+<a name="2187"><span class="lineNum">    2187 </span>            : </a>
+<a name="2188"><span class="lineNum">    2188 </span>            :   //! Get TiedReg list (all).</a>
+<a name="2189"><span class="lineNum">    2189 </span>            :   ASMJIT_INLINE TiedReg* getTiedArray() const { return _tiedArray[0]; }</a>
+<a name="2190"><span class="lineNum">    2190 </span>            :   //! Get TiedReg list (per class).</a>
+<a name="2191"><span class="lineNum">    2191 </span><span class="lineCov">     333940 :   ASMJIT_INLINE TiedReg* getTiedArrayByKind(uint32_t kind) const { return _tiedArray[kind]; }</span></a>
+<a name="2192"><span class="lineNum">    2192 </span>            : </a>
+<a name="2193"><span class="lineNum">    2193 </span>            :   //! Get TiedReg count (all).</a>
+<a name="2194"><span class="lineNum">    2194 </span>            :   ASMJIT_INLINE uint32_t getTiedCount() const { return _tiedTotal; }</a>
+<a name="2195"><span class="lineNum">    2195 </span>            :   //! Get TiedReg count (per class).</a>
+<a name="2196"><span class="lineNum">    2196 </span>            :   ASMJIT_INLINE uint32_t getTiedCountByKind(uint32_t kind) const { return _tiedCount.get(kind); }</a>
+<a name="2197"><span class="lineNum">    2197 </span>            : </a>
+<a name="2198"><span class="lineNum">    2198 </span>            :   //! Get if all variables of the given register `kind` are done.</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :   ASMJIT_INLINE bool isTiedDone(uint32_t kind) const { return _tiedDone.get(kind) == _tiedCount.get(kind); }</a>
+<a name="2200"><span class="lineNum">    2200 </span>            : </a>
+<a name="2201"><span class="lineNum">    2201 </span>            :   //! Get how many variables have been allocated.</a>
+<a name="2202"><span class="lineNum">    2202 </span>            :   ASMJIT_INLINE uint32_t getTiedDone(uint32_t kind) const { return _tiedDone.get(kind); }</a>
+<a name="2203"><span class="lineNum">    2203 </span>            :   //! Add to the count of variables allocated.</a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineCov">      26078 :   ASMJIT_INLINE void addTiedDone(uint32_t kind, uint32_t n = 1) { _tiedDone.add(kind, n); }</span></a>
+<a name="2205"><span class="lineNum">    2205 </span>            : </a>
+<a name="2206"><span class="lineNum">    2206 </span>            :   //! Get number of allocable registers per class.</a>
+<a name="2207"><span class="lineNum">    2207 </span>            :   ASMJIT_INLINE uint32_t getGaRegs(uint32_t kind) const {</a>
+<a name="2208"><span class="lineNum">    2208 </span>            :     return _context-&gt;_gaRegs[kind];</a>
+<a name="2209"><span class="lineNum">    2209 </span>            :   }</a>
+<a name="2210"><span class="lineNum">    2210 </span>            : </a>
+<a name="2211"><span class="lineNum">    2211 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2212"><span class="lineNum">    2212 </span>            :   // [Init / Cleanup]</a>
+<a name="2213"><span class="lineNum">    2213 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2214"><span class="lineNum">    2214 </span>            : </a>
+<a name="2215"><span class="lineNum">    2215 </span>            : protected:</a>
+<a name="2216"><span class="lineNum">    2216 </span>            :   // Just to prevent calling these methods by X86RAPass::translate().</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :   ASMJIT_INLINE void init(CBNode* node, X86RAData* map);</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :   ASMJIT_INLINE void cleanup();</a>
+<a name="2219"><span class="lineNum">    2219 </span>            : </a>
+<a name="2220"><span class="lineNum">    2220 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2221"><span class="lineNum">    2221 </span>            :   // [Unuse]</a>
+<a name="2222"><span class="lineNum">    2222 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2223"><span class="lineNum">    2223 </span>            : </a>
+<a name="2224"><span class="lineNum">    2224 </span>            :   template&lt;int C&gt;</a>
+<a name="2225"><span class="lineNum">    2225 </span>            :   ASMJIT_INLINE void unuseBefore();</a>
+<a name="2226"><span class="lineNum">    2226 </span>            : </a>
+<a name="2227"><span class="lineNum">    2227 </span>            :   template&lt;int C&gt;</a>
+<a name="2228"><span class="lineNum">    2228 </span>            :   ASMJIT_INLINE void unuseAfter();</a>
+<a name="2229"><span class="lineNum">    2229 </span>            : </a>
+<a name="2230"><span class="lineNum">    2230 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2231"><span class="lineNum">    2231 </span>            :   // [Members]</a>
+<a name="2232"><span class="lineNum">    2232 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2233"><span class="lineNum">    2233 </span>            : </a>
+<a name="2234"><span class="lineNum">    2234 </span>            :   //! RA context.</a>
+<a name="2235"><span class="lineNum">    2235 </span>            :   X86RAPass* _context;</a>
+<a name="2236"><span class="lineNum">    2236 </span>            :   //! Compiler.</a>
+<a name="2237"><span class="lineNum">    2237 </span>            :   X86Compiler* _cc;</a>
+<a name="2238"><span class="lineNum">    2238 </span>            : </a>
+<a name="2239"><span class="lineNum">    2239 </span>            :   //! Node.</a>
+<a name="2240"><span class="lineNum">    2240 </span>            :   CBNode* _node;</a>
+<a name="2241"><span class="lineNum">    2241 </span>            : </a>
+<a name="2242"><span class="lineNum">    2242 </span>            :   //! Register allocator (RA) data.</a>
+<a name="2243"><span class="lineNum">    2243 </span>            :   X86RAData* _raData;</a>
+<a name="2244"><span class="lineNum">    2244 </span>            :   //! TiedReg list (per register kind).</a>
+<a name="2245"><span class="lineNum">    2245 </span>            :   TiedReg* _tiedArray[Globals::kMaxVRegKinds];</a>
+<a name="2246"><span class="lineNum">    2246 </span>            : </a>
+<a name="2247"><span class="lineNum">    2247 </span>            :   //! Count of all TiedReg's.</a>
+<a name="2248"><span class="lineNum">    2248 </span>            :   uint32_t _tiedTotal;</a>
+<a name="2249"><span class="lineNum">    2249 </span>            : </a>
+<a name="2250"><span class="lineNum">    2250 </span>            :   //! TiedReg's total counter.</a>
+<a name="2251"><span class="lineNum">    2251 </span>            :   X86RegCount _tiedCount;</a>
+<a name="2252"><span class="lineNum">    2252 </span>            :   //! TiedReg's done counter.</a>
+<a name="2253"><span class="lineNum">    2253 </span>            :   X86RegCount _tiedDone;</a>
+<a name="2254"><span class="lineNum">    2254 </span>            : };</a>
+<a name="2255"><span class="lineNum">    2255 </span>            : </a>
+<a name="2256"><span class="lineNum">    2256 </span>            : // ============================================================================</a>
+<a name="2257"><span class="lineNum">    2257 </span>            : // [asmjit::X86BaseAlloc - Init / Cleanup]</a>
+<a name="2258"><span class="lineNum">    2258 </span>            : // ============================================================================</a>
+<a name="2259"><span class="lineNum">    2259 </span>            : </a>
+<a name="2260"><span class="lineNum">    2260 </span>            : ASMJIT_INLINE void X86BaseAlloc::init(CBNode* node, X86RAData* raData) {</a>
+<a name="2261"><span class="lineNum">    2261 </span><span class="lineCov">      36702 :   _node = node;</span></a>
+<a name="2262"><span class="lineNum">    2262 </span><span class="lineCov">      36702 :   _raData = raData;</span></a>
+<a name="2263"><span class="lineNum">    2263 </span>            : </a>
+<a name="2264"><span class="lineNum">    2264 </span>            :   // We have to set the correct cursor in case any instruction is emitted</a>
+<a name="2265"><span class="lineNum">    2265 </span>            :   // during the allocation phase; it has to be emitted before the current</a>
+<a name="2266"><span class="lineNum">    2266 </span>            :   // instruction.</a>
+<a name="2267"><span class="lineNum">    2267 </span><span class="lineCov">      36702 :   _cc-&gt;_setCursor(node-&gt;getPrev());</span></a>
+<a name="2268"><span class="lineNum">    2268 </span>            : </a>
+<a name="2269"><span class="lineNum">    2269 </span>            :   // Setup the lists of variables.</a>
+<a name="2270"><span class="lineNum">    2270 </span>            :   {</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :     TiedReg* tied = raData-&gt;getTiedArray();</a>
+<a name="2272"><span class="lineNum">    2272 </span><span class="lineCov">      36702 :     _tiedArray[X86Reg::kKindGp ] = tied;</span></a>
+<a name="2273"><span class="lineNum">    2273 </span><span class="lineCov">      36702 :     _tiedArray[X86Reg::kKindMm ] = tied + raData-&gt;getTiedStart(X86Reg::kKindMm );</span></a>
+<a name="2274"><span class="lineNum">    2274 </span><span class="lineCov">      36702 :     _tiedArray[X86Reg::kKindK  ] = tied + raData-&gt;getTiedStart(X86Reg::kKindK  );</span></a>
+<a name="2275"><span class="lineNum">    2275 </span><span class="lineCov">      36702 :     _tiedArray[X86Reg::kKindVec] = tied + raData-&gt;getTiedStart(X86Reg::kKindVec);</span></a>
+<a name="2276"><span class="lineNum">    2276 </span>            :   }</a>
+<a name="2277"><span class="lineNum">    2277 </span>            : </a>
+<a name="2278"><span class="lineNum">    2278 </span>            :   // Setup counters.</a>
+<a name="2279"><span class="lineNum">    2279 </span><span class="lineCov">      36702 :   _tiedTotal = raData-&gt;tiedTotal;</span></a>
+<a name="2280"><span class="lineNum">    2280 </span><span class="lineCov">      36702 :   _tiedCount = raData-&gt;tiedCount;</span></a>
+<a name="2281"><span class="lineNum">    2281 </span>            :   _tiedDone.reset();</a>
+<a name="2282"><span class="lineNum">    2282 </span>            : </a>
+<a name="2283"><span class="lineNum">    2283 </span>            :   // Connect VREG-&gt;TIED.</a>
+<a name="2284"><span class="lineNum">    2284 </span><span class="lineCov">      98196 :   for (uint32_t i = 0; i &lt; _tiedTotal; i++) {</span></a>
+<a name="2285"><span class="lineNum">    2285 </span><span class="lineCov">      61494 :     TiedReg* tied = &amp;_tiedArray[0][i];</span></a>
+<a name="2286"><span class="lineNum">    2286 </span><span class="lineCov">      61494 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="2287"><span class="lineNum">    2287 </span><span class="lineCov">      61494 :     vreg-&gt;_tied = tied;</span></a>
+<a name="2288"><span class="lineNum">    2288 </span>            :   }</a>
+<a name="2289"><span class="lineNum">    2289 </span>            : }</a>
+<a name="2290"><span class="lineNum">    2290 </span>            : </a>
+<a name="2291"><span class="lineNum">    2291 </span>            : ASMJIT_INLINE void X86BaseAlloc::cleanup() {</a>
+<a name="2292"><span class="lineNum">    2292 </span>            :   // Disconnect VREG-&gt;TIED.</a>
+<a name="2293"><span class="lineNum">    2293 </span><span class="lineCov">      96248 :   for (uint32_t i = 0; i &lt; _tiedTotal; i++) {</span></a>
+<a name="2294"><span class="lineNum">    2294 </span><span class="lineCov">      61494 :     TiedReg* tied = &amp;_tiedArray[0][i];</span></a>
+<a name="2295"><span class="lineNum">    2295 </span><span class="lineCov">      61494 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="2296"><span class="lineNum">    2296 </span><span class="lineCov">      61494 :     vreg-&gt;_tied = nullptr;</span></a>
+<a name="2297"><span class="lineNum">    2297 </span>            :   }</a>
+<a name="2298"><span class="lineNum">    2298 </span>            : }</a>
+<a name="2299"><span class="lineNum">    2299 </span>            : </a>
+<a name="2300"><span class="lineNum">    2300 </span>            : // ============================================================================</a>
+<a name="2301"><span class="lineNum">    2301 </span>            : // [asmjit::X86BaseAlloc - Unuse]</a>
+<a name="2302"><span class="lineNum">    2302 </span>            : // ============================================================================</a>
+<a name="2303"><span class="lineNum">    2303 </span>            : </a>
+<a name="2304"><span class="lineNum">    2304 </span>            : template&lt;int C&gt;</a>
+<a name="2305"><span class="lineNum">    2305 </span>            : ASMJIT_INLINE void X86BaseAlloc::unuseBefore() {</a>
+<a name="2306"><span class="lineNum">    2306 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="2307"><span class="lineNum">    2307 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="2308"><span class="lineNum">    2308 </span>            : </a>
+<a name="2309"><span class="lineNum">    2309 </span>            :   const uint32_t checkFlags = TiedReg::kXReg  |</a>
+<a name="2310"><span class="lineNum">    2310 </span>            :                               TiedReg::kRMem  |</a>
+<a name="2311"><span class="lineNum">    2311 </span>            :                               TiedReg::kRFunc |</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :                               TiedReg::kRCall ;</a>
+<a name="2313"><span class="lineNum">    2313 </span>            : </a>
+<a name="2314"><span class="lineNum">    2314 </span><span class="lineCov">      89854 :   for (uint32_t i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2315"><span class="lineNum">    2315 </span><span class="lineCov">      56748 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="2316"><span class="lineNum">    2316 </span><span class="lineCov">      56748 :     if ((tied-&gt;flags &amp; checkFlags) == TiedReg::kWReg)</span></a>
+<a name="2317"><span class="lineNum">    2317 </span><span class="lineCov">      22140 :       _context-&gt;unuse&lt;C&gt;(tied-&gt;vreg);</span></a>
+<a name="2318"><span class="lineNum">    2318 </span>            :   }</a>
+<a name="2319"><span class="lineNum">    2319 </span>            : }</a>
+<a name="2320"><span class="lineNum">    2320 </span>            : </a>
+<a name="2321"><span class="lineNum">    2321 </span>            : template&lt;int C&gt;</a>
+<a name="2322"><span class="lineNum">    2322 </span>            : ASMJIT_INLINE void X86BaseAlloc::unuseAfter() {</a>
+<a name="2323"><span class="lineNum">    2323 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="2324"><span class="lineNum">    2324 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="2325"><span class="lineNum">    2325 </span>            : </a>
+<a name="2326"><span class="lineNum">    2326 </span><span class="lineCov">      96248 :   for (uint32_t i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2327"><span class="lineNum">    2327 </span><span class="lineCov">      61494 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="2328"><span class="lineNum">    2328 </span><span class="lineCov">      61494 :     if (tied-&gt;flags &amp; TiedReg::kUnuse)</span></a>
+<a name="2329"><span class="lineNum">    2329 </span><span class="lineCov">      21840 :       _context-&gt;unuse&lt;C&gt;(tied-&gt;vreg);</span></a>
+<a name="2330"><span class="lineNum">    2330 </span>            :   }</a>
+<a name="2331"><span class="lineNum">    2331 </span>            : }</a>
+<a name="2332"><span class="lineNum">    2332 </span>            : </a>
+<a name="2333"><span class="lineNum">    2333 </span>            : // ============================================================================</a>
+<a name="2334"><span class="lineNum">    2334 </span>            : // [asmjit::X86VarAlloc]</a>
+<a name="2335"><span class="lineNum">    2335 </span>            : // ============================================================================</a>
+<a name="2336"><span class="lineNum">    2336 </span>            : </a>
+<a name="2337"><span class="lineNum">    2337 </span>            : //! \internal</a>
+<a name="2338"><span class="lineNum">    2338 </span>            : //!</a>
+<a name="2339"><span class="lineNum">    2339 </span>            : //! Register allocator context (asm instructions).</a>
+<a name="2340"><span class="lineNum">    2340 </span>            : struct X86VarAlloc : public X86BaseAlloc {</a>
+<a name="2341"><span class="lineNum">    2341 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2342"><span class="lineNum">    2342 </span>            :   // [Construction / Destruction]</a>
+<a name="2343"><span class="lineNum">    2343 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2344"><span class="lineNum">    2344 </span>            : </a>
+<a name="2345"><span class="lineNum">    2345 </span><span class="lineCov">       1948 :   ASMJIT_INLINE X86VarAlloc(X86RAPass* context) : X86BaseAlloc(context) {}</span></a>
+<a name="2346"><span class="lineNum">    2346 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ~X86VarAlloc() {}</span></a>
+<a name="2347"><span class="lineNum">    2347 </span>            : </a>
+<a name="2348"><span class="lineNum">    2348 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2349"><span class="lineNum">    2349 </span>            :   // [Run]</a>
+<a name="2350"><span class="lineNum">    2350 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2351"><span class="lineNum">    2351 </span>            : </a>
+<a name="2352"><span class="lineNum">    2352 </span>            :   Error run(CBNode* node);</a>
+<a name="2353"><span class="lineNum">    2353 </span>            : </a>
+<a name="2354"><span class="lineNum">    2354 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2355"><span class="lineNum">    2355 </span>            :   // [Init / Cleanup]</a>
+<a name="2356"><span class="lineNum">    2356 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2357"><span class="lineNum">    2357 </span>            : </a>
+<a name="2358"><span class="lineNum">    2358 </span>            : protected:</a>
+<a name="2359"><span class="lineNum">    2359 </span>            :   // Just to prevent calling these methods by X86RAPass::translate().</a>
+<a name="2360"><span class="lineNum">    2360 </span>            :   ASMJIT_INLINE void init(CBNode* node, X86RAData* map);</a>
+<a name="2361"><span class="lineNum">    2361 </span>            :   ASMJIT_INLINE void cleanup();</a>
+<a name="2362"><span class="lineNum">    2362 </span>            : </a>
+<a name="2363"><span class="lineNum">    2363 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2364"><span class="lineNum">    2364 </span>            :   // [Plan / Spill / Alloc]</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2366"><span class="lineNum">    2366 </span>            : </a>
+<a name="2367"><span class="lineNum">    2367 </span>            :   template&lt;int C&gt;</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :   ASMJIT_INLINE void plan();</a>
+<a name="2369"><span class="lineNum">    2369 </span>            : </a>
+<a name="2370"><span class="lineNum">    2370 </span>            :   template&lt;int C&gt;</a>
+<a name="2371"><span class="lineNum">    2371 </span>            :   ASMJIT_INLINE void spill();</a>
+<a name="2372"><span class="lineNum">    2372 </span>            : </a>
+<a name="2373"><span class="lineNum">    2373 </span>            :   template&lt;int C&gt;</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :   ASMJIT_INLINE void alloc();</a>
+<a name="2375"><span class="lineNum">    2375 </span>            : </a>
+<a name="2376"><span class="lineNum">    2376 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2377"><span class="lineNum">    2377 </span>            :   // [GuessAlloc / GuessSpill]</a>
+<a name="2378"><span class="lineNum">    2378 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2379"><span class="lineNum">    2379 </span>            : </a>
+<a name="2380"><span class="lineNum">    2380 </span>            :   //! Guess which register is the best candidate for `vreg` from `allocableRegs`.</a>
+<a name="2381"><span class="lineNum">    2381 </span>            :   //!</a>
+<a name="2382"><span class="lineNum">    2382 </span>            :   //! The guess is based on looking ahead and inspecting register allocator</a>
+<a name="2383"><span class="lineNum">    2383 </span>            :   //! instructions. The main reason is to prevent allocation to a register</a>
+<a name="2384"><span class="lineNum">    2384 </span>            :   //! which is needed by next instruction(s). The guess look tries to go as far</a>
+<a name="2385"><span class="lineNum">    2385 </span>            :   //! as possible, after the remaining registers are zero, the mask of previous</a>
+<a name="2386"><span class="lineNum">    2386 </span>            :   //! registers (called 'safeRegs') is returned.</a>
+<a name="2387"><span class="lineNum">    2387 </span>            :   template&lt;int C&gt;</a>
+<a name="2388"><span class="lineNum">    2388 </span>            :   ASMJIT_INLINE uint32_t guessAlloc(VirtReg* vreg, uint32_t allocableRegs);</a>
+<a name="2389"><span class="lineNum">    2389 </span>            : </a>
+<a name="2390"><span class="lineNum">    2390 </span>            :   //! Guess whether to move the given `vreg` instead of spill.</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :   template&lt;int C&gt;</a>
+<a name="2392"><span class="lineNum">    2392 </span>            :   ASMJIT_INLINE uint32_t guessSpill(VirtReg* vreg, uint32_t allocableRegs);</a>
+<a name="2393"><span class="lineNum">    2393 </span>            : </a>
+<a name="2394"><span class="lineNum">    2394 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2395"><span class="lineNum">    2395 </span>            :   // [Modified]</a>
+<a name="2396"><span class="lineNum">    2396 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2397"><span class="lineNum">    2397 </span>            : </a>
+<a name="2398"><span class="lineNum">    2398 </span>            :   template&lt;int C&gt;</a>
+<a name="2399"><span class="lineNum">    2399 </span>            :   ASMJIT_INLINE void modified();</a>
+<a name="2400"><span class="lineNum">    2400 </span>            : </a>
+<a name="2401"><span class="lineNum">    2401 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2402"><span class="lineNum">    2402 </span>            :   // [Members]</a>
+<a name="2403"><span class="lineNum">    2403 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2404"><span class="lineNum">    2404 </span>            : </a>
+<a name="2405"><span class="lineNum">    2405 </span>            :   //! Will alloc to these registers.</a>
+<a name="2406"><span class="lineNum">    2406 </span>            :   X86RegMask _willAlloc;</a>
+<a name="2407"><span class="lineNum">    2407 </span>            :   //! Will spill these registers.</a>
+<a name="2408"><span class="lineNum">    2408 </span>            :   X86RegMask _willSpill;</a>
+<a name="2409"><span class="lineNum">    2409 </span>            : };</a>
+<a name="2410"><span class="lineNum">    2410 </span>            : </a>
+<a name="2411"><span class="lineNum">    2411 </span>            : // ============================================================================</a>
+<a name="2412"><span class="lineNum">    2412 </span>            : // [asmjit::X86VarAlloc - Run]</a>
+<a name="2413"><span class="lineNum">    2413 </span>            : // ============================================================================</a>
+<a name="2414"><span class="lineNum">    2414 </span>            : </a>
+<a name="2415"><span class="lineNum">    2415 </span><span class="lineCov">      35054 : Error X86VarAlloc::run(CBNode* node_) {</span></a>
+<a name="2416"><span class="lineNum">    2416 </span>            :   // Initialize.</a>
+<a name="2417"><span class="lineNum">    2417 </span>            :   X86RAData* raData = node_-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="2418"><span class="lineNum">    2418 </span>            :   // Initialize the allocator; connect Vd-&gt;Va.</a>
+<a name="2419"><span class="lineNum">    2419 </span>            :   init(node_, raData);</a>
+<a name="2420"><span class="lineNum">    2420 </span>            : </a>
+<a name="2421"><span class="lineNum">    2421 </span><span class="lineCov">      35054 :   if (raData-&gt;tiedTotal != 0) {</span></a>
+<a name="2422"><span class="lineNum">    2422 </span>            :     // Unuse overwritten variables.</a>
+<a name="2423"><span class="lineNum">    2423 </span>            :     unuseBefore&lt;X86Reg::kKindGp&gt;();</a>
+<a name="2424"><span class="lineNum">    2424 </span>            :     unuseBefore&lt;X86Reg::kKindMm&gt;();</a>
+<a name="2425"><span class="lineNum">    2425 </span>            :     unuseBefore&lt;X86Reg::kKindVec&gt;();</a>
+<a name="2426"><span class="lineNum">    2426 </span>            : </a>
+<a name="2427"><span class="lineNum">    2427 </span>            :     // Plan the allocation. Planner assigns input/output registers for each</a>
+<a name="2428"><span class="lineNum">    2428 </span>            :     // variable and decides whether to allocate it in register or stack.</a>
+<a name="2429"><span class="lineNum">    2429 </span>            :     plan&lt;X86Reg::kKindGp&gt;();</a>
+<a name="2430"><span class="lineNum">    2430 </span>            :     plan&lt;X86Reg::kKindMm&gt;();</a>
+<a name="2431"><span class="lineNum">    2431 </span>            :     plan&lt;X86Reg::kKindVec&gt;();</a>
+<a name="2432"><span class="lineNum">    2432 </span>            : </a>
+<a name="2433"><span class="lineNum">    2433 </span>            :     // Spill all variables marked by plan().</a>
+<a name="2434"><span class="lineNum">    2434 </span>            :     spill&lt;X86Reg::kKindGp&gt;();</a>
+<a name="2435"><span class="lineNum">    2435 </span>            :     spill&lt;X86Reg::kKindMm&gt;();</a>
+<a name="2436"><span class="lineNum">    2436 </span>            :     spill&lt;X86Reg::kKindVec&gt;();</a>
+<a name="2437"><span class="lineNum">    2437 </span>            : </a>
+<a name="2438"><span class="lineNum">    2438 </span>            :     // Alloc all variables marked by plan().</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :     alloc&lt;X86Reg::kKindGp&gt;();</a>
+<a name="2440"><span class="lineNum">    2440 </span>            :     alloc&lt;X86Reg::kKindMm&gt;();</a>
+<a name="2441"><span class="lineNum">    2441 </span>            :     alloc&lt;X86Reg::kKindVec&gt;();</a>
+<a name="2442"><span class="lineNum">    2442 </span>            : </a>
+<a name="2443"><span class="lineNum">    2443 </span>            :     // Translate node operands.</a>
+<a name="2444"><span class="lineNum">    2444 </span><span class="lineCov">      33106 :     if (node_-&gt;getType() == CBNode::kNodeInst) {</span></a>
+<a name="2445"><span class="lineNum">    2445 </span>            :       CBInst* node = static_cast&lt;CBInst*&gt;(node_);</a>
+<a name="2446"><span class="lineNum">    2446 </span><span class="lineCov">      31158 :       if (node-&gt;hasExtraReg()) {</span></a>
+<a name="2447"><span class="lineNum">    2447 </span>            :         Reg reg = node-&gt;getExtraReg().toReg&lt;Reg&gt;();</a>
+<a name="2448"><span class="lineNum">    2448 </span><span class="lineNoCov">          0 :         ASMJIT_PROPAGATE(X86RAPass_translateOperands(_context, &amp;reg, 1));</span></a>
+<a name="2449"><span class="lineNum">    2449 </span>            :         node-&gt;setExtraReg(reg);</a>
+<a name="2450"><span class="lineNum">    2450 </span>            :       }</a>
+<a name="2451"><span class="lineNum">    2451 </span><span class="lineCov">      31158 :       ASMJIT_PROPAGATE(X86RAPass_translateOperands(_context, node-&gt;getOpArray(), node-&gt;getOpCount()));</span></a>
+<a name="2452"><span class="lineNum">    2452 </span>            :     }</a>
+<a name="2453"><span class="lineNum">    2453 </span><span class="lineCov">       1948 :     else if (node_-&gt;getType() == CBNode::kNodePushArg) {</span></a>
+<a name="2454"><span class="lineNum">    2454 </span>            :       CCPushArg* node = static_cast&lt;CCPushArg*&gt;(node_);</a>
+<a name="2455"><span class="lineNum">    2455 </span>            : </a>
+<a name="2456"><span class="lineNum">    2456 </span>            :       CCFuncCall* call = static_cast&lt;CCFuncCall*&gt;(node-&gt;getCall());</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :       FuncDetail&amp; fd = call-&gt;getDetail();</a>
+<a name="2458"><span class="lineNum">    2458 </span>            : </a>
+<a name="2459"><span class="lineNum">    2459 </span>            :       uint32_t argIndex = 0;</a>
+<a name="2460"><span class="lineNum">    2460 </span><span class="lineNoCov">          0 :       uint32_t argMask = node-&gt;_args;</span></a>
+<a name="2461"><span class="lineNum">    2461 </span>            : </a>
+<a name="2462"><span class="lineNum">    2462 </span>            :       VirtReg* cvtReg = node-&gt;getCvtReg();</a>
+<a name="2463"><span class="lineNum">    2463 </span>            :       VirtReg* srcReg = node-&gt;getSrcReg();</a>
+<a name="2464"><span class="lineNum">    2464 </span>            : </a>
+<a name="2465"><span class="lineNum">    2465 </span>            :       // Convert first.</a>
+<a name="2466"><span class="lineNum">    2466 </span>            :       ASMJIT_ASSERT(srcReg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="2467"><span class="lineNum">    2467 </span>            : </a>
+<a name="2468"><span class="lineNum">    2468 </span><span class="lineNoCov">          0 :       if (cvtReg) {</span></a>
+<a name="2469"><span class="lineNum">    2469 </span>            :         ASMJIT_ASSERT(cvtReg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="2470"><span class="lineNum">    2470 </span>            : </a>
+<a name="2471"><span class="lineNum">    2471 </span>            :         X86Reg dstOp(X86Reg::fromSignature(cvtReg-&gt;getSignature(), cvtReg-&gt;getId()));</a>
+<a name="2472"><span class="lineNum">    2472 </span>            :         X86Reg srcOp(X86Reg::fromSignature(srcReg-&gt;getSignature(), srcReg-&gt;getId()));</a>
+<a name="2473"><span class="lineNum">    2473 </span>            : </a>
+<a name="2474"><span class="lineNum">    2474 </span>            :         // Emit conversion after the prolog.</a>
+<a name="2475"><span class="lineNum">    2475 </span><span class="lineNoCov">          0 :         X86Internal::emitArgMove(reinterpret_cast&lt;X86Emitter*&gt;(_context-&gt;cc()),</span></a>
+<a name="2476"><span class="lineNum">    2476 </span>            :           dstOp, cvtReg-&gt;getTypeId(),</a>
+<a name="2477"><span class="lineNum">    2477 </span><span class="lineNoCov">          0 :           srcOp, srcReg-&gt;getTypeId(), _context-&gt;_avxEnabled);</span></a>
+<a name="2478"><span class="lineNum">    2478 </span>            :         srcReg = cvtReg;</a>
+<a name="2479"><span class="lineNum">    2479 </span>            :       }</a>
+<a name="2480"><span class="lineNum">    2480 </span>            : </a>
+<a name="2481"><span class="lineNum">    2481 </span><span class="lineNoCov">          0 :       while (argMask != 0) {</span></a>
+<a name="2482"><span class="lineNum">    2482 </span><span class="lineNoCov">          0 :         if (argMask &amp; 0x1) {</span></a>
+<a name="2483"><span class="lineNum">    2483 </span><span class="lineNoCov">          0 :           FuncDetail::Value&amp; arg = fd.getArg(argIndex);</span></a>
+<a name="2484"><span class="lineNum">    2484 </span>            :           ASMJIT_ASSERT(arg.byStack());</a>
+<a name="2485"><span class="lineNum">    2485 </span>            : </a>
+<a name="2486"><span class="lineNum">    2486 </span><span class="lineNoCov">          0 :           X86Mem dst = x86::ptr(_context-&gt;_zsp, -static_cast&lt;int&gt;(_context-&gt;getGpSize()) + arg.getStackOffset());</span></a>
+<a name="2487"><span class="lineNum">    2487 </span><span class="lineNoCov">          0 :           _context-&gt;emitRegToStack(arg.getTypeId(), &amp;dst, srcReg-&gt;getTypeId(), srcReg-&gt;getPhysId());</span></a>
+<a name="2488"><span class="lineNum">    2488 </span>            :         }</a>
+<a name="2489"><span class="lineNum">    2489 </span>            : </a>
+<a name="2490"><span class="lineNum">    2490 </span><span class="lineNoCov">          0 :         argIndex++;</span></a>
+<a name="2491"><span class="lineNum">    2491 </span><span class="lineNoCov">          0 :         argMask &gt;&gt;= 1;</span></a>
+<a name="2492"><span class="lineNum">    2492 </span>            :       }</a>
+<a name="2493"><span class="lineNum">    2493 </span>            :     }</a>
+<a name="2494"><span class="lineNum">    2494 </span>            : </a>
+<a name="2495"><span class="lineNum">    2495 </span>            :     // Mark variables as modified.</a>
+<a name="2496"><span class="lineNum">    2496 </span>            :     modified&lt;X86Reg::kKindGp&gt;();</a>
+<a name="2497"><span class="lineNum">    2497 </span>            :     modified&lt;X86Reg::kKindMm&gt;();</a>
+<a name="2498"><span class="lineNum">    2498 </span>            :     modified&lt;X86Reg::kKindVec&gt;();</a>
+<a name="2499"><span class="lineNum">    2499 </span>            : </a>
+<a name="2500"><span class="lineNum">    2500 </span>            :     // Cleanup; disconnect Vd-&gt;Va.</a>
+<a name="2501"><span class="lineNum">    2501 </span>            :     cleanup();</a>
+<a name="2502"><span class="lineNum">    2502 </span>            : </a>
+<a name="2503"><span class="lineNum">    2503 </span>            :     // Update clobbered mask.</a>
+<a name="2504"><span class="lineNum">    2504 </span><span class="lineCov">      33106 :     _context-&gt;_clobberedRegs.or_(_willAlloc);</span></a>
+<a name="2505"><span class="lineNum">    2505 </span>            :   }</a>
+<a name="2506"><span class="lineNum">    2506 </span>            : </a>
+<a name="2507"><span class="lineNum">    2507 </span>            :   // Update clobbered mask.</a>
+<a name="2508"><span class="lineNum">    2508 </span><span class="lineCov">      35054 :   _context-&gt;_clobberedRegs.or_(raData-&gt;clobberedRegs);</span></a>
+<a name="2509"><span class="lineNum">    2509 </span>            : </a>
+<a name="2510"><span class="lineNum">    2510 </span>            :   // Unuse.</a>
+<a name="2511"><span class="lineNum">    2511 </span><span class="lineCov">      35054 :   if (raData-&gt;tiedTotal != 0) {</span></a>
+<a name="2512"><span class="lineNum">    2512 </span>            :     unuseAfter&lt;X86Reg::kKindGp&gt;();</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :     unuseAfter&lt;X86Reg::kKindMm&gt;();</a>
+<a name="2514"><span class="lineNum">    2514 </span>            :     unuseAfter&lt;X86Reg::kKindVec&gt;();</a>
+<a name="2515"><span class="lineNum">    2515 </span>            :   }</a>
+<a name="2516"><span class="lineNum">    2516 </span>            : </a>
+<a name="2517"><span class="lineNum">    2517 </span>            :   return kErrorOk;</a>
+<a name="2518"><span class="lineNum">    2518 </span>            : }</a>
+<a name="2519"><span class="lineNum">    2519 </span>            : </a>
+<a name="2520"><span class="lineNum">    2520 </span>            : // ============================================================================</a>
+<a name="2521"><span class="lineNum">    2521 </span>            : // [asmjit::X86VarAlloc - Init / Cleanup]</a>
+<a name="2522"><span class="lineNum">    2522 </span>            : // ============================================================================</a>
+<a name="2523"><span class="lineNum">    2523 </span>            : </a>
+<a name="2524"><span class="lineNum">    2524 </span>            : ASMJIT_INLINE void X86VarAlloc::init(CBNode* node, X86RAData* raData) {</a>
+<a name="2525"><span class="lineNum">    2525 </span>            :   X86BaseAlloc::init(node, raData);</a>
+<a name="2526"><span class="lineNum">    2526 </span>            : </a>
+<a name="2527"><span class="lineNum">    2527 </span>            :   // These will block planner from assigning them during planning. Planner will</a>
+<a name="2528"><span class="lineNum">    2528 </span>            :   // add more registers when assigning registers to variables that don't need</a>
+<a name="2529"><span class="lineNum">    2529 </span>            :   // any specific register.</a>
+<a name="2530"><span class="lineNum">    2530 </span><span class="lineCov">      35054 :   _willAlloc = raData-&gt;inRegs;</span></a>
+<a name="2531"><span class="lineNum">    2531 </span>            :   _willAlloc.or_(raData-&gt;outRegs);</a>
+<a name="2532"><span class="lineNum">    2532 </span>            :   _willSpill.reset();</a>
+<a name="2533"><span class="lineNum">    2533 </span>            : }</a>
+<a name="2534"><span class="lineNum">    2534 </span>            : </a>
+<a name="2535"><span class="lineNum">    2535 </span>            : ASMJIT_INLINE void X86VarAlloc::cleanup() {</a>
+<a name="2536"><span class="lineNum">    2536 </span>            :   X86BaseAlloc::cleanup();</a>
+<a name="2537"><span class="lineNum">    2537 </span>            : }</a>
+<a name="2538"><span class="lineNum">    2538 </span>            : </a>
+<a name="2539"><span class="lineNum">    2539 </span>            : // ============================================================================</a>
+<a name="2540"><span class="lineNum">    2540 </span>            : // [asmjit::X86VarAlloc - Plan / Spill / Alloc]</a>
+<a name="2541"><span class="lineNum">    2541 </span>            : // ============================================================================</a>
+<a name="2542"><span class="lineNum">    2542 </span>            : </a>
+<a name="2543"><span class="lineNum">    2543 </span>            : template&lt;int C&gt;</a>
+<a name="2544"><span class="lineNum">    2544 </span>            : ASMJIT_INLINE void X86VarAlloc::plan() {</a>
+<a name="2545"><span class="lineNum">    2545 </span><span class="lineCov">      46474 :   if (isTiedDone(C)) return;</span></a>
+<a name="2546"><span class="lineNum">    2546 </span>            : </a>
+<a name="2547"><span class="lineNum">    2547 </span>            :   uint32_t i;</a>
+<a name="2548"><span class="lineNum">    2548 </span>            :   uint32_t willAlloc = _willAlloc.get(C);</a>
+<a name="2549"><span class="lineNum">    2549 </span>            :   uint32_t willFree = 0;</a>
+<a name="2550"><span class="lineNum">    2550 </span>            : </a>
+<a name="2551"><span class="lineNum">    2551 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="2552"><span class="lineNum">    2552 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="2553"><span class="lineNum">    2553 </span>            :   X86RAState* state = getState();</a>
+<a name="2554"><span class="lineNum">    2554 </span>            : </a>
+<a name="2555"><span class="lineNum">    2555 </span>            :   // Calculate 'willAlloc' and 'willFree' masks based on mandatory masks.</a>
+<a name="2556"><span class="lineNum">    2556 </span><span class="lineCov">      95954 :   for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2557"><span class="lineNum">    2557 </span><span class="lineCov">      56748 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="2558"><span class="lineNum">    2558 </span><span class="lineCov">      56748 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="2559"><span class="lineNum">    2559 </span>            : </a>
+<a name="2560"><span class="lineNum">    2560 </span><span class="lineCov">      56748 :     uint32_t vaFlags = tied-&gt;flags;</span></a>
+<a name="2561"><span class="lineNum">    2561 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="2562"><span class="lineNum">    2562 </span><span class="lineCov">      56748 :     uint32_t regMask = (physId != Globals::kInvalidRegId) ? Utils::mask(physId) : 0;</span></a>
+<a name="2563"><span class="lineNum">    2563 </span>            : </a>
+<a name="2564"><span class="lineNum">    2564 </span><span class="lineCov">      56748 :     if ((vaFlags &amp; TiedReg::kXReg) != 0) {</span></a>
+<a name="2565"><span class="lineNum">    2565 </span>            :       // Planning register allocation. First check whether the variable is</a>
+<a name="2566"><span class="lineNum">    2566 </span>            :       // already allocated in register and if it can stay allocated there.</a>
+<a name="2567"><span class="lineNum">    2567 </span>            :       //</a>
+<a name="2568"><span class="lineNum">    2568 </span>            :       // The following conditions may happen:</a>
+<a name="2569"><span class="lineNum">    2569 </span>            :       //</a>
+<a name="2570"><span class="lineNum">    2570 </span>            :       // a) Allocated register is one of the mandatoryRegs.</a>
+<a name="2571"><span class="lineNum">    2571 </span>            :       // b) Allocated register is one of the allocableRegs.</a>
+<a name="2572"><span class="lineNum">    2572 </span><span class="lineCov">      56748 :       uint32_t mandatoryRegs = tied-&gt;inRegs;</span></a>
+<a name="2573"><span class="lineNum">    2573 </span><span class="lineCov">      56748 :       uint32_t allocableRegs = tied-&gt;allocableRegs;</span></a>
+<a name="2574"><span class="lineNum">    2574 </span>            : </a>
+<a name="2575"><span class="lineNum">    2575 </span><span class="lineCov">      56748 :       if (regMask != 0) {</span></a>
+<a name="2576"><span class="lineNum">    2576 </span>            :         // Special path for planning output-only registers.</a>
+<a name="2577"><span class="lineNum">    2577 </span><span class="lineCov">      30670 :         if ((vaFlags &amp; TiedReg::kXReg) == TiedReg::kWReg) {</span></a>
+<a name="2578"><span class="lineNum">    2578 </span><span class="lineNoCov">          0 :           uint32_t outPhysId = tied-&gt;outPhysId;</span></a>
+<a name="2579"><span class="lineNum">    2579 </span><span class="lineNoCov">          0 :           mandatoryRegs = (outPhysId != Globals::kInvalidRegId) ? Utils::mask(outPhysId) : 0;</span></a>
+<a name="2580"><span class="lineNum">    2580 </span>            : </a>
+<a name="2581"><span class="lineNum">    2581 </span><span class="lineNoCov">          0 :           if ((mandatoryRegs | allocableRegs) &amp; regMask) {</span></a>
+<a name="2582"><span class="lineNum">    2582 </span>            :             tied-&gt;setOutPhysId(physId);</a>
+<a name="2583"><span class="lineNum">    2583 </span><span class="lineNoCov">          0 :             tied-&gt;flags |= TiedReg::kWDone;</span></a>
+<a name="2584"><span class="lineNum">    2584 </span>            : </a>
+<a name="2585"><span class="lineNum">    2585 </span><span class="lineNoCov">          0 :             if (mandatoryRegs &amp; regMask) {</span></a>
+<a name="2586"><span class="lineNum">    2586 </span>            :               // Case 'a' - 'willAlloc' contains initially all inRegs from all TiedReg's.</a>
+<a name="2587"><span class="lineNum">    2587 </span>            :               ASMJIT_ASSERT((willAlloc &amp; regMask) != 0);</a>
+<a name="2588"><span class="lineNum">    2588 </span>            :             }</a>
+<a name="2589"><span class="lineNum">    2589 </span>            :             else {</a>
+<a name="2590"><span class="lineNum">    2590 </span>            :               // Case 'b'.</a>
+<a name="2591"><span class="lineNum">    2591 </span>            :               tied-&gt;setOutPhysId(physId);</a>
+<a name="2592"><span class="lineNum">    2592 </span><span class="lineNoCov">          0 :               willAlloc |= regMask;</span></a>
+<a name="2593"><span class="lineNum">    2593 </span>            :             }</a>
+<a name="2594"><span class="lineNum">    2594 </span>            : </a>
+<a name="2595"><span class="lineNum">    2595 </span>            :             addTiedDone(C);</a>
+<a name="2596"><span class="lineNum">    2596 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="2597"><span class="lineNum">    2597 </span>            :           }</a>
+<a name="2598"><span class="lineNum">    2598 </span>            :         }</a>
+<a name="2599"><span class="lineNum">    2599 </span>            :         else {</a>
+<a name="2600"><span class="lineNum">    2600 </span><span class="lineCov">      30670 :           if ((mandatoryRegs | allocableRegs) &amp; regMask) {</span></a>
+<a name="2601"><span class="lineNum">    2601 </span>            :             tied-&gt;setInPhysId(physId);</a>
+<a name="2602"><span class="lineNum">    2602 </span><span class="lineCov">      30336 :             tied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="2603"><span class="lineNum">    2603 </span>            : </a>
+<a name="2604"><span class="lineNum">    2604 </span><span class="lineCov">      30336 :             if (mandatoryRegs &amp; regMask) {</span></a>
+<a name="2605"><span class="lineNum">    2605 </span>            :               // Case 'a' - 'willAlloc' contains initially all inRegs from all TiedReg's.</a>
+<a name="2606"><span class="lineNum">    2606 </span>            :               ASMJIT_ASSERT((willAlloc &amp; regMask) != 0);</a>
+<a name="2607"><span class="lineNum">    2607 </span>            :             }</a>
+<a name="2608"><span class="lineNum">    2608 </span>            :             else {</a>
+<a name="2609"><span class="lineNum">    2609 </span>            :               // Case 'b'.</a>
+<a name="2610"><span class="lineNum">    2610 </span><span class="lineCov">      28722 :               tied-&gt;inRegs |= regMask;</span></a>
+<a name="2611"><span class="lineNum">    2611 </span><span class="lineCov">      28722 :               willAlloc |= regMask;</span></a>
+<a name="2612"><span class="lineNum">    2612 </span>            :             }</a>
+<a name="2613"><span class="lineNum">    2613 </span>            : </a>
+<a name="2614"><span class="lineNum">    2614 </span>            :             addTiedDone(C);</a>
+<a name="2615"><span class="lineNum">    2615 </span><span class="lineCov">      30336 :             continue;</span></a>
+<a name="2616"><span class="lineNum">    2616 </span>            :           }</a>
+<a name="2617"><span class="lineNum">    2617 </span>            :         }</a>
+<a name="2618"><span class="lineNum">    2618 </span>            :       }</a>
+<a name="2619"><span class="lineNum">    2619 </span>            : </a>
+<a name="2620"><span class="lineNum">    2620 </span>            :       // Variable is not allocated or allocated in register that doesn't</a>
+<a name="2621"><span class="lineNum">    2621 </span>            :       // match inRegs or allocableRegs. The next step is to pick the best</a>
+<a name="2622"><span class="lineNum">    2622 </span>            :       // register for this variable. If `inRegs` contains any register the</a>
+<a name="2623"><span class="lineNum">    2623 </span>            :       // decision is simple - we have to follow, in other case will use</a>
+<a name="2624"><span class="lineNum">    2624 </span>            :       // the advantage of `guessAlloc()` to find a register (or registers)</a>
+<a name="2625"><span class="lineNum">    2625 </span>            :       // by looking ahead. But the best way to find a good register is not</a>
+<a name="2626"><span class="lineNum">    2626 </span>            :       // here since now we have no information about the registers that</a>
+<a name="2627"><span class="lineNum">    2627 </span>            :       // will be freed. So instead of finding register here, we just mark</a>
+<a name="2628"><span class="lineNum">    2628 </span>            :       // the current register (if variable is allocated) as `willFree` so</a>
+<a name="2629"><span class="lineNum">    2629 </span>            :       // the planner can use this information in the second step to plan the</a>
+<a name="2630"><span class="lineNum">    2630 </span>            :       // allocation as a whole.</a>
+<a name="2631"><span class="lineNum">    2631 </span><span class="lineCov">      26412 :       willFree |= regMask;</span></a>
+<a name="2632"><span class="lineNum">    2632 </span><span class="lineCov">      26412 :       continue;</span></a>
+<a name="2633"><span class="lineNum">    2633 </span><span class="lineCov">      26412 :     }</span></a>
+<a name="2634"><span class="lineNum">    2634 </span>            :     else {</a>
+<a name="2635"><span class="lineNum">    2635 </span><span class="lineNoCov">          0 :       if (regMask != 0) {</span></a>
+<a name="2636"><span class="lineNum">    2636 </span><span class="lineNoCov">          0 :         willFree |= regMask;</span></a>
+<a name="2637"><span class="lineNum">    2637 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="2638"><span class="lineNum">    2638 </span>            :       }</a>
+<a name="2639"><span class="lineNum">    2639 </span>            :       else {</a>
+<a name="2640"><span class="lineNum">    2640 </span><span class="lineNoCov">          0 :         tied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="2641"><span class="lineNum">    2641 </span>            :         addTiedDone(C);</a>
+<a name="2642"><span class="lineNum">    2642 </span><span class="lineNoCov">          0 :         continue;</span></a>
+<a name="2643"><span class="lineNum">    2643 </span>            :       }</a>
+<a name="2644"><span class="lineNum">    2644 </span>            :     }</a>
+<a name="2645"><span class="lineNum">    2645 </span>            :   }</a>
+<a name="2646"><span class="lineNum">    2646 </span>            : </a>
+<a name="2647"><span class="lineNum">    2647 </span>            :   // Occupied registers without 'willFree' registers; contains basically</a>
+<a name="2648"><span class="lineNum">    2648 </span>            :   // all the registers we can use to allocate variables without inRegs</a>
+<a name="2649"><span class="lineNum">    2649 </span>            :   // specified.</a>
+<a name="2650"><span class="lineNum">    2650 </span><span class="lineCov">      39206 :   uint32_t occupied = state-&gt;_occupied.get(C) &amp; ~willFree;</span></a>
+<a name="2651"><span class="lineNum">    2651 </span>            :   uint32_t willSpill = 0;</a>
+<a name="2652"><span class="lineNum">    2652 </span>            : </a>
+<a name="2653"><span class="lineNum">    2653 </span>            :   // Find the best registers for variables that are not allocated yet.</a>
+<a name="2654"><span class="lineNum">    2654 </span><span class="lineCov">      95954 :   for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2655"><span class="lineNum">    2655 </span><span class="lineCov">      56748 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="2656"><span class="lineNum">    2656 </span><span class="lineCov">      56748 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="2657"><span class="lineNum">    2657 </span><span class="lineCov">      56748 :     uint32_t vaFlags = tied-&gt;flags;</span></a>
+<a name="2658"><span class="lineNum">    2658 </span>            : </a>
+<a name="2659"><span class="lineNum">    2659 </span><span class="lineCov">      56748 :     if ((vaFlags &amp; TiedReg::kXReg) != 0) {</span></a>
+<a name="2660"><span class="lineNum">    2660 </span><span class="lineCov">      56748 :       if ((vaFlags &amp; TiedReg::kXReg) == TiedReg::kWReg) {</span></a>
+<a name="2661"><span class="lineNum">    2661 </span><span class="lineCov">      22140 :         if (vaFlags &amp; TiedReg::kWDone)</span></a>
+<a name="2662"><span class="lineNum">    2662 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="2663"><span class="lineNum">    2663 </span>            : </a>
+<a name="2664"><span class="lineNum">    2664 </span>            :         // Skip all registers that have assigned outPhysId. Spill if occupied.</a>
+<a name="2665"><span class="lineNum">    2665 </span><span class="lineCov">      22140 :         if (tied-&gt;hasOutPhysId()) {</span></a>
+<a name="2666"><span class="lineNum">    2666 </span><span class="lineNoCov">          0 :           uint32_t outRegs = Utils::mask(tied-&gt;outPhysId);</span></a>
+<a name="2667"><span class="lineNum">    2667 </span><span class="lineNoCov">          0 :           willSpill |= occupied &amp; outRegs;</span></a>
+<a name="2668"><span class="lineNum">    2668 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="2669"><span class="lineNum">    2669 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="2670"><span class="lineNum">    2670 </span>            :       }</a>
+<a name="2671"><span class="lineNum">    2671 </span>            :       else {</a>
+<a name="2672"><span class="lineNum">    2672 </span><span class="lineCov">      34608 :         if (vaFlags &amp; TiedReg::kRDone)</span></a>
+<a name="2673"><span class="lineNum">    2673 </span><span class="lineCov">      30336 :           continue;</span></a>
+<a name="2674"><span class="lineNum">    2674 </span>            : </a>
+<a name="2675"><span class="lineNum">    2675 </span>            :         // We skip all registers that have assigned inPhysId, indicates that</a>
+<a name="2676"><span class="lineNum">    2676 </span>            :         // the register to allocate in is known.</a>
+<a name="2677"><span class="lineNum">    2677 </span><span class="lineCov">       4272 :         if (tied-&gt;hasInPhysId()) {</span></a>
+<a name="2678"><span class="lineNum">    2678 </span><span class="lineNoCov">          0 :           uint32_t inRegs = tied-&gt;inRegs;</span></a>
+<a name="2679"><span class="lineNum">    2679 </span><span class="lineNoCov">          0 :           willSpill |= occupied &amp; inRegs;</span></a>
+<a name="2680"><span class="lineNum">    2680 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="2681"><span class="lineNum">    2681 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="2682"><span class="lineNum">    2682 </span>            :       }</a>
+<a name="2683"><span class="lineNum">    2683 </span>            : </a>
+<a name="2684"><span class="lineNum">    2684 </span><span class="lineCov">      26412 :       uint32_t m = tied-&gt;inRegs;</span></a>
+<a name="2685"><span class="lineNum">    2685 </span><span class="lineCov">      26412 :       if (tied-&gt;hasOutPhysId())</span></a>
+<a name="2686"><span class="lineNum">    2686 </span><span class="lineNoCov">          0 :         m |= Utils::mask(tied-&gt;outPhysId);</span></a>
+<a name="2687"><span class="lineNum">    2687 </span>            : </a>
+<a name="2688"><span class="lineNum">    2688 </span><span class="lineCov">      26412 :       m = tied-&gt;allocableRegs &amp; ~(willAlloc ^ m);</span></a>
+<a name="2689"><span class="lineNum">    2689 </span>            :       m = guessAlloc&lt;C&gt;(vreg, m);</a>
+<a name="2690"><span class="lineNum">    2690 </span>            :       ASMJIT_ASSERT(m != 0);</a>
+<a name="2691"><span class="lineNum">    2691 </span>            : </a>
+<a name="2692"><span class="lineNum">    2692 </span><span class="lineCov">      26412 :       uint32_t candidateRegs = m &amp; ~occupied;</span></a>
+<a name="2693"><span class="lineNum">    2693 </span>            :       uint32_t homeMask = vreg-&gt;getHomeMask();</a>
+<a name="2694"><span class="lineNum">    2694 </span>            : </a>
+<a name="2695"><span class="lineNum">    2695 </span>            :       uint32_t physId;</a>
+<a name="2696"><span class="lineNum">    2696 </span>            :       uint32_t regMask;</a>
+<a name="2697"><span class="lineNum">    2697 </span>            : </a>
+<a name="2698"><span class="lineNum">    2698 </span><span class="lineCov">      26412 :       if (candidateRegs == 0) {</span></a>
+<a name="2699"><span class="lineNum">    2699 </span><span class="lineCov">        138 :         candidateRegs = m &amp; occupied &amp; ~state-&gt;_modified.get(C);</span></a>
+<a name="2700"><span class="lineNum">    2700 </span><span class="lineCov">        138 :         if (candidateRegs == 0)</span></a>
+<a name="2701"><span class="lineNum">    2701 </span>            :           candidateRegs = m;</a>
+<a name="2702"><span class="lineNum">    2702 </span>            :       }</a>
+<a name="2703"><span class="lineNum">    2703 </span><span class="lineCov">      26412 :       if (candidateRegs &amp; homeMask) candidateRegs &amp;= homeMask;</span></a>
+<a name="2704"><span class="lineNum">    2704 </span>            : </a>
+<a name="2705"><span class="lineNum">    2705 </span>            :       physId = Utils::findFirstBit(candidateRegs);</a>
+<a name="2706"><span class="lineNum">    2706 </span>            :       regMask = Utils::mask(physId);</a>
+<a name="2707"><span class="lineNum">    2707 </span>            : </a>
+<a name="2708"><span class="lineNum">    2708 </span><span class="lineCov">      26412 :       if ((vaFlags &amp; TiedReg::kXReg) == TiedReg::kWReg) {</span></a>
+<a name="2709"><span class="lineNum">    2709 </span>            :         tied-&gt;setOutPhysId(physId);</a>
+<a name="2710"><span class="lineNum">    2710 </span>            :       }</a>
+<a name="2711"><span class="lineNum">    2711 </span>            :       else {</a>
+<a name="2712"><span class="lineNum">    2712 </span>            :         tied-&gt;setInPhysId(physId);</a>
+<a name="2713"><span class="lineNum">    2713 </span><span class="lineCov">       4272 :         tied-&gt;inRegs = regMask;</span></a>
+<a name="2714"><span class="lineNum">    2714 </span>            :       }</a>
+<a name="2715"><span class="lineNum">    2715 </span>            : </a>
+<a name="2716"><span class="lineNum">    2716 </span><span class="lineCov">      26412 :       willAlloc |= regMask;</span></a>
+<a name="2717"><span class="lineNum">    2717 </span><span class="lineCov">      26412 :       willSpill |= regMask &amp; occupied;</span></a>
+<a name="2718"><span class="lineNum">    2718 </span>            :       willFree  &amp;=~regMask;</a>
+<a name="2719"><span class="lineNum">    2719 </span><span class="lineCov">      26412 :       occupied  |= regMask;</span></a>
+<a name="2720"><span class="lineNum">    2720 </span>            : </a>
+<a name="2721"><span class="lineNum">    2721 </span><span class="lineCov">      26412 :       continue;</span></a>
+<a name="2722"><span class="lineNum">    2722 </span><span class="lineCov">      26412 :     }</span></a>
+<a name="2723"><span class="lineNum">    2723 </span><span class="lineNoCov">          0 :     else if ((vaFlags &amp; TiedReg::kXMem) != 0) {</span></a>
+<a name="2724"><span class="lineNum">    2724 </span>            :       uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="2725"><span class="lineNum">    2725 </span><span class="lineNoCov">          0 :       if (physId != Globals::kInvalidRegId &amp;&amp; (vaFlags &amp; TiedReg::kXMem) != TiedReg::kWMem) {</span></a>
+<a name="2726"><span class="lineNum">    2726 </span><span class="lineNoCov">          0 :         willSpill |= Utils::mask(physId);</span></a>
+<a name="2727"><span class="lineNum">    2727 </span>            :       }</a>
+<a name="2728"><span class="lineNum">    2728 </span>            :     }</a>
+<a name="2729"><span class="lineNum">    2729 </span>            :   }</a>
+<a name="2730"><span class="lineNum">    2730 </span>            : </a>
+<a name="2731"><span class="lineNum">    2731 </span>            :   // Set calculated masks back to the allocator; needed by spill() and alloc().</a>
+<a name="2732"><span class="lineNum">    2732 </span>            :   _willSpill.set(C, willSpill);</a>
+<a name="2733"><span class="lineNum">    2733 </span>            :   _willAlloc.set(C, willAlloc);</a>
+<a name="2734"><span class="lineNum">    2734 </span>            : }</a>
+<a name="2735"><span class="lineNum">    2735 </span>            : </a>
+<a name="2736"><span class="lineNum">    2736 </span>            : template&lt;int C&gt;</a>
+<a name="2737"><span class="lineNum">    2737 </span>            : ASMJIT_INLINE void X86VarAlloc::spill() {</a>
+<a name="2738"><span class="lineNum">    2738 </span>            :   uint32_t m = _willSpill.get(C);</a>
+<a name="2739"><span class="lineNum">    2739 </span>            :   uint32_t i = static_cast&lt;uint32_t&gt;(0) - 1;</a>
+<a name="2740"><span class="lineNum">    2740 </span><span class="lineCov">      33106 :   if (m == 0) return;</span></a>
+<a name="2741"><span class="lineNum">    2741 </span>            : </a>
+<a name="2742"><span class="lineNum">    2742 </span>            :   X86RAState* state = getState();</a>
+<a name="2743"><span class="lineNum">    2743 </span>            :   VirtReg** vregs = state-&gt;getListByKind(C);</a>
+<a name="2744"><span class="lineNum">    2744 </span>            : </a>
+<a name="2745"><span class="lineNum">    2745 </span>            :   // Available registers for decision if move has any benefit over spill.</a>
+<a name="2746"><span class="lineNum">    2746 </span>            :   uint32_t availableRegs = getGaRegs(C) &amp; ~(state-&gt;_occupied.get(C) | m | _willAlloc.get(C));</a>
+<a name="2747"><span class="lineNum">    2747 </span>            : </a>
+<a name="2748"><span class="lineNum">    2748 </span>            :   do {</a>
+<a name="2749"><span class="lineNum">    2749 </span>            :     // We always advance one more to destroy the bit that we have found.</a>
+<a name="2750"><span class="lineNum">    2750 </span><span class="lineCov">        138 :     uint32_t bitIndex = Utils::findFirstBit(m) + 1;</span></a>
+<a name="2751"><span class="lineNum">    2751 </span>            : </a>
+<a name="2752"><span class="lineNum">    2752 </span><span class="lineCov">        138 :     i += bitIndex;</span></a>
+<a name="2753"><span class="lineNum">    2753 </span><span class="lineCov">        138 :     m &gt;&gt;= bitIndex;</span></a>
+<a name="2754"><span class="lineNum">    2754 </span>            : </a>
+<a name="2755"><span class="lineNum">    2755 </span><span class="lineCov">        138 :     VirtReg* vreg = vregs[i];</span></a>
+<a name="2756"><span class="lineNum">    2756 </span>            :     ASMJIT_ASSERT(vreg);</a>
+<a name="2757"><span class="lineNum">    2757 </span>            : </a>
+<a name="2758"><span class="lineNum">    2758 </span>            :     TiedReg* tied = vreg-&gt;_tied;</a>
+<a name="2759"><span class="lineNum">    2759 </span>            :     ASMJIT_ASSERT(!tied || (tied-&gt;flags &amp; TiedReg::kXReg) == 0);</a>
+<a name="2760"><span class="lineNum">    2760 </span>            : </a>
+<a name="2761"><span class="lineNum">    2761 </span>            :     if (vreg-&gt;isModified() &amp;&amp; availableRegs) {</a>
+<a name="2762"><span class="lineNum">    2762 </span>            :       // Don't check for alternatives if the variable has to be spilled.</a>
+<a name="2763"><span class="lineNum">    2763 </span>            :       if (!tied || (tied-&gt;flags &amp; TiedReg::kSpill) == 0) {</a>
+<a name="2764"><span class="lineNum">    2764 </span>            :         uint32_t altRegs = guessSpill&lt;C&gt;(vreg, availableRegs);</a>
+<a name="2765"><span class="lineNum">    2765 </span>            : </a>
+<a name="2766"><span class="lineNum">    2766 </span>            :         if (altRegs != 0) {</a>
+<a name="2767"><span class="lineNum">    2767 </span>            :           uint32_t physId = Utils::findFirstBit(altRegs);</a>
+<a name="2768"><span class="lineNum">    2768 </span>            :           uint32_t regMask = Utils::mask(physId);</a>
+<a name="2769"><span class="lineNum">    2769 </span>            : </a>
+<a name="2770"><span class="lineNum">    2770 </span>            :           _context-&gt;move&lt;C&gt;(vreg, physId);</a>
+<a name="2771"><span class="lineNum">    2771 </span>            :           availableRegs ^= regMask;</a>
+<a name="2772"><span class="lineNum">    2772 </span>            :           continue;</a>
+<a name="2773"><span class="lineNum">    2773 </span>            :         }</a>
+<a name="2774"><span class="lineNum">    2774 </span>            :       }</a>
+<a name="2775"><span class="lineNum">    2775 </span>            :     }</a>
+<a name="2776"><span class="lineNum">    2776 </span>            : </a>
+<a name="2777"><span class="lineNum">    2777 </span><span class="lineCov">        138 :     _context-&gt;spill&lt;C&gt;(vreg);</span></a>
+<a name="2778"><span class="lineNum">    2778 </span><span class="lineCov">        138 :   } while (m != 0);</span></a>
+<a name="2779"><span class="lineNum">    2779 </span>            : }</a>
+<a name="2780"><span class="lineNum">    2780 </span>            : </a>
+<a name="2781"><span class="lineNum">    2781 </span>            : template&lt;int C&gt;</a>
+<a name="2782"><span class="lineNum">    2782 </span>            : ASMJIT_INLINE void X86VarAlloc::alloc() {</a>
+<a name="2783"><span class="lineNum">    2783 </span><span class="lineCov">      40374 :   if (isTiedDone(C)) return;</span></a>
+<a name="2784"><span class="lineNum">    2784 </span>            : </a>
+<a name="2785"><span class="lineNum">    2785 </span>            :   uint32_t i;</a>
+<a name="2786"><span class="lineNum">    2786 </span>            :   bool didWork;</a>
+<a name="2787"><span class="lineNum">    2787 </span>            : </a>
+<a name="2788"><span class="lineNum">    2788 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="2789"><span class="lineNum">    2789 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="2790"><span class="lineNum">    2790 </span>            : </a>
+<a name="2791"><span class="lineNum">    2791 </span>            :   // Alloc `in` regs.</a>
+<a name="2792"><span class="lineNum">    2792 </span><span class="lineCov">      29562 :   do {</span></a>
+<a name="2793"><span class="lineNum">    2793 </span>            :     didWork = false;</a>
+<a name="2794"><span class="lineNum">    2794 </span><span class="lineCov">      74600 :     for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2795"><span class="lineNum">    2795 </span><span class="lineCov">      45038 :       TiedReg* aTied = &amp;tiedArray[i];</span></a>
+<a name="2796"><span class="lineNum">    2796 </span><span class="lineCov">      45038 :       VirtReg* aVReg = aTied-&gt;vreg;</span></a>
+<a name="2797"><span class="lineNum">    2797 </span>            : </a>
+<a name="2798"><span class="lineNum">    2798 </span><span class="lineCov">      45038 :       if ((aTied-&gt;flags &amp; (TiedReg::kRReg | TiedReg::kRDone)) != TiedReg::kRReg)</span></a>
+<a name="2799"><span class="lineNum">    2799 </span><span class="lineCov">      40766 :         continue;</span></a>
+<a name="2800"><span class="lineNum">    2800 </span>            : </a>
+<a name="2801"><span class="lineNum">    2801 </span>            :       uint32_t aPhysId = aVReg-&gt;getPhysId();</a>
+<a name="2802"><span class="lineNum">    2802 </span><span class="lineCov">       4272 :       uint32_t bPhysId = aTied-&gt;inPhysId;</span></a>
+<a name="2803"><span class="lineNum">    2803 </span>            : </a>
+<a name="2804"><span class="lineNum">    2804 </span>            :       // Shouldn't be the same.</a>
+<a name="2805"><span class="lineNum">    2805 </span>            :       ASMJIT_ASSERT(aPhysId != bPhysId);</a>
+<a name="2806"><span class="lineNum">    2806 </span>            : </a>
+<a name="2807"><span class="lineNum">    2807 </span><span class="lineCov">       4272 :       VirtReg* bVReg = getState()-&gt;getListByKind(C)[bPhysId];</span></a>
+<a name="2808"><span class="lineNum">    2808 </span><span class="lineCov">       4272 :       if (bVReg) {</span></a>
+<a name="2809"><span class="lineNum">    2809 </span>            :         // Gp registers only - Swap two registers if we can solve two</a>
+<a name="2810"><span class="lineNum">    2810 </span>            :         // allocation tasks by a single 'xchg' instruction, swapping</a>
+<a name="2811"><span class="lineNum">    2811 </span>            :         // two registers required by the instruction/node or one register</a>
+<a name="2812"><span class="lineNum">    2812 </span>            :         // required with another non-required.</a>
+<a name="2813"><span class="lineNum">    2813 </span><span class="lineNoCov">          0 :         if (C == X86Reg::kKindGp &amp;&amp; aPhysId != Globals::kInvalidRegId) {</span></a>
+<a name="2814"><span class="lineNum">    2814 </span><span class="lineNoCov">          0 :           TiedReg* bTied = bVReg-&gt;_tied;</span></a>
+<a name="2815"><span class="lineNum">    2815 </span>            :           _context-&gt;swapGp(aVReg, bVReg);</a>
+<a name="2816"><span class="lineNum">    2816 </span>            : </a>
+<a name="2817"><span class="lineNum">    2817 </span><span class="lineNoCov">          0 :           aTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="2818"><span class="lineNum">    2818 </span>            :           addTiedDone(C);</a>
+<a name="2819"><span class="lineNum">    2819 </span>            : </a>
+<a name="2820"><span class="lineNum">    2820 </span>            :           // Double-hit, two registers allocated by a single xchg.</a>
+<a name="2821"><span class="lineNum">    2821 </span><span class="lineNoCov">          0 :           if (bTied &amp;&amp; bTied-&gt;inPhysId == aPhysId) {</span></a>
+<a name="2822"><span class="lineNum">    2822 </span><span class="lineNoCov">          0 :             bTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="2823"><span class="lineNum">    2823 </span>            :             addTiedDone(C);</a>
+<a name="2824"><span class="lineNum">    2824 </span>            :           }</a>
+<a name="2825"><span class="lineNum">    2825 </span>            : </a>
+<a name="2826"><span class="lineNum">    2826 </span>            :           didWork = true;</a>
+<a name="2827"><span class="lineNum">    2827 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="2828"><span class="lineNum">    2828 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="2829"><span class="lineNum">    2829 </span>            :       }</a>
+<a name="2830"><span class="lineNum">    2830 </span><span class="lineCov">       4272 :       else if (aPhysId != Globals::kInvalidRegId) {</span></a>
+<a name="2831"><span class="lineNum">    2831 </span>            :         _context-&gt;move&lt;C&gt;(aVReg, bPhysId);</a>
+<a name="2832"><span class="lineNum">    2832 </span>            : </a>
+<a name="2833"><span class="lineNum">    2833 </span><span class="lineCov">        334 :         aTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="2834"><span class="lineNum">    2834 </span>            :         addTiedDone(C);</a>
+<a name="2835"><span class="lineNum">    2835 </span>            : </a>
+<a name="2836"><span class="lineNum">    2836 </span>            :         didWork = true;</a>
+<a name="2837"><span class="lineNum">    2837 </span><span class="lineCov">        334 :         continue;</span></a>
+<a name="2838"><span class="lineNum">    2838 </span>            :       }</a>
+<a name="2839"><span class="lineNum">    2839 </span>            :       else {</a>
+<a name="2840"><span class="lineNum">    2840 </span>            :         _context-&gt;alloc&lt;C&gt;(aVReg, bPhysId);</a>
+<a name="2841"><span class="lineNum">    2841 </span>            : </a>
+<a name="2842"><span class="lineNum">    2842 </span><span class="lineCov">       3938 :         aTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="2843"><span class="lineNum">    2843 </span>            :         addTiedDone(C);</a>
+<a name="2844"><span class="lineNum">    2844 </span>            : </a>
+<a name="2845"><span class="lineNum">    2845 </span>            :         didWork = true;</a>
+<a name="2846"><span class="lineNum">    2846 </span><span class="lineCov">       3938 :         continue;</span></a>
+<a name="2847"><span class="lineNum">    2847 </span>            :       }</a>
+<a name="2848"><span class="lineNum">    2848 </span>            :     }</a>
+<a name="2849"><span class="lineNum">    2849 </span>            :   } while (didWork);</a>
+<a name="2850"><span class="lineNum">    2850 </span>            : </a>
+<a name="2851"><span class="lineNum">    2851 </span>            :   // Alloc 'out' regs.</a>
+<a name="2852"><span class="lineNum">    2852 </span><span class="lineCov">      62152 :   for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2853"><span class="lineNum">    2853 </span><span class="lineCov">      36862 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="2854"><span class="lineNum">    2854 </span><span class="lineCov">      36862 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="2855"><span class="lineNum">    2855 </span>            : </a>
+<a name="2856"><span class="lineNum">    2856 </span><span class="lineCov">      36862 :     if ((tied-&gt;flags &amp; (TiedReg::kXReg | TiedReg::kWDone)) != TiedReg::kWReg)</span></a>
+<a name="2857"><span class="lineNum">    2857 </span><span class="lineCov">      14722 :       continue;</span></a>
+<a name="2858"><span class="lineNum">    2858 </span>            : </a>
+<a name="2859"><span class="lineNum">    2859 </span><span class="lineCov">      22140 :     uint32_t physId = tied-&gt;outPhysId;</span></a>
+<a name="2860"><span class="lineNum">    2860 </span>            :     ASMJIT_ASSERT(physId != Globals::kInvalidRegId);</a>
+<a name="2861"><span class="lineNum">    2861 </span>            : </a>
+<a name="2862"><span class="lineNum">    2862 </span><span class="lineCov">      22140 :     if (vreg-&gt;getPhysId() != physId) {</span></a>
+<a name="2863"><span class="lineNum">    2863 </span>            :       ASMJIT_ASSERT(getState()-&gt;getListByKind(C)[physId] == nullptr);</a>
+<a name="2864"><span class="lineNum">    2864 </span><span class="lineCov">      22140 :       _context-&gt;attach&lt;C&gt;(vreg, physId, false);</span></a>
+<a name="2865"><span class="lineNum">    2865 </span>            :     }</a>
+<a name="2866"><span class="lineNum">    2866 </span>            : </a>
+<a name="2867"><span class="lineNum">    2867 </span><span class="lineCov">      22140 :     tied-&gt;flags |= TiedReg::kWDone;</span></a>
+<a name="2868"><span class="lineNum">    2868 </span>            :     addTiedDone(C);</a>
+<a name="2869"><span class="lineNum">    2869 </span>            :   }</a>
+<a name="2870"><span class="lineNum">    2870 </span>            : }</a>
+<a name="2871"><span class="lineNum">    2871 </span>            : </a>
+<a name="2872"><span class="lineNum">    2872 </span>            : // ============================================================================</a>
+<a name="2873"><span class="lineNum">    2873 </span>            : // [asmjit::X86VarAlloc - GuessAlloc / GuessSpill]</a>
+<a name="2874"><span class="lineNum">    2874 </span>            : // ============================================================================</a>
+<a name="2875"><span class="lineNum">    2875 </span>            : </a>
+<a name="2876"><span class="lineNum">    2876 </span>            : template&lt;int C&gt;</a>
+<a name="2877"><span class="lineNum">    2877 </span>            : ASMJIT_INLINE uint32_t X86VarAlloc::guessAlloc(VirtReg* vreg, uint32_t allocableRegs) {</a>
+<a name="2878"><span class="lineNum">    2878 </span>            :   ASMJIT_ASSERT(allocableRegs != 0);</a>
+<a name="2879"><span class="lineNum">    2879 </span>            : </a>
+<a name="2880"><span class="lineNum">    2880 </span>            :   // Stop now if there is only one bit (register) set in `allocableRegs` mask.</a>
+<a name="2881"><span class="lineNum">    2881 </span>            :   if (Utils::isPowerOf2(allocableRegs)) return allocableRegs;</a>
+<a name="2882"><span class="lineNum">    2882 </span>            : </a>
+<a name="2883"><span class="lineNum">    2883 </span><span class="lineCov">      26078 :   uint32_t raId = vreg-&gt;_raId;</span></a>
+<a name="2884"><span class="lineNum">    2884 </span>            :   uint32_t safeRegs = allocableRegs;</a>
+<a name="2885"><span class="lineNum">    2885 </span>            : </a>
+<a name="2886"><span class="lineNum">    2886 </span>            :   uint32_t i;</a>
+<a name="2887"><span class="lineNum">    2887 </span>            :   uint32_t maxLookAhead = kCompilerDefaultLookAhead;</a>
+<a name="2888"><span class="lineNum">    2888 </span>            : </a>
+<a name="2889"><span class="lineNum">    2889 </span>            :   // Look ahead and calculate mask of special registers on both - input/output.</a>
+<a name="2890"><span class="lineNum">    2890 </span><span class="lineCov">      26078 :   CBNode* node = _node;</span></a>
+<a name="2891"><span class="lineNum">    2891 </span><span class="lineCov">     119272 :   for (i = 0; i &lt; maxLookAhead; i++) {</span></a>
+<a name="2892"><span class="lineNum">    2892 </span>            :     X86RAData* raData = node-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="2893"><span class="lineNum">    2893 </span><span class="lineCov">     119200 :     RABits* liveness = raData ? raData-&gt;liveness : static_cast&lt;RABits*&gt;(nullptr);</span></a>
+<a name="2894"><span class="lineNum">    2894 </span>            : </a>
+<a name="2895"><span class="lineNum">    2895 </span>            :     // If the variable becomes dead it doesn't make sense to continue.</a>
+<a name="2896"><span class="lineNum">    2896 </span><span class="lineCov">     119200 :     if (liveness &amp;&amp; !liveness-&gt;getBit(raId)) break;</span></a>
+<a name="2897"><span class="lineNum">    2897 </span>            : </a>
+<a name="2898"><span class="lineNum">    2898 </span>            :     // Stop on `CBSentinel` and `CCFuncRet`.</a>
+<a name="2899"><span class="lineNum">    2899 </span><span class="lineCov">      99342 :     if (node-&gt;hasFlag(CBNode::kFlagIsRet)) break;</span></a>
+<a name="2900"><span class="lineNum">    2900 </span>            : </a>
+<a name="2901"><span class="lineNum">    2901 </span>            :     // Stop on conditional jump, we don't follow them.</a>
+<a name="2902"><span class="lineNum">    2902 </span><span class="lineCov">      99342 :     if (node-&gt;hasFlag(CBNode::kFlagIsJcc)) break;</span></a>
+<a name="2903"><span class="lineNum">    2903 </span>            : </a>
+<a name="2904"><span class="lineNum">    2904 </span>            :     // Advance on non-conditional jump.</a>
+<a name="2905"><span class="lineNum">    2905 </span><span class="lineCov">      99342 :     if (node-&gt;hasFlag(CBNode::kFlagIsJmp)) {</span></a>
+<a name="2906"><span class="lineNum">    2906 </span>            :       node = static_cast&lt;CBJump*&gt;(node)-&gt;getTarget();</a>
+<a name="2907"><span class="lineNum">    2907 </span>            :       // Stop on jump that is not followed.</a>
+<a name="2908"><span class="lineNum">    2908 </span><span class="lineNoCov">          0 :       if (!node) break;</span></a>
+<a name="2909"><span class="lineNum">    2909 </span>            :     }</a>
+<a name="2910"><span class="lineNum">    2910 </span>            : </a>
+<a name="2911"><span class="lineNum">    2911 </span>            :     node = node-&gt;getNext();</a>
+<a name="2912"><span class="lineNum">    2912 </span>            :     ASMJIT_ASSERT(node != nullptr);</a>
+<a name="2913"><span class="lineNum">    2913 </span>            : </a>
+<a name="2914"><span class="lineNum">    2914 </span>            :     raData = node-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="2915"><span class="lineNum">    2915 </span><span class="lineCov">      99342 :     if (raData) {</span></a>
+<a name="2916"><span class="lineNum">    2916 </span>            :       TiedReg* tied = raData-&gt;findTiedByKind(C, vreg);</a>
+<a name="2917"><span class="lineNum">    2917 </span>            :       uint32_t mask;</a>
+<a name="2918"><span class="lineNum">    2918 </span>            : </a>
+<a name="2919"><span class="lineNum">    2919 </span><span class="lineCov">      99342 :       if (tied) {</span></a>
+<a name="2920"><span class="lineNum">    2920 </span>            :         // If the variable is overwritten it doesn't make sense to continue.</a>
+<a name="2921"><span class="lineNum">    2921 </span><span class="lineCov">      29928 :         if ((tied-&gt;flags &amp; TiedReg::kRAll) == 0)</span></a>
+<a name="2922"><span class="lineNum">    2922 </span>            :           break;</a>
+<a name="2923"><span class="lineNum">    2923 </span>            : </a>
+<a name="2924"><span class="lineNum">    2924 </span><span class="lineCov">      29928 :         mask = tied-&gt;allocableRegs;</span></a>
+<a name="2925"><span class="lineNum">    2925 </span><span class="lineCov">      29928 :         if (mask != 0) {</span></a>
+<a name="2926"><span class="lineNum">    2926 </span><span class="lineCov">      29928 :           allocableRegs &amp;= mask;</span></a>
+<a name="2927"><span class="lineNum">    2927 </span><span class="lineCov">      29928 :           if (allocableRegs == 0) break;</span></a>
+<a name="2928"><span class="lineNum">    2928 </span>            :           safeRegs = allocableRegs;</a>
+<a name="2929"><span class="lineNum">    2929 </span>            :         }</a>
+<a name="2930"><span class="lineNum">    2930 </span>            : </a>
+<a name="2931"><span class="lineNum">    2931 </span><span class="lineCov">      29272 :         mask = tied-&gt;inRegs;</span></a>
+<a name="2932"><span class="lineNum">    2932 </span><span class="lineCov">      29272 :         if (mask != 0) {</span></a>
+<a name="2933"><span class="lineNum">    2933 </span><span class="lineCov">       2088 :           allocableRegs &amp;= mask;</span></a>
+<a name="2934"><span class="lineNum">    2934 </span><span class="lineCov">       2088 :           if (allocableRegs == 0) break;</span></a>
+<a name="2935"><span class="lineNum">    2935 </span>            :           safeRegs = allocableRegs;</a>
+<a name="2936"><span class="lineNum">    2936 </span><span class="lineCov">       2088 :           break;</span></a>
+<a name="2937"><span class="lineNum">    2937 </span>            :         }</a>
+<a name="2938"><span class="lineNum">    2938 </span>            : </a>
+<a name="2939"><span class="lineNum">    2939 </span><span class="lineCov">      27184 :         allocableRegs &amp;= ~(raData-&gt;outRegs.get(C) | raData-&gt;clobberedRegs.get(C));</span></a>
+<a name="2940"><span class="lineNum">    2940 </span><span class="lineCov">      27184 :         if (allocableRegs == 0) break;</span></a>
+<a name="2941"><span class="lineNum">    2941 </span>            :       }</a>
+<a name="2942"><span class="lineNum">    2942 </span>            :       else {</a>
+<a name="2943"><span class="lineNum">    2943 </span><span class="lineCov">      69414 :         allocableRegs &amp;= ~(raData-&gt;inRegs.get(C) | raData-&gt;outRegs.get(C) | raData-&gt;clobberedRegs.get(C));</span></a>
+<a name="2944"><span class="lineNum">    2944 </span><span class="lineCov">      69414 :         if (allocableRegs == 0) break;</span></a>
+<a name="2945"><span class="lineNum">    2945 </span>            :       }</a>
+<a name="2946"><span class="lineNum">    2946 </span>            : </a>
+<a name="2947"><span class="lineNum">    2947 </span>            :       safeRegs = allocableRegs;</a>
+<a name="2948"><span class="lineNum">    2948 </span>            :     }</a>
+<a name="2949"><span class="lineNum">    2949 </span>            :   }</a>
+<a name="2950"><span class="lineNum">    2950 </span>            : </a>
+<a name="2951"><span class="lineNum">    2951 </span>            :   return safeRegs;</a>
+<a name="2952"><span class="lineNum">    2952 </span>            : }</a>
+<a name="2953"><span class="lineNum">    2953 </span>            : </a>
+<a name="2954"><span class="lineNum">    2954 </span>            : template&lt;int C&gt;</a>
+<a name="2955"><span class="lineNum">    2955 </span>            : ASMJIT_INLINE uint32_t X86VarAlloc::guessSpill(VirtReg* vreg, uint32_t allocableRegs) {</a>
+<a name="2956"><span class="lineNum">    2956 </span>            :   ASMJIT_ASSERT(allocableRegs != 0);</a>
+<a name="2957"><span class="lineNum">    2957 </span>            : </a>
+<a name="2958"><span class="lineNum">    2958 </span>            :   return 0;</a>
+<a name="2959"><span class="lineNum">    2959 </span>            : }</a>
+<a name="2960"><span class="lineNum">    2960 </span>            : </a>
+<a name="2961"><span class="lineNum">    2961 </span>            : // ============================================================================</a>
+<a name="2962"><span class="lineNum">    2962 </span>            : // [asmjit::X86VarAlloc - Modified]</a>
+<a name="2963"><span class="lineNum">    2963 </span>            : // ============================================================================</a>
+<a name="2964"><span class="lineNum">    2964 </span>            : </a>
+<a name="2965"><span class="lineNum">    2965 </span>            : template&lt;int C&gt;</a>
+<a name="2966"><span class="lineNum">    2966 </span>            : ASMJIT_INLINE void X86VarAlloc::modified() {</a>
+<a name="2967"><span class="lineNum">    2967 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="2968"><span class="lineNum">    2968 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="2969"><span class="lineNum">    2969 </span>            : </a>
+<a name="2970"><span class="lineNum">    2970 </span><span class="lineCov">      89854 :   for (uint32_t i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="2971"><span class="lineNum">    2971 </span><span class="lineCov">      56748 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="2972"><span class="lineNum">    2972 </span>            : </a>
+<a name="2973"><span class="lineNum">    2973 </span><span class="lineCov">      56748 :     if (tied-&gt;flags &amp; TiedReg::kWReg) {</span></a>
+<a name="2974"><span class="lineNum">    2974 </span><span class="lineCov">      30892 :       VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="2975"><span class="lineNum">    2975 </span>            : </a>
+<a name="2976"><span class="lineNum">    2976 </span>            :       uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="2977"><span class="lineNum">    2977 </span>            :       uint32_t regMask = Utils::mask(physId);</a>
+<a name="2978"><span class="lineNum">    2978 </span>            : </a>
+<a name="2979"><span class="lineNum">    2979 </span>            :       vreg-&gt;setModified(true);</a>
+<a name="2980"><span class="lineNum">    2980 </span><span class="lineCov">      30892 :       _context-&gt;_x86State._modified.or_(C, regMask);</span></a>
+<a name="2981"><span class="lineNum">    2981 </span>            :     }</a>
+<a name="2982"><span class="lineNum">    2982 </span>            :   }</a>
+<a name="2983"><span class="lineNum">    2983 </span>            : }</a>
+<a name="2984"><span class="lineNum">    2984 </span>            : </a>
+<a name="2985"><span class="lineNum">    2985 </span>            : // ============================================================================</a>
+<a name="2986"><span class="lineNum">    2986 </span>            : // [asmjit::X86CallAlloc]</a>
+<a name="2987"><span class="lineNum">    2987 </span>            : // ============================================================================</a>
+<a name="2988"><span class="lineNum">    2988 </span>            : </a>
+<a name="2989"><span class="lineNum">    2989 </span>            : //! \internal</a>
+<a name="2990"><span class="lineNum">    2990 </span>            : //!</a>
+<a name="2991"><span class="lineNum">    2991 </span>            : //! Register allocator context (function call).</a>
+<a name="2992"><span class="lineNum">    2992 </span>            : struct X86CallAlloc : public X86BaseAlloc {</a>
+<a name="2993"><span class="lineNum">    2993 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2994"><span class="lineNum">    2994 </span>            :   // [Construction / Destruction]</a>
+<a name="2995"><span class="lineNum">    2995 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="2996"><span class="lineNum">    2996 </span>            : </a>
+<a name="2997"><span class="lineNum">    2997 </span><span class="lineCov">       1948 :   ASMJIT_INLINE X86CallAlloc(X86RAPass* context) : X86BaseAlloc(context) {}</span></a>
+<a name="2998"><span class="lineNum">    2998 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ~X86CallAlloc() {}</span></a>
+<a name="2999"><span class="lineNum">    2999 </span>            : </a>
+<a name="3000"><span class="lineNum">    3000 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3001"><span class="lineNum">    3001 </span>            :   // [Accessors]</a>
+<a name="3002"><span class="lineNum">    3002 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3003"><span class="lineNum">    3003 </span>            : </a>
+<a name="3004"><span class="lineNum">    3004 </span>            :   //! Get the node.</a>
+<a name="3005"><span class="lineNum">    3005 </span><span class="lineCov">       1648 :   ASMJIT_INLINE CCFuncCall* getNode() const { return static_cast&lt;CCFuncCall*&gt;(_node); }</span></a>
+<a name="3006"><span class="lineNum">    3006 </span>            : </a>
+<a name="3007"><span class="lineNum">    3007 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3008"><span class="lineNum">    3008 </span>            :   // [Run]</a>
+<a name="3009"><span class="lineNum">    3009 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3010"><span class="lineNum">    3010 </span>            : </a>
+<a name="3011"><span class="lineNum">    3011 </span>            :   Error run(CCFuncCall* node);</a>
+<a name="3012"><span class="lineNum">    3012 </span>            : </a>
+<a name="3013"><span class="lineNum">    3013 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3014"><span class="lineNum">    3014 </span>            :   // [Init / Cleanup]</a>
+<a name="3015"><span class="lineNum">    3015 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3016"><span class="lineNum">    3016 </span>            : </a>
+<a name="3017"><span class="lineNum">    3017 </span>            : protected:</a>
+<a name="3018"><span class="lineNum">    3018 </span>            :   // Just to prevent calling these methods from X86RAPass::translate().</a>
+<a name="3019"><span class="lineNum">    3019 </span>            :   ASMJIT_INLINE void init(CCFuncCall* node, X86RAData* raData);</a>
+<a name="3020"><span class="lineNum">    3020 </span>            :   ASMJIT_INLINE void cleanup();</a>
+<a name="3021"><span class="lineNum">    3021 </span>            : </a>
+<a name="3022"><span class="lineNum">    3022 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3023"><span class="lineNum">    3023 </span>            :   // [Plan / Alloc / Spill / Move]</a>
+<a name="3024"><span class="lineNum">    3024 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3025"><span class="lineNum">    3025 </span>            : </a>
+<a name="3026"><span class="lineNum">    3026 </span>            :   template&lt;int C&gt;</a>
+<a name="3027"><span class="lineNum">    3027 </span>            :   ASMJIT_INLINE void plan();</a>
+<a name="3028"><span class="lineNum">    3028 </span>            : </a>
+<a name="3029"><span class="lineNum">    3029 </span>            :   template&lt;int C&gt;</a>
+<a name="3030"><span class="lineNum">    3030 </span>            :   ASMJIT_INLINE void spill();</a>
+<a name="3031"><span class="lineNum">    3031 </span>            : </a>
+<a name="3032"><span class="lineNum">    3032 </span>            :   template&lt;int C&gt;</a>
+<a name="3033"><span class="lineNum">    3033 </span>            :   ASMJIT_INLINE void alloc();</a>
+<a name="3034"><span class="lineNum">    3034 </span>            : </a>
+<a name="3035"><span class="lineNum">    3035 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3036"><span class="lineNum">    3036 </span>            :   // [AllocImmsOnStack]</a>
+<a name="3037"><span class="lineNum">    3037 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3038"><span class="lineNum">    3038 </span>            : </a>
+<a name="3039"><span class="lineNum">    3039 </span>            :   ASMJIT_INLINE void allocImmsOnStack();</a>
+<a name="3040"><span class="lineNum">    3040 </span>            : </a>
+<a name="3041"><span class="lineNum">    3041 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3042"><span class="lineNum">    3042 </span>            :   // [Duplicate]</a>
+<a name="3043"><span class="lineNum">    3043 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3044"><span class="lineNum">    3044 </span>            : </a>
+<a name="3045"><span class="lineNum">    3045 </span>            :   template&lt;int C&gt;</a>
+<a name="3046"><span class="lineNum">    3046 </span>            :   ASMJIT_INLINE void duplicate();</a>
+<a name="3047"><span class="lineNum">    3047 </span>            : </a>
+<a name="3048"><span class="lineNum">    3048 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3049"><span class="lineNum">    3049 </span>            :   // [GuessAlloc / GuessSpill]</a>
+<a name="3050"><span class="lineNum">    3050 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3051"><span class="lineNum">    3051 </span>            : </a>
+<a name="3052"><span class="lineNum">    3052 </span>            :   template&lt;int C&gt;</a>
+<a name="3053"><span class="lineNum">    3053 </span>            :   ASMJIT_INLINE uint32_t guessAlloc(VirtReg* vreg, uint32_t allocableRegs);</a>
+<a name="3054"><span class="lineNum">    3054 </span>            : </a>
+<a name="3055"><span class="lineNum">    3055 </span>            :   template&lt;int C&gt;</a>
+<a name="3056"><span class="lineNum">    3056 </span>            :   ASMJIT_INLINE uint32_t guessSpill(VirtReg* vreg, uint32_t allocableRegs);</a>
+<a name="3057"><span class="lineNum">    3057 </span>            : </a>
+<a name="3058"><span class="lineNum">    3058 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3059"><span class="lineNum">    3059 </span>            :   // [Save]</a>
+<a name="3060"><span class="lineNum">    3060 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3061"><span class="lineNum">    3061 </span>            : </a>
+<a name="3062"><span class="lineNum">    3062 </span>            :   template&lt;int C&gt;</a>
+<a name="3063"><span class="lineNum">    3063 </span>            :   ASMJIT_INLINE void save();</a>
+<a name="3064"><span class="lineNum">    3064 </span>            : </a>
+<a name="3065"><span class="lineNum">    3065 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3066"><span class="lineNum">    3066 </span>            :   // [Clobber]</a>
+<a name="3067"><span class="lineNum">    3067 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3068"><span class="lineNum">    3068 </span>            : </a>
+<a name="3069"><span class="lineNum">    3069 </span>            :   template&lt;int C&gt;</a>
+<a name="3070"><span class="lineNum">    3070 </span>            :   ASMJIT_INLINE void clobber();</a>
+<a name="3071"><span class="lineNum">    3071 </span>            : </a>
+<a name="3072"><span class="lineNum">    3072 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3073"><span class="lineNum">    3073 </span>            :   // [Ret]</a>
+<a name="3074"><span class="lineNum">    3074 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3075"><span class="lineNum">    3075 </span>            : </a>
+<a name="3076"><span class="lineNum">    3076 </span>            :   ASMJIT_INLINE void ret();</a>
+<a name="3077"><span class="lineNum">    3077 </span>            : </a>
+<a name="3078"><span class="lineNum">    3078 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3079"><span class="lineNum">    3079 </span>            :   // [Members]</a>
+<a name="3080"><span class="lineNum">    3080 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="3081"><span class="lineNum">    3081 </span>            : </a>
+<a name="3082"><span class="lineNum">    3082 </span>            :   //! Will alloc to these registers.</a>
+<a name="3083"><span class="lineNum">    3083 </span>            :   X86RegMask _willAlloc;</a>
+<a name="3084"><span class="lineNum">    3084 </span>            :   //! Will spill these registers.</a>
+<a name="3085"><span class="lineNum">    3085 </span>            :   X86RegMask _willSpill;</a>
+<a name="3086"><span class="lineNum">    3086 </span>            : };</a>
+<a name="3087"><span class="lineNum">    3087 </span>            : </a>
+<a name="3088"><span class="lineNum">    3088 </span>            : // ============================================================================</a>
+<a name="3089"><span class="lineNum">    3089 </span>            : // [asmjit::X86CallAlloc - Run]</a>
+<a name="3090"><span class="lineNum">    3090 </span>            : // ============================================================================</a>
+<a name="3091"><span class="lineNum">    3091 </span>            : </a>
+<a name="3092"><span class="lineNum">    3092 </span><span class="lineCov">       1648 : Error X86CallAlloc::run(CCFuncCall* node) {</span></a>
+<a name="3093"><span class="lineNum">    3093 </span>            :   // Initialize the allocator; prepare basics and connect Vd-&gt;Va.</a>
+<a name="3094"><span class="lineNum">    3094 </span>            :   X86RAData* raData = node-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="3095"><span class="lineNum">    3095 </span>            :   init(node, raData);</a>
+<a name="3096"><span class="lineNum">    3096 </span>            : </a>
+<a name="3097"><span class="lineNum">    3097 </span>            :   // Plan register allocation. Planner is only able to assign one register per</a>
+<a name="3098"><span class="lineNum">    3098 </span>            :   // variable. If any variable is used multiple times it will be handled later.</a>
+<a name="3099"><span class="lineNum">    3099 </span>            :   plan&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3100"><span class="lineNum">    3100 </span>            :   plan&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3101"><span class="lineNum">    3101 </span>            :   plan&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3102"><span class="lineNum">    3102 </span>            : </a>
+<a name="3103"><span class="lineNum">    3103 </span>            :   // Spill.</a>
+<a name="3104"><span class="lineNum">    3104 </span>            :   spill&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3105"><span class="lineNum">    3105 </span>            :   spill&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3106"><span class="lineNum">    3106 </span>            :   spill&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3107"><span class="lineNum">    3107 </span>            : </a>
+<a name="3108"><span class="lineNum">    3108 </span>            :   // Alloc.</a>
+<a name="3109"><span class="lineNum">    3109 </span>            :   alloc&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3110"><span class="lineNum">    3110 </span>            :   alloc&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3111"><span class="lineNum">    3111 </span>            :   alloc&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3112"><span class="lineNum">    3112 </span>            : </a>
+<a name="3113"><span class="lineNum">    3113 </span>            :   // Unuse clobbered registers that are not used to pass function arguments and</a>
+<a name="3114"><span class="lineNum">    3114 </span>            :   // save variables used to pass function arguments that will be reused later on.</a>
+<a name="3115"><span class="lineNum">    3115 </span>            :   save&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3116"><span class="lineNum">    3116 </span>            :   save&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3117"><span class="lineNum">    3117 </span>            :   save&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3118"><span class="lineNum">    3118 </span>            : </a>
+<a name="3119"><span class="lineNum">    3119 </span>            :   // Allocate immediates in registers and on the stack.</a>
+<a name="3120"><span class="lineNum">    3120 </span>            :   allocImmsOnStack();</a>
+<a name="3121"><span class="lineNum">    3121 </span>            : </a>
+<a name="3122"><span class="lineNum">    3122 </span>            :   // Duplicate.</a>
+<a name="3123"><span class="lineNum">    3123 </span>            :   duplicate&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3124"><span class="lineNum">    3124 </span>            :   duplicate&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3125"><span class="lineNum">    3125 </span>            :   duplicate&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3126"><span class="lineNum">    3126 </span>            : </a>
+<a name="3127"><span class="lineNum">    3127 </span>            :   // Translate call operand.</a>
+<a name="3128"><span class="lineNum">    3128 </span><span class="lineCov">       1648 :   ASMJIT_PROPAGATE(X86RAPass_translateOperands(_context, node-&gt;getOpArray(), node-&gt;getOpCount()));</span></a>
+<a name="3129"><span class="lineNum">    3129 </span>            : </a>
+<a name="3130"><span class="lineNum">    3130 </span>            :   // To emit instructions after call.</a>
+<a name="3131"><span class="lineNum">    3131 </span><span class="lineCov">       1648 :   _cc-&gt;_setCursor(node);</span></a>
+<a name="3132"><span class="lineNum">    3132 </span>            : </a>
+<a name="3133"><span class="lineNum">    3133 </span>            :   // If the callee pops stack it has to be manually adjusted back.</a>
+<a name="3134"><span class="lineNum">    3134 </span>            :   FuncDetail&amp; fd = node-&gt;getDetail();</a>
+<a name="3135"><span class="lineNum">    3135 </span><span class="lineCov">       1648 :   if (fd.hasFlag(CallConv::kFlagCalleePopsStack) &amp;&amp; fd.getArgStackSize() != 0)</span></a>
+<a name="3136"><span class="lineNum">    3136 </span><span class="lineNoCov">          0 :     _cc-&gt;emit(X86Inst::kIdSub, _context-&gt;_zsp, static_cast&lt;int&gt;(fd.getArgStackSize()));</span></a>
+<a name="3137"><span class="lineNum">    3137 </span>            : </a>
+<a name="3138"><span class="lineNum">    3138 </span>            :   // Clobber.</a>
+<a name="3139"><span class="lineNum">    3139 </span>            :   clobber&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3140"><span class="lineNum">    3140 </span>            :   clobber&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3141"><span class="lineNum">    3141 </span>            :   clobber&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3142"><span class="lineNum">    3142 </span>            : </a>
+<a name="3143"><span class="lineNum">    3143 </span>            :   // Return.</a>
+<a name="3144"><span class="lineNum">    3144 </span>            :   ret();</a>
+<a name="3145"><span class="lineNum">    3145 </span>            : </a>
+<a name="3146"><span class="lineNum">    3146 </span>            :   // Unuse.</a>
+<a name="3147"><span class="lineNum">    3147 </span>            :   unuseAfter&lt;X86Reg::kKindGp &gt;();</a>
+<a name="3148"><span class="lineNum">    3148 </span>            :   unuseAfter&lt;X86Reg::kKindMm &gt;();</a>
+<a name="3149"><span class="lineNum">    3149 </span>            :   unuseAfter&lt;X86Reg::kKindVec&gt;();</a>
+<a name="3150"><span class="lineNum">    3150 </span>            : </a>
+<a name="3151"><span class="lineNum">    3151 </span>            :   // Cleanup; disconnect Vd-&gt;Va.</a>
+<a name="3152"><span class="lineNum">    3152 </span>            :   cleanup();</a>
+<a name="3153"><span class="lineNum">    3153 </span>            : </a>
+<a name="3154"><span class="lineNum">    3154 </span>            :   return kErrorOk;</a>
+<a name="3155"><span class="lineNum">    3155 </span>            : }</a>
+<a name="3156"><span class="lineNum">    3156 </span>            : </a>
+<a name="3157"><span class="lineNum">    3157 </span>            : // ============================================================================</a>
+<a name="3158"><span class="lineNum">    3158 </span>            : // [asmjit::X86CallAlloc - Init / Cleanup]</a>
+<a name="3159"><span class="lineNum">    3159 </span>            : // ============================================================================</a>
+<a name="3160"><span class="lineNum">    3160 </span>            : </a>
+<a name="3161"><span class="lineNum">    3161 </span>            : ASMJIT_INLINE void X86CallAlloc::init(CCFuncCall* node, X86RAData* raData) {</a>
+<a name="3162"><span class="lineNum">    3162 </span>            :   X86BaseAlloc::init(node, raData);</a>
+<a name="3163"><span class="lineNum">    3163 </span>            : </a>
+<a name="3164"><span class="lineNum">    3164 </span>            :   // Create mask of all registers that will be used to pass function arguments.</a>
+<a name="3165"><span class="lineNum">    3165 </span>            :   _willAlloc.reset();</a>
+<a name="3166"><span class="lineNum">    3166 </span>            :   _willAlloc.set(X86Reg::kKindGp , node-&gt;getDetail().getUsedRegs(X86Reg::kKindGp ));</a>
+<a name="3167"><span class="lineNum">    3167 </span>            :   _willAlloc.set(X86Reg::kKindMm , node-&gt;getDetail().getUsedRegs(X86Reg::kKindMm ));</a>
+<a name="3168"><span class="lineNum">    3168 </span>            :   _willAlloc.set(X86Reg::kKindK  , node-&gt;getDetail().getUsedRegs(X86Reg::kKindK  ));</a>
+<a name="3169"><span class="lineNum">    3169 </span>            :   _willAlloc.set(X86Reg::kKindVec, node-&gt;getDetail().getUsedRegs(X86Reg::kKindVec));</a>
+<a name="3170"><span class="lineNum">    3170 </span>            :   _willSpill.reset();</a>
+<a name="3171"><span class="lineNum">    3171 </span>            : }</a>
+<a name="3172"><span class="lineNum">    3172 </span>            : </a>
+<a name="3173"><span class="lineNum">    3173 </span>            : ASMJIT_INLINE void X86CallAlloc::cleanup() {</a>
+<a name="3174"><span class="lineNum">    3174 </span>            :   X86BaseAlloc::cleanup();</a>
+<a name="3175"><span class="lineNum">    3175 </span>            : }</a>
+<a name="3176"><span class="lineNum">    3176 </span>            : </a>
+<a name="3177"><span class="lineNum">    3177 </span>            : // ============================================================================</a>
+<a name="3178"><span class="lineNum">    3178 </span>            : // [asmjit::X86CallAlloc - Plan / Spill / Alloc]</a>
+<a name="3179"><span class="lineNum">    3179 </span>            : // ============================================================================</a>
+<a name="3180"><span class="lineNum">    3180 </span>            : </a>
+<a name="3181"><span class="lineNum">    3181 </span>            : template&lt;int C&gt;</a>
+<a name="3182"><span class="lineNum">    3182 </span>            : ASMJIT_INLINE void X86CallAlloc::plan() {</a>
+<a name="3183"><span class="lineNum">    3183 </span>            :   uint32_t i;</a>
+<a name="3184"><span class="lineNum">    3184 </span><span class="lineCov">       4944 :   uint32_t clobbered = _raData-&gt;clobberedRegs.get(C);</span></a>
+<a name="3185"><span class="lineNum">    3185 </span>            : </a>
+<a name="3186"><span class="lineNum">    3186 </span>            :   uint32_t willAlloc = _willAlloc.get(C);</a>
+<a name="3187"><span class="lineNum">    3187 </span><span class="lineCov">       4944 :   uint32_t willFree = clobbered &amp; ~willAlloc;</span></a>
+<a name="3188"><span class="lineNum">    3188 </span>            : </a>
+<a name="3189"><span class="lineNum">    3189 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="3190"><span class="lineNum">    3190 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="3191"><span class="lineNum">    3191 </span>            : </a>
+<a name="3192"><span class="lineNum">    3192 </span>            :   X86RAState* state = getState();</a>
+<a name="3193"><span class="lineNum">    3193 </span>            : </a>
+<a name="3194"><span class="lineNum">    3194 </span>            :   // Calculate 'willAlloc' and 'willFree' masks based on mandatory masks.</a>
+<a name="3195"><span class="lineNum">    3195 </span><span class="lineCov">       9690 :   for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="3196"><span class="lineNum">    3196 </span><span class="lineCov">       4746 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="3197"><span class="lineNum">    3197 </span><span class="lineCov">       4746 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="3198"><span class="lineNum">    3198 </span>            : </a>
+<a name="3199"><span class="lineNum">    3199 </span><span class="lineCov">       4746 :     uint32_t vaFlags = tied-&gt;flags;</span></a>
+<a name="3200"><span class="lineNum">    3200 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="3201"><span class="lineNum">    3201 </span><span class="lineCov">       4746 :     uint32_t regMask = (physId != Globals::kInvalidRegId) ? Utils::mask(physId) : 0;</span></a>
+<a name="3202"><span class="lineNum">    3202 </span>            : </a>
+<a name="3203"><span class="lineNum">    3203 </span><span class="lineCov">       4746 :     if ((vaFlags &amp; TiedReg::kRReg) != 0) {</span></a>
+<a name="3204"><span class="lineNum">    3204 </span>            :       // Planning register allocation. First check whether the variable is</a>
+<a name="3205"><span class="lineNum">    3205 </span>            :       // already allocated in register and if it can stay there. Function</a>
+<a name="3206"><span class="lineNum">    3206 </span>            :       // arguments are passed either in a specific register or in stack so</a>
+<a name="3207"><span class="lineNum">    3207 </span>            :       // we care mostly of mandatory registers.</a>
+<a name="3208"><span class="lineNum">    3208 </span><span class="lineCov">       3098 :       uint32_t inRegs = tied-&gt;inRegs;</span></a>
+<a name="3209"><span class="lineNum">    3209 </span>            : </a>
+<a name="3210"><span class="lineNum">    3210 </span><span class="lineCov">       3098 :       if (inRegs == 0) {</span></a>
+<a name="3211"><span class="lineNum">    3211 </span><span class="lineCov">       1648 :         inRegs = tied-&gt;allocableRegs;</span></a>
+<a name="3212"><span class="lineNum">    3212 </span>            :       }</a>
+<a name="3213"><span class="lineNum">    3213 </span>            : </a>
+<a name="3214"><span class="lineNum">    3214 </span>            :       // Optimize situation where the variable has to be allocated in a</a>
+<a name="3215"><span class="lineNum">    3215 </span>            :       // mandatory register, but it's already allocated in register that</a>
+<a name="3216"><span class="lineNum">    3216 </span>            :       // is not clobbered (i.e. it will survive function call).</a>
+<a name="3217"><span class="lineNum">    3217 </span><span class="lineCov">       3098 :       if ((regMask &amp; inRegs) != 0 || ((regMask &amp; ~clobbered) != 0 &amp;&amp; (vaFlags &amp; TiedReg::kUnuse) == 0)) {</span></a>
+<a name="3218"><span class="lineNum">    3218 </span>            :         tied-&gt;setInPhysId(physId);</a>
+<a name="3219"><span class="lineNum">    3219 </span><span class="lineCov">       2290 :         tied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="3220"><span class="lineNum">    3220 </span>            :         addTiedDone(C);</a>
+<a name="3221"><span class="lineNum">    3221 </span>            :       }</a>
+<a name="3222"><span class="lineNum">    3222 </span>            :       else {</a>
+<a name="3223"><span class="lineNum">    3223 </span><span class="lineCov">        808 :         willFree |= regMask;</span></a>
+<a name="3224"><span class="lineNum">    3224 </span>            :       }</a>
+<a name="3225"><span class="lineNum">    3225 </span>            :     }</a>
+<a name="3226"><span class="lineNum">    3226 </span>            :     else {</a>
+<a name="3227"><span class="lineNum">    3227 </span>            :       // Memory access - if variable is allocated it has to be freed.</a>
+<a name="3228"><span class="lineNum">    3228 </span><span class="lineCov">       1648 :       if (regMask != 0) {</span></a>
+<a name="3229"><span class="lineNum">    3229 </span><span class="lineNoCov">          0 :         willFree |= regMask;</span></a>
+<a name="3230"><span class="lineNum">    3230 </span>            :       }</a>
+<a name="3231"><span class="lineNum">    3231 </span>            :       else {</a>
+<a name="3232"><span class="lineNum">    3232 </span><span class="lineCov">       1648 :         tied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="3233"><span class="lineNum">    3233 </span>            :         addTiedDone(C);</a>
+<a name="3234"><span class="lineNum">    3234 </span>            :       }</a>
+<a name="3235"><span class="lineNum">    3235 </span>            :     }</a>
+<a name="3236"><span class="lineNum">    3236 </span>            :   }</a>
+<a name="3237"><span class="lineNum">    3237 </span>            : </a>
+<a name="3238"><span class="lineNum">    3238 </span>            :   // Occupied registers without 'willFree' registers; contains basically</a>
+<a name="3239"><span class="lineNum">    3239 </span>            :   // all the registers we can use to allocate variables without inRegs</a>
+<a name="3240"><span class="lineNum">    3240 </span>            :   // speficied.</a>
+<a name="3241"><span class="lineNum">    3241 </span><span class="lineCov">       4944 :   uint32_t occupied = state-&gt;_occupied.get(C) &amp; ~willFree;</span></a>
+<a name="3242"><span class="lineNum">    3242 </span>            :   uint32_t willSpill = 0;</a>
+<a name="3243"><span class="lineNum">    3243 </span>            : </a>
+<a name="3244"><span class="lineNum">    3244 </span>            :   // Find the best registers for variables that are not allocated yet. Only</a>
+<a name="3245"><span class="lineNum">    3245 </span>            :   // useful for Gp registers used as call operand.</a>
+<a name="3246"><span class="lineNum">    3246 </span><span class="lineCov">       9690 :   for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="3247"><span class="lineNum">    3247 </span><span class="lineCov">       4746 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="3248"><span class="lineNum">    3248 </span><span class="lineCov">       1648 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="3249"><span class="lineNum">    3249 </span>            : </a>
+<a name="3250"><span class="lineNum">    3250 </span><span class="lineCov">       4746 :     uint32_t vaFlags = tied-&gt;flags;</span></a>
+<a name="3251"><span class="lineNum">    3251 </span><span class="lineCov">       4746 :     if ((vaFlags &amp; TiedReg::kRDone) != 0 || (vaFlags &amp; TiedReg::kRReg) == 0)</span></a>
+<a name="3252"><span class="lineNum">    3252 </span><span class="lineCov">       3938 :       continue;</span></a>
+<a name="3253"><span class="lineNum">    3253 </span>            : </a>
+<a name="3254"><span class="lineNum">    3254 </span>            :     // All registers except Gp used by call itself must have inPhysId.</a>
+<a name="3255"><span class="lineNum">    3255 </span><span class="lineCov">        808 :     uint32_t m = tied-&gt;inRegs;</span></a>
+<a name="3256"><span class="lineNum">    3256 </span><span class="lineNoCov">          0 :     if (C != X86Reg::kKindGp || m) {</span></a>
+<a name="3257"><span class="lineNum">    3257 </span>            :       ASMJIT_ASSERT(m != 0);</a>
+<a name="3258"><span class="lineNum">    3258 </span>            :       tied-&gt;setInPhysId(Utils::findFirstBit(m));</a>
+<a name="3259"><span class="lineNum">    3259 </span><span class="lineCov">        808 :       willSpill |= occupied &amp; m;</span></a>
+<a name="3260"><span class="lineNum">    3260 </span><span class="lineCov">        808 :       continue;</span></a>
+<a name="3261"><span class="lineNum">    3261 </span>            :     }</a>
+<a name="3262"><span class="lineNum">    3262 </span>            : </a>
+<a name="3263"><span class="lineNum">    3263 </span><span class="lineNoCov">          0 :     m = tied-&gt;allocableRegs &amp; ~(willAlloc ^ m);</span></a>
+<a name="3264"><span class="lineNum">    3264 </span>            :     m = guessAlloc&lt;C&gt;(vreg, m);</a>
+<a name="3265"><span class="lineNum">    3265 </span>            :     ASMJIT_ASSERT(m != 0);</a>
+<a name="3266"><span class="lineNum">    3266 </span>            : </a>
+<a name="3267"><span class="lineNum">    3267 </span><span class="lineNoCov">          0 :     uint32_t candidateRegs = m &amp; ~occupied;</span></a>
+<a name="3268"><span class="lineNum">    3268 </span><span class="lineNoCov">          0 :     if (candidateRegs == 0) {</span></a>
+<a name="3269"><span class="lineNum">    3269 </span><span class="lineNoCov">          0 :       candidateRegs = m &amp; occupied &amp; ~state-&gt;_modified.get(C);</span></a>
+<a name="3270"><span class="lineNum">    3270 </span><span class="lineNoCov">          0 :       if (candidateRegs == 0)</span></a>
+<a name="3271"><span class="lineNum">    3271 </span>            :         candidateRegs = m;</a>
+<a name="3272"><span class="lineNum">    3272 </span>            :     }</a>
+<a name="3273"><span class="lineNum">    3273 </span>            : </a>
+<a name="3274"><span class="lineNum">    3274 </span><span class="lineNoCov">          0 :     if (!(vaFlags &amp; (TiedReg::kWReg | TiedReg::kUnuse)) &amp;&amp; (candidateRegs &amp; ~clobbered))</span></a>
+<a name="3275"><span class="lineNum">    3275 </span>            :       candidateRegs &amp;= ~clobbered;</a>
+<a name="3276"><span class="lineNum">    3276 </span>            : </a>
+<a name="3277"><span class="lineNum">    3277 </span>            :     uint32_t physId = Utils::findFirstBit(candidateRegs);</a>
+<a name="3278"><span class="lineNum">    3278 </span>            :     uint32_t regMask = Utils::mask(physId);</a>
+<a name="3279"><span class="lineNum">    3279 </span>            : </a>
+<a name="3280"><span class="lineNum">    3280 </span>            :     tied-&gt;setInPhysId(physId);</a>
+<a name="3281"><span class="lineNum">    3281 </span><span class="lineNoCov">          0 :     tied-&gt;inRegs = regMask;</span></a>
+<a name="3282"><span class="lineNum">    3282 </span>            : </a>
+<a name="3283"><span class="lineNum">    3283 </span><span class="lineNoCov">          0 :     willAlloc |= regMask;</span></a>
+<a name="3284"><span class="lineNum">    3284 </span><span class="lineNoCov">          0 :     willSpill |= regMask &amp; occupied;</span></a>
+<a name="3285"><span class="lineNum">    3285 </span>            :     willFree &amp;= ~regMask;</a>
+<a name="3286"><span class="lineNum">    3286 </span>            : </a>
+<a name="3287"><span class="lineNum">    3287 </span><span class="lineNoCov">          0 :     occupied |= regMask;</span></a>
+<a name="3288"><span class="lineNum">    3288 </span><span class="lineNoCov">          0 :     continue;</span></a>
+<a name="3289"><span class="lineNum">    3289 </span>            :   }</a>
+<a name="3290"><span class="lineNum">    3290 </span>            : </a>
+<a name="3291"><span class="lineNum">    3291 </span>            :   // Set calculated masks back to the allocator; needed by spill() and alloc().</a>
+<a name="3292"><span class="lineNum">    3292 </span>            :   _willSpill.set(C, willSpill);</a>
+<a name="3293"><span class="lineNum">    3293 </span>            :   _willAlloc.set(C, willAlloc);</a>
+<a name="3294"><span class="lineNum">    3294 </span>            : }</a>
+<a name="3295"><span class="lineNum">    3295 </span>            : </a>
+<a name="3296"><span class="lineNum">    3296 </span>            : template&lt;int C&gt;</a>
+<a name="3297"><span class="lineNum">    3297 </span>            : ASMJIT_INLINE void X86CallAlloc::spill() {</a>
+<a name="3298"><span class="lineNum">    3298 </span>            :   uint32_t m = _willSpill.get(C);</a>
+<a name="3299"><span class="lineNum">    3299 </span>            :   uint32_t i = static_cast&lt;uint32_t&gt;(0) - 1;</a>
+<a name="3300"><span class="lineNum">    3300 </span>            : </a>
+<a name="3301"><span class="lineNum">    3301 </span><span class="lineCov">       1648 :   if (m == 0)</span></a>
+<a name="3302"><span class="lineNum">    3302 </span>            :     return;</a>
+<a name="3303"><span class="lineNum">    3303 </span>            : </a>
+<a name="3304"><span class="lineNum">    3304 </span>            :   X86RAState* state = getState();</a>
+<a name="3305"><span class="lineNum">    3305 </span>            :   VirtReg** sVars = state-&gt;getListByKind(C);</a>
+<a name="3306"><span class="lineNum">    3306 </span>            : </a>
+<a name="3307"><span class="lineNum">    3307 </span>            :   // Available registers for decision if move has any benefit over spill.</a>
+<a name="3308"><span class="lineNum">    3308 </span>            :   uint32_t availableRegs = getGaRegs(C) &amp; ~(state-&gt;_occupied.get(C) | m | _willAlloc.get(C));</a>
+<a name="3309"><span class="lineNum">    3309 </span>            : </a>
+<a name="3310"><span class="lineNum">    3310 </span>            :   do {</a>
+<a name="3311"><span class="lineNum">    3311 </span>            :     // We always advance one more to destroy the bit that we have found.</a>
+<a name="3312"><span class="lineNum">    3312 </span><span class="lineCov">        410 :     uint32_t bitIndex = Utils::findFirstBit(m) + 1;</span></a>
+<a name="3313"><span class="lineNum">    3313 </span>            : </a>
+<a name="3314"><span class="lineNum">    3314 </span><span class="lineCov">        410 :     i += bitIndex;</span></a>
+<a name="3315"><span class="lineNum">    3315 </span><span class="lineCov">        410 :     m &gt;&gt;= bitIndex;</span></a>
+<a name="3316"><span class="lineNum">    3316 </span>            : </a>
+<a name="3317"><span class="lineNum">    3317 </span><span class="lineCov">        410 :     VirtReg* vreg = sVars[i];</span></a>
+<a name="3318"><span class="lineNum">    3318 </span>            :     ASMJIT_ASSERT(vreg &amp;&amp; !vreg-&gt;_tied);</a>
+<a name="3319"><span class="lineNum">    3319 </span>            : </a>
+<a name="3320"><span class="lineNum">    3320 </span>            :     if (vreg-&gt;isModified() &amp;&amp; availableRegs) {</a>
+<a name="3321"><span class="lineNum">    3321 </span>            :       uint32_t available = guessSpill&lt;C&gt;(vreg, availableRegs);</a>
+<a name="3322"><span class="lineNum">    3322 </span>            :       if (available != 0) {</a>
+<a name="3323"><span class="lineNum">    3323 </span>            :         uint32_t physId = Utils::findFirstBit(available);</a>
+<a name="3324"><span class="lineNum">    3324 </span>            :         uint32_t regMask = Utils::mask(physId);</a>
+<a name="3325"><span class="lineNum">    3325 </span>            : </a>
+<a name="3326"><span class="lineNum">    3326 </span>            :         _context-&gt;move&lt;C&gt;(vreg, physId);</a>
+<a name="3327"><span class="lineNum">    3327 </span>            :         availableRegs ^= regMask;</a>
+<a name="3328"><span class="lineNum">    3328 </span>            :         continue;</a>
+<a name="3329"><span class="lineNum">    3329 </span>            :       }</a>
+<a name="3330"><span class="lineNum">    3330 </span>            :     }</a>
+<a name="3331"><span class="lineNum">    3331 </span>            : </a>
+<a name="3332"><span class="lineNum">    3332 </span><span class="lineCov">        410 :     _context-&gt;spill&lt;C&gt;(vreg);</span></a>
+<a name="3333"><span class="lineNum">    3333 </span><span class="lineCov">        410 :   } while (m != 0);</span></a>
+<a name="3334"><span class="lineNum">    3334 </span>            : }</a>
+<a name="3335"><span class="lineNum">    3335 </span>            : </a>
+<a name="3336"><span class="lineNum">    3336 </span>            : template&lt;int C&gt;</a>
+<a name="3337"><span class="lineNum">    3337 </span>            : ASMJIT_INLINE void X86CallAlloc::alloc() {</a>
+<a name="3338"><span class="lineNum">    3338 </span><span class="lineCov">       1648 :   if (isTiedDone(C)) return;</span></a>
+<a name="3339"><span class="lineNum">    3339 </span>            : </a>
+<a name="3340"><span class="lineNum">    3340 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="3341"><span class="lineNum">    3341 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="3342"><span class="lineNum">    3342 </span>            : </a>
+<a name="3343"><span class="lineNum">    3343 </span>            :   uint32_t i;</a>
+<a name="3344"><span class="lineNum">    3344 </span>            :   bool didWork;</a>
+<a name="3345"><span class="lineNum">    3345 </span>            : </a>
+<a name="3346"><span class="lineNum">    3346 </span><span class="lineCov">       1616 :   do {</span></a>
+<a name="3347"><span class="lineNum">    3347 </span>            :     didWork = false;</a>
+<a name="3348"><span class="lineNum">    3348 </span><span class="lineCov">       4872 :     for (i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="3349"><span class="lineNum">    3349 </span><span class="lineCov">       3256 :       TiedReg* aTied = &amp;tiedArray[i];</span></a>
+<a name="3350"><span class="lineNum">    3350 </span><span class="lineCov">       3256 :       VirtReg* aVReg = aTied-&gt;vreg;</span></a>
+<a name="3351"><span class="lineNum">    3351 </span><span class="lineCov">       3256 :       if ((aTied-&gt;flags &amp; (TiedReg::kRReg | TiedReg::kRDone)) != TiedReg::kRReg) continue;</span></a>
+<a name="3352"><span class="lineNum">    3352 </span>            : </a>
+<a name="3353"><span class="lineNum">    3353 </span>            :       uint32_t sPhysId = aVReg-&gt;getPhysId();</a>
+<a name="3354"><span class="lineNum">    3354 </span><span class="lineCov">        808 :       uint32_t bPhysId = aTied-&gt;inPhysId;</span></a>
+<a name="3355"><span class="lineNum">    3355 </span>            : </a>
+<a name="3356"><span class="lineNum">    3356 </span>            :       // Shouldn't be the same.</a>
+<a name="3357"><span class="lineNum">    3357 </span>            :       ASMJIT_ASSERT(sPhysId != bPhysId);</a>
+<a name="3358"><span class="lineNum">    3358 </span>            : </a>
+<a name="3359"><span class="lineNum">    3359 </span><span class="lineCov">        808 :       VirtReg* bVReg = getState()-&gt;getListByKind(C)[bPhysId];</span></a>
+<a name="3360"><span class="lineNum">    3360 </span><span class="lineCov">        808 :       if (bVReg) {</span></a>
+<a name="3361"><span class="lineNum">    3361 </span><span class="lineNoCov">          0 :         TiedReg* bTied = bVReg-&gt;_tied;</span></a>
+<a name="3362"><span class="lineNum">    3362 </span>            : </a>
+<a name="3363"><span class="lineNum">    3363 </span>            :         // GP registers only - Swap two registers if we can solve two</a>
+<a name="3364"><span class="lineNum">    3364 </span>            :         // allocation tasks by a single 'xchg' instruction, swapping</a>
+<a name="3365"><span class="lineNum">    3365 </span>            :         // two registers required by the instruction/node or one register</a>
+<a name="3366"><span class="lineNum">    3366 </span>            :         // required with another non-required.</a>
+<a name="3367"><span class="lineNum">    3367 </span>            :         if (C == X86Reg::kKindGp) {</a>
+<a name="3368"><span class="lineNum">    3368 </span>            :           _context-&gt;swapGp(aVReg, bVReg);</a>
+<a name="3369"><span class="lineNum">    3369 </span>            : </a>
+<a name="3370"><span class="lineNum">    3370 </span><span class="lineNoCov">          0 :           aTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="3371"><span class="lineNum">    3371 </span>            :           addTiedDone(C);</a>
+<a name="3372"><span class="lineNum">    3372 </span>            : </a>
+<a name="3373"><span class="lineNum">    3373 </span>            :           // Double-hit, two registers allocated by a single swap.</a>
+<a name="3374"><span class="lineNum">    3374 </span><span class="lineNoCov">          0 :           if (bTied &amp;&amp; bTied-&gt;inPhysId == sPhysId) {</span></a>
+<a name="3375"><span class="lineNum">    3375 </span><span class="lineNoCov">          0 :             bTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="3376"><span class="lineNum">    3376 </span>            :             addTiedDone(C);</a>
+<a name="3377"><span class="lineNum">    3377 </span>            :           }</a>
+<a name="3378"><span class="lineNum">    3378 </span>            : </a>
+<a name="3379"><span class="lineNum">    3379 </span>            :           didWork = true;</a>
+<a name="3380"><span class="lineNum">    3380 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="3381"><span class="lineNum">    3381 </span>            :         }</a>
+<a name="3382"><span class="lineNum">    3382 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="3383"><span class="lineNum">    3383 </span><span class="lineCov">        808 :       else if (sPhysId != Globals::kInvalidRegId) {</span></a>
+<a name="3384"><span class="lineNum">    3384 </span>            :         _context-&gt;move&lt;C&gt;(aVReg, bPhysId);</a>
+<a name="3385"><span class="lineNum">    3385 </span><span class="lineCov">        322 :         _context-&gt;_clobberedRegs.or_(C, Utils::mask(bPhysId));</span></a>
+<a name="3386"><span class="lineNum">    3386 </span>            : </a>
+<a name="3387"><span class="lineNum">    3387 </span><span class="lineCov">        322 :         aTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="3388"><span class="lineNum">    3388 </span>            :         addTiedDone(C);</a>
+<a name="3389"><span class="lineNum">    3389 </span>            : </a>
+<a name="3390"><span class="lineNum">    3390 </span>            :         didWork = true;</a>
+<a name="3391"><span class="lineNum">    3391 </span><span class="lineCov">        322 :         continue;</span></a>
+<a name="3392"><span class="lineNum">    3392 </span>            :       }</a>
+<a name="3393"><span class="lineNum">    3393 </span>            :       else {</a>
+<a name="3394"><span class="lineNum">    3394 </span>            :         _context-&gt;alloc&lt;C&gt;(aVReg, bPhysId);</a>
+<a name="3395"><span class="lineNum">    3395 </span><span class="lineCov">        486 :         _context-&gt;_clobberedRegs.or_(C, Utils::mask(bPhysId));</span></a>
+<a name="3396"><span class="lineNum">    3396 </span>            : </a>
+<a name="3397"><span class="lineNum">    3397 </span><span class="lineCov">        486 :         aTied-&gt;flags |= TiedReg::kRDone;</span></a>
+<a name="3398"><span class="lineNum">    3398 </span>            :         addTiedDone(C);</a>
+<a name="3399"><span class="lineNum">    3399 </span>            : </a>
+<a name="3400"><span class="lineNum">    3400 </span>            :         didWork = true;</a>
+<a name="3401"><span class="lineNum">    3401 </span><span class="lineCov">        486 :         continue;</span></a>
+<a name="3402"><span class="lineNum">    3402 </span>            :       }</a>
+<a name="3403"><span class="lineNum">    3403 </span>            :     }</a>
+<a name="3404"><span class="lineNum">    3404 </span>            :   } while (didWork);</a>
+<a name="3405"><span class="lineNum">    3405 </span>            : }</a>
+<a name="3406"><span class="lineNum">    3406 </span>            : </a>
+<a name="3407"><span class="lineNum">    3407 </span>            : // ============================================================================</a>
+<a name="3408"><span class="lineNum">    3408 </span>            : // [asmjit::X86CallAlloc - AllocImmsOnStack]</a>
+<a name="3409"><span class="lineNum">    3409 </span>            : // ============================================================================</a>
+<a name="3410"><span class="lineNum">    3410 </span>            : </a>
+<a name="3411"><span class="lineNum">    3411 </span>            : ASMJIT_INLINE void X86CallAlloc::allocImmsOnStack() {</a>
+<a name="3412"><span class="lineNum">    3412 </span>            :   CCFuncCall* node = getNode();</a>
+<a name="3413"><span class="lineNum">    3413 </span>            :   FuncDetail&amp; fd = node-&gt;getDetail();</a>
+<a name="3414"><span class="lineNum">    3414 </span>            : </a>
+<a name="3415"><span class="lineNum">    3415 </span>            :   uint32_t argCount = fd.getArgCount();</a>
+<a name="3416"><span class="lineNum">    3416 </span><span class="lineCov">       1648 :   Operand_* args = node-&gt;_args;</span></a>
+<a name="3417"><span class="lineNum">    3417 </span>            : </a>
+<a name="3418"><span class="lineNum">    3418 </span><span class="lineCov">       3518 :   for (uint32_t i = 0; i &lt; argCount; i++) {</span></a>
+<a name="3419"><span class="lineNum">    3419 </span><span class="lineCov">       1870 :     Operand_&amp; op = args[i];</span></a>
+<a name="3420"><span class="lineNum">    3420 </span><span class="lineCov">       1870 :     if (!op.isImm()) continue;</span></a>
+<a name="3421"><span class="lineNum">    3421 </span>            : </a>
+<a name="3422"><span class="lineNum">    3422 </span>            :     const Imm&amp; imm = static_cast&lt;const Imm&amp;&gt;(op);</a>
+<a name="3423"><span class="lineNum">    3423 </span>            :     const FuncDetail::Value&amp; arg = fd.getArg(i);</a>
+<a name="3424"><span class="lineNum">    3424 </span>            :     uint32_t varType = arg.getTypeId();</a>
+<a name="3425"><span class="lineNum">    3425 </span>            : </a>
+<a name="3426"><span class="lineNum">    3426 </span><span class="lineCov">        420 :     if (arg.byReg()) {</span></a>
+<a name="3427"><span class="lineNum">    3427 </span><span class="lineCov">        420 :       _context-&gt;emitImmToReg(varType, arg.getRegId(), &amp;imm);</span></a>
+<a name="3428"><span class="lineNum">    3428 </span>            :     }</a>
+<a name="3429"><span class="lineNum">    3429 </span>            :     else {</a>
+<a name="3430"><span class="lineNum">    3430 </span><span class="lineNoCov">          0 :       X86Mem dst = x86::ptr(_context-&gt;_zsp, -static_cast&lt;int&gt;(_context-&gt;getGpSize()) + arg.getStackOffset());</span></a>
+<a name="3431"><span class="lineNum">    3431 </span><span class="lineNoCov">          0 :       _context-&gt;emitImmToStack(varType, &amp;dst, &amp;imm);</span></a>
+<a name="3432"><span class="lineNum">    3432 </span>            :     }</a>
+<a name="3433"><span class="lineNum">    3433 </span>            :   }</a>
+<a name="3434"><span class="lineNum">    3434 </span>            : }</a>
+<a name="3435"><span class="lineNum">    3435 </span>            : </a>
+<a name="3436"><span class="lineNum">    3436 </span>            : // ============================================================================</a>
+<a name="3437"><span class="lineNum">    3437 </span>            : // [asmjit::X86CallAlloc - Duplicate]</a>
+<a name="3438"><span class="lineNum">    3438 </span>            : // ============================================================================</a>
+<a name="3439"><span class="lineNum">    3439 </span>            : </a>
+<a name="3440"><span class="lineNum">    3440 </span>            : template&lt;int C&gt;</a>
+<a name="3441"><span class="lineNum">    3441 </span>            : ASMJIT_INLINE void X86CallAlloc::duplicate() {</a>
+<a name="3442"><span class="lineNum">    3442 </span>            :   TiedReg* tiedArray = getTiedArrayByKind(C);</a>
+<a name="3443"><span class="lineNum">    3443 </span>            :   uint32_t tiedCount = getTiedCountByKind(C);</a>
+<a name="3444"><span class="lineNum">    3444 </span>            : </a>
+<a name="3445"><span class="lineNum">    3445 </span><span class="lineCov">       6394 :   for (uint32_t i = 0; i &lt; tiedCount; i++) {</span></a>
+<a name="3446"><span class="lineNum">    3446 </span><span class="lineCov">       4746 :     TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="3447"><span class="lineNum">    3447 </span><span class="lineCov">       4746 :     if ((tied-&gt;flags &amp; TiedReg::kRReg) == 0) continue;</span></a>
+<a name="3448"><span class="lineNum">    3448 </span>            : </a>
+<a name="3449"><span class="lineNum">    3449 </span><span class="lineCov">       3098 :     uint32_t inRegs = tied-&gt;inRegs;</span></a>
+<a name="3450"><span class="lineNum">    3450 </span><span class="lineCov">       3098 :     if (!inRegs) continue;</span></a>
+<a name="3451"><span class="lineNum">    3451 </span>            : </a>
+<a name="3452"><span class="lineNum">    3452 </span><span class="lineCov">       1450 :     VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="3453"><span class="lineNum">    3453 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="3454"><span class="lineNum">    3454 </span>            : </a>
+<a name="3455"><span class="lineNum">    3455 </span>            :     ASMJIT_ASSERT(physId != Globals::kInvalidRegId);</a>
+<a name="3456"><span class="lineNum">    3456 </span>            : </a>
+<a name="3457"><span class="lineNum">    3457 </span><span class="lineCov">       1450 :     inRegs &amp;= ~Utils::mask(physId);</span></a>
+<a name="3458"><span class="lineNum">    3458 </span><span class="lineCov">       1450 :     if (!inRegs) continue;</span></a>
+<a name="3459"><span class="lineNum">    3459 </span>            : </a>
+<a name="3460"><span class="lineNum">    3460 </span><span class="lineNoCov">          0 :     for (uint32_t dupIndex = 0; inRegs != 0; dupIndex++, inRegs &gt;&gt;= 1) {</span></a>
+<a name="3461"><span class="lineNum">    3461 </span><span class="lineNoCov">          0 :       if (inRegs &amp; 0x1) {</span></a>
+<a name="3462"><span class="lineNum">    3462 </span><span class="lineNoCov">          0 :         _context-&gt;emitMove(vreg, dupIndex, physId, &quot;Duplicate&quot;);</span></a>
+<a name="3463"><span class="lineNum">    3463 </span><span class="lineNoCov">          0 :         _context-&gt;_clobberedRegs.or_(C, Utils::mask(dupIndex));</span></a>
+<a name="3464"><span class="lineNum">    3464 </span>            :       }</a>
+<a name="3465"><span class="lineNum">    3465 </span>            :     }</a>
+<a name="3466"><span class="lineNum">    3466 </span>            :   }</a>
+<a name="3467"><span class="lineNum">    3467 </span>            : }</a>
+<a name="3468"><span class="lineNum">    3468 </span>            : </a>
+<a name="3469"><span class="lineNum">    3469 </span>            : // ============================================================================</a>
+<a name="3470"><span class="lineNum">    3470 </span>            : // [asmjit::X86CallAlloc - GuessAlloc / GuessSpill]</a>
+<a name="3471"><span class="lineNum">    3471 </span>            : // ============================================================================</a>
+<a name="3472"><span class="lineNum">    3472 </span>            : </a>
+<a name="3473"><span class="lineNum">    3473 </span>            : template&lt;int C&gt;</a>
+<a name="3474"><span class="lineNum">    3474 </span>            : ASMJIT_INLINE uint32_t X86CallAlloc::guessAlloc(VirtReg* vreg, uint32_t allocableRegs) {</a>
+<a name="3475"><span class="lineNum">    3475 </span>            :   ASMJIT_ASSERT(allocableRegs != 0);</a>
+<a name="3476"><span class="lineNum">    3476 </span>            : </a>
+<a name="3477"><span class="lineNum">    3477 </span>            :   // Stop now if there is only one bit (register) set in 'allocableRegs' mask.</a>
+<a name="3478"><span class="lineNum">    3478 </span>            :   if (Utils::isPowerOf2(allocableRegs))</a>
+<a name="3479"><span class="lineNum">    3479 </span>            :     return allocableRegs;</a>
+<a name="3480"><span class="lineNum">    3480 </span>            : </a>
+<a name="3481"><span class="lineNum">    3481 </span>            :   uint32_t i;</a>
+<a name="3482"><span class="lineNum">    3482 </span>            :   uint32_t safeRegs = allocableRegs;</a>
+<a name="3483"><span class="lineNum">    3483 </span>            :   uint32_t maxLookAhead = kCompilerDefaultLookAhead;</a>
+<a name="3484"><span class="lineNum">    3484 </span>            : </a>
+<a name="3485"><span class="lineNum">    3485 </span>            :   // Look ahead and calculate mask of special registers on both - input/output.</a>
+<a name="3486"><span class="lineNum">    3486 </span><span class="lineNoCov">          0 :   CBNode* node = _node;</span></a>
+<a name="3487"><span class="lineNum">    3487 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; maxLookAhead; i++) {</span></a>
+<a name="3488"><span class="lineNum">    3488 </span>            :     // Stop on `CCFuncRet` and `CBSentinel`.</a>
+<a name="3489"><span class="lineNum">    3489 </span><span class="lineNoCov">          0 :     if (node-&gt;hasFlag(CBNode::kFlagIsRet))</span></a>
+<a name="3490"><span class="lineNum">    3490 </span>            :       break;</a>
+<a name="3491"><span class="lineNum">    3491 </span>            : </a>
+<a name="3492"><span class="lineNum">    3492 </span>            :     // Stop on conditional jump, we don't follow them.</a>
+<a name="3493"><span class="lineNum">    3493 </span><span class="lineNoCov">          0 :     if (node-&gt;hasFlag(CBNode::kFlagIsJcc))</span></a>
+<a name="3494"><span class="lineNum">    3494 </span>            :       break;</a>
+<a name="3495"><span class="lineNum">    3495 </span>            : </a>
+<a name="3496"><span class="lineNum">    3496 </span>            :     // Advance on non-conditional jump.</a>
+<a name="3497"><span class="lineNum">    3497 </span><span class="lineNoCov">          0 :     if (node-&gt;hasFlag(CBNode::kFlagIsJmp)) {</span></a>
+<a name="3498"><span class="lineNum">    3498 </span>            :       node = static_cast&lt;CBJump*&gt;(node)-&gt;getTarget();</a>
+<a name="3499"><span class="lineNum">    3499 </span>            :       // Stop on jump that is not followed.</a>
+<a name="3500"><span class="lineNum">    3500 </span><span class="lineNoCov">          0 :       if (!node) break;</span></a>
+<a name="3501"><span class="lineNum">    3501 </span>            :     }</a>
+<a name="3502"><span class="lineNum">    3502 </span>            : </a>
+<a name="3503"><span class="lineNum">    3503 </span>            :     node = node-&gt;getNext();</a>
+<a name="3504"><span class="lineNum">    3504 </span>            :     ASMJIT_ASSERT(node != nullptr);</a>
+<a name="3505"><span class="lineNum">    3505 </span>            : </a>
+<a name="3506"><span class="lineNum">    3506 </span>            :     X86RAData* raData = node-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="3507"><span class="lineNum">    3507 </span><span class="lineNoCov">          0 :     if (raData) {</span></a>
+<a name="3508"><span class="lineNum">    3508 </span>            :       TiedReg* tied = raData-&gt;findTiedByKind(C, vreg);</a>
+<a name="3509"><span class="lineNum">    3509 </span><span class="lineNoCov">          0 :       if (tied) {</span></a>
+<a name="3510"><span class="lineNum">    3510 </span><span class="lineNoCov">          0 :         uint32_t inRegs = tied-&gt;inRegs;</span></a>
+<a name="3511"><span class="lineNum">    3511 </span><span class="lineNoCov">          0 :         if (inRegs != 0) {</span></a>
+<a name="3512"><span class="lineNum">    3512 </span>            :           safeRegs = allocableRegs;</a>
+<a name="3513"><span class="lineNum">    3513 </span><span class="lineNoCov">          0 :           allocableRegs &amp;= inRegs;</span></a>
+<a name="3514"><span class="lineNum">    3514 </span>            : </a>
+<a name="3515"><span class="lineNum">    3515 </span><span class="lineNoCov">          0 :           if (allocableRegs == 0)</span></a>
+<a name="3516"><span class="lineNum">    3516 </span><span class="lineNoCov">          0 :             goto _UseSafeRegs;</span></a>
+<a name="3517"><span class="lineNum">    3517 </span>            :           else</a>
+<a name="3518"><span class="lineNum">    3518 </span>            :             return allocableRegs;</a>
+<a name="3519"><span class="lineNum">    3519 </span>            :         }</a>
+<a name="3520"><span class="lineNum">    3520 </span>            :       }</a>
+<a name="3521"><span class="lineNum">    3521 </span>            : </a>
+<a name="3522"><span class="lineNum">    3522 </span>            :       safeRegs = allocableRegs;</a>
+<a name="3523"><span class="lineNum">    3523 </span><span class="lineNoCov">          0 :       allocableRegs &amp;= ~(raData-&gt;inRegs.get(C) | raData-&gt;outRegs.get(C) | raData-&gt;clobberedRegs.get(C));</span></a>
+<a name="3524"><span class="lineNum">    3524 </span>            : </a>
+<a name="3525"><span class="lineNum">    3525 </span><span class="lineNoCov">          0 :       if (allocableRegs == 0)</span></a>
+<a name="3526"><span class="lineNum">    3526 </span>            :         break;</a>
+<a name="3527"><span class="lineNum">    3527 </span>            :     }</a>
+<a name="3528"><span class="lineNum">    3528 </span>            :   }</a>
+<a name="3529"><span class="lineNum">    3529 </span>            : </a>
+<a name="3530"><span class="lineNum">    3530 </span><span class="lineNoCov">          0 : _UseSafeRegs:</span></a>
+<a name="3531"><span class="lineNum">    3531 </span>            :   return safeRegs;</a>
+<a name="3532"><span class="lineNum">    3532 </span>            : }</a>
+<a name="3533"><span class="lineNum">    3533 </span>            : </a>
+<a name="3534"><span class="lineNum">    3534 </span>            : template&lt;int C&gt;</a>
+<a name="3535"><span class="lineNum">    3535 </span>            : ASMJIT_INLINE uint32_t X86CallAlloc::guessSpill(VirtReg* vreg, uint32_t allocableRegs) {</a>
+<a name="3536"><span class="lineNum">    3536 </span>            :   ASMJIT_ASSERT(allocableRegs != 0);</a>
+<a name="3537"><span class="lineNum">    3537 </span>            :   return 0;</a>
+<a name="3538"><span class="lineNum">    3538 </span>            : }</a>
+<a name="3539"><span class="lineNum">    3539 </span>            : </a>
+<a name="3540"><span class="lineNum">    3540 </span>            : // ============================================================================</a>
+<a name="3541"><span class="lineNum">    3541 </span>            : // [asmjit::X86CallAlloc - Save]</a>
+<a name="3542"><span class="lineNum">    3542 </span>            : // ============================================================================</a>
+<a name="3543"><span class="lineNum">    3543 </span>            : </a>
+<a name="3544"><span class="lineNum">    3544 </span>            : template&lt;int C&gt;</a>
+<a name="3545"><span class="lineNum">    3545 </span>            : ASMJIT_INLINE void X86CallAlloc::save() {</a>
+<a name="3546"><span class="lineNum">    3546 </span>            :   X86RAState* state = getState();</a>
+<a name="3547"><span class="lineNum">    3547 </span>            :   VirtReg** sVars = state-&gt;getListByKind(C);</a>
+<a name="3548"><span class="lineNum">    3548 </span>            : </a>
+<a name="3549"><span class="lineNum">    3549 </span>            :   uint32_t i;</a>
+<a name="3550"><span class="lineNum">    3550 </span><span class="lineCov">       4944 :   uint32_t affected = _raData-&gt;clobberedRegs.get(C) &amp; state-&gt;_occupied.get(C) &amp; state-&gt;_modified.get(C);</span></a>
+<a name="3551"><span class="lineNum">    3551 </span>            : </a>
+<a name="3552"><span class="lineNum">    3552 </span><span class="lineCov">       6460 :   for (i = 0; affected != 0; i++, affected &gt;&gt;= 1) {</span></a>
+<a name="3553"><span class="lineNum">    3553 </span><span class="lineCov">       4812 :     if (affected &amp; 0x1) {</span></a>
+<a name="3554"><span class="lineNum">    3554 </span><span class="lineCov">       3940 :       VirtReg* vreg = sVars[i];</span></a>
+<a name="3555"><span class="lineNum">    3555 </span>            :       ASMJIT_ASSERT(vreg != nullptr);</a>
+<a name="3556"><span class="lineNum">    3556 </span>            :       ASMJIT_ASSERT(vreg-&gt;isModified());</a>
+<a name="3557"><span class="lineNum">    3557 </span>            : </a>
+<a name="3558"><span class="lineNum">    3558 </span><span class="lineCov">       3940 :       TiedReg* tied = vreg-&gt;_tied;</span></a>
+<a name="3559"><span class="lineNum">    3559 </span><span class="lineCov">       3940 :       if (!tied || (tied-&gt;flags &amp; (TiedReg::kWReg | TiedReg::kUnuse)) == 0)</span></a>
+<a name="3560"><span class="lineNum">    3560 </span><span class="lineCov">       3468 :         _context-&gt;save&lt;C&gt;(vreg);</span></a>
+<a name="3561"><span class="lineNum">    3561 </span>            :     }</a>
+<a name="3562"><span class="lineNum">    3562 </span>            :   }</a>
+<a name="3563"><span class="lineNum">    3563 </span>            : }</a>
+<a name="3564"><span class="lineNum">    3564 </span>            : </a>
+<a name="3565"><span class="lineNum">    3565 </span>            : // ============================================================================</a>
+<a name="3566"><span class="lineNum">    3566 </span>            : // [asmjit::X86CallAlloc - Clobber]</a>
+<a name="3567"><span class="lineNum">    3567 </span>            : // ============================================================================</a>
+<a name="3568"><span class="lineNum">    3568 </span>            : </a>
+<a name="3569"><span class="lineNum">    3569 </span>            : template&lt;int C&gt;</a>
+<a name="3570"><span class="lineNum">    3570 </span>            : ASMJIT_INLINE void X86CallAlloc::clobber() {</a>
+<a name="3571"><span class="lineNum">    3571 </span>            :   X86RAState* state = getState();</a>
+<a name="3572"><span class="lineNum">    3572 </span>            :   VirtReg** sVars = state-&gt;getListByKind(C);</a>
+<a name="3573"><span class="lineNum">    3573 </span>            : </a>
+<a name="3574"><span class="lineNum">    3574 </span>            :   uint32_t i;</a>
+<a name="3575"><span class="lineNum">    3575 </span><span class="lineCov">       4944 :   uint32_t affected = _raData-&gt;clobberedRegs.get(C) &amp; state-&gt;_occupied.get(C);</span></a>
+<a name="3576"><span class="lineNum">    3576 </span>            : </a>
+<a name="3577"><span class="lineNum">    3577 </span><span class="lineCov">       6886 :   for (i = 0; affected != 0; i++, affected &gt;&gt;= 1) {</span></a>
+<a name="3578"><span class="lineNum">    3578 </span><span class="lineCov">       5238 :     if (affected &amp; 0x1) {</span></a>
+<a name="3579"><span class="lineNum">    3579 </span><span class="lineCov">       4834 :       VirtReg* vreg = sVars[i];</span></a>
+<a name="3580"><span class="lineNum">    3580 </span>            :       ASMJIT_ASSERT(vreg != nullptr);</a>
+<a name="3581"><span class="lineNum">    3581 </span>            : </a>
+<a name="3582"><span class="lineNum">    3582 </span><span class="lineCov">       4834 :       TiedReg* tied = vreg-&gt;_tied;</span></a>
+<a name="3583"><span class="lineNum">    3583 </span>            :       uint32_t vdState = VirtReg::kStateNone;</a>
+<a name="3584"><span class="lineNum">    3584 </span>            : </a>
+<a name="3585"><span class="lineNum">    3585 </span><span class="lineCov">       4834 :       if (!vreg-&gt;isModified() || (tied &amp;&amp; (tied-&gt;flags &amp; (TiedReg::kWAll | TiedReg::kUnuse)) != 0))</span></a>
+<a name="3586"><span class="lineNum">    3586 </span>            :         vdState = VirtReg::kStateMem;</a>
+<a name="3587"><span class="lineNum">    3587 </span><span class="lineCov">       4834 :       _context-&gt;unuse&lt;C&gt;(vreg, vdState);</span></a>
+<a name="3588"><span class="lineNum">    3588 </span>            :     }</a>
+<a name="3589"><span class="lineNum">    3589 </span>            :   }</a>
+<a name="3590"><span class="lineNum">    3590 </span>            : }</a>
+<a name="3591"><span class="lineNum">    3591 </span>            : </a>
+<a name="3592"><span class="lineNum">    3592 </span>            : // ============================================================================</a>
+<a name="3593"><span class="lineNum">    3593 </span>            : // [asmjit::X86CallAlloc - Ret]</a>
+<a name="3594"><span class="lineNum">    3594 </span>            : // ============================================================================</a>
+<a name="3595"><span class="lineNum">    3595 </span>            : </a>
+<a name="3596"><span class="lineNum">    3596 </span>            : ASMJIT_INLINE void X86CallAlloc::ret() {</a>
+<a name="3597"><span class="lineNum">    3597 </span>            :   CCFuncCall* node = getNode();</a>
+<a name="3598"><span class="lineNum">    3598 </span>            :   FuncDetail&amp; fd = node-&gt;getDetail();</a>
+<a name="3599"><span class="lineNum">    3599 </span><span class="lineCov">       1648 :   Operand_* rets = node-&gt;_ret;</span></a>
+<a name="3600"><span class="lineNum">    3600 </span>            : </a>
+<a name="3601"><span class="lineNum">    3601 </span><span class="lineCov">       4944 :   for (uint32_t i = 0; i &lt; 2; i++) {</span></a>
+<a name="3602"><span class="lineNum">    3602 </span><span class="lineCov">       3296 :     const FuncDetail::Value&amp; ret = fd.getRet(i);</span></a>
+<a name="3603"><span class="lineNum">    3603 </span><span class="lineCov">       3296 :     Operand_* op = &amp;rets[i];</span></a>
+<a name="3604"><span class="lineNum">    3604 </span>            : </a>
+<a name="3605"><span class="lineNum">    3605 </span><span class="lineCov">       3296 :     if (!ret.byReg() || !op-&gt;isVirtReg())</span></a>
+<a name="3606"><span class="lineNum">    3606 </span><span class="lineCov">       1648 :       continue;</span></a>
+<a name="3607"><span class="lineNum">    3607 </span>            : </a>
+<a name="3608"><span class="lineNum">    3608 </span><span class="lineCov">       1648 :     VirtReg* vreg = _cc-&gt;getVirtRegById(op-&gt;getId());</span></a>
+<a name="3609"><span class="lineNum">    3609 </span>            :     uint32_t regId = ret.getRegId();</a>
+<a name="3610"><span class="lineNum">    3610 </span>            : </a>
+<a name="3611"><span class="lineNum">    3611 </span><span class="lineCov">       1648 :     switch (vreg-&gt;getKind()) {</span></a>
+<a name="3612"><span class="lineNum">    3612 </span><span class="lineNoCov">          0 :       case X86Reg::kKindGp:</span></a>
+<a name="3613"><span class="lineNum">    3613 </span><span class="lineNoCov">          0 :         _context-&gt;unuse&lt;X86Reg::kKindGp&gt;(vreg);</span></a>
+<a name="3614"><span class="lineNum">    3614 </span><span class="lineNoCov">          0 :         _context-&gt;attach&lt;X86Reg::kKindGp&gt;(vreg, regId, true);</span></a>
+<a name="3615"><span class="lineNum">    3615 </span>            :         break;</a>
+<a name="3616"><span class="lineNum">    3616 </span>            : </a>
+<a name="3617"><span class="lineNum">    3617 </span><span class="lineNoCov">          0 :       case X86Reg::kKindMm:</span></a>
+<a name="3618"><span class="lineNum">    3618 </span><span class="lineNoCov">          0 :         _context-&gt;unuse&lt;X86Reg::kKindMm&gt;(vreg);</span></a>
+<a name="3619"><span class="lineNum">    3619 </span><span class="lineNoCov">          0 :         _context-&gt;attach&lt;X86Reg::kKindMm&gt;(vreg, regId, true);</span></a>
+<a name="3620"><span class="lineNum">    3620 </span>            :         break;</a>
+<a name="3621"><span class="lineNum">    3621 </span>            : </a>
+<a name="3622"><span class="lineNum">    3622 </span>            :       case X86Reg::kKindVec:</a>
+<a name="3623"><span class="lineNum">    3623 </span><span class="lineCov">       1648 :         if (X86Reg::kindOf(ret.getRegType()) == X86Reg::kKindVec) {</span></a>
+<a name="3624"><span class="lineNum">    3624 </span><span class="lineCov">       1648 :           _context-&gt;unuse&lt;X86Reg::kKindVec&gt;(vreg);</span></a>
+<a name="3625"><span class="lineNum">    3625 </span><span class="lineCov">       1648 :           _context-&gt;attach&lt;X86Reg::kKindVec&gt;(vreg, regId, true);</span></a>
+<a name="3626"><span class="lineNum">    3626 </span>            :         }</a>
+<a name="3627"><span class="lineNum">    3627 </span>            :         else {</a>
+<a name="3628"><span class="lineNum">    3628 </span>            :           uint32_t elementId = TypeId::elementOf(vreg-&gt;getTypeId());</a>
+<a name="3629"><span class="lineNum">    3629 </span><span class="lineNoCov">          0 :           uint32_t size = (elementId == TypeId::kF32) ? 4 : 8;</span></a>
+<a name="3630"><span class="lineNum">    3630 </span>            : </a>
+<a name="3631"><span class="lineNum">    3631 </span><span class="lineNoCov">          0 :           X86Mem m = _context-&gt;getVarMem(vreg);</span></a>
+<a name="3632"><span class="lineNum">    3632 </span>            :           m.setSize(size);</a>
+<a name="3633"><span class="lineNum">    3633 </span>            : </a>
+<a name="3634"><span class="lineNum">    3634 </span><span class="lineNoCov">          0 :           _context-&gt;unuse&lt;X86Reg::kKindVec&gt;(vreg, VirtReg::kStateMem);</span></a>
+<a name="3635"><span class="lineNum">    3635 </span><span class="lineNoCov">          0 :           _cc-&gt;fstp(m);</span></a>
+<a name="3636"><span class="lineNum">    3636 </span>            :         }</a>
+<a name="3637"><span class="lineNum">    3637 </span>            :         break;</a>
+<a name="3638"><span class="lineNum">    3638 </span>            :     }</a>
+<a name="3639"><span class="lineNum">    3639 </span>            :   }</a>
+<a name="3640"><span class="lineNum">    3640 </span>            : }</a>
+<a name="3641"><span class="lineNum">    3641 </span>            : </a>
+<a name="3642"><span class="lineNum">    3642 </span>            : // ============================================================================</a>
+<a name="3643"><span class="lineNum">    3643 </span>            : // [asmjit::X86RAPass - TranslateOperands]</a>
+<a name="3644"><span class="lineNum">    3644 </span>            : // ============================================================================</a>
+<a name="3645"><span class="lineNum">    3645 </span>            : </a>
+<a name="3646"><span class="lineNum">    3646 </span>            : //! \internal</a>
+<a name="3647"><span class="lineNum">    3647 </span><span class="lineCov">      32806 : static Error X86RAPass_translateOperands(X86RAPass* self, Operand_* opArray, uint32_t opCount) {</span></a>
+<a name="3648"><span class="lineNum">    3648 </span>            :   X86Compiler* cc = self-&gt;cc();</a>
+<a name="3649"><span class="lineNum">    3649 </span>            : </a>
+<a name="3650"><span class="lineNum">    3650 </span>            :   // Translate variables into registers.</a>
+<a name="3651"><span class="lineNum">    3651 </span><span class="lineCov">      96890 :   for (uint32_t i = 0; i &lt; opCount; i++) {</span></a>
+<a name="3652"><span class="lineNum">    3652 </span><span class="lineCov">      64084 :     Operand_* op = &amp;opArray[i];</span></a>
+<a name="3653"><span class="lineNum">    3653 </span>            :     if (op-&gt;isVirtReg()) {</a>
+<a name="3654"><span class="lineNum">    3654 </span>            :       VirtReg* vreg = cc-&gt;getVirtRegById(op-&gt;getId());</a>
+<a name="3655"><span class="lineNum">    3655 </span>            :       ASMJIT_ASSERT(vreg != nullptr);</a>
+<a name="3656"><span class="lineNum">    3656 </span>            :       ASMJIT_ASSERT(vreg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="3657"><span class="lineNum">    3657 </span><span class="lineCov">      50596 :       op-&gt;_reg.id = vreg-&gt;getPhysId();</span></a>
+<a name="3658"><span class="lineNum">    3658 </span>            :     }</a>
+<a name="3659"><span class="lineNum">    3659 </span><span class="lineCov">      13488 :     else if (op-&gt;isMem()) {</span></a>
+<a name="3660"><span class="lineNum">    3660 </span>            :       X86Mem* m = static_cast&lt;X86Mem*&gt;(op);</a>
+<a name="3661"><span class="lineNum">    3661 </span>            : </a>
+<a name="3662"><span class="lineNum">    3662 </span><span class="lineCov">       6100 :       if (m-&gt;hasBaseReg() &amp;&amp; cc-&gt;isVirtRegValid(m-&gt;getBaseId())) {</span></a>
+<a name="3663"><span class="lineNum">    3663 </span>            :         VirtReg* vreg = cc-&gt;getVirtRegById(m-&gt;getBaseId());</a>
+<a name="3664"><span class="lineNum">    3664 </span>            : </a>
+<a name="3665"><span class="lineNum">    3665 </span><span class="lineCov">       6100 :         if (m-&gt;isRegHome()) {</span></a>
+<a name="3666"><span class="lineNum">    3666 </span><span class="lineNoCov">          0 :           self-&gt;getVarCell(vreg);</span></a>
+<a name="3667"><span class="lineNum">    3667 </span>            :         }</a>
+<a name="3668"><span class="lineNum">    3668 </span>            :         else {</a>
+<a name="3669"><span class="lineNum">    3669 </span>            :           ASMJIT_ASSERT(vreg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="3670"><span class="lineNum">    3670 </span><span class="lineCov">       6100 :           op-&gt;_mem.base = vreg-&gt;getPhysId();</span></a>
+<a name="3671"><span class="lineNum">    3671 </span>            :         }</a>
+<a name="3672"><span class="lineNum">    3672 </span>            :       }</a>
+<a name="3673"><span class="lineNum">    3673 </span>            : </a>
+<a name="3674"><span class="lineNum">    3674 </span><span class="lineCov">       6100 :       if (m-&gt;hasIndexReg() &amp;&amp; cc-&gt;isVirtRegValid(m-&gt;getIndexId())) {</span></a>
+<a name="3675"><span class="lineNum">    3675 </span>            :         VirtReg* vreg = cc-&gt;getVirtRegById(m-&gt;getIndexId());</a>
+<a name="3676"><span class="lineNum">    3676 </span><span class="lineNoCov">          0 :         op-&gt;_mem.index = vreg-&gt;getPhysId();</span></a>
+<a name="3677"><span class="lineNum">    3677 </span>            :       }</a>
+<a name="3678"><span class="lineNum">    3678 </span>            :     }</a>
+<a name="3679"><span class="lineNum">    3679 </span>            :   }</a>
+<a name="3680"><span class="lineNum">    3680 </span>            : </a>
+<a name="3681"><span class="lineNum">    3681 </span><span class="lineCov">      32806 :   return kErrorOk;</span></a>
+<a name="3682"><span class="lineNum">    3682 </span>            : }</a>
+<a name="3683"><span class="lineNum">    3683 </span>            : </a>
+<a name="3684"><span class="lineNum">    3684 </span>            : // ============================================================================</a>
+<a name="3685"><span class="lineNum">    3685 </span>            : // [asmjit::X86RAPass - TranslatePrologEpilog]</a>
+<a name="3686"><span class="lineNum">    3686 </span>            : // ============================================================================</a>
+<a name="3687"><span class="lineNum">    3687 </span>            : </a>
+<a name="3688"><span class="lineNum">    3688 </span>            : //! \internal</a>
+<a name="3689"><span class="lineNum">    3689 </span><span class="lineCov">       1948 : static Error X86RAPass_prepareFuncFrame(X86RAPass* self, CCFunc* func) {</span></a>
+<a name="3690"><span class="lineNum">    3690 </span>            :   FuncFrameInfo&amp; ffi = func-&gt;getFrameInfo();</a>
+<a name="3691"><span class="lineNum">    3691 </span>            : </a>
+<a name="3692"><span class="lineNum">    3692 </span>            :   X86RegMask&amp; clobberedRegs = self-&gt;_clobberedRegs;</a>
+<a name="3693"><span class="lineNum">    3693 </span>            : </a>
+<a name="3694"><span class="lineNum">    3694 </span>            :   // Initialize dirty registers.</a>
+<a name="3695"><span class="lineNum">    3695 </span>            :   ffi.setDirtyRegs(X86Reg::kKindGp , clobberedRegs.get(X86Reg::kKindGp ));</a>
+<a name="3696"><span class="lineNum">    3696 </span>            :   ffi.setDirtyRegs(X86Reg::kKindMm , clobberedRegs.get(X86Reg::kKindMm ));</a>
+<a name="3697"><span class="lineNum">    3697 </span>            :   ffi.setDirtyRegs(X86Reg::kKindK  , clobberedRegs.get(X86Reg::kKindK  ));</a>
+<a name="3698"><span class="lineNum">    3698 </span>            :   ffi.setDirtyRegs(X86Reg::kKindVec, clobberedRegs.get(X86Reg::kKindVec));</a>
+<a name="3699"><span class="lineNum">    3699 </span>            : </a>
+<a name="3700"><span class="lineNum">    3700 </span>            :   // Initialize stack size &amp; alignment.</a>
+<a name="3701"><span class="lineNum">    3701 </span><span class="lineCov">       1948 :   ffi.setStackFrameSize(self-&gt;_memAllTotal);</span></a>
+<a name="3702"><span class="lineNum">    3702 </span><span class="lineCov">       1948 :   ffi.setStackFrameAlignment(self-&gt;_memMaxAlign);</span></a>
+<a name="3703"><span class="lineNum">    3703 </span>            : </a>
+<a name="3704"><span class="lineNum">    3704 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="3705"><span class="lineNum">    3705 </span>            : }</a>
+<a name="3706"><span class="lineNum">    3706 </span>            : </a>
+<a name="3707"><span class="lineNum">    3707 </span>            : //! \internal</a>
+<a name="3708"><span class="lineNum">    3708 </span><span class="lineCov">       1948 : static Error X86RAPass_patchFuncMem(X86RAPass* self, CCFunc* func, CBNode* stop, FuncFrameLayout&amp; layout) {</span></a>
+<a name="3709"><span class="lineNum">    3709 </span>            :   X86Compiler* cc = self-&gt;cc();</a>
+<a name="3710"><span class="lineNum">    3710 </span>            :   CBNode* node = func;</a>
+<a name="3711"><span class="lineNum">    3711 </span>            : </a>
+<a name="3712"><span class="lineNum">    3712 </span>            :   do {</a>
+<a name="3713"><span class="lineNum">    3713 </span><span class="lineCov">      50102 :     if (node-&gt;getType() == CBNode::kNodeInst) {</span></a>
+<a name="3714"><span class="lineNum">    3714 </span>            :       CBInst* iNode = static_cast&lt;CBInst*&gt;(node);</a>
+<a name="3715"><span class="lineNum">    3715 </span>            : </a>
+<a name="3716"><span class="lineNum">    3716 </span><span class="lineCov">      40662 :       if (iNode-&gt;hasMemOp()) {</span></a>
+<a name="3717"><span class="lineNum">    3717 </span>            :         X86Mem* m = iNode-&gt;getMemOp&lt;X86Mem&gt;();</a>
+<a name="3718"><span class="lineNum">    3718 </span>            : </a>
+<a name="3719"><span class="lineNum">    3719 </span><span class="lineCov">      14528 :         if (m-&gt;isArgHome()) {</span></a>
+<a name="3720"><span class="lineNum">    3720 </span>            :           m-&gt;addOffsetLo32(layout.getStackArgsOffset());</a>
+<a name="3721"><span class="lineNum">    3721 </span>            :           m-&gt;clearArgHome();</a>
+<a name="3722"><span class="lineNum">    3722 </span>            :         }</a>
+<a name="3723"><span class="lineNum">    3723 </span>            : </a>
+<a name="3724"><span class="lineNum">    3724 </span><span class="lineCov">      14528 :         if (m-&gt;isRegHome() &amp;&amp; Operand::isPackedId(m-&gt;getBaseId())) {</span></a>
+<a name="3725"><span class="lineNum">    3725 </span>            :           VirtReg* vreg = cc-&gt;getVirtRegById(m-&gt;getBaseId());</a>
+<a name="3726"><span class="lineNum">    3726 </span>            :           ASMJIT_ASSERT(vreg != nullptr);</a>
+<a name="3727"><span class="lineNum">    3727 </span>            : </a>
+<a name="3728"><span class="lineNum">    3728 </span>            :           RACell* cell = vreg-&gt;getMemCell();</a>
+<a name="3729"><span class="lineNum">    3729 </span>            :           ASMJIT_ASSERT(cell != nullptr);</a>
+<a name="3730"><span class="lineNum">    3730 </span>            : </a>
+<a name="3731"><span class="lineNum">    3731 </span><span class="lineCov">       8428 :           m-&gt;_setBase(cc-&gt;_nativeGpReg.getType(), self-&gt;_varBaseRegId);</span></a>
+<a name="3732"><span class="lineNum">    3732 </span><span class="lineCov">       8428 :           m-&gt;addOffsetLo32(self-&gt;_varBaseOffset + cell-&gt;offset);</span></a>
+<a name="3733"><span class="lineNum">    3733 </span>            :           m-&gt;clearRegHome();</a>
+<a name="3734"><span class="lineNum">    3734 </span>            :         }</a>
+<a name="3735"><span class="lineNum">    3735 </span>            :       }</a>
+<a name="3736"><span class="lineNum">    3736 </span>            :     }</a>
+<a name="3737"><span class="lineNum">    3737 </span>            : </a>
+<a name="3738"><span class="lineNum">    3738 </span>            :     node = node-&gt;getNext();</a>
+<a name="3739"><span class="lineNum">    3739 </span><span class="lineCov">      50102 :   } while (node != stop);</span></a>
+<a name="3740"><span class="lineNum">    3740 </span>            : </a>
+<a name="3741"><span class="lineNum">    3741 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="3742"><span class="lineNum">    3742 </span>            : }</a>
+<a name="3743"><span class="lineNum">    3743 </span>            : </a>
+<a name="3744"><span class="lineNum">    3744 </span>            : // ============================================================================</a>
+<a name="3745"><span class="lineNum">    3745 </span>            : // [asmjit::X86RAPass - Translate - Jump]</a>
+<a name="3746"><span class="lineNum">    3746 </span>            : // ============================================================================</a>
+<a name="3747"><span class="lineNum">    3747 </span>            : </a>
+<a name="3748"><span class="lineNum">    3748 </span>            : //! \internal</a>
+<a name="3749"><span class="lineNum">    3749 </span><span class="lineNoCov">          0 : static void X86RAPass_translateJump(X86RAPass* self, CBJump* jNode, CBLabel* jTarget) {</span></a>
+<a name="3750"><span class="lineNum">    3750 </span>            :   X86Compiler* cc = self-&gt;cc();</a>
+<a name="3751"><span class="lineNum">    3751 </span>            : </a>
+<a name="3752"><span class="lineNum">    3752 </span>            :   CBNode* injectRef = self-&gt;getFunc()-&gt;getEnd()-&gt;getPrev();</a>
+<a name="3753"><span class="lineNum">    3753 </span><span class="lineNoCov">          0 :   CBNode* prevCursor = cc-&gt;setCursor(injectRef);</span></a>
+<a name="3754"><span class="lineNum">    3754 </span>            : </a>
+<a name="3755"><span class="lineNum">    3755 </span><span class="lineNoCov">          0 :   self-&gt;switchState(jTarget-&gt;getPassData&lt;RAData&gt;()-&gt;state);</span></a>
+<a name="3756"><span class="lineNum">    3756 </span>            : </a>
+<a name="3757"><span class="lineNum">    3757 </span>            :   // Any code necessary to `switchState()` will be added at the end of the function.</a>
+<a name="3758"><span class="lineNum">    3758 </span><span class="lineNoCov">          0 :   if (cc-&gt;getCursor() != injectRef) {</span></a>
+<a name="3759"><span class="lineNum">    3759 </span>            :     // TODO: Can fail.</a>
+<a name="3760"><span class="lineNum">    3760 </span><span class="lineNoCov">          0 :     CBLabel* injectLabel = cc-&gt;newLabelNode();</span></a>
+<a name="3761"><span class="lineNum">    3761 </span>            : </a>
+<a name="3762"><span class="lineNum">    3762 </span>            :     // Add the jump to the target.</a>
+<a name="3763"><span class="lineNum">    3763 </span><span class="lineNoCov">          0 :     cc-&gt;jmp(jTarget-&gt;getLabel());</span></a>
+<a name="3764"><span class="lineNum">    3764 </span>            : </a>
+<a name="3765"><span class="lineNum">    3765 </span>            :     // Inject the label.</a>
+<a name="3766"><span class="lineNum">    3766 </span>            :     cc-&gt;_setCursor(injectRef);</a>
+<a name="3767"><span class="lineNum">    3767 </span><span class="lineNoCov">          0 :     cc-&gt;addNode(injectLabel);</span></a>
+<a name="3768"><span class="lineNum">    3768 </span>            : </a>
+<a name="3769"><span class="lineNum">    3769 </span>            :     // Finally, patch `jNode` target.</a>
+<a name="3770"><span class="lineNum">    3770 </span>            :     ASMJIT_ASSERT(jNode-&gt;getOpCount() &gt; 0);</a>
+<a name="3771"><span class="lineNum">    3771 </span><span class="lineNoCov">          0 :     jNode-&gt;_opArray[jNode-&gt;getOpCount() - 1] = injectLabel-&gt;getLabel();</span></a>
+<a name="3772"><span class="lineNum">    3772 </span><span class="lineNoCov">          0 :     jNode-&gt;_target = injectLabel;</span></a>
+<a name="3773"><span class="lineNum">    3773 </span>            :     // If we injected any code it may not satisfy short form anymore.</a>
+<a name="3774"><span class="lineNum">    3774 </span>            :     jNode-&gt;delOptions(X86Inst::kOptionShortForm);</a>
+<a name="3775"><span class="lineNum">    3775 </span>            :   }</a>
+<a name="3776"><span class="lineNum">    3776 </span>            : </a>
+<a name="3777"><span class="lineNum">    3777 </span>            :   cc-&gt;_setCursor(prevCursor);</a>
+<a name="3778"><span class="lineNum">    3778 </span><span class="lineNoCov">          0 :   self-&gt;loadState(jNode-&gt;getPassData&lt;RAData&gt;()-&gt;state);</span></a>
+<a name="3779"><span class="lineNum">    3779 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="3780"><span class="lineNum">    3780 </span>            : </a>
+<a name="3781"><span class="lineNum">    3781 </span>            : // ============================================================================</a>
+<a name="3782"><span class="lineNum">    3782 </span>            : // [asmjit::X86RAPass - Translate - Ret]</a>
+<a name="3783"><span class="lineNum">    3783 </span>            : // ============================================================================</a>
+<a name="3784"><span class="lineNum">    3784 </span>            : </a>
+<a name="3785"><span class="lineNum">    3785 </span><span class="lineCov">       1948 : static Error X86RAPass_translateRet(X86RAPass* self, CCFuncRet* rNode, CBLabel* exitTarget) {</span></a>
+<a name="3786"><span class="lineNum">    3786 </span>            :   X86Compiler* cc = self-&gt;cc();</a>
+<a name="3787"><span class="lineNum">    3787 </span>            :   CBNode* node = rNode-&gt;getNext();</a>
+<a name="3788"><span class="lineNum">    3788 </span>            : </a>
+<a name="3789"><span class="lineNum">    3789 </span>            :   // 32-bit mode requires to push floating point return value(s), handle it</a>
+<a name="3790"><span class="lineNum">    3790 </span>            :   // here as it's a special case.</a>
+<a name="3791"><span class="lineNum">    3791 </span>            :   X86RAData* raData = rNode-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="3792"><span class="lineNum">    3792 </span><span class="lineCov">       1948 :   if (raData) {</span></a>
+<a name="3793"><span class="lineNum">    3793 </span><span class="lineCov">       1948 :     TiedReg* tiedArray = raData-&gt;tiedArray;</span></a>
+<a name="3794"><span class="lineNum">    3794 </span><span class="lineCov">       1948 :     uint32_t tiedTotal = raData-&gt;tiedTotal;</span></a>
+<a name="3795"><span class="lineNum">    3795 </span>            : </a>
+<a name="3796"><span class="lineNum">    3796 </span><span class="lineCov">       3896 :     for (uint32_t i = 0; i &lt; tiedTotal; i++) {</span></a>
+<a name="3797"><span class="lineNum">    3797 </span><span class="lineCov">       1948 :       TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="3798"><span class="lineNum">    3798 </span><span class="lineCov">       1948 :       if (tied-&gt;flags &amp; (TiedReg::kX86Fld4 | TiedReg::kX86Fld8)) {</span></a>
+<a name="3799"><span class="lineNum">    3799 </span><span class="lineNoCov">          0 :         VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="3800"><span class="lineNum">    3800 </span>            :         X86Mem m(self-&gt;getVarMem(vreg));</a>
+<a name="3801"><span class="lineNum">    3801 </span>            : </a>
+<a name="3802"><span class="lineNum">    3802 </span>            :         uint32_t elementId = TypeId::elementOf(vreg-&gt;getTypeId());</a>
+<a name="3803"><span class="lineNum">    3803 </span><span class="lineNoCov">          0 :         m.setSize(elementId == TypeId::kF32 ? 4 :</span></a>
+<a name="3804"><span class="lineNum">    3804 </span>            :                   elementId == TypeId::kF64 ? 8 :</a>
+<a name="3805"><span class="lineNum">    3805 </span><span class="lineNoCov">          0 :                   (tied-&gt;flags &amp; TiedReg::kX86Fld4) ? 4 : 8);</span></a>
+<a name="3806"><span class="lineNum">    3806 </span>            : </a>
+<a name="3807"><span class="lineNum">    3807 </span>            :         cc-&gt;fld(m);</a>
+<a name="3808"><span class="lineNum">    3808 </span>            :       }</a>
+<a name="3809"><span class="lineNum">    3809 </span>            :     }</a>
+<a name="3810"><span class="lineNum">    3810 </span>            :   }</a>
+<a name="3811"><span class="lineNum">    3811 </span>            : </a>
+<a name="3812"><span class="lineNum">    3812 </span>            :   // Decide whether to `jmp` or not in case we are next to the return label.</a>
+<a name="3813"><span class="lineNum">    3813 </span><span class="lineCov">       1948 :   while (node) {</span></a>
+<a name="3814"><span class="lineNum">    3814 </span><span class="lineCov">       1948 :     switch (node-&gt;getType()) {</span></a>
+<a name="3815"><span class="lineNum">    3815 </span>            :       // If we have found an exit label we just return, there is no need to</a>
+<a name="3816"><span class="lineNum">    3816 </span>            :       // emit jump to that.</a>
+<a name="3817"><span class="lineNum">    3817 </span><span class="lineCov">       1948 :       case CBNode::kNodeLabel:</span></a>
+<a name="3818"><span class="lineNum">    3818 </span><span class="lineCov">       1948 :         if (static_cast&lt;CBLabel*&gt;(node) == exitTarget)</span></a>
+<a name="3819"><span class="lineNum">    3819 </span>            :           return kErrorOk;</a>
+<a name="3820"><span class="lineNum">    3820 </span><span class="lineNoCov">          0 :         goto _EmitRet;</span></a>
+<a name="3821"><span class="lineNum">    3821 </span>            : </a>
+<a name="3822"><span class="lineNum">    3822 </span><span class="lineNoCov">          0 :       case CBNode::kNodeData:</span></a>
+<a name="3823"><span class="lineNum">    3823 </span>            :       case CBNode::kNodeInst:</a>
+<a name="3824"><span class="lineNum">    3824 </span>            :       case CBNode::kNodeFuncCall:</a>
+<a name="3825"><span class="lineNum">    3825 </span>            :       case CBNode::kNodeFuncExit:</a>
+<a name="3826"><span class="lineNum">    3826 </span><span class="lineNoCov">          0 :         goto _EmitRet;</span></a>
+<a name="3827"><span class="lineNum">    3827 </span>            : </a>
+<a name="3828"><span class="lineNum">    3828 </span>            :       // Continue iterating.</a>
+<a name="3829"><span class="lineNum">    3829 </span>            :       case CBNode::kNodeComment:</a>
+<a name="3830"><span class="lineNum">    3830 </span>            :       case CBNode::kNodeAlign:</a>
+<a name="3831"><span class="lineNum">    3831 </span>            :       case CBNode::kNodeHint:</a>
+<a name="3832"><span class="lineNum">    3832 </span>            :         break;</a>
+<a name="3833"><span class="lineNum">    3833 </span>            : </a>
+<a name="3834"><span class="lineNum">    3834 </span>            :       // Invalid node to be here.</a>
+<a name="3835"><span class="lineNum">    3835 </span>            :       case CBNode::kNodeFunc:</a>
+<a name="3836"><span class="lineNum">    3836 </span>            :         return DebugUtils::errored(kErrorInvalidState);</a>
+<a name="3837"><span class="lineNum">    3837 </span>            : </a>
+<a name="3838"><span class="lineNum">    3838 </span>            :       // We can't go forward from here.</a>
+<a name="3839"><span class="lineNum">    3839 </span><span class="lineNoCov">          0 :       case CBNode::kNodeSentinel:</span></a>
+<a name="3840"><span class="lineNum">    3840 </span><span class="lineNoCov">          0 :         return kErrorOk;</span></a>
+<a name="3841"><span class="lineNum">    3841 </span>            :     }</a>
+<a name="3842"><span class="lineNum">    3842 </span>            : </a>
+<a name="3843"><span class="lineNum">    3843 </span>            :     node = node-&gt;getNext();</a>
+<a name="3844"><span class="lineNum">    3844 </span>            :   }</a>
+<a name="3845"><span class="lineNum">    3845 </span>            : </a>
+<a name="3846"><span class="lineNum">    3846 </span><span class="lineNoCov">          0 : _EmitRet:</span></a>
+<a name="3847"><span class="lineNum">    3847 </span>            :   {</a>
+<a name="3848"><span class="lineNum">    3848 </span>            :     cc-&gt;_setCursor(rNode);</a>
+<a name="3849"><span class="lineNum">    3849 </span><span class="lineNoCov">          0 :     cc-&gt;jmp(exitTarget-&gt;getLabel());</span></a>
+<a name="3850"><span class="lineNum">    3850 </span>            :   }</a>
+<a name="3851"><span class="lineNum">    3851 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="3852"><span class="lineNum">    3852 </span>            : }</a>
+<a name="3853"><span class="lineNum">    3853 </span>            : </a>
+<a name="3854"><span class="lineNum">    3854 </span>            : // ============================================================================</a>
+<a name="3855"><span class="lineNum">    3855 </span>            : // [asmjit::X86RAPass - Translate - Func]</a>
+<a name="3856"><span class="lineNum">    3856 </span>            : // ============================================================================</a>
+<a name="3857"><span class="lineNum">    3857 </span>            : </a>
+<a name="3858"><span class="lineNum">    3858 </span><span class="lineCov">       1948 : Error X86RAPass::translate() {</span></a>
+<a name="3859"><span class="lineNum">    3859 </span>            :   X86Compiler* cc = this-&gt;cc();</a>
+<a name="3860"><span class="lineNum">    3860 </span>            :   CCFunc* func = getFunc();</a>
+<a name="3861"><span class="lineNum">    3861 </span>            : </a>
+<a name="3862"><span class="lineNum">    3862 </span>            :   // Register allocator contexts.</a>
+<a name="3863"><span class="lineNum">    3863 </span>            :   X86VarAlloc vAlloc(this);</a>
+<a name="3864"><span class="lineNum">    3864 </span>            :   X86CallAlloc cAlloc(this);</a>
+<a name="3865"><span class="lineNum">    3865 </span>            : </a>
+<a name="3866"><span class="lineNum">    3866 </span>            :   // Flow.</a>
+<a name="3867"><span class="lineNum">    3867 </span>            :   CBNode* node_ = func;</a>
+<a name="3868"><span class="lineNum">    3868 </span>            :   CBNode* next = nullptr;</a>
+<a name="3869"><span class="lineNum">    3869 </span>            :   CBNode* stop = getStop();</a>
+<a name="3870"><span class="lineNum">    3870 </span>            : </a>
+<a name="3871"><span class="lineNum">    3871 </span>            :   ZoneList&lt;CBNode*&gt;::Link* jLink = _jccList.getFirst();</a>
+<a name="3872"><span class="lineNum">    3872 </span>            : </a>
+<a name="3873"><span class="lineNum">    3873 </span>            :   for (;;) {</a>
+<a name="3874"><span class="lineNum">    3874 </span><span class="lineCov">      36702 :     while (node_-&gt;isTranslated()) {</span></a>
+<a name="3875"><span class="lineNum">    3875 </span>            :       // Switch state if we went to a node that is already translated.</a>
+<a name="3876"><span class="lineNum">    3876 </span><span class="lineNoCov">          0 :       if (node_-&gt;getType() == CBNode::kNodeLabel) {</span></a>
+<a name="3877"><span class="lineNum">    3877 </span>            :         CBLabel* node = static_cast&lt;CBLabel*&gt;(node_);</a>
+<a name="3878"><span class="lineNum">    3878 </span>            :         cc-&gt;_setCursor(node-&gt;getPrev());</a>
+<a name="3879"><span class="lineNum">    3879 </span><span class="lineNoCov">          0 :         switchState(node-&gt;getPassData&lt;RAData&gt;()-&gt;state);</span></a>
+<a name="3880"><span class="lineNum">    3880 </span>            :       }</a>
+<a name="3881"><span class="lineNum">    3881 </span>            : </a>
+<a name="3882"><span class="lineNum">    3882 </span><span class="lineNoCov">          0 : _NextGroup:</span></a>
+<a name="3883"><span class="lineNum">    3883 </span><span class="lineCov">       1948 :       if (!jLink) {</span></a>
+<a name="3884"><span class="lineNum">    3884 </span><span class="lineCov">       1948 :         goto _Done;</span></a>
+<a name="3885"><span class="lineNum">    3885 </span>            :       }</a>
+<a name="3886"><span class="lineNum">    3886 </span>            :       else {</a>
+<a name="3887"><span class="lineNum">    3887 </span>            :         node_ = jLink-&gt;getValue();</a>
+<a name="3888"><span class="lineNum">    3888 </span>            :         jLink = jLink-&gt;getNext();</a>
+<a name="3889"><span class="lineNum">    3889 </span>            : </a>
+<a name="3890"><span class="lineNum">    3890 </span>            :         CBNode* jFlow = X86RAPass_getOppositeJccFlow(static_cast&lt;CBJump*&gt;(node_));</a>
+<a name="3891"><span class="lineNum">    3891 </span><span class="lineNoCov">          0 :         loadState(node_-&gt;getPassData&lt;RAData&gt;()-&gt;state);</span></a>
+<a name="3892"><span class="lineNum">    3892 </span>            : </a>
+<a name="3893"><span class="lineNum">    3893 </span><span class="lineNoCov">          0 :         if (jFlow-&gt;hasPassData() &amp;&amp; jFlow-&gt;getPassData&lt;RAData&gt;()-&gt;state) {</span></a>
+<a name="3894"><span class="lineNum">    3894 </span><span class="lineNoCov">          0 :           X86RAPass_translateJump(this, static_cast&lt;CBJump*&gt;(node_), static_cast&lt;CBLabel*&gt;(jFlow));</span></a>
+<a name="3895"><span class="lineNum">    3895 </span>            : </a>
+<a name="3896"><span class="lineNum">    3896 </span>            :           node_ = jFlow;</a>
+<a name="3897"><span class="lineNum">    3897 </span><span class="lineNoCov">          0 :           if (node_-&gt;isTranslated())</span></a>
+<a name="3898"><span class="lineNum">    3898 </span><span class="lineNoCov">          0 :             goto _NextGroup;</span></a>
+<a name="3899"><span class="lineNum">    3899 </span>            :         }</a>
+<a name="3900"><span class="lineNum">    3900 </span>            :         else {</a>
+<a name="3901"><span class="lineNum">    3901 </span>            :           node_ = jFlow;</a>
+<a name="3902"><span class="lineNum">    3902 </span>            :         }</a>
+<a name="3903"><span class="lineNum">    3903 </span>            : </a>
+<a name="3904"><span class="lineNum">    3904 </span>            :         break;</a>
+<a name="3905"><span class="lineNum">    3905 </span>            :       }</a>
+<a name="3906"><span class="lineNum">    3906 </span>            :     }</a>
+<a name="3907"><span class="lineNum">    3907 </span>            : </a>
+<a name="3908"><span class="lineNum">    3908 </span>            :     next = node_-&gt;getNext();</a>
+<a name="3909"><span class="lineNum">    3909 </span><span class="lineCov">      36702 :     node_-&gt;_flags |= CBNode::kFlagIsTranslated;</span></a>
+<a name="3910"><span class="lineNum">    3910 </span>            : </a>
+<a name="3911"><span class="lineNum">    3911 </span><span class="lineCov">      36702 :     if (node_-&gt;hasPassData()) {</span></a>
+<a name="3912"><span class="lineNum">    3912 </span><span class="lineCov">      36702 :       switch (node_-&gt;getType()) {</span></a>
+<a name="3913"><span class="lineNum">    3913 </span>            :         // --------------------------------------------------------------------</a>
+<a name="3914"><span class="lineNum">    3914 </span>            :         // [Align / Embed]</a>
+<a name="3915"><span class="lineNum">    3915 </span>            :         // --------------------------------------------------------------------</a>
+<a name="3916"><span class="lineNum">    3916 </span>            : </a>
+<a name="3917"><span class="lineNum">    3917 </span>            :         case CBNode::kNodeAlign:</a>
+<a name="3918"><span class="lineNum">    3918 </span>            :         case CBNode::kNodeData:</a>
+<a name="3919"><span class="lineNum">    3919 </span>            :           break;</a>
+<a name="3920"><span class="lineNum">    3920 </span>            : </a>
+<a name="3921"><span class="lineNum">    3921 </span>            :         // --------------------------------------------------------------------</a>
+<a name="3922"><span class="lineNum">    3922 </span>            :         // [Label]</a>
+<a name="3923"><span class="lineNum">    3923 </span>            :         // --------------------------------------------------------------------</a>
+<a name="3924"><span class="lineNum">    3924 </span>            : </a>
+<a name="3925"><span class="lineNum">    3925 </span><span class="lineNoCov">          0 :         case CBNode::kNodeLabel: {</span></a>
+<a name="3926"><span class="lineNum">    3926 </span>            :           CBLabel* node = static_cast&lt;CBLabel*&gt;(node_);</a>
+<a name="3927"><span class="lineNum">    3927 </span>            :           ASMJIT_ASSERT(node-&gt;getPassData&lt;RAData&gt;()-&gt;state == nullptr);</a>
+<a name="3928"><span class="lineNum">    3928 </span><span class="lineNoCov">          0 :           node-&gt;getPassData&lt;RAData&gt;()-&gt;state = saveState();</span></a>
+<a name="3929"><span class="lineNum">    3929 </span>            : </a>
+<a name="3930"><span class="lineNum">    3930 </span><span class="lineNoCov">          0 :           if (node == func-&gt;getExitNode())</span></a>
+<a name="3931"><span class="lineNum">    3931 </span><span class="lineNoCov">          0 :             goto _NextGroup;</span></a>
+<a name="3932"><span class="lineNum">    3932 </span>            :           break;</a>
+<a name="3933"><span class="lineNum">    3933 </span>            :         }</a>
+<a name="3934"><span class="lineNum">    3934 </span>            : </a>
+<a name="3935"><span class="lineNum">    3935 </span>            :         // --------------------------------------------------------------------</a>
+<a name="3936"><span class="lineNum">    3936 </span>            :         // [Inst/Call/SArg/Ret]</a>
+<a name="3937"><span class="lineNum">    3937 </span>            :         // --------------------------------------------------------------------</a>
+<a name="3938"><span class="lineNum">    3938 </span>            : </a>
+<a name="3939"><span class="lineNum">    3939 </span>            :         case CBNode::kNodeInst:</a>
+<a name="3940"><span class="lineNum">    3940 </span>            :         case CBNode::kNodeFunc:</a>
+<a name="3941"><span class="lineNum">    3941 </span>            :         case CBNode::kNodeFuncCall:</a>
+<a name="3942"><span class="lineNum">    3942 </span>            :         case CBNode::kNodePushArg:</a>
+<a name="3943"><span class="lineNum">    3943 </span>            :           // Update TiedReg's unuse flags based on liveness of the next node.</a>
+<a name="3944"><span class="lineNum">    3944 </span><span class="lineCov">      34754 :           if (!node_-&gt;isJcc()) {</span></a>
+<a name="3945"><span class="lineNum">    3945 </span>            :             X86RAData* raData = node_-&gt;getPassData&lt;X86RAData&gt;();</a>
+<a name="3946"><span class="lineNum">    3946 </span>            :             RABits* liveness;</a>
+<a name="3947"><span class="lineNum">    3947 </span>            : </a>
+<a name="3948"><span class="lineNum">    3948 </span><span class="lineCov">      34754 :             if (raData &amp;&amp; next &amp;&amp; next-&gt;hasPassData() &amp;&amp; (liveness = next-&gt;getPassData&lt;RAData&gt;()-&gt;liveness)) {</span></a>
+<a name="3949"><span class="lineNum">    3949 </span><span class="lineCov">      34754 :               TiedReg* tiedArray = raData-&gt;tiedArray;</span></a>
+<a name="3950"><span class="lineNum">    3950 </span><span class="lineCov">      34754 :               uint32_t tiedTotal = raData-&gt;tiedTotal;</span></a>
+<a name="3951"><span class="lineNum">    3951 </span>            : </a>
+<a name="3952"><span class="lineNum">    3952 </span><span class="lineCov">      94300 :               for (uint32_t i = 0; i &lt; tiedTotal; i++) {</span></a>
+<a name="3953"><span class="lineNum">    3953 </span><span class="lineCov">      59546 :                 TiedReg* tied = &amp;tiedArray[i];</span></a>
+<a name="3954"><span class="lineNum">    3954 </span><span class="lineCov">      59546 :                 VirtReg* vreg = tied-&gt;vreg;</span></a>
+<a name="3955"><span class="lineNum">    3955 </span>            : </a>
+<a name="3956"><span class="lineNum">    3956 </span><span class="lineCov">      59546 :                 if (!liveness-&gt;getBit(vreg-&gt;_raId) &amp;&amp; !vreg-&gt;isFixed())</span></a>
+<a name="3957"><span class="lineNum">    3957 </span><span class="lineCov">      21840 :                   tied-&gt;flags |= TiedReg::kUnuse;</span></a>
+<a name="3958"><span class="lineNum">    3958 </span>            :               }</a>
+<a name="3959"><span class="lineNum">    3959 </span>            :             }</a>
+<a name="3960"><span class="lineNum">    3960 </span>            :           }</a>
+<a name="3961"><span class="lineNum">    3961 </span>            : </a>
+<a name="3962"><span class="lineNum">    3962 </span><span class="lineCov">      34754 :           if (node_-&gt;getType() == CBNode::kNodeFuncCall) {</span></a>
+<a name="3963"><span class="lineNum">    3963 </span><span class="lineCov">       1648 :             ASMJIT_PROPAGATE(cAlloc.run(static_cast&lt;CCFuncCall*&gt;(node_)));</span></a>
+<a name="3964"><span class="lineNum">    3964 </span>            :             break;</a>
+<a name="3965"><span class="lineNum">    3965 </span>            :           }</a>
+<a name="3966"><span class="lineNum">    3966 </span>            :           ASMJIT_FALLTHROUGH;</a>
+<a name="3967"><span class="lineNum">    3967 </span>            : </a>
+<a name="3968"><span class="lineNum">    3968 </span>            :         case CBNode::kNodeHint:</a>
+<a name="3969"><span class="lineNum">    3969 </span>            :         case CBNode::kNodeFuncExit: {</a>
+<a name="3970"><span class="lineNum">    3970 </span><span class="lineCov">      35054 :           ASMJIT_PROPAGATE(vAlloc.run(node_));</span></a>
+<a name="3971"><span class="lineNum">    3971 </span>            : </a>
+<a name="3972"><span class="lineNum">    3972 </span>            :           // Handle conditional/unconditional jump.</a>
+<a name="3973"><span class="lineNum">    3973 </span><span class="lineCov">      35054 :           if (node_-&gt;isJmpOrJcc()) {</span></a>
+<a name="3974"><span class="lineNum">    3974 </span>            :             CBJump* node = static_cast&lt;CBJump*&gt;(node_);</a>
+<a name="3975"><span class="lineNum">    3975 </span>            :             CBLabel* jTarget = node-&gt;getTarget();</a>
+<a name="3976"><span class="lineNum">    3976 </span>            : </a>
+<a name="3977"><span class="lineNum">    3977 </span>            :             // Target not followed.</a>
+<a name="3978"><span class="lineNum">    3978 </span><span class="lineNoCov">          0 :             if (!jTarget) {</span></a>
+<a name="3979"><span class="lineNum">    3979 </span><span class="lineNoCov">          0 :               if (node-&gt;isJmp())</span></a>
+<a name="3980"><span class="lineNum">    3980 </span><span class="lineNoCov">          0 :                 goto _NextGroup;</span></a>
+<a name="3981"><span class="lineNum">    3981 </span>            :               else</a>
+<a name="3982"><span class="lineNum">    3982 </span>            :                 break;</a>
+<a name="3983"><span class="lineNum">    3983 </span>            :             }</a>
+<a name="3984"><span class="lineNum">    3984 </span>            : </a>
+<a name="3985"><span class="lineNum">    3985 </span><span class="lineNoCov">          0 :             if (node-&gt;isJmp()) {</span></a>
+<a name="3986"><span class="lineNum">    3986 </span><span class="lineNoCov">          0 :               if (jTarget-&gt;hasPassData() &amp;&amp; jTarget-&gt;getPassData&lt;RAData&gt;()-&gt;state) {</span></a>
+<a name="3987"><span class="lineNum">    3987 </span>            :                 cc-&gt;_setCursor(node-&gt;getPrev());</a>
+<a name="3988"><span class="lineNum">    3988 </span><span class="lineNoCov">          0 :                 switchState(jTarget-&gt;getPassData&lt;RAData&gt;()-&gt;state);</span></a>
+<a name="3989"><span class="lineNum">    3989 </span>            : </a>
+<a name="3990"><span class="lineNum">    3990 </span><span class="lineNoCov">          0 :                 goto _NextGroup;</span></a>
+<a name="3991"><span class="lineNum">    3991 </span>            :               }</a>
+<a name="3992"><span class="lineNum">    3992 </span>            :               else {</a>
+<a name="3993"><span class="lineNum">    3993 </span>            :                 next = jTarget;</a>
+<a name="3994"><span class="lineNum">    3994 </span>            :               }</a>
+<a name="3995"><span class="lineNum">    3995 </span>            :             }</a>
+<a name="3996"><span class="lineNum">    3996 </span>            :             else {</a>
+<a name="3997"><span class="lineNum">    3997 </span>            :               CBNode* jNext = node-&gt;getNext();</a>
+<a name="3998"><span class="lineNum">    3998 </span>            : </a>
+<a name="3999"><span class="lineNum">    3999 </span><span class="lineNoCov">          0 :               if (jTarget-&gt;isTranslated()) {</span></a>
+<a name="4000"><span class="lineNum">    4000 </span><span class="lineNoCov">          0 :                 if (jNext-&gt;isTranslated()) {</span></a>
+<a name="4001"><span class="lineNum">    4001 </span>            :                   ASMJIT_ASSERT(jNext-&gt;getType() == CBNode::kNodeLabel);</a>
+<a name="4002"><span class="lineNum">    4002 </span>            :                   cc-&gt;_setCursor(node-&gt;getPrev());</a>
+<a name="4003"><span class="lineNum">    4003 </span><span class="lineNoCov">          0 :                   intersectStates(</span></a>
+<a name="4004"><span class="lineNum">    4004 </span>            :                     jTarget-&gt;getPassData&lt;RAData&gt;()-&gt;state,</a>
+<a name="4005"><span class="lineNum">    4005 </span>            :                     jNext-&gt;getPassData&lt;RAData&gt;()-&gt;state);</a>
+<a name="4006"><span class="lineNum">    4006 </span>            :                 }</a>
+<a name="4007"><span class="lineNum">    4007 </span>            : </a>
+<a name="4008"><span class="lineNum">    4008 </span><span class="lineNoCov">          0 :                 RAState* savedState = saveState();</span></a>
+<a name="4009"><span class="lineNum">    4009 </span><span class="lineNoCov">          0 :                 node-&gt;getPassData&lt;RAData&gt;()-&gt;state = savedState;</span></a>
+<a name="4010"><span class="lineNum">    4010 </span>            : </a>
+<a name="4011"><span class="lineNum">    4011 </span><span class="lineNoCov">          0 :                 X86RAPass_translateJump(this, node, jTarget);</span></a>
+<a name="4012"><span class="lineNum">    4012 </span>            :                 next = jNext;</a>
+<a name="4013"><span class="lineNum">    4013 </span>            :               }</a>
+<a name="4014"><span class="lineNum">    4014 </span><span class="lineNoCov">          0 :               else if (jNext-&gt;isTranslated()) {</span></a>
+<a name="4015"><span class="lineNum">    4015 </span>            :                 ASMJIT_ASSERT(jNext-&gt;getType() == CBNode::kNodeLabel);</a>
+<a name="4016"><span class="lineNum">    4016 </span>            : </a>
+<a name="4017"><span class="lineNum">    4017 </span><span class="lineNoCov">          0 :                 RAState* savedState = saveState();</span></a>
+<a name="4018"><span class="lineNum">    4018 </span><span class="lineNoCov">          0 :                 node-&gt;getPassData&lt;RAData&gt;()-&gt;state = savedState;</span></a>
+<a name="4019"><span class="lineNum">    4019 </span>            : </a>
+<a name="4020"><span class="lineNum">    4020 </span>            :                 cc-&gt;_setCursor(node);</a>
+<a name="4021"><span class="lineNum">    4021 </span><span class="lineNoCov">          0 :                 switchState(jNext-&gt;getPassData&lt;RAData&gt;()-&gt;state);</span></a>
+<a name="4022"><span class="lineNum">    4022 </span>            :                 next = jTarget;</a>
+<a name="4023"><span class="lineNum">    4023 </span>            :               }</a>
+<a name="4024"><span class="lineNum">    4024 </span>            :               else {</a>
+<a name="4025"><span class="lineNum">    4025 </span><span class="lineNoCov">          0 :                 node-&gt;getPassData&lt;RAData&gt;()-&gt;state = saveState();</span></a>
+<a name="4026"><span class="lineNum">    4026 </span>            :                 next = X86RAPass_getJccFlow(node);</a>
+<a name="4027"><span class="lineNum">    4027 </span>            :               }</a>
+<a name="4028"><span class="lineNum">    4028 </span>            :             }</a>
+<a name="4029"><span class="lineNum">    4029 </span>            :           }</a>
+<a name="4030"><span class="lineNum">    4030 </span><span class="lineCov">      35054 :           else if (node_-&gt;isRet()) {</span></a>
+<a name="4031"><span class="lineNum">    4031 </span><span class="lineCov">       1948 :             ASMJIT_PROPAGATE(</span></a>
+<a name="4032"><span class="lineNum">    4032 </span>            :               X86RAPass_translateRet(this, static_cast&lt;CCFuncRet*&gt;(node_), func-&gt;getExitNode()));</a>
+<a name="4033"><span class="lineNum">    4033 </span><span class="lineCov">       1948 :             goto _NextGroup;</span></a>
+<a name="4034"><span class="lineNum">    4034 </span>            :           }</a>
+<a name="4035"><span class="lineNum">    4035 </span>            :           break;</a>
+<a name="4036"><span class="lineNum">    4036 </span>            :         }</a>
+<a name="4037"><span class="lineNum">    4037 </span>            : </a>
+<a name="4038"><span class="lineNum">    4038 </span>            :         // --------------------------------------------------------------------</a>
+<a name="4039"><span class="lineNum">    4039 </span>            :         // [End]</a>
+<a name="4040"><span class="lineNum">    4040 </span>            :         // --------------------------------------------------------------------</a>
+<a name="4041"><span class="lineNum">    4041 </span>            : </a>
+<a name="4042"><span class="lineNum">    4042 </span><span class="lineNoCov">          0 :         case CBNode::kNodeSentinel: {</span></a>
+<a name="4043"><span class="lineNum">    4043 </span><span class="lineNoCov">          0 :           goto _NextGroup;</span></a>
+<a name="4044"><span class="lineNum">    4044 </span>            :         }</a>
+<a name="4045"><span class="lineNum">    4045 </span>            : </a>
+<a name="4046"><span class="lineNum">    4046 </span>            :         default:</a>
+<a name="4047"><span class="lineNum">    4047 </span>            :           break;</a>
+<a name="4048"><span class="lineNum">    4048 </span>            :       }</a>
+<a name="4049"><span class="lineNum">    4049 </span>            :     }</a>
+<a name="4050"><span class="lineNum">    4050 </span>            : </a>
+<a name="4051"><span class="lineNum">    4051 </span><span class="lineCov">      34754 :     if (next == stop)</span></a>
+<a name="4052"><span class="lineNum">    4052 </span><span class="lineNoCov">          0 :       goto _NextGroup;</span></a>
+<a name="4053"><span class="lineNum">    4053 </span>            :     node_ = next;</a>
+<a name="4054"><span class="lineNum">    4054 </span>            :   }</a>
+<a name="4055"><span class="lineNum">    4055 </span>            : </a>
+<a name="4056"><span class="lineNum">    4056 </span>            : _Done:</a>
+<a name="4057"><span class="lineNum">    4057 </span>            :   {</a>
+<a name="4058"><span class="lineNum">    4058 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(resolveCellOffsets());</span></a>
+<a name="4059"><span class="lineNum">    4059 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(X86RAPass_prepareFuncFrame(this, func));</span></a>
+<a name="4060"><span class="lineNum">    4060 </span>            : </a>
+<a name="4061"><span class="lineNum">    4061 </span>            :     FuncFrameLayout layout;</a>
+<a name="4062"><span class="lineNum">    4062 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(layout.init(func-&gt;getDetail(), func-&gt;getFrameInfo()));</span></a>
+<a name="4063"><span class="lineNum">    4063 </span>            : </a>
+<a name="4064"><span class="lineNum">    4064 </span><span class="lineCov">       1948 :     _varBaseRegId = layout._stackBaseRegId;</span></a>
+<a name="4065"><span class="lineNum">    4065 </span><span class="lineCov">       1948 :     _varBaseOffset = layout._stackBaseOffset;</span></a>
+<a name="4066"><span class="lineNum">    4066 </span>            : </a>
+<a name="4067"><span class="lineNum">    4067 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(X86RAPass_patchFuncMem(this, func, stop, layout));</span></a>
+<a name="4068"><span class="lineNum">    4068 </span>            : </a>
+<a name="4069"><span class="lineNum">    4069 </span>            :     cc-&gt;_setCursor(func);</a>
+<a name="4070"><span class="lineNum">    4070 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(FuncUtils::emitProlog(this-&gt;cc(), layout));</span></a>
+<a name="4071"><span class="lineNum">    4071 </span>            : </a>
+<a name="4072"><span class="lineNum">    4072 </span>            :     cc-&gt;_setCursor(func-&gt;getExitNode());</a>
+<a name="4073"><span class="lineNum">    4073 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(FuncUtils::emitEpilog(this-&gt;cc(), layout));</span></a>
+<a name="4074"><span class="lineNum">    4074 </span>            :   }</a>
+<a name="4075"><span class="lineNum">    4075 </span>            : </a>
+<a name="4076"><span class="lineNum">    4076 </span><span class="lineCov">       1948 :   return kErrorOk;</span></a>
+<a name="4077"><span class="lineNum">    4077 </span>            : }</a>
+<a name="4078"><span class="lineNum">    4078 </span>            : </a>
+<a name="4079"><span class="lineNum">    4079 </span>            : } // asmjit namespace</a>
+<a name="4080"><span class="lineNum">    4080 </span>            : } // namespace PLMD</a>
+<a name="4081"><span class="lineNum">    4081 </span>            : </a>
+<a name="4082"><span class="lineNum">    4082 </span>            : // [Api-End]</a>
+<a name="4083"><span class="lineNum">    4083 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="4084"><span class="lineNum">    4084 </span>            : </a>
+<a name="4085"><span class="lineNum">    4085 </span>            : // [Guard]</a>
+<a name="4086"><span class="lineNum">    4086 </span>            : #endif // ASMJIT_BUILD_X86 &amp;&amp; !ASMJIT_DISABLE_COMPILER</a>
+<a name="4087"><span class="lineNum">    4087 </span>            : #pragma GCC diagnostic pop</a>
+<a name="4088"><span class="lineNum">    4088 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86regalloc_p.h.func-sort-c.html b/coverage-libs/asmjit/x86regalloc_p.h.func-sort-c.html
new file mode 100644
index 0000000000..610b47c230
--- /dev/null
+++ b/coverage-libs/asmjit/x86regalloc_p.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86regalloc_p.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86regalloc_p.h<span style="font-size: 80%;"> (<a href="x86regalloc_p.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryLo">69.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="x86regalloc_p.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86regalloc_p.h.func.html b/coverage-libs/asmjit/x86regalloc_p.h.func.html
new file mode 100644
index 0000000000..1db1cbb8b0
--- /dev/null
+++ b/coverage-libs/asmjit/x86regalloc_p.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86regalloc_p.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86regalloc_p.h<span style="font-size: 80%;"> (<a href="x86regalloc_p.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryLo">69.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="x86regalloc_p.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/x86regalloc_p.h.gcov.html b/coverage-libs/asmjit/x86regalloc_p.h.gcov.html
new file mode 100644
index 0000000000..169c50efae
--- /dev/null
+++ b/coverage-libs/asmjit/x86regalloc_p.h.gcov.html
@@ -0,0 +1,810 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/x86regalloc_p.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - x86regalloc_p.h<span style="font-size: 80%;"> (source / <a href="x86regalloc_p.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryLo">69.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_x86regalloc_p_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_x86regalloc_p_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_X86_X86REGALLOC_P_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_X86_X86REGALLOC_P_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;./asmjit_build.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if !defined(ASMJIT_DISABLE_COMPILER)</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Dependencies]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./codecompiler.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;./regalloc_p.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;./x86assembler.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;./x86compiler.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;./x86misc.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : // [Api-Begin]</a>
+<a name="47"><span class="lineNum">      47 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : namespace PLMD {</a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace asmjit {</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : //! \addtogroup asmjit_x86</a>
+<a name="53"><span class="lineNum">      53 </span>            : //! \{</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // ============================================================================</a>
+<a name="56"><span class="lineNum">      56 </span>            : // [asmjit::X86RAData]</a>
+<a name="57"><span class="lineNum">      57 </span>            : // ============================================================================</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : struct X86RAData : public RAData {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      81196 :   ASMJIT_INLINE X86RAData(uint32_t tiedTotal) noexcept : RAData(tiedTotal) {</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :     inRegs.reset();</a>
+<a name="62"><span class="lineNum">      62 </span>            :     outRegs.reset();</a>
+<a name="63"><span class="lineNum">      63 </span>            :     clobberedRegs.reset();</a>
+<a name="64"><span class="lineNum">      64 </span>            :     tiedIndex.reset();</a>
+<a name="65"><span class="lineNum">      65 </span>            :     tiedCount.reset();</a>
+<a name="66"><span class="lineNum">      66 </span>            :   }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // [Accessors]</a>
+<a name="70"><span class="lineNum">      70 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :   //! Get TiedReg array.</a>
+<a name="73"><span class="lineNum">      73 </span>            :   ASMJIT_INLINE TiedReg* getTiedArray() const noexcept {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      36702 :     return const_cast&lt;TiedReg*&gt;(tiedArray);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :   //! Get TiedReg array for a given register `kind`.</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ASMJIT_INLINE TiedReg* getTiedArrayByKind(uint32_t kind) const noexcept {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      99342 :     return const_cast&lt;TiedReg*&gt;(tiedArray) + tiedIndex.get(kind);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   //! Get TiedReg index for a given register `kind`.</a>
+<a name="83"><span class="lineNum">      83 </span>            :   ASMJIT_INLINE uint32_t getTiedStart(uint32_t kind) const noexcept {</a>
+<a name="84"><span class="lineNum">      84 </span>            :     return tiedIndex.get(kind);</a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   //! Get TiedReg count for a given register `kind`.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ASMJIT_INLINE uint32_t getTiedCountByKind(uint32_t kind) const noexcept {</a>
+<a name="89"><span class="lineNum">      89 </span>            :     return tiedCount.get(kind);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   //! Get TiedReg at the specified `index`.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   ASMJIT_INLINE TiedReg* getTiedAt(uint32_t index) const noexcept {</a>
+<a name="94"><span class="lineNum">      94 </span>            :     ASMJIT_ASSERT(index &lt; tiedTotal);</a>
+<a name="95"><span class="lineNum">      95 </span>            :     return getTiedArray() + index;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   //! Get TiedReg at the specified index for a given register `kind`.</a>
+<a name="99"><span class="lineNum">      99 </span>            :   ASMJIT_INLINE TiedReg* getTiedAtByKind(uint32_t kind, uint32_t index) const noexcept {</a>
+<a name="100"><span class="lineNum">     100 </span>            :     ASMJIT_ASSERT(index &lt; tiedCount._regs[kind]);</a>
+<a name="101"><span class="lineNum">     101 </span>            :     return getTiedArrayByKind(kind) + index;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   ASMJIT_INLINE void setTiedAt(uint32_t index, TiedReg&amp; tied) noexcept {</a>
+<a name="105"><span class="lineNum">     105 </span>            :     ASMJIT_ASSERT(index &lt; tiedTotal);</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      61494 :     tiedArray[index] = tied;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // [Utils]</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Find TiedReg.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_INLINE TiedReg* findTied(VirtReg* vreg) const noexcept {</a>
+<a name="115"><span class="lineNum">     115 </span>            :     TiedReg* tiedArray = getTiedArray();</a>
+<a name="116"><span class="lineNum">     116 </span>            :     uint32_t tiedCount = tiedTotal;</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :     for (uint32_t i = 0; i &lt; tiedCount; i++)</a>
+<a name="119"><span class="lineNum">     119 </span>            :       if (tiedArray[i].vreg == vreg)</a>
+<a name="120"><span class="lineNum">     120 </span>            :         return &amp;tiedArray[i];</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :     return nullptr;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   //! Find TiedReg (by class).</a>
+<a name="126"><span class="lineNum">     126 </span>            :   ASMJIT_INLINE TiedReg* findTiedByKind(uint32_t kind, VirtReg* vreg) const noexcept {</a>
+<a name="127"><span class="lineNum">     127 </span>            :     TiedReg* tiedArray = getTiedArrayByKind(kind);</a>
+<a name="128"><span class="lineNum">     128 </span>            :     uint32_t tiedCount = getTiedCountByKind(kind);</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     209940 :     for (uint32_t i = 0; i &lt; tiedCount; i++)</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     140526 :       if (tiedArray[i].vreg == vreg)</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :         return &amp;tiedArray[i];</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :     return nullptr;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="138"><span class="lineNum">     138 </span>            :   // [Members]</a>
+<a name="139"><span class="lineNum">     139 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   //! Special registers on input.</a>
+<a name="142"><span class="lineNum">     142 </span>            :   //!</a>
+<a name="143"><span class="lineNum">     143 </span>            :   //! Special register(s) restricted to one or more physical register. If there</a>
+<a name="144"><span class="lineNum">     144 </span>            :   //! is more than one special register it means that we have to duplicate the</a>
+<a name="145"><span class="lineNum">     145 </span>            :   //! variable content to all of them (it means that the same variable was used</a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! by two or more operands). We forget about duplicates after the register</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //! allocation finishes and marks all duplicates as non-assigned.</a>
+<a name="148"><span class="lineNum">     148 </span>            :   X86RegMask inRegs;</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   //! Special registers on output.</a>
+<a name="151"><span class="lineNum">     151 </span>            :   //!</a>
+<a name="152"><span class="lineNum">     152 </span>            :   //! Special register(s) used on output. Each variable can have only one</a>
+<a name="153"><span class="lineNum">     153 </span>            :   //! special register on the output, 'X86RAData' contains all registers from</a>
+<a name="154"><span class="lineNum">     154 </span>            :   //! all 'TiedReg's.</a>
+<a name="155"><span class="lineNum">     155 </span>            :   X86RegMask outRegs;</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   //! Clobbered registers (by a function call).</a>
+<a name="158"><span class="lineNum">     158 </span>            :   X86RegMask clobberedRegs;</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   //! Start indexes of `TiedReg`s per register kind.</a>
+<a name="161"><span class="lineNum">     161 </span>            :   X86RegCount tiedIndex;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! Count of variables per register kind.</a>
+<a name="163"><span class="lineNum">     163 </span>            :   X86RegCount tiedCount;</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            :   //! Linked registers.</a>
+<a name="166"><span class="lineNum">     166 </span>            :   TiedReg tiedArray[1];</a>
+<a name="167"><span class="lineNum">     167 </span>            : };</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : // ============================================================================</a>
+<a name="170"><span class="lineNum">     170 </span>            : // [asmjit::X86StateCell]</a>
+<a name="171"><span class="lineNum">     171 </span>            : // ============================================================================</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : //! X86/X64 state-cell.</a>
+<a name="174"><span class="lineNum">     174 </span>            : union X86StateCell {</a>
+<a name="175"><span class="lineNum">     175 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="176"><span class="lineNum">     176 </span>            :   // [Accessors]</a>
+<a name="177"><span class="lineNum">     177 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE uint32_t getState() const noexcept { return _state; }</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void setState(uint32_t state) noexcept { _state = static_cast&lt;uint8_t&gt;(state); }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="183"><span class="lineNum">     183 </span>            :   // [Reset]</a>
+<a name="184"><span class="lineNum">     184 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE void reset() noexcept { _packed = 0; }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // [Members]</a>
+<a name="190"><span class="lineNum">     190 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   uint8_t _packed;</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            :   struct {</a>
+<a name="195"><span class="lineNum">     195 </span>            :     uint8_t _state : 2;</a>
+<a name="196"><span class="lineNum">     196 </span>            :     uint8_t _unused : 6;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   };</a>
+<a name="198"><span class="lineNum">     198 </span>            : };</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : // ============================================================================</a>
+<a name="201"><span class="lineNum">     201 </span>            : // [asmjit::X86RAState]</a>
+<a name="202"><span class="lineNum">     202 </span>            : // ============================================================================</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : //! X86/X64 state.</a>
+<a name="205"><span class="lineNum">     205 </span>            : struct X86RAState : RAState {</a>
+<a name="206"><span class="lineNum">     206 </span>            :   enum {</a>
+<a name="207"><span class="lineNum">     207 </span>            :     //! Base index of GP registers.</a>
+<a name="208"><span class="lineNum">     208 </span>            :     kGpIndex = 0,</a>
+<a name="209"><span class="lineNum">     209 </span>            :     //! Count of GP registers.</a>
+<a name="210"><span class="lineNum">     210 </span>            :     kGpCount = 16,</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :     //! Base index of MMX registers.</a>
+<a name="213"><span class="lineNum">     213 </span>            :     kMmIndex = kGpIndex + kGpCount,</a>
+<a name="214"><span class="lineNum">     214 </span>            :     //! Count of Mm registers.</a>
+<a name="215"><span class="lineNum">     215 </span>            :     kMmCount = 8,</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :     //! Base index of XMM registers.</a>
+<a name="218"><span class="lineNum">     218 </span>            :     kXmmIndex = kMmIndex + kMmCount,</a>
+<a name="219"><span class="lineNum">     219 </span>            :     //! Count of XMM registers.</a>
+<a name="220"><span class="lineNum">     220 </span>            :     kXmmCount = 16,</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :     //! Count of all registers in `X86RAState`.</a>
+<a name="223"><span class="lineNum">     223 </span>            :     kAllCount = kXmmIndex + kXmmCount</a>
+<a name="224"><span class="lineNum">     224 </span>            :   };</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="227"><span class="lineNum">     227 </span>            :   // [Accessors]</a>
+<a name="228"><span class="lineNum">     228 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   ASMJIT_INLINE VirtReg** getList() {</a>
+<a name="231"><span class="lineNum">     231 </span>            :     return _list;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            :   ASMJIT_INLINE VirtReg** getListByKind(uint32_t kind) {</a>
+<a name="235"><span class="lineNum">     235 </span>            :     switch (kind) {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       3296 :       case X86Reg::kKindGp : return _listGp;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       3296 :       case X86Reg::kKindMm : return _listMm;</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       8920 :       case X86Reg::kKindVec: return _listXmm;</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :       default:</a>
+<a name="241"><span class="lineNum">     241 </span>            :         return nullptr;</a>
+<a name="242"><span class="lineNum">     242 </span>            :     }</a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="246"><span class="lineNum">     246 </span>            :   // [Clear]</a>
+<a name="247"><span class="lineNum">     247 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   ASMJIT_INLINE void reset(size_t numCells) {</a>
+<a name="250"><span class="lineNum">     250 </span>            :     ::memset(this, 0, kAllCount * sizeof(VirtReg*) +</a>
+<a name="251"><span class="lineNum">     251 </span>            :                       2         * sizeof(X86RegMask) +</a>
+<a name="252"><span class="lineNum">     252 </span>            :                       numCells  * sizeof(X86StateCell));</a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // [Members]</a>
+<a name="257"><span class="lineNum">     257 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            :   union {</a>
+<a name="260"><span class="lineNum">     260 </span>            :     //! List of all allocated variables in one array.</a>
+<a name="261"><span class="lineNum">     261 </span>            :     VirtReg* _list[kAllCount];</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :     struct {</a>
+<a name="264"><span class="lineNum">     264 </span>            :       //! Allocated GP registers.</a>
+<a name="265"><span class="lineNum">     265 </span>            :       VirtReg* _listGp[kGpCount];</a>
+<a name="266"><span class="lineNum">     266 </span>            :       //! Allocated MMX registers.</a>
+<a name="267"><span class="lineNum">     267 </span>            :       VirtReg* _listMm[kMmCount];</a>
+<a name="268"><span class="lineNum">     268 </span>            :       //! Allocated XMM registers.</a>
+<a name="269"><span class="lineNum">     269 </span>            :       VirtReg* _listXmm[kXmmCount];</a>
+<a name="270"><span class="lineNum">     270 </span>            :     };</a>
+<a name="271"><span class="lineNum">     271 </span>            :   };</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   //! Occupied registers (mask).</a>
+<a name="274"><span class="lineNum">     274 </span>            :   X86RegMask _occupied;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   //! Modified registers (mask).</a>
+<a name="276"><span class="lineNum">     276 </span>            :   X86RegMask _modified;</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   //! Variables data, the length is stored in `X86RAPass`.</a>
+<a name="279"><span class="lineNum">     279 </span>            :   X86StateCell _cells[1];</a>
+<a name="280"><span class="lineNum">     280 </span>            : };</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            : // ============================================================================</a>
+<a name="283"><span class="lineNum">     283 </span>            : // [asmjit::X86RAPass]</a>
+<a name="284"><span class="lineNum">     284 </span>            : // ============================================================================</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : #if defined(ASMJIT_DEBUG)</a>
+<a name="287"><span class="lineNum">     287 </span>            : # define ASMJIT_X86_CHECK_STATE _checkState();</a>
+<a name="288"><span class="lineNum">     288 </span>            : #else</a>
+<a name="289"><span class="lineNum">     289 </span>            : # define ASMJIT_X86_CHECK_STATE</a>
+<a name="290"><span class="lineNum">     290 </span>            : #endif // ASMJIT_DEBUG</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            : //! \internal</a>
+<a name="293"><span class="lineNum">     293 </span>            : //!</a>
+<a name="294"><span class="lineNum">     294 </span>            : //! X86 register allocator pipeline.</a>
+<a name="295"><span class="lineNum">     295 </span>            : //!</a>
+<a name="296"><span class="lineNum">     296 </span>            : //! Takes care of generating function prologs and epilogs, and also performs</a>
+<a name="297"><span class="lineNum">     297 </span>            : //! register allocation.</a>
+<a name="298"><span class="lineNum">     298 </span>            : class X86RAPass : public RAPass {</a>
+<a name="299"><span class="lineNum">     299 </span>            : public:</a>
+<a name="300"><span class="lineNum">     300 </span>            :   ASMJIT_NONCOPYABLE(X86RAPass)</a>
+<a name="301"><span class="lineNum">     301 </span>            :   typedef RAPass Base;</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            :   enum RegOp {</a>
+<a name="304"><span class="lineNum">     304 </span>            :     kRegOpMove,</a>
+<a name="305"><span class="lineNum">     305 </span>            :     kRegOpLoad,</a>
+<a name="306"><span class="lineNum">     306 </span>            :     kRegOpSave</a>
+<a name="307"><span class="lineNum">     307 </span>            :   };</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="310"><span class="lineNum">     310 </span>            :   // [Construction / Destruction]</a>
+<a name="311"><span class="lineNum">     311 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   X86RAPass() noexcept;</a>
+<a name="314"><span class="lineNum">     314 </span>            :   virtual ~X86RAPass() noexcept;</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="317"><span class="lineNum">     317 </span>            :   // [Interface]</a>
+<a name="318"><span class="lineNum">     318 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :   virtual Error process(Zone* zone) noexcept override;</a>
+<a name="321"><span class="lineNum">     321 </span>            :   virtual Error prepare(CCFunc* func) noexcept override;</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="324"><span class="lineNum">     324 </span>            :   // [ArchInfo]</a>
+<a name="325"><span class="lineNum">     325 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            :   ASMJIT_INLINE uint32_t getGpSize() const noexcept { return _zsp.getSize(); }</a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="330"><span class="lineNum">     330 </span>            :   // [Accessors]</a>
+<a name="331"><span class="lineNum">     331 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   //! Get compiler as `X86Compiler`.</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">     119636 :   ASMJIT_INLINE X86Compiler* cc() const noexcept { return static_cast&lt;X86Compiler*&gt;(_cb); }</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :   //! Get clobbered registers (global).</a>
+<a name="336"><span class="lineNum">     336 </span>            :   ASMJIT_INLINE uint32_t getClobberedRegs(uint32_t kind) noexcept { return _clobberedRegs.get(kind); }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="339"><span class="lineNum">     339 </span>            :   // [Helpers]</a>
+<a name="340"><span class="lineNum">     340 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            :   ASMJIT_INLINE X86RAData* newRAData(uint32_t tiedTotal) noexcept {</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">      40598 :     return new(_zone-&gt;alloc(sizeof(X86RAData) + tiedTotal * sizeof(TiedReg))) X86RAData(tiedTotal);</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :   }</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="347"><span class="lineNum">     347 </span>            :   // [Emit]</a>
+<a name="348"><span class="lineNum">     348 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            :   // Tiny wrappers that call `X86Internal::emit...()`.</a>
+<a name="351"><span class="lineNum">     351 </span>            :   Error emitMove(VirtReg* vreg, uint32_t dstId, uint32_t srcId, const char* reason);</a>
+<a name="352"><span class="lineNum">     352 </span>            :   Error emitLoad(VirtReg* vreg, uint32_t id, const char* reason);</a>
+<a name="353"><span class="lineNum">     353 </span>            :   Error emitSave(VirtReg* vreg, uint32_t id, const char* reason);</a>
+<a name="354"><span class="lineNum">     354 </span>            :   Error emitSwapGp(VirtReg* aVReg, VirtReg* bVReg, uint32_t aId, uint32_t bId, const char* reason) noexcept;</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            :   Error emitImmToReg(uint32_t dstTypeId, uint32_t dstPhysId, const Imm* src) noexcept;</a>
+<a name="357"><span class="lineNum">     357 </span>            :   Error emitImmToStack(uint32_t dstTypeId, const X86Mem* dst, const Imm* src) noexcept;</a>
+<a name="358"><span class="lineNum">     358 </span>            :   Error emitRegToStack(uint32_t dstTypeId, const X86Mem* dst, uint32_t srcTypeId, uint32_t srcPhysId) noexcept;</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="361"><span class="lineNum">     361 </span>            :   // [Register Management]</a>
+<a name="362"><span class="lineNum">     362 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :   void _checkState();</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="367"><span class="lineNum">     367 </span>            :   // [Attach / Detach]</a>
+<a name="368"><span class="lineNum">     368 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span>            :   //! Attach.</a>
+<a name="371"><span class="lineNum">     371 </span>            :   //!</a>
+<a name="372"><span class="lineNum">     372 </span>            :   //! Attach a register to the 'VirtReg', changing 'VirtReg' members to show</a>
+<a name="373"><span class="lineNum">     373 </span>            :   //! that the variable is currently alive and linking variable with the</a>
+<a name="374"><span class="lineNum">     374 </span>            :   //! current 'X86RAState'.</a>
+<a name="375"><span class="lineNum">     375 </span>            :   template&lt;int C&gt;</a>
+<a name="376"><span class="lineNum">     376 </span>            :   ASMJIT_INLINE void attach(VirtReg* vreg, uint32_t physId, bool modified) {</a>
+<a name="377"><span class="lineNum">     377 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="378"><span class="lineNum">     378 </span>            :     ASMJIT_ASSERT(physId != Globals::kInvalidRegId);</a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span>            :     // Prevent Esp allocation if C==Gp.</a>
+<a name="381"><span class="lineNum">     381 </span>            :     ASMJIT_ASSERT(C != X86Reg::kKindGp || physId != X86Gp::kIdSp);</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            :     uint32_t regMask = Utils::mask(physId);</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            :     vreg-&gt;setState(VirtReg::kStateReg);</a>
+<a name="386"><span class="lineNum">     386 </span>            :     vreg-&gt;setModified(modified);</a>
+<a name="387"><span class="lineNum">     387 </span>            :     vreg-&gt;setPhysId(physId);</a>
+<a name="388"><span class="lineNum">     388 </span>            :     vreg-&gt;addHomeId(physId);</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      23788 :     _x86State.getListByKind(C)[physId] = vreg;</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     _x86State._occupied.or_(C, regMask);</a>
+<a name="392"><span class="lineNum">     392 </span>            :     _x86State._modified.or_(C, static_cast&lt;uint32_t&gt;(modified) &lt;&lt; physId);</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">      23788 :   }</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :   //! Detach.</a>
+<a name="398"><span class="lineNum">     398 </span>            :   //!</a>
+<a name="399"><span class="lineNum">     399 </span>            :   //! The opposite of 'Attach'. Detach resets the members in 'VirtReg'</a>
+<a name="400"><span class="lineNum">     400 </span>            :   //! (physId, state and changed flags) and unlinks the variable with the</a>
+<a name="401"><span class="lineNum">     401 </span>            :   //! current 'X86RAState'.</a>
+<a name="402"><span class="lineNum">     402 </span>            :   template&lt;int C&gt;</a>
+<a name="403"><span class="lineNum">     403 </span>            :   ASMJIT_INLINE void detach(VirtReg* vreg, uint32_t physId, uint32_t vState) {</a>
+<a name="404"><span class="lineNum">     404 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="405"><span class="lineNum">     405 </span>            :     ASMJIT_ASSERT(vreg-&gt;getPhysId() == physId);</a>
+<a name="406"><span class="lineNum">     406 </span>            :     ASMJIT_ASSERT(vState != VirtReg::kStateReg);</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :     uint32_t regMask = Utils::mask(physId);</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :     vreg-&gt;setState(vState);</a>
+<a name="411"><span class="lineNum">     411 </span>            :     vreg-&gt;resetPhysId();</a>
+<a name="412"><span class="lineNum">     412 </span>            :     vreg-&gt;setModified(false);</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">      26264 :     _x86State.getListByKind(C)[physId] = nullptr;</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :     _x86State._occupied.andNot(C, regMask);</a>
+<a name="416"><span class="lineNum">     416 </span>            :     _x86State._modified.andNot(C, regMask);</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      26264 :   }</span></a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="422"><span class="lineNum">     422 </span>            :   // [Rebase]</a>
+<a name="423"><span class="lineNum">     423 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            :   //! Rebase.</a>
+<a name="426"><span class="lineNum">     426 </span>            :   //!</a>
+<a name="427"><span class="lineNum">     427 </span>            :   //! Change the register of the 'VirtReg' changing also the current 'X86RAState'.</a>
+<a name="428"><span class="lineNum">     428 </span>            :   //! Rebase is nearly identical to 'Detach' and 'Attach' sequence, but doesn't</a>
+<a name="429"><span class="lineNum">     429 </span>            :   //! change the `VirtReg`s modified flag.</a>
+<a name="430"><span class="lineNum">     430 </span>            :   template&lt;int C&gt;</a>
+<a name="431"><span class="lineNum">     431 </span>            :   ASMJIT_INLINE void rebase(VirtReg* vreg, uint32_t newPhysId, uint32_t oldPhysId) {</a>
+<a name="432"><span class="lineNum">     432 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span>            :     uint32_t newRegMask = Utils::mask(newPhysId);</a>
+<a name="435"><span class="lineNum">     435 </span>            :     uint32_t oldRegMask = Utils::mask(oldPhysId);</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">        656 :     uint32_t bothRegMask = newRegMask ^ oldRegMask;</span></a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            :     vreg-&gt;setPhysId(newPhysId);</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        656 :     _x86State.getListByKind(C)[oldPhysId] = nullptr;</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">        656 :     _x86State.getListByKind(C)[newPhysId] = vreg;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            :     _x86State._occupied.xor_(C, bothRegMask);</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">        656 :     _x86State._modified.xor_(C, bothRegMask &amp; -static_cast&lt;int32_t&gt;(vreg-&gt;isModified()));</span></a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        656 :   }</span></a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="450"><span class="lineNum">     450 </span>            :   // [Load / Save]</a>
+<a name="451"><span class="lineNum">     451 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            :   //! Load.</a>
+<a name="454"><span class="lineNum">     454 </span>            :   //!</a>
+<a name="455"><span class="lineNum">     455 </span>            :   //! Load variable from its memory slot to a register, emitting 'Load'</a>
+<a name="456"><span class="lineNum">     456 </span>            :   //! instruction and changing the variable state to allocated.</a>
+<a name="457"><span class="lineNum">     457 </span>            :   template&lt;int C&gt;</a>
+<a name="458"><span class="lineNum">     458 </span>            :   ASMJIT_INLINE void load(VirtReg* vreg, uint32_t physId) {</a>
+<a name="459"><span class="lineNum">     459 </span>            :     // Can be only called if variable is not allocated.</a>
+<a name="460"><span class="lineNum">     460 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="461"><span class="lineNum">     461 </span>            :     ASMJIT_ASSERT(vreg-&gt;getState() != VirtReg::kStateReg);</a>
+<a name="462"><span class="lineNum">     462 </span>            :     ASMJIT_ASSERT(vreg-&gt;getPhysId() == Globals::kInvalidRegId);</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :     emitLoad(vreg, physId, &quot;Load&quot;);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :     attach&lt;C&gt;(vreg, physId, false);</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            :   //! Save.</a>
+<a name="471"><span class="lineNum">     471 </span>            :   //!</a>
+<a name="472"><span class="lineNum">     472 </span>            :   //! Save the variable into its home location, but keep it as allocated.</a>
+<a name="473"><span class="lineNum">     473 </span>            :   template&lt;int C&gt;</a>
+<a name="474"><span class="lineNum">     474 </span>            :   ASMJIT_INLINE void save(VirtReg* vreg) {</a>
+<a name="475"><span class="lineNum">     475 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="476"><span class="lineNum">     476 </span>            :     ASMJIT_ASSERT(vreg-&gt;getState() == VirtReg::kStateReg);</a>
+<a name="477"><span class="lineNum">     477 </span>            :     ASMJIT_ASSERT(vreg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="480"><span class="lineNum">     480 </span>            :     uint32_t regMask = Utils::mask(physId);</a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">       3468 :     emitSave(vreg, physId, &quot;Save&quot;);</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :     vreg-&gt;setModified(false);</a>
+<a name="484"><span class="lineNum">     484 </span>            :     _x86State._modified.andNot(C, regMask);</a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">       3468 :   }</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="490"><span class="lineNum">     490 </span>            :   // [Move / Swap]</a>
+<a name="491"><span class="lineNum">     491 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            :   //! Move a register.</a>
+<a name="494"><span class="lineNum">     494 </span>            :   //!</a>
+<a name="495"><span class="lineNum">     495 </span>            :   //! Move register from one index to another, emitting 'Move' if needed. This</a>
+<a name="496"><span class="lineNum">     496 </span>            :   //! function does nothing if register is already at the given index.</a>
+<a name="497"><span class="lineNum">     497 </span>            :   template&lt;int C&gt;</a>
+<a name="498"><span class="lineNum">     498 </span>            :   ASMJIT_INLINE void move(VirtReg* vreg, uint32_t newPhysId) {</a>
+<a name="499"><span class="lineNum">     499 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="500"><span class="lineNum">     500 </span>            :     ASMJIT_ASSERT(vreg-&gt;getState() == VirtReg::kStateReg);</a>
+<a name="501"><span class="lineNum">     501 </span>            :     ASMJIT_ASSERT(vreg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            :     uint32_t oldPhysId = vreg-&gt;getPhysId();</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        656 :     if (newPhysId != oldPhysId) {</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        656 :       emitMove(vreg, newPhysId, oldPhysId, &quot;Move&quot;);</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :       rebase&lt;C&gt;(vreg, newPhysId, oldPhysId);</a>
+<a name="507"><span class="lineNum">     507 </span>            :     }</a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="510"><span class="lineNum">     510 </span>            :   }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            :   //! Swap two registers</a>
+<a name="513"><span class="lineNum">     513 </span>            :   //!</a>
+<a name="514"><span class="lineNum">     514 </span>            :   //! It's only possible to swap Gp registers.</a>
+<a name="515"><span class="lineNum">     515 </span>            :   ASMJIT_INLINE void swapGp(VirtReg* aVReg, VirtReg* bVReg) {</a>
+<a name="516"><span class="lineNum">     516 </span>            :     ASMJIT_ASSERT(aVReg != bVReg);</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            :     ASMJIT_ASSERT(aVReg-&gt;getKind() == X86Reg::kKindGp);</a>
+<a name="519"><span class="lineNum">     519 </span>            :     ASMJIT_ASSERT(aVReg-&gt;getState() == VirtReg::kStateReg);</a>
+<a name="520"><span class="lineNum">     520 </span>            :     ASMJIT_ASSERT(aVReg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            :     ASMJIT_ASSERT(bVReg-&gt;getKind() == X86Reg::kKindGp);</a>
+<a name="523"><span class="lineNum">     523 </span>            :     ASMJIT_ASSERT(bVReg-&gt;getState() == VirtReg::kStateReg);</a>
+<a name="524"><span class="lineNum">     524 </span>            :     ASMJIT_ASSERT(bVReg-&gt;getPhysId() != Globals::kInvalidRegId);</a>
+<a name="525"><span class="lineNum">     525 </span>            : </a>
+<a name="526"><span class="lineNum">     526 </span>            :     uint32_t aIndex = aVReg-&gt;getPhysId();</a>
+<a name="527"><span class="lineNum">     527 </span>            :     uint32_t bIndex = bVReg-&gt;getPhysId();</a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :     emitSwapGp(aVReg, bVReg, aIndex, bIndex, &quot;Swap&quot;);</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :     aVReg-&gt;setPhysId(bIndex);</a>
+<a name="532"><span class="lineNum">     532 </span>            :     bVReg-&gt;setPhysId(aIndex);</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :     _x86State.getListByKind(X86Reg::kKindGp)[aIndex] = bVReg;</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :     _x86State.getListByKind(X86Reg::kKindGp)[bIndex] = aVReg;</span></a>
+<a name="536"><span class="lineNum">     536 </span>            : </a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :     uint32_t m = aVReg-&gt;isModified() ^ bVReg-&gt;isModified();</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :     _x86State._modified.xor_(X86Reg::kKindGp, (m &lt;&lt; aIndex) | (m &lt;&lt; bIndex));</span></a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="541"><span class="lineNum">     541 </span>            :   }</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="544"><span class="lineNum">     544 </span>            :   // [Alloc / Spill]</a>
+<a name="545"><span class="lineNum">     545 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :   //! Alloc.</a>
+<a name="548"><span class="lineNum">     548 </span>            :   template&lt;int C&gt;</a>
+<a name="549"><span class="lineNum">     549 </span>            :   ASMJIT_INLINE void alloc(VirtReg* vreg, uint32_t physId) {</a>
+<a name="550"><span class="lineNum">     550 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="551"><span class="lineNum">     551 </span>            :     ASMJIT_ASSERT(physId != Globals::kInvalidRegId);</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span>            :     uint32_t oldPhysId = vreg-&gt;getPhysId();</a>
+<a name="554"><span class="lineNum">     554 </span>            :     uint32_t oldState = vreg-&gt;getState();</a>
+<a name="555"><span class="lineNum">     555 </span>            :     uint32_t regMask = Utils::mask(physId);</a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span>            :     ASMJIT_ASSERT(_x86State.getListByKind(C)[physId] == nullptr || physId == oldPhysId);</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">       4424 :     if (oldState != VirtReg::kStateReg) {</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">       4424 :       if (oldState == VirtReg::kStateMem)</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">       4424 :         emitLoad(vreg, physId, &quot;Alloc&quot;);</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :       vreg-&gt;setModified(false);</a>
+<a name="563"><span class="lineNum">     563 </span>            :     }</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :     else if (oldPhysId != physId) {</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :       emitMove(vreg, physId, oldPhysId, &quot;Alloc&quot;);</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineNoCov">          0 :       _x86State.getListByKind(C)[oldPhysId] = nullptr;</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineNoCov">          0 :       regMask ^= Utils::mask(oldPhysId);</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :     }</a>
+<a name="570"><span class="lineNum">     570 </span>            :     else {</a>
+<a name="571"><span class="lineNum">     571 </span>            :       ASMJIT_X86_CHECK_STATE</a>
+<a name="572"><span class="lineNum">     572 </span>            :       return;</a>
+<a name="573"><span class="lineNum">     573 </span>            :     }</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span>            :     vreg-&gt;setState(VirtReg::kStateReg);</a>
+<a name="576"><span class="lineNum">     576 </span>            :     vreg-&gt;setPhysId(physId);</a>
+<a name="577"><span class="lineNum">     577 </span>            :     vreg-&gt;addHomeId(physId);</a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">       4424 :     _x86State.getListByKind(C)[physId] = vreg;</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :     _x86State._occupied.xor_(C, regMask);</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">       4424 :     _x86State._modified.xor_(C, regMask &amp; -static_cast&lt;int32_t&gt;(vreg-&gt;isModified()));</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="584"><span class="lineNum">     584 </span>            :   }</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span>            :   //! Spill.</a>
+<a name="587"><span class="lineNum">     587 </span>            :   //!</a>
+<a name="588"><span class="lineNum">     588 </span>            :   //! Spill variable/register, saves the content to the memory-home if modified.</a>
+<a name="589"><span class="lineNum">     589 </span>            :   template&lt;int C&gt;</a>
+<a name="590"><span class="lineNum">     590 </span>            :   ASMJIT_INLINE void spill(VirtReg* vreg) {</a>
+<a name="591"><span class="lineNum">     591 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">        548 :     if (vreg-&gt;getState() != VirtReg::kStateReg) {</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :       ASMJIT_X86_CHECK_STATE</a>
+<a name="595"><span class="lineNum">     595 </span>            :       return;</a>
+<a name="596"><span class="lineNum">     596 </span>            :     }</a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="599"><span class="lineNum">     599 </span>            :     ASMJIT_ASSERT(physId != Globals::kInvalidRegId);</a>
+<a name="600"><span class="lineNum">     600 </span>            :     ASMJIT_ASSERT(_x86State.getListByKind(C)[physId] == vreg);</a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">        548 :     if (vreg-&gt;isModified())</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">        536 :       emitSave(vreg, physId, &quot;Spill&quot;);</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :     detach&lt;C&gt;(vreg, physId, VirtReg::kStateMem);</a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="607"><span class="lineNum">     607 </span>            :   }</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="610"><span class="lineNum">     610 </span>            :   // [Modify]</a>
+<a name="611"><span class="lineNum">     611 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span>            :   template&lt;int C&gt;</a>
+<a name="614"><span class="lineNum">     614 </span>            :   ASMJIT_INLINE void modify(VirtReg* vreg) {</a>
+<a name="615"><span class="lineNum">     615 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="618"><span class="lineNum">     618 </span>            :     uint32_t regMask = Utils::mask(physId);</a>
+<a name="619"><span class="lineNum">     619 </span>            : </a>
+<a name="620"><span class="lineNum">     620 </span>            :     vreg-&gt;setModified(true);</a>
+<a name="621"><span class="lineNum">     621 </span>            :     _x86State._modified.or_(C, regMask);</a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="624"><span class="lineNum">     624 </span>            :   }</a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="627"><span class="lineNum">     627 </span>            :   // [Unuse]</a>
+<a name="628"><span class="lineNum">     628 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            :   //! Unuse.</a>
+<a name="631"><span class="lineNum">     631 </span>            :   //!</a>
+<a name="632"><span class="lineNum">     632 </span>            :   //! Unuse variable, it will be detached it if it's allocated then its state</a>
+<a name="633"><span class="lineNum">     633 </span>            :   //! will be changed to VirtReg::kStateNone.</a>
+<a name="634"><span class="lineNum">     634 </span>            :   template&lt;int C&gt;</a>
+<a name="635"><span class="lineNum">     635 </span>            :   ASMJIT_INLINE void unuse(VirtReg* vreg, uint32_t vState = VirtReg::kStateNone) {</a>
+<a name="636"><span class="lineNum">     636 </span>            :     ASMJIT_ASSERT(vreg-&gt;getKind() == C);</a>
+<a name="637"><span class="lineNum">     637 </span>            :     ASMJIT_ASSERT(vState != VirtReg::kStateReg);</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            :     uint32_t physId = vreg-&gt;getPhysId();</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">      50462 :     if (physId != Globals::kInvalidRegId)</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :       detach&lt;C&gt;(vreg, physId, vState);</a>
+<a name="642"><span class="lineNum">     642 </span>            :     else</a>
+<a name="643"><span class="lineNum">     643 </span>            :       vreg-&gt;setState(vState);</a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span>            :     ASMJIT_X86_CHECK_STATE</a>
+<a name="646"><span class="lineNum">     646 </span>            :   }</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="649"><span class="lineNum">     649 </span>            :   // [State]</a>
+<a name="650"><span class="lineNum">     650 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :   //! Get state as `X86RAState`.</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE X86RAState* getState() const { return const_cast&lt;X86RAState*&gt;(&amp;_x86State); }</span></a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :   virtual void loadState(RAState* src) override;</a>
+<a name="656"><span class="lineNum">     656 </span>            :   virtual RAState* saveState() override;</a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span>            :   virtual void switchState(RAState* src) override;</a>
+<a name="659"><span class="lineNum">     659 </span>            :   virtual void intersectStates(RAState* a, RAState* b) override;</a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="662"><span class="lineNum">     662 </span>            :   // [Memory]</a>
+<a name="663"><span class="lineNum">     663 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="664"><span class="lineNum">     664 </span>            : </a>
+<a name="665"><span class="lineNum">     665 </span>            :   ASMJIT_INLINE X86Mem getVarMem(VirtReg* vreg) {</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">       8428 :     (void)getVarCell(vreg);</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :     return X86Mem(Init,</a>
+<a name="668"><span class="lineNum">     668 </span>            :       cc()-&gt;_nativeGpReg.getType(), vreg-&gt;getId(),</a>
+<a name="669"><span class="lineNum">     669 </span>            :       Reg::kRegNone, kInvalidValue,</a>
+<a name="670"><span class="lineNum">     670 </span>            :       0, 0, Mem::kSignatureMemRegHomeFlag);</a>
+<a name="671"><span class="lineNum">     671 </span>            :   }</a>
+<a name="672"><span class="lineNum">     672 </span>            : </a>
+<a name="673"><span class="lineNum">     673 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="674"><span class="lineNum">     674 </span>            :   // [Fetch]</a>
+<a name="675"><span class="lineNum">     675 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span>            :   virtual Error fetch() override;</a>
+<a name="678"><span class="lineNum">     678 </span>            : </a>
+<a name="679"><span class="lineNum">     679 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="680"><span class="lineNum">     680 </span>            :   // [Annotate]</a>
+<a name="681"><span class="lineNum">     681 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="682"><span class="lineNum">     682 </span>            : </a>
+<a name="683"><span class="lineNum">     683 </span>            :   virtual Error annotate() override;</a>
+<a name="684"><span class="lineNum">     684 </span>            : </a>
+<a name="685"><span class="lineNum">     685 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="686"><span class="lineNum">     686 </span>            :   // [Translate]</a>
+<a name="687"><span class="lineNum">     687 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span>            :   virtual Error translate() override;</a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="692"><span class="lineNum">     692 </span>            :   // [Members]</a>
+<a name="693"><span class="lineNum">     693 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span>            :   //! Count of X86/X64 registers.</a>
+<a name="696"><span class="lineNum">     696 </span>            :   X86RegCount _regCount;</a>
+<a name="697"><span class="lineNum">     697 </span>            :   //! X86/X64 stack-pointer (esp or rsp).</a>
+<a name="698"><span class="lineNum">     698 </span>            :   X86Gp _zsp;</a>
+<a name="699"><span class="lineNum">     699 </span>            :   //! X86/X64 frame-pointer (ebp or rbp).</a>
+<a name="700"><span class="lineNum">     700 </span>            :   X86Gp _zbp;</a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            :   //! X86/X64 specific compiler state, linked to `_state`.</a>
+<a name="703"><span class="lineNum">     703 </span>            :   X86RAState _x86State;</a>
+<a name="704"><span class="lineNum">     704 </span>            :   //! Clobbered registers (for the whole function).</a>
+<a name="705"><span class="lineNum">     705 </span>            :   X86RegMask _clobberedRegs;</a>
+<a name="706"><span class="lineNum">     706 </span>            : </a>
+<a name="707"><span class="lineNum">     707 </span>            :   //! Global allocable registers mask.</a>
+<a name="708"><span class="lineNum">     708 </span>            :   uint32_t _gaRegs[Globals::kMaxVRegKinds];</a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span>            :   bool _avxEnabled;</a>
+<a name="711"><span class="lineNum">     711 </span>            : </a>
+<a name="712"><span class="lineNum">     712 </span>            :   //! Function variables base pointer (register).</a>
+<a name="713"><span class="lineNum">     713 </span>            :   uint8_t _varBaseRegId;</a>
+<a name="714"><span class="lineNum">     714 </span>            :   //! Function variables base offset.</a>
+<a name="715"><span class="lineNum">     715 </span>            :   int32_t _varBaseOffset;</a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            :   //! Temporary string builder used for logging.</a>
+<a name="718"><span class="lineNum">     718 </span>            :   StringBuilderTmp&lt;256&gt; _stringBuilder;</a>
+<a name="719"><span class="lineNum">     719 </span>            : };</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span>            : //! \}</a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            : } // asmjit namespace</a>
+<a name="724"><span class="lineNum">     724 </span>            : } // namespace PLMD</a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            : // [Api-End]</a>
+<a name="727"><span class="lineNum">     727 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span>            : // [Guard]</a>
+<a name="730"><span class="lineNum">     730 </span>            : #endif // !ASMJIT_DISABLE_COMPILER</a>
+<a name="731"><span class="lineNum">     731 </span>            : #endif // _ASMJIT_X86_X86REGALLOC_P_H</a>
+<a name="732"><span class="lineNum">     732 </span>            : #pragma GCC diagnostic pop</a>
+<a name="733"><span class="lineNum">     733 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="734"><span class="lineNum">     734 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/zone.cpp.func-sort-c.html b/coverage-libs/asmjit/zone.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b58ceb3115
--- /dev/null
+++ b/coverage-libs/asmjit/zone.cpp.func-sort-c.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/zone.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - zone.cpp<span style="font-size: 80%;"> (<a href="zone.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">136</td>
+            <td class="headerCovTableEntry">298</td>
+            <td class="headerCovTableEntryLo">45.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryLo">59.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="zone.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#750">_ZN4PLMD6asmjit12ZoneHashBase4_delEPNS0_12ZoneHashNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#734">_ZN4PLMD6asmjit12ZoneHashBase4_putEPNS0_12ZoneHashNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#692">_ZN4PLMD6asmjit12ZoneHashBase7_rehashEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#584">_ZN4PLMD6asmjit13ZoneBitVector4fillEmmb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#563">_ZN4PLMD6asmjit13ZoneBitVector7_appendEPNS0_8ZoneHeapEb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#462">_ZN4PLMD6asmjit13ZoneBitVector7_resizeEPNS0_8ZoneHeapEmmb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#201">_ZN4PLMD6asmjit4Zone7sformatEPKcz</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#352">_ZN4PLMD6asmjit8ZoneHeap15_releaseDynamicEPvm</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#675">_ZN4PLMD6asmjit12ZoneHashBase5resetEPNS0_8ZoneHeapE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#444">_ZN4PLMD6asmjit14ZoneVectorBase7_resizeEPNS0_8ZoneHeapEmm</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#344">_ZN4PLMD6asmjit8ZoneHeap12_allocZeroedEmRm</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#118">_ZN4PLMD6asmjit4Zone6_allocEm</a></td>
+              <td class="coverFnHi">7796</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#235">_ZN4PLMD6asmjit8ZoneHeap5resetEPNS0_4ZoneE</a></td>
+              <td class="coverFnHi">9740</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#61">_ZN4PLMD6asmjit4ZoneC2Ejj</a></td>
+              <td class="coverFnHi">11688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#68">_ZN4PLMD6asmjit4ZoneD2Ev</a></td>
+              <td class="coverFnHi">11688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#76">_ZN4PLMD6asmjit4Zone5resetEb</a></td>
+              <td class="coverFnHi">17532</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#379">_ZN4PLMD6asmjit14ZoneVectorBase5_growEPNS0_8ZoneHeapEmm</a></td>
+              <td class="coverFnHi">18288</td>
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+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#416">_ZN4PLMD6asmjit14ZoneVectorBase8_reserveEPNS0_8ZoneHeapEmm</a></td>
+              <td class="coverFnHi">18288</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#182">_ZN4PLMD6asmjit4Zone11allocZeroedEm</a></td>
+              <td class="coverFnHi">27684</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#188">_ZN4PLMD6asmjit4Zone3dupEPKvmb</a></td>
+              <td class="coverFnHi">36702</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#253">_ZN4PLMD6asmjit8ZoneHeap6_allocEmRm</a></td>
+              <td class="coverFnHi">79986</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/zone.cpp.func.html b/coverage-libs/asmjit/zone.cpp.func.html
new file mode 100644
index 0000000000..f075588705
--- /dev/null
+++ b/coverage-libs/asmjit/zone.cpp.func.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/zone.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - zone.cpp<span style="font-size: 80%;"> (<a href="zone.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">136</td>
+            <td class="headerCovTableEntry">298</td>
+            <td class="headerCovTableEntryLo">45.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryLo">59.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="zone.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#750">_ZN4PLMD6asmjit12ZoneHashBase4_delEPNS0_12ZoneHashNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#734">_ZN4PLMD6asmjit12ZoneHashBase4_putEPNS0_12ZoneHashNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#675">_ZN4PLMD6asmjit12ZoneHashBase5resetEPNS0_8ZoneHeapE</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#692">_ZN4PLMD6asmjit12ZoneHashBase7_rehashEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#584">_ZN4PLMD6asmjit13ZoneBitVector4fillEmmb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#563">_ZN4PLMD6asmjit13ZoneBitVector7_appendEPNS0_8ZoneHeapEb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#462">_ZN4PLMD6asmjit13ZoneBitVector7_resizeEPNS0_8ZoneHeapEmmb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#379">_ZN4PLMD6asmjit14ZoneVectorBase5_growEPNS0_8ZoneHeapEmm</a></td>
+              <td class="coverFnHi">18288</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#444">_ZN4PLMD6asmjit14ZoneVectorBase7_resizeEPNS0_8ZoneHeapEmm</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#416">_ZN4PLMD6asmjit14ZoneVectorBase8_reserveEPNS0_8ZoneHeapEmm</a></td>
+              <td class="coverFnHi">18288</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#182">_ZN4PLMD6asmjit4Zone11allocZeroedEm</a></td>
+              <td class="coverFnHi">27684</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#188">_ZN4PLMD6asmjit4Zone3dupEPKvmb</a></td>
+              <td class="coverFnHi">36702</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#76">_ZN4PLMD6asmjit4Zone5resetEb</a></td>
+              <td class="coverFnHi">17532</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#118">_ZN4PLMD6asmjit4Zone6_allocEm</a></td>
+              <td class="coverFnHi">7796</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#201">_ZN4PLMD6asmjit4Zone7sformatEPKcz</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#61">_ZN4PLMD6asmjit4ZoneC2Ejj</a></td>
+              <td class="coverFnHi">11688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#68">_ZN4PLMD6asmjit4ZoneD2Ev</a></td>
+              <td class="coverFnHi">11688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#344">_ZN4PLMD6asmjit8ZoneHeap12_allocZeroedEmRm</a></td>
+              <td class="coverFnHi">3896</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#352">_ZN4PLMD6asmjit8ZoneHeap15_releaseDynamicEPvm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#235">_ZN4PLMD6asmjit8ZoneHeap5resetEPNS0_4ZoneE</a></td>
+              <td class="coverFnHi">9740</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#253">_ZN4PLMD6asmjit8ZoneHeap6_allocEmRm</a></td>
+              <td class="coverFnHi">79986</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.cpp.gcov.html#655">_ZN4PLMD6asmjitL24ZoneHash_getClosestPrimeEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/zone.cpp.gcov.html b/coverage-libs/asmjit/zone.cpp.gcov.html
new file mode 100644
index 0000000000..2941f806a1
--- /dev/null
+++ b/coverage-libs/asmjit/zone.cpp.gcov.html
@@ -0,0 +1,935 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/zone.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - zone.cpp<span style="font-size: 80%;"> (source / <a href="zone.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">136</td>
+            <td class="headerCovTableEntry">298</td>
+            <td class="headerCovTableEntryLo">45.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryLo">59.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="21"><span class="lineNum">      21 </span>            : #pragma GCC diagnostic push</a>
+<a name="22"><span class="lineNum">      22 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : // [AsmJit]</a>
+<a name="24"><span class="lineNum">      24 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="25"><span class="lineNum">      25 </span>            : //</a>
+<a name="26"><span class="lineNum">      26 </span>            : // [License]</a>
+<a name="27"><span class="lineNum">      27 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : // [Export]</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define ASMJIT_EXPORTS</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // [Dependencies]</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;./zone.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // [Api-Begin]</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace asmjit {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : //! Zero size block used by `Zone` that doesn't have any memory allocated.</a>
+<a name="43"><span class="lineNum">      43 </span>            : static const Zone::Block Zone_zeroBlock = { nullptr, nullptr, 0, { 0 } };</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : static ASMJIT_INLINE uint32_t Zone_getAlignmentOffsetFromAlignment(uint32_t x) noexcept {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      11688 :   switch (x) {</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :     default: return 0;</a>
+<a name="48"><span class="lineNum">      48 </span>            :     case 0 : return 0;</a>
+<a name="49"><span class="lineNum">      49 </span>            :     case 1 : return 0;</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :     case 2 : return 1;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :     case 4 : return 2;</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :     case 8 : return 3;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :     case 16: return 4;</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :     case 32: return 5;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :     case 64: return 6;</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : // ============================================================================</a>
+<a name="60"><span class="lineNum">      60 </span>            : // [asmjit::Zone - Construction / Destruction]</a>
+<a name="61"><span class="lineNum">      61 </span>            : // ============================================================================</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      11688 : Zone::Zone(uint32_t blockSize, uint32_t blockAlignment) noexcept</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      11688 :   : _ptr(nullptr),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      11688 :     _end(nullptr),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      11688 :     _block(const_cast&lt;Zone::Block*&gt;(&amp;Zone_zeroBlock)),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      11688 :     _blockSize(blockSize),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      11688 :     _blockAlignmentShift(Zone_getAlignmentOffsetFromAlignment(blockAlignment)) {}</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      11688 : Zone::~Zone() noexcept {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      11688 :   reset(true);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      11688 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : // ============================================================================</a>
+<a name="75"><span class="lineNum">      75 </span>            : // [asmjit::Zone - Reset]</a>
+<a name="76"><span class="lineNum">      76 </span>            : // ============================================================================</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      17532 : void Zone::reset(bool releaseMemory) noexcept {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      17532 :   Block* cur = _block;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   // Can't be altered.</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      17532 :   if (cur == &amp;Zone_zeroBlock)</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :     return;</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      11688 :   if (releaseMemory) {</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     // Since cur can be in the middle of the double-linked list, we have to</a>
+<a name="87"><span class="lineNum">      87 </span>            :     // traverse to both directions `prev` and `next` separately.</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       7792 :     Block* next = cur-&gt;next;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     do {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       7796 :       Block* prev = cur-&gt;prev;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :       Internal::releaseMemory(cur);</a>
+<a name="92"><span class="lineNum">      92 </span>            :       cur = prev;</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       7796 :     } while (cur);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :     cur = next;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       7792 :     while (cur) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :       next = cur-&gt;next;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :       Internal::releaseMemory(cur);</a>
+<a name="99"><span class="lineNum">      99 </span>            :       cur = next;</a>
+<a name="100"><span class="lineNum">     100 </span>            :     }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       7792 :     _ptr = nullptr;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       7792 :     _end = nullptr;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       7792 :     _block = const_cast&lt;Zone::Block*&gt;(&amp;Zone_zeroBlock);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span>            :   else {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       3896 :     while (cur-&gt;prev)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :       cur = cur-&gt;prev;</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       3896 :     _ptr = cur-&gt;data;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       3896 :     _end = _ptr + cur-&gt;size;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       3896 :     _block = cur;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : // ============================================================================</a>
+<a name="117"><span class="lineNum">     117 </span>            : // [asmjit::Zone - Alloc]</a>
+<a name="118"><span class="lineNum">     118 </span>            : // ============================================================================</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       7796 : void* Zone::_alloc(size_t size) noexcept {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       7796 :   Block* curBlock = _block;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   uint8_t* p;</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       7796 :   size_t blockSize = std::max&lt;size_t&gt;(_blockSize, size);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       7796 :   size_t blockAlignment = getBlockAlignment();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // The `_alloc()` method can only be called if there is not enough space</a>
+<a name="128"><span class="lineNum">     128 </span>            :   // in the current block, see `alloc()` implementation for more details.</a>
+<a name="129"><span class="lineNum">     129 </span>            :   ASMJIT_ASSERT(curBlock == &amp;Zone_zeroBlock || getRemainingSize() &lt; size);</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   // If the `Zone` has been cleared the current block doesn't have to be the</a>
+<a name="132"><span class="lineNum">     132 </span>            :   // last one. Check if there is a block that can be used instead of allocating</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // a new one. If there is a `next` block it's completely unused, we don't have</a>
+<a name="134"><span class="lineNum">     134 </span>            :   // to check for remaining bytes.</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       7796 :   Block* next = curBlock-&gt;next;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       7796 :   if (next &amp;&amp; next-&gt;size &gt;= size) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     p = Utils::alignTo(next-&gt;data, blockAlignment);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     _block = next;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     _ptr = p + size;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     _end = next-&gt;data + next-&gt;size;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     return static_cast&lt;void*&gt;(p);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Prevent arithmetic overflow.</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       7796 :   if (ASMJIT_UNLIKELY(blockSize &gt; (~static_cast&lt;size_t&gt;(0) - sizeof(Block) - blockAlignment)))</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     return nullptr;</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       7796 :   blockSize += blockAlignment;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       7796 :   Block* newBlock = static_cast&lt;Block*&gt;(Internal::allocMemory(sizeof(Block) + blockSize));</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       7796 :   if (ASMJIT_UNLIKELY(!newBlock))</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     return nullptr;</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Align the pointer to `blockAlignment` and adjust the size of this block</a>
+<a name="157"><span class="lineNum">     157 </span>            :   // accordingly. It's the same as using `blockAlignment - Utils::alignDiff()`,</a>
+<a name="158"><span class="lineNum">     158 </span>            :   // just written differently.</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       7796 :   p = Utils::alignTo(newBlock-&gt;data, blockAlignment);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       7796 :   newBlock-&gt;prev = nullptr;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       7796 :   newBlock-&gt;next = nullptr;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       7796 :   newBlock-&gt;size = blockSize;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       7796 :   if (curBlock != &amp;Zone_zeroBlock) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          4 :     newBlock-&gt;prev = curBlock;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          4 :     curBlock-&gt;next = newBlock;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :     // Does only happen if there is a next block, but the requested memory</a>
+<a name="169"><span class="lineNum">     169 </span>            :     // can't fit into it. In this case a new buffer is allocated and inserted</a>
+<a name="170"><span class="lineNum">     170 </span>            :     // between the current block and the next one.</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 :     if (next) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :       newBlock-&gt;next = next;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :       next-&gt;prev = newBlock;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     }</a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       7796 :   _block = newBlock;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       7796 :   _ptr = p + size;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       7796 :   _end = newBlock-&gt;data + blockSize;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       7796 :   return static_cast&lt;void*&gt;(p);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      27684 : void* Zone::allocZeroed(size_t size) noexcept {</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   void* p = alloc(size);</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">      27684 :   if (ASMJIT_UNLIKELY(!p)) return p;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      27684 :   return ::memset(p, 0, size);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      36702 : void* Zone::dup(const void* data, size_t size, bool nullTerminate) noexcept {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      36702 :   if (ASMJIT_UNLIKELY(!data || !size)) return nullptr;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   ASMJIT_ASSERT(size != IntTraits&lt;size_t&gt;::maxValue());</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      36702 :   uint8_t* m = allocT&lt;uint8_t&gt;(size + nullTerminate);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      36702 :   if (ASMJIT_UNLIKELY(!m)) return nullptr;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   ::memcpy(m, data, size);</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      36702 :   if (nullTerminate) m[size] = '\0';</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   return static_cast&lt;void*&gt;(m);</a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 : char* Zone::sformat(const char* fmt, ...) noexcept {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(!fmt)) return nullptr;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   char buf[512];</a>
+<a name="207"><span class="lineNum">     207 </span>            :   size_t len;</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   va_list ap;</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   va_start(ap, fmt);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   len = vsnprintf(buf, ASMJIT_ARRAY_SIZE(buf) - 1, fmt, ap);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   buf[len++] = 0;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   va_end(ap);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   return static_cast&lt;char*&gt;(dup(buf, len));</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            : // ============================================================================</a>
+<a name="220"><span class="lineNum">     220 </span>            : // [asmjit::ZoneHeap - Helpers]</a>
+<a name="221"><span class="lineNum">     221 </span>            : // ============================================================================</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : static bool ZoneHeap_hasDynamicBlock(ZoneHeap* self, ZoneHeap::DynamicBlock* block) noexcept {</a>
+<a name="224"><span class="lineNum">     224 </span>            :   ZoneHeap::DynamicBlock* cur = self-&gt;_dynamicBlocks;</a>
+<a name="225"><span class="lineNum">     225 </span>            :   while (cur) {</a>
+<a name="226"><span class="lineNum">     226 </span>            :     if (cur == block)</a>
+<a name="227"><span class="lineNum">     227 </span>            :       return true;</a>
+<a name="228"><span class="lineNum">     228 </span>            :     cur = cur-&gt;next;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            :   return false;</a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : // ============================================================================</a>
+<a name="234"><span class="lineNum">     234 </span>            : // [asmjit::ZoneHeap - Init / Reset]</a>
+<a name="235"><span class="lineNum">     235 </span>            : // ============================================================================</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       9740 : void ZoneHeap::reset(Zone* zone) noexcept {</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   // Free dynamic blocks.</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       9740 :   DynamicBlock* block = _dynamicBlocks;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       9748 :   while (block) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          8 :     DynamicBlock* next = block-&gt;next;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     Internal::releaseMemory(block);</a>
+<a name="243"><span class="lineNum">     243 </span>            :     block = next;</a>
+<a name="244"><span class="lineNum">     244 </span>            :   }</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :   // Zero the entire class and initialize to the given `zone`.</a>
+<a name="247"><span class="lineNum">     247 </span>            :   ::memset(this, 0, sizeof(*this));</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       9740 :   _zone = zone;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       9740 : }</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : // ============================================================================</a>
+<a name="252"><span class="lineNum">     252 </span>            : // [asmjit::ZoneHeap - Alloc / Release]</a>
+<a name="253"><span class="lineNum">     253 </span>            : // ============================================================================</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">      79986 : void* ZoneHeap::_alloc(size_t size, size_t&amp; allocatedSize) noexcept {</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   ASMJIT_ASSERT(isInitialized());</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // We use our memory pool only if the requested block is of a reasonable size.</a>
+<a name="259"><span class="lineNum">     259 </span>            :   uint32_t slot;</a>
+<a name="260"><span class="lineNum">     260 </span>            :   if (_getSlotIndex(size, slot, allocatedSize)) {</a>
+<a name="261"><span class="lineNum">     261 </span>            :     // Slot reuse.</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      79978 :     uint8_t* p = reinterpret_cast&lt;uint8_t*&gt;(_slots[slot]);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">      79978 :     size = allocatedSize;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      79978 :     if (p) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       1688 :       _slots[slot] = reinterpret_cast&lt;Slot*&gt;(p)-&gt;next;</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :       //printf(&quot;ALLOCATED %p of size %d (SLOT %d)\n&quot;, p, int(size), slot);</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       1688 :       return p;</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :     // So use Zone to allocate a new chunk for us. But before we use it, we</a>
+<a name="272"><span class="lineNum">     272 </span>            :     // check if there is enough room for the new chunk in zone, and if not,</a>
+<a name="273"><span class="lineNum">     273 </span>            :     // we redistribute the remaining memory in Zone's current block into slots.</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      78290 :     Zone* zone = _zone;</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :     p = Utils::alignTo(zone-&gt;getCursor(), kBlockAlignment);</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      78290 :     size_t remain = (p &lt;= zone-&gt;getEnd()) ? (size_t)(zone-&gt;getEnd() - p) : size_t(0);</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      78290 :     if (ASMJIT_LIKELY(remain &gt;= size)) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">      74394 :       zone-&gt;setCursor(p + size);</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :       //printf(&quot;ALLOCATED %p of size %d (SLOT %d)\n&quot;, p, int(size), slot);</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">      74394 :       return p;</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :     }</a>
+<a name="283"><span class="lineNum">     283 </span>            :     else {</a>
+<a name="284"><span class="lineNum">     284 </span>            :       // Distribute the remaining memory to suitable slots.</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       3896 :       if (remain &gt;= kLoGranularity) {</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :         do {</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :           size_t distSize = std::min&lt;size_t&gt;(remain, kLoMaxSize);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :           uint32_t distSlot = static_cast&lt;uint32_t&gt;((distSize - kLoGranularity) / kLoGranularity);</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :           ASMJIT_ASSERT(distSlot &lt; kLoCount);</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :           reinterpret_cast&lt;Slot*&gt;(p)-&gt;next = _slots[distSlot];</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :           _slots[distSlot] = reinterpret_cast&lt;Slot*&gt;(p);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :           p += distSize;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :           remain -= distSize;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :         } while (remain &gt;= kLoGranularity);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :         zone-&gt;setCursor(p);</a>
+<a name="298"><span class="lineNum">     298 </span>            :       }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       3896 :       p = static_cast&lt;uint8_t*&gt;(zone-&gt;_alloc(size));</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       3896 :       if (ASMJIT_UNLIKELY(!p)) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :         allocatedSize = 0;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :         return nullptr;</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :       }</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :       //printf(&quot;ALLOCATED %p of size %d (SLOT %d)\n&quot;, p, int(size), slot);</a>
+<a name="307"><span class="lineNum">     307 </span>            :       return p;</a>
+<a name="308"><span class="lineNum">     308 </span>            :     }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   }</a>
+<a name="310"><span class="lineNum">     310 </span>            :   else {</a>
+<a name="311"><span class="lineNum">     311 </span>            :     // Allocate a dynamic block.</a>
+<a name="312"><span class="lineNum">     312 </span>            :     size_t overhead = sizeof(DynamicBlock) + sizeof(DynamicBlock*) + kBlockAlignment;</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :     // Handle a possible overflow.</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          8 :     if (ASMJIT_UNLIKELY(overhead &gt;= ~static_cast&lt;size_t&gt;(0) - size))</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :       return nullptr;</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          8 :     void* p = Internal::allocMemory(size + overhead);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          8 :     if (ASMJIT_UNLIKELY(!p)) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :       allocatedSize = 0;</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :       return nullptr;</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :     }</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            :     // Link as first in `_dynamicBlocks` double-linked list.</a>
+<a name="325"><span class="lineNum">     325 </span>            :     DynamicBlock* block = static_cast&lt;DynamicBlock*&gt;(p);</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          8 :     DynamicBlock* next = _dynamicBlocks;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          8 :     if (next)</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :       next-&gt;prev = block;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          8 :     block-&gt;prev = nullptr;</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          8 :     block-&gt;next = next;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          8 :     _dynamicBlocks = block;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :     // Align the pointer to the guaranteed alignment and store `DynamicBlock`</a>
+<a name="336"><span class="lineNum">     336 </span>            :     // at the end of the memory block, so `_releaseDynamic()` can find it.</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          8 :     p = Utils::alignTo(static_cast&lt;uint8_t*&gt;(p) + sizeof(DynamicBlock) + sizeof(DynamicBlock*), kBlockAlignment);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          8 :     reinterpret_cast&lt;DynamicBlock**&gt;(p)[-1] = block;</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          8 :     allocatedSize = size;</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :     //printf(&quot;ALLOCATED DYNAMIC %p of size %d\n&quot;, p, int(size));</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          8 :     return p;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span>            : }</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">       3896 : void* ZoneHeap::_allocZeroed(size_t size, size_t&amp; allocatedSize) noexcept {</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :   ASMJIT_ASSERT(isInitialized());</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">       3896 :   void* p = _alloc(size, allocatedSize);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">       3896 :   if (ASMJIT_UNLIKELY(!p)) return p;</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">       3896 :   return ::memset(p, 0, allocatedSize);</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : }</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 : void ZoneHeap::_releaseDynamic(void* p, size_t size) noexcept {</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :   ASMJIT_ASSERT(isInitialized());</a>
+<a name="356"><span class="lineNum">     356 </span>            :   //printf(&quot;RELEASING DYNAMIC %p of size %d\n&quot;, p, int(size));</a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            :   // Pointer to `DynamicBlock` is stored at [-1].</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :   DynamicBlock* block = reinterpret_cast&lt;DynamicBlock**&gt;(p)[-1];</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :   ASMJIT_ASSERT(ZoneHeap_hasDynamicBlock(this, block));</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   // Unlink and free.</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   DynamicBlock* prev = block-&gt;prev;</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :   DynamicBlock* next = block-&gt;next;</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :   if (prev)</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :     prev-&gt;next = next;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   else</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     _dynamicBlocks = next;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :   if (next)</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     next-&gt;prev = prev;</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            :   Internal::releaseMemory(block);</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : // ============================================================================</a>
+<a name="378"><span class="lineNum">     378 </span>            : // [asmjit::ZoneVectorBase - Helpers]</a>
+<a name="379"><span class="lineNum">     379 </span>            : // ============================================================================</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">      18288 : Error ZoneVectorBase::_grow(ZoneHeap* heap, size_t sizeOfT, size_t n) noexcept {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">      18288 :   size_t threshold = Globals::kAllocThreshold / sizeOfT;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">      18288 :   size_t capacity = _capacity;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">      18288 :   size_t after = _length;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">      18288 :   if (ASMJIT_UNLIKELY(IntTraits&lt;size_t&gt;::maxValue() - n &lt; after))</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      18288 :   after += n;</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      18288 :   if (capacity &gt;= after)</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     return kErrorOk;</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span>            :   // ZoneVector is used as an array to hold short-lived data structures used</a>
+<a name="394"><span class="lineNum">     394 </span>            :   // during code generation. The growing strategy is simple - use small capacity</a>
+<a name="395"><span class="lineNum">     395 </span>            :   // at the beginning (very good for ZoneHeap) and then grow quicker to prevent</a>
+<a name="396"><span class="lineNum">     396 </span>            :   // successive reallocations.</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">      18288 :   if (capacity &lt; 4)</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :     capacity = 4;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       6600 :   else if (capacity &lt; 8)</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :     capacity = 8;</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       3500 :   else if (capacity &lt; 16)</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :     capacity = 16;</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       1232 :   else if (capacity &lt; 64)</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :     capacity = 64;</a>
+<a name="405"><span class="lineNum">     405 </span>            :   else if (capacity &lt; 256)</a>
+<a name="406"><span class="lineNum">     406 </span>            :     capacity = 256;</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">      18288 :   while (capacity &lt; after) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :     if (capacity &lt; threshold)</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :       capacity *= 2;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :     else</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :       capacity += threshold;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :   }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">      18288 :   return _reserve(heap, sizeOfT, capacity);</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : }</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">      18288 : Error ZoneVectorBase::_reserve(ZoneHeap* heap, size_t sizeOfT, size_t n) noexcept {</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      18288 :   size_t oldCapacity = _capacity;</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      18288 :   if (oldCapacity &gt;= n) return kErrorOk;</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">      18288 :   size_t nBytes = n * sizeOfT;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">      18288 :   if (ASMJIT_UNLIKELY(nBytes &lt; n))</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            :   size_t allocatedBytes;</a>
+<a name="427"><span class="lineNum">     427 </span>            :   uint8_t* newData = static_cast&lt;uint8_t*&gt;(heap-&gt;alloc(nBytes, allocatedBytes));</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">      18288 :   if (ASMJIT_UNLIKELY(!newData))</span></a>
+<a name="430"><span class="lineNum">     430 </span>            :     return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">      18288 :   void* oldData = _data;</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">      18288 :   if (_length)</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">       6600 :     ::memcpy(newData, oldData, _length * sizeOfT);</span></a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">      18288 :   if (oldData)</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">       6600 :     heap-&gt;release(oldData, oldCapacity * sizeOfT);</span></a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">      18288 :   _capacity = allocatedBytes / sizeOfT;</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   ASMJIT_ASSERT(_capacity &gt;= n);</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">      18288 :   _data = newData;</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">      18288 :   return kErrorOk;</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : }</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">       3896 : Error ZoneVectorBase::_resize(ZoneHeap* heap, size_t sizeOfT, size_t n) noexcept {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">       3896 :   size_t length = _length;</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">       3896 :   if (_capacity &lt; n) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">       1948 :     ASMJIT_PROPAGATE(_grow(heap, sizeOfT, n - length));</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :     ASMJIT_ASSERT(_capacity &gt;= n);</a>
+<a name="451"><span class="lineNum">     451 </span>            :   }</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">       3896 :   if (length &lt; n)</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">       3896 :     ::memset(static_cast&lt;uint8_t*&gt;(_data) + length * sizeOfT, 0, (n - length) * sizeOfT);</span></a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">       3896 :   _length = n;</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">       3896 :   return kErrorOk;</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            : // ============================================================================</a>
+<a name="461"><span class="lineNum">     461 </span>            : // [asmjit::ZoneBitVector - Ops]</a>
+<a name="462"><span class="lineNum">     462 </span>            : // ============================================================================</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 : Error ZoneBitVector::_resize(ZoneHeap* heap, size_t newLength, size_t idealCapacity, bool newBitsValue) noexcept {</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :   ASMJIT_ASSERT(idealCapacity &gt;= newLength);</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :   if (newLength &lt;= _length) {</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :     // The size after the resize is lesser than or equal to the current length.</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :     size_t idx = newLength / kBitsPerWord;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 :     size_t bit = newLength % kBitsPerWord;</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :     // Just set all bits outside of the new length in the last word to zero.</a>
+<a name="473"><span class="lineNum">     473 </span>            :     // There is a case that there are not bits to set if `bit` is zero. This</a>
+<a name="474"><span class="lineNum">     474 </span>            :     // happens when `newLength` is a multiply of `kBitsPerWord` like 64, 128,</a>
+<a name="475"><span class="lineNum">     475 </span>            :     // and so on. In that case don't change anything as that would mean settings</a>
+<a name="476"><span class="lineNum">     476 </span>            :     // bits outside of the `_length`.</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :     if (bit)</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :       _data[idx] &amp;= (static_cast&lt;uintptr_t&gt;(1) &lt;&lt; bit) - 1U;</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 :     _length = newLength;</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :     return kErrorOk;</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   }</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :   size_t oldLength = _length;</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :   BitWord* data = _data;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :   if (newLength &gt; _capacity) {</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :     // Realloc needed... Calculate the minimum capacity (in bytes) requied.</a>
+<a name="489"><span class="lineNum">     489 </span>            :     size_t minimumCapacityInBits = Utils::alignTo&lt;size_t&gt;(idealCapacity, kBitsPerWord);</a>
+<a name="490"><span class="lineNum">     490 </span>            :     size_t allocatedCapacity;</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(minimumCapacityInBits &lt; newLength))</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :       return DebugUtils::errored(kErrorNoHeapMemory);</span></a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :     // Normalize to bytes.</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :     size_t minimumCapacity = minimumCapacityInBits / 8;</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :     BitWord* newData = static_cast&lt;BitWord*&gt;(heap-&gt;alloc(minimumCapacity, allocatedCapacity));</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(!newData))</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :       return DebugUtils::errored(kErrorNoHeapMemory);</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            :     // `allocatedCapacity` now contains number in bytes, we need bits.</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :     size_t allocatedCapacityInBits = allocatedCapacity * 8;</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            :     // Arithmetic overflow should normally not happen. If it happens we just</a>
+<a name="506"><span class="lineNum">     506 </span>            :     // change the `allocatedCapacityInBits` to the `minimumCapacityInBits` as</a>
+<a name="507"><span class="lineNum">     507 </span>            :     // this value is still safe to be used to call `_heap-&gt;release(...)`.</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineNoCov">          0 :     if (ASMJIT_UNLIKELY(allocatedCapacityInBits &lt; allocatedCapacity))</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :       allocatedCapacityInBits = minimumCapacityInBits;</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :     if (oldLength)</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :       ::memcpy(newData, data, _wordsPerBits(oldLength));</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :     if (data)</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :       heap-&gt;release(data, _capacity / 8);</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :     data = newData;</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :     _data = data;</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :     _capacity = allocatedCapacityInBits;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :   }</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            :   // Start (of the old length) and end (of the new length) bits</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :   size_t idx = oldLength / kBitsPerWord;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :   size_t startBit = oldLength % kBitsPerWord;</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :   size_t endBit = newLength % kBitsPerWord;</span></a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            :   // Set new bits to either 0 or 1. The `pattern` is used to set multiple</a>
+<a name="528"><span class="lineNum">     528 </span>            :   // bits per bit-word and contains either all zeros or all ones.</a>
+<a name="529"><span class="lineNum">     529 </span>            :   BitWord pattern = _patternFromBit(newBitsValue);</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :   // First initialize the last bit-word of the old length.</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :   if (startBit) {</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :     size_t nBits = 0;</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :     if (idx == (newLength / kBitsPerWord)) {</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :       // The number of bit-words is the same after the resize. In that case</a>
+<a name="537"><span class="lineNum">     537 </span>            :       // we need to set only bits necessary in the current last bit-word.</a>
+<a name="538"><span class="lineNum">     538 </span>            :       ASMJIT_ASSERT(startBit &lt; endBit);</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :       nBits = endBit - startBit;</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :     }</a>
+<a name="541"><span class="lineNum">     541 </span>            :     else {</a>
+<a name="542"><span class="lineNum">     542 </span>            :       // There is be more bit-words after the resize. In that case we don't</a>
+<a name="543"><span class="lineNum">     543 </span>            :       // have to be extra careful about the last bit-word of the old length.</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :       nBits = kBitsPerWord - startBit;</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :     }</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :     data[idx++] |= pattern &lt;&lt; nBits;</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :   }</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            :   // Initialize all bit-words after the last bit-word of the old length.</a>
+<a name="551"><span class="lineNum">     551 </span>            :   size_t endIdx = _wordsPerBits(newLength);</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :   endIdx -= static_cast&lt;size_t&gt;(endIdx * kBitsPerWord == newLength);</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :   while (idx &lt;= endIdx)</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineNoCov">          0 :     data[idx++] = pattern;</span></a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span>            :   // Clear unused bits of the last bit-word.</a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineNoCov">          0 :   if (endBit)</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :     data[endIdx] &amp;= (static_cast&lt;BitWord&gt;(1) &lt;&lt; endBit) - 1;</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :   _length = newLength;</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :   return kErrorOk;</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : }</a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 : Error ZoneBitVector::_append(ZoneHeap* heap, bool value) noexcept {</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :   size_t kThreshold = Globals::kAllocThreshold * 8;</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineNoCov">          0 :   size_t newLength = _length + 1;</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineNoCov">          0 :   size_t idealCapacity = _capacity;</span></a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :   if (idealCapacity &lt; 128)</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :     idealCapacity = 128;</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineNoCov">          0 :   else if (idealCapacity &lt;= kThreshold)</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :     idealCapacity *= 2;</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :   else</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :     idealCapacity += kThreshold;</span></a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(idealCapacity &lt; _capacity)) {</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :     // It's technically impossible that `_length + 1` overflows.</a>
+<a name="579"><span class="lineNum">     579 </span>            :     idealCapacity = newLength;</a>
+<a name="580"><span class="lineNum">     580 </span>            :     ASMJIT_ASSERT(idealCapacity &gt; _capacity);</a>
+<a name="581"><span class="lineNum">     581 </span>            :   }</a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :   return _resize(heap, newLength, idealCapacity, value);</span></a>
+<a name="584"><span class="lineNum">     584 </span>            : }</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 : Error ZoneBitVector::fill(size_t from, size_t to, bool value) noexcept {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(from &gt;= to)) {</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :     if (from &gt; to)</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :       return DebugUtils::errored(kErrorInvalidArgument);</a>
+<a name="590"><span class="lineNum">     590 </span>            :     else</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :       return kErrorOk;</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :   }</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span>            :   ASMJIT_ASSERT(from &lt;= _length);</a>
+<a name="595"><span class="lineNum">     595 </span>            :   ASMJIT_ASSERT(to &lt;= _length);</a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            :   // This is very similar to `ZoneBitVector::_fill()`, however, since we</a>
+<a name="598"><span class="lineNum">     598 </span>            :   // actually set bits that are already part of the container we need to</a>
+<a name="599"><span class="lineNum">     599 </span>            :   // special case filiing to zeros and ones.</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :   size_t idx = from / kBitsPerWord;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :   size_t startBit = from % kBitsPerWord;</span></a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :   size_t endIdx = to / kBitsPerWord;</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :   size_t endBit = to % kBitsPerWord;</span></a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :   BitWord* data = _data;</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :   ASMJIT_ASSERT(data != nullptr);</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            :   // Special case for non-zero `startBit`.</a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 :   if (startBit) {</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :     if (idx == endIdx) {</span></a>
+<a name="612"><span class="lineNum">     612 </span>            :       ASMJIT_ASSERT(startBit &lt; endBit);</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineNoCov">          0 :       size_t nBits = endBit - startBit;</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineNoCov">          0 :       BitWord mask = ((static_cast&lt;BitWord&gt;(1) &lt;&lt; nBits) - 1) &lt;&lt; startBit;</span></a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :       if (value)</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :         data[idx] |= mask;</span></a>
+<a name="619"><span class="lineNum">     619 </span>            :       else</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :         data[idx] &amp;= ~mask;</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :       return kErrorOk;</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :     }</a>
+<a name="623"><span class="lineNum">     623 </span>            :     else {</a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineNoCov">          0 :       BitWord mask = (static_cast&lt;BitWord&gt;(0) - 1) &lt;&lt; startBit;</span></a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :       if (value)</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :         data[idx++] |= mask;</span></a>
+<a name="628"><span class="lineNum">     628 </span>            :       else</a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :         data[idx++] &amp;= ~mask;</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :     }</a>
+<a name="631"><span class="lineNum">     631 </span>            :   }</a>
+<a name="632"><span class="lineNum">     632 </span>            : </a>
+<a name="633"><span class="lineNum">     633 </span>            :   // Fill all bits in case there is a gap between the current `idx` and `endIdx`.</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :   if (idx &lt; endIdx) {</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :     BitWord pattern = _patternFromBit(value);</a>
+<a name="636"><span class="lineNum">     636 </span>            :     do {</a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :       data[idx++] = pattern;</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineNoCov">          0 :     } while (idx &lt; endIdx);</span></a>
+<a name="639"><span class="lineNum">     639 </span>            :   }</a>
+<a name="640"><span class="lineNum">     640 </span>            : </a>
+<a name="641"><span class="lineNum">     641 </span>            :   // Special case for non-zero `endBit`.</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :   if (endBit) {</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :     BitWord mask = ((static_cast&lt;BitWord&gt;(1) &lt;&lt; endBit) - 1);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :     if (value)</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :       data[endIdx] |= mask;</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :     else</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineNoCov">          0 :       data[endIdx] &amp;= ~mask;</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :   }</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span>            :   return kErrorOk;</a>
+<a name="651"><span class="lineNum">     651 </span>            : }</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            : // ============================================================================</a>
+<a name="654"><span class="lineNum">     654 </span>            : // [asmjit::ZoneHashBase - Utilities]</a>
+<a name="655"><span class="lineNum">     655 </span>            : // ============================================================================</a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 : static uint32_t ZoneHash_getClosestPrime(uint32_t x) noexcept {</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :   static const uint32_t primeTable[] = {</a>
+<a name="659"><span class="lineNum">     659 </span>            :     23, 53, 193, 389, 769, 1543, 3079, 6151, 12289, 24593</a>
+<a name="660"><span class="lineNum">     660 </span>            :   };</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span>            :   size_t i = 0;</a>
+<a name="663"><span class="lineNum">     663 </span>            :   uint32_t p;</a>
+<a name="664"><span class="lineNum">     664 </span>            : </a>
+<a name="665"><span class="lineNum">     665 </span>            :   do {</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :     if ((p = primeTable[i]) &gt; x)</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :       break;</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :   } while (++i &lt; ASMJIT_ARRAY_SIZE(primeTable));</span></a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :   return p;</span></a>
+<a name="671"><span class="lineNum">     671 </span>            : }</a>
+<a name="672"><span class="lineNum">     672 </span>            : </a>
+<a name="673"><span class="lineNum">     673 </span>            : // ============================================================================</a>
+<a name="674"><span class="lineNum">     674 </span>            : // [asmjit::ZoneHashBase - Reset]</a>
+<a name="675"><span class="lineNum">     675 </span>            : // ============================================================================</a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">       3896 : void ZoneHashBase::reset(ZoneHeap* heap) noexcept {</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">       3896 :   ZoneHashNode** oldData = _data;</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">       3896 :   if (oldData != _embedded)</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :     _heap-&gt;release(oldData, _bucketsCount * sizeof(ZoneHashNode*));</span></a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">       3896 :   _heap = heap;</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">       3896 :   _size = 0;</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">       3896 :   _bucketsCount = 1;</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">       3896 :   _bucketsGrow = 1;</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">       3896 :   _data = _embedded;</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">       3896 :   _embedded[0] = nullptr;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">       3896 : }</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span>            : // ============================================================================</a>
+<a name="691"><span class="lineNum">     691 </span>            : // [asmjit::ZoneHashBase - Rehash]</a>
+<a name="692"><span class="lineNum">     692 </span>            : // ============================================================================</a>
+<a name="693"><span class="lineNum">     693 </span>            : </a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 : void ZoneHashBase::_rehash(uint32_t newCount) noexcept {</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :   ASMJIT_ASSERT(isInitialized());</a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :   ZoneHashNode** oldData = _data;</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :   ZoneHashNode** newData = reinterpret_cast&lt;ZoneHashNode**&gt;(</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :     _heap-&gt;allocZeroed(static_cast&lt;size_t&gt;(newCount) * sizeof(ZoneHashNode*)));</span></a>
+<a name="700"><span class="lineNum">     700 </span>            : </a>
+<a name="701"><span class="lineNum">     701 </span>            :   // We can still store nodes into the table, but it will degrade.</a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineNoCov">          0 :   if (ASMJIT_UNLIKELY(newData == nullptr))</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :     return;</a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span>            :   uint32_t i;</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineNoCov">          0 :   uint32_t oldCount = _bucketsCount;</span></a>
+<a name="707"><span class="lineNum">     707 </span>            : </a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; oldCount; i++) {</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :     ZoneHashNode* node = oldData[i];</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :     while (node) {</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineNoCov">          0 :       ZoneHashNode* next = node-&gt;_hashNext;</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :       uint32_t hMod = node-&gt;_hVal % newCount;</span></a>
+<a name="713"><span class="lineNum">     713 </span>            : </a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :       node-&gt;_hashNext = newData[hMod];</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :       newData[hMod] = node;</span></a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            :       node = next;</a>
+<a name="718"><span class="lineNum">     718 </span>            :     }</a>
+<a name="719"><span class="lineNum">     719 </span>            :   }</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span>            :   // 90% is the maximum occupancy, can't overflow since the maximum capacity</a>
+<a name="722"><span class="lineNum">     722 </span>            :   // is limited to the last prime number stored in the prime table.</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :   if (oldData != _embedded)</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineNoCov">          0 :     _heap-&gt;release(oldData, _bucketsCount * sizeof(ZoneHashNode*));</span></a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :   _bucketsCount = newCount;</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :   _bucketsGrow = newCount * 9 / 10;</span></a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineNoCov">          0 :   _data = newData;</span></a>
+<a name="730"><span class="lineNum">     730 </span>            : }</a>
+<a name="731"><span class="lineNum">     731 </span>            : </a>
+<a name="732"><span class="lineNum">     732 </span>            : // ============================================================================</a>
+<a name="733"><span class="lineNum">     733 </span>            : // [asmjit::ZoneHashBase - Ops]</a>
+<a name="734"><span class="lineNum">     734 </span>            : // ============================================================================</a>
+<a name="735"><span class="lineNum">     735 </span>            : </a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 : ZoneHashNode* ZoneHashBase::_put(ZoneHashNode* node) noexcept {</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineNoCov">          0 :   uint32_t hMod = node-&gt;_hVal % _bucketsCount;</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :   ZoneHashNode* next = _data[hMod];</span></a>
+<a name="739"><span class="lineNum">     739 </span>            : </a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :   node-&gt;_hashNext = next;</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 :   _data[hMod] = node;</span></a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineNoCov">          0 :   if (++_size &gt;= _bucketsGrow &amp;&amp; next) {</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :     uint32_t newCapacity = ZoneHash_getClosestPrime(_bucketsCount);</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :     if (newCapacity != _bucketsCount)</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 :       _rehash(newCapacity);</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :   }</a>
+<a name="748"><span class="lineNum">     748 </span>            : </a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineNoCov">          0 :   return node;</span></a>
+<a name="750"><span class="lineNum">     750 </span>            : }</a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineNoCov">          0 : ZoneHashNode* ZoneHashBase::_del(ZoneHashNode* node) noexcept {</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :   uint32_t hMod = node-&gt;_hVal % _bucketsCount;</span></a>
+<a name="754"><span class="lineNum">     754 </span>            : </a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :   ZoneHashNode** pPrev = &amp;_data[hMod];</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineNoCov">          0 :   ZoneHashNode* p = *pPrev;</span></a>
+<a name="757"><span class="lineNum">     757 </span>            : </a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :   while (p) {</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineNoCov">          0 :     if (p == node) {</span></a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineNoCov">          0 :       *pPrev = p-&gt;_hashNext;</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineNoCov">          0 :       return node;</span></a>
+<a name="762"><span class="lineNum">     762 </span>            :     }</a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineNoCov">          0 :     pPrev = &amp;p-&gt;_hashNext;</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineNoCov">          0 :     p = *pPrev;</span></a>
+<a name="766"><span class="lineNum">     766 </span>            :   }</a>
+<a name="767"><span class="lineNum">     767 </span>            : </a>
+<a name="768"><span class="lineNum">     768 </span>            :   return nullptr;</a>
+<a name="769"><span class="lineNum">     769 </span>            : }</a>
+<a name="770"><span class="lineNum">     770 </span>            : </a>
+<a name="771"><span class="lineNum">     771 </span>            : // ============================================================================</a>
+<a name="772"><span class="lineNum">     772 </span>            : // [asmjit::Zone - Test]</a>
+<a name="773"><span class="lineNum">     773 </span>            : // ============================================================================</a>
+<a name="774"><span class="lineNum">     774 </span>            : </a>
+<a name="775"><span class="lineNum">     775 </span>            : #if defined(ASMJIT_TEST)</a>
+<a name="776"><span class="lineNum">     776 </span>            : UNIT(base_zonevector) {</a>
+<a name="777"><span class="lineNum">     777 </span>            :   Zone zone(8096 - Zone::kZoneOverhead);</a>
+<a name="778"><span class="lineNum">     778 </span>            :   ZoneHeap heap(&amp;zone);</a>
+<a name="779"><span class="lineNum">     779 </span>            : </a>
+<a name="780"><span class="lineNum">     780 </span>            :   int i;</a>
+<a name="781"><span class="lineNum">     781 </span>            :   int kMax = 100000;</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            :   ZoneVector&lt;int&gt; vec;</a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            :   INFO(&quot;ZoneVector&lt;int&gt; basic tests&quot;);</a>
+<a name="786"><span class="lineNum">     786 </span>            :   EXPECT(vec.append(&amp;heap, 0) == kErrorOk);</a>
+<a name="787"><span class="lineNum">     787 </span>            :   EXPECT(vec.isEmpty() == false);</a>
+<a name="788"><span class="lineNum">     788 </span>            :   EXPECT(vec.getLength() == 1);</a>
+<a name="789"><span class="lineNum">     789 </span>            :   EXPECT(vec.getCapacity() &gt;= 1);</a>
+<a name="790"><span class="lineNum">     790 </span>            :   EXPECT(vec.indexOf(0) == 0);</a>
+<a name="791"><span class="lineNum">     791 </span>            :   EXPECT(vec.indexOf(-11) == Globals::kInvalidIndex);</a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span>            :   vec.clear();</a>
+<a name="794"><span class="lineNum">     794 </span>            :   EXPECT(vec.isEmpty());</a>
+<a name="795"><span class="lineNum">     795 </span>            :   EXPECT(vec.getLength() == 0);</a>
+<a name="796"><span class="lineNum">     796 </span>            :   EXPECT(vec.indexOf(0) == Globals::kInvalidIndex);</a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span>            :   for (i = 0; i &lt; kMax; i++) {</a>
+<a name="799"><span class="lineNum">     799 </span>            :     EXPECT(vec.append(&amp;heap, i) == kErrorOk);</a>
+<a name="800"><span class="lineNum">     800 </span>            :   }</a>
+<a name="801"><span class="lineNum">     801 </span>            :   EXPECT(vec.isEmpty() == false);</a>
+<a name="802"><span class="lineNum">     802 </span>            :   EXPECT(vec.getLength() == static_cast&lt;size_t&gt;(kMax));</a>
+<a name="803"><span class="lineNum">     803 </span>            :   EXPECT(vec.indexOf(kMax - 1) == static_cast&lt;size_t&gt;(kMax - 1));</a>
+<a name="804"><span class="lineNum">     804 </span>            : }</a>
+<a name="805"><span class="lineNum">     805 </span>            : </a>
+<a name="806"><span class="lineNum">     806 </span>            : UNIT(base_ZoneBitVector) {</a>
+<a name="807"><span class="lineNum">     807 </span>            :   Zone zone(8096 - Zone::kZoneOverhead);</a>
+<a name="808"><span class="lineNum">     808 </span>            :   ZoneHeap heap(&amp;zone);</a>
+<a name="809"><span class="lineNum">     809 </span>            : </a>
+<a name="810"><span class="lineNum">     810 </span>            :   size_t i, count;</a>
+<a name="811"><span class="lineNum">     811 </span>            :   size_t kMaxCount = 100;</a>
+<a name="812"><span class="lineNum">     812 </span>            : </a>
+<a name="813"><span class="lineNum">     813 </span>            :   ZoneBitVector vec;</a>
+<a name="814"><span class="lineNum">     814 </span>            :   EXPECT(vec.isEmpty());</a>
+<a name="815"><span class="lineNum">     815 </span>            :   EXPECT(vec.getLength() == 0);</a>
+<a name="816"><span class="lineNum">     816 </span>            : </a>
+<a name="817"><span class="lineNum">     817 </span>            :   INFO(&quot;ZoneBitVector::resize()&quot;);</a>
+<a name="818"><span class="lineNum">     818 </span>            :   for (count = 1; count &lt; kMaxCount; count++) {</a>
+<a name="819"><span class="lineNum">     819 </span>            :     vec.clear();</a>
+<a name="820"><span class="lineNum">     820 </span>            :     EXPECT(vec.resize(&amp;heap, count, false) == kErrorOk);</a>
+<a name="821"><span class="lineNum">     821 </span>            :     EXPECT(vec.getLength() == count);</a>
+<a name="822"><span class="lineNum">     822 </span>            : </a>
+<a name="823"><span class="lineNum">     823 </span>            :     for (i = 0; i &lt; count; i++)</a>
+<a name="824"><span class="lineNum">     824 </span>            :       EXPECT(vec.getAt(i) == false);</a>
+<a name="825"><span class="lineNum">     825 </span>            : </a>
+<a name="826"><span class="lineNum">     826 </span>            :     vec.clear();</a>
+<a name="827"><span class="lineNum">     827 </span>            :     EXPECT(vec.resize(&amp;heap, count, true) == kErrorOk);</a>
+<a name="828"><span class="lineNum">     828 </span>            :     EXPECT(vec.getLength() == count);</a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span>            :     for (i = 0; i &lt; count; i++)</a>
+<a name="831"><span class="lineNum">     831 </span>            :       EXPECT(vec.getAt(i) == true);</a>
+<a name="832"><span class="lineNum">     832 </span>            :   }</a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span>            :   INFO(&quot;ZoneBitVector::fill()&quot;);</a>
+<a name="835"><span class="lineNum">     835 </span>            :   for (count = 1; count &lt; kMaxCount; count += 2) {</a>
+<a name="836"><span class="lineNum">     836 </span>            :     vec.clear();</a>
+<a name="837"><span class="lineNum">     837 </span>            :     EXPECT(vec.resize(&amp;heap, count) == kErrorOk);</a>
+<a name="838"><span class="lineNum">     838 </span>            :     EXPECT(vec.getLength() == count);</a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span>            :     for (i = 0; i &lt; (count + 1) / 2; i++) {</a>
+<a name="841"><span class="lineNum">     841 </span>            :       bool value = static_cast&lt;bool&gt;(i &amp; 1);</a>
+<a name="842"><span class="lineNum">     842 </span>            :       EXPECT(vec.fill(i, count - i, value) == kErrorOk);</a>
+<a name="843"><span class="lineNum">     843 </span>            :     }</a>
+<a name="844"><span class="lineNum">     844 </span>            : </a>
+<a name="845"><span class="lineNum">     845 </span>            :     for (i = 0; i &lt; count; i++) {</a>
+<a name="846"><span class="lineNum">     846 </span>            :       EXPECT(vec.getAt(i) == static_cast&lt;bool&gt;(i &amp; 1));</a>
+<a name="847"><span class="lineNum">     847 </span>            :     }</a>
+<a name="848"><span class="lineNum">     848 </span>            :   }</a>
+<a name="849"><span class="lineNum">     849 </span>            : }</a>
+<a name="850"><span class="lineNum">     850 </span>            : </a>
+<a name="851"><span class="lineNum">     851 </span>            : #endif // ASMJIT_TEST</a>
+<a name="852"><span class="lineNum">     852 </span>            : </a>
+<a name="853"><span class="lineNum">     853 </span>            : } // asmjit namespace</a>
+<a name="854"><span class="lineNum">     854 </span>            : } // namespace PLMD</a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span>            : // [Api-End]</a>
+<a name="857"><span class="lineNum">     857 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="858"><span class="lineNum">     858 </span>            : #pragma GCC diagnostic pop</a>
+<a name="859"><span class="lineNum">     859 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/zone.h.func-sort-c.html b/coverage-libs/asmjit/zone.h.func-sort-c.html
new file mode 100644
index 0000000000..f4a2a49a67
--- /dev/null
+++ b/coverage-libs/asmjit/zone.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/zone.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - zone.h<span style="font-size: 80%;"> (<a href="zone.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryMed">78.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="zone.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.h.gcov.html#719">_ZN4PLMD6asmjit10ZoneVectorIPNS0_6CBPassEE6appendEPNS0_8ZoneHeapERKS3_</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.h.gcov.html#719">_ZN4PLMD6asmjit10ZoneVectorIPNS0_7VirtRegEE6appendEPNS0_8ZoneHeapERKS3_</a></td>
+              <td class="coverFnHi">23788</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/zone.h.func.html b/coverage-libs/asmjit/zone.h.func.html
new file mode 100644
index 0000000000..93adfaa200
--- /dev/null
+++ b/coverage-libs/asmjit/zone.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/zone.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - zone.h<span style="font-size: 80%;"> (<a href="zone.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryMed">78.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="zone.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.h.gcov.html#719">_ZN4PLMD6asmjit10ZoneVectorIPNS0_6CBPassEE6appendEPNS0_8ZoneHeapERKS3_</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="zone.h.gcov.html#719">_ZN4PLMD6asmjit10ZoneVectorIPNS0_7VirtRegEE6appendEPNS0_8ZoneHeapERKS3_</a></td>
+              <td class="coverFnHi">23788</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/asmjit/zone.h.gcov.html b/coverage-libs/asmjit/zone.h.gcov.html
new file mode 100644
index 0000000000..b5c7fc9a30
--- /dev/null
+++ b/coverage-libs/asmjit/zone.h.gcov.html
@@ -0,0 +1,1233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - asmjit/zone.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">asmjit</a> - zone.h<span style="font-size: 80%;"> (source / <a href="zone.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryMed">78.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2008-2017, Petr Kobalicek</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : #ifndef __PLUMED_asmjit_zone_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : #define __PLUMED_asmjit_zone_h</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="23"><span class="lineNum">      23 </span>            : #pragma GCC diagnostic push</a>
+<a name="24"><span class="lineNum">      24 </span>            : #pragma GCC diagnostic ignored &quot;-Wpedantic&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : // [AsmJit]</a>
+<a name="26"><span class="lineNum">      26 </span>            : // Complete x86/x64 JIT and Remote Assembler for C++.</a>
+<a name="27"><span class="lineNum">      27 </span>            : //</a>
+<a name="28"><span class="lineNum">      28 </span>            : // [License]</a>
+<a name="29"><span class="lineNum">      29 </span>            : // Zlib - See LICENSE.md file in the package.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // [Guard]</a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifndef _ASMJIT_BASE_ZONE_H</a>
+<a name="33"><span class="lineNum">      33 </span>            : #define _ASMJIT_BASE_ZONE_H</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // [Dependencies]</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;./utils.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // [Api-Begin]</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;./asmjit_apibegin.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace asmjit {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //! \addtogroup asmjit_base</a>
+<a name="45"><span class="lineNum">      45 </span>            : //! \{</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : // ============================================================================</a>
+<a name="48"><span class="lineNum">      48 </span>            : // [asmjit::Zone]</a>
+<a name="49"><span class="lineNum">      49 </span>            : // ============================================================================</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : //! Memory zone.</a>
+<a name="52"><span class="lineNum">      52 </span>            : //!</a>
+<a name="53"><span class="lineNum">      53 </span>            : //! Zone is an incremental memory allocator that allocates memory by simply</a>
+<a name="54"><span class="lineNum">      54 </span>            : //! incrementing a pointer. It allocates blocks of memory by using standard</a>
+<a name="55"><span class="lineNum">      55 </span>            : //! C `malloc`, but divides these blocks into smaller segments requested by</a>
+<a name="56"><span class="lineNum">      56 </span>            : //! calling `Zone::alloc()` and friends.</a>
+<a name="57"><span class="lineNum">      57 </span>            : //!</a>
+<a name="58"><span class="lineNum">      58 </span>            : //! Zone has no function to release the allocated memory. It has to be released</a>
+<a name="59"><span class="lineNum">      59 </span>            : //! all at once by calling `reset()`. If you need a more friendly allocator that</a>
+<a name="60"><span class="lineNum">      60 </span>            : //! also supports `release()`, consider using \ref Zone with \ref ZoneHeap.</a>
+<a name="61"><span class="lineNum">      61 </span>            : class Zone {</a>
+<a name="62"><span class="lineNum">      62 </span>            : public:</a>
+<a name="63"><span class="lineNum">      63 </span>            :   //! \internal</a>
+<a name="64"><span class="lineNum">      64 </span>            :   //!</a>
+<a name="65"><span class="lineNum">      65 </span>            :   //! A single block of memory.</a>
+<a name="66"><span class="lineNum">      66 </span>            :   struct Block {</a>
+<a name="67"><span class="lineNum">      67 </span>            :     Block* prev;                         //!&lt; Link to the previous block.</a>
+<a name="68"><span class="lineNum">      68 </span>            :     Block* next;                         //!&lt; Link to the next block.</a>
+<a name="69"><span class="lineNum">      69 </span>            :     size_t size;                         //!&lt; Size of the block.</a>
+<a name="70"><span class="lineNum">      70 </span>            :     uint8_t data[sizeof(void*)];         //!&lt; Data.</a>
+<a name="71"><span class="lineNum">      71 </span>            :   };</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   enum {</a>
+<a name="74"><span class="lineNum">      74 </span>            :     //! Zone allocator overhead.</a>
+<a name="75"><span class="lineNum">      75 </span>            :     kZoneOverhead = Globals::kAllocOverhead + static_cast&lt;int&gt;(sizeof(Block))</a>
+<a name="76"><span class="lineNum">      76 </span>            :   };</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="79"><span class="lineNum">      79 </span>            :   // [Construction / Destruction]</a>
+<a name="80"><span class="lineNum">      80 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   //! Create a new instance of `Zone` allocator.</a>
+<a name="83"><span class="lineNum">      83 </span>            :   //!</a>
+<a name="84"><span class="lineNum">      84 </span>            :   //! The `blockSize` parameter describes the default size of the block. If the</a>
+<a name="85"><span class="lineNum">      85 </span>            :   //! `size` parameter passed to `alloc()` is greater than the default size</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //! `Zone` will allocate and use a larger block, but it will not change the</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //! default `blockSize`.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   //!</a>
+<a name="89"><span class="lineNum">      89 </span>            :   //! It's not required, but it's good practice to set `blockSize` to a</a>
+<a name="90"><span class="lineNum">      90 </span>            :   //! reasonable value that depends on the usage of `Zone`. Greater block sizes</a>
+<a name="91"><span class="lineNum">      91 </span>            :   //! are generally safer and perform better than unreasonably low values.</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ASMJIT_API Zone(uint32_t blockSize, uint32_t blockAlignment = 0) noexcept;</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Destroy the `Zone` instance.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   //!</a>
+<a name="96"><span class="lineNum">      96 </span>            :   //! This will destroy the `Zone` instance and release all blocks of memory</a>
+<a name="97"><span class="lineNum">      97 </span>            :   //! allocated by it. It performs implicit `reset(true)`.</a>
+<a name="98"><span class="lineNum">      98 </span>            :   ASMJIT_API ~Zone() noexcept;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="101"><span class="lineNum">     101 </span>            :   // [Reset]</a>
+<a name="102"><span class="lineNum">     102 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   //! Reset the `Zone` invalidating all blocks allocated.</a>
+<a name="105"><span class="lineNum">     105 </span>            :   //!</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //! If `releaseMemory` is true all buffers will be released to the system.</a>
+<a name="107"><span class="lineNum">     107 </span>            :   ASMJIT_API void reset(bool releaseMemory = false) noexcept;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // [Accessors]</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   //! Get the default block size.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ASMJIT_INLINE uint32_t getBlockSize() const noexcept { return _blockSize; }</a>
+<a name="115"><span class="lineNum">     115 </span>            :   //! Get the default block alignment.</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       7796 :   ASMJIT_INLINE uint32_t getBlockAlignment() const noexcept { return (uint32_t)1 &lt;&lt; _blockAlignmentShift; }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   //! Get remaining size of the current block.</a>
+<a name="118"><span class="lineNum">     118 </span>            :   ASMJIT_INLINE size_t getRemainingSize() const noexcept { return (size_t)(_end - _ptr); }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   //! Get the current zone cursor (dangerous).</a>
+<a name="121"><span class="lineNum">     121 </span>            :   //!</a>
+<a name="122"><span class="lineNum">     122 </span>            :   //! This is a function that can be used to get exclusive access to the current</a>
+<a name="123"><span class="lineNum">     123 </span>            :   //! block's memory buffer.</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      78290 :   ASMJIT_INLINE uint8_t* getCursor() noexcept { return _ptr; }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   //! Get the end of the current zone block, only useful if you use `getCursor()`.</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      78290 :   ASMJIT_INLINE uint8_t* getEnd() noexcept { return _end; }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   //! Set the current zone cursor to `p` (must match the current block).</a>
+<a name="129"><span class="lineNum">     129 </span>            :   //!</a>
+<a name="130"><span class="lineNum">     130 </span>            :   //! This is a counterpart of `getZoneCursor()`.</a>
+<a name="131"><span class="lineNum">     131 </span>            :   ASMJIT_INLINE void setCursor(uint8_t* p) noexcept {</a>
+<a name="132"><span class="lineNum">     132 </span>            :     ASMJIT_ASSERT(p &gt;= _ptr &amp;&amp; p &lt;= _end);</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      74394 :     _ptr = p;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="137"><span class="lineNum">     137 </span>            :   // [Alloc]</a>
+<a name="138"><span class="lineNum">     138 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   //! Allocate `size` bytes of memory.</a>
+<a name="141"><span class="lineNum">     141 </span>            :   //!</a>
+<a name="142"><span class="lineNum">     142 </span>            :   //! Pointer returned is valid until the `Zone` instance is destroyed or reset</a>
+<a name="143"><span class="lineNum">     143 </span>            :   //! by calling `reset()`. If you plan to make an instance of C++ from the</a>
+<a name="144"><span class="lineNum">     144 </span>            :   //! given pointer use placement `new` and `delete` operators:</a>
+<a name="145"><span class="lineNum">     145 </span>            :   //!</a>
+<a name="146"><span class="lineNum">     146 </span>            :   //! ~~~</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //! using namespace asmjit;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   //!</a>
+<a name="149"><span class="lineNum">     149 </span>            :   //! class Object { ... };</a>
+<a name="150"><span class="lineNum">     150 </span>            :   //!</a>
+<a name="151"><span class="lineNum">     151 </span>            :   //! // Create Zone with default block size of approximately 65536 bytes.</a>
+<a name="152"><span class="lineNum">     152 </span>            :   //! Zone zone(65536 - Zone::kZoneOverhead);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   //!</a>
+<a name="154"><span class="lineNum">     154 </span>            :   //! // Create your objects using zone object allocating, for example:</a>
+<a name="155"><span class="lineNum">     155 </span>            :   //! Object* obj = static_cast&lt;Object*&gt;( zone.alloc(sizeof(Object)) );</a>
+<a name="156"><span class="lineNum">     156 </span>            :   //</a>
+<a name="157"><span class="lineNum">     157 </span>            :   //! if (!obj) {</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //!   // Handle out of memory error.</a>
+<a name="159"><span class="lineNum">     159 </span>            :   //! }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   //!</a>
+<a name="161"><span class="lineNum">     161 </span>            :   //! // Placement `new` and `delete` operators can be used to instantiate it.</a>
+<a name="162"><span class="lineNum">     162 </span>            :   //! new(obj) Object();</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //!</a>
+<a name="164"><span class="lineNum">     164 </span>            :   //! // ... lifetime of your objects ...</a>
+<a name="165"><span class="lineNum">     165 </span>            :   //!</a>
+<a name="166"><span class="lineNum">     166 </span>            :   //! // To destroy the instance (if required).</a>
+<a name="167"><span class="lineNum">     167 </span>            :   //! obj-&gt;~Object();</a>
+<a name="168"><span class="lineNum">     168 </span>            :   //!</a>
+<a name="169"><span class="lineNum">     169 </span>            :   //! // Reset or destroy `Zone`.</a>
+<a name="170"><span class="lineNum">     170 </span>            :   //! zone.reset();</a>
+<a name="171"><span class="lineNum">     171 </span>            :   //! ~~~</a>
+<a name="172"><span class="lineNum">     172 </span>            :   ASMJIT_INLINE void* alloc(size_t size) noexcept {</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     114832 :     uint8_t* ptr = _ptr;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     114832 :     size_t remainingBytes = (size_t)(_end - ptr);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     114832 :     if (ASMJIT_UNLIKELY(remainingBytes &lt; size))</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       3900 :       return _alloc(size);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     110932 :     _ptr += size;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     ASMJIT_ASSERT(_ptr &lt;= _end);</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">     110932 :     return static_cast&lt;void*&gt;(ptr);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   }</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   //! Allocate `size` bytes without any checks.</a>
+<a name="186"><span class="lineNum">     186 </span>            :   //!</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //! Can only be called if `getRemainingSize()` returns size at least equal</a>
+<a name="188"><span class="lineNum">     188 </span>            :   //! to `size`.</a>
+<a name="189"><span class="lineNum">     189 </span>            :   ASMJIT_INLINE void* allocNoCheck(size_t size) noexcept {</a>
+<a name="190"><span class="lineNum">     190 </span>            :     ASMJIT_ASSERT((size_t)(_end - _ptr) &gt;= size);</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :     uint8_t* ptr = _ptr;</a>
+<a name="193"><span class="lineNum">     193 </span>            :     _ptr += size;</a>
+<a name="194"><span class="lineNum">     194 </span>            :     return static_cast&lt;void*&gt;(ptr);</a>
+<a name="195"><span class="lineNum">     195 </span>            :   }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   //! Allocate `size` bytes of zeroed memory.</a>
+<a name="198"><span class="lineNum">     198 </span>            :   //!</a>
+<a name="199"><span class="lineNum">     199 </span>            :   //! See \ref alloc() for more details.</a>
+<a name="200"><span class="lineNum">     200 </span>            :   ASMJIT_API void* allocZeroed(size_t size) noexcept;</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   //! Like `alloc()`, but the return pointer is casted to `T*`.</a>
+<a name="203"><span class="lineNum">     203 </span>            :   template&lt;typename T&gt;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   ASMJIT_INLINE T* allocT(size_t size = sizeof(T)) noexcept {</a>
+<a name="205"><span class="lineNum">     205 </span>            :     return static_cast&lt;T*&gt;(alloc(size));</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   //! Like `allocNoCheck()`, but the return pointer is casted to `T*`.</a>
+<a name="209"><span class="lineNum">     209 </span>            :   template&lt;typename T&gt;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   ASMJIT_INLINE T* allocNoCheckT(size_t size = sizeof(T)) noexcept {</a>
+<a name="211"><span class="lineNum">     211 </span>            :     return static_cast&lt;T*&gt;(allocNoCheck(size));</a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   //! Like `allocZeroed()`, but the return pointer is casted to `T*`.</a>
+<a name="215"><span class="lineNum">     215 </span>            :   template&lt;typename T&gt;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   ASMJIT_INLINE T* allocZeroedT(size_t size = sizeof(T)) noexcept {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      25736 :     return static_cast&lt;T*&gt;(allocZeroed(size));</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :   //! Like `new(std::nothrow) T(...)`, but allocated by `Zone`.</a>
+<a name="221"><span class="lineNum">     221 </span>            :   template&lt;typename T&gt;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   ASMJIT_INLINE T* newT() noexcept {</a>
+<a name="223"><span class="lineNum">     223 </span>            :     void* p = alloc(sizeof(T));</a>
+<a name="224"><span class="lineNum">     224 </span>            :     if (ASMJIT_UNLIKELY(!p))</a>
+<a name="225"><span class="lineNum">     225 </span>            :       return nullptr;</a>
+<a name="226"><span class="lineNum">     226 </span>            :     return new(p) T();</a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span>            :   //! Like `new(std::nothrow) T(...)`, but allocated by `Zone`.</a>
+<a name="229"><span class="lineNum">     229 </span>            :   template&lt;typename T, typename P1&gt;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   ASMJIT_INLINE T* newT(P1 p1) noexcept {</a>
+<a name="231"><span class="lineNum">     231 </span>            :     void* p = alloc(sizeof(T));</a>
+<a name="232"><span class="lineNum">     232 </span>            :     if (ASMJIT_UNLIKELY(!p))</a>
+<a name="233"><span class="lineNum">     233 </span>            :       return nullptr;</a>
+<a name="234"><span class="lineNum">     234 </span>            :     return new(p) T(p1);</a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   //! \internal</a>
+<a name="238"><span class="lineNum">     238 </span>            :   ASMJIT_API void* _alloc(size_t size) noexcept;</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   //! Helper to duplicate data.</a>
+<a name="241"><span class="lineNum">     241 </span>            :   ASMJIT_API void* dup(const void* data, size_t size, bool nullTerminate = false) noexcept;</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   //! Helper to duplicate formatted string, maximum length is 256 bytes.</a>
+<a name="244"><span class="lineNum">     244 </span>            :   ASMJIT_API char* sformat(const char* str, ...) noexcept;</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="247"><span class="lineNum">     247 </span>            :   // [Members]</a>
+<a name="248"><span class="lineNum">     248 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            :   uint8_t* _ptr;                         //!&lt; Pointer in the current block's buffer.</a>
+<a name="251"><span class="lineNum">     251 </span>            :   uint8_t* _end;                         //!&lt; End of the current block's buffer.</a>
+<a name="252"><span class="lineNum">     252 </span>            :   Block* _block;                         //!&lt; Current block.</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : #if ASMJIT_ARCH_64BIT</a>
+<a name="255"><span class="lineNum">     255 </span>            :   uint32_t _blockSize;                   //!&lt; Default size of a newly allocated block.</a>
+<a name="256"><span class="lineNum">     256 </span>            :   uint32_t _blockAlignmentShift;         //!&lt; Minimum alignment of each block.</a>
+<a name="257"><span class="lineNum">     257 </span>            : #else</a>
+<a name="258"><span class="lineNum">     258 </span>            :   uint32_t _blockSize : 29;              //!&lt; Default size of a newly allocated block.</a>
+<a name="259"><span class="lineNum">     259 </span>            :   uint32_t _blockAlignmentShift : 3;     //!&lt; Minimum alignment of each block.</a>
+<a name="260"><span class="lineNum">     260 </span>            : #endif</a>
+<a name="261"><span class="lineNum">     261 </span>            : };</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : // ============================================================================</a>
+<a name="264"><span class="lineNum">     264 </span>            : // [asmjit::ZoneHeap]</a>
+<a name="265"><span class="lineNum">     265 </span>            : // ============================================================================</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : //! Zone-based memory allocator that uses an existing \ref Zone and provides</a>
+<a name="268"><span class="lineNum">     268 </span>            : //! a `release()` functionality on top of it. It uses \ref Zone only for chunks</a>
+<a name="269"><span class="lineNum">     269 </span>            : //! that can be pooled, and uses libc `malloc()` for chunks that are large.</a>
+<a name="270"><span class="lineNum">     270 </span>            : //!</a>
+<a name="271"><span class="lineNum">     271 </span>            : //! The advantage of ZoneHeap is that it can allocate small chunks of memory</a>
+<a name="272"><span class="lineNum">     272 </span>            : //! really fast, and these chunks, when released, will be reused by consecutive</a>
+<a name="273"><span class="lineNum">     273 </span>            : //! calls to `alloc()`. Also, since ZoneHeap uses \ref Zone, you can turn any</a>
+<a name="274"><span class="lineNum">     274 </span>            : //! \ref Zone into a \ref ZoneHeap, and use it in your \ref Pass when necessary.</a>
+<a name="275"><span class="lineNum">     275 </span>            : //!</a>
+<a name="276"><span class="lineNum">     276 </span>            : //! ZoneHeap is used by AsmJit containers to make containers having only</a>
+<a name="277"><span class="lineNum">     277 </span>            : //! few elements fast (and lightweight) and to allow them to grow and use</a>
+<a name="278"><span class="lineNum">     278 </span>            : //! dynamic blocks when require more storage.</a>
+<a name="279"><span class="lineNum">     279 </span>            : class ZoneHeap {</a>
+<a name="280"><span class="lineNum">     280 </span>            :   ASMJIT_NONCOPYABLE(ZoneHeap)</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   enum {</a>
+<a name="283"><span class="lineNum">     283 </span>            :     // In short, we pool chunks of these sizes:</a>
+<a name="284"><span class="lineNum">     284 </span>            :     //   [32, 64, 96, 128, 192, 256, 320, 384, 448, 512]</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :     //! How many bytes per a low granularity pool (has to be at least 16).</a>
+<a name="287"><span class="lineNum">     287 </span>            :     kLoGranularity = 32,</a>
+<a name="288"><span class="lineNum">     288 </span>            :     //! Number of slots of a low granularity pool.</a>
+<a name="289"><span class="lineNum">     289 </span>            :     kLoCount = 4,</a>
+<a name="290"><span class="lineNum">     290 </span>            :     //! Maximum size of a block that can be allocated in a low granularity pool.</a>
+<a name="291"><span class="lineNum">     291 </span>            :     kLoMaxSize = kLoGranularity * kLoCount,</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            :     //! How many bytes per a high granularity pool.</a>
+<a name="294"><span class="lineNum">     294 </span>            :     kHiGranularity = 64,</a>
+<a name="295"><span class="lineNum">     295 </span>            :     //! Number of slots of a high granularity pool.</a>
+<a name="296"><span class="lineNum">     296 </span>            :     kHiCount = 6,</a>
+<a name="297"><span class="lineNum">     297 </span>            :     //! Maximum size of a block that can be allocated in a high granularity pool.</a>
+<a name="298"><span class="lineNum">     298 </span>            :     kHiMaxSize = kLoMaxSize + kHiGranularity * kHiCount,</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :     //! Alignment of every pointer returned by `alloc()`.</a>
+<a name="301"><span class="lineNum">     301 </span>            :     kBlockAlignment = kLoGranularity</a>
+<a name="302"><span class="lineNum">     302 </span>            :   };</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   //! Single-linked list used to store unused chunks.</a>
+<a name="305"><span class="lineNum">     305 </span>            :   struct Slot {</a>
+<a name="306"><span class="lineNum">     306 </span>            :     //! Link to a next slot in a single-linked list.</a>
+<a name="307"><span class="lineNum">     307 </span>            :     Slot* next;</a>
+<a name="308"><span class="lineNum">     308 </span>            :   };</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            :   //! A block of memory that has been allocated dynamically and is not part of</a>
+<a name="311"><span class="lineNum">     311 </span>            :   //! block-list used by the allocator. This is used to keep track of all these</a>
+<a name="312"><span class="lineNum">     312 </span>            :   //! blocks so they can be freed by `reset()` if not freed explicitly.</a>
+<a name="313"><span class="lineNum">     313 </span>            :   struct DynamicBlock {</a>
+<a name="314"><span class="lineNum">     314 </span>            :     DynamicBlock* prev;</a>
+<a name="315"><span class="lineNum">     315 </span>            :     DynamicBlock* next;</a>
+<a name="316"><span class="lineNum">     316 </span>            :   };</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="319"><span class="lineNum">     319 </span>            :   // [Construction / Destruction]</a>
+<a name="320"><span class="lineNum">     320 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            :   //! Create a new `ZoneHeap`.</a>
+<a name="323"><span class="lineNum">     323 </span>            :   //!</a>
+<a name="324"><span class="lineNum">     324 </span>            :   //! NOTE: To use it, you must first `init()` it.</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ZoneHeap() noexcept {</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :     ::memset(this, 0, sizeof(*this));</a>
+<a name="327"><span class="lineNum">     327 </span>            :   }</a>
+<a name="328"><span class="lineNum">     328 </span>            :   //! Create a new `ZoneHeap` initialized to use `zone`.</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       3896 :   explicit ASMJIT_INLINE ZoneHeap(Zone* zone) noexcept {</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     ::memset(this, 0, sizeof(*this));</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       3896 :     _zone = zone;</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :   }</a>
+<a name="333"><span class="lineNum">     333 </span>            :   //! Destroy the `ZoneHeap`.</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       3896 :   ASMJIT_INLINE ~ZoneHeap() noexcept { reset(); }</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="337"><span class="lineNum">     337 </span>            :   // [Init / Reset]</a>
+<a name="338"><span class="lineNum">     338 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            :   //! Get if the `ZoneHeap` is initialized (i.e. has `Zone`).</a>
+<a name="341"><span class="lineNum">     341 </span>            :   ASMJIT_INLINE bool isInitialized() const noexcept { return _zone != nullptr; }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :   //! Convenience method to initialize the `ZoneHeap` with `zone`.</a>
+<a name="344"><span class="lineNum">     344 </span>            :   //!</a>
+<a name="345"><span class="lineNum">     345 </span>            :   //! It's the same as calling `reset(zone)`.</a>
+<a name="346"><span class="lineNum">     346 </span>            :   ASMJIT_INLINE void init(Zone* zone) noexcept { reset(zone); }</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            :   //! Reset this `ZoneHeap` and also forget about the current `Zone` which</a>
+<a name="349"><span class="lineNum">     349 </span>            :   //! is attached (if any). Reset optionally attaches a new `zone` passed, or</a>
+<a name="350"><span class="lineNum">     350 </span>            :   //! keeps the `ZoneHeap` in an uninitialized state, if `zone` is null.</a>
+<a name="351"><span class="lineNum">     351 </span>            :   ASMJIT_API void reset(Zone* zone = nullptr) noexcept;</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="354"><span class="lineNum">     354 </span>            :   // [Accessors]</a>
+<a name="355"><span class="lineNum">     355 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   //! Get the `Zone` the `ZoneHeap` is using, or null if it's not initialized.</a>
+<a name="358"><span class="lineNum">     358 </span>            :   ASMJIT_INLINE Zone* getZone() const noexcept { return _zone; }</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="361"><span class="lineNum">     361 </span>            :   // [Utilities]</a>
+<a name="362"><span class="lineNum">     362 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :   //! \internal</a>
+<a name="365"><span class="lineNum">     365 </span>            :   //!</a>
+<a name="366"><span class="lineNum">     366 </span>            :   //! Get the slot index to be used for `size`. Returns `true` if a valid slot</a>
+<a name="367"><span class="lineNum">     367 </span>            :   //! has been written to `slot` and `allocatedSize` has been filled with slot</a>
+<a name="368"><span class="lineNum">     368 </span>            :   //! exact size (`allocatedSize` can be equal or slightly greater than `size`).</a>
+<a name="369"><span class="lineNum">     369 </span>            :   static ASMJIT_INLINE bool _getSlotIndex(size_t size, uint32_t&amp; slot) noexcept {</a>
+<a name="370"><span class="lineNum">     370 </span>            :     ASMJIT_ASSERT(size &gt; 0);</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">       6600 :     if (size &gt; kHiMaxSize)</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :       return false;</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">       6600 :     if (size &lt;= kLoMaxSize)</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">       6592 :       slot = static_cast&lt;uint32_t&gt;((size - 1) / kLoGranularity);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     else</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          8 :       slot = static_cast&lt;uint32_t&gt;((size - kLoMaxSize - 1) / kHiGranularity) + kLoCount;</span></a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :     return true;</a>
+<a name="380"><span class="lineNum">     380 </span>            :   }</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            :   //! \overload</a>
+<a name="383"><span class="lineNum">     383 </span>            :   static ASMJIT_INLINE bool _getSlotIndex(size_t size, uint32_t&amp; slot, size_t&amp; allocatedSize) noexcept {</a>
+<a name="384"><span class="lineNum">     384 </span>            :     ASMJIT_ASSERT(size &gt; 0);</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      79986 :     if (size &gt; kHiMaxSize)</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :       return false;</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">      79978 :     if (size &lt;= kLoMaxSize) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      75158 :       slot = static_cast&lt;uint32_t&gt;((size - 1) / kLoGranularity);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      75158 :       allocatedSize = Utils::alignTo(size, kLoGranularity);</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     }</a>
+<a name="392"><span class="lineNum">     392 </span>            :     else {</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       4820 :       slot = static_cast&lt;uint32_t&gt;((size - kLoMaxSize - 1) / kHiGranularity) + kLoCount;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       4820 :       allocatedSize = Utils::alignTo(size, kHiGranularity);</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :     }</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :     return true;</a>
+<a name="398"><span class="lineNum">     398 </span>            :   }</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="401"><span class="lineNum">     401 </span>            :   // [Alloc / Release]</a>
+<a name="402"><span class="lineNum">     402 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            :   ASMJIT_API void* _alloc(size_t size, size_t&amp; allocatedSize) noexcept;</a>
+<a name="405"><span class="lineNum">     405 </span>            :   ASMJIT_API void* _allocZeroed(size_t size, size_t&amp; allocatedSize) noexcept;</a>
+<a name="406"><span class="lineNum">     406 </span>            :   ASMJIT_API void _releaseDynamic(void* p, size_t size) noexcept;</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :   //! Allocate `size` bytes of memory, ideally from an available pool.</a>
+<a name="409"><span class="lineNum">     409 </span>            :   //!</a>
+<a name="410"><span class="lineNum">     410 </span>            :   //! NOTE: `size` can't be zero, it will assert in debug mode in such case.</a>
+<a name="411"><span class="lineNum">     411 </span>            :   ASMJIT_INLINE void* alloc(size_t size) noexcept {</a>
+<a name="412"><span class="lineNum">     412 </span>            :     ASMJIT_ASSERT(isInitialized());</a>
+<a name="413"><span class="lineNum">     413 </span>            :     size_t allocatedSize;</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">      57802 :     return _alloc(size, allocatedSize);</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   //! Like `alloc(size)`, but provides a second argument `allocatedSize` that</a>
+<a name="418"><span class="lineNum">     418 </span>            :   //! provides a way to know how big the block returned actually is. This is</a>
+<a name="419"><span class="lineNum">     419 </span>            :   //! useful for containers to prevent growing too early.</a>
+<a name="420"><span class="lineNum">     420 </span>            :   ASMJIT_INLINE void* alloc(size_t size, size_t&amp; allocatedSize) noexcept {</a>
+<a name="421"><span class="lineNum">     421 </span>            :     ASMJIT_ASSERT(isInitialized());</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">      18288 :     return _alloc(size, allocatedSize);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :   }</a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            :   //! Like `alloc()`, but the return pointer is casted to `T*`.</a>
+<a name="426"><span class="lineNum">     426 </span>            :   template&lt;typename T&gt;</a>
+<a name="427"><span class="lineNum">     427 </span>            :   ASMJIT_INLINE T* allocT(size_t size = sizeof(T)) noexcept {</a>
+<a name="428"><span class="lineNum">     428 </span>            :     return static_cast&lt;T*&gt;(alloc(size));</a>
+<a name="429"><span class="lineNum">     429 </span>            :   }</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            :   //! Like `alloc(size)`, but returns zeroed memory.</a>
+<a name="432"><span class="lineNum">     432 </span>            :   ASMJIT_INLINE void* allocZeroed(size_t size) noexcept {</a>
+<a name="433"><span class="lineNum">     433 </span>            :     ASMJIT_ASSERT(isInitialized());</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :     size_t allocatedSize;</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">       3896 :     return _allocZeroed(size, allocatedSize);</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :   }</a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span>            :   //! Like `alloc(size, allocatedSize)`, but returns zeroed memory.</a>
+<a name="440"><span class="lineNum">     440 </span>            :   ASMJIT_INLINE void* allocZeroed(size_t size, size_t&amp; allocatedSize) noexcept {</a>
+<a name="441"><span class="lineNum">     441 </span>            :     ASMJIT_ASSERT(isInitialized());</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            :     return _allocZeroed(size, allocatedSize);</a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            :   //! Like `allocZeroed()`, but the return pointer is casted to `T*`.</a>
+<a name="447"><span class="lineNum">     447 </span>            :   template&lt;typename T&gt;</a>
+<a name="448"><span class="lineNum">     448 </span>            :   ASMJIT_INLINE T* allocZeroedT(size_t size = sizeof(T)) noexcept {</a>
+<a name="449"><span class="lineNum">     449 </span>            :     return static_cast&lt;T*&gt;(allocZeroed(size));</a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :   //! Release the memory previously allocated by `alloc()`. The `size` argument</a>
+<a name="453"><span class="lineNum">     453 </span>            :   //! has to be the same as used to call `alloc()` or `allocatedSize` returned</a>
+<a name="454"><span class="lineNum">     454 </span>            :   //! by `alloc()`.</a>
+<a name="455"><span class="lineNum">     455 </span>            :   ASMJIT_INLINE void release(void* p, size_t size) noexcept {</a>
+<a name="456"><span class="lineNum">     456 </span>            :     ASMJIT_ASSERT(isInitialized());</a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span>            :     ASMJIT_ASSERT(p != nullptr);</a>
+<a name="459"><span class="lineNum">     459 </span>            :     ASMJIT_ASSERT(size != 0);</a>
+<a name="460"><span class="lineNum">     460 </span>            : </a>
+<a name="461"><span class="lineNum">     461 </span>            :     uint32_t slot;</a>
+<a name="462"><span class="lineNum">     462 </span>            :     if (_getSlotIndex(size, slot)) {</a>
+<a name="463"><span class="lineNum">     463 </span>            :       //printf(&quot;RELEASING %p of size %d (SLOT %u)\n&quot;, p, int(size), slot);</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">       6600 :       static_cast&lt;Slot*&gt;(p)-&gt;next = static_cast&lt;Slot*&gt;(_slots[slot]);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">       6600 :       _slots[slot] = static_cast&lt;Slot*&gt;(p);</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :     }</a>
+<a name="467"><span class="lineNum">     467 </span>            :     else {</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :       _releaseDynamic(p, size);</span></a>
+<a name="469"><span class="lineNum">     469 </span>            :     }</a>
+<a name="470"><span class="lineNum">     470 </span>            :   }</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="473"><span class="lineNum">     473 </span>            :   // [Members]</a>
+<a name="474"><span class="lineNum">     474 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            :   Zone* _zone;                           //!&lt; Zone used to allocate memory that fits into slots.</a>
+<a name="477"><span class="lineNum">     477 </span>            :   Slot* _slots[kLoCount + kHiCount];     //!&lt; Indexed slots containing released memory.</a>
+<a name="478"><span class="lineNum">     478 </span>            :   DynamicBlock* _dynamicBlocks;          //!&lt; Dynamic blocks for larger allocations (no slots).</a>
+<a name="479"><span class="lineNum">     479 </span>            : };</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            : // ============================================================================</a>
+<a name="482"><span class="lineNum">     482 </span>            : // [asmjit::ZoneList&lt;T&gt;]</a>
+<a name="483"><span class="lineNum">     483 </span>            : // ============================================================================</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            : //! \internal</a>
+<a name="486"><span class="lineNum">     486 </span>            : template &lt;typename T&gt;</a>
+<a name="487"><span class="lineNum">     487 </span>            : class ZoneList {</a>
+<a name="488"><span class="lineNum">     488 </span>            : public:</a>
+<a name="489"><span class="lineNum">     489 </span>            :   ASMJIT_NONCOPYABLE(ZoneList&lt;T&gt;)</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="492"><span class="lineNum">     492 </span>            :   // [Link]</a>
+<a name="493"><span class="lineNum">     493 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :   //! ZoneList node.</a>
+<a name="496"><span class="lineNum">     496 </span>            :   struct Link {</a>
+<a name="497"><span class="lineNum">     497 </span>            :     //! Get next node.</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">       3896 :     ASMJIT_INLINE Link* getNext() const noexcept { return _next; }</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :     //! Get value.</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">       1948 :     ASMJIT_INLINE T getValue() const noexcept { return _value; }</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :     //! Set value to `value`.</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">       3896 :     ASMJIT_INLINE void setValue(const T&amp; value) noexcept { _value = value; }</span></a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span>            :     Link* _next;</a>
+<a name="505"><span class="lineNum">     505 </span>            :     T _value;</a>
+<a name="506"><span class="lineNum">     506 </span>            :   };</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="509"><span class="lineNum">     509 </span>            :   // [Appender]</a>
+<a name="510"><span class="lineNum">     510 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            :   //! Specialized appender that takes advantage of ZoneList structure. You must</a>
+<a name="513"><span class="lineNum">     513 </span>            :   //! initialize it and then call done().</a>
+<a name="514"><span class="lineNum">     514 </span>            :   struct Appender {</a>
+<a name="515"><span class="lineNum">     515 </span>            :     ASMJIT_INLINE Appender(ZoneList&lt;T&gt;&amp; list) noexcept { init(list); }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span>            :     ASMJIT_INLINE void init(ZoneList&lt;T&gt;&amp; list) noexcept {</a>
+<a name="518"><span class="lineNum">     518 </span>            :       pPrev = &amp;list._first;</a>
+<a name="519"><span class="lineNum">     519 </span>            :     }</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            :     ASMJIT_INLINE void done(ZoneList&lt;T&gt;&amp; list) noexcept {</a>
+<a name="522"><span class="lineNum">     522 </span>            :       list._last = *pPrev;</a>
+<a name="523"><span class="lineNum">     523 </span>            :       *pPrev = nullptr;</a>
+<a name="524"><span class="lineNum">     524 </span>            :     }</a>
+<a name="525"><span class="lineNum">     525 </span>            : </a>
+<a name="526"><span class="lineNum">     526 </span>            :     ASMJIT_INLINE void append(Link* node) noexcept {</a>
+<a name="527"><span class="lineNum">     527 </span>            :       *pPrev = node;</a>
+<a name="528"><span class="lineNum">     528 </span>            :       pPrev = &amp;node-&gt;_next;</a>
+<a name="529"><span class="lineNum">     529 </span>            :     }</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :     Link** pPrev;</a>
+<a name="532"><span class="lineNum">     532 </span>            :   };</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="535"><span class="lineNum">     535 </span>            :   // [Construction / Destruction]</a>
+<a name="536"><span class="lineNum">     536 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ZoneList() noexcept : _first(nullptr), _last(nullptr) {}</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE ~ZoneList() noexcept {}</span></a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="542"><span class="lineNum">     542 </span>            :   // [Data]</a>
+<a name="543"><span class="lineNum">     543 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span>            :   ASMJIT_INLINE bool isEmpty() const noexcept { return _first != nullptr; }</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">       7792 :   ASMJIT_INLINE Link* getFirst() const noexcept { return _first; }</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :   ASMJIT_INLINE Link* getLast() const noexcept { return _last; }</a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="550"><span class="lineNum">     550 </span>            :   // [Ops]</a>
+<a name="551"><span class="lineNum">     551 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">       1948 :     _first = nullptr;</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">       1948 :     _last = nullptr;</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :   }</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            :   ASMJIT_INLINE void prepend(Link* link) noexcept {</a>
+<a name="559"><span class="lineNum">     559 </span>            :     link-&gt;_next = _first;</a>
+<a name="560"><span class="lineNum">     560 </span>            :     if (!_first) _last = link;</a>
+<a name="561"><span class="lineNum">     561 </span>            :     _first = link;</a>
+<a name="562"><span class="lineNum">     562 </span>            :   }</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :   ASMJIT_INLINE void append(Link* link) noexcept {</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">       3896 :     link-&gt;_next = nullptr;</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">       3896 :     if (!_first)</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">       3896 :       _first = link;</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :     else</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :       _last-&gt;_next = link;</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">       3896 :     _last = link;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :   }</a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="574"><span class="lineNum">     574 </span>            :   // [Members]</a>
+<a name="575"><span class="lineNum">     575 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span>            :   Link* _first;</a>
+<a name="578"><span class="lineNum">     578 </span>            :   Link* _last;</a>
+<a name="579"><span class="lineNum">     579 </span>            : };</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            : // ============================================================================</a>
+<a name="582"><span class="lineNum">     582 </span>            : // [asmjit::ZoneVectorBase]</a>
+<a name="583"><span class="lineNum">     583 </span>            : // ============================================================================</a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span>            : //! \internal</a>
+<a name="586"><span class="lineNum">     586 </span>            : class ZoneVectorBase {</a>
+<a name="587"><span class="lineNum">     587 </span>            : public:</a>
+<a name="588"><span class="lineNum">     588 </span>            :   ASMJIT_NONCOPYABLE(ZoneVectorBase)</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span>            : protected:</a>
+<a name="591"><span class="lineNum">     591 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="592"><span class="lineNum">     592 </span>            :   // [Construction / Destruction]</a>
+<a name="593"><span class="lineNum">     593 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span>            :   //! Create a new instance of `ZoneVectorBase`.</a>
+<a name="596"><span class="lineNum">     596 </span>            :   explicit ASMJIT_INLINE ZoneVectorBase() noexcept</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">       7792 :     : _data(nullptr),</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">       7792 :       _length(0),</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">       7792 :       _capacity(0) {}</span></a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="602"><span class="lineNum">     602 </span>            :   // [Accessors]</a>
+<a name="603"><span class="lineNum">     603 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span>            : public:</a>
+<a name="606"><span class="lineNum">     606 </span>            :   //! Get if the vector is empty.</a>
+<a name="607"><span class="lineNum">     607 </span>            :   ASMJIT_INLINE bool isEmpty() const noexcept { return _length == 0; }</a>
+<a name="608"><span class="lineNum">     608 </span>            :   //! Get vector length.</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">      73412 :   ASMJIT_INLINE size_t getLength() const noexcept { return _length; }</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :   //! Get vector capacity.</a>
+<a name="611"><span class="lineNum">     611 </span>            :   ASMJIT_INLINE size_t getCapacity() const noexcept { return _capacity; }</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="614"><span class="lineNum">     614 </span>            :   // [Ops]</a>
+<a name="615"><span class="lineNum">     615 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            :   //! Makes the vector empty (won't change the capacity or data pointer).</a>
+<a name="618"><span class="lineNum">     618 </span>            :   ASMJIT_INLINE void clear() noexcept { _length = 0; }</a>
+<a name="619"><span class="lineNum">     619 </span>            :   //! Reset the vector data and set its `length` to zero.</a>
+<a name="620"><span class="lineNum">     620 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">       5844 :     _data = nullptr;</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">       5844 :     _length = 0;</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">       5844 :     _capacity = 0;</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :   }</a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span>            :   //! Truncate the vector to at most `n` items.</a>
+<a name="627"><span class="lineNum">     627 </span>            :   ASMJIT_INLINE void truncate(size_t n) noexcept {</a>
+<a name="628"><span class="lineNum">     628 </span>            :     _length = std::min(_length, n);</a>
+<a name="629"><span class="lineNum">     629 </span>            :   }</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="632"><span class="lineNum">     632 </span>            :   // [Memory Management]</a>
+<a name="633"><span class="lineNum">     633 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            : protected:</a>
+<a name="636"><span class="lineNum">     636 </span>            :   ASMJIT_INLINE void _release(ZoneHeap* heap, size_t sizeOfT) noexcept {</a>
+<a name="637"><span class="lineNum">     637 </span>            :     if (_data != nullptr) {</a>
+<a name="638"><span class="lineNum">     638 </span>            :       heap-&gt;release(_data, _capacity * sizeOfT);</a>
+<a name="639"><span class="lineNum">     639 </span>            :       reset();</a>
+<a name="640"><span class="lineNum">     640 </span>            :     }</a>
+<a name="641"><span class="lineNum">     641 </span>            :   }</a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span>            :   ASMJIT_API Error _grow(ZoneHeap* heap, size_t sizeOfT, size_t n) noexcept;</a>
+<a name="644"><span class="lineNum">     644 </span>            :   ASMJIT_API Error _resize(ZoneHeap* heap, size_t sizeOfT, size_t n) noexcept;</a>
+<a name="645"><span class="lineNum">     645 </span>            :   ASMJIT_API Error _reserve(ZoneHeap* heap, size_t sizeOfT, size_t n) noexcept;</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="648"><span class="lineNum">     648 </span>            :   // [Members]</a>
+<a name="649"><span class="lineNum">     649 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="650"><span class="lineNum">     650 </span>            : </a>
+<a name="651"><span class="lineNum">     651 </span>            : public:</a>
+<a name="652"><span class="lineNum">     652 </span>            :   void* _data;                           //!&lt; Vector data.</a>
+<a name="653"><span class="lineNum">     653 </span>            :   size_t _length;                        //!&lt; Length of the vector.</a>
+<a name="654"><span class="lineNum">     654 </span>            :   size_t _capacity;                      //!&lt; Capacity of the vector.</a>
+<a name="655"><span class="lineNum">     655 </span>            : };</a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            : // ============================================================================</a>
+<a name="658"><span class="lineNum">     658 </span>            : // [asmjit::ZoneVector&lt;T&gt;]</a>
+<a name="659"><span class="lineNum">     659 </span>            : // ============================================================================</a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span>            : //! Template used to store and manage array of Zone allocated data.</a>
+<a name="662"><span class="lineNum">     662 </span>            : //!</a>
+<a name="663"><span class="lineNum">     663 </span>            : //! This template has these advantages over other std::vector&lt;&gt;:</a>
+<a name="664"><span class="lineNum">     664 </span>            : //! - Always non-copyable (designed to be non-copyable, we want it).</a>
+<a name="665"><span class="lineNum">     665 </span>            : //! - No copy-on-write (some implementations of STL can use it).</a>
+<a name="666"><span class="lineNum">     666 </span>            : //! - Optimized for working only with POD types.</a>
+<a name="667"><span class="lineNum">     667 </span>            : //! - Uses ZoneHeap, thus small vectors are basically for free.</a>
+<a name="668"><span class="lineNum">     668 </span>            : template &lt;typename T&gt;</a>
+<a name="669"><span class="lineNum">     669 </span>            : class ZoneVector : public ZoneVectorBase {</a>
+<a name="670"><span class="lineNum">     670 </span>            : public:</a>
+<a name="671"><span class="lineNum">     671 </span>            :   ASMJIT_NONCOPYABLE(ZoneVector&lt;T&gt;)</a>
+<a name="672"><span class="lineNum">     672 </span>            : </a>
+<a name="673"><span class="lineNum">     673 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="674"><span class="lineNum">     674 </span>            :   // [Construction / Destruction]</a>
+<a name="675"><span class="lineNum">     675 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span>            :   //! Create a new instance of `ZoneVector&lt;T&gt;`.</a>
+<a name="678"><span class="lineNum">     678 </span>            :   explicit ASMJIT_INLINE ZoneVector() noexcept : ZoneVectorBase() {}</a>
+<a name="679"><span class="lineNum">     679 </span>            : </a>
+<a name="680"><span class="lineNum">     680 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="681"><span class="lineNum">     681 </span>            :   // [Accessors]</a>
+<a name="682"><span class="lineNum">     682 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="683"><span class="lineNum">     683 </span>            : </a>
+<a name="684"><span class="lineNum">     684 </span>            :   //! Get data.</a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">      11688 :   ASMJIT_INLINE T* getData() noexcept { return static_cast&lt;T*&gt;(_data); }</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :   //! \overload</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">     136306 :   ASMJIT_INLINE const T* getData() const noexcept { return static_cast&lt;const T*&gt;(_data); }</span></a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="690"><span class="lineNum">     690 </span>            :   // [Ops]</a>
+<a name="691"><span class="lineNum">     691 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :   //! Prepend `item` to the vector.</a>
+<a name="694"><span class="lineNum">     694 </span>            :   Error prepend(ZoneHeap* heap, const T&amp; item) noexcept {</a>
+<a name="695"><span class="lineNum">     695 </span>            :     if (ASMJIT_UNLIKELY(_length == _capacity))</a>
+<a name="696"><span class="lineNum">     696 </span>            :       ASMJIT_PROPAGATE(grow(heap, 1));</a>
+<a name="697"><span class="lineNum">     697 </span>            : </a>
+<a name="698"><span class="lineNum">     698 </span>            :     ::memmove(static_cast&lt;T*&gt;(_data) + 1, _data, _length * sizeof(T));</a>
+<a name="699"><span class="lineNum">     699 </span>            :     ::memcpy(_data, &amp;item, sizeof(T));</a>
+<a name="700"><span class="lineNum">     700 </span>            : </a>
+<a name="701"><span class="lineNum">     701 </span>            :     _length++;</a>
+<a name="702"><span class="lineNum">     702 </span>            :     return kErrorOk;</a>
+<a name="703"><span class="lineNum">     703 </span>            :   }</a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span>            :   //! Insert an `item` at the specified `index`.</a>
+<a name="706"><span class="lineNum">     706 </span>            :   Error insert(ZoneHeap* heap, size_t index, const T&amp; item) noexcept {</a>
+<a name="707"><span class="lineNum">     707 </span>            :     ASMJIT_ASSERT(index &lt;= _length);</a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span>            :     if (ASMJIT_UNLIKELY(_length == _capacity))</a>
+<a name="710"><span class="lineNum">     710 </span>            :       ASMJIT_PROPAGATE(grow(heap, 1));</a>
+<a name="711"><span class="lineNum">     711 </span>            : </a>
+<a name="712"><span class="lineNum">     712 </span>            :     T* dst = static_cast&lt;T*&gt;(_data) + index;</a>
+<a name="713"><span class="lineNum">     713 </span>            :     ::memmove(dst + 1, dst, _length - index);</a>
+<a name="714"><span class="lineNum">     714 </span>            :     ::memcpy(dst, &amp;item, sizeof(T));</a>
+<a name="715"><span class="lineNum">     715 </span>            : </a>
+<a name="716"><span class="lineNum">     716 </span>            :     _length++;</a>
+<a name="717"><span class="lineNum">     717 </span>            :     return kErrorOk;</a>
+<a name="718"><span class="lineNum">     718 </span>            :   }</a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span>            :   //! Append `item` to the vector.</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">      25736 :   Error append(ZoneHeap* heap, const T&amp; item) noexcept {</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">      25736 :     if (ASMJIT_UNLIKELY(_length == _capacity))</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">       5248 :       ASMJIT_PROPAGATE(grow(heap, 1));</span></a>
+<a name="724"><span class="lineNum">     724 </span>            : </a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">      25736 :     ::memcpy(static_cast&lt;T*&gt;(_data) + _length, &amp;item, sizeof(T));</span></a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">      25736 :     _length++;</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">      25736 :     return kErrorOk;</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :   }</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span>            :   Error concat(ZoneHeap* heap, const ZoneVector&lt;T&gt;&amp; other) noexcept {</a>
+<a name="732"><span class="lineNum">     732 </span>            :     size_t count = other._length;</a>
+<a name="733"><span class="lineNum">     733 </span>            :     if (_capacity - _length &lt; count)</a>
+<a name="734"><span class="lineNum">     734 </span>            :       ASMJIT_PROPAGATE(grow(heap, count));</a>
+<a name="735"><span class="lineNum">     735 </span>            : </a>
+<a name="736"><span class="lineNum">     736 </span>            :     ::memcpy(static_cast&lt;T*&gt;(_data) + _length, other._data, count * sizeof(T));</a>
+<a name="737"><span class="lineNum">     737 </span>            : </a>
+<a name="738"><span class="lineNum">     738 </span>            :     _length += count;</a>
+<a name="739"><span class="lineNum">     739 </span>            :     return kErrorOk;</a>
+<a name="740"><span class="lineNum">     740 </span>            :   }</a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span>            :   //! Prepend `item` to the vector (unsafe case).</a>
+<a name="743"><span class="lineNum">     743 </span>            :   //!</a>
+<a name="744"><span class="lineNum">     744 </span>            :   //! Can only be used together with `willGrow()`. If `willGrow(N)` returns</a>
+<a name="745"><span class="lineNum">     745 </span>            :   //! `kErrorOk` then N elements can be added to the vector without checking</a>
+<a name="746"><span class="lineNum">     746 </span>            :   //! if there is a place for them. Used mostly internally.</a>
+<a name="747"><span class="lineNum">     747 </span>            :   ASMJIT_INLINE void prependUnsafe(const T&amp; item) noexcept {</a>
+<a name="748"><span class="lineNum">     748 </span>            :     ASMJIT_ASSERT(_length &lt; _capacity);</a>
+<a name="749"><span class="lineNum">     749 </span>            :     T* data = static_cast&lt;T*&gt;(_data);</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            :     if (_length)</a>
+<a name="752"><span class="lineNum">     752 </span>            :       ::memmove(data + 1, data, _length * sizeof(T));</a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span>            :     ::memcpy(data, &amp;item, sizeof(T));</a>
+<a name="755"><span class="lineNum">     755 </span>            :     _length++;</a>
+<a name="756"><span class="lineNum">     756 </span>            :   }</a>
+<a name="757"><span class="lineNum">     757 </span>            : </a>
+<a name="758"><span class="lineNum">     758 </span>            :   //! Append `item` to the vector (unsafe case).</a>
+<a name="759"><span class="lineNum">     759 </span>            :   //!</a>
+<a name="760"><span class="lineNum">     760 </span>            :   //! Can only be used together with `willGrow()`. If `willGrow(N)` returns</a>
+<a name="761"><span class="lineNum">     761 </span>            :   //! `kErrorOk` then N elements can be added to the vector without checking</a>
+<a name="762"><span class="lineNum">     762 </span>            :   //! if there is a place for them. Used mostly internally.</a>
+<a name="763"><span class="lineNum">     763 </span>            :   ASMJIT_INLINE void appendUnsafe(const T&amp; item) noexcept {</a>
+<a name="764"><span class="lineNum">     764 </span>            :     ASMJIT_ASSERT(_length &lt; _capacity);</a>
+<a name="765"><span class="lineNum">     765 </span>            : </a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">      29632 :     ::memcpy(static_cast&lt;T*&gt;(_data) + _length, &amp;item, sizeof(T));</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">      27684 :     _length++;</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">       1948 :   }</span></a>
+<a name="769"><span class="lineNum">     769 </span>            : </a>
+<a name="770"><span class="lineNum">     770 </span>            :   //! Concatenate all items of `other` at the end of the vector.</a>
+<a name="771"><span class="lineNum">     771 </span>            :   ASMJIT_INLINE void concatUnsafe(const ZoneVector&lt;T&gt;&amp; other) noexcept {</a>
+<a name="772"><span class="lineNum">     772 </span>            :     size_t count = other._length;</a>
+<a name="773"><span class="lineNum">     773 </span>            :     ASMJIT_ASSERT(_capacity - _length &gt;= count);</a>
+<a name="774"><span class="lineNum">     774 </span>            : </a>
+<a name="775"><span class="lineNum">     775 </span>            :     ::memcpy(static_cast&lt;T*&gt;(_data) + _length, other._data, count * sizeof(T));</a>
+<a name="776"><span class="lineNum">     776 </span>            :     _length += count;</a>
+<a name="777"><span class="lineNum">     777 </span>            :   }</a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span>            :   //! Get index of `val` or `kInvalidIndex` if not found.</a>
+<a name="780"><span class="lineNum">     780 </span>            :   ASMJIT_INLINE size_t indexOf(const T&amp; val) const noexcept {</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineNoCov">          0 :     const T* data = static_cast&lt;const T*&gt;(_data);</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineNoCov">          0 :     size_t length = _length;</span></a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineNoCov">          0 :     for (size_t i = 0; i &lt; length; i++)</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineNoCov">          0 :       if (data[i] == val)</span></a>
+<a name="786"><span class="lineNum">     786 </span>            :         return i;</a>
+<a name="787"><span class="lineNum">     787 </span>            : </a>
+<a name="788"><span class="lineNum">     788 </span>            :     return Globals::kInvalidIndex;</a>
+<a name="789"><span class="lineNum">     789 </span>            :   }</a>
+<a name="790"><span class="lineNum">     790 </span>            : </a>
+<a name="791"><span class="lineNum">     791 </span>            :   //! Get whether the vector contains `val`.</a>
+<a name="792"><span class="lineNum">     792 </span>            :   ASMJIT_INLINE bool contains(const T&amp; val) const noexcept {</a>
+<a name="793"><span class="lineNum">     793 </span>            :     return indexOf(val) != Globals::kInvalidIndex;</a>
+<a name="794"><span class="lineNum">     794 </span>            :   }</a>
+<a name="795"><span class="lineNum">     795 </span>            : </a>
+<a name="796"><span class="lineNum">     796 </span>            :   //! Remove item at index `i`.</a>
+<a name="797"><span class="lineNum">     797 </span>            :   ASMJIT_INLINE void removeAt(size_t i) noexcept {</a>
+<a name="798"><span class="lineNum">     798 </span>            :     ASMJIT_ASSERT(i &lt; _length);</a>
+<a name="799"><span class="lineNum">     799 </span>            : </a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineNoCov">          0 :     T* data = static_cast&lt;T*&gt;(_data) + i;</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineNoCov">          0 :     _length--;</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineNoCov">          0 :     ::memmove(data, data + 1, _length - i);</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="804"><span class="lineNum">     804 </span>            : </a>
+<a name="805"><span class="lineNum">     805 </span>            :   //! Swap this pod-vector with `other`.</a>
+<a name="806"><span class="lineNum">     806 </span>            :   ASMJIT_INLINE void swap(ZoneVector&lt;T&gt;&amp; other) noexcept {</a>
+<a name="807"><span class="lineNum">     807 </span>            :     Utils::swap(_length, other._length);</a>
+<a name="808"><span class="lineNum">     808 </span>            :     Utils::swap(_capacity, other._capacity);</a>
+<a name="809"><span class="lineNum">     809 </span>            :     Utils::swap(_data, other._data);</a>
+<a name="810"><span class="lineNum">     810 </span>            :   }</a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span>            :   //! Get item at index `i` (const).</a>
+<a name="813"><span class="lineNum">     813 </span>            :   ASMJIT_INLINE const T&amp; getAt(size_t i) const noexcept {</a>
+<a name="814"><span class="lineNum">     814 </span>            :     ASMJIT_ASSERT(i &lt; _length);</a>
+<a name="815"><span class="lineNum">     815 </span>            :     return getData()[i];</a>
+<a name="816"><span class="lineNum">     816 </span>            :   }</a>
+<a name="817"><span class="lineNum">     817 </span>            : </a>
+<a name="818"><span class="lineNum">     818 </span>            :   //! Get item at index `i`.</a>
+<a name="819"><span class="lineNum">     819 </span>            :   ASMJIT_INLINE T&amp; operator[](size_t i) noexcept {</a>
+<a name="820"><span class="lineNum">     820 </span>            :     ASMJIT_ASSERT(i &lt; _length);</a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">       7792 :     return getData()[i];</span></a>
+<a name="822"><span class="lineNum">     822 </span>            :   }</a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span>            :   //! Get item at index `i`.</a>
+<a name="825"><span class="lineNum">     825 </span>            :   ASMJIT_INLINE const T&amp; operator[](size_t i) const noexcept {</a>
+<a name="826"><span class="lineNum">     826 </span>            :     ASMJIT_ASSERT(i &lt; _length);</a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">     132410 :     return getData()[i];</span></a>
+<a name="828"><span class="lineNum">     828 </span>            :   }</a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="831"><span class="lineNum">     831 </span>            :   // [Memory Management]</a>
+<a name="832"><span class="lineNum">     832 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span>            :   //! Release the memory held by `ZoneVector&lt;T&gt;` back to the `heap`.</a>
+<a name="835"><span class="lineNum">     835 </span>            :   ASMJIT_INLINE void release(ZoneHeap* heap) noexcept { _release(heap, sizeof(T)); }</a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            :   //! Called to grow the buffer to fit at least `n` elements more.</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">      16340 :   ASMJIT_INLINE Error grow(ZoneHeap* heap, size_t n) noexcept { return ZoneVectorBase::_grow(heap, sizeof(T), n); }</span></a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span>            :   //! Resize the vector to hold `n` elements.</a>
+<a name="841"><span class="lineNum">     841 </span>            :   //!</a>
+<a name="842"><span class="lineNum">     842 </span>            :   //! If `n` is greater than the current length then the additional elements'</a>
+<a name="843"><span class="lineNum">     843 </span>            :   //! content will be initialized to zero. If `n` is less than the current</a>
+<a name="844"><span class="lineNum">     844 </span>            :   //! length then the vector will be truncated to exactly `n` elements.</a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">       3896 :   ASMJIT_INLINE Error resize(ZoneHeap* heap, size_t n) noexcept { return ZoneVectorBase::_resize(heap, sizeof(T), n); }</span></a>
+<a name="846"><span class="lineNum">     846 </span>            : </a>
+<a name="847"><span class="lineNum">     847 </span>            :   //! Realloc internal array to fit at least `n` items.</a>
+<a name="848"><span class="lineNum">     848 </span>            :   ASMJIT_INLINE Error reserve(ZoneHeap* heap, size_t n) noexcept { return ZoneVectorBase::_reserve(heap, sizeof(T), n); }</a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span>            :   ASMJIT_INLINE Error willGrow(ZoneHeap* heap, size_t n = 1) noexcept {</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">      31580 :     return _capacity - _length &lt; n ? grow(heap, n) : static_cast&lt;Error&gt;(kErrorOk);</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :   }</a>
+<a name="853"><span class="lineNum">     853 </span>            : };</a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span>            : // ============================================================================</a>
+<a name="856"><span class="lineNum">     856 </span>            : // [asmjit::ZoneBitVector]</a>
+<a name="857"><span class="lineNum">     857 </span>            : // ============================================================================</a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span>            : class ZoneBitVector {</a>
+<a name="860"><span class="lineNum">     860 </span>            : public:</a>
+<a name="861"><span class="lineNum">     861 </span>            :   ASMJIT_NONCOPYABLE(ZoneBitVector)</a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span>            :   //! Storage used to store a pack of bits (should by compatible with a machine word).</a>
+<a name="864"><span class="lineNum">     864 </span>            :   typedef uintptr_t BitWord;</a>
+<a name="865"><span class="lineNum">     865 </span>            :   enum { kBitsPerWord = static_cast&lt;int&gt;(sizeof(BitWord)) * 8 };</a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span>            :   static ASMJIT_INLINE size_t _wordsPerBits(size_t nBits) noexcept {</a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineNoCov">          0 :     return ((nBits + kBitsPerWord) / kBitsPerWord) - 1;</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :   }</a>
+<a name="870"><span class="lineNum">     870 </span>            : </a>
+<a name="871"><span class="lineNum">     871 </span>            :   // Return all bits zero if 0 and all bits set if 1.</a>
+<a name="872"><span class="lineNum">     872 </span>            :   static ASMJIT_INLINE BitWord _patternFromBit(bool bit) noexcept {</a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineNoCov">          0 :     BitWord bitAsWord = static_cast&lt;BitWord&gt;(bit);</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :     ASMJIT_ASSERT(bitAsWord == 0 || bitAsWord == 1);</a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineNoCov">          0 :     return static_cast&lt;BitWord&gt;(0) - bitAsWord;</span></a>
+<a name="876"><span class="lineNum">     876 </span>            :   }</a>
+<a name="877"><span class="lineNum">     877 </span>            : </a>
+<a name="878"><span class="lineNum">     878 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="879"><span class="lineNum">     879 </span>            :   // [Construction / Destruction]</a>
+<a name="880"><span class="lineNum">     880 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span>            :   explicit ASMJIT_INLINE ZoneBitVector() noexcept :</a>
+<a name="883"><span class="lineNum">     883 </span>            :     _data(nullptr),</a>
+<a name="884"><span class="lineNum">     884 </span>            :     _length(0),</a>
+<a name="885"><span class="lineNum">     885 </span>            :     _capacity(0) {}</a>
+<a name="886"><span class="lineNum">     886 </span>            : </a>
+<a name="887"><span class="lineNum">     887 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="888"><span class="lineNum">     888 </span>            :   // [Accessors]</a>
+<a name="889"><span class="lineNum">     889 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="890"><span class="lineNum">     890 </span>            : </a>
+<a name="891"><span class="lineNum">     891 </span>            :   //! Get if the bit-vector is empty (has no bits).</a>
+<a name="892"><span class="lineNum">     892 </span>            :   ASMJIT_INLINE bool isEmpty() const noexcept { return _length == 0; }</a>
+<a name="893"><span class="lineNum">     893 </span>            :   //! Get a length of this bit-vector (in bits).</a>
+<a name="894"><span class="lineNum">     894 </span>            :   ASMJIT_INLINE size_t getLength() const noexcept { return _length; }</a>
+<a name="895"><span class="lineNum">     895 </span>            :   //! Get a capacity of this bit-vector (in bits).</a>
+<a name="896"><span class="lineNum">     896 </span>            :   ASMJIT_INLINE size_t getCapacity() const noexcept { return _capacity; }</a>
+<a name="897"><span class="lineNum">     897 </span>            : </a>
+<a name="898"><span class="lineNum">     898 </span>            :   //! Get data.</a>
+<a name="899"><span class="lineNum">     899 </span>            :   ASMJIT_INLINE BitWord* getData() noexcept { return _data; }</a>
+<a name="900"><span class="lineNum">     900 </span>            :   //! \overload</a>
+<a name="901"><span class="lineNum">     901 </span>            :   ASMJIT_INLINE const BitWord* getData() const noexcept { return _data; }</a>
+<a name="902"><span class="lineNum">     902 </span>            : </a>
+<a name="903"><span class="lineNum">     903 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="904"><span class="lineNum">     904 </span>            :   // [Ops]</a>
+<a name="905"><span class="lineNum">     905 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="906"><span class="lineNum">     906 </span>            : </a>
+<a name="907"><span class="lineNum">     907 </span>            :   ASMJIT_INLINE void clear() noexcept {</a>
+<a name="908"><span class="lineNum">     908 </span>            :     _length = 0;</a>
+<a name="909"><span class="lineNum">     909 </span>            :   }</a>
+<a name="910"><span class="lineNum">     910 </span>            : </a>
+<a name="911"><span class="lineNum">     911 </span>            :   ASMJIT_INLINE void reset() noexcept {</a>
+<a name="912"><span class="lineNum">     912 </span>            :     _data = nullptr;</a>
+<a name="913"><span class="lineNum">     913 </span>            :     _length = 0;</a>
+<a name="914"><span class="lineNum">     914 </span>            :     _capacity = 0;</a>
+<a name="915"><span class="lineNum">     915 </span>            :   }</a>
+<a name="916"><span class="lineNum">     916 </span>            : </a>
+<a name="917"><span class="lineNum">     917 </span>            :   ASMJIT_INLINE void truncate(size_t newLength) noexcept {</a>
+<a name="918"><span class="lineNum">     918 </span>            :     _length = std::min(_length, newLength);</a>
+<a name="919"><span class="lineNum">     919 </span>            :     _clearUnusedBits();</a>
+<a name="920"><span class="lineNum">     920 </span>            :   }</a>
+<a name="921"><span class="lineNum">     921 </span>            : </a>
+<a name="922"><span class="lineNum">     922 </span>            :   ASMJIT_INLINE bool getAt(size_t index) const noexcept {</a>
+<a name="923"><span class="lineNum">     923 </span>            :     ASMJIT_ASSERT(index &lt; _length);</a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span>            :     size_t idx = index / kBitsPerWord;</a>
+<a name="926"><span class="lineNum">     926 </span>            :     size_t bit = index % kBitsPerWord;</a>
+<a name="927"><span class="lineNum">     927 </span>            :     return static_cast&lt;bool&gt;((_data[idx] &gt;&gt; bit) &amp; 1);</a>
+<a name="928"><span class="lineNum">     928 </span>            :   }</a>
+<a name="929"><span class="lineNum">     929 </span>            : </a>
+<a name="930"><span class="lineNum">     930 </span>            :   ASMJIT_INLINE void setAt(size_t index, bool value) noexcept {</a>
+<a name="931"><span class="lineNum">     931 </span>            :     ASMJIT_ASSERT(index &lt; _length);</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span>            :     size_t idx = index / kBitsPerWord;</a>
+<a name="934"><span class="lineNum">     934 </span>            :     size_t bit = index % kBitsPerWord;</a>
+<a name="935"><span class="lineNum">     935 </span>            :     if (value)</a>
+<a name="936"><span class="lineNum">     936 </span>            :       _data[idx] |= static_cast&lt;BitWord&gt;(1) &lt;&lt; bit;</a>
+<a name="937"><span class="lineNum">     937 </span>            :     else</a>
+<a name="938"><span class="lineNum">     938 </span>            :       _data[idx] &amp;= ~(static_cast&lt;BitWord&gt;(1) &lt;&lt; bit);</a>
+<a name="939"><span class="lineNum">     939 </span>            :   }</a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span>            :   ASMJIT_INLINE void toggleAt(size_t index) noexcept {</a>
+<a name="942"><span class="lineNum">     942 </span>            :     ASMJIT_ASSERT(index &lt; _length);</a>
+<a name="943"><span class="lineNum">     943 </span>            : </a>
+<a name="944"><span class="lineNum">     944 </span>            :     size_t idx = index / kBitsPerWord;</a>
+<a name="945"><span class="lineNum">     945 </span>            :     size_t bit = index % kBitsPerWord;</a>
+<a name="946"><span class="lineNum">     946 </span>            :     _data[idx] ^= static_cast&lt;BitWord&gt;(1) &lt;&lt; bit;</a>
+<a name="947"><span class="lineNum">     947 </span>            :   }</a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span>            :   ASMJIT_INLINE Error append(ZoneHeap* heap, bool value) noexcept {</a>
+<a name="950"><span class="lineNum">     950 </span>            :     size_t index = _length;</a>
+<a name="951"><span class="lineNum">     951 </span>            :     if (ASMJIT_UNLIKELY(index &gt;= _capacity))</a>
+<a name="952"><span class="lineNum">     952 </span>            :       return _append(heap, value);</a>
+<a name="953"><span class="lineNum">     953 </span>            : </a>
+<a name="954"><span class="lineNum">     954 </span>            :     size_t idx = index / kBitsPerWord;</a>
+<a name="955"><span class="lineNum">     955 </span>            :     size_t bit = index % kBitsPerWord;</a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            :     if (bit == 0)</a>
+<a name="958"><span class="lineNum">     958 </span>            :       _data[idx] = static_cast&lt;BitWord&gt;(value) &lt;&lt; bit;</a>
+<a name="959"><span class="lineNum">     959 </span>            :     else</a>
+<a name="960"><span class="lineNum">     960 </span>            :       _data[idx] |= static_cast&lt;BitWord&gt;(value) &lt;&lt; bit;</a>
+<a name="961"><span class="lineNum">     961 </span>            : </a>
+<a name="962"><span class="lineNum">     962 </span>            :     _length++;</a>
+<a name="963"><span class="lineNum">     963 </span>            :     return kErrorOk;</a>
+<a name="964"><span class="lineNum">     964 </span>            :   }</a>
+<a name="965"><span class="lineNum">     965 </span>            : </a>
+<a name="966"><span class="lineNum">     966 </span>            :   ASMJIT_API Error fill(size_t fromIndex, size_t toIndex, bool value) noexcept;</a>
+<a name="967"><span class="lineNum">     967 </span>            : </a>
+<a name="968"><span class="lineNum">     968 </span>            :   ASMJIT_INLINE void and_(const ZoneBitVector&amp; other) noexcept {</a>
+<a name="969"><span class="lineNum">     969 </span>            :     BitWord* dst = _data;</a>
+<a name="970"><span class="lineNum">     970 </span>            :     const BitWord* src = other._data;</a>
+<a name="971"><span class="lineNum">     971 </span>            : </a>
+<a name="972"><span class="lineNum">     972 </span>            :     size_t numWords = (std::min(_length, other._length) + kBitsPerWord - 1) / kBitsPerWord;</a>
+<a name="973"><span class="lineNum">     973 </span>            :     for (size_t i = 0; i &lt; numWords; i++)</a>
+<a name="974"><span class="lineNum">     974 </span>            :       dst[i] = dst[i] &amp; src[i];</a>
+<a name="975"><span class="lineNum">     975 </span>            :     _clearUnusedBits();</a>
+<a name="976"><span class="lineNum">     976 </span>            :   }</a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span>            :   ASMJIT_INLINE void andNot(const ZoneBitVector&amp; other) noexcept {</a>
+<a name="979"><span class="lineNum">     979 </span>            :     BitWord* dst = _data;</a>
+<a name="980"><span class="lineNum">     980 </span>            :     const BitWord* src = other._data;</a>
+<a name="981"><span class="lineNum">     981 </span>            : </a>
+<a name="982"><span class="lineNum">     982 </span>            :     size_t numWords = (std::min(_length, other._length) + kBitsPerWord - 1) / kBitsPerWord;</a>
+<a name="983"><span class="lineNum">     983 </span>            :     for (size_t i = 0; i &lt; numWords; i++)</a>
+<a name="984"><span class="lineNum">     984 </span>            :       dst[i] = dst[i] &amp; ~src[i];</a>
+<a name="985"><span class="lineNum">     985 </span>            :     _clearUnusedBits();</a>
+<a name="986"><span class="lineNum">     986 </span>            :   }</a>
+<a name="987"><span class="lineNum">     987 </span>            : </a>
+<a name="988"><span class="lineNum">     988 </span>            :   ASMJIT_INLINE void or_(const ZoneBitVector&amp; other) noexcept {</a>
+<a name="989"><span class="lineNum">     989 </span>            :     BitWord* dst = _data;</a>
+<a name="990"><span class="lineNum">     990 </span>            :     const BitWord* src = other._data;</a>
+<a name="991"><span class="lineNum">     991 </span>            : </a>
+<a name="992"><span class="lineNum">     992 </span>            :     size_t numWords = (std::min(_length, other._length) + kBitsPerWord - 1) / kBitsPerWord;</a>
+<a name="993"><span class="lineNum">     993 </span>            :     for (size_t i = 0; i &lt; numWords; i++)</a>
+<a name="994"><span class="lineNum">     994 </span>            :       dst[i] = dst[i] | src[i];</a>
+<a name="995"><span class="lineNum">     995 </span>            :     _clearUnusedBits();</a>
+<a name="996"><span class="lineNum">     996 </span>            :   }</a>
+<a name="997"><span class="lineNum">     997 </span>            : </a>
+<a name="998"><span class="lineNum">     998 </span>            :   ASMJIT_INLINE void _clearUnusedBits() noexcept {</a>
+<a name="999"><span class="lineNum">     999 </span>            :     size_t idx = _length / kBitsPerWord;</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :     size_t bit = _length % kBitsPerWord;</a>
+<a name="1001"><span class="lineNum">    1001 </span>            : </a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     if (!bit) return;</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :     _data[idx] &amp;= (static_cast&lt;BitWord&gt;(1) &lt;&lt; bit) - 1U;</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :   }</a>
+<a name="1005"><span class="lineNum">    1005 </span>            : </a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :   // [Memory Management]</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1009"><span class="lineNum">    1009 </span>            : </a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   ASMJIT_INLINE void release(ZoneHeap* heap) noexcept {</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :     if (_data != nullptr) {</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :       heap-&gt;release(_data, _capacity / 8);</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :       reset();</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :     }</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   }</a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   ASMJIT_INLINE Error resize(ZoneHeap* heap, size_t newLength, bool newBitsValue = false) noexcept {</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :     return _resize(heap, newLength, newLength, newBitsValue);</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   }</a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span>            :   ASMJIT_API Error _resize(ZoneHeap* heap, size_t newLength, size_t idealCapacity, bool newBitsValue) noexcept;</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :   ASMJIT_API Error _append(ZoneHeap* heap, bool value) noexcept;</a>
+<a name="1023"><span class="lineNum">    1023 </span>            : </a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   // [Members]</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1027"><span class="lineNum">    1027 </span>            : </a>
+<a name="1028"><span class="lineNum">    1028 </span>            :   BitWord* _data;                        //!&lt; Bits.</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :   size_t _length;                        //!&lt; Length of the bit-vector (in bits).</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :   size_t _capacity;                      //!&lt; Capacity of the bit-vector (in bits).</a>
+<a name="1031"><span class="lineNum">    1031 </span>            : };</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : </a>
+<a name="1033"><span class="lineNum">    1033 </span>            : // ============================================================================</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : // [asmjit::ZoneHashNode]</a>
+<a name="1035"><span class="lineNum">    1035 </span>            : // ============================================================================</a>
+<a name="1036"><span class="lineNum">    1036 </span>            : </a>
+<a name="1037"><span class="lineNum">    1037 </span>            : //! Node used by \ref ZoneHash&lt;&gt; template.</a>
+<a name="1038"><span class="lineNum">    1038 </span>            : //!</a>
+<a name="1039"><span class="lineNum">    1039 </span>            : //! You must provide function `bool eq(const Key&amp; key)` in order to make</a>
+<a name="1040"><span class="lineNum">    1040 </span>            : //! `ZoneHash::get()` working.</a>
+<a name="1041"><span class="lineNum">    1041 </span>            : class ZoneHashNode {</a>
+<a name="1042"><span class="lineNum">    1042 </span>            : public:</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :   ASMJIT_INLINE ZoneHashNode(uint32_t hVal = 0) noexcept</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     : _hashNext(nullptr),</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :       _hVal(hVal) {}</a>
+<a name="1046"><span class="lineNum">    1046 </span>            : </a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   //! Next node in the chain, null if it terminates the chain.</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :   ZoneHashNode* _hashNext;</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :   //! Key hash.</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   uint32_t _hVal;</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   //! Should be used by Node that inherits ZoneHashNode, it aligns ZoneHashNode.</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   uint32_t _customData;</a>
+<a name="1053"><span class="lineNum">    1053 </span>            : };</a>
+<a name="1054"><span class="lineNum">    1054 </span>            : </a>
+<a name="1055"><span class="lineNum">    1055 </span>            : // ============================================================================</a>
+<a name="1056"><span class="lineNum">    1056 </span>            : // [asmjit::ZoneHashBase]</a>
+<a name="1057"><span class="lineNum">    1057 </span>            : // ============================================================================</a>
+<a name="1058"><span class="lineNum">    1058 </span>            : </a>
+<a name="1059"><span class="lineNum">    1059 </span>            : class ZoneHashBase {</a>
+<a name="1060"><span class="lineNum">    1060 </span>            : public:</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   ASMJIT_NONCOPYABLE(ZoneHashBase)</a>
+<a name="1062"><span class="lineNum">    1062 </span>            : </a>
+<a name="1063"><span class="lineNum">    1063 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   // [Construction / Destruction]</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : </a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ZoneHashBase(ZoneHeap* heap) noexcept {</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">       1948 :     _heap = heap;</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">       1948 :     _size = 0;</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">       1948 :     _bucketsCount = 1;</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">       1948 :     _bucketsGrow = 1;</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">       1948 :     _data = _embedded;</span></a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">       1948 :     _embedded[0] = nullptr;</span></a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   }</a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ~ZoneHashBase() noexcept { reset(nullptr); }</span></a>
+<a name="1076"><span class="lineNum">    1076 </span>            : </a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :   // [Reset]</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : </a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   ASMJIT_INLINE bool isInitialized() const noexcept { return _heap != nullptr; }</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   ASMJIT_API void reset(ZoneHeap* heap) noexcept;</a>
+<a name="1083"><span class="lineNum">    1083 </span>            : </a>
+<a name="1084"><span class="lineNum">    1084 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   // [Accessors]</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1087"><span class="lineNum">    1087 </span>            : </a>
+<a name="1088"><span class="lineNum">    1088 </span>            :   //! Get a `ZoneHeap` attached to this container.</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :   ASMJIT_INLINE ZoneHeap* getHeap() const noexcept { return _heap; }</a>
+<a name="1090"><span class="lineNum">    1090 </span>            : </a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   ASMJIT_INLINE size_t getSize() const noexcept { return _size; }</a>
+<a name="1092"><span class="lineNum">    1092 </span>            : </a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   // [Ops]</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1096"><span class="lineNum">    1096 </span>            : </a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   ASMJIT_API void _rehash(uint32_t newCount) noexcept;</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   ASMJIT_API ZoneHashNode* _put(ZoneHashNode* node) noexcept;</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :   ASMJIT_API ZoneHashNode* _del(ZoneHashNode* node) noexcept;</a>
+<a name="1100"><span class="lineNum">    1100 </span>            : </a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   // [Members]</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   // --------------------------------------------------------------------------</a>
+<a name="1104"><span class="lineNum">    1104 </span>            : </a>
+<a name="1105"><span class="lineNum">    1105 </span>            :   ZoneHeap* _heap;                       //!&lt; ZoneHeap used to allocate data.</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   size_t _size;                          //!&lt; Count of records inserted into the hash table.</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   uint32_t _bucketsCount;                //!&lt; Count of hash buckets.</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   uint32_t _bucketsGrow;                 //!&lt; When buckets array should grow.</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   ZoneHashNode** _data;                  //!&lt; Buckets data.</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   ZoneHashNode* _embedded[1];            //!&lt; Embedded data, used by empty hash tables.</a>
+<a name="1112"><span class="lineNum">    1112 </span>            : };</a>
+<a name="1113"><span class="lineNum">    1113 </span>            : </a>
+<a name="1114"><span class="lineNum">    1114 </span>            : // ============================================================================</a>
+<a name="1115"><span class="lineNum">    1115 </span>            : // [asmjit::ZoneHash&lt;Key, Node&gt;]</a>
+<a name="1116"><span class="lineNum">    1116 </span>            : // ============================================================================</a>
+<a name="1117"><span class="lineNum">    1117 </span>            : </a>
+<a name="1118"><span class="lineNum">    1118 </span>            : //! Low-level hash table specialized for storing string keys and POD values.</a>
+<a name="1119"><span class="lineNum">    1119 </span>            : //!</a>
+<a name="1120"><span class="lineNum">    1120 </span>            : //! This hash table allows duplicates to be inserted (the API is so low</a>
+<a name="1121"><span class="lineNum">    1121 </span>            : //! level that it's up to you if you allow it or not, as you should first</a>
+<a name="1122"><span class="lineNum">    1122 </span>            : //! `get()` the node and then modify it or insert a new node by using `put()`,</a>
+<a name="1123"><span class="lineNum">    1123 </span>            : //! depending on the intention).</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : template&lt;typename Node&gt;</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : class ZoneHash : public ZoneHashBase {</a>
+<a name="1126"><span class="lineNum">    1126 </span>            : public:</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   explicit ASMJIT_INLINE ZoneHash(ZoneHeap* heap = nullptr) noexcept</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :     : ZoneHashBase(heap) {}</a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">       1948 :   ASMJIT_INLINE ~ZoneHash() noexcept {}</span></a>
+<a name="1130"><span class="lineNum">    1130 </span>            : </a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   template&lt;typename Key&gt;</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   ASMJIT_INLINE Node* get(const Key&amp; key) const noexcept {</a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineNoCov">          0 :     uint32_t hMod = key.hVal % _bucketsCount;</span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineNoCov">          0 :     Node* node = static_cast&lt;Node*&gt;(_data[hMod]);</span></a>
+<a name="1135"><span class="lineNum">    1135 </span>            : </a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineNoCov">          0 :     while (node &amp;&amp; !key.matches(node))</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineNoCov">          0 :       node = static_cast&lt;Node*&gt;(node-&gt;_hashNext);</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     return node;</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :   }</a>
+<a name="1140"><span class="lineNum">    1140 </span>            : </a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineNoCov">          0 :   ASMJIT_INLINE Node* put(Node* node) noexcept { return static_cast&lt;Node*&gt;(_put(node)); }</span></a>
+<a name="1142"><span class="lineNum">    1142 </span>            :   ASMJIT_INLINE Node* del(Node* node) noexcept { return static_cast&lt;Node*&gt;(_del(node)); }</a>
+<a name="1143"><span class="lineNum">    1143 </span>            : };</a>
+<a name="1144"><span class="lineNum">    1144 </span>            : </a>
+<a name="1145"><span class="lineNum">    1145 </span>            : //! \}</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : </a>
+<a name="1147"><span class="lineNum">    1147 </span>            : } // asmjit namespace</a>
+<a name="1148"><span class="lineNum">    1148 </span>            : } // namespace PLMD</a>
+<a name="1149"><span class="lineNum">    1149 </span>            : </a>
+<a name="1150"><span class="lineNum">    1150 </span>            : // [Api-End]</a>
+<a name="1151"><span class="lineNum">    1151 </span>            : #include &quot;./asmjit_apiend.h&quot;</a>
+<a name="1152"><span class="lineNum">    1152 </span>            : </a>
+<a name="1153"><span class="lineNum">    1153 </span>            : // [Guard]</a>
+<a name="1154"><span class="lineNum">    1154 </span>            : #endif // _ASMJIT_BASE_ZONE_H</a>
+<a name="1155"><span class="lineNum">    1155 </span>            : #pragma GCC diagnostic pop</a>
+<a name="1156"><span class="lineNum">    1156 </span>            : #endif // __PLUMED_HAS_ASMJIT</a>
+<a name="1157"><span class="lineNum">    1157 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/blas/blas.cpp.func-sort-c.html b/coverage-libs/blas/blas.cpp.func-sort-c.html
new file mode 100644
index 0000000000..98b1fa0585
--- /dev/null
+++ b/coverage-libs/blas/blas.cpp.func-sort-c.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - blas/blas.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">blas</a> - blas.cpp<span style="font-size: 80%;"> (<a href="blas.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">405</td>
+            <td class="headerCovTableEntry">1605</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">47.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="blas.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
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+
+</body>
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diff --git a/coverage-libs/blas/blas.cpp.func.html b/coverage-libs/blas/blas.cpp.func.html
new file mode 100644
index 0000000000..d8f5fc91fe
--- /dev/null
+++ b/coverage-libs/blas/blas.cpp.func.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - blas/blas.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">blas</a> - blas.cpp<span style="font-size: 80%;"> (<a href="blas.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">405</td>
+            <td class="headerCovTableEntry">1605</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">47.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage-libs/blas/blas.cpp.gcov.html b/coverage-libs/blas/blas.cpp.gcov.html
new file mode 100644
index 0000000000..aeb291abd3
--- /dev/null
+++ b/coverage-libs/blas/blas.cpp.gcov.html
@@ -0,0 +1,3766 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - blas/blas.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">blas</a> - blas.cpp<span style="font-size: 80%;"> (source / <a href="blas.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">405</td>
+            <td class="headerCovTableEntry">1605</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">47.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : These files are semi-automatic translations by f2c from the original netlib BLAS library.</a>
+<a name="3"><span class="lineNum">       3 </span>            : The source has been modified to (mostly) use modern C formatting, and to get rid of</a>
+<a name="4"><span class="lineNum">       4 </span>            : compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and</a>
+<a name="5"><span class="lineNum">       5 </span>            : not the reference BLAS implementation.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            : The reference BLAS implementation is available from http://www.netlib.org/blas </a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : BLAS does not come with a formal named &quot;license&quot;, but a general statement that </a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            : &quot;The reference BLAS is a freely-available software package. It is available from netlib</a>
+<a name="12"><span class="lineNum">      12 </span>            : via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software</a>
+<a name="13"><span class="lineNum">      13 </span>            : packages (and has been). We only ask that proper credit be given to the authors.&quot;</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            : While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to</a>
+<a name="16"><span class="lineNum">      16 </span>            : our modified BLAS files as the original netlib versions, so do what you want with them.</a>
+<a name="17"><span class="lineNum">      17 </span>            : However, be warned that we have only tested that they to the right thing in the cases used</a>
+<a name="18"><span class="lineNum">      18 </span>            : in GROMACS (primarily full &amp; sparse matrix diagonalization), so in most cases it is a much</a>
+<a name="19"><span class="lineNum">      19 </span>            : better idea to use the full reference implementation.</a>
+<a name="20"><span class="lineNum">      20 </span>            : </a>
+<a name="21"><span class="lineNum">      21 </span>            : Erik Lindahl, 2008-10-07.</a>
+<a name="22"><span class="lineNum">      22 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="23"><span class="lineNum">      23 </span>            : #if ! defined (__PLUMED_HAS_EXTERNAL_BLAS)</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cmath&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;blas.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD{</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace blas{</a>
+<a name="29"><span class="lineNum">      29 </span>            : double</a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dasum,DASUM)(int *n__, </span></a>
+<a name="31"><span class="lineNum">      31 </span>            :                       double *dx, </a>
+<a name="32"><span class="lineNum">      32 </span>            :                       int *incx__)</a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span>            :     int i__1, i__2;</a>
+<a name="35"><span class="lineNum">      35 </span>            :     </a>
+<a name="36"><span class="lineNum">      36 </span>            :     int i__, m, mp1;</a>
+<a name="37"><span class="lineNum">      37 </span>            :     double dtemp;</a>
+<a name="38"><span class="lineNum">      38 </span>            :     int nincx;</a>
+<a name="39"><span class="lineNum">      39 </span>            :     </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :     </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :     --dx;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :     </a>
+<a name="45"><span class="lineNum">      45 </span>            :     dtemp = 0.;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 :     if (n &lt;= 0 || incx &lt;= 0) {</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :         return 0.0;</a>
+<a name="48"><span class="lineNum">      48 </span>            :     }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 :     if (incx != 1) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :         nincx = n * incx;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :         i__1 = nincx;</a>
+<a name="52"><span class="lineNum">      52 </span>            :         i__2 = incx;</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :             dtemp += std::abs(dx[i__]);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :         }</a>
+<a name="56"><span class="lineNum">      56 </span>            :         return dtemp;</a>
+<a name="57"><span class="lineNum">      57 </span>            :     }</a>
+<a name="58"><span class="lineNum">      58 </span>            :     </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :     m = n % 6;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :     if (m != 0) {</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :         i__2 = m;</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :             dtemp += std::abs(dx[i__]);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :         }</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :         if (n &lt; 6) {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :             return dtemp;</a>
+<a name="67"><span class="lineNum">      67 </span>            :         }</a>
+<a name="68"><span class="lineNum">      68 </span>            :     }</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :     mp1 = m + 1;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     i__2 = n;</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :     for (i__ = mp1; i__ &lt;= i__2; i__ += 6) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :         dtemp = dtemp + std::abs(dx[i__]) + std::abs(dx[i__ + 1]) + </span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :         std::abs(dx[i__ + 2]) + std::abs(dx[i__+ 3]) + std::abs(dx[i__ + 4]) +</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :         std::abs(dx[i__ + 5]);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     }</a>
+<a name="76"><span class="lineNum">      76 </span>            :     return dtemp;</a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : #include &quot;blas.h&quot;</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : namespace PLMD{</a>
+<a name="86"><span class="lineNum">      86 </span>            : namespace blas{</a>
+<a name="87"><span class="lineNum">      87 </span>            : void</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    1114408 : PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(int   *   n_arg,</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :                       double *   da_arg,</a>
+<a name="90"><span class="lineNum">      90 </span>            :                       double *   dx,</a>
+<a name="91"><span class="lineNum">      91 </span>            :                       int *      incx_arg,</a>
+<a name="92"><span class="lineNum">      92 </span>            :                       double *   dy,</a>
+<a name="93"><span class="lineNum">      93 </span>            :                       int *      incy_arg)</a>
+<a name="94"><span class="lineNum">      94 </span>            : {</a>
+<a name="95"><span class="lineNum">      95 </span>            :   int i,ix,iy;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    1114408 :   int n=*n_arg;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    1114408 :   double da=*da_arg;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">    1114408 :   int incx = *incx_arg;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">    1114408 :   int incy = *incy_arg;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">    1114408 :   if (n&lt;=0)</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     return;</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">    1114408 :   if(incx!=1 || incy!=1) {</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :     ix = 0;</a>
+<a name="106"><span class="lineNum">     106 </span>            :     iy = 0;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     if(incx&lt;0)</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :       ix = (1-n)*incx;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     if(incy&lt;0)</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :       iy = (1-n)*incy;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) </span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       dy[iy] += da*dx[ix];</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :     return;</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   } else {</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :     /* unroll */</a>
+<a name="120"><span class="lineNum">     120 </span>            :     </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    1162445 :     for(i=0;i&lt;(n-4);i+=4) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      48037 :       dy[i]   += da*dx[i];</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      48037 :       dy[i+1] += da*dx[i+1];</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      48037 :       dy[i+2] += da*dx[i+2];</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      48037 :       dy[i+3] += da*dx[i+3];</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     }</a>
+<a name="127"><span class="lineNum">     127 </span>            :     /* continue with current value of i */</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">    3900117 :     for(;i&lt;n;i++)</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">    2785709 :       dy[i]   += da*dx[i];</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   }</a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : #include &quot;blas.h&quot;</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : namespace PLMD{</a>
+<a name="137"><span class="lineNum">     137 </span>            : namespace blas{</a>
+<a name="138"><span class="lineNum">     138 </span>            : void</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">    4000772 : PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(int *n__,</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :                       double *dx,</a>
+<a name="141"><span class="lineNum">     141 </span>            :                       int *incx__,</a>
+<a name="142"><span class="lineNum">     142 </span>            :                       double *dy,</a>
+<a name="143"><span class="lineNum">     143 </span>            :                       int *incy__)</a>
+<a name="144"><span class="lineNum">     144 </span>            : {</a>
+<a name="145"><span class="lineNum">     145 </span>            :     int i,ix,iy;</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">    4000772 :     int n= *n__;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">    4000772 :     int incx = *incx__;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">    4000772 :     int incy = *incy__;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     </a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">    4000772 :     if(incx!=1 || incy!=1) {</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :         ix = 0;</a>
+<a name="154"><span class="lineNum">     154 </span>            :         iy = 0;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       6132 :         if(incx&lt;0)</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :             ix = (1-n)*(incx);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       6132 :         if(incy&lt;0)</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :             iy = (1-n)*(incy);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :         </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    1183902 :         for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) </span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    1177770 :             dy[iy] = dx[ix];</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :         </a>
+<a name="163"><span class="lineNum">     163 </span>            :         return;</a>
+<a name="164"><span class="lineNum">     164 </span>            :         </a>
+<a name="165"><span class="lineNum">     165 </span>            :     } else {</a>
+<a name="166"><span class="lineNum">     166 </span>            :         </a>
+<a name="167"><span class="lineNum">     167 </span>            :         /* unroll */</a>
+<a name="168"><span class="lineNum">     168 </span>            :         </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">    4101553 :         for(i=0;i&lt;(n-8);i+=8) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     106913 :             dy[i]   = dx[i];</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     106913 :             dy[i+1] = dx[i+1];</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     106913 :             dy[i+2] = dx[i+2];</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     106913 :             dy[i+3] = dx[i+3];</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     106913 :             dy[i+4] = dx[i+4];</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     106913 :             dy[i+5] = dx[i+5];</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     106913 :             dy[i+6] = dx[i+6];</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     106913 :             dy[i+7] = dx[i+7];</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :         }</a>
+<a name="179"><span class="lineNum">     179 </span>            :         /* continue with current value of i */</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">   16426655 :         for(;i&lt;n;i++)</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">   12432015 :             dy[i] = dx[i];</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+<a name="185"><span class="lineNum">     185 </span>            : }</a>
+<a name="186"><span class="lineNum">     186 </span>            : #include &quot;blas.h&quot;</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : namespace PLMD{</a>
+<a name="189"><span class="lineNum">     189 </span>            : namespace blas{</a>
+<a name="190"><span class="lineNum">     190 </span>            : double</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">    1114409 : PLUMED_BLAS_F77_FUNC(ddot,DDOT)(int *n_arg,</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :                     double *dx,</a>
+<a name="193"><span class="lineNum">     193 </span>            :                     int *incx_arg,</a>
+<a name="194"><span class="lineNum">     194 </span>            :                     double *dy,</a>
+<a name="195"><span class="lineNum">     195 </span>            :                     int *incy_arg)</a>
+<a name="196"><span class="lineNum">     196 </span>            : {</a>
+<a name="197"><span class="lineNum">     197 </span>            :     int i,ix,iy,m;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">    1114409 :     int n=*n_arg;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">    1114409 :     int incx = *incx_arg;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">    1114409 :     int incy = *incy_arg;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :     double t1;</a>
+<a name="202"><span class="lineNum">     202 </span>            :     </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">    1114409 :     if(n&lt;=0)</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :         return 0.0;</a>
+<a name="205"><span class="lineNum">     205 </span>            :     </a>
+<a name="206"><span class="lineNum">     206 </span>            :     t1 = 0.0;</a>
+<a name="207"><span class="lineNum">     207 </span>            :     </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">    1114409 :     if(incx!=1 || incy!=1) {</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :         ix = 0;</a>
+<a name="210"><span class="lineNum">     210 </span>            :         iy = 0;</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :         if(incx&lt;0)</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :             ix = (1-n)*incx;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :         if(incy&lt;0)</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :             iy = (1-n)*incy;</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :         </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) </span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :             t1 += dx[ix] * dy[iy];</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :         </a>
+<a name="219"><span class="lineNum">     219 </span>            :         return t1;</a>
+<a name="220"><span class="lineNum">     220 </span>            :         </a>
+<a name="221"><span class="lineNum">     221 </span>            :     } else {</a>
+<a name="222"><span class="lineNum">     222 </span>            :         </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">    1114409 :         m = n%5;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :         </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">    3899271 :         for(i=0;i&lt;m;i++)</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">    2784862 :             t1 += dx[i] * dy[i];</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :         </a>
+<a name="228"><span class="lineNum">     228 </span>            :         /* unroll */</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">    1153009 :         for(i=m;i&lt;n;i+=5) </span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      38600 :             t1  =  t1 + dx[i] * dy[i]   </span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      38600 :                 +    dx[i+1] * dy[i+1] </span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      38600 :                 +    dx[i+2] * dy[i+2] </span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      38600 :                 +    dx[i+3] * dy[i+3]   </span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      38600 :                 +    dx[i+4] * dy[i+4];   </span></a>
+<a name="235"><span class="lineNum">     235 </span>            :         </a>
+<a name="236"><span class="lineNum">     236 </span>            :         return t1;</a>
+<a name="237"><span class="lineNum">     237 </span>            :     }</a>
+<a name="238"><span class="lineNum">     238 </span>            : }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :  </a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : #include &lt;cctype&gt;</a>
+<a name="244"><span class="lineNum">     244 </span>            : #include &lt;cmath&gt;</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : #include &quot;real.h&quot;</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : #include &quot;blas.h&quot;</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : namespace PLMD{</a>
+<a name="251"><span class="lineNum">     251 </span>            : namespace blas{</a>
+<a name="252"><span class="lineNum">     252 </span>            : void</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        520 : PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(const char *transa,</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :                       const char *transb,</a>
+<a name="255"><span class="lineNum">     255 </span>            :                       int *m__,</a>
+<a name="256"><span class="lineNum">     256 </span>            :                       int *n__,</a>
+<a name="257"><span class="lineNum">     257 </span>            :                       int *k__,</a>
+<a name="258"><span class="lineNum">     258 </span>            :                       double *alpha__,</a>
+<a name="259"><span class="lineNum">     259 </span>            :                       double *a,</a>
+<a name="260"><span class="lineNum">     260 </span>            :                       int *lda__,</a>
+<a name="261"><span class="lineNum">     261 </span>            :                       double *b,</a>
+<a name="262"><span class="lineNum">     262 </span>            :                       int *ldb__,</a>
+<a name="263"><span class="lineNum">     263 </span>            :                       double *beta__,</a>
+<a name="264"><span class="lineNum">     264 </span>            :                       double *c,</a>
+<a name="265"><span class="lineNum">     265 </span>            :                       int *ldc__)</a>
+<a name="266"><span class="lineNum">     266 </span>            : {</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        520 :   const char tra=std::toupper(*transa);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        520 :   const char trb=std::toupper(*transb);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   double temp;</a>
+<a name="270"><span class="lineNum">     270 </span>            :   int i,j,l;</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        520 :   int m = *m__;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        520 :   int n = *n__;</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        520 :   int k = *k__;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        520 :   int lda = *lda__;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        520 :   int ldb = *ldb__;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        520 :   int ldc = *ldc__;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :   </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        520 :   double alpha = *alpha__;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        520 :   double beta  = *beta__;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        520 :   if(m==0 || n==0 || (( std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN || k==0) &amp;&amp; std::abs(beta-1.0)&lt;PLUMED_GMX_DOUBLE_EPS))</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     return;</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        471 :   if(std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :     if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++)</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++)</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :           c[j*(ldc)+i] = 0.0;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :     } else {</a>
+<a name="291"><span class="lineNum">     291 </span>            :       /* nonzero beta */</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++)</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++)</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :           c[j*(ldc)+i] *= beta;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :     }</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        471 :   if(trb=='N') {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">        354 :     if(tra=='N') {</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :       </a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">      17396 :       for(j=0;j&lt;n;j++) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">      17120 :         if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     934292 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     924369 :             c[j*(ldc)+i] = 0.0;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       7197 :         } else if(std::abs(beta-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] *= beta;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :         } </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">     898860 :         for(l=0;l&lt;k;l++) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">     881740 :           if( std::abs(b[ j*(ldb) + l ])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">     879210 :             temp = alpha * b[ j*(ldb) + l ];</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">  223022936 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">  222143726 :               c[j*(ldc)+i] += temp * a[l*(lda)+i]; </span></a>
+<a name="315"><span class="lineNum">     315 </span>            :           }</a>
+<a name="316"><span class="lineNum">     316 </span>            :         }</a>
+<a name="317"><span class="lineNum">     317 </span>            :       }</a>
+<a name="318"><span class="lineNum">     318 </span>            :     } else {</a>
+<a name="319"><span class="lineNum">     319 </span>            :       /* transpose A, but not B */</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       2290 :       for(j=0;j&lt;n;j++) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">     599172 :         for(i=0;i&lt;m;i++) {</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :           temp = 0.0;</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">  126807456 :           for(l=0;l&lt;k;l++) </span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">  126210496 :             temp += a[i*(lda)+l] * b[j*(ldb)+l];</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">     596960 :           if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :           else</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">     596960 :             c[j*(ldc)+i] = alpha * temp + beta * c[j*(ldc)+i];</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :         }</a>
+<a name="330"><span class="lineNum">     330 </span>            :       }</a>
+<a name="331"><span class="lineNum">     331 </span>            :     }</a>
+<a name="332"><span class="lineNum">     332 </span>            :   } else {</a>
+<a name="333"><span class="lineNum">     333 </span>            :     /* transpose B */</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">        117 :     if(tra=='N') {</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :       /* transpose B, but not A */</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      24143 :       for(j=0;j&lt;n;j++) {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      24026 :         if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = 0.0;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">      24026 :         } else if(std::abs(beta-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] *= beta;</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :         } </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">     851290 :         for(l=0;l&lt;k;l++) {</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">     827264 :           if( std::abs(b[ l*(ldb) + j ])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">     714770 :             temp = alpha * b[ l*(ldb) + j ];</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">  208051270 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">  207336500 :               c[j*(ldc)+i] += temp * a[l*(lda)+i]; </span></a>
+<a name="351"><span class="lineNum">     351 </span>            :           }</a>
+<a name="352"><span class="lineNum">     352 </span>            :         }</a>
+<a name="353"><span class="lineNum">     353 </span>            :       }</a>
+<a name="354"><span class="lineNum">     354 </span>            :  </a>
+<a name="355"><span class="lineNum">     355 </span>            :     } else {</a>
+<a name="356"><span class="lineNum">     356 </span>            :       /* Transpose both A and B */</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :        for(j=0;j&lt;n;j++) {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++) {</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :           temp = 0.0;</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :           for(l=0;l&lt;k;l++) </span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :             temp += a[i*(lda)+l] * b[l*(ldb)+j];</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :           else</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp + beta * c[j*(ldc)+i];</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :         }</a>
+<a name="367"><span class="lineNum">     367 </span>            :        }</a>
+<a name="368"><span class="lineNum">     368 </span>            :     }</a>
+<a name="369"><span class="lineNum">     369 </span>            :   }</a>
+<a name="370"><span class="lineNum">     370 </span>            : }</a>
+<a name="371"><span class="lineNum">     371 </span>            : }</a>
+<a name="372"><span class="lineNum">     372 </span>            : }</a>
+<a name="373"><span class="lineNum">     373 </span>            : #include &lt;cctype&gt;</a>
+<a name="374"><span class="lineNum">     374 </span>            : #include &lt;cmath&gt;</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : #include &quot;real.h&quot;</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : #include &quot;blas.h&quot;</a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span>            : namespace PLMD{</a>
+<a name="381"><span class="lineNum">     381 </span>            : namespace blas{</a>
+<a name="382"><span class="lineNum">     382 </span>            : void</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">    1131535 : PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(const char *trans, </span></a>
+<a name="384"><span class="lineNum">     384 </span>            :        int *m__,</a>
+<a name="385"><span class="lineNum">     385 </span>            :        int *n__,</a>
+<a name="386"><span class="lineNum">     386 </span>            :        double *alpha__,</a>
+<a name="387"><span class="lineNum">     387 </span>            :        double *a,</a>
+<a name="388"><span class="lineNum">     388 </span>            :        int *lda__,</a>
+<a name="389"><span class="lineNum">     389 </span>            :        double *x,</a>
+<a name="390"><span class="lineNum">     390 </span>            :        int *incx__,</a>
+<a name="391"><span class="lineNum">     391 </span>            :        double *beta__,</a>
+<a name="392"><span class="lineNum">     392 </span>            :        double *y,</a>
+<a name="393"><span class="lineNum">     393 </span>            :        int *incy__)</a>
+<a name="394"><span class="lineNum">     394 </span>            : {</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">    1131535 :   const char ch=std::toupper(*trans);</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :   int lenx,leny,kx,ky;</a>
+<a name="397"><span class="lineNum">     397 </span>            :   int i,j,jx,jy,ix,iy;</a>
+<a name="398"><span class="lineNum">     398 </span>            :   double temp;</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">    1131535 :   int m = *m__;</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">    1131535 :   int n = *n__;</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">    1131535 :   double alpha = *alpha__;</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">    1131535 :   double beta = *beta__;</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">    1131535 :   int incx = *incx__;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">    1131535 :   int incy = *incy__;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">    1131535 :   int lda = *lda__;</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :   </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">    1131535 :   if(n&lt;=0 || m&lt;=0 || (std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN &amp;&amp; std::abs(beta-1.0)&lt;PLUMED_GMX_DOUBLE_EPS))</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     return;</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">    1131343 :   if(ch=='N') {</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :     lenx = n;</a>
+<a name="413"><span class="lineNum">     413 </span>            :     leny = m;</a>
+<a name="414"><span class="lineNum">     414 </span>            :   } else {</a>
+<a name="415"><span class="lineNum">     415 </span>            :     lenx = m;</a>
+<a name="416"><span class="lineNum">     416 </span>            :     leny = n;</a>
+<a name="417"><span class="lineNum">     417 </span>            :   }</a>
+<a name="418"><span class="lineNum">     418 </span>            :   </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">    1131343 :    if(incx&gt;0)</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :     kx = 1;</a>
+<a name="421"><span class="lineNum">     421 </span>            :   else</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :     kx = 1 - (lenx -1)*(incx);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">    1131343 :   if(incy&gt;0)</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :     ky = 1;</a>
+<a name="426"><span class="lineNum">     426 </span>            :   else</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :     ky = 1 - (leny -1)*(incy);</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :  </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">    1131343 :   if(std::abs(beta-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">    1126310 :     if(incy==1) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">    1126310 :       if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">    2736412 :         for(i=0;i&lt;leny;i++)</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">    1610102 :           y[i] = 0.0;</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :       else</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++)</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :           y[i] *= beta;</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :     } else {</a>
+<a name="438"><span class="lineNum">     438 </span>            :       /* non-unit incr. */</a>
+<a name="439"><span class="lineNum">     439 </span>            :       iy = ky;</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++,iy+=incy)</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :           y[iy] = 0.0;</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :       else</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++,iy+=incy)</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :           y[iy] *= beta;</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :     }</a>
+<a name="447"><span class="lineNum">     447 </span>            :   }</a>
+<a name="448"><span class="lineNum">     448 </span>            :   </a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">    1131343 :   if(std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :     return;</a>
+<a name="451"><span class="lineNum">     451 </span>            :   </a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">    1131343 :   if(ch=='N') {</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     jx = kx;</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">       9325 :     if(incy==1) {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">     474392 :       for(j=1;j&lt;=n;j++,jx+=incx) </span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">     465451 :         if(std::abs(x[jx-1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">     465451 :           temp = alpha * x[jx-1];</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">   63040550 :           for(i=1;i&lt;=m;i++)</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">   62575099 :             y[i-1] += temp * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :         }</a>
+<a name="461"><span class="lineNum">     461 </span>            :     } else {</a>
+<a name="462"><span class="lineNum">     462 </span>            :       /* non-unit y incr. */</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">       6720 :       for(j=1;j&lt;=n;j++,jx+=incx) </span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">       6336 :         if(std::abs(x[jx-1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">       6336 :           temp = alpha * x[jx-1];</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :           iy = ky;</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">    1921920 :           for(i=1;i&lt;=m;i++,iy+=incy)</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">    1915584 :             y[iy-1] += temp * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="469"><span class="lineNum">     469 </span>            :         }</a>
+<a name="470"><span class="lineNum">     470 </span>            :     }</a>
+<a name="471"><span class="lineNum">     471 </span>            :   } else {</a>
+<a name="472"><span class="lineNum">     472 </span>            :     /* transpose */</a>
+<a name="473"><span class="lineNum">     473 </span>            :     jy = ky;</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">    1122018 :     if(incx==1) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">    2638116 :       for(j=1;j&lt;=n;j++,jy+=incy) {</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :         temp = 0.0;</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">   60769798 :         for(i=1;i&lt;=m;i++)</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">   59252944 :           temp += a[(j-1)*(lda)+(i-1)] * x[i-1];</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">    1516854 :         y[jy-1] += alpha * temp;</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :       }</a>
+<a name="481"><span class="lineNum">     481 </span>            :     } else {</a>
+<a name="482"><span class="lineNum">     482 </span>            :       /* non-unit y incr. */</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">     121296 :       for(j=1;j&lt;=n;j++,jy+=incy) {</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :         temp = 0.0;</a>
+<a name="485"><span class="lineNum">     485 </span>            :         ix = kx;</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">    3833628 :         for(i=1;i&lt;=m;i++,ix+=incx)</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">    3713088 :           temp += a[(j-1)*(lda)+(i-1)] * x[ix-1];</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">     120540 :         y[jy-1] += alpha * temp;</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :       }</a>
+<a name="490"><span class="lineNum">     490 </span>            :     }</a>
+<a name="491"><span class="lineNum">     491 </span>            :   }</a>
+<a name="492"><span class="lineNum">     492 </span>            : } </a>
+<a name="493"><span class="lineNum">     493 </span>            :    </a>
+<a name="494"><span class="lineNum">     494 </span>            : }</a>
+<a name="495"><span class="lineNum">     495 </span>            : }</a>
+<a name="496"><span class="lineNum">     496 </span>            : #include &lt;cmath&gt;</a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span>            : #include &quot;real.h&quot;</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            : #include &quot;blas.h&quot;</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            : namespace PLMD{</a>
+<a name="503"><span class="lineNum">     503 </span>            : namespace blas{</a>
+<a name="504"><span class="lineNum">     504 </span>            : void</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">    1119685 : PLUMED_BLAS_F77_FUNC(dger,DGER)(int *m__,</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :                     int *n__,</a>
+<a name="507"><span class="lineNum">     507 </span>            :                     double *alpha__,</a>
+<a name="508"><span class="lineNum">     508 </span>            :                     double *x,</a>
+<a name="509"><span class="lineNum">     509 </span>            :                     int *incx__,</a>
+<a name="510"><span class="lineNum">     510 </span>            :                     double *y,</a>
+<a name="511"><span class="lineNum">     511 </span>            :                     int *incy__,</a>
+<a name="512"><span class="lineNum">     512 </span>            :                     double *a,</a>
+<a name="513"><span class="lineNum">     513 </span>            :                     int *lda__)</a>
+<a name="514"><span class="lineNum">     514 </span>            : {</a>
+<a name="515"><span class="lineNum">     515 </span>            :     int ix,kx,jy;</a>
+<a name="516"><span class="lineNum">     516 </span>            :     int i,j;</a>
+<a name="517"><span class="lineNum">     517 </span>            :     double temp;</a>
+<a name="518"><span class="lineNum">     518 </span>            :     </a>
+<a name="519"><span class="lineNum">     519 </span>            :     </a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">    1119685 :     int m = *m__;</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">    1119685 :     int n = *n__;</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">    1119685 :     int incx = *incx__;</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">    1119685 :     int incy = *incy__;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">    1119685 :     int lda = *lda__;</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">    1119685 :     double alpha = *alpha__;</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :     </a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">    1119685 :     if(m&lt;=0 || n&lt;=0 || std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :         return;</a>
+<a name="529"><span class="lineNum">     529 </span>            :     </a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">    1119685 :     if(incy&gt;0)</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :         jy = 0;</a>
+<a name="532"><span class="lineNum">     532 </span>            :     else</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :         jy = incy * (1 - n);</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :     </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">    1119685 :     if(incx==1) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">    2387900 :         for(j=0;j&lt;n;j++,jy+=incy)</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">    1268215 :             if(std::abs(y[jy])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">    1268207 :                 temp = alpha * y[jy];</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">    6935852 :                 for(i=0;i&lt;m;i++)</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">    5667645 :                     a[j*(lda)+i] += temp*x[i];</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :             }</a>
+<a name="542"><span class="lineNum">     542 </span>            :     } else {</a>
+<a name="543"><span class="lineNum">     543 </span>            :         /* non-unit incx */</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :         if(incx&gt;0) </span></a>
+<a name="545"><span class="lineNum">     545 </span>            :             kx = 0;</a>
+<a name="546"><span class="lineNum">     546 </span>            :         else</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :             kx = incx * (1 - m);</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :         </a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++,jy+=incy) {</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :             if(std::abs(y[jy])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :                 temp = alpha * y[jy];</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :                 ix = kx;</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :                 for(i=0;i&lt;m;i++,ix+=incx)</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :                     a[j*(lda)+i] += temp*x[ix];</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :             }</a>
+<a name="556"><span class="lineNum">     556 </span>            :         }</a>
+<a name="557"><span class="lineNum">     557 </span>            :     }</a>
+<a name="558"><span class="lineNum">     558 </span>            :         return;</a>
+<a name="559"><span class="lineNum">     559 </span>            : }</a>
+<a name="560"><span class="lineNum">     560 </span>            : }</a>
+<a name="561"><span class="lineNum">     561 </span>            : }</a>
+<a name="562"><span class="lineNum">     562 </span>            : #include &lt;cmath&gt;</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            : #include &quot;real.h&quot;</a>
+<a name="565"><span class="lineNum">     565 </span>            : #include &quot;blas.h&quot;</a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            : namespace PLMD{</a>
+<a name="568"><span class="lineNum">     568 </span>            : namespace blas{</a>
+<a name="569"><span class="lineNum">     569 </span>            : double</a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">    1125776 : PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(int  *     n__,</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :                       double *    x,</a>
+<a name="572"><span class="lineNum">     572 </span>            :                       int    *    incx__)</a>
+<a name="573"><span class="lineNum">     573 </span>            : {</a>
+<a name="574"><span class="lineNum">     574 </span>            :     int ix,max_ix;</a>
+<a name="575"><span class="lineNum">     575 </span>            :     double ssq,scale,absxi,t;</a>
+<a name="576"><span class="lineNum">     576 </span>            :     </a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">    1125776 :     int n = *n__;</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">    1125776 :     int incx = *incx__;</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :     </a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">    1125776 :     if(n&lt;1 || incx&lt;1)</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :         return 0;</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">    1125776 :     else if (n==1) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">     556841 :         t = x[0];</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">     556841 :         if(t&gt;=0)</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :             return t;</a>
+<a name="586"><span class="lineNum">     586 </span>            :         else </a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">     417149 :             return -t;</span></a>
+<a name="588"><span class="lineNum">     588 </span>            :     }</a>
+<a name="589"><span class="lineNum">     589 </span>            :     </a>
+<a name="590"><span class="lineNum">     590 </span>            :     scale = 0.0;</a>
+<a name="591"><span class="lineNum">     591 </span>            :     ssq   = 1.0;</a>
+<a name="592"><span class="lineNum">     592 </span>            :     </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">     568935 :     max_ix = 1+(n-1)*(incx);</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">    3017084 :     for(ix=1;ix&lt;=max_ix;ix+=incx) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">    2448149 :         t = x[ix-1];</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">    2448149 :         if(std::abs(t)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">    2447162 :             absxi = (t&gt;=0) ? t : (-t);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">    2447162 :             if(scale&lt;absxi) {</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">     823386 :                 t = scale/absxi;</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">     823386 :                 t = t*t;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">     823386 :                 ssq = ssq*t + 1.0;</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :                 scale = absxi;</a>
+<a name="603"><span class="lineNum">     603 </span>            :             } else {</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">    1623776 :                 t = absxi/scale;</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">    1623776 :                 ssq += t*t;</span></a>
+<a name="606"><span class="lineNum">     606 </span>            :             }</a>
+<a name="607"><span class="lineNum">     607 </span>            :         }</a>
+<a name="608"><span class="lineNum">     608 </span>            :     }</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">     568935 :     return scale*std::sqrt(ssq);</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :     </a>
+<a name="611"><span class="lineNum">     611 </span>            : }</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            :  </a>
+<a name="615"><span class="lineNum">     615 </span>            : }</a>
+<a name="616"><span class="lineNum">     616 </span>            : }</a>
+<a name="617"><span class="lineNum">     617 </span>            : #include &quot;blas.h&quot;</a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span>            : namespace PLMD{</a>
+<a name="620"><span class="lineNum">     620 </span>            : namespace blas{</a>
+<a name="621"><span class="lineNum">     621 </span>            : void</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        360 : PLUMED_BLAS_F77_FUNC(drot,DROT)(int *n__,</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :       double *dx,</a>
+<a name="624"><span class="lineNum">     624 </span>            :       int *incx__,</a>
+<a name="625"><span class="lineNum">     625 </span>            :       double *dy,</a>
+<a name="626"><span class="lineNum">     626 </span>            :       int *incy__,</a>
+<a name="627"><span class="lineNum">     627 </span>            :       double *c__,</a>
+<a name="628"><span class="lineNum">     628 </span>            :       double *s__)</a>
+<a name="629"><span class="lineNum">     629 </span>            : {</a>
+<a name="630"><span class="lineNum">     630 </span>            :   int i,ix,iy;</a>
+<a name="631"><span class="lineNum">     631 </span>            :   double dtemp;</a>
+<a name="632"><span class="lineNum">     632 </span>            : </a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">        360 :   int n = *n__;</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">        360 :   int incx = *incx__;</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">        360 :   int incy = *incy__;</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">        360 :   double c = *c__;</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">        360 :   double s = *s__;</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :   </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">        360 :   if(incx!=1 || incy!=1) {</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :     ix = 0;</a>
+<a name="641"><span class="lineNum">     641 </span>            :     iy = 0;</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">        180 :     if(incx&lt;0)</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :       ix = (1-n)*(incx);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">        180 :     if(incy&lt;0)</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :       iy = (1-n)*(incy);</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :     </a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">       3136 :     for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) {</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">       2956 :       dtemp  = (c) * dx[ix] + (s) * dy[iy];</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">       2956 :       dy[iy] = (c) * dy[iy] - (s) * dx[ix];</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">       2956 :       dx[ix] = dtemp;</span></a>
+<a name="651"><span class="lineNum">     651 </span>            :     }</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            :     return;</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            :   } else {</a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            :     /* unit increments */   </a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">       3075 :     for(i=0;i&lt;n;i++) {</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       2895 :       dtemp = (c) * dx[i] + (s) * dy[i];</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">       2895 :       dy[i] = (c) * dy[i] - (s) * dx[i];</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">       2895 :       dx[i] = dtemp;      </span></a>
+<a name="662"><span class="lineNum">     662 </span>            :     }</a>
+<a name="663"><span class="lineNum">     663 </span>            : </a>
+<a name="664"><span class="lineNum">     664 </span>            :   }</a>
+<a name="665"><span class="lineNum">     665 </span>            : }</a>
+<a name="666"><span class="lineNum">     666 </span>            : }</a>
+<a name="667"><span class="lineNum">     667 </span>            : }</a>
+<a name="668"><span class="lineNum">     668 </span>            : #include &quot;blas.h&quot;</a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span>            : namespace PLMD{</a>
+<a name="671"><span class="lineNum">     671 </span>            : namespace blas{</a>
+<a name="672"><span class="lineNum">     672 </span>            : void </a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">    1728060 : PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(int  *    n__,</span></a>
+<a name="674"><span class="lineNum">     674 </span>            :                       double *   fact__,</a>
+<a name="675"><span class="lineNum">     675 </span>            :                       double *   dx,</a>
+<a name="676"><span class="lineNum">     676 </span>            :                       int    *   incx__)</a>
+<a name="677"><span class="lineNum">     677 </span>            : {</a>
+<a name="678"><span class="lineNum">     678 </span>            :     int nincx,i;</a>
+<a name="679"><span class="lineNum">     679 </span>            : </a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">    1728060 :     int n = *n__;</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">    1728060 :     double fact = *fact__;</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">    1728060 :     int incx = *incx__;</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :     </a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">    1728060 :     if(n&lt;=0 || incx&lt;=0)</span></a>
+<a name="685"><span class="lineNum">     685 </span>            :         return;</a>
+<a name="686"><span class="lineNum">     686 </span>            :     </a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">    1728003 :     if(incx==1) {</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :         /* Unrool factor 5 */</a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">    1912122 :         for(i=0;i&lt;(n-5);i+=5) {</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">     187002 :             dx[i]   *= fact;</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">     187002 :             dx[i+1] *= fact;</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">     187002 :             dx[i+2] *= fact;</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">     187002 :             dx[i+3] *= fact;</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">     187002 :             dx[i+4] *= fact;</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :         }    </a>
+<a name="696"><span class="lineNum">     696 </span>            :         /* continue with current value of i */</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">    5781798 :         for(;i&lt;n;i++)</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">    4056678 :             dx[i]   *= fact;</span></a>
+<a name="699"><span class="lineNum">     699 </span>            :         </a>
+<a name="700"><span class="lineNum">     700 </span>            :         return;</a>
+<a name="701"><span class="lineNum">     701 </span>            :     } else {</a>
+<a name="702"><span class="lineNum">     702 </span>            :         /* inc != 1 */</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">       2883 :         nincx = n * (incx);</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">     159270 :         for (i=0;i&lt;nincx;i+=incx)</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">     156387 :             dx[i] *= fact;</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :         </a>
+<a name="707"><span class="lineNum">     707 </span>            :         return;</a>
+<a name="708"><span class="lineNum">     708 </span>            :     } </a>
+<a name="709"><span class="lineNum">     709 </span>            :     </a>
+<a name="710"><span class="lineNum">     710 </span>            : }</a>
+<a name="711"><span class="lineNum">     711 </span>            : }</a>
+<a name="712"><span class="lineNum">     712 </span>            : }</a>
+<a name="713"><span class="lineNum">     713 </span>            : #include &quot;blas.h&quot;</a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            : namespace PLMD{</a>
+<a name="716"><span class="lineNum">     716 </span>            : namespace blas{</a>
+<a name="717"><span class="lineNum">     717 </span>            : void</a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">       5884 : PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(int *n__,</span></a>
+<a name="719"><span class="lineNum">     719 </span>            :                       double *dx,</a>
+<a name="720"><span class="lineNum">     720 </span>            :                       int *incx__,</a>
+<a name="721"><span class="lineNum">     721 </span>            :                       double *dy,</a>
+<a name="722"><span class="lineNum">     722 </span>            :                       int *incy__)</a>
+<a name="723"><span class="lineNum">     723 </span>            : {</a>
+<a name="724"><span class="lineNum">     724 </span>            :   int i,ix,iy;</a>
+<a name="725"><span class="lineNum">     725 </span>            :   double d1,d2,d3;</a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">       5884 :   int n = *n__;</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">       5884 :   int incx = *incx__;</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">       5884 :   int incy = *incy__;</span></a>
+<a name="730"><span class="lineNum">     730 </span>            :   </a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">       5884 :   if(n&lt;=0)</span></a>
+<a name="732"><span class="lineNum">     732 </span>            :     return;</a>
+<a name="733"><span class="lineNum">     733 </span>            : </a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">       5884 :   if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">      85127 :     for(i=0;i&lt;(n-3);i+=3) {</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">      81866 :       d1      = dx[i];</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">      81866 :       d2      = dx[i+1];</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">      81866 :       d3      = dx[i+2];</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">      81866 :       dx[i]   = dy[i];</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">      81866 :       dx[i+1] = dy[i+1];</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">      81866 :       dx[i+2] = dy[i+2];</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">      81866 :       dy[i]   = d1;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">      81866 :       dy[i+1] = d2;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">      81866 :       dy[i+2] = d3;</span></a>
+<a name="745"><span class="lineNum">     745 </span>            :     }</a>
+<a name="746"><span class="lineNum">     746 </span>            :     /* continue with last i value */</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">       9150 :     for(;i&lt;n;i++) {</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">       5889 :       d1      = dx[i];</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">       5889 :       dx[i]   = dy[i];</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">       5889 :       dy[i]   = d1;</span></a>
+<a name="751"><span class="lineNum">     751 </span>            :     }</a>
+<a name="752"><span class="lineNum">     752 </span>            : </a>
+<a name="753"><span class="lineNum">     753 </span>            :   } else {</a>
+<a name="754"><span class="lineNum">     754 </span>            :     ix = 0;</a>
+<a name="755"><span class="lineNum">     755 </span>            :     iy = 0;</a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">       2623 :     if(incx&lt;0)</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 :       ix = incx * (1 - n);</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">       2623 :     if(incy&lt;0)</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineNoCov">          0 :       iy = incy * (1 - n);</span></a>
+<a name="760"><span class="lineNum">     760 </span>            : </a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">     195103 :     for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) {</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">     192480 :       d1     = dx[ix];</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">     192480 :       dx[ix] = dy[iy];</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">     192480 :       dy[iy] = d1;</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :     }</a>
+<a name="766"><span class="lineNum">     766 </span>            :   }</a>
+<a name="767"><span class="lineNum">     767 </span>            :   return;</a>
+<a name="768"><span class="lineNum">     768 </span>            : }</a>
+<a name="769"><span class="lineNum">     769 </span>            :  </a>
+<a name="770"><span class="lineNum">     770 </span>            : }</a>
+<a name="771"><span class="lineNum">     771 </span>            : }</a>
+<a name="772"><span class="lineNum">     772 </span>            : #include &lt;cctype&gt;</a>
+<a name="773"><span class="lineNum">     773 </span>            : #include &lt;cmath&gt;</a>
+<a name="774"><span class="lineNum">     774 </span>            : </a>
+<a name="775"><span class="lineNum">     775 </span>            : #include &quot;real.h&quot;</a>
+<a name="776"><span class="lineNum">     776 </span>            : #include &quot;blas.h&quot;</a>
+<a name="777"><span class="lineNum">     777 </span>            : </a>
+<a name="778"><span class="lineNum">     778 </span>            : namespace PLMD{</a>
+<a name="779"><span class="lineNum">     779 </span>            : namespace blas{</a>
+<a name="780"><span class="lineNum">     780 </span>            : void</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">    1114408 : PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)(const char *uplo,</span></a>
+<a name="782"><span class="lineNum">     782 </span>            :        int *n__,</a>
+<a name="783"><span class="lineNum">     783 </span>            :        double *alpha__,</a>
+<a name="784"><span class="lineNum">     784 </span>            :        double *a,</a>
+<a name="785"><span class="lineNum">     785 </span>            :        int *lda__,</a>
+<a name="786"><span class="lineNum">     786 </span>            :        double *x,</a>
+<a name="787"><span class="lineNum">     787 </span>            :        int *incx__,</a>
+<a name="788"><span class="lineNum">     788 </span>            :        double *beta__,</a>
+<a name="789"><span class="lineNum">     789 </span>            :        double *y,</a>
+<a name="790"><span class="lineNum">     790 </span>            :        int *incy__)</a>
+<a name="791"><span class="lineNum">     791 </span>            : {</a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">    1114408 :     const char ch=std::toupper(*uplo);</span></a>
+<a name="793"><span class="lineNum">     793 </span>            :     int kx,ky,i,j,ix,iy,jx,jy;</a>
+<a name="794"><span class="lineNum">     794 </span>            :     double temp1,temp2;</a>
+<a name="795"><span class="lineNum">     795 </span>            :     </a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">    1114408 :     int n = *n__;</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">    1114408 :     int lda = *lda__;</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">    1114408 :     int incx = *incx__;</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">    1114408 :     int incy = *incy__;</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">    1114408 :     double alpha = *alpha__;</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">    1114408 :     double beta  = *beta__;</span></a>
+<a name="802"><span class="lineNum">     802 </span>            :     </a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">    1114408 :     if(n&lt;=0 || incx==0 || incy==0)</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :         return;</a>
+<a name="805"><span class="lineNum">     805 </span>            :     </a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">    1114408 :     if(incx&gt;0)</span></a>
+<a name="807"><span class="lineNum">     807 </span>            :         kx = 1;</a>
+<a name="808"><span class="lineNum">     808 </span>            :     else</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineNoCov">          0 :         kx = 1 - (n -1)*(incx);</span></a>
+<a name="810"><span class="lineNum">     810 </span>            :     </a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">    1114408 :     if(incy&gt;0)</span></a>
+<a name="812"><span class="lineNum">     812 </span>            :         ky = 1;</a>
+<a name="813"><span class="lineNum">     813 </span>            :     else</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineNoCov">          0 :         ky = 1 - (n -1)*(incy);</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :     </a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">    1114408 :     if(std::abs(beta-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">    1114408 :         if(incy==1) {</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">    1114408 :             if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">    4092265 :                 for(i=1;i&lt;=n;i++)</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">    2977857 :                     y[i-1] = 0.0;</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :             else</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineNoCov">          0 :                 for(i=1;i&lt;=n;i++)</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 :                     y[i-1] *= beta;</span></a>
+<a name="824"><span class="lineNum">     824 </span>            :         } else {</a>
+<a name="825"><span class="lineNum">     825 </span>            :             /* non-unit incr. */</a>
+<a name="826"><span class="lineNum">     826 </span>            :             iy = ky;</a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineNoCov">          0 :             if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineNoCov">          0 :                 for(i=1;i&lt;=n;i++) {</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineNoCov">          0 :                     y[iy-1] = 0.0;</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineNoCov">          0 :                     iy += incy;</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :                 }</a>
+<a name="832"><span class="lineNum">     832 </span>            :                     else</a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineNoCov">          0 :                         for(i=1;i&lt;=n;i++) {</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineNoCov">          0 :                             y[iy-1] *= beta;</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineNoCov">          0 :                             iy += incy;</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :                         }</a>
+<a name="837"><span class="lineNum">     837 </span>            :         }</a>
+<a name="838"><span class="lineNum">     838 </span>            :     }</a>
+<a name="839"><span class="lineNum">     839 </span>            :         </a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">    1114408 :         if(std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="841"><span class="lineNum">     841 </span>            :             return;</a>
+<a name="842"><span class="lineNum">     842 </span>            :         </a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">    1114408 :         if(ch=='U') {</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">    1114408 :             if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">    4092265 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">    2977857 :                     temp1 = alpha * x[j-1];</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :                     temp2 = 0.0;</a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">   29707007 :                     for(i=1;i&lt;j;i++) {</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">   26729150 :                         y[i-1] += temp1*a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">   26729150 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[i-1];</span></a>
+<a name="851"><span class="lineNum">     851 </span>            :                     }</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">    2977857 :                     y[j-1] += temp1*a[(j-1)*(lda)+(j-1)] + alpha *temp2;</span></a>
+<a name="853"><span class="lineNum">     853 </span>            :                 }</a>
+<a name="854"><span class="lineNum">     854 </span>            :             } else {</a>
+<a name="855"><span class="lineNum">     855 </span>            :                 /* non-unit incr. */</a>
+<a name="856"><span class="lineNum">     856 </span>            :                 jx = kx;</a>
+<a name="857"><span class="lineNum">     857 </span>            :                 jy = ky;</a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[jx-1];</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :                     temp2 = 0.0;</a>
+<a name="861"><span class="lineNum">     861 </span>            :                     ix = kx;</a>
+<a name="862"><span class="lineNum">     862 </span>            :                     iy = ky;</a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineNoCov">          0 :                     for(i=1;i&lt;j;i++) {</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineNoCov">          0 :                         y[iy-1] += temp1 * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[ix-1];</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="868"><span class="lineNum">     868 </span>            :                     }</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineNoCov">          0 :                     y[jy-1] += temp1*a[(j-1)*(lda)+(j-1)] + alpha*temp2;</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :                     jy += incy;</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :                 }</a>
+<a name="873"><span class="lineNum">     873 </span>            :             }</a>
+<a name="874"><span class="lineNum">     874 </span>            :         } else {</a>
+<a name="875"><span class="lineNum">     875 </span>            :             /* lower */</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineNoCov">          0 :             if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[j-1];</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :                     temp2 = 0.0;</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :                     y[j-1] += temp1 * a[(j-1)*(lda)+(j-1)];</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineNoCov">          0 :                     for(i=j+1;i&lt;=n;i++) {</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineNoCov">          0 :                         y[i-1] += temp1*a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[i-1];</span></a>
+<a name="884"><span class="lineNum">     884 </span>            :                     }</a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineNoCov">          0 :                     y[j-1] += alpha *temp2;</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :                 }</a>
+<a name="887"><span class="lineNum">     887 </span>            :             } else {</a>
+<a name="888"><span class="lineNum">     888 </span>            :                 /* non-unit incr. */</a>
+<a name="889"><span class="lineNum">     889 </span>            :                 jx = kx;</a>
+<a name="890"><span class="lineNum">     890 </span>            :                 jy = ky;</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[jx-1];</span></a>
+<a name="893"><span class="lineNum">     893 </span>            :                     temp2 = 0.0;</a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineNoCov">          0 :                     y[jy-1] += temp1 * a[(j-1)*(lda)+(j-1)];</span></a>
+<a name="895"><span class="lineNum">     895 </span>            :                     ix = jx;</a>
+<a name="896"><span class="lineNum">     896 </span>            :                     iy = jy;</a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineNoCov">          0 :                     for(i=j+1;i&lt;=n;i++) {</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :                         y[iy-1] += temp1 * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[ix-1];</span></a>
+<a name="902"><span class="lineNum">     902 </span>            :                     }</a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineNoCov">          0 :                     y[jy-1] += alpha*temp2;</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineNoCov">          0 :                     jy += incy;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :                 }</a>
+<a name="907"><span class="lineNum">     907 </span>            :             }</a>
+<a name="908"><span class="lineNum">     908 </span>            :         }</a>
+<a name="909"><span class="lineNum">     909 </span>            :         return;</a>
+<a name="910"><span class="lineNum">     910 </span>            : }    </a>
+<a name="911"><span class="lineNum">     911 </span>            : }</a>
+<a name="912"><span class="lineNum">     912 </span>            : }</a>
+<a name="913"><span class="lineNum">     913 </span>            : #include &lt;cctype&gt;</a>
+<a name="914"><span class="lineNum">     914 </span>            : #include &lt;cmath&gt;</a>
+<a name="915"><span class="lineNum">     915 </span>            : </a>
+<a name="916"><span class="lineNum">     916 </span>            : #include &quot;real.h&quot;</a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span>            : #include &quot;blas.h&quot;</a>
+<a name="919"><span class="lineNum">     919 </span>            : </a>
+<a name="920"><span class="lineNum">     920 </span>            : namespace PLMD{</a>
+<a name="921"><span class="lineNum">     921 </span>            : namespace blas{</a>
+<a name="922"><span class="lineNum">     922 </span>            : void</a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">    1113895 : PLUMED_BLAS_F77_FUNC(dsyr2,DSYR2)(const char *    uplo,</span></a>
+<a name="924"><span class="lineNum">     924 </span>            :                       int *     n__,</a>
+<a name="925"><span class="lineNum">     925 </span>            :                       double *  alpha__,</a>
+<a name="926"><span class="lineNum">     926 </span>            :                       double *  x,</a>
+<a name="927"><span class="lineNum">     927 </span>            :                       int *     incx__,</a>
+<a name="928"><span class="lineNum">     928 </span>            :                       double *  y,</a>
+<a name="929"><span class="lineNum">     929 </span>            :                       int *     incy__,</a>
+<a name="930"><span class="lineNum">     930 </span>            :                       double *  a,</a>
+<a name="931"><span class="lineNum">     931 </span>            :                       int *     lda__)</a>
+<a name="932"><span class="lineNum">     932 </span>            : {</a>
+<a name="933"><span class="lineNum">     933 </span>            :     int kx,ky,ix,iy,jx,jy,j,i;</a>
+<a name="934"><span class="lineNum">     934 </span>            :     double temp1,temp2;</a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">    1113895 :     const char ch=std::toupper(*uplo);</span></a>
+<a name="936"><span class="lineNum">     936 </span>            :     </a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">    1113895 :     int n = *n__;</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">    1113895 :     int lda = *lda__;</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">    1113895 :     int incx = *incx__;</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">    1113895 :     int incy = *incy__;</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">    1113895 :     float alpha = *alpha__;</span></a>
+<a name="942"><span class="lineNum">     942 </span>            :     </a>
+<a name="943"><span class="lineNum">     943 </span>            :     </a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">    1113895 :     if(n&lt;=0 || std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN || incx==0 || incy==0 ||</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">    1113895 :        (ch != 'U' &amp;&amp; ch != 'L'))</span></a>
+<a name="946"><span class="lineNum">     946 </span>            :         return;</a>
+<a name="947"><span class="lineNum">     947 </span>            :     </a>
+<a name="948"><span class="lineNum">     948 </span>            :     jx = jy = kx = ky = 0;</a>
+<a name="949"><span class="lineNum">     949 </span>            :     </a>
+<a name="950"><span class="lineNum">     950 </span>            :     /* init start points for non-unit increments */</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">    1113895 :     if(incx!=1 || incy!=1) {</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineNoCov">          0 :         if(incx&gt;0)</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :             kx = 1;</a>
+<a name="954"><span class="lineNum">     954 </span>            :         else</a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineNoCov">          0 :             kx = 1 - (n - 1)*(incx);</span></a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineNoCov">          0 :         if(incy&gt;0)</span></a>
+<a name="957"><span class="lineNum">     957 </span>            :             ky = 1;</a>
+<a name="958"><span class="lineNum">     958 </span>            :         else</a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineNoCov">          0 :             ky = 1 - (n - 1)*(incy);</span></a>
+<a name="960"><span class="lineNum">     960 </span>            :         </a>
+<a name="961"><span class="lineNum">     961 </span>            :         jx = kx;</a>
+<a name="962"><span class="lineNum">     962 </span>            :         jy = ky;</a>
+<a name="963"><span class="lineNum">     963 </span>            :     }</a>
+<a name="964"><span class="lineNum">     964 </span>            :     </a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">    1113895 :     if(ch == 'U') {</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :         /* Data in upper part of A */</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">    1113895 :         if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="968"><span class="lineNum">     968 </span>            :             /* Unit increments for both x and y */</a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">    3949813 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">    2835918 :                 if( std::abs(x[j-1])&gt;PLUMED_GMX_DOUBLE_MIN  || std::abs(y[j-1])&gt;PLUMED_GMX_DOUBLE_MIN ) {</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">    2835918 :                     temp1 = alpha * y[j-1];</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">    2835918 :                     temp2 = alpha * x[j-1];</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">    9661631 :                     for(i=1;i&lt;=j;i++)</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">    6825713 :                         a[(j-1)*(lda)+(i-1)] += x[i-1]*temp1 + y[i-1]*temp2;</span></a>
+<a name="975"><span class="lineNum">     975 </span>            :                 }</a>
+<a name="976"><span class="lineNum">     976 </span>            :             }</a>
+<a name="977"><span class="lineNum">     977 </span>            :         } else {</a>
+<a name="978"><span class="lineNum">     978 </span>            :             </a>
+<a name="979"><span class="lineNum">     979 </span>            :             /* non-unit increments */</a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="981"><span class="lineNum">     981 </span>            :                 </a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineNoCov">          0 :                 if( std::abs(x[jx-1])&gt;PLUMED_GMX_DOUBLE_MIN || std::abs(y[jy-1])&gt;PLUMED_GMX_DOUBLE_MIN ) {</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[jy-1];</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[jx-1];</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :                     ix = kx;</a>
+<a name="986"><span class="lineNum">     986 </span>            :                     iy = ky;</a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineNoCov">          0 :                     for(i=1;i&lt;=j;i++) {</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[ix-1]*temp1 + y[iy-1]*temp2;</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :                     }</a>
+<a name="992"><span class="lineNum">     992 </span>            :                 }</a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineNoCov">          0 :                 jx += incx;</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineNoCov">          0 :                 jy += incy;</span></a>
+<a name="995"><span class="lineNum">     995 </span>            :             }</a>
+<a name="996"><span class="lineNum">     996 </span>            :         }</a>
+<a name="997"><span class="lineNum">     997 </span>            :     } else {</a>
+<a name="998"><span class="lineNum">     998 </span>            :         /* Data in lower part of A */</a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineNoCov">          0 :         if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            :             /* Unit increments for both x and y */</a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineNoCov">          0 :                 if( std::abs(x[j-1])&gt;PLUMED_GMX_DOUBLE_MIN  || std::abs(y[j-1])&gt;PLUMED_GMX_DOUBLE_MIN ) {</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[j-1];</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[j-1];</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineNoCov">          0 :                     for(i=j;i&lt;=n;i++)</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[i-1]*temp1 + y[i-1]*temp2;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span>            :                 }</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :             }</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :         } else {</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :             </a>
+<a name="1011"><span class="lineNum">    1011 </span>            :             /* non-unit increments */</a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :                 </a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineNoCov">          0 :                 if( std::abs(x[jx-1])&gt;PLUMED_GMX_DOUBLE_MIN || std::abs(y[jy-1])&gt;PLUMED_GMX_DOUBLE_MIN ) {</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[jy-1];</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[jx-1];</span></a>
+<a name="1017"><span class="lineNum">    1017 </span>            :                     ix = jx;</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :                     iy = jy;</a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineNoCov">          0 :                     for(i=j;i&lt;=n;i++) {</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[ix-1]*temp1 + y[iy-1]*temp2;</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            :                     }</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :                 }</a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineNoCov">          0 :                 jx += incx;</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineNoCov">          0 :                 jy += incy;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span>            :             }</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :         }</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     }</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     </a>
+<a name="1031"><span class="lineNum">    1031 </span>            :     return;</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : }</a>
+<a name="1033"><span class="lineNum">    1033 </span>            : }</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : }</a>
+<a name="1035"><span class="lineNum">    1035 </span>            : #include &lt;cctype&gt;</a>
+<a name="1036"><span class="lineNum">    1036 </span>            : #include &lt;cmath&gt;</a>
+<a name="1037"><span class="lineNum">    1037 </span>            : </a>
+<a name="1038"><span class="lineNum">    1038 </span>            : #include &quot;real.h&quot;</a>
+<a name="1039"><span class="lineNum">    1039 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1040"><span class="lineNum">    1040 </span>            : </a>
+<a name="1041"><span class="lineNum">    1041 </span>            : namespace PLMD{</a>
+<a name="1042"><span class="lineNum">    1042 </span>            : namespace blas{</a>
+<a name="1043"><span class="lineNum">    1043 </span>            : void</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">         19 : PLUMED_BLAS_F77_FUNC(dsyr2k,DSYR2K)(const char *uplo, </span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            :         const char *trans,</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :         int *n__,</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :         int *k__,</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :         double *alpha__,</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :         double *a,</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :         int *lda__,</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :         double *b,</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :         int *ldb__,</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :         double *beta__,</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :         double *c,</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :         int *ldc__)</a>
+<a name="1056"><span class="lineNum">    1056 </span>            : {</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   char ch1,ch2;</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   int i,j,l;</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   double temp1,temp2;</a>
+<a name="1060"><span class="lineNum">    1060 </span>            : </a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   </a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">         19 :   int n = *n__;</span></a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">         19 :   int k = *k__;</span></a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">         19 :   int lda = *lda__;</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">         19 :   int ldb = *ldb__;</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">         19 :   int ldc = *ldc__;</span></a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   </a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">         19 :   double alpha = *alpha__;</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">         19 :   double beta  = *beta__;</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   </a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         19 :   ch1 = std::toupper(*uplo);</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         19 :   ch2 = std::toupper(*trans);</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            : </a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">         19 :   if(n==0 || ( ( std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN || k==0 ) &amp;&amp; std::abs(beta-1.0)&lt;PLUMED_GMX_DOUBLE_EPS))</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     return;</a>
+<a name="1076"><span class="lineNum">    1076 </span>            : </a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">         19 :   if(std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN ) {</span></a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineNoCov">          0 :     if(ch1=='U') {</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="1083"><span class="lineNum">    1083 </span>            :       else</a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="1087"><span class="lineNum">    1087 </span>            :     } else {</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :       /* lower */</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="1093"><span class="lineNum">    1093 </span>            :       else</a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="1097"><span class="lineNum">    1097 </span>            :     }</a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            :   }</a>
+<a name="1100"><span class="lineNum">    1100 </span>            : </a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">         19 :   if(ch2=='N') {</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">         19 :     if(ch1=='U') {</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">       5029 :       for(j=1;j&lt;=n;j++) {</span></a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">       5010 :         if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineNoCov">          0 :              c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">       5010 :         else if(std::abs(beta-1.0)&gt;PLUMED_GMX_DOUBLE_EPS)</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">     140280 :         for(l=1;l&lt;=k;l++) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">     135270 :           if( std::abs(a[(l-1)*(lda)+(j-1)])&gt;PLUMED_GMX_DOUBLE_MIN ||</span></a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineNoCov">          0 :               std::abs(b[(l-1)*(ldb)+(j-1)])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">     135270 :             temp1 = alpha * b[(l-1)*(ldb)+(j-1)];</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">     135270 :             temp2 = alpha * a[(l-1)*(lda)+(j-1)];</span></a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">   21195810 :             for(i=1;i&lt;=j;i++)</span></a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">   21060540 :               c[(j-1)*(ldc)+(i-1)] += </span></a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineCov">   21060540 :                 a[(l-1)*(lda)+(i-1)] * temp1 + </span></a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">   21060540 :                 b[(l-1)*(ldb)+(i-1)] * temp2;</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :           }</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :         }</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :       }</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     } else {</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :       /* lower */</a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) {</span></a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineNoCov">          0 :         if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineNoCov">          0 :         else if(std::abs(beta-1.0)&gt;PLUMED_GMX_DOUBLE_EPS)</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineNoCov">          0 :         for(l=1;l&lt;=k;l++) {</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineNoCov">          0 :           if( std::abs(a[(l-1)*(lda)+(j-1)])&gt;PLUMED_GMX_DOUBLE_MIN ||</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineNoCov">          0 :               std::abs(b[(l-1)*(ldb)+(j-1)])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineNoCov">          0 :             temp1 = alpha * b[(l-1)*(ldb)+(j-1)];</span></a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineNoCov">          0 :             temp2 = alpha * a[(l-1)*(lda)+(j-1)];</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineNoCov">          0 :             for(i=j;i&lt;=n;i++)</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineNoCov">          0 :               c[(j-1)*(ldc)+(i-1)] += </span></a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineNoCov">          0 :                 a[(l-1)*(lda)+(i-1)] * temp1 + </span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineNoCov">          0 :                 b[(l-1)*(ldb)+(i-1)] * temp2;</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            :           }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :         }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :       }</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :     }</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   } else {</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :     /* transpose */</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineNoCov">          0 :     if(ch1=='U') {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) </span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineNoCov">          0 :         for(i=1;i&lt;=j;i++) {</span></a>
+<a name="1149"><span class="lineNum">    1149 </span>            :           temp1 = 0.0;</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :           temp2 = 0.0;</a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineNoCov">          0 :           for (l=1;l&lt;=k;l++) {</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineNoCov">          0 :              temp1 += a[(i-1)*(lda)+(l-1)] * b[(j-1)*(ldb)+(l-1)];</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineNoCov">          0 :              temp2 += b[(i-1)*(ldb)+(l-1)] * a[(j-1)*(lda)+(l-1)];</span></a>
+<a name="1154"><span class="lineNum">    1154 </span>            :           }</a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = alpha * (temp1 + temp2);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span>            :           else</a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = beta * c[(j-1)*(ldc)+(i-1)] +</span></a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineNoCov">          0 :               alpha * (temp1 + temp2);</span></a>
+<a name="1160"><span class="lineNum">    1160 </span>            :         }</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :     } else {</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :       /* lower */</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) </span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineNoCov">          0 :         for(i=j;i&lt;=n;i++) {</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            :           temp1 = 0.0;</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :           temp2 = 0.0;</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineNoCov">          0 :           for (l=1;l&lt;=k;l++) {</span></a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineNoCov">          0 :              temp1 += a[(i-1)*(lda)+(l-1)] * b[(j-1)*(ldb)+(l-1)];</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :              temp2 += b[(i-1)*(ldb)+(l-1)] * a[(j-1)*(lda)+(l-1)];</span></a>
+<a name="1170"><span class="lineNum">    1170 </span>            :           }</a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = alpha * (temp1 + temp2);</span></a>
+<a name="1173"><span class="lineNum">    1173 </span>            :           else</a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = beta * c[(j-1)*(ldc)+(i-1)] +</span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineNoCov">          0 :               alpha * (temp1 + temp2);</span></a>
+<a name="1176"><span class="lineNum">    1176 </span>            :         }</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :     }</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :   }</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :   return;</a>
+<a name="1180"><span class="lineNum">    1180 </span>            : }</a>
+<a name="1181"><span class="lineNum">    1181 </span>            : }</a>
+<a name="1182"><span class="lineNum">    1182 </span>            : }</a>
+<a name="1183"><span class="lineNum">    1183 </span>            : #include &lt;cmath&gt;</a>
+<a name="1184"><span class="lineNum">    1184 </span>            : </a>
+<a name="1185"><span class="lineNum">    1185 </span>            : #include &quot;real.h&quot;</a>
+<a name="1186"><span class="lineNum">    1186 </span>            : </a>
+<a name="1187"><span class="lineNum">    1187 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1188"><span class="lineNum">    1188 </span>            : </a>
+<a name="1189"><span class="lineNum">    1189 </span>            : namespace PLMD{</a>
+<a name="1190"><span class="lineNum">    1190 </span>            : namespace blas{</a>
+<a name="1191"><span class="lineNum">    1191 </span>            : void </a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineCov">        441 : PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(const char *side, </span></a>
+<a name="1193"><span class="lineNum">    1193 </span>            :        const char *uplo, </a>
+<a name="1194"><span class="lineNum">    1194 </span>            :        const char *transa, </a>
+<a name="1195"><span class="lineNum">    1195 </span>            :        const char *diag, </a>
+<a name="1196"><span class="lineNum">    1196 </span>            :        int *m__, </a>
+<a name="1197"><span class="lineNum">    1197 </span>            :        int *n__, </a>
+<a name="1198"><span class="lineNum">    1198 </span>            :        double *alpha__, </a>
+<a name="1199"><span class="lineNum">    1199 </span>            :        double *a, </a>
+<a name="1200"><span class="lineNum">    1200 </span>            :        int *lda__, </a>
+<a name="1201"><span class="lineNum">    1201 </span>            :        double *b, </a>
+<a name="1202"><span class="lineNum">    1202 </span>            :        int *ldb__)</a>
+<a name="1203"><span class="lineNum">    1203 </span>            : {</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     int a_dim1, a_offset, b_dim1, b_offset, i__1, i__2, i__3;</a>
+<a name="1205"><span class="lineNum">    1205 </span>            : </a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">        441 :     int m = *m__;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">        441 :     int n = *n__;</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">        441 :     int lda = *lda__;</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">        441 :     int ldb = *ldb__;</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">        441 :     double alpha = *alpha__;</span></a>
+<a name="1211"><span class="lineNum">    1211 </span>            :     </a>
+<a name="1212"><span class="lineNum">    1212 </span>            :     /* Local variables */</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :     int i__, j, k;</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :     double temp;</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :     int lside;</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :     int upper;</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :     int nounit;</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :     a_dim1 = lda;</a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">        441 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">        441 :     a -= a_offset;</span></a>
+<a name="1221"><span class="lineNum">    1221 </span>            :     b_dim1 = ldb;</a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">        441 :     b_offset = 1 + b_dim1;</span></a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">        441 :     b -= b_offset;</span></a>
+<a name="1224"><span class="lineNum">    1224 </span>            : </a>
+<a name="1225"><span class="lineNum">    1225 </span>            :     /* Function Body */</a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">        441 :     lside = (*side=='L' || *side=='l');</span></a>
+<a name="1227"><span class="lineNum">    1227 </span>            : </a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">        441 :     nounit = (*diag=='N' || *diag=='n');</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">        441 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            : </a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">        441 :     if (n == 0) {</span></a>
+<a name="1232"><span class="lineNum">    1232 </span>            :         return;</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     }</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">        441 :     if (std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            :         i__1 = n;</a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1237"><span class="lineNum">    1237 </span>            :             i__2 = m;</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineNoCov">          0 :                 b[i__ + j * b_dim1] = 0.;</span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            :             }</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :         }</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :         return;</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :     }</a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">        441 :     if (lside) {</span></a>
+<a name="1245"><span class="lineNum">    1245 </span><span class="lineNoCov">          0 :         if (*transa=='N' || *transa=='n') {</span></a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineNoCov">          0 :             if (upper) {</span></a>
+<a name="1247"><span class="lineNum">    1247 </span>            :                 i__1 = n;</a>
+<a name="1248"><span class="lineNum">    1248 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1249"><span class="lineNum">    1249 </span>            :                     i__2 = m;</a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineNoCov">          0 :                     for (k = 1; k &lt;= i__2; ++k) {</span></a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineNoCov">          0 :                         if (std::abs(b[k + j * b_dim1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineNoCov">          0 :                             temp = alpha * b[k + j * b_dim1];</span></a>
+<a name="1253"><span class="lineNum">    1253 </span>            :                             i__3 = k - 1;</a>
+<a name="1254"><span class="lineNum">    1254 </span><span class="lineNoCov">          0 :                             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * a[i__ + k * a_dim1];</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            :                             }</a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineNoCov">          0 :                             if (nounit) {</span></a>
+<a name="1258"><span class="lineNum">    1258 </span><span class="lineNoCov">          0 :                                 temp *= a[k + k * a_dim1];</span></a>
+<a name="1259"><span class="lineNum">    1259 </span>            :                             }</a>
+<a name="1260"><span class="lineNum">    1260 </span><span class="lineNoCov">          0 :                             b[k + j * b_dim1] = temp;</span></a>
+<a name="1261"><span class="lineNum">    1261 </span>            :                         }</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :                     }</a>
+<a name="1263"><span class="lineNum">    1263 </span>            :                 }</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :             } else {</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :                 i__1 = n;</a>
+<a name="1266"><span class="lineNum">    1266 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineNoCov">          0 :                     for (k = m; k &gt;= 1; --k) {</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineNoCov">          0 :                         if (std::abs(b[k + j * b_dim1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1269"><span class="lineNum">    1269 </span><span class="lineNoCov">          0 :                             temp = alpha * b[k + j * b_dim1];</span></a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineNoCov">          0 :                             b[k + j * b_dim1] = temp;</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineNoCov">          0 :                             if (nounit) {</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineNoCov">          0 :                                 b[k + j * b_dim1] *= a[k + k * a_dim1];</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :                             }</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :                             i__2 = m;</a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineNoCov">          0 :                             for (i__ = k + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * a[i__ + k * </span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineNoCov">          0 :                                         a_dim1];</span></a>
+<a name="1278"><span class="lineNum">    1278 </span>            :                             }</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :                         }</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :                     }</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :                 }</a>
+<a name="1282"><span class="lineNum">    1282 </span>            :             }</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :         } else {</a>
+<a name="1284"><span class="lineNum">    1284 </span>            : </a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineNoCov">          0 :             if (upper) {</span></a>
+<a name="1286"><span class="lineNum">    1286 </span>            :                 i__1 = n;</a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineNoCov">          0 :                     for (i__ = m; i__ &gt;= 1; --i__) {</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineNoCov">          0 :                         temp = b[i__ + j * b_dim1];</span></a>
+<a name="1290"><span class="lineNum">    1290 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="1291"><span class="lineNum">    1291 </span><span class="lineNoCov">          0 :                             temp *= a[i__ + i__ * a_dim1];</span></a>
+<a name="1292"><span class="lineNum">    1292 </span>            :                         }</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :                         i__2 = i__ - 1;</a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineNoCov">          0 :                         for (k = 1; k &lt;= i__2; ++k) {</span></a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineNoCov">          0 :                             temp += a[k + i__ * a_dim1] * b[k + j * b_dim1];</span></a>
+<a name="1296"><span class="lineNum">    1296 </span>            :                         }</a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineNoCov">          0 :                         b[i__ + j * b_dim1] = alpha * temp;</span></a>
+<a name="1298"><span class="lineNum">    1298 </span>            :                     }</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :                 }</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :             } else {</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :                 i__1 = n;</a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1303"><span class="lineNum">    1303 </span>            :                     i__2 = m;</a>
+<a name="1304"><span class="lineNum">    1304 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1305"><span class="lineNum">    1305 </span><span class="lineNoCov">          0 :                         temp = b[i__ + j * b_dim1];</span></a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="1307"><span class="lineNum">    1307 </span><span class="lineNoCov">          0 :                             temp *= a[i__ + i__ * a_dim1];</span></a>
+<a name="1308"><span class="lineNum">    1308 </span>            :                         }</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :                         i__3 = m;</a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineNoCov">          0 :                         for (k = i__ + 1; k &lt;= i__3; ++k) {</span></a>
+<a name="1311"><span class="lineNum">    1311 </span><span class="lineNoCov">          0 :                             temp += a[k + i__ * a_dim1] * b[k + j * b_dim1];</span></a>
+<a name="1312"><span class="lineNum">    1312 </span>            :                         }</a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineNoCov">          0 :                         b[i__ + j * b_dim1] = alpha * temp;</span></a>
+<a name="1314"><span class="lineNum">    1314 </span>            :                     }</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :                 }</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :             }</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :         }</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :     } else {</a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">        441 :         if (*transa=='N' || *transa=='n') {</span></a>
+<a name="1320"><span class="lineNum">    1320 </span>            : </a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">        147 :             if (upper) {</span></a>
+<a name="1322"><span class="lineNum">    1322 </span><span class="lineCov">       2634 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="1323"><span class="lineNum">    1323 </span>            :                     temp = alpha;</a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">       2535 :                     if (nounit) {</span></a>
+<a name="1325"><span class="lineNum">    1325 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="1326"><span class="lineNum">    1326 </span>            :                     }</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :                     i__1 = m;</a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineCov">     658291 :                     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineCov">     655756 :                         b[i__ + j * b_dim1] = temp * b[i__ + j * b_dim1];</span></a>
+<a name="1330"><span class="lineNum">    1330 </span>            :                     }</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :                     i__1 = j - 1;</a>
+<a name="1332"><span class="lineNum">    1332 </span><span class="lineCov">      40262 :                     for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineCov">      37727 :                         if (std::abs(a[k + j * a_dim1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">      37727 :                             temp = alpha * a[k + j * a_dim1];</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            :                             i__2 = m;</a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineCov">    9987691 :                             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1337"><span class="lineNum">    1337 </span><span class="lineCov">    9949964 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineCov">    9949964 :                                         b_dim1];</span></a>
+<a name="1339"><span class="lineNum">    1339 </span>            :                             }</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :                         }</a>
+<a name="1341"><span class="lineNum">    1341 </span>            :                     }</a>
+<a name="1342"><span class="lineNum">    1342 </span>            :                 }</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :             } else {</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :                 i__1 = n;</a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineCov">       1124 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1346"><span class="lineNum">    1346 </span>            :                     temp = alpha;</a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">       1076 :                     if (nounit) {</span></a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="1349"><span class="lineNum">    1349 </span>            :                     }</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :                     i__2 = m;</a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineCov">     271892 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">     270816 :                         b[i__ + j * b_dim1] = temp * b[i__ + j * b_dim1];</span></a>
+<a name="1353"><span class="lineNum">    1353 </span>            :                     }</a>
+<a name="1354"><span class="lineNum">    1354 </span>            :                     i__2 = n;</a>
+<a name="1355"><span class="lineNum">    1355 </span><span class="lineCov">      16778 :                     for (k = j + 1; k &lt;= i__2; ++k) {</span></a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineCov">      15702 :                         if (std::abs(a[k + j * a_dim1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineCov">      15486 :                             temp = alpha * a[k + j * a_dim1];</span></a>
+<a name="1358"><span class="lineNum">    1358 </span>            :                             i__3 = m;</a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineCov">    4113622 :                             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineCov">    4098136 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineCov">    4098136 :                                         b_dim1];</span></a>
+<a name="1362"><span class="lineNum">    1362 </span>            :                             }</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :                         }</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :                     }</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :                 }</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :             }</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :         } else {</a>
+<a name="1368"><span class="lineNum">    1368 </span>            : </a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineCov">        294 :             if (upper) {</span></a>
+<a name="1370"><span class="lineNum">    1370 </span>            :                 i__1 = n;</a>
+<a name="1371"><span class="lineNum">    1371 </span><span class="lineCov">       4729 :                 for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="1372"><span class="lineNum">    1372 </span>            :                     i__2 = k - 1;</a>
+<a name="1373"><span class="lineNum">    1373 </span><span class="lineCov">      71622 :                     for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineCov">      67080 :                         if (std::abs(a[j + k * a_dim1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1375"><span class="lineNum">    1375 </span><span class="lineCov">      66959 :                             temp = alpha * a[j + k * a_dim1];</span></a>
+<a name="1376"><span class="lineNum">    1376 </span>            :                             i__3 = m;</a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">   18130215 :                             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineCov">   18063256 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="1379"><span class="lineNum">    1379 </span><span class="lineCov">   18063256 :                                         b_dim1];</span></a>
+<a name="1380"><span class="lineNum">    1380 </span>            :                             }</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :                         }</a>
+<a name="1382"><span class="lineNum">    1382 </span>            :                     }</a>
+<a name="1383"><span class="lineNum">    1383 </span>            :                     temp = alpha;</a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineCov">       4542 :                     if (nounit) {</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineCov">       2007 :                         temp *= a[k + k * a_dim1];</span></a>
+<a name="1386"><span class="lineNum">    1386 </span>            :                     }</a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineCov">       4542 :                     if (std::abs(temp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="1388"><span class="lineNum">    1388 </span>            :                         i__2 = m;</a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineCov">     538339 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineCov">     536332 :                             b[i__ + k * b_dim1] = temp * b[i__ + k * b_dim1];</span></a>
+<a name="1391"><span class="lineNum">    1391 </span>            :                         }</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :                     }</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :                 }</a>
+<a name="1394"><span class="lineNum">    1394 </span>            :             } else {</a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineCov">       2787 :                 for (k = n; k &gt;= 1; --k) {</span></a>
+<a name="1396"><span class="lineNum">    1396 </span>            :                     i__1 = n;</a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">      42458 :                     for (j = k + 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineCov">      39778 :                         if (std::abs(a[j + k * a_dim1])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1399"><span class="lineNum">    1399 </span><span class="lineCov">      39190 :                             temp = alpha * a[j + k * a_dim1];</span></a>
+<a name="1400"><span class="lineNum">    1400 </span>            :                             i__2 = m;</a>
+<a name="1401"><span class="lineNum">    1401 </span><span class="lineCov">   10008102 :                             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">    9968912 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="1403"><span class="lineNum">    1403 </span><span class="lineCov">    9968912 :                                         b_dim1];</span></a>
+<a name="1404"><span class="lineNum">    1404 </span>            :                             }</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :                         }</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :                     }</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :                     temp = alpha;</a>
+<a name="1408"><span class="lineNum">    1408 </span><span class="lineCov">       2680 :                     if (nounit) {</span></a>
+<a name="1409"><span class="lineNum">    1409 </span><span class="lineCov">       1604 :                         temp *= a[k + k * a_dim1];</span></a>
+<a name="1410"><span class="lineNum">    1410 </span>            :                     }</a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineCov">       2680 :                     if (std::abs(temp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="1412"><span class="lineNum">    1412 </span>            :                         i__1 = m;</a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineCov">     391844 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineCov">     390240 :                             b[i__ + k * b_dim1] = temp * b[i__ + k * b_dim1];</span></a>
+<a name="1415"><span class="lineNum">    1415 </span>            :                         }</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :                     }</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :                 }</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :             }</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :         }</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :     }</a>
+<a name="1421"><span class="lineNum">    1421 </span>            : </a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     return;</a>
+<a name="1423"><span class="lineNum">    1423 </span>            : </a>
+<a name="1424"><span class="lineNum">    1424 </span>            : }</a>
+<a name="1425"><span class="lineNum">    1425 </span>            : </a>
+<a name="1426"><span class="lineNum">    1426 </span>            : </a>
+<a name="1427"><span class="lineNum">    1427 </span>            : }</a>
+<a name="1428"><span class="lineNum">    1428 </span>            : }</a>
+<a name="1429"><span class="lineNum">    1429 </span>            : #include &lt;cmath&gt;</a>
+<a name="1430"><span class="lineNum">    1430 </span>            : </a>
+<a name="1431"><span class="lineNum">    1431 </span>            : #include &quot;real.h&quot;</a>
+<a name="1432"><span class="lineNum">    1432 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1433"><span class="lineNum">    1433 </span>            : </a>
+<a name="1434"><span class="lineNum">    1434 </span>            : namespace PLMD{</a>
+<a name="1435"><span class="lineNum">    1435 </span>            : namespace blas{</a>
+<a name="1436"><span class="lineNum">    1436 </span>            : void </a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">       3624 : PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)(const char *uplo, </span></a>
+<a name="1438"><span class="lineNum">    1438 </span>            :        const char *trans,</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :        const char *diag, </a>
+<a name="1440"><span class="lineNum">    1440 </span>            :        int *n__, </a>
+<a name="1441"><span class="lineNum">    1441 </span>            :        double *a, </a>
+<a name="1442"><span class="lineNum">    1442 </span>            :        int *lda__, </a>
+<a name="1443"><span class="lineNum">    1443 </span>            :        double *x, </a>
+<a name="1444"><span class="lineNum">    1444 </span>            :        int *incx__)</a>
+<a name="1445"><span class="lineNum">    1445 </span>            : {</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="1447"><span class="lineNum">    1447 </span>            : </a>
+<a name="1448"><span class="lineNum">    1448 </span>            :     int i__, j, ix, jx, kx;</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :     double temp;</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :     int nounit;</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :     </a>
+<a name="1452"><span class="lineNum">    1452 </span><span class="lineCov">       3624 :     int n = *n__;</span></a>
+<a name="1453"><span class="lineNum">    1453 </span><span class="lineCov">       3624 :     int lda = *lda__;</span></a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineCov">       3624 :     int incx = *incx__;</span></a>
+<a name="1455"><span class="lineNum">    1455 </span>            :     </a>
+<a name="1456"><span class="lineNum">    1456 </span>            :     a_dim1 = lda;</a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineCov">       3624 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineCov">       3624 :     a -= a_offset;</span></a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineCov">       3624 :     --x;</span></a>
+<a name="1460"><span class="lineNum">    1460 </span>            : </a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineCov">       3624 :     if (n == 0) {</span></a>
+<a name="1462"><span class="lineNum">    1462 </span>            :         return;</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :     }</a>
+<a name="1464"><span class="lineNum">    1464 </span>            : </a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineCov">       3483 :     nounit = (*diag=='n' || *diag=='N');</span></a>
+<a name="1466"><span class="lineNum">    1466 </span>            : </a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">       3483 :     if (incx &lt;= 0) {</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineNoCov">          0 :         kx = 1 - (n - 1) * incx;</span></a>
+<a name="1469"><span class="lineNum">    1469 </span>            :     } else {</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :         kx = 1;</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :     }</a>
+<a name="1472"><span class="lineNum">    1472 </span>            : </a>
+<a name="1473"><span class="lineNum">    1473 </span><span class="lineCov">       3483 :     if (*trans=='N' || *trans=='n') {</span></a>
+<a name="1474"><span class="lineNum">    1474 </span>            : </a>
+<a name="1475"><span class="lineNum">    1475 </span><span class="lineCov">       3483 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="1476"><span class="lineNum">    1476 </span><span class="lineCov">       1950 :             if (incx == 1) {</span></a>
+<a name="1477"><span class="lineNum">    1477 </span>            :                 i__1 = n;</a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineCov">      31239 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1479"><span class="lineNum">    1479 </span><span class="lineCov">      29289 :                     if (std::abs(x[j])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1480"><span class="lineNum">    1480 </span>            :                         temp = x[j];</a>
+<a name="1481"><span class="lineNum">    1481 </span>            :                         i__2 = j - 1;</a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineCov">     318678 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1483"><span class="lineNum">    1483 </span><span class="lineCov">     289605 :                             x[i__] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="1484"><span class="lineNum">    1484 </span>            :                         }</a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineCov">      29073 :                         if (nounit) {</span></a>
+<a name="1486"><span class="lineNum">    1486 </span><span class="lineCov">      29073 :                             x[j] *= a[j + j * a_dim1];</span></a>
+<a name="1487"><span class="lineNum">    1487 </span>            :                         }</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :                     }</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :                 }</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :             } else {</a>
+<a name="1491"><span class="lineNum">    1491 </span>            :                 jx = kx;</a>
+<a name="1492"><span class="lineNum">    1492 </span>            :                 i__1 = n;</a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineNoCov">          0 :                     if (std::abs(x[jx])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1495"><span class="lineNum">    1495 </span>            :                         temp = x[jx];</a>
+<a name="1496"><span class="lineNum">    1496 </span>            :                         ix = kx;</a>
+<a name="1497"><span class="lineNum">    1497 </span>            :                         i__2 = j - 1;</a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineNoCov">          0 :                             x[ix] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineNoCov">          0 :                             ix += incx;</span></a>
+<a name="1501"><span class="lineNum">    1501 </span>            :                         }</a>
+<a name="1502"><span class="lineNum">    1502 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineNoCov">          0 :                             x[jx] *= a[j + j * a_dim1];</span></a>
+<a name="1504"><span class="lineNum">    1504 </span>            :                         }</a>
+<a name="1505"><span class="lineNum">    1505 </span>            :                     }</a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="1507"><span class="lineNum">    1507 </span>            :                 }</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :             }</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :         } else {</a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineCov">       1533 :             if (incx == 1) {</span></a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineCov">      25237 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineCov">      23704 :                     if (std::abs(x[j])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1513"><span class="lineNum">    1513 </span>            :                         temp = x[j];</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :                         i__1 = j + 1;</a>
+<a name="1515"><span class="lineNum">    1515 </span><span class="lineCov">     255880 :                         for (i__ = n; i__ &gt;= i__1; --i__) {</span></a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">     232176 :                             x[i__] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="1517"><span class="lineNum">    1517 </span>            :                         }</a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineCov">      23704 :                         if (nounit) {</span></a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineCov">      23704 :                             x[j] *= a[j + j * a_dim1];</span></a>
+<a name="1520"><span class="lineNum">    1520 </span>            :                         }</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :                     }</a>
+<a name="1522"><span class="lineNum">    1522 </span>            :                 }</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :             } else {</a>
+<a name="1524"><span class="lineNum">    1524 </span><span class="lineNoCov">          0 :                 kx += (n - 1) * incx;</span></a>
+<a name="1525"><span class="lineNum">    1525 </span>            :                 jx = kx;</a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineNoCov">          0 :                     if (std::abs(x[jx])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1528"><span class="lineNum">    1528 </span>            :                         temp = x[jx];</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :                         ix = kx;</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :                         i__1 = j + 1;</a>
+<a name="1531"><span class="lineNum">    1531 </span><span class="lineNoCov">          0 :                         for (i__ = n; i__ &gt;= i__1; --i__) {</span></a>
+<a name="1532"><span class="lineNum">    1532 </span><span class="lineNoCov">          0 :                             x[ix] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineNoCov">          0 :                             ix -= incx;</span></a>
+<a name="1534"><span class="lineNum">    1534 </span>            :                         }</a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineNoCov">          0 :                             x[jx] *= a[j + j * a_dim1];</span></a>
+<a name="1537"><span class="lineNum">    1537 </span>            :                         }</a>
+<a name="1538"><span class="lineNum">    1538 </span>            :                     }</a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineNoCov">          0 :                     jx -= incx;</span></a>
+<a name="1540"><span class="lineNum">    1540 </span>            :                 }</a>
+<a name="1541"><span class="lineNum">    1541 </span>            :             }</a>
+<a name="1542"><span class="lineNum">    1542 </span>            :         }</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :     } else {</a>
+<a name="1544"><span class="lineNum">    1544 </span>            : </a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineNoCov">          0 :             if (incx == 1) {</span></a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineNoCov">          0 :                     temp = x[j];</span></a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="1551"><span class="lineNum">    1551 </span>            :                     }</a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineNoCov">          0 :                     for (i__ = j - 1; i__ &gt;= 1; --i__) {</span></a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[i__];</span></a>
+<a name="1554"><span class="lineNum">    1554 </span>            :                     }</a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineNoCov">          0 :                     x[j] = temp;</span></a>
+<a name="1556"><span class="lineNum">    1556 </span>            :                 }</a>
+<a name="1557"><span class="lineNum">    1557 </span>            :             } else {</a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineNoCov">          0 :                 jx = kx + (n - 1) * incx;</span></a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineNoCov">          0 :                     temp = x[jx];</span></a>
+<a name="1561"><span class="lineNum">    1561 </span>            :                     ix = jx;</a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="1564"><span class="lineNum">    1564 </span>            :                     }</a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineNoCov">          0 :                     for (i__ = j - 1; i__ &gt;= 1; --i__) {</span></a>
+<a name="1566"><span class="lineNum">    1566 </span><span class="lineNoCov">          0 :                         ix -= incx;</span></a>
+<a name="1567"><span class="lineNum">    1567 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[ix];</span></a>
+<a name="1568"><span class="lineNum">    1568 </span>            :                     }</a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineNoCov">          0 :                     x[jx] = temp;</span></a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineNoCov">          0 :                     jx -= incx;</span></a>
+<a name="1571"><span class="lineNum">    1571 </span>            :                 }</a>
+<a name="1572"><span class="lineNum">    1572 </span>            :             }</a>
+<a name="1573"><span class="lineNum">    1573 </span>            :         } else {</a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineNoCov">          0 :             if (incx == 1) {</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            :                 i__1 = n;</a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1577"><span class="lineNum">    1577 </span><span class="lineNoCov">          0 :                     temp = x[j];</span></a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="1580"><span class="lineNum">    1580 </span>            :                     }</a>
+<a name="1581"><span class="lineNum">    1581 </span>            :                     i__2 = n;</a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineNoCov">          0 :                     for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[i__];</span></a>
+<a name="1584"><span class="lineNum">    1584 </span>            :                     }</a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineNoCov">          0 :                     x[j] = temp;</span></a>
+<a name="1586"><span class="lineNum">    1586 </span>            :                 }</a>
+<a name="1587"><span class="lineNum">    1587 </span>            :             } else {</a>
+<a name="1588"><span class="lineNum">    1588 </span>            :                 jx = kx;</a>
+<a name="1589"><span class="lineNum">    1589 </span>            :                 i__1 = n;</a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineNoCov">          0 :                     temp = x[jx];</span></a>
+<a name="1592"><span class="lineNum">    1592 </span>            :                     ix = jx;</a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="1594"><span class="lineNum">    1594 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="1595"><span class="lineNum">    1595 </span>            :                     }</a>
+<a name="1596"><span class="lineNum">    1596 </span>            :                     i__2 = n;</a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineNoCov">          0 :                     for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="1599"><span class="lineNum">    1599 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[ix];</span></a>
+<a name="1600"><span class="lineNum">    1600 </span>            :                     }</a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineNoCov">          0 :                     x[jx] = temp;</span></a>
+<a name="1602"><span class="lineNum">    1602 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="1603"><span class="lineNum">    1603 </span>            :                 }</a>
+<a name="1604"><span class="lineNum">    1604 </span>            :             }</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :         }</a>
+<a name="1606"><span class="lineNum">    1606 </span>            :     }</a>
+<a name="1607"><span class="lineNum">    1607 </span>            : </a>
+<a name="1608"><span class="lineNum">    1608 </span>            :     return;</a>
+<a name="1609"><span class="lineNum">    1609 </span>            : </a>
+<a name="1610"><span class="lineNum">    1610 </span>            : }</a>
+<a name="1611"><span class="lineNum">    1611 </span>            : </a>
+<a name="1612"><span class="lineNum">    1612 </span>            : </a>
+<a name="1613"><span class="lineNum">    1613 </span>            : }</a>
+<a name="1614"><span class="lineNum">    1614 </span>            : }</a>
+<a name="1615"><span class="lineNum">    1615 </span>            : #include &lt;cctype&gt;</a>
+<a name="1616"><span class="lineNum">    1616 </span>            : #include &lt;cmath&gt;</a>
+<a name="1617"><span class="lineNum">    1617 </span>            : </a>
+<a name="1618"><span class="lineNum">    1618 </span>            : #include &quot;real.h&quot;</a>
+<a name="1619"><span class="lineNum">    1619 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1620"><span class="lineNum">    1620 </span>            : </a>
+<a name="1621"><span class="lineNum">    1621 </span>            : namespace PLMD{</a>
+<a name="1622"><span class="lineNum">    1622 </span>            : namespace blas{</a>
+<a name="1623"><span class="lineNum">    1623 </span>            : void</a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(const char * side,</span></a>
+<a name="1625"><span class="lineNum">    1625 </span>            :        const char * uplo,</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :        const char * transa,</a>
+<a name="1627"><span class="lineNum">    1627 </span>            :        const char * diag,</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :        int *  m__,</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :        int *  n__,</a>
+<a name="1630"><span class="lineNum">    1630 </span>            :        double *alpha__,</a>
+<a name="1631"><span class="lineNum">    1631 </span>            :        double *a,</a>
+<a name="1632"><span class="lineNum">    1632 </span>            :        int *  lda__,</a>
+<a name="1633"><span class="lineNum">    1633 </span>            :        double *b,</a>
+<a name="1634"><span class="lineNum">    1634 </span>            :        int *  ldb__)</a>
+<a name="1635"><span class="lineNum">    1635 </span>            : {</a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineNoCov">          0 :   const char xside  = std::toupper(*side);</span></a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineNoCov">          0 :   const char xuplo  = std::toupper(*uplo);</span></a>
+<a name="1638"><span class="lineNum">    1638 </span><span class="lineNoCov">          0 :   const char xtrans = std::toupper(*transa);</span></a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineNoCov">          0 :   const char xdiag  = std::toupper(*diag);</span></a>
+<a name="1640"><span class="lineNum">    1640 </span>            :   int i,j,k;</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :   double temp;</a>
+<a name="1642"><span class="lineNum">    1642 </span>            : </a>
+<a name="1643"><span class="lineNum">    1643 </span>            :   </a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineNoCov">          0 :   int m = *m__;</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineNoCov">          0 :   int n = *n__;</span></a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineNoCov">          0 :   int lda = *lda__;</span></a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineNoCov">          0 :   int ldb = *ldb__;</span></a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineNoCov">          0 :   double alpha = *alpha__;</span></a>
+<a name="1649"><span class="lineNum">    1649 </span>            : </a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineNoCov">          0 :   if(n&lt;=0)</span></a>
+<a name="1651"><span class="lineNum">    1651 </span>            :     return;</a>
+<a name="1652"><span class="lineNum">    1652 </span>            :   </a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineNoCov">          0 :   if(std::abs(alpha)&lt;PLUMED_GMX_DOUBLE_MIN) { </span></a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;n;j++)</span></a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;m;i++)</span></a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineNoCov">          0 :         b[j*(ldb)+i] = 0.0;</span></a>
+<a name="1657"><span class="lineNum">    1657 </span>            :     return;</a>
+<a name="1658"><span class="lineNum">    1658 </span>            :   }</a>
+<a name="1659"><span class="lineNum">    1659 </span>            : </a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineNoCov">          0 :   if(xside=='L') {</span></a>
+<a name="1661"><span class="lineNum">    1661 </span>            :     /* left side */</a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineNoCov">          0 :     if(xtrans=='N') {</span></a>
+<a name="1663"><span class="lineNum">    1663 </span>            :       /* No transpose */</a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="1665"><span class="lineNum">    1665 </span>            :         /* upper */</a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="1670"><span class="lineNum">    1670 </span>            :           }</a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineNoCov">          0 :           for(k=m-1;k&gt;=0;k--) {</span></a>
+<a name="1672"><span class="lineNum">    1672 </span><span class="lineNoCov">          0 :             if(std::abs(b[j*(ldb)+k])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1673"><span class="lineNum">    1673 </span><span class="lineNoCov">          0 :               if(xdiag=='N')</span></a>
+<a name="1674"><span class="lineNum">    1674 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+k] /= a[k*(lda)+k];</span></a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;k;i++)</span></a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= b[j*(ldb)+k]*a[k*(lda)+i];</span></a>
+<a name="1677"><span class="lineNum">    1677 </span>            :             }</a>
+<a name="1678"><span class="lineNum">    1678 </span>            :           }</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :         }</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :       } else {</a>
+<a name="1681"><span class="lineNum">    1681 </span>            :         /* lower */</a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_DOUBLE_EPS)</span></a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineNoCov">          0 :           for(k=0;k&lt;m;k++) {</span></a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineNoCov">          0 :             if(std::abs(b[j*(ldb)+k])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1688"><span class="lineNum">    1688 </span><span class="lineNoCov">          0 :               if(xdiag=='N')</span></a>
+<a name="1689"><span class="lineNum">    1689 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+k] /= a[k*(lda)+k];</span></a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineNoCov">          0 :               for(i=k+1;i&lt;m;i++)</span></a>
+<a name="1691"><span class="lineNum">    1691 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= b[j*(ldb)+k]*a[k*(lda)+i];</span></a>
+<a name="1692"><span class="lineNum">    1692 </span>            :             }</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :           }</a>
+<a name="1694"><span class="lineNum">    1694 </span>            :         }</a>
+<a name="1695"><span class="lineNum">    1695 </span>            :       }</a>
+<a name="1696"><span class="lineNum">    1696 </span>            :     } else {</a>
+<a name="1697"><span class="lineNum">    1697 </span>            :       /* Transpose */</a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="1699"><span class="lineNum">    1699 </span>            :         /* upper */</a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++) {</span></a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineNoCov">          0 :             temp = alpha * b[j*(ldb)+i];</span></a>
+<a name="1703"><span class="lineNum">    1703 </span><span class="lineNoCov">          0 :             for(k=0;k&lt;i;k++)</span></a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineNoCov">          0 :               temp -= a[i*(lda)+k] * b[j*(ldb)+k];</span></a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineNoCov">          0 :             if(xdiag=='N')</span></a>
+<a name="1706"><span class="lineNum">    1706 </span><span class="lineNoCov">          0 :                 temp /= a[i*(lda)+i];</span></a>
+<a name="1707"><span class="lineNum">    1707 </span><span class="lineNoCov">          0 :             b[j*(ldb)+i] = temp;</span></a>
+<a name="1708"><span class="lineNum">    1708 </span>            :           }</a>
+<a name="1709"><span class="lineNum">    1709 </span>            :         }</a>
+<a name="1710"><span class="lineNum">    1710 </span>            :       } else {</a>
+<a name="1711"><span class="lineNum">    1711 </span>            :         /* lower */</a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineNoCov">          0 :           for(i=m-1;i&gt;=0;i--) {</span></a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineNoCov">          0 :             temp = alpha * b[j*(ldb)+i];</span></a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineNoCov">          0 :             for(k=i+1;k&lt;m;k++)</span></a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineNoCov">          0 :               temp -= a[i*(lda)+k] * b[j*(ldb)+k];</span></a>
+<a name="1717"><span class="lineNum">    1717 </span><span class="lineNoCov">          0 :             if(xdiag=='N')</span></a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineNoCov">          0 :                 temp /= a[i*(lda)+i];</span></a>
+<a name="1719"><span class="lineNum">    1719 </span><span class="lineNoCov">          0 :             b[j*(ldb)+i] = temp;</span></a>
+<a name="1720"><span class="lineNum">    1720 </span>            :           }</a>
+<a name="1721"><span class="lineNum">    1721 </span>            :         }</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :       }</a>
+<a name="1723"><span class="lineNum">    1723 </span>            :     }</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :   } else {</a>
+<a name="1725"><span class="lineNum">    1725 </span>            :     /* right side */</a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineNoCov">          0 :     if(xtrans=='N') {</span></a>
+<a name="1727"><span class="lineNum">    1727 </span>            :       /* No transpose */</a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="1729"><span class="lineNum">    1729 </span>            :         /* upper */</a>
+<a name="1730"><span class="lineNum">    1730 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_DOUBLE_EPS)</span></a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1733"><span class="lineNum">    1733 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineNoCov">          0 :           for(k=0;k&lt;j;k++) {</span></a>
+<a name="1735"><span class="lineNum">    1735 </span><span class="lineNoCov">          0 :             if(std::abs(a[j*(lda)+k])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1736"><span class="lineNum">    1736 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= a[j*(lda)+k]*b[k*(ldb)+i];</span></a>
+<a name="1738"><span class="lineNum">    1738 </span>            :             }</a>
+<a name="1739"><span class="lineNum">    1739 </span>            :           }</a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineNoCov">          0 :             temp = 1.0/a[j*(lda)+j];</span></a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1743"><span class="lineNum">    1743 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= temp;</span></a>
+<a name="1744"><span class="lineNum">    1744 </span>            :           }</a>
+<a name="1745"><span class="lineNum">    1745 </span>            :         }</a>
+<a name="1746"><span class="lineNum">    1746 </span>            :       } else {</a>
+<a name="1747"><span class="lineNum">    1747 </span>            :         /* lower */</a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineNoCov">          0 :         for(j=n-1;j&gt;=0;j--) {</span></a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineNoCov">          0 :           if(std::abs(alpha)&gt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1751"><span class="lineNum">    1751 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineNoCov">          0 :           for(k=j+1;k&lt;n;k++) {</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineNoCov">          0 :             if(std::abs(a[j*(lda)+k])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= a[j*(lda)+k]*b[k*(ldb)+i];</span></a>
+<a name="1756"><span class="lineNum">    1756 </span>            :             }</a>
+<a name="1757"><span class="lineNum">    1757 </span>            :           }</a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineNoCov">          0 :             temp = 1.0/a[j*(lda)+j];</span></a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= temp;</span></a>
+<a name="1762"><span class="lineNum">    1762 </span>            :           }</a>
+<a name="1763"><span class="lineNum">    1763 </span>            :         }</a>
+<a name="1764"><span class="lineNum">    1764 </span>            :       }</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :     } else {</a>
+<a name="1766"><span class="lineNum">    1766 </span>            :       /* Transpose */</a>
+<a name="1767"><span class="lineNum">    1767 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="1768"><span class="lineNum">    1768 </span>            :         /* upper */</a>
+<a name="1769"><span class="lineNum">    1769 </span><span class="lineNoCov">          0 :         for(k=n-1;k&gt;=0;k--) {</span></a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="1771"><span class="lineNum">    1771 </span><span class="lineNoCov">          0 :             temp = 1.0/a[k*(lda)+k];</span></a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1773"><span class="lineNum">    1773 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= temp;</span></a>
+<a name="1774"><span class="lineNum">    1774 </span>            :           }</a>
+<a name="1775"><span class="lineNum">    1775 </span><span class="lineNoCov">          0 :           for(j=0;j&lt;k;j++) {</span></a>
+<a name="1776"><span class="lineNum">    1776 </span><span class="lineNoCov">          0 :             if(std::abs(a[k*(lda)+j])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1777"><span class="lineNum">    1777 </span>            :               temp = a[k*(lda)+j];</a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="1779"><span class="lineNum">    1779 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= temp * b[k*(ldb)+i];</span></a>
+<a name="1780"><span class="lineNum">    1780 </span>            :             }</a>
+<a name="1781"><span class="lineNum">    1781 </span>            :           }</a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_DOUBLE_EPS)</span></a>
+<a name="1783"><span class="lineNum">    1783 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= alpha;</span></a>
+<a name="1785"><span class="lineNum">    1785 </span>            :         }</a>
+<a name="1786"><span class="lineNum">    1786 </span>            :       } else {</a>
+<a name="1787"><span class="lineNum">    1787 </span>            :         /* lower */</a>
+<a name="1788"><span class="lineNum">    1788 </span><span class="lineNoCov">          0 :         for(k=0;k&lt;n;k++) {</span></a>
+<a name="1789"><span class="lineNum">    1789 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="1790"><span class="lineNum">    1790 </span><span class="lineNoCov">          0 :             temp = 1.0/a[k*(lda)+k];</span></a>
+<a name="1791"><span class="lineNum">    1791 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1792"><span class="lineNum">    1792 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= temp;</span></a>
+<a name="1793"><span class="lineNum">    1793 </span>            :           }</a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineNoCov">          0 :           for(j=k+1;j&lt;n;j++) {</span></a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineNoCov">          0 :             if(std::abs(a[k*(lda)+j])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="1796"><span class="lineNum">    1796 </span>            :               temp = a[k*(lda)+j];</a>
+<a name="1797"><span class="lineNum">    1797 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="1798"><span class="lineNum">    1798 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= temp * b[k*(ldb)+i];</span></a>
+<a name="1799"><span class="lineNum">    1799 </span>            :             }</a>
+<a name="1800"><span class="lineNum">    1800 </span>            :           }</a>
+<a name="1801"><span class="lineNum">    1801 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_DOUBLE_EPS)</span></a>
+<a name="1802"><span class="lineNum">    1802 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= alpha;</span></a>
+<a name="1804"><span class="lineNum">    1804 </span>            :         }</a>
+<a name="1805"><span class="lineNum">    1805 </span>            :       }      </a>
+<a name="1806"><span class="lineNum">    1806 </span>            :     }</a>
+<a name="1807"><span class="lineNum">    1807 </span>            :   }    </a>
+<a name="1808"><span class="lineNum">    1808 </span>            : }</a>
+<a name="1809"><span class="lineNum">    1809 </span>            : }</a>
+<a name="1810"><span class="lineNum">    1810 </span>            : }</a>
+<a name="1811"><span class="lineNum">    1811 </span>            : #include &lt;cmath&gt;</a>
+<a name="1812"><span class="lineNum">    1812 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1813"><span class="lineNum">    1813 </span>            : </a>
+<a name="1814"><span class="lineNum">    1814 </span>            : namespace PLMD{</a>
+<a name="1815"><span class="lineNum">    1815 </span>            : namespace blas{</a>
+<a name="1816"><span class="lineNum">    1816 </span>            : int</a>
+<a name="1817"><span class="lineNum">    1817 </span><span class="lineCov">        114 : PLUMED_BLAS_F77_FUNC(idamax,IDAMAX)(int *n__,</span></a>
+<a name="1818"><span class="lineNum">    1818 </span>            :                         double *dx,</a>
+<a name="1819"><span class="lineNum">    1819 </span>            :                         int *incx__)</a>
+<a name="1820"><span class="lineNum">    1820 </span>            : {</a>
+<a name="1821"><span class="lineNum">    1821 </span>            :   int i,ix,idxmax;</a>
+<a name="1822"><span class="lineNum">    1822 </span>            :   double dmax,tmp;</a>
+<a name="1823"><span class="lineNum">    1823 </span>            : </a>
+<a name="1824"><span class="lineNum">    1824 </span><span class="lineCov">        114 :   int n    = *n__;</span></a>
+<a name="1825"><span class="lineNum">    1825 </span><span class="lineCov">        114 :   int incx = *incx__;</span></a>
+<a name="1826"><span class="lineNum">    1826 </span>            :   </a>
+<a name="1827"><span class="lineNum">    1827 </span><span class="lineCov">        114 :   if(n&lt;1 || incx&lt;=0)</span></a>
+<a name="1828"><span class="lineNum">    1828 </span>            :     return -1;</a>
+<a name="1829"><span class="lineNum">    1829 </span>            : </a>
+<a name="1830"><span class="lineNum">    1830 </span><span class="lineCov">        114 :   if(n==1)</span></a>
+<a name="1831"><span class="lineNum">    1831 </span>            :     return 1;</a>
+<a name="1832"><span class="lineNum">    1832 </span>            : </a>
+<a name="1833"><span class="lineNum">    1833 </span><span class="lineCov">         57 :   dmax = std::abs(dx[0]);</span></a>
+<a name="1834"><span class="lineNum">    1834 </span>            :   idxmax = 1;</a>
+<a name="1835"><span class="lineNum">    1835 </span>            : </a>
+<a name="1836"><span class="lineNum">    1836 </span><span class="lineCov">         57 :   if(incx==1) {</span></a>
+<a name="1837"><span class="lineNum">    1837 </span><span class="lineCov">        114 :     for(i=1;i&lt;n;i++) {</span></a>
+<a name="1838"><span class="lineNum">    1838 </span><span class="lineCov">         57 :       tmp = std::abs(dx[i]);</span></a>
+<a name="1839"><span class="lineNum">    1839 </span><span class="lineCov">         57 :       if(tmp&gt;dmax) {</span></a>
+<a name="1840"><span class="lineNum">    1840 </span>            :         dmax = tmp;</a>
+<a name="1841"><span class="lineNum">    1841 </span><span class="lineNoCov">          0 :         idxmax = i+1;</span></a>
+<a name="1842"><span class="lineNum">    1842 </span>            :       }</a>
+<a name="1843"><span class="lineNum">    1843 </span>            :     }</a>
+<a name="1844"><span class="lineNum">    1844 </span>            :   } else {</a>
+<a name="1845"><span class="lineNum">    1845 </span>            :     /* Non-unit increments */</a>
+<a name="1846"><span class="lineNum">    1846 </span>            :     ix = incx; /* this is really 0 + an increment */</a>
+<a name="1847"><span class="lineNum">    1847 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;n;i++,ix+=incx) {</span></a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineNoCov">          0 :       tmp = std::abs(dx[ix]);</span></a>
+<a name="1849"><span class="lineNum">    1849 </span><span class="lineNoCov">          0 :       if(tmp&gt;dmax) {</span></a>
+<a name="1850"><span class="lineNum">    1850 </span>            :         dmax = tmp;</a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineNoCov">          0 :         idxmax = ix+1;</span></a>
+<a name="1852"><span class="lineNum">    1852 </span>            :       }</a>
+<a name="1853"><span class="lineNum">    1853 </span>            :     }    </a>
+<a name="1854"><span class="lineNum">    1854 </span>            :   }</a>
+<a name="1855"><span class="lineNum">    1855 </span>            :   return idxmax;</a>
+<a name="1856"><span class="lineNum">    1856 </span>            : }</a>
+<a name="1857"><span class="lineNum">    1857 </span>            : }</a>
+<a name="1858"><span class="lineNum">    1858 </span>            : }</a>
+<a name="1859"><span class="lineNum">    1859 </span>            : #include &lt;cmath&gt;</a>
+<a name="1860"><span class="lineNum">    1860 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1861"><span class="lineNum">    1861 </span>            : </a>
+<a name="1862"><span class="lineNum">    1862 </span>            : namespace PLMD{</a>
+<a name="1863"><span class="lineNum">    1863 </span>            : namespace blas{</a>
+<a name="1864"><span class="lineNum">    1864 </span>            : int</a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)(int *n__,</span></a>
+<a name="1866"><span class="lineNum">    1866 </span>            :        float *dx,</a>
+<a name="1867"><span class="lineNum">    1867 </span>            :        int *incx__)</a>
+<a name="1868"><span class="lineNum">    1868 </span>            : {</a>
+<a name="1869"><span class="lineNum">    1869 </span>            :   int i,ix,idxmax;</a>
+<a name="1870"><span class="lineNum">    1870 </span>            :   float dmax,tmp;</a>
+<a name="1871"><span class="lineNum">    1871 </span>            : </a>
+<a name="1872"><span class="lineNum">    1872 </span><span class="lineNoCov">          0 :   int n    = *n__;</span></a>
+<a name="1873"><span class="lineNum">    1873 </span><span class="lineNoCov">          0 :   int incx = *incx__;</span></a>
+<a name="1874"><span class="lineNum">    1874 </span>            :   </a>
+<a name="1875"><span class="lineNum">    1875 </span><span class="lineNoCov">          0 :   if(n&lt;1 || incx&lt;=0)</span></a>
+<a name="1876"><span class="lineNum">    1876 </span>            :     return -1;</a>
+<a name="1877"><span class="lineNum">    1877 </span>            : </a>
+<a name="1878"><span class="lineNum">    1878 </span><span class="lineNoCov">          0 :   if(n==1)</span></a>
+<a name="1879"><span class="lineNum">    1879 </span>            :     return 1;</a>
+<a name="1880"><span class="lineNum">    1880 </span>            : </a>
+<a name="1881"><span class="lineNum">    1881 </span><span class="lineNoCov">          0 :   dmax = std::abs(dx[0]);</span></a>
+<a name="1882"><span class="lineNum">    1882 </span>            :   idxmax = 1;</a>
+<a name="1883"><span class="lineNum">    1883 </span>            : </a>
+<a name="1884"><span class="lineNum">    1884 </span><span class="lineNoCov">          0 :   if(incx==1) {</span></a>
+<a name="1885"><span class="lineNum">    1885 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;n;i++) {</span></a>
+<a name="1886"><span class="lineNum">    1886 </span><span class="lineNoCov">          0 :       tmp = std::abs(dx[i]);</span></a>
+<a name="1887"><span class="lineNum">    1887 </span><span class="lineNoCov">          0 :       if(tmp&gt;dmax) {</span></a>
+<a name="1888"><span class="lineNum">    1888 </span>            :         dmax = tmp;</a>
+<a name="1889"><span class="lineNum">    1889 </span><span class="lineNoCov">          0 :         idxmax = i+1;</span></a>
+<a name="1890"><span class="lineNum">    1890 </span>            :       }</a>
+<a name="1891"><span class="lineNum">    1891 </span>            :     }</a>
+<a name="1892"><span class="lineNum">    1892 </span>            :   } else {</a>
+<a name="1893"><span class="lineNum">    1893 </span>            :     /* Non-unit increments */</a>
+<a name="1894"><span class="lineNum">    1894 </span>            :     ix = incx; /* this is really 0 + an increment */</a>
+<a name="1895"><span class="lineNum">    1895 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;n;i++,ix+=incx) {</span></a>
+<a name="1896"><span class="lineNum">    1896 </span><span class="lineNoCov">          0 :       tmp = std::abs(dx[ix]);</span></a>
+<a name="1897"><span class="lineNum">    1897 </span><span class="lineNoCov">          0 :       if(tmp&gt;dmax) {</span></a>
+<a name="1898"><span class="lineNum">    1898 </span>            :         dmax = tmp;</a>
+<a name="1899"><span class="lineNum">    1899 </span><span class="lineNoCov">          0 :         idxmax = ix+1;</span></a>
+<a name="1900"><span class="lineNum">    1900 </span>            :       }</a>
+<a name="1901"><span class="lineNum">    1901 </span>            :     }    </a>
+<a name="1902"><span class="lineNum">    1902 </span>            :   }</a>
+<a name="1903"><span class="lineNum">    1903 </span>            :   return idxmax;</a>
+<a name="1904"><span class="lineNum">    1904 </span>            : }</a>
+<a name="1905"><span class="lineNum">    1905 </span>            : }</a>
+<a name="1906"><span class="lineNum">    1906 </span>            : }</a>
+<a name="1907"><span class="lineNum">    1907 </span>            : #include &lt;cmath&gt;</a>
+<a name="1908"><span class="lineNum">    1908 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1909"><span class="lineNum">    1909 </span>            : </a>
+<a name="1910"><span class="lineNum">    1910 </span>            : namespace PLMD{</a>
+<a name="1911"><span class="lineNum">    1911 </span>            : namespace blas{</a>
+<a name="1912"><span class="lineNum">    1912 </span>            : float</a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sasum,SASUM)(int *n__, </span></a>
+<a name="1914"><span class="lineNum">    1914 </span>            :        float *dx, </a>
+<a name="1915"><span class="lineNum">    1915 </span>            :        int *incx__)</a>
+<a name="1916"><span class="lineNum">    1916 </span>            : {</a>
+<a name="1917"><span class="lineNum">    1917 </span>            :     int i__1, i__2;</a>
+<a name="1918"><span class="lineNum">    1918 </span>            :     </a>
+<a name="1919"><span class="lineNum">    1919 </span>            :     int i__, m, mp1;</a>
+<a name="1920"><span class="lineNum">    1920 </span>            :     float dtemp;</a>
+<a name="1921"><span class="lineNum">    1921 </span>            :     int nincx;</a>
+<a name="1922"><span class="lineNum">    1922 </span>            :     </a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="1925"><span class="lineNum">    1925 </span>            :     </a>
+<a name="1926"><span class="lineNum">    1926 </span>            :     </a>
+<a name="1927"><span class="lineNum">    1927 </span><span class="lineNoCov">          0 :     --dx;</span></a>
+<a name="1928"><span class="lineNum">    1928 </span>            :     </a>
+<a name="1929"><span class="lineNum">    1929 </span>            :     dtemp = 0.;</a>
+<a name="1930"><span class="lineNum">    1930 </span><span class="lineNoCov">          0 :     if (n &lt;= 0 || incx &lt;= 0) {</span></a>
+<a name="1931"><span class="lineNum">    1931 </span>            :         return 0.0;</a>
+<a name="1932"><span class="lineNum">    1932 </span>            :     }</a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineNoCov">          0 :     if (incx != 1) {</span></a>
+<a name="1934"><span class="lineNum">    1934 </span><span class="lineNoCov">          0 :         nincx = n * incx;</span></a>
+<a name="1935"><span class="lineNum">    1935 </span>            :         i__1 = nincx;</a>
+<a name="1936"><span class="lineNum">    1936 </span>            :         i__2 = incx;</a>
+<a name="1937"><span class="lineNum">    1937 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="1938"><span class="lineNum">    1938 </span><span class="lineNoCov">          0 :             dtemp += std::abs(dx[i__]);</span></a>
+<a name="1939"><span class="lineNum">    1939 </span>            :         }</a>
+<a name="1940"><span class="lineNum">    1940 </span>            :         return dtemp;</a>
+<a name="1941"><span class="lineNum">    1941 </span>            :     }</a>
+<a name="1942"><span class="lineNum">    1942 </span>            :     </a>
+<a name="1943"><span class="lineNum">    1943 </span><span class="lineNoCov">          0 :     m = n % 6;</span></a>
+<a name="1944"><span class="lineNum">    1944 </span><span class="lineNoCov">          0 :     if (m != 0) {</span></a>
+<a name="1945"><span class="lineNum">    1945 </span>            :         i__2 = m;</a>
+<a name="1946"><span class="lineNum">    1946 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="1947"><span class="lineNum">    1947 </span><span class="lineNoCov">          0 :             dtemp += std::abs(dx[i__]);</span></a>
+<a name="1948"><span class="lineNum">    1948 </span>            :         }</a>
+<a name="1949"><span class="lineNum">    1949 </span><span class="lineNoCov">          0 :         if (n &lt; 6) {</span></a>
+<a name="1950"><span class="lineNum">    1950 </span>            :             return dtemp;</a>
+<a name="1951"><span class="lineNum">    1951 </span>            :         }</a>
+<a name="1952"><span class="lineNum">    1952 </span>            :     }</a>
+<a name="1953"><span class="lineNum">    1953 </span><span class="lineNoCov">          0 :     mp1 = m + 1;</span></a>
+<a name="1954"><span class="lineNum">    1954 </span>            :     i__2 = n;</a>
+<a name="1955"><span class="lineNum">    1955 </span><span class="lineNoCov">          0 :     for (i__ = mp1; i__ &lt;= i__2; i__ += 6) {</span></a>
+<a name="1956"><span class="lineNum">    1956 </span><span class="lineNoCov">          0 :         dtemp = dtemp + std::abs(dx[i__]) + std::abs(dx[i__ + 1]) + </span></a>
+<a name="1957"><span class="lineNum">    1957 </span><span class="lineNoCov">          0 :         std::abs(dx[i__ + 2]) + std::abs(dx[i__+ 3]) + std::abs(dx[i__ + 4]) +</span></a>
+<a name="1958"><span class="lineNum">    1958 </span><span class="lineNoCov">          0 :         std::abs(dx[i__ + 5]);</span></a>
+<a name="1959"><span class="lineNum">    1959 </span>            :     }</a>
+<a name="1960"><span class="lineNum">    1960 </span>            :     return dtemp;</a>
+<a name="1961"><span class="lineNum">    1961 </span>            : }</a>
+<a name="1962"><span class="lineNum">    1962 </span>            : </a>
+<a name="1963"><span class="lineNum">    1963 </span>            : </a>
+<a name="1964"><span class="lineNum">    1964 </span>            : }</a>
+<a name="1965"><span class="lineNum">    1965 </span>            : }</a>
+<a name="1966"><span class="lineNum">    1966 </span>            : #include &quot;blas.h&quot;</a>
+<a name="1967"><span class="lineNum">    1967 </span>            : </a>
+<a name="1968"><span class="lineNum">    1968 </span>            : </a>
+<a name="1969"><span class="lineNum">    1969 </span>            : namespace PLMD{</a>
+<a name="1970"><span class="lineNum">    1970 </span>            : namespace blas{</a>
+<a name="1971"><span class="lineNum">    1971 </span>            : void</a>
+<a name="1972"><span class="lineNum">    1972 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(int   *   n_arg,</span></a>
+<a name="1973"><span class="lineNum">    1973 </span>            :                       float *   da_arg,</a>
+<a name="1974"><span class="lineNum">    1974 </span>            :                       float *   dx,</a>
+<a name="1975"><span class="lineNum">    1975 </span>            :                       int *      incx_arg,</a>
+<a name="1976"><span class="lineNum">    1976 </span>            :                       float *   dy,</a>
+<a name="1977"><span class="lineNum">    1977 </span>            :                       int *      incy_arg)</a>
+<a name="1978"><span class="lineNum">    1978 </span>            : {</a>
+<a name="1979"><span class="lineNum">    1979 </span>            :   int i,ix,iy;</a>
+<a name="1980"><span class="lineNum">    1980 </span><span class="lineNoCov">          0 :   int n=*n_arg;</span></a>
+<a name="1981"><span class="lineNum">    1981 </span><span class="lineNoCov">          0 :   float da=*da_arg;</span></a>
+<a name="1982"><span class="lineNum">    1982 </span><span class="lineNoCov">          0 :   int incx = *incx_arg;</span></a>
+<a name="1983"><span class="lineNum">    1983 </span><span class="lineNoCov">          0 :   int incy = *incy_arg;</span></a>
+<a name="1984"><span class="lineNum">    1984 </span>            : </a>
+<a name="1985"><span class="lineNum">    1985 </span><span class="lineNoCov">          0 :   if (n&lt;=0)</span></a>
+<a name="1986"><span class="lineNum">    1986 </span>            :     return;</a>
+<a name="1987"><span class="lineNum">    1987 </span>            : </a>
+<a name="1988"><span class="lineNum">    1988 </span><span class="lineNoCov">          0 :   if(incx!=1 || incy!=1) {</span></a>
+<a name="1989"><span class="lineNum">    1989 </span>            :     ix = 0;</a>
+<a name="1990"><span class="lineNum">    1990 </span>            :     iy = 0;</a>
+<a name="1991"><span class="lineNum">    1991 </span><span class="lineNoCov">          0 :     if(incx&lt;0)</span></a>
+<a name="1992"><span class="lineNum">    1992 </span><span class="lineNoCov">          0 :       ix = (1-n)*incx;</span></a>
+<a name="1993"><span class="lineNum">    1993 </span><span class="lineNoCov">          0 :     if(incy&lt;0)</span></a>
+<a name="1994"><span class="lineNum">    1994 </span><span class="lineNoCov">          0 :       iy = (1-n)*incy;</span></a>
+<a name="1995"><span class="lineNum">    1995 </span>            :     </a>
+<a name="1996"><span class="lineNum">    1996 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) </span></a>
+<a name="1997"><span class="lineNum">    1997 </span><span class="lineNoCov">          0 :       dy[iy] += da*dx[ix];</span></a>
+<a name="1998"><span class="lineNum">    1998 </span>            : </a>
+<a name="1999"><span class="lineNum">    1999 </span>            :     return;</a>
+<a name="2000"><span class="lineNum">    2000 </span>            : </a>
+<a name="2001"><span class="lineNum">    2001 </span>            :   } else {</a>
+<a name="2002"><span class="lineNum">    2002 </span>            : </a>
+<a name="2003"><span class="lineNum">    2003 </span>            :     /* unroll */</a>
+<a name="2004"><span class="lineNum">    2004 </span>            :     </a>
+<a name="2005"><span class="lineNum">    2005 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;(n-4);i+=4) {</span></a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineNoCov">          0 :       dy[i]   += da*dx[i];</span></a>
+<a name="2007"><span class="lineNum">    2007 </span><span class="lineNoCov">          0 :       dy[i+1] += da*dx[i+1];</span></a>
+<a name="2008"><span class="lineNum">    2008 </span><span class="lineNoCov">          0 :       dy[i+2] += da*dx[i+2];</span></a>
+<a name="2009"><span class="lineNum">    2009 </span><span class="lineNoCov">          0 :       dy[i+3] += da*dx[i+3];</span></a>
+<a name="2010"><span class="lineNum">    2010 </span>            :     }</a>
+<a name="2011"><span class="lineNum">    2011 </span>            :     /* continue with current value of i */</a>
+<a name="2012"><span class="lineNum">    2012 </span><span class="lineNoCov">          0 :     for(;i&lt;n;i++)</span></a>
+<a name="2013"><span class="lineNum">    2013 </span><span class="lineNoCov">          0 :       dy[i]   += da*dx[i];</span></a>
+<a name="2014"><span class="lineNum">    2014 </span>            :   }</a>
+<a name="2015"><span class="lineNum">    2015 </span>            : }</a>
+<a name="2016"><span class="lineNum">    2016 </span>            : }</a>
+<a name="2017"><span class="lineNum">    2017 </span>            : }</a>
+<a name="2018"><span class="lineNum">    2018 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2019"><span class="lineNum">    2019 </span>            : </a>
+<a name="2020"><span class="lineNum">    2020 </span>            : namespace PLMD{</a>
+<a name="2021"><span class="lineNum">    2021 </span>            : namespace blas{</a>
+<a name="2022"><span class="lineNum">    2022 </span>            : void</a>
+<a name="2023"><span class="lineNum">    2023 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(int *n__,</span></a>
+<a name="2024"><span class="lineNum">    2024 </span>            :                       float *dx,</a>
+<a name="2025"><span class="lineNum">    2025 </span>            :                       int *incx__,</a>
+<a name="2026"><span class="lineNum">    2026 </span>            :                       float *dy,</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :                       int *incy__)</a>
+<a name="2028"><span class="lineNum">    2028 </span>            : {</a>
+<a name="2029"><span class="lineNum">    2029 </span>            :     int i,ix,iy;</a>
+<a name="2030"><span class="lineNum">    2030 </span>            : </a>
+<a name="2031"><span class="lineNum">    2031 </span><span class="lineNoCov">          0 :     int n= *n__;</span></a>
+<a name="2032"><span class="lineNum">    2032 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="2033"><span class="lineNum">    2033 </span><span class="lineNoCov">          0 :     int incy = *incy__;</span></a>
+<a name="2034"><span class="lineNum">    2034 </span>            :     </a>
+<a name="2035"><span class="lineNum">    2035 </span><span class="lineNoCov">          0 :     if(incx!=1 || incy!=1) </span></a>
+<a name="2036"><span class="lineNum">    2036 </span>            :     {</a>
+<a name="2037"><span class="lineNum">    2037 </span>            :         ix = 0;</a>
+<a name="2038"><span class="lineNum">    2038 </span>            :         iy = 0;</a>
+<a name="2039"><span class="lineNum">    2039 </span><span class="lineNoCov">          0 :         if(incx&lt;0)</span></a>
+<a name="2040"><span class="lineNum">    2040 </span><span class="lineNoCov">          0 :             ix = (1-n)*(incx);</span></a>
+<a name="2041"><span class="lineNum">    2041 </span><span class="lineNoCov">          0 :         if(incy&lt;0)</span></a>
+<a name="2042"><span class="lineNum">    2042 </span><span class="lineNoCov">          0 :             iy = (1-n)*(incy);</span></a>
+<a name="2043"><span class="lineNum">    2043 </span>            :         </a>
+<a name="2044"><span class="lineNum">    2044 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) </span></a>
+<a name="2045"><span class="lineNum">    2045 </span><span class="lineNoCov">          0 :             dy[iy] = dx[ix];</span></a>
+<a name="2046"><span class="lineNum">    2046 </span>            :         </a>
+<a name="2047"><span class="lineNum">    2047 </span>            :         return;</a>
+<a name="2048"><span class="lineNum">    2048 </span>            :         </a>
+<a name="2049"><span class="lineNum">    2049 </span>            :     } else {</a>
+<a name="2050"><span class="lineNum">    2050 </span>            :         </a>
+<a name="2051"><span class="lineNum">    2051 </span>            :         /* unroll */</a>
+<a name="2052"><span class="lineNum">    2052 </span>            :         </a>
+<a name="2053"><span class="lineNum">    2053 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;(n-8);i+=8) {</span></a>
+<a name="2054"><span class="lineNum">    2054 </span><span class="lineNoCov">          0 :             dy[i]   = dx[i];</span></a>
+<a name="2055"><span class="lineNum">    2055 </span><span class="lineNoCov">          0 :             dy[i+1] = dx[i+1];</span></a>
+<a name="2056"><span class="lineNum">    2056 </span><span class="lineNoCov">          0 :             dy[i+2] = dx[i+2];</span></a>
+<a name="2057"><span class="lineNum">    2057 </span><span class="lineNoCov">          0 :             dy[i+3] = dx[i+3];</span></a>
+<a name="2058"><span class="lineNum">    2058 </span><span class="lineNoCov">          0 :             dy[i+4] = dx[i+4];</span></a>
+<a name="2059"><span class="lineNum">    2059 </span><span class="lineNoCov">          0 :             dy[i+5] = dx[i+5];</span></a>
+<a name="2060"><span class="lineNum">    2060 </span><span class="lineNoCov">          0 :             dy[i+6] = dx[i+6];</span></a>
+<a name="2061"><span class="lineNum">    2061 </span><span class="lineNoCov">          0 :             dy[i+7] = dx[i+7];</span></a>
+<a name="2062"><span class="lineNum">    2062 </span>            :         }</a>
+<a name="2063"><span class="lineNum">    2063 </span>            :         /* continue with current value of i */</a>
+<a name="2064"><span class="lineNum">    2064 </span><span class="lineNoCov">          0 :         for(;i&lt;n;i++)</span></a>
+<a name="2065"><span class="lineNum">    2065 </span><span class="lineNoCov">          0 :             dy[i] = dx[i];</span></a>
+<a name="2066"><span class="lineNum">    2066 </span>            :     }</a>
+<a name="2067"><span class="lineNum">    2067 </span>            : }</a>
+<a name="2068"><span class="lineNum">    2068 </span>            : }</a>
+<a name="2069"><span class="lineNum">    2069 </span>            : }</a>
+<a name="2070"><span class="lineNum">    2070 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2071"><span class="lineNum">    2071 </span>            : </a>
+<a name="2072"><span class="lineNum">    2072 </span>            : </a>
+<a name="2073"><span class="lineNum">    2073 </span>            : namespace PLMD{</a>
+<a name="2074"><span class="lineNum">    2074 </span>            : namespace blas{</a>
+<a name="2075"><span class="lineNum">    2075 </span>            : float</a>
+<a name="2076"><span class="lineNum">    2076 </span><span class="lineCov">          1 : PLUMED_BLAS_F77_FUNC(sdot,SDOT)(int *n_arg,</span></a>
+<a name="2077"><span class="lineNum">    2077 </span>            :                     float *dx,</a>
+<a name="2078"><span class="lineNum">    2078 </span>            :                     int *incx_arg,</a>
+<a name="2079"><span class="lineNum">    2079 </span>            :                     float *dy,</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :                     int *incy_arg)</a>
+<a name="2081"><span class="lineNum">    2081 </span>            : {</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :     int i,ix,iy,m;</a>
+<a name="2083"><span class="lineNum">    2083 </span><span class="lineCov">          1 :     int n=*n_arg;</span></a>
+<a name="2084"><span class="lineNum">    2084 </span><span class="lineCov">          1 :     int incx = *incx_arg;</span></a>
+<a name="2085"><span class="lineNum">    2085 </span><span class="lineCov">          1 :     int incy = *incy_arg;</span></a>
+<a name="2086"><span class="lineNum">    2086 </span>            :     float t1;</a>
+<a name="2087"><span class="lineNum">    2087 </span>            :     </a>
+<a name="2088"><span class="lineNum">    2088 </span><span class="lineCov">          1 :     if(n&lt;=0)</span></a>
+<a name="2089"><span class="lineNum">    2089 </span>            :         return 0.0;</a>
+<a name="2090"><span class="lineNum">    2090 </span>            :     </a>
+<a name="2091"><span class="lineNum">    2091 </span>            :     t1 = 0.0;</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :     </a>
+<a name="2093"><span class="lineNum">    2093 </span><span class="lineCov">          1 :     if(incx!=1 || incy!=1) {</span></a>
+<a name="2094"><span class="lineNum">    2094 </span>            :         ix = 0;</a>
+<a name="2095"><span class="lineNum">    2095 </span>            :         iy = 0;</a>
+<a name="2096"><span class="lineNum">    2096 </span><span class="lineNoCov">          0 :         if(incx&lt;0)</span></a>
+<a name="2097"><span class="lineNum">    2097 </span><span class="lineNoCov">          0 :             ix = (1-n)*incx;</span></a>
+<a name="2098"><span class="lineNum">    2098 </span><span class="lineNoCov">          0 :         if(incy&lt;0)</span></a>
+<a name="2099"><span class="lineNum">    2099 </span><span class="lineNoCov">          0 :             iy = (1-n)*incy;</span></a>
+<a name="2100"><span class="lineNum">    2100 </span>            :         </a>
+<a name="2101"><span class="lineNum">    2101 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) </span></a>
+<a name="2102"><span class="lineNum">    2102 </span><span class="lineNoCov">          0 :             t1 += dx[ix] * dy[iy];</span></a>
+<a name="2103"><span class="lineNum">    2103 </span>            :         </a>
+<a name="2104"><span class="lineNum">    2104 </span>            :         return t1;</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :         </a>
+<a name="2106"><span class="lineNum">    2106 </span>            :     } else {</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :         </a>
+<a name="2108"><span class="lineNum">    2108 </span><span class="lineCov">          1 :         m = n%5;</span></a>
+<a name="2109"><span class="lineNum">    2109 </span>            :         </a>
+<a name="2110"><span class="lineNum">    2110 </span><span class="lineCov">          1 :         for(i=0;i&lt;m;i++)</span></a>
+<a name="2111"><span class="lineNum">    2111 </span><span class="lineNoCov">          0 :             t1 += dx[i] * dy[i];</span></a>
+<a name="2112"><span class="lineNum">    2112 </span>            :         </a>
+<a name="2113"><span class="lineNum">    2113 </span>            :         /* unroll */</a>
+<a name="2114"><span class="lineNum">    2114 </span><span class="lineCov">          2 :         for(i=m;i&lt;n;i+=5) </span></a>
+<a name="2115"><span class="lineNum">    2115 </span><span class="lineCov">          1 :             t1  =  t1 + dx[i] * dy[i]   </span></a>
+<a name="2116"><span class="lineNum">    2116 </span><span class="lineCov">          1 :                 +    dx[i+1] * dy[i+1] </span></a>
+<a name="2117"><span class="lineNum">    2117 </span><span class="lineCov">          1 :                 +    dx[i+2] * dy[i+2] </span></a>
+<a name="2118"><span class="lineNum">    2118 </span><span class="lineCov">          1 :                 +    dx[i+3] * dy[i+3]   </span></a>
+<a name="2119"><span class="lineNum">    2119 </span><span class="lineCov">          1 :                 +    dx[i+4] * dy[i+4];   </span></a>
+<a name="2120"><span class="lineNum">    2120 </span>            :         </a>
+<a name="2121"><span class="lineNum">    2121 </span>            :         return t1;</a>
+<a name="2122"><span class="lineNum">    2122 </span>            :     }</a>
+<a name="2123"><span class="lineNum">    2123 </span>            : }</a>
+<a name="2124"><span class="lineNum">    2124 </span>            : </a>
+<a name="2125"><span class="lineNum">    2125 </span>            : </a>
+<a name="2126"><span class="lineNum">    2126 </span>            : }</a>
+<a name="2127"><span class="lineNum">    2127 </span>            : }</a>
+<a name="2128"><span class="lineNum">    2128 </span>            : #include &lt;cctype&gt;</a>
+<a name="2129"><span class="lineNum">    2129 </span>            : #include &lt;cmath&gt;</a>
+<a name="2130"><span class="lineNum">    2130 </span>            : </a>
+<a name="2131"><span class="lineNum">    2131 </span>            : #include &quot;real.h&quot;</a>
+<a name="2132"><span class="lineNum">    2132 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2133"><span class="lineNum">    2133 </span>            : </a>
+<a name="2134"><span class="lineNum">    2134 </span>            : namespace PLMD{</a>
+<a name="2135"><span class="lineNum">    2135 </span>            : namespace blas{</a>
+<a name="2136"><span class="lineNum">    2136 </span>            : void</a>
+<a name="2137"><span class="lineNum">    2137 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(const char *transa,</span></a>
+<a name="2138"><span class="lineNum">    2138 </span>            :        const char *transb,</a>
+<a name="2139"><span class="lineNum">    2139 </span>            :        int *m__,</a>
+<a name="2140"><span class="lineNum">    2140 </span>            :        int *n__,</a>
+<a name="2141"><span class="lineNum">    2141 </span>            :        int *k__,</a>
+<a name="2142"><span class="lineNum">    2142 </span>            :        float *alpha__,</a>
+<a name="2143"><span class="lineNum">    2143 </span>            :        float *a,</a>
+<a name="2144"><span class="lineNum">    2144 </span>            :        int *lda__,</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :        float *b,</a>
+<a name="2146"><span class="lineNum">    2146 </span>            :        int *ldb__,</a>
+<a name="2147"><span class="lineNum">    2147 </span>            :        float *beta__,</a>
+<a name="2148"><span class="lineNum">    2148 </span>            :        float *c,</a>
+<a name="2149"><span class="lineNum">    2149 </span>            :        int *ldc__)</a>
+<a name="2150"><span class="lineNum">    2150 </span>            : {</a>
+<a name="2151"><span class="lineNum">    2151 </span><span class="lineNoCov">          0 :   const char tra=std::toupper(*transa);</span></a>
+<a name="2152"><span class="lineNum">    2152 </span><span class="lineNoCov">          0 :   const char trb=std::toupper(*transb);</span></a>
+<a name="2153"><span class="lineNum">    2153 </span>            :   float temp;</a>
+<a name="2154"><span class="lineNum">    2154 </span>            :   int i,j,l;</a>
+<a name="2155"><span class="lineNum">    2155 </span>            : </a>
+<a name="2156"><span class="lineNum">    2156 </span><span class="lineNoCov">          0 :   int m   = *m__;</span></a>
+<a name="2157"><span class="lineNum">    2157 </span><span class="lineNoCov">          0 :   int n   = *n__;</span></a>
+<a name="2158"><span class="lineNum">    2158 </span><span class="lineNoCov">          0 :   int k   = *k__;</span></a>
+<a name="2159"><span class="lineNum">    2159 </span><span class="lineNoCov">          0 :   int lda = *lda__;</span></a>
+<a name="2160"><span class="lineNum">    2160 </span><span class="lineNoCov">          0 :   int ldb = *ldb__;</span></a>
+<a name="2161"><span class="lineNum">    2161 </span><span class="lineNoCov">          0 :   int ldc = *ldc__;</span></a>
+<a name="2162"><span class="lineNum">    2162 </span>            :   </a>
+<a name="2163"><span class="lineNum">    2163 </span><span class="lineNoCov">          0 :   float alpha = *alpha__;</span></a>
+<a name="2164"><span class="lineNum">    2164 </span><span class="lineNoCov">          0 :   float beta  = *beta__;</span></a>
+<a name="2165"><span class="lineNum">    2165 </span>            :   </a>
+<a name="2166"><span class="lineNum">    2166 </span><span class="lineNoCov">          0 :   if(m==0 || n==0 || (( std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN || k==0) &amp;&amp; std::abs(beta-1.0)&lt;PLUMED_GMX_FLOAT_EPS))</span></a>
+<a name="2167"><span class="lineNum">    2167 </span>            :     return;</a>
+<a name="2168"><span class="lineNum">    2168 </span>            : </a>
+<a name="2169"><span class="lineNum">    2169 </span><span class="lineNoCov">          0 :   if(std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2170"><span class="lineNum">    2170 </span><span class="lineNoCov">          0 :     if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2171"><span class="lineNum">    2171 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++)</span></a>
+<a name="2172"><span class="lineNum">    2172 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++)</span></a>
+<a name="2173"><span class="lineNum">    2173 </span><span class="lineNoCov">          0 :           c[j*(ldc)+i] = 0.0;</span></a>
+<a name="2174"><span class="lineNum">    2174 </span>            :     } else {</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :       /* nonzero beta */</a>
+<a name="2176"><span class="lineNum">    2176 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++)</span></a>
+<a name="2177"><span class="lineNum">    2177 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++)</span></a>
+<a name="2178"><span class="lineNum">    2178 </span><span class="lineNoCov">          0 :           c[j*(ldc)+i] *= beta;</span></a>
+<a name="2179"><span class="lineNum">    2179 </span>            :     }</a>
+<a name="2180"><span class="lineNum">    2180 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="2181"><span class="lineNum">    2181 </span>            :   }</a>
+<a name="2182"><span class="lineNum">    2182 </span>            : </a>
+<a name="2183"><span class="lineNum">    2183 </span><span class="lineNoCov">          0 :   if(trb=='N') {</span></a>
+<a name="2184"><span class="lineNum">    2184 </span><span class="lineNoCov">          0 :     if(tra=='N') {</span></a>
+<a name="2185"><span class="lineNum">    2185 </span>            :       </a>
+<a name="2186"><span class="lineNum">    2186 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++) {</span></a>
+<a name="2187"><span class="lineNum">    2187 </span><span class="lineNoCov">          0 :         if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2188"><span class="lineNum">    2188 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="2189"><span class="lineNum">    2189 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = 0.0;</span></a>
+<a name="2190"><span class="lineNum">    2190 </span><span class="lineNoCov">          0 :         } else if(std::abs(beta-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="2191"><span class="lineNum">    2191 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="2192"><span class="lineNum">    2192 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] *= beta;</span></a>
+<a name="2193"><span class="lineNum">    2193 </span>            :         } </a>
+<a name="2194"><span class="lineNum">    2194 </span><span class="lineNoCov">          0 :         for(l=0;l&lt;k;l++) {</span></a>
+<a name="2195"><span class="lineNum">    2195 </span><span class="lineNoCov">          0 :           if( std::abs(b[ j*(ldb) + l ])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2196"><span class="lineNum">    2196 </span><span class="lineNoCov">          0 :             temp = alpha * b[ j*(ldb) + l ];</span></a>
+<a name="2197"><span class="lineNum">    2197 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="2198"><span class="lineNum">    2198 </span><span class="lineNoCov">          0 :               c[j*(ldc)+i] += temp * a[l*(lda)+i]; </span></a>
+<a name="2199"><span class="lineNum">    2199 </span>            :           }</a>
+<a name="2200"><span class="lineNum">    2200 </span>            :         }</a>
+<a name="2201"><span class="lineNum">    2201 </span>            :       }</a>
+<a name="2202"><span class="lineNum">    2202 </span>            :     } else {</a>
+<a name="2203"><span class="lineNum">    2203 </span>            :       /* transpose A, but not B */</a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++) {</span></a>
+<a name="2205"><span class="lineNum">    2205 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++) {</span></a>
+<a name="2206"><span class="lineNum">    2206 </span>            :           temp = 0.0;</a>
+<a name="2207"><span class="lineNum">    2207 </span><span class="lineNoCov">          0 :           for(l=0;l&lt;k;l++) </span></a>
+<a name="2208"><span class="lineNum">    2208 </span><span class="lineNoCov">          0 :             temp += a[i*(lda)+l] * b[j*(ldb)+l];</span></a>
+<a name="2209"><span class="lineNum">    2209 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="2210"><span class="lineNum">    2210 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp;</span></a>
+<a name="2211"><span class="lineNum">    2211 </span>            :           else</a>
+<a name="2212"><span class="lineNum">    2212 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp + beta * c[j*(ldc)+i];</span></a>
+<a name="2213"><span class="lineNum">    2213 </span>            :         }</a>
+<a name="2214"><span class="lineNum">    2214 </span>            :       }</a>
+<a name="2215"><span class="lineNum">    2215 </span>            :     }</a>
+<a name="2216"><span class="lineNum">    2216 </span>            :   } else {</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :     /* transpose B */</a>
+<a name="2218"><span class="lineNum">    2218 </span><span class="lineNoCov">          0 :     if(tra=='N') {</span></a>
+<a name="2219"><span class="lineNum">    2219 </span>            : </a>
+<a name="2220"><span class="lineNum">    2220 </span>            :       /* transpose B, but not A */</a>
+<a name="2221"><span class="lineNum">    2221 </span>            : </a>
+<a name="2222"><span class="lineNum">    2222 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;n;j++) {</span></a>
+<a name="2223"><span class="lineNum">    2223 </span><span class="lineNoCov">          0 :         if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2224"><span class="lineNum">    2224 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="2225"><span class="lineNum">    2225 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = 0.0;</span></a>
+<a name="2226"><span class="lineNum">    2226 </span><span class="lineNoCov">          0 :         } else if(std::abs(beta-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="2227"><span class="lineNum">    2227 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++)</span></a>
+<a name="2228"><span class="lineNum">    2228 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] *= beta;</span></a>
+<a name="2229"><span class="lineNum">    2229 </span>            :         } </a>
+<a name="2230"><span class="lineNum">    2230 </span><span class="lineNoCov">          0 :         for(l=0;l&lt;k;l++) {</span></a>
+<a name="2231"><span class="lineNum">    2231 </span><span class="lineNoCov">          0 :           if( std::abs(b[ l*(ldb) + j ])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2232"><span class="lineNum">    2232 </span><span class="lineNoCov">          0 :             temp = alpha * b[ l*(ldb) + j ];</span></a>
+<a name="2233"><span class="lineNum">    2233 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="2234"><span class="lineNum">    2234 </span><span class="lineNoCov">          0 :               c[j*(ldc)+i] += temp * a[l*(lda)+i]; </span></a>
+<a name="2235"><span class="lineNum">    2235 </span>            :           }</a>
+<a name="2236"><span class="lineNum">    2236 </span>            :         }</a>
+<a name="2237"><span class="lineNum">    2237 </span>            :       }</a>
+<a name="2238"><span class="lineNum">    2238 </span>            :  </a>
+<a name="2239"><span class="lineNum">    2239 </span>            :     } else {</a>
+<a name="2240"><span class="lineNum">    2240 </span>            :       /* Transpose both A and B */</a>
+<a name="2241"><span class="lineNum">    2241 </span><span class="lineNoCov">          0 :        for(j=0;j&lt;n;j++) {</span></a>
+<a name="2242"><span class="lineNum">    2242 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;m;i++) {</span></a>
+<a name="2243"><span class="lineNum">    2243 </span>            :           temp = 0.0;</a>
+<a name="2244"><span class="lineNum">    2244 </span><span class="lineNoCov">          0 :           for(l=0;l&lt;k;l++) </span></a>
+<a name="2245"><span class="lineNum">    2245 </span><span class="lineNoCov">          0 :             temp += a[i*(lda)+l] * b[l*(ldb)+j];</span></a>
+<a name="2246"><span class="lineNum">    2246 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="2247"><span class="lineNum">    2247 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp;</span></a>
+<a name="2248"><span class="lineNum">    2248 </span>            :           else</a>
+<a name="2249"><span class="lineNum">    2249 </span><span class="lineNoCov">          0 :             c[j*(ldc)+i] = alpha * temp + beta * c[j*(ldc)+i];</span></a>
+<a name="2250"><span class="lineNum">    2250 </span>            :         }</a>
+<a name="2251"><span class="lineNum">    2251 </span>            :        }</a>
+<a name="2252"><span class="lineNum">    2252 </span>            :     }</a>
+<a name="2253"><span class="lineNum">    2253 </span>            :   }</a>
+<a name="2254"><span class="lineNum">    2254 </span>            : }</a>
+<a name="2255"><span class="lineNum">    2255 </span>            : }</a>
+<a name="2256"><span class="lineNum">    2256 </span>            : }</a>
+<a name="2257"><span class="lineNum">    2257 </span>            : #include &lt;cctype&gt;</a>
+<a name="2258"><span class="lineNum">    2258 </span>            : #include &lt;cmath&gt;</a>
+<a name="2259"><span class="lineNum">    2259 </span>            : </a>
+<a name="2260"><span class="lineNum">    2260 </span>            : #include &quot;real.h&quot;</a>
+<a name="2261"><span class="lineNum">    2261 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2262"><span class="lineNum">    2262 </span>            : </a>
+<a name="2263"><span class="lineNum">    2263 </span>            : namespace PLMD{</a>
+<a name="2264"><span class="lineNum">    2264 </span>            : namespace blas{</a>
+<a name="2265"><span class="lineNum">    2265 </span>            : void</a>
+<a name="2266"><span class="lineNum">    2266 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(const char *trans, </span></a>
+<a name="2267"><span class="lineNum">    2267 </span>            :                       int *m__,</a>
+<a name="2268"><span class="lineNum">    2268 </span>            :                       int *n__,</a>
+<a name="2269"><span class="lineNum">    2269 </span>            :                       float *alpha__,</a>
+<a name="2270"><span class="lineNum">    2270 </span>            :                       float *a,</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :                       int *lda__,</a>
+<a name="2272"><span class="lineNum">    2272 </span>            :                       float *x,</a>
+<a name="2273"><span class="lineNum">    2273 </span>            :                       int *incx__,</a>
+<a name="2274"><span class="lineNum">    2274 </span>            :                       float *beta__,</a>
+<a name="2275"><span class="lineNum">    2275 </span>            :                       float *y,</a>
+<a name="2276"><span class="lineNum">    2276 </span>            :                       int *incy__)</a>
+<a name="2277"><span class="lineNum">    2277 </span>            : {</a>
+<a name="2278"><span class="lineNum">    2278 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*trans);</span></a>
+<a name="2279"><span class="lineNum">    2279 </span>            :   int lenx,leny,kx,ky;</a>
+<a name="2280"><span class="lineNum">    2280 </span>            :   int i,j,jx,jy,ix,iy;</a>
+<a name="2281"><span class="lineNum">    2281 </span>            :   float temp;</a>
+<a name="2282"><span class="lineNum">    2282 </span>            : </a>
+<a name="2283"><span class="lineNum">    2283 </span><span class="lineNoCov">          0 :   int m = *m__;</span></a>
+<a name="2284"><span class="lineNum">    2284 </span><span class="lineNoCov">          0 :   int n = *n__;</span></a>
+<a name="2285"><span class="lineNum">    2285 </span><span class="lineNoCov">          0 :   float alpha = *alpha__;</span></a>
+<a name="2286"><span class="lineNum">    2286 </span><span class="lineNoCov">          0 :   float beta = *beta__;</span></a>
+<a name="2287"><span class="lineNum">    2287 </span><span class="lineNoCov">          0 :   int incx = *incx__;</span></a>
+<a name="2288"><span class="lineNum">    2288 </span><span class="lineNoCov">          0 :   int incy = *incy__;</span></a>
+<a name="2289"><span class="lineNum">    2289 </span><span class="lineNoCov">          0 :   int lda = *lda__;</span></a>
+<a name="2290"><span class="lineNum">    2290 </span>            :   </a>
+<a name="2291"><span class="lineNum">    2291 </span><span class="lineNoCov">          0 :   if(n&lt;=0 || m&lt;=0 || (std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN &amp;&amp; std::abs(beta-1.0)&lt;PLUMED_GMX_FLOAT_EPS))</span></a>
+<a name="2292"><span class="lineNum">    2292 </span>            :     return;</a>
+<a name="2293"><span class="lineNum">    2293 </span>            : </a>
+<a name="2294"><span class="lineNum">    2294 </span><span class="lineNoCov">          0 :   if(ch=='N') {</span></a>
+<a name="2295"><span class="lineNum">    2295 </span>            :     lenx = n;</a>
+<a name="2296"><span class="lineNum">    2296 </span>            :     leny = m;</a>
+<a name="2297"><span class="lineNum">    2297 </span>            :   } else {</a>
+<a name="2298"><span class="lineNum">    2298 </span>            :     lenx = m;</a>
+<a name="2299"><span class="lineNum">    2299 </span>            :     leny = n;</a>
+<a name="2300"><span class="lineNum">    2300 </span>            :   }</a>
+<a name="2301"><span class="lineNum">    2301 </span>            :   </a>
+<a name="2302"><span class="lineNum">    2302 </span><span class="lineNoCov">          0 :    if(incx&gt;0)</span></a>
+<a name="2303"><span class="lineNum">    2303 </span>            :     kx = 1;</a>
+<a name="2304"><span class="lineNum">    2304 </span>            :   else</a>
+<a name="2305"><span class="lineNum">    2305 </span><span class="lineNoCov">          0 :     kx = 1 - (lenx -1)*(incx);</span></a>
+<a name="2306"><span class="lineNum">    2306 </span>            : </a>
+<a name="2307"><span class="lineNum">    2307 </span><span class="lineNoCov">          0 :   if(incy&gt;0)</span></a>
+<a name="2308"><span class="lineNum">    2308 </span>            :     ky = 1;</a>
+<a name="2309"><span class="lineNum">    2309 </span>            :   else</a>
+<a name="2310"><span class="lineNum">    2310 </span><span class="lineNoCov">          0 :     ky = 1 - (leny -1)*(incy);</span></a>
+<a name="2311"><span class="lineNum">    2311 </span>            :  </a>
+<a name="2312"><span class="lineNum">    2312 </span><span class="lineNoCov">          0 :   if(std::abs(beta-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="2313"><span class="lineNum">    2313 </span><span class="lineNoCov">          0 :     if(incy==1) {</span></a>
+<a name="2314"><span class="lineNum">    2314 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="2315"><span class="lineNum">    2315 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++)</span></a>
+<a name="2316"><span class="lineNum">    2316 </span><span class="lineNoCov">          0 :           y[i] = 0.0;</span></a>
+<a name="2317"><span class="lineNum">    2317 </span>            :       else</a>
+<a name="2318"><span class="lineNum">    2318 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++)</span></a>
+<a name="2319"><span class="lineNum">    2319 </span><span class="lineNoCov">          0 :           y[i] *= beta;</span></a>
+<a name="2320"><span class="lineNum">    2320 </span>            :     } else {</a>
+<a name="2321"><span class="lineNum">    2321 </span>            :       /* non-unit incr. */</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :       iy = ky;</a>
+<a name="2323"><span class="lineNum">    2323 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="2324"><span class="lineNum">    2324 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++,iy+=incy)</span></a>
+<a name="2325"><span class="lineNum">    2325 </span><span class="lineNoCov">          0 :           y[iy] = 0.0;</span></a>
+<a name="2326"><span class="lineNum">    2326 </span>            :       else</a>
+<a name="2327"><span class="lineNum">    2327 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;leny;i++,iy+=incy)</span></a>
+<a name="2328"><span class="lineNum">    2328 </span><span class="lineNoCov">          0 :           y[iy] *= beta;</span></a>
+<a name="2329"><span class="lineNum">    2329 </span>            :     }</a>
+<a name="2330"><span class="lineNum">    2330 </span>            :   }</a>
+<a name="2331"><span class="lineNum">    2331 </span>            :   </a>
+<a name="2332"><span class="lineNum">    2332 </span><span class="lineNoCov">          0 :   if(std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="2333"><span class="lineNum">    2333 </span>            :     return;</a>
+<a name="2334"><span class="lineNum">    2334 </span>            :   </a>
+<a name="2335"><span class="lineNum">    2335 </span><span class="lineNoCov">          0 :   if(ch=='N') {</span></a>
+<a name="2336"><span class="lineNum">    2336 </span>            :     jx = kx;</a>
+<a name="2337"><span class="lineNum">    2337 </span><span class="lineNoCov">          0 :     if(incy==1) {</span></a>
+<a name="2338"><span class="lineNum">    2338 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++,jx+=incx) </span></a>
+<a name="2339"><span class="lineNum">    2339 </span><span class="lineNoCov">          0 :         if( std::abs(x[jx-1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2340"><span class="lineNum">    2340 </span><span class="lineNoCov">          0 :           temp = alpha * x[jx-1];</span></a>
+<a name="2341"><span class="lineNum">    2341 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=m;i++)</span></a>
+<a name="2342"><span class="lineNum">    2342 </span><span class="lineNoCov">          0 :             y[i-1] += temp * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="2343"><span class="lineNum">    2343 </span>            :         }</a>
+<a name="2344"><span class="lineNum">    2344 </span>            :     } else {</a>
+<a name="2345"><span class="lineNum">    2345 </span>            :       /* non-unit y incr. */</a>
+<a name="2346"><span class="lineNum">    2346 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++,jx+=incx) </span></a>
+<a name="2347"><span class="lineNum">    2347 </span><span class="lineNoCov">          0 :         if( std::abs(x[jx-1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2348"><span class="lineNum">    2348 </span><span class="lineNoCov">          0 :           temp = alpha * x[jx-1];</span></a>
+<a name="2349"><span class="lineNum">    2349 </span>            :           iy = ky;</a>
+<a name="2350"><span class="lineNum">    2350 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=m;i++,iy+=incy)</span></a>
+<a name="2351"><span class="lineNum">    2351 </span><span class="lineNoCov">          0 :             y[iy-1] += temp * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="2352"><span class="lineNum">    2352 </span>            :         }</a>
+<a name="2353"><span class="lineNum">    2353 </span>            :     }</a>
+<a name="2354"><span class="lineNum">    2354 </span>            :   } else {</a>
+<a name="2355"><span class="lineNum">    2355 </span>            :     /* transpose */</a>
+<a name="2356"><span class="lineNum">    2356 </span>            :     jy = ky;</a>
+<a name="2357"><span class="lineNum">    2357 </span><span class="lineNoCov">          0 :     if(incx==1) {</span></a>
+<a name="2358"><span class="lineNum">    2358 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++,jy+=incy) {</span></a>
+<a name="2359"><span class="lineNum">    2359 </span>            :         temp = 0.0;</a>
+<a name="2360"><span class="lineNum">    2360 </span><span class="lineNoCov">          0 :         for(i=1;i&lt;=m;i++)</span></a>
+<a name="2361"><span class="lineNum">    2361 </span><span class="lineNoCov">          0 :           temp += a[(j-1)*(lda)+(i-1)] * x[i-1];</span></a>
+<a name="2362"><span class="lineNum">    2362 </span><span class="lineNoCov">          0 :         y[jy-1] += alpha * temp;</span></a>
+<a name="2363"><span class="lineNum">    2363 </span>            :       }</a>
+<a name="2364"><span class="lineNum">    2364 </span>            :     } else {</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :       /* non-unit y incr. */</a>
+<a name="2366"><span class="lineNum">    2366 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++,jy+=incy) {</span></a>
+<a name="2367"><span class="lineNum">    2367 </span>            :         temp = 0.0;</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :         ix = kx;</a>
+<a name="2369"><span class="lineNum">    2369 </span><span class="lineNoCov">          0 :         for(i=1;i&lt;=m;i++,ix+=incx)</span></a>
+<a name="2370"><span class="lineNum">    2370 </span><span class="lineNoCov">          0 :           temp += a[(j-1)*(lda)+(i-1)] * x[ix-1];</span></a>
+<a name="2371"><span class="lineNum">    2371 </span><span class="lineNoCov">          0 :         y[jy-1] += alpha * temp;</span></a>
+<a name="2372"><span class="lineNum">    2372 </span>            :       }</a>
+<a name="2373"><span class="lineNum">    2373 </span>            :     }</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :   }</a>
+<a name="2375"><span class="lineNum">    2375 </span>            : } </a>
+<a name="2376"><span class="lineNum">    2376 </span>            :    </a>
+<a name="2377"><span class="lineNum">    2377 </span>            : }</a>
+<a name="2378"><span class="lineNum">    2378 </span>            : }</a>
+<a name="2379"><span class="lineNum">    2379 </span>            : #include &lt;cmath&gt;</a>
+<a name="2380"><span class="lineNum">    2380 </span>            : </a>
+<a name="2381"><span class="lineNum">    2381 </span>            : #include &quot;real.h&quot;</a>
+<a name="2382"><span class="lineNum">    2382 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2383"><span class="lineNum">    2383 </span>            : </a>
+<a name="2384"><span class="lineNum">    2384 </span>            : namespace PLMD{</a>
+<a name="2385"><span class="lineNum">    2385 </span>            : namespace blas{</a>
+<a name="2386"><span class="lineNum">    2386 </span>            : void</a>
+<a name="2387"><span class="lineNum">    2387 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sger,SGER)(int *m__,</span></a>
+<a name="2388"><span class="lineNum">    2388 </span>            :                     int *n__,</a>
+<a name="2389"><span class="lineNum">    2389 </span>            :                     float *alpha__,</a>
+<a name="2390"><span class="lineNum">    2390 </span>            :                     float *x,</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :                     int *incx__,</a>
+<a name="2392"><span class="lineNum">    2392 </span>            :                     float *y,</a>
+<a name="2393"><span class="lineNum">    2393 </span>            :                     int *incy__,</a>
+<a name="2394"><span class="lineNum">    2394 </span>            :                     float *a,</a>
+<a name="2395"><span class="lineNum">    2395 </span>            :                     int *lda__)</a>
+<a name="2396"><span class="lineNum">    2396 </span>            : {</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :     int ix,kx,jy;</a>
+<a name="2398"><span class="lineNum">    2398 </span>            :     int i,j;</a>
+<a name="2399"><span class="lineNum">    2399 </span>            :     float temp;</a>
+<a name="2400"><span class="lineNum">    2400 </span>            :     </a>
+<a name="2401"><span class="lineNum">    2401 </span><span class="lineNoCov">          0 :     int m = *m__;</span></a>
+<a name="2402"><span class="lineNum">    2402 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="2403"><span class="lineNum">    2403 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="2404"><span class="lineNum">    2404 </span><span class="lineNoCov">          0 :     int incy = *incy__;</span></a>
+<a name="2405"><span class="lineNum">    2405 </span><span class="lineNoCov">          0 :     int lda = *lda__;</span></a>
+<a name="2406"><span class="lineNum">    2406 </span><span class="lineNoCov">          0 :     float alpha = *alpha__;</span></a>
+<a name="2407"><span class="lineNum">    2407 </span>            :     </a>
+<a name="2408"><span class="lineNum">    2408 </span><span class="lineNoCov">          0 :     if(m&lt;=0 || n&lt;=0 || std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="2409"><span class="lineNum">    2409 </span>            :         return;</a>
+<a name="2410"><span class="lineNum">    2410 </span>            :     </a>
+<a name="2411"><span class="lineNum">    2411 </span><span class="lineNoCov">          0 :     if(incy&gt;0)</span></a>
+<a name="2412"><span class="lineNum">    2412 </span>            :         jy = 0;</a>
+<a name="2413"><span class="lineNum">    2413 </span>            :     else</a>
+<a name="2414"><span class="lineNum">    2414 </span><span class="lineNoCov">          0 :         jy = incy * (1 - n);</span></a>
+<a name="2415"><span class="lineNum">    2415 </span>            :     </a>
+<a name="2416"><span class="lineNum">    2416 </span><span class="lineNoCov">          0 :     if(incx==1) {</span></a>
+<a name="2417"><span class="lineNum">    2417 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++,jy+=incy)</span></a>
+<a name="2418"><span class="lineNum">    2418 </span><span class="lineNoCov">          0 :             if(std::abs(y[jy])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2419"><span class="lineNum">    2419 </span><span class="lineNoCov">          0 :                 temp = alpha * y[jy];</span></a>
+<a name="2420"><span class="lineNum">    2420 </span><span class="lineNoCov">          0 :                 for(i=0;i&lt;m;i++)</span></a>
+<a name="2421"><span class="lineNum">    2421 </span><span class="lineNoCov">          0 :                     a[j*(lda)+i] += temp*x[i];</span></a>
+<a name="2422"><span class="lineNum">    2422 </span>            :             }</a>
+<a name="2423"><span class="lineNum">    2423 </span>            :     } else {</a>
+<a name="2424"><span class="lineNum">    2424 </span>            :         /* non-unit incx */</a>
+<a name="2425"><span class="lineNum">    2425 </span><span class="lineNoCov">          0 :         if(incx&gt;0) </span></a>
+<a name="2426"><span class="lineNum">    2426 </span>            :             kx = 0;</a>
+<a name="2427"><span class="lineNum">    2427 </span>            :         else</a>
+<a name="2428"><span class="lineNum">    2428 </span><span class="lineNoCov">          0 :             kx = incx * (1 - m);</span></a>
+<a name="2429"><span class="lineNum">    2429 </span>            :         </a>
+<a name="2430"><span class="lineNum">    2430 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++,jy+=incy) {</span></a>
+<a name="2431"><span class="lineNum">    2431 </span><span class="lineNoCov">          0 :             if(std::abs(y[jy])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2432"><span class="lineNum">    2432 </span><span class="lineNoCov">          0 :                 temp = alpha * y[jy];</span></a>
+<a name="2433"><span class="lineNum">    2433 </span>            :                 ix = kx;</a>
+<a name="2434"><span class="lineNum">    2434 </span><span class="lineNoCov">          0 :                 for(i=0;i&lt;m;i++,ix+=incx)</span></a>
+<a name="2435"><span class="lineNum">    2435 </span><span class="lineNoCov">          0 :                     a[j*(lda)+i] += temp*x[ix];</span></a>
+<a name="2436"><span class="lineNum">    2436 </span>            :             }</a>
+<a name="2437"><span class="lineNum">    2437 </span>            :         }</a>
+<a name="2438"><span class="lineNum">    2438 </span>            :     }</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :         return;</a>
+<a name="2440"><span class="lineNum">    2440 </span>            : }</a>
+<a name="2441"><span class="lineNum">    2441 </span>            : }</a>
+<a name="2442"><span class="lineNum">    2442 </span>            : }</a>
+<a name="2443"><span class="lineNum">    2443 </span>            : #include &lt;cmath&gt;</a>
+<a name="2444"><span class="lineNum">    2444 </span>            : </a>
+<a name="2445"><span class="lineNum">    2445 </span>            : </a>
+<a name="2446"><span class="lineNum">    2446 </span>            : #include &quot;real.h&quot;</a>
+<a name="2447"><span class="lineNum">    2447 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2448"><span class="lineNum">    2448 </span>            : </a>
+<a name="2449"><span class="lineNum">    2449 </span>            : namespace PLMD{</a>
+<a name="2450"><span class="lineNum">    2450 </span>            : namespace blas{</a>
+<a name="2451"><span class="lineNum">    2451 </span>            : float</a>
+<a name="2452"><span class="lineNum">    2452 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(int  *     n__,</span></a>
+<a name="2453"><span class="lineNum">    2453 </span>            :                       float *    x,</a>
+<a name="2454"><span class="lineNum">    2454 </span>            :                       int    *    incx__)</a>
+<a name="2455"><span class="lineNum">    2455 </span>            : {</a>
+<a name="2456"><span class="lineNum">    2456 </span>            :     int ix,max_ix;</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :     float ssq,scale,absxi,t;</a>
+<a name="2458"><span class="lineNum">    2458 </span>            :     </a>
+<a name="2459"><span class="lineNum">    2459 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="2460"><span class="lineNum">    2460 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="2461"><span class="lineNum">    2461 </span>            :     </a>
+<a name="2462"><span class="lineNum">    2462 </span><span class="lineNoCov">          0 :     if(n&lt;1 || incx&lt;1)</span></a>
+<a name="2463"><span class="lineNum">    2463 </span>            :         return 0;</a>
+<a name="2464"><span class="lineNum">    2464 </span><span class="lineNoCov">          0 :     else if (n==1) {</span></a>
+<a name="2465"><span class="lineNum">    2465 </span><span class="lineNoCov">          0 :         t = x[0];</span></a>
+<a name="2466"><span class="lineNum">    2466 </span><span class="lineNoCov">          0 :         if(t&gt;=0)</span></a>
+<a name="2467"><span class="lineNum">    2467 </span>            :             return t;</a>
+<a name="2468"><span class="lineNum">    2468 </span>            :         else </a>
+<a name="2469"><span class="lineNum">    2469 </span><span class="lineNoCov">          0 :             return -t;</span></a>
+<a name="2470"><span class="lineNum">    2470 </span>            :     }</a>
+<a name="2471"><span class="lineNum">    2471 </span>            :     </a>
+<a name="2472"><span class="lineNum">    2472 </span>            :     scale = 0.0;</a>
+<a name="2473"><span class="lineNum">    2473 </span>            :     ssq   = 1.0;</a>
+<a name="2474"><span class="lineNum">    2474 </span>            :     </a>
+<a name="2475"><span class="lineNum">    2475 </span><span class="lineNoCov">          0 :     max_ix = 1+(n-1)*(incx);</span></a>
+<a name="2476"><span class="lineNum">    2476 </span><span class="lineNoCov">          0 :     for(ix=1;ix&lt;=max_ix;ix+=incx) {</span></a>
+<a name="2477"><span class="lineNum">    2477 </span><span class="lineNoCov">          0 :         t = x[ix-1];</span></a>
+<a name="2478"><span class="lineNum">    2478 </span><span class="lineNoCov">          0 :         if(std::abs(t)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2479"><span class="lineNum">    2479 </span><span class="lineNoCov">          0 :             absxi = (t&gt;=0) ? t : (-t);</span></a>
+<a name="2480"><span class="lineNum">    2480 </span><span class="lineNoCov">          0 :             if(scale&lt;absxi) {</span></a>
+<a name="2481"><span class="lineNum">    2481 </span><span class="lineNoCov">          0 :                 t = scale/absxi;</span></a>
+<a name="2482"><span class="lineNum">    2482 </span><span class="lineNoCov">          0 :                 t = t*t;</span></a>
+<a name="2483"><span class="lineNum">    2483 </span><span class="lineNoCov">          0 :                 ssq = ssq*t + 1.0;</span></a>
+<a name="2484"><span class="lineNum">    2484 </span>            :                 scale = absxi;</a>
+<a name="2485"><span class="lineNum">    2485 </span>            :             } else {</a>
+<a name="2486"><span class="lineNum">    2486 </span><span class="lineNoCov">          0 :                 t = absxi/scale;</span></a>
+<a name="2487"><span class="lineNum">    2487 </span><span class="lineNoCov">          0 :                 ssq += t*t;</span></a>
+<a name="2488"><span class="lineNum">    2488 </span>            :             }</a>
+<a name="2489"><span class="lineNum">    2489 </span>            :         }</a>
+<a name="2490"><span class="lineNum">    2490 </span>            :     }</a>
+<a name="2491"><span class="lineNum">    2491 </span><span class="lineNoCov">          0 :     return scale*std::sqrt(ssq);</span></a>
+<a name="2492"><span class="lineNum">    2492 </span>            :     </a>
+<a name="2493"><span class="lineNum">    2493 </span>            : }</a>
+<a name="2494"><span class="lineNum">    2494 </span>            : </a>
+<a name="2495"><span class="lineNum">    2495 </span>            : </a>
+<a name="2496"><span class="lineNum">    2496 </span>            :  </a>
+<a name="2497"><span class="lineNum">    2497 </span>            : }</a>
+<a name="2498"><span class="lineNum">    2498 </span>            : }</a>
+<a name="2499"><span class="lineNum">    2499 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2500"><span class="lineNum">    2500 </span>            : </a>
+<a name="2501"><span class="lineNum">    2501 </span>            : namespace PLMD{</a>
+<a name="2502"><span class="lineNum">    2502 </span>            : namespace blas{</a>
+<a name="2503"><span class="lineNum">    2503 </span>            : void</a>
+<a name="2504"><span class="lineNum">    2504 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(srot,SROT)(int *n__,</span></a>
+<a name="2505"><span class="lineNum">    2505 </span>            :                     float *dx,</a>
+<a name="2506"><span class="lineNum">    2506 </span>            :                     int *incx__,</a>
+<a name="2507"><span class="lineNum">    2507 </span>            :                     float *dy,</a>
+<a name="2508"><span class="lineNum">    2508 </span>            :                     int *incy__,</a>
+<a name="2509"><span class="lineNum">    2509 </span>            :                     float *c__,</a>
+<a name="2510"><span class="lineNum">    2510 </span>            :                     float *s__)</a>
+<a name="2511"><span class="lineNum">    2511 </span>            : {</a>
+<a name="2512"><span class="lineNum">    2512 </span>            :   int i,ix,iy;</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :   float dtemp;</a>
+<a name="2514"><span class="lineNum">    2514 </span>            : </a>
+<a name="2515"><span class="lineNum">    2515 </span><span class="lineNoCov">          0 :   int n = *n__;</span></a>
+<a name="2516"><span class="lineNum">    2516 </span><span class="lineNoCov">          0 :   int incx = *incx__;</span></a>
+<a name="2517"><span class="lineNum">    2517 </span><span class="lineNoCov">          0 :   int incy = *incy__;</span></a>
+<a name="2518"><span class="lineNum">    2518 </span><span class="lineNoCov">          0 :   float c = *c__;</span></a>
+<a name="2519"><span class="lineNum">    2519 </span><span class="lineNoCov">          0 :   float s = *s__;</span></a>
+<a name="2520"><span class="lineNum">    2520 </span>            :   </a>
+<a name="2521"><span class="lineNum">    2521 </span><span class="lineNoCov">          0 :   if(incx!=1 || incy!=1) {</span></a>
+<a name="2522"><span class="lineNum">    2522 </span>            :     ix = 0;</a>
+<a name="2523"><span class="lineNum">    2523 </span>            :     iy = 0;</a>
+<a name="2524"><span class="lineNum">    2524 </span><span class="lineNoCov">          0 :     if(incx&lt;0)</span></a>
+<a name="2525"><span class="lineNum">    2525 </span><span class="lineNoCov">          0 :       ix = (1-n)*(incx);</span></a>
+<a name="2526"><span class="lineNum">    2526 </span><span class="lineNoCov">          0 :     if(incy&lt;0)</span></a>
+<a name="2527"><span class="lineNum">    2527 </span><span class="lineNoCov">          0 :       iy = (1-n)*(incy);</span></a>
+<a name="2528"><span class="lineNum">    2528 </span>            :     </a>
+<a name="2529"><span class="lineNum">    2529 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) {</span></a>
+<a name="2530"><span class="lineNum">    2530 </span><span class="lineNoCov">          0 :       dtemp  = (c) * dx[ix] + (s) * dy[iy];</span></a>
+<a name="2531"><span class="lineNum">    2531 </span><span class="lineNoCov">          0 :       dy[iy] = (c) * dy[iy] - (s) * dx[ix];</span></a>
+<a name="2532"><span class="lineNum">    2532 </span><span class="lineNoCov">          0 :       dx[ix] = dtemp;</span></a>
+<a name="2533"><span class="lineNum">    2533 </span>            :     }</a>
+<a name="2534"><span class="lineNum">    2534 </span>            : </a>
+<a name="2535"><span class="lineNum">    2535 </span>            :     return;</a>
+<a name="2536"><span class="lineNum">    2536 </span>            : </a>
+<a name="2537"><span class="lineNum">    2537 </span>            :   } else {</a>
+<a name="2538"><span class="lineNum">    2538 </span>            : </a>
+<a name="2539"><span class="lineNum">    2539 </span>            :     /* unit increments */   </a>
+<a name="2540"><span class="lineNum">    2540 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;n;i++) {</span></a>
+<a name="2541"><span class="lineNum">    2541 </span><span class="lineNoCov">          0 :       dtemp = (c) * dx[i] + (s) * dy[i];</span></a>
+<a name="2542"><span class="lineNum">    2542 </span><span class="lineNoCov">          0 :       dy[i] = (c) * dy[i] - (s) * dx[i];</span></a>
+<a name="2543"><span class="lineNum">    2543 </span><span class="lineNoCov">          0 :       dx[i] = dtemp;      </span></a>
+<a name="2544"><span class="lineNum">    2544 </span>            :     }</a>
+<a name="2545"><span class="lineNum">    2545 </span>            : </a>
+<a name="2546"><span class="lineNum">    2546 </span>            :   }</a>
+<a name="2547"><span class="lineNum">    2547 </span>            : }</a>
+<a name="2548"><span class="lineNum">    2548 </span>            : }</a>
+<a name="2549"><span class="lineNum">    2549 </span>            : }</a>
+<a name="2550"><span class="lineNum">    2550 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2551"><span class="lineNum">    2551 </span>            : </a>
+<a name="2552"><span class="lineNum">    2552 </span>            : namespace PLMD{</a>
+<a name="2553"><span class="lineNum">    2553 </span>            : namespace blas{</a>
+<a name="2554"><span class="lineNum">    2554 </span>            : void </a>
+<a name="2555"><span class="lineNum">    2555 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(int  *n__,</span></a>
+<a name="2556"><span class="lineNum">    2556 </span>            :                       float *fact__,</a>
+<a name="2557"><span class="lineNum">    2557 </span>            :                       float *dx,</a>
+<a name="2558"><span class="lineNum">    2558 </span>            :                       int   *incx__)</a>
+<a name="2559"><span class="lineNum">    2559 </span>            : {</a>
+<a name="2560"><span class="lineNum">    2560 </span>            :     int nincx,i;</a>
+<a name="2561"><span class="lineNum">    2561 </span>            : </a>
+<a name="2562"><span class="lineNum">    2562 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="2563"><span class="lineNum">    2563 </span><span class="lineNoCov">          0 :     float fact = *fact__;</span></a>
+<a name="2564"><span class="lineNum">    2564 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="2565"><span class="lineNum">    2565 </span>            :     </a>
+<a name="2566"><span class="lineNum">    2566 </span><span class="lineNoCov">          0 :     if(n&lt;=0 || incx&lt;=0)</span></a>
+<a name="2567"><span class="lineNum">    2567 </span>            :         return;</a>
+<a name="2568"><span class="lineNum">    2568 </span>            :     </a>
+<a name="2569"><span class="lineNum">    2569 </span><span class="lineNoCov">          0 :     if(incx==1) {</span></a>
+<a name="2570"><span class="lineNum">    2570 </span>            :         /* Unrool factor 5 */</a>
+<a name="2571"><span class="lineNum">    2571 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;(n-5);i+=5) {</span></a>
+<a name="2572"><span class="lineNum">    2572 </span><span class="lineNoCov">          0 :             dx[i]   *= fact;</span></a>
+<a name="2573"><span class="lineNum">    2573 </span><span class="lineNoCov">          0 :             dx[i+1] *= fact;</span></a>
+<a name="2574"><span class="lineNum">    2574 </span><span class="lineNoCov">          0 :             dx[i+2] *= fact;</span></a>
+<a name="2575"><span class="lineNum">    2575 </span><span class="lineNoCov">          0 :             dx[i+3] *= fact;</span></a>
+<a name="2576"><span class="lineNum">    2576 </span><span class="lineNoCov">          0 :             dx[i+4] *= fact;</span></a>
+<a name="2577"><span class="lineNum">    2577 </span>            :         }    </a>
+<a name="2578"><span class="lineNum">    2578 </span>            :         /* continue with current value of i */</a>
+<a name="2579"><span class="lineNum">    2579 </span><span class="lineNoCov">          0 :         for(;i&lt;n;i++)</span></a>
+<a name="2580"><span class="lineNum">    2580 </span><span class="lineNoCov">          0 :             dx[i]   *= fact;</span></a>
+<a name="2581"><span class="lineNum">    2581 </span>            :         </a>
+<a name="2582"><span class="lineNum">    2582 </span>            :         return;</a>
+<a name="2583"><span class="lineNum">    2583 </span>            :     } else {</a>
+<a name="2584"><span class="lineNum">    2584 </span>            :         /* inc != 1 */</a>
+<a name="2585"><span class="lineNum">    2585 </span><span class="lineNoCov">          0 :         nincx = n * (incx);</span></a>
+<a name="2586"><span class="lineNum">    2586 </span><span class="lineNoCov">          0 :         for (i=0;i&lt;nincx;i+=incx)</span></a>
+<a name="2587"><span class="lineNum">    2587 </span><span class="lineNoCov">          0 :             dx[i] *= fact;</span></a>
+<a name="2588"><span class="lineNum">    2588 </span>            :         </a>
+<a name="2589"><span class="lineNum">    2589 </span>            :         return;</a>
+<a name="2590"><span class="lineNum">    2590 </span>            :     } </a>
+<a name="2591"><span class="lineNum">    2591 </span>            :     </a>
+<a name="2592"><span class="lineNum">    2592 </span>            : }</a>
+<a name="2593"><span class="lineNum">    2593 </span>            : }</a>
+<a name="2594"><span class="lineNum">    2594 </span>            : }</a>
+<a name="2595"><span class="lineNum">    2595 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2596"><span class="lineNum">    2596 </span>            : </a>
+<a name="2597"><span class="lineNum">    2597 </span>            : namespace PLMD{</a>
+<a name="2598"><span class="lineNum">    2598 </span>            : namespace blas{</a>
+<a name="2599"><span class="lineNum">    2599 </span>            : void</a>
+<a name="2600"><span class="lineNum">    2600 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(int *n__,</span></a>
+<a name="2601"><span class="lineNum">    2601 </span>            :                       float *dx,</a>
+<a name="2602"><span class="lineNum">    2602 </span>            :                       int *incx__,</a>
+<a name="2603"><span class="lineNum">    2603 </span>            :                       float *dy,</a>
+<a name="2604"><span class="lineNum">    2604 </span>            :                       int *incy__)</a>
+<a name="2605"><span class="lineNum">    2605 </span>            : {</a>
+<a name="2606"><span class="lineNum">    2606 </span>            :   int i,ix,iy;</a>
+<a name="2607"><span class="lineNum">    2607 </span>            :   float d1,d2,d3;</a>
+<a name="2608"><span class="lineNum">    2608 </span>            : </a>
+<a name="2609"><span class="lineNum">    2609 </span><span class="lineNoCov">          0 :   int n = *n__;</span></a>
+<a name="2610"><span class="lineNum">    2610 </span><span class="lineNoCov">          0 :   int incx = *incx__;</span></a>
+<a name="2611"><span class="lineNum">    2611 </span><span class="lineNoCov">          0 :   int incy = *incy__;</span></a>
+<a name="2612"><span class="lineNum">    2612 </span>            :   </a>
+<a name="2613"><span class="lineNum">    2613 </span><span class="lineNoCov">          0 :   if(n&lt;=0)</span></a>
+<a name="2614"><span class="lineNum">    2614 </span>            :     return;</a>
+<a name="2615"><span class="lineNum">    2615 </span>            : </a>
+<a name="2616"><span class="lineNum">    2616 </span><span class="lineNoCov">          0 :   if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="2617"><span class="lineNum">    2617 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;(n-3);i+=3) {</span></a>
+<a name="2618"><span class="lineNum">    2618 </span><span class="lineNoCov">          0 :       d1      = dx[i];</span></a>
+<a name="2619"><span class="lineNum">    2619 </span><span class="lineNoCov">          0 :       d2      = dx[i+1];</span></a>
+<a name="2620"><span class="lineNum">    2620 </span><span class="lineNoCov">          0 :       d3      = dx[i+2];</span></a>
+<a name="2621"><span class="lineNum">    2621 </span><span class="lineNoCov">          0 :       dx[i]   = dy[i];</span></a>
+<a name="2622"><span class="lineNum">    2622 </span><span class="lineNoCov">          0 :       dx[i+1] = dy[i+1];</span></a>
+<a name="2623"><span class="lineNum">    2623 </span><span class="lineNoCov">          0 :       dx[i+2] = dy[i+2];</span></a>
+<a name="2624"><span class="lineNum">    2624 </span><span class="lineNoCov">          0 :       dy[i]   = d1;</span></a>
+<a name="2625"><span class="lineNum">    2625 </span><span class="lineNoCov">          0 :       dy[i+1] = d2;</span></a>
+<a name="2626"><span class="lineNum">    2626 </span><span class="lineNoCov">          0 :       dy[i+2] = d3;</span></a>
+<a name="2627"><span class="lineNum">    2627 </span>            :     }</a>
+<a name="2628"><span class="lineNum">    2628 </span>            :     /* continue with last i value */</a>
+<a name="2629"><span class="lineNum">    2629 </span><span class="lineNoCov">          0 :     for(;i&lt;n;i++) {</span></a>
+<a name="2630"><span class="lineNum">    2630 </span><span class="lineNoCov">          0 :       d1      = dx[i];</span></a>
+<a name="2631"><span class="lineNum">    2631 </span><span class="lineNoCov">          0 :       dx[i]   = dy[i];</span></a>
+<a name="2632"><span class="lineNum">    2632 </span><span class="lineNoCov">          0 :       dy[i]   = d1;</span></a>
+<a name="2633"><span class="lineNum">    2633 </span>            :     }</a>
+<a name="2634"><span class="lineNum">    2634 </span>            : </a>
+<a name="2635"><span class="lineNum">    2635 </span>            :   } else {</a>
+<a name="2636"><span class="lineNum">    2636 </span>            :     ix = 0;</a>
+<a name="2637"><span class="lineNum">    2637 </span>            :     iy = 0;</a>
+<a name="2638"><span class="lineNum">    2638 </span><span class="lineNoCov">          0 :     if(incx&lt;0)</span></a>
+<a name="2639"><span class="lineNum">    2639 </span><span class="lineNoCov">          0 :       ix = incx * (1 - n);</span></a>
+<a name="2640"><span class="lineNum">    2640 </span><span class="lineNoCov">          0 :     if(incy&lt;0)</span></a>
+<a name="2641"><span class="lineNum">    2641 </span><span class="lineNoCov">          0 :       iy = incy * (1 - n);</span></a>
+<a name="2642"><span class="lineNum">    2642 </span>            : </a>
+<a name="2643"><span class="lineNum">    2643 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;n;i++,ix+=incx,iy+=incy) {</span></a>
+<a name="2644"><span class="lineNum">    2644 </span><span class="lineNoCov">          0 :       d1     = dx[ix];</span></a>
+<a name="2645"><span class="lineNum">    2645 </span><span class="lineNoCov">          0 :       dx[ix] = dy[iy];</span></a>
+<a name="2646"><span class="lineNum">    2646 </span><span class="lineNoCov">          0 :       dy[iy] = d1;</span></a>
+<a name="2647"><span class="lineNum">    2647 </span>            :     }</a>
+<a name="2648"><span class="lineNum">    2648 </span>            :   }</a>
+<a name="2649"><span class="lineNum">    2649 </span>            :   return;</a>
+<a name="2650"><span class="lineNum">    2650 </span>            : }</a>
+<a name="2651"><span class="lineNum">    2651 </span>            :  </a>
+<a name="2652"><span class="lineNum">    2652 </span>            : }</a>
+<a name="2653"><span class="lineNum">    2653 </span>            : }</a>
+<a name="2654"><span class="lineNum">    2654 </span>            : #include &lt;cctype&gt;</a>
+<a name="2655"><span class="lineNum">    2655 </span>            : #include &lt;cmath&gt;</a>
+<a name="2656"><span class="lineNum">    2656 </span>            : </a>
+<a name="2657"><span class="lineNum">    2657 </span>            : #include &quot;real.h&quot;</a>
+<a name="2658"><span class="lineNum">    2658 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2659"><span class="lineNum">    2659 </span>            : </a>
+<a name="2660"><span class="lineNum">    2660 </span>            : namespace PLMD{</a>
+<a name="2661"><span class="lineNum">    2661 </span>            : namespace blas{</a>
+<a name="2662"><span class="lineNum">    2662 </span>            : void</a>
+<a name="2663"><span class="lineNum">    2663 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)(const char *uplo,</span></a>
+<a name="2664"><span class="lineNum">    2664 </span>            :                       int *n__,</a>
+<a name="2665"><span class="lineNum">    2665 </span>            :                       float *alpha__,</a>
+<a name="2666"><span class="lineNum">    2666 </span>            :                       float *a,</a>
+<a name="2667"><span class="lineNum">    2667 </span>            :                       int *lda__,</a>
+<a name="2668"><span class="lineNum">    2668 </span>            :                       float *x,</a>
+<a name="2669"><span class="lineNum">    2669 </span>            :                       int *incx__,</a>
+<a name="2670"><span class="lineNum">    2670 </span>            :                       float *beta__,</a>
+<a name="2671"><span class="lineNum">    2671 </span>            :                       float *y,</a>
+<a name="2672"><span class="lineNum">    2672 </span>            :                       int *incy__)</a>
+<a name="2673"><span class="lineNum">    2673 </span>            : {</a>
+<a name="2674"><span class="lineNum">    2674 </span><span class="lineNoCov">          0 :     const char ch=std::toupper(*uplo);</span></a>
+<a name="2675"><span class="lineNum">    2675 </span>            :     int kx,ky,i,j,ix,iy,jx,jy;</a>
+<a name="2676"><span class="lineNum">    2676 </span>            :     float temp1,temp2;</a>
+<a name="2677"><span class="lineNum">    2677 </span>            :     </a>
+<a name="2678"><span class="lineNum">    2678 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="2679"><span class="lineNum">    2679 </span><span class="lineNoCov">          0 :     int lda = *lda__;</span></a>
+<a name="2680"><span class="lineNum">    2680 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="2681"><span class="lineNum">    2681 </span><span class="lineNoCov">          0 :     int incy = *incy__;</span></a>
+<a name="2682"><span class="lineNum">    2682 </span><span class="lineNoCov">          0 :     float alpha = *alpha__;</span></a>
+<a name="2683"><span class="lineNum">    2683 </span><span class="lineNoCov">          0 :     float beta  = *beta__;</span></a>
+<a name="2684"><span class="lineNum">    2684 </span>            :     </a>
+<a name="2685"><span class="lineNum">    2685 </span><span class="lineNoCov">          0 :     if(n&lt;=0 || incx==0 || incy==0)</span></a>
+<a name="2686"><span class="lineNum">    2686 </span>            :         return;</a>
+<a name="2687"><span class="lineNum">    2687 </span>            :     </a>
+<a name="2688"><span class="lineNum">    2688 </span><span class="lineNoCov">          0 :     if(incx&gt;0)</span></a>
+<a name="2689"><span class="lineNum">    2689 </span>            :         kx = 1;</a>
+<a name="2690"><span class="lineNum">    2690 </span>            :     else</a>
+<a name="2691"><span class="lineNum">    2691 </span><span class="lineNoCov">          0 :         kx = 1 - (n -1)*(incx);</span></a>
+<a name="2692"><span class="lineNum">    2692 </span>            :     </a>
+<a name="2693"><span class="lineNum">    2693 </span><span class="lineNoCov">          0 :     if(incy&gt;0)</span></a>
+<a name="2694"><span class="lineNum">    2694 </span>            :         ky = 1;</a>
+<a name="2695"><span class="lineNum">    2695 </span>            :     else</a>
+<a name="2696"><span class="lineNum">    2696 </span><span class="lineNoCov">          0 :         ky = 1 - (n -1)*(incy);</span></a>
+<a name="2697"><span class="lineNum">    2697 </span>            :     </a>
+<a name="2698"><span class="lineNum">    2698 </span><span class="lineNoCov">          0 :     if(std::abs(beta-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="2699"><span class="lineNum">    2699 </span><span class="lineNoCov">          0 :         if(incy==1) {</span></a>
+<a name="2700"><span class="lineNum">    2700 </span><span class="lineNoCov">          0 :             if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="2701"><span class="lineNum">    2701 </span><span class="lineNoCov">          0 :                 for(i=1;i&lt;=n;i++)</span></a>
+<a name="2702"><span class="lineNum">    2702 </span><span class="lineNoCov">          0 :                     y[i-1] = 0.0;</span></a>
+<a name="2703"><span class="lineNum">    2703 </span>            :             else</a>
+<a name="2704"><span class="lineNum">    2704 </span><span class="lineNoCov">          0 :                 for(i=1;i&lt;=n;i++)</span></a>
+<a name="2705"><span class="lineNum">    2705 </span><span class="lineNoCov">          0 :                     y[i-1] *= beta;</span></a>
+<a name="2706"><span class="lineNum">    2706 </span>            :         } else {</a>
+<a name="2707"><span class="lineNum">    2707 </span>            :             /* non-unit incr. */</a>
+<a name="2708"><span class="lineNum">    2708 </span>            :             iy = ky;</a>
+<a name="2709"><span class="lineNum">    2709 </span><span class="lineNoCov">          0 :             if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="2710"><span class="lineNum">    2710 </span><span class="lineNoCov">          0 :                 for(i=1;i&lt;=n;i++) {</span></a>
+<a name="2711"><span class="lineNum">    2711 </span><span class="lineNoCov">          0 :                     y[iy-1] = 0.0;</span></a>
+<a name="2712"><span class="lineNum">    2712 </span><span class="lineNoCov">          0 :                     iy += incy;</span></a>
+<a name="2713"><span class="lineNum">    2713 </span>            :                 }</a>
+<a name="2714"><span class="lineNum">    2714 </span>            :                     else</a>
+<a name="2715"><span class="lineNum">    2715 </span><span class="lineNoCov">          0 :                         for(i=1;i&lt;=n;i++) {</span></a>
+<a name="2716"><span class="lineNum">    2716 </span><span class="lineNoCov">          0 :                             y[iy-1] *= beta;</span></a>
+<a name="2717"><span class="lineNum">    2717 </span><span class="lineNoCov">          0 :                             iy += incy;</span></a>
+<a name="2718"><span class="lineNum">    2718 </span>            :                         }</a>
+<a name="2719"><span class="lineNum">    2719 </span>            :         }</a>
+<a name="2720"><span class="lineNum">    2720 </span>            :     }</a>
+<a name="2721"><span class="lineNum">    2721 </span>            :         </a>
+<a name="2722"><span class="lineNum">    2722 </span><span class="lineNoCov">          0 :         if(std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="2723"><span class="lineNum">    2723 </span>            :             return;</a>
+<a name="2724"><span class="lineNum">    2724 </span>            :         </a>
+<a name="2725"><span class="lineNum">    2725 </span><span class="lineNoCov">          0 :         if(ch=='U') {</span></a>
+<a name="2726"><span class="lineNum">    2726 </span><span class="lineNoCov">          0 :             if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="2727"><span class="lineNum">    2727 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2728"><span class="lineNum">    2728 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[j-1];</span></a>
+<a name="2729"><span class="lineNum">    2729 </span>            :                     temp2 = 0.0;</a>
+<a name="2730"><span class="lineNum">    2730 </span><span class="lineNoCov">          0 :                     for(i=1;i&lt;j;i++) {</span></a>
+<a name="2731"><span class="lineNum">    2731 </span><span class="lineNoCov">          0 :                         y[i-1] += temp1*a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="2732"><span class="lineNum">    2732 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[i-1];</span></a>
+<a name="2733"><span class="lineNum">    2733 </span>            :                     }</a>
+<a name="2734"><span class="lineNum">    2734 </span><span class="lineNoCov">          0 :                     y[j-1] += temp1*a[(j-1)*(lda)+(j-1)] + alpha *temp2;</span></a>
+<a name="2735"><span class="lineNum">    2735 </span>            :                 }</a>
+<a name="2736"><span class="lineNum">    2736 </span>            :             } else {</a>
+<a name="2737"><span class="lineNum">    2737 </span>            :                 /* non-unit incr. */</a>
+<a name="2738"><span class="lineNum">    2738 </span>            :                 jx = kx;</a>
+<a name="2739"><span class="lineNum">    2739 </span>            :                 jy = ky;</a>
+<a name="2740"><span class="lineNum">    2740 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2741"><span class="lineNum">    2741 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[jx-1];</span></a>
+<a name="2742"><span class="lineNum">    2742 </span>            :                     temp2 = 0.0;</a>
+<a name="2743"><span class="lineNum">    2743 </span>            :                     ix = kx;</a>
+<a name="2744"><span class="lineNum">    2744 </span>            :                     iy = ky;</a>
+<a name="2745"><span class="lineNum">    2745 </span><span class="lineNoCov">          0 :                     for(i=1;i&lt;j;i++) {</span></a>
+<a name="2746"><span class="lineNum">    2746 </span><span class="lineNoCov">          0 :                         y[iy-1] += temp1 * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="2747"><span class="lineNum">    2747 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[ix-1];</span></a>
+<a name="2748"><span class="lineNum">    2748 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="2749"><span class="lineNum">    2749 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="2750"><span class="lineNum">    2750 </span>            :                     }</a>
+<a name="2751"><span class="lineNum">    2751 </span><span class="lineNoCov">          0 :                     y[jy-1] += temp1*a[(j-1)*(lda)+(j-1)] + alpha*temp2;</span></a>
+<a name="2752"><span class="lineNum">    2752 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="2753"><span class="lineNum">    2753 </span><span class="lineNoCov">          0 :                     jy += incy;</span></a>
+<a name="2754"><span class="lineNum">    2754 </span>            :                 }</a>
+<a name="2755"><span class="lineNum">    2755 </span>            :             }</a>
+<a name="2756"><span class="lineNum">    2756 </span>            :         } else {</a>
+<a name="2757"><span class="lineNum">    2757 </span>            :             /* lower */</a>
+<a name="2758"><span class="lineNum">    2758 </span><span class="lineNoCov">          0 :             if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="2759"><span class="lineNum">    2759 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2760"><span class="lineNum">    2760 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[j-1];</span></a>
+<a name="2761"><span class="lineNum">    2761 </span>            :                     temp2 = 0.0;</a>
+<a name="2762"><span class="lineNum">    2762 </span><span class="lineNoCov">          0 :                     y[j-1] += temp1 * a[(j-1)*(lda)+(j-1)];</span></a>
+<a name="2763"><span class="lineNum">    2763 </span><span class="lineNoCov">          0 :                     for(i=j+1;i&lt;=n;i++) {</span></a>
+<a name="2764"><span class="lineNum">    2764 </span><span class="lineNoCov">          0 :                         y[i-1] += temp1*a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="2765"><span class="lineNum">    2765 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[i-1];</span></a>
+<a name="2766"><span class="lineNum">    2766 </span>            :                     }</a>
+<a name="2767"><span class="lineNum">    2767 </span><span class="lineNoCov">          0 :                     y[j-1] += alpha *temp2;</span></a>
+<a name="2768"><span class="lineNum">    2768 </span>            :                 }</a>
+<a name="2769"><span class="lineNum">    2769 </span>            :             } else {</a>
+<a name="2770"><span class="lineNum">    2770 </span>            :                 /* non-unit incr. */</a>
+<a name="2771"><span class="lineNum">    2771 </span>            :                 jx = kx;</a>
+<a name="2772"><span class="lineNum">    2772 </span>            :                 jy = ky;</a>
+<a name="2773"><span class="lineNum">    2773 </span><span class="lineNoCov">          0 :                 for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2774"><span class="lineNum">    2774 </span><span class="lineNoCov">          0 :                     temp1 = alpha * x[jx-1];</span></a>
+<a name="2775"><span class="lineNum">    2775 </span>            :                     temp2 = 0.0;</a>
+<a name="2776"><span class="lineNum">    2776 </span><span class="lineNoCov">          0 :                     y[jy-1] += temp1 * a[(j-1)*(lda)+(j-1)];</span></a>
+<a name="2777"><span class="lineNum">    2777 </span>            :                     ix = jx;</a>
+<a name="2778"><span class="lineNum">    2778 </span>            :                     iy = jy;</a>
+<a name="2779"><span class="lineNum">    2779 </span><span class="lineNoCov">          0 :                     for(i=j+1;i&lt;=n;i++) {</span></a>
+<a name="2780"><span class="lineNum">    2780 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="2781"><span class="lineNum">    2781 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="2782"><span class="lineNum">    2782 </span><span class="lineNoCov">          0 :                         y[iy-1] += temp1 * a[(j-1)*(lda)+(i-1)];</span></a>
+<a name="2783"><span class="lineNum">    2783 </span><span class="lineNoCov">          0 :                         temp2 += a[(j-1)*(lda)+(i-1)] * x[ix-1];</span></a>
+<a name="2784"><span class="lineNum">    2784 </span>            :                     }</a>
+<a name="2785"><span class="lineNum">    2785 </span><span class="lineNoCov">          0 :                     y[jy-1] += alpha*temp2;</span></a>
+<a name="2786"><span class="lineNum">    2786 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="2787"><span class="lineNum">    2787 </span><span class="lineNoCov">          0 :                     jy += incy;</span></a>
+<a name="2788"><span class="lineNum">    2788 </span>            :                 }</a>
+<a name="2789"><span class="lineNum">    2789 </span>            :             }</a>
+<a name="2790"><span class="lineNum">    2790 </span>            :         }</a>
+<a name="2791"><span class="lineNum">    2791 </span>            :         return;</a>
+<a name="2792"><span class="lineNum">    2792 </span>            : }    </a>
+<a name="2793"><span class="lineNum">    2793 </span>            : }</a>
+<a name="2794"><span class="lineNum">    2794 </span>            : }</a>
+<a name="2795"><span class="lineNum">    2795 </span>            : #include &lt;cctype&gt;</a>
+<a name="2796"><span class="lineNum">    2796 </span>            : #include &lt;cmath&gt;</a>
+<a name="2797"><span class="lineNum">    2797 </span>            : </a>
+<a name="2798"><span class="lineNum">    2798 </span>            : #include &quot;real.h&quot;</a>
+<a name="2799"><span class="lineNum">    2799 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2800"><span class="lineNum">    2800 </span>            : </a>
+<a name="2801"><span class="lineNum">    2801 </span>            : namespace PLMD{</a>
+<a name="2802"><span class="lineNum">    2802 </span>            : namespace blas{</a>
+<a name="2803"><span class="lineNum">    2803 </span>            : void</a>
+<a name="2804"><span class="lineNum">    2804 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssyr2,SSYR2)(const char *    uplo,</span></a>
+<a name="2805"><span class="lineNum">    2805 </span>            :                       int *     n__,</a>
+<a name="2806"><span class="lineNum">    2806 </span>            :                       float *  alpha__,</a>
+<a name="2807"><span class="lineNum">    2807 </span>            :                       float *  x,</a>
+<a name="2808"><span class="lineNum">    2808 </span>            :                       int *     incx__,</a>
+<a name="2809"><span class="lineNum">    2809 </span>            :                       float *  y,</a>
+<a name="2810"><span class="lineNum">    2810 </span>            :                       int *     incy__,</a>
+<a name="2811"><span class="lineNum">    2811 </span>            :                       float *  a,</a>
+<a name="2812"><span class="lineNum">    2812 </span>            :                       int *     lda__)</a>
+<a name="2813"><span class="lineNum">    2813 </span>            : {</a>
+<a name="2814"><span class="lineNum">    2814 </span>            :     int kx,ky,ix,iy,jx,jy,j,i;</a>
+<a name="2815"><span class="lineNum">    2815 </span>            :     float temp1,temp2;</a>
+<a name="2816"><span class="lineNum">    2816 </span><span class="lineNoCov">          0 :     const char ch=std::toupper(*uplo);</span></a>
+<a name="2817"><span class="lineNum">    2817 </span>            :     </a>
+<a name="2818"><span class="lineNum">    2818 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="2819"><span class="lineNum">    2819 </span><span class="lineNoCov">          0 :     int lda = *lda__;</span></a>
+<a name="2820"><span class="lineNum">    2820 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="2821"><span class="lineNum">    2821 </span><span class="lineNoCov">          0 :     int incy = *incy__;</span></a>
+<a name="2822"><span class="lineNum">    2822 </span><span class="lineNoCov">          0 :     float alpha = *alpha__;</span></a>
+<a name="2823"><span class="lineNum">    2823 </span>            :     </a>
+<a name="2824"><span class="lineNum">    2824 </span><span class="lineNoCov">          0 :     if(n&lt;=0 || std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN || incx==0 || incy==0 ||</span></a>
+<a name="2825"><span class="lineNum">    2825 </span><span class="lineNoCov">          0 :        (ch != 'U' &amp;&amp; ch != 'L'))</span></a>
+<a name="2826"><span class="lineNum">    2826 </span>            :         return;</a>
+<a name="2827"><span class="lineNum">    2827 </span>            :     </a>
+<a name="2828"><span class="lineNum">    2828 </span>            :     jx = jy = kx = ky = 0;</a>
+<a name="2829"><span class="lineNum">    2829 </span>            :     </a>
+<a name="2830"><span class="lineNum">    2830 </span>            :     /* init start points for non-unit increments */</a>
+<a name="2831"><span class="lineNum">    2831 </span><span class="lineNoCov">          0 :     if(incx!=1 || incy!=1) {</span></a>
+<a name="2832"><span class="lineNum">    2832 </span><span class="lineNoCov">          0 :         if(incx&gt;0)</span></a>
+<a name="2833"><span class="lineNum">    2833 </span>            :             kx = 1;</a>
+<a name="2834"><span class="lineNum">    2834 </span>            :         else</a>
+<a name="2835"><span class="lineNum">    2835 </span><span class="lineNoCov">          0 :             kx = 1 - (n - 1)*(incx);</span></a>
+<a name="2836"><span class="lineNum">    2836 </span><span class="lineNoCov">          0 :         if(incy&gt;0)</span></a>
+<a name="2837"><span class="lineNum">    2837 </span>            :             ky = 1;</a>
+<a name="2838"><span class="lineNum">    2838 </span>            :         else</a>
+<a name="2839"><span class="lineNum">    2839 </span><span class="lineNoCov">          0 :             ky = 1 - (n - 1)*(incy);</span></a>
+<a name="2840"><span class="lineNum">    2840 </span>            :         </a>
+<a name="2841"><span class="lineNum">    2841 </span>            :         jx = kx;</a>
+<a name="2842"><span class="lineNum">    2842 </span>            :         jy = ky;</a>
+<a name="2843"><span class="lineNum">    2843 </span>            :     }</a>
+<a name="2844"><span class="lineNum">    2844 </span>            :     </a>
+<a name="2845"><span class="lineNum">    2845 </span><span class="lineNoCov">          0 :     if(ch == 'U') {</span></a>
+<a name="2846"><span class="lineNum">    2846 </span>            :         /* Data in upper part of A */</a>
+<a name="2847"><span class="lineNum">    2847 </span><span class="lineNoCov">          0 :         if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="2848"><span class="lineNum">    2848 </span>            :             /* Unit increments for both x and y */</a>
+<a name="2849"><span class="lineNum">    2849 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2850"><span class="lineNum">    2850 </span><span class="lineNoCov">          0 :                 if( std::abs(x[j-1])&gt;PLUMED_GMX_FLOAT_MIN  || std::abs(y[j-1])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="2851"><span class="lineNum">    2851 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[j-1];</span></a>
+<a name="2852"><span class="lineNum">    2852 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[j-1];</span></a>
+<a name="2853"><span class="lineNum">    2853 </span><span class="lineNoCov">          0 :                     for(i=1;i&lt;=j;i++)</span></a>
+<a name="2854"><span class="lineNum">    2854 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[i-1]*temp1 + y[i-1]*temp2;</span></a>
+<a name="2855"><span class="lineNum">    2855 </span>            :                 }</a>
+<a name="2856"><span class="lineNum">    2856 </span>            :             }</a>
+<a name="2857"><span class="lineNum">    2857 </span>            :         } else {</a>
+<a name="2858"><span class="lineNum">    2858 </span>            :             </a>
+<a name="2859"><span class="lineNum">    2859 </span>            :             /* non-unit increments */</a>
+<a name="2860"><span class="lineNum">    2860 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2861"><span class="lineNum">    2861 </span>            :                 </a>
+<a name="2862"><span class="lineNum">    2862 </span><span class="lineNoCov">          0 :                 if( std::abs(x[jx-1])&gt;PLUMED_GMX_FLOAT_MIN || std::abs(y[jy-1])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="2863"><span class="lineNum">    2863 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[jy-1];</span></a>
+<a name="2864"><span class="lineNum">    2864 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[jx-1];</span></a>
+<a name="2865"><span class="lineNum">    2865 </span>            :                     ix = kx;</a>
+<a name="2866"><span class="lineNum">    2866 </span>            :                     iy = ky;</a>
+<a name="2867"><span class="lineNum">    2867 </span><span class="lineNoCov">          0 :                     for(i=1;i&lt;=j;i++) {</span></a>
+<a name="2868"><span class="lineNum">    2868 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[ix-1]*temp1 + y[iy-1]*temp2;</span></a>
+<a name="2869"><span class="lineNum">    2869 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="2870"><span class="lineNum">    2870 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="2871"><span class="lineNum">    2871 </span>            :                     }</a>
+<a name="2872"><span class="lineNum">    2872 </span>            :                 }</a>
+<a name="2873"><span class="lineNum">    2873 </span><span class="lineNoCov">          0 :                 jx += incx;</span></a>
+<a name="2874"><span class="lineNum">    2874 </span><span class="lineNoCov">          0 :                 jy += incy;</span></a>
+<a name="2875"><span class="lineNum">    2875 </span>            :             }</a>
+<a name="2876"><span class="lineNum">    2876 </span>            :         }</a>
+<a name="2877"><span class="lineNum">    2877 </span>            :     } else {</a>
+<a name="2878"><span class="lineNum">    2878 </span>            :         /* Data in lower part of A */</a>
+<a name="2879"><span class="lineNum">    2879 </span><span class="lineNoCov">          0 :         if(incx==1 &amp;&amp; incy==1) {</span></a>
+<a name="2880"><span class="lineNum">    2880 </span>            :             /* Unit increments for both x and y */</a>
+<a name="2881"><span class="lineNum">    2881 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2882"><span class="lineNum">    2882 </span><span class="lineNoCov">          0 :                 if( std::abs(x[j-1])&gt;PLUMED_GMX_FLOAT_MIN  || std::abs(y[j-1])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="2883"><span class="lineNum">    2883 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[j-1];</span></a>
+<a name="2884"><span class="lineNum">    2884 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[j-1];</span></a>
+<a name="2885"><span class="lineNum">    2885 </span><span class="lineNoCov">          0 :                     for(i=j;i&lt;=n;i++)</span></a>
+<a name="2886"><span class="lineNum">    2886 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[i-1]*temp1 + y[i-1]*temp2;</span></a>
+<a name="2887"><span class="lineNum">    2887 </span>            :                 }</a>
+<a name="2888"><span class="lineNum">    2888 </span>            :             }</a>
+<a name="2889"><span class="lineNum">    2889 </span>            :         } else {</a>
+<a name="2890"><span class="lineNum">    2890 </span>            :             </a>
+<a name="2891"><span class="lineNum">    2891 </span>            :             /* non-unit increments */</a>
+<a name="2892"><span class="lineNum">    2892 </span><span class="lineNoCov">          0 :             for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2893"><span class="lineNum">    2893 </span>            :                 </a>
+<a name="2894"><span class="lineNum">    2894 </span><span class="lineNoCov">          0 :                 if( std::abs(x[jx-1])&gt;PLUMED_GMX_FLOAT_MIN || std::abs(y[jy-1])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="2895"><span class="lineNum">    2895 </span><span class="lineNoCov">          0 :                     temp1 = alpha * y[jy-1];</span></a>
+<a name="2896"><span class="lineNum">    2896 </span><span class="lineNoCov">          0 :                     temp2 = alpha * x[jx-1];</span></a>
+<a name="2897"><span class="lineNum">    2897 </span>            :                     ix = jx;</a>
+<a name="2898"><span class="lineNum">    2898 </span>            :                     iy = jy;</a>
+<a name="2899"><span class="lineNum">    2899 </span><span class="lineNoCov">          0 :                     for(i=j;i&lt;=n;i++) {</span></a>
+<a name="2900"><span class="lineNum">    2900 </span><span class="lineNoCov">          0 :                         a[(j-1)*(lda)+(i-1)] += x[ix-1]*temp1 + y[iy-1]*temp2;</span></a>
+<a name="2901"><span class="lineNum">    2901 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="2902"><span class="lineNum">    2902 </span><span class="lineNoCov">          0 :                         iy += incy;</span></a>
+<a name="2903"><span class="lineNum">    2903 </span>            :                     }</a>
+<a name="2904"><span class="lineNum">    2904 </span>            :                 }</a>
+<a name="2905"><span class="lineNum">    2905 </span><span class="lineNoCov">          0 :                 jx += incx;</span></a>
+<a name="2906"><span class="lineNum">    2906 </span><span class="lineNoCov">          0 :                 jy += incy;</span></a>
+<a name="2907"><span class="lineNum">    2907 </span>            :             }</a>
+<a name="2908"><span class="lineNum">    2908 </span>            :         }</a>
+<a name="2909"><span class="lineNum">    2909 </span>            :     }</a>
+<a name="2910"><span class="lineNum">    2910 </span>            :     </a>
+<a name="2911"><span class="lineNum">    2911 </span>            :     return;</a>
+<a name="2912"><span class="lineNum">    2912 </span>            : }</a>
+<a name="2913"><span class="lineNum">    2913 </span>            : }</a>
+<a name="2914"><span class="lineNum">    2914 </span>            : }</a>
+<a name="2915"><span class="lineNum">    2915 </span>            : #include &lt;cctype&gt;</a>
+<a name="2916"><span class="lineNum">    2916 </span>            : #include &lt;cmath&gt;</a>
+<a name="2917"><span class="lineNum">    2917 </span>            : </a>
+<a name="2918"><span class="lineNum">    2918 </span>            : #include &quot;real.h&quot;</a>
+<a name="2919"><span class="lineNum">    2919 </span>            : #include &quot;blas.h&quot;</a>
+<a name="2920"><span class="lineNum">    2920 </span>            : </a>
+<a name="2921"><span class="lineNum">    2921 </span>            : namespace PLMD{</a>
+<a name="2922"><span class="lineNum">    2922 </span>            : namespace blas{</a>
+<a name="2923"><span class="lineNum">    2923 </span>            : void</a>
+<a name="2924"><span class="lineNum">    2924 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssyr2k,SSYR2K)(const char *uplo, </span></a>
+<a name="2925"><span class="lineNum">    2925 </span>            :                         const char *trans,</a>
+<a name="2926"><span class="lineNum">    2926 </span>            :                         int *n__,</a>
+<a name="2927"><span class="lineNum">    2927 </span>            :                         int *k__,</a>
+<a name="2928"><span class="lineNum">    2928 </span>            :                         float *alpha__,</a>
+<a name="2929"><span class="lineNum">    2929 </span>            :                         float *a,</a>
+<a name="2930"><span class="lineNum">    2930 </span>            :                         int *lda__,</a>
+<a name="2931"><span class="lineNum">    2931 </span>            :                         float *b,</a>
+<a name="2932"><span class="lineNum">    2932 </span>            :                         int *ldb__,</a>
+<a name="2933"><span class="lineNum">    2933 </span>            :                         float *beta__,</a>
+<a name="2934"><span class="lineNum">    2934 </span>            :                         float *c,</a>
+<a name="2935"><span class="lineNum">    2935 </span>            :                         int *ldc__)</a>
+<a name="2936"><span class="lineNum">    2936 </span>            : {</a>
+<a name="2937"><span class="lineNum">    2937 </span>            :   char ch1,ch2;</a>
+<a name="2938"><span class="lineNum">    2938 </span>            :   int i,j,l;</a>
+<a name="2939"><span class="lineNum">    2939 </span>            :   float temp1,temp2;</a>
+<a name="2940"><span class="lineNum">    2940 </span>            : </a>
+<a name="2941"><span class="lineNum">    2941 </span><span class="lineNoCov">          0 :   int n = *n__;</span></a>
+<a name="2942"><span class="lineNum">    2942 </span><span class="lineNoCov">          0 :   int k = *k__;</span></a>
+<a name="2943"><span class="lineNum">    2943 </span><span class="lineNoCov">          0 :   int lda = *lda__;</span></a>
+<a name="2944"><span class="lineNum">    2944 </span><span class="lineNoCov">          0 :   int ldb = *ldb__;</span></a>
+<a name="2945"><span class="lineNum">    2945 </span><span class="lineNoCov">          0 :   int ldc = *ldc__;</span></a>
+<a name="2946"><span class="lineNum">    2946 </span>            :   </a>
+<a name="2947"><span class="lineNum">    2947 </span><span class="lineNoCov">          0 :   float alpha = *alpha__;</span></a>
+<a name="2948"><span class="lineNum">    2948 </span><span class="lineNoCov">          0 :   float beta  = *beta__;</span></a>
+<a name="2949"><span class="lineNum">    2949 </span>            :   </a>
+<a name="2950"><span class="lineNum">    2950 </span><span class="lineNoCov">          0 :   ch1 = std::toupper(*uplo);</span></a>
+<a name="2951"><span class="lineNum">    2951 </span><span class="lineNoCov">          0 :   ch2 = std::toupper(*trans);</span></a>
+<a name="2952"><span class="lineNum">    2952 </span>            : </a>
+<a name="2953"><span class="lineNum">    2953 </span><span class="lineNoCov">          0 :   if(n==0 || ( ( std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN || k==0 ) &amp;&amp; std::abs(beta-1.0)&lt;PLUMED_GMX_FLOAT_EPS))</span></a>
+<a name="2954"><span class="lineNum">    2954 </span>            :     return;</a>
+<a name="2955"><span class="lineNum">    2955 </span>            : </a>
+<a name="2956"><span class="lineNum">    2956 </span><span class="lineNoCov">          0 :   if(std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2957"><span class="lineNum">    2957 </span><span class="lineNoCov">          0 :     if(ch1=='U') {</span></a>
+<a name="2958"><span class="lineNum">    2958 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="2959"><span class="lineNum">    2959 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="2960"><span class="lineNum">    2960 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="2961"><span class="lineNum">    2961 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="2962"><span class="lineNum">    2962 </span>            :       else</a>
+<a name="2963"><span class="lineNum">    2963 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="2964"><span class="lineNum">    2964 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="2965"><span class="lineNum">    2965 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="2966"><span class="lineNum">    2966 </span>            :     } else {</a>
+<a name="2967"><span class="lineNum">    2967 </span>            :       /* lower */</a>
+<a name="2968"><span class="lineNum">    2968 </span><span class="lineNoCov">          0 :       if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="2969"><span class="lineNum">    2969 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="2970"><span class="lineNum">    2970 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="2971"><span class="lineNum">    2971 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="2972"><span class="lineNum">    2972 </span>            :       else</a>
+<a name="2973"><span class="lineNum">    2973 </span><span class="lineNoCov">          0 :         for(j=1;j&lt;=n;j++) </span></a>
+<a name="2974"><span class="lineNum">    2974 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="2975"><span class="lineNum">    2975 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="2976"><span class="lineNum">    2976 </span>            :     }</a>
+<a name="2977"><span class="lineNum">    2977 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="2978"><span class="lineNum">    2978 </span>            :   }</a>
+<a name="2979"><span class="lineNum">    2979 </span>            : </a>
+<a name="2980"><span class="lineNum">    2980 </span><span class="lineNoCov">          0 :   if(ch2=='N') {</span></a>
+<a name="2981"><span class="lineNum">    2981 </span><span class="lineNoCov">          0 :     if(ch1=='U') {</span></a>
+<a name="2982"><span class="lineNum">    2982 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) {</span></a>
+<a name="2983"><span class="lineNum">    2983 </span><span class="lineNoCov">          0 :         if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="2984"><span class="lineNum">    2984 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="2985"><span class="lineNum">    2985 </span><span class="lineNoCov">          0 :              c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="2986"><span class="lineNum">    2986 </span><span class="lineNoCov">          0 :         else if(std::abs(beta-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="2987"><span class="lineNum">    2987 </span><span class="lineNoCov">          0 :           for(i=1;i&lt;=j;i++)</span></a>
+<a name="2988"><span class="lineNum">    2988 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="2989"><span class="lineNum">    2989 </span><span class="lineNoCov">          0 :         for(l=1;l&lt;=k;l++) {</span></a>
+<a name="2990"><span class="lineNum">    2990 </span><span class="lineNoCov">          0 :           if( std::abs(a[(l-1)*(lda)+(j-1)])&gt;PLUMED_GMX_FLOAT_MIN ||</span></a>
+<a name="2991"><span class="lineNum">    2991 </span><span class="lineNoCov">          0 :               std::abs(b[(l-1)*(ldb)+(j-1)])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="2992"><span class="lineNum">    2992 </span><span class="lineNoCov">          0 :             temp1 = alpha * b[(l-1)*(ldb)+(j-1)];</span></a>
+<a name="2993"><span class="lineNum">    2993 </span><span class="lineNoCov">          0 :             temp2 = alpha * a[(l-1)*(lda)+(j-1)];</span></a>
+<a name="2994"><span class="lineNum">    2994 </span><span class="lineNoCov">          0 :             for(i=1;i&lt;=j;i++)</span></a>
+<a name="2995"><span class="lineNum">    2995 </span><span class="lineNoCov">          0 :               c[(j-1)*(ldc)+(i-1)] += </span></a>
+<a name="2996"><span class="lineNum">    2996 </span><span class="lineNoCov">          0 :                 a[(l-1)*(lda)+(i-1)] * temp1 + </span></a>
+<a name="2997"><span class="lineNum">    2997 </span><span class="lineNoCov">          0 :                 b[(l-1)*(ldb)+(i-1)] * temp2;</span></a>
+<a name="2998"><span class="lineNum">    2998 </span>            :           }</a>
+<a name="2999"><span class="lineNum">    2999 </span>            :         }</a>
+<a name="3000"><span class="lineNum">    3000 </span>            :       }</a>
+<a name="3001"><span class="lineNum">    3001 </span>            :     } else {</a>
+<a name="3002"><span class="lineNum">    3002 </span>            :       /* lower */</a>
+<a name="3003"><span class="lineNum">    3003 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) {</span></a>
+<a name="3004"><span class="lineNum">    3004 </span><span class="lineNoCov">          0 :         if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="3005"><span class="lineNum">    3005 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="3006"><span class="lineNum">    3006 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = 0.0;</span></a>
+<a name="3007"><span class="lineNum">    3007 </span><span class="lineNoCov">          0 :         else if(std::abs(beta-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="3008"><span class="lineNum">    3008 </span><span class="lineNoCov">          0 :           for(i=j;i&lt;=n;i++)</span></a>
+<a name="3009"><span class="lineNum">    3009 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] *= beta;</span></a>
+<a name="3010"><span class="lineNum">    3010 </span><span class="lineNoCov">          0 :         for(l=1;l&lt;=k;l++) {</span></a>
+<a name="3011"><span class="lineNum">    3011 </span><span class="lineNoCov">          0 :           if( std::abs(a[(l-1)*(lda)+(j-1)])&gt;PLUMED_GMX_FLOAT_MIN ||</span></a>
+<a name="3012"><span class="lineNum">    3012 </span><span class="lineNoCov">          0 :               std::abs(b[(l-1)*(ldb)+(j-1)])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3013"><span class="lineNum">    3013 </span><span class="lineNoCov">          0 :             temp1 = alpha * b[(l-1)*(ldb)+(j-1)];</span></a>
+<a name="3014"><span class="lineNum">    3014 </span><span class="lineNoCov">          0 :             temp2 = alpha * a[(l-1)*(lda)+(j-1)];</span></a>
+<a name="3015"><span class="lineNum">    3015 </span><span class="lineNoCov">          0 :             for(i=j;i&lt;=n;i++)</span></a>
+<a name="3016"><span class="lineNum">    3016 </span><span class="lineNoCov">          0 :               c[(j-1)*(ldc)+(i-1)] += </span></a>
+<a name="3017"><span class="lineNum">    3017 </span><span class="lineNoCov">          0 :                 a[(l-1)*(lda)+(i-1)] * temp1 + </span></a>
+<a name="3018"><span class="lineNum">    3018 </span><span class="lineNoCov">          0 :                 b[(l-1)*(ldb)+(i-1)] * temp2;</span></a>
+<a name="3019"><span class="lineNum">    3019 </span>            :           }</a>
+<a name="3020"><span class="lineNum">    3020 </span>            :         }</a>
+<a name="3021"><span class="lineNum">    3021 </span>            :       }</a>
+<a name="3022"><span class="lineNum">    3022 </span>            :     }</a>
+<a name="3023"><span class="lineNum">    3023 </span>            :   } else {</a>
+<a name="3024"><span class="lineNum">    3024 </span>            :     /* transpose */</a>
+<a name="3025"><span class="lineNum">    3025 </span><span class="lineNoCov">          0 :     if(ch1=='U') {</span></a>
+<a name="3026"><span class="lineNum">    3026 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) </span></a>
+<a name="3027"><span class="lineNum">    3027 </span><span class="lineNoCov">          0 :         for(i=1;i&lt;=j;i++) {</span></a>
+<a name="3028"><span class="lineNum">    3028 </span>            :           temp1 = 0.0;</a>
+<a name="3029"><span class="lineNum">    3029 </span>            :           temp2 = 0.0;</a>
+<a name="3030"><span class="lineNum">    3030 </span><span class="lineNoCov">          0 :           for (l=1;l&lt;=k;l++) {</span></a>
+<a name="3031"><span class="lineNum">    3031 </span><span class="lineNoCov">          0 :              temp1 += a[(i-1)*(lda)+(l-1)] * b[(j-1)*(ldb)+(l-1)];</span></a>
+<a name="3032"><span class="lineNum">    3032 </span><span class="lineNoCov">          0 :              temp2 += b[(i-1)*(ldb)+(l-1)] * a[(j-1)*(lda)+(l-1)];</span></a>
+<a name="3033"><span class="lineNum">    3033 </span>            :           }</a>
+<a name="3034"><span class="lineNum">    3034 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="3035"><span class="lineNum">    3035 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = alpha * (temp1 + temp2);</span></a>
+<a name="3036"><span class="lineNum">    3036 </span>            :           else</a>
+<a name="3037"><span class="lineNum">    3037 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = beta * c[(j-1)*(ldc)+(i-1)] +</span></a>
+<a name="3038"><span class="lineNum">    3038 </span><span class="lineNoCov">          0 :               alpha * (temp1 + temp2);</span></a>
+<a name="3039"><span class="lineNum">    3039 </span>            :         }</a>
+<a name="3040"><span class="lineNum">    3040 </span>            :     } else {</a>
+<a name="3041"><span class="lineNum">    3041 </span>            :       /* lower */</a>
+<a name="3042"><span class="lineNum">    3042 </span><span class="lineNoCov">          0 :       for(j=1;j&lt;=n;j++) </span></a>
+<a name="3043"><span class="lineNum">    3043 </span><span class="lineNoCov">          0 :         for(i=j;i&lt;=n;i++) {</span></a>
+<a name="3044"><span class="lineNum">    3044 </span>            :           temp1 = 0.0;</a>
+<a name="3045"><span class="lineNum">    3045 </span>            :           temp2 = 0.0;</a>
+<a name="3046"><span class="lineNum">    3046 </span><span class="lineNoCov">          0 :           for (l=1;l&lt;=k;l++) {</span></a>
+<a name="3047"><span class="lineNum">    3047 </span><span class="lineNoCov">          0 :              temp1 += a[(i-1)*(lda)+(l-1)] * b[(j-1)*(ldb)+(l-1)];</span></a>
+<a name="3048"><span class="lineNum">    3048 </span><span class="lineNoCov">          0 :              temp2 += b[(i-1)*(ldb)+(l-1)] * a[(j-1)*(lda)+(l-1)];</span></a>
+<a name="3049"><span class="lineNum">    3049 </span>            :           }</a>
+<a name="3050"><span class="lineNum">    3050 </span><span class="lineNoCov">          0 :           if(std::abs(beta)&lt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="3051"><span class="lineNum">    3051 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = alpha * (temp1 + temp2);</span></a>
+<a name="3052"><span class="lineNum">    3052 </span>            :           else</a>
+<a name="3053"><span class="lineNum">    3053 </span><span class="lineNoCov">          0 :             c[(j-1)*(ldc)+(i-1)] = beta * c[(j-1)*(ldc)+(i-1)] +</span></a>
+<a name="3054"><span class="lineNum">    3054 </span><span class="lineNoCov">          0 :               alpha * (temp1 + temp2);</span></a>
+<a name="3055"><span class="lineNum">    3055 </span>            :         }</a>
+<a name="3056"><span class="lineNum">    3056 </span>            :     }</a>
+<a name="3057"><span class="lineNum">    3057 </span>            :   }</a>
+<a name="3058"><span class="lineNum">    3058 </span>            :   return;</a>
+<a name="3059"><span class="lineNum">    3059 </span>            : }</a>
+<a name="3060"><span class="lineNum">    3060 </span>            : }</a>
+<a name="3061"><span class="lineNum">    3061 </span>            : }</a>
+<a name="3062"><span class="lineNum">    3062 </span>            : #include &lt;cmath&gt;</a>
+<a name="3063"><span class="lineNum">    3063 </span>            : </a>
+<a name="3064"><span class="lineNum">    3064 </span>            : #include &quot;real.h&quot;</a>
+<a name="3065"><span class="lineNum">    3065 </span>            : #include &quot;blas.h&quot;</a>
+<a name="3066"><span class="lineNum">    3066 </span>            : </a>
+<a name="3067"><span class="lineNum">    3067 </span>            : namespace PLMD{</a>
+<a name="3068"><span class="lineNum">    3068 </span>            : namespace blas{</a>
+<a name="3069"><span class="lineNum">    3069 </span>            : void </a>
+<a name="3070"><span class="lineNum">    3070 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(strmm,STRMM)(const char *side, </span></a>
+<a name="3071"><span class="lineNum">    3071 </span>            :                       const char *uplo, </a>
+<a name="3072"><span class="lineNum">    3072 </span>            :                       const char *transa, </a>
+<a name="3073"><span class="lineNum">    3073 </span>            :                       const char *diag, </a>
+<a name="3074"><span class="lineNum">    3074 </span>            :                       int *m__, </a>
+<a name="3075"><span class="lineNum">    3075 </span>            :                       int *n__, </a>
+<a name="3076"><span class="lineNum">    3076 </span>            :                       float *alpha__, </a>
+<a name="3077"><span class="lineNum">    3077 </span>            :                       float *a, </a>
+<a name="3078"><span class="lineNum">    3078 </span>            :                       int *lda__, </a>
+<a name="3079"><span class="lineNum">    3079 </span>            :                       float *b, </a>
+<a name="3080"><span class="lineNum">    3080 </span>            :                       int *ldb__)</a>
+<a name="3081"><span class="lineNum">    3081 </span>            : {</a>
+<a name="3082"><span class="lineNum">    3082 </span>            :     int a_dim1, a_offset, b_dim1, b_offset, i__1, i__2, i__3;</a>
+<a name="3083"><span class="lineNum">    3083 </span>            :     </a>
+<a name="3084"><span class="lineNum">    3084 </span><span class="lineNoCov">          0 :     int m = *m__;</span></a>
+<a name="3085"><span class="lineNum">    3085 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="3086"><span class="lineNum">    3086 </span><span class="lineNoCov">          0 :     int lda = *lda__;</span></a>
+<a name="3087"><span class="lineNum">    3087 </span><span class="lineNoCov">          0 :     int ldb = *ldb__;</span></a>
+<a name="3088"><span class="lineNum">    3088 </span><span class="lineNoCov">          0 :     float alpha = *alpha__;</span></a>
+<a name="3089"><span class="lineNum">    3089 </span>            :     </a>
+<a name="3090"><span class="lineNum">    3090 </span>            :     /* Local variables */</a>
+<a name="3091"><span class="lineNum">    3091 </span>            :     int i__, j, k;</a>
+<a name="3092"><span class="lineNum">    3092 </span>            :     float temp;</a>
+<a name="3093"><span class="lineNum">    3093 </span>            :     int lside;</a>
+<a name="3094"><span class="lineNum">    3094 </span>            :     int upper;</a>
+<a name="3095"><span class="lineNum">    3095 </span>            :     int nounit;</a>
+<a name="3096"><span class="lineNum">    3096 </span>            :     a_dim1 = lda;</a>
+<a name="3097"><span class="lineNum">    3097 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="3098"><span class="lineNum">    3098 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="3099"><span class="lineNum">    3099 </span>            :     b_dim1 = ldb;</a>
+<a name="3100"><span class="lineNum">    3100 </span><span class="lineNoCov">          0 :     b_offset = 1 + b_dim1;</span></a>
+<a name="3101"><span class="lineNum">    3101 </span><span class="lineNoCov">          0 :     b -= b_offset;</span></a>
+<a name="3102"><span class="lineNum">    3102 </span>            : </a>
+<a name="3103"><span class="lineNum">    3103 </span>            :     /* Function Body */</a>
+<a name="3104"><span class="lineNum">    3104 </span><span class="lineNoCov">          0 :     lside = (*side=='L' || *side=='l');</span></a>
+<a name="3105"><span class="lineNum">    3105 </span>            : </a>
+<a name="3106"><span class="lineNum">    3106 </span><span class="lineNoCov">          0 :     nounit = (*diag=='N' || *diag=='n');</span></a>
+<a name="3107"><span class="lineNum">    3107 </span><span class="lineNoCov">          0 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="3108"><span class="lineNum">    3108 </span>            : </a>
+<a name="3109"><span class="lineNum">    3109 </span><span class="lineNoCov">          0 :     if (n == 0) {</span></a>
+<a name="3110"><span class="lineNum">    3110 </span>            :         return;</a>
+<a name="3111"><span class="lineNum">    3111 </span>            :     }</a>
+<a name="3112"><span class="lineNum">    3112 </span><span class="lineNoCov">          0 :     if (std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3113"><span class="lineNum">    3113 </span>            :         i__1 = n;</a>
+<a name="3114"><span class="lineNum">    3114 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3115"><span class="lineNum">    3115 </span>            :             i__2 = m;</a>
+<a name="3116"><span class="lineNum">    3116 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3117"><span class="lineNum">    3117 </span><span class="lineNoCov">          0 :                 b[i__ + j * b_dim1] = 0.;</span></a>
+<a name="3118"><span class="lineNum">    3118 </span>            :             }</a>
+<a name="3119"><span class="lineNum">    3119 </span>            :         }</a>
+<a name="3120"><span class="lineNum">    3120 </span>            :         return;</a>
+<a name="3121"><span class="lineNum">    3121 </span>            :     }</a>
+<a name="3122"><span class="lineNum">    3122 </span><span class="lineNoCov">          0 :     if (lside) {</span></a>
+<a name="3123"><span class="lineNum">    3123 </span><span class="lineNoCov">          0 :         if (*transa=='N' || *transa=='n') {</span></a>
+<a name="3124"><span class="lineNum">    3124 </span><span class="lineNoCov">          0 :             if (upper) {</span></a>
+<a name="3125"><span class="lineNum">    3125 </span>            :                 i__1 = n;</a>
+<a name="3126"><span class="lineNum">    3126 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3127"><span class="lineNum">    3127 </span>            :                     i__2 = m;</a>
+<a name="3128"><span class="lineNum">    3128 </span><span class="lineNoCov">          0 :                     for (k = 1; k &lt;= i__2; ++k) {</span></a>
+<a name="3129"><span class="lineNum">    3129 </span><span class="lineNoCov">          0 :                         if ( std::abs(b[k + j * b_dim1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3130"><span class="lineNum">    3130 </span><span class="lineNoCov">          0 :                             temp = alpha * b[k + j * b_dim1];</span></a>
+<a name="3131"><span class="lineNum">    3131 </span>            :                             i__3 = k - 1;</a>
+<a name="3132"><span class="lineNum">    3132 </span><span class="lineNoCov">          0 :                             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="3133"><span class="lineNum">    3133 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * a[i__ + k * </span></a>
+<a name="3134"><span class="lineNum">    3134 </span><span class="lineNoCov">          0 :                                         a_dim1];</span></a>
+<a name="3135"><span class="lineNum">    3135 </span>            :                             }</a>
+<a name="3136"><span class="lineNum">    3136 </span><span class="lineNoCov">          0 :                             if (nounit) {</span></a>
+<a name="3137"><span class="lineNum">    3137 </span><span class="lineNoCov">          0 :                                 temp *= a[k + k * a_dim1];</span></a>
+<a name="3138"><span class="lineNum">    3138 </span>            :                             }</a>
+<a name="3139"><span class="lineNum">    3139 </span><span class="lineNoCov">          0 :                             b[k + j * b_dim1] = temp;</span></a>
+<a name="3140"><span class="lineNum">    3140 </span>            :                         }</a>
+<a name="3141"><span class="lineNum">    3141 </span>            :                     }</a>
+<a name="3142"><span class="lineNum">    3142 </span>            :                 }</a>
+<a name="3143"><span class="lineNum">    3143 </span>            :             } else {</a>
+<a name="3144"><span class="lineNum">    3144 </span>            :                 i__1 = n;</a>
+<a name="3145"><span class="lineNum">    3145 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3146"><span class="lineNum">    3146 </span><span class="lineNoCov">          0 :                     for (k = m; k &gt;= 1; --k) {</span></a>
+<a name="3147"><span class="lineNum">    3147 </span><span class="lineNoCov">          0 :                         if (std::abs(b[k + j * b_dim1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3148"><span class="lineNum">    3148 </span><span class="lineNoCov">          0 :                             temp = alpha * b[k + j * b_dim1];</span></a>
+<a name="3149"><span class="lineNum">    3149 </span><span class="lineNoCov">          0 :                             b[k + j * b_dim1] = temp;</span></a>
+<a name="3150"><span class="lineNum">    3150 </span><span class="lineNoCov">          0 :                             if (nounit) {</span></a>
+<a name="3151"><span class="lineNum">    3151 </span><span class="lineNoCov">          0 :                                 b[k + j * b_dim1] *= a[k + k * a_dim1];</span></a>
+<a name="3152"><span class="lineNum">    3152 </span>            :                             }</a>
+<a name="3153"><span class="lineNum">    3153 </span>            :                             i__2 = m;</a>
+<a name="3154"><span class="lineNum">    3154 </span><span class="lineNoCov">          0 :                             for (i__ = k + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3155"><span class="lineNum">    3155 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * a[i__ + k * </span></a>
+<a name="3156"><span class="lineNum">    3156 </span><span class="lineNoCov">          0 :                                         a_dim1];</span></a>
+<a name="3157"><span class="lineNum">    3157 </span>            :                             }</a>
+<a name="3158"><span class="lineNum">    3158 </span>            :                         }</a>
+<a name="3159"><span class="lineNum">    3159 </span>            :                     }</a>
+<a name="3160"><span class="lineNum">    3160 </span>            :                 }</a>
+<a name="3161"><span class="lineNum">    3161 </span>            :             }</a>
+<a name="3162"><span class="lineNum">    3162 </span>            :         } else {</a>
+<a name="3163"><span class="lineNum">    3163 </span>            : </a>
+<a name="3164"><span class="lineNum">    3164 </span><span class="lineNoCov">          0 :             if (upper) {</span></a>
+<a name="3165"><span class="lineNum">    3165 </span>            :                 i__1 = n;</a>
+<a name="3166"><span class="lineNum">    3166 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3167"><span class="lineNum">    3167 </span><span class="lineNoCov">          0 :                     for (i__ = m; i__ &gt;= 1; --i__) {</span></a>
+<a name="3168"><span class="lineNum">    3168 </span><span class="lineNoCov">          0 :                         temp = b[i__ + j * b_dim1];</span></a>
+<a name="3169"><span class="lineNum">    3169 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="3170"><span class="lineNum">    3170 </span><span class="lineNoCov">          0 :                             temp *= a[i__ + i__ * a_dim1];</span></a>
+<a name="3171"><span class="lineNum">    3171 </span>            :                         }</a>
+<a name="3172"><span class="lineNum">    3172 </span>            :                         i__2 = i__ - 1;</a>
+<a name="3173"><span class="lineNum">    3173 </span><span class="lineNoCov">          0 :                         for (k = 1; k &lt;= i__2; ++k) {</span></a>
+<a name="3174"><span class="lineNum">    3174 </span><span class="lineNoCov">          0 :                             temp += a[k + i__ * a_dim1] * b[k + j * b_dim1];</span></a>
+<a name="3175"><span class="lineNum">    3175 </span>            :                         }</a>
+<a name="3176"><span class="lineNum">    3176 </span><span class="lineNoCov">          0 :                         b[i__ + j * b_dim1] = alpha * temp;</span></a>
+<a name="3177"><span class="lineNum">    3177 </span>            :                     }</a>
+<a name="3178"><span class="lineNum">    3178 </span>            :                 }</a>
+<a name="3179"><span class="lineNum">    3179 </span>            :             } else {</a>
+<a name="3180"><span class="lineNum">    3180 </span>            :                 i__1 = n;</a>
+<a name="3181"><span class="lineNum">    3181 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3182"><span class="lineNum">    3182 </span>            :                     i__2 = m;</a>
+<a name="3183"><span class="lineNum">    3183 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3184"><span class="lineNum">    3184 </span><span class="lineNoCov">          0 :                         temp = b[i__ + j * b_dim1];</span></a>
+<a name="3185"><span class="lineNum">    3185 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="3186"><span class="lineNum">    3186 </span><span class="lineNoCov">          0 :                             temp *= a[i__ + i__ * a_dim1];</span></a>
+<a name="3187"><span class="lineNum">    3187 </span>            :                         }</a>
+<a name="3188"><span class="lineNum">    3188 </span>            :                         i__3 = m;</a>
+<a name="3189"><span class="lineNum">    3189 </span><span class="lineNoCov">          0 :                         for (k = i__ + 1; k &lt;= i__3; ++k) {</span></a>
+<a name="3190"><span class="lineNum">    3190 </span><span class="lineNoCov">          0 :                             temp += a[k + i__ * a_dim1] * b[k + j * b_dim1];</span></a>
+<a name="3191"><span class="lineNum">    3191 </span>            :                         }</a>
+<a name="3192"><span class="lineNum">    3192 </span><span class="lineNoCov">          0 :                         b[i__ + j * b_dim1] = alpha * temp;</span></a>
+<a name="3193"><span class="lineNum">    3193 </span>            :                     }</a>
+<a name="3194"><span class="lineNum">    3194 </span>            :                 }</a>
+<a name="3195"><span class="lineNum">    3195 </span>            :             }</a>
+<a name="3196"><span class="lineNum">    3196 </span>            :         }</a>
+<a name="3197"><span class="lineNum">    3197 </span>            :     } else {</a>
+<a name="3198"><span class="lineNum">    3198 </span><span class="lineNoCov">          0 :         if (*transa=='N' || *transa=='n') {</span></a>
+<a name="3199"><span class="lineNum">    3199 </span>            : </a>
+<a name="3200"><span class="lineNum">    3200 </span><span class="lineNoCov">          0 :             if (upper) {</span></a>
+<a name="3201"><span class="lineNum">    3201 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="3202"><span class="lineNum">    3202 </span>            :                     temp = alpha;</a>
+<a name="3203"><span class="lineNum">    3203 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3204"><span class="lineNum">    3204 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="3205"><span class="lineNum">    3205 </span>            :                     }</a>
+<a name="3206"><span class="lineNum">    3206 </span>            :                     i__1 = m;</a>
+<a name="3207"><span class="lineNum">    3207 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3208"><span class="lineNum">    3208 </span><span class="lineNoCov">          0 :                         b[i__ + j * b_dim1] = temp * b[i__ + j * b_dim1];</span></a>
+<a name="3209"><span class="lineNum">    3209 </span>            :                     }</a>
+<a name="3210"><span class="lineNum">    3210 </span>            :                     i__1 = j - 1;</a>
+<a name="3211"><span class="lineNum">    3211 </span><span class="lineNoCov">          0 :                     for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="3212"><span class="lineNum">    3212 </span><span class="lineNoCov">          0 :                         if ( std::abs(a[k + j * a_dim1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3213"><span class="lineNum">    3213 </span><span class="lineNoCov">          0 :                             temp = alpha * a[k + j * a_dim1];</span></a>
+<a name="3214"><span class="lineNum">    3214 </span>            :                             i__2 = m;</a>
+<a name="3215"><span class="lineNum">    3215 </span><span class="lineNoCov">          0 :                             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3216"><span class="lineNum">    3216 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="3217"><span class="lineNum">    3217 </span><span class="lineNoCov">          0 :                                         b_dim1];</span></a>
+<a name="3218"><span class="lineNum">    3218 </span>            :                             }</a>
+<a name="3219"><span class="lineNum">    3219 </span>            :                         }</a>
+<a name="3220"><span class="lineNum">    3220 </span>            :                     }</a>
+<a name="3221"><span class="lineNum">    3221 </span>            :                 }</a>
+<a name="3222"><span class="lineNum">    3222 </span>            :             } else {</a>
+<a name="3223"><span class="lineNum">    3223 </span>            :                 i__1 = n;</a>
+<a name="3224"><span class="lineNum">    3224 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3225"><span class="lineNum">    3225 </span>            :                     temp = alpha;</a>
+<a name="3226"><span class="lineNum">    3226 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3227"><span class="lineNum">    3227 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="3228"><span class="lineNum">    3228 </span>            :                     }</a>
+<a name="3229"><span class="lineNum">    3229 </span>            :                     i__2 = m;</a>
+<a name="3230"><span class="lineNum">    3230 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3231"><span class="lineNum">    3231 </span><span class="lineNoCov">          0 :                         b[i__ + j * b_dim1] = temp * b[i__ + j * b_dim1];</span></a>
+<a name="3232"><span class="lineNum">    3232 </span>            :                     }</a>
+<a name="3233"><span class="lineNum">    3233 </span>            :                     i__2 = n;</a>
+<a name="3234"><span class="lineNum">    3234 </span><span class="lineNoCov">          0 :                     for (k = j + 1; k &lt;= i__2; ++k) {</span></a>
+<a name="3235"><span class="lineNum">    3235 </span><span class="lineNoCov">          0 :                         if ( std::abs(a[k + j * a_dim1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3236"><span class="lineNum">    3236 </span><span class="lineNoCov">          0 :                             temp = alpha * a[k + j * a_dim1];</span></a>
+<a name="3237"><span class="lineNum">    3237 </span>            :                             i__3 = m;</a>
+<a name="3238"><span class="lineNum">    3238 </span><span class="lineNoCov">          0 :                             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="3239"><span class="lineNum">    3239 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="3240"><span class="lineNum">    3240 </span><span class="lineNoCov">          0 :                                         b_dim1];</span></a>
+<a name="3241"><span class="lineNum">    3241 </span>            :                             }</a>
+<a name="3242"><span class="lineNum">    3242 </span>            :                         }</a>
+<a name="3243"><span class="lineNum">    3243 </span>            :                     }</a>
+<a name="3244"><span class="lineNum">    3244 </span>            :                 }</a>
+<a name="3245"><span class="lineNum">    3245 </span>            :             }</a>
+<a name="3246"><span class="lineNum">    3246 </span>            :         } else {</a>
+<a name="3247"><span class="lineNum">    3247 </span>            : </a>
+<a name="3248"><span class="lineNum">    3248 </span><span class="lineNoCov">          0 :             if (upper) {</span></a>
+<a name="3249"><span class="lineNum">    3249 </span>            :                 i__1 = n;</a>
+<a name="3250"><span class="lineNum">    3250 </span><span class="lineNoCov">          0 :                 for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="3251"><span class="lineNum">    3251 </span>            :                     i__2 = k - 1;</a>
+<a name="3252"><span class="lineNum">    3252 </span><span class="lineNoCov">          0 :                     for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="3253"><span class="lineNum">    3253 </span><span class="lineNoCov">          0 :                         if ( std::abs(a[j + k * a_dim1])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="3254"><span class="lineNum">    3254 </span><span class="lineNoCov">          0 :                             temp = alpha * a[j + k * a_dim1];</span></a>
+<a name="3255"><span class="lineNum">    3255 </span>            :                             i__3 = m;</a>
+<a name="3256"><span class="lineNum">    3256 </span><span class="lineNoCov">          0 :                             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="3257"><span class="lineNum">    3257 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="3258"><span class="lineNum">    3258 </span><span class="lineNoCov">          0 :                                         b_dim1];</span></a>
+<a name="3259"><span class="lineNum">    3259 </span>            :                             }</a>
+<a name="3260"><span class="lineNum">    3260 </span>            :                         }</a>
+<a name="3261"><span class="lineNum">    3261 </span>            :                     }</a>
+<a name="3262"><span class="lineNum">    3262 </span>            :                     temp = alpha;</a>
+<a name="3263"><span class="lineNum">    3263 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3264"><span class="lineNum">    3264 </span><span class="lineNoCov">          0 :                         temp *= a[k + k * a_dim1];</span></a>
+<a name="3265"><span class="lineNum">    3265 </span>            :                     }</a>
+<a name="3266"><span class="lineNum">    3266 </span><span class="lineNoCov">          0 :                     if ( std::abs(temp-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="3267"><span class="lineNum">    3267 </span>            :                         i__2 = m;</a>
+<a name="3268"><span class="lineNum">    3268 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3269"><span class="lineNum">    3269 </span><span class="lineNoCov">          0 :                             b[i__ + k * b_dim1] = temp * b[i__ + k * b_dim1];</span></a>
+<a name="3270"><span class="lineNum">    3270 </span>            :                         }</a>
+<a name="3271"><span class="lineNum">    3271 </span>            :                     }</a>
+<a name="3272"><span class="lineNum">    3272 </span>            :                 }</a>
+<a name="3273"><span class="lineNum">    3273 </span>            :             } else {</a>
+<a name="3274"><span class="lineNum">    3274 </span><span class="lineNoCov">          0 :                 for (k = n; k &gt;= 1; --k) {</span></a>
+<a name="3275"><span class="lineNum">    3275 </span>            :                     i__1 = n;</a>
+<a name="3276"><span class="lineNum">    3276 </span><span class="lineNoCov">          0 :                     for (j = k + 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3277"><span class="lineNum">    3277 </span><span class="lineNoCov">          0 :                         if ( std::abs(a[j + k * a_dim1])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3278"><span class="lineNum">    3278 </span><span class="lineNoCov">          0 :                             temp = alpha * a[j + k * a_dim1];</span></a>
+<a name="3279"><span class="lineNum">    3279 </span>            :                             i__2 = m;</a>
+<a name="3280"><span class="lineNum">    3280 </span><span class="lineNoCov">          0 :                             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3281"><span class="lineNum">    3281 </span><span class="lineNoCov">          0 :                                 b[i__ + j * b_dim1] += temp * b[i__ + k * </span></a>
+<a name="3282"><span class="lineNum">    3282 </span><span class="lineNoCov">          0 :                                         b_dim1];</span></a>
+<a name="3283"><span class="lineNum">    3283 </span>            :                             }</a>
+<a name="3284"><span class="lineNum">    3284 </span>            :                         }</a>
+<a name="3285"><span class="lineNum">    3285 </span>            :                     }</a>
+<a name="3286"><span class="lineNum">    3286 </span>            :                     temp = alpha;</a>
+<a name="3287"><span class="lineNum">    3287 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3288"><span class="lineNum">    3288 </span><span class="lineNoCov">          0 :                         temp *= a[k + k * a_dim1];</span></a>
+<a name="3289"><span class="lineNum">    3289 </span>            :                     }</a>
+<a name="3290"><span class="lineNum">    3290 </span><span class="lineNoCov">          0 :                     if ( std::abs(temp-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="3291"><span class="lineNum">    3291 </span>            :                         i__1 = m;</a>
+<a name="3292"><span class="lineNum">    3292 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3293"><span class="lineNum">    3293 </span><span class="lineNoCov">          0 :                             b[i__ + k * b_dim1] = temp * b[i__ + k * b_dim1];</span></a>
+<a name="3294"><span class="lineNum">    3294 </span>            :                         }</a>
+<a name="3295"><span class="lineNum">    3295 </span>            :                     }</a>
+<a name="3296"><span class="lineNum">    3296 </span>            :                 }</a>
+<a name="3297"><span class="lineNum">    3297 </span>            :             }</a>
+<a name="3298"><span class="lineNum">    3298 </span>            :         }</a>
+<a name="3299"><span class="lineNum">    3299 </span>            :     }</a>
+<a name="3300"><span class="lineNum">    3300 </span>            : </a>
+<a name="3301"><span class="lineNum">    3301 </span>            :     return;</a>
+<a name="3302"><span class="lineNum">    3302 </span>            : </a>
+<a name="3303"><span class="lineNum">    3303 </span>            : }</a>
+<a name="3304"><span class="lineNum">    3304 </span>            : </a>
+<a name="3305"><span class="lineNum">    3305 </span>            : </a>
+<a name="3306"><span class="lineNum">    3306 </span>            : }</a>
+<a name="3307"><span class="lineNum">    3307 </span>            : }</a>
+<a name="3308"><span class="lineNum">    3308 </span>            : #include &lt;cmath&gt;</a>
+<a name="3309"><span class="lineNum">    3309 </span>            : </a>
+<a name="3310"><span class="lineNum">    3310 </span>            : #include &quot;real.h&quot;</a>
+<a name="3311"><span class="lineNum">    3311 </span>            : #include &quot;blas.h&quot;</a>
+<a name="3312"><span class="lineNum">    3312 </span>            : </a>
+<a name="3313"><span class="lineNum">    3313 </span>            : namespace PLMD{</a>
+<a name="3314"><span class="lineNum">    3314 </span>            : namespace blas{</a>
+<a name="3315"><span class="lineNum">    3315 </span>            : void </a>
+<a name="3316"><span class="lineNum">    3316 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(strmv,STRMV)(const char *uplo, </span></a>
+<a name="3317"><span class="lineNum">    3317 </span>            :                       const char *trans,</a>
+<a name="3318"><span class="lineNum">    3318 </span>            :                       const char *diag, </a>
+<a name="3319"><span class="lineNum">    3319 </span>            :                       int *n__, </a>
+<a name="3320"><span class="lineNum">    3320 </span>            :                       float *a, </a>
+<a name="3321"><span class="lineNum">    3321 </span>            :                       int *lda__, </a>
+<a name="3322"><span class="lineNum">    3322 </span>            :                       float *x, </a>
+<a name="3323"><span class="lineNum">    3323 </span>            :                       int *incx__)</a>
+<a name="3324"><span class="lineNum">    3324 </span>            : {</a>
+<a name="3325"><span class="lineNum">    3325 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="3326"><span class="lineNum">    3326 </span>            : </a>
+<a name="3327"><span class="lineNum">    3327 </span>            :     int i__, j, ix, jx, kx;</a>
+<a name="3328"><span class="lineNum">    3328 </span>            :     float temp;</a>
+<a name="3329"><span class="lineNum">    3329 </span>            :     int nounit;</a>
+<a name="3330"><span class="lineNum">    3330 </span>            :     </a>
+<a name="3331"><span class="lineNum">    3331 </span><span class="lineNoCov">          0 :     int n = *n__;</span></a>
+<a name="3332"><span class="lineNum">    3332 </span><span class="lineNoCov">          0 :     int lda = *lda__;</span></a>
+<a name="3333"><span class="lineNum">    3333 </span><span class="lineNoCov">          0 :     int incx = *incx__;</span></a>
+<a name="3334"><span class="lineNum">    3334 </span>            :     </a>
+<a name="3335"><span class="lineNum">    3335 </span>            :     a_dim1 = lda;</a>
+<a name="3336"><span class="lineNum">    3336 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="3337"><span class="lineNum">    3337 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="3338"><span class="lineNum">    3338 </span><span class="lineNoCov">          0 :     --x;</span></a>
+<a name="3339"><span class="lineNum">    3339 </span>            : </a>
+<a name="3340"><span class="lineNum">    3340 </span><span class="lineNoCov">          0 :     if (n == 0) {</span></a>
+<a name="3341"><span class="lineNum">    3341 </span>            :         return;</a>
+<a name="3342"><span class="lineNum">    3342 </span>            :     }</a>
+<a name="3343"><span class="lineNum">    3343 </span>            : </a>
+<a name="3344"><span class="lineNum">    3344 </span><span class="lineNoCov">          0 :     nounit = (*diag=='n' || *diag=='N');</span></a>
+<a name="3345"><span class="lineNum">    3345 </span>            : </a>
+<a name="3346"><span class="lineNum">    3346 </span><span class="lineNoCov">          0 :     if (incx &lt;= 0) {</span></a>
+<a name="3347"><span class="lineNum">    3347 </span><span class="lineNoCov">          0 :         kx = 1 - (n - 1) * incx;</span></a>
+<a name="3348"><span class="lineNum">    3348 </span>            :     } else {</a>
+<a name="3349"><span class="lineNum">    3349 </span>            :         kx = 1;</a>
+<a name="3350"><span class="lineNum">    3350 </span>            :     }</a>
+<a name="3351"><span class="lineNum">    3351 </span>            : </a>
+<a name="3352"><span class="lineNum">    3352 </span><span class="lineNoCov">          0 :     if (*trans=='N' || *trans=='n') {</span></a>
+<a name="3353"><span class="lineNum">    3353 </span>            : </a>
+<a name="3354"><span class="lineNum">    3354 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="3355"><span class="lineNum">    3355 </span><span class="lineNoCov">          0 :             if (incx == 1) {</span></a>
+<a name="3356"><span class="lineNum">    3356 </span>            :                 i__1 = n;</a>
+<a name="3357"><span class="lineNum">    3357 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3358"><span class="lineNum">    3358 </span><span class="lineNoCov">          0 :                     if (std::abs(x[j])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3359"><span class="lineNum">    3359 </span>            :                         temp = x[j];</a>
+<a name="3360"><span class="lineNum">    3360 </span>            :                         i__2 = j - 1;</a>
+<a name="3361"><span class="lineNum">    3361 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3362"><span class="lineNum">    3362 </span><span class="lineNoCov">          0 :                             x[i__] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="3363"><span class="lineNum">    3363 </span>            :                         }</a>
+<a name="3364"><span class="lineNum">    3364 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="3365"><span class="lineNum">    3365 </span><span class="lineNoCov">          0 :                             x[j] *= a[j + j * a_dim1];</span></a>
+<a name="3366"><span class="lineNum">    3366 </span>            :                         }</a>
+<a name="3367"><span class="lineNum">    3367 </span>            :                     }</a>
+<a name="3368"><span class="lineNum">    3368 </span>            :                 }</a>
+<a name="3369"><span class="lineNum">    3369 </span>            :             } else {</a>
+<a name="3370"><span class="lineNum">    3370 </span>            :                 jx = kx;</a>
+<a name="3371"><span class="lineNum">    3371 </span>            :                 i__1 = n;</a>
+<a name="3372"><span class="lineNum">    3372 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3373"><span class="lineNum">    3373 </span><span class="lineNoCov">          0 :                     if (std::abs(x[jx])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3374"><span class="lineNum">    3374 </span>            :                         temp = x[jx];</a>
+<a name="3375"><span class="lineNum">    3375 </span>            :                         ix = kx;</a>
+<a name="3376"><span class="lineNum">    3376 </span>            :                         i__2 = j - 1;</a>
+<a name="3377"><span class="lineNum">    3377 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3378"><span class="lineNum">    3378 </span><span class="lineNoCov">          0 :                             x[ix] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="3379"><span class="lineNum">    3379 </span><span class="lineNoCov">          0 :                             ix += incx;</span></a>
+<a name="3380"><span class="lineNum">    3380 </span>            :                         }</a>
+<a name="3381"><span class="lineNum">    3381 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="3382"><span class="lineNum">    3382 </span><span class="lineNoCov">          0 :                             x[jx] *= a[j + j * a_dim1];</span></a>
+<a name="3383"><span class="lineNum">    3383 </span>            :                         }</a>
+<a name="3384"><span class="lineNum">    3384 </span>            :                     }</a>
+<a name="3385"><span class="lineNum">    3385 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="3386"><span class="lineNum">    3386 </span>            :                 }</a>
+<a name="3387"><span class="lineNum">    3387 </span>            :             }</a>
+<a name="3388"><span class="lineNum">    3388 </span>            :         } else {</a>
+<a name="3389"><span class="lineNum">    3389 </span><span class="lineNoCov">          0 :             if (incx == 1) {</span></a>
+<a name="3390"><span class="lineNum">    3390 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="3391"><span class="lineNum">    3391 </span><span class="lineNoCov">          0 :                     if (std::abs(x[j])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3392"><span class="lineNum">    3392 </span>            :                         temp = x[j];</a>
+<a name="3393"><span class="lineNum">    3393 </span>            :                         i__1 = j + 1;</a>
+<a name="3394"><span class="lineNum">    3394 </span><span class="lineNoCov">          0 :                         for (i__ = n; i__ &gt;= i__1; --i__) {</span></a>
+<a name="3395"><span class="lineNum">    3395 </span><span class="lineNoCov">          0 :                             x[i__] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="3396"><span class="lineNum">    3396 </span>            :                         }</a>
+<a name="3397"><span class="lineNum">    3397 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="3398"><span class="lineNum">    3398 </span><span class="lineNoCov">          0 :                             x[j] *= a[j + j * a_dim1];</span></a>
+<a name="3399"><span class="lineNum">    3399 </span>            :                         }</a>
+<a name="3400"><span class="lineNum">    3400 </span>            :                     }</a>
+<a name="3401"><span class="lineNum">    3401 </span>            :                 }</a>
+<a name="3402"><span class="lineNum">    3402 </span>            :             } else {</a>
+<a name="3403"><span class="lineNum">    3403 </span><span class="lineNoCov">          0 :                 kx += (n - 1) * incx;</span></a>
+<a name="3404"><span class="lineNum">    3404 </span>            :                 jx = kx;</a>
+<a name="3405"><span class="lineNum">    3405 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="3406"><span class="lineNum">    3406 </span><span class="lineNoCov">          0 :                     if (std::abs(x[jx])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3407"><span class="lineNum">    3407 </span>            :                         temp = x[jx];</a>
+<a name="3408"><span class="lineNum">    3408 </span>            :                         ix = kx;</a>
+<a name="3409"><span class="lineNum">    3409 </span>            :                         i__1 = j + 1;</a>
+<a name="3410"><span class="lineNum">    3410 </span><span class="lineNoCov">          0 :                         for (i__ = n; i__ &gt;= i__1; --i__) {</span></a>
+<a name="3411"><span class="lineNum">    3411 </span><span class="lineNoCov">          0 :                             x[ix] += temp * a[i__ + j * a_dim1];</span></a>
+<a name="3412"><span class="lineNum">    3412 </span><span class="lineNoCov">          0 :                             ix -= incx;</span></a>
+<a name="3413"><span class="lineNum">    3413 </span>            :                         }</a>
+<a name="3414"><span class="lineNum">    3414 </span><span class="lineNoCov">          0 :                         if (nounit) {</span></a>
+<a name="3415"><span class="lineNum">    3415 </span><span class="lineNoCov">          0 :                             x[jx] *= a[j + j * a_dim1];</span></a>
+<a name="3416"><span class="lineNum">    3416 </span>            :                         }</a>
+<a name="3417"><span class="lineNum">    3417 </span>            :                     }</a>
+<a name="3418"><span class="lineNum">    3418 </span><span class="lineNoCov">          0 :                     jx -= incx;</span></a>
+<a name="3419"><span class="lineNum">    3419 </span>            :                 }</a>
+<a name="3420"><span class="lineNum">    3420 </span>            :             }</a>
+<a name="3421"><span class="lineNum">    3421 </span>            :         }</a>
+<a name="3422"><span class="lineNum">    3422 </span>            :     } else {</a>
+<a name="3423"><span class="lineNum">    3423 </span>            : </a>
+<a name="3424"><span class="lineNum">    3424 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="3425"><span class="lineNum">    3425 </span><span class="lineNoCov">          0 :             if (incx == 1) {</span></a>
+<a name="3426"><span class="lineNum">    3426 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="3427"><span class="lineNum">    3427 </span><span class="lineNoCov">          0 :                     temp = x[j];</span></a>
+<a name="3428"><span class="lineNum">    3428 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3429"><span class="lineNum">    3429 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="3430"><span class="lineNum">    3430 </span>            :                     }</a>
+<a name="3431"><span class="lineNum">    3431 </span><span class="lineNoCov">          0 :                     for (i__ = j - 1; i__ &gt;= 1; --i__) {</span></a>
+<a name="3432"><span class="lineNum">    3432 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[i__];</span></a>
+<a name="3433"><span class="lineNum">    3433 </span>            :                     }</a>
+<a name="3434"><span class="lineNum">    3434 </span><span class="lineNoCov">          0 :                     x[j] = temp;</span></a>
+<a name="3435"><span class="lineNum">    3435 </span>            :                 }</a>
+<a name="3436"><span class="lineNum">    3436 </span>            :             } else {</a>
+<a name="3437"><span class="lineNum">    3437 </span><span class="lineNoCov">          0 :                 jx = kx + (n - 1) * incx;</span></a>
+<a name="3438"><span class="lineNum">    3438 </span><span class="lineNoCov">          0 :                 for (j = n; j &gt;= 1; --j) {</span></a>
+<a name="3439"><span class="lineNum">    3439 </span><span class="lineNoCov">          0 :                     temp = x[jx];</span></a>
+<a name="3440"><span class="lineNum">    3440 </span>            :                     ix = jx;</a>
+<a name="3441"><span class="lineNum">    3441 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3442"><span class="lineNum">    3442 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="3443"><span class="lineNum">    3443 </span>            :                     }</a>
+<a name="3444"><span class="lineNum">    3444 </span><span class="lineNoCov">          0 :                     for (i__ = j - 1; i__ &gt;= 1; --i__) {</span></a>
+<a name="3445"><span class="lineNum">    3445 </span><span class="lineNoCov">          0 :                         ix -= incx;</span></a>
+<a name="3446"><span class="lineNum">    3446 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[ix];</span></a>
+<a name="3447"><span class="lineNum">    3447 </span>            :                     }</a>
+<a name="3448"><span class="lineNum">    3448 </span><span class="lineNoCov">          0 :                     x[jx] = temp;</span></a>
+<a name="3449"><span class="lineNum">    3449 </span><span class="lineNoCov">          0 :                     jx -= incx;</span></a>
+<a name="3450"><span class="lineNum">    3450 </span>            :                 }</a>
+<a name="3451"><span class="lineNum">    3451 </span>            :             }</a>
+<a name="3452"><span class="lineNum">    3452 </span>            :         } else {</a>
+<a name="3453"><span class="lineNum">    3453 </span><span class="lineNoCov">          0 :             if (incx == 1) {</span></a>
+<a name="3454"><span class="lineNum">    3454 </span>            :                 i__1 = n;</a>
+<a name="3455"><span class="lineNum">    3455 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3456"><span class="lineNum">    3456 </span><span class="lineNoCov">          0 :                     temp = x[j];</span></a>
+<a name="3457"><span class="lineNum">    3457 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3458"><span class="lineNum">    3458 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="3459"><span class="lineNum">    3459 </span>            :                     }</a>
+<a name="3460"><span class="lineNum">    3460 </span>            :                     i__2 = n;</a>
+<a name="3461"><span class="lineNum">    3461 </span><span class="lineNoCov">          0 :                     for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3462"><span class="lineNum">    3462 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[i__];</span></a>
+<a name="3463"><span class="lineNum">    3463 </span>            :                     }</a>
+<a name="3464"><span class="lineNum">    3464 </span><span class="lineNoCov">          0 :                     x[j] = temp;</span></a>
+<a name="3465"><span class="lineNum">    3465 </span>            :                 }</a>
+<a name="3466"><span class="lineNum">    3466 </span>            :             } else {</a>
+<a name="3467"><span class="lineNum">    3467 </span>            :                 jx = kx;</a>
+<a name="3468"><span class="lineNum">    3468 </span>            :                 i__1 = n;</a>
+<a name="3469"><span class="lineNum">    3469 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3470"><span class="lineNum">    3470 </span><span class="lineNoCov">          0 :                     temp = x[jx];</span></a>
+<a name="3471"><span class="lineNum">    3471 </span>            :                     ix = jx;</a>
+<a name="3472"><span class="lineNum">    3472 </span><span class="lineNoCov">          0 :                     if (nounit) {</span></a>
+<a name="3473"><span class="lineNum">    3473 </span><span class="lineNoCov">          0 :                         temp *= a[j + j * a_dim1];</span></a>
+<a name="3474"><span class="lineNum">    3474 </span>            :                     }</a>
+<a name="3475"><span class="lineNum">    3475 </span>            :                     i__2 = n;</a>
+<a name="3476"><span class="lineNum">    3476 </span><span class="lineNoCov">          0 :                     for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3477"><span class="lineNum">    3477 </span><span class="lineNoCov">          0 :                         ix += incx;</span></a>
+<a name="3478"><span class="lineNum">    3478 </span><span class="lineNoCov">          0 :                         temp += a[i__ + j * a_dim1] * x[ix];</span></a>
+<a name="3479"><span class="lineNum">    3479 </span>            :                     }</a>
+<a name="3480"><span class="lineNum">    3480 </span><span class="lineNoCov">          0 :                     x[jx] = temp;</span></a>
+<a name="3481"><span class="lineNum">    3481 </span><span class="lineNoCov">          0 :                     jx += incx;</span></a>
+<a name="3482"><span class="lineNum">    3482 </span>            :                 }</a>
+<a name="3483"><span class="lineNum">    3483 </span>            :             }</a>
+<a name="3484"><span class="lineNum">    3484 </span>            :         }</a>
+<a name="3485"><span class="lineNum">    3485 </span>            :     }</a>
+<a name="3486"><span class="lineNum">    3486 </span>            : </a>
+<a name="3487"><span class="lineNum">    3487 </span>            :     return;</a>
+<a name="3488"><span class="lineNum">    3488 </span>            : </a>
+<a name="3489"><span class="lineNum">    3489 </span>            : }</a>
+<a name="3490"><span class="lineNum">    3490 </span>            : </a>
+<a name="3491"><span class="lineNum">    3491 </span>            : </a>
+<a name="3492"><span class="lineNum">    3492 </span>            : }</a>
+<a name="3493"><span class="lineNum">    3493 </span>            : }</a>
+<a name="3494"><span class="lineNum">    3494 </span>            : #include &lt;cctype&gt;</a>
+<a name="3495"><span class="lineNum">    3495 </span>            : #include &lt;cmath&gt;</a>
+<a name="3496"><span class="lineNum">    3496 </span>            : </a>
+<a name="3497"><span class="lineNum">    3497 </span>            : #include &quot;real.h&quot;</a>
+<a name="3498"><span class="lineNum">    3498 </span>            : #include &quot;blas.h&quot;</a>
+<a name="3499"><span class="lineNum">    3499 </span>            : </a>
+<a name="3500"><span class="lineNum">    3500 </span>            : namespace PLMD{</a>
+<a name="3501"><span class="lineNum">    3501 </span>            : namespace blas{</a>
+<a name="3502"><span class="lineNum">    3502 </span>            : void</a>
+<a name="3503"><span class="lineNum">    3503 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(strsm,STRSM)(const char * side,</span></a>
+<a name="3504"><span class="lineNum">    3504 </span>            :                       const char * uplo,</a>
+<a name="3505"><span class="lineNum">    3505 </span>            :                       const char * transa,</a>
+<a name="3506"><span class="lineNum">    3506 </span>            :                       const char * diag,</a>
+<a name="3507"><span class="lineNum">    3507 </span>            :                       int *  m__,</a>
+<a name="3508"><span class="lineNum">    3508 </span>            :                       int *  n__,</a>
+<a name="3509"><span class="lineNum">    3509 </span>            :                       float *alpha__,</a>
+<a name="3510"><span class="lineNum">    3510 </span>            :                       float *a,</a>
+<a name="3511"><span class="lineNum">    3511 </span>            :                       int *  lda__,</a>
+<a name="3512"><span class="lineNum">    3512 </span>            :                       float *b,</a>
+<a name="3513"><span class="lineNum">    3513 </span>            :                       int *  ldb__)</a>
+<a name="3514"><span class="lineNum">    3514 </span>            : {</a>
+<a name="3515"><span class="lineNum">    3515 </span><span class="lineNoCov">          0 :   const char xside  = std::toupper(*side);</span></a>
+<a name="3516"><span class="lineNum">    3516 </span><span class="lineNoCov">          0 :   const char xuplo  = std::toupper(*uplo);</span></a>
+<a name="3517"><span class="lineNum">    3517 </span><span class="lineNoCov">          0 :   const char xtrans = std::toupper(*transa);</span></a>
+<a name="3518"><span class="lineNum">    3518 </span><span class="lineNoCov">          0 :   const char xdiag  = std::toupper(*diag);</span></a>
+<a name="3519"><span class="lineNum">    3519 </span>            :   int i,j,k;</a>
+<a name="3520"><span class="lineNum">    3520 </span>            :   float temp;</a>
+<a name="3521"><span class="lineNum">    3521 </span>            : </a>
+<a name="3522"><span class="lineNum">    3522 </span><span class="lineNoCov">          0 :   int m = *m__;</span></a>
+<a name="3523"><span class="lineNum">    3523 </span><span class="lineNoCov">          0 :   int n = *n__;</span></a>
+<a name="3524"><span class="lineNum">    3524 </span><span class="lineNoCov">          0 :   int lda = *lda__;</span></a>
+<a name="3525"><span class="lineNum">    3525 </span><span class="lineNoCov">          0 :   int ldb = *ldb__;</span></a>
+<a name="3526"><span class="lineNum">    3526 </span><span class="lineNoCov">          0 :   float alpha = *alpha__;</span></a>
+<a name="3527"><span class="lineNum">    3527 </span>            :   </a>
+<a name="3528"><span class="lineNum">    3528 </span><span class="lineNoCov">          0 :   if(n&lt;=0)</span></a>
+<a name="3529"><span class="lineNum">    3529 </span>            :     return;</a>
+<a name="3530"><span class="lineNum">    3530 </span>            : </a>
+<a name="3531"><span class="lineNum">    3531 </span>            :   </a>
+<a name="3532"><span class="lineNum">    3532 </span><span class="lineNoCov">          0 :   if(std::abs(alpha)&lt;PLUMED_GMX_FLOAT_MIN) { </span></a>
+<a name="3533"><span class="lineNum">    3533 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;n;j++)</span></a>
+<a name="3534"><span class="lineNum">    3534 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;m;i++)</span></a>
+<a name="3535"><span class="lineNum">    3535 </span><span class="lineNoCov">          0 :         b[j*(ldb)+i] = 0.0;</span></a>
+<a name="3536"><span class="lineNum">    3536 </span>            :     return;</a>
+<a name="3537"><span class="lineNum">    3537 </span>            :   }</a>
+<a name="3538"><span class="lineNum">    3538 </span>            : </a>
+<a name="3539"><span class="lineNum">    3539 </span><span class="lineNoCov">          0 :   if(xside=='L') {</span></a>
+<a name="3540"><span class="lineNum">    3540 </span>            :     /* left side */</a>
+<a name="3541"><span class="lineNum">    3541 </span><span class="lineNoCov">          0 :     if(xtrans=='N') {</span></a>
+<a name="3542"><span class="lineNum">    3542 </span>            :       /* No transpose */</a>
+<a name="3543"><span class="lineNum">    3543 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="3544"><span class="lineNum">    3544 </span>            :         /* upper */</a>
+<a name="3545"><span class="lineNum">    3545 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="3546"><span class="lineNum">    3546 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="3547"><span class="lineNum">    3547 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3548"><span class="lineNum">    3548 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="3549"><span class="lineNum">    3549 </span>            :           }</a>
+<a name="3550"><span class="lineNum">    3550 </span><span class="lineNoCov">          0 :           for(k=m-1;k&gt;=0;k--) {</span></a>
+<a name="3551"><span class="lineNum">    3551 </span><span class="lineNoCov">          0 :             if( std::abs(b[j*(ldb)+k])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3552"><span class="lineNum">    3552 </span><span class="lineNoCov">          0 :               if(xdiag=='N')</span></a>
+<a name="3553"><span class="lineNum">    3553 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+k] /= a[k*(lda)+k];</span></a>
+<a name="3554"><span class="lineNum">    3554 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;k;i++)</span></a>
+<a name="3555"><span class="lineNum">    3555 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= b[j*(ldb)+k]*a[k*(lda)+i];</span></a>
+<a name="3556"><span class="lineNum">    3556 </span>            :             }</a>
+<a name="3557"><span class="lineNum">    3557 </span>            :           }</a>
+<a name="3558"><span class="lineNum">    3558 </span>            :         }</a>
+<a name="3559"><span class="lineNum">    3559 </span>            :       } else {</a>
+<a name="3560"><span class="lineNum">    3560 </span>            :         /* lower */</a>
+<a name="3561"><span class="lineNum">    3561 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="3562"><span class="lineNum">    3562 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="3563"><span class="lineNum">    3563 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3564"><span class="lineNum">    3564 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="3565"><span class="lineNum">    3565 </span><span class="lineNoCov">          0 :           for(k=0;k&lt;m;k++) {</span></a>
+<a name="3566"><span class="lineNum">    3566 </span><span class="lineNoCov">          0 :             if( std::abs(b[j*(ldb)+k])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3567"><span class="lineNum">    3567 </span><span class="lineNoCov">          0 :               if(xdiag=='N')</span></a>
+<a name="3568"><span class="lineNum">    3568 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+k] /= a[k*(lda)+k];</span></a>
+<a name="3569"><span class="lineNum">    3569 </span><span class="lineNoCov">          0 :               for(i=k+1;i&lt;m;i++)</span></a>
+<a name="3570"><span class="lineNum">    3570 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= b[j*(ldb)+k]*a[k*(lda)+i];</span></a>
+<a name="3571"><span class="lineNum">    3571 </span>            :             }</a>
+<a name="3572"><span class="lineNum">    3572 </span>            :           }</a>
+<a name="3573"><span class="lineNum">    3573 </span>            :         }</a>
+<a name="3574"><span class="lineNum">    3574 </span>            :       }</a>
+<a name="3575"><span class="lineNum">    3575 </span>            :     } else {</a>
+<a name="3576"><span class="lineNum">    3576 </span>            :       /* Transpose */</a>
+<a name="3577"><span class="lineNum">    3577 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="3578"><span class="lineNum">    3578 </span>            :         /* upper */</a>
+<a name="3579"><span class="lineNum">    3579 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="3580"><span class="lineNum">    3580 </span><span class="lineNoCov">          0 :           for(i=0;i&lt;m;i++) {</span></a>
+<a name="3581"><span class="lineNum">    3581 </span><span class="lineNoCov">          0 :             temp = alpha * b[j*(ldb)+i];</span></a>
+<a name="3582"><span class="lineNum">    3582 </span><span class="lineNoCov">          0 :             for(k=0;k&lt;i;k++)</span></a>
+<a name="3583"><span class="lineNum">    3583 </span><span class="lineNoCov">          0 :               temp -= a[i*(lda)+k] * b[j*(ldb)+k];</span></a>
+<a name="3584"><span class="lineNum">    3584 </span><span class="lineNoCov">          0 :             if(xdiag=='N')</span></a>
+<a name="3585"><span class="lineNum">    3585 </span><span class="lineNoCov">          0 :                 temp /= a[i*(lda)+i];</span></a>
+<a name="3586"><span class="lineNum">    3586 </span><span class="lineNoCov">          0 :             b[j*(ldb)+i] = temp;</span></a>
+<a name="3587"><span class="lineNum">    3587 </span>            :           }</a>
+<a name="3588"><span class="lineNum">    3588 </span>            :         }</a>
+<a name="3589"><span class="lineNum">    3589 </span>            :       } else {</a>
+<a name="3590"><span class="lineNum">    3590 </span>            :         /* lower */</a>
+<a name="3591"><span class="lineNum">    3591 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="3592"><span class="lineNum">    3592 </span><span class="lineNoCov">          0 :           for(i=m-1;i&gt;=0;i--) {</span></a>
+<a name="3593"><span class="lineNum">    3593 </span><span class="lineNoCov">          0 :             temp = alpha * b[j*(ldb)+i];</span></a>
+<a name="3594"><span class="lineNum">    3594 </span><span class="lineNoCov">          0 :             for(k=i+1;k&lt;m;k++)</span></a>
+<a name="3595"><span class="lineNum">    3595 </span><span class="lineNoCov">          0 :               temp -= a[i*(lda)+k] * b[j*(ldb)+k];</span></a>
+<a name="3596"><span class="lineNum">    3596 </span><span class="lineNoCov">          0 :             if(xdiag=='N')</span></a>
+<a name="3597"><span class="lineNum">    3597 </span><span class="lineNoCov">          0 :                 temp /= a[i*(lda)+i];</span></a>
+<a name="3598"><span class="lineNum">    3598 </span><span class="lineNoCov">          0 :             b[j*(ldb)+i] = temp;</span></a>
+<a name="3599"><span class="lineNum">    3599 </span>            :           }</a>
+<a name="3600"><span class="lineNum">    3600 </span>            :         }</a>
+<a name="3601"><span class="lineNum">    3601 </span>            :       }</a>
+<a name="3602"><span class="lineNum">    3602 </span>            :     }</a>
+<a name="3603"><span class="lineNum">    3603 </span>            :   } else {</a>
+<a name="3604"><span class="lineNum">    3604 </span>            :     /* right side */</a>
+<a name="3605"><span class="lineNum">    3605 </span><span class="lineNoCov">          0 :     if(xtrans=='N') {</span></a>
+<a name="3606"><span class="lineNum">    3606 </span>            :       /* No transpose */</a>
+<a name="3607"><span class="lineNum">    3607 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="3608"><span class="lineNum">    3608 </span>            :         /* upper */</a>
+<a name="3609"><span class="lineNum">    3609 </span><span class="lineNoCov">          0 :         for(j=0;j&lt;n;j++) {</span></a>
+<a name="3610"><span class="lineNum">    3610 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="3611"><span class="lineNum">    3611 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3612"><span class="lineNum">    3612 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="3613"><span class="lineNum">    3613 </span><span class="lineNoCov">          0 :           for(k=0;k&lt;j;k++) {</span></a>
+<a name="3614"><span class="lineNum">    3614 </span><span class="lineNoCov">          0 :             if( std::abs(a[j*(lda)+k])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3615"><span class="lineNum">    3615 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="3616"><span class="lineNum">    3616 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= a[j*(lda)+k]*b[k*(ldb)+i];</span></a>
+<a name="3617"><span class="lineNum">    3617 </span>            :             }</a>
+<a name="3618"><span class="lineNum">    3618 </span>            :           }</a>
+<a name="3619"><span class="lineNum">    3619 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="3620"><span class="lineNum">    3620 </span><span class="lineNoCov">          0 :             temp = 1.0/a[j*(lda)+j];</span></a>
+<a name="3621"><span class="lineNum">    3621 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3622"><span class="lineNum">    3622 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= temp;</span></a>
+<a name="3623"><span class="lineNum">    3623 </span>            :           }</a>
+<a name="3624"><span class="lineNum">    3624 </span>            :         }</a>
+<a name="3625"><span class="lineNum">    3625 </span>            :       } else {</a>
+<a name="3626"><span class="lineNum">    3626 </span>            :         /* lower */</a>
+<a name="3627"><span class="lineNum">    3627 </span><span class="lineNoCov">          0 :         for(j=n-1;j&gt;=0;j--) {</span></a>
+<a name="3628"><span class="lineNum">    3628 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="3629"><span class="lineNum">    3629 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3630"><span class="lineNum">    3630 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= alpha;</span></a>
+<a name="3631"><span class="lineNum">    3631 </span><span class="lineNoCov">          0 :           for(k=j+1;k&lt;n;k++) {</span></a>
+<a name="3632"><span class="lineNum">    3632 </span><span class="lineNoCov">          0 :             if( std::abs(a[j*(lda)+k])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="3633"><span class="lineNum">    3633 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="3634"><span class="lineNum">    3634 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= a[j*(lda)+k]*b[k*(ldb)+i];</span></a>
+<a name="3635"><span class="lineNum">    3635 </span>            :             }</a>
+<a name="3636"><span class="lineNum">    3636 </span>            :           }</a>
+<a name="3637"><span class="lineNum">    3637 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="3638"><span class="lineNum">    3638 </span><span class="lineNoCov">          0 :             temp = 1.0/a[j*(lda)+j];</span></a>
+<a name="3639"><span class="lineNum">    3639 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3640"><span class="lineNum">    3640 </span><span class="lineNoCov">          0 :               b[j*(ldb)+i] *= temp;</span></a>
+<a name="3641"><span class="lineNum">    3641 </span>            :           }</a>
+<a name="3642"><span class="lineNum">    3642 </span>            :         }</a>
+<a name="3643"><span class="lineNum">    3643 </span>            :       }</a>
+<a name="3644"><span class="lineNum">    3644 </span>            :     } else {</a>
+<a name="3645"><span class="lineNum">    3645 </span>            :       /* Transpose */</a>
+<a name="3646"><span class="lineNum">    3646 </span><span class="lineNoCov">          0 :       if(xuplo=='U') {</span></a>
+<a name="3647"><span class="lineNum">    3647 </span>            :         /* upper */</a>
+<a name="3648"><span class="lineNum">    3648 </span><span class="lineNoCov">          0 :         for(k=n-1;k&gt;=0;k--) {</span></a>
+<a name="3649"><span class="lineNum">    3649 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="3650"><span class="lineNum">    3650 </span><span class="lineNoCov">          0 :             temp = 1.0/a[k*(lda)+k];</span></a>
+<a name="3651"><span class="lineNum">    3651 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3652"><span class="lineNum">    3652 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= temp;</span></a>
+<a name="3653"><span class="lineNum">    3653 </span>            :           }</a>
+<a name="3654"><span class="lineNum">    3654 </span><span class="lineNoCov">          0 :           for(j=0;j&lt;k;j++) {</span></a>
+<a name="3655"><span class="lineNum">    3655 </span><span class="lineNoCov">          0 :             if( std::abs(a[k*(lda)+j])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3656"><span class="lineNum">    3656 </span>            :               temp = a[k*(lda)+j];</a>
+<a name="3657"><span class="lineNum">    3657 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="3658"><span class="lineNum">    3658 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= temp * b[k*(ldb)+i];</span></a>
+<a name="3659"><span class="lineNum">    3659 </span>            :             }</a>
+<a name="3660"><span class="lineNum">    3660 </span>            :           }</a>
+<a name="3661"><span class="lineNum">    3661 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="3662"><span class="lineNum">    3662 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3663"><span class="lineNum">    3663 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= alpha;</span></a>
+<a name="3664"><span class="lineNum">    3664 </span>            :         }</a>
+<a name="3665"><span class="lineNum">    3665 </span>            :       } else {</a>
+<a name="3666"><span class="lineNum">    3666 </span>            :         /* lower */</a>
+<a name="3667"><span class="lineNum">    3667 </span><span class="lineNoCov">          0 :         for(k=0;k&lt;n;k++) {</span></a>
+<a name="3668"><span class="lineNum">    3668 </span><span class="lineNoCov">          0 :           if(xdiag=='N') {</span></a>
+<a name="3669"><span class="lineNum">    3669 </span><span class="lineNoCov">          0 :             temp = 1.0/a[k*(lda)+k];</span></a>
+<a name="3670"><span class="lineNum">    3670 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3671"><span class="lineNum">    3671 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= temp;</span></a>
+<a name="3672"><span class="lineNum">    3672 </span>            :           }</a>
+<a name="3673"><span class="lineNum">    3673 </span><span class="lineNoCov">          0 :           for(j=k+1;j&lt;n;j++) {</span></a>
+<a name="3674"><span class="lineNum">    3674 </span><span class="lineNoCov">          0 :             if( std::abs(a[k*(lda)+j])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="3675"><span class="lineNum">    3675 </span>            :               temp = a[k*(lda)+j];</a>
+<a name="3676"><span class="lineNum">    3676 </span><span class="lineNoCov">          0 :               for(i=0;i&lt;m;i++)</span></a>
+<a name="3677"><span class="lineNum">    3677 </span><span class="lineNoCov">          0 :                 b[j*(ldb)+i] -= temp * b[k*(ldb)+i];</span></a>
+<a name="3678"><span class="lineNum">    3678 </span>            :             }</a>
+<a name="3679"><span class="lineNum">    3679 </span>            :           }</a>
+<a name="3680"><span class="lineNum">    3680 </span><span class="lineNoCov">          0 :           if(std::abs(alpha-1.0)&gt;PLUMED_GMX_FLOAT_EPS)</span></a>
+<a name="3681"><span class="lineNum">    3681 </span><span class="lineNoCov">          0 :             for(i=0;i&lt;m;i++)</span></a>
+<a name="3682"><span class="lineNum">    3682 </span><span class="lineNoCov">          0 :               b[k*(ldb)+i] *= alpha;</span></a>
+<a name="3683"><span class="lineNum">    3683 </span>            :         }</a>
+<a name="3684"><span class="lineNum">    3684 </span>            :       }      </a>
+<a name="3685"><span class="lineNum">    3685 </span>            :     }</a>
+<a name="3686"><span class="lineNum">    3686 </span>            :   }    </a>
+<a name="3687"><span class="lineNum">    3687 </span>            : }</a>
+<a name="3688"><span class="lineNum">    3688 </span>            : }</a>
+<a name="3689"><span class="lineNum">    3689 </span>            : }</a>
+<a name="3690"><span class="lineNum">    3690 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/blas/index-sort-f.html b/coverage-libs/blas/index-sort-f.html
new file mode 100644
index 0000000000..675717de0a
--- /dev/null
+++ b/coverage-libs/blas/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - blas</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - blas</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">405</td>
+            <td class="headerCovTableEntry">1605</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">47.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="blas.cpp.gcov.html">blas.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.2%"><img src="../snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">405 / 1605</td>
+      <td class="coverPerLo">47.2&nbsp;%</td>
+      <td class="coverNumLo">17 / 36</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/blas/index-sort-l.html b/coverage-libs/blas/index-sort-l.html
new file mode 100644
index 0000000000..a95b777232
--- /dev/null
+++ b/coverage-libs/blas/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - blas</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - blas</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">405</td>
+            <td class="headerCovTableEntry">1605</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">47.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="blas.cpp.gcov.html">blas.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.2%"><img src="../snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">405 / 1605</td>
+      <td class="coverPerLo">47.2&nbsp;%</td>
+      <td class="coverNumLo">17 / 36</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/blas/index.html b/coverage-libs/blas/index.html
new file mode 100644
index 0000000000..5247c1858c
--- /dev/null
+++ b/coverage-libs/blas/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - blas</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - blas</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">405</td>
+            <td class="headerCovTableEntry">1605</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">47.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="blas.cpp.gcov.html">blas.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.2%"><img src="../snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">405 / 1605</td>
+      <td class="coverPerLo">47.2&nbsp;%</td>
+      <td class="coverNumLo">17 / 36</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/emerald.png b/coverage-libs/emerald.png
new file mode 100644
index 0000000000000000000000000000000000000000..38ad4f4068b935643d2486f323005fb294a9bd7e
GIT binary patch
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diff --git a/coverage-libs/gcov.css b/coverage-libs/gcov.css
new file mode 100644
index 0000000000..0fcdff13ce
--- /dev/null
+++ b/coverage-libs/gcov.css
@@ -0,0 +1,519 @@
+/* All views: initial background and text color */
+body
+{
+  color: #000000;
+  background-color: #ffffff;
+}
+
+/* All views: standard link format*/
+a:link
+{
+  color: #284fa8;
+  text-decoration: underline;
+}
+
+/* All views: standard link - visited format */
+a:visited
+{
+  color: #00cb40;
+  text-decoration: underline;
+}
+
+/* All views: standard link - activated format */
+a:active
+{
+  color: #ff0040;
+  text-decoration: underline;
+}
+
+/* All views: main title format */
+td.title
+{
+  text-align: center;
+  padding-bottom: 10px;
+  font-family: sans-serif;
+  font-size: 20pt;
+  font-style: italic;
+  font-weight: bold;
+}
+
+/* All views: header item format */
+td.headerItem
+{
+  text-align: right;
+  padding-right: 6px;
+  font-family: sans-serif;
+  font-weight: bold;
+  vertical-align: top;
+  white-space: nowrap;
+}
+
+/* All views: header item value format */
+td.headerValue
+{
+  text-align: left;
+  color: #284fa8;
+  font-family: sans-serif;
+  font-weight: bold;
+  white-space: nowrap;
+}
+
+/* All views: header item coverage table heading */
+td.headerCovTableHead
+{
+  text-align: center;
+  padding-right: 6px;
+  padding-left: 6px;
+  padding-bottom: 0px;
+  font-family: sans-serif;
+  font-size: 80%;
+  white-space: nowrap;
+}
+
+/* All views: header item coverage table entry */
+td.headerCovTableEntry
+{
+  text-align: right;
+  color: #284fa8;
+  font-family: sans-serif;
+  font-weight: bold;
+  white-space: nowrap;
+  padding-left: 12px;
+  padding-right: 4px;
+  background-color: #dae7fe;
+}
+
+/* All views: header item coverage table entry for high coverage rate */
+td.headerCovTableEntryHi
+{
+  text-align: right;
+  color: #000000;
+  font-family: sans-serif;
+  font-weight: bold;
+  white-space: nowrap;
+  padding-left: 12px;
+  padding-right: 4px;
+  background-color: #a7fc9d;
+}
+
+/* All views: header item coverage table entry for medium coverage rate */
+td.headerCovTableEntryMed
+{
+  text-align: right;
+  color: #000000;
+  font-family: sans-serif;
+  font-weight: bold;
+  white-space: nowrap;
+  padding-left: 12px;
+  padding-right: 4px;
+  background-color: #ffea20;
+}
+
+/* All views: header item coverage table entry for ow coverage rate */
+td.headerCovTableEntryLo
+{
+  text-align: right;
+  color: #000000;
+  font-family: sans-serif;
+  font-weight: bold;
+  white-space: nowrap;
+  padding-left: 12px;
+  padding-right: 4px;
+  background-color: #ff0000;
+}
+
+/* All views: header legend value for legend entry */
+td.headerValueLeg
+{
+  text-align: left;
+  color: #000000;
+  font-family: sans-serif;
+  font-size: 80%;
+  white-space: nowrap;
+  padding-top: 4px;
+}
+
+/* All views: color of horizontal ruler */
+td.ruler
+{
+  background-color: #6688d4;
+}
+
+/* All views: version string format */
+td.versionInfo
+{
+  text-align: center;
+  padding-top: 2px;
+  font-family: sans-serif;
+  font-style: italic;
+}
+
+/* Directory view/File view (all)/Test case descriptions:
+   table headline format */
+td.tableHead
+{
+  text-align: center;
+  color: #ffffff;
+  background-color: #6688d4;
+  font-family: sans-serif;
+  font-size: 120%;
+  font-weight: bold;
+  white-space: nowrap;
+  padding-left: 4px;
+  padding-right: 4px;
+}
+
+span.tableHeadSort
+{
+  padding-right: 4px;
+}
+
+/* Directory view/File view (all): filename entry format */
+td.coverFile
+{
+  text-align: left;
+  padding-left: 10px;
+  padding-right: 20px; 
+  color: #284fa8;
+  background-color: #dae7fe;
+  font-family: monospace;
+}
+
+/* Directory view/File view (all): bar-graph entry format*/
+td.coverBar
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #dae7fe;
+}
+
+/* Directory view/File view (all): bar-graph outline color */
+td.coverBarOutline
+{
+  background-color: #000000;
+}
+
+/* Directory view/File view (all): percentage entry for files with
+   high coverage rate */
+td.coverPerHi
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #a7fc9d;
+  font-weight: bold;
+  font-family: sans-serif;
+}
+
+/* Directory view/File view (all): line count entry for files with
+   high coverage rate */
+td.coverNumHi
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #a7fc9d;
+  white-space: nowrap;
+  font-family: sans-serif;
+}
+
+/* Directory view/File view (all): percentage entry for files with
+   medium coverage rate */
+td.coverPerMed
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #ffea20;
+  font-weight: bold;
+  font-family: sans-serif;
+}
+
+/* Directory view/File view (all): line count entry for files with
+   medium coverage rate */
+td.coverNumMed
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #ffea20;
+  white-space: nowrap;
+  font-family: sans-serif;
+}
+
+/* Directory view/File view (all): percentage entry for files with
+   low coverage rate */
+td.coverPerLo
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #ff0000;
+  font-weight: bold;
+  font-family: sans-serif;
+}
+
+/* Directory view/File view (all): line count entry for files with
+   low coverage rate */
+td.coverNumLo
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #ff0000;
+  white-space: nowrap;
+  font-family: sans-serif;
+}
+
+/* File view (all): "show/hide details" link format */
+a.detail:link
+{
+  color: #B8D0FF;
+  font-size:80%;
+}
+
+/* File view (all): "show/hide details" link - visited format */
+a.detail:visited
+{
+  color: #B8D0FF;
+  font-size:80%;
+}
+
+/* File view (all): "show/hide details" link - activated format */
+a.detail:active
+{
+  color: #ffffff;
+  font-size:80%;
+}
+
+/* File view (detail): test name entry */
+td.testName
+{
+  text-align: right;
+  padding-right: 10px;
+  background-color: #dae7fe;
+  font-family: sans-serif;
+}
+
+/* File view (detail): test percentage entry */
+td.testPer
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px; 
+  background-color: #dae7fe;
+  font-family: sans-serif;
+}
+
+/* File view (detail): test lines count entry */
+td.testNum
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px; 
+  background-color: #dae7fe;
+  font-family: sans-serif;
+}
+
+/* Test case descriptions: test name format*/
+dt
+{
+  font-family: sans-serif;
+  font-weight: bold;
+}
+
+/* Test case descriptions: description table body */
+td.testDescription
+{
+  padding-top: 10px;
+  padding-left: 30px;
+  padding-bottom: 10px;
+  padding-right: 30px;
+  background-color: #dae7fe;
+}
+
+/* Source code view: function entry */
+td.coverFn
+{
+  text-align: left;
+  padding-left: 10px;
+  padding-right: 20px; 
+  color: #284fa8;
+  background-color: #dae7fe;
+  font-family: monospace;
+}
+
+/* Source code view: function entry zero count*/
+td.coverFnLo
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #ff0000;
+  font-weight: bold;
+  font-family: sans-serif;
+}
+
+/* Source code view: function entry nonzero count*/
+td.coverFnHi
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px;
+  background-color: #dae7fe;
+  font-weight: bold;
+  font-family: sans-serif;
+}
+
+/* Source code view: source code format */
+pre.source
+{
+  font-family: monospace;
+  white-space: pre;
+  margin-top: 2px;
+}
+
+/* Source code view: line number format */
+span.lineNum
+{
+  background-color: #efe383;
+}
+
+/* Source code view: format for lines which were executed */
+td.lineCov,
+span.lineCov
+{
+  background-color: #cad7fe;
+}
+
+/* Source code view: format for Cov legend */
+span.coverLegendCov
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-bottom: 2px;
+  background-color: #cad7fe;
+}
+
+/* Source code view: format for lines which were not executed */
+td.lineNoCov,
+span.lineNoCov
+{
+  background-color: #ff6230;
+}
+
+/* Source code view: format for NoCov legend */
+span.coverLegendNoCov
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-bottom: 2px;
+  background-color: #ff6230;
+}
+
+/* Source code view (function table): standard link - visited format */
+td.lineNoCov > a:visited,
+td.lineCov > a:visited
+{  
+  color: #000000;
+  text-decoration: underline;
+}  
+
+/* Source code view: format for lines which were executed only in a
+   previous version */
+span.lineDiffCov
+{
+  background-color: #b5f7af;
+}
+
+/* Source code view: format for branches which were executed
+ * and taken */
+span.branchCov
+{
+  background-color: #cad7fe;
+}
+
+/* Source code view: format for branches which were executed
+ * but not taken */
+span.branchNoCov
+{
+  background-color: #ff6230;
+}
+
+/* Source code view: format for branches which were not executed */
+span.branchNoExec
+{
+  background-color: #ff6230;
+}
+
+/* Source code view: format for the source code heading line */
+pre.sourceHeading
+{
+  white-space: pre;
+  font-family: monospace;
+  font-weight: bold;
+  margin: 0px;
+}
+
+/* All views: header legend value for low rate */
+td.headerValueLegL
+{
+  font-family: sans-serif;
+  text-align: center;
+  white-space: nowrap;
+  padding-left: 4px;
+  padding-right: 2px;
+  background-color: #ff0000;
+  font-size: 80%;
+}
+
+/* All views: header legend value for med rate */
+td.headerValueLegM
+{
+  font-family: sans-serif;
+  text-align: center;
+  white-space: nowrap;
+  padding-left: 2px;
+  padding-right: 2px;
+  background-color: #ffea20;
+  font-size: 80%;
+}
+
+/* All views: header legend value for hi rate */
+td.headerValueLegH
+{
+  font-family: sans-serif;
+  text-align: center;
+  white-space: nowrap;
+  padding-left: 2px;
+  padding-right: 4px;
+  background-color: #a7fc9d;
+  font-size: 80%;
+}
+
+/* All views except source code view: legend format for low coverage */
+span.coverLegendCovLo
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-top: 2px;
+  background-color: #ff0000;
+}
+
+/* All views except source code view: legend format for med coverage */
+span.coverLegendCovMed
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-top: 2px;
+  background-color: #ffea20;
+}
+
+/* All views except source code view: legend format for hi coverage */
+span.coverLegendCovHi
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-top: 2px;
+  background-color: #a7fc9d;
+}
diff --git a/coverage-libs/glass.png b/coverage-libs/glass.png
new file mode 100644
index 0000000000000000000000000000000000000000..e1abc00680a3093c49fdb775ae6bdb6764c95af2
GIT binary patch
literal 167
zcmeAS@N?(olHy`uVBq!ia0vp^j3CU&3?x-=hn)gaEa{HEjtmSN`?>!lvI6;R0X`wF
z|Ns97GD8ntt^-nxB|(0{3=Yq3q=7g|-tI089jvk*Kn`btM`SSr1Gf+eGhVt|_XjA*
zUgGKN%6^Gmn4d%Ph(nkFP>9RZ#WAE}PI3Z}&BVayv3^M*kj3EX>gTe~DWM4f=_Dpv

literal 0
HcmV?d00001

diff --git a/coverage-libs/index-sort-f.html b/coverage-libs/index-sort-f.html
new file mode 100644
index 0000000000..8b20e97f83
--- /dev/null
+++ b/coverage-libs/index-sort-f.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules)</title>
+  <link rel="stylesheet" type="text/css" href="gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue">top level</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9495</td>
+            <td class="headerCovTableEntry">29014</td>
+            <td class="headerCovTableEntryLo">32.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">715</td>
+            <td class="headerCovTableEntry">1214</td>
+            <td class="headerCovTableEntryLo">58.9 %</td>
+          </tr>
+          <tr><td><img src="glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Directory <span class="tableHeadSort"><a href="index.html"><img src="updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lapack/index.html">lapack</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=25 height=10 alt="25.2%"><img src="snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">3838 / 15226</td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">65 / 181</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="asmjit/index.html">asmjit</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=31 height=10 alt="31.4%"><img src="snow.png" width=69 height=10 alt="31.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.4&nbsp;%</td>
+      <td class="coverNumLo">2235 / 7124</td>
+      <td class="coverPerLo">39.5&nbsp;%</td>
+      <td class="coverNumLo">139 / 352</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="molfile/index.html">molfile</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=41 height=10 alt="40.9%"><img src="snow.png" width=59 height=10 alt="40.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">40.9&nbsp;%</td>
+      <td class="coverNumLo">861 / 2104</td>
+      <td class="coverPerLo">45.2&nbsp;%</td>
+      <td class="coverNumLo">56 / 124</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile/index.html">xdrfile</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=48 height=10 alt="48.3%"><img src="snow.png" width=52 height=10 alt="48.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">48.3&nbsp;%</td>
+      <td class="coverNumLo">563 / 1166</td>
+      <td class="coverPerLo">46.2&nbsp;%</td>
+      <td class="coverNumLo">43 / 93</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="blas/index.html">blas</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=25 height=10 alt="25.2%"><img src="snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">405 / 1605</td>
+      <td class="coverPerLo">47.2&nbsp;%</td>
+      <td class="coverNumLo">17 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lepton/index.html">lepton</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=89 height=10 alt="89.0%"><img src="snow.png" width=11 height=10 alt="89.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.0&nbsp;%</td>
+      <td class="coverNumMed">1593 / 1789</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">395 / 428</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/index-sort-l.html b/coverage-libs/index-sort-l.html
new file mode 100644
index 0000000000..b1a62a3bd4
--- /dev/null
+++ b/coverage-libs/index-sort-l.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules)</title>
+  <link rel="stylesheet" type="text/css" href="gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue">top level</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9495</td>
+            <td class="headerCovTableEntry">29014</td>
+            <td class="headerCovTableEntryLo">32.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">715</td>
+            <td class="headerCovTableEntry">1214</td>
+            <td class="headerCovTableEntryLo">58.9 %</td>
+          </tr>
+          <tr><td><img src="glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Directory <span class="tableHeadSort"><a href="index.html"><img src="updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="blas/index.html">blas</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=25 height=10 alt="25.2%"><img src="snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">405 / 1605</td>
+      <td class="coverPerLo">47.2&nbsp;%</td>
+      <td class="coverNumLo">17 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lapack/index.html">lapack</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=25 height=10 alt="25.2%"><img src="snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">3838 / 15226</td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">65 / 181</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="asmjit/index.html">asmjit</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=31 height=10 alt="31.4%"><img src="snow.png" width=69 height=10 alt="31.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.4&nbsp;%</td>
+      <td class="coverNumLo">2235 / 7124</td>
+      <td class="coverPerLo">39.5&nbsp;%</td>
+      <td class="coverNumLo">139 / 352</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="molfile/index.html">molfile</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=41 height=10 alt="40.9%"><img src="snow.png" width=59 height=10 alt="40.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">40.9&nbsp;%</td>
+      <td class="coverNumLo">861 / 2104</td>
+      <td class="coverPerLo">45.2&nbsp;%</td>
+      <td class="coverNumLo">56 / 124</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile/index.html">xdrfile</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=48 height=10 alt="48.3%"><img src="snow.png" width=52 height=10 alt="48.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">48.3&nbsp;%</td>
+      <td class="coverNumLo">563 / 1166</td>
+      <td class="coverPerLo">46.2&nbsp;%</td>
+      <td class="coverNumLo">43 / 93</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lepton/index.html">lepton</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=89 height=10 alt="89.0%"><img src="snow.png" width=11 height=10 alt="89.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.0&nbsp;%</td>
+      <td class="coverNumMed">1593 / 1789</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">395 / 428</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/index.html b/coverage-libs/index.html
new file mode 100644
index 0000000000..e9b673a11f
--- /dev/null
+++ b/coverage-libs/index.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules)</title>
+  <link rel="stylesheet" type="text/css" href="gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue">top level</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9495</td>
+            <td class="headerCovTableEntry">29014</td>
+            <td class="headerCovTableEntryLo">32.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">715</td>
+            <td class="headerCovTableEntry">1214</td>
+            <td class="headerCovTableEntryLo">58.9 %</td>
+          </tr>
+          <tr><td><img src="glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Directory <span class="tableHeadSort"><img src="glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="asmjit/index.html">asmjit</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=31 height=10 alt="31.4%"><img src="snow.png" width=69 height=10 alt="31.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.4&nbsp;%</td>
+      <td class="coverNumLo">2235 / 7124</td>
+      <td class="coverPerLo">39.5&nbsp;%</td>
+      <td class="coverNumLo">139 / 352</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="blas/index.html">blas</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=25 height=10 alt="25.2%"><img src="snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">405 / 1605</td>
+      <td class="coverPerLo">47.2&nbsp;%</td>
+      <td class="coverNumLo">17 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lapack/index.html">lapack</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=25 height=10 alt="25.2%"><img src="snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">3838 / 15226</td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">65 / 181</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lepton/index.html">lepton</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=89 height=10 alt="89.0%"><img src="snow.png" width=11 height=10 alt="89.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.0&nbsp;%</td>
+      <td class="coverNumMed">1593 / 1789</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">395 / 428</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="molfile/index.html">molfile</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=41 height=10 alt="40.9%"><img src="snow.png" width=59 height=10 alt="40.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">40.9&nbsp;%</td>
+      <td class="coverNumLo">861 / 2104</td>
+      <td class="coverPerLo">45.2&nbsp;%</td>
+      <td class="coverNumLo">56 / 124</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile/index.html">xdrfile</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=48 height=10 alt="48.3%"><img src="snow.png" width=52 height=10 alt="48.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">48.3&nbsp;%</td>
+      <td class="coverNumLo">563 / 1166</td>
+      <td class="coverPerLo">46.2&nbsp;%</td>
+      <td class="coverNumLo">43 / 93</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lapack/index-sort-f.html b/coverage-libs/lapack/index-sort-f.html
new file mode 100644
index 0000000000..02e0483fbe
--- /dev/null
+++ b/coverage-libs/lapack/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lapack</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - lapack</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3838</td>
+            <td class="headerCovTableEntry">15226</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">181</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lapack.cpp.gcov.html">lapack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.2%"><img src="../snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">3838 / 15226</td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">65 / 181</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lapack/index-sort-l.html b/coverage-libs/lapack/index-sort-l.html
new file mode 100644
index 0000000000..b7f0a3d24d
--- /dev/null
+++ b/coverage-libs/lapack/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lapack</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - lapack</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3838</td>
+            <td class="headerCovTableEntry">15226</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">181</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lapack.cpp.gcov.html">lapack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.2%"><img src="../snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">3838 / 15226</td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">65 / 181</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lapack/index.html b/coverage-libs/lapack/index.html
new file mode 100644
index 0000000000..7e73986845
--- /dev/null
+++ b/coverage-libs/lapack/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lapack</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - lapack</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3838</td>
+            <td class="headerCovTableEntry">15226</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">181</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="lapack.cpp.gcov.html">lapack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.2%"><img src="../snow.png" width=75 height=10 alt="25.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.2&nbsp;%</td>
+      <td class="coverNumLo">3838 / 15226</td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">65 / 181</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lapack/lapack.cpp.func-sort-c.html b/coverage-libs/lapack/lapack.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fccfbefaa5
--- /dev/null
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lapack/lapack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lapack</a> - lapack.cpp<span style="font-size: 80%;"> (<a href="lapack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
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+            <td class="headerCovTableEntry">15226</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
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+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
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+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage-libs/lapack/lapack.cpp.func.html b/coverage-libs/lapack/lapack.cpp.func.html
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+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage-libs/lapack/lapack.cpp.gcov.html b/coverage-libs/lapack/lapack.cpp.gcov.html
new file mode 100644
index 0000000000..3c94d57865
--- /dev/null
+++ b/coverage-libs/lapack/lapack.cpp.gcov.html
@@ -0,0 +1,31099 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lapack/lapack.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lapack</a> - lapack.cpp<span style="font-size: 80%;"> (source / <a href="lapack.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3838</td>
+            <td class="headerCovTableEntry">15226</td>
+            <td class="headerCovTableEntryLo">25.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">181</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : These files are semi-automatic translations by f2c from the original netlib LAPACK library.</a>
+<a name="3"><span class="lineNum">       3 </span>            : The source has been modified to (mostly) use modern C formatting, and to get rid of</a>
+<a name="4"><span class="lineNum">       4 </span>            : compiler warnings. Any errors in doing this should be blamed on the GROMACS developers, and</a>
+<a name="5"><span class="lineNum">       5 </span>            : not the reference LAPACK implementation.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            : The reference LAPACK implementation is available from http://www.netlib.org/lapack </a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : LAPACK does not come with a formal named &quot;license&quot;, but a general statement saying:</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            : &quot;The reference LAPACK is a freely-available software package. It is available from netlib</a>
+<a name="12"><span class="lineNum">      12 </span>            : via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software</a>
+<a name="13"><span class="lineNum">      13 </span>            : packages (and has been). We only ask that proper credit be given to the authors.&quot;</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            : While the rest of GROMACS is LGPL, we think it's only fair to give you the same rights to</a>
+<a name="16"><span class="lineNum">      16 </span>            : our modified LAPACK files as the original netlib versions, so do what you want with them.</a>
+<a name="17"><span class="lineNum">      17 </span>            : </a>
+<a name="18"><span class="lineNum">      18 </span>            : However, be warned that we have only tested that they to the right thing in the cases used</a>
+<a name="19"><span class="lineNum">      19 </span>            : in GROMACS (primarily full &amp; sparse matrix diagonalization), so in most cases it is a much</a>
+<a name="20"><span class="lineNum">      20 </span>            : better idea to use the full reference implementation.</a>
+<a name="21"><span class="lineNum">      21 </span>            : </a>
+<a name="22"><span class="lineNum">      22 </span>            : Erik Lindahl, 2008-10-07.</a>
+<a name="23"><span class="lineNum">      23 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="24"><span class="lineNum">      24 </span>            : #if ! defined(__PLUMED_HAS_EXTERNAL_LAPACK)</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cctype&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;real.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD{</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace lapack{</a>
+<a name="36"><span class="lineNum">      36 </span>            : using namespace blas;</a>
+<a name="37"><span class="lineNum">      37 </span>            : void</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         96 : PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(const char *uplo, </span></a>
+<a name="39"><span class="lineNum">      39 </span>            :         const char *compq, </a>
+<a name="40"><span class="lineNum">      40 </span>            :         int *n,</a>
+<a name="41"><span class="lineNum">      41 </span>            :         double *d__, </a>
+<a name="42"><span class="lineNum">      42 </span>            :         double *e, </a>
+<a name="43"><span class="lineNum">      43 </span>            :         double *u, </a>
+<a name="44"><span class="lineNum">      44 </span>            :         int *ldu,</a>
+<a name="45"><span class="lineNum">      45 </span>            :         double *vt, </a>
+<a name="46"><span class="lineNum">      46 </span>            :         int *ldvt,</a>
+<a name="47"><span class="lineNum">      47 </span>            :         double *q,</a>
+<a name="48"><span class="lineNum">      48 </span>            :         int *iq,</a>
+<a name="49"><span class="lineNum">      49 </span>            :         double *work, </a>
+<a name="50"><span class="lineNum">      50 </span>            :         int *iwork, </a>
+<a name="51"><span class="lineNum">      51 </span>            :         int *info)</a>
+<a name="52"><span class="lineNum">      52 </span>            : {</a>
+<a name="53"><span class="lineNum">      53 </span>            :     int u_dim1, u_offset, vt_dim1, vt_offset, i__1, i__2;</a>
+<a name="54"><span class="lineNum">      54 </span>            :     int i__, j, k;</a>
+<a name="55"><span class="lineNum">      55 </span>            :     double p, r__;</a>
+<a name="56"><span class="lineNum">      56 </span>            :     int z__, ic, ii, kk;</a>
+<a name="57"><span class="lineNum">      57 </span>            :     double cs;</a>
+<a name="58"><span class="lineNum">      58 </span>            :     int is, iu;</a>
+<a name="59"><span class="lineNum">      59 </span>            :     double sn;</a>
+<a name="60"><span class="lineNum">      60 </span>            :     int nm1;</a>
+<a name="61"><span class="lineNum">      61 </span>            :     double eps;</a>
+<a name="62"><span class="lineNum">      62 </span>            :     int ivt, difl, difr, ierr, perm, mlvl, sqre;</a>
+<a name="63"><span class="lineNum">      63 </span>            :     int poles, iuplo, nsize, start;</a>
+<a name="64"><span class="lineNum">      64 </span>            :     int givcol;</a>
+<a name="65"><span class="lineNum">      65 </span>            :     int icompq;</a>
+<a name="66"><span class="lineNum">      66 </span>            :     double orgnrm;</a>
+<a name="67"><span class="lineNum">      67 </span>            :     int givnum, givptr, qstart, smlsiz, wstart, smlszp;</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         96 :     double zero = 0.0;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         96 :     double one = 1.0;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         96 :     int c_0 = 0;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         96 :     int c_1 = 1;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         96 :     --d__;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         96 :     --e;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         96 :     u_dim1 = *ldu;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         96 :     u_offset = 1 + u_dim1;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         96 :     u -= u_offset;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         96 :     vt_dim1 = *ldvt;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         96 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         96 :     vt -= vt_offset;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         96 :     --q;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         96 :     --iq;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         96 :     --work;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :     --iwork;</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :     k = iu = z__ = ic = is = ivt = difl = difr = perm = 0;</a>
+<a name="87"><span class="lineNum">      87 </span>            :     poles = givnum = givptr = givcol = 0;</a>
+<a name="88"><span class="lineNum">      88 </span>            :     </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         96 :     smlsiz = DBDSDC_SMALLSIZE;</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         96 :     *info = 0;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         96 :     iuplo = (*uplo=='U' || *uplo=='u') ? 1 : 2;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         96 :     switch(*compq) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     case 'n':</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :     case 'N':</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :       icompq = 0;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     case 'p':</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :     case 'P':</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :       icompq = 1;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         96 :     case 'i':</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :     case 'I':</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         96 :       icompq = 2;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         96 :       break;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     default:</a>
+<a name="108"><span class="lineNum">     108 </span>            :       return;</a>
+<a name="109"><span class="lineNum">     109 </span>            :     }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         96 :     if (*n &lt;= 0) </span></a>
+<a name="112"><span class="lineNum">     112 </span>            :         return;</a>
+<a name="113"><span class="lineNum">     113 </span>            :     </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         96 :     if (*n == 1) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :         if (icompq == 1) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :           q[1] = (d__[1]&gt;0) ? 1.0 : -1.0;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :           q[smlsiz * *n + 1] = 1.;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :         } else if (icompq == 2) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :           u[u_dim1 + 1] = (d__[1]&gt;0) ? 1.0 : -1.0;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :           vt[vt_dim1 + 1] = 1.;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :         }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :         d__[1] = std::abs(d__[1]);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :     }</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         96 :     nm1 = *n - 1;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     wstart = 1;</a>
+<a name="127"><span class="lineNum">     127 </span>            :     qstart = 3;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         96 :     if (icompq == 1) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;d__[1], &amp;c_1, &amp;q[1], &amp;c_1);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;e[1], &amp;c_1, &amp;q[*n + 1], &amp;c_1);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     }</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         96 :     if (iuplo == 2) {</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :         qstart = 5;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :         wstart = (*n &lt;&lt; 1) - 1;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :             d__[i__] = r__;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :             if (icompq == 1) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :                 q[i__ + (*n &lt;&lt; 1)] = cs;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :                 q[i__ + *n * 3] = sn;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :             } else if (icompq == 2) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :                 work[i__] = cs;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :                 work[nm1 + i__] = -sn;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :             }</a>
+<a name="149"><span class="lineNum">     149 </span>            :         }</a>
+<a name="150"><span class="lineNum">     150 </span>            :     }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         96 :     if (icompq == 0) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;,&amp;c_0,n,&amp;c_0,&amp;c_0,&amp;c_0,&amp;d__[1],&amp;e[1],&amp;vt[vt_offset],ldvt,</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :               &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;work[wstart], info);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         96 :     if (*n &lt;= smlsiz) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         67 :         if (icompq == 2) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         67 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;u[u_offset], ldu);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         67 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         67 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;,&amp;c_0,n,n,n,&amp;c_0,&amp;d__[1],&amp;e[1],&amp;vt[vt_offset],ldvt,</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         67 :                     &amp;u[u_offset],ldu,&amp;u[u_offset],ldu,&amp;work[wstart],info);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :         } else if (icompq == 1) {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :             iu = 1;</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :             ivt = iu + *n;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;q[iu + (qstart - 1) * *n], n);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;q[ivt + (qstart - 1) * *n], n);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;c_0, n, n, n, &amp;c_0, &amp;d__[1], &amp;e[1], </span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :                     &amp;q[ivt + (qstart - 1) * *n], n, &amp;q[iu + (qstart - 1) * *n], </span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :                     n, &amp;q[iu + (qstart - 1) * *n], n, &amp;work[wstart], info);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :         }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         67 :         goto L40;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         29 :     if (icompq == 2) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         29 :         PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;u[u_offset], ldu);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         29 :         PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :     }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         29 :     orgnrm = PLUMED_BLAS_F77_FUNC(dlanst,DLANST)(&quot;M&quot;, n, &amp;d__[1], &amp;e[1]);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         29 :     if ( std::abs(orgnrm)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :         return;</a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         29 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c_0, &amp;c_0, &amp;orgnrm, &amp;one, n, &amp;c_1, &amp;d__[1], n, &amp;ierr);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         29 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c_0, &amp;c_0, &amp;orgnrm, &amp;one, &amp;nm1, &amp;c_1, &amp;e[1], &amp;nm1, &amp;ierr);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         29 :     mlvl = (int) (std::log((double) (*n) / (double) (smlsiz + 1)) / </span></a>
+<a name="189"><span class="lineNum">     189 </span>            :                   std::log(2.)) + 1;</a>
+<a name="190"><span class="lineNum">     190 </span>            :     smlszp = smlsiz + 1;</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         29 :     if (icompq == 1) {</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :         iu = 1;</a>
+<a name="194"><span class="lineNum">     194 </span>            :         ivt = smlsiz + 1;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :         difl = ivt + smlszp;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :         difr = difl + mlvl;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :         z__ = difr + (mlvl &lt;&lt; 1);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :         ic = z__ + mlvl;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :         is = ic + 1;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :         poles = is + 1;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :         givnum = poles + (mlvl &lt;&lt; 1);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :         k = 1;</a>
+<a name="204"><span class="lineNum">     204 </span>            :         givptr = 2;</a>
+<a name="205"><span class="lineNum">     205 </span>            :         perm = 3;</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :         givcol = perm + mlvl;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         29 :     i__1 = *n;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       1453 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       1424 :         if (std::abs(d__[i__]) &lt; eps) </span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         40 :             d__[i__] = (d__[i__]&gt;0) ? eps : -eps;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :     start = 1;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         29 :     sqre = 0;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         29 :     i__1 = nm1;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1424 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       1395 :         if (std::abs(e[i__]) &lt; eps || i__ == nm1) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         29 :             if (i__ &lt; nm1) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :                 nsize = i__ - start + 1;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         29 :             } else if (std::abs(e[i__]) &gt;= eps) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         24 :                 nsize = *n - start + 1;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :             } else {</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          5 :                 nsize = i__ - start + 1;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          5 :                 if (icompq == 2) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          5 :                     u[*n + *n * u_dim1] = (d__[*n]&gt;0) ? 1.0 : -1.0; </span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          5 :                     vt[*n + *n * vt_dim1] = 1.;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :                 } else if (icompq == 1) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :                     q[*n + (qstart - 1) * *n] = (d__[*n]&gt;0) ? 1.0 : -1.0; </span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :                     q[*n + (smlsiz + qstart - 1) * *n] = 1.;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :                 }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          5 :                 d__[*n] = std::abs(d__[*n]);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :             }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         29 :             if (icompq == 2) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         29 :                 PLUMED_BLAS_F77_FUNC(dlasd0,DLASD0)(&amp;nsize, &amp;sqre, &amp;d__[start], &amp;e[start], </span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         29 :                         &amp;u[start + start * u_dim1], ldu, </span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         29 :                         &amp;vt[start + start * vt_dim1], </span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         29 :                         ldvt, &amp;smlsiz, &amp;iwork[1], &amp;work[wstart], info);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :             } else {</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasda,DLASDA)(&amp;icompq, &amp;smlsiz, &amp;nsize, &amp;sqre, &amp;d__[start], </span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :                         &amp;e[start], &amp;q[start + (iu + qstart - 2) * *n], n, </span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :                         &amp;q[start + (ivt + qstart - 2) * *n], &amp;iq[start + k * *n],</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :                         &amp;q[start + (difl + qstart - 2) * *n], </span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :                         &amp;q[start + (difr + qstart - 2) * *n], </span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :                         &amp;q[start + (z__ + qstart - 2) * *n], </span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :                         &amp;q[start + (poles + qstart - 2) * *n], </span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :                         &amp;iq[start + givptr * *n], &amp;iq[start + givcol * *n], n, </span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :                         &amp;iq[start + perm * *n], </span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :                         &amp;q[start + (givnum + qstart - 2) * *n], </span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :                         &amp;q[start + (ic + qstart - 2) * *n], </span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :                         &amp;q[start + (is + qstart - 2) * *n], &amp;work[wstart], </span></a>
+<a name="254"><span class="lineNum">     254 </span>            :                         &amp;iwork[1], info);</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :                 if (*info != 0) {</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :                     return;</a>
+<a name="257"><span class="lineNum">     257 </span>            :                 }</a>
+<a name="258"><span class="lineNum">     258 </span>            :             }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         29 :             start = i__ + 1;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :         }</a>
+<a name="261"><span class="lineNum">     261 </span>            :     }</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         29 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c_0, &amp;c_0, &amp;one, &amp;orgnrm, n, &amp;c_1, &amp;d__[1], n, &amp;ierr);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         96 : L40:</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         96 :     i__1 = *n;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       2544 :     for (ii = 2; ii &lt;= i__1; ++ii) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       2448 :         i__ = ii - 1;</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :         kk = i__;</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       2448 :         p = d__[i__];</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       2448 :         i__2 = *n;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">     152041 :         for (j = ii; j &lt;= i__2; ++j) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">     149593 :             if (d__[j] &gt; p) {</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :                 kk = j;</a>
+<a name="273"><span class="lineNum">     273 </span>            :                 p = d__[j];</a>
+<a name="274"><span class="lineNum">     274 </span>            :             }</a>
+<a name="275"><span class="lineNum">     275 </span>            :         }</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       2448 :         if (kk != i__) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       1263 :             d__[kk] = d__[i__];</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       1263 :             d__[i__] = p;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       1263 :             if (icompq == 1) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :                 iq[i__] = kk;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       1263 :             } else if (icompq == 2) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       1263 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n, &amp;u[i__ * u_dim1 + 1],&amp;c_1,&amp;u[kk*u_dim1+1],&amp;c_1);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       1263 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n, &amp;vt[i__ + vt_dim1], ldvt, &amp;vt[kk + vt_dim1], ldvt);</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :             }</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       1185 :         } else if (icompq == 1) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :             iq[i__] = i__;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :         }</a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         96 :     if (icompq == 1) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :         if (iuplo == 1) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :             iq[*n] = 1;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :         } else {</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :             iq[*n] = 0;</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :         }</a>
+<a name="295"><span class="lineNum">     295 </span>            :     }</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         96 :     if (iuplo == 2 &amp;&amp; icompq == 2) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, n, n, &amp;work[1], &amp;work[*n], &amp;u[u_offset], ldu);</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :     return;</a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : }</a>
+<a name="303"><span class="lineNum">     303 </span>            : }</a>
+<a name="304"><span class="lineNum">     304 </span>            : #include &lt;cctype&gt;</a>
+<a name="305"><span class="lineNum">     305 </span>            : #include &lt;cmath&gt;</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="308"><span class="lineNum">     308 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : #include &quot;real.h&quot;</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="313"><span class="lineNum">     313 </span>            : namespace PLMD{</a>
+<a name="314"><span class="lineNum">     314 </span>            : namespace lapack{</a>
+<a name="315"><span class="lineNum">     315 </span>            : using namespace blas;</a>
+<a name="316"><span class="lineNum">     316 </span>            : void </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        155 : PLUMED_BLAS_F77_FUNC(dbdsqr,DBDSQR)(const char *uplo,</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :                         int *n,</a>
+<a name="319"><span class="lineNum">     319 </span>            :                         int *ncvt,</a>
+<a name="320"><span class="lineNum">     320 </span>            :                         int *nru, </a>
+<a name="321"><span class="lineNum">     321 </span>            :                         int *ncc, </a>
+<a name="322"><span class="lineNum">     322 </span>            :                         double *d__,</a>
+<a name="323"><span class="lineNum">     323 </span>            :                         double *e,</a>
+<a name="324"><span class="lineNum">     324 </span>            :                         double *vt, </a>
+<a name="325"><span class="lineNum">     325 </span>            :                         int *ldvt,</a>
+<a name="326"><span class="lineNum">     326 </span>            :                         double *u, </a>
+<a name="327"><span class="lineNum">     327 </span>            :                         int *ldu,</a>
+<a name="328"><span class="lineNum">     328 </span>            :                         double *c__, </a>
+<a name="329"><span class="lineNum">     329 </span>            :                         int *ldc,</a>
+<a name="330"><span class="lineNum">     330 </span>            :                         double *work,</a>
+<a name="331"><span class="lineNum">     331 </span>            :                         int *info)</a>
+<a name="332"><span class="lineNum">     332 </span>            : {</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        155 :     const char xuplo = std::toupper(*uplo);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :     int c_dim1, c_offset, u_dim1, u_offset, vt_dim1, vt_offset, i__1, </a>
+<a name="335"><span class="lineNum">     335 </span>            :             i__2;</a>
+<a name="336"><span class="lineNum">     336 </span>            :     double r__1, r__2, r__3, r__4;</a>
+<a name="337"><span class="lineNum">     337 </span>            :     double c_b15 = -.125;</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">        155 :     int c__1 = 1;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :     double c_b49 = 1.f;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        155 :     double c_b72 = -1.f;</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :     double f, g, h__;</a>
+<a name="344"><span class="lineNum">     344 </span>            :     int i__, j, m;</a>
+<a name="345"><span class="lineNum">     345 </span>            :     double r__, cs;</a>
+<a name="346"><span class="lineNum">     346 </span>            :     int ll;</a>
+<a name="347"><span class="lineNum">     347 </span>            :     double sn, mu;</a>
+<a name="348"><span class="lineNum">     348 </span>            :     int nm1, nm12, nm13, lll;</a>
+<a name="349"><span class="lineNum">     349 </span>            :     double eps, sll, tol, abse;</a>
+<a name="350"><span class="lineNum">     350 </span>            :     int idir;</a>
+<a name="351"><span class="lineNum">     351 </span>            :     double abss;</a>
+<a name="352"><span class="lineNum">     352 </span>            :     int oldm;</a>
+<a name="353"><span class="lineNum">     353 </span>            :     double cosl;</a>
+<a name="354"><span class="lineNum">     354 </span>            :     int isub, iter;</a>
+<a name="355"><span class="lineNum">     355 </span>            :     double unfl, sinl, cosr, smin, smax, sinr;</a>
+<a name="356"><span class="lineNum">     356 </span>            :     double oldcs;</a>
+<a name="357"><span class="lineNum">     357 </span>            :     int oldll;</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        155 :     double shift, sigmn, oldsn = 0.;</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :     int maxit;</a>
+<a name="360"><span class="lineNum">     360 </span>            :     double sminl;</a>
+<a name="361"><span class="lineNum">     361 </span>            :     double sigmx;</a>
+<a name="362"><span class="lineNum">     362 </span>            :     int lower;</a>
+<a name="363"><span class="lineNum">     363 </span>            :     double sminoa;</a>
+<a name="364"><span class="lineNum">     364 </span>            :     double thresh;</a>
+<a name="365"><span class="lineNum">     365 </span>            :     int rotate;</a>
+<a name="366"><span class="lineNum">     366 </span>            :     double tolmul;</a>
+<a name="367"><span class="lineNum">     367 </span>            :     int itmp1,itmp2;</a>
+<a name="368"><span class="lineNum">     368 </span>            :     </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        155 :     --d__;</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        155 :     --e;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        155 :     vt_dim1 = *ldvt;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        155 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        155 :     vt -= vt_offset;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        155 :     u_dim1 = *ldu;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        155 :     u_offset = 1 + u_dim1;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        155 :     u -= u_offset;</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        155 :     c_dim1 = *ldc;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">        155 :     c_offset = 1 + c_dim1;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        155 :     c__ -= c_offset;</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        155 :     --work;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        155 :     *info = 0;</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        155 :     itmp1 = (*n &gt; 1) ? *n : 1;</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        155 :     itmp2 = (*nru &gt; 1) ? *nru : 1;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :     </a>
+<a name="387"><span class="lineNum">     387 </span>            :     lower = (xuplo == 'L');</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        155 :     if ( (xuplo!='U') &amp;&amp; !lower) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        155 :     } else if (*n &lt; 0) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        155 :     } else if (*ncvt &lt; 0) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        155 :     } else if (*nru &lt; 0) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        155 :     } else if (*ncc &lt; 0) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        155 :     } else if ( ((*ncvt == 0) &amp;&amp; (*ldvt &lt; 1)) || ((*ncvt &gt; 0) &amp;&amp; (*ldvt &lt; itmp1)) ) {</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        155 :     } else if (*ldu &lt; itmp2) {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :         *info = -11;</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">        155 :     } else if ( ((*ncc == 0) &amp;&amp; (*ldc &lt; 1)) || ((*ncc &gt; 0) &amp;&amp; (*ldc &lt; itmp1))) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :         *info = -13;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :     }</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">        155 :     if (*info != 0) {</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :         return;</a>
+<a name="407"><span class="lineNum">     407 </span>            :     }</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">        155 :     if (*n == 0) {</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :         return;</a>
+<a name="410"><span class="lineNum">     410 </span>            :     }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        155 :     if (*n == 1) {</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :         goto L160;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :     }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        155 :     rotate = *ncvt &gt; 0 || *nru &gt; 0 || *ncc &gt; 0;</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :     if (! rotate) {</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasq1,DLASQ1)(n, &amp;d__[1], &amp;e[1], &amp;work[1], info);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :     }</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        155 :     nm1 = *n - 1;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        155 :     nm12 = nm1 + nm1;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        155 :     nm13 = nm12 + nm1;</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :     idir = 0;</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="428"><span class="lineNum">     428 </span>            :     unfl = PLUMED_GMX_DOUBLE_MIN/PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        155 :     if (lower) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :             d__[i__] = r__;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :             work[i__] = cs;</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :             work[nm1 + i__] = sn;</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :         }</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :         if (*nru &gt; 0) {</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, n, &amp;work[1], &amp;work[*n], &amp;u[u_offset], </span></a>
+<a name="443"><span class="lineNum">     443 </span>            :                     ldu);</a>
+<a name="444"><span class="lineNum">     444 </span>            :         }</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :         if (*ncc &gt; 0) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, n, ncc, &amp;work[1], &amp;work[*n], &amp;c__[c_offset],</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :                      ldc);</a>
+<a name="448"><span class="lineNum">     448 </span>            :         }</a>
+<a name="449"><span class="lineNum">     449 </span>            :     }</a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            :     r__3 = 100.f, r__4 = std::pow(PLUMED_GMX_DOUBLE_EPS,c_b15);</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">        155 :     r__1 = 10.f, r__2 = (r__3&lt;r__4) ? r__3 : r__4;</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     tolmul = (r__1&gt;r__2) ? r__1 : r__2;</a>
+<a name="454"><span class="lineNum">     454 </span>            :     tol = tolmul * eps;</a>
+<a name="455"><span class="lineNum">     455 </span>            :     smax = 0.f;</a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        155 :     i__1 = *n;</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">       2635 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">       2480 :         r__2 = smax, r__3 = (r__1 = d__[i__], std::abs(r__1));</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">       2480 :         smax = (r__2&gt;r__3) ? r__2 : r__3;</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :     }</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">        155 :     i__1 = *n - 1;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">       2480 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">       2325 :         r__2 = smax, r__3 = (r__1 = e[i__], std::abs(r__1));</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">       2325 :         smax = (r__2&gt;r__3) ? r__2 : r__3;</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :     }</a>
+<a name="466"><span class="lineNum">     466 </span>            :     sminl = 0.f;</a>
+<a name="467"><span class="lineNum">     467 </span>            :     if (tol &gt;= 0.f) {</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">        155 :         sminoa = std::abs(d__[1]);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        155 :         if (sminoa == 0.f) {</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 :             goto L50;</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :         }</a>
+<a name="472"><span class="lineNum">     472 </span>            :         mu = sminoa;</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">        155 :         i__1 = *n;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">       2480 :         for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">       2325 :             mu = (r__2 = d__[i__], std::abs(r__2)) * (mu / (mu + (r__1 = e[i__ - </span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">       2325 :                     1], std::abs(r__1))));</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">       2325 :             sminoa = (sminoa&lt;mu) ? sminoa : mu;</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">       2325 :             if (sminoa == 0.f) {</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :                 goto L50;</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :             }</a>
+<a name="481"><span class="lineNum">     481 </span>            :         }</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">        155 : L50:</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">        155 :         sminoa /=  std::sqrt((double) (*n));</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        155 :         r__1 = tol * sminoa, r__2 = *n * 6 * *n * unfl;</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">        155 :         thresh = (r__1&gt;r__2) ? r__1 : r__2;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :     } else {</a>
+<a name="487"><span class="lineNum">     487 </span>            :         r__1 = std::abs(tol) * smax, r__2 = *n * 6 * *n * unfl;</a>
+<a name="488"><span class="lineNum">     488 </span>            :         thresh = (r__1&gt;r__2) ? r__1 : r__2;</a>
+<a name="489"><span class="lineNum">     489 </span>            :     }</a>
+<a name="490"><span class="lineNum">     490 </span>            :     maxit = *n * 6 * *n;</a>
+<a name="491"><span class="lineNum">     491 </span>            :     iter = 0;</a>
+<a name="492"><span class="lineNum">     492 </span>            :     oldll = -1;</a>
+<a name="493"><span class="lineNum">     493 </span>            :     oldm = -1;</a>
+<a name="494"><span class="lineNum">     494 </span>            :     m = *n;</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">       8153 : L60:</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">       8308 :     if (m &lt;= 1) {</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        155 :         goto L160;</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :     }</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">       8153 :     if (iter &gt; maxit) {</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 :         goto L200;</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :     }</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            :     if (tol &lt; 0.f &amp;&amp; (r__1 = d__[m], std::abs(r__1)) &lt;= thresh) {</a>
+<a name="506"><span class="lineNum">     506 </span>            :         d__[m] = 0.f;</a>
+<a name="507"><span class="lineNum">     507 </span>            :     }</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">       8153 :     smax = (r__1 = d__[m], std::abs(r__1));</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :     smin = smax;</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">       8153 :     i__1 = m - 1;</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">      64129 :     for (lll = 1; lll &lt;= i__1; ++lll) {</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">      58204 :         ll = m - lll;</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">      58204 :         abss = (r__1 = d__[ll], std::abs(r__1));</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">      58204 :         abse = (r__1 = e[ll], std::abs(r__1));</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :         if (tol &lt; 0.f &amp;&amp; abss &lt;= thresh) {</a>
+<a name="516"><span class="lineNum">     516 </span>            :             d__[ll] = 0.f;</a>
+<a name="517"><span class="lineNum">     517 </span>            :         }</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">      58204 :         if (abse &lt;= thresh) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">       2228 :             goto L80;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :         }</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">      55976 :         smin = (smin&lt;abss) ? smin : abss;</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">      55976 :         r__1 = (smax&gt;abss) ? smax : abss;</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">      55976 :         smax = (r__1&gt;abse) ? r__1 : abse;</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :     }</a>
+<a name="525"><span class="lineNum">     525 </span>            :     ll = 0;</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">       5925 :     goto L90;</span></a>
+<a name="527"><span class="lineNum">     527 </span>            : L80:</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">       2228 :     e[ll] = 0.f;</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">       2228 :     if (ll == m - 1) {</span></a>
+<a name="530"><span class="lineNum">     530 </span>            :         --m;</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">       2119 :         goto L60;</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :     }</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        109 : L90:</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">       6034 :     ++ll;</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">       6034 :     if (ll == m - 1) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">        180 :         PLUMED_BLAS_F77_FUNC(dlasv2,DLASV2)(&amp;d__[m - 1], &amp;e[m - 1], &amp;d__[m], &amp;sigmn, &amp;sigmx, &amp;sinr, &amp;cosr,</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :                  &amp;sinl, &amp;cosl);</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">        180 :         d__[m - 1] = sigmx;</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">        180 :         e[m - 1] = 0.f;</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">        180 :         d__[m] = sigmn;</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">        180 :         if (*ncvt &gt; 0) {</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">        180 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(ncvt, &amp;vt[m - 1 + vt_dim1], ldvt, &amp;vt[m + vt_dim1], ldvt, &amp;</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :                     cosr, &amp;sinr);</a>
+<a name="544"><span class="lineNum">     544 </span>            :         }</a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">        180 :         if (*nru &gt; 0) {</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">        180 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(nru, &amp;u[(m - 1) * u_dim1 + 1], &amp;c__1, &amp;u[m * u_dim1 + 1], &amp;</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :                     c__1, &amp;cosl, &amp;sinl);</a>
+<a name="548"><span class="lineNum">     548 </span>            :         }</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">        180 :         if (*ncc &gt; 0) {</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(ncc, &amp;c__[m - 1 + c_dim1], ldc, &amp;c__[m + c_dim1], ldc, &amp;</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :                     cosl, &amp;sinl);</a>
+<a name="552"><span class="lineNum">     552 </span>            :         }</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">        180 :         m += -2;</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">        180 :         goto L60;</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :     }</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">       5854 :     if (ll &gt; oldm || m &lt; oldll) {</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        182 :         if ((r__1 = d__[ll], std::abs(r__1)) &gt;= (r__2 = d__[m], std::abs(r__2))) {</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :             idir = 1;</a>
+<a name="559"><span class="lineNum">     559 </span>            :         } else {</a>
+<a name="560"><span class="lineNum">     560 </span>            :             idir = 2;</a>
+<a name="561"><span class="lineNum">     561 </span>            :         }</a>
+<a name="562"><span class="lineNum">     562 </span>            :     }</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">       5672 :     if (idir == 1) {</span></a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">       5821 :         if( (std::abs(e[m-1]) &lt;= std::abs(tol) * std::abs(d__[m])) ||</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :             (tol&lt;0.0 &amp;&amp; std::abs(e[m-1])&lt;=thresh)) {</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">       1172 :             e[m - 1] = 0.f;</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">       1172 :             goto L60;</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :         }</a>
+<a name="570"><span class="lineNum">     570 </span>            :         if (tol &gt;= 0.f) {</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">       4649 :             mu = (r__1 = d__[ll], std::abs(r__1));</span></a>
+<a name="572"><span class="lineNum">     572 </span>            :             sminl = mu;</a>
+<a name="573"><span class="lineNum">     573 </span>            :             i__1 = m - 1;</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">      49166 :             for (lll = ll; lll &lt;= i__1; ++lll) {</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">      44567 :                 if ((r__1 = e[lll], std::abs(r__1)) &lt;= tol * mu) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         50 :                     e[lll] = 0.f;</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         50 :                     goto L60;</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :                 }</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">      44517 :                 mu = (r__2 = d__[lll + 1], std::abs(r__2)) * (mu / (mu + (r__1 = </span></a>
+<a name="580"><span class="lineNum">     580 </span>            :                         e[lll], std::abs(r__1))));</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">      44517 :                 sminl = (sminl&lt;mu) ? sminl : mu;</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :             }</a>
+<a name="583"><span class="lineNum">     583 </span>            :         }</a>
+<a name="584"><span class="lineNum">     584 </span>            :     } else {</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         33 :         if( (std::abs(e[ll]) &lt;= std::abs(tol)*std::abs(d__[ll])) ||</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :             (tol&lt;0.0 &amp;&amp; std::abs(e[ll])&lt;=thresh)) {</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineNoCov">          0 :             e[ll] = 0.f;</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :             goto L60;</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :         }</a>
+<a name="590"><span class="lineNum">     590 </span>            :         if (tol &gt;= 0.f) {</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         33 :             mu = (r__1 = d__[m], std::abs(r__1));</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :             sminl = mu;</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         33 :             i__1 = ll;</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">        305 :             for (lll = m - 1; lll &gt;= i__1; --lll) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">        272 :                 if ((r__1 = e[lll], std::abs(r__1)) &lt;= tol * mu) {</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :                     e[lll] = 0.f;</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="598"><span class="lineNum">     598 </span>            :                 }</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">        272 :                 mu = (r__2 = d__[lll], std::abs(r__2)) * (mu / (mu + (r__1 = e[</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :                         lll], std::abs(r__1))));</a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">        272 :                 sminl = (sminl&lt;mu) ? sminl : mu;</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :             }</a>
+<a name="603"><span class="lineNum">     603 </span>            :         }</a>
+<a name="604"><span class="lineNum">     604 </span>            :     }</a>
+<a name="605"><span class="lineNum">     605 </span>            :     oldll = ll;</a>
+<a name="606"><span class="lineNum">     606 </span>            :     oldm = m;</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">       4632 :     r__1 = eps, r__2 = tol * .01f;</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">       4632 :     if (tol &gt;= 0.f &amp;&amp; *n * tol * (sminl / smax) &lt;= ((r__1&gt;r__2) ? r__1 : r__2)) {</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         80 :         shift = 0.f;</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :     } else {</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">       4552 :         if (idir == 1) {</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       4519 :             sll = (r__1 = d__[ll], std::abs(r__1));</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">       4519 :             PLUMED_BLAS_F77_FUNC(dlas2,DLAS2)(&amp;d__[m - 1], &amp;e[m - 1], &amp;d__[m], &amp;shift, &amp;r__);</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :         } else {</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         33 :             sll = (r__1 = d__[m], std::abs(r__1));</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         33 :             PLUMED_BLAS_F77_FUNC(dlas2,DLAS2)(&amp;d__[ll], &amp;e[ll], &amp;d__[ll + 1], &amp;shift, &amp;r__);</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :         }</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">       4552 :         if (sll &gt; 0.f) {</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">       4552 :             r__1 = shift / sll;</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">       4552 :             if (r__1 * r__1 &lt; eps) {</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :                 shift = 0.f;</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :             }</a>
+<a name="624"><span class="lineNum">     624 </span>            :         }</a>
+<a name="625"><span class="lineNum">     625 </span>            :     }</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">       4632 :     iter = iter + m - ll;</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">       4632 :     if (shift == 0.f) {</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         80 :         if (idir == 1) {</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">         80 :             cs = 1.f;</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         80 :             oldcs = 1.f;</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         80 :             i__1 = m - 1;</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">       1346 :             for (i__ = ll; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">       1266 :                 r__1 = d__[i__] * cs;</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">       1266 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;r__1, &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">       1266 :                 if (i__ &gt; ll) {</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       1186 :                     e[i__ - 1] = oldsn * r__;</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :                 }</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">       1266 :                 r__1 = oldcs * r__;</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">       1266 :                 r__2 = d__[i__ + 1] * sn;</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">       1266 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;r__1, &amp;r__2, &amp;oldcs, &amp;oldsn, &amp;d__[i__]);</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">       1266 :                 work[i__ - ll + 1] = cs;</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">       1266 :                 work[i__ - ll + 1 + nm1] = sn;</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">       1266 :                 work[i__ - ll + 1 + nm12] = oldcs;</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">       1266 :                 work[i__ - ll + 1 + nm13] = oldsn;</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :             }</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">         80 :             h__ = d__[m] * cs;</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         80 :             d__[m] = h__ * oldcs;</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">         80 :             e[m - 1] = h__ * oldsn;</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">         80 :             if (*ncvt &gt; 0) {</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         80 :                 i__1 = m - ll + 1;</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         80 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncvt, &amp;work[1], &amp;work[*n], &amp;vt[</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         80 :                         ll + vt_dim1], ldvt);</span></a>
+<a name="653"><span class="lineNum">     653 </span>            :             }</a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">         80 :             if (*nru &gt; 0) {</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         80 :                 i__1 = m - ll + 1;</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">         80 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, &amp;i__1, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">         80 :                         + 1], &amp;u[ll * u_dim1 + 1], ldu);</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :             }</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">         80 :             if (*ncc &gt; 0) {</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncc, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :                         + 1], &amp;c__[ll + c_dim1], ldc);</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :             }</a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         80 :             if ((r__1 = e[m - 1], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">         75 :                 e[m - 1] = 0.f;</span></a>
+<a name="666"><span class="lineNum">     666 </span>            :             }</a>
+<a name="667"><span class="lineNum">     667 </span>            :         } else {</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :             cs = 1.f;</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :             oldcs = 1.f;</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :             i__1 = ll + 1;</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :             for (i__ = m; i__ &gt;= i__1; --i__) {</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :                 r__1 = d__[i__] * cs;</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;r__1, &amp;e[i__ - 1], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :                 if (i__ &lt; m) {</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :                     e[i__] = oldsn * r__;</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :                 }</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :                 r__1 = oldcs * r__;</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :                 r__2 = d__[i__ - 1] * sn;</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;r__1, &amp;r__2, &amp;oldcs, &amp;oldsn, &amp;d__[i__]);</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :                 work[i__ - ll] = cs;</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm1] = -sn;</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm12] = oldcs;</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm13] = -oldsn;</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :             }</a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :             h__ = d__[ll] * cs;</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :             d__[ll] = h__ * oldcs;</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :             e[ll] = h__ * oldsn;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncvt, &amp;work[nm12 + 1], &amp;work[</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :                         nm13 + 1], &amp;vt[ll + vt_dim1], ldvt);</span></a>
+<a name="692"><span class="lineNum">     692 </span>            :             }</a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, nru, &amp;i__1, &amp;work[1], &amp;work[*n], &amp;u[ll *</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :                          u_dim1 + 1], ldu);</span></a>
+<a name="697"><span class="lineNum">     697 </span>            :             }</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncc, &amp;work[1], &amp;work[*n], &amp;c__[</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :                         ll + c_dim1], ldc);</span></a>
+<a name="702"><span class="lineNum">     702 </span>            :             }</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :             if ((r__1 = e[ll], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineNoCov">          0 :                 e[ll] = 0.f;</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :             }</a>
+<a name="706"><span class="lineNum">     706 </span>            :         }</a>
+<a name="707"><span class="lineNum">     707 </span>            :     } else {</a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">       4552 :         if (idir == 1) {</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">       4519 :             f = ((r__1 = d__[ll], std::abs(r__1)) - shift) * ( ((d__[ll] &gt; 0) ? c_b49 : -c_b49) + shift / d__[ll]);</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">       4519 :             g = e[ll];</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">       4519 :             i__1 = m - 1;</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">      47367 :             for (i__ = ll; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">      42848 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;f, &amp;g, &amp;cosr, &amp;sinr, &amp;r__);</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">      42848 :                 if (i__ &gt; ll) {</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">      38329 :                     e[i__ - 1] = r__;</span></a>
+<a name="717"><span class="lineNum">     717 </span>            :                 }</a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">      42848 :                 f = cosr * d__[i__] + sinr * e[i__];</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">      42848 :                 e[i__] = cosr * e[i__] - sinr * d__[i__];</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">      42848 :                 g = sinr * d__[i__ + 1];</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">      42848 :                 d__[i__ + 1] = cosr * d__[i__ + 1];</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">      42848 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;f, &amp;g, &amp;cosl, &amp;sinl, &amp;r__);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">      42848 :                 d__[i__] = r__;</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">      42848 :                 f = cosl * e[i__] + sinl * d__[i__ + 1];</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">      42848 :                 d__[i__ + 1] = cosl * d__[i__ + 1] - sinl * e[i__];</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">      42848 :                 if (i__ &lt; m - 1) {</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">      38329 :                     g = sinl * e[i__ + 1];</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">      38329 :                     e[i__ + 1] = cosl * e[i__ + 1];</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :                 }</a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">      42848 :                 work[i__ - ll + 1] = cosr;</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">      42848 :                 work[i__ - ll + 1 + nm1] = sinr;</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">      42848 :                 work[i__ - ll + 1 + nm12] = cosl;</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">      42848 :                 work[i__ - ll + 1 + nm13] = sinl;</span></a>
+<a name="734"><span class="lineNum">     734 </span>            :             }</a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">       4519 :             e[m - 1] = f;</span></a>
+<a name="736"><span class="lineNum">     736 </span>            : </a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">       4519 :             if (*ncvt &gt; 0) {</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">       4519 :                 i__1 = m - ll + 1;</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">       4519 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncvt, &amp;work[1], &amp;work[*n], &amp;vt[</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">       4519 :                         ll + vt_dim1], ldvt);</span></a>
+<a name="741"><span class="lineNum">     741 </span>            :             }</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">       4519 :             if (*nru &gt; 0) {</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">       4519 :                 i__1 = m - ll + 1;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">       4519 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, &amp;i__1, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">       4519 :                         + 1], &amp;u[ll * u_dim1 + 1], ldu);</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :             }</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">       4519 :             if (*ncc &gt; 0) {</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncc, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :                         + 1], &amp;c__[ll + c_dim1], ldc);</span></a>
+<a name="751"><span class="lineNum">     751 </span>            :             }</a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">       4519 :             if ((r__1 = e[m - 1], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">        834 :                 e[m - 1] = 0.f;</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :             }</a>
+<a name="755"><span class="lineNum">     755 </span>            :         } else {</a>
+<a name="756"><span class="lineNum">     756 </span>            : </a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">         33 :             f = ((r__1 = d__[m], std::abs(r__1)) - shift) * ( ((d__[m] &gt; 0) ? c_b49 : -c_b49) + shift / d__[m]);</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">         33 :             g = e[m - 1];</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">         33 :             i__1 = ll + 1;</span></a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">        305 :             for (i__ = m; i__ &gt;= i__1; --i__) {</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">        272 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;f, &amp;g, &amp;cosr, &amp;sinr, &amp;r__);</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">        272 :                 if (i__ &lt; m) {</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">        239 :                     e[i__] = r__;</span></a>
+<a name="764"><span class="lineNum">     764 </span>            :                 }</a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">        272 :                 f = cosr * d__[i__] + sinr * e[i__ - 1];</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">        272 :                 e[i__ - 1] = cosr * e[i__ - 1] - sinr * d__[i__];</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">        272 :                 g = sinr * d__[i__ - 1];</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">        272 :                 d__[i__ - 1] = cosr * d__[i__ - 1];</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">        272 :                 PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;f, &amp;g, &amp;cosl, &amp;sinl, &amp;r__);</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">        272 :                 d__[i__] = r__;</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">        272 :                 f = cosl * e[i__ - 1] + sinl * d__[i__ - 1];</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">        272 :                 d__[i__ - 1] = cosl * d__[i__ - 1] - sinl * e[i__ - 1];</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">        272 :                 if (i__ &gt; ll + 1) {</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">        239 :                     g = sinl * e[i__ - 2];</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">        239 :                     e[i__ - 2] = cosl * e[i__ - 2];</span></a>
+<a name="776"><span class="lineNum">     776 </span>            :                 }</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">        272 :                 work[i__ - ll] = cosr;</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">        272 :                 work[i__ - ll + nm1] = -sinr;</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">        272 :                 work[i__ - ll + nm12] = cosl;</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">        272 :                 work[i__ - ll + nm13] = -sinl;</span></a>
+<a name="781"><span class="lineNum">     781 </span>            :             }</a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">         33 :             e[ll] = f;</span></a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">         33 :             if ((r__1 = e[ll], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">         12 :                 e[ll] = 0.f;</span></a>
+<a name="786"><span class="lineNum">     786 </span>            :             }</a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">         33 :             if (*ncvt &gt; 0) {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">         33 :                 i__1 = m - ll + 1;</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">         33 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncvt, &amp;work[nm12 + 1], &amp;work[</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">         33 :                         nm13 + 1], &amp;vt[ll + vt_dim1], ldvt);</span></a>
+<a name="791"><span class="lineNum">     791 </span>            :             }</a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">         33 :             if (*nru &gt; 0) {</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">         33 :                 i__1 = m - ll + 1;</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">         33 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, nru, &amp;i__1, &amp;work[1], &amp;work[*n], &amp;u[ll *</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">         33 :                          u_dim1 + 1], ldu);</span></a>
+<a name="796"><span class="lineNum">     796 </span>            :             }</a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">         33 :             if (*ncc &gt; 0) {</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncc, &amp;work[1], &amp;work[*n], &amp;c__[</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineNoCov">          0 :                         ll + c_dim1], ldc);</span></a>
+<a name="801"><span class="lineNum">     801 </span>            :             }</a>
+<a name="802"><span class="lineNum">     802 </span>            :         }</a>
+<a name="803"><span class="lineNum">     803 </span>            :     }</a>
+<a name="804"><span class="lineNum">     804 </span>            : </a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">       4632 :     goto L60;</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">        155 : L160:</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">        155 :     i__1 = *n;</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">       2635 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">       2480 :         if (d__[i__] &lt; 0.f) {</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">        531 :             d__[i__] = -d__[i__];</span></a>
+<a name="812"><span class="lineNum">     812 </span>            : </a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">        531 :             if (*ncvt &gt; 0) {</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">        531 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(ncvt, &amp;c_b72, &amp;vt[i__ + vt_dim1], ldvt);</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :             }</a>
+<a name="816"><span class="lineNum">     816 </span>            :         }</a>
+<a name="817"><span class="lineNum">     817 </span>            :     }</a>
+<a name="818"><span class="lineNum">     818 </span>            : </a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">        155 :     i__1 = *n - 1;</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">       2480 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="821"><span class="lineNum">     821 </span>            : </a>
+<a name="822"><span class="lineNum">     822 </span>            :         isub = 1;</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">       2325 :         smin = d__[1];</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">       2325 :         i__2 = *n + 1 - i__;</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">      22122 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">      19797 :             if (d__[j] &lt;= smin) {</span></a>
+<a name="827"><span class="lineNum">     827 </span>            :                 isub = j;</a>
+<a name="828"><span class="lineNum">     828 </span>            :                 smin = d__[j];</a>
+<a name="829"><span class="lineNum">     829 </span>            :             }</a>
+<a name="830"><span class="lineNum">     830 </span>            :         }</a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">       2325 :         if (isub != *n + 1 - i__) {</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">        179 :             d__[isub] = d__[*n + 1 - i__];</span></a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">        179 :             d__[*n + 1 - i__] = smin;</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">        179 :             if (*ncvt &gt; 0) {</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">        179 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(ncvt, &amp;vt[isub + vt_dim1], ldvt, &amp;vt[*n + 1 - i__ + </span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">        179 :                         vt_dim1], ldvt);</span></a>
+<a name="837"><span class="lineNum">     837 </span>            :             }</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">        179 :             if (*nru &gt; 0) {</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">        179 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(nru, &amp;u[isub * u_dim1 + 1], &amp;c__1, &amp;u[(*n + 1 - i__) * </span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">        179 :                         u_dim1 + 1], &amp;c__1);</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :             }</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">        179 :             if (*ncc &gt; 0) {</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(ncc, &amp;c__[isub + c_dim1], ldc, &amp;c__[*n + 1 - i__ + </span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineNoCov">          0 :                         c_dim1], ldc);</span></a>
+<a name="845"><span class="lineNum">     845 </span>            :             }</a>
+<a name="846"><span class="lineNum">     846 </span>            :         }</a>
+<a name="847"><span class="lineNum">     847 </span>            :     }</a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">        155 :     goto L220;</span></a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span>            : L200:</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :         if (e[i__] != 0.f) {</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="856"><span class="lineNum">     856 </span>            :         }</a>
+<a name="857"><span class="lineNum">     857 </span>            :     }</a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 : L220:</span></a>
+<a name="859"><span class="lineNum">     859 </span>            :     return;</a>
+<a name="860"><span class="lineNum">     860 </span>            : </a>
+<a name="861"><span class="lineNum">     861 </span>            : }</a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span>            : }</a>
+<a name="865"><span class="lineNum">     865 </span>            : }</a>
+<a name="866"><span class="lineNum">     866 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="867"><span class="lineNum">     867 </span>            : </a>
+<a name="868"><span class="lineNum">     868 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="869"><span class="lineNum">     869 </span>            : namespace PLMD{</a>
+<a name="870"><span class="lineNum">     870 </span>            : namespace lapack{</a>
+<a name="871"><span class="lineNum">     871 </span>            : using namespace blas;</a>
+<a name="872"><span class="lineNum">     872 </span>            : void</a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">         96 : PLUMED_BLAS_F77_FUNC(dgebd2,DGEBD2)(int *m,</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :         int *n,</a>
+<a name="875"><span class="lineNum">     875 </span>            :         double *a,</a>
+<a name="876"><span class="lineNum">     876 </span>            :         int *lda,</a>
+<a name="877"><span class="lineNum">     877 </span>            :         double *d,</a>
+<a name="878"><span class="lineNum">     878 </span>            :         double *e,</a>
+<a name="879"><span class="lineNum">     879 </span>            :         double *tauq,</a>
+<a name="880"><span class="lineNum">     880 </span>            :         double *taup,</a>
+<a name="881"><span class="lineNum">     881 </span>            :         double *work,</a>
+<a name="882"><span class="lineNum">     882 </span>            :         int *info)</a>
+<a name="883"><span class="lineNum">     883 </span>            : {</a>
+<a name="884"><span class="lineNum">     884 </span>            :   int i,i1,i2,i3;</a>
+<a name="885"><span class="lineNum">     885 </span>            :     </a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">         96 :     *info = 0;</span></a>
+<a name="887"><span class="lineNum">     887 </span>            : </a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineCov">         96 :   if(*m&gt;=*n) {</span></a>
+<a name="889"><span class="lineNum">     889 </span>            :     /* reduce to upper bidiag. form */</a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">       2256 :     for(i=0;i&lt;*n;i++) {</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">       2160 :       i1 = *m - i;</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">       2160 :       i2 = ( (i+1) &lt; (*m-1)) ? (i+1) : (*m-1);</span></a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">       2160 :       i3 = 1;</span></a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">       2160 :       PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i1,&amp;(a[i*(*lda)+i]),&amp;(a[i*(*lda)+i2]),&amp;i3,&amp;(tauq[i]));</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">       2160 :       d[i] = a[i*(*lda)+i];</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">       2160 :       a[i*(*lda)+i] = 1.0;</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">       2160 :       i2 = *n - i - 1;</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">       2160 :       PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;L&quot;,&amp;i1,&amp;i2,&amp;(a[i*(*lda)+i]),&amp;i3,&amp;(tauq[i]),&amp;(a[(i+1)*(*lda)+i]),lda,work);</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">       2160 :       a[i*(*lda)+i] = d[i];</span></a>
+<a name="900"><span class="lineNum">     900 </span>            : </a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">       2160 :       if(i&lt;(*n-1)) {</span></a>
+<a name="902"><span class="lineNum">     902 </span>            : </a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">       2064 :         i1 = *n - i -1;</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">       2064 :         i2 = ( (i+2) &lt; (*n-1)) ? (i+2) : (*n-1); </span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">       2064 :         PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i1,&amp;(a[(i+1)*(*lda)+i]),&amp;(a[i2*(*lda)+i]),lda,&amp;(taup[i]));</span></a>
+<a name="906"><span class="lineNum">     906 </span>            : </a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">       2064 :         e[i] = a[(i+1)*(*lda)+i];</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">       2064 :         a[(i+1)*(*lda)+i] = 1.0;</span></a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">       2064 :         i1 = *m - i - 1;</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">       2064 :         i2 = *n - i - 1;</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">       2064 :         PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;R&quot;,&amp;i1,&amp;i2,&amp;(a[(i+1)*(*lda)+i]),lda,&amp;(taup[i]),&amp;(a[(i+1)*(*lda)+i+1]),lda,work);</span></a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">       2064 :         a[(i+1)*(*lda)+i] = e[i];</span></a>
+<a name="914"><span class="lineNum">     914 </span>            :       } else</a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">         96 :         taup[i] = 0.0;</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :     }</a>
+<a name="917"><span class="lineNum">     917 </span>            :   } else {</a>
+<a name="918"><span class="lineNum">     918 </span>            :     /* reduce to lower bidiag. form */</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*m;i++) {</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :       i1 = *n - i;</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineNoCov">          0 :       i2 = ( (i+1) &lt; (*n-1)) ? (i+1) : (*n-1);</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i1,&amp;(a[i*(*lda)+i]),&amp;(a[i2*(*lda)+i]),lda,&amp;(taup[i]));</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineNoCov">          0 :       d[i] = a[i*(*lda)+i];</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = 1.0;</span></a>
+<a name="925"><span class="lineNum">     925 </span>            : </a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineNoCov">          0 :       i2 = *m - i - 1;</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineNoCov">          0 :       i3 = ( (i+1) &lt; (*m-1)) ? (i+1) : (*m-1);</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;R&quot;,&amp;i2,&amp;i1,&amp;(a[i*(*lda)+i]),lda,&amp;(taup[i]),&amp;(a[(i)*(*lda)+i3]),lda,work);</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = d[i];</span></a>
+<a name="930"><span class="lineNum">     930 </span>            : </a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineNoCov">          0 :       if(i&lt;(*m-1)) {</span></a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineNoCov">          0 :         i1 = *m - i - 1;</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :         i2 = ( (i+2) &lt; (*m-1)) ? (i+2) : (*m-1);</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineNoCov">          0 :         i3 = 1;</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i1,&amp;(a[(i)*(*lda)+i+1]),&amp;(a[i*(*lda)+i2]),&amp;i3,&amp;(tauq[i]));</span></a>
+<a name="937"><span class="lineNum">     937 </span>            : </a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 :         e[i] = a[(i)*(*lda)+i+1];</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineNoCov">          0 :         a[(i)*(*lda)+i+1] = 1.0;</span></a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineNoCov">          0 :         i1 = *m - i - 1;</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :         i2 = *n - i - 1;</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineNoCov">          0 :         i3 = 1;</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;L&quot;,&amp;i1,&amp;i2,&amp;(a[(i)*(*lda)+i+1]),&amp;i3,&amp;(tauq[i]),&amp;(a[(i+1)*(*lda)+i+1]),lda,work);</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineNoCov">          0 :         a[(i)*(*lda)+i+1] = e[i];</span></a>
+<a name="946"><span class="lineNum">     946 </span>            :       } else</a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineNoCov">          0 :         tauq[i] = 0.0;</span></a>
+<a name="948"><span class="lineNum">     948 </span>            :     }</a>
+<a name="949"><span class="lineNum">     949 </span>            :   }</a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">         96 :   return;</span></a>
+<a name="951"><span class="lineNum">     951 </span>            : }</a>
+<a name="952"><span class="lineNum">     952 </span>            : }</a>
+<a name="953"><span class="lineNum">     953 </span>            : }</a>
+<a name="954"><span class="lineNum">     954 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="955"><span class="lineNum">     955 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="956"><span class="lineNum">     956 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="957"><span class="lineNum">     957 </span>            : </a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="960"><span class="lineNum">     960 </span>            : namespace PLMD{</a>
+<a name="961"><span class="lineNum">     961 </span>            : namespace lapack{</a>
+<a name="962"><span class="lineNum">     962 </span>            : using namespace blas;</a>
+<a name="963"><span class="lineNum">     963 </span>            : void</a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">         96 : PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(int *m, </span></a>
+<a name="965"><span class="lineNum">     965 </span>            :         int *n, </a>
+<a name="966"><span class="lineNum">     966 </span>            :         double *a, </a>
+<a name="967"><span class="lineNum">     967 </span>            :         int *lda, </a>
+<a name="968"><span class="lineNum">     968 </span>            :         double *d__, </a>
+<a name="969"><span class="lineNum">     969 </span>            :         double *e,</a>
+<a name="970"><span class="lineNum">     970 </span>            :         double *tauq, </a>
+<a name="971"><span class="lineNum">     971 </span>            :         double *taup,</a>
+<a name="972"><span class="lineNum">     972 </span>            :         double *work, </a>
+<a name="973"><span class="lineNum">     973 </span>            :         int *lwork,</a>
+<a name="974"><span class="lineNum">     974 </span>            :         int *info)</a>
+<a name="975"><span class="lineNum">     975 </span>            : {</a>
+<a name="976"><span class="lineNum">     976 </span>            :     /* System generated locals */</a>
+<a name="977"><span class="lineNum">     977 </span>            :     int a_dim1, a_offset, i_1, i_2, i_3, i_4;</a>
+<a name="978"><span class="lineNum">     978 </span>            : </a>
+<a name="979"><span class="lineNum">     979 </span>            :     /* Local variables */</a>
+<a name="980"><span class="lineNum">     980 </span>            :     int i_, j, nx,nb;</a>
+<a name="981"><span class="lineNum">     981 </span>            :     double ws;</a>
+<a name="982"><span class="lineNum">     982 </span>            :     int nbmin, iinfo, minmn;</a>
+<a name="983"><span class="lineNum">     983 </span>            :     int ldwrkx, ldwrky;</a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">         96 :     double one = 1.0;</span></a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">         96 :     double minusone = -1.0;</span></a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">         96 :     a_dim1 = *lda;</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">         96 :     a_offset = 1 + a_dim1;</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">         96 :     a -= a_offset;</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">         96 :     --d__;</span></a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">         96 :     --e;</span></a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">         96 :     --tauq;</span></a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">         96 :     --taup;</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">         96 :     --work;</span></a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">         96 :     nb = DGEBRD_BLOCKSIZE;</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">         96 :     *info = 0;</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">         96 :     if (*lwork==-1) {</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineNoCov">          0 :       work[1] = (double) ( (*m + *n) * nb);</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="1001"><span class="lineNum">    1001 </span>            :     }</a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">         96 :     minmn = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">         96 :     if (minmn == 0) {</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineNoCov">          0 :       work[1] = 1.;</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="1006"><span class="lineNum">    1006 </span>            :     }</a>
+<a name="1007"><span class="lineNum">    1007 </span>            : </a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineCov">         96 :     ws = (*m &gt; *n) ? *m : *n;</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">         96 :     ldwrkx = *m;</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">         96 :     ldwrky = *n;</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            : </a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">         96 :     if (nb &gt; 1 &amp;&amp; nb &lt; minmn) {</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :         nx = DGEBRD_CROSSOVER;</a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">         17 :         if (nx &lt; minmn) {</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">          1 :             ws = (double) ((*m + *n) * nb);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">          1 :             if ((double) (*lwork) &lt; ws) {</span></a>
+<a name="1017"><span class="lineNum">    1017 </span>            :               nbmin = DGEBRD_MINBLOCKSIZE;</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineNoCov">          0 :                 if (*lwork &gt;= (*m + *n) * nbmin) {</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineNoCov">          0 :                     nb = *lwork / (*m + *n);</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            :                 } else {</a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineNoCov">          0 :                     nb = 1;</span></a>
+<a name="1022"><span class="lineNum">    1022 </span>            :                     nx = minmn;</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :                 }</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :             }</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :         }</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :     } else {</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :         nx = minmn;</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     }</a>
+<a name="1029"><span class="lineNum">    1029 </span>            : </a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">         96 :     i_1 = minmn - nx;</span></a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">         96 :     i_2 = nb;</span></a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">        108 :     for (i_ = 1; i_2 &lt; 0 ? i_ &gt;= i_1 : i_ &lt;= i_1; i_ += i_2) {</span></a>
+<a name="1033"><span class="lineNum">    1033 </span>            : </a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">         12 :         i_3 = *m - i_ + 1;</span></a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">         12 :         i_4 = *n - i_ + 1;</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">         12 :         PLUMED_BLAS_F77_FUNC(dlabrd,DLABRD)(&amp;i_3, &amp;i_4, &amp;nb, &amp;a[i_ + i_ * a_dim1], lda, &amp;d__[i_], </span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">         12 :                 &amp;e[i_], &amp;tauq[i_], &amp;taup[i_], &amp;work[1], &amp;ldwrkx, </span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">         12 :                 &amp;work[ldwrkx * nb + 1], &amp;ldwrky);</span></a>
+<a name="1039"><span class="lineNum">    1039 </span>            : </a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">         12 :         i_3 = *m - i_ - nb + 1;</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">         12 :         i_4 = *n - i_ - nb + 1;</span></a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">         12 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;T&quot;, &amp;i_3, &amp;i_4, &amp;nb, &amp;minusone, </span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">         12 :                &amp;a[i_ + nb + i_ * a_dim1], lda, &amp;work[ldwrkx * nb + nb + 1],</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">         12 :                &amp;ldwrky, &amp;one, &amp;a[i_ + nb + (i_ + nb) * a_dim1], lda);</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">         12 :         i_3 = *m - i_ - nb + 1;</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">         12 :         i_4 = *n - i_ - nb + 1;</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">         12 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, &amp;i_3, &amp;i_4, &amp;nb, &amp;minusone, &amp;work[nb + 1], &amp;ldwrkx,</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">         12 :                &amp;a[i_ + (i_ + nb) * a_dim1], lda, &amp;one, </span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">         12 :                &amp;a[i_ + nb + (i_ + nb) * a_dim1], lda);</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            : </a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">         12 :         if (*m &gt;= *n) {</span></a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">         12 :             i_3 = i_ + nb - 1;</span></a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">        396 :             for (j = i_; j &lt;= i_3; ++j) {</span></a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">        384 :                 a[j + j * a_dim1] = d__[j];</span></a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">        384 :                 a[j + (j + 1) * a_dim1] = e[j];</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            :             }</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :         } else {</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineNoCov">          0 :             i_3 = i_ + nb - 1;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineNoCov">          0 :             for (j = i_; j &lt;= i_3; ++j) {</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = d__[j];</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineNoCov">          0 :                 a[j + 1 + j * a_dim1] = e[j];</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            :             }</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :         }</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     }</a>
+<a name="1065"><span class="lineNum">    1065 </span>            : </a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">         96 :     i_2 = *m - i_ + 1;</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">         96 :     i_1 = *n - i_ + 1;</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">         96 :     PLUMED_BLAS_F77_FUNC(dgebd2,DGEBD2)(&amp;i_2, &amp;i_1, &amp;a[i_ + i_ * a_dim1], lda, &amp;d__[i_], &amp;e[i_], &amp;</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">         96 :             tauq[i_], &amp;taup[i_], &amp;work[1], &amp;iinfo);</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">         96 :     work[1] = ws;</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         96 :     return;</span></a>
+<a name="1072"><span class="lineNum">    1072 </span>            : </a>
+<a name="1073"><span class="lineNum">    1073 </span>            : }</a>
+<a name="1074"><span class="lineNum">    1074 </span>            : }</a>
+<a name="1075"><span class="lineNum">    1075 </span>            : }</a>
+<a name="1076"><span class="lineNum">    1076 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1079"><span class="lineNum">    1079 </span>            : namespace PLMD{</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : namespace lapack{</a>
+<a name="1081"><span class="lineNum">    1081 </span>            : using namespace blas;</a>
+<a name="1082"><span class="lineNum">    1082 </span>            : void </a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dgelq2,DGELQ2)(int *m, </span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :                         int *n, </a>
+<a name="1085"><span class="lineNum">    1085 </span>            :                         double *a,</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :                         int *lda, </a>
+<a name="1087"><span class="lineNum">    1087 </span>            :                         double *tau, </a>
+<a name="1088"><span class="lineNum">    1088 </span>            :                         double *work, </a>
+<a name="1089"><span class="lineNum">    1089 </span>            :                         int *info)</a>
+<a name="1090"><span class="lineNum">    1090 </span>            : {</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :     /* System generated locals */</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3, i__4;</a>
+<a name="1093"><span class="lineNum">    1093 </span>            : </a>
+<a name="1094"><span class="lineNum">    1094 </span>            :     /* Local variables */</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :     int i__, k;</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :     double aii;</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : </a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     --work;</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : </a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            :     </a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineNoCov">          0 :     i__4 = (*m &gt; 1) ? *m : 1;</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            :     </a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; i__4) {</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            :     }</a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            :         return;</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     }</a>
+<a name="1118"><span class="lineNum">    1118 </span>            : </a>
+<a name="1119"><span class="lineNum">    1119 </span>            :     </a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineNoCov">          0 :     k = (*m &lt; *n ) ? *m : *n;</span></a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     i__1 = k;</a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineNoCov">          0 :         i__2 = *n - i__ + 1;</span></a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineNoCov">          0 :         i__3 = i__ + 1;</span></a>
+<a name="1125"><span class="lineNum">    1125 </span>            :     i__4 = (i__3 &lt; *n) ? i__3 : *n;</a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i__2, &amp;a[i__ + i__ * a_dim1], &amp;a[i__ + i__4 * a_dim1],</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineNoCov">          0 :                             lda, &amp;tau[i__]);</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineNoCov">          0 :         if (i__ &lt; *m) {</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineNoCov">          0 :             aii = a[i__ + i__ * a_dim1];</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineNoCov">          0 :             a[i__ + i__ * a_dim1] = 1.f;</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineNoCov">          0 :             i__2 = *m - i__;</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;R&quot;, &amp;i__2, &amp;i__3, &amp;a[i__ + i__ * a_dim1], lda, </span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineNoCov">          0 :                               &amp;tau[i__], &amp;a[i__ + 1 + i__ * a_dim1], lda, &amp;work[1]);</span></a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineNoCov">          0 :             a[i__ + i__ * a_dim1] = aii;</span></a>
+<a name="1136"><span class="lineNum">    1136 </span>            :         }</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :     }</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     return;</a>
+<a name="1139"><span class="lineNum">    1139 </span>            : }</a>
+<a name="1140"><span class="lineNum">    1140 </span>            : </a>
+<a name="1141"><span class="lineNum">    1141 </span>            : </a>
+<a name="1142"><span class="lineNum">    1142 </span>            : }</a>
+<a name="1143"><span class="lineNum">    1143 </span>            : }</a>
+<a name="1144"><span class="lineNum">    1144 </span>            : #include &lt;cmath&gt;</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="1147"><span class="lineNum">    1147 </span>            : </a>
+<a name="1148"><span class="lineNum">    1148 </span>            : </a>
+<a name="1149"><span class="lineNum">    1149 </span>            : </a>
+<a name="1150"><span class="lineNum">    1150 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1151"><span class="lineNum">    1151 </span>            : namespace PLMD{</a>
+<a name="1152"><span class="lineNum">    1152 </span>            : namespace lapack{</a>
+<a name="1153"><span class="lineNum">    1153 </span>            : using namespace blas;</a>
+<a name="1154"><span class="lineNum">    1154 </span>            : void</a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dgelqf,DGELQF)(int *m,</span></a>
+<a name="1156"><span class="lineNum">    1156 </span>            :         int *n, </a>
+<a name="1157"><span class="lineNum">    1157 </span>            :         double *a, </a>
+<a name="1158"><span class="lineNum">    1158 </span>            :         int *lda, </a>
+<a name="1159"><span class="lineNum">    1159 </span>            :         double *tau,</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :         double *work, </a>
+<a name="1161"><span class="lineNum">    1161 </span>            :         int *lwork, </a>
+<a name="1162"><span class="lineNum">    1162 </span>            :         int *info)</a>
+<a name="1163"><span class="lineNum">    1163 </span>            : {</a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3, i__4;</a>
+<a name="1165"><span class="lineNum">    1165 </span>            : </a>
+<a name="1166"><span class="lineNum">    1166 </span>            :     int i__, k, ib, nb, nx, iws, nbmin, iinfo;</a>
+<a name="1167"><span class="lineNum">    1167 </span>            :     int ldwork, lwkopt;</a>
+<a name="1168"><span class="lineNum">    1168 </span>            : </a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="1173"><span class="lineNum">    1173 </span>            :     --work;</a>
+<a name="1174"><span class="lineNum">    1174 </span>            : </a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     nb = DGELQF_BLOCKSIZE;</a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 :     lwkopt = *m * nb;</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineNoCov">          0 :     work[1] = (double) lwkopt;</span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            : </a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :     if (*lwork==-1) {</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            :         return;</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :     }</a>
+<a name="1183"><span class="lineNum">    1183 </span>            : </a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineNoCov">          0 :     k =(*m &lt; *n) ? *m : *n;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineNoCov">          0 :     if (k == 0) {</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :     }</a>
+<a name="1189"><span class="lineNum">    1189 </span>            : </a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     nbmin = 2;</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :     nx = 0;</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :     iws = *m;</a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; k) {</span></a>
+<a name="1194"><span class="lineNum">    1194 </span>            :         nx = DGELQF_CROSSOVER;</a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineNoCov">          0 :         if (nx &lt; k) {</span></a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineNoCov">          0 :             ldwork = *m;</span></a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="1199"><span class="lineNum">    1199 </span>            : </a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            :                 nbmin = DGELQF_MINBLOCKSIZE;</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :             }</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :         }</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     }</a>
+<a name="1205"><span class="lineNum">    1205 </span>            : </a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; k &amp;&amp; nx &lt; k) {</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            : </a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineNoCov">          0 :         i__1 = k - nx;</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineNoCov">          0 :         i__2 = nb;</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineNoCov">          0 :             i__3 = k - i__ + 1;</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineNoCov">          0 :             ib = (i__3 &lt; nb) ? i__3 : nb;</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            : </a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dgelq2,DGELQ2)(&amp;ib, &amp;i__3, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[</span></a>
+<a name="1216"><span class="lineNum">    1216 </span>            :                     1], &amp;iinfo);</a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *m) {</span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            : </a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__3, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="1221"><span class="lineNum">    1221 </span>            :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</a>
+<a name="1222"><span class="lineNum">    1222 </span>            : </a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineNoCov">          0 :                 i__3 = *m - i__ - ib + 1;</span></a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineNoCov">          0 :                 i__4 = *n - i__ + 1;</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(&quot;Right&quot;, &quot;No transpose&quot;, &quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__3, </span></a>
+<a name="1226"><span class="lineNum">    1226 </span>            :                         &amp;i__4, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[1], &amp;</a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineNoCov">          0 :                         ldwork, &amp;a[i__ + ib + i__ * a_dim1], lda, &amp;work[ib + </span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineNoCov">          0 :                         1], &amp;ldwork);</span></a>
+<a name="1229"><span class="lineNum">    1229 </span>            :             }</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :         }</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :     } else {</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :         i__ = 1;</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     }</a>
+<a name="1234"><span class="lineNum">    1234 </span>            : </a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineNoCov">          0 :     if (i__ &lt;= k) {</span></a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineNoCov">          0 :         i__2 = *m - i__ + 1;</span></a>
+<a name="1237"><span class="lineNum">    1237 </span><span class="lineNoCov">          0 :         i__1 = *n - i__ + 1;</span></a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgelq2,DGELQ2)(&amp;i__2, &amp;i__1, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[1]</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            :                 , &amp;iinfo);</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :     }</a>
+<a name="1241"><span class="lineNum">    1241 </span>            : </a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineNoCov">          0 :     work[1] = (double) iws;</span></a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            : </a>
+<a name="1245"><span class="lineNum">    1245 </span>            : }</a>
+<a name="1246"><span class="lineNum">    1246 </span>            : }</a>
+<a name="1247"><span class="lineNum">    1247 </span>            : }</a>
+<a name="1248"><span class="lineNum">    1248 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1249"><span class="lineNum">    1249 </span>            : </a>
+<a name="1250"><span class="lineNum">    1250 </span>            : </a>
+<a name="1251"><span class="lineNum">    1251 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1252"><span class="lineNum">    1252 </span>            : namespace PLMD{</a>
+<a name="1253"><span class="lineNum">    1253 </span>            : namespace lapack{</a>
+<a name="1254"><span class="lineNum">    1254 </span>            : using namespace blas;</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : void</a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineCov">          1 : PLUMED_BLAS_F77_FUNC(dgeqr2,DGEQR2)(int *m,</span></a>
+<a name="1257"><span class="lineNum">    1257 </span>            :         int *n,</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :         double *a,</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :         int *lda,</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :         double *tau,</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :         double *work,</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :         int *info)</a>
+<a name="1263"><span class="lineNum">    1263 </span>            : {</a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineCov">          1 :   int k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="1265"><span class="lineNum">    1265 </span>            :   int i,i1,i2,i3;</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   double aii;</a>
+<a name="1267"><span class="lineNum">    1267 </span>            : </a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineCov">          1 :   *info = 0;</span></a>
+<a name="1269"><span class="lineNum">    1269 </span>            :   </a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineCov">          3 :   for(i=0;i&lt;k;i++) {</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">          2 :     i1 = *m - i;</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineCov">          2 :     i2 = ( (i+1) &lt; (*m-1) ) ? (i+1) : (*m-1);</span></a>
+<a name="1273"><span class="lineNum">    1273 </span><span class="lineCov">          2 :     i3 = 1;</span></a>
+<a name="1274"><span class="lineNum">    1274 </span><span class="lineCov">          2 :     PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i1,&amp;(a[i*(*lda)+i]),&amp;(a[i*(*lda)+i2]),&amp;i3,&amp;(tau[i]));</span></a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">          2 :     if(i&lt;(*n-1)) {</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">          1 :       aii = a[i*(*lda)+i];</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineCov">          1 :       a[i*(*lda)+i] = 1.0;</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">          1 :       i2 = *n - i - 1;</span></a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">          1 :       PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;L&quot;,&amp;i1,&amp;i2,&amp;(a[i*(*lda)+i]),&amp;i3,&amp;(tau[i]),</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">          1 :              &amp;(a[(i+1)*(*lda)+i]),lda,work);</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">          1 :       a[i*(*lda)+i] = aii;</span></a>
+<a name="1282"><span class="lineNum">    1282 </span>            :     }</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   }</a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">          1 :   return;</span></a>
+<a name="1285"><span class="lineNum">    1285 </span>            : }</a>
+<a name="1286"><span class="lineNum">    1286 </span>            : }</a>
+<a name="1287"><span class="lineNum">    1287 </span>            : }</a>
+<a name="1288"><span class="lineNum">    1288 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1289"><span class="lineNum">    1289 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="1290"><span class="lineNum">    1290 </span>            : </a>
+<a name="1291"><span class="lineNum">    1291 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1292"><span class="lineNum">    1292 </span>            : namespace PLMD{</a>
+<a name="1293"><span class="lineNum">    1293 </span>            : namespace lapack{</a>
+<a name="1294"><span class="lineNum">    1294 </span>            : using namespace blas;</a>
+<a name="1295"><span class="lineNum">    1295 </span>            : void </a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineCov">          1 : PLUMED_BLAS_F77_FUNC(dgeqrf,DGEQRF)(int *m, </span></a>
+<a name="1297"><span class="lineNum">    1297 </span>            :         int *n, </a>
+<a name="1298"><span class="lineNum">    1298 </span>            :         double *a, </a>
+<a name="1299"><span class="lineNum">    1299 </span>            :         int *lda, </a>
+<a name="1300"><span class="lineNum">    1300 </span>            :         double *tau,</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :         double *work, </a>
+<a name="1302"><span class="lineNum">    1302 </span>            :         int *lwork, </a>
+<a name="1303"><span class="lineNum">    1303 </span>            :         int *info)</a>
+<a name="1304"><span class="lineNum">    1304 </span>            : {</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3, i__4;</a>
+<a name="1306"><span class="lineNum">    1306 </span>            : </a>
+<a name="1307"><span class="lineNum">    1307 </span>            :     int i__, k, ib, nb, nx, iws, nbmin, iinfo;</a>
+<a name="1308"><span class="lineNum">    1308 </span>            :     int ldwork, lwkopt;</a>
+<a name="1309"><span class="lineNum">    1309 </span>            : </a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineCov">          1 :     a_dim1 = *lda;</span></a>
+<a name="1311"><span class="lineNum">    1311 </span><span class="lineCov">          1 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">          1 :     a -= a_offset;</span></a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineCov">          1 :     --tau;</span></a>
+<a name="1314"><span class="lineNum">    1314 </span>            :     --work;</a>
+<a name="1315"><span class="lineNum">    1315 </span>            : </a>
+<a name="1316"><span class="lineNum">    1316 </span><span class="lineCov">          1 :     *info = 0;</span></a>
+<a name="1317"><span class="lineNum">    1317 </span>            :     nb = DGEQRF_BLOCKSIZE;</a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineCov">          1 :     lwkopt = *n * nb;</span></a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">          1 :     work[1] = (double) lwkopt;</span></a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">          1 :         if (*lwork==-1)</span></a>
+<a name="1321"><span class="lineNum">    1321 </span>            :         return;</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :     </a>
+<a name="1323"><span class="lineNum">    1323 </span>            : </a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">          1 :     k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="1325"><span class="lineNum">    1325 </span><span class="lineCov">          1 :     if (k == 0) {</span></a>
+<a name="1326"><span class="lineNum">    1326 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="1327"><span class="lineNum">    1327 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="1328"><span class="lineNum">    1328 </span>            :     }</a>
+<a name="1329"><span class="lineNum">    1329 </span>            : </a>
+<a name="1330"><span class="lineNum">    1330 </span>            :     nbmin = 2;</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :     nx = 0;</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :     iws = *n;</a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineCov">          1 :     if (nb &gt; 1 &amp;&amp; nb &lt; k) {</span></a>
+<a name="1334"><span class="lineNum">    1334 </span>            :         </a>
+<a name="1335"><span class="lineNum">    1335 </span>            :       nx = DGEQRF_CROSSOVER;</a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineNoCov">          0 :         if (nx &lt; k) {</span></a>
+<a name="1337"><span class="lineNum">    1337 </span>            : </a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineNoCov">          0 :             ldwork = *n;</span></a>
+<a name="1339"><span class="lineNum">    1339 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="1340"><span class="lineNum">    1340 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="1341"><span class="lineNum">    1341 </span>            : </a>
+<a name="1342"><span class="lineNum">    1342 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="1343"><span class="lineNum">    1343 </span>            :                 nbmin = DGEQRF_MINBLOCKSIZE;</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :             }</a>
+<a name="1345"><span class="lineNum">    1345 </span>            :         }</a>
+<a name="1346"><span class="lineNum">    1346 </span>            :     }</a>
+<a name="1347"><span class="lineNum">    1347 </span>            : </a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineCov">          1 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; k &amp;&amp; nx &lt; k) {</span></a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineNoCov">          0 :         i__1 = k - nx;</span></a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineNoCov">          0 :         i__2 = nb;</span></a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="1352"><span class="lineNum">    1352 </span>            : </a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineNoCov">          0 :             i__3 = k - i__ + 1;</span></a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineNoCov">          0 :             ib = (i__3 &lt; nb) ? i__3 : nb;</span></a>
+<a name="1355"><span class="lineNum">    1355 </span>            : </a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineNoCov">          0 :             i__3 = *m - i__ + 1;</span></a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dgeqr2,DGEQR2)(&amp;i__3, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[</span></a>
+<a name="1358"><span class="lineNum">    1358 </span>            :                     1], &amp;iinfo);</a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *n) {</span></a>
+<a name="1360"><span class="lineNum">    1360 </span>            : </a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineNoCov">          0 :                 i__3 = *m - i__ + 1;</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__3, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="1363"><span class="lineNum">    1363 </span>            :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</a>
+<a name="1364"><span class="lineNum">    1364 </span>            : </a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineNoCov">          0 :                 i__3 = *m - i__ + 1;</span></a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineNoCov">          0 :                 i__4 = *n - i__ - ib + 1;</span></a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(&quot;Left&quot;, &quot;Transpose&quot;, &quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__3, &amp;</span></a>
+<a name="1368"><span class="lineNum">    1368 </span>            :                         i__4, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[1], &amp;</a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineNoCov">          0 :                         ldwork, &amp;a[i__ + (i__ + ib) * a_dim1], lda, &amp;work[ib </span></a>
+<a name="1370"><span class="lineNum">    1370 </span><span class="lineNoCov">          0 :                         + 1], &amp;ldwork);</span></a>
+<a name="1371"><span class="lineNum">    1371 </span>            :             }</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :         }</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :     } else {</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :         i__ = 1;</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :     }</a>
+<a name="1376"><span class="lineNum">    1376 </span>            : </a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">          1 :     if (i__ &lt;= k) {</span></a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineCov">          1 :         i__2 = *m - i__ + 1;</span></a>
+<a name="1379"><span class="lineNum">    1379 </span><span class="lineCov">          1 :         i__1 = *n - i__ + 1;</span></a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">          1 :         PLUMED_BLAS_F77_FUNC(dgeqr2,DGEQR2)(&amp;i__2, &amp;i__1, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[1]</span></a>
+<a name="1381"><span class="lineNum">    1381 </span>            :                 , &amp;iinfo);</a>
+<a name="1382"><span class="lineNum">    1382 </span>            :     }</a>
+<a name="1383"><span class="lineNum">    1383 </span>            : </a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineCov">          1 :     work[1] = (double) iws;</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineCov">          1 :     return;</span></a>
+<a name="1386"><span class="lineNum">    1386 </span>            : </a>
+<a name="1387"><span class="lineNum">    1387 </span>            : } </a>
+<a name="1388"><span class="lineNum">    1388 </span>            : </a>
+<a name="1389"><span class="lineNum">    1389 </span>            : }</a>
+<a name="1390"><span class="lineNum">    1390 </span>            : }</a>
+<a name="1391"><span class="lineNum">    1391 </span>            : #include &lt;cmath&gt;</a>
+<a name="1392"><span class="lineNum">    1392 </span>            : #include &quot;real.h&quot;</a>
+<a name="1393"><span class="lineNum">    1393 </span>            : </a>
+<a name="1394"><span class="lineNum">    1394 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1395"><span class="lineNum">    1395 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1396"><span class="lineNum">    1396 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="1397"><span class="lineNum">    1397 </span>            : </a>
+<a name="1398"><span class="lineNum">    1398 </span>            : </a>
+<a name="1399"><span class="lineNum">    1399 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1400"><span class="lineNum">    1400 </span>            : namespace PLMD{</a>
+<a name="1401"><span class="lineNum">    1401 </span>            : namespace lapack{</a>
+<a name="1402"><span class="lineNum">    1402 </span>            : using namespace blas;</a>
+<a name="1403"><span class="lineNum">    1403 </span>            : void </a>
+<a name="1404"><span class="lineNum">    1404 </span><span class="lineCov">        192 : PLUMED_BLAS_F77_FUNC(dgesdd,DGESDD)(const char *jobz, </span></a>
+<a name="1405"><span class="lineNum">    1405 </span>            :         int *m, </a>
+<a name="1406"><span class="lineNum">    1406 </span>            :         int *n, </a>
+<a name="1407"><span class="lineNum">    1407 </span>            :         double *a, </a>
+<a name="1408"><span class="lineNum">    1408 </span>            :         int *lda, </a>
+<a name="1409"><span class="lineNum">    1409 </span>            :         double *s,</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :         double *u, </a>
+<a name="1411"><span class="lineNum">    1411 </span>            :         int *ldu, </a>
+<a name="1412"><span class="lineNum">    1412 </span>            :         double *vt, </a>
+<a name="1413"><span class="lineNum">    1413 </span>            :         int *ldvt, </a>
+<a name="1414"><span class="lineNum">    1414 </span>            :         double *work,</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :         int *lwork, </a>
+<a name="1416"><span class="lineNum">    1416 </span>            :         int *iwork, </a>
+<a name="1417"><span class="lineNum">    1417 </span>            :         int *info)</a>
+<a name="1418"><span class="lineNum">    1418 </span>            : {</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     int a_dim1, a_offset, u_dim1, u_offset, vt_dim1, vt_offset, i__1, i__2;</a>
+<a name="1420"><span class="lineNum">    1420 </span>            : </a>
+<a name="1421"><span class="lineNum">    1421 </span>            :     int ie, iu;</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     double dum[1], eps;</a>
+<a name="1423"><span class="lineNum">    1423 </span>            :     int ivt, iscl;</a>
+<a name="1424"><span class="lineNum">    1424 </span>            :     double anrm;</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :     int idum[1], ierr, itau;</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :     int minmn, wrkbl, itaup, itauq, mnthr;</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :     int nwork;</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :     int wntqn;</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :     int bdspac;</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :     double bignum;</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :     int ldwrku, maxwrk, ldwkvt;</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :     double smlnum,minval, safemin;</a>
+<a name="1433"><span class="lineNum">    1433 </span>            :     int lquery;</a>
+<a name="1434"><span class="lineNum">    1434 </span><span class="lineCov">        192 :     int c__0 = 0;</span></a>
+<a name="1435"><span class="lineNum">    1435 </span><span class="lineCov">        192 :     int c__1 = 1;</span></a>
+<a name="1436"><span class="lineNum">    1436 </span><span class="lineCov">        192 :     double zero = 0.0;</span></a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">        192 :     double one = 1.0;</span></a>
+<a name="1438"><span class="lineNum">    1438 </span>            : </a>
+<a name="1439"><span class="lineNum">    1439 </span>            : </a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineCov">        192 :     a_dim1 = *lda;</span></a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineCov">        192 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineCov">        192 :     a -= a_offset;</span></a>
+<a name="1443"><span class="lineNum">    1443 </span>            :     --s;</a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineCov">        192 :     u_dim1 = *ldu;</span></a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineCov">        192 :     u_offset = 1 + u_dim1;</span></a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineCov">        192 :     u -= u_offset;</span></a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineCov">        192 :     vt_dim1 = *ldvt;</span></a>
+<a name="1448"><span class="lineNum">    1448 </span><span class="lineCov">        192 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineCov">        192 :     vt -= vt_offset;</span></a>
+<a name="1450"><span class="lineNum">    1450 </span><span class="lineCov">        192 :     --work;</span></a>
+<a name="1451"><span class="lineNum">    1451 </span>            :     --iwork;</a>
+<a name="1452"><span class="lineNum">    1452 </span>            : </a>
+<a name="1453"><span class="lineNum">    1453 </span><span class="lineCov">        192 :     *info = 0;</span></a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineCov">        192 :     minmn = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineCov">        192 :     mnthr = (int) (minmn * 11. / 6.);</span></a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineCov">        192 :     wntqn = (*jobz=='o' || *jobz=='O');</span></a>
+<a name="1457"><span class="lineNum">    1457 </span>            : </a>
+<a name="1458"><span class="lineNum">    1458 </span>            :     maxwrk = 1;</a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineCov">        192 :     lquery = *lwork == -1;</span></a>
+<a name="1460"><span class="lineNum">    1460 </span>            : </a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineCov">        192 :     if (*info == 0 &amp;&amp; *m &gt; 0 &amp;&amp; *n &gt; 0) {</span></a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">        192 :         if (*m &gt;= *n) {</span></a>
+<a name="1463"><span class="lineNum">    1463 </span>            : </a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineCov">        192 :             if (wntqn) {</span></a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineNoCov">          0 :                 bdspac = *n * 7;</span></a>
+<a name="1466"><span class="lineNum">    1466 </span>            :             } else {</a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">        192 :                 bdspac = *n * 3 * *n + (*n &lt;&lt; 2);</span></a>
+<a name="1468"><span class="lineNum">    1468 </span>            :             }</a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineCov">        192 :             if (*m &gt;= mnthr) {</span></a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineCov">          2 :                 if (wntqn) {</span></a>
+<a name="1471"><span class="lineNum">    1471 </span>            : </a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineNoCov">          0 :                     wrkbl = *n * 67;</span></a>
+<a name="1473"><span class="lineNum">    1473 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *n;</span></a>
+<a name="1474"><span class="lineNum">    1474 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :                 } else {</a>
+<a name="1476"><span class="lineNum">    1476 </span>            : </a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">          2 :                     wrkbl = *n * 67;</span></a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineCov">          2 :                     i__1 = wrkbl, i__2 = *n + (*m &lt;&lt; 5);</span></a>
+<a name="1479"><span class="lineNum">    1479 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">          2 :                     i__1 = wrkbl, i__2 = bdspac + *n * 3;</span></a>
+<a name="1481"><span class="lineNum">    1481 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineCov">          2 :                     maxwrk = wrkbl + *n * *n;</span></a>
+<a name="1483"><span class="lineNum">    1483 </span>            :                 }</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :             } else {</a>
+<a name="1485"><span class="lineNum">    1485 </span>            : </a>
+<a name="1486"><span class="lineNum">    1486 </span><span class="lineCov">        190 :                 wrkbl = *n * 3 + (*m + *n*32);</span></a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineCov">        190 :                 if (wntqn) {</span></a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *n * 3;</span></a>
+<a name="1489"><span class="lineNum">    1489 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :                 } else {</a>
+<a name="1491"><span class="lineNum">    1491 </span><span class="lineCov">        190 :                     i__1 = maxwrk, i__2 = bdspac + *n * 3;</span></a>
+<a name="1492"><span class="lineNum">    1492 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1493"><span class="lineNum">    1493 </span>            :                 }</a>
+<a name="1494"><span class="lineNum">    1494 </span>            :             }</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :         } else {</a>
+<a name="1496"><span class="lineNum">    1496 </span>            : </a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineNoCov">          0 :                 bdspac = *m * 7;</span></a>
+<a name="1499"><span class="lineNum">    1499 </span>            :             } else {</a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineNoCov">          0 :                 bdspac = *m * 3 * *m + (*m*4);</span></a>
+<a name="1501"><span class="lineNum">    1501 </span>            :             }</a>
+<a name="1502"><span class="lineNum">    1502 </span><span class="lineNoCov">          0 :             if (*n &gt;= mnthr) {</span></a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineNoCov">          0 :                 if (wntqn) {</span></a>
+<a name="1504"><span class="lineNum">    1504 </span>            : </a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineNoCov">          0 :                     wrkbl = *m * 67;</span></a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m;</span></a>
+<a name="1507"><span class="lineNum">    1507 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :                 } else {</a>
+<a name="1509"><span class="lineNum">    1509 </span>            : </a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineNoCov">          0 :                     wrkbl = *m * 67;</span></a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = *m + (*n*32);</span></a>
+<a name="1512"><span class="lineNum">    1512 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1513"><span class="lineNum">    1513 </span>            : </a>
+<a name="1514"><span class="lineNum">    1514 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m * 3;</span></a>
+<a name="1515"><span class="lineNum">    1515 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineNoCov">          0 :                     maxwrk = wrkbl + *m * *m;</span></a>
+<a name="1517"><span class="lineNum">    1517 </span>            :                 }</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :             } else {</a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineNoCov">          0 :                 wrkbl = *m * 3 + (*m + *n*32);</span></a>
+<a name="1520"><span class="lineNum">    1520 </span><span class="lineNoCov">          0 :                 if (wntqn) {</span></a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m * 3;</span></a>
+<a name="1522"><span class="lineNum">    1522 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :                 } else {</a>
+<a name="1524"><span class="lineNum">    1524 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m * 3;</span></a>
+<a name="1525"><span class="lineNum">    1525 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :                 }</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :             }</a>
+<a name="1528"><span class="lineNum">    1528 </span>            :         }</a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">        192 :         work[1] = (double) maxwrk;</span></a>
+<a name="1530"><span class="lineNum">    1530 </span>            :     }</a>
+<a name="1531"><span class="lineNum">    1531 </span>            : </a>
+<a name="1532"><span class="lineNum">    1532 </span>            :     </a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineCov">        192 :     if( lquery != 0)</span></a>
+<a name="1534"><span class="lineNum">    1534 </span>            :     {</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :         return;</a>
+<a name="1536"><span class="lineNum">    1536 </span>            :     }</a>
+<a name="1537"><span class="lineNum">    1537 </span>            :     </a>
+<a name="1538"><span class="lineNum">    1538 </span>            : </a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineCov">         96 :     if (*m == 0 || *n == 0) {</span></a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineNoCov">          0 :         if (*lwork &gt;= 1) {</span></a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineNoCov">          0 :             work[1] = 1.;</span></a>
+<a name="1542"><span class="lineNum">    1542 </span>            :         }</a>
+<a name="1543"><span class="lineNum">    1543 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="1544"><span class="lineNum">    1544 </span>            :     }</a>
+<a name="1545"><span class="lineNum">    1545 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="1547"><span class="lineNum">    1547 </span>            :     safemin = minval / eps;</a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineCov">         96 :     smlnum =  std::sqrt(safemin) / eps;</span></a>
+<a name="1549"><span class="lineNum">    1549 </span>            : </a>
+<a name="1550"><span class="lineNum">    1550 </span>            : </a>
+<a name="1551"><span class="lineNum">    1551 </span><span class="lineCov">         96 :     bignum = 1. / smlnum;</span></a>
+<a name="1552"><span class="lineNum">    1552 </span>            : </a>
+<a name="1553"><span class="lineNum">    1553 </span>            : </a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineCov">         96 :     anrm = PLUMED_BLAS_F77_FUNC(dlange,DLANGE)(&quot;M&quot;, m, n, &amp;a[a_offset], lda, dum);</span></a>
+<a name="1555"><span class="lineNum">    1555 </span>            :     iscl = 0;</a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineCov">         96 :     if (anrm &gt; 0. &amp;&amp; anrm &lt; smlnum) {</span></a>
+<a name="1557"><span class="lineNum">    1557 </span>            :         iscl = 1;</a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;,&amp;c__0,&amp;c__0,&amp;anrm,&amp;smlnum,m,n,&amp;a[a_offset],lda,&amp;ierr);</span></a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineCov">         96 :     } else if (anrm &gt; bignum) {</span></a>
+<a name="1560"><span class="lineNum">    1560 </span>            :         iscl = 1;</a>
+<a name="1561"><span class="lineNum">    1561 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;,&amp;c__0,&amp;c__0,&amp;anrm,&amp;bignum,m,n,&amp;a[a_offset],lda,&amp;ierr);</span></a>
+<a name="1562"><span class="lineNum">    1562 </span>            :     }</a>
+<a name="1563"><span class="lineNum">    1563 </span>            : </a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineCov">         96 :     if (*m &gt;= *n) {</span></a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineCov">         96 :         if (*m &gt;= mnthr) {</span></a>
+<a name="1566"><span class="lineNum">    1566 </span>            : </a>
+<a name="1567"><span class="lineNum">    1567 </span><span class="lineCov">          1 :             if (wntqn) {</span></a>
+<a name="1568"><span class="lineNum">    1568 </span>            : </a>
+<a name="1569"><span class="lineNum">    1569 </span>            :                 itau = 1;</a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineNoCov">          0 :                 nwork = itau + *n;</span></a>
+<a name="1571"><span class="lineNum">    1571 </span>            : </a>
+<a name="1572"><span class="lineNum">    1572 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgeqrf,DGEQRF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="1574"><span class="lineNum">    1574 </span>            :                         i__1, &amp;ierr);</a>
+<a name="1575"><span class="lineNum">    1575 </span>            : </a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineNoCov">          0 :                 i__1 = *n - 1;</span></a>
+<a name="1577"><span class="lineNum">    1577 </span><span class="lineNoCov">          0 :                 i__2 = *n - 1;</span></a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;L&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[a_dim1 + 2], </span></a>
+<a name="1579"><span class="lineNum">    1579 </span>            :                         lda);</a>
+<a name="1580"><span class="lineNum">    1580 </span>            :                 ie = 1;</a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineNoCov">          0 :                 itauq = ie + *n;</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineNoCov">          0 :                 itaup = itauq + *n;</span></a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineNoCov">          0 :                 nwork = itaup + *n;</span></a>
+<a name="1584"><span class="lineNum">    1584 </span>            : </a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(n, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="1587"><span class="lineNum">    1587 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineNoCov">          0 :                 nwork = ie + *n;</span></a>
+<a name="1589"><span class="lineNum">    1589 </span>            : </a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;U&quot;, &quot;N&quot;, n, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineNoCov">          0 :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</span></a>
+<a name="1592"><span class="lineNum">    1592 </span>            : </a>
+<a name="1593"><span class="lineNum">    1593 </span>            :             } else {</a>
+<a name="1594"><span class="lineNum">    1594 </span>            :                 iu = 1;</a>
+<a name="1595"><span class="lineNum">    1595 </span>            : </a>
+<a name="1596"><span class="lineNum">    1596 </span><span class="lineCov">          1 :                 ldwrku = *n;</span></a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineCov">          1 :                 itau = iu + ldwrku * *n;</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineCov">          1 :                 nwork = itau + *n;</span></a>
+<a name="1599"><span class="lineNum">    1599 </span>            : </a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineCov">          1 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dgeqrf,DGEQRF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="1602"><span class="lineNum">    1602 </span>            :                         i__1, &amp;ierr);</a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;L&quot;, m, n, &amp;a[a_offset], lda, &amp;u[u_offset], ldu);</span></a>
+<a name="1604"><span class="lineNum">    1604 </span>            : </a>
+<a name="1605"><span class="lineNum">    1605 </span><span class="lineCov">          1 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dorgqr,DORGQR)(m, m, n, &amp;u[u_offset], ldu, &amp;work[itau], &amp;work[nwork],</span></a>
+<a name="1607"><span class="lineNum">    1607 </span>            :                          &amp;i__1, &amp;ierr);</a>
+<a name="1608"><span class="lineNum">    1608 </span>            : </a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineCov">          1 :                 i__1 = *n - 1;</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineCov">          1 :                 i__2 = *n - 1;</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;L&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[a_dim1 + 2], </span></a>
+<a name="1612"><span class="lineNum">    1612 </span>            :                         lda);</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :                 ie = itau;</a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineCov">          1 :                 itauq = ie + *n;</span></a>
+<a name="1615"><span class="lineNum">    1615 </span><span class="lineCov">          1 :                 itaup = itauq + *n;</span></a>
+<a name="1616"><span class="lineNum">    1616 </span><span class="lineCov">          1 :                 nwork = itaup + *n;</span></a>
+<a name="1617"><span class="lineNum">    1617 </span>            : </a>
+<a name="1618"><span class="lineNum">    1618 </span><span class="lineCov">          1 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(n, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineCov">          1 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="1621"><span class="lineNum">    1621 </span>            : </a>
+<a name="1622"><span class="lineNum">    1622 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;U&quot;, &quot;I&quot;, n, &amp;s[1], &amp;work[ie], &amp;work[iu], n, &amp;vt[</span></a>
+<a name="1623"><span class="lineNum">    1623 </span>            :                         vt_offset], ldvt, dum, idum, &amp;work[nwork], &amp;iwork[1], </a>
+<a name="1624"><span class="lineNum">    1624 </span>            :                         info);</a>
+<a name="1625"><span class="lineNum">    1625 </span>            : </a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineCov">          1 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1627"><span class="lineNum">    1627 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, n, n, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1628"><span class="lineNum">    1628 </span>            :                         itauq], &amp;work[iu], &amp;ldwrku, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :                         ierr);</a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineCov">          1 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1631"><span class="lineNum">    1631 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, n, n, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1632"><span class="lineNum">    1632 </span>            :                         itaup], &amp;vt[vt_offset], ldvt, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="1633"><span class="lineNum">    1633 </span>            :                         ierr);</a>
+<a name="1634"><span class="lineNum">    1634 </span>            : </a>
+<a name="1635"><span class="lineNum">    1635 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, m, n, n, &amp;one, &amp;u[u_offset], ldu, &amp;work[iu]</span></a>
+<a name="1636"><span class="lineNum">    1636 </span>            :                         , &amp;ldwrku, &amp;zero, &amp;a[a_offset], lda);</a>
+<a name="1637"><span class="lineNum">    1637 </span>            : </a>
+<a name="1638"><span class="lineNum">    1638 </span><span class="lineCov">          1 :                 PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;F&quot;, m, n, &amp;a[a_offset], lda, &amp;u[u_offset], ldu);</span></a>
+<a name="1639"><span class="lineNum">    1639 </span>            : </a>
+<a name="1640"><span class="lineNum">    1640 </span>            :             }</a>
+<a name="1641"><span class="lineNum">    1641 </span>            : </a>
+<a name="1642"><span class="lineNum">    1642 </span>            :         } else {</a>
+<a name="1643"><span class="lineNum">    1643 </span>            :             ie = 1;</a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineCov">         95 :             itauq = ie + *n;</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineCov">         95 :             itaup = itauq + *n;</span></a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineCov">         95 :             nwork = itaup + *n;</span></a>
+<a name="1647"><span class="lineNum">    1647 </span>            : </a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">         95 :             i__1 = *lwork - nwork + 1;</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">         95 :             PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(m, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[itauq], &amp;</span></a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineCov">         95 :                     work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineCov">         95 :             if (wntqn) {</span></a>
+<a name="1652"><span class="lineNum">    1652 </span>            : </a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;U&quot;, &quot;N&quot;, n, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="1654"><span class="lineNum">    1654 </span>            :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</a>
+<a name="1655"><span class="lineNum">    1655 </span>            :             } else {</a>
+<a name="1656"><span class="lineNum">    1656 </span>            : </a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">         95 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;F&quot;, m, m, &amp;zero, &amp;zero, &amp;u[u_offset], ldu);</span></a>
+<a name="1658"><span class="lineNum">    1658 </span><span class="lineCov">         95 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;U&quot;, &quot;I&quot;, n, &amp;s[1], &amp;work[ie], &amp;u[u_offset], ldu, &amp;vt[</span></a>
+<a name="1659"><span class="lineNum">    1659 </span>            :                         vt_offset], ldvt, dum, idum, &amp;work[nwork], &amp;iwork[1], </a>
+<a name="1660"><span class="lineNum">    1660 </span>            :                         info);</a>
+<a name="1661"><span class="lineNum">    1661 </span>            : </a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineCov">         95 :                 i__1 = *m - *n;</span></a>
+<a name="1663"><span class="lineNum">    1663 </span><span class="lineCov">         95 :                 i__2 = *m - *n;</span></a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">         95 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;F&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;one, &amp;u[*n + 1 + (*n + </span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">         95 :                         1) * u_dim1], ldu);</span></a>
+<a name="1666"><span class="lineNum">    1666 </span>            : </a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineCov">         95 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">         95 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, m, m, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1669"><span class="lineNum">    1669 </span>            :                         itauq], &amp;u[u_offset], ldu, &amp;work[nwork], &amp;i__1, &amp;ierr);</a>
+<a name="1670"><span class="lineNum">    1670 </span><span class="lineCov">         95 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineCov">         95 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, n, n, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1672"><span class="lineNum">    1672 </span>            :                         itaup], &amp;vt[vt_offset],ldvt,&amp;work[nwork],&amp;i__1,&amp;ierr);</a>
+<a name="1673"><span class="lineNum">    1673 </span>            :             }</a>
+<a name="1674"><span class="lineNum">    1674 </span>            : </a>
+<a name="1675"><span class="lineNum">    1675 </span>            :         }</a>
+<a name="1676"><span class="lineNum">    1676 </span>            : </a>
+<a name="1677"><span class="lineNum">    1677 </span>            :     } else {</a>
+<a name="1678"><span class="lineNum">    1678 </span>            : </a>
+<a name="1679"><span class="lineNum">    1679 </span><span class="lineNoCov">          0 :         if (*n &gt;= mnthr) {</span></a>
+<a name="1680"><span class="lineNum">    1680 </span>            : </a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="1682"><span class="lineNum">    1682 </span>            : </a>
+<a name="1683"><span class="lineNum">    1683 </span>            :                 itau = 1;</a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineNoCov">          0 :                 nwork = itau + *m;</span></a>
+<a name="1685"><span class="lineNum">    1685 </span>            : </a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgelqf,DGELQF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="1688"><span class="lineNum">    1688 </span>            :                         i__1, &amp;ierr);</a>
+<a name="1689"><span class="lineNum">    1689 </span>            : </a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineNoCov">          0 :                 i__1 = *m - 1;</span></a>
+<a name="1691"><span class="lineNum">    1691 </span><span class="lineNoCov">          0 :                 i__2 = *m - 1;</span></a>
+<a name="1692"><span class="lineNum">    1692 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;U&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[(a_dim1*2) + </span></a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineNoCov">          0 :                         1], lda);</span></a>
+<a name="1694"><span class="lineNum">    1694 </span>            :                 ie = 1;</a>
+<a name="1695"><span class="lineNum">    1695 </span><span class="lineNoCov">          0 :                 itauq = ie + *m;</span></a>
+<a name="1696"><span class="lineNum">    1696 </span><span class="lineNoCov">          0 :                 itaup = itauq + *m;</span></a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineNoCov">          0 :                 nwork = itaup + *m;</span></a>
+<a name="1698"><span class="lineNum">    1698 </span>            : </a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(m, m, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineNoCov">          0 :                 nwork = ie + *m;</span></a>
+<a name="1703"><span class="lineNum">    1703 </span>            : </a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;U&quot;, &quot;N&quot;, m, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineNoCov">          0 :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</span></a>
+<a name="1706"><span class="lineNum">    1706 </span>            : </a>
+<a name="1707"><span class="lineNum">    1707 </span>            :             } else {</a>
+<a name="1708"><span class="lineNum">    1708 </span>            : </a>
+<a name="1709"><span class="lineNum">    1709 </span>            :                 ivt = 1;</a>
+<a name="1710"><span class="lineNum">    1710 </span>            : </a>
+<a name="1711"><span class="lineNum">    1711 </span><span class="lineNoCov">          0 :                 ldwkvt = *m;</span></a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineNoCov">          0 :                 itau = ivt + ldwkvt * *m;</span></a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineNoCov">          0 :                 nwork = itau + *m;</span></a>
+<a name="1714"><span class="lineNum">    1714 </span>            : </a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgelqf,DGELQF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="1717"><span class="lineNum">    1717 </span>            :                         i__1, &amp;ierr);</a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;U&quot;, m, n, &amp;a[a_offset], lda, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="1719"><span class="lineNum">    1719 </span>            : </a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1721"><span class="lineNum">    1721 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dorglq,DORGLQ)(n, n, m, &amp;vt[vt_offset], ldvt, &amp;work[itau], &amp;work[</span></a>
+<a name="1722"><span class="lineNum">    1722 </span>            :                         nwork], &amp;i__1, &amp;ierr);</a>
+<a name="1723"><span class="lineNum">    1723 </span>            : </a>
+<a name="1724"><span class="lineNum">    1724 </span><span class="lineNoCov">          0 :                 i__1 = *m - 1;</span></a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineNoCov">          0 :                 i__2 = *m - 1;</span></a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;U&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[(a_dim1*2) + </span></a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineNoCov">          0 :                         1], lda);</span></a>
+<a name="1728"><span class="lineNum">    1728 </span>            :                 ie = itau;</a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineNoCov">          0 :                 itauq = ie + *m;</span></a>
+<a name="1730"><span class="lineNum">    1730 </span><span class="lineNoCov">          0 :                 itaup = itauq + *m;</span></a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineNoCov">          0 :                 nwork = itaup + *m;</span></a>
+<a name="1732"><span class="lineNum">    1732 </span>            : </a>
+<a name="1733"><span class="lineNum">    1733 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(m, m, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="1735"><span class="lineNum">    1735 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="1736"><span class="lineNum">    1736 </span>            : </a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;U&quot;, &quot;I&quot;, m, &amp;s[1], &amp;work[ie], &amp;u[u_offset], ldu, &amp;</span></a>
+<a name="1738"><span class="lineNum">    1738 </span>            :                         work[ivt], &amp;ldwkvt, dum, idum, &amp;work[nwork], &amp;iwork[1]</a>
+<a name="1739"><span class="lineNum">    1739 </span>            :                         , info);</a>
+<a name="1740"><span class="lineNum">    1740 </span>            : </a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, m, m, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1743"><span class="lineNum">    1743 </span>            :                         itauq], &amp;u[u_offset], ldu, &amp;work[nwork], &amp;i__1, &amp;ierr);</a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, m, m, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1746"><span class="lineNum">    1746 </span>            :                         itaup], &amp;work[ivt], &amp;ldwkvt, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="1747"><span class="lineNum">    1747 </span>            :                         ierr);</a>
+<a name="1748"><span class="lineNum">    1748 </span>            : </a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, m, n, m, &amp;one, &amp;work[ivt], &amp;ldwkvt, &amp;vt[</span></a>
+<a name="1750"><span class="lineNum">    1750 </span>            :                         vt_offset], ldvt, &amp;zero, &amp;a[a_offset], lda);</a>
+<a name="1751"><span class="lineNum">    1751 </span>            : </a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;F&quot;, m, n, &amp;a[a_offset], lda, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="1753"><span class="lineNum">    1753 </span>            : </a>
+<a name="1754"><span class="lineNum">    1754 </span>            :             }</a>
+<a name="1755"><span class="lineNum">    1755 </span>            : </a>
+<a name="1756"><span class="lineNum">    1756 </span>            :         } else {</a>
+<a name="1757"><span class="lineNum">    1757 </span>            : </a>
+<a name="1758"><span class="lineNum">    1758 </span>            :             ie = 1;</a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineNoCov">          0 :             itauq = ie + *m;</span></a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineNoCov">          0 :             itaup = itauq + *m;</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineNoCov">          0 :             nwork = itaup + *m;</span></a>
+<a name="1762"><span class="lineNum">    1762 </span>            : </a>
+<a name="1763"><span class="lineNum">    1763 </span><span class="lineNoCov">          0 :             i__1 = *lwork - nwork + 1;</span></a>
+<a name="1764"><span class="lineNum">    1764 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dgebrd,DGEBRD)(m, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[itauq], &amp;</span></a>
+<a name="1765"><span class="lineNum">    1765 </span><span class="lineNoCov">          0 :                     work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="1766"><span class="lineNum">    1766 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="1767"><span class="lineNum">    1767 </span>            : </a>
+<a name="1768"><span class="lineNum">    1768 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;L&quot;, &quot;N&quot;, m, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="1769"><span class="lineNum">    1769 </span>            :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</a>
+<a name="1770"><span class="lineNum">    1770 </span>            :             } else {</a>
+<a name="1771"><span class="lineNum">    1771 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;F&quot;, n, n, &amp;zero, &amp;zero, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dbdsdc,DBDSDC)(&quot;L&quot;, &quot;I&quot;, m, &amp;s[1], &amp;work[ie], &amp;u[u_offset], ldu, &amp;vt[</span></a>
+<a name="1773"><span class="lineNum">    1773 </span>            :                         vt_offset], ldvt, dum, idum, &amp;work[nwork], &amp;iwork[1], </a>
+<a name="1774"><span class="lineNum">    1774 </span>            :                         info);</a>
+<a name="1775"><span class="lineNum">    1775 </span>            : </a>
+<a name="1776"><span class="lineNum">    1776 </span><span class="lineNoCov">          0 :                 i__1 = *n - *m;</span></a>
+<a name="1777"><span class="lineNum">    1777 </span><span class="lineNoCov">          0 :                 i__2 = *n - *m;</span></a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;F&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;one, &amp;vt[*m + 1 + (*m + </span></a>
+<a name="1779"><span class="lineNum">    1779 </span><span class="lineNoCov">          0 :                         1) * vt_dim1], ldvt);</span></a>
+<a name="1780"><span class="lineNum">    1780 </span>            : </a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, m, m, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1783"><span class="lineNum">    1783 </span>            :                         itauq], &amp;u[u_offset], ldu, &amp;work[nwork], &amp;i__1, &amp;ierr);</a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, n, n, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="1786"><span class="lineNum">    1786 </span>            :                         itaup], &amp;vt[vt_offset], ldvt, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="1787"><span class="lineNum">    1787 </span>            :                         ierr);</a>
+<a name="1788"><span class="lineNum">    1788 </span>            :             }</a>
+<a name="1789"><span class="lineNum">    1789 </span>            : </a>
+<a name="1790"><span class="lineNum">    1790 </span>            :         }</a>
+<a name="1791"><span class="lineNum">    1791 </span>            : </a>
+<a name="1792"><span class="lineNum">    1792 </span>            :     }</a>
+<a name="1793"><span class="lineNum">    1793 </span>            : </a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineCov">         96 :     if (iscl == 1) {</span></a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineNoCov">          0 :         if (anrm &gt; bignum) {</span></a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;bignum, &amp;anrm, &amp;minmn, &amp;c__1, &amp;s[1], &amp;</span></a>
+<a name="1797"><span class="lineNum">    1797 </span>            :                     minmn, &amp;ierr);</a>
+<a name="1798"><span class="lineNum">    1798 </span>            :         }</a>
+<a name="1799"><span class="lineNum">    1799 </span><span class="lineNoCov">          0 :         if (anrm &lt; smlnum) {</span></a>
+<a name="1800"><span class="lineNum">    1800 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;smlnum, &amp;anrm, &amp;minmn, &amp;c__1, &amp;s[1], &amp;</span></a>
+<a name="1801"><span class="lineNum">    1801 </span>            :                     minmn, &amp;ierr);</a>
+<a name="1802"><span class="lineNum">    1802 </span>            :         }</a>
+<a name="1803"><span class="lineNum">    1803 </span>            :     }</a>
+<a name="1804"><span class="lineNum">    1804 </span>            : </a>
+<a name="1805"><span class="lineNum">    1805 </span><span class="lineCov">         96 :     work[1] = (double) maxwrk;</span></a>
+<a name="1806"><span class="lineNum">    1806 </span>            : </a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineCov">         96 :     return;</span></a>
+<a name="1808"><span class="lineNum">    1808 </span>            : </a>
+<a name="1809"><span class="lineNum">    1809 </span>            : }</a>
+<a name="1810"><span class="lineNum">    1810 </span>            : </a>
+<a name="1811"><span class="lineNum">    1811 </span>            : </a>
+<a name="1812"><span class="lineNum">    1812 </span>            : }</a>
+<a name="1813"><span class="lineNum">    1813 </span>            : }</a>
+<a name="1814"><span class="lineNum">    1814 </span>            : #include &lt;cmath&gt;</a>
+<a name="1815"><span class="lineNum">    1815 </span>            : #include &quot;real.h&quot;</a>
+<a name="1816"><span class="lineNum">    1816 </span>            : </a>
+<a name="1817"><span class="lineNum">    1817 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1818"><span class="lineNum">    1818 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1819"><span class="lineNum">    1819 </span>            : </a>
+<a name="1820"><span class="lineNum">    1820 </span>            : </a>
+<a name="1821"><span class="lineNum">    1821 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1822"><span class="lineNum">    1822 </span>            : namespace PLMD{</a>
+<a name="1823"><span class="lineNum">    1823 </span>            : namespace lapack{</a>
+<a name="1824"><span class="lineNum">    1824 </span>            : using namespace blas;</a>
+<a name="1825"><span class="lineNum">    1825 </span>            : void</a>
+<a name="1826"><span class="lineNum">    1826 </span><span class="lineCov">         57 : PLUMED_BLAS_F77_FUNC(dgetf2,DGETF2)(int *m,</span></a>
+<a name="1827"><span class="lineNum">    1827 </span>            :         int *n,</a>
+<a name="1828"><span class="lineNum">    1828 </span>            :         double *a,</a>
+<a name="1829"><span class="lineNum">    1829 </span>            :         int *lda,</a>
+<a name="1830"><span class="lineNum">    1830 </span>            :         int *ipiv,</a>
+<a name="1831"><span class="lineNum">    1831 </span>            :         int *info)</a>
+<a name="1832"><span class="lineNum">    1832 </span>            : {</a>
+<a name="1833"><span class="lineNum">    1833 </span>            :   int j,jp,k,t1,t2,t3;</a>
+<a name="1834"><span class="lineNum">    1834 </span>            :   double minusone;</a>
+<a name="1835"><span class="lineNum">    1835 </span>            :   double tmp;</a>
+<a name="1836"><span class="lineNum">    1836 </span>            : </a>
+<a name="1837"><span class="lineNum">    1837 </span><span class="lineCov">         57 :   minusone = -1.0;</span></a>
+<a name="1838"><span class="lineNum">    1838 </span>            : </a>
+<a name="1839"><span class="lineNum">    1839 </span><span class="lineCov">         57 :   if(*m&lt;=0 || *n&lt;=0)</span></a>
+<a name="1840"><span class="lineNum">    1840 </span>            :     return;</a>
+<a name="1841"><span class="lineNum">    1841 </span>            : </a>
+<a name="1842"><span class="lineNum">    1842 </span>            :   k = (*m &lt; *n) ? *m : *n;</a>
+<a name="1843"><span class="lineNum">    1843 </span><span class="lineCov">        171 :   for(j=1;j&lt;=k;j++) {</span></a>
+<a name="1844"><span class="lineNum">    1844 </span><span class="lineCov">        114 :     t1 = *m-j+1;</span></a>
+<a name="1845"><span class="lineNum">    1845 </span><span class="lineCov">        114 :     t2 = 1;</span></a>
+<a name="1846"><span class="lineNum">    1846 </span><span class="lineCov">        114 :     jp = j - 1 + PLUMED_BLAS_F77_FUNC(idamax,IDAMAX)(&amp;t1,&amp;(a[(j-1)*(*lda)+(j-1)]),&amp;t2);</span></a>
+<a name="1847"><span class="lineNum">    1847 </span><span class="lineCov">        114 :     ipiv[j-1] = jp;</span></a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineCov">        114 :     if( std::abs(a[(j-1)*(*lda)+(jp-1)])&gt;PLUMED_GMX_DOUBLE_MIN ) {</span></a>
+<a name="1849"><span class="lineNum">    1849 </span><span class="lineCov">        114 :       if(jp != j)</span></a>
+<a name="1850"><span class="lineNum">    1850 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n,&amp;(a[ j-1 ]),lda,&amp;(a[ jp-1 ]),lda);</span></a>
+<a name="1851"><span class="lineNum">    1851 </span>            :       </a>
+<a name="1852"><span class="lineNum">    1852 </span><span class="lineCov">        114 :       if(j&lt;*m) {</span></a>
+<a name="1853"><span class="lineNum">    1853 </span><span class="lineCov">         57 :         t1 = *m-j;</span></a>
+<a name="1854"><span class="lineNum">    1854 </span><span class="lineCov">         57 :         t2 = 1;</span></a>
+<a name="1855"><span class="lineNum">    1855 </span><span class="lineCov">         57 :         tmp = 1.0/a[(j-1)*(*lda)+(j-1)];</span></a>
+<a name="1856"><span class="lineNum">    1856 </span><span class="lineCov">         57 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;t1,&amp;tmp,&amp;(a[(j-1)*(*lda)+(j)]),&amp;t2);</span></a>
+<a name="1857"><span class="lineNum">    1857 </span>            :       }</a>
+<a name="1858"><span class="lineNum">    1858 </span>            :     } else {</a>
+<a name="1859"><span class="lineNum">    1859 </span><span class="lineNoCov">          0 :       *info = j;</span></a>
+<a name="1860"><span class="lineNum">    1860 </span>            :     }</a>
+<a name="1861"><span class="lineNum">    1861 </span>            : </a>
+<a name="1862"><span class="lineNum">    1862 </span><span class="lineCov">        114 :     if(j&lt;k) {</span></a>
+<a name="1863"><span class="lineNum">    1863 </span><span class="lineCov">         57 :       t1 = *m-j;</span></a>
+<a name="1864"><span class="lineNum">    1864 </span><span class="lineCov">         57 :       t2 = *n-j;</span></a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineCov">         57 :       t3 = 1;</span></a>
+<a name="1866"><span class="lineNum">    1866 </span><span class="lineCov">         57 :       PLUMED_BLAS_F77_FUNC(dger,DGER)(&amp;t1,&amp;t2,&amp;minusone,&amp;(a[(j-1)*(*lda)+(j)]),&amp;t3,</span></a>
+<a name="1867"><span class="lineNum">    1867 </span><span class="lineCov">         57 :             &amp;(a[(j)*(*lda)+(j-1)]),lda, &amp;(a[(j)*(*lda)+(j)]),lda);</span></a>
+<a name="1868"><span class="lineNum">    1868 </span>            :     }</a>
+<a name="1869"><span class="lineNum">    1869 </span>            :   }</a>
+<a name="1870"><span class="lineNum">    1870 </span>            :   return;</a>
+<a name="1871"><span class="lineNum">    1871 </span>            : }</a>
+<a name="1872"><span class="lineNum">    1872 </span>            : }</a>
+<a name="1873"><span class="lineNum">    1873 </span>            : }</a>
+<a name="1874"><span class="lineNum">    1874 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1875"><span class="lineNum">    1875 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1876"><span class="lineNum">    1876 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="1877"><span class="lineNum">    1877 </span>            : </a>
+<a name="1878"><span class="lineNum">    1878 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1879"><span class="lineNum">    1879 </span>            : namespace PLMD{</a>
+<a name="1880"><span class="lineNum">    1880 </span>            : namespace lapack{</a>
+<a name="1881"><span class="lineNum">    1881 </span>            : using namespace blas;</a>
+<a name="1882"><span class="lineNum">    1882 </span>            : void</a>
+<a name="1883"><span class="lineNum">    1883 </span><span class="lineCov">         57 : PLUMED_BLAS_F77_FUNC(dgetrf,DGETRF)(int *m,</span></a>
+<a name="1884"><span class="lineNum">    1884 </span>            :         int *n,</a>
+<a name="1885"><span class="lineNum">    1885 </span>            :         double *a,</a>
+<a name="1886"><span class="lineNum">    1886 </span>            :         int *lda,</a>
+<a name="1887"><span class="lineNum">    1887 </span>            :         int *ipiv,</a>
+<a name="1888"><span class="lineNum">    1888 </span>            :         int *info)</a>
+<a name="1889"><span class="lineNum">    1889 </span>            : {</a>
+<a name="1890"><span class="lineNum">    1890 </span>            :   int mindim,jb;</a>
+<a name="1891"><span class="lineNum">    1891 </span>            :   int i,j,k,l;</a>
+<a name="1892"><span class="lineNum">    1892 </span>            :   int iinfo;</a>
+<a name="1893"><span class="lineNum">    1893 </span><span class="lineCov">         57 :   double minusone = -1.0;</span></a>
+<a name="1894"><span class="lineNum">    1894 </span><span class="lineCov">         57 :   double one = 1.0;</span></a>
+<a name="1895"><span class="lineNum">    1895 </span>            : </a>
+<a name="1896"><span class="lineNum">    1896 </span><span class="lineCov">         57 :   if(*m&lt;=0 || *n&lt;=0)</span></a>
+<a name="1897"><span class="lineNum">    1897 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="1898"><span class="lineNum">    1898 </span>            : </a>
+<a name="1899"><span class="lineNum">    1899 </span><span class="lineCov">         57 :   *info = 0;</span></a>
+<a name="1900"><span class="lineNum">    1900 </span>            : </a>
+<a name="1901"><span class="lineNum">    1901 </span><span class="lineCov">         57 :   mindim = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="1902"><span class="lineNum">    1902 </span>            : </a>
+<a name="1903"><span class="lineNum">    1903 </span><span class="lineCov">         57 :   if(DGETRF_BLOCKSIZE&gt;=mindim) {</span></a>
+<a name="1904"><span class="lineNum">    1904 </span>            : </a>
+<a name="1905"><span class="lineNum">    1905 </span>            :     /* unblocked code */</a>
+<a name="1906"><span class="lineNum">    1906 </span><span class="lineCov">         57 :     PLUMED_BLAS_F77_FUNC(dgetf2,DGETF2)(m,n,a,lda,ipiv,info);</span></a>
+<a name="1907"><span class="lineNum">    1907 </span>            : </a>
+<a name="1908"><span class="lineNum">    1908 </span>            :   } else {</a>
+<a name="1909"><span class="lineNum">    1909 </span>            : </a>
+<a name="1910"><span class="lineNum">    1910 </span>            :     /* blocked case */</a>
+<a name="1911"><span class="lineNum">    1911 </span>            : </a>
+<a name="1912"><span class="lineNum">    1912 </span><span class="lineNoCov">          0 :     for(j=1;j&lt;=mindim;j+=DGETRF_BLOCKSIZE) {</span></a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineNoCov">          0 :       jb = ( DGETRF_BLOCKSIZE &lt; (mindim-j+1)) ? DGETRF_BLOCKSIZE : (mindim-j+1);</span></a>
+<a name="1914"><span class="lineNum">    1914 </span>            :       /* factor diag. and subdiag blocks and test for singularity */</a>
+<a name="1915"><span class="lineNum">    1915 </span><span class="lineNoCov">          0 :       k = *m-j+1;</span></a>
+<a name="1916"><span class="lineNum">    1916 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dgetf2,DGETF2)(&amp;k,&amp;jb,&amp;(a[(j-1)*(*lda)+(j-1)]),lda,&amp;(ipiv[j-1]),&amp;iinfo);</span></a>
+<a name="1917"><span class="lineNum">    1917 </span>            :       </a>
+<a name="1918"><span class="lineNum">    1918 </span><span class="lineNoCov">          0 :       if(*info==0 &amp;&amp; iinfo&gt;0)</span></a>
+<a name="1919"><span class="lineNum">    1919 </span><span class="lineNoCov">          0 :         *info = iinfo + j - 1;</span></a>
+<a name="1920"><span class="lineNum">    1920 </span>            : </a>
+<a name="1921"><span class="lineNum">    1921 </span>            :       /* adjust pivot indices */</a>
+<a name="1922"><span class="lineNum">    1922 </span><span class="lineNoCov">          0 :       k = (*m &lt; (j+jb-1)) ? *m : (j+jb-1);</span></a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineNoCov">          0 :       for(i=j;i&lt;=k;i++)</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineNoCov">          0 :         ipiv[i-1] += j - 1;</span></a>
+<a name="1925"><span class="lineNum">    1925 </span>            : </a>
+<a name="1926"><span class="lineNum">    1926 </span>            :       /* Apply to columns 1 throughj j-1 */</a>
+<a name="1927"><span class="lineNum">    1927 </span><span class="lineNoCov">          0 :       k = j - 1;</span></a>
+<a name="1928"><span class="lineNum">    1928 </span><span class="lineNoCov">          0 :       i = j + jb - 1;</span></a>
+<a name="1929"><span class="lineNum">    1929 </span><span class="lineNoCov">          0 :       l = 1;</span></a>
+<a name="1930"><span class="lineNum">    1930 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlaswp,DLASWP)(&amp;k,a,lda,&amp;j,&amp;i,ipiv,&amp;l);</span></a>
+<a name="1931"><span class="lineNum">    1931 </span><span class="lineNoCov">          0 :       if((j+jb)&lt;=*n) {</span></a>
+<a name="1932"><span class="lineNum">    1932 </span>            :         /* Apply to cols. j+jb through n */</a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineNoCov">          0 :         k = *n-j-jb+1;</span></a>
+<a name="1934"><span class="lineNum">    1934 </span><span class="lineNoCov">          0 :         i = j+jb-1;</span></a>
+<a name="1935"><span class="lineNum">    1935 </span><span class="lineNoCov">          0 :         l = 1;</span></a>
+<a name="1936"><span class="lineNum">    1936 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlaswp,DLASWP)(&amp;k,&amp;(a[(j+jb-1)*(*lda)+0]),lda,&amp;j,&amp;i,ipiv,&amp;l);</span></a>
+<a name="1937"><span class="lineNum">    1937 </span>            :         /* Compute block row of U */</a>
+<a name="1938"><span class="lineNum">    1938 </span><span class="lineNoCov">          0 :         k = *n-j-jb+1;</span></a>
+<a name="1939"><span class="lineNum">    1939 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Left&quot;,&quot;Lower&quot;,&quot;No transpose&quot;,&quot;Unit&quot;,&amp;jb,&amp;k,&amp;one,</span></a>
+<a name="1940"><span class="lineNum">    1940 </span><span class="lineNoCov">          0 :                &amp;(a[(j-1)*(*lda)+(j-1)]),lda,&amp;(a[(j+jb-1)*(*lda)+(j-1)]),lda);</span></a>
+<a name="1941"><span class="lineNum">    1941 </span>            : </a>
+<a name="1942"><span class="lineNum">    1942 </span><span class="lineNoCov">          0 :         if((j+jb)&lt;=*m) {</span></a>
+<a name="1943"><span class="lineNum">    1943 </span>            :           /* Update trailing submatrix */</a>
+<a name="1944"><span class="lineNum">    1944 </span><span class="lineNoCov">          0 :           k = *m-j-jb+1;</span></a>
+<a name="1945"><span class="lineNum">    1945 </span><span class="lineNoCov">          0 :           i = *n-j-jb+1;</span></a>
+<a name="1946"><span class="lineNum">    1946 </span><span class="lineNoCov">          0 :           PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;,&quot;No transpose&quot;,&amp;k,&amp;i,&amp;jb,&amp;minusone,</span></a>
+<a name="1947"><span class="lineNum">    1947 </span><span class="lineNoCov">          0 :                  &amp;(a[(j-1)*(*lda)+(j+jb-1)]),lda,</span></a>
+<a name="1948"><span class="lineNum">    1948 </span><span class="lineNoCov">          0 :                  &amp;(a[(j+jb-1)*(*lda)+(j-1)]),lda,&amp;one,</span></a>
+<a name="1949"><span class="lineNum">    1949 </span><span class="lineNoCov">          0 :                  &amp;(a[(j+jb-1)*(*lda)+(j+jb-1)]),lda);</span></a>
+<a name="1950"><span class="lineNum">    1950 </span>            :         }</a>
+<a name="1951"><span class="lineNum">    1951 </span>            : </a>
+<a name="1952"><span class="lineNum">    1952 </span>            :       }</a>
+<a name="1953"><span class="lineNum">    1953 </span>            :     }</a>
+<a name="1954"><span class="lineNum">    1954 </span>            :   }</a>
+<a name="1955"><span class="lineNum">    1955 </span>            : }</a>
+<a name="1956"><span class="lineNum">    1956 </span>            : }</a>
+<a name="1957"><span class="lineNum">    1957 </span>            : }</a>
+<a name="1958"><span class="lineNum">    1958 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1959"><span class="lineNum">    1959 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="1960"><span class="lineNum">    1960 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="1961"><span class="lineNum">    1961 </span>            : </a>
+<a name="1962"><span class="lineNum">    1962 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="1963"><span class="lineNum">    1963 </span>            : namespace PLMD{</a>
+<a name="1964"><span class="lineNum">    1964 </span>            : namespace lapack{</a>
+<a name="1965"><span class="lineNum">    1965 </span>            : using namespace blas;</a>
+<a name="1966"><span class="lineNum">    1966 </span>            : void</a>
+<a name="1967"><span class="lineNum">    1967 </span><span class="lineCov">        114 : PLUMED_BLAS_F77_FUNC(dgetri,DGETRI)(int *n, </span></a>
+<a name="1968"><span class="lineNum">    1968 </span>            :         double *a, </a>
+<a name="1969"><span class="lineNum">    1969 </span>            :         int *lda, </a>
+<a name="1970"><span class="lineNum">    1970 </span>            :         int *ipiv, </a>
+<a name="1971"><span class="lineNum">    1971 </span>            :         double *work, </a>
+<a name="1972"><span class="lineNum">    1972 </span>            :         int *lwork, </a>
+<a name="1973"><span class="lineNum">    1973 </span>            :         int *info)</a>
+<a name="1974"><span class="lineNum">    1974 </span>            : {</a>
+<a name="1975"><span class="lineNum">    1975 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="1976"><span class="lineNum">    1976 </span>            : </a>
+<a name="1977"><span class="lineNum">    1977 </span>            :     int i__, j, jb, nb, jj, jp, nn, iws;</a>
+<a name="1978"><span class="lineNum">    1978 </span>            :     int nbmin;</a>
+<a name="1979"><span class="lineNum">    1979 </span>            :     int ldwork;</a>
+<a name="1980"><span class="lineNum">    1980 </span>            :     int lwkopt;</a>
+<a name="1981"><span class="lineNum">    1981 </span><span class="lineCov">        114 :     int c__1 = 1;</span></a>
+<a name="1982"><span class="lineNum">    1982 </span><span class="lineCov">        114 :     double c_b20 = -1.;</span></a>
+<a name="1983"><span class="lineNum">    1983 </span><span class="lineCov">        114 :     double c_b22 = 1.;</span></a>
+<a name="1984"><span class="lineNum">    1984 </span>            : </a>
+<a name="1985"><span class="lineNum">    1985 </span><span class="lineCov">        114 :     a_dim1 = *lda;</span></a>
+<a name="1986"><span class="lineNum">    1986 </span><span class="lineCov">        114 :     a_offset = 1 + a_dim1;</span></a>
+<a name="1987"><span class="lineNum">    1987 </span><span class="lineCov">        114 :     a -= a_offset;</span></a>
+<a name="1988"><span class="lineNum">    1988 </span>            :     --ipiv;</a>
+<a name="1989"><span class="lineNum">    1989 </span><span class="lineCov">        114 :     --work;</span></a>
+<a name="1990"><span class="lineNum">    1990 </span>            : </a>
+<a name="1991"><span class="lineNum">    1991 </span><span class="lineCov">        114 :     *info = 0;</span></a>
+<a name="1992"><span class="lineNum">    1992 </span>            :     nb = DGETRI_BLOCKSIZE;</a>
+<a name="1993"><span class="lineNum">    1993 </span><span class="lineCov">        114 :     lwkopt = *n * nb;</span></a>
+<a name="1994"><span class="lineNum">    1994 </span><span class="lineCov">        114 :     work[1] = (double) lwkopt;</span></a>
+<a name="1995"><span class="lineNum">    1995 </span>            : </a>
+<a name="1996"><span class="lineNum">    1996 </span><span class="lineCov">        114 :     if (*n &lt; 0) {</span></a>
+<a name="1997"><span class="lineNum">    1997 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="1998"><span class="lineNum">    1998 </span><span class="lineCov">        114 :     } else if (*lda &lt; (*n)) {</span></a>
+<a name="1999"><span class="lineNum">    1999 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="2000"><span class="lineNum">    2000 </span><span class="lineCov">        114 :     } else if (*lwork &lt; (*n) &amp;&amp; *lwork!=-1) {</span></a>
+<a name="2001"><span class="lineNum">    2001 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="2002"><span class="lineNum">    2002 </span>            :     }</a>
+<a name="2003"><span class="lineNum">    2003 </span><span class="lineCov">        114 :     if (*info != 0) {</span></a>
+<a name="2004"><span class="lineNum">    2004 </span>            :         i__1 = -(*info);</a>
+<a name="2005"><span class="lineNum">    2005 </span>            :         return;</a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineCov">        114 :     } else if (*lwork == -1) {</span></a>
+<a name="2007"><span class="lineNum">    2007 </span>            :         return;</a>
+<a name="2008"><span class="lineNum">    2008 </span>            :     }</a>
+<a name="2009"><span class="lineNum">    2009 </span>            : </a>
+<a name="2010"><span class="lineNum">    2010 </span><span class="lineCov">         57 :     if (*n == 0) {</span></a>
+<a name="2011"><span class="lineNum">    2011 </span>            :         return;</a>
+<a name="2012"><span class="lineNum">    2012 </span>            :     }</a>
+<a name="2013"><span class="lineNum">    2013 </span>            : </a>
+<a name="2014"><span class="lineNum">    2014 </span><span class="lineCov">         57 :     PLUMED_BLAS_F77_FUNC(dtrtri,DTRTRI)(&quot;Upper&quot;, &quot;Non-unit&quot;, n, &amp;a[a_offset], lda, info);</span></a>
+<a name="2015"><span class="lineNum">    2015 </span><span class="lineCov">         57 :     if (*info &gt; 0) {</span></a>
+<a name="2016"><span class="lineNum">    2016 </span>            :         return;</a>
+<a name="2017"><span class="lineNum">    2017 </span>            :     }</a>
+<a name="2018"><span class="lineNum">    2018 </span>            : </a>
+<a name="2019"><span class="lineNum">    2019 </span>            :     nbmin = 2;</a>
+<a name="2020"><span class="lineNum">    2020 </span><span class="lineCov">         57 :     ldwork = *n;</span></a>
+<a name="2021"><span class="lineNum">    2021 </span><span class="lineCov">         57 :     if (nb &gt; 1 &amp;&amp; nb &lt; *n) {</span></a>
+<a name="2022"><span class="lineNum">    2022 </span><span class="lineNoCov">          0 :         i__1 = ldwork * nb;</span></a>
+<a name="2023"><span class="lineNum">    2023 </span><span class="lineNoCov">          0 :         iws = (i__1&gt;1) ? i__1 : 1;</span></a>
+<a name="2024"><span class="lineNum">    2024 </span><span class="lineNoCov">          0 :         if (*lwork &lt; iws) {</span></a>
+<a name="2025"><span class="lineNum">    2025 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="2026"><span class="lineNum">    2026 </span>            :             nbmin = DGETRI_MINBLOCKSIZE;</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :         }</a>
+<a name="2028"><span class="lineNum">    2028 </span>            :     } else {</a>
+<a name="2029"><span class="lineNum">    2029 </span>            :         iws = *n;</a>
+<a name="2030"><span class="lineNum">    2030 </span>            :     }</a>
+<a name="2031"><span class="lineNum">    2031 </span>            : </a>
+<a name="2032"><span class="lineNum">    2032 </span><span class="lineCov">         57 :     if (nb &lt; nbmin || nb &gt;= *n) {</span></a>
+<a name="2033"><span class="lineNum">    2033 </span>            : </a>
+<a name="2034"><span class="lineNum">    2034 </span><span class="lineCov">        171 :         for (j = *n; j &gt;= 1; --j) {</span></a>
+<a name="2035"><span class="lineNum">    2035 </span>            : </a>
+<a name="2036"><span class="lineNum">    2036 </span><span class="lineCov">        114 :             i__1 = *n;</span></a>
+<a name="2037"><span class="lineNum">    2037 </span><span class="lineCov">        171 :             for (i__ = j + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="2038"><span class="lineNum">    2038 </span><span class="lineCov">         57 :                 work[i__] = a[i__ + j * a_dim1];</span></a>
+<a name="2039"><span class="lineNum">    2039 </span><span class="lineCov">         57 :                 a[i__ + j * a_dim1] = 0.;</span></a>
+<a name="2040"><span class="lineNum">    2040 </span>            :             }</a>
+<a name="2041"><span class="lineNum">    2041 </span>            : </a>
+<a name="2042"><span class="lineNum">    2042 </span><span class="lineCov">        114 :             if (j &lt; *n) {</span></a>
+<a name="2043"><span class="lineNum">    2043 </span><span class="lineCov">         57 :                 i__1 = *n - j;</span></a>
+<a name="2044"><span class="lineNum">    2044 </span><span class="lineCov">         57 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, n, &amp;i__1, &amp;c_b20, &amp;a[(j + 1) * a_dim1 </span></a>
+<a name="2045"><span class="lineNum">    2045 </span><span class="lineCov">         57 :                         + 1], lda, &amp;work[j + 1], &amp;c__1, &amp;c_b22, &amp;a[j * a_dim1 </span></a>
+<a name="2046"><span class="lineNum">    2046 </span><span class="lineCov">         57 :                         + 1], &amp;c__1);</span></a>
+<a name="2047"><span class="lineNum">    2047 </span>            :             }</a>
+<a name="2048"><span class="lineNum">    2048 </span>            :         }</a>
+<a name="2049"><span class="lineNum">    2049 </span>            :     } else {</a>
+<a name="2050"><span class="lineNum">    2050 </span>            : </a>
+<a name="2051"><span class="lineNum">    2051 </span><span class="lineNoCov">          0 :         nn = (*n - 1) / nb * nb + 1;</span></a>
+<a name="2052"><span class="lineNum">    2052 </span><span class="lineNoCov">          0 :         i__1 = -nb;</span></a>
+<a name="2053"><span class="lineNum">    2053 </span><span class="lineNoCov">          0 :         for (j = nn; i__1 &lt; 0 ? j &gt;= 1 : j &lt;= 1; j += i__1) {</span></a>
+<a name="2054"><span class="lineNum">    2054 </span><span class="lineNoCov">          0 :             i__2 = nb, i__3 = *n - j + 1;</span></a>
+<a name="2055"><span class="lineNum">    2055 </span><span class="lineNoCov">          0 :             jb = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="2056"><span class="lineNum">    2056 </span>            : </a>
+<a name="2057"><span class="lineNum">    2057 </span><span class="lineNoCov">          0 :             i__2 = j + jb - 1;</span></a>
+<a name="2058"><span class="lineNum">    2058 </span><span class="lineNoCov">          0 :             for (jj = j; jj &lt;= i__2; ++jj) {</span></a>
+<a name="2059"><span class="lineNum">    2059 </span><span class="lineNoCov">          0 :                 i__3 = *n;</span></a>
+<a name="2060"><span class="lineNum">    2060 </span><span class="lineNoCov">          0 :                 for (i__ = jj + 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="2061"><span class="lineNum">    2061 </span><span class="lineNoCov">          0 :                     work[i__ + (jj - j) * ldwork] = a[i__ + jj * a_dim1];</span></a>
+<a name="2062"><span class="lineNum">    2062 </span><span class="lineNoCov">          0 :                     a[i__ + jj * a_dim1] = 0.;</span></a>
+<a name="2063"><span class="lineNum">    2063 </span>            :                 }</a>
+<a name="2064"><span class="lineNum">    2064 </span>            :             }</a>
+<a name="2065"><span class="lineNum">    2065 </span>            : </a>
+<a name="2066"><span class="lineNum">    2066 </span><span class="lineNoCov">          0 :             if (j + jb &lt;= *n) {</span></a>
+<a name="2067"><span class="lineNum">    2067 </span><span class="lineNoCov">          0 :                 i__2 = *n - j - jb + 1;</span></a>
+<a name="2068"><span class="lineNum">    2068 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, n, &amp;jb, &amp;i__2, &amp;c_b20, </span></a>
+<a name="2069"><span class="lineNum">    2069 </span><span class="lineNoCov">          0 :                         &amp;a[(j + jb) * a_dim1 + 1], lda, &amp;work[j + jb], &amp;</span></a>
+<a name="2070"><span class="lineNum">    2070 </span><span class="lineNoCov">          0 :                         ldwork, &amp;c_b22, &amp;a[j * a_dim1 + 1], lda);</span></a>
+<a name="2071"><span class="lineNum">    2071 </span>            :             }</a>
+<a name="2072"><span class="lineNum">    2072 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, &amp;jb, &amp;c_b22, &amp;</span></a>
+<a name="2073"><span class="lineNum">    2073 </span><span class="lineNoCov">          0 :                     work[j], &amp;ldwork, &amp;a[j * a_dim1 + 1], lda);</span></a>
+<a name="2074"><span class="lineNum">    2074 </span>            :         }</a>
+<a name="2075"><span class="lineNum">    2075 </span>            :     }</a>
+<a name="2076"><span class="lineNum">    2076 </span>            : </a>
+<a name="2077"><span class="lineNum">    2077 </span><span class="lineCov">        114 :     for (j = *n - 1; j &gt;= 1; --j) {</span></a>
+<a name="2078"><span class="lineNum">    2078 </span><span class="lineCov">         57 :         jp = ipiv[j];</span></a>
+<a name="2079"><span class="lineNum">    2079 </span><span class="lineCov">         57 :         if (jp != j) {</span></a>
+<a name="2080"><span class="lineNum">    2080 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n, &amp;a[j * a_dim1 + 1], &amp;c__1, &amp;a[jp * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="2081"><span class="lineNum">    2081 </span>            :         }</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :     }</a>
+<a name="2083"><span class="lineNum">    2083 </span>            : </a>
+<a name="2084"><span class="lineNum">    2084 </span><span class="lineCov">         57 :     work[1] = (double) iws;</span></a>
+<a name="2085"><span class="lineNum">    2085 </span><span class="lineCov">         57 :     return;</span></a>
+<a name="2086"><span class="lineNum">    2086 </span>            : </a>
+<a name="2087"><span class="lineNum">    2087 </span>            : }</a>
+<a name="2088"><span class="lineNum">    2088 </span>            : </a>
+<a name="2089"><span class="lineNum">    2089 </span>            : </a>
+<a name="2090"><span class="lineNum">    2090 </span>            : }</a>
+<a name="2091"><span class="lineNum">    2091 </span>            : }</a>
+<a name="2092"><span class="lineNum">    2092 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2093"><span class="lineNum">    2093 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="2094"><span class="lineNum">    2094 </span>            : </a>
+<a name="2095"><span class="lineNum">    2095 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2096"><span class="lineNum">    2096 </span>            : namespace PLMD{</a>
+<a name="2097"><span class="lineNum">    2097 </span>            : namespace lapack{</a>
+<a name="2098"><span class="lineNum">    2098 </span>            : using namespace blas;</a>
+<a name="2099"><span class="lineNum">    2099 </span>            : void</a>
+<a name="2100"><span class="lineNum">    2100 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dgetrs,DGETRS)(const char *trans, </span></a>
+<a name="2101"><span class="lineNum">    2101 </span>            :         int *n, </a>
+<a name="2102"><span class="lineNum">    2102 </span>            :         int *nrhs, </a>
+<a name="2103"><span class="lineNum">    2103 </span>            :         double *a, </a>
+<a name="2104"><span class="lineNum">    2104 </span>            :         int *lda, </a>
+<a name="2105"><span class="lineNum">    2105 </span>            :         int *ipiv,</a>
+<a name="2106"><span class="lineNum">    2106 </span>            :         double *b, </a>
+<a name="2107"><span class="lineNum">    2107 </span>            :         int *ldb, </a>
+<a name="2108"><span class="lineNum">    2108 </span>            :         int *info)</a>
+<a name="2109"><span class="lineNum">    2109 </span>            : {</a>
+<a name="2110"><span class="lineNum">    2110 </span>            :     int a_dim1, a_offset, b_dim1, b_offset;</a>
+<a name="2111"><span class="lineNum">    2111 </span>            :     int notran;</a>
+<a name="2112"><span class="lineNum">    2112 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="2113"><span class="lineNum">    2113 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="2114"><span class="lineNum">    2114 </span><span class="lineNoCov">          0 :     double one = 1.0;</span></a>
+<a name="2115"><span class="lineNum">    2115 </span>            : </a>
+<a name="2116"><span class="lineNum">    2116 </span>            :     a_dim1 = *lda;</a>
+<a name="2117"><span class="lineNum">    2117 </span>            :     a_offset = 1 + a_dim1;</a>
+<a name="2118"><span class="lineNum">    2118 </span>            :     a -= a_offset;</a>
+<a name="2119"><span class="lineNum">    2119 </span>            :     --ipiv;</a>
+<a name="2120"><span class="lineNum">    2120 </span>            :     b_dim1 = *ldb;</a>
+<a name="2121"><span class="lineNum">    2121 </span>            :     b_offset = 1 + b_dim1;</a>
+<a name="2122"><span class="lineNum">    2122 </span>            :     b -= b_offset;</a>
+<a name="2123"><span class="lineNum">    2123 </span>            : </a>
+<a name="2124"><span class="lineNum">    2124 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="2125"><span class="lineNum">    2125 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="2126"><span class="lineNum">    2126 </span>            : </a>
+<a name="2127"><span class="lineNum">    2127 </span><span class="lineNoCov">          0 :     if (*n &lt;= 0 || *nrhs &lt;= 0) </span></a>
+<a name="2128"><span class="lineNum">    2128 </span>            :         return;</a>
+<a name="2129"><span class="lineNum">    2129 </span>            : </a>
+<a name="2130"><span class="lineNum">    2130 </span><span class="lineNoCov">          0 :     if (notran) {</span></a>
+<a name="2131"><span class="lineNum">    2131 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlaswp,DLASWP)(nrhs, &amp;b[b_offset], ldb, &amp;c__1, n, &amp;ipiv[1], &amp;c__1);</span></a>
+<a name="2132"><span class="lineNum">    2132 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Left&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="2133"><span class="lineNum">    2133 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="2134"><span class="lineNum">    2134 </span>            : </a>
+<a name="2135"><span class="lineNum">    2135 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Left&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Non-unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="2136"><span class="lineNum">    2136 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="2137"><span class="lineNum">    2137 </span>            :     } else {</a>
+<a name="2138"><span class="lineNum">    2138 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Left&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Non-unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="2139"><span class="lineNum">    2139 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="2140"><span class="lineNum">    2140 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Left&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="2141"><span class="lineNum">    2141 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="2142"><span class="lineNum">    2142 </span>            : </a>
+<a name="2143"><span class="lineNum">    2143 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlaswp,DLASWP)(nrhs, &amp;b[b_offset], ldb, &amp;c__1, n, &amp;ipiv[1], &amp;c_n1);</span></a>
+<a name="2144"><span class="lineNum">    2144 </span>            :     }</a>
+<a name="2145"><span class="lineNum">    2145 </span>            : </a>
+<a name="2146"><span class="lineNum">    2146 </span>            :     return;</a>
+<a name="2147"><span class="lineNum">    2147 </span>            : </a>
+<a name="2148"><span class="lineNum">    2148 </span>            : } </a>
+<a name="2149"><span class="lineNum">    2149 </span>            : }</a>
+<a name="2150"><span class="lineNum">    2150 </span>            : }</a>
+<a name="2151"><span class="lineNum">    2151 </span>            : #include &lt;cmath&gt;</a>
+<a name="2152"><span class="lineNum">    2152 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2153"><span class="lineNum">    2153 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="2154"><span class="lineNum">    2154 </span>            : </a>
+<a name="2155"><span class="lineNum">    2155 </span>            : </a>
+<a name="2156"><span class="lineNum">    2156 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2157"><span class="lineNum">    2157 </span>            : namespace PLMD{</a>
+<a name="2158"><span class="lineNum">    2158 </span>            : namespace lapack{</a>
+<a name="2159"><span class="lineNum">    2159 </span>            : using namespace blas;</a>
+<a name="2160"><span class="lineNum">    2160 </span>            : void </a>
+<a name="2161"><span class="lineNum">    2161 </span><span class="lineCov">         12 : PLUMED_BLAS_F77_FUNC(dlabrd,DLABRD)(int *m, </span></a>
+<a name="2162"><span class="lineNum">    2162 </span>            :         int *n, </a>
+<a name="2163"><span class="lineNum">    2163 </span>            :         int *nb,</a>
+<a name="2164"><span class="lineNum">    2164 </span>            :         double *a, </a>
+<a name="2165"><span class="lineNum">    2165 </span>            :         int *lda, </a>
+<a name="2166"><span class="lineNum">    2166 </span>            :         double *d__,</a>
+<a name="2167"><span class="lineNum">    2167 </span>            :         double *e,</a>
+<a name="2168"><span class="lineNum">    2168 </span>            :         double *tauq, </a>
+<a name="2169"><span class="lineNum">    2169 </span>            :         double *taup,</a>
+<a name="2170"><span class="lineNum">    2170 </span>            :         double *x,</a>
+<a name="2171"><span class="lineNum">    2171 </span>            :         int *ldx,</a>
+<a name="2172"><span class="lineNum">    2172 </span>            :         double *y,</a>
+<a name="2173"><span class="lineNum">    2173 </span>            :         int *ldy)</a>
+<a name="2174"><span class="lineNum">    2174 </span>            : {</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :     int a_dim1, a_offset, x_dim1, x_offset, y_dim1, y_offset;</a>
+<a name="2176"><span class="lineNum">    2176 </span>            :     int i__1, i__2, i__3;</a>
+<a name="2177"><span class="lineNum">    2177 </span><span class="lineCov">         12 :     double one = 1.0;</span></a>
+<a name="2178"><span class="lineNum">    2178 </span><span class="lineCov">         12 :     double minusone = -1.0;</span></a>
+<a name="2179"><span class="lineNum">    2179 </span><span class="lineCov">         12 :     double zero = 0.0;</span></a>
+<a name="2180"><span class="lineNum">    2180 </span><span class="lineCov">         12 :     int c__1 = 1;</span></a>
+<a name="2181"><span class="lineNum">    2181 </span>            :     int i__;</a>
+<a name="2182"><span class="lineNum">    2182 </span>            : </a>
+<a name="2183"><span class="lineNum">    2183 </span><span class="lineCov">         12 :     a_dim1 = *lda;</span></a>
+<a name="2184"><span class="lineNum">    2184 </span><span class="lineCov">         12 :     a_offset = 1 + a_dim1;</span></a>
+<a name="2185"><span class="lineNum">    2185 </span><span class="lineCov">         12 :     a -= a_offset;</span></a>
+<a name="2186"><span class="lineNum">    2186 </span><span class="lineCov">         12 :     --d__;</span></a>
+<a name="2187"><span class="lineNum">    2187 </span><span class="lineCov">         12 :     --e;</span></a>
+<a name="2188"><span class="lineNum">    2188 </span><span class="lineCov">         12 :     --tauq;</span></a>
+<a name="2189"><span class="lineNum">    2189 </span><span class="lineCov">         12 :     --taup;</span></a>
+<a name="2190"><span class="lineNum">    2190 </span><span class="lineCov">         12 :     x_dim1 = *ldx;</span></a>
+<a name="2191"><span class="lineNum">    2191 </span><span class="lineCov">         12 :     x_offset = 1 + x_dim1;</span></a>
+<a name="2192"><span class="lineNum">    2192 </span><span class="lineCov">         12 :     x -= x_offset;</span></a>
+<a name="2193"><span class="lineNum">    2193 </span><span class="lineCov">         12 :     y_dim1 = *ldy;</span></a>
+<a name="2194"><span class="lineNum">    2194 </span><span class="lineCov">         12 :     y_offset = 1 + y_dim1;</span></a>
+<a name="2195"><span class="lineNum">    2195 </span><span class="lineCov">         12 :     y -= y_offset;</span></a>
+<a name="2196"><span class="lineNum">    2196 </span>            : </a>
+<a name="2197"><span class="lineNum">    2197 </span><span class="lineCov">         12 :     if (*m &lt;= 0 || *n &lt;= 0) {</span></a>
+<a name="2198"><span class="lineNum">    2198 </span>            :         return;</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :     }</a>
+<a name="2200"><span class="lineNum">    2200 </span>            : </a>
+<a name="2201"><span class="lineNum">    2201 </span><span class="lineCov">         12 :     if (*m &gt;= *n) {</span></a>
+<a name="2202"><span class="lineNum">    2202 </span>            : </a>
+<a name="2203"><span class="lineNum">    2203 </span><span class="lineCov">         12 :         i__1 = *nb;</span></a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineCov">        396 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="2205"><span class="lineNum">    2205 </span>            : </a>
+<a name="2206"><span class="lineNum">    2206 </span><span class="lineCov">        384 :             i__2 = *m - i__ + 1;</span></a>
+<a name="2207"><span class="lineNum">    2207 </span><span class="lineCov">        384 :             i__3 = i__ - 1;</span></a>
+<a name="2208"><span class="lineNum">    2208 </span><span class="lineCov">        384 :             PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ + a_dim1], lda,</span></a>
+<a name="2209"><span class="lineNum">    2209 </span><span class="lineCov">        384 :                      &amp;y[i__ + y_dim1], ldy, &amp;one, &amp;a[i__ + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="2210"><span class="lineNum">    2210 </span><span class="lineCov">        384 :             i__2 = *m - i__ + 1;</span></a>
+<a name="2211"><span class="lineNum">    2211 </span><span class="lineCov">        384 :             i__3 = i__ - 1;</span></a>
+<a name="2212"><span class="lineNum">    2212 </span><span class="lineCov">        384 :             PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;x[i__ + x_dim1], ldx,</span></a>
+<a name="2213"><span class="lineNum">    2213 </span><span class="lineCov">        384 :                    &amp;a[i__*a_dim1+1],&amp;c__1,&amp;one,&amp;a[i__+i__*a_dim1],&amp;c__1);</span></a>
+<a name="2214"><span class="lineNum">    2214 </span>            : </a>
+<a name="2215"><span class="lineNum">    2215 </span><span class="lineCov">        384 :             i__2 = *m - i__ + 1;</span></a>
+<a name="2216"><span class="lineNum">    2216 </span><span class="lineCov">        384 :             i__3 = i__ + 1;</span></a>
+<a name="2217"><span class="lineNum">    2217 </span><span class="lineCov">        384 :             if(*m&lt;i__3)</span></a>
+<a name="2218"><span class="lineNum">    2218 </span><span class="lineNoCov">          0 :               i__3 = *m;</span></a>
+<a name="2219"><span class="lineNum">    2219 </span><span class="lineCov">        384 :             PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i__2, &amp;a[i__ + i__ * a_dim1], &amp;a[i__3 + i__ * a_dim1], </span></a>
+<a name="2220"><span class="lineNum">    2220 </span><span class="lineCov">        384 :                     &amp;c__1, &amp;tauq[i__]);</span></a>
+<a name="2221"><span class="lineNum">    2221 </span><span class="lineCov">        384 :             d__[i__] = a[i__ + i__ * a_dim1];</span></a>
+<a name="2222"><span class="lineNum">    2222 </span><span class="lineCov">        384 :             if (i__ &lt; *n) {</span></a>
+<a name="2223"><span class="lineNum">    2223 </span><span class="lineCov">        384 :                 a[i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="2224"><span class="lineNum">    2224 </span>            : </a>
+<a name="2225"><span class="lineNum">    2225 </span><span class="lineCov">        384 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="2226"><span class="lineNum">    2226 </span><span class="lineCov">        384 :                 i__3 = *n - i__;</span></a>
+<a name="2227"><span class="lineNum">    2227 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + (i__ + 1) * </span></a>
+<a name="2228"><span class="lineNum">    2228 </span><span class="lineCov">        384 :                         a_dim1], lda, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;</span></a>
+<a name="2229"><span class="lineNum">    2229 </span><span class="lineCov">        384 :                         y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2230"><span class="lineNum">    2230 </span><span class="lineCov">        384 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="2231"><span class="lineNum">    2231 </span><span class="lineCov">        384 :                 i__3 = i__ - 1;</span></a>
+<a name="2232"><span class="lineNum">    2232 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + a_dim1], </span></a>
+<a name="2233"><span class="lineNum">    2233 </span><span class="lineCov">        384 :                         lda, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[i__ * </span></a>
+<a name="2234"><span class="lineNum">    2234 </span><span class="lineCov">        384 :                         y_dim1 + 1], &amp;c__1);</span></a>
+<a name="2235"><span class="lineNum">    2235 </span><span class="lineCov">        384 :                 i__2 = *n - i__;</span></a>
+<a name="2236"><span class="lineNum">    2236 </span><span class="lineCov">        384 :                 i__3 = i__ - 1;</span></a>
+<a name="2237"><span class="lineNum">    2237 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;y[i__ + 1 + </span></a>
+<a name="2238"><span class="lineNum">    2238 </span><span class="lineCov">        384 :                         y_dim1], ldy, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, &amp;y[</span></a>
+<a name="2239"><span class="lineNum">    2239 </span><span class="lineCov">        384 :                         i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2240"><span class="lineNum">    2240 </span><span class="lineCov">        384 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="2241"><span class="lineNum">    2241 </span><span class="lineCov">        384 :                 i__3 = i__ - 1;</span></a>
+<a name="2242"><span class="lineNum">    2242 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;x[i__ + x_dim1], </span></a>
+<a name="2243"><span class="lineNum">    2243 </span><span class="lineCov">        384 :                         ldx, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[i__ * </span></a>
+<a name="2244"><span class="lineNum">    2244 </span><span class="lineCov">        384 :                         y_dim1 + 1], &amp;c__1);</span></a>
+<a name="2245"><span class="lineNum">    2245 </span><span class="lineCov">        384 :                 i__2 = i__ - 1;</span></a>
+<a name="2246"><span class="lineNum">    2246 </span><span class="lineCov">        384 :                 i__3 = *n - i__;</span></a>
+<a name="2247"><span class="lineNum">    2247 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[(i__ + 1) * </span></a>
+<a name="2248"><span class="lineNum">    2248 </span><span class="lineCov">        384 :                         a_dim1 + 1], lda, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, </span></a>
+<a name="2249"><span class="lineNum">    2249 </span><span class="lineCov">        384 :                         &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2250"><span class="lineNum">    2250 </span><span class="lineCov">        384 :                 i__2 = *n - i__;</span></a>
+<a name="2251"><span class="lineNum">    2251 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__2, &amp;tauq[i__], &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2252"><span class="lineNum">    2252 </span>            : </a>
+<a name="2253"><span class="lineNum">    2253 </span><span class="lineCov">        384 :                 i__2 = *n - i__;</span></a>
+<a name="2254"><span class="lineNum">    2254 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__, &amp;minusone, &amp;y[i__ + 1 + </span></a>
+<a name="2255"><span class="lineNum">    2255 </span><span class="lineCov">        384 :                         y_dim1], ldy, &amp;a[i__ + a_dim1], lda, &amp;one, &amp;a[i__ + (</span></a>
+<a name="2256"><span class="lineNum">    2256 </span><span class="lineCov">        384 :                         i__ + 1) * a_dim1], lda);</span></a>
+<a name="2257"><span class="lineNum">    2257 </span><span class="lineCov">        384 :                 i__2 = i__ - 1;</span></a>
+<a name="2258"><span class="lineNum">    2258 </span><span class="lineCov">        384 :                 i__3 = *n - i__;</span></a>
+<a name="2259"><span class="lineNum">    2259 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[(i__ + 1) * </span></a>
+<a name="2260"><span class="lineNum">    2260 </span><span class="lineCov">        384 :                         a_dim1 + 1], lda, &amp;x[i__ + x_dim1], ldx, &amp;one, &amp;a[</span></a>
+<a name="2261"><span class="lineNum">    2261 </span><span class="lineCov">        384 :                         i__ + (i__ + 1) * a_dim1], lda);</span></a>
+<a name="2262"><span class="lineNum">    2262 </span>            : </a>
+<a name="2263"><span class="lineNum">    2263 </span><span class="lineCov">        384 :                 i__2 = *n - i__;</span></a>
+<a name="2264"><span class="lineNum">    2264 </span><span class="lineCov">        384 :                 i__3 = i__ + 2;</span></a>
+<a name="2265"><span class="lineNum">    2265 </span><span class="lineCov">        384 :                 if(*n&lt;i__3)</span></a>
+<a name="2266"><span class="lineNum">    2266 </span><span class="lineNoCov">          0 :                   i__3 = *n;</span></a>
+<a name="2267"><span class="lineNum">    2267 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i__2, &amp;a[i__ + (i__ + 1) * a_dim1], </span></a>
+<a name="2268"><span class="lineNum">    2268 </span><span class="lineCov">        384 :                         &amp;a[i__ + i__3 * a_dim1], lda, &amp;taup[i__]);</span></a>
+<a name="2269"><span class="lineNum">    2269 </span><span class="lineCov">        384 :                 e[i__] = a[i__ + (i__ + 1) * a_dim1];</span></a>
+<a name="2270"><span class="lineNum">    2270 </span><span class="lineCov">        384 :                 a[i__ + (i__ + 1) * a_dim1] = 1.;</span></a>
+<a name="2271"><span class="lineNum">    2271 </span>            : </a>
+<a name="2272"><span class="lineNum">    2272 </span><span class="lineCov">        384 :                 i__2 = *m - i__;</span></a>
+<a name="2273"><span class="lineNum">    2273 </span><span class="lineCov">        384 :                 i__3 = *n - i__;</span></a>
+<a name="2274"><span class="lineNum">    2274 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + 1 + (i__ </span></a>
+<a name="2275"><span class="lineNum">    2275 </span><span class="lineCov">        384 :                         + 1) * a_dim1], lda, &amp;a[i__ + (i__ + 1) * a_dim1], </span></a>
+<a name="2276"><span class="lineNum">    2276 </span><span class="lineCov">        384 :                         lda, &amp;zero, &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2277"><span class="lineNum">    2277 </span><span class="lineCov">        384 :                 i__2 = *n - i__;</span></a>
+<a name="2278"><span class="lineNum">    2278 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__, &amp;one, &amp;y[i__ + 1 + y_dim1], </span></a>
+<a name="2279"><span class="lineNum">    2279 </span><span class="lineCov">        384 :                         ldy, &amp;a[i__ + (i__ + 1) * a_dim1], lda, &amp;zero, &amp;x[</span></a>
+<a name="2280"><span class="lineNum">    2280 </span><span class="lineCov">        384 :                         i__ * x_dim1 + 1], &amp;c__1);</span></a>
+<a name="2281"><span class="lineNum">    2281 </span><span class="lineCov">        384 :                 i__2 = *m - i__;</span></a>
+<a name="2282"><span class="lineNum">    2282 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__, &amp;minusone, &amp;a[i__ + 1 + </span></a>
+<a name="2283"><span class="lineNum">    2283 </span><span class="lineCov">        384 :                         a_dim1], lda, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="2284"><span class="lineNum">    2284 </span><span class="lineCov">        384 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2285"><span class="lineNum">    2285 </span><span class="lineCov">        384 :                 i__2 = i__ - 1;</span></a>
+<a name="2286"><span class="lineNum">    2286 </span><span class="lineCov">        384 :                 i__3 = *n - i__;</span></a>
+<a name="2287"><span class="lineNum">    2287 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[(i__ + 1) * </span></a>
+<a name="2288"><span class="lineNum">    2288 </span><span class="lineCov">        384 :                         a_dim1 + 1], lda, &amp;a[i__ + (i__ + 1) * a_dim1], lda, &amp;</span></a>
+<a name="2289"><span class="lineNum">    2289 </span><span class="lineCov">        384 :                         zero, &amp;x[i__ * x_dim1 + 1], &amp;c__1);</span></a>
+<a name="2290"><span class="lineNum">    2290 </span><span class="lineCov">        384 :                 i__2 = *m - i__;</span></a>
+<a name="2291"><span class="lineNum">    2291 </span><span class="lineCov">        384 :                 i__3 = i__ - 1;</span></a>
+<a name="2292"><span class="lineNum">    2292 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;x[i__ + 1 + </span></a>
+<a name="2293"><span class="lineNum">    2293 </span><span class="lineCov">        384 :                         x_dim1], ldx, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="2294"><span class="lineNum">    2294 </span><span class="lineCov">        384 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2295"><span class="lineNum">    2295 </span><span class="lineCov">        384 :                 i__2 = *m - i__;</span></a>
+<a name="2296"><span class="lineNum">    2296 </span><span class="lineCov">        384 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__2, &amp;taup[i__], &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2297"><span class="lineNum">    2297 </span>            :             }</a>
+<a name="2298"><span class="lineNum">    2298 </span>            :         }</a>
+<a name="2299"><span class="lineNum">    2299 </span>            :     } else {</a>
+<a name="2300"><span class="lineNum">    2300 </span>            : </a>
+<a name="2301"><span class="lineNum">    2301 </span><span class="lineNoCov">          0 :         i__1 = *nb;</span></a>
+<a name="2302"><span class="lineNum">    2302 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="2303"><span class="lineNum">    2303 </span>            : </a>
+<a name="2304"><span class="lineNum">    2304 </span><span class="lineNoCov">          0 :             i__2 = *n - i__ + 1;</span></a>
+<a name="2305"><span class="lineNum">    2305 </span><span class="lineNoCov">          0 :             i__3 = i__ - 1;</span></a>
+<a name="2306"><span class="lineNum">    2306 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;y[i__ + y_dim1], ldy,</span></a>
+<a name="2307"><span class="lineNum">    2307 </span><span class="lineNoCov">          0 :                      &amp;a[i__ + a_dim1], lda, &amp;one, &amp;a[i__ + i__ * a_dim1],lda);</span></a>
+<a name="2308"><span class="lineNum">    2308 </span><span class="lineNoCov">          0 :             i__2 = i__ - 1;</span></a>
+<a name="2309"><span class="lineNum">    2309 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="2310"><span class="lineNum">    2310 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ * a_dim1 + 1], </span></a>
+<a name="2311"><span class="lineNum">    2311 </span><span class="lineNoCov">          0 :                     lda, &amp;x[i__ + x_dim1], ldx, &amp;one,&amp;a[i__+i__*a_dim1],lda);</span></a>
+<a name="2312"><span class="lineNum">    2312 </span>            : </a>
+<a name="2313"><span class="lineNum">    2313 </span><span class="lineNoCov">          0 :             i__2 = *n - i__ + 1;</span></a>
+<a name="2314"><span class="lineNum">    2314 </span><span class="lineNoCov">          0 :             i__3 = i__ + 1;</span></a>
+<a name="2315"><span class="lineNum">    2315 </span><span class="lineNoCov">          0 :             if(*n&lt;i__3)</span></a>
+<a name="2316"><span class="lineNum">    2316 </span><span class="lineNoCov">          0 :               i__3 = *n;</span></a>
+<a name="2317"><span class="lineNum">    2317 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i__2, &amp;a[i__ + i__ * a_dim1], </span></a>
+<a name="2318"><span class="lineNum">    2318 </span><span class="lineNoCov">          0 :                     &amp;a[i__ + i__3 * a_dim1], lda, &amp;taup[i__]);</span></a>
+<a name="2319"><span class="lineNum">    2319 </span><span class="lineNoCov">          0 :             d__[i__] = a[i__ + i__ * a_dim1];</span></a>
+<a name="2320"><span class="lineNum">    2320 </span><span class="lineNoCov">          0 :             if (i__ &lt; *m) {</span></a>
+<a name="2321"><span class="lineNum">    2321 </span><span class="lineNoCov">          0 :                 a[i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="2322"><span class="lineNum">    2322 </span>            : </a>
+<a name="2323"><span class="lineNum">    2323 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2324"><span class="lineNum">    2324 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="2325"><span class="lineNum">    2325 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;,&amp;i__2,&amp;i__3,&amp;one,&amp;a[i__+1+i__*a_dim1], </span></a>
+<a name="2326"><span class="lineNum">    2326 </span>            :                        lda, &amp;a[i__ + i__ * a_dim1], lda, &amp;zero, </a>
+<a name="2327"><span class="lineNum">    2327 </span><span class="lineNoCov">          0 :                        &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2328"><span class="lineNum">    2328 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__ + 1;</span></a>
+<a name="2329"><span class="lineNum">    2329 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="2330"><span class="lineNum">    2330 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;y[i__ + y_dim1], </span></a>
+<a name="2331"><span class="lineNum">    2331 </span><span class="lineNoCov">          0 :                         ldy, &amp;a[i__ + i__ * a_dim1], lda, &amp;zero, &amp;x[i__ * </span></a>
+<a name="2332"><span class="lineNum">    2332 </span><span class="lineNoCov">          0 :                         x_dim1 + 1], &amp;c__1);</span></a>
+<a name="2333"><span class="lineNum">    2333 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2334"><span class="lineNum">    2334 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="2335"><span class="lineNum">    2335 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ + 1 + </span></a>
+<a name="2336"><span class="lineNum">    2336 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="2337"><span class="lineNum">    2337 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2338"><span class="lineNum">    2338 </span><span class="lineNoCov">          0 :                 i__2 = i__ - 1;</span></a>
+<a name="2339"><span class="lineNum">    2339 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="2340"><span class="lineNum">    2340 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ * a_dim1 + </span></a>
+<a name="2341"><span class="lineNum">    2341 </span><span class="lineNoCov">          0 :                         1], lda, &amp;a[i__ + i__ * a_dim1], lda, &amp;zero, &amp;x[i__ *</span></a>
+<a name="2342"><span class="lineNum">    2342 </span><span class="lineNoCov">          0 :                          x_dim1 + 1], &amp;c__1);</span></a>
+<a name="2343"><span class="lineNum">    2343 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2344"><span class="lineNum">    2344 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="2345"><span class="lineNum">    2345 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;x[i__ + 1 + </span></a>
+<a name="2346"><span class="lineNum">    2346 </span><span class="lineNoCov">          0 :                         x_dim1], ldx, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="2347"><span class="lineNum">    2347 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2348"><span class="lineNum">    2348 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2349"><span class="lineNum">    2349 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__2, &amp;taup[i__], &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="2350"><span class="lineNum">    2350 </span>            : </a>
+<a name="2351"><span class="lineNum">    2351 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2352"><span class="lineNum">    2352 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="2353"><span class="lineNum">    2353 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ + 1 + </span></a>
+<a name="2354"><span class="lineNum">    2354 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;y[i__ + y_dim1], ldy, &amp;one, &amp;a[i__ + </span></a>
+<a name="2355"><span class="lineNum">    2355 </span><span class="lineNoCov">          0 :                         1 + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="2356"><span class="lineNum">    2356 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2357"><span class="lineNum">    2357 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__, &amp;minusone, &amp;x[i__ + 1 + </span></a>
+<a name="2358"><span class="lineNum">    2358 </span><span class="lineNoCov">          0 :                         x_dim1], ldx, &amp;a[i__ * a_dim1 + 1], &amp;c__1, &amp;one, &amp;a[</span></a>
+<a name="2359"><span class="lineNum">    2359 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="2360"><span class="lineNum">    2360 </span>            : </a>
+<a name="2361"><span class="lineNum">    2361 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2362"><span class="lineNum">    2362 </span><span class="lineNoCov">          0 :                 i__3 = i__ + 2;</span></a>
+<a name="2363"><span class="lineNum">    2363 </span><span class="lineNoCov">          0 :                 if(*m&lt;i__3)</span></a>
+<a name="2364"><span class="lineNum">    2364 </span><span class="lineNoCov">          0 :                   i__3 = *m;</span></a>
+<a name="2365"><span class="lineNum">    2365 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i__2, &amp;a[i__ + 1 + i__ * a_dim1], </span></a>
+<a name="2366"><span class="lineNum">    2366 </span><span class="lineNoCov">          0 :                         &amp;a[i__3 + i__ * a_dim1], &amp;c__1, &amp;tauq[i__]);</span></a>
+<a name="2367"><span class="lineNum">    2367 </span><span class="lineNoCov">          0 :                 e[i__] = a[i__ + 1 + i__ * a_dim1];</span></a>
+<a name="2368"><span class="lineNum">    2368 </span><span class="lineNoCov">          0 :                 a[i__ + 1 + i__ * a_dim1] = 1.;</span></a>
+<a name="2369"><span class="lineNum">    2369 </span>            : </a>
+<a name="2370"><span class="lineNum">    2370 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2371"><span class="lineNum">    2371 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="2372"><span class="lineNum">    2372 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + 1 + (i__ + </span></a>
+<a name="2373"><span class="lineNum">    2373 </span><span class="lineNoCov">          0 :                         1) * a_dim1], lda, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1, </span></a>
+<a name="2374"><span class="lineNum">    2374 </span><span class="lineNoCov">          0 :                         &amp;zero, &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2375"><span class="lineNum">    2375 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2376"><span class="lineNum">    2376 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="2377"><span class="lineNum">    2377 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + 1 + a_dim1],</span></a>
+<a name="2378"><span class="lineNum">    2378 </span><span class="lineNoCov">          0 :                          lda, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[</span></a>
+<a name="2379"><span class="lineNum">    2379 </span><span class="lineNoCov">          0 :                         i__ * y_dim1 + 1], &amp;c__1);</span></a>
+<a name="2380"><span class="lineNum">    2380 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="2381"><span class="lineNum">    2381 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="2382"><span class="lineNum">    2382 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;y[i__ + 1 + </span></a>
+<a name="2383"><span class="lineNum">    2383 </span><span class="lineNoCov">          0 :                         y_dim1], ldy, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, &amp;y[</span></a>
+<a name="2384"><span class="lineNum">    2384 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2385"><span class="lineNum">    2385 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="2386"><span class="lineNum">    2386 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__, &amp;one, &amp;x[i__ + 1 + x_dim1], </span></a>
+<a name="2387"><span class="lineNum">    2387 </span><span class="lineNoCov">          0 :                         ldx, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[</span></a>
+<a name="2388"><span class="lineNum">    2388 </span><span class="lineNoCov">          0 :                         i__ * y_dim1 + 1], &amp;c__1);</span></a>
+<a name="2389"><span class="lineNum">    2389 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="2390"><span class="lineNum">    2390 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__, &amp;i__2, &amp;minusone, &amp;a[(i__ + 1) * a_dim1 </span></a>
+<a name="2391"><span class="lineNum">    2391 </span><span class="lineNoCov">          0 :                         + 1], lda, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, &amp;y[i__ </span></a>
+<a name="2392"><span class="lineNum">    2392 </span><span class="lineNoCov">          0 :                         + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2393"><span class="lineNum">    2393 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="2394"><span class="lineNum">    2394 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__2, &amp;tauq[i__], &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="2395"><span class="lineNum">    2395 </span>            :             }</a>
+<a name="2396"><span class="lineNum">    2396 </span>            :         }</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :     }</a>
+<a name="2398"><span class="lineNum">    2398 </span>            :     return;</a>
+<a name="2399"><span class="lineNum">    2399 </span>            : } </a>
+<a name="2400"><span class="lineNum">    2400 </span>            : </a>
+<a name="2401"><span class="lineNum">    2401 </span>            : }</a>
+<a name="2402"><span class="lineNum">    2402 </span>            : }</a>
+<a name="2403"><span class="lineNum">    2403 </span>            : #include &lt;cctype&gt;</a>
+<a name="2404"><span class="lineNum">    2404 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="2405"><span class="lineNum">    2405 </span>            : </a>
+<a name="2406"><span class="lineNum">    2406 </span>            : /* LAPACK */</a>
+<a name="2407"><span class="lineNum">    2407 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2408"><span class="lineNum">    2408 </span>            : namespace PLMD{</a>
+<a name="2409"><span class="lineNum">    2409 </span>            : namespace lapack{</a>
+<a name="2410"><span class="lineNum">    2410 </span>            : using namespace blas;</a>
+<a name="2411"><span class="lineNum">    2411 </span>            : void</a>
+<a name="2412"><span class="lineNum">    2412 </span><span class="lineCov">         54 : PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(const char *uplo,</span></a>
+<a name="2413"><span class="lineNum">    2413 </span>            :         int *m,</a>
+<a name="2414"><span class="lineNum">    2414 </span>            :         int *n,</a>
+<a name="2415"><span class="lineNum">    2415 </span>            :         double *a,</a>
+<a name="2416"><span class="lineNum">    2416 </span>            :         int *lda,</a>
+<a name="2417"><span class="lineNum">    2417 </span>            :         double *b,</a>
+<a name="2418"><span class="lineNum">    2418 </span>            :         int *ldb)</a>
+<a name="2419"><span class="lineNum">    2419 </span>            : {</a>
+<a name="2420"><span class="lineNum">    2420 </span>            :   int i,j,minjm;</a>
+<a name="2421"><span class="lineNum">    2421 </span><span class="lineCov">         54 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="2422"><span class="lineNum">    2422 </span>            : </a>
+<a name="2423"><span class="lineNum">    2423 </span><span class="lineCov">         54 :   if(ch=='U') {</span></a>
+<a name="2424"><span class="lineNum">    2424 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="2425"><span class="lineNum">    2425 </span><span class="lineNoCov">          0 :       minjm = (j &lt; (*m-1)) ? j : (*m-1);</span></a>
+<a name="2426"><span class="lineNum">    2426 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;=minjm;i++)</span></a>
+<a name="2427"><span class="lineNum">    2427 </span><span class="lineNoCov">          0 :         b[j*(*ldb)+i] = a[j*(*lda)+i];</span></a>
+<a name="2428"><span class="lineNum">    2428 </span>            :     }</a>
+<a name="2429"><span class="lineNum">    2429 </span><span class="lineCov">         54 :   } else if(ch=='L') {</span></a>
+<a name="2430"><span class="lineNum">    2430 </span><span class="lineCov">          3 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="2431"><span class="lineNum">    2431 </span><span class="lineCov">          7 :       for(i=j;i&lt;*m;i++)</span></a>
+<a name="2432"><span class="lineNum">    2432 </span><span class="lineCov">          5 :         b[j*(*ldb)+i] = a[j*(*lda)+i];</span></a>
+<a name="2433"><span class="lineNum">    2433 </span>            :     }</a>
+<a name="2434"><span class="lineNum">    2434 </span>            :   } else {</a>
+<a name="2435"><span class="lineNum">    2435 </span><span class="lineCov">       2222 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="2436"><span class="lineNum">    2436 </span><span class="lineCov">      99977 :       for(i=0;i&lt;*m;i++)</span></a>
+<a name="2437"><span class="lineNum">    2437 </span><span class="lineCov">      97808 :         b[j*(*ldb)+i] = a[j*(*lda)+i];</span></a>
+<a name="2438"><span class="lineNum">    2438 </span>            :     }    </a>
+<a name="2439"><span class="lineNum">    2439 </span>            :   }</a>
+<a name="2440"><span class="lineNum">    2440 </span><span class="lineCov">         54 : }</span></a>
+<a name="2441"><span class="lineNum">    2441 </span>            : }</a>
+<a name="2442"><span class="lineNum">    2442 </span>            : }</a>
+<a name="2443"><span class="lineNum">    2443 </span>            : #include &lt;cmath&gt;</a>
+<a name="2444"><span class="lineNum">    2444 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="2445"><span class="lineNum">    2445 </span>            : </a>
+<a name="2446"><span class="lineNum">    2446 </span>            : </a>
+<a name="2447"><span class="lineNum">    2447 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2448"><span class="lineNum">    2448 </span>            : namespace PLMD{</a>
+<a name="2449"><span class="lineNum">    2449 </span>            : namespace lapack{</a>
+<a name="2450"><span class="lineNum">    2450 </span>            : using namespace blas;</a>
+<a name="2451"><span class="lineNum">    2451 </span>            : void</a>
+<a name="2452"><span class="lineNum">    2452 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlae2,DLAE2)(double *a, </span></a>
+<a name="2453"><span class="lineNum">    2453 </span>            :        double *b,</a>
+<a name="2454"><span class="lineNum">    2454 </span>            :        double *c__, </a>
+<a name="2455"><span class="lineNum">    2455 </span>            :        double *rt1, </a>
+<a name="2456"><span class="lineNum">    2456 </span>            :        double *rt2)</a>
+<a name="2457"><span class="lineNum">    2457 </span>            : {</a>
+<a name="2458"><span class="lineNum">    2458 </span>            :     double d__1;</a>
+<a name="2459"><span class="lineNum">    2459 </span>            :     double ab, df, tb, sm, rt, adf, acmn, acmx;</a>
+<a name="2460"><span class="lineNum">    2460 </span>            : </a>
+<a name="2461"><span class="lineNum">    2461 </span>            : </a>
+<a name="2462"><span class="lineNum">    2462 </span><span class="lineNoCov">          0 :     sm = *a + *c__;</span></a>
+<a name="2463"><span class="lineNum">    2463 </span><span class="lineNoCov">          0 :     df = *a - *c__;</span></a>
+<a name="2464"><span class="lineNum">    2464 </span>            :     adf = std::abs(df);</a>
+<a name="2465"><span class="lineNum">    2465 </span><span class="lineNoCov">          0 :     tb = *b + *b;</span></a>
+<a name="2466"><span class="lineNum">    2466 </span>            :     ab = std::abs(tb);</a>
+<a name="2467"><span class="lineNum">    2467 </span><span class="lineNoCov">          0 :     if (std::abs(*a) &gt; std::abs(*c__)) {</span></a>
+<a name="2468"><span class="lineNum">    2468 </span>            :         acmx = *a;</a>
+<a name="2469"><span class="lineNum">    2469 </span>            :         acmn = *c__;</a>
+<a name="2470"><span class="lineNum">    2470 </span>            :     } else {</a>
+<a name="2471"><span class="lineNum">    2471 </span>            :         acmx = *c__;</a>
+<a name="2472"><span class="lineNum">    2472 </span>            :         acmn = *a;</a>
+<a name="2473"><span class="lineNum">    2473 </span>            :     }</a>
+<a name="2474"><span class="lineNum">    2474 </span><span class="lineNoCov">          0 :     if (adf &gt; ab) {</span></a>
+<a name="2475"><span class="lineNum">    2475 </span><span class="lineNoCov">          0 :         d__1 = ab / adf;</span></a>
+<a name="2476"><span class="lineNum">    2476 </span><span class="lineNoCov">          0 :         rt = adf *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="2477"><span class="lineNum">    2477 </span><span class="lineNoCov">          0 :     } else if (adf &lt; ab) {</span></a>
+<a name="2478"><span class="lineNum">    2478 </span><span class="lineNoCov">          0 :         d__1 = adf / ab;</span></a>
+<a name="2479"><span class="lineNum">    2479 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="2480"><span class="lineNum">    2480 </span>            :     } else {</a>
+<a name="2481"><span class="lineNum">    2481 </span>            : </a>
+<a name="2482"><span class="lineNum">    2482 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(2.);</span></a>
+<a name="2483"><span class="lineNum">    2483 </span>            :     }</a>
+<a name="2484"><span class="lineNum">    2484 </span><span class="lineNoCov">          0 :     if (sm &lt; 0.) {</span></a>
+<a name="2485"><span class="lineNum">    2485 </span><span class="lineNoCov">          0 :         *rt1 = (sm - rt) * .5;</span></a>
+<a name="2486"><span class="lineNum">    2486 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="2487"><span class="lineNum">    2487 </span><span class="lineNoCov">          0 :     } else if (sm &gt; 0.) {</span></a>
+<a name="2488"><span class="lineNum">    2488 </span><span class="lineNoCov">          0 :         *rt1 = (sm + rt) * .5;</span></a>
+<a name="2489"><span class="lineNum">    2489 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="2490"><span class="lineNum">    2490 </span>            :     } else {</a>
+<a name="2491"><span class="lineNum">    2491 </span><span class="lineNoCov">          0 :         *rt1 = rt * .5;</span></a>
+<a name="2492"><span class="lineNum">    2492 </span><span class="lineNoCov">          0 :         *rt2 = rt * -.5;</span></a>
+<a name="2493"><span class="lineNum">    2493 </span>            :     }</a>
+<a name="2494"><span class="lineNum">    2494 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="2495"><span class="lineNum">    2495 </span>            : </a>
+<a name="2496"><span class="lineNum">    2496 </span>            : }</a>
+<a name="2497"><span class="lineNum">    2497 </span>            : </a>
+<a name="2498"><span class="lineNum">    2498 </span>            : </a>
+<a name="2499"><span class="lineNum">    2499 </span>            : }</a>
+<a name="2500"><span class="lineNum">    2500 </span>            : }</a>
+<a name="2501"><span class="lineNum">    2501 </span>            : #include &lt;cmath&gt;</a>
+<a name="2502"><span class="lineNum">    2502 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="2503"><span class="lineNum">    2503 </span>            : </a>
+<a name="2504"><span class="lineNum">    2504 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2505"><span class="lineNum">    2505 </span>            : namespace PLMD{</a>
+<a name="2506"><span class="lineNum">    2506 </span>            : namespace lapack{</a>
+<a name="2507"><span class="lineNum">    2507 </span>            : using namespace blas;</a>
+<a name="2508"><span class="lineNum">    2508 </span>            : void</a>
+<a name="2509"><span class="lineNum">    2509 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlaebz,DLAEBZ)(int *ijob,</span></a>
+<a name="2510"><span class="lineNum">    2510 </span>            :         int *nitmax,</a>
+<a name="2511"><span class="lineNum">    2511 </span>            :         int *n, </a>
+<a name="2512"><span class="lineNum">    2512 </span>            :         int *mmax,</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :         int *minp,</a>
+<a name="2514"><span class="lineNum">    2514 </span>            :         int *nbmin,</a>
+<a name="2515"><span class="lineNum">    2515 </span>            :         double *abstol, </a>
+<a name="2516"><span class="lineNum">    2516 </span>            :         double *reltol, </a>
+<a name="2517"><span class="lineNum">    2517 </span>            :         double *pivmin, </a>
+<a name="2518"><span class="lineNum">    2518 </span>            :         double *d__,</a>
+<a name="2519"><span class="lineNum">    2519 </span>            :         double *e,</a>
+<a name="2520"><span class="lineNum">    2520 </span>            :         double *e2, </a>
+<a name="2521"><span class="lineNum">    2521 </span>            :         int *nval,</a>
+<a name="2522"><span class="lineNum">    2522 </span>            :         double *ab, </a>
+<a name="2523"><span class="lineNum">    2523 </span>            :         double *c__, </a>
+<a name="2524"><span class="lineNum">    2524 </span>            :         int *mout, </a>
+<a name="2525"><span class="lineNum">    2525 </span>            :         int *nab,</a>
+<a name="2526"><span class="lineNum">    2526 </span>            :         double *work,</a>
+<a name="2527"><span class="lineNum">    2527 </span>            :         int *iwork, </a>
+<a name="2528"><span class="lineNum">    2528 </span>            :         int *info)</a>
+<a name="2529"><span class="lineNum">    2529 </span>            : {</a>
+<a name="2530"><span class="lineNum">    2530 </span>            :     int nab_dim1, nab_offset, ab_dim1, ab_offset, i__1, i__2, i__3, i__4, </a>
+<a name="2531"><span class="lineNum">    2531 </span>            :             i__5, i__6;</a>
+<a name="2532"><span class="lineNum">    2532 </span>            :     double d__1, d__2, d__3, d__4;</a>
+<a name="2533"><span class="lineNum">    2533 </span>            : </a>
+<a name="2534"><span class="lineNum">    2534 </span>            :     int j, kf, ji, kl, jp, jit;</a>
+<a name="2535"><span class="lineNum">    2535 </span>            :     double tmp1, tmp2;</a>
+<a name="2536"><span class="lineNum">    2536 </span>            :     int itmp1, itmp2, kfnew, klnew;</a>
+<a name="2537"><span class="lineNum">    2537 </span>            : </a>
+<a name="2538"><span class="lineNum">    2538 </span><span class="lineNoCov">          0 :     nab_dim1 = *mmax;</span></a>
+<a name="2539"><span class="lineNum">    2539 </span><span class="lineNoCov">          0 :     nab_offset = 1 + nab_dim1;</span></a>
+<a name="2540"><span class="lineNum">    2540 </span><span class="lineNoCov">          0 :     nab -= nab_offset;</span></a>
+<a name="2541"><span class="lineNum">    2541 </span>            :     ab_dim1 = *mmax;</a>
+<a name="2542"><span class="lineNum">    2542 </span>            :     ab_offset = 1 + ab_dim1;</a>
+<a name="2543"><span class="lineNum">    2543 </span><span class="lineNoCov">          0 :     ab -= ab_offset;</span></a>
+<a name="2544"><span class="lineNum">    2544 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="2545"><span class="lineNum">    2545 </span>            :     --e;</a>
+<a name="2546"><span class="lineNum">    2546 </span><span class="lineNoCov">          0 :     --e2;</span></a>
+<a name="2547"><span class="lineNum">    2547 </span><span class="lineNoCov">          0 :     --nval;</span></a>
+<a name="2548"><span class="lineNum">    2548 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="2549"><span class="lineNum">    2549 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="2550"><span class="lineNum">    2550 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="2551"><span class="lineNum">    2551 </span>            : </a>
+<a name="2552"><span class="lineNum">    2552 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="2553"><span class="lineNum">    2553 </span><span class="lineNoCov">          0 :     if (*ijob &lt; 1 || *ijob &gt; 3) {</span></a>
+<a name="2554"><span class="lineNum">    2554 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="2555"><span class="lineNum">    2555 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="2556"><span class="lineNum">    2556 </span>            :     }</a>
+<a name="2557"><span class="lineNum">    2557 </span>            : </a>
+<a name="2558"><span class="lineNum">    2558 </span><span class="lineNoCov">          0 :     if (*ijob == 1) {</span></a>
+<a name="2559"><span class="lineNum">    2559 </span>            : </a>
+<a name="2560"><span class="lineNum">    2560 </span><span class="lineNoCov">          0 :         *mout = 0;</span></a>
+<a name="2561"><span class="lineNum">    2561 </span>            : </a>
+<a name="2562"><span class="lineNum">    2562 </span><span class="lineNoCov">          0 :         i__1 = *minp;</span></a>
+<a name="2563"><span class="lineNum">    2563 </span><span class="lineNoCov">          0 :         for (ji = 1; ji &lt;= i__1; ++ji) {</span></a>
+<a name="2564"><span class="lineNum">    2564 </span><span class="lineNoCov">          0 :             for (jp = 1; jp &lt;= 2; ++jp) {</span></a>
+<a name="2565"><span class="lineNum">    2565 </span><span class="lineNoCov">          0 :                 tmp1 = d__[1] - ab[ji + jp * ab_dim1];</span></a>
+<a name="2566"><span class="lineNum">    2566 </span><span class="lineNoCov">          0 :                 if (std::abs(tmp1) &lt; *pivmin) {</span></a>
+<a name="2567"><span class="lineNum">    2567 </span><span class="lineNoCov">          0 :                     tmp1 = -(*pivmin);</span></a>
+<a name="2568"><span class="lineNum">    2568 </span>            :                 }</a>
+<a name="2569"><span class="lineNum">    2569 </span><span class="lineNoCov">          0 :                 nab[ji + jp * nab_dim1] = 0;</span></a>
+<a name="2570"><span class="lineNum">    2570 </span><span class="lineNoCov">          0 :                 if (tmp1 &lt;= 0.) {</span></a>
+<a name="2571"><span class="lineNum">    2571 </span><span class="lineNoCov">          0 :                     nab[ji + jp * nab_dim1] = 1;</span></a>
+<a name="2572"><span class="lineNum">    2572 </span>            :                 }</a>
+<a name="2573"><span class="lineNum">    2573 </span>            : </a>
+<a name="2574"><span class="lineNum">    2574 </span><span class="lineNoCov">          0 :                 i__2 = *n;</span></a>
+<a name="2575"><span class="lineNum">    2575 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="2576"><span class="lineNum">    2576 </span><span class="lineNoCov">          0 :                     tmp1 = d__[j] - e2[j - 1] / tmp1 - ab[ji + jp * ab_dim1];</span></a>
+<a name="2577"><span class="lineNum">    2577 </span><span class="lineNoCov">          0 :                     if (std::abs(tmp1) &lt; *pivmin) {</span></a>
+<a name="2578"><span class="lineNum">    2578 </span><span class="lineNoCov">          0 :                         tmp1 = -(*pivmin);</span></a>
+<a name="2579"><span class="lineNum">    2579 </span>            :                     }</a>
+<a name="2580"><span class="lineNum">    2580 </span><span class="lineNoCov">          0 :                     if (tmp1 &lt;= 0.) {</span></a>
+<a name="2581"><span class="lineNum">    2581 </span><span class="lineNoCov">          0 :                         ++nab[ji + jp * nab_dim1];</span></a>
+<a name="2582"><span class="lineNum">    2582 </span>            :                     }</a>
+<a name="2583"><span class="lineNum">    2583 </span>            :                 }</a>
+<a name="2584"><span class="lineNum">    2584 </span>            :             }</a>
+<a name="2585"><span class="lineNum">    2585 </span><span class="lineNoCov">          0 :             *mout = *mout + nab[ji + (nab_dim1 &lt;&lt; 1)] - nab[ji + nab_dim1];</span></a>
+<a name="2586"><span class="lineNum">    2586 </span>            :         }</a>
+<a name="2587"><span class="lineNum">    2587 </span>            :         return;</a>
+<a name="2588"><span class="lineNum">    2588 </span>            :     }</a>
+<a name="2589"><span class="lineNum">    2589 </span>            : </a>
+<a name="2590"><span class="lineNum">    2590 </span>            :     kf = 1;</a>
+<a name="2591"><span class="lineNum">    2591 </span><span class="lineNoCov">          0 :     kl = *minp;</span></a>
+<a name="2592"><span class="lineNum">    2592 </span>            : </a>
+<a name="2593"><span class="lineNum">    2593 </span><span class="lineNoCov">          0 :     if (*ijob == 2) {</span></a>
+<a name="2594"><span class="lineNum">    2594 </span>            :         i__1 = *minp;</a>
+<a name="2595"><span class="lineNum">    2595 </span><span class="lineNoCov">          0 :         for (ji = 1; ji &lt;= i__1; ++ji) {</span></a>
+<a name="2596"><span class="lineNum">    2596 </span><span class="lineNoCov">          0 :             c__[ji] = (ab[ji + ab_dim1] + ab[ji + (ab_dim1 &lt;&lt; 1)]) * .5;</span></a>
+<a name="2597"><span class="lineNum">    2597 </span>            :         }</a>
+<a name="2598"><span class="lineNum">    2598 </span>            :     }</a>
+<a name="2599"><span class="lineNum">    2599 </span>            : </a>
+<a name="2600"><span class="lineNum">    2600 </span><span class="lineNoCov">          0 :     i__1 = *nitmax;</span></a>
+<a name="2601"><span class="lineNum">    2601 </span><span class="lineNoCov">          0 :     for (jit = 1; jit &lt;= i__1; ++jit) {</span></a>
+<a name="2602"><span class="lineNum">    2602 </span>            : </a>
+<a name="2603"><span class="lineNum">    2603 </span><span class="lineNoCov">          0 :         if (kl - kf + 1 &gt;= *nbmin &amp;&amp; *nbmin &gt; 0) {</span></a>
+<a name="2604"><span class="lineNum">    2604 </span>            : </a>
+<a name="2605"><span class="lineNum">    2605 </span>            :             i__2 = kl;</a>
+<a name="2606"><span class="lineNum">    2606 </span><span class="lineNoCov">          0 :             for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="2607"><span class="lineNum">    2607 </span>            : </a>
+<a name="2608"><span class="lineNum">    2608 </span><span class="lineNoCov">          0 :                 work[ji] = d__[1] - c__[ji];</span></a>
+<a name="2609"><span class="lineNum">    2609 </span><span class="lineNoCov">          0 :                 iwork[ji] = 0;</span></a>
+<a name="2610"><span class="lineNum">    2610 </span><span class="lineNoCov">          0 :                 if (work[ji] &lt;= *pivmin) {</span></a>
+<a name="2611"><span class="lineNum">    2611 </span><span class="lineNoCov">          0 :                     iwork[ji] = 1;</span></a>
+<a name="2612"><span class="lineNum">    2612 </span><span class="lineNoCov">          0 :                     d__1 = work[ji], d__2 = -(*pivmin);</span></a>
+<a name="2613"><span class="lineNum">    2613 </span><span class="lineNoCov">          0 :                     work[ji] = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="2614"><span class="lineNum">    2614 </span>            :                 }</a>
+<a name="2615"><span class="lineNum">    2615 </span>            : </a>
+<a name="2616"><span class="lineNum">    2616 </span><span class="lineNoCov">          0 :                 i__3 = *n;</span></a>
+<a name="2617"><span class="lineNum">    2617 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__3; ++j) {</span></a>
+<a name="2618"><span class="lineNum">    2618 </span><span class="lineNoCov">          0 :                     work[ji] = d__[j] - e2[j - 1] / work[ji] - c__[ji];</span></a>
+<a name="2619"><span class="lineNum">    2619 </span><span class="lineNoCov">          0 :                     if (work[ji] &lt;= *pivmin) {</span></a>
+<a name="2620"><span class="lineNum">    2620 </span><span class="lineNoCov">          0 :                         ++iwork[ji];</span></a>
+<a name="2621"><span class="lineNum">    2621 </span><span class="lineNoCov">          0 :                         d__1 = work[ji], d__2 = -(*pivmin);</span></a>
+<a name="2622"><span class="lineNum">    2622 </span><span class="lineNoCov">          0 :                         work[ji] = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="2623"><span class="lineNum">    2623 </span>            :                     }</a>
+<a name="2624"><span class="lineNum">    2624 </span>            :                 }</a>
+<a name="2625"><span class="lineNum">    2625 </span>            :             }</a>
+<a name="2626"><span class="lineNum">    2626 </span>            : </a>
+<a name="2627"><span class="lineNum">    2627 </span><span class="lineNoCov">          0 :             if (*ijob &lt;= 2) {</span></a>
+<a name="2628"><span class="lineNum">    2628 </span>            : </a>
+<a name="2629"><span class="lineNum">    2629 </span>            :                 klnew = kl;</a>
+<a name="2630"><span class="lineNum">    2630 </span>            :                 i__2 = kl;</a>
+<a name="2631"><span class="lineNum">    2631 </span><span class="lineNoCov">          0 :                 for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="2632"><span class="lineNum">    2632 </span>            : </a>
+<a name="2633"><span class="lineNum">    2633 </span><span class="lineNoCov">          0 :                   i__5 = nab[ji + nab_dim1];</span></a>
+<a name="2634"><span class="lineNum">    2634 </span><span class="lineNoCov">          0 :                   i__6 = iwork[ji];</span></a>
+<a name="2635"><span class="lineNum">    2635 </span><span class="lineNoCov">          0 :                   i__3 = nab[ji + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="2636"><span class="lineNum">    2636 </span>            :                   i__4 = (i__5&gt;i__6) ? i__5 : i__6;</a>
+<a name="2637"><span class="lineNum">    2637 </span><span class="lineNoCov">          0 :                     iwork[ji] = (i__3&lt;i__4) ? i__3 : i__4;</span></a>
+<a name="2638"><span class="lineNum">    2638 </span>            : </a>
+<a name="2639"><span class="lineNum">    2639 </span><span class="lineNoCov">          0 :                     if (iwork[ji] == nab[ji + (nab_dim1 &lt;&lt; 1)]) {</span></a>
+<a name="2640"><span class="lineNum">    2640 </span>            : </a>
+<a name="2641"><span class="lineNum">    2641 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = c__[ji];</span></a>
+<a name="2642"><span class="lineNum">    2642 </span>            : </a>
+<a name="2643"><span class="lineNum">    2643 </span><span class="lineNoCov">          0 :                     } else if (iwork[ji] == nab[ji + nab_dim1]) {</span></a>
+<a name="2644"><span class="lineNum">    2644 </span>            : </a>
+<a name="2645"><span class="lineNum">    2645 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = c__[ji];</span></a>
+<a name="2646"><span class="lineNum">    2646 </span>            :                     } else {</a>
+<a name="2647"><span class="lineNum">    2647 </span><span class="lineNoCov">          0 :                         ++klnew;</span></a>
+<a name="2648"><span class="lineNum">    2648 </span><span class="lineNoCov">          0 :                         if (klnew &lt;= *mmax) {</span></a>
+<a name="2649"><span class="lineNum">    2649 </span>            : </a>
+<a name="2650"><span class="lineNum">    2650 </span><span class="lineNoCov">          0 :                             ab[klnew + (ab_dim1 &lt;&lt; 1)] = ab[ji + (ab_dim1 &lt;&lt; </span></a>
+<a name="2651"><span class="lineNum">    2651 </span><span class="lineNoCov">          0 :                                     1)];</span></a>
+<a name="2652"><span class="lineNum">    2652 </span><span class="lineNoCov">          0 :                             nab[klnew + (nab_dim1 &lt;&lt; 1)] = nab[ji + (nab_dim1 </span></a>
+<a name="2653"><span class="lineNum">    2653 </span><span class="lineNoCov">          0 :                                     &lt;&lt; 1)];</span></a>
+<a name="2654"><span class="lineNum">    2654 </span><span class="lineNoCov">          0 :                             ab[klnew + ab_dim1] = c__[ji];</span></a>
+<a name="2655"><span class="lineNum">    2655 </span><span class="lineNoCov">          0 :                             nab[klnew + nab_dim1] = iwork[ji];</span></a>
+<a name="2656"><span class="lineNum">    2656 </span><span class="lineNoCov">          0 :                             ab[ji + (ab_dim1 &lt;&lt; 1)] = c__[ji];</span></a>
+<a name="2657"><span class="lineNum">    2657 </span><span class="lineNoCov">          0 :                             nab[ji + (nab_dim1 &lt;&lt; 1)] = iwork[ji];</span></a>
+<a name="2658"><span class="lineNum">    2658 </span>            :                         } else {</a>
+<a name="2659"><span class="lineNum">    2659 </span><span class="lineNoCov">          0 :                             *info = *mmax + 1;</span></a>
+<a name="2660"><span class="lineNum">    2660 </span>            :                         }</a>
+<a name="2661"><span class="lineNum">    2661 </span>            :                     }</a>
+<a name="2662"><span class="lineNum">    2662 </span>            :                 }</a>
+<a name="2663"><span class="lineNum">    2663 </span><span class="lineNoCov">          0 :                 if (*info != 0) {</span></a>
+<a name="2664"><span class="lineNum">    2664 </span>            :                     return;</a>
+<a name="2665"><span class="lineNum">    2665 </span>            :                 }</a>
+<a name="2666"><span class="lineNum">    2666 </span>            :                 kl = klnew;</a>
+<a name="2667"><span class="lineNum">    2667 </span>            :             } else {</a>
+<a name="2668"><span class="lineNum">    2668 </span>            : </a>
+<a name="2669"><span class="lineNum">    2669 </span>            :                 i__2 = kl;</a>
+<a name="2670"><span class="lineNum">    2670 </span><span class="lineNoCov">          0 :                 for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="2671"><span class="lineNum">    2671 </span><span class="lineNoCov">          0 :                     if (iwork[ji] &lt;= nval[ji]) {</span></a>
+<a name="2672"><span class="lineNum">    2672 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = c__[ji];</span></a>
+<a name="2673"><span class="lineNum">    2673 </span><span class="lineNoCov">          0 :                         nab[ji + nab_dim1] = iwork[ji];</span></a>
+<a name="2674"><span class="lineNum">    2674 </span>            :                     }</a>
+<a name="2675"><span class="lineNum">    2675 </span><span class="lineNoCov">          0 :                     if (iwork[ji] &gt;= nval[ji]) {</span></a>
+<a name="2676"><span class="lineNum">    2676 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = c__[ji];</span></a>
+<a name="2677"><span class="lineNum">    2677 </span><span class="lineNoCov">          0 :                         nab[ji + (nab_dim1 &lt;&lt; 1)] = iwork[ji];</span></a>
+<a name="2678"><span class="lineNum">    2678 </span>            :                     }</a>
+<a name="2679"><span class="lineNum">    2679 </span>            :                 }</a>
+<a name="2680"><span class="lineNum">    2680 </span>            :             }</a>
+<a name="2681"><span class="lineNum">    2681 </span>            : </a>
+<a name="2682"><span class="lineNum">    2682 </span>            :         } else {</a>
+<a name="2683"><span class="lineNum">    2683 </span>            : </a>
+<a name="2684"><span class="lineNum">    2684 </span>            :             klnew = kl;</a>
+<a name="2685"><span class="lineNum">    2685 </span>            :             i__2 = kl;</a>
+<a name="2686"><span class="lineNum">    2686 </span><span class="lineNoCov">          0 :             for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="2687"><span class="lineNum">    2687 </span>            : </a>
+<a name="2688"><span class="lineNum">    2688 </span><span class="lineNoCov">          0 :                 tmp1 = c__[ji];</span></a>
+<a name="2689"><span class="lineNum">    2689 </span><span class="lineNoCov">          0 :                 tmp2 = d__[1] - tmp1;</span></a>
+<a name="2690"><span class="lineNum">    2690 </span>            :                 itmp1 = 0;</a>
+<a name="2691"><span class="lineNum">    2691 </span><span class="lineNoCov">          0 :                 if (tmp2 &lt;= *pivmin) {</span></a>
+<a name="2692"><span class="lineNum">    2692 </span>            :                     itmp1 = 1;</a>
+<a name="2693"><span class="lineNum">    2693 </span><span class="lineNoCov">          0 :                     d__1 = tmp2, d__2 = -(*pivmin);</span></a>
+<a name="2694"><span class="lineNum">    2694 </span><span class="lineNoCov">          0 :                     tmp2 = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="2695"><span class="lineNum">    2695 </span>            :                 }</a>
+<a name="2696"><span class="lineNum">    2696 </span>            : </a>
+<a name="2697"><span class="lineNum">    2697 </span><span class="lineNoCov">          0 :                 i__3 = *n;</span></a>
+<a name="2698"><span class="lineNum">    2698 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__3; ++j) {</span></a>
+<a name="2699"><span class="lineNum">    2699 </span><span class="lineNoCov">          0 :                     tmp2 = d__[j] - e2[j - 1] / tmp2 - tmp1;</span></a>
+<a name="2700"><span class="lineNum">    2700 </span><span class="lineNoCov">          0 :                     if (tmp2 &lt;= *pivmin) {</span></a>
+<a name="2701"><span class="lineNum">    2701 </span><span class="lineNoCov">          0 :                         ++itmp1;</span></a>
+<a name="2702"><span class="lineNum">    2702 </span><span class="lineNoCov">          0 :                         d__1 = tmp2, d__2 = -(*pivmin);</span></a>
+<a name="2703"><span class="lineNum">    2703 </span><span class="lineNoCov">          0 :                         tmp2 = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="2704"><span class="lineNum">    2704 </span>            :                     }</a>
+<a name="2705"><span class="lineNum">    2705 </span>            :                 }</a>
+<a name="2706"><span class="lineNum">    2706 </span>            : </a>
+<a name="2707"><span class="lineNum">    2707 </span><span class="lineNoCov">          0 :                 if (*ijob &lt;= 2) {</span></a>
+<a name="2708"><span class="lineNum">    2708 </span>            : </a>
+<a name="2709"><span class="lineNum">    2709 </span><span class="lineNoCov">          0 :                     i__5 = nab[ji + nab_dim1];</span></a>
+<a name="2710"><span class="lineNum">    2710 </span><span class="lineNoCov">          0 :                     i__3 = nab[ji + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="2711"><span class="lineNum">    2711 </span>            :                     i__4 = (i__5&gt;itmp1) ? i__5 : itmp1;</a>
+<a name="2712"><span class="lineNum">    2712 </span>            :                     itmp1 = (i__3&lt;i__4) ? i__3 : i__4;</a>
+<a name="2713"><span class="lineNum">    2713 </span>            : </a>
+<a name="2714"><span class="lineNum">    2714 </span><span class="lineNoCov">          0 :                     if (itmp1 == nab[ji + (nab_dim1 &lt;&lt; 1)]) {</span></a>
+<a name="2715"><span class="lineNum">    2715 </span>            : </a>
+<a name="2716"><span class="lineNum">    2716 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = tmp1;</span></a>
+<a name="2717"><span class="lineNum">    2717 </span>            : </a>
+<a name="2718"><span class="lineNum">    2718 </span><span class="lineNoCov">          0 :                     } else if (itmp1 == nab[ji + nab_dim1]) {</span></a>
+<a name="2719"><span class="lineNum">    2719 </span>            : </a>
+<a name="2720"><span class="lineNum">    2720 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = tmp1;</span></a>
+<a name="2721"><span class="lineNum">    2721 </span><span class="lineNoCov">          0 :                     } else if (klnew &lt; *mmax) {</span></a>
+<a name="2722"><span class="lineNum">    2722 </span>            : </a>
+<a name="2723"><span class="lineNum">    2723 </span><span class="lineNoCov">          0 :                         ++klnew;</span></a>
+<a name="2724"><span class="lineNum">    2724 </span><span class="lineNoCov">          0 :                         ab[klnew + (ab_dim1 &lt;&lt; 1)] = ab[ji + (ab_dim1 &lt;&lt; 1)];</span></a>
+<a name="2725"><span class="lineNum">    2725 </span><span class="lineNoCov">          0 :                         nab[klnew + (nab_dim1 &lt;&lt; 1)] = nab[ji + (nab_dim1 &lt;&lt; </span></a>
+<a name="2726"><span class="lineNum">    2726 </span><span class="lineNoCov">          0 :                                 1)];</span></a>
+<a name="2727"><span class="lineNum">    2727 </span><span class="lineNoCov">          0 :                         ab[klnew + ab_dim1] = tmp1;</span></a>
+<a name="2728"><span class="lineNum">    2728 </span><span class="lineNoCov">          0 :                         nab[klnew + nab_dim1] = itmp1;</span></a>
+<a name="2729"><span class="lineNum">    2729 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = tmp1;</span></a>
+<a name="2730"><span class="lineNum">    2730 </span><span class="lineNoCov">          0 :                         nab[ji + (nab_dim1 &lt;&lt; 1)] = itmp1;</span></a>
+<a name="2731"><span class="lineNum">    2731 </span>            :                     } else {</a>
+<a name="2732"><span class="lineNum">    2732 </span><span class="lineNoCov">          0 :                         *info = *mmax + 1;</span></a>
+<a name="2733"><span class="lineNum">    2733 </span><span class="lineNoCov">          0 :                         return;</span></a>
+<a name="2734"><span class="lineNum">    2734 </span>            :                     }</a>
+<a name="2735"><span class="lineNum">    2735 </span>            :                 } else {</a>
+<a name="2736"><span class="lineNum">    2736 </span>            : </a>
+<a name="2737"><span class="lineNum">    2737 </span><span class="lineNoCov">          0 :                     if (itmp1 &lt;= nval[ji]) {</span></a>
+<a name="2738"><span class="lineNum">    2738 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = tmp1;</span></a>
+<a name="2739"><span class="lineNum">    2739 </span><span class="lineNoCov">          0 :                         nab[ji + nab_dim1] = itmp1;</span></a>
+<a name="2740"><span class="lineNum">    2740 </span>            :                     }</a>
+<a name="2741"><span class="lineNum">    2741 </span><span class="lineNoCov">          0 :                     if (itmp1 &gt;= nval[ji]) {</span></a>
+<a name="2742"><span class="lineNum">    2742 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = tmp1;</span></a>
+<a name="2743"><span class="lineNum">    2743 </span><span class="lineNoCov">          0 :                         nab[ji + (nab_dim1 &lt;&lt; 1)] = itmp1;</span></a>
+<a name="2744"><span class="lineNum">    2744 </span>            :                     }</a>
+<a name="2745"><span class="lineNum">    2745 </span>            :                 }</a>
+<a name="2746"><span class="lineNum">    2746 </span>            :             }</a>
+<a name="2747"><span class="lineNum">    2747 </span>            :             kl = klnew;</a>
+<a name="2748"><span class="lineNum">    2748 </span>            : </a>
+<a name="2749"><span class="lineNum">    2749 </span>            :         }</a>
+<a name="2750"><span class="lineNum">    2750 </span>            : </a>
+<a name="2751"><span class="lineNum">    2751 </span>            :         kfnew = kf;</a>
+<a name="2752"><span class="lineNum">    2752 </span>            :         i__2 = kl;</a>
+<a name="2753"><span class="lineNum">    2753 </span><span class="lineNoCov">          0 :         for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="2754"><span class="lineNum">    2754 </span><span class="lineNoCov">          0 :             tmp1 = std::abs(ab[ji + (ab_dim1 &lt;&lt; 1)] - ab[ji + ab_dim1]);</span></a>
+<a name="2755"><span class="lineNum">    2755 </span>            :             d__3 = std::abs(ab[ji + (ab_dim1 &lt;&lt; 1)]);</a>
+<a name="2756"><span class="lineNum">    2756 </span>            :             d__4 = std::abs(ab[ji + ab_dim1]);</a>
+<a name="2757"><span class="lineNum">    2757 </span><span class="lineNoCov">          0 :             tmp2 = (d__3&gt;d__4) ? d__3 : d__4;</span></a>
+<a name="2758"><span class="lineNum">    2758 </span><span class="lineNoCov">          0 :             d__1 = (*abstol&gt;*pivmin) ? *abstol : *pivmin;</span></a>
+<a name="2759"><span class="lineNum">    2759 </span><span class="lineNoCov">          0 :             d__2 = *reltol * tmp2;</span></a>
+<a name="2760"><span class="lineNum">    2760 </span><span class="lineNoCov">          0 :             if (tmp1 &lt; ((d__1&gt;d__2) ? d__1 : d__2) || nab[ji + nab_dim1] &gt;= nab[ji + (</span></a>
+<a name="2761"><span class="lineNum">    2761 </span><span class="lineNoCov">          0 :                     nab_dim1 &lt;&lt; 1)]) {</span></a>
+<a name="2762"><span class="lineNum">    2762 </span>            : </a>
+<a name="2763"><span class="lineNum">    2763 </span><span class="lineNoCov">          0 :                 if (ji &gt; kfnew) {</span></a>
+<a name="2764"><span class="lineNum">    2764 </span>            :                     tmp1 = ab[ji + ab_dim1];</a>
+<a name="2765"><span class="lineNum">    2765 </span>            :                     tmp2 = ab[ji + (ab_dim1 &lt;&lt; 1)];</a>
+<a name="2766"><span class="lineNum">    2766 </span><span class="lineNoCov">          0 :                     itmp1 = nab[ji + nab_dim1];</span></a>
+<a name="2767"><span class="lineNum">    2767 </span><span class="lineNoCov">          0 :                     itmp2 = nab[ji + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="2768"><span class="lineNum">    2768 </span><span class="lineNoCov">          0 :                     ab[ji + ab_dim1] = ab[kfnew + ab_dim1];</span></a>
+<a name="2769"><span class="lineNum">    2769 </span><span class="lineNoCov">          0 :                     ab[ji + (ab_dim1 &lt;&lt; 1)] = ab[kfnew + (ab_dim1 &lt;&lt; 1)];</span></a>
+<a name="2770"><span class="lineNum">    2770 </span><span class="lineNoCov">          0 :                     nab[ji + nab_dim1] = nab[kfnew + nab_dim1];</span></a>
+<a name="2771"><span class="lineNum">    2771 </span><span class="lineNoCov">          0 :                     nab[ji + (nab_dim1 &lt;&lt; 1)] = nab[kfnew + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="2772"><span class="lineNum">    2772 </span><span class="lineNoCov">          0 :                     ab[kfnew + ab_dim1] = tmp1;</span></a>
+<a name="2773"><span class="lineNum">    2773 </span><span class="lineNoCov">          0 :                     ab[kfnew + (ab_dim1 &lt;&lt; 1)] = tmp2;</span></a>
+<a name="2774"><span class="lineNum">    2774 </span><span class="lineNoCov">          0 :                     nab[kfnew + nab_dim1] = itmp1;</span></a>
+<a name="2775"><span class="lineNum">    2775 </span><span class="lineNoCov">          0 :                     nab[kfnew + (nab_dim1 &lt;&lt; 1)] = itmp2;</span></a>
+<a name="2776"><span class="lineNum">    2776 </span><span class="lineNoCov">          0 :                     if (*ijob == 3) {</span></a>
+<a name="2777"><span class="lineNum">    2777 </span><span class="lineNoCov">          0 :                         itmp1 = nval[ji];</span></a>
+<a name="2778"><span class="lineNum">    2778 </span><span class="lineNoCov">          0 :                         nval[ji] = nval[kfnew];</span></a>
+<a name="2779"><span class="lineNum">    2779 </span><span class="lineNoCov">          0 :                         nval[kfnew] = itmp1;</span></a>
+<a name="2780"><span class="lineNum">    2780 </span>            :                     }</a>
+<a name="2781"><span class="lineNum">    2781 </span>            :                 }</a>
+<a name="2782"><span class="lineNum">    2782 </span><span class="lineNoCov">          0 :                 ++kfnew;</span></a>
+<a name="2783"><span class="lineNum">    2783 </span>            :             }</a>
+<a name="2784"><span class="lineNum">    2784 </span>            :         }</a>
+<a name="2785"><span class="lineNum">    2785 </span>            :         kf = kfnew;</a>
+<a name="2786"><span class="lineNum">    2786 </span>            : </a>
+<a name="2787"><span class="lineNum">    2787 </span>            :         i__2 = kl;</a>
+<a name="2788"><span class="lineNum">    2788 </span><span class="lineNoCov">          0 :         for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="2789"><span class="lineNum">    2789 </span><span class="lineNoCov">          0 :             c__[ji] = (ab[ji + ab_dim1] + ab[ji + (ab_dim1 &lt;&lt; 1)]) * .5;</span></a>
+<a name="2790"><span class="lineNum">    2790 </span>            :         }</a>
+<a name="2791"><span class="lineNum">    2791 </span>            : </a>
+<a name="2792"><span class="lineNum">    2792 </span><span class="lineNoCov">          0 :         if (kf &gt; kl) {</span></a>
+<a name="2793"><span class="lineNum">    2793 </span>            :             break;</a>
+<a name="2794"><span class="lineNum">    2794 </span>            :         }</a>
+<a name="2795"><span class="lineNum">    2795 </span>            :     }</a>
+<a name="2796"><span class="lineNum">    2796 </span>            : </a>
+<a name="2797"><span class="lineNum">    2797 </span><span class="lineNoCov">          0 :     i__1 = kl + 1 - kf;</span></a>
+<a name="2798"><span class="lineNum">    2798 </span><span class="lineNoCov">          0 :     if(i__1&gt;0)</span></a>
+<a name="2799"><span class="lineNum">    2799 </span><span class="lineNoCov">          0 :       *info = i__1;</span></a>
+<a name="2800"><span class="lineNum">    2800 </span>            : </a>
+<a name="2801"><span class="lineNum">    2801 </span><span class="lineNoCov">          0 :     *mout = kl;</span></a>
+<a name="2802"><span class="lineNum">    2802 </span>            : </a>
+<a name="2803"><span class="lineNum">    2803 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="2804"><span class="lineNum">    2804 </span>            : </a>
+<a name="2805"><span class="lineNum">    2805 </span>            : }</a>
+<a name="2806"><span class="lineNum">    2806 </span>            : </a>
+<a name="2807"><span class="lineNum">    2807 </span>            : </a>
+<a name="2808"><span class="lineNum">    2808 </span>            : }</a>
+<a name="2809"><span class="lineNum">    2809 </span>            : }</a>
+<a name="2810"><span class="lineNum">    2810 </span>            : #include &lt;cmath&gt;</a>
+<a name="2811"><span class="lineNum">    2811 </span>            : </a>
+<a name="2812"><span class="lineNum">    2812 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="2813"><span class="lineNum">    2813 </span>            : </a>
+<a name="2814"><span class="lineNum">    2814 </span>            : #include &quot;real.h&quot;</a>
+<a name="2815"><span class="lineNum">    2815 </span>            : </a>
+<a name="2816"><span class="lineNum">    2816 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="2817"><span class="lineNum">    2817 </span>            : namespace PLMD{</a>
+<a name="2818"><span class="lineNum">    2818 </span>            : namespace lapack{</a>
+<a name="2819"><span class="lineNum">    2819 </span>            : using namespace blas;</a>
+<a name="2820"><span class="lineNum">    2820 </span>            : void</a>
+<a name="2821"><span class="lineNum">    2821 </span><span class="lineCov">       1387 : PLUMED_BLAS_F77_FUNC(dlaed6,DLAED6)(int *kniter, </span></a>
+<a name="2822"><span class="lineNum">    2822 </span>            :                         int *orgati, </a>
+<a name="2823"><span class="lineNum">    2823 </span>            :                         double *rho, </a>
+<a name="2824"><span class="lineNum">    2824 </span>            :                         double *d__,</a>
+<a name="2825"><span class="lineNum">    2825 </span>            :                         double *z__, </a>
+<a name="2826"><span class="lineNum">    2826 </span>            :                         double *finit, </a>
+<a name="2827"><span class="lineNum">    2827 </span>            :                         double *tau, </a>
+<a name="2828"><span class="lineNum">    2828 </span>            :                         int *info)</a>
+<a name="2829"><span class="lineNum">    2829 </span>            : {</a>
+<a name="2830"><span class="lineNum">    2830 </span>            :     int i__1;</a>
+<a name="2831"><span class="lineNum">    2831 </span>            :     double r__1, r__2, r__3, r__4;</a>
+<a name="2832"><span class="lineNum">    2832 </span>            : </a>
+<a name="2833"><span class="lineNum">    2833 </span>            :     double a, b, c__, f;</a>
+<a name="2834"><span class="lineNum">    2834 </span>            :     int i__;</a>
+<a name="2835"><span class="lineNum">    2835 </span>            :     double fc, df, ddf, eta, eps, base;</a>
+<a name="2836"><span class="lineNum">    2836 </span>            :     int iter;</a>
+<a name="2837"><span class="lineNum">    2837 </span>            :     double temp, temp1, temp2, temp3, temp4;</a>
+<a name="2838"><span class="lineNum">    2838 </span>            :     int scale;</a>
+<a name="2839"><span class="lineNum">    2839 </span>            :     int niter;</a>
+<a name="2840"><span class="lineNum">    2840 </span>            :     double small1, small2, sminv1, sminv2, dscale[3], sclfac;</a>
+<a name="2841"><span class="lineNum">    2841 </span>            :     double zscale[3], erretm;</a>
+<a name="2842"><span class="lineNum">    2842 </span>            :     double safemin;</a>
+<a name="2843"><span class="lineNum">    2843 </span>            :     double sclinv = 0;</a>
+<a name="2844"><span class="lineNum">    2844 </span>            :     </a>
+<a name="2845"><span class="lineNum">    2845 </span><span class="lineCov">       1387 :     --z__;</span></a>
+<a name="2846"><span class="lineNum">    2846 </span><span class="lineCov">       1387 :     --d__;</span></a>
+<a name="2847"><span class="lineNum">    2847 </span>            : </a>
+<a name="2848"><span class="lineNum">    2848 </span><span class="lineCov">       1387 :     *info = 0;</span></a>
+<a name="2849"><span class="lineNum">    2849 </span>            : </a>
+<a name="2850"><span class="lineNum">    2850 </span>            :     niter = 1;</a>
+<a name="2851"><span class="lineNum">    2851 </span><span class="lineCov">       1387 :     *tau = 0.f;</span></a>
+<a name="2852"><span class="lineNum">    2852 </span><span class="lineCov">       1387 :     if (*kniter == 2) {</span></a>
+<a name="2853"><span class="lineNum">    2853 </span><span class="lineCov">        342 :         if (*orgati) {</span></a>
+<a name="2854"><span class="lineNum">    2854 </span><span class="lineCov">        173 :             temp = (d__[3] - d__[2]) / 2.f;</span></a>
+<a name="2855"><span class="lineNum">    2855 </span><span class="lineCov">        173 :             c__ = *rho + z__[1] / (d__[1] - d__[2] - temp);</span></a>
+<a name="2856"><span class="lineNum">    2856 </span><span class="lineCov">        173 :             a = c__ * (d__[2] + d__[3]) + z__[2] + z__[3];</span></a>
+<a name="2857"><span class="lineNum">    2857 </span><span class="lineCov">        173 :             b = c__ * d__[2] * d__[3] + z__[2] * d__[3] + z__[3] * d__[2];</span></a>
+<a name="2858"><span class="lineNum">    2858 </span>            :         } else {</a>
+<a name="2859"><span class="lineNum">    2859 </span><span class="lineCov">        169 :             temp = (d__[1] - d__[2]) / 2.f;</span></a>
+<a name="2860"><span class="lineNum">    2860 </span><span class="lineCov">        169 :             c__ = *rho + z__[3] / (d__[3] - d__[2] - temp);</span></a>
+<a name="2861"><span class="lineNum">    2861 </span><span class="lineCov">        169 :             a = c__ * (d__[1] + d__[2]) + z__[1] + z__[2];</span></a>
+<a name="2862"><span class="lineNum">    2862 </span><span class="lineCov">        169 :             b = c__ * d__[1] * d__[2] + z__[1] * d__[2] + z__[2] * d__[1];</span></a>
+<a name="2863"><span class="lineNum">    2863 </span>            :         }</a>
+<a name="2864"><span class="lineNum">    2864 </span><span class="lineCov">        342 :         r__1 = std::abs(a), r__2 = std::abs(b), r__1 = ((r__1&gt;r__2)? r__1:r__2), r__2 = std::abs(c__);</span></a>
+<a name="2865"><span class="lineNum">    2865 </span><span class="lineCov">        342 :         temp = (r__1&gt;r__2) ? r__1 : r__2;</span></a>
+<a name="2866"><span class="lineNum">    2866 </span><span class="lineCov">        342 :         a /= temp;</span></a>
+<a name="2867"><span class="lineNum">    2867 </span><span class="lineCov">        342 :         b /= temp;</span></a>
+<a name="2868"><span class="lineNum">    2868 </span><span class="lineCov">        342 :         c__ /= temp;</span></a>
+<a name="2869"><span class="lineNum">    2869 </span><span class="lineCov">        342 :         if (c__ == 0.f) {</span></a>
+<a name="2870"><span class="lineNum">    2870 </span><span class="lineNoCov">          0 :             *tau = b / a;</span></a>
+<a name="2871"><span class="lineNum">    2871 </span><span class="lineCov">        342 :         } else if (a &lt;= 0.f) {</span></a>
+<a name="2872"><span class="lineNum">    2872 </span><span class="lineCov">        113 :             *tau = (a -  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs(r__1)))) / (</span></a>
+<a name="2873"><span class="lineNum">    2873 </span><span class="lineCov">        113 :                     c__ * 2.f);</span></a>
+<a name="2874"><span class="lineNum">    2874 </span>            :         } else {</a>
+<a name="2875"><span class="lineNum">    2875 </span><span class="lineCov">        229 :             *tau = b * 2.f / (a +  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs(r__1))));</span></a>
+<a name="2876"><span class="lineNum">    2876 </span>            :         }</a>
+<a name="2877"><span class="lineNum">    2877 </span>            : </a>
+<a name="2878"><span class="lineNum">    2878 </span><span class="lineCov">        342 :         temp = *rho + z__[1] / (d__[1] - *tau) + z__[2] / (d__[2] - *tau) + </span></a>
+<a name="2879"><span class="lineNum">    2879 </span><span class="lineCov">        342 :                 z__[3] / (d__[3] - *tau);</span></a>
+<a name="2880"><span class="lineNum">    2880 </span><span class="lineCov">        342 :         if (std::abs(*finit) &lt;= std::abs(temp)) {</span></a>
+<a name="2881"><span class="lineNum">    2881 </span><span class="lineNoCov">          0 :             *tau = 0.f;</span></a>
+<a name="2882"><span class="lineNum">    2882 </span>            :         }</a>
+<a name="2883"><span class="lineNum">    2883 </span>            :     }</a>
+<a name="2884"><span class="lineNum">    2884 </span>            : </a>
+<a name="2885"><span class="lineNum">    2885 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="2886"><span class="lineNum">    2886 </span>            :     base = 2;</a>
+<a name="2887"><span class="lineNum">    2887 </span>            :     safemin = PLUMED_GMX_DOUBLE_MIN*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="2888"><span class="lineNum">    2888 </span>            :     i__1 = static_cast&lt;int&gt;(std::log(safemin) / std::log(base) / 3.f);</a>
+<a name="2889"><span class="lineNum">    2889 </span>            :     small1 = std::pow(base, static_cast&lt;double&gt;(i__1));</a>
+<a name="2890"><span class="lineNum">    2890 </span>            :     sminv1 = 1.f / small1;</a>
+<a name="2891"><span class="lineNum">    2891 </span>            :     small2 = small1 * small1;</a>
+<a name="2892"><span class="lineNum">    2892 </span>            :     sminv2 = sminv1 * sminv1;</a>
+<a name="2893"><span class="lineNum">    2893 </span>            : </a>
+<a name="2894"><span class="lineNum">    2894 </span><span class="lineCov">       1387 :     if (*orgati) {</span></a>
+<a name="2895"><span class="lineNum">    2895 </span><span class="lineCov">        706 :         r__3 = (r__1 = d__[2] - *tau, std::abs(r__1)), r__4 = (r__2 = d__[3] - *</span></a>
+<a name="2896"><span class="lineNum">    2896 </span>            :                 tau, std::abs(r__2));</a>
+<a name="2897"><span class="lineNum">    2897 </span><span class="lineCov">        706 :         temp = (r__3&lt;r__4) ? r__3 : r__4;</span></a>
+<a name="2898"><span class="lineNum">    2898 </span>            :     } else {</a>
+<a name="2899"><span class="lineNum">    2899 </span><span class="lineCov">        681 :         r__3 = (r__1 = d__[1] - *tau, std::abs(r__1)), r__4 = (r__2 = d__[2] - *</span></a>
+<a name="2900"><span class="lineNum">    2900 </span>            :                 tau, std::abs(r__2));</a>
+<a name="2901"><span class="lineNum">    2901 </span><span class="lineCov">        681 :         temp = (r__3&lt;r__4) ? r__3 : r__4;</span></a>
+<a name="2902"><span class="lineNum">    2902 </span>            :     }</a>
+<a name="2903"><span class="lineNum">    2903 </span>            :     scale = 0;</a>
+<a name="2904"><span class="lineNum">    2904 </span><span class="lineCov">       1387 :     if (temp &lt;= small1) {</span></a>
+<a name="2905"><span class="lineNum">    2905 </span>            :         scale = 1;</a>
+<a name="2906"><span class="lineNum">    2906 </span><span class="lineNoCov">          0 :         if (temp &lt;= small2) {</span></a>
+<a name="2907"><span class="lineNum">    2907 </span>            : </a>
+<a name="2908"><span class="lineNum">    2908 </span>            :             sclfac = sminv2;</a>
+<a name="2909"><span class="lineNum">    2909 </span>            :             sclinv = small2;</a>
+<a name="2910"><span class="lineNum">    2910 </span>            :         } else {</a>
+<a name="2911"><span class="lineNum">    2911 </span>            : </a>
+<a name="2912"><span class="lineNum">    2912 </span>            :             sclfac = sminv1;</a>
+<a name="2913"><span class="lineNum">    2913 </span>            :             sclinv = small1;</a>
+<a name="2914"><span class="lineNum">    2914 </span>            : </a>
+<a name="2915"><span class="lineNum">    2915 </span>            :         }</a>
+<a name="2916"><span class="lineNum">    2916 </span>            : </a>
+<a name="2917"><span class="lineNum">    2917 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="2918"><span class="lineNum">    2918 </span><span class="lineNoCov">          0 :             dscale[i__ - 1] = d__[i__] * sclfac;</span></a>
+<a name="2919"><span class="lineNum">    2919 </span><span class="lineNoCov">          0 :             zscale[i__ - 1] = z__[i__] * sclfac;</span></a>
+<a name="2920"><span class="lineNum">    2920 </span>            :         }</a>
+<a name="2921"><span class="lineNum">    2921 </span><span class="lineNoCov">          0 :         *tau *= sclfac;</span></a>
+<a name="2922"><span class="lineNum">    2922 </span>            :     } else {</a>
+<a name="2923"><span class="lineNum">    2923 </span>            : </a>
+<a name="2924"><span class="lineNum">    2924 </span><span class="lineCov">       5548 :         for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="2925"><span class="lineNum">    2925 </span><span class="lineCov">       4161 :             dscale[i__ - 1] = d__[i__];</span></a>
+<a name="2926"><span class="lineNum">    2926 </span><span class="lineCov">       4161 :             zscale[i__ - 1] = z__[i__];</span></a>
+<a name="2927"><span class="lineNum">    2927 </span>            :         }</a>
+<a name="2928"><span class="lineNum">    2928 </span>            :     }</a>
+<a name="2929"><span class="lineNum">    2929 </span>            :     fc = 0.f;</a>
+<a name="2930"><span class="lineNum">    2930 </span>            :     df = 0.f;</a>
+<a name="2931"><span class="lineNum">    2931 </span>            :     ddf = 0.f;</a>
+<a name="2932"><span class="lineNum">    2932 </span><span class="lineCov">       5548 :     for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="2933"><span class="lineNum">    2933 </span><span class="lineCov">       4161 :         temp = 1.f / (dscale[i__ - 1] - *tau);</span></a>
+<a name="2934"><span class="lineNum">    2934 </span><span class="lineCov">       4161 :         temp1 = zscale[i__ - 1] * temp;</span></a>
+<a name="2935"><span class="lineNum">    2935 </span><span class="lineCov">       4161 :         temp2 = temp1 * temp;</span></a>
+<a name="2936"><span class="lineNum">    2936 </span><span class="lineCov">       4161 :         temp3 = temp2 * temp;</span></a>
+<a name="2937"><span class="lineNum">    2937 </span><span class="lineCov">       4161 :         fc += temp1 / dscale[i__ - 1];</span></a>
+<a name="2938"><span class="lineNum">    2938 </span><span class="lineCov">       4161 :         df += temp2;</span></a>
+<a name="2939"><span class="lineNum">    2939 </span><span class="lineCov">       4161 :         ddf += temp3;</span></a>
+<a name="2940"><span class="lineNum">    2940 </span>            :     }</a>
+<a name="2941"><span class="lineNum">    2941 </span><span class="lineCov">       1387 :     f = *finit + *tau * fc;</span></a>
+<a name="2942"><span class="lineNum">    2942 </span>            : </a>
+<a name="2943"><span class="lineNum">    2943 </span><span class="lineCov">       1387 :     if (std::abs(f) &lt;= 0.f) {</span></a>
+<a name="2944"><span class="lineNum">    2944 </span><span class="lineNoCov">          0 :         goto L60;</span></a>
+<a name="2945"><span class="lineNum">    2945 </span>            :     }</a>
+<a name="2946"><span class="lineNum">    2946 </span>            :     iter = niter + 1;</a>
+<a name="2947"><span class="lineNum">    2947 </span><span class="lineCov">       2782 :     for (niter = iter; niter &lt;= 20; ++niter) {</span></a>
+<a name="2948"><span class="lineNum">    2948 </span><span class="lineCov">       2782 :         if (*orgati) {</span></a>
+<a name="2949"><span class="lineNum">    2949 </span><span class="lineCov">       1436 :             temp1 = dscale[1] - *tau;</span></a>
+<a name="2950"><span class="lineNum">    2950 </span><span class="lineCov">       1436 :             temp2 = dscale[2] - *tau;</span></a>
+<a name="2951"><span class="lineNum">    2951 </span>            :         } else {</a>
+<a name="2952"><span class="lineNum">    2952 </span><span class="lineCov">       1346 :             temp1 = dscale[0] - *tau;</span></a>
+<a name="2953"><span class="lineNum">    2953 </span><span class="lineCov">       1346 :             temp2 = dscale[1] - *tau;</span></a>
+<a name="2954"><span class="lineNum">    2954 </span>            :         }</a>
+<a name="2955"><span class="lineNum">    2955 </span><span class="lineCov">       2782 :         a = (temp1 + temp2) * f - temp1 * temp2 * df;</span></a>
+<a name="2956"><span class="lineNum">    2956 </span><span class="lineCov">       2782 :         b = temp1 * temp2 * f;</span></a>
+<a name="2957"><span class="lineNum">    2957 </span><span class="lineCov">       2782 :         c__ = f - (temp1 + temp2) * df + temp1 * temp2 * ddf;</span></a>
+<a name="2958"><span class="lineNum">    2958 </span><span class="lineCov">       2782 :         r__1 = std::abs(a), r__2 = std::abs(b), r__1 = ((r__1&gt;r__2)? r__1:r__2), r__2 = std::abs(c__);</span></a>
+<a name="2959"><span class="lineNum">    2959 </span><span class="lineCov">       2782 :         temp = (r__1&gt;r__2) ? r__1 : r__2;</span></a>
+<a name="2960"><span class="lineNum">    2960 </span><span class="lineCov">       2782 :         a /= temp;</span></a>
+<a name="2961"><span class="lineNum">    2961 </span><span class="lineCov">       2782 :         b /= temp;</span></a>
+<a name="2962"><span class="lineNum">    2962 </span><span class="lineCov">       2782 :         c__ /= temp;</span></a>
+<a name="2963"><span class="lineNum">    2963 </span><span class="lineCov">       2782 :         if (c__ == 0.f) {</span></a>
+<a name="2964"><span class="lineNum">    2964 </span><span class="lineNoCov">          0 :             eta = b / a;</span></a>
+<a name="2965"><span class="lineNum">    2965 </span><span class="lineCov">       2782 :         } else if (a &lt;= 0.f) {</span></a>
+<a name="2966"><span class="lineNum">    2966 </span><span class="lineCov">         46 :             eta = (a -  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs(r__1)))) / ( c__ * 2.f);</span></a>
+<a name="2967"><span class="lineNum">    2967 </span>            :         } else {</a>
+<a name="2968"><span class="lineNum">    2968 </span><span class="lineCov">       2736 :             eta = b * 2.f / (a +  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs( r__1))));</span></a>
+<a name="2969"><span class="lineNum">    2969 </span>            :         }</a>
+<a name="2970"><span class="lineNum">    2970 </span><span class="lineCov">       2782 :         if (f * eta &gt;= 0.f) {</span></a>
+<a name="2971"><span class="lineNum">    2971 </span><span class="lineNoCov">          0 :             eta = -f / df;</span></a>
+<a name="2972"><span class="lineNum">    2972 </span>            :         }</a>
+<a name="2973"><span class="lineNum">    2973 </span><span class="lineCov">       2782 :         temp = eta + *tau;</span></a>
+<a name="2974"><span class="lineNum">    2974 </span><span class="lineCov">       2782 :         if (*orgati) {</span></a>
+<a name="2975"><span class="lineNum">    2975 </span><span class="lineCov">       1436 :             if (eta &gt; 0.f &amp;&amp; temp &gt;= dscale[2]) {</span></a>
+<a name="2976"><span class="lineNum">    2976 </span><span class="lineNoCov">          0 :                 eta = (dscale[2] - *tau) / 2.f;</span></a>
+<a name="2977"><span class="lineNum">    2977 </span>            :             }</a>
+<a name="2978"><span class="lineNum">    2978 </span>            : </a>
+<a name="2979"><span class="lineNum">    2979 </span><span class="lineCov">       1436 :             if (eta &lt; 0.f &amp;&amp; temp &lt;= dscale[1]) {</span></a>
+<a name="2980"><span class="lineNum">    2980 </span><span class="lineNoCov">          0 :                 eta = (dscale[1] - *tau) / 2.f;</span></a>
+<a name="2981"><span class="lineNum">    2981 </span>            :             }</a>
+<a name="2982"><span class="lineNum">    2982 </span>            :         } else {</a>
+<a name="2983"><span class="lineNum">    2983 </span><span class="lineCov">       1346 :             if (eta &gt; 0.f &amp;&amp; temp &gt;= dscale[1]) {</span></a>
+<a name="2984"><span class="lineNum">    2984 </span><span class="lineNoCov">          0 :                 eta = (dscale[1] - *tau) / 2.f;</span></a>
+<a name="2985"><span class="lineNum">    2985 </span>            :             }</a>
+<a name="2986"><span class="lineNum">    2986 </span><span class="lineCov">       1346 :             if (eta &lt; 0.f &amp;&amp; temp &lt;= dscale[0]) {</span></a>
+<a name="2987"><span class="lineNum">    2987 </span><span class="lineNoCov">          0 :                 eta = (dscale[0] - *tau) / 2.f;</span></a>
+<a name="2988"><span class="lineNum">    2988 </span>            :             }</a>
+<a name="2989"><span class="lineNum">    2989 </span>            :         }</a>
+<a name="2990"><span class="lineNum">    2990 </span><span class="lineCov">       2782 :         *tau += eta;</span></a>
+<a name="2991"><span class="lineNum">    2991 </span>            :         fc = 0.f;</a>
+<a name="2992"><span class="lineNum">    2992 </span>            :         erretm = 0.f;</a>
+<a name="2993"><span class="lineNum">    2993 </span>            :         df = 0.f;</a>
+<a name="2994"><span class="lineNum">    2994 </span>            :         ddf = 0.f;</a>
+<a name="2995"><span class="lineNum">    2995 </span><span class="lineCov">      11128 :         for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="2996"><span class="lineNum">    2996 </span><span class="lineCov">       8346 :             temp = 1.f / (dscale[i__ - 1] - *tau);</span></a>
+<a name="2997"><span class="lineNum">    2997 </span><span class="lineCov">       8346 :             temp1 = zscale[i__ - 1] * temp;</span></a>
+<a name="2998"><span class="lineNum">    2998 </span><span class="lineCov">       8346 :             temp2 = temp1 * temp;</span></a>
+<a name="2999"><span class="lineNum">    2999 </span><span class="lineCov">       8346 :             temp3 = temp2 * temp;</span></a>
+<a name="3000"><span class="lineNum">    3000 </span><span class="lineCov">       8346 :             temp4 = temp1 / dscale[i__ - 1];</span></a>
+<a name="3001"><span class="lineNum">    3001 </span><span class="lineCov">       8346 :             fc += temp4;</span></a>
+<a name="3002"><span class="lineNum">    3002 </span><span class="lineCov">       8346 :             erretm += std::abs(temp4);</span></a>
+<a name="3003"><span class="lineNum">    3003 </span><span class="lineCov">       8346 :             df += temp2;</span></a>
+<a name="3004"><span class="lineNum">    3004 </span><span class="lineCov">       8346 :             ddf += temp3;</span></a>
+<a name="3005"><span class="lineNum">    3005 </span>            :         }</a>
+<a name="3006"><span class="lineNum">    3006 </span><span class="lineCov">       2782 :         f = *finit + *tau * fc;</span></a>
+<a name="3007"><span class="lineNum">    3007 </span><span class="lineCov">       2782 :         erretm = (std::abs(*finit) + std::abs(*tau) * erretm) * 8.f + std::abs(*tau) * df;</span></a>
+<a name="3008"><span class="lineNum">    3008 </span><span class="lineCov">       2782 :         if (std::abs(f) &lt;= eps * erretm) {</span></a>
+<a name="3009"><span class="lineNum">    3009 </span><span class="lineCov">       1387 :             goto L60;</span></a>
+<a name="3010"><span class="lineNum">    3010 </span>            :         }</a>
+<a name="3011"><span class="lineNum">    3011 </span>            :     }</a>
+<a name="3012"><span class="lineNum">    3012 </span><span class="lineNoCov">          0 :     *info = 1;</span></a>
+<a name="3013"><span class="lineNum">    3013 </span><span class="lineCov">       1387 : L60:</span></a>
+<a name="3014"><span class="lineNum">    3014 </span><span class="lineCov">       1387 :     if (scale) {</span></a>
+<a name="3015"><span class="lineNum">    3015 </span><span class="lineNoCov">          0 :         *tau *= sclinv;</span></a>
+<a name="3016"><span class="lineNum">    3016 </span>            :     }</a>
+<a name="3017"><span class="lineNum">    3017 </span><span class="lineCov">       1387 :     return;</span></a>
+<a name="3018"><span class="lineNum">    3018 </span>            : } </a>
+<a name="3019"><span class="lineNum">    3019 </span>            : </a>
+<a name="3020"><span class="lineNum">    3020 </span>            : </a>
+<a name="3021"><span class="lineNum">    3021 </span>            : }</a>
+<a name="3022"><span class="lineNum">    3022 </span>            : }</a>
+<a name="3023"><span class="lineNum">    3023 </span>            : #include &lt;cmath&gt;</a>
+<a name="3024"><span class="lineNum">    3024 </span>            : #include &quot;real.h&quot;</a>
+<a name="3025"><span class="lineNum">    3025 </span>            : </a>
+<a name="3026"><span class="lineNum">    3026 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3027"><span class="lineNum">    3027 </span>            : </a>
+<a name="3028"><span class="lineNum">    3028 </span>            : </a>
+<a name="3029"><span class="lineNum">    3029 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3030"><span class="lineNum">    3030 </span>            : namespace PLMD{</a>
+<a name="3031"><span class="lineNum">    3031 </span>            : namespace lapack{</a>
+<a name="3032"><span class="lineNum">    3032 </span>            : using namespace blas;</a>
+<a name="3033"><span class="lineNum">    3033 </span>            : void</a>
+<a name="3034"><span class="lineNum">    3034 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlaev2,DLAEV2)(double *   a, </span></a>
+<a name="3035"><span class="lineNum">    3035 </span>            :         double *   b, </a>
+<a name="3036"><span class="lineNum">    3036 </span>            :         double *   c__, </a>
+<a name="3037"><span class="lineNum">    3037 </span>            :         double *   rt1, </a>
+<a name="3038"><span class="lineNum">    3038 </span>            :         double *   rt2, </a>
+<a name="3039"><span class="lineNum">    3039 </span>            :         double *   cs1, </a>
+<a name="3040"><span class="lineNum">    3040 </span>            :         double *   sn1)</a>
+<a name="3041"><span class="lineNum">    3041 </span>            : {</a>
+<a name="3042"><span class="lineNum">    3042 </span>            :     double d__1;</a>
+<a name="3043"><span class="lineNum">    3043 </span>            : </a>
+<a name="3044"><span class="lineNum">    3044 </span>            :     double ab, df, cs, ct, tb, sm, tn, rt, adf, acs;</a>
+<a name="3045"><span class="lineNum">    3045 </span>            :     int sgn1, sgn2;</a>
+<a name="3046"><span class="lineNum">    3046 </span>            :     double acmn, acmx;</a>
+<a name="3047"><span class="lineNum">    3047 </span>            : </a>
+<a name="3048"><span class="lineNum">    3048 </span><span class="lineNoCov">          0 :     sm = *a + *c__;</span></a>
+<a name="3049"><span class="lineNum">    3049 </span><span class="lineNoCov">          0 :     df = *a - *c__;</span></a>
+<a name="3050"><span class="lineNum">    3050 </span>            :     adf = std::abs(df);</a>
+<a name="3051"><span class="lineNum">    3051 </span><span class="lineNoCov">          0 :     tb = *b + *b;</span></a>
+<a name="3052"><span class="lineNum">    3052 </span>            :     ab = std::abs(tb);</a>
+<a name="3053"><span class="lineNum">    3053 </span><span class="lineNoCov">          0 :     if (std::abs(*a) &gt; std::abs(*c__)) {</span></a>
+<a name="3054"><span class="lineNum">    3054 </span>            :         acmx = *a;</a>
+<a name="3055"><span class="lineNum">    3055 </span>            :         acmn = *c__;</a>
+<a name="3056"><span class="lineNum">    3056 </span>            :     } else {</a>
+<a name="3057"><span class="lineNum">    3057 </span>            :         acmx = *c__;</a>
+<a name="3058"><span class="lineNum">    3058 </span>            :         acmn = *a;</a>
+<a name="3059"><span class="lineNum">    3059 </span>            :     }</a>
+<a name="3060"><span class="lineNum">    3060 </span><span class="lineNoCov">          0 :     if (adf &gt; ab) {</span></a>
+<a name="3061"><span class="lineNum">    3061 </span><span class="lineNoCov">          0 :         d__1 = ab / adf;</span></a>
+<a name="3062"><span class="lineNum">    3062 </span><span class="lineNoCov">          0 :         rt = adf *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="3063"><span class="lineNum">    3063 </span><span class="lineNoCov">          0 :     } else if (adf &lt; ab) {</span></a>
+<a name="3064"><span class="lineNum">    3064 </span><span class="lineNoCov">          0 :         d__1 = adf / ab;</span></a>
+<a name="3065"><span class="lineNum">    3065 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="3066"><span class="lineNum">    3066 </span>            :     } else {</a>
+<a name="3067"><span class="lineNum">    3067 </span>            : </a>
+<a name="3068"><span class="lineNum">    3068 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(2.);</span></a>
+<a name="3069"><span class="lineNum">    3069 </span>            :     }</a>
+<a name="3070"><span class="lineNum">    3070 </span><span class="lineNoCov">          0 :     if (sm &lt; 0.) {</span></a>
+<a name="3071"><span class="lineNum">    3071 </span><span class="lineNoCov">          0 :         *rt1 = (sm - rt) * .5;</span></a>
+<a name="3072"><span class="lineNum">    3072 </span>            :         sgn1 = -1;</a>
+<a name="3073"><span class="lineNum">    3073 </span>            : </a>
+<a name="3074"><span class="lineNum">    3074 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="3075"><span class="lineNum">    3075 </span><span class="lineNoCov">          0 :     } else if (sm &gt; 0.) {</span></a>
+<a name="3076"><span class="lineNum">    3076 </span><span class="lineNoCov">          0 :         *rt1 = (sm + rt) * .5;</span></a>
+<a name="3077"><span class="lineNum">    3077 </span>            :         sgn1 = 1;</a>
+<a name="3078"><span class="lineNum">    3078 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="3079"><span class="lineNum">    3079 </span>            :     } else {</a>
+<a name="3080"><span class="lineNum">    3080 </span><span class="lineNoCov">          0 :         *rt1 = rt * .5;</span></a>
+<a name="3081"><span class="lineNum">    3081 </span><span class="lineNoCov">          0 :         *rt2 = rt * -.5;</span></a>
+<a name="3082"><span class="lineNum">    3082 </span>            :         sgn1 = 1;</a>
+<a name="3083"><span class="lineNum">    3083 </span>            :     }</a>
+<a name="3084"><span class="lineNum">    3084 </span><span class="lineNoCov">          0 :     if (df &gt;= 0.) {</span></a>
+<a name="3085"><span class="lineNum">    3085 </span><span class="lineNoCov">          0 :         cs = df + rt;</span></a>
+<a name="3086"><span class="lineNum">    3086 </span>            :         sgn2 = 1;</a>
+<a name="3087"><span class="lineNum">    3087 </span>            :     } else {</a>
+<a name="3088"><span class="lineNum">    3088 </span><span class="lineNoCov">          0 :         cs = df - rt;</span></a>
+<a name="3089"><span class="lineNum">    3089 </span>            :         sgn2 = -1;</a>
+<a name="3090"><span class="lineNum">    3090 </span>            :     }</a>
+<a name="3091"><span class="lineNum">    3091 </span>            :     acs = std::abs(cs);</a>
+<a name="3092"><span class="lineNum">    3092 </span><span class="lineNoCov">          0 :     if (acs &gt; ab) {</span></a>
+<a name="3093"><span class="lineNum">    3093 </span><span class="lineNoCov">          0 :         ct = -tb / cs;</span></a>
+<a name="3094"><span class="lineNum">    3094 </span><span class="lineNoCov">          0 :         *sn1 = 1. /  std::sqrt(ct * ct + 1.);</span></a>
+<a name="3095"><span class="lineNum">    3095 </span><span class="lineNoCov">          0 :         *cs1 = ct * *sn1;</span></a>
+<a name="3096"><span class="lineNum">    3096 </span>            :     } else {</a>
+<a name="3097"><span class="lineNum">    3097 </span><span class="lineNoCov">          0 :         if (std::abs(ab)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3098"><span class="lineNum">    3098 </span><span class="lineNoCov">          0 :             *cs1 = 1.;</span></a>
+<a name="3099"><span class="lineNum">    3099 </span><span class="lineNoCov">          0 :             *sn1 = 0.;</span></a>
+<a name="3100"><span class="lineNum">    3100 </span>            :         } else {</a>
+<a name="3101"><span class="lineNum">    3101 </span><span class="lineNoCov">          0 :             tn = -cs / tb;</span></a>
+<a name="3102"><span class="lineNum">    3102 </span><span class="lineNoCov">          0 :             *cs1 = 1. /  std::sqrt(tn * tn + 1.);</span></a>
+<a name="3103"><span class="lineNum">    3103 </span><span class="lineNoCov">          0 :             *sn1 = tn * *cs1;</span></a>
+<a name="3104"><span class="lineNum">    3104 </span>            :         }</a>
+<a name="3105"><span class="lineNum">    3105 </span>            :     }</a>
+<a name="3106"><span class="lineNum">    3106 </span><span class="lineNoCov">          0 :     if (sgn1 == sgn2) {</span></a>
+<a name="3107"><span class="lineNum">    3107 </span><span class="lineNoCov">          0 :         tn = *cs1;</span></a>
+<a name="3108"><span class="lineNum">    3108 </span><span class="lineNoCov">          0 :         *cs1 = -(*sn1);</span></a>
+<a name="3109"><span class="lineNum">    3109 </span><span class="lineNoCov">          0 :         *sn1 = tn;</span></a>
+<a name="3110"><span class="lineNum">    3110 </span>            :     }</a>
+<a name="3111"><span class="lineNum">    3111 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="3112"><span class="lineNum">    3112 </span>            : </a>
+<a name="3113"><span class="lineNum">    3113 </span>            : }</a>
+<a name="3114"><span class="lineNum">    3114 </span>            : </a>
+<a name="3115"><span class="lineNum">    3115 </span>            : </a>
+<a name="3116"><span class="lineNum">    3116 </span>            : }</a>
+<a name="3117"><span class="lineNum">    3117 </span>            : }</a>
+<a name="3118"><span class="lineNum">    3118 </span>            : #include &lt;cmath&gt;</a>
+<a name="3119"><span class="lineNum">    3119 </span>            : #include &quot;real.h&quot;</a>
+<a name="3120"><span class="lineNum">    3120 </span>            : </a>
+<a name="3121"><span class="lineNum">    3121 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3122"><span class="lineNum">    3122 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="3123"><span class="lineNum">    3123 </span>            : </a>
+<a name="3124"><span class="lineNum">    3124 </span>            : </a>
+<a name="3125"><span class="lineNum">    3125 </span>            : </a>
+<a name="3126"><span class="lineNum">    3126 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3127"><span class="lineNum">    3127 </span>            : namespace PLMD{</a>
+<a name="3128"><span class="lineNum">    3128 </span>            : namespace lapack{</a>
+<a name="3129"><span class="lineNum">    3129 </span>            : using namespace blas;</a>
+<a name="3130"><span class="lineNum">    3130 </span>            : void</a>
+<a name="3131"><span class="lineNum">    3131 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlagtf,DLAGTF)(int *n, </span></a>
+<a name="3132"><span class="lineNum">    3132 </span>            :         double *a, </a>
+<a name="3133"><span class="lineNum">    3133 </span>            :         double *lambda, </a>
+<a name="3134"><span class="lineNum">    3134 </span>            :         double *b, </a>
+<a name="3135"><span class="lineNum">    3135 </span>            :         double *c__, </a>
+<a name="3136"><span class="lineNum">    3136 </span>            :         double *tol, </a>
+<a name="3137"><span class="lineNum">    3137 </span>            :         double *d__, </a>
+<a name="3138"><span class="lineNum">    3138 </span>            :         int *in, </a>
+<a name="3139"><span class="lineNum">    3139 </span>            :         int *info)</a>
+<a name="3140"><span class="lineNum">    3140 </span>            : {</a>
+<a name="3141"><span class="lineNum">    3141 </span>            :     int i__1;</a>
+<a name="3142"><span class="lineNum">    3142 </span>            : </a>
+<a name="3143"><span class="lineNum">    3143 </span>            :     int k;</a>
+<a name="3144"><span class="lineNum">    3144 </span>            :     double tl, eps, piv1, piv2, temp, mult, scale1, scale2;</a>
+<a name="3145"><span class="lineNum">    3145 </span>            : </a>
+<a name="3146"><span class="lineNum">    3146 </span><span class="lineNoCov">          0 :     --in;</span></a>
+<a name="3147"><span class="lineNum">    3147 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="3148"><span class="lineNum">    3148 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="3149"><span class="lineNum">    3149 </span><span class="lineNoCov">          0 :     --b;</span></a>
+<a name="3150"><span class="lineNum">    3150 </span><span class="lineNoCov">          0 :     --a;</span></a>
+<a name="3151"><span class="lineNum">    3151 </span>            : </a>
+<a name="3152"><span class="lineNum">    3152 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="3153"><span class="lineNum">    3153 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="3154"><span class="lineNum">    3154 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="3155"><span class="lineNum">    3155 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="3156"><span class="lineNum">    3156 </span>            :     }</a>
+<a name="3157"><span class="lineNum">    3157 </span>            : </a>
+<a name="3158"><span class="lineNum">    3158 </span><span class="lineNoCov">          0 :     if (*n == 0) </span></a>
+<a name="3159"><span class="lineNum">    3159 </span>            :         return;</a>
+<a name="3160"><span class="lineNum">    3160 </span>            :     </a>
+<a name="3161"><span class="lineNum">    3161 </span><span class="lineNoCov">          0 :     a[1] -= *lambda;</span></a>
+<a name="3162"><span class="lineNum">    3162 </span><span class="lineNoCov">          0 :     in[*n] = 0;</span></a>
+<a name="3163"><span class="lineNum">    3163 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="3164"><span class="lineNum">    3164 </span><span class="lineNoCov">          0 :         if (std::abs(a[1])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3165"><span class="lineNum">    3165 </span><span class="lineNoCov">          0 :             in[1] = 1;</span></a>
+<a name="3166"><span class="lineNum">    3166 </span>            :         }</a>
+<a name="3167"><span class="lineNum">    3167 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="3168"><span class="lineNum">    3168 </span>            :     }</a>
+<a name="3169"><span class="lineNum">    3169 </span>            : </a>
+<a name="3170"><span class="lineNum">    3170 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="3171"><span class="lineNum">    3171 </span>            : </a>
+<a name="3172"><span class="lineNum">    3172 </span><span class="lineNoCov">          0 :     tl = (*tol&gt;eps) ? *tol : eps;</span></a>
+<a name="3173"><span class="lineNum">    3173 </span><span class="lineNoCov">          0 :     scale1 = std::abs(a[1]) + std::abs(b[1]);</span></a>
+<a name="3174"><span class="lineNum">    3174 </span>            :     i__1 = *n - 1;</a>
+<a name="3175"><span class="lineNum">    3175 </span><span class="lineNoCov">          0 :     for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="3176"><span class="lineNum">    3176 </span><span class="lineNoCov">          0 :         a[k + 1] -= *lambda;</span></a>
+<a name="3177"><span class="lineNum">    3177 </span><span class="lineNoCov">          0 :         scale2 = std::abs(c__[k]) + std::abs(a[k + 1]);</span></a>
+<a name="3178"><span class="lineNum">    3178 </span><span class="lineNoCov">          0 :         if (k &lt; *n - 1) {</span></a>
+<a name="3179"><span class="lineNum">    3179 </span><span class="lineNoCov">          0 :             scale2 += std::abs(b[k + 1]);</span></a>
+<a name="3180"><span class="lineNum">    3180 </span>            :         }</a>
+<a name="3181"><span class="lineNum">    3181 </span><span class="lineNoCov">          0 :         if (std::abs(a[k])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3182"><span class="lineNum">    3182 </span>            :             piv1 = 0.;</a>
+<a name="3183"><span class="lineNum">    3183 </span>            :         } else {</a>
+<a name="3184"><span class="lineNum">    3184 </span><span class="lineNoCov">          0 :             piv1 = std::abs(a[k]) / scale1;</span></a>
+<a name="3185"><span class="lineNum">    3185 </span>            :         }</a>
+<a name="3186"><span class="lineNum">    3186 </span><span class="lineNoCov">          0 :         if (std::abs(c__[k])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3187"><span class="lineNum">    3187 </span><span class="lineNoCov">          0 :             in[k] = 0;</span></a>
+<a name="3188"><span class="lineNum">    3188 </span>            :             piv2 = 0.;</a>
+<a name="3189"><span class="lineNum">    3189 </span>            :             scale1 = scale2;</a>
+<a name="3190"><span class="lineNum">    3190 </span><span class="lineNoCov">          0 :             if (k &lt; *n - 1) {</span></a>
+<a name="3191"><span class="lineNum">    3191 </span><span class="lineNoCov">          0 :                 d__[k] = 0.;</span></a>
+<a name="3192"><span class="lineNum">    3192 </span>            :             }</a>
+<a name="3193"><span class="lineNum">    3193 </span>            :         } else {</a>
+<a name="3194"><span class="lineNum">    3194 </span><span class="lineNoCov">          0 :             piv2 = std::abs(c__[k]) / scale2;</span></a>
+<a name="3195"><span class="lineNum">    3195 </span><span class="lineNoCov">          0 :             if (piv2 &lt;= piv1) {</span></a>
+<a name="3196"><span class="lineNum">    3196 </span><span class="lineNoCov">          0 :                 in[k] = 0;</span></a>
+<a name="3197"><span class="lineNum">    3197 </span>            :                 scale1 = scale2;</a>
+<a name="3198"><span class="lineNum">    3198 </span><span class="lineNoCov">          0 :                 c__[k] /= a[k];</span></a>
+<a name="3199"><span class="lineNum">    3199 </span><span class="lineNoCov">          0 :                 a[k + 1] -= c__[k] * b[k];</span></a>
+<a name="3200"><span class="lineNum">    3200 </span><span class="lineNoCov">          0 :                 if (k &lt; *n - 1) {</span></a>
+<a name="3201"><span class="lineNum">    3201 </span><span class="lineNoCov">          0 :                     d__[k] = 0.;</span></a>
+<a name="3202"><span class="lineNum">    3202 </span>            :                 }</a>
+<a name="3203"><span class="lineNum">    3203 </span>            :             } else {</a>
+<a name="3204"><span class="lineNum">    3204 </span><span class="lineNoCov">          0 :                 in[k] = 1;</span></a>
+<a name="3205"><span class="lineNum">    3205 </span><span class="lineNoCov">          0 :                 mult = a[k] / c__[k];</span></a>
+<a name="3206"><span class="lineNum">    3206 </span><span class="lineNoCov">          0 :                 a[k] = c__[k];</span></a>
+<a name="3207"><span class="lineNum">    3207 </span><span class="lineNoCov">          0 :                 temp = a[k + 1];</span></a>
+<a name="3208"><span class="lineNum">    3208 </span><span class="lineNoCov">          0 :                 a[k + 1] = b[k] - mult * temp;</span></a>
+<a name="3209"><span class="lineNum">    3209 </span><span class="lineNoCov">          0 :                 if (k &lt; *n - 1) {</span></a>
+<a name="3210"><span class="lineNum">    3210 </span><span class="lineNoCov">          0 :                     d__[k] = b[k + 1];</span></a>
+<a name="3211"><span class="lineNum">    3211 </span><span class="lineNoCov">          0 :                     b[k + 1] = -mult * d__[k];</span></a>
+<a name="3212"><span class="lineNum">    3212 </span>            :                 }</a>
+<a name="3213"><span class="lineNum">    3213 </span><span class="lineNoCov">          0 :                 b[k] = temp;</span></a>
+<a name="3214"><span class="lineNum">    3214 </span><span class="lineNoCov">          0 :                 c__[k] = mult;</span></a>
+<a name="3215"><span class="lineNum">    3215 </span>            :             }</a>
+<a name="3216"><span class="lineNum">    3216 </span>            :         }</a>
+<a name="3217"><span class="lineNum">    3217 </span><span class="lineNoCov">          0 :         if (((piv1&gt;piv2) ? piv1 : piv2) &lt;= tl &amp;&amp; in[*n] == 0) {</span></a>
+<a name="3218"><span class="lineNum">    3218 </span><span class="lineNoCov">          0 :             in[*n] = k;</span></a>
+<a name="3219"><span class="lineNum">    3219 </span>            :         }</a>
+<a name="3220"><span class="lineNum">    3220 </span>            :     }</a>
+<a name="3221"><span class="lineNum">    3221 </span><span class="lineNoCov">          0 :     if (std::abs(a[*n]) &lt;= scale1 * tl &amp;&amp; in[*n] == 0) {</span></a>
+<a name="3222"><span class="lineNum">    3222 </span><span class="lineNoCov">          0 :         in[*n] = *n;</span></a>
+<a name="3223"><span class="lineNum">    3223 </span>            :     }</a>
+<a name="3224"><span class="lineNum">    3224 </span>            : </a>
+<a name="3225"><span class="lineNum">    3225 </span>            :     return;</a>
+<a name="3226"><span class="lineNum">    3226 </span>            : </a>
+<a name="3227"><span class="lineNum">    3227 </span>            : }</a>
+<a name="3228"><span class="lineNum">    3228 </span>            : </a>
+<a name="3229"><span class="lineNum">    3229 </span>            : </a>
+<a name="3230"><span class="lineNum">    3230 </span>            : }</a>
+<a name="3231"><span class="lineNum">    3231 </span>            : }</a>
+<a name="3232"><span class="lineNum">    3232 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="3233"><span class="lineNum">    3233 </span>            : #include &lt;cmath&gt;</a>
+<a name="3234"><span class="lineNum">    3234 </span>            : #include &quot;real.h&quot;</a>
+<a name="3235"><span class="lineNum">    3235 </span>            : </a>
+<a name="3236"><span class="lineNum">    3236 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3237"><span class="lineNum">    3237 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="3238"><span class="lineNum">    3238 </span>            : </a>
+<a name="3239"><span class="lineNum">    3239 </span>            : </a>
+<a name="3240"><span class="lineNum">    3240 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3241"><span class="lineNum">    3241 </span>            : namespace PLMD{</a>
+<a name="3242"><span class="lineNum">    3242 </span>            : namespace lapack{</a>
+<a name="3243"><span class="lineNum">    3243 </span>            : using namespace blas;</a>
+<a name="3244"><span class="lineNum">    3244 </span>            : void</a>
+<a name="3245"><span class="lineNum">    3245 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlagts,DLAGTS)(int *job, </span></a>
+<a name="3246"><span class="lineNum">    3246 </span>            :         int *n, </a>
+<a name="3247"><span class="lineNum">    3247 </span>            :         double *a, </a>
+<a name="3248"><span class="lineNum">    3248 </span>            :         double *b, </a>
+<a name="3249"><span class="lineNum">    3249 </span>            :         double *c__, </a>
+<a name="3250"><span class="lineNum">    3250 </span>            :         double *d__, </a>
+<a name="3251"><span class="lineNum">    3251 </span>            :         int *in, </a>
+<a name="3252"><span class="lineNum">    3252 </span>            :         double *y, </a>
+<a name="3253"><span class="lineNum">    3253 </span>            :         double *tol, </a>
+<a name="3254"><span class="lineNum">    3254 </span>            :         int *info)</a>
+<a name="3255"><span class="lineNum">    3255 </span>            : {</a>
+<a name="3256"><span class="lineNum">    3256 </span>            :     int i__1;</a>
+<a name="3257"><span class="lineNum">    3257 </span>            :     double d__1, d__2, d__4, d__5;</a>
+<a name="3258"><span class="lineNum">    3258 </span>            : </a>
+<a name="3259"><span class="lineNum">    3259 </span>            :     int k;</a>
+<a name="3260"><span class="lineNum">    3260 </span>            :     double ak, eps, temp, pert, absak, sfmin;</a>
+<a name="3261"><span class="lineNum">    3261 </span>            :     double bignum,minval;</a>
+<a name="3262"><span class="lineNum">    3262 </span><span class="lineNoCov">          0 :     --y;</span></a>
+<a name="3263"><span class="lineNum">    3263 </span><span class="lineNoCov">          0 :     --in;</span></a>
+<a name="3264"><span class="lineNum">    3264 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="3265"><span class="lineNum">    3265 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="3266"><span class="lineNum">    3266 </span><span class="lineNoCov">          0 :     --b;</span></a>
+<a name="3267"><span class="lineNum">    3267 </span><span class="lineNoCov">          0 :     --a;</span></a>
+<a name="3268"><span class="lineNum">    3268 </span>            : </a>
+<a name="3269"><span class="lineNum">    3269 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="3270"><span class="lineNum">    3270 </span><span class="lineNoCov">          0 :     if (abs(*job) &gt; 2 || *job == 0) {</span></a>
+<a name="3271"><span class="lineNum">    3271 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="3272"><span class="lineNum">    3272 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="3273"><span class="lineNum">    3273 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="3274"><span class="lineNum">    3274 </span>            :     }</a>
+<a name="3275"><span class="lineNum">    3275 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="3276"><span class="lineNum">    3276 </span>            :         return;</a>
+<a name="3277"><span class="lineNum">    3277 </span>            :     }</a>
+<a name="3278"><span class="lineNum">    3278 </span>            : </a>
+<a name="3279"><span class="lineNum">    3279 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="3280"><span class="lineNum">    3280 </span>            :         return;</a>
+<a name="3281"><span class="lineNum">    3281 </span>            :     }</a>
+<a name="3282"><span class="lineNum">    3282 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="3283"><span class="lineNum">    3283 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="3284"><span class="lineNum">    3284 </span>            :     sfmin = minval / eps;</a>
+<a name="3285"><span class="lineNum">    3285 </span>            : </a>
+<a name="3286"><span class="lineNum">    3286 </span>            :     bignum = 1. / sfmin;</a>
+<a name="3287"><span class="lineNum">    3287 </span>            : </a>
+<a name="3288"><span class="lineNum">    3288 </span><span class="lineNoCov">          0 :     if (*job &lt; 0) {</span></a>
+<a name="3289"><span class="lineNum">    3289 </span><span class="lineNoCov">          0 :         if (*tol &lt;= 0.) {</span></a>
+<a name="3290"><span class="lineNum">    3290 </span><span class="lineNoCov">          0 :             *tol = std::abs(a[1]);</span></a>
+<a name="3291"><span class="lineNum">    3291 </span><span class="lineNoCov">          0 :             if (*n &gt; 1) {</span></a>
+<a name="3292"><span class="lineNum">    3292 </span>            :                 d__1 = *tol;</a>
+<a name="3293"><span class="lineNum">    3293 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(a[2]);</span></a>
+<a name="3294"><span class="lineNum">    3294 </span><span class="lineNoCov">          0 :                 d__1 = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="3295"><span class="lineNum">    3295 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(b[1]);</span></a>
+<a name="3296"><span class="lineNum">    3296 </span><span class="lineNoCov">          0 :                 *tol = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="3297"><span class="lineNum">    3297 </span>            :             }</a>
+<a name="3298"><span class="lineNum">    3298 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3299"><span class="lineNum">    3299 </span><span class="lineNoCov">          0 :             for (k = 3; k &lt;= i__1; ++k) {</span></a>
+<a name="3300"><span class="lineNum">    3300 </span><span class="lineNoCov">          0 :               d__4 = *tol;</span></a>
+<a name="3301"><span class="lineNum">    3301 </span><span class="lineNoCov">          0 :               d__5 = std::abs(a[k]);</span></a>
+<a name="3302"><span class="lineNum">    3302 </span><span class="lineNoCov">          0 :               d__4 = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="3303"><span class="lineNum">    3303 </span><span class="lineNoCov">          0 :               d__5 = std::abs(b[k - 1]);</span></a>
+<a name="3304"><span class="lineNum">    3304 </span><span class="lineNoCov">          0 :               d__4 = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="3305"><span class="lineNum">    3305 </span><span class="lineNoCov">          0 :               d__5 = std::abs(d__[k - 2]);</span></a>
+<a name="3306"><span class="lineNum">    3306 </span><span class="lineNoCov">          0 :               *tol = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="3307"><span class="lineNum">    3307 </span>            :             }</a>
+<a name="3308"><span class="lineNum">    3308 </span><span class="lineNoCov">          0 :             *tol *= eps;</span></a>
+<a name="3309"><span class="lineNum">    3309 </span><span class="lineNoCov">          0 :             if (std::abs(*tol)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3310"><span class="lineNum">    3310 </span><span class="lineNoCov">          0 :                 *tol = eps;</span></a>
+<a name="3311"><span class="lineNum">    3311 </span>            :             }</a>
+<a name="3312"><span class="lineNum">    3312 </span>            :         }</a>
+<a name="3313"><span class="lineNum">    3313 </span>            :     }</a>
+<a name="3314"><span class="lineNum">    3314 </span>            : </a>
+<a name="3315"><span class="lineNum">    3315 </span><span class="lineNoCov">          0 :     if (1 == abs(*job)) {</span></a>
+<a name="3316"><span class="lineNum">    3316 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="3317"><span class="lineNum">    3317 </span><span class="lineNoCov">          0 :         for (k = 2; k &lt;= i__1; ++k) {</span></a>
+<a name="3318"><span class="lineNum">    3318 </span><span class="lineNoCov">          0 :             if (in[k - 1] == 0) {</span></a>
+<a name="3319"><span class="lineNum">    3319 </span><span class="lineNoCov">          0 :                 y[k] -= c__[k - 1] * y[k - 1];</span></a>
+<a name="3320"><span class="lineNum">    3320 </span>            :             } else {</a>
+<a name="3321"><span class="lineNum">    3321 </span><span class="lineNoCov">          0 :                 temp = y[k - 1];</span></a>
+<a name="3322"><span class="lineNum">    3322 </span><span class="lineNoCov">          0 :                 y[k - 1] = y[k];</span></a>
+<a name="3323"><span class="lineNum">    3323 </span><span class="lineNoCov">          0 :                 y[k] = temp - c__[k - 1] * y[k];</span></a>
+<a name="3324"><span class="lineNum">    3324 </span>            :             }</a>
+<a name="3325"><span class="lineNum">    3325 </span>            :         }</a>
+<a name="3326"><span class="lineNum">    3326 </span><span class="lineNoCov">          0 :         if (*job == 1) {</span></a>
+<a name="3327"><span class="lineNum">    3327 </span><span class="lineNoCov">          0 :             for (k = *n; k &gt;= 1; --k) {</span></a>
+<a name="3328"><span class="lineNum">    3328 </span><span class="lineNoCov">          0 :                 if (k &lt;= *n - 2) {</span></a>
+<a name="3329"><span class="lineNum">    3329 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1] - d__[k] * y[k + 2];</span></a>
+<a name="3330"><span class="lineNum">    3330 </span><span class="lineNoCov">          0 :                 } else if (k == *n - 1) {</span></a>
+<a name="3331"><span class="lineNum">    3331 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1];</span></a>
+<a name="3332"><span class="lineNum">    3332 </span>            :                 } else {</a>
+<a name="3333"><span class="lineNum">    3333 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="3334"><span class="lineNum">    3334 </span>            :                 }</a>
+<a name="3335"><span class="lineNum">    3335 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="3336"><span class="lineNum">    3336 </span>            :                 absak = std::abs(ak);</a>
+<a name="3337"><span class="lineNum">    3337 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="3338"><span class="lineNum">    3338 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="3339"><span class="lineNum">    3339 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_DOUBLE_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="3340"><span class="lineNum">    3340 </span><span class="lineNoCov">          0 :                             *info = k;</span></a>
+<a name="3341"><span class="lineNum">    3341 </span><span class="lineNoCov">          0 :                             return;</span></a>
+<a name="3342"><span class="lineNum">    3342 </span>            :                         } else {</a>
+<a name="3343"><span class="lineNum">    3343 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="3344"><span class="lineNum">    3344 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="3345"><span class="lineNum">    3345 </span>            :                         }</a>
+<a name="3346"><span class="lineNum">    3346 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="3347"><span class="lineNum">    3347 </span><span class="lineNoCov">          0 :                         *info = k;</span></a>
+<a name="3348"><span class="lineNum">    3348 </span><span class="lineNoCov">          0 :                         return;</span></a>
+<a name="3349"><span class="lineNum">    3349 </span>            :                     }</a>
+<a name="3350"><span class="lineNum">    3350 </span>            :                 }</a>
+<a name="3351"><span class="lineNum">    3351 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="3352"><span class="lineNum">    3352 </span>            :             }</a>
+<a name="3353"><span class="lineNum">    3353 </span>            :         } else {</a>
+<a name="3354"><span class="lineNum">    3354 </span><span class="lineNoCov">          0 :             for (k = *n; k &gt;= 1; --k) {</span></a>
+<a name="3355"><span class="lineNum">    3355 </span><span class="lineNoCov">          0 :                 if (k + 2 &lt;= *n) {</span></a>
+<a name="3356"><span class="lineNum">    3356 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1] - d__[k] * y[k + 2];</span></a>
+<a name="3357"><span class="lineNum">    3357 </span><span class="lineNoCov">          0 :                 } else if (k + 1 == *n) {</span></a>
+<a name="3358"><span class="lineNum">    3358 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1];</span></a>
+<a name="3359"><span class="lineNum">    3359 </span>            :                 } else {</a>
+<a name="3360"><span class="lineNum">    3360 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="3361"><span class="lineNum">    3361 </span>            :                 }</a>
+<a name="3362"><span class="lineNum">    3362 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="3363"><span class="lineNum">    3363 </span>            : </a>
+<a name="3364"><span class="lineNum">    3364 </span><span class="lineNoCov">          0 :                 pert = *tol;</span></a>
+<a name="3365"><span class="lineNum">    3365 </span><span class="lineNoCov">          0 :                 if(ak&lt;0)</span></a>
+<a name="3366"><span class="lineNum">    3366 </span><span class="lineNoCov">          0 :                   pert *= -1.0;</span></a>
+<a name="3367"><span class="lineNum">    3367 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="3368"><span class="lineNum">    3368 </span>            :                 absak = std::abs(ak);</a>
+<a name="3369"><span class="lineNum">    3369 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="3370"><span class="lineNum">    3370 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="3371"><span class="lineNum">    3371 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_DOUBLE_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="3372"><span class="lineNum">    3372 </span><span class="lineNoCov">          0 :                             ak += pert;</span></a>
+<a name="3373"><span class="lineNum">    3373 </span><span class="lineNoCov">          0 :                             pert *= 2;</span></a>
+<a name="3374"><span class="lineNum">    3374 </span><span class="lineNoCov">          0 :                             goto L40;</span></a>
+<a name="3375"><span class="lineNum">    3375 </span>            :                         } else {</a>
+<a name="3376"><span class="lineNum">    3376 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="3377"><span class="lineNum">    3377 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="3378"><span class="lineNum">    3378 </span>            :                         }</a>
+<a name="3379"><span class="lineNum">    3379 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="3380"><span class="lineNum">    3380 </span><span class="lineNoCov">          0 :                         ak += pert;</span></a>
+<a name="3381"><span class="lineNum">    3381 </span><span class="lineNoCov">          0 :                         pert *= 2;</span></a>
+<a name="3382"><span class="lineNum">    3382 </span><span class="lineNoCov">          0 :                         goto L40;</span></a>
+<a name="3383"><span class="lineNum">    3383 </span>            :                     }</a>
+<a name="3384"><span class="lineNum">    3384 </span>            :                 }</a>
+<a name="3385"><span class="lineNum">    3385 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="3386"><span class="lineNum">    3386 </span>            :             }</a>
+<a name="3387"><span class="lineNum">    3387 </span>            :         }</a>
+<a name="3388"><span class="lineNum">    3388 </span>            :     } else {</a>
+<a name="3389"><span class="lineNum">    3389 </span>            : </a>
+<a name="3390"><span class="lineNum">    3390 </span><span class="lineNoCov">          0 :         if (*job == 2) {</span></a>
+<a name="3391"><span class="lineNum">    3391 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3392"><span class="lineNum">    3392 </span><span class="lineNoCov">          0 :             for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="3393"><span class="lineNum">    3393 </span><span class="lineNoCov">          0 :                 if (k &gt;= 3) {</span></a>
+<a name="3394"><span class="lineNum">    3394 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1] - d__[k - 2] * y[k - 2];</span></a>
+<a name="3395"><span class="lineNum">    3395 </span><span class="lineNoCov">          0 :                 } else if (k == 2) {</span></a>
+<a name="3396"><span class="lineNum">    3396 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1];</span></a>
+<a name="3397"><span class="lineNum">    3397 </span>            :                 } else {</a>
+<a name="3398"><span class="lineNum">    3398 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="3399"><span class="lineNum">    3399 </span>            :                 }</a>
+<a name="3400"><span class="lineNum">    3400 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="3401"><span class="lineNum">    3401 </span>            :                 absak = std::abs(ak);</a>
+<a name="3402"><span class="lineNum">    3402 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="3403"><span class="lineNum">    3403 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="3404"><span class="lineNum">    3404 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_DOUBLE_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="3405"><span class="lineNum">    3405 </span><span class="lineNoCov">          0 :                             *info = k;</span></a>
+<a name="3406"><span class="lineNum">    3406 </span><span class="lineNoCov">          0 :                             return;</span></a>
+<a name="3407"><span class="lineNum">    3407 </span>            :                         } else {</a>
+<a name="3408"><span class="lineNum">    3408 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="3409"><span class="lineNum">    3409 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="3410"><span class="lineNum">    3410 </span>            :                         }</a>
+<a name="3411"><span class="lineNum">    3411 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="3412"><span class="lineNum">    3412 </span><span class="lineNoCov">          0 :                         *info = k;</span></a>
+<a name="3413"><span class="lineNum">    3413 </span><span class="lineNoCov">          0 :                         return;</span></a>
+<a name="3414"><span class="lineNum">    3414 </span>            :                     }</a>
+<a name="3415"><span class="lineNum">    3415 </span>            :                 }</a>
+<a name="3416"><span class="lineNum">    3416 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="3417"><span class="lineNum">    3417 </span>            :             }</a>
+<a name="3418"><span class="lineNum">    3418 </span>            :         } else {</a>
+<a name="3419"><span class="lineNum">    3419 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3420"><span class="lineNum">    3420 </span><span class="lineNoCov">          0 :             for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="3421"><span class="lineNum">    3421 </span><span class="lineNoCov">          0 :                 if (k &gt;= 3) {</span></a>
+<a name="3422"><span class="lineNum">    3422 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1] - d__[k - 2] * y[k - 2];</span></a>
+<a name="3423"><span class="lineNum">    3423 </span><span class="lineNoCov">          0 :                 } else if (k == 2) {</span></a>
+<a name="3424"><span class="lineNum">    3424 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1];</span></a>
+<a name="3425"><span class="lineNum">    3425 </span>            :                 } else {</a>
+<a name="3426"><span class="lineNum">    3426 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="3427"><span class="lineNum">    3427 </span>            :                 }</a>
+<a name="3428"><span class="lineNum">    3428 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="3429"><span class="lineNum">    3429 </span>            : </a>
+<a name="3430"><span class="lineNum">    3430 </span><span class="lineNoCov">          0 :                 pert = *tol;</span></a>
+<a name="3431"><span class="lineNum">    3431 </span><span class="lineNoCov">          0 :                 if(ak&lt;0)</span></a>
+<a name="3432"><span class="lineNum">    3432 </span><span class="lineNoCov">          0 :                   pert *= -1.0;</span></a>
+<a name="3433"><span class="lineNum">    3433 </span>            : </a>
+<a name="3434"><span class="lineNum">    3434 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="3435"><span class="lineNum">    3435 </span>            :                 absak = std::abs(ak);</a>
+<a name="3436"><span class="lineNum">    3436 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="3437"><span class="lineNum">    3437 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="3438"><span class="lineNum">    3438 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_DOUBLE_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="3439"><span class="lineNum">    3439 </span><span class="lineNoCov">          0 :                             ak += pert;</span></a>
+<a name="3440"><span class="lineNum">    3440 </span><span class="lineNoCov">          0 :                             pert *= 2;</span></a>
+<a name="3441"><span class="lineNum">    3441 </span><span class="lineNoCov">          0 :                             goto L70;</span></a>
+<a name="3442"><span class="lineNum">    3442 </span>            :                         } else {</a>
+<a name="3443"><span class="lineNum">    3443 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="3444"><span class="lineNum">    3444 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="3445"><span class="lineNum">    3445 </span>            :                         }</a>
+<a name="3446"><span class="lineNum">    3446 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="3447"><span class="lineNum">    3447 </span><span class="lineNoCov">          0 :                         ak += pert;</span></a>
+<a name="3448"><span class="lineNum">    3448 </span><span class="lineNoCov">          0 :                         pert *= 2;</span></a>
+<a name="3449"><span class="lineNum">    3449 </span><span class="lineNoCov">          0 :                         goto L70;</span></a>
+<a name="3450"><span class="lineNum">    3450 </span>            :                     }</a>
+<a name="3451"><span class="lineNum">    3451 </span>            :                 }</a>
+<a name="3452"><span class="lineNum">    3452 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="3453"><span class="lineNum">    3453 </span>            :             }</a>
+<a name="3454"><span class="lineNum">    3454 </span>            :         }</a>
+<a name="3455"><span class="lineNum">    3455 </span>            : </a>
+<a name="3456"><span class="lineNum">    3456 </span><span class="lineNoCov">          0 :         for (k = *n; k &gt;= 2; --k) {</span></a>
+<a name="3457"><span class="lineNum">    3457 </span><span class="lineNoCov">          0 :             if (in[k - 1] == 0) {</span></a>
+<a name="3458"><span class="lineNum">    3458 </span><span class="lineNoCov">          0 :                 y[k - 1] -= c__[k - 1] * y[k];</span></a>
+<a name="3459"><span class="lineNum">    3459 </span>            :             } else {</a>
+<a name="3460"><span class="lineNum">    3460 </span><span class="lineNoCov">          0 :                 temp = y[k - 1];</span></a>
+<a name="3461"><span class="lineNum">    3461 </span><span class="lineNoCov">          0 :                 y[k - 1] = y[k];</span></a>
+<a name="3462"><span class="lineNum">    3462 </span><span class="lineNoCov">          0 :                 y[k] = temp - c__[k - 1] * y[k];</span></a>
+<a name="3463"><span class="lineNum">    3463 </span>            :             }</a>
+<a name="3464"><span class="lineNum">    3464 </span>            :         }</a>
+<a name="3465"><span class="lineNum">    3465 </span>            :     }</a>
+<a name="3466"><span class="lineNum">    3466 </span>            : </a>
+<a name="3467"><span class="lineNum">    3467 </span>            :     return;</a>
+<a name="3468"><span class="lineNum">    3468 </span>            : }</a>
+<a name="3469"><span class="lineNum">    3469 </span>            : </a>
+<a name="3470"><span class="lineNum">    3470 </span>            : </a>
+<a name="3471"><span class="lineNum">    3471 </span>            : }</a>
+<a name="3472"><span class="lineNum">    3472 </span>            : }</a>
+<a name="3473"><span class="lineNum">    3473 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3474"><span class="lineNum">    3474 </span>            : </a>
+<a name="3475"><span class="lineNum">    3475 </span>            : </a>
+<a name="3476"><span class="lineNum">    3476 </span>            : /* LAPACK */</a>
+<a name="3477"><span class="lineNum">    3477 </span>            : </a>
+<a name="3478"><span class="lineNum">    3478 </span>            : </a>
+<a name="3479"><span class="lineNum">    3479 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3480"><span class="lineNum">    3480 </span>            : namespace PLMD{</a>
+<a name="3481"><span class="lineNum">    3481 </span>            : namespace lapack{</a>
+<a name="3482"><span class="lineNum">    3482 </span>            : using namespace blas;</a>
+<a name="3483"><span class="lineNum">    3483 </span>            : void</a>
+<a name="3484"><span class="lineNum">    3484 </span><span class="lineCov">        118 : PLUMED_BLAS_F77_FUNC(dlamrg,DLAMRG)(int *n1,</span></a>
+<a name="3485"><span class="lineNum">    3485 </span>            :                         int *n2,</a>
+<a name="3486"><span class="lineNum">    3486 </span>            :                         double *a,</a>
+<a name="3487"><span class="lineNum">    3487 </span>            :                         int *dtrd1,</a>
+<a name="3488"><span class="lineNum">    3488 </span>            :                         int *dtrd2,</a>
+<a name="3489"><span class="lineNum">    3489 </span>            :                         int *index)</a>
+<a name="3490"><span class="lineNum">    3490 </span>            : {</a>
+<a name="3491"><span class="lineNum">    3491 </span><span class="lineCov">        118 :   int n1sv = *n1;</span></a>
+<a name="3492"><span class="lineNum">    3492 </span><span class="lineCov">        118 :   int n2sv = *n2;</span></a>
+<a name="3493"><span class="lineNum">    3493 </span>            :   int i,ind1,ind2;</a>
+<a name="3494"><span class="lineNum">    3494 </span>            : </a>
+<a name="3495"><span class="lineNum">    3495 </span><span class="lineCov">        118 :   if(*dtrd1&gt;0)</span></a>
+<a name="3496"><span class="lineNum">    3496 </span>            :     ind1 = 0;</a>
+<a name="3497"><span class="lineNum">    3497 </span>            :   else</a>
+<a name="3498"><span class="lineNum">    3498 </span><span class="lineNoCov">          0 :     ind1 = *n1-1;</span></a>
+<a name="3499"><span class="lineNum">    3499 </span>            : </a>
+<a name="3500"><span class="lineNum">    3500 </span><span class="lineCov">        118 :   if(*dtrd2&gt;0)</span></a>
+<a name="3501"><span class="lineNum">    3501 </span>            :     ind2 = *n1;</a>
+<a name="3502"><span class="lineNum">    3502 </span>            :   else</a>
+<a name="3503"><span class="lineNum">    3503 </span><span class="lineCov">         59 :     ind2 = *n1+*n2-1;</span></a>
+<a name="3504"><span class="lineNum">    3504 </span>            : </a>
+<a name="3505"><span class="lineNum">    3505 </span>            :   i = 0;</a>
+<a name="3506"><span class="lineNum">    3506 </span>            :   </a>
+<a name="3507"><span class="lineNum">    3507 </span><span class="lineCov">       4270 :   while(n1sv&gt;0 &amp;&amp; n2sv&gt;0) {</span></a>
+<a name="3508"><span class="lineNum">    3508 </span><span class="lineCov">       4152 :     if(a[ind1]&lt;=a[ind2]) {</span></a>
+<a name="3509"><span class="lineNum">    3509 </span><span class="lineCov">       2476 :       index[i] = ind1 + 1;</span></a>
+<a name="3510"><span class="lineNum">    3510 </span><span class="lineCov">       2476 :       i++;</span></a>
+<a name="3511"><span class="lineNum">    3511 </span><span class="lineCov">       2476 :       ind1 += *dtrd1;</span></a>
+<a name="3512"><span class="lineNum">    3512 </span><span class="lineCov">       2476 :       n1sv--;</span></a>
+<a name="3513"><span class="lineNum">    3513 </span>            :     } else {</a>
+<a name="3514"><span class="lineNum">    3514 </span><span class="lineCov">       1676 :       index[i] = ind2 + 1;</span></a>
+<a name="3515"><span class="lineNum">    3515 </span><span class="lineCov">       1676 :       i++;</span></a>
+<a name="3516"><span class="lineNum">    3516 </span><span class="lineCov">       1676 :       ind2 += *dtrd2;</span></a>
+<a name="3517"><span class="lineNum">    3517 </span><span class="lineCov">       1676 :       n2sv--;</span></a>
+<a name="3518"><span class="lineNum">    3518 </span>            :     }</a>
+<a name="3519"><span class="lineNum">    3519 </span>            :   }</a>
+<a name="3520"><span class="lineNum">    3520 </span>            : </a>
+<a name="3521"><span class="lineNum">    3521 </span><span class="lineCov">        118 :   if(n1sv==0) {</span></a>
+<a name="3522"><span class="lineNum">    3522 </span><span class="lineCov">        126 :     for(n1sv=1;n1sv&lt;=n2sv;n1sv++) {</span></a>
+<a name="3523"><span class="lineNum">    3523 </span><span class="lineCov">        120 :       index[i] = ind2 + 1;</span></a>
+<a name="3524"><span class="lineNum">    3524 </span><span class="lineCov">        120 :       i++;</span></a>
+<a name="3525"><span class="lineNum">    3525 </span><span class="lineCov">        120 :       ind2 += *dtrd2;</span></a>
+<a name="3526"><span class="lineNum">    3526 </span>            :     } </a>
+<a name="3527"><span class="lineNum">    3527 </span>            :   } else {</a>
+<a name="3528"><span class="lineNum">    3528 </span><span class="lineCov">       2567 :     for(n2sv=1;n2sv&lt;=n1sv;n2sv++) {</span></a>
+<a name="3529"><span class="lineNum">    3529 </span><span class="lineCov">       2455 :       index[i] = ind1 + 1;</span></a>
+<a name="3530"><span class="lineNum">    3530 </span><span class="lineCov">       2455 :       i++;</span></a>
+<a name="3531"><span class="lineNum">    3531 </span><span class="lineCov">       2455 :       ind1 += *dtrd1;</span></a>
+<a name="3532"><span class="lineNum">    3532 </span>            :     } </a>
+<a name="3533"><span class="lineNum">    3533 </span>            :   }</a>
+<a name="3534"><span class="lineNum">    3534 </span><span class="lineCov">        118 :   return;</span></a>
+<a name="3535"><span class="lineNum">    3535 </span>            : }</a>
+<a name="3536"><span class="lineNum">    3536 </span>            : }</a>
+<a name="3537"><span class="lineNum">    3537 </span>            : }</a>
+<a name="3538"><span class="lineNum">    3538 </span>            : #include &lt;cctype&gt;</a>
+<a name="3539"><span class="lineNum">    3539 </span>            : #include &lt;cmath&gt;</a>
+<a name="3540"><span class="lineNum">    3540 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3541"><span class="lineNum">    3541 </span>            : </a>
+<a name="3542"><span class="lineNum">    3542 </span>            : </a>
+<a name="3543"><span class="lineNum">    3543 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3544"><span class="lineNum">    3544 </span>            : namespace PLMD{</a>
+<a name="3545"><span class="lineNum">    3545 </span>            : namespace lapack{</a>
+<a name="3546"><span class="lineNum">    3546 </span>            : using namespace blas;</a>
+<a name="3547"><span class="lineNum">    3547 </span>            : double</a>
+<a name="3548"><span class="lineNum">    3548 </span><span class="lineCov">         96 : PLUMED_BLAS_F77_FUNC(dlange,DLANGE)(const char *norm,</span></a>
+<a name="3549"><span class="lineNum">    3549 </span>            :         int *m,</a>
+<a name="3550"><span class="lineNum">    3550 </span>            :         int *n,</a>
+<a name="3551"><span class="lineNum">    3551 </span>            :         double *a,</a>
+<a name="3552"><span class="lineNum">    3552 </span>            :         int *lda,</a>
+<a name="3553"><span class="lineNum">    3553 </span>            :         double *work)</a>
+<a name="3554"><span class="lineNum">    3554 </span>            : {</a>
+<a name="3555"><span class="lineNum">    3555 </span><span class="lineCov">         96 :   const char ch=std::toupper(*norm);</span></a>
+<a name="3556"><span class="lineNum">    3556 </span>            :   double dtemp,sum,max,val,scale;</a>
+<a name="3557"><span class="lineNum">    3557 </span>            :   int i,j;</a>
+<a name="3558"><span class="lineNum">    3558 </span>            : </a>
+<a name="3559"><span class="lineNum">    3559 </span><span class="lineCov">         96 :   switch(ch) {</span></a>
+<a name="3560"><span class="lineNum">    3560 </span>            :   case 'M':</a>
+<a name="3561"><span class="lineNum">    3561 </span>            :     max = 0.0;</a>
+<a name="3562"><span class="lineNum">    3562 </span><span class="lineCov">       2640 :     for(j=0;j&lt;*n;j++)</span></a>
+<a name="3563"><span class="lineNum">    3563 </span><span class="lineCov">     304276 :       for(i=0;i&lt;*m;i++) {</span></a>
+<a name="3564"><span class="lineNum">    3564 </span><span class="lineCov">     301732 :         dtemp = std::abs(a[j*(*lda)+i]);</span></a>
+<a name="3565"><span class="lineNum">    3565 </span><span class="lineCov">     301732 :         if(dtemp&gt;max)</span></a>
+<a name="3566"><span class="lineNum">    3566 </span>            :           max = dtemp;</a>
+<a name="3567"><span class="lineNum">    3567 </span>            :       }</a>
+<a name="3568"><span class="lineNum">    3568 </span>            :     val = max;</a>
+<a name="3569"><span class="lineNum">    3569 </span>            :     break;</a>
+<a name="3570"><span class="lineNum">    3570 </span>            : </a>
+<a name="3571"><span class="lineNum">    3571 </span>            :   case 'O':</a>
+<a name="3572"><span class="lineNum">    3572 </span>            :   case '1':</a>
+<a name="3573"><span class="lineNum">    3573 </span>            :     max = 0.0;</a>
+<a name="3574"><span class="lineNum">    3574 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="3575"><span class="lineNum">    3575 </span><span class="lineNoCov">          0 :       sum = 0.0;</span></a>
+<a name="3576"><span class="lineNum">    3576 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++) </span></a>
+<a name="3577"><span class="lineNum">    3577 </span><span class="lineNoCov">          0 :         sum += std::abs(a[j*(*lda)+i]);</span></a>
+<a name="3578"><span class="lineNum">    3578 </span><span class="lineNoCov">          0 :       if(sum&gt;max)</span></a>
+<a name="3579"><span class="lineNum">    3579 </span>            :         max = sum;</a>
+<a name="3580"><span class="lineNum">    3580 </span>            :     }</a>
+<a name="3581"><span class="lineNum">    3581 </span>            :     val = max;</a>
+<a name="3582"><span class="lineNum">    3582 </span>            :     break;</a>
+<a name="3583"><span class="lineNum">    3583 </span>            : </a>
+<a name="3584"><span class="lineNum">    3584 </span><span class="lineNoCov">          0 :   case 'I':</span></a>
+<a name="3585"><span class="lineNum">    3585 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*m;i++)</span></a>
+<a name="3586"><span class="lineNum">    3586 </span><span class="lineNoCov">          0 :       work[i] = 0.0;</span></a>
+<a name="3587"><span class="lineNum">    3587 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++)</span></a>
+<a name="3588"><span class="lineNum">    3588 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++)</span></a>
+<a name="3589"><span class="lineNum">    3589 </span><span class="lineNoCov">          0 :         work[i] += std::abs(a[j*(*lda)+i]);</span></a>
+<a name="3590"><span class="lineNum">    3590 </span>            :     max = 0;</a>
+<a name="3591"><span class="lineNum">    3591 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*m;i++)</span></a>
+<a name="3592"><span class="lineNum">    3592 </span><span class="lineNoCov">          0 :       if(work[i]&gt;max)</span></a>
+<a name="3593"><span class="lineNum">    3593 </span>            :         max=work[i];</a>
+<a name="3594"><span class="lineNum">    3594 </span>            :     val = max;</a>
+<a name="3595"><span class="lineNum">    3595 </span>            :     break;</a>
+<a name="3596"><span class="lineNum">    3596 </span>            : </a>
+<a name="3597"><span class="lineNum">    3597 </span><span class="lineNoCov">          0 :   case 'F':</span></a>
+<a name="3598"><span class="lineNum">    3598 </span>            :   case 'E':</a>
+<a name="3599"><span class="lineNum">    3599 </span><span class="lineNoCov">          0 :     scale = 0.0;</span></a>
+<a name="3600"><span class="lineNum">    3600 </span><span class="lineNoCov">          0 :     sum   = 1.0;</span></a>
+<a name="3601"><span class="lineNum">    3601 </span><span class="lineNoCov">          0 :     i = 1;</span></a>
+<a name="3602"><span class="lineNum">    3602 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) </span></a>
+<a name="3603"><span class="lineNum">    3603 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(m,&amp;(a[j*(*lda)+0]),&amp;i,&amp;scale,&amp;sum);</span></a>
+<a name="3604"><span class="lineNum">    3604 </span><span class="lineNoCov">          0 :     val = scale* std::sqrt(sum);</span></a>
+<a name="3605"><span class="lineNum">    3605 </span><span class="lineNoCov">          0 :     break;</span></a>
+<a name="3606"><span class="lineNum">    3606 </span>            : </a>
+<a name="3607"><span class="lineNum">    3607 </span>            :   default:</a>
+<a name="3608"><span class="lineNum">    3608 </span>            :     val = 0.0;</a>
+<a name="3609"><span class="lineNum">    3609 </span>            :     break;</a>
+<a name="3610"><span class="lineNum">    3610 </span>            :   }</a>
+<a name="3611"><span class="lineNum">    3611 </span><span class="lineCov">         96 :   return val;</span></a>
+<a name="3612"><span class="lineNum">    3612 </span>            : }</a>
+<a name="3613"><span class="lineNum">    3613 </span>            : }</a>
+<a name="3614"><span class="lineNum">    3614 </span>            : }</a>
+<a name="3615"><span class="lineNum">    3615 </span>            : #include &lt;cctype&gt;</a>
+<a name="3616"><span class="lineNum">    3616 </span>            : #include &lt;cmath&gt;</a>
+<a name="3617"><span class="lineNum">    3617 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3618"><span class="lineNum">    3618 </span>            : </a>
+<a name="3619"><span class="lineNum">    3619 </span>            : </a>
+<a name="3620"><span class="lineNum">    3620 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3621"><span class="lineNum">    3621 </span>            : namespace PLMD{</a>
+<a name="3622"><span class="lineNum">    3622 </span>            : namespace lapack{</a>
+<a name="3623"><span class="lineNum">    3623 </span>            : using namespace blas;</a>
+<a name="3624"><span class="lineNum">    3624 </span>            : double</a>
+<a name="3625"><span class="lineNum">    3625 </span><span class="lineCov">     570037 : PLUMED_BLAS_F77_FUNC(dlanst,DLANST)(const char *norm,</span></a>
+<a name="3626"><span class="lineNum">    3626 </span>            :         int *n,</a>
+<a name="3627"><span class="lineNum">    3627 </span>            :         double *d,</a>
+<a name="3628"><span class="lineNum">    3628 </span>            :         double *e)</a>
+<a name="3629"><span class="lineNum">    3629 </span>            : {</a>
+<a name="3630"><span class="lineNum">    3630 </span><span class="lineCov">     570037 :   const char ch=std::toupper(*norm);</span></a>
+<a name="3631"><span class="lineNum">    3631 </span>            :   double dtemp,max,val,scale,sum;</a>
+<a name="3632"><span class="lineNum">    3632 </span>            :   int i,j;</a>
+<a name="3633"><span class="lineNum">    3633 </span>            : </a>
+<a name="3634"><span class="lineNum">    3634 </span>            : </a>
+<a name="3635"><span class="lineNum">    3635 </span><span class="lineCov">     570037 :   if(*n&lt;=0)</span></a>
+<a name="3636"><span class="lineNum">    3636 </span>            :     return 0.0;</a>
+<a name="3637"><span class="lineNum">    3637 </span>            :   </a>
+<a name="3638"><span class="lineNum">    3638 </span><span class="lineCov">     570037 :   switch(ch) {</span></a>
+<a name="3639"><span class="lineNum">    3639 </span><span class="lineCov">     570037 :   case 'M':</span></a>
+<a name="3640"><span class="lineNum">    3640 </span><span class="lineCov">     570037 :     max = std::abs(d[*n-1]);</span></a>
+<a name="3641"><span class="lineNum">    3641 </span><span class="lineCov">    2255853 :       for(i=0;i&lt;(*n-1);i++) {</span></a>
+<a name="3642"><span class="lineNum">    3642 </span><span class="lineCov">    1685816 :         dtemp = std::abs(d[i]);</span></a>
+<a name="3643"><span class="lineNum">    3643 </span><span class="lineCov">    1685816 :         if(dtemp&gt;max)</span></a>
+<a name="3644"><span class="lineNum">    3644 </span>            :           max = dtemp;</a>
+<a name="3645"><span class="lineNum">    3645 </span><span class="lineCov">    1685816 :         dtemp = std::abs(e[i]);</span></a>
+<a name="3646"><span class="lineNum">    3646 </span><span class="lineCov">    1685816 :         if(dtemp&gt;max)</span></a>
+<a name="3647"><span class="lineNum">    3647 </span>            :           max = dtemp;</a>
+<a name="3648"><span class="lineNum">    3648 </span>            :       }</a>
+<a name="3649"><span class="lineNum">    3649 </span>            :     val = max;</a>
+<a name="3650"><span class="lineNum">    3650 </span>            :     break;</a>
+<a name="3651"><span class="lineNum">    3651 </span>            :     </a>
+<a name="3652"><span class="lineNum">    3652 </span><span class="lineNoCov">          0 :   case 'O':</span></a>
+<a name="3653"><span class="lineNum">    3653 </span>            :   case '1':</a>
+<a name="3654"><span class="lineNum">    3654 </span>            :   case 'I':</a>
+<a name="3655"><span class="lineNum">    3655 </span>            : </a>
+<a name="3656"><span class="lineNum">    3656 </span><span class="lineNoCov">          0 :     if(*n==1)</span></a>
+<a name="3657"><span class="lineNum">    3657 </span><span class="lineNoCov">          0 :       val = std::abs(d[0]);</span></a>
+<a name="3658"><span class="lineNum">    3658 </span>            :     else {</a>
+<a name="3659"><span class="lineNum">    3659 </span><span class="lineNoCov">          0 :       max = std::abs(d[0]) + std::abs(e[0]);</span></a>
+<a name="3660"><span class="lineNum">    3660 </span><span class="lineNoCov">          0 :       dtemp = std::abs(e[*n-2]) + std::abs(d[*n-1]);</span></a>
+<a name="3661"><span class="lineNum">    3661 </span><span class="lineNoCov">          0 :       if(dtemp&gt;max)</span></a>
+<a name="3662"><span class="lineNum">    3662 </span>            :         max = dtemp;</a>
+<a name="3663"><span class="lineNum">    3663 </span><span class="lineNoCov">          0 :       for(i=1;i&lt;(*n-1);i++) {</span></a>
+<a name="3664"><span class="lineNum">    3664 </span><span class="lineNoCov">          0 :         dtemp = std::abs(d[i]) + std::abs(e[i]) + std::abs(e[i-1]);</span></a>
+<a name="3665"><span class="lineNum">    3665 </span><span class="lineNoCov">          0 :         if(dtemp&gt;max)</span></a>
+<a name="3666"><span class="lineNum">    3666 </span>            :           max = dtemp;</a>
+<a name="3667"><span class="lineNum">    3667 </span>            :       }</a>
+<a name="3668"><span class="lineNum">    3668 </span>            :       val = max;</a>
+<a name="3669"><span class="lineNum">    3669 </span>            :     }</a>
+<a name="3670"><span class="lineNum">    3670 </span>            :     break;</a>
+<a name="3671"><span class="lineNum">    3671 </span>            : </a>
+<a name="3672"><span class="lineNum">    3672 </span><span class="lineNoCov">          0 :   case 'F':</span></a>
+<a name="3673"><span class="lineNum">    3673 </span>            :   case 'E':</a>
+<a name="3674"><span class="lineNum">    3674 </span><span class="lineNoCov">          0 :     scale = 0.0;</span></a>
+<a name="3675"><span class="lineNum">    3675 </span><span class="lineNoCov">          0 :     sum   = 1.0;</span></a>
+<a name="3676"><span class="lineNum">    3676 </span><span class="lineNoCov">          0 :     i = *n-1;</span></a>
+<a name="3677"><span class="lineNum">    3677 </span><span class="lineNoCov">          0 :     j = 1;</span></a>
+<a name="3678"><span class="lineNum">    3678 </span><span class="lineNoCov">          0 :     if(*n&gt;1) {</span></a>
+<a name="3679"><span class="lineNum">    3679 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(&amp;i,e,&amp;j,&amp;scale,&amp;sum);</span></a>
+<a name="3680"><span class="lineNum">    3680 </span><span class="lineNoCov">          0 :       sum *= 2;</span></a>
+<a name="3681"><span class="lineNum">    3681 </span>            :     }</a>
+<a name="3682"><span class="lineNum">    3682 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(n,d,&amp;j,&amp;scale,&amp;sum);</span></a>
+<a name="3683"><span class="lineNum">    3683 </span><span class="lineNoCov">          0 :     val = scale *  std::sqrt(sum);</span></a>
+<a name="3684"><span class="lineNum">    3684 </span><span class="lineNoCov">          0 :     break;</span></a>
+<a name="3685"><span class="lineNum">    3685 </span>            :     </a>
+<a name="3686"><span class="lineNum">    3686 </span>            :   default:</a>
+<a name="3687"><span class="lineNum">    3687 </span>            :     val = 0.0;</a>
+<a name="3688"><span class="lineNum">    3688 </span>            :     break;</a>
+<a name="3689"><span class="lineNum">    3689 </span>            :   }</a>
+<a name="3690"><span class="lineNum">    3690 </span>            :   return val;</a>
+<a name="3691"><span class="lineNum">    3691 </span>            : }</a>
+<a name="3692"><span class="lineNum">    3692 </span>            : }</a>
+<a name="3693"><span class="lineNum">    3693 </span>            : }</a>
+<a name="3694"><span class="lineNum">    3694 </span>            : #include &lt;cmath&gt;</a>
+<a name="3695"><span class="lineNum">    3695 </span>            : </a>
+<a name="3696"><span class="lineNum">    3696 </span>            : </a>
+<a name="3697"><span class="lineNum">    3697 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3698"><span class="lineNum">    3698 </span>            : </a>
+<a name="3699"><span class="lineNum">    3699 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3700"><span class="lineNum">    3700 </span>            : namespace PLMD{</a>
+<a name="3701"><span class="lineNum">    3701 </span>            : namespace lapack{</a>
+<a name="3702"><span class="lineNum">    3702 </span>            : using namespace blas;</a>
+<a name="3703"><span class="lineNum">    3703 </span>            : double </a>
+<a name="3704"><span class="lineNum">    3704 </span><span class="lineCov">     570008 : PLUMED_BLAS_F77_FUNC(dlansy,DLANSY)(const char *norm, const char *uplo, int *n, double *a, int </span></a>
+<a name="3705"><span class="lineNum">    3705 </span>            :         *lda, double *work)</a>
+<a name="3706"><span class="lineNum">    3706 </span>            : {</a>
+<a name="3707"><span class="lineNum">    3707 </span>            :     /* System generated locals */</a>
+<a name="3708"><span class="lineNum">    3708 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="3709"><span class="lineNum">    3709 </span>            :     double ret_val, d__1, d__2, d__3;</a>
+<a name="3710"><span class="lineNum">    3710 </span><span class="lineCov">     570008 :     int c__1 = 1;</span></a>
+<a name="3711"><span class="lineNum">    3711 </span>            : </a>
+<a name="3712"><span class="lineNum">    3712 </span>            :     /* Local variables */</a>
+<a name="3713"><span class="lineNum">    3713 </span>            :     int i__, j;</a>
+<a name="3714"><span class="lineNum">    3714 </span>            :     double sum, absa, scale;</a>
+<a name="3715"><span class="lineNum">    3715 </span>            :     double value =0.0;</a>
+<a name="3716"><span class="lineNum">    3716 </span>            : </a>
+<a name="3717"><span class="lineNum">    3717 </span><span class="lineCov">     570008 :     a_dim1 = *lda;</span></a>
+<a name="3718"><span class="lineNum">    3718 </span><span class="lineCov">     570008 :     a_offset = 1 + a_dim1;</span></a>
+<a name="3719"><span class="lineNum">    3719 </span><span class="lineCov">     570008 :     a -= a_offset;</span></a>
+<a name="3720"><span class="lineNum">    3720 </span><span class="lineCov">     570008 :     --work;</span></a>
+<a name="3721"><span class="lineNum">    3721 </span>            : </a>
+<a name="3722"><span class="lineNum">    3722 </span><span class="lineCov">     570008 :     if (*n == 0) {</span></a>
+<a name="3723"><span class="lineNum">    3723 </span>            :         value = 0.;</a>
+<a name="3724"><span class="lineNum">    3724 </span><span class="lineCov">     570008 :     } else if (*norm=='M' || *norm=='m') {</span></a>
+<a name="3725"><span class="lineNum">    3725 </span>            : </a>
+<a name="3726"><span class="lineNum">    3726 </span>            :         value = 0.;</a>
+<a name="3727"><span class="lineNum">    3727 </span><span class="lineCov">     570008 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="3728"><span class="lineNum">    3728 </span><span class="lineCov">     570008 :             i__1 = *n;</span></a>
+<a name="3729"><span class="lineNum">    3729 </span><span class="lineCov">    2824437 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3730"><span class="lineNum">    3730 </span>            :                 i__2 = j;</a>
+<a name="3731"><span class="lineNum">    3731 </span><span class="lineCov">    8056735 :                 for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3732"><span class="lineNum">    3732 </span>            :                   d__2 = value;</a>
+<a name="3733"><span class="lineNum">    3733 </span><span class="lineCov">    5802306 :                   d__3 = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="3734"><span class="lineNum">    3734 </span><span class="lineCov">    5802306 :                   value = (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="3735"><span class="lineNum">    3735 </span>            :                 }</a>
+<a name="3736"><span class="lineNum">    3736 </span>            :             }</a>
+<a name="3737"><span class="lineNum">    3737 </span>            :         } else {</a>
+<a name="3738"><span class="lineNum">    3738 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3739"><span class="lineNum">    3739 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3740"><span class="lineNum">    3740 </span>            :                 i__2 = *n;</a>
+<a name="3741"><span class="lineNum">    3741 </span><span class="lineNoCov">          0 :                 for (i__ = j; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3742"><span class="lineNum">    3742 </span>            :                   d__2 = value;</a>
+<a name="3743"><span class="lineNum">    3743 </span><span class="lineNoCov">          0 :                   d__3 = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="3744"><span class="lineNum">    3744 </span><span class="lineNoCov">          0 :                     value =  (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="3745"><span class="lineNum">    3745 </span>            :                 }</a>
+<a name="3746"><span class="lineNum">    3746 </span>            :             }</a>
+<a name="3747"><span class="lineNum">    3747 </span>            :         }</a>
+<a name="3748"><span class="lineNum">    3748 </span><span class="lineNoCov">          0 :     } else if (*norm=='I' || *norm=='i' || *norm=='O' || *norm=='o' || *norm=='1') {</span></a>
+<a name="3749"><span class="lineNum">    3749 </span>            : </a>
+<a name="3750"><span class="lineNum">    3750 </span>            :         value = 0.;</a>
+<a name="3751"><span class="lineNum">    3751 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="3752"><span class="lineNum">    3752 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3753"><span class="lineNum">    3753 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3754"><span class="lineNum">    3754 </span><span class="lineNoCov">          0 :                 sum = 0.;</span></a>
+<a name="3755"><span class="lineNum">    3755 </span><span class="lineNoCov">          0 :                 i__2 = j - 1;</span></a>
+<a name="3756"><span class="lineNum">    3756 </span><span class="lineNoCov">          0 :                 for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3757"><span class="lineNum">    3757 </span><span class="lineNoCov">          0 :                     absa = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="3758"><span class="lineNum">    3758 </span><span class="lineNoCov">          0 :                     sum += absa;</span></a>
+<a name="3759"><span class="lineNum">    3759 </span><span class="lineNoCov">          0 :                     work[i__] += absa;</span></a>
+<a name="3760"><span class="lineNum">    3760 </span>            :                 }</a>
+<a name="3761"><span class="lineNum">    3761 </span><span class="lineNoCov">          0 :                 work[j] = sum + std::abs(a[j + j * a_dim1]);</span></a>
+<a name="3762"><span class="lineNum">    3762 </span>            :             }</a>
+<a name="3763"><span class="lineNum">    3763 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3764"><span class="lineNum">    3764 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3765"><span class="lineNum">    3765 </span><span class="lineNoCov">          0 :                 d__1 = value, d__2 = work[i__];</span></a>
+<a name="3766"><span class="lineNum">    3766 </span><span class="lineNoCov">          0 :                 value =  (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="3767"><span class="lineNum">    3767 </span>            :             }</a>
+<a name="3768"><span class="lineNum">    3768 </span>            :         } else {</a>
+<a name="3769"><span class="lineNum">    3769 </span>            :             i__1 = *n;</a>
+<a name="3770"><span class="lineNum">    3770 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3771"><span class="lineNum">    3771 </span><span class="lineNoCov">          0 :                 work[i__] = 0.;</span></a>
+<a name="3772"><span class="lineNum">    3772 </span>            :             }</a>
+<a name="3773"><span class="lineNum">    3773 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3774"><span class="lineNum">    3774 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3775"><span class="lineNum">    3775 </span><span class="lineNoCov">          0 :                 sum = work[j] + std::abs(a[j + j * a_dim1]);</span></a>
+<a name="3776"><span class="lineNum">    3776 </span><span class="lineNoCov">          0 :                 i__2 = *n;</span></a>
+<a name="3777"><span class="lineNum">    3777 </span><span class="lineNoCov">          0 :                 for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="3778"><span class="lineNum">    3778 </span><span class="lineNoCov">          0 :                     absa = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="3779"><span class="lineNum">    3779 </span><span class="lineNoCov">          0 :                     sum += absa;</span></a>
+<a name="3780"><span class="lineNum">    3780 </span><span class="lineNoCov">          0 :                     work[i__] += absa;</span></a>
+<a name="3781"><span class="lineNum">    3781 </span>            :                 }</a>
+<a name="3782"><span class="lineNum">    3782 </span><span class="lineNoCov">          0 :                 if(sum&gt;value)</span></a>
+<a name="3783"><span class="lineNum">    3783 </span>            :                   value = sum;</a>
+<a name="3784"><span class="lineNum">    3784 </span>            :             }</a>
+<a name="3785"><span class="lineNum">    3785 </span>            :         }</a>
+<a name="3786"><span class="lineNum">    3786 </span>            :     } else if (*norm=='F' || *norm=='f' || *norm=='E' || *norm=='e') {</a>
+<a name="3787"><span class="lineNum">    3787 </span>            : </a>
+<a name="3788"><span class="lineNum">    3788 </span><span class="lineNoCov">          0 :         scale = 0.;</span></a>
+<a name="3789"><span class="lineNum">    3789 </span><span class="lineNoCov">          0 :         sum = 1.;</span></a>
+<a name="3790"><span class="lineNum">    3790 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="3791"><span class="lineNum">    3791 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="3792"><span class="lineNum">    3792 </span><span class="lineNoCov">          0 :             for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="3793"><span class="lineNum">    3793 </span><span class="lineNoCov">          0 :                 i__2 = j - 1;</span></a>
+<a name="3794"><span class="lineNum">    3794 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(&amp;i__2, &amp;a[j * a_dim1 + 1], &amp;c__1, &amp;scale, &amp;sum);</span></a>
+<a name="3795"><span class="lineNum">    3795 </span>            :             }</a>
+<a name="3796"><span class="lineNum">    3796 </span>            :         } else {</a>
+<a name="3797"><span class="lineNum">    3797 </span><span class="lineNoCov">          0 :             i__1 = *n - 1;</span></a>
+<a name="3798"><span class="lineNum">    3798 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="3799"><span class="lineNum">    3799 </span><span class="lineNoCov">          0 :                 i__2 = *n - j;</span></a>
+<a name="3800"><span class="lineNum">    3800 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(&amp;i__2, &amp;a[j + 1 + j * a_dim1], &amp;c__1, &amp;scale, &amp;sum);</span></a>
+<a name="3801"><span class="lineNum">    3801 </span>            :             }</a>
+<a name="3802"><span class="lineNum">    3802 </span>            :         }</a>
+<a name="3803"><span class="lineNum">    3803 </span><span class="lineNoCov">          0 :         sum *= 2;</span></a>
+<a name="3804"><span class="lineNum">    3804 </span><span class="lineNoCov">          0 :         i__1 = *lda + 1;</span></a>
+<a name="3805"><span class="lineNum">    3805 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(n, &amp;a[a_offset], &amp;i__1, &amp;scale, &amp;sum);</span></a>
+<a name="3806"><span class="lineNum">    3806 </span><span class="lineNoCov">          0 :         value = scale *  std::sqrt(sum);</span></a>
+<a name="3807"><span class="lineNum">    3807 </span>            :     }</a>
+<a name="3808"><span class="lineNum">    3808 </span>            : </a>
+<a name="3809"><span class="lineNum">    3809 </span>            :     ret_val = value;</a>
+<a name="3810"><span class="lineNum">    3810 </span><span class="lineCov">     570008 :     return ret_val;</span></a>
+<a name="3811"><span class="lineNum">    3811 </span>            : }</a>
+<a name="3812"><span class="lineNum">    3812 </span>            : </a>
+<a name="3813"><span class="lineNum">    3813 </span>            : </a>
+<a name="3814"><span class="lineNum">    3814 </span>            : }</a>
+<a name="3815"><span class="lineNum">    3815 </span>            : }</a>
+<a name="3816"><span class="lineNum">    3816 </span>            : #include &lt;cmath&gt;</a>
+<a name="3817"><span class="lineNum">    3817 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3818"><span class="lineNum">    3818 </span>            : </a>
+<a name="3819"><span class="lineNum">    3819 </span>            : #include &quot;real.h&quot;</a>
+<a name="3820"><span class="lineNum">    3820 </span>            : </a>
+<a name="3821"><span class="lineNum">    3821 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3822"><span class="lineNum">    3822 </span>            : namespace PLMD{</a>
+<a name="3823"><span class="lineNum">    3823 </span>            : namespace lapack{</a>
+<a name="3824"><span class="lineNum">    3824 </span>            : using namespace blas;</a>
+<a name="3825"><span class="lineNum">    3825 </span>            : double</a>
+<a name="3826"><span class="lineNum">    3826 </span><span class="lineCov">    1119236 : PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(double * x, double * y)</span></a>
+<a name="3827"><span class="lineNum">    3827 </span>            : {</a>
+<a name="3828"><span class="lineNum">    3828 </span>            :   double xabs,yabs;</a>
+<a name="3829"><span class="lineNum">    3829 </span>            :   double w,z;</a>
+<a name="3830"><span class="lineNum">    3830 </span>            : </a>
+<a name="3831"><span class="lineNum">    3831 </span><span class="lineCov">    1119236 :   xabs = std::abs(*x);</span></a>
+<a name="3832"><span class="lineNum">    3832 </span><span class="lineCov">    1119236 :   yabs = std::abs(*y);</span></a>
+<a name="3833"><span class="lineNum">    3833 </span>            :   </a>
+<a name="3834"><span class="lineNum">    3834 </span><span class="lineCov">    1119236 :   if(xabs&gt;yabs) {</span></a>
+<a name="3835"><span class="lineNum">    3835 </span>            :     w = xabs;</a>
+<a name="3836"><span class="lineNum">    3836 </span>            :     z = yabs;</a>
+<a name="3837"><span class="lineNum">    3837 </span>            :   } else {</a>
+<a name="3838"><span class="lineNum">    3838 </span>            :     w = yabs;</a>
+<a name="3839"><span class="lineNum">    3839 </span>            :     z = xabs;</a>
+<a name="3840"><span class="lineNum">    3840 </span>            :   }</a>
+<a name="3841"><span class="lineNum">    3841 </span>            : </a>
+<a name="3842"><span class="lineNum">    3842 </span><span class="lineCov">    1119236 :   if( std::abs(z)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="3843"><span class="lineNum">    3843 </span>            :     return w;</a>
+<a name="3844"><span class="lineNum">    3844 </span>            :   else {</a>
+<a name="3845"><span class="lineNum">    3845 </span><span class="lineCov">    1119236 :     z = z/w;</span></a>
+<a name="3846"><span class="lineNum">    3846 </span><span class="lineCov">    1119236 :     return w* std::sqrt(1.0+z*z);</span></a>
+<a name="3847"><span class="lineNum">    3847 </span>            :   }</a>
+<a name="3848"><span class="lineNum">    3848 </span>            : }</a>
+<a name="3849"><span class="lineNum">    3849 </span>            :   </a>
+<a name="3850"><span class="lineNum">    3850 </span>            : }</a>
+<a name="3851"><span class="lineNum">    3851 </span>            : }</a>
+<a name="3852"><span class="lineNum">    3852 </span>            : #include &lt;cmath&gt;</a>
+<a name="3853"><span class="lineNum">    3853 </span>            : </a>
+<a name="3854"><span class="lineNum">    3854 </span>            : #include &quot;real.h&quot;</a>
+<a name="3855"><span class="lineNum">    3855 </span>            : </a>
+<a name="3856"><span class="lineNum">    3856 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="3857"><span class="lineNum">    3857 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="3858"><span class="lineNum">    3858 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="3859"><span class="lineNum">    3859 </span>            : namespace PLMD{</a>
+<a name="3860"><span class="lineNum">    3860 </span>            : namespace lapack{</a>
+<a name="3861"><span class="lineNum">    3861 </span>            : using namespace blas;</a>
+<a name="3862"><span class="lineNum">    3862 </span>            : </a>
+<a name="3863"><span class="lineNum">    3863 </span><span class="lineCov">     608139 : void PLUMED_BLAS_F77_FUNC(dlar1vx,DLAR1VX)(int *n, </span></a>
+<a name="3864"><span class="lineNum">    3864 </span>            :               int *b1, </a>
+<a name="3865"><span class="lineNum">    3865 </span>            :               int *bn,</a>
+<a name="3866"><span class="lineNum">    3866 </span>            :               double *sigma, </a>
+<a name="3867"><span class="lineNum">    3867 </span>            :               double *d__, </a>
+<a name="3868"><span class="lineNum">    3868 </span>            :               double *l, </a>
+<a name="3869"><span class="lineNum">    3869 </span>            :               double *ld, </a>
+<a name="3870"><span class="lineNum">    3870 </span>            :               double *lld, </a>
+<a name="3871"><span class="lineNum">    3871 </span>            :               double *eval, </a>
+<a name="3872"><span class="lineNum">    3872 </span>            :               double *gersch, </a>
+<a name="3873"><span class="lineNum">    3873 </span>            :               double *z__, </a>
+<a name="3874"><span class="lineNum">    3874 </span>            :               double *ztz, </a>
+<a name="3875"><span class="lineNum">    3875 </span>            :               double *mingma, </a>
+<a name="3876"><span class="lineNum">    3876 </span>            :               int *r__, </a>
+<a name="3877"><span class="lineNum">    3877 </span>            :               int *isuppz, </a>
+<a name="3878"><span class="lineNum">    3878 </span>            :               double *work)</a>
+<a name="3879"><span class="lineNum">    3879 </span>            : {</a>
+<a name="3880"><span class="lineNum">    3880 </span>            :     int i__1;</a>
+<a name="3881"><span class="lineNum">    3881 </span>            : </a>
+<a name="3882"><span class="lineNum">    3882 </span>            :     int i__, j;</a>
+<a name="3883"><span class="lineNum">    3883 </span>            :     double s;</a>
+<a name="3884"><span class="lineNum">    3884 </span>            :     int r1, r2;</a>
+<a name="3885"><span class="lineNum">    3885 </span>            :     int to;</a>
+<a name="3886"><span class="lineNum">    3886 </span>            :     double eps, tmp;</a>
+<a name="3887"><span class="lineNum">    3887 </span>            :     int indp, inds, from;</a>
+<a name="3888"><span class="lineNum">    3888 </span>            :     double dplus;</a>
+<a name="3889"><span class="lineNum">    3889 </span>            :     int sawnan;</a>
+<a name="3890"><span class="lineNum">    3890 </span>            :     int indumn;</a>
+<a name="3891"><span class="lineNum">    3891 </span>            :     double dminus;</a>
+<a name="3892"><span class="lineNum">    3892 </span>            : </a>
+<a name="3893"><span class="lineNum">    3893 </span><span class="lineCov">     608139 :     --work;</span></a>
+<a name="3894"><span class="lineNum">    3894 </span>            :     --isuppz;</a>
+<a name="3895"><span class="lineNum">    3895 </span><span class="lineCov">     608139 :     --z__;</span></a>
+<a name="3896"><span class="lineNum">    3896 </span><span class="lineCov">     608139 :     --gersch;</span></a>
+<a name="3897"><span class="lineNum">    3897 </span><span class="lineCov">     608139 :     --lld;</span></a>
+<a name="3898"><span class="lineNum">    3898 </span><span class="lineCov">     608139 :     --ld;</span></a>
+<a name="3899"><span class="lineNum">    3899 </span><span class="lineCov">     608139 :     --l;</span></a>
+<a name="3900"><span class="lineNum">    3900 </span><span class="lineCov">     608139 :     --d__;</span></a>
+<a name="3901"><span class="lineNum">    3901 </span>            : </a>
+<a name="3902"><span class="lineNum">    3902 </span>            :     /* Function Body */</a>
+<a name="3903"><span class="lineNum">    3903 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="3904"><span class="lineNum">    3904 </span><span class="lineCov">     608139 :     if (*r__ == 0) {</span></a>
+<a name="3905"><span class="lineNum">    3905 </span>            : </a>
+<a name="3906"><span class="lineNum">    3906 </span><span class="lineCov">     606866 :         r1 = *b1;</span></a>
+<a name="3907"><span class="lineNum">    3907 </span><span class="lineCov">     606866 :         r2 = *bn;</span></a>
+<a name="3908"><span class="lineNum">    3908 </span>            :         i__1 = *bn;</a>
+<a name="3909"><span class="lineNum">    3909 </span><span class="lineCov">    1399107 :         for (i__ = *b1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3910"><span class="lineNum">    3910 </span><span class="lineCov">    1399107 :             if (*eval &gt;= gersch[(i__ &lt;&lt; 1) - 1] &amp;&amp; *eval &lt;= gersch[i__ * 2]) {</span></a>
+<a name="3911"><span class="lineNum">    3911 </span>            :                 r1 = i__;</a>
+<a name="3912"><span class="lineNum">    3912 </span><span class="lineCov">     606866 :                 goto L20;</span></a>
+<a name="3913"><span class="lineNum">    3913 </span>            :             }</a>
+<a name="3914"><span class="lineNum">    3914 </span>            :         }</a>
+<a name="3915"><span class="lineNum">    3915 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="3916"><span class="lineNum">    3916 </span>            : L20:</a>
+<a name="3917"><span class="lineNum">    3917 </span>            :         i__1 = *b1;</a>
+<a name="3918"><span class="lineNum">    3918 </span><span class="lineCov">    1557137 :         for (i__ = *bn; i__ &gt;= i__1; --i__) {</span></a>
+<a name="3919"><span class="lineNum">    3919 </span><span class="lineCov">    1557137 :             if (*eval &gt;= gersch[(i__ &lt;&lt; 1) - 1] &amp;&amp; *eval &lt;= gersch[i__ * 2]) {</span></a>
+<a name="3920"><span class="lineNum">    3920 </span>            :                 r2 = i__;</a>
+<a name="3921"><span class="lineNum">    3921 </span><span class="lineCov">     606866 :                 goto L40;</span></a>
+<a name="3922"><span class="lineNum">    3922 </span>            :             }</a>
+<a name="3923"><span class="lineNum">    3923 </span>            :         }</a>
+<a name="3924"><span class="lineNum">    3924 </span>            :     } else {</a>
+<a name="3925"><span class="lineNum">    3925 </span>            :         r1 = *r__;</a>
+<a name="3926"><span class="lineNum">    3926 </span>            :         r2 = *r__;</a>
+<a name="3927"><span class="lineNum">    3927 </span>            :     }</a>
+<a name="3928"><span class="lineNum">    3928 </span>            : </a>
+<a name="3929"><span class="lineNum">    3929 </span><span class="lineCov">     608139 : L40:</span></a>
+<a name="3930"><span class="lineNum">    3930 </span><span class="lineCov">     608139 :     indumn = *n;</span></a>
+<a name="3931"><span class="lineNum">    3931 </span><span class="lineCov">     608139 :     inds = (*n &lt;&lt; 1) + 1;</span></a>
+<a name="3932"><span class="lineNum">    3932 </span><span class="lineCov">     608139 :     indp = *n * 3 + 1;</span></a>
+<a name="3933"><span class="lineNum">    3933 </span>            :     sawnan = 0;</a>
+<a name="3934"><span class="lineNum">    3934 </span>            : </a>
+<a name="3935"><span class="lineNum">    3935 </span><span class="lineCov">     608139 :     if (*b1 == 1) {</span></a>
+<a name="3936"><span class="lineNum">    3936 </span><span class="lineCov">     608139 :         work[inds] = 0.;</span></a>
+<a name="3937"><span class="lineNum">    3937 </span>            :     } else {</a>
+<a name="3938"><span class="lineNum">    3938 </span><span class="lineNoCov">          0 :         work[inds] = lld[*b1 - 1];</span></a>
+<a name="3939"><span class="lineNum">    3939 </span>            :     }</a>
+<a name="3940"><span class="lineNum">    3940 </span><span class="lineCov">     608139 :     s = work[inds] - *sigma;</span></a>
+<a name="3941"><span class="lineNum">    3941 </span>            :     i__1 = r2 - 1;</a>
+<a name="3942"><span class="lineNum">    3942 </span><span class="lineCov">    1842521 :     for (i__ = *b1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3943"><span class="lineNum">    3943 </span><span class="lineCov">    1234382 :         dplus = d__[i__] + s;</span></a>
+<a name="3944"><span class="lineNum">    3944 </span><span class="lineCov">    1234382 :         work[i__] = ld[i__] / dplus;</span></a>
+<a name="3945"><span class="lineNum">    3945 </span><span class="lineCov">    1234382 :         work[inds + i__] = s * work[i__] * l[i__];</span></a>
+<a name="3946"><span class="lineNum">    3946 </span><span class="lineCov">    1234382 :         s = work[inds + i__] - *sigma;</span></a>
+<a name="3947"><span class="lineNum">    3947 </span>            :     }</a>
+<a name="3948"><span class="lineNum">    3948 </span>            : </a>
+<a name="3949"><span class="lineNum">    3949 </span><span class="lineCov">     608139 :     if (std::isnan(s)) {</span></a>
+<a name="3950"><span class="lineNum">    3950 </span>            : </a>
+<a name="3951"><span class="lineNum">    3951 </span>            :         sawnan = 1;</a>
+<a name="3952"><span class="lineNum">    3952 </span><span class="lineNoCov">          0 :         j = *b1 + 1;</span></a>
+<a name="3953"><span class="lineNum">    3953 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="3954"><span class="lineNum">    3954 </span><span class="lineNoCov">          0 :     if (!std::isnan(work[inds + j])) {</span></a>
+<a name="3955"><span class="lineNum">    3955 </span><span class="lineNoCov">          0 :             ++j;</span></a>
+<a name="3956"><span class="lineNum">    3956 </span><span class="lineNoCov">          0 :             goto L60;</span></a>
+<a name="3957"><span class="lineNum">    3957 </span>            :         }</a>
+<a name="3958"><span class="lineNum">    3958 </span><span class="lineNoCov">          0 :         work[inds + j] = lld[j];</span></a>
+<a name="3959"><span class="lineNum">    3959 </span><span class="lineNoCov">          0 :         s = work[inds + j] - *sigma;</span></a>
+<a name="3960"><span class="lineNum">    3960 </span>            :         i__1 = r2 - 1;</a>
+<a name="3961"><span class="lineNum">    3961 </span><span class="lineNoCov">          0 :         for (i__ = j + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="3962"><span class="lineNum">    3962 </span><span class="lineNoCov">          0 :             dplus = d__[i__] + s;</span></a>
+<a name="3963"><span class="lineNum">    3963 </span><span class="lineNoCov">          0 :             work[i__] = ld[i__] / dplus;</span></a>
+<a name="3964"><span class="lineNum">    3964 </span><span class="lineNoCov">          0 :             if (std::abs(work[i__])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3965"><span class="lineNum">    3965 </span><span class="lineNoCov">          0 :                 work[inds + i__] = lld[i__];</span></a>
+<a name="3966"><span class="lineNum">    3966 </span>            :             } else {</a>
+<a name="3967"><span class="lineNum">    3967 </span><span class="lineNoCov">          0 :                 work[inds + i__] = s * work[i__] * l[i__];</span></a>
+<a name="3968"><span class="lineNum">    3968 </span>            :             }</a>
+<a name="3969"><span class="lineNum">    3969 </span><span class="lineNoCov">          0 :             s = work[inds + i__] - *sigma;</span></a>
+<a name="3970"><span class="lineNum">    3970 </span>            :         }</a>
+<a name="3971"><span class="lineNum">    3971 </span>            :     }</a>
+<a name="3972"><span class="lineNum">    3972 </span>            : </a>
+<a name="3973"><span class="lineNum">    3973 </span><span class="lineCov">     608139 :     work[indp + *bn - 1] = d__[*bn] - *sigma;</span></a>
+<a name="3974"><span class="lineNum">    3974 </span>            :     i__1 = r1;</a>
+<a name="3975"><span class="lineNum">    3975 </span><span class="lineCov">    2110778 :     for (i__ = *bn - 1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="3976"><span class="lineNum">    3976 </span><span class="lineCov">    1502639 :         dminus = lld[i__] + work[indp + i__];</span></a>
+<a name="3977"><span class="lineNum">    3977 </span><span class="lineCov">    1502639 :         tmp = d__[i__] / dminus;</span></a>
+<a name="3978"><span class="lineNum">    3978 </span><span class="lineCov">    1502639 :         work[indumn + i__] = l[i__] * tmp;</span></a>
+<a name="3979"><span class="lineNum">    3979 </span><span class="lineCov">    1502639 :         work[indp + i__ - 1] = work[indp + i__] * tmp - *sigma;</span></a>
+<a name="3980"><span class="lineNum">    3980 </span>            :     }</a>
+<a name="3981"><span class="lineNum">    3981 </span><span class="lineCov">     608139 :     tmp = work[indp + r1 - 1];</span></a>
+<a name="3982"><span class="lineNum">    3982 </span><span class="lineCov">     608139 :     if (std::isnan(tmp)) {</span></a>
+<a name="3983"><span class="lineNum">    3983 </span>            : </a>
+<a name="3984"><span class="lineNum">    3984 </span>            :         sawnan = 1;</a>
+<a name="3985"><span class="lineNum">    3985 </span><span class="lineNoCov">          0 :         j = *bn - 3;</span></a>
+<a name="3986"><span class="lineNum">    3986 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="3987"><span class="lineNum">    3987 </span><span class="lineNoCov">          0 :     if (!std::isnan(work[indp + j])) {</span></a>
+<a name="3988"><span class="lineNum">    3988 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="3989"><span class="lineNum">    3989 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="3990"><span class="lineNum">    3990 </span>            :         }</a>
+<a name="3991"><span class="lineNum">    3991 </span><span class="lineNoCov">          0 :         work[indp + j] = d__[j + 1] - *sigma;</span></a>
+<a name="3992"><span class="lineNum">    3992 </span>            :         i__1 = r1;</a>
+<a name="3993"><span class="lineNum">    3993 </span><span class="lineNoCov">          0 :         for (i__ = j; i__ &gt;= i__1; --i__) {</span></a>
+<a name="3994"><span class="lineNum">    3994 </span><span class="lineNoCov">          0 :             dminus = lld[i__] + work[indp + i__];</span></a>
+<a name="3995"><span class="lineNum">    3995 </span><span class="lineNoCov">          0 :             tmp = d__[i__] / dminus;</span></a>
+<a name="3996"><span class="lineNum">    3996 </span><span class="lineNoCov">          0 :             work[indumn + i__] = l[i__] * tmp;</span></a>
+<a name="3997"><span class="lineNum">    3997 </span><span class="lineNoCov">          0 :             if (std::abs(tmp)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="3998"><span class="lineNum">    3998 </span><span class="lineNoCov">          0 :                 work[indp + i__ - 1] = d__[i__] - *sigma;</span></a>
+<a name="3999"><span class="lineNum">    3999 </span>            :             } else {</a>
+<a name="4000"><span class="lineNum">    4000 </span><span class="lineNoCov">          0 :                 work[indp + i__ - 1] = work[indp + i__] * tmp - *sigma;</span></a>
+<a name="4001"><span class="lineNum">    4001 </span>            :             }</a>
+<a name="4002"><span class="lineNum">    4002 </span>            :         }</a>
+<a name="4003"><span class="lineNum">    4003 </span>            :     }</a>
+<a name="4004"><span class="lineNum">    4004 </span>            : </a>
+<a name="4005"><span class="lineNum">    4005 </span><span class="lineCov">     608139 :     *mingma = work[inds + r1 - 1] + work[indp + r1 - 1];</span></a>
+<a name="4006"><span class="lineNum">    4006 </span><span class="lineCov">     608139 :     if (std::abs(*mingma)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4007"><span class="lineNum">    4007 </span><span class="lineCov">      45745 :         *mingma = eps * work[inds + r1 - 1];</span></a>
+<a name="4008"><span class="lineNum">    4008 </span>            :     }</a>
+<a name="4009"><span class="lineNum">    4009 </span><span class="lineCov">     608139 :     *r__ = r1;</span></a>
+<a name="4010"><span class="lineNum">    4010 </span>            :     i__1 = r2 - 1;</a>
+<a name="4011"><span class="lineNum">    4011 </span><span class="lineCov">     956212 :     for (i__ = r1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="4012"><span class="lineNum">    4012 </span><span class="lineCov">     348073 :         tmp = work[inds + i__] + work[indp + i__];</span></a>
+<a name="4013"><span class="lineNum">    4013 </span><span class="lineCov">     348073 :         if (std::abs(tmp)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4014"><span class="lineNum">    4014 </span><span class="lineCov">      23351 :             tmp = eps * work[inds + i__];</span></a>
+<a name="4015"><span class="lineNum">    4015 </span>            :         }</a>
+<a name="4016"><span class="lineNum">    4016 </span><span class="lineCov">     348073 :         if (std::abs(tmp) &lt; std::abs(*mingma)) {</span></a>
+<a name="4017"><span class="lineNum">    4017 </span><span class="lineCov">      50702 :             *mingma = tmp;</span></a>
+<a name="4018"><span class="lineNum">    4018 </span><span class="lineCov">      50702 :             *r__ = i__ + 1;</span></a>
+<a name="4019"><span class="lineNum">    4019 </span>            :         }</a>
+<a name="4020"><span class="lineNum">    4020 </span>            :     }</a>
+<a name="4021"><span class="lineNum">    4021 </span>            : </a>
+<a name="4022"><span class="lineNum">    4022 </span><span class="lineCov">     608139 :     isuppz[1] = *b1;</span></a>
+<a name="4023"><span class="lineNum">    4023 </span><span class="lineCov">     608139 :     isuppz[2] = *bn;</span></a>
+<a name="4024"><span class="lineNum">    4024 </span><span class="lineCov">     608139 :     z__[*r__] = 1.;</span></a>
+<a name="4025"><span class="lineNum">    4025 </span><span class="lineCov">     608139 :     *ztz = 1.;</span></a>
+<a name="4026"><span class="lineNum">    4026 </span><span class="lineCov">     608139 :     if (! sawnan) {</span></a>
+<a name="4027"><span class="lineNum">    4027 </span><span class="lineCov">     608139 :         from = *r__ - 1;</span></a>
+<a name="4028"><span class="lineNum">    4028 </span><span class="lineCov">     608139 :         i__1 = *r__ - 32;</span></a>
+<a name="4029"><span class="lineNum">    4029 </span><span class="lineCov">     608139 :         to = (i__1&gt;(*b1)) ? i__1 : (*b1);</span></a>
+<a name="4030"><span class="lineNum">    4030 </span>            : L120:</a>
+<a name="4031"><span class="lineNum">    4031 </span><span class="lineCov">    1148734 :         if (from &gt;= *b1) {</span></a>
+<a name="4032"><span class="lineNum">    4032 </span>            :             i__1 = to;</a>
+<a name="4033"><span class="lineNum">    4033 </span><span class="lineCov">    1355280 :             for (i__ = from; i__ &gt;= i__1; --i__) {</span></a>
+<a name="4034"><span class="lineNum">    4034 </span><span class="lineCov">     813473 :                 z__[i__] = -(work[i__] * z__[i__ + 1]);</span></a>
+<a name="4035"><span class="lineNum">    4035 </span><span class="lineCov">     813473 :                 *ztz += z__[i__] * z__[i__];</span></a>
+<a name="4036"><span class="lineNum">    4036 </span>            :             }</a>
+<a name="4037"><span class="lineNum">    4037 </span><span class="lineCov">     541807 :             if (std::abs(z__[to]) &lt;= eps &amp;&amp; std::abs(z__[to + 1]) &lt;= eps) {</span></a>
+<a name="4038"><span class="lineNum">    4038 </span><span class="lineCov">       1212 :                 isuppz[1] = to + 2;</span></a>
+<a name="4039"><span class="lineNum">    4039 </span>            :             } else {</a>
+<a name="4040"><span class="lineNum">    4040 </span><span class="lineCov">     540595 :                 from = to - 1;</span></a>
+<a name="4041"><span class="lineNum">    4041 </span><span class="lineCov">     540595 :                 i__1 = to - 32;</span></a>
+<a name="4042"><span class="lineNum">    4042 </span><span class="lineCov">     540595 :                 to = (i__1&gt;*b1) ? i__1 : *b1;</span></a>
+<a name="4043"><span class="lineNum">    4043 </span><span class="lineCov">     540595 :                 goto L120;</span></a>
+<a name="4044"><span class="lineNum">    4044 </span>            :             }</a>
+<a name="4045"><span class="lineNum">    4045 </span>            :         }</a>
+<a name="4046"><span class="lineNum">    4046 </span><span class="lineCov">     608139 :         from = *r__ + 1;</span></a>
+<a name="4047"><span class="lineNum">    4047 </span><span class="lineCov">     608139 :         i__1 = *r__ + 32;</span></a>
+<a name="4048"><span class="lineNum">    4048 </span><span class="lineCov">     608139 :         to = (i__1&lt;*bn) ? i__1 : *bn;</span></a>
+<a name="4049"><span class="lineNum">    4049 </span>            : L140:</a>
+<a name="4050"><span class="lineNum">    4050 </span><span class="lineCov">    1192356 :         if (from &lt;= *bn) {</span></a>
+<a name="4051"><span class="lineNum">    4051 </span>            :             i__1 = to;</a>
+<a name="4052"><span class="lineNum">    4052 </span><span class="lineCov">    2016537 :             for (i__ = from; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="4053"><span class="lineNum">    4053 </span><span class="lineCov">    1432314 :                 z__[i__] = -(work[indumn + i__ - 1] * z__[i__ - 1]);</span></a>
+<a name="4054"><span class="lineNum">    4054 </span><span class="lineCov">    1432314 :                 *ztz += z__[i__] * z__[i__];</span></a>
+<a name="4055"><span class="lineNum">    4055 </span>            :             }</a>
+<a name="4056"><span class="lineNum">    4056 </span><span class="lineCov">     584223 :             if (std::abs(z__[to]) &lt;= eps &amp;&amp; std::abs(z__[to - 1]) &lt;= eps) {</span></a>
+<a name="4057"><span class="lineNum">    4057 </span><span class="lineCov">          6 :                 isuppz[2] = to - 2;</span></a>
+<a name="4058"><span class="lineNum">    4058 </span>            :             } else {</a>
+<a name="4059"><span class="lineNum">    4059 </span><span class="lineCov">     584217 :                 from = to + 1;</span></a>
+<a name="4060"><span class="lineNum">    4060 </span><span class="lineCov">     584217 :                 i__1 = to + 32;</span></a>
+<a name="4061"><span class="lineNum">    4061 </span><span class="lineCov">     584217 :                 to = (i__1&lt;*bn) ? i__1 : *bn;</span></a>
+<a name="4062"><span class="lineNum">    4062 </span><span class="lineCov">     584217 :                 goto L140;</span></a>
+<a name="4063"><span class="lineNum">    4063 </span>            :             }</a>
+<a name="4064"><span class="lineNum">    4064 </span>            :         }</a>
+<a name="4065"><span class="lineNum">    4065 </span>            :     } else {</a>
+<a name="4066"><span class="lineNum">    4066 </span><span class="lineNoCov">          0 :         i__1 = *b1;</span></a>
+<a name="4067"><span class="lineNum">    4067 </span><span class="lineNoCov">          0 :         for (i__ = *r__ - 1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="4068"><span class="lineNum">    4068 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__ + 1])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4069"><span class="lineNum">    4069 </span><span class="lineNoCov">          0 :                 z__[i__] = -(ld[i__ + 1] / ld[i__]) * z__[i__ + 2];</span></a>
+<a name="4070"><span class="lineNum">    4070 </span>            :             } else {</a>
+<a name="4071"><span class="lineNum">    4071 </span><span class="lineNoCov">          0 :                 z__[i__] = -(work[i__] * z__[i__ + 1]);</span></a>
+<a name="4072"><span class="lineNum">    4072 </span>            :             }</a>
+<a name="4073"><span class="lineNum">    4073 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__]) &lt;= eps &amp;&amp; std::abs(z__[i__ + 1]) &lt;= eps) {</span></a>
+<a name="4074"><span class="lineNum">    4074 </span><span class="lineNoCov">          0 :                 isuppz[1] = i__ + 2;</span></a>
+<a name="4075"><span class="lineNum">    4075 </span><span class="lineNoCov">          0 :                 goto L170;</span></a>
+<a name="4076"><span class="lineNum">    4076 </span>            :             }</a>
+<a name="4077"><span class="lineNum">    4077 </span><span class="lineNoCov">          0 :             *ztz += z__[i__] * z__[i__];</span></a>
+<a name="4078"><span class="lineNum">    4078 </span>            :         }</a>
+<a name="4079"><span class="lineNum">    4079 </span><span class="lineNoCov">          0 : L170:</span></a>
+<a name="4080"><span class="lineNum">    4080 </span><span class="lineNoCov">          0 :         i__1 = *bn - 1;</span></a>
+<a name="4081"><span class="lineNum">    4081 </span><span class="lineNoCov">          0 :         for (i__ = *r__; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="4082"><span class="lineNum">    4082 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4083"><span class="lineNum">    4083 </span><span class="lineNoCov">          0 :                 z__[i__ + 1] = -(ld[i__ - 1] / ld[i__]) * z__[i__ - 1];</span></a>
+<a name="4084"><span class="lineNum">    4084 </span>            :             } else {</a>
+<a name="4085"><span class="lineNum">    4085 </span><span class="lineNoCov">          0 :                 z__[i__ + 1] = -(work[indumn + i__] * z__[i__]);</span></a>
+<a name="4086"><span class="lineNum">    4086 </span>            :             }</a>
+<a name="4087"><span class="lineNum">    4087 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__]) &lt;= eps &amp;&amp; std::abs(z__[i__ + 1]) &lt;= eps) {</span></a>
+<a name="4088"><span class="lineNum">    4088 </span><span class="lineNoCov">          0 :                 isuppz[2] = i__ - 1;</span></a>
+<a name="4089"><span class="lineNum">    4089 </span><span class="lineNoCov">          0 :                 break;</span></a>
+<a name="4090"><span class="lineNum">    4090 </span>            :             }</a>
+<a name="4091"><span class="lineNum">    4091 </span><span class="lineNoCov">          0 :             *ztz += z__[i__ + 1] * z__[i__ + 1];</span></a>
+<a name="4092"><span class="lineNum">    4092 </span>            :         }</a>
+<a name="4093"><span class="lineNum">    4093 </span>            :     }</a>
+<a name="4094"><span class="lineNum">    4094 </span>            : </a>
+<a name="4095"><span class="lineNum">    4095 </span><span class="lineCov">     608139 :     return;</span></a>
+<a name="4096"><span class="lineNum">    4096 </span>            : </a>
+<a name="4097"><span class="lineNum">    4097 </span>            : }</a>
+<a name="4098"><span class="lineNum">    4098 </span>            : </a>
+<a name="4099"><span class="lineNum">    4099 </span>            : </a>
+<a name="4100"><span class="lineNum">    4100 </span>            : }</a>
+<a name="4101"><span class="lineNum">    4101 </span>            : }</a>
+<a name="4102"><span class="lineNum">    4102 </span>            : #include &lt;cctype&gt;</a>
+<a name="4103"><span class="lineNum">    4103 </span>            : #include &lt;cmath&gt;</a>
+<a name="4104"><span class="lineNum">    4104 </span>            : </a>
+<a name="4105"><span class="lineNum">    4105 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4106"><span class="lineNum">    4106 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="4107"><span class="lineNum">    4107 </span>            : </a>
+<a name="4108"><span class="lineNum">    4108 </span>            : #include &quot;real.h&quot;</a>
+<a name="4109"><span class="lineNum">    4109 </span>            : </a>
+<a name="4110"><span class="lineNum">    4110 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4111"><span class="lineNum">    4111 </span>            : namespace PLMD{</a>
+<a name="4112"><span class="lineNum">    4112 </span>            : namespace lapack{</a>
+<a name="4113"><span class="lineNum">    4113 </span>            : using namespace blas;</a>
+<a name="4114"><span class="lineNum">    4114 </span>            : void</a>
+<a name="4115"><span class="lineNum">    4115 </span><span class="lineCov">    1689941 : PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(const char *side,</span></a>
+<a name="4116"><span class="lineNum">    4116 </span>            :        int *m,</a>
+<a name="4117"><span class="lineNum">    4117 </span>            :        int *n,</a>
+<a name="4118"><span class="lineNum">    4118 </span>            :        double *v,</a>
+<a name="4119"><span class="lineNum">    4119 </span>            :        int *incv,</a>
+<a name="4120"><span class="lineNum">    4120 </span>            :        double *tau,</a>
+<a name="4121"><span class="lineNum">    4121 </span>            :        double *c,</a>
+<a name="4122"><span class="lineNum">    4122 </span>            :        int *ldc,</a>
+<a name="4123"><span class="lineNum">    4123 </span>            :        double *work)</a>
+<a name="4124"><span class="lineNum">    4124 </span>            : {</a>
+<a name="4125"><span class="lineNum">    4125 </span><span class="lineCov">    1689941 :   const char ch=std::toupper(*side);</span></a>
+<a name="4126"><span class="lineNum">    4126 </span><span class="lineCov">    1689941 :   double one = 1.0;</span></a>
+<a name="4127"><span class="lineNum">    4127 </span><span class="lineCov">    1689941 :   double zero = 0.0;</span></a>
+<a name="4128"><span class="lineNum">    4128 </span><span class="lineCov">    1689941 :   double minustau = -(*tau);</span></a>
+<a name="4129"><span class="lineNum">    4129 </span><span class="lineCov">    1689941 :   int i1 = 1;</span></a>
+<a name="4130"><span class="lineNum">    4130 </span>            : </a>
+<a name="4131"><span class="lineNum">    4131 </span>            : </a>
+<a name="4132"><span class="lineNum">    4132 </span><span class="lineCov">    1689941 :   if(ch=='L') {</span></a>
+<a name="4133"><span class="lineNum">    4133 </span><span class="lineCov">    1686360 :     if(std::abs(*tau)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4134"><span class="lineNum">    4134 </span><span class="lineCov">    1116226 :       PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;T&quot;,m,n,&amp;one,c,ldc,v,incv,&amp;zero,work,&amp;i1);</span></a>
+<a name="4135"><span class="lineNum">    4135 </span><span class="lineCov">    1116226 :       PLUMED_BLAS_F77_FUNC(dger,DGER)(m,n,&amp;minustau,v,incv,work,&amp;i1,c,ldc);</span></a>
+<a name="4136"><span class="lineNum">    4136 </span>            :     }</a>
+<a name="4137"><span class="lineNum">    4137 </span>            :   } else {</a>
+<a name="4138"><span class="lineNum">    4138 </span><span class="lineCov">       3581 :     if(std::abs(*tau)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4139"><span class="lineNum">    4139 </span><span class="lineCov">       3402 :       PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,m,n,&amp;one,c,ldc,v,incv,&amp;zero,work,&amp;i1);</span></a>
+<a name="4140"><span class="lineNum">    4140 </span><span class="lineCov">       3402 :       PLUMED_BLAS_F77_FUNC(dger,DGER)(m,n,&amp;minustau,work,&amp;i1,v,incv,c,ldc);</span></a>
+<a name="4141"><span class="lineNum">    4141 </span>            :     }</a>
+<a name="4142"><span class="lineNum">    4142 </span>            :   }</a>
+<a name="4143"><span class="lineNum">    4143 </span><span class="lineCov">    1689941 :   return;</span></a>
+<a name="4144"><span class="lineNum">    4144 </span>            : }</a>
+<a name="4145"><span class="lineNum">    4145 </span>            : }</a>
+<a name="4146"><span class="lineNum">    4146 </span>            : }</a>
+<a name="4147"><span class="lineNum">    4147 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4148"><span class="lineNum">    4148 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="4149"><span class="lineNum">    4149 </span>            : </a>
+<a name="4150"><span class="lineNum">    4150 </span>            : </a>
+<a name="4151"><span class="lineNum">    4151 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4152"><span class="lineNum">    4152 </span>            : namespace PLMD{</a>
+<a name="4153"><span class="lineNum">    4153 </span>            : namespace lapack{</a>
+<a name="4154"><span class="lineNum">    4154 </span>            : using namespace blas;</a>
+<a name="4155"><span class="lineNum">    4155 </span>            : void </a>
+<a name="4156"><span class="lineNum">    4156 </span><span class="lineCov">        147 : PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(const char *side, </span></a>
+<a name="4157"><span class="lineNum">    4157 </span>            :         const char *trans, </a>
+<a name="4158"><span class="lineNum">    4158 </span>            :         const char *direct, </a>
+<a name="4159"><span class="lineNum">    4159 </span>            :         const char *storev, </a>
+<a name="4160"><span class="lineNum">    4160 </span>            :         int *m, </a>
+<a name="4161"><span class="lineNum">    4161 </span>            :         int *n, </a>
+<a name="4162"><span class="lineNum">    4162 </span>            :         int *k, </a>
+<a name="4163"><span class="lineNum">    4163 </span>            :         double *v, </a>
+<a name="4164"><span class="lineNum">    4164 </span>            :         int *ldv, </a>
+<a name="4165"><span class="lineNum">    4165 </span>            :         double *t, </a>
+<a name="4166"><span class="lineNum">    4166 </span>            :         int *ldt, </a>
+<a name="4167"><span class="lineNum">    4167 </span>            :         double *c__,</a>
+<a name="4168"><span class="lineNum">    4168 </span>            :         int *ldc, </a>
+<a name="4169"><span class="lineNum">    4169 </span>            :         double *work, </a>
+<a name="4170"><span class="lineNum">    4170 </span>            :         int *ldwork)</a>
+<a name="4171"><span class="lineNum">    4171 </span>            : {</a>
+<a name="4172"><span class="lineNum">    4172 </span>            :     int c_dim1, c_offset, t_dim1, t_offset, v_dim1, v_offset, work_dim1, </a>
+<a name="4173"><span class="lineNum">    4173 </span>            :             work_offset, i__1, i__2;</a>
+<a name="4174"><span class="lineNum">    4174 </span>            : </a>
+<a name="4175"><span class="lineNum">    4175 </span>            :     int i__, j;</a>
+<a name="4176"><span class="lineNum">    4176 </span>            :     char transt[1];</a>
+<a name="4177"><span class="lineNum">    4177 </span><span class="lineCov">        147 :     int c__1 = 1;</span></a>
+<a name="4178"><span class="lineNum">    4178 </span><span class="lineCov">        147 :     double one = 1.0;</span></a>
+<a name="4179"><span class="lineNum">    4179 </span><span class="lineCov">        147 :     double minusone = -1.0;</span></a>
+<a name="4180"><span class="lineNum">    4180 </span>            : </a>
+<a name="4181"><span class="lineNum">    4181 </span><span class="lineCov">        147 :     v_dim1 = *ldv;</span></a>
+<a name="4182"><span class="lineNum">    4182 </span><span class="lineCov">        147 :     v_offset = 1 + v_dim1;</span></a>
+<a name="4183"><span class="lineNum">    4183 </span><span class="lineCov">        147 :     v -= v_offset;</span></a>
+<a name="4184"><span class="lineNum">    4184 </span>            :     t_dim1 = *ldt;</a>
+<a name="4185"><span class="lineNum">    4185 </span>            :     t_offset = 1 + t_dim1;</a>
+<a name="4186"><span class="lineNum">    4186 </span>            :     t -= t_offset;</a>
+<a name="4187"><span class="lineNum">    4187 </span><span class="lineCov">        147 :     c_dim1 = *ldc;</span></a>
+<a name="4188"><span class="lineNum">    4188 </span><span class="lineCov">        147 :     c_offset = 1 + c_dim1;</span></a>
+<a name="4189"><span class="lineNum">    4189 </span><span class="lineCov">        147 :     c__ -= c_offset;</span></a>
+<a name="4190"><span class="lineNum">    4190 </span><span class="lineCov">        147 :     work_dim1 = *ldwork;</span></a>
+<a name="4191"><span class="lineNum">    4191 </span><span class="lineCov">        147 :     work_offset = 1 + work_dim1;</span></a>
+<a name="4192"><span class="lineNum">    4192 </span><span class="lineCov">        147 :     work -= work_offset;</span></a>
+<a name="4193"><span class="lineNum">    4193 </span>            : </a>
+<a name="4194"><span class="lineNum">    4194 </span><span class="lineCov">        147 :     if (*m &lt;= 0 || *n &lt;= 0) {</span></a>
+<a name="4195"><span class="lineNum">    4195 </span>            :         return;</a>
+<a name="4196"><span class="lineNum">    4196 </span>            :     }</a>
+<a name="4197"><span class="lineNum">    4197 </span><span class="lineCov">        147 :     if (*trans=='N' || *trans=='n') {</span></a>
+<a name="4198"><span class="lineNum">    4198 </span><span class="lineCov">        107 :       *(unsigned char *)transt = 'T';</span></a>
+<a name="4199"><span class="lineNum">    4199 </span>            :     } else {</a>
+<a name="4200"><span class="lineNum">    4200 </span><span class="lineCov">         40 :         *(unsigned char *)transt = 'N';</span></a>
+<a name="4201"><span class="lineNum">    4201 </span>            :     }</a>
+<a name="4202"><span class="lineNum">    4202 </span>            :     </a>
+<a name="4203"><span class="lineNum">    4203 </span><span class="lineCov">        147 :     if (*storev=='C' || *storev=='c') {</span></a>
+<a name="4204"><span class="lineNum">    4204 </span>            : </a>
+<a name="4205"><span class="lineNum">    4205 </span><span class="lineCov">        107 :         if (*direct=='F' || *direct=='f') {</span></a>
+<a name="4206"><span class="lineNum">    4206 </span><span class="lineCov">         48 :           if (*side=='l' || *side=='L') {</span></a>
+<a name="4207"><span class="lineNum">    4207 </span>            : </a>
+<a name="4208"><span class="lineNum">    4208 </span><span class="lineCov">         48 :                 i__1 = *k;</span></a>
+<a name="4209"><span class="lineNum">    4209 </span><span class="lineCov">       1124 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4210"><span class="lineNum">    4210 </span><span class="lineCov">       1076 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;c__[j + c_dim1], ldc, &amp;work[j * work_dim1 + 1],</span></a>
+<a name="4211"><span class="lineNum">    4211 </span>            :                              &amp;c__1);</a>
+<a name="4212"><span class="lineNum">    4212 </span>            :                 }</a>
+<a name="4213"><span class="lineNum">    4213 </span>            : </a>
+<a name="4214"><span class="lineNum">    4214 </span><span class="lineCov">         48 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="4215"><span class="lineNum">    4215 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4216"><span class="lineNum">    4216 </span><span class="lineCov">         48 :                 if (*m &gt; *k) {</span></a>
+<a name="4217"><span class="lineNum">    4217 </span>            : </a>
+<a name="4218"><span class="lineNum">    4218 </span><span class="lineCov">         31 :                     i__1 = *m - *k;</span></a>
+<a name="4219"><span class="lineNum">    4219 </span><span class="lineCov">         31 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;Transpose&quot;, &quot;No transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="4220"><span class="lineNum">    4220 </span><span class="lineCov">         31 :                             c__[*k + 1 + c_dim1], ldc, &amp;v[*k + 1 + v_dim1], </span></a>
+<a name="4221"><span class="lineNum">    4221 </span>            :                             ldv, &amp;one, &amp;work[work_offset], ldwork);</a>
+<a name="4222"><span class="lineNum">    4222 </span>            :                 }</a>
+<a name="4223"><span class="lineNum">    4223 </span>            : </a>
+<a name="4224"><span class="lineNum">    4224 </span><span class="lineCov">         48 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="4225"><span class="lineNum">    4225 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4226"><span class="lineNum">    4226 </span>            : </a>
+<a name="4227"><span class="lineNum">    4227 </span><span class="lineCov">         48 :                 if (*m &gt; *k) {</span></a>
+<a name="4228"><span class="lineNum">    4228 </span><span class="lineCov">         31 :                     i__1 = *m - *k;</span></a>
+<a name="4229"><span class="lineNum">    4229 </span><span class="lineCov">         31 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;</span></a>
+<a name="4230"><span class="lineNum">    4230 </span><span class="lineCov">         31 :                             v[*k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="4231"><span class="lineNum">    4231 </span><span class="lineCov">         31 :                             ldwork, &amp;one, &amp;c__[*k + 1 + c_dim1], ldc);</span></a>
+<a name="4232"><span class="lineNum">    4232 </span>            :                 }</a>
+<a name="4233"><span class="lineNum">    4233 </span>            : </a>
+<a name="4234"><span class="lineNum">    4234 </span><span class="lineCov">         48 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="4235"><span class="lineNum">    4235 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4236"><span class="lineNum">    4236 </span>            : </a>
+<a name="4237"><span class="lineNum">    4237 </span><span class="lineCov">         48 :                 i__1 = *k;</span></a>
+<a name="4238"><span class="lineNum">    4238 </span><span class="lineCov">       1124 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4239"><span class="lineNum">    4239 </span><span class="lineCov">       1076 :                     i__2 = *n;</span></a>
+<a name="4240"><span class="lineNum">    4240 </span><span class="lineCov">     271892 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4241"><span class="lineNum">    4241 </span><span class="lineCov">     270816 :                         c__[j + i__ * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="4242"><span class="lineNum">    4242 </span>            :                     }</a>
+<a name="4243"><span class="lineNum">    4243 </span>            :                 }</a>
+<a name="4244"><span class="lineNum">    4244 </span>            : </a>
+<a name="4245"><span class="lineNum">    4245 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="4246"><span class="lineNum">    4246 </span>            : </a>
+<a name="4247"><span class="lineNum">    4247 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4248"><span class="lineNum">    4248 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4249"><span class="lineNum">    4249 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(m, &amp;c__[j * c_dim1 + 1], &amp;c__1, &amp;work[j * </span></a>
+<a name="4250"><span class="lineNum">    4250 </span><span class="lineNoCov">          0 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="4251"><span class="lineNum">    4251 </span>            :                 }</a>
+<a name="4252"><span class="lineNum">    4252 </span>            : </a>
+<a name="4253"><span class="lineNum">    4253 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="4254"><span class="lineNum">    4254 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4255"><span class="lineNum">    4255 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="4256"><span class="lineNum">    4256 </span>            : </a>
+<a name="4257"><span class="lineNum">    4257 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="4258"><span class="lineNum">    4258 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, k, &amp;i__1, &amp;</span></a>
+<a name="4259"><span class="lineNum">    4259 </span><span class="lineNoCov">          0 :                             one, &amp;c__[(*k + 1) * c_dim1 + 1], ldc, &amp;v[*k + </span></a>
+<a name="4260"><span class="lineNum">    4260 </span><span class="lineNoCov">          0 :                             1 + v_dim1], ldv, &amp;one, &amp;work[work_offset], </span></a>
+<a name="4261"><span class="lineNum">    4261 </span>            :                             ldwork);</a>
+<a name="4262"><span class="lineNum">    4262 </span>            :                 }</a>
+<a name="4263"><span class="lineNum">    4263 </span>            : </a>
+<a name="4264"><span class="lineNum">    4264 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="4265"><span class="lineNum">    4265 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4266"><span class="lineNum">    4266 </span>            : </a>
+<a name="4267"><span class="lineNum">    4267 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="4268"><span class="lineNum">    4268 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="4269"><span class="lineNum">    4269 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, &amp;i__1, k, &amp;minusone, &amp;</span></a>
+<a name="4270"><span class="lineNum">    4270 </span><span class="lineNoCov">          0 :                             work[work_offset], ldwork, &amp;v[*k + 1 + v_dim1], </span></a>
+<a name="4271"><span class="lineNum">    4271 </span><span class="lineNoCov">          0 :                             ldv, &amp;one, &amp;c__[(*k + 1) * c_dim1 + 1], ldc);</span></a>
+<a name="4272"><span class="lineNum">    4272 </span>            :                 }</a>
+<a name="4273"><span class="lineNum">    4273 </span>            : </a>
+<a name="4274"><span class="lineNum">    4274 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="4275"><span class="lineNum">    4275 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4276"><span class="lineNum">    4276 </span>            : </a>
+<a name="4277"><span class="lineNum">    4277 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4278"><span class="lineNum">    4278 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4279"><span class="lineNum">    4279 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="4280"><span class="lineNum">    4280 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4281"><span class="lineNum">    4281 </span><span class="lineNoCov">          0 :                         c__[i__ + j * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="4282"><span class="lineNum">    4282 </span>            :                     }</a>
+<a name="4283"><span class="lineNum">    4283 </span>            :                 }</a>
+<a name="4284"><span class="lineNum">    4284 </span>            :             }</a>
+<a name="4285"><span class="lineNum">    4285 </span>            : </a>
+<a name="4286"><span class="lineNum">    4286 </span>            :         } else {</a>
+<a name="4287"><span class="lineNum">    4287 </span>            : </a>
+<a name="4288"><span class="lineNum">    4288 </span><span class="lineCov">         59 :           if (*side=='l' || *side=='L') {</span></a>
+<a name="4289"><span class="lineNum">    4289 </span><span class="lineCov">         59 :                 i__1 = *k;</span></a>
+<a name="4290"><span class="lineNum">    4290 </span><span class="lineCov">       1663 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4291"><span class="lineNum">    4291 </span><span class="lineCov">       1604 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;c__[*m - *k + j + c_dim1], ldc, &amp;work[j * </span></a>
+<a name="4292"><span class="lineNum">    4292 </span><span class="lineCov">       1604 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="4293"><span class="lineNum">    4293 </span>            :                 }</a>
+<a name="4294"><span class="lineNum">    4294 </span>            : </a>
+<a name="4295"><span class="lineNum">    4295 </span><span class="lineCov">         59 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="4296"><span class="lineNum">    4296 </span><span class="lineCov">         59 :                          &amp;v[*m - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="4297"><span class="lineNum">    4297 </span>            :                         ldwork);</a>
+<a name="4298"><span class="lineNum">    4298 </span><span class="lineCov">         59 :                 if (*m &gt; *k) {</span></a>
+<a name="4299"><span class="lineNum">    4299 </span><span class="lineCov">         47 :                     i__1 = *m - *k;</span></a>
+<a name="4300"><span class="lineNum">    4300 </span><span class="lineCov">         47 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;Transpose&quot;, &quot;No transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="4301"><span class="lineNum">    4301 </span>            :                             c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;one, &amp;</a>
+<a name="4302"><span class="lineNum">    4302 </span>            :                             work[work_offset], ldwork);</a>
+<a name="4303"><span class="lineNum">    4303 </span>            :                 }</a>
+<a name="4304"><span class="lineNum">    4304 </span>            : </a>
+<a name="4305"><span class="lineNum">    4305 </span><span class="lineCov">         59 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="4306"><span class="lineNum">    4306 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4307"><span class="lineNum">    4307 </span>            : </a>
+<a name="4308"><span class="lineNum">    4308 </span><span class="lineCov">         59 :                 if (*m &gt; *k) {</span></a>
+<a name="4309"><span class="lineNum">    4309 </span>            : </a>
+<a name="4310"><span class="lineNum">    4310 </span><span class="lineCov">         47 :                     i__1 = *m - *k;</span></a>
+<a name="4311"><span class="lineNum">    4311 </span><span class="lineCov">         47 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;</span></a>
+<a name="4312"><span class="lineNum">    4312 </span>            :                             v[v_offset], ldv, &amp;work[work_offset], ldwork, &amp;</a>
+<a name="4313"><span class="lineNum">    4313 </span>            :                             one, &amp;c__[c_offset], ldc)</a>
+<a name="4314"><span class="lineNum">    4314 </span>            :                             ;</a>
+<a name="4315"><span class="lineNum">    4315 </span>            :                 }</a>
+<a name="4316"><span class="lineNum">    4316 </span>            : </a>
+<a name="4317"><span class="lineNum">    4317 </span><span class="lineCov">         59 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="4318"><span class="lineNum">    4318 </span><span class="lineCov">         59 :                         v[*m - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="4319"><span class="lineNum">    4319 </span>            :                         ldwork);</a>
+<a name="4320"><span class="lineNum">    4320 </span>            : </a>
+<a name="4321"><span class="lineNum">    4321 </span><span class="lineCov">         59 :                 i__1 = *k;</span></a>
+<a name="4322"><span class="lineNum">    4322 </span><span class="lineCov">       1663 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4323"><span class="lineNum">    4323 </span><span class="lineCov">       1604 :                     i__2 = *n;</span></a>
+<a name="4324"><span class="lineNum">    4324 </span><span class="lineCov">     391844 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4325"><span class="lineNum">    4325 </span><span class="lineCov">     390240 :                         c__[*m - *k + j + i__ * c_dim1] -= work[i__ + j * </span></a>
+<a name="4326"><span class="lineNum">    4326 </span><span class="lineCov">     390240 :                                 work_dim1];</span></a>
+<a name="4327"><span class="lineNum">    4327 </span>            :                     }</a>
+<a name="4328"><span class="lineNum">    4328 </span>            :                 }</a>
+<a name="4329"><span class="lineNum">    4329 </span>            : </a>
+<a name="4330"><span class="lineNum">    4330 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="4331"><span class="lineNum">    4331 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4332"><span class="lineNum">    4332 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4333"><span class="lineNum">    4333 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(m, &amp;c__[(*n - *k + j) * c_dim1 + 1], &amp;c__1, &amp;work[</span></a>
+<a name="4334"><span class="lineNum">    4334 </span><span class="lineNoCov">          0 :                             j * work_dim1 + 1], &amp;c__1);</span></a>
+<a name="4335"><span class="lineNum">    4335 </span>            :                 }</a>
+<a name="4336"><span class="lineNum">    4336 </span>            : </a>
+<a name="4337"><span class="lineNum">    4337 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="4338"><span class="lineNum">    4338 </span><span class="lineNoCov">          0 :                          &amp;v[*n - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="4339"><span class="lineNum">    4339 </span>            :                         ldwork);</a>
+<a name="4340"><span class="lineNum">    4340 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="4341"><span class="lineNum">    4341 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="4342"><span class="lineNum">    4342 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, k, &amp;i__1, &amp;</span></a>
+<a name="4343"><span class="lineNum">    4343 </span>            :                             one, &amp;c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;</a>
+<a name="4344"><span class="lineNum">    4344 </span>            :                             one, &amp;work[work_offset], ldwork);</a>
+<a name="4345"><span class="lineNum">    4345 </span>            :                 }</a>
+<a name="4346"><span class="lineNum">    4346 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="4347"><span class="lineNum">    4347 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4348"><span class="lineNum">    4348 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="4349"><span class="lineNum">    4349 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="4350"><span class="lineNum">    4350 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, &amp;i__1, k, &amp;minusone, &amp;</span></a>
+<a name="4351"><span class="lineNum">    4351 </span>            :                             work[work_offset], ldwork, &amp;v[v_offset], ldv, &amp;</a>
+<a name="4352"><span class="lineNum">    4352 </span>            :                             one, &amp;c__[c_offset], ldc)</a>
+<a name="4353"><span class="lineNum">    4353 </span>            :                             ;</a>
+<a name="4354"><span class="lineNum">    4354 </span>            :                 }</a>
+<a name="4355"><span class="lineNum">    4355 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="4356"><span class="lineNum">    4356 </span><span class="lineNoCov">          0 :                         v[*n - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="4357"><span class="lineNum">    4357 </span>            :                         ldwork);</a>
+<a name="4358"><span class="lineNum">    4358 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4359"><span class="lineNum">    4359 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4360"><span class="lineNum">    4360 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="4361"><span class="lineNum">    4361 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4362"><span class="lineNum">    4362 </span><span class="lineNoCov">          0 :                         c__[i__ + (*n - *k + j) * c_dim1] -= work[i__ + j * </span></a>
+<a name="4363"><span class="lineNum">    4363 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="4364"><span class="lineNum">    4364 </span>            :                     }</a>
+<a name="4365"><span class="lineNum">    4365 </span>            :                 }</a>
+<a name="4366"><span class="lineNum">    4366 </span>            :             }</a>
+<a name="4367"><span class="lineNum">    4367 </span>            :         }</a>
+<a name="4368"><span class="lineNum">    4368 </span>            : </a>
+<a name="4369"><span class="lineNum">    4369 </span><span class="lineCov">         40 :     } else  if (*storev=='r' || *storev=='R') {</span></a>
+<a name="4370"><span class="lineNum">    4370 </span><span class="lineCov">         40 :       if (*direct=='F' || *direct=='f') {</span></a>
+<a name="4371"><span class="lineNum">    4371 </span><span class="lineCov">         40 :           if (*side=='l' || *side=='L') {</span></a>
+<a name="4372"><span class="lineNum">    4372 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4373"><span class="lineNum">    4373 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4374"><span class="lineNum">    4374 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;c__[j + c_dim1], ldc, &amp;work[j * work_dim1 + 1],</span></a>
+<a name="4375"><span class="lineNum">    4375 </span>            :                              &amp;c__1);</a>
+<a name="4376"><span class="lineNum">    4376 </span>            :                 }</a>
+<a name="4377"><span class="lineNum">    4377 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="4378"><span class="lineNum">    4378 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4379"><span class="lineNum">    4379 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="4380"><span class="lineNum">    4380 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="4381"><span class="lineNum">    4381 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="4382"><span class="lineNum">    4382 </span><span class="lineNoCov">          0 :                             c__[*k + 1 + c_dim1], ldc, &amp;v[(*k + 1) * v_dim1 + </span></a>
+<a name="4383"><span class="lineNum">    4383 </span><span class="lineNoCov">          0 :                             1], ldv, &amp;one, &amp;work[work_offset], ldwork);</span></a>
+<a name="4384"><span class="lineNum">    4384 </span>            :                 }</a>
+<a name="4385"><span class="lineNum">    4385 </span>            : </a>
+<a name="4386"><span class="lineNum">    4386 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="4387"><span class="lineNum">    4387 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4388"><span class="lineNum">    4388 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="4389"><span class="lineNum">    4389 </span>            : </a>
+<a name="4390"><span class="lineNum">    4390 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="4391"><span class="lineNum">    4391 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;v[(</span></a>
+<a name="4392"><span class="lineNum">    4392 </span><span class="lineNoCov">          0 :                             *k + 1) * v_dim1 + 1], ldv, &amp;work[work_offset], </span></a>
+<a name="4393"><span class="lineNum">    4393 </span><span class="lineNoCov">          0 :                             ldwork, &amp;one, &amp;c__[*k + 1 + c_dim1], ldc);</span></a>
+<a name="4394"><span class="lineNum">    4394 </span>            :                 }</a>
+<a name="4395"><span class="lineNum">    4395 </span>            : </a>
+<a name="4396"><span class="lineNum">    4396 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="4397"><span class="lineNum">    4397 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4398"><span class="lineNum">    4398 </span>            : </a>
+<a name="4399"><span class="lineNum">    4399 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4400"><span class="lineNum">    4400 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4401"><span class="lineNum">    4401 </span><span class="lineNoCov">          0 :                     i__2 = *n;</span></a>
+<a name="4402"><span class="lineNum">    4402 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4403"><span class="lineNum">    4403 </span><span class="lineNoCov">          0 :                         c__[j + i__ * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="4404"><span class="lineNum">    4404 </span>            :                     }</a>
+<a name="4405"><span class="lineNum">    4405 </span>            :                 }</a>
+<a name="4406"><span class="lineNum">    4406 </span>            : </a>
+<a name="4407"><span class="lineNum">    4407 </span><span class="lineCov">         40 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="4408"><span class="lineNum">    4408 </span>            : </a>
+<a name="4409"><span class="lineNum">    4409 </span><span class="lineCov">         40 :                 i__1 = *k;</span></a>
+<a name="4410"><span class="lineNum">    4410 </span><span class="lineCov">        971 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4411"><span class="lineNum">    4411 </span><span class="lineCov">        931 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(m, &amp;c__[j * c_dim1 + 1], &amp;c__1, &amp;work[j * </span></a>
+<a name="4412"><span class="lineNum">    4412 </span><span class="lineCov">        931 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="4413"><span class="lineNum">    4413 </span>            :                 }</a>
+<a name="4414"><span class="lineNum">    4414 </span>            : </a>
+<a name="4415"><span class="lineNum">    4415 </span><span class="lineCov">         40 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="4416"><span class="lineNum">    4416 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4417"><span class="lineNum">    4417 </span><span class="lineCov">         40 :                 if (*n &gt; *k) {</span></a>
+<a name="4418"><span class="lineNum">    4418 </span>            : </a>
+<a name="4419"><span class="lineNum">    4419 </span><span class="lineCov">         27 :                     i__1 = *n - *k;</span></a>
+<a name="4420"><span class="lineNum">    4420 </span><span class="lineCov">         27 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="4421"><span class="lineNum">    4421 </span><span class="lineCov">         27 :                             c__[(*k + 1) * c_dim1 + 1], ldc, &amp;v[(*k + 1) * </span></a>
+<a name="4422"><span class="lineNum">    4422 </span><span class="lineCov">         27 :                             v_dim1 + 1], ldv, &amp;one, &amp;work[work_offset], </span></a>
+<a name="4423"><span class="lineNum">    4423 </span>            :                             ldwork);</a>
+<a name="4424"><span class="lineNum">    4424 </span>            :                 }</a>
+<a name="4425"><span class="lineNum">    4425 </span>            : </a>
+<a name="4426"><span class="lineNum">    4426 </span><span class="lineCov">         40 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="4427"><span class="lineNum">    4427 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4428"><span class="lineNum">    4428 </span>            : </a>
+<a name="4429"><span class="lineNum">    4429 </span><span class="lineCov">         40 :                 if (*n &gt; *k) {</span></a>
+<a name="4430"><span class="lineNum">    4430 </span>            : </a>
+<a name="4431"><span class="lineNum">    4431 </span><span class="lineCov">         27 :                     i__1 = *n - *k;</span></a>
+<a name="4432"><span class="lineNum">    4432 </span><span class="lineCov">         27 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, &amp;i__1, k, &amp;</span></a>
+<a name="4433"><span class="lineNum">    4433 </span><span class="lineCov">         27 :                             minusone, &amp;work[work_offset], ldwork, &amp;v[(*k + 1) * </span></a>
+<a name="4434"><span class="lineNum">    4434 </span><span class="lineCov">         27 :                             v_dim1 + 1], ldv, &amp;one, &amp;c__[(*k + 1) * c_dim1 </span></a>
+<a name="4435"><span class="lineNum">    4435 </span><span class="lineCov">         27 :                             + 1], ldc);</span></a>
+<a name="4436"><span class="lineNum">    4436 </span>            :                 }</a>
+<a name="4437"><span class="lineNum">    4437 </span><span class="lineCov">         40 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="4438"><span class="lineNum">    4438 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="4439"><span class="lineNum">    4439 </span><span class="lineCov">         40 :                 i__1 = *k;</span></a>
+<a name="4440"><span class="lineNum">    4440 </span><span class="lineCov">        971 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4441"><span class="lineNum">    4441 </span><span class="lineCov">        931 :                     i__2 = *m;</span></a>
+<a name="4442"><span class="lineNum">    4442 </span><span class="lineCov">     266447 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4443"><span class="lineNum">    4443 </span><span class="lineCov">     265516 :                         c__[i__ + j * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="4444"><span class="lineNum">    4444 </span>            :                     }</a>
+<a name="4445"><span class="lineNum">    4445 </span>            :                 }</a>
+<a name="4446"><span class="lineNum">    4446 </span>            : </a>
+<a name="4447"><span class="lineNum">    4447 </span>            :             }</a>
+<a name="4448"><span class="lineNum">    4448 </span>            : </a>
+<a name="4449"><span class="lineNum">    4449 </span>            :         } else {</a>
+<a name="4450"><span class="lineNum">    4450 </span>            : </a>
+<a name="4451"><span class="lineNum">    4451 </span><span class="lineNoCov">          0 :             if (*side=='l' || *side=='L') {</span></a>
+<a name="4452"><span class="lineNum">    4452 </span>            : </a>
+<a name="4453"><span class="lineNum">    4453 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4454"><span class="lineNum">    4454 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4455"><span class="lineNum">    4455 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;c__[*m - *k + j + c_dim1], ldc, &amp;work[j * </span></a>
+<a name="4456"><span class="lineNum">    4456 </span><span class="lineNoCov">          0 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="4457"><span class="lineNum">    4457 </span>            :                 }</a>
+<a name="4458"><span class="lineNum">    4458 </span>            : </a>
+<a name="4459"><span class="lineNum">    4459 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="4460"><span class="lineNum">    4460 </span><span class="lineNoCov">          0 :                         v[(*m - *k + 1) * v_dim1 + 1], ldv, &amp;work[work_offset]</span></a>
+<a name="4461"><span class="lineNum">    4461 </span>            :                         , ldwork);</a>
+<a name="4462"><span class="lineNum">    4462 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="4463"><span class="lineNum">    4463 </span>            : </a>
+<a name="4464"><span class="lineNum">    4464 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="4465"><span class="lineNum">    4465 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="4466"><span class="lineNum">    4466 </span>            :                             c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;one, &amp;</a>
+<a name="4467"><span class="lineNum">    4467 </span>            :                             work[work_offset], ldwork);</a>
+<a name="4468"><span class="lineNum">    4468 </span>            :                 }</a>
+<a name="4469"><span class="lineNum">    4469 </span>            : </a>
+<a name="4470"><span class="lineNum">    4470 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="4471"><span class="lineNum">    4471 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4472"><span class="lineNum">    4472 </span>            : </a>
+<a name="4473"><span class="lineNum">    4473 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="4474"><span class="lineNum">    4474 </span>            : </a>
+<a name="4475"><span class="lineNum">    4475 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="4476"><span class="lineNum">    4476 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;v[</span></a>
+<a name="4477"><span class="lineNum">    4477 </span>            :                             v_offset], ldv, &amp;work[work_offset], ldwork, &amp;</a>
+<a name="4478"><span class="lineNum">    4478 </span>            :                             one, &amp;c__[c_offset], ldc);</a>
+<a name="4479"><span class="lineNum">    4479 </span>            :                 }</a>
+<a name="4480"><span class="lineNum">    4480 </span>            : </a>
+<a name="4481"><span class="lineNum">    4481 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="4482"><span class="lineNum">    4482 </span><span class="lineNoCov">          0 :                          &amp;v[(*m - *k + 1) * v_dim1 + 1], ldv, &amp;work[</span></a>
+<a name="4483"><span class="lineNum">    4483 </span>            :                         work_offset], ldwork);</a>
+<a name="4484"><span class="lineNum">    4484 </span>            : </a>
+<a name="4485"><span class="lineNum">    4485 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4486"><span class="lineNum">    4486 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4487"><span class="lineNum">    4487 </span><span class="lineNoCov">          0 :                     i__2 = *n;</span></a>
+<a name="4488"><span class="lineNum">    4488 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4489"><span class="lineNum">    4489 </span><span class="lineNoCov">          0 :                         c__[*m - *k + j + i__ * c_dim1] -= work[i__ + j * </span></a>
+<a name="4490"><span class="lineNum">    4490 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="4491"><span class="lineNum">    4491 </span>            :                     }</a>
+<a name="4492"><span class="lineNum">    4492 </span>            :                 }</a>
+<a name="4493"><span class="lineNum">    4493 </span>            : </a>
+<a name="4494"><span class="lineNum">    4494 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="4495"><span class="lineNum">    4495 </span>            : </a>
+<a name="4496"><span class="lineNum">    4496 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4497"><span class="lineNum">    4497 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4498"><span class="lineNum">    4498 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(m, &amp;c__[(*n - *k + j) * c_dim1 + 1], &amp;c__1, &amp;work[</span></a>
+<a name="4499"><span class="lineNum">    4499 </span><span class="lineNoCov">          0 :                             j * work_dim1 + 1], &amp;c__1);</span></a>
+<a name="4500"><span class="lineNum">    4500 </span>            :                 }</a>
+<a name="4501"><span class="lineNum">    4501 </span>            : </a>
+<a name="4502"><span class="lineNum">    4502 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="4503"><span class="lineNum">    4503 </span><span class="lineNoCov">          0 :                         v[(*n - *k + 1) * v_dim1 + 1], ldv, &amp;work[work_offset]</span></a>
+<a name="4504"><span class="lineNum">    4504 </span>            :                         , ldwork);</a>
+<a name="4505"><span class="lineNum">    4505 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="4506"><span class="lineNum">    4506 </span>            : </a>
+<a name="4507"><span class="lineNum">    4507 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="4508"><span class="lineNum">    4508 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="4509"><span class="lineNum">    4509 </span>            :                             c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;one, &amp;</a>
+<a name="4510"><span class="lineNum">    4510 </span>            :                             work[work_offset], ldwork);</a>
+<a name="4511"><span class="lineNum">    4511 </span>            :                 }</a>
+<a name="4512"><span class="lineNum">    4512 </span>            : </a>
+<a name="4513"><span class="lineNum">    4513 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="4514"><span class="lineNum">    4514 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="4515"><span class="lineNum">    4515 </span>            : </a>
+<a name="4516"><span class="lineNum">    4516 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="4517"><span class="lineNum">    4517 </span>            : </a>
+<a name="4518"><span class="lineNum">    4518 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="4519"><span class="lineNum">    4519 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, &amp;i__1, k, &amp;</span></a>
+<a name="4520"><span class="lineNum">    4520 </span>            :                             minusone, &amp;work[work_offset], ldwork, &amp;v[v_offset], </a>
+<a name="4521"><span class="lineNum">    4521 </span>            :                             ldv, &amp;one, &amp;c__[c_offset], ldc);</a>
+<a name="4522"><span class="lineNum">    4522 </span>            :                 }</a>
+<a name="4523"><span class="lineNum">    4523 </span>            : </a>
+<a name="4524"><span class="lineNum">    4524 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="4525"><span class="lineNum">    4525 </span><span class="lineNoCov">          0 :                          &amp;v[(*n - *k + 1) * v_dim1 + 1], ldv, &amp;work[</span></a>
+<a name="4526"><span class="lineNum">    4526 </span>            :                         work_offset], ldwork);</a>
+<a name="4527"><span class="lineNum">    4527 </span>            : </a>
+<a name="4528"><span class="lineNum">    4528 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="4529"><span class="lineNum">    4529 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4530"><span class="lineNum">    4530 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="4531"><span class="lineNum">    4531 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4532"><span class="lineNum">    4532 </span><span class="lineNoCov">          0 :                         c__[i__ + (*n - *k + j) * c_dim1] -= work[i__ + j * </span></a>
+<a name="4533"><span class="lineNum">    4533 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="4534"><span class="lineNum">    4534 </span>            :                     }</a>
+<a name="4535"><span class="lineNum">    4535 </span>            :                 }</a>
+<a name="4536"><span class="lineNum">    4536 </span>            : </a>
+<a name="4537"><span class="lineNum">    4537 </span>            :             }</a>
+<a name="4538"><span class="lineNum">    4538 </span>            : </a>
+<a name="4539"><span class="lineNum">    4539 </span>            :         }</a>
+<a name="4540"><span class="lineNum">    4540 </span>            :     }</a>
+<a name="4541"><span class="lineNum">    4541 </span>            : </a>
+<a name="4542"><span class="lineNum">    4542 </span>            :     return;</a>
+<a name="4543"><span class="lineNum">    4543 </span>            : </a>
+<a name="4544"><span class="lineNum">    4544 </span>            : </a>
+<a name="4545"><span class="lineNum">    4545 </span>            : }</a>
+<a name="4546"><span class="lineNum">    4546 </span>            : </a>
+<a name="4547"><span class="lineNum">    4547 </span>            : }</a>
+<a name="4548"><span class="lineNum">    4548 </span>            : }</a>
+<a name="4549"><span class="lineNum">    4549 </span>            : #include &lt;cmath&gt;</a>
+<a name="4550"><span class="lineNum">    4550 </span>            : #include &quot;real.h&quot;</a>
+<a name="4551"><span class="lineNum">    4551 </span>            : </a>
+<a name="4552"><span class="lineNum">    4552 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4553"><span class="lineNum">    4553 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="4554"><span class="lineNum">    4554 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="4555"><span class="lineNum">    4555 </span>            : </a>
+<a name="4556"><span class="lineNum">    4556 </span>            : </a>
+<a name="4557"><span class="lineNum">    4557 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4558"><span class="lineNum">    4558 </span>            : namespace PLMD{</a>
+<a name="4559"><span class="lineNum">    4559 </span>            : namespace lapack{</a>
+<a name="4560"><span class="lineNum">    4560 </span>            : using namespace blas;</a>
+<a name="4561"><span class="lineNum">    4561 </span>            : void</a>
+<a name="4562"><span class="lineNum">    4562 </span><span class="lineCov">    1689415 : PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(int   *n,</span></a>
+<a name="4563"><span class="lineNum">    4563 </span>            :                         double *alpha,</a>
+<a name="4564"><span class="lineNum">    4564 </span>            :                         double *x,</a>
+<a name="4565"><span class="lineNum">    4565 </span>            :                         int    *incx,</a>
+<a name="4566"><span class="lineNum">    4566 </span>            :                         double *tau)</a>
+<a name="4567"><span class="lineNum">    4567 </span>            : {</a>
+<a name="4568"><span class="lineNum">    4568 </span>            :   double xnorm,t;</a>
+<a name="4569"><span class="lineNum">    4569 </span>            :   int    ti1,knt,j;</a>
+<a name="4570"><span class="lineNum">    4570 </span>            :   double minval,safmin,rsafmn,beta;</a>
+<a name="4571"><span class="lineNum">    4571 </span>            : </a>
+<a name="4572"><span class="lineNum">    4572 </span><span class="lineCov">    1689415 :   if(*n&lt;=1) {</span></a>
+<a name="4573"><span class="lineNum">    4573 </span><span class="lineCov">     570200 :     *tau = 0;</span></a>
+<a name="4574"><span class="lineNum">    4574 </span><span class="lineCov">     570200 :     return;</span></a>
+<a name="4575"><span class="lineNum">    4575 </span>            :   }</a>
+<a name="4576"><span class="lineNum">    4576 </span>            : </a>
+<a name="4577"><span class="lineNum">    4577 </span><span class="lineCov">    1119215 :   ti1 = *n-1;</span></a>
+<a name="4578"><span class="lineNum">    4578 </span>            : </a>
+<a name="4579"><span class="lineNum">    4579 </span><span class="lineCov">    1119215 :   xnorm = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(&amp;ti1,x,incx);</span></a>
+<a name="4580"><span class="lineNum">    4580 </span>            : </a>
+<a name="4581"><span class="lineNum">    4581 </span><span class="lineCov">    1119215 :   if(std::abs(xnorm)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4582"><span class="lineNum">    4582 </span><span class="lineCov">          6 :     *tau = 0.0;</span></a>
+<a name="4583"><span class="lineNum">    4583 </span>            :   } else {</a>
+<a name="4584"><span class="lineNum">    4584 </span>            : </a>
+<a name="4585"><span class="lineNum">    4585 </span><span class="lineCov">    1119209 :     t = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(alpha,&amp;xnorm);</span></a>
+<a name="4586"><span class="lineNum">    4586 </span>            : </a>
+<a name="4587"><span class="lineNum">    4587 </span><span class="lineCov">    1119209 :     if(*alpha&lt;0)</span></a>
+<a name="4588"><span class="lineNum">    4588 </span>            :       beta = t;</a>
+<a name="4589"><span class="lineNum">    4589 </span>            :     else</a>
+<a name="4590"><span class="lineNum">    4590 </span><span class="lineCov">     453492 :       beta = -t;</span></a>
+<a name="4591"><span class="lineNum">    4591 </span>            : </a>
+<a name="4592"><span class="lineNum">    4592 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="4593"><span class="lineNum">    4593 </span>            :     </a>
+<a name="4594"><span class="lineNum">    4594 </span>            :     safmin = minval*(1.0+PLUMED_GMX_DOUBLE_EPS) / PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="4595"><span class="lineNum">    4595 </span>            : </a>
+<a name="4596"><span class="lineNum">    4596 </span>            :         </a>
+<a name="4597"><span class="lineNum">    4597 </span><span class="lineCov">    1119209 :     if(std::abs(beta)&lt;safmin) {</span></a>
+<a name="4598"><span class="lineNum">    4598 </span>            : </a>
+<a name="4599"><span class="lineNum">    4599 </span>            :       knt = 0;</a>
+<a name="4600"><span class="lineNum">    4600 </span><span class="lineNoCov">          0 :       rsafmn = 1.0 / safmin;</span></a>
+<a name="4601"><span class="lineNum">    4601 </span>            :       </a>
+<a name="4602"><span class="lineNum">    4602 </span><span class="lineNoCov">          0 :       while(std::abs(beta)&lt;safmin) {</span></a>
+<a name="4603"><span class="lineNum">    4603 </span><span class="lineNoCov">          0 :         knt++;</span></a>
+<a name="4604"><span class="lineNum">    4604 </span><span class="lineNoCov">          0 :         ti1 = *n-1;</span></a>
+<a name="4605"><span class="lineNum">    4605 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;ti1,&amp;rsafmn,x,incx);</span></a>
+<a name="4606"><span class="lineNum">    4606 </span><span class="lineNoCov">          0 :         beta *= rsafmn;</span></a>
+<a name="4607"><span class="lineNum">    4607 </span><span class="lineNoCov">          0 :         *alpha *= rsafmn;</span></a>
+<a name="4608"><span class="lineNum">    4608 </span>            :       }</a>
+<a name="4609"><span class="lineNum">    4609 </span>            :       </a>
+<a name="4610"><span class="lineNum">    4610 </span>            :       /* safmin &lt;= beta &lt;= 1 now */</a>
+<a name="4611"><span class="lineNum">    4611 </span><span class="lineNoCov">          0 :       ti1 = *n-1;</span></a>
+<a name="4612"><span class="lineNum">    4612 </span><span class="lineNoCov">          0 :       xnorm = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(&amp;ti1,x,incx);</span></a>
+<a name="4613"><span class="lineNum">    4613 </span><span class="lineNoCov">          0 :       t = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(alpha,&amp;xnorm);</span></a>
+<a name="4614"><span class="lineNum">    4614 </span>            :       </a>
+<a name="4615"><span class="lineNum">    4615 </span><span class="lineNoCov">          0 :       if(*alpha&lt;0)</span></a>
+<a name="4616"><span class="lineNum">    4616 </span>            :         beta = t;</a>
+<a name="4617"><span class="lineNum">    4617 </span>            :       else</a>
+<a name="4618"><span class="lineNum">    4618 </span><span class="lineNoCov">          0 :         beta = -t;</span></a>
+<a name="4619"><span class="lineNum">    4619 </span>            :       </a>
+<a name="4620"><span class="lineNum">    4620 </span><span class="lineNoCov">          0 :       *tau = (beta-*alpha)/beta;</span></a>
+<a name="4621"><span class="lineNum">    4621 </span>            : </a>
+<a name="4622"><span class="lineNum">    4622 </span><span class="lineNoCov">          0 :       ti1= *n-1;</span></a>
+<a name="4623"><span class="lineNum">    4623 </span><span class="lineNoCov">          0 :       t = 1.0/(*alpha-beta);</span></a>
+<a name="4624"><span class="lineNum">    4624 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;ti1,&amp;t,x,incx);</span></a>
+<a name="4625"><span class="lineNum">    4625 </span>            :    </a>
+<a name="4626"><span class="lineNum">    4626 </span><span class="lineNoCov">          0 :       *alpha = beta;</span></a>
+<a name="4627"><span class="lineNum">    4627 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;knt;j++)</span></a>
+<a name="4628"><span class="lineNum">    4628 </span><span class="lineNoCov">          0 :         *alpha *= safmin;</span></a>
+<a name="4629"><span class="lineNum">    4629 </span>            :     } else {</a>
+<a name="4630"><span class="lineNum">    4630 </span><span class="lineCov">    1119209 :       *tau = (beta-*alpha)/beta;</span></a>
+<a name="4631"><span class="lineNum">    4631 </span><span class="lineCov">    1119209 :       ti1= *n-1;</span></a>
+<a name="4632"><span class="lineNum">    4632 </span><span class="lineCov">    1119209 :       t = 1.0/(*alpha-beta);</span></a>
+<a name="4633"><span class="lineNum">    4633 </span><span class="lineCov">    1119209 :       PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;ti1,&amp;t,x,incx);</span></a>
+<a name="4634"><span class="lineNum">    4634 </span><span class="lineCov">    1119209 :       *alpha = beta;</span></a>
+<a name="4635"><span class="lineNum">    4635 </span>            :     }</a>
+<a name="4636"><span class="lineNum">    4636 </span>            :   }</a>
+<a name="4637"><span class="lineNum">    4637 </span>            :    </a>
+<a name="4638"><span class="lineNum">    4638 </span>            :   return;</a>
+<a name="4639"><span class="lineNum">    4639 </span>            : }</a>
+<a name="4640"><span class="lineNum">    4640 </span>            : }</a>
+<a name="4641"><span class="lineNum">    4641 </span>            : }</a>
+<a name="4642"><span class="lineNum">    4642 </span>            : #include &lt;cmath&gt;</a>
+<a name="4643"><span class="lineNum">    4643 </span>            : #include &quot;real.h&quot;</a>
+<a name="4644"><span class="lineNum">    4644 </span>            : </a>
+<a name="4645"><span class="lineNum">    4645 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4646"><span class="lineNum">    4646 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="4647"><span class="lineNum">    4647 </span>            : </a>
+<a name="4648"><span class="lineNum">    4648 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4649"><span class="lineNum">    4649 </span>            : namespace PLMD{</a>
+<a name="4650"><span class="lineNum">    4650 </span>            : namespace lapack{</a>
+<a name="4651"><span class="lineNum">    4651 </span>            : using namespace blas;</a>
+<a name="4652"><span class="lineNum">    4652 </span>            : void </a>
+<a name="4653"><span class="lineNum">    4653 </span><span class="lineCov">        147 : PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(const char *direct, </span></a>
+<a name="4654"><span class="lineNum">    4654 </span>            :         const char *storev, </a>
+<a name="4655"><span class="lineNum">    4655 </span>            :         int *n, </a>
+<a name="4656"><span class="lineNum">    4656 </span>            :         int *k, </a>
+<a name="4657"><span class="lineNum">    4657 </span>            :         double *v, </a>
+<a name="4658"><span class="lineNum">    4658 </span>            :         int *ldv, </a>
+<a name="4659"><span class="lineNum">    4659 </span>            :         double *tau, </a>
+<a name="4660"><span class="lineNum">    4660 </span>            :         double *t, </a>
+<a name="4661"><span class="lineNum">    4661 </span>            :         int *ldt)</a>
+<a name="4662"><span class="lineNum">    4662 </span>            : {</a>
+<a name="4663"><span class="lineNum">    4663 </span>            :     /* System generated locals */</a>
+<a name="4664"><span class="lineNum">    4664 </span>            :     int t_dim1, t_offset, v_dim1, v_offset, i__1, i__2, i__3;</a>
+<a name="4665"><span class="lineNum">    4665 </span>            :     double d__1;</a>
+<a name="4666"><span class="lineNum">    4666 </span>            : </a>
+<a name="4667"><span class="lineNum">    4667 </span>            :     /* Local variables */</a>
+<a name="4668"><span class="lineNum">    4668 </span>            :     int i__, j;</a>
+<a name="4669"><span class="lineNum">    4669 </span>            :     double vii;</a>
+<a name="4670"><span class="lineNum">    4670 </span><span class="lineCov">        147 :     int c__1 = 1;</span></a>
+<a name="4671"><span class="lineNum">    4671 </span><span class="lineCov">        147 :     double zero = 0.0;</span></a>
+<a name="4672"><span class="lineNum">    4672 </span>            : </a>
+<a name="4673"><span class="lineNum">    4673 </span><span class="lineCov">        147 :     v_dim1 = *ldv;</span></a>
+<a name="4674"><span class="lineNum">    4674 </span><span class="lineCov">        147 :     v_offset = 1 + v_dim1;</span></a>
+<a name="4675"><span class="lineNum">    4675 </span><span class="lineCov">        147 :     v -= v_offset;</span></a>
+<a name="4676"><span class="lineNum">    4676 </span><span class="lineCov">        147 :     --tau;</span></a>
+<a name="4677"><span class="lineNum">    4677 </span><span class="lineCov">        147 :     t_dim1 = *ldt;</span></a>
+<a name="4678"><span class="lineNum">    4678 </span><span class="lineCov">        147 :     t_offset = 1 + t_dim1;</span></a>
+<a name="4679"><span class="lineNum">    4679 </span><span class="lineCov">        147 :     t -= t_offset;</span></a>
+<a name="4680"><span class="lineNum">    4680 </span>            : </a>
+<a name="4681"><span class="lineNum">    4681 </span><span class="lineCov">        147 :     if (*n == 0) {</span></a>
+<a name="4682"><span class="lineNum">    4682 </span>            :         return;</a>
+<a name="4683"><span class="lineNum">    4683 </span>            :     }</a>
+<a name="4684"><span class="lineNum">    4684 </span>            : </a>
+<a name="4685"><span class="lineNum">    4685 </span><span class="lineCov">        147 :     if (*direct=='F' || *direct=='f') {</span></a>
+<a name="4686"><span class="lineNum">    4686 </span><span class="lineCov">         88 :         i__1 = *k;</span></a>
+<a name="4687"><span class="lineNum">    4687 </span><span class="lineCov">       2095 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="4688"><span class="lineNum">    4688 </span><span class="lineCov">       2007 :             if (std::abs(tau[i__])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4689"><span class="lineNum">    4689 </span>            : </a>
+<a name="4690"><span class="lineNum">    4690 </span><span class="lineCov">         30 :                 i__2 = i__;</span></a>
+<a name="4691"><span class="lineNum">    4691 </span><span class="lineCov">        181 :                 for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="4692"><span class="lineNum">    4692 </span><span class="lineCov">        151 :                     t[j + i__ * t_dim1] = 0.;</span></a>
+<a name="4693"><span class="lineNum">    4693 </span>            :                 }</a>
+<a name="4694"><span class="lineNum">    4694 </span>            :             } else {</a>
+<a name="4695"><span class="lineNum">    4695 </span>            : </a>
+<a name="4696"><span class="lineNum">    4696 </span><span class="lineCov">       1977 :                 vii = v[i__ + i__ * v_dim1];</span></a>
+<a name="4697"><span class="lineNum">    4697 </span><span class="lineCov">       1977 :                 v[i__ + i__ * v_dim1] = 1.;</span></a>
+<a name="4698"><span class="lineNum">    4698 </span><span class="lineCov">       1977 :                 if (*storev=='C' || *storev=='c') {</span></a>
+<a name="4699"><span class="lineNum">    4699 </span>            : </a>
+<a name="4700"><span class="lineNum">    4700 </span><span class="lineCov">       1059 :                     i__2 = *n - i__ + 1;</span></a>
+<a name="4701"><span class="lineNum">    4701 </span><span class="lineCov">       1059 :                     i__3 = i__ - 1;</span></a>
+<a name="4702"><span class="lineNum">    4702 </span><span class="lineCov">       1059 :                     d__1 = -tau[i__];</span></a>
+<a name="4703"><span class="lineNum">    4703 </span><span class="lineCov">       1059 :                     PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;d__1, &amp;v[i__ + v_dim1],</span></a>
+<a name="4704"><span class="lineNum">    4704 </span>            :                              ldv, &amp;v[i__ + i__ * v_dim1], &amp;c__1, &amp;zero, &amp;t[</a>
+<a name="4705"><span class="lineNum">    4705 </span><span class="lineCov">       1059 :                             i__ * t_dim1 + 1], &amp;c__1);</span></a>
+<a name="4706"><span class="lineNum">    4706 </span>            :                 } else {</a>
+<a name="4707"><span class="lineNum">    4707 </span>            : </a>
+<a name="4708"><span class="lineNum">    4708 </span><span class="lineCov">        918 :                     i__2 = i__ - 1;</span></a>
+<a name="4709"><span class="lineNum">    4709 </span><span class="lineCov">        918 :                     i__3 = *n - i__ + 1;</span></a>
+<a name="4710"><span class="lineNum">    4710 </span><span class="lineCov">        918 :                     d__1 = -tau[i__];</span></a>
+<a name="4711"><span class="lineNum">    4711 </span><span class="lineCov">        918 :                     PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;d__1, &amp;v[i__ * </span></a>
+<a name="4712"><span class="lineNum">    4712 </span><span class="lineCov">        918 :                             v_dim1 + 1], ldv, &amp;v[i__ + i__ * v_dim1], ldv, &amp;</span></a>
+<a name="4713"><span class="lineNum">    4713 </span><span class="lineCov">        918 :                             zero, &amp;t[i__ * t_dim1 + 1], &amp;c__1);</span></a>
+<a name="4714"><span class="lineNum">    4714 </span>            :                 }</a>
+<a name="4715"><span class="lineNum">    4715 </span><span class="lineCov">       1977 :                 v[i__ + i__ * v_dim1] = vii;</span></a>
+<a name="4716"><span class="lineNum">    4716 </span>            : </a>
+<a name="4717"><span class="lineNum">    4717 </span>            : </a>
+<a name="4718"><span class="lineNum">    4718 </span><span class="lineCov">       1977 :                 i__2 = i__ - 1;</span></a>
+<a name="4719"><span class="lineNum">    4719 </span><span class="lineCov">       1977 :                 PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)(&quot;Upper&quot;, &quot;No transpose&quot;, &quot;Non-unit&quot;, &amp;i__2, &amp;t[</span></a>
+<a name="4720"><span class="lineNum">    4720 </span><span class="lineCov">       1977 :                         t_offset], ldt, &amp;t[i__ * t_dim1 + 1], &amp;c__1);</span></a>
+<a name="4721"><span class="lineNum">    4721 </span><span class="lineCov">       1977 :                 t[i__ + i__ * t_dim1] = tau[i__];</span></a>
+<a name="4722"><span class="lineNum">    4722 </span>            :             }</a>
+<a name="4723"><span class="lineNum">    4723 </span>            :         }</a>
+<a name="4724"><span class="lineNum">    4724 </span>            :     } else {</a>
+<a name="4725"><span class="lineNum">    4725 </span><span class="lineCov">       1663 :         for (i__ = *k; i__ &gt;= 1; --i__) {</span></a>
+<a name="4726"><span class="lineNum">    4726 </span><span class="lineCov">       1604 :             if (std::abs(tau[i__])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4727"><span class="lineNum">    4727 </span>            : </a>
+<a name="4728"><span class="lineNum">    4728 </span><span class="lineCov">         12 :                 i__1 = *k;</span></a>
+<a name="4729"><span class="lineNum">    4729 </span><span class="lineCov">        396 :                 for (j = i__; j &lt;= i__1; ++j) {</span></a>
+<a name="4730"><span class="lineNum">    4730 </span><span class="lineCov">        384 :                     t[j + i__ * t_dim1] = 0.;</span></a>
+<a name="4731"><span class="lineNum">    4731 </span>            :                 }</a>
+<a name="4732"><span class="lineNum">    4732 </span>            :             } else {</a>
+<a name="4733"><span class="lineNum">    4733 </span>            : </a>
+<a name="4734"><span class="lineNum">    4734 </span><span class="lineCov">       1592 :                 if (i__ &lt; *k) {</span></a>
+<a name="4735"><span class="lineNum">    4735 </span><span class="lineCov">       1533 :                     if (*storev=='C' || *storev=='c') {</span></a>
+<a name="4736"><span class="lineNum">    4736 </span><span class="lineCov">       1533 :                         vii = v[*n - *k + i__ + i__ * v_dim1];</span></a>
+<a name="4737"><span class="lineNum">    4737 </span><span class="lineCov">       1533 :                         v[*n - *k + i__ + i__ * v_dim1] = 1.;</span></a>
+<a name="4738"><span class="lineNum">    4738 </span>            : </a>
+<a name="4739"><span class="lineNum">    4739 </span><span class="lineCov">       1533 :                         i__1 = *n - *k + i__;</span></a>
+<a name="4740"><span class="lineNum">    4740 </span><span class="lineCov">       1533 :                         i__2 = *k - i__;</span></a>
+<a name="4741"><span class="lineNum">    4741 </span><span class="lineCov">       1533 :                         d__1 = -tau[i__];</span></a>
+<a name="4742"><span class="lineNum">    4742 </span><span class="lineCov">       1533 :                         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;Transpose&quot;, &amp;i__1, &amp;i__2, &amp;d__1, &amp;v[(i__ + 1) </span></a>
+<a name="4743"><span class="lineNum">    4743 </span><span class="lineCov">       1533 :                                 * v_dim1 + 1], ldv, &amp;v[i__ * v_dim1 + 1], &amp;</span></a>
+<a name="4744"><span class="lineNum">    4744 </span><span class="lineCov">       1533 :                                 c__1, &amp;zero, &amp;t[i__ + 1 + i__ * t_dim1], &amp;</span></a>
+<a name="4745"><span class="lineNum">    4745 </span>            :                                 c__1);</a>
+<a name="4746"><span class="lineNum">    4746 </span><span class="lineCov">       1533 :                         v[*n - *k + i__ + i__ * v_dim1] = vii;</span></a>
+<a name="4747"><span class="lineNum">    4747 </span>            :                     } else {</a>
+<a name="4748"><span class="lineNum">    4748 </span><span class="lineNoCov">          0 :                         vii = v[i__ + (*n - *k + i__) * v_dim1];</span></a>
+<a name="4749"><span class="lineNum">    4749 </span><span class="lineNoCov">          0 :                         v[i__ + (*n - *k + i__) * v_dim1] = 1.;</span></a>
+<a name="4750"><span class="lineNum">    4750 </span>            : </a>
+<a name="4751"><span class="lineNum">    4751 </span><span class="lineNoCov">          0 :                         i__1 = *k - i__;</span></a>
+<a name="4752"><span class="lineNum">    4752 </span><span class="lineNoCov">          0 :                         i__2 = *n - *k + i__;</span></a>
+<a name="4753"><span class="lineNum">    4753 </span><span class="lineNoCov">          0 :                         d__1 = -tau[i__];</span></a>
+<a name="4754"><span class="lineNum">    4754 </span><span class="lineNoCov">          0 :                         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;No transpose&quot;, &amp;i__1, &amp;i__2, &amp;d__1, &amp;v[i__ + </span></a>
+<a name="4755"><span class="lineNum">    4755 </span><span class="lineNoCov">          0 :                                 1 + v_dim1], ldv, &amp;v[i__ + v_dim1], ldv, &amp;</span></a>
+<a name="4756"><span class="lineNum">    4756 </span><span class="lineNoCov">          0 :                                 zero, &amp;t[i__ + 1 + i__ * t_dim1], &amp;c__1);</span></a>
+<a name="4757"><span class="lineNum">    4757 </span><span class="lineNoCov">          0 :                         v[i__ + (*n - *k + i__) * v_dim1] = vii;</span></a>
+<a name="4758"><span class="lineNum">    4758 </span>            :                     }</a>
+<a name="4759"><span class="lineNum">    4759 </span>            : </a>
+<a name="4760"><span class="lineNum">    4760 </span><span class="lineCov">       1533 :                     i__1 = *k - i__;</span></a>
+<a name="4761"><span class="lineNum">    4761 </span><span class="lineCov">       1533 :                     PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)(&quot;Lower&quot;, &quot;No transpose&quot;, &quot;Non-unit&quot;, &amp;i__1, &amp;t[i__ </span></a>
+<a name="4762"><span class="lineNum">    4762 </span><span class="lineCov">       1533 :                             + 1 + (i__ + 1) * t_dim1], ldt, &amp;t[i__ + 1 + i__ *</span></a>
+<a name="4763"><span class="lineNum">    4763 </span><span class="lineCov">       1533 :                              t_dim1], &amp;c__1)</span></a>
+<a name="4764"><span class="lineNum">    4764 </span>            :                             ;</a>
+<a name="4765"><span class="lineNum">    4765 </span>            :                 }</a>
+<a name="4766"><span class="lineNum">    4766 </span><span class="lineCov">       1592 :                 t[i__ + i__ * t_dim1] = tau[i__];</span></a>
+<a name="4767"><span class="lineNum">    4767 </span>            :             }</a>
+<a name="4768"><span class="lineNum">    4768 </span>            :         }</a>
+<a name="4769"><span class="lineNum">    4769 </span>            :     }</a>
+<a name="4770"><span class="lineNum">    4770 </span>            :     return;</a>
+<a name="4771"><span class="lineNum">    4771 </span>            : </a>
+<a name="4772"><span class="lineNum">    4772 </span>            : </a>
+<a name="4773"><span class="lineNum">    4773 </span>            : }</a>
+<a name="4774"><span class="lineNum">    4774 </span>            : }</a>
+<a name="4775"><span class="lineNum">    4775 </span>            : }</a>
+<a name="4776"><span class="lineNum">    4776 </span>            : #include &lt;cmath&gt;</a>
+<a name="4777"><span class="lineNum">    4777 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="4778"><span class="lineNum">    4778 </span>            : </a>
+<a name="4779"><span class="lineNum">    4779 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4780"><span class="lineNum">    4780 </span>            : namespace PLMD{</a>
+<a name="4781"><span class="lineNum">    4781 </span>            : namespace lapack{</a>
+<a name="4782"><span class="lineNum">    4782 </span>            : using namespace blas;</a>
+<a name="4783"><span class="lineNum">    4783 </span>            : void</a>
+<a name="4784"><span class="lineNum">    4784 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlarnv,DLARNV)(int *idist, </span></a>
+<a name="4785"><span class="lineNum">    4785 </span>            :         int *iseed, </a>
+<a name="4786"><span class="lineNum">    4786 </span>            :         int *n, </a>
+<a name="4787"><span class="lineNum">    4787 </span>            :         double *x)</a>
+<a name="4788"><span class="lineNum">    4788 </span>            : {</a>
+<a name="4789"><span class="lineNum">    4789 </span>            :     int i__1, i__2, i__3;</a>
+<a name="4790"><span class="lineNum">    4790 </span>            : </a>
+<a name="4791"><span class="lineNum">    4791 </span>            :     int i__;</a>
+<a name="4792"><span class="lineNum">    4792 </span>            :     double u[128];</a>
+<a name="4793"><span class="lineNum">    4793 </span>            :     int il, iv, il2;</a>
+<a name="4794"><span class="lineNum">    4794 </span>            : </a>
+<a name="4795"><span class="lineNum">    4795 </span><span class="lineNoCov">          0 :     --x;</span></a>
+<a name="4796"><span class="lineNum">    4796 </span>            :     --iseed;</a>
+<a name="4797"><span class="lineNum">    4797 </span>            : </a>
+<a name="4798"><span class="lineNum">    4798 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="4799"><span class="lineNum">    4799 </span><span class="lineNoCov">          0 :     for (iv = 1; iv &lt;= i__1; iv += 64) {</span></a>
+<a name="4800"><span class="lineNum">    4800 </span><span class="lineNoCov">          0 :         i__2 = 64, i__3 = *n - iv + 1;</span></a>
+<a name="4801"><span class="lineNum">    4801 </span>            :         il = (i__2&lt;i__3) ? i__2 : i__3;</a>
+<a name="4802"><span class="lineNum">    4802 </span><span class="lineNoCov">          0 :         if (*idist == 3) {</span></a>
+<a name="4803"><span class="lineNum">    4803 </span><span class="lineNoCov">          0 :             il2 = il &lt;&lt; 1;</span></a>
+<a name="4804"><span class="lineNum">    4804 </span>            :         } else {</a>
+<a name="4805"><span class="lineNum">    4805 </span><span class="lineNoCov">          0 :             il2 = il;</span></a>
+<a name="4806"><span class="lineNum">    4806 </span>            :         }</a>
+<a name="4807"><span class="lineNum">    4807 </span>            : </a>
+<a name="4808"><span class="lineNum">    4808 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlaruv,DLARUV)(&amp;iseed[1], &amp;il2, u);</span></a>
+<a name="4809"><span class="lineNum">    4809 </span>            : </a>
+<a name="4810"><span class="lineNum">    4810 </span><span class="lineNoCov">          0 :         if (*idist == 1) {</span></a>
+<a name="4811"><span class="lineNum">    4811 </span>            : </a>
+<a name="4812"><span class="lineNum">    4812 </span>            :             i__2 = il;</a>
+<a name="4813"><span class="lineNum">    4813 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4814"><span class="lineNum">    4814 </span><span class="lineNoCov">          0 :                 x[iv + i__ - 1] = u[i__ - 1];</span></a>
+<a name="4815"><span class="lineNum">    4815 </span>            :             }</a>
+<a name="4816"><span class="lineNum">    4816 </span><span class="lineNoCov">          0 :         } else if (*idist == 2) {</span></a>
+<a name="4817"><span class="lineNum">    4817 </span>            : </a>
+<a name="4818"><span class="lineNum">    4818 </span>            :             i__2 = il;</a>
+<a name="4819"><span class="lineNum">    4819 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4820"><span class="lineNum">    4820 </span><span class="lineNoCov">          0 :                 x[iv + i__ - 1] = u[i__ - 1] * 2. - 1.;</span></a>
+<a name="4821"><span class="lineNum">    4821 </span>            :             }</a>
+<a name="4822"><span class="lineNum">    4822 </span><span class="lineNoCov">          0 :         } else if (*idist == 3) {</span></a>
+<a name="4823"><span class="lineNum">    4823 </span>            : </a>
+<a name="4824"><span class="lineNum">    4824 </span>            :             i__2 = il;</a>
+<a name="4825"><span class="lineNum">    4825 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="4826"><span class="lineNum">    4826 </span><span class="lineNoCov">          0 :                 x[iv + i__ - 1] =  std::sqrt(std::log(u[(i__ &lt;&lt; 1) - 2]) * -2.) * </span></a>
+<a name="4827"><span class="lineNum">    4827 </span><span class="lineNoCov">          0 :                   std::cos(u[(i__ &lt;&lt; 1) - 1] * (double)6.2831853071795864769252867663);</span></a>
+<a name="4828"><span class="lineNum">    4828 </span>            :             }</a>
+<a name="4829"><span class="lineNum">    4829 </span>            :         }</a>
+<a name="4830"><span class="lineNum">    4830 </span>            :     }</a>
+<a name="4831"><span class="lineNum">    4831 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="4832"><span class="lineNum">    4832 </span>            : </a>
+<a name="4833"><span class="lineNum">    4833 </span>            : }</a>
+<a name="4834"><span class="lineNum">    4834 </span>            : }</a>
+<a name="4835"><span class="lineNum">    4835 </span>            : }</a>
+<a name="4836"><span class="lineNum">    4836 </span>            : #include &lt;cmath&gt;</a>
+<a name="4837"><span class="lineNum">    4837 </span>            : </a>
+<a name="4838"><span class="lineNum">    4838 </span>            : #include &quot;real.h&quot;</a>
+<a name="4839"><span class="lineNum">    4839 </span>            : </a>
+<a name="4840"><span class="lineNum">    4840 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="4841"><span class="lineNum">    4841 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="4842"><span class="lineNum">    4842 </span>            : </a>
+<a name="4843"><span class="lineNum">    4843 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="4844"><span class="lineNum">    4844 </span>            : namespace PLMD{</a>
+<a name="4845"><span class="lineNum">    4845 </span>            : namespace lapack{</a>
+<a name="4846"><span class="lineNum">    4846 </span>            : using namespace blas;</a>
+<a name="4847"><span class="lineNum">    4847 </span>            : void</a>
+<a name="4848"><span class="lineNum">    4848 </span><span class="lineCov">     570080 : PLUMED_BLAS_F77_FUNC(dlarrbx,DLARRBX)(int *n, </span></a>
+<a name="4849"><span class="lineNum">    4849 </span>            :          double *d__, </a>
+<a name="4850"><span class="lineNum">    4850 </span>            :          double *l, </a>
+<a name="4851"><span class="lineNum">    4851 </span>            :          double *ld, </a>
+<a name="4852"><span class="lineNum">    4852 </span>            :          double *lld, </a>
+<a name="4853"><span class="lineNum">    4853 </span>            :          int *ifirst, </a>
+<a name="4854"><span class="lineNum">    4854 </span>            :          int *ilast, </a>
+<a name="4855"><span class="lineNum">    4855 </span>            :          double *rtol1, </a>
+<a name="4856"><span class="lineNum">    4856 </span>            :          double *rtol2, </a>
+<a name="4857"><span class="lineNum">    4857 </span>            :          int *offset, </a>
+<a name="4858"><span class="lineNum">    4858 </span>            :          double *w, </a>
+<a name="4859"><span class="lineNum">    4859 </span>            :          double *wgap, </a>
+<a name="4860"><span class="lineNum">    4860 </span>            :          double *werr, </a>
+<a name="4861"><span class="lineNum">    4861 </span>            :          double *work,</a>
+<a name="4862"><span class="lineNum">    4862 </span>            :          int *iwork, </a>
+<a name="4863"><span class="lineNum">    4863 </span>            :          int *info)</a>
+<a name="4864"><span class="lineNum">    4864 </span>            : {</a>
+<a name="4865"><span class="lineNum">    4865 </span>            :     int i__1, i__2, i__3;</a>
+<a name="4866"><span class="lineNum">    4866 </span>            :     double d__1, d__2;</a>
+<a name="4867"><span class="lineNum">    4867 </span>            : </a>
+<a name="4868"><span class="lineNum">    4868 </span>            :     int i__, j, k, p;</a>
+<a name="4869"><span class="lineNum">    4869 </span>            :     double s;</a>
+<a name="4870"><span class="lineNum">    4870 </span>            :     int i1, i2, ii, kk;</a>
+<a name="4871"><span class="lineNum">    4871 </span>            :     double fac, gap, mid;</a>
+<a name="4872"><span class="lineNum">    4872 </span>            :     int cnt;</a>
+<a name="4873"><span class="lineNum">    4873 </span>            :     double tmp, left;</a>
+<a name="4874"><span class="lineNum">    4874 </span>            :     int nint, prev, next, nleft;</a>
+<a name="4875"><span class="lineNum">    4875 </span>            :     double right, width, dplus;</a>
+<a name="4876"><span class="lineNum">    4876 </span>            :     int nright, olnint;</a>
+<a name="4877"><span class="lineNum">    4877 </span>            :     k = 0;</a>
+<a name="4878"><span class="lineNum">    4878 </span>            :     right = 0.0;</a>
+<a name="4879"><span class="lineNum">    4879 </span>            : </a>
+<a name="4880"><span class="lineNum">    4880 </span><span class="lineCov">     570080 :     --iwork;</span></a>
+<a name="4881"><span class="lineNum">    4881 </span><span class="lineCov">     570080 :     --work;</span></a>
+<a name="4882"><span class="lineNum">    4882 </span><span class="lineCov">     570080 :     --werr;</span></a>
+<a name="4883"><span class="lineNum">    4883 </span><span class="lineCov">     570080 :     --wgap;</span></a>
+<a name="4884"><span class="lineNum">    4884 </span><span class="lineCov">     570080 :     --w;</span></a>
+<a name="4885"><span class="lineNum">    4885 </span><span class="lineCov">     570080 :     --lld;</span></a>
+<a name="4886"><span class="lineNum">    4886 </span>            :     --ld;</a>
+<a name="4887"><span class="lineNum">    4887 </span>            :     --l;</a>
+<a name="4888"><span class="lineNum">    4888 </span><span class="lineCov">     570080 :     --d__;</span></a>
+<a name="4889"><span class="lineNum">    4889 </span>            : </a>
+<a name="4890"><span class="lineNum">    4890 </span><span class="lineCov">     570080 :     *info = 0;</span></a>
+<a name="4891"><span class="lineNum">    4891 </span><span class="lineCov">     570080 :     i__1 = *n &lt;&lt; 1;</span></a>
+<a name="4892"><span class="lineNum">    4892 </span><span class="lineCov">    5134164 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="4893"><span class="lineNum">    4893 </span><span class="lineCov">    4564084 :         iwork[i__] = 0;</span></a>
+<a name="4894"><span class="lineNum">    4894 </span>            :     }</a>
+<a name="4895"><span class="lineNum">    4895 </span><span class="lineCov">     570080 :     i1 = *ifirst;</span></a>
+<a name="4896"><span class="lineNum">    4896 </span>            :     i2 = *ifirst;</a>
+<a name="4897"><span class="lineNum">    4897 </span>            :     prev = 0;</a>
+<a name="4898"><span class="lineNum">    4898 </span><span class="lineCov">     570080 :     i__1 = *ilast;</span></a>
+<a name="4899"><span class="lineNum">    4899 </span><span class="lineCov">    1141026 :     for (i__ = *ifirst; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="4900"><span class="lineNum">    4900 </span><span class="lineCov">     570946 :         k = i__ &lt;&lt; 1;</span></a>
+<a name="4901"><span class="lineNum">    4901 </span><span class="lineCov">     570946 :         iwork[k - 1] = 1;</span></a>
+<a name="4902"><span class="lineNum">    4902 </span>            :         i2 = i__;</a>
+<a name="4903"><span class="lineNum">    4903 </span>            :     }</a>
+<a name="4904"><span class="lineNum">    4904 </span>            : </a>
+<a name="4905"><span class="lineNum">    4905 </span>            :     i__ = i1;</a>
+<a name="4906"><span class="lineNum">    4906 </span>            :     nint = 0;</a>
+<a name="4907"><span class="lineNum">    4907 </span><span class="lineCov">    1141026 : L30:</span></a>
+<a name="4908"><span class="lineNum">    4908 </span><span class="lineCov">    1141026 :     if (i__ &lt;= i2) {</span></a>
+<a name="4909"><span class="lineNum">    4909 </span><span class="lineCov">     570946 :         ii = i__ - *offset;</span></a>
+<a name="4910"><span class="lineNum">    4910 </span><span class="lineCov">     570946 :         if (iwork[(i__ &lt;&lt; 1) - 1] == 1) {</span></a>
+<a name="4911"><span class="lineNum">    4911 </span>            :             fac = 1.;</a>
+<a name="4912"><span class="lineNum">    4912 </span><span class="lineCov">     570946 :             left = w[ii] - werr[ii];</span></a>
+<a name="4913"><span class="lineNum">    4913 </span>            : </a>
+<a name="4914"><span class="lineNum">    4914 </span>            : </a>
+<a name="4915"><span class="lineNum">    4915 </span><span class="lineCov">     571036 : L40:</span></a>
+<a name="4916"><span class="lineNum">    4916 </span><span class="lineCov">     571036 :             if (i__ &gt; i1 &amp;&amp; left &lt;= right) {</span></a>
+<a name="4917"><span class="lineNum">    4917 </span>            :                 left = right;</a>
+<a name="4918"><span class="lineNum">    4918 </span><span class="lineNoCov">          0 :                 cnt = i__ - 1;</span></a>
+<a name="4919"><span class="lineNum">    4919 </span>            :             } else {</a>
+<a name="4920"><span class="lineNum">    4920 </span><span class="lineCov">     571036 :                 s = -left;</span></a>
+<a name="4921"><span class="lineNum">    4921 </span>            :                 cnt = 0;</a>
+<a name="4922"><span class="lineNum">    4922 </span><span class="lineCov">     571036 :                 i__1 = *n - 1;</span></a>
+<a name="4923"><span class="lineNum">    4923 </span><span class="lineCov">    2677334 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4924"><span class="lineNum">    4924 </span><span class="lineCov">    2106298 :                     dplus = d__[j] + s;</span></a>
+<a name="4925"><span class="lineNum">    4925 </span><span class="lineCov">    2106298 :                     s = s * lld[j] / dplus - left;</span></a>
+<a name="4926"><span class="lineNum">    4926 </span><span class="lineCov">    2106298 :                     if (dplus &lt; 0.) {</span></a>
+<a name="4927"><span class="lineNum">    4927 </span><span class="lineCov">     209478 :                         ++cnt;</span></a>
+<a name="4928"><span class="lineNum">    4928 </span>            :                     }</a>
+<a name="4929"><span class="lineNum">    4929 </span>            :                 }</a>
+<a name="4930"><span class="lineNum">    4930 </span><span class="lineCov">     571036 :                 dplus = d__[*n] + s;</span></a>
+<a name="4931"><span class="lineNum">    4931 </span><span class="lineCov">     571036 :                 if (dplus &lt; 0.) {</span></a>
+<a name="4932"><span class="lineNum">    4932 </span><span class="lineCov">         90 :                     ++cnt;</span></a>
+<a name="4933"><span class="lineNum">    4933 </span>            :                 }</a>
+<a name="4934"><span class="lineNum">    4934 </span><span class="lineCov">     571036 :         if (std::isnan(s)) {</span></a>
+<a name="4935"><span class="lineNum">    4935 </span>            : </a>
+<a name="4936"><span class="lineNum">    4936 </span>            :                     cnt = 0;</a>
+<a name="4937"><span class="lineNum">    4937 </span>            :                     s = -left;</a>
+<a name="4938"><span class="lineNum">    4938 </span>            :                     i__1 = *n - 1;</a>
+<a name="4939"><span class="lineNum">    4939 </span><span class="lineNoCov">          0 :                     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4940"><span class="lineNum">    4940 </span><span class="lineNoCov">          0 :                         dplus = d__[j] + s;</span></a>
+<a name="4941"><span class="lineNum">    4941 </span><span class="lineNoCov">          0 :                         if (dplus &lt; 0.) {</span></a>
+<a name="4942"><span class="lineNum">    4942 </span><span class="lineNoCov">          0 :                             ++cnt;</span></a>
+<a name="4943"><span class="lineNum">    4943 </span>            :                         }</a>
+<a name="4944"><span class="lineNum">    4944 </span><span class="lineNoCov">          0 :                         tmp = lld[j] / dplus;</span></a>
+<a name="4945"><span class="lineNum">    4945 </span><span class="lineNoCov">          0 :                         if (std::abs(tmp)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4946"><span class="lineNum">    4946 </span><span class="lineNoCov">          0 :                             s = lld[j] - left;</span></a>
+<a name="4947"><span class="lineNum">    4947 </span>            :                         } else {</a>
+<a name="4948"><span class="lineNum">    4948 </span><span class="lineNoCov">          0 :                             s = s * tmp - left;</span></a>
+<a name="4949"><span class="lineNum">    4949 </span>            :                         }</a>
+<a name="4950"><span class="lineNum">    4950 </span>            :                     }</a>
+<a name="4951"><span class="lineNum">    4951 </span><span class="lineNoCov">          0 :                     dplus = d__[*n] + s;</span></a>
+<a name="4952"><span class="lineNum">    4952 </span><span class="lineNoCov">          0 :                     if (dplus &lt; 0.) {</span></a>
+<a name="4953"><span class="lineNum">    4953 </span><span class="lineNoCov">          0 :                         ++cnt;</span></a>
+<a name="4954"><span class="lineNum">    4954 </span>            :                     }</a>
+<a name="4955"><span class="lineNum">    4955 </span>            :                 }</a>
+<a name="4956"><span class="lineNum">    4956 </span><span class="lineCov">     571036 :                 if (cnt &gt; i__ - 1) {</span></a>
+<a name="4957"><span class="lineNum">    4957 </span><span class="lineCov">         90 :                     left -= werr[ii] * fac;</span></a>
+<a name="4958"><span class="lineNum">    4958 </span><span class="lineCov">         90 :                     fac *= 2.;</span></a>
+<a name="4959"><span class="lineNum">    4959 </span><span class="lineCov">         90 :                     goto L40;</span></a>
+<a name="4960"><span class="lineNum">    4960 </span>            :                 }</a>
+<a name="4961"><span class="lineNum">    4961 </span>            :             }</a>
+<a name="4962"><span class="lineNum">    4962 </span><span class="lineCov">     570946 :             nleft = cnt + 1;</span></a>
+<a name="4963"><span class="lineNum">    4963 </span>            :             i1 = (i1&lt;nleft) ? i1 : nleft;</a>
+<a name="4964"><span class="lineNum">    4964 </span>            :             fac = 1.;</a>
+<a name="4965"><span class="lineNum">    4965 </span><span class="lineCov">     570946 :             right = w[ii] + werr[ii];</span></a>
+<a name="4966"><span class="lineNum">    4966 </span><span class="lineCov">     570962 : L60:</span></a>
+<a name="4967"><span class="lineNum">    4967 </span><span class="lineCov">     570962 :             s = -right;</span></a>
+<a name="4968"><span class="lineNum">    4968 </span>            :             cnt = 0;</a>
+<a name="4969"><span class="lineNum">    4969 </span><span class="lineCov">     570962 :             i__1 = *n - 1;</span></a>
+<a name="4970"><span class="lineNum">    4970 </span><span class="lineCov">    2654334 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4971"><span class="lineNum">    4971 </span><span class="lineCov">    2083372 :                 dplus = d__[j] + s;</span></a>
+<a name="4972"><span class="lineNum">    4972 </span><span class="lineCov">    2083372 :                 s = s * lld[j] / dplus - right;</span></a>
+<a name="4973"><span class="lineNum">    4973 </span><span class="lineCov">    2083372 :                 if (dplus &lt; 0.) {</span></a>
+<a name="4974"><span class="lineNum">    4974 </span><span class="lineCov">    1882767 :                     ++cnt;</span></a>
+<a name="4975"><span class="lineNum">    4975 </span>            :                 }</a>
+<a name="4976"><span class="lineNum">    4976 </span>            :             }</a>
+<a name="4977"><span class="lineNum">    4977 </span><span class="lineCov">     570962 :             dplus = d__[*n] + s;</span></a>
+<a name="4978"><span class="lineNum">    4978 </span><span class="lineCov">     570962 :             if (dplus &lt; 0.) {</span></a>
+<a name="4979"><span class="lineNum">    4979 </span><span class="lineCov">     570942 :                 ++cnt;</span></a>
+<a name="4980"><span class="lineNum">    4980 </span>            :             }</a>
+<a name="4981"><span class="lineNum">    4981 </span><span class="lineCov">     570962 :             if (std::isnan(s)) {</span></a>
+<a name="4982"><span class="lineNum">    4982 </span>            : </a>
+<a name="4983"><span class="lineNum">    4983 </span>            :                 cnt = 0;</a>
+<a name="4984"><span class="lineNum">    4984 </span>            :                 s = -right;</a>
+<a name="4985"><span class="lineNum">    4985 </span>            :                 i__1 = *n - 1;</a>
+<a name="4986"><span class="lineNum">    4986 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="4987"><span class="lineNum">    4987 </span><span class="lineNoCov">          0 :                     dplus = d__[j] + s;</span></a>
+<a name="4988"><span class="lineNum">    4988 </span><span class="lineNoCov">          0 :                     if (dplus &lt; 0.) {</span></a>
+<a name="4989"><span class="lineNum">    4989 </span><span class="lineNoCov">          0 :                         ++cnt;</span></a>
+<a name="4990"><span class="lineNum">    4990 </span>            :                     }</a>
+<a name="4991"><span class="lineNum">    4991 </span><span class="lineNoCov">          0 :                     tmp = lld[j] / dplus;</span></a>
+<a name="4992"><span class="lineNum">    4992 </span><span class="lineNoCov">          0 :                     if (std::abs(tmp)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="4993"><span class="lineNum">    4993 </span><span class="lineNoCov">          0 :                         s = lld[j] - right;</span></a>
+<a name="4994"><span class="lineNum">    4994 </span>            :                     } else {</a>
+<a name="4995"><span class="lineNum">    4995 </span><span class="lineNoCov">          0 :                         s = s * tmp - right;</span></a>
+<a name="4996"><span class="lineNum">    4996 </span>            :                     }</a>
+<a name="4997"><span class="lineNum">    4997 </span>            :                 }</a>
+<a name="4998"><span class="lineNum">    4998 </span><span class="lineNoCov">          0 :                 dplus = d__[*n] + s;</span></a>
+<a name="4999"><span class="lineNum">    4999 </span><span class="lineNoCov">          0 :                 if (dplus &lt; 0.) {</span></a>
+<a name="5000"><span class="lineNum">    5000 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="5001"><span class="lineNum">    5001 </span>            :                 }</a>
+<a name="5002"><span class="lineNum">    5002 </span>            :             }</a>
+<a name="5003"><span class="lineNum">    5003 </span><span class="lineCov">     570962 :             if (cnt &lt; i__) {</span></a>
+<a name="5004"><span class="lineNum">    5004 </span><span class="lineCov">         16 :                 right += werr[ii] * fac;</span></a>
+<a name="5005"><span class="lineNum">    5005 </span><span class="lineCov">         16 :                 fac *= 2.;</span></a>
+<a name="5006"><span class="lineNum">    5006 </span><span class="lineCov">         16 :                 goto L60;</span></a>
+<a name="5007"><span class="lineNum">    5007 </span>            :             }</a>
+<a name="5008"><span class="lineNum">    5008 </span>            :             cnt = (cnt&lt;i2) ? cnt : i2;</a>
+<a name="5009"><span class="lineNum">    5009 </span><span class="lineCov">     570946 :             ++nint;</span></a>
+<a name="5010"><span class="lineNum">    5010 </span><span class="lineCov">     570946 :             k = nleft &lt;&lt; 1;</span></a>
+<a name="5011"><span class="lineNum">    5011 </span><span class="lineCov">     570946 :             work[k - 1] = left;</span></a>
+<a name="5012"><span class="lineNum">    5012 </span><span class="lineCov">     570946 :             work[k] = right;</span></a>
+<a name="5013"><span class="lineNum">    5013 </span><span class="lineCov">     570946 :             i__ = cnt + 1;</span></a>
+<a name="5014"><span class="lineNum">    5014 </span><span class="lineCov">     570946 :             iwork[k - 1] = i__;</span></a>
+<a name="5015"><span class="lineNum">    5015 </span><span class="lineCov">     570946 :             iwork[k] = cnt;</span></a>
+<a name="5016"><span class="lineNum">    5016 </span><span class="lineCov">     570946 :             if (prev != nleft - 1) {</span></a>
+<a name="5017"><span class="lineNum">    5017 </span><span class="lineCov">         70 :                 work[k - 2] = left;</span></a>
+<a name="5018"><span class="lineNum">    5018 </span>            :             }</a>
+<a name="5019"><span class="lineNum">    5019 </span>            :             prev = nleft;</a>
+<a name="5020"><span class="lineNum">    5020 </span>            :         } else {</a>
+<a name="5021"><span class="lineNum">    5021 </span><span class="lineNoCov">          0 :             right = work[i__ * 2];</span></a>
+<a name="5022"><span class="lineNum">    5022 </span>            : </a>
+<a name="5023"><span class="lineNum">    5023 </span><span class="lineNoCov">          0 :             ++iwork[k - 1];</span></a>
+<a name="5024"><span class="lineNum">    5024 </span>            :             prev = i__;</a>
+<a name="5025"><span class="lineNum">    5025 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="5026"><span class="lineNum">    5026 </span>            :         }</a>
+<a name="5027"><span class="lineNum">    5027 </span><span class="lineCov">     570946 :         goto L30;</span></a>
+<a name="5028"><span class="lineNum">    5028 </span>            :     }</a>
+<a name="5029"><span class="lineNum">    5029 </span><span class="lineCov">     570080 :     if (i__ &lt;= *n &amp;&amp; iwork[(i__ &lt;&lt; 1) - 1] != -1) {</span></a>
+<a name="5030"><span class="lineNum">    5030 </span><span class="lineCov">     490521 :         work[(i__ &lt;&lt; 1) - 1] = work[prev * 2];</span></a>
+<a name="5031"><span class="lineNum">    5031 </span>            :     }</a>
+<a name="5032"><span class="lineNum">    5032 </span>            : </a>
+<a name="5033"><span class="lineNum">    5033 </span><span class="lineCov">      79559 : L80:</span></a>
+<a name="5034"><span class="lineNum">    5034 </span><span class="lineCov">   29310201 :     prev = i1 - 1;</span></a>
+<a name="5035"><span class="lineNum">    5035 </span>            :     olnint = nint;</a>
+<a name="5036"><span class="lineNum">    5036 </span>            :     i__ = i1;</a>
+<a name="5037"><span class="lineNum">    5037 </span>            :     i__1 = olnint;</a>
+<a name="5038"><span class="lineNum">    5038 </span><span class="lineCov">   58621950 :     for (p = 1; p &lt;= i__1; ++p) {</span></a>
+<a name="5039"><span class="lineNum">    5039 </span><span class="lineCov">   29311749 :         k = i__ &lt;&lt; 1;</span></a>
+<a name="5040"><span class="lineNum">    5040 </span><span class="lineCov">   29311749 :         left = work[k - 1];</span></a>
+<a name="5041"><span class="lineNum">    5041 </span><span class="lineCov">   29311749 :         right = work[k];</span></a>
+<a name="5042"><span class="lineNum">    5042 </span><span class="lineCov">   29311749 :         next = iwork[k - 1];</span></a>
+<a name="5043"><span class="lineNum">    5043 </span><span class="lineCov">   29311749 :         nright = iwork[k];</span></a>
+<a name="5044"><span class="lineNum">    5044 </span><span class="lineCov">   29311749 :         mid = (left + right) * .5;</span></a>
+<a name="5045"><span class="lineNum">    5045 </span><span class="lineCov">   29311749 :         width = right - mid;</span></a>
+<a name="5046"><span class="lineNum">    5046 </span>            :         d__1 = std::abs(left);</a>
+<a name="5047"><span class="lineNum">    5047 </span>            :         d__2 = std::abs(right);</a>
+<a name="5048"><span class="lineNum">    5048 </span><span class="lineCov">   29311749 :         tmp = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="5049"><span class="lineNum">    5049 </span>            : </a>
+<a name="5050"><span class="lineNum">    5050 </span>            :         gap = 0.;</a>
+<a name="5051"><span class="lineNum">    5051 </span><span class="lineCov">   29311749 :         if (i__ == nright) {</span></a>
+<a name="5052"><span class="lineNum">    5052 </span><span class="lineCov">   29071087 :             if (prev &gt; 0 &amp;&amp; next &lt;= *n) {</span></a>
+<a name="5053"><span class="lineNum">    5053 </span><span class="lineCov">       2391 :                 d__1 = left - work[k - 2], d__2 = work[k + 1] - right;</span></a>
+<a name="5054"><span class="lineNum">    5054 </span><span class="lineCov">       2391 :                 gap = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="5055"><span class="lineNum">    5055 </span><span class="lineCov">   29068696 :             } else if (prev &gt; 0) {</span></a>
+<a name="5056"><span class="lineNum">    5056 </span><span class="lineCov">    4055695 :                 gap = left - work[k - 2];</span></a>
+<a name="5057"><span class="lineNum">    5057 </span><span class="lineCov">   25013001 :             } else if (next &lt;= *n) {</span></a>
+<a name="5058"><span class="lineNum">    5058 </span><span class="lineCov">   25013001 :                 gap = work[k + 1] - right;</span></a>
+<a name="5059"><span class="lineNum">    5059 </span>            :             }</a>
+<a name="5060"><span class="lineNum">    5060 </span>            :         }</a>
+<a name="5061"><span class="lineNum">    5061 </span><span class="lineCov">   29311749 :         d__1 = *rtol1 * gap, d__2 = *rtol2 * tmp;</span></a>
+<a name="5062"><span class="lineNum">    5062 </span><span class="lineCov">   32850455 :         if (width &lt; ((d__1&gt;d__2) ? d__1 : d__2)) {</span></a>
+<a name="5063"><span class="lineNum">    5063 </span><span class="lineCov">     570946 :             --nint;</span></a>
+<a name="5064"><span class="lineNum">    5064 </span><span class="lineCov">     570946 :             iwork[k - 1] = 0;</span></a>
+<a name="5065"><span class="lineNum">    5065 </span>            :             kk = k;</a>
+<a name="5066"><span class="lineNum">    5066 </span>            :             i__2 = nright;</a>
+<a name="5067"><span class="lineNum">    5067 </span><span class="lineCov">     570946 :             for (j = i__ + 1; j &lt;= i__2; ++j) {</span></a>
+<a name="5068"><span class="lineNum">    5068 </span><span class="lineNoCov">          0 :                 kk += 2;</span></a>
+<a name="5069"><span class="lineNum">    5069 </span><span class="lineNoCov">          0 :                 iwork[kk - 1] = 0;</span></a>
+<a name="5070"><span class="lineNum">    5070 </span><span class="lineNoCov">          0 :                 work[kk - 1] = left;</span></a>
+<a name="5071"><span class="lineNum">    5071 </span><span class="lineNoCov">          0 :                 work[kk] = right;</span></a>
+<a name="5072"><span class="lineNum">    5072 </span><span class="lineNoCov">          0 :                 wgap[j - 1 - *offset] = 0.;</span></a>
+<a name="5073"><span class="lineNum">    5073 </span>            :             }</a>
+<a name="5074"><span class="lineNum">    5074 </span><span class="lineCov">     570946 :             if (i1 == i__) {</span></a>
+<a name="5075"><span class="lineNum">    5075 </span>            :                 i1 = next;</a>
+<a name="5076"><span class="lineNum">    5076 </span>            :             } else {</a>
+<a name="5077"><span class="lineNum">    5077 </span><span class="lineCov">        831 :                 iwork[(prev &lt;&lt; 1) - 1] = next;</span></a>
+<a name="5078"><span class="lineNum">    5078 </span>            :             }</a>
+<a name="5079"><span class="lineNum">    5079 </span>            :             i__ = next;</a>
+<a name="5080"><span class="lineNum">    5080 </span><span class="lineCov">     570946 :             continue;</span></a>
+<a name="5081"><span class="lineNum">    5081 </span>            :         }</a>
+<a name="5082"><span class="lineNum">    5082 </span>            :         prev = i__;</a>
+<a name="5083"><span class="lineNum">    5083 </span>            : </a>
+<a name="5084"><span class="lineNum">    5084 </span><span class="lineCov">   28740803 :         s = -mid;</span></a>
+<a name="5085"><span class="lineNum">    5085 </span>            :         cnt = 0;</a>
+<a name="5086"><span class="lineNum">    5086 </span><span class="lineCov">   28740803 :         i__2 = *n - 1;</span></a>
+<a name="5087"><span class="lineNum">    5087 </span><span class="lineCov">  114233046 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="5088"><span class="lineNum">    5088 </span><span class="lineCov">   85492243 :             dplus = d__[j] + s;</span></a>
+<a name="5089"><span class="lineNum">    5089 </span><span class="lineCov">   85492243 :             s = s * lld[j] / dplus - mid;</span></a>
+<a name="5090"><span class="lineNum">    5090 </span><span class="lineCov">   85492243 :             if (dplus &lt; 0.) {</span></a>
+<a name="5091"><span class="lineNum">    5091 </span><span class="lineCov">   15245070 :                 ++cnt;</span></a>
+<a name="5092"><span class="lineNum">    5092 </span>            :             }</a>
+<a name="5093"><span class="lineNum">    5093 </span>            :         }</a>
+<a name="5094"><span class="lineNum">    5094 </span><span class="lineCov">   28740803 :         dplus = d__[*n] + s;</span></a>
+<a name="5095"><span class="lineNum">    5095 </span><span class="lineCov">   28740803 :         if (dplus &lt; 0.) {</span></a>
+<a name="5096"><span class="lineNum">    5096 </span><span class="lineCov">   12605322 :             ++cnt;</span></a>
+<a name="5097"><span class="lineNum">    5097 </span>            :         }</a>
+<a name="5098"><span class="lineNum">    5098 </span><span class="lineCov">   28740803 :         if (std::isnan(s)) {</span></a>
+<a name="5099"><span class="lineNum">    5099 </span>            :             cnt = 0;</a>
+<a name="5100"><span class="lineNum">    5100 </span>            :             s = -mid;</a>
+<a name="5101"><span class="lineNum">    5101 </span>            :             i__2 = *n - 1;</a>
+<a name="5102"><span class="lineNum">    5102 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="5103"><span class="lineNum">    5103 </span><span class="lineNoCov">          0 :                 dplus = d__[j] + s;</span></a>
+<a name="5104"><span class="lineNum">    5104 </span><span class="lineNoCov">          0 :                 if (dplus &lt; 0.) {</span></a>
+<a name="5105"><span class="lineNum">    5105 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="5106"><span class="lineNum">    5106 </span>            :                 }</a>
+<a name="5107"><span class="lineNum">    5107 </span><span class="lineNoCov">          0 :                 tmp = lld[j] / dplus;</span></a>
+<a name="5108"><span class="lineNum">    5108 </span><span class="lineNoCov">          0 :                 if (std::abs(tmp)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="5109"><span class="lineNum">    5109 </span><span class="lineNoCov">          0 :                     s = lld[j] - mid;</span></a>
+<a name="5110"><span class="lineNum">    5110 </span>            :                 } else {</a>
+<a name="5111"><span class="lineNum">    5111 </span><span class="lineNoCov">          0 :                     s = s * tmp - mid;</span></a>
+<a name="5112"><span class="lineNum">    5112 </span>            :                 }</a>
+<a name="5113"><span class="lineNum">    5113 </span>            :             }</a>
+<a name="5114"><span class="lineNum">    5114 </span><span class="lineNoCov">          0 :             dplus = d__[*n] + s;</span></a>
+<a name="5115"><span class="lineNum">    5115 </span><span class="lineNoCov">          0 :             if (dplus &lt; 0.) {</span></a>
+<a name="5116"><span class="lineNum">    5116 </span><span class="lineNoCov">          0 :                 ++cnt;</span></a>
+<a name="5117"><span class="lineNum">    5117 </span>            :             }</a>
+<a name="5118"><span class="lineNum">    5118 </span>            :         }</a>
+<a name="5119"><span class="lineNum">    5119 </span><span class="lineCov">   28740803 :         i__2 = i__ - 1, i__3 = (nright&lt;cnt) ? nright : cnt;</span></a>
+<a name="5120"><span class="lineNum">    5120 </span>            :         cnt = (i__2&gt;i__3) ? i__2 : i__3;</a>
+<a name="5121"><span class="lineNum">    5121 </span><span class="lineCov">   28740803 :         if (cnt == i__ - 1) {</span></a>
+<a name="5122"><span class="lineNum">    5122 </span><span class="lineCov">   13873747 :             work[k - 1] = mid;</span></a>
+<a name="5123"><span class="lineNum">    5123 </span><span class="lineCov">   14867056 :         } else if (cnt == nright) {</span></a>
+<a name="5124"><span class="lineNum">    5124 </span><span class="lineCov">   14658917 :             work[k] = mid;</span></a>
+<a name="5125"><span class="lineNum">    5125 </span>            :         } else {</a>
+<a name="5126"><span class="lineNum">    5126 </span><span class="lineCov">     208139 :             iwork[k] = cnt;</span></a>
+<a name="5127"><span class="lineNum">    5127 </span><span class="lineCov">     208139 :             ++cnt;</span></a>
+<a name="5128"><span class="lineNum">    5128 </span><span class="lineCov">     208139 :             iwork[k - 1] = cnt;</span></a>
+<a name="5129"><span class="lineNum">    5129 </span><span class="lineCov">     208139 :             kk = cnt &lt;&lt; 1;</span></a>
+<a name="5130"><span class="lineNum">    5130 </span><span class="lineCov">     208139 :             iwork[kk - 1] = next;</span></a>
+<a name="5131"><span class="lineNum">    5131 </span><span class="lineCov">     208139 :             iwork[kk] = nright;</span></a>
+<a name="5132"><span class="lineNum">    5132 </span><span class="lineCov">     208139 :             work[k] = mid;</span></a>
+<a name="5133"><span class="lineNum">    5133 </span><span class="lineCov">     208139 :             work[kk - 1] = mid;</span></a>
+<a name="5134"><span class="lineNum">    5134 </span><span class="lineCov">     208139 :             work[kk] = right;</span></a>
+<a name="5135"><span class="lineNum">    5135 </span>            :             prev = cnt;</a>
+<a name="5136"><span class="lineNum">    5136 </span><span class="lineCov">     208139 :             if (cnt - 1 &gt; i__) {</span></a>
+<a name="5137"><span class="lineNum">    5137 </span><span class="lineCov">      30298 :                 work[kk - 2] = mid;</span></a>
+<a name="5138"><span class="lineNum">    5138 </span>            :             }</a>
+<a name="5139"><span class="lineNum">    5139 </span><span class="lineCov">     208139 :             if (cnt &gt; *ifirst &amp;&amp; cnt &lt;= *ilast) {</span></a>
+<a name="5140"><span class="lineNum">    5140 </span><span class="lineNoCov">          0 :                 ++nint;</span></a>
+<a name="5141"><span class="lineNum">    5141 </span><span class="lineCov">     208139 :             } else if (cnt &lt;= *ifirst) {</span></a>
+<a name="5142"><span class="lineNum">    5142 </span>            :                 i1 = cnt;</a>
+<a name="5143"><span class="lineNum">    5143 </span>            :             }</a>
+<a name="5144"><span class="lineNum">    5144 </span>            :         }</a>
+<a name="5145"><span class="lineNum">    5145 </span>            :         i__ = next;</a>
+<a name="5146"><span class="lineNum">    5146 </span>            :     }</a>
+<a name="5147"><span class="lineNum">    5147 </span><span class="lineCov">   29310201 :     if (nint &gt; 0) {</span></a>
+<a name="5148"><span class="lineNum">    5148 </span><span class="lineCov">   28740121 :         goto L80;</span></a>
+<a name="5149"><span class="lineNum">    5149 </span>            :     }</a>
+<a name="5150"><span class="lineNum">    5150 </span><span class="lineCov">     570080 :     i__1 = *ilast;</span></a>
+<a name="5151"><span class="lineNum">    5151 </span><span class="lineCov">    1141026 :     for (i__ = *ifirst; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5152"><span class="lineNum">    5152 </span><span class="lineCov">     570946 :         k = i__ &lt;&lt; 1;</span></a>
+<a name="5153"><span class="lineNum">    5153 </span><span class="lineCov">     570946 :         ii = i__ - *offset;</span></a>
+<a name="5154"><span class="lineNum">    5154 </span><span class="lineCov">     570946 :         if (iwork[k - 1] != -1) {</span></a>
+<a name="5155"><span class="lineNum">    5155 </span><span class="lineCov">     570946 :             w[ii] = (work[k - 1] + work[k]) * .5;</span></a>
+<a name="5156"><span class="lineNum">    5156 </span><span class="lineCov">     570946 :             werr[ii] = work[k] - w[ii];</span></a>
+<a name="5157"><span class="lineNum">    5157 </span><span class="lineCov">     570946 :             if (i__ != *ilast) {</span></a>
+<a name="5158"><span class="lineNum">    5158 </span><span class="lineCov">        866 :                 wgap[ii] = work[k + 1] - work[k];</span></a>
+<a name="5159"><span class="lineNum">    5159 </span>            :             }</a>
+<a name="5160"><span class="lineNum">    5160 </span>            :         }</a>
+<a name="5161"><span class="lineNum">    5161 </span>            :     }</a>
+<a name="5162"><span class="lineNum">    5162 </span>            : </a>
+<a name="5163"><span class="lineNum">    5163 </span><span class="lineCov">     570080 :     return;</span></a>
+<a name="5164"><span class="lineNum">    5164 </span>            : </a>
+<a name="5165"><span class="lineNum">    5165 </span>            : } </a>
+<a name="5166"><span class="lineNum">    5166 </span>            : }</a>
+<a name="5167"><span class="lineNum">    5167 </span>            : }</a>
+<a name="5168"><span class="lineNum">    5168 </span>            : #include &lt;cctype&gt;</a>
+<a name="5169"><span class="lineNum">    5169 </span>            : #include &lt;cmath&gt;</a>
+<a name="5170"><span class="lineNum">    5170 </span>            : </a>
+<a name="5171"><span class="lineNum">    5171 </span>            : #include &quot;real.h&quot;</a>
+<a name="5172"><span class="lineNum">    5172 </span>            : </a>
+<a name="5173"><span class="lineNum">    5173 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="5174"><span class="lineNum">    5174 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="5175"><span class="lineNum">    5175 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="5176"><span class="lineNum">    5176 </span>            : </a>
+<a name="5177"><span class="lineNum">    5177 </span>            : </a>
+<a name="5178"><span class="lineNum">    5178 </span>            : </a>
+<a name="5179"><span class="lineNum">    5179 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="5180"><span class="lineNum">    5180 </span>            : namespace PLMD{</a>
+<a name="5181"><span class="lineNum">    5181 </span>            : namespace lapack{</a>
+<a name="5182"><span class="lineNum">    5182 </span>            : using namespace blas;</a>
+<a name="5183"><span class="lineNum">    5183 </span>            : void</a>
+<a name="5184"><span class="lineNum">    5184 </span><span class="lineCov">     570008 : PLUMED_BLAS_F77_FUNC(dlarrex,DLARREX)(const char *range,</span></a>
+<a name="5185"><span class="lineNum">    5185 </span>            :          int *n, </a>
+<a name="5186"><span class="lineNum">    5186 </span>            :          double *vl, </a>
+<a name="5187"><span class="lineNum">    5187 </span>            :          double *vu, </a>
+<a name="5188"><span class="lineNum">    5188 </span>            :          int *il, </a>
+<a name="5189"><span class="lineNum">    5189 </span>            :          int *iu, </a>
+<a name="5190"><span class="lineNum">    5190 </span>            :          double *d__, </a>
+<a name="5191"><span class="lineNum">    5191 </span>            :          double *e, </a>
+<a name="5192"><span class="lineNum">    5192 </span>            :          double *tol, </a>
+<a name="5193"><span class="lineNum">    5193 </span>            :          int *nsplit, </a>
+<a name="5194"><span class="lineNum">    5194 </span>            :          int *isplit, </a>
+<a name="5195"><span class="lineNum">    5195 </span>            :          int *m, </a>
+<a name="5196"><span class="lineNum">    5196 </span>            :          double *w, </a>
+<a name="5197"><span class="lineNum">    5197 </span>            :          int *iblock, </a>
+<a name="5198"><span class="lineNum">    5198 </span>            :          int *indexw, </a>
+<a name="5199"><span class="lineNum">    5199 </span>            :          double *gersch, </a>
+<a name="5200"><span class="lineNum">    5200 </span>            :          double *work,</a>
+<a name="5201"><span class="lineNum">    5201 </span>            :          int *iwork, </a>
+<a name="5202"><span class="lineNum">    5202 </span>            :          int *info)</a>
+<a name="5203"><span class="lineNum">    5203 </span>            : {</a>
+<a name="5204"><span class="lineNum">    5204 </span>            :     int i__1, i__2, i__3;</a>
+<a name="5205"><span class="lineNum">    5205 </span>            :     double d__1, d__2;</a>
+<a name="5206"><span class="lineNum">    5206 </span><span class="lineCov">     570008 :     int c__1 = 1;</span></a>
+<a name="5207"><span class="lineNum">    5207 </span><span class="lineCov">     570008 :     int c__0 = 0;</span></a>
+<a name="5208"><span class="lineNum">    5208 </span>            : </a>
+<a name="5209"><span class="lineNum">    5209 </span>            :     int i__, j, k;</a>
+<a name="5210"><span class="lineNum">    5210 </span>            :     double s, gl;</a>
+<a name="5211"><span class="lineNum">    5211 </span>            :     int in;</a>
+<a name="5212"><span class="lineNum">    5212 </span>            :     double gu;</a>
+<a name="5213"><span class="lineNum">    5213 </span>            :     int cnt;</a>
+<a name="5214"><span class="lineNum">    5214 </span>            :     double eps, tau, nrm, tmp, vvl, vvu, offd;</a>
+<a name="5215"><span class="lineNum">    5215 </span>            :     int iend, jblk, till, itmp;</a>
+<a name="5216"><span class="lineNum">    5216 </span>            :     double rtol, delta, sigma;</a>
+<a name="5217"><span class="lineNum">    5217 </span>            :     int iinfo;</a>
+<a name="5218"><span class="lineNum">    5218 </span>            :     double width;</a>
+<a name="5219"><span class="lineNum">    5219 </span>            :     int ibegin;</a>
+<a name="5220"><span class="lineNum">    5220 </span>            :     int irange;</a>
+<a name="5221"><span class="lineNum">    5221 </span>            :     double sgndef;</a>
+<a name="5222"><span class="lineNum">    5222 </span>            :     int maxcnt;</a>
+<a name="5223"><span class="lineNum">    5223 </span><span class="lineCov">     570008 :     --iwork;</span></a>
+<a name="5224"><span class="lineNum">    5224 </span><span class="lineCov">     570008 :     --work;</span></a>
+<a name="5225"><span class="lineNum">    5225 </span><span class="lineCov">     570008 :     --gersch;</span></a>
+<a name="5226"><span class="lineNum">    5226 </span><span class="lineCov">     570008 :     --indexw;</span></a>
+<a name="5227"><span class="lineNum">    5227 </span><span class="lineCov">     570008 :     --iblock;</span></a>
+<a name="5228"><span class="lineNum">    5228 </span><span class="lineCov">     570008 :     --w;</span></a>
+<a name="5229"><span class="lineNum">    5229 </span><span class="lineCov">     570008 :     --isplit;</span></a>
+<a name="5230"><span class="lineNum">    5230 </span><span class="lineCov">     570008 :     --e;</span></a>
+<a name="5231"><span class="lineNum">    5231 </span><span class="lineCov">     570008 :     --d__;</span></a>
+<a name="5232"><span class="lineNum">    5232 </span>            : </a>
+<a name="5233"><span class="lineNum">    5233 </span>            :     sigma = 0;</a>
+<a name="5234"><span class="lineNum">    5234 </span>            :     irange = 0;</a>
+<a name="5235"><span class="lineNum">    5235 </span>            :     sgndef = 0;</a>
+<a name="5236"><span class="lineNum">    5236 </span>            :     maxcnt = 0;</a>
+<a name="5237"><span class="lineNum">    5237 </span>            : </a>
+<a name="5238"><span class="lineNum">    5238 </span><span class="lineCov">     570008 :     *info = 0;</span></a>
+<a name="5239"><span class="lineNum">    5239 </span>            : </a>
+<a name="5240"><span class="lineNum">    5240 </span><span class="lineCov">     570008 :     if (*range=='A' || *range=='a')</span></a>
+<a name="5241"><span class="lineNum">    5241 </span>            :         irange = 1;</a>
+<a name="5242"><span class="lineNum">    5242 </span><span class="lineCov">     562533 :     else if (*range=='V' || *range=='v')</span></a>
+<a name="5243"><span class="lineNum">    5243 </span>            :         irange = 2;</a>
+<a name="5244"><span class="lineNum">    5244 </span><span class="lineCov">     562533 :     else if (*range=='I' || *range=='i')</span></a>
+<a name="5245"><span class="lineNum">    5245 </span>            :         irange = 3;</a>
+<a name="5246"><span class="lineNum">    5246 </span>            :     </a>
+<a name="5247"><span class="lineNum">    5247 </span>            : </a>
+<a name="5248"><span class="lineNum">    5248 </span><span class="lineCov">     570008 :     *m = 0;</span></a>
+<a name="5249"><span class="lineNum">    5249 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="5250"><span class="lineNum">    5250 </span>            : </a>
+<a name="5251"><span class="lineNum">    5251 </span><span class="lineCov">     570008 :     *nsplit = 1;</span></a>
+<a name="5252"><span class="lineNum">    5252 </span><span class="lineCov">     570008 :     i__1 = *n - 1;</span></a>
+<a name="5253"><span class="lineNum">    5253 </span><span class="lineCov">    2254429 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5254"><span class="lineNum">    5254 </span><span class="lineCov">    1684421 :         if (std::abs(e[i__]) &lt;= *tol) {</span></a>
+<a name="5255"><span class="lineNum">    5255 </span><span class="lineCov">        667 :             isplit[*nsplit] = i__;</span></a>
+<a name="5256"><span class="lineNum">    5256 </span><span class="lineCov">        667 :             ++(*nsplit);</span></a>
+<a name="5257"><span class="lineNum">    5257 </span>            :         }</a>
+<a name="5258"><span class="lineNum">    5258 </span>            :     }</a>
+<a name="5259"><span class="lineNum">    5259 </span><span class="lineCov">     570008 :     isplit[*nsplit] = *n;</span></a>
+<a name="5260"><span class="lineNum">    5260 </span>            : </a>
+<a name="5261"><span class="lineNum">    5261 </span>            :     ibegin = 1;</a>
+<a name="5262"><span class="lineNum">    5262 </span><span class="lineCov">     570008 :     i__1 = *nsplit;</span></a>
+<a name="5263"><span class="lineNum">    5263 </span><span class="lineCov">    1140683 :     for (jblk = 1; jblk &lt;= i__1; ++jblk) {</span></a>
+<a name="5264"><span class="lineNum">    5264 </span><span class="lineCov">     570675 :         iend = isplit[jblk];</span></a>
+<a name="5265"><span class="lineNum">    5265 </span><span class="lineCov">     570675 :         if (ibegin == iend) {</span></a>
+<a name="5266"><span class="lineNum">    5266 </span><span class="lineCov">        665 :             ++(*m);</span></a>
+<a name="5267"><span class="lineNum">    5267 </span><span class="lineCov">        665 :             w[*m] = d__[ibegin];</span></a>
+<a name="5268"><span class="lineNum">    5268 </span><span class="lineCov">        665 :             iblock[*m] = jblk;</span></a>
+<a name="5269"><span class="lineNum">    5269 </span><span class="lineCov">        665 :             indexw[*m] = 1;</span></a>
+<a name="5270"><span class="lineNum">    5270 </span><span class="lineCov">        665 :             e[iend] = 0.;</span></a>
+<a name="5271"><span class="lineNum">    5271 </span><span class="lineCov">        665 :             ibegin = iend + 1;</span></a>
+<a name="5272"><span class="lineNum">    5272 </span><span class="lineCov">        665 :             goto L170;</span></a>
+<a name="5273"><span class="lineNum">    5273 </span>            :         }</a>
+<a name="5274"><span class="lineNum">    5274 </span><span class="lineCov">     570010 :         in = iend - ibegin + 1;</span></a>
+<a name="5275"><span class="lineNum">    5275 </span>            : </a>
+<a name="5276"><span class="lineNum">    5276 </span><span class="lineCov">     570010 :         gl = d__[ibegin] - std::abs(e[ibegin]);</span></a>
+<a name="5277"><span class="lineNum">    5277 </span><span class="lineCov">     570010 :         gu = d__[ibegin] + std::abs(e[ibegin]);</span></a>
+<a name="5278"><span class="lineNum">    5278 </span><span class="lineCov">     570010 :         gersch[(ibegin &lt;&lt; 1) - 1] = gl;</span></a>
+<a name="5279"><span class="lineNum">    5279 </span><span class="lineCov">     570010 :         gersch[ibegin * 2] = gu;</span></a>
+<a name="5280"><span class="lineNum">    5280 </span><span class="lineCov">     570010 :         gersch[(iend &lt;&lt; 1) - 1] = d__[iend] - std::abs(e[iend - 1]);</span></a>
+<a name="5281"><span class="lineNum">    5281 </span><span class="lineCov">     570010 :         gersch[iend * 2] = d__[iend] + std::abs(e[iend - 1]);</span></a>
+<a name="5282"><span class="lineNum">    5282 </span><span class="lineCov">     570010 :         d__1 = gersch[(iend &lt;&lt; 1) - 1];</span></a>
+<a name="5283"><span class="lineNum">    5283 </span><span class="lineCov">     570010 :         gl = (d__1&lt;gl) ? d__1 : gl;</span></a>
+<a name="5284"><span class="lineNum">    5284 </span>            :         d__1 = gersch[iend * 2];</a>
+<a name="5285"><span class="lineNum">    5285 </span><span class="lineCov">     570010 :         gu = (d__1&gt;gu) ? d__1 : gu;</span></a>
+<a name="5286"><span class="lineNum">    5286 </span><span class="lineCov">     570010 :         i__2 = iend - 1;</span></a>
+<a name="5287"><span class="lineNum">    5287 </span><span class="lineCov">    1683754 :         for (i__ = ibegin + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5288"><span class="lineNum">    5288 </span><span class="lineCov">    1113744 :             offd = std::abs(e[i__ - 1]) + std::abs(e[i__]);</span></a>
+<a name="5289"><span class="lineNum">    5289 </span><span class="lineCov">    1113744 :             gersch[(i__ &lt;&lt; 1) - 1] = d__[i__] - offd;</span></a>
+<a name="5290"><span class="lineNum">    5290 </span>            :             d__1 = gersch[(i__ &lt;&lt; 1) - 1];</a>
+<a name="5291"><span class="lineNum">    5291 </span><span class="lineCov">    1113744 :             gl = (d__1&lt;gl) ? d__1 : gl;</span></a>
+<a name="5292"><span class="lineNum">    5292 </span><span class="lineCov">    1113744 :             gersch[i__ * 2] = d__[i__] + offd;</span></a>
+<a name="5293"><span class="lineNum">    5293 </span>            :             d__1 = gersch[i__ * 2];</a>
+<a name="5294"><span class="lineNum">    5294 </span><span class="lineCov">    1113744 :             gu = (d__1&gt;gu) ? d__1 : gu;</span></a>
+<a name="5295"><span class="lineNum">    5295 </span>            :         }</a>
+<a name="5296"><span class="lineNum">    5296 </span>            :         d__1 = std::abs(gl), d__2 = std::abs(gu);</a>
+<a name="5297"><span class="lineNum">    5297 </span><span class="lineCov">     570010 :         nrm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="5298"><span class="lineNum">    5298 </span>            : </a>
+<a name="5299"><span class="lineNum">    5299 </span><span class="lineCov">     570010 :         width = gu - gl;</span></a>
+<a name="5300"><span class="lineNum">    5300 </span>            :         i__2 = iend - 1;</a>
+<a name="5301"><span class="lineNum">    5301 </span><span class="lineCov">    2253764 :         for (i__ = ibegin; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5302"><span class="lineNum">    5302 </span><span class="lineCov">    1683754 :             work[i__] = e[i__] * e[i__];</span></a>
+<a name="5303"><span class="lineNum">    5303 </span>            :         }</a>
+<a name="5304"><span class="lineNum">    5304 </span><span class="lineCov">    1710030 :         for (j = 1; j &lt;= 2; ++j) {</span></a>
+<a name="5305"><span class="lineNum">    5305 </span><span class="lineCov">    1140020 :             if (j == 1) {</span></a>
+<a name="5306"><span class="lineNum">    5306 </span><span class="lineCov">     570010 :                 tau = gl + width * .25;</span></a>
+<a name="5307"><span class="lineNum">    5307 </span>            :             } else {</a>
+<a name="5308"><span class="lineNum">    5308 </span><span class="lineCov">     570010 :                 tau = gu - width * .25;</span></a>
+<a name="5309"><span class="lineNum">    5309 </span>            :             }</a>
+<a name="5310"><span class="lineNum">    5310 </span><span class="lineCov">    1140020 :             tmp = d__[ibegin] - tau;</span></a>
+<a name="5311"><span class="lineNum">    5311 </span><span class="lineCov">    1140020 :             if (tmp &lt; 0.) {</span></a>
+<a name="5312"><span class="lineNum">    5312 </span><span class="lineCov">     596324 :                 cnt = 1;</span></a>
+<a name="5313"><span class="lineNum">    5313 </span>            :             } else {</a>
+<a name="5314"><span class="lineNum">    5314 </span><span class="lineCov">     543696 :                 cnt = 0;</span></a>
+<a name="5315"><span class="lineNum">    5315 </span>            :             }</a>
+<a name="5316"><span class="lineNum">    5316 </span><span class="lineCov">    1140020 :             i__2 = iend;</span></a>
+<a name="5317"><span class="lineNum">    5317 </span><span class="lineCov">    4507528 :             for (i__ = ibegin + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5318"><span class="lineNum">    5318 </span><span class="lineCov">    3367508 :                 tmp = d__[i__] - tau - work[i__ - 1] / tmp;</span></a>
+<a name="5319"><span class="lineNum">    5319 </span><span class="lineCov">    3367508 :                 if (tmp &lt; 0.) {</span></a>
+<a name="5320"><span class="lineNum">    5320 </span><span class="lineCov">    1585168 :                     ++cnt;</span></a>
+<a name="5321"><span class="lineNum">    5321 </span>            :                 }</a>
+<a name="5322"><span class="lineNum">    5322 </span>            :             }</a>
+<a name="5323"><span class="lineNum">    5323 </span><span class="lineCov">    1140020 :             if (cnt == 0) {</span></a>
+<a name="5324"><span class="lineNum">    5324 </span>            :                 gl = tau;</a>
+<a name="5325"><span class="lineNum">    5325 </span><span class="lineCov">    1140020 :             } else if (cnt == in) {</span></a>
+<a name="5326"><span class="lineNum">    5326 </span>            :                 gu = tau;</a>
+<a name="5327"><span class="lineNum">    5327 </span>            :             }</a>
+<a name="5328"><span class="lineNum">    5328 </span><span class="lineCov">    1140020 :             if (j == 1) {</span></a>
+<a name="5329"><span class="lineNum">    5329 </span>            :                 maxcnt = cnt;</a>
+<a name="5330"><span class="lineNum">    5330 </span>            :                 sigma = gl;</a>
+<a name="5331"><span class="lineNum">    5331 </span>            :                 sgndef = 1.;</a>
+<a name="5332"><span class="lineNum">    5332 </span>            :             } else {</a>
+<a name="5333"><span class="lineNum">    5333 </span><span class="lineCov">     570010 :                 if (in - cnt &gt; maxcnt) {</span></a>
+<a name="5334"><span class="lineNum">    5334 </span>            :                     sigma = gu;</a>
+<a name="5335"><span class="lineNum">    5335 </span>            :                     sgndef = -1.;</a>
+<a name="5336"><span class="lineNum">    5336 </span>            :                 }</a>
+<a name="5337"><span class="lineNum">    5337 </span>            :             }</a>
+<a name="5338"><span class="lineNum">    5338 </span>            :         }</a>
+<a name="5339"><span class="lineNum">    5339 </span>            : </a>
+<a name="5340"><span class="lineNum">    5340 </span><span class="lineCov">     570010 :         work[in * 3] = 1.;</span></a>
+<a name="5341"><span class="lineNum">    5341 </span>            :         delta = eps;</a>
+<a name="5342"><span class="lineNum">    5342 </span><span class="lineCov">     570010 :         tau = sgndef * nrm;</span></a>
+<a name="5343"><span class="lineNum">    5343 </span><span class="lineCov">     570010 : L60:</span></a>
+<a name="5344"><span class="lineNum">    5344 </span><span class="lineCov">     570010 :         sigma -= delta * tau;</span></a>
+<a name="5345"><span class="lineNum">    5345 </span><span class="lineCov">     570010 :         work[1] = d__[ibegin] - sigma;</span></a>
+<a name="5346"><span class="lineNum">    5346 </span>            :         j = ibegin;</a>
+<a name="5347"><span class="lineNum">    5347 </span><span class="lineCov">     570010 :         i__2 = in - 1;</span></a>
+<a name="5348"><span class="lineNum">    5348 </span><span class="lineCov">    2253764 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5349"><span class="lineNum">    5349 </span><span class="lineCov">    1683754 :             work[(in &lt;&lt; 1) + i__] = 1. / work[i__];</span></a>
+<a name="5350"><span class="lineNum">    5350 </span><span class="lineCov">    1683754 :             tmp = e[j] * work[(in &lt;&lt; 1) + i__];</span></a>
+<a name="5351"><span class="lineNum">    5351 </span><span class="lineCov">    1683754 :             work[i__ + 1] = d__[j + 1] - sigma - tmp * e[j];</span></a>
+<a name="5352"><span class="lineNum">    5352 </span><span class="lineCov">    1683754 :             work[in + i__] = tmp;</span></a>
+<a name="5353"><span class="lineNum">    5353 </span><span class="lineCov">    1683754 :             ++j;</span></a>
+<a name="5354"><span class="lineNum">    5354 </span>            :         }</a>
+<a name="5355"><span class="lineNum">    5355 </span><span class="lineCov">    2823774 :         for (i__ = in; i__ &gt;= 1; --i__) {</span></a>
+<a name="5356"><span class="lineNum">    5356 </span><span class="lineCov">    2253764 :             tmp = sgndef * work[i__];</span></a>
+<a name="5357"><span class="lineNum">    5357 </span><span class="lineCov">    2253764 :         if (tmp &lt; 0. || std::abs(work[(in &lt;&lt; 1) + i__])&lt;PLUMED_GMX_DOUBLE_MIN || std::isnan(tmp)) {</span></a>
+<a name="5358"><span class="lineNum">    5358 </span><span class="lineNoCov">          0 :                 delta *= 2.;</span></a>
+<a name="5359"><span class="lineNum">    5359 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="5360"><span class="lineNum">    5360 </span>            :             }</a>
+<a name="5361"><span class="lineNum">    5361 </span>            :         }</a>
+<a name="5362"><span class="lineNum">    5362 </span>            : </a>
+<a name="5363"><span class="lineNum">    5363 </span><span class="lineCov">     570010 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;in, &amp;work[1], &amp;c__1, &amp;d__[ibegin], &amp;c__1);</span></a>
+<a name="5364"><span class="lineNum">    5364 </span><span class="lineCov">     570010 :         i__2 = in - 1;</span></a>
+<a name="5365"><span class="lineNum">    5365 </span><span class="lineCov">     570010 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__2, &amp;work[in + 1], &amp;c__1, &amp;e[ibegin], &amp;c__1);</span></a>
+<a name="5366"><span class="lineNum">    5366 </span><span class="lineCov">     570010 :         i__2 = in - 1;</span></a>
+<a name="5367"><span class="lineNum">    5367 </span><span class="lineCov">    2253764 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5368"><span class="lineNum">    5368 </span><span class="lineCov">    1683754 :             work[in * 3 + i__] = work[i__] * work[in + i__];</span></a>
+<a name="5369"><span class="lineNum">    5369 </span><span class="lineCov">    1683754 :             work[(in &lt;&lt; 2) + i__] = work[in * 3 + i__] * work[in + i__];</span></a>
+<a name="5370"><span class="lineNum">    5370 </span>            :         }</a>
+<a name="5371"><span class="lineNum">    5371 </span><span class="lineCov">     570010 :         if (sgndef &gt; 0.) {</span></a>
+<a name="5372"><span class="lineNum">    5372 </span><span class="lineCov">     490451 :             cnt = 1;</span></a>
+<a name="5373"><span class="lineNum">    5373 </span><span class="lineCov">     490451 :             work[1] = (gl + gu) / 2. - sigma;</span></a>
+<a name="5374"><span class="lineNum">    5374 </span><span class="lineCov">     490451 :             work[in + 1] = 0.;</span></a>
+<a name="5375"><span class="lineNum">    5375 </span><span class="lineCov">     490451 :             work[(in &lt;&lt; 1) + 1] = (gu - gl) / 2.;</span></a>
+<a name="5376"><span class="lineNum">    5376 </span>            :         } else {</a>
+<a name="5377"><span class="lineNum">    5377 </span><span class="lineCov">      79559 :             cnt = in;</span></a>
+<a name="5378"><span class="lineNum">    5378 </span><span class="lineCov">      79559 :             work[in] = (gl + gu) / 2. - sigma;</span></a>
+<a name="5379"><span class="lineNum">    5379 </span><span class="lineCov">      79559 :             work[in * 2] = 0.;</span></a>
+<a name="5380"><span class="lineNum">    5380 </span><span class="lineCov">      79559 :             work[in * 3] = (gu - gl) / 2.;</span></a>
+<a name="5381"><span class="lineNum">    5381 </span>            :         }</a>
+<a name="5382"><span class="lineNum">    5382 </span><span class="lineCov">     570010 :         rtol = eps * 4.;</span></a>
+<a name="5383"><span class="lineNum">    5383 </span><span class="lineCov">     570010 :         PLUMED_BLAS_F77_FUNC(dlarrbx,DLARRBX)(&amp;in, &amp;d__[ibegin], &amp;e[ibegin], &amp;work[in * 3 + 1], &amp;work[(in &lt;&lt;</span></a>
+<a name="5384"><span class="lineNum">    5384 </span><span class="lineCov">     570010 :                  2) + 1], &amp;cnt, &amp;cnt, &amp;rtol, &amp;rtol, &amp;c__0, &amp;work[1], &amp;work[in </span></a>
+<a name="5385"><span class="lineNum">    5385 </span><span class="lineCov">     570010 :                 + 1], &amp;work[(in &lt;&lt; 1) + 1], &amp;work[in * 5 + 1], &amp;iwork[1], &amp;</span></a>
+<a name="5386"><span class="lineNum">    5386 </span>            :                 iinfo);</a>
+<a name="5387"><span class="lineNum">    5387 </span><span class="lineCov">     570010 :         if (sgndef &gt; 0.) {</span></a>
+<a name="5388"><span class="lineNum">    5388 </span><span class="lineCov">     490451 :             tau = work[1] - work[(in &lt;&lt; 1) + 1];</span></a>
+<a name="5389"><span class="lineNum">    5389 </span>            :         } else {</a>
+<a name="5390"><span class="lineNum">    5390 </span><span class="lineCov">      79559 :             tau = work[in] + work[in * 3];</span></a>
+<a name="5391"><span class="lineNum">    5391 </span>            :         }</a>
+<a name="5392"><span class="lineNum">    5392 </span>            : </a>
+<a name="5393"><span class="lineNum">    5393 </span><span class="lineCov">     570010 :         work[in * 3] = 1.;</span></a>
+<a name="5394"><span class="lineNum">    5394 </span>            :         delta = eps * 2.;</a>
+<a name="5395"><span class="lineNum">    5395 </span><span class="lineCov">     570010 : L100:</span></a>
+<a name="5396"><span class="lineNum">    5396 </span><span class="lineCov">     570010 :         tau *= 1. - delta;</span></a>
+<a name="5397"><span class="lineNum">    5397 </span>            : </a>
+<a name="5398"><span class="lineNum">    5398 </span><span class="lineCov">     570010 :         s = -tau;</span></a>
+<a name="5399"><span class="lineNum">    5399 </span>            :         j = ibegin;</a>
+<a name="5400"><span class="lineNum">    5400 </span><span class="lineCov">     570010 :         i__2 = in - 1;</span></a>
+<a name="5401"><span class="lineNum">    5401 </span><span class="lineCov">    2253764 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5402"><span class="lineNum">    5402 </span><span class="lineCov">    1683754 :             work[i__] = d__[j] + s;</span></a>
+<a name="5403"><span class="lineNum">    5403 </span><span class="lineCov">    1683754 :             work[(in &lt;&lt; 1) + i__] = 1. / work[i__];</span></a>
+<a name="5404"><span class="lineNum">    5404 </span><span class="lineCov">    1683754 :             work[in + i__] = e[j] * d__[j] * work[(in &lt;&lt; 1) + i__];</span></a>
+<a name="5405"><span class="lineNum">    5405 </span><span class="lineCov">    1683754 :             s = s * work[in + i__] * e[j] - tau;</span></a>
+<a name="5406"><span class="lineNum">    5406 </span><span class="lineCov">    1683754 :             ++j;</span></a>
+<a name="5407"><span class="lineNum">    5407 </span>            :         }</a>
+<a name="5408"><span class="lineNum">    5408 </span><span class="lineCov">     570010 :         work[in] = d__[iend] + s;</span></a>
+<a name="5409"><span class="lineNum">    5409 </span>            : </a>
+<a name="5410"><span class="lineNum">    5410 </span><span class="lineCov">    2823774 :         for (i__ = in; i__ &gt;= 1; --i__) {</span></a>
+<a name="5411"><span class="lineNum">    5411 </span><span class="lineCov">    2253764 :             tmp = sgndef * work[i__];</span></a>
+<a name="5412"><span class="lineNum">    5412 </span><span class="lineCov">    2253764 :             if (tmp &lt; 0. || std::abs(work[(in &lt;&lt; 1) + i__])&lt;PLUMED_GMX_DOUBLE_MIN || std::isnan(tmp)) {</span></a>
+<a name="5413"><span class="lineNum">    5413 </span><span class="lineNoCov">          0 :                 delta *= 2.;</span></a>
+<a name="5414"><span class="lineNum">    5414 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="5415"><span class="lineNum">    5415 </span>            :             }</a>
+<a name="5416"><span class="lineNum">    5416 </span>            :         }</a>
+<a name="5417"><span class="lineNum">    5417 </span>            : </a>
+<a name="5418"><span class="lineNum">    5418 </span><span class="lineCov">     570010 :         sigma += tau;</span></a>
+<a name="5419"><span class="lineNum">    5419 </span><span class="lineCov">     570010 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;in, &amp;work[1], &amp;c__1, &amp;d__[ibegin], &amp;c__1);</span></a>
+<a name="5420"><span class="lineNum">    5420 </span><span class="lineCov">     570010 :         i__2 = in - 1;</span></a>
+<a name="5421"><span class="lineNum">    5421 </span><span class="lineCov">     570010 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__2, &amp;work[in + 1], &amp;c__1, &amp;e[ibegin], &amp;c__1);</span></a>
+<a name="5422"><span class="lineNum">    5422 </span><span class="lineCov">     570010 :         e[iend] = sigma;</span></a>
+<a name="5423"><span class="lineNum">    5423 </span><span class="lineCov">     570010 :         tmp = (double) in * 4. * eps * (std::abs(sigma) + std::abs(tau));</span></a>
+<a name="5424"><span class="lineNum">    5424 </span>            :         i__2 = iend;</a>
+<a name="5425"><span class="lineNum">    5425 </span><span class="lineCov">    2823774 :         for (i__ = ibegin; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5426"><span class="lineNum">    5426 </span><span class="lineCov">    2253764 :             gersch[(i__ &lt;&lt; 1) - 1] = gersch[(i__ &lt;&lt; 1) - 1] - sigma - tmp;</span></a>
+<a name="5427"><span class="lineNum">    5427 </span><span class="lineCov">    2253764 :             gersch[i__ * 2] = gersch[i__ * 2] - sigma + tmp;</span></a>
+<a name="5428"><span class="lineNum">    5428 </span>            :         }</a>
+<a name="5429"><span class="lineNum">    5429 </span>            : </a>
+<a name="5430"><span class="lineNum">    5430 </span>            :         j = ibegin;</a>
+<a name="5431"><span class="lineNum">    5431 </span><span class="lineCov">     570010 :         i__2 = in - 1;</span></a>
+<a name="5432"><span class="lineNum">    5432 </span><span class="lineCov">    2253764 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5433"><span class="lineNum">    5433 </span><span class="lineCov">    1683754 :             work[(i__ &lt;&lt; 1) - 1] = std::abs(d__[j]);</span></a>
+<a name="5434"><span class="lineNum">    5434 </span><span class="lineCov">    1683754 :             work[i__ * 2] = e[j] * e[j] * work[(i__ &lt;&lt; 1) - 1];</span></a>
+<a name="5435"><span class="lineNum">    5435 </span><span class="lineCov">    1683754 :             ++j;</span></a>
+<a name="5436"><span class="lineNum">    5436 </span>            :         }</a>
+<a name="5437"><span class="lineNum">    5437 </span><span class="lineCov">     570010 :         work[(in &lt;&lt; 1) - 1] = std::abs(d__[iend]);</span></a>
+<a name="5438"><span class="lineNum">    5438 </span>            : </a>
+<a name="5439"><span class="lineNum">    5439 </span><span class="lineCov">     570010 :         PLUMED_BLAS_F77_FUNC(dlasq2,DLASQ2)(&amp;in, &amp;work[1], info);</span></a>
+<a name="5440"><span class="lineNum">    5440 </span><span class="lineCov">     570010 :         if (*info != 0) {</span></a>
+<a name="5441"><span class="lineNum">    5441 </span>            :             return;</a>
+<a name="5442"><span class="lineNum">    5442 </span>            :         }</a>
+<a name="5443"><span class="lineNum">    5443 </span>            : </a>
+<a name="5444"><span class="lineNum">    5444 </span><span class="lineCov">     570010 :         if (sgndef &gt; 0.) {</span></a>
+<a name="5445"><span class="lineNum">    5445 </span><span class="lineCov">     490451 :             i__2 = in;</span></a>
+<a name="5446"><span class="lineNum">    5446 </span><span class="lineCov">    2426219 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5447"><span class="lineNum">    5447 </span><span class="lineCov">    1935768 :                 ++(*m);</span></a>
+<a name="5448"><span class="lineNum">    5448 </span><span class="lineCov">    1935768 :                 w[*m] = work[in - i__ + 1];</span></a>
+<a name="5449"><span class="lineNum">    5449 </span><span class="lineCov">    1935768 :                 iblock[*m] = jblk;</span></a>
+<a name="5450"><span class="lineNum">    5450 </span><span class="lineCov">    1935768 :                 indexw[*m] = i__;</span></a>
+<a name="5451"><span class="lineNum">    5451 </span>            :             }</a>
+<a name="5452"><span class="lineNum">    5452 </span>            :         } else {</a>
+<a name="5453"><span class="lineNum">    5453 </span><span class="lineCov">      79559 :             i__2 = in;</span></a>
+<a name="5454"><span class="lineNum">    5454 </span><span class="lineCov">     397555 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5455"><span class="lineNum">    5455 </span><span class="lineCov">     317996 :                 ++(*m);</span></a>
+<a name="5456"><span class="lineNum">    5456 </span><span class="lineCov">     317996 :                 w[*m] = -work[i__];</span></a>
+<a name="5457"><span class="lineNum">    5457 </span><span class="lineCov">     317996 :                 iblock[*m] = jblk;</span></a>
+<a name="5458"><span class="lineNum">    5458 </span><span class="lineCov">     317996 :                 indexw[*m] = i__;</span></a>
+<a name="5459"><span class="lineNum">    5459 </span>            :             }</a>
+<a name="5460"><span class="lineNum">    5460 </span>            :         }</a>
+<a name="5461"><span class="lineNum">    5461 </span><span class="lineCov">     570010 :         ibegin = iend + 1;</span></a>
+<a name="5462"><span class="lineNum">    5462 </span><span class="lineCov">     570675 : L170:</span></a>
+<a name="5463"><span class="lineNum">    5463 </span>            :         ;</a>
+<a name="5464"><span class="lineNum">    5464 </span>            :     }</a>
+<a name="5465"><span class="lineNum">    5465 </span><span class="lineCov">     570008 :     if (irange == 2) {</span></a>
+<a name="5466"><span class="lineNum">    5466 </span><span class="lineNoCov">          0 :         *m = 0;</span></a>
+<a name="5467"><span class="lineNum">    5467 </span>            :         ibegin = 1;</a>
+<a name="5468"><span class="lineNum">    5468 </span><span class="lineNoCov">          0 :         i__1 = *nsplit;</span></a>
+<a name="5469"><span class="lineNum">    5469 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5470"><span class="lineNum">    5470 </span><span class="lineNoCov">          0 :             iend = isplit[i__];</span></a>
+<a name="5471"><span class="lineNum">    5471 </span><span class="lineNoCov">          0 :             vvl = *vl - e[iend];</span></a>
+<a name="5472"><span class="lineNum">    5472 </span><span class="lineNoCov">          0 :             vvu = *vu - e[iend];</span></a>
+<a name="5473"><span class="lineNum">    5473 </span><span class="lineNoCov">          0 :             i__2 = iend;</span></a>
+<a name="5474"><span class="lineNum">    5474 </span><span class="lineNoCov">          0 :             for (j = ibegin; j &lt;= i__2; ++j) {</span></a>
+<a name="5475"><span class="lineNum">    5475 </span><span class="lineNoCov">          0 :                 if (vvl &lt;= w[j] &amp;&amp; w[j] &lt;= vvu) {</span></a>
+<a name="5476"><span class="lineNum">    5476 </span><span class="lineNoCov">          0 :                     ++(*m);</span></a>
+<a name="5477"><span class="lineNum">    5477 </span><span class="lineNoCov">          0 :                     w[*m] = w[j];</span></a>
+<a name="5478"><span class="lineNum">    5478 </span><span class="lineNoCov">          0 :                     iblock[*m] = i__;</span></a>
+<a name="5479"><span class="lineNum">    5479 </span><span class="lineNoCov">          0 :                     indexw[*m] = j - ibegin + 1;</span></a>
+<a name="5480"><span class="lineNum">    5480 </span>            :                 }</a>
+<a name="5481"><span class="lineNum">    5481 </span>            :             }</a>
+<a name="5482"><span class="lineNum">    5482 </span><span class="lineNoCov">          0 :             ibegin = iend + 1;</span></a>
+<a name="5483"><span class="lineNum">    5483 </span>            :         }</a>
+<a name="5484"><span class="lineNum">    5484 </span><span class="lineCov">     570008 :     } else if (irange == 3) {</span></a>
+<a name="5485"><span class="lineNum">    5485 </span><span class="lineCov">     562533 :         *m = *iu - *il + 1;</span></a>
+<a name="5486"><span class="lineNum">    5486 </span><span class="lineCov">     562533 :         if (*nsplit == 1) {</span></a>
+<a name="5487"><span class="lineNum">    5487 </span>            :             i__1 = *m;</a>
+<a name="5488"><span class="lineNum">    5488 </span><span class="lineCov">    1139915 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5489"><span class="lineNum">    5489 </span><span class="lineCov">     577394 :                 w[i__] = w[*il + i__ - 1];</span></a>
+<a name="5490"><span class="lineNum">    5490 </span><span class="lineCov">     577394 :                 indexw[i__] = *il + i__ - 1;</span></a>
+<a name="5491"><span class="lineNum">    5491 </span>            :             }</a>
+<a name="5492"><span class="lineNum">    5492 </span>            :         } else {</a>
+<a name="5493"><span class="lineNum">    5493 </span>            :             ibegin = 1;</a>
+<a name="5494"><span class="lineNum">    5494 </span>            :             i__1 = *nsplit;</a>
+<a name="5495"><span class="lineNum">    5495 </span><span class="lineCov">        685 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5496"><span class="lineNum">    5496 </span><span class="lineCov">        673 :                 iend = isplit[i__];</span></a>
+<a name="5497"><span class="lineNum">    5497 </span><span class="lineCov">        673 :                 i__2 = iend;</span></a>
+<a name="5498"><span class="lineNum">    5498 </span><span class="lineCov">       1451 :                 for (j = ibegin; j &lt;= i__2; ++j) {</span></a>
+<a name="5499"><span class="lineNum">    5499 </span><span class="lineCov">        778 :                     work[j] = w[j] + e[iend];</span></a>
+<a name="5500"><span class="lineNum">    5500 </span>            :                 }</a>
+<a name="5501"><span class="lineNum">    5501 </span><span class="lineCov">        673 :                 ibegin = iend + 1;</span></a>
+<a name="5502"><span class="lineNum">    5502 </span>            :             }</a>
+<a name="5503"><span class="lineNum">    5503 </span><span class="lineCov">         12 :             i__1 = *n;</span></a>
+<a name="5504"><span class="lineNum">    5504 </span><span class="lineCov">        790 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5505"><span class="lineNum">    5505 </span><span class="lineCov">        778 :                 iwork[i__] = i__;</span></a>
+<a name="5506"><span class="lineNum">    5506 </span><span class="lineCov">        778 :                 iwork[*n + i__] = iblock[i__];</span></a>
+<a name="5507"><span class="lineNum">    5507 </span>            :             }</a>
+<a name="5508"><span class="lineNum">    5508 </span><span class="lineCov">         12 :             PLUMED_BLAS_F77_FUNC(dlasrt2,DLASRT2)(&quot;I&quot;, n, &amp;work[1], &amp;iwork[1], &amp;iinfo);</span></a>
+<a name="5509"><span class="lineNum">    5509 </span><span class="lineCov">         12 :             i__1 = *m;</span></a>
+<a name="5510"><span class="lineNum">    5510 </span><span class="lineCov">        781 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5511"><span class="lineNum">    5511 </span><span class="lineCov">        769 :                 itmp = iwork[*il + i__ - 1];</span></a>
+<a name="5512"><span class="lineNum">    5512 </span><span class="lineCov">        769 :                 work[i__] = w[itmp];</span></a>
+<a name="5513"><span class="lineNum">    5513 </span><span class="lineCov">        769 :                 iblock[i__] = iwork[*n + itmp];</span></a>
+<a name="5514"><span class="lineNum">    5514 </span>            :             }</a>
+<a name="5515"><span class="lineNum">    5515 </span><span class="lineCov">         12 :             i__1 = *m;</span></a>
+<a name="5516"><span class="lineNum">    5516 </span><span class="lineCov">        781 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5517"><span class="lineNum">    5517 </span><span class="lineCov">        769 :                 iwork[*n + i__] = iwork[*il + i__ - 1];</span></a>
+<a name="5518"><span class="lineNum">    5518 </span><span class="lineCov">        769 :                 iwork[i__] = i__;</span></a>
+<a name="5519"><span class="lineNum">    5519 </span>            :             }</a>
+<a name="5520"><span class="lineNum">    5520 </span><span class="lineCov">         12 :             PLUMED_BLAS_F77_FUNC(ilasrt2,ILASRT2)(&quot;I&quot;, m, &amp;iblock[1], &amp;iwork[1], &amp;iinfo);</span></a>
+<a name="5521"><span class="lineNum">    5521 </span>            :             j = 1;</a>
+<a name="5522"><span class="lineNum">    5522 </span><span class="lineCov">         12 :             itmp = iblock[j];</span></a>
+<a name="5523"><span class="lineNum">    5523 </span><span class="lineCov">         12 :             cnt = iwork[*n + iwork[j]];</span></a>
+<a name="5524"><span class="lineNum">    5524 </span><span class="lineCov">         12 :             if (itmp == 1) {</span></a>
+<a name="5525"><span class="lineNum">    5525 </span>            :                 ibegin = 1;</a>
+<a name="5526"><span class="lineNum">    5526 </span>            :             } else {</a>
+<a name="5527"><span class="lineNum">    5527 </span><span class="lineNoCov">          0 :                 ibegin = isplit[itmp - 1] + 1;</span></a>
+<a name="5528"><span class="lineNum">    5528 </span>            :             }</a>
+<a name="5529"><span class="lineNum">    5529 </span><span class="lineCov">         12 :             i__1 = *m;</span></a>
+<a name="5530"><span class="lineNum">    5530 </span><span class="lineCov">        781 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5531"><span class="lineNum">    5531 </span><span class="lineCov">        769 :                 w[i__] = work[iwork[i__]];</span></a>
+<a name="5532"><span class="lineNum">    5532 </span><span class="lineCov">        769 :                 if (iblock[i__] != itmp || i__ == *m) {</span></a>
+<a name="5533"><span class="lineNum">    5533 </span><span class="lineCov">        670 :                     if (iblock[i__] == itmp) {</span></a>
+<a name="5534"><span class="lineNum">    5534 </span><span class="lineCov">         12 :                         till = *m;</span></a>
+<a name="5535"><span class="lineNum">    5535 </span>            :                     } else {</a>
+<a name="5536"><span class="lineNum">    5536 </span><span class="lineCov">        658 :                         till = i__ - 1;</span></a>
+<a name="5537"><span class="lineNum">    5537 </span>            :                     }</a>
+<a name="5538"><span class="lineNum">    5538 </span><span class="lineCov">        670 :                     i__2 = till - j + 1;</span></a>
+<a name="5539"><span class="lineNum">    5539 </span><span class="lineCov">        670 :                     PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(&quot;I&quot;, &amp;i__2, &amp;w[j], &amp;iinfo);</span></a>
+<a name="5540"><span class="lineNum">    5540 </span><span class="lineCov">        670 :                     cnt = cnt - ibegin + 1;</span></a>
+<a name="5541"><span class="lineNum">    5541 </span><span class="lineCov">        670 :                     i__2 = till;</span></a>
+<a name="5542"><span class="lineNum">    5542 </span><span class="lineCov">       1439 :                     for (k = j; k &lt;= i__2; ++k) {</span></a>
+<a name="5543"><span class="lineNum">    5543 </span><span class="lineCov">        769 :                         indexw[k] = cnt + k - j;</span></a>
+<a name="5544"><span class="lineNum">    5544 </span>            :                     }</a>
+<a name="5545"><span class="lineNum">    5545 </span>            :                     j = i__;</a>
+<a name="5546"><span class="lineNum">    5546 </span><span class="lineCov">        670 :                     itmp = iblock[j];</span></a>
+<a name="5547"><span class="lineNum">    5547 </span><span class="lineCov">        670 :                     cnt = iwork[*n + iwork[j]];</span></a>
+<a name="5548"><span class="lineNum">    5548 </span><span class="lineCov">        670 :                     ibegin = isplit[itmp - 1] + 1;</span></a>
+<a name="5549"><span class="lineNum">    5549 </span><span class="lineCov">        670 :                     if (i__ == *m &amp;&amp; till &lt; *m) {</span></a>
+<a name="5550"><span class="lineNum">    5550 </span><span class="lineNoCov">          0 :                         indexw[*m] = cnt - ibegin + 1;</span></a>
+<a name="5551"><span class="lineNum">    5551 </span>            :                     }</a>
+<a name="5552"><span class="lineNum">    5552 </span>            :                 } else {</a>
+<a name="5553"><span class="lineNum">    5553 </span><span class="lineCov">         99 :                     i__2 = cnt, i__3 = iwork[*n + iwork[i__]];</span></a>
+<a name="5554"><span class="lineNum">    5554 </span><span class="lineCov">         99 :                     cnt = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="5555"><span class="lineNum">    5555 </span>            :                 }</a>
+<a name="5556"><span class="lineNum">    5556 </span>            :             }</a>
+<a name="5557"><span class="lineNum">    5557 </span>            :         }</a>
+<a name="5558"><span class="lineNum">    5558 </span>            :     }</a>
+<a name="5559"><span class="lineNum">    5559 </span>            : </a>
+<a name="5560"><span class="lineNum">    5560 </span>            :     return;</a>
+<a name="5561"><span class="lineNum">    5561 </span>            : </a>
+<a name="5562"><span class="lineNum">    5562 </span>            : }</a>
+<a name="5563"><span class="lineNum">    5563 </span>            : </a>
+<a name="5564"><span class="lineNum">    5564 </span>            : </a>
+<a name="5565"><span class="lineNum">    5565 </span>            : }</a>
+<a name="5566"><span class="lineNum">    5566 </span>            : }</a>
+<a name="5567"><span class="lineNum">    5567 </span>            : #include &lt;cmath&gt;</a>
+<a name="5568"><span class="lineNum">    5568 </span>            : </a>
+<a name="5569"><span class="lineNum">    5569 </span>            : #include &quot;real.h&quot;</a>
+<a name="5570"><span class="lineNum">    5570 </span>            : </a>
+<a name="5571"><span class="lineNum">    5571 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="5572"><span class="lineNum">    5572 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="5573"><span class="lineNum">    5573 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="5574"><span class="lineNum">    5574 </span>            : </a>
+<a name="5575"><span class="lineNum">    5575 </span>            : </a>
+<a name="5576"><span class="lineNum">    5576 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="5577"><span class="lineNum">    5577 </span>            : namespace PLMD{</a>
+<a name="5578"><span class="lineNum">    5578 </span>            : namespace lapack{</a>
+<a name="5579"><span class="lineNum">    5579 </span>            : using namespace blas;</a>
+<a name="5580"><span class="lineNum">    5580 </span>            : void</a>
+<a name="5581"><span class="lineNum">    5581 </span><span class="lineCov">         70 : PLUMED_BLAS_F77_FUNC(dlarrfx,DLARRFX)(int *n, </span></a>
+<a name="5582"><span class="lineNum">    5582 </span>            :         double *d__, </a>
+<a name="5583"><span class="lineNum">    5583 </span>            :         double *l, </a>
+<a name="5584"><span class="lineNum">    5584 </span>            :         double *ld, </a>
+<a name="5585"><span class="lineNum">    5585 </span>            :         double *lld, </a>
+<a name="5586"><span class="lineNum">    5586 </span>            :         int *ifirst, </a>
+<a name="5587"><span class="lineNum">    5587 </span>            :         int *ilast, </a>
+<a name="5588"><span class="lineNum">    5588 </span>            :         double *w, </a>
+<a name="5589"><span class="lineNum">    5589 </span>            :         double *sigma, </a>
+<a name="5590"><span class="lineNum">    5590 </span>            :         double *dplus, </a>
+<a name="5591"><span class="lineNum">    5591 </span>            :         double *lplus, </a>
+<a name="5592"><span class="lineNum">    5592 </span>            :         double *work,</a>
+<a name="5593"><span class="lineNum">    5593 </span>            :         int *info)</a>
+<a name="5594"><span class="lineNum">    5594 </span>            : {</a>
+<a name="5595"><span class="lineNum">    5595 </span><span class="lineCov">         70 :     int i1 = 1;</span></a>
+<a name="5596"><span class="lineNum">    5596 </span>            :     int i__1;</a>
+<a name="5597"><span class="lineNum">    5597 </span>            :     double d__2, d__3;</a>
+<a name="5598"><span class="lineNum">    5598 </span>            : </a>
+<a name="5599"><span class="lineNum">    5599 </span>            :     int i__;</a>
+<a name="5600"><span class="lineNum">    5600 </span>            :     double s, eps, tmp, dmax1, dmax2, delta;</a>
+<a name="5601"><span class="lineNum">    5601 </span><span class="lineCov">         70 :     --work;</span></a>
+<a name="5602"><span class="lineNum">    5602 </span><span class="lineCov">         70 :     --lplus;</span></a>
+<a name="5603"><span class="lineNum">    5603 </span><span class="lineCov">         70 :     --dplus;</span></a>
+<a name="5604"><span class="lineNum">    5604 </span><span class="lineCov">         70 :     --w;</span></a>
+<a name="5605"><span class="lineNum">    5605 </span>            :     --lld;</a>
+<a name="5606"><span class="lineNum">    5606 </span><span class="lineCov">         70 :     --ld;</span></a>
+<a name="5607"><span class="lineNum">    5607 </span><span class="lineCov">         70 :     --l;</span></a>
+<a name="5608"><span class="lineNum">    5608 </span><span class="lineCov">         70 :     --d__;</span></a>
+<a name="5609"><span class="lineNum">    5609 </span><span class="lineCov">         70 :     *info = 0;</span></a>
+<a name="5610"><span class="lineNum">    5610 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="5611"><span class="lineNum">    5611 </span><span class="lineCov">         70 :     *sigma = w[*ifirst];</span></a>
+<a name="5612"><span class="lineNum">    5612 </span>            :     delta = eps * 2.;</a>
+<a name="5613"><span class="lineNum">    5613 </span>            : </a>
+<a name="5614"><span class="lineNum">    5614 </span><span class="lineCov">         70 : L10:</span></a>
+<a name="5615"><span class="lineNum">    5615 </span><span class="lineCov">         70 :     s = -(*sigma);</span></a>
+<a name="5616"><span class="lineNum">    5616 </span><span class="lineCov">         70 :     dplus[1] = d__[1] + s;</span></a>
+<a name="5617"><span class="lineNum">    5617 </span>            :     dmax1 = std::abs(dplus[1]);</a>
+<a name="5618"><span class="lineNum">    5618 </span><span class="lineCov">         70 :     i__1 = *n - 1;</span></a>
+<a name="5619"><span class="lineNum">    5619 </span><span class="lineCov">      28278 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5620"><span class="lineNum">    5620 </span><span class="lineCov">      28208 :         lplus[i__] = ld[i__] / dplus[i__];</span></a>
+<a name="5621"><span class="lineNum">    5621 </span><span class="lineCov">      28208 :         s = s * lplus[i__] * l[i__] - *sigma;</span></a>
+<a name="5622"><span class="lineNum">    5622 </span><span class="lineCov">      28208 :         dplus[i__ + 1] = d__[i__ + 1] + s;</span></a>
+<a name="5623"><span class="lineNum">    5623 </span>            :         d__2 = dmax1, d__3 = std::abs(dplus[i__ + 1]);</a>
+<a name="5624"><span class="lineNum">    5624 </span><span class="lineCov">      28208 :         dmax1 = (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="5625"><span class="lineNum">    5625 </span>            :     }</a>
+<a name="5626"><span class="lineNum">    5626 </span><span class="lineCov">         70 :     if (std::isnan(dmax1)) {</span></a>
+<a name="5627"><span class="lineNum">    5627 </span><span class="lineNoCov">          0 :         *sigma -= std::abs(*sigma) * delta;</span></a>
+<a name="5628"><span class="lineNum">    5628 </span><span class="lineNoCov">          0 :         delta *= 2.;</span></a>
+<a name="5629"><span class="lineNum">    5629 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="5630"><span class="lineNum">    5630 </span>            :     }</a>
+<a name="5631"><span class="lineNum">    5631 </span>            : </a>
+<a name="5632"><span class="lineNum">    5632 </span><span class="lineCov">         70 :     tmp = w[*ilast];</span></a>
+<a name="5633"><span class="lineNum">    5633 </span>            :     delta = eps * 2.;</a>
+<a name="5634"><span class="lineNum">    5634 </span><span class="lineCov">         70 : L30:</span></a>
+<a name="5635"><span class="lineNum">    5635 </span><span class="lineCov">         70 :     s = -tmp;</span></a>
+<a name="5636"><span class="lineNum">    5636 </span><span class="lineCov">         70 :     work[1] = d__[1] + s;</span></a>
+<a name="5637"><span class="lineNum">    5637 </span>            :     dmax2 = std::abs(work[1]);</a>
+<a name="5638"><span class="lineNum">    5638 </span><span class="lineCov">         70 :     i__1 = *n - 1;</span></a>
+<a name="5639"><span class="lineNum">    5639 </span><span class="lineCov">      28278 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5640"><span class="lineNum">    5640 </span><span class="lineCov">      28208 :         work[*n + i__] = ld[i__] / work[i__];</span></a>
+<a name="5641"><span class="lineNum">    5641 </span><span class="lineCov">      28208 :         s = s * work[*n + i__] * l[i__] - tmp;</span></a>
+<a name="5642"><span class="lineNum">    5642 </span><span class="lineCov">      28208 :         work[i__ + 1] = d__[i__ + 1] + s;</span></a>
+<a name="5643"><span class="lineNum">    5643 </span>            :         d__2 = dmax2, d__3 = std::abs(work[i__ + 1]);</a>
+<a name="5644"><span class="lineNum">    5644 </span><span class="lineCov">      28208 :         dmax2 = (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="5645"><span class="lineNum">    5645 </span>            :     }</a>
+<a name="5646"><span class="lineNum">    5646 </span><span class="lineCov">         70 :     if (std::isnan(dmax2)) {</span></a>
+<a name="5647"><span class="lineNum">    5647 </span><span class="lineNoCov">          0 :         tmp += std::abs(tmp) * delta;</span></a>
+<a name="5648"><span class="lineNum">    5648 </span><span class="lineNoCov">          0 :         delta *= 2.;</span></a>
+<a name="5649"><span class="lineNum">    5649 </span><span class="lineNoCov">          0 :         goto L30;</span></a>
+<a name="5650"><span class="lineNum">    5650 </span>            :     }</a>
+<a name="5651"><span class="lineNum">    5651 </span><span class="lineCov">         70 :     if (dmax2 &lt; dmax1) {</span></a>
+<a name="5652"><span class="lineNum">    5652 </span><span class="lineCov">         36 :         *sigma = tmp;</span></a>
+<a name="5653"><span class="lineNum">    5653 </span><span class="lineCov">         36 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;work[1], &amp;i1, &amp;dplus[1], &amp;i1);</span></a>
+<a name="5654"><span class="lineNum">    5654 </span><span class="lineCov">         36 :         i__1 = *n - 1;</span></a>
+<a name="5655"><span class="lineNum">    5655 </span><span class="lineCov">         36 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;work[*n + 1], &amp;i1, &amp;lplus[1], &amp;i1);</span></a>
+<a name="5656"><span class="lineNum">    5656 </span>            :     }</a>
+<a name="5657"><span class="lineNum">    5657 </span>            : </a>
+<a name="5658"><span class="lineNum">    5658 </span><span class="lineCov">         70 :     return;</span></a>
+<a name="5659"><span class="lineNum">    5659 </span>            : }</a>
+<a name="5660"><span class="lineNum">    5660 </span>            : }</a>
+<a name="5661"><span class="lineNum">    5661 </span>            : }</a>
+<a name="5662"><span class="lineNum">    5662 </span>            : #include &lt;cmath&gt;</a>
+<a name="5663"><span class="lineNum">    5663 </span>            : </a>
+<a name="5664"><span class="lineNum">    5664 </span>            : #include &quot;real.h&quot;</a>
+<a name="5665"><span class="lineNum">    5665 </span>            : </a>
+<a name="5666"><span class="lineNum">    5666 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="5667"><span class="lineNum">    5667 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="5668"><span class="lineNum">    5668 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="5669"><span class="lineNum">    5669 </span>            : </a>
+<a name="5670"><span class="lineNum">    5670 </span>            : </a>
+<a name="5671"><span class="lineNum">    5671 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="5672"><span class="lineNum">    5672 </span>            : namespace PLMD{</a>
+<a name="5673"><span class="lineNum">    5673 </span>            : namespace lapack{</a>
+<a name="5674"><span class="lineNum">    5674 </span>            : using namespace blas;</a>
+<a name="5675"><span class="lineNum">    5675 </span>            : void</a>
+<a name="5676"><span class="lineNum">    5676 </span><span class="lineCov">     569964 : PLUMED_BLAS_F77_FUNC(dlarrvx,DLARRVX)(int *n, </span></a>
+<a name="5677"><span class="lineNum">    5677 </span>            :         double *d__, </a>
+<a name="5678"><span class="lineNum">    5678 </span>            :         double *l, </a>
+<a name="5679"><span class="lineNum">    5679 </span>            :         int *isplit,</a>
+<a name="5680"><span class="lineNum">    5680 </span>            :         int *m, </a>
+<a name="5681"><span class="lineNum">    5681 </span>            :         double *w,</a>
+<a name="5682"><span class="lineNum">    5682 </span>            :         int *iblock, </a>
+<a name="5683"><span class="lineNum">    5683 </span>            :         int *indexw, </a>
+<a name="5684"><span class="lineNum">    5684 </span>            :         double *gersch, </a>
+<a name="5685"><span class="lineNum">    5685 </span>            :         double *tol, </a>
+<a name="5686"><span class="lineNum">    5686 </span>            :         double *z__, </a>
+<a name="5687"><span class="lineNum">    5687 </span>            :         int *ldz, </a>
+<a name="5688"><span class="lineNum">    5688 </span>            :         int *isuppz, </a>
+<a name="5689"><span class="lineNum">    5689 </span>            :         double *work, </a>
+<a name="5690"><span class="lineNum">    5690 </span>            :         int *iwork, </a>
+<a name="5691"><span class="lineNum">    5691 </span>            :         int *info)</a>
+<a name="5692"><span class="lineNum">    5692 </span>            : {</a>
+<a name="5693"><span class="lineNum">    5693 </span>            :     int z_dim1, z_offset, i__1, i__2, i__3, i__4, i__5, i__6;</a>
+<a name="5694"><span class="lineNum">    5694 </span>            :     double d__1, d__2;</a>
+<a name="5695"><span class="lineNum">    5695 </span><span class="lineCov">     569964 :     double c_b5 = 0.;</span></a>
+<a name="5696"><span class="lineNum">    5696 </span><span class="lineCov">     569964 :     int c__1 = 1;</span></a>
+<a name="5697"><span class="lineNum">    5697 </span><span class="lineCov">     569964 :     int c__2 = 2;</span></a>
+<a name="5698"><span class="lineNum">    5698 </span>            : </a>
+<a name="5699"><span class="lineNum">    5699 </span>            :     int i__, j, k, p, q;</a>
+<a name="5700"><span class="lineNum">    5700 </span>            :     int im, in;</a>
+<a name="5701"><span class="lineNum">    5701 </span>            :     double gap, eps, tmp;</a>
+<a name="5702"><span class="lineNum">    5702 </span>            :     int zto;</a>
+<a name="5703"><span class="lineNum">    5703 </span>            :     double ztz;</a>
+<a name="5704"><span class="lineNum">    5704 </span>            :     int iend, jblk;</a>
+<a name="5705"><span class="lineNum">    5705 </span>            :     int wend, iter, temp[1], ktot;</a>
+<a name="5706"><span class="lineNum">    5706 </span>            :     int itmp1, itmp2;</a>
+<a name="5707"><span class="lineNum">    5707 </span>            :     int indld;</a>
+<a name="5708"><span class="lineNum">    5708 </span>            :     double sigma;</a>
+<a name="5709"><span class="lineNum">    5709 </span>            :     int ndone, iinfo, iindr;</a>
+<a name="5710"><span class="lineNum">    5710 </span>            :     double resid;</a>
+<a name="5711"><span class="lineNum">    5711 </span>            :     int nomgs;</a>
+<a name="5712"><span class="lineNum">    5712 </span>            :     int nclus;</a>
+<a name="5713"><span class="lineNum">    5713 </span>            :     int zfrom, iindc1, iindc2;</a>
+<a name="5714"><span class="lineNum">    5714 </span>            :     double lambda;</a>
+<a name="5715"><span class="lineNum">    5715 </span>            :     int ibegin;</a>
+<a name="5716"><span class="lineNum">    5716 </span>            :     int indgap, indlld;</a>
+<a name="5717"><span class="lineNum">    5717 </span>            :     double mingma;</a>
+<a name="5718"><span class="lineNum">    5718 </span>            :     int oldien, oldncl, wbegin;</a>
+<a name="5719"><span class="lineNum">    5719 </span>            :     double relgap;</a>
+<a name="5720"><span class="lineNum">    5720 </span>            :     int oldcls;</a>
+<a name="5721"><span class="lineNum">    5721 </span>            :     int ndepth, inderr, iindwk;</a>
+<a name="5722"><span class="lineNum">    5722 </span>            :     int newcls, oldfst;</a>
+<a name="5723"><span class="lineNum">    5723 </span>            :     double minrgp=0.0;</a>
+<a name="5724"><span class="lineNum">    5724 </span>            :     int indwrk, oldlst;</a>
+<a name="5725"><span class="lineNum">    5725 </span>            :     double reltol;</a>
+<a name="5726"><span class="lineNum">    5726 </span>            :     int newfrs, newftt, parity;</a>
+<a name="5727"><span class="lineNum">    5727 </span>            :     double mgstol, nrminv, rqcorr;</a>
+<a name="5728"><span class="lineNum">    5728 </span>            :     int newlst, newsiz;</a>
+<a name="5729"><span class="lineNum">    5729 </span>            : </a>
+<a name="5730"><span class="lineNum">    5730 </span>            : </a>
+<a name="5731"><span class="lineNum">    5731 </span><span class="lineCov">     569964 :     --d__;</span></a>
+<a name="5732"><span class="lineNum">    5732 </span><span class="lineCov">     569964 :     --l;</span></a>
+<a name="5733"><span class="lineNum">    5733 </span>            :     --isplit;</a>
+<a name="5734"><span class="lineNum">    5734 </span><span class="lineCov">     569964 :     --w;</span></a>
+<a name="5735"><span class="lineNum">    5735 </span><span class="lineCov">     569964 :     --iblock;</span></a>
+<a name="5736"><span class="lineNum">    5736 </span><span class="lineCov">     569964 :     --indexw;</span></a>
+<a name="5737"><span class="lineNum">    5737 </span>            :     --gersch;</a>
+<a name="5738"><span class="lineNum">    5738 </span><span class="lineCov">     569964 :     z_dim1 = *ldz;</span></a>
+<a name="5739"><span class="lineNum">    5739 </span><span class="lineCov">     569964 :     z_offset = 1 + z_dim1;</span></a>
+<a name="5740"><span class="lineNum">    5740 </span><span class="lineCov">     569964 :     z__ -= z_offset;</span></a>
+<a name="5741"><span class="lineNum">    5741 </span><span class="lineCov">     569964 :     --isuppz;</span></a>
+<a name="5742"><span class="lineNum">    5742 </span><span class="lineCov">     569964 :     --work;</span></a>
+<a name="5743"><span class="lineNum">    5743 </span><span class="lineCov">     569964 :     --iwork;</span></a>
+<a name="5744"><span class="lineNum">    5744 </span>            : </a>
+<a name="5745"><span class="lineNum">    5745 </span><span class="lineCov">     569964 :     inderr = *n;</span></a>
+<a name="5746"><span class="lineNum">    5746 </span><span class="lineCov">     569964 :     indld = *n &lt;&lt; 1;</span></a>
+<a name="5747"><span class="lineNum">    5747 </span><span class="lineCov">     569964 :     indlld = *n * 3;</span></a>
+<a name="5748"><span class="lineNum">    5748 </span><span class="lineCov">     569964 :     indgap = *n &lt;&lt; 2;</span></a>
+<a name="5749"><span class="lineNum">    5749 </span><span class="lineCov">     569964 :     indwrk = *n * 5 + 1;</span></a>
+<a name="5750"><span class="lineNum">    5750 </span>            : </a>
+<a name="5751"><span class="lineNum">    5751 </span>            :     iindr = *n;</a>
+<a name="5752"><span class="lineNum">    5752 </span>            :     iindc1 = *n &lt;&lt; 1;</a>
+<a name="5753"><span class="lineNum">    5753 </span>            :     iindc2 = *n * 3;</a>
+<a name="5754"><span class="lineNum">    5754 </span><span class="lineCov">     569964 :     iindwk = (*n &lt;&lt; 2) + 1;</span></a>
+<a name="5755"><span class="lineNum">    5755 </span>            : </a>
+<a name="5756"><span class="lineNum">    5756 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="5757"><span class="lineNum">    5757 </span>            : </a>
+<a name="5758"><span class="lineNum">    5758 </span>            :     i__1 = *n &lt;&lt; 1;</a>
+<a name="5759"><span class="lineNum">    5759 </span><span class="lineCov">    5078558 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="5760"><span class="lineNum">    5760 </span><span class="lineCov">    4508594 :         iwork[i__] = 0;</span></a>
+<a name="5761"><span class="lineNum">    5761 </span>            :     }</a>
+<a name="5762"><span class="lineNum">    5762 </span><span class="lineCov">     569964 :     PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;Full&quot;, n, m, &amp;c_b5, &amp;c_b5, &amp;z__[z_offset], ldz);</span></a>
+<a name="5763"><span class="lineNum">    5763 </span>            :     mgstol = eps * 100.;</a>
+<a name="5764"><span class="lineNum">    5764 </span>            : </a>
+<a name="5765"><span class="lineNum">    5765 </span>            :     ibegin = 1;</a>
+<a name="5766"><span class="lineNum">    5766 </span>            :     wbegin = 1;</a>
+<a name="5767"><span class="lineNum">    5767 </span><span class="lineCov">     569964 :     i__1 = iblock[*m];</span></a>
+<a name="5768"><span class="lineNum">    5768 </span><span class="lineCov">    1140592 :     for (jblk = 1; jblk &lt;= i__1; ++jblk) {</span></a>
+<a name="5769"><span class="lineNum">    5769 </span><span class="lineCov">     570628 :         iend = isplit[jblk];</span></a>
+<a name="5770"><span class="lineNum">    5770 </span>            : </a>
+<a name="5771"><span class="lineNum">    5771 </span><span class="lineCov">     570628 :         wend = wbegin - 1;</span></a>
+<a name="5772"><span class="lineNum">    5772 </span><span class="lineCov">    1178159 : L171:</span></a>
+<a name="5773"><span class="lineNum">    5773 </span><span class="lineCov">    1178159 :         if (wend &lt; *m) {</span></a>
+<a name="5774"><span class="lineNum">    5774 </span><span class="lineCov">     608195 :             if (iblock[wend + 1] == jblk) {</span></a>
+<a name="5775"><span class="lineNum">    5775 </span><span class="lineCov">     607531 :                 ++wend;</span></a>
+<a name="5776"><span class="lineNum">    5776 </span><span class="lineCov">     607531 :                 goto L171;</span></a>
+<a name="5777"><span class="lineNum">    5777 </span>            :             }</a>
+<a name="5778"><span class="lineNum">    5778 </span>            :         }</a>
+<a name="5779"><span class="lineNum">    5779 </span><span class="lineCov">     570628 :         if (wend &lt; wbegin) {</span></a>
+<a name="5780"><span class="lineNum">    5780 </span><span class="lineNoCov">          0 :             ibegin = iend + 1;</span></a>
+<a name="5781"><span class="lineNum">    5781 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="5782"><span class="lineNum">    5782 </span>            :         }</a>
+<a name="5783"><span class="lineNum">    5783 </span>            : </a>
+<a name="5784"><span class="lineNum">    5784 </span><span class="lineCov">     570628 :         if (ibegin == iend) {</span></a>
+<a name="5785"><span class="lineNum">    5785 </span><span class="lineCov">        665 :             z__[ibegin + wbegin * z_dim1] = 1.;</span></a>
+<a name="5786"><span class="lineNum">    5786 </span><span class="lineCov">        665 :             isuppz[(wbegin &lt;&lt; 1) - 1] = ibegin;</span></a>
+<a name="5787"><span class="lineNum">    5787 </span><span class="lineCov">        665 :             isuppz[wbegin * 2] = ibegin;</span></a>
+<a name="5788"><span class="lineNum">    5788 </span><span class="lineCov">        665 :             ibegin = iend + 1;</span></a>
+<a name="5789"><span class="lineNum">    5789 </span><span class="lineCov">        665 :             wbegin = wend + 1;</span></a>
+<a name="5790"><span class="lineNum">    5790 </span><span class="lineCov">        665 :             continue;</span></a>
+<a name="5791"><span class="lineNum">    5791 </span>            :         }</a>
+<a name="5792"><span class="lineNum">    5792 </span><span class="lineCov">     569963 :         oldien = ibegin - 1;</span></a>
+<a name="5793"><span class="lineNum">    5793 </span><span class="lineCov">     569963 :         in = iend - oldien;</span></a>
+<a name="5794"><span class="lineNum">    5794 </span><span class="lineCov">     569963 :         d__1 = .001, d__2 = 1. / (double) in;</span></a>
+<a name="5795"><span class="lineNum">    5795 </span><span class="lineCov">     569963 :         reltol = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="5796"><span class="lineNum">    5796 </span><span class="lineCov">     569963 :         im = wend - wbegin + 1;</span></a>
+<a name="5797"><span class="lineNum">    5797 </span><span class="lineCov">     569963 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;im, &amp;w[wbegin], &amp;c__1, &amp;work[1], &amp;c__1);</span></a>
+<a name="5798"><span class="lineNum">    5798 </span><span class="lineCov">     569963 :         i__2 = im - 1;</span></a>
+<a name="5799"><span class="lineNum">    5799 </span><span class="lineCov">     606866 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5800"><span class="lineNum">    5800 </span><span class="lineCov">      36903 :             work[inderr + i__] = eps * std::abs(work[i__]);</span></a>
+<a name="5801"><span class="lineNum">    5801 </span><span class="lineCov">      36903 :             work[indgap + i__] = work[i__ + 1] - work[i__];</span></a>
+<a name="5802"><span class="lineNum">    5802 </span>            :         }</a>
+<a name="5803"><span class="lineNum">    5803 </span><span class="lineCov">     569963 :         work[inderr + im] = eps * std::abs(work[im]);</span></a>
+<a name="5804"><span class="lineNum">    5804 </span><span class="lineCov">     569963 :         d__2 = std::abs(work[im]);</span></a>
+<a name="5805"><span class="lineNum">    5805 </span><span class="lineCov">     569963 :         work[indgap + im] = (d__2&gt;eps) ? d__2 : eps;</span></a>
+<a name="5806"><span class="lineNum">    5806 </span>            :         ndone = 0;</a>
+<a name="5807"><span class="lineNum">    5807 </span>            : </a>
+<a name="5808"><span class="lineNum">    5808 </span>            :         ndepth = 0;</a>
+<a name="5809"><span class="lineNum">    5809 </span>            :         parity = 1;</a>
+<a name="5810"><span class="lineNum">    5810 </span>            :         nclus = 1;</a>
+<a name="5811"><span class="lineNum">    5811 </span><span class="lineCov">     569963 :         iwork[iindc1 + 1] = 1;</span></a>
+<a name="5812"><span class="lineNum">    5812 </span><span class="lineCov">     569963 :         iwork[iindc1 + 2] = im;</span></a>
+<a name="5813"><span class="lineNum">    5813 </span>            : </a>
+<a name="5814"><span class="lineNum">    5814 </span><span class="lineCov">    1139933 : L40:</span></a>
+<a name="5815"><span class="lineNum">    5815 </span><span class="lineCov">    1139933 :         if (ndone &lt; im) {</span></a>
+<a name="5816"><span class="lineNum">    5816 </span>            :             oldncl = nclus;</a>
+<a name="5817"><span class="lineNum">    5817 </span>            :             nclus = 0;</a>
+<a name="5818"><span class="lineNum">    5818 </span><span class="lineCov">     569970 :             parity = 1 - parity;</span></a>
+<a name="5819"><span class="lineNum">    5819 </span><span class="lineCov">     569970 :             if (parity == 0) {</span></a>
+<a name="5820"><span class="lineNum">    5820 </span>            :                 oldcls = iindc1;</a>
+<a name="5821"><span class="lineNum">    5821 </span>            :                 newcls = iindc2;</a>
+<a name="5822"><span class="lineNum">    5822 </span>            :             } else {</a>
+<a name="5823"><span class="lineNum">    5823 </span>            :                 oldcls = iindc2;</a>
+<a name="5824"><span class="lineNum">    5824 </span>            :                 newcls = iindc1;</a>
+<a name="5825"><span class="lineNum">    5825 </span>            :             }</a>
+<a name="5826"><span class="lineNum">    5826 </span>            :             i__2 = oldncl;</a>
+<a name="5827"><span class="lineNum">    5827 </span><span class="lineCov">    1140003 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="5828"><span class="lineNum">    5828 </span>            : </a>
+<a name="5829"><span class="lineNum">    5829 </span><span class="lineCov">     570033 :                 j = oldcls + (i__ &lt;&lt; 1);</span></a>
+<a name="5830"><span class="lineNum">    5830 </span><span class="lineCov">     570033 :                 oldfst = iwork[j - 1];</span></a>
+<a name="5831"><span class="lineNum">    5831 </span><span class="lineCov">     570033 :                 oldlst = iwork[j];</span></a>
+<a name="5832"><span class="lineNum">    5832 </span><span class="lineCov">     570033 :                 if (ndepth &gt; 0) {</span></a>
+<a name="5833"><span class="lineNum">    5833 </span><span class="lineCov">         70 :                     j = wbegin + oldfst - 1;</span></a>
+<a name="5834"><span class="lineNum">    5834 </span><span class="lineCov">         70 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;in, &amp;z__[ibegin + j * z_dim1], &amp;c__1, &amp;d__[ibegin]</span></a>
+<a name="5835"><span class="lineNum">    5835 </span>            :                             , &amp;c__1);</a>
+<a name="5836"><span class="lineNum">    5836 </span><span class="lineCov">         70 :                     i__3 = in - 1;</span></a>
+<a name="5837"><span class="lineNum">    5837 </span><span class="lineCov">         70 :                     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__3, &amp;z__[ibegin + (j + 1) * z_dim1], &amp;c__1, &amp;l[</span></a>
+<a name="5838"><span class="lineNum">    5838 </span>            :                             ibegin], &amp;c__1);</a>
+<a name="5839"><span class="lineNum">    5839 </span><span class="lineCov">         70 :                     PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;Full&quot;, &amp;in, &amp;c__2, &amp;c_b5, &amp;c_b5, &amp;z__[ibegin + j </span></a>
+<a name="5840"><span class="lineNum">    5840 </span>            :                             * z_dim1], ldz);</a>
+<a name="5841"><span class="lineNum">    5841 </span>            :                 }</a>
+<a name="5842"><span class="lineNum">    5842 </span>            :                 k = ibegin;</a>
+<a name="5843"><span class="lineNum">    5843 </span><span class="lineCov">     570033 :                 i__3 = in - 1;</span></a>
+<a name="5844"><span class="lineNum">    5844 </span><span class="lineCov">    2281903 :                 for (j = 1; j &lt;= i__3; ++j) {</span></a>
+<a name="5845"><span class="lineNum">    5845 </span><span class="lineCov">    1711870 :                     tmp = d__[k] * l[k];</span></a>
+<a name="5846"><span class="lineNum">    5846 </span><span class="lineCov">    1711870 :                     work[indld + j] = tmp;</span></a>
+<a name="5847"><span class="lineNum">    5847 </span><span class="lineCov">    1711870 :                     work[indlld + j] = tmp * l[k];</span></a>
+<a name="5848"><span class="lineNum">    5848 </span><span class="lineCov">    1711870 :                     ++k;</span></a>
+<a name="5849"><span class="lineNum">    5849 </span>            :                 }</a>
+<a name="5850"><span class="lineNum">    5850 </span><span class="lineCov">     570033 :                 if (ndepth &gt; 0) {</span></a>
+<a name="5851"><span class="lineNum">    5851 </span>            : </a>
+<a name="5852"><span class="lineNum">    5852 </span><span class="lineCov">         70 :                     p = indexw[wbegin - 1 + oldfst];</span></a>
+<a name="5853"><span class="lineNum">    5853 </span><span class="lineCov">         70 :                     q = indexw[wbegin - 1 + oldlst];</span></a>
+<a name="5854"><span class="lineNum">    5854 </span><span class="lineCov">         70 :                     d__1 = eps * 4.;</span></a>
+<a name="5855"><span class="lineNum">    5855 </span><span class="lineCov">         70 :                     i__3 = p - oldfst;</span></a>
+<a name="5856"><span class="lineNum">    5856 </span><span class="lineCov">         70 :                     PLUMED_BLAS_F77_FUNC(dlarrbx,DLARRBX)(&amp;in, &amp;d__[ibegin], &amp;l[ibegin], &amp;work[indld + 1], &amp;</span></a>
+<a name="5857"><span class="lineNum">    5857 </span><span class="lineCov">         70 :                             work[indlld + 1], &amp;p, &amp;q, &amp;reltol, &amp;d__1, &amp;i__3, &amp;</span></a>
+<a name="5858"><span class="lineNum">    5858 </span><span class="lineCov">         70 :                             work[1], &amp;work[indgap + 1], &amp;work[inderr + 1], &amp;</span></a>
+<a name="5859"><span class="lineNum">    5859 </span><span class="lineCov">         70 :                             work[indwrk + in], &amp;iwork[iindwk], &amp;iinfo);</span></a>
+<a name="5860"><span class="lineNum">    5860 </span>            :                 }</a>
+<a name="5861"><span class="lineNum">    5861 </span><span class="lineCov">     570033 :                 newfrs = oldfst;</span></a>
+<a name="5862"><span class="lineNum">    5862 </span><span class="lineCov">     570033 :                 i__3 = oldlst;</span></a>
+<a name="5863"><span class="lineNum">    5863 </span><span class="lineCov">    1177835 :                 for (j = oldfst; j &lt;= i__3; ++j) {</span></a>
+<a name="5864"><span class="lineNum">    5864 </span><span class="lineCov">     607802 :                     if (j == oldlst || work[indgap + j] &gt;= </span></a>
+<a name="5865"><span class="lineNum">    5865 </span><span class="lineCov">      37769 :                         reltol * std::abs(work[j])) {</span></a>
+<a name="5866"><span class="lineNum">    5866 </span><span class="lineCov">     606936 :                         newlst = j;</span></a>
+<a name="5867"><span class="lineNum">    5867 </span>            :                     } else {</a>
+<a name="5868"><span class="lineNum">    5868 </span>            : </a>
+<a name="5869"><span class="lineNum">    5869 </span><span class="lineCov">        866 :                         relgap = work[indgap + j] / std::abs(work[j]);</span></a>
+<a name="5870"><span class="lineNum">    5870 </span><span class="lineCov">        866 :                         if (j == newfrs) {</span></a>
+<a name="5871"><span class="lineNum">    5871 </span>            :                             minrgp = relgap;</a>
+<a name="5872"><span class="lineNum">    5872 </span>            :                         } else {</a>
+<a name="5873"><span class="lineNum">    5873 </span><span class="lineCov">        796 :                             minrgp = (minrgp&lt;relgap) ? minrgp : relgap;</span></a>
+<a name="5874"><span class="lineNum">    5874 </span>            :                         }</a>
+<a name="5875"><span class="lineNum">    5875 </span><span class="lineCov">        866 :                         continue;</span></a>
+<a name="5876"><span class="lineNum">    5876 </span>            :                     }</a>
+<a name="5877"><span class="lineNum">    5877 </span><span class="lineCov">     606936 :                     newsiz = newlst - newfrs + 1;</span></a>
+<a name="5878"><span class="lineNum">    5878 </span><span class="lineCov">     606936 :                     newftt = wbegin + newfrs - 1;</span></a>
+<a name="5879"><span class="lineNum">    5879 </span><span class="lineCov">     606936 :                     nomgs = newsiz == 1 || newsiz &gt; 1 || minrgp &lt; mgstol;</span></a>
+<a name="5880"><span class="lineNum">    5880 </span><span class="lineCov">     606936 :                     if (newsiz &gt; 1 &amp;&amp; nomgs) {</span></a>
+<a name="5881"><span class="lineNum">    5881 </span>            : </a>
+<a name="5882"><span class="lineNum">    5882 </span><span class="lineCov">         70 :                         PLUMED_BLAS_F77_FUNC(dlarrfx,DLARRFX)(&amp;in, &amp;d__[ibegin], &amp;l[ibegin], &amp;work[indld + </span></a>
+<a name="5883"><span class="lineNum">    5883 </span><span class="lineCov">         70 :                                 1], &amp;work[indlld + 1], &amp;newfrs, &amp;newlst, &amp;</span></a>
+<a name="5884"><span class="lineNum">    5884 </span><span class="lineCov">         70 :                                 work[1], &amp;sigma, &amp;z__[ibegin + newftt * </span></a>
+<a name="5885"><span class="lineNum">    5885 </span><span class="lineCov">         70 :                                 z_dim1], &amp;z__[ibegin + (newftt + 1) * z_dim1],</span></a>
+<a name="5886"><span class="lineNum">    5886 </span><span class="lineCov">         70 :                                  &amp;work[indwrk], info);</span></a>
+<a name="5887"><span class="lineNum">    5887 </span><span class="lineCov">         70 :                         if (*info == 0) {</span></a>
+<a name="5888"><span class="lineNum">    5888 </span><span class="lineCov">         70 :                             tmp = eps * std::abs(sigma);</span></a>
+<a name="5889"><span class="lineNum">    5889 </span><span class="lineCov">         70 :                             i__4 = newlst;</span></a>
+<a name="5890"><span class="lineNum">    5890 </span><span class="lineCov">       1006 :                             for (k = newfrs; k &lt;= i__4; ++k) {</span></a>
+<a name="5891"><span class="lineNum">    5891 </span><span class="lineCov">        936 :                                 work[k] -= sigma;</span></a>
+<a name="5892"><span class="lineNum">    5892 </span><span class="lineCov">        936 :                                 d__1 = work[indgap + k];</span></a>
+<a name="5893"><span class="lineNum">    5893 </span><span class="lineCov">        936 :                                 work[indgap + k] = (d__1&gt;tmp) ? d__1 : tmp;</span></a>
+<a name="5894"><span class="lineNum">    5894 </span><span class="lineCov">        936 :                                 work[inderr + k] += tmp;</span></a>
+<a name="5895"><span class="lineNum">    5895 </span>            :                             }</a>
+<a name="5896"><span class="lineNum">    5896 </span><span class="lineCov">         70 :                             ++nclus;</span></a>
+<a name="5897"><span class="lineNum">    5897 </span><span class="lineCov">         70 :                             k = newcls + (nclus &lt;&lt; 1);</span></a>
+<a name="5898"><span class="lineNum">    5898 </span><span class="lineCov">         70 :                             iwork[k - 1] = newfrs;</span></a>
+<a name="5899"><span class="lineNum">    5899 </span><span class="lineCov">         70 :                             iwork[k] = newlst;</span></a>
+<a name="5900"><span class="lineNum">    5900 </span>            :                         } else {</a>
+<a name="5901"><span class="lineNum">    5901 </span><span class="lineNoCov">          0 :                             *info = 0;</span></a>
+<a name="5902"><span class="lineNum">    5902 </span><span class="lineNoCov">          0 :                             if (minrgp &lt; mgstol) {</span></a>
+<a name="5903"><span class="lineNum">    5903 </span><span class="lineNoCov">          0 :                                 work[indwrk] = d__[ibegin];</span></a>
+<a name="5904"><span class="lineNum">    5904 </span><span class="lineNoCov">          0 :                                 i__4 = in - 1;</span></a>
+<a name="5905"><span class="lineNum">    5905 </span><span class="lineNoCov">          0 :                                 for (k = 1; k &lt;= i__4; ++k) {</span></a>
+<a name="5906"><span class="lineNum">    5906 </span><span class="lineNoCov">          0 :                                     work[indwrk + k] = d__[ibegin + k] + work[</span></a>
+<a name="5907"><span class="lineNum">    5907 </span><span class="lineNoCov">          0 :                                             indlld + k];</span></a>
+<a name="5908"><span class="lineNum">    5908 </span>            :                                 }</a>
+<a name="5909"><span class="lineNum">    5909 </span><span class="lineNoCov">          0 :                                 i__4 = newsiz;</span></a>
+<a name="5910"><span class="lineNum">    5910 </span><span class="lineNoCov">          0 :                                 for (k = 1; k &lt;= i__4; ++k) {</span></a>
+<a name="5911"><span class="lineNum">    5911 </span><span class="lineNoCov">          0 :                                     iwork[iindwk + k - 1] = 1;</span></a>
+<a name="5912"><span class="lineNum">    5912 </span>            :                                 }</a>
+<a name="5913"><span class="lineNum">    5913 </span><span class="lineNoCov">          0 :                                 i__4 = newlst;</span></a>
+<a name="5914"><span class="lineNum">    5914 </span><span class="lineNoCov">          0 :                                 for (k = newfrs; k &lt;= i__4; ++k) {</span></a>
+<a name="5915"><span class="lineNum">    5915 </span><span class="lineNoCov">          0 :                                     isuppz[2*(oldien + k) - 1] = 1;</span></a>
+<a name="5916"><span class="lineNum">    5916 </span><span class="lineNoCov">          0 :                                     isuppz[(oldien + k) * 2] = in;</span></a>
+<a name="5917"><span class="lineNum">    5917 </span>            :                                 }</a>
+<a name="5918"><span class="lineNum">    5918 </span><span class="lineNoCov">          0 :                                 temp[0] = in;</span></a>
+<a name="5919"><span class="lineNum">    5919 </span><span class="lineNoCov">          0 :                                 PLUMED_BLAS_F77_FUNC(dstein,DSTEIN)(&amp;in, &amp;work[indwrk], &amp;work[indld + 1], </span></a>
+<a name="5920"><span class="lineNum">    5920 </span><span class="lineNoCov">          0 :                                         &amp;newsiz, &amp;work[newfrs], &amp;iwork[iindwk]</span></a>
+<a name="5921"><span class="lineNum">    5921 </span>            :                                         , temp, &amp;z__[ibegin + newftt * z_dim1]</a>
+<a name="5922"><span class="lineNum">    5922 </span><span class="lineNoCov">          0 :                                         , ldz, &amp;work[indwrk + in], &amp;iwork[</span></a>
+<a name="5923"><span class="lineNum">    5923 </span><span class="lineNoCov">          0 :                                         iindwk + in], &amp;iwork[iindwk + (in*2)], &amp;iinfo);</span></a>
+<a name="5924"><span class="lineNum">    5924 </span><span class="lineNoCov">          0 :                                 if (iinfo != 0) {</span></a>
+<a name="5925"><span class="lineNum">    5925 </span><span class="lineNoCov">          0 :                                     *info = 2;</span></a>
+<a name="5926"><span class="lineNum">    5926 </span><span class="lineNoCov">          0 :                                     return;</span></a>
+<a name="5927"><span class="lineNum">    5927 </span>            :                                 }</a>
+<a name="5928"><span class="lineNum">    5928 </span><span class="lineNoCov">          0 :                                 ndone += newsiz;</span></a>
+<a name="5929"><span class="lineNum">    5929 </span>            :                             }</a>
+<a name="5930"><span class="lineNum">    5930 </span>            :                         }</a>
+<a name="5931"><span class="lineNum">    5931 </span>            :                     } else {</a>
+<a name="5932"><span class="lineNum">    5932 </span>            :                         ktot = newftt;</a>
+<a name="5933"><span class="lineNum">    5933 </span>            :                         i__4 = newlst;</a>
+<a name="5934"><span class="lineNum">    5934 </span><span class="lineCov">    1213732 :                         for (k = newfrs; k &lt;= i__4; ++k) {</span></a>
+<a name="5935"><span class="lineNum">    5935 </span>            :                             iter = 0;</a>
+<a name="5936"><span class="lineNum">    5936 </span><span class="lineCov">     608139 : L90:</span></a>
+<a name="5937"><span class="lineNum">    5937 </span><span class="lineCov">     608139 :                             lambda = work[k];</span></a>
+<a name="5938"><span class="lineNum">    5938 </span>            : </a>
+<a name="5939"><span class="lineNum">    5939 </span><span class="lineCov">     608139 :                             PLUMED_BLAS_F77_FUNC(dlar1vx,DLAR1VX)(&amp;in, &amp;c__1, &amp;in, &amp;lambda, &amp;d__[ibegin], &amp;</span></a>
+<a name="5940"><span class="lineNum">    5940 </span><span class="lineCov">     608139 :                                     l[ibegin], &amp;work[indld + 1], &amp;work[indlld </span></a>
+<a name="5941"><span class="lineNum">    5941 </span><span class="lineCov">     608139 :                                     + 1], &amp;w[wbegin + k - 1], &amp;gersch[(oldien </span></a>
+<a name="5942"><span class="lineNum">    5942 </span><span class="lineCov">     608139 :                                     &lt;&lt; 1) + 1], &amp;z__[ibegin + ktot * z_dim1], </span></a>
+<a name="5943"><span class="lineNum">    5943 </span><span class="lineCov">     608139 :                                     &amp;ztz, &amp;mingma, &amp;iwork[iindr + ktot], &amp;</span></a>
+<a name="5944"><span class="lineNum">    5944 </span><span class="lineCov">     608139 :                                     isuppz[(ktot &lt;&lt; 1) - 1], &amp;work[indwrk]);</span></a>
+<a name="5945"><span class="lineNum">    5945 </span><span class="lineCov">     608139 :                             tmp = 1. / ztz;</span></a>
+<a name="5946"><span class="lineNum">    5946 </span><span class="lineCov">     608139 :                             nrminv =  std::sqrt(tmp);</span></a>
+<a name="5947"><span class="lineNum">    5947 </span><span class="lineCov">     608139 :                             resid = std::abs(mingma) * nrminv;</span></a>
+<a name="5948"><span class="lineNum">    5948 </span><span class="lineCov">     608139 :                             rqcorr = mingma * tmp;</span></a>
+<a name="5949"><span class="lineNum">    5949 </span><span class="lineCov">     608139 :                             if (k == in) {</span></a>
+<a name="5950"><span class="lineNum">    5950 </span><span class="lineCov">      21047 :                                 gap = work[indgap + k - 1];</span></a>
+<a name="5951"><span class="lineNum">    5951 </span><span class="lineCov">     587092 :                             } else if (k == 1) {</span></a>
+<a name="5952"><span class="lineNum">    5952 </span><span class="lineCov">     570469 :                                 gap = work[indgap + k];</span></a>
+<a name="5953"><span class="lineNum">    5953 </span>            :                             } else {</a>
+<a name="5954"><span class="lineNum">    5954 </span><span class="lineCov">      16623 :                                 d__1 = work[indgap + k - 1], d__2 = work[</span></a>
+<a name="5955"><span class="lineNum">    5955 </span><span class="lineCov">      16623 :                                         indgap + k];</span></a>
+<a name="5956"><span class="lineNum">    5956 </span><span class="lineCov">      16623 :                                 gap = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="5957"><span class="lineNum">    5957 </span>            :                             }</a>
+<a name="5958"><span class="lineNum">    5958 </span><span class="lineCov">     608139 :                             ++iter;</span></a>
+<a name="5959"><span class="lineNum">    5959 </span><span class="lineCov">     608139 :                             if (resid &gt; *tol * gap &amp;&amp; std::abs(rqcorr) &gt; eps * 4. *</span></a>
+<a name="5960"><span class="lineNum">    5960 </span><span class="lineCov">       8164 :                                      std::abs(lambda)) {</span></a>
+<a name="5961"><span class="lineNum">    5961 </span><span class="lineCov">       1285 :                                 work[k] = lambda + rqcorr;</span></a>
+<a name="5962"><span class="lineNum">    5962 </span><span class="lineCov">       1285 :                                 if (iter &lt; 8) {</span></a>
+<a name="5963"><span class="lineNum">    5963 </span><span class="lineCov">       1273 :                                     goto L90;</span></a>
+<a name="5964"><span class="lineNum">    5964 </span>            :                                 }</a>
+<a name="5965"><span class="lineNum">    5965 </span>            :                             }</a>
+<a name="5966"><span class="lineNum">    5966 </span><span class="lineCov">     606866 :                             iwork[ktot] = 1;</span></a>
+<a name="5967"><span class="lineNum">    5967 </span><span class="lineCov">     606866 :                             if (newsiz == 1) {</span></a>
+<a name="5968"><span class="lineNum">    5968 </span><span class="lineCov">     606866 :                                 ++ndone;</span></a>
+<a name="5969"><span class="lineNum">    5969 </span>            :                             }</a>
+<a name="5970"><span class="lineNum">    5970 </span><span class="lineCov">     606866 :                             zfrom = isuppz[(ktot &lt;&lt; 1) - 1];</span></a>
+<a name="5971"><span class="lineNum">    5971 </span><span class="lineCov">     606866 :                             zto = isuppz[ktot * 2];</span></a>
+<a name="5972"><span class="lineNum">    5972 </span><span class="lineCov">     606866 :                             i__5 = zto - zfrom + 1;</span></a>
+<a name="5973"><span class="lineNum">    5973 </span><span class="lineCov">     606866 :                             PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__5, &amp;nrminv, &amp;z__[ibegin + zfrom - 1 + </span></a>
+<a name="5974"><span class="lineNum">    5974 </span><span class="lineCov">     606866 :                                     ktot * z_dim1], &amp;c__1);</span></a>
+<a name="5975"><span class="lineNum">    5975 </span><span class="lineCov">     606866 :                             ++ktot;</span></a>
+<a name="5976"><span class="lineNum">    5976 </span>            :                         }</a>
+<a name="5977"><span class="lineNum">    5977 </span><span class="lineCov">     606866 :                         if (newsiz &gt; 1) {</span></a>
+<a name="5978"><span class="lineNum">    5978 </span><span class="lineNoCov">          0 :                             itmp1 = isuppz[(newftt &lt;&lt; 1) - 1];</span></a>
+<a name="5979"><span class="lineNum">    5979 </span><span class="lineNoCov">          0 :                             itmp2 = isuppz[newftt * 2];</span></a>
+<a name="5980"><span class="lineNum">    5980 </span><span class="lineNoCov">          0 :                             ktot = oldien + newlst;</span></a>
+<a name="5981"><span class="lineNum">    5981 </span>            :                             i__4 = ktot;</a>
+<a name="5982"><span class="lineNum">    5982 </span><span class="lineNoCov">          0 :                             for (p = newftt + 1; p &lt;= i__4; ++p) {</span></a>
+<a name="5983"><span class="lineNum">    5983 </span><span class="lineNoCov">          0 :                                 i__5 = p - 1;</span></a>
+<a name="5984"><span class="lineNum">    5984 </span><span class="lineNoCov">          0 :                                 for (q = newftt; q &lt;= i__5; ++q) {</span></a>
+<a name="5985"><span class="lineNum">    5985 </span><span class="lineNoCov">          0 :                                     tmp = -PLUMED_BLAS_F77_FUNC(ddot,DDOT)(&amp;in, &amp;z__[ibegin + p * </span></a>
+<a name="5986"><span class="lineNum">    5986 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1, &amp;z__[ibegin + q * </span></a>
+<a name="5987"><span class="lineNum">    5987 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1);</span></a>
+<a name="5988"><span class="lineNum">    5988 </span><span class="lineNoCov">          0 :                                     PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(&amp;in, &amp;tmp, &amp;z__[ibegin + q * </span></a>
+<a name="5989"><span class="lineNum">    5989 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1, &amp;z__[ibegin + p * </span></a>
+<a name="5990"><span class="lineNum">    5990 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1);</span></a>
+<a name="5991"><span class="lineNum">    5991 </span>            :                                 }</a>
+<a name="5992"><span class="lineNum">    5992 </span><span class="lineNoCov">          0 :                                 tmp = 1. / PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(&amp;in, &amp;z__[ibegin + p * </span></a>
+<a name="5993"><span class="lineNum">    5993 </span><span class="lineNoCov">          0 :                                         z_dim1], &amp;c__1);</span></a>
+<a name="5994"><span class="lineNum">    5994 </span><span class="lineNoCov">          0 :                                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;in, &amp;tmp, &amp;z__[ibegin + p * z_dim1], &amp;</span></a>
+<a name="5995"><span class="lineNum">    5995 </span>            :                                         c__1);</a>
+<a name="5996"><span class="lineNum">    5996 </span><span class="lineNoCov">          0 :                                 i__5 = itmp1, i__6 = isuppz[(p &lt;&lt; 1) - 1];</span></a>
+<a name="5997"><span class="lineNum">    5997 </span>            :                                 itmp1 = (i__5&lt;i__6) ? i__5 : i__6;</a>
+<a name="5998"><span class="lineNum">    5998 </span><span class="lineNoCov">          0 :                                 i__5 = itmp2, i__6 = isuppz[p * 2];</span></a>
+<a name="5999"><span class="lineNum">    5999 </span>            :                                 itmp2 = (i__5&gt;i__6) ? i__5 : i__6;</a>
+<a name="6000"><span class="lineNum">    6000 </span>            :                             }</a>
+<a name="6001"><span class="lineNum">    6001 </span>            :                             i__4 = ktot;</a>
+<a name="6002"><span class="lineNum">    6002 </span><span class="lineNoCov">          0 :                             for (p = newftt; p &lt;= i__4; ++p) {</span></a>
+<a name="6003"><span class="lineNum">    6003 </span><span class="lineNoCov">          0 :                                 isuppz[(p &lt;&lt; 1) - 1] = itmp1;</span></a>
+<a name="6004"><span class="lineNum">    6004 </span><span class="lineNoCov">          0 :                                 isuppz[p * 2] = itmp2;</span></a>
+<a name="6005"><span class="lineNum">    6005 </span>            :                             }</a>
+<a name="6006"><span class="lineNum">    6006 </span><span class="lineNoCov">          0 :                             ndone += newsiz;</span></a>
+<a name="6007"><span class="lineNum">    6007 </span>            :                         }</a>
+<a name="6008"><span class="lineNum">    6008 </span>            :                     }</a>
+<a name="6009"><span class="lineNum">    6009 </span><span class="lineCov">     606936 :                     newfrs = j + 1;</span></a>
+<a name="6010"><span class="lineNum">    6010 </span>            :                 }</a>
+<a name="6011"><span class="lineNum">    6011 </span>            :             }</a>
+<a name="6012"><span class="lineNum">    6012 </span><span class="lineCov">     569970 :             ++ndepth;</span></a>
+<a name="6013"><span class="lineNum">    6013 </span><span class="lineCov">     569970 :             goto L40;</span></a>
+<a name="6014"><span class="lineNum">    6014 </span>            :         }</a>
+<a name="6015"><span class="lineNum">    6015 </span><span class="lineCov">     569963 :         j = wbegin &lt;&lt; 1;</span></a>
+<a name="6016"><span class="lineNum">    6016 </span>            :         i__2 = wend;</a>
+<a name="6017"><span class="lineNum">    6017 </span><span class="lineCov">    1176829 :         for (i__ = wbegin; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="6018"><span class="lineNum">    6018 </span><span class="lineCov">     606866 :             isuppz[j - 1] += oldien;</span></a>
+<a name="6019"><span class="lineNum">    6019 </span><span class="lineCov">     606866 :             isuppz[j] += oldien;</span></a>
+<a name="6020"><span class="lineNum">    6020 </span><span class="lineCov">     606866 :             j += 2;</span></a>
+<a name="6021"><span class="lineNum">    6021 </span>            : </a>
+<a name="6022"><span class="lineNum">    6022 </span>            :         }</a>
+<a name="6023"><span class="lineNum">    6023 </span><span class="lineCov">     569963 :         ibegin = iend + 1;</span></a>
+<a name="6024"><span class="lineNum">    6024 </span><span class="lineCov">     569963 :         wbegin = wend + 1;</span></a>
+<a name="6025"><span class="lineNum">    6025 </span>            :     }</a>
+<a name="6026"><span class="lineNum">    6026 </span>            : </a>
+<a name="6027"><span class="lineNum">    6027 </span>            :     return;</a>
+<a name="6028"><span class="lineNum">    6028 </span>            : </a>
+<a name="6029"><span class="lineNum">    6029 </span>            : } </a>
+<a name="6030"><span class="lineNum">    6030 </span>            : }</a>
+<a name="6031"><span class="lineNum">    6031 </span>            : }</a>
+<a name="6032"><span class="lineNum">    6032 </span>            : #include &lt;cmath&gt;</a>
+<a name="6033"><span class="lineNum">    6033 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6034"><span class="lineNum">    6034 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="6035"><span class="lineNum">    6035 </span>            : </a>
+<a name="6036"><span class="lineNum">    6036 </span>            : #include &quot;real.h&quot;</a>
+<a name="6037"><span class="lineNum">    6037 </span>            : </a>
+<a name="6038"><span class="lineNum">    6038 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6039"><span class="lineNum">    6039 </span>            : namespace PLMD{</a>
+<a name="6040"><span class="lineNum">    6040 </span>            : namespace lapack{</a>
+<a name="6041"><span class="lineNum">    6041 </span>            : using namespace blas;</a>
+<a name="6042"><span class="lineNum">    6042 </span>            : void</a>
+<a name="6043"><span class="lineNum">    6043 </span><span class="lineCov">      90519 : PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(double *f,</span></a>
+<a name="6044"><span class="lineNum">    6044 </span>            :         double *g,</a>
+<a name="6045"><span class="lineNum">    6045 </span>            :         double *cs,</a>
+<a name="6046"><span class="lineNum">    6046 </span>            :         double *sn,</a>
+<a name="6047"><span class="lineNum">    6047 </span>            :         double *r)</a>
+<a name="6048"><span class="lineNum">    6048 </span>            : {</a>
+<a name="6049"><span class="lineNum">    6049 </span>            :   double minval,safemin, safemin2, safemx2, eps;</a>
+<a name="6050"><span class="lineNum">    6050 </span>            :   double f1,g1,f1a,g1a,scale;</a>
+<a name="6051"><span class="lineNum">    6051 </span>            :   int i,n,count;</a>
+<a name="6052"><span class="lineNum">    6052 </span>            : </a>
+<a name="6053"><span class="lineNum">    6053 </span>            :   eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="6054"><span class="lineNum">    6054 </span>            :   minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="6055"><span class="lineNum">    6055 </span>            :   safemin = minval*(1.0+eps);</a>
+<a name="6056"><span class="lineNum">    6056 </span>            :   n = static_cast&lt;int&gt;(0.5*std::log( safemin/eps ) / std::log(2.0));</a>
+<a name="6057"><span class="lineNum">    6057 </span>            :   safemin2 = std::pow(2.0,static_cast&lt;double&gt;(n));</a>
+<a name="6058"><span class="lineNum">    6058 </span>            : </a>
+<a name="6059"><span class="lineNum">    6059 </span>            :   safemx2 = 1.0 / safemin2;</a>
+<a name="6060"><span class="lineNum">    6060 </span>            : </a>
+<a name="6061"><span class="lineNum">    6061 </span><span class="lineCov">      90519 :   if(std::abs(*g)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="6062"><span class="lineNum">    6062 </span><span class="lineNoCov">          0 :     *cs = 1.0;</span></a>
+<a name="6063"><span class="lineNum">    6063 </span><span class="lineNoCov">          0 :     *sn = 0.0;</span></a>
+<a name="6064"><span class="lineNum">    6064 </span><span class="lineNoCov">          0 :     *r = *f;</span></a>
+<a name="6065"><span class="lineNum">    6065 </span><span class="lineCov">      90519 :   } else if (std::abs(*f)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="6066"><span class="lineNum">    6066 </span><span class="lineCov">          1 :     *cs = 0.0;</span></a>
+<a name="6067"><span class="lineNum">    6067 </span><span class="lineCov">          1 :     *sn = 1.0;</span></a>
+<a name="6068"><span class="lineNum">    6068 </span><span class="lineCov">          1 :     *r = *g;</span></a>
+<a name="6069"><span class="lineNum">    6069 </span>            :   } else {</a>
+<a name="6070"><span class="lineNum">    6070 </span>            :     f1 = *f;</a>
+<a name="6071"><span class="lineNum">    6071 </span>            :     g1 = *g;</a>
+<a name="6072"><span class="lineNum">    6072 </span>            :     f1a = std::abs(f1);</a>
+<a name="6073"><span class="lineNum">    6073 </span>            :     g1a = std::abs(g1);</a>
+<a name="6074"><span class="lineNum">    6074 </span><span class="lineCov">      90518 :     scale = (f1a &gt; g1a) ? f1a : g1a;</span></a>
+<a name="6075"><span class="lineNum">    6075 </span><span class="lineCov">      90518 :     if(scale &gt;= safemx2) {</span></a>
+<a name="6076"><span class="lineNum">    6076 </span>            :       count = 0;</a>
+<a name="6077"><span class="lineNum">    6077 </span><span class="lineNoCov">          0 :       while(scale &gt;= safemx2) {</span></a>
+<a name="6078"><span class="lineNum">    6078 </span><span class="lineNoCov">          0 :         count++;</span></a>
+<a name="6079"><span class="lineNum">    6079 </span><span class="lineNoCov">          0 :         f1 *= safemin2;</span></a>
+<a name="6080"><span class="lineNum">    6080 </span><span class="lineNoCov">          0 :         g1 *= safemin2;</span></a>
+<a name="6081"><span class="lineNum">    6081 </span>            :         f1a = std::abs(f1);</a>
+<a name="6082"><span class="lineNum">    6082 </span>            :         g1a = std::abs(g1);</a>
+<a name="6083"><span class="lineNum">    6083 </span><span class="lineNoCov">          0 :         scale = (f1a &gt; g1a) ? f1a : g1a;</span></a>
+<a name="6084"><span class="lineNum">    6084 </span>            :       }</a>
+<a name="6085"><span class="lineNum">    6085 </span><span class="lineNoCov">          0 :       *r =  std::sqrt(f1*f1 + g1*g1);</span></a>
+<a name="6086"><span class="lineNum">    6086 </span><span class="lineNoCov">          0 :       *cs = f1 / *r;</span></a>
+<a name="6087"><span class="lineNum">    6087 </span><span class="lineNoCov">          0 :       *sn = g1 / *r;</span></a>
+<a name="6088"><span class="lineNum">    6088 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;count;i++)</span></a>
+<a name="6089"><span class="lineNum">    6089 </span><span class="lineNoCov">          0 :         *r *= safemx2;</span></a>
+<a name="6090"><span class="lineNum">    6090 </span><span class="lineCov">      90518 :     } else if (scale&lt;=safemin2) {</span></a>
+<a name="6091"><span class="lineNum">    6091 </span>            :       count = 0;</a>
+<a name="6092"><span class="lineNum">    6092 </span><span class="lineNoCov">          0 :       while(scale &lt;= safemin2) {</span></a>
+<a name="6093"><span class="lineNum">    6093 </span><span class="lineNoCov">          0 :         count++;</span></a>
+<a name="6094"><span class="lineNum">    6094 </span><span class="lineNoCov">          0 :         f1 *= safemx2;</span></a>
+<a name="6095"><span class="lineNum">    6095 </span><span class="lineNoCov">          0 :         g1 *= safemx2;</span></a>
+<a name="6096"><span class="lineNum">    6096 </span>            :         f1a = std::abs(f1);</a>
+<a name="6097"><span class="lineNum">    6097 </span>            :         g1a = std::abs(g1);</a>
+<a name="6098"><span class="lineNum">    6098 </span><span class="lineNoCov">          0 :         scale = (f1a &gt; g1a) ? f1a : g1a;</span></a>
+<a name="6099"><span class="lineNum">    6099 </span>            :       }</a>
+<a name="6100"><span class="lineNum">    6100 </span><span class="lineNoCov">          0 :       *r =  std::sqrt(f1*f1 + g1*g1);</span></a>
+<a name="6101"><span class="lineNum">    6101 </span><span class="lineNoCov">          0 :       *cs = f1 / *r;</span></a>
+<a name="6102"><span class="lineNum">    6102 </span><span class="lineNoCov">          0 :       *sn = g1 / *r;</span></a>
+<a name="6103"><span class="lineNum">    6103 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;count;i++)</span></a>
+<a name="6104"><span class="lineNum">    6104 </span><span class="lineNoCov">          0 :         *r *= safemin2;</span></a>
+<a name="6105"><span class="lineNum">    6105 </span>            :     } else {</a>
+<a name="6106"><span class="lineNum">    6106 </span><span class="lineCov">      90518 :       *r =  std::sqrt(f1*f1 + g1*g1);</span></a>
+<a name="6107"><span class="lineNum">    6107 </span><span class="lineCov">      90518 :       *cs = f1 / *r;</span></a>
+<a name="6108"><span class="lineNum">    6108 </span><span class="lineCov">      90518 :       *sn = g1 / *r;</span></a>
+<a name="6109"><span class="lineNum">    6109 </span>            :     }</a>
+<a name="6110"><span class="lineNum">    6110 </span><span class="lineCov">      90518 :     if(std::abs(*f)&gt;std::abs(*g) &amp;&amp; *cs&lt;0.0) {</span></a>
+<a name="6111"><span class="lineNum">    6111 </span><span class="lineCov">      18497 :       *cs *= -1.0;</span></a>
+<a name="6112"><span class="lineNum">    6112 </span><span class="lineCov">      18497 :       *sn *= -1.0;</span></a>
+<a name="6113"><span class="lineNum">    6113 </span><span class="lineCov">      18497 :       *r  *= -1.0;</span></a>
+<a name="6114"><span class="lineNum">    6114 </span>            :     }</a>
+<a name="6115"><span class="lineNum">    6115 </span>            :   }</a>
+<a name="6116"><span class="lineNum">    6116 </span><span class="lineCov">      90519 :   return;</span></a>
+<a name="6117"><span class="lineNum">    6117 </span>            : }</a>
+<a name="6118"><span class="lineNum">    6118 </span>            :       </a>
+<a name="6119"><span class="lineNum">    6119 </span>            : }</a>
+<a name="6120"><span class="lineNum">    6120 </span>            : }</a>
+<a name="6121"><span class="lineNum">    6121 </span>            : #include &lt;cmath&gt;</a>
+<a name="6122"><span class="lineNum">    6122 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6123"><span class="lineNum">    6123 </span>            : </a>
+<a name="6124"><span class="lineNum">    6124 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6125"><span class="lineNum">    6125 </span>            : namespace PLMD{</a>
+<a name="6126"><span class="lineNum">    6126 </span>            : namespace lapack{</a>
+<a name="6127"><span class="lineNum">    6127 </span>            : using namespace blas;</a>
+<a name="6128"><span class="lineNum">    6128 </span>            : void</a>
+<a name="6129"><span class="lineNum">    6129 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlaruv,DLARUV)(int *iseed, int *n, double *x)</span></a>
+<a name="6130"><span class="lineNum">    6130 </span>            : {</a>
+<a name="6131"><span class="lineNum">    6131 </span>            :   const int</a>
+<a name="6132"><span class="lineNum">    6132 </span><span class="lineNoCov">          0 :     mm[512] = {</span></a>
+<a name="6133"><span class="lineNum">    6133 </span>            :       494,2637,255,2008,1253,</a>
+<a name="6134"><span class="lineNum">    6134 </span>            :       3344,4084,1739,3143,3468,688,1657,1238,3166,1292,3422,1270,2016,</a>
+<a name="6135"><span class="lineNum">    6135 </span>            :       154,2862,697,1706,491,931,1444,444,3577,3944,2184,1661,3482,657,</a>
+<a name="6136"><span class="lineNum">    6136 </span>            :       3023,3618,1267,1828,164,3798,3087,2400,2870,3876,1905,1593,1797,</a>
+<a name="6137"><span class="lineNum">    6137 </span>            :       1234,3460,328,2861,1950,617,2070,3331,769,1558,2412,2800,189,287,</a>
+<a name="6138"><span class="lineNum">    6138 </span>            :       2045,1227,2838,209,2770,3654,3993,192,2253,3491,2889,2857,2094,</a>
+<a name="6139"><span class="lineNum">    6139 </span>            :       1818,688,1407,634,3231,815,3524,1914,516,164,303,2144,3480,119,</a>
+<a name="6140"><span class="lineNum">    6140 </span>            :       3357,837,2826,2332,2089,3780,1700,3712,150,2000,3375,1621,3090,</a>
+<a name="6141"><span class="lineNum">    6141 </span>            :       3765,1149,3146,33,3082,2741,359,3316,1749,185,2784,2202,2199,1364,</a>
+<a name="6142"><span class="lineNum">    6142 </span>            :       1244,2020,3160,2785,2772,1217,1822,1245,2252,3904,2774,997,2573,</a>
+<a name="6143"><span class="lineNum">    6143 </span>            :       1148,545,322,789,1440,752,2859,123,1848,643,2405,2638,2344,46,</a>
+<a name="6144"><span class="lineNum">    6144 </span>            :       3814,913,3649,339,3808,822,2832,3078,3633,2970,637,2249,2081,4019,</a>
+<a name="6145"><span class="lineNum">    6145 </span>            :       1478,242,481,2075,4058,622,3376,812,234,641,4005,1122,3135,2640,</a>
+<a name="6146"><span class="lineNum">    6146 </span>            :       2302,40,1832,2247,2034,2637,1287,1691,496,1597,2394,2584,1843,336,</a>
+<a name="6147"><span class="lineNum">    6147 </span>            :       1472,2407,433,2096,1761,2810,566,442,41,1238,1086,603,840,3168,</a>
+<a name="6148"><span class="lineNum">    6148 </span>            :       1499,1084,3438,2408,1589,2391,288,26,512,1456,171,1677,2657,2270,</a>
+<a name="6149"><span class="lineNum">    6149 </span>            :       2587,2961,1970,1817,676,1410,3723,2803,3185,184,663,499,3784,1631,</a>
+<a name="6150"><span class="lineNum">    6150 </span>            :       1925,3912,1398,1349,1441,2224,2411,1907,3192,2786,382,37,759,2948,</a>
+<a name="6151"><span class="lineNum">    6151 </span>            :       1862,3802,2423,2051,2295,1332,1832,2405,3638,3661,327,3660,716,</a>
+<a name="6152"><span class="lineNum">    6152 </span>            :       1842,3987,1368,1848,2366,2508,3754,1766,3572,2893,307,1297,3966,</a>
+<a name="6153"><span class="lineNum">    6153 </span>            :       758,2598,3406,2922,1038,2934,2091,2451,1580,1958,2055,1507,1078,</a>
+<a name="6154"><span class="lineNum">    6154 </span>            :       3273,17,854,2916,3971,2889,3831,2621,1541,893,736,3992,787,2125,</a>
+<a name="6155"><span class="lineNum">    6155 </span>            :       2364,2460,257,1574,3912,1216,3248,3401,2124,2762,149,2245,166,466,</a>
+<a name="6156"><span class="lineNum">    6156 </span>            :       4018,1399,190,2879,153,2320,18,712,2159,2318,2091,3443,1510,449,</a>
+<a name="6157"><span class="lineNum">    6157 </span>            :       1956,2201,3137,3399,1321,2271,3667,2703,629,2365,2431,1113,3922,</a>
+<a name="6158"><span class="lineNum">    6158 </span>            :       2554,184,2099,3228,4012,1921,3452,3901,572,3309,3171,817,3039,</a>
+<a name="6159"><span class="lineNum">    6159 </span>            :       1696,1256,3715,2077,3019,1497,1101,717,51,981,1978,1813,3881,76,</a>
+<a name="6160"><span class="lineNum">    6160 </span>            :       3846,3694,1682,124,1660,3997,479,1141,886,3514,1301,3604,1888,</a>
+<a name="6161"><span class="lineNum">    6161 </span>            :       1836,1990,2058,692,1194,20,3285,2046,2107,3508,3525,3801,2549,</a>
+<a name="6162"><span class="lineNum">    6162 </span>            :       1145,2253,305,3301,1065,3133,2913,3285,1241,1197,3729,2501,1673,</a>
+<a name="6163"><span class="lineNum">    6163 </span>            :       541,2753,949,2361,1165,4081,2725,3305,3069,3617,3733,409,2157,</a>
+<a name="6164"><span class="lineNum">    6164 </span>            :       1361,3973,1865,2525,1409,3445,3577,77,3761,2149,1449,3005,225,85,</a>
+<a name="6165"><span class="lineNum">    6165 </span>            :       3673,3117,3089,1349,2057,413,65,1845,697,3085,3441,1573,3689,2941,</a>
+<a name="6166"><span class="lineNum">    6166 </span>            :       929,533,2841,4077,721,2821,2249,2397,2817,245,1913,1997,3121,997,</a>
+<a name="6167"><span class="lineNum">    6167 </span>            :       1833,2877,1633,981,2009,941,2449,197,2441,285,1473,2741,3129,909,</a>
+<a name="6168"><span class="lineNum">    6168 </span>            :       2801,421,4073,2813,2337,1429,1177,1901,81,1669,2633,2269,129,1141,</a>
+<a name="6169"><span class="lineNum">    6169 </span>            :       249,3917,2481,3941,2217,2749,3041,1877,345,2861,1809,3141,2825,</a>
+<a name="6170"><span class="lineNum">    6170 </span>            :       157,2881,3637,1465,2829,2161,3365,361,2685,3745,2325,3609,3821,</a>
+<a name="6171"><span class="lineNum">    6171 </span>            :       3537,517,3017,2141,1537 </a>
+<a name="6172"><span class="lineNum">    6172 </span>            :     };</a>
+<a name="6173"><span class="lineNum">    6173 </span>            : </a>
+<a name="6174"><span class="lineNum">    6174 </span>            :     int i__1;</a>
+<a name="6175"><span class="lineNum">    6175 </span>            : </a>
+<a name="6176"><span class="lineNum">    6176 </span>            :     int i__, i1, i2, i3, i4, it1, it2, it3, it4;</a>
+<a name="6177"><span class="lineNum">    6177 </span>            : </a>
+<a name="6178"><span class="lineNum">    6178 </span>            : </a>
+<a name="6179"><span class="lineNum">    6179 </span>            :     --iseed;</a>
+<a name="6180"><span class="lineNum">    6180 </span>            :     --x;</a>
+<a name="6181"><span class="lineNum">    6181 </span>            : </a>
+<a name="6182"><span class="lineNum">    6182 </span>            :     it1 = it2 = it3 = it4 = 0;</a>
+<a name="6183"><span class="lineNum">    6183 </span>            : </a>
+<a name="6184"><span class="lineNum">    6184 </span><span class="lineNoCov">          0 :     i1 = iseed[1];</span></a>
+<a name="6185"><span class="lineNum">    6185 </span><span class="lineNoCov">          0 :     i2 = iseed[2];</span></a>
+<a name="6186"><span class="lineNum">    6186 </span><span class="lineNoCov">          0 :     i3 = iseed[3];</span></a>
+<a name="6187"><span class="lineNum">    6187 </span><span class="lineNoCov">          0 :     i4 = iseed[4];</span></a>
+<a name="6188"><span class="lineNum">    6188 </span>            : </a>
+<a name="6189"><span class="lineNum">    6189 </span><span class="lineNoCov">          0 :     i__1 = (*n&lt;128) ? *n : 128;</span></a>
+<a name="6190"><span class="lineNum">    6190 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6191"><span class="lineNum">    6191 </span>            : </a>
+<a name="6192"><span class="lineNum">    6192 </span><span class="lineNoCov">          0 :         it4 = i4 * mm[i__ + 383];</span></a>
+<a name="6193"><span class="lineNum">    6193 </span><span class="lineNoCov">          0 :         it3 = it4 / 4096;</span></a>
+<a name="6194"><span class="lineNum">    6194 </span><span class="lineNoCov">          0 :         it4 -= it3 &lt;&lt; 12;</span></a>
+<a name="6195"><span class="lineNum">    6195 </span><span class="lineNoCov">          0 :         it3 = it3 + i3 * mm[i__ + 383] + i4 * mm[i__ + 255];</span></a>
+<a name="6196"><span class="lineNum">    6196 </span><span class="lineNoCov">          0 :         it2 = it3 / 4096;</span></a>
+<a name="6197"><span class="lineNum">    6197 </span><span class="lineNoCov">          0 :         it3 -= it2 &lt;&lt; 12;</span></a>
+<a name="6198"><span class="lineNum">    6198 </span><span class="lineNoCov">          0 :         it2 = it2 + i2 * mm[i__ + 383] + i3 * mm[i__ + 255] + </span></a>
+<a name="6199"><span class="lineNum">    6199 </span><span class="lineNoCov">          0 :           i4 * mm[i__ + 127];</span></a>
+<a name="6200"><span class="lineNum">    6200 </span><span class="lineNoCov">          0 :         it1 = it2 / 4096;</span></a>
+<a name="6201"><span class="lineNum">    6201 </span><span class="lineNoCov">          0 :         it2 -= it1 &lt;&lt; 12;</span></a>
+<a name="6202"><span class="lineNum">    6202 </span><span class="lineNoCov">          0 :         it1 = it1 + i1 * mm[i__ + 383] + i2 * mm[i__ + 255] + </span></a>
+<a name="6203"><span class="lineNum">    6203 </span><span class="lineNoCov">          0 :           i3 * mm[i__ + 127] + i4 * mm[i__ - 1];</span></a>
+<a name="6204"><span class="lineNum">    6204 </span><span class="lineNoCov">          0 :         it1 %= 4096;</span></a>
+<a name="6205"><span class="lineNum">    6205 </span>            : </a>
+<a name="6206"><span class="lineNum">    6206 </span><span class="lineNoCov">          0 :         x[i__] = ((double) it1 + ((double) it2 + ((double) it3 + (</span></a>
+<a name="6207"><span class="lineNum">    6207 </span><span class="lineNoCov">          0 :                 double) it4 * 2.44140625e-4) * 2.44140625e-4) * </span></a>
+<a name="6208"><span class="lineNum">    6208 </span><span class="lineNoCov">          0 :                 2.44140625e-4) * 2.44140625e-4;</span></a>
+<a name="6209"><span class="lineNum">    6209 </span>            :     }</a>
+<a name="6210"><span class="lineNum">    6210 </span>            : </a>
+<a name="6211"><span class="lineNum">    6211 </span><span class="lineNoCov">          0 :     iseed[1] = it1;</span></a>
+<a name="6212"><span class="lineNum">    6212 </span><span class="lineNoCov">          0 :     iseed[2] = it2;</span></a>
+<a name="6213"><span class="lineNum">    6213 </span><span class="lineNoCov">          0 :     iseed[3] = it3;</span></a>
+<a name="6214"><span class="lineNum">    6214 </span><span class="lineNoCov">          0 :     iseed[4] = it4;</span></a>
+<a name="6215"><span class="lineNum">    6215 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="6216"><span class="lineNum">    6216 </span>            : </a>
+<a name="6217"><span class="lineNum">    6217 </span>            : } </a>
+<a name="6218"><span class="lineNum">    6218 </span>            : }</a>
+<a name="6219"><span class="lineNum">    6219 </span>            : }</a>
+<a name="6220"><span class="lineNum">    6220 </span>            : #include &lt;cmath&gt;</a>
+<a name="6221"><span class="lineNum">    6221 </span>            : #include &quot;real.h&quot;</a>
+<a name="6222"><span class="lineNum">    6222 </span>            : </a>
+<a name="6223"><span class="lineNum">    6223 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6224"><span class="lineNum">    6224 </span>            : </a>
+<a name="6225"><span class="lineNum">    6225 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6226"><span class="lineNum">    6226 </span>            : namespace PLMD{</a>
+<a name="6227"><span class="lineNum">    6227 </span>            : namespace lapack{</a>
+<a name="6228"><span class="lineNum">    6228 </span>            : using namespace blas;</a>
+<a name="6229"><span class="lineNum">    6229 </span>            : void</a>
+<a name="6230"><span class="lineNum">    6230 </span><span class="lineCov">       4552 : PLUMED_BLAS_F77_FUNC(dlas2,DLAS2)(double *f,</span></a>
+<a name="6231"><span class="lineNum">    6231 </span>            :        double *g,</a>
+<a name="6232"><span class="lineNum">    6232 </span>            :        double *h,</a>
+<a name="6233"><span class="lineNum">    6233 </span>            :        double *ssmin,</a>
+<a name="6234"><span class="lineNum">    6234 </span>            :        double *ssmax)</a>
+<a name="6235"><span class="lineNum">    6235 </span>            : {</a>
+<a name="6236"><span class="lineNum">    6236 </span><span class="lineCov">       4552 :   double fa = std::abs(*f);</span></a>
+<a name="6237"><span class="lineNum">    6237 </span><span class="lineCov">       4552 :   double ga = std::abs(*g);</span></a>
+<a name="6238"><span class="lineNum">    6238 </span><span class="lineCov">       4552 :   double ha = std::abs(*h);</span></a>
+<a name="6239"><span class="lineNum">    6239 </span>            :   double fhmin,fhmax,tmax,tmin,tmp1,tmp2;</a>
+<a name="6240"><span class="lineNum">    6240 </span>            :   double as,at,au,c;</a>
+<a name="6241"><span class="lineNum">    6241 </span>            : </a>
+<a name="6242"><span class="lineNum">    6242 </span><span class="lineCov">       4552 :   fhmin = (fa&lt;ha) ? fa : ha;</span></a>
+<a name="6243"><span class="lineNum">    6243 </span><span class="lineCov">       4552 :   fhmax = (fa&gt;ha) ? fa : ha;</span></a>
+<a name="6244"><span class="lineNum">    6244 </span>            :   </a>
+<a name="6245"><span class="lineNum">    6245 </span><span class="lineCov">       4552 :   if(std::abs(fhmin)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="6246"><span class="lineNum">    6246 </span><span class="lineNoCov">          0 :     *ssmin = 0.0;</span></a>
+<a name="6247"><span class="lineNum">    6247 </span><span class="lineNoCov">          0 :     if(std::abs(fhmax)&lt;PLUMED_GMX_DOUBLE_MIN) </span></a>
+<a name="6248"><span class="lineNum">    6248 </span><span class="lineNoCov">          0 :       *ssmax = ga;</span></a>
+<a name="6249"><span class="lineNum">    6249 </span>            :     else {</a>
+<a name="6250"><span class="lineNum">    6250 </span><span class="lineNoCov">          0 :       tmax = (fhmax&gt;ga) ? fhmax : ga;</span></a>
+<a name="6251"><span class="lineNum">    6251 </span><span class="lineNoCov">          0 :       tmin = (fhmax&lt;ga) ? fhmax : ga;</span></a>
+<a name="6252"><span class="lineNum">    6252 </span><span class="lineNoCov">          0 :       tmp1 = tmin / tmax;</span></a>
+<a name="6253"><span class="lineNum">    6253 </span><span class="lineNoCov">          0 :       tmp1 = tmp1 * tmp1;</span></a>
+<a name="6254"><span class="lineNum">    6254 </span><span class="lineNoCov">          0 :       *ssmax = tmax* std::sqrt(1.0 + tmp1);</span></a>
+<a name="6255"><span class="lineNum">    6255 </span>            :     }</a>
+<a name="6256"><span class="lineNum">    6256 </span>            :   } else {</a>
+<a name="6257"><span class="lineNum">    6257 </span><span class="lineCov">       4552 :     if(ga&lt;fhmax) {</span></a>
+<a name="6258"><span class="lineNum">    6258 </span><span class="lineCov">       4526 :       as = 1.0 + fhmin / fhmax;</span></a>
+<a name="6259"><span class="lineNum">    6259 </span><span class="lineCov">       4526 :       at = (fhmax-fhmin) / fhmax;</span></a>
+<a name="6260"><span class="lineNum">    6260 </span><span class="lineCov">       4526 :       au = (ga/fhmax);</span></a>
+<a name="6261"><span class="lineNum">    6261 </span><span class="lineCov">       4526 :       au = au * au;</span></a>
+<a name="6262"><span class="lineNum">    6262 </span><span class="lineCov">       4526 :       c = 2.0 / (  std::sqrt(as*as+au) + std::sqrt(at*at+au) );</span></a>
+<a name="6263"><span class="lineNum">    6263 </span><span class="lineCov">       4526 :       *ssmin = fhmin * c;</span></a>
+<a name="6264"><span class="lineNum">    6264 </span><span class="lineCov">       4526 :       *ssmax = fhmax / c;</span></a>
+<a name="6265"><span class="lineNum">    6265 </span>            :     } else {</a>
+<a name="6266"><span class="lineNum">    6266 </span><span class="lineCov">         26 :       au = fhmax / ga;</span></a>
+<a name="6267"><span class="lineNum">    6267 </span><span class="lineCov">         26 :       if(std::abs(au)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="6268"><span class="lineNum">    6268 </span><span class="lineNoCov">          0 :         *ssmin = (fhmin*fhmax)/ga;</span></a>
+<a name="6269"><span class="lineNum">    6269 </span><span class="lineNoCov">          0 :         *ssmax = ga;</span></a>
+<a name="6270"><span class="lineNum">    6270 </span>            :       } else {</a>
+<a name="6271"><span class="lineNum">    6271 </span><span class="lineCov">         26 :         as = 1.0 + fhmin / fhmax;</span></a>
+<a name="6272"><span class="lineNum">    6272 </span><span class="lineCov">         26 :         at = (fhmax-fhmin)/fhmax;</span></a>
+<a name="6273"><span class="lineNum">    6273 </span><span class="lineCov">         26 :         tmp1 = as*au;</span></a>
+<a name="6274"><span class="lineNum">    6274 </span><span class="lineCov">         26 :         tmp2 = at*au;</span></a>
+<a name="6275"><span class="lineNum">    6275 </span><span class="lineCov">         26 :         c = 1.0 / (  std::sqrt(1.0+tmp1*tmp1) + std::sqrt(1.0+tmp2*tmp2));</span></a>
+<a name="6276"><span class="lineNum">    6276 </span><span class="lineCov">         26 :         *ssmin = (fhmin*c)*au;</span></a>
+<a name="6277"><span class="lineNum">    6277 </span><span class="lineCov">         26 :         *ssmin = *ssmin + *ssmin;</span></a>
+<a name="6278"><span class="lineNum">    6278 </span><span class="lineCov">         26 :         *ssmax = ga / (c+c);</span></a>
+<a name="6279"><span class="lineNum">    6279 </span>            :       }</a>
+<a name="6280"><span class="lineNum">    6280 </span>            :     }</a>
+<a name="6281"><span class="lineNum">    6281 </span>            :   }</a>
+<a name="6282"><span class="lineNum">    6282 </span><span class="lineCov">       4552 :   return;</span></a>
+<a name="6283"><span class="lineNum">    6283 </span>            : }</a>
+<a name="6284"><span class="lineNum">    6284 </span>            : }</a>
+<a name="6285"><span class="lineNum">    6285 </span>            : }</a>
+<a name="6286"><span class="lineNum">    6286 </span>            : #include &lt;cctype&gt;</a>
+<a name="6287"><span class="lineNum">    6287 </span>            : #include &lt;cmath&gt;</a>
+<a name="6288"><span class="lineNum">    6288 </span>            : #include &quot;real.h&quot;</a>
+<a name="6289"><span class="lineNum">    6289 </span>            : </a>
+<a name="6290"><span class="lineNum">    6290 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6291"><span class="lineNum">    6291 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="6292"><span class="lineNum">    6292 </span>            : </a>
+<a name="6293"><span class="lineNum">    6293 </span>            : </a>
+<a name="6294"><span class="lineNum">    6294 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6295"><span class="lineNum">    6295 </span>            : namespace PLMD{</a>
+<a name="6296"><span class="lineNum">    6296 </span>            : namespace lapack{</a>
+<a name="6297"><span class="lineNum">    6297 </span>            : using namespace blas;</a>
+<a name="6298"><span class="lineNum">    6298 </span>            : void</a>
+<a name="6299"><span class="lineNum">    6299 </span><span class="lineCov">        264 : PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(const char *type,</span></a>
+<a name="6300"><span class="lineNum">    6300 </span>            :                         int *kl,</a>
+<a name="6301"><span class="lineNum">    6301 </span>            :                         int *ku,</a>
+<a name="6302"><span class="lineNum">    6302 </span>            :                         double *cfrom,</a>
+<a name="6303"><span class="lineNum">    6303 </span>            :                         double *cto,</a>
+<a name="6304"><span class="lineNum">    6304 </span>            :                         int *m,</a>
+<a name="6305"><span class="lineNum">    6305 </span>            :                         int *n,</a>
+<a name="6306"><span class="lineNum">    6306 </span>            :                         double *a,</a>
+<a name="6307"><span class="lineNum">    6307 </span>            :                         int *lda,</a>
+<a name="6308"><span class="lineNum">    6308 </span>            :                         int *info)</a>
+<a name="6309"><span class="lineNum">    6309 </span>            : {</a>
+<a name="6310"><span class="lineNum">    6310 </span><span class="lineCov">        264 :   const char ch=std::toupper(*type);</span></a>
+<a name="6311"><span class="lineNum">    6311 </span>            :   int i,j,k,l,k1,k2,k3,k4;</a>
+<a name="6312"><span class="lineNum">    6312 </span>            :   int done=0;</a>
+<a name="6313"><span class="lineNum">    6313 </span>            :   double minval,smlnum,bignum;</a>
+<a name="6314"><span class="lineNum">    6314 </span>            :   double cfromc, ctoc, cfrom1, cto1, mul;</a>
+<a name="6315"><span class="lineNum">    6315 </span>            : </a>
+<a name="6316"><span class="lineNum">    6316 </span><span class="lineCov">        264 :   if(*n&lt;=0 || *m&lt;=0)</span></a>
+<a name="6317"><span class="lineNum">    6317 </span>            :     return;</a>
+<a name="6318"><span class="lineNum">    6318 </span>            : </a>
+<a name="6319"><span class="lineNum">    6319 </span>            :   minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="6320"><span class="lineNum">    6320 </span>            :   smlnum = minval / PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="6321"><span class="lineNum">    6321 </span>            :   bignum = 1.0 / smlnum;</a>
+<a name="6322"><span class="lineNum">    6322 </span>            : </a>
+<a name="6323"><span class="lineNum">    6323 </span><span class="lineCov">        264 :   cfromc = *cfrom;</span></a>
+<a name="6324"><span class="lineNum">    6324 </span><span class="lineCov">        264 :   ctoc   = *cto;</span></a>
+<a name="6325"><span class="lineNum">    6325 </span>            : </a>
+<a name="6326"><span class="lineNum">    6326 </span><span class="lineCov">        528 :   while(!done) {</span></a>
+<a name="6327"><span class="lineNum">    6327 </span>            :     </a>
+<a name="6328"><span class="lineNum">    6328 </span><span class="lineCov">        264 :     cfrom1 = cfromc * smlnum;</span></a>
+<a name="6329"><span class="lineNum">    6329 </span><span class="lineCov">        264 :     cto1   = ctoc / bignum;</span></a>
+<a name="6330"><span class="lineNum">    6330 </span>            : </a>
+<a name="6331"><span class="lineNum">    6331 </span><span class="lineCov">        264 :     if(std::abs(cfrom1)&gt;std::abs(ctoc) &amp;&amp; std::abs(ctoc)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="6332"><span class="lineNum">    6332 </span>            :       mul = smlnum;</a>
+<a name="6333"><span class="lineNum">    6333 </span>            :       done = 0;</a>
+<a name="6334"><span class="lineNum">    6334 </span>            :       cfromc = cfrom1;</a>
+<a name="6335"><span class="lineNum">    6335 </span><span class="lineCov">        264 :     } else if(std::abs(cto1)&gt;std::abs(cfromc)) {</span></a>
+<a name="6336"><span class="lineNum">    6336 </span>            :       mul = bignum;</a>
+<a name="6337"><span class="lineNum">    6337 </span>            :       done = 0;</a>
+<a name="6338"><span class="lineNum">    6338 </span>            :       ctoc = cto1;</a>
+<a name="6339"><span class="lineNum">    6339 </span>            :     } else {</a>
+<a name="6340"><span class="lineNum">    6340 </span><span class="lineCov">        264 :       mul = ctoc / cfromc;</span></a>
+<a name="6341"><span class="lineNum">    6341 </span>            :       done = 1;</a>
+<a name="6342"><span class="lineNum">    6342 </span>            :     }</a>
+<a name="6343"><span class="lineNum">    6343 </span>            : </a>
+<a name="6344"><span class="lineNum">    6344 </span><span class="lineCov">        264 :     switch(ch) {</span></a>
+<a name="6345"><span class="lineNum">    6345 </span>            :     case 'G': </a>
+<a name="6346"><span class="lineNum">    6346 </span>            :       /* Full matrix */</a>
+<a name="6347"><span class="lineNum">    6347 </span><span class="lineCov">        528 :       for(j=0;j&lt;*n;j++)</span></a>
+<a name="6348"><span class="lineNum">    6348 </span><span class="lineCov">      14544 :         for(i=0;i&lt;*m;i++)</span></a>
+<a name="6349"><span class="lineNum">    6349 </span><span class="lineCov">      14280 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6350"><span class="lineNum">    6350 </span>            :       break;</a>
+<a name="6351"><span class="lineNum">    6351 </span>            : </a>
+<a name="6352"><span class="lineNum">    6352 </span>            :     case 'L': </a>
+<a name="6353"><span class="lineNum">    6353 </span>            :       /* Lower triangular matrix */</a>
+<a name="6354"><span class="lineNum">    6354 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++)</span></a>
+<a name="6355"><span class="lineNum">    6355 </span><span class="lineNoCov">          0 :         for(i=j;i&lt;*m;i++)</span></a>
+<a name="6356"><span class="lineNum">    6356 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6357"><span class="lineNum">    6357 </span>            :       break;</a>
+<a name="6358"><span class="lineNum">    6358 </span>            : </a>
+<a name="6359"><span class="lineNum">    6359 </span>            :     case 'U': </a>
+<a name="6360"><span class="lineNum">    6360 </span>            :       /* Upper triangular matrix */</a>
+<a name="6361"><span class="lineNum">    6361 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="6362"><span class="lineNum">    6362 </span><span class="lineNoCov">          0 :         k = (j &lt; (*m-1)) ? j : (*m-1);</span></a>
+<a name="6363"><span class="lineNum">    6363 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;=k;i++)</span></a>
+<a name="6364"><span class="lineNum">    6364 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6365"><span class="lineNum">    6365 </span>            :       }</a>
+<a name="6366"><span class="lineNum">    6366 </span>            :       break;</a>
+<a name="6367"><span class="lineNum">    6367 </span>            : </a>
+<a name="6368"><span class="lineNum">    6368 </span>            :     case 'H': </a>
+<a name="6369"><span class="lineNum">    6369 </span>            :       /* Upper Hessenberg matrix */</a>
+<a name="6370"><span class="lineNum">    6370 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="6371"><span class="lineNum">    6371 </span><span class="lineNoCov">          0 :         k = ((j+1) &lt; (*m-1)) ? (j+1) : (*m-1);</span></a>
+<a name="6372"><span class="lineNum">    6372 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;=k;i++)</span></a>
+<a name="6373"><span class="lineNum">    6373 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6374"><span class="lineNum">    6374 </span>            :       }</a>
+<a name="6375"><span class="lineNum">    6375 </span>            :       break;</a>
+<a name="6376"><span class="lineNum">    6376 </span>            : </a>
+<a name="6377"><span class="lineNum">    6377 </span><span class="lineNoCov">          0 :     case 'B': </span></a>
+<a name="6378"><span class="lineNum">    6378 </span>            :       /* Symmetric band matrix, lower bandwidth KL, upper KU,</a>
+<a name="6379"><span class="lineNum">    6379 </span>            :        * only the lower half stored.</a>
+<a name="6380"><span class="lineNum">    6380 </span>            :        */</a>
+<a name="6381"><span class="lineNum">    6381 </span><span class="lineNoCov">          0 :       k3 = *kl;</span></a>
+<a name="6382"><span class="lineNum">    6382 </span><span class="lineNoCov">          0 :       k4 = *n - 1;</span></a>
+<a name="6383"><span class="lineNum">    6383 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="6384"><span class="lineNum">    6384 </span><span class="lineNoCov">          0 :         k = (k3 &lt; (k4-j)) ? k3 : (k4-j);</span></a>
+<a name="6385"><span class="lineNum">    6385 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;=k;i++)</span></a>
+<a name="6386"><span class="lineNum">    6386 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6387"><span class="lineNum">    6387 </span>            :       }</a>
+<a name="6388"><span class="lineNum">    6388 </span>            :       break;</a>
+<a name="6389"><span class="lineNum">    6389 </span>            : </a>
+<a name="6390"><span class="lineNum">    6390 </span><span class="lineNoCov">          0 :     case 'Q': </span></a>
+<a name="6391"><span class="lineNum">    6391 </span>            :       /* Symmetric band matrix, lower bandwidth KL, upper KU,</a>
+<a name="6392"><span class="lineNum">    6392 </span>            :        * only the upper half stored.</a>
+<a name="6393"><span class="lineNum">    6393 </span>            :        */</a>
+<a name="6394"><span class="lineNum">    6394 </span><span class="lineNoCov">          0 :       k1 = *ku;</span></a>
+<a name="6395"><span class="lineNum">    6395 </span>            :       k3 = *ku;</a>
+<a name="6396"><span class="lineNum">    6396 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="6397"><span class="lineNum">    6397 </span><span class="lineNoCov">          0 :         k = ((k1-j) &gt; 0) ? (k1-j) : 0;</span></a>
+<a name="6398"><span class="lineNum">    6398 </span><span class="lineNoCov">          0 :         for(i=k;i&lt;=k3;i++)</span></a>
+<a name="6399"><span class="lineNum">    6399 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6400"><span class="lineNum">    6400 </span>            :       }</a>
+<a name="6401"><span class="lineNum">    6401 </span>            :       break;</a>
+<a name="6402"><span class="lineNum">    6402 </span>            : </a>
+<a name="6403"><span class="lineNum">    6403 </span><span class="lineNoCov">          0 :     case 'Z': </span></a>
+<a name="6404"><span class="lineNum">    6404 </span>            :       /* Band matrix, lower bandwidth KL, upper KU. */</a>
+<a name="6405"><span class="lineNum">    6405 </span>            : </a>
+<a name="6406"><span class="lineNum">    6406 </span><span class="lineNoCov">          0 :       k1 = *kl + *ku;</span></a>
+<a name="6407"><span class="lineNum">    6407 </span>            :       k2 = *kl;</a>
+<a name="6408"><span class="lineNum">    6408 </span><span class="lineNoCov">          0 :       k3 = 2*(*kl) + *ku;</span></a>
+<a name="6409"><span class="lineNum">    6409 </span><span class="lineNoCov">          0 :       k4 = *kl + *ku - 1 + *m;</span></a>
+<a name="6410"><span class="lineNum">    6410 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="6411"><span class="lineNum">    6411 </span><span class="lineNoCov">          0 :         k = ((k1-j) &gt; k2) ? (k1-j) : k2;</span></a>
+<a name="6412"><span class="lineNum">    6412 </span><span class="lineNoCov">          0 :         l = (k3 &lt; (k4-j)) ? k3 : (k4-j);</span></a>
+<a name="6413"><span class="lineNum">    6413 </span><span class="lineNoCov">          0 :         for(i=k;i&lt;=l;i++)</span></a>
+<a name="6414"><span class="lineNum">    6414 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="6415"><span class="lineNum">    6415 </span>            :       }</a>
+<a name="6416"><span class="lineNum">    6416 </span>            :       break;</a>
+<a name="6417"><span class="lineNum">    6417 </span>            : </a>
+<a name="6418"><span class="lineNum">    6418 </span><span class="lineNoCov">          0 :     default:</span></a>
+<a name="6419"><span class="lineNum">    6419 </span><span class="lineNoCov">          0 :       *info = -1;</span></a>
+<a name="6420"><span class="lineNum">    6420 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="6421"><span class="lineNum">    6421 </span>            :     }</a>
+<a name="6422"><span class="lineNum">    6422 </span>            :   } /* finished */</a>
+<a name="6423"><span class="lineNum">    6423 </span>            : </a>
+<a name="6424"><span class="lineNum">    6424 </span><span class="lineCov">        264 :   *info = 0;</span></a>
+<a name="6425"><span class="lineNum">    6425 </span><span class="lineCov">        264 :   return;</span></a>
+<a name="6426"><span class="lineNum">    6426 </span>            : }</a>
+<a name="6427"><span class="lineNum">    6427 </span>            : }</a>
+<a name="6428"><span class="lineNum">    6428 </span>            : }</a>
+<a name="6429"><span class="lineNum">    6429 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6430"><span class="lineNum">    6430 </span>            : </a>
+<a name="6431"><span class="lineNum">    6431 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6432"><span class="lineNum">    6432 </span>            : namespace PLMD{</a>
+<a name="6433"><span class="lineNum">    6433 </span>            : namespace lapack{</a>
+<a name="6434"><span class="lineNum">    6434 </span>            : using namespace blas;</a>
+<a name="6435"><span class="lineNum">    6435 </span>            : void </a>
+<a name="6436"><span class="lineNum">    6436 </span><span class="lineCov">         29 : PLUMED_BLAS_F77_FUNC(dlasd0,DLASD0)(int *n, </span></a>
+<a name="6437"><span class="lineNum">    6437 </span>            :         int *sqre, </a>
+<a name="6438"><span class="lineNum">    6438 </span>            :         double *d__, </a>
+<a name="6439"><span class="lineNum">    6439 </span>            :         double *e, </a>
+<a name="6440"><span class="lineNum">    6440 </span>            :         double *u, </a>
+<a name="6441"><span class="lineNum">    6441 </span>            :         int *ldu, </a>
+<a name="6442"><span class="lineNum">    6442 </span>            :         double *vt, </a>
+<a name="6443"><span class="lineNum">    6443 </span>            :         int *ldvt,</a>
+<a name="6444"><span class="lineNum">    6444 </span>            :         int *smlsiz, </a>
+<a name="6445"><span class="lineNum">    6445 </span>            :         int *iwork,</a>
+<a name="6446"><span class="lineNum">    6446 </span>            :         double *work, </a>
+<a name="6447"><span class="lineNum">    6447 </span>            :         int *info)</a>
+<a name="6448"><span class="lineNum">    6448 </span>            : {</a>
+<a name="6449"><span class="lineNum">    6449 </span>            :     int u_dim1, u_offset, vt_dim1, vt_offset, i__1, i__2;</a>
+<a name="6450"><span class="lineNum">    6450 </span>            : </a>
+<a name="6451"><span class="lineNum">    6451 </span>            :     int i__, j, m, i1, ic, lf, nd, ll, nl, nr, im1, ncc, nlf, nrf, </a>
+<a name="6452"><span class="lineNum">    6452 </span>            :             iwk, lvl, ndb1, nlp1, nrp1;</a>
+<a name="6453"><span class="lineNum">    6453 </span>            :     double beta;</a>
+<a name="6454"><span class="lineNum">    6454 </span>            :     int idxq, nlvl;</a>
+<a name="6455"><span class="lineNum">    6455 </span>            :     double alpha;</a>
+<a name="6456"><span class="lineNum">    6456 </span>            :     int inode, ndiml, idxqc, ndimr, itemp, sqrei;</a>
+<a name="6457"><span class="lineNum">    6457 </span><span class="lineCov">         29 :     int c__0 = 0;</span></a>
+<a name="6458"><span class="lineNum">    6458 </span>            : </a>
+<a name="6459"><span class="lineNum">    6459 </span>            : </a>
+<a name="6460"><span class="lineNum">    6460 </span><span class="lineCov">         29 :     --d__;</span></a>
+<a name="6461"><span class="lineNum">    6461 </span><span class="lineCov">         29 :     --e;</span></a>
+<a name="6462"><span class="lineNum">    6462 </span><span class="lineCov">         29 :     u_dim1 = *ldu;</span></a>
+<a name="6463"><span class="lineNum">    6463 </span><span class="lineCov">         29 :     u_offset = 1 + u_dim1;</span></a>
+<a name="6464"><span class="lineNum">    6464 </span><span class="lineCov">         29 :     u -= u_offset;</span></a>
+<a name="6465"><span class="lineNum">    6465 </span><span class="lineCov">         29 :     vt_dim1 = *ldvt;</span></a>
+<a name="6466"><span class="lineNum">    6466 </span><span class="lineCov">         29 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="6467"><span class="lineNum">    6467 </span><span class="lineCov">         29 :     vt -= vt_offset;</span></a>
+<a name="6468"><span class="lineNum">    6468 </span><span class="lineCov">         29 :     --iwork;</span></a>
+<a name="6469"><span class="lineNum">    6469 </span>            :     --work;</a>
+<a name="6470"><span class="lineNum">    6470 </span>            : </a>
+<a name="6471"><span class="lineNum">    6471 </span><span class="lineCov">         29 :     *info = 0;</span></a>
+<a name="6472"><span class="lineNum">    6472 </span>            : </a>
+<a name="6473"><span class="lineNum">    6473 </span><span class="lineCov">         29 :     if (*n &lt; 0) {</span></a>
+<a name="6474"><span class="lineNum">    6474 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="6475"><span class="lineNum">    6475 </span><span class="lineCov">         29 :     } else if (*sqre &lt; 0 || *sqre &gt; 1) {</span></a>
+<a name="6476"><span class="lineNum">    6476 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="6477"><span class="lineNum">    6477 </span>            :     }</a>
+<a name="6478"><span class="lineNum">    6478 </span>            : </a>
+<a name="6479"><span class="lineNum">    6479 </span><span class="lineCov">         29 :     m = *n + *sqre;</span></a>
+<a name="6480"><span class="lineNum">    6480 </span>            : </a>
+<a name="6481"><span class="lineNum">    6481 </span><span class="lineCov">         29 :     if (*ldu &lt; *n) {</span></a>
+<a name="6482"><span class="lineNum">    6482 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="6483"><span class="lineNum">    6483 </span><span class="lineCov">         29 :     } else if (*ldvt &lt; m) {</span></a>
+<a name="6484"><span class="lineNum">    6484 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="6485"><span class="lineNum">    6485 </span><span class="lineCov">         29 :     } else if (*smlsiz &lt; 3) {</span></a>
+<a name="6486"><span class="lineNum">    6486 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="6487"><span class="lineNum">    6487 </span>            :     }</a>
+<a name="6488"><span class="lineNum">    6488 </span><span class="lineCov">         29 :     if (*info != 0) {</span></a>
+<a name="6489"><span class="lineNum">    6489 </span>            :         return;</a>
+<a name="6490"><span class="lineNum">    6490 </span>            :     }</a>
+<a name="6491"><span class="lineNum">    6491 </span>            : </a>
+<a name="6492"><span class="lineNum">    6492 </span><span class="lineCov">         29 :     if (*n &lt;= *smlsiz) {</span></a>
+<a name="6493"><span class="lineNum">    6493 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, sqre, n, &amp;m, n, &amp;c__0, &amp;d__[1], &amp;e[1], &amp;vt[vt_offset], </span></a>
+<a name="6494"><span class="lineNum">    6494 </span>            :                 ldvt, &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;work[1], info);</a>
+<a name="6495"><span class="lineNum">    6495 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="6496"><span class="lineNum">    6496 </span>            :     }</a>
+<a name="6497"><span class="lineNum">    6497 </span>            : </a>
+<a name="6498"><span class="lineNum">    6498 </span>            :     inode = 1;</a>
+<a name="6499"><span class="lineNum">    6499 </span><span class="lineCov">         29 :     ndiml = inode + *n;</span></a>
+<a name="6500"><span class="lineNum">    6500 </span><span class="lineCov">         29 :     ndimr = ndiml + *n;</span></a>
+<a name="6501"><span class="lineNum">    6501 </span><span class="lineCov">         29 :     idxq = ndimr + *n;</span></a>
+<a name="6502"><span class="lineNum">    6502 </span><span class="lineCov">         29 :     iwk = idxq + *n;</span></a>
+<a name="6503"><span class="lineNum">    6503 </span><span class="lineCov">         29 :     PLUMED_BLAS_F77_FUNC(dlasdt,DLASDT)(n, &amp;nlvl, &amp;nd, &amp;iwork[inode], &amp;iwork[ndiml], &amp;iwork[ndimr], </span></a>
+<a name="6504"><span class="lineNum">    6504 </span>            :             smlsiz);</a>
+<a name="6505"><span class="lineNum">    6505 </span>            : </a>
+<a name="6506"><span class="lineNum">    6506 </span><span class="lineCov">         29 :     ndb1 = (nd + 1) / 2;</span></a>
+<a name="6507"><span class="lineNum">    6507 </span><span class="lineCov">         29 :     ncc = 0;</span></a>
+<a name="6508"><span class="lineNum">    6508 </span>            :     i__1 = nd;</a>
+<a name="6509"><span class="lineNum">    6509 </span><span class="lineCov">         73 :     for (i__ = ndb1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6510"><span class="lineNum">    6510 </span>            : </a>
+<a name="6511"><span class="lineNum">    6511 </span><span class="lineCov">         44 :         i1 = i__ - 1;</span></a>
+<a name="6512"><span class="lineNum">    6512 </span><span class="lineCov">         44 :         ic = iwork[inode + i1];</span></a>
+<a name="6513"><span class="lineNum">    6513 </span><span class="lineCov">         44 :         nl = iwork[ndiml + i1];</span></a>
+<a name="6514"><span class="lineNum">    6514 </span><span class="lineCov">         44 :         nlp1 = nl + 1;</span></a>
+<a name="6515"><span class="lineNum">    6515 </span><span class="lineCov">         44 :         nr = iwork[ndimr + i1];</span></a>
+<a name="6516"><span class="lineNum">    6516 </span><span class="lineCov">         44 :         nrp1 = nr + 1;</span></a>
+<a name="6517"><span class="lineNum">    6517 </span><span class="lineCov">         44 :         nlf = ic - nl;</span></a>
+<a name="6518"><span class="lineNum">    6518 </span><span class="lineCov">         44 :         nrf = ic + 1;</span></a>
+<a name="6519"><span class="lineNum">    6519 </span><span class="lineCov">         44 :         sqrei = 1;</span></a>
+<a name="6520"><span class="lineNum">    6520 </span><span class="lineCov">         44 :         PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nl, &amp;nlp1, &amp;nl, &amp;ncc, &amp;d__[nlf], &amp;e[nlf], &amp;vt[</span></a>
+<a name="6521"><span class="lineNum">    6521 </span><span class="lineCov">         44 :                 nlf + nlf * vt_dim1], ldvt, &amp;u[nlf + nlf * u_dim1], ldu, &amp;u[</span></a>
+<a name="6522"><span class="lineNum">    6522 </span><span class="lineCov">         44 :                 nlf + nlf * u_dim1], ldu, &amp;work[1], info);</span></a>
+<a name="6523"><span class="lineNum">    6523 </span><span class="lineCov">         44 :         if (*info != 0) {</span></a>
+<a name="6524"><span class="lineNum">    6524 </span>            :             return;</a>
+<a name="6525"><span class="lineNum">    6525 </span>            :         }</a>
+<a name="6526"><span class="lineNum">    6526 </span><span class="lineCov">         44 :         itemp = idxq + nlf - 2;</span></a>
+<a name="6527"><span class="lineNum">    6527 </span><span class="lineCov">         44 :         i__2 = nl;</span></a>
+<a name="6528"><span class="lineNum">    6528 </span><span class="lineCov">        732 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="6529"><span class="lineNum">    6529 </span><span class="lineCov">        688 :             iwork[itemp + j] = j;</span></a>
+<a name="6530"><span class="lineNum">    6530 </span>            :         }</a>
+<a name="6531"><span class="lineNum">    6531 </span><span class="lineCov">         44 :         if (i__ == nd) {</span></a>
+<a name="6532"><span class="lineNum">    6532 </span><span class="lineCov">         29 :             sqrei = *sqre;</span></a>
+<a name="6533"><span class="lineNum">    6533 </span>            :         } else {</a>
+<a name="6534"><span class="lineNum">    6534 </span><span class="lineCov">         15 :             sqrei = 1;</span></a>
+<a name="6535"><span class="lineNum">    6535 </span>            :         }</a>
+<a name="6536"><span class="lineNum">    6536 </span><span class="lineCov">         44 :         nrp1 = nr + sqrei;</span></a>
+<a name="6537"><span class="lineNum">    6537 </span><span class="lineCov">         44 :         PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nr, &amp;nrp1, &amp;nr, &amp;ncc, &amp;d__[nrf], &amp;e[nrf], &amp;vt[</span></a>
+<a name="6538"><span class="lineNum">    6538 </span><span class="lineCov">         44 :                 nrf + nrf * vt_dim1], ldvt, &amp;u[nrf + nrf * u_dim1], ldu, &amp;u[</span></a>
+<a name="6539"><span class="lineNum">    6539 </span><span class="lineCov">         44 :                 nrf + nrf * u_dim1], ldu, &amp;work[1], info);</span></a>
+<a name="6540"><span class="lineNum">    6540 </span><span class="lineCov">         44 :         if (*info != 0) {</span></a>
+<a name="6541"><span class="lineNum">    6541 </span>            :             return;</a>
+<a name="6542"><span class="lineNum">    6542 </span>            :         }</a>
+<a name="6543"><span class="lineNum">    6543 </span><span class="lineCov">         44 :         itemp = idxq + ic;</span></a>
+<a name="6544"><span class="lineNum">    6544 </span><span class="lineCov">         44 :         i__2 = nr;</span></a>
+<a name="6545"><span class="lineNum">    6545 </span><span class="lineCov">        716 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="6546"><span class="lineNum">    6546 </span><span class="lineCov">        672 :             iwork[itemp + j - 1] = j;</span></a>
+<a name="6547"><span class="lineNum">    6547 </span>            :         }</a>
+<a name="6548"><span class="lineNum">    6548 </span>            :     }</a>
+<a name="6549"><span class="lineNum">    6549 </span>            : </a>
+<a name="6550"><span class="lineNum">    6550 </span><span class="lineCov">         62 :     for (lvl = nlvl; lvl &gt;= 1; --lvl) {</span></a>
+<a name="6551"><span class="lineNum">    6551 </span>            : </a>
+<a name="6552"><span class="lineNum">    6552 </span><span class="lineCov">         33 :         if (lvl == 1) {</span></a>
+<a name="6553"><span class="lineNum">    6553 </span>            :             lf = 1;</a>
+<a name="6554"><span class="lineNum">    6554 </span>            :             ll = 1;</a>
+<a name="6555"><span class="lineNum">    6555 </span>            :         } else {</a>
+<a name="6556"><span class="lineNum">    6556 </span><span class="lineCov">          4 :             i__1 = lvl - 1;</span></a>
+<a name="6557"><span class="lineNum">    6557 </span><span class="lineCov">          4 :             lf = (1 &lt;&lt; i__1);</span></a>
+<a name="6558"><span class="lineNum">    6558 </span><span class="lineCov">          4 :             ll = (lf &lt;&lt; 1) - 1;</span></a>
+<a name="6559"><span class="lineNum">    6559 </span>            :         }</a>
+<a name="6560"><span class="lineNum">    6560 </span>            :         i__1 = ll;</a>
+<a name="6561"><span class="lineNum">    6561 </span><span class="lineCov">         92 :         for (i__ = lf; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6562"><span class="lineNum">    6562 </span><span class="lineCov">         59 :             im1 = i__ - 1;</span></a>
+<a name="6563"><span class="lineNum">    6563 </span><span class="lineCov">         59 :             ic = iwork[inode + im1];</span></a>
+<a name="6564"><span class="lineNum">    6564 </span><span class="lineCov">         59 :             nl = iwork[ndiml + im1];</span></a>
+<a name="6565"><span class="lineNum">    6565 </span><span class="lineCov">         59 :             nr = iwork[ndimr + im1];</span></a>
+<a name="6566"><span class="lineNum">    6566 </span><span class="lineCov">         59 :             nlf = ic - nl;</span></a>
+<a name="6567"><span class="lineNum">    6567 </span><span class="lineCov">         59 :             if (*sqre == 0 &amp;&amp; i__ == ll) {</span></a>
+<a name="6568"><span class="lineNum">    6568 </span><span class="lineCov">         33 :                 sqrei = *sqre;</span></a>
+<a name="6569"><span class="lineNum">    6569 </span>            :             } else {</a>
+<a name="6570"><span class="lineNum">    6570 </span><span class="lineCov">         26 :                 sqrei = 1;</span></a>
+<a name="6571"><span class="lineNum">    6571 </span>            :             }</a>
+<a name="6572"><span class="lineNum">    6572 </span><span class="lineCov">         59 :             idxqc = idxq + nlf - 1;</span></a>
+<a name="6573"><span class="lineNum">    6573 </span><span class="lineCov">         59 :             alpha = d__[ic];</span></a>
+<a name="6574"><span class="lineNum">    6574 </span><span class="lineCov">         59 :             beta = e[ic];</span></a>
+<a name="6575"><span class="lineNum">    6575 </span><span class="lineCov">         59 :             PLUMED_BLAS_F77_FUNC(dlasd1,DLASD1)(&amp;nl, &amp;nr, &amp;sqrei, &amp;d__[nlf], &amp;alpha, &amp;beta, &amp;u[nlf + nlf *</span></a>
+<a name="6576"><span class="lineNum">    6576 </span><span class="lineCov">         59 :                      u_dim1], ldu, &amp;vt[nlf + nlf * vt_dim1], ldvt, &amp;iwork[</span></a>
+<a name="6577"><span class="lineNum">    6577 </span><span class="lineCov">         59 :                     idxqc], &amp;iwork[iwk], &amp;work[1], info);</span></a>
+<a name="6578"><span class="lineNum">    6578 </span><span class="lineCov">         59 :             if (*info != 0) {</span></a>
+<a name="6579"><span class="lineNum">    6579 </span>            :                 return;</a>
+<a name="6580"><span class="lineNum">    6580 </span>            :             }</a>
+<a name="6581"><span class="lineNum">    6581 </span>            :         }</a>
+<a name="6582"><span class="lineNum">    6582 </span>            :     }</a>
+<a name="6583"><span class="lineNum">    6583 </span>            : </a>
+<a name="6584"><span class="lineNum">    6584 </span>            :     return;</a>
+<a name="6585"><span class="lineNum">    6585 </span>            : </a>
+<a name="6586"><span class="lineNum">    6586 </span>            : }</a>
+<a name="6587"><span class="lineNum">    6587 </span>            : }</a>
+<a name="6588"><span class="lineNum">    6588 </span>            : }</a>
+<a name="6589"><span class="lineNum">    6589 </span>            : #include &lt;cmath&gt;</a>
+<a name="6590"><span class="lineNum">    6590 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6591"><span class="lineNum">    6591 </span>            : </a>
+<a name="6592"><span class="lineNum">    6592 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6593"><span class="lineNum">    6593 </span>            : namespace PLMD{</a>
+<a name="6594"><span class="lineNum">    6594 </span>            : namespace lapack{</a>
+<a name="6595"><span class="lineNum">    6595 </span>            : using namespace blas;</a>
+<a name="6596"><span class="lineNum">    6596 </span>            : void </a>
+<a name="6597"><span class="lineNum">    6597 </span><span class="lineCov">         59 : PLUMED_BLAS_F77_FUNC(dlasd1,DLASD1)(int *nl, </span></a>
+<a name="6598"><span class="lineNum">    6598 </span>            :         int *nr, </a>
+<a name="6599"><span class="lineNum">    6599 </span>            :         int *sqre, </a>
+<a name="6600"><span class="lineNum">    6600 </span>            :         double *d__, </a>
+<a name="6601"><span class="lineNum">    6601 </span>            :         double *alpha, </a>
+<a name="6602"><span class="lineNum">    6602 </span>            :         double *beta, </a>
+<a name="6603"><span class="lineNum">    6603 </span>            :         double *u, </a>
+<a name="6604"><span class="lineNum">    6604 </span>            :         int *ldu, </a>
+<a name="6605"><span class="lineNum">    6605 </span>            :         double *vt, </a>
+<a name="6606"><span class="lineNum">    6606 </span>            :         int *ldvt, </a>
+<a name="6607"><span class="lineNum">    6607 </span>            :         int *idxq, </a>
+<a name="6608"><span class="lineNum">    6608 </span>            :         int *iwork, </a>
+<a name="6609"><span class="lineNum">    6609 </span>            :         double *work, </a>
+<a name="6610"><span class="lineNum">    6610 </span>            :         int *info)</a>
+<a name="6611"><span class="lineNum">    6611 </span>            : {</a>
+<a name="6612"><span class="lineNum">    6612 </span>            :     int u_dim1, u_offset, vt_dim1, vt_offset, i__1;</a>
+<a name="6613"><span class="lineNum">    6613 </span>            :     double d__1, d__2;</a>
+<a name="6614"><span class="lineNum">    6614 </span>            : </a>
+<a name="6615"><span class="lineNum">    6615 </span>            :     int i__, k, m, n, n1, n2, iq, iz, iu2, ldq, idx, ldu2, ivt2, </a>
+<a name="6616"><span class="lineNum">    6616 </span>            :             idxc, idxp, ldvt2;</a>
+<a name="6617"><span class="lineNum">    6617 </span>            :     int isigma;</a>
+<a name="6618"><span class="lineNum">    6618 </span>            :     double orgnrm;</a>
+<a name="6619"><span class="lineNum">    6619 </span>            :     int coltyp;</a>
+<a name="6620"><span class="lineNum">    6620 </span><span class="lineCov">         59 :     int c__0 = 0;</span></a>
+<a name="6621"><span class="lineNum">    6621 </span><span class="lineCov">         59 :     double one = 1.0;</span></a>
+<a name="6622"><span class="lineNum">    6622 </span><span class="lineCov">         59 :     int c__1 = 1;</span></a>
+<a name="6623"><span class="lineNum">    6623 </span><span class="lineCov">         59 :     int c_n1 = -1;</span></a>
+<a name="6624"><span class="lineNum">    6624 </span>            : </a>
+<a name="6625"><span class="lineNum">    6625 </span><span class="lineCov">         59 :     --d__;</span></a>
+<a name="6626"><span class="lineNum">    6626 </span>            :     u_dim1 = *ldu;</a>
+<a name="6627"><span class="lineNum">    6627 </span>            :     u_offset = 1 + u_dim1;</a>
+<a name="6628"><span class="lineNum">    6628 </span>            :     u -= u_offset;</a>
+<a name="6629"><span class="lineNum">    6629 </span>            :     vt_dim1 = *ldvt;</a>
+<a name="6630"><span class="lineNum">    6630 </span>            :     vt_offset = 1 + vt_dim1;</a>
+<a name="6631"><span class="lineNum">    6631 </span>            :     vt -= vt_offset;</a>
+<a name="6632"><span class="lineNum">    6632 </span>            :     --idxq;</a>
+<a name="6633"><span class="lineNum">    6633 </span><span class="lineCov">         59 :     --iwork;</span></a>
+<a name="6634"><span class="lineNum">    6634 </span><span class="lineCov">         59 :     --work;</span></a>
+<a name="6635"><span class="lineNum">    6635 </span>            : </a>
+<a name="6636"><span class="lineNum">    6636 </span><span class="lineCov">         59 :     *info = 0;</span></a>
+<a name="6637"><span class="lineNum">    6637 </span>            : </a>
+<a name="6638"><span class="lineNum">    6638 </span><span class="lineCov">         59 :     if (*nl &lt; 1) {</span></a>
+<a name="6639"><span class="lineNum">    6639 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="6640"><span class="lineNum">    6640 </span><span class="lineCov">         59 :     } else if (*nr &lt; 1) {</span></a>
+<a name="6641"><span class="lineNum">    6641 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="6642"><span class="lineNum">    6642 </span><span class="lineCov">         59 :     } else if (*sqre &lt; 0 || *sqre &gt; 1) {</span></a>
+<a name="6643"><span class="lineNum">    6643 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="6644"><span class="lineNum">    6644 </span>            :     }</a>
+<a name="6645"><span class="lineNum">    6645 </span><span class="lineCov">         59 :     if (*info != 0) {</span></a>
+<a name="6646"><span class="lineNum">    6646 </span>            :         return;</a>
+<a name="6647"><span class="lineNum">    6647 </span>            :     }</a>
+<a name="6648"><span class="lineNum">    6648 </span>            : </a>
+<a name="6649"><span class="lineNum">    6649 </span><span class="lineCov">         59 :     n = *nl + *nr + 1;</span></a>
+<a name="6650"><span class="lineNum">    6650 </span><span class="lineCov">         59 :     m = n + *sqre;</span></a>
+<a name="6651"><span class="lineNum">    6651 </span>            : </a>
+<a name="6652"><span class="lineNum">    6652 </span>            : </a>
+<a name="6653"><span class="lineNum">    6653 </span><span class="lineCov">         59 :     ldu2 = n;</span></a>
+<a name="6654"><span class="lineNum">    6654 </span><span class="lineCov">         59 :     ldvt2 = m;</span></a>
+<a name="6655"><span class="lineNum">    6655 </span>            : </a>
+<a name="6656"><span class="lineNum">    6656 </span>            :     iz = 1;</a>
+<a name="6657"><span class="lineNum">    6657 </span><span class="lineCov">         59 :     isigma = iz + m;</span></a>
+<a name="6658"><span class="lineNum">    6658 </span><span class="lineCov">         59 :     iu2 = isigma + n;</span></a>
+<a name="6659"><span class="lineNum">    6659 </span><span class="lineCov">         59 :     ivt2 = iu2 + ldu2 * n;</span></a>
+<a name="6660"><span class="lineNum">    6660 </span><span class="lineCov">         59 :     iq = ivt2 + ldvt2 * m;</span></a>
+<a name="6661"><span class="lineNum">    6661 </span>            : </a>
+<a name="6662"><span class="lineNum">    6662 </span>            :     idx = 1;</a>
+<a name="6663"><span class="lineNum">    6663 </span><span class="lineCov">         59 :     idxc = idx + n;</span></a>
+<a name="6664"><span class="lineNum">    6664 </span><span class="lineCov">         59 :     coltyp = idxc + n;</span></a>
+<a name="6665"><span class="lineNum">    6665 </span><span class="lineCov">         59 :     idxp = coltyp + n;</span></a>
+<a name="6666"><span class="lineNum">    6666 </span>            : </a>
+<a name="6667"><span class="lineNum">    6667 </span><span class="lineCov">         59 :     d__1 = std::abs(*alpha);</span></a>
+<a name="6668"><span class="lineNum">    6668 </span><span class="lineCov">         59 :     d__2 = std::abs(*beta);</span></a>
+<a name="6669"><span class="lineNum">    6669 </span><span class="lineCov">         59 :     orgnrm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="6670"><span class="lineNum">    6670 </span><span class="lineCov">         59 :     d__[*nl + 1] = 0.;</span></a>
+<a name="6671"><span class="lineNum">    6671 </span>            :     i__1 = n;</a>
+<a name="6672"><span class="lineNum">    6672 </span><span class="lineCov">       3452 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6673"><span class="lineNum">    6673 </span><span class="lineCov">       3393 :         if (std::abs(d__[i__]) &gt; orgnrm) {</span></a>
+<a name="6674"><span class="lineNum">    6674 </span><span class="lineCov">       1098 :             orgnrm = std::abs(d__[i__]);</span></a>
+<a name="6675"><span class="lineNum">    6675 </span>            :         }</a>
+<a name="6676"><span class="lineNum">    6676 </span>            :     }</a>
+<a name="6677"><span class="lineNum">    6677 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;orgnrm, &amp;one, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="6678"><span class="lineNum">    6678 </span><span class="lineCov">         59 :     *alpha /= orgnrm;</span></a>
+<a name="6679"><span class="lineNum">    6679 </span><span class="lineCov">         59 :     *beta /= orgnrm;</span></a>
+<a name="6680"><span class="lineNum">    6680 </span>            : </a>
+<a name="6681"><span class="lineNum">    6681 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlasd2,DLASD2)(nl, nr, sqre, &amp;k, &amp;d__[1], &amp;work[iz], alpha, beta, &amp;u[u_offset], </span></a>
+<a name="6682"><span class="lineNum">    6682 </span><span class="lineCov">         59 :             ldu, &amp;vt[vt_offset], ldvt, &amp;work[isigma], &amp;work[iu2], &amp;ldu2, &amp;</span></a>
+<a name="6683"><span class="lineNum">    6683 </span><span class="lineCov">         59 :             work[ivt2], &amp;ldvt2, &amp;iwork[idxp], &amp;iwork[idx], &amp;iwork[idxc], &amp;</span></a>
+<a name="6684"><span class="lineNum">    6684 </span><span class="lineCov">         59 :             idxq[1], &amp;iwork[coltyp], info);</span></a>
+<a name="6685"><span class="lineNum">    6685 </span>            : </a>
+<a name="6686"><span class="lineNum">    6686 </span><span class="lineCov">         59 :     ldq = k;</span></a>
+<a name="6687"><span class="lineNum">    6687 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlasd3,DLASD3)(nl, nr, sqre, &amp;k, &amp;d__[1], &amp;work[iq], &amp;ldq, &amp;work[isigma], &amp;u[</span></a>
+<a name="6688"><span class="lineNum">    6688 </span>            :             u_offset], ldu, &amp;work[iu2], &amp;ldu2, &amp;vt[vt_offset], ldvt, &amp;work[</a>
+<a name="6689"><span class="lineNum">    6689 </span>            :             ivt2], &amp;ldvt2, &amp;iwork[idxc], &amp;iwork[coltyp], &amp;work[iz], info);</a>
+<a name="6690"><span class="lineNum">    6690 </span><span class="lineCov">         59 :     if (*info != 0) {</span></a>
+<a name="6691"><span class="lineNum">    6691 </span>            :         return;</a>
+<a name="6692"><span class="lineNum">    6692 </span>            :     }</a>
+<a name="6693"><span class="lineNum">    6693 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;one, &amp;orgnrm, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="6694"><span class="lineNum">    6694 </span>            : </a>
+<a name="6695"><span class="lineNum">    6695 </span><span class="lineCov">         59 :     n1 = k;</span></a>
+<a name="6696"><span class="lineNum">    6696 </span><span class="lineCov">         59 :     n2 = n - k;</span></a>
+<a name="6697"><span class="lineNum">    6697 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlamrg,DLAMRG)(&amp;n1, &amp;n2, &amp;d__[1], &amp;c__1, &amp;c_n1, &amp;idxq[1]);</span></a>
+<a name="6698"><span class="lineNum">    6698 </span>            : </a>
+<a name="6699"><span class="lineNum">    6699 </span>            :     return;</a>
+<a name="6700"><span class="lineNum">    6700 </span>            : </a>
+<a name="6701"><span class="lineNum">    6701 </span>            : }</a>
+<a name="6702"><span class="lineNum">    6702 </span>            : }</a>
+<a name="6703"><span class="lineNum">    6703 </span>            : }</a>
+<a name="6704"><span class="lineNum">    6704 </span>            : #include &lt;cmath&gt;</a>
+<a name="6705"><span class="lineNum">    6705 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6706"><span class="lineNum">    6706 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="6707"><span class="lineNum">    6707 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="6708"><span class="lineNum">    6708 </span>            : </a>
+<a name="6709"><span class="lineNum">    6709 </span>            : #include &quot;real.h&quot;</a>
+<a name="6710"><span class="lineNum">    6710 </span>            : </a>
+<a name="6711"><span class="lineNum">    6711 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="6712"><span class="lineNum">    6712 </span>            : namespace PLMD{</a>
+<a name="6713"><span class="lineNum">    6713 </span>            : namespace lapack{</a>
+<a name="6714"><span class="lineNum">    6714 </span>            : using namespace blas;</a>
+<a name="6715"><span class="lineNum">    6715 </span>            : void </a>
+<a name="6716"><span class="lineNum">    6716 </span><span class="lineCov">         59 : PLUMED_BLAS_F77_FUNC(dlasd2,DLASD2)(int *nl, </span></a>
+<a name="6717"><span class="lineNum">    6717 </span>            :                         int *nr, </a>
+<a name="6718"><span class="lineNum">    6718 </span>            :                         int *sqre, </a>
+<a name="6719"><span class="lineNum">    6719 </span>            :                         int *k, </a>
+<a name="6720"><span class="lineNum">    6720 </span>            :                         double *d__, </a>
+<a name="6721"><span class="lineNum">    6721 </span>            :                         double *z__, </a>
+<a name="6722"><span class="lineNum">    6722 </span>            :                         double *alpha, </a>
+<a name="6723"><span class="lineNum">    6723 </span>            :                         double *beta, </a>
+<a name="6724"><span class="lineNum">    6724 </span>            :                         double *u, </a>
+<a name="6725"><span class="lineNum">    6725 </span>            :                         int *ldu, </a>
+<a name="6726"><span class="lineNum">    6726 </span>            :                         double *vt, </a>
+<a name="6727"><span class="lineNum">    6727 </span>            :                         int *ldvt, </a>
+<a name="6728"><span class="lineNum">    6728 </span>            :                         double *dsigma, </a>
+<a name="6729"><span class="lineNum">    6729 </span>            :                         double *u2, </a>
+<a name="6730"><span class="lineNum">    6730 </span>            :                         int *ldu2, </a>
+<a name="6731"><span class="lineNum">    6731 </span>            :                         double *vt2, </a>
+<a name="6732"><span class="lineNum">    6732 </span>            :                         int *ldvt2, </a>
+<a name="6733"><span class="lineNum">    6733 </span>            :                         int *idxp, </a>
+<a name="6734"><span class="lineNum">    6734 </span>            :                         int *idx, </a>
+<a name="6735"><span class="lineNum">    6735 </span>            :                         int *idxc, </a>
+<a name="6736"><span class="lineNum">    6736 </span>            :                         int *idxq, </a>
+<a name="6737"><span class="lineNum">    6737 </span>            :                         int *coltyp, </a>
+<a name="6738"><span class="lineNum">    6738 </span>            :                         int *info)</a>
+<a name="6739"><span class="lineNum">    6739 </span>            : {</a>
+<a name="6740"><span class="lineNum">    6740 </span>            :     int u_dim1, u_offset, u2_dim1, u2_offset, vt_dim1, vt_offset;</a>
+<a name="6741"><span class="lineNum">    6741 </span>            :     int vt2_dim1, vt2_offset, i__1;</a>
+<a name="6742"><span class="lineNum">    6742 </span>            :     double d__1, d__2;</a>
+<a name="6743"><span class="lineNum">    6743 </span>            : </a>
+<a name="6744"><span class="lineNum">    6744 </span>            :     double c__;</a>
+<a name="6745"><span class="lineNum">    6745 </span>            :     int i__, j, m, n;</a>
+<a name="6746"><span class="lineNum">    6746 </span>            :     double s;</a>
+<a name="6747"><span class="lineNum">    6747 </span>            :     int k2;</a>
+<a name="6748"><span class="lineNum">    6748 </span>            :     double z1;</a>
+<a name="6749"><span class="lineNum">    6749 </span>            :     int ct, jp;</a>
+<a name="6750"><span class="lineNum">    6750 </span>            :     double eps, tau, tol;</a>
+<a name="6751"><span class="lineNum">    6751 </span>            :     int psm[4], nlp1, nlp2, idxi, idxj;</a>
+<a name="6752"><span class="lineNum">    6752 </span>            :     int ctot[4], idxjp;</a>
+<a name="6753"><span class="lineNum">    6753 </span>            :     int jprev = 0;</a>
+<a name="6754"><span class="lineNum">    6754 </span>            :     double hlftol;</a>
+<a name="6755"><span class="lineNum">    6755 </span><span class="lineCov">         59 :     double zero = 0.0;</span></a>
+<a name="6756"><span class="lineNum">    6756 </span><span class="lineCov">         59 :     int c__1 = 1;</span></a>
+<a name="6757"><span class="lineNum">    6757 </span>            : </a>
+<a name="6758"><span class="lineNum">    6758 </span>            : </a>
+<a name="6759"><span class="lineNum">    6759 </span><span class="lineCov">         59 :     --d__;</span></a>
+<a name="6760"><span class="lineNum">    6760 </span><span class="lineCov">         59 :     --z__;</span></a>
+<a name="6761"><span class="lineNum">    6761 </span><span class="lineCov">         59 :     u_dim1 = *ldu;</span></a>
+<a name="6762"><span class="lineNum">    6762 </span><span class="lineCov">         59 :     u_offset = 1 + u_dim1;</span></a>
+<a name="6763"><span class="lineNum">    6763 </span><span class="lineCov">         59 :     u -= u_offset;</span></a>
+<a name="6764"><span class="lineNum">    6764 </span><span class="lineCov">         59 :     vt_dim1 = *ldvt;</span></a>
+<a name="6765"><span class="lineNum">    6765 </span><span class="lineCov">         59 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="6766"><span class="lineNum">    6766 </span><span class="lineCov">         59 :     vt -= vt_offset;</span></a>
+<a name="6767"><span class="lineNum">    6767 </span><span class="lineCov">         59 :     --dsigma;</span></a>
+<a name="6768"><span class="lineNum">    6768 </span><span class="lineCov">         59 :     u2_dim1 = *ldu2;</span></a>
+<a name="6769"><span class="lineNum">    6769 </span><span class="lineCov">         59 :     u2_offset = 1 + u2_dim1;</span></a>
+<a name="6770"><span class="lineNum">    6770 </span><span class="lineCov">         59 :     u2 -= u2_offset;</span></a>
+<a name="6771"><span class="lineNum">    6771 </span><span class="lineCov">         59 :     vt2_dim1 = *ldvt2;</span></a>
+<a name="6772"><span class="lineNum">    6772 </span><span class="lineCov">         59 :     vt2_offset = 1 + vt2_dim1;</span></a>
+<a name="6773"><span class="lineNum">    6773 </span><span class="lineCov">         59 :     vt2 -= vt2_offset;</span></a>
+<a name="6774"><span class="lineNum">    6774 </span><span class="lineCov">         59 :     --idxp;</span></a>
+<a name="6775"><span class="lineNum">    6775 </span><span class="lineCov">         59 :     --idx;</span></a>
+<a name="6776"><span class="lineNum">    6776 </span><span class="lineCov">         59 :     --idxc;</span></a>
+<a name="6777"><span class="lineNum">    6777 </span><span class="lineCov">         59 :     --idxq;</span></a>
+<a name="6778"><span class="lineNum">    6778 </span><span class="lineCov">         59 :     --coltyp;</span></a>
+<a name="6779"><span class="lineNum">    6779 </span>            : </a>
+<a name="6780"><span class="lineNum">    6780 </span><span class="lineCov">         59 :     *info = 0;</span></a>
+<a name="6781"><span class="lineNum">    6781 </span>            : </a>
+<a name="6782"><span class="lineNum">    6782 </span><span class="lineCov">         59 :     n = *nl + *nr + 1;</span></a>
+<a name="6783"><span class="lineNum">    6783 </span><span class="lineCov">         59 :     m = n + *sqre;</span></a>
+<a name="6784"><span class="lineNum">    6784 </span>            : </a>
+<a name="6785"><span class="lineNum">    6785 </span><span class="lineCov">         59 :     nlp1 = *nl + 1;</span></a>
+<a name="6786"><span class="lineNum">    6786 </span><span class="lineCov">         59 :     nlp2 = *nl + 2;</span></a>
+<a name="6787"><span class="lineNum">    6787 </span>            : </a>
+<a name="6788"><span class="lineNum">    6788 </span><span class="lineCov">         59 :     z1 = *alpha * vt[nlp1 + nlp1 * vt_dim1];</span></a>
+<a name="6789"><span class="lineNum">    6789 </span><span class="lineCov">         59 :     z__[1] = z1;</span></a>
+<a name="6790"><span class="lineNum">    6790 </span><span class="lineCov">       1739 :     for (i__ = *nl; i__ &gt;= 1; --i__) {</span></a>
+<a name="6791"><span class="lineNum">    6791 </span><span class="lineCov">       1680 :         z__[i__ + 1] = *alpha * vt[i__ + nlp1 * vt_dim1];</span></a>
+<a name="6792"><span class="lineNum">    6792 </span><span class="lineCov">       1680 :         d__[i__ + 1] = d__[i__];</span></a>
+<a name="6793"><span class="lineNum">    6793 </span><span class="lineCov">       1680 :         idxq[i__ + 1] = idxq[i__] + 1;</span></a>
+<a name="6794"><span class="lineNum">    6794 </span>            :     }</a>
+<a name="6795"><span class="lineNum">    6795 </span>            : </a>
+<a name="6796"><span class="lineNum">    6796 </span>            :     i__1 = m;</a>
+<a name="6797"><span class="lineNum">    6797 </span><span class="lineCov">       1739 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6798"><span class="lineNum">    6798 </span><span class="lineCov">       1680 :         z__[i__] = *beta * vt[i__ + nlp2 * vt_dim1];</span></a>
+<a name="6799"><span class="lineNum">    6799 </span>            :     }</a>
+<a name="6800"><span class="lineNum">    6800 </span>            : </a>
+<a name="6801"><span class="lineNum">    6801 </span>            :     i__1 = nlp1;</a>
+<a name="6802"><span class="lineNum">    6802 </span><span class="lineCov">       1739 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6803"><span class="lineNum">    6803 </span><span class="lineCov">       1680 :         coltyp[i__] = 1;</span></a>
+<a name="6804"><span class="lineNum">    6804 </span>            :     }</a>
+<a name="6805"><span class="lineNum">    6805 </span><span class="lineCov">         59 :     i__1 = n;</span></a>
+<a name="6806"><span class="lineNum">    6806 </span><span class="lineCov">       1713 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6807"><span class="lineNum">    6807 </span><span class="lineCov">       1654 :         coltyp[i__] = 2;</span></a>
+<a name="6808"><span class="lineNum">    6808 </span>            :     }</a>
+<a name="6809"><span class="lineNum">    6809 </span>            : </a>
+<a name="6810"><span class="lineNum">    6810 </span>            :     i__1 = n;</a>
+<a name="6811"><span class="lineNum">    6811 </span><span class="lineCov">       1713 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6812"><span class="lineNum">    6812 </span><span class="lineCov">       1654 :         idxq[i__] += nlp1;</span></a>
+<a name="6813"><span class="lineNum">    6813 </span>            :     }</a>
+<a name="6814"><span class="lineNum">    6814 </span>            : </a>
+<a name="6815"><span class="lineNum">    6815 </span>            :     i__1 = n;</a>
+<a name="6816"><span class="lineNum">    6816 </span><span class="lineCov">       3393 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6817"><span class="lineNum">    6817 </span><span class="lineCov">       3334 :         dsigma[i__] = d__[idxq[i__]];</span></a>
+<a name="6818"><span class="lineNum">    6818 </span><span class="lineCov">       3334 :         u2[i__ + u2_dim1] = z__[idxq[i__]];</span></a>
+<a name="6819"><span class="lineNum">    6819 </span><span class="lineCov">       3334 :         idxc[i__] = coltyp[idxq[i__]];</span></a>
+<a name="6820"><span class="lineNum">    6820 </span>            :     }</a>
+<a name="6821"><span class="lineNum">    6821 </span>            : </a>
+<a name="6822"><span class="lineNum">    6822 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlamrg,DLAMRG)(nl, nr, &amp;dsigma[2], &amp;c__1, &amp;c__1, &amp;idx[2]);</span></a>
+<a name="6823"><span class="lineNum">    6823 </span>            : </a>
+<a name="6824"><span class="lineNum">    6824 </span><span class="lineCov">         59 :     i__1 = n;</span></a>
+<a name="6825"><span class="lineNum">    6825 </span><span class="lineCov">       3393 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6826"><span class="lineNum">    6826 </span><span class="lineCov">       3334 :         idxi = idx[i__] + 1;</span></a>
+<a name="6827"><span class="lineNum">    6827 </span><span class="lineCov">       3334 :         d__[i__] = dsigma[idxi];</span></a>
+<a name="6828"><span class="lineNum">    6828 </span><span class="lineCov">       3334 :         z__[i__] = u2[idxi + u2_dim1];</span></a>
+<a name="6829"><span class="lineNum">    6829 </span><span class="lineCov">       3334 :         coltyp[i__] = idxc[idxi];</span></a>
+<a name="6830"><span class="lineNum">    6830 </span>            :     }</a>
+<a name="6831"><span class="lineNum">    6831 </span>            : </a>
+<a name="6832"><span class="lineNum">    6832 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="6833"><span class="lineNum">    6833 </span><span class="lineCov">         59 :     d__1 = std::abs(*alpha), d__2 = std::abs(*beta);</span></a>
+<a name="6834"><span class="lineNum">    6834 </span><span class="lineCov">         59 :     tol = (d__1 &gt; d__2) ? d__1 : d__2;</span></a>
+<a name="6835"><span class="lineNum">    6835 </span><span class="lineCov">         59 :     d__2 = std::abs(d__[n]);</span></a>
+<a name="6836"><span class="lineNum">    6836 </span><span class="lineCov">         59 :     tol = eps * 8. * ((d__2 &gt; tol) ? d__2 : tol);</span></a>
+<a name="6837"><span class="lineNum">    6837 </span>            : </a>
+<a name="6838"><span class="lineNum">    6838 </span><span class="lineCov">         59 :     *k = 1;</span></a>
+<a name="6839"><span class="lineNum">    6839 </span><span class="lineCov">         59 :     k2 = n + 1;</span></a>
+<a name="6840"><span class="lineNum">    6840 </span>            :     i__1 = n;</a>
+<a name="6841"><span class="lineNum">    6841 </span><span class="lineCov">         79 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="6842"><span class="lineNum">    6842 </span><span class="lineCov">         79 :         if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="6843"><span class="lineNum">    6843 </span>            : </a>
+<a name="6844"><span class="lineNum">    6844 </span><span class="lineCov">         20 :             --k2;</span></a>
+<a name="6845"><span class="lineNum">    6845 </span><span class="lineCov">         20 :             idxp[k2] = j;</span></a>
+<a name="6846"><span class="lineNum">    6846 </span><span class="lineCov">         20 :             coltyp[j] = 4;</span></a>
+<a name="6847"><span class="lineNum">    6847 </span><span class="lineCov">         20 :             if (j == n) {</span></a>
+<a name="6848"><span class="lineNum">    6848 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="6849"><span class="lineNum">    6849 </span>            :             }</a>
+<a name="6850"><span class="lineNum">    6850 </span>            :         } else {</a>
+<a name="6851"><span class="lineNum">    6851 </span>            :             jprev = j;</a>
+<a name="6852"><span class="lineNum">    6852 </span><span class="lineCov">         59 :             goto L90;</span></a>
+<a name="6853"><span class="lineNum">    6853 </span>            :         }</a>
+<a name="6854"><span class="lineNum">    6854 </span>            :     }</a>
+<a name="6855"><span class="lineNum">    6855 </span><span class="lineCov">         59 : L90:</span></a>
+<a name="6856"><span class="lineNum">    6856 </span>            :     j = jprev;</a>
+<a name="6857"><span class="lineNum">    6857 </span><span class="lineCov">       3314 : L100:</span></a>
+<a name="6858"><span class="lineNum">    6858 </span><span class="lineCov">       3314 :     ++j;</span></a>
+<a name="6859"><span class="lineNum">    6859 </span><span class="lineCov">       3314 :     if (j &gt; n) {</span></a>
+<a name="6860"><span class="lineNum">    6860 </span><span class="lineCov">         59 :         goto L110;</span></a>
+<a name="6861"><span class="lineNum">    6861 </span>            :     }</a>
+<a name="6862"><span class="lineNum">    6862 </span><span class="lineCov">       3255 :     if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="6863"><span class="lineNum">    6863 </span>            : </a>
+<a name="6864"><span class="lineNum">    6864 </span><span class="lineCov">        122 :         --k2;</span></a>
+<a name="6865"><span class="lineNum">    6865 </span><span class="lineCov">        122 :         idxp[k2] = j;</span></a>
+<a name="6866"><span class="lineNum">    6866 </span><span class="lineCov">        122 :         coltyp[j] = 4;</span></a>
+<a name="6867"><span class="lineNum">    6867 </span>            :     } else {</a>
+<a name="6868"><span class="lineNum">    6868 </span>            : </a>
+<a name="6869"><span class="lineNum">    6869 </span><span class="lineCov">       3133 :         if (std::abs(d__[j] - d__[jprev]) &lt;= tol) {</span></a>
+<a name="6870"><span class="lineNum">    6870 </span>            : </a>
+<a name="6871"><span class="lineNum">    6871 </span><span class="lineNoCov">          0 :             s = z__[jprev];</span></a>
+<a name="6872"><span class="lineNum">    6872 </span><span class="lineNoCov">          0 :             c__ = z__[j];</span></a>
+<a name="6873"><span class="lineNum">    6873 </span>            : </a>
+<a name="6874"><span class="lineNum">    6874 </span><span class="lineNoCov">          0 :             tau = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;c__, &amp;s);</span></a>
+<a name="6875"><span class="lineNum">    6875 </span><span class="lineNoCov">          0 :             c__ /= tau;</span></a>
+<a name="6876"><span class="lineNum">    6876 </span><span class="lineNoCov">          0 :             s = -s / tau;</span></a>
+<a name="6877"><span class="lineNum">    6877 </span><span class="lineNoCov">          0 :             z__[j] = tau;</span></a>
+<a name="6878"><span class="lineNum">    6878 </span><span class="lineNoCov">          0 :             z__[jprev] = 0.;</span></a>
+<a name="6879"><span class="lineNum">    6879 </span>            : </a>
+<a name="6880"><span class="lineNum">    6880 </span><span class="lineNoCov">          0 :             idxjp = idxq[idx[jprev] + 1];</span></a>
+<a name="6881"><span class="lineNum">    6881 </span><span class="lineNoCov">          0 :             idxj = idxq[idx[j] + 1];</span></a>
+<a name="6882"><span class="lineNum">    6882 </span><span class="lineNoCov">          0 :             if (idxjp &lt;= nlp1) {</span></a>
+<a name="6883"><span class="lineNum">    6883 </span><span class="lineNoCov">          0 :                 --idxjp;</span></a>
+<a name="6884"><span class="lineNum">    6884 </span>            :             }</a>
+<a name="6885"><span class="lineNum">    6885 </span><span class="lineNoCov">          0 :             if (idxj &lt;= nlp1) {</span></a>
+<a name="6886"><span class="lineNum">    6886 </span><span class="lineNoCov">          0 :                 --idxj;</span></a>
+<a name="6887"><span class="lineNum">    6887 </span>            :             }</a>
+<a name="6888"><span class="lineNum">    6888 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(&amp;n, &amp;u[idxjp * u_dim1 + 1], &amp;c__1, &amp;u[idxj * u_dim1 + 1], &amp;</span></a>
+<a name="6889"><span class="lineNum">    6889 </span>            :                     c__1, &amp;c__, &amp;s);</a>
+<a name="6890"><span class="lineNum">    6890 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(&amp;m, &amp;vt[idxjp + vt_dim1], ldvt, &amp;vt[idxj + vt_dim1], ldvt, &amp;</span></a>
+<a name="6891"><span class="lineNum">    6891 </span>            :                     c__, &amp;s);</a>
+<a name="6892"><span class="lineNum">    6892 </span><span class="lineNoCov">          0 :             if (coltyp[j] != coltyp[jprev]) {</span></a>
+<a name="6893"><span class="lineNum">    6893 </span><span class="lineNoCov">          0 :                 coltyp[j] = 3;</span></a>
+<a name="6894"><span class="lineNum">    6894 </span>            :             }</a>
+<a name="6895"><span class="lineNum">    6895 </span><span class="lineNoCov">          0 :             coltyp[jprev] = 4;</span></a>
+<a name="6896"><span class="lineNum">    6896 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="6897"><span class="lineNum">    6897 </span><span class="lineNoCov">          0 :             idxp[k2] = jprev;</span></a>
+<a name="6898"><span class="lineNum">    6898 </span>            :             jprev = j;</a>
+<a name="6899"><span class="lineNum">    6899 </span>            :         } else {</a>
+<a name="6900"><span class="lineNum">    6900 </span><span class="lineCov">       3133 :             ++(*k);</span></a>
+<a name="6901"><span class="lineNum">    6901 </span><span class="lineCov">       3133 :             u2[*k + u2_dim1] = z__[jprev];</span></a>
+<a name="6902"><span class="lineNum">    6902 </span><span class="lineCov">       3133 :             dsigma[*k] = d__[jprev];</span></a>
+<a name="6903"><span class="lineNum">    6903 </span><span class="lineCov">       3133 :             idxp[*k] = jprev;</span></a>
+<a name="6904"><span class="lineNum">    6904 </span>            :             jprev = j;</a>
+<a name="6905"><span class="lineNum">    6905 </span>            :         }</a>
+<a name="6906"><span class="lineNum">    6906 </span>            :     }</a>
+<a name="6907"><span class="lineNum">    6907 </span><span class="lineCov">       3255 :     goto L100;</span></a>
+<a name="6908"><span class="lineNum">    6908 </span>            : L110:</a>
+<a name="6909"><span class="lineNum">    6909 </span>            : </a>
+<a name="6910"><span class="lineNum">    6910 </span><span class="lineCov">         59 :     ++(*k);</span></a>
+<a name="6911"><span class="lineNum">    6911 </span><span class="lineCov">         59 :     u2[*k + u2_dim1] = z__[jprev];</span></a>
+<a name="6912"><span class="lineNum">    6912 </span><span class="lineCov">         59 :     dsigma[*k] = d__[jprev];</span></a>
+<a name="6913"><span class="lineNum">    6913 </span><span class="lineCov">         59 :     idxp[*k] = jprev;</span></a>
+<a name="6914"><span class="lineNum">    6914 </span>            : </a>
+<a name="6915"><span class="lineNum">    6915 </span>            : L120:</a>
+<a name="6916"><span class="lineNum">    6916 </span>            : </a>
+<a name="6917"><span class="lineNum">    6917 </span><span class="lineCov">        295 :     for (j = 1; j &lt;= 4; ++j) {</span></a>
+<a name="6918"><span class="lineNum">    6918 </span><span class="lineCov">        236 :         ctot[j - 1] = 0;</span></a>
+<a name="6919"><span class="lineNum">    6919 </span>            :     }</a>
+<a name="6920"><span class="lineNum">    6920 </span><span class="lineCov">         59 :     i__1 = n;</span></a>
+<a name="6921"><span class="lineNum">    6921 </span><span class="lineCov">       3393 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="6922"><span class="lineNum">    6922 </span><span class="lineCov">       3334 :         ct = coltyp[j];</span></a>
+<a name="6923"><span class="lineNum">    6923 </span><span class="lineCov">       3334 :         ++ctot[ct - 1];</span></a>
+<a name="6924"><span class="lineNum">    6924 </span>            :     }</a>
+<a name="6925"><span class="lineNum">    6925 </span>            : </a>
+<a name="6926"><span class="lineNum">    6926 </span><span class="lineCov">         59 :     psm[0] = 2;</span></a>
+<a name="6927"><span class="lineNum">    6927 </span><span class="lineCov">         59 :     psm[1] = ctot[0] + 2;</span></a>
+<a name="6928"><span class="lineNum">    6928 </span><span class="lineCov">         59 :     psm[2] = psm[1] + ctot[1];</span></a>
+<a name="6929"><span class="lineNum">    6929 </span><span class="lineCov">         59 :     psm[3] = psm[2] + ctot[2];</span></a>
+<a name="6930"><span class="lineNum">    6930 </span>            : </a>
+<a name="6931"><span class="lineNum">    6931 </span>            :     i__1 = n;</a>
+<a name="6932"><span class="lineNum">    6932 </span><span class="lineCov">       3393 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="6933"><span class="lineNum">    6933 </span><span class="lineCov">       3334 :         jp = idxp[j];</span></a>
+<a name="6934"><span class="lineNum">    6934 </span><span class="lineCov">       3334 :         ct = coltyp[jp];</span></a>
+<a name="6935"><span class="lineNum">    6935 </span><span class="lineCov">       3334 :         idxc[psm[ct - 1]] = j;</span></a>
+<a name="6936"><span class="lineNum">    6936 </span><span class="lineCov">       3334 :         ++psm[ct - 1];</span></a>
+<a name="6937"><span class="lineNum">    6937 </span>            :     }</a>
+<a name="6938"><span class="lineNum">    6938 </span>            : </a>
+<a name="6939"><span class="lineNum">    6939 </span>            :     i__1 = n;</a>
+<a name="6940"><span class="lineNum">    6940 </span><span class="lineCov">       3393 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="6941"><span class="lineNum">    6941 </span><span class="lineCov">       3334 :         jp = idxp[j];</span></a>
+<a name="6942"><span class="lineNum">    6942 </span><span class="lineCov">       3334 :         dsigma[j] = d__[jp];</span></a>
+<a name="6943"><span class="lineNum">    6943 </span><span class="lineCov">       3334 :         idxj = idxq[idx[idxp[idxc[j]]] + 1];</span></a>
+<a name="6944"><span class="lineNum">    6944 </span><span class="lineCov">       3334 :         if (idxj &lt;= nlp1) {</span></a>
+<a name="6945"><span class="lineNum">    6945 </span><span class="lineCov">       1680 :             --idxj;</span></a>
+<a name="6946"><span class="lineNum">    6946 </span>            :         }</a>
+<a name="6947"><span class="lineNum">    6947 </span><span class="lineCov">       3334 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;n, &amp;u[idxj * u_dim1 + 1], &amp;c__1, &amp;u2[j * u2_dim1 + 1], &amp;c__1);</span></a>
+<a name="6948"><span class="lineNum">    6948 </span><span class="lineCov">       3334 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;m, &amp;vt[idxj + vt_dim1], ldvt, &amp;vt2[j + vt2_dim1], ldvt2);</span></a>
+<a name="6949"><span class="lineNum">    6949 </span>            :     }</a>
+<a name="6950"><span class="lineNum">    6950 </span>            : </a>
+<a name="6951"><span class="lineNum">    6951 </span><span class="lineCov">         59 :     dsigma[1] = 0.;</span></a>
+<a name="6952"><span class="lineNum">    6952 </span><span class="lineCov">         59 :     hlftol = tol / 2.;</span></a>
+<a name="6953"><span class="lineNum">    6953 </span><span class="lineCov">         59 :     if (std::abs(dsigma[2]) &lt;= hlftol) {</span></a>
+<a name="6954"><span class="lineNum">    6954 </span><span class="lineCov">          5 :         dsigma[2] = hlftol;</span></a>
+<a name="6955"><span class="lineNum">    6955 </span>            :     }</a>
+<a name="6956"><span class="lineNum">    6956 </span><span class="lineCov">         59 :     if (m &gt; n) {</span></a>
+<a name="6957"><span class="lineNum">    6957 </span><span class="lineCov">         26 :         z__[1] = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;z1, &amp;z__[m]);</span></a>
+<a name="6958"><span class="lineNum">    6958 </span><span class="lineCov">         26 :         if (z__[1] &lt;= tol) {</span></a>
+<a name="6959"><span class="lineNum">    6959 </span><span class="lineNoCov">          0 :             c__ = 1.;</span></a>
+<a name="6960"><span class="lineNum">    6960 </span><span class="lineNoCov">          0 :             s = 0.;</span></a>
+<a name="6961"><span class="lineNum">    6961 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="6962"><span class="lineNum">    6962 </span>            :         } else {</a>
+<a name="6963"><span class="lineNum">    6963 </span><span class="lineCov">         26 :             c__ = z1 / z__[1];</span></a>
+<a name="6964"><span class="lineNum">    6964 </span><span class="lineCov">         26 :             s = z__[m] / z__[1];</span></a>
+<a name="6965"><span class="lineNum">    6965 </span>            :         }</a>
+<a name="6966"><span class="lineNum">    6966 </span>            :     } else {</a>
+<a name="6967"><span class="lineNum">    6967 </span><span class="lineCov">         33 :         if (std::abs(z1) &lt;= tol) {</span></a>
+<a name="6968"><span class="lineNum">    6968 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="6969"><span class="lineNum">    6969 </span>            :         } else {</a>
+<a name="6970"><span class="lineNum">    6970 </span><span class="lineCov">         33 :             z__[1] = z1;</span></a>
+<a name="6971"><span class="lineNum">    6971 </span>            :         }</a>
+<a name="6972"><span class="lineNum">    6972 </span>            :     }</a>
+<a name="6973"><span class="lineNum">    6973 </span>            : </a>
+<a name="6974"><span class="lineNum">    6974 </span><span class="lineCov">         59 :     i__1 = *k - 1;</span></a>
+<a name="6975"><span class="lineNum">    6975 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;u2[u2_dim1 + 2], &amp;c__1, &amp;z__[2], &amp;c__1);</span></a>
+<a name="6976"><span class="lineNum">    6976 </span>            : </a>
+<a name="6977"><span class="lineNum">    6977 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;n, &amp;c__1, &amp;zero, &amp;zero, &amp;u2[u2_offset], ldu2);</span></a>
+<a name="6978"><span class="lineNum">    6978 </span><span class="lineCov">         59 :     u2[nlp1 + u2_dim1] = 1.;</span></a>
+<a name="6979"><span class="lineNum">    6979 </span><span class="lineCov">         59 :     if (m &gt; n) {</span></a>
+<a name="6980"><span class="lineNum">    6980 </span>            :         i__1 = nlp1;</a>
+<a name="6981"><span class="lineNum">    6981 </span><span class="lineCov">        803 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6982"><span class="lineNum">    6982 </span><span class="lineCov">        777 :             vt[m + i__ * vt_dim1] = -s * vt[nlp1 + i__ * vt_dim1];</span></a>
+<a name="6983"><span class="lineNum">    6983 </span><span class="lineCov">        777 :             vt2[i__ * vt2_dim1 + 1] = c__ * vt[nlp1 + i__ * vt_dim1];</span></a>
+<a name="6984"><span class="lineNum">    6984 </span>            :         }</a>
+<a name="6985"><span class="lineNum">    6985 </span><span class="lineCov">         26 :         i__1 = m;</span></a>
+<a name="6986"><span class="lineNum">    6986 </span><span class="lineCov">        785 :         for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="6987"><span class="lineNum">    6987 </span><span class="lineCov">        759 :             vt2[i__ * vt2_dim1 + 1] = s * vt[m + i__ * vt_dim1];</span></a>
+<a name="6988"><span class="lineNum">    6988 </span><span class="lineCov">        759 :             vt[m + i__ * vt_dim1] = c__ * vt[m + i__ * vt_dim1];</span></a>
+<a name="6989"><span class="lineNum">    6989 </span>            :         }</a>
+<a name="6990"><span class="lineNum">    6990 </span>            :     } else {</a>
+<a name="6991"><span class="lineNum">    6991 </span><span class="lineCov">         33 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;m, &amp;vt[nlp1 + vt_dim1], ldvt, &amp;vt2[vt2_dim1 + 1], ldvt2);</span></a>
+<a name="6992"><span class="lineNum">    6992 </span>            :     }</a>
+<a name="6993"><span class="lineNum">    6993 </span><span class="lineCov">         59 :     if (m &gt; n) {</span></a>
+<a name="6994"><span class="lineNum">    6994 </span><span class="lineCov">         26 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;m, &amp;vt[m + vt_dim1], ldvt, &amp;vt2[m + vt2_dim1], ldvt2);</span></a>
+<a name="6995"><span class="lineNum">    6995 </span>            :     }</a>
+<a name="6996"><span class="lineNum">    6996 </span>            : </a>
+<a name="6997"><span class="lineNum">    6997 </span><span class="lineCov">         59 :     if (n &gt; *k) {</span></a>
+<a name="6998"><span class="lineNum">    6998 </span><span class="lineCov">         26 :         i__1 = n - *k;</span></a>
+<a name="6999"><span class="lineNum">    6999 </span><span class="lineCov">         26 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;dsigma[*k + 1], &amp;c__1, &amp;d__[*k + 1], &amp;c__1);</span></a>
+<a name="7000"><span class="lineNum">    7000 </span><span class="lineCov">         26 :         i__1 = n - *k;</span></a>
+<a name="7001"><span class="lineNum">    7001 </span><span class="lineCov">         26 :         PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;A&quot;, &amp;n, &amp;i__1, &amp;u2[(*k + 1) * u2_dim1 + 1], ldu2, &amp;u[(*k + 1)</span></a>
+<a name="7002"><span class="lineNum">    7002 </span><span class="lineCov">         26 :                  * u_dim1 + 1], ldu);</span></a>
+<a name="7003"><span class="lineNum">    7003 </span><span class="lineCov">         26 :         i__1 = n - *k;</span></a>
+<a name="7004"><span class="lineNum">    7004 </span><span class="lineCov">         26 :         PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;A&quot;, &amp;i__1, &amp;m, &amp;vt2[*k + 1 + vt2_dim1], ldvt2, &amp;vt[*k + 1 + </span></a>
+<a name="7005"><span class="lineNum">    7005 </span><span class="lineCov">         26 :                 vt_dim1], ldvt);</span></a>
+<a name="7006"><span class="lineNum">    7006 </span>            :     }</a>
+<a name="7007"><span class="lineNum">    7007 </span><span class="lineCov">        295 :     for (j = 1; j &lt;= 4; ++j) {</span></a>
+<a name="7008"><span class="lineNum">    7008 </span><span class="lineCov">        236 :         coltyp[j] = ctot[j - 1];</span></a>
+<a name="7009"><span class="lineNum">    7009 </span>            :     }</a>
+<a name="7010"><span class="lineNum">    7010 </span>            : </a>
+<a name="7011"><span class="lineNum">    7011 </span><span class="lineCov">         59 :     return;</span></a>
+<a name="7012"><span class="lineNum">    7012 </span>            : </a>
+<a name="7013"><span class="lineNum">    7013 </span>            : }</a>
+<a name="7014"><span class="lineNum">    7014 </span>            : </a>
+<a name="7015"><span class="lineNum">    7015 </span>            : </a>
+<a name="7016"><span class="lineNum">    7016 </span>            : }</a>
+<a name="7017"><span class="lineNum">    7017 </span>            : }</a>
+<a name="7018"><span class="lineNum">    7018 </span>            : #include &lt;cmath&gt;</a>
+<a name="7019"><span class="lineNum">    7019 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="7020"><span class="lineNum">    7020 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="7021"><span class="lineNum">    7021 </span>            : </a>
+<a name="7022"><span class="lineNum">    7022 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="7023"><span class="lineNum">    7023 </span>            : namespace PLMD{</a>
+<a name="7024"><span class="lineNum">    7024 </span>            : namespace lapack{</a>
+<a name="7025"><span class="lineNum">    7025 </span>            : using namespace blas;</a>
+<a name="7026"><span class="lineNum">    7026 </span>            : void </a>
+<a name="7027"><span class="lineNum">    7027 </span><span class="lineCov">         59 : PLUMED_BLAS_F77_FUNC(dlasd3,DLASD3)(int *nl, </span></a>
+<a name="7028"><span class="lineNum">    7028 </span>            :         int *nr,</a>
+<a name="7029"><span class="lineNum">    7029 </span>            :         int *sqre, </a>
+<a name="7030"><span class="lineNum">    7030 </span>            :         int *k, </a>
+<a name="7031"><span class="lineNum">    7031 </span>            :         double *d__, </a>
+<a name="7032"><span class="lineNum">    7032 </span>            :         double *q, </a>
+<a name="7033"><span class="lineNum">    7033 </span>            :         int *ldq, </a>
+<a name="7034"><span class="lineNum">    7034 </span>            :         double *dsigma, </a>
+<a name="7035"><span class="lineNum">    7035 </span>            :         double *u, </a>
+<a name="7036"><span class="lineNum">    7036 </span>            :         int *ldu, </a>
+<a name="7037"><span class="lineNum">    7037 </span>            :         double *u2, </a>
+<a name="7038"><span class="lineNum">    7038 </span>            :         int *ldu2, </a>
+<a name="7039"><span class="lineNum">    7039 </span>            :         double *vt, </a>
+<a name="7040"><span class="lineNum">    7040 </span>            :         int *ldvt, </a>
+<a name="7041"><span class="lineNum">    7041 </span>            :         double *vt2, </a>
+<a name="7042"><span class="lineNum">    7042 </span>            :         int *ldvt2, </a>
+<a name="7043"><span class="lineNum">    7043 </span>            :         int *idxc, </a>
+<a name="7044"><span class="lineNum">    7044 </span>            :         int *ctot, </a>
+<a name="7045"><span class="lineNum">    7045 </span>            :         double *z__, </a>
+<a name="7046"><span class="lineNum">    7046 </span>            :         int *info)</a>
+<a name="7047"><span class="lineNum">    7047 </span>            : {</a>
+<a name="7048"><span class="lineNum">    7048 </span>            :     int q_dim1, q_offset, u_dim1, u_offset, u2_dim1, u2_offset, vt_dim1, </a>
+<a name="7049"><span class="lineNum">    7049 </span>            :             vt_offset, vt2_dim1, vt2_offset, i__1, i__2;</a>
+<a name="7050"><span class="lineNum">    7050 </span>            :     double d__2;</a>
+<a name="7051"><span class="lineNum">    7051 </span>            : </a>
+<a name="7052"><span class="lineNum">    7052 </span>            :     int i__, j, m, n, jc;</a>
+<a name="7053"><span class="lineNum">    7053 </span>            :     double rho;</a>
+<a name="7054"><span class="lineNum">    7054 </span>            :     int nlp1, nlp2, nrp1;</a>
+<a name="7055"><span class="lineNum">    7055 </span>            :     double temp;</a>
+<a name="7056"><span class="lineNum">    7056 </span>            :     int ctemp;</a>
+<a name="7057"><span class="lineNum">    7057 </span>            :     int ktemp;</a>
+<a name="7058"><span class="lineNum">    7058 </span><span class="lineCov">         59 :     int c__1 = 1;</span></a>
+<a name="7059"><span class="lineNum">    7059 </span><span class="lineCov">         59 :     int c__0 = 0;</span></a>
+<a name="7060"><span class="lineNum">    7060 </span><span class="lineCov">         59 :     double zero = 0.0;</span></a>
+<a name="7061"><span class="lineNum">    7061 </span><span class="lineCov">         59 :     double one = 1.0;</span></a>
+<a name="7062"><span class="lineNum">    7062 </span>            : </a>
+<a name="7063"><span class="lineNum">    7063 </span>            :     --d__;</a>
+<a name="7064"><span class="lineNum">    7064 </span><span class="lineCov">         59 :     q_dim1 = *ldq;</span></a>
+<a name="7065"><span class="lineNum">    7065 </span><span class="lineCov">         59 :     q_offset = 1 + q_dim1;</span></a>
+<a name="7066"><span class="lineNum">    7066 </span><span class="lineCov">         59 :     q -= q_offset;</span></a>
+<a name="7067"><span class="lineNum">    7067 </span><span class="lineCov">         59 :     --dsigma;</span></a>
+<a name="7068"><span class="lineNum">    7068 </span><span class="lineCov">         59 :     u_dim1 = *ldu;</span></a>
+<a name="7069"><span class="lineNum">    7069 </span><span class="lineCov">         59 :     u_offset = 1 + u_dim1;</span></a>
+<a name="7070"><span class="lineNum">    7070 </span><span class="lineCov">         59 :     u -= u_offset;</span></a>
+<a name="7071"><span class="lineNum">    7071 </span><span class="lineCov">         59 :     u2_dim1 = *ldu2;</span></a>
+<a name="7072"><span class="lineNum">    7072 </span><span class="lineCov">         59 :     u2_offset = 1 + u2_dim1;</span></a>
+<a name="7073"><span class="lineNum">    7073 </span><span class="lineCov">         59 :     u2 -= u2_offset;</span></a>
+<a name="7074"><span class="lineNum">    7074 </span><span class="lineCov">         59 :     vt_dim1 = *ldvt;</span></a>
+<a name="7075"><span class="lineNum">    7075 </span><span class="lineCov">         59 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="7076"><span class="lineNum">    7076 </span><span class="lineCov">         59 :     vt -= vt_offset;</span></a>
+<a name="7077"><span class="lineNum">    7077 </span><span class="lineCov">         59 :     vt2_dim1 = *ldvt2;</span></a>
+<a name="7078"><span class="lineNum">    7078 </span><span class="lineCov">         59 :     vt2_offset = 1 + vt2_dim1;</span></a>
+<a name="7079"><span class="lineNum">    7079 </span><span class="lineCov">         59 :     vt2 -= vt2_offset;</span></a>
+<a name="7080"><span class="lineNum">    7080 </span><span class="lineCov">         59 :     --idxc;</span></a>
+<a name="7081"><span class="lineNum">    7081 </span>            :     --ctot;</a>
+<a name="7082"><span class="lineNum">    7082 </span><span class="lineCov">         59 :     --z__;</span></a>
+<a name="7083"><span class="lineNum">    7083 </span>            : </a>
+<a name="7084"><span class="lineNum">    7084 </span>            :     /* Function Body */</a>
+<a name="7085"><span class="lineNum">    7085 </span><span class="lineCov">         59 :     *info = 0;</span></a>
+<a name="7086"><span class="lineNum">    7086 </span>            : </a>
+<a name="7087"><span class="lineNum">    7087 </span><span class="lineCov">         59 :     if (*nl &lt; 1) {</span></a>
+<a name="7088"><span class="lineNum">    7088 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="7089"><span class="lineNum">    7089 </span><span class="lineCov">         59 :     } else if (*nr &lt; 1) {</span></a>
+<a name="7090"><span class="lineNum">    7090 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="7091"><span class="lineNum">    7091 </span><span class="lineCov">         59 :     } else if (*sqre != 1 &amp;&amp; *sqre != 0) {</span></a>
+<a name="7092"><span class="lineNum">    7092 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="7093"><span class="lineNum">    7093 </span>            :     }</a>
+<a name="7094"><span class="lineNum">    7094 </span>            : </a>
+<a name="7095"><span class="lineNum">    7095 </span><span class="lineCov">         59 :     n = *nl + *nr + 1;</span></a>
+<a name="7096"><span class="lineNum">    7096 </span><span class="lineCov">         59 :     m = n + *sqre;</span></a>
+<a name="7097"><span class="lineNum">    7097 </span><span class="lineCov">         59 :     nlp1 = *nl + 1;</span></a>
+<a name="7098"><span class="lineNum">    7098 </span><span class="lineCov">         59 :     nlp2 = *nl + 2;</span></a>
+<a name="7099"><span class="lineNum">    7099 </span>            : </a>
+<a name="7100"><span class="lineNum">    7100 </span><span class="lineCov">         59 :     if (*k == 1) {</span></a>
+<a name="7101"><span class="lineNum">    7101 </span><span class="lineNoCov">          0 :         d__[1] = std::abs(z__[1]);</span></a>
+<a name="7102"><span class="lineNum">    7102 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;m, &amp;vt2[vt2_dim1 + 1], ldvt2, &amp;vt[vt_dim1 + 1], ldvt);</span></a>
+<a name="7103"><span class="lineNum">    7103 </span><span class="lineNoCov">          0 :         if (z__[1] &gt; 0.) {</span></a>
+<a name="7104"><span class="lineNum">    7104 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;n, &amp;u2[u2_dim1 + 1], &amp;c__1, &amp;u[u_dim1 + 1], &amp;c__1);</span></a>
+<a name="7105"><span class="lineNum">    7105 </span>            :         } else {</a>
+<a name="7106"><span class="lineNum">    7106 </span><span class="lineNoCov">          0 :             i__1 = n;</span></a>
+<a name="7107"><span class="lineNum">    7107 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="7108"><span class="lineNum">    7108 </span><span class="lineNoCov">          0 :                 u[i__ + u_dim1] = -u2[i__ + u2_dim1];</span></a>
+<a name="7109"><span class="lineNum">    7109 </span>            :             }</a>
+<a name="7110"><span class="lineNum">    7110 </span>            :         }</a>
+<a name="7111"><span class="lineNum">    7111 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="7112"><span class="lineNum">    7112 </span>            :     }</a>
+<a name="7113"><span class="lineNum">    7113 </span>            : </a>
+<a name="7114"><span class="lineNum">    7114 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(k, &amp;z__[1], &amp;c__1, &amp;q[q_offset], &amp;c__1);</span></a>
+<a name="7115"><span class="lineNum">    7115 </span>            : </a>
+<a name="7116"><span class="lineNum">    7116 </span><span class="lineCov">         59 :     rho = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(k, &amp;z__[1], &amp;c__1);</span></a>
+<a name="7117"><span class="lineNum">    7117 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;rho, &amp;one, k, &amp;c__1, &amp;z__[1], k, info);</span></a>
+<a name="7118"><span class="lineNum">    7118 </span><span class="lineCov">         59 :     rho *= rho;</span></a>
+<a name="7119"><span class="lineNum">    7119 </span>            : </a>
+<a name="7120"><span class="lineNum">    7120 </span>            : </a>
+<a name="7121"><span class="lineNum">    7121 </span><span class="lineCov">         59 :     i__1 = *k;</span></a>
+<a name="7122"><span class="lineNum">    7122 </span><span class="lineCov">       3310 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7123"><span class="lineNum">    7123 </span><span class="lineCov">       3251 :         PLUMED_BLAS_F77_FUNC(dlasd4,DLASD4)(k, &amp;j, &amp;dsigma[1], &amp;z__[1], &amp;u[j * u_dim1 + 1], &amp;rho, &amp;d__[j],</span></a>
+<a name="7124"><span class="lineNum">    7124 </span><span class="lineCov">       3251 :                  &amp;vt[j * vt_dim1 + 1], info);</span></a>
+<a name="7125"><span class="lineNum">    7125 </span>            : </a>
+<a name="7126"><span class="lineNum">    7126 </span><span class="lineCov">       3251 :         if (*info != 0) {</span></a>
+<a name="7127"><span class="lineNum">    7127 </span>            :             return;</a>
+<a name="7128"><span class="lineNum">    7128 </span>            :         }</a>
+<a name="7129"><span class="lineNum">    7129 </span>            :     }</a>
+<a name="7130"><span class="lineNum">    7130 </span>            : </a>
+<a name="7131"><span class="lineNum">    7131 </span><span class="lineCov">         59 :     i__1 = *k;</span></a>
+<a name="7132"><span class="lineNum">    7132 </span><span class="lineCov">       3310 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="7133"><span class="lineNum">    7133 </span><span class="lineCov">       3251 :         z__[i__] = u[i__ + *k * u_dim1] * vt[i__ + *k * vt_dim1];</span></a>
+<a name="7134"><span class="lineNum">    7134 </span>            :         i__2 = i__ - 1;</a>
+<a name="7135"><span class="lineNum">    7135 </span><span class="lineCov">     212011 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="7136"><span class="lineNum">    7136 </span><span class="lineCov">     208760 :             z__[i__] *= u[i__ + j * u_dim1] * vt[i__ + j * vt_dim1] / (dsigma[</span></a>
+<a name="7137"><span class="lineNum">    7137 </span><span class="lineCov">     208760 :                     i__] - dsigma[j]) / (dsigma[i__] + dsigma[j]);</span></a>
+<a name="7138"><span class="lineNum">    7138 </span>            :         }</a>
+<a name="7139"><span class="lineNum">    7139 </span><span class="lineCov">       3251 :         i__2 = *k - 1;</span></a>
+<a name="7140"><span class="lineNum">    7140 </span><span class="lineCov">     212011 :         for (j = i__; j &lt;= i__2; ++j) {</span></a>
+<a name="7141"><span class="lineNum">    7141 </span><span class="lineCov">     208760 :             z__[i__] *= u[i__ + j * u_dim1] * vt[i__ + j * vt_dim1] / (dsigma[</span></a>
+<a name="7142"><span class="lineNum">    7142 </span><span class="lineCov">     208760 :                     i__] - dsigma[j + 1]) / (dsigma[i__] + dsigma[j + 1]);</span></a>
+<a name="7143"><span class="lineNum">    7143 </span>            :         }</a>
+<a name="7144"><span class="lineNum">    7144 </span><span class="lineCov">       3251 :         d__2 =  std::sqrt(std::abs(z__[i__]));</span></a>
+<a name="7145"><span class="lineNum">    7145 </span><span class="lineCov">       3251 :         z__[i__] = (q[i__ + q_dim1] &gt; 0) ? d__2 : -d__2;</span></a>
+<a name="7146"><span class="lineNum">    7146 </span>            :     }</a>
+<a name="7147"><span class="lineNum">    7147 </span>            : </a>
+<a name="7148"><span class="lineNum">    7148 </span><span class="lineCov">         59 :     i__1 = *k;</span></a>
+<a name="7149"><span class="lineNum">    7149 </span><span class="lineCov">       3310 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="7150"><span class="lineNum">    7150 </span><span class="lineCov">       3251 :         vt[i__ * vt_dim1 + 1] = z__[1] / u[i__ * u_dim1 + 1] / vt[i__ * </span></a>
+<a name="7151"><span class="lineNum">    7151 </span><span class="lineCov">       3251 :                 vt_dim1 + 1];</span></a>
+<a name="7152"><span class="lineNum">    7152 </span><span class="lineCov">       3251 :         u[i__ * u_dim1 + 1] = -1.;</span></a>
+<a name="7153"><span class="lineNum">    7153 </span><span class="lineCov">       3251 :         i__2 = *k;</span></a>
+<a name="7154"><span class="lineNum">    7154 </span><span class="lineCov">     420771 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="7155"><span class="lineNum">    7155 </span><span class="lineCov">     417520 :             vt[j + i__ * vt_dim1] = z__[j] / u[j + i__ * u_dim1] / vt[j + i__ </span></a>
+<a name="7156"><span class="lineNum">    7156 </span><span class="lineCov">     417520 :                     * vt_dim1];</span></a>
+<a name="7157"><span class="lineNum">    7157 </span><span class="lineCov">     417520 :             u[j + i__ * u_dim1] = dsigma[j] * vt[j + i__ * vt_dim1];</span></a>
+<a name="7158"><span class="lineNum">    7158 </span>            :         }</a>
+<a name="7159"><span class="lineNum">    7159 </span><span class="lineCov">       3251 :         temp = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(k, &amp;u[i__ * u_dim1 + 1], &amp;c__1);</span></a>
+<a name="7160"><span class="lineNum">    7160 </span><span class="lineCov">       3251 :         q[i__ * q_dim1 + 1] = u[i__ * u_dim1 + 1] / temp;</span></a>
+<a name="7161"><span class="lineNum">    7161 </span><span class="lineCov">       3251 :         i__2 = *k;</span></a>
+<a name="7162"><span class="lineNum">    7162 </span><span class="lineCov">     420771 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="7163"><span class="lineNum">    7163 </span><span class="lineCov">     417520 :             jc = idxc[j];</span></a>
+<a name="7164"><span class="lineNum">    7164 </span><span class="lineCov">     417520 :             q[j + i__ * q_dim1] = u[jc + i__ * u_dim1] / temp;</span></a>
+<a name="7165"><span class="lineNum">    7165 </span>            :         }</a>
+<a name="7166"><span class="lineNum">    7166 </span>            :     }</a>
+<a name="7167"><span class="lineNum">    7167 </span>            : </a>
+<a name="7168"><span class="lineNum">    7168 </span><span class="lineCov">         59 :     if (*k == 2) {</span></a>
+<a name="7169"><span class="lineNum">    7169 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, &amp;n, k, k, &amp;one, &amp;u2[u2_offset], ldu2, &amp;q[q_offset],</span></a>
+<a name="7170"><span class="lineNum">    7170 </span>            :                  ldq, &amp;zero, &amp;u[u_offset], ldu);</a>
+<a name="7171"><span class="lineNum">    7171 </span><span class="lineNoCov">          0 :         goto L100;</span></a>
+<a name="7172"><span class="lineNum">    7172 </span>            :     }</a>
+<a name="7173"><span class="lineNum">    7173 </span><span class="lineCov">         59 :     if (ctot[1] &gt; 0) {</span></a>
+<a name="7174"><span class="lineNum">    7174 </span><span class="lineCov">         59 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, nl, k, &amp;ctot[1], &amp;one, &amp;u2[(u2_dim1 &lt;&lt; 1) + 1], </span></a>
+<a name="7175"><span class="lineNum">    7175 </span><span class="lineCov">         59 :                 ldu2, &amp;q[q_dim1 + 2], ldq, &amp;zero, &amp;u[u_dim1 + 1], ldu);</span></a>
+<a name="7176"><span class="lineNum">    7176 </span><span class="lineCov">         59 :         if (ctot[3] &gt; 0) {</span></a>
+<a name="7177"><span class="lineNum">    7177 </span><span class="lineNoCov">          0 :             ktemp = ctot[1] + 2 + ctot[2];</span></a>
+<a name="7178"><span class="lineNum">    7178 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, nl, k, &amp;ctot[3], &amp;one, &amp;u2[ktemp * u2_dim1 + 1]</span></a>
+<a name="7179"><span class="lineNum">    7179 </span><span class="lineNoCov">          0 :                     , ldu2, &amp;q[ktemp + q_dim1], ldq, &amp;one, &amp;u[u_dim1 + 1], </span></a>
+<a name="7180"><span class="lineNum">    7180 </span>            :                     ldu);</a>
+<a name="7181"><span class="lineNum">    7181 </span>            :         }</a>
+<a name="7182"><span class="lineNum">    7182 </span><span class="lineNoCov">          0 :     } else if (ctot[3] &gt; 0) {</span></a>
+<a name="7183"><span class="lineNum">    7183 </span><span class="lineNoCov">          0 :         ktemp = ctot[1] + 2 + ctot[2];</span></a>
+<a name="7184"><span class="lineNum">    7184 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, nl, k, &amp;ctot[3], &amp;one, &amp;u2[ktemp * u2_dim1 + 1], </span></a>
+<a name="7185"><span class="lineNum">    7185 </span><span class="lineNoCov">          0 :                 ldu2, &amp;q[ktemp + q_dim1], ldq, &amp;zero, &amp;u[u_dim1 + 1], ldu);</span></a>
+<a name="7186"><span class="lineNum">    7186 </span>            :     } else {</a>
+<a name="7187"><span class="lineNum">    7187 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlacpy,DLACPY)(&quot;F&quot;, nl, k, &amp;u2[u2_offset], ldu2, &amp;u[u_offset], ldu);</span></a>
+<a name="7188"><span class="lineNum">    7188 </span>            :     }</a>
+<a name="7189"><span class="lineNum">    7189 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(k, &amp;q[q_dim1 + 1], ldq, &amp;u[nlp1 + u_dim1], ldu);</span></a>
+<a name="7190"><span class="lineNum">    7190 </span><span class="lineCov">         59 :     ktemp = ctot[1] + 2;</span></a>
+<a name="7191"><span class="lineNum">    7191 </span><span class="lineCov">         59 :     ctemp = ctot[2] + ctot[3];</span></a>
+<a name="7192"><span class="lineNum">    7192 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, nr, k, &amp;ctemp, &amp;one, &amp;u2[nlp2 + ktemp * u2_dim1], ldu2,</span></a>
+<a name="7193"><span class="lineNum">    7193 </span><span class="lineCov">         59 :              &amp;q[ktemp + q_dim1], ldq, &amp;zero, &amp;u[nlp2 + u_dim1], ldu);</span></a>
+<a name="7194"><span class="lineNum">    7194 </span>            : </a>
+<a name="7195"><span class="lineNum">    7195 </span><span class="lineCov">         59 : L100:</span></a>
+<a name="7196"><span class="lineNum">    7196 </span><span class="lineCov">         59 :     i__1 = *k;</span></a>
+<a name="7197"><span class="lineNum">    7197 </span><span class="lineCov">       3310 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="7198"><span class="lineNum">    7198 </span><span class="lineCov">       3251 :         temp = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(k, &amp;vt[i__ * vt_dim1 + 1], &amp;c__1);</span></a>
+<a name="7199"><span class="lineNum">    7199 </span><span class="lineCov">       3251 :         q[i__ + q_dim1] = vt[i__ * vt_dim1 + 1] / temp;</span></a>
+<a name="7200"><span class="lineNum">    7200 </span><span class="lineCov">       3251 :         i__2 = *k;</span></a>
+<a name="7201"><span class="lineNum">    7201 </span><span class="lineCov">     420771 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="7202"><span class="lineNum">    7202 </span><span class="lineCov">     417520 :             jc = idxc[j];</span></a>
+<a name="7203"><span class="lineNum">    7203 </span><span class="lineCov">     417520 :             q[i__ + j * q_dim1] = vt[jc + i__ * vt_dim1] / temp;</span></a>
+<a name="7204"><span class="lineNum">    7204 </span>            :         }</a>
+<a name="7205"><span class="lineNum">    7205 </span>            :     }</a>
+<a name="7206"><span class="lineNum">    7206 </span>            : </a>
+<a name="7207"><span class="lineNum">    7207 </span><span class="lineCov">         59 :     if (*k == 2) {</span></a>
+<a name="7208"><span class="lineNum">    7208 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;m, k, &amp;one, &amp;q[q_offset], ldq, &amp;vt2[vt2_offset]</span></a>
+<a name="7209"><span class="lineNum">    7209 </span>            :                 , ldvt2, &amp;zero, &amp;vt[vt_offset], ldvt);</a>
+<a name="7210"><span class="lineNum">    7210 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="7211"><span class="lineNum">    7211 </span>            :     }</a>
+<a name="7212"><span class="lineNum">    7212 </span><span class="lineCov">         59 :     ktemp = ctot[1] + 1;</span></a>
+<a name="7213"><span class="lineNum">    7213 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;nlp1, &amp;ktemp, &amp;one, &amp;q[q_dim1 + 1], ldq, &amp;vt2[</span></a>
+<a name="7214"><span class="lineNum">    7214 </span><span class="lineCov">         59 :             vt2_dim1 + 1], ldvt2, &amp;zero, &amp;vt[vt_dim1 + 1], ldvt);</span></a>
+<a name="7215"><span class="lineNum">    7215 </span><span class="lineCov">         59 :     ktemp = ctot[1] + 2 + ctot[2];</span></a>
+<a name="7216"><span class="lineNum">    7216 </span><span class="lineCov">         59 :     if (ktemp &lt;= *ldvt2) {</span></a>
+<a name="7217"><span class="lineNum">    7217 </span><span class="lineCov">         49 :         PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;nlp1, &amp;ctot[3], &amp;one, &amp;q[ktemp * q_dim1 + 1], </span></a>
+<a name="7218"><span class="lineNum">    7218 </span><span class="lineCov">         49 :                 ldq, &amp;vt2[ktemp + vt2_dim1], ldvt2, &amp;one, &amp;vt[vt_dim1 + 1], </span></a>
+<a name="7219"><span class="lineNum">    7219 </span>            :                 ldvt);</a>
+<a name="7220"><span class="lineNum">    7220 </span>            :     }</a>
+<a name="7221"><span class="lineNum">    7221 </span>            : </a>
+<a name="7222"><span class="lineNum">    7222 </span><span class="lineCov">         59 :     ktemp = ctot[1] + 1;</span></a>
+<a name="7223"><span class="lineNum">    7223 </span><span class="lineCov">         59 :     nrp1 = *nr + *sqre;</span></a>
+<a name="7224"><span class="lineNum">    7224 </span><span class="lineCov">         59 :     if (ktemp &gt; 1) {</span></a>
+<a name="7225"><span class="lineNum">    7225 </span><span class="lineCov">         59 :         i__1 = *k;</span></a>
+<a name="7226"><span class="lineNum">    7226 </span><span class="lineCov">       3310 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="7227"><span class="lineNum">    7227 </span><span class="lineCov">       3251 :             q[i__ + ktemp * q_dim1] = q[i__ + q_dim1];</span></a>
+<a name="7228"><span class="lineNum">    7228 </span>            :         }</a>
+<a name="7229"><span class="lineNum">    7229 </span><span class="lineCov">         59 :         i__1 = m;</span></a>
+<a name="7230"><span class="lineNum">    7230 </span><span class="lineCov">       1739 :         for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="7231"><span class="lineNum">    7231 </span><span class="lineCov">       1680 :             vt2[ktemp + i__ * vt2_dim1] = vt2[i__ * vt2_dim1 + 1];</span></a>
+<a name="7232"><span class="lineNum">    7232 </span>            :         }</a>
+<a name="7233"><span class="lineNum">    7233 </span>            :     }</a>
+<a name="7234"><span class="lineNum">    7234 </span><span class="lineCov">         59 :     ctemp = ctot[2] + 1 + ctot[3];</span></a>
+<a name="7235"><span class="lineNum">    7235 </span><span class="lineCov">         59 :     PLUMED_BLAS_F77_FUNC(dgemm,DGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;nrp1, &amp;ctemp, &amp;one, &amp;q[ktemp * q_dim1 + 1], ldq, &amp;</span></a>
+<a name="7236"><span class="lineNum">    7236 </span><span class="lineCov">         59 :             vt2[ktemp + nlp2 * vt2_dim1], ldvt2, &amp;zero, &amp;vt[nlp2 * vt_dim1 + </span></a>
+<a name="7237"><span class="lineNum">    7237 </span><span class="lineCov">         59 :             1], ldvt);</span></a>
+<a name="7238"><span class="lineNum">    7238 </span>            : </a>
+<a name="7239"><span class="lineNum">    7239 </span>            :     return;</a>
+<a name="7240"><span class="lineNum">    7240 </span>            : </a>
+<a name="7241"><span class="lineNum">    7241 </span>            : </a>
+<a name="7242"><span class="lineNum">    7242 </span>            : }</a>
+<a name="7243"><span class="lineNum">    7243 </span>            : </a>
+<a name="7244"><span class="lineNum">    7244 </span>            : </a>
+<a name="7245"><span class="lineNum">    7245 </span>            : }</a>
+<a name="7246"><span class="lineNum">    7246 </span>            : }</a>
+<a name="7247"><span class="lineNum">    7247 </span>            : #include &lt;cmath&gt;</a>
+<a name="7248"><span class="lineNum">    7248 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="7249"><span class="lineNum">    7249 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="7250"><span class="lineNum">    7250 </span>            : </a>
+<a name="7251"><span class="lineNum">    7251 </span>            : #include &quot;real.h&quot;</a>
+<a name="7252"><span class="lineNum">    7252 </span>            : </a>
+<a name="7253"><span class="lineNum">    7253 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="7254"><span class="lineNum">    7254 </span>            : namespace PLMD{</a>
+<a name="7255"><span class="lineNum">    7255 </span>            : namespace lapack{</a>
+<a name="7256"><span class="lineNum">    7256 </span>            : using namespace blas;</a>
+<a name="7257"><span class="lineNum">    7257 </span>            : void </a>
+<a name="7258"><span class="lineNum">    7258 </span><span class="lineCov">       3251 : PLUMED_BLAS_F77_FUNC(dlasd4,DLASD4)(int *n, </span></a>
+<a name="7259"><span class="lineNum">    7259 </span>            :         int *i__, </a>
+<a name="7260"><span class="lineNum">    7260 </span>            :         double *d__, </a>
+<a name="7261"><span class="lineNum">    7261 </span>            :         double *z__, </a>
+<a name="7262"><span class="lineNum">    7262 </span>            :         double *delta, </a>
+<a name="7263"><span class="lineNum">    7263 </span>            :         double *rho, </a>
+<a name="7264"><span class="lineNum">    7264 </span>            :         double *sigma, </a>
+<a name="7265"><span class="lineNum">    7265 </span>            :         double *work, </a>
+<a name="7266"><span class="lineNum">    7266 </span>            :         int *info)</a>
+<a name="7267"><span class="lineNum">    7267 </span>            : {</a>
+<a name="7268"><span class="lineNum">    7268 </span>            :     int i__1;</a>
+<a name="7269"><span class="lineNum">    7269 </span>            :     double d__1;</a>
+<a name="7270"><span class="lineNum">    7270 </span>            : </a>
+<a name="7271"><span class="lineNum">    7271 </span>            :     double a, b, c__;</a>
+<a name="7272"><span class="lineNum">    7272 </span>            :     int j;</a>
+<a name="7273"><span class="lineNum">    7273 </span>            :     double w, dd[3];</a>
+<a name="7274"><span class="lineNum">    7274 </span>            :     int ii;</a>
+<a name="7275"><span class="lineNum">    7275 </span>            :     double dw, zz[3];</a>
+<a name="7276"><span class="lineNum">    7276 </span>            :     int ip1;</a>
+<a name="7277"><span class="lineNum">    7277 </span>            :     double eta, phi, eps, tau, psi;</a>
+<a name="7278"><span class="lineNum">    7278 </span>            :     int iim1, iip1;</a>
+<a name="7279"><span class="lineNum">    7279 </span>            :     double dphi, dpsi;</a>
+<a name="7280"><span class="lineNum">    7280 </span>            :     int iter;</a>
+<a name="7281"><span class="lineNum">    7281 </span>            :     double temp, prew, sg2lb, sg2ub, temp1, temp2, dtiim, delsq, </a>
+<a name="7282"><span class="lineNum">    7282 </span>            :             dtiip;</a>
+<a name="7283"><span class="lineNum">    7283 </span>            :     int niter;</a>
+<a name="7284"><span class="lineNum">    7284 </span>            :     double dtisq;</a>
+<a name="7285"><span class="lineNum">    7285 </span>            :     int swtch;</a>
+<a name="7286"><span class="lineNum">    7286 </span>            :     double dtnsq;</a>
+<a name="7287"><span class="lineNum">    7287 </span>            :     double delsq2, dtnsq1;</a>
+<a name="7288"><span class="lineNum">    7288 </span>            :     int swtch3;</a>
+<a name="7289"><span class="lineNum">    7289 </span>            :     int orgati;</a>
+<a name="7290"><span class="lineNum">    7290 </span>            :     double erretm, dtipsq, rhoinv;</a>
+<a name="7291"><span class="lineNum">    7291 </span>            : </a>
+<a name="7292"><span class="lineNum">    7292 </span><span class="lineCov">       3251 :     --work;</span></a>
+<a name="7293"><span class="lineNum">    7293 </span><span class="lineCov">       3251 :     --delta;</span></a>
+<a name="7294"><span class="lineNum">    7294 </span><span class="lineCov">       3251 :     --z__;</span></a>
+<a name="7295"><span class="lineNum">    7295 </span><span class="lineCov">       3251 :     --d__;</span></a>
+<a name="7296"><span class="lineNum">    7296 </span>            : </a>
+<a name="7297"><span class="lineNum">    7297 </span><span class="lineCov">       3251 :     *info = 0;</span></a>
+<a name="7298"><span class="lineNum">    7298 </span><span class="lineCov">       3251 :     if (*n == 1) {</span></a>
+<a name="7299"><span class="lineNum">    7299 </span>            : </a>
+<a name="7300"><span class="lineNum">    7300 </span><span class="lineNoCov">          0 :         *sigma =  std::sqrt(d__[1] * d__[1] + *rho * z__[1] * z__[1]);</span></a>
+<a name="7301"><span class="lineNum">    7301 </span><span class="lineNoCov">          0 :         delta[1] = 1.;</span></a>
+<a name="7302"><span class="lineNum">    7302 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="7303"><span class="lineNum">    7303 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="7304"><span class="lineNum">    7304 </span>            :     }</a>
+<a name="7305"><span class="lineNum">    7305 </span><span class="lineCov">       3251 :     if (*n == 2) {</span></a>
+<a name="7306"><span class="lineNum">    7306 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasd5,DLASD5)(i__, &amp;d__[1], &amp;z__[1], &amp;delta[1], rho, sigma, &amp;work[1]);</span></a>
+<a name="7307"><span class="lineNum">    7307 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="7308"><span class="lineNum">    7308 </span>            :     }</a>
+<a name="7309"><span class="lineNum">    7309 </span>            : </a>
+<a name="7310"><span class="lineNum">    7310 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="7311"><span class="lineNum">    7311 </span><span class="lineCov">       3251 :     rhoinv = 1. / *rho;</span></a>
+<a name="7312"><span class="lineNum">    7312 </span>            : </a>
+<a name="7313"><span class="lineNum">    7313 </span><span class="lineCov">       3251 :     if (*i__ == *n) {</span></a>
+<a name="7314"><span class="lineNum">    7314 </span>            : </a>
+<a name="7315"><span class="lineNum">    7315 </span><span class="lineCov">         59 :         ii = *n - 1;</span></a>
+<a name="7316"><span class="lineNum">    7316 </span><span class="lineCov">         59 :         niter = 1;</span></a>
+<a name="7317"><span class="lineNum">    7317 </span>            : </a>
+<a name="7318"><span class="lineNum">    7318 </span><span class="lineCov">         59 :         temp = *rho / 2.;</span></a>
+<a name="7319"><span class="lineNum">    7319 </span>            : </a>
+<a name="7320"><span class="lineNum">    7320 </span><span class="lineCov">         59 :         temp1 = temp / (d__[*n] +  std::sqrt(d__[*n] * d__[*n] + temp));</span></a>
+<a name="7321"><span class="lineNum">    7321 </span><span class="lineCov">         59 :         i__1 = *n;</span></a>
+<a name="7322"><span class="lineNum">    7322 </span><span class="lineCov">       3310 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7323"><span class="lineNum">    7323 </span><span class="lineCov">       3251 :             work[j] = d__[j] + d__[*n] + temp1;</span></a>
+<a name="7324"><span class="lineNum">    7324 </span><span class="lineCov">       3251 :             delta[j] = d__[j] - d__[*n] - temp1;</span></a>
+<a name="7325"><span class="lineNum">    7325 </span>            :         }</a>
+<a name="7326"><span class="lineNum">    7326 </span>            : </a>
+<a name="7327"><span class="lineNum">    7327 </span>            :         psi = 0.;</a>
+<a name="7328"><span class="lineNum">    7328 </span><span class="lineCov">         59 :         i__1 = *n - 2;</span></a>
+<a name="7329"><span class="lineNum">    7329 </span><span class="lineCov">       3192 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7330"><span class="lineNum">    7330 </span><span class="lineCov">       3133 :             psi += z__[j] * z__[j] / (delta[j] * work[j]);</span></a>
+<a name="7331"><span class="lineNum">    7331 </span>            :         }</a>
+<a name="7332"><span class="lineNum">    7332 </span>            : </a>
+<a name="7333"><span class="lineNum">    7333 </span><span class="lineCov">         59 :         c__ = rhoinv + psi;</span></a>
+<a name="7334"><span class="lineNum">    7334 </span><span class="lineCov">         59 :         w = c__ + z__[ii] * z__[ii] / (delta[ii] * work[ii]) + z__[*n] * z__[*</span></a>
+<a name="7335"><span class="lineNum">    7335 </span><span class="lineCov">         59 :                 n] / (delta[*n] * work[*n]);</span></a>
+<a name="7336"><span class="lineNum">    7336 </span>            : </a>
+<a name="7337"><span class="lineNum">    7337 </span><span class="lineCov">         59 :         if (w &lt;= 0.) {</span></a>
+<a name="7338"><span class="lineNum">    7338 </span><span class="lineNoCov">          0 :             temp1 =  std::sqrt(d__[*n] * d__[*n] + *rho);</span></a>
+<a name="7339"><span class="lineNum">    7339 </span><span class="lineNoCov">          0 :             temp = z__[*n - 1] * z__[*n - 1] / ((d__[*n - 1] + temp1) * (d__[*</span></a>
+<a name="7340"><span class="lineNum">    7340 </span><span class="lineNoCov">          0 :                     n] - d__[*n - 1] + *rho / (d__[*n] + temp1))) + z__[*n] * </span></a>
+<a name="7341"><span class="lineNum">    7341 </span><span class="lineNoCov">          0 :                     z__[*n] / *rho;</span></a>
+<a name="7342"><span class="lineNum">    7342 </span>            : </a>
+<a name="7343"><span class="lineNum">    7343 </span><span class="lineNoCov">          0 :             if (c__ &lt;= temp) {</span></a>
+<a name="7344"><span class="lineNum">    7344 </span>            :                 tau = *rho;</a>
+<a name="7345"><span class="lineNum">    7345 </span>            :             } else {</a>
+<a name="7346"><span class="lineNum">    7346 </span><span class="lineNoCov">          0 :                 delsq = (d__[*n] - d__[*n - 1]) * (d__[*n] + d__[*n - 1]);</span></a>
+<a name="7347"><span class="lineNum">    7347 </span><span class="lineNoCov">          0 :                 a = -c__ * delsq + z__[*n - 1] * z__[*n - 1] + z__[*n] * z__[*</span></a>
+<a name="7348"><span class="lineNum">    7348 </span>            :                         n];</a>
+<a name="7349"><span class="lineNum">    7349 </span><span class="lineNoCov">          0 :                 b = z__[*n] * z__[*n] * delsq;</span></a>
+<a name="7350"><span class="lineNum">    7350 </span><span class="lineNoCov">          0 :                 if (a &lt; 0.) {</span></a>
+<a name="7351"><span class="lineNum">    7351 </span><span class="lineNoCov">          0 :                     tau = b * 2. / ( std::sqrt(a * a + b * 4. * c__) - a);</span></a>
+<a name="7352"><span class="lineNum">    7352 </span>            :                 } else {</a>
+<a name="7353"><span class="lineNum">    7353 </span><span class="lineNoCov">          0 :                     tau = (a +  std::sqrt(a * a + b * 4. * c__)) / (c__ * 2.);</span></a>
+<a name="7354"><span class="lineNum">    7354 </span>            :                 }</a>
+<a name="7355"><span class="lineNum">    7355 </span>            :             }</a>
+<a name="7356"><span class="lineNum">    7356 </span>            : </a>
+<a name="7357"><span class="lineNum">    7357 </span>            :         } else {</a>
+<a name="7358"><span class="lineNum">    7358 </span><span class="lineCov">         59 :             delsq = (d__[*n] - d__[*n - 1]) * (d__[*n] + d__[*n - 1]);</span></a>
+<a name="7359"><span class="lineNum">    7359 </span><span class="lineCov">         59 :             a = -c__ * delsq + z__[*n - 1] * z__[*n - 1] + z__[*n] * z__[*n];</span></a>
+<a name="7360"><span class="lineNum">    7360 </span><span class="lineCov">         59 :             b = z__[*n] * z__[*n] * delsq;</span></a>
+<a name="7361"><span class="lineNum">    7361 </span>            : </a>
+<a name="7362"><span class="lineNum">    7362 </span><span class="lineCov">         59 :             if (a &lt; 0.) {</span></a>
+<a name="7363"><span class="lineNum">    7363 </span><span class="lineCov">         59 :                 tau = b * 2. / ( std::sqrt(a * a + b * 4. * c__) - a);</span></a>
+<a name="7364"><span class="lineNum">    7364 </span>            :             } else {</a>
+<a name="7365"><span class="lineNum">    7365 </span><span class="lineNoCov">          0 :                 tau = (a +  std::sqrt(a * a + b * 4. * c__)) / (c__ * 2.);</span></a>
+<a name="7366"><span class="lineNum">    7366 </span>            :             }</a>
+<a name="7367"><span class="lineNum">    7367 </span>            : </a>
+<a name="7368"><span class="lineNum">    7368 </span>            :         }</a>
+<a name="7369"><span class="lineNum">    7369 </span>            : </a>
+<a name="7370"><span class="lineNum">    7370 </span><span class="lineCov">         59 :         eta = tau / (d__[*n] +  std::sqrt(d__[*n] * d__[*n] + tau));</span></a>
+<a name="7371"><span class="lineNum">    7371 </span>            : </a>
+<a name="7372"><span class="lineNum">    7372 </span><span class="lineCov">         59 :         *sigma = d__[*n] + eta;</span></a>
+<a name="7373"><span class="lineNum">    7373 </span><span class="lineCov">         59 :         i__1 = *n;</span></a>
+<a name="7374"><span class="lineNum">    7374 </span><span class="lineCov">       3310 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7375"><span class="lineNum">    7375 </span><span class="lineCov">       3251 :             delta[j] = d__[j] - d__[*i__] - eta;</span></a>
+<a name="7376"><span class="lineNum">    7376 </span><span class="lineCov">       3251 :             work[j] = d__[j] + d__[*i__] + eta;</span></a>
+<a name="7377"><span class="lineNum">    7377 </span>            :         }</a>
+<a name="7378"><span class="lineNum">    7378 </span>            : </a>
+<a name="7379"><span class="lineNum">    7379 </span>            :         dpsi = 0.;</a>
+<a name="7380"><span class="lineNum">    7380 </span>            :         psi = 0.;</a>
+<a name="7381"><span class="lineNum">    7381 </span>            :         erretm = 0.;</a>
+<a name="7382"><span class="lineNum">    7382 </span>            :         i__1 = ii;</a>
+<a name="7383"><span class="lineNum">    7383 </span><span class="lineCov">       3251 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7384"><span class="lineNum">    7384 </span><span class="lineCov">       3192 :             temp = z__[j] / (delta[j] * work[j]);</span></a>
+<a name="7385"><span class="lineNum">    7385 </span><span class="lineCov">       3192 :             psi += z__[j] * temp;</span></a>
+<a name="7386"><span class="lineNum">    7386 </span><span class="lineCov">       3192 :             dpsi += temp * temp;</span></a>
+<a name="7387"><span class="lineNum">    7387 </span><span class="lineCov">       3192 :             erretm += psi;</span></a>
+<a name="7388"><span class="lineNum">    7388 </span>            :         }</a>
+<a name="7389"><span class="lineNum">    7389 </span>            :         erretm = std::abs(erretm);</a>
+<a name="7390"><span class="lineNum">    7390 </span>            : </a>
+<a name="7391"><span class="lineNum">    7391 </span><span class="lineCov">         59 :         temp = z__[*n] / (delta[*n] * work[*n]);</span></a>
+<a name="7392"><span class="lineNum">    7392 </span><span class="lineCov">         59 :         phi = z__[*n] * temp;</span></a>
+<a name="7393"><span class="lineNum">    7393 </span><span class="lineCov">         59 :         dphi = temp * temp;</span></a>
+<a name="7394"><span class="lineNum">    7394 </span><span class="lineCov">         59 :         erretm = (-phi - psi) * 8. + erretm - phi + rhoinv + std::abs(tau) * (dpsi </span></a>
+<a name="7395"><span class="lineNum">    7395 </span><span class="lineCov">         59 :                 + dphi);</span></a>
+<a name="7396"><span class="lineNum">    7396 </span>            : </a>
+<a name="7397"><span class="lineNum">    7397 </span><span class="lineCov">         59 :         w = rhoinv + phi + psi;</span></a>
+<a name="7398"><span class="lineNum">    7398 </span>            : </a>
+<a name="7399"><span class="lineNum">    7399 </span><span class="lineCov">         59 :         if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="7400"><span class="lineNum">    7400 </span><span class="lineNoCov">          0 :             goto L240;</span></a>
+<a name="7401"><span class="lineNum">    7401 </span>            :         }</a>
+<a name="7402"><span class="lineNum">    7402 </span>            : </a>
+<a name="7403"><span class="lineNum">    7403 </span><span class="lineCov">         59 :         ++niter;</span></a>
+<a name="7404"><span class="lineNum">    7404 </span><span class="lineCov">         59 :         dtnsq1 = work[*n - 1] * delta[*n - 1];</span></a>
+<a name="7405"><span class="lineNum">    7405 </span>            :         dtnsq = work[*n] * delta[*n];</a>
+<a name="7406"><span class="lineNum">    7406 </span><span class="lineCov">         59 :         c__ = w - dtnsq1 * dpsi - dtnsq * dphi;</span></a>
+<a name="7407"><span class="lineNum">    7407 </span><span class="lineCov">         59 :         a = (dtnsq + dtnsq1) * w - dtnsq * dtnsq1 * (dpsi + dphi);</span></a>
+<a name="7408"><span class="lineNum">    7408 </span><span class="lineCov">         59 :         b = dtnsq * dtnsq1 * w;</span></a>
+<a name="7409"><span class="lineNum">    7409 </span><span class="lineCov">         59 :         if (c__ &lt; 0.) {</span></a>
+<a name="7410"><span class="lineNum">    7410 </span><span class="lineNoCov">          0 :             c__ = std::abs(c__);</span></a>
+<a name="7411"><span class="lineNum">    7411 </span>            :         }</a>
+<a name="7412"><span class="lineNum">    7412 </span><span class="lineCov">         59 :         if ( std::abs(c__)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="7413"><span class="lineNum">    7413 </span><span class="lineNoCov">          0 :             eta = *rho - *sigma * *sigma;</span></a>
+<a name="7414"><span class="lineNum">    7414 </span><span class="lineCov">         59 :         } else if (a &gt;= 0.) {</span></a>
+<a name="7415"><span class="lineNum">    7415 </span><span class="lineCov">          1 :             eta = (a +  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__  * 2.);</span></a>
+<a name="7416"><span class="lineNum">    7416 </span>            :         } else {</a>
+<a name="7417"><span class="lineNum">    7417 </span><span class="lineCov">         58 :           eta = b * 2. / (a -  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="7418"><span class="lineNum">    7418 </span>            :         }</a>
+<a name="7419"><span class="lineNum">    7419 </span>            : </a>
+<a name="7420"><span class="lineNum">    7420 </span><span class="lineCov">         59 :         if (w * eta &gt; 0.) {</span></a>
+<a name="7421"><span class="lineNum">    7421 </span><span class="lineNoCov">          0 :             eta = -w / (dpsi + dphi);</span></a>
+<a name="7422"><span class="lineNum">    7422 </span>            :         }</a>
+<a name="7423"><span class="lineNum">    7423 </span><span class="lineCov">         59 :         temp = eta - dtnsq;</span></a>
+<a name="7424"><span class="lineNum">    7424 </span><span class="lineCov">         59 :         if (temp &gt; *rho) {</span></a>
+<a name="7425"><span class="lineNum">    7425 </span><span class="lineNoCov">          0 :             eta = *rho + dtnsq;</span></a>
+<a name="7426"><span class="lineNum">    7426 </span>            :         }</a>
+<a name="7427"><span class="lineNum">    7427 </span>            : </a>
+<a name="7428"><span class="lineNum">    7428 </span><span class="lineCov">         59 :         tau += eta;</span></a>
+<a name="7429"><span class="lineNum">    7429 </span><span class="lineCov">         59 :         eta /= *sigma +  std::sqrt(eta + *sigma * *sigma);</span></a>
+<a name="7430"><span class="lineNum">    7430 </span><span class="lineCov">         59 :         i__1 = *n;</span></a>
+<a name="7431"><span class="lineNum">    7431 </span><span class="lineCov">       3310 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7432"><span class="lineNum">    7432 </span><span class="lineCov">       3251 :             delta[j] -= eta;</span></a>
+<a name="7433"><span class="lineNum">    7433 </span><span class="lineCov">       3251 :             work[j] += eta;</span></a>
+<a name="7434"><span class="lineNum">    7434 </span>            :         }</a>
+<a name="7435"><span class="lineNum">    7435 </span>            : </a>
+<a name="7436"><span class="lineNum">    7436 </span><span class="lineCov">         59 :         *sigma += eta;</span></a>
+<a name="7437"><span class="lineNum">    7437 </span>            : </a>
+<a name="7438"><span class="lineNum">    7438 </span>            :         dpsi = 0.;</a>
+<a name="7439"><span class="lineNum">    7439 </span>            :         psi = 0.;</a>
+<a name="7440"><span class="lineNum">    7440 </span>            :         erretm = 0.;</a>
+<a name="7441"><span class="lineNum">    7441 </span>            :         i__1 = ii;</a>
+<a name="7442"><span class="lineNum">    7442 </span><span class="lineCov">       3251 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7443"><span class="lineNum">    7443 </span><span class="lineCov">       3192 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7444"><span class="lineNum">    7444 </span><span class="lineCov">       3192 :             psi += z__[j] * temp;</span></a>
+<a name="7445"><span class="lineNum">    7445 </span><span class="lineCov">       3192 :             dpsi += temp * temp;</span></a>
+<a name="7446"><span class="lineNum">    7446 </span><span class="lineCov">       3192 :             erretm += psi;</span></a>
+<a name="7447"><span class="lineNum">    7447 </span>            :         }</a>
+<a name="7448"><span class="lineNum">    7448 </span>            :         erretm = std::abs(erretm);</a>
+<a name="7449"><span class="lineNum">    7449 </span>            : </a>
+<a name="7450"><span class="lineNum">    7450 </span><span class="lineCov">         59 :         temp = z__[*n] / (work[*n] * delta[*n]);</span></a>
+<a name="7451"><span class="lineNum">    7451 </span><span class="lineCov">         59 :         phi = z__[*n] * temp;</span></a>
+<a name="7452"><span class="lineNum">    7452 </span><span class="lineCov">         59 :         dphi = temp * temp;</span></a>
+<a name="7453"><span class="lineNum">    7453 </span><span class="lineCov">         59 :         erretm = (-phi - psi) * 8. + erretm - phi + rhoinv + std::abs(tau) * (dpsi </span></a>
+<a name="7454"><span class="lineNum">    7454 </span><span class="lineCov">         59 :                 + dphi);</span></a>
+<a name="7455"><span class="lineNum">    7455 </span>            : </a>
+<a name="7456"><span class="lineNum">    7456 </span><span class="lineCov">         59 :         w = rhoinv + phi + psi;</span></a>
+<a name="7457"><span class="lineNum">    7457 </span>            : </a>
+<a name="7458"><span class="lineNum">    7458 </span>            :         iter = niter + 1;</a>
+<a name="7459"><span class="lineNum">    7459 </span>            : </a>
+<a name="7460"><span class="lineNum">    7460 </span><span class="lineCov">        113 :         for (niter = iter; niter &lt;= 20; ++niter) {</span></a>
+<a name="7461"><span class="lineNum">    7461 </span>            : </a>
+<a name="7462"><span class="lineNum">    7462 </span><span class="lineCov">        113 :             if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="7463"><span class="lineNum">    7463 </span><span class="lineCov">         59 :                 goto L240;</span></a>
+<a name="7464"><span class="lineNum">    7464 </span>            :             }</a>
+<a name="7465"><span class="lineNum">    7465 </span><span class="lineCov">         54 :             dtnsq1 = work[*n - 1] * delta[*n - 1];</span></a>
+<a name="7466"><span class="lineNum">    7466 </span><span class="lineCov">         54 :             dtnsq = work[*n] * delta[*n];</span></a>
+<a name="7467"><span class="lineNum">    7467 </span><span class="lineCov">         54 :             c__ = w - dtnsq1 * dpsi - dtnsq * dphi;</span></a>
+<a name="7468"><span class="lineNum">    7468 </span><span class="lineCov">         54 :             a = (dtnsq + dtnsq1) * w - dtnsq1 * dtnsq * (dpsi + dphi);</span></a>
+<a name="7469"><span class="lineNum">    7469 </span><span class="lineCov">         54 :             b = dtnsq1 * dtnsq * w;</span></a>
+<a name="7470"><span class="lineNum">    7470 </span><span class="lineCov">         54 :             if (a &gt;= 0.) {</span></a>
+<a name="7471"><span class="lineNum">    7471 </span><span class="lineNoCov">          0 :                 eta = (a +  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="7472"><span class="lineNum">    7472 </span>            :             } else {</a>
+<a name="7473"><span class="lineNum">    7473 </span><span class="lineCov">         54 :               eta = b * 2. / (a -  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="7474"><span class="lineNum">    7474 </span>            :             }</a>
+<a name="7475"><span class="lineNum">    7475 </span>            : </a>
+<a name="7476"><span class="lineNum">    7476 </span><span class="lineCov">         54 :             if (w * eta &gt; 0.) {</span></a>
+<a name="7477"><span class="lineNum">    7477 </span><span class="lineNoCov">          0 :                 eta = -w / (dpsi + dphi);</span></a>
+<a name="7478"><span class="lineNum">    7478 </span>            :             }</a>
+<a name="7479"><span class="lineNum">    7479 </span><span class="lineCov">         54 :             temp = eta - dtnsq;</span></a>
+<a name="7480"><span class="lineNum">    7480 </span><span class="lineCov">         54 :             if (temp &lt;= 0.) {</span></a>
+<a name="7481"><span class="lineNum">    7481 </span><span class="lineNoCov">          0 :                 eta /= 2.;</span></a>
+<a name="7482"><span class="lineNum">    7482 </span>            :             }</a>
+<a name="7483"><span class="lineNum">    7483 </span>            : </a>
+<a name="7484"><span class="lineNum">    7484 </span><span class="lineCov">         54 :             tau += eta;</span></a>
+<a name="7485"><span class="lineNum">    7485 </span><span class="lineCov">         54 :             eta /= *sigma +  std::sqrt(eta + *sigma * *sigma);</span></a>
+<a name="7486"><span class="lineNum">    7486 </span><span class="lineCov">         54 :             i__1 = *n;</span></a>
+<a name="7487"><span class="lineNum">    7487 </span><span class="lineCov">       1745 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7488"><span class="lineNum">    7488 </span><span class="lineCov">       1691 :                 delta[j] -= eta;</span></a>
+<a name="7489"><span class="lineNum">    7489 </span><span class="lineCov">       1691 :                 work[j] += eta;</span></a>
+<a name="7490"><span class="lineNum">    7490 </span>            :             }</a>
+<a name="7491"><span class="lineNum">    7491 </span>            : </a>
+<a name="7492"><span class="lineNum">    7492 </span><span class="lineCov">         54 :             *sigma += eta;</span></a>
+<a name="7493"><span class="lineNum">    7493 </span>            : </a>
+<a name="7494"><span class="lineNum">    7494 </span>            :             dpsi = 0.;</a>
+<a name="7495"><span class="lineNum">    7495 </span>            :             psi = 0.;</a>
+<a name="7496"><span class="lineNum">    7496 </span>            :             erretm = 0.;</a>
+<a name="7497"><span class="lineNum">    7497 </span>            :             i__1 = ii;</a>
+<a name="7498"><span class="lineNum">    7498 </span><span class="lineCov">       1691 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7499"><span class="lineNum">    7499 </span><span class="lineCov">       1637 :                 temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7500"><span class="lineNum">    7500 </span><span class="lineCov">       1637 :                 psi += z__[j] * temp;</span></a>
+<a name="7501"><span class="lineNum">    7501 </span><span class="lineCov">       1637 :                 dpsi += temp * temp;</span></a>
+<a name="7502"><span class="lineNum">    7502 </span><span class="lineCov">       1637 :                 erretm += psi;</span></a>
+<a name="7503"><span class="lineNum">    7503 </span>            :             }</a>
+<a name="7504"><span class="lineNum">    7504 </span>            :             erretm = std::abs(erretm);</a>
+<a name="7505"><span class="lineNum">    7505 </span>            : </a>
+<a name="7506"><span class="lineNum">    7506 </span><span class="lineCov">         54 :             temp = z__[*n] / (work[*n] * delta[*n]);</span></a>
+<a name="7507"><span class="lineNum">    7507 </span><span class="lineCov">         54 :             phi = z__[*n] * temp;</span></a>
+<a name="7508"><span class="lineNum">    7508 </span><span class="lineCov">         54 :             dphi = temp * temp;</span></a>
+<a name="7509"><span class="lineNum">    7509 </span><span class="lineCov">         54 :             erretm = (-phi - psi) * 8. + erretm - phi + rhoinv + std::abs(tau) * (</span></a>
+<a name="7510"><span class="lineNum">    7510 </span><span class="lineCov">         54 :                     dpsi + dphi);</span></a>
+<a name="7511"><span class="lineNum">    7511 </span>            : </a>
+<a name="7512"><span class="lineNum">    7512 </span><span class="lineCov">         54 :             w = rhoinv + phi + psi;</span></a>
+<a name="7513"><span class="lineNum">    7513 </span>            :         }</a>
+<a name="7514"><span class="lineNum">    7514 </span>            : </a>
+<a name="7515"><span class="lineNum">    7515 </span><span class="lineNoCov">          0 :         *info = 1;</span></a>
+<a name="7516"><span class="lineNum">    7516 </span><span class="lineNoCov">          0 :         goto L240;</span></a>
+<a name="7517"><span class="lineNum">    7517 </span>            : </a>
+<a name="7518"><span class="lineNum">    7518 </span>            :     } else {</a>
+<a name="7519"><span class="lineNum">    7519 </span>            : </a>
+<a name="7520"><span class="lineNum">    7520 </span><span class="lineCov">       3192 :         niter = 1;</span></a>
+<a name="7521"><span class="lineNum">    7521 </span><span class="lineCov">       3192 :         ip1 = *i__ + 1;</span></a>
+<a name="7522"><span class="lineNum">    7522 </span>            : </a>
+<a name="7523"><span class="lineNum">    7523 </span><span class="lineCov">       3192 :         delsq = (d__[ip1] - d__[*i__]) * (d__[ip1] + d__[*i__]);</span></a>
+<a name="7524"><span class="lineNum">    7524 </span><span class="lineCov">       3192 :         delsq2 = delsq / 2.;</span></a>
+<a name="7525"><span class="lineNum">    7525 </span><span class="lineCov">       3192 :         temp = delsq2 / (d__[*i__] +  std::sqrt(d__[*i__] * d__[*i__] + delsq2));</span></a>
+<a name="7526"><span class="lineNum">    7526 </span><span class="lineCov">       3192 :         i__1 = *n;</span></a>
+<a name="7527"><span class="lineNum">    7527 </span><span class="lineCov">     420712 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7528"><span class="lineNum">    7528 </span><span class="lineCov">     417520 :             work[j] = d__[j] + d__[*i__] + temp;</span></a>
+<a name="7529"><span class="lineNum">    7529 </span><span class="lineCov">     417520 :             delta[j] = d__[j] - d__[*i__] - temp;</span></a>
+<a name="7530"><span class="lineNum">    7530 </span>            :         }</a>
+<a name="7531"><span class="lineNum">    7531 </span>            : </a>
+<a name="7532"><span class="lineNum">    7532 </span>            :         psi = 0.;</a>
+<a name="7533"><span class="lineNum">    7533 </span><span class="lineCov">       3192 :         i__1 = *i__ - 1;</span></a>
+<a name="7534"><span class="lineNum">    7534 </span><span class="lineCov">     208760 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7535"><span class="lineNum">    7535 </span><span class="lineCov">     205568 :             psi += z__[j] * z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7536"><span class="lineNum">    7536 </span>            :         }</a>
+<a name="7537"><span class="lineNum">    7537 </span>            : </a>
+<a name="7538"><span class="lineNum">    7538 </span>            :         phi = 0.;</a>
+<a name="7539"><span class="lineNum">    7539 </span><span class="lineCov">       3192 :         i__1 = *i__ + 2;</span></a>
+<a name="7540"><span class="lineNum">    7540 </span><span class="lineCov">     208760 :         for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="7541"><span class="lineNum">    7541 </span><span class="lineCov">     205568 :             phi += z__[j] * z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7542"><span class="lineNum">    7542 </span>            :         }</a>
+<a name="7543"><span class="lineNum">    7543 </span><span class="lineCov">       3192 :         c__ = rhoinv + psi + phi;</span></a>
+<a name="7544"><span class="lineNum">    7544 </span><span class="lineCov">       3192 :         w = c__ + z__[*i__] * z__[*i__] / (work[*i__] * delta[*i__]) + z__[</span></a>
+<a name="7545"><span class="lineNum">    7545 </span><span class="lineCov">       3192 :                 ip1] * z__[ip1] / (work[ip1] * delta[ip1]);</span></a>
+<a name="7546"><span class="lineNum">    7546 </span>            : </a>
+<a name="7547"><span class="lineNum">    7547 </span><span class="lineCov">       3192 :         if (w &gt; 0.) {</span></a>
+<a name="7548"><span class="lineNum">    7548 </span>            : </a>
+<a name="7549"><span class="lineNum">    7549 </span><span class="lineCov">       1684 :             orgati = 1;</span></a>
+<a name="7550"><span class="lineNum">    7550 </span>            :             sg2lb = 0.;</a>
+<a name="7551"><span class="lineNum">    7551 </span>            :             sg2ub = delsq2;</a>
+<a name="7552"><span class="lineNum">    7552 </span><span class="lineCov">       1684 :             a = c__ * delsq + z__[*i__] * z__[*i__] + z__[ip1] * z__[ip1];</span></a>
+<a name="7553"><span class="lineNum">    7553 </span><span class="lineCov">       1684 :             b = z__[*i__] * z__[*i__] * delsq;</span></a>
+<a name="7554"><span class="lineNum">    7554 </span><span class="lineCov">       1684 :             if (a &gt; 0.) {</span></a>
+<a name="7555"><span class="lineNum">    7555 </span><span class="lineCov">       1655 :                 tau = b * 2. / (a +  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="7556"><span class="lineNum">    7556 </span>            :             } else {</a>
+<a name="7557"><span class="lineNum">    7557 </span><span class="lineCov">         29 :                 tau = (a -  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="7558"><span class="lineNum">    7558 </span>            :             }</a>
+<a name="7559"><span class="lineNum">    7559 </span><span class="lineCov">       1684 :             eta = tau / (d__[*i__] +  std::sqrt(d__[*i__] * d__[*i__] + tau));</span></a>
+<a name="7560"><span class="lineNum">    7560 </span>            :         } else {</a>
+<a name="7561"><span class="lineNum">    7561 </span>            : </a>
+<a name="7562"><span class="lineNum">    7562 </span><span class="lineCov">       1508 :             orgati = 0;</span></a>
+<a name="7563"><span class="lineNum">    7563 </span><span class="lineCov">       1508 :             sg2lb = -delsq2;</span></a>
+<a name="7564"><span class="lineNum">    7564 </span>            :             sg2ub = 0.;</a>
+<a name="7565"><span class="lineNum">    7565 </span><span class="lineCov">       1508 :             a = c__ * delsq - z__[*i__] * z__[*i__] - z__[ip1] * z__[ip1];</span></a>
+<a name="7566"><span class="lineNum">    7566 </span><span class="lineCov">       1508 :             b = z__[ip1] * z__[ip1] * delsq;</span></a>
+<a name="7567"><span class="lineNum">    7567 </span><span class="lineCov">       1508 :             if (a &lt; 0.) {</span></a>
+<a name="7568"><span class="lineNum">    7568 </span><span class="lineCov">       1480 :                 tau = b * 2. / (a -  std::sqrt(std::abs(a * a + b * 4. * c__)));</span></a>
+<a name="7569"><span class="lineNum">    7569 </span>            :             } else {</a>
+<a name="7570"><span class="lineNum">    7570 </span><span class="lineCov">         28 :                 tau = -(a +  std::sqrt(std::abs(a * a + b * 4. * c__))) /       (c__ * 2.);</span></a>
+<a name="7571"><span class="lineNum">    7571 </span>            :             }</a>
+<a name="7572"><span class="lineNum">    7572 </span><span class="lineCov">       1508 :             eta = tau / (d__[ip1] +  std::sqrt(std::abs(d__[ip1] * d__[ip1] + tau)));</span></a>
+<a name="7573"><span class="lineNum">    7573 </span>            :         }</a>
+<a name="7574"><span class="lineNum">    7574 </span>            : </a>
+<a name="7575"><span class="lineNum">    7575 </span><span class="lineCov">       3192 :         if (orgati) {</span></a>
+<a name="7576"><span class="lineNum">    7576 </span><span class="lineCov">       1684 :             ii = *i__;</span></a>
+<a name="7577"><span class="lineNum">    7577 </span><span class="lineCov">       1684 :             *sigma = d__[*i__] + eta;</span></a>
+<a name="7578"><span class="lineNum">    7578 </span><span class="lineCov">       1684 :             i__1 = *n;</span></a>
+<a name="7579"><span class="lineNum">    7579 </span><span class="lineCov">     220971 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7580"><span class="lineNum">    7580 </span><span class="lineCov">     219287 :                 work[j] = d__[j] + d__[*i__] + eta;</span></a>
+<a name="7581"><span class="lineNum">    7581 </span><span class="lineCov">     219287 :                 delta[j] = d__[j] - d__[*i__] - eta;</span></a>
+<a name="7582"><span class="lineNum">    7582 </span>            :             }</a>
+<a name="7583"><span class="lineNum">    7583 </span>            :         } else {</a>
+<a name="7584"><span class="lineNum">    7584 </span><span class="lineCov">       1508 :             ii = *i__ + 1;</span></a>
+<a name="7585"><span class="lineNum">    7585 </span><span class="lineCov">       1508 :             *sigma = d__[ip1] + eta;</span></a>
+<a name="7586"><span class="lineNum">    7586 </span><span class="lineCov">       1508 :             i__1 = *n;</span></a>
+<a name="7587"><span class="lineNum">    7587 </span><span class="lineCov">     199741 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7588"><span class="lineNum">    7588 </span><span class="lineCov">     198233 :                 work[j] = d__[j] + d__[ip1] + eta;</span></a>
+<a name="7589"><span class="lineNum">    7589 </span><span class="lineCov">     198233 :                 delta[j] = d__[j] - d__[ip1] - eta;</span></a>
+<a name="7590"><span class="lineNum">    7590 </span>            :             }</a>
+<a name="7591"><span class="lineNum">    7591 </span>            :         }</a>
+<a name="7592"><span class="lineNum">    7592 </span><span class="lineCov">       3192 :         iim1 = ii - 1;</span></a>
+<a name="7593"><span class="lineNum">    7593 </span><span class="lineCov">       3192 :         iip1 = ii + 1;</span></a>
+<a name="7594"><span class="lineNum">    7594 </span>            : </a>
+<a name="7595"><span class="lineNum">    7595 </span>            :         dpsi = 0.;</a>
+<a name="7596"><span class="lineNum">    7596 </span>            :         psi = 0.;</a>
+<a name="7597"><span class="lineNum">    7597 </span>            :         erretm = 0.;</a>
+<a name="7598"><span class="lineNum">    7598 </span>            :         i__1 = iim1;</a>
+<a name="7599"><span class="lineNum">    7599 </span><span class="lineCov">     210268 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7600"><span class="lineNum">    7600 </span><span class="lineCov">     207076 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7601"><span class="lineNum">    7601 </span><span class="lineCov">     207076 :             psi += z__[j] * temp;</span></a>
+<a name="7602"><span class="lineNum">    7602 </span><span class="lineCov">     207076 :             dpsi += temp * temp;</span></a>
+<a name="7603"><span class="lineNum">    7603 </span><span class="lineCov">     207076 :             erretm += psi;</span></a>
+<a name="7604"><span class="lineNum">    7604 </span>            :         }</a>
+<a name="7605"><span class="lineNum">    7605 </span>            :         erretm = std::abs(erretm);</a>
+<a name="7606"><span class="lineNum">    7606 </span>            : </a>
+<a name="7607"><span class="lineNum">    7607 </span>            :         dphi = 0.;</a>
+<a name="7608"><span class="lineNum">    7608 </span>            :         phi = 0.;</a>
+<a name="7609"><span class="lineNum">    7609 </span>            :         i__1 = iip1;</a>
+<a name="7610"><span class="lineNum">    7610 </span><span class="lineCov">     210444 :         for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="7611"><span class="lineNum">    7611 </span><span class="lineCov">     207252 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7612"><span class="lineNum">    7612 </span><span class="lineCov">     207252 :             phi += z__[j] * temp;</span></a>
+<a name="7613"><span class="lineNum">    7613 </span><span class="lineCov">     207252 :             dphi += temp * temp;</span></a>
+<a name="7614"><span class="lineNum">    7614 </span><span class="lineCov">     207252 :             erretm += phi;</span></a>
+<a name="7615"><span class="lineNum">    7615 </span>            :         }</a>
+<a name="7616"><span class="lineNum">    7616 </span>            : </a>
+<a name="7617"><span class="lineNum">    7617 </span><span class="lineCov">       3192 :         w = rhoinv + phi + psi;</span></a>
+<a name="7618"><span class="lineNum">    7618 </span>            : </a>
+<a name="7619"><span class="lineNum">    7619 </span>            :         swtch3 = 0;</a>
+<a name="7620"><span class="lineNum">    7620 </span><span class="lineCov">       3192 :         if (orgati) {</span></a>
+<a name="7621"><span class="lineNum">    7621 </span><span class="lineCov">       1684 :             if (w &lt; 0.) {</span></a>
+<a name="7622"><span class="lineNum">    7622 </span>            :                 swtch3 = 1;</a>
+<a name="7623"><span class="lineNum">    7623 </span>            :             }</a>
+<a name="7624"><span class="lineNum">    7624 </span>            :         } else {</a>
+<a name="7625"><span class="lineNum">    7625 </span><span class="lineCov">       1508 :             if (w &gt; 0.) {</span></a>
+<a name="7626"><span class="lineNum">    7626 </span>            :                 swtch3 = 1;</a>
+<a name="7627"><span class="lineNum">    7627 </span>            :             }</a>
+<a name="7628"><span class="lineNum">    7628 </span>            :         }</a>
+<a name="7629"><span class="lineNum">    7629 </span><span class="lineCov">       3192 :         if (ii == 1 || ii == *n) {</span></a>
+<a name="7630"><span class="lineNum">    7630 </span>            :             swtch3 = 0;</a>
+<a name="7631"><span class="lineNum">    7631 </span>            :         }</a>
+<a name="7632"><span class="lineNum">    7632 </span>            : </a>
+<a name="7633"><span class="lineNum">    7633 </span><span class="lineCov">       3192 :         temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="7634"><span class="lineNum">    7634 </span><span class="lineCov">       3192 :         dw = dpsi + dphi + temp * temp;</span></a>
+<a name="7635"><span class="lineNum">    7635 </span><span class="lineCov">       3192 :         temp = z__[ii] * temp;</span></a>
+<a name="7636"><span class="lineNum">    7636 </span><span class="lineCov">       3192 :         w += temp;</span></a>
+<a name="7637"><span class="lineNum">    7637 </span><span class="lineCov">       3192 :         erretm = (phi - psi) * 8. + erretm + rhoinv * 2. + std::abs(temp) * 3. + </span></a>
+<a name="7638"><span class="lineNum">    7638 </span><span class="lineCov">       3192 :                 std::abs(tau) * dw;</span></a>
+<a name="7639"><span class="lineNum">    7639 </span>            : </a>
+<a name="7640"><span class="lineNum">    7640 </span><span class="lineCov">       3192 :         if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="7641"><span class="lineNum">    7641 </span><span class="lineCov">          7 :             goto L240;</span></a>
+<a name="7642"><span class="lineNum">    7642 </span>            :         }</a>
+<a name="7643"><span class="lineNum">    7643 </span>            : </a>
+<a name="7644"><span class="lineNum">    7644 </span><span class="lineCov">       3185 :         if (w &lt;= 0.) {</span></a>
+<a name="7645"><span class="lineNum">    7645 </span><span class="lineCov">       1683 :             sg2lb = (sg2lb &gt; tau) ? sg2lb : tau;</span></a>
+<a name="7646"><span class="lineNum">    7646 </span>            :         } else {</a>
+<a name="7647"><span class="lineNum">    7647 </span><span class="lineCov">       1502 :             sg2ub = (sg2ub &lt; tau) ? sg2ub : tau;</span></a>
+<a name="7648"><span class="lineNum">    7648 </span>            :         }</a>
+<a name="7649"><span class="lineNum">    7649 </span>            : </a>
+<a name="7650"><span class="lineNum">    7650 </span><span class="lineCov">       3185 :         ++niter;</span></a>
+<a name="7651"><span class="lineNum">    7651 </span><span class="lineCov">       3185 :         if (! swtch3) {</span></a>
+<a name="7652"><span class="lineNum">    7652 </span><span class="lineCov">       2843 :             dtipsq = work[ip1] * delta[ip1];</span></a>
+<a name="7653"><span class="lineNum">    7653 </span><span class="lineCov">       2843 :             dtisq = work[*i__] * delta[*i__];</span></a>
+<a name="7654"><span class="lineNum">    7654 </span><span class="lineCov">       2843 :             if (orgati) {</span></a>
+<a name="7655"><span class="lineNum">    7655 </span><span class="lineCov">       1510 :                 d__1 = z__[*i__] / dtisq;</span></a>
+<a name="7656"><span class="lineNum">    7656 </span><span class="lineCov">       1510 :                 c__ = w - dtipsq * dw + delsq * (d__1 * d__1);</span></a>
+<a name="7657"><span class="lineNum">    7657 </span>            :             } else {</a>
+<a name="7658"><span class="lineNum">    7658 </span><span class="lineCov">       1333 :                 d__1 = z__[ip1] / dtipsq;</span></a>
+<a name="7659"><span class="lineNum">    7659 </span><span class="lineCov">       1333 :                 c__ = w - dtisq * dw - delsq * (d__1 * d__1);</span></a>
+<a name="7660"><span class="lineNum">    7660 </span>            :             }</a>
+<a name="7661"><span class="lineNum">    7661 </span><span class="lineCov">       2843 :             a = (dtipsq + dtisq) * w - dtipsq * dtisq * dw;</span></a>
+<a name="7662"><span class="lineNum">    7662 </span><span class="lineCov">       2843 :             b = dtipsq * dtisq * w;</span></a>
+<a name="7663"><span class="lineNum">    7663 </span><span class="lineCov">       2843 :             if ( std::abs(c__)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="7664"><span class="lineNum">    7664 </span><span class="lineCov">         23 :                 if ( std::abs(a)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="7665"><span class="lineNum">    7665 </span><span class="lineNoCov">          0 :                     if (orgati) {</span></a>
+<a name="7666"><span class="lineNum">    7666 </span><span class="lineNoCov">          0 :                         a = z__[*i__] * z__[*i__] + dtipsq * dtipsq * (dpsi + </span></a>
+<a name="7667"><span class="lineNum">    7667 </span>            :                                 dphi);</a>
+<a name="7668"><span class="lineNum">    7668 </span>            :                     } else {</a>
+<a name="7669"><span class="lineNum">    7669 </span><span class="lineNoCov">          0 :                         a = z__[ip1] * z__[ip1] + dtisq * dtisq * (dpsi + </span></a>
+<a name="7670"><span class="lineNum">    7670 </span>            :                                 dphi);</a>
+<a name="7671"><span class="lineNum">    7671 </span>            :                     }</a>
+<a name="7672"><span class="lineNum">    7672 </span>            :                 }</a>
+<a name="7673"><span class="lineNum">    7673 </span><span class="lineCov">         23 :                 eta = b / a;</span></a>
+<a name="7674"><span class="lineNum">    7674 </span><span class="lineCov">       2820 :             } else if (a &lt;= 0.) {</span></a>
+<a name="7675"><span class="lineNum">    7675 </span><span class="lineNoCov">          0 :                 eta = (a -  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="7676"><span class="lineNum">    7676 </span>            :             } else {</a>
+<a name="7677"><span class="lineNum">    7677 </span><span class="lineCov">       2820 :                 eta = b * 2. / (a +  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="7678"><span class="lineNum">    7678 </span>            :             }</a>
+<a name="7679"><span class="lineNum">    7679 </span>            :         } else {</a>
+<a name="7680"><span class="lineNum">    7680 </span>            : </a>
+<a name="7681"><span class="lineNum">    7681 </span><span class="lineCov">        342 :             dtiim = work[iim1] * delta[iim1];</span></a>
+<a name="7682"><span class="lineNum">    7682 </span><span class="lineCov">        342 :             dtiip = work[iip1] * delta[iip1];</span></a>
+<a name="7683"><span class="lineNum">    7683 </span><span class="lineCov">        342 :             temp = rhoinv + psi + phi;</span></a>
+<a name="7684"><span class="lineNum">    7684 </span><span class="lineCov">        342 :             if (orgati) {</span></a>
+<a name="7685"><span class="lineNum">    7685 </span><span class="lineCov">        173 :                 temp1 = z__[iim1] / dtiim;</span></a>
+<a name="7686"><span class="lineNum">    7686 </span><span class="lineCov">        173 :                 temp1 *= temp1;</span></a>
+<a name="7687"><span class="lineNum">    7687 </span><span class="lineCov">        173 :                 c__ = temp - dtiip * (dpsi + dphi) - (d__[iim1] - d__[iip1]) *</span></a>
+<a name="7688"><span class="lineNum">    7688 </span><span class="lineCov">        173 :                          (d__[iim1] + d__[iip1]) * temp1;</span></a>
+<a name="7689"><span class="lineNum">    7689 </span><span class="lineCov">        173 :                 zz[0] = z__[iim1] * z__[iim1];</span></a>
+<a name="7690"><span class="lineNum">    7690 </span><span class="lineCov">        173 :                 if (dpsi &lt; temp1) {</span></a>
+<a name="7691"><span class="lineNum">    7691 </span><span class="lineNoCov">          0 :                     zz[2] = dtiip * dtiip * dphi;</span></a>
+<a name="7692"><span class="lineNum">    7692 </span>            :                 } else {</a>
+<a name="7693"><span class="lineNum">    7693 </span><span class="lineCov">        173 :                     zz[2] = dtiip * dtiip * (dpsi - temp1 + dphi);</span></a>
+<a name="7694"><span class="lineNum">    7694 </span>            :                 }</a>
+<a name="7695"><span class="lineNum">    7695 </span>            :             } else {</a>
+<a name="7696"><span class="lineNum">    7696 </span><span class="lineCov">        169 :                 temp1 = z__[iip1] / dtiip;</span></a>
+<a name="7697"><span class="lineNum">    7697 </span><span class="lineCov">        169 :                 temp1 *= temp1;</span></a>
+<a name="7698"><span class="lineNum">    7698 </span><span class="lineCov">        169 :                 c__ = temp - dtiim * (dpsi + dphi) - (d__[iip1] - d__[iim1]) *</span></a>
+<a name="7699"><span class="lineNum">    7699 </span><span class="lineCov">        169 :                          (d__[iim1] + d__[iip1]) * temp1;</span></a>
+<a name="7700"><span class="lineNum">    7700 </span><span class="lineCov">        169 :                 if (dphi &lt; temp1) {</span></a>
+<a name="7701"><span class="lineNum">    7701 </span><span class="lineNoCov">          0 :                     zz[0] = dtiim * dtiim * dpsi;</span></a>
+<a name="7702"><span class="lineNum">    7702 </span>            :                 } else {</a>
+<a name="7703"><span class="lineNum">    7703 </span><span class="lineCov">        169 :                     zz[0] = dtiim * dtiim * (dpsi + (dphi - temp1));</span></a>
+<a name="7704"><span class="lineNum">    7704 </span>            :                 }</a>
+<a name="7705"><span class="lineNum">    7705 </span><span class="lineCov">        169 :                 zz[2] = z__[iip1] * z__[iip1];</span></a>
+<a name="7706"><span class="lineNum">    7706 </span>            :             }</a>
+<a name="7707"><span class="lineNum">    7707 </span><span class="lineCov">        342 :             zz[1] = z__[ii] * z__[ii];</span></a>
+<a name="7708"><span class="lineNum">    7708 </span><span class="lineCov">        342 :             dd[0] = dtiim;</span></a>
+<a name="7709"><span class="lineNum">    7709 </span><span class="lineCov">        342 :             dd[1] = delta[ii] * work[ii];</span></a>
+<a name="7710"><span class="lineNum">    7710 </span><span class="lineCov">        342 :             dd[2] = dtiip;</span></a>
+<a name="7711"><span class="lineNum">    7711 </span><span class="lineCov">        342 :             PLUMED_BLAS_F77_FUNC(dlaed6,DLAED6)(&amp;niter, &amp;orgati, &amp;c__, dd, zz, &amp;w, &amp;eta, info);</span></a>
+<a name="7712"><span class="lineNum">    7712 </span><span class="lineCov">        342 :             if (*info != 0) {</span></a>
+<a name="7713"><span class="lineNum">    7713 </span><span class="lineNoCov">          0 :                 goto L240;</span></a>
+<a name="7714"><span class="lineNum">    7714 </span>            :             }</a>
+<a name="7715"><span class="lineNum">    7715 </span>            :         }</a>
+<a name="7716"><span class="lineNum">    7716 </span>            : </a>
+<a name="7717"><span class="lineNum">    7717 </span><span class="lineCov">       3185 :         if (w * eta &gt;= 0.) {</span></a>
+<a name="7718"><span class="lineNum">    7718 </span><span class="lineNoCov">          0 :             eta = -w / dw;</span></a>
+<a name="7719"><span class="lineNum">    7719 </span>            :         }</a>
+<a name="7720"><span class="lineNum">    7720 </span><span class="lineCov">       3185 :         if (orgati) {</span></a>
+<a name="7721"><span class="lineNum">    7721 </span><span class="lineCov">       1683 :             temp1 = work[*i__] * delta[*i__];</span></a>
+<a name="7722"><span class="lineNum">    7722 </span><span class="lineCov">       1683 :             temp = eta - temp1;</span></a>
+<a name="7723"><span class="lineNum">    7723 </span>            :         } else {</a>
+<a name="7724"><span class="lineNum">    7724 </span><span class="lineCov">       1502 :             temp1 = work[ip1] * delta[ip1];</span></a>
+<a name="7725"><span class="lineNum">    7725 </span><span class="lineCov">       1502 :             temp = eta - temp1;</span></a>
+<a name="7726"><span class="lineNum">    7726 </span>            :         }</a>
+<a name="7727"><span class="lineNum">    7727 </span><span class="lineCov">       3185 :         if (temp &gt; sg2ub || temp &lt; sg2lb) {</span></a>
+<a name="7728"><span class="lineNum">    7728 </span><span class="lineNoCov">          0 :             if (w &lt; 0.) {</span></a>
+<a name="7729"><span class="lineNum">    7729 </span><span class="lineNoCov">          0 :                 eta = (sg2ub - tau) / 2.;</span></a>
+<a name="7730"><span class="lineNum">    7730 </span>            :             } else {</a>
+<a name="7731"><span class="lineNum">    7731 </span><span class="lineNoCov">          0 :                 eta = (sg2lb - tau) / 2.;</span></a>
+<a name="7732"><span class="lineNum">    7732 </span>            :             }</a>
+<a name="7733"><span class="lineNum">    7733 </span>            :         }</a>
+<a name="7734"><span class="lineNum">    7734 </span>            : </a>
+<a name="7735"><span class="lineNum">    7735 </span><span class="lineCov">       3185 :         tau += eta;</span></a>
+<a name="7736"><span class="lineNum">    7736 </span><span class="lineCov">       3185 :         eta /= *sigma +  std::sqrt(*sigma * *sigma + eta);</span></a>
+<a name="7737"><span class="lineNum">    7737 </span>            : </a>
+<a name="7738"><span class="lineNum">    7738 </span>            :         prew = w;</a>
+<a name="7739"><span class="lineNum">    7739 </span>            : </a>
+<a name="7740"><span class="lineNum">    7740 </span><span class="lineCov">       3185 :         *sigma += eta;</span></a>
+<a name="7741"><span class="lineNum">    7741 </span><span class="lineCov">       3185 :         i__1 = *n;</span></a>
+<a name="7742"><span class="lineNum">    7742 </span><span class="lineCov">     419753 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7743"><span class="lineNum">    7743 </span><span class="lineCov">     416568 :             work[j] += eta;</span></a>
+<a name="7744"><span class="lineNum">    7744 </span><span class="lineCov">     416568 :             delta[j] -= eta;</span></a>
+<a name="7745"><span class="lineNum">    7745 </span>            :         }</a>
+<a name="7746"><span class="lineNum">    7746 </span>            : </a>
+<a name="7747"><span class="lineNum">    7747 </span>            :         dpsi = 0.;</a>
+<a name="7748"><span class="lineNum">    7748 </span>            :         psi = 0.;</a>
+<a name="7749"><span class="lineNum">    7749 </span>            :         erretm = 0.;</a>
+<a name="7750"><span class="lineNum">    7750 </span>            :         i__1 = iim1;</a>
+<a name="7751"><span class="lineNum">    7751 </span><span class="lineCov">     210255 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7752"><span class="lineNum">    7752 </span><span class="lineCov">     207070 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7753"><span class="lineNum">    7753 </span><span class="lineCov">     207070 :             psi += z__[j] * temp;</span></a>
+<a name="7754"><span class="lineNum">    7754 </span><span class="lineCov">     207070 :             dpsi += temp * temp;</span></a>
+<a name="7755"><span class="lineNum">    7755 </span><span class="lineCov">     207070 :             erretm += psi;</span></a>
+<a name="7756"><span class="lineNum">    7756 </span>            :         }</a>
+<a name="7757"><span class="lineNum">    7757 </span>            :         erretm = std::abs(erretm);</a>
+<a name="7758"><span class="lineNum">    7758 </span>            : </a>
+<a name="7759"><span class="lineNum">    7759 </span>            :         dphi = 0.;</a>
+<a name="7760"><span class="lineNum">    7760 </span>            :         phi = 0.;</a>
+<a name="7761"><span class="lineNum">    7761 </span>            :         i__1 = iip1;</a>
+<a name="7762"><span class="lineNum">    7762 </span><span class="lineCov">     209498 :         for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="7763"><span class="lineNum">    7763 </span><span class="lineCov">     206313 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7764"><span class="lineNum">    7764 </span><span class="lineCov">     206313 :             phi += z__[j] * temp;</span></a>
+<a name="7765"><span class="lineNum">    7765 </span><span class="lineCov">     206313 :             dphi += temp * temp;</span></a>
+<a name="7766"><span class="lineNum">    7766 </span><span class="lineCov">     206313 :             erretm += phi;</span></a>
+<a name="7767"><span class="lineNum">    7767 </span>            :         }</a>
+<a name="7768"><span class="lineNum">    7768 </span>            : </a>
+<a name="7769"><span class="lineNum">    7769 </span><span class="lineCov">       3185 :         temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="7770"><span class="lineNum">    7770 </span><span class="lineCov">       3185 :         dw = dpsi + dphi + temp * temp;</span></a>
+<a name="7771"><span class="lineNum">    7771 </span><span class="lineCov">       3185 :         temp = z__[ii] * temp;</span></a>
+<a name="7772"><span class="lineNum">    7772 </span><span class="lineCov">       3185 :         w = rhoinv + phi + psi + temp;</span></a>
+<a name="7773"><span class="lineNum">    7773 </span><span class="lineCov">       3185 :         erretm = (phi - psi) * 8. + erretm + rhoinv * 2. + std::abs(temp) * 3. + </span></a>
+<a name="7774"><span class="lineNum">    7774 </span><span class="lineCov">       3185 :                 std::abs(tau) * dw;</span></a>
+<a name="7775"><span class="lineNum">    7775 </span>            : </a>
+<a name="7776"><span class="lineNum">    7776 </span><span class="lineCov">       3185 :         if (w &lt;= 0.) {</span></a>
+<a name="7777"><span class="lineNum">    7777 </span><span class="lineCov">       1672 :             sg2lb = (sg2lb &gt; tau) ? sg2lb : tau;</span></a>
+<a name="7778"><span class="lineNum">    7778 </span>            :         } else {</a>
+<a name="7779"><span class="lineNum">    7779 </span><span class="lineCov">       1513 :             sg2ub = (sg2ub &lt; tau) ? sg2ub : tau;</span></a>
+<a name="7780"><span class="lineNum">    7780 </span>            :         }</a>
+<a name="7781"><span class="lineNum">    7781 </span>            : </a>
+<a name="7782"><span class="lineNum">    7782 </span>            :         swtch = 0;</a>
+<a name="7783"><span class="lineNum">    7783 </span><span class="lineCov">       3185 :         if (orgati) {</span></a>
+<a name="7784"><span class="lineNum">    7784 </span><span class="lineCov">       1683 :             if (-w &gt; std::abs(prew) / 10.) {</span></a>
+<a name="7785"><span class="lineNum">    7785 </span>            :                 swtch = 1;</a>
+<a name="7786"><span class="lineNum">    7786 </span>            :             }</a>
+<a name="7787"><span class="lineNum">    7787 </span>            :         } else {</a>
+<a name="7788"><span class="lineNum">    7788 </span><span class="lineCov">       1502 :             if (w &gt; std::abs(prew) / 10.) {</span></a>
+<a name="7789"><span class="lineNum">    7789 </span>            :                 swtch = 1;</a>
+<a name="7790"><span class="lineNum">    7790 </span>            :             }</a>
+<a name="7791"><span class="lineNum">    7791 </span>            :         }</a>
+<a name="7792"><span class="lineNum">    7792 </span>            : </a>
+<a name="7793"><span class="lineNum">    7793 </span><span class="lineCov">       3185 :         iter = niter + 1;</span></a>
+<a name="7794"><span class="lineNum">    7794 </span>            : </a>
+<a name="7795"><span class="lineNum">    7795 </span><span class="lineCov">       9406 :         for (niter = iter; niter &lt;= 20; ++niter) {</span></a>
+<a name="7796"><span class="lineNum">    7796 </span>            : </a>
+<a name="7797"><span class="lineNum">    7797 </span><span class="lineCov">       9406 :             if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="7798"><span class="lineNum">    7798 </span><span class="lineCov">       3185 :                 goto L240;</span></a>
+<a name="7799"><span class="lineNum">    7799 </span>            :             }</a>
+<a name="7800"><span class="lineNum">    7800 </span>            : </a>
+<a name="7801"><span class="lineNum">    7801 </span><span class="lineCov">       6221 :             if (! swtch3) {</span></a>
+<a name="7802"><span class="lineNum">    7802 </span><span class="lineCov">       5176 :                 dtipsq = work[ip1] * delta[ip1];</span></a>
+<a name="7803"><span class="lineNum">    7803 </span><span class="lineCov">       5176 :                 dtisq = work[*i__] * delta[*i__];</span></a>
+<a name="7804"><span class="lineNum">    7804 </span><span class="lineCov">       5176 :                 if (! swtch) {</span></a>
+<a name="7805"><span class="lineNum">    7805 </span><span class="lineCov">       5069 :                     if (orgati) {</span></a>
+<a name="7806"><span class="lineNum">    7806 </span><span class="lineCov">       2626 :                         d__1 = z__[*i__] / dtisq;</span></a>
+<a name="7807"><span class="lineNum">    7807 </span><span class="lineCov">       2626 :                         c__ = w - dtipsq * dw + delsq * (d__1 * d__1);</span></a>
+<a name="7808"><span class="lineNum">    7808 </span>            :                     } else {</a>
+<a name="7809"><span class="lineNum">    7809 </span><span class="lineCov">       2443 :                         d__1 = z__[ip1] / dtipsq;</span></a>
+<a name="7810"><span class="lineNum">    7810 </span><span class="lineCov">       2443 :                         c__ = w - dtisq * dw - delsq * (d__1 * d__1);</span></a>
+<a name="7811"><span class="lineNum">    7811 </span>            :                     }</a>
+<a name="7812"><span class="lineNum">    7812 </span>            :                 } else {</a>
+<a name="7813"><span class="lineNum">    7813 </span><span class="lineCov">        107 :                     temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="7814"><span class="lineNum">    7814 </span><span class="lineCov">        107 :                     if (orgati) {</span></a>
+<a name="7815"><span class="lineNum">    7815 </span><span class="lineCov">         69 :                         dpsi += temp * temp;</span></a>
+<a name="7816"><span class="lineNum">    7816 </span>            :                     } else {</a>
+<a name="7817"><span class="lineNum">    7817 </span><span class="lineCov">         38 :                         dphi += temp * temp;</span></a>
+<a name="7818"><span class="lineNum">    7818 </span>            :                     }</a>
+<a name="7819"><span class="lineNum">    7819 </span><span class="lineCov">        107 :                     c__ = w - dtisq * dpsi - dtipsq * dphi;</span></a>
+<a name="7820"><span class="lineNum">    7820 </span>            :                 }</a>
+<a name="7821"><span class="lineNum">    7821 </span><span class="lineCov">       5176 :                 a = (dtipsq + dtisq) * w - dtipsq * dtisq * dw;</span></a>
+<a name="7822"><span class="lineNum">    7822 </span><span class="lineCov">       5176 :                 b = dtipsq * dtisq * w;</span></a>
+<a name="7823"><span class="lineNum">    7823 </span><span class="lineCov">       5176 :                 if (std::abs(c__)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="7824"><span class="lineNum">    7824 </span><span class="lineNoCov">          0 :                     if (std::abs(a)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="7825"><span class="lineNum">    7825 </span><span class="lineNoCov">          0 :                         if (! swtch) {</span></a>
+<a name="7826"><span class="lineNum">    7826 </span><span class="lineNoCov">          0 :                             if (orgati) {</span></a>
+<a name="7827"><span class="lineNum">    7827 </span><span class="lineNoCov">          0 :                                 a = z__[*i__] * z__[*i__] + dtipsq * dtipsq * </span></a>
+<a name="7828"><span class="lineNum">    7828 </span><span class="lineNoCov">          0 :                                         (dpsi + dphi);</span></a>
+<a name="7829"><span class="lineNum">    7829 </span>            :                             } else {</a>
+<a name="7830"><span class="lineNum">    7830 </span><span class="lineNoCov">          0 :                                 a = z__[ip1] * z__[ip1] + dtisq * dtisq * (</span></a>
+<a name="7831"><span class="lineNum">    7831 </span><span class="lineNoCov">          0 :                                         dpsi + dphi);</span></a>
+<a name="7832"><span class="lineNum">    7832 </span>            :                             }</a>
+<a name="7833"><span class="lineNum">    7833 </span>            :                         } else {</a>
+<a name="7834"><span class="lineNum">    7834 </span><span class="lineNoCov">          0 :                             a = dtisq * dtisq * dpsi + dtipsq * dtipsq * dphi;</span></a>
+<a name="7835"><span class="lineNum">    7835 </span>            :                         }</a>
+<a name="7836"><span class="lineNum">    7836 </span>            :                     }</a>
+<a name="7837"><span class="lineNum">    7837 </span><span class="lineNoCov">          0 :                     eta = b / a;</span></a>
+<a name="7838"><span class="lineNum">    7838 </span><span class="lineCov">       5176 :                 } else if (a &lt;= 0.) {</span></a>
+<a name="7839"><span class="lineNum">    7839 </span><span class="lineNoCov">          0 :                   eta = (a -  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="7840"><span class="lineNum">    7840 </span>            :                 } else {</a>
+<a name="7841"><span class="lineNum">    7841 </span><span class="lineCov">       5176 :                   eta = b * 2. / (a +  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="7842"><span class="lineNum">    7842 </span>            :                 }</a>
+<a name="7843"><span class="lineNum">    7843 </span>            :             } else {</a>
+<a name="7844"><span class="lineNum">    7844 </span>            : </a>
+<a name="7845"><span class="lineNum">    7845 </span><span class="lineCov">       1045 :                 dtiim = work[iim1] * delta[iim1];</span></a>
+<a name="7846"><span class="lineNum">    7846 </span><span class="lineCov">       1045 :                 dtiip = work[iip1] * delta[iip1];</span></a>
+<a name="7847"><span class="lineNum">    7847 </span><span class="lineCov">       1045 :                 temp = rhoinv + psi + phi;</span></a>
+<a name="7848"><span class="lineNum">    7848 </span><span class="lineCov">       1045 :                 if (swtch) {</span></a>
+<a name="7849"><span class="lineNum">    7849 </span><span class="lineCov">        250 :                     c__ = temp - dtiim * dpsi - dtiip * dphi;</span></a>
+<a name="7850"><span class="lineNum">    7850 </span><span class="lineCov">        250 :                     zz[0] = dtiim * dtiim * dpsi;</span></a>
+<a name="7851"><span class="lineNum">    7851 </span><span class="lineCov">        250 :                     zz[2] = dtiip * dtiip * dphi;</span></a>
+<a name="7852"><span class="lineNum">    7852 </span>            :                 } else {</a>
+<a name="7853"><span class="lineNum">    7853 </span><span class="lineCov">        795 :                     if (orgati) {</span></a>
+<a name="7854"><span class="lineNum">    7854 </span><span class="lineCov">        399 :                         temp1 = z__[iim1] / dtiim;</span></a>
+<a name="7855"><span class="lineNum">    7855 </span><span class="lineCov">        399 :                         temp1 *= temp1;</span></a>
+<a name="7856"><span class="lineNum">    7856 </span><span class="lineCov">        399 :                         temp2 = (d__[iim1] - d__[iip1]) * (d__[iim1] + d__[</span></a>
+<a name="7857"><span class="lineNum">    7857 </span>            :                                 iip1]) * temp1;</a>
+<a name="7858"><span class="lineNum">    7858 </span><span class="lineCov">        399 :                         c__ = temp - dtiip * (dpsi + dphi) - temp2;</span></a>
+<a name="7859"><span class="lineNum">    7859 </span><span class="lineCov">        399 :                         zz[0] = z__[iim1] * z__[iim1];</span></a>
+<a name="7860"><span class="lineNum">    7860 </span><span class="lineCov">        399 :                         if (dpsi &lt; temp1) {</span></a>
+<a name="7861"><span class="lineNum">    7861 </span><span class="lineNoCov">          0 :                             zz[2] = dtiip * dtiip * dphi;</span></a>
+<a name="7862"><span class="lineNum">    7862 </span>            :                         } else {</a>
+<a name="7863"><span class="lineNum">    7863 </span><span class="lineCov">        399 :                             zz[2] = dtiip * dtiip * (dpsi - temp1 + dphi);</span></a>
+<a name="7864"><span class="lineNum">    7864 </span>            :                         }</a>
+<a name="7865"><span class="lineNum">    7865 </span>            :                     } else {</a>
+<a name="7866"><span class="lineNum">    7866 </span><span class="lineCov">        396 :                         temp1 = z__[iip1] / dtiip;</span></a>
+<a name="7867"><span class="lineNum">    7867 </span><span class="lineCov">        396 :                         temp1 *= temp1;</span></a>
+<a name="7868"><span class="lineNum">    7868 </span><span class="lineCov">        396 :                         temp2 = (d__[iip1] - d__[iim1]) * (d__[iim1] + d__[</span></a>
+<a name="7869"><span class="lineNum">    7869 </span>            :                                 iip1]) * temp1;</a>
+<a name="7870"><span class="lineNum">    7870 </span><span class="lineCov">        396 :                         c__ = temp - dtiim * (dpsi + dphi) - temp2;</span></a>
+<a name="7871"><span class="lineNum">    7871 </span><span class="lineCov">        396 :                         if (dphi &lt; temp1) {</span></a>
+<a name="7872"><span class="lineNum">    7872 </span><span class="lineNoCov">          0 :                             zz[0] = dtiim * dtiim * dpsi;</span></a>
+<a name="7873"><span class="lineNum">    7873 </span>            :                         } else {</a>
+<a name="7874"><span class="lineNum">    7874 </span><span class="lineCov">        396 :                             zz[0] = dtiim * dtiim * (dpsi + (dphi - temp1));</span></a>
+<a name="7875"><span class="lineNum">    7875 </span>            :                         }</a>
+<a name="7876"><span class="lineNum">    7876 </span><span class="lineCov">        396 :                         zz[2] = z__[iip1] * z__[iip1];</span></a>
+<a name="7877"><span class="lineNum">    7877 </span>            :                     }</a>
+<a name="7878"><span class="lineNum">    7878 </span>            :                 }</a>
+<a name="7879"><span class="lineNum">    7879 </span><span class="lineCov">       1045 :                 dd[0] = dtiim;</span></a>
+<a name="7880"><span class="lineNum">    7880 </span><span class="lineCov">       1045 :                 dd[1] = delta[ii] * work[ii];</span></a>
+<a name="7881"><span class="lineNum">    7881 </span><span class="lineCov">       1045 :                 dd[2] = dtiip;</span></a>
+<a name="7882"><span class="lineNum">    7882 </span><span class="lineCov">       1045 :                 PLUMED_BLAS_F77_FUNC(dlaed6,DLAED6)(&amp;niter, &amp;orgati, &amp;c__, dd, zz, &amp;w, &amp;eta, info);</span></a>
+<a name="7883"><span class="lineNum">    7883 </span><span class="lineCov">       1045 :                 if (*info != 0) {</span></a>
+<a name="7884"><span class="lineNum">    7884 </span><span class="lineNoCov">          0 :                     goto L240;</span></a>
+<a name="7885"><span class="lineNum">    7885 </span>            :                 }</a>
+<a name="7886"><span class="lineNum">    7886 </span>            :             }</a>
+<a name="7887"><span class="lineNum">    7887 </span>            : </a>
+<a name="7888"><span class="lineNum">    7888 </span><span class="lineCov">       6221 :             if (w * eta &gt;= 0.) {</span></a>
+<a name="7889"><span class="lineNum">    7889 </span><span class="lineNoCov">          0 :                 eta = -w / dw;</span></a>
+<a name="7890"><span class="lineNum">    7890 </span>            :             }</a>
+<a name="7891"><span class="lineNum">    7891 </span><span class="lineCov">       6221 :             if (orgati) {</span></a>
+<a name="7892"><span class="lineNum">    7892 </span><span class="lineCov">       3228 :                 temp1 = work[*i__] * delta[*i__];</span></a>
+<a name="7893"><span class="lineNum">    7893 </span><span class="lineCov">       3228 :                 temp = eta - temp1;</span></a>
+<a name="7894"><span class="lineNum">    7894 </span>            :             } else {</a>
+<a name="7895"><span class="lineNum">    7895 </span><span class="lineCov">       2993 :                 temp1 = work[ip1] * delta[ip1];</span></a>
+<a name="7896"><span class="lineNum">    7896 </span><span class="lineCov">       2993 :                 temp = eta - temp1;</span></a>
+<a name="7897"><span class="lineNum">    7897 </span>            :             }</a>
+<a name="7898"><span class="lineNum">    7898 </span><span class="lineCov">       6221 :             if (temp &gt; sg2ub || temp &lt; sg2lb) {</span></a>
+<a name="7899"><span class="lineNum">    7899 </span><span class="lineCov">          1 :                 if (w &lt; 0.) {</span></a>
+<a name="7900"><span class="lineNum">    7900 </span><span class="lineCov">          1 :                     eta = (sg2ub - tau) / 2.;</span></a>
+<a name="7901"><span class="lineNum">    7901 </span>            :                 } else {</a>
+<a name="7902"><span class="lineNum">    7902 </span><span class="lineNoCov">          0 :                     eta = (sg2lb - tau) / 2.;</span></a>
+<a name="7903"><span class="lineNum">    7903 </span>            :                 }</a>
+<a name="7904"><span class="lineNum">    7904 </span>            :             }</a>
+<a name="7905"><span class="lineNum">    7905 </span>            : </a>
+<a name="7906"><span class="lineNum">    7906 </span><span class="lineCov">       6221 :             tau += eta;</span></a>
+<a name="7907"><span class="lineNum">    7907 </span><span class="lineCov">       6221 :             eta /= *sigma +  std::sqrt(*sigma * *sigma + eta);</span></a>
+<a name="7908"><span class="lineNum">    7908 </span>            : </a>
+<a name="7909"><span class="lineNum">    7909 </span><span class="lineCov">       6221 :             *sigma += eta;</span></a>
+<a name="7910"><span class="lineNum">    7910 </span><span class="lineCov">       6221 :             i__1 = *n;</span></a>
+<a name="7911"><span class="lineNum">    7911 </span><span class="lineCov">     819441 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7912"><span class="lineNum">    7912 </span><span class="lineCov">     813220 :                 work[j] += eta;</span></a>
+<a name="7913"><span class="lineNum">    7913 </span><span class="lineCov">     813220 :                 delta[j] -= eta;</span></a>
+<a name="7914"><span class="lineNum">    7914 </span>            :             }</a>
+<a name="7915"><span class="lineNum">    7915 </span>            : </a>
+<a name="7916"><span class="lineNum">    7916 </span>            :             prew = w;</a>
+<a name="7917"><span class="lineNum">    7917 </span>            : </a>
+<a name="7918"><span class="lineNum">    7918 </span>            :             dpsi = 0.;</a>
+<a name="7919"><span class="lineNum">    7919 </span>            :             psi = 0.;</a>
+<a name="7920"><span class="lineNum">    7920 </span>            :             erretm = 0.;</a>
+<a name="7921"><span class="lineNum">    7921 </span>            :             i__1 = iim1;</a>
+<a name="7922"><span class="lineNum">    7922 </span><span class="lineCov">     391937 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="7923"><span class="lineNum">    7923 </span><span class="lineCov">     385716 :                 temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7924"><span class="lineNum">    7924 </span><span class="lineCov">     385716 :                 psi += z__[j] * temp;</span></a>
+<a name="7925"><span class="lineNum">    7925 </span><span class="lineCov">     385716 :                 dpsi += temp * temp;</span></a>
+<a name="7926"><span class="lineNum">    7926 </span><span class="lineCov">     385716 :                 erretm += psi;</span></a>
+<a name="7927"><span class="lineNum">    7927 </span>            :             }</a>
+<a name="7928"><span class="lineNum">    7928 </span>            :             erretm = std::abs(erretm);</a>
+<a name="7929"><span class="lineNum">    7929 </span>            : </a>
+<a name="7930"><span class="lineNum">    7930 </span>            :             dphi = 0.;</a>
+<a name="7931"><span class="lineNum">    7931 </span>            :             phi = 0.;</a>
+<a name="7932"><span class="lineNum">    7932 </span>            :             i__1 = iip1;</a>
+<a name="7933"><span class="lineNum">    7933 </span><span class="lineCov">     427504 :             for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="7934"><span class="lineNum">    7934 </span><span class="lineCov">     421283 :                 temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="7935"><span class="lineNum">    7935 </span><span class="lineCov">     421283 :                 phi += z__[j] * temp;</span></a>
+<a name="7936"><span class="lineNum">    7936 </span><span class="lineCov">     421283 :                 dphi += temp * temp;</span></a>
+<a name="7937"><span class="lineNum">    7937 </span><span class="lineCov">     421283 :                 erretm += phi;</span></a>
+<a name="7938"><span class="lineNum">    7938 </span>            :             }</a>
+<a name="7939"><span class="lineNum">    7939 </span>            : </a>
+<a name="7940"><span class="lineNum">    7940 </span><span class="lineCov">       6221 :             temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="7941"><span class="lineNum">    7941 </span><span class="lineCov">       6221 :             dw = dpsi + dphi + temp * temp;</span></a>
+<a name="7942"><span class="lineNum">    7942 </span><span class="lineCov">       6221 :             temp = z__[ii] * temp;</span></a>
+<a name="7943"><span class="lineNum">    7943 </span><span class="lineCov">       6221 :             w = rhoinv + phi + psi + temp;</span></a>
+<a name="7944"><span class="lineNum">    7944 </span><span class="lineCov">       6221 :             erretm = (phi - psi) * 8. + erretm + rhoinv * 2. + std::abs(temp) * 3. </span></a>
+<a name="7945"><span class="lineNum">    7945 </span><span class="lineCov">       6221 :                     + std::abs(tau) * dw;</span></a>
+<a name="7946"><span class="lineNum">    7946 </span><span class="lineCov">       6221 :             if (w * prew &gt; 0. &amp;&amp; std::abs(w) &gt; std::abs(prew) / 10.) {</span></a>
+<a name="7947"><span class="lineNum">    7947 </span><span class="lineCov">          2 :                 swtch = ! swtch;</span></a>
+<a name="7948"><span class="lineNum">    7948 </span>            :             }</a>
+<a name="7949"><span class="lineNum">    7949 </span>            : </a>
+<a name="7950"><span class="lineNum">    7950 </span><span class="lineCov">       6221 :             if (w &lt;= 0.) {</span></a>
+<a name="7951"><span class="lineNum">    7951 </span><span class="lineCov">       3250 :                 sg2lb = (sg2lb &gt; tau) ? sg2lb : tau;</span></a>
+<a name="7952"><span class="lineNum">    7952 </span>            :             } else {</a>
+<a name="7953"><span class="lineNum">    7953 </span><span class="lineCov">       2971 :                 sg2ub = (sg2ub &lt; tau) ? sg2ub : tau;</span></a>
+<a name="7954"><span class="lineNum">    7954 </span>            :             }</a>
+<a name="7955"><span class="lineNum">    7955 </span>            :         }</a>
+<a name="7956"><span class="lineNum">    7956 </span>            : </a>
+<a name="7957"><span class="lineNum">    7957 </span><span class="lineNoCov">          0 :         *info = 1;</span></a>
+<a name="7958"><span class="lineNum">    7958 </span>            : </a>
+<a name="7959"><span class="lineNum">    7959 </span>            :     }</a>
+<a name="7960"><span class="lineNum">    7960 </span>            : </a>
+<a name="7961"><span class="lineNum">    7961 </span><span class="lineCov">       3251 : L240:</span></a>
+<a name="7962"><span class="lineNum">    7962 </span>            :     return;</a>
+<a name="7963"><span class="lineNum">    7963 </span>            : </a>
+<a name="7964"><span class="lineNum">    7964 </span>            : } </a>
+<a name="7965"><span class="lineNum">    7965 </span>            : }</a>
+<a name="7966"><span class="lineNum">    7966 </span>            : }</a>
+<a name="7967"><span class="lineNum">    7967 </span>            : #include &lt;cmath&gt;</a>
+<a name="7968"><span class="lineNum">    7968 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="7969"><span class="lineNum">    7969 </span>            : </a>
+<a name="7970"><span class="lineNum">    7970 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="7971"><span class="lineNum">    7971 </span>            : namespace PLMD{</a>
+<a name="7972"><span class="lineNum">    7972 </span>            : namespace lapack{</a>
+<a name="7973"><span class="lineNum">    7973 </span>            : using namespace blas;</a>
+<a name="7974"><span class="lineNum">    7974 </span>            : void </a>
+<a name="7975"><span class="lineNum">    7975 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasd5,DLASD5)(int *i__, </span></a>
+<a name="7976"><span class="lineNum">    7976 </span>            :         double *d__, </a>
+<a name="7977"><span class="lineNum">    7977 </span>            :         double *z__, </a>
+<a name="7978"><span class="lineNum">    7978 </span>            :         double *delta, </a>
+<a name="7979"><span class="lineNum">    7979 </span>            :         double *rho, </a>
+<a name="7980"><span class="lineNum">    7980 </span>            :         double *dsigma, </a>
+<a name="7981"><span class="lineNum">    7981 </span>            :         double *work)</a>
+<a name="7982"><span class="lineNum">    7982 </span>            : {</a>
+<a name="7983"><span class="lineNum">    7983 </span>            :     double b, c__, w, del, tau, delsq;</a>
+<a name="7984"><span class="lineNum">    7984 </span>            : </a>
+<a name="7985"><span class="lineNum">    7985 </span>            :     --work;</a>
+<a name="7986"><span class="lineNum">    7986 </span>            :     --delta;</a>
+<a name="7987"><span class="lineNum">    7987 </span>            :     --z__;</a>
+<a name="7988"><span class="lineNum">    7988 </span>            :     --d__;</a>
+<a name="7989"><span class="lineNum">    7989 </span>            : </a>
+<a name="7990"><span class="lineNum">    7990 </span><span class="lineNoCov">          0 :     del = d__[2] - d__[1];</span></a>
+<a name="7991"><span class="lineNum">    7991 </span><span class="lineNoCov">          0 :     delsq = del * (d__[2] + d__[1]);</span></a>
+<a name="7992"><span class="lineNum">    7992 </span><span class="lineNoCov">          0 :     if (*i__ == 1) {</span></a>
+<a name="7993"><span class="lineNum">    7993 </span><span class="lineNoCov">          0 :         w = *rho * 4. * (z__[2] * z__[2] / (d__[1] + d__[2] * 3.) - z__[1] * </span></a>
+<a name="7994"><span class="lineNum">    7994 </span><span class="lineNoCov">          0 :                 z__[1] / (d__[1] * 3. + d__[2])) / del + 1.;</span></a>
+<a name="7995"><span class="lineNum">    7995 </span><span class="lineNoCov">          0 :         if (w &gt; 0.) {</span></a>
+<a name="7996"><span class="lineNum">    7996 </span><span class="lineNoCov">          0 :             b = delsq + *rho * (z__[1] * z__[1] + z__[2] * z__[2]);</span></a>
+<a name="7997"><span class="lineNum">    7997 </span><span class="lineNoCov">          0 :             c__ = *rho * z__[1] * z__[1] * delsq;</span></a>
+<a name="7998"><span class="lineNum">    7998 </span>            : </a>
+<a name="7999"><span class="lineNum">    7999 </span><span class="lineNoCov">          0 :             tau = c__ * 2. / (b +  std::sqrt(std::abs(b * b - c__ * 4.)));</span></a>
+<a name="8000"><span class="lineNum">    8000 </span>            : </a>
+<a name="8001"><span class="lineNum">    8001 </span><span class="lineNoCov">          0 :             tau /= d__[1] +  std::sqrt(d__[1] * d__[1] + tau);</span></a>
+<a name="8002"><span class="lineNum">    8002 </span><span class="lineNoCov">          0 :             *dsigma = d__[1] + tau;</span></a>
+<a name="8003"><span class="lineNum">    8003 </span><span class="lineNoCov">          0 :             delta[1] = -tau;</span></a>
+<a name="8004"><span class="lineNum">    8004 </span><span class="lineNoCov">          0 :             delta[2] = del - tau;</span></a>
+<a name="8005"><span class="lineNum">    8005 </span><span class="lineNoCov">          0 :             work[1] = d__[1] * 2. + tau;</span></a>
+<a name="8006"><span class="lineNum">    8006 </span><span class="lineNoCov">          0 :             work[2] = d__[1] + tau + d__[2];</span></a>
+<a name="8007"><span class="lineNum">    8007 </span>            :         } else {</a>
+<a name="8008"><span class="lineNum">    8008 </span><span class="lineNoCov">          0 :             b = -delsq + *rho * (z__[1] * z__[1] + z__[2] * z__[2]);</span></a>
+<a name="8009"><span class="lineNum">    8009 </span><span class="lineNoCov">          0 :             c__ = *rho * z__[2] * z__[2] * delsq;</span></a>
+<a name="8010"><span class="lineNum">    8010 </span>            : </a>
+<a name="8011"><span class="lineNum">    8011 </span><span class="lineNoCov">          0 :             if (b &gt; 0.) {</span></a>
+<a name="8012"><span class="lineNum">    8012 </span><span class="lineNoCov">          0 :                 tau = c__ * -2. / (b +  std::sqrt(b * b + c__ * 4.));</span></a>
+<a name="8013"><span class="lineNum">    8013 </span>            :             } else {</a>
+<a name="8014"><span class="lineNum">    8014 </span><span class="lineNoCov">          0 :                 tau = (b -  std::sqrt(b * b + c__ * 4.)) / 2.;</span></a>
+<a name="8015"><span class="lineNum">    8015 </span>            :             }</a>
+<a name="8016"><span class="lineNum">    8016 </span>            : </a>
+<a name="8017"><span class="lineNum">    8017 </span><span class="lineNoCov">          0 :             tau /= d__[2] +  std::sqrt(std::abs(d__[2] * d__[2] + tau));</span></a>
+<a name="8018"><span class="lineNum">    8018 </span><span class="lineNoCov">          0 :             *dsigma = d__[2] + tau;</span></a>
+<a name="8019"><span class="lineNum">    8019 </span><span class="lineNoCov">          0 :             delta[1] = -(del + tau);</span></a>
+<a name="8020"><span class="lineNum">    8020 </span><span class="lineNoCov">          0 :             delta[2] = -tau;</span></a>
+<a name="8021"><span class="lineNum">    8021 </span><span class="lineNoCov">          0 :             work[1] = d__[1] + tau + d__[2];</span></a>
+<a name="8022"><span class="lineNum">    8022 </span><span class="lineNoCov">          0 :             work[2] = d__[2] * 2. + tau;</span></a>
+<a name="8023"><span class="lineNum">    8023 </span>            :         }</a>
+<a name="8024"><span class="lineNum">    8024 </span>            :     } else {</a>
+<a name="8025"><span class="lineNum">    8025 </span>            : </a>
+<a name="8026"><span class="lineNum">    8026 </span><span class="lineNoCov">          0 :         b = -delsq + *rho * (z__[1] * z__[1] + z__[2] * z__[2]);</span></a>
+<a name="8027"><span class="lineNum">    8027 </span><span class="lineNoCov">          0 :         c__ = *rho * z__[2] * z__[2] * delsq;</span></a>
+<a name="8028"><span class="lineNum">    8028 </span>            : </a>
+<a name="8029"><span class="lineNum">    8029 </span><span class="lineNoCov">          0 :         if (b &gt; 0.) {</span></a>
+<a name="8030"><span class="lineNum">    8030 </span><span class="lineNoCov">          0 :             tau = (b +  std::sqrt(b * b + c__ * 4.)) / 2.;</span></a>
+<a name="8031"><span class="lineNum">    8031 </span>            :         } else {</a>
+<a name="8032"><span class="lineNum">    8032 </span><span class="lineNoCov">          0 :             tau = c__ * 2. / (-b +  std::sqrt(b * b + c__ * 4.));</span></a>
+<a name="8033"><span class="lineNum">    8033 </span>            :         }</a>
+<a name="8034"><span class="lineNum">    8034 </span><span class="lineNoCov">          0 :         tau /= d__[2] +  std::sqrt(d__[2] * d__[2] + tau);</span></a>
+<a name="8035"><span class="lineNum">    8035 </span><span class="lineNoCov">          0 :         *dsigma = d__[2] + tau;</span></a>
+<a name="8036"><span class="lineNum">    8036 </span><span class="lineNoCov">          0 :         delta[1] = -(del + tau);</span></a>
+<a name="8037"><span class="lineNum">    8037 </span><span class="lineNoCov">          0 :         delta[2] = -tau;</span></a>
+<a name="8038"><span class="lineNum">    8038 </span><span class="lineNoCov">          0 :         work[1] = d__[1] + tau + d__[2];</span></a>
+<a name="8039"><span class="lineNum">    8039 </span><span class="lineNoCov">          0 :         work[2] = d__[2] * 2. + tau;</span></a>
+<a name="8040"><span class="lineNum">    8040 </span>            :     }</a>
+<a name="8041"><span class="lineNum">    8041 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="8042"><span class="lineNum">    8042 </span>            : </a>
+<a name="8043"><span class="lineNum">    8043 </span>            : } </a>
+<a name="8044"><span class="lineNum">    8044 </span>            : }</a>
+<a name="8045"><span class="lineNum">    8045 </span>            : }</a>
+<a name="8046"><span class="lineNum">    8046 </span>            : #include &lt;cmath&gt;</a>
+<a name="8047"><span class="lineNum">    8047 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8048"><span class="lineNum">    8048 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="8049"><span class="lineNum">    8049 </span>            : </a>
+<a name="8050"><span class="lineNum">    8050 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8051"><span class="lineNum">    8051 </span>            : namespace PLMD{</a>
+<a name="8052"><span class="lineNum">    8052 </span>            : namespace lapack{</a>
+<a name="8053"><span class="lineNum">    8053 </span>            : using namespace blas;</a>
+<a name="8054"><span class="lineNum">    8054 </span>            : void </a>
+<a name="8055"><span class="lineNum">    8055 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasd6,DLASD6)(int *icompq, </span></a>
+<a name="8056"><span class="lineNum">    8056 </span>            :         int *nl, </a>
+<a name="8057"><span class="lineNum">    8057 </span>            :         int *nr, </a>
+<a name="8058"><span class="lineNum">    8058 </span>            :         int *sqre, </a>
+<a name="8059"><span class="lineNum">    8059 </span>            :         double *d__, </a>
+<a name="8060"><span class="lineNum">    8060 </span>            :         double *vf, </a>
+<a name="8061"><span class="lineNum">    8061 </span>            :         double *vl, </a>
+<a name="8062"><span class="lineNum">    8062 </span>            :         double *alpha, </a>
+<a name="8063"><span class="lineNum">    8063 </span>            :         double *beta, </a>
+<a name="8064"><span class="lineNum">    8064 </span>            :         int *idxq, </a>
+<a name="8065"><span class="lineNum">    8065 </span>            :         int *perm, </a>
+<a name="8066"><span class="lineNum">    8066 </span>            :         int *givptr, </a>
+<a name="8067"><span class="lineNum">    8067 </span>            :         int *givcol, </a>
+<a name="8068"><span class="lineNum">    8068 </span>            :         int *ldgcol, </a>
+<a name="8069"><span class="lineNum">    8069 </span>            :         double *givnum,</a>
+<a name="8070"><span class="lineNum">    8070 </span>            :         int *ldgnum, </a>
+<a name="8071"><span class="lineNum">    8071 </span>            :         double *poles, </a>
+<a name="8072"><span class="lineNum">    8072 </span>            :         double *difl, </a>
+<a name="8073"><span class="lineNum">    8073 </span>            :         double *difr, </a>
+<a name="8074"><span class="lineNum">    8074 </span>            :         double *z__, </a>
+<a name="8075"><span class="lineNum">    8075 </span>            :         int *k, </a>
+<a name="8076"><span class="lineNum">    8076 </span>            :         double *c__, </a>
+<a name="8077"><span class="lineNum">    8077 </span>            :         double *s, </a>
+<a name="8078"><span class="lineNum">    8078 </span>            :         double *work, </a>
+<a name="8079"><span class="lineNum">    8079 </span>            :         int *iwork, </a>
+<a name="8080"><span class="lineNum">    8080 </span>            :         int *info)</a>
+<a name="8081"><span class="lineNum">    8081 </span>            : {</a>
+<a name="8082"><span class="lineNum">    8082 </span>            :     int givcol_dim1, givcol_offset, givnum_dim1, givnum_offset, </a>
+<a name="8083"><span class="lineNum">    8083 </span>            :             poles_dim1, poles_offset, i__1;</a>
+<a name="8084"><span class="lineNum">    8084 </span>            :     double d__1, d__2;</a>
+<a name="8085"><span class="lineNum">    8085 </span>            : </a>
+<a name="8086"><span class="lineNum">    8086 </span>            :     int i__, m, n, n1, n2, iw, idx, idxc, idxp, ivfw, ivlw;</a>
+<a name="8087"><span class="lineNum">    8087 </span>            :     int isigma;</a>
+<a name="8088"><span class="lineNum">    8088 </span>            :     double orgnrm;</a>
+<a name="8089"><span class="lineNum">    8089 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="8090"><span class="lineNum">    8090 </span><span class="lineNoCov">          0 :     double one = 1.0;</span></a>
+<a name="8091"><span class="lineNum">    8091 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="8092"><span class="lineNum">    8092 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="8093"><span class="lineNum">    8093 </span>            : </a>
+<a name="8094"><span class="lineNum">    8094 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="8095"><span class="lineNum">    8095 </span>            :     --vf;</a>
+<a name="8096"><span class="lineNum">    8096 </span>            :     --vl;</a>
+<a name="8097"><span class="lineNum">    8097 </span>            :     --idxq;</a>
+<a name="8098"><span class="lineNum">    8098 </span>            :     --perm;</a>
+<a name="8099"><span class="lineNum">    8099 </span>            :     givcol_dim1 = *ldgcol;</a>
+<a name="8100"><span class="lineNum">    8100 </span>            :     givcol_offset = 1 + givcol_dim1;</a>
+<a name="8101"><span class="lineNum">    8101 </span>            :     givcol -= givcol_offset;</a>
+<a name="8102"><span class="lineNum">    8102 </span><span class="lineNoCov">          0 :     poles_dim1 = *ldgnum;</span></a>
+<a name="8103"><span class="lineNum">    8103 </span><span class="lineNoCov">          0 :     poles_offset = 1 + poles_dim1;</span></a>
+<a name="8104"><span class="lineNum">    8104 </span><span class="lineNoCov">          0 :     poles -= poles_offset;</span></a>
+<a name="8105"><span class="lineNum">    8105 </span>            :     givnum_dim1 = *ldgnum;</a>
+<a name="8106"><span class="lineNum">    8106 </span>            :     givnum_offset = 1 + givnum_dim1;</a>
+<a name="8107"><span class="lineNum">    8107 </span>            :     givnum -= givnum_offset;</a>
+<a name="8108"><span class="lineNum">    8108 </span>            :     --difl;</a>
+<a name="8109"><span class="lineNum">    8109 </span>            :     --difr;</a>
+<a name="8110"><span class="lineNum">    8110 </span>            :     --z__;</a>
+<a name="8111"><span class="lineNum">    8111 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="8112"><span class="lineNum">    8112 </span>            :     --iwork;</a>
+<a name="8113"><span class="lineNum">    8113 </span>            : </a>
+<a name="8114"><span class="lineNum">    8114 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="8115"><span class="lineNum">    8115 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="8116"><span class="lineNum">    8116 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="8117"><span class="lineNum">    8117 </span>            : </a>
+<a name="8118"><span class="lineNum">    8118 </span>            :     isigma = 1;</a>
+<a name="8119"><span class="lineNum">    8119 </span><span class="lineNoCov">          0 :     iw = isigma + n;</span></a>
+<a name="8120"><span class="lineNum">    8120 </span><span class="lineNoCov">          0 :     ivfw = iw + m;</span></a>
+<a name="8121"><span class="lineNum">    8121 </span><span class="lineNoCov">          0 :     ivlw = ivfw + m;</span></a>
+<a name="8122"><span class="lineNum">    8122 </span>            : </a>
+<a name="8123"><span class="lineNum">    8123 </span>            :     idx = 1;</a>
+<a name="8124"><span class="lineNum">    8124 </span>            :     idxc = idx + n;</a>
+<a name="8125"><span class="lineNum">    8125 </span><span class="lineNoCov">          0 :     idxp = idxc + n;</span></a>
+<a name="8126"><span class="lineNum">    8126 </span>            : </a>
+<a name="8127"><span class="lineNum">    8127 </span><span class="lineNoCov">          0 :     d__1 = std::abs(*alpha); </span></a>
+<a name="8128"><span class="lineNum">    8128 </span><span class="lineNoCov">          0 :     d__2 = std::abs(*beta);</span></a>
+<a name="8129"><span class="lineNum">    8129 </span><span class="lineNoCov">          0 :     orgnrm = (d__1 &gt; d__2) ? d__1 : d__2;</span></a>
+<a name="8130"><span class="lineNum">    8130 </span><span class="lineNoCov">          0 :     d__[*nl + 1] = 0.;</span></a>
+<a name="8131"><span class="lineNum">    8131 </span>            :     i__1 = n;</a>
+<a name="8132"><span class="lineNum">    8132 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8133"><span class="lineNum">    8133 </span><span class="lineNoCov">          0 :       d__1 = std::abs(d__[i__]);</span></a>
+<a name="8134"><span class="lineNum">    8134 </span><span class="lineNoCov">          0 :         if (d__1 &gt; orgnrm)</span></a>
+<a name="8135"><span class="lineNum">    8135 </span><span class="lineNoCov">          0 :             orgnrm = d__1;</span></a>
+<a name="8136"><span class="lineNum">    8136 </span>            :     }</a>
+<a name="8137"><span class="lineNum">    8137 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;orgnrm, &amp;one, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="8138"><span class="lineNum">    8138 </span><span class="lineNoCov">          0 :     *alpha /= orgnrm;</span></a>
+<a name="8139"><span class="lineNum">    8139 </span><span class="lineNoCov">          0 :     *beta /= orgnrm;</span></a>
+<a name="8140"><span class="lineNum">    8140 </span>            : </a>
+<a name="8141"><span class="lineNum">    8141 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlasd7,DLASD7)(icompq, nl, nr, sqre, k, &amp;d__[1], &amp;z__[1], &amp;work[iw], &amp;vf[1], &amp;</span></a>
+<a name="8142"><span class="lineNum">    8142 </span><span class="lineNoCov">          0 :             work[ivfw], &amp;vl[1], &amp;work[ivlw], alpha, beta, &amp;work[isigma], &amp;</span></a>
+<a name="8143"><span class="lineNum">    8143 </span><span class="lineNoCov">          0 :             iwork[idx], &amp;iwork[idxp], &amp;idxq[1], &amp;perm[1], givptr, &amp;givcol[</span></a>
+<a name="8144"><span class="lineNum">    8144 </span>            :             givcol_offset], ldgcol, &amp;givnum[givnum_offset], ldgnum, c__, s, </a>
+<a name="8145"><span class="lineNum">    8145 </span>            :             info);</a>
+<a name="8146"><span class="lineNum">    8146 </span>            : </a>
+<a name="8147"><span class="lineNum">    8147 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlasd8,DLASD8)(icompq, k, &amp;d__[1], &amp;z__[1], &amp;vf[1], &amp;vl[1], &amp;difl[1], &amp;difr[1], </span></a>
+<a name="8148"><span class="lineNum">    8148 </span>            :             ldgnum, &amp;work[isigma], &amp;work[iw], info);</a>
+<a name="8149"><span class="lineNum">    8149 </span>            : </a>
+<a name="8150"><span class="lineNum">    8150 </span><span class="lineNoCov">          0 :     if (*icompq == 1) {</span></a>
+<a name="8151"><span class="lineNum">    8151 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(k, &amp;d__[1], &amp;c__1, &amp;poles[poles_dim1 + 1], &amp;c__1);</span></a>
+<a name="8152"><span class="lineNum">    8152 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(k, &amp;work[isigma], &amp;c__1, &amp;poles[(poles_dim1 &lt;&lt; 1) + 1], &amp;c__1);</span></a>
+<a name="8153"><span class="lineNum">    8153 </span>            :     }</a>
+<a name="8154"><span class="lineNum">    8154 </span>            : </a>
+<a name="8155"><span class="lineNum">    8155 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;one, &amp;orgnrm, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="8156"><span class="lineNum">    8156 </span>            : </a>
+<a name="8157"><span class="lineNum">    8157 </span><span class="lineNoCov">          0 :     n1 = *k;</span></a>
+<a name="8158"><span class="lineNum">    8158 </span><span class="lineNoCov">          0 :     n2 = n - *k;</span></a>
+<a name="8159"><span class="lineNum">    8159 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlamrg,DLAMRG)(&amp;n1, &amp;n2, &amp;d__[1], &amp;c__1, &amp;c_n1, &amp;idxq[1]);</span></a>
+<a name="8160"><span class="lineNum">    8160 </span>            : </a>
+<a name="8161"><span class="lineNum">    8161 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="8162"><span class="lineNum">    8162 </span>            : </a>
+<a name="8163"><span class="lineNum">    8163 </span>            : }</a>
+<a name="8164"><span class="lineNum">    8164 </span>            : </a>
+<a name="8165"><span class="lineNum">    8165 </span>            : </a>
+<a name="8166"><span class="lineNum">    8166 </span>            : }</a>
+<a name="8167"><span class="lineNum">    8167 </span>            : }</a>
+<a name="8168"><span class="lineNum">    8168 </span>            : #include &lt;cmath&gt;</a>
+<a name="8169"><span class="lineNum">    8169 </span>            : #include &quot;real.h&quot;</a>
+<a name="8170"><span class="lineNum">    8170 </span>            : </a>
+<a name="8171"><span class="lineNum">    8171 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8172"><span class="lineNum">    8172 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="8173"><span class="lineNum">    8173 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="8174"><span class="lineNum">    8174 </span>            : </a>
+<a name="8175"><span class="lineNum">    8175 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8176"><span class="lineNum">    8176 </span>            : namespace PLMD{</a>
+<a name="8177"><span class="lineNum">    8177 </span>            : namespace lapack{</a>
+<a name="8178"><span class="lineNum">    8178 </span>            : using namespace blas;</a>
+<a name="8179"><span class="lineNum">    8179 </span>            : void </a>
+<a name="8180"><span class="lineNum">    8180 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasd7,DLASD7)(int *icompq, </span></a>
+<a name="8181"><span class="lineNum">    8181 </span>            :         int *nl, </a>
+<a name="8182"><span class="lineNum">    8182 </span>            :         int *nr, </a>
+<a name="8183"><span class="lineNum">    8183 </span>            :         int *sqre, </a>
+<a name="8184"><span class="lineNum">    8184 </span>            :         int *k, </a>
+<a name="8185"><span class="lineNum">    8185 </span>            :         double *d__, </a>
+<a name="8186"><span class="lineNum">    8186 </span>            :         double *z__, </a>
+<a name="8187"><span class="lineNum">    8187 </span>            :         double *zw, </a>
+<a name="8188"><span class="lineNum">    8188 </span>            :         double *vf, </a>
+<a name="8189"><span class="lineNum">    8189 </span>            :         double *vfw,</a>
+<a name="8190"><span class="lineNum">    8190 </span>            :         double *vl, </a>
+<a name="8191"><span class="lineNum">    8191 </span>            :         double *vlw,</a>
+<a name="8192"><span class="lineNum">    8192 </span>            :         double *alpha, </a>
+<a name="8193"><span class="lineNum">    8193 </span>            :         double *beta,</a>
+<a name="8194"><span class="lineNum">    8194 </span>            :         double *dsigma, </a>
+<a name="8195"><span class="lineNum">    8195 </span>            :         int *idx, </a>
+<a name="8196"><span class="lineNum">    8196 </span>            :         int *idxp,</a>
+<a name="8197"><span class="lineNum">    8197 </span>            :         int *idxq, </a>
+<a name="8198"><span class="lineNum">    8198 </span>            :         int *perm, </a>
+<a name="8199"><span class="lineNum">    8199 </span>            :         int *givptr,</a>
+<a name="8200"><span class="lineNum">    8200 </span>            :         int *givcol, </a>
+<a name="8201"><span class="lineNum">    8201 </span>            :         int *ldgcol, </a>
+<a name="8202"><span class="lineNum">    8202 </span>            :         double *givnum,</a>
+<a name="8203"><span class="lineNum">    8203 </span>            :         int *ldgnum, </a>
+<a name="8204"><span class="lineNum">    8204 </span>            :         double *c__, </a>
+<a name="8205"><span class="lineNum">    8205 </span>            :         double *s, </a>
+<a name="8206"><span class="lineNum">    8206 </span>            :         int *info)</a>
+<a name="8207"><span class="lineNum">    8207 </span>            : {</a>
+<a name="8208"><span class="lineNum">    8208 </span>            :     int givcol_dim1, givcol_offset, givnum_dim1, givnum_offset, i__1;</a>
+<a name="8209"><span class="lineNum">    8209 </span>            :     double d__1, d__2;</a>
+<a name="8210"><span class="lineNum">    8210 </span>            : </a>
+<a name="8211"><span class="lineNum">    8211 </span>            :     int i__, j, m, n, k2;</a>
+<a name="8212"><span class="lineNum">    8212 </span>            :     double z1;</a>
+<a name="8213"><span class="lineNum">    8213 </span>            :     int jp;</a>
+<a name="8214"><span class="lineNum">    8214 </span>            :     double eps, tau, tol;</a>
+<a name="8215"><span class="lineNum">    8215 </span>            :     int nlp1, nlp2, idxi, idxj;</a>
+<a name="8216"><span class="lineNum">    8216 </span>            :     int idxjp;</a>
+<a name="8217"><span class="lineNum">    8217 </span>            :     int jprev = 0;</a>
+<a name="8218"><span class="lineNum">    8218 </span>            :     double hlftol;</a>
+<a name="8219"><span class="lineNum">    8219 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="8220"><span class="lineNum">    8220 </span>            : </a>
+<a name="8221"><span class="lineNum">    8221 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="8222"><span class="lineNum">    8222 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="8223"><span class="lineNum">    8223 </span><span class="lineNoCov">          0 :     --zw;</span></a>
+<a name="8224"><span class="lineNum">    8224 </span><span class="lineNoCov">          0 :     --vf;</span></a>
+<a name="8225"><span class="lineNum">    8225 </span><span class="lineNoCov">          0 :     --vfw;</span></a>
+<a name="8226"><span class="lineNum">    8226 </span><span class="lineNoCov">          0 :     --vl;</span></a>
+<a name="8227"><span class="lineNum">    8227 </span><span class="lineNoCov">          0 :     --vlw;</span></a>
+<a name="8228"><span class="lineNum">    8228 </span><span class="lineNoCov">          0 :     --dsigma;</span></a>
+<a name="8229"><span class="lineNum">    8229 </span><span class="lineNoCov">          0 :     --idx;</span></a>
+<a name="8230"><span class="lineNum">    8230 </span><span class="lineNoCov">          0 :     --idxp;</span></a>
+<a name="8231"><span class="lineNum">    8231 </span><span class="lineNoCov">          0 :     --idxq;</span></a>
+<a name="8232"><span class="lineNum">    8232 </span><span class="lineNoCov">          0 :     --perm;</span></a>
+<a name="8233"><span class="lineNum">    8233 </span><span class="lineNoCov">          0 :     givcol_dim1 = *ldgcol;</span></a>
+<a name="8234"><span class="lineNum">    8234 </span><span class="lineNoCov">          0 :     givcol_offset = 1 + givcol_dim1;</span></a>
+<a name="8235"><span class="lineNum">    8235 </span><span class="lineNoCov">          0 :     givcol -= givcol_offset;</span></a>
+<a name="8236"><span class="lineNum">    8236 </span><span class="lineNoCov">          0 :     givnum_dim1 = *ldgnum;</span></a>
+<a name="8237"><span class="lineNum">    8237 </span><span class="lineNoCov">          0 :     givnum_offset = 1 + givnum_dim1;</span></a>
+<a name="8238"><span class="lineNum">    8238 </span><span class="lineNoCov">          0 :     givnum -= givnum_offset;</span></a>
+<a name="8239"><span class="lineNum">    8239 </span>            : </a>
+<a name="8240"><span class="lineNum">    8240 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="8241"><span class="lineNum">    8241 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="8242"><span class="lineNum">    8242 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="8243"><span class="lineNum">    8243 </span>            : </a>
+<a name="8244"><span class="lineNum">    8244 </span><span class="lineNoCov">          0 :     nlp1 = *nl + 1;</span></a>
+<a name="8245"><span class="lineNum">    8245 </span><span class="lineNoCov">          0 :     nlp2 = *nl + 2;</span></a>
+<a name="8246"><span class="lineNum">    8246 </span><span class="lineNoCov">          0 :     if (*icompq == 1) {</span></a>
+<a name="8247"><span class="lineNum">    8247 </span><span class="lineNoCov">          0 :         *givptr = 0;</span></a>
+<a name="8248"><span class="lineNum">    8248 </span>            :     }</a>
+<a name="8249"><span class="lineNum">    8249 </span>            : </a>
+<a name="8250"><span class="lineNum">    8250 </span><span class="lineNoCov">          0 :     z1 = *alpha * vl[nlp1];</span></a>
+<a name="8251"><span class="lineNum">    8251 </span><span class="lineNoCov">          0 :     vl[nlp1] = 0.;</span></a>
+<a name="8252"><span class="lineNum">    8252 </span><span class="lineNoCov">          0 :     tau = vf[nlp1];</span></a>
+<a name="8253"><span class="lineNum">    8253 </span><span class="lineNoCov">          0 :     for (i__ = *nl; i__ &gt;= 1; --i__) {</span></a>
+<a name="8254"><span class="lineNum">    8254 </span><span class="lineNoCov">          0 :         z__[i__ + 1] = *alpha * vl[i__];</span></a>
+<a name="8255"><span class="lineNum">    8255 </span><span class="lineNoCov">          0 :         vl[i__] = 0.;</span></a>
+<a name="8256"><span class="lineNum">    8256 </span><span class="lineNoCov">          0 :         vf[i__ + 1] = vf[i__];</span></a>
+<a name="8257"><span class="lineNum">    8257 </span><span class="lineNoCov">          0 :         d__[i__ + 1] = d__[i__];</span></a>
+<a name="8258"><span class="lineNum">    8258 </span><span class="lineNoCov">          0 :         idxq[i__ + 1] = idxq[i__] + 1;</span></a>
+<a name="8259"><span class="lineNum">    8259 </span>            :     }</a>
+<a name="8260"><span class="lineNum">    8260 </span><span class="lineNoCov">          0 :     vf[1] = tau;</span></a>
+<a name="8261"><span class="lineNum">    8261 </span>            : </a>
+<a name="8262"><span class="lineNum">    8262 </span>            :     i__1 = m;</a>
+<a name="8263"><span class="lineNum">    8263 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8264"><span class="lineNum">    8264 </span><span class="lineNoCov">          0 :         z__[i__] = *beta * vf[i__];</span></a>
+<a name="8265"><span class="lineNum">    8265 </span><span class="lineNoCov">          0 :         vf[i__] = 0.;</span></a>
+<a name="8266"><span class="lineNum">    8266 </span>            :     }</a>
+<a name="8267"><span class="lineNum">    8267 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="8268"><span class="lineNum">    8268 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8269"><span class="lineNum">    8269 </span><span class="lineNoCov">          0 :         idxq[i__] += nlp1;</span></a>
+<a name="8270"><span class="lineNum">    8270 </span>            :     }</a>
+<a name="8271"><span class="lineNum">    8271 </span>            : </a>
+<a name="8272"><span class="lineNum">    8272 </span>            :     i__1 = n;</a>
+<a name="8273"><span class="lineNum">    8273 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8274"><span class="lineNum">    8274 </span><span class="lineNoCov">          0 :         dsigma[i__] = d__[idxq[i__]];</span></a>
+<a name="8275"><span class="lineNum">    8275 </span><span class="lineNoCov">          0 :         zw[i__] = z__[idxq[i__]];</span></a>
+<a name="8276"><span class="lineNum">    8276 </span><span class="lineNoCov">          0 :         vfw[i__] = vf[idxq[i__]];</span></a>
+<a name="8277"><span class="lineNum">    8277 </span><span class="lineNoCov">          0 :         vlw[i__] = vl[idxq[i__]];</span></a>
+<a name="8278"><span class="lineNum">    8278 </span>            :     }</a>
+<a name="8279"><span class="lineNum">    8279 </span>            : </a>
+<a name="8280"><span class="lineNum">    8280 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlamrg,DLAMRG)(nl, nr, &amp;dsigma[2], &amp;c__1, &amp;c__1, &amp;idx[2]);</span></a>
+<a name="8281"><span class="lineNum">    8281 </span>            : </a>
+<a name="8282"><span class="lineNum">    8282 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="8283"><span class="lineNum">    8283 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8284"><span class="lineNum">    8284 </span><span class="lineNoCov">          0 :         idxi = idx[i__] + 1;</span></a>
+<a name="8285"><span class="lineNum">    8285 </span><span class="lineNoCov">          0 :         d__[i__] = dsigma[idxi];</span></a>
+<a name="8286"><span class="lineNum">    8286 </span><span class="lineNoCov">          0 :         z__[i__] = zw[idxi];</span></a>
+<a name="8287"><span class="lineNum">    8287 </span><span class="lineNoCov">          0 :         vf[i__] = vfw[idxi];</span></a>
+<a name="8288"><span class="lineNum">    8288 </span><span class="lineNoCov">          0 :         vl[i__] = vlw[idxi];</span></a>
+<a name="8289"><span class="lineNum">    8289 </span>            :     }</a>
+<a name="8290"><span class="lineNum">    8290 </span>            : </a>
+<a name="8291"><span class="lineNum">    8291 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="8292"><span class="lineNum">    8292 </span>            : </a>
+<a name="8293"><span class="lineNum">    8293 </span><span class="lineNoCov">          0 :     d__1 = std::abs(*alpha);</span></a>
+<a name="8294"><span class="lineNum">    8294 </span><span class="lineNoCov">          0 :     d__2 = std::abs(*beta);</span></a>
+<a name="8295"><span class="lineNum">    8295 </span><span class="lineNoCov">          0 :     tol = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="8296"><span class="lineNum">    8296 </span><span class="lineNoCov">          0 :     d__2 = std::abs(d__[n]);</span></a>
+<a name="8297"><span class="lineNum">    8297 </span><span class="lineNoCov">          0 :     tol = eps * 64. * ((d__2&gt;tol) ? d__2 : tol);</span></a>
+<a name="8298"><span class="lineNum">    8298 </span>            : </a>
+<a name="8299"><span class="lineNum">    8299 </span><span class="lineNoCov">          0 :     *k = 1;</span></a>
+<a name="8300"><span class="lineNum">    8300 </span><span class="lineNoCov">          0 :     k2 = n + 1;</span></a>
+<a name="8301"><span class="lineNum">    8301 </span>            :     i__1 = n;</a>
+<a name="8302"><span class="lineNum">    8302 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="8303"><span class="lineNum">    8303 </span><span class="lineNoCov">          0 :         if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="8304"><span class="lineNum">    8304 </span>            : </a>
+<a name="8305"><span class="lineNum">    8305 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="8306"><span class="lineNum">    8306 </span><span class="lineNoCov">          0 :             idxp[k2] = j;</span></a>
+<a name="8307"><span class="lineNum">    8307 </span><span class="lineNoCov">          0 :             if (j == n) {</span></a>
+<a name="8308"><span class="lineNum">    8308 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="8309"><span class="lineNum">    8309 </span>            :             }</a>
+<a name="8310"><span class="lineNum">    8310 </span>            :         } else {</a>
+<a name="8311"><span class="lineNum">    8311 </span>            :             jprev = j;</a>
+<a name="8312"><span class="lineNum">    8312 </span><span class="lineNoCov">          0 :             goto L70;</span></a>
+<a name="8313"><span class="lineNum">    8313 </span>            :         }</a>
+<a name="8314"><span class="lineNum">    8314 </span>            :     }</a>
+<a name="8315"><span class="lineNum">    8315 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="8316"><span class="lineNum">    8316 </span>            :     j = jprev;</a>
+<a name="8317"><span class="lineNum">    8317 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="8318"><span class="lineNum">    8318 </span><span class="lineNoCov">          0 :     ++j;</span></a>
+<a name="8319"><span class="lineNum">    8319 </span><span class="lineNoCov">          0 :     if (j &gt; n) {</span></a>
+<a name="8320"><span class="lineNum">    8320 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="8321"><span class="lineNum">    8321 </span>            :     }</a>
+<a name="8322"><span class="lineNum">    8322 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="8323"><span class="lineNum">    8323 </span>            : </a>
+<a name="8324"><span class="lineNum">    8324 </span><span class="lineNoCov">          0 :         --k2;</span></a>
+<a name="8325"><span class="lineNum">    8325 </span><span class="lineNoCov">          0 :         idxp[k2] = j;</span></a>
+<a name="8326"><span class="lineNum">    8326 </span>            :     } else {</a>
+<a name="8327"><span class="lineNum">    8327 </span>            : </a>
+<a name="8328"><span class="lineNum">    8328 </span><span class="lineNoCov">          0 :         if (std::abs(d__[j] - d__[jprev]) &lt;= tol) {</span></a>
+<a name="8329"><span class="lineNum">    8329 </span>            : </a>
+<a name="8330"><span class="lineNum">    8330 </span><span class="lineNoCov">          0 :             *s = z__[jprev];</span></a>
+<a name="8331"><span class="lineNum">    8331 </span><span class="lineNoCov">          0 :             *c__ = z__[j];</span></a>
+<a name="8332"><span class="lineNum">    8332 </span>            : </a>
+<a name="8333"><span class="lineNum">    8333 </span><span class="lineNoCov">          0 :             tau = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(c__, s);</span></a>
+<a name="8334"><span class="lineNum">    8334 </span><span class="lineNoCov">          0 :             z__[j] = tau;</span></a>
+<a name="8335"><span class="lineNum">    8335 </span><span class="lineNoCov">          0 :             z__[jprev] = 0.;</span></a>
+<a name="8336"><span class="lineNum">    8336 </span><span class="lineNoCov">          0 :             *c__ /= tau;</span></a>
+<a name="8337"><span class="lineNum">    8337 </span><span class="lineNoCov">          0 :             *s = -(*s) / tau;</span></a>
+<a name="8338"><span class="lineNum">    8338 </span>            : </a>
+<a name="8339"><span class="lineNum">    8339 </span>            : </a>
+<a name="8340"><span class="lineNum">    8340 </span><span class="lineNoCov">          0 :             if (*icompq == 1) {</span></a>
+<a name="8341"><span class="lineNum">    8341 </span><span class="lineNoCov">          0 :                 ++(*givptr);</span></a>
+<a name="8342"><span class="lineNum">    8342 </span><span class="lineNoCov">          0 :                 idxjp = idxq[idx[jprev] + 1];</span></a>
+<a name="8343"><span class="lineNum">    8343 </span><span class="lineNoCov">          0 :                 idxj = idxq[idx[j] + 1];</span></a>
+<a name="8344"><span class="lineNum">    8344 </span><span class="lineNoCov">          0 :                 if (idxjp &lt;= nlp1) {</span></a>
+<a name="8345"><span class="lineNum">    8345 </span><span class="lineNoCov">          0 :                     --idxjp;</span></a>
+<a name="8346"><span class="lineNum">    8346 </span>            :                 }</a>
+<a name="8347"><span class="lineNum">    8347 </span><span class="lineNoCov">          0 :                 if (idxj &lt;= nlp1) {</span></a>
+<a name="8348"><span class="lineNum">    8348 </span><span class="lineNoCov">          0 :                     --idxj;</span></a>
+<a name="8349"><span class="lineNum">    8349 </span>            :                 }</a>
+<a name="8350"><span class="lineNum">    8350 </span><span class="lineNoCov">          0 :                 givcol[*givptr + (givcol_dim1 &lt;&lt; 1)] = idxjp;</span></a>
+<a name="8351"><span class="lineNum">    8351 </span><span class="lineNoCov">          0 :                 givcol[*givptr + givcol_dim1] = idxj;</span></a>
+<a name="8352"><span class="lineNum">    8352 </span><span class="lineNoCov">          0 :                 givnum[*givptr + (givnum_dim1 &lt;&lt; 1)] = *c__;</span></a>
+<a name="8353"><span class="lineNum">    8353 </span><span class="lineNoCov">          0 :                 givnum[*givptr + givnum_dim1] = *s;</span></a>
+<a name="8354"><span class="lineNum">    8354 </span>            :             }</a>
+<a name="8355"><span class="lineNum">    8355 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(&amp;c__1, &amp;vf[jprev], &amp;c__1, &amp;vf[j], &amp;c__1, c__, s);</span></a>
+<a name="8356"><span class="lineNum">    8356 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(drot,DROT)(&amp;c__1, &amp;vl[jprev], &amp;c__1, &amp;vl[j], &amp;c__1, c__, s);</span></a>
+<a name="8357"><span class="lineNum">    8357 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="8358"><span class="lineNum">    8358 </span><span class="lineNoCov">          0 :             idxp[k2] = jprev;</span></a>
+<a name="8359"><span class="lineNum">    8359 </span>            :             jprev = j;</a>
+<a name="8360"><span class="lineNum">    8360 </span>            :         } else {</a>
+<a name="8361"><span class="lineNum">    8361 </span><span class="lineNoCov">          0 :             ++(*k);</span></a>
+<a name="8362"><span class="lineNum">    8362 </span><span class="lineNoCov">          0 :             zw[*k] = z__[jprev];</span></a>
+<a name="8363"><span class="lineNum">    8363 </span><span class="lineNoCov">          0 :             dsigma[*k] = d__[jprev];</span></a>
+<a name="8364"><span class="lineNum">    8364 </span><span class="lineNoCov">          0 :             idxp[*k] = jprev;</span></a>
+<a name="8365"><span class="lineNum">    8365 </span>            :             jprev = j;</a>
+<a name="8366"><span class="lineNum">    8366 </span>            :         }</a>
+<a name="8367"><span class="lineNum">    8367 </span>            :     }</a>
+<a name="8368"><span class="lineNum">    8368 </span><span class="lineNoCov">          0 :     goto L80;</span></a>
+<a name="8369"><span class="lineNum">    8369 </span>            : L90:</a>
+<a name="8370"><span class="lineNum">    8370 </span>            : </a>
+<a name="8371"><span class="lineNum">    8371 </span><span class="lineNoCov">          0 :     ++(*k);</span></a>
+<a name="8372"><span class="lineNum">    8372 </span><span class="lineNoCov">          0 :     zw[*k] = z__[jprev];</span></a>
+<a name="8373"><span class="lineNum">    8373 </span><span class="lineNoCov">          0 :     dsigma[*k] = d__[jprev];</span></a>
+<a name="8374"><span class="lineNum">    8374 </span><span class="lineNoCov">          0 :     idxp[*k] = jprev;</span></a>
+<a name="8375"><span class="lineNum">    8375 </span>            : </a>
+<a name="8376"><span class="lineNum">    8376 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="8377"><span class="lineNum">    8377 </span>            : </a>
+<a name="8378"><span class="lineNum">    8378 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="8379"><span class="lineNum">    8379 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="8380"><span class="lineNum">    8380 </span><span class="lineNoCov">          0 :         jp = idxp[j];</span></a>
+<a name="8381"><span class="lineNum">    8381 </span><span class="lineNoCov">          0 :         dsigma[j] = d__[jp];</span></a>
+<a name="8382"><span class="lineNum">    8382 </span><span class="lineNoCov">          0 :         vfw[j] = vf[jp];</span></a>
+<a name="8383"><span class="lineNum">    8383 </span><span class="lineNoCov">          0 :         vlw[j] = vl[jp];</span></a>
+<a name="8384"><span class="lineNum">    8384 </span>            :     }</a>
+<a name="8385"><span class="lineNum">    8385 </span><span class="lineNoCov">          0 :     if (*icompq == 1) {</span></a>
+<a name="8386"><span class="lineNum">    8386 </span>            :         i__1 = n;</a>
+<a name="8387"><span class="lineNum">    8387 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="8388"><span class="lineNum">    8388 </span><span class="lineNoCov">          0 :             jp = idxp[j];</span></a>
+<a name="8389"><span class="lineNum">    8389 </span><span class="lineNoCov">          0 :             perm[j] = idxq[idx[jp] + 1];</span></a>
+<a name="8390"><span class="lineNum">    8390 </span><span class="lineNoCov">          0 :             if (perm[j] &lt;= nlp1) {</span></a>
+<a name="8391"><span class="lineNum">    8391 </span><span class="lineNoCov">          0 :                 --perm[j];</span></a>
+<a name="8392"><span class="lineNum">    8392 </span>            :             }</a>
+<a name="8393"><span class="lineNum">    8393 </span>            :         }</a>
+<a name="8394"><span class="lineNum">    8394 </span>            :     }</a>
+<a name="8395"><span class="lineNum">    8395 </span><span class="lineNoCov">          0 :     i__1 = n - *k;</span></a>
+<a name="8396"><span class="lineNum">    8396 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;dsigma[*k + 1], &amp;c__1, &amp;d__[*k + 1], &amp;c__1);</span></a>
+<a name="8397"><span class="lineNum">    8397 </span>            : </a>
+<a name="8398"><span class="lineNum">    8398 </span><span class="lineNoCov">          0 :     dsigma[1] = 0.;</span></a>
+<a name="8399"><span class="lineNum">    8399 </span><span class="lineNoCov">          0 :     hlftol = tol / 2.;</span></a>
+<a name="8400"><span class="lineNum">    8400 </span><span class="lineNoCov">          0 :     if (std::abs(dsigma[2]) &lt;= hlftol) {</span></a>
+<a name="8401"><span class="lineNum">    8401 </span><span class="lineNoCov">          0 :         dsigma[2] = hlftol;</span></a>
+<a name="8402"><span class="lineNum">    8402 </span>            :     }</a>
+<a name="8403"><span class="lineNum">    8403 </span><span class="lineNoCov">          0 :     if (m &gt; n) {</span></a>
+<a name="8404"><span class="lineNum">    8404 </span><span class="lineNoCov">          0 :         z__[1] = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;z1, &amp;z__[m]);</span></a>
+<a name="8405"><span class="lineNum">    8405 </span><span class="lineNoCov">          0 :         if (z__[1] &lt;= tol) {</span></a>
+<a name="8406"><span class="lineNum">    8406 </span><span class="lineNoCov">          0 :             *c__ = 1.;</span></a>
+<a name="8407"><span class="lineNum">    8407 </span><span class="lineNoCov">          0 :             *s = 0.;</span></a>
+<a name="8408"><span class="lineNum">    8408 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="8409"><span class="lineNum">    8409 </span>            :         } else {</a>
+<a name="8410"><span class="lineNum">    8410 </span><span class="lineNoCov">          0 :             *c__ = z1 / z__[1];</span></a>
+<a name="8411"><span class="lineNum">    8411 </span><span class="lineNoCov">          0 :             *s = -z__[m] / z__[1];</span></a>
+<a name="8412"><span class="lineNum">    8412 </span>            :         }</a>
+<a name="8413"><span class="lineNum">    8413 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(drot,DROT)(&amp;c__1, &amp;vf[m], &amp;c__1, &amp;vf[1], &amp;c__1, c__, s);</span></a>
+<a name="8414"><span class="lineNum">    8414 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(drot,DROT)(&amp;c__1, &amp;vl[m], &amp;c__1, &amp;vl[1], &amp;c__1, c__, s);</span></a>
+<a name="8415"><span class="lineNum">    8415 </span>            :     } else {</a>
+<a name="8416"><span class="lineNum">    8416 </span><span class="lineNoCov">          0 :         if (std::abs(z1) &lt;= tol) {</span></a>
+<a name="8417"><span class="lineNum">    8417 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="8418"><span class="lineNum">    8418 </span>            :         } else {</a>
+<a name="8419"><span class="lineNum">    8419 </span><span class="lineNoCov">          0 :             z__[1] = z1;</span></a>
+<a name="8420"><span class="lineNum">    8420 </span>            :         }</a>
+<a name="8421"><span class="lineNum">    8421 </span>            :     }</a>
+<a name="8422"><span class="lineNum">    8422 </span>            : </a>
+<a name="8423"><span class="lineNum">    8423 </span><span class="lineNoCov">          0 :     i__1 = *k - 1;</span></a>
+<a name="8424"><span class="lineNum">    8424 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;zw[2], &amp;c__1, &amp;z__[2], &amp;c__1);</span></a>
+<a name="8425"><span class="lineNum">    8425 </span><span class="lineNoCov">          0 :     i__1 = n - 1;</span></a>
+<a name="8426"><span class="lineNum">    8426 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;vfw[2], &amp;c__1, &amp;vf[2], &amp;c__1);</span></a>
+<a name="8427"><span class="lineNum">    8427 </span><span class="lineNoCov">          0 :     i__1 = n - 1;</span></a>
+<a name="8428"><span class="lineNum">    8428 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;vlw[2], &amp;c__1, &amp;vl[2], &amp;c__1);</span></a>
+<a name="8429"><span class="lineNum">    8429 </span>            : </a>
+<a name="8430"><span class="lineNum">    8430 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="8431"><span class="lineNum">    8431 </span>            : </a>
+<a name="8432"><span class="lineNum">    8432 </span>            : }</a>
+<a name="8433"><span class="lineNum">    8433 </span>            : </a>
+<a name="8434"><span class="lineNum">    8434 </span>            : </a>
+<a name="8435"><span class="lineNum">    8435 </span>            : }</a>
+<a name="8436"><span class="lineNum">    8436 </span>            : }</a>
+<a name="8437"><span class="lineNum">    8437 </span>            : #include &lt;cmath&gt;</a>
+<a name="8438"><span class="lineNum">    8438 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8439"><span class="lineNum">    8439 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="8440"><span class="lineNum">    8440 </span>            : </a>
+<a name="8441"><span class="lineNum">    8441 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8442"><span class="lineNum">    8442 </span>            : namespace PLMD{</a>
+<a name="8443"><span class="lineNum">    8443 </span>            : namespace lapack{</a>
+<a name="8444"><span class="lineNum">    8444 </span>            : using namespace blas;</a>
+<a name="8445"><span class="lineNum">    8445 </span>            : void </a>
+<a name="8446"><span class="lineNum">    8446 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasd8,DLASD8)(int *icompq, </span></a>
+<a name="8447"><span class="lineNum">    8447 </span>            :         int *k, </a>
+<a name="8448"><span class="lineNum">    8448 </span>            :         double *d__, </a>
+<a name="8449"><span class="lineNum">    8449 </span>            :         double *z__, </a>
+<a name="8450"><span class="lineNum">    8450 </span>            :         double *vf, </a>
+<a name="8451"><span class="lineNum">    8451 </span>            :         double *vl, </a>
+<a name="8452"><span class="lineNum">    8452 </span>            :         double *difl, </a>
+<a name="8453"><span class="lineNum">    8453 </span>            :         double *difr, </a>
+<a name="8454"><span class="lineNum">    8454 </span>            :         int *lddifr, </a>
+<a name="8455"><span class="lineNum">    8455 </span>            :         double *dsigma, </a>
+<a name="8456"><span class="lineNum">    8456 </span>            :         double *work, </a>
+<a name="8457"><span class="lineNum">    8457 </span>            :         int *info)</a>
+<a name="8458"><span class="lineNum">    8458 </span>            : {</a>
+<a name="8459"><span class="lineNum">    8459 </span>            :     int difr_dim1, difr_offset, i__1, i__2;</a>
+<a name="8460"><span class="lineNum">    8460 </span>            :     double d__2;</a>
+<a name="8461"><span class="lineNum">    8461 </span>            : </a>
+<a name="8462"><span class="lineNum">    8462 </span>            :     int i__, j;</a>
+<a name="8463"><span class="lineNum">    8463 </span>            :     double dj, rho;</a>
+<a name="8464"><span class="lineNum">    8464 </span>            :     int iwk1, iwk2, iwk3;</a>
+<a name="8465"><span class="lineNum">    8465 </span>            :     double temp;</a>
+<a name="8466"><span class="lineNum">    8466 </span>            :     int iwk2i, iwk3i;</a>
+<a name="8467"><span class="lineNum">    8467 </span>            :     double diflj, difrj, dsigj;</a>
+<a name="8468"><span class="lineNum">    8468 </span>            :     double dsigjp;</a>
+<a name="8469"><span class="lineNum">    8469 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="8470"><span class="lineNum">    8470 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="8471"><span class="lineNum">    8471 </span><span class="lineNoCov">          0 :     double one = 1.;</span></a>
+<a name="8472"><span class="lineNum">    8472 </span>            : </a>
+<a name="8473"><span class="lineNum">    8473 </span>            :     /* avoid warnings on high gcc optimization levels */</a>
+<a name="8474"><span class="lineNum">    8474 </span>            :     difrj = dsigjp = 0;</a>
+<a name="8475"><span class="lineNum">    8475 </span>            : </a>
+<a name="8476"><span class="lineNum">    8476 </span><span class="lineNoCov">          0 :      --d__;</span></a>
+<a name="8477"><span class="lineNum">    8477 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="8478"><span class="lineNum">    8478 </span>            :     --vf;</a>
+<a name="8479"><span class="lineNum">    8479 </span>            :     --vl;</a>
+<a name="8480"><span class="lineNum">    8480 </span><span class="lineNoCov">          0 :     --difl;</span></a>
+<a name="8481"><span class="lineNum">    8481 </span><span class="lineNoCov">          0 :     difr_dim1 = *lddifr;</span></a>
+<a name="8482"><span class="lineNum">    8482 </span><span class="lineNoCov">          0 :     difr_offset = 1 + difr_dim1;</span></a>
+<a name="8483"><span class="lineNum">    8483 </span><span class="lineNoCov">          0 :     difr -= difr_offset;</span></a>
+<a name="8484"><span class="lineNum">    8484 </span><span class="lineNoCov">          0 :     --dsigma;</span></a>
+<a name="8485"><span class="lineNum">    8485 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="8486"><span class="lineNum">    8486 </span>            : </a>
+<a name="8487"><span class="lineNum">    8487 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="8488"><span class="lineNum">    8488 </span>            : </a>
+<a name="8489"><span class="lineNum">    8489 </span><span class="lineNoCov">          0 :     if (*k == 1) {</span></a>
+<a name="8490"><span class="lineNum">    8490 </span><span class="lineNoCov">          0 :         d__[1] = std::abs(z__[1]);</span></a>
+<a name="8491"><span class="lineNum">    8491 </span><span class="lineNoCov">          0 :         difl[1] = d__[1];</span></a>
+<a name="8492"><span class="lineNum">    8492 </span><span class="lineNoCov">          0 :         if (*icompq == 1) {</span></a>
+<a name="8493"><span class="lineNum">    8493 </span><span class="lineNoCov">          0 :             difl[2] = 1.;</span></a>
+<a name="8494"><span class="lineNum">    8494 </span><span class="lineNoCov">          0 :             difr[(difr_dim1 &lt;&lt; 1) + 1] = 1.;</span></a>
+<a name="8495"><span class="lineNum">    8495 </span>            :         }</a>
+<a name="8496"><span class="lineNum">    8496 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="8497"><span class="lineNum">    8497 </span>            :     }</a>
+<a name="8498"><span class="lineNum">    8498 </span>            : </a>
+<a name="8499"><span class="lineNum">    8499 </span>            :     iwk1 = 1;</a>
+<a name="8500"><span class="lineNum">    8500 </span><span class="lineNoCov">          0 :     iwk2 = iwk1 + *k;</span></a>
+<a name="8501"><span class="lineNum">    8501 </span><span class="lineNoCov">          0 :     iwk3 = iwk2 + *k;</span></a>
+<a name="8502"><span class="lineNum">    8502 </span>            :     iwk2i = iwk2 - 1;</a>
+<a name="8503"><span class="lineNum">    8503 </span><span class="lineNoCov">          0 :     iwk3i = iwk3 - 1;</span></a>
+<a name="8504"><span class="lineNum">    8504 </span>            : </a>
+<a name="8505"><span class="lineNum">    8505 </span><span class="lineNoCov">          0 :     rho = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(k, &amp;z__[1], &amp;c__1);</span></a>
+<a name="8506"><span class="lineNum">    8506 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;rho, &amp;one, k, &amp;c__1, &amp;z__[1], k, info);</span></a>
+<a name="8507"><span class="lineNum">    8507 </span><span class="lineNoCov">          0 :     rho *= rho;</span></a>
+<a name="8508"><span class="lineNum">    8508 </span>            : </a>
+<a name="8509"><span class="lineNum">    8509 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, k, &amp;c__1, &amp;one, &amp;one, &amp;work[iwk3], k);</span></a>
+<a name="8510"><span class="lineNum">    8510 </span>            : </a>
+<a name="8511"><span class="lineNum">    8511 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="8512"><span class="lineNum">    8512 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="8513"><span class="lineNum">    8513 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasd4,DLASD4)(k, &amp;j, &amp;dsigma[1], &amp;z__[1], &amp;work[iwk1], &amp;rho, &amp;d__[j], &amp;work[</span></a>
+<a name="8514"><span class="lineNum">    8514 </span><span class="lineNoCov">          0 :                 iwk2], info);</span></a>
+<a name="8515"><span class="lineNum">    8515 </span>            : </a>
+<a name="8516"><span class="lineNum">    8516 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="8517"><span class="lineNum">    8517 </span>            :             return;</a>
+<a name="8518"><span class="lineNum">    8518 </span>            :         }</a>
+<a name="8519"><span class="lineNum">    8519 </span><span class="lineNoCov">          0 :         work[iwk3i + j] = work[iwk3i + j] * work[j] * work[iwk2i + j];</span></a>
+<a name="8520"><span class="lineNum">    8520 </span><span class="lineNoCov">          0 :         difl[j] = -work[j];</span></a>
+<a name="8521"><span class="lineNum">    8521 </span><span class="lineNoCov">          0 :         difr[j + difr_dim1] = -work[j + 1];</span></a>
+<a name="8522"><span class="lineNum">    8522 </span>            :         i__2 = j - 1;</a>
+<a name="8523"><span class="lineNum">    8523 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="8524"><span class="lineNum">    8524 </span><span class="lineNoCov">          0 :             work[iwk3i + i__] = work[iwk3i + i__] * work[i__] * work[iwk2i + </span></a>
+<a name="8525"><span class="lineNum">    8525 </span><span class="lineNoCov">          0 :                     i__] / (dsigma[i__] - dsigma[j]) / (dsigma[i__] + dsigma[</span></a>
+<a name="8526"><span class="lineNum">    8526 </span>            :                     j]);</a>
+<a name="8527"><span class="lineNum">    8527 </span>            :         }</a>
+<a name="8528"><span class="lineNum">    8528 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="8529"><span class="lineNum">    8529 </span><span class="lineNoCov">          0 :         for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="8530"><span class="lineNum">    8530 </span><span class="lineNoCov">          0 :             work[iwk3i + i__] = work[iwk3i + i__] * work[i__] * work[iwk2i + </span></a>
+<a name="8531"><span class="lineNum">    8531 </span><span class="lineNoCov">          0 :                     i__] / (dsigma[i__] - dsigma[j]) / (dsigma[i__] + dsigma[</span></a>
+<a name="8532"><span class="lineNum">    8532 </span>            :                     j]);</a>
+<a name="8533"><span class="lineNum">    8533 </span>            :         }</a>
+<a name="8534"><span class="lineNum">    8534 </span>            :     }</a>
+<a name="8535"><span class="lineNum">    8535 </span>            : </a>
+<a name="8536"><span class="lineNum">    8536 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="8537"><span class="lineNum">    8537 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8538"><span class="lineNum">    8538 </span><span class="lineNoCov">          0 :         d__2 =  std::sqrt(std::abs(work[iwk3i + i__]));</span></a>
+<a name="8539"><span class="lineNum">    8539 </span><span class="lineNoCov">          0 :         z__[i__] = (z__[i__] &gt; 0) ? d__2 : -d__2;</span></a>
+<a name="8540"><span class="lineNum">    8540 </span>            :     }</a>
+<a name="8541"><span class="lineNum">    8541 </span>            : </a>
+<a name="8542"><span class="lineNum">    8542 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="8543"><span class="lineNum">    8543 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="8544"><span class="lineNum">    8544 </span><span class="lineNoCov">          0 :         diflj = difl[j];</span></a>
+<a name="8545"><span class="lineNum">    8545 </span><span class="lineNoCov">          0 :         dj = d__[j];</span></a>
+<a name="8546"><span class="lineNum">    8546 </span><span class="lineNoCov">          0 :         dsigj = -dsigma[j];</span></a>
+<a name="8547"><span class="lineNum">    8547 </span><span class="lineNoCov">          0 :         if (j &lt; *k) {</span></a>
+<a name="8548"><span class="lineNum">    8548 </span><span class="lineNoCov">          0 :             difrj = -difr[j + difr_dim1];</span></a>
+<a name="8549"><span class="lineNum">    8549 </span><span class="lineNoCov">          0 :             dsigjp = -dsigma[j + 1];</span></a>
+<a name="8550"><span class="lineNum">    8550 </span>            :         }</a>
+<a name="8551"><span class="lineNum">    8551 </span><span class="lineNoCov">          0 :         work[j] = -z__[j] / diflj / (dsigma[j] + dj);</span></a>
+<a name="8552"><span class="lineNum">    8552 </span>            :         i__2 = j - 1;</a>
+<a name="8553"><span class="lineNum">    8553 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="8554"><span class="lineNum">    8554 </span><span class="lineNoCov">          0 :         work[i__] = z__[i__] / (dsigma[i__] + dsigj - diflj) / ( dsigma[i__] + dj);</span></a>
+<a name="8555"><span class="lineNum">    8555 </span>            :         }</a>
+<a name="8556"><span class="lineNum">    8556 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="8557"><span class="lineNum">    8557 </span><span class="lineNoCov">          0 :         for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="8558"><span class="lineNum">    8558 </span><span class="lineNoCov">          0 :             work[i__] = z__[i__] / (dsigma[i__] + dsigjp - difrj) / (dsigma[i__] + dj);</span></a>
+<a name="8559"><span class="lineNum">    8559 </span>            :         }</a>
+<a name="8560"><span class="lineNum">    8560 </span><span class="lineNoCov">          0 :         temp = PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(k, &amp;work[1], &amp;c__1);</span></a>
+<a name="8561"><span class="lineNum">    8561 </span><span class="lineNoCov">          0 :         work[iwk2i + j] = PLUMED_BLAS_F77_FUNC(ddot,DDOT)(k, &amp;work[1], &amp;c__1, &amp;vf[1], &amp;c__1) / temp;</span></a>
+<a name="8562"><span class="lineNum">    8562 </span><span class="lineNoCov">          0 :         work[iwk3i + j] = PLUMED_BLAS_F77_FUNC(ddot,DDOT)(k, &amp;work[1], &amp;c__1, &amp;vl[1], &amp;c__1) / temp;</span></a>
+<a name="8563"><span class="lineNum">    8563 </span><span class="lineNoCov">          0 :         if (*icompq == 1) {</span></a>
+<a name="8564"><span class="lineNum">    8564 </span><span class="lineNoCov">          0 :             difr[j + (difr_dim1 &lt;&lt; 1)] = temp;</span></a>
+<a name="8565"><span class="lineNum">    8565 </span>            :         }</a>
+<a name="8566"><span class="lineNum">    8566 </span>            :     }</a>
+<a name="8567"><span class="lineNum">    8567 </span>            : </a>
+<a name="8568"><span class="lineNum">    8568 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(k, &amp;work[iwk2], &amp;c__1, &amp;vf[1], &amp;c__1);</span></a>
+<a name="8569"><span class="lineNum">    8569 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(k, &amp;work[iwk3], &amp;c__1, &amp;vl[1], &amp;c__1);</span></a>
+<a name="8570"><span class="lineNum">    8570 </span>            : </a>
+<a name="8571"><span class="lineNum">    8571 </span>            :     return;</a>
+<a name="8572"><span class="lineNum">    8572 </span>            : </a>
+<a name="8573"><span class="lineNum">    8573 </span>            : } </a>
+<a name="8574"><span class="lineNum">    8574 </span>            : }</a>
+<a name="8575"><span class="lineNum">    8575 </span>            : }</a>
+<a name="8576"><span class="lineNum">    8576 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8577"><span class="lineNum">    8577 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="8578"><span class="lineNum">    8578 </span>            : </a>
+<a name="8579"><span class="lineNum">    8579 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8580"><span class="lineNum">    8580 </span>            : namespace PLMD{</a>
+<a name="8581"><span class="lineNum">    8581 </span>            : namespace lapack{</a>
+<a name="8582"><span class="lineNum">    8582 </span>            : using namespace blas;</a>
+<a name="8583"><span class="lineNum">    8583 </span>            : void </a>
+<a name="8584"><span class="lineNum">    8584 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasda,DLASDA)(int *icompq, </span></a>
+<a name="8585"><span class="lineNum">    8585 </span>            :         int *smlsiz, </a>
+<a name="8586"><span class="lineNum">    8586 </span>            :         int *n, </a>
+<a name="8587"><span class="lineNum">    8587 </span>            :         int *sqre, </a>
+<a name="8588"><span class="lineNum">    8588 </span>            :         double *d__, </a>
+<a name="8589"><span class="lineNum">    8589 </span>            :         double *e, </a>
+<a name="8590"><span class="lineNum">    8590 </span>            :         double *u, </a>
+<a name="8591"><span class="lineNum">    8591 </span>            :         int *ldu, </a>
+<a name="8592"><span class="lineNum">    8592 </span>            :         double *vt, </a>
+<a name="8593"><span class="lineNum">    8593 </span>            :         int *k, </a>
+<a name="8594"><span class="lineNum">    8594 </span>            :         double *difl, </a>
+<a name="8595"><span class="lineNum">    8595 </span>            :         double *difr, </a>
+<a name="8596"><span class="lineNum">    8596 </span>            :         double *z__, </a>
+<a name="8597"><span class="lineNum">    8597 </span>            :         double *poles, </a>
+<a name="8598"><span class="lineNum">    8598 </span>            :         int *givptr, </a>
+<a name="8599"><span class="lineNum">    8599 </span>            :         int *givcol, </a>
+<a name="8600"><span class="lineNum">    8600 </span>            :         int *ldgcol, </a>
+<a name="8601"><span class="lineNum">    8601 </span>            :         int *perm, </a>
+<a name="8602"><span class="lineNum">    8602 </span>            :         double *givnum, </a>
+<a name="8603"><span class="lineNum">    8603 </span>            :         double *c__, </a>
+<a name="8604"><span class="lineNum">    8604 </span>            :         double *s, </a>
+<a name="8605"><span class="lineNum">    8605 </span>            :         double *work, </a>
+<a name="8606"><span class="lineNum">    8606 </span>            :         int *iwork, </a>
+<a name="8607"><span class="lineNum">    8607 </span>            :         int *info)</a>
+<a name="8608"><span class="lineNum">    8608 </span>            : {</a>
+<a name="8609"><span class="lineNum">    8609 </span>            :     int givcol_dim1, givcol_offset, perm_dim1, perm_offset, difl_dim1, </a>
+<a name="8610"><span class="lineNum">    8610 </span>            :             difl_offset, difr_dim1, difr_offset, givnum_dim1, givnum_offset, </a>
+<a name="8611"><span class="lineNum">    8611 </span>            :             poles_dim1, poles_offset, u_dim1, u_offset, vt_dim1, vt_offset, </a>
+<a name="8612"><span class="lineNum">    8612 </span>            :             z_dim1, z_offset, i__1, i__2;</a>
+<a name="8613"><span class="lineNum">    8613 </span>            : </a>
+<a name="8614"><span class="lineNum">    8614 </span>            :     int i__, j, m, i1, ic, lf, nd, ll, nl, vf, nr, vl, im1, ncc, </a>
+<a name="8615"><span class="lineNum">    8615 </span>            :             nlf, nrf, vfi, iwk, vli, lvl, nru, ndb1, nlp1, lvl2, nrp1;</a>
+<a name="8616"><span class="lineNum">    8616 </span>            :     double beta;</a>
+<a name="8617"><span class="lineNum">    8617 </span>            :     int idxq, nlvl;</a>
+<a name="8618"><span class="lineNum">    8618 </span>            :     double alpha;</a>
+<a name="8619"><span class="lineNum">    8619 </span>            :     int inode, ndiml, ndimr, idxqi, itemp;</a>
+<a name="8620"><span class="lineNum">    8620 </span>            :     int sqrei;</a>
+<a name="8621"><span class="lineNum">    8621 </span>            :     int nwork1, nwork2;</a>
+<a name="8622"><span class="lineNum">    8622 </span>            :     int smlszp;</a>
+<a name="8623"><span class="lineNum">    8623 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="8624"><span class="lineNum">    8624 </span><span class="lineNoCov">          0 :     double zero = 0.0;</span></a>
+<a name="8625"><span class="lineNum">    8625 </span><span class="lineNoCov">          0 :     double one = 1.;</span></a>
+<a name="8626"><span class="lineNum">    8626 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="8627"><span class="lineNum">    8627 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="8628"><span class="lineNum">    8628 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="8629"><span class="lineNum">    8629 </span><span class="lineNoCov">          0 :     givnum_dim1 = *ldu;</span></a>
+<a name="8630"><span class="lineNum">    8630 </span><span class="lineNoCov">          0 :     givnum_offset = 1 + givnum_dim1;</span></a>
+<a name="8631"><span class="lineNum">    8631 </span><span class="lineNoCov">          0 :     givnum -= givnum_offset;</span></a>
+<a name="8632"><span class="lineNum">    8632 </span>            :     poles_dim1 = *ldu;</a>
+<a name="8633"><span class="lineNum">    8633 </span>            :     poles_offset = 1 + poles_dim1;</a>
+<a name="8634"><span class="lineNum">    8634 </span>            :     poles -= poles_offset;</a>
+<a name="8635"><span class="lineNum">    8635 </span>            :     z_dim1 = *ldu;</a>
+<a name="8636"><span class="lineNum">    8636 </span>            :     z_offset = 1 + z_dim1;</a>
+<a name="8637"><span class="lineNum">    8637 </span>            :     z__ -= z_offset;</a>
+<a name="8638"><span class="lineNum">    8638 </span>            :     difr_dim1 = *ldu;</a>
+<a name="8639"><span class="lineNum">    8639 </span>            :     difr_offset = 1 + difr_dim1;</a>
+<a name="8640"><span class="lineNum">    8640 </span>            :     difr -= difr_offset;</a>
+<a name="8641"><span class="lineNum">    8641 </span>            :     difl_dim1 = *ldu;</a>
+<a name="8642"><span class="lineNum">    8642 </span>            :     difl_offset = 1 + difl_dim1;</a>
+<a name="8643"><span class="lineNum">    8643 </span>            :     difl -= difl_offset;</a>
+<a name="8644"><span class="lineNum">    8644 </span>            :     vt_dim1 = *ldu;</a>
+<a name="8645"><span class="lineNum">    8645 </span>            :     vt_offset = 1 + vt_dim1;</a>
+<a name="8646"><span class="lineNum">    8646 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="8647"><span class="lineNum">    8647 </span>            :     u_dim1 = *ldu;</a>
+<a name="8648"><span class="lineNum">    8648 </span>            :     u_offset = 1 + u_dim1;</a>
+<a name="8649"><span class="lineNum">    8649 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="8650"><span class="lineNum">    8650 </span>            :     --k;</a>
+<a name="8651"><span class="lineNum">    8651 </span>            :     --givptr;</a>
+<a name="8652"><span class="lineNum">    8652 </span><span class="lineNoCov">          0 :     perm_dim1 = *ldgcol;</span></a>
+<a name="8653"><span class="lineNum">    8653 </span><span class="lineNoCov">          0 :     perm_offset = 1 + perm_dim1;</span></a>
+<a name="8654"><span class="lineNum">    8654 </span><span class="lineNoCov">          0 :     perm -= perm_offset;</span></a>
+<a name="8655"><span class="lineNum">    8655 </span>            :     givcol_dim1 = *ldgcol;</a>
+<a name="8656"><span class="lineNum">    8656 </span>            :     givcol_offset = 1 + givcol_dim1;</a>
+<a name="8657"><span class="lineNum">    8657 </span>            :     givcol -= givcol_offset;</a>
+<a name="8658"><span class="lineNum">    8658 </span>            :     --c__;</a>
+<a name="8659"><span class="lineNum">    8659 </span>            :     --s;</a>
+<a name="8660"><span class="lineNum">    8660 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="8661"><span class="lineNum">    8661 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="8662"><span class="lineNum">    8662 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="8663"><span class="lineNum">    8663 </span>            : </a>
+<a name="8664"><span class="lineNum">    8664 </span><span class="lineNoCov">          0 :     m = *n + *sqre;</span></a>
+<a name="8665"><span class="lineNum">    8665 </span>            : </a>
+<a name="8666"><span class="lineNum">    8666 </span><span class="lineNoCov">          0 :     if (*n &lt;= *smlsiz) {</span></a>
+<a name="8667"><span class="lineNum">    8667 </span><span class="lineNoCov">          0 :         if (*icompq == 0) {</span></a>
+<a name="8668"><span class="lineNum">    8668 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, sqre, n, &amp;c__0, &amp;c__0, &amp;c__0, &amp;d__[1], &amp;e[1], &amp;vt[</span></a>
+<a name="8669"><span class="lineNum">    8669 </span>            :                     vt_offset], ldu, &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;</a>
+<a name="8670"><span class="lineNum">    8670 </span>            :                     work[1], info);</a>
+<a name="8671"><span class="lineNum">    8671 </span>            :         } else {</a>
+<a name="8672"><span class="lineNum">    8672 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, sqre, n, &amp;m, n, &amp;c__0, &amp;d__[1], &amp;e[1], &amp;vt[vt_offset]</span></a>
+<a name="8673"><span class="lineNum">    8673 </span>            :                     , ldu, &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;work[1], </a>
+<a name="8674"><span class="lineNum">    8674 </span>            :                     info);</a>
+<a name="8675"><span class="lineNum">    8675 </span>            :         }</a>
+<a name="8676"><span class="lineNum">    8676 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="8677"><span class="lineNum">    8677 </span>            :     }</a>
+<a name="8678"><span class="lineNum">    8678 </span>            : </a>
+<a name="8679"><span class="lineNum">    8679 </span>            :     inode = 1;</a>
+<a name="8680"><span class="lineNum">    8680 </span><span class="lineNoCov">          0 :     ndiml = inode + *n;</span></a>
+<a name="8681"><span class="lineNum">    8681 </span><span class="lineNoCov">          0 :     ndimr = ndiml + *n;</span></a>
+<a name="8682"><span class="lineNum">    8682 </span><span class="lineNoCov">          0 :     idxq = ndimr + *n;</span></a>
+<a name="8683"><span class="lineNum">    8683 </span><span class="lineNoCov">          0 :     iwk = idxq + *n;</span></a>
+<a name="8684"><span class="lineNum">    8684 </span>            : </a>
+<a name="8685"><span class="lineNum">    8685 </span><span class="lineNoCov">          0 :     ncc = 0;</span></a>
+<a name="8686"><span class="lineNum">    8686 </span><span class="lineNoCov">          0 :     nru = 0;</span></a>
+<a name="8687"><span class="lineNum">    8687 </span>            : </a>
+<a name="8688"><span class="lineNum">    8688 </span><span class="lineNoCov">          0 :     smlszp = *smlsiz + 1;</span></a>
+<a name="8689"><span class="lineNum">    8689 </span>            :     vf = 1;</a>
+<a name="8690"><span class="lineNum">    8690 </span><span class="lineNoCov">          0 :     vl = vf + m;</span></a>
+<a name="8691"><span class="lineNum">    8691 </span><span class="lineNoCov">          0 :     nwork1 = vl + m;</span></a>
+<a name="8692"><span class="lineNum">    8692 </span><span class="lineNoCov">          0 :     nwork2 = nwork1 + smlszp * smlszp;</span></a>
+<a name="8693"><span class="lineNum">    8693 </span>            : </a>
+<a name="8694"><span class="lineNum">    8694 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlasdt,DLASDT)(n, &amp;nlvl, &amp;nd, &amp;iwork[inode], &amp;iwork[ndiml], &amp;iwork[ndimr], </span></a>
+<a name="8695"><span class="lineNum">    8695 </span>            :             smlsiz);</a>
+<a name="8696"><span class="lineNum">    8696 </span>            : </a>
+<a name="8697"><span class="lineNum">    8697 </span><span class="lineNoCov">          0 :     ndb1 = (nd + 1) / 2;</span></a>
+<a name="8698"><span class="lineNum">    8698 </span>            :     i__1 = nd;</a>
+<a name="8699"><span class="lineNum">    8699 </span><span class="lineNoCov">          0 :     for (i__ = ndb1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8700"><span class="lineNum">    8700 </span><span class="lineNoCov">          0 :         i1 = i__ - 1;</span></a>
+<a name="8701"><span class="lineNum">    8701 </span><span class="lineNoCov">          0 :         ic = iwork[inode + i1];</span></a>
+<a name="8702"><span class="lineNum">    8702 </span><span class="lineNoCov">          0 :         nl = iwork[ndiml + i1];</span></a>
+<a name="8703"><span class="lineNum">    8703 </span><span class="lineNoCov">          0 :         nlp1 = nl + 1;</span></a>
+<a name="8704"><span class="lineNum">    8704 </span><span class="lineNoCov">          0 :         nr = iwork[ndimr + i1];</span></a>
+<a name="8705"><span class="lineNum">    8705 </span><span class="lineNoCov">          0 :         nlf = ic - nl;</span></a>
+<a name="8706"><span class="lineNum">    8706 </span><span class="lineNoCov">          0 :         nrf = ic + 1;</span></a>
+<a name="8707"><span class="lineNum">    8707 </span><span class="lineNoCov">          0 :         idxqi = idxq + nlf - 2;</span></a>
+<a name="8708"><span class="lineNum">    8708 </span>            :         vfi = vf + nlf - 1;</a>
+<a name="8709"><span class="lineNum">    8709 </span><span class="lineNoCov">          0 :         vli = vl + nlf - 1;</span></a>
+<a name="8710"><span class="lineNum">    8710 </span><span class="lineNoCov">          0 :         sqrei = 1;</span></a>
+<a name="8711"><span class="lineNum">    8711 </span><span class="lineNoCov">          0 :         if (*icompq == 0) {</span></a>
+<a name="8712"><span class="lineNum">    8712 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;nlp1, &amp;nlp1, &amp;zero, &amp;one, &amp;work[nwork1], &amp;smlszp);</span></a>
+<a name="8713"><span class="lineNum">    8713 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nl, &amp;nlp1, &amp;nru, &amp;ncc, &amp;d__[nlf], &amp;e[nlf], &amp;</span></a>
+<a name="8714"><span class="lineNum">    8714 </span>            :                     work[nwork1], &amp;smlszp, &amp;work[nwork2], &amp;nl, &amp;work[nwork2], </a>
+<a name="8715"><span class="lineNum">    8715 </span><span class="lineNoCov">          0 :                     &amp;nl, &amp;work[nwork2], info);</span></a>
+<a name="8716"><span class="lineNum">    8716 </span><span class="lineNoCov">          0 :             itemp = nwork1 + nl * smlszp;</span></a>
+<a name="8717"><span class="lineNum">    8717 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nlp1, &amp;work[nwork1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="8718"><span class="lineNum">    8718 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nlp1, &amp;work[itemp], &amp;c__1, &amp;work[vli], &amp;c__1);</span></a>
+<a name="8719"><span class="lineNum">    8719 </span>            :         } else {</a>
+<a name="8720"><span class="lineNum">    8720 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;nl, &amp;nl, &amp;zero, &amp;one, &amp;u[nlf + u_dim1], ldu);</span></a>
+<a name="8721"><span class="lineNum">    8721 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;nlp1, &amp;nlp1, &amp;zero, &amp;one, &amp;vt[nlf + vt_dim1], </span></a>
+<a name="8722"><span class="lineNum">    8722 </span>            :                     ldu);</a>
+<a name="8723"><span class="lineNum">    8723 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nl, &amp;nlp1, &amp;nl, &amp;ncc, &amp;d__[nlf], &amp;e[nlf], &amp;</span></a>
+<a name="8724"><span class="lineNum">    8724 </span>            :                     vt[nlf + vt_dim1], ldu, &amp;u[nlf + u_dim1], ldu, &amp;u[nlf + </a>
+<a name="8725"><span class="lineNum">    8725 </span><span class="lineNoCov">          0 :                     u_dim1], ldu, &amp;work[nwork1], info);</span></a>
+<a name="8726"><span class="lineNum">    8726 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nlp1, &amp;vt[nlf + vt_dim1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="8727"><span class="lineNum">    8727 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nlp1, &amp;vt[nlf + nlp1 * vt_dim1], &amp;c__1, &amp;work[vli], &amp;c__1)</span></a>
+<a name="8728"><span class="lineNum">    8728 </span>            :                     ;</a>
+<a name="8729"><span class="lineNum">    8729 </span>            :         }</a>
+<a name="8730"><span class="lineNum">    8730 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="8731"><span class="lineNum">    8731 </span>            :             return;</a>
+<a name="8732"><span class="lineNum">    8732 </span>            :         }</a>
+<a name="8733"><span class="lineNum">    8733 </span><span class="lineNoCov">          0 :         i__2 = nl;</span></a>
+<a name="8734"><span class="lineNum">    8734 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="8735"><span class="lineNum">    8735 </span><span class="lineNoCov">          0 :             iwork[idxqi + j] = j;</span></a>
+<a name="8736"><span class="lineNum">    8736 </span>            :         }</a>
+<a name="8737"><span class="lineNum">    8737 </span><span class="lineNoCov">          0 :         if (i__ == nd &amp;&amp; *sqre == 0) {</span></a>
+<a name="8738"><span class="lineNum">    8738 </span><span class="lineNoCov">          0 :             sqrei = 0;</span></a>
+<a name="8739"><span class="lineNum">    8739 </span>            :         } else {</a>
+<a name="8740"><span class="lineNum">    8740 </span><span class="lineNoCov">          0 :             sqrei = 1;</span></a>
+<a name="8741"><span class="lineNum">    8741 </span>            :         }</a>
+<a name="8742"><span class="lineNum">    8742 </span><span class="lineNoCov">          0 :         idxqi += nlp1;</span></a>
+<a name="8743"><span class="lineNum">    8743 </span><span class="lineNoCov">          0 :         vfi += nlp1;</span></a>
+<a name="8744"><span class="lineNum">    8744 </span><span class="lineNoCov">          0 :         vli += nlp1;</span></a>
+<a name="8745"><span class="lineNum">    8745 </span><span class="lineNoCov">          0 :         nrp1 = nr + sqrei;</span></a>
+<a name="8746"><span class="lineNum">    8746 </span><span class="lineNoCov">          0 :         if (*icompq == 0) {</span></a>
+<a name="8747"><span class="lineNum">    8747 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;nrp1, &amp;nrp1, &amp;zero, &amp;one, &amp;work[nwork1], &amp;smlszp);</span></a>
+<a name="8748"><span class="lineNum">    8748 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nr, &amp;nrp1, &amp;nru, &amp;ncc, &amp;d__[nrf], &amp;e[nrf], &amp;</span></a>
+<a name="8749"><span class="lineNum">    8749 </span>            :                     work[nwork1], &amp;smlszp, &amp;work[nwork2], &amp;nr, &amp;work[nwork2], </a>
+<a name="8750"><span class="lineNum">    8750 </span><span class="lineNoCov">          0 :                     &amp;nr, &amp;work[nwork2], info);</span></a>
+<a name="8751"><span class="lineNum">    8751 </span><span class="lineNoCov">          0 :             itemp = nwork1 + (nrp1 - 1) * smlszp;</span></a>
+<a name="8752"><span class="lineNum">    8752 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nrp1, &amp;work[nwork1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="8753"><span class="lineNum">    8753 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nrp1, &amp;work[itemp], &amp;c__1, &amp;work[vli], &amp;c__1);</span></a>
+<a name="8754"><span class="lineNum">    8754 </span>            :         } else {</a>
+<a name="8755"><span class="lineNum">    8755 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;nr, &amp;nr, &amp;zero, &amp;one, &amp;u[nrf + u_dim1], ldu);</span></a>
+<a name="8756"><span class="lineNum">    8756 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;A&quot;, &amp;nrp1, &amp;nrp1, &amp;zero, &amp;one, &amp;vt[nrf + vt_dim1], </span></a>
+<a name="8757"><span class="lineNum">    8757 </span>            :                     ldu);</a>
+<a name="8758"><span class="lineNum">    8758 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nr, &amp;nrp1, &amp;nr, &amp;ncc, &amp;d__[nrf], &amp;e[nrf], &amp;</span></a>
+<a name="8759"><span class="lineNum">    8759 </span>            :                     vt[nrf + vt_dim1], ldu, &amp;u[nrf + u_dim1], ldu, &amp;u[nrf + </a>
+<a name="8760"><span class="lineNum">    8760 </span><span class="lineNoCov">          0 :                     u_dim1], ldu, &amp;work[nwork1], info);</span></a>
+<a name="8761"><span class="lineNum">    8761 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nrp1, &amp;vt[nrf + vt_dim1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="8762"><span class="lineNum">    8762 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;nrp1, &amp;vt[nrf + nrp1 * vt_dim1], &amp;c__1, &amp;work[vli], &amp;c__1)</span></a>
+<a name="8763"><span class="lineNum">    8763 </span>            :                     ;</a>
+<a name="8764"><span class="lineNum">    8764 </span>            :         }</a>
+<a name="8765"><span class="lineNum">    8765 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="8766"><span class="lineNum">    8766 </span>            :             return;</a>
+<a name="8767"><span class="lineNum">    8767 </span>            :         }</a>
+<a name="8768"><span class="lineNum">    8768 </span><span class="lineNoCov">          0 :         i__2 = nr;</span></a>
+<a name="8769"><span class="lineNum">    8769 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="8770"><span class="lineNum">    8770 </span><span class="lineNoCov">          0 :             iwork[idxqi + j] = j;</span></a>
+<a name="8771"><span class="lineNum">    8771 </span>            :         }</a>
+<a name="8772"><span class="lineNum">    8772 </span>            :     }</a>
+<a name="8773"><span class="lineNum">    8773 </span>            : </a>
+<a name="8774"><span class="lineNum">    8774 </span><span class="lineNoCov">          0 :     j = (1 &lt;&lt; nlvl);</span></a>
+<a name="8775"><span class="lineNum">    8775 </span>            : </a>
+<a name="8776"><span class="lineNum">    8776 </span><span class="lineNoCov">          0 :     for (lvl = nlvl; lvl &gt;= 1; --lvl) {</span></a>
+<a name="8777"><span class="lineNum">    8777 </span><span class="lineNoCov">          0 :         lvl2 = (lvl &lt;&lt; 1) - 1;</span></a>
+<a name="8778"><span class="lineNum">    8778 </span>            : </a>
+<a name="8779"><span class="lineNum">    8779 </span><span class="lineNoCov">          0 :         if (lvl == 1) {</span></a>
+<a name="8780"><span class="lineNum">    8780 </span>            :             lf = 1;</a>
+<a name="8781"><span class="lineNum">    8781 </span>            :             ll = 1;</a>
+<a name="8782"><span class="lineNum">    8782 </span>            :         } else {</a>
+<a name="8783"><span class="lineNum">    8783 </span><span class="lineNoCov">          0 :             lf = (1 &lt;&lt; (lvl-1));</span></a>
+<a name="8784"><span class="lineNum">    8784 </span><span class="lineNoCov">          0 :             ll = (lf &lt;&lt; 1) - 1;</span></a>
+<a name="8785"><span class="lineNum">    8785 </span>            :         }</a>
+<a name="8786"><span class="lineNum">    8786 </span>            :         i__1 = ll;</a>
+<a name="8787"><span class="lineNum">    8787 </span><span class="lineNoCov">          0 :         for (i__ = lf; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8788"><span class="lineNum">    8788 </span><span class="lineNoCov">          0 :             im1 = i__ - 1;</span></a>
+<a name="8789"><span class="lineNum">    8789 </span><span class="lineNoCov">          0 :             ic = iwork[inode + im1];</span></a>
+<a name="8790"><span class="lineNum">    8790 </span><span class="lineNoCov">          0 :             nl = iwork[ndiml + im1];</span></a>
+<a name="8791"><span class="lineNum">    8791 </span><span class="lineNoCov">          0 :             nr = iwork[ndimr + im1];</span></a>
+<a name="8792"><span class="lineNum">    8792 </span><span class="lineNoCov">          0 :             nlf = ic - nl;</span></a>
+<a name="8793"><span class="lineNum">    8793 </span><span class="lineNoCov">          0 :             if (i__ == ll) {</span></a>
+<a name="8794"><span class="lineNum">    8794 </span><span class="lineNoCov">          0 :                 sqrei = *sqre;</span></a>
+<a name="8795"><span class="lineNum">    8795 </span>            :             } else {</a>
+<a name="8796"><span class="lineNum">    8796 </span><span class="lineNoCov">          0 :                 sqrei = 1;</span></a>
+<a name="8797"><span class="lineNum">    8797 </span>            :             }</a>
+<a name="8798"><span class="lineNum">    8798 </span>            :             vfi = vf + nlf - 1;</a>
+<a name="8799"><span class="lineNum">    8799 </span><span class="lineNoCov">          0 :             vli = vl + nlf - 1;</span></a>
+<a name="8800"><span class="lineNum">    8800 </span><span class="lineNoCov">          0 :             idxqi = idxq + nlf - 1;</span></a>
+<a name="8801"><span class="lineNum">    8801 </span><span class="lineNoCov">          0 :             alpha = d__[ic];</span></a>
+<a name="8802"><span class="lineNum">    8802 </span><span class="lineNoCov">          0 :             beta = e[ic];</span></a>
+<a name="8803"><span class="lineNum">    8803 </span><span class="lineNoCov">          0 :             if (*icompq == 0) {</span></a>
+<a name="8804"><span class="lineNum">    8804 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasd6,DLASD6)(icompq, &amp;nl, &amp;nr, &amp;sqrei, &amp;d__[nlf], &amp;work[vfi], &amp;</span></a>
+<a name="8805"><span class="lineNum">    8805 </span><span class="lineNoCov">          0 :                         work[vli], &amp;alpha, &amp;beta, &amp;iwork[idxqi], &amp;perm[</span></a>
+<a name="8806"><span class="lineNum">    8806 </span>            :                         perm_offset], &amp;givptr[1], &amp;givcol[givcol_offset], </a>
+<a name="8807"><span class="lineNum">    8807 </span>            :                         ldgcol, &amp;givnum[givnum_offset], ldu, &amp;poles[</a>
+<a name="8808"><span class="lineNum">    8808 </span>            :                         poles_offset], &amp;difl[difl_offset], &amp;difr[difr_offset],</a>
+<a name="8809"><span class="lineNum">    8809 </span><span class="lineNoCov">          0 :                          &amp;z__[z_offset], &amp;k[1], &amp;c__[1], &amp;s[1], &amp;work[nwork1],</span></a>
+<a name="8810"><span class="lineNum">    8810 </span><span class="lineNoCov">          0 :                          &amp;iwork[iwk], info);</span></a>
+<a name="8811"><span class="lineNum">    8811 </span>            :             } else {</a>
+<a name="8812"><span class="lineNum">    8812 </span><span class="lineNoCov">          0 :                 --j;</span></a>
+<a name="8813"><span class="lineNum">    8813 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasd6,DLASD6)(icompq, &amp;nl, &amp;nr, &amp;sqrei, &amp;d__[nlf], &amp;work[vfi], &amp;</span></a>
+<a name="8814"><span class="lineNum">    8814 </span><span class="lineNoCov">          0 :                         work[vli], &amp;alpha, &amp;beta, &amp;iwork[idxqi], &amp;perm[nlf + </span></a>
+<a name="8815"><span class="lineNum">    8815 </span><span class="lineNoCov">          0 :                         lvl * perm_dim1], &amp;givptr[j], &amp;givcol[nlf + lvl2 * </span></a>
+<a name="8816"><span class="lineNum">    8816 </span>            :                         givcol_dim1], ldgcol, &amp;givnum[nlf + lvl2 * </a>
+<a name="8817"><span class="lineNum">    8817 </span>            :                         givnum_dim1], ldu, &amp;poles[nlf + lvl2 * poles_dim1], &amp;</a>
+<a name="8818"><span class="lineNum">    8818 </span><span class="lineNoCov">          0 :                         difl[nlf + lvl * difl_dim1], &amp;difr[nlf + lvl2 * </span></a>
+<a name="8819"><span class="lineNum">    8819 </span><span class="lineNoCov">          0 :                         difr_dim1], &amp;z__[nlf + lvl * z_dim1], &amp;k[j], &amp;c__[j], </span></a>
+<a name="8820"><span class="lineNum">    8820 </span><span class="lineNoCov">          0 :                         &amp;s[j], &amp;work[nwork1], &amp;iwork[iwk], info);</span></a>
+<a name="8821"><span class="lineNum">    8821 </span>            :             }</a>
+<a name="8822"><span class="lineNum">    8822 </span><span class="lineNoCov">          0 :             if (*info != 0) {</span></a>
+<a name="8823"><span class="lineNum">    8823 </span>            :                 return;</a>
+<a name="8824"><span class="lineNum">    8824 </span>            :             }</a>
+<a name="8825"><span class="lineNum">    8825 </span>            :         }</a>
+<a name="8826"><span class="lineNum">    8826 </span>            :     }</a>
+<a name="8827"><span class="lineNum">    8827 </span>            : </a>
+<a name="8828"><span class="lineNum">    8828 </span>            :     return;</a>
+<a name="8829"><span class="lineNum">    8829 </span>            : </a>
+<a name="8830"><span class="lineNum">    8830 </span>            : }</a>
+<a name="8831"><span class="lineNum">    8831 </span>            : </a>
+<a name="8832"><span class="lineNum">    8832 </span>            : </a>
+<a name="8833"><span class="lineNum">    8833 </span>            : }</a>
+<a name="8834"><span class="lineNum">    8834 </span>            : }</a>
+<a name="8835"><span class="lineNum">    8835 </span>            : #include &lt;cctype&gt;</a>
+<a name="8836"><span class="lineNum">    8836 </span>            : </a>
+<a name="8837"><span class="lineNum">    8837 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8838"><span class="lineNum">    8838 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="8839"><span class="lineNum">    8839 </span>            : </a>
+<a name="8840"><span class="lineNum">    8840 </span>            : </a>
+<a name="8841"><span class="lineNum">    8841 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="8842"><span class="lineNum">    8842 </span>            : namespace PLMD{</a>
+<a name="8843"><span class="lineNum">    8843 </span>            : namespace lapack{</a>
+<a name="8844"><span class="lineNum">    8844 </span>            : using namespace blas;</a>
+<a name="8845"><span class="lineNum">    8845 </span>            : void </a>
+<a name="8846"><span class="lineNum">    8846 </span><span class="lineCov">        155 : PLUMED_BLAS_F77_FUNC(dlasdq,DLASDQ)(const char *uplo,</span></a>
+<a name="8847"><span class="lineNum">    8847 </span>            :                         int *sqre,</a>
+<a name="8848"><span class="lineNum">    8848 </span>            :                         int *n,</a>
+<a name="8849"><span class="lineNum">    8849 </span>            :                         int *ncvt,</a>
+<a name="8850"><span class="lineNum">    8850 </span>            :                         int *nru,</a>
+<a name="8851"><span class="lineNum">    8851 </span>            :                         int *ncc,</a>
+<a name="8852"><span class="lineNum">    8852 </span>            :                         double *d__,</a>
+<a name="8853"><span class="lineNum">    8853 </span>            :                         double *e, </a>
+<a name="8854"><span class="lineNum">    8854 </span>            :                         double *vt, </a>
+<a name="8855"><span class="lineNum">    8855 </span>            :                         int *ldvt, </a>
+<a name="8856"><span class="lineNum">    8856 </span>            :                         double *u,</a>
+<a name="8857"><span class="lineNum">    8857 </span>            :                         int *ldu, </a>
+<a name="8858"><span class="lineNum">    8858 </span>            :                         double *c__,</a>
+<a name="8859"><span class="lineNum">    8859 </span>            :                         int *ldc,</a>
+<a name="8860"><span class="lineNum">    8860 </span>            :                         double *work, </a>
+<a name="8861"><span class="lineNum">    8861 </span>            :                         int *info)</a>
+<a name="8862"><span class="lineNum">    8862 </span>            : {</a>
+<a name="8863"><span class="lineNum">    8863 </span><span class="lineCov">        155 :     const char xuplo=std::toupper(*uplo);</span></a>
+<a name="8864"><span class="lineNum">    8864 </span>            :     int c_dim1, c_offset, u_dim1, u_offset, vt_dim1, vt_offset, i__1, </a>
+<a name="8865"><span class="lineNum">    8865 </span>            :             i__2;</a>
+<a name="8866"><span class="lineNum">    8866 </span><span class="lineCov">        155 :     int c__1 = 1;</span></a>
+<a name="8867"><span class="lineNum">    8867 </span>            :     int itmp1,itmp2;</a>
+<a name="8868"><span class="lineNum">    8868 </span>            :     int i__, j;</a>
+<a name="8869"><span class="lineNum">    8869 </span>            :     double r__, cs, sn;</a>
+<a name="8870"><span class="lineNum">    8870 </span>            :     int np1, isub;</a>
+<a name="8871"><span class="lineNum">    8871 </span>            :     double smin;</a>
+<a name="8872"><span class="lineNum">    8872 </span>            :     int sqre1;</a>
+<a name="8873"><span class="lineNum">    8873 </span>            :     int iuplo;</a>
+<a name="8874"><span class="lineNum">    8874 </span>            :     int rotate;</a>
+<a name="8875"><span class="lineNum">    8875 </span>            : </a>
+<a name="8876"><span class="lineNum">    8876 </span><span class="lineCov">        155 :     --d__;</span></a>
+<a name="8877"><span class="lineNum">    8877 </span><span class="lineCov">        155 :     --e;</span></a>
+<a name="8878"><span class="lineNum">    8878 </span><span class="lineCov">        155 :     vt_dim1 = *ldvt;</span></a>
+<a name="8879"><span class="lineNum">    8879 </span><span class="lineCov">        155 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="8880"><span class="lineNum">    8880 </span><span class="lineCov">        155 :     vt -= vt_offset;</span></a>
+<a name="8881"><span class="lineNum">    8881 </span><span class="lineCov">        155 :     u_dim1 = *ldu;</span></a>
+<a name="8882"><span class="lineNum">    8882 </span><span class="lineCov">        155 :     u_offset = 1 + u_dim1;</span></a>
+<a name="8883"><span class="lineNum">    8883 </span><span class="lineCov">        155 :     u -= u_offset;</span></a>
+<a name="8884"><span class="lineNum">    8884 </span><span class="lineCov">        155 :     c_dim1 = *ldc;</span></a>
+<a name="8885"><span class="lineNum">    8885 </span><span class="lineCov">        155 :     c_offset = 1 + c_dim1;</span></a>
+<a name="8886"><span class="lineNum">    8886 </span><span class="lineCov">        155 :     c__ -= c_offset;</span></a>
+<a name="8887"><span class="lineNum">    8887 </span><span class="lineCov">        155 :     --work;</span></a>
+<a name="8888"><span class="lineNum">    8888 </span>            : </a>
+<a name="8889"><span class="lineNum">    8889 </span><span class="lineCov">        155 :     *info = 0;</span></a>
+<a name="8890"><span class="lineNum">    8890 </span>            :     iuplo = 0;</a>
+<a name="8891"><span class="lineNum">    8891 </span><span class="lineCov">        155 :     if (xuplo == 'U') {</span></a>
+<a name="8892"><span class="lineNum">    8892 </span>            :         iuplo = 1;</a>
+<a name="8893"><span class="lineNum">    8893 </span>            :     }</a>
+<a name="8894"><span class="lineNum">    8894 </span><span class="lineCov">        155 :     if (xuplo == 'L') {</span></a>
+<a name="8895"><span class="lineNum">    8895 </span>            :         iuplo = 2;</a>
+<a name="8896"><span class="lineNum">    8896 </span>            :     }</a>
+<a name="8897"><span class="lineNum">    8897 </span>            :     </a>
+<a name="8898"><span class="lineNum">    8898 </span><span class="lineCov">        155 :     itmp1 = (*n &gt; 1) ? *n : 1;</span></a>
+<a name="8899"><span class="lineNum">    8899 </span><span class="lineCov">        155 :     itmp2 = (*nru &gt; 1) ? *nru : 1;</span></a>
+<a name="8900"><span class="lineNum">    8900 </span><span class="lineCov">        155 :     if (iuplo == 0) {</span></a>
+<a name="8901"><span class="lineNum">    8901 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="8902"><span class="lineNum">    8902 </span><span class="lineCov">        155 :     } else if (*sqre &lt; 0 || *sqre &gt; 1) {</span></a>
+<a name="8903"><span class="lineNum">    8903 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="8904"><span class="lineNum">    8904 </span><span class="lineCov">        155 :     } else if (*n &lt; 0) {</span></a>
+<a name="8905"><span class="lineNum">    8905 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="8906"><span class="lineNum">    8906 </span><span class="lineCov">        155 :     } else if (*ncvt &lt; 0) {</span></a>
+<a name="8907"><span class="lineNum">    8907 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="8908"><span class="lineNum">    8908 </span><span class="lineCov">        155 :     } else if (*nru &lt; 0) {</span></a>
+<a name="8909"><span class="lineNum">    8909 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="8910"><span class="lineNum">    8910 </span><span class="lineCov">        155 :     } else if (*ncc &lt; 0) {</span></a>
+<a name="8911"><span class="lineNum">    8911 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="8912"><span class="lineNum">    8912 </span><span class="lineCov">        155 :     } else if ((*ncvt == 0 &amp;&amp; *ldvt &lt; 1) || (*ncvt &gt; 0 &amp;&amp; *ldvt &lt; itmp1)) {</span></a>
+<a name="8913"><span class="lineNum">    8913 </span><span class="lineNoCov">          0 :         *info = -10;</span></a>
+<a name="8914"><span class="lineNum">    8914 </span><span class="lineCov">        155 :     } else if (*ldu &lt; itmp2) {</span></a>
+<a name="8915"><span class="lineNum">    8915 </span><span class="lineNoCov">          0 :         *info = -12;</span></a>
+<a name="8916"><span class="lineNum">    8916 </span><span class="lineCov">        155 :     } else if ((*ncc == 0 &amp;&amp; *ldc &lt; 1) || (*ncc &gt; 0 &amp;&amp; *ldc &lt; itmp1)) {</span></a>
+<a name="8917"><span class="lineNum">    8917 </span><span class="lineNoCov">          0 :         *info = -14;</span></a>
+<a name="8918"><span class="lineNum">    8918 </span>            :     }</a>
+<a name="8919"><span class="lineNum">    8919 </span><span class="lineCov">        155 :     if (*info != 0) {</span></a>
+<a name="8920"><span class="lineNum">    8920 </span>            :         return;</a>
+<a name="8921"><span class="lineNum">    8921 </span>            :     }</a>
+<a name="8922"><span class="lineNum">    8922 </span><span class="lineCov">        155 :     if (*n == 0) {</span></a>
+<a name="8923"><span class="lineNum">    8923 </span>            :         return;</a>
+<a name="8924"><span class="lineNum">    8924 </span>            :     }</a>
+<a name="8925"><span class="lineNum">    8925 </span>            : </a>
+<a name="8926"><span class="lineNum">    8926 </span><span class="lineCov">        155 :     rotate = *ncvt &gt; 0 || *nru &gt; 0 || *ncc &gt; 0;</span></a>
+<a name="8927"><span class="lineNum">    8927 </span><span class="lineCov">        155 :     np1 = *n + 1;</span></a>
+<a name="8928"><span class="lineNum">    8928 </span><span class="lineCov">        155 :     sqre1 = *sqre;</span></a>
+<a name="8929"><span class="lineNum">    8929 </span>            : </a>
+<a name="8930"><span class="lineNum">    8930 </span><span class="lineCov">        155 :     if (iuplo == 1 &amp;&amp; sqre1 == 1) {</span></a>
+<a name="8931"><span class="lineNum">    8931 </span>            :         i__1 = *n - 1;</a>
+<a name="8932"><span class="lineNum">    8932 </span><span class="lineCov">        903 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8933"><span class="lineNum">    8933 </span><span class="lineCov">        844 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="8934"><span class="lineNum">    8934 </span><span class="lineCov">        844 :             d__[i__] = r__;</span></a>
+<a name="8935"><span class="lineNum">    8935 </span><span class="lineCov">        844 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="8936"><span class="lineNum">    8936 </span><span class="lineCov">        844 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="8937"><span class="lineNum">    8937 </span><span class="lineCov">        844 :             if (rotate) {</span></a>
+<a name="8938"><span class="lineNum">    8938 </span><span class="lineCov">        844 :                 work[i__] = cs;</span></a>
+<a name="8939"><span class="lineNum">    8939 </span><span class="lineCov">        844 :                 work[*n + i__] = sn;</span></a>
+<a name="8940"><span class="lineNum">    8940 </span>            :             }</a>
+<a name="8941"><span class="lineNum">    8941 </span>            :         }</a>
+<a name="8942"><span class="lineNum">    8942 </span><span class="lineCov">         59 :         PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;d__[*n], &amp;e[*n], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="8943"><span class="lineNum">    8943 </span><span class="lineCov">         59 :         d__[*n] = r__;</span></a>
+<a name="8944"><span class="lineNum">    8944 </span><span class="lineCov">         59 :         e[*n] = 0.f;</span></a>
+<a name="8945"><span class="lineNum">    8945 </span><span class="lineCov">         59 :         if (rotate) {</span></a>
+<a name="8946"><span class="lineNum">    8946 </span><span class="lineCov">         59 :             work[*n] = cs;</span></a>
+<a name="8947"><span class="lineNum">    8947 </span><span class="lineCov">         59 :             work[*n + *n] = sn;</span></a>
+<a name="8948"><span class="lineNum">    8948 </span>            :         }</a>
+<a name="8949"><span class="lineNum">    8949 </span>            :         iuplo = 2;</a>
+<a name="8950"><span class="lineNum">    8950 </span>            :         sqre1 = 0;</a>
+<a name="8951"><span class="lineNum">    8951 </span>            : </a>
+<a name="8952"><span class="lineNum">    8952 </span><span class="lineCov">         59 :         if (*ncvt &gt; 0) {</span></a>
+<a name="8953"><span class="lineNum">    8953 </span><span class="lineCov">         59 :             PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;np1, ncvt, &amp;work[1], &amp;work[np1], &amp;vt[</span></a>
+<a name="8954"><span class="lineNum">    8954 </span>            :                     vt_offset], ldvt);</a>
+<a name="8955"><span class="lineNum">    8955 </span>            :         }</a>
+<a name="8956"><span class="lineNum">    8956 </span>            :     }</a>
+<a name="8957"><span class="lineNum">    8957 </span><span class="lineCov">         96 :     if (iuplo == 2) {</span></a>
+<a name="8958"><span class="lineNum">    8958 </span><span class="lineCov">         59 :         i__1 = *n - 1;</span></a>
+<a name="8959"><span class="lineNum">    8959 </span><span class="lineCov">        903 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="8960"><span class="lineNum">    8960 </span><span class="lineCov">        844 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="8961"><span class="lineNum">    8961 </span><span class="lineCov">        844 :             d__[i__] = r__;</span></a>
+<a name="8962"><span class="lineNum">    8962 </span><span class="lineCov">        844 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="8963"><span class="lineNum">    8963 </span><span class="lineCov">        844 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="8964"><span class="lineNum">    8964 </span><span class="lineCov">        844 :             if (rotate) {</span></a>
+<a name="8965"><span class="lineNum">    8965 </span><span class="lineCov">        844 :                 work[i__] = cs;</span></a>
+<a name="8966"><span class="lineNum">    8966 </span><span class="lineCov">        844 :                 work[*n + i__] = sn;</span></a>
+<a name="8967"><span class="lineNum">    8967 </span>            :             }</a>
+<a name="8968"><span class="lineNum">    8968 </span>            :         }</a>
+<a name="8969"><span class="lineNum">    8969 </span>            : </a>
+<a name="8970"><span class="lineNum">    8970 </span><span class="lineCov">         59 :         if (sqre1 == 1) {</span></a>
+<a name="8971"><span class="lineNum">    8971 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;d__[*n], &amp;e[*n], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="8972"><span class="lineNum">    8972 </span><span class="lineNoCov">          0 :             d__[*n] = r__;</span></a>
+<a name="8973"><span class="lineNum">    8973 </span><span class="lineNoCov">          0 :             if (rotate) {</span></a>
+<a name="8974"><span class="lineNum">    8974 </span><span class="lineNoCov">          0 :                 work[*n] = cs;</span></a>
+<a name="8975"><span class="lineNum">    8975 </span><span class="lineNoCov">          0 :                 work[*n + *n] = sn;</span></a>
+<a name="8976"><span class="lineNum">    8976 </span>            :             }</a>
+<a name="8977"><span class="lineNum">    8977 </span>            :         }</a>
+<a name="8978"><span class="lineNum">    8978 </span><span class="lineCov">         59 :         if (*nru &gt; 0) {</span></a>
+<a name="8979"><span class="lineNum">    8979 </span><span class="lineCov">         59 :             if (sqre1 == 0) {</span></a>
+<a name="8980"><span class="lineNum">    8980 </span><span class="lineCov">         59 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, n, &amp;work[1], &amp;work[np1], &amp;u[</span></a>
+<a name="8981"><span class="lineNum">    8981 </span>            :                         u_offset], ldu);</a>
+<a name="8982"><span class="lineNum">    8982 </span>            :             } else {</a>
+<a name="8983"><span class="lineNum">    8983 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, &amp;np1, &amp;work[1], &amp;work[np1], &amp;u[</span></a>
+<a name="8984"><span class="lineNum">    8984 </span>            :                         u_offset], ldu);</a>
+<a name="8985"><span class="lineNum">    8985 </span>            :             }</a>
+<a name="8986"><span class="lineNum">    8986 </span>            :         }</a>
+<a name="8987"><span class="lineNum">    8987 </span><span class="lineCov">         59 :         if (*ncc &gt; 0) {</span></a>
+<a name="8988"><span class="lineNum">    8988 </span><span class="lineNoCov">          0 :             if (sqre1 == 0) {</span></a>
+<a name="8989"><span class="lineNum">    8989 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, n, ncc, &amp;work[1], &amp;work[np1], &amp;c__[</span></a>
+<a name="8990"><span class="lineNum">    8990 </span>            :                         c_offset], ldc);</a>
+<a name="8991"><span class="lineNum">    8991 </span>            :             } else {</a>
+<a name="8992"><span class="lineNum">    8992 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;np1, ncc, &amp;work[1], &amp;work[np1], &amp;c__[</span></a>
+<a name="8993"><span class="lineNum">    8993 </span>            :                         c_offset], ldc);</a>
+<a name="8994"><span class="lineNum">    8994 </span>            :             }</a>
+<a name="8995"><span class="lineNum">    8995 </span>            :         }</a>
+<a name="8996"><span class="lineNum">    8996 </span>            :     }</a>
+<a name="8997"><span class="lineNum">    8997 </span>            : </a>
+<a name="8998"><span class="lineNum">    8998 </span><span class="lineCov">        155 :     PLUMED_BLAS_F77_FUNC(dbdsqr,DBDSQR)(&quot;U&quot;, n, ncvt, nru, ncc, &amp;d__[1], &amp;e[1], &amp;vt[vt_offset], ldvt, &amp;u[</span></a>
+<a name="8999"><span class="lineNum">    8999 </span>            :             u_offset], ldu, &amp;c__[c_offset], ldc, &amp;work[1], info);</a>
+<a name="9000"><span class="lineNum">    9000 </span>            : </a>
+<a name="9001"><span class="lineNum">    9001 </span><span class="lineCov">        155 :     i__1 = *n;</span></a>
+<a name="9002"><span class="lineNum">    9002 </span><span class="lineCov">       2635 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="9003"><span class="lineNum">    9003 </span>            : </a>
+<a name="9004"><span class="lineNum">    9004 </span>            :         isub = i__;</a>
+<a name="9005"><span class="lineNum">    9005 </span><span class="lineCov">       2480 :         smin = d__[i__];</span></a>
+<a name="9006"><span class="lineNum">    9006 </span><span class="lineCov">       2480 :         i__2 = *n;</span></a>
+<a name="9007"><span class="lineNum">    9007 </span><span class="lineCov">      22277 :         for (j = i__ + 1; j &lt;= i__2; ++j) {</span></a>
+<a name="9008"><span class="lineNum">    9008 </span><span class="lineCov">      19797 :             if (d__[j] &lt; smin) {</span></a>
+<a name="9009"><span class="lineNum">    9009 </span>            :                 isub = j;</a>
+<a name="9010"><span class="lineNum">    9010 </span>            :                 smin = d__[j];</a>
+<a name="9011"><span class="lineNum">    9011 </span>            :             }</a>
+<a name="9012"><span class="lineNum">    9012 </span>            :         }</a>
+<a name="9013"><span class="lineNum">    9013 </span><span class="lineCov">       2480 :         if (isub != i__) {</span></a>
+<a name="9014"><span class="lineNum">    9014 </span><span class="lineCov">       1181 :             d__[isub] = d__[i__];</span></a>
+<a name="9015"><span class="lineNum">    9015 </span><span class="lineCov">       1181 :             d__[i__] = smin;</span></a>
+<a name="9016"><span class="lineNum">    9016 </span><span class="lineCov">       1181 :             if (*ncvt &gt; 0) {</span></a>
+<a name="9017"><span class="lineNum">    9017 </span><span class="lineCov">       1181 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(ncvt, &amp;vt[isub + vt_dim1], ldvt, &amp;vt[i__ + vt_dim1], </span></a>
+<a name="9018"><span class="lineNum">    9018 </span>            :                         ldvt);</a>
+<a name="9019"><span class="lineNum">    9019 </span>            :             }</a>
+<a name="9020"><span class="lineNum">    9020 </span><span class="lineCov">       1181 :             if (*nru &gt; 0) {</span></a>
+<a name="9021"><span class="lineNum">    9021 </span><span class="lineCov">       1181 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(nru, &amp;u[isub * u_dim1 + 1], &amp;c__1, &amp;u[i__ * u_dim1 + 1]</span></a>
+<a name="9022"><span class="lineNum">    9022 </span>            :                         , &amp;c__1);</a>
+<a name="9023"><span class="lineNum">    9023 </span>            :             }</a>
+<a name="9024"><span class="lineNum">    9024 </span><span class="lineCov">       1181 :             if (*ncc &gt; 0) {</span></a>
+<a name="9025"><span class="lineNum">    9025 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(ncc, &amp;c__[isub + c_dim1], ldc, &amp;c__[i__ + c_dim1], ldc)</span></a>
+<a name="9026"><span class="lineNum">    9026 </span>            :                         ;</a>
+<a name="9027"><span class="lineNum">    9027 </span>            :             }</a>
+<a name="9028"><span class="lineNum">    9028 </span>            :         }</a>
+<a name="9029"><span class="lineNum">    9029 </span>            :     }</a>
+<a name="9030"><span class="lineNum">    9030 </span>            : </a>
+<a name="9031"><span class="lineNum">    9031 </span>            :     return;</a>
+<a name="9032"><span class="lineNum">    9032 </span>            : }</a>
+<a name="9033"><span class="lineNum">    9033 </span>            : </a>
+<a name="9034"><span class="lineNum">    9034 </span>            : </a>
+<a name="9035"><span class="lineNum">    9035 </span>            : }</a>
+<a name="9036"><span class="lineNum">    9036 </span>            : }</a>
+<a name="9037"><span class="lineNum">    9037 </span>            : #include &lt;cmath&gt;</a>
+<a name="9038"><span class="lineNum">    9038 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="9039"><span class="lineNum">    9039 </span>            : </a>
+<a name="9040"><span class="lineNum">    9040 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9041"><span class="lineNum">    9041 </span>            : namespace PLMD{</a>
+<a name="9042"><span class="lineNum">    9042 </span>            : namespace lapack{</a>
+<a name="9043"><span class="lineNum">    9043 </span>            : using namespace blas;</a>
+<a name="9044"><span class="lineNum">    9044 </span>            : void</a>
+<a name="9045"><span class="lineNum">    9045 </span><span class="lineCov">         29 : PLUMED_BLAS_F77_FUNC(dlasdt,DLASDT)(int *n,</span></a>
+<a name="9046"><span class="lineNum">    9046 </span>            :         int *lvl,</a>
+<a name="9047"><span class="lineNum">    9047 </span>            :         int *nd,</a>
+<a name="9048"><span class="lineNum">    9048 </span>            :         int *inode,</a>
+<a name="9049"><span class="lineNum">    9049 </span>            :         int *ndiml,</a>
+<a name="9050"><span class="lineNum">    9050 </span>            :         int *ndimr,</a>
+<a name="9051"><span class="lineNum">    9051 </span>            :         int *msub)</a>
+<a name="9052"><span class="lineNum">    9052 </span>            : {</a>
+<a name="9053"><span class="lineNum">    9053 </span><span class="lineCov">         29 :   int maxn = (*n &gt; 1) ? *n : 1;</span></a>
+<a name="9054"><span class="lineNum">    9054 </span>            :   double temp;</a>
+<a name="9055"><span class="lineNum">    9055 </span>            :   int i,il,ir,llst,nlvl,ncrnt;</a>
+<a name="9056"><span class="lineNum">    9056 </span>            : </a>
+<a name="9057"><span class="lineNum">    9057 </span><span class="lineCov">         29 :   temp = std::log( ((double) maxn) / ((double)(*msub+1))) / std::log(2.0);</span></a>
+<a name="9058"><span class="lineNum">    9058 </span>            :   </a>
+<a name="9059"><span class="lineNum">    9059 </span><span class="lineCov">         29 :   *lvl = 1 + (int) temp;</span></a>
+<a name="9060"><span class="lineNum">    9060 </span>            : </a>
+<a name="9061"><span class="lineNum">    9061 </span><span class="lineCov">         29 :   i = *n / 2;</span></a>
+<a name="9062"><span class="lineNum">    9062 </span><span class="lineCov">         29 :   inode[0] = i + 1;</span></a>
+<a name="9063"><span class="lineNum">    9063 </span><span class="lineCov">         29 :   ndiml[0] = i;</span></a>
+<a name="9064"><span class="lineNum">    9064 </span><span class="lineCov">         29 :   ndimr[0] = *n - i - 1;</span></a>
+<a name="9065"><span class="lineNum">    9065 </span>            :   il = -1;</a>
+<a name="9066"><span class="lineNum">    9066 </span>            :   ir = 0;</a>
+<a name="9067"><span class="lineNum">    9067 </span>            :   llst = 1;</a>
+<a name="9068"><span class="lineNum">    9068 </span>            : </a>
+<a name="9069"><span class="lineNum">    9069 </span><span class="lineCov">         33 :   for(nlvl=1;nlvl&lt;*lvl;nlvl++) {</span></a>
+<a name="9070"><span class="lineNum">    9070 </span><span class="lineCov">         19 :     for(i=0;i&lt;llst;i++) {</span></a>
+<a name="9071"><span class="lineNum">    9071 </span><span class="lineCov">         15 :       il += 2;</span></a>
+<a name="9072"><span class="lineNum">    9072 </span><span class="lineCov">         15 :       ir += 2;</span></a>
+<a name="9073"><span class="lineNum">    9073 </span><span class="lineCov">         15 :       ncrnt = llst + i - 1;</span></a>
+<a name="9074"><span class="lineNum">    9074 </span><span class="lineCov">         15 :       ndiml[il] = ndiml[ncrnt] / 2;</span></a>
+<a name="9075"><span class="lineNum">    9075 </span><span class="lineCov">         15 :       ndimr[il] = ndiml[ncrnt] - ndiml[il] - 1;</span></a>
+<a name="9076"><span class="lineNum">    9076 </span><span class="lineCov">         15 :       inode[il] = inode[ncrnt] - ndimr[il] - 1;</span></a>
+<a name="9077"><span class="lineNum">    9077 </span><span class="lineCov">         15 :       ndiml[ir] = ndimr[ncrnt] / 2;</span></a>
+<a name="9078"><span class="lineNum">    9078 </span><span class="lineCov">         15 :       ndimr[ir] = ndimr[ncrnt] - ndiml[ir] - 1;</span></a>
+<a name="9079"><span class="lineNum">    9079 </span><span class="lineCov">         15 :       inode[ir] = inode[ncrnt] + ndiml[ir] + 1;</span></a>
+<a name="9080"><span class="lineNum">    9080 </span>            :     }</a>
+<a name="9081"><span class="lineNum">    9081 </span><span class="lineCov">          4 :     llst *= 2;</span></a>
+<a name="9082"><span class="lineNum">    9082 </span>            :   }</a>
+<a name="9083"><span class="lineNum">    9083 </span><span class="lineCov">         29 :   *nd = llst*2 - 1;</span></a>
+<a name="9084"><span class="lineNum">    9084 </span><span class="lineCov">         29 :   return;</span></a>
+<a name="9085"><span class="lineNum">    9085 </span>            : }</a>
+<a name="9086"><span class="lineNum">    9086 </span>            : }</a>
+<a name="9087"><span class="lineNum">    9087 </span>            : }</a>
+<a name="9088"><span class="lineNum">    9088 </span>            : #include &lt;cctype&gt;</a>
+<a name="9089"><span class="lineNum">    9089 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="9090"><span class="lineNum">    9090 </span>            : </a>
+<a name="9091"><span class="lineNum">    9091 </span>            : </a>
+<a name="9092"><span class="lineNum">    9092 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9093"><span class="lineNum">    9093 </span>            : namespace PLMD{</a>
+<a name="9094"><span class="lineNum">    9094 </span>            : namespace lapack{</a>
+<a name="9095"><span class="lineNum">    9095 </span>            : using namespace blas;</a>
+<a name="9096"><span class="lineNum">    9096 </span>            : void</a>
+<a name="9097"><span class="lineNum">    9097 </span><span class="lineCov">     570476 : PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(const char *uplo,</span></a>
+<a name="9098"><span class="lineNum">    9098 </span>            :         int *m,</a>
+<a name="9099"><span class="lineNum">    9099 </span>            :         int *n,</a>
+<a name="9100"><span class="lineNum">    9100 </span>            :         double *alpha,</a>
+<a name="9101"><span class="lineNum">    9101 </span>            :         double *beta,</a>
+<a name="9102"><span class="lineNum">    9102 </span>            :         double *a,</a>
+<a name="9103"><span class="lineNum">    9103 </span>            :         int *lda)</a>
+<a name="9104"><span class="lineNum">    9104 </span>            : {</a>
+<a name="9105"><span class="lineNum">    9105 </span>            :   int i,j,k;</a>
+<a name="9106"><span class="lineNum">    9106 </span><span class="lineCov">     570476 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="9107"><span class="lineNum">    9107 </span>            : </a>
+<a name="9108"><span class="lineNum">    9108 </span><span class="lineCov">     570476 :   if(ch=='U') {</span></a>
+<a name="9109"><span class="lineNum">    9109 </span><span class="lineNoCov">          0 :     for(j=1;j&lt;*n;j++) {</span></a>
+<a name="9110"><span class="lineNum">    9110 </span><span class="lineNoCov">          0 :       k = (j &lt; *m) ? j : *m;</span></a>
+<a name="9111"><span class="lineNum">    9111 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;k;i++)</span></a>
+<a name="9112"><span class="lineNum">    9112 </span><span class="lineNoCov">          0 :         a[j*(*lda)+i] = *alpha;</span></a>
+<a name="9113"><span class="lineNum">    9113 </span>            :     }</a>
+<a name="9114"><span class="lineNum">    9114 </span><span class="lineCov">     570476 :   } else if(ch=='L') {</span></a>
+<a name="9115"><span class="lineNum">    9115 </span><span class="lineCov">          1 :     k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="9116"><span class="lineNum">    9116 </span><span class="lineCov">          2 :     for(j=0;j&lt;k;j++) {</span></a>
+<a name="9117"><span class="lineNum">    9117 </span><span class="lineCov">          1 :       for(i=j+1;i&lt;*m;i++)</span></a>
+<a name="9118"><span class="lineNum">    9118 </span><span class="lineNoCov">          0 :         a[j*(*lda)+i] = *alpha;</span></a>
+<a name="9119"><span class="lineNum">    9119 </span>            :     }</a>
+<a name="9120"><span class="lineNum">    9120 </span>            :   } else {</a>
+<a name="9121"><span class="lineNum">    9121 </span><span class="lineCov">    1185835 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="9122"><span class="lineNum">    9122 </span><span class="lineCov">    4343218 :       for(i=0;i&lt;*m;i++)</span></a>
+<a name="9123"><span class="lineNum">    9123 </span><span class="lineCov">    3727858 :         a[j*(*lda)+i] = *alpha;</span></a>
+<a name="9124"><span class="lineNum">    9124 </span>            :     }    </a>
+<a name="9125"><span class="lineNum">    9125 </span>            :   }</a>
+<a name="9126"><span class="lineNum">    9126 </span>            : </a>
+<a name="9127"><span class="lineNum">    9127 </span><span class="lineCov">     570476 :   k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="9128"><span class="lineNum">    9128 </span><span class="lineCov">    1185837 :   for(i=0;i&lt;k;i++)</span></a>
+<a name="9129"><span class="lineNum">    9129 </span><span class="lineCov">     615361 :     a[i*(*lda)+i] = *beta;</span></a>
+<a name="9130"><span class="lineNum">    9130 </span><span class="lineCov">     570476 : }</span></a>
+<a name="9131"><span class="lineNum">    9131 </span>            : }</a>
+<a name="9132"><span class="lineNum">    9132 </span>            : }</a>
+<a name="9133"><span class="lineNum">    9133 </span>            : #include &lt;cmath&gt;</a>
+<a name="9134"><span class="lineNum">    9134 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9135"><span class="lineNum">    9135 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="9136"><span class="lineNum">    9136 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="9137"><span class="lineNum">    9137 </span>            : </a>
+<a name="9138"><span class="lineNum">    9138 </span>            : #include &quot;real.h&quot;</a>
+<a name="9139"><span class="lineNum">    9139 </span>            : </a>
+<a name="9140"><span class="lineNum">    9140 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9141"><span class="lineNum">    9141 </span>            : namespace PLMD{</a>
+<a name="9142"><span class="lineNum">    9142 </span>            : namespace lapack{</a>
+<a name="9143"><span class="lineNum">    9143 </span>            : using namespace blas;</a>
+<a name="9144"><span class="lineNum">    9144 </span>            : void</a>
+<a name="9145"><span class="lineNum">    9145 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasq1,DLASQ1)(int *n,</span></a>
+<a name="9146"><span class="lineNum">    9146 </span>            :         double *d,</a>
+<a name="9147"><span class="lineNum">    9147 </span>            :         double *e,</a>
+<a name="9148"><span class="lineNum">    9148 </span>            :         double *work,</a>
+<a name="9149"><span class="lineNum">    9149 </span>            :         int *info)</a>
+<a name="9150"><span class="lineNum">    9150 </span>            : {</a>
+<a name="9151"><span class="lineNum">    9151 </span><span class="lineNoCov">          0 :   double sigmx = 0.0;</span></a>
+<a name="9152"><span class="lineNum">    9152 </span>            :   int i,j,k,iinfo;</a>
+<a name="9153"><span class="lineNum">    9153 </span>            :   double minval,safemin;</a>
+<a name="9154"><span class="lineNum">    9154 </span>            :   double dtemp,scale;</a>
+<a name="9155"><span class="lineNum">    9155 </span>            :   double eps;</a>
+<a name="9156"><span class="lineNum">    9156 </span>            : </a>
+<a name="9157"><span class="lineNum">    9157 </span>            :   eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="9158"><span class="lineNum">    9158 </span>            :   minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="9159"><span class="lineNum">    9159 </span>            :   safemin = minval*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="9160"><span class="lineNum">    9160 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="9161"><span class="lineNum">    9161 </span>            : </a>
+<a name="9162"><span class="lineNum">    9162 </span><span class="lineNoCov">          0 :   if(*n&lt;0) {</span></a>
+<a name="9163"><span class="lineNum">    9163 </span><span class="lineNoCov">          0 :     *info = -2;</span></a>
+<a name="9164"><span class="lineNum">    9164 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="9165"><span class="lineNum">    9165 </span>            :   }</a>
+<a name="9166"><span class="lineNum">    9166 </span>            :   </a>
+<a name="9167"><span class="lineNum">    9167 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;*n-1;i++) {</span></a>
+<a name="9168"><span class="lineNum">    9168 </span><span class="lineNoCov">          0 :     d[i] = std::abs(d[i]);</span></a>
+<a name="9169"><span class="lineNum">    9169 </span><span class="lineNoCov">          0 :     dtemp = std::abs(e[i]);</span></a>
+<a name="9170"><span class="lineNum">    9170 </span><span class="lineNoCov">          0 :     if(dtemp&gt;sigmx)</span></a>
+<a name="9171"><span class="lineNum">    9171 </span><span class="lineNoCov">          0 :       sigmx=dtemp;</span></a>
+<a name="9172"><span class="lineNum">    9172 </span>            :   }</a>
+<a name="9173"><span class="lineNum">    9173 </span><span class="lineNoCov">          0 :   d[*n-1] = std::abs(d[*n-1]);</span></a>
+<a name="9174"><span class="lineNum">    9174 </span>            :   </a>
+<a name="9175"><span class="lineNum">    9175 </span><span class="lineNoCov">          0 :   if(std::abs(sigmx)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="9176"><span class="lineNum">    9176 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(&quot;D&quot;,n,d,&amp;iinfo);</span></a>
+<a name="9177"><span class="lineNum">    9177 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="9178"><span class="lineNum">    9178 </span>            :   }</a>
+<a name="9179"><span class="lineNum">    9179 </span>            : </a>
+<a name="9180"><span class="lineNum">    9180 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;*n;i++) {</span></a>
+<a name="9181"><span class="lineNum">    9181 </span><span class="lineNoCov">          0 :     if(d[i]&gt;sigmx)</span></a>
+<a name="9182"><span class="lineNum">    9182 </span><span class="lineNoCov">          0 :       sigmx=d[i];</span></a>
+<a name="9183"><span class="lineNum">    9183 </span>            :   }</a>
+<a name="9184"><span class="lineNum">    9184 </span>            : </a>
+<a name="9185"><span class="lineNum">    9185 </span>            :   /* Copy d and e into work (z format) and scale.</a>
+<a name="9186"><span class="lineNum">    9186 </span>            :    * Squaring input data makes scaling by a power of the</a>
+<a name="9187"><span class="lineNum">    9187 </span>            :    * radix pointless.</a>
+<a name="9188"><span class="lineNum">    9188 </span>            :    */</a>
+<a name="9189"><span class="lineNum">    9189 </span><span class="lineNoCov">          0 :   scale =  std::sqrt(eps/safemin);</span></a>
+<a name="9190"><span class="lineNum">    9190 </span><span class="lineNoCov">          0 :   i = 1;</span></a>
+<a name="9191"><span class="lineNum">    9191 </span><span class="lineNoCov">          0 :   j = 2;</span></a>
+<a name="9192"><span class="lineNum">    9192 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n,d,&amp;i,work,&amp;j);</span></a>
+<a name="9193"><span class="lineNum">    9193 </span><span class="lineNoCov">          0 :   k = *n-1;</span></a>
+<a name="9194"><span class="lineNum">    9194 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;k,e,&amp;i,work+1,&amp;j);</span></a>
+<a name="9195"><span class="lineNum">    9195 </span><span class="lineNoCov">          0 :   i = 0;</span></a>
+<a name="9196"><span class="lineNum">    9196 </span><span class="lineNoCov">          0 :   j = 2*(*n)-1;</span></a>
+<a name="9197"><span class="lineNum">    9197 </span><span class="lineNoCov">          0 :   k = 1;</span></a>
+<a name="9198"><span class="lineNum">    9198 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;,&amp;i,&amp;i,&amp;sigmx,&amp;scale,&amp;j,&amp;k,work,&amp;j,&amp;iinfo);</span></a>
+<a name="9199"><span class="lineNum">    9199 </span>            : </a>
+<a name="9200"><span class="lineNum">    9200 </span>            : </a>
+<a name="9201"><span class="lineNum">    9201 </span>            :   /* Compute q and e elements */</a>
+<a name="9202"><span class="lineNum">    9202 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;2*(*n)-1;i++)</span></a>
+<a name="9203"><span class="lineNum">    9203 </span><span class="lineNoCov">          0 :     work[i] = work[i]*work[i];</span></a>
+<a name="9204"><span class="lineNum">    9204 </span>            : </a>
+<a name="9205"><span class="lineNum">    9205 </span><span class="lineNoCov">          0 :   work[2*(*n)-1] = 0.0;</span></a>
+<a name="9206"><span class="lineNum">    9206 </span>            : </a>
+<a name="9207"><span class="lineNum">    9207 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(dlasq2,DLASQ2)(n,work,info);</span></a>
+<a name="9208"><span class="lineNum">    9208 </span>            : </a>
+<a name="9209"><span class="lineNum">    9209 </span><span class="lineNoCov">          0 :   j = 0;</span></a>
+<a name="9210"><span class="lineNum">    9210 </span><span class="lineNoCov">          0 :   k = 1;</span></a>
+<a name="9211"><span class="lineNum">    9211 </span><span class="lineNoCov">          0 :   if(*info==0) {</span></a>
+<a name="9212"><span class="lineNum">    9212 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*n;i++)</span></a>
+<a name="9213"><span class="lineNum">    9213 </span><span class="lineNoCov">          0 :       d[i]= std::sqrt(work[i]);</span></a>
+<a name="9214"><span class="lineNum">    9214 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;,&amp;j,&amp;j,&amp;scale,&amp;sigmx,n,&amp;k,d,n,&amp;iinfo);</span></a>
+<a name="9215"><span class="lineNum">    9215 </span>            :   }</a>
+<a name="9216"><span class="lineNum">    9216 </span>            :   return;</a>
+<a name="9217"><span class="lineNum">    9217 </span>            : }</a>
+<a name="9218"><span class="lineNum">    9218 </span>            : }</a>
+<a name="9219"><span class="lineNum">    9219 </span>            : }</a>
+<a name="9220"><span class="lineNum">    9220 </span>            : #include &lt;cmath&gt;</a>
+<a name="9221"><span class="lineNum">    9221 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="9222"><span class="lineNum">    9222 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="9223"><span class="lineNum">    9223 </span>            : </a>
+<a name="9224"><span class="lineNum">    9224 </span>            : #include &quot;real.h&quot;</a>
+<a name="9225"><span class="lineNum">    9225 </span>            : </a>
+<a name="9226"><span class="lineNum">    9226 </span>            : #ifdef _MSC_VER</a>
+<a name="9227"><span class="lineNum">    9227 </span>            : #pragma warning(disable: 4723) /*division by zero - is used on purpose here*/</a>
+<a name="9228"><span class="lineNum">    9228 </span>            : #endif</a>
+<a name="9229"><span class="lineNum">    9229 </span>            : </a>
+<a name="9230"><span class="lineNum">    9230 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9231"><span class="lineNum">    9231 </span>            : namespace PLMD{</a>
+<a name="9232"><span class="lineNum">    9232 </span>            : namespace lapack{</a>
+<a name="9233"><span class="lineNum">    9233 </span>            : using namespace blas;</a>
+<a name="9234"><span class="lineNum">    9234 </span>            : void </a>
+<a name="9235"><span class="lineNum">    9235 </span><span class="lineCov">     570010 : PLUMED_BLAS_F77_FUNC(dlasq2,DLASQ2)(int *n, </span></a>
+<a name="9236"><span class="lineNum">    9236 </span>            :                         double *z__, </a>
+<a name="9237"><span class="lineNum">    9237 </span>            :                         int *info)</a>
+<a name="9238"><span class="lineNum">    9238 </span>            : {</a>
+<a name="9239"><span class="lineNum">    9239 </span>            :     int i__1, i__2, i__3;</a>
+<a name="9240"><span class="lineNum">    9240 </span>            :     double d__1, d__2;</a>
+<a name="9241"><span class="lineNum">    9241 </span>            : </a>
+<a name="9242"><span class="lineNum">    9242 </span>            :     double d__, e;</a>
+<a name="9243"><span class="lineNum">    9243 </span>            :     int k;</a>
+<a name="9244"><span class="lineNum">    9244 </span>            :     double s, t;</a>
+<a name="9245"><span class="lineNum">    9245 </span>            :     int i0, i4, n0, pp;</a>
+<a name="9246"><span class="lineNum">    9246 </span>            :     double dee, eps, tol;</a>
+<a name="9247"><span class="lineNum">    9247 </span>            :     int ipn4;</a>
+<a name="9248"><span class="lineNum">    9248 </span>            :     double tol2;</a>
+<a name="9249"><span class="lineNum">    9249 </span>            :     int ieee;</a>
+<a name="9250"><span class="lineNum">    9250 </span>            :     int nbig;</a>
+<a name="9251"><span class="lineNum">    9251 </span>            :     double dmin__, emin, emax;</a>
+<a name="9252"><span class="lineNum">    9252 </span>            :     int kmin, ndiv, iter;</a>
+<a name="9253"><span class="lineNum">    9253 </span>            :     double qmin, temp, qmax, zmax;</a>
+<a name="9254"><span class="lineNum">    9254 </span>            :     int splt, nfail;</a>
+<a name="9255"><span class="lineNum">    9255 </span>            :     double desig, trace, sigma;</a>
+<a name="9256"><span class="lineNum">    9256 </span>            :     int iinfo;</a>
+<a name="9257"><span class="lineNum">    9257 </span>            :     double deemin;</a>
+<a name="9258"><span class="lineNum">    9258 </span>            :     int iwhila, iwhilb;</a>
+<a name="9259"><span class="lineNum">    9259 </span>            :     double oldemn, safmin, minval;</a>
+<a name="9260"><span class="lineNum">    9260 </span>            :     double posinf,neginf,negzro,newzro;</a>
+<a name="9261"><span class="lineNum">    9261 </span>            :     double zero = 0.0;</a>
+<a name="9262"><span class="lineNum">    9262 </span>            :     double one = 1.0;</a>
+<a name="9263"><span class="lineNum">    9263 </span>            : </a>
+<a name="9264"><span class="lineNum">    9264 </span><span class="lineCov">     570010 :     --z__;</span></a>
+<a name="9265"><span class="lineNum">    9265 </span>            : </a>
+<a name="9266"><span class="lineNum">    9266 </span><span class="lineCov">     570010 :     *info = 0;</span></a>
+<a name="9267"><span class="lineNum">    9267 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="9268"><span class="lineNum">    9268 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="9269"><span class="lineNum">    9269 </span>            :     safmin = minval*(1.0+eps);</a>
+<a name="9270"><span class="lineNum">    9270 </span>            : </a>
+<a name="9271"><span class="lineNum">    9271 </span>            :     tol = eps * 100.;</a>
+<a name="9272"><span class="lineNum">    9272 </span>            : </a>
+<a name="9273"><span class="lineNum">    9273 </span>            :     d__1 = tol;</a>
+<a name="9274"><span class="lineNum">    9274 </span>            :     tol2 = d__1 * d__1;</a>
+<a name="9275"><span class="lineNum">    9275 </span>            : </a>
+<a name="9276"><span class="lineNum">    9276 </span><span class="lineCov">     570010 :     if (*n &lt; 0) {</span></a>
+<a name="9277"><span class="lineNum">    9277 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="9278"><span class="lineNum">    9278 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="9279"><span class="lineNum">    9279 </span><span class="lineCov">     570010 :     } else if (*n == 0) {</span></a>
+<a name="9280"><span class="lineNum">    9280 </span>            :         return;</a>
+<a name="9281"><span class="lineNum">    9281 </span><span class="lineCov">     570010 :     } else if (*n == 1) {</span></a>
+<a name="9282"><span class="lineNum">    9282 </span>            : </a>
+<a name="9283"><span class="lineNum">    9283 </span><span class="lineNoCov">          0 :         if (z__[1] &lt; 0.) {</span></a>
+<a name="9284"><span class="lineNum">    9284 </span><span class="lineNoCov">          0 :             *info = -201;</span></a>
+<a name="9285"><span class="lineNum">    9285 </span>            :         }</a>
+<a name="9286"><span class="lineNum">    9286 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="9287"><span class="lineNum">    9287 </span><span class="lineCov">     570010 :     } else if (*n == 2) {</span></a>
+<a name="9288"><span class="lineNum">    9288 </span>            : </a>
+<a name="9289"><span class="lineNum">    9289 </span><span class="lineCov">      13363 :         if (z__[2] &lt; 0. || z__[3] &lt; 0.) {</span></a>
+<a name="9290"><span class="lineNum">    9290 </span><span class="lineNoCov">          0 :             *info = -2;</span></a>
+<a name="9291"><span class="lineNum">    9291 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="9292"><span class="lineNum">    9292 </span><span class="lineCov">      13363 :         } else if (z__[3] &gt; z__[1]) {</span></a>
+<a name="9293"><span class="lineNum">    9293 </span>            :             d__ = z__[3];</a>
+<a name="9294"><span class="lineNum">    9294 </span><span class="lineNoCov">          0 :             z__[3] = z__[1];</span></a>
+<a name="9295"><span class="lineNum">    9295 </span><span class="lineNoCov">          0 :             z__[1] = d__;</span></a>
+<a name="9296"><span class="lineNum">    9296 </span>            :         }</a>
+<a name="9297"><span class="lineNum">    9297 </span><span class="lineCov">      13363 :         z__[5] = z__[1] + z__[2] + z__[3];</span></a>
+<a name="9298"><span class="lineNum">    9298 </span><span class="lineCov">      13363 :         if (z__[2] &gt; z__[3] * tol2) {</span></a>
+<a name="9299"><span class="lineNum">    9299 </span><span class="lineCov">      13363 :             t = (z__[1] - z__[3] + z__[2]) * .5;</span></a>
+<a name="9300"><span class="lineNum">    9300 </span><span class="lineCov">      13363 :             s = z__[3] * (z__[2] / t);</span></a>
+<a name="9301"><span class="lineNum">    9301 </span><span class="lineCov">      13363 :             if (s &lt;= t) {</span></a>
+<a name="9302"><span class="lineNum">    9302 </span><span class="lineCov">      13363 :                 s = z__[3] * (z__[2] / (t * ( std::sqrt(s / t + 1.) + 1.)));</span></a>
+<a name="9303"><span class="lineNum">    9303 </span>            :             } else {</a>
+<a name="9304"><span class="lineNum">    9304 </span><span class="lineNoCov">          0 :                 s = z__[3] * (z__[2] / (t +  std::sqrt(t) * std::sqrt(t + s)));</span></a>
+<a name="9305"><span class="lineNum">    9305 </span>            :             }</a>
+<a name="9306"><span class="lineNum">    9306 </span><span class="lineCov">      13363 :             t = z__[1] + (s + z__[2]);</span></a>
+<a name="9307"><span class="lineNum">    9307 </span><span class="lineCov">      13363 :             z__[3] *= z__[1] / t;</span></a>
+<a name="9308"><span class="lineNum">    9308 </span><span class="lineCov">      13363 :             z__[1] = t;</span></a>
+<a name="9309"><span class="lineNum">    9309 </span>            :         }</a>
+<a name="9310"><span class="lineNum">    9310 </span><span class="lineCov">      13363 :         z__[2] = z__[3];</span></a>
+<a name="9311"><span class="lineNum">    9311 </span><span class="lineCov">      13363 :         z__[6] = z__[2] + z__[1];</span></a>
+<a name="9312"><span class="lineNum">    9312 </span><span class="lineCov">      13363 :         return;</span></a>
+<a name="9313"><span class="lineNum">    9313 </span>            :     }</a>
+<a name="9314"><span class="lineNum">    9314 </span><span class="lineCov">     556647 :     z__[*n * 2] = 0.;</span></a>
+<a name="9315"><span class="lineNum">    9315 </span><span class="lineCov">     556647 :     emin = z__[2];</span></a>
+<a name="9316"><span class="lineNum">    9316 </span><span class="lineCov">     556647 :     qmax = 0.;</span></a>
+<a name="9317"><span class="lineNum">    9317 </span>            :     zmax = 0.;</a>
+<a name="9318"><span class="lineNum">    9318 </span>            :     d__ = 0.;</a>
+<a name="9319"><span class="lineNum">    9319 </span>            :     e = 0.;</a>
+<a name="9320"><span class="lineNum">    9320 </span>            : </a>
+<a name="9321"><span class="lineNum">    9321 </span><span class="lineCov">     556647 :     i__1 = 2*(*n - 1);</span></a>
+<a name="9322"><span class="lineNum">    9322 </span><span class="lineCov">    2227038 :     for (k = 1; k &lt;= i__1; k += 2) {</span></a>
+<a name="9323"><span class="lineNum">    9323 </span><span class="lineCov">    1670391 :         if (z__[k] &lt; 0.) {</span></a>
+<a name="9324"><span class="lineNum">    9324 </span><span class="lineNoCov">          0 :             *info = -(k + 200);</span></a>
+<a name="9325"><span class="lineNum">    9325 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="9326"><span class="lineNum">    9326 </span><span class="lineCov">    1670391 :         } else if (z__[k + 1] &lt; 0.) {</span></a>
+<a name="9327"><span class="lineNum">    9327 </span><span class="lineNoCov">          0 :             *info = -(k + 201);</span></a>
+<a name="9328"><span class="lineNum">    9328 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="9329"><span class="lineNum">    9329 </span>            :         }</a>
+<a name="9330"><span class="lineNum">    9330 </span><span class="lineCov">    1670391 :         d__ += z__[k];</span></a>
+<a name="9331"><span class="lineNum">    9331 </span><span class="lineCov">    1670391 :         e += z__[k + 1];</span></a>
+<a name="9332"><span class="lineNum">    9332 </span><span class="lineCov">    1670391 :         d__1 = qmax, d__2 = z__[k];</span></a>
+<a name="9333"><span class="lineNum">    9333 </span><span class="lineCov">    1670391 :         qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9334"><span class="lineNum">    9334 </span>            :         d__1 = emin, d__2 = z__[k + 1];</a>
+<a name="9335"><span class="lineNum">    9335 </span><span class="lineCov">    1670391 :         emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9336"><span class="lineNum">    9336 </span><span class="lineCov">    1670391 :         d__1 = (qmax&gt;zmax) ? qmax : zmax;</span></a>
+<a name="9337"><span class="lineNum">    9337 </span>            :         d__2 = z__[k + 1];</a>
+<a name="9338"><span class="lineNum">    9338 </span><span class="lineCov">    1670391 :         zmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9339"><span class="lineNum">    9339 </span>            :     }</a>
+<a name="9340"><span class="lineNum">    9340 </span><span class="lineCov">     556647 :     if (z__[(*n &lt;&lt; 1) - 1] &lt; 0.) {</span></a>
+<a name="9341"><span class="lineNum">    9341 </span><span class="lineNoCov">          0 :         *info = -((*n &lt;&lt; 1) + 199);</span></a>
+<a name="9342"><span class="lineNum">    9342 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="9343"><span class="lineNum">    9343 </span>            :     }</a>
+<a name="9344"><span class="lineNum">    9344 </span><span class="lineCov">     556647 :     d__ += z__[(*n &lt;&lt; 1) - 1];</span></a>
+<a name="9345"><span class="lineNum">    9345 </span><span class="lineCov">     556647 :     d__1 = qmax, d__2 = z__[(*n &lt;&lt; 1) - 1];</span></a>
+<a name="9346"><span class="lineNum">    9346 </span><span class="lineCov">     556658 :     qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9347"><span class="lineNum">    9347 </span>            : </a>
+<a name="9348"><span class="lineNum">    9348 </span><span class="lineCov">     556647 :     if (std::abs(e)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="9349"><span class="lineNum">    9349 </span>            :         i__1 = *n;</a>
+<a name="9350"><span class="lineNum">    9350 </span><span class="lineNoCov">          0 :         for (k = 2; k &lt;= i__1; ++k) {</span></a>
+<a name="9351"><span class="lineNum">    9351 </span><span class="lineNoCov">          0 :             z__[k] = z__[(k &lt;&lt; 1) - 1];</span></a>
+<a name="9352"><span class="lineNum">    9352 </span>            :         }</a>
+<a name="9353"><span class="lineNum">    9353 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(&quot;D&quot;, n, &amp;z__[1], &amp;iinfo);</span></a>
+<a name="9354"><span class="lineNum">    9354 </span><span class="lineNoCov">          0 :         z__[(*n &lt;&lt; 1) - 1] = d__;</span></a>
+<a name="9355"><span class="lineNum">    9355 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="9356"><span class="lineNum">    9356 </span>            :     }</a>
+<a name="9357"><span class="lineNum">    9357 </span>            : </a>
+<a name="9358"><span class="lineNum">    9358 </span><span class="lineCov">     556647 :     trace = d__ + e;</span></a>
+<a name="9359"><span class="lineNum">    9359 </span>            : </a>
+<a name="9360"><span class="lineNum">    9360 </span><span class="lineCov">     556647 :     if (std::abs(trace)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="9361"><span class="lineNum">    9361 </span><span class="lineNoCov">          0 :         z__[(*n &lt;&lt; 1) - 1] = 0.;</span></a>
+<a name="9362"><span class="lineNum">    9362 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="9363"><span class="lineNum">    9363 </span>            :     }</a>
+<a name="9364"><span class="lineNum">    9364 </span>            : </a>
+<a name="9365"><span class="lineNum">    9365 </span><span class="lineCov">     556647 :     ieee = 1;</span></a>
+<a name="9366"><span class="lineNum">    9366 </span><span class="lineCov">     556647 :     posinf = one/zero;</span></a>
+<a name="9367"><span class="lineNum">    9367 </span><span class="lineCov">     556647 :     if(posinf&lt;=1.0)</span></a>
+<a name="9368"><span class="lineNum">    9368 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9369"><span class="lineNum">    9369 </span>            :     neginf = -one/zero;</a>
+<a name="9370"><span class="lineNum">    9370 </span><span class="lineCov">     556647 :     if(neginf&gt;=0.0)</span></a>
+<a name="9371"><span class="lineNum">    9371 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9372"><span class="lineNum">    9372 </span><span class="lineCov">     556647 :     negzro = one/(neginf+one);</span></a>
+<a name="9373"><span class="lineNum">    9373 </span><span class="lineCov">     556647 :     if(std::abs(negzro)&gt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="9374"><span class="lineNum">    9374 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9375"><span class="lineNum">    9375 </span><span class="lineCov">     556647 :     neginf = one/negzro;</span></a>
+<a name="9376"><span class="lineNum">    9376 </span><span class="lineCov">     556647 :     if(neginf&gt;=0)</span></a>
+<a name="9377"><span class="lineNum">    9377 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9378"><span class="lineNum">    9378 </span><span class="lineCov">     556647 :     newzro = negzro + zero;</span></a>
+<a name="9379"><span class="lineNum">    9379 </span><span class="lineCov">     556647 :     if(std::abs(newzro-zero)&gt;PLUMED_GMX_DOUBLE_MIN)</span></a>
+<a name="9380"><span class="lineNum">    9380 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9381"><span class="lineNum">    9381 </span><span class="lineCov">     556647 :     posinf = one /newzro;</span></a>
+<a name="9382"><span class="lineNum">    9382 </span><span class="lineCov">     556647 :     if(posinf&lt;=one)</span></a>
+<a name="9383"><span class="lineNum">    9383 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9384"><span class="lineNum">    9384 </span><span class="lineCov">     556647 :     neginf = neginf*posinf;</span></a>
+<a name="9385"><span class="lineNum">    9385 </span><span class="lineCov">     556647 :     if(neginf&gt;=zero)</span></a>
+<a name="9386"><span class="lineNum">    9386 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9387"><span class="lineNum">    9387 </span><span class="lineCov">     556647 :     posinf = posinf*posinf;</span></a>
+<a name="9388"><span class="lineNum">    9388 </span><span class="lineCov">     556647 :     if(posinf&lt;=1.0)</span></a>
+<a name="9389"><span class="lineNum">    9389 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="9390"><span class="lineNum">    9390 </span>            : </a>
+<a name="9391"><span class="lineNum">    9391 </span><span class="lineCov">    2783685 :     for (k = *n &lt;&lt; 1; k &gt;= 2; k += -2) {</span></a>
+<a name="9392"><span class="lineNum">    9392 </span><span class="lineCov">    2227038 :         z__[k * 2] = 0.;</span></a>
+<a name="9393"><span class="lineNum">    9393 </span><span class="lineCov">    2227038 :         z__[(k &lt;&lt; 1) - 1] = z__[k];</span></a>
+<a name="9394"><span class="lineNum">    9394 </span><span class="lineCov">    2227038 :         z__[(k &lt;&lt; 1) - 2] = 0.;</span></a>
+<a name="9395"><span class="lineNum">    9395 </span><span class="lineCov">    2227038 :         z__[(k &lt;&lt; 1) - 3] = z__[k - 1];</span></a>
+<a name="9396"><span class="lineNum">    9396 </span>            :     }</a>
+<a name="9397"><span class="lineNum">    9397 </span>            : </a>
+<a name="9398"><span class="lineNum">    9398 </span><span class="lineCov">     556647 :     i0 = 1;</span></a>
+<a name="9399"><span class="lineNum">    9399 </span><span class="lineCov">     556647 :     n0 = *n;</span></a>
+<a name="9400"><span class="lineNum">    9400 </span>            : </a>
+<a name="9401"><span class="lineNum">    9401 </span><span class="lineCov">     556647 :     if (z__[(i0 &lt;&lt; 2) - 3] * 1.5 &lt; z__[(n0 &lt;&lt; 2) - 3]) {</span></a>
+<a name="9402"><span class="lineNum">    9402 </span><span class="lineCov">        121 :         ipn4 = 4*(i0 + n0);</span></a>
+<a name="9403"><span class="lineNum">    9403 </span><span class="lineCov">        121 :         i__1 = 2*(i0 + n0 - 1);</span></a>
+<a name="9404"><span class="lineNum">    9404 </span><span class="lineCov">        362 :         for (i4 = i0 &lt;&lt; 2; i4 &lt;= i__1; i4 += 4) {</span></a>
+<a name="9405"><span class="lineNum">    9405 </span><span class="lineCov">        241 :             temp = z__[i4 - 3];</span></a>
+<a name="9406"><span class="lineNum">    9406 </span><span class="lineCov">        241 :             z__[i4 - 3] = z__[ipn4 - i4 - 3];</span></a>
+<a name="9407"><span class="lineNum">    9407 </span><span class="lineCov">        241 :             z__[ipn4 - i4 - 3] = temp;</span></a>
+<a name="9408"><span class="lineNum">    9408 </span><span class="lineCov">        241 :             temp = z__[i4 - 1];</span></a>
+<a name="9409"><span class="lineNum">    9409 </span><span class="lineCov">        241 :             z__[i4 - 1] = z__[ipn4 - i4 - 5];</span></a>
+<a name="9410"><span class="lineNum">    9410 </span><span class="lineCov">        241 :             z__[ipn4 - i4 - 5] = temp;</span></a>
+<a name="9411"><span class="lineNum">    9411 </span>            :         }</a>
+<a name="9412"><span class="lineNum">    9412 </span>            :     }</a>
+<a name="9413"><span class="lineNum">    9413 </span>            : </a>
+<a name="9414"><span class="lineNum">    9414 </span><span class="lineCov">     556647 :     pp = 0;</span></a>
+<a name="9415"><span class="lineNum">    9415 </span>            : </a>
+<a name="9416"><span class="lineNum">    9416 </span><span class="lineCov">    1669941 :     for (k = 1; k &lt;= 2; ++k) {</span></a>
+<a name="9417"><span class="lineNum">    9417 </span>            : </a>
+<a name="9418"><span class="lineNum">    9418 </span><span class="lineCov">    1113294 :         d__ = z__[(n0 &lt;&lt; 2) + pp - 3];</span></a>
+<a name="9419"><span class="lineNum">    9419 </span><span class="lineCov">    1113294 :         i__1 = (i0 &lt;&lt; 2) + pp;</span></a>
+<a name="9420"><span class="lineNum">    9420 </span><span class="lineCov">    4454076 :         for (i4 = 4*(n0 - 1) + pp; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="9421"><span class="lineNum">    9421 </span><span class="lineCov">    3340782 :             if (z__[i4 - 1] &lt;= tol2 * d__) {</span></a>
+<a name="9422"><span class="lineNum">    9422 </span><span class="lineCov">          4 :                 z__[i4 - 1] = -0.;</span></a>
+<a name="9423"><span class="lineNum">    9423 </span><span class="lineCov">          4 :                 d__ = z__[i4 - 3];</span></a>
+<a name="9424"><span class="lineNum">    9424 </span>            :             } else {</a>
+<a name="9425"><span class="lineNum">    9425 </span><span class="lineCov">    3340778 :                 d__ = z__[i4 - 3] * (d__ / (d__ + z__[i4 - 1]));</span></a>
+<a name="9426"><span class="lineNum">    9426 </span>            :             }</a>
+<a name="9427"><span class="lineNum">    9427 </span>            :         }</a>
+<a name="9428"><span class="lineNum">    9428 </span>            : </a>
+<a name="9429"><span class="lineNum">    9429 </span><span class="lineCov">    1113294 :         emin = z__[(i0 &lt;&lt; 2) + pp + 1];</span></a>
+<a name="9430"><span class="lineNum">    9430 </span><span class="lineCov">    1113294 :         d__ = z__[(i0 &lt;&lt; 2) + pp - 3];</span></a>
+<a name="9431"><span class="lineNum">    9431 </span>            :         i__1 = 4*(n0 - 1) + pp;</a>
+<a name="9432"><span class="lineNum">    9432 </span><span class="lineCov">    4454076 :         for (i4 = (i0 &lt;&lt; 2) + pp; i4 &lt;= i__1; i4 += 4) {</span></a>
+<a name="9433"><span class="lineNum">    9433 </span><span class="lineCov">    3340782 :             z__[i4 - (pp &lt;&lt; 1) - 2] = d__ + z__[i4 - 1];</span></a>
+<a name="9434"><span class="lineNum">    9434 </span><span class="lineCov">    3340782 :             if (z__[i4 - 1] &lt;= tol2 * d__) {</span></a>
+<a name="9435"><span class="lineNum">    9435 </span><span class="lineCov">         23 :                 z__[i4 - 1] = -0.;</span></a>
+<a name="9436"><span class="lineNum">    9436 </span><span class="lineCov">         23 :                 z__[i4 - (pp &lt;&lt; 1) - 2] = d__;</span></a>
+<a name="9437"><span class="lineNum">    9437 </span><span class="lineCov">         23 :                 z__[i4 - (pp &lt;&lt; 1)] = 0.;</span></a>
+<a name="9438"><span class="lineNum">    9438 </span><span class="lineCov">         23 :                 d__ = z__[i4 + 1];</span></a>
+<a name="9439"><span class="lineNum">    9439 </span><span class="lineCov">    3340759 :             } else if (safmin * z__[i4 + 1] &lt; z__[i4 - (pp &lt;&lt; 1) - 2] &amp;&amp; </span></a>
+<a name="9440"><span class="lineNum">    9440 </span><span class="lineCov">    3340759 :                     safmin * z__[i4 - (pp &lt;&lt; 1) - 2] &lt; z__[i4 + 1]) {</span></a>
+<a name="9441"><span class="lineNum">    9441 </span><span class="lineCov">    3340755 :                 temp = z__[i4 + 1] / z__[i4 - (pp &lt;&lt; 1) - 2];</span></a>
+<a name="9442"><span class="lineNum">    9442 </span><span class="lineCov">    3340755 :                 z__[i4 - (pp &lt;&lt; 1)] = z__[i4 - 1] * temp;</span></a>
+<a name="9443"><span class="lineNum">    9443 </span><span class="lineCov">    3340755 :                 d__ *= temp;</span></a>
+<a name="9444"><span class="lineNum">    9444 </span>            :             } else {</a>
+<a name="9445"><span class="lineNum">    9445 </span><span class="lineCov">          4 :                 z__[i4 - (pp &lt;&lt; 1)] = z__[i4 + 1] * (z__[i4 - 1] / z__[i4 - (</span></a>
+<a name="9446"><span class="lineNum">    9446 </span>            :                         pp &lt;&lt; 1) - 2]);</a>
+<a name="9447"><span class="lineNum">    9447 </span><span class="lineCov">          4 :                 d__ = z__[i4 + 1] * (d__ / z__[i4 - (pp &lt;&lt; 1) - 2]);</span></a>
+<a name="9448"><span class="lineNum">    9448 </span>            :             }</a>
+<a name="9449"><span class="lineNum">    9449 </span><span class="lineCov">    3340782 :             d__1 = emin, d__2 = z__[i4 - (pp &lt;&lt; 1)];</span></a>
+<a name="9450"><span class="lineNum">    9450 </span><span class="lineCov">    3340782 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9451"><span class="lineNum">    9451 </span>            :         }</a>
+<a name="9452"><span class="lineNum">    9452 </span><span class="lineCov">    1113294 :         z__[(n0 &lt;&lt; 2) - pp - 2] = d__;</span></a>
+<a name="9453"><span class="lineNum">    9453 </span>            : </a>
+<a name="9454"><span class="lineNum">    9454 </span>            : </a>
+<a name="9455"><span class="lineNum">    9455 </span><span class="lineCov">    1113294 :         qmax = z__[(i0 &lt;&lt; 2) - pp - 2];</span></a>
+<a name="9456"><span class="lineNum">    9456 </span><span class="lineCov">    1113294 :         i__1 = (n0 &lt;&lt; 2) - pp - 2;</span></a>
+<a name="9457"><span class="lineNum">    9457 </span><span class="lineCov">    4454076 :         for (i4 = (i0 &lt;&lt; 2) - pp + 2; i4 &lt;= i__1; i4 += 4) {</span></a>
+<a name="9458"><span class="lineNum">    9458 </span><span class="lineCov">    3340782 :             d__1 = qmax, d__2 = z__[i4];</span></a>
+<a name="9459"><span class="lineNum">    9459 </span><span class="lineCov">    4475369 :             qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9460"><span class="lineNum">    9460 </span>            :         }</a>
+<a name="9461"><span class="lineNum">    9461 </span>            : </a>
+<a name="9462"><span class="lineNum">    9462 </span><span class="lineCov">    1113294 :         pp = 1 - pp;</span></a>
+<a name="9463"><span class="lineNum">    9463 </span>            :     }</a>
+<a name="9464"><span class="lineNum">    9464 </span>            : </a>
+<a name="9465"><span class="lineNum">    9465 </span><span class="lineCov">     556647 :     iter = 2;</span></a>
+<a name="9466"><span class="lineNum">    9466 </span><span class="lineCov">     556647 :     nfail = 0;</span></a>
+<a name="9467"><span class="lineNum">    9467 </span><span class="lineCov">     556647 :     ndiv = 2*(n0 - i0);</span></a>
+<a name="9468"><span class="lineNum">    9468 </span>            : </a>
+<a name="9469"><span class="lineNum">    9469 </span><span class="lineCov">     556647 :     i__1 = *n + 1;</span></a>
+<a name="9470"><span class="lineNum">    9470 </span><span class="lineCov">    1113433 :     for (iwhila = 1; iwhila &lt;= i__1; ++iwhila) {</span></a>
+<a name="9471"><span class="lineNum">    9471 </span><span class="lineCov">    1113433 :         if (n0 &lt; 1) {</span></a>
+<a name="9472"><span class="lineNum">    9472 </span><span class="lineCov">     556647 :             goto L170;</span></a>
+<a name="9473"><span class="lineNum">    9473 </span>            :         }</a>
+<a name="9474"><span class="lineNum">    9474 </span>            : </a>
+<a name="9475"><span class="lineNum">    9475 </span><span class="lineCov">     556786 :         desig = 0.;</span></a>
+<a name="9476"><span class="lineNum">    9476 </span><span class="lineCov">     556786 :         if (n0 == *n) {</span></a>
+<a name="9477"><span class="lineNum">    9477 </span><span class="lineCov">     556647 :             sigma = 0.;</span></a>
+<a name="9478"><span class="lineNum">    9478 </span>            :         } else {</a>
+<a name="9479"><span class="lineNum">    9479 </span><span class="lineCov">        139 :             sigma = -z__[(n0 &lt;&lt; 2) - 1];</span></a>
+<a name="9480"><span class="lineNum">    9480 </span>            :         }</a>
+<a name="9481"><span class="lineNum">    9481 </span><span class="lineCov">     556786 :         if (sigma &lt; 0.) {</span></a>
+<a name="9482"><span class="lineNum">    9482 </span><span class="lineNoCov">          0 :             *info = 1;</span></a>
+<a name="9483"><span class="lineNum">    9483 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="9484"><span class="lineNum">    9484 </span>            :         }</a>
+<a name="9485"><span class="lineNum">    9485 </span>            : </a>
+<a name="9486"><span class="lineNum">    9486 </span>            :         emax = 0.;</a>
+<a name="9487"><span class="lineNum">    9487 </span><span class="lineCov">     556786 :         if (n0 &gt; i0) {</span></a>
+<a name="9488"><span class="lineNum">    9488 </span><span class="lineCov">     556647 :             emin = std::abs(z__[(n0 &lt;&lt; 2) - 5]);</span></a>
+<a name="9489"><span class="lineNum">    9489 </span>            :         } else {</a>
+<a name="9490"><span class="lineNum">    9490 </span>            :             emin = 0.;</a>
+<a name="9491"><span class="lineNum">    9491 </span>            :         }</a>
+<a name="9492"><span class="lineNum">    9492 </span><span class="lineCov">     556786 :         qmin = z__[(n0 &lt;&lt; 2) - 3];</span></a>
+<a name="9493"><span class="lineNum">    9493 </span><span class="lineCov">     556786 :         qmax = qmin;</span></a>
+<a name="9494"><span class="lineNum">    9494 </span><span class="lineCov">    2232257 :         for (i4 = n0 &lt;&lt; 2; i4 &gt;= 8; i4 += -4) {</span></a>
+<a name="9495"><span class="lineNum">    9495 </span><span class="lineCov">    1675584 :             if (z__[i4 - 5] &lt;= 0.) {</span></a>
+<a name="9496"><span class="lineNum">    9496 </span><span class="lineCov">        113 :                 goto L100;</span></a>
+<a name="9497"><span class="lineNum">    9497 </span>            :             }</a>
+<a name="9498"><span class="lineNum">    9498 </span><span class="lineCov">    1675471 :             if (qmin &gt;= emax * 4.) {</span></a>
+<a name="9499"><span class="lineNum">    9499 </span><span class="lineCov">    1116327 :                 d__1 = qmin, d__2 = z__[i4 - 3];</span></a>
+<a name="9500"><span class="lineNum">    9500 </span><span class="lineCov">    1116327 :                 qmin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9501"><span class="lineNum">    9501 </span>            :                 d__1 = emax, d__2 = z__[i4 - 5];</a>
+<a name="9502"><span class="lineNum">    9502 </span><span class="lineCov">    1116327 :                 emax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9503"><span class="lineNum">    9503 </span>            :             }</a>
+<a name="9504"><span class="lineNum">    9504 </span><span class="lineCov">    1675471 :             d__1 = qmax, d__2 = z__[i4 - 7] + z__[i4 - 5];</span></a>
+<a name="9505"><span class="lineNum">    9505 </span><span class="lineCov">    1675471 :             qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9506"><span class="lineNum">    9506 </span>            :             d__1 = emin, d__2 = z__[i4 - 5];</a>
+<a name="9507"><span class="lineNum">    9507 </span><span class="lineCov">    1675471 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9508"><span class="lineNum">    9508 </span>            :         }</a>
+<a name="9509"><span class="lineNum">    9509 </span>            :         i4 = 4;</a>
+<a name="9510"><span class="lineNum">    9510 </span>            : </a>
+<a name="9511"><span class="lineNum">    9511 </span><span class="lineCov">     556786 : L100:</span></a>
+<a name="9512"><span class="lineNum">    9512 </span><span class="lineCov">     556786 :         i0 = i4 / 4;</span></a>
+<a name="9513"><span class="lineNum">    9513 </span><span class="lineCov">     556786 :         pp = 0;</span></a>
+<a name="9514"><span class="lineNum">    9514 </span>            : </a>
+<a name="9515"><span class="lineNum">    9515 </span><span class="lineCov">     556786 :         if (n0 - i0 &gt; 1) {</span></a>
+<a name="9516"><span class="lineNum">    9516 </span><span class="lineCov">     556742 :             dee = z__[(i0 &lt;&lt; 2) - 3];</span></a>
+<a name="9517"><span class="lineNum">    9517 </span>            :             deemin = dee;</a>
+<a name="9518"><span class="lineNum">    9518 </span>            :             kmin = i0;</a>
+<a name="9519"><span class="lineNum">    9519 </span><span class="lineCov">     556742 :             i__2 = (n0 &lt;&lt; 2) - 3;</span></a>
+<a name="9520"><span class="lineNum">    9520 </span><span class="lineCov">    2788949 :             for (i4 = (i0 &lt;&lt; 2) - 3; i4 &lt;= i__2; i4 += 4) {</span></a>
+<a name="9521"><span class="lineNum">    9521 </span><span class="lineCov">    2232207 :                 dee = z__[i4] * (dee / (dee + z__[i4 - 2]));</span></a>
+<a name="9522"><span class="lineNum">    9522 </span><span class="lineCov">    2232207 :                 if (dee &lt;= deemin) {</span></a>
+<a name="9523"><span class="lineNum">    9523 </span>            :                     deemin = dee;</a>
+<a name="9524"><span class="lineNum">    9524 </span><span class="lineCov">    1206053 :                     kmin = (i4 + 3) / 4;</span></a>
+<a name="9525"><span class="lineNum">    9525 </span>            :                 }</a>
+<a name="9526"><span class="lineNum">    9526 </span>            :             }</a>
+<a name="9527"><span class="lineNum">    9527 </span><span class="lineCov">     556742 :             if (2*(kmin - i0) &lt; n0 - kmin &amp;&amp; deemin &lt;= z__[(n0 &lt;&lt; 2) - 3] * </span></a>
+<a name="9528"><span class="lineNum">    9528 </span>            :                     .5) {</a>
+<a name="9529"><span class="lineNum">    9529 </span><span class="lineCov">       7987 :                 ipn4 = 4*(i0 + n0);</span></a>
+<a name="9530"><span class="lineNum">    9530 </span><span class="lineCov">       7987 :                 pp = 2;</span></a>
+<a name="9531"><span class="lineNum">    9531 </span><span class="lineCov">       7987 :                 i__2 = 2*(i0 + n0 - 1);</span></a>
+<a name="9532"><span class="lineNum">    9532 </span><span class="lineCov">      25756 :                 for (i4 = i0 &lt;&lt; 2; i4 &lt;= i__2; i4 += 4) {</span></a>
+<a name="9533"><span class="lineNum">    9533 </span><span class="lineCov">      17769 :                     temp = z__[i4 - 3];</span></a>
+<a name="9534"><span class="lineNum">    9534 </span><span class="lineCov">      17769 :                     z__[i4 - 3] = z__[ipn4 - i4 - 3];</span></a>
+<a name="9535"><span class="lineNum">    9535 </span><span class="lineCov">      17769 :                     z__[ipn4 - i4 - 3] = temp;</span></a>
+<a name="9536"><span class="lineNum">    9536 </span><span class="lineCov">      17769 :                     temp = z__[i4 - 2];</span></a>
+<a name="9537"><span class="lineNum">    9537 </span><span class="lineCov">      17769 :                     z__[i4 - 2] = z__[ipn4 - i4 - 2];</span></a>
+<a name="9538"><span class="lineNum">    9538 </span><span class="lineCov">      17769 :                     z__[ipn4 - i4 - 2] = temp;</span></a>
+<a name="9539"><span class="lineNum">    9539 </span><span class="lineCov">      17769 :                     temp = z__[i4 - 1];</span></a>
+<a name="9540"><span class="lineNum">    9540 </span><span class="lineCov">      17769 :                     z__[i4 - 1] = z__[ipn4 - i4 - 5];</span></a>
+<a name="9541"><span class="lineNum">    9541 </span><span class="lineCov">      17769 :                     z__[ipn4 - i4 - 5] = temp;</span></a>
+<a name="9542"><span class="lineNum">    9542 </span><span class="lineCov">      17769 :                     temp = z__[i4];</span></a>
+<a name="9543"><span class="lineNum">    9543 </span><span class="lineCov">      17769 :                     z__[i4] = z__[ipn4 - i4 - 4];</span></a>
+<a name="9544"><span class="lineNum">    9544 </span><span class="lineCov">      17769 :                     z__[ipn4 - i4 - 4] = temp;</span></a>
+<a name="9545"><span class="lineNum">    9545 </span>            :                 }</a>
+<a name="9546"><span class="lineNum">    9546 </span>            :             }</a>
+<a name="9547"><span class="lineNum">    9547 </span>            :         }</a>
+<a name="9548"><span class="lineNum">    9548 </span>            : </a>
+<a name="9549"><span class="lineNum">    9549 </span>            : </a>
+<a name="9550"><span class="lineNum">    9550 </span><span class="lineCov">     556786 :         d__1 = 0., d__2 = qmin -  std::sqrt(qmin) * 2. * std::sqrt(emax);</span></a>
+<a name="9551"><span class="lineNum">    9551 </span><span class="lineCov">     556786 :         dmin__ = -((d__1&gt;d__2) ? d__1 : d__2);</span></a>
+<a name="9552"><span class="lineNum">    9552 </span>            : </a>
+<a name="9553"><span class="lineNum">    9553 </span><span class="lineCov">     556786 :         nbig = (n0 - i0 + 1) * 30;</span></a>
+<a name="9554"><span class="lineNum">    9554 </span>            :         i__2 = nbig;</a>
+<a name="9555"><span class="lineNum">    9555 </span><span class="lineCov">   13682334 :         for (iwhilb = 1; iwhilb &lt;= i__2; ++iwhilb) {</span></a>
+<a name="9556"><span class="lineNum">    9556 </span><span class="lineCov">   13682334 :             if (i0 &gt; n0) {</span></a>
+<a name="9557"><span class="lineNum">    9557 </span><span class="lineCov">     556786 :                 goto L150;</span></a>
+<a name="9558"><span class="lineNum">    9558 </span>            :             }</a>
+<a name="9559"><span class="lineNum">    9559 </span>            : </a>
+<a name="9560"><span class="lineNum">    9560 </span><span class="lineCov">   13125548 :             PLUMED_BLAS_F77_FUNC(dlasq3,DLASQ3)(&amp;i0, &amp;n0, &amp;z__[1], &amp;pp, &amp;dmin__, &amp;sigma, &amp;desig, &amp;qmax, &amp;</span></a>
+<a name="9561"><span class="lineNum">    9561 </span>            :                     nfail, &amp;iter, &amp;ndiv, &amp;ieee);</a>
+<a name="9562"><span class="lineNum">    9562 </span>            : </a>
+<a name="9563"><span class="lineNum">    9563 </span><span class="lineCov">   13125548 :             pp = 1 - pp;</span></a>
+<a name="9564"><span class="lineNum">    9564 </span>            : </a>
+<a name="9565"><span class="lineNum">    9565 </span><span class="lineCov">   13125548 :             if (pp == 0 &amp;&amp; n0 - i0 &gt;= 3) {</span></a>
+<a name="9566"><span class="lineNum">    9566 </span><span class="lineCov">     162508 :                 if (z__[n0 * 4] &lt;= tol2 * qmax || z__[(n0 &lt;&lt; 2) - 1] &lt;= tol2 *</span></a>
+<a name="9567"><span class="lineNum">    9567 </span>            :                          sigma) {</a>
+<a name="9568"><span class="lineNum">    9568 </span><span class="lineCov">        301 :                     splt = i0 - 1;</span></a>
+<a name="9569"><span class="lineNum">    9569 </span><span class="lineCov">        301 :                     qmax = z__[(i0 &lt;&lt; 2) - 3];</span></a>
+<a name="9570"><span class="lineNum">    9570 </span><span class="lineCov">        301 :                     emin = z__[(i0 &lt;&lt; 2) - 1];</span></a>
+<a name="9571"><span class="lineNum">    9571 </span><span class="lineCov">        301 :                     oldemn = z__[i0 * 4];</span></a>
+<a name="9572"><span class="lineNum">    9572 </span><span class="lineCov">        301 :                     i__3 = 4*(n0 - 3);</span></a>
+<a name="9573"><span class="lineNum">    9573 </span><span class="lineCov">      41906 :                     for (i4 = i0 &lt;&lt; 2; i4 &lt;= i__3; i4 += 4) {</span></a>
+<a name="9574"><span class="lineNum">    9574 </span><span class="lineCov">      41605 :                         if (z__[i4] &lt;= tol2 * z__[i4 - 3] || z__[i4 - 1] &lt;= </span></a>
+<a name="9575"><span class="lineNum">    9575 </span><span class="lineCov">      41576 :                                 tol2 * sigma) {</span></a>
+<a name="9576"><span class="lineNum">    9576 </span><span class="lineCov">        116 :                             z__[i4 - 1] = -sigma;</span></a>
+<a name="9577"><span class="lineNum">    9577 </span><span class="lineCov">        116 :                             splt = i4 / 4;</span></a>
+<a name="9578"><span class="lineNum">    9578 </span><span class="lineCov">        116 :                             qmax = 0.;</span></a>
+<a name="9579"><span class="lineNum">    9579 </span><span class="lineCov">        116 :                             emin = z__[i4 + 3];</span></a>
+<a name="9580"><span class="lineNum">    9580 </span><span class="lineCov">        116 :                             oldemn = z__[i4 + 4];</span></a>
+<a name="9581"><span class="lineNum">    9581 </span>            :                         } else {</a>
+<a name="9582"><span class="lineNum">    9582 </span><span class="lineCov">      41489 :                             d__1 = qmax, d__2 = z__[i4 + 1];</span></a>
+<a name="9583"><span class="lineNum">    9583 </span><span class="lineCov">      41489 :                             qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9584"><span class="lineNum">    9584 </span>            :                             d__1 = emin, d__2 = z__[i4 - 1];</a>
+<a name="9585"><span class="lineNum">    9585 </span><span class="lineCov">      41489 :                             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9586"><span class="lineNum">    9586 </span>            :                             d__1 = oldemn, d__2 = z__[i4];</a>
+<a name="9587"><span class="lineNum">    9587 </span><span class="lineCov">      41489 :                             oldemn = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9588"><span class="lineNum">    9588 </span>            :                         }</a>
+<a name="9589"><span class="lineNum">    9589 </span>            :                     }</a>
+<a name="9590"><span class="lineNum">    9590 </span><span class="lineCov">        301 :                     z__[(n0 &lt;&lt; 2) - 1] = emin;</span></a>
+<a name="9591"><span class="lineNum">    9591 </span><span class="lineCov">        301 :                     z__[n0 * 4] = oldemn;</span></a>
+<a name="9592"><span class="lineNum">    9592 </span><span class="lineCov">        301 :                     i0 = splt + 1;</span></a>
+<a name="9593"><span class="lineNum">    9593 </span>            :                 }</a>
+<a name="9594"><span class="lineNum">    9594 </span>            :             }</a>
+<a name="9595"><span class="lineNum">    9595 </span>            :         }</a>
+<a name="9596"><span class="lineNum">    9596 </span>            : </a>
+<a name="9597"><span class="lineNum">    9597 </span><span class="lineNoCov">          0 :         *info = 2;</span></a>
+<a name="9598"><span class="lineNum">    9598 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="9599"><span class="lineNum">    9599 </span>            : </a>
+<a name="9600"><span class="lineNum">    9600 </span>            : L150:</a>
+<a name="9601"><span class="lineNum">    9601 </span>            :         ;</a>
+<a name="9602"><span class="lineNum">    9602 </span>            :     }</a>
+<a name="9603"><span class="lineNum">    9603 </span>            : </a>
+<a name="9604"><span class="lineNum">    9604 </span><span class="lineNoCov">          0 :     *info = 3;</span></a>
+<a name="9605"><span class="lineNum">    9605 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="9606"><span class="lineNum">    9606 </span>            : </a>
+<a name="9607"><span class="lineNum">    9607 </span>            : </a>
+<a name="9608"><span class="lineNum">    9608 </span>            : L170:</a>
+<a name="9609"><span class="lineNum">    9609 </span>            : </a>
+<a name="9610"><span class="lineNum">    9610 </span><span class="lineCov">     556647 :     i__1 = *n;</span></a>
+<a name="9611"><span class="lineNum">    9611 </span><span class="lineCov">    2227038 :     for (k = 2; k &lt;= i__1; ++k) {</span></a>
+<a name="9612"><span class="lineNum">    9612 </span><span class="lineCov">    1670391 :         z__[k] = z__[(k &lt;&lt; 2) - 3];</span></a>
+<a name="9613"><span class="lineNum">    9613 </span>            :     }</a>
+<a name="9614"><span class="lineNum">    9614 </span>            : </a>
+<a name="9615"><span class="lineNum">    9615 </span><span class="lineCov">     556647 :     PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(&quot;D&quot;, n, &amp;z__[1], &amp;iinfo);</span></a>
+<a name="9616"><span class="lineNum">    9616 </span>            : </a>
+<a name="9617"><span class="lineNum">    9617 </span>            :     e = 0.;</a>
+<a name="9618"><span class="lineNum">    9618 </span><span class="lineCov">    2783685 :     for (k = *n; k &gt;= 1; --k) {</span></a>
+<a name="9619"><span class="lineNum">    9619 </span><span class="lineCov">    2227038 :         e += z__[k];</span></a>
+<a name="9620"><span class="lineNum">    9620 </span>            :     }</a>
+<a name="9621"><span class="lineNum">    9621 </span>            : </a>
+<a name="9622"><span class="lineNum">    9622 </span>            : </a>
+<a name="9623"><span class="lineNum">    9623 </span><span class="lineCov">     556647 :     z__[(*n &lt;&lt; 1) + 1] = trace;</span></a>
+<a name="9624"><span class="lineNum">    9624 </span><span class="lineCov">     556647 :     z__[(*n &lt;&lt; 1) + 2] = e;</span></a>
+<a name="9625"><span class="lineNum">    9625 </span><span class="lineCov">     556647 :     z__[(*n &lt;&lt; 1) + 3] = (double) iter;</span></a>
+<a name="9626"><span class="lineNum">    9626 </span><span class="lineCov">     556647 :     i__1 = *n;</span></a>
+<a name="9627"><span class="lineNum">    9627 </span><span class="lineCov">     556647 :     z__[(*n &lt;&lt; 1) + 4] = (double) ndiv / (double) (i__1 * i__1);</span></a>
+<a name="9628"><span class="lineNum">    9628 </span><span class="lineCov">     556647 :     z__[(*n &lt;&lt; 1) + 5] = nfail * 100. / (double) iter;</span></a>
+<a name="9629"><span class="lineNum">    9629 </span>            : </a>
+<a name="9630"><span class="lineNum">    9630 </span><span class="lineCov">     556647 :     return;</span></a>
+<a name="9631"><span class="lineNum">    9631 </span>            : </a>
+<a name="9632"><span class="lineNum">    9632 </span>            : }</a>
+<a name="9633"><span class="lineNum">    9633 </span>            : </a>
+<a name="9634"><span class="lineNum">    9634 </span>            : </a>
+<a name="9635"><span class="lineNum">    9635 </span>            : </a>
+<a name="9636"><span class="lineNum">    9636 </span>            : }</a>
+<a name="9637"><span class="lineNum">    9637 </span>            : }</a>
+<a name="9638"><span class="lineNum">    9638 </span>            : #include &lt;cmath&gt;</a>
+<a name="9639"><span class="lineNum">    9639 </span>            : #include &quot;real.h&quot;</a>
+<a name="9640"><span class="lineNum">    9640 </span>            : </a>
+<a name="9641"><span class="lineNum">    9641 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="9642"><span class="lineNum">    9642 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="9643"><span class="lineNum">    9643 </span>            : </a>
+<a name="9644"><span class="lineNum">    9644 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9645"><span class="lineNum">    9645 </span>            : namespace PLMD{</a>
+<a name="9646"><span class="lineNum">    9646 </span>            : namespace lapack{</a>
+<a name="9647"><span class="lineNum">    9647 </span>            : using namespace blas;</a>
+<a name="9648"><span class="lineNum">    9648 </span>            : void</a>
+<a name="9649"><span class="lineNum">    9649 </span><span class="lineCov">   13125548 : PLUMED_BLAS_F77_FUNC(dlasq3,DLASQ3)(int *i0, </span></a>
+<a name="9650"><span class="lineNum">    9650 </span>            :                         int *n0, </a>
+<a name="9651"><span class="lineNum">    9651 </span>            :                         double *z__, </a>
+<a name="9652"><span class="lineNum">    9652 </span>            :                         int *pp, </a>
+<a name="9653"><span class="lineNum">    9653 </span>            :                         double *dmin__, </a>
+<a name="9654"><span class="lineNum">    9654 </span>            :                         double *sigma,</a>
+<a name="9655"><span class="lineNum">    9655 </span>            :                         double *desig,</a>
+<a name="9656"><span class="lineNum">    9656 </span>            :                         double *qmax, </a>
+<a name="9657"><span class="lineNum">    9657 </span>            :                         int *nfail, </a>
+<a name="9658"><span class="lineNum">    9658 </span>            :                         int *iter, </a>
+<a name="9659"><span class="lineNum">    9659 </span>            :                         int *ndiv, </a>
+<a name="9660"><span class="lineNum">    9660 </span>            :         int *ieee)</a>
+<a name="9661"><span class="lineNum">    9661 </span>            : {</a>
+<a name="9662"><span class="lineNum">    9662 </span>            : </a>
+<a name="9663"><span class="lineNum">    9663 </span><span class="lineCov">   13125548 :     int ttype = 0;</span></a>
+<a name="9664"><span class="lineNum">    9664 </span><span class="lineCov">   13125548 :     double dmin1 = 0.;</span></a>
+<a name="9665"><span class="lineNum">    9665 </span><span class="lineCov">   13125548 :     double dmin2 = 0.;</span></a>
+<a name="9666"><span class="lineNum">    9666 </span><span class="lineCov">   13125548 :     double dn = 0.;</span></a>
+<a name="9667"><span class="lineNum">    9667 </span><span class="lineCov">   13125548 :     double dn1 = 0.;</span></a>
+<a name="9668"><span class="lineNum">    9668 </span><span class="lineCov">   13125548 :     double dn2 = 0.;</span></a>
+<a name="9669"><span class="lineNum">    9669 </span><span class="lineCov">   13125548 :     double tau = 0.;</span></a>
+<a name="9670"><span class="lineNum">    9670 </span>            : </a>
+<a name="9671"><span class="lineNum">    9671 </span>            :     int i__1;</a>
+<a name="9672"><span class="lineNum">    9672 </span>            :     double d__1, d__2;</a>
+<a name="9673"><span class="lineNum">    9673 </span>            :     double s, t;</a>
+<a name="9674"><span class="lineNum">    9674 </span>            :     int j4, nn;</a>
+<a name="9675"><span class="lineNum">    9675 </span>            :     double eps, tol;</a>
+<a name="9676"><span class="lineNum">    9676 </span>            :     int n0in, ipn4;</a>
+<a name="9677"><span class="lineNum">    9677 </span>            :     double tol2, temp;</a>
+<a name="9678"><span class="lineNum">    9678 </span><span class="lineCov">   13125548 :     --z__;</span></a>
+<a name="9679"><span class="lineNum">    9679 </span>            : </a>
+<a name="9680"><span class="lineNum">    9680 </span><span class="lineCov">   13125548 :     n0in = *n0;</span></a>
+<a name="9681"><span class="lineNum">    9681 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="9682"><span class="lineNum">    9682 </span>            :     tol = eps * 100.;</a>
+<a name="9683"><span class="lineNum">    9683 </span>            :     d__1 = tol;</a>
+<a name="9684"><span class="lineNum">    9684 </span>            :     tol2 = d__1 * d__1;</a>
+<a name="9685"><span class="lineNum">    9685 </span>            : </a>
+<a name="9686"><span class="lineNum">    9686 </span>            : </a>
+<a name="9687"><span class="lineNum">    9687 </span><span class="lineCov">    1670177 : L10:</span></a>
+<a name="9688"><span class="lineNum">    9688 </span>            : </a>
+<a name="9689"><span class="lineNum">    9689 </span><span class="lineCov">   14795725 :     if (*n0 &lt; *i0) {</span></a>
+<a name="9690"><span class="lineNum">    9690 </span>            :         return;</a>
+<a name="9691"><span class="lineNum">    9691 </span>            :     }</a>
+<a name="9692"><span class="lineNum">    9692 </span><span class="lineCov">   14238939 :     if (*n0 == *i0) {</span></a>
+<a name="9693"><span class="lineNum">    9693 </span><span class="lineCov">         82 :         goto L20;</span></a>
+<a name="9694"><span class="lineNum">    9694 </span>            :     }</a>
+<a name="9695"><span class="lineNum">    9695 </span><span class="lineCov">   14238857 :     nn = (*n0 &lt;&lt; 2) + *pp;</span></a>
+<a name="9696"><span class="lineNum">    9696 </span><span class="lineCov">   14238857 :     if (*n0 == *i0 + 1) {</span></a>
+<a name="9697"><span class="lineNum">    9697 </span><span class="lineCov">     556704 :         goto L40;</span></a>
+<a name="9698"><span class="lineNum">    9698 </span>            :     }</a>
+<a name="9699"><span class="lineNum">    9699 </span>            : </a>
+<a name="9700"><span class="lineNum">    9700 </span><span class="lineCov">   13682153 :     if (z__[nn - 5] &gt; tol2 * (*sigma + z__[nn - 3]) &amp;&amp; z__[nn - (*pp &lt;&lt; 1) - </span></a>
+<a name="9701"><span class="lineNum">    9701 </span><span class="lineCov">   12568919 :             4] &gt; tol2 * z__[nn - 7]) {</span></a>
+<a name="9702"><span class="lineNum">    9702 </span><span class="lineCov">   12568919 :         goto L30;</span></a>
+<a name="9703"><span class="lineNum">    9703 </span>            :     }</a>
+<a name="9704"><span class="lineNum">    9704 </span>            : </a>
+<a name="9705"><span class="lineNum">    9705 </span><span class="lineCov">    1113234 : L20:</span></a>
+<a name="9706"><span class="lineNum">    9706 </span>            : </a>
+<a name="9707"><span class="lineNum">    9707 </span><span class="lineCov">    1113316 :     z__[(*n0 &lt;&lt; 2) - 3] = z__[(*n0 &lt;&lt; 2) + *pp - 3] + *sigma;</span></a>
+<a name="9708"><span class="lineNum">    9708 </span><span class="lineCov">    1113316 :     --(*n0);</span></a>
+<a name="9709"><span class="lineNum">    9709 </span><span class="lineCov">    1113316 :     goto L10;</span></a>
+<a name="9710"><span class="lineNum">    9710 </span>            : </a>
+<a name="9711"><span class="lineNum">    9711 </span>            : L30:</a>
+<a name="9712"><span class="lineNum">    9712 </span>            : </a>
+<a name="9713"><span class="lineNum">    9713 </span><span class="lineCov">   12568919 :     if (z__[nn - 9] &gt; tol2 * *sigma &amp;&amp; z__[nn - (*pp &lt;&lt; 1) - 8] &gt; tol2 * z__[</span></a>
+<a name="9714"><span class="lineNum">    9714 </span><span class="lineCov">   12568762 :             nn - 11]) {</span></a>
+<a name="9715"><span class="lineNum">    9715 </span><span class="lineCov">   12568762 :         goto L50;</span></a>
+<a name="9716"><span class="lineNum">    9716 </span>            :     }</a>
+<a name="9717"><span class="lineNum">    9717 </span>            : </a>
+<a name="9718"><span class="lineNum">    9718 </span><span class="lineCov">        157 : L40:</span></a>
+<a name="9719"><span class="lineNum">    9719 </span>            : </a>
+<a name="9720"><span class="lineNum">    9720 </span><span class="lineCov">     556861 :     if (z__[nn - 3] &gt; z__[nn - 7]) {</span></a>
+<a name="9721"><span class="lineNum">    9721 </span>            :         s = z__[nn - 3];</a>
+<a name="9722"><span class="lineNum">    9722 </span><span class="lineCov">      21586 :         z__[nn - 3] = z__[nn - 7];</span></a>
+<a name="9723"><span class="lineNum">    9723 </span><span class="lineCov">      21586 :         z__[nn - 7] = s;</span></a>
+<a name="9724"><span class="lineNum">    9724 </span>            :     }</a>
+<a name="9725"><span class="lineNum">    9725 </span><span class="lineCov">     556861 :     if (z__[nn - 5] &gt; z__[nn - 3] * tol2) {</span></a>
+<a name="9726"><span class="lineNum">    9726 </span><span class="lineCov">     556861 :         t = (z__[nn - 7] - z__[nn - 3] + z__[nn - 5]) * .5;</span></a>
+<a name="9727"><span class="lineNum">    9727 </span><span class="lineCov">     556861 :         s = z__[nn - 3] * (z__[nn - 5] / t);</span></a>
+<a name="9728"><span class="lineNum">    9728 </span><span class="lineCov">     556861 :         if (s &lt;= t) {</span></a>
+<a name="9729"><span class="lineNum">    9729 </span><span class="lineCov">     539402 :             s = z__[nn - 3] * (z__[nn - 5] / (t * ( std::sqrt(s / t + 1.) + 1.)));</span></a>
+<a name="9730"><span class="lineNum">    9730 </span>            :         } else {</a>
+<a name="9731"><span class="lineNum">    9731 </span><span class="lineCov">      17459 :             s = z__[nn - 3] * (z__[nn - 5] / (t +  std::sqrt(t) * std::sqrt(t + s)));</span></a>
+<a name="9732"><span class="lineNum">    9732 </span>            :         }</a>
+<a name="9733"><span class="lineNum">    9733 </span><span class="lineCov">     556861 :         t = z__[nn - 7] + (s + z__[nn - 5]);</span></a>
+<a name="9734"><span class="lineNum">    9734 </span><span class="lineCov">     556861 :         z__[nn - 3] *= z__[nn - 7] / t;</span></a>
+<a name="9735"><span class="lineNum">    9735 </span><span class="lineCov">     556861 :         z__[nn - 7] = t;</span></a>
+<a name="9736"><span class="lineNum">    9736 </span>            :     }</a>
+<a name="9737"><span class="lineNum">    9737 </span><span class="lineCov">     556861 :     z__[(*n0 &lt;&lt; 2) - 7] = z__[nn - 7] + *sigma;</span></a>
+<a name="9738"><span class="lineNum">    9738 </span><span class="lineCov">     556861 :     z__[(*n0 &lt;&lt; 2) - 3] = z__[nn - 3] + *sigma;</span></a>
+<a name="9739"><span class="lineNum">    9739 </span><span class="lineCov">     556861 :     *n0 += -2;</span></a>
+<a name="9740"><span class="lineNum">    9740 </span><span class="lineCov">     556861 :     goto L10;</span></a>
+<a name="9741"><span class="lineNum">    9741 </span>            : </a>
+<a name="9742"><span class="lineNum">    9742 </span>            : L50:</a>
+<a name="9743"><span class="lineNum">    9743 </span><span class="lineCov">   12568762 :     if (*pp == 2) {</span></a>
+<a name="9744"><span class="lineNum">    9744 </span><span class="lineCov">       7987 :         *pp = 0;</span></a>
+<a name="9745"><span class="lineNum">    9745 </span>            :     }</a>
+<a name="9746"><span class="lineNum">    9746 </span>            : </a>
+<a name="9747"><span class="lineNum">    9747 </span><span class="lineCov">   12568762 :     if (*dmin__ &lt;= 0. || *n0 &lt; n0in) {</span></a>
+<a name="9748"><span class="lineNum">    9748 </span><span class="lineCov">    1113380 :         if (z__[(*i0 &lt;&lt; 2) + *pp - 3] * 1.5 &lt; z__[(*n0 &lt;&lt; 2) + *pp - 3]) {</span></a>
+<a name="9749"><span class="lineNum">    9749 </span><span class="lineCov">     299487 :             ipn4 = 4*(*i0 + *n0);</span></a>
+<a name="9750"><span class="lineNum">    9750 </span><span class="lineCov">     299487 :             i__1 = 2*(*i0 + *n0 - 1);</span></a>
+<a name="9751"><span class="lineNum">    9751 </span><span class="lineCov">     608758 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="9752"><span class="lineNum">    9752 </span><span class="lineCov">     309271 :                 temp = z__[j4 - 3];</span></a>
+<a name="9753"><span class="lineNum">    9753 </span><span class="lineCov">     309271 :                 z__[j4 - 3] = z__[ipn4 - j4 - 3];</span></a>
+<a name="9754"><span class="lineNum">    9754 </span><span class="lineCov">     309271 :                 z__[ipn4 - j4 - 3] = temp;</span></a>
+<a name="9755"><span class="lineNum">    9755 </span><span class="lineCov">     309271 :                 temp = z__[j4 - 2];</span></a>
+<a name="9756"><span class="lineNum">    9756 </span><span class="lineCov">     309271 :                 z__[j4 - 2] = z__[ipn4 - j4 - 2];</span></a>
+<a name="9757"><span class="lineNum">    9757 </span><span class="lineCov">     309271 :                 z__[ipn4 - j4 - 2] = temp;</span></a>
+<a name="9758"><span class="lineNum">    9758 </span><span class="lineCov">     309271 :                 temp = z__[j4 - 1];</span></a>
+<a name="9759"><span class="lineNum">    9759 </span><span class="lineCov">     309271 :                 z__[j4 - 1] = z__[ipn4 - j4 - 5];</span></a>
+<a name="9760"><span class="lineNum">    9760 </span><span class="lineCov">     309271 :                 z__[ipn4 - j4 - 5] = temp;</span></a>
+<a name="9761"><span class="lineNum">    9761 </span><span class="lineCov">     309271 :                 temp = z__[j4];</span></a>
+<a name="9762"><span class="lineNum">    9762 </span><span class="lineCov">     309271 :                 z__[j4] = z__[ipn4 - j4 - 4];</span></a>
+<a name="9763"><span class="lineNum">    9763 </span><span class="lineCov">     309271 :                 z__[ipn4 - j4 - 4] = temp;</span></a>
+<a name="9764"><span class="lineNum">    9764 </span>            :             }</a>
+<a name="9765"><span class="lineNum">    9765 </span><span class="lineCov">     299487 :             if (*n0 - *i0 &lt;= 4) {</span></a>
+<a name="9766"><span class="lineNum">    9766 </span><span class="lineCov">     299438 :                 z__[(*n0 &lt;&lt; 2) + *pp - 1] = z__[(*i0 &lt;&lt; 2) + *pp - 1];</span></a>
+<a name="9767"><span class="lineNum">    9767 </span><span class="lineCov">     299438 :                 z__[(*n0 &lt;&lt; 2) - *pp] = z__[(*i0 &lt;&lt; 2) - *pp];</span></a>
+<a name="9768"><span class="lineNum">    9768 </span>            :             }</a>
+<a name="9769"><span class="lineNum">    9769 </span><span class="lineCov">     299487 :             d__1 = dmin2, d__2 = z__[(*n0 &lt;&lt; 2) + *pp - 1];</span></a>
+<a name="9770"><span class="lineNum">    9770 </span><span class="lineCov">     299487 :             dmin2 = ((d__1&lt;d__2) ? d__1 : d__2);</span></a>
+<a name="9771"><span class="lineNum">    9771 </span><span class="lineCov">     299487 :             d__1 = z__[(*n0 &lt;&lt; 2) + *pp - 1], d__2 = z__[(*i0 &lt;&lt; 2) + *pp - 1]</span></a>
+<a name="9772"><span class="lineNum">    9772 </span><span class="lineCov">     299487 :                     , d__1 = ((d__1&lt;d__2) ? d__1 : d__2), d__2 = z__[(*i0 &lt;&lt; 2) + *pp + 3];</span></a>
+<a name="9773"><span class="lineNum">    9773 </span><span class="lineCov">     299487 :             z__[(*n0 &lt;&lt; 2) + *pp - 1] = ((d__1&lt;d__2) ? d__1 : d__2);</span></a>
+<a name="9774"><span class="lineNum">    9774 </span><span class="lineCov">     299487 :             d__1 = z__[(*n0 &lt;&lt; 2) - *pp], d__2 = z__[(*i0 &lt;&lt; 2) - *pp], d__1 =</span></a>
+<a name="9775"><span class="lineNum">    9775 </span><span class="lineCov">     299487 :                      ((d__1&lt;d__2) ? d__1 : d__2), d__2 = z__[(*i0 &lt;&lt; 2) - *pp + 4];</span></a>
+<a name="9776"><span class="lineNum">    9776 </span><span class="lineCov">     299487 :             z__[(*n0 &lt;&lt; 2) - *pp] = ((d__1&lt;d__2) ? d__1 : d__2);</span></a>
+<a name="9777"><span class="lineNum">    9777 </span><span class="lineCov">     299487 :             d__1 = *qmax;</span></a>
+<a name="9778"><span class="lineNum">    9778 </span><span class="lineCov">     299487 :             d__2 = z__[(*i0 &lt;&lt; 2) + *pp - 3];</span></a>
+<a name="9779"><span class="lineNum">    9779 </span><span class="lineCov">     299487 :             d__1 = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9780"><span class="lineNum">    9780 </span><span class="lineCov">     299487 :             d__2 = z__[(*i0 &lt;&lt; 2) + *pp + 1];</span></a>
+<a name="9781"><span class="lineNum">    9781 </span><span class="lineCov">     299487 :             *qmax = ((d__1&gt;d__2) ? d__1 : d__2);</span></a>
+<a name="9782"><span class="lineNum">    9782 </span><span class="lineCov">     299487 :             *dmin__ = -0.;</span></a>
+<a name="9783"><span class="lineNum">    9783 </span>            :         }</a>
+<a name="9784"><span class="lineNum">    9784 </span>            :     }</a>
+<a name="9785"><span class="lineNum">    9785 </span>            : </a>
+<a name="9786"><span class="lineNum">    9786 </span>            : </a>
+<a name="9787"><span class="lineNum">    9787 </span><span class="lineCov">   12568762 :     PLUMED_BLAS_F77_FUNC(dlasq4,DLASQ4)(i0, n0, &amp;z__[1], pp, &amp;n0in, dmin__, &amp;dmin1, &amp;dmin2, &amp;dn, &amp;dn1, &amp;</span></a>
+<a name="9788"><span class="lineNum">    9788 </span>            :             dn2, &amp;tau, &amp;ttype);</a>
+<a name="9789"><span class="lineNum">    9789 </span>            : </a>
+<a name="9790"><span class="lineNum">    9790 </span><span class="lineCov">   12568766 : L70:</span></a>
+<a name="9791"><span class="lineNum">    9791 </span>            : </a>
+<a name="9792"><span class="lineNum">    9792 </span><span class="lineCov">   12568766 :     PLUMED_BLAS_F77_FUNC(dlasq5,DLASQ5)(i0, n0, &amp;z__[1], pp, &amp;tau, dmin__, &amp;dmin1, &amp;dmin2, &amp;dn, &amp;dn1, &amp;</span></a>
+<a name="9793"><span class="lineNum">    9793 </span>            :             dn2, ieee);</a>
+<a name="9794"><span class="lineNum">    9794 </span>            : </a>
+<a name="9795"><span class="lineNum">    9795 </span><span class="lineCov">   12568766 :     *ndiv += *n0 - *i0 + 2;</span></a>
+<a name="9796"><span class="lineNum">    9796 </span><span class="lineCov">   12568766 :     ++(*iter);</span></a>
+<a name="9797"><span class="lineNum">    9797 </span>            : </a>
+<a name="9798"><span class="lineNum">    9798 </span><span class="lineCov">   12568766 :     if (*dmin__ &gt;= 0. &amp;&amp; dmin1 &gt; 0.) {</span></a>
+<a name="9799"><span class="lineNum">    9799 </span>            : </a>
+<a name="9800"><span class="lineNum">    9800 </span><span class="lineCov">   12568762 :         goto L90;</span></a>
+<a name="9801"><span class="lineNum">    9801 </span>            : </a>
+<a name="9802"><span class="lineNum">    9802 </span><span class="lineCov">          4 :     } else if (*dmin__ &lt; 0. &amp;&amp; dmin1 &gt; 0. &amp;&amp; z__[4*(*n0 - 1) - *pp] &lt; tol *</span></a>
+<a name="9803"><span class="lineNum">    9803 </span><span class="lineCov">          6 :              (*sigma + dn1) &amp;&amp; std::abs(dn) &lt; tol * *sigma) {</span></a>
+<a name="9804"><span class="lineNum">    9804 </span>            : </a>
+<a name="9805"><span class="lineNum">    9805 </span><span class="lineNoCov">          0 :         z__[4*(*n0 - 1) - *pp + 2] = 0.;</span></a>
+<a name="9806"><span class="lineNum">    9806 </span><span class="lineNoCov">          0 :         *dmin__ = 0.;</span></a>
+<a name="9807"><span class="lineNum">    9807 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="9808"><span class="lineNum">    9808 </span><span class="lineCov">          4 :     } else if (*dmin__ &lt; 0.) {</span></a>
+<a name="9809"><span class="lineNum">    9809 </span>            : </a>
+<a name="9810"><span class="lineNum">    9810 </span><span class="lineCov">          4 :         ++(*nfail);</span></a>
+<a name="9811"><span class="lineNum">    9811 </span><span class="lineCov">          4 :         if (ttype &lt; -22) {</span></a>
+<a name="9812"><span class="lineNum">    9812 </span>            : </a>
+<a name="9813"><span class="lineNum">    9813 </span><span class="lineNoCov">          0 :             tau = 0.;</span></a>
+<a name="9814"><span class="lineNum">    9814 </span><span class="lineCov">          4 :         } else if (dmin1 &gt; 0.) {</span></a>
+<a name="9815"><span class="lineNum">    9815 </span>            : </a>
+<a name="9816"><span class="lineNum">    9816 </span><span class="lineCov">          2 :             tau = (tau + *dmin__) * (1. - eps * 2.);</span></a>
+<a name="9817"><span class="lineNum">    9817 </span><span class="lineCov">          2 :             ttype += -11;</span></a>
+<a name="9818"><span class="lineNum">    9818 </span>            :         } else {</a>
+<a name="9819"><span class="lineNum">    9819 </span>            : </a>
+<a name="9820"><span class="lineNum">    9820 </span><span class="lineCov">          2 :             tau *= .25;</span></a>
+<a name="9821"><span class="lineNum">    9821 </span><span class="lineCov">          2 :             ttype += -12;</span></a>
+<a name="9822"><span class="lineNum">    9822 </span>            :         }</a>
+<a name="9823"><span class="lineNum">    9823 </span><span class="lineCov">          4 :         goto L70;</span></a>
+<a name="9824"><span class="lineNum">    9824 </span>            :     }</a>
+<a name="9825"><span class="lineNum">    9825 </span>            :     else {</a>
+<a name="9826"><span class="lineNum">    9826 </span>            :         </a>
+<a name="9827"><span class="lineNum">    9827 </span><span class="lineNoCov">          0 :         goto L80;</span></a>
+<a name="9828"><span class="lineNum">    9828 </span>            :     }</a>
+<a name="9829"><span class="lineNum">    9829 </span>            : </a>
+<a name="9830"><span class="lineNum">    9830 </span>            : L80:</a>
+<a name="9831"><span class="lineNum">    9831 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(dlasq6,DLASQ6)(i0, n0, &amp;z__[1], pp, dmin__, &amp;dmin1, &amp;dmin2, &amp;dn, &amp;dn1, &amp;dn2);</span></a>
+<a name="9832"><span class="lineNum">    9832 </span><span class="lineNoCov">          0 :     *ndiv += *n0 - *i0 + 2;</span></a>
+<a name="9833"><span class="lineNum">    9833 </span><span class="lineNoCov">          0 :     ++(*iter);</span></a>
+<a name="9834"><span class="lineNum">    9834 </span><span class="lineNoCov">          0 :     tau = 0.;</span></a>
+<a name="9835"><span class="lineNum">    9835 </span>            : </a>
+<a name="9836"><span class="lineNum">    9836 </span><span class="lineCov">   12568762 : L90:</span></a>
+<a name="9837"><span class="lineNum">    9837 </span><span class="lineCov">   12568762 :     if (tau &lt; *sigma) {</span></a>
+<a name="9838"><span class="lineNum">    9838 </span><span class="lineCov">   10899823 :         *desig += tau;</span></a>
+<a name="9839"><span class="lineNum">    9839 </span><span class="lineCov">   10899823 :         t = *sigma + *desig;</span></a>
+<a name="9840"><span class="lineNum">    9840 </span><span class="lineCov">   10899823 :         *desig -= t - *sigma;</span></a>
+<a name="9841"><span class="lineNum">    9841 </span>            :     } else {</a>
+<a name="9842"><span class="lineNum">    9842 </span><span class="lineCov">    1668939 :         t = *sigma + tau;</span></a>
+<a name="9843"><span class="lineNum">    9843 </span><span class="lineCov">    1668939 :         *desig = *sigma - (t - tau) + *desig;</span></a>
+<a name="9844"><span class="lineNum">    9844 </span>            :     }</a>
+<a name="9845"><span class="lineNum">    9845 </span><span class="lineCov">   12568762 :     *sigma = t;</span></a>
+<a name="9846"><span class="lineNum">    9846 </span>            : </a>
+<a name="9847"><span class="lineNum">    9847 </span><span class="lineCov">   12568762 :     return;</span></a>
+<a name="9848"><span class="lineNum">    9848 </span>            : }</a>
+<a name="9849"><span class="lineNum">    9849 </span>            : }</a>
+<a name="9850"><span class="lineNum">    9850 </span>            : }</a>
+<a name="9851"><span class="lineNum">    9851 </span>            : #include &lt;cmath&gt;</a>
+<a name="9852"><span class="lineNum">    9852 </span>            : #include &quot;real.h&quot;</a>
+<a name="9853"><span class="lineNum">    9853 </span>            : </a>
+<a name="9854"><span class="lineNum">    9854 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="9855"><span class="lineNum">    9855 </span>            : </a>
+<a name="9856"><span class="lineNum">    9856 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="9857"><span class="lineNum">    9857 </span>            : namespace PLMD{</a>
+<a name="9858"><span class="lineNum">    9858 </span>            : namespace lapack{</a>
+<a name="9859"><span class="lineNum">    9859 </span>            : using namespace blas;</a>
+<a name="9860"><span class="lineNum">    9860 </span>            : void </a>
+<a name="9861"><span class="lineNum">    9861 </span><span class="lineCov">   12568762 : PLUMED_BLAS_F77_FUNC(dlasq4,DLASQ4)(int *i0, </span></a>
+<a name="9862"><span class="lineNum">    9862 </span>            :         int *n0, </a>
+<a name="9863"><span class="lineNum">    9863 </span>            :         double *z__, </a>
+<a name="9864"><span class="lineNum">    9864 </span>            :         int *pp, </a>
+<a name="9865"><span class="lineNum">    9865 </span>            :         int *n0in, </a>
+<a name="9866"><span class="lineNum">    9866 </span>            :         double *dmin__, </a>
+<a name="9867"><span class="lineNum">    9867 </span>            :         double *dmin1, </a>
+<a name="9868"><span class="lineNum">    9868 </span>            :         double *dmin2, </a>
+<a name="9869"><span class="lineNum">    9869 </span>            :         double *dn, </a>
+<a name="9870"><span class="lineNum">    9870 </span>            :         double *dn1, </a>
+<a name="9871"><span class="lineNum">    9871 </span>            :         double *dn2, </a>
+<a name="9872"><span class="lineNum">    9872 </span>            :         double *tau, </a>
+<a name="9873"><span class="lineNum">    9873 </span>            :         int *ttype)</a>
+<a name="9874"><span class="lineNum">    9874 </span>            : {</a>
+<a name="9875"><span class="lineNum">    9875 </span>            :     double g = 0.;</a>
+<a name="9876"><span class="lineNum">    9876 </span>            :     int i__1;</a>
+<a name="9877"><span class="lineNum">    9877 </span>            :     double d__1, d__2;</a>
+<a name="9878"><span class="lineNum">    9878 </span>            : </a>
+<a name="9879"><span class="lineNum">    9879 </span>            :     double s, a2, b1, b2;</a>
+<a name="9880"><span class="lineNum">    9880 </span>            :     int i4, nn, np;</a>
+<a name="9881"><span class="lineNum">    9881 </span>            :     double gam, gap1, gap2;</a>
+<a name="9882"><span class="lineNum">    9882 </span>            : </a>
+<a name="9883"><span class="lineNum">    9883 </span>            : </a>
+<a name="9884"><span class="lineNum">    9884 </span><span class="lineCov">   12568762 :     if (*dmin__ &lt;= 0.) {</span></a>
+<a name="9885"><span class="lineNum">    9885 </span><span class="lineCov">     848266 :         *tau = -(*dmin__);</span></a>
+<a name="9886"><span class="lineNum">    9886 </span><span class="lineCov">     848266 :         *ttype = -1;</span></a>
+<a name="9887"><span class="lineNum">    9887 </span><span class="lineCov">     848266 :         return;</span></a>
+<a name="9888"><span class="lineNum">    9888 </span>            :     }</a>
+<a name="9889"><span class="lineNum">    9889 </span>            : </a>
+<a name="9890"><span class="lineNum">    9890 </span>            :     s = 0.0;</a>
+<a name="9891"><span class="lineNum">    9891 </span>            : </a>
+<a name="9892"><span class="lineNum">    9892 </span><span class="lineCov">   11720496 :     nn = (*n0 &lt;&lt; 2) + *pp;</span></a>
+<a name="9893"><span class="lineNum">    9893 </span><span class="lineCov">   11720496 :     if (*n0in == *n0) {</span></a>
+<a name="9894"><span class="lineNum">    9894 </span>            : </a>
+<a name="9895"><span class="lineNum">    9895 </span><span class="lineCov">   11455382 :         if ( std::abs(*dmin__ - *dn)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin__ + *dn) ||</span></a>
+<a name="9896"><span class="lineNum">    9896 </span><span class="lineCov">   11455382 :          std::abs(*dmin__ - *dn1)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin__ + *dn1)) {</span></a>
+<a name="9897"><span class="lineNum">    9897 </span>            : </a>
+<a name="9898"><span class="lineNum">    9898 </span><span class="lineNoCov">          0 :             b1 =  std::sqrt(z__[nn - 3]) * std::sqrt(z__[nn - 5]);</span></a>
+<a name="9899"><span class="lineNum">    9899 </span><span class="lineNoCov">          0 :             b2 =  std::sqrt(z__[nn - 7]) * std::sqrt(z__[nn - 9]);</span></a>
+<a name="9900"><span class="lineNum">    9900 </span><span class="lineNoCov">          0 :             a2 = z__[nn - 7] + z__[nn - 5];</span></a>
+<a name="9901"><span class="lineNum">    9901 </span>            : </a>
+<a name="9902"><span class="lineNum">    9902 </span><span class="lineNoCov">          0 :         if ( std::abs(*dmin__ - *dn)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin__ + *dn) &amp;&amp;</span></a>
+<a name="9903"><span class="lineNum">    9903 </span><span class="lineNoCov">          0 :              std::abs(*dmin1 - *dn1)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin1 + *dn1)) {</span></a>
+<a name="9904"><span class="lineNum">    9904 </span>            : </a>
+<a name="9905"><span class="lineNum">    9905 </span><span class="lineNoCov">          0 :             gap2 = *dmin2 - a2 - *dmin2 * .25;</span></a>
+<a name="9906"><span class="lineNum">    9906 </span><span class="lineNoCov">          0 :                 if (gap2 &gt; 0. &amp;&amp; gap2 &gt; b2) {</span></a>
+<a name="9907"><span class="lineNum">    9907 </span><span class="lineNoCov">          0 :                     gap1 = a2 - *dn - b2 / gap2 * b2;</span></a>
+<a name="9908"><span class="lineNum">    9908 </span>            :                 } else {</a>
+<a name="9909"><span class="lineNum">    9909 </span><span class="lineNoCov">          0 :                     gap1 = a2 - *dn - (b1 + b2);</span></a>
+<a name="9910"><span class="lineNum">    9910 </span>            :                 }</a>
+<a name="9911"><span class="lineNum">    9911 </span><span class="lineNoCov">          0 :                 if (gap1 &gt; 0. &amp;&amp; gap1 &gt; b1) {</span></a>
+<a name="9912"><span class="lineNum">    9912 </span><span class="lineNoCov">          0 :                     d__1 = *dn - b1 / gap1 * b1, d__2 = *dmin__ * .5;</span></a>
+<a name="9913"><span class="lineNum">    9913 </span><span class="lineNoCov">          0 :                     s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9914"><span class="lineNum">    9914 </span><span class="lineNoCov">          0 :                     *ttype = -2;</span></a>
+<a name="9915"><span class="lineNum">    9915 </span>            :                 } else {</a>
+<a name="9916"><span class="lineNum">    9916 </span>            :                     s = 0.;</a>
+<a name="9917"><span class="lineNum">    9917 </span><span class="lineNoCov">          0 :                     if (*dn &gt; b1) {</span></a>
+<a name="9918"><span class="lineNum">    9918 </span><span class="lineNoCov">          0 :                         s = *dn - b1;</span></a>
+<a name="9919"><span class="lineNum">    9919 </span>            :                     }</a>
+<a name="9920"><span class="lineNum">    9920 </span><span class="lineNoCov">          0 :                     if (a2 &gt; b1 + b2) {</span></a>
+<a name="9921"><span class="lineNum">    9921 </span><span class="lineNoCov">          0 :                         d__1 = s, d__2 = a2 - (b1 + b2);</span></a>
+<a name="9922"><span class="lineNum">    9922 </span><span class="lineNoCov">          0 :                         s = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="9923"><span class="lineNum">    9923 </span>            :                     }</a>
+<a name="9924"><span class="lineNum">    9924 </span><span class="lineNoCov">          0 :                     d__1 = s, d__2 = *dmin__ * .333;</span></a>
+<a name="9925"><span class="lineNum">    9925 </span><span class="lineNoCov">          0 :                     s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="9926"><span class="lineNum">    9926 </span><span class="lineNoCov">          0 :                     *ttype = -3;</span></a>
+<a name="9927"><span class="lineNum">    9927 </span>            :                 }</a>
+<a name="9928"><span class="lineNum">    9928 </span>            :             } else {</a>
+<a name="9929"><span class="lineNum">    9929 </span>            : </a>
+<a name="9930"><span class="lineNum">    9930 </span>            : </a>
+<a name="9931"><span class="lineNum">    9931 </span><span class="lineNoCov">          0 :                 *ttype = -4;</span></a>
+<a name="9932"><span class="lineNum">    9932 </span><span class="lineNoCov">          0 :                 s = *dmin__ * .25;</span></a>
+<a name="9933"><span class="lineNum">    9933 </span><span class="lineNoCov">          0 :                 if (std::abs(*dmin__ - *dn)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin__ + *dn)) {</span></a>
+<a name="9934"><span class="lineNum">    9934 </span>            :                     gam = *dn;</a>
+<a name="9935"><span class="lineNum">    9935 </span>            :                     a2 = 0.;</a>
+<a name="9936"><span class="lineNum">    9936 </span><span class="lineNoCov">          0 :                     if (z__[nn - 5] &gt; z__[nn - 7]) {</span></a>
+<a name="9937"><span class="lineNum">    9937 </span>            :                         return;</a>
+<a name="9938"><span class="lineNum">    9938 </span>            :                     }</a>
+<a name="9939"><span class="lineNum">    9939 </span><span class="lineNoCov">          0 :                     b2 = z__[nn - 5] / z__[nn - 7];</span></a>
+<a name="9940"><span class="lineNum">    9940 </span><span class="lineNoCov">          0 :                     np = nn - 9;</span></a>
+<a name="9941"><span class="lineNum">    9941 </span>            :                 } else {</a>
+<a name="9942"><span class="lineNum">    9942 </span><span class="lineNoCov">          0 :                     np = nn - (*pp &lt;&lt; 1);</span></a>
+<a name="9943"><span class="lineNum">    9943 </span><span class="lineNoCov">          0 :                     gam = *dn1;</span></a>
+<a name="9944"><span class="lineNum">    9944 </span><span class="lineNoCov">          0 :                     if (z__[np - 4] &gt; z__[np - 2]) {</span></a>
+<a name="9945"><span class="lineNum">    9945 </span>            :                         return;</a>
+<a name="9946"><span class="lineNum">    9946 </span>            :                     }</a>
+<a name="9947"><span class="lineNum">    9947 </span><span class="lineNoCov">          0 :                     a2 = z__[np - 4] / z__[np - 2];</span></a>
+<a name="9948"><span class="lineNum">    9948 </span><span class="lineNoCov">          0 :                     if (z__[nn - 9] &gt; z__[nn - 11]) {</span></a>
+<a name="9949"><span class="lineNum">    9949 </span>            :                         return;</a>
+<a name="9950"><span class="lineNum">    9950 </span>            :                     }</a>
+<a name="9951"><span class="lineNum">    9951 </span><span class="lineNoCov">          0 :                     b2 = z__[nn - 9] / z__[nn - 11];</span></a>
+<a name="9952"><span class="lineNum">    9952 </span><span class="lineNoCov">          0 :                     np = nn - 13;</span></a>
+<a name="9953"><span class="lineNum">    9953 </span>            :                 }</a>
+<a name="9954"><span class="lineNum">    9954 </span>            : </a>
+<a name="9955"><span class="lineNum">    9955 </span>            : </a>
+<a name="9956"><span class="lineNum">    9956 </span><span class="lineNoCov">          0 :                 a2 += b2;</span></a>
+<a name="9957"><span class="lineNum">    9957 </span><span class="lineNoCov">          0 :                 i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="9958"><span class="lineNum">    9958 </span><span class="lineNoCov">          0 :                 for (i4 = np; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="9959"><span class="lineNum">    9959 </span><span class="lineNoCov">          0 :                     if (std::abs(b2)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="9960"><span class="lineNum">    9960 </span><span class="lineNoCov">          0 :                         goto L20;</span></a>
+<a name="9961"><span class="lineNum">    9961 </span>            :                     }</a>
+<a name="9962"><span class="lineNum">    9962 </span>            :                     b1 = b2;</a>
+<a name="9963"><span class="lineNum">    9963 </span><span class="lineNoCov">          0 :                     if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="9964"><span class="lineNum">    9964 </span>            :                         return;</a>
+<a name="9965"><span class="lineNum">    9965 </span>            :                     }</a>
+<a name="9966"><span class="lineNum">    9966 </span><span class="lineNoCov">          0 :                     b2 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="9967"><span class="lineNum">    9967 </span><span class="lineNoCov">          0 :                     a2 += b2;</span></a>
+<a name="9968"><span class="lineNum">    9968 </span><span class="lineNoCov">          0 :                     if (((b2&gt;b1) ? b2 : b1) * 100. &lt; a2 || .563 &lt; a2) {</span></a>
+<a name="9969"><span class="lineNum">    9969 </span><span class="lineNoCov">          0 :                         goto L20;</span></a>
+<a name="9970"><span class="lineNum">    9970 </span>            :                     }</a>
+<a name="9971"><span class="lineNum">    9971 </span>            :                 }</a>
+<a name="9972"><span class="lineNum">    9972 </span><span class="lineNoCov">          0 : L20:</span></a>
+<a name="9973"><span class="lineNum">    9973 </span><span class="lineNoCov">          0 :                 a2 *= 1.05;</span></a>
+<a name="9974"><span class="lineNum">    9974 </span>            : </a>
+<a name="9975"><span class="lineNum">    9975 </span>            : </a>
+<a name="9976"><span class="lineNum">    9976 </span><span class="lineNoCov">          0 :                 if (a2 &lt; .563) {</span></a>
+<a name="9977"><span class="lineNum">    9977 </span><span class="lineNoCov">          0 :                     s = gam * (1. -  std::sqrt(a2)) / (a2 + 1.);</span></a>
+<a name="9978"><span class="lineNum">    9978 </span>            :                 }</a>
+<a name="9979"><span class="lineNum">    9979 </span>            :             }</a>
+<a name="9980"><span class="lineNum">    9980 </span><span class="lineCov">   11455382 :         } else if (std::abs(*dmin__ - *dn2)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin__ + *dn2)) {</span></a>
+<a name="9981"><span class="lineNum">    9981 </span>            : </a>
+<a name="9982"><span class="lineNum">    9982 </span><span class="lineNoCov">          0 :             *ttype = -5;</span></a>
+<a name="9983"><span class="lineNum">    9983 </span><span class="lineNoCov">          0 :             s = *dmin__ * .25;</span></a>
+<a name="9984"><span class="lineNum">    9984 </span>            : </a>
+<a name="9985"><span class="lineNum">    9985 </span><span class="lineNoCov">          0 :             np = nn - (*pp &lt;&lt; 1);</span></a>
+<a name="9986"><span class="lineNum">    9986 </span><span class="lineNoCov">          0 :             b1 = z__[np - 2];</span></a>
+<a name="9987"><span class="lineNum">    9987 </span><span class="lineNoCov">          0 :             b2 = z__[np - 6];</span></a>
+<a name="9988"><span class="lineNum">    9988 </span><span class="lineNoCov">          0 :             gam = *dn2;</span></a>
+<a name="9989"><span class="lineNum">    9989 </span><span class="lineNoCov">          0 :             if (z__[np - 8] &gt; b2 || z__[np - 4] &gt; b1) {</span></a>
+<a name="9990"><span class="lineNum">    9990 </span>            :                 return;</a>
+<a name="9991"><span class="lineNum">    9991 </span>            :             }</a>
+<a name="9992"><span class="lineNum">    9992 </span><span class="lineNoCov">          0 :             a2 = z__[np - 8] / b2 * (z__[np - 4] / b1 + 1.);</span></a>
+<a name="9993"><span class="lineNum">    9993 </span>            : </a>
+<a name="9994"><span class="lineNum">    9994 </span>            : </a>
+<a name="9995"><span class="lineNum">    9995 </span><span class="lineNoCov">          0 :             if (*n0 - *i0 &gt; 2) {</span></a>
+<a name="9996"><span class="lineNum">    9996 </span><span class="lineNoCov">          0 :                 b2 = z__[nn - 13] / z__[nn - 15];</span></a>
+<a name="9997"><span class="lineNum">    9997 </span><span class="lineNoCov">          0 :                 a2 += b2;</span></a>
+<a name="9998"><span class="lineNum">    9998 </span><span class="lineNoCov">          0 :                 i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="9999"><span class="lineNum">    9999 </span><span class="lineNoCov">          0 :                 for (i4 = nn - 17; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="10000"><span class="lineNum">   10000 </span><span class="lineNoCov">          0 :                     if (std::abs(b2)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10001"><span class="lineNum">   10001 </span><span class="lineNoCov">          0 :                         goto L40;</span></a>
+<a name="10002"><span class="lineNum">   10002 </span>            :                     }</a>
+<a name="10003"><span class="lineNum">   10003 </span>            :                     b1 = b2;</a>
+<a name="10004"><span class="lineNum">   10004 </span><span class="lineNoCov">          0 :                     if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="10005"><span class="lineNum">   10005 </span>            :                         return;</a>
+<a name="10006"><span class="lineNum">   10006 </span>            :                     }</a>
+<a name="10007"><span class="lineNum">   10007 </span><span class="lineNoCov">          0 :                     b2 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="10008"><span class="lineNum">   10008 </span><span class="lineNoCov">          0 :                     a2 += b2;</span></a>
+<a name="10009"><span class="lineNum">   10009 </span><span class="lineNoCov">          0 :                     if (((b2&gt;b1) ? b2 : b1) * 100. &lt; a2 || .563 &lt; a2) {</span></a>
+<a name="10010"><span class="lineNum">   10010 </span><span class="lineNoCov">          0 :                         goto L40;</span></a>
+<a name="10011"><span class="lineNum">   10011 </span>            :                     }</a>
+<a name="10012"><span class="lineNum">   10012 </span>            :                 }</a>
+<a name="10013"><span class="lineNum">   10013 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="10014"><span class="lineNum">   10014 </span><span class="lineNoCov">          0 :                 a2 *= 1.05;</span></a>
+<a name="10015"><span class="lineNum">   10015 </span>            :             }</a>
+<a name="10016"><span class="lineNum">   10016 </span>            : </a>
+<a name="10017"><span class="lineNum">   10017 </span><span class="lineNoCov">          0 :             if (a2 &lt; .563) {</span></a>
+<a name="10018"><span class="lineNum">   10018 </span><span class="lineNoCov">          0 :                 s = gam * (1. -  std::sqrt(a2)) / (a2 + 1.);</span></a>
+<a name="10019"><span class="lineNum">   10019 </span>            :             }</a>
+<a name="10020"><span class="lineNum">   10020 </span>            :         } else {</a>
+<a name="10021"><span class="lineNum">   10021 </span>            : </a>
+<a name="10022"><span class="lineNum">   10022 </span><span class="lineCov">   11455382 :             if (*ttype == -6) {</span></a>
+<a name="10023"><span class="lineNum">   10023 </span>            :                 g += (1. - g) * .333;</a>
+<a name="10024"><span class="lineNum">   10024 </span><span class="lineCov">   11455382 :             } else if (*ttype == -18) {</span></a>
+<a name="10025"><span class="lineNum">   10025 </span>            :                 g = .083250000000000005;</a>
+<a name="10026"><span class="lineNum">   10026 </span>            :             } else {</a>
+<a name="10027"><span class="lineNum">   10027 </span>            :                 g = .25;</a>
+<a name="10028"><span class="lineNum">   10028 </span>            :             }</a>
+<a name="10029"><span class="lineNum">   10029 </span><span class="lineCov">   11455382 :             s = g * *dmin__;</span></a>
+<a name="10030"><span class="lineNum">   10030 </span><span class="lineCov">   11455382 :             *ttype = -6;</span></a>
+<a name="10031"><span class="lineNum">   10031 </span>            :         }</a>
+<a name="10032"><span class="lineNum">   10032 </span>            : </a>
+<a name="10033"><span class="lineNum">   10033 </span><span class="lineCov">     265114 :     } else if (*n0in == *n0 + 1) {</span></a>
+<a name="10034"><span class="lineNum">   10034 </span>            : </a>
+<a name="10035"><span class="lineNum">   10035 </span><span class="lineCov">     265005 :         if ( std::abs(*dmin1 - *dn1)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin1 + *dn1) &amp;&amp;</span></a>
+<a name="10036"><span class="lineNum">   10036 </span><span class="lineNoCov">          0 :              std::abs(*dmin2 - *dn2)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin2 + *dn2)) {</span></a>
+<a name="10037"><span class="lineNum">   10037 </span>            : </a>
+<a name="10038"><span class="lineNum">   10038 </span><span class="lineNoCov">          0 :             *ttype = -7;</span></a>
+<a name="10039"><span class="lineNum">   10039 </span><span class="lineNoCov">          0 :             s = *dmin1 * .333;</span></a>
+<a name="10040"><span class="lineNum">   10040 </span><span class="lineNoCov">          0 :             if (z__[nn - 5] &gt; z__[nn - 7]) {</span></a>
+<a name="10041"><span class="lineNum">   10041 </span>            :                 return;</a>
+<a name="10042"><span class="lineNum">   10042 </span>            :             }</a>
+<a name="10043"><span class="lineNum">   10043 </span><span class="lineNoCov">          0 :             b1 = z__[nn - 5] / z__[nn - 7];</span></a>
+<a name="10044"><span class="lineNum">   10044 </span>            :             b2 = b1;</a>
+<a name="10045"><span class="lineNum">   10045 </span><span class="lineNoCov">          0 :             if (std::abs(b2)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10046"><span class="lineNum">   10046 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="10047"><span class="lineNum">   10047 </span>            :             }</a>
+<a name="10048"><span class="lineNum">   10048 </span><span class="lineNoCov">          0 :             i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="10049"><span class="lineNum">   10049 </span><span class="lineNoCov">          0 :             for (i4 = (*n0 &lt;&lt; 2) - 9 + *pp; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="10050"><span class="lineNum">   10050 </span>            :                 a2 = b1;</a>
+<a name="10051"><span class="lineNum">   10051 </span><span class="lineNoCov">          0 :                 if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="10052"><span class="lineNum">   10052 </span>            :                     return;</a>
+<a name="10053"><span class="lineNum">   10053 </span>            :                 }</a>
+<a name="10054"><span class="lineNum">   10054 </span><span class="lineNoCov">          0 :                 b1 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="10055"><span class="lineNum">   10055 </span><span class="lineNoCov">          0 :                 b2 += b1;</span></a>
+<a name="10056"><span class="lineNum">   10056 </span><span class="lineNoCov">          0 :                 if (((a2&gt;b1) ? a2 : b1) * 100. &lt; b2) {</span></a>
+<a name="10057"><span class="lineNum">   10057 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="10058"><span class="lineNum">   10058 </span>            :                 }</a>
+<a name="10059"><span class="lineNum">   10059 </span>            :             }</a>
+<a name="10060"><span class="lineNum">   10060 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="10061"><span class="lineNum">   10061 </span><span class="lineNoCov">          0 :             b2 =  std::sqrt(b2 * 1.05);</span></a>
+<a name="10062"><span class="lineNum">   10062 </span>            :             d__1 = b2;</a>
+<a name="10063"><span class="lineNum">   10063 </span><span class="lineNoCov">          0 :             a2 = *dmin1 / (d__1 * d__1 + 1.);</span></a>
+<a name="10064"><span class="lineNum">   10064 </span><span class="lineNoCov">          0 :             gap2 = *dmin2 * .5 - a2;</span></a>
+<a name="10065"><span class="lineNum">   10065 </span><span class="lineNoCov">          0 :             if (gap2 &gt; 0. &amp;&amp; gap2 &gt; b2 * a2) {</span></a>
+<a name="10066"><span class="lineNum">   10066 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - a2 * 1.01 * (b2 / gap2) * b2);</span></a>
+<a name="10067"><span class="lineNum">   10067 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="10068"><span class="lineNum">   10068 </span>            :             } else {</a>
+<a name="10069"><span class="lineNum">   10069 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - b2 * 1.01);</span></a>
+<a name="10070"><span class="lineNum">   10070 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="10071"><span class="lineNum">   10071 </span><span class="lineNoCov">          0 :                 *ttype = -8;</span></a>
+<a name="10072"><span class="lineNum">   10072 </span>            :             }</a>
+<a name="10073"><span class="lineNum">   10073 </span>            :         } else {</a>
+<a name="10074"><span class="lineNum">   10074 </span>            : </a>
+<a name="10075"><span class="lineNum">   10075 </span><span class="lineCov">     265005 :             s = *dmin1 * .25;</span></a>
+<a name="10076"><span class="lineNum">   10076 </span><span class="lineCov">     265005 :             if (std::abs(*dmin1 - *dn1)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin1 + *dn1)) {</span></a>
+<a name="10077"><span class="lineNum">   10077 </span><span class="lineNoCov">          0 :                 s = *dmin1 * .5;</span></a>
+<a name="10078"><span class="lineNum">   10078 </span>            :             }</a>
+<a name="10079"><span class="lineNum">   10079 </span><span class="lineCov">     265005 :             *ttype = -9;</span></a>
+<a name="10080"><span class="lineNum">   10080 </span>            :         }</a>
+<a name="10081"><span class="lineNum">   10081 </span>            : </a>
+<a name="10082"><span class="lineNum">   10082 </span><span class="lineCov">        109 :     } else if (*n0in == *n0 + 2) {</span></a>
+<a name="10083"><span class="lineNum">   10083 </span>            : </a>
+<a name="10084"><span class="lineNum">   10084 </span><span class="lineCov">        108 :         if (std::abs(*dmin2 - *dn2)&lt;PLUMED_GMX_DOUBLE_EPS*std::abs(*dmin2 + *dn2) &amp;&amp;</span></a>
+<a name="10085"><span class="lineNum">   10085 </span><span class="lineNoCov">          0 :         z__[nn - 5] * 2. &lt; z__[nn - 7]) {</span></a>
+<a name="10086"><span class="lineNum">   10086 </span><span class="lineNoCov">          0 :             *ttype = -10;</span></a>
+<a name="10087"><span class="lineNum">   10087 </span><span class="lineNoCov">          0 :             s = *dmin2 * .333;</span></a>
+<a name="10088"><span class="lineNum">   10088 </span><span class="lineNoCov">          0 :             if (z__[nn - 5] &gt; z__[nn - 7]) {</span></a>
+<a name="10089"><span class="lineNum">   10089 </span>            :                 return;</a>
+<a name="10090"><span class="lineNum">   10090 </span>            :             }</a>
+<a name="10091"><span class="lineNum">   10091 </span><span class="lineNoCov">          0 :             b1 = z__[nn - 5] / z__[nn - 7];</span></a>
+<a name="10092"><span class="lineNum">   10092 </span>            :             b2 = b1;</a>
+<a name="10093"><span class="lineNum">   10093 </span><span class="lineNoCov">          0 :             if (std::abs(b2)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10094"><span class="lineNum">   10094 </span><span class="lineNoCov">          0 :                 goto L80;</span></a>
+<a name="10095"><span class="lineNum">   10095 </span>            :             }</a>
+<a name="10096"><span class="lineNum">   10096 </span><span class="lineNoCov">          0 :             i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="10097"><span class="lineNum">   10097 </span><span class="lineNoCov">          0 :             for (i4 = (*n0 &lt;&lt; 2) - 9 + *pp; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="10098"><span class="lineNum">   10098 </span><span class="lineNoCov">          0 :                 if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="10099"><span class="lineNum">   10099 </span>            :                     return;</a>
+<a name="10100"><span class="lineNum">   10100 </span>            :                 }</a>
+<a name="10101"><span class="lineNum">   10101 </span><span class="lineNoCov">          0 :                 b1 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="10102"><span class="lineNum">   10102 </span><span class="lineNoCov">          0 :                 b2 += b1;</span></a>
+<a name="10103"><span class="lineNum">   10103 </span><span class="lineNoCov">          0 :                 if (b1 * 100. &lt; b2) {</span></a>
+<a name="10104"><span class="lineNum">   10104 </span><span class="lineNoCov">          0 :                     goto L80;</span></a>
+<a name="10105"><span class="lineNum">   10105 </span>            :                 }</a>
+<a name="10106"><span class="lineNum">   10106 </span>            :             }</a>
+<a name="10107"><span class="lineNum">   10107 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="10108"><span class="lineNum">   10108 </span><span class="lineNoCov">          0 :             b2 =  std::sqrt(b2 * 1.05);</span></a>
+<a name="10109"><span class="lineNum">   10109 </span>            :             d__1 = b2;</a>
+<a name="10110"><span class="lineNum">   10110 </span><span class="lineNoCov">          0 :             a2 = *dmin2 / (d__1 * d__1 + 1.);</span></a>
+<a name="10111"><span class="lineNum">   10111 </span><span class="lineNoCov">          0 :             gap2 = z__[nn - 7] + z__[nn - 9] -  std::sqrt(z__[nn - 11]) * std::sqrt(z__[</span></a>
+<a name="10112"><span class="lineNum">   10112 </span>            :                     nn - 9]) - a2;</a>
+<a name="10113"><span class="lineNum">   10113 </span><span class="lineNoCov">          0 :             if (gap2 &gt; 0. &amp;&amp; gap2 &gt; b2 * a2) {</span></a>
+<a name="10114"><span class="lineNum">   10114 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - a2 * 1.01 * (b2 / gap2) * b2);</span></a>
+<a name="10115"><span class="lineNum">   10115 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="10116"><span class="lineNum">   10116 </span>            :             } else {</a>
+<a name="10117"><span class="lineNum">   10117 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - b2 * 1.01);</span></a>
+<a name="10118"><span class="lineNum">   10118 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="10119"><span class="lineNum">   10119 </span>            :             }</a>
+<a name="10120"><span class="lineNum">   10120 </span>            :         } else {</a>
+<a name="10121"><span class="lineNum">   10121 </span><span class="lineCov">        108 :             s = *dmin2 * .25;</span></a>
+<a name="10122"><span class="lineNum">   10122 </span><span class="lineCov">        108 :             *ttype = -11;</span></a>
+<a name="10123"><span class="lineNum">   10123 </span>            :         }</a>
+<a name="10124"><span class="lineNum">   10124 </span><span class="lineCov">          1 :     } else if (*n0in &gt; *n0 + 2) {</span></a>
+<a name="10125"><span class="lineNum">   10125 </span>            : </a>
+<a name="10126"><span class="lineNum">   10126 </span>            :         s = 0.;</a>
+<a name="10127"><span class="lineNum">   10127 </span><span class="lineCov">          1 :         *ttype = -12;</span></a>
+<a name="10128"><span class="lineNum">   10128 </span>            :     }</a>
+<a name="10129"><span class="lineNum">   10129 </span>            : </a>
+<a name="10130"><span class="lineNum">   10130 </span><span class="lineCov">   11720496 :     *tau = s;</span></a>
+<a name="10131"><span class="lineNum">   10131 </span><span class="lineCov">   11720496 :     return;</span></a>
+<a name="10132"><span class="lineNum">   10132 </span>            : </a>
+<a name="10133"><span class="lineNum">   10133 </span>            : }</a>
+<a name="10134"><span class="lineNum">   10134 </span>            : </a>
+<a name="10135"><span class="lineNum">   10135 </span>            : </a>
+<a name="10136"><span class="lineNum">   10136 </span>            : }</a>
+<a name="10137"><span class="lineNum">   10137 </span>            : }</a>
+<a name="10138"><span class="lineNum">   10138 </span>            : #include &lt;cmath&gt;</a>
+<a name="10139"><span class="lineNum">   10139 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="10140"><span class="lineNum">   10140 </span>            : </a>
+<a name="10141"><span class="lineNum">   10141 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="10142"><span class="lineNum">   10142 </span>            : namespace PLMD{</a>
+<a name="10143"><span class="lineNum">   10143 </span>            : namespace lapack{</a>
+<a name="10144"><span class="lineNum">   10144 </span>            : using namespace blas;</a>
+<a name="10145"><span class="lineNum">   10145 </span>            : void</a>
+<a name="10146"><span class="lineNum">   10146 </span><span class="lineCov">   12568766 : PLUMED_BLAS_F77_FUNC(dlasq5,DLASQ5)(int *i0, </span></a>
+<a name="10147"><span class="lineNum">   10147 </span>            :         int *n0,</a>
+<a name="10148"><span class="lineNum">   10148 </span>            :         double *z__, </a>
+<a name="10149"><span class="lineNum">   10149 </span>            :         int *pp, </a>
+<a name="10150"><span class="lineNum">   10150 </span>            :         double *tau,</a>
+<a name="10151"><span class="lineNum">   10151 </span>            :         double *dmin__, </a>
+<a name="10152"><span class="lineNum">   10152 </span>            :         double *dmin1, </a>
+<a name="10153"><span class="lineNum">   10153 </span>            :         double *dmin2, </a>
+<a name="10154"><span class="lineNum">   10154 </span>            :         double *dn,</a>
+<a name="10155"><span class="lineNum">   10155 </span>            :         double *dnm1, </a>
+<a name="10156"><span class="lineNum">   10156 </span>            :         double *dnm2,</a>
+<a name="10157"><span class="lineNum">   10157 </span>            :         int *ieee)</a>
+<a name="10158"><span class="lineNum">   10158 </span>            : {</a>
+<a name="10159"><span class="lineNum">   10159 </span>            :     int i__1;</a>
+<a name="10160"><span class="lineNum">   10160 </span>            :     double d__1, d__2;</a>
+<a name="10161"><span class="lineNum">   10161 </span>            : </a>
+<a name="10162"><span class="lineNum">   10162 </span>            :     double d__;</a>
+<a name="10163"><span class="lineNum">   10163 </span>            :     int    j4, j4p2;</a>
+<a name="10164"><span class="lineNum">   10164 </span>            :     double emin, temp;</a>
+<a name="10165"><span class="lineNum">   10165 </span>            : </a>
+<a name="10166"><span class="lineNum">   10166 </span><span class="lineCov">   12568766 :     --z__;</span></a>
+<a name="10167"><span class="lineNum">   10167 </span>            : </a>
+<a name="10168"><span class="lineNum">   10168 </span><span class="lineCov">   12568766 :     if (*n0 - *i0 - 1 &lt;= 0) {</span></a>
+<a name="10169"><span class="lineNum">   10169 </span>            :         return;</a>
+<a name="10170"><span class="lineNum">   10170 </span>            :     }</a>
+<a name="10171"><span class="lineNum">   10171 </span>            : </a>
+<a name="10172"><span class="lineNum">   10172 </span><span class="lineCov">   12568766 :     j4 = (*i0 &lt;&lt; 2) + *pp - 3;</span></a>
+<a name="10173"><span class="lineNum">   10173 </span><span class="lineCov">   12568766 :     emin = z__[j4 + 4];</span></a>
+<a name="10174"><span class="lineNum">   10174 </span><span class="lineCov">   12568766 :     d__ = z__[j4] - *tau;</span></a>
+<a name="10175"><span class="lineNum">   10175 </span><span class="lineCov">   12568766 :     *dmin__ = d__;</span></a>
+<a name="10176"><span class="lineNum">   10176 </span><span class="lineCov">   12568766 :     *dmin1 = -z__[j4];</span></a>
+<a name="10177"><span class="lineNum">   10177 </span>            : </a>
+<a name="10178"><span class="lineNum">   10178 </span><span class="lineCov">   12568766 :     if (*ieee) {</span></a>
+<a name="10179"><span class="lineNum">   10179 </span>            : </a>
+<a name="10180"><span class="lineNum">   10180 </span><span class="lineCov">   12568766 :         if (*pp == 0) {</span></a>
+<a name="10181"><span class="lineNum">   10181 </span><span class="lineCov">    6430794 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="10182"><span class="lineNum">   10182 </span><span class="lineCov">    7707680 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="10183"><span class="lineNum">   10183 </span><span class="lineCov">    1276886 :                 z__[j4 - 2] = d__ + z__[j4 - 1];</span></a>
+<a name="10184"><span class="lineNum">   10184 </span><span class="lineCov">    1276886 :                 temp = z__[j4 + 1] / z__[j4 - 2];</span></a>
+<a name="10185"><span class="lineNum">   10185 </span><span class="lineCov">    1276886 :                 d__ = d__ * temp - *tau;</span></a>
+<a name="10186"><span class="lineNum">   10186 </span><span class="lineCov">    1276886 :                 if(d__&lt;*dmin__)</span></a>
+<a name="10187"><span class="lineNum">   10187 </span><span class="lineCov">     328487 :                   *dmin__ = d__;</span></a>
+<a name="10188"><span class="lineNum">   10188 </span><span class="lineCov">    1276886 :                 z__[j4] = z__[j4 - 1] * temp;</span></a>
+<a name="10189"><span class="lineNum">   10189 </span>            :                 d__1 = z__[j4];</a>
+<a name="10190"><span class="lineNum">   10190 </span><span class="lineCov">    1276886 :                 if(d__1&lt;emin)</span></a>
+<a name="10191"><span class="lineNum">   10191 </span>            :                   emin = d__1;</a>
+<a name="10192"><span class="lineNum">   10192 </span>            :             }</a>
+<a name="10193"><span class="lineNum">   10193 </span>            :         } else {</a>
+<a name="10194"><span class="lineNum">   10194 </span><span class="lineCov">    6137972 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="10195"><span class="lineNum">   10195 </span><span class="lineCov">    7015854 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="10196"><span class="lineNum">   10196 </span><span class="lineCov">     877882 :                 z__[j4 - 3] = d__ + z__[j4];</span></a>
+<a name="10197"><span class="lineNum">   10197 </span><span class="lineCov">     877882 :                 temp = z__[j4 + 2] / z__[j4 - 3];</span></a>
+<a name="10198"><span class="lineNum">   10198 </span><span class="lineCov">     877882 :                 d__ = d__ * temp - *tau;</span></a>
+<a name="10199"><span class="lineNum">   10199 </span><span class="lineCov">     877882 :                 if(d__&lt;*dmin__)</span></a>
+<a name="10200"><span class="lineNum">   10200 </span><span class="lineCov">     239959 :                   *dmin__ = d__;</span></a>
+<a name="10201"><span class="lineNum">   10201 </span><span class="lineCov">     877882 :                 z__[j4 - 1] = z__[j4] * temp;</span></a>
+<a name="10202"><span class="lineNum">   10202 </span>            :                 d__1 = z__[j4 - 1];</a>
+<a name="10203"><span class="lineNum">   10203 </span><span class="lineCov">     877882 :                 if(d__1&lt;emin)</span></a>
+<a name="10204"><span class="lineNum">   10204 </span>            :                   emin = d__1;</a>
+<a name="10205"><span class="lineNum">   10205 </span>            :             }</a>
+<a name="10206"><span class="lineNum">   10206 </span>            :         }</a>
+<a name="10207"><span class="lineNum">   10207 </span>            : </a>
+<a name="10208"><span class="lineNum">   10208 </span><span class="lineCov">   12568766 :         *dnm2 = d__;</span></a>
+<a name="10209"><span class="lineNum">   10209 </span><span class="lineCov">   12568766 :         *dmin2 = *dmin__;</span></a>
+<a name="10210"><span class="lineNum">   10210 </span><span class="lineCov">   12568766 :         j4 = 4*(*n0 - 2) - *pp;</span></a>
+<a name="10211"><span class="lineNum">   10211 </span><span class="lineCov">   12568766 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="10212"><span class="lineNum">   10212 </span><span class="lineCov">   12568766 :         z__[j4 - 2] = *dnm2 + z__[j4p2];</span></a>
+<a name="10213"><span class="lineNum">   10213 </span><span class="lineCov">   12568766 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="10214"><span class="lineNum">   10214 </span><span class="lineCov">   12568766 :         *dnm1 = z__[j4p2 + 2] * (*dnm2 / z__[j4 - 2]) - *tau;</span></a>
+<a name="10215"><span class="lineNum">   10215 </span><span class="lineCov">   12568766 :         if(*dnm1&lt;*dmin__)</span></a>
+<a name="10216"><span class="lineNum">   10216 </span><span class="lineCov">    9958646 :           *dmin__ = *dnm1;</span></a>
+<a name="10217"><span class="lineNum">   10217 </span>            : </a>
+<a name="10218"><span class="lineNum">   10218 </span><span class="lineCov">   12568766 :         *dmin1 = *dmin__;</span></a>
+<a name="10219"><span class="lineNum">   10219 </span><span class="lineCov">   12568766 :         j4 += 4;</span></a>
+<a name="10220"><span class="lineNum">   10220 </span><span class="lineCov">   12568766 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="10221"><span class="lineNum">   10221 </span><span class="lineCov">   12568766 :         z__[j4 - 2] = *dnm1 + z__[j4p2];</span></a>
+<a name="10222"><span class="lineNum">   10222 </span><span class="lineCov">   12568766 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="10223"><span class="lineNum">   10223 </span><span class="lineCov">   12568766 :         *dn = z__[j4p2 + 2] * (*dnm1 / z__[j4 - 2]) - *tau;</span></a>
+<a name="10224"><span class="lineNum">   10224 </span><span class="lineCov">   12568766 :         if(*dn&lt;*dmin__)</span></a>
+<a name="10225"><span class="lineNum">   10225 </span><span class="lineCov">   12019828 :           *dmin__ = *dn;</span></a>
+<a name="10226"><span class="lineNum">   10226 </span>            : </a>
+<a name="10227"><span class="lineNum">   10227 </span>            :     } else {</a>
+<a name="10228"><span class="lineNum">   10228 </span>            : </a>
+<a name="10229"><span class="lineNum">   10229 </span><span class="lineNoCov">          0 :         if (*pp == 0) {</span></a>
+<a name="10230"><span class="lineNum">   10230 </span><span class="lineNoCov">          0 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="10231"><span class="lineNum">   10231 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="10232"><span class="lineNum">   10232 </span><span class="lineNoCov">          0 :                 z__[j4 - 2] = d__ + z__[j4 - 1];</span></a>
+<a name="10233"><span class="lineNum">   10233 </span><span class="lineNoCov">          0 :                 if (d__ &lt; 0.) {</span></a>
+<a name="10234"><span class="lineNum">   10234 </span>            :                     return;</a>
+<a name="10235"><span class="lineNum">   10235 </span>            :                 } else {</a>
+<a name="10236"><span class="lineNum">   10236 </span><span class="lineNoCov">          0 :                     z__[j4] = z__[j4 + 1] * (z__[j4 - 1] / z__[j4 - 2]);</span></a>
+<a name="10237"><span class="lineNum">   10237 </span><span class="lineNoCov">          0 :                     d__ = z__[j4 + 1] * (d__ / z__[j4 - 2]) - *tau;</span></a>
+<a name="10238"><span class="lineNum">   10238 </span>            :                 }</a>
+<a name="10239"><span class="lineNum">   10239 </span><span class="lineNoCov">          0 :                 if(d__&lt;*dmin__)</span></a>
+<a name="10240"><span class="lineNum">   10240 </span><span class="lineNoCov">          0 :                   *dmin__ = d__;</span></a>
+<a name="10241"><span class="lineNum">   10241 </span><span class="lineNoCov">          0 :                 d__1 = emin, d__2 = z__[j4];</span></a>
+<a name="10242"><span class="lineNum">   10242 </span><span class="lineNoCov">          0 :                 emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="10243"><span class="lineNum">   10243 </span>            :             }</a>
+<a name="10244"><span class="lineNum">   10244 </span>            :         } else {</a>
+<a name="10245"><span class="lineNum">   10245 </span><span class="lineNoCov">          0 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="10246"><span class="lineNum">   10246 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="10247"><span class="lineNum">   10247 </span><span class="lineNoCov">          0 :                 z__[j4 - 3] = d__ + z__[j4];</span></a>
+<a name="10248"><span class="lineNum">   10248 </span><span class="lineNoCov">          0 :                 if (d__ &lt; 0.) {</span></a>
+<a name="10249"><span class="lineNum">   10249 </span>            :                     return;</a>
+<a name="10250"><span class="lineNum">   10250 </span>            :                 } else {</a>
+<a name="10251"><span class="lineNum">   10251 </span><span class="lineNoCov">          0 :                     z__[j4 - 1] = z__[j4 + 2] * (z__[j4] / z__[j4 - 3]);</span></a>
+<a name="10252"><span class="lineNum">   10252 </span><span class="lineNoCov">          0 :                     d__ = z__[j4 + 2] * (d__ / z__[j4 - 3]) - *tau;</span></a>
+<a name="10253"><span class="lineNum">   10253 </span>            :                 }</a>
+<a name="10254"><span class="lineNum">   10254 </span><span class="lineNoCov">          0 :                 if(d__&lt;*dmin__)</span></a>
+<a name="10255"><span class="lineNum">   10255 </span><span class="lineNoCov">          0 :                   *dmin__ = d__;</span></a>
+<a name="10256"><span class="lineNum">   10256 </span><span class="lineNoCov">          0 :                 d__1 = emin, d__2 = z__[j4 - 1];</span></a>
+<a name="10257"><span class="lineNum">   10257 </span><span class="lineNoCov">          0 :                 emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="10258"><span class="lineNum">   10258 </span>            :             }</a>
+<a name="10259"><span class="lineNum">   10259 </span>            :         }</a>
+<a name="10260"><span class="lineNum">   10260 </span>            : </a>
+<a name="10261"><span class="lineNum">   10261 </span><span class="lineNoCov">          0 :         *dnm2 = d__;</span></a>
+<a name="10262"><span class="lineNum">   10262 </span><span class="lineNoCov">          0 :         *dmin2 = *dmin__;</span></a>
+<a name="10263"><span class="lineNum">   10263 </span><span class="lineNoCov">          0 :         j4 = 4*(*n0 - 2) - *pp;</span></a>
+<a name="10264"><span class="lineNum">   10264 </span><span class="lineNoCov">          0 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="10265"><span class="lineNum">   10265 </span><span class="lineNoCov">          0 :         z__[j4 - 2] = *dnm2 + z__[j4p2];</span></a>
+<a name="10266"><span class="lineNum">   10266 </span><span class="lineNoCov">          0 :         if (*dnm2 &lt; 0.) {</span></a>
+<a name="10267"><span class="lineNum">   10267 </span>            :             return;</a>
+<a name="10268"><span class="lineNum">   10268 </span>            :         } else {</a>
+<a name="10269"><span class="lineNum">   10269 </span><span class="lineNoCov">          0 :             z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="10270"><span class="lineNum">   10270 </span><span class="lineNoCov">          0 :             *dnm1 = z__[j4p2 + 2] * (*dnm2 / z__[j4 - 2]) - *tau;</span></a>
+<a name="10271"><span class="lineNum">   10271 </span>            :         }</a>
+<a name="10272"><span class="lineNum">   10272 </span><span class="lineNoCov">          0 :         if(*dnm1&lt;*dmin__)</span></a>
+<a name="10273"><span class="lineNum">   10273 </span><span class="lineNoCov">          0 :           *dmin__ = *dnm1;</span></a>
+<a name="10274"><span class="lineNum">   10274 </span>            : </a>
+<a name="10275"><span class="lineNum">   10275 </span><span class="lineNoCov">          0 :         *dmin1 = *dmin__;</span></a>
+<a name="10276"><span class="lineNum">   10276 </span><span class="lineNoCov">          0 :         j4 += 4;</span></a>
+<a name="10277"><span class="lineNum">   10277 </span><span class="lineNoCov">          0 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="10278"><span class="lineNum">   10278 </span><span class="lineNoCov">          0 :         z__[j4 - 2] = *dnm1 + z__[j4p2];</span></a>
+<a name="10279"><span class="lineNum">   10279 </span><span class="lineNoCov">          0 :         if (*dnm1 &lt; 0.) {</span></a>
+<a name="10280"><span class="lineNum">   10280 </span>            :             return;</a>
+<a name="10281"><span class="lineNum">   10281 </span>            :         } else {</a>
+<a name="10282"><span class="lineNum">   10282 </span><span class="lineNoCov">          0 :             z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="10283"><span class="lineNum">   10283 </span><span class="lineNoCov">          0 :             *dn = z__[j4p2 + 2] * (*dnm1 / z__[j4 - 2]) - *tau;</span></a>
+<a name="10284"><span class="lineNum">   10284 </span>            :         }</a>
+<a name="10285"><span class="lineNum">   10285 </span><span class="lineNoCov">          0 :         if(*dn&lt;*dmin__)</span></a>
+<a name="10286"><span class="lineNum">   10286 </span><span class="lineNoCov">          0 :           *dmin__ = *dn;</span></a>
+<a name="10287"><span class="lineNum">   10287 </span>            : </a>
+<a name="10288"><span class="lineNum">   10288 </span>            :     }</a>
+<a name="10289"><span class="lineNum">   10289 </span>            : </a>
+<a name="10290"><span class="lineNum">   10290 </span><span class="lineCov">   12568766 :     z__[j4 + 2] = *dn;</span></a>
+<a name="10291"><span class="lineNum">   10291 </span><span class="lineCov">   12568766 :     z__[(*n0 &lt;&lt; 2) - *pp] = emin;</span></a>
+<a name="10292"><span class="lineNum">   10292 </span><span class="lineCov">   12568766 :     return;</span></a>
+<a name="10293"><span class="lineNum">   10293 </span>            : </a>
+<a name="10294"><span class="lineNum">   10294 </span>            : }</a>
+<a name="10295"><span class="lineNum">   10295 </span>            : </a>
+<a name="10296"><span class="lineNum">   10296 </span>            : }</a>
+<a name="10297"><span class="lineNum">   10297 </span>            : }</a>
+<a name="10298"><span class="lineNum">   10298 </span>            : #include &lt;cmath&gt;</a>
+<a name="10299"><span class="lineNum">   10299 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="10300"><span class="lineNum">   10300 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="10301"><span class="lineNum">   10301 </span>            : </a>
+<a name="10302"><span class="lineNum">   10302 </span>            : #include &quot;real.h&quot;</a>
+<a name="10303"><span class="lineNum">   10303 </span>            : </a>
+<a name="10304"><span class="lineNum">   10304 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="10305"><span class="lineNum">   10305 </span>            : namespace PLMD{</a>
+<a name="10306"><span class="lineNum">   10306 </span>            : namespace lapack{</a>
+<a name="10307"><span class="lineNum">   10307 </span>            : using namespace blas;</a>
+<a name="10308"><span class="lineNum">   10308 </span>            : void </a>
+<a name="10309"><span class="lineNum">   10309 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlasq6,DLASQ6)(int *i0, </span></a>
+<a name="10310"><span class="lineNum">   10310 </span>            :         int *n0, </a>
+<a name="10311"><span class="lineNum">   10311 </span>            :         double *z__, </a>
+<a name="10312"><span class="lineNum">   10312 </span>            :         int *pp, </a>
+<a name="10313"><span class="lineNum">   10313 </span>            :         double *dmin__, </a>
+<a name="10314"><span class="lineNum">   10314 </span>            :         double *dmin1, </a>
+<a name="10315"><span class="lineNum">   10315 </span>            :         double *dmin2,</a>
+<a name="10316"><span class="lineNum">   10316 </span>            :         double *dn, </a>
+<a name="10317"><span class="lineNum">   10317 </span>            :         double *dnm1, </a>
+<a name="10318"><span class="lineNum">   10318 </span>            :         double *dnm2)</a>
+<a name="10319"><span class="lineNum">   10319 </span>            : {</a>
+<a name="10320"><span class="lineNum">   10320 </span>            :     int i__1;</a>
+<a name="10321"><span class="lineNum">   10321 </span>            :     double d__1, d__2;</a>
+<a name="10322"><span class="lineNum">   10322 </span>            : </a>
+<a name="10323"><span class="lineNum">   10323 </span>            :     /* Local variables */</a>
+<a name="10324"><span class="lineNum">   10324 </span>            :     double d__;</a>
+<a name="10325"><span class="lineNum">   10325 </span>            :     int j4, j4p2;</a>
+<a name="10326"><span class="lineNum">   10326 </span>            :     double emin, temp;</a>
+<a name="10327"><span class="lineNum">   10327 </span>            :     const double safemin = PLUMED_GMX_DOUBLE_MIN*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="10328"><span class="lineNum">   10328 </span>            : </a>
+<a name="10329"><span class="lineNum">   10329 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="10330"><span class="lineNum">   10330 </span>            : </a>
+<a name="10331"><span class="lineNum">   10331 </span><span class="lineNoCov">          0 :     if (*n0 - *i0 - 1 &lt;= 0) {</span></a>
+<a name="10332"><span class="lineNum">   10332 </span>            :         return;</a>
+<a name="10333"><span class="lineNum">   10333 </span>            :     }</a>
+<a name="10334"><span class="lineNum">   10334 </span>            : </a>
+<a name="10335"><span class="lineNum">   10335 </span><span class="lineNoCov">          0 :     j4 = (*i0 &lt;&lt; 2) + *pp - 3;</span></a>
+<a name="10336"><span class="lineNum">   10336 </span><span class="lineNoCov">          0 :     emin = z__[j4 + 4];</span></a>
+<a name="10337"><span class="lineNum">   10337 </span><span class="lineNoCov">          0 :     d__ = z__[j4];</span></a>
+<a name="10338"><span class="lineNum">   10338 </span><span class="lineNoCov">          0 :     *dmin__ = d__;</span></a>
+<a name="10339"><span class="lineNum">   10339 </span>            : </a>
+<a name="10340"><span class="lineNum">   10340 </span><span class="lineNoCov">          0 :     if (*pp == 0) {</span></a>
+<a name="10341"><span class="lineNum">   10341 </span><span class="lineNoCov">          0 :         i__1 = 4*(*n0 - 3);</span></a>
+<a name="10342"><span class="lineNum">   10342 </span><span class="lineNoCov">          0 :         for (j4 = *i0*4; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="10343"><span class="lineNum">   10343 </span><span class="lineNoCov">          0 :             z__[j4 - 2] = d__ + z__[j4 - 1];</span></a>
+<a name="10344"><span class="lineNum">   10344 </span><span class="lineNoCov">          0 :             if (std::abs(z__[j4 - 2])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10345"><span class="lineNum">   10345 </span><span class="lineNoCov">          0 :                 z__[j4] = 0.;</span></a>
+<a name="10346"><span class="lineNum">   10346 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 1];</span></a>
+<a name="10347"><span class="lineNum">   10347 </span><span class="lineNoCov">          0 :                 *dmin__ = d__;</span></a>
+<a name="10348"><span class="lineNum">   10348 </span>            :                 emin = 0.;</a>
+<a name="10349"><span class="lineNum">   10349 </span><span class="lineNoCov">          0 :             } else if (safemin * z__[j4 + 1] &lt; z__[j4 - 2] &amp;&amp; safemin * z__[j4 </span></a>
+<a name="10350"><span class="lineNum">   10350 </span>            :                     - 2] &lt; z__[j4 + 1]) {</a>
+<a name="10351"><span class="lineNum">   10351 </span><span class="lineNoCov">          0 :                 temp = z__[j4 + 1] / z__[j4 - 2];</span></a>
+<a name="10352"><span class="lineNum">   10352 </span><span class="lineNoCov">          0 :                 z__[j4] = z__[j4 - 1] * temp;</span></a>
+<a name="10353"><span class="lineNum">   10353 </span><span class="lineNoCov">          0 :                 d__ *= temp;</span></a>
+<a name="10354"><span class="lineNum">   10354 </span>            :             } else {</a>
+<a name="10355"><span class="lineNum">   10355 </span><span class="lineNoCov">          0 :                 z__[j4] = z__[j4 + 1] * (z__[j4 - 1] / z__[j4 - 2]);</span></a>
+<a name="10356"><span class="lineNum">   10356 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 1] * (d__ / z__[j4 - 2]);</span></a>
+<a name="10357"><span class="lineNum">   10357 </span>            :             }</a>
+<a name="10358"><span class="lineNum">   10358 </span><span class="lineNoCov">          0 :             if(d__&lt;*dmin__)</span></a>
+<a name="10359"><span class="lineNum">   10359 </span><span class="lineNoCov">          0 :               *dmin__ = d__;</span></a>
+<a name="10360"><span class="lineNum">   10360 </span>            : </a>
+<a name="10361"><span class="lineNum">   10361 </span><span class="lineNoCov">          0 :             d__1 = emin, d__2 = z__[j4];</span></a>
+<a name="10362"><span class="lineNum">   10362 </span><span class="lineNoCov">          0 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="10363"><span class="lineNum">   10363 </span>            :         }</a>
+<a name="10364"><span class="lineNum">   10364 </span>            :     } else {</a>
+<a name="10365"><span class="lineNum">   10365 </span><span class="lineNoCov">          0 :         i__1 = 4*(*n0 - 3);</span></a>
+<a name="10366"><span class="lineNum">   10366 </span><span class="lineNoCov">          0 :         for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="10367"><span class="lineNum">   10367 </span><span class="lineNoCov">          0 :             z__[j4 - 3] = d__ + z__[j4];</span></a>
+<a name="10368"><span class="lineNum">   10368 </span><span class="lineNoCov">          0 :             if (std::abs(z__[j4 - 3])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10369"><span class="lineNum">   10369 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = 0.;</span></a>
+<a name="10370"><span class="lineNum">   10370 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 2];</span></a>
+<a name="10371"><span class="lineNum">   10371 </span><span class="lineNoCov">          0 :                 *dmin__ = d__;</span></a>
+<a name="10372"><span class="lineNum">   10372 </span>            :                 emin = 0.;</a>
+<a name="10373"><span class="lineNum">   10373 </span><span class="lineNoCov">          0 :             } else if (safemin * z__[j4 + 2] &lt; z__[j4 - 3] &amp;&amp; safemin * z__[j4 </span></a>
+<a name="10374"><span class="lineNum">   10374 </span>            :                     - 3] &lt; z__[j4 + 2]) {</a>
+<a name="10375"><span class="lineNum">   10375 </span><span class="lineNoCov">          0 :                 temp = z__[j4 + 2] / z__[j4 - 3];</span></a>
+<a name="10376"><span class="lineNum">   10376 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = z__[j4] * temp;</span></a>
+<a name="10377"><span class="lineNum">   10377 </span><span class="lineNoCov">          0 :                 d__ *= temp;</span></a>
+<a name="10378"><span class="lineNum">   10378 </span>            :             } else {</a>
+<a name="10379"><span class="lineNum">   10379 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = z__[j4 + 2] * (z__[j4] / z__[j4 - 3]);</span></a>
+<a name="10380"><span class="lineNum">   10380 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 2] * (d__ / z__[j4 - 3]);</span></a>
+<a name="10381"><span class="lineNum">   10381 </span>            :             }</a>
+<a name="10382"><span class="lineNum">   10382 </span><span class="lineNoCov">          0 :             if(d__&lt;*dmin__)</span></a>
+<a name="10383"><span class="lineNum">   10383 </span><span class="lineNoCov">          0 :               *dmin__ = d__;</span></a>
+<a name="10384"><span class="lineNum">   10384 </span><span class="lineNoCov">          0 :             d__1 = emin, d__2 = z__[j4 - 1];</span></a>
+<a name="10385"><span class="lineNum">   10385 </span><span class="lineNoCov">          0 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="10386"><span class="lineNum">   10386 </span>            :         }</a>
+<a name="10387"><span class="lineNum">   10387 </span>            :     }</a>
+<a name="10388"><span class="lineNum">   10388 </span>            : </a>
+<a name="10389"><span class="lineNum">   10389 </span><span class="lineNoCov">          0 :     *dnm2 = d__;</span></a>
+<a name="10390"><span class="lineNum">   10390 </span><span class="lineNoCov">          0 :     *dmin2 = *dmin__;</span></a>
+<a name="10391"><span class="lineNum">   10391 </span><span class="lineNoCov">          0 :     j4 = 4*(*n0 - 2) - *pp;</span></a>
+<a name="10392"><span class="lineNum">   10392 </span><span class="lineNoCov">          0 :     j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="10393"><span class="lineNum">   10393 </span><span class="lineNoCov">          0 :     z__[j4 - 2] = *dnm2 + z__[j4p2];</span></a>
+<a name="10394"><span class="lineNum">   10394 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j4 - 2])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10395"><span class="lineNum">   10395 </span><span class="lineNoCov">          0 :         z__[j4] = 0.;</span></a>
+<a name="10396"><span class="lineNum">   10396 </span><span class="lineNoCov">          0 :         *dnm1 = z__[j4p2 + 2];</span></a>
+<a name="10397"><span class="lineNum">   10397 </span><span class="lineNoCov">          0 :         *dmin__ = *dnm1;</span></a>
+<a name="10398"><span class="lineNum">   10398 </span>            :         emin = 0.;</a>
+<a name="10399"><span class="lineNum">   10399 </span><span class="lineNoCov">          0 :     } else if (safemin * z__[j4p2 + 2] &lt; z__[j4 - 2] &amp;&amp; safemin * z__[j4 - 2] &lt; </span></a>
+<a name="10400"><span class="lineNum">   10400 </span>            :             z__[j4p2 + 2]) {</a>
+<a name="10401"><span class="lineNum">   10401 </span><span class="lineNoCov">          0 :         temp = z__[j4p2 + 2] / z__[j4 - 2];</span></a>
+<a name="10402"><span class="lineNum">   10402 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2] * temp;</span></a>
+<a name="10403"><span class="lineNum">   10403 </span><span class="lineNoCov">          0 :         *dnm1 = *dnm2 * temp;</span></a>
+<a name="10404"><span class="lineNum">   10404 </span>            :     } else {</a>
+<a name="10405"><span class="lineNum">   10405 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="10406"><span class="lineNum">   10406 </span><span class="lineNoCov">          0 :         *dnm1 = z__[j4p2 + 2] * (*dnm2 / z__[j4 - 2]);</span></a>
+<a name="10407"><span class="lineNum">   10407 </span>            :     }</a>
+<a name="10408"><span class="lineNum">   10408 </span><span class="lineNoCov">          0 :     if(*dnm1&lt;*dmin__)</span></a>
+<a name="10409"><span class="lineNum">   10409 </span><span class="lineNoCov">          0 :       *dmin__ = *dnm1;</span></a>
+<a name="10410"><span class="lineNum">   10410 </span>            : </a>
+<a name="10411"><span class="lineNum">   10411 </span><span class="lineNoCov">          0 :     *dmin1 = *dmin__;</span></a>
+<a name="10412"><span class="lineNum">   10412 </span><span class="lineNoCov">          0 :     j4 += 4;</span></a>
+<a name="10413"><span class="lineNum">   10413 </span><span class="lineNoCov">          0 :     j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="10414"><span class="lineNum">   10414 </span><span class="lineNoCov">          0 :     z__[j4 - 2] = *dnm1 + z__[j4p2];</span></a>
+<a name="10415"><span class="lineNum">   10415 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j4 - 2])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10416"><span class="lineNum">   10416 </span><span class="lineNoCov">          0 :         z__[j4] = 0.;</span></a>
+<a name="10417"><span class="lineNum">   10417 </span><span class="lineNoCov">          0 :         *dn = z__[j4p2 + 2];</span></a>
+<a name="10418"><span class="lineNum">   10418 </span><span class="lineNoCov">          0 :         *dmin__ = *dn;</span></a>
+<a name="10419"><span class="lineNum">   10419 </span>            :         emin = 0.;</a>
+<a name="10420"><span class="lineNum">   10420 </span><span class="lineNoCov">          0 :     } else if (safemin * z__[j4p2 + 2] &lt; z__[j4 - 2] &amp;&amp; safemin * z__[j4 - 2] &lt; </span></a>
+<a name="10421"><span class="lineNum">   10421 </span>            :             z__[j4p2 + 2]) {</a>
+<a name="10422"><span class="lineNum">   10422 </span><span class="lineNoCov">          0 :         temp = z__[j4p2 + 2] / z__[j4 - 2];</span></a>
+<a name="10423"><span class="lineNum">   10423 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2] * temp;</span></a>
+<a name="10424"><span class="lineNum">   10424 </span><span class="lineNoCov">          0 :         *dn = *dnm1 * temp;</span></a>
+<a name="10425"><span class="lineNum">   10425 </span>            :     } else {</a>
+<a name="10426"><span class="lineNum">   10426 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="10427"><span class="lineNum">   10427 </span><span class="lineNoCov">          0 :         *dn = z__[j4p2 + 2] * (*dnm1 / z__[j4 - 2]);</span></a>
+<a name="10428"><span class="lineNum">   10428 </span>            :     }</a>
+<a name="10429"><span class="lineNum">   10429 </span><span class="lineNoCov">          0 :     if(*dn&lt;*dmin__)</span></a>
+<a name="10430"><span class="lineNum">   10430 </span><span class="lineNoCov">          0 :       *dmin__ = *dn;</span></a>
+<a name="10431"><span class="lineNum">   10431 </span>            : </a>
+<a name="10432"><span class="lineNum">   10432 </span><span class="lineNoCov">          0 :     z__[j4 + 2] = *dn;</span></a>
+<a name="10433"><span class="lineNum">   10433 </span><span class="lineNoCov">          0 :     z__[(*n0 &lt;&lt; 2) - *pp] = emin;</span></a>
+<a name="10434"><span class="lineNum">   10434 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="10435"><span class="lineNum">   10435 </span>            : </a>
+<a name="10436"><span class="lineNum">   10436 </span>            : </a>
+<a name="10437"><span class="lineNum">   10437 </span>            : } </a>
+<a name="10438"><span class="lineNum">   10438 </span>            : }</a>
+<a name="10439"><span class="lineNum">   10439 </span>            : }</a>
+<a name="10440"><span class="lineNum">   10440 </span>            : #include &lt;cmath&gt;</a>
+<a name="10441"><span class="lineNum">   10441 </span>            : </a>
+<a name="10442"><span class="lineNum">   10442 </span>            : #include &quot;real.h&quot;</a>
+<a name="10443"><span class="lineNum">   10443 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="10444"><span class="lineNum">   10444 </span>            : </a>
+<a name="10445"><span class="lineNum">   10445 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="10446"><span class="lineNum">   10446 </span>            : namespace PLMD{</a>
+<a name="10447"><span class="lineNum">   10447 </span>            : namespace lapack{</a>
+<a name="10448"><span class="lineNum">   10448 </span>            : using namespace blas;</a>
+<a name="10449"><span class="lineNum">   10449 </span>            : void </a>
+<a name="10450"><span class="lineNum">   10450 </span><span class="lineCov">       9382 : PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(const char *side, </span></a>
+<a name="10451"><span class="lineNum">   10451 </span>            :        const char *pivot, </a>
+<a name="10452"><span class="lineNum">   10452 </span>            :        const char *direct, </a>
+<a name="10453"><span class="lineNum">   10453 </span>            :        int *m,</a>
+<a name="10454"><span class="lineNum">   10454 </span>            :        int *n, </a>
+<a name="10455"><span class="lineNum">   10455 </span>            :        double *c__, </a>
+<a name="10456"><span class="lineNum">   10456 </span>            :        double *s, </a>
+<a name="10457"><span class="lineNum">   10457 </span>            :        double *a, </a>
+<a name="10458"><span class="lineNum">   10458 </span>            :        int *lda)</a>
+<a name="10459"><span class="lineNum">   10459 </span>            : {</a>
+<a name="10460"><span class="lineNum">   10460 </span>            :     /* System generated locals */</a>
+<a name="10461"><span class="lineNum">   10461 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="10462"><span class="lineNum">   10462 </span>            : </a>
+<a name="10463"><span class="lineNum">   10463 </span>            :     /* Local variables */</a>
+<a name="10464"><span class="lineNum">   10464 </span>            :     int i__, j;</a>
+<a name="10465"><span class="lineNum">   10465 </span>            :     double temp;</a>
+<a name="10466"><span class="lineNum">   10466 </span>            :     double ctemp, stemp;</a>
+<a name="10467"><span class="lineNum">   10467 </span>            : </a>
+<a name="10468"><span class="lineNum">   10468 </span><span class="lineCov">       9382 :     --c__;</span></a>
+<a name="10469"><span class="lineNum">   10469 </span><span class="lineCov">       9382 :     --s;</span></a>
+<a name="10470"><span class="lineNum">   10470 </span><span class="lineCov">       9382 :     a_dim1 = *lda;</span></a>
+<a name="10471"><span class="lineNum">   10471 </span><span class="lineCov">       9382 :     a_offset = 1 + a_dim1;</span></a>
+<a name="10472"><span class="lineNum">   10472 </span><span class="lineCov">       9382 :     a -= a_offset;</span></a>
+<a name="10473"><span class="lineNum">   10473 </span>            : </a>
+<a name="10474"><span class="lineNum">   10474 </span>            :     /* Function Body */</a>
+<a name="10475"><span class="lineNum">   10475 </span>            : </a>
+<a name="10476"><span class="lineNum">   10476 </span><span class="lineCov">       9382 :     if (*m == 0 || *n == 0) {</span></a>
+<a name="10477"><span class="lineNum">   10477 </span>            :         return;</a>
+<a name="10478"><span class="lineNum">   10478 </span>            :     }</a>
+<a name="10479"><span class="lineNum">   10479 </span><span class="lineCov">       9382 :     if (*side=='L' || *side=='l') {</span></a>
+<a name="10480"><span class="lineNum">   10480 </span>            : </a>
+<a name="10481"><span class="lineNum">   10481 </span><span class="lineCov">       4691 :         if (*pivot=='V' || *pivot=='v') {</span></a>
+<a name="10482"><span class="lineNum">   10482 </span><span class="lineCov">       4691 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="10483"><span class="lineNum">   10483 </span>            :                 i__1 = *m - 1;</a>
+<a name="10484"><span class="lineNum">   10484 </span><span class="lineCov">      49675 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="10485"><span class="lineNum">   10485 </span><span class="lineCov">      45017 :                     ctemp = c__[j];</span></a>
+<a name="10486"><span class="lineNum">   10486 </span><span class="lineCov">      45017 :                     stemp = s[j];</span></a>
+<a name="10487"><span class="lineNum">   10487 </span><span class="lineCov">      45017 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10488"><span class="lineNum">   10488 </span><span class="lineCov">      45017 :                         i__2 = *n;</span></a>
+<a name="10489"><span class="lineNum">   10489 </span><span class="lineCov">     861025 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="10490"><span class="lineNum">   10490 </span><span class="lineCov">     816008 :                             temp = a[j + 1 + i__ * a_dim1];</span></a>
+<a name="10491"><span class="lineNum">   10491 </span><span class="lineCov">     816008 :                             a[j + 1 + i__ * a_dim1] = ctemp * temp - stemp * </span></a>
+<a name="10492"><span class="lineNum">   10492 </span><span class="lineCov">     816008 :                                     a[j + i__ * a_dim1];</span></a>
+<a name="10493"><span class="lineNum">   10493 </span><span class="lineCov">     816008 :                             a[j + i__ * a_dim1] = stemp * temp + ctemp * a[j </span></a>
+<a name="10494"><span class="lineNum">   10494 </span><span class="lineCov">     816008 :                                     + i__ * a_dim1];</span></a>
+<a name="10495"><span class="lineNum">   10495 </span>            :                         }</a>
+<a name="10496"><span class="lineNum">   10496 </span>            :                     }</a>
+<a name="10497"><span class="lineNum">   10497 </span>            :                 }</a>
+<a name="10498"><span class="lineNum">   10498 </span><span class="lineCov">         33 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="10499"><span class="lineNum">   10499 </span><span class="lineCov">        305 :                 for (j = *m - 1; j &gt;= 1; --j) {</span></a>
+<a name="10500"><span class="lineNum">   10500 </span><span class="lineCov">        272 :                     ctemp = c__[j];</span></a>
+<a name="10501"><span class="lineNum">   10501 </span><span class="lineCov">        272 :                     stemp = s[j];</span></a>
+<a name="10502"><span class="lineNum">   10502 </span><span class="lineCov">        272 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10503"><span class="lineNum">   10503 </span><span class="lineCov">        272 :                         i__1 = *n;</span></a>
+<a name="10504"><span class="lineNum">   10504 </span><span class="lineCov">       4080 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10505"><span class="lineNum">   10505 </span><span class="lineCov">       3808 :                             temp = a[j + 1 + i__ * a_dim1];</span></a>
+<a name="10506"><span class="lineNum">   10506 </span><span class="lineCov">       3808 :                             a[j + 1 + i__ * a_dim1] = ctemp * temp - stemp * </span></a>
+<a name="10507"><span class="lineNum">   10507 </span><span class="lineCov">       3808 :                                     a[j + i__ * a_dim1];</span></a>
+<a name="10508"><span class="lineNum">   10508 </span><span class="lineCov">       3808 :                             a[j + i__ * a_dim1] = stemp * temp + ctemp * a[j </span></a>
+<a name="10509"><span class="lineNum">   10509 </span><span class="lineCov">       3808 :                                     + i__ * a_dim1];</span></a>
+<a name="10510"><span class="lineNum">   10510 </span>            :                         }</a>
+<a name="10511"><span class="lineNum">   10511 </span>            :                     }</a>
+<a name="10512"><span class="lineNum">   10512 </span>            :                 }</a>
+<a name="10513"><span class="lineNum">   10513 </span>            :             }</a>
+<a name="10514"><span class="lineNum">   10514 </span><span class="lineNoCov">          0 :         } else if (*pivot=='T' || *pivot=='t') {</span></a>
+<a name="10515"><span class="lineNum">   10515 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="10516"><span class="lineNum">   10516 </span>            :                 i__1 = *m;</a>
+<a name="10517"><span class="lineNum">   10517 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="10518"><span class="lineNum">   10518 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="10519"><span class="lineNum">   10519 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="10520"><span class="lineNum">   10520 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10521"><span class="lineNum">   10521 </span><span class="lineNoCov">          0 :                         i__2 = *n;</span></a>
+<a name="10522"><span class="lineNum">   10522 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="10523"><span class="lineNum">   10523 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="10524"><span class="lineNum">   10524 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="10525"><span class="lineNum">   10525 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="10526"><span class="lineNum">   10526 </span><span class="lineNoCov">          0 :                             a[i__ * a_dim1 + 1] = stemp * temp + ctemp * a[</span></a>
+<a name="10527"><span class="lineNum">   10527 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="10528"><span class="lineNum">   10528 </span>            :                         }</a>
+<a name="10529"><span class="lineNum">   10529 </span>            :                     }</a>
+<a name="10530"><span class="lineNum">   10530 </span>            :                 }</a>
+<a name="10531"><span class="lineNum">   10531 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="10532"><span class="lineNum">   10532 </span><span class="lineNoCov">          0 :                 for (j = *m; j &gt;= 2; --j) {</span></a>
+<a name="10533"><span class="lineNum">   10533 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="10534"><span class="lineNum">   10534 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="10535"><span class="lineNum">   10535 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10536"><span class="lineNum">   10536 </span><span class="lineNoCov">          0 :                         i__1 = *n;</span></a>
+<a name="10537"><span class="lineNum">   10537 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10538"><span class="lineNum">   10538 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="10539"><span class="lineNum">   10539 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="10540"><span class="lineNum">   10540 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="10541"><span class="lineNum">   10541 </span><span class="lineNoCov">          0 :                             a[i__ * a_dim1 + 1] = stemp * temp + ctemp * a[</span></a>
+<a name="10542"><span class="lineNum">   10542 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="10543"><span class="lineNum">   10543 </span>            :                         }</a>
+<a name="10544"><span class="lineNum">   10544 </span>            :                     }</a>
+<a name="10545"><span class="lineNum">   10545 </span>            :                 }</a>
+<a name="10546"><span class="lineNum">   10546 </span>            :             }</a>
+<a name="10547"><span class="lineNum">   10547 </span><span class="lineNoCov">          0 :         } else if (*pivot=='B' || *pivot=='b') {</span></a>
+<a name="10548"><span class="lineNum">   10548 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="10549"><span class="lineNum">   10549 </span>            :                 i__1 = *m - 1;</a>
+<a name="10550"><span class="lineNum">   10550 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="10551"><span class="lineNum">   10551 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="10552"><span class="lineNum">   10552 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="10553"><span class="lineNum">   10553 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10554"><span class="lineNum">   10554 </span><span class="lineNoCov">          0 :                         i__2 = *n;</span></a>
+<a name="10555"><span class="lineNum">   10555 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="10556"><span class="lineNum">   10556 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="10557"><span class="lineNum">   10557 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = stemp * a[*m + i__ * a_dim1]</span></a>
+<a name="10558"><span class="lineNum">   10558 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="10559"><span class="lineNum">   10559 </span><span class="lineNoCov">          0 :                             a[*m + i__ * a_dim1] = ctemp * a[*m + i__ * </span></a>
+<a name="10560"><span class="lineNum">   10560 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="10561"><span class="lineNum">   10561 </span>            :                         }</a>
+<a name="10562"><span class="lineNum">   10562 </span>            :                     }</a>
+<a name="10563"><span class="lineNum">   10563 </span>            :                 }</a>
+<a name="10564"><span class="lineNum">   10564 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="10565"><span class="lineNum">   10565 </span><span class="lineNoCov">          0 :                 for (j = *m - 1; j &gt;= 1; --j) {</span></a>
+<a name="10566"><span class="lineNum">   10566 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="10567"><span class="lineNum">   10567 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="10568"><span class="lineNum">   10568 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10569"><span class="lineNum">   10569 </span><span class="lineNoCov">          0 :                         i__1 = *n;</span></a>
+<a name="10570"><span class="lineNum">   10570 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10571"><span class="lineNum">   10571 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="10572"><span class="lineNum">   10572 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = stemp * a[*m + i__ * a_dim1]</span></a>
+<a name="10573"><span class="lineNum">   10573 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="10574"><span class="lineNum">   10574 </span><span class="lineNoCov">          0 :                             a[*m + i__ * a_dim1] = ctemp * a[*m + i__ * </span></a>
+<a name="10575"><span class="lineNum">   10575 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="10576"><span class="lineNum">   10576 </span>            :                         }</a>
+<a name="10577"><span class="lineNum">   10577 </span>            :                     }</a>
+<a name="10578"><span class="lineNum">   10578 </span>            :                 }</a>
+<a name="10579"><span class="lineNum">   10579 </span>            :             }</a>
+<a name="10580"><span class="lineNum">   10580 </span>            :         }</a>
+<a name="10581"><span class="lineNum">   10581 </span><span class="lineCov">       4691 :     } else if (*side=='R' || *side=='r') {</span></a>
+<a name="10582"><span class="lineNum">   10582 </span>            : </a>
+<a name="10583"><span class="lineNum">   10583 </span><span class="lineCov">       4691 :         if (*pivot=='V' || *pivot=='v') {</span></a>
+<a name="10584"><span class="lineNum">   10584 </span><span class="lineCov">       4691 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="10585"><span class="lineNum">   10585 </span>            :                 i__1 = *n - 1;</a>
+<a name="10586"><span class="lineNum">   10586 </span><span class="lineCov">      49616 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="10587"><span class="lineNum">   10587 </span><span class="lineCov">      44958 :                     ctemp = c__[j];</span></a>
+<a name="10588"><span class="lineNum">   10588 </span><span class="lineCov">      44958 :                     stemp = s[j];</span></a>
+<a name="10589"><span class="lineNum">   10589 </span><span class="lineCov">      44958 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10590"><span class="lineNum">   10590 </span><span class="lineCov">      44958 :                         i__2 = *m;</span></a>
+<a name="10591"><span class="lineNum">   10591 </span><span class="lineCov">     843208 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="10592"><span class="lineNum">   10592 </span><span class="lineCov">     798250 :                             temp = a[i__ + (j + 1) * a_dim1];</span></a>
+<a name="10593"><span class="lineNum">   10593 </span><span class="lineCov">     798250 :                             a[i__ + (j + 1) * a_dim1] = ctemp * temp - stemp *</span></a>
+<a name="10594"><span class="lineNum">   10594 </span><span class="lineCov">     798250 :                                      a[i__ + j * a_dim1];</span></a>
+<a name="10595"><span class="lineNum">   10595 </span><span class="lineCov">     798250 :                             a[i__ + j * a_dim1] = stemp * temp + ctemp * a[</span></a>
+<a name="10596"><span class="lineNum">   10596 </span><span class="lineCov">     798250 :                                     i__ + j * a_dim1];</span></a>
+<a name="10597"><span class="lineNum">   10597 </span>            :                         }</a>
+<a name="10598"><span class="lineNum">   10598 </span>            :                     }</a>
+<a name="10599"><span class="lineNum">   10599 </span>            :                 }</a>
+<a name="10600"><span class="lineNum">   10600 </span><span class="lineCov">         33 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="10601"><span class="lineNum">   10601 </span><span class="lineCov">        305 :                 for (j = *n - 1; j &gt;= 1; --j) {</span></a>
+<a name="10602"><span class="lineNum">   10602 </span><span class="lineCov">        272 :                     ctemp = c__[j];</span></a>
+<a name="10603"><span class="lineNum">   10603 </span><span class="lineCov">        272 :                     stemp = s[j];</span></a>
+<a name="10604"><span class="lineNum">   10604 </span><span class="lineCov">        272 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10605"><span class="lineNum">   10605 </span><span class="lineCov">        272 :                         i__1 = *m;</span></a>
+<a name="10606"><span class="lineNum">   10606 </span><span class="lineCov">       4080 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10607"><span class="lineNum">   10607 </span><span class="lineCov">       3808 :                             temp = a[i__ + (j + 1) * a_dim1];</span></a>
+<a name="10608"><span class="lineNum">   10608 </span><span class="lineCov">       3808 :                             a[i__ + (j + 1) * a_dim1] = ctemp * temp - stemp *</span></a>
+<a name="10609"><span class="lineNum">   10609 </span><span class="lineCov">       3808 :                                      a[i__ + j * a_dim1];</span></a>
+<a name="10610"><span class="lineNum">   10610 </span><span class="lineCov">       3808 :                             a[i__ + j * a_dim1] = stemp * temp + ctemp * a[</span></a>
+<a name="10611"><span class="lineNum">   10611 </span><span class="lineCov">       3808 :                                     i__ + j * a_dim1];</span></a>
+<a name="10612"><span class="lineNum">   10612 </span>            :                         }</a>
+<a name="10613"><span class="lineNum">   10613 </span>            :                     }</a>
+<a name="10614"><span class="lineNum">   10614 </span>            :                 }</a>
+<a name="10615"><span class="lineNum">   10615 </span>            :             }</a>
+<a name="10616"><span class="lineNum">   10616 </span><span class="lineNoCov">          0 :         } else if (*pivot=='T' || *pivot=='t') {</span></a>
+<a name="10617"><span class="lineNum">   10617 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="10618"><span class="lineNum">   10618 </span>            :                 i__1 = *n;</a>
+<a name="10619"><span class="lineNum">   10619 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="10620"><span class="lineNum">   10620 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="10621"><span class="lineNum">   10621 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="10622"><span class="lineNum">   10622 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10623"><span class="lineNum">   10623 </span><span class="lineNoCov">          0 :                         i__2 = *m;</span></a>
+<a name="10624"><span class="lineNum">   10624 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="10625"><span class="lineNum">   10625 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="10626"><span class="lineNum">   10626 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="10627"><span class="lineNum">   10627 </span><span class="lineNoCov">          0 :                                     i__ + a_dim1];</span></a>
+<a name="10628"><span class="lineNum">   10628 </span><span class="lineNoCov">          0 :                             a[i__ + a_dim1] = stemp * temp + ctemp * a[i__ + </span></a>
+<a name="10629"><span class="lineNum">   10629 </span><span class="lineNoCov">          0 :                                     a_dim1];</span></a>
+<a name="10630"><span class="lineNum">   10630 </span>            :                         }</a>
+<a name="10631"><span class="lineNum">   10631 </span>            :                     }</a>
+<a name="10632"><span class="lineNum">   10632 </span>            :                 }</a>
+<a name="10633"><span class="lineNum">   10633 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="10634"><span class="lineNum">   10634 </span><span class="lineNoCov">          0 :                 for (j = *n; j &gt;= 2; --j) {</span></a>
+<a name="10635"><span class="lineNum">   10635 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="10636"><span class="lineNum">   10636 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="10637"><span class="lineNum">   10637 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10638"><span class="lineNum">   10638 </span><span class="lineNoCov">          0 :                         i__1 = *m;</span></a>
+<a name="10639"><span class="lineNum">   10639 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10640"><span class="lineNum">   10640 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="10641"><span class="lineNum">   10641 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="10642"><span class="lineNum">   10642 </span><span class="lineNoCov">          0 :                                     i__ + a_dim1];</span></a>
+<a name="10643"><span class="lineNum">   10643 </span><span class="lineNoCov">          0 :                             a[i__ + a_dim1] = stemp * temp + ctemp * a[i__ + </span></a>
+<a name="10644"><span class="lineNum">   10644 </span><span class="lineNoCov">          0 :                                     a_dim1];</span></a>
+<a name="10645"><span class="lineNum">   10645 </span>            :                         }</a>
+<a name="10646"><span class="lineNum">   10646 </span>            :                     }</a>
+<a name="10647"><span class="lineNum">   10647 </span>            :                 }</a>
+<a name="10648"><span class="lineNum">   10648 </span>            :             }</a>
+<a name="10649"><span class="lineNum">   10649 </span><span class="lineNoCov">          0 :         } else if (*pivot=='B' || *pivot=='b') {</span></a>
+<a name="10650"><span class="lineNum">   10650 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="10651"><span class="lineNum">   10651 </span>            :                 i__1 = *n - 1;</a>
+<a name="10652"><span class="lineNum">   10652 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="10653"><span class="lineNum">   10653 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="10654"><span class="lineNum">   10654 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="10655"><span class="lineNum">   10655 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10656"><span class="lineNum">   10656 </span><span class="lineNoCov">          0 :                         i__2 = *m;</span></a>
+<a name="10657"><span class="lineNum">   10657 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="10658"><span class="lineNum">   10658 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="10659"><span class="lineNum">   10659 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = stemp * a[i__ + *n * a_dim1]</span></a>
+<a name="10660"><span class="lineNum">   10660 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="10661"><span class="lineNum">   10661 </span><span class="lineNoCov">          0 :                             a[i__ + *n * a_dim1] = ctemp * a[i__ + *n * </span></a>
+<a name="10662"><span class="lineNum">   10662 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="10663"><span class="lineNum">   10663 </span>            :                         }</a>
+<a name="10664"><span class="lineNum">   10664 </span>            :                     }</a>
+<a name="10665"><span class="lineNum">   10665 </span>            :                 }</a>
+<a name="10666"><span class="lineNum">   10666 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="10667"><span class="lineNum">   10667 </span><span class="lineNoCov">          0 :                 for (j = *n - 1; j &gt;= 1; --j) {</span></a>
+<a name="10668"><span class="lineNum">   10668 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="10669"><span class="lineNum">   10669 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="10670"><span class="lineNum">   10670 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_DOUBLE_EPS || std::abs(stemp)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="10671"><span class="lineNum">   10671 </span><span class="lineNoCov">          0 :                         i__1 = *m;</span></a>
+<a name="10672"><span class="lineNum">   10672 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10673"><span class="lineNum">   10673 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="10674"><span class="lineNum">   10674 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = stemp * a[i__ + *n * a_dim1]</span></a>
+<a name="10675"><span class="lineNum">   10675 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="10676"><span class="lineNum">   10676 </span><span class="lineNoCov">          0 :                             a[i__ + *n * a_dim1] = ctemp * a[i__ + *n * </span></a>
+<a name="10677"><span class="lineNum">   10677 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="10678"><span class="lineNum">   10678 </span>            :                         }</a>
+<a name="10679"><span class="lineNum">   10679 </span>            :                     }</a>
+<a name="10680"><span class="lineNum">   10680 </span>            :                 }</a>
+<a name="10681"><span class="lineNum">   10681 </span>            :             }</a>
+<a name="10682"><span class="lineNum">   10682 </span>            :         }</a>
+<a name="10683"><span class="lineNum">   10683 </span>            :     }</a>
+<a name="10684"><span class="lineNum">   10684 </span>            : </a>
+<a name="10685"><span class="lineNum">   10685 </span>            :     return;</a>
+<a name="10686"><span class="lineNum">   10686 </span>            : </a>
+<a name="10687"><span class="lineNum">   10687 </span>            : }</a>
+<a name="10688"><span class="lineNum">   10688 </span>            : </a>
+<a name="10689"><span class="lineNum">   10689 </span>            : </a>
+<a name="10690"><span class="lineNum">   10690 </span>            : }</a>
+<a name="10691"><span class="lineNum">   10691 </span>            : }</a>
+<a name="10692"><span class="lineNum">   10692 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="10693"><span class="lineNum">   10693 </span>            : </a>
+<a name="10694"><span class="lineNum">   10694 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="10695"><span class="lineNum">   10695 </span>            : namespace PLMD{</a>
+<a name="10696"><span class="lineNum">   10696 </span>            : namespace lapack{</a>
+<a name="10697"><span class="lineNum">   10697 </span>            : using namespace blas;</a>
+<a name="10698"><span class="lineNum">   10698 </span>            : void </a>
+<a name="10699"><span class="lineNum">   10699 </span><span class="lineCov">     557317 : PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(const char *id, </span></a>
+<a name="10700"><span class="lineNum">   10700 </span>            :         int *n, </a>
+<a name="10701"><span class="lineNum">   10701 </span>            :         double *d__, </a>
+<a name="10702"><span class="lineNum">   10702 </span>            :         int *info)</a>
+<a name="10703"><span class="lineNum">   10703 </span>            : {</a>
+<a name="10704"><span class="lineNum">   10704 </span>            :     int i__1, i__2;</a>
+<a name="10705"><span class="lineNum">   10705 </span>            : </a>
+<a name="10706"><span class="lineNum">   10706 </span>            :     int i__, j;</a>
+<a name="10707"><span class="lineNum">   10707 </span>            :     double d1, d2, d3;</a>
+<a name="10708"><span class="lineNum">   10708 </span>            :     int dir;</a>
+<a name="10709"><span class="lineNum">   10709 </span>            :     double tmp;</a>
+<a name="10710"><span class="lineNum">   10710 </span>            :     int endd;</a>
+<a name="10711"><span class="lineNum">   10711 </span>            :     int stack[64];</a>
+<a name="10712"><span class="lineNum">   10712 </span>            :     double dmnmx;</a>
+<a name="10713"><span class="lineNum">   10713 </span>            :     int start;</a>
+<a name="10714"><span class="lineNum">   10714 </span>            :     int stkpnt;</a>
+<a name="10715"><span class="lineNum">   10715 </span>            : </a>
+<a name="10716"><span class="lineNum">   10716 </span><span class="lineCov">     557317 :     --d__;</span></a>
+<a name="10717"><span class="lineNum">   10717 </span>            : </a>
+<a name="10718"><span class="lineNum">   10718 </span><span class="lineCov">     557317 :     *info = 0;</span></a>
+<a name="10719"><span class="lineNum">   10719 </span>            :     dir = -1;</a>
+<a name="10720"><span class="lineNum">   10720 </span><span class="lineCov">     557317 :     if (*id=='D' || *id=='d') </span></a>
+<a name="10721"><span class="lineNum">   10721 </span>            :         dir = 0;</a>
+<a name="10722"><span class="lineNum">   10722 </span><span class="lineCov">        670 :     else if (*id=='I' || *id=='i') </span></a>
+<a name="10723"><span class="lineNum">   10723 </span>            :         dir = 1;</a>
+<a name="10724"><span class="lineNum">   10724 </span>            :    </a>
+<a name="10725"><span class="lineNum">   10725 </span>            :     if (dir == -1) {</a>
+<a name="10726"><span class="lineNum">   10726 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="10727"><span class="lineNum">   10727 </span><span class="lineCov">     557317 :     } else if (*n &lt; 0) {</span></a>
+<a name="10728"><span class="lineNum">   10728 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="10729"><span class="lineNum">   10729 </span>            :     }</a>
+<a name="10730"><span class="lineNum">   10730 </span><span class="lineCov">     557317 :     if (*info != 0) {</span></a>
+<a name="10731"><span class="lineNum">   10731 </span>            :         return;</a>
+<a name="10732"><span class="lineNum">   10732 </span>            :     }</a>
+<a name="10733"><span class="lineNum">   10733 </span><span class="lineCov">     557317 :     if (*n &lt;= 1) {</span></a>
+<a name="10734"><span class="lineNum">   10734 </span>            :         return;</a>
+<a name="10735"><span class="lineNum">   10735 </span>            :     }</a>
+<a name="10736"><span class="lineNum">   10736 </span>            : </a>
+<a name="10737"><span class="lineNum">   10737 </span>            :     stkpnt = 1;</a>
+<a name="10738"><span class="lineNum">   10738 </span><span class="lineCov">     556656 :     stack[0] = 1;</span></a>
+<a name="10739"><span class="lineNum">   10739 </span><span class="lineCov">     556656 :     stack[1] = *n;</span></a>
+<a name="10740"><span class="lineNum">   10740 </span><span class="lineCov">     556774 : L10:</span></a>
+<a name="10741"><span class="lineNum">   10741 </span><span class="lineCov">     556774 :     start = stack[(stkpnt &lt;&lt; 1) - 2];</span></a>
+<a name="10742"><span class="lineNum">   10742 </span><span class="lineCov">     556774 :     endd = stack[(stkpnt &lt;&lt; 1) - 1];</span></a>
+<a name="10743"><span class="lineNum">   10743 </span><span class="lineCov">     556774 :     --stkpnt;</span></a>
+<a name="10744"><span class="lineNum">   10744 </span><span class="lineCov">     556774 :     if (endd - start &lt;= 20 &amp;&amp; endd - start &gt; 0) {</span></a>
+<a name="10745"><span class="lineNum">   10745 </span>            : </a>
+<a name="10746"><span class="lineNum">   10746 </span>            : </a>
+<a name="10747"><span class="lineNum">   10747 </span><span class="lineCov">     556715 :         if (dir == 0) {</span></a>
+<a name="10748"><span class="lineNum">   10748 </span>            : </a>
+<a name="10749"><span class="lineNum">   10749 </span>            :             i__1 = endd;</a>
+<a name="10750"><span class="lineNum">   10750 </span><span class="lineCov">    2227038 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10751"><span class="lineNum">   10751 </span>            :                 i__2 = start + 1;</a>
+<a name="10752"><span class="lineNum">   10752 </span><span class="lineCov">    1670335 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="10753"><span class="lineNum">   10753 </span><span class="lineCov">    1670335 :                     if (d__[j] &gt; d__[j - 1]) {</span></a>
+<a name="10754"><span class="lineNum">   10754 </span>            :                         dmnmx = d__[j];</a>
+<a name="10755"><span class="lineNum">   10755 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="10756"><span class="lineNum">   10756 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="10757"><span class="lineNum">   10757 </span>            :                     } else {</a>
+<a name="10758"><span class="lineNum">   10758 </span><span class="lineCov">    1670335 :                         goto L30;</span></a>
+<a name="10759"><span class="lineNum">   10759 </span>            :                     }</a>
+<a name="10760"><span class="lineNum">   10760 </span>            :                 }</a>
+<a name="10761"><span class="lineNum">   10761 </span><span class="lineCov">    1670335 : L30:</span></a>
+<a name="10762"><span class="lineNum">   10762 </span>            :                 ;</a>
+<a name="10763"><span class="lineNum">   10763 </span>            :             }</a>
+<a name="10764"><span class="lineNum">   10764 </span>            : </a>
+<a name="10765"><span class="lineNum">   10765 </span>            :         } else {</a>
+<a name="10766"><span class="lineNum">   10766 </span>            : </a>
+<a name="10767"><span class="lineNum">   10767 </span>            :             i__1 = endd;</a>
+<a name="10768"><span class="lineNum">   10768 </span><span class="lineCov">        108 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10769"><span class="lineNum">   10769 </span>            :                 i__2 = start + 1;</a>
+<a name="10770"><span class="lineNum">   10770 </span><span class="lineCov">         96 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="10771"><span class="lineNum">   10771 </span><span class="lineCov">         96 :                     if (d__[j] &lt; d__[j - 1]) {</span></a>
+<a name="10772"><span class="lineNum">   10772 </span>            :                         dmnmx = d__[j];</a>
+<a name="10773"><span class="lineNum">   10773 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="10774"><span class="lineNum">   10774 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="10775"><span class="lineNum">   10775 </span>            :                     } else {</a>
+<a name="10776"><span class="lineNum">   10776 </span><span class="lineCov">         96 :                         goto L50;</span></a>
+<a name="10777"><span class="lineNum">   10777 </span>            :                     }</a>
+<a name="10778"><span class="lineNum">   10778 </span>            :                 }</a>
+<a name="10779"><span class="lineNum">   10779 </span><span class="lineCov">         96 : L50:</span></a>
+<a name="10780"><span class="lineNum">   10780 </span>            :                 ;</a>
+<a name="10781"><span class="lineNum">   10781 </span>            :             }</a>
+<a name="10782"><span class="lineNum">   10782 </span>            : </a>
+<a name="10783"><span class="lineNum">   10783 </span>            :         }</a>
+<a name="10784"><span class="lineNum">   10784 </span>            : </a>
+<a name="10785"><span class="lineNum">   10785 </span><span class="lineCov">         59 :     } else if (endd - start &gt; 20) {</span></a>
+<a name="10786"><span class="lineNum">   10786 </span>            : </a>
+<a name="10787"><span class="lineNum">   10787 </span><span class="lineCov">         59 :         d1 = d__[start];</span></a>
+<a name="10788"><span class="lineNum">   10788 </span><span class="lineCov">         59 :         d2 = d__[endd];</span></a>
+<a name="10789"><span class="lineNum">   10789 </span><span class="lineCov">         59 :         i__ = (start + endd) / 2;</span></a>
+<a name="10790"><span class="lineNum">   10790 </span><span class="lineCov">         59 :         d3 = d__[i__];</span></a>
+<a name="10791"><span class="lineNum">   10791 </span><span class="lineCov">         59 :         if (d1 &lt; d2) {</span></a>
+<a name="10792"><span class="lineNum">   10792 </span><span class="lineCov">          3 :             if (d3 &lt; d1) {</span></a>
+<a name="10793"><span class="lineNum">   10793 </span>            :                 dmnmx = d1;</a>
+<a name="10794"><span class="lineNum">   10794 </span><span class="lineCov">          3 :             } else if (d3 &lt; d2) {</span></a>
+<a name="10795"><span class="lineNum">   10795 </span>            :                 dmnmx = d3;</a>
+<a name="10796"><span class="lineNum">   10796 </span>            :             } else {</a>
+<a name="10797"><span class="lineNum">   10797 </span>            :                 dmnmx = d2;</a>
+<a name="10798"><span class="lineNum">   10798 </span>            :             }</a>
+<a name="10799"><span class="lineNum">   10799 </span>            :         } else {</a>
+<a name="10800"><span class="lineNum">   10800 </span><span class="lineCov">         56 :             if (d3 &lt; d2) {</span></a>
+<a name="10801"><span class="lineNum">   10801 </span>            :                 dmnmx = d2;</a>
+<a name="10802"><span class="lineNum">   10802 </span><span class="lineCov">         56 :             } else if (d3 &lt; d1) {</span></a>
+<a name="10803"><span class="lineNum">   10803 </span>            :                 dmnmx = d3;</a>
+<a name="10804"><span class="lineNum">   10804 </span>            :             } else {</a>
+<a name="10805"><span class="lineNum">   10805 </span>            :                 dmnmx = d1;</a>
+<a name="10806"><span class="lineNum">   10806 </span>            :             }</a>
+<a name="10807"><span class="lineNum">   10807 </span>            :         }</a>
+<a name="10808"><span class="lineNum">   10808 </span>            : </a>
+<a name="10809"><span class="lineNum">   10809 </span><span class="lineCov">         59 :         if (dir == 0) {</span></a>
+<a name="10810"><span class="lineNum">   10810 </span>            : </a>
+<a name="10811"><span class="lineNum">   10811 </span><span class="lineCov">         56 :             i__ = start - 1;</span></a>
+<a name="10812"><span class="lineNum">   10812 </span><span class="lineCov">         56 :             j = endd + 1;</span></a>
+<a name="10813"><span class="lineNum">   10813 </span><span class="lineCov">       1944 : L60:</span></a>
+<a name="10814"><span class="lineNum">   10814 </span><span class="lineCov">       1944 : L70:</span></a>
+<a name="10815"><span class="lineNum">   10815 </span><span class="lineCov">       2000 :             --j;</span></a>
+<a name="10816"><span class="lineNum">   10816 </span><span class="lineCov">       2000 :             if (d__[j] &lt; dmnmx) {</span></a>
+<a name="10817"><span class="lineNum">   10817 </span><span class="lineCov">       1944 :                 goto L70;</span></a>
+<a name="10818"><span class="lineNum">   10818 </span>            :             }</a>
+<a name="10819"><span class="lineNum">   10819 </span><span class="lineCov">         56 : L80:</span></a>
+<a name="10820"><span class="lineNum">   10820 </span><span class="lineCov">       1980 :             ++i__;</span></a>
+<a name="10821"><span class="lineNum">   10821 </span><span class="lineCov">       1980 :             if (d__[i__] &gt; dmnmx) {</span></a>
+<a name="10822"><span class="lineNum">   10822 </span><span class="lineCov">       1924 :                 goto L80;</span></a>
+<a name="10823"><span class="lineNum">   10823 </span>            :             }</a>
+<a name="10824"><span class="lineNum">   10824 </span><span class="lineCov">         56 :             if (i__ &lt; j) {</span></a>
+<a name="10825"><span class="lineNum">   10825 </span>            :                 tmp = d__[i__];</a>
+<a name="10826"><span class="lineNum">   10826 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="10827"><span class="lineNum">   10827 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="10828"><span class="lineNum">   10828 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="10829"><span class="lineNum">   10829 </span>            :             }</a>
+<a name="10830"><span class="lineNum">   10830 </span><span class="lineCov">         56 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="10831"><span class="lineNum">   10831 </span>            :                 ++stkpnt;</a>
+<a name="10832"><span class="lineNum">   10832 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="10833"><span class="lineNum">   10833 </span><span class="lineCov">         36 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="10834"><span class="lineNum">   10834 </span><span class="lineCov">         36 :                 ++stkpnt;</span></a>
+<a name="10835"><span class="lineNum">   10835 </span><span class="lineCov">         36 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="10836"><span class="lineNum">   10836 </span><span class="lineCov">         36 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="10837"><span class="lineNum">   10837 </span>            :             } else {</a>
+<a name="10838"><span class="lineNum">   10838 </span>            :                 ++stkpnt;</a>
+<a name="10839"><span class="lineNum">   10839 </span><span class="lineCov">         20 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="10840"><span class="lineNum">   10840 </span><span class="lineCov">         20 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="10841"><span class="lineNum">   10841 </span><span class="lineCov">         20 :                 ++stkpnt;</span></a>
+<a name="10842"><span class="lineNum">   10842 </span><span class="lineCov">         20 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="10843"><span class="lineNum">   10843 </span><span class="lineCov">         20 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="10844"><span class="lineNum">   10844 </span>            :             }</a>
+<a name="10845"><span class="lineNum">   10845 </span>            :         } else {</a>
+<a name="10846"><span class="lineNum">   10846 </span>            : </a>
+<a name="10847"><span class="lineNum">   10847 </span><span class="lineCov">          3 :             i__ = start - 1;</span></a>
+<a name="10848"><span class="lineNum">   10848 </span><span class="lineCov">          3 :             j = endd + 1;</span></a>
+<a name="10849"><span class="lineNum">   10849 </span><span class="lineCov">         61 : L90:</span></a>
+<a name="10850"><span class="lineNum">   10850 </span><span class="lineCov">         61 : L100:</span></a>
+<a name="10851"><span class="lineNum">   10851 </span><span class="lineCov">         64 :             --j;</span></a>
+<a name="10852"><span class="lineNum">   10852 </span><span class="lineCov">         64 :             if (d__[j] &gt; dmnmx) {</span></a>
+<a name="10853"><span class="lineNum">   10853 </span><span class="lineCov">         61 :                 goto L100;</span></a>
+<a name="10854"><span class="lineNum">   10854 </span>            :             }</a>
+<a name="10855"><span class="lineNum">   10855 </span><span class="lineCov">          3 : L110:</span></a>
+<a name="10856"><span class="lineNum">   10856 </span><span class="lineCov">         63 :             ++i__;</span></a>
+<a name="10857"><span class="lineNum">   10857 </span><span class="lineCov">         63 :             if (d__[i__] &lt; dmnmx) {</span></a>
+<a name="10858"><span class="lineNum">   10858 </span><span class="lineCov">         60 :                 goto L110;</span></a>
+<a name="10859"><span class="lineNum">   10859 </span>            :             }</a>
+<a name="10860"><span class="lineNum">   10860 </span><span class="lineCov">          3 :             if (i__ &lt; j) {</span></a>
+<a name="10861"><span class="lineNum">   10861 </span>            :                 tmp = d__[i__];</a>
+<a name="10862"><span class="lineNum">   10862 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="10863"><span class="lineNum">   10863 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="10864"><span class="lineNum">   10864 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="10865"><span class="lineNum">   10865 </span>            :             }</a>
+<a name="10866"><span class="lineNum">   10866 </span><span class="lineCov">          3 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="10867"><span class="lineNum">   10867 </span>            :                 ++stkpnt;</a>
+<a name="10868"><span class="lineNum">   10868 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="10869"><span class="lineNum">   10869 </span><span class="lineCov">          2 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="10870"><span class="lineNum">   10870 </span><span class="lineCov">          2 :                 ++stkpnt;</span></a>
+<a name="10871"><span class="lineNum">   10871 </span><span class="lineCov">          2 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="10872"><span class="lineNum">   10872 </span><span class="lineCov">          2 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="10873"><span class="lineNum">   10873 </span>            :             } else {</a>
+<a name="10874"><span class="lineNum">   10874 </span>            :                 ++stkpnt;</a>
+<a name="10875"><span class="lineNum">   10875 </span><span class="lineCov">          1 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="10876"><span class="lineNum">   10876 </span><span class="lineCov">          1 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="10877"><span class="lineNum">   10877 </span><span class="lineCov">          1 :                 ++stkpnt;</span></a>
+<a name="10878"><span class="lineNum">   10878 </span><span class="lineCov">          1 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="10879"><span class="lineNum">   10879 </span><span class="lineCov">          1 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="10880"><span class="lineNum">   10880 </span>            :             }</a>
+<a name="10881"><span class="lineNum">   10881 </span>            :         }</a>
+<a name="10882"><span class="lineNum">   10882 </span>            :     }</a>
+<a name="10883"><span class="lineNum">   10883 </span><span class="lineCov">     556774 :     if (stkpnt &gt; 0) {</span></a>
+<a name="10884"><span class="lineNum">   10884 </span><span class="lineCov">        118 :         goto L10;</span></a>
+<a name="10885"><span class="lineNum">   10885 </span>            :     }</a>
+<a name="10886"><span class="lineNum">   10886 </span>            :     return;</a>
+<a name="10887"><span class="lineNum">   10887 </span>            : </a>
+<a name="10888"><span class="lineNum">   10888 </span>            : }</a>
+<a name="10889"><span class="lineNum">   10889 </span>            : }</a>
+<a name="10890"><span class="lineNum">   10890 </span>            : }</a>
+<a name="10891"><span class="lineNum">   10891 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="10892"><span class="lineNum">   10892 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="10893"><span class="lineNum">   10893 </span>            : namespace PLMD{</a>
+<a name="10894"><span class="lineNum">   10894 </span>            : namespace lapack{</a>
+<a name="10895"><span class="lineNum">   10895 </span>            : using namespace blas;</a>
+<a name="10896"><span class="lineNum">   10896 </span>            : </a>
+<a name="10897"><span class="lineNum">   10897 </span><span class="lineCov">         12 : void PLUMED_BLAS_F77_FUNC(dlasrt2,DLASRT2)(const char *id, </span></a>
+<a name="10898"><span class="lineNum">   10898 </span>            :               int *n, </a>
+<a name="10899"><span class="lineNum">   10899 </span>            :               double *d__, </a>
+<a name="10900"><span class="lineNum">   10900 </span>            :               int * key, </a>
+<a name="10901"><span class="lineNum">   10901 </span>            :               int *info)</a>
+<a name="10902"><span class="lineNum">   10902 </span>            : {</a>
+<a name="10903"><span class="lineNum">   10903 </span>            :     int i__1, i__2;</a>
+<a name="10904"><span class="lineNum">   10904 </span>            : </a>
+<a name="10905"><span class="lineNum">   10905 </span>            :     int i__, j;</a>
+<a name="10906"><span class="lineNum">   10906 </span>            :     double d1, d2, d3;</a>
+<a name="10907"><span class="lineNum">   10907 </span>            :     int dir;</a>
+<a name="10908"><span class="lineNum">   10908 </span>            :     double tmp;</a>
+<a name="10909"><span class="lineNum">   10909 </span>            :     int endd;</a>
+<a name="10910"><span class="lineNum">   10910 </span>            :     int stack[64];</a>
+<a name="10911"><span class="lineNum">   10911 </span>            :     double dmnmx;</a>
+<a name="10912"><span class="lineNum">   10912 </span>            :     int start;</a>
+<a name="10913"><span class="lineNum">   10913 </span>            :     int tmpkey, stkpnt;</a>
+<a name="10914"><span class="lineNum">   10914 </span>            : </a>
+<a name="10915"><span class="lineNum">   10915 </span><span class="lineCov">         12 :     --key;</span></a>
+<a name="10916"><span class="lineNum">   10916 </span><span class="lineCov">         12 :     --d__;</span></a>
+<a name="10917"><span class="lineNum">   10917 </span>            : </a>
+<a name="10918"><span class="lineNum">   10918 </span><span class="lineCov">         12 :     *info = 0;</span></a>
+<a name="10919"><span class="lineNum">   10919 </span>            :     dir = -1;</a>
+<a name="10920"><span class="lineNum">   10920 </span><span class="lineCov">         12 :     if (*id=='D' || *id=='d')</span></a>
+<a name="10921"><span class="lineNum">   10921 </span>            :         dir = 0;</a>
+<a name="10922"><span class="lineNum">   10922 </span><span class="lineCov">         12 :     else if (*id=='I' || *id=='i')</span></a>
+<a name="10923"><span class="lineNum">   10923 </span>            :         dir = 1;</a>
+<a name="10924"><span class="lineNum">   10924 </span>            :     </a>
+<a name="10925"><span class="lineNum">   10925 </span>            :     if (dir == -1) {</a>
+<a name="10926"><span class="lineNum">   10926 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="10927"><span class="lineNum">   10927 </span><span class="lineCov">         12 :     } else if (*n &lt; 0) {</span></a>
+<a name="10928"><span class="lineNum">   10928 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="10929"><span class="lineNum">   10929 </span>            :     }</a>
+<a name="10930"><span class="lineNum">   10930 </span><span class="lineCov">         12 :     if (*info != 0) {</span></a>
+<a name="10931"><span class="lineNum">   10931 </span>            :         return;</a>
+<a name="10932"><span class="lineNum">   10932 </span>            :     }</a>
+<a name="10933"><span class="lineNum">   10933 </span>            : </a>
+<a name="10934"><span class="lineNum">   10934 </span><span class="lineCov">         12 :     if (*n &lt;= 1) {</span></a>
+<a name="10935"><span class="lineNum">   10935 </span>            :         return;</a>
+<a name="10936"><span class="lineNum">   10936 </span>            :     }</a>
+<a name="10937"><span class="lineNum">   10937 </span>            : </a>
+<a name="10938"><span class="lineNum">   10938 </span>            :     stkpnt = 1;</a>
+<a name="10939"><span class="lineNum">   10939 </span><span class="lineCov">         12 :     stack[0] = 1;</span></a>
+<a name="10940"><span class="lineNum">   10940 </span><span class="lineCov">         12 :     stack[1] = *n;</span></a>
+<a name="10941"><span class="lineNum">   10941 </span><span class="lineCov">         12 : L10:</span></a>
+<a name="10942"><span class="lineNum">   10942 </span><span class="lineCov">         12 :     start = stack[(stkpnt &lt;&lt; 1) - 2];</span></a>
+<a name="10943"><span class="lineNum">   10943 </span><span class="lineCov">         12 :     endd = stack[(stkpnt &lt;&lt; 1) - 1];</span></a>
+<a name="10944"><span class="lineNum">   10944 </span><span class="lineCov">         12 :     --stkpnt;</span></a>
+<a name="10945"><span class="lineNum">   10945 </span><span class="lineCov">         12 :     if (endd - start &gt; 0) {</span></a>
+<a name="10946"><span class="lineNum">   10946 </span>            : </a>
+<a name="10947"><span class="lineNum">   10947 </span><span class="lineCov">         12 :         if (dir == 0) {</span></a>
+<a name="10948"><span class="lineNum">   10948 </span>            : </a>
+<a name="10949"><span class="lineNum">   10949 </span>            :             i__1 = endd;</a>
+<a name="10950"><span class="lineNum">   10950 </span><span class="lineNoCov">          0 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10951"><span class="lineNum">   10951 </span>            :                 i__2 = start + 1;</a>
+<a name="10952"><span class="lineNum">   10952 </span><span class="lineNoCov">          0 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="10953"><span class="lineNum">   10953 </span><span class="lineNoCov">          0 :                     if (d__[j] &gt; d__[j - 1]) {</span></a>
+<a name="10954"><span class="lineNum">   10954 </span>            :                         dmnmx = d__[j];</a>
+<a name="10955"><span class="lineNum">   10955 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="10956"><span class="lineNum">   10956 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="10957"><span class="lineNum">   10957 </span><span class="lineNoCov">          0 :                         tmpkey = key[j];</span></a>
+<a name="10958"><span class="lineNum">   10958 </span><span class="lineNoCov">          0 :                         key[j] = key[j - 1];</span></a>
+<a name="10959"><span class="lineNum">   10959 </span><span class="lineNoCov">          0 :                         key[j - 1] = tmpkey;</span></a>
+<a name="10960"><span class="lineNum">   10960 </span>            :                     } else {</a>
+<a name="10961"><span class="lineNum">   10961 </span>            :                         break;</a>
+<a name="10962"><span class="lineNum">   10962 </span>            :                     }</a>
+<a name="10963"><span class="lineNum">   10963 </span>            :                 }</a>
+<a name="10964"><span class="lineNum">   10964 </span>            :             }</a>
+<a name="10965"><span class="lineNum">   10965 </span>            : </a>
+<a name="10966"><span class="lineNum">   10966 </span>            :         } else {</a>
+<a name="10967"><span class="lineNum">   10967 </span>            : </a>
+<a name="10968"><span class="lineNum">   10968 </span>            :             i__1 = endd;</a>
+<a name="10969"><span class="lineNum">   10969 </span><span class="lineCov">        778 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="10970"><span class="lineNum">   10970 </span>            :                 i__2 = start + 1;</a>
+<a name="10971"><span class="lineNum">   10971 </span><span class="lineCov">      14906 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="10972"><span class="lineNum">   10972 </span><span class="lineCov">      14840 :                     if (d__[j] &lt; d__[j - 1]) {</span></a>
+<a name="10973"><span class="lineNum">   10973 </span>            :                         dmnmx = d__[j];</a>
+<a name="10974"><span class="lineNum">   10974 </span><span class="lineCov">      14140 :                         d__[j] = d__[j - 1];</span></a>
+<a name="10975"><span class="lineNum">   10975 </span><span class="lineCov">      14140 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="10976"><span class="lineNum">   10976 </span><span class="lineCov">      14140 :                         tmpkey = key[j];</span></a>
+<a name="10977"><span class="lineNum">   10977 </span><span class="lineCov">      14140 :                         key[j] = key[j - 1];</span></a>
+<a name="10978"><span class="lineNum">   10978 </span><span class="lineCov">      14140 :                         key[j - 1] = tmpkey;</span></a>
+<a name="10979"><span class="lineNum">   10979 </span>            :                     } else {</a>
+<a name="10980"><span class="lineNum">   10980 </span>            :                         break;</a>
+<a name="10981"><span class="lineNum">   10981 </span>            :                     }</a>
+<a name="10982"><span class="lineNum">   10982 </span>            :                 }</a>
+<a name="10983"><span class="lineNum">   10983 </span>            :             }</a>
+<a name="10984"><span class="lineNum">   10984 </span>            : </a>
+<a name="10985"><span class="lineNum">   10985 </span>            :         }</a>
+<a name="10986"><span class="lineNum">   10986 </span>            : </a>
+<a name="10987"><span class="lineNum">   10987 </span><span class="lineNoCov">          0 :     } else if (endd - start &gt; 20) {</span></a>
+<a name="10988"><span class="lineNum">   10988 </span>            : </a>
+<a name="10989"><span class="lineNum">   10989 </span><span class="lineNoCov">          0 :         d1 = d__[start];</span></a>
+<a name="10990"><span class="lineNum">   10990 </span><span class="lineNoCov">          0 :         d2 = d__[endd];</span></a>
+<a name="10991"><span class="lineNum">   10991 </span><span class="lineNoCov">          0 :         i__ = (start + endd) / 2;</span></a>
+<a name="10992"><span class="lineNum">   10992 </span><span class="lineNoCov">          0 :         d3 = d__[i__];</span></a>
+<a name="10993"><span class="lineNum">   10993 </span><span class="lineNoCov">          0 :         if (d1 &lt; d2) {</span></a>
+<a name="10994"><span class="lineNum">   10994 </span><span class="lineNoCov">          0 :             if (d3 &lt; d1) {</span></a>
+<a name="10995"><span class="lineNum">   10995 </span>            :                 dmnmx = d1;</a>
+<a name="10996"><span class="lineNum">   10996 </span><span class="lineNoCov">          0 :             } else if (d3 &lt; d2) {</span></a>
+<a name="10997"><span class="lineNum">   10997 </span>            :                 dmnmx = d3;</a>
+<a name="10998"><span class="lineNum">   10998 </span>            :             } else {</a>
+<a name="10999"><span class="lineNum">   10999 </span>            :                 dmnmx = d2;</a>
+<a name="11000"><span class="lineNum">   11000 </span>            :             }</a>
+<a name="11001"><span class="lineNum">   11001 </span>            :         } else {</a>
+<a name="11002"><span class="lineNum">   11002 </span><span class="lineNoCov">          0 :             if (d3 &lt; d2) {</span></a>
+<a name="11003"><span class="lineNum">   11003 </span>            :                 dmnmx = d2;</a>
+<a name="11004"><span class="lineNum">   11004 </span><span class="lineNoCov">          0 :             } else if (d3 &lt; d1) {</span></a>
+<a name="11005"><span class="lineNum">   11005 </span>            :                 dmnmx = d3;</a>
+<a name="11006"><span class="lineNum">   11006 </span>            :             } else {</a>
+<a name="11007"><span class="lineNum">   11007 </span>            :                 dmnmx = d1;</a>
+<a name="11008"><span class="lineNum">   11008 </span>            :             }</a>
+<a name="11009"><span class="lineNum">   11009 </span>            :         }</a>
+<a name="11010"><span class="lineNum">   11010 </span>            : </a>
+<a name="11011"><span class="lineNum">   11011 </span><span class="lineNoCov">          0 :         if (dir == 0) {</span></a>
+<a name="11012"><span class="lineNum">   11012 </span>            : </a>
+<a name="11013"><span class="lineNum">   11013 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="11014"><span class="lineNum">   11014 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="11015"><span class="lineNum">   11015 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="11016"><span class="lineNum">   11016 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="11017"><span class="lineNum">   11017 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="11018"><span class="lineNum">   11018 </span><span class="lineNoCov">          0 :             if (d__[j] &lt; dmnmx) {</span></a>
+<a name="11019"><span class="lineNum">   11019 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="11020"><span class="lineNum">   11020 </span>            :             }</a>
+<a name="11021"><span class="lineNum">   11021 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="11022"><span class="lineNum">   11022 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="11023"><span class="lineNum">   11023 </span><span class="lineNoCov">          0 :             if (d__[i__] &gt; dmnmx) {</span></a>
+<a name="11024"><span class="lineNum">   11024 </span><span class="lineNoCov">          0 :                 goto L80;</span></a>
+<a name="11025"><span class="lineNum">   11025 </span>            :             }</a>
+<a name="11026"><span class="lineNum">   11026 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="11027"><span class="lineNum">   11027 </span>            :                 tmp = d__[i__];</a>
+<a name="11028"><span class="lineNum">   11028 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="11029"><span class="lineNum">   11029 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="11030"><span class="lineNum">   11030 </span><span class="lineNoCov">          0 :                 tmpkey = key[j];</span></a>
+<a name="11031"><span class="lineNum">   11031 </span><span class="lineNoCov">          0 :                 key[j] = key[i__];</span></a>
+<a name="11032"><span class="lineNum">   11032 </span><span class="lineNoCov">          0 :                 key[i__] = tmpkey;</span></a>
+<a name="11033"><span class="lineNum">   11033 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="11034"><span class="lineNum">   11034 </span>            :             }</a>
+<a name="11035"><span class="lineNum">   11035 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="11036"><span class="lineNum">   11036 </span>            :                 ++stkpnt;</a>
+<a name="11037"><span class="lineNum">   11037 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="11038"><span class="lineNum">   11038 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="11039"><span class="lineNum">   11039 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="11040"><span class="lineNum">   11040 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="11041"><span class="lineNum">   11041 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="11042"><span class="lineNum">   11042 </span>            :             } else {</a>
+<a name="11043"><span class="lineNum">   11043 </span>            :                 ++stkpnt;</a>
+<a name="11044"><span class="lineNum">   11044 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="11045"><span class="lineNum">   11045 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="11046"><span class="lineNum">   11046 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="11047"><span class="lineNum">   11047 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="11048"><span class="lineNum">   11048 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="11049"><span class="lineNum">   11049 </span>            :             }</a>
+<a name="11050"><span class="lineNum">   11050 </span>            :         } else {</a>
+<a name="11051"><span class="lineNum">   11051 </span>            : </a>
+<a name="11052"><span class="lineNum">   11052 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="11053"><span class="lineNum">   11053 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="11054"><span class="lineNum">   11054 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="11055"><span class="lineNum">   11055 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="11056"><span class="lineNum">   11056 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="11057"><span class="lineNum">   11057 </span><span class="lineNoCov">          0 :             if (d__[j] &gt; dmnmx) {</span></a>
+<a name="11058"><span class="lineNum">   11058 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="11059"><span class="lineNum">   11059 </span>            :             }</a>
+<a name="11060"><span class="lineNum">   11060 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="11061"><span class="lineNum">   11061 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="11062"><span class="lineNum">   11062 </span><span class="lineNoCov">          0 :             if (d__[i__] &lt; dmnmx) {</span></a>
+<a name="11063"><span class="lineNum">   11063 </span><span class="lineNoCov">          0 :                 goto L110;</span></a>
+<a name="11064"><span class="lineNum">   11064 </span>            :             }</a>
+<a name="11065"><span class="lineNum">   11065 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="11066"><span class="lineNum">   11066 </span>            :                 tmp = d__[i__];</a>
+<a name="11067"><span class="lineNum">   11067 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="11068"><span class="lineNum">   11068 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="11069"><span class="lineNum">   11069 </span><span class="lineNoCov">          0 :                 tmpkey = key[j];</span></a>
+<a name="11070"><span class="lineNum">   11070 </span><span class="lineNoCov">          0 :                 key[j] = key[i__];</span></a>
+<a name="11071"><span class="lineNum">   11071 </span><span class="lineNoCov">          0 :                 key[i__] = tmpkey;</span></a>
+<a name="11072"><span class="lineNum">   11072 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="11073"><span class="lineNum">   11073 </span>            :             }</a>
+<a name="11074"><span class="lineNum">   11074 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="11075"><span class="lineNum">   11075 </span>            :                 ++stkpnt;</a>
+<a name="11076"><span class="lineNum">   11076 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="11077"><span class="lineNum">   11077 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="11078"><span class="lineNum">   11078 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="11079"><span class="lineNum">   11079 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="11080"><span class="lineNum">   11080 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="11081"><span class="lineNum">   11081 </span>            :             } else {</a>
+<a name="11082"><span class="lineNum">   11082 </span>            :                 ++stkpnt;</a>
+<a name="11083"><span class="lineNum">   11083 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="11084"><span class="lineNum">   11084 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="11085"><span class="lineNum">   11085 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="11086"><span class="lineNum">   11086 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="11087"><span class="lineNum">   11087 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="11088"><span class="lineNum">   11088 </span>            :             }</a>
+<a name="11089"><span class="lineNum">   11089 </span>            :         }</a>
+<a name="11090"><span class="lineNum">   11090 </span>            :     }</a>
+<a name="11091"><span class="lineNum">   11091 </span><span class="lineCov">         12 :     if (stkpnt &gt; 0) {</span></a>
+<a name="11092"><span class="lineNum">   11092 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="11093"><span class="lineNum">   11093 </span>            :     }</a>
+<a name="11094"><span class="lineNum">   11094 </span>            : </a>
+<a name="11095"><span class="lineNum">   11095 </span>            :     return;</a>
+<a name="11096"><span class="lineNum">   11096 </span>            : }</a>
+<a name="11097"><span class="lineNum">   11097 </span>            : }</a>
+<a name="11098"><span class="lineNum">   11098 </span>            : }</a>
+<a name="11099"><span class="lineNum">   11099 </span>            : #include &lt;cmath&gt;</a>
+<a name="11100"><span class="lineNum">   11100 </span>            : #include &quot;real.h&quot;</a>
+<a name="11101"><span class="lineNum">   11101 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11102"><span class="lineNum">   11102 </span>            : </a>
+<a name="11103"><span class="lineNum">   11103 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11104"><span class="lineNum">   11104 </span>            : namespace PLMD{</a>
+<a name="11105"><span class="lineNum">   11105 </span>            : namespace lapack{</a>
+<a name="11106"><span class="lineNum">   11106 </span>            : using namespace blas;</a>
+<a name="11107"><span class="lineNum">   11107 </span>            : void</a>
+<a name="11108"><span class="lineNum">   11108 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlassq,DLASSQ)(int *n,</span></a>
+<a name="11109"><span class="lineNum">   11109 </span>            :                         double *x,</a>
+<a name="11110"><span class="lineNum">   11110 </span>            :                         int *incx,</a>
+<a name="11111"><span class="lineNum">   11111 </span>            :                         double *scale,</a>
+<a name="11112"><span class="lineNum">   11112 </span>            :                         double *sumsq)</a>
+<a name="11113"><span class="lineNum">   11113 </span>            : {</a>
+<a name="11114"><span class="lineNum">   11114 </span>            :   int ix;</a>
+<a name="11115"><span class="lineNum">   11115 </span>            :   double absxi,t;</a>
+<a name="11116"><span class="lineNum">   11116 </span>            : </a>
+<a name="11117"><span class="lineNum">   11117 </span><span class="lineNoCov">          0 :   if(*n&gt;0) {</span></a>
+<a name="11118"><span class="lineNum">   11118 </span><span class="lineNoCov">          0 :     for(ix=0;ix&lt;=(*n-1)*(*incx);ix+=*incx) {</span></a>
+<a name="11119"><span class="lineNum">   11119 </span><span class="lineNoCov">          0 :       if(std::abs(x[ix])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="11120"><span class="lineNum">   11120 </span>            :         absxi = std::abs(x[ix]);</a>
+<a name="11121"><span class="lineNum">   11121 </span><span class="lineNoCov">          0 :         if(*scale&lt;absxi) {</span></a>
+<a name="11122"><span class="lineNum">   11122 </span><span class="lineNoCov">          0 :           t = *scale/absxi;</span></a>
+<a name="11123"><span class="lineNum">   11123 </span><span class="lineNoCov">          0 :           t = t*t;</span></a>
+<a name="11124"><span class="lineNum">   11124 </span><span class="lineNoCov">          0 :           *sumsq = 1.0 + (*sumsq)*t;</span></a>
+<a name="11125"><span class="lineNum">   11125 </span><span class="lineNoCov">          0 :           *scale = absxi;</span></a>
+<a name="11126"><span class="lineNum">   11126 </span>            :         } else {</a>
+<a name="11127"><span class="lineNum">   11127 </span><span class="lineNoCov">          0 :           t = absxi/(*scale);</span></a>
+<a name="11128"><span class="lineNum">   11128 </span><span class="lineNoCov">          0 :           *sumsq += t*t;</span></a>
+<a name="11129"><span class="lineNum">   11129 </span>            :         }</a>
+<a name="11130"><span class="lineNum">   11130 </span>            :       }</a>
+<a name="11131"><span class="lineNum">   11131 </span>            :     }</a>
+<a name="11132"><span class="lineNum">   11132 </span>            :   }</a>
+<a name="11133"><span class="lineNum">   11133 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="11134"><span class="lineNum">   11134 </span>            : }</a>
+<a name="11135"><span class="lineNum">   11135 </span>            : }</a>
+<a name="11136"><span class="lineNum">   11136 </span>            : }</a>
+<a name="11137"><span class="lineNum">   11137 </span>            : #include &lt;cmath&gt;</a>
+<a name="11138"><span class="lineNum">   11138 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11139"><span class="lineNum">   11139 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="11140"><span class="lineNum">   11140 </span>            : </a>
+<a name="11141"><span class="lineNum">   11141 </span>            : #include &quot;real.h&quot;</a>
+<a name="11142"><span class="lineNum">   11142 </span>            : </a>
+<a name="11143"><span class="lineNum">   11143 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11144"><span class="lineNum">   11144 </span>            : namespace PLMD{</a>
+<a name="11145"><span class="lineNum">   11145 </span>            : namespace lapack{</a>
+<a name="11146"><span class="lineNum">   11146 </span>            : using namespace blas;</a>
+<a name="11147"><span class="lineNum">   11147 </span>            : void </a>
+<a name="11148"><span class="lineNum">   11148 </span><span class="lineCov">        180 : PLUMED_BLAS_F77_FUNC(dlasv2,DLASV2)(double *f, </span></a>
+<a name="11149"><span class="lineNum">   11149 </span>            :                         double *g, </a>
+<a name="11150"><span class="lineNum">   11150 </span>            :                         double *h__, </a>
+<a name="11151"><span class="lineNum">   11151 </span>            :                         double *ssmin, </a>
+<a name="11152"><span class="lineNum">   11152 </span>            :                         double *ssmax, </a>
+<a name="11153"><span class="lineNum">   11153 </span>            :                         double *snr, </a>
+<a name="11154"><span class="lineNum">   11154 </span>            :                         double *csr, </a>
+<a name="11155"><span class="lineNum">   11155 </span>            :                         double *snl, </a>
+<a name="11156"><span class="lineNum">   11156 </span>            :                         double *csl)</a>
+<a name="11157"><span class="lineNum">   11157 </span>            : {</a>
+<a name="11158"><span class="lineNum">   11158 </span>            :     double d__1;</a>
+<a name="11159"><span class="lineNum">   11159 </span>            : </a>
+<a name="11160"><span class="lineNum">   11160 </span>            :     double a, d__, l, m, r__, s, t, fa, ga, ha, ft, gt, ht, mm, tt,</a>
+<a name="11161"><span class="lineNum">   11161 </span>            :              clt, crt, slt, srt;</a>
+<a name="11162"><span class="lineNum">   11162 </span>            :     int pmax;</a>
+<a name="11163"><span class="lineNum">   11163 </span>            :     double temp;</a>
+<a name="11164"><span class="lineNum">   11164 </span>            :     int swap;</a>
+<a name="11165"><span class="lineNum">   11165 </span>            :     double tsign=1.0;</a>
+<a name="11166"><span class="lineNum">   11166 </span>            :     int gasmal;</a>
+<a name="11167"><span class="lineNum">   11167 </span>            : </a>
+<a name="11168"><span class="lineNum">   11168 </span><span class="lineCov">        180 :     ft = *f;</span></a>
+<a name="11169"><span class="lineNum">   11169 </span>            :     fa = std::abs(ft);</a>
+<a name="11170"><span class="lineNum">   11170 </span><span class="lineCov">        180 :     ht = *h__;</span></a>
+<a name="11171"><span class="lineNum">   11171 </span>            :     ha = std::abs(*h__);</a>
+<a name="11172"><span class="lineNum">   11172 </span>            : </a>
+<a name="11173"><span class="lineNum">   11173 </span>            :     pmax = 1;</a>
+<a name="11174"><span class="lineNum">   11174 </span>            :     swap = ha &gt; fa;</a>
+<a name="11175"><span class="lineNum">   11175 </span><span class="lineCov">        180 :     if (swap) {</span></a>
+<a name="11176"><span class="lineNum">   11176 </span>            :         pmax = 3;</a>
+<a name="11177"><span class="lineNum">   11177 </span>            :         temp = ft;</a>
+<a name="11178"><span class="lineNum">   11178 </span>            :         ft = ht;</a>
+<a name="11179"><span class="lineNum">   11179 </span>            :         ht = temp;</a>
+<a name="11180"><span class="lineNum">   11180 </span>            :         temp = fa;</a>
+<a name="11181"><span class="lineNum">   11181 </span>            :         fa = ha;</a>
+<a name="11182"><span class="lineNum">   11182 </span>            :         ha = temp;</a>
+<a name="11183"><span class="lineNum">   11183 </span>            : </a>
+<a name="11184"><span class="lineNum">   11184 </span>            :     }</a>
+<a name="11185"><span class="lineNum">   11185 </span><span class="lineCov">        180 :     gt = *g;</span></a>
+<a name="11186"><span class="lineNum">   11186 </span>            :     ga = std::abs(gt);</a>
+<a name="11187"><span class="lineNum">   11187 </span><span class="lineCov">        180 :     if (std::abs(ga)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="11188"><span class="lineNum">   11188 </span>            : </a>
+<a name="11189"><span class="lineNum">   11189 </span><span class="lineNoCov">          0 :         *ssmin = ha;</span></a>
+<a name="11190"><span class="lineNum">   11190 </span><span class="lineNoCov">          0 :         *ssmax = fa;</span></a>
+<a name="11191"><span class="lineNum">   11191 </span>            :         clt = 1.;</a>
+<a name="11192"><span class="lineNum">   11192 </span>            :         crt = 1.;</a>
+<a name="11193"><span class="lineNum">   11193 </span>            :         slt = 0.;</a>
+<a name="11194"><span class="lineNum">   11194 </span>            :         srt = 0.;</a>
+<a name="11195"><span class="lineNum">   11195 </span>            :     } else {</a>
+<a name="11196"><span class="lineNum">   11196 </span>            :         gasmal = 1;</a>
+<a name="11197"><span class="lineNum">   11197 </span><span class="lineCov">        180 :         if (ga &gt; fa) {</span></a>
+<a name="11198"><span class="lineNum">   11198 </span>            :             pmax = 2;</a>
+<a name="11199"><span class="lineNum">   11199 </span><span class="lineCov">          1 :             if (fa / ga &lt; PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="11200"><span class="lineNum">   11200 </span>            : </a>
+<a name="11201"><span class="lineNum">   11201 </span>            :                 gasmal = 0;</a>
+<a name="11202"><span class="lineNum">   11202 </span><span class="lineNoCov">          0 :                 *ssmax = ga;</span></a>
+<a name="11203"><span class="lineNum">   11203 </span><span class="lineNoCov">          0 :                 if (ha &gt; 1.) {</span></a>
+<a name="11204"><span class="lineNum">   11204 </span><span class="lineNoCov">          0 :                     *ssmin = fa / (ga / ha);</span></a>
+<a name="11205"><span class="lineNum">   11205 </span>            :                 } else {</a>
+<a name="11206"><span class="lineNum">   11206 </span><span class="lineNoCov">          0 :                     *ssmin = fa / ga * ha;</span></a>
+<a name="11207"><span class="lineNum">   11207 </span>            :                 }</a>
+<a name="11208"><span class="lineNum">   11208 </span>            :                 clt = 1.;</a>
+<a name="11209"><span class="lineNum">   11209 </span><span class="lineNoCov">          0 :                 slt = ht / gt;</span></a>
+<a name="11210"><span class="lineNum">   11210 </span>            :                 srt = 1.;</a>
+<a name="11211"><span class="lineNum">   11211 </span><span class="lineNoCov">          0 :                 crt = ft / gt;</span></a>
+<a name="11212"><span class="lineNum">   11212 </span>            :             }</a>
+<a name="11213"><span class="lineNum">   11213 </span>            :         }</a>
+<a name="11214"><span class="lineNum">   11214 </span><span class="lineCov">        180 :         if (gasmal) {</span></a>
+<a name="11215"><span class="lineNum">   11215 </span>            : </a>
+<a name="11216"><span class="lineNum">   11216 </span><span class="lineCov">        180 :             d__ = fa - ha;</span></a>
+<a name="11217"><span class="lineNum">   11217 </span><span class="lineCov">        180 :             if ( std::abs( fa - d__ )&lt;PLUMED_GMX_DOUBLE_EPS*std::abs( fa + d__ )) {</span></a>
+<a name="11218"><span class="lineNum">   11218 </span>            :                 l = 1.;</a>
+<a name="11219"><span class="lineNum">   11219 </span>            :             } else {</a>
+<a name="11220"><span class="lineNum">   11220 </span><span class="lineCov">        180 :                 l = d__ / fa;</span></a>
+<a name="11221"><span class="lineNum">   11221 </span>            :             }</a>
+<a name="11222"><span class="lineNum">   11222 </span>            : </a>
+<a name="11223"><span class="lineNum">   11223 </span><span class="lineCov">        180 :             m = gt / ft;</span></a>
+<a name="11224"><span class="lineNum">   11224 </span><span class="lineCov">        180 :             t = 2. - l;</span></a>
+<a name="11225"><span class="lineNum">   11225 </span>            : </a>
+<a name="11226"><span class="lineNum">   11226 </span><span class="lineCov">        180 :             mm = m * m;</span></a>
+<a name="11227"><span class="lineNum">   11227 </span><span class="lineCov">        180 :             tt = t * t;</span></a>
+<a name="11228"><span class="lineNum">   11228 </span><span class="lineCov">        180 :             s =  std::sqrt(tt + mm);</span></a>
+<a name="11229"><span class="lineNum">   11229 </span>            : </a>
+<a name="11230"><span class="lineNum">   11230 </span><span class="lineCov">        180 :             if ( std::abs(l)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="11231"><span class="lineNum">   11231 </span>            :                 r__ = std::abs(m);</a>
+<a name="11232"><span class="lineNum">   11232 </span>            :             } else {</a>
+<a name="11233"><span class="lineNum">   11233 </span><span class="lineCov">        180 :                 r__ =  std::sqrt(l * l + mm);</span></a>
+<a name="11234"><span class="lineNum">   11234 </span>            :             }</a>
+<a name="11235"><span class="lineNum">   11235 </span><span class="lineCov">        180 :             a = (s + r__) * .5;</span></a>
+<a name="11236"><span class="lineNum">   11236 </span>            : </a>
+<a name="11237"><span class="lineNum">   11237 </span><span class="lineCov">        180 :             *ssmin = ha / a;</span></a>
+<a name="11238"><span class="lineNum">   11238 </span><span class="lineCov">        180 :             *ssmax = fa * a;</span></a>
+<a name="11239"><span class="lineNum">   11239 </span><span class="lineCov">        180 :             if ( std::abs(mm)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="11240"><span class="lineNum">   11240 </span>            : </a>
+<a name="11241"><span class="lineNum">   11241 </span><span class="lineNoCov">          0 :                 if (std::abs(l)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="11242"><span class="lineNum">   11242 </span><span class="lineNoCov">          0 :                     t = ( (ft&gt;0) ? 2.0 : -2.0) * ( (gt&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="11243"><span class="lineNum">   11243 </span>            :                 } else {</a>
+<a name="11244"><span class="lineNum">   11244 </span><span class="lineNoCov">          0 :                     t = gt / ( (ft&gt;0) ? d__ : -d__) + m / t;</span></a>
+<a name="11245"><span class="lineNum">   11245 </span>            :                 }</a>
+<a name="11246"><span class="lineNum">   11246 </span>            :             } else {</a>
+<a name="11247"><span class="lineNum">   11247 </span><span class="lineCov">        180 :                 t = (m / (s + t) + m / (r__ + l)) * (a + 1.);</span></a>
+<a name="11248"><span class="lineNum">   11248 </span>            :             }</a>
+<a name="11249"><span class="lineNum">   11249 </span><span class="lineCov">        180 :             l =  std::sqrt(t * t + 4.);</span></a>
+<a name="11250"><span class="lineNum">   11250 </span><span class="lineCov">        180 :             crt = 2. / l;</span></a>
+<a name="11251"><span class="lineNum">   11251 </span><span class="lineCov">        180 :             srt = t / l;</span></a>
+<a name="11252"><span class="lineNum">   11252 </span><span class="lineCov">        180 :             clt = (crt + srt * m) / a;</span></a>
+<a name="11253"><span class="lineNum">   11253 </span><span class="lineCov">        180 :             slt = ht / ft * srt / a;</span></a>
+<a name="11254"><span class="lineNum">   11254 </span>            :         }</a>
+<a name="11255"><span class="lineNum">   11255 </span>            :     }</a>
+<a name="11256"><span class="lineNum">   11256 </span><span class="lineCov">        180 :     if (swap) {</span></a>
+<a name="11257"><span class="lineNum">   11257 </span><span class="lineCov">         12 :         *csl = srt;</span></a>
+<a name="11258"><span class="lineNum">   11258 </span><span class="lineCov">         12 :         *snl = crt;</span></a>
+<a name="11259"><span class="lineNum">   11259 </span><span class="lineCov">         12 :         *csr = slt;</span></a>
+<a name="11260"><span class="lineNum">   11260 </span><span class="lineCov">         12 :         *snr = clt;</span></a>
+<a name="11261"><span class="lineNum">   11261 </span>            :     } else {</a>
+<a name="11262"><span class="lineNum">   11262 </span><span class="lineCov">        168 :         *csl = clt;</span></a>
+<a name="11263"><span class="lineNum">   11263 </span><span class="lineCov">        168 :         *snl = slt;</span></a>
+<a name="11264"><span class="lineNum">   11264 </span><span class="lineCov">        168 :         *csr = crt;</span></a>
+<a name="11265"><span class="lineNum">   11265 </span><span class="lineCov">        168 :         *snr = srt;</span></a>
+<a name="11266"><span class="lineNum">   11266 </span>            :     }</a>
+<a name="11267"><span class="lineNum">   11267 </span>            : </a>
+<a name="11268"><span class="lineNum">   11268 </span><span class="lineCov">        180 :     if (pmax == 1) {</span></a>
+<a name="11269"><span class="lineNum">   11269 </span><span class="lineCov">        187 :         tsign = ( (*csr&gt;0) ? 1.0 : -1.0) * ( (*csl&gt;0) ? 1.0 : -1.0) * ( (*f&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="11270"><span class="lineNum">   11270 </span>            :     }</a>
+<a name="11271"><span class="lineNum">   11271 </span><span class="lineCov">        180 :     if (pmax == 2) {</span></a>
+<a name="11272"><span class="lineNum">   11272 </span><span class="lineCov">          2 :         tsign = ( (*snr&gt;0) ? 1.0 : -1.0) * ( (*csl&gt;0) ? 1.0 : -1.0) * ( (*g&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="11273"><span class="lineNum">   11273 </span>            :     }</a>
+<a name="11274"><span class="lineNum">   11274 </span><span class="lineCov">        180 :     if (pmax == 3) {</span></a>
+<a name="11275"><span class="lineNum">   11275 </span><span class="lineCov">         16 :         tsign = ( (*snr&gt;0) ? 1.0 : -1.0) * ( (*snl&gt;0) ? 1.0 : -1.0) * ( (*h__&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="11276"><span class="lineNum">   11276 </span>            :     }</a>
+<a name="11277"><span class="lineNum">   11277 </span><span class="lineCov">        180 :     if(tsign&lt;0)</span></a>
+<a name="11278"><span class="lineNum">   11278 </span><span class="lineCov">         25 :       *ssmax *= -1.0;</span></a>
+<a name="11279"><span class="lineNum">   11279 </span><span class="lineCov">        205 :     d__1 = tsign * ( (*f&gt;0) ? 1.0 : -1.0) * ( (*h__&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="11280"><span class="lineNum">   11280 </span><span class="lineCov">        180 :     if(d__1&lt;0)</span></a>
+<a name="11281"><span class="lineNum">   11281 </span><span class="lineCov">         65 :       *ssmin *= -1.0;</span></a>
+<a name="11282"><span class="lineNum">   11282 </span><span class="lineCov">        180 :     return;</span></a>
+<a name="11283"><span class="lineNum">   11283 </span>            : </a>
+<a name="11284"><span class="lineNum">   11284 </span>            : }</a>
+<a name="11285"><span class="lineNum">   11285 </span>            : }</a>
+<a name="11286"><span class="lineNum">   11286 </span>            : }</a>
+<a name="11287"><span class="lineNum">   11287 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11288"><span class="lineNum">   11288 </span>            : </a>
+<a name="11289"><span class="lineNum">   11289 </span>            : /* LAPACK */</a>
+<a name="11290"><span class="lineNum">   11290 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11291"><span class="lineNum">   11291 </span>            : namespace PLMD{</a>
+<a name="11292"><span class="lineNum">   11292 </span>            : namespace lapack{</a>
+<a name="11293"><span class="lineNum">   11293 </span>            : using namespace blas;</a>
+<a name="11294"><span class="lineNum">   11294 </span>            : void</a>
+<a name="11295"><span class="lineNum">   11295 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dlaswp,DLASWP)(int *n,</span></a>
+<a name="11296"><span class="lineNum">   11296 </span>            :         double *a,</a>
+<a name="11297"><span class="lineNum">   11297 </span>            :         int *lda,</a>
+<a name="11298"><span class="lineNum">   11298 </span>            :         int *k1,</a>
+<a name="11299"><span class="lineNum">   11299 </span>            :         int *k2,</a>
+<a name="11300"><span class="lineNum">   11300 </span>            :         int *ipiv,</a>
+<a name="11301"><span class="lineNum">   11301 </span>            :         int *incx)</a>
+<a name="11302"><span class="lineNum">   11302 </span>            : {</a>
+<a name="11303"><span class="lineNum">   11303 </span>            :   int ix0,i1,i2,inc,n32;</a>
+<a name="11304"><span class="lineNum">   11304 </span>            :   int ix,i,j,ip,k;</a>
+<a name="11305"><span class="lineNum">   11305 </span>            :   double temp;</a>
+<a name="11306"><span class="lineNum">   11306 </span>            : </a>
+<a name="11307"><span class="lineNum">   11307 </span><span class="lineNoCov">          0 :   if(*incx&gt;0) {</span></a>
+<a name="11308"><span class="lineNum">   11308 </span><span class="lineNoCov">          0 :     ix0 = *k1 - 1;</span></a>
+<a name="11309"><span class="lineNum">   11309 </span>            :     i1 = *k1 - 1;</a>
+<a name="11310"><span class="lineNum">   11310 </span><span class="lineNoCov">          0 :     i2 = *k2;</span></a>
+<a name="11311"><span class="lineNum">   11311 </span>            :     inc = 1;</a>
+<a name="11312"><span class="lineNum">   11312 </span><span class="lineNoCov">          0 :   } else if(*incx&lt;0) {</span></a>
+<a name="11313"><span class="lineNum">   11313 </span><span class="lineNoCov">          0 :     ix0 = *incx * (1- *k2);</span></a>
+<a name="11314"><span class="lineNum">   11314 </span><span class="lineNoCov">          0 :     i1 = *k2 - 1;</span></a>
+<a name="11315"><span class="lineNum">   11315 </span><span class="lineNoCov">          0 :     i2 = *k1;</span></a>
+<a name="11316"><span class="lineNum">   11316 </span>            :     inc = -1;</a>
+<a name="11317"><span class="lineNum">   11317 </span>            :   } else</a>
+<a name="11318"><span class="lineNum">   11318 </span>            :     return;</a>
+<a name="11319"><span class="lineNum">   11319 </span>            : </a>
+<a name="11320"><span class="lineNum">   11320 </span><span class="lineNoCov">          0 :   n32 = *n / 32;</span></a>
+<a name="11321"><span class="lineNum">   11321 </span>            :   </a>
+<a name="11322"><span class="lineNum">   11322 </span><span class="lineNoCov">          0 :   n32 *= 32;</span></a>
+<a name="11323"><span class="lineNum">   11323 </span>            : </a>
+<a name="11324"><span class="lineNum">   11324 </span>            : </a>
+<a name="11325"><span class="lineNum">   11325 </span><span class="lineNoCov">          0 :   if(n32!=0) {</span></a>
+<a name="11326"><span class="lineNum">   11326 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;n32;j+=32) {</span></a>
+<a name="11327"><span class="lineNum">   11327 </span>            :       ix = ix0;</a>
+<a name="11328"><span class="lineNum">   11328 </span><span class="lineNoCov">          0 :       for(i=i1;i&lt;i2;i+=inc,ix+=*incx) {</span></a>
+<a name="11329"><span class="lineNum">   11329 </span><span class="lineNoCov">          0 :         ip = ipiv[ix] - 1;</span></a>
+<a name="11330"><span class="lineNum">   11330 </span><span class="lineNoCov">          0 :         if(ip != i) {</span></a>
+<a name="11331"><span class="lineNum">   11331 </span><span class="lineNoCov">          0 :           for(k=j;k&lt;j+32;k++) {</span></a>
+<a name="11332"><span class="lineNum">   11332 </span><span class="lineNoCov">          0 :             temp = a[(k)*(*lda)+i];</span></a>
+<a name="11333"><span class="lineNum">   11333 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+i] = a[(k)*(*lda)+ip];</span></a>
+<a name="11334"><span class="lineNum">   11334 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+ip] = temp;</span></a>
+<a name="11335"><span class="lineNum">   11335 </span>            :           }</a>
+<a name="11336"><span class="lineNum">   11336 </span>            :         }</a>
+<a name="11337"><span class="lineNum">   11337 </span>            :       }</a>
+<a name="11338"><span class="lineNum">   11338 </span>            :     }</a>
+<a name="11339"><span class="lineNum">   11339 </span>            :   }</a>
+<a name="11340"><span class="lineNum">   11340 </span><span class="lineNoCov">          0 :   if(n32!=*n) {</span></a>
+<a name="11341"><span class="lineNum">   11341 </span>            :     ix = ix0;</a>
+<a name="11342"><span class="lineNum">   11342 </span><span class="lineNoCov">          0 :     for(i=i1;i&lt;i2;i+=inc,ix+=*incx) {</span></a>
+<a name="11343"><span class="lineNum">   11343 </span><span class="lineNoCov">          0 :       ip = ipiv[ix] - 1;</span></a>
+<a name="11344"><span class="lineNum">   11344 </span><span class="lineNoCov">          0 :       if(ip != i) {</span></a>
+<a name="11345"><span class="lineNum">   11345 </span><span class="lineNoCov">          0 :         for(k=n32;k&lt;*n;k++) {</span></a>
+<a name="11346"><span class="lineNum">   11346 </span><span class="lineNoCov">          0 :             temp = a[(k)*(*lda)+i];</span></a>
+<a name="11347"><span class="lineNum">   11347 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+i] = a[(k)*(*lda)+ip];</span></a>
+<a name="11348"><span class="lineNum">   11348 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+ip] = temp;</span></a>
+<a name="11349"><span class="lineNum">   11349 </span>            :         }</a>
+<a name="11350"><span class="lineNum">   11350 </span>            :       }</a>
+<a name="11351"><span class="lineNum">   11351 </span>            :     }</a>
+<a name="11352"><span class="lineNum">   11352 </span>            :   }</a>
+<a name="11353"><span class="lineNum">   11353 </span>            :   return;</a>
+<a name="11354"><span class="lineNum">   11354 </span>            : }</a>
+<a name="11355"><span class="lineNum">   11355 </span>            : }</a>
+<a name="11356"><span class="lineNum">   11356 </span>            : }</a>
+<a name="11357"><span class="lineNum">   11357 </span>            : #include &lt;cctype&gt;</a>
+<a name="11358"><span class="lineNum">   11358 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11359"><span class="lineNum">   11359 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11360"><span class="lineNum">   11360 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="11361"><span class="lineNum">   11361 </span>            : </a>
+<a name="11362"><span class="lineNum">   11362 </span>            : </a>
+<a name="11363"><span class="lineNum">   11363 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11364"><span class="lineNum">   11364 </span>            : namespace PLMD{</a>
+<a name="11365"><span class="lineNum">   11365 </span>            : namespace lapack{</a>
+<a name="11366"><span class="lineNum">   11366 </span>            : using namespace blas;</a>
+<a name="11367"><span class="lineNum">   11367 </span>            : void</a>
+<a name="11368"><span class="lineNum">   11368 </span><span class="lineCov">         19 : PLUMED_BLAS_F77_FUNC(dlatrd,DLATRD)(const char *  uplo,</span></a>
+<a name="11369"><span class="lineNum">   11369 </span>            :        int  *   n,</a>
+<a name="11370"><span class="lineNum">   11370 </span>            :        int  *   nb,</a>
+<a name="11371"><span class="lineNum">   11371 </span>            :        double * a,</a>
+<a name="11372"><span class="lineNum">   11372 </span>            :        int *    lda,</a>
+<a name="11373"><span class="lineNum">   11373 </span>            :        double * e,</a>
+<a name="11374"><span class="lineNum">   11374 </span>            :        double * tau,</a>
+<a name="11375"><span class="lineNum">   11375 </span>            :        double * w,</a>
+<a name="11376"><span class="lineNum">   11376 </span>            :        int *    ldw)</a>
+<a name="11377"><span class="lineNum">   11377 </span>            : {</a>
+<a name="11378"><span class="lineNum">   11378 </span>            :   int i,iw;</a>
+<a name="11379"><span class="lineNum">   11379 </span>            :   int ti1,ti2,ti3;</a>
+<a name="11380"><span class="lineNum">   11380 </span>            :   double one,zero,minusone,alpha;</a>
+<a name="11381"><span class="lineNum">   11381 </span><span class="lineCov">         19 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="11382"><span class="lineNum">   11382 </span>            : </a>
+<a name="11383"><span class="lineNum">   11383 </span><span class="lineCov">         19 :   one=1.0;</span></a>
+<a name="11384"><span class="lineNum">   11384 </span><span class="lineCov">         19 :   minusone=-1.0;</span></a>
+<a name="11385"><span class="lineNum">   11385 </span><span class="lineCov">         19 :   zero=0.0;</span></a>
+<a name="11386"><span class="lineNum">   11386 </span>            : </a>
+<a name="11387"><span class="lineNum">   11387 </span><span class="lineCov">         19 :   if(*n&lt;=0)</span></a>
+<a name="11388"><span class="lineNum">   11388 </span>            :     return;</a>
+<a name="11389"><span class="lineNum">   11389 </span>            : </a>
+<a name="11390"><span class="lineNum">   11390 </span><span class="lineCov">         19 :   if(ch=='U') {</span></a>
+<a name="11391"><span class="lineNum">   11391 </span><span class="lineCov">        532 :     for(i=*n;i&gt;=(*n-*nb+1);i--) {</span></a>
+<a name="11392"><span class="lineNum">   11392 </span><span class="lineCov">        513 :       iw = i -*n + *nb;</span></a>
+<a name="11393"><span class="lineNum">   11393 </span>            :       </a>
+<a name="11394"><span class="lineNum">   11394 </span><span class="lineCov">        513 :       if(i&lt;*n) {</span></a>
+<a name="11395"><span class="lineNum">   11395 </span><span class="lineCov">        494 :         ti1 = *n-i;</span></a>
+<a name="11396"><span class="lineNum">   11396 </span><span class="lineCov">        494 :         ti2 = 1;</span></a>
+<a name="11397"><span class="lineNum">   11397 </span>            :         /* BLAS */</a>
+<a name="11398"><span class="lineNum">   11398 </span><span class="lineCov">        494 :         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;i,&amp;ti1,&amp;minusone, &amp;(a[ i*(*lda) + 0]),lda,&amp;(w[iw*(*ldw)+(i-1)]),</span></a>
+<a name="11399"><span class="lineNum">   11399 </span><span class="lineCov">        494 :                ldw,&amp;one, &amp;(a[ (i-1)*(*lda) + 0]), &amp;ti2);</span></a>
+<a name="11400"><span class="lineNum">   11400 </span>            :         /* BLAS */</a>
+<a name="11401"><span class="lineNum">   11401 </span><span class="lineCov">        494 :         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;i,&amp;ti1,&amp;minusone, &amp;(w[ iw*(*ldw) + 0]),ldw,&amp;(a[i*(*lda)+(i-1)]),</span></a>
+<a name="11402"><span class="lineNum">   11402 </span><span class="lineCov">        494 :                lda,&amp;one, &amp;(a[ (i-1)*(*lda) + 0]), &amp;ti2);</span></a>
+<a name="11403"><span class="lineNum">   11403 </span>            :       }</a>
+<a name="11404"><span class="lineNum">   11404 </span>            : </a>
+<a name="11405"><span class="lineNum">   11405 </span><span class="lineCov">        513 :       if(i&gt;1) {</span></a>
+<a name="11406"><span class="lineNum">   11406 </span>            :         /*  Generate elementary reflector H(i) to annihilate</a>
+<a name="11407"><span class="lineNum">   11407 </span>            :          *              A(1:i-2,i) </a>
+<a name="11408"><span class="lineNum">   11408 </span>            :          */</a>
+<a name="11409"><span class="lineNum">   11409 </span><span class="lineCov">        513 :         ti1 = i-1;</span></a>
+<a name="11410"><span class="lineNum">   11410 </span><span class="lineCov">        513 :         ti2 = 1;</span></a>
+<a name="11411"><span class="lineNum">   11411 </span>            : </a>
+<a name="11412"><span class="lineNum">   11412 </span>            :         /* LAPACK */</a>
+<a name="11413"><span class="lineNum">   11413 </span><span class="lineCov">        513 :         PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;ti1,&amp;(a[(i-1)*(*lda)+(i-2)]),&amp;(a[(i-1)*(*lda)+0]),&amp;ti2,&amp;(tau[i-2]));</span></a>
+<a name="11414"><span class="lineNum">   11414 </span>            :       </a>
+<a name="11415"><span class="lineNum">   11415 </span><span class="lineCov">        513 :         e[i-2] = a[(i-1)*(*lda)+(i-2)];</span></a>
+<a name="11416"><span class="lineNum">   11416 </span><span class="lineCov">        513 :         a[(i-1)*(*lda)+(i-2)] = 1.0;</span></a>
+<a name="11417"><span class="lineNum">   11417 </span>            : </a>
+<a name="11418"><span class="lineNum">   11418 </span>            :         /* Compute W(1:i-1,i) */</a>
+<a name="11419"><span class="lineNum">   11419 </span><span class="lineCov">        513 :         ti1 = i-1;</span></a>
+<a name="11420"><span class="lineNum">   11420 </span><span class="lineCov">        513 :         ti2 = 1;</span></a>
+<a name="11421"><span class="lineNum">   11421 </span>            : </a>
+<a name="11422"><span class="lineNum">   11422 </span>            :         /* BLAS */</a>
+<a name="11423"><span class="lineNum">   11423 </span><span class="lineCov">        513 :         PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)(&quot;U&quot;,&amp;ti1,&amp;one,a,lda,&amp;(a[(i-1)*(*lda)+0]),&amp;ti2,&amp;zero,</span></a>
+<a name="11424"><span class="lineNum">   11424 </span><span class="lineCov">        513 :                &amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2);</span></a>
+<a name="11425"><span class="lineNum">   11425 </span><span class="lineCov">        513 :         if(i&lt;*n) {</span></a>
+<a name="11426"><span class="lineNum">   11426 </span><span class="lineCov">        494 :           ti1 = i-1;</span></a>
+<a name="11427"><span class="lineNum">   11427 </span><span class="lineCov">        494 :           ti2 = *n-i;</span></a>
+<a name="11428"><span class="lineNum">   11428 </span><span class="lineCov">        494 :           ti3 = 1;</span></a>
+<a name="11429"><span class="lineNum">   11429 </span>            :           /* BLAS */</a>
+<a name="11430"><span class="lineNum">   11430 </span><span class="lineCov">        494 :           PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(w[iw*(*ldw)+0]),ldw,&amp;(a[(i-1)*(*lda)+0]),&amp;ti3,</span></a>
+<a name="11431"><span class="lineNum">   11431 </span><span class="lineCov">        494 :                  &amp;zero,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="11432"><span class="lineNum">   11432 </span>            :         </a>
+<a name="11433"><span class="lineNum">   11433 </span>            :           /* BLAS */</a>
+<a name="11434"><span class="lineNum">   11434 </span><span class="lineCov">        494 :           PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(a[i*(*lda)+0]),lda,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3,</span></a>
+<a name="11435"><span class="lineNum">   11435 </span><span class="lineCov">        494 :                  &amp;one,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="11436"><span class="lineNum">   11436 </span>            :         </a>
+<a name="11437"><span class="lineNum">   11437 </span>            :           /* BLAS */</a>
+<a name="11438"><span class="lineNum">   11438 </span><span class="lineCov">        494 :           PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(a[i*(*lda)+0]),lda,&amp;(a[(i-1)*(*lda)+0]),&amp;ti3,</span></a>
+<a name="11439"><span class="lineNum">   11439 </span><span class="lineCov">        494 :                  &amp;zero,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="11440"><span class="lineNum">   11440 </span>            :         </a>
+<a name="11441"><span class="lineNum">   11441 </span>            :           /* BLAS */</a>
+<a name="11442"><span class="lineNum">   11442 </span><span class="lineCov">        494 :           PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(w[iw*(*ldw)+0]),ldw,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3,</span></a>
+<a name="11443"><span class="lineNum">   11443 </span><span class="lineCov">        494 :                  &amp;one,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="11444"><span class="lineNum">   11444 </span>            :         }</a>
+<a name="11445"><span class="lineNum">   11445 </span>            :       </a>
+<a name="11446"><span class="lineNum">   11446 </span><span class="lineCov">        513 :         ti1 = i-1;</span></a>
+<a name="11447"><span class="lineNum">   11447 </span><span class="lineCov">        513 :         ti2 = 1;</span></a>
+<a name="11448"><span class="lineNum">   11448 </span>            :         /* BLAS */</a>
+<a name="11449"><span class="lineNum">   11449 </span><span class="lineCov">        513 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;ti1,&amp;(tau[i-2]),&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2);</span></a>
+<a name="11450"><span class="lineNum">   11450 </span>            :       </a>
+<a name="11451"><span class="lineNum">   11451 </span><span class="lineCov">       1026 :         alpha = -0.5*tau[i-2]*PLUMED_BLAS_F77_FUNC(ddot,DDOT)(&amp;ti1,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2,</span></a>
+<a name="11452"><span class="lineNum">   11452 </span><span class="lineCov">        513 :                                     &amp;(a[(i-1)*(*lda)+0]),&amp;ti2);</span></a>
+<a name="11453"><span class="lineNum">   11453 </span>            :       </a>
+<a name="11454"><span class="lineNum">   11454 </span>            :         /* BLAS */</a>
+<a name="11455"><span class="lineNum">   11455 </span><span class="lineCov">        513 :         PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(&amp;ti1,&amp;alpha,&amp;(a[(i-1)*(*lda)+0]),&amp;ti2,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2);</span></a>
+<a name="11456"><span class="lineNum">   11456 </span>            : </a>
+<a name="11457"><span class="lineNum">   11457 </span>            :       }</a>
+<a name="11458"><span class="lineNum">   11458 </span>            :     }</a>
+<a name="11459"><span class="lineNum">   11459 </span>            :   } else {</a>
+<a name="11460"><span class="lineNum">   11460 </span>            :     /* lower */</a>
+<a name="11461"><span class="lineNum">   11461 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;=*nb;i++) {</span></a>
+<a name="11462"><span class="lineNum">   11462 </span>            : </a>
+<a name="11463"><span class="lineNum">   11463 </span><span class="lineNoCov">          0 :       ti1 = *n-i+1;</span></a>
+<a name="11464"><span class="lineNum">   11464 </span><span class="lineNoCov">          0 :       ti2 = i-1;</span></a>
+<a name="11465"><span class="lineNum">   11465 </span><span class="lineNoCov">          0 :       ti3 = 1;</span></a>
+<a name="11466"><span class="lineNum">   11466 </span>            :       /* BLAS */</a>
+<a name="11467"><span class="lineNum">   11467 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone, &amp;(a[ i-1 ]),lda,&amp;(w[ i-1 ]),</span></a>
+<a name="11468"><span class="lineNum">   11468 </span><span class="lineNoCov">          0 :                ldw,&amp;one, &amp;(a[ (i-1)*(*lda) + (i-1)]), &amp;ti3);</span></a>
+<a name="11469"><span class="lineNum">   11469 </span>            :       /* BLAS */</a>
+<a name="11470"><span class="lineNum">   11470 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone, &amp;(w[ i-1 ]),ldw,&amp;(a[ i-1 ]),</span></a>
+<a name="11471"><span class="lineNum">   11471 </span><span class="lineNoCov">          0 :                lda,&amp;one, &amp;(a[ (i-1)*(*lda) + (i-1)]), &amp;ti3);</span></a>
+<a name="11472"><span class="lineNum">   11472 </span>            : </a>
+<a name="11473"><span class="lineNum">   11473 </span><span class="lineNoCov">          0 :       if(i&lt;*n) {</span></a>
+<a name="11474"><span class="lineNum">   11474 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="11475"><span class="lineNum">   11475 </span><span class="lineNoCov">          0 :         ti2 = (*n &lt; i+2 ) ? *n : (i+2);</span></a>
+<a name="11476"><span class="lineNum">   11476 </span><span class="lineNoCov">          0 :         ti3 = 1;</span></a>
+<a name="11477"><span class="lineNum">   11477 </span>            :         /* LAPACK */</a>
+<a name="11478"><span class="lineNum">   11478 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;ti1,&amp;(a[(i-1)*(*lda)+(i)]),&amp;(a[(i-1)*(*lda)+(ti2-1)]),&amp;ti3,&amp;(tau[i-1]));</span></a>
+<a name="11479"><span class="lineNum">   11479 </span><span class="lineNoCov">          0 :         e[i-1] = a[(i-1)*(*lda)+(i)];</span></a>
+<a name="11480"><span class="lineNum">   11480 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i)] = 1.0;</span></a>
+<a name="11481"><span class="lineNum">   11481 </span>            :         </a>
+<a name="11482"><span class="lineNum">   11482 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="11483"><span class="lineNum">   11483 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="11484"><span class="lineNum">   11484 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)(&quot;L&quot;,&amp;ti1,&amp;one,&amp;(a[i*(*lda)+i]),lda,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2,</span></a>
+<a name="11485"><span class="lineNum">   11485 </span><span class="lineNoCov">          0 :                &amp;zero,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti2);</span></a>
+<a name="11486"><span class="lineNum">   11486 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="11487"><span class="lineNum">   11487 </span><span class="lineNoCov">          0 :         ti2 = i-1;</span></a>
+<a name="11488"><span class="lineNum">   11488 </span><span class="lineNoCov">          0 :         ti3 = 1;</span></a>
+<a name="11489"><span class="lineNum">   11489 </span>            :         /* BLAS */</a>
+<a name="11490"><span class="lineNum">   11490 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(w[ i ]),ldw,&amp;(a[(i-1)*(*lda)+i]),&amp;ti3,</span></a>
+<a name="11491"><span class="lineNum">   11491 </span><span class="lineNoCov">          0 :                &amp;zero,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="11492"><span class="lineNum">   11492 </span>            :         </a>
+<a name="11493"><span class="lineNum">   11493 </span>            :         /* BLAS */</a>
+<a name="11494"><span class="lineNum">   11494 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(a[ i ]),lda,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3,</span></a>
+<a name="11495"><span class="lineNum">   11495 </span><span class="lineNoCov">          0 :                &amp;one,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="11496"><span class="lineNum">   11496 </span>            :         </a>
+<a name="11497"><span class="lineNum">   11497 </span>            :         /* BLAS */</a>
+<a name="11498"><span class="lineNum">   11498 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(a[ i ]),lda,&amp;(a[(i-1)*(*lda)+i]),&amp;ti3,</span></a>
+<a name="11499"><span class="lineNum">   11499 </span><span class="lineNoCov">          0 :                &amp;zero,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="11500"><span class="lineNum">   11500 </span>            :         </a>
+<a name="11501"><span class="lineNum">   11501 </span>            :         /* BLAS */</a>
+<a name="11502"><span class="lineNum">   11502 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dgemv,DGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(w[ i ]),ldw,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3,</span></a>
+<a name="11503"><span class="lineNum">   11503 </span><span class="lineNoCov">          0 :                &amp;one,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="11504"><span class="lineNum">   11504 </span>            : </a>
+<a name="11505"><span class="lineNum">   11505 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;ti1,&amp;(tau[i-1]),&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="11506"><span class="lineNum">   11506 </span><span class="lineNoCov">          0 :         alpha = -0.5*tau[i-1]*PLUMED_BLAS_F77_FUNC(ddot,DDOT)(&amp;ti1,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3,</span></a>
+<a name="11507"><span class="lineNum">   11507 </span><span class="lineNoCov">          0 :                                    &amp;(a[(i-1)*(*lda)+i]),&amp;ti3);</span></a>
+<a name="11508"><span class="lineNum">   11508 </span>            :         </a>
+<a name="11509"><span class="lineNum">   11509 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(&amp;ti1,&amp;alpha,&amp;(a[(i-1)*(*lda)+i]),&amp;ti3,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="11510"><span class="lineNum">   11510 </span>            :       }</a>
+<a name="11511"><span class="lineNum">   11511 </span>            :     }</a>
+<a name="11512"><span class="lineNum">   11512 </span>            :   }</a>
+<a name="11513"><span class="lineNum">   11513 </span>            :   return;</a>
+<a name="11514"><span class="lineNum">   11514 </span>            : }</a>
+<a name="11515"><span class="lineNum">   11515 </span>            :         </a>
+<a name="11516"><span class="lineNum">   11516 </span>            : </a>
+<a name="11517"><span class="lineNum">   11517 </span>            : </a>
+<a name="11518"><span class="lineNum">   11518 </span>            :   </a>
+<a name="11519"><span class="lineNum">   11519 </span>            : }</a>
+<a name="11520"><span class="lineNum">   11520 </span>            : }</a>
+<a name="11521"><span class="lineNum">   11521 </span>            : #include &lt;cmath&gt;</a>
+<a name="11522"><span class="lineNum">   11522 </span>            : </a>
+<a name="11523"><span class="lineNum">   11523 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11524"><span class="lineNum">   11524 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11525"><span class="lineNum">   11525 </span>            : </a>
+<a name="11526"><span class="lineNum">   11526 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11527"><span class="lineNum">   11527 </span>            : namespace PLMD{</a>
+<a name="11528"><span class="lineNum">   11528 </span>            : namespace lapack{</a>
+<a name="11529"><span class="lineNum">   11529 </span>            : using namespace blas;</a>
+<a name="11530"><span class="lineNum">   11530 </span>            : void </a>
+<a name="11531"><span class="lineNum">   11531 </span><span class="lineCov">          1 : PLUMED_BLAS_F77_FUNC(dorg2r,DORG2R)(int *m, </span></a>
+<a name="11532"><span class="lineNum">   11532 </span>            :                         int *n,</a>
+<a name="11533"><span class="lineNum">   11533 </span>            :                         int *k, </a>
+<a name="11534"><span class="lineNum">   11534 </span>            :                         double *a, </a>
+<a name="11535"><span class="lineNum">   11535 </span>            :                         int *lda,</a>
+<a name="11536"><span class="lineNum">   11536 </span>            :                         double *tau,</a>
+<a name="11537"><span class="lineNum">   11537 </span>            :                         double *work,</a>
+<a name="11538"><span class="lineNum">   11538 </span>            :                         int *info)</a>
+<a name="11539"><span class="lineNum">   11539 </span>            : {</a>
+<a name="11540"><span class="lineNum">   11540 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="11541"><span class="lineNum">   11541 </span>            :     double r__1;</a>
+<a name="11542"><span class="lineNum">   11542 </span><span class="lineCov">          1 :     int c__1 = 1;</span></a>
+<a name="11543"><span class="lineNum">   11543 </span>            : </a>
+<a name="11544"><span class="lineNum">   11544 </span>            :     int i__, j, l;</a>
+<a name="11545"><span class="lineNum">   11545 </span>            : </a>
+<a name="11546"><span class="lineNum">   11546 </span><span class="lineCov">          1 :     a_dim1 = *lda;</span></a>
+<a name="11547"><span class="lineNum">   11547 </span><span class="lineCov">          1 :     a_offset = 1 + a_dim1;</span></a>
+<a name="11548"><span class="lineNum">   11548 </span><span class="lineCov">          1 :     a -= a_offset;</span></a>
+<a name="11549"><span class="lineNum">   11549 </span><span class="lineCov">          1 :     --tau;</span></a>
+<a name="11550"><span class="lineNum">   11550 </span>            :     --work;</a>
+<a name="11551"><span class="lineNum">   11551 </span>            : </a>
+<a name="11552"><span class="lineNum">   11552 </span><span class="lineCov">          1 :     *info = 0;</span></a>
+<a name="11553"><span class="lineNum">   11553 </span>            : </a>
+<a name="11554"><span class="lineNum">   11554 </span><span class="lineCov">          1 :     if (*n &lt;= 0) {</span></a>
+<a name="11555"><span class="lineNum">   11555 </span>            :         return;</a>
+<a name="11556"><span class="lineNum">   11556 </span>            :     }</a>
+<a name="11557"><span class="lineNum">   11557 </span>            : </a>
+<a name="11558"><span class="lineNum">   11558 </span><span class="lineCov">          1 :     i__1 = *n;</span></a>
+<a name="11559"><span class="lineNum">   11559 </span><span class="lineCov">          2 :     for (j = *k + 1; j &lt;= i__1; ++j) {</span></a>
+<a name="11560"><span class="lineNum">   11560 </span><span class="lineCov">          1 :         i__2 = *m;</span></a>
+<a name="11561"><span class="lineNum">   11561 </span><span class="lineCov">          4 :         for (l = 1; l &lt;= i__2; ++l) {</span></a>
+<a name="11562"><span class="lineNum">   11562 </span><span class="lineCov">          3 :             a[l + j * a_dim1] = 0.0;</span></a>
+<a name="11563"><span class="lineNum">   11563 </span>            :         }</a>
+<a name="11564"><span class="lineNum">   11564 </span><span class="lineCov">          1 :         a[j + j * a_dim1] = 1.0;</span></a>
+<a name="11565"><span class="lineNum">   11565 </span>            :     }</a>
+<a name="11566"><span class="lineNum">   11566 </span><span class="lineCov">          3 :     for (i__ = *k; i__ &gt;= 1; --i__) {</span></a>
+<a name="11567"><span class="lineNum">   11567 </span><span class="lineCov">          2 :         if (i__ &lt; *n) {</span></a>
+<a name="11568"><span class="lineNum">   11568 </span><span class="lineCov">          2 :             a[i__ + i__ * a_dim1] = 1.0;</span></a>
+<a name="11569"><span class="lineNum">   11569 </span><span class="lineCov">          2 :             i__1 = *m - i__ + 1;</span></a>
+<a name="11570"><span class="lineNum">   11570 </span><span class="lineCov">          2 :             i__2 = *n - i__;</span></a>
+<a name="11571"><span class="lineNum">   11571 </span><span class="lineCov">          2 :             PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;L&quot;, &amp;i__1, &amp;i__2, &amp;a[i__ + i__ * a_dim1], &amp;c__1, </span></a>
+<a name="11572"><span class="lineNum">   11572 </span><span class="lineCov">          2 :                               &amp;tau[i__], &amp;a[i__ + (i__ + 1) * a_dim1], lda, &amp;work[1]);</span></a>
+<a name="11573"><span class="lineNum">   11573 </span>            :         }</a>
+<a name="11574"><span class="lineNum">   11574 </span><span class="lineCov">          2 :         if (i__ &lt; *m) {</span></a>
+<a name="11575"><span class="lineNum">   11575 </span><span class="lineCov">          2 :             i__1 = *m - i__;</span></a>
+<a name="11576"><span class="lineNum">   11576 </span><span class="lineCov">          2 :             r__1 = -tau[i__];</span></a>
+<a name="11577"><span class="lineNum">   11577 </span><span class="lineCov">          2 :             PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__1, &amp;r__1, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="11578"><span class="lineNum">   11578 </span>            :         }</a>
+<a name="11579"><span class="lineNum">   11579 </span><span class="lineCov">          2 :         a[i__ + i__ * a_dim1] = 1.0 - tau[i__];</span></a>
+<a name="11580"><span class="lineNum">   11580 </span><span class="lineCov">          2 :         i__1 = i__ - 1;</span></a>
+<a name="11581"><span class="lineNum">   11581 </span><span class="lineCov">          3 :         for (l = 1; l &lt;= i__1; ++l) {</span></a>
+<a name="11582"><span class="lineNum">   11582 </span><span class="lineCov">          1 :             a[l + i__ * a_dim1] = 0.0;</span></a>
+<a name="11583"><span class="lineNum">   11583 </span>            :         }</a>
+<a name="11584"><span class="lineNum">   11584 </span>            :     }</a>
+<a name="11585"><span class="lineNum">   11585 </span>            :     return;</a>
+<a name="11586"><span class="lineNum">   11586 </span>            : </a>
+<a name="11587"><span class="lineNum">   11587 </span>            : }</a>
+<a name="11588"><span class="lineNum">   11588 </span>            : </a>
+<a name="11589"><span class="lineNum">   11589 </span>            : </a>
+<a name="11590"><span class="lineNum">   11590 </span>            : }</a>
+<a name="11591"><span class="lineNum">   11591 </span>            : }</a>
+<a name="11592"><span class="lineNum">   11592 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11593"><span class="lineNum">   11593 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="11594"><span class="lineNum">   11594 </span>            : </a>
+<a name="11595"><span class="lineNum">   11595 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11596"><span class="lineNum">   11596 </span>            : namespace PLMD{</a>
+<a name="11597"><span class="lineNum">   11597 </span>            : namespace lapack{</a>
+<a name="11598"><span class="lineNum">   11598 </span>            : using namespace blas;</a>
+<a name="11599"><span class="lineNum">   11599 </span>            : void</a>
+<a name="11600"><span class="lineNum">   11600 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dorgbr,DORGBR)(const char *vect,</span></a>
+<a name="11601"><span class="lineNum">   11601 </span>            :         int *m,</a>
+<a name="11602"><span class="lineNum">   11602 </span>            :         int *n,</a>
+<a name="11603"><span class="lineNum">   11603 </span>            :         int *k,</a>
+<a name="11604"><span class="lineNum">   11604 </span>            :         double *a,</a>
+<a name="11605"><span class="lineNum">   11605 </span>            :         int *lda,</a>
+<a name="11606"><span class="lineNum">   11606 </span>            :         double *tau,</a>
+<a name="11607"><span class="lineNum">   11607 </span>            :         double *work,</a>
+<a name="11608"><span class="lineNum">   11608 </span>            :         int *lwork,</a>
+<a name="11609"><span class="lineNum">   11609 </span>            :         int *info)</a>
+<a name="11610"><span class="lineNum">   11610 </span>            : {</a>
+<a name="11611"><span class="lineNum">   11611 </span>            :   int wantq,iinfo,j,i,i1,wrksz;</a>
+<a name="11612"><span class="lineNum">   11612 </span><span class="lineNoCov">          0 :   int mn = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="11613"><span class="lineNum">   11613 </span>            : </a>
+<a name="11614"><span class="lineNum">   11614 </span><span class="lineNoCov">          0 :   wantq = (*vect=='Q' || *vect=='q');</span></a>
+<a name="11615"><span class="lineNum">   11615 </span>            : </a>
+<a name="11616"><span class="lineNum">   11616 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="11617"><span class="lineNum">   11617 </span><span class="lineNoCov">          0 :   wrksz = mn*DORGBR_BLOCKSIZE;</span></a>
+<a name="11618"><span class="lineNum">   11618 </span><span class="lineNoCov">          0 :   if(*lwork==-1) {</span></a>
+<a name="11619"><span class="lineNum">   11619 </span><span class="lineNoCov">          0 :     work[0] = wrksz;</span></a>
+<a name="11620"><span class="lineNum">   11620 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="11621"><span class="lineNum">   11621 </span>            :   }</a>
+<a name="11622"><span class="lineNum">   11622 </span>            :   </a>
+<a name="11623"><span class="lineNum">   11623 </span><span class="lineNoCov">          0 :   if(*m==0 || *n==0)</span></a>
+<a name="11624"><span class="lineNum">   11624 </span>            :     return;</a>
+<a name="11625"><span class="lineNum">   11625 </span>            : </a>
+<a name="11626"><span class="lineNum">   11626 </span><span class="lineNoCov">          0 :   if(wantq) {</span></a>
+<a name="11627"><span class="lineNum">   11627 </span><span class="lineNoCov">          0 :     if(*m&gt;=*k)</span></a>
+<a name="11628"><span class="lineNum">   11628 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dorgqr,DORGQR)(m,n,k,a,lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="11629"><span class="lineNum">   11629 </span>            :     else {</a>
+<a name="11630"><span class="lineNum">   11630 </span><span class="lineNoCov">          0 :       for(j=*m;j&gt;=2;j--) {</span></a>
+<a name="11631"><span class="lineNum">   11631 </span><span class="lineNoCov">          0 :         a[(j-1)*(*lda)+0] = 0.0;</span></a>
+<a name="11632"><span class="lineNum">   11632 </span><span class="lineNoCov">          0 :         for(i=j+1;i&lt;=*m;i++)</span></a>
+<a name="11633"><span class="lineNum">   11633 </span><span class="lineNoCov">          0 :           a[(j-1)*(*lda)+(i-1)] = a[(j-2)*(*lda)+(i-1)]; </span></a>
+<a name="11634"><span class="lineNum">   11634 </span>            :       }</a>
+<a name="11635"><span class="lineNum">   11635 </span><span class="lineNoCov">          0 :       a[0] = 1.0;</span></a>
+<a name="11636"><span class="lineNum">   11636 </span><span class="lineNoCov">          0 :       for(i=2;i&lt;=*m;i++)</span></a>
+<a name="11637"><span class="lineNum">   11637 </span><span class="lineNoCov">          0 :         a[i-1] = 0.0;</span></a>
+<a name="11638"><span class="lineNum">   11638 </span><span class="lineNoCov">          0 :       if(*m&gt;1) {</span></a>
+<a name="11639"><span class="lineNum">   11639 </span><span class="lineNoCov">          0 :         i1 = *m-1;</span></a>
+<a name="11640"><span class="lineNum">   11640 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dorgqr,DORGQR)(&amp;i1,&amp;i1,&amp;i1,&amp;(a[*lda+1]),lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="11641"><span class="lineNum">   11641 </span>            :       }</a>
+<a name="11642"><span class="lineNum">   11642 </span>            :     }</a>
+<a name="11643"><span class="lineNum">   11643 </span>            :   } else {</a>
+<a name="11644"><span class="lineNum">   11644 </span><span class="lineNoCov">          0 :     if(*k&lt;*n)</span></a>
+<a name="11645"><span class="lineNum">   11645 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dorglq,DORGLQ)(m,n,k,a,lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="11646"><span class="lineNum">   11646 </span>            :     else {</a>
+<a name="11647"><span class="lineNum">   11647 </span><span class="lineNoCov">          0 :       a[0] = 1.0;</span></a>
+<a name="11648"><span class="lineNum">   11648 </span><span class="lineNoCov">          0 :       for(i=2;i&lt;=*m;i++)</span></a>
+<a name="11649"><span class="lineNum">   11649 </span><span class="lineNoCov">          0 :         a[i-1] = 0.0;</span></a>
+<a name="11650"><span class="lineNum">   11650 </span><span class="lineNoCov">          0 :       for(j=2;j&lt;=*n;j++) {</span></a>
+<a name="11651"><span class="lineNum">   11651 </span><span class="lineNoCov">          0 :         for(i=j-1;i&gt;=2;i--)</span></a>
+<a name="11652"><span class="lineNum">   11652 </span><span class="lineNoCov">          0 :           a[(j-1)*(*lda)+(i-1)] = a[(j-1)*(*lda)+(i-2)]; </span></a>
+<a name="11653"><span class="lineNum">   11653 </span><span class="lineNoCov">          0 :         a[(j-1)*(*lda)+0] = 0.0;</span></a>
+<a name="11654"><span class="lineNum">   11654 </span>            :       }</a>
+<a name="11655"><span class="lineNum">   11655 </span><span class="lineNoCov">          0 :       if(*n&gt;1) {</span></a>
+<a name="11656"><span class="lineNum">   11656 </span><span class="lineNoCov">          0 :         i1 = *n-1;</span></a>
+<a name="11657"><span class="lineNum">   11657 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dorglq,DORGLQ)(&amp;i1,&amp;i1,&amp;i1,&amp;(a[*lda+1]),lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="11658"><span class="lineNum">   11658 </span>            :       }</a>
+<a name="11659"><span class="lineNum">   11659 </span>            :     }</a>
+<a name="11660"><span class="lineNum">   11660 </span>            :   }</a>
+<a name="11661"><span class="lineNum">   11661 </span><span class="lineNoCov">          0 :   work[0] = wrksz;</span></a>
+<a name="11662"><span class="lineNum">   11662 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="11663"><span class="lineNum">   11663 </span>            : }</a>
+<a name="11664"><span class="lineNum">   11664 </span>            :  </a>
+<a name="11665"><span class="lineNum">   11665 </span>            : }</a>
+<a name="11666"><span class="lineNum">   11666 </span>            : }</a>
+<a name="11667"><span class="lineNum">   11667 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11668"><span class="lineNum">   11668 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11669"><span class="lineNum">   11669 </span>            : </a>
+<a name="11670"><span class="lineNum">   11670 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11671"><span class="lineNum">   11671 </span>            : namespace PLMD{</a>
+<a name="11672"><span class="lineNum">   11672 </span>            : namespace lapack{</a>
+<a name="11673"><span class="lineNum">   11673 </span>            : using namespace blas;</a>
+<a name="11674"><span class="lineNum">   11674 </span>            : void</a>
+<a name="11675"><span class="lineNum">   11675 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dorgl2,DORGL2)(int *m,</span></a>
+<a name="11676"><span class="lineNum">   11676 </span>            :                         int *n, </a>
+<a name="11677"><span class="lineNum">   11677 </span>            :                         int *k, </a>
+<a name="11678"><span class="lineNum">   11678 </span>            :                         double *a, </a>
+<a name="11679"><span class="lineNum">   11679 </span>            :                         int *lda, </a>
+<a name="11680"><span class="lineNum">   11680 </span>            :                         double *tau, </a>
+<a name="11681"><span class="lineNum">   11681 </span>            :                         double *work, </a>
+<a name="11682"><span class="lineNum">   11682 </span>            :                         int *info)</a>
+<a name="11683"><span class="lineNum">   11683 </span>            : {</a>
+<a name="11684"><span class="lineNum">   11684 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="11685"><span class="lineNum">   11685 </span>            :     double r__1;</a>
+<a name="11686"><span class="lineNum">   11686 </span>            : </a>
+<a name="11687"><span class="lineNum">   11687 </span>            :     int i__, j, l;</a>
+<a name="11688"><span class="lineNum">   11688 </span>            : </a>
+<a name="11689"><span class="lineNum">   11689 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="11690"><span class="lineNum">   11690 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="11691"><span class="lineNum">   11691 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="11692"><span class="lineNum">   11692 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="11693"><span class="lineNum">   11693 </span>            :     --work;</a>
+<a name="11694"><span class="lineNum">   11694 </span>            : </a>
+<a name="11695"><span class="lineNum">   11695 </span><span class="lineNoCov">          0 :     i__ = (*m &gt; 1) ? *m : 1;</span></a>
+<a name="11696"><span class="lineNum">   11696 </span>            :     </a>
+<a name="11697"><span class="lineNum">   11697 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="11698"><span class="lineNum">   11698 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="11699"><span class="lineNum">   11699 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="11700"><span class="lineNum">   11700 </span><span class="lineNoCov">          0 :     } else if (*n &lt; *m) {</span></a>
+<a name="11701"><span class="lineNum">   11701 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="11702"><span class="lineNum">   11702 </span><span class="lineNoCov">          0 :     } else if (*k &lt; 0 || *k &gt; *m) {</span></a>
+<a name="11703"><span class="lineNum">   11703 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="11704"><span class="lineNum">   11704 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; i__) {</span></a>
+<a name="11705"><span class="lineNum">   11705 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="11706"><span class="lineNum">   11706 </span>            :     }</a>
+<a name="11707"><span class="lineNum">   11707 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="11708"><span class="lineNum">   11708 </span>            :         return;</a>
+<a name="11709"><span class="lineNum">   11709 </span>            :     }</a>
+<a name="11710"><span class="lineNum">   11710 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0) {</span></a>
+<a name="11711"><span class="lineNum">   11711 </span>            :         return;</a>
+<a name="11712"><span class="lineNum">   11712 </span>            :     }</a>
+<a name="11713"><span class="lineNum">   11713 </span>            : </a>
+<a name="11714"><span class="lineNum">   11714 </span><span class="lineNoCov">          0 :     if (*k &lt; *m) {</span></a>
+<a name="11715"><span class="lineNum">   11715 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="11716"><span class="lineNum">   11716 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="11717"><span class="lineNum">   11717 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="11718"><span class="lineNum">   11718 </span><span class="lineNoCov">          0 :             for (l = *k + 1; l &lt;= i__2; ++l) {</span></a>
+<a name="11719"><span class="lineNum">   11719 </span><span class="lineNoCov">          0 :                 a[l + j * a_dim1] = 0.0;</span></a>
+<a name="11720"><span class="lineNum">   11720 </span>            :             }</a>
+<a name="11721"><span class="lineNum">   11721 </span><span class="lineNoCov">          0 :             if (j &gt; *k &amp;&amp; j &lt;= *m) {</span></a>
+<a name="11722"><span class="lineNum">   11722 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = 1.0;</span></a>
+<a name="11723"><span class="lineNum">   11723 </span>            :             }</a>
+<a name="11724"><span class="lineNum">   11724 </span>            :         }</a>
+<a name="11725"><span class="lineNum">   11725 </span>            :     }</a>
+<a name="11726"><span class="lineNum">   11726 </span>            : </a>
+<a name="11727"><span class="lineNum">   11727 </span><span class="lineNoCov">          0 :     for (i__ = *k; i__ &gt;= 1; --i__) {</span></a>
+<a name="11728"><span class="lineNum">   11728 </span><span class="lineNoCov">          0 :         if (i__ &lt; *n) {</span></a>
+<a name="11729"><span class="lineNum">   11729 </span><span class="lineNoCov">          0 :             if (i__ &lt; *m) {</span></a>
+<a name="11730"><span class="lineNum">   11730 </span><span class="lineNoCov">          0 :                 a[i__ + i__ * a_dim1] = 1.0;</span></a>
+<a name="11731"><span class="lineNum">   11731 </span><span class="lineNoCov">          0 :                 i__1 = *m - i__;</span></a>
+<a name="11732"><span class="lineNum">   11732 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__ + 1;</span></a>
+<a name="11733"><span class="lineNum">   11733 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(&quot;R&quot;, &amp;i__1, &amp;i__2, &amp;a[i__ + i__ * a_dim1], lda, </span></a>
+<a name="11734"><span class="lineNum">   11734 </span><span class="lineNoCov">          0 :                &amp;tau[i__], &amp;a[i__ + 1 + i__ * a_dim1], lda, &amp;work[1]);</span></a>
+<a name="11735"><span class="lineNum">   11735 </span>            :             }</a>
+<a name="11736"><span class="lineNum">   11736 </span><span class="lineNoCov">          0 :             i__1 = *n - i__;</span></a>
+<a name="11737"><span class="lineNum">   11737 </span><span class="lineNoCov">          0 :             r__1 = -tau[i__];</span></a>
+<a name="11738"><span class="lineNum">   11738 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__1, &amp;r__1, &amp;a[i__ + (i__ + 1) * a_dim1], lda);</span></a>
+<a name="11739"><span class="lineNum">   11739 </span>            :         }</a>
+<a name="11740"><span class="lineNum">   11740 </span><span class="lineNoCov">          0 :         a[i__ + i__ * a_dim1] = 1.0 - tau[i__];</span></a>
+<a name="11741"><span class="lineNum">   11741 </span><span class="lineNoCov">          0 :         i__1 = i__ - 1;</span></a>
+<a name="11742"><span class="lineNum">   11742 </span><span class="lineNoCov">          0 :         for (l = 1; l &lt;= i__1; ++l) {</span></a>
+<a name="11743"><span class="lineNum">   11743 </span><span class="lineNoCov">          0 :             a[i__ + l * a_dim1] = 0.0;</span></a>
+<a name="11744"><span class="lineNum">   11744 </span>            :         }</a>
+<a name="11745"><span class="lineNum">   11745 </span>            :     }</a>
+<a name="11746"><span class="lineNum">   11746 </span>            :     return;</a>
+<a name="11747"><span class="lineNum">   11747 </span>            : </a>
+<a name="11748"><span class="lineNum">   11748 </span>            : }</a>
+<a name="11749"><span class="lineNum">   11749 </span>            : </a>
+<a name="11750"><span class="lineNum">   11750 </span>            : </a>
+<a name="11751"><span class="lineNum">   11751 </span>            : </a>
+<a name="11752"><span class="lineNum">   11752 </span>            : }</a>
+<a name="11753"><span class="lineNum">   11753 </span>            : }</a>
+<a name="11754"><span class="lineNum">   11754 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11755"><span class="lineNum">   11755 </span>            : </a>
+<a name="11756"><span class="lineNum">   11756 </span>            : #define DORGLQ_BLOCKSIZE    32</a>
+<a name="11757"><span class="lineNum">   11757 </span>            : #define DORGLQ_MINBLOCKSIZE 2</a>
+<a name="11758"><span class="lineNum">   11758 </span>            : #define DORGLQ_CROSSOVER    128</a>
+<a name="11759"><span class="lineNum">   11759 </span>            : </a>
+<a name="11760"><span class="lineNum">   11760 </span>            : </a>
+<a name="11761"><span class="lineNum">   11761 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11762"><span class="lineNum">   11762 </span>            : namespace PLMD{</a>
+<a name="11763"><span class="lineNum">   11763 </span>            : namespace lapack{</a>
+<a name="11764"><span class="lineNum">   11764 </span>            : using namespace blas;</a>
+<a name="11765"><span class="lineNum">   11765 </span>            : void </a>
+<a name="11766"><span class="lineNum">   11766 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dorglq,DORGLQ)(int *m, </span></a>
+<a name="11767"><span class="lineNum">   11767 </span>            :         int *n, </a>
+<a name="11768"><span class="lineNum">   11768 </span>            :         int *k, </a>
+<a name="11769"><span class="lineNum">   11769 </span>            :         double *a, </a>
+<a name="11770"><span class="lineNum">   11770 </span>            :         int *lda, </a>
+<a name="11771"><span class="lineNum">   11771 </span>            :         double *tau, </a>
+<a name="11772"><span class="lineNum">   11772 </span>            :         double *work, </a>
+<a name="11773"><span class="lineNum">   11773 </span>            :         int *lwork, </a>
+<a name="11774"><span class="lineNum">   11774 </span>            :         int *info)</a>
+<a name="11775"><span class="lineNum">   11775 </span>            : {</a>
+<a name="11776"><span class="lineNum">   11776 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="11777"><span class="lineNum">   11777 </span>            : </a>
+<a name="11778"><span class="lineNum">   11778 </span>            :     int i__, j, l, ib, nb, ki, kk, nx, iws, nbmin, iinfo;</a>
+<a name="11779"><span class="lineNum">   11779 </span>            : </a>
+<a name="11780"><span class="lineNum">   11780 </span>            :     int ldwork, lwkopt;</a>
+<a name="11781"><span class="lineNum">   11781 </span>            :     int lquery;</a>
+<a name="11782"><span class="lineNum">   11782 </span>            :     </a>
+<a name="11783"><span class="lineNum">   11783 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="11784"><span class="lineNum">   11784 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="11785"><span class="lineNum">   11785 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="11786"><span class="lineNum">   11786 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="11787"><span class="lineNum">   11787 </span>            :     --work;</a>
+<a name="11788"><span class="lineNum">   11788 </span>            : </a>
+<a name="11789"><span class="lineNum">   11789 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="11790"><span class="lineNum">   11790 </span>            :     ki = 0;</a>
+<a name="11791"><span class="lineNum">   11791 </span>            :     nb = DORGLQ_BLOCKSIZE;</a>
+<a name="11792"><span class="lineNum">   11792 </span><span class="lineNoCov">          0 :     lwkopt = (*m) * nb;</span></a>
+<a name="11793"><span class="lineNum">   11793 </span><span class="lineNoCov">          0 :     work[1] = (double) lwkopt;</span></a>
+<a name="11794"><span class="lineNum">   11794 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="11795"><span class="lineNum">   11795 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="11796"><span class="lineNum">   11796 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="11797"><span class="lineNum">   11797 </span><span class="lineNoCov">          0 :     } else if (*n &lt; *m) {</span></a>
+<a name="11798"><span class="lineNum">   11798 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="11799"><span class="lineNum">   11799 </span><span class="lineNoCov">          0 :     } else if (*k &lt; 0 || *k &gt; *m) {</span></a>
+<a name="11800"><span class="lineNum">   11800 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="11801"><span class="lineNum">   11801 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; (*m)) {</span></a>
+<a name="11802"><span class="lineNum">   11802 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="11803"><span class="lineNum">   11803 </span><span class="lineNoCov">          0 :     } else if (*lwork &lt; (*m) &amp;&amp; ! lquery) {</span></a>
+<a name="11804"><span class="lineNum">   11804 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="11805"><span class="lineNum">   11805 </span>            :     }</a>
+<a name="11806"><span class="lineNum">   11806 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="11807"><span class="lineNum">   11807 </span>            :         i__1 = -(*info);</a>
+<a name="11808"><span class="lineNum">   11808 </span>            :         return;</a>
+<a name="11809"><span class="lineNum">   11809 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="11810"><span class="lineNum">   11810 </span>            :         return;</a>
+<a name="11811"><span class="lineNum">   11811 </span>            :     }</a>
+<a name="11812"><span class="lineNum">   11812 </span>            : </a>
+<a name="11813"><span class="lineNum">   11813 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0) {</span></a>
+<a name="11814"><span class="lineNum">   11814 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="11815"><span class="lineNum">   11815 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="11816"><span class="lineNum">   11816 </span>            :     }</a>
+<a name="11817"><span class="lineNum">   11817 </span>            : </a>
+<a name="11818"><span class="lineNum">   11818 </span>            :     nbmin = 2;</a>
+<a name="11819"><span class="lineNum">   11819 </span>            :     nx = 0;</a>
+<a name="11820"><span class="lineNum">   11820 </span>            :     iws = *m;</a>
+<a name="11821"><span class="lineNum">   11821 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="11822"><span class="lineNum">   11822 </span>            : </a>
+<a name="11823"><span class="lineNum">   11823 </span>            :         nx = DORGLQ_CROSSOVER;</a>
+<a name="11824"><span class="lineNum">   11824 </span><span class="lineNoCov">          0 :         if (nx &lt; *k) {</span></a>
+<a name="11825"><span class="lineNum">   11825 </span>            : </a>
+<a name="11826"><span class="lineNum">   11826 </span><span class="lineNoCov">          0 :             ldwork = *m;</span></a>
+<a name="11827"><span class="lineNum">   11827 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="11828"><span class="lineNum">   11828 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="11829"><span class="lineNum">   11829 </span>            : </a>
+<a name="11830"><span class="lineNum">   11830 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="11831"><span class="lineNum">   11831 </span>            :                 nbmin = DORGLQ_MINBLOCKSIZE;</a>
+<a name="11832"><span class="lineNum">   11832 </span>            :             }</a>
+<a name="11833"><span class="lineNum">   11833 </span>            :         }</a>
+<a name="11834"><span class="lineNum">   11834 </span>            :     }</a>
+<a name="11835"><span class="lineNum">   11835 </span>            : </a>
+<a name="11836"><span class="lineNum">   11836 </span><span class="lineNoCov">          0 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; *k &amp;&amp; nx &lt; *k) {</span></a>
+<a name="11837"><span class="lineNum">   11837 </span>            : </a>
+<a name="11838"><span class="lineNum">   11838 </span><span class="lineNoCov">          0 :         ki = (*k - nx - 1) / nb * nb;</span></a>
+<a name="11839"><span class="lineNum">   11839 </span><span class="lineNoCov">          0 :         i__1 = *k, i__2 = ki + nb;</span></a>
+<a name="11840"><span class="lineNum">   11840 </span>            :         kk = (i__1&lt;i__2) ? i__1 : i__2;</a>
+<a name="11841"><span class="lineNum">   11841 </span>            : </a>
+<a name="11842"><span class="lineNum">   11842 </span><span class="lineNoCov">          0 :         i__1 = kk;</span></a>
+<a name="11843"><span class="lineNum">   11843 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="11844"><span class="lineNum">   11844 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="11845"><span class="lineNum">   11845 </span><span class="lineNoCov">          0 :             for (i__ = kk + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="11846"><span class="lineNum">   11846 </span><span class="lineNoCov">          0 :                 a[i__ + j * a_dim1] = 0.;</span></a>
+<a name="11847"><span class="lineNum">   11847 </span>            :             }</a>
+<a name="11848"><span class="lineNum">   11848 </span>            :         }</a>
+<a name="11849"><span class="lineNum">   11849 </span>            :     } else {</a>
+<a name="11850"><span class="lineNum">   11850 </span>            :         kk = 0;</a>
+<a name="11851"><span class="lineNum">   11851 </span>            :     }</a>
+<a name="11852"><span class="lineNum">   11852 </span><span class="lineNoCov">          0 :     if (kk &lt; *m) {</span></a>
+<a name="11853"><span class="lineNum">   11853 </span><span class="lineNoCov">          0 :         i__1 = *m - kk;</span></a>
+<a name="11854"><span class="lineNum">   11854 </span><span class="lineNoCov">          0 :         i__2 = *n - kk;</span></a>
+<a name="11855"><span class="lineNum">   11855 </span><span class="lineNoCov">          0 :         i__3 = *k - kk;</span></a>
+<a name="11856"><span class="lineNum">   11856 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dorgl2,DORGL2)(&amp;i__1, &amp;i__2, &amp;i__3, &amp;a[kk + 1 + (kk + 1) * a_dim1], lda, &amp;</span></a>
+<a name="11857"><span class="lineNum">   11857 </span><span class="lineNoCov">          0 :                 tau[kk + 1], &amp;work[1], &amp;iinfo);</span></a>
+<a name="11858"><span class="lineNum">   11858 </span>            :     }</a>
+<a name="11859"><span class="lineNum">   11859 </span>            : </a>
+<a name="11860"><span class="lineNum">   11860 </span><span class="lineNoCov">          0 :     if (kk &gt; 0) {</span></a>
+<a name="11861"><span class="lineNum">   11861 </span>            : </a>
+<a name="11862"><span class="lineNum">   11862 </span><span class="lineNoCov">          0 :         i__1 = -nb;</span></a>
+<a name="11863"><span class="lineNum">   11863 </span><span class="lineNoCov">          0 :         for (i__ = ki + 1; i__1 &lt; 0 ? i__ &gt;= 1 : i__ &lt;= 1; i__ += i__1) {</span></a>
+<a name="11864"><span class="lineNum">   11864 </span><span class="lineNoCov">          0 :             i__2 = nb, i__3 = *k - i__ + 1;</span></a>
+<a name="11865"><span class="lineNum">   11865 </span><span class="lineNoCov">          0 :             ib = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="11866"><span class="lineNum">   11866 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *m) {</span></a>
+<a name="11867"><span class="lineNum">   11867 </span>            : </a>
+<a name="11868"><span class="lineNum">   11868 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__ + 1;</span></a>
+<a name="11869"><span class="lineNum">   11869 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__2, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="11870"><span class="lineNum">   11870 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</span></a>
+<a name="11871"><span class="lineNum">   11871 </span>            : </a>
+<a name="11872"><span class="lineNum">   11872 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ - ib + 1;</span></a>
+<a name="11873"><span class="lineNum">   11873 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="11874"><span class="lineNum">   11874 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(&quot;Right&quot;, &quot;Transpose&quot;, &quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__2, &amp;</span></a>
+<a name="11875"><span class="lineNum">   11875 </span>            :                         i__3, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[1], &amp;</a>
+<a name="11876"><span class="lineNum">   11876 </span><span class="lineNoCov">          0 :                         ldwork, &amp;a[i__ + ib + i__ * a_dim1], lda, &amp;work[ib + </span></a>
+<a name="11877"><span class="lineNum">   11877 </span><span class="lineNoCov">          0 :                         1], &amp;ldwork);</span></a>
+<a name="11878"><span class="lineNum">   11878 </span>            :             }</a>
+<a name="11879"><span class="lineNum">   11879 </span>            : </a>
+<a name="11880"><span class="lineNum">   11880 </span><span class="lineNoCov">          0 :             i__2 = *n - i__ + 1;</span></a>
+<a name="11881"><span class="lineNum">   11881 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dorgl2,DORGL2)(&amp;ib, &amp;i__2, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;</span></a>
+<a name="11882"><span class="lineNum">   11882 </span>            :                     work[1], &amp;iinfo);</a>
+<a name="11883"><span class="lineNum">   11883 </span>            : </a>
+<a name="11884"><span class="lineNum">   11884 </span><span class="lineNoCov">          0 :             i__2 = i__ - 1;</span></a>
+<a name="11885"><span class="lineNum">   11885 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="11886"><span class="lineNum">   11886 </span><span class="lineNoCov">          0 :                 i__3 = i__ + ib - 1;</span></a>
+<a name="11887"><span class="lineNum">   11887 </span><span class="lineNoCov">          0 :                 for (l = i__; l &lt;= i__3; ++l) {</span></a>
+<a name="11888"><span class="lineNum">   11888 </span><span class="lineNoCov">          0 :                     a[l + j * a_dim1] = 0.;</span></a>
+<a name="11889"><span class="lineNum">   11889 </span>            :                 }</a>
+<a name="11890"><span class="lineNum">   11890 </span>            :             }</a>
+<a name="11891"><span class="lineNum">   11891 </span>            :         }</a>
+<a name="11892"><span class="lineNum">   11892 </span>            :     }</a>
+<a name="11893"><span class="lineNum">   11893 </span>            : </a>
+<a name="11894"><span class="lineNum">   11894 </span><span class="lineNoCov">          0 :     work[1] = (double) iws;</span></a>
+<a name="11895"><span class="lineNum">   11895 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="11896"><span class="lineNum">   11896 </span>            : </a>
+<a name="11897"><span class="lineNum">   11897 </span>            : }</a>
+<a name="11898"><span class="lineNum">   11898 </span>            : </a>
+<a name="11899"><span class="lineNum">   11899 </span>            : </a>
+<a name="11900"><span class="lineNum">   11900 </span>            : }</a>
+<a name="11901"><span class="lineNum">   11901 </span>            : }</a>
+<a name="11902"><span class="lineNum">   11902 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="11903"><span class="lineNum">   11903 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="11904"><span class="lineNum">   11904 </span>            : </a>
+<a name="11905"><span class="lineNum">   11905 </span>            : </a>
+<a name="11906"><span class="lineNum">   11906 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="11907"><span class="lineNum">   11907 </span>            : namespace PLMD{</a>
+<a name="11908"><span class="lineNum">   11908 </span>            : namespace lapack{</a>
+<a name="11909"><span class="lineNum">   11909 </span>            : using namespace blas;</a>
+<a name="11910"><span class="lineNum">   11910 </span>            : void </a>
+<a name="11911"><span class="lineNum">   11911 </span><span class="lineCov">          1 : PLUMED_BLAS_F77_FUNC(dorgqr,DORGQR)(int *m, </span></a>
+<a name="11912"><span class="lineNum">   11912 </span>            :         int *n, </a>
+<a name="11913"><span class="lineNum">   11913 </span>            :         int *k, </a>
+<a name="11914"><span class="lineNum">   11914 </span>            :         double *a, </a>
+<a name="11915"><span class="lineNum">   11915 </span>            :         int *lda, </a>
+<a name="11916"><span class="lineNum">   11916 </span>            :         double *tau, </a>
+<a name="11917"><span class="lineNum">   11917 </span>            :         double *work, </a>
+<a name="11918"><span class="lineNum">   11918 </span>            :         int *lwork, </a>
+<a name="11919"><span class="lineNum">   11919 </span>            :         int *info)</a>
+<a name="11920"><span class="lineNum">   11920 </span>            : {</a>
+<a name="11921"><span class="lineNum">   11921 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="11922"><span class="lineNum">   11922 </span>            : </a>
+<a name="11923"><span class="lineNum">   11923 </span>            :     int i__, j, l, ib, nb, ki, kk, nx, iws, nbmin, iinfo;</a>
+<a name="11924"><span class="lineNum">   11924 </span>            :     int ldwork, lwkopt;</a>
+<a name="11925"><span class="lineNum">   11925 </span>            :     int lquery;</a>
+<a name="11926"><span class="lineNum">   11926 </span>            :  </a>
+<a name="11927"><span class="lineNum">   11927 </span><span class="lineCov">          1 :     a_dim1 = *lda;</span></a>
+<a name="11928"><span class="lineNum">   11928 </span><span class="lineCov">          1 :     a_offset = 1 + a_dim1;</span></a>
+<a name="11929"><span class="lineNum">   11929 </span><span class="lineCov">          1 :     a -= a_offset;</span></a>
+<a name="11930"><span class="lineNum">   11930 </span><span class="lineCov">          1 :     --tau;</span></a>
+<a name="11931"><span class="lineNum">   11931 </span>            :     --work;</a>
+<a name="11932"><span class="lineNum">   11932 </span>            : </a>
+<a name="11933"><span class="lineNum">   11933 </span>            :     ki = 0;</a>
+<a name="11934"><span class="lineNum">   11934 </span><span class="lineCov">          1 :     *info = 0;</span></a>
+<a name="11935"><span class="lineNum">   11935 </span>            :     nb = DORGQR_BLOCKSIZE;</a>
+<a name="11936"><span class="lineNum">   11936 </span><span class="lineCov">          1 :     lwkopt = (*n) * nb;</span></a>
+<a name="11937"><span class="lineNum">   11937 </span><span class="lineCov">          1 :     work[1] = (double) lwkopt;</span></a>
+<a name="11938"><span class="lineNum">   11938 </span><span class="lineCov">          1 :     lquery = *lwork == -1;</span></a>
+<a name="11939"><span class="lineNum">   11939 </span><span class="lineCov">          1 :     if (*m &lt; 0) {</span></a>
+<a name="11940"><span class="lineNum">   11940 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="11941"><span class="lineNum">   11941 </span><span class="lineCov">          1 :     } else if (*n &lt; 0 || *n &gt; *m) {</span></a>
+<a name="11942"><span class="lineNum">   11942 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="11943"><span class="lineNum">   11943 </span><span class="lineCov">          1 :     } else if (*k &lt; 0 || *k &gt; *n) {</span></a>
+<a name="11944"><span class="lineNum">   11944 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="11945"><span class="lineNum">   11945 </span><span class="lineCov">          1 :     } else if (*lda &lt; (*m)) {</span></a>
+<a name="11946"><span class="lineNum">   11946 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="11947"><span class="lineNum">   11947 </span><span class="lineCov">          1 :     } else if (*lwork &lt; (*n) &amp;&amp; ! lquery) {</span></a>
+<a name="11948"><span class="lineNum">   11948 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="11949"><span class="lineNum">   11949 </span>            :     }</a>
+<a name="11950"><span class="lineNum">   11950 </span><span class="lineCov">          1 :     if (*info != 0) {</span></a>
+<a name="11951"><span class="lineNum">   11951 </span>            :         i__1 = -(*info);</a>
+<a name="11952"><span class="lineNum">   11952 </span>            :         return;</a>
+<a name="11953"><span class="lineNum">   11953 </span><span class="lineCov">          1 :     } else if (lquery) {</span></a>
+<a name="11954"><span class="lineNum">   11954 </span>            :         return;</a>
+<a name="11955"><span class="lineNum">   11955 </span>            :     }</a>
+<a name="11956"><span class="lineNum">   11956 </span>            : </a>
+<a name="11957"><span class="lineNum">   11957 </span><span class="lineCov">          1 :     if (*n &lt;= 0) {</span></a>
+<a name="11958"><span class="lineNum">   11958 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="11959"><span class="lineNum">   11959 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="11960"><span class="lineNum">   11960 </span>            :     }</a>
+<a name="11961"><span class="lineNum">   11961 </span>            : </a>
+<a name="11962"><span class="lineNum">   11962 </span>            :     nbmin = 2;</a>
+<a name="11963"><span class="lineNum">   11963 </span>            :     nx = 0;</a>
+<a name="11964"><span class="lineNum">   11964 </span>            :     iws = *n;</a>
+<a name="11965"><span class="lineNum">   11965 </span><span class="lineCov">          1 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="11966"><span class="lineNum">   11966 </span>            : </a>
+<a name="11967"><span class="lineNum">   11967 </span>            :         nx = DORGQR_CROSSOVER;</a>
+<a name="11968"><span class="lineNum">   11968 </span><span class="lineNoCov">          0 :         if (nx &lt; *k) {</span></a>
+<a name="11969"><span class="lineNum">   11969 </span>            : </a>
+<a name="11970"><span class="lineNum">   11970 </span><span class="lineNoCov">          0 :             ldwork = *n;</span></a>
+<a name="11971"><span class="lineNum">   11971 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="11972"><span class="lineNum">   11972 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="11973"><span class="lineNum">   11973 </span>            : </a>
+<a name="11974"><span class="lineNum">   11974 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="11975"><span class="lineNum">   11975 </span>            :                 nbmin = DORGQR_MINBLOCKSIZE;</a>
+<a name="11976"><span class="lineNum">   11976 </span>            :             }</a>
+<a name="11977"><span class="lineNum">   11977 </span>            :         }</a>
+<a name="11978"><span class="lineNum">   11978 </span>            :     }</a>
+<a name="11979"><span class="lineNum">   11979 </span>            : </a>
+<a name="11980"><span class="lineNum">   11980 </span><span class="lineCov">          1 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; *k &amp;&amp; nx &lt; *k) {</span></a>
+<a name="11981"><span class="lineNum">   11981 </span>            : </a>
+<a name="11982"><span class="lineNum">   11982 </span><span class="lineNoCov">          0 :         ki = (*k - nx - 1) / nb * nb;</span></a>
+<a name="11983"><span class="lineNum">   11983 </span><span class="lineNoCov">          0 :         i__1 = *k, i__2 = ki + nb;</span></a>
+<a name="11984"><span class="lineNum">   11984 </span>            :         kk = (i__1&lt;i__2) ? i__1 : i__2;</a>
+<a name="11985"><span class="lineNum">   11985 </span>            : </a>
+<a name="11986"><span class="lineNum">   11986 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="11987"><span class="lineNum">   11987 </span><span class="lineNoCov">          0 :         for (j = kk + 1; j &lt;= i__1; ++j) {</span></a>
+<a name="11988"><span class="lineNum">   11988 </span><span class="lineNoCov">          0 :             i__2 = kk;</span></a>
+<a name="11989"><span class="lineNum">   11989 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="11990"><span class="lineNum">   11990 </span><span class="lineNoCov">          0 :                 a[i__ + j * a_dim1] = 0.;</span></a>
+<a name="11991"><span class="lineNum">   11991 </span>            :             }</a>
+<a name="11992"><span class="lineNum">   11992 </span>            :         }</a>
+<a name="11993"><span class="lineNum">   11993 </span>            :     } else {</a>
+<a name="11994"><span class="lineNum">   11994 </span>            :         kk = 0;</a>
+<a name="11995"><span class="lineNum">   11995 </span>            :     }</a>
+<a name="11996"><span class="lineNum">   11996 </span>            : </a>
+<a name="11997"><span class="lineNum">   11997 </span><span class="lineCov">          1 :     if (kk &lt; *n) {</span></a>
+<a name="11998"><span class="lineNum">   11998 </span><span class="lineCov">          1 :         i__1 = *m - kk;</span></a>
+<a name="11999"><span class="lineNum">   11999 </span><span class="lineCov">          1 :         i__2 = *n - kk;</span></a>
+<a name="12000"><span class="lineNum">   12000 </span><span class="lineCov">          1 :         i__3 = *k - kk;</span></a>
+<a name="12001"><span class="lineNum">   12001 </span><span class="lineCov">          1 :         PLUMED_BLAS_F77_FUNC(dorg2r,DORG2R)(&amp;i__1, &amp;i__2, &amp;i__3, &amp;a[kk + 1 + (kk + 1) * a_dim1], lda, &amp;</span></a>
+<a name="12002"><span class="lineNum">   12002 </span><span class="lineCov">          1 :                 tau[kk + 1], &amp;work[1], &amp;iinfo);</span></a>
+<a name="12003"><span class="lineNum">   12003 </span>            :     }</a>
+<a name="12004"><span class="lineNum">   12004 </span>            : </a>
+<a name="12005"><span class="lineNum">   12005 </span><span class="lineCov">          1 :     if (kk &gt; 0) {</span></a>
+<a name="12006"><span class="lineNum">   12006 </span>            : </a>
+<a name="12007"><span class="lineNum">   12007 </span><span class="lineNoCov">          0 :         i__1 = -nb;</span></a>
+<a name="12008"><span class="lineNum">   12008 </span><span class="lineNoCov">          0 :         for (i__ = ki + 1; i__1 &lt; 0 ? i__ &gt;= 1 : i__ &lt;= 1; i__ += i__1) {</span></a>
+<a name="12009"><span class="lineNum">   12009 </span><span class="lineNoCov">          0 :             i__2 = nb, i__3 = *k - i__ + 1;</span></a>
+<a name="12010"><span class="lineNum">   12010 </span><span class="lineNoCov">          0 :             ib = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="12011"><span class="lineNum">   12011 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *n) {</span></a>
+<a name="12012"><span class="lineNum">   12012 </span>            : </a>
+<a name="12013"><span class="lineNum">   12013 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="12014"><span class="lineNum">   12014 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__2, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="12015"><span class="lineNum">   12015 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</span></a>
+<a name="12016"><span class="lineNum">   12016 </span>            : </a>
+<a name="12017"><span class="lineNum">   12017 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="12018"><span class="lineNum">   12018 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ - ib + 1;</span></a>
+<a name="12019"><span class="lineNum">   12019 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(&quot;Left&quot;, &quot;No transpose&quot;, &quot;Forward&quot;, &quot;Columnwise&quot;, &amp;</span></a>
+<a name="12020"><span class="lineNum">   12020 </span>            :                         i__2, &amp;i__3, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[</a>
+<a name="12021"><span class="lineNum">   12021 </span><span class="lineNoCov">          0 :                         1], &amp;ldwork, &amp;a[i__ + (i__ + ib) * a_dim1], lda, &amp;</span></a>
+<a name="12022"><span class="lineNum">   12022 </span><span class="lineNoCov">          0 :                         work[ib + 1], &amp;ldwork);</span></a>
+<a name="12023"><span class="lineNum">   12023 </span>            :             }</a>
+<a name="12024"><span class="lineNum">   12024 </span>            : </a>
+<a name="12025"><span class="lineNum">   12025 </span><span class="lineNoCov">          0 :             i__2 = *m - i__ + 1;</span></a>
+<a name="12026"><span class="lineNum">   12026 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dorg2r,DORG2R)(&amp;i__2, &amp;ib, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;</span></a>
+<a name="12027"><span class="lineNum">   12027 </span>            :                     work[1], &amp;iinfo);</a>
+<a name="12028"><span class="lineNum">   12028 </span>            : </a>
+<a name="12029"><span class="lineNum">   12029 </span><span class="lineNoCov">          0 :             i__2 = i__ + ib - 1;</span></a>
+<a name="12030"><span class="lineNum">   12030 </span><span class="lineNoCov">          0 :             for (j = i__; j &lt;= i__2; ++j) {</span></a>
+<a name="12031"><span class="lineNum">   12031 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="12032"><span class="lineNum">   12032 </span><span class="lineNoCov">          0 :                 for (l = 1; l &lt;= i__3; ++l) {</span></a>
+<a name="12033"><span class="lineNum">   12033 </span><span class="lineNoCov">          0 :                     a[l + j * a_dim1] = 0.;</span></a>
+<a name="12034"><span class="lineNum">   12034 </span>            :                 }</a>
+<a name="12035"><span class="lineNum">   12035 </span>            :             }</a>
+<a name="12036"><span class="lineNum">   12036 </span>            :         }</a>
+<a name="12037"><span class="lineNum">   12037 </span>            :     }</a>
+<a name="12038"><span class="lineNum">   12038 </span>            : </a>
+<a name="12039"><span class="lineNum">   12039 </span><span class="lineCov">          1 :     work[1] = (double) iws;</span></a>
+<a name="12040"><span class="lineNum">   12040 </span><span class="lineCov">          1 :     return;</span></a>
+<a name="12041"><span class="lineNum">   12041 </span>            : </a>
+<a name="12042"><span class="lineNum">   12042 </span>            : } </a>
+<a name="12043"><span class="lineNum">   12043 </span>            : }</a>
+<a name="12044"><span class="lineNum">   12044 </span>            : }</a>
+<a name="12045"><span class="lineNum">   12045 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12046"><span class="lineNum">   12046 </span>            : </a>
+<a name="12047"><span class="lineNum">   12047 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12048"><span class="lineNum">   12048 </span>            : namespace PLMD{</a>
+<a name="12049"><span class="lineNum">   12049 </span>            : namespace lapack{</a>
+<a name="12050"><span class="lineNum">   12050 </span>            : using namespace blas;</a>
+<a name="12051"><span class="lineNum">   12051 </span>            : void</a>
+<a name="12052"><span class="lineNum">   12052 </span><span class="lineCov">     569952 : PLUMED_BLAS_F77_FUNC(dorm2l,DORM2L)(const char *side, </span></a>
+<a name="12053"><span class="lineNum">   12053 </span>            :         const char *trans, </a>
+<a name="12054"><span class="lineNum">   12054 </span>            :         int *m, </a>
+<a name="12055"><span class="lineNum">   12055 </span>            :         int *n, </a>
+<a name="12056"><span class="lineNum">   12056 </span>            :         int *k, </a>
+<a name="12057"><span class="lineNum">   12057 </span>            :         double *a,</a>
+<a name="12058"><span class="lineNum">   12058 </span>            :         int *lda, </a>
+<a name="12059"><span class="lineNum">   12059 </span>            :         double *tau,</a>
+<a name="12060"><span class="lineNum">   12060 </span>            :         double *c__,</a>
+<a name="12061"><span class="lineNum">   12061 </span>            :         int *ldc, </a>
+<a name="12062"><span class="lineNum">   12062 </span>            :         double *work, </a>
+<a name="12063"><span class="lineNum">   12063 </span>            :         int *info)</a>
+<a name="12064"><span class="lineNum">   12064 </span>            : {</a>
+<a name="12065"><span class="lineNum">   12065 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2;</a>
+<a name="12066"><span class="lineNum">   12066 </span><span class="lineCov">     569952 :     int c__1 = 1;</span></a>
+<a name="12067"><span class="lineNum">   12067 </span>            : </a>
+<a name="12068"><span class="lineNum">   12068 </span>            :     int i__, i1, i2, i3, mi, ni, nq;</a>
+<a name="12069"><span class="lineNum">   12069 </span>            :     double aii;</a>
+<a name="12070"><span class="lineNum">   12070 </span>            :     int left;</a>
+<a name="12071"><span class="lineNum">   12071 </span>            :     int notran;</a>
+<a name="12072"><span class="lineNum">   12072 </span>            : </a>
+<a name="12073"><span class="lineNum">   12073 </span><span class="lineCov">     569952 :     a_dim1 = *lda;</span></a>
+<a name="12074"><span class="lineNum">   12074 </span><span class="lineCov">     569952 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12075"><span class="lineNum">   12075 </span><span class="lineCov">     569952 :     a -= a_offset;</span></a>
+<a name="12076"><span class="lineNum">   12076 </span>            :     --tau;</a>
+<a name="12077"><span class="lineNum">   12077 </span>            :     c_dim1 = *ldc;</a>
+<a name="12078"><span class="lineNum">   12078 </span>            :     c_offset = 1 + c_dim1;</a>
+<a name="12079"><span class="lineNum">   12079 </span>            :     c__ -= c_offset;</a>
+<a name="12080"><span class="lineNum">   12080 </span>            :     --work;</a>
+<a name="12081"><span class="lineNum">   12081 </span>            : </a>
+<a name="12082"><span class="lineNum">   12082 </span>            :     /* Function Body */</a>
+<a name="12083"><span class="lineNum">   12083 </span><span class="lineCov">     569952 :     *info = 0;</span></a>
+<a name="12084"><span class="lineNum">   12084 </span><span class="lineCov">     569952 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12085"><span class="lineNum">   12085 </span><span class="lineCov">     569952 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="12086"><span class="lineNum">   12086 </span>            : </a>
+<a name="12087"><span class="lineNum">   12087 </span><span class="lineCov">     569952 :     if (left) {</span></a>
+<a name="12088"><span class="lineNum">   12088 </span><span class="lineCov">     569952 :         nq = *m;</span></a>
+<a name="12089"><span class="lineNum">   12089 </span>            :     } else {</a>
+<a name="12090"><span class="lineNum">   12090 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="12091"><span class="lineNum">   12091 </span>            :     }</a>
+<a name="12092"><span class="lineNum">   12092 </span>            :     if (*info != 0) {</a>
+<a name="12093"><span class="lineNum">   12093 </span>            :         return;</a>
+<a name="12094"><span class="lineNum">   12094 </span>            :     }</a>
+<a name="12095"><span class="lineNum">   12095 </span>            : </a>
+<a name="12096"><span class="lineNum">   12096 </span><span class="lineCov">     569952 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="12097"><span class="lineNum">   12097 </span>            :         return;</a>
+<a name="12098"><span class="lineNum">   12098 </span>            :     }</a>
+<a name="12099"><span class="lineNum">   12099 </span>            : </a>
+<a name="12100"><span class="lineNum">   12100 </span><span class="lineCov">     569952 :     if ((left &amp;&amp; notran) || (! left &amp;&amp; ! notran)) {</span></a>
+<a name="12101"><span class="lineNum">   12101 </span>            :         i1 = 1;</a>
+<a name="12102"><span class="lineNum">   12102 </span>            :         i2 = *k;</a>
+<a name="12103"><span class="lineNum">   12103 </span>            :         i3 = 1;</a>
+<a name="12104"><span class="lineNum">   12104 </span>            :     } else {</a>
+<a name="12105"><span class="lineNum">   12105 </span>            :         i1 = *k;</a>
+<a name="12106"><span class="lineNum">   12106 </span>            :         i2 = 1;</a>
+<a name="12107"><span class="lineNum">   12107 </span>            :         i3 = -1;</a>
+<a name="12108"><span class="lineNum">   12108 </span>            :     }</a>
+<a name="12109"><span class="lineNum">   12109 </span>            : </a>
+<a name="12110"><span class="lineNum">   12110 </span><span class="lineCov">     569952 :     if (left) {</span></a>
+<a name="12111"><span class="lineNum">   12111 </span><span class="lineCov">     569952 :         ni = *n;</span></a>
+<a name="12112"><span class="lineNum">   12112 </span>            :     } else {</a>
+<a name="12113"><span class="lineNum">   12113 </span><span class="lineNoCov">          0 :         mi = *m;</span></a>
+<a name="12114"><span class="lineNum">   12114 </span>            :     }</a>
+<a name="12115"><span class="lineNum">   12115 </span>            : </a>
+<a name="12116"><span class="lineNum">   12116 </span>            :     i__1 = i2;</a>
+<a name="12117"><span class="lineNum">   12117 </span>            :     i__2 = i3;</a>
+<a name="12118"><span class="lineNum">   12118 </span><span class="lineCov">    2252681 :     for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="12119"><span class="lineNum">   12119 </span><span class="lineCov">    1682729 :         if (left) {</span></a>
+<a name="12120"><span class="lineNum">   12120 </span>            : </a>
+<a name="12121"><span class="lineNum">   12121 </span><span class="lineCov">    1682729 :             mi = *m - *k + i__;</span></a>
+<a name="12122"><span class="lineNum">   12122 </span>            :         } else {</a>
+<a name="12123"><span class="lineNum">   12123 </span>            : </a>
+<a name="12124"><span class="lineNum">   12124 </span><span class="lineNoCov">          0 :             ni = *n - *k + i__;</span></a>
+<a name="12125"><span class="lineNum">   12125 </span>            :         }</a>
+<a name="12126"><span class="lineNum">   12126 </span>            : </a>
+<a name="12127"><span class="lineNum">   12127 </span><span class="lineCov">    1682729 :         aii = a[nq - *k + i__ + i__ * a_dim1];</span></a>
+<a name="12128"><span class="lineNum">   12128 </span><span class="lineCov">    1682729 :         a[nq - *k + i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="12129"><span class="lineNum">   12129 </span><span class="lineCov">    1682729 :         PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(side, &amp;mi, &amp;ni, &amp;a[i__ * a_dim1 + 1], &amp;c__1, &amp;tau[i__], &amp;c__[</span></a>
+<a name="12130"><span class="lineNum">   12130 </span>            :                 c_offset], ldc, &amp;work[1]);</a>
+<a name="12131"><span class="lineNum">   12131 </span><span class="lineCov">    1682729 :         a[nq - *k + i__ + i__ * a_dim1] = aii;</span></a>
+<a name="12132"><span class="lineNum">   12132 </span>            :     }</a>
+<a name="12133"><span class="lineNum">   12133 </span>            :     return;</a>
+<a name="12134"><span class="lineNum">   12134 </span>            : }</a>
+<a name="12135"><span class="lineNum">   12135 </span>            : }</a>
+<a name="12136"><span class="lineNum">   12136 </span>            : }</a>
+<a name="12137"><span class="lineNum">   12137 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12138"><span class="lineNum">   12138 </span>            : </a>
+<a name="12139"><span class="lineNum">   12139 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12140"><span class="lineNum">   12140 </span>            : namespace PLMD{</a>
+<a name="12141"><span class="lineNum">   12141 </span>            : namespace lapack{</a>
+<a name="12142"><span class="lineNum">   12142 </span>            : using namespace blas;</a>
+<a name="12143"><span class="lineNum">   12143 </span>            : void </a>
+<a name="12144"><span class="lineNum">   12144 </span><span class="lineCov">         79 : PLUMED_BLAS_F77_FUNC(dorm2r,DORM2R)(const char *side, </span></a>
+<a name="12145"><span class="lineNum">   12145 </span>            :         const char *trans, </a>
+<a name="12146"><span class="lineNum">   12146 </span>            :         int *m, </a>
+<a name="12147"><span class="lineNum">   12147 </span>            :         int *n, </a>
+<a name="12148"><span class="lineNum">   12148 </span>            :         int *k, </a>
+<a name="12149"><span class="lineNum">   12149 </span>            :         double *a, </a>
+<a name="12150"><span class="lineNum">   12150 </span>            :         int *lda, </a>
+<a name="12151"><span class="lineNum">   12151 </span>            :         double *tau, </a>
+<a name="12152"><span class="lineNum">   12152 </span>            :         double *c__, </a>
+<a name="12153"><span class="lineNum">   12153 </span>            :         int *ldc, </a>
+<a name="12154"><span class="lineNum">   12154 </span>            :         double *work, </a>
+<a name="12155"><span class="lineNum">   12155 </span>            :         int *info)</a>
+<a name="12156"><span class="lineNum">   12156 </span>            : {</a>
+<a name="12157"><span class="lineNum">   12157 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2;</a>
+<a name="12158"><span class="lineNum">   12158 </span>            : </a>
+<a name="12159"><span class="lineNum">   12159 </span>            :     int i__, i1, i2, i3, ic, jc, mi, ni;</a>
+<a name="12160"><span class="lineNum">   12160 </span>            :     double aii;</a>
+<a name="12161"><span class="lineNum">   12161 </span>            :     int left;</a>
+<a name="12162"><span class="lineNum">   12162 </span>            :     int notran;</a>
+<a name="12163"><span class="lineNum">   12163 </span><span class="lineCov">         79 :     int c__1 = 1;</span></a>
+<a name="12164"><span class="lineNum">   12164 </span>            : </a>
+<a name="12165"><span class="lineNum">   12165 </span><span class="lineCov">         79 :     a_dim1 = *lda;</span></a>
+<a name="12166"><span class="lineNum">   12166 </span><span class="lineCov">         79 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12167"><span class="lineNum">   12167 </span><span class="lineCov">         79 :     a -= a_offset;</span></a>
+<a name="12168"><span class="lineNum">   12168 </span>            :     --tau;</a>
+<a name="12169"><span class="lineNum">   12169 </span><span class="lineCov">         79 :     c_dim1 = *ldc;</span></a>
+<a name="12170"><span class="lineNum">   12170 </span><span class="lineCov">         79 :     c_offset = 1 + c_dim1;</span></a>
+<a name="12171"><span class="lineNum">   12171 </span><span class="lineCov">         79 :     c__ -= c_offset;</span></a>
+<a name="12172"><span class="lineNum">   12172 </span>            :     --work;</a>
+<a name="12173"><span class="lineNum">   12173 </span><span class="lineCov">         79 :     *info = 0;</span></a>
+<a name="12174"><span class="lineNum">   12174 </span><span class="lineCov">         79 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12175"><span class="lineNum">   12175 </span><span class="lineCov">         79 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="12176"><span class="lineNum">   12176 </span>            : </a>
+<a name="12177"><span class="lineNum">   12177 </span>            :     ic = jc = 0;</a>
+<a name="12178"><span class="lineNum">   12178 </span>            : </a>
+<a name="12179"><span class="lineNum">   12179 </span><span class="lineCov">         79 :     if (*m &lt;= 0 || *n &lt;= 0 || *k &lt;= 0) {</span></a>
+<a name="12180"><span class="lineNum">   12180 </span>            :         return;</a>
+<a name="12181"><span class="lineNum">   12181 </span>            :     }</a>
+<a name="12182"><span class="lineNum">   12182 </span>            : </a>
+<a name="12183"><span class="lineNum">   12183 </span><span class="lineCov">         79 :     if ((left &amp;&amp; !notran) || (!left &amp;&amp; notran)) {</span></a>
+<a name="12184"><span class="lineNum">   12184 </span>            :         i1 = 1;</a>
+<a name="12185"><span class="lineNum">   12185 </span>            :         i2 = *k;</a>
+<a name="12186"><span class="lineNum">   12186 </span>            :         i3 = 1;</a>
+<a name="12187"><span class="lineNum">   12187 </span>            :     } else {</a>
+<a name="12188"><span class="lineNum">   12188 </span>            :         i1 = *k;</a>
+<a name="12189"><span class="lineNum">   12189 </span>            :         i2 = 1;</a>
+<a name="12190"><span class="lineNum">   12190 </span>            :         i3 = -1;</a>
+<a name="12191"><span class="lineNum">   12191 </span>            :     }</a>
+<a name="12192"><span class="lineNum">   12192 </span>            : </a>
+<a name="12193"><span class="lineNum">   12193 </span><span class="lineCov">         79 :     if (left) {</span></a>
+<a name="12194"><span class="lineNum">   12194 </span><span class="lineCov">         79 :         ni = *n;</span></a>
+<a name="12195"><span class="lineNum">   12195 </span>            :         jc = 1;</a>
+<a name="12196"><span class="lineNum">   12196 </span>            :     } else {</a>
+<a name="12197"><span class="lineNum">   12197 </span><span class="lineNoCov">          0 :         mi = *m;</span></a>
+<a name="12198"><span class="lineNum">   12198 </span>            :         ic = 1;</a>
+<a name="12199"><span class="lineNum">   12199 </span>            :     }</a>
+<a name="12200"><span class="lineNum">   12200 </span>            : </a>
+<a name="12201"><span class="lineNum">   12201 </span>            :     i__1 = i2;</a>
+<a name="12202"><span class="lineNum">   12202 </span>            :     i__2 = i3;</a>
+<a name="12203"><span class="lineNum">   12203 </span><span class="lineCov">       1547 :     for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="12204"><span class="lineNum">   12204 </span><span class="lineCov">       1468 :         if (left) {</span></a>
+<a name="12205"><span class="lineNum">   12205 </span>            : </a>
+<a name="12206"><span class="lineNum">   12206 </span><span class="lineCov">       1468 :             mi = *m - i__ + 1;</span></a>
+<a name="12207"><span class="lineNum">   12207 </span>            :             ic = i__;</a>
+<a name="12208"><span class="lineNum">   12208 </span>            :         } else {</a>
+<a name="12209"><span class="lineNum">   12209 </span>            : </a>
+<a name="12210"><span class="lineNum">   12210 </span><span class="lineNoCov">          0 :             ni = *n - i__ + 1;</span></a>
+<a name="12211"><span class="lineNum">   12211 </span>            :             jc = i__;</a>
+<a name="12212"><span class="lineNum">   12212 </span>            :         }</a>
+<a name="12213"><span class="lineNum">   12213 </span>            : </a>
+<a name="12214"><span class="lineNum">   12214 </span>            : </a>
+<a name="12215"><span class="lineNum">   12215 </span><span class="lineCov">       1468 :         aii = a[i__ + i__ * a_dim1];</span></a>
+<a name="12216"><span class="lineNum">   12216 </span><span class="lineCov">       1468 :         a[i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="12217"><span class="lineNum">   12217 </span><span class="lineCov">       1468 :         PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(side, &amp;mi, &amp;ni, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;tau[i__], &amp;c__[</span></a>
+<a name="12218"><span class="lineNum">   12218 </span><span class="lineCov">       1468 :                 ic + jc * c_dim1], ldc, &amp;work[1]);</span></a>
+<a name="12219"><span class="lineNum">   12219 </span><span class="lineCov">       1468 :         a[i__ + i__ * a_dim1] = aii;</span></a>
+<a name="12220"><span class="lineNum">   12220 </span>            :     }</a>
+<a name="12221"><span class="lineNum">   12221 </span>            :     return;</a>
+<a name="12222"><span class="lineNum">   12222 </span>            : </a>
+<a name="12223"><span class="lineNum">   12223 </span>            : } </a>
+<a name="12224"><span class="lineNum">   12224 </span>            : }</a>
+<a name="12225"><span class="lineNum">   12225 </span>            : }</a>
+<a name="12226"><span class="lineNum">   12226 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12227"><span class="lineNum">   12227 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="12228"><span class="lineNum">   12228 </span>            : </a>
+<a name="12229"><span class="lineNum">   12229 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12230"><span class="lineNum">   12230 </span>            : namespace PLMD{</a>
+<a name="12231"><span class="lineNum">   12231 </span>            : namespace lapack{</a>
+<a name="12232"><span class="lineNum">   12232 </span>            : using namespace blas;</a>
+<a name="12233"><span class="lineNum">   12233 </span>            : void </a>
+<a name="12234"><span class="lineNum">   12234 </span><span class="lineCov">        192 : PLUMED_BLAS_F77_FUNC(dormbr,DORMBR)(const char *vect, </span></a>
+<a name="12235"><span class="lineNum">   12235 </span>            :         const char *side, </a>
+<a name="12236"><span class="lineNum">   12236 </span>            :         const char *trans, </a>
+<a name="12237"><span class="lineNum">   12237 </span>            :         int *m, </a>
+<a name="12238"><span class="lineNum">   12238 </span>            :         int *n, </a>
+<a name="12239"><span class="lineNum">   12239 </span>            :         int *k, </a>
+<a name="12240"><span class="lineNum">   12240 </span>            :         double *a, </a>
+<a name="12241"><span class="lineNum">   12241 </span>            :         int *lda, </a>
+<a name="12242"><span class="lineNum">   12242 </span>            :         double *tau, </a>
+<a name="12243"><span class="lineNum">   12243 </span>            :         double *c__, </a>
+<a name="12244"><span class="lineNum">   12244 </span>            :         int *ldc, </a>
+<a name="12245"><span class="lineNum">   12245 </span>            :         double *work, </a>
+<a name="12246"><span class="lineNum">   12246 </span>            :         int *lwork, </a>
+<a name="12247"><span class="lineNum">   12247 </span>            :         int *info)</a>
+<a name="12248"><span class="lineNum">   12248 </span>            : {</a>
+<a name="12249"><span class="lineNum">   12249 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1;</a>
+<a name="12250"><span class="lineNum">   12250 </span>            :  </a>
+<a name="12251"><span class="lineNum">   12251 </span>            : </a>
+<a name="12252"><span class="lineNum">   12252 </span>            :     int i1, i2, nb, mi, ni, nq, nw;</a>
+<a name="12253"><span class="lineNum">   12253 </span>            :     int left;</a>
+<a name="12254"><span class="lineNum">   12254 </span>            :     int iinfo;</a>
+<a name="12255"><span class="lineNum">   12255 </span>            :     int notran;</a>
+<a name="12256"><span class="lineNum">   12256 </span>            :     int applyq;</a>
+<a name="12257"><span class="lineNum">   12257 </span>            :     char transt[1];</a>
+<a name="12258"><span class="lineNum">   12258 </span>            :     int lwkopt;</a>
+<a name="12259"><span class="lineNum">   12259 </span>            :     int lquery;</a>
+<a name="12260"><span class="lineNum">   12260 </span>            : </a>
+<a name="12261"><span class="lineNum">   12261 </span><span class="lineCov">        192 :     a_dim1 = *lda;</span></a>
+<a name="12262"><span class="lineNum">   12262 </span><span class="lineCov">        192 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12263"><span class="lineNum">   12263 </span><span class="lineCov">        192 :     a -= a_offset;</span></a>
+<a name="12264"><span class="lineNum">   12264 </span>            :     --tau;</a>
+<a name="12265"><span class="lineNum">   12265 </span><span class="lineCov">        192 :     c_dim1 = *ldc;</span></a>
+<a name="12266"><span class="lineNum">   12266 </span><span class="lineCov">        192 :     c_offset = 1 + c_dim1;</span></a>
+<a name="12267"><span class="lineNum">   12267 </span><span class="lineCov">        192 :     c__ -= c_offset;</span></a>
+<a name="12268"><span class="lineNum">   12268 </span>            :     --work;</a>
+<a name="12269"><span class="lineNum">   12269 </span><span class="lineCov">        192 :     *info = 0;</span></a>
+<a name="12270"><span class="lineNum">   12270 </span><span class="lineCov">        192 :     applyq = (*vect=='Q' || *vect=='q');</span></a>
+<a name="12271"><span class="lineNum">   12271 </span><span class="lineCov">        192 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12272"><span class="lineNum">   12272 </span><span class="lineCov">        192 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="12273"><span class="lineNum">   12273 </span><span class="lineCov">        192 :     lquery = *lwork == -1;</span></a>
+<a name="12274"><span class="lineNum">   12274 </span>            : </a>
+<a name="12275"><span class="lineNum">   12275 </span><span class="lineCov">        192 :     if (left) {</span></a>
+<a name="12276"><span class="lineNum">   12276 </span><span class="lineCov">         96 :         nq = *m;</span></a>
+<a name="12277"><span class="lineNum">   12277 </span><span class="lineCov">         96 :         nw = *n;</span></a>
+<a name="12278"><span class="lineNum">   12278 </span>            :     } else {</a>
+<a name="12279"><span class="lineNum">   12279 </span><span class="lineCov">         96 :         nq = *n;</span></a>
+<a name="12280"><span class="lineNum">   12280 </span><span class="lineCov">         96 :         nw = *m;</span></a>
+<a name="12281"><span class="lineNum">   12281 </span>            :     }</a>
+<a name="12282"><span class="lineNum">   12282 </span>            : </a>
+<a name="12283"><span class="lineNum">   12283 </span>            :     nb = DORMQR_BLOCKSIZE;</a>
+<a name="12284"><span class="lineNum">   12284 </span><span class="lineCov">        192 :     lwkopt = nw * nb;</span></a>
+<a name="12285"><span class="lineNum">   12285 </span><span class="lineCov">        192 :     work[1] = (double) lwkopt;</span></a>
+<a name="12286"><span class="lineNum">   12286 </span>            :     </a>
+<a name="12287"><span class="lineNum">   12287 </span><span class="lineCov">        192 :     if (*info != 0) {</span></a>
+<a name="12288"><span class="lineNum">   12288 </span>            :         i__1 = -(*info);</a>
+<a name="12289"><span class="lineNum">   12289 </span>            :         return;</a>
+<a name="12290"><span class="lineNum">   12290 </span><span class="lineCov">        192 :     } else if (lquery) {</span></a>
+<a name="12291"><span class="lineNum">   12291 </span>            :         return;</a>
+<a name="12292"><span class="lineNum">   12292 </span>            :     }</a>
+<a name="12293"><span class="lineNum">   12293 </span>            : </a>
+<a name="12294"><span class="lineNum">   12294 </span><span class="lineCov">        192 :     work[1] = 1.;</span></a>
+<a name="12295"><span class="lineNum">   12295 </span><span class="lineCov">        192 :     if (*m == 0 || *n == 0) {</span></a>
+<a name="12296"><span class="lineNum">   12296 </span>            :         return;</a>
+<a name="12297"><span class="lineNum">   12297 </span>            :     }</a>
+<a name="12298"><span class="lineNum">   12298 </span>            : </a>
+<a name="12299"><span class="lineNum">   12299 </span><span class="lineCov">        192 :     if (applyq) {</span></a>
+<a name="12300"><span class="lineNum">   12300 </span>            : </a>
+<a name="12301"><span class="lineNum">   12301 </span><span class="lineCov">         96 :         if (nq &gt;= *k) {</span></a>
+<a name="12302"><span class="lineNum">   12302 </span>            : </a>
+<a name="12303"><span class="lineNum">   12303 </span><span class="lineCov">         96 :             PLUMED_BLAS_F77_FUNC(dormqr,DORMQR)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="12304"><span class="lineNum">   12304 </span>            :                     c_offset], ldc, &amp;work[1], lwork, &amp;iinfo);</a>
+<a name="12305"><span class="lineNum">   12305 </span><span class="lineNoCov">          0 :         } else if (nq &gt; 1) {</span></a>
+<a name="12306"><span class="lineNum">   12306 </span>            : </a>
+<a name="12307"><span class="lineNum">   12307 </span><span class="lineNoCov">          0 :             if (left) {</span></a>
+<a name="12308"><span class="lineNum">   12308 </span><span class="lineNoCov">          0 :                 mi = *m - 1;</span></a>
+<a name="12309"><span class="lineNum">   12309 </span><span class="lineNoCov">          0 :                 ni = *n;</span></a>
+<a name="12310"><span class="lineNum">   12310 </span>            :                 i1 = 2;</a>
+<a name="12311"><span class="lineNum">   12311 </span>            :                 i2 = 1;</a>
+<a name="12312"><span class="lineNum">   12312 </span>            :             } else {</a>
+<a name="12313"><span class="lineNum">   12313 </span><span class="lineNoCov">          0 :                 mi = *m;</span></a>
+<a name="12314"><span class="lineNum">   12314 </span><span class="lineNoCov">          0 :                 ni = *n - 1;</span></a>
+<a name="12315"><span class="lineNum">   12315 </span>            :                 i1 = 1;</a>
+<a name="12316"><span class="lineNum">   12316 </span>            :                 i2 = 2;</a>
+<a name="12317"><span class="lineNum">   12317 </span>            :             }</a>
+<a name="12318"><span class="lineNum">   12318 </span><span class="lineNoCov">          0 :             i__1 = nq - 1;</span></a>
+<a name="12319"><span class="lineNum">   12319 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dormqr,DORMQR)(side, trans, &amp;mi, &amp;ni, &amp;i__1, &amp;a[a_dim1 + 2], lda, &amp;tau[1]</span></a>
+<a name="12320"><span class="lineNum">   12320 </span><span class="lineNoCov">          0 :                     , &amp;c__[i1 + i2 * c_dim1], ldc, &amp;work[1], lwork, &amp;iinfo);</span></a>
+<a name="12321"><span class="lineNum">   12321 </span>            :         }</a>
+<a name="12322"><span class="lineNum">   12322 </span>            :     } else {</a>
+<a name="12323"><span class="lineNum">   12323 </span>            : </a>
+<a name="12324"><span class="lineNum">   12324 </span><span class="lineCov">         96 :         if (notran) {</span></a>
+<a name="12325"><span class="lineNum">   12325 </span><span class="lineNoCov">          0 :             *(unsigned char *)transt = 'T';</span></a>
+<a name="12326"><span class="lineNum">   12326 </span>            :         } else {</a>
+<a name="12327"><span class="lineNum">   12327 </span><span class="lineCov">         96 :             *(unsigned char *)transt = 'N';</span></a>
+<a name="12328"><span class="lineNum">   12328 </span>            :         }</a>
+<a name="12329"><span class="lineNum">   12329 </span><span class="lineCov">         96 :         if (nq &gt; *k) {</span></a>
+<a name="12330"><span class="lineNum">   12330 </span>            : </a>
+<a name="12331"><span class="lineNum">   12331 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dormlq,DORMLQ)(side, transt, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="12332"><span class="lineNum">   12332 </span>            :                     c_offset], ldc, &amp;work[1], lwork, &amp;iinfo);</a>
+<a name="12333"><span class="lineNum">   12333 </span><span class="lineCov">         96 :         } else if (nq &gt; 1) {</span></a>
+<a name="12334"><span class="lineNum">   12334 </span>            : </a>
+<a name="12335"><span class="lineNum">   12335 </span><span class="lineCov">         96 :             if (left) {</span></a>
+<a name="12336"><span class="lineNum">   12336 </span><span class="lineNoCov">          0 :                 mi = *m - 1;</span></a>
+<a name="12337"><span class="lineNum">   12337 </span><span class="lineNoCov">          0 :                 ni = *n;</span></a>
+<a name="12338"><span class="lineNum">   12338 </span>            :                 i1 = 2;</a>
+<a name="12339"><span class="lineNum">   12339 </span>            :                 i2 = 1;</a>
+<a name="12340"><span class="lineNum">   12340 </span>            :             } else {</a>
+<a name="12341"><span class="lineNum">   12341 </span><span class="lineCov">         96 :                 mi = *m;</span></a>
+<a name="12342"><span class="lineNum">   12342 </span><span class="lineCov">         96 :                 ni = *n - 1;</span></a>
+<a name="12343"><span class="lineNum">   12343 </span>            :                 i1 = 1;</a>
+<a name="12344"><span class="lineNum">   12344 </span>            :                 i2 = 2;</a>
+<a name="12345"><span class="lineNum">   12345 </span>            :             }</a>
+<a name="12346"><span class="lineNum">   12346 </span><span class="lineCov">         96 :             i__1 = nq - 1;</span></a>
+<a name="12347"><span class="lineNum">   12347 </span><span class="lineCov">         96 :             PLUMED_BLAS_F77_FUNC(dormlq,DORMLQ)(side, transt, &amp;mi, &amp;ni, &amp;i__1, &amp;a[(a_dim1 &lt;&lt; 1) + 1], lda,</span></a>
+<a name="12348"><span class="lineNum">   12348 </span><span class="lineCov">         96 :                      &amp;tau[1], &amp;c__[i1 + i2 * c_dim1], ldc, &amp;work[1], lwork, &amp;</span></a>
+<a name="12349"><span class="lineNum">   12349 </span>            :                     iinfo);</a>
+<a name="12350"><span class="lineNum">   12350 </span>            :         }</a>
+<a name="12351"><span class="lineNum">   12351 </span>            :     }</a>
+<a name="12352"><span class="lineNum">   12352 </span><span class="lineCov">        192 :     work[1] = (double) lwkopt;</span></a>
+<a name="12353"><span class="lineNum">   12353 </span><span class="lineCov">        192 :     return;</span></a>
+<a name="12354"><span class="lineNum">   12354 </span>            : </a>
+<a name="12355"><span class="lineNum">   12355 </span>            : </a>
+<a name="12356"><span class="lineNum">   12356 </span>            : }</a>
+<a name="12357"><span class="lineNum">   12357 </span>            : </a>
+<a name="12358"><span class="lineNum">   12358 </span>            : </a>
+<a name="12359"><span class="lineNum">   12359 </span>            : }</a>
+<a name="12360"><span class="lineNum">   12360 </span>            : }</a>
+<a name="12361"><span class="lineNum">   12361 </span>            : #include &lt;cctype&gt;</a>
+<a name="12362"><span class="lineNum">   12362 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12363"><span class="lineNum">   12363 </span>            : #include &quot;real.h&quot;</a>
+<a name="12364"><span class="lineNum">   12364 </span>            : </a>
+<a name="12365"><span class="lineNum">   12365 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12366"><span class="lineNum">   12366 </span>            : namespace PLMD{</a>
+<a name="12367"><span class="lineNum">   12367 </span>            : namespace lapack{</a>
+<a name="12368"><span class="lineNum">   12368 </span>            : using namespace blas;</a>
+<a name="12369"><span class="lineNum">   12369 </span>            : void</a>
+<a name="12370"><span class="lineNum">   12370 </span><span class="lineCov">         83 : PLUMED_BLAS_F77_FUNC(dorml2,DORML2)(const char *side,</span></a>
+<a name="12371"><span class="lineNum">   12371 </span>            :         const char *trans,</a>
+<a name="12372"><span class="lineNum">   12372 </span>            :         int *m,</a>
+<a name="12373"><span class="lineNum">   12373 </span>            :         int *n,</a>
+<a name="12374"><span class="lineNum">   12374 </span>            :         int *k,</a>
+<a name="12375"><span class="lineNum">   12375 </span>            :         double *a,</a>
+<a name="12376"><span class="lineNum">   12376 </span>            :         int *lda,</a>
+<a name="12377"><span class="lineNum">   12377 </span>            :         double *tau,</a>
+<a name="12378"><span class="lineNum">   12378 </span>            :         double *c,</a>
+<a name="12379"><span class="lineNum">   12379 </span>            :         int *ldc,</a>
+<a name="12380"><span class="lineNum">   12380 </span>            :         double *work,</a>
+<a name="12381"><span class="lineNum">   12381 </span>            :     int *info)</a>
+<a name="12382"><span class="lineNum">   12382 </span>            : {</a>
+<a name="12383"><span class="lineNum">   12383 </span><span class="lineCov">         83 :   const char xside=std::toupper(*side);</span></a>
+<a name="12384"><span class="lineNum">   12384 </span><span class="lineCov">         83 :   const char xtrans=std::toupper(*trans);</span></a>
+<a name="12385"><span class="lineNum">   12385 </span>            :   int i,i1,i2,i3,ni,mi,ic,jc;</a>
+<a name="12386"><span class="lineNum">   12386 </span>            :   double aii;</a>
+<a name="12387"><span class="lineNum">   12387 </span>            : </a>
+<a name="12388"><span class="lineNum">   12388 </span><span class="lineCov">         83 :   if(*m&lt;=0 || *n&lt;=0 || *k&lt;=0)</span></a>
+<a name="12389"><span class="lineNum">   12389 </span>            :     return;</a>
+<a name="12390"><span class="lineNum">   12390 </span>            : </a>
+<a name="12391"><span class="lineNum">   12391 </span>            :   ic = jc = 0;</a>
+<a name="12392"><span class="lineNum">   12392 </span>            : </a>
+<a name="12393"><span class="lineNum">   12393 </span><span class="lineCov">         83 :   if((xside=='L' &amp;&amp; xtrans=='N') || (xside!='L' &amp;&amp; xtrans!='N')) {</span></a>
+<a name="12394"><span class="lineNum">   12394 </span>            :     i1 = 0;</a>
+<a name="12395"><span class="lineNum">   12395 </span>            :     i2 = *k;</a>
+<a name="12396"><span class="lineNum">   12396 </span>            :     i3 = 1;</a>
+<a name="12397"><span class="lineNum">   12397 </span>            :   } else {</a>
+<a name="12398"><span class="lineNum">   12398 </span><span class="lineCov">         83 :     i1 = *k-1;</span></a>
+<a name="12399"><span class="lineNum">   12399 </span>            :     i2 = -1;</a>
+<a name="12400"><span class="lineNum">   12400 </span>            :     i3 = -1;</a>
+<a name="12401"><span class="lineNum">   12401 </span>            :   }</a>
+<a name="12402"><span class="lineNum">   12402 </span>            :   </a>
+<a name="12403"><span class="lineNum">   12403 </span><span class="lineCov">         83 :   if(xside=='L') {</span></a>
+<a name="12404"><span class="lineNum">   12404 </span><span class="lineNoCov">          0 :     ni = *n;</span></a>
+<a name="12405"><span class="lineNum">   12405 </span>            :     jc = 0;</a>
+<a name="12406"><span class="lineNum">   12406 </span>            :   } else {</a>
+<a name="12407"><span class="lineNum">   12407 </span><span class="lineCov">         83 :     mi = *m;</span></a>
+<a name="12408"><span class="lineNum">   12408 </span>            :     ic = 0;</a>
+<a name="12409"><span class="lineNum">   12409 </span>            :   }</a>
+<a name="12410"><span class="lineNum">   12410 </span>            : </a>
+<a name="12411"><span class="lineNum">   12411 </span><span class="lineCov">       1600 :   for(i=i1;i!=i2;i+=i3) {</span></a>
+<a name="12412"><span class="lineNum">   12412 </span><span class="lineCov">       1517 :     if(xside=='L') {</span></a>
+<a name="12413"><span class="lineNum">   12413 </span><span class="lineNoCov">          0 :       mi = *m - i;</span></a>
+<a name="12414"><span class="lineNum">   12414 </span>            :       ic = i;</a>
+<a name="12415"><span class="lineNum">   12415 </span>            :     } else {</a>
+<a name="12416"><span class="lineNum">   12416 </span><span class="lineCov">       1517 :       ni = *n - i;</span></a>
+<a name="12417"><span class="lineNum">   12417 </span>            :       jc = i;</a>
+<a name="12418"><span class="lineNum">   12418 </span>            :     }</a>
+<a name="12419"><span class="lineNum">   12419 </span><span class="lineCov">       1517 :     aii = a[i*(*lda)+i];</span></a>
+<a name="12420"><span class="lineNum">   12420 </span><span class="lineCov">       1517 :     a[i*(*lda)+i] = 1.0;</span></a>
+<a name="12421"><span class="lineNum">   12421 </span><span class="lineCov">       1517 :     PLUMED_BLAS_F77_FUNC(dlarf,DLARF)(side,&amp;mi,&amp;ni,&amp;(a[i*(*lda)+i]),lda,tau+i,</span></a>
+<a name="12422"><span class="lineNum">   12422 </span><span class="lineCov">       1517 :            &amp;(c[jc*(*ldc)+ic]),ldc,work);</span></a>
+<a name="12423"><span class="lineNum">   12423 </span><span class="lineCov">       1517 :     a[i*(*lda)+i] = aii;</span></a>
+<a name="12424"><span class="lineNum">   12424 </span>            :   }</a>
+<a name="12425"><span class="lineNum">   12425 </span>            :   return;</a>
+<a name="12426"><span class="lineNum">   12426 </span>            : }</a>
+<a name="12427"><span class="lineNum">   12427 </span>            :              </a>
+<a name="12428"><span class="lineNum">   12428 </span>            : }</a>
+<a name="12429"><span class="lineNum">   12429 </span>            : }</a>
+<a name="12430"><span class="lineNum">   12430 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12431"><span class="lineNum">   12431 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="12432"><span class="lineNum">   12432 </span>            : </a>
+<a name="12433"><span class="lineNum">   12433 </span>            : </a>
+<a name="12434"><span class="lineNum">   12434 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12435"><span class="lineNum">   12435 </span>            : namespace PLMD{</a>
+<a name="12436"><span class="lineNum">   12436 </span>            : namespace lapack{</a>
+<a name="12437"><span class="lineNum">   12437 </span>            : using namespace blas;</a>
+<a name="12438"><span class="lineNum">   12438 </span>            : void </a>
+<a name="12439"><span class="lineNum">   12439 </span><span class="lineCov">         96 : PLUMED_BLAS_F77_FUNC(dormlq,DORMLQ)(const char *side, </span></a>
+<a name="12440"><span class="lineNum">   12440 </span>            :         const char *trans,</a>
+<a name="12441"><span class="lineNum">   12441 </span>            :         int *m, </a>
+<a name="12442"><span class="lineNum">   12442 </span>            :         int *n, </a>
+<a name="12443"><span class="lineNum">   12443 </span>            :         int *k,</a>
+<a name="12444"><span class="lineNum">   12444 </span>            :         double *a,</a>
+<a name="12445"><span class="lineNum">   12445 </span>            :         int *lda, </a>
+<a name="12446"><span class="lineNum">   12446 </span>            :         double *tau, </a>
+<a name="12447"><span class="lineNum">   12447 </span>            :         double *c__, </a>
+<a name="12448"><span class="lineNum">   12448 </span>            :         int *ldc, </a>
+<a name="12449"><span class="lineNum">   12449 </span>            :         double *work, </a>
+<a name="12450"><span class="lineNum">   12450 </span>            :         int *lwork, </a>
+<a name="12451"><span class="lineNum">   12451 </span>            :         int *info)</a>
+<a name="12452"><span class="lineNum">   12452 </span>            : {</a>
+<a name="12453"><span class="lineNum">   12453 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2, i__4, </a>
+<a name="12454"><span class="lineNum">   12454 </span>            :             i__5;</a>
+<a name="12455"><span class="lineNum">   12455 </span>            :   </a>
+<a name="12456"><span class="lineNum">   12456 </span>            : </a>
+<a name="12457"><span class="lineNum">   12457 </span>            :     int i__;</a>
+<a name="12458"><span class="lineNum">   12458 </span>            :     double t[4160]      /* was [65][64] */;</a>
+<a name="12459"><span class="lineNum">   12459 </span>            :     int i1, i2, i3, ib, ic, jc, nb, mi, ni, nq, nw, iws;</a>
+<a name="12460"><span class="lineNum">   12460 </span>            :     int left;</a>
+<a name="12461"><span class="lineNum">   12461 </span>            :     int nbmin, iinfo;</a>
+<a name="12462"><span class="lineNum">   12462 </span>            :     int notran;</a>
+<a name="12463"><span class="lineNum">   12463 </span>            :     int ldwork;</a>
+<a name="12464"><span class="lineNum">   12464 </span>            :     char transt[1];</a>
+<a name="12465"><span class="lineNum">   12465 </span>            :     int lwkopt;</a>
+<a name="12466"><span class="lineNum">   12466 </span>            :     int lquery;</a>
+<a name="12467"><span class="lineNum">   12467 </span><span class="lineCov">         96 :     int ldt = 65;</span></a>
+<a name="12468"><span class="lineNum">   12468 </span>            : </a>
+<a name="12469"><span class="lineNum">   12469 </span><span class="lineCov">         96 :     a_dim1 = *lda;</span></a>
+<a name="12470"><span class="lineNum">   12470 </span><span class="lineCov">         96 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12471"><span class="lineNum">   12471 </span><span class="lineCov">         96 :     a -= a_offset;</span></a>
+<a name="12472"><span class="lineNum">   12472 </span>            :     --tau;</a>
+<a name="12473"><span class="lineNum">   12473 </span><span class="lineCov">         96 :     c_dim1 = *ldc;</span></a>
+<a name="12474"><span class="lineNum">   12474 </span><span class="lineCov">         96 :     c_offset = 1 + c_dim1;</span></a>
+<a name="12475"><span class="lineNum">   12475 </span><span class="lineCov">         96 :     c__ -= c_offset;</span></a>
+<a name="12476"><span class="lineNum">   12476 </span>            :     --work;</a>
+<a name="12477"><span class="lineNum">   12477 </span>            : </a>
+<a name="12478"><span class="lineNum">   12478 </span>            :     ic = jc = 0;</a>
+<a name="12479"><span class="lineNum">   12479 </span>            : </a>
+<a name="12480"><span class="lineNum">   12480 </span><span class="lineCov">         96 :     *info = 0;</span></a>
+<a name="12481"><span class="lineNum">   12481 </span><span class="lineCov">         96 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12482"><span class="lineNum">   12482 </span><span class="lineCov">         96 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="12483"><span class="lineNum">   12483 </span><span class="lineCov">         96 :     lquery = *lwork == -1;</span></a>
+<a name="12484"><span class="lineNum">   12484 </span>            : </a>
+<a name="12485"><span class="lineNum">   12485 </span><span class="lineCov">         96 :     if (left) {</span></a>
+<a name="12486"><span class="lineNum">   12486 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="12487"><span class="lineNum">   12487 </span><span class="lineNoCov">          0 :         nw = *n;</span></a>
+<a name="12488"><span class="lineNum">   12488 </span>            :     } else {</a>
+<a name="12489"><span class="lineNum">   12489 </span><span class="lineCov">         96 :         nq = *n;</span></a>
+<a name="12490"><span class="lineNum">   12490 </span><span class="lineCov">         96 :         nw = *m;</span></a>
+<a name="12491"><span class="lineNum">   12491 </span>            :     }</a>
+<a name="12492"><span class="lineNum">   12492 </span>            : </a>
+<a name="12493"><span class="lineNum">   12493 </span>            :     nb = DORMLQ_BLOCKSIZE;</a>
+<a name="12494"><span class="lineNum">   12494 </span><span class="lineCov">         96 :     lwkopt = nw * nb;</span></a>
+<a name="12495"><span class="lineNum">   12495 </span><span class="lineCov">         96 :     work[1] = (double) lwkopt;</span></a>
+<a name="12496"><span class="lineNum">   12496 </span>            :     </a>
+<a name="12497"><span class="lineNum">   12497 </span><span class="lineCov">         96 :     if (*info != 0) {</span></a>
+<a name="12498"><span class="lineNum">   12498 </span>            :         return;</a>
+<a name="12499"><span class="lineNum">   12499 </span><span class="lineCov">         96 :     } else if (lquery) {</span></a>
+<a name="12500"><span class="lineNum">   12500 </span>            :         return;</a>
+<a name="12501"><span class="lineNum">   12501 </span>            :     }</a>
+<a name="12502"><span class="lineNum">   12502 </span>            : </a>
+<a name="12503"><span class="lineNum">   12503 </span><span class="lineCov">         96 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="12504"><span class="lineNum">   12504 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="12505"><span class="lineNum">   12505 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="12506"><span class="lineNum">   12506 </span>            :     }</a>
+<a name="12507"><span class="lineNum">   12507 </span>            : </a>
+<a name="12508"><span class="lineNum">   12508 </span>            :     nbmin = 2;</a>
+<a name="12509"><span class="lineNum">   12509 </span><span class="lineCov">         96 :     ldwork = nw;</span></a>
+<a name="12510"><span class="lineNum">   12510 </span><span class="lineCov">         96 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="12511"><span class="lineNum">   12511 </span>            :         iws = nw * nb;</a>
+<a name="12512"><span class="lineNum">   12512 </span><span class="lineCov">         13 :         if (*lwork &lt; iws) {</span></a>
+<a name="12513"><span class="lineNum">   12513 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="12514"><span class="lineNum">   12514 </span>            :             nbmin = DORMLQ_MINBLOCKSIZE;</a>
+<a name="12515"><span class="lineNum">   12515 </span>            :         }</a>
+<a name="12516"><span class="lineNum">   12516 </span>            :     }</a>
+<a name="12517"><span class="lineNum">   12517 </span>            : </a>
+<a name="12518"><span class="lineNum">   12518 </span><span class="lineCov">         96 :     if (nb &lt; nbmin || nb &gt;= *k) {</span></a>
+<a name="12519"><span class="lineNum">   12519 </span>            : </a>
+<a name="12520"><span class="lineNum">   12520 </span>            : </a>
+<a name="12521"><span class="lineNum">   12521 </span><span class="lineCov">         83 :         PLUMED_BLAS_F77_FUNC(dorml2,DORML2)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="12522"><span class="lineNum">   12522 </span>            :                 c_offset], ldc, &amp;work[1], &amp;iinfo);</a>
+<a name="12523"><span class="lineNum">   12523 </span>            :     } else {</a>
+<a name="12524"><span class="lineNum">   12524 </span>            : </a>
+<a name="12525"><span class="lineNum">   12525 </span><span class="lineCov">         13 :         if ((left &amp;&amp; notran) || (!left &amp;&amp; !notran)) {</span></a>
+<a name="12526"><span class="lineNum">   12526 </span>            :             i1 = 1;</a>
+<a name="12527"><span class="lineNum">   12527 </span>            :             i2 = *k;</a>
+<a name="12528"><span class="lineNum">   12528 </span>            :             i3 = nb;</a>
+<a name="12529"><span class="lineNum">   12529 </span>            :         } else {</a>
+<a name="12530"><span class="lineNum">   12530 </span><span class="lineCov">         13 :             i1 = (*k - 1) / nb * nb + 1;</span></a>
+<a name="12531"><span class="lineNum">   12531 </span>            :             i2 = 1;</a>
+<a name="12532"><span class="lineNum">   12532 </span><span class="lineCov">         13 :             i3 = -nb;</span></a>
+<a name="12533"><span class="lineNum">   12533 </span>            :         }</a>
+<a name="12534"><span class="lineNum">   12534 </span>            : </a>
+<a name="12535"><span class="lineNum">   12535 </span><span class="lineCov">         13 :         if (left) {</span></a>
+<a name="12536"><span class="lineNum">   12536 </span><span class="lineNoCov">          0 :             ni = *n;</span></a>
+<a name="12537"><span class="lineNum">   12537 </span>            :             jc = 1;</a>
+<a name="12538"><span class="lineNum">   12538 </span>            :         } else {</a>
+<a name="12539"><span class="lineNum">   12539 </span><span class="lineCov">         13 :             mi = *m;</span></a>
+<a name="12540"><span class="lineNum">   12540 </span>            :             ic = 1;</a>
+<a name="12541"><span class="lineNum">   12541 </span>            :         }</a>
+<a name="12542"><span class="lineNum">   12542 </span>            : </a>
+<a name="12543"><span class="lineNum">   12543 </span><span class="lineCov">         13 :         if (notran) {</span></a>
+<a name="12544"><span class="lineNum">   12544 </span><span class="lineCov">         13 :             *(unsigned char *)transt = 'T';</span></a>
+<a name="12545"><span class="lineNum">   12545 </span>            :         } else {</a>
+<a name="12546"><span class="lineNum">   12546 </span><span class="lineNoCov">          0 :             *(unsigned char *)transt = 'N';</span></a>
+<a name="12547"><span class="lineNum">   12547 </span>            :         }</a>
+<a name="12548"><span class="lineNum">   12548 </span>            : </a>
+<a name="12549"><span class="lineNum">   12549 </span>            :         i__1 = i2;</a>
+<a name="12550"><span class="lineNum">   12550 </span>            :         i__2 = i3;</a>
+<a name="12551"><span class="lineNum">   12551 </span><span class="lineCov">         53 :         for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="12552"><span class="lineNum">   12552 </span><span class="lineCov">         40 :             i__4 = nb, i__5 = *k - i__ + 1;</span></a>
+<a name="12553"><span class="lineNum">   12553 </span><span class="lineCov">         40 :             ib = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="12554"><span class="lineNum">   12554 </span>            : </a>
+<a name="12555"><span class="lineNum">   12555 </span><span class="lineCov">         40 :             i__4 = nq - i__ + 1;</span></a>
+<a name="12556"><span class="lineNum">   12556 </span><span class="lineCov">         40 :             PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__4, &amp;ib, &amp;a[i__ + i__ * a_dim1], </span></a>
+<a name="12557"><span class="lineNum">   12557 </span><span class="lineCov">         40 :                     lda, &amp;tau[i__], t, &amp;ldt);</span></a>
+<a name="12558"><span class="lineNum">   12558 </span><span class="lineCov">         40 :             if (left) {</span></a>
+<a name="12559"><span class="lineNum">   12559 </span>            : </a>
+<a name="12560"><span class="lineNum">   12560 </span><span class="lineNoCov">          0 :                 mi = *m - i__ + 1;</span></a>
+<a name="12561"><span class="lineNum">   12561 </span>            :                 ic = i__;</a>
+<a name="12562"><span class="lineNum">   12562 </span>            :             } else {</a>
+<a name="12563"><span class="lineNum">   12563 </span>            : </a>
+<a name="12564"><span class="lineNum">   12564 </span><span class="lineCov">         40 :                 ni = *n - i__ + 1;</span></a>
+<a name="12565"><span class="lineNum">   12565 </span>            :                 jc = i__;</a>
+<a name="12566"><span class="lineNum">   12566 </span>            :             }</a>
+<a name="12567"><span class="lineNum">   12567 </span>            : </a>
+<a name="12568"><span class="lineNum">   12568 </span><span class="lineCov">         40 :             PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(side, transt, &quot;Forward&quot;, &quot;Rowwise&quot;, &amp;mi, &amp;ni, &amp;ib, &amp;a[i__ </span></a>
+<a name="12569"><span class="lineNum">   12569 </span><span class="lineCov">         40 :                     + i__ * a_dim1], lda, t, &amp;ldt, &amp;c__[ic + jc * c_dim1], </span></a>
+<a name="12570"><span class="lineNum">   12570 </span>            :                     ldc, &amp;work[1], &amp;ldwork);</a>
+<a name="12571"><span class="lineNum">   12571 </span>            :         }</a>
+<a name="12572"><span class="lineNum">   12572 </span>            :     }</a>
+<a name="12573"><span class="lineNum">   12573 </span><span class="lineCov">         96 :     work[1] = (double) lwkopt;</span></a>
+<a name="12574"><span class="lineNum">   12574 </span><span class="lineCov">         96 :     return;</span></a>
+<a name="12575"><span class="lineNum">   12575 </span>            : </a>
+<a name="12576"><span class="lineNum">   12576 </span>            : }</a>
+<a name="12577"><span class="lineNum">   12577 </span>            : </a>
+<a name="12578"><span class="lineNum">   12578 </span>            : </a>
+<a name="12579"><span class="lineNum">   12579 </span>            : }</a>
+<a name="12580"><span class="lineNum">   12580 </span>            : }</a>
+<a name="12581"><span class="lineNum">   12581 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12582"><span class="lineNum">   12582 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="12583"><span class="lineNum">   12583 </span>            : </a>
+<a name="12584"><span class="lineNum">   12584 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12585"><span class="lineNum">   12585 </span>            : namespace PLMD{</a>
+<a name="12586"><span class="lineNum">   12586 </span>            : namespace lapack{</a>
+<a name="12587"><span class="lineNum">   12587 </span>            : using namespace blas;</a>
+<a name="12588"><span class="lineNum">   12588 </span>            : void</a>
+<a name="12589"><span class="lineNum">   12589 </span><span class="lineCov">     569964 : PLUMED_BLAS_F77_FUNC(dormql,DORMQL)(const char *side, const char *trans, int *m, int *n, </span></a>
+<a name="12590"><span class="lineNum">   12590 </span>            :         int *k, double *a, int *lda, double *tau, double *</a>
+<a name="12591"><span class="lineNum">   12591 </span>            :         c__, int *ldc, double *work, int *lwork, int *info)</a>
+<a name="12592"><span class="lineNum">   12592 </span>            : {</a>
+<a name="12593"><span class="lineNum">   12593 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2, i__4, i__5;</a>
+<a name="12594"><span class="lineNum">   12594 </span><span class="lineCov">     569964 :     int c__65 = 65;</span></a>
+<a name="12595"><span class="lineNum">   12595 </span>            : </a>
+<a name="12596"><span class="lineNum">   12596 </span>            :     int i__;</a>
+<a name="12597"><span class="lineNum">   12597 </span>            :     double t[4160];</a>
+<a name="12598"><span class="lineNum">   12598 </span>            :     int i1, i2, i3, ib, nb, mi, ni, nq, nw, iws;</a>
+<a name="12599"><span class="lineNum">   12599 </span>            :     int left;</a>
+<a name="12600"><span class="lineNum">   12600 </span>            :     int nbmin, iinfo;</a>
+<a name="12601"><span class="lineNum">   12601 </span>            :     int notran;</a>
+<a name="12602"><span class="lineNum">   12602 </span>            :     int ldwork, lwkopt;</a>
+<a name="12603"><span class="lineNum">   12603 </span>            :     int lquery;</a>
+<a name="12604"><span class="lineNum">   12604 </span>            : </a>
+<a name="12605"><span class="lineNum">   12605 </span>            : </a>
+<a name="12606"><span class="lineNum">   12606 </span><span class="lineCov">     569964 :     a_dim1 = *lda;</span></a>
+<a name="12607"><span class="lineNum">   12607 </span><span class="lineCov">     569964 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12608"><span class="lineNum">   12608 </span><span class="lineCov">     569964 :     a -= a_offset;</span></a>
+<a name="12609"><span class="lineNum">   12609 </span>            :     --tau;</a>
+<a name="12610"><span class="lineNum">   12610 </span>            :     c_dim1 = *ldc;</a>
+<a name="12611"><span class="lineNum">   12611 </span>            :     c_offset = 1 + c_dim1;</a>
+<a name="12612"><span class="lineNum">   12612 </span>            :     c__ -= c_offset;</a>
+<a name="12613"><span class="lineNum">   12613 </span>            :     --work;</a>
+<a name="12614"><span class="lineNum">   12614 </span>            : </a>
+<a name="12615"><span class="lineNum">   12615 </span><span class="lineCov">     569964 :     *info = 0;</span></a>
+<a name="12616"><span class="lineNum">   12616 </span><span class="lineCov">     569964 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12617"><span class="lineNum">   12617 </span><span class="lineCov">     569964 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="12618"><span class="lineNum">   12618 </span><span class="lineCov">     569964 :     lquery = *lwork == -1;</span></a>
+<a name="12619"><span class="lineNum">   12619 </span>            : </a>
+<a name="12620"><span class="lineNum">   12620 </span><span class="lineCov">     569964 :     if (left) {</span></a>
+<a name="12621"><span class="lineNum">   12621 </span><span class="lineCov">     569964 :         nq = *m;</span></a>
+<a name="12622"><span class="lineNum">   12622 </span><span class="lineCov">     569964 :         nw = *n;</span></a>
+<a name="12623"><span class="lineNum">   12623 </span>            :     } else {</a>
+<a name="12624"><span class="lineNum">   12624 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="12625"><span class="lineNum">   12625 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="12626"><span class="lineNum">   12626 </span>            :     }</a>
+<a name="12627"><span class="lineNum">   12627 </span>            : </a>
+<a name="12628"><span class="lineNum">   12628 </span>            :     nb = DORMQL_BLOCKSIZE;</a>
+<a name="12629"><span class="lineNum">   12629 </span><span class="lineCov">     569964 :     lwkopt = nw * nb;</span></a>
+<a name="12630"><span class="lineNum">   12630 </span><span class="lineCov">     569964 :     work[1] = (double) lwkopt;</span></a>
+<a name="12631"><span class="lineNum">   12631 </span>            :     </a>
+<a name="12632"><span class="lineNum">   12632 </span><span class="lineCov">     569964 :     if (*info != 0) {</span></a>
+<a name="12633"><span class="lineNum">   12633 </span>            :         return;</a>
+<a name="12634"><span class="lineNum">   12634 </span><span class="lineCov">     569964 :     } else if (lquery) {</span></a>
+<a name="12635"><span class="lineNum">   12635 </span>            :         return;</a>
+<a name="12636"><span class="lineNum">   12636 </span>            :     }</a>
+<a name="12637"><span class="lineNum">   12637 </span>            : </a>
+<a name="12638"><span class="lineNum">   12638 </span><span class="lineCov">     569964 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="12639"><span class="lineNum">   12639 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="12640"><span class="lineNum">   12640 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="12641"><span class="lineNum">   12641 </span>            :     }</a>
+<a name="12642"><span class="lineNum">   12642 </span>            : </a>
+<a name="12643"><span class="lineNum">   12643 </span>            :     nbmin = 2;</a>
+<a name="12644"><span class="lineNum">   12644 </span><span class="lineCov">     569964 :     ldwork = nw;</span></a>
+<a name="12645"><span class="lineNum">   12645 </span><span class="lineCov">     569964 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="12646"><span class="lineNum">   12646 </span>            :         iws = nw * nb;</a>
+<a name="12647"><span class="lineNum">   12647 </span><span class="lineCov">         12 :         if (*lwork &lt; iws) {</span></a>
+<a name="12648"><span class="lineNum">   12648 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="12649"><span class="lineNum">   12649 </span>            :             nbmin = DORMQL_MINBLOCKSIZE;</a>
+<a name="12650"><span class="lineNum">   12650 </span>            :         }</a>
+<a name="12651"><span class="lineNum">   12651 </span>            :     }</a>
+<a name="12652"><span class="lineNum">   12652 </span>            : </a>
+<a name="12653"><span class="lineNum">   12653 </span><span class="lineCov">     569964 :     if (nb &lt; nbmin || nb &gt;= *k) {</span></a>
+<a name="12654"><span class="lineNum">   12654 </span>            : </a>
+<a name="12655"><span class="lineNum">   12655 </span><span class="lineCov">     569952 :         PLUMED_BLAS_F77_FUNC(dorm2l,DORM2L)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="12656"><span class="lineNum">   12656 </span>            :                 c_offset], ldc, &amp;work[1], &amp;iinfo);</a>
+<a name="12657"><span class="lineNum">   12657 </span>            :     } else {</a>
+<a name="12658"><span class="lineNum">   12658 </span>            : </a>
+<a name="12659"><span class="lineNum">   12659 </span><span class="lineCov">         12 :         if ((left &amp;&amp; notran) || (! left &amp;&amp; ! notran)) {</span></a>
+<a name="12660"><span class="lineNum">   12660 </span>            :             i1 = 1;</a>
+<a name="12661"><span class="lineNum">   12661 </span>            :             i2 = *k;</a>
+<a name="12662"><span class="lineNum">   12662 </span>            :             i3 = nb;</a>
+<a name="12663"><span class="lineNum">   12663 </span>            :         } else {</a>
+<a name="12664"><span class="lineNum">   12664 </span><span class="lineNoCov">          0 :             i1 = (*k - 1) / nb * nb + 1;</span></a>
+<a name="12665"><span class="lineNum">   12665 </span>            :             i2 = 1;</a>
+<a name="12666"><span class="lineNum">   12666 </span><span class="lineNoCov">          0 :             i3 = -nb;</span></a>
+<a name="12667"><span class="lineNum">   12667 </span>            :         }</a>
+<a name="12668"><span class="lineNum">   12668 </span>            : </a>
+<a name="12669"><span class="lineNum">   12669 </span><span class="lineCov">         12 :         if (left) {</span></a>
+<a name="12670"><span class="lineNum">   12670 </span><span class="lineCov">         12 :             ni = *n;</span></a>
+<a name="12671"><span class="lineNum">   12671 </span>            :         } else {</a>
+<a name="12672"><span class="lineNum">   12672 </span><span class="lineNoCov">          0 :             mi = *m;</span></a>
+<a name="12673"><span class="lineNum">   12673 </span>            :         }</a>
+<a name="12674"><span class="lineNum">   12674 </span>            : </a>
+<a name="12675"><span class="lineNum">   12675 </span>            :         i__1 = i2;</a>
+<a name="12676"><span class="lineNum">   12676 </span>            :         i__2 = i3;</a>
+<a name="12677"><span class="lineNum">   12677 </span><span class="lineCov">         71 :         for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="12678"><span class="lineNum">   12678 </span><span class="lineCov">         59 :             i__4 = nb, i__5 = *k - i__ + 1;</span></a>
+<a name="12679"><span class="lineNum">   12679 </span><span class="lineCov">         59 :             ib = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="12680"><span class="lineNum">   12680 </span>            : </a>
+<a name="12681"><span class="lineNum">   12681 </span><span class="lineCov">         59 :             i__4 = nq - *k + i__ + ib - 1;</span></a>
+<a name="12682"><span class="lineNum">   12682 </span><span class="lineCov">         59 :             PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Backward&quot;, &quot;Columnwise&quot;, &amp;i__4, &amp;ib, &amp;a[i__ * a_dim1 + 1]</span></a>
+<a name="12683"><span class="lineNum">   12683 </span><span class="lineCov">         59 :                     , lda, &amp;tau[i__], t, &amp;c__65);</span></a>
+<a name="12684"><span class="lineNum">   12684 </span><span class="lineCov">         59 :             if (left) {</span></a>
+<a name="12685"><span class="lineNum">   12685 </span>            : </a>
+<a name="12686"><span class="lineNum">   12686 </span><span class="lineCov">         59 :                 mi = *m - *k + i__ + ib - 1;</span></a>
+<a name="12687"><span class="lineNum">   12687 </span>            :             } else {</a>
+<a name="12688"><span class="lineNum">   12688 </span>            : </a>
+<a name="12689"><span class="lineNum">   12689 </span><span class="lineNoCov">          0 :                 ni = *n - *k + i__ + ib - 1;</span></a>
+<a name="12690"><span class="lineNum">   12690 </span>            :             }</a>
+<a name="12691"><span class="lineNum">   12691 </span>            : </a>
+<a name="12692"><span class="lineNum">   12692 </span><span class="lineCov">         59 :             PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(side, trans, &quot;Backward&quot;, &quot;Columnwise&quot;, &amp;mi, &amp;ni, &amp;ib, &amp;a[</span></a>
+<a name="12693"><span class="lineNum">   12693 </span>            :                     i__ * a_dim1 + 1], lda, t, &amp;c__65, &amp;c__[c_offset], ldc, &amp;</a>
+<a name="12694"><span class="lineNum">   12694 </span>            :                     work[1], &amp;ldwork);</a>
+<a name="12695"><span class="lineNum">   12695 </span>            :         }</a>
+<a name="12696"><span class="lineNum">   12696 </span>            :     }</a>
+<a name="12697"><span class="lineNum">   12697 </span><span class="lineCov">     569964 :     work[1] = (double) lwkopt;</span></a>
+<a name="12698"><span class="lineNum">   12698 </span><span class="lineCov">     569964 :     return;</span></a>
+<a name="12699"><span class="lineNum">   12699 </span>            : </a>
+<a name="12700"><span class="lineNum">   12700 </span>            : }</a>
+<a name="12701"><span class="lineNum">   12701 </span>            : </a>
+<a name="12702"><span class="lineNum">   12702 </span>            : </a>
+<a name="12703"><span class="lineNum">   12703 </span>            : }</a>
+<a name="12704"><span class="lineNum">   12704 </span>            : }</a>
+<a name="12705"><span class="lineNum">   12705 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12706"><span class="lineNum">   12706 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="12707"><span class="lineNum">   12707 </span>            : </a>
+<a name="12708"><span class="lineNum">   12708 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12709"><span class="lineNum">   12709 </span>            : namespace PLMD{</a>
+<a name="12710"><span class="lineNum">   12710 </span>            : namespace lapack{</a>
+<a name="12711"><span class="lineNum">   12711 </span>            : using namespace blas;</a>
+<a name="12712"><span class="lineNum">   12712 </span>            : void </a>
+<a name="12713"><span class="lineNum">   12713 </span><span class="lineCov">         96 : PLUMED_BLAS_F77_FUNC(dormqr,DORMQR)(const char *side, </span></a>
+<a name="12714"><span class="lineNum">   12714 </span>            :         const char *trans, </a>
+<a name="12715"><span class="lineNum">   12715 </span>            :         int *m, </a>
+<a name="12716"><span class="lineNum">   12716 </span>            :         int *n, </a>
+<a name="12717"><span class="lineNum">   12717 </span>            :         int *k, </a>
+<a name="12718"><span class="lineNum">   12718 </span>            :         double *a, </a>
+<a name="12719"><span class="lineNum">   12719 </span>            :         int *lda, </a>
+<a name="12720"><span class="lineNum">   12720 </span>            :         double *tau, </a>
+<a name="12721"><span class="lineNum">   12721 </span>            :         double *c__, </a>
+<a name="12722"><span class="lineNum">   12722 </span>            :         int *ldc, </a>
+<a name="12723"><span class="lineNum">   12723 </span>            :         double *work, </a>
+<a name="12724"><span class="lineNum">   12724 </span>            :         int *lwork, </a>
+<a name="12725"><span class="lineNum">   12725 </span>            :         int *info)</a>
+<a name="12726"><span class="lineNum">   12726 </span>            : {</a>
+<a name="12727"><span class="lineNum">   12727 </span>            :    int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2, i__4, i__5;</a>
+<a name="12728"><span class="lineNum">   12728 </span>            : </a>
+<a name="12729"><span class="lineNum">   12729 </span>            :     int i__;</a>
+<a name="12730"><span class="lineNum">   12730 </span>            :     double t[4160];</a>
+<a name="12731"><span class="lineNum">   12731 </span>            :     int i1, i2, i3, ib, ic, jc, nb, mi, ni, nq, nw, iws;</a>
+<a name="12732"><span class="lineNum">   12732 </span>            :     int left;</a>
+<a name="12733"><span class="lineNum">   12733 </span>            :     int nbmin, iinfo;</a>
+<a name="12734"><span class="lineNum">   12734 </span>            :     int notran;</a>
+<a name="12735"><span class="lineNum">   12735 </span>            :     int ldwork, lwkopt;</a>
+<a name="12736"><span class="lineNum">   12736 </span>            :     int lquery;</a>
+<a name="12737"><span class="lineNum">   12737 </span><span class="lineCov">         96 :     int ldt = 65;</span></a>
+<a name="12738"><span class="lineNum">   12738 </span>            : </a>
+<a name="12739"><span class="lineNum">   12739 </span><span class="lineCov">         96 :     a_dim1 = *lda;</span></a>
+<a name="12740"><span class="lineNum">   12740 </span><span class="lineCov">         96 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12741"><span class="lineNum">   12741 </span><span class="lineCov">         96 :     a -= a_offset;</span></a>
+<a name="12742"><span class="lineNum">   12742 </span>            :     --tau;</a>
+<a name="12743"><span class="lineNum">   12743 </span><span class="lineCov">         96 :     c_dim1 = *ldc;</span></a>
+<a name="12744"><span class="lineNum">   12744 </span><span class="lineCov">         96 :     c_offset = 1 + c_dim1;</span></a>
+<a name="12745"><span class="lineNum">   12745 </span><span class="lineCov">         96 :     c__ -= c_offset;</span></a>
+<a name="12746"><span class="lineNum">   12746 </span>            :     --work;</a>
+<a name="12747"><span class="lineNum">   12747 </span>            : </a>
+<a name="12748"><span class="lineNum">   12748 </span><span class="lineCov">         96 :     *info = 0;</span></a>
+<a name="12749"><span class="lineNum">   12749 </span><span class="lineCov">         96 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12750"><span class="lineNum">   12750 </span><span class="lineCov">         96 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="12751"><span class="lineNum">   12751 </span><span class="lineCov">         96 :     lquery = *lwork == -1;</span></a>
+<a name="12752"><span class="lineNum">   12752 </span>            : </a>
+<a name="12753"><span class="lineNum">   12753 </span><span class="lineCov">         96 :     if (left) {</span></a>
+<a name="12754"><span class="lineNum">   12754 </span><span class="lineCov">         96 :         nq = *m;</span></a>
+<a name="12755"><span class="lineNum">   12755 </span><span class="lineCov">         96 :         nw = *n;</span></a>
+<a name="12756"><span class="lineNum">   12756 </span>            :     } else {</a>
+<a name="12757"><span class="lineNum">   12757 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="12758"><span class="lineNum">   12758 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="12759"><span class="lineNum">   12759 </span>            :     }</a>
+<a name="12760"><span class="lineNum">   12760 </span>            : </a>
+<a name="12761"><span class="lineNum">   12761 </span>            :      ic = jc = 0;</a>
+<a name="12762"><span class="lineNum">   12762 </span>            :      nb = DORMQR_BLOCKSIZE;</a>
+<a name="12763"><span class="lineNum">   12763 </span><span class="lineCov">         96 :      lwkopt = nw * nb;</span></a>
+<a name="12764"><span class="lineNum">   12764 </span><span class="lineCov">         96 :      work[1] = (double) lwkopt;</span></a>
+<a name="12765"><span class="lineNum">   12765 </span>            : </a>
+<a name="12766"><span class="lineNum">   12766 </span><span class="lineCov">         96 :     if (*info != 0) {</span></a>
+<a name="12767"><span class="lineNum">   12767 </span>            :         return;</a>
+<a name="12768"><span class="lineNum">   12768 </span><span class="lineCov">         96 :     } else if (lquery) {</span></a>
+<a name="12769"><span class="lineNum">   12769 </span>            :       return;</a>
+<a name="12770"><span class="lineNum">   12770 </span>            :     }</a>
+<a name="12771"><span class="lineNum">   12771 </span>            : </a>
+<a name="12772"><span class="lineNum">   12772 </span><span class="lineCov">         96 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="12773"><span class="lineNum">   12773 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="12774"><span class="lineNum">   12774 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="12775"><span class="lineNum">   12775 </span>            :     }</a>
+<a name="12776"><span class="lineNum">   12776 </span>            : </a>
+<a name="12777"><span class="lineNum">   12777 </span>            :     nbmin = 2;</a>
+<a name="12778"><span class="lineNum">   12778 </span><span class="lineCov">         96 :     ldwork = nw;</span></a>
+<a name="12779"><span class="lineNum">   12779 </span><span class="lineCov">         96 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="12780"><span class="lineNum">   12780 </span>            :         iws = nw * nb;</a>
+<a name="12781"><span class="lineNum">   12781 </span><span class="lineCov">         17 :         if (*lwork &lt; iws) {</span></a>
+<a name="12782"><span class="lineNum">   12782 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="12783"><span class="lineNum">   12783 </span>            :             nbmin = DORMQR_MINBLOCKSIZE;</a>
+<a name="12784"><span class="lineNum">   12784 </span>            :         }</a>
+<a name="12785"><span class="lineNum">   12785 </span>            :     }</a>
+<a name="12786"><span class="lineNum">   12786 </span>            : </a>
+<a name="12787"><span class="lineNum">   12787 </span><span class="lineCov">         96 :     if (nb &lt; nbmin || nb &gt;= *k) {</span></a>
+<a name="12788"><span class="lineNum">   12788 </span>            : </a>
+<a name="12789"><span class="lineNum">   12789 </span><span class="lineCov">         79 :         PLUMED_BLAS_F77_FUNC(dorm2r,DORM2R)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="12790"><span class="lineNum">   12790 </span>            :                 c_offset], ldc, &amp;work[1], &amp;iinfo);</a>
+<a name="12791"><span class="lineNum">   12791 </span>            :     } else {</a>
+<a name="12792"><span class="lineNum">   12792 </span>            : </a>
+<a name="12793"><span class="lineNum">   12793 </span><span class="lineCov">         17 :         if ((left &amp;&amp; !notran) || (!left &amp;&amp; notran)) {</span></a>
+<a name="12794"><span class="lineNum">   12794 </span>            :             i1 = 1;</a>
+<a name="12795"><span class="lineNum">   12795 </span>            :             i2 = *k;</a>
+<a name="12796"><span class="lineNum">   12796 </span>            :             i3 = nb;</a>
+<a name="12797"><span class="lineNum">   12797 </span>            :         } else {</a>
+<a name="12798"><span class="lineNum">   12798 </span><span class="lineCov">         17 :             i1 = (*k - 1) / nb * nb + 1;</span></a>
+<a name="12799"><span class="lineNum">   12799 </span>            :             i2 = 1;</a>
+<a name="12800"><span class="lineNum">   12800 </span><span class="lineCov">         17 :             i3 = -nb;</span></a>
+<a name="12801"><span class="lineNum">   12801 </span>            :         }</a>
+<a name="12802"><span class="lineNum">   12802 </span>            : </a>
+<a name="12803"><span class="lineNum">   12803 </span><span class="lineCov">         17 :         if (left) {</span></a>
+<a name="12804"><span class="lineNum">   12804 </span><span class="lineCov">         17 :             ni = *n;</span></a>
+<a name="12805"><span class="lineNum">   12805 </span>            :             jc = 1;</a>
+<a name="12806"><span class="lineNum">   12806 </span>            :         } else {</a>
+<a name="12807"><span class="lineNum">   12807 </span><span class="lineNoCov">          0 :             mi = *m;</span></a>
+<a name="12808"><span class="lineNum">   12808 </span>            :             ic = 1;</a>
+<a name="12809"><span class="lineNum">   12809 </span>            :         }</a>
+<a name="12810"><span class="lineNum">   12810 </span>            : </a>
+<a name="12811"><span class="lineNum">   12811 </span>            :         i__1 = i2;</a>
+<a name="12812"><span class="lineNum">   12812 </span>            :         i__2 = i3;</a>
+<a name="12813"><span class="lineNum">   12813 </span><span class="lineCov">         65 :         for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="12814"><span class="lineNum">   12814 </span><span class="lineCov">         48 :             i__4 = nb, i__5 = *k - i__ + 1;</span></a>
+<a name="12815"><span class="lineNum">   12815 </span><span class="lineCov">         48 :             ib = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="12816"><span class="lineNum">   12816 </span>            : </a>
+<a name="12817"><span class="lineNum">   12817 </span><span class="lineCov">         48 :             i__4 = nq - i__ + 1;</span></a>
+<a name="12818"><span class="lineNum">   12818 </span><span class="lineCov">         48 :             PLUMED_BLAS_F77_FUNC(dlarft,DLARFT)(&quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__4, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="12819"><span class="lineNum">   12819 </span><span class="lineCov">         48 :                     a_dim1], lda, &amp;tau[i__], t, &amp;ldt);</span></a>
+<a name="12820"><span class="lineNum">   12820 </span><span class="lineCov">         48 :             if (left) {</span></a>
+<a name="12821"><span class="lineNum">   12821 </span>            : </a>
+<a name="12822"><span class="lineNum">   12822 </span><span class="lineCov">         48 :                 mi = *m - i__ + 1;</span></a>
+<a name="12823"><span class="lineNum">   12823 </span>            :                 ic = i__;</a>
+<a name="12824"><span class="lineNum">   12824 </span>            :             } else {</a>
+<a name="12825"><span class="lineNum">   12825 </span><span class="lineNoCov">          0 :                 ni = *n - i__ + 1;</span></a>
+<a name="12826"><span class="lineNum">   12826 </span>            :                 jc = i__;</a>
+<a name="12827"><span class="lineNum">   12827 </span>            :             }</a>
+<a name="12828"><span class="lineNum">   12828 </span>            : </a>
+<a name="12829"><span class="lineNum">   12829 </span><span class="lineCov">         48 :             PLUMED_BLAS_F77_FUNC(dlarfb,DLARFB)(side, trans, &quot;Forward&quot;, &quot;Columnwise&quot;, &amp;mi, &amp;ni, &amp;ib, &amp;a[</span></a>
+<a name="12830"><span class="lineNum">   12830 </span><span class="lineCov">         48 :                     i__ + i__ * a_dim1], lda, t, &amp;ldt, &amp;c__[ic + jc * </span></a>
+<a name="12831"><span class="lineNum">   12831 </span>            :                     c_dim1], ldc, &amp;work[1], &amp;ldwork);</a>
+<a name="12832"><span class="lineNum">   12832 </span>            :         }</a>
+<a name="12833"><span class="lineNum">   12833 </span>            :     }</a>
+<a name="12834"><span class="lineNum">   12834 </span><span class="lineCov">         96 :     work[1] = (double) lwkopt;</span></a>
+<a name="12835"><span class="lineNum">   12835 </span><span class="lineCov">         96 :     return;</span></a>
+<a name="12836"><span class="lineNum">   12836 </span>            : </a>
+<a name="12837"><span class="lineNum">   12837 </span>            : </a>
+<a name="12838"><span class="lineNum">   12838 </span>            : }</a>
+<a name="12839"><span class="lineNum">   12839 </span>            : </a>
+<a name="12840"><span class="lineNum">   12840 </span>            : </a>
+<a name="12841"><span class="lineNum">   12841 </span>            : }</a>
+<a name="12842"><span class="lineNum">   12842 </span>            : }</a>
+<a name="12843"><span class="lineNum">   12843 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12844"><span class="lineNum">   12844 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="12845"><span class="lineNum">   12845 </span>            : </a>
+<a name="12846"><span class="lineNum">   12846 </span>            : </a>
+<a name="12847"><span class="lineNum">   12847 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12848"><span class="lineNum">   12848 </span>            : namespace PLMD{</a>
+<a name="12849"><span class="lineNum">   12849 </span>            : namespace lapack{</a>
+<a name="12850"><span class="lineNum">   12850 </span>            : using namespace blas;</a>
+<a name="12851"><span class="lineNum">   12851 </span>            : void</a>
+<a name="12852"><span class="lineNum">   12852 </span><span class="lineCov">     569964 : PLUMED_BLAS_F77_FUNC(dormtr,DORMTR)(const char *side, </span></a>
+<a name="12853"><span class="lineNum">   12853 </span>            :         const char *uplo,</a>
+<a name="12854"><span class="lineNum">   12854 </span>            :         const char *trans, </a>
+<a name="12855"><span class="lineNum">   12855 </span>            :         int *m, </a>
+<a name="12856"><span class="lineNum">   12856 </span>            :         int *n,</a>
+<a name="12857"><span class="lineNum">   12857 </span>            :         double *a, </a>
+<a name="12858"><span class="lineNum">   12858 </span>            :         int *lda, </a>
+<a name="12859"><span class="lineNum">   12859 </span>            :         double *tau, </a>
+<a name="12860"><span class="lineNum">   12860 </span>            :         double *c__, </a>
+<a name="12861"><span class="lineNum">   12861 </span>            :         int *ldc,</a>
+<a name="12862"><span class="lineNum">   12862 </span>            :         double *work, </a>
+<a name="12863"><span class="lineNum">   12863 </span>            :         int *lwork, </a>
+<a name="12864"><span class="lineNum">   12864 </span>            :         int *info)</a>
+<a name="12865"><span class="lineNum">   12865 </span>            : {</a>
+<a name="12866"><span class="lineNum">   12866 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__2;</a>
+<a name="12867"><span class="lineNum">   12867 </span>            : </a>
+<a name="12868"><span class="lineNum">   12868 </span>            :     int i1, i2, nb, mi, ni, nq, nw;</a>
+<a name="12869"><span class="lineNum">   12869 </span>            :     int left;</a>
+<a name="12870"><span class="lineNum">   12870 </span>            :     int iinfo;</a>
+<a name="12871"><span class="lineNum">   12871 </span>            :     int upper;</a>
+<a name="12872"><span class="lineNum">   12872 </span>            :     int lwkopt;</a>
+<a name="12873"><span class="lineNum">   12873 </span>            :     int lquery;</a>
+<a name="12874"><span class="lineNum">   12874 </span>            : </a>
+<a name="12875"><span class="lineNum">   12875 </span>            : </a>
+<a name="12876"><span class="lineNum">   12876 </span><span class="lineCov">     569964 :     a_dim1 = *lda;</span></a>
+<a name="12877"><span class="lineNum">   12877 </span><span class="lineCov">     569964 :     a_offset = 1 + a_dim1;</span></a>
+<a name="12878"><span class="lineNum">   12878 </span><span class="lineCov">     569964 :     a -= a_offset;</span></a>
+<a name="12879"><span class="lineNum">   12879 </span>            :     --tau;</a>
+<a name="12880"><span class="lineNum">   12880 </span><span class="lineCov">     569964 :     c_dim1 = *ldc;</span></a>
+<a name="12881"><span class="lineNum">   12881 </span><span class="lineCov">     569964 :     c_offset = 1 + c_dim1;</span></a>
+<a name="12882"><span class="lineNum">   12882 </span><span class="lineCov">     569964 :     c__ -= c_offset;</span></a>
+<a name="12883"><span class="lineNum">   12883 </span>            :     --work;</a>
+<a name="12884"><span class="lineNum">   12884 </span>            : </a>
+<a name="12885"><span class="lineNum">   12885 </span><span class="lineCov">     569964 :     *info = 0;</span></a>
+<a name="12886"><span class="lineNum">   12886 </span><span class="lineCov">     569964 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="12887"><span class="lineNum">   12887 </span><span class="lineCov">     569964 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="12888"><span class="lineNum">   12888 </span><span class="lineCov">     569964 :     lquery = *lwork == -1;</span></a>
+<a name="12889"><span class="lineNum">   12889 </span>            : </a>
+<a name="12890"><span class="lineNum">   12890 </span><span class="lineCov">     569964 :     if (left) {</span></a>
+<a name="12891"><span class="lineNum">   12891 </span><span class="lineCov">     569964 :         nq = *m;</span></a>
+<a name="12892"><span class="lineNum">   12892 </span><span class="lineCov">     569964 :         nw = *n;</span></a>
+<a name="12893"><span class="lineNum">   12893 </span>            :     } else {</a>
+<a name="12894"><span class="lineNum">   12894 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="12895"><span class="lineNum">   12895 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="12896"><span class="lineNum">   12896 </span>            :     }</a>
+<a name="12897"><span class="lineNum">   12897 </span>            : </a>
+<a name="12898"><span class="lineNum">   12898 </span>            : </a>
+<a name="12899"><span class="lineNum">   12899 </span>            :     nb = DORMQL_BLOCKSIZE;</a>
+<a name="12900"><span class="lineNum">   12900 </span><span class="lineCov">     569964 :     lwkopt = nw * nb;</span></a>
+<a name="12901"><span class="lineNum">   12901 </span><span class="lineCov">     569964 :     work[1] = (double) lwkopt;</span></a>
+<a name="12902"><span class="lineNum">   12902 </span>            :     </a>
+<a name="12903"><span class="lineNum">   12903 </span><span class="lineCov">     569964 :     if (*info != 0) {</span></a>
+<a name="12904"><span class="lineNum">   12904 </span>            :         i__2 = -(*info);</a>
+<a name="12905"><span class="lineNum">   12905 </span>            :         return;</a>
+<a name="12906"><span class="lineNum">   12906 </span><span class="lineCov">     569964 :     } else if (lquery) {</span></a>
+<a name="12907"><span class="lineNum">   12907 </span>            :         return;</a>
+<a name="12908"><span class="lineNum">   12908 </span>            :     }</a>
+<a name="12909"><span class="lineNum">   12909 </span>            : </a>
+<a name="12910"><span class="lineNum">   12910 </span><span class="lineCov">     569964 :     if (*m == 0 || *n == 0 || nq == 1) {</span></a>
+<a name="12911"><span class="lineNum">   12911 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="12912"><span class="lineNum">   12912 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="12913"><span class="lineNum">   12913 </span>            :     }</a>
+<a name="12914"><span class="lineNum">   12914 </span>            : </a>
+<a name="12915"><span class="lineNum">   12915 </span><span class="lineCov">     569964 :     if (left) {</span></a>
+<a name="12916"><span class="lineNum">   12916 </span><span class="lineCov">     569964 :         mi = *m - 1;</span></a>
+<a name="12917"><span class="lineNum">   12917 </span><span class="lineCov">     569964 :         ni = *n;</span></a>
+<a name="12918"><span class="lineNum">   12918 </span>            :     } else {</a>
+<a name="12919"><span class="lineNum">   12919 </span><span class="lineNoCov">          0 :         mi = *m;</span></a>
+<a name="12920"><span class="lineNum">   12920 </span><span class="lineNoCov">          0 :         ni = *n - 1;</span></a>
+<a name="12921"><span class="lineNum">   12921 </span>            :     }</a>
+<a name="12922"><span class="lineNum">   12922 </span>            : </a>
+<a name="12923"><span class="lineNum">   12923 </span><span class="lineCov">     569964 :     if (upper) {</span></a>
+<a name="12924"><span class="lineNum">   12924 </span><span class="lineCov">     569964 :         i__2 = nq - 1;</span></a>
+<a name="12925"><span class="lineNum">   12925 </span><span class="lineCov">     569964 :         PLUMED_BLAS_F77_FUNC(dormql,DORMQL)(side, trans, &amp;mi, &amp;ni, &amp;i__2, &amp;a[(a_dim1 &lt;&lt; 1) + 1], lda, &amp;</span></a>
+<a name="12926"><span class="lineNum">   12926 </span>            :                 tau[1], &amp;c__[c_offset], ldc, &amp;work[1], lwork, &amp;iinfo);</a>
+<a name="12927"><span class="lineNum">   12927 </span>            :     } else {</a>
+<a name="12928"><span class="lineNum">   12928 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="12929"><span class="lineNum">   12929 </span>            :             i1 = 2;</a>
+<a name="12930"><span class="lineNum">   12930 </span>            :             i2 = 1;</a>
+<a name="12931"><span class="lineNum">   12931 </span>            :         } else {</a>
+<a name="12932"><span class="lineNum">   12932 </span>            :             i1 = 1;</a>
+<a name="12933"><span class="lineNum">   12933 </span>            :             i2 = 2;</a>
+<a name="12934"><span class="lineNum">   12934 </span>            :         }</a>
+<a name="12935"><span class="lineNum">   12935 </span><span class="lineNoCov">          0 :         i__2 = nq - 1;</span></a>
+<a name="12936"><span class="lineNum">   12936 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dormqr,DORMQR)(side, trans, &amp;mi, &amp;ni, &amp;i__2, &amp;a[a_dim1 + 2], lda, &amp;tau[1], &amp;</span></a>
+<a name="12937"><span class="lineNum">   12937 </span><span class="lineNoCov">          0 :                 c__[i1 + i2 * c_dim1], ldc, &amp;work[1], lwork, &amp;iinfo);</span></a>
+<a name="12938"><span class="lineNum">   12938 </span>            :     }</a>
+<a name="12939"><span class="lineNum">   12939 </span><span class="lineCov">     569964 :     work[1] = (double) lwkopt;</span></a>
+<a name="12940"><span class="lineNum">   12940 </span><span class="lineCov">     569964 :     return;</span></a>
+<a name="12941"><span class="lineNum">   12941 </span>            : </a>
+<a name="12942"><span class="lineNum">   12942 </span>            : }</a>
+<a name="12943"><span class="lineNum">   12943 </span>            : </a>
+<a name="12944"><span class="lineNum">   12944 </span>            : </a>
+<a name="12945"><span class="lineNum">   12945 </span>            : }</a>
+<a name="12946"><span class="lineNum">   12946 </span>            : }</a>
+<a name="12947"><span class="lineNum">   12947 </span>            : #include &lt;cmath&gt;</a>
+<a name="12948"><span class="lineNum">   12948 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="12949"><span class="lineNum">   12949 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="12950"><span class="lineNum">   12950 </span>            : </a>
+<a name="12951"><span class="lineNum">   12951 </span>            : #include &quot;real.h&quot;</a>
+<a name="12952"><span class="lineNum">   12952 </span>            : </a>
+<a name="12953"><span class="lineNum">   12953 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="12954"><span class="lineNum">   12954 </span>            : namespace PLMD{</a>
+<a name="12955"><span class="lineNum">   12955 </span>            : namespace lapack{</a>
+<a name="12956"><span class="lineNum">   12956 </span>            : using namespace blas;</a>
+<a name="12957"><span class="lineNum">   12957 </span>            : void</a>
+<a name="12958"><span class="lineNum">   12958 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dstebz,DSTEBZ)(const char *range, </span></a>
+<a name="12959"><span class="lineNum">   12959 </span>            :                         const char *order,</a>
+<a name="12960"><span class="lineNum">   12960 </span>            :                         int *n,</a>
+<a name="12961"><span class="lineNum">   12961 </span>            :                         double *vl, </a>
+<a name="12962"><span class="lineNum">   12962 </span>            :                         double *vu, </a>
+<a name="12963"><span class="lineNum">   12963 </span>            :                         int *il,</a>
+<a name="12964"><span class="lineNum">   12964 </span>            :                         int *iu,</a>
+<a name="12965"><span class="lineNum">   12965 </span>            :                         double *abstol, </a>
+<a name="12966"><span class="lineNum">   12966 </span>            :                         double *d__,</a>
+<a name="12967"><span class="lineNum">   12967 </span>            :                         double *e,</a>
+<a name="12968"><span class="lineNum">   12968 </span>            :                         int *m, </a>
+<a name="12969"><span class="lineNum">   12969 </span>            :                         int *nsplit, </a>
+<a name="12970"><span class="lineNum">   12970 </span>            :                         double *w,</a>
+<a name="12971"><span class="lineNum">   12971 </span>            :                         int *iblock,</a>
+<a name="12972"><span class="lineNum">   12972 </span>            :                         int *isplit,</a>
+<a name="12973"><span class="lineNum">   12973 </span>            :                         double *work, </a>
+<a name="12974"><span class="lineNum">   12974 </span>            :                         int *iwork, </a>
+<a name="12975"><span class="lineNum">   12975 </span>            :                         int *info)</a>
+<a name="12976"><span class="lineNum">   12976 </span>            : {</a>
+<a name="12977"><span class="lineNum">   12977 </span>            :     int i__1, i__2, i__3;</a>
+<a name="12978"><span class="lineNum">   12978 </span>            :     double d__1, d__2, d__3, d__4, d__5;</a>
+<a name="12979"><span class="lineNum">   12979 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="12980"><span class="lineNum">   12980 </span><span class="lineNoCov">          0 :     int c__3 = 3;</span></a>
+<a name="12981"><span class="lineNum">   12981 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="12982"><span class="lineNum">   12982 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="12983"><span class="lineNum">   12983 </span>            : </a>
+<a name="12984"><span class="lineNum">   12984 </span>            :     int j, ib, jb, ie, je, nb;</a>
+<a name="12985"><span class="lineNum">   12985 </span>            :     double gl;</a>
+<a name="12986"><span class="lineNum">   12986 </span>            :     int im, in;</a>
+<a name="12987"><span class="lineNum">   12987 </span>            :     double gu;</a>
+<a name="12988"><span class="lineNum">   12988 </span>            :     int iw;</a>
+<a name="12989"><span class="lineNum">   12989 </span>            :     double wl, wu;</a>
+<a name="12990"><span class="lineNum">   12990 </span>            :     int nwl;</a>
+<a name="12991"><span class="lineNum">   12991 </span>            :     double ulp, wlu, wul;</a>
+<a name="12992"><span class="lineNum">   12992 </span>            :     int nwu;</a>
+<a name="12993"><span class="lineNum">   12993 </span>            :     double tmp1, tmp2;</a>
+<a name="12994"><span class="lineNum">   12994 </span>            :     int iend, ioff, iout, itmp1, jdisc;</a>
+<a name="12995"><span class="lineNum">   12995 </span>            :     int iinfo;</a>
+<a name="12996"><span class="lineNum">   12996 </span>            :     double atoli;</a>
+<a name="12997"><span class="lineNum">   12997 </span>            :     int iwoff;</a>
+<a name="12998"><span class="lineNum">   12998 </span>            :     double bnorm;</a>
+<a name="12999"><span class="lineNum">   12999 </span>            :     int itmax;</a>
+<a name="13000"><span class="lineNum">   13000 </span>            :     double wkill, rtoli, tnorm;</a>
+<a name="13001"><span class="lineNum">   13001 </span>            :     int ibegin;</a>
+<a name="13002"><span class="lineNum">   13002 </span>            :     int irange, idiscl;</a>
+<a name="13003"><span class="lineNum">   13003 </span>            :     int idumma[1];</a>
+<a name="13004"><span class="lineNum">   13004 </span>            :     int idiscu, iorder;</a>
+<a name="13005"><span class="lineNum">   13005 </span>            :     int ncnvrg;</a>
+<a name="13006"><span class="lineNum">   13006 </span>            :     double pivmin;</a>
+<a name="13007"><span class="lineNum">   13007 </span>            :     int toofew;</a>
+<a name="13008"><span class="lineNum">   13008 </span>            :     const double safemn = PLUMED_GMX_DOUBLE_MIN*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="13009"><span class="lineNum">   13009 </span>            : </a>
+<a name="13010"><span class="lineNum">   13010 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="13011"><span class="lineNum">   13011 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="13012"><span class="lineNum">   13012 </span><span class="lineNoCov">          0 :     --isplit;</span></a>
+<a name="13013"><span class="lineNum">   13013 </span><span class="lineNoCov">          0 :     --iblock;</span></a>
+<a name="13014"><span class="lineNum">   13014 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="13015"><span class="lineNum">   13015 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="13016"><span class="lineNum">   13016 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="13017"><span class="lineNum">   13017 </span>            : </a>
+<a name="13018"><span class="lineNum">   13018 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="13019"><span class="lineNum">   13019 </span>            : </a>
+<a name="13020"><span class="lineNum">   13020 </span><span class="lineNoCov">          0 :     if (*range=='A' || *range=='a') {</span></a>
+<a name="13021"><span class="lineNum">   13021 </span>            :         irange = 1;</a>
+<a name="13022"><span class="lineNum">   13022 </span><span class="lineNoCov">          0 :     } else if (*range=='V' || *range=='v') {</span></a>
+<a name="13023"><span class="lineNum">   13023 </span>            :         irange = 2;</a>
+<a name="13024"><span class="lineNum">   13024 </span>            :     } else if (*range=='I' || *range=='i') {</a>
+<a name="13025"><span class="lineNum">   13025 </span>            :         irange = 3;</a>
+<a name="13026"><span class="lineNum">   13026 </span>            :     } else {</a>
+<a name="13027"><span class="lineNum">   13027 </span>            :         irange = 0;</a>
+<a name="13028"><span class="lineNum">   13028 </span>            :     }</a>
+<a name="13029"><span class="lineNum">   13029 </span>            : </a>
+<a name="13030"><span class="lineNum">   13030 </span><span class="lineNoCov">          0 :     if (*order=='B' || *order=='b') {</span></a>
+<a name="13031"><span class="lineNum">   13031 </span>            :         iorder = 2;</a>
+<a name="13032"><span class="lineNum">   13032 </span><span class="lineNoCov">          0 :     } else if (*order=='E' || *order=='e') {</span></a>
+<a name="13033"><span class="lineNum">   13033 </span>            :         iorder = 1;</a>
+<a name="13034"><span class="lineNum">   13034 </span>            :     } else {</a>
+<a name="13035"><span class="lineNum">   13035 </span>            :         iorder = 0;</a>
+<a name="13036"><span class="lineNum">   13036 </span>            :     }</a>
+<a name="13037"><span class="lineNum">   13037 </span>            : </a>
+<a name="13038"><span class="lineNum">   13038 </span><span class="lineNoCov">          0 :     if (irange &lt;= 0) {</span></a>
+<a name="13039"><span class="lineNum">   13039 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="13040"><span class="lineNum">   13040 </span><span class="lineNoCov">          0 :     } else if (iorder &lt;= 0) {</span></a>
+<a name="13041"><span class="lineNum">   13041 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="13042"><span class="lineNum">   13042 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="13043"><span class="lineNum">   13043 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="13044"><span class="lineNum">   13044 </span><span class="lineNoCov">          0 :     } else if (irange == 2) {</span></a>
+<a name="13045"><span class="lineNum">   13045 </span><span class="lineNoCov">          0 :         if (*vl &gt;= *vu) {</span></a>
+<a name="13046"><span class="lineNum">   13046 </span><span class="lineNoCov">          0 :             *info = -5;</span></a>
+<a name="13047"><span class="lineNum">   13047 </span>            :         }</a>
+<a name="13048"><span class="lineNum">   13048 </span><span class="lineNoCov">          0 :     } else if (irange == 3 &amp;&amp; (*il &lt; 1 || *il &gt; (*n))) {</span></a>
+<a name="13049"><span class="lineNum">   13049 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="13050"><span class="lineNum">   13050 </span><span class="lineNoCov">          0 :     } else if (irange == 3 &amp;&amp; (*iu &lt; ((*n&lt;*il) ? *n : *il) || *iu &gt; *n)) {</span></a>
+<a name="13051"><span class="lineNum">   13051 </span><span class="lineNoCov">          0 :         *info = -7;</span></a>
+<a name="13052"><span class="lineNum">   13052 </span>            :     }</a>
+<a name="13053"><span class="lineNum">   13053 </span>            : </a>
+<a name="13054"><span class="lineNum">   13054 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="13055"><span class="lineNum">   13055 </span>            :         return;</a>
+<a name="13056"><span class="lineNum">   13056 </span>            :     }</a>
+<a name="13057"><span class="lineNum">   13057 </span>            : </a>
+<a name="13058"><span class="lineNum">   13058 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="13059"><span class="lineNum">   13059 </span>            :     ncnvrg = 0;</a>
+<a name="13060"><span class="lineNum">   13060 </span>            :     toofew = 0;</a>
+<a name="13061"><span class="lineNum">   13061 </span>            : </a>
+<a name="13062"><span class="lineNum">   13062 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="13063"><span class="lineNum">   13063 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="13064"><span class="lineNum">   13064 </span>            :         return;</a>
+<a name="13065"><span class="lineNum">   13065 </span>            :     }</a>
+<a name="13066"><span class="lineNum">   13066 </span>            : </a>
+<a name="13067"><span class="lineNum">   13067 </span><span class="lineNoCov">          0 :     if (irange == 3 &amp;&amp; *il == 1 &amp;&amp; *iu == *n) {</span></a>
+<a name="13068"><span class="lineNum">   13068 </span>            :         irange = 1;</a>
+<a name="13069"><span class="lineNum">   13069 </span>            :     }</a>
+<a name="13070"><span class="lineNum">   13070 </span>            : </a>
+<a name="13071"><span class="lineNum">   13071 </span>            :     ulp = 2*PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="13072"><span class="lineNum">   13072 </span><span class="lineNoCov">          0 :     rtoli = ulp * 2.;</span></a>
+<a name="13073"><span class="lineNum">   13073 </span>            :     nb = DSTEBZ_BLOCKSIZE;</a>
+<a name="13074"><span class="lineNum">   13074 </span>            :     // cppcheck-suppress knownConditionTrueFalse</a>
+<a name="13075"><span class="lineNum">   13075 </span>            :     if (nb &lt;= 1) {</a>
+<a name="13076"><span class="lineNum">   13076 </span><span class="lineNoCov">          0 :         nb = 0;</span></a>
+<a name="13077"><span class="lineNum">   13077 </span>            :     }</a>
+<a name="13078"><span class="lineNum">   13078 </span>            : </a>
+<a name="13079"><span class="lineNum">   13079 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="13080"><span class="lineNum">   13080 </span><span class="lineNoCov">          0 :         *nsplit = 1;</span></a>
+<a name="13081"><span class="lineNum">   13081 </span><span class="lineNoCov">          0 :         isplit[1] = 1;</span></a>
+<a name="13082"><span class="lineNum">   13082 </span><span class="lineNoCov">          0 :         if (irange == 2 &amp;&amp; (*vl &gt;= d__[1] || *vu &lt; d__[1])) {</span></a>
+<a name="13083"><span class="lineNum">   13083 </span><span class="lineNoCov">          0 :             *m = 0;</span></a>
+<a name="13084"><span class="lineNum">   13084 </span>            :         } else {</a>
+<a name="13085"><span class="lineNum">   13085 </span><span class="lineNoCov">          0 :             w[1] = d__[1];</span></a>
+<a name="13086"><span class="lineNum">   13086 </span><span class="lineNoCov">          0 :             iblock[1] = 1;</span></a>
+<a name="13087"><span class="lineNum">   13087 </span><span class="lineNoCov">          0 :             *m = 1;</span></a>
+<a name="13088"><span class="lineNum">   13088 </span>            :         }</a>
+<a name="13089"><span class="lineNum">   13089 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="13090"><span class="lineNum">   13090 </span>            :     }</a>
+<a name="13091"><span class="lineNum">   13091 </span>            : </a>
+<a name="13092"><span class="lineNum">   13092 </span><span class="lineNoCov">          0 :     *nsplit = 1;</span></a>
+<a name="13093"><span class="lineNum">   13093 </span><span class="lineNoCov">          0 :     work[*n] = 0.;</span></a>
+<a name="13094"><span class="lineNum">   13094 </span><span class="lineNoCov">          0 :     pivmin = 1.;</span></a>
+<a name="13095"><span class="lineNum">   13095 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="13096"><span class="lineNum">   13096 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="13097"><span class="lineNum">   13097 </span><span class="lineNoCov">          0 :         d__1 = e[j - 1];</span></a>
+<a name="13098"><span class="lineNum">   13098 </span><span class="lineNoCov">          0 :         tmp1 = d__1 * d__1;</span></a>
+<a name="13099"><span class="lineNum">   13099 </span>            :         d__2 = ulp;</a>
+<a name="13100"><span class="lineNum">   13100 </span><span class="lineNoCov">          0 :         if (std::abs(d__[j] * d__[j - 1]) * (d__2 * d__2) + safemn </span></a>
+<a name="13101"><span class="lineNum">   13101 </span>            :                 &gt; tmp1) {</a>
+<a name="13102"><span class="lineNum">   13102 </span><span class="lineNoCov">          0 :             isplit[*nsplit] = j - 1;</span></a>
+<a name="13103"><span class="lineNum">   13103 </span><span class="lineNoCov">          0 :             ++(*nsplit);</span></a>
+<a name="13104"><span class="lineNum">   13104 </span><span class="lineNoCov">          0 :             work[j - 1] = 0.;</span></a>
+<a name="13105"><span class="lineNum">   13105 </span>            :         } else {</a>
+<a name="13106"><span class="lineNum">   13106 </span><span class="lineNoCov">          0 :             work[j - 1] = tmp1;</span></a>
+<a name="13107"><span class="lineNum">   13107 </span><span class="lineNoCov">          0 :             pivmin = (pivmin&gt;tmp1) ? pivmin : tmp1;</span></a>
+<a name="13108"><span class="lineNum">   13108 </span>            :         }</a>
+<a name="13109"><span class="lineNum">   13109 </span>            :     }</a>
+<a name="13110"><span class="lineNum">   13110 </span><span class="lineNoCov">          0 :     isplit[*nsplit] = *n;</span></a>
+<a name="13111"><span class="lineNum">   13111 </span><span class="lineNoCov">          0 :     pivmin *= safemn;</span></a>
+<a name="13112"><span class="lineNum">   13112 </span>            : </a>
+<a name="13113"><span class="lineNum">   13113 </span><span class="lineNoCov">          0 :     if (irange == 3) {</span></a>
+<a name="13114"><span class="lineNum">   13114 </span>            : </a>
+<a name="13115"><span class="lineNum">   13115 </span><span class="lineNoCov">          0 :         gu = d__[1];</span></a>
+<a name="13116"><span class="lineNum">   13116 </span>            :         gl = d__[1];</a>
+<a name="13117"><span class="lineNum">   13117 </span>            :         tmp1 = 0.;</a>
+<a name="13118"><span class="lineNum">   13118 </span>            : </a>
+<a name="13119"><span class="lineNum">   13119 </span>            :         i__1 = *n - 1;</a>
+<a name="13120"><span class="lineNum">   13120 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="13121"><span class="lineNum">   13121 </span><span class="lineNoCov">          0 :             tmp2 =  std::sqrt(work[j]);</span></a>
+<a name="13122"><span class="lineNum">   13122 </span><span class="lineNoCov">          0 :             d__1 = gu, d__2 = d__[j] + tmp1 + tmp2;</span></a>
+<a name="13123"><span class="lineNum">   13123 </span><span class="lineNoCov">          0 :             gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13124"><span class="lineNum">   13124 </span><span class="lineNoCov">          0 :             d__1 = gl, d__2 = d__[j] - tmp1 - tmp2;</span></a>
+<a name="13125"><span class="lineNum">   13125 </span><span class="lineNoCov">          0 :             gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="13126"><span class="lineNum">   13126 </span>            :             tmp1 = tmp2;</a>
+<a name="13127"><span class="lineNum">   13127 </span>            :         }</a>
+<a name="13128"><span class="lineNum">   13128 </span>            : </a>
+<a name="13129"><span class="lineNum">   13129 </span><span class="lineNoCov">          0 :         d__1 = gu, d__2 = d__[*n] + tmp1;</span></a>
+<a name="13130"><span class="lineNum">   13130 </span><span class="lineNoCov">          0 :         gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13131"><span class="lineNum">   13131 </span><span class="lineNoCov">          0 :         d__1 = gl, d__2 = d__[*n] - tmp1;</span></a>
+<a name="13132"><span class="lineNum">   13132 </span><span class="lineNoCov">          0 :         gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="13133"><span class="lineNum">   13133 </span>            :         d__1 = std::abs(gl);</a>
+<a name="13134"><span class="lineNum">   13134 </span>            :         d__2 = std::abs(gu);</a>
+<a name="13135"><span class="lineNum">   13135 </span><span class="lineNoCov">          0 :         tnorm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13136"><span class="lineNum">   13136 </span><span class="lineNoCov">          0 :         gl = gl - tnorm * 2. * ulp * *n - pivmin * 4.;</span></a>
+<a name="13137"><span class="lineNum">   13137 </span><span class="lineNoCov">          0 :         gu = gu + tnorm * 2. * ulp * *n + pivmin * 2.;</span></a>
+<a name="13138"><span class="lineNum">   13138 </span>            : </a>
+<a name="13139"><span class="lineNum">   13139 </span><span class="lineNoCov">          0 :         itmax = (int) ((std::log(tnorm + pivmin) - std::log(pivmin)) / std::log(2.)) + 2;</span></a>
+<a name="13140"><span class="lineNum">   13140 </span><span class="lineNoCov">          0 :         if (*abstol &lt;= 0.) {</span></a>
+<a name="13141"><span class="lineNum">   13141 </span><span class="lineNoCov">          0 :             atoli = ulp * tnorm;</span></a>
+<a name="13142"><span class="lineNum">   13142 </span>            :         } else {</a>
+<a name="13143"><span class="lineNum">   13143 </span><span class="lineNoCov">          0 :             atoli = *abstol;</span></a>
+<a name="13144"><span class="lineNum">   13144 </span>            :         }</a>
+<a name="13145"><span class="lineNum">   13145 </span>            : </a>
+<a name="13146"><span class="lineNum">   13146 </span><span class="lineNoCov">          0 :         work[*n + 1] = gl;</span></a>
+<a name="13147"><span class="lineNum">   13147 </span><span class="lineNoCov">          0 :         work[*n + 2] = gl;</span></a>
+<a name="13148"><span class="lineNum">   13148 </span><span class="lineNoCov">          0 :         work[*n + 3] = gu;</span></a>
+<a name="13149"><span class="lineNum">   13149 </span><span class="lineNoCov">          0 :         work[*n + 4] = gu;</span></a>
+<a name="13150"><span class="lineNum">   13150 </span><span class="lineNoCov">          0 :         work[*n + 5] = gl;</span></a>
+<a name="13151"><span class="lineNum">   13151 </span><span class="lineNoCov">          0 :         work[*n + 6] = gu;</span></a>
+<a name="13152"><span class="lineNum">   13152 </span><span class="lineNoCov">          0 :         iwork[1] = -1;</span></a>
+<a name="13153"><span class="lineNum">   13153 </span><span class="lineNoCov">          0 :         iwork[2] = -1;</span></a>
+<a name="13154"><span class="lineNum">   13154 </span><span class="lineNoCov">          0 :         iwork[3] = *n + 1;</span></a>
+<a name="13155"><span class="lineNum">   13155 </span><span class="lineNoCov">          0 :         iwork[4] = *n + 1;</span></a>
+<a name="13156"><span class="lineNum">   13156 </span><span class="lineNoCov">          0 :         iwork[5] = *il - 1;</span></a>
+<a name="13157"><span class="lineNum">   13157 </span><span class="lineNoCov">          0 :         iwork[6] = *iu;</span></a>
+<a name="13158"><span class="lineNum">   13158 </span>            : </a>
+<a name="13159"><span class="lineNum">   13159 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlaebz,DLAEBZ)(&amp;c__3, &amp;itmax, n, &amp;c__2, &amp;c__2, &amp;nb, &amp;atoli, &amp;rtoli, &amp;pivmin, </span></a>
+<a name="13160"><span class="lineNum">   13160 </span><span class="lineNoCov">          0 :                 &amp;d__[1], &amp;e[1], &amp;work[1], &amp;iwork[5], &amp;work[*n + 1], &amp;work[*n </span></a>
+<a name="13161"><span class="lineNum">   13161 </span><span class="lineNoCov">          0 :                 + 5], &amp;iout, &amp;iwork[1], &amp;w[1], &amp;iblock[1], &amp;iinfo);</span></a>
+<a name="13162"><span class="lineNum">   13162 </span>            : </a>
+<a name="13163"><span class="lineNum">   13163 </span><span class="lineNoCov">          0 :         if (iwork[6] == *iu) {</span></a>
+<a name="13164"><span class="lineNum">   13164 </span><span class="lineNoCov">          0 :             wl = work[*n + 1];</span></a>
+<a name="13165"><span class="lineNum">   13165 </span><span class="lineNoCov">          0 :             wlu = work[*n + 3];</span></a>
+<a name="13166"><span class="lineNum">   13166 </span><span class="lineNoCov">          0 :             nwl = iwork[1];</span></a>
+<a name="13167"><span class="lineNum">   13167 </span><span class="lineNoCov">          0 :             wu = work[*n + 4];</span></a>
+<a name="13168"><span class="lineNum">   13168 </span><span class="lineNoCov">          0 :             wul = work[*n + 2];</span></a>
+<a name="13169"><span class="lineNum">   13169 </span><span class="lineNoCov">          0 :             nwu = iwork[4];</span></a>
+<a name="13170"><span class="lineNum">   13170 </span>            :         } else {</a>
+<a name="13171"><span class="lineNum">   13171 </span><span class="lineNoCov">          0 :             wl = work[*n + 2];</span></a>
+<a name="13172"><span class="lineNum">   13172 </span><span class="lineNoCov">          0 :             wlu = work[*n + 4];</span></a>
+<a name="13173"><span class="lineNum">   13173 </span><span class="lineNoCov">          0 :             nwl = iwork[2];</span></a>
+<a name="13174"><span class="lineNum">   13174 </span><span class="lineNoCov">          0 :             wu = work[*n + 3];</span></a>
+<a name="13175"><span class="lineNum">   13175 </span><span class="lineNoCov">          0 :             wul = work[*n + 1];</span></a>
+<a name="13176"><span class="lineNum">   13176 </span><span class="lineNoCov">          0 :             nwu = iwork[3];</span></a>
+<a name="13177"><span class="lineNum">   13177 </span>            :         }</a>
+<a name="13178"><span class="lineNum">   13178 </span>            : </a>
+<a name="13179"><span class="lineNum">   13179 </span><span class="lineNoCov">          0 :         if (nwl &lt; 0 || nwl &gt;= *n || nwu &lt; 1 || nwu &gt; *n) {</span></a>
+<a name="13180"><span class="lineNum">   13180 </span><span class="lineNoCov">          0 :             *info = 4;</span></a>
+<a name="13181"><span class="lineNum">   13181 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="13182"><span class="lineNum">   13182 </span>            :         }</a>
+<a name="13183"><span class="lineNum">   13183 </span>            :     } else {</a>
+<a name="13184"><span class="lineNum">   13184 </span>            : </a>
+<a name="13185"><span class="lineNum">   13185 </span>            : </a>
+<a name="13186"><span class="lineNum">   13186 </span>            :       /* avoid warnings for high gcc optimization */</a>
+<a name="13187"><span class="lineNum">   13187 </span>            :       wlu = wul = 1.0;</a>
+<a name="13188"><span class="lineNum">   13188 </span>            : </a>
+<a name="13189"><span class="lineNum">   13189 </span><span class="lineNoCov">          0 :         d__3 = std::abs(d__[1]) + std::abs(e[1]);</span></a>
+<a name="13190"><span class="lineNum">   13190 </span><span class="lineNoCov">          0 :         d__4 = std::abs(d__[*n]) + std::abs(e[*n - 1]);</span></a>
+<a name="13191"><span class="lineNum">   13191 </span><span class="lineNoCov">          0 :         tnorm = (d__3&gt;d__4) ? d__3 : d__4;</span></a>
+<a name="13192"><span class="lineNum">   13192 </span>            : </a>
+<a name="13193"><span class="lineNum">   13193 </span>            :         i__1 = *n - 1;</a>
+<a name="13194"><span class="lineNum">   13194 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="13195"><span class="lineNum">   13195 </span>            :             d__4 = tnorm;</a>
+<a name="13196"><span class="lineNum">   13196 </span><span class="lineNoCov">          0 :             d__5 = std::abs(d__[j]) + std::abs(e[j - 1]) + std::abs(e[j]);</span></a>
+<a name="13197"><span class="lineNum">   13197 </span><span class="lineNoCov">          0 :             tnorm = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="13198"><span class="lineNum">   13198 </span>            :         }</a>
+<a name="13199"><span class="lineNum">   13199 </span>            : </a>
+<a name="13200"><span class="lineNum">   13200 </span><span class="lineNoCov">          0 :         if (*abstol &lt;= 0.) {</span></a>
+<a name="13201"><span class="lineNum">   13201 </span><span class="lineNoCov">          0 :             atoli = ulp * tnorm;</span></a>
+<a name="13202"><span class="lineNum">   13202 </span>            :         } else {</a>
+<a name="13203"><span class="lineNum">   13203 </span><span class="lineNoCov">          0 :             atoli = *abstol;</span></a>
+<a name="13204"><span class="lineNum">   13204 </span>            :         }</a>
+<a name="13205"><span class="lineNum">   13205 </span>            : </a>
+<a name="13206"><span class="lineNum">   13206 </span><span class="lineNoCov">          0 :         if (irange == 2) {</span></a>
+<a name="13207"><span class="lineNum">   13207 </span><span class="lineNoCov">          0 :             wl = *vl;</span></a>
+<a name="13208"><span class="lineNum">   13208 </span><span class="lineNoCov">          0 :             wu = *vu;</span></a>
+<a name="13209"><span class="lineNum">   13209 </span>            :         } else {</a>
+<a name="13210"><span class="lineNum">   13210 </span>            :             wl = 0.;</a>
+<a name="13211"><span class="lineNum">   13211 </span>            :             wu = 0.;</a>
+<a name="13212"><span class="lineNum">   13212 </span>            :         }</a>
+<a name="13213"><span class="lineNum">   13213 </span>            :     }</a>
+<a name="13214"><span class="lineNum">   13214 </span>            : </a>
+<a name="13215"><span class="lineNum">   13215 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="13216"><span class="lineNum">   13216 </span>            :     iend = 0;</a>
+<a name="13217"><span class="lineNum">   13217 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="13218"><span class="lineNum">   13218 </span>            :     nwl = 0;</a>
+<a name="13219"><span class="lineNum">   13219 </span>            :     nwu = 0;</a>
+<a name="13220"><span class="lineNum">   13220 </span>            : </a>
+<a name="13221"><span class="lineNum">   13221 </span><span class="lineNoCov">          0 :     i__1 = *nsplit;</span></a>
+<a name="13222"><span class="lineNum">   13222 </span><span class="lineNoCov">          0 :     for (jb = 1; jb &lt;= i__1; ++jb) {</span></a>
+<a name="13223"><span class="lineNum">   13223 </span>            :         ioff = iend;</a>
+<a name="13224"><span class="lineNum">   13224 </span><span class="lineNoCov">          0 :         ibegin = ioff + 1;</span></a>
+<a name="13225"><span class="lineNum">   13225 </span><span class="lineNoCov">          0 :         iend = isplit[jb];</span></a>
+<a name="13226"><span class="lineNum">   13226 </span><span class="lineNoCov">          0 :         in = iend - ioff;</span></a>
+<a name="13227"><span class="lineNum">   13227 </span>            : </a>
+<a name="13228"><span class="lineNum">   13228 </span><span class="lineNoCov">          0 :         if (in == 1) {</span></a>
+<a name="13229"><span class="lineNum">   13229 </span>            : </a>
+<a name="13230"><span class="lineNum">   13230 </span><span class="lineNoCov">          0 :             if (irange == 1 || wl &gt;= d__[ibegin] - pivmin) {</span></a>
+<a name="13231"><span class="lineNum">   13231 </span><span class="lineNoCov">          0 :                 ++nwl;</span></a>
+<a name="13232"><span class="lineNum">   13232 </span>            :             }</a>
+<a name="13233"><span class="lineNum">   13233 </span><span class="lineNoCov">          0 :             if (irange == 1 || wu &gt;= d__[ibegin] - pivmin) {</span></a>
+<a name="13234"><span class="lineNum">   13234 </span><span class="lineNoCov">          0 :                 ++nwu;</span></a>
+<a name="13235"><span class="lineNum">   13235 </span>            :             }</a>
+<a name="13236"><span class="lineNum">   13236 </span><span class="lineNoCov">          0 :             if (irange == 1 || ((wl &lt; d__[ibegin] - pivmin) &amp;&amp; (wu &gt;= d__[ibegin] - pivmin))) {</span></a>
+<a name="13237"><span class="lineNum">   13237 </span><span class="lineNoCov">          0 :                 ++(*m);</span></a>
+<a name="13238"><span class="lineNum">   13238 </span><span class="lineNoCov">          0 :                 w[*m] = d__[ibegin];</span></a>
+<a name="13239"><span class="lineNum">   13239 </span><span class="lineNoCov">          0 :                 iblock[*m] = jb;</span></a>
+<a name="13240"><span class="lineNum">   13240 </span>            :             }</a>
+<a name="13241"><span class="lineNum">   13241 </span>            :         } else {</a>
+<a name="13242"><span class="lineNum">   13242 </span>            : </a>
+<a name="13243"><span class="lineNum">   13243 </span><span class="lineNoCov">          0 :             gu = d__[ibegin];</span></a>
+<a name="13244"><span class="lineNum">   13244 </span>            :             gl = d__[ibegin];</a>
+<a name="13245"><span class="lineNum">   13245 </span>            :             tmp1 = 0.;</a>
+<a name="13246"><span class="lineNum">   13246 </span>            : </a>
+<a name="13247"><span class="lineNum">   13247 </span>            :             i__2 = iend - 1;</a>
+<a name="13248"><span class="lineNum">   13248 </span><span class="lineNoCov">          0 :             for (j = ibegin; j &lt;= i__2; ++j) {</span></a>
+<a name="13249"><span class="lineNum">   13249 </span><span class="lineNoCov">          0 :                 tmp2 = std::abs(e[j]);</span></a>
+<a name="13250"><span class="lineNum">   13250 </span><span class="lineNoCov">          0 :                 d__1 = gu, d__2 = d__[j] + tmp1 + tmp2;</span></a>
+<a name="13251"><span class="lineNum">   13251 </span><span class="lineNoCov">          0 :                 gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13252"><span class="lineNum">   13252 </span><span class="lineNoCov">          0 :                 d__1 = gl, d__2 = d__[j] - tmp1 - tmp2;</span></a>
+<a name="13253"><span class="lineNum">   13253 </span><span class="lineNoCov">          0 :                 gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="13254"><span class="lineNum">   13254 </span>            :                 tmp1 = tmp2;</a>
+<a name="13255"><span class="lineNum">   13255 </span>            :             }</a>
+<a name="13256"><span class="lineNum">   13256 </span>            : </a>
+<a name="13257"><span class="lineNum">   13257 </span><span class="lineNoCov">          0 :             d__1 = gu, d__2 = d__[iend] + tmp1;</span></a>
+<a name="13258"><span class="lineNum">   13258 </span><span class="lineNoCov">          0 :             gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13259"><span class="lineNum">   13259 </span><span class="lineNoCov">          0 :             d__1 = gl, d__2 = d__[iend] - tmp1;</span></a>
+<a name="13260"><span class="lineNum">   13260 </span><span class="lineNoCov">          0 :             gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="13261"><span class="lineNum">   13261 </span>            :             d__1 = std::abs(gl);</a>
+<a name="13262"><span class="lineNum">   13262 </span>            :             d__2 = std::abs(gu);</a>
+<a name="13263"><span class="lineNum">   13263 </span><span class="lineNoCov">          0 :             bnorm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13264"><span class="lineNum">   13264 </span><span class="lineNoCov">          0 :             gl = gl - bnorm * 2. * ulp * in - pivmin * 2.;</span></a>
+<a name="13265"><span class="lineNum">   13265 </span><span class="lineNoCov">          0 :             gu = gu + bnorm * 2. * ulp * in + pivmin * 2.;</span></a>
+<a name="13266"><span class="lineNum">   13266 </span>            : </a>
+<a name="13267"><span class="lineNum">   13267 </span><span class="lineNoCov">          0 :             if (*abstol &lt;= 0.) {</span></a>
+<a name="13268"><span class="lineNum">   13268 </span>            :                 d__1 = std::abs(gl);</a>
+<a name="13269"><span class="lineNum">   13269 </span>            :                 d__2 = std::abs(gu);</a>
+<a name="13270"><span class="lineNum">   13270 </span><span class="lineNoCov">          0 :                 atoli = ulp * ((d__1&gt;d__2) ? d__1 : d__2);</span></a>
+<a name="13271"><span class="lineNum">   13271 </span>            :             } else {</a>
+<a name="13272"><span class="lineNum">   13272 </span><span class="lineNoCov">          0 :                 atoli = *abstol;</span></a>
+<a name="13273"><span class="lineNum">   13273 </span>            :             }</a>
+<a name="13274"><span class="lineNum">   13274 </span>            : </a>
+<a name="13275"><span class="lineNum">   13275 </span><span class="lineNoCov">          0 :             if (irange &gt; 1) {</span></a>
+<a name="13276"><span class="lineNum">   13276 </span><span class="lineNoCov">          0 :                 if (gu &lt; wl) {</span></a>
+<a name="13277"><span class="lineNum">   13277 </span><span class="lineNoCov">          0 :                     nwl += in;</span></a>
+<a name="13278"><span class="lineNum">   13278 </span><span class="lineNoCov">          0 :                     nwu += in;</span></a>
+<a name="13279"><span class="lineNum">   13279 </span>            :                 }</a>
+<a name="13280"><span class="lineNum">   13280 </span>            :                 gl = (gl&gt;wl) ? gl : wl;</a>
+<a name="13281"><span class="lineNum">   13281 </span>            :                 gu = (gu&lt;wu) ? gu : wu;</a>
+<a name="13282"><span class="lineNum">   13282 </span>            :                 if (gl &gt;= gu) {</a>
+<a name="13283"><span class="lineNum">   13283 </span>            :                 }</a>
+<a name="13284"><span class="lineNum">   13284 </span><span class="lineNoCov">          0 :                 continue;</span></a>
+<a name="13285"><span class="lineNum">   13285 </span>            :             }</a>
+<a name="13286"><span class="lineNum">   13286 </span>            : </a>
+<a name="13287"><span class="lineNum">   13287 </span><span class="lineNoCov">          0 :             work[*n + 1] = gl;</span></a>
+<a name="13288"><span class="lineNum">   13288 </span><span class="lineNoCov">          0 :             work[*n + in + 1] = gu;</span></a>
+<a name="13289"><span class="lineNum">   13289 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaebz,DLAEBZ)(&amp;c__1, &amp;c__0, &amp;in, &amp;in, &amp;c__1, &amp;nb, &amp;atoli, &amp;rtoli, &amp;</span></a>
+<a name="13290"><span class="lineNum">   13290 </span>            :                     pivmin, &amp;d__[ibegin], &amp;e[ibegin], &amp;work[ibegin], idumma, &amp;</a>
+<a name="13291"><span class="lineNum">   13291 </span><span class="lineNoCov">          0 :                     work[*n + 1], &amp;work[*n + (in &lt;&lt; 1) + 1], &amp;im, &amp;iwork[1], &amp;</span></a>
+<a name="13292"><span class="lineNum">   13292 </span><span class="lineNoCov">          0 :                     w[*m + 1], &amp;iblock[*m + 1], &amp;iinfo);</span></a>
+<a name="13293"><span class="lineNum">   13293 </span>            : </a>
+<a name="13294"><span class="lineNum">   13294 </span><span class="lineNoCov">          0 :             nwl += iwork[1];</span></a>
+<a name="13295"><span class="lineNum">   13295 </span><span class="lineNoCov">          0 :             nwu += iwork[in + 1];</span></a>
+<a name="13296"><span class="lineNum">   13296 </span><span class="lineNoCov">          0 :             iwoff = *m - iwork[1];</span></a>
+<a name="13297"><span class="lineNum">   13297 </span>            : </a>
+<a name="13298"><span class="lineNum">   13298 </span><span class="lineNoCov">          0 :             itmax = (int) ((std::log(gu - gl + pivmin) - std::log(pivmin)) / std::log(2.)</span></a>
+<a name="13299"><span class="lineNum">   13299 </span><span class="lineNoCov">          0 :                     ) + 2;</span></a>
+<a name="13300"><span class="lineNum">   13300 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlaebz,DLAEBZ)(&amp;c__2, &amp;itmax, &amp;in, &amp;in, &amp;c__1, &amp;nb, &amp;atoli, &amp;rtoli, &amp;</span></a>
+<a name="13301"><span class="lineNum">   13301 </span>            :                     pivmin, &amp;d__[ibegin], &amp;e[ibegin], &amp;work[ibegin], idumma, &amp;</a>
+<a name="13302"><span class="lineNum">   13302 </span><span class="lineNoCov">          0 :                     work[*n + 1], &amp;work[*n + (in &lt;&lt; 1) + 1], &amp;iout, &amp;iwork[1],</span></a>
+<a name="13303"><span class="lineNum">   13303 </span><span class="lineNoCov">          0 :                      &amp;w[*m + 1], &amp;iblock[*m + 1], &amp;iinfo);</span></a>
+<a name="13304"><span class="lineNum">   13304 </span>            : </a>
+<a name="13305"><span class="lineNum">   13305 </span><span class="lineNoCov">          0 :             i__2 = iout;</span></a>
+<a name="13306"><span class="lineNum">   13306 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="13307"><span class="lineNum">   13307 </span><span class="lineNoCov">          0 :                 tmp1 = (work[j + *n] + work[j + in + *n]) * .5;</span></a>
+<a name="13308"><span class="lineNum">   13308 </span>            : </a>
+<a name="13309"><span class="lineNum">   13309 </span><span class="lineNoCov">          0 :                 if (j &gt; iout - iinfo) {</span></a>
+<a name="13310"><span class="lineNum">   13310 </span>            :                     ncnvrg = 1;</a>
+<a name="13311"><span class="lineNum">   13311 </span><span class="lineNoCov">          0 :                     ib = -jb;</span></a>
+<a name="13312"><span class="lineNum">   13312 </span>            :                 } else {</a>
+<a name="13313"><span class="lineNum">   13313 </span>            :                     ib = jb;</a>
+<a name="13314"><span class="lineNum">   13314 </span>            :                 }</a>
+<a name="13315"><span class="lineNum">   13315 </span><span class="lineNoCov">          0 :                 i__3 = iwork[j + in] + iwoff;</span></a>
+<a name="13316"><span class="lineNum">   13316 </span><span class="lineNoCov">          0 :                 for (je = iwork[j] + 1 + iwoff; je &lt;= i__3; ++je) {</span></a>
+<a name="13317"><span class="lineNum">   13317 </span><span class="lineNoCov">          0 :                     w[je] = tmp1;</span></a>
+<a name="13318"><span class="lineNum">   13318 </span><span class="lineNoCov">          0 :                     iblock[je] = ib;</span></a>
+<a name="13319"><span class="lineNum">   13319 </span>            :                 }</a>
+<a name="13320"><span class="lineNum">   13320 </span>            :             }</a>
+<a name="13321"><span class="lineNum">   13321 </span>            : </a>
+<a name="13322"><span class="lineNum">   13322 </span><span class="lineNoCov">          0 :             *m += im;</span></a>
+<a name="13323"><span class="lineNum">   13323 </span>            :         }</a>
+<a name="13324"><span class="lineNum">   13324 </span>            :     }</a>
+<a name="13325"><span class="lineNum">   13325 </span>            : </a>
+<a name="13326"><span class="lineNum">   13326 </span><span class="lineNoCov">          0 :     if (irange == 3) {</span></a>
+<a name="13327"><span class="lineNum">   13327 </span><span class="lineNoCov">          0 :         im = 0;</span></a>
+<a name="13328"><span class="lineNum">   13328 </span><span class="lineNoCov">          0 :         idiscl = *il - 1 - nwl;</span></a>
+<a name="13329"><span class="lineNum">   13329 </span><span class="lineNoCov">          0 :         idiscu = nwu - *iu;</span></a>
+<a name="13330"><span class="lineNum">   13330 </span>            : </a>
+<a name="13331"><span class="lineNum">   13331 </span><span class="lineNoCov">          0 :         if (idiscl &gt; 0 || idiscu &gt; 0) {</span></a>
+<a name="13332"><span class="lineNum">   13332 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="13333"><span class="lineNum">   13333 </span><span class="lineNoCov">          0 :             for (je = 1; je &lt;= i__1; ++je) {</span></a>
+<a name="13334"><span class="lineNum">   13334 </span><span class="lineNoCov">          0 :                 if (w[je] &lt;= wlu &amp;&amp; idiscl &gt; 0) {</span></a>
+<a name="13335"><span class="lineNum">   13335 </span><span class="lineNoCov">          0 :                     --idiscl;</span></a>
+<a name="13336"><span class="lineNum">   13336 </span><span class="lineNoCov">          0 :                 } else if (w[je] &gt;= wul &amp;&amp; idiscu &gt; 0) {</span></a>
+<a name="13337"><span class="lineNum">   13337 </span><span class="lineNoCov">          0 :                     --idiscu;</span></a>
+<a name="13338"><span class="lineNum">   13338 </span>            :                 } else {</a>
+<a name="13339"><span class="lineNum">   13339 </span><span class="lineNoCov">          0 :                     ++im;</span></a>
+<a name="13340"><span class="lineNum">   13340 </span><span class="lineNoCov">          0 :                     w[im] = w[je];</span></a>
+<a name="13341"><span class="lineNum">   13341 </span><span class="lineNoCov">          0 :                     iblock[im] = iblock[je];</span></a>
+<a name="13342"><span class="lineNum">   13342 </span>            :                 }</a>
+<a name="13343"><span class="lineNum">   13343 </span>            :             }</a>
+<a name="13344"><span class="lineNum">   13344 </span><span class="lineNoCov">          0 :             *m = im;</span></a>
+<a name="13345"><span class="lineNum">   13345 </span>            :         }</a>
+<a name="13346"><span class="lineNum">   13346 </span><span class="lineNoCov">          0 :         if (idiscl &gt; 0 || idiscu &gt; 0) {</span></a>
+<a name="13347"><span class="lineNum">   13347 </span>            : </a>
+<a name="13348"><span class="lineNum">   13348 </span><span class="lineNoCov">          0 :             if (idiscl &gt; 0) {</span></a>
+<a name="13349"><span class="lineNum">   13349 </span>            :                 wkill = wu;</a>
+<a name="13350"><span class="lineNum">   13350 </span>            :                 i__1 = idiscl;</a>
+<a name="13351"><span class="lineNum">   13351 </span><span class="lineNoCov">          0 :                 for (jdisc = 1; jdisc &lt;= i__1; ++jdisc) {</span></a>
+<a name="13352"><span class="lineNum">   13352 </span>            :                     iw = 0;</a>
+<a name="13353"><span class="lineNum">   13353 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="13354"><span class="lineNum">   13354 </span><span class="lineNoCov">          0 :                     for (je = 1; je &lt;= i__2; ++je) {</span></a>
+<a name="13355"><span class="lineNum">   13355 </span><span class="lineNoCov">          0 :                         if (iblock[je] != 0 &amp;&amp; (w[je] &lt; wkill || iw == 0)) {</span></a>
+<a name="13356"><span class="lineNum">   13356 </span>            :                             iw = je;</a>
+<a name="13357"><span class="lineNum">   13357 </span>            :                             wkill = w[je];</a>
+<a name="13358"><span class="lineNum">   13358 </span>            :                         }</a>
+<a name="13359"><span class="lineNum">   13359 </span>            :                     }</a>
+<a name="13360"><span class="lineNum">   13360 </span><span class="lineNoCov">          0 :                     iblock[iw] = 0;</span></a>
+<a name="13361"><span class="lineNum">   13361 </span>            :                 }</a>
+<a name="13362"><span class="lineNum">   13362 </span>            :             }</a>
+<a name="13363"><span class="lineNum">   13363 </span><span class="lineNoCov">          0 :             if (idiscu &gt; 0) {</span></a>
+<a name="13364"><span class="lineNum">   13364 </span>            : </a>
+<a name="13365"><span class="lineNum">   13365 </span>            :                 wkill = wl;</a>
+<a name="13366"><span class="lineNum">   13366 </span>            :                 i__1 = idiscu;</a>
+<a name="13367"><span class="lineNum">   13367 </span><span class="lineNoCov">          0 :                 for (jdisc = 1; jdisc &lt;= i__1; ++jdisc) {</span></a>
+<a name="13368"><span class="lineNum">   13368 </span>            :                     iw = 0;</a>
+<a name="13369"><span class="lineNum">   13369 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="13370"><span class="lineNum">   13370 </span><span class="lineNoCov">          0 :                     for (je = 1; je &lt;= i__2; ++je) {</span></a>
+<a name="13371"><span class="lineNum">   13371 </span><span class="lineNoCov">          0 :                         if (iblock[je] != 0 &amp;&amp; (w[je] &gt; wkill || iw == 0)) {</span></a>
+<a name="13372"><span class="lineNum">   13372 </span>            :                             iw = je;</a>
+<a name="13373"><span class="lineNum">   13373 </span>            :                             wkill = w[je];</a>
+<a name="13374"><span class="lineNum">   13374 </span>            :                         }</a>
+<a name="13375"><span class="lineNum">   13375 </span>            :                     }</a>
+<a name="13376"><span class="lineNum">   13376 </span><span class="lineNoCov">          0 :                     iblock[iw] = 0;</span></a>
+<a name="13377"><span class="lineNum">   13377 </span>            :                 }</a>
+<a name="13378"><span class="lineNum">   13378 </span>            :             }</a>
+<a name="13379"><span class="lineNum">   13379 </span><span class="lineNoCov">          0 :             im = 0;</span></a>
+<a name="13380"><span class="lineNum">   13380 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="13381"><span class="lineNum">   13381 </span><span class="lineNoCov">          0 :             for (je = 1; je &lt;= i__1; ++je) {</span></a>
+<a name="13382"><span class="lineNum">   13382 </span><span class="lineNoCov">          0 :                 if (iblock[je] != 0) {</span></a>
+<a name="13383"><span class="lineNum">   13383 </span><span class="lineNoCov">          0 :                     ++im;</span></a>
+<a name="13384"><span class="lineNum">   13384 </span><span class="lineNoCov">          0 :                     w[im] = w[je];</span></a>
+<a name="13385"><span class="lineNum">   13385 </span><span class="lineNoCov">          0 :                     iblock[im] = iblock[je];</span></a>
+<a name="13386"><span class="lineNum">   13386 </span>            :                 }</a>
+<a name="13387"><span class="lineNum">   13387 </span>            :             }</a>
+<a name="13388"><span class="lineNum">   13388 </span><span class="lineNoCov">          0 :             *m = im;</span></a>
+<a name="13389"><span class="lineNum">   13389 </span>            :         }</a>
+<a name="13390"><span class="lineNum">   13390 </span><span class="lineNoCov">          0 :         if (idiscl &lt; 0 || idiscu &lt; 0) {</span></a>
+<a name="13391"><span class="lineNum">   13391 </span>            :             toofew = 1;</a>
+<a name="13392"><span class="lineNum">   13392 </span>            :         }</a>
+<a name="13393"><span class="lineNum">   13393 </span>            :     }</a>
+<a name="13394"><span class="lineNum">   13394 </span>            : </a>
+<a name="13395"><span class="lineNum">   13395 </span><span class="lineNoCov">          0 :     if (iorder == 1 &amp;&amp; *nsplit &gt; 1) {</span></a>
+<a name="13396"><span class="lineNum">   13396 </span><span class="lineNoCov">          0 :         i__1 = *m - 1;</span></a>
+<a name="13397"><span class="lineNum">   13397 </span><span class="lineNoCov">          0 :         for (je = 1; je &lt;= i__1; ++je) {</span></a>
+<a name="13398"><span class="lineNum">   13398 </span>            :             ie = 0;</a>
+<a name="13399"><span class="lineNum">   13399 </span><span class="lineNoCov">          0 :             tmp1 = w[je];</span></a>
+<a name="13400"><span class="lineNum">   13400 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="13401"><span class="lineNum">   13401 </span><span class="lineNoCov">          0 :             for (j = je + 1; j &lt;= i__2; ++j) {</span></a>
+<a name="13402"><span class="lineNum">   13402 </span><span class="lineNoCov">          0 :                 if (w[j] &lt; tmp1) {</span></a>
+<a name="13403"><span class="lineNum">   13403 </span>            :                     ie = j;</a>
+<a name="13404"><span class="lineNum">   13404 </span>            :                     tmp1 = w[j];</a>
+<a name="13405"><span class="lineNum">   13405 </span>            :                 }</a>
+<a name="13406"><span class="lineNum">   13406 </span>            :             }</a>
+<a name="13407"><span class="lineNum">   13407 </span>            : </a>
+<a name="13408"><span class="lineNum">   13408 </span><span class="lineNoCov">          0 :             if (ie != 0) {</span></a>
+<a name="13409"><span class="lineNum">   13409 </span><span class="lineNoCov">          0 :                 itmp1 = iblock[ie];</span></a>
+<a name="13410"><span class="lineNum">   13410 </span><span class="lineNoCov">          0 :                 w[ie] = w[je];</span></a>
+<a name="13411"><span class="lineNum">   13411 </span><span class="lineNoCov">          0 :                 iblock[ie] = iblock[je];</span></a>
+<a name="13412"><span class="lineNum">   13412 </span><span class="lineNoCov">          0 :                 w[je] = tmp1;</span></a>
+<a name="13413"><span class="lineNum">   13413 </span><span class="lineNoCov">          0 :                 iblock[je] = itmp1;</span></a>
+<a name="13414"><span class="lineNum">   13414 </span>            :             }</a>
+<a name="13415"><span class="lineNum">   13415 </span>            :         }</a>
+<a name="13416"><span class="lineNum">   13416 </span>            :     }</a>
+<a name="13417"><span class="lineNum">   13417 </span>            : </a>
+<a name="13418"><span class="lineNum">   13418 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="13419"><span class="lineNum">   13419 </span><span class="lineNoCov">          0 :     if (ncnvrg) {</span></a>
+<a name="13420"><span class="lineNum">   13420 </span><span class="lineNoCov">          0 :         ++(*info);</span></a>
+<a name="13421"><span class="lineNum">   13421 </span>            :     }</a>
+<a name="13422"><span class="lineNum">   13422 </span><span class="lineNoCov">          0 :     if (toofew) {</span></a>
+<a name="13423"><span class="lineNum">   13423 </span><span class="lineNoCov">          0 :         *info += 2;</span></a>
+<a name="13424"><span class="lineNum">   13424 </span>            :     }</a>
+<a name="13425"><span class="lineNum">   13425 </span>            :     return;</a>
+<a name="13426"><span class="lineNum">   13426 </span>            : </a>
+<a name="13427"><span class="lineNum">   13427 </span>            : }</a>
+<a name="13428"><span class="lineNum">   13428 </span>            : </a>
+<a name="13429"><span class="lineNum">   13429 </span>            : </a>
+<a name="13430"><span class="lineNum">   13430 </span>            : }</a>
+<a name="13431"><span class="lineNum">   13431 </span>            : }</a>
+<a name="13432"><span class="lineNum">   13432 </span>            : #include &lt;cmath&gt;</a>
+<a name="13433"><span class="lineNum">   13433 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="13434"><span class="lineNum">   13434 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="13435"><span class="lineNum">   13435 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="13436"><span class="lineNum">   13436 </span>            : </a>
+<a name="13437"><span class="lineNum">   13437 </span>            : #include &quot;real.h&quot;</a>
+<a name="13438"><span class="lineNum">   13438 </span>            : </a>
+<a name="13439"><span class="lineNum">   13439 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="13440"><span class="lineNum">   13440 </span>            : namespace PLMD{</a>
+<a name="13441"><span class="lineNum">   13441 </span>            : namespace lapack{</a>
+<a name="13442"><span class="lineNum">   13442 </span>            : using namespace blas;</a>
+<a name="13443"><span class="lineNum">   13443 </span>            : void</a>
+<a name="13444"><span class="lineNum">   13444 </span><span class="lineCov">     570008 : PLUMED_BLAS_F77_FUNC(dstegr,DSTEGR)(const char *jobz, </span></a>
+<a name="13445"><span class="lineNum">   13445 </span>            :         const char *range, </a>
+<a name="13446"><span class="lineNum">   13446 </span>            :         int *n, </a>
+<a name="13447"><span class="lineNum">   13447 </span>            :         double *d__, </a>
+<a name="13448"><span class="lineNum">   13448 </span>            :         double *e, </a>
+<a name="13449"><span class="lineNum">   13449 </span>            :         double *vl, </a>
+<a name="13450"><span class="lineNum">   13450 </span>            :         double *vu, </a>
+<a name="13451"><span class="lineNum">   13451 </span>            :         int *il, </a>
+<a name="13452"><span class="lineNum">   13452 </span>            :         int *iu, </a>
+<a name="13453"><span class="lineNum">   13453 </span>            :         double *abstol, </a>
+<a name="13454"><span class="lineNum">   13454 </span>            :         int *m, </a>
+<a name="13455"><span class="lineNum">   13455 </span>            :         double *w, </a>
+<a name="13456"><span class="lineNum">   13456 </span>            :         double *z__, </a>
+<a name="13457"><span class="lineNum">   13457 </span>            :         int *ldz, </a>
+<a name="13458"><span class="lineNum">   13458 </span>            :         int *isuppz,</a>
+<a name="13459"><span class="lineNum">   13459 </span>            :         double *work, </a>
+<a name="13460"><span class="lineNum">   13460 </span>            :         int *lwork, </a>
+<a name="13461"><span class="lineNum">   13461 </span>            :         int *iwork, </a>
+<a name="13462"><span class="lineNum">   13462 </span>            :         int *liwork, </a>
+<a name="13463"><span class="lineNum">   13463 </span>            :         int *info)</a>
+<a name="13464"><span class="lineNum">   13464 </span>            : {</a>
+<a name="13465"><span class="lineNum">   13465 </span>            :     int z_dim1, z_offset, i__1, i__2;</a>
+<a name="13466"><span class="lineNum">   13466 </span>            :     double d__1, d__2;</a>
+<a name="13467"><span class="lineNum">   13467 </span><span class="lineCov">     570008 :     int c__1 = 1;</span></a>
+<a name="13468"><span class="lineNum">   13468 </span>            : </a>
+<a name="13469"><span class="lineNum">   13469 </span>            :     int i__, j;</a>
+<a name="13470"><span class="lineNum">   13470 </span>            :     int jj;</a>
+<a name="13471"><span class="lineNum">   13471 </span>            :     double eps, tol, tmp, rmin, rmax;</a>
+<a name="13472"><span class="lineNum">   13472 </span>            :     int itmp;</a>
+<a name="13473"><span class="lineNum">   13473 </span>            :     double tnrm;</a>
+<a name="13474"><span class="lineNum">   13474 </span>            :     double scale;</a>
+<a name="13475"><span class="lineNum">   13475 </span>            :     int iinfo, iindw;</a>
+<a name="13476"><span class="lineNum">   13476 </span>            :     int lwmin;</a>
+<a name="13477"><span class="lineNum">   13477 </span>            :     int wantz;</a>
+<a name="13478"><span class="lineNum">   13478 </span>            :     int iindbl;</a>
+<a name="13479"><span class="lineNum">   13479 </span>            :     int valeig,alleig,indeig;</a>
+<a name="13480"><span class="lineNum">   13480 </span>            :     double safmin,minval;</a>
+<a name="13481"><span class="lineNum">   13481 </span>            :     double bignum;</a>
+<a name="13482"><span class="lineNum">   13482 </span>            :     int iindwk, indgrs;</a>
+<a name="13483"><span class="lineNum">   13483 </span>            :     double thresh;</a>
+<a name="13484"><span class="lineNum">   13484 </span>            :     int iinspl, indwrk, liwmin, nsplit;</a>
+<a name="13485"><span class="lineNum">   13485 </span>            :     double smlnum;</a>
+<a name="13486"><span class="lineNum">   13486 </span>            :     int lquery;</a>
+<a name="13487"><span class="lineNum">   13487 </span>            : </a>
+<a name="13488"><span class="lineNum">   13488 </span>            : </a>
+<a name="13489"><span class="lineNum">   13489 </span>            :     --d__;</a>
+<a name="13490"><span class="lineNum">   13490 </span>            :     --e;</a>
+<a name="13491"><span class="lineNum">   13491 </span><span class="lineCov">     570008 :     --w;</span></a>
+<a name="13492"><span class="lineNum">   13492 </span><span class="lineCov">     570008 :     z_dim1 = *ldz;</span></a>
+<a name="13493"><span class="lineNum">   13493 </span><span class="lineCov">     570008 :     z_offset = 1 + z_dim1;</span></a>
+<a name="13494"><span class="lineNum">   13494 </span><span class="lineCov">     570008 :     z__ -= z_offset;</span></a>
+<a name="13495"><span class="lineNum">   13495 </span><span class="lineCov">     570008 :     --isuppz;</span></a>
+<a name="13496"><span class="lineNum">   13496 </span><span class="lineCov">     570008 :     --work;</span></a>
+<a name="13497"><span class="lineNum">   13497 </span><span class="lineCov">     570008 :     --iwork;</span></a>
+<a name="13498"><span class="lineNum">   13498 </span>            : </a>
+<a name="13499"><span class="lineNum">   13499 </span><span class="lineCov">     570008 :     wantz = (*jobz=='V' || *jobz=='v');</span></a>
+<a name="13500"><span class="lineNum">   13500 </span><span class="lineCov">     570008 :     alleig = (*range=='A' || *range=='a');</span></a>
+<a name="13501"><span class="lineNum">   13501 </span><span class="lineCov">     570008 :     valeig = (*range=='V' || *range=='v');</span></a>
+<a name="13502"><span class="lineNum">   13502 </span><span class="lineCov">     570008 :     indeig = (*range=='I' || *range=='i');</span></a>
+<a name="13503"><span class="lineNum">   13503 </span>            : </a>
+<a name="13504"><span class="lineNum">   13504 </span><span class="lineCov">     570008 :     lquery = *lwork == -1 || *liwork == -1;</span></a>
+<a name="13505"><span class="lineNum">   13505 </span><span class="lineCov">     570008 :     lwmin = *n * 17;</span></a>
+<a name="13506"><span class="lineNum">   13506 </span><span class="lineCov">     570008 :     liwmin = *n * 10;</span></a>
+<a name="13507"><span class="lineNum">   13507 </span>            : </a>
+<a name="13508"><span class="lineNum">   13508 </span><span class="lineCov">     570008 :     *info = 0;</span></a>
+<a name="13509"><span class="lineNum">   13509 </span><span class="lineCov">     570008 :     if (! (wantz || (*jobz=='N' || *jobz=='n'))) {</span></a>
+<a name="13510"><span class="lineNum">   13510 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="13511"><span class="lineNum">   13511 </span><span class="lineCov">     570008 :     } else if (! (alleig || valeig || indeig)) {</span></a>
+<a name="13512"><span class="lineNum">   13512 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="13513"><span class="lineNum">   13513 </span><span class="lineCov">     570008 :     } else if (*n &lt; 0) {</span></a>
+<a name="13514"><span class="lineNum">   13514 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="13515"><span class="lineNum">   13515 </span><span class="lineCov">     570008 :     } else if (valeig &amp;&amp; *n &gt; 0 &amp;&amp; *vu &lt;= *vl) {</span></a>
+<a name="13516"><span class="lineNum">   13516 </span><span class="lineNoCov">          0 :         *info = -7;</span></a>
+<a name="13517"><span class="lineNum">   13517 </span><span class="lineCov">     570008 :     } else if (indeig &amp;&amp; (*il &lt; 1 || *il &gt; *n)) {</span></a>
+<a name="13518"><span class="lineNum">   13518 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="13519"><span class="lineNum">   13519 </span><span class="lineCov">     570008 :     } else if (indeig &amp;&amp; (*iu &lt; *il || *iu &gt; *n)) {</span></a>
+<a name="13520"><span class="lineNum">   13520 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="13521"><span class="lineNum">   13521 </span><span class="lineCov">     570008 :     } else if (*ldz &lt; 1 || (wantz &amp;&amp; *ldz &lt; *n)) {</span></a>
+<a name="13522"><span class="lineNum">   13522 </span><span class="lineNoCov">          0 :         *info = -14;</span></a>
+<a name="13523"><span class="lineNum">   13523 </span><span class="lineCov">     570008 :     } else if (*lwork &lt; lwmin &amp;&amp; ! lquery) {</span></a>
+<a name="13524"><span class="lineNum">   13524 </span><span class="lineNoCov">          0 :         *info = -17;</span></a>
+<a name="13525"><span class="lineNum">   13525 </span><span class="lineCov">     570008 :     } else if (*liwork &lt; liwmin &amp;&amp; ! lquery) {</span></a>
+<a name="13526"><span class="lineNum">   13526 </span><span class="lineNoCov">          0 :         *info = -19;</span></a>
+<a name="13527"><span class="lineNum">   13527 </span>            :     }</a>
+<a name="13528"><span class="lineNum">   13528 </span><span class="lineCov">     570008 :     if (*info == 0) {</span></a>
+<a name="13529"><span class="lineNum">   13529 </span><span class="lineCov">     570008 :         work[1] = (double) lwmin;</span></a>
+<a name="13530"><span class="lineNum">   13530 </span><span class="lineCov">     570008 :         iwork[1] = liwmin;</span></a>
+<a name="13531"><span class="lineNum">   13531 </span>            :     }</a>
+<a name="13532"><span class="lineNum">   13532 </span>            : </a>
+<a name="13533"><span class="lineNum">   13533 </span><span class="lineCov">     570008 :     if (*info != 0) {</span></a>
+<a name="13534"><span class="lineNum">   13534 </span>            :         i__1 = -(*info);</a>
+<a name="13535"><span class="lineNum">   13535 </span>            :         return;</a>
+<a name="13536"><span class="lineNum">   13536 </span><span class="lineCov">     570008 :     } else if (lquery) {</span></a>
+<a name="13537"><span class="lineNum">   13537 </span>            :         return;</a>
+<a name="13538"><span class="lineNum">   13538 </span>            :     }</a>
+<a name="13539"><span class="lineNum">   13539 </span>            : </a>
+<a name="13540"><span class="lineNum">   13540 </span><span class="lineCov">     570008 :     *m = 0;</span></a>
+<a name="13541"><span class="lineNum">   13541 </span><span class="lineCov">     570008 :     if (*n == 0) {</span></a>
+<a name="13542"><span class="lineNum">   13542 </span>            :         return;</a>
+<a name="13543"><span class="lineNum">   13543 </span>            :     }</a>
+<a name="13544"><span class="lineNum">   13544 </span>            : </a>
+<a name="13545"><span class="lineNum">   13545 </span><span class="lineCov">     570008 :     if (*n == 1) {</span></a>
+<a name="13546"><span class="lineNum">   13546 </span><span class="lineNoCov">          0 :         if (alleig || indeig) {</span></a>
+<a name="13547"><span class="lineNum">   13547 </span><span class="lineNoCov">          0 :             *m = 1;</span></a>
+<a name="13548"><span class="lineNum">   13548 </span><span class="lineNoCov">          0 :             w[1] = d__[1];</span></a>
+<a name="13549"><span class="lineNum">   13549 </span>            :         } else {</a>
+<a name="13550"><span class="lineNum">   13550 </span><span class="lineNoCov">          0 :             if (*vl &lt; d__[1] &amp;&amp; *vu &gt;= d__[1]) {</span></a>
+<a name="13551"><span class="lineNum">   13551 </span><span class="lineNoCov">          0 :                 *m = 1;</span></a>
+<a name="13552"><span class="lineNum">   13552 </span><span class="lineNoCov">          0 :                 w[1] = d__[1];</span></a>
+<a name="13553"><span class="lineNum">   13553 </span>            :             }</a>
+<a name="13554"><span class="lineNum">   13554 </span>            :         }</a>
+<a name="13555"><span class="lineNum">   13555 </span><span class="lineNoCov">          0 :         if (wantz) {</span></a>
+<a name="13556"><span class="lineNum">   13556 </span><span class="lineNoCov">          0 :             z__[z_dim1 + 1] = 1.;</span></a>
+<a name="13557"><span class="lineNum">   13557 </span>            :         }</a>
+<a name="13558"><span class="lineNum">   13558 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="13559"><span class="lineNum">   13559 </span>            :     }</a>
+<a name="13560"><span class="lineNum">   13560 </span>            : </a>
+<a name="13561"><span class="lineNum">   13561 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="13562"><span class="lineNum">   13562 </span>            :     safmin = minval*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="13563"><span class="lineNum">   13563 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="13564"><span class="lineNum">   13564 </span>            :     smlnum = safmin / eps;</a>
+<a name="13565"><span class="lineNum">   13565 </span>            :     bignum = 1. / smlnum;</a>
+<a name="13566"><span class="lineNum">   13566 </span>            :     rmin =  std::sqrt(smlnum);</a>
+<a name="13567"><span class="lineNum">   13567 </span><span class="lineCov">     570008 :     d__1 =  std::sqrt(bignum), d__2 = 1. / std::sqrt(sqrt(safmin));</span></a>
+<a name="13568"><span class="lineNum">   13568 </span>            :     rmax = (d__1&lt;d__2) ? d__1 : d__2;</a>
+<a name="13569"><span class="lineNum">   13569 </span><span class="lineCov">     570008 :     scale = 1.;</span></a>
+<a name="13570"><span class="lineNum">   13570 </span><span class="lineCov">     570008 :     tnrm = PLUMED_BLAS_F77_FUNC(dlanst,DLANST)(&quot;M&quot;, n, &amp;d__[1], &amp;e[1]);</span></a>
+<a name="13571"><span class="lineNum">   13571 </span><span class="lineCov">     570008 :     if (tnrm &gt; 0. &amp;&amp; tnrm &lt; rmin) {</span></a>
+<a name="13572"><span class="lineNum">   13572 </span><span class="lineNoCov">          0 :         scale = rmin / tnrm;</span></a>
+<a name="13573"><span class="lineNum">   13573 </span><span class="lineCov">     570008 :     } else if (tnrm &gt; rmax) {</span></a>
+<a name="13574"><span class="lineNum">   13574 </span><span class="lineNoCov">          0 :         scale = rmax / tnrm;</span></a>
+<a name="13575"><span class="lineNum">   13575 </span>            :     }</a>
+<a name="13576"><span class="lineNum">   13576 </span><span class="lineCov">     570008 :     if ( std::abs(scale-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="13577"><span class="lineNum">   13577 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(n, &amp;scale, &amp;d__[1], &amp;c__1);</span></a>
+<a name="13578"><span class="lineNum">   13578 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="13579"><span class="lineNum">   13579 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__1, &amp;scale, &amp;e[1], &amp;c__1);</span></a>
+<a name="13580"><span class="lineNum">   13580 </span><span class="lineNoCov">          0 :         tnrm *= scale;</span></a>
+<a name="13581"><span class="lineNum">   13581 </span>            :     }</a>
+<a name="13582"><span class="lineNum">   13582 </span>            :     indgrs = 1;</a>
+<a name="13583"><span class="lineNum">   13583 </span><span class="lineCov">     570008 :     indwrk = (*n &lt;&lt; 1) + 1;</span></a>
+<a name="13584"><span class="lineNum">   13584 </span>            : </a>
+<a name="13585"><span class="lineNum">   13585 </span>            :     iinspl = 1;</a>
+<a name="13586"><span class="lineNum">   13586 </span><span class="lineCov">     570008 :     iindbl = *n + 1;</span></a>
+<a name="13587"><span class="lineNum">   13587 </span>            :     iindw = (*n &lt;&lt; 1) + 1;</a>
+<a name="13588"><span class="lineNum">   13588 </span><span class="lineCov">     570008 :     iindwk = *n * 3 + 1;</span></a>
+<a name="13589"><span class="lineNum">   13589 </span>            : </a>
+<a name="13590"><span class="lineNum">   13590 </span><span class="lineCov">     570008 :     thresh = eps * tnrm;</span></a>
+<a name="13591"><span class="lineNum">   13591 </span><span class="lineCov">     570008 :     PLUMED_BLAS_F77_FUNC(dlarrex,DLARREX)(range, n, vl, vu, il, iu, &amp;d__[1], &amp;e[1], &amp;thresh, &amp;nsplit, &amp;</span></a>
+<a name="13592"><span class="lineNum">   13592 </span><span class="lineCov">     570008 :             iwork[iinspl], m, &amp;w[1], &amp;iwork[iindbl], &amp;iwork[iindw], &amp;work[</span></a>
+<a name="13593"><span class="lineNum">   13593 </span><span class="lineCov">     570008 :             indgrs], &amp;work[indwrk], &amp;iwork[iindwk], &amp;iinfo);</span></a>
+<a name="13594"><span class="lineNum">   13594 </span>            :     </a>
+<a name="13595"><span class="lineNum">   13595 </span><span class="lineCov">     570008 :     if (iinfo != 0) {</span></a>
+<a name="13596"><span class="lineNum">   13596 </span><span class="lineNoCov">          0 :         *info = 1;</span></a>
+<a name="13597"><span class="lineNum">   13597 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="13598"><span class="lineNum">   13598 </span>            :     }</a>
+<a name="13599"><span class="lineNum">   13599 </span>            : </a>
+<a name="13600"><span class="lineNum">   13600 </span><span class="lineCov">     570008 :     if (wantz) {</span></a>
+<a name="13601"><span class="lineNum">   13601 </span><span class="lineCov">     569964 :         d__1 = *abstol, d__2 = (double) (*n) * eps;</span></a>
+<a name="13602"><span class="lineNum">   13602 </span><span class="lineCov">     569964 :         tol = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="13603"><span class="lineNum">   13603 </span><span class="lineCov">     569964 :         PLUMED_BLAS_F77_FUNC(dlarrvx,DLARRVX)(n, &amp;d__[1], &amp;e[1], &amp;iwork[iinspl], m, &amp;w[1], &amp;iwork[iindbl], &amp;</span></a>
+<a name="13604"><span class="lineNum">   13604 </span>            :                 iwork[iindw], &amp;work[indgrs], &amp;tol, &amp;z__[z_offset], ldz, &amp;</a>
+<a name="13605"><span class="lineNum">   13605 </span>            :                 isuppz[1], &amp;work[indwrk], &amp;iwork[iindwk], &amp;iinfo);</a>
+<a name="13606"><span class="lineNum">   13606 </span><span class="lineCov">     569964 :         if (iinfo != 0) {</span></a>
+<a name="13607"><span class="lineNum">   13607 </span><span class="lineNoCov">          0 :             *info = 2;</span></a>
+<a name="13608"><span class="lineNum">   13608 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="13609"><span class="lineNum">   13609 </span>            :         }</a>
+<a name="13610"><span class="lineNum">   13610 </span>            :     }</a>
+<a name="13611"><span class="lineNum">   13611 </span>            : </a>
+<a name="13612"><span class="lineNum">   13612 </span><span class="lineCov">     570008 :     i__1 = *m;</span></a>
+<a name="13613"><span class="lineNum">   13613 </span><span class="lineCov">    1177671 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="13614"><span class="lineNum">   13614 </span><span class="lineCov">     607663 :         itmp = iwork[iindbl + j - 1];</span></a>
+<a name="13615"><span class="lineNum">   13615 </span><span class="lineCov">     607663 :         w[j] += e[iwork[iinspl + itmp - 1]];</span></a>
+<a name="13616"><span class="lineNum">   13616 </span>            :     } </a>
+<a name="13617"><span class="lineNum">   13617 </span>            : </a>
+<a name="13618"><span class="lineNum">   13618 </span><span class="lineCov">     570008 :     if (std::abs(scale-1.0)&gt;PLUMED_GMX_DOUBLE_EPS) {</span></a>
+<a name="13619"><span class="lineNum">   13619 </span><span class="lineNoCov">          0 :         d__1 = 1. / scale;</span></a>
+<a name="13620"><span class="lineNum">   13620 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(m, &amp;d__1, &amp;w[1], &amp;c__1);</span></a>
+<a name="13621"><span class="lineNum">   13621 </span>            :     }</a>
+<a name="13622"><span class="lineNum">   13622 </span><span class="lineCov">     570008 :     if (nsplit &gt; 1) {</span></a>
+<a name="13623"><span class="lineNum">   13623 </span><span class="lineCov">         18 :         i__1 = *m - 1;</span></a>
+<a name="13624"><span class="lineNum">   13624 </span><span class="lineCov">        793 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="13625"><span class="lineNum">   13625 </span>            :             i__ = 0;</a>
+<a name="13626"><span class="lineNum">   13626 </span><span class="lineCov">        775 :             tmp = w[j];</span></a>
+<a name="13627"><span class="lineNum">   13627 </span><span class="lineCov">        775 :             i__2 = *m;</span></a>
+<a name="13628"><span class="lineNum">   13628 </span><span class="lineCov">      35106 :             for (jj = j + 1; jj &lt;= i__2; ++jj) {</span></a>
+<a name="13629"><span class="lineNum">   13629 </span><span class="lineCov">      34331 :                 if (w[jj] &lt; tmp) {</span></a>
+<a name="13630"><span class="lineNum">   13630 </span>            :                     i__ = jj;</a>
+<a name="13631"><span class="lineNum">   13631 </span>            :                     tmp = w[jj];</a>
+<a name="13632"><span class="lineNum">   13632 </span>            :                 }</a>
+<a name="13633"><span class="lineNum">   13633 </span>            :             }</a>
+<a name="13634"><span class="lineNum">   13634 </span><span class="lineCov">        775 :             if (i__ != 0) {</span></a>
+<a name="13635"><span class="lineNum">   13635 </span><span class="lineCov">        638 :                 w[i__] = w[j];</span></a>
+<a name="13636"><span class="lineNum">   13636 </span><span class="lineCov">        638 :                 w[j] = tmp;</span></a>
+<a name="13637"><span class="lineNum">   13637 </span><span class="lineCov">        638 :                 if (wantz) {</span></a>
+<a name="13638"><span class="lineNum">   13638 </span><span class="lineCov">        638 :                     PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n, &amp;z__[i__ * z_dim1 + 1], &amp;c__1, &amp;z__[j * z_dim1 </span></a>
+<a name="13639"><span class="lineNum">   13639 </span><span class="lineCov">        638 :                             + 1], &amp;c__1);</span></a>
+<a name="13640"><span class="lineNum">   13640 </span><span class="lineCov">        638 :                     itmp = isuppz[(i__ &lt;&lt; 1) - 1];</span></a>
+<a name="13641"><span class="lineNum">   13641 </span><span class="lineCov">        638 :                     isuppz[(i__ &lt;&lt; 1) - 1] = isuppz[(j &lt;&lt; 1) - 1];</span></a>
+<a name="13642"><span class="lineNum">   13642 </span><span class="lineCov">        638 :                     isuppz[(j &lt;&lt; 1) - 1] = itmp;</span></a>
+<a name="13643"><span class="lineNum">   13643 </span><span class="lineCov">        638 :                     itmp = isuppz[i__ * 2];</span></a>
+<a name="13644"><span class="lineNum">   13644 </span><span class="lineCov">        638 :                     isuppz[i__ * 2] = isuppz[j * 2];</span></a>
+<a name="13645"><span class="lineNum">   13645 </span><span class="lineCov">        638 :                     isuppz[j * 2] = itmp;</span></a>
+<a name="13646"><span class="lineNum">   13646 </span>            :                 }</a>
+<a name="13647"><span class="lineNum">   13647 </span>            :             }</a>
+<a name="13648"><span class="lineNum">   13648 </span>            :         }</a>
+<a name="13649"><span class="lineNum">   13649 </span>            :     }</a>
+<a name="13650"><span class="lineNum">   13650 </span>            : </a>
+<a name="13651"><span class="lineNum">   13651 </span><span class="lineCov">     570008 :     work[1] = (double) lwmin;</span></a>
+<a name="13652"><span class="lineNum">   13652 </span><span class="lineCov">     570008 :     iwork[1] = liwmin;</span></a>
+<a name="13653"><span class="lineNum">   13653 </span><span class="lineCov">     570008 :     return;</span></a>
+<a name="13654"><span class="lineNum">   13654 </span>            : </a>
+<a name="13655"><span class="lineNum">   13655 </span>            : } </a>
+<a name="13656"><span class="lineNum">   13656 </span>            : }</a>
+<a name="13657"><span class="lineNum">   13657 </span>            : }</a>
+<a name="13658"><span class="lineNum">   13658 </span>            : #include &lt;cmath&gt;</a>
+<a name="13659"><span class="lineNum">   13659 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="13660"><span class="lineNum">   13660 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="13661"><span class="lineNum">   13661 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="13662"><span class="lineNum">   13662 </span>            : </a>
+<a name="13663"><span class="lineNum">   13663 </span>            : #include &quot;real.h&quot;</a>
+<a name="13664"><span class="lineNum">   13664 </span>            : </a>
+<a name="13665"><span class="lineNum">   13665 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="13666"><span class="lineNum">   13666 </span>            : namespace PLMD{</a>
+<a name="13667"><span class="lineNum">   13667 </span>            : namespace lapack{</a>
+<a name="13668"><span class="lineNum">   13668 </span>            : using namespace blas;</a>
+<a name="13669"><span class="lineNum">   13669 </span>            : void</a>
+<a name="13670"><span class="lineNum">   13670 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dstein,DSTEIN)(int *n, </span></a>
+<a name="13671"><span class="lineNum">   13671 </span>            :         double *d__, </a>
+<a name="13672"><span class="lineNum">   13672 </span>            :         double *e, </a>
+<a name="13673"><span class="lineNum">   13673 </span>            :         int *m, </a>
+<a name="13674"><span class="lineNum">   13674 </span>            :         double *w, </a>
+<a name="13675"><span class="lineNum">   13675 </span>            :         int *iblock,</a>
+<a name="13676"><span class="lineNum">   13676 </span>            :         int *isplit, </a>
+<a name="13677"><span class="lineNum">   13677 </span>            :         double *z__,</a>
+<a name="13678"><span class="lineNum">   13678 </span>            :         int *ldz, </a>
+<a name="13679"><span class="lineNum">   13679 </span>            :         double *work,</a>
+<a name="13680"><span class="lineNum">   13680 </span>            :         int *iwork, </a>
+<a name="13681"><span class="lineNum">   13681 </span>            :         int *ifail,</a>
+<a name="13682"><span class="lineNum">   13682 </span>            :         int *info)</a>
+<a name="13683"><span class="lineNum">   13683 </span>            : {</a>
+<a name="13684"><span class="lineNum">   13684 </span>            :     int z_dim1, z_offset, i__1, i__2, i__3;</a>
+<a name="13685"><span class="lineNum">   13685 </span>            :     double d__2, d__3, d__4, d__5;</a>
+<a name="13686"><span class="lineNum">   13686 </span>            : </a>
+<a name="13687"><span class="lineNum">   13687 </span>            :     int i__, j, b1, j1, bn;</a>
+<a name="13688"><span class="lineNum">   13688 </span>            :     double xj, scl, eps, sep, nrm, tol;</a>
+<a name="13689"><span class="lineNum">   13689 </span>            :     int its;</a>
+<a name="13690"><span class="lineNum">   13690 </span>            :     double xjm, ztr, eps1;</a>
+<a name="13691"><span class="lineNum">   13691 </span>            :     int jblk, nblk;</a>
+<a name="13692"><span class="lineNum">   13692 </span>            :     int jmax;</a>
+<a name="13693"><span class="lineNum">   13693 </span>            : </a>
+<a name="13694"><span class="lineNum">   13694 </span>            :     int iseed[4], gpind, iinfo;</a>
+<a name="13695"><span class="lineNum">   13695 </span>            :     double ortol;</a>
+<a name="13696"><span class="lineNum">   13696 </span>            :     int indrv1, indrv2, indrv3, indrv4, indrv5;</a>
+<a name="13697"><span class="lineNum">   13697 </span>            :     int nrmchk;</a>
+<a name="13698"><span class="lineNum">   13698 </span>            :     int blksiz;</a>
+<a name="13699"><span class="lineNum">   13699 </span>            :     double onenrm, dtpcrt, pertol;</a>
+<a name="13700"><span class="lineNum">   13700 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="13701"><span class="lineNum">   13701 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="13702"><span class="lineNum">   13702 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="13703"><span class="lineNum">   13703 </span>            : </a>
+<a name="13704"><span class="lineNum">   13704 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="13705"><span class="lineNum">   13705 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="13706"><span class="lineNum">   13706 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="13707"><span class="lineNum">   13707 </span><span class="lineNoCov">          0 :     --iblock;</span></a>
+<a name="13708"><span class="lineNum">   13708 </span><span class="lineNoCov">          0 :     --isplit;</span></a>
+<a name="13709"><span class="lineNum">   13709 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="13710"><span class="lineNum">   13710 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="13711"><span class="lineNum">   13711 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="13712"><span class="lineNum">   13712 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="13713"><span class="lineNum">   13713 </span>            :     --iwork;</a>
+<a name="13714"><span class="lineNum">   13714 </span><span class="lineNoCov">          0 :     --ifail;</span></a>
+<a name="13715"><span class="lineNum">   13715 </span>            : </a>
+<a name="13716"><span class="lineNum">   13716 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="13717"><span class="lineNum">   13717 </span>            : </a>
+<a name="13718"><span class="lineNum">   13718 </span>            :     xjm = 0.0;</a>
+<a name="13719"><span class="lineNum">   13719 </span><span class="lineNoCov">          0 :     i__1 = *m;</span></a>
+<a name="13720"><span class="lineNum">   13720 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="13721"><span class="lineNum">   13721 </span><span class="lineNoCov">          0 :         ifail[i__] = 0;</span></a>
+<a name="13722"><span class="lineNum">   13722 </span>            :     }</a>
+<a name="13723"><span class="lineNum">   13723 </span>            : </a>
+<a name="13724"><span class="lineNum">   13724 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="13725"><span class="lineNum">   13725 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="13726"><span class="lineNum">   13726 </span><span class="lineNoCov">          0 :     } else if (*m &lt; 0 || *m &gt; *n) {</span></a>
+<a name="13727"><span class="lineNum">   13727 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="13728"><span class="lineNum">   13728 </span><span class="lineNoCov">          0 :     } else if (*ldz &lt; (*n)) {</span></a>
+<a name="13729"><span class="lineNum">   13729 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="13730"><span class="lineNum">   13730 </span>            :     } else {</a>
+<a name="13731"><span class="lineNum">   13731 </span>            :         i__1 = *m;</a>
+<a name="13732"><span class="lineNum">   13732 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="13733"><span class="lineNum">   13733 </span><span class="lineNoCov">          0 :             if (iblock[j] &lt; iblock[j - 1]) {</span></a>
+<a name="13734"><span class="lineNum">   13734 </span><span class="lineNoCov">          0 :                 *info = -6;</span></a>
+<a name="13735"><span class="lineNum">   13735 </span><span class="lineNoCov">          0 :                 break;</span></a>
+<a name="13736"><span class="lineNum">   13736 </span>            :             }</a>
+<a name="13737"><span class="lineNum">   13737 </span><span class="lineNoCov">          0 :             if (iblock[j] == iblock[j - 1] &amp;&amp; w[j] &lt; w[j - 1]) {</span></a>
+<a name="13738"><span class="lineNum">   13738 </span><span class="lineNoCov">          0 :                 *info = -5;</span></a>
+<a name="13739"><span class="lineNum">   13739 </span><span class="lineNoCov">          0 :                 break;</span></a>
+<a name="13740"><span class="lineNum">   13740 </span>            :             }</a>
+<a name="13741"><span class="lineNum">   13741 </span>            :         }</a>
+<a name="13742"><span class="lineNum">   13742 </span>            :     }</a>
+<a name="13743"><span class="lineNum">   13743 </span>            : </a>
+<a name="13744"><span class="lineNum">   13744 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="13745"><span class="lineNum">   13745 </span>            :         return;</a>
+<a name="13746"><span class="lineNum">   13746 </span>            :     }</a>
+<a name="13747"><span class="lineNum">   13747 </span>            : </a>
+<a name="13748"><span class="lineNum">   13748 </span><span class="lineNoCov">          0 :     if (*n == 0 || *m == 0) {</span></a>
+<a name="13749"><span class="lineNum">   13749 </span>            :         return;</a>
+<a name="13750"><span class="lineNum">   13750 </span><span class="lineNoCov">          0 :     } else if (*n == 1) {</span></a>
+<a name="13751"><span class="lineNum">   13751 </span><span class="lineNoCov">          0 :         z__[z_dim1 + 1] = 1.;</span></a>
+<a name="13752"><span class="lineNum">   13752 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="13753"><span class="lineNum">   13753 </span>            :     }</a>
+<a name="13754"><span class="lineNum">   13754 </span>            : </a>
+<a name="13755"><span class="lineNum">   13755 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="13756"><span class="lineNum">   13756 </span>            : </a>
+<a name="13757"><span class="lineNum">   13757 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= 4; ++i__) {</span></a>
+<a name="13758"><span class="lineNum">   13758 </span><span class="lineNoCov">          0 :         iseed[i__ - 1] = 1;</span></a>
+<a name="13759"><span class="lineNum">   13759 </span>            :     }</a>
+<a name="13760"><span class="lineNum">   13760 </span>            : </a>
+<a name="13761"><span class="lineNum">   13761 </span>            :     indrv1 = 0;</a>
+<a name="13762"><span class="lineNum">   13762 </span>            :     indrv2 = indrv1 + *n;</a>
+<a name="13763"><span class="lineNum">   13763 </span><span class="lineNoCov">          0 :     indrv3 = indrv2 + *n;</span></a>
+<a name="13764"><span class="lineNum">   13764 </span><span class="lineNoCov">          0 :     indrv4 = indrv3 + *n;</span></a>
+<a name="13765"><span class="lineNum">   13765 </span><span class="lineNoCov">          0 :     indrv5 = indrv4 + *n;</span></a>
+<a name="13766"><span class="lineNum">   13766 </span>            : </a>
+<a name="13767"><span class="lineNum">   13767 </span>            :     j1 = 1;</a>
+<a name="13768"><span class="lineNum">   13768 </span><span class="lineNoCov">          0 :     i__1 = iblock[*m];</span></a>
+<a name="13769"><span class="lineNum">   13769 </span><span class="lineNoCov">          0 :     for (nblk = 1; nblk &lt;= i__1; ++nblk) {</span></a>
+<a name="13770"><span class="lineNum">   13770 </span>            : </a>
+<a name="13771"><span class="lineNum">   13771 </span><span class="lineNoCov">          0 :         if (nblk == 1) {</span></a>
+<a name="13772"><span class="lineNum">   13772 </span>            :             b1 = 1;</a>
+<a name="13773"><span class="lineNum">   13773 </span>            :         } else {</a>
+<a name="13774"><span class="lineNum">   13774 </span><span class="lineNoCov">          0 :             b1 = isplit[nblk - 1] + 1;</span></a>
+<a name="13775"><span class="lineNum">   13775 </span>            :         }</a>
+<a name="13776"><span class="lineNum">   13776 </span><span class="lineNoCov">          0 :         bn = isplit[nblk];</span></a>
+<a name="13777"><span class="lineNum">   13777 </span><span class="lineNoCov">          0 :         blksiz = bn - b1 + 1;</span></a>
+<a name="13778"><span class="lineNum">   13778 </span><span class="lineNoCov">          0 :         if (blksiz == 1) {</span></a>
+<a name="13779"><span class="lineNum">   13779 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="13780"><span class="lineNum">   13780 </span>            :         }</a>
+<a name="13781"><span class="lineNum">   13781 </span>            :         gpind = b1;</a>
+<a name="13782"><span class="lineNum">   13782 </span>            : </a>
+<a name="13783"><span class="lineNum">   13783 </span><span class="lineNoCov">          0 :         onenrm = std::abs(d__[b1]) + std::abs(e[b1]);</span></a>
+<a name="13784"><span class="lineNum">   13784 </span>            :         d__3 = onenrm;</a>
+<a name="13785"><span class="lineNum">   13785 </span><span class="lineNoCov">          0 :         d__4 = std::abs(d__[bn]) + std::abs(e[bn - 1]);</span></a>
+<a name="13786"><span class="lineNum">   13786 </span><span class="lineNoCov">          0 :         onenrm = (d__3&gt;d__4) ? d__3 : d__4;</span></a>
+<a name="13787"><span class="lineNum">   13787 </span>            :         i__2 = bn - 1;</a>
+<a name="13788"><span class="lineNum">   13788 </span><span class="lineNoCov">          0 :         for (i__ = b1 + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="13789"><span class="lineNum">   13789 </span>            :           d__4 = onenrm;</a>
+<a name="13790"><span class="lineNum">   13790 </span><span class="lineNoCov">          0 :           d__5 = std::abs(d__[i__]) + std::abs(e[i__ - 1]) + std::abs(e[i__]);</span></a>
+<a name="13791"><span class="lineNum">   13791 </span><span class="lineNoCov">          0 :             onenrm = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="13792"><span class="lineNum">   13792 </span>            :         }</a>
+<a name="13793"><span class="lineNum">   13793 </span><span class="lineNoCov">          0 :         ortol = onenrm * .001;</span></a>
+<a name="13794"><span class="lineNum">   13794 </span>            : </a>
+<a name="13795"><span class="lineNum">   13795 </span><span class="lineNoCov">          0 :         dtpcrt =  std::sqrt(.1 / blksiz);</span></a>
+<a name="13796"><span class="lineNum">   13796 </span>            : </a>
+<a name="13797"><span class="lineNum">   13797 </span>            :         jblk = 0;</a>
+<a name="13798"><span class="lineNum">   13798 </span><span class="lineNoCov">          0 :         i__2 = *m;</span></a>
+<a name="13799"><span class="lineNum">   13799 </span><span class="lineNoCov">          0 :         for (j = j1; j &lt;= i__2; ++j) {</span></a>
+<a name="13800"><span class="lineNum">   13800 </span><span class="lineNoCov">          0 :             if (iblock[j] != nblk) {</span></a>
+<a name="13801"><span class="lineNum">   13801 </span>            :                 j1 = j;</a>
+<a name="13802"><span class="lineNum">   13802 </span>            :                 break;</a>
+<a name="13803"><span class="lineNum">   13803 </span>            :             }</a>
+<a name="13804"><span class="lineNum">   13804 </span><span class="lineNoCov">          0 :             ++jblk;</span></a>
+<a name="13805"><span class="lineNum">   13805 </span><span class="lineNoCov">          0 :             xj = w[j];</span></a>
+<a name="13806"><span class="lineNum">   13806 </span>            : </a>
+<a name="13807"><span class="lineNum">   13807 </span><span class="lineNoCov">          0 :             if (blksiz == 1) {</span></a>
+<a name="13808"><span class="lineNum">   13808 </span><span class="lineNoCov">          0 :                 work[indrv1 + 1] = 1.;</span></a>
+<a name="13809"><span class="lineNum">   13809 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="13810"><span class="lineNum">   13810 </span>            :             }</a>
+<a name="13811"><span class="lineNum">   13811 </span>            : </a>
+<a name="13812"><span class="lineNum">   13812 </span><span class="lineNoCov">          0 :             if (jblk &gt; 1) {</span></a>
+<a name="13813"><span class="lineNum">   13813 </span><span class="lineNoCov">          0 :                 eps1 = std::abs(eps * xj);</span></a>
+<a name="13814"><span class="lineNum">   13814 </span><span class="lineNoCov">          0 :                 pertol = eps1 * 10.;</span></a>
+<a name="13815"><span class="lineNum">   13815 </span><span class="lineNoCov">          0 :                 sep = xj - xjm;</span></a>
+<a name="13816"><span class="lineNum">   13816 </span><span class="lineNoCov">          0 :                 if (sep &lt; pertol) {</span></a>
+<a name="13817"><span class="lineNum">   13817 </span><span class="lineNoCov">          0 :                     xj = xjm + pertol;</span></a>
+<a name="13818"><span class="lineNum">   13818 </span>            :                 }</a>
+<a name="13819"><span class="lineNum">   13819 </span>            :             }</a>
+<a name="13820"><span class="lineNum">   13820 </span>            : </a>
+<a name="13821"><span class="lineNum">   13821 </span>            :             its = 0;</a>
+<a name="13822"><span class="lineNum">   13822 </span>            :             nrmchk = 0;</a>
+<a name="13823"><span class="lineNum">   13823 </span>            : </a>
+<a name="13824"><span class="lineNum">   13824 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlarnv,DLARNV)(&amp;c__2, iseed, &amp;blksiz, &amp;work[indrv1 + 1]);</span></a>
+<a name="13825"><span class="lineNum">   13825 </span>            : </a>
+<a name="13826"><span class="lineNum">   13826 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;blksiz, &amp;d__[b1], &amp;c__1, &amp;work[indrv4 + 1], &amp;c__1);</span></a>
+<a name="13827"><span class="lineNum">   13827 </span><span class="lineNoCov">          0 :             i__3 = blksiz - 1;</span></a>
+<a name="13828"><span class="lineNum">   13828 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__3, &amp;e[b1], &amp;c__1, &amp;work[indrv2 + 2], &amp;c__1);</span></a>
+<a name="13829"><span class="lineNum">   13829 </span><span class="lineNoCov">          0 :             i__3 = blksiz - 1;</span></a>
+<a name="13830"><span class="lineNum">   13830 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__3, &amp;e[b1], &amp;c__1, &amp;work[indrv3 + 1], &amp;c__1);</span></a>
+<a name="13831"><span class="lineNum">   13831 </span>            : </a>
+<a name="13832"><span class="lineNum">   13832 </span><span class="lineNoCov">          0 :             tol = 0.;</span></a>
+<a name="13833"><span class="lineNum">   13833 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlagtf,DLAGTF)(&amp;blksiz, &amp;work[indrv4 + 1], &amp;xj, &amp;work[indrv2 + 2], &amp;work[</span></a>
+<a name="13834"><span class="lineNum">   13834 </span><span class="lineNoCov">          0 :                     indrv3 + 1], &amp;tol, &amp;work[indrv5 + 1], &amp;iwork[1], &amp;iinfo);</span></a>
+<a name="13835"><span class="lineNum">   13835 </span>            : </a>
+<a name="13836"><span class="lineNum">   13836 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="13837"><span class="lineNum">   13837 </span><span class="lineNoCov">          0 :             ++its;</span></a>
+<a name="13838"><span class="lineNum">   13838 </span><span class="lineNoCov">          0 :             if (its &gt; 5) {</span></a>
+<a name="13839"><span class="lineNum">   13839 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="13840"><span class="lineNum">   13840 </span>            :             }</a>
+<a name="13841"><span class="lineNum">   13841 </span>            : </a>
+<a name="13842"><span class="lineNum">   13842 </span>            :             d__2 = eps;</a>
+<a name="13843"><span class="lineNum">   13843 </span><span class="lineNoCov">          0 :             d__3 = std::abs(work[indrv4 + blksiz]);</span></a>
+<a name="13844"><span class="lineNum">   13844 </span><span class="lineNoCov">          0 :             scl = blksiz * onenrm * ((d__2&gt;d__3) ? d__2 : d__3) / PLUMED_BLAS_F77_FUNC(dasum,DASUM)(&amp;blksiz, &amp;work[</span></a>
+<a name="13845"><span class="lineNum">   13845 </span>            :                     indrv1 + 1], &amp;c__1);</a>
+<a name="13846"><span class="lineNum">   13846 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;blksiz, &amp;scl, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="13847"><span class="lineNum">   13847 </span>            : </a>
+<a name="13848"><span class="lineNum">   13848 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlagts,DLAGTS)(&amp;c_n1, &amp;blksiz, &amp;work[indrv4 + 1], &amp;work[indrv2 + 2], &amp;</span></a>
+<a name="13849"><span class="lineNum">   13849 </span>            :                     work[indrv3 + 1], &amp;work[indrv5 + 1], &amp;iwork[1], &amp;work[</a>
+<a name="13850"><span class="lineNum">   13850 </span>            :                     indrv1 + 1], &amp;tol, &amp;iinfo);</a>
+<a name="13851"><span class="lineNum">   13851 </span>            : </a>
+<a name="13852"><span class="lineNum">   13852 </span><span class="lineNoCov">          0 :             if (jblk == 1) {</span></a>
+<a name="13853"><span class="lineNum">   13853 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="13854"><span class="lineNum">   13854 </span>            :             }</a>
+<a name="13855"><span class="lineNum">   13855 </span><span class="lineNoCov">          0 :             if (std::abs(xj - xjm) &gt; ortol) {</span></a>
+<a name="13856"><span class="lineNum">   13856 </span>            :                 gpind = j;</a>
+<a name="13857"><span class="lineNum">   13857 </span>            :             }</a>
+<a name="13858"><span class="lineNum">   13858 </span><span class="lineNoCov">          0 :             if (gpind != j) {</span></a>
+<a name="13859"><span class="lineNum">   13859 </span><span class="lineNoCov">          0 :                 i__3 = j - 1;</span></a>
+<a name="13860"><span class="lineNum">   13860 </span><span class="lineNoCov">          0 :                 for (i__ = gpind; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="13861"><span class="lineNum">   13861 </span><span class="lineNoCov">          0 :                     ztr = -PLUMED_BLAS_F77_FUNC(ddot,DDOT)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1, &amp;z__[b1 + </span></a>
+<a name="13862"><span class="lineNum">   13862 </span><span class="lineNoCov">          0 :                             i__ * z_dim1], &amp;c__1);</span></a>
+<a name="13863"><span class="lineNum">   13863 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(&amp;blksiz, &amp;ztr, &amp;z__[b1 + i__ * z_dim1], &amp;c__1, &amp;</span></a>
+<a name="13864"><span class="lineNum">   13864 </span>            :                             work[indrv1 + 1], &amp;c__1);</a>
+<a name="13865"><span class="lineNum">   13865 </span>            :                 }</a>
+<a name="13866"><span class="lineNum">   13866 </span>            :             }</a>
+<a name="13867"><span class="lineNum">   13867 </span>            : </a>
+<a name="13868"><span class="lineNum">   13868 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="13869"><span class="lineNum">   13869 </span><span class="lineNoCov">          0 :             jmax = PLUMED_BLAS_F77_FUNC(idamax,IDAMAX)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="13870"><span class="lineNum">   13870 </span><span class="lineNoCov">          0 :             nrm = std::abs(work[indrv1 + jmax]);</span></a>
+<a name="13871"><span class="lineNum">   13871 </span>            : </a>
+<a name="13872"><span class="lineNum">   13872 </span><span class="lineNoCov">          0 :             if (nrm &lt; dtpcrt) {</span></a>
+<a name="13873"><span class="lineNum">   13873 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="13874"><span class="lineNum">   13874 </span>            :             }</a>
+<a name="13875"><span class="lineNum">   13875 </span><span class="lineNoCov">          0 :             ++nrmchk;</span></a>
+<a name="13876"><span class="lineNum">   13876 </span><span class="lineNoCov">          0 :             if (nrmchk &lt; 3) {</span></a>
+<a name="13877"><span class="lineNum">   13877 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="13878"><span class="lineNum">   13878 </span>            :             }</a>
+<a name="13879"><span class="lineNum">   13879 </span>            : </a>
+<a name="13880"><span class="lineNum">   13880 </span><span class="lineNoCov">          0 :             goto L110;</span></a>
+<a name="13881"><span class="lineNum">   13881 </span>            : </a>
+<a name="13882"><span class="lineNum">   13882 </span>            : L100:</a>
+<a name="13883"><span class="lineNum">   13883 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="13884"><span class="lineNum">   13884 </span><span class="lineNoCov">          0 :             ifail[*info] = j;</span></a>
+<a name="13885"><span class="lineNum">   13885 </span>            : </a>
+<a name="13886"><span class="lineNum">   13886 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="13887"><span class="lineNum">   13887 </span><span class="lineNoCov">          0 :             scl = 1. / PLUMED_BLAS_F77_FUNC(dnrm2,DNRM2)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="13888"><span class="lineNum">   13888 </span><span class="lineNoCov">          0 :             jmax = PLUMED_BLAS_F77_FUNC(idamax,IDAMAX)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="13889"><span class="lineNum">   13889 </span><span class="lineNoCov">          0 :             if (work[indrv1 + jmax] &lt; 0.) {</span></a>
+<a name="13890"><span class="lineNum">   13890 </span><span class="lineNoCov">          0 :                 scl = -scl;</span></a>
+<a name="13891"><span class="lineNum">   13891 </span>            :             }</a>
+<a name="13892"><span class="lineNum">   13892 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;blksiz, &amp;scl, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="13893"><span class="lineNum">   13893 </span><span class="lineNoCov">          0 : L120:</span></a>
+<a name="13894"><span class="lineNum">   13894 </span><span class="lineNoCov">          0 :             i__3 = *n;</span></a>
+<a name="13895"><span class="lineNum">   13895 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="13896"><span class="lineNum">   13896 </span><span class="lineNoCov">          0 :                 z__[i__ + j * z_dim1] = 0.;</span></a>
+<a name="13897"><span class="lineNum">   13897 </span>            :             }</a>
+<a name="13898"><span class="lineNum">   13898 </span><span class="lineNoCov">          0 :             i__3 = blksiz;</span></a>
+<a name="13899"><span class="lineNum">   13899 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="13900"><span class="lineNum">   13900 </span><span class="lineNoCov">          0 :                 z__[b1 + i__ - 1 + j * z_dim1] = work[indrv1 + i__];</span></a>
+<a name="13901"><span class="lineNum">   13901 </span>            :             }</a>
+<a name="13902"><span class="lineNum">   13902 </span>            : </a>
+<a name="13903"><span class="lineNum">   13903 </span><span class="lineNoCov">          0 :             xjm = xj;</span></a>
+<a name="13904"><span class="lineNum">   13904 </span>            :         }</a>
+<a name="13905"><span class="lineNum">   13905 </span>            :     }</a>
+<a name="13906"><span class="lineNum">   13906 </span>            : </a>
+<a name="13907"><span class="lineNum">   13907 </span>            :     return;</a>
+<a name="13908"><span class="lineNum">   13908 </span>            : </a>
+<a name="13909"><span class="lineNum">   13909 </span>            : }</a>
+<a name="13910"><span class="lineNum">   13910 </span>            : </a>
+<a name="13911"><span class="lineNum">   13911 </span>            : </a>
+<a name="13912"><span class="lineNum">   13912 </span>            : }</a>
+<a name="13913"><span class="lineNum">   13913 </span>            : }</a>
+<a name="13914"><span class="lineNum">   13914 </span>            : #include &lt;cmath&gt;</a>
+<a name="13915"><span class="lineNum">   13915 </span>            : #include &quot;real.h&quot;</a>
+<a name="13916"><span class="lineNum">   13916 </span>            : </a>
+<a name="13917"><span class="lineNum">   13917 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="13918"><span class="lineNum">   13918 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="13919"><span class="lineNum">   13919 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="13920"><span class="lineNum">   13920 </span>            : </a>
+<a name="13921"><span class="lineNum">   13921 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="13922"><span class="lineNum">   13922 </span>            : namespace PLMD{</a>
+<a name="13923"><span class="lineNum">   13923 </span>            : namespace lapack{</a>
+<a name="13924"><span class="lineNum">   13924 </span>            : using namespace blas;</a>
+<a name="13925"><span class="lineNum">   13925 </span>            : void</a>
+<a name="13926"><span class="lineNum">   13926 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dsteqr,DSTEQR)(const char *    compz, </span></a>
+<a name="13927"><span class="lineNum">   13927 </span>            :         int *     n, </a>
+<a name="13928"><span class="lineNum">   13928 </span>            :         double *  d__, </a>
+<a name="13929"><span class="lineNum">   13929 </span>            :         double *  e, </a>
+<a name="13930"><span class="lineNum">   13930 </span>            :         double *  z__, </a>
+<a name="13931"><span class="lineNum">   13931 </span>            :         int *     ldz, </a>
+<a name="13932"><span class="lineNum">   13932 </span>            :         double *  work, </a>
+<a name="13933"><span class="lineNum">   13933 </span>            :         int *     info)</a>
+<a name="13934"><span class="lineNum">   13934 </span>            : {</a>
+<a name="13935"><span class="lineNum">   13935 </span><span class="lineNoCov">          0 :     double c_b9 = 0.;</span></a>
+<a name="13936"><span class="lineNum">   13936 </span><span class="lineNoCov">          0 :     double c_b10 = 1.;</span></a>
+<a name="13937"><span class="lineNum">   13937 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="13938"><span class="lineNum">   13938 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="13939"><span class="lineNum">   13939 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="13940"><span class="lineNum">   13940 </span>            :     int z_dim1, z_offset, i__1, i__2;</a>
+<a name="13941"><span class="lineNum">   13941 </span>            :     double d__1, d__2;</a>
+<a name="13942"><span class="lineNum">   13942 </span>            : </a>
+<a name="13943"><span class="lineNum">   13943 </span>            :     double b, c__, f, g;</a>
+<a name="13944"><span class="lineNum">   13944 </span>            :     int i__, j, k, l, m;</a>
+<a name="13945"><span class="lineNum">   13945 </span>            :     double p, r__, s;</a>
+<a name="13946"><span class="lineNum">   13946 </span>            :     int l1, ii, mm, lm1, mm1, nm1;</a>
+<a name="13947"><span class="lineNum">   13947 </span>            :     double rt1, rt2, eps;</a>
+<a name="13948"><span class="lineNum">   13948 </span>            :     int lsv;</a>
+<a name="13949"><span class="lineNum">   13949 </span>            :     double tst, eps2;</a>
+<a name="13950"><span class="lineNum">   13950 </span>            :     int lend, jtot;</a>
+<a name="13951"><span class="lineNum">   13951 </span>            :     double anorm;</a>
+<a name="13952"><span class="lineNum">   13952 </span>            :     int lendm1, lendp1;</a>
+<a name="13953"><span class="lineNum">   13953 </span>            :     int iscale;</a>
+<a name="13954"><span class="lineNum">   13954 </span>            :     double safmin,minval;</a>
+<a name="13955"><span class="lineNum">   13955 </span>            :     double safmax;</a>
+<a name="13956"><span class="lineNum">   13956 </span>            :     int lendsv;</a>
+<a name="13957"><span class="lineNum">   13957 </span>            :     double ssfmin;</a>
+<a name="13958"><span class="lineNum">   13958 </span>            :     int nmaxit, icompz;</a>
+<a name="13959"><span class="lineNum">   13959 </span>            :     double ssfmax;</a>
+<a name="13960"><span class="lineNum">   13960 </span>            : </a>
+<a name="13961"><span class="lineNum">   13961 </span>            : </a>
+<a name="13962"><span class="lineNum">   13962 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="13963"><span class="lineNum">   13963 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="13964"><span class="lineNum">   13964 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="13965"><span class="lineNum">   13965 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="13966"><span class="lineNum">   13966 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="13967"><span class="lineNum">   13967 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="13968"><span class="lineNum">   13968 </span>            : </a>
+<a name="13969"><span class="lineNum">   13969 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="13970"><span class="lineNum">   13970 </span>            : </a>
+<a name="13971"><span class="lineNum">   13971 </span><span class="lineNoCov">          0 :     if (*compz=='N' || *compz=='n') {</span></a>
+<a name="13972"><span class="lineNum">   13972 </span>            :         icompz = 0;</a>
+<a name="13973"><span class="lineNum">   13973 </span><span class="lineNoCov">          0 :     } else if (*compz=='V' || *compz=='v') {</span></a>
+<a name="13974"><span class="lineNum">   13974 </span>            :         icompz = 1;</a>
+<a name="13975"><span class="lineNum">   13975 </span>            :     } else if (*compz=='I' || *compz=='i') {</a>
+<a name="13976"><span class="lineNum">   13976 </span>            :         icompz = 2;</a>
+<a name="13977"><span class="lineNum">   13977 </span>            :     } else {</a>
+<a name="13978"><span class="lineNum">   13978 </span>            :         icompz = -1;</a>
+<a name="13979"><span class="lineNum">   13979 </span>            :     }</a>
+<a name="13980"><span class="lineNum">   13980 </span>            :     if (icompz &lt; 0) {</a>
+<a name="13981"><span class="lineNum">   13981 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="13982"><span class="lineNum">   13982 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="13983"><span class="lineNum">   13983 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="13984"><span class="lineNum">   13984 </span><span class="lineNoCov">          0 :     } else if (*ldz &lt; 1 || (icompz &gt; 0 &amp;&amp; *ldz &lt; ((*n&gt;1) ? *n : 1))) {</span></a>
+<a name="13985"><span class="lineNum">   13985 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="13986"><span class="lineNum">   13986 </span>            :     }</a>
+<a name="13987"><span class="lineNum">   13987 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="13988"><span class="lineNum">   13988 </span>            :         return;</a>
+<a name="13989"><span class="lineNum">   13989 </span>            :     }</a>
+<a name="13990"><span class="lineNum">   13990 </span>            : </a>
+<a name="13991"><span class="lineNum">   13991 </span>            : </a>
+<a name="13992"><span class="lineNum">   13992 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="13993"><span class="lineNum">   13993 </span>            :         return;</a>
+<a name="13994"><span class="lineNum">   13994 </span>            :     }</a>
+<a name="13995"><span class="lineNum">   13995 </span>            : </a>
+<a name="13996"><span class="lineNum">   13996 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="13997"><span class="lineNum">   13997 </span><span class="lineNoCov">          0 :         if (icompz == 2) {</span></a>
+<a name="13998"><span class="lineNum">   13998 </span><span class="lineNoCov">          0 :             z__[z_dim1 + 1] = 1.;</span></a>
+<a name="13999"><span class="lineNum">   13999 </span>            :         }</a>
+<a name="14000"><span class="lineNum">   14000 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="14001"><span class="lineNum">   14001 </span>            :     }</a>
+<a name="14002"><span class="lineNum">   14002 </span>            : </a>
+<a name="14003"><span class="lineNum">   14003 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="14004"><span class="lineNum">   14004 </span>            :     d__1 = eps;</a>
+<a name="14005"><span class="lineNum">   14005 </span>            :     eps2 = d__1 * d__1;</a>
+<a name="14006"><span class="lineNum">   14006 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="14007"><span class="lineNum">   14007 </span>            :     safmin = minval*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="14008"><span class="lineNum">   14008 </span>            : </a>
+<a name="14009"><span class="lineNum">   14009 </span>            :     safmax = 1. / safmin;</a>
+<a name="14010"><span class="lineNum">   14010 </span><span class="lineNoCov">          0 :     ssfmax =  std::sqrt(safmax) / 3.;</span></a>
+<a name="14011"><span class="lineNum">   14011 </span><span class="lineNoCov">          0 :     ssfmin =  std::sqrt(safmin) / eps2;</span></a>
+<a name="14012"><span class="lineNum">   14012 </span>            : </a>
+<a name="14013"><span class="lineNum">   14013 </span><span class="lineNoCov">          0 :     if (icompz == 2) {</span></a>
+<a name="14014"><span class="lineNum">   14014 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlaset,DLASET)(&quot;Full&quot;, n, n, &amp;c_b9, &amp;c_b10, &amp;z__[z_offset], ldz);</span></a>
+<a name="14015"><span class="lineNum">   14015 </span>            :     }</a>
+<a name="14016"><span class="lineNum">   14016 </span>            : </a>
+<a name="14017"><span class="lineNum">   14017 </span><span class="lineNoCov">          0 :     nmaxit = *n * 30;</span></a>
+<a name="14018"><span class="lineNum">   14018 </span>            :     jtot = 0;</a>
+<a name="14019"><span class="lineNum">   14019 </span>            : </a>
+<a name="14020"><span class="lineNum">   14020 </span>            :     l1 = 1;</a>
+<a name="14021"><span class="lineNum">   14021 </span><span class="lineNoCov">          0 :     nm1 = *n - 1;</span></a>
+<a name="14022"><span class="lineNum">   14022 </span>            : </a>
+<a name="14023"><span class="lineNum">   14023 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="14024"><span class="lineNum">   14024 </span><span class="lineNoCov">          0 :     if (l1 &gt; *n) {</span></a>
+<a name="14025"><span class="lineNum">   14025 </span><span class="lineNoCov">          0 :         goto L160;</span></a>
+<a name="14026"><span class="lineNum">   14026 </span>            :     }</a>
+<a name="14027"><span class="lineNum">   14027 </span><span class="lineNoCov">          0 :     if (l1 &gt; 1) {</span></a>
+<a name="14028"><span class="lineNum">   14028 </span><span class="lineNoCov">          0 :         e[l1 - 1] = 0.;</span></a>
+<a name="14029"><span class="lineNum">   14029 </span>            :     }</a>
+<a name="14030"><span class="lineNum">   14030 </span><span class="lineNoCov">          0 :     if (l1 &lt;= nm1) {</span></a>
+<a name="14031"><span class="lineNum">   14031 </span><span class="lineNoCov">          0 :         i__1 = nm1;</span></a>
+<a name="14032"><span class="lineNum">   14032 </span><span class="lineNoCov">          0 :         for (m = l1; m &lt;= i__1; ++m) {</span></a>
+<a name="14033"><span class="lineNum">   14033 </span><span class="lineNoCov">          0 :             tst = std::abs(e[m]);</span></a>
+<a name="14034"><span class="lineNum">   14034 </span><span class="lineNoCov">          0 :             if (std::abs(tst)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="14035"><span class="lineNum">   14035 </span><span class="lineNoCov">          0 :                 goto L30;</span></a>
+<a name="14036"><span class="lineNum">   14036 </span>            :             }</a>
+<a name="14037"><span class="lineNum">   14037 </span><span class="lineNoCov">          0 :             if (tst &lt;=  std::sqrt(std::abs(d__[m])) * std::sqrt(std::abs(d__[m + 1])) * eps) {</span></a>
+<a name="14038"><span class="lineNum">   14038 </span><span class="lineNoCov">          0 :                 e[m] = 0.;</span></a>
+<a name="14039"><span class="lineNum">   14039 </span><span class="lineNoCov">          0 :                 goto L30;</span></a>
+<a name="14040"><span class="lineNum">   14040 </span>            :             }</a>
+<a name="14041"><span class="lineNum">   14041 </span>            :         }</a>
+<a name="14042"><span class="lineNum">   14042 </span>            :     }</a>
+<a name="14043"><span class="lineNum">   14043 </span><span class="lineNoCov">          0 :     m = *n;</span></a>
+<a name="14044"><span class="lineNum">   14044 </span>            : </a>
+<a name="14045"><span class="lineNum">   14045 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="14046"><span class="lineNum">   14046 </span>            :     l = l1;</a>
+<a name="14047"><span class="lineNum">   14047 </span>            :     lsv = l;</a>
+<a name="14048"><span class="lineNum">   14048 </span>            :     lend = m;</a>
+<a name="14049"><span class="lineNum">   14049 </span>            :     lendsv = lend;</a>
+<a name="14050"><span class="lineNum">   14050 </span><span class="lineNoCov">          0 :     l1 = m + 1;</span></a>
+<a name="14051"><span class="lineNum">   14051 </span><span class="lineNoCov">          0 :     if (lend == l) {</span></a>
+<a name="14052"><span class="lineNum">   14052 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="14053"><span class="lineNum">   14053 </span>            :     }</a>
+<a name="14054"><span class="lineNum">   14054 </span>            : </a>
+<a name="14055"><span class="lineNum">   14055 </span><span class="lineNoCov">          0 :     i__1 = lend - l + 1;</span></a>
+<a name="14056"><span class="lineNum">   14056 </span><span class="lineNoCov">          0 :     anorm = PLUMED_BLAS_F77_FUNC(dlanst,DLANST)(&quot;I&quot;, &amp;i__1, &amp;d__[l], &amp;e[l]);</span></a>
+<a name="14057"><span class="lineNum">   14057 </span>            :     iscale = 0;</a>
+<a name="14058"><span class="lineNum">   14058 </span><span class="lineNoCov">          0 :     if (std::abs(anorm)&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="14059"><span class="lineNum">   14059 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="14060"><span class="lineNum">   14060 </span>            :     }</a>
+<a name="14061"><span class="lineNum">   14061 </span><span class="lineNoCov">          0 :     if (anorm &gt; ssfmax) {</span></a>
+<a name="14062"><span class="lineNum">   14062 </span>            :         iscale = 1;</a>
+<a name="14063"><span class="lineNum">   14063 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="14064"><span class="lineNum">   14064 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="14065"><span class="lineNum">   14065 </span>            :                 info);</a>
+<a name="14066"><span class="lineNum">   14066 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="14067"><span class="lineNum">   14067 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="14068"><span class="lineNum">   14068 </span>            :                 info);</a>
+<a name="14069"><span class="lineNum">   14069 </span><span class="lineNoCov">          0 :     } else if (anorm &lt; ssfmin) {</span></a>
+<a name="14070"><span class="lineNum">   14070 </span>            :         iscale = 2;</a>
+<a name="14071"><span class="lineNum">   14071 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="14072"><span class="lineNum">   14072 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="14073"><span class="lineNum">   14073 </span>            :                 info);</a>
+<a name="14074"><span class="lineNum">   14074 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="14075"><span class="lineNum">   14075 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="14076"><span class="lineNum">   14076 </span>            :                 info);</a>
+<a name="14077"><span class="lineNum">   14077 </span>            :     }</a>
+<a name="14078"><span class="lineNum">   14078 </span>            : </a>
+<a name="14079"><span class="lineNum">   14079 </span><span class="lineNoCov">          0 :     if (std::abs(d__[lend]) &lt; std::abs(d__[l])) {</span></a>
+<a name="14080"><span class="lineNum">   14080 </span>            :         lend = lsv;</a>
+<a name="14081"><span class="lineNum">   14081 </span>            :         l = lendsv;</a>
+<a name="14082"><span class="lineNum">   14082 </span>            :     }</a>
+<a name="14083"><span class="lineNum">   14083 </span>            : </a>
+<a name="14084"><span class="lineNum">   14084 </span><span class="lineNoCov">          0 :     if (lend &gt; l) {</span></a>
+<a name="14085"><span class="lineNum">   14085 </span>            : </a>
+<a name="14086"><span class="lineNum">   14086 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="14087"><span class="lineNum">   14087 </span><span class="lineNoCov">          0 :         if (l != lend) {</span></a>
+<a name="14088"><span class="lineNum">   14088 </span><span class="lineNoCov">          0 :             lendm1 = lend - 1;</span></a>
+<a name="14089"><span class="lineNum">   14089 </span><span class="lineNoCov">          0 :             i__1 = lendm1;</span></a>
+<a name="14090"><span class="lineNum">   14090 </span><span class="lineNoCov">          0 :             for (m = l; m &lt;= i__1; ++m) {</span></a>
+<a name="14091"><span class="lineNum">   14091 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(e[m]);</span></a>
+<a name="14092"><span class="lineNum">   14092 </span><span class="lineNoCov">          0 :                 tst = d__2 * d__2;</span></a>
+<a name="14093"><span class="lineNum">   14093 </span><span class="lineNoCov">          0 :                 if (tst &lt;= eps2 * std::abs(d__[m]) * std::abs(d__[m+ 1]) + safmin) {</span></a>
+<a name="14094"><span class="lineNum">   14094 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="14095"><span class="lineNum">   14095 </span>            :                 }</a>
+<a name="14096"><span class="lineNum">   14096 </span>            :             }</a>
+<a name="14097"><span class="lineNum">   14097 </span>            :         }</a>
+<a name="14098"><span class="lineNum">   14098 </span>            : </a>
+<a name="14099"><span class="lineNum">   14099 </span>            :         m = lend;</a>
+<a name="14100"><span class="lineNum">   14100 </span>            : </a>
+<a name="14101"><span class="lineNum">   14101 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="14102"><span class="lineNum">   14102 </span><span class="lineNoCov">          0 :         if (m &lt; lend) {</span></a>
+<a name="14103"><span class="lineNum">   14103 </span><span class="lineNoCov">          0 :             e[m] = 0.;</span></a>
+<a name="14104"><span class="lineNum">   14104 </span>            :         }</a>
+<a name="14105"><span class="lineNum">   14105 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="14106"><span class="lineNum">   14106 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="14107"><span class="lineNum">   14107 </span><span class="lineNoCov">          0 :             goto L80;</span></a>
+<a name="14108"><span class="lineNum">   14108 </span>            :         }</a>
+<a name="14109"><span class="lineNum">   14109 </span>            : </a>
+<a name="14110"><span class="lineNum">   14110 </span><span class="lineNoCov">          0 :         if (m == l + 1) {</span></a>
+<a name="14111"><span class="lineNum">   14111 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="14112"><span class="lineNum">   14112 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaev2,DLAEV2)(&amp;d__[l], &amp;e[l], &amp;d__[l + 1], &amp;rt1, &amp;rt2, &amp;c__, &amp;s);</span></a>
+<a name="14113"><span class="lineNum">   14113 </span><span class="lineNoCov">          0 :                 work[l] = c__;</span></a>
+<a name="14114"><span class="lineNum">   14114 </span><span class="lineNoCov">          0 :                 work[*n - 1 + l] = s;</span></a>
+<a name="14115"><span class="lineNum">   14115 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, n, &amp;c__2, &amp;work[l], &amp;work[*n - 1 + l], &amp;</span></a>
+<a name="14116"><span class="lineNum">   14116 </span><span class="lineNoCov">          0 :                         z__[l * z_dim1 + 1], ldz);</span></a>
+<a name="14117"><span class="lineNum">   14117 </span>            :             } else {</a>
+<a name="14118"><span class="lineNum">   14118 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlae2,DLAE2)(&amp;d__[l], &amp;e[l], &amp;d__[l + 1], &amp;rt1, &amp;rt2);</span></a>
+<a name="14119"><span class="lineNum">   14119 </span>            :             }</a>
+<a name="14120"><span class="lineNum">   14120 </span><span class="lineNoCov">          0 :             d__[l] = rt1;</span></a>
+<a name="14121"><span class="lineNum">   14121 </span><span class="lineNoCov">          0 :             d__[l + 1] = rt2;</span></a>
+<a name="14122"><span class="lineNum">   14122 </span><span class="lineNoCov">          0 :             e[l] = 0.;</span></a>
+<a name="14123"><span class="lineNum">   14123 </span><span class="lineNoCov">          0 :             l += 2;</span></a>
+<a name="14124"><span class="lineNum">   14124 </span><span class="lineNoCov">          0 :             if (l &lt;= lend) {</span></a>
+<a name="14125"><span class="lineNum">   14125 </span><span class="lineNoCov">          0 :                 goto L40;</span></a>
+<a name="14126"><span class="lineNum">   14126 </span>            :             }</a>
+<a name="14127"><span class="lineNum">   14127 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="14128"><span class="lineNum">   14128 </span>            :         }</a>
+<a name="14129"><span class="lineNum">   14129 </span>            : </a>
+<a name="14130"><span class="lineNum">   14130 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="14131"><span class="lineNum">   14131 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="14132"><span class="lineNum">   14132 </span>            :         }</a>
+<a name="14133"><span class="lineNum">   14133 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="14134"><span class="lineNum">   14134 </span>            : </a>
+<a name="14135"><span class="lineNum">   14135 </span><span class="lineNoCov">          0 :         g = (d__[l + 1] - p) / (e[l] * 2.);</span></a>
+<a name="14136"><span class="lineNum">   14136 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;g, &amp;c_b10);</span></a>
+<a name="14137"><span class="lineNum">   14137 </span><span class="lineNoCov">          0 :         g = d__[m] - p + e[l] / (g + ( (g&gt;0) ? r__ : -r__ ) );</span></a>
+<a name="14138"><span class="lineNum">   14138 </span>            : </a>
+<a name="14139"><span class="lineNum">   14139 </span><span class="lineNoCov">          0 :         s = 1.;</span></a>
+<a name="14140"><span class="lineNum">   14140 </span><span class="lineNoCov">          0 :         c__ = 1.;</span></a>
+<a name="14141"><span class="lineNum">   14141 </span>            :         p = 0.;</a>
+<a name="14142"><span class="lineNum">   14142 </span>            : </a>
+<a name="14143"><span class="lineNum">   14143 </span><span class="lineNoCov">          0 :         mm1 = m - 1;</span></a>
+<a name="14144"><span class="lineNum">   14144 </span><span class="lineNoCov">          0 :         i__1 = l;</span></a>
+<a name="14145"><span class="lineNum">   14145 </span><span class="lineNoCov">          0 :         for (i__ = mm1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="14146"><span class="lineNum">   14146 </span><span class="lineNoCov">          0 :             f = s * e[i__];</span></a>
+<a name="14147"><span class="lineNum">   14147 </span><span class="lineNoCov">          0 :             b = c__ * e[i__];</span></a>
+<a name="14148"><span class="lineNum">   14148 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;g, &amp;f, &amp;c__, &amp;s, &amp;r__);</span></a>
+<a name="14149"><span class="lineNum">   14149 </span><span class="lineNoCov">          0 :             if (i__ != m - 1) {</span></a>
+<a name="14150"><span class="lineNum">   14150 </span><span class="lineNoCov">          0 :                 e[i__ + 1] = r__;</span></a>
+<a name="14151"><span class="lineNum">   14151 </span>            :             }</a>
+<a name="14152"><span class="lineNum">   14152 </span><span class="lineNoCov">          0 :             g = d__[i__ + 1] - p;</span></a>
+<a name="14153"><span class="lineNum">   14153 </span><span class="lineNoCov">          0 :             r__ = (d__[i__] - g) * s + c__ * 2. * b;</span></a>
+<a name="14154"><span class="lineNum">   14154 </span><span class="lineNoCov">          0 :             p = s * r__;</span></a>
+<a name="14155"><span class="lineNum">   14155 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = g + p;</span></a>
+<a name="14156"><span class="lineNum">   14156 </span><span class="lineNoCov">          0 :             g = c__ * r__ - b;</span></a>
+<a name="14157"><span class="lineNum">   14157 </span>            : </a>
+<a name="14158"><span class="lineNum">   14158 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="14159"><span class="lineNum">   14159 </span><span class="lineNoCov">          0 :                 work[i__] = c__;</span></a>
+<a name="14160"><span class="lineNum">   14160 </span><span class="lineNoCov">          0 :                 work[*n - 1 + i__] = -s;</span></a>
+<a name="14161"><span class="lineNum">   14161 </span>            :             }</a>
+<a name="14162"><span class="lineNum">   14162 </span>            :         }</a>
+<a name="14163"><span class="lineNum">   14163 </span>            : </a>
+<a name="14164"><span class="lineNum">   14164 </span><span class="lineNoCov">          0 :         if (icompz &gt; 0) {</span></a>
+<a name="14165"><span class="lineNum">   14165 </span><span class="lineNoCov">          0 :             mm = m - l + 1;</span></a>
+<a name="14166"><span class="lineNum">   14166 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, n, &amp;mm, &amp;work[l], &amp;work[*n - 1 + l], &amp;z__[l </span></a>
+<a name="14167"><span class="lineNum">   14167 </span><span class="lineNoCov">          0 :                     * z_dim1 + 1], ldz);</span></a>
+<a name="14168"><span class="lineNum">   14168 </span>            :         }</a>
+<a name="14169"><span class="lineNum">   14169 </span>            : </a>
+<a name="14170"><span class="lineNum">   14170 </span><span class="lineNoCov">          0 :         d__[l] -= p;</span></a>
+<a name="14171"><span class="lineNum">   14171 </span><span class="lineNoCov">          0 :         e[l] = g;</span></a>
+<a name="14172"><span class="lineNum">   14172 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="14173"><span class="lineNum">   14173 </span>            : </a>
+<a name="14174"><span class="lineNum">   14174 </span>            : L80:</a>
+<a name="14175"><span class="lineNum">   14175 </span>            :         d__[l] = p;</a>
+<a name="14176"><span class="lineNum">   14176 </span>            : </a>
+<a name="14177"><span class="lineNum">   14177 </span><span class="lineNoCov">          0 :         ++l;</span></a>
+<a name="14178"><span class="lineNum">   14178 </span><span class="lineNoCov">          0 :         if (l &lt;= lend) {</span></a>
+<a name="14179"><span class="lineNum">   14179 </span><span class="lineNoCov">          0 :             goto L40;</span></a>
+<a name="14180"><span class="lineNum">   14180 </span>            :         }</a>
+<a name="14181"><span class="lineNum">   14181 </span><span class="lineNoCov">          0 :         goto L140;</span></a>
+<a name="14182"><span class="lineNum">   14182 </span>            : </a>
+<a name="14183"><span class="lineNum">   14183 </span>            :     } else {</a>
+<a name="14184"><span class="lineNum">   14184 </span>            : </a>
+<a name="14185"><span class="lineNum">   14185 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="14186"><span class="lineNum">   14186 </span><span class="lineNoCov">          0 :         if (l != lend) {</span></a>
+<a name="14187"><span class="lineNum">   14187 </span><span class="lineNoCov">          0 :             lendp1 = lend + 1;</span></a>
+<a name="14188"><span class="lineNum">   14188 </span><span class="lineNoCov">          0 :             i__1 = lendp1;</span></a>
+<a name="14189"><span class="lineNum">   14189 </span><span class="lineNoCov">          0 :             for (m = l; m &gt;= i__1; --m) {</span></a>
+<a name="14190"><span class="lineNum">   14190 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(e[m - 1]);</span></a>
+<a name="14191"><span class="lineNum">   14191 </span><span class="lineNoCov">          0 :                 tst = d__2 * d__2;</span></a>
+<a name="14192"><span class="lineNum">   14192 </span><span class="lineNoCov">          0 :                 if (tst &lt;= eps2 * std::abs(d__[m]) * std::abs(d__[m- 1]) + safmin) {</span></a>
+<a name="14193"><span class="lineNum">   14193 </span><span class="lineNoCov">          0 :                     goto L110;</span></a>
+<a name="14194"><span class="lineNum">   14194 </span>            :                 }</a>
+<a name="14195"><span class="lineNum">   14195 </span>            :             }</a>
+<a name="14196"><span class="lineNum">   14196 </span>            :         }</a>
+<a name="14197"><span class="lineNum">   14197 </span>            : </a>
+<a name="14198"><span class="lineNum">   14198 </span>            :         m = lend;</a>
+<a name="14199"><span class="lineNum">   14199 </span>            : </a>
+<a name="14200"><span class="lineNum">   14200 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="14201"><span class="lineNum">   14201 </span><span class="lineNoCov">          0 :         if (m &gt; lend) {</span></a>
+<a name="14202"><span class="lineNum">   14202 </span><span class="lineNoCov">          0 :             e[m - 1] = 0.;</span></a>
+<a name="14203"><span class="lineNum">   14203 </span>            :         }</a>
+<a name="14204"><span class="lineNum">   14204 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="14205"><span class="lineNum">   14205 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="14206"><span class="lineNum">   14206 </span><span class="lineNoCov">          0 :             goto L130;</span></a>
+<a name="14207"><span class="lineNum">   14207 </span>            :         }</a>
+<a name="14208"><span class="lineNum">   14208 </span><span class="lineNoCov">          0 :         if (m == l - 1) {</span></a>
+<a name="14209"><span class="lineNum">   14209 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="14210"><span class="lineNum">   14210 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlaev2,DLAEV2)(&amp;d__[l - 1], &amp;e[l - 1], &amp;d__[l], &amp;rt1, &amp;rt2, &amp;c__, &amp;s)</span></a>
+<a name="14211"><span class="lineNum">   14211 </span>            :                         ;</a>
+<a name="14212"><span class="lineNum">   14212 </span><span class="lineNoCov">          0 :                 work[m] = c__;</span></a>
+<a name="14213"><span class="lineNum">   14213 </span><span class="lineNoCov">          0 :                 work[*n - 1 + m] = s;</span></a>
+<a name="14214"><span class="lineNum">   14214 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, n, &amp;c__2, &amp;work[m], &amp;work[*n - 1 + m], &amp;</span></a>
+<a name="14215"><span class="lineNum">   14215 </span><span class="lineNoCov">          0 :                         z__[(l - 1) * z_dim1 + 1], ldz);</span></a>
+<a name="14216"><span class="lineNum">   14216 </span>            :             } else {</a>
+<a name="14217"><span class="lineNum">   14217 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dlae2,DLAE2)(&amp;d__[l - 1], &amp;e[l - 1], &amp;d__[l], &amp;rt1, &amp;rt2);</span></a>
+<a name="14218"><span class="lineNum">   14218 </span>            :             }</a>
+<a name="14219"><span class="lineNum">   14219 </span><span class="lineNoCov">          0 :             d__[l - 1] = rt1;</span></a>
+<a name="14220"><span class="lineNum">   14220 </span><span class="lineNoCov">          0 :             d__[l] = rt2;</span></a>
+<a name="14221"><span class="lineNum">   14221 </span><span class="lineNoCov">          0 :             e[l - 1] = 0.;</span></a>
+<a name="14222"><span class="lineNum">   14222 </span><span class="lineNoCov">          0 :             l += -2;</span></a>
+<a name="14223"><span class="lineNum">   14223 </span><span class="lineNoCov">          0 :             if (l &gt;= lend) {</span></a>
+<a name="14224"><span class="lineNum">   14224 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="14225"><span class="lineNum">   14225 </span>            :             }</a>
+<a name="14226"><span class="lineNum">   14226 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="14227"><span class="lineNum">   14227 </span>            :         }</a>
+<a name="14228"><span class="lineNum">   14228 </span>            : </a>
+<a name="14229"><span class="lineNum">   14229 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="14230"><span class="lineNum">   14230 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="14231"><span class="lineNum">   14231 </span>            :         }</a>
+<a name="14232"><span class="lineNum">   14232 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="14233"><span class="lineNum">   14233 </span>            : </a>
+<a name="14234"><span class="lineNum">   14234 </span><span class="lineNoCov">          0 :         g = (d__[l - 1] - p) / (e[l - 1] * 2.);</span></a>
+<a name="14235"><span class="lineNum">   14235 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;g, &amp;c_b10);</span></a>
+<a name="14236"><span class="lineNum">   14236 </span><span class="lineNoCov">          0 :         g = d__[m] - p + e[l - 1] / (g + ( (g&gt;0) ? r__ : -r__ ));</span></a>
+<a name="14237"><span class="lineNum">   14237 </span>            : </a>
+<a name="14238"><span class="lineNum">   14238 </span><span class="lineNoCov">          0 :         s = 1.;</span></a>
+<a name="14239"><span class="lineNum">   14239 </span><span class="lineNoCov">          0 :         c__ = 1.;</span></a>
+<a name="14240"><span class="lineNum">   14240 </span>            :         p = 0.;</a>
+<a name="14241"><span class="lineNum">   14241 </span>            : </a>
+<a name="14242"><span class="lineNum">   14242 </span>            :         lm1 = l - 1;</a>
+<a name="14243"><span class="lineNum">   14243 </span><span class="lineNoCov">          0 :         i__1 = lm1;</span></a>
+<a name="14244"><span class="lineNum">   14244 </span><span class="lineNoCov">          0 :         for (i__ = m; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="14245"><span class="lineNum">   14245 </span><span class="lineNoCov">          0 :             f = s * e[i__];</span></a>
+<a name="14246"><span class="lineNum">   14246 </span><span class="lineNoCov">          0 :             b = c__ * e[i__];</span></a>
+<a name="14247"><span class="lineNum">   14247 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlartg,DLARTG)(&amp;g, &amp;f, &amp;c__, &amp;s, &amp;r__);</span></a>
+<a name="14248"><span class="lineNum">   14248 </span><span class="lineNoCov">          0 :             if (i__ != m) {</span></a>
+<a name="14249"><span class="lineNum">   14249 </span><span class="lineNoCov">          0 :                 e[i__ - 1] = r__;</span></a>
+<a name="14250"><span class="lineNum">   14250 </span>            :             }</a>
+<a name="14251"><span class="lineNum">   14251 </span><span class="lineNoCov">          0 :             g = d__[i__] - p;</span></a>
+<a name="14252"><span class="lineNum">   14252 </span><span class="lineNoCov">          0 :             r__ = (d__[i__ + 1] - g) * s + c__ * 2. * b;</span></a>
+<a name="14253"><span class="lineNum">   14253 </span><span class="lineNoCov">          0 :             p = s * r__;</span></a>
+<a name="14254"><span class="lineNum">   14254 </span><span class="lineNoCov">          0 :             d__[i__] = g + p;</span></a>
+<a name="14255"><span class="lineNum">   14255 </span><span class="lineNoCov">          0 :             g = c__ * r__ - b;</span></a>
+<a name="14256"><span class="lineNum">   14256 </span>            : </a>
+<a name="14257"><span class="lineNum">   14257 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="14258"><span class="lineNum">   14258 </span><span class="lineNoCov">          0 :                 work[i__] = c__;</span></a>
+<a name="14259"><span class="lineNum">   14259 </span><span class="lineNoCov">          0 :                 work[*n - 1 + i__] = s;</span></a>
+<a name="14260"><span class="lineNum">   14260 </span>            :             }</a>
+<a name="14261"><span class="lineNum">   14261 </span>            :         }</a>
+<a name="14262"><span class="lineNum">   14262 </span>            : </a>
+<a name="14263"><span class="lineNum">   14263 </span><span class="lineNoCov">          0 :         if (icompz &gt; 0) {</span></a>
+<a name="14264"><span class="lineNum">   14264 </span><span class="lineNoCov">          0 :             mm = l - m + 1;</span></a>
+<a name="14265"><span class="lineNum">   14265 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlasr,DLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, n, &amp;mm, &amp;work[m], &amp;work[*n - 1 + m], &amp;z__[m </span></a>
+<a name="14266"><span class="lineNum">   14266 </span><span class="lineNoCov">          0 :                     * z_dim1 + 1], ldz);</span></a>
+<a name="14267"><span class="lineNum">   14267 </span>            :         }</a>
+<a name="14268"><span class="lineNum">   14268 </span>            : </a>
+<a name="14269"><span class="lineNum">   14269 </span><span class="lineNoCov">          0 :         d__[l] -= p;</span></a>
+<a name="14270"><span class="lineNum">   14270 </span><span class="lineNoCov">          0 :         e[lm1] = g;</span></a>
+<a name="14271"><span class="lineNum">   14271 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="14272"><span class="lineNum">   14272 </span>            : </a>
+<a name="14273"><span class="lineNum">   14273 </span>            : L130:</a>
+<a name="14274"><span class="lineNum">   14274 </span>            :         d__[l] = p;</a>
+<a name="14275"><span class="lineNum">   14275 </span>            : </a>
+<a name="14276"><span class="lineNum">   14276 </span><span class="lineNoCov">          0 :         --l;</span></a>
+<a name="14277"><span class="lineNum">   14277 </span><span class="lineNoCov">          0 :         if (l &gt;= lend) {</span></a>
+<a name="14278"><span class="lineNum">   14278 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="14279"><span class="lineNum">   14279 </span>            :         }</a>
+<a name="14280"><span class="lineNum">   14280 </span><span class="lineNoCov">          0 :         goto L140;</span></a>
+<a name="14281"><span class="lineNum">   14281 </span>            : </a>
+<a name="14282"><span class="lineNum">   14282 </span>            :     }</a>
+<a name="14283"><span class="lineNum">   14283 </span>            : </a>
+<a name="14284"><span class="lineNum">   14284 </span><span class="lineNoCov">          0 : L140:</span></a>
+<a name="14285"><span class="lineNum">   14285 </span><span class="lineNoCov">          0 :     if (iscale == 1) {</span></a>
+<a name="14286"><span class="lineNum">   14286 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="14287"><span class="lineNum">   14287 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmax, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="14288"><span class="lineNum">   14288 </span>            :                 n, info);</a>
+<a name="14289"><span class="lineNum">   14289 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv;</span></a>
+<a name="14290"><span class="lineNum">   14290 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmax, &amp;anorm, &amp;i__1, &amp;c__1, &amp;e[lsv], n, </span></a>
+<a name="14291"><span class="lineNum">   14291 </span>            :                 info);</a>
+<a name="14292"><span class="lineNum">   14292 </span><span class="lineNoCov">          0 :     } else if (iscale == 2) {</span></a>
+<a name="14293"><span class="lineNum">   14293 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="14294"><span class="lineNum">   14294 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmin, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="14295"><span class="lineNum">   14295 </span>            :                 n, info);</a>
+<a name="14296"><span class="lineNum">   14296 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv;</span></a>
+<a name="14297"><span class="lineNum">   14297 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmin, &amp;anorm, &amp;i__1, &amp;c__1, &amp;e[lsv], n, </span></a>
+<a name="14298"><span class="lineNum">   14298 </span>            :                 info);</a>
+<a name="14299"><span class="lineNum">   14299 </span>            :     }</a>
+<a name="14300"><span class="lineNum">   14300 </span>            : </a>
+<a name="14301"><span class="lineNum">   14301 </span><span class="lineNoCov">          0 :     if (jtot &lt; nmaxit) {</span></a>
+<a name="14302"><span class="lineNum">   14302 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="14303"><span class="lineNum">   14303 </span>            :     }</a>
+<a name="14304"><span class="lineNum">   14304 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="14305"><span class="lineNum">   14305 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="14306"><span class="lineNum">   14306 </span><span class="lineNoCov">          0 :         if (std::abs(e[i__])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="14307"><span class="lineNum">   14307 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="14308"><span class="lineNum">   14308 </span>            :         }</a>
+<a name="14309"><span class="lineNum">   14309 </span>            :     }</a>
+<a name="14310"><span class="lineNum">   14310 </span><span class="lineNoCov">          0 :     goto L190;</span></a>
+<a name="14311"><span class="lineNum">   14311 </span>            : </a>
+<a name="14312"><span class="lineNum">   14312 </span>            : L160:</a>
+<a name="14313"><span class="lineNum">   14313 </span><span class="lineNoCov">          0 :     if (icompz == 0) {</span></a>
+<a name="14314"><span class="lineNum">   14314 </span>            : </a>
+<a name="14315"><span class="lineNum">   14315 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(&quot;I&quot;, n, &amp;d__[1], info);</span></a>
+<a name="14316"><span class="lineNum">   14316 </span>            : </a>
+<a name="14317"><span class="lineNum">   14317 </span>            :     } else {</a>
+<a name="14318"><span class="lineNum">   14318 </span>            : </a>
+<a name="14319"><span class="lineNum">   14319 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="14320"><span class="lineNum">   14320 </span><span class="lineNoCov">          0 :         for (ii = 2; ii &lt;= i__1; ++ii) {</span></a>
+<a name="14321"><span class="lineNum">   14321 </span><span class="lineNoCov">          0 :             i__ = ii - 1;</span></a>
+<a name="14322"><span class="lineNum">   14322 </span>            :             k = i__;</a>
+<a name="14323"><span class="lineNum">   14323 </span><span class="lineNoCov">          0 :             p = d__[i__];</span></a>
+<a name="14324"><span class="lineNum">   14324 </span><span class="lineNoCov">          0 :             i__2 = *n;</span></a>
+<a name="14325"><span class="lineNum">   14325 </span><span class="lineNoCov">          0 :             for (j = ii; j &lt;= i__2; ++j) {</span></a>
+<a name="14326"><span class="lineNum">   14326 </span><span class="lineNoCov">          0 :                 if (d__[j] &lt; p) {</span></a>
+<a name="14327"><span class="lineNum">   14327 </span>            :                     k = j;</a>
+<a name="14328"><span class="lineNum">   14328 </span>            :                     p = d__[j];</a>
+<a name="14329"><span class="lineNum">   14329 </span>            :                 }</a>
+<a name="14330"><span class="lineNum">   14330 </span>            :             }</a>
+<a name="14331"><span class="lineNum">   14331 </span><span class="lineNoCov">          0 :             if (k != i__) {</span></a>
+<a name="14332"><span class="lineNum">   14332 </span><span class="lineNoCov">          0 :                 d__[k] = d__[i__];</span></a>
+<a name="14333"><span class="lineNum">   14333 </span><span class="lineNoCov">          0 :                 d__[i__] = p;</span></a>
+<a name="14334"><span class="lineNum">   14334 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n, &amp;z__[i__ * z_dim1 + 1], &amp;c__1, &amp;z__[k * z_dim1 + 1],</span></a>
+<a name="14335"><span class="lineNum">   14335 </span>            :                          &amp;c__1);</a>
+<a name="14336"><span class="lineNum">   14336 </span>            :             }</a>
+<a name="14337"><span class="lineNum">   14337 </span>            :         }</a>
+<a name="14338"><span class="lineNum">   14338 </span>            :     }</a>
+<a name="14339"><span class="lineNum">   14339 </span>            : </a>
+<a name="14340"><span class="lineNum">   14340 </span><span class="lineNoCov">          0 : L190:</span></a>
+<a name="14341"><span class="lineNum">   14341 </span>            :     return;</a>
+<a name="14342"><span class="lineNum">   14342 </span>            : }</a>
+<a name="14343"><span class="lineNum">   14343 </span>            : </a>
+<a name="14344"><span class="lineNum">   14344 </span>            : </a>
+<a name="14345"><span class="lineNum">   14345 </span>            : }</a>
+<a name="14346"><span class="lineNum">   14346 </span>            : }</a>
+<a name="14347"><span class="lineNum">   14347 </span>            : #include &lt;cmath&gt;</a>
+<a name="14348"><span class="lineNum">   14348 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="14349"><span class="lineNum">   14349 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="14350"><span class="lineNum">   14350 </span>            : </a>
+<a name="14351"><span class="lineNum">   14351 </span>            : #include &quot;real.h&quot;</a>
+<a name="14352"><span class="lineNum">   14352 </span>            : </a>
+<a name="14353"><span class="lineNum">   14353 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="14354"><span class="lineNum">   14354 </span>            : namespace PLMD{</a>
+<a name="14355"><span class="lineNum">   14355 </span>            : namespace lapack{</a>
+<a name="14356"><span class="lineNum">   14356 </span>            : using namespace blas;</a>
+<a name="14357"><span class="lineNum">   14357 </span>            : void</a>
+<a name="14358"><span class="lineNum">   14358 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dsterf,DSTERF)(int *n, </span></a>
+<a name="14359"><span class="lineNum">   14359 </span>            :         double *d__, </a>
+<a name="14360"><span class="lineNum">   14360 </span>            :         double *e, </a>
+<a name="14361"><span class="lineNum">   14361 </span>            :         int *info)</a>
+<a name="14362"><span class="lineNum">   14362 </span>            : {</a>
+<a name="14363"><span class="lineNum">   14363 </span>            :     int i__1;</a>
+<a name="14364"><span class="lineNum">   14364 </span>            :     double d__1;</a>
+<a name="14365"><span class="lineNum">   14365 </span>            : </a>
+<a name="14366"><span class="lineNum">   14366 </span>            :     double c__;</a>
+<a name="14367"><span class="lineNum">   14367 </span>            :     int i__, l, m;</a>
+<a name="14368"><span class="lineNum">   14368 </span>            :     double p, r__, s;</a>
+<a name="14369"><span class="lineNum">   14369 </span>            :     int l1;</a>
+<a name="14370"><span class="lineNum">   14370 </span>            :     double bb, rt1, rt2, eps, rte;</a>
+<a name="14371"><span class="lineNum">   14371 </span>            :     int lsv;</a>
+<a name="14372"><span class="lineNum">   14372 </span>            :     double eps2, oldc;</a>
+<a name="14373"><span class="lineNum">   14373 </span>            :     int lend, jtot;</a>
+<a name="14374"><span class="lineNum">   14374 </span>            :     double gamma, alpha, sigma, anorm;</a>
+<a name="14375"><span class="lineNum">   14375 </span>            :       int iscale;</a>
+<a name="14376"><span class="lineNum">   14376 </span>            :     double oldgam;</a>
+<a name="14377"><span class="lineNum">   14377 </span>            :     double safmax;</a>
+<a name="14378"><span class="lineNum">   14378 </span>            :     int lendsv;</a>
+<a name="14379"><span class="lineNum">   14379 </span>            :     double ssfmin;</a>
+<a name="14380"><span class="lineNum">   14380 </span>            :     int nmaxit;</a>
+<a name="14381"><span class="lineNum">   14381 </span>            :     double ssfmax;</a>
+<a name="14382"><span class="lineNum">   14382 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="14383"><span class="lineNum">   14383 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="14384"><span class="lineNum">   14384 </span><span class="lineNoCov">          0 :     double c_b32 = 1.;</span></a>
+<a name="14385"><span class="lineNum">   14385 </span>            :     const double safmin = PLUMED_GMX_DOUBLE_MIN*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="14386"><span class="lineNum">   14386 </span>            : </a>
+<a name="14387"><span class="lineNum">   14387 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="14388"><span class="lineNum">   14388 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="14389"><span class="lineNum">   14389 </span>            : </a>
+<a name="14390"><span class="lineNum">   14390 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="14391"><span class="lineNum">   14391 </span>            : </a>
+<a name="14392"><span class="lineNum">   14392 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="14393"><span class="lineNum">   14393 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="14394"><span class="lineNum">   14394 </span>            :         i__1 = -(*info);</a>
+<a name="14395"><span class="lineNum">   14395 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="14396"><span class="lineNum">   14396 </span>            :     }</a>
+<a name="14397"><span class="lineNum">   14397 </span><span class="lineNoCov">          0 :     if (*n &lt;= 1) {</span></a>
+<a name="14398"><span class="lineNum">   14398 </span>            :         return;</a>
+<a name="14399"><span class="lineNum">   14399 </span>            :     }</a>
+<a name="14400"><span class="lineNum">   14400 </span>            : </a>
+<a name="14401"><span class="lineNum">   14401 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="14402"><span class="lineNum">   14402 </span>            :     d__1 = eps;</a>
+<a name="14403"><span class="lineNum">   14403 </span>            :     eps2 = d__1 * d__1;</a>
+<a name="14404"><span class="lineNum">   14404 </span>            :     safmax = 1. / safmin;</a>
+<a name="14405"><span class="lineNum">   14405 </span><span class="lineNoCov">          0 :     ssfmax =  std::sqrt(safmax) / 3.;</span></a>
+<a name="14406"><span class="lineNum">   14406 </span><span class="lineNoCov">          0 :     ssfmin =  std::sqrt(safmin) / eps2;</span></a>
+<a name="14407"><span class="lineNum">   14407 </span>            : </a>
+<a name="14408"><span class="lineNum">   14408 </span><span class="lineNoCov">          0 :     nmaxit = *n * 30;</span></a>
+<a name="14409"><span class="lineNum">   14409 </span><span class="lineNoCov">          0 :     sigma = 0.;</span></a>
+<a name="14410"><span class="lineNum">   14410 </span>            :     jtot = 0;</a>
+<a name="14411"><span class="lineNum">   14411 </span>            : </a>
+<a name="14412"><span class="lineNum">   14412 </span>            :     l1 = 1;</a>
+<a name="14413"><span class="lineNum">   14413 </span>            : </a>
+<a name="14414"><span class="lineNum">   14414 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="14415"><span class="lineNum">   14415 </span><span class="lineNoCov">          0 :     if (l1 &gt; *n) {</span></a>
+<a name="14416"><span class="lineNum">   14416 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlasrt,DLASRT)(&quot;I&quot;, n, &amp;d__[1], info);</span></a>
+<a name="14417"><span class="lineNum">   14417 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="14418"><span class="lineNum">   14418 </span>            :     }</a>
+<a name="14419"><span class="lineNum">   14419 </span><span class="lineNoCov">          0 :     if (l1 &gt; 1) {</span></a>
+<a name="14420"><span class="lineNum">   14420 </span><span class="lineNoCov">          0 :         e[l1 - 1] = 0.;</span></a>
+<a name="14421"><span class="lineNum">   14421 </span>            :     }</a>
+<a name="14422"><span class="lineNum">   14422 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="14423"><span class="lineNum">   14423 </span><span class="lineNoCov">          0 :     for (m = l1; m &lt;= i__1; ++m) {</span></a>
+<a name="14424"><span class="lineNum">   14424 </span><span class="lineNoCov">          0 :         if (std::abs(e[m]) &lt;=  std::sqrt(std::abs(d__[m])) * </span></a>
+<a name="14425"><span class="lineNum">   14425 </span><span class="lineNoCov">          0 :                  std::sqrt(std::abs(d__[m + 1])) * eps) {</span></a>
+<a name="14426"><span class="lineNum">   14426 </span><span class="lineNoCov">          0 :             e[m] = 0.;</span></a>
+<a name="14427"><span class="lineNum">   14427 </span><span class="lineNoCov">          0 :             goto L30;</span></a>
+<a name="14428"><span class="lineNum">   14428 </span>            :         }</a>
+<a name="14429"><span class="lineNum">   14429 </span>            :     }</a>
+<a name="14430"><span class="lineNum">   14430 </span><span class="lineNoCov">          0 :     m = *n;</span></a>
+<a name="14431"><span class="lineNum">   14431 </span>            : </a>
+<a name="14432"><span class="lineNum">   14432 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="14433"><span class="lineNum">   14433 </span>            :     l = l1;</a>
+<a name="14434"><span class="lineNum">   14434 </span>            :     lsv = l;</a>
+<a name="14435"><span class="lineNum">   14435 </span>            :     lend = m;</a>
+<a name="14436"><span class="lineNum">   14436 </span>            :     lendsv = lend;</a>
+<a name="14437"><span class="lineNum">   14437 </span><span class="lineNoCov">          0 :     l1 = m + 1;</span></a>
+<a name="14438"><span class="lineNum">   14438 </span><span class="lineNoCov">          0 :     if (lend == l) {</span></a>
+<a name="14439"><span class="lineNum">   14439 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="14440"><span class="lineNum">   14440 </span>            :     }</a>
+<a name="14441"><span class="lineNum">   14441 </span>            : </a>
+<a name="14442"><span class="lineNum">   14442 </span><span class="lineNoCov">          0 :     i__1 = lend - l + 1;</span></a>
+<a name="14443"><span class="lineNum">   14443 </span><span class="lineNoCov">          0 :     anorm = PLUMED_BLAS_F77_FUNC(dlanst,DLANST)(&quot;I&quot;, &amp;i__1, &amp;d__[l], &amp;e[l]);</span></a>
+<a name="14444"><span class="lineNum">   14444 </span>            :     iscale = 0;</a>
+<a name="14445"><span class="lineNum">   14445 </span><span class="lineNoCov">          0 :     if (anorm &gt; ssfmax) {</span></a>
+<a name="14446"><span class="lineNum">   14446 </span>            :         iscale = 1;</a>
+<a name="14447"><span class="lineNum">   14447 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="14448"><span class="lineNum">   14448 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="14449"><span class="lineNum">   14449 </span>            :                 info);</a>
+<a name="14450"><span class="lineNum">   14450 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="14451"><span class="lineNum">   14451 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="14452"><span class="lineNum">   14452 </span>            :                 info);</a>
+<a name="14453"><span class="lineNum">   14453 </span><span class="lineNoCov">          0 :     } else if (anorm &lt; ssfmin) {</span></a>
+<a name="14454"><span class="lineNum">   14454 </span>            :         iscale = 2;</a>
+<a name="14455"><span class="lineNum">   14455 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="14456"><span class="lineNum">   14456 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="14457"><span class="lineNum">   14457 </span>            :                 info);</a>
+<a name="14458"><span class="lineNum">   14458 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="14459"><span class="lineNum">   14459 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="14460"><span class="lineNum">   14460 </span>            :                 info);</a>
+<a name="14461"><span class="lineNum">   14461 </span>            :     }</a>
+<a name="14462"><span class="lineNum">   14462 </span>            : </a>
+<a name="14463"><span class="lineNum">   14463 </span><span class="lineNoCov">          0 :     i__1 = lend - 1;</span></a>
+<a name="14464"><span class="lineNum">   14464 </span><span class="lineNoCov">          0 :     for (i__ = l; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="14465"><span class="lineNum">   14465 </span><span class="lineNoCov">          0 :         d__1 = e[i__];</span></a>
+<a name="14466"><span class="lineNum">   14466 </span><span class="lineNoCov">          0 :         e[i__] = d__1 * d__1;</span></a>
+<a name="14467"><span class="lineNum">   14467 </span>            :     }</a>
+<a name="14468"><span class="lineNum">   14468 </span>            : </a>
+<a name="14469"><span class="lineNum">   14469 </span><span class="lineNoCov">          0 :     if (std::abs(d__[lend]) &lt; std::abs(d__[l])) {</span></a>
+<a name="14470"><span class="lineNum">   14470 </span>            :         lend = lsv;</a>
+<a name="14471"><span class="lineNum">   14471 </span>            :         l = lendsv;</a>
+<a name="14472"><span class="lineNum">   14472 </span>            :     }</a>
+<a name="14473"><span class="lineNum">   14473 </span>            : </a>
+<a name="14474"><span class="lineNum">   14474 </span><span class="lineNoCov">          0 :     if (lend &gt;= l) {</span></a>
+<a name="14475"><span class="lineNum">   14475 </span>            : </a>
+<a name="14476"><span class="lineNum">   14476 </span><span class="lineNoCov">          0 : L50:</span></a>
+<a name="14477"><span class="lineNum">   14477 </span><span class="lineNoCov">          0 :         if (l != lend) {</span></a>
+<a name="14478"><span class="lineNum">   14478 </span><span class="lineNoCov">          0 :             i__1 = lend - 1;</span></a>
+<a name="14479"><span class="lineNum">   14479 </span><span class="lineNoCov">          0 :             for (m = l; m &lt;= i__1; ++m) {</span></a>
+<a name="14480"><span class="lineNum">   14480 </span><span class="lineNoCov">          0 :                 if (std::abs(e[m]) &lt;= eps2 * std::abs(d__[m] * d__[m + 1])) {</span></a>
+<a name="14481"><span class="lineNum">   14481 </span><span class="lineNoCov">          0 :                     goto L70;</span></a>
+<a name="14482"><span class="lineNum">   14482 </span>            :                 }</a>
+<a name="14483"><span class="lineNum">   14483 </span>            :             }</a>
+<a name="14484"><span class="lineNum">   14484 </span>            :         }</a>
+<a name="14485"><span class="lineNum">   14485 </span>            :         m = lend;</a>
+<a name="14486"><span class="lineNum">   14486 </span>            : </a>
+<a name="14487"><span class="lineNum">   14487 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="14488"><span class="lineNum">   14488 </span><span class="lineNoCov">          0 :         if (m &lt; lend) {</span></a>
+<a name="14489"><span class="lineNum">   14489 </span><span class="lineNoCov">          0 :             e[m] = 0.;</span></a>
+<a name="14490"><span class="lineNum">   14490 </span>            :         }</a>
+<a name="14491"><span class="lineNum">   14491 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="14492"><span class="lineNum">   14492 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="14493"><span class="lineNum">   14493 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="14494"><span class="lineNum">   14494 </span>            :         }</a>
+<a name="14495"><span class="lineNum">   14495 </span><span class="lineNoCov">          0 :         if (m == l + 1) {</span></a>
+<a name="14496"><span class="lineNum">   14496 </span><span class="lineNoCov">          0 :             rte =  std::sqrt(e[l]);</span></a>
+<a name="14497"><span class="lineNum">   14497 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlae2,DLAE2)(&amp;d__[l], &amp;rte, &amp;d__[l + 1], &amp;rt1, &amp;rt2);</span></a>
+<a name="14498"><span class="lineNum">   14498 </span><span class="lineNoCov">          0 :             d__[l] = rt1;</span></a>
+<a name="14499"><span class="lineNum">   14499 </span><span class="lineNoCov">          0 :             d__[l + 1] = rt2;</span></a>
+<a name="14500"><span class="lineNum">   14500 </span><span class="lineNoCov">          0 :             e[l] = 0.;</span></a>
+<a name="14501"><span class="lineNum">   14501 </span><span class="lineNoCov">          0 :             l += 2;</span></a>
+<a name="14502"><span class="lineNum">   14502 </span><span class="lineNoCov">          0 :             if (l &lt;= lend) {</span></a>
+<a name="14503"><span class="lineNum">   14503 </span><span class="lineNoCov">          0 :                 goto L50;</span></a>
+<a name="14504"><span class="lineNum">   14504 </span>            :             }</a>
+<a name="14505"><span class="lineNum">   14505 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="14506"><span class="lineNum">   14506 </span>            :         }</a>
+<a name="14507"><span class="lineNum">   14507 </span>            : </a>
+<a name="14508"><span class="lineNum">   14508 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="14509"><span class="lineNum">   14509 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="14510"><span class="lineNum">   14510 </span>            :         }</a>
+<a name="14511"><span class="lineNum">   14511 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="14512"><span class="lineNum">   14512 </span>            : </a>
+<a name="14513"><span class="lineNum">   14513 </span><span class="lineNoCov">          0 :         rte =  std::sqrt(e[l]);</span></a>
+<a name="14514"><span class="lineNum">   14514 </span><span class="lineNoCov">          0 :         sigma = (d__[l + 1] - p) / (rte * 2.);</span></a>
+<a name="14515"><span class="lineNum">   14515 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;sigma, &amp;c_b32);</span></a>
+<a name="14516"><span class="lineNum">   14516 </span><span class="lineNoCov">          0 :         sigma = p - rte / (sigma + ( (sigma&gt;0) ? r__ : -r__));</span></a>
+<a name="14517"><span class="lineNum">   14517 </span>            : </a>
+<a name="14518"><span class="lineNum">   14518 </span>            :         c__ = 1.;</a>
+<a name="14519"><span class="lineNum">   14519 </span>            :         s = 0.;</a>
+<a name="14520"><span class="lineNum">   14520 </span><span class="lineNoCov">          0 :         gamma = d__[m] - sigma;</span></a>
+<a name="14521"><span class="lineNum">   14521 </span><span class="lineNoCov">          0 :         p = gamma * gamma;</span></a>
+<a name="14522"><span class="lineNum">   14522 </span>            : </a>
+<a name="14523"><span class="lineNum">   14523 </span><span class="lineNoCov">          0 :         i__1 = l;</span></a>
+<a name="14524"><span class="lineNum">   14524 </span><span class="lineNoCov">          0 :         for (i__ = m - 1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="14525"><span class="lineNum">   14525 </span><span class="lineNoCov">          0 :             bb = e[i__];</span></a>
+<a name="14526"><span class="lineNum">   14526 </span><span class="lineNoCov">          0 :             r__ = p + bb;</span></a>
+<a name="14527"><span class="lineNum">   14527 </span><span class="lineNoCov">          0 :             if (i__ != m - 1) {</span></a>
+<a name="14528"><span class="lineNum">   14528 </span><span class="lineNoCov">          0 :                 e[i__ + 1] = s * r__;</span></a>
+<a name="14529"><span class="lineNum">   14529 </span>            :             }</a>
+<a name="14530"><span class="lineNum">   14530 </span>            :             oldc = c__;</a>
+<a name="14531"><span class="lineNum">   14531 </span><span class="lineNoCov">          0 :             c__ = p / r__;</span></a>
+<a name="14532"><span class="lineNum">   14532 </span><span class="lineNoCov">          0 :             s = bb / r__;</span></a>
+<a name="14533"><span class="lineNum">   14533 </span>            :             oldgam = gamma;</a>
+<a name="14534"><span class="lineNum">   14534 </span><span class="lineNoCov">          0 :             alpha = d__[i__];</span></a>
+<a name="14535"><span class="lineNum">   14535 </span><span class="lineNoCov">          0 :             gamma = c__ * (alpha - sigma) - s * oldgam;</span></a>
+<a name="14536"><span class="lineNum">   14536 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = oldgam + (alpha - gamma);</span></a>
+<a name="14537"><span class="lineNum">   14537 </span><span class="lineNoCov">          0 :             if (std::abs(c__)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="14538"><span class="lineNum">   14538 </span><span class="lineNoCov">          0 :                 p = gamma * gamma / c__;</span></a>
+<a name="14539"><span class="lineNum">   14539 </span>            :             } else {</a>
+<a name="14540"><span class="lineNum">   14540 </span><span class="lineNoCov">          0 :                 p = oldc * bb;</span></a>
+<a name="14541"><span class="lineNum">   14541 </span>            :             }</a>
+<a name="14542"><span class="lineNum">   14542 </span>            :         }</a>
+<a name="14543"><span class="lineNum">   14543 </span>            : </a>
+<a name="14544"><span class="lineNum">   14544 </span><span class="lineNoCov">          0 :         e[l] = s * p;</span></a>
+<a name="14545"><span class="lineNum">   14545 </span><span class="lineNoCov">          0 :         d__[l] = sigma + gamma;</span></a>
+<a name="14546"><span class="lineNum">   14546 </span><span class="lineNoCov">          0 :         goto L50;</span></a>
+<a name="14547"><span class="lineNum">   14547 </span>            : </a>
+<a name="14548"><span class="lineNum">   14548 </span>            : L90:</a>
+<a name="14549"><span class="lineNum">   14549 </span>            :         d__[l] = p;</a>
+<a name="14550"><span class="lineNum">   14550 </span>            : </a>
+<a name="14551"><span class="lineNum">   14551 </span><span class="lineNoCov">          0 :         ++l;</span></a>
+<a name="14552"><span class="lineNum">   14552 </span><span class="lineNoCov">          0 :         if (l &lt;= lend) {</span></a>
+<a name="14553"><span class="lineNum">   14553 </span><span class="lineNoCov">          0 :             goto L50;</span></a>
+<a name="14554"><span class="lineNum">   14554 </span>            :         }</a>
+<a name="14555"><span class="lineNum">   14555 </span><span class="lineNoCov">          0 :         goto L150;</span></a>
+<a name="14556"><span class="lineNum">   14556 </span>            : </a>
+<a name="14557"><span class="lineNum">   14557 </span>            :     } else {</a>
+<a name="14558"><span class="lineNum">   14558 </span>            : </a>
+<a name="14559"><span class="lineNum">   14559 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="14560"><span class="lineNum">   14560 </span><span class="lineNoCov">          0 :         i__1 = lend + 1;</span></a>
+<a name="14561"><span class="lineNum">   14561 </span><span class="lineNoCov">          0 :         for (m = l; m &gt;= i__1; --m) {</span></a>
+<a name="14562"><span class="lineNum">   14562 </span><span class="lineNoCov">          0 :             if (std::abs(e[m - 1]) &lt;= eps2 * std::abs(d__[m] * d__[m - 1])) {</span></a>
+<a name="14563"><span class="lineNum">   14563 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="14564"><span class="lineNum">   14564 </span>            :             }</a>
+<a name="14565"><span class="lineNum">   14565 </span>            :         }</a>
+<a name="14566"><span class="lineNum">   14566 </span>            :         m = lend;</a>
+<a name="14567"><span class="lineNum">   14567 </span>            : </a>
+<a name="14568"><span class="lineNum">   14568 </span><span class="lineNoCov">          0 : L120:</span></a>
+<a name="14569"><span class="lineNum">   14569 </span><span class="lineNoCov">          0 :         if (m &gt; lend) {</span></a>
+<a name="14570"><span class="lineNum">   14570 </span><span class="lineNoCov">          0 :             e[m - 1] = 0.;</span></a>
+<a name="14571"><span class="lineNum">   14571 </span>            :         }</a>
+<a name="14572"><span class="lineNum">   14572 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="14573"><span class="lineNum">   14573 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="14574"><span class="lineNum">   14574 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="14575"><span class="lineNum">   14575 </span>            :         }</a>
+<a name="14576"><span class="lineNum">   14576 </span>            : </a>
+<a name="14577"><span class="lineNum">   14577 </span><span class="lineNoCov">          0 :         if (m == l - 1) {</span></a>
+<a name="14578"><span class="lineNum">   14578 </span><span class="lineNoCov">          0 :             rte =  std::sqrt(e[l - 1]);</span></a>
+<a name="14579"><span class="lineNum">   14579 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlae2,DLAE2)(&amp;d__[l], &amp;rte, &amp;d__[l - 1], &amp;rt1, &amp;rt2);</span></a>
+<a name="14580"><span class="lineNum">   14580 </span><span class="lineNoCov">          0 :             d__[l] = rt1;</span></a>
+<a name="14581"><span class="lineNum">   14581 </span><span class="lineNoCov">          0 :             d__[l - 1] = rt2;</span></a>
+<a name="14582"><span class="lineNum">   14582 </span><span class="lineNoCov">          0 :             e[l - 1] = 0.;</span></a>
+<a name="14583"><span class="lineNum">   14583 </span><span class="lineNoCov">          0 :             l += -2;</span></a>
+<a name="14584"><span class="lineNum">   14584 </span><span class="lineNoCov">          0 :             if (l &gt;= lend) {</span></a>
+<a name="14585"><span class="lineNum">   14585 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="14586"><span class="lineNum">   14586 </span>            :             }</a>
+<a name="14587"><span class="lineNum">   14587 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="14588"><span class="lineNum">   14588 </span>            :         }</a>
+<a name="14589"><span class="lineNum">   14589 </span>            : </a>
+<a name="14590"><span class="lineNum">   14590 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="14591"><span class="lineNum">   14591 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="14592"><span class="lineNum">   14592 </span>            :         }</a>
+<a name="14593"><span class="lineNum">   14593 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="14594"><span class="lineNum">   14594 </span>            : </a>
+<a name="14595"><span class="lineNum">   14595 </span><span class="lineNoCov">          0 :         rte =  std::sqrt(e[l - 1]);</span></a>
+<a name="14596"><span class="lineNum">   14596 </span><span class="lineNoCov">          0 :         sigma = (d__[l - 1] - p) / (rte * 2.);</span></a>
+<a name="14597"><span class="lineNum">   14597 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(dlapy2,DLAPY2)(&amp;sigma, &amp;c_b32);</span></a>
+<a name="14598"><span class="lineNum">   14598 </span><span class="lineNoCov">          0 :         sigma = p - rte / (sigma + ( (sigma&gt;0) ? r__ : -r__));</span></a>
+<a name="14599"><span class="lineNum">   14599 </span>            : </a>
+<a name="14600"><span class="lineNum">   14600 </span>            :         c__ = 1.;</a>
+<a name="14601"><span class="lineNum">   14601 </span>            :         s = 0.;</a>
+<a name="14602"><span class="lineNum">   14602 </span><span class="lineNoCov">          0 :         gamma = d__[m] - sigma;</span></a>
+<a name="14603"><span class="lineNum">   14603 </span><span class="lineNoCov">          0 :         p = gamma * gamma;</span></a>
+<a name="14604"><span class="lineNum">   14604 </span>            : </a>
+<a name="14605"><span class="lineNum">   14605 </span><span class="lineNoCov">          0 :         i__1 = l - 1;</span></a>
+<a name="14606"><span class="lineNum">   14606 </span><span class="lineNoCov">          0 :         for (i__ = m; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="14607"><span class="lineNum">   14607 </span><span class="lineNoCov">          0 :             bb = e[i__];</span></a>
+<a name="14608"><span class="lineNum">   14608 </span><span class="lineNoCov">          0 :             r__ = p + bb;</span></a>
+<a name="14609"><span class="lineNum">   14609 </span><span class="lineNoCov">          0 :             if (i__ != m) {</span></a>
+<a name="14610"><span class="lineNum">   14610 </span><span class="lineNoCov">          0 :                 e[i__ - 1] = s * r__;</span></a>
+<a name="14611"><span class="lineNum">   14611 </span>            :             }</a>
+<a name="14612"><span class="lineNum">   14612 </span>            :             oldc = c__;</a>
+<a name="14613"><span class="lineNum">   14613 </span><span class="lineNoCov">          0 :             c__ = p / r__;</span></a>
+<a name="14614"><span class="lineNum">   14614 </span><span class="lineNoCov">          0 :             s = bb / r__;</span></a>
+<a name="14615"><span class="lineNum">   14615 </span>            :             oldgam = gamma;</a>
+<a name="14616"><span class="lineNum">   14616 </span><span class="lineNoCov">          0 :             alpha = d__[i__ + 1];</span></a>
+<a name="14617"><span class="lineNum">   14617 </span><span class="lineNoCov">          0 :             gamma = c__ * (alpha - sigma) - s * oldgam;</span></a>
+<a name="14618"><span class="lineNum">   14618 </span><span class="lineNoCov">          0 :             d__[i__] = oldgam + (alpha - gamma);</span></a>
+<a name="14619"><span class="lineNum">   14619 </span><span class="lineNoCov">          0 :             if (std::abs(c__)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="14620"><span class="lineNum">   14620 </span><span class="lineNoCov">          0 :                 p = gamma * gamma / c__;</span></a>
+<a name="14621"><span class="lineNum">   14621 </span>            :             } else {</a>
+<a name="14622"><span class="lineNum">   14622 </span><span class="lineNoCov">          0 :                 p = oldc * bb;</span></a>
+<a name="14623"><span class="lineNum">   14623 </span>            :             }</a>
+<a name="14624"><span class="lineNum">   14624 </span>            :         }</a>
+<a name="14625"><span class="lineNum">   14625 </span>            : </a>
+<a name="14626"><span class="lineNum">   14626 </span><span class="lineNoCov">          0 :         e[l - 1] = s * p;</span></a>
+<a name="14627"><span class="lineNum">   14627 </span><span class="lineNoCov">          0 :         d__[l] = sigma + gamma;</span></a>
+<a name="14628"><span class="lineNum">   14628 </span><span class="lineNoCov">          0 :         goto L100;</span></a>
+<a name="14629"><span class="lineNum">   14629 </span>            : </a>
+<a name="14630"><span class="lineNum">   14630 </span>            : L140:</a>
+<a name="14631"><span class="lineNum">   14631 </span>            :         d__[l] = p;</a>
+<a name="14632"><span class="lineNum">   14632 </span>            : </a>
+<a name="14633"><span class="lineNum">   14633 </span><span class="lineNoCov">          0 :         --l;</span></a>
+<a name="14634"><span class="lineNum">   14634 </span><span class="lineNoCov">          0 :         if (l &gt;= lend) {</span></a>
+<a name="14635"><span class="lineNum">   14635 </span><span class="lineNoCov">          0 :             goto L100;</span></a>
+<a name="14636"><span class="lineNum">   14636 </span>            :         }</a>
+<a name="14637"><span class="lineNum">   14637 </span><span class="lineNoCov">          0 :         goto L150;</span></a>
+<a name="14638"><span class="lineNum">   14638 </span>            : </a>
+<a name="14639"><span class="lineNum">   14639 </span>            :     }</a>
+<a name="14640"><span class="lineNum">   14640 </span>            : </a>
+<a name="14641"><span class="lineNum">   14641 </span><span class="lineNoCov">          0 : L150:</span></a>
+<a name="14642"><span class="lineNum">   14642 </span><span class="lineNoCov">          0 :     if (iscale == 1) {</span></a>
+<a name="14643"><span class="lineNum">   14643 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="14644"><span class="lineNum">   14644 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmax, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="14645"><span class="lineNum">   14645 </span>            :                 n, info);</a>
+<a name="14646"><span class="lineNum">   14646 </span>            :     }</a>
+<a name="14647"><span class="lineNum">   14647 </span><span class="lineNoCov">          0 :     if (iscale == 2) {</span></a>
+<a name="14648"><span class="lineNum">   14648 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="14649"><span class="lineNum">   14649 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dlascl,DLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmin, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="14650"><span class="lineNum">   14650 </span>            :                 n, info);</a>
+<a name="14651"><span class="lineNum">   14651 </span>            :     }</a>
+<a name="14652"><span class="lineNum">   14652 </span>            : </a>
+<a name="14653"><span class="lineNum">   14653 </span><span class="lineNoCov">          0 :     if (jtot &lt; nmaxit) {</span></a>
+<a name="14654"><span class="lineNum">   14654 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="14655"><span class="lineNum">   14655 </span>            :     }</a>
+<a name="14656"><span class="lineNum">   14656 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="14657"><span class="lineNum">   14657 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="14658"><span class="lineNum">   14658 </span><span class="lineNoCov">          0 :         if (std::abs(e[i__])&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="14659"><span class="lineNum">   14659 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="14660"><span class="lineNum">   14660 </span>            :         }</a>
+<a name="14661"><span class="lineNum">   14661 </span>            :     }</a>
+<a name="14662"><span class="lineNum">   14662 </span>            :     return;</a>
+<a name="14663"><span class="lineNum">   14663 </span>            : }</a>
+<a name="14664"><span class="lineNum">   14664 </span>            : </a>
+<a name="14665"><span class="lineNum">   14665 </span>            : </a>
+<a name="14666"><span class="lineNum">   14666 </span>            : }</a>
+<a name="14667"><span class="lineNum">   14667 </span>            : }</a>
+<a name="14668"><span class="lineNum">   14668 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="14669"><span class="lineNum">   14669 </span>            : </a>
+<a name="14670"><span class="lineNum">   14670 </span>            : </a>
+<a name="14671"><span class="lineNum">   14671 </span>            : /* Normally, DSTEVR is the LAPACK wrapper which calls one</a>
+<a name="14672"><span class="lineNum">   14672 </span>            :  * of the eigenvalue methods. However, our code includes a</a>
+<a name="14673"><span class="lineNum">   14673 </span>            :  * version of DSTEGR which is never than LAPACK 3.0 and can</a>
+<a name="14674"><span class="lineNum">   14674 </span>            :  * handle requests for a subset of eigenvalues/vectors too,</a>
+<a name="14675"><span class="lineNum">   14675 </span>            :  * and it should not need to call DSTEIN.</a>
+<a name="14676"><span class="lineNum">   14676 </span>            :  * Just in case somebody has a faster version in their lapack</a>
+<a name="14677"><span class="lineNum">   14677 </span>            :  * library we still call the driver routine, but in our own</a>
+<a name="14678"><span class="lineNum">   14678 </span>            :  * case this is just a wrapper to dstegr.</a>
+<a name="14679"><span class="lineNum">   14679 </span>            :  */</a>
+<a name="14680"><span class="lineNum">   14680 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="14681"><span class="lineNum">   14681 </span>            : namespace PLMD{</a>
+<a name="14682"><span class="lineNum">   14682 </span>            : namespace lapack{</a>
+<a name="14683"><span class="lineNum">   14683 </span>            : using namespace blas;</a>
+<a name="14684"><span class="lineNum">   14684 </span>            : void</a>
+<a name="14685"><span class="lineNum">   14685 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(dstevr,DSTEVR)(const char *jobz, </span></a>
+<a name="14686"><span class="lineNum">   14686 </span>            :         const char *range,</a>
+<a name="14687"><span class="lineNum">   14687 </span>            :         int *n,</a>
+<a name="14688"><span class="lineNum">   14688 </span>            :         double *d,</a>
+<a name="14689"><span class="lineNum">   14689 </span>            :         double *e,</a>
+<a name="14690"><span class="lineNum">   14690 </span>            :         double *vl, </a>
+<a name="14691"><span class="lineNum">   14691 </span>            :         double *vu,</a>
+<a name="14692"><span class="lineNum">   14692 </span>            :         int *il, </a>
+<a name="14693"><span class="lineNum">   14693 </span>            :         int *iu, </a>
+<a name="14694"><span class="lineNum">   14694 </span>            :         double *abstol,</a>
+<a name="14695"><span class="lineNum">   14695 </span>            :         int *m,</a>
+<a name="14696"><span class="lineNum">   14696 </span>            :         double *w, </a>
+<a name="14697"><span class="lineNum">   14697 </span>            :         double *z,</a>
+<a name="14698"><span class="lineNum">   14698 </span>            :         int *ldz,</a>
+<a name="14699"><span class="lineNum">   14699 </span>            :         int *isuppz, </a>
+<a name="14700"><span class="lineNum">   14700 </span>            :         double *work, </a>
+<a name="14701"><span class="lineNum">   14701 </span>            :         int *lwork, </a>
+<a name="14702"><span class="lineNum">   14702 </span>            :         int *iwork,</a>
+<a name="14703"><span class="lineNum">   14703 </span>            :         int *liwork, </a>
+<a name="14704"><span class="lineNum">   14704 </span>            :         int *info)</a>
+<a name="14705"><span class="lineNum">   14705 </span>            : {</a>
+<a name="14706"><span class="lineNum">   14706 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(dstegr,DSTEGR)(jobz, range, n, d, e, vl, vu, il, iu, abstol, m, w,</span></a>
+<a name="14707"><span class="lineNum">   14707 </span>            :           z, ldz, isuppz, work, lwork, iwork, liwork, info);</a>
+<a name="14708"><span class="lineNum">   14708 </span>            :   </a>
+<a name="14709"><span class="lineNum">   14709 </span>            : </a>
+<a name="14710"><span class="lineNum">   14710 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="14711"><span class="lineNum">   14711 </span>            : </a>
+<a name="14712"><span class="lineNum">   14712 </span>            : }</a>
+<a name="14713"><span class="lineNum">   14713 </span>            : </a>
+<a name="14714"><span class="lineNum">   14714 </span>            : </a>
+<a name="14715"><span class="lineNum">   14715 </span>            : }</a>
+<a name="14716"><span class="lineNum">   14716 </span>            : }</a>
+<a name="14717"><span class="lineNum">   14717 </span>            : #include &lt;cmath&gt;</a>
+<a name="14718"><span class="lineNum">   14718 </span>            : </a>
+<a name="14719"><span class="lineNum">   14719 </span>            : #include &quot;real.h&quot;</a>
+<a name="14720"><span class="lineNum">   14720 </span>            : </a>
+<a name="14721"><span class="lineNum">   14721 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="14722"><span class="lineNum">   14722 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="14723"><span class="lineNum">   14723 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="14724"><span class="lineNum">   14724 </span>            : </a>
+<a name="14725"><span class="lineNum">   14725 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="14726"><span class="lineNum">   14726 </span>            : namespace PLMD{</a>
+<a name="14727"><span class="lineNum">   14727 </span>            : namespace lapack{</a>
+<a name="14728"><span class="lineNum">   14728 </span>            : using namespace blas;</a>
+<a name="14729"><span class="lineNum">   14729 </span>            : void</a>
+<a name="14730"><span class="lineNum">   14730 </span><span class="lineCov">     584795 : PLUMED_BLAS_F77_FUNC(dsyevr,DSYEVR)(const char *jobz, const char *range, const char *uplo, int *n, </span></a>
+<a name="14731"><span class="lineNum">   14731 </span>            :         double *a, int *lda, double *vl, double *vu, int *</a>
+<a name="14732"><span class="lineNum">   14732 </span>            :         il, int *iu, double *abstol, int *m, double *w, </a>
+<a name="14733"><span class="lineNum">   14733 </span>            :         double *z__, int *ldz, int *isuppz, double *work, </a>
+<a name="14734"><span class="lineNum">   14734 </span>            :         int *lwork, int *iwork, int *liwork, int *info)</a>
+<a name="14735"><span class="lineNum">   14735 </span>            : {</a>
+<a name="14736"><span class="lineNum">   14736 </span>            :     /* System generated locals */</a>
+<a name="14737"><span class="lineNum">   14737 </span>            :     int a_dim1, a_offset, z_dim1, z_offset, i__1, i__2;</a>
+<a name="14738"><span class="lineNum">   14738 </span>            :     double d__1, d__2;</a>
+<a name="14739"><span class="lineNum">   14739 </span>            : </a>
+<a name="14740"><span class="lineNum">   14740 </span>            :     /* Local variables */</a>
+<a name="14741"><span class="lineNum">   14741 </span><span class="lineCov">     584795 :     int c__1 = 1;</span></a>
+<a name="14742"><span class="lineNum">   14742 </span>            :     int i__, j, nb, jj;</a>
+<a name="14743"><span class="lineNum">   14743 </span>            :     double eps, tmp1;</a>
+<a name="14744"><span class="lineNum">   14744 </span>            :     int indd, inde;</a>
+<a name="14745"><span class="lineNum">   14745 </span>            :     double anrm;</a>
+<a name="14746"><span class="lineNum">   14746 </span>            :     int imax;</a>
+<a name="14747"><span class="lineNum">   14747 </span>            :     double rmin, rmax;</a>
+<a name="14748"><span class="lineNum">   14748 </span>            :     int itmp1, inddd, indee;</a>
+<a name="14749"><span class="lineNum">   14749 </span>            :     double sigma;</a>
+<a name="14750"><span class="lineNum">   14750 </span>            :     int iinfo;</a>
+<a name="14751"><span class="lineNum">   14751 </span>            :     int indwk;</a>
+<a name="14752"><span class="lineNum">   14752 </span>            :     int lwmin;</a>
+<a name="14753"><span class="lineNum">   14753 </span>            :     int lower, wantz;</a>
+<a name="14754"><span class="lineNum">   14754 </span>            :     int alleig, indeig;</a>
+<a name="14755"><span class="lineNum">   14755 </span>            :     int iscale, indibl, indifl;</a>
+<a name="14756"><span class="lineNum">   14756 </span>            :     int valeig;</a>
+<a name="14757"><span class="lineNum">   14757 </span>            :     double safmin,minval;</a>
+<a name="14758"><span class="lineNum">   14758 </span>            :     double bignum;</a>
+<a name="14759"><span class="lineNum">   14759 </span>            :     int indtau;</a>
+<a name="14760"><span class="lineNum">   14760 </span>            :     int indwkn;</a>
+<a name="14761"><span class="lineNum">   14761 </span>            :     int liwmin;</a>
+<a name="14762"><span class="lineNum">   14762 </span>            :     int llwrkn, llwork;</a>
+<a name="14763"><span class="lineNum">   14763 </span>            :     double smlnum;</a>
+<a name="14764"><span class="lineNum">   14764 </span>            :     int lwkopt;</a>
+<a name="14765"><span class="lineNum">   14765 </span>            :     int lquery;</a>
+<a name="14766"><span class="lineNum">   14766 </span>            :     </a>
+<a name="14767"><span class="lineNum">   14767 </span>            :     /* Parameter adjustments */</a>
+<a name="14768"><span class="lineNum">   14768 </span><span class="lineCov">     584795 :     a_dim1 = *lda;</span></a>
+<a name="14769"><span class="lineNum">   14769 </span><span class="lineCov">     584795 :     a_offset = 1 + a_dim1;</span></a>
+<a name="14770"><span class="lineNum">   14770 </span><span class="lineCov">     584795 :     a -= a_offset;</span></a>
+<a name="14771"><span class="lineNum">   14771 </span><span class="lineCov">     584795 :     --w;</span></a>
+<a name="14772"><span class="lineNum">   14772 </span><span class="lineCov">     584795 :     z_dim1 = *ldz;</span></a>
+<a name="14773"><span class="lineNum">   14773 </span><span class="lineCov">     584795 :     z_offset = 1 + z_dim1;</span></a>
+<a name="14774"><span class="lineNum">   14774 </span><span class="lineCov">     584795 :     z__ -= z_offset;</span></a>
+<a name="14775"><span class="lineNum">   14775 </span>            :     --isuppz;</a>
+<a name="14776"><span class="lineNum">   14776 </span><span class="lineCov">     584795 :     --work;</span></a>
+<a name="14777"><span class="lineNum">   14777 </span><span class="lineCov">     584795 :     --iwork;</span></a>
+<a name="14778"><span class="lineNum">   14778 </span>            : </a>
+<a name="14779"><span class="lineNum">   14779 </span><span class="lineCov">     584795 :     lower = (*uplo=='L' || *uplo=='l');</span></a>
+<a name="14780"><span class="lineNum">   14780 </span><span class="lineCov">     584795 :     wantz = (*jobz=='V' || *jobz=='v');</span></a>
+<a name="14781"><span class="lineNum">   14781 </span><span class="lineCov">     584795 :     alleig = (*range=='A' || *range=='a');</span></a>
+<a name="14782"><span class="lineNum">   14782 </span><span class="lineCov">     584795 :     valeig = (*range=='V' || *range=='v');</span></a>
+<a name="14783"><span class="lineNum">   14783 </span><span class="lineCov">     584795 :     indeig = (*range=='I' || *range=='i');</span></a>
+<a name="14784"><span class="lineNum">   14784 </span>            : </a>
+<a name="14785"><span class="lineNum">   14785 </span>            :     indibl = 0;</a>
+<a name="14786"><span class="lineNum">   14786 </span><span class="lineCov">     584795 :     lquery = *lwork == -1 || *liwork == -1;</span></a>
+<a name="14787"><span class="lineNum">   14787 </span>            : </a>
+<a name="14788"><span class="lineNum">   14788 </span>            :     i__1 = 1;</a>
+<a name="14789"><span class="lineNum">   14789 </span><span class="lineCov">     584795 :     i__2 = *n * 26;</span></a>
+<a name="14790"><span class="lineNum">   14790 </span>            : </a>
+<a name="14791"><span class="lineNum">   14791 </span><span class="lineCov">     584795 :     if(*n&gt;0) </span></a>
+<a name="14792"><span class="lineNum">   14792 </span>            :       lwmin = *n * 26;</a>
+<a name="14793"><span class="lineNum">   14793 </span>            :     else</a>
+<a name="14794"><span class="lineNum">   14794 </span>            :       lwmin = 1;</a>
+<a name="14795"><span class="lineNum">   14795 </span>            : </a>
+<a name="14796"><span class="lineNum">   14796 </span><span class="lineCov">     584795 :     if(*n&gt;0) </span></a>
+<a name="14797"><span class="lineNum">   14797 </span><span class="lineCov">     584795 :       liwmin = *n * 10;</span></a>
+<a name="14798"><span class="lineNum">   14798 </span>            :     else</a>
+<a name="14799"><span class="lineNum">   14799 </span>            :       liwmin = 1;</a>
+<a name="14800"><span class="lineNum">   14800 </span>            : </a>
+<a name="14801"><span class="lineNum">   14801 </span><span class="lineCov">     584795 :     *info = 0;</span></a>
+<a name="14802"><span class="lineNum">   14802 </span><span class="lineCov">     584795 :     if (! (wantz || (*jobz=='N' || *jobz=='n'))) {</span></a>
+<a name="14803"><span class="lineNum">   14803 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="14804"><span class="lineNum">   14804 </span><span class="lineCov">     584795 :     } else if (! (alleig || valeig || indeig)) {</span></a>
+<a name="14805"><span class="lineNum">   14805 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="14806"><span class="lineNum">   14806 </span><span class="lineCov">     584795 :     } else if (! (lower || (*uplo=='U' || *uplo=='u'))) {</span></a>
+<a name="14807"><span class="lineNum">   14807 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="14808"><span class="lineNum">   14808 </span><span class="lineCov">     584795 :     } else if (*n &lt; 0) {</span></a>
+<a name="14809"><span class="lineNum">   14809 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="14810"><span class="lineNum">   14810 </span><span class="lineCov">     584795 :     } else if (*lda &lt; ((*n&gt;1) ? *n : 1) ) {</span></a>
+<a name="14811"><span class="lineNum">   14811 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="14812"><span class="lineNum">   14812 </span>            :     } else {</a>
+<a name="14813"><span class="lineNum">   14813 </span><span class="lineCov">     584795 :         if (valeig) {</span></a>
+<a name="14814"><span class="lineNum">   14814 </span><span class="lineNoCov">          0 :             if (*n &gt; 0 &amp;&amp; *vu &lt;= *vl) {</span></a>
+<a name="14815"><span class="lineNum">   14815 </span><span class="lineNoCov">          0 :                 *info = -8;</span></a>
+<a name="14816"><span class="lineNum">   14816 </span>            :             }</a>
+<a name="14817"><span class="lineNum">   14817 </span><span class="lineCov">     584795 :         } else if (indeig) {</span></a>
+<a name="14818"><span class="lineNum">   14818 </span><span class="lineCov">     577320 :           if (*il &lt; 1 || *il &gt; ((*n&gt;1) ? *n : 1)) {</span></a>
+<a name="14819"><span class="lineNum">   14819 </span><span class="lineNoCov">          0 :                 *info = -9;</span></a>
+<a name="14820"><span class="lineNum">   14820 </span><span class="lineCov">     577320 :             } else if (*iu &lt; ((*n&lt;*il) ? *n : *il) || *iu &gt; *n) {</span></a>
+<a name="14821"><span class="lineNum">   14821 </span><span class="lineNoCov">          0 :                 *info = -10;</span></a>
+<a name="14822"><span class="lineNum">   14822 </span>            :             }</a>
+<a name="14823"><span class="lineNum">   14823 </span>            :         }</a>
+<a name="14824"><span class="lineNum">   14824 </span>            :     }</a>
+<a name="14825"><span class="lineNum">   14825 </span><span class="lineCov">     584795 :     if (*info == 0) {</span></a>
+<a name="14826"><span class="lineNum">   14826 </span><span class="lineCov">     584795 :       if (*ldz &lt; 1 || (wantz &amp;&amp; *ldz &lt; *n)) {</span></a>
+<a name="14827"><span class="lineNum">   14827 </span><span class="lineNoCov">          0 :             *info = -15;</span></a>
+<a name="14828"><span class="lineNum">   14828 </span><span class="lineCov">     584795 :         } else if (*lwork &lt; lwmin &amp;&amp; ! lquery) {</span></a>
+<a name="14829"><span class="lineNum">   14829 </span><span class="lineNoCov">          0 :             *info = -18;</span></a>
+<a name="14830"><span class="lineNum">   14830 </span><span class="lineCov">     584795 :         } else if (*liwork &lt; liwmin &amp;&amp; ! lquery) {</span></a>
+<a name="14831"><span class="lineNum">   14831 </span><span class="lineNoCov">          0 :             *info = -20;</span></a>
+<a name="14832"><span class="lineNum">   14832 </span>            :         }</a>
+<a name="14833"><span class="lineNum">   14833 </span>            :     }</a>
+<a name="14834"><span class="lineNum">   14834 </span>            : </a>
+<a name="14835"><span class="lineNum">   14835 </span><span class="lineCov">     584795 :     if (*info == 0) {</span></a>
+<a name="14836"><span class="lineNum">   14836 </span>            :       nb = 32;</a>
+<a name="14837"><span class="lineNum">   14837 </span>            :       /* Computing MAX */</a>
+<a name="14838"><span class="lineNum">   14838 </span><span class="lineCov">     584795 :       i__1 = (nb + 1) * *n;</span></a>
+<a name="14839"><span class="lineNum">   14839 </span>            :       lwkopt = (i__1&gt;lwmin) ? i__1 : lwmin;</a>
+<a name="14840"><span class="lineNum">   14840 </span><span class="lineCov">     584795 :       work[1] = (double) lwkopt;</span></a>
+<a name="14841"><span class="lineNum">   14841 </span><span class="lineCov">     584795 :       iwork[1] = liwmin;</span></a>
+<a name="14842"><span class="lineNum">   14842 </span>            :     } else </a>
+<a name="14843"><span class="lineNum">   14843 </span>            :       return;</a>
+<a name="14844"><span class="lineNum">   14844 </span>            : </a>
+<a name="14845"><span class="lineNum">   14845 </span><span class="lineCov">     584795 :     if (lquery) </span></a>
+<a name="14846"><span class="lineNum">   14846 </span>            :         return;</a>
+<a name="14847"><span class="lineNum">   14847 </span>            :     </a>
+<a name="14848"><span class="lineNum">   14848 </span><span class="lineCov">     570596 :     *m = 0;</span></a>
+<a name="14849"><span class="lineNum">   14849 </span><span class="lineCov">     570596 :     if (*n == 0) {</span></a>
+<a name="14850"><span class="lineNum">   14850 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="14851"><span class="lineNum">   14851 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="14852"><span class="lineNum">   14852 </span>            :     }</a>
+<a name="14853"><span class="lineNum">   14853 </span>            : </a>
+<a name="14854"><span class="lineNum">   14854 </span><span class="lineCov">     570596 :     if (*n == 1) {</span></a>
+<a name="14855"><span class="lineNum">   14855 </span><span class="lineCov">        588 :         work[1] = 7.;</span></a>
+<a name="14856"><span class="lineNum">   14856 </span><span class="lineCov">        588 :         if (alleig || indeig) {</span></a>
+<a name="14857"><span class="lineNum">   14857 </span><span class="lineCov">        588 :             *m = 1;</span></a>
+<a name="14858"><span class="lineNum">   14858 </span><span class="lineCov">        588 :             w[1] = a[a_dim1 + 1];</span></a>
+<a name="14859"><span class="lineNum">   14859 </span>            :         } else {</a>
+<a name="14860"><span class="lineNum">   14860 </span><span class="lineNoCov">          0 :             if (*vl &lt; a[a_dim1 + 1] &amp;&amp; *vu &gt;= a[a_dim1 + 1]) {</span></a>
+<a name="14861"><span class="lineNum">   14861 </span><span class="lineNoCov">          0 :                 *m = 1;</span></a>
+<a name="14862"><span class="lineNum">   14862 </span><span class="lineNoCov">          0 :                 w[1] = a[a_dim1 + 1];</span></a>
+<a name="14863"><span class="lineNum">   14863 </span>            :             }</a>
+<a name="14864"><span class="lineNum">   14864 </span>            :         }</a>
+<a name="14865"><span class="lineNum">   14865 </span><span class="lineCov">        588 :         if (wantz) {</span></a>
+<a name="14866"><span class="lineNum">   14866 </span><span class="lineCov">        586 :             z__[z_dim1 + 1] = 1.;</span></a>
+<a name="14867"><span class="lineNum">   14867 </span>            :         }</a>
+<a name="14868"><span class="lineNum">   14868 </span><span class="lineCov">        588 :         return;</span></a>
+<a name="14869"><span class="lineNum">   14869 </span>            :     }</a>
+<a name="14870"><span class="lineNum">   14870 </span>            :     minval = PLUMED_GMX_DOUBLE_MIN;</a>
+<a name="14871"><span class="lineNum">   14871 </span>            :     safmin = minval*(1.0+PLUMED_GMX_DOUBLE_EPS);</a>
+<a name="14872"><span class="lineNum">   14872 </span>            :     eps = PLUMED_GMX_DOUBLE_EPS;</a>
+<a name="14873"><span class="lineNum">   14873 </span>            : </a>
+<a name="14874"><span class="lineNum">   14874 </span>            :     smlnum = safmin / eps;</a>
+<a name="14875"><span class="lineNum">   14875 </span>            :     bignum = 1. / smlnum;</a>
+<a name="14876"><span class="lineNum">   14876 </span>            :     rmin =  std::sqrt(smlnum);</a>
+<a name="14877"><span class="lineNum">   14877 </span>            : </a>
+<a name="14878"><span class="lineNum">   14878 </span><span class="lineCov">     570008 :     d__1 =  std::sqrt(bignum), d__2 = 1. / std::sqrt(sqrt(safmin));</span></a>
+<a name="14879"><span class="lineNum">   14879 </span>            :     rmax = (d__1&lt;d__2) ? d__1 : d__2;</a>
+<a name="14880"><span class="lineNum">   14880 </span>            : </a>
+<a name="14881"><span class="lineNum">   14881 </span>            :     iscale = 0;</a>
+<a name="14882"><span class="lineNum">   14882 </span><span class="lineCov">     570008 :     anrm = PLUMED_BLAS_F77_FUNC(dlansy,DLANSY)(&quot;M&quot;, uplo, n, &amp;a[a_offset], lda, &amp;work[1]);</span></a>
+<a name="14883"><span class="lineNum">   14883 </span><span class="lineCov">     570008 :     if (anrm &gt; 0. &amp;&amp; anrm &lt; rmin) {</span></a>
+<a name="14884"><span class="lineNum">   14884 </span>            :         iscale = 1;</a>
+<a name="14885"><span class="lineNum">   14885 </span><span class="lineNoCov">          0 :         sigma = rmin / anrm;</span></a>
+<a name="14886"><span class="lineNum">   14886 </span><span class="lineCov">     570008 :     } else if (anrm &gt; rmax) {</span></a>
+<a name="14887"><span class="lineNum">   14887 </span>            :         iscale = 1;</a>
+<a name="14888"><span class="lineNum">   14888 </span><span class="lineNoCov">          0 :         sigma = rmax / anrm; </span></a>
+<a name="14889"><span class="lineNum">   14889 </span>            :     }</a>
+<a name="14890"><span class="lineNum">   14890 </span>            :     if (iscale == 1) {</a>
+<a name="14891"><span class="lineNum">   14891 </span><span class="lineNoCov">          0 :         if (lower) {</span></a>
+<a name="14892"><span class="lineNum">   14892 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="14893"><span class="lineNum">   14893 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="14894"><span class="lineNum">   14894 </span><span class="lineNoCov">          0 :                 i__2 = *n - j + 1;</span></a>
+<a name="14895"><span class="lineNum">   14895 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__2, &amp;sigma, &amp;a[j + j * a_dim1], &amp;c__1);</span></a>
+<a name="14896"><span class="lineNum">   14896 </span>            :             }</a>
+<a name="14897"><span class="lineNum">   14897 </span>            :         } else {</a>
+<a name="14898"><span class="lineNum">   14898 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="14899"><span class="lineNum">   14899 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="14900"><span class="lineNum">   14900 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;j, &amp;sigma, &amp;a[j * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="14901"><span class="lineNum">   14901 </span>            : </a>
+<a name="14902"><span class="lineNum">   14902 </span>            :             }</a>
+<a name="14903"><span class="lineNum">   14903 </span>            :         }</a>
+<a name="14904"><span class="lineNum">   14904 </span>            :     }</a>
+<a name="14905"><span class="lineNum">   14905 </span>            : </a>
+<a name="14906"><span class="lineNum">   14906 </span>            :     indtau = 1;</a>
+<a name="14907"><span class="lineNum">   14907 </span><span class="lineCov">     570008 :     inde = indtau + *n;</span></a>
+<a name="14908"><span class="lineNum">   14908 </span><span class="lineCov">     570008 :     indd = inde + *n;</span></a>
+<a name="14909"><span class="lineNum">   14909 </span><span class="lineCov">     570008 :     indee = indd + *n;</span></a>
+<a name="14910"><span class="lineNum">   14910 </span><span class="lineCov">     570008 :     inddd = indee + *n;</span></a>
+<a name="14911"><span class="lineNum">   14911 </span><span class="lineCov">     570008 :     indifl = inddd + *n;</span></a>
+<a name="14912"><span class="lineNum">   14912 </span><span class="lineCov">     570008 :     indwk = indifl + *n;</span></a>
+<a name="14913"><span class="lineNum">   14913 </span><span class="lineCov">     570008 :     llwork = *lwork - indwk + 1;</span></a>
+<a name="14914"><span class="lineNum">   14914 </span><span class="lineCov">     570008 :     PLUMED_BLAS_F77_FUNC(dsytrd,DSYTRD)(uplo, n, &amp;a[a_offset], lda, &amp;work[indd], &amp;work[inde], &amp;work[</span></a>
+<a name="14915"><span class="lineNum">   14915 </span><span class="lineCov">     570008 :             indtau], &amp;work[indwk], &amp;llwork, &amp;iinfo);</span></a>
+<a name="14916"><span class="lineNum">   14916 </span>            : </a>
+<a name="14917"><span class="lineNum">   14917 </span><span class="lineCov">     570008 :     i__1 = *n - 1;</span></a>
+<a name="14918"><span class="lineNum">   14918 </span><span class="lineCov">     570008 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(&amp;i__1, &amp;work[inde], &amp;c__1, &amp;work[indee], &amp;c__1);</span></a>
+<a name="14919"><span class="lineNum">   14919 </span><span class="lineCov">     570008 :     PLUMED_BLAS_F77_FUNC(dcopy,DCOPY)(n, &amp;work[indd], &amp;c__1, &amp;work[inddd], &amp;c__1);</span></a>
+<a name="14920"><span class="lineNum">   14920 </span>            : </a>
+<a name="14921"><span class="lineNum">   14921 </span><span class="lineCov">     570008 :     PLUMED_BLAS_F77_FUNC(dstegr,DSTEGR)(jobz, range, n, &amp;work[inddd], &amp;work[indee], vl, vu, il, iu, </span></a>
+<a name="14922"><span class="lineNum">   14922 </span>            :             abstol, m, &amp;w[1], &amp;z__[z_offset], ldz, &amp;isuppz[1], </a>
+<a name="14923"><span class="lineNum">   14923 </span>            :             &amp;work[indwk], lwork, &amp;iwork[1], liwork, info);</a>
+<a name="14924"><span class="lineNum">   14924 </span><span class="lineCov">     570008 :     if (wantz &amp;&amp; *info == 0) {</span></a>
+<a name="14925"><span class="lineNum">   14925 </span>            :       indwkn = inde;</a>
+<a name="14926"><span class="lineNum">   14926 </span><span class="lineCov">     569964 :       llwrkn = *lwork - indwkn + 1;</span></a>
+<a name="14927"><span class="lineNum">   14927 </span><span class="lineCov">     569964 :       PLUMED_BLAS_F77_FUNC(dormtr,DORMTR)(&quot;L&quot;, uplo, &quot;N&quot;, n, m, &amp;a[a_offset], lda, &amp;work[indtau]</span></a>
+<a name="14928"><span class="lineNum">   14928 </span>            :               , &amp;z__[z_offset], ldz, &amp;work[indwkn], &amp;llwrkn, &amp;iinfo);</a>
+<a name="14929"><span class="lineNum">   14929 </span>            :     }</a>
+<a name="14930"><span class="lineNum">   14930 </span>            : </a>
+<a name="14931"><span class="lineNum">   14931 </span><span class="lineCov">     570008 :     if (*info != 0) </span></a>
+<a name="14932"><span class="lineNum">   14932 </span>            :       return;</a>
+<a name="14933"><span class="lineNum">   14933 </span>            : </a>
+<a name="14934"><span class="lineNum">   14934 </span><span class="lineCov">     570008 :     if (iscale == 1) {</span></a>
+<a name="14935"><span class="lineNum">   14935 </span>            :         if (*info == 0) {</a>
+<a name="14936"><span class="lineNum">   14936 </span><span class="lineNoCov">          0 :             imax = *m;</span></a>
+<a name="14937"><span class="lineNum">   14937 </span>            :         } else {</a>
+<a name="14938"><span class="lineNum">   14938 </span>            :             imax = *info - 1;</a>
+<a name="14939"><span class="lineNum">   14939 </span>            :         }</a>
+<a name="14940"><span class="lineNum">   14940 </span><span class="lineNoCov">          0 :         d__1 = 1. / sigma;</span></a>
+<a name="14941"><span class="lineNum">   14941 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;imax, &amp;d__1, &amp;w[1], &amp;c__1);</span></a>
+<a name="14942"><span class="lineNum">   14942 </span>            :     }</a>
+<a name="14943"><span class="lineNum">   14943 </span>            : </a>
+<a name="14944"><span class="lineNum">   14944 </span><span class="lineCov">     570008 :     if (wantz) {</span></a>
+<a name="14945"><span class="lineNum">   14945 </span><span class="lineCov">     569964 :         i__1 = *m - 1;</span></a>
+<a name="14946"><span class="lineNum">   14946 </span>            :         </a>
+<a name="14947"><span class="lineNum">   14947 </span><span class="lineCov">     607531 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="14948"><span class="lineNum">   14948 </span>            :             i__ = 0;</a>
+<a name="14949"><span class="lineNum">   14949 </span><span class="lineCov">      37567 :             tmp1 = w[j];</span></a>
+<a name="14950"><span class="lineNum">   14950 </span><span class="lineCov">      37567 :             i__2 = *m;</span></a>
+<a name="14951"><span class="lineNum">   14951 </span><span class="lineCov">     291780 :             for (jj = j + 1; jj &lt;= i__2; ++jj) {</span></a>
+<a name="14952"><span class="lineNum">   14952 </span><span class="lineCov">     254213 :                 if (w[jj] &lt; tmp1) {</span></a>
+<a name="14953"><span class="lineNum">   14953 </span>            :                     i__ = jj;</a>
+<a name="14954"><span class="lineNum">   14954 </span>            :                     tmp1 = w[jj];</a>
+<a name="14955"><span class="lineNum">   14955 </span>            :                 }</a>
+<a name="14956"><span class="lineNum">   14956 </span>            :             }</a>
+<a name="14957"><span class="lineNum">   14957 </span>            : </a>
+<a name="14958"><span class="lineNum">   14958 </span><span class="lineCov">      37567 :             if (i__ != 0) {</span></a>
+<a name="14959"><span class="lineNum">   14959 </span><span class="lineNoCov">          0 :                 itmp1 = iwork[indibl + i__ - 1];</span></a>
+<a name="14960"><span class="lineNum">   14960 </span><span class="lineNoCov">          0 :                 w[i__] = w[j];</span></a>
+<a name="14961"><span class="lineNum">   14961 </span><span class="lineNoCov">          0 :                 iwork[indibl + i__ - 1] = iwork[indibl + j - 1];</span></a>
+<a name="14962"><span class="lineNum">   14962 </span><span class="lineNoCov">          0 :                 w[j] = tmp1;</span></a>
+<a name="14963"><span class="lineNum">   14963 </span><span class="lineNoCov">          0 :                 iwork[indibl + j - 1] = itmp1;</span></a>
+<a name="14964"><span class="lineNum">   14964 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dswap,DSWAP)(n, &amp;z__[i__ * z_dim1 + 1], &amp;c__1, &amp;z__[j * z_dim1 + 1],</span></a>
+<a name="14965"><span class="lineNum">   14965 </span>            :                          &amp;c__1);</a>
+<a name="14966"><span class="lineNum">   14966 </span>            :             }</a>
+<a name="14967"><span class="lineNum">   14967 </span>            :         }</a>
+<a name="14968"><span class="lineNum">   14968 </span>            :     }</a>
+<a name="14969"><span class="lineNum">   14969 </span>            : </a>
+<a name="14970"><span class="lineNum">   14970 </span><span class="lineCov">     570008 :     work[1] = (double) lwkopt;</span></a>
+<a name="14971"><span class="lineNum">   14971 </span><span class="lineCov">     570008 :     iwork[1] = liwmin;</span></a>
+<a name="14972"><span class="lineNum">   14972 </span><span class="lineCov">     570008 :     return;</span></a>
+<a name="14973"><span class="lineNum">   14973 </span>            : </a>
+<a name="14974"><span class="lineNum">   14974 </span>            : }</a>
+<a name="14975"><span class="lineNum">   14975 </span>            : }</a>
+<a name="14976"><span class="lineNum">   14976 </span>            : }</a>
+<a name="14977"><span class="lineNum">   14977 </span>            : #include &lt;cctype&gt;</a>
+<a name="14978"><span class="lineNum">   14978 </span>            : #include &lt;cmath&gt;</a>
+<a name="14979"><span class="lineNum">   14979 </span>            : </a>
+<a name="14980"><span class="lineNum">   14980 </span>            : #include &quot;real.h&quot;</a>
+<a name="14981"><span class="lineNum">   14981 </span>            : </a>
+<a name="14982"><span class="lineNum">   14982 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="14983"><span class="lineNum">   14983 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="14984"><span class="lineNum">   14984 </span>            : </a>
+<a name="14985"><span class="lineNum">   14985 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="14986"><span class="lineNum">   14986 </span>            : namespace PLMD{</a>
+<a name="14987"><span class="lineNum">   14987 </span>            : namespace lapack{</a>
+<a name="14988"><span class="lineNum">   14988 </span>            : using namespace blas;</a>
+<a name="14989"><span class="lineNum">   14989 </span>            : void</a>
+<a name="14990"><span class="lineNum">   14990 </span><span class="lineCov">     570008 : PLUMED_BLAS_F77_FUNC(dsytd2,DSYTD2)(const char *    uplo,</span></a>
+<a name="14991"><span class="lineNum">   14991 </span>            :         int *     n,</a>
+<a name="14992"><span class="lineNum">   14992 </span>            :         double *  a,</a>
+<a name="14993"><span class="lineNum">   14993 </span>            :         int *     lda,</a>
+<a name="14994"><span class="lineNum">   14994 </span>            :         double *  d,</a>
+<a name="14995"><span class="lineNum">   14995 </span>            :         double *  e,</a>
+<a name="14996"><span class="lineNum">   14996 </span>            :         double *  tau,</a>
+<a name="14997"><span class="lineNum">   14997 </span>            :     int *     info)</a>
+<a name="14998"><span class="lineNum">   14998 </span>            : {</a>
+<a name="14999"><span class="lineNum">   14999 </span>            :   double minusone,zero;</a>
+<a name="15000"><span class="lineNum">   15000 </span>            :   double taui,alpha,tmp;</a>
+<a name="15001"><span class="lineNum">   15001 </span>            :   int ti1,ti2,ti3,i;</a>
+<a name="15002"><span class="lineNum">   15002 </span><span class="lineCov">     570008 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="15003"><span class="lineNum">   15003 </span>            : </a>
+<a name="15004"><span class="lineNum">   15004 </span><span class="lineCov">     570008 :   zero = 0.0;</span></a>
+<a name="15005"><span class="lineNum">   15005 </span><span class="lineCov">     570008 :   minusone = -1.0;</span></a>
+<a name="15006"><span class="lineNum">   15006 </span>            : </a>
+<a name="15007"><span class="lineNum">   15007 </span><span class="lineCov">     570008 :   if(*n&lt;=0)</span></a>
+<a name="15008"><span class="lineNum">   15008 </span>            :     return;</a>
+<a name="15009"><span class="lineNum">   15009 </span>            : </a>
+<a name="15010"><span class="lineNum">   15010 </span><span class="lineCov">     570008 :   if(ch=='U') {</span></a>
+<a name="15011"><span class="lineNum">   15011 </span><span class="lineCov">    2253916 :     for(i=*n-1;i&gt;=1;i--) {</span></a>
+<a name="15012"><span class="lineNum">   15012 </span>            : </a>
+<a name="15013"><span class="lineNum">   15013 </span><span class="lineCov">    1683908 :       ti1 = 1;</span></a>
+<a name="15014"><span class="lineNum">   15014 </span><span class="lineCov">    1683908 :       PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;i,&amp;(a[i*(*lda)+(i-1)]),&amp;(a[i*(*lda)+0]),&amp;ti1,&amp;taui);</span></a>
+<a name="15015"><span class="lineNum">   15015 </span><span class="lineCov">    1683908 :       e[i-1] = a[i*(*lda) + (i-1)];</span></a>
+<a name="15016"><span class="lineNum">   15016 </span><span class="lineCov">    1683908 :       if(std::abs(taui)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="15017"><span class="lineNum">   15017 </span><span class="lineCov">    1113895 :         a[i*(*lda)+(i-1)] = 1.0;</span></a>
+<a name="15018"><span class="lineNum">   15018 </span>            :       </a>
+<a name="15019"><span class="lineNum">   15019 </span><span class="lineCov">    1113895 :         ti1 = 1;</span></a>
+<a name="15020"><span class="lineNum">   15020 </span><span class="lineCov">    1113895 :         PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)(&quot;U&quot;,&amp;i,&amp;taui,a,lda,&amp;(a[i*(*lda)+0]),&amp;ti1,&amp;zero,tau,&amp;ti1);</span></a>
+<a name="15021"><span class="lineNum">   15021 </span>            : </a>
+<a name="15022"><span class="lineNum">   15022 </span><span class="lineCov">    1113895 :         tmp = PLUMED_BLAS_F77_FUNC(ddot,DDOT)(&amp;i,tau,&amp;ti1,&amp;(a[i*(*lda)+0]),&amp;ti1);</span></a>
+<a name="15023"><span class="lineNum">   15023 </span>            : </a>
+<a name="15024"><span class="lineNum">   15024 </span><span class="lineCov">    1113895 :         alpha = -0.5*taui*tmp;</span></a>
+<a name="15025"><span class="lineNum">   15025 </span>            : </a>
+<a name="15026"><span class="lineNum">   15026 </span><span class="lineCov">    1113895 :         PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(&amp;i,&amp;alpha,&amp;(a[i*(*lda)+0]),&amp;ti1,tau,&amp;ti1);</span></a>
+<a name="15027"><span class="lineNum">   15027 </span>            : </a>
+<a name="15028"><span class="lineNum">   15028 </span><span class="lineCov">    1113895 :         PLUMED_BLAS_F77_FUNC(dsyr2,DSYR2)(&quot;U&quot;,&amp;i,&amp;minusone,&amp;(a[i*(*lda)+0]),&amp;ti1,tau,&amp;ti1,a,lda);</span></a>
+<a name="15029"><span class="lineNum">   15029 </span>            : </a>
+<a name="15030"><span class="lineNum">   15030 </span><span class="lineCov">    1113895 :         a[i*(*lda)+(i-1)] = e[i-1]; </span></a>
+<a name="15031"><span class="lineNum">   15031 </span>            : </a>
+<a name="15032"><span class="lineNum">   15032 </span>            :       }</a>
+<a name="15033"><span class="lineNum">   15033 </span><span class="lineCov">    1683908 :       d[i] = a[i*(*lda)+i];</span></a>
+<a name="15034"><span class="lineNum">   15034 </span><span class="lineCov">    1683908 :       tau[i-1] = taui;</span></a>
+<a name="15035"><span class="lineNum">   15035 </span>            :     }</a>
+<a name="15036"><span class="lineNum">   15036 </span><span class="lineCov">     570008 :     d[0] = a[0];</span></a>
+<a name="15037"><span class="lineNum">   15037 </span>            :     </a>
+<a name="15038"><span class="lineNum">   15038 </span>            :   } else {</a>
+<a name="15039"><span class="lineNum">   15039 </span>            :     /* lower */</a>
+<a name="15040"><span class="lineNum">   15040 </span>            : </a>
+<a name="15041"><span class="lineNum">   15041 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;*n;i++) {</span></a>
+<a name="15042"><span class="lineNum">   15042 </span>            : </a>
+<a name="15043"><span class="lineNum">   15043 </span><span class="lineNoCov">          0 :       ti1 = *n - i;</span></a>
+<a name="15044"><span class="lineNum">   15044 </span><span class="lineNoCov">          0 :       ti2 = ( *n &lt; i+2) ? *n : i+2;</span></a>
+<a name="15045"><span class="lineNum">   15045 </span><span class="lineNoCov">          0 :       ti3 = 1;</span></a>
+<a name="15046"><span class="lineNum">   15046 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(dlarfg,DLARFG)(&amp;ti1,&amp;(a[(i-1)*(*lda)+(i)]),&amp;(a[(i-1)*(*lda)+ti2-1]),&amp;ti3,&amp;taui);</span></a>
+<a name="15047"><span class="lineNum">   15047 </span>            : </a>
+<a name="15048"><span class="lineNum">   15048 </span><span class="lineNoCov">          0 :       e[i-1] = a[(i-1)*(*lda) + (i)];</span></a>
+<a name="15049"><span class="lineNum">   15049 </span>            : </a>
+<a name="15050"><span class="lineNum">   15050 </span><span class="lineNoCov">          0 :       if(std::abs(taui)&gt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="15051"><span class="lineNum">   15051 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i)] = 1.0;</span></a>
+<a name="15052"><span class="lineNum">   15052 </span>            :       </a>
+<a name="15053"><span class="lineNum">   15053 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="15054"><span class="lineNum">   15054 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="15055"><span class="lineNum">   15055 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dsymv,DSYMV)(uplo,&amp;ti1,&amp;taui,&amp;(a[i*(*lda)+i]),lda,&amp;(a[(i-1)*(*lda)+i]),</span></a>
+<a name="15056"><span class="lineNum">   15056 </span>            :                &amp;ti2,&amp;zero,&amp;(tau[i-1]),&amp;ti2);</a>
+<a name="15057"><span class="lineNum">   15057 </span>            :         </a>
+<a name="15058"><span class="lineNum">   15058 </span><span class="lineNoCov">          0 :         tmp = PLUMED_BLAS_F77_FUNC(ddot,DDOT)(&amp;ti1,&amp;(tau[i-1]),&amp;ti2,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2);</span></a>
+<a name="15059"><span class="lineNum">   15059 </span>            : </a>
+<a name="15060"><span class="lineNum">   15060 </span><span class="lineNoCov">          0 :         alpha = -0.5*taui*tmp;</span></a>
+<a name="15061"><span class="lineNum">   15061 </span>            : </a>
+<a name="15062"><span class="lineNum">   15062 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(daxpy,DAXPY)(&amp;ti1,&amp;alpha,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2,&amp;(tau[i-1]),&amp;ti2);</span></a>
+<a name="15063"><span class="lineNum">   15063 </span>            : </a>
+<a name="15064"><span class="lineNum">   15064 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dsyr2,DSYR2)(uplo,&amp;ti1,&amp;minusone,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2,&amp;(tau[i-1]),&amp;ti2,</span></a>
+<a name="15065"><span class="lineNum">   15065 </span><span class="lineNoCov">          0 :                &amp;(a[(i)*(*lda)+i]),lda);</span></a>
+<a name="15066"><span class="lineNum">   15066 </span>            : </a>
+<a name="15067"><span class="lineNum">   15067 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i)] = e[i-1]; </span></a>
+<a name="15068"><span class="lineNum">   15068 </span>            : </a>
+<a name="15069"><span class="lineNum">   15069 </span>            :       }</a>
+<a name="15070"><span class="lineNum">   15070 </span><span class="lineNoCov">          0 :       d[i-1] = a[(i-1)*(*lda)+i-1];</span></a>
+<a name="15071"><span class="lineNum">   15071 </span><span class="lineNoCov">          0 :       tau[i-1] = taui;</span></a>
+<a name="15072"><span class="lineNum">   15072 </span>            :     }</a>
+<a name="15073"><span class="lineNum">   15073 </span><span class="lineNoCov">          0 :     d[*n-1] = a[(*n-1)*(*lda)+(*n-1)];</span></a>
+<a name="15074"><span class="lineNum">   15074 </span>            :  </a>
+<a name="15075"><span class="lineNum">   15075 </span>            :   }</a>
+<a name="15076"><span class="lineNum">   15076 </span>            :   return;</a>
+<a name="15077"><span class="lineNum">   15077 </span>            : }</a>
+<a name="15078"><span class="lineNum">   15078 </span>            : }</a>
+<a name="15079"><span class="lineNum">   15079 </span>            : }</a>
+<a name="15080"><span class="lineNum">   15080 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15081"><span class="lineNum">   15081 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="15082"><span class="lineNum">   15082 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="15083"><span class="lineNum">   15083 </span>            : </a>
+<a name="15084"><span class="lineNum">   15084 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15085"><span class="lineNum">   15085 </span>            : namespace PLMD{</a>
+<a name="15086"><span class="lineNum">   15086 </span>            : namespace lapack{</a>
+<a name="15087"><span class="lineNum">   15087 </span>            : using namespace blas;</a>
+<a name="15088"><span class="lineNum">   15088 </span>            : void</a>
+<a name="15089"><span class="lineNum">   15089 </span><span class="lineCov">     570008 : PLUMED_BLAS_F77_FUNC(dsytrd,DSYTRD)(const char *uplo, int *n, double *a, int *</span></a>
+<a name="15090"><span class="lineNum">   15090 </span>            :         lda, double *d__, double *e, double *tau, double *</a>
+<a name="15091"><span class="lineNum">   15091 </span>            :         work, int *lwork, int *info)</a>
+<a name="15092"><span class="lineNum">   15092 </span>            : {</a>
+<a name="15093"><span class="lineNum">   15093 </span>            :     /* System generated locals */</a>
+<a name="15094"><span class="lineNum">   15094 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="15095"><span class="lineNum">   15095 </span>            : </a>
+<a name="15096"><span class="lineNum">   15096 </span>            :     /* Local variables */</a>
+<a name="15097"><span class="lineNum">   15097 </span>            :     int i__, j, nb, kk, nx, iws;</a>
+<a name="15098"><span class="lineNum">   15098 </span>            :     int nbmin, iinfo;</a>
+<a name="15099"><span class="lineNum">   15099 </span>            :     int upper;</a>
+<a name="15100"><span class="lineNum">   15100 </span>            :     int ldwork, lwkopt;</a>
+<a name="15101"><span class="lineNum">   15101 </span>            :     int lquery;</a>
+<a name="15102"><span class="lineNum">   15102 </span><span class="lineCov">     570008 :     double c_b22 = -1.;</span></a>
+<a name="15103"><span class="lineNum">   15103 </span><span class="lineCov">     570008 :     double c_b23 = 1.;</span></a>
+<a name="15104"><span class="lineNum">   15104 </span>            : </a>
+<a name="15105"><span class="lineNum">   15105 </span>            : </a>
+<a name="15106"><span class="lineNum">   15106 </span>            :     /* Parameter adjustments */</a>
+<a name="15107"><span class="lineNum">   15107 </span><span class="lineCov">     570008 :     a_dim1 = *lda;</span></a>
+<a name="15108"><span class="lineNum">   15108 </span><span class="lineCov">     570008 :     a_offset = 1 + a_dim1;</span></a>
+<a name="15109"><span class="lineNum">   15109 </span><span class="lineCov">     570008 :     a -= a_offset;</span></a>
+<a name="15110"><span class="lineNum">   15110 </span><span class="lineCov">     570008 :     --d__;</span></a>
+<a name="15111"><span class="lineNum">   15111 </span><span class="lineCov">     570008 :     --e;</span></a>
+<a name="15112"><span class="lineNum">   15112 </span><span class="lineCov">     570008 :     --tau;</span></a>
+<a name="15113"><span class="lineNum">   15113 </span>            :     --work;</a>
+<a name="15114"><span class="lineNum">   15114 </span>            : </a>
+<a name="15115"><span class="lineNum">   15115 </span>            :     /* Function Body */</a>
+<a name="15116"><span class="lineNum">   15116 </span><span class="lineCov">     570008 :     *info = 0;</span></a>
+<a name="15117"><span class="lineNum">   15117 </span><span class="lineCov">     570008 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="15118"><span class="lineNum">   15118 </span><span class="lineCov">     570008 :     lquery = (*lwork == -1);</span></a>
+<a name="15119"><span class="lineNum">   15119 </span>            : </a>
+<a name="15120"><span class="lineNum">   15120 </span><span class="lineCov">     570008 :     if (! upper &amp;&amp; ! (*uplo=='L' || *uplo=='l')) {</span></a>
+<a name="15121"><span class="lineNum">   15121 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="15122"><span class="lineNum">   15122 </span><span class="lineCov">     570008 :     } else if (*n &lt; 0) {</span></a>
+<a name="15123"><span class="lineNum">   15123 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="15124"><span class="lineNum">   15124 </span><span class="lineCov">     570008 :     } else if (*lda &lt; ((1&gt;*n) ? 1 : *n)) {</span></a>
+<a name="15125"><span class="lineNum">   15125 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="15126"><span class="lineNum">   15126 </span><span class="lineCov">     570008 :     } else if (*lwork &lt; 1 &amp;&amp; ! lquery) {</span></a>
+<a name="15127"><span class="lineNum">   15127 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="15128"><span class="lineNum">   15128 </span>            :     }</a>
+<a name="15129"><span class="lineNum">   15129 </span>            : </a>
+<a name="15130"><span class="lineNum">   15130 </span><span class="lineCov">     570008 :     if (*info == 0) {</span></a>
+<a name="15131"><span class="lineNum">   15131 </span>            : </a>
+<a name="15132"><span class="lineNum">   15132 </span><span class="lineCov">     570008 :       nb = DSYTRD_BLOCKSIZE;</span></a>
+<a name="15133"><span class="lineNum">   15133 </span><span class="lineCov">     570008 :       lwkopt = *n * nb;</span></a>
+<a name="15134"><span class="lineNum">   15134 </span><span class="lineCov">     570008 :       work[1] = (double) lwkopt;</span></a>
+<a name="15135"><span class="lineNum">   15135 </span>            :     } else</a>
+<a name="15136"><span class="lineNum">   15136 </span>            :       return;</a>
+<a name="15137"><span class="lineNum">   15137 </span>            : </a>
+<a name="15138"><span class="lineNum">   15138 </span><span class="lineCov">     570008 :     if (lquery) </span></a>
+<a name="15139"><span class="lineNum">   15139 </span>            :       return;</a>
+<a name="15140"><span class="lineNum">   15140 </span>            :   </a>
+<a name="15141"><span class="lineNum">   15141 </span><span class="lineCov">     570008 :     if (*n == 0) {</span></a>
+<a name="15142"><span class="lineNum">   15142 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="15143"><span class="lineNum">   15143 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="15144"><span class="lineNum">   15144 </span>            :     }</a>
+<a name="15145"><span class="lineNum">   15145 </span>            : </a>
+<a name="15146"><span class="lineNum">   15146 </span>            :     nx = *n;</a>
+<a name="15147"><span class="lineNum">   15147 </span><span class="lineCov">     570008 :     if (nb &gt; 1 &amp;&amp; nb &lt; *n) {</span></a>
+<a name="15148"><span class="lineNum">   15148 </span>            : </a>
+<a name="15149"><span class="lineNum">   15149 </span>            :         nx = DSYTRD_CROSSOVER;</a>
+<a name="15150"><span class="lineNum">   15150 </span><span class="lineCov">         12 :         if (nx &lt; *n) {</span></a>
+<a name="15151"><span class="lineNum">   15151 </span>            : </a>
+<a name="15152"><span class="lineNum">   15152 </span><span class="lineCov">          2 :             ldwork = *n;</span></a>
+<a name="15153"><span class="lineNum">   15153 </span><span class="lineCov">          2 :             iws = ldwork * nb;</span></a>
+<a name="15154"><span class="lineNum">   15154 </span><span class="lineCov">          2 :             if (*lwork &lt; iws) {</span></a>
+<a name="15155"><span class="lineNum">   15155 </span>            : </a>
+<a name="15156"><span class="lineNum">   15156 </span><span class="lineCov">          2 :                 i__1 = *lwork / ldwork;</span></a>
+<a name="15157"><span class="lineNum">   15157 </span><span class="lineCov">          2 :                 nb = (i__1&gt;1) ? i__1 : 1;</span></a>
+<a name="15158"><span class="lineNum">   15158 </span>            :                 nbmin = DSYTRD_MINBLOCKSIZE;</a>
+<a name="15159"><span class="lineNum">   15159 </span><span class="lineCov">          2 :                 if (nb &lt; nbmin) {</span></a>
+<a name="15160"><span class="lineNum">   15160 </span>            :                     nx = *n;</a>
+<a name="15161"><span class="lineNum">   15161 </span>            :                 }</a>
+<a name="15162"><span class="lineNum">   15162 </span>            :             }</a>
+<a name="15163"><span class="lineNum">   15163 </span>            :         } else {</a>
+<a name="15164"><span class="lineNum">   15164 </span>            :             nx = *n;</a>
+<a name="15165"><span class="lineNum">   15165 </span>            :         }</a>
+<a name="15166"><span class="lineNum">   15166 </span>            :     } else {</a>
+<a name="15167"><span class="lineNum">   15167 </span><span class="lineCov">     569996 :         nb = 1;</span></a>
+<a name="15168"><span class="lineNum">   15168 </span>            :     }</a>
+<a name="15169"><span class="lineNum">   15169 </span>            : </a>
+<a name="15170"><span class="lineNum">   15170 </span><span class="lineCov">     570008 :     if (upper) {</span></a>
+<a name="15171"><span class="lineNum">   15171 </span>            : </a>
+<a name="15172"><span class="lineNum">   15172 </span><span class="lineCov">     570008 :         kk = *n - (*n - nx + nb - 1) / nb * nb;</span></a>
+<a name="15173"><span class="lineNum">   15173 </span><span class="lineCov">     570008 :         i__1 = kk + 1;</span></a>
+<a name="15174"><span class="lineNum">   15174 </span>            :         i__2 = -nb;</a>
+<a name="15175"><span class="lineNum">   15175 </span><span class="lineCov">     570027 :         for (i__ = *n - nb + 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += </span></a>
+<a name="15176"><span class="lineNum">   15176 </span>            :                 i__2) {</a>
+<a name="15177"><span class="lineNum">   15177 </span>            : </a>
+<a name="15178"><span class="lineNum">   15178 </span><span class="lineCov">         19 :             i__3 = i__ + nb - 1;</span></a>
+<a name="15179"><span class="lineNum">   15179 </span><span class="lineCov">         19 :             PLUMED_BLAS_F77_FUNC(dlatrd,DLATRD)(uplo, &amp;i__3, &amp;nb, &amp;a[a_offset], lda, &amp;e[1], &amp;tau[1], &amp;</span></a>
+<a name="15180"><span class="lineNum">   15180 </span>            :                     work[1], &amp;ldwork);</a>
+<a name="15181"><span class="lineNum">   15181 </span>            : </a>
+<a name="15182"><span class="lineNum">   15182 </span><span class="lineCov">         19 :             i__3 = i__ - 1;</span></a>
+<a name="15183"><span class="lineNum">   15183 </span><span class="lineCov">         19 :             PLUMED_BLAS_F77_FUNC(dsyr2k,DSYR2K)(uplo, &quot;No transpose&quot;, &amp;i__3, &amp;nb, &amp;c_b22, &amp;a[i__ * a_dim1 </span></a>
+<a name="15184"><span class="lineNum">   15184 </span><span class="lineCov">         19 :                     + 1], lda, &amp;work[1], &amp;ldwork, &amp;c_b23, &amp;a[a_offset], lda);</span></a>
+<a name="15185"><span class="lineNum">   15185 </span>            : </a>
+<a name="15186"><span class="lineNum">   15186 </span><span class="lineCov">         19 :             i__3 = i__ + nb - 1;</span></a>
+<a name="15187"><span class="lineNum">   15187 </span><span class="lineCov">        532 :             for (j = i__; j &lt;= i__3; ++j) {</span></a>
+<a name="15188"><span class="lineNum">   15188 </span><span class="lineCov">        513 :                 a[j - 1 + j * a_dim1] = e[j - 1];</span></a>
+<a name="15189"><span class="lineNum">   15189 </span><span class="lineCov">        513 :                 d__[j] = a[j + j * a_dim1];</span></a>
+<a name="15190"><span class="lineNum">   15190 </span>            : </a>
+<a name="15191"><span class="lineNum">   15191 </span>            :             }</a>
+<a name="15192"><span class="lineNum">   15192 </span>            : </a>
+<a name="15193"><span class="lineNum">   15193 </span>            :         }</a>
+<a name="15194"><span class="lineNum">   15194 </span>            : </a>
+<a name="15195"><span class="lineNum">   15195 </span><span class="lineCov">     570008 :         PLUMED_BLAS_F77_FUNC(dsytd2,DSYTD2)(uplo, &amp;kk, &amp;a[a_offset], lda, &amp;d__[1], &amp;e[1], &amp;tau[1], &amp;iinfo);</span></a>
+<a name="15196"><span class="lineNum">   15196 </span>            :     } else {</a>
+<a name="15197"><span class="lineNum">   15197 </span>            : </a>
+<a name="15198"><span class="lineNum">   15198 </span><span class="lineNoCov">          0 :         i__2 = *n - nx;</span></a>
+<a name="15199"><span class="lineNum">   15199 </span><span class="lineNoCov">          0 :         i__1 = nb;</span></a>
+<a name="15200"><span class="lineNum">   15200 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__1 &lt; 0 ? i__ &gt;= i__2 : i__ &lt;= i__2; i__ += i__1) {</span></a>
+<a name="15201"><span class="lineNum">   15201 </span>            : </a>
+<a name="15202"><span class="lineNum">   15202 </span>            : </a>
+<a name="15203"><span class="lineNum">   15203 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="15204"><span class="lineNum">   15204 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dlatrd,DLATRD)(uplo, &amp;i__3, &amp;nb, &amp;a[i__ + i__ * a_dim1], lda, &amp;e[i__], &amp;</span></a>
+<a name="15205"><span class="lineNum">   15205 </span><span class="lineNoCov">          0 :                     tau[i__], &amp;work[1], &amp;ldwork);</span></a>
+<a name="15206"><span class="lineNum">   15206 </span>            : </a>
+<a name="15207"><span class="lineNum">   15207 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ - nb + 1;</span></a>
+<a name="15208"><span class="lineNum">   15208 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(dsyr2k,DSYR2K)(uplo, &quot;No transpose&quot;, &amp;i__3, &amp;nb, &amp;c_b22, &amp;a[i__ + nb + </span></a>
+<a name="15209"><span class="lineNum">   15209 </span><span class="lineNoCov">          0 :                     i__ * a_dim1], lda, &amp;work[nb + 1], &amp;ldwork, &amp;c_b23, &amp;a[</span></a>
+<a name="15210"><span class="lineNum">   15210 </span><span class="lineNoCov">          0 :                     i__ + nb + (i__ + nb) * a_dim1], lda);</span></a>
+<a name="15211"><span class="lineNum">   15211 </span>            : </a>
+<a name="15212"><span class="lineNum">   15212 </span>            : </a>
+<a name="15213"><span class="lineNum">   15213 </span><span class="lineNoCov">          0 :             i__3 = i__ + nb - 1;</span></a>
+<a name="15214"><span class="lineNum">   15214 </span><span class="lineNoCov">          0 :             for (j = i__; j &lt;= i__3; ++j) {</span></a>
+<a name="15215"><span class="lineNum">   15215 </span><span class="lineNoCov">          0 :                 a[j + 1 + j * a_dim1] = e[j];</span></a>
+<a name="15216"><span class="lineNum">   15216 </span><span class="lineNoCov">          0 :                 d__[j] = a[j + j * a_dim1];</span></a>
+<a name="15217"><span class="lineNum">   15217 </span>            : </a>
+<a name="15218"><span class="lineNum">   15218 </span>            :             }</a>
+<a name="15219"><span class="lineNum">   15219 </span>            : </a>
+<a name="15220"><span class="lineNum">   15220 </span>            :         }</a>
+<a name="15221"><span class="lineNum">   15221 </span>            : </a>
+<a name="15222"><span class="lineNum">   15222 </span>            : </a>
+<a name="15223"><span class="lineNum">   15223 </span><span class="lineNoCov">          0 :         i__1 = *n - i__ + 1;</span></a>
+<a name="15224"><span class="lineNum">   15224 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(dsytd2,DSYTD2)(uplo, &amp;i__1, &amp;a[i__ + i__ * a_dim1], lda, &amp;d__[i__], &amp;e[i__], </span></a>
+<a name="15225"><span class="lineNum">   15225 </span><span class="lineNoCov">          0 :                 &amp;tau[i__], &amp;iinfo);</span></a>
+<a name="15226"><span class="lineNum">   15226 </span>            :     }</a>
+<a name="15227"><span class="lineNum">   15227 </span>            : </a>
+<a name="15228"><span class="lineNum">   15228 </span><span class="lineCov">     570008 :     work[1] = (double) lwkopt;</span></a>
+<a name="15229"><span class="lineNum">   15229 </span><span class="lineCov">     570008 :     return;</span></a>
+<a name="15230"><span class="lineNum">   15230 </span>            : </a>
+<a name="15231"><span class="lineNum">   15231 </span>            : }</a>
+<a name="15232"><span class="lineNum">   15232 </span>            : </a>
+<a name="15233"><span class="lineNum">   15233 </span>            : </a>
+<a name="15234"><span class="lineNum">   15234 </span>            : }</a>
+<a name="15235"><span class="lineNum">   15235 </span>            : }</a>
+<a name="15236"><span class="lineNum">   15236 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15237"><span class="lineNum">   15237 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="15238"><span class="lineNum">   15238 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="15239"><span class="lineNum">   15239 </span>            : </a>
+<a name="15240"><span class="lineNum">   15240 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15241"><span class="lineNum">   15241 </span>            : namespace PLMD{</a>
+<a name="15242"><span class="lineNum">   15242 </span>            : namespace lapack{</a>
+<a name="15243"><span class="lineNum">   15243 </span>            : using namespace blas;</a>
+<a name="15244"><span class="lineNum">   15244 </span>            : void</a>
+<a name="15245"><span class="lineNum">   15245 </span><span class="lineCov">         57 : PLUMED_BLAS_F77_FUNC(dtrti2,DTRTI2)(const char *uplo,</span></a>
+<a name="15246"><span class="lineNum">   15246 </span>            :         const char *diag, </a>
+<a name="15247"><span class="lineNum">   15247 </span>            :         int *n, </a>
+<a name="15248"><span class="lineNum">   15248 </span>            :         double *a,</a>
+<a name="15249"><span class="lineNum">   15249 </span>            :         int *lda,</a>
+<a name="15250"><span class="lineNum">   15250 </span>            :         int *info)</a>
+<a name="15251"><span class="lineNum">   15251 </span>            : {</a>
+<a name="15252"><span class="lineNum">   15252 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="15253"><span class="lineNum">   15253 </span>            : </a>
+<a name="15254"><span class="lineNum">   15254 </span>            :     int j;</a>
+<a name="15255"><span class="lineNum">   15255 </span>            :     double ajj;</a>
+<a name="15256"><span class="lineNum">   15256 </span>            :     int upper, nounit;</a>
+<a name="15257"><span class="lineNum">   15257 </span><span class="lineCov">         57 :     int c__1 = 1;</span></a>
+<a name="15258"><span class="lineNum">   15258 </span>            : </a>
+<a name="15259"><span class="lineNum">   15259 </span>            : </a>
+<a name="15260"><span class="lineNum">   15260 </span><span class="lineCov">         57 :     a_dim1 = *lda;</span></a>
+<a name="15261"><span class="lineNum">   15261 </span><span class="lineCov">         57 :     a_offset = 1 + a_dim1;</span></a>
+<a name="15262"><span class="lineNum">   15262 </span><span class="lineCov">         57 :     a -= a_offset;</span></a>
+<a name="15263"><span class="lineNum">   15263 </span>            : </a>
+<a name="15264"><span class="lineNum">   15264 </span><span class="lineCov">         57 :     *info = 0;</span></a>
+<a name="15265"><span class="lineNum">   15265 </span><span class="lineCov">         57 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="15266"><span class="lineNum">   15266 </span><span class="lineCov">         57 :     nounit = (*diag=='N' || *diag=='n');</span></a>
+<a name="15267"><span class="lineNum">   15267 </span>            : </a>
+<a name="15268"><span class="lineNum">   15268 </span>            :     if (*info != 0) {</a>
+<a name="15269"><span class="lineNum">   15269 </span>            :         i__1 = -(*info);</a>
+<a name="15270"><span class="lineNum">   15270 </span>            :         return;</a>
+<a name="15271"><span class="lineNum">   15271 </span>            :     }</a>
+<a name="15272"><span class="lineNum">   15272 </span>            : </a>
+<a name="15273"><span class="lineNum">   15273 </span><span class="lineCov">         57 :     if (upper) {</span></a>
+<a name="15274"><span class="lineNum">   15274 </span>            : </a>
+<a name="15275"><span class="lineNum">   15275 </span><span class="lineCov">         57 :         i__1 = *n;</span></a>
+<a name="15276"><span class="lineNum">   15276 </span><span class="lineCov">        171 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="15277"><span class="lineNum">   15277 </span><span class="lineCov">        114 :             if (nounit) {</span></a>
+<a name="15278"><span class="lineNum">   15278 </span><span class="lineCov">        114 :                 a[j + j * a_dim1] = 1. / a[j + j * a_dim1];</span></a>
+<a name="15279"><span class="lineNum">   15279 </span><span class="lineCov">        114 :                 ajj = -a[j + j * a_dim1];</span></a>
+<a name="15280"><span class="lineNum">   15280 </span>            :             } else {</a>
+<a name="15281"><span class="lineNum">   15281 </span><span class="lineNoCov">          0 :                 ajj = -1.;</span></a>
+<a name="15282"><span class="lineNum">   15282 </span>            :             }</a>
+<a name="15283"><span class="lineNum">   15283 </span>            : </a>
+<a name="15284"><span class="lineNum">   15284 </span><span class="lineCov">        114 :             i__2 = j - 1;</span></a>
+<a name="15285"><span class="lineNum">   15285 </span><span class="lineCov">        114 :             PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)(&quot;Upper&quot;, &quot;No transpose&quot;, diag, &amp;i__2, &amp;a[a_offset], lda, &amp;</span></a>
+<a name="15286"><span class="lineNum">   15286 </span><span class="lineCov">        114 :                     a[j * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="15287"><span class="lineNum">   15287 </span><span class="lineCov">        114 :             i__2 = j - 1;</span></a>
+<a name="15288"><span class="lineNum">   15288 </span><span class="lineCov">        114 :             PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__2, &amp;ajj, &amp;a[j * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="15289"><span class="lineNum">   15289 </span>            :         }</a>
+<a name="15290"><span class="lineNum">   15290 </span>            :     } else {</a>
+<a name="15291"><span class="lineNum">   15291 </span>            : </a>
+<a name="15292"><span class="lineNum">   15292 </span><span class="lineNoCov">          0 :         for (j = *n; j &gt;= 1; --j) {</span></a>
+<a name="15293"><span class="lineNum">   15293 </span><span class="lineNoCov">          0 :             if (nounit) {</span></a>
+<a name="15294"><span class="lineNum">   15294 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = 1. / a[j + j * a_dim1];</span></a>
+<a name="15295"><span class="lineNum">   15295 </span><span class="lineNoCov">          0 :                 ajj = -a[j + j * a_dim1];</span></a>
+<a name="15296"><span class="lineNum">   15296 </span>            :             } else {</a>
+<a name="15297"><span class="lineNum">   15297 </span><span class="lineNoCov">          0 :                 ajj = -1.;</span></a>
+<a name="15298"><span class="lineNum">   15298 </span>            :             }</a>
+<a name="15299"><span class="lineNum">   15299 </span><span class="lineNoCov">          0 :             if (j &lt; *n) {</span></a>
+<a name="15300"><span class="lineNum">   15300 </span>            : </a>
+<a name="15301"><span class="lineNum">   15301 </span><span class="lineNoCov">          0 :                 i__1 = *n - j;</span></a>
+<a name="15302"><span class="lineNum">   15302 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmv,DTRMV)(&quot;Lower&quot;, &quot;No transpose&quot;, diag, &amp;i__1, &amp;a[j + 1 + (j + </span></a>
+<a name="15303"><span class="lineNum">   15303 </span><span class="lineNoCov">          0 :                         1) * a_dim1], lda, &amp;a[j + 1 + j * a_dim1], &amp;c__1);</span></a>
+<a name="15304"><span class="lineNum">   15304 </span><span class="lineNoCov">          0 :                 i__1 = *n - j;</span></a>
+<a name="15305"><span class="lineNum">   15305 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dscal,DSCAL)(&amp;i__1, &amp;ajj, &amp;a[j + 1 + j * a_dim1], &amp;c__1);</span></a>
+<a name="15306"><span class="lineNum">   15306 </span>            :             }</a>
+<a name="15307"><span class="lineNum">   15307 </span>            :         }</a>
+<a name="15308"><span class="lineNum">   15308 </span>            :     }</a>
+<a name="15309"><span class="lineNum">   15309 </span>            :     return;</a>
+<a name="15310"><span class="lineNum">   15310 </span>            : }</a>
+<a name="15311"><span class="lineNum">   15311 </span>            : }</a>
+<a name="15312"><span class="lineNum">   15312 </span>            : }</a>
+<a name="15313"><span class="lineNum">   15313 </span>            : #include &lt;cmath&gt;</a>
+<a name="15314"><span class="lineNum">   15314 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15315"><span class="lineNum">   15315 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="15316"><span class="lineNum">   15316 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="15317"><span class="lineNum">   15317 </span>            : </a>
+<a name="15318"><span class="lineNum">   15318 </span>            : #include &quot;real.h&quot;</a>
+<a name="15319"><span class="lineNum">   15319 </span>            : </a>
+<a name="15320"><span class="lineNum">   15320 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15321"><span class="lineNum">   15321 </span>            : namespace PLMD{</a>
+<a name="15322"><span class="lineNum">   15322 </span>            : namespace lapack{</a>
+<a name="15323"><span class="lineNum">   15323 </span>            : using namespace blas;</a>
+<a name="15324"><span class="lineNum">   15324 </span>            : void</a>
+<a name="15325"><span class="lineNum">   15325 </span><span class="lineCov">         57 : PLUMED_BLAS_F77_FUNC(dtrtri,DTRTRI)(const char *uplo,</span></a>
+<a name="15326"><span class="lineNum">   15326 </span>            :         const char *diag, </a>
+<a name="15327"><span class="lineNum">   15327 </span>            :         int *n,</a>
+<a name="15328"><span class="lineNum">   15328 </span>            :         double *a, </a>
+<a name="15329"><span class="lineNum">   15329 </span>            :         int *lda,</a>
+<a name="15330"><span class="lineNum">   15330 </span>            :         int *info)</a>
+<a name="15331"><span class="lineNum">   15331 </span>            : {</a>
+<a name="15332"><span class="lineNum">   15332 </span>            :     int a_dim1, a_offset, i__1, i__3, i__4, i__5;</a>
+<a name="15333"><span class="lineNum">   15333 </span>            :     int j, jb, nb, nn;</a>
+<a name="15334"><span class="lineNum">   15334 </span><span class="lineCov">         57 :     double c_b18 = 1.;</span></a>
+<a name="15335"><span class="lineNum">   15335 </span><span class="lineCov">         57 :     double c_b22 = -1.;</span></a>
+<a name="15336"><span class="lineNum">   15336 </span>            : </a>
+<a name="15337"><span class="lineNum">   15337 </span>            :     int upper;</a>
+<a name="15338"><span class="lineNum">   15338 </span>            :     int nounit;</a>
+<a name="15339"><span class="lineNum">   15339 </span>            : </a>
+<a name="15340"><span class="lineNum">   15340 </span><span class="lineCov">         57 :     a_dim1 = *lda;</span></a>
+<a name="15341"><span class="lineNum">   15341 </span><span class="lineCov">         57 :     a_offset = 1 + a_dim1;</span></a>
+<a name="15342"><span class="lineNum">   15342 </span><span class="lineCov">         57 :     a -= a_offset;</span></a>
+<a name="15343"><span class="lineNum">   15343 </span>            : </a>
+<a name="15344"><span class="lineNum">   15344 </span><span class="lineCov">         57 :     *info = 0;</span></a>
+<a name="15345"><span class="lineNum">   15345 </span><span class="lineCov">         57 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="15346"><span class="lineNum">   15346 </span><span class="lineCov">         57 :     nounit = (*diag=='N' || *diag=='n');</span></a>
+<a name="15347"><span class="lineNum">   15347 </span>            : </a>
+<a name="15348"><span class="lineNum">   15348 </span>            :     if (*info != 0) {</a>
+<a name="15349"><span class="lineNum">   15349 </span>            :         i__1 = -(*info);</a>
+<a name="15350"><span class="lineNum">   15350 </span>            :         return;</a>
+<a name="15351"><span class="lineNum">   15351 </span>            :     }</a>
+<a name="15352"><span class="lineNum">   15352 </span>            : </a>
+<a name="15353"><span class="lineNum">   15353 </span><span class="lineCov">         57 :     if (*n == 0) {</span></a>
+<a name="15354"><span class="lineNum">   15354 </span>            :         return;</a>
+<a name="15355"><span class="lineNum">   15355 </span>            :     }</a>
+<a name="15356"><span class="lineNum">   15356 </span>            : </a>
+<a name="15357"><span class="lineNum">   15357 </span><span class="lineCov">         57 :     if (nounit) {</span></a>
+<a name="15358"><span class="lineNum">   15358 </span><span class="lineCov">         57 :         i__1 = *n;</span></a>
+<a name="15359"><span class="lineNum">   15359 </span><span class="lineCov">        171 :         for (*info = 1; *info &lt;= i__1; ++(*info)) {</span></a>
+<a name="15360"><span class="lineNum">   15360 </span><span class="lineCov">        114 :             if (std::abs(a[*info + *info * a_dim1])&lt;PLUMED_GMX_DOUBLE_MIN) {</span></a>
+<a name="15361"><span class="lineNum">   15361 </span>            :                 return;</a>
+<a name="15362"><span class="lineNum">   15362 </span>            :             }</a>
+<a name="15363"><span class="lineNum">   15363 </span>            :         }</a>
+<a name="15364"><span class="lineNum">   15364 </span><span class="lineCov">         57 :         *info = 0;</span></a>
+<a name="15365"><span class="lineNum">   15365 </span>            :     }</a>
+<a name="15366"><span class="lineNum">   15366 </span>            : </a>
+<a name="15367"><span class="lineNum">   15367 </span>            :     nb = DTRTRI_BLOCKSIZE;</a>
+<a name="15368"><span class="lineNum">   15368 </span><span class="lineCov">         57 :     if (nb &lt;= 1 || nb &gt;= *n) {</span></a>
+<a name="15369"><span class="lineNum">   15369 </span>            : </a>
+<a name="15370"><span class="lineNum">   15370 </span><span class="lineCov">         57 :         PLUMED_BLAS_F77_FUNC(dtrti2,DTRTI2)(uplo, diag, n, &amp;a[a_offset], lda, info);</span></a>
+<a name="15371"><span class="lineNum">   15371 </span>            :     } else {</a>
+<a name="15372"><span class="lineNum">   15372 </span>            : </a>
+<a name="15373"><span class="lineNum">   15373 </span><span class="lineNoCov">          0 :         if (upper) {</span></a>
+<a name="15374"><span class="lineNum">   15374 </span>            : </a>
+<a name="15375"><span class="lineNum">   15375 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="15376"><span class="lineNum">   15376 </span>            :             i__3 = nb;</a>
+<a name="15377"><span class="lineNum">   15377 </span><span class="lineNoCov">          0 :             for (j = 1; i__3 &lt; 0 ? j &gt;= i__1 : j &lt;= i__1; j += i__3) {</span></a>
+<a name="15378"><span class="lineNum">   15378 </span><span class="lineNoCov">          0 :                 i__4 = nb, i__5 = *n - j + 1;</span></a>
+<a name="15379"><span class="lineNum">   15379 </span><span class="lineNoCov">          0 :                 jb = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="15380"><span class="lineNum">   15380 </span>            : </a>
+<a name="15381"><span class="lineNum">   15381 </span><span class="lineNoCov">          0 :                 i__4 = j - 1;</span></a>
+<a name="15382"><span class="lineNum">   15382 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Left&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, diag, &amp;i__4, &amp;jb, &amp;</span></a>
+<a name="15383"><span class="lineNum">   15383 </span><span class="lineNoCov">          0 :                         c_b18, &amp;a[a_offset], lda, &amp;a[j * a_dim1 + 1], lda);</span></a>
+<a name="15384"><span class="lineNum">   15384 </span><span class="lineNoCov">          0 :                 i__4 = j - 1;</span></a>
+<a name="15385"><span class="lineNum">   15385 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, diag, &amp;i__4, &amp;jb, &amp;</span></a>
+<a name="15386"><span class="lineNum">   15386 </span><span class="lineNoCov">          0 :                         c_b22, &amp;a[j + j * a_dim1], lda, &amp;a[j * a_dim1 + 1], </span></a>
+<a name="15387"><span class="lineNum">   15387 </span>            :                         lda);</a>
+<a name="15388"><span class="lineNum">   15388 </span>            : </a>
+<a name="15389"><span class="lineNum">   15389 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrti2,DTRTI2)(&quot;Upper&quot;, diag, &amp;jb, &amp;a[j + j * a_dim1], lda, info);</span></a>
+<a name="15390"><span class="lineNum">   15390 </span>            :             }</a>
+<a name="15391"><span class="lineNum">   15391 </span>            :         } else {</a>
+<a name="15392"><span class="lineNum">   15392 </span>            : </a>
+<a name="15393"><span class="lineNum">   15393 </span><span class="lineNoCov">          0 :             nn = (*n - 1) / nb * nb + 1;</span></a>
+<a name="15394"><span class="lineNum">   15394 </span>            :             i__3 = -nb;</a>
+<a name="15395"><span class="lineNum">   15395 </span><span class="lineNoCov">          0 :             for (j = nn; i__3 &lt; 0 ? j &gt;= 1 : j &lt;= 1; j += i__3) {</span></a>
+<a name="15396"><span class="lineNum">   15396 </span><span class="lineNoCov">          0 :                 i__1 = nb, i__4 = *n - j + 1;</span></a>
+<a name="15397"><span class="lineNum">   15397 </span><span class="lineNoCov">          0 :                 jb = (i__1&lt;i__4) ? i__1 : i__4;</span></a>
+<a name="15398"><span class="lineNum">   15398 </span><span class="lineNoCov">          0 :                 if (j + jb &lt;= *n) {</span></a>
+<a name="15399"><span class="lineNum">   15399 </span>            : </a>
+<a name="15400"><span class="lineNum">   15400 </span><span class="lineNoCov">          0 :                     i__1 = *n - j - jb + 1;</span></a>
+<a name="15401"><span class="lineNum">   15401 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dtrmm,DTRMM)(&quot;Left&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, diag, &amp;i__1, &amp;jb, </span></a>
+<a name="15402"><span class="lineNum">   15402 </span><span class="lineNoCov">          0 :                             &amp;c_b18, &amp;a[j + jb + (j + jb) * a_dim1], lda, &amp;a[j </span></a>
+<a name="15403"><span class="lineNum">   15403 </span><span class="lineNoCov">          0 :                             + jb + j * a_dim1], lda);</span></a>
+<a name="15404"><span class="lineNum">   15404 </span><span class="lineNoCov">          0 :                     i__1 = *n - j - jb + 1;</span></a>
+<a name="15405"><span class="lineNum">   15405 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(dtrsm,DTRSM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, diag, &amp;i__1, &amp;jb,</span></a>
+<a name="15406"><span class="lineNum">   15406 </span><span class="lineNoCov">          0 :                              &amp;c_b22, &amp;a[j + j * a_dim1], lda, &amp;a[j + jb + j * </span></a>
+<a name="15407"><span class="lineNum">   15407 </span><span class="lineNoCov">          0 :                             a_dim1], lda);</span></a>
+<a name="15408"><span class="lineNum">   15408 </span>            :                 }</a>
+<a name="15409"><span class="lineNum">   15409 </span>            : </a>
+<a name="15410"><span class="lineNum">   15410 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(dtrti2,DTRTI2)(&quot;Lower&quot;, diag, &amp;jb, &amp;a[j + j * a_dim1], lda, info);</span></a>
+<a name="15411"><span class="lineNum">   15411 </span>            :             }</a>
+<a name="15412"><span class="lineNum">   15412 </span>            :         }</a>
+<a name="15413"><span class="lineNum">   15413 </span>            :     }</a>
+<a name="15414"><span class="lineNum">   15414 </span>            :     return;</a>
+<a name="15415"><span class="lineNum">   15415 </span>            : }</a>
+<a name="15416"><span class="lineNum">   15416 </span>            : </a>
+<a name="15417"><span class="lineNum">   15417 </span>            : </a>
+<a name="15418"><span class="lineNum">   15418 </span>            : }</a>
+<a name="15419"><span class="lineNum">   15419 </span>            : }</a>
+<a name="15420"><span class="lineNum">   15420 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="15421"><span class="lineNum">   15421 </span>            : </a>
+<a name="15422"><span class="lineNum">   15422 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15423"><span class="lineNum">   15423 </span>            : namespace PLMD{</a>
+<a name="15424"><span class="lineNum">   15424 </span>            : namespace lapack{</a>
+<a name="15425"><span class="lineNum">   15425 </span>            : using namespace blas;</a>
+<a name="15426"><span class="lineNum">   15426 </span>            : void </a>
+<a name="15427"><span class="lineNum">   15427 </span><span class="lineCov">         12 : PLUMED_BLAS_F77_FUNC(ilasrt2,ILASRT2)(const char *id, </span></a>
+<a name="15428"><span class="lineNum">   15428 </span>            :          int *n, </a>
+<a name="15429"><span class="lineNum">   15429 </span>            :          int *d__, </a>
+<a name="15430"><span class="lineNum">   15430 </span>            :          int *key, </a>
+<a name="15431"><span class="lineNum">   15431 </span>            :          int *info)</a>
+<a name="15432"><span class="lineNum">   15432 </span>            : {</a>
+<a name="15433"><span class="lineNum">   15433 </span>            :     int i__1, i__2;</a>
+<a name="15434"><span class="lineNum">   15434 </span>            :     int i__, j, d1, d2, d3, dir, tmp, endd;</a>
+<a name="15435"><span class="lineNum">   15435 </span>            :     int stack[64], dmnmx, start;</a>
+<a name="15436"><span class="lineNum">   15436 </span>            :     int tmpkey, stkpnt;</a>
+<a name="15437"><span class="lineNum">   15437 </span>            : </a>
+<a name="15438"><span class="lineNum">   15438 </span><span class="lineCov">         12 :     --key;</span></a>
+<a name="15439"><span class="lineNum">   15439 </span><span class="lineCov">         12 :     --d__;</span></a>
+<a name="15440"><span class="lineNum">   15440 </span>            : </a>
+<a name="15441"><span class="lineNum">   15441 </span><span class="lineCov">         12 :     *info = 0;</span></a>
+<a name="15442"><span class="lineNum">   15442 </span>            :     dir = -1;</a>
+<a name="15443"><span class="lineNum">   15443 </span><span class="lineCov">         12 :     if (*id=='D' || *id=='d') </span></a>
+<a name="15444"><span class="lineNum">   15444 </span>            :         dir = 0;</a>
+<a name="15445"><span class="lineNum">   15445 </span><span class="lineCov">         12 :     else if (*id=='I' || *id=='i') </span></a>
+<a name="15446"><span class="lineNum">   15446 </span>            :         dir = 1;</a>
+<a name="15447"><span class="lineNum">   15447 </span>            :     </a>
+<a name="15448"><span class="lineNum">   15448 </span>            :     if (dir == -1) {</a>
+<a name="15449"><span class="lineNum">   15449 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="15450"><span class="lineNum">   15450 </span><span class="lineCov">         12 :     } else if (*n &lt; 0) {</span></a>
+<a name="15451"><span class="lineNum">   15451 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="15452"><span class="lineNum">   15452 </span>            :     }</a>
+<a name="15453"><span class="lineNum">   15453 </span><span class="lineCov">         12 :     if (*info != 0) {</span></a>
+<a name="15454"><span class="lineNum">   15454 </span>            :         return;</a>
+<a name="15455"><span class="lineNum">   15455 </span>            :     }</a>
+<a name="15456"><span class="lineNum">   15456 </span>            : </a>
+<a name="15457"><span class="lineNum">   15457 </span><span class="lineCov">         12 :     if (*n &lt;= 1) {</span></a>
+<a name="15458"><span class="lineNum">   15458 </span>            :         return;</a>
+<a name="15459"><span class="lineNum">   15459 </span>            :     }</a>
+<a name="15460"><span class="lineNum">   15460 </span>            : </a>
+<a name="15461"><span class="lineNum">   15461 </span>            :     stkpnt = 1;</a>
+<a name="15462"><span class="lineNum">   15462 </span><span class="lineCov">          9 :     stack[0] = 1;</span></a>
+<a name="15463"><span class="lineNum">   15463 </span><span class="lineCov">          9 :     stack[1] = *n;</span></a>
+<a name="15464"><span class="lineNum">   15464 </span><span class="lineCov">          9 : L10:</span></a>
+<a name="15465"><span class="lineNum">   15465 </span><span class="lineCov">          9 :     start = stack[(stkpnt &lt;&lt; 1) - 2];</span></a>
+<a name="15466"><span class="lineNum">   15466 </span><span class="lineCov">          9 :     endd = stack[(stkpnt &lt;&lt; 1) - 1];</span></a>
+<a name="15467"><span class="lineNum">   15467 </span><span class="lineCov">          9 :     --stkpnt;</span></a>
+<a name="15468"><span class="lineNum">   15468 </span><span class="lineCov">          9 :     if (endd - start &gt; 0) {</span></a>
+<a name="15469"><span class="lineNum">   15469 </span>            : </a>
+<a name="15470"><span class="lineNum">   15470 </span><span class="lineCov">          9 :         if (dir == 0) {</span></a>
+<a name="15471"><span class="lineNum">   15471 </span>            : </a>
+<a name="15472"><span class="lineNum">   15472 </span>            :             i__1 = endd;</a>
+<a name="15473"><span class="lineNum">   15473 </span><span class="lineNoCov">          0 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="15474"><span class="lineNum">   15474 </span>            :                 i__2 = start + 1;</a>
+<a name="15475"><span class="lineNum">   15475 </span><span class="lineNoCov">          0 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="15476"><span class="lineNum">   15476 </span><span class="lineNoCov">          0 :                     if (d__[j] &gt; d__[j - 1]) {</span></a>
+<a name="15477"><span class="lineNum">   15477 </span>            :                         dmnmx = d__[j];</a>
+<a name="15478"><span class="lineNum">   15478 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="15479"><span class="lineNum">   15479 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="15480"><span class="lineNum">   15480 </span><span class="lineNoCov">          0 :                         tmpkey = key[j];</span></a>
+<a name="15481"><span class="lineNum">   15481 </span><span class="lineNoCov">          0 :                         key[j] = key[j - 1];</span></a>
+<a name="15482"><span class="lineNum">   15482 </span><span class="lineNoCov">          0 :                         key[j - 1] = tmpkey;</span></a>
+<a name="15483"><span class="lineNum">   15483 </span>            :                     } else {</a>
+<a name="15484"><span class="lineNum">   15484 </span><span class="lineNoCov">          0 :                         goto L30;</span></a>
+<a name="15485"><span class="lineNum">   15485 </span>            :                     }</a>
+<a name="15486"><span class="lineNum">   15486 </span>            :                 }</a>
+<a name="15487"><span class="lineNum">   15487 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="15488"><span class="lineNum">   15488 </span>            :                 ;</a>
+<a name="15489"><span class="lineNum">   15489 </span>            :             }</a>
+<a name="15490"><span class="lineNum">   15490 </span>            : </a>
+<a name="15491"><span class="lineNum">   15491 </span>            :         } else {</a>
+<a name="15492"><span class="lineNum">   15492 </span>            : </a>
+<a name="15493"><span class="lineNum">   15493 </span>            :             i__1 = endd;</a>
+<a name="15494"><span class="lineNum">   15494 </span><span class="lineCov">        766 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="15495"><span class="lineNum">   15495 </span>            :                 i__2 = start + 1;</a>
+<a name="15496"><span class="lineNum">   15496 </span><span class="lineCov">      14895 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="15497"><span class="lineNum">   15497 </span><span class="lineCov">      14829 :                     if (d__[j] &lt; d__[j - 1]) {</span></a>
+<a name="15498"><span class="lineNum">   15498 </span>            :                         dmnmx = d__[j];</a>
+<a name="15499"><span class="lineNum">   15499 </span><span class="lineCov">      14138 :                         d__[j] = d__[j - 1];</span></a>
+<a name="15500"><span class="lineNum">   15500 </span><span class="lineCov">      14138 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="15501"><span class="lineNum">   15501 </span><span class="lineCov">      14138 :                         tmpkey = key[j];</span></a>
+<a name="15502"><span class="lineNum">   15502 </span><span class="lineCov">      14138 :                         key[j] = key[j - 1];</span></a>
+<a name="15503"><span class="lineNum">   15503 </span><span class="lineCov">      14138 :                         key[j - 1] = tmpkey;</span></a>
+<a name="15504"><span class="lineNum">   15504 </span>            :                     } else {</a>
+<a name="15505"><span class="lineNum">   15505 </span><span class="lineCov">        691 :                         goto L50;</span></a>
+<a name="15506"><span class="lineNum">   15506 </span>            :                     }</a>
+<a name="15507"><span class="lineNum">   15507 </span>            :                 }</a>
+<a name="15508"><span class="lineNum">   15508 </span><span class="lineCov">        757 : L50:</span></a>
+<a name="15509"><span class="lineNum">   15509 </span>            :                 ;</a>
+<a name="15510"><span class="lineNum">   15510 </span>            :             }</a>
+<a name="15511"><span class="lineNum">   15511 </span>            : </a>
+<a name="15512"><span class="lineNum">   15512 </span>            :         }</a>
+<a name="15513"><span class="lineNum">   15513 </span>            : </a>
+<a name="15514"><span class="lineNum">   15514 </span><span class="lineNoCov">          0 :     } else if (endd - start &gt; 20) {</span></a>
+<a name="15515"><span class="lineNum">   15515 </span>            : </a>
+<a name="15516"><span class="lineNum">   15516 </span><span class="lineNoCov">          0 :         d1 = d__[start];</span></a>
+<a name="15517"><span class="lineNum">   15517 </span><span class="lineNoCov">          0 :         d2 = d__[endd];</span></a>
+<a name="15518"><span class="lineNum">   15518 </span><span class="lineNoCov">          0 :         i__ = (start + endd) / 2;</span></a>
+<a name="15519"><span class="lineNum">   15519 </span><span class="lineNoCov">          0 :         d3 = d__[i__];</span></a>
+<a name="15520"><span class="lineNum">   15520 </span><span class="lineNoCov">          0 :         if (d1 &lt; d2) {</span></a>
+<a name="15521"><span class="lineNum">   15521 </span><span class="lineNoCov">          0 :             if (d3 &lt; d1) {</span></a>
+<a name="15522"><span class="lineNum">   15522 </span>            :                 dmnmx = d1;</a>
+<a name="15523"><span class="lineNum">   15523 </span>            :             } else if (d3 &lt; d2) {</a>
+<a name="15524"><span class="lineNum">   15524 </span>            :                 dmnmx = d3;</a>
+<a name="15525"><span class="lineNum">   15525 </span>            :             } else {</a>
+<a name="15526"><span class="lineNum">   15526 </span>            :                 dmnmx = d2;</a>
+<a name="15527"><span class="lineNum">   15527 </span>            :             }</a>
+<a name="15528"><span class="lineNum">   15528 </span>            :         } else {</a>
+<a name="15529"><span class="lineNum">   15529 </span><span class="lineNoCov">          0 :             if (d3 &lt; d2) {</span></a>
+<a name="15530"><span class="lineNum">   15530 </span>            :                 dmnmx = d2;</a>
+<a name="15531"><span class="lineNum">   15531 </span>            :             } else if (d3 &lt; d1) {</a>
+<a name="15532"><span class="lineNum">   15532 </span>            :                 dmnmx = d3;</a>
+<a name="15533"><span class="lineNum">   15533 </span>            :             } else {</a>
+<a name="15534"><span class="lineNum">   15534 </span>            :                 dmnmx = d1;</a>
+<a name="15535"><span class="lineNum">   15535 </span>            :             }</a>
+<a name="15536"><span class="lineNum">   15536 </span>            :         }</a>
+<a name="15537"><span class="lineNum">   15537 </span>            : </a>
+<a name="15538"><span class="lineNum">   15538 </span><span class="lineNoCov">          0 :         if (dir == 0) {</span></a>
+<a name="15539"><span class="lineNum">   15539 </span>            : </a>
+<a name="15540"><span class="lineNum">   15540 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="15541"><span class="lineNum">   15541 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="15542"><span class="lineNum">   15542 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="15543"><span class="lineNum">   15543 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="15544"><span class="lineNum">   15544 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="15545"><span class="lineNum">   15545 </span><span class="lineNoCov">          0 :             if (d__[j] &lt; dmnmx) {</span></a>
+<a name="15546"><span class="lineNum">   15546 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="15547"><span class="lineNum">   15547 </span>            :             }</a>
+<a name="15548"><span class="lineNum">   15548 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="15549"><span class="lineNum">   15549 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="15550"><span class="lineNum">   15550 </span><span class="lineNoCov">          0 :             if (d__[i__] &gt; dmnmx) {</span></a>
+<a name="15551"><span class="lineNum">   15551 </span><span class="lineNoCov">          0 :                 goto L80;</span></a>
+<a name="15552"><span class="lineNum">   15552 </span>            :             }</a>
+<a name="15553"><span class="lineNum">   15553 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="15554"><span class="lineNum">   15554 </span>            :                 tmp = d__[i__];</a>
+<a name="15555"><span class="lineNum">   15555 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="15556"><span class="lineNum">   15556 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="15557"><span class="lineNum">   15557 </span><span class="lineNoCov">          0 :                 tmpkey = key[j];</span></a>
+<a name="15558"><span class="lineNum">   15558 </span><span class="lineNoCov">          0 :                 key[j] = key[i__];</span></a>
+<a name="15559"><span class="lineNum">   15559 </span><span class="lineNoCov">          0 :                 key[i__] = tmpkey;</span></a>
+<a name="15560"><span class="lineNum">   15560 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="15561"><span class="lineNum">   15561 </span>            :             }</a>
+<a name="15562"><span class="lineNum">   15562 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="15563"><span class="lineNum">   15563 </span>            :                 ++stkpnt;</a>
+<a name="15564"><span class="lineNum">   15564 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="15565"><span class="lineNum">   15565 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="15566"><span class="lineNum">   15566 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="15567"><span class="lineNum">   15567 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="15568"><span class="lineNum">   15568 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="15569"><span class="lineNum">   15569 </span>            :             } else {</a>
+<a name="15570"><span class="lineNum">   15570 </span>            :                 ++stkpnt;</a>
+<a name="15571"><span class="lineNum">   15571 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="15572"><span class="lineNum">   15572 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="15573"><span class="lineNum">   15573 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="15574"><span class="lineNum">   15574 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="15575"><span class="lineNum">   15575 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="15576"><span class="lineNum">   15576 </span>            :             }</a>
+<a name="15577"><span class="lineNum">   15577 </span>            :         } else {</a>
+<a name="15578"><span class="lineNum">   15578 </span>            : </a>
+<a name="15579"><span class="lineNum">   15579 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="15580"><span class="lineNum">   15580 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="15581"><span class="lineNum">   15581 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="15582"><span class="lineNum">   15582 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="15583"><span class="lineNum">   15583 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="15584"><span class="lineNum">   15584 </span><span class="lineNoCov">          0 :             if (d__[j] &gt; dmnmx) {</span></a>
+<a name="15585"><span class="lineNum">   15585 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="15586"><span class="lineNum">   15586 </span>            :             }</a>
+<a name="15587"><span class="lineNum">   15587 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="15588"><span class="lineNum">   15588 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="15589"><span class="lineNum">   15589 </span><span class="lineNoCov">          0 :             if (d__[i__] &lt; dmnmx) {</span></a>
+<a name="15590"><span class="lineNum">   15590 </span><span class="lineNoCov">          0 :                 goto L110;</span></a>
+<a name="15591"><span class="lineNum">   15591 </span>            :             }</a>
+<a name="15592"><span class="lineNum">   15592 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="15593"><span class="lineNum">   15593 </span>            :                 tmp = d__[i__];</a>
+<a name="15594"><span class="lineNum">   15594 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="15595"><span class="lineNum">   15595 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="15596"><span class="lineNum">   15596 </span><span class="lineNoCov">          0 :                 tmpkey = key[j];</span></a>
+<a name="15597"><span class="lineNum">   15597 </span><span class="lineNoCov">          0 :                 key[j] = key[i__];</span></a>
+<a name="15598"><span class="lineNum">   15598 </span><span class="lineNoCov">          0 :                 key[i__] = tmpkey;</span></a>
+<a name="15599"><span class="lineNum">   15599 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="15600"><span class="lineNum">   15600 </span>            :             }</a>
+<a name="15601"><span class="lineNum">   15601 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="15602"><span class="lineNum">   15602 </span>            :                 ++stkpnt;</a>
+<a name="15603"><span class="lineNum">   15603 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="15604"><span class="lineNum">   15604 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="15605"><span class="lineNum">   15605 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="15606"><span class="lineNum">   15606 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="15607"><span class="lineNum">   15607 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="15608"><span class="lineNum">   15608 </span>            :             } else {</a>
+<a name="15609"><span class="lineNum">   15609 </span>            :                 ++stkpnt;</a>
+<a name="15610"><span class="lineNum">   15610 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="15611"><span class="lineNum">   15611 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="15612"><span class="lineNum">   15612 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="15613"><span class="lineNum">   15613 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="15614"><span class="lineNum">   15614 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="15615"><span class="lineNum">   15615 </span>            :             }</a>
+<a name="15616"><span class="lineNum">   15616 </span>            :         }</a>
+<a name="15617"><span class="lineNum">   15617 </span>            :     }</a>
+<a name="15618"><span class="lineNum">   15618 </span><span class="lineCov">          9 :     if (stkpnt &gt; 0) {</span></a>
+<a name="15619"><span class="lineNum">   15619 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="15620"><span class="lineNum">   15620 </span>            :     }</a>
+<a name="15621"><span class="lineNum">   15621 </span>            : </a>
+<a name="15622"><span class="lineNum">   15622 </span>            : </a>
+<a name="15623"><span class="lineNum">   15623 </span>            :     return;</a>
+<a name="15624"><span class="lineNum">   15624 </span>            : }</a>
+<a name="15625"><span class="lineNum">   15625 </span>            : }</a>
+<a name="15626"><span class="lineNum">   15626 </span>            : }</a>
+<a name="15627"><span class="lineNum">   15627 </span>            : #include &lt;cctype&gt;</a>
+<a name="15628"><span class="lineNum">   15628 </span>            : #include &lt;cmath&gt;</a>
+<a name="15629"><span class="lineNum">   15629 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15630"><span class="lineNum">   15630 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="15631"><span class="lineNum">   15631 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="15632"><span class="lineNum">   15632 </span>            : </a>
+<a name="15633"><span class="lineNum">   15633 </span>            : #include &quot;real.h&quot;</a>
+<a name="15634"><span class="lineNum">   15634 </span>            : </a>
+<a name="15635"><span class="lineNum">   15635 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15636"><span class="lineNum">   15636 </span>            : namespace PLMD{</a>
+<a name="15637"><span class="lineNum">   15637 </span>            : namespace lapack{</a>
+<a name="15638"><span class="lineNum">   15638 </span>            : using namespace blas;</a>
+<a name="15639"><span class="lineNum">   15639 </span>            : void</a>
+<a name="15640"><span class="lineNum">   15640 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(const char *uplo, </span></a>
+<a name="15641"><span class="lineNum">   15641 </span>            :         const char *compq, </a>
+<a name="15642"><span class="lineNum">   15642 </span>            :         int *n,</a>
+<a name="15643"><span class="lineNum">   15643 </span>            :         float *d__, </a>
+<a name="15644"><span class="lineNum">   15644 </span>            :         float *e, </a>
+<a name="15645"><span class="lineNum">   15645 </span>            :         float *u, </a>
+<a name="15646"><span class="lineNum">   15646 </span>            :         int *ldu,</a>
+<a name="15647"><span class="lineNum">   15647 </span>            :         float *vt, </a>
+<a name="15648"><span class="lineNum">   15648 </span>            :         int *ldvt,</a>
+<a name="15649"><span class="lineNum">   15649 </span>            :         float *q,</a>
+<a name="15650"><span class="lineNum">   15650 </span>            :         int *iq,</a>
+<a name="15651"><span class="lineNum">   15651 </span>            :         float *work, </a>
+<a name="15652"><span class="lineNum">   15652 </span>            :         int *iwork, </a>
+<a name="15653"><span class="lineNum">   15653 </span>            :         int *info)</a>
+<a name="15654"><span class="lineNum">   15654 </span>            : {</a>
+<a name="15655"><span class="lineNum">   15655 </span>            :     int u_dim1, u_offset, vt_dim1, vt_offset, i__1, i__2;</a>
+<a name="15656"><span class="lineNum">   15656 </span>            :     int i__, j, k;</a>
+<a name="15657"><span class="lineNum">   15657 </span>            :     float p, r__;</a>
+<a name="15658"><span class="lineNum">   15658 </span>            :     int z__, ic, ii, kk;</a>
+<a name="15659"><span class="lineNum">   15659 </span>            :     float cs;</a>
+<a name="15660"><span class="lineNum">   15660 </span>            :     int is, iu;</a>
+<a name="15661"><span class="lineNum">   15661 </span>            :     float sn;</a>
+<a name="15662"><span class="lineNum">   15662 </span>            :     int nm1;</a>
+<a name="15663"><span class="lineNum">   15663 </span>            :     float eps;</a>
+<a name="15664"><span class="lineNum">   15664 </span>            :     int ivt, difl, difr, ierr, perm, mlvl, sqre;</a>
+<a name="15665"><span class="lineNum">   15665 </span>            :     int poles, iuplo, nsize, start;</a>
+<a name="15666"><span class="lineNum">   15666 </span>            :     int givcol;</a>
+<a name="15667"><span class="lineNum">   15667 </span>            :     int icompq;</a>
+<a name="15668"><span class="lineNum">   15668 </span>            :     float orgnrm;</a>
+<a name="15669"><span class="lineNum">   15669 </span>            :     int givnum, givptr, qstart, smlsiz, wstart, smlszp;</a>
+<a name="15670"><span class="lineNum">   15670 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="15671"><span class="lineNum">   15671 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="15672"><span class="lineNum">   15672 </span><span class="lineNoCov">          0 :     int c_0 = 0;</span></a>
+<a name="15673"><span class="lineNum">   15673 </span><span class="lineNoCov">          0 :     int c_1 = 1;</span></a>
+<a name="15674"><span class="lineNum">   15674 </span>            : </a>
+<a name="15675"><span class="lineNum">   15675 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="15676"><span class="lineNum">   15676 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="15677"><span class="lineNum">   15677 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="15678"><span class="lineNum">   15678 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="15679"><span class="lineNum">   15679 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="15680"><span class="lineNum">   15680 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="15681"><span class="lineNum">   15681 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="15682"><span class="lineNum">   15682 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="15683"><span class="lineNum">   15683 </span><span class="lineNoCov">          0 :     --q;</span></a>
+<a name="15684"><span class="lineNum">   15684 </span><span class="lineNoCov">          0 :     --iq;</span></a>
+<a name="15685"><span class="lineNum">   15685 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="15686"><span class="lineNum">   15686 </span>            :     --iwork;</a>
+<a name="15687"><span class="lineNum">   15687 </span>            : </a>
+<a name="15688"><span class="lineNum">   15688 </span>            :     k = iu = z__ = ic = is = ivt = difl = difr = perm = 0;</a>
+<a name="15689"><span class="lineNum">   15689 </span>            :     poles = givnum = givptr = givcol = 0;</a>
+<a name="15690"><span class="lineNum">   15690 </span>            :     </a>
+<a name="15691"><span class="lineNum">   15691 </span><span class="lineNoCov">          0 :     smlsiz = DBDSDC_SMALLSIZE;</span></a>
+<a name="15692"><span class="lineNum">   15692 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="15693"><span class="lineNum">   15693 </span>            : </a>
+<a name="15694"><span class="lineNum">   15694 </span><span class="lineNoCov">          0 :     iuplo = (*uplo=='U' || *uplo=='u') ? 1 : 2;</span></a>
+<a name="15695"><span class="lineNum">   15695 </span>            : </a>
+<a name="15696"><span class="lineNum">   15696 </span><span class="lineNoCov">          0 :     switch(*compq) {</span></a>
+<a name="15697"><span class="lineNum">   15697 </span><span class="lineNoCov">          0 :     case 'n':</span></a>
+<a name="15698"><span class="lineNum">   15698 </span>            :     case 'N':</a>
+<a name="15699"><span class="lineNum">   15699 </span><span class="lineNoCov">          0 :       icompq = 0;</span></a>
+<a name="15700"><span class="lineNum">   15700 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="15701"><span class="lineNum">   15701 </span><span class="lineNoCov">          0 :     case 'p':</span></a>
+<a name="15702"><span class="lineNum">   15702 </span>            :     case 'P':</a>
+<a name="15703"><span class="lineNum">   15703 </span><span class="lineNoCov">          0 :       icompq = 1;</span></a>
+<a name="15704"><span class="lineNum">   15704 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="15705"><span class="lineNum">   15705 </span><span class="lineNoCov">          0 :     case 'i':</span></a>
+<a name="15706"><span class="lineNum">   15706 </span>            :     case 'I':</a>
+<a name="15707"><span class="lineNum">   15707 </span><span class="lineNoCov">          0 :       icompq = 2;</span></a>
+<a name="15708"><span class="lineNum">   15708 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="15709"><span class="lineNum">   15709 </span>            :     default:</a>
+<a name="15710"><span class="lineNum">   15710 </span>            :       return;</a>
+<a name="15711"><span class="lineNum">   15711 </span>            :     }</a>
+<a name="15712"><span class="lineNum">   15712 </span>            : </a>
+<a name="15713"><span class="lineNum">   15713 </span><span class="lineNoCov">          0 :     if (*n &lt;= 0) </span></a>
+<a name="15714"><span class="lineNum">   15714 </span>            :         return;</a>
+<a name="15715"><span class="lineNum">   15715 </span>            :     </a>
+<a name="15716"><span class="lineNum">   15716 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="15717"><span class="lineNum">   15717 </span><span class="lineNoCov">          0 :         if (icompq == 1) {</span></a>
+<a name="15718"><span class="lineNum">   15718 </span><span class="lineNoCov">          0 :           q[1] = (d__[1]&gt;0) ? 1.0 : -1.0;</span></a>
+<a name="15719"><span class="lineNum">   15719 </span><span class="lineNoCov">          0 :           q[smlsiz * *n + 1] = 1.;</span></a>
+<a name="15720"><span class="lineNum">   15720 </span><span class="lineNoCov">          0 :         } else if (icompq == 2) {</span></a>
+<a name="15721"><span class="lineNum">   15721 </span><span class="lineNoCov">          0 :           u[u_dim1 + 1] = (d__[1]&gt;0) ? 1.0 : -1.0;</span></a>
+<a name="15722"><span class="lineNum">   15722 </span><span class="lineNoCov">          0 :           vt[vt_dim1 + 1] = 1.;</span></a>
+<a name="15723"><span class="lineNum">   15723 </span>            :         }</a>
+<a name="15724"><span class="lineNum">   15724 </span><span class="lineNoCov">          0 :         d__[1] = std::abs(d__[1]);</span></a>
+<a name="15725"><span class="lineNum">   15725 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="15726"><span class="lineNum">   15726 </span>            :     }</a>
+<a name="15727"><span class="lineNum">   15727 </span><span class="lineNoCov">          0 :     nm1 = *n - 1;</span></a>
+<a name="15728"><span class="lineNum">   15728 </span>            :     wstart = 1;</a>
+<a name="15729"><span class="lineNum">   15729 </span>            :     qstart = 3;</a>
+<a name="15730"><span class="lineNum">   15730 </span><span class="lineNoCov">          0 :     if (icompq == 1) {</span></a>
+<a name="15731"><span class="lineNum">   15731 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;d__[1], &amp;c_1, &amp;q[1], &amp;c_1);</span></a>
+<a name="15732"><span class="lineNum">   15732 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="15733"><span class="lineNum">   15733 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;e[1], &amp;c_1, &amp;q[*n + 1], &amp;c_1);</span></a>
+<a name="15734"><span class="lineNum">   15734 </span>            :     }</a>
+<a name="15735"><span class="lineNum">   15735 </span><span class="lineNoCov">          0 :     if (iuplo == 2) {</span></a>
+<a name="15736"><span class="lineNum">   15736 </span>            :         qstart = 5;</a>
+<a name="15737"><span class="lineNum">   15737 </span><span class="lineNoCov">          0 :         wstart = (*n &lt;&lt; 1) - 1;</span></a>
+<a name="15738"><span class="lineNum">   15738 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="15739"><span class="lineNum">   15739 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="15740"><span class="lineNum">   15740 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="15741"><span class="lineNum">   15741 </span><span class="lineNoCov">          0 :             d__[i__] = r__;</span></a>
+<a name="15742"><span class="lineNum">   15742 </span><span class="lineNoCov">          0 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="15743"><span class="lineNum">   15743 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="15744"><span class="lineNum">   15744 </span><span class="lineNoCov">          0 :             if (icompq == 1) {</span></a>
+<a name="15745"><span class="lineNum">   15745 </span><span class="lineNoCov">          0 :                 q[i__ + (*n &lt;&lt; 1)] = cs;</span></a>
+<a name="15746"><span class="lineNum">   15746 </span><span class="lineNoCov">          0 :                 q[i__ + *n * 3] = sn;</span></a>
+<a name="15747"><span class="lineNum">   15747 </span><span class="lineNoCov">          0 :             } else if (icompq == 2) {</span></a>
+<a name="15748"><span class="lineNum">   15748 </span><span class="lineNoCov">          0 :                 work[i__] = cs;</span></a>
+<a name="15749"><span class="lineNum">   15749 </span><span class="lineNoCov">          0 :                 work[nm1 + i__] = -sn;</span></a>
+<a name="15750"><span class="lineNum">   15750 </span>            :             }</a>
+<a name="15751"><span class="lineNum">   15751 </span>            :         }</a>
+<a name="15752"><span class="lineNum">   15752 </span>            :     }</a>
+<a name="15753"><span class="lineNum">   15753 </span><span class="lineNoCov">          0 :     if (icompq == 0) {</span></a>
+<a name="15754"><span class="lineNum">   15754 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;,&amp;c_0,n,&amp;c_0,&amp;c_0,&amp;c_0,&amp;d__[1],&amp;e[1],&amp;vt[vt_offset],ldvt,</span></a>
+<a name="15755"><span class="lineNum">   15755 </span><span class="lineNoCov">          0 :               &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;work[wstart], info);</span></a>
+<a name="15756"><span class="lineNum">   15756 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="15757"><span class="lineNum">   15757 </span>            :     }</a>
+<a name="15758"><span class="lineNum">   15758 </span><span class="lineNoCov">          0 :     if (*n &lt;= smlsiz) {</span></a>
+<a name="15759"><span class="lineNum">   15759 </span><span class="lineNoCov">          0 :         if (icompq == 2) {</span></a>
+<a name="15760"><span class="lineNum">   15760 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;u[u_offset], ldu);</span></a>
+<a name="15761"><span class="lineNum">   15761 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="15762"><span class="lineNum">   15762 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;,&amp;c_0,n,n,n,&amp;c_0,&amp;d__[1],&amp;e[1],&amp;vt[vt_offset],ldvt,</span></a>
+<a name="15763"><span class="lineNum">   15763 </span><span class="lineNoCov">          0 :                     &amp;u[u_offset],ldu,&amp;u[u_offset],ldu,&amp;work[wstart],info);</span></a>
+<a name="15764"><span class="lineNum">   15764 </span><span class="lineNoCov">          0 :         } else if (icompq == 1) {</span></a>
+<a name="15765"><span class="lineNum">   15765 </span>            :             iu = 1;</a>
+<a name="15766"><span class="lineNum">   15766 </span><span class="lineNoCov">          0 :             ivt = iu + *n;</span></a>
+<a name="15767"><span class="lineNum">   15767 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;q[iu + (qstart - 1) * *n], n);</span></a>
+<a name="15768"><span class="lineNum">   15768 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;q[ivt + (qstart - 1) * *n], n);</span></a>
+<a name="15769"><span class="lineNum">   15769 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;c_0, n, n, n, &amp;c_0, &amp;d__[1], &amp;e[1], </span></a>
+<a name="15770"><span class="lineNum">   15770 </span><span class="lineNoCov">          0 :                     &amp;q[ivt + (qstart - 1) * *n], n, &amp;q[iu + (qstart - 1) * *n], </span></a>
+<a name="15771"><span class="lineNum">   15771 </span><span class="lineNoCov">          0 :                     n, &amp;q[iu + (qstart - 1) * *n], n, &amp;work[wstart], info);</span></a>
+<a name="15772"><span class="lineNum">   15772 </span>            :         }</a>
+<a name="15773"><span class="lineNum">   15773 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="15774"><span class="lineNum">   15774 </span>            :     }</a>
+<a name="15775"><span class="lineNum">   15775 </span>            : </a>
+<a name="15776"><span class="lineNum">   15776 </span><span class="lineNoCov">          0 :     if (icompq == 2) {</span></a>
+<a name="15777"><span class="lineNum">   15777 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;u[u_offset], ldu);</span></a>
+<a name="15778"><span class="lineNum">   15778 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, n, n, &amp;zero, &amp;one, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="15779"><span class="lineNum">   15779 </span>            :     }</a>
+<a name="15780"><span class="lineNum">   15780 </span>            : </a>
+<a name="15781"><span class="lineNum">   15781 </span><span class="lineNoCov">          0 :     orgnrm = PLUMED_BLAS_F77_FUNC(slanst,SLANST)(&quot;M&quot;, n, &amp;d__[1], &amp;e[1]);</span></a>
+<a name="15782"><span class="lineNum">   15782 </span><span class="lineNoCov">          0 :     if ( std::abs(orgnrm)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="15783"><span class="lineNum">   15783 </span>            :         return;</a>
+<a name="15784"><span class="lineNum">   15784 </span>            :     }</a>
+<a name="15785"><span class="lineNum">   15785 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c_0, &amp;c_0, &amp;orgnrm, &amp;one, n, &amp;c_1, &amp;d__[1], n, &amp;ierr);</span></a>
+<a name="15786"><span class="lineNum">   15786 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c_0, &amp;c_0, &amp;orgnrm, &amp;one, &amp;nm1, &amp;c_1, &amp;e[1], &amp;nm1, &amp;ierr);</span></a>
+<a name="15787"><span class="lineNum">   15787 </span>            : </a>
+<a name="15788"><span class="lineNum">   15788 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="15789"><span class="lineNum">   15789 </span>            : </a>
+<a name="15790"><span class="lineNum">   15790 </span><span class="lineNoCov">          0 :     mlvl = (int) (std::log((float) (*n) / (float) (smlsiz + 1)) / std::log(2.)) + 1;</span></a>
+<a name="15791"><span class="lineNum">   15791 </span>            :     smlszp = smlsiz + 1;</a>
+<a name="15792"><span class="lineNum">   15792 </span>            : </a>
+<a name="15793"><span class="lineNum">   15793 </span><span class="lineNoCov">          0 :     if (icompq == 1) {</span></a>
+<a name="15794"><span class="lineNum">   15794 </span>            :         iu = 1;</a>
+<a name="15795"><span class="lineNum">   15795 </span>            :         ivt = smlsiz + 1;</a>
+<a name="15796"><span class="lineNum">   15796 </span><span class="lineNoCov">          0 :         difl = ivt + smlszp;</span></a>
+<a name="15797"><span class="lineNum">   15797 </span><span class="lineNoCov">          0 :         difr = difl + mlvl;</span></a>
+<a name="15798"><span class="lineNum">   15798 </span><span class="lineNoCov">          0 :         z__ = difr + (mlvl &lt;&lt; 1);</span></a>
+<a name="15799"><span class="lineNum">   15799 </span><span class="lineNoCov">          0 :         ic = z__ + mlvl;</span></a>
+<a name="15800"><span class="lineNum">   15800 </span><span class="lineNoCov">          0 :         is = ic + 1;</span></a>
+<a name="15801"><span class="lineNum">   15801 </span><span class="lineNoCov">          0 :         poles = is + 1;</span></a>
+<a name="15802"><span class="lineNum">   15802 </span><span class="lineNoCov">          0 :         givnum = poles + (mlvl &lt;&lt; 1);</span></a>
+<a name="15803"><span class="lineNum">   15803 </span>            : </a>
+<a name="15804"><span class="lineNum">   15804 </span>            :         k = 1;</a>
+<a name="15805"><span class="lineNum">   15805 </span>            :         givptr = 2;</a>
+<a name="15806"><span class="lineNum">   15806 </span>            :         perm = 3;</a>
+<a name="15807"><span class="lineNum">   15807 </span><span class="lineNoCov">          0 :         givcol = perm + mlvl;</span></a>
+<a name="15808"><span class="lineNum">   15808 </span>            :     }</a>
+<a name="15809"><span class="lineNum">   15809 </span>            : </a>
+<a name="15810"><span class="lineNum">   15810 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="15811"><span class="lineNum">   15811 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="15812"><span class="lineNum">   15812 </span><span class="lineNoCov">          0 :         if (std::abs(d__[i__]) &lt; eps) </span></a>
+<a name="15813"><span class="lineNum">   15813 </span><span class="lineNoCov">          0 :             d__[i__] = (d__[i__]&gt;0) ? eps : -eps;</span></a>
+<a name="15814"><span class="lineNum">   15814 </span>            :     }</a>
+<a name="15815"><span class="lineNum">   15815 </span>            : </a>
+<a name="15816"><span class="lineNum">   15816 </span>            :     start = 1;</a>
+<a name="15817"><span class="lineNum">   15817 </span><span class="lineNoCov">          0 :     sqre = 0;</span></a>
+<a name="15818"><span class="lineNum">   15818 </span>            : </a>
+<a name="15819"><span class="lineNum">   15819 </span><span class="lineNoCov">          0 :     i__1 = nm1;</span></a>
+<a name="15820"><span class="lineNum">   15820 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="15821"><span class="lineNum">   15821 </span><span class="lineNoCov">          0 :         if (std::abs(e[i__]) &lt; eps || i__ == nm1) {</span></a>
+<a name="15822"><span class="lineNum">   15822 </span><span class="lineNoCov">          0 :             if (i__ &lt; nm1) {</span></a>
+<a name="15823"><span class="lineNum">   15823 </span><span class="lineNoCov">          0 :                 nsize = i__ - start + 1;</span></a>
+<a name="15824"><span class="lineNum">   15824 </span><span class="lineNoCov">          0 :             } else if (std::abs(e[i__]) &gt;= eps) {</span></a>
+<a name="15825"><span class="lineNum">   15825 </span><span class="lineNoCov">          0 :                 nsize = *n - start + 1;</span></a>
+<a name="15826"><span class="lineNum">   15826 </span>            :             } else {</a>
+<a name="15827"><span class="lineNum">   15827 </span><span class="lineNoCov">          0 :                 nsize = i__ - start + 1;</span></a>
+<a name="15828"><span class="lineNum">   15828 </span><span class="lineNoCov">          0 :                 if (icompq == 2) {</span></a>
+<a name="15829"><span class="lineNum">   15829 </span><span class="lineNoCov">          0 :                     u[*n + *n * u_dim1] = (d__[*n]&gt;0) ? 1.0 : -1.0; </span></a>
+<a name="15830"><span class="lineNum">   15830 </span><span class="lineNoCov">          0 :                     vt[*n + *n * vt_dim1] = 1.;</span></a>
+<a name="15831"><span class="lineNum">   15831 </span><span class="lineNoCov">          0 :                 } else if (icompq == 1) {</span></a>
+<a name="15832"><span class="lineNum">   15832 </span><span class="lineNoCov">          0 :                     q[*n + (qstart - 1) * *n] = (d__[*n]&gt;0) ? 1.0 : -1.0; </span></a>
+<a name="15833"><span class="lineNum">   15833 </span><span class="lineNoCov">          0 :                     q[*n + (smlsiz + qstart - 1) * *n] = 1.;</span></a>
+<a name="15834"><span class="lineNum">   15834 </span>            :                 }</a>
+<a name="15835"><span class="lineNum">   15835 </span><span class="lineNoCov">          0 :                 d__[*n] = std::abs(d__[*n]);</span></a>
+<a name="15836"><span class="lineNum">   15836 </span>            :             }</a>
+<a name="15837"><span class="lineNum">   15837 </span><span class="lineNoCov">          0 :             if (icompq == 2) {</span></a>
+<a name="15838"><span class="lineNum">   15838 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasd0,SLASD0)(&amp;nsize, &amp;sqre, &amp;d__[start], &amp;e[start], </span></a>
+<a name="15839"><span class="lineNum">   15839 </span><span class="lineNoCov">          0 :                         &amp;u[start + start * u_dim1], ldu, </span></a>
+<a name="15840"><span class="lineNum">   15840 </span><span class="lineNoCov">          0 :                         &amp;vt[start + start * vt_dim1], </span></a>
+<a name="15841"><span class="lineNum">   15841 </span><span class="lineNoCov">          0 :                         ldvt, &amp;smlsiz, &amp;iwork[1], &amp;work[wstart], info);</span></a>
+<a name="15842"><span class="lineNum">   15842 </span>            :             } else {</a>
+<a name="15843"><span class="lineNum">   15843 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasda,SLASDA)(&amp;icompq, &amp;smlsiz, &amp;nsize, &amp;sqre, &amp;d__[start], </span></a>
+<a name="15844"><span class="lineNum">   15844 </span><span class="lineNoCov">          0 :                         &amp;e[start], &amp;q[start + (iu + qstart - 2) * *n], n, </span></a>
+<a name="15845"><span class="lineNum">   15845 </span><span class="lineNoCov">          0 :                         &amp;q[start + (ivt + qstart - 2) * *n], &amp;iq[start + k * *n],</span></a>
+<a name="15846"><span class="lineNum">   15846 </span><span class="lineNoCov">          0 :                         &amp;q[start + (difl + qstart - 2) * *n], </span></a>
+<a name="15847"><span class="lineNum">   15847 </span><span class="lineNoCov">          0 :                         &amp;q[start + (difr + qstart - 2) * *n], </span></a>
+<a name="15848"><span class="lineNum">   15848 </span><span class="lineNoCov">          0 :                         &amp;q[start + (z__ + qstart - 2) * *n], </span></a>
+<a name="15849"><span class="lineNum">   15849 </span><span class="lineNoCov">          0 :                         &amp;q[start + (poles + qstart - 2) * *n], </span></a>
+<a name="15850"><span class="lineNum">   15850 </span><span class="lineNoCov">          0 :                         &amp;iq[start + givptr * *n], &amp;iq[start + givcol * *n], n, </span></a>
+<a name="15851"><span class="lineNum">   15851 </span><span class="lineNoCov">          0 :                         &amp;iq[start + perm * *n], </span></a>
+<a name="15852"><span class="lineNum">   15852 </span><span class="lineNoCov">          0 :                         &amp;q[start + (givnum + qstart - 2) * *n], </span></a>
+<a name="15853"><span class="lineNum">   15853 </span><span class="lineNoCov">          0 :                         &amp;q[start + (ic + qstart - 2) * *n], </span></a>
+<a name="15854"><span class="lineNum">   15854 </span><span class="lineNoCov">          0 :                         &amp;q[start + (is + qstart - 2) * *n], &amp;work[wstart], </span></a>
+<a name="15855"><span class="lineNum">   15855 </span>            :                         &amp;iwork[1], info);</a>
+<a name="15856"><span class="lineNum">   15856 </span><span class="lineNoCov">          0 :                 if (*info != 0) {</span></a>
+<a name="15857"><span class="lineNum">   15857 </span>            :                     return;</a>
+<a name="15858"><span class="lineNum">   15858 </span>            :                 }</a>
+<a name="15859"><span class="lineNum">   15859 </span>            :             }</a>
+<a name="15860"><span class="lineNum">   15860 </span><span class="lineNoCov">          0 :             start = i__ + 1;</span></a>
+<a name="15861"><span class="lineNum">   15861 </span>            :         }</a>
+<a name="15862"><span class="lineNum">   15862 </span>            :     }</a>
+<a name="15863"><span class="lineNum">   15863 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c_0, &amp;c_0, &amp;one, &amp;orgnrm, n, &amp;c_1, &amp;d__[1], n, &amp;ierr);</span></a>
+<a name="15864"><span class="lineNum">   15864 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="15865"><span class="lineNum">   15865 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="15866"><span class="lineNum">   15866 </span><span class="lineNoCov">          0 :     for (ii = 2; ii &lt;= i__1; ++ii) {</span></a>
+<a name="15867"><span class="lineNum">   15867 </span><span class="lineNoCov">          0 :         i__ = ii - 1;</span></a>
+<a name="15868"><span class="lineNum">   15868 </span>            :         kk = i__;</a>
+<a name="15869"><span class="lineNum">   15869 </span><span class="lineNoCov">          0 :         p = d__[i__];</span></a>
+<a name="15870"><span class="lineNum">   15870 </span><span class="lineNoCov">          0 :         i__2 = *n;</span></a>
+<a name="15871"><span class="lineNum">   15871 </span><span class="lineNoCov">          0 :         for (j = ii; j &lt;= i__2; ++j) {</span></a>
+<a name="15872"><span class="lineNum">   15872 </span><span class="lineNoCov">          0 :             if (d__[j] &gt; p) {</span></a>
+<a name="15873"><span class="lineNum">   15873 </span>            :                 kk = j;</a>
+<a name="15874"><span class="lineNum">   15874 </span>            :                 p = d__[j];</a>
+<a name="15875"><span class="lineNum">   15875 </span>            :             }</a>
+<a name="15876"><span class="lineNum">   15876 </span>            :         }</a>
+<a name="15877"><span class="lineNum">   15877 </span><span class="lineNoCov">          0 :         if (kk != i__) {</span></a>
+<a name="15878"><span class="lineNum">   15878 </span><span class="lineNoCov">          0 :             d__[kk] = d__[i__];</span></a>
+<a name="15879"><span class="lineNum">   15879 </span><span class="lineNoCov">          0 :             d__[i__] = p;</span></a>
+<a name="15880"><span class="lineNum">   15880 </span><span class="lineNoCov">          0 :             if (icompq == 1) {</span></a>
+<a name="15881"><span class="lineNum">   15881 </span><span class="lineNoCov">          0 :                 iq[i__] = kk;</span></a>
+<a name="15882"><span class="lineNum">   15882 </span><span class="lineNoCov">          0 :             } else if (icompq == 2) {</span></a>
+<a name="15883"><span class="lineNum">   15883 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n, &amp;u[i__ * u_dim1 + 1],&amp;c_1,&amp;u[kk*u_dim1+1],&amp;c_1);</span></a>
+<a name="15884"><span class="lineNum">   15884 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n, &amp;vt[i__ + vt_dim1], ldvt, &amp;vt[kk + vt_dim1], ldvt);</span></a>
+<a name="15885"><span class="lineNum">   15885 </span>            :             }</a>
+<a name="15886"><span class="lineNum">   15886 </span><span class="lineNoCov">          0 :         } else if (icompq == 1) {</span></a>
+<a name="15887"><span class="lineNum">   15887 </span><span class="lineNoCov">          0 :             iq[i__] = i__;</span></a>
+<a name="15888"><span class="lineNum">   15888 </span>            :         }</a>
+<a name="15889"><span class="lineNum">   15889 </span>            :     }</a>
+<a name="15890"><span class="lineNum">   15890 </span><span class="lineNoCov">          0 :     if (icompq == 1) {</span></a>
+<a name="15891"><span class="lineNum">   15891 </span><span class="lineNoCov">          0 :         if (iuplo == 1) {</span></a>
+<a name="15892"><span class="lineNum">   15892 </span><span class="lineNoCov">          0 :             iq[*n] = 1;</span></a>
+<a name="15893"><span class="lineNum">   15893 </span>            :         } else {</a>
+<a name="15894"><span class="lineNum">   15894 </span><span class="lineNoCov">          0 :             iq[*n] = 0;</span></a>
+<a name="15895"><span class="lineNum">   15895 </span>            :         }</a>
+<a name="15896"><span class="lineNum">   15896 </span>            :     }</a>
+<a name="15897"><span class="lineNum">   15897 </span><span class="lineNoCov">          0 :     if (iuplo == 2 &amp;&amp; icompq == 2) {</span></a>
+<a name="15898"><span class="lineNum">   15898 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, n, n, &amp;work[1], &amp;work[*n], &amp;u[u_offset], ldu);</span></a>
+<a name="15899"><span class="lineNum">   15899 </span>            :     }</a>
+<a name="15900"><span class="lineNum">   15900 </span>            : </a>
+<a name="15901"><span class="lineNum">   15901 </span>            :     return;</a>
+<a name="15902"><span class="lineNum">   15902 </span>            : }</a>
+<a name="15903"><span class="lineNum">   15903 </span>            : }</a>
+<a name="15904"><span class="lineNum">   15904 </span>            : }</a>
+<a name="15905"><span class="lineNum">   15905 </span>            : #include &lt;cctype&gt;</a>
+<a name="15906"><span class="lineNum">   15906 </span>            : #include &lt;cmath&gt;</a>
+<a name="15907"><span class="lineNum">   15907 </span>            : </a>
+<a name="15908"><span class="lineNum">   15908 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15909"><span class="lineNum">   15909 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="15910"><span class="lineNum">   15910 </span>            : </a>
+<a name="15911"><span class="lineNum">   15911 </span>            : #include &quot;real.h&quot;</a>
+<a name="15912"><span class="lineNum">   15912 </span>            : </a>
+<a name="15913"><span class="lineNum">   15913 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="15914"><span class="lineNum">   15914 </span>            : namespace PLMD{</a>
+<a name="15915"><span class="lineNum">   15915 </span>            : namespace lapack{</a>
+<a name="15916"><span class="lineNum">   15916 </span>            : using namespace blas;</a>
+<a name="15917"><span class="lineNum">   15917 </span>            : void </a>
+<a name="15918"><span class="lineNum">   15918 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sbdsqr,SBDSQR)(const char *uplo,</span></a>
+<a name="15919"><span class="lineNum">   15919 </span>            :                         int *n,</a>
+<a name="15920"><span class="lineNum">   15920 </span>            :                         int *ncvt,</a>
+<a name="15921"><span class="lineNum">   15921 </span>            :                         int *nru, </a>
+<a name="15922"><span class="lineNum">   15922 </span>            :                         int *ncc, </a>
+<a name="15923"><span class="lineNum">   15923 </span>            :                         float *d__,</a>
+<a name="15924"><span class="lineNum">   15924 </span>            :                         float *e,</a>
+<a name="15925"><span class="lineNum">   15925 </span>            :                         float *vt, </a>
+<a name="15926"><span class="lineNum">   15926 </span>            :                         int *ldvt,</a>
+<a name="15927"><span class="lineNum">   15927 </span>            :                         float *u, </a>
+<a name="15928"><span class="lineNum">   15928 </span>            :                         int *ldu,</a>
+<a name="15929"><span class="lineNum">   15929 </span>            :                         float *c__, </a>
+<a name="15930"><span class="lineNum">   15930 </span>            :                         int *ldc,</a>
+<a name="15931"><span class="lineNum">   15931 </span>            :                         float *work,</a>
+<a name="15932"><span class="lineNum">   15932 </span>            :                         int *info)</a>
+<a name="15933"><span class="lineNum">   15933 </span>            : {</a>
+<a name="15934"><span class="lineNum">   15934 </span><span class="lineNoCov">          0 :     const char xuplo = std::toupper(*uplo);</span></a>
+<a name="15935"><span class="lineNum">   15935 </span>            :     int c_dim1, c_offset, u_dim1, u_offset, vt_dim1, vt_offset, i__1, </a>
+<a name="15936"><span class="lineNum">   15936 </span>            :             i__2;</a>
+<a name="15937"><span class="lineNum">   15937 </span>            :     float r__1, r__2, r__3, r__4;</a>
+<a name="15938"><span class="lineNum">   15938 </span>            :     float c_b15 = -.125;</a>
+<a name="15939"><span class="lineNum">   15939 </span>            : </a>
+<a name="15940"><span class="lineNum">   15940 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="15941"><span class="lineNum">   15941 </span>            :     float c_b49 = 1.f;</a>
+<a name="15942"><span class="lineNum">   15942 </span><span class="lineNoCov">          0 :     float c_b72 = -1.f;</span></a>
+<a name="15943"><span class="lineNum">   15943 </span>            : </a>
+<a name="15944"><span class="lineNum">   15944 </span>            :     float f, g, h__;</a>
+<a name="15945"><span class="lineNum">   15945 </span>            :     int i__, j, m;</a>
+<a name="15946"><span class="lineNum">   15946 </span>            :     float r__, cs;</a>
+<a name="15947"><span class="lineNum">   15947 </span>            :     int ll;</a>
+<a name="15948"><span class="lineNum">   15948 </span>            :     float sn, mu;</a>
+<a name="15949"><span class="lineNum">   15949 </span>            :     int nm1, nm12, nm13, lll;</a>
+<a name="15950"><span class="lineNum">   15950 </span>            :     float eps, sll, tol, abse;</a>
+<a name="15951"><span class="lineNum">   15951 </span>            :     int idir;</a>
+<a name="15952"><span class="lineNum">   15952 </span>            :     float abss;</a>
+<a name="15953"><span class="lineNum">   15953 </span>            :     int oldm;</a>
+<a name="15954"><span class="lineNum">   15954 </span>            :     float cosl;</a>
+<a name="15955"><span class="lineNum">   15955 </span>            :     int isub, iter;</a>
+<a name="15956"><span class="lineNum">   15956 </span>            :     float unfl, sinl, cosr, smin, smax, sinr;</a>
+<a name="15957"><span class="lineNum">   15957 </span>            :     float oldcs;</a>
+<a name="15958"><span class="lineNum">   15958 </span>            :     int oldll;</a>
+<a name="15959"><span class="lineNum">   15959 </span><span class="lineNoCov">          0 :     float shift, sigmn, oldsn = 0.;</span></a>
+<a name="15960"><span class="lineNum">   15960 </span>            :     int maxit;</a>
+<a name="15961"><span class="lineNum">   15961 </span>            :     float sminl;</a>
+<a name="15962"><span class="lineNum">   15962 </span>            :     float sigmx;</a>
+<a name="15963"><span class="lineNum">   15963 </span>            :     int lower;</a>
+<a name="15964"><span class="lineNum">   15964 </span>            :     float sminoa;</a>
+<a name="15965"><span class="lineNum">   15965 </span>            :     float thresh;</a>
+<a name="15966"><span class="lineNum">   15966 </span>            :     int rotate;</a>
+<a name="15967"><span class="lineNum">   15967 </span>            :     float tolmul;</a>
+<a name="15968"><span class="lineNum">   15968 </span>            :     int itmp1,itmp2;</a>
+<a name="15969"><span class="lineNum">   15969 </span>            :     </a>
+<a name="15970"><span class="lineNum">   15970 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="15971"><span class="lineNum">   15971 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="15972"><span class="lineNum">   15972 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="15973"><span class="lineNum">   15973 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="15974"><span class="lineNum">   15974 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="15975"><span class="lineNum">   15975 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="15976"><span class="lineNum">   15976 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="15977"><span class="lineNum">   15977 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="15978"><span class="lineNum">   15978 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="15979"><span class="lineNum">   15979 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="15980"><span class="lineNum">   15980 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="15981"><span class="lineNum">   15981 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="15982"><span class="lineNum">   15982 </span>            : </a>
+<a name="15983"><span class="lineNum">   15983 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="15984"><span class="lineNum">   15984 </span>            :     </a>
+<a name="15985"><span class="lineNum">   15985 </span><span class="lineNoCov">          0 :     itmp1 = (*n &gt; 1) ? *n : 1;</span></a>
+<a name="15986"><span class="lineNum">   15986 </span><span class="lineNoCov">          0 :     itmp2 = (*nru &gt; 1) ? *nru : 1;</span></a>
+<a name="15987"><span class="lineNum">   15987 </span>            :     </a>
+<a name="15988"><span class="lineNum">   15988 </span>            :     lower = (xuplo == 'L');</a>
+<a name="15989"><span class="lineNum">   15989 </span><span class="lineNoCov">          0 :     if ( (xuplo!='U') &amp;&amp; !lower) {</span></a>
+<a name="15990"><span class="lineNum">   15990 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="15991"><span class="lineNum">   15991 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="15992"><span class="lineNum">   15992 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="15993"><span class="lineNum">   15993 </span><span class="lineNoCov">          0 :     } else if (*ncvt &lt; 0) {</span></a>
+<a name="15994"><span class="lineNum">   15994 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="15995"><span class="lineNum">   15995 </span><span class="lineNoCov">          0 :     } else if (*nru &lt; 0) {</span></a>
+<a name="15996"><span class="lineNum">   15996 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="15997"><span class="lineNum">   15997 </span><span class="lineNoCov">          0 :     } else if (*ncc &lt; 0) {</span></a>
+<a name="15998"><span class="lineNum">   15998 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="15999"><span class="lineNum">   15999 </span><span class="lineNoCov">          0 :     } else if ( ((*ncvt == 0) &amp;&amp; (*ldvt &lt; 1)) || ((*ncvt &gt; 0) &amp;&amp; (*ldvt &lt; itmp1)) ) {</span></a>
+<a name="16000"><span class="lineNum">   16000 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="16001"><span class="lineNum">   16001 </span><span class="lineNoCov">          0 :     } else if (*ldu &lt; itmp2) {</span></a>
+<a name="16002"><span class="lineNum">   16002 </span><span class="lineNoCov">          0 :         *info = -11;</span></a>
+<a name="16003"><span class="lineNum">   16003 </span><span class="lineNoCov">          0 :     } else if ( ((*ncc == 0) &amp;&amp; (*ldc &lt; 1)) || ((*ncc &gt; 0) &amp;&amp; (*ldc &lt; itmp1))) {</span></a>
+<a name="16004"><span class="lineNum">   16004 </span><span class="lineNoCov">          0 :         *info = -13;</span></a>
+<a name="16005"><span class="lineNum">   16005 </span>            :     }</a>
+<a name="16006"><span class="lineNum">   16006 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="16007"><span class="lineNum">   16007 </span>            :         return;</a>
+<a name="16008"><span class="lineNum">   16008 </span>            :     }</a>
+<a name="16009"><span class="lineNum">   16009 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="16010"><span class="lineNum">   16010 </span>            :         return;</a>
+<a name="16011"><span class="lineNum">   16011 </span>            :     }</a>
+<a name="16012"><span class="lineNum">   16012 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="16013"><span class="lineNum">   16013 </span><span class="lineNoCov">          0 :         goto L160;</span></a>
+<a name="16014"><span class="lineNum">   16014 </span>            :     }</a>
+<a name="16015"><span class="lineNum">   16015 </span>            : </a>
+<a name="16016"><span class="lineNum">   16016 </span><span class="lineNoCov">          0 :     rotate = *ncvt &gt; 0 || *nru &gt; 0 || *ncc &gt; 0;</span></a>
+<a name="16017"><span class="lineNum">   16017 </span>            : </a>
+<a name="16018"><span class="lineNum">   16018 </span>            :     if (! rotate) {</a>
+<a name="16019"><span class="lineNum">   16019 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasq1,SLASQ1)(n, &amp;d__[1], &amp;e[1], &amp;work[1], info);</span></a>
+<a name="16020"><span class="lineNum">   16020 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="16021"><span class="lineNum">   16021 </span>            :     }</a>
+<a name="16022"><span class="lineNum">   16022 </span>            : </a>
+<a name="16023"><span class="lineNum">   16023 </span><span class="lineNoCov">          0 :     nm1 = *n - 1;</span></a>
+<a name="16024"><span class="lineNum">   16024 </span><span class="lineNoCov">          0 :     nm12 = nm1 + nm1;</span></a>
+<a name="16025"><span class="lineNum">   16025 </span><span class="lineNoCov">          0 :     nm13 = nm12 + nm1;</span></a>
+<a name="16026"><span class="lineNum">   16026 </span>            :     idir = 0;</a>
+<a name="16027"><span class="lineNum">   16027 </span>            : </a>
+<a name="16028"><span class="lineNum">   16028 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="16029"><span class="lineNum">   16029 </span>            :     unfl = PLUMED_GMX_FLOAT_MIN/PLUMED_GMX_FLOAT_EPS;</a>
+<a name="16030"><span class="lineNum">   16030 </span>            : </a>
+<a name="16031"><span class="lineNum">   16031 </span><span class="lineNoCov">          0 :     if (lower) {</span></a>
+<a name="16032"><span class="lineNum">   16032 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="16033"><span class="lineNum">   16033 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16034"><span class="lineNum">   16034 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="16035"><span class="lineNum">   16035 </span><span class="lineNoCov">          0 :             d__[i__] = r__;</span></a>
+<a name="16036"><span class="lineNum">   16036 </span><span class="lineNoCov">          0 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="16037"><span class="lineNum">   16037 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="16038"><span class="lineNum">   16038 </span><span class="lineNoCov">          0 :             work[i__] = cs;</span></a>
+<a name="16039"><span class="lineNum">   16039 </span><span class="lineNoCov">          0 :             work[nm1 + i__] = sn;</span></a>
+<a name="16040"><span class="lineNum">   16040 </span>            :         }</a>
+<a name="16041"><span class="lineNum">   16041 </span>            : </a>
+<a name="16042"><span class="lineNum">   16042 </span><span class="lineNoCov">          0 :         if (*nru &gt; 0) {</span></a>
+<a name="16043"><span class="lineNum">   16043 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, n, &amp;work[1], &amp;work[*n], &amp;u[u_offset], </span></a>
+<a name="16044"><span class="lineNum">   16044 </span>            :                     ldu);</a>
+<a name="16045"><span class="lineNum">   16045 </span>            :         }</a>
+<a name="16046"><span class="lineNum">   16046 </span><span class="lineNoCov">          0 :         if (*ncc &gt; 0) {</span></a>
+<a name="16047"><span class="lineNum">   16047 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, n, ncc, &amp;work[1], &amp;work[*n], &amp;c__[c_offset],</span></a>
+<a name="16048"><span class="lineNum">   16048 </span>            :                      ldc);</a>
+<a name="16049"><span class="lineNum">   16049 </span>            :         }</a>
+<a name="16050"><span class="lineNum">   16050 </span>            :     }</a>
+<a name="16051"><span class="lineNum">   16051 </span>            : </a>
+<a name="16052"><span class="lineNum">   16052 </span>            :     r__3 = 100.f, r__4 = std::pow(static_cast&lt;float&gt;(PLUMED_GMX_FLOAT_EPS),c_b15);</a>
+<a name="16053"><span class="lineNum">   16053 </span><span class="lineNoCov">          0 :     r__1 = 10.f, r__2 = (r__3&lt;r__4) ? r__3 : r__4;</span></a>
+<a name="16054"><span class="lineNum">   16054 </span>            :     tolmul = (r__1&gt;r__2) ? r__1 : r__2;</a>
+<a name="16055"><span class="lineNum">   16055 </span>            :     tol = tolmul * eps;</a>
+<a name="16056"><span class="lineNum">   16056 </span>            :     smax = 0.f;</a>
+<a name="16057"><span class="lineNum">   16057 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="16058"><span class="lineNum">   16058 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16059"><span class="lineNum">   16059 </span><span class="lineNoCov">          0 :         r__2 = smax, r__3 = (r__1 = d__[i__], std::abs(r__1));</span></a>
+<a name="16060"><span class="lineNum">   16060 </span><span class="lineNoCov">          0 :         smax = (r__2&gt;r__3) ? r__2 : r__3;</span></a>
+<a name="16061"><span class="lineNum">   16061 </span>            :     }</a>
+<a name="16062"><span class="lineNum">   16062 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="16063"><span class="lineNum">   16063 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16064"><span class="lineNum">   16064 </span><span class="lineNoCov">          0 :         r__2 = smax, r__3 = (r__1 = e[i__], std::abs(r__1));</span></a>
+<a name="16065"><span class="lineNum">   16065 </span><span class="lineNoCov">          0 :         smax = (r__2&gt;r__3) ? r__2 : r__3;</span></a>
+<a name="16066"><span class="lineNum">   16066 </span>            :     }</a>
+<a name="16067"><span class="lineNum">   16067 </span>            :     sminl = 0.f;</a>
+<a name="16068"><span class="lineNum">   16068 </span>            :     if (tol &gt;= 0.f) {</a>
+<a name="16069"><span class="lineNum">   16069 </span><span class="lineNoCov">          0 :         sminoa = std::abs(d__[1]);</span></a>
+<a name="16070"><span class="lineNum">   16070 </span><span class="lineNoCov">          0 :         if (sminoa == 0.f) {</span></a>
+<a name="16071"><span class="lineNum">   16071 </span><span class="lineNoCov">          0 :             goto L50;</span></a>
+<a name="16072"><span class="lineNum">   16072 </span>            :         }</a>
+<a name="16073"><span class="lineNum">   16073 </span>            :         mu = sminoa;</a>
+<a name="16074"><span class="lineNum">   16074 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="16075"><span class="lineNum">   16075 </span><span class="lineNoCov">          0 :         for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16076"><span class="lineNum">   16076 </span><span class="lineNoCov">          0 :             mu = (r__2 = d__[i__], std::abs(r__2)) * (mu / (mu + (r__1 = e[i__ - </span></a>
+<a name="16077"><span class="lineNum">   16077 </span><span class="lineNoCov">          0 :                     1], std::abs(r__1))));</span></a>
+<a name="16078"><span class="lineNum">   16078 </span><span class="lineNoCov">          0 :             sminoa = (sminoa&lt;mu) ? sminoa : mu;</span></a>
+<a name="16079"><span class="lineNum">   16079 </span><span class="lineNoCov">          0 :             if (sminoa == 0.f) {</span></a>
+<a name="16080"><span class="lineNum">   16080 </span><span class="lineNoCov">          0 :                 goto L50;</span></a>
+<a name="16081"><span class="lineNum">   16081 </span>            :             }</a>
+<a name="16082"><span class="lineNum">   16082 </span>            :         }</a>
+<a name="16083"><span class="lineNum">   16083 </span><span class="lineNoCov">          0 : L50:</span></a>
+<a name="16084"><span class="lineNum">   16084 </span><span class="lineNoCov">          0 :         sminoa /=  std::sqrt((float) (*n));</span></a>
+<a name="16085"><span class="lineNum">   16085 </span><span class="lineNoCov">          0 :         r__1 = tol * sminoa, r__2 = *n * 6 * *n * unfl;</span></a>
+<a name="16086"><span class="lineNum">   16086 </span><span class="lineNoCov">          0 :         thresh = (r__1&gt;r__2) ? r__1 : r__2;</span></a>
+<a name="16087"><span class="lineNum">   16087 </span>            :     } else {</a>
+<a name="16088"><span class="lineNum">   16088 </span>            :         r__1 = std::abs(tol) * smax, r__2 = *n * 6 * *n * unfl;</a>
+<a name="16089"><span class="lineNum">   16089 </span>            :         thresh = (r__1&gt;r__2) ? r__1 : r__2;</a>
+<a name="16090"><span class="lineNum">   16090 </span>            :     }</a>
+<a name="16091"><span class="lineNum">   16091 </span>            :     maxit = *n * 6 * *n;</a>
+<a name="16092"><span class="lineNum">   16092 </span>            :     iter = 0;</a>
+<a name="16093"><span class="lineNum">   16093 </span>            :     oldll = -1;</a>
+<a name="16094"><span class="lineNum">   16094 </span>            :     oldm = -1;</a>
+<a name="16095"><span class="lineNum">   16095 </span>            :     m = *n;</a>
+<a name="16096"><span class="lineNum">   16096 </span>            : </a>
+<a name="16097"><span class="lineNum">   16097 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="16098"><span class="lineNum">   16098 </span>            : </a>
+<a name="16099"><span class="lineNum">   16099 </span><span class="lineNoCov">          0 :     if (m &lt;= 1) {</span></a>
+<a name="16100"><span class="lineNum">   16100 </span><span class="lineNoCov">          0 :         goto L160;</span></a>
+<a name="16101"><span class="lineNum">   16101 </span>            :     }</a>
+<a name="16102"><span class="lineNum">   16102 </span><span class="lineNoCov">          0 :     if (iter &gt; maxit) {</span></a>
+<a name="16103"><span class="lineNum">   16103 </span><span class="lineNoCov">          0 :         goto L200;</span></a>
+<a name="16104"><span class="lineNum">   16104 </span>            :     }</a>
+<a name="16105"><span class="lineNum">   16105 </span>            : </a>
+<a name="16106"><span class="lineNum">   16106 </span>            :     if (tol &lt; 0.f &amp;&amp; (r__1 = d__[m], std::abs(r__1)) &lt;= thresh) {</a>
+<a name="16107"><span class="lineNum">   16107 </span>            :         d__[m] = 0.f;</a>
+<a name="16108"><span class="lineNum">   16108 </span>            :     }</a>
+<a name="16109"><span class="lineNum">   16109 </span><span class="lineNoCov">          0 :     smax = (r__1 = d__[m], std::abs(r__1));</span></a>
+<a name="16110"><span class="lineNum">   16110 </span>            :     smin = smax;</a>
+<a name="16111"><span class="lineNum">   16111 </span><span class="lineNoCov">          0 :     i__1 = m - 1;</span></a>
+<a name="16112"><span class="lineNum">   16112 </span><span class="lineNoCov">          0 :     for (lll = 1; lll &lt;= i__1; ++lll) {</span></a>
+<a name="16113"><span class="lineNum">   16113 </span><span class="lineNoCov">          0 :         ll = m - lll;</span></a>
+<a name="16114"><span class="lineNum">   16114 </span><span class="lineNoCov">          0 :         abss = (r__1 = d__[ll], std::abs(r__1));</span></a>
+<a name="16115"><span class="lineNum">   16115 </span><span class="lineNoCov">          0 :         abse = (r__1 = e[ll], std::abs(r__1));</span></a>
+<a name="16116"><span class="lineNum">   16116 </span>            :         if (tol &lt; 0.f &amp;&amp; abss &lt;= thresh) {</a>
+<a name="16117"><span class="lineNum">   16117 </span>            :             d__[ll] = 0.f;</a>
+<a name="16118"><span class="lineNum">   16118 </span>            :         }</a>
+<a name="16119"><span class="lineNum">   16119 </span><span class="lineNoCov">          0 :         if (abse &lt;= thresh) {</span></a>
+<a name="16120"><span class="lineNum">   16120 </span><span class="lineNoCov">          0 :             goto L80;</span></a>
+<a name="16121"><span class="lineNum">   16121 </span>            :         }</a>
+<a name="16122"><span class="lineNum">   16122 </span><span class="lineNoCov">          0 :         smin = (smin&lt;abss) ? smin : abss;</span></a>
+<a name="16123"><span class="lineNum">   16123 </span><span class="lineNoCov">          0 :         r__1 = (smax&gt;abss) ? smax : abss;</span></a>
+<a name="16124"><span class="lineNum">   16124 </span><span class="lineNoCov">          0 :         smax = (r__1&gt;abse) ? r__1 : abse;</span></a>
+<a name="16125"><span class="lineNum">   16125 </span>            :     }</a>
+<a name="16126"><span class="lineNum">   16126 </span>            :     ll = 0;</a>
+<a name="16127"><span class="lineNum">   16127 </span><span class="lineNoCov">          0 :     goto L90;</span></a>
+<a name="16128"><span class="lineNum">   16128 </span>            : L80:</a>
+<a name="16129"><span class="lineNum">   16129 </span><span class="lineNoCov">          0 :     e[ll] = 0.f;</span></a>
+<a name="16130"><span class="lineNum">   16130 </span><span class="lineNoCov">          0 :     if (ll == m - 1) {</span></a>
+<a name="16131"><span class="lineNum">   16131 </span>            :         --m;</a>
+<a name="16132"><span class="lineNum">   16132 </span><span class="lineNoCov">          0 :         goto L60;</span></a>
+<a name="16133"><span class="lineNum">   16133 </span>            :     }</a>
+<a name="16134"><span class="lineNum">   16134 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="16135"><span class="lineNum">   16135 </span><span class="lineNoCov">          0 :     ++ll;</span></a>
+<a name="16136"><span class="lineNum">   16136 </span><span class="lineNoCov">          0 :     if (ll == m - 1) {</span></a>
+<a name="16137"><span class="lineNum">   16137 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasv2,SLASV2)(&amp;d__[m - 1], &amp;e[m - 1], &amp;d__[m], &amp;sigmn, &amp;sigmx, &amp;sinr, &amp;cosr,</span></a>
+<a name="16138"><span class="lineNum">   16138 </span>            :                  &amp;sinl, &amp;cosl);</a>
+<a name="16139"><span class="lineNum">   16139 </span><span class="lineNoCov">          0 :         d__[m - 1] = sigmx;</span></a>
+<a name="16140"><span class="lineNum">   16140 </span><span class="lineNoCov">          0 :         e[m - 1] = 0.f;</span></a>
+<a name="16141"><span class="lineNum">   16141 </span><span class="lineNoCov">          0 :         d__[m] = sigmn;</span></a>
+<a name="16142"><span class="lineNum">   16142 </span><span class="lineNoCov">          0 :         if (*ncvt &gt; 0) {</span></a>
+<a name="16143"><span class="lineNum">   16143 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(ncvt, &amp;vt[m - 1 + vt_dim1], ldvt, &amp;vt[m + vt_dim1], ldvt, &amp;</span></a>
+<a name="16144"><span class="lineNum">   16144 </span>            :                     cosr, &amp;sinr);</a>
+<a name="16145"><span class="lineNum">   16145 </span>            :         }</a>
+<a name="16146"><span class="lineNum">   16146 </span><span class="lineNoCov">          0 :         if (*nru &gt; 0) {</span></a>
+<a name="16147"><span class="lineNum">   16147 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(nru, &amp;u[(m - 1) * u_dim1 + 1], &amp;c__1, &amp;u[m * u_dim1 + 1], &amp;</span></a>
+<a name="16148"><span class="lineNum">   16148 </span>            :                     c__1, &amp;cosl, &amp;sinl);</a>
+<a name="16149"><span class="lineNum">   16149 </span>            :         }</a>
+<a name="16150"><span class="lineNum">   16150 </span><span class="lineNoCov">          0 :         if (*ncc &gt; 0) {</span></a>
+<a name="16151"><span class="lineNum">   16151 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(ncc, &amp;c__[m - 1 + c_dim1], ldc, &amp;c__[m + c_dim1], ldc, &amp;</span></a>
+<a name="16152"><span class="lineNum">   16152 </span>            :                     cosl, &amp;sinl);</a>
+<a name="16153"><span class="lineNum">   16153 </span>            :         }</a>
+<a name="16154"><span class="lineNum">   16154 </span><span class="lineNoCov">          0 :         m += -2;</span></a>
+<a name="16155"><span class="lineNum">   16155 </span><span class="lineNoCov">          0 :         goto L60;</span></a>
+<a name="16156"><span class="lineNum">   16156 </span>            :     }</a>
+<a name="16157"><span class="lineNum">   16157 </span><span class="lineNoCov">          0 :     if (ll &gt; oldm || m &lt; oldll) {</span></a>
+<a name="16158"><span class="lineNum">   16158 </span><span class="lineNoCov">          0 :         if ((r__1 = d__[ll], std::abs(r__1)) &gt;= (r__2 = d__[m], std::abs(r__2))) {</span></a>
+<a name="16159"><span class="lineNum">   16159 </span>            :             idir = 1;</a>
+<a name="16160"><span class="lineNum">   16160 </span>            :         } else {</a>
+<a name="16161"><span class="lineNum">   16161 </span>            :             idir = 2;</a>
+<a name="16162"><span class="lineNum">   16162 </span>            :         }</a>
+<a name="16163"><span class="lineNum">   16163 </span>            :     }</a>
+<a name="16164"><span class="lineNum">   16164 </span><span class="lineNoCov">          0 :     if (idir == 1) {</span></a>
+<a name="16165"><span class="lineNum">   16165 </span>            : </a>
+<a name="16166"><span class="lineNum">   16166 </span><span class="lineNoCov">          0 :         if( (std::abs(e[m-1]) &lt;= std::abs(tol) * std::abs(d__[m])) ||</span></a>
+<a name="16167"><span class="lineNum">   16167 </span>            :             (tol&lt;0.0 &amp;&amp; std::abs(e[m-1])&lt;=thresh)) {</a>
+<a name="16168"><span class="lineNum">   16168 </span><span class="lineNoCov">          0 :             e[m - 1] = 0.f;</span></a>
+<a name="16169"><span class="lineNum">   16169 </span><span class="lineNoCov">          0 :             goto L60;</span></a>
+<a name="16170"><span class="lineNum">   16170 </span>            :         }</a>
+<a name="16171"><span class="lineNum">   16171 </span>            :         if (tol &gt;= 0.f) {</a>
+<a name="16172"><span class="lineNum">   16172 </span><span class="lineNoCov">          0 :             mu = (r__1 = d__[ll], std::abs(r__1));</span></a>
+<a name="16173"><span class="lineNum">   16173 </span>            :             sminl = mu;</a>
+<a name="16174"><span class="lineNum">   16174 </span>            :             i__1 = m - 1;</a>
+<a name="16175"><span class="lineNum">   16175 </span><span class="lineNoCov">          0 :             for (lll = ll; lll &lt;= i__1; ++lll) {</span></a>
+<a name="16176"><span class="lineNum">   16176 </span><span class="lineNoCov">          0 :                 if ((r__1 = e[lll], std::abs(r__1)) &lt;= tol * mu) {</span></a>
+<a name="16177"><span class="lineNum">   16177 </span><span class="lineNoCov">          0 :                     e[lll] = 0.f;</span></a>
+<a name="16178"><span class="lineNum">   16178 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="16179"><span class="lineNum">   16179 </span>            :                 }</a>
+<a name="16180"><span class="lineNum">   16180 </span><span class="lineNoCov">          0 :                 mu = (r__2 = d__[lll + 1], std::abs(r__2)) * (mu / (mu + (r__1 = </span></a>
+<a name="16181"><span class="lineNum">   16181 </span>            :                         e[lll], std::abs(r__1))));</a>
+<a name="16182"><span class="lineNum">   16182 </span><span class="lineNoCov">          0 :                 sminl = (sminl&lt;mu) ? sminl : mu;</span></a>
+<a name="16183"><span class="lineNum">   16183 </span>            :             }</a>
+<a name="16184"><span class="lineNum">   16184 </span>            :         }</a>
+<a name="16185"><span class="lineNum">   16185 </span>            :     } else {</a>
+<a name="16186"><span class="lineNum">   16186 </span><span class="lineNoCov">          0 :         if( (std::abs(e[ll]) &lt;= std::abs(tol)*std::abs(d__[ll])) ||</span></a>
+<a name="16187"><span class="lineNum">   16187 </span>            :             (tol&lt;0.0 &amp;&amp; std::abs(e[ll])&lt;=thresh)) {</a>
+<a name="16188"><span class="lineNum">   16188 </span><span class="lineNoCov">          0 :             e[ll] = 0.f;</span></a>
+<a name="16189"><span class="lineNum">   16189 </span><span class="lineNoCov">          0 :             goto L60;</span></a>
+<a name="16190"><span class="lineNum">   16190 </span>            :         }</a>
+<a name="16191"><span class="lineNum">   16191 </span>            :         if (tol &gt;= 0.f) {</a>
+<a name="16192"><span class="lineNum">   16192 </span><span class="lineNoCov">          0 :             mu = (r__1 = d__[m], std::abs(r__1));</span></a>
+<a name="16193"><span class="lineNum">   16193 </span>            :             sminl = mu;</a>
+<a name="16194"><span class="lineNum">   16194 </span><span class="lineNoCov">          0 :             i__1 = ll;</span></a>
+<a name="16195"><span class="lineNum">   16195 </span><span class="lineNoCov">          0 :             for (lll = m - 1; lll &gt;= i__1; --lll) {</span></a>
+<a name="16196"><span class="lineNum">   16196 </span><span class="lineNoCov">          0 :                 if ((r__1 = e[lll], std::abs(r__1)) &lt;= tol * mu) {</span></a>
+<a name="16197"><span class="lineNum">   16197 </span><span class="lineNoCov">          0 :                     e[lll] = 0.f;</span></a>
+<a name="16198"><span class="lineNum">   16198 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="16199"><span class="lineNum">   16199 </span>            :                 }</a>
+<a name="16200"><span class="lineNum">   16200 </span><span class="lineNoCov">          0 :                 mu = (r__2 = d__[lll], std::abs(r__2)) * (mu / (mu + (r__1 = e[</span></a>
+<a name="16201"><span class="lineNum">   16201 </span>            :                         lll], std::abs(r__1))));</a>
+<a name="16202"><span class="lineNum">   16202 </span><span class="lineNoCov">          0 :                 sminl = (sminl&lt;mu) ? sminl : mu;</span></a>
+<a name="16203"><span class="lineNum">   16203 </span>            :             }</a>
+<a name="16204"><span class="lineNum">   16204 </span>            :         }</a>
+<a name="16205"><span class="lineNum">   16205 </span>            :     }</a>
+<a name="16206"><span class="lineNum">   16206 </span>            :     oldll = ll;</a>
+<a name="16207"><span class="lineNum">   16207 </span>            :     oldm = m;</a>
+<a name="16208"><span class="lineNum">   16208 </span>            : </a>
+<a name="16209"><span class="lineNum">   16209 </span><span class="lineNoCov">          0 :     r__1 = eps, r__2 = tol * .01f;</span></a>
+<a name="16210"><span class="lineNum">   16210 </span><span class="lineNoCov">          0 :     if (tol &gt;= 0.f &amp;&amp; *n * tol * (sminl / smax) &lt;= ((r__1&gt;r__2) ? r__1 : r__2)) {</span></a>
+<a name="16211"><span class="lineNum">   16211 </span><span class="lineNoCov">          0 :         shift = 0.f;</span></a>
+<a name="16212"><span class="lineNum">   16212 </span>            :     } else {</a>
+<a name="16213"><span class="lineNum">   16213 </span><span class="lineNoCov">          0 :         if (idir == 1) {</span></a>
+<a name="16214"><span class="lineNum">   16214 </span><span class="lineNoCov">          0 :             sll = (r__1 = d__[ll], std::abs(r__1));</span></a>
+<a name="16215"><span class="lineNum">   16215 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slas2,SLAS2)(&amp;d__[m - 1], &amp;e[m - 1], &amp;d__[m], &amp;shift, &amp;r__);</span></a>
+<a name="16216"><span class="lineNum">   16216 </span>            :         } else {</a>
+<a name="16217"><span class="lineNum">   16217 </span><span class="lineNoCov">          0 :             sll = (r__1 = d__[m], std::abs(r__1));</span></a>
+<a name="16218"><span class="lineNum">   16218 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slas2,SLAS2)(&amp;d__[ll], &amp;e[ll], &amp;d__[ll + 1], &amp;shift, &amp;r__);</span></a>
+<a name="16219"><span class="lineNum">   16219 </span>            :         }</a>
+<a name="16220"><span class="lineNum">   16220 </span><span class="lineNoCov">          0 :         if (sll &gt; 0.f) {</span></a>
+<a name="16221"><span class="lineNum">   16221 </span><span class="lineNoCov">          0 :             r__1 = shift / sll;</span></a>
+<a name="16222"><span class="lineNum">   16222 </span><span class="lineNoCov">          0 :             if (r__1 * r__1 &lt; eps) {</span></a>
+<a name="16223"><span class="lineNum">   16223 </span><span class="lineNoCov">          0 :                 shift = 0.f;</span></a>
+<a name="16224"><span class="lineNum">   16224 </span>            :             }</a>
+<a name="16225"><span class="lineNum">   16225 </span>            :         }</a>
+<a name="16226"><span class="lineNum">   16226 </span>            :     }</a>
+<a name="16227"><span class="lineNum">   16227 </span><span class="lineNoCov">          0 :     iter = iter + m - ll;</span></a>
+<a name="16228"><span class="lineNum">   16228 </span><span class="lineNoCov">          0 :     if (shift == 0.f) {</span></a>
+<a name="16229"><span class="lineNum">   16229 </span><span class="lineNoCov">          0 :         if (idir == 1) {</span></a>
+<a name="16230"><span class="lineNum">   16230 </span><span class="lineNoCov">          0 :             cs = 1.f;</span></a>
+<a name="16231"><span class="lineNum">   16231 </span><span class="lineNoCov">          0 :             oldcs = 1.f;</span></a>
+<a name="16232"><span class="lineNum">   16232 </span><span class="lineNoCov">          0 :             i__1 = m - 1;</span></a>
+<a name="16233"><span class="lineNum">   16233 </span><span class="lineNoCov">          0 :             for (i__ = ll; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16234"><span class="lineNum">   16234 </span><span class="lineNoCov">          0 :                 r__1 = d__[i__] * cs;</span></a>
+<a name="16235"><span class="lineNum">   16235 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;r__1, &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="16236"><span class="lineNum">   16236 </span><span class="lineNoCov">          0 :                 if (i__ &gt; ll) {</span></a>
+<a name="16237"><span class="lineNum">   16237 </span><span class="lineNoCov">          0 :                     e[i__ - 1] = oldsn * r__;</span></a>
+<a name="16238"><span class="lineNum">   16238 </span>            :                 }</a>
+<a name="16239"><span class="lineNum">   16239 </span><span class="lineNoCov">          0 :                 r__1 = oldcs * r__;</span></a>
+<a name="16240"><span class="lineNum">   16240 </span><span class="lineNoCov">          0 :                 r__2 = d__[i__ + 1] * sn;</span></a>
+<a name="16241"><span class="lineNum">   16241 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;r__1, &amp;r__2, &amp;oldcs, &amp;oldsn, &amp;d__[i__]);</span></a>
+<a name="16242"><span class="lineNum">   16242 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1] = cs;</span></a>
+<a name="16243"><span class="lineNum">   16243 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1 + nm1] = sn;</span></a>
+<a name="16244"><span class="lineNum">   16244 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1 + nm12] = oldcs;</span></a>
+<a name="16245"><span class="lineNum">   16245 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1 + nm13] = oldsn;</span></a>
+<a name="16246"><span class="lineNum">   16246 </span>            :             }</a>
+<a name="16247"><span class="lineNum">   16247 </span><span class="lineNoCov">          0 :             h__ = d__[m] * cs;</span></a>
+<a name="16248"><span class="lineNum">   16248 </span><span class="lineNoCov">          0 :             d__[m] = h__ * oldcs;</span></a>
+<a name="16249"><span class="lineNum">   16249 </span><span class="lineNoCov">          0 :             e[m - 1] = h__ * oldsn;</span></a>
+<a name="16250"><span class="lineNum">   16250 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="16251"><span class="lineNum">   16251 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16252"><span class="lineNum">   16252 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncvt, &amp;work[1], &amp;work[*n], &amp;vt[</span></a>
+<a name="16253"><span class="lineNum">   16253 </span><span class="lineNoCov">          0 :                         ll + vt_dim1], ldvt);</span></a>
+<a name="16254"><span class="lineNum">   16254 </span>            :             }</a>
+<a name="16255"><span class="lineNum">   16255 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="16256"><span class="lineNum">   16256 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16257"><span class="lineNum">   16257 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, &amp;i__1, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="16258"><span class="lineNum">   16258 </span><span class="lineNoCov">          0 :                         + 1], &amp;u[ll * u_dim1 + 1], ldu);</span></a>
+<a name="16259"><span class="lineNum">   16259 </span>            :             }</a>
+<a name="16260"><span class="lineNum">   16260 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="16261"><span class="lineNum">   16261 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16262"><span class="lineNum">   16262 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncc, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="16263"><span class="lineNum">   16263 </span><span class="lineNoCov">          0 :                         + 1], &amp;c__[ll + c_dim1], ldc);</span></a>
+<a name="16264"><span class="lineNum">   16264 </span>            :             }</a>
+<a name="16265"><span class="lineNum">   16265 </span><span class="lineNoCov">          0 :             if ((r__1 = e[m - 1], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="16266"><span class="lineNum">   16266 </span><span class="lineNoCov">          0 :                 e[m - 1] = 0.f;</span></a>
+<a name="16267"><span class="lineNum">   16267 </span>            :             }</a>
+<a name="16268"><span class="lineNum">   16268 </span>            :         } else {</a>
+<a name="16269"><span class="lineNum">   16269 </span><span class="lineNoCov">          0 :             cs = 1.f;</span></a>
+<a name="16270"><span class="lineNum">   16270 </span><span class="lineNoCov">          0 :             oldcs = 1.f;</span></a>
+<a name="16271"><span class="lineNum">   16271 </span><span class="lineNoCov">          0 :             i__1 = ll + 1;</span></a>
+<a name="16272"><span class="lineNum">   16272 </span><span class="lineNoCov">          0 :             for (i__ = m; i__ &gt;= i__1; --i__) {</span></a>
+<a name="16273"><span class="lineNum">   16273 </span><span class="lineNoCov">          0 :                 r__1 = d__[i__] * cs;</span></a>
+<a name="16274"><span class="lineNum">   16274 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;r__1, &amp;e[i__ - 1], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="16275"><span class="lineNum">   16275 </span><span class="lineNoCov">          0 :                 if (i__ &lt; m) {</span></a>
+<a name="16276"><span class="lineNum">   16276 </span><span class="lineNoCov">          0 :                     e[i__] = oldsn * r__;</span></a>
+<a name="16277"><span class="lineNum">   16277 </span>            :                 }</a>
+<a name="16278"><span class="lineNum">   16278 </span><span class="lineNoCov">          0 :                 r__1 = oldcs * r__;</span></a>
+<a name="16279"><span class="lineNum">   16279 </span><span class="lineNoCov">          0 :                 r__2 = d__[i__ - 1] * sn;</span></a>
+<a name="16280"><span class="lineNum">   16280 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;r__1, &amp;r__2, &amp;oldcs, &amp;oldsn, &amp;d__[i__]);</span></a>
+<a name="16281"><span class="lineNum">   16281 </span><span class="lineNoCov">          0 :                 work[i__ - ll] = cs;</span></a>
+<a name="16282"><span class="lineNum">   16282 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm1] = -sn;</span></a>
+<a name="16283"><span class="lineNum">   16283 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm12] = oldcs;</span></a>
+<a name="16284"><span class="lineNum">   16284 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm13] = -oldsn;</span></a>
+<a name="16285"><span class="lineNum">   16285 </span>            :             }</a>
+<a name="16286"><span class="lineNum">   16286 </span><span class="lineNoCov">          0 :             h__ = d__[ll] * cs;</span></a>
+<a name="16287"><span class="lineNum">   16287 </span><span class="lineNoCov">          0 :             d__[ll] = h__ * oldcs;</span></a>
+<a name="16288"><span class="lineNum">   16288 </span><span class="lineNoCov">          0 :             e[ll] = h__ * oldsn;</span></a>
+<a name="16289"><span class="lineNum">   16289 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="16290"><span class="lineNum">   16290 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16291"><span class="lineNum">   16291 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncvt, &amp;work[nm12 + 1], &amp;work[</span></a>
+<a name="16292"><span class="lineNum">   16292 </span><span class="lineNoCov">          0 :                         nm13 + 1], &amp;vt[ll + vt_dim1], ldvt);</span></a>
+<a name="16293"><span class="lineNum">   16293 </span>            :             }</a>
+<a name="16294"><span class="lineNum">   16294 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="16295"><span class="lineNum">   16295 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16296"><span class="lineNum">   16296 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, nru, &amp;i__1, &amp;work[1], &amp;work[*n], &amp;u[ll *</span></a>
+<a name="16297"><span class="lineNum">   16297 </span><span class="lineNoCov">          0 :                          u_dim1 + 1], ldu);</span></a>
+<a name="16298"><span class="lineNum">   16298 </span>            :             }</a>
+<a name="16299"><span class="lineNum">   16299 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="16300"><span class="lineNum">   16300 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16301"><span class="lineNum">   16301 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncc, &amp;work[1], &amp;work[*n], &amp;c__[</span></a>
+<a name="16302"><span class="lineNum">   16302 </span><span class="lineNoCov">          0 :                         ll + c_dim1], ldc);</span></a>
+<a name="16303"><span class="lineNum">   16303 </span>            :             }</a>
+<a name="16304"><span class="lineNum">   16304 </span><span class="lineNoCov">          0 :             if ((r__1 = e[ll], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="16305"><span class="lineNum">   16305 </span><span class="lineNoCov">          0 :                 e[ll] = 0.f;</span></a>
+<a name="16306"><span class="lineNum">   16306 </span>            :             }</a>
+<a name="16307"><span class="lineNum">   16307 </span>            :         }</a>
+<a name="16308"><span class="lineNum">   16308 </span>            :     } else {</a>
+<a name="16309"><span class="lineNum">   16309 </span>            : </a>
+<a name="16310"><span class="lineNum">   16310 </span><span class="lineNoCov">          0 :         if (idir == 1) {</span></a>
+<a name="16311"><span class="lineNum">   16311 </span><span class="lineNoCov">          0 :             f = ((r__1 = d__[ll], std::abs(r__1)) - shift) * ( ((d__[ll] &gt; 0) ? c_b49 : -c_b49) + shift / d__[ll]);</span></a>
+<a name="16312"><span class="lineNum">   16312 </span><span class="lineNoCov">          0 :             g = e[ll];</span></a>
+<a name="16313"><span class="lineNum">   16313 </span><span class="lineNoCov">          0 :             i__1 = m - 1;</span></a>
+<a name="16314"><span class="lineNum">   16314 </span><span class="lineNoCov">          0 :             for (i__ = ll; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16315"><span class="lineNum">   16315 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;f, &amp;g, &amp;cosr, &amp;sinr, &amp;r__);</span></a>
+<a name="16316"><span class="lineNum">   16316 </span><span class="lineNoCov">          0 :                 if (i__ &gt; ll) {</span></a>
+<a name="16317"><span class="lineNum">   16317 </span><span class="lineNoCov">          0 :                     e[i__ - 1] = r__;</span></a>
+<a name="16318"><span class="lineNum">   16318 </span>            :                 }</a>
+<a name="16319"><span class="lineNum">   16319 </span><span class="lineNoCov">          0 :                 f = cosr * d__[i__] + sinr * e[i__];</span></a>
+<a name="16320"><span class="lineNum">   16320 </span><span class="lineNoCov">          0 :                 e[i__] = cosr * e[i__] - sinr * d__[i__];</span></a>
+<a name="16321"><span class="lineNum">   16321 </span><span class="lineNoCov">          0 :                 g = sinr * d__[i__ + 1];</span></a>
+<a name="16322"><span class="lineNum">   16322 </span><span class="lineNoCov">          0 :                 d__[i__ + 1] = cosr * d__[i__ + 1];</span></a>
+<a name="16323"><span class="lineNum">   16323 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;f, &amp;g, &amp;cosl, &amp;sinl, &amp;r__);</span></a>
+<a name="16324"><span class="lineNum">   16324 </span><span class="lineNoCov">          0 :                 d__[i__] = r__;</span></a>
+<a name="16325"><span class="lineNum">   16325 </span><span class="lineNoCov">          0 :                 f = cosl * e[i__] + sinl * d__[i__ + 1];</span></a>
+<a name="16326"><span class="lineNum">   16326 </span><span class="lineNoCov">          0 :                 d__[i__ + 1] = cosl * d__[i__ + 1] - sinl * e[i__];</span></a>
+<a name="16327"><span class="lineNum">   16327 </span><span class="lineNoCov">          0 :                 if (i__ &lt; m - 1) {</span></a>
+<a name="16328"><span class="lineNum">   16328 </span><span class="lineNoCov">          0 :                     g = sinl * e[i__ + 1];</span></a>
+<a name="16329"><span class="lineNum">   16329 </span><span class="lineNoCov">          0 :                     e[i__ + 1] = cosl * e[i__ + 1];</span></a>
+<a name="16330"><span class="lineNum">   16330 </span>            :                 }</a>
+<a name="16331"><span class="lineNum">   16331 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1] = cosr;</span></a>
+<a name="16332"><span class="lineNum">   16332 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1 + nm1] = sinr;</span></a>
+<a name="16333"><span class="lineNum">   16333 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1 + nm12] = cosl;</span></a>
+<a name="16334"><span class="lineNum">   16334 </span><span class="lineNoCov">          0 :                 work[i__ - ll + 1 + nm13] = sinl;</span></a>
+<a name="16335"><span class="lineNum">   16335 </span>            :             }</a>
+<a name="16336"><span class="lineNum">   16336 </span><span class="lineNoCov">          0 :             e[m - 1] = f;</span></a>
+<a name="16337"><span class="lineNum">   16337 </span>            : </a>
+<a name="16338"><span class="lineNum">   16338 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="16339"><span class="lineNum">   16339 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16340"><span class="lineNum">   16340 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncvt, &amp;work[1], &amp;work[*n], &amp;vt[</span></a>
+<a name="16341"><span class="lineNum">   16341 </span><span class="lineNoCov">          0 :                         ll + vt_dim1], ldvt);</span></a>
+<a name="16342"><span class="lineNum">   16342 </span>            :             }</a>
+<a name="16343"><span class="lineNum">   16343 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="16344"><span class="lineNum">   16344 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16345"><span class="lineNum">   16345 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, &amp;i__1, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="16346"><span class="lineNum">   16346 </span><span class="lineNoCov">          0 :                         + 1], &amp;u[ll * u_dim1 + 1], ldu);</span></a>
+<a name="16347"><span class="lineNum">   16347 </span>            :             }</a>
+<a name="16348"><span class="lineNum">   16348 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="16349"><span class="lineNum">   16349 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16350"><span class="lineNum">   16350 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;i__1, ncc, &amp;work[nm12 + 1], &amp;work[nm13 </span></a>
+<a name="16351"><span class="lineNum">   16351 </span><span class="lineNoCov">          0 :                         + 1], &amp;c__[ll + c_dim1], ldc);</span></a>
+<a name="16352"><span class="lineNum">   16352 </span>            :             }</a>
+<a name="16353"><span class="lineNum">   16353 </span><span class="lineNoCov">          0 :             if ((r__1 = e[m - 1], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="16354"><span class="lineNum">   16354 </span><span class="lineNoCov">          0 :                 e[m - 1] = 0.f;</span></a>
+<a name="16355"><span class="lineNum">   16355 </span>            :             }</a>
+<a name="16356"><span class="lineNum">   16356 </span>            :         } else {</a>
+<a name="16357"><span class="lineNum">   16357 </span>            : </a>
+<a name="16358"><span class="lineNum">   16358 </span><span class="lineNoCov">          0 :             f = ((r__1 = d__[m], std::abs(r__1)) - shift) * ( ((d__[m] &gt; 0) ? c_b49 : -c_b49) + shift / d__[m]);</span></a>
+<a name="16359"><span class="lineNum">   16359 </span><span class="lineNoCov">          0 :             g = e[m - 1];</span></a>
+<a name="16360"><span class="lineNum">   16360 </span><span class="lineNoCov">          0 :             i__1 = ll + 1;</span></a>
+<a name="16361"><span class="lineNum">   16361 </span><span class="lineNoCov">          0 :             for (i__ = m; i__ &gt;= i__1; --i__) {</span></a>
+<a name="16362"><span class="lineNum">   16362 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;f, &amp;g, &amp;cosr, &amp;sinr, &amp;r__);</span></a>
+<a name="16363"><span class="lineNum">   16363 </span><span class="lineNoCov">          0 :                 if (i__ &lt; m) {</span></a>
+<a name="16364"><span class="lineNum">   16364 </span><span class="lineNoCov">          0 :                     e[i__] = r__;</span></a>
+<a name="16365"><span class="lineNum">   16365 </span>            :                 }</a>
+<a name="16366"><span class="lineNum">   16366 </span><span class="lineNoCov">          0 :                 f = cosr * d__[i__] + sinr * e[i__ - 1];</span></a>
+<a name="16367"><span class="lineNum">   16367 </span><span class="lineNoCov">          0 :                 e[i__ - 1] = cosr * e[i__ - 1] - sinr * d__[i__];</span></a>
+<a name="16368"><span class="lineNum">   16368 </span><span class="lineNoCov">          0 :                 g = sinr * d__[i__ - 1];</span></a>
+<a name="16369"><span class="lineNum">   16369 </span><span class="lineNoCov">          0 :                 d__[i__ - 1] = cosr * d__[i__ - 1];</span></a>
+<a name="16370"><span class="lineNum">   16370 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;f, &amp;g, &amp;cosl, &amp;sinl, &amp;r__);</span></a>
+<a name="16371"><span class="lineNum">   16371 </span><span class="lineNoCov">          0 :                 d__[i__] = r__;</span></a>
+<a name="16372"><span class="lineNum">   16372 </span><span class="lineNoCov">          0 :                 f = cosl * e[i__ - 1] + sinl * d__[i__ - 1];</span></a>
+<a name="16373"><span class="lineNum">   16373 </span><span class="lineNoCov">          0 :                 d__[i__ - 1] = cosl * d__[i__ - 1] - sinl * e[i__ - 1];</span></a>
+<a name="16374"><span class="lineNum">   16374 </span><span class="lineNoCov">          0 :                 if (i__ &gt; ll + 1) {</span></a>
+<a name="16375"><span class="lineNum">   16375 </span><span class="lineNoCov">          0 :                     g = sinl * e[i__ - 2];</span></a>
+<a name="16376"><span class="lineNum">   16376 </span><span class="lineNoCov">          0 :                     e[i__ - 2] = cosl * e[i__ - 2];</span></a>
+<a name="16377"><span class="lineNum">   16377 </span>            :                 }</a>
+<a name="16378"><span class="lineNum">   16378 </span><span class="lineNoCov">          0 :                 work[i__ - ll] = cosr;</span></a>
+<a name="16379"><span class="lineNum">   16379 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm1] = -sinr;</span></a>
+<a name="16380"><span class="lineNum">   16380 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm12] = cosl;</span></a>
+<a name="16381"><span class="lineNum">   16381 </span><span class="lineNoCov">          0 :                 work[i__ - ll + nm13] = -sinl;</span></a>
+<a name="16382"><span class="lineNum">   16382 </span>            :             }</a>
+<a name="16383"><span class="lineNum">   16383 </span><span class="lineNoCov">          0 :             e[ll] = f;</span></a>
+<a name="16384"><span class="lineNum">   16384 </span>            : </a>
+<a name="16385"><span class="lineNum">   16385 </span><span class="lineNoCov">          0 :             if ((r__1 = e[ll], std::abs(r__1)) &lt;= thresh) {</span></a>
+<a name="16386"><span class="lineNum">   16386 </span><span class="lineNoCov">          0 :                 e[ll] = 0.f;</span></a>
+<a name="16387"><span class="lineNum">   16387 </span>            :             }</a>
+<a name="16388"><span class="lineNum">   16388 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="16389"><span class="lineNum">   16389 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16390"><span class="lineNum">   16390 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncvt, &amp;work[nm12 + 1], &amp;work[</span></a>
+<a name="16391"><span class="lineNum">   16391 </span><span class="lineNoCov">          0 :                         nm13 + 1], &amp;vt[ll + vt_dim1], ldvt);</span></a>
+<a name="16392"><span class="lineNum">   16392 </span>            :             }</a>
+<a name="16393"><span class="lineNum">   16393 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="16394"><span class="lineNum">   16394 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16395"><span class="lineNum">   16395 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, nru, &amp;i__1, &amp;work[1], &amp;work[*n], &amp;u[ll *</span></a>
+<a name="16396"><span class="lineNum">   16396 </span><span class="lineNoCov">          0 :                          u_dim1 + 1], ldu);</span></a>
+<a name="16397"><span class="lineNum">   16397 </span>            :             }</a>
+<a name="16398"><span class="lineNum">   16398 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="16399"><span class="lineNum">   16399 </span><span class="lineNoCov">          0 :                 i__1 = m - ll + 1;</span></a>
+<a name="16400"><span class="lineNum">   16400 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;B&quot;, &amp;i__1, ncc, &amp;work[1], &amp;work[*n], &amp;c__[</span></a>
+<a name="16401"><span class="lineNum">   16401 </span><span class="lineNoCov">          0 :                         ll + c_dim1], ldc);</span></a>
+<a name="16402"><span class="lineNum">   16402 </span>            :             }</a>
+<a name="16403"><span class="lineNum">   16403 </span>            :         }</a>
+<a name="16404"><span class="lineNum">   16404 </span>            :     }</a>
+<a name="16405"><span class="lineNum">   16405 </span>            : </a>
+<a name="16406"><span class="lineNum">   16406 </span><span class="lineNoCov">          0 :     goto L60;</span></a>
+<a name="16407"><span class="lineNum">   16407 </span>            : </a>
+<a name="16408"><span class="lineNum">   16408 </span><span class="lineNoCov">          0 : L160:</span></a>
+<a name="16409"><span class="lineNum">   16409 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="16410"><span class="lineNum">   16410 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16411"><span class="lineNum">   16411 </span><span class="lineNoCov">          0 :         if (d__[i__] &lt; 0.f) {</span></a>
+<a name="16412"><span class="lineNum">   16412 </span><span class="lineNoCov">          0 :             d__[i__] = -d__[i__];</span></a>
+<a name="16413"><span class="lineNum">   16413 </span>            : </a>
+<a name="16414"><span class="lineNum">   16414 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="16415"><span class="lineNum">   16415 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(ncvt, &amp;c_b72, &amp;vt[i__ + vt_dim1], ldvt);</span></a>
+<a name="16416"><span class="lineNum">   16416 </span>            :             }</a>
+<a name="16417"><span class="lineNum">   16417 </span>            :         }</a>
+<a name="16418"><span class="lineNum">   16418 </span>            :     }</a>
+<a name="16419"><span class="lineNum">   16419 </span>            : </a>
+<a name="16420"><span class="lineNum">   16420 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="16421"><span class="lineNum">   16421 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16422"><span class="lineNum">   16422 </span>            : </a>
+<a name="16423"><span class="lineNum">   16423 </span>            :         isub = 1;</a>
+<a name="16424"><span class="lineNum">   16424 </span><span class="lineNoCov">          0 :         smin = d__[1];</span></a>
+<a name="16425"><span class="lineNum">   16425 </span><span class="lineNoCov">          0 :         i__2 = *n + 1 - i__;</span></a>
+<a name="16426"><span class="lineNum">   16426 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="16427"><span class="lineNum">   16427 </span><span class="lineNoCov">          0 :             if (d__[j] &lt;= smin) {</span></a>
+<a name="16428"><span class="lineNum">   16428 </span>            :                 isub = j;</a>
+<a name="16429"><span class="lineNum">   16429 </span>            :                 smin = d__[j];</a>
+<a name="16430"><span class="lineNum">   16430 </span>            :             }</a>
+<a name="16431"><span class="lineNum">   16431 </span>            :         }</a>
+<a name="16432"><span class="lineNum">   16432 </span><span class="lineNoCov">          0 :         if (isub != *n + 1 - i__) {</span></a>
+<a name="16433"><span class="lineNum">   16433 </span><span class="lineNoCov">          0 :             d__[isub] = d__[*n + 1 - i__];</span></a>
+<a name="16434"><span class="lineNum">   16434 </span><span class="lineNoCov">          0 :             d__[*n + 1 - i__] = smin;</span></a>
+<a name="16435"><span class="lineNum">   16435 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="16436"><span class="lineNum">   16436 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(ncvt, &amp;vt[isub + vt_dim1], ldvt, &amp;vt[*n + 1 - i__ + </span></a>
+<a name="16437"><span class="lineNum">   16437 </span><span class="lineNoCov">          0 :                         vt_dim1], ldvt);</span></a>
+<a name="16438"><span class="lineNum">   16438 </span>            :             }</a>
+<a name="16439"><span class="lineNum">   16439 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="16440"><span class="lineNum">   16440 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(nru, &amp;u[isub * u_dim1 + 1], &amp;c__1, &amp;u[(*n + 1 - i__) * </span></a>
+<a name="16441"><span class="lineNum">   16441 </span><span class="lineNoCov">          0 :                         u_dim1 + 1], &amp;c__1);</span></a>
+<a name="16442"><span class="lineNum">   16442 </span>            :             }</a>
+<a name="16443"><span class="lineNum">   16443 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="16444"><span class="lineNum">   16444 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(ncc, &amp;c__[isub + c_dim1], ldc, &amp;c__[*n + 1 - i__ + </span></a>
+<a name="16445"><span class="lineNum">   16445 </span><span class="lineNoCov">          0 :                         c_dim1], ldc);</span></a>
+<a name="16446"><span class="lineNum">   16446 </span>            :             }</a>
+<a name="16447"><span class="lineNum">   16447 </span>            :         }</a>
+<a name="16448"><span class="lineNum">   16448 </span>            :     }</a>
+<a name="16449"><span class="lineNum">   16449 </span><span class="lineNoCov">          0 :     goto L220;</span></a>
+<a name="16450"><span class="lineNum">   16450 </span>            : </a>
+<a name="16451"><span class="lineNum">   16451 </span>            : L200:</a>
+<a name="16452"><span class="lineNum">   16452 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="16453"><span class="lineNum">   16453 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="16454"><span class="lineNum">   16454 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16455"><span class="lineNum">   16455 </span><span class="lineNoCov">          0 :         if (e[i__] != 0.f) {</span></a>
+<a name="16456"><span class="lineNum">   16456 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="16457"><span class="lineNum">   16457 </span>            :         }</a>
+<a name="16458"><span class="lineNum">   16458 </span>            :     }</a>
+<a name="16459"><span class="lineNum">   16459 </span><span class="lineNoCov">          0 : L220:</span></a>
+<a name="16460"><span class="lineNum">   16460 </span>            :     return;</a>
+<a name="16461"><span class="lineNum">   16461 </span>            : </a>
+<a name="16462"><span class="lineNum">   16462 </span>            : }</a>
+<a name="16463"><span class="lineNum">   16463 </span>            : </a>
+<a name="16464"><span class="lineNum">   16464 </span>            : </a>
+<a name="16465"><span class="lineNum">   16465 </span>            : }</a>
+<a name="16466"><span class="lineNum">   16466 </span>            : }</a>
+<a name="16467"><span class="lineNum">   16467 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16468"><span class="lineNum">   16468 </span>            : </a>
+<a name="16469"><span class="lineNum">   16469 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16470"><span class="lineNum">   16470 </span>            : namespace PLMD{</a>
+<a name="16471"><span class="lineNum">   16471 </span>            : namespace lapack{</a>
+<a name="16472"><span class="lineNum">   16472 </span>            : using namespace blas;</a>
+<a name="16473"><span class="lineNum">   16473 </span>            : void</a>
+<a name="16474"><span class="lineNum">   16474 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgebd2,SGEBD2)(int *m,</span></a>
+<a name="16475"><span class="lineNum">   16475 </span>            :         int *n,</a>
+<a name="16476"><span class="lineNum">   16476 </span>            :         float *a,</a>
+<a name="16477"><span class="lineNum">   16477 </span>            :         int *lda,</a>
+<a name="16478"><span class="lineNum">   16478 </span>            :         float *d,</a>
+<a name="16479"><span class="lineNum">   16479 </span>            :         float *e,</a>
+<a name="16480"><span class="lineNum">   16480 </span>            :         float *tauq,</a>
+<a name="16481"><span class="lineNum">   16481 </span>            :         float *taup,</a>
+<a name="16482"><span class="lineNum">   16482 </span>            :         float *work,</a>
+<a name="16483"><span class="lineNum">   16483 </span>            :         int *info)</a>
+<a name="16484"><span class="lineNum">   16484 </span>            : {</a>
+<a name="16485"><span class="lineNum">   16485 </span>            : </a>
+<a name="16486"><span class="lineNum">   16486 </span>            :   int i,i1,i2,i3;</a>
+<a name="16487"><span class="lineNum">   16487 </span>            : </a>
+<a name="16488"><span class="lineNum">   16488 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="16489"><span class="lineNum">   16489 </span>            : </a>
+<a name="16490"><span class="lineNum">   16490 </span><span class="lineNoCov">          0 :   if(*m&gt;=*n) {</span></a>
+<a name="16491"><span class="lineNum">   16491 </span>            :     /* reduce to upper bidiag. form */</a>
+<a name="16492"><span class="lineNum">   16492 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*n;i++) {</span></a>
+<a name="16493"><span class="lineNum">   16493 </span><span class="lineNoCov">          0 :       i1 = *m - i;</span></a>
+<a name="16494"><span class="lineNum">   16494 </span><span class="lineNoCov">          0 :       i2 = ( (i+1) &lt; (*m-1)) ? (i+1) : (*m-1);</span></a>
+<a name="16495"><span class="lineNum">   16495 </span><span class="lineNoCov">          0 :       i3 = 1;</span></a>
+<a name="16496"><span class="lineNum">   16496 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i1,&amp;(a[i*(*lda)+i]),&amp;(a[i*(*lda)+i2]),&amp;i3,&amp;(tauq[i]));</span></a>
+<a name="16497"><span class="lineNum">   16497 </span><span class="lineNoCov">          0 :       d[i] = a[i*(*lda)+i];</span></a>
+<a name="16498"><span class="lineNum">   16498 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = 1.0;</span></a>
+<a name="16499"><span class="lineNum">   16499 </span><span class="lineNoCov">          0 :       i2 = *n - i - 1;</span></a>
+<a name="16500"><span class="lineNum">   16500 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;L&quot;,&amp;i1,&amp;i2,&amp;(a[i*(*lda)+i]),&amp;i3,&amp;(tauq[i]),&amp;(a[(i+1)*(*lda)+i]),lda,work);</span></a>
+<a name="16501"><span class="lineNum">   16501 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = d[i];</span></a>
+<a name="16502"><span class="lineNum">   16502 </span>            : </a>
+<a name="16503"><span class="lineNum">   16503 </span><span class="lineNoCov">          0 :       if(i&lt;(*n-1)) {</span></a>
+<a name="16504"><span class="lineNum">   16504 </span>            : </a>
+<a name="16505"><span class="lineNum">   16505 </span><span class="lineNoCov">          0 :         i1 = *n - i -1;</span></a>
+<a name="16506"><span class="lineNum">   16506 </span><span class="lineNoCov">          0 :         i2 = ( (i+2) &lt; (*n-1)) ? (i+2) : (*n-1); </span></a>
+<a name="16507"><span class="lineNum">   16507 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i1,&amp;(a[(i+1)*(*lda)+i]),&amp;(a[i2*(*lda)+i]),lda,&amp;(taup[i]));</span></a>
+<a name="16508"><span class="lineNum">   16508 </span>            : </a>
+<a name="16509"><span class="lineNum">   16509 </span><span class="lineNoCov">          0 :         e[i] = a[(i+1)*(*lda)+i];</span></a>
+<a name="16510"><span class="lineNum">   16510 </span><span class="lineNoCov">          0 :         a[(i+1)*(*lda)+i] = 1.0;</span></a>
+<a name="16511"><span class="lineNum">   16511 </span>            : </a>
+<a name="16512"><span class="lineNum">   16512 </span><span class="lineNoCov">          0 :         i1 = *m - i - 1;</span></a>
+<a name="16513"><span class="lineNum">   16513 </span><span class="lineNoCov">          0 :         i2 = *n - i - 1;</span></a>
+<a name="16514"><span class="lineNum">   16514 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;R&quot;,&amp;i1,&amp;i2,&amp;(a[(i+1)*(*lda)+i]),lda,&amp;(taup[i]),&amp;(a[(i+1)*(*lda)+i+1]),lda,work);</span></a>
+<a name="16515"><span class="lineNum">   16515 </span><span class="lineNoCov">          0 :         a[(i+1)*(*lda)+i] = e[i];</span></a>
+<a name="16516"><span class="lineNum">   16516 </span>            :       } else</a>
+<a name="16517"><span class="lineNum">   16517 </span><span class="lineNoCov">          0 :         taup[i] = 0.0;</span></a>
+<a name="16518"><span class="lineNum">   16518 </span>            :     }</a>
+<a name="16519"><span class="lineNum">   16519 </span>            :   } else {</a>
+<a name="16520"><span class="lineNum">   16520 </span>            :     /* reduce to lower bidiag. form */</a>
+<a name="16521"><span class="lineNum">   16521 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*m;i++) {</span></a>
+<a name="16522"><span class="lineNum">   16522 </span><span class="lineNoCov">          0 :       i1 = *n - i;</span></a>
+<a name="16523"><span class="lineNum">   16523 </span><span class="lineNoCov">          0 :       i2 = ( (i+1) &lt; (*n-1)) ? (i+1) : (*n-1);</span></a>
+<a name="16524"><span class="lineNum">   16524 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i1,&amp;(a[i*(*lda)+i]),&amp;(a[i2*(*lda)+i]),lda,&amp;(taup[i]));</span></a>
+<a name="16525"><span class="lineNum">   16525 </span><span class="lineNoCov">          0 :       d[i] = a[i*(*lda)+i];</span></a>
+<a name="16526"><span class="lineNum">   16526 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = 1.0;</span></a>
+<a name="16527"><span class="lineNum">   16527 </span>            : </a>
+<a name="16528"><span class="lineNum">   16528 </span><span class="lineNoCov">          0 :       i2 = *m - i - 1;</span></a>
+<a name="16529"><span class="lineNum">   16529 </span><span class="lineNoCov">          0 :       i3 = ( (i+1) &lt; (*m-1)) ? (i+1) : (*m-1);</span></a>
+<a name="16530"><span class="lineNum">   16530 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;R&quot;,&amp;i2,&amp;i1,&amp;(a[i*(*lda)+i]),lda,&amp;(taup[i]),&amp;(a[(i)*(*lda)+i3]),lda,work);</span></a>
+<a name="16531"><span class="lineNum">   16531 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = d[i];</span></a>
+<a name="16532"><span class="lineNum">   16532 </span>            : </a>
+<a name="16533"><span class="lineNum">   16533 </span><span class="lineNoCov">          0 :       if(i&lt;(*m-1)) {</span></a>
+<a name="16534"><span class="lineNum">   16534 </span>            : </a>
+<a name="16535"><span class="lineNum">   16535 </span><span class="lineNoCov">          0 :         i1 = *m - i - 1;</span></a>
+<a name="16536"><span class="lineNum">   16536 </span><span class="lineNoCov">          0 :         i2 = ( (i+2) &lt; (*m-1)) ? (i+2) : (*m-1);</span></a>
+<a name="16537"><span class="lineNum">   16537 </span><span class="lineNoCov">          0 :         i3 = 1;</span></a>
+<a name="16538"><span class="lineNum">   16538 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i1,&amp;(a[(i)*(*lda)+i+1]),&amp;(a[i*(*lda)+i2]),&amp;i3,&amp;(tauq[i]));</span></a>
+<a name="16539"><span class="lineNum">   16539 </span>            : </a>
+<a name="16540"><span class="lineNum">   16540 </span><span class="lineNoCov">          0 :         e[i] = a[(i)*(*lda)+i+1];</span></a>
+<a name="16541"><span class="lineNum">   16541 </span><span class="lineNoCov">          0 :         a[(i)*(*lda)+i+1] = 1.0;</span></a>
+<a name="16542"><span class="lineNum">   16542 </span>            : </a>
+<a name="16543"><span class="lineNum">   16543 </span><span class="lineNoCov">          0 :         i1 = *m - i - 1;</span></a>
+<a name="16544"><span class="lineNum">   16544 </span><span class="lineNoCov">          0 :         i2 = *n - i - 1;</span></a>
+<a name="16545"><span class="lineNum">   16545 </span><span class="lineNoCov">          0 :         i3 = 1;</span></a>
+<a name="16546"><span class="lineNum">   16546 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;L&quot;,&amp;i1,&amp;i2,&amp;(a[(i)*(*lda)+i+1]),&amp;i3,&amp;(tauq[i]),&amp;(a[(i+1)*(*lda)+i+1]),lda,work);</span></a>
+<a name="16547"><span class="lineNum">   16547 </span><span class="lineNoCov">          0 :         a[(i)*(*lda)+i+1] = e[i];</span></a>
+<a name="16548"><span class="lineNum">   16548 </span>            :       } else</a>
+<a name="16549"><span class="lineNum">   16549 </span><span class="lineNoCov">          0 :         tauq[i] = 0.0;</span></a>
+<a name="16550"><span class="lineNum">   16550 </span>            :     }</a>
+<a name="16551"><span class="lineNum">   16551 </span>            :   }</a>
+<a name="16552"><span class="lineNum">   16552 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="16553"><span class="lineNum">   16553 </span>            : }</a>
+<a name="16554"><span class="lineNum">   16554 </span>            : }</a>
+<a name="16555"><span class="lineNum">   16555 </span>            : }</a>
+<a name="16556"><span class="lineNum">   16556 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16557"><span class="lineNum">   16557 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16558"><span class="lineNum">   16558 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="16559"><span class="lineNum">   16559 </span>            : </a>
+<a name="16560"><span class="lineNum">   16560 </span>            : </a>
+<a name="16561"><span class="lineNum">   16561 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16562"><span class="lineNum">   16562 </span>            : namespace PLMD{</a>
+<a name="16563"><span class="lineNum">   16563 </span>            : namespace lapack{</a>
+<a name="16564"><span class="lineNum">   16564 </span>            : using namespace blas;</a>
+<a name="16565"><span class="lineNum">   16565 </span>            : void</a>
+<a name="16566"><span class="lineNum">   16566 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(int *m, </span></a>
+<a name="16567"><span class="lineNum">   16567 </span>            :         int *n, </a>
+<a name="16568"><span class="lineNum">   16568 </span>            :         float *a, </a>
+<a name="16569"><span class="lineNum">   16569 </span>            :         int *lda, </a>
+<a name="16570"><span class="lineNum">   16570 </span>            :         float *d__, </a>
+<a name="16571"><span class="lineNum">   16571 </span>            :         float *e,</a>
+<a name="16572"><span class="lineNum">   16572 </span>            :         float *tauq, </a>
+<a name="16573"><span class="lineNum">   16573 </span>            :         float *taup,</a>
+<a name="16574"><span class="lineNum">   16574 </span>            :         float *work, </a>
+<a name="16575"><span class="lineNum">   16575 </span>            :         int *lwork,</a>
+<a name="16576"><span class="lineNum">   16576 </span>            :         int *info)</a>
+<a name="16577"><span class="lineNum">   16577 </span>            : {</a>
+<a name="16578"><span class="lineNum">   16578 </span>            :     /* System generated locals */</a>
+<a name="16579"><span class="lineNum">   16579 </span>            :     int a_dim1, a_offset, i_1, i_2, i_3, i_4;</a>
+<a name="16580"><span class="lineNum">   16580 </span>            : </a>
+<a name="16581"><span class="lineNum">   16581 </span>            :     /* Local variables */</a>
+<a name="16582"><span class="lineNum">   16582 </span>            :     int i_, j, nx,nb;</a>
+<a name="16583"><span class="lineNum">   16583 </span>            :     float ws;</a>
+<a name="16584"><span class="lineNum">   16584 </span>            :     int nbmin, iinfo, minmn;</a>
+<a name="16585"><span class="lineNum">   16585 </span>            :     int ldwrkx, ldwrky;</a>
+<a name="16586"><span class="lineNum">   16586 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="16587"><span class="lineNum">   16587 </span><span class="lineNoCov">          0 :     float minusone = -1.0;</span></a>
+<a name="16588"><span class="lineNum">   16588 </span>            : </a>
+<a name="16589"><span class="lineNum">   16589 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="16590"><span class="lineNum">   16590 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="16591"><span class="lineNum">   16591 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="16592"><span class="lineNum">   16592 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="16593"><span class="lineNum">   16593 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="16594"><span class="lineNum">   16594 </span><span class="lineNoCov">          0 :     --tauq;</span></a>
+<a name="16595"><span class="lineNum">   16595 </span><span class="lineNoCov">          0 :     --taup;</span></a>
+<a name="16596"><span class="lineNum">   16596 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="16597"><span class="lineNum">   16597 </span>            : </a>
+<a name="16598"><span class="lineNum">   16598 </span><span class="lineNoCov">          0 :     nb = DGEBRD_BLOCKSIZE;</span></a>
+<a name="16599"><span class="lineNum">   16599 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="16600"><span class="lineNum">   16600 </span><span class="lineNoCov">          0 :     if (*lwork==-1) {</span></a>
+<a name="16601"><span class="lineNum">   16601 </span><span class="lineNoCov">          0 :       work[1] = (float) ( (*m + *n) * nb);</span></a>
+<a name="16602"><span class="lineNum">   16602 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="16603"><span class="lineNum">   16603 </span>            :     }</a>
+<a name="16604"><span class="lineNum">   16604 </span><span class="lineNoCov">          0 :     minmn = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="16605"><span class="lineNum">   16605 </span><span class="lineNoCov">          0 :     if (minmn == 0) {</span></a>
+<a name="16606"><span class="lineNum">   16606 </span><span class="lineNoCov">          0 :       work[1] = 1.;</span></a>
+<a name="16607"><span class="lineNum">   16607 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="16608"><span class="lineNum">   16608 </span>            :     }</a>
+<a name="16609"><span class="lineNum">   16609 </span>            : </a>
+<a name="16610"><span class="lineNum">   16610 </span><span class="lineNoCov">          0 :     ws = (*m &gt; *n) ? *m : *n;</span></a>
+<a name="16611"><span class="lineNum">   16611 </span><span class="lineNoCov">          0 :     ldwrkx = *m;</span></a>
+<a name="16612"><span class="lineNum">   16612 </span><span class="lineNoCov">          0 :     ldwrky = *n;</span></a>
+<a name="16613"><span class="lineNum">   16613 </span>            : </a>
+<a name="16614"><span class="lineNum">   16614 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; minmn) {</span></a>
+<a name="16615"><span class="lineNum">   16615 </span>            :         nx = DGEBRD_CROSSOVER;</a>
+<a name="16616"><span class="lineNum">   16616 </span><span class="lineNoCov">          0 :         if (nx &lt; minmn) {</span></a>
+<a name="16617"><span class="lineNum">   16617 </span><span class="lineNoCov">          0 :             ws = (float) ((*m + *n) * nb);</span></a>
+<a name="16618"><span class="lineNum">   16618 </span><span class="lineNoCov">          0 :             if ((float) (*lwork) &lt; ws) {</span></a>
+<a name="16619"><span class="lineNum">   16619 </span>            :               nbmin = DGEBRD_MINBLOCKSIZE;</a>
+<a name="16620"><span class="lineNum">   16620 </span><span class="lineNoCov">          0 :                 if (*lwork &gt;= (*m + *n) * nbmin) {</span></a>
+<a name="16621"><span class="lineNum">   16621 </span><span class="lineNoCov">          0 :                     nb = *lwork / (*m + *n);</span></a>
+<a name="16622"><span class="lineNum">   16622 </span>            :                 } else {</a>
+<a name="16623"><span class="lineNum">   16623 </span><span class="lineNoCov">          0 :                     nb = 1;</span></a>
+<a name="16624"><span class="lineNum">   16624 </span>            :                     nx = minmn;</a>
+<a name="16625"><span class="lineNum">   16625 </span>            :                 }</a>
+<a name="16626"><span class="lineNum">   16626 </span>            :             }</a>
+<a name="16627"><span class="lineNum">   16627 </span>            :         }</a>
+<a name="16628"><span class="lineNum">   16628 </span>            :     } else {</a>
+<a name="16629"><span class="lineNum">   16629 </span>            :         nx = minmn;</a>
+<a name="16630"><span class="lineNum">   16630 </span>            :     }</a>
+<a name="16631"><span class="lineNum">   16631 </span>            : </a>
+<a name="16632"><span class="lineNum">   16632 </span><span class="lineNoCov">          0 :     i_1 = minmn - nx;</span></a>
+<a name="16633"><span class="lineNum">   16633 </span><span class="lineNoCov">          0 :     i_2 = nb;</span></a>
+<a name="16634"><span class="lineNum">   16634 </span><span class="lineNoCov">          0 :     for (i_ = 1; i_2 &lt; 0 ? i_ &gt;= i_1 : i_ &lt;= i_1; i_ += i_2) {</span></a>
+<a name="16635"><span class="lineNum">   16635 </span>            : </a>
+<a name="16636"><span class="lineNum">   16636 </span><span class="lineNoCov">          0 :         i_3 = *m - i_ + 1;</span></a>
+<a name="16637"><span class="lineNum">   16637 </span><span class="lineNoCov">          0 :         i_4 = *n - i_ + 1;</span></a>
+<a name="16638"><span class="lineNum">   16638 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slabrd,SLABRD)(&amp;i_3, &amp;i_4, &amp;nb, &amp;a[i_ + i_ * a_dim1], lda, &amp;d__[i_], </span></a>
+<a name="16639"><span class="lineNum">   16639 </span><span class="lineNoCov">          0 :                 &amp;e[i_], &amp;tauq[i_], &amp;taup[i_], &amp;work[1], &amp;ldwrkx, </span></a>
+<a name="16640"><span class="lineNum">   16640 </span><span class="lineNoCov">          0 :                 &amp;work[ldwrkx * nb + 1], &amp;ldwrky);</span></a>
+<a name="16641"><span class="lineNum">   16641 </span>            : </a>
+<a name="16642"><span class="lineNum">   16642 </span><span class="lineNoCov">          0 :         i_3 = *m - i_ - nb + 1;</span></a>
+<a name="16643"><span class="lineNum">   16643 </span><span class="lineNoCov">          0 :         i_4 = *n - i_ - nb + 1;</span></a>
+<a name="16644"><span class="lineNum">   16644 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;T&quot;, &amp;i_3, &amp;i_4, &amp;nb, &amp;minusone, </span></a>
+<a name="16645"><span class="lineNum">   16645 </span><span class="lineNoCov">          0 :                &amp;a[i_ + nb + i_ * a_dim1], lda, &amp;work[ldwrkx * nb + nb + 1],</span></a>
+<a name="16646"><span class="lineNum">   16646 </span><span class="lineNoCov">          0 :                &amp;ldwrky, &amp;one, &amp;a[i_ + nb + (i_ + nb) * a_dim1], lda);</span></a>
+<a name="16647"><span class="lineNum">   16647 </span><span class="lineNoCov">          0 :         i_3 = *m - i_ - nb + 1;</span></a>
+<a name="16648"><span class="lineNum">   16648 </span><span class="lineNoCov">          0 :         i_4 = *n - i_ - nb + 1;</span></a>
+<a name="16649"><span class="lineNum">   16649 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, &amp;i_3, &amp;i_4, &amp;nb, &amp;minusone, &amp;work[nb + 1], &amp;ldwrkx,</span></a>
+<a name="16650"><span class="lineNum">   16650 </span><span class="lineNoCov">          0 :                &amp;a[i_ + (i_ + nb) * a_dim1], lda, &amp;one, </span></a>
+<a name="16651"><span class="lineNum">   16651 </span><span class="lineNoCov">          0 :                &amp;a[i_ + nb + (i_ + nb) * a_dim1], lda);</span></a>
+<a name="16652"><span class="lineNum">   16652 </span>            : </a>
+<a name="16653"><span class="lineNum">   16653 </span><span class="lineNoCov">          0 :         if (*m &gt;= *n) {</span></a>
+<a name="16654"><span class="lineNum">   16654 </span><span class="lineNoCov">          0 :             i_3 = i_ + nb - 1;</span></a>
+<a name="16655"><span class="lineNum">   16655 </span><span class="lineNoCov">          0 :             for (j = i_; j &lt;= i_3; ++j) {</span></a>
+<a name="16656"><span class="lineNum">   16656 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = d__[j];</span></a>
+<a name="16657"><span class="lineNum">   16657 </span><span class="lineNoCov">          0 :                 a[j + (j + 1) * a_dim1] = e[j];</span></a>
+<a name="16658"><span class="lineNum">   16658 </span>            :             }</a>
+<a name="16659"><span class="lineNum">   16659 </span>            :         } else {</a>
+<a name="16660"><span class="lineNum">   16660 </span><span class="lineNoCov">          0 :             i_3 = i_ + nb - 1;</span></a>
+<a name="16661"><span class="lineNum">   16661 </span><span class="lineNoCov">          0 :             for (j = i_; j &lt;= i_3; ++j) {</span></a>
+<a name="16662"><span class="lineNum">   16662 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = d__[j];</span></a>
+<a name="16663"><span class="lineNum">   16663 </span><span class="lineNoCov">          0 :                 a[j + 1 + j * a_dim1] = e[j];</span></a>
+<a name="16664"><span class="lineNum">   16664 </span>            :             }</a>
+<a name="16665"><span class="lineNum">   16665 </span>            :         }</a>
+<a name="16666"><span class="lineNum">   16666 </span>            :     }</a>
+<a name="16667"><span class="lineNum">   16667 </span>            : </a>
+<a name="16668"><span class="lineNum">   16668 </span><span class="lineNoCov">          0 :     i_2 = *m - i_ + 1;</span></a>
+<a name="16669"><span class="lineNum">   16669 </span><span class="lineNoCov">          0 :     i_1 = *n - i_ + 1;</span></a>
+<a name="16670"><span class="lineNum">   16670 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sgebd2,SGEBD2)(&amp;i_2, &amp;i_1, &amp;a[i_ + i_ * a_dim1], lda, &amp;d__[i_], &amp;e[i_], &amp;</span></a>
+<a name="16671"><span class="lineNum">   16671 </span><span class="lineNoCov">          0 :             tauq[i_], &amp;taup[i_], &amp;work[1], &amp;iinfo);</span></a>
+<a name="16672"><span class="lineNum">   16672 </span><span class="lineNoCov">          0 :     work[1] = ws;</span></a>
+<a name="16673"><span class="lineNum">   16673 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="16674"><span class="lineNum">   16674 </span>            : </a>
+<a name="16675"><span class="lineNum">   16675 </span>            : }</a>
+<a name="16676"><span class="lineNum">   16676 </span>            : }</a>
+<a name="16677"><span class="lineNum">   16677 </span>            : }</a>
+<a name="16678"><span class="lineNum">   16678 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16679"><span class="lineNum">   16679 </span>            : </a>
+<a name="16680"><span class="lineNum">   16680 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16681"><span class="lineNum">   16681 </span>            : namespace PLMD{</a>
+<a name="16682"><span class="lineNum">   16682 </span>            : namespace lapack{</a>
+<a name="16683"><span class="lineNum">   16683 </span>            : using namespace blas;</a>
+<a name="16684"><span class="lineNum">   16684 </span>            : void </a>
+<a name="16685"><span class="lineNum">   16685 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgelq2,SGELQ2)(int *m, </span></a>
+<a name="16686"><span class="lineNum">   16686 </span>            :                         int *n, </a>
+<a name="16687"><span class="lineNum">   16687 </span>            :                         float *a,</a>
+<a name="16688"><span class="lineNum">   16688 </span>            :                         int *lda, </a>
+<a name="16689"><span class="lineNum">   16689 </span>            :                         float *tau, </a>
+<a name="16690"><span class="lineNum">   16690 </span>            :                         float *work, </a>
+<a name="16691"><span class="lineNum">   16691 </span>            :                         int *info)</a>
+<a name="16692"><span class="lineNum">   16692 </span>            : {</a>
+<a name="16693"><span class="lineNum">   16693 </span>            :     /* System generated locals */</a>
+<a name="16694"><span class="lineNum">   16694 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3, i__4;</a>
+<a name="16695"><span class="lineNum">   16695 </span>            : </a>
+<a name="16696"><span class="lineNum">   16696 </span>            :     /* Local variables */</a>
+<a name="16697"><span class="lineNum">   16697 </span>            :     int i__, k;</a>
+<a name="16698"><span class="lineNum">   16698 </span>            :     float aii;</a>
+<a name="16699"><span class="lineNum">   16699 </span>            : </a>
+<a name="16700"><span class="lineNum">   16700 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="16701"><span class="lineNum">   16701 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="16702"><span class="lineNum">   16702 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="16703"><span class="lineNum">   16703 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="16704"><span class="lineNum">   16704 </span>            :     --work;</a>
+<a name="16705"><span class="lineNum">   16705 </span>            : </a>
+<a name="16706"><span class="lineNum">   16706 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="16707"><span class="lineNum">   16707 </span>            :     </a>
+<a name="16708"><span class="lineNum">   16708 </span><span class="lineNoCov">          0 :     i__4 = (*m &gt; 1) ? *m : 1;</span></a>
+<a name="16709"><span class="lineNum">   16709 </span>            :     </a>
+<a name="16710"><span class="lineNum">   16710 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="16711"><span class="lineNum">   16711 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="16712"><span class="lineNum">   16712 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="16713"><span class="lineNum">   16713 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="16714"><span class="lineNum">   16714 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; i__4) {</span></a>
+<a name="16715"><span class="lineNum">   16715 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="16716"><span class="lineNum">   16716 </span>            :     }</a>
+<a name="16717"><span class="lineNum">   16717 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="16718"><span class="lineNum">   16718 </span>            :         return;</a>
+<a name="16719"><span class="lineNum">   16719 </span>            :     }</a>
+<a name="16720"><span class="lineNum">   16720 </span>            : </a>
+<a name="16721"><span class="lineNum">   16721 </span>            :     </a>
+<a name="16722"><span class="lineNum">   16722 </span><span class="lineNoCov">          0 :     k = (*m &lt; *n ) ? *m : *n;</span></a>
+<a name="16723"><span class="lineNum">   16723 </span>            :     i__1 = k;</a>
+<a name="16724"><span class="lineNum">   16724 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="16725"><span class="lineNum">   16725 </span><span class="lineNoCov">          0 :         i__2 = *n - i__ + 1;</span></a>
+<a name="16726"><span class="lineNum">   16726 </span><span class="lineNoCov">          0 :         i__3 = i__ + 1;</span></a>
+<a name="16727"><span class="lineNum">   16727 </span>            :     i__4 = (i__3 &lt; *n) ? i__3 : *n;</a>
+<a name="16728"><span class="lineNum">   16728 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i__2, &amp;a[i__ + i__ * a_dim1], &amp;a[i__ + i__4 * a_dim1],</span></a>
+<a name="16729"><span class="lineNum">   16729 </span><span class="lineNoCov">          0 :             lda, &amp;tau[i__]);</span></a>
+<a name="16730"><span class="lineNum">   16730 </span><span class="lineNoCov">          0 :         if (i__ &lt; *m) {</span></a>
+<a name="16731"><span class="lineNum">   16731 </span><span class="lineNoCov">          0 :             aii = a[i__ + i__ * a_dim1];</span></a>
+<a name="16732"><span class="lineNum">   16732 </span><span class="lineNoCov">          0 :             a[i__ + i__ * a_dim1] = 1.f;</span></a>
+<a name="16733"><span class="lineNum">   16733 </span><span class="lineNoCov">          0 :             i__2 = *m - i__;</span></a>
+<a name="16734"><span class="lineNum">   16734 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="16735"><span class="lineNum">   16735 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;R&quot;, &amp;i__2, &amp;i__3, &amp;a[i__ + i__ * a_dim1], lda, </span></a>
+<a name="16736"><span class="lineNum">   16736 </span><span class="lineNoCov">          0 :                &amp;tau[i__], &amp;a[i__ + 1 + i__ * a_dim1], lda, &amp;work[1]);</span></a>
+<a name="16737"><span class="lineNum">   16737 </span><span class="lineNoCov">          0 :             a[i__ + i__ * a_dim1] = aii;</span></a>
+<a name="16738"><span class="lineNum">   16738 </span>            :         }</a>
+<a name="16739"><span class="lineNum">   16739 </span>            :     }</a>
+<a name="16740"><span class="lineNum">   16740 </span>            :     return;</a>
+<a name="16741"><span class="lineNum">   16741 </span>            : }</a>
+<a name="16742"><span class="lineNum">   16742 </span>            : </a>
+<a name="16743"><span class="lineNum">   16743 </span>            : </a>
+<a name="16744"><span class="lineNum">   16744 </span>            : }</a>
+<a name="16745"><span class="lineNum">   16745 </span>            : }</a>
+<a name="16746"><span class="lineNum">   16746 </span>            : #include &lt;cmath&gt;</a>
+<a name="16747"><span class="lineNum">   16747 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16748"><span class="lineNum">   16748 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="16749"><span class="lineNum">   16749 </span>            : </a>
+<a name="16750"><span class="lineNum">   16750 </span>            : </a>
+<a name="16751"><span class="lineNum">   16751 </span>            : </a>
+<a name="16752"><span class="lineNum">   16752 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16753"><span class="lineNum">   16753 </span>            : namespace PLMD{</a>
+<a name="16754"><span class="lineNum">   16754 </span>            : namespace lapack{</a>
+<a name="16755"><span class="lineNum">   16755 </span>            : using namespace blas;</a>
+<a name="16756"><span class="lineNum">   16756 </span>            : void</a>
+<a name="16757"><span class="lineNum">   16757 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgelqf,SGELQF)(int *m,</span></a>
+<a name="16758"><span class="lineNum">   16758 </span>            :         int *n, </a>
+<a name="16759"><span class="lineNum">   16759 </span>            :         float *a, </a>
+<a name="16760"><span class="lineNum">   16760 </span>            :         int *lda, </a>
+<a name="16761"><span class="lineNum">   16761 </span>            :         float *tau,</a>
+<a name="16762"><span class="lineNum">   16762 </span>            :         float *work, </a>
+<a name="16763"><span class="lineNum">   16763 </span>            :         int *lwork, </a>
+<a name="16764"><span class="lineNum">   16764 </span>            :         int *info)</a>
+<a name="16765"><span class="lineNum">   16765 </span>            : {</a>
+<a name="16766"><span class="lineNum">   16766 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3, i__4;</a>
+<a name="16767"><span class="lineNum">   16767 </span>            : </a>
+<a name="16768"><span class="lineNum">   16768 </span>            :     int i__, k, ib, nb, nx, iws, nbmin, iinfo;</a>
+<a name="16769"><span class="lineNum">   16769 </span>            :     int ldwork, lwkopt;</a>
+<a name="16770"><span class="lineNum">   16770 </span>            : </a>
+<a name="16771"><span class="lineNum">   16771 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="16772"><span class="lineNum">   16772 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="16773"><span class="lineNum">   16773 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="16774"><span class="lineNum">   16774 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="16775"><span class="lineNum">   16775 </span>            :     --work;</a>
+<a name="16776"><span class="lineNum">   16776 </span>            : </a>
+<a name="16777"><span class="lineNum">   16777 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="16778"><span class="lineNum">   16778 </span>            :     nb = DGELQF_BLOCKSIZE;</a>
+<a name="16779"><span class="lineNum">   16779 </span><span class="lineNoCov">          0 :     lwkopt = *m * nb;</span></a>
+<a name="16780"><span class="lineNum">   16780 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="16781"><span class="lineNum">   16781 </span>            : </a>
+<a name="16782"><span class="lineNum">   16782 </span><span class="lineNoCov">          0 :     if (*lwork==-1) {</span></a>
+<a name="16783"><span class="lineNum">   16783 </span>            :         return;</a>
+<a name="16784"><span class="lineNum">   16784 </span>            :     }</a>
+<a name="16785"><span class="lineNum">   16785 </span>            : </a>
+<a name="16786"><span class="lineNum">   16786 </span><span class="lineNoCov">          0 :     k =(*m &lt; *n) ? *m : *n;</span></a>
+<a name="16787"><span class="lineNum">   16787 </span><span class="lineNoCov">          0 :     if (k == 0) {</span></a>
+<a name="16788"><span class="lineNum">   16788 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="16789"><span class="lineNum">   16789 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="16790"><span class="lineNum">   16790 </span>            :     }</a>
+<a name="16791"><span class="lineNum">   16791 </span>            : </a>
+<a name="16792"><span class="lineNum">   16792 </span>            :     nbmin = 2;</a>
+<a name="16793"><span class="lineNum">   16793 </span>            :     nx = 0;</a>
+<a name="16794"><span class="lineNum">   16794 </span>            :     iws = *m;</a>
+<a name="16795"><span class="lineNum">   16795 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; k) {</span></a>
+<a name="16796"><span class="lineNum">   16796 </span>            :         nx = DGELQF_CROSSOVER;</a>
+<a name="16797"><span class="lineNum">   16797 </span><span class="lineNoCov">          0 :         if (nx &lt; k) {</span></a>
+<a name="16798"><span class="lineNum">   16798 </span><span class="lineNoCov">          0 :             ldwork = *m;</span></a>
+<a name="16799"><span class="lineNum">   16799 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="16800"><span class="lineNum">   16800 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="16801"><span class="lineNum">   16801 </span>            : </a>
+<a name="16802"><span class="lineNum">   16802 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="16803"><span class="lineNum">   16803 </span>            :                 nbmin = DGELQF_MINBLOCKSIZE;</a>
+<a name="16804"><span class="lineNum">   16804 </span>            :             }</a>
+<a name="16805"><span class="lineNum">   16805 </span>            :         }</a>
+<a name="16806"><span class="lineNum">   16806 </span>            :     }</a>
+<a name="16807"><span class="lineNum">   16807 </span>            : </a>
+<a name="16808"><span class="lineNum">   16808 </span><span class="lineNoCov">          0 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; k &amp;&amp; nx &lt; k) {</span></a>
+<a name="16809"><span class="lineNum">   16809 </span>            : </a>
+<a name="16810"><span class="lineNum">   16810 </span><span class="lineNoCov">          0 :         i__1 = k - nx;</span></a>
+<a name="16811"><span class="lineNum">   16811 </span><span class="lineNoCov">          0 :         i__2 = nb;</span></a>
+<a name="16812"><span class="lineNum">   16812 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="16813"><span class="lineNum">   16813 </span><span class="lineNoCov">          0 :             i__3 = k - i__ + 1;</span></a>
+<a name="16814"><span class="lineNum">   16814 </span><span class="lineNoCov">          0 :             ib = (i__3 &lt; nb) ? i__3 : nb;</span></a>
+<a name="16815"><span class="lineNum">   16815 </span>            : </a>
+<a name="16816"><span class="lineNum">   16816 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="16817"><span class="lineNum">   16817 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgelq2,SGELQ2)(&amp;ib, &amp;i__3, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[</span></a>
+<a name="16818"><span class="lineNum">   16818 </span>            :                     1], &amp;iinfo);</a>
+<a name="16819"><span class="lineNum">   16819 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *m) {</span></a>
+<a name="16820"><span class="lineNum">   16820 </span>            : </a>
+<a name="16821"><span class="lineNum">   16821 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="16822"><span class="lineNum">   16822 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__3, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="16823"><span class="lineNum">   16823 </span>            :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</a>
+<a name="16824"><span class="lineNum">   16824 </span>            : </a>
+<a name="16825"><span class="lineNum">   16825 </span><span class="lineNoCov">          0 :                 i__3 = *m - i__ - ib + 1;</span></a>
+<a name="16826"><span class="lineNum">   16826 </span><span class="lineNoCov">          0 :                 i__4 = *n - i__ + 1;</span></a>
+<a name="16827"><span class="lineNum">   16827 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(&quot;Right&quot;, &quot;No transpose&quot;, &quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__3, </span></a>
+<a name="16828"><span class="lineNum">   16828 </span>            :                         &amp;i__4, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[1], &amp;</a>
+<a name="16829"><span class="lineNum">   16829 </span><span class="lineNoCov">          0 :                         ldwork, &amp;a[i__ + ib + i__ * a_dim1], lda, &amp;work[ib + </span></a>
+<a name="16830"><span class="lineNum">   16830 </span><span class="lineNoCov">          0 :                         1], &amp;ldwork);</span></a>
+<a name="16831"><span class="lineNum">   16831 </span>            :             }</a>
+<a name="16832"><span class="lineNum">   16832 </span>            :         }</a>
+<a name="16833"><span class="lineNum">   16833 </span>            :     } else {</a>
+<a name="16834"><span class="lineNum">   16834 </span>            :         i__ = 1;</a>
+<a name="16835"><span class="lineNum">   16835 </span>            :     }</a>
+<a name="16836"><span class="lineNum">   16836 </span>            : </a>
+<a name="16837"><span class="lineNum">   16837 </span><span class="lineNoCov">          0 :     if (i__ &lt;= k) {</span></a>
+<a name="16838"><span class="lineNum">   16838 </span><span class="lineNoCov">          0 :         i__2 = *m - i__ + 1;</span></a>
+<a name="16839"><span class="lineNum">   16839 </span><span class="lineNoCov">          0 :         i__1 = *n - i__ + 1;</span></a>
+<a name="16840"><span class="lineNum">   16840 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgelq2,SGELQ2)(&amp;i__2, &amp;i__1, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[1]</span></a>
+<a name="16841"><span class="lineNum">   16841 </span>            :                 , &amp;iinfo);</a>
+<a name="16842"><span class="lineNum">   16842 </span>            :     }</a>
+<a name="16843"><span class="lineNum">   16843 </span>            : </a>
+<a name="16844"><span class="lineNum">   16844 </span><span class="lineNoCov">          0 :     work[1] = (float) iws;</span></a>
+<a name="16845"><span class="lineNum">   16845 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="16846"><span class="lineNum">   16846 </span>            : </a>
+<a name="16847"><span class="lineNum">   16847 </span>            : }</a>
+<a name="16848"><span class="lineNum">   16848 </span>            : }</a>
+<a name="16849"><span class="lineNum">   16849 </span>            : }</a>
+<a name="16850"><span class="lineNum">   16850 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16851"><span class="lineNum">   16851 </span>            : </a>
+<a name="16852"><span class="lineNum">   16852 </span>            : </a>
+<a name="16853"><span class="lineNum">   16853 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16854"><span class="lineNum">   16854 </span>            : namespace PLMD{</a>
+<a name="16855"><span class="lineNum">   16855 </span>            : namespace lapack{</a>
+<a name="16856"><span class="lineNum">   16856 </span>            : using namespace blas;</a>
+<a name="16857"><span class="lineNum">   16857 </span>            : void</a>
+<a name="16858"><span class="lineNum">   16858 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgeqr2,SGEQR2)(int *m,</span></a>
+<a name="16859"><span class="lineNum">   16859 </span>            :         int *n,</a>
+<a name="16860"><span class="lineNum">   16860 </span>            :         float *a,</a>
+<a name="16861"><span class="lineNum">   16861 </span>            :         int *lda,</a>
+<a name="16862"><span class="lineNum">   16862 </span>            :         float *tau,</a>
+<a name="16863"><span class="lineNum">   16863 </span>            :         float *work,</a>
+<a name="16864"><span class="lineNum">   16864 </span>            :         int *info)</a>
+<a name="16865"><span class="lineNum">   16865 </span>            : {</a>
+<a name="16866"><span class="lineNum">   16866 </span><span class="lineNoCov">          0 :   int k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="16867"><span class="lineNum">   16867 </span>            :   int i,i1,i2,i3;</a>
+<a name="16868"><span class="lineNum">   16868 </span>            :   float aii;</a>
+<a name="16869"><span class="lineNum">   16869 </span>            : </a>
+<a name="16870"><span class="lineNum">   16870 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="16871"><span class="lineNum">   16871 </span>            :   </a>
+<a name="16872"><span class="lineNum">   16872 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;k;i++) {</span></a>
+<a name="16873"><span class="lineNum">   16873 </span><span class="lineNoCov">          0 :     i1 = *m - i;</span></a>
+<a name="16874"><span class="lineNum">   16874 </span><span class="lineNoCov">          0 :     i2 = ( (i+1) &lt; (*m-1) ) ? (i+1) : (*m-1);</span></a>
+<a name="16875"><span class="lineNum">   16875 </span><span class="lineNoCov">          0 :     i3 = 1;</span></a>
+<a name="16876"><span class="lineNum">   16876 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i1,&amp;(a[i*(*lda)+i]),&amp;(a[i*(*lda)+i2]),&amp;i3,&amp;(tau[i]));</span></a>
+<a name="16877"><span class="lineNum">   16877 </span><span class="lineNoCov">          0 :     if(i&lt;(*n-1)) {</span></a>
+<a name="16878"><span class="lineNum">   16878 </span><span class="lineNoCov">          0 :       aii = a[i*(*lda)+i];</span></a>
+<a name="16879"><span class="lineNum">   16879 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = 1.0;</span></a>
+<a name="16880"><span class="lineNum">   16880 </span><span class="lineNoCov">          0 :       i2 = *n - i - 1;</span></a>
+<a name="16881"><span class="lineNum">   16881 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;L&quot;,&amp;i1,&amp;i2,&amp;(a[i*(*lda)+i]),&amp;i3,&amp;(tau[i]),</span></a>
+<a name="16882"><span class="lineNum">   16882 </span><span class="lineNoCov">          0 :              &amp;(a[(i+1)*(*lda)+i]),lda,work);</span></a>
+<a name="16883"><span class="lineNum">   16883 </span><span class="lineNoCov">          0 :       a[i*(*lda)+i] = aii;</span></a>
+<a name="16884"><span class="lineNum">   16884 </span>            :     }</a>
+<a name="16885"><span class="lineNum">   16885 </span>            :   }</a>
+<a name="16886"><span class="lineNum">   16886 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="16887"><span class="lineNum">   16887 </span>            : }</a>
+<a name="16888"><span class="lineNum">   16888 </span>            : }</a>
+<a name="16889"><span class="lineNum">   16889 </span>            : }</a>
+<a name="16890"><span class="lineNum">   16890 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16891"><span class="lineNum">   16891 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="16892"><span class="lineNum">   16892 </span>            : </a>
+<a name="16893"><span class="lineNum">   16893 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16894"><span class="lineNum">   16894 </span>            : namespace PLMD{</a>
+<a name="16895"><span class="lineNum">   16895 </span>            : namespace lapack{</a>
+<a name="16896"><span class="lineNum">   16896 </span>            : using namespace blas;</a>
+<a name="16897"><span class="lineNum">   16897 </span>            : void </a>
+<a name="16898"><span class="lineNum">   16898 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgeqrf,SGEQRF)(int *m, </span></a>
+<a name="16899"><span class="lineNum">   16899 </span>            :         int *n, </a>
+<a name="16900"><span class="lineNum">   16900 </span>            :         float *a, </a>
+<a name="16901"><span class="lineNum">   16901 </span>            :         int *lda, </a>
+<a name="16902"><span class="lineNum">   16902 </span>            :         float *tau,</a>
+<a name="16903"><span class="lineNum">   16903 </span>            :         float *work, </a>
+<a name="16904"><span class="lineNum">   16904 </span>            :         int *lwork, </a>
+<a name="16905"><span class="lineNum">   16905 </span>            :         int *info)</a>
+<a name="16906"><span class="lineNum">   16906 </span>            : {</a>
+<a name="16907"><span class="lineNum">   16907 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3, i__4;</a>
+<a name="16908"><span class="lineNum">   16908 </span>            : </a>
+<a name="16909"><span class="lineNum">   16909 </span>            :     int i__, k, ib, nb, nx, iws, nbmin, iinfo;</a>
+<a name="16910"><span class="lineNum">   16910 </span>            :     int ldwork, lwkopt;</a>
+<a name="16911"><span class="lineNum">   16911 </span>            : </a>
+<a name="16912"><span class="lineNum">   16912 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="16913"><span class="lineNum">   16913 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="16914"><span class="lineNum">   16914 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="16915"><span class="lineNum">   16915 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="16916"><span class="lineNum">   16916 </span>            :     --work;</a>
+<a name="16917"><span class="lineNum">   16917 </span>            : </a>
+<a name="16918"><span class="lineNum">   16918 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="16919"><span class="lineNum">   16919 </span>            :     nb = DGEQRF_BLOCKSIZE;</a>
+<a name="16920"><span class="lineNum">   16920 </span><span class="lineNoCov">          0 :     lwkopt = *n * nb;</span></a>
+<a name="16921"><span class="lineNum">   16921 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="16922"><span class="lineNum">   16922 </span><span class="lineNoCov">          0 :         if (*lwork==-1)</span></a>
+<a name="16923"><span class="lineNum">   16923 </span>            :         return;</a>
+<a name="16924"><span class="lineNum">   16924 </span>            :     </a>
+<a name="16925"><span class="lineNum">   16925 </span>            : </a>
+<a name="16926"><span class="lineNum">   16926 </span><span class="lineNoCov">          0 :     k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="16927"><span class="lineNum">   16927 </span><span class="lineNoCov">          0 :     if (k == 0) {</span></a>
+<a name="16928"><span class="lineNum">   16928 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="16929"><span class="lineNum">   16929 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="16930"><span class="lineNum">   16930 </span>            :     }</a>
+<a name="16931"><span class="lineNum">   16931 </span>            : </a>
+<a name="16932"><span class="lineNum">   16932 </span>            :     nbmin = 2;</a>
+<a name="16933"><span class="lineNum">   16933 </span>            :     nx = 0;</a>
+<a name="16934"><span class="lineNum">   16934 </span>            :     iws = *n;</a>
+<a name="16935"><span class="lineNum">   16935 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; k) {</span></a>
+<a name="16936"><span class="lineNum">   16936 </span>            :         </a>
+<a name="16937"><span class="lineNum">   16937 </span>            :       nx = DGEQRF_CROSSOVER;</a>
+<a name="16938"><span class="lineNum">   16938 </span><span class="lineNoCov">          0 :         if (nx &lt; k) {</span></a>
+<a name="16939"><span class="lineNum">   16939 </span>            : </a>
+<a name="16940"><span class="lineNum">   16940 </span><span class="lineNoCov">          0 :             ldwork = *n;</span></a>
+<a name="16941"><span class="lineNum">   16941 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="16942"><span class="lineNum">   16942 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="16943"><span class="lineNum">   16943 </span>            : </a>
+<a name="16944"><span class="lineNum">   16944 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="16945"><span class="lineNum">   16945 </span>            :                 nbmin = DGEQRF_MINBLOCKSIZE;</a>
+<a name="16946"><span class="lineNum">   16946 </span>            :             }</a>
+<a name="16947"><span class="lineNum">   16947 </span>            :         }</a>
+<a name="16948"><span class="lineNum">   16948 </span>            :     }</a>
+<a name="16949"><span class="lineNum">   16949 </span>            : </a>
+<a name="16950"><span class="lineNum">   16950 </span><span class="lineNoCov">          0 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; k &amp;&amp; nx &lt; k) {</span></a>
+<a name="16951"><span class="lineNum">   16951 </span><span class="lineNoCov">          0 :         i__1 = k - nx;</span></a>
+<a name="16952"><span class="lineNum">   16952 </span><span class="lineNoCov">          0 :         i__2 = nb;</span></a>
+<a name="16953"><span class="lineNum">   16953 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="16954"><span class="lineNum">   16954 </span>            : </a>
+<a name="16955"><span class="lineNum">   16955 </span><span class="lineNoCov">          0 :             i__3 = k - i__ + 1;</span></a>
+<a name="16956"><span class="lineNum">   16956 </span><span class="lineNoCov">          0 :             ib = (i__3 &lt; nb) ? i__3 : nb;</span></a>
+<a name="16957"><span class="lineNum">   16957 </span>            : </a>
+<a name="16958"><span class="lineNum">   16958 </span><span class="lineNoCov">          0 :             i__3 = *m - i__ + 1;</span></a>
+<a name="16959"><span class="lineNum">   16959 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgeqr2,SGEQR2)(&amp;i__3, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[</span></a>
+<a name="16960"><span class="lineNum">   16960 </span>            :                     1], &amp;iinfo);</a>
+<a name="16961"><span class="lineNum">   16961 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *n) {</span></a>
+<a name="16962"><span class="lineNum">   16962 </span>            : </a>
+<a name="16963"><span class="lineNum">   16963 </span><span class="lineNoCov">          0 :                 i__3 = *m - i__ + 1;</span></a>
+<a name="16964"><span class="lineNum">   16964 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__3, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="16965"><span class="lineNum">   16965 </span>            :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</a>
+<a name="16966"><span class="lineNum">   16966 </span>            : </a>
+<a name="16967"><span class="lineNum">   16967 </span><span class="lineNoCov">          0 :                 i__3 = *m - i__ + 1;</span></a>
+<a name="16968"><span class="lineNum">   16968 </span><span class="lineNoCov">          0 :                 i__4 = *n - i__ - ib + 1;</span></a>
+<a name="16969"><span class="lineNum">   16969 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(&quot;Left&quot;, &quot;Transpose&quot;, &quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__3, &amp;</span></a>
+<a name="16970"><span class="lineNum">   16970 </span>            :                         i__4, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[1], &amp;</a>
+<a name="16971"><span class="lineNum">   16971 </span><span class="lineNoCov">          0 :                         ldwork, &amp;a[i__ + (i__ + ib) * a_dim1], lda, &amp;work[ib </span></a>
+<a name="16972"><span class="lineNum">   16972 </span><span class="lineNoCov">          0 :                         + 1], &amp;ldwork);</span></a>
+<a name="16973"><span class="lineNum">   16973 </span>            :             }</a>
+<a name="16974"><span class="lineNum">   16974 </span>            :         }</a>
+<a name="16975"><span class="lineNum">   16975 </span>            :     } else {</a>
+<a name="16976"><span class="lineNum">   16976 </span>            :         i__ = 1;</a>
+<a name="16977"><span class="lineNum">   16977 </span>            :     }</a>
+<a name="16978"><span class="lineNum">   16978 </span>            : </a>
+<a name="16979"><span class="lineNum">   16979 </span><span class="lineNoCov">          0 :     if (i__ &lt;= k) {</span></a>
+<a name="16980"><span class="lineNum">   16980 </span><span class="lineNoCov">          0 :         i__2 = *m - i__ + 1;</span></a>
+<a name="16981"><span class="lineNum">   16981 </span><span class="lineNoCov">          0 :         i__1 = *n - i__ + 1;</span></a>
+<a name="16982"><span class="lineNum">   16982 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgeqr2,SGEQR2)(&amp;i__2, &amp;i__1, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;work[1]</span></a>
+<a name="16983"><span class="lineNum">   16983 </span>            :                 , &amp;iinfo);</a>
+<a name="16984"><span class="lineNum">   16984 </span>            :     }</a>
+<a name="16985"><span class="lineNum">   16985 </span>            : </a>
+<a name="16986"><span class="lineNum">   16986 </span><span class="lineNoCov">          0 :     work[1] = (float) iws;</span></a>
+<a name="16987"><span class="lineNum">   16987 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="16988"><span class="lineNum">   16988 </span>            : </a>
+<a name="16989"><span class="lineNum">   16989 </span>            : } </a>
+<a name="16990"><span class="lineNum">   16990 </span>            : </a>
+<a name="16991"><span class="lineNum">   16991 </span>            : }</a>
+<a name="16992"><span class="lineNum">   16992 </span>            : }</a>
+<a name="16993"><span class="lineNum">   16993 </span>            : #include &lt;cmath&gt;</a>
+<a name="16994"><span class="lineNum">   16994 </span>            : #include &quot;real.h&quot;</a>
+<a name="16995"><span class="lineNum">   16995 </span>            : </a>
+<a name="16996"><span class="lineNum">   16996 </span>            : </a>
+<a name="16997"><span class="lineNum">   16997 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="16998"><span class="lineNum">   16998 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="16999"><span class="lineNum">   16999 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="17000"><span class="lineNum">   17000 </span>            : </a>
+<a name="17001"><span class="lineNum">   17001 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17002"><span class="lineNum">   17002 </span>            : namespace PLMD{</a>
+<a name="17003"><span class="lineNum">   17003 </span>            : namespace lapack{</a>
+<a name="17004"><span class="lineNum">   17004 </span>            : using namespace blas;</a>
+<a name="17005"><span class="lineNum">   17005 </span>            : void</a>
+<a name="17006"><span class="lineNum">   17006 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgesdd,SGESDD)(const char *jobz, </span></a>
+<a name="17007"><span class="lineNum">   17007 </span>            :                         int *m, </a>
+<a name="17008"><span class="lineNum">   17008 </span>            :                         int *n, </a>
+<a name="17009"><span class="lineNum">   17009 </span>            :                         float *a, </a>
+<a name="17010"><span class="lineNum">   17010 </span>            :                         int *lda, </a>
+<a name="17011"><span class="lineNum">   17011 </span>            :                         float *s,</a>
+<a name="17012"><span class="lineNum">   17012 </span>            :                         float *u, </a>
+<a name="17013"><span class="lineNum">   17013 </span>            :                         int *ldu, </a>
+<a name="17014"><span class="lineNum">   17014 </span>            :                         float *vt, </a>
+<a name="17015"><span class="lineNum">   17015 </span>            :                         int *ldvt, </a>
+<a name="17016"><span class="lineNum">   17016 </span>            :                         float *work,</a>
+<a name="17017"><span class="lineNum">   17017 </span>            :                         int *lwork, </a>
+<a name="17018"><span class="lineNum">   17018 </span>            :                         int *iwork, </a>
+<a name="17019"><span class="lineNum">   17019 </span>            :                         int *info)</a>
+<a name="17020"><span class="lineNum">   17020 </span>            : {</a>
+<a name="17021"><span class="lineNum">   17021 </span>            :     int a_dim1, a_offset, u_dim1, u_offset, vt_dim1, vt_offset, i__1, i__2;</a>
+<a name="17022"><span class="lineNum">   17022 </span>            : </a>
+<a name="17023"><span class="lineNum">   17023 </span>            :     int ie, iu;</a>
+<a name="17024"><span class="lineNum">   17024 </span>            :     float dum[1], eps;</a>
+<a name="17025"><span class="lineNum">   17025 </span>            :     int ivt, iscl;</a>
+<a name="17026"><span class="lineNum">   17026 </span>            :     float anrm;</a>
+<a name="17027"><span class="lineNum">   17027 </span>            :     int idum[1], ierr, itau;</a>
+<a name="17028"><span class="lineNum">   17028 </span>            :     int minmn, wrkbl, itaup, itauq, mnthr;</a>
+<a name="17029"><span class="lineNum">   17029 </span>            :     int nwork;</a>
+<a name="17030"><span class="lineNum">   17030 </span>            :     int wntqn;</a>
+<a name="17031"><span class="lineNum">   17031 </span>            :     int bdspac;</a>
+<a name="17032"><span class="lineNum">   17032 </span>            :     float bignum;</a>
+<a name="17033"><span class="lineNum">   17033 </span>            :     int ldwrku, maxwrk, ldwkvt;</a>
+<a name="17034"><span class="lineNum">   17034 </span>            :     float smlnum,minval, safemin;</a>
+<a name="17035"><span class="lineNum">   17035 </span>            :     int lquery;</a>
+<a name="17036"><span class="lineNum">   17036 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="17037"><span class="lineNum">   17037 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="17038"><span class="lineNum">   17038 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="17039"><span class="lineNum">   17039 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="17040"><span class="lineNum">   17040 </span>            : </a>
+<a name="17041"><span class="lineNum">   17041 </span>            : </a>
+<a name="17042"><span class="lineNum">   17042 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="17043"><span class="lineNum">   17043 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="17044"><span class="lineNum">   17044 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="17045"><span class="lineNum">   17045 </span>            :     --s;</a>
+<a name="17046"><span class="lineNum">   17046 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="17047"><span class="lineNum">   17047 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="17048"><span class="lineNum">   17048 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="17049"><span class="lineNum">   17049 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="17050"><span class="lineNum">   17050 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="17051"><span class="lineNum">   17051 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="17052"><span class="lineNum">   17052 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="17053"><span class="lineNum">   17053 </span>            :     --iwork;</a>
+<a name="17054"><span class="lineNum">   17054 </span>            : </a>
+<a name="17055"><span class="lineNum">   17055 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="17056"><span class="lineNum">   17056 </span><span class="lineNoCov">          0 :     minmn = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="17057"><span class="lineNum">   17057 </span><span class="lineNoCov">          0 :     mnthr = (int) (minmn * 11. / 6.);</span></a>
+<a name="17058"><span class="lineNum">   17058 </span><span class="lineNoCov">          0 :     wntqn = (*jobz=='o' || *jobz=='O');</span></a>
+<a name="17059"><span class="lineNum">   17059 </span>            : </a>
+<a name="17060"><span class="lineNum">   17060 </span>            :     maxwrk = 1;</a>
+<a name="17061"><span class="lineNum">   17061 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="17062"><span class="lineNum">   17062 </span>            : </a>
+<a name="17063"><span class="lineNum">   17063 </span><span class="lineNoCov">          0 :     if (*info == 0 &amp;&amp; *m &gt; 0 &amp;&amp; *n &gt; 0) {</span></a>
+<a name="17064"><span class="lineNum">   17064 </span><span class="lineNoCov">          0 :         if (*m &gt;= *n) {</span></a>
+<a name="17065"><span class="lineNum">   17065 </span>            : </a>
+<a name="17066"><span class="lineNum">   17066 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="17067"><span class="lineNum">   17067 </span><span class="lineNoCov">          0 :                 bdspac = *n * 7;</span></a>
+<a name="17068"><span class="lineNum">   17068 </span>            :             } else {</a>
+<a name="17069"><span class="lineNum">   17069 </span><span class="lineNoCov">          0 :                 bdspac = *n * 3 * *n + (*n &lt;&lt; 2);</span></a>
+<a name="17070"><span class="lineNum">   17070 </span>            :             }</a>
+<a name="17071"><span class="lineNum">   17071 </span><span class="lineNoCov">          0 :             if (*m &gt;= mnthr) {</span></a>
+<a name="17072"><span class="lineNum">   17072 </span><span class="lineNoCov">          0 :                 if (wntqn) {</span></a>
+<a name="17073"><span class="lineNum">   17073 </span>            : </a>
+<a name="17074"><span class="lineNum">   17074 </span><span class="lineNoCov">          0 :                     wrkbl = *n * 67;</span></a>
+<a name="17075"><span class="lineNum">   17075 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *n;</span></a>
+<a name="17076"><span class="lineNum">   17076 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17077"><span class="lineNum">   17077 </span>            :                 } else {</a>
+<a name="17078"><span class="lineNum">   17078 </span>            : </a>
+<a name="17079"><span class="lineNum">   17079 </span><span class="lineNoCov">          0 :                     wrkbl = *n * 67;</span></a>
+<a name="17080"><span class="lineNum">   17080 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = *n + (*m &lt;&lt; 5);</span></a>
+<a name="17081"><span class="lineNum">   17081 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17082"><span class="lineNum">   17082 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *n * 3;</span></a>
+<a name="17083"><span class="lineNum">   17083 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17084"><span class="lineNum">   17084 </span><span class="lineNoCov">          0 :                     maxwrk = wrkbl + *n * *n;</span></a>
+<a name="17085"><span class="lineNum">   17085 </span>            :                 }</a>
+<a name="17086"><span class="lineNum">   17086 </span>            :             } else {</a>
+<a name="17087"><span class="lineNum">   17087 </span>            : </a>
+<a name="17088"><span class="lineNum">   17088 </span><span class="lineNoCov">          0 :                 wrkbl = *n * 3 + (*m + *n*32);</span></a>
+<a name="17089"><span class="lineNum">   17089 </span><span class="lineNoCov">          0 :                 if (wntqn) {</span></a>
+<a name="17090"><span class="lineNum">   17090 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *n * 3;</span></a>
+<a name="17091"><span class="lineNum">   17091 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17092"><span class="lineNum">   17092 </span>            :                 } else {</a>
+<a name="17093"><span class="lineNum">   17093 </span><span class="lineNoCov">          0 :                     i__1 = maxwrk, i__2 = bdspac + *n * 3;</span></a>
+<a name="17094"><span class="lineNum">   17094 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17095"><span class="lineNum">   17095 </span>            :                 }</a>
+<a name="17096"><span class="lineNum">   17096 </span>            :             }</a>
+<a name="17097"><span class="lineNum">   17097 </span>            :         } else {</a>
+<a name="17098"><span class="lineNum">   17098 </span>            : </a>
+<a name="17099"><span class="lineNum">   17099 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="17100"><span class="lineNum">   17100 </span><span class="lineNoCov">          0 :                 bdspac = *m * 7;</span></a>
+<a name="17101"><span class="lineNum">   17101 </span>            :             } else {</a>
+<a name="17102"><span class="lineNum">   17102 </span><span class="lineNoCov">          0 :                 bdspac = *m * 3 * *m + (*m*4);</span></a>
+<a name="17103"><span class="lineNum">   17103 </span>            :             }</a>
+<a name="17104"><span class="lineNum">   17104 </span><span class="lineNoCov">          0 :             if (*n &gt;= mnthr) {</span></a>
+<a name="17105"><span class="lineNum">   17105 </span><span class="lineNoCov">          0 :                 if (wntqn) {</span></a>
+<a name="17106"><span class="lineNum">   17106 </span>            : </a>
+<a name="17107"><span class="lineNum">   17107 </span><span class="lineNoCov">          0 :                     wrkbl = *m * 67;</span></a>
+<a name="17108"><span class="lineNum">   17108 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m;</span></a>
+<a name="17109"><span class="lineNum">   17109 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17110"><span class="lineNum">   17110 </span>            :                 } else {</a>
+<a name="17111"><span class="lineNum">   17111 </span>            : </a>
+<a name="17112"><span class="lineNum">   17112 </span><span class="lineNoCov">          0 :                     wrkbl = *m * 67;</span></a>
+<a name="17113"><span class="lineNum">   17113 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = *m + (*n*32);</span></a>
+<a name="17114"><span class="lineNum">   17114 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17115"><span class="lineNum">   17115 </span>            : </a>
+<a name="17116"><span class="lineNum">   17116 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m * 3;</span></a>
+<a name="17117"><span class="lineNum">   17117 </span>            :                     wrkbl = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17118"><span class="lineNum">   17118 </span><span class="lineNoCov">          0 :                     maxwrk = wrkbl + *m * *m;</span></a>
+<a name="17119"><span class="lineNum">   17119 </span>            :                 }</a>
+<a name="17120"><span class="lineNum">   17120 </span>            :             } else {</a>
+<a name="17121"><span class="lineNum">   17121 </span><span class="lineNoCov">          0 :                 wrkbl = *m * 3 + (*m + *n*32);</span></a>
+<a name="17122"><span class="lineNum">   17122 </span><span class="lineNoCov">          0 :                 if (wntqn) {</span></a>
+<a name="17123"><span class="lineNum">   17123 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m * 3;</span></a>
+<a name="17124"><span class="lineNum">   17124 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17125"><span class="lineNum">   17125 </span>            :                 } else {</a>
+<a name="17126"><span class="lineNum">   17126 </span><span class="lineNoCov">          0 :                     i__1 = wrkbl, i__2 = bdspac + *m * 3;</span></a>
+<a name="17127"><span class="lineNum">   17127 </span>            :                     maxwrk = (i__1 &gt; i__2) ? i__1 : i__2;</a>
+<a name="17128"><span class="lineNum">   17128 </span>            :                 }</a>
+<a name="17129"><span class="lineNum">   17129 </span>            :             }</a>
+<a name="17130"><span class="lineNum">   17130 </span>            :         }</a>
+<a name="17131"><span class="lineNum">   17131 </span><span class="lineNoCov">          0 :         work[1] = (float) maxwrk;</span></a>
+<a name="17132"><span class="lineNum">   17132 </span>            :     }</a>
+<a name="17133"><span class="lineNum">   17133 </span>            :     </a>
+<a name="17134"><span class="lineNum">   17134 </span><span class="lineNoCov">          0 :     if( lquery != 0)</span></a>
+<a name="17135"><span class="lineNum">   17135 </span>            :     {</a>
+<a name="17136"><span class="lineNum">   17136 </span>            :         return;</a>
+<a name="17137"><span class="lineNum">   17137 </span>            :     }</a>
+<a name="17138"><span class="lineNum">   17138 </span>            :     </a>
+<a name="17139"><span class="lineNum">   17139 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0) {</span></a>
+<a name="17140"><span class="lineNum">   17140 </span><span class="lineNoCov">          0 :         if (*lwork &gt;= 1) {</span></a>
+<a name="17141"><span class="lineNum">   17141 </span><span class="lineNoCov">          0 :             work[1] = 1.;</span></a>
+<a name="17142"><span class="lineNum">   17142 </span>            :         }</a>
+<a name="17143"><span class="lineNum">   17143 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="17144"><span class="lineNum">   17144 </span>            :     }</a>
+<a name="17145"><span class="lineNum">   17145 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="17146"><span class="lineNum">   17146 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="17147"><span class="lineNum">   17147 </span>            :     safemin = minval / eps;</a>
+<a name="17148"><span class="lineNum">   17148 </span><span class="lineNoCov">          0 :     smlnum =  std::sqrt(safemin) / eps;</span></a>
+<a name="17149"><span class="lineNum">   17149 </span>            : </a>
+<a name="17150"><span class="lineNum">   17150 </span>            : </a>
+<a name="17151"><span class="lineNum">   17151 </span><span class="lineNoCov">          0 :     bignum = 1. / smlnum;</span></a>
+<a name="17152"><span class="lineNum">   17152 </span>            : </a>
+<a name="17153"><span class="lineNum">   17153 </span>            : </a>
+<a name="17154"><span class="lineNum">   17154 </span><span class="lineNoCov">          0 :     anrm = PLUMED_BLAS_F77_FUNC(slange,SLANGE)(&quot;M&quot;, m, n, &amp;a[a_offset], lda, dum);</span></a>
+<a name="17155"><span class="lineNum">   17155 </span>            :     iscl = 0;</a>
+<a name="17156"><span class="lineNum">   17156 </span><span class="lineNoCov">          0 :     if (anrm &gt; 0. &amp;&amp; anrm &lt; smlnum) {</span></a>
+<a name="17157"><span class="lineNum">   17157 </span>            :         iscl = 1;</a>
+<a name="17158"><span class="lineNum">   17158 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;,&amp;c__0,&amp;c__0,&amp;anrm,&amp;smlnum,m,n,&amp;a[a_offset],lda,&amp;ierr);</span></a>
+<a name="17159"><span class="lineNum">   17159 </span><span class="lineNoCov">          0 :     } else if (anrm &gt; bignum) {</span></a>
+<a name="17160"><span class="lineNum">   17160 </span>            :         iscl = 1;</a>
+<a name="17161"><span class="lineNum">   17161 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;,&amp;c__0,&amp;c__0,&amp;anrm,&amp;bignum,m,n,&amp;a[a_offset],lda,&amp;ierr);</span></a>
+<a name="17162"><span class="lineNum">   17162 </span>            :     }</a>
+<a name="17163"><span class="lineNum">   17163 </span>            : </a>
+<a name="17164"><span class="lineNum">   17164 </span><span class="lineNoCov">          0 :     if (*m &gt;= *n) {</span></a>
+<a name="17165"><span class="lineNum">   17165 </span><span class="lineNoCov">          0 :         if (*m &gt;= mnthr) {</span></a>
+<a name="17166"><span class="lineNum">   17166 </span>            : </a>
+<a name="17167"><span class="lineNum">   17167 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="17168"><span class="lineNum">   17168 </span>            : </a>
+<a name="17169"><span class="lineNum">   17169 </span>            :                 itau = 1;</a>
+<a name="17170"><span class="lineNum">   17170 </span><span class="lineNoCov">          0 :                 nwork = itau + *n;</span></a>
+<a name="17171"><span class="lineNum">   17171 </span>            : </a>
+<a name="17172"><span class="lineNum">   17172 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17173"><span class="lineNum">   17173 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgeqrf,SGEQRF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="17174"><span class="lineNum">   17174 </span>            :                         i__1, &amp;ierr);</a>
+<a name="17175"><span class="lineNum">   17175 </span>            : </a>
+<a name="17176"><span class="lineNum">   17176 </span><span class="lineNoCov">          0 :                 i__1 = *n - 1;</span></a>
+<a name="17177"><span class="lineNum">   17177 </span><span class="lineNoCov">          0 :                 i__2 = *n - 1;</span></a>
+<a name="17178"><span class="lineNum">   17178 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;L&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[a_dim1 + 2], </span></a>
+<a name="17179"><span class="lineNum">   17179 </span>            :                         lda);</a>
+<a name="17180"><span class="lineNum">   17180 </span>            :                 ie = 1;</a>
+<a name="17181"><span class="lineNum">   17181 </span><span class="lineNoCov">          0 :                 itauq = ie + *n;</span></a>
+<a name="17182"><span class="lineNum">   17182 </span><span class="lineNoCov">          0 :                 itaup = itauq + *n;</span></a>
+<a name="17183"><span class="lineNum">   17183 </span><span class="lineNoCov">          0 :                 nwork = itaup + *n;</span></a>
+<a name="17184"><span class="lineNum">   17184 </span>            : </a>
+<a name="17185"><span class="lineNum">   17185 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17186"><span class="lineNum">   17186 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(n, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="17187"><span class="lineNum">   17187 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="17188"><span class="lineNum">   17188 </span><span class="lineNoCov">          0 :                 nwork = ie + *n;</span></a>
+<a name="17189"><span class="lineNum">   17189 </span>            : </a>
+<a name="17190"><span class="lineNum">   17190 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;U&quot;, &quot;N&quot;, n, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="17191"><span class="lineNum">   17191 </span><span class="lineNoCov">          0 :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</span></a>
+<a name="17192"><span class="lineNum">   17192 </span>            : </a>
+<a name="17193"><span class="lineNum">   17193 </span>            :             } else {</a>
+<a name="17194"><span class="lineNum">   17194 </span>            :                 iu = 1;</a>
+<a name="17195"><span class="lineNum">   17195 </span>            : </a>
+<a name="17196"><span class="lineNum">   17196 </span><span class="lineNoCov">          0 :                 ldwrku = *n;</span></a>
+<a name="17197"><span class="lineNum">   17197 </span><span class="lineNoCov">          0 :                 itau = iu + ldwrku * *n;</span></a>
+<a name="17198"><span class="lineNum">   17198 </span><span class="lineNoCov">          0 :                 nwork = itau + *n;</span></a>
+<a name="17199"><span class="lineNum">   17199 </span>            : </a>
+<a name="17200"><span class="lineNum">   17200 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17201"><span class="lineNum">   17201 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgeqrf,SGEQRF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="17202"><span class="lineNum">   17202 </span>            :                         i__1, &amp;ierr);</a>
+<a name="17203"><span class="lineNum">   17203 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;L&quot;, m, n, &amp;a[a_offset], lda, &amp;u[u_offset], ldu);</span></a>
+<a name="17204"><span class="lineNum">   17204 </span>            : </a>
+<a name="17205"><span class="lineNum">   17205 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17206"><span class="lineNum">   17206 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sorgqr,SORGQR)(m, m, n, &amp;u[u_offset], ldu, &amp;work[itau], &amp;work[nwork],</span></a>
+<a name="17207"><span class="lineNum">   17207 </span>            :                          &amp;i__1, &amp;ierr);</a>
+<a name="17208"><span class="lineNum">   17208 </span>            : </a>
+<a name="17209"><span class="lineNum">   17209 </span><span class="lineNoCov">          0 :                 i__1 = *n - 1;</span></a>
+<a name="17210"><span class="lineNum">   17210 </span><span class="lineNoCov">          0 :                 i__2 = *n - 1;</span></a>
+<a name="17211"><span class="lineNum">   17211 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;L&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[a_dim1 + 2], </span></a>
+<a name="17212"><span class="lineNum">   17212 </span>            :                         lda);</a>
+<a name="17213"><span class="lineNum">   17213 </span>            :                 ie = itau;</a>
+<a name="17214"><span class="lineNum">   17214 </span><span class="lineNoCov">          0 :                 itauq = ie + *n;</span></a>
+<a name="17215"><span class="lineNum">   17215 </span><span class="lineNoCov">          0 :                 itaup = itauq + *n;</span></a>
+<a name="17216"><span class="lineNum">   17216 </span><span class="lineNoCov">          0 :                 nwork = itaup + *n;</span></a>
+<a name="17217"><span class="lineNum">   17217 </span>            : </a>
+<a name="17218"><span class="lineNum">   17218 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17219"><span class="lineNum">   17219 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(n, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="17220"><span class="lineNum">   17220 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="17221"><span class="lineNum">   17221 </span>            : </a>
+<a name="17222"><span class="lineNum">   17222 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;U&quot;, &quot;I&quot;, n, &amp;s[1], &amp;work[ie], &amp;work[iu], n, &amp;vt[</span></a>
+<a name="17223"><span class="lineNum">   17223 </span>            :                         vt_offset], ldvt, dum, idum, &amp;work[nwork], &amp;iwork[1], </a>
+<a name="17224"><span class="lineNum">   17224 </span>            :                         info);</a>
+<a name="17225"><span class="lineNum">   17225 </span>            : </a>
+<a name="17226"><span class="lineNum">   17226 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17227"><span class="lineNum">   17227 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, n, n, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17228"><span class="lineNum">   17228 </span>            :                         itauq], &amp;work[iu], &amp;ldwrku, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="17229"><span class="lineNum">   17229 </span>            :                         ierr);</a>
+<a name="17230"><span class="lineNum">   17230 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17231"><span class="lineNum">   17231 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, n, n, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17232"><span class="lineNum">   17232 </span>            :                         itaup], &amp;vt[vt_offset], ldvt, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="17233"><span class="lineNum">   17233 </span>            :                         ierr);</a>
+<a name="17234"><span class="lineNum">   17234 </span>            : </a>
+<a name="17235"><span class="lineNum">   17235 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, m, n, n, &amp;one, &amp;u[u_offset], ldu, &amp;work[iu]</span></a>
+<a name="17236"><span class="lineNum">   17236 </span>            :                         , &amp;ldwrku, &amp;zero, &amp;a[a_offset], lda);</a>
+<a name="17237"><span class="lineNum">   17237 </span>            : </a>
+<a name="17238"><span class="lineNum">   17238 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;F&quot;, m, n, &amp;a[a_offset], lda, &amp;u[u_offset], ldu);</span></a>
+<a name="17239"><span class="lineNum">   17239 </span>            : </a>
+<a name="17240"><span class="lineNum">   17240 </span>            :             }</a>
+<a name="17241"><span class="lineNum">   17241 </span>            : </a>
+<a name="17242"><span class="lineNum">   17242 </span>            :         } else {</a>
+<a name="17243"><span class="lineNum">   17243 </span>            :             ie = 1;</a>
+<a name="17244"><span class="lineNum">   17244 </span><span class="lineNoCov">          0 :             itauq = ie + *n;</span></a>
+<a name="17245"><span class="lineNum">   17245 </span><span class="lineNoCov">          0 :             itaup = itauq + *n;</span></a>
+<a name="17246"><span class="lineNum">   17246 </span><span class="lineNoCov">          0 :             nwork = itaup + *n;</span></a>
+<a name="17247"><span class="lineNum">   17247 </span>            : </a>
+<a name="17248"><span class="lineNum">   17248 </span><span class="lineNoCov">          0 :             i__1 = *lwork - nwork + 1;</span></a>
+<a name="17249"><span class="lineNum">   17249 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(m, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[itauq], &amp;</span></a>
+<a name="17250"><span class="lineNum">   17250 </span><span class="lineNoCov">          0 :                     work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="17251"><span class="lineNum">   17251 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="17252"><span class="lineNum">   17252 </span>            : </a>
+<a name="17253"><span class="lineNum">   17253 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;U&quot;, &quot;N&quot;, n, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="17254"><span class="lineNum">   17254 </span>            :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</a>
+<a name="17255"><span class="lineNum">   17255 </span>            :             } else {</a>
+<a name="17256"><span class="lineNum">   17256 </span>            : </a>
+<a name="17257"><span class="lineNum">   17257 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;F&quot;, m, m, &amp;zero, &amp;zero, &amp;u[u_offset], ldu);</span></a>
+<a name="17258"><span class="lineNum">   17258 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;U&quot;, &quot;I&quot;, n, &amp;s[1], &amp;work[ie], &amp;u[u_offset], ldu, &amp;vt[</span></a>
+<a name="17259"><span class="lineNum">   17259 </span>            :                         vt_offset], ldvt, dum, idum, &amp;work[nwork], &amp;iwork[1], </a>
+<a name="17260"><span class="lineNum">   17260 </span>            :                         info);</a>
+<a name="17261"><span class="lineNum">   17261 </span>            : </a>
+<a name="17262"><span class="lineNum">   17262 </span><span class="lineNoCov">          0 :                 i__1 = *m - *n;</span></a>
+<a name="17263"><span class="lineNum">   17263 </span><span class="lineNoCov">          0 :                 i__2 = *m - *n;</span></a>
+<a name="17264"><span class="lineNum">   17264 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;F&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;one, &amp;u[*n + 1 + (*n + </span></a>
+<a name="17265"><span class="lineNum">   17265 </span><span class="lineNoCov">          0 :                         1) * u_dim1], ldu);</span></a>
+<a name="17266"><span class="lineNum">   17266 </span>            : </a>
+<a name="17267"><span class="lineNum">   17267 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17268"><span class="lineNum">   17268 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, m, m, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17269"><span class="lineNum">   17269 </span>            :                         itauq], &amp;u[u_offset], ldu, &amp;work[nwork], &amp;i__1, &amp;ierr);</a>
+<a name="17270"><span class="lineNum">   17270 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17271"><span class="lineNum">   17271 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, n, n, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17272"><span class="lineNum">   17272 </span>            :                         itaup], &amp;vt[vt_offset],ldvt,&amp;work[nwork],&amp;i__1,&amp;ierr);</a>
+<a name="17273"><span class="lineNum">   17273 </span>            :             }</a>
+<a name="17274"><span class="lineNum">   17274 </span>            : </a>
+<a name="17275"><span class="lineNum">   17275 </span>            :         }</a>
+<a name="17276"><span class="lineNum">   17276 </span>            : </a>
+<a name="17277"><span class="lineNum">   17277 </span>            :     } else {</a>
+<a name="17278"><span class="lineNum">   17278 </span>            : </a>
+<a name="17279"><span class="lineNum">   17279 </span><span class="lineNoCov">          0 :         if (*n &gt;= mnthr) {</span></a>
+<a name="17280"><span class="lineNum">   17280 </span>            : </a>
+<a name="17281"><span class="lineNum">   17281 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="17282"><span class="lineNum">   17282 </span>            : </a>
+<a name="17283"><span class="lineNum">   17283 </span>            :                 itau = 1;</a>
+<a name="17284"><span class="lineNum">   17284 </span><span class="lineNoCov">          0 :                 nwork = itau + *m;</span></a>
+<a name="17285"><span class="lineNum">   17285 </span>            : </a>
+<a name="17286"><span class="lineNum">   17286 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17287"><span class="lineNum">   17287 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgelqf,SGELQF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="17288"><span class="lineNum">   17288 </span>            :                         i__1, &amp;ierr);</a>
+<a name="17289"><span class="lineNum">   17289 </span>            : </a>
+<a name="17290"><span class="lineNum">   17290 </span><span class="lineNoCov">          0 :                 i__1 = *m - 1;</span></a>
+<a name="17291"><span class="lineNum">   17291 </span><span class="lineNoCov">          0 :                 i__2 = *m - 1;</span></a>
+<a name="17292"><span class="lineNum">   17292 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;U&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[(a_dim1*2) + </span></a>
+<a name="17293"><span class="lineNum">   17293 </span><span class="lineNoCov">          0 :                         1], lda);</span></a>
+<a name="17294"><span class="lineNum">   17294 </span>            :                 ie = 1;</a>
+<a name="17295"><span class="lineNum">   17295 </span><span class="lineNoCov">          0 :                 itauq = ie + *m;</span></a>
+<a name="17296"><span class="lineNum">   17296 </span><span class="lineNoCov">          0 :                 itaup = itauq + *m;</span></a>
+<a name="17297"><span class="lineNum">   17297 </span><span class="lineNoCov">          0 :                 nwork = itaup + *m;</span></a>
+<a name="17298"><span class="lineNum">   17298 </span>            : </a>
+<a name="17299"><span class="lineNum">   17299 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17300"><span class="lineNum">   17300 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(m, m, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="17301"><span class="lineNum">   17301 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="17302"><span class="lineNum">   17302 </span><span class="lineNoCov">          0 :                 nwork = ie + *m;</span></a>
+<a name="17303"><span class="lineNum">   17303 </span>            : </a>
+<a name="17304"><span class="lineNum">   17304 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;U&quot;, &quot;N&quot;, m, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="17305"><span class="lineNum">   17305 </span><span class="lineNoCov">          0 :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</span></a>
+<a name="17306"><span class="lineNum">   17306 </span>            : </a>
+<a name="17307"><span class="lineNum">   17307 </span>            :             } else {</a>
+<a name="17308"><span class="lineNum">   17308 </span>            : </a>
+<a name="17309"><span class="lineNum">   17309 </span>            :                 ivt = 1;</a>
+<a name="17310"><span class="lineNum">   17310 </span>            : </a>
+<a name="17311"><span class="lineNum">   17311 </span><span class="lineNoCov">          0 :                 ldwkvt = *m;</span></a>
+<a name="17312"><span class="lineNum">   17312 </span><span class="lineNoCov">          0 :                 itau = ivt + ldwkvt * *m;</span></a>
+<a name="17313"><span class="lineNum">   17313 </span><span class="lineNoCov">          0 :                 nwork = itau + *m;</span></a>
+<a name="17314"><span class="lineNum">   17314 </span>            : </a>
+<a name="17315"><span class="lineNum">   17315 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17316"><span class="lineNum">   17316 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgelqf,SGELQF)(m, n, &amp;a[a_offset], lda, &amp;work[itau], &amp;work[nwork], &amp;</span></a>
+<a name="17317"><span class="lineNum">   17317 </span>            :                         i__1, &amp;ierr);</a>
+<a name="17318"><span class="lineNum">   17318 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;U&quot;, m, n, &amp;a[a_offset], lda, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="17319"><span class="lineNum">   17319 </span>            : </a>
+<a name="17320"><span class="lineNum">   17320 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17321"><span class="lineNum">   17321 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sorglq,SORGLQ)(n, n, m, &amp;vt[vt_offset], ldvt, &amp;work[itau], &amp;work[</span></a>
+<a name="17322"><span class="lineNum">   17322 </span>            :                         nwork], &amp;i__1, &amp;ierr);</a>
+<a name="17323"><span class="lineNum">   17323 </span>            : </a>
+<a name="17324"><span class="lineNum">   17324 </span><span class="lineNoCov">          0 :                 i__1 = *m - 1;</span></a>
+<a name="17325"><span class="lineNum">   17325 </span><span class="lineNoCov">          0 :                 i__2 = *m - 1;</span></a>
+<a name="17326"><span class="lineNum">   17326 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;U&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;zero, &amp;a[(a_dim1*2) + </span></a>
+<a name="17327"><span class="lineNum">   17327 </span><span class="lineNoCov">          0 :                         1], lda);</span></a>
+<a name="17328"><span class="lineNum">   17328 </span>            :                 ie = itau;</a>
+<a name="17329"><span class="lineNum">   17329 </span><span class="lineNoCov">          0 :                 itauq = ie + *m;</span></a>
+<a name="17330"><span class="lineNum">   17330 </span><span class="lineNoCov">          0 :                 itaup = itauq + *m;</span></a>
+<a name="17331"><span class="lineNum">   17331 </span><span class="lineNoCov">          0 :                 nwork = itaup + *m;</span></a>
+<a name="17332"><span class="lineNum">   17332 </span>            : </a>
+<a name="17333"><span class="lineNum">   17333 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17334"><span class="lineNum">   17334 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(m, m, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[</span></a>
+<a name="17335"><span class="lineNum">   17335 </span><span class="lineNoCov">          0 :                         itauq], &amp;work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="17336"><span class="lineNum">   17336 </span>            : </a>
+<a name="17337"><span class="lineNum">   17337 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;U&quot;, &quot;I&quot;, m, &amp;s[1], &amp;work[ie], &amp;u[u_offset], ldu, &amp;</span></a>
+<a name="17338"><span class="lineNum">   17338 </span>            :                         work[ivt], &amp;ldwkvt, dum, idum, &amp;work[nwork], &amp;iwork[1]</a>
+<a name="17339"><span class="lineNum">   17339 </span>            :                         , info);</a>
+<a name="17340"><span class="lineNum">   17340 </span>            : </a>
+<a name="17341"><span class="lineNum">   17341 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17342"><span class="lineNum">   17342 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, m, m, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17343"><span class="lineNum">   17343 </span>            :                         itauq], &amp;u[u_offset], ldu, &amp;work[nwork], &amp;i__1, &amp;ierr);</a>
+<a name="17344"><span class="lineNum">   17344 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17345"><span class="lineNum">   17345 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, m, m, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17346"><span class="lineNum">   17346 </span>            :                         itaup], &amp;work[ivt], &amp;ldwkvt, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="17347"><span class="lineNum">   17347 </span>            :                         ierr);</a>
+<a name="17348"><span class="lineNum">   17348 </span>            : </a>
+<a name="17349"><span class="lineNum">   17349 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, m, n, m, &amp;one, &amp;work[ivt], &amp;ldwkvt, &amp;vt[</span></a>
+<a name="17350"><span class="lineNum">   17350 </span>            :                         vt_offset], ldvt, &amp;zero, &amp;a[a_offset], lda);</a>
+<a name="17351"><span class="lineNum">   17351 </span>            : </a>
+<a name="17352"><span class="lineNum">   17352 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;F&quot;, m, n, &amp;a[a_offset], lda, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="17353"><span class="lineNum">   17353 </span>            : </a>
+<a name="17354"><span class="lineNum">   17354 </span>            :             }</a>
+<a name="17355"><span class="lineNum">   17355 </span>            : </a>
+<a name="17356"><span class="lineNum">   17356 </span>            :         } else {</a>
+<a name="17357"><span class="lineNum">   17357 </span>            : </a>
+<a name="17358"><span class="lineNum">   17358 </span>            :             ie = 1;</a>
+<a name="17359"><span class="lineNum">   17359 </span><span class="lineNoCov">          0 :             itauq = ie + *m;</span></a>
+<a name="17360"><span class="lineNum">   17360 </span><span class="lineNoCov">          0 :             itaup = itauq + *m;</span></a>
+<a name="17361"><span class="lineNum">   17361 </span><span class="lineNoCov">          0 :             nwork = itaup + *m;</span></a>
+<a name="17362"><span class="lineNum">   17362 </span>            : </a>
+<a name="17363"><span class="lineNum">   17363 </span><span class="lineNoCov">          0 :             i__1 = *lwork - nwork + 1;</span></a>
+<a name="17364"><span class="lineNum">   17364 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgebrd,SGEBRD)(m, n, &amp;a[a_offset], lda, &amp;s[1], &amp;work[ie], &amp;work[itauq], &amp;</span></a>
+<a name="17365"><span class="lineNum">   17365 </span><span class="lineNoCov">          0 :                     work[itaup], &amp;work[nwork], &amp;i__1, &amp;ierr);</span></a>
+<a name="17366"><span class="lineNum">   17366 </span><span class="lineNoCov">          0 :             if (wntqn) {</span></a>
+<a name="17367"><span class="lineNum">   17367 </span>            : </a>
+<a name="17368"><span class="lineNum">   17368 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;L&quot;, &quot;N&quot;, m, &amp;s[1], &amp;work[ie], dum, &amp;c__1, dum, &amp;c__1,</span></a>
+<a name="17369"><span class="lineNum">   17369 </span>            :                          dum, idum, &amp;work[nwork], &amp;iwork[1], info);</a>
+<a name="17370"><span class="lineNum">   17370 </span>            :             } else {</a>
+<a name="17371"><span class="lineNum">   17371 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;F&quot;, n, n, &amp;zero, &amp;zero, &amp;vt[vt_offset], ldvt);</span></a>
+<a name="17372"><span class="lineNum">   17372 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sbdsdc,SBDSDC)(&quot;L&quot;, &quot;I&quot;, m, &amp;s[1], &amp;work[ie], &amp;u[u_offset], ldu, &amp;vt[</span></a>
+<a name="17373"><span class="lineNum">   17373 </span>            :                         vt_offset], ldvt, dum, idum, &amp;work[nwork], &amp;iwork[1], </a>
+<a name="17374"><span class="lineNum">   17374 </span>            :                         info);</a>
+<a name="17375"><span class="lineNum">   17375 </span>            : </a>
+<a name="17376"><span class="lineNum">   17376 </span><span class="lineNoCov">          0 :                 i__1 = *n - *m;</span></a>
+<a name="17377"><span class="lineNum">   17377 </span><span class="lineNoCov">          0 :                 i__2 = *n - *m;</span></a>
+<a name="17378"><span class="lineNum">   17378 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;F&quot;, &amp;i__1, &amp;i__2, &amp;zero, &amp;one, &amp;vt[*m + 1 + (*m + </span></a>
+<a name="17379"><span class="lineNum">   17379 </span><span class="lineNoCov">          0 :                         1) * vt_dim1], ldvt);</span></a>
+<a name="17380"><span class="lineNum">   17380 </span>            : </a>
+<a name="17381"><span class="lineNum">   17381 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17382"><span class="lineNum">   17382 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;Q&quot;, &quot;L&quot;, &quot;N&quot;, m, m, n, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17383"><span class="lineNum">   17383 </span>            :                         itauq], &amp;u[u_offset], ldu, &amp;work[nwork], &amp;i__1, &amp;ierr);</a>
+<a name="17384"><span class="lineNum">   17384 </span><span class="lineNoCov">          0 :                 i__1 = *lwork - nwork + 1;</span></a>
+<a name="17385"><span class="lineNum">   17385 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(&quot;P&quot;, &quot;R&quot;, &quot;T&quot;, n, n, m, &amp;a[a_offset], lda, &amp;work[</span></a>
+<a name="17386"><span class="lineNum">   17386 </span>            :                         itaup], &amp;vt[vt_offset], ldvt, &amp;work[nwork], &amp;i__1, &amp;</a>
+<a name="17387"><span class="lineNum">   17387 </span>            :                         ierr);</a>
+<a name="17388"><span class="lineNum">   17388 </span>            :             }</a>
+<a name="17389"><span class="lineNum">   17389 </span>            : </a>
+<a name="17390"><span class="lineNum">   17390 </span>            :         }</a>
+<a name="17391"><span class="lineNum">   17391 </span>            : </a>
+<a name="17392"><span class="lineNum">   17392 </span>            :     }</a>
+<a name="17393"><span class="lineNum">   17393 </span>            : </a>
+<a name="17394"><span class="lineNum">   17394 </span><span class="lineNoCov">          0 :     if (iscl == 1) {</span></a>
+<a name="17395"><span class="lineNum">   17395 </span><span class="lineNoCov">          0 :         if (anrm &gt; bignum) {</span></a>
+<a name="17396"><span class="lineNum">   17396 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;bignum, &amp;anrm, &amp;minmn, &amp;c__1, &amp;s[1], &amp;</span></a>
+<a name="17397"><span class="lineNum">   17397 </span>            :                     minmn, &amp;ierr);</a>
+<a name="17398"><span class="lineNum">   17398 </span>            :         }</a>
+<a name="17399"><span class="lineNum">   17399 </span><span class="lineNoCov">          0 :         if (anrm &lt; smlnum) {</span></a>
+<a name="17400"><span class="lineNum">   17400 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;smlnum, &amp;anrm, &amp;minmn, &amp;c__1, &amp;s[1], &amp;</span></a>
+<a name="17401"><span class="lineNum">   17401 </span>            :                     minmn, &amp;ierr);</a>
+<a name="17402"><span class="lineNum">   17402 </span>            :         }</a>
+<a name="17403"><span class="lineNum">   17403 </span>            :     }</a>
+<a name="17404"><span class="lineNum">   17404 </span>            : </a>
+<a name="17405"><span class="lineNum">   17405 </span><span class="lineNoCov">          0 :     work[1] = (float) maxwrk;</span></a>
+<a name="17406"><span class="lineNum">   17406 </span>            : </a>
+<a name="17407"><span class="lineNum">   17407 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="17408"><span class="lineNum">   17408 </span>            : </a>
+<a name="17409"><span class="lineNum">   17409 </span>            : }</a>
+<a name="17410"><span class="lineNum">   17410 </span>            : </a>
+<a name="17411"><span class="lineNum">   17411 </span>            : </a>
+<a name="17412"><span class="lineNum">   17412 </span>            : }</a>
+<a name="17413"><span class="lineNum">   17413 </span>            : }</a>
+<a name="17414"><span class="lineNum">   17414 </span>            : #include &lt;cmath&gt;</a>
+<a name="17415"><span class="lineNum">   17415 </span>            : #include &quot;real.h&quot;</a>
+<a name="17416"><span class="lineNum">   17416 </span>            : </a>
+<a name="17417"><span class="lineNum">   17417 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17418"><span class="lineNum">   17418 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="17419"><span class="lineNum">   17419 </span>            : </a>
+<a name="17420"><span class="lineNum">   17420 </span>            : </a>
+<a name="17421"><span class="lineNum">   17421 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17422"><span class="lineNum">   17422 </span>            : namespace PLMD{</a>
+<a name="17423"><span class="lineNum">   17423 </span>            : namespace lapack{</a>
+<a name="17424"><span class="lineNum">   17424 </span>            : using namespace blas;</a>
+<a name="17425"><span class="lineNum">   17425 </span>            : void</a>
+<a name="17426"><span class="lineNum">   17426 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgetf2,SGETF2)(int *m,</span></a>
+<a name="17427"><span class="lineNum">   17427 </span>            :         int *n,</a>
+<a name="17428"><span class="lineNum">   17428 </span>            :         float *a,</a>
+<a name="17429"><span class="lineNum">   17429 </span>            :         int *lda,</a>
+<a name="17430"><span class="lineNum">   17430 </span>            :         int *ipiv,</a>
+<a name="17431"><span class="lineNum">   17431 </span>            :         int *info)</a>
+<a name="17432"><span class="lineNum">   17432 </span>            : {</a>
+<a name="17433"><span class="lineNum">   17433 </span>            :   int j,jp,k,t1,t2,t3;</a>
+<a name="17434"><span class="lineNum">   17434 </span>            :   float minusone;</a>
+<a name="17435"><span class="lineNum">   17435 </span>            :   float tmp;</a>
+<a name="17436"><span class="lineNum">   17436 </span>            : </a>
+<a name="17437"><span class="lineNum">   17437 </span><span class="lineNoCov">          0 :   minusone = -1.0;</span></a>
+<a name="17438"><span class="lineNum">   17438 </span>            : </a>
+<a name="17439"><span class="lineNum">   17439 </span><span class="lineNoCov">          0 :   if(*m&lt;=0 || *n&lt;=0)</span></a>
+<a name="17440"><span class="lineNum">   17440 </span>            :     return;</a>
+<a name="17441"><span class="lineNum">   17441 </span>            : </a>
+<a name="17442"><span class="lineNum">   17442 </span>            :   k = (*m &lt; *n) ? *m : *n;</a>
+<a name="17443"><span class="lineNum">   17443 </span><span class="lineNoCov">          0 :   for(j=1;j&lt;=k;j++) {</span></a>
+<a name="17444"><span class="lineNum">   17444 </span><span class="lineNoCov">          0 :     t1 = *m-j+1;</span></a>
+<a name="17445"><span class="lineNum">   17445 </span><span class="lineNoCov">          0 :     t2 = 1;</span></a>
+<a name="17446"><span class="lineNum">   17446 </span><span class="lineNoCov">          0 :     jp = j - 1 + PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)(&amp;t1,&amp;(a[(j-1)*(*lda)+(j-1)]),&amp;t2);</span></a>
+<a name="17447"><span class="lineNum">   17447 </span><span class="lineNoCov">          0 :     ipiv[j-1] = jp;</span></a>
+<a name="17448"><span class="lineNum">   17448 </span><span class="lineNoCov">          0 :     if( std::abs(a[(j-1)*(*lda)+(jp-1)])&gt;PLUMED_GMX_FLOAT_MIN ) {</span></a>
+<a name="17449"><span class="lineNum">   17449 </span><span class="lineNoCov">          0 :       if(jp != j)</span></a>
+<a name="17450"><span class="lineNum">   17450 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n,&amp;(a[ j-1 ]),lda,&amp;(a[ jp-1 ]),lda);</span></a>
+<a name="17451"><span class="lineNum">   17451 </span>            :       </a>
+<a name="17452"><span class="lineNum">   17452 </span><span class="lineNoCov">          0 :       if(j&lt;*m) {</span></a>
+<a name="17453"><span class="lineNum">   17453 </span><span class="lineNoCov">          0 :         t1 = *m-j;</span></a>
+<a name="17454"><span class="lineNum">   17454 </span><span class="lineNoCov">          0 :         t2 = 1;</span></a>
+<a name="17455"><span class="lineNum">   17455 </span><span class="lineNoCov">          0 :         tmp = 1.0/a[(j-1)*(*lda)+(j-1)];</span></a>
+<a name="17456"><span class="lineNum">   17456 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;t1,&amp;tmp,&amp;(a[(j-1)*(*lda)+(j)]),&amp;t2);</span></a>
+<a name="17457"><span class="lineNum">   17457 </span>            :       }</a>
+<a name="17458"><span class="lineNum">   17458 </span>            :     } else {</a>
+<a name="17459"><span class="lineNum">   17459 </span><span class="lineNoCov">          0 :       *info = j;</span></a>
+<a name="17460"><span class="lineNum">   17460 </span>            :     }</a>
+<a name="17461"><span class="lineNum">   17461 </span>            : </a>
+<a name="17462"><span class="lineNum">   17462 </span><span class="lineNoCov">          0 :     if(j&lt;k) {</span></a>
+<a name="17463"><span class="lineNum">   17463 </span><span class="lineNoCov">          0 :       t1 = *m-j;</span></a>
+<a name="17464"><span class="lineNum">   17464 </span><span class="lineNoCov">          0 :       t2 = *n-j;</span></a>
+<a name="17465"><span class="lineNum">   17465 </span><span class="lineNoCov">          0 :       t3 = 1;</span></a>
+<a name="17466"><span class="lineNum">   17466 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sger,SGER)(&amp;t1,&amp;t2,&amp;minusone,&amp;(a[(j-1)*(*lda)+(j)]),&amp;t3,</span></a>
+<a name="17467"><span class="lineNum">   17467 </span><span class="lineNoCov">          0 :             &amp;(a[(j)*(*lda)+(j-1)]),lda, &amp;(a[(j)*(*lda)+(j)]),lda);</span></a>
+<a name="17468"><span class="lineNum">   17468 </span>            :     }</a>
+<a name="17469"><span class="lineNum">   17469 </span>            :   }</a>
+<a name="17470"><span class="lineNum">   17470 </span>            :   return;</a>
+<a name="17471"><span class="lineNum">   17471 </span>            : }</a>
+<a name="17472"><span class="lineNum">   17472 </span>            : }</a>
+<a name="17473"><span class="lineNum">   17473 </span>            : }</a>
+<a name="17474"><span class="lineNum">   17474 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17475"><span class="lineNum">   17475 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="17476"><span class="lineNum">   17476 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="17477"><span class="lineNum">   17477 </span>            : </a>
+<a name="17478"><span class="lineNum">   17478 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17479"><span class="lineNum">   17479 </span>            : namespace PLMD{</a>
+<a name="17480"><span class="lineNum">   17480 </span>            : namespace lapack{</a>
+<a name="17481"><span class="lineNum">   17481 </span>            : using namespace blas;</a>
+<a name="17482"><span class="lineNum">   17482 </span>            : void</a>
+<a name="17483"><span class="lineNum">   17483 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgetrf,SGETRF)(int *m,</span></a>
+<a name="17484"><span class="lineNum">   17484 </span>            :         int *n,</a>
+<a name="17485"><span class="lineNum">   17485 </span>            :         float *a,</a>
+<a name="17486"><span class="lineNum">   17486 </span>            :         int *lda,</a>
+<a name="17487"><span class="lineNum">   17487 </span>            :         int *ipiv,</a>
+<a name="17488"><span class="lineNum">   17488 </span>            :         int *info)</a>
+<a name="17489"><span class="lineNum">   17489 </span>            : {</a>
+<a name="17490"><span class="lineNum">   17490 </span>            :   int mindim,jb;</a>
+<a name="17491"><span class="lineNum">   17491 </span>            :   int i,j,k,l;</a>
+<a name="17492"><span class="lineNum">   17492 </span>            :   int iinfo;</a>
+<a name="17493"><span class="lineNum">   17493 </span><span class="lineNoCov">          0 :   float minusone = -1.0;</span></a>
+<a name="17494"><span class="lineNum">   17494 </span><span class="lineNoCov">          0 :   float one = 1.0;</span></a>
+<a name="17495"><span class="lineNum">   17495 </span>            : </a>
+<a name="17496"><span class="lineNum">   17496 </span><span class="lineNoCov">          0 :   if(*m&lt;=0 || *n&lt;=0)</span></a>
+<a name="17497"><span class="lineNum">   17497 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="17498"><span class="lineNum">   17498 </span>            : </a>
+<a name="17499"><span class="lineNum">   17499 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="17500"><span class="lineNum">   17500 </span>            : </a>
+<a name="17501"><span class="lineNum">   17501 </span><span class="lineNoCov">          0 :   mindim = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="17502"><span class="lineNum">   17502 </span>            : </a>
+<a name="17503"><span class="lineNum">   17503 </span><span class="lineNoCov">          0 :   if(DGETRF_BLOCKSIZE&gt;=mindim) {</span></a>
+<a name="17504"><span class="lineNum">   17504 </span>            : </a>
+<a name="17505"><span class="lineNum">   17505 </span>            :     /* unblocked code */</a>
+<a name="17506"><span class="lineNum">   17506 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sgetf2,SGETF2)(m,n,a,lda,ipiv,info);</span></a>
+<a name="17507"><span class="lineNum">   17507 </span>            : </a>
+<a name="17508"><span class="lineNum">   17508 </span>            :   } else {</a>
+<a name="17509"><span class="lineNum">   17509 </span>            : </a>
+<a name="17510"><span class="lineNum">   17510 </span>            :     /* blocked case */</a>
+<a name="17511"><span class="lineNum">   17511 </span>            : </a>
+<a name="17512"><span class="lineNum">   17512 </span><span class="lineNoCov">          0 :     for(j=1;j&lt;=mindim;j+=DGETRF_BLOCKSIZE) {</span></a>
+<a name="17513"><span class="lineNum">   17513 </span><span class="lineNoCov">          0 :       jb = ( DGETRF_BLOCKSIZE &lt; (mindim-j+1)) ? DGETRF_BLOCKSIZE : (mindim-j+1);</span></a>
+<a name="17514"><span class="lineNum">   17514 </span>            :       /* factor diag. and subdiag blocks and test for singularity */</a>
+<a name="17515"><span class="lineNum">   17515 </span><span class="lineNoCov">          0 :       k = *m-j+1;</span></a>
+<a name="17516"><span class="lineNum">   17516 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sgetf2,SGETF2)(&amp;k,&amp;jb,&amp;(a[(j-1)*(*lda)+(j-1)]),lda,&amp;(ipiv[j-1]),&amp;iinfo);</span></a>
+<a name="17517"><span class="lineNum">   17517 </span>            :       </a>
+<a name="17518"><span class="lineNum">   17518 </span><span class="lineNoCov">          0 :       if(*info==0 &amp;&amp; iinfo&gt;0)</span></a>
+<a name="17519"><span class="lineNum">   17519 </span><span class="lineNoCov">          0 :         *info = iinfo + j - 1;</span></a>
+<a name="17520"><span class="lineNum">   17520 </span>            : </a>
+<a name="17521"><span class="lineNum">   17521 </span>            :       /* adjust pivot indices */</a>
+<a name="17522"><span class="lineNum">   17522 </span><span class="lineNoCov">          0 :       k = (*m &lt; (j+jb-1)) ? *m : (j+jb-1);</span></a>
+<a name="17523"><span class="lineNum">   17523 </span><span class="lineNoCov">          0 :       for(i=j;i&lt;=k;i++)</span></a>
+<a name="17524"><span class="lineNum">   17524 </span><span class="lineNoCov">          0 :         ipiv[i-1] += j - 1;</span></a>
+<a name="17525"><span class="lineNum">   17525 </span>            : </a>
+<a name="17526"><span class="lineNum">   17526 </span>            :       /* Apply to columns 1 throughj j-1 */</a>
+<a name="17527"><span class="lineNum">   17527 </span><span class="lineNoCov">          0 :       k = j - 1;</span></a>
+<a name="17528"><span class="lineNum">   17528 </span><span class="lineNoCov">          0 :       i = j + jb - 1;</span></a>
+<a name="17529"><span class="lineNum">   17529 </span><span class="lineNoCov">          0 :       l = 1;</span></a>
+<a name="17530"><span class="lineNum">   17530 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slaswp,SLASWP)(&amp;k,a,lda,&amp;j,&amp;i,ipiv,&amp;l);</span></a>
+<a name="17531"><span class="lineNum">   17531 </span><span class="lineNoCov">          0 :       if((j+jb)&lt;=*n) {</span></a>
+<a name="17532"><span class="lineNum">   17532 </span>            :         /* Apply to cols. j+jb through n */</a>
+<a name="17533"><span class="lineNum">   17533 </span><span class="lineNoCov">          0 :         k = *n-j-jb+1;</span></a>
+<a name="17534"><span class="lineNum">   17534 </span><span class="lineNoCov">          0 :         i = j+jb-1;</span></a>
+<a name="17535"><span class="lineNum">   17535 </span><span class="lineNoCov">          0 :         l = 1;</span></a>
+<a name="17536"><span class="lineNum">   17536 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaswp,SLASWP)(&amp;k,&amp;(a[(j+jb-1)*(*lda)+0]),lda,&amp;j,&amp;i,ipiv,&amp;l);</span></a>
+<a name="17537"><span class="lineNum">   17537 </span>            :         /* Compute block row of U */</a>
+<a name="17538"><span class="lineNum">   17538 </span><span class="lineNoCov">          0 :         k = *n-j-jb+1;</span></a>
+<a name="17539"><span class="lineNum">   17539 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Left&quot;,&quot;Lower&quot;,&quot;No transpose&quot;,&quot;Unit&quot;,&amp;jb,&amp;k,&amp;one,</span></a>
+<a name="17540"><span class="lineNum">   17540 </span><span class="lineNoCov">          0 :                &amp;(a[(j-1)*(*lda)+(j-1)]),lda,&amp;(a[(j+jb-1)*(*lda)+(j-1)]),lda);</span></a>
+<a name="17541"><span class="lineNum">   17541 </span>            : </a>
+<a name="17542"><span class="lineNum">   17542 </span><span class="lineNoCov">          0 :         if((j+jb)&lt;=*m) {</span></a>
+<a name="17543"><span class="lineNum">   17543 </span>            :           /* Update trailing submatrix */</a>
+<a name="17544"><span class="lineNum">   17544 </span><span class="lineNoCov">          0 :           k = *m-j-jb+1;</span></a>
+<a name="17545"><span class="lineNum">   17545 </span><span class="lineNoCov">          0 :           i = *n-j-jb+1;</span></a>
+<a name="17546"><span class="lineNum">   17546 </span><span class="lineNoCov">          0 :           PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;,&quot;No transpose&quot;,&amp;k,&amp;i,&amp;jb,&amp;minusone,</span></a>
+<a name="17547"><span class="lineNum">   17547 </span><span class="lineNoCov">          0 :                  &amp;(a[(j-1)*(*lda)+(j+jb-1)]),lda,</span></a>
+<a name="17548"><span class="lineNum">   17548 </span><span class="lineNoCov">          0 :                  &amp;(a[(j+jb-1)*(*lda)+(j-1)]),lda,&amp;one,</span></a>
+<a name="17549"><span class="lineNum">   17549 </span><span class="lineNoCov">          0 :                  &amp;(a[(j+jb-1)*(*lda)+(j+jb-1)]),lda);</span></a>
+<a name="17550"><span class="lineNum">   17550 </span>            :         }</a>
+<a name="17551"><span class="lineNum">   17551 </span>            : </a>
+<a name="17552"><span class="lineNum">   17552 </span>            :       }</a>
+<a name="17553"><span class="lineNum">   17553 </span>            :     }</a>
+<a name="17554"><span class="lineNum">   17554 </span>            :   }</a>
+<a name="17555"><span class="lineNum">   17555 </span>            : }</a>
+<a name="17556"><span class="lineNum">   17556 </span>            : }</a>
+<a name="17557"><span class="lineNum">   17557 </span>            : }</a>
+<a name="17558"><span class="lineNum">   17558 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17559"><span class="lineNum">   17559 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="17560"><span class="lineNum">   17560 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="17561"><span class="lineNum">   17561 </span>            : </a>
+<a name="17562"><span class="lineNum">   17562 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17563"><span class="lineNum">   17563 </span>            : namespace PLMD{</a>
+<a name="17564"><span class="lineNum">   17564 </span>            : namespace lapack{</a>
+<a name="17565"><span class="lineNum">   17565 </span>            : using namespace blas;</a>
+<a name="17566"><span class="lineNum">   17566 </span>            : void</a>
+<a name="17567"><span class="lineNum">   17567 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgetri,SGETRI)(int *n, </span></a>
+<a name="17568"><span class="lineNum">   17568 </span>            :         float *a, </a>
+<a name="17569"><span class="lineNum">   17569 </span>            :         int *lda, </a>
+<a name="17570"><span class="lineNum">   17570 </span>            :         int *ipiv, </a>
+<a name="17571"><span class="lineNum">   17571 </span>            :         float *work, </a>
+<a name="17572"><span class="lineNum">   17572 </span>            :         int *lwork, </a>
+<a name="17573"><span class="lineNum">   17573 </span>            :         int *info)</a>
+<a name="17574"><span class="lineNum">   17574 </span>            : {</a>
+<a name="17575"><span class="lineNum">   17575 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="17576"><span class="lineNum">   17576 </span>            : </a>
+<a name="17577"><span class="lineNum">   17577 </span>            :     int i__, j, jb, nb, jj, jp, nn, iws;</a>
+<a name="17578"><span class="lineNum">   17578 </span>            :     int nbmin;</a>
+<a name="17579"><span class="lineNum">   17579 </span>            :     int ldwork;</a>
+<a name="17580"><span class="lineNum">   17580 </span>            :     int lwkopt;</a>
+<a name="17581"><span class="lineNum">   17581 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="17582"><span class="lineNum">   17582 </span><span class="lineNoCov">          0 :     float c_b20 = -1.;</span></a>
+<a name="17583"><span class="lineNum">   17583 </span><span class="lineNoCov">          0 :     float c_b22 = 1.;</span></a>
+<a name="17584"><span class="lineNum">   17584 </span>            : </a>
+<a name="17585"><span class="lineNum">   17585 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="17586"><span class="lineNum">   17586 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="17587"><span class="lineNum">   17587 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="17588"><span class="lineNum">   17588 </span>            :     --ipiv;</a>
+<a name="17589"><span class="lineNum">   17589 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="17590"><span class="lineNum">   17590 </span>            : </a>
+<a name="17591"><span class="lineNum">   17591 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="17592"><span class="lineNum">   17592 </span>            :     nb = DGETRI_BLOCKSIZE;</a>
+<a name="17593"><span class="lineNum">   17593 </span><span class="lineNoCov">          0 :     lwkopt = *n * nb;</span></a>
+<a name="17594"><span class="lineNum">   17594 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="17595"><span class="lineNum">   17595 </span>            : </a>
+<a name="17596"><span class="lineNum">   17596 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="17597"><span class="lineNum">   17597 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="17598"><span class="lineNum">   17598 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; (*n)) {</span></a>
+<a name="17599"><span class="lineNum">   17599 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="17600"><span class="lineNum">   17600 </span><span class="lineNoCov">          0 :     } else if (*lwork &lt; (*n) &amp;&amp; *lwork!=-1) {</span></a>
+<a name="17601"><span class="lineNum">   17601 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="17602"><span class="lineNum">   17602 </span>            :     }</a>
+<a name="17603"><span class="lineNum">   17603 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="17604"><span class="lineNum">   17604 </span>            :         i__1 = -(*info);</a>
+<a name="17605"><span class="lineNum">   17605 </span>            :         return;</a>
+<a name="17606"><span class="lineNum">   17606 </span><span class="lineNoCov">          0 :     } else if (*lwork == -1) {</span></a>
+<a name="17607"><span class="lineNum">   17607 </span>            :         return;</a>
+<a name="17608"><span class="lineNum">   17608 </span>            :     }</a>
+<a name="17609"><span class="lineNum">   17609 </span>            : </a>
+<a name="17610"><span class="lineNum">   17610 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="17611"><span class="lineNum">   17611 </span>            :         return;</a>
+<a name="17612"><span class="lineNum">   17612 </span>            :     }</a>
+<a name="17613"><span class="lineNum">   17613 </span>            : </a>
+<a name="17614"><span class="lineNum">   17614 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(strtri,STRTRI)(&quot;Upper&quot;, &quot;Non-unit&quot;, n, &amp;a[a_offset], lda, info);</span></a>
+<a name="17615"><span class="lineNum">   17615 </span><span class="lineNoCov">          0 :     if (*info &gt; 0) {</span></a>
+<a name="17616"><span class="lineNum">   17616 </span>            :         return;</a>
+<a name="17617"><span class="lineNum">   17617 </span>            :     }</a>
+<a name="17618"><span class="lineNum">   17618 </span>            : </a>
+<a name="17619"><span class="lineNum">   17619 </span>            :     nbmin = 2;</a>
+<a name="17620"><span class="lineNum">   17620 </span><span class="lineNoCov">          0 :     ldwork = *n;</span></a>
+<a name="17621"><span class="lineNum">   17621 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *n) {</span></a>
+<a name="17622"><span class="lineNum">   17622 </span><span class="lineNoCov">          0 :         i__1 = ldwork * nb;</span></a>
+<a name="17623"><span class="lineNum">   17623 </span><span class="lineNoCov">          0 :         iws = (i__1&gt;1) ? i__1 : 1;</span></a>
+<a name="17624"><span class="lineNum">   17624 </span><span class="lineNoCov">          0 :         if (*lwork &lt; iws) {</span></a>
+<a name="17625"><span class="lineNum">   17625 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="17626"><span class="lineNum">   17626 </span>            :             nbmin = DGETRI_MINBLOCKSIZE;</a>
+<a name="17627"><span class="lineNum">   17627 </span>            :         }</a>
+<a name="17628"><span class="lineNum">   17628 </span>            :     } else {</a>
+<a name="17629"><span class="lineNum">   17629 </span>            :         iws = *n;</a>
+<a name="17630"><span class="lineNum">   17630 </span>            :     }</a>
+<a name="17631"><span class="lineNum">   17631 </span>            : </a>
+<a name="17632"><span class="lineNum">   17632 </span><span class="lineNoCov">          0 :     if (nb &lt; nbmin || nb &gt;= *n) {</span></a>
+<a name="17633"><span class="lineNum">   17633 </span>            : </a>
+<a name="17634"><span class="lineNum">   17634 </span><span class="lineNoCov">          0 :         for (j = *n; j &gt;= 1; --j) {</span></a>
+<a name="17635"><span class="lineNum">   17635 </span>            : </a>
+<a name="17636"><span class="lineNum">   17636 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="17637"><span class="lineNum">   17637 </span><span class="lineNoCov">          0 :             for (i__ = j + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="17638"><span class="lineNum">   17638 </span><span class="lineNoCov">          0 :                 work[i__] = a[i__ + j * a_dim1];</span></a>
+<a name="17639"><span class="lineNum">   17639 </span><span class="lineNoCov">          0 :                 a[i__ + j * a_dim1] = 0.;</span></a>
+<a name="17640"><span class="lineNum">   17640 </span>            :             }</a>
+<a name="17641"><span class="lineNum">   17641 </span>            : </a>
+<a name="17642"><span class="lineNum">   17642 </span><span class="lineNoCov">          0 :             if (j &lt; *n) {</span></a>
+<a name="17643"><span class="lineNum">   17643 </span><span class="lineNoCov">          0 :                 i__1 = *n - j;</span></a>
+<a name="17644"><span class="lineNum">   17644 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, n, &amp;i__1, &amp;c_b20, &amp;a[(j + 1) * a_dim1 </span></a>
+<a name="17645"><span class="lineNum">   17645 </span><span class="lineNoCov">          0 :                         + 1], lda, &amp;work[j + 1], &amp;c__1, &amp;c_b22, &amp;a[j * a_dim1 </span></a>
+<a name="17646"><span class="lineNum">   17646 </span><span class="lineNoCov">          0 :                         + 1], &amp;c__1);</span></a>
+<a name="17647"><span class="lineNum">   17647 </span>            :             }</a>
+<a name="17648"><span class="lineNum">   17648 </span>            :         }</a>
+<a name="17649"><span class="lineNum">   17649 </span>            :     } else {</a>
+<a name="17650"><span class="lineNum">   17650 </span>            : </a>
+<a name="17651"><span class="lineNum">   17651 </span><span class="lineNoCov">          0 :         nn = (*n - 1) / nb * nb + 1;</span></a>
+<a name="17652"><span class="lineNum">   17652 </span><span class="lineNoCov">          0 :         i__1 = -nb;</span></a>
+<a name="17653"><span class="lineNum">   17653 </span><span class="lineNoCov">          0 :         for (j = nn; i__1 &lt; 0 ? j &gt;= 1 : j &lt;= 1; j += i__1) {</span></a>
+<a name="17654"><span class="lineNum">   17654 </span><span class="lineNoCov">          0 :             i__2 = nb, i__3 = *n - j + 1;</span></a>
+<a name="17655"><span class="lineNum">   17655 </span><span class="lineNoCov">          0 :             jb = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="17656"><span class="lineNum">   17656 </span>            : </a>
+<a name="17657"><span class="lineNum">   17657 </span><span class="lineNoCov">          0 :             i__2 = j + jb - 1;</span></a>
+<a name="17658"><span class="lineNum">   17658 </span><span class="lineNoCov">          0 :             for (jj = j; jj &lt;= i__2; ++jj) {</span></a>
+<a name="17659"><span class="lineNum">   17659 </span><span class="lineNoCov">          0 :                 i__3 = *n;</span></a>
+<a name="17660"><span class="lineNum">   17660 </span><span class="lineNoCov">          0 :                 for (i__ = jj + 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="17661"><span class="lineNum">   17661 </span><span class="lineNoCov">          0 :                     work[i__ + (jj - j) * ldwork] = a[i__ + jj * a_dim1];</span></a>
+<a name="17662"><span class="lineNum">   17662 </span><span class="lineNoCov">          0 :                     a[i__ + jj * a_dim1] = 0.;</span></a>
+<a name="17663"><span class="lineNum">   17663 </span>            :                 }</a>
+<a name="17664"><span class="lineNum">   17664 </span>            :             }</a>
+<a name="17665"><span class="lineNum">   17665 </span>            : </a>
+<a name="17666"><span class="lineNum">   17666 </span><span class="lineNoCov">          0 :             if (j + jb &lt;= *n) {</span></a>
+<a name="17667"><span class="lineNum">   17667 </span><span class="lineNoCov">          0 :                 i__2 = *n - j - jb + 1;</span></a>
+<a name="17668"><span class="lineNum">   17668 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, n, &amp;jb, &amp;i__2, &amp;c_b20, </span></a>
+<a name="17669"><span class="lineNum">   17669 </span><span class="lineNoCov">          0 :                         &amp;a[(j + jb) * a_dim1 + 1], lda, &amp;work[j + jb], &amp;</span></a>
+<a name="17670"><span class="lineNum">   17670 </span><span class="lineNoCov">          0 :                         ldwork, &amp;c_b22, &amp;a[j * a_dim1 + 1], lda);</span></a>
+<a name="17671"><span class="lineNum">   17671 </span>            :             }</a>
+<a name="17672"><span class="lineNum">   17672 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, &amp;jb, &amp;c_b22, &amp;</span></a>
+<a name="17673"><span class="lineNum">   17673 </span><span class="lineNoCov">          0 :                     work[j], &amp;ldwork, &amp;a[j * a_dim1 + 1], lda);</span></a>
+<a name="17674"><span class="lineNum">   17674 </span>            :         }</a>
+<a name="17675"><span class="lineNum">   17675 </span>            :     }</a>
+<a name="17676"><span class="lineNum">   17676 </span>            : </a>
+<a name="17677"><span class="lineNum">   17677 </span><span class="lineNoCov">          0 :     for (j = *n - 1; j &gt;= 1; --j) {</span></a>
+<a name="17678"><span class="lineNum">   17678 </span><span class="lineNoCov">          0 :         jp = ipiv[j];</span></a>
+<a name="17679"><span class="lineNum">   17679 </span><span class="lineNoCov">          0 :         if (jp != j) {</span></a>
+<a name="17680"><span class="lineNum">   17680 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n, &amp;a[j * a_dim1 + 1], &amp;c__1, &amp;a[jp * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="17681"><span class="lineNum">   17681 </span>            :         }</a>
+<a name="17682"><span class="lineNum">   17682 </span>            :     }</a>
+<a name="17683"><span class="lineNum">   17683 </span>            : </a>
+<a name="17684"><span class="lineNum">   17684 </span><span class="lineNoCov">          0 :     work[1] = (float) iws;</span></a>
+<a name="17685"><span class="lineNum">   17685 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="17686"><span class="lineNum">   17686 </span>            : </a>
+<a name="17687"><span class="lineNum">   17687 </span>            : }</a>
+<a name="17688"><span class="lineNum">   17688 </span>            : </a>
+<a name="17689"><span class="lineNum">   17689 </span>            : </a>
+<a name="17690"><span class="lineNum">   17690 </span>            : }</a>
+<a name="17691"><span class="lineNum">   17691 </span>            : }</a>
+<a name="17692"><span class="lineNum">   17692 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17693"><span class="lineNum">   17693 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="17694"><span class="lineNum">   17694 </span>            : </a>
+<a name="17695"><span class="lineNum">   17695 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17696"><span class="lineNum">   17696 </span>            : namespace PLMD{</a>
+<a name="17697"><span class="lineNum">   17697 </span>            : namespace lapack{</a>
+<a name="17698"><span class="lineNum">   17698 </span>            : using namespace blas;</a>
+<a name="17699"><span class="lineNum">   17699 </span>            : void</a>
+<a name="17700"><span class="lineNum">   17700 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sgetrs,SGETRS)(const char *trans, </span></a>
+<a name="17701"><span class="lineNum">   17701 </span>            :         int *n, </a>
+<a name="17702"><span class="lineNum">   17702 </span>            :         int *nrhs, </a>
+<a name="17703"><span class="lineNum">   17703 </span>            :         float *a, </a>
+<a name="17704"><span class="lineNum">   17704 </span>            :         int *lda, </a>
+<a name="17705"><span class="lineNum">   17705 </span>            :         int *ipiv,</a>
+<a name="17706"><span class="lineNum">   17706 </span>            :         float *b, </a>
+<a name="17707"><span class="lineNum">   17707 </span>            :         int *ldb, </a>
+<a name="17708"><span class="lineNum">   17708 </span>            :         int *info)</a>
+<a name="17709"><span class="lineNum">   17709 </span>            : {</a>
+<a name="17710"><span class="lineNum">   17710 </span>            :     int a_dim1, a_offset, b_dim1, b_offset;</a>
+<a name="17711"><span class="lineNum">   17711 </span>            :     int notran;</a>
+<a name="17712"><span class="lineNum">   17712 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="17713"><span class="lineNum">   17713 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="17714"><span class="lineNum">   17714 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="17715"><span class="lineNum">   17715 </span>            : </a>
+<a name="17716"><span class="lineNum">   17716 </span>            :     a_dim1 = *lda;</a>
+<a name="17717"><span class="lineNum">   17717 </span>            :     a_offset = 1 + a_dim1;</a>
+<a name="17718"><span class="lineNum">   17718 </span>            :     a -= a_offset;</a>
+<a name="17719"><span class="lineNum">   17719 </span>            :     --ipiv;</a>
+<a name="17720"><span class="lineNum">   17720 </span>            :     b_dim1 = *ldb;</a>
+<a name="17721"><span class="lineNum">   17721 </span>            :     b_offset = 1 + b_dim1;</a>
+<a name="17722"><span class="lineNum">   17722 </span>            :     b -= b_offset;</a>
+<a name="17723"><span class="lineNum">   17723 </span>            : </a>
+<a name="17724"><span class="lineNum">   17724 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="17725"><span class="lineNum">   17725 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="17726"><span class="lineNum">   17726 </span>            : </a>
+<a name="17727"><span class="lineNum">   17727 </span><span class="lineNoCov">          0 :     if (*n &lt;= 0 || *nrhs &lt;= 0) </span></a>
+<a name="17728"><span class="lineNum">   17728 </span>            :         return;</a>
+<a name="17729"><span class="lineNum">   17729 </span>            : </a>
+<a name="17730"><span class="lineNum">   17730 </span><span class="lineNoCov">          0 :     if (notran) {</span></a>
+<a name="17731"><span class="lineNum">   17731 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaswp,SLASWP)(nrhs, &amp;b[b_offset], ldb, &amp;c__1, n, &amp;ipiv[1], &amp;c__1);</span></a>
+<a name="17732"><span class="lineNum">   17732 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Left&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="17733"><span class="lineNum">   17733 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="17734"><span class="lineNum">   17734 </span>            : </a>
+<a name="17735"><span class="lineNum">   17735 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Left&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Non-unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="17736"><span class="lineNum">   17736 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="17737"><span class="lineNum">   17737 </span>            :     } else {</a>
+<a name="17738"><span class="lineNum">   17738 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Left&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Non-unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="17739"><span class="lineNum">   17739 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="17740"><span class="lineNum">   17740 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Left&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, nrhs, &amp;one, </span></a>
+<a name="17741"><span class="lineNum">   17741 </span>            :                &amp;a[a_offset], lda, &amp;b[b_offset], ldb);</a>
+<a name="17742"><span class="lineNum">   17742 </span>            : </a>
+<a name="17743"><span class="lineNum">   17743 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaswp,SLASWP)(nrhs, &amp;b[b_offset], ldb, &amp;c__1, n, &amp;ipiv[1], &amp;c_n1);</span></a>
+<a name="17744"><span class="lineNum">   17744 </span>            :     }</a>
+<a name="17745"><span class="lineNum">   17745 </span>            : </a>
+<a name="17746"><span class="lineNum">   17746 </span>            :     return;</a>
+<a name="17747"><span class="lineNum">   17747 </span>            : </a>
+<a name="17748"><span class="lineNum">   17748 </span>            : } </a>
+<a name="17749"><span class="lineNum">   17749 </span>            : }</a>
+<a name="17750"><span class="lineNum">   17750 </span>            : }</a>
+<a name="17751"><span class="lineNum">   17751 </span>            : #include &lt;cmath&gt;</a>
+<a name="17752"><span class="lineNum">   17752 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17753"><span class="lineNum">   17753 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="17754"><span class="lineNum">   17754 </span>            : </a>
+<a name="17755"><span class="lineNum">   17755 </span>            : </a>
+<a name="17756"><span class="lineNum">   17756 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="17757"><span class="lineNum">   17757 </span>            : namespace PLMD{</a>
+<a name="17758"><span class="lineNum">   17758 </span>            : namespace lapack{</a>
+<a name="17759"><span class="lineNum">   17759 </span>            : using namespace blas;</a>
+<a name="17760"><span class="lineNum">   17760 </span>            : void </a>
+<a name="17761"><span class="lineNum">   17761 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slabrd,SLABRD)(int *m, </span></a>
+<a name="17762"><span class="lineNum">   17762 </span>            :         int *n, </a>
+<a name="17763"><span class="lineNum">   17763 </span>            :         int *nb,</a>
+<a name="17764"><span class="lineNum">   17764 </span>            :         float *a, </a>
+<a name="17765"><span class="lineNum">   17765 </span>            :         int *lda, </a>
+<a name="17766"><span class="lineNum">   17766 </span>            :         float *d__,</a>
+<a name="17767"><span class="lineNum">   17767 </span>            :         float *e,</a>
+<a name="17768"><span class="lineNum">   17768 </span>            :         float *tauq, </a>
+<a name="17769"><span class="lineNum">   17769 </span>            :         float *taup,</a>
+<a name="17770"><span class="lineNum">   17770 </span>            :         float *x,</a>
+<a name="17771"><span class="lineNum">   17771 </span>            :         int *ldx,</a>
+<a name="17772"><span class="lineNum">   17772 </span>            :         float *y,</a>
+<a name="17773"><span class="lineNum">   17773 </span>            :         int *ldy)</a>
+<a name="17774"><span class="lineNum">   17774 </span>            : {</a>
+<a name="17775"><span class="lineNum">   17775 </span>            :     int a_dim1, a_offset, x_dim1, x_offset, y_dim1, y_offset;</a>
+<a name="17776"><span class="lineNum">   17776 </span>            :     int i__1, i__2, i__3;</a>
+<a name="17777"><span class="lineNum">   17777 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="17778"><span class="lineNum">   17778 </span><span class="lineNoCov">          0 :     float minusone = -1.0;</span></a>
+<a name="17779"><span class="lineNum">   17779 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="17780"><span class="lineNum">   17780 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="17781"><span class="lineNum">   17781 </span>            :     int i__;</a>
+<a name="17782"><span class="lineNum">   17782 </span>            : </a>
+<a name="17783"><span class="lineNum">   17783 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="17784"><span class="lineNum">   17784 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="17785"><span class="lineNum">   17785 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="17786"><span class="lineNum">   17786 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="17787"><span class="lineNum">   17787 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="17788"><span class="lineNum">   17788 </span><span class="lineNoCov">          0 :     --tauq;</span></a>
+<a name="17789"><span class="lineNum">   17789 </span><span class="lineNoCov">          0 :     --taup;</span></a>
+<a name="17790"><span class="lineNum">   17790 </span><span class="lineNoCov">          0 :     x_dim1 = *ldx;</span></a>
+<a name="17791"><span class="lineNum">   17791 </span><span class="lineNoCov">          0 :     x_offset = 1 + x_dim1;</span></a>
+<a name="17792"><span class="lineNum">   17792 </span><span class="lineNoCov">          0 :     x -= x_offset;</span></a>
+<a name="17793"><span class="lineNum">   17793 </span><span class="lineNoCov">          0 :     y_dim1 = *ldy;</span></a>
+<a name="17794"><span class="lineNum">   17794 </span><span class="lineNoCov">          0 :     y_offset = 1 + y_dim1;</span></a>
+<a name="17795"><span class="lineNum">   17795 </span><span class="lineNoCov">          0 :     y -= y_offset;</span></a>
+<a name="17796"><span class="lineNum">   17796 </span>            : </a>
+<a name="17797"><span class="lineNum">   17797 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0 || *n &lt;= 0) {</span></a>
+<a name="17798"><span class="lineNum">   17798 </span>            :         return;</a>
+<a name="17799"><span class="lineNum">   17799 </span>            :     }</a>
+<a name="17800"><span class="lineNum">   17800 </span>            : </a>
+<a name="17801"><span class="lineNum">   17801 </span><span class="lineNoCov">          0 :     if (*m &gt;= *n) {</span></a>
+<a name="17802"><span class="lineNum">   17802 </span>            : </a>
+<a name="17803"><span class="lineNum">   17803 </span><span class="lineNoCov">          0 :         i__1 = *nb;</span></a>
+<a name="17804"><span class="lineNum">   17804 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="17805"><span class="lineNum">   17805 </span>            : </a>
+<a name="17806"><span class="lineNum">   17806 </span><span class="lineNoCov">          0 :             i__2 = *m - i__ + 1;</span></a>
+<a name="17807"><span class="lineNum">   17807 </span><span class="lineNoCov">          0 :             i__3 = i__ - 1;</span></a>
+<a name="17808"><span class="lineNum">   17808 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ + a_dim1], lda,</span></a>
+<a name="17809"><span class="lineNum">   17809 </span><span class="lineNoCov">          0 :                      &amp;y[i__ + y_dim1], ldy, &amp;one, &amp;a[i__ + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="17810"><span class="lineNum">   17810 </span><span class="lineNoCov">          0 :             i__2 = *m - i__ + 1;</span></a>
+<a name="17811"><span class="lineNum">   17811 </span><span class="lineNoCov">          0 :             i__3 = i__ - 1;</span></a>
+<a name="17812"><span class="lineNum">   17812 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;x[i__ + x_dim1], ldx,</span></a>
+<a name="17813"><span class="lineNum">   17813 </span><span class="lineNoCov">          0 :                    &amp;a[i__*a_dim1+1],&amp;c__1,&amp;one,&amp;a[i__+i__*a_dim1],&amp;c__1);</span></a>
+<a name="17814"><span class="lineNum">   17814 </span>            : </a>
+<a name="17815"><span class="lineNum">   17815 </span><span class="lineNoCov">          0 :             i__2 = *m - i__ + 1;</span></a>
+<a name="17816"><span class="lineNum">   17816 </span><span class="lineNoCov">          0 :             i__3 = i__ + 1;</span></a>
+<a name="17817"><span class="lineNum">   17817 </span><span class="lineNoCov">          0 :             if(*m&lt;i__3)</span></a>
+<a name="17818"><span class="lineNum">   17818 </span><span class="lineNoCov">          0 :               i__3 = *m;</span></a>
+<a name="17819"><span class="lineNum">   17819 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i__2, &amp;a[i__ + i__ * a_dim1], &amp;a[i__3 + i__ * a_dim1], </span></a>
+<a name="17820"><span class="lineNum">   17820 </span><span class="lineNoCov">          0 :                     &amp;c__1, &amp;tauq[i__]);</span></a>
+<a name="17821"><span class="lineNum">   17821 </span><span class="lineNoCov">          0 :             d__[i__] = a[i__ + i__ * a_dim1];</span></a>
+<a name="17822"><span class="lineNum">   17822 </span><span class="lineNoCov">          0 :             if (i__ &lt; *n) {</span></a>
+<a name="17823"><span class="lineNum">   17823 </span><span class="lineNoCov">          0 :                 a[i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="17824"><span class="lineNum">   17824 </span>            : </a>
+<a name="17825"><span class="lineNum">   17825 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="17826"><span class="lineNum">   17826 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="17827"><span class="lineNum">   17827 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + (i__ + 1) * </span></a>
+<a name="17828"><span class="lineNum">   17828 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;</span></a>
+<a name="17829"><span class="lineNum">   17829 </span><span class="lineNoCov">          0 :                         y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17830"><span class="lineNum">   17830 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="17831"><span class="lineNum">   17831 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17832"><span class="lineNum">   17832 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + a_dim1], </span></a>
+<a name="17833"><span class="lineNum">   17833 </span><span class="lineNoCov">          0 :                         lda, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[i__ * </span></a>
+<a name="17834"><span class="lineNum">   17834 </span><span class="lineNoCov">          0 :                         y_dim1 + 1], &amp;c__1);</span></a>
+<a name="17835"><span class="lineNum">   17835 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17836"><span class="lineNum">   17836 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17837"><span class="lineNum">   17837 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;y[i__ + 1 + </span></a>
+<a name="17838"><span class="lineNum">   17838 </span><span class="lineNoCov">          0 :                         y_dim1], ldy, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, &amp;y[</span></a>
+<a name="17839"><span class="lineNum">   17839 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17840"><span class="lineNum">   17840 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="17841"><span class="lineNum">   17841 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17842"><span class="lineNum">   17842 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;x[i__ + x_dim1], </span></a>
+<a name="17843"><span class="lineNum">   17843 </span><span class="lineNoCov">          0 :                         ldx, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[i__ * </span></a>
+<a name="17844"><span class="lineNum">   17844 </span><span class="lineNoCov">          0 :                         y_dim1 + 1], &amp;c__1);</span></a>
+<a name="17845"><span class="lineNum">   17845 </span><span class="lineNoCov">          0 :                 i__2 = i__ - 1;</span></a>
+<a name="17846"><span class="lineNum">   17846 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="17847"><span class="lineNum">   17847 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[(i__ + 1) * </span></a>
+<a name="17848"><span class="lineNum">   17848 </span><span class="lineNoCov">          0 :                         a_dim1 + 1], lda, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, </span></a>
+<a name="17849"><span class="lineNum">   17849 </span><span class="lineNoCov">          0 :                         &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17850"><span class="lineNum">   17850 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17851"><span class="lineNum">   17851 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__2, &amp;tauq[i__], &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17852"><span class="lineNum">   17852 </span>            : </a>
+<a name="17853"><span class="lineNum">   17853 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17854"><span class="lineNum">   17854 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__, &amp;minusone, &amp;y[i__ + 1 + </span></a>
+<a name="17855"><span class="lineNum">   17855 </span><span class="lineNoCov">          0 :                         y_dim1], ldy, &amp;a[i__ + a_dim1], lda, &amp;one, &amp;a[i__ + (</span></a>
+<a name="17856"><span class="lineNum">   17856 </span><span class="lineNoCov">          0 :                         i__ + 1) * a_dim1], lda);</span></a>
+<a name="17857"><span class="lineNum">   17857 </span><span class="lineNoCov">          0 :                 i__2 = i__ - 1;</span></a>
+<a name="17858"><span class="lineNum">   17858 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="17859"><span class="lineNum">   17859 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[(i__ + 1) * </span></a>
+<a name="17860"><span class="lineNum">   17860 </span><span class="lineNoCov">          0 :                         a_dim1 + 1], lda, &amp;x[i__ + x_dim1], ldx, &amp;one, &amp;a[</span></a>
+<a name="17861"><span class="lineNum">   17861 </span><span class="lineNoCov">          0 :                         i__ + (i__ + 1) * a_dim1], lda);</span></a>
+<a name="17862"><span class="lineNum">   17862 </span>            : </a>
+<a name="17863"><span class="lineNum">   17863 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17864"><span class="lineNum">   17864 </span><span class="lineNoCov">          0 :                 i__3 = i__ + 2;</span></a>
+<a name="17865"><span class="lineNum">   17865 </span><span class="lineNoCov">          0 :                 if(*n&lt;i__3)</span></a>
+<a name="17866"><span class="lineNum">   17866 </span><span class="lineNoCov">          0 :                   i__3 = *n;</span></a>
+<a name="17867"><span class="lineNum">   17867 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i__2, &amp;a[i__ + (i__ + 1) * a_dim1], </span></a>
+<a name="17868"><span class="lineNum">   17868 </span><span class="lineNoCov">          0 :                         &amp;a[i__ + i__3 * a_dim1], lda, &amp;taup[i__]);</span></a>
+<a name="17869"><span class="lineNum">   17869 </span><span class="lineNoCov">          0 :                 e[i__] = a[i__ + (i__ + 1) * a_dim1];</span></a>
+<a name="17870"><span class="lineNum">   17870 </span><span class="lineNoCov">          0 :                 a[i__ + (i__ + 1) * a_dim1] = 1.;</span></a>
+<a name="17871"><span class="lineNum">   17871 </span>            : </a>
+<a name="17872"><span class="lineNum">   17872 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17873"><span class="lineNum">   17873 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="17874"><span class="lineNum">   17874 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + 1 + (i__ </span></a>
+<a name="17875"><span class="lineNum">   17875 </span><span class="lineNoCov">          0 :                         + 1) * a_dim1], lda, &amp;a[i__ + (i__ + 1) * a_dim1], </span></a>
+<a name="17876"><span class="lineNum">   17876 </span><span class="lineNoCov">          0 :                         lda, &amp;zero, &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17877"><span class="lineNum">   17877 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17878"><span class="lineNum">   17878 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__, &amp;one, &amp;y[i__ + 1 + y_dim1], </span></a>
+<a name="17879"><span class="lineNum">   17879 </span><span class="lineNoCov">          0 :                         ldy, &amp;a[i__ + (i__ + 1) * a_dim1], lda, &amp;zero, &amp;x[</span></a>
+<a name="17880"><span class="lineNum">   17880 </span><span class="lineNoCov">          0 :                         i__ * x_dim1 + 1], &amp;c__1);</span></a>
+<a name="17881"><span class="lineNum">   17881 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17882"><span class="lineNum">   17882 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__, &amp;minusone, &amp;a[i__ + 1 + </span></a>
+<a name="17883"><span class="lineNum">   17883 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="17884"><span class="lineNum">   17884 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17885"><span class="lineNum">   17885 </span><span class="lineNoCov">          0 :                 i__2 = i__ - 1;</span></a>
+<a name="17886"><span class="lineNum">   17886 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="17887"><span class="lineNum">   17887 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[(i__ + 1) * </span></a>
+<a name="17888"><span class="lineNum">   17888 </span><span class="lineNoCov">          0 :                         a_dim1 + 1], lda, &amp;a[i__ + (i__ + 1) * a_dim1], lda, &amp;</span></a>
+<a name="17889"><span class="lineNum">   17889 </span><span class="lineNoCov">          0 :                         zero, &amp;x[i__ * x_dim1 + 1], &amp;c__1);</span></a>
+<a name="17890"><span class="lineNum">   17890 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17891"><span class="lineNum">   17891 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17892"><span class="lineNum">   17892 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;x[i__ + 1 + </span></a>
+<a name="17893"><span class="lineNum">   17893 </span><span class="lineNoCov">          0 :                         x_dim1], ldx, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="17894"><span class="lineNum">   17894 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17895"><span class="lineNum">   17895 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17896"><span class="lineNum">   17896 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__2, &amp;taup[i__], &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17897"><span class="lineNum">   17897 </span>            :             }</a>
+<a name="17898"><span class="lineNum">   17898 </span>            :         }</a>
+<a name="17899"><span class="lineNum">   17899 </span>            :     } else {</a>
+<a name="17900"><span class="lineNum">   17900 </span>            : </a>
+<a name="17901"><span class="lineNum">   17901 </span><span class="lineNoCov">          0 :         i__1 = *nb;</span></a>
+<a name="17902"><span class="lineNum">   17902 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="17903"><span class="lineNum">   17903 </span>            : </a>
+<a name="17904"><span class="lineNum">   17904 </span><span class="lineNoCov">          0 :             i__2 = *n - i__ + 1;</span></a>
+<a name="17905"><span class="lineNum">   17905 </span><span class="lineNoCov">          0 :             i__3 = i__ - 1;</span></a>
+<a name="17906"><span class="lineNum">   17906 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;y[i__ + y_dim1], ldy,</span></a>
+<a name="17907"><span class="lineNum">   17907 </span><span class="lineNoCov">          0 :                      &amp;a[i__ + a_dim1], lda, &amp;one, &amp;a[i__ + i__ * a_dim1],lda);</span></a>
+<a name="17908"><span class="lineNum">   17908 </span><span class="lineNoCov">          0 :             i__2 = i__ - 1;</span></a>
+<a name="17909"><span class="lineNum">   17909 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="17910"><span class="lineNum">   17910 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ * a_dim1 + 1], </span></a>
+<a name="17911"><span class="lineNum">   17911 </span><span class="lineNoCov">          0 :                     lda, &amp;x[i__ + x_dim1], ldx, &amp;one,&amp;a[i__+i__*a_dim1],lda);</span></a>
+<a name="17912"><span class="lineNum">   17912 </span>            : </a>
+<a name="17913"><span class="lineNum">   17913 </span><span class="lineNoCov">          0 :             i__2 = *n - i__ + 1;</span></a>
+<a name="17914"><span class="lineNum">   17914 </span><span class="lineNoCov">          0 :             i__3 = i__ + 1;</span></a>
+<a name="17915"><span class="lineNum">   17915 </span><span class="lineNoCov">          0 :             if(*n&lt;i__3)</span></a>
+<a name="17916"><span class="lineNum">   17916 </span><span class="lineNoCov">          0 :               i__3 = *n;</span></a>
+<a name="17917"><span class="lineNum">   17917 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i__2, &amp;a[i__ + i__ * a_dim1], </span></a>
+<a name="17918"><span class="lineNum">   17918 </span><span class="lineNoCov">          0 :                     &amp;a[i__ + i__3 * a_dim1], lda, &amp;taup[i__]);</span></a>
+<a name="17919"><span class="lineNum">   17919 </span><span class="lineNoCov">          0 :             d__[i__] = a[i__ + i__ * a_dim1];</span></a>
+<a name="17920"><span class="lineNum">   17920 </span><span class="lineNoCov">          0 :             if (i__ &lt; *m) {</span></a>
+<a name="17921"><span class="lineNum">   17921 </span><span class="lineNoCov">          0 :                 a[i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="17922"><span class="lineNum">   17922 </span>            : </a>
+<a name="17923"><span class="lineNum">   17923 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17924"><span class="lineNum">   17924 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="17925"><span class="lineNum">   17925 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;,&amp;i__2,&amp;i__3,&amp;one,&amp;a[i__+1+i__*a_dim1], </span></a>
+<a name="17926"><span class="lineNum">   17926 </span>            :                        lda, &amp;a[i__ + i__ * a_dim1], lda, &amp;zero, </a>
+<a name="17927"><span class="lineNum">   17927 </span><span class="lineNoCov">          0 :                        &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17928"><span class="lineNum">   17928 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__ + 1;</span></a>
+<a name="17929"><span class="lineNum">   17929 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17930"><span class="lineNum">   17930 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;y[i__ + y_dim1], </span></a>
+<a name="17931"><span class="lineNum">   17931 </span><span class="lineNoCov">          0 :                         ldy, &amp;a[i__ + i__ * a_dim1], lda, &amp;zero, &amp;x[i__ * </span></a>
+<a name="17932"><span class="lineNum">   17932 </span><span class="lineNoCov">          0 :                         x_dim1 + 1], &amp;c__1);</span></a>
+<a name="17933"><span class="lineNum">   17933 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17934"><span class="lineNum">   17934 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17935"><span class="lineNum">   17935 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ + 1 + </span></a>
+<a name="17936"><span class="lineNum">   17936 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="17937"><span class="lineNum">   17937 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17938"><span class="lineNum">   17938 </span><span class="lineNoCov">          0 :                 i__2 = i__ - 1;</span></a>
+<a name="17939"><span class="lineNum">   17939 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="17940"><span class="lineNum">   17940 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ * a_dim1 + </span></a>
+<a name="17941"><span class="lineNum">   17941 </span><span class="lineNoCov">          0 :                         1], lda, &amp;a[i__ + i__ * a_dim1], lda, &amp;zero, &amp;x[i__ *</span></a>
+<a name="17942"><span class="lineNum">   17942 </span><span class="lineNoCov">          0 :                          x_dim1 + 1], &amp;c__1);</span></a>
+<a name="17943"><span class="lineNum">   17943 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17944"><span class="lineNum">   17944 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17945"><span class="lineNum">   17945 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;x[i__ + 1 + </span></a>
+<a name="17946"><span class="lineNum">   17946 </span><span class="lineNoCov">          0 :                         x_dim1], ldx, &amp;x[i__ * x_dim1 + 1], &amp;c__1, &amp;one, &amp;x[</span></a>
+<a name="17947"><span class="lineNum">   17947 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17948"><span class="lineNum">   17948 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17949"><span class="lineNum">   17949 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__2, &amp;taup[i__], &amp;x[i__ + 1 + i__ * x_dim1], &amp;c__1);</span></a>
+<a name="17950"><span class="lineNum">   17950 </span>            : </a>
+<a name="17951"><span class="lineNum">   17951 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17952"><span class="lineNum">   17952 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17953"><span class="lineNum">   17953 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;a[i__ + 1 + </span></a>
+<a name="17954"><span class="lineNum">   17954 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;y[i__ + y_dim1], ldy, &amp;one, &amp;a[i__ + </span></a>
+<a name="17955"><span class="lineNum">   17955 </span><span class="lineNoCov">          0 :                         1 + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="17956"><span class="lineNum">   17956 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17957"><span class="lineNum">   17957 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__, &amp;minusone, &amp;x[i__ + 1 + </span></a>
+<a name="17958"><span class="lineNum">   17958 </span><span class="lineNoCov">          0 :                         x_dim1], ldx, &amp;a[i__ * a_dim1 + 1], &amp;c__1, &amp;one, &amp;a[</span></a>
+<a name="17959"><span class="lineNum">   17959 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="17960"><span class="lineNum">   17960 </span>            : </a>
+<a name="17961"><span class="lineNum">   17961 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17962"><span class="lineNum">   17962 </span><span class="lineNoCov">          0 :                 i__3 = i__ + 2;</span></a>
+<a name="17963"><span class="lineNum">   17963 </span><span class="lineNoCov">          0 :                 if(*m&lt;i__3)</span></a>
+<a name="17964"><span class="lineNum">   17964 </span><span class="lineNoCov">          0 :                   i__3 = *m;</span></a>
+<a name="17965"><span class="lineNum">   17965 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i__2, &amp;a[i__ + 1 + i__ * a_dim1], </span></a>
+<a name="17966"><span class="lineNum">   17966 </span><span class="lineNoCov">          0 :                         &amp;a[i__3 + i__ * a_dim1], &amp;c__1, &amp;tauq[i__]);</span></a>
+<a name="17967"><span class="lineNum">   17967 </span><span class="lineNoCov">          0 :                 e[i__] = a[i__ + 1 + i__ * a_dim1];</span></a>
+<a name="17968"><span class="lineNum">   17968 </span><span class="lineNoCov">          0 :                 a[i__ + 1 + i__ * a_dim1] = 1.;</span></a>
+<a name="17969"><span class="lineNum">   17969 </span>            : </a>
+<a name="17970"><span class="lineNum">   17970 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17971"><span class="lineNum">   17971 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__;</span></a>
+<a name="17972"><span class="lineNum">   17972 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + 1 + (i__ + </span></a>
+<a name="17973"><span class="lineNum">   17973 </span><span class="lineNoCov">          0 :                         1) * a_dim1], lda, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1, </span></a>
+<a name="17974"><span class="lineNum">   17974 </span><span class="lineNoCov">          0 :                         &amp;zero, &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17975"><span class="lineNum">   17975 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17976"><span class="lineNum">   17976 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17977"><span class="lineNum">   17977 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;one, &amp;a[i__ + 1 + a_dim1],</span></a>
+<a name="17978"><span class="lineNum">   17978 </span><span class="lineNoCov">          0 :                          lda, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[</span></a>
+<a name="17979"><span class="lineNum">   17979 </span><span class="lineNoCov">          0 :                         i__ * y_dim1 + 1], &amp;c__1);</span></a>
+<a name="17980"><span class="lineNum">   17980 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17981"><span class="lineNum">   17981 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="17982"><span class="lineNum">   17982 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;minusone, &amp;y[i__ + 1 + </span></a>
+<a name="17983"><span class="lineNum">   17983 </span><span class="lineNoCov">          0 :                         y_dim1], ldy, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, &amp;y[</span></a>
+<a name="17984"><span class="lineNum">   17984 </span><span class="lineNoCov">          0 :                         i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17985"><span class="lineNum">   17985 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__;</span></a>
+<a name="17986"><span class="lineNum">   17986 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__, &amp;one, &amp;x[i__ + 1 + x_dim1], </span></a>
+<a name="17987"><span class="lineNum">   17987 </span><span class="lineNoCov">          0 :                         ldx, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1, &amp;zero, &amp;y[</span></a>
+<a name="17988"><span class="lineNum">   17988 </span><span class="lineNoCov">          0 :                         i__ * y_dim1 + 1], &amp;c__1);</span></a>
+<a name="17989"><span class="lineNum">   17989 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17990"><span class="lineNum">   17990 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__, &amp;i__2, &amp;minusone, &amp;a[(i__ + 1) * a_dim1 </span></a>
+<a name="17991"><span class="lineNum">   17991 </span><span class="lineNoCov">          0 :                         + 1], lda, &amp;y[i__ * y_dim1 + 1], &amp;c__1, &amp;one, &amp;y[i__ </span></a>
+<a name="17992"><span class="lineNum">   17992 </span><span class="lineNoCov">          0 :                         + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17993"><span class="lineNum">   17993 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__;</span></a>
+<a name="17994"><span class="lineNum">   17994 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__2, &amp;tauq[i__], &amp;y[i__ + 1 + i__ * y_dim1], &amp;c__1);</span></a>
+<a name="17995"><span class="lineNum">   17995 </span>            :             }</a>
+<a name="17996"><span class="lineNum">   17996 </span>            :         }</a>
+<a name="17997"><span class="lineNum">   17997 </span>            :     }</a>
+<a name="17998"><span class="lineNum">   17998 </span>            :     return;</a>
+<a name="17999"><span class="lineNum">   17999 </span>            : } </a>
+<a name="18000"><span class="lineNum">   18000 </span>            : </a>
+<a name="18001"><span class="lineNum">   18001 </span>            : }</a>
+<a name="18002"><span class="lineNum">   18002 </span>            : }</a>
+<a name="18003"><span class="lineNum">   18003 </span>            : #include &lt;cctype&gt;</a>
+<a name="18004"><span class="lineNum">   18004 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18005"><span class="lineNum">   18005 </span>            : </a>
+<a name="18006"><span class="lineNum">   18006 </span>            : /* LAPACK */</a>
+<a name="18007"><span class="lineNum">   18007 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18008"><span class="lineNum">   18008 </span>            : namespace PLMD{</a>
+<a name="18009"><span class="lineNum">   18009 </span>            : namespace lapack{</a>
+<a name="18010"><span class="lineNum">   18010 </span>            : using namespace blas;</a>
+<a name="18011"><span class="lineNum">   18011 </span>            : void</a>
+<a name="18012"><span class="lineNum">   18012 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(const char *uplo,</span></a>
+<a name="18013"><span class="lineNum">   18013 </span>            :         int *m,</a>
+<a name="18014"><span class="lineNum">   18014 </span>            :         int *n,</a>
+<a name="18015"><span class="lineNum">   18015 </span>            :         float *a,</a>
+<a name="18016"><span class="lineNum">   18016 </span>            :         int *lda,</a>
+<a name="18017"><span class="lineNum">   18017 </span>            :         float *b,</a>
+<a name="18018"><span class="lineNum">   18018 </span>            :         int *ldb)</a>
+<a name="18019"><span class="lineNum">   18019 </span>            : {</a>
+<a name="18020"><span class="lineNum">   18020 </span>            :   int i,j,minjm;</a>
+<a name="18021"><span class="lineNum">   18021 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="18022"><span class="lineNum">   18022 </span>            : </a>
+<a name="18023"><span class="lineNum">   18023 </span><span class="lineNoCov">          0 :   if(ch=='U') {</span></a>
+<a name="18024"><span class="lineNum">   18024 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="18025"><span class="lineNum">   18025 </span><span class="lineNoCov">          0 :       minjm = (j &lt; (*m-1)) ? j : (*m-1);</span></a>
+<a name="18026"><span class="lineNum">   18026 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;=minjm;i++)</span></a>
+<a name="18027"><span class="lineNum">   18027 </span><span class="lineNoCov">          0 :         b[j*(*ldb)+i] = a[j*(*lda)+i];</span></a>
+<a name="18028"><span class="lineNum">   18028 </span>            :     }</a>
+<a name="18029"><span class="lineNum">   18029 </span><span class="lineNoCov">          0 :   } else if(ch=='L') {</span></a>
+<a name="18030"><span class="lineNum">   18030 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="18031"><span class="lineNum">   18031 </span><span class="lineNoCov">          0 :       for(i=j;i&lt;*m;i++)</span></a>
+<a name="18032"><span class="lineNum">   18032 </span><span class="lineNoCov">          0 :         b[j*(*ldb)+i] = a[j*(*lda)+i];</span></a>
+<a name="18033"><span class="lineNum">   18033 </span>            :     }</a>
+<a name="18034"><span class="lineNum">   18034 </span>            :   } else {</a>
+<a name="18035"><span class="lineNum">   18035 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="18036"><span class="lineNum">   18036 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++)</span></a>
+<a name="18037"><span class="lineNum">   18037 </span><span class="lineNoCov">          0 :         b[j*(*ldb)+i] = a[j*(*lda)+i];</span></a>
+<a name="18038"><span class="lineNum">   18038 </span>            :     }    </a>
+<a name="18039"><span class="lineNum">   18039 </span>            :   }</a>
+<a name="18040"><span class="lineNum">   18040 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="18041"><span class="lineNum">   18041 </span>            : }</a>
+<a name="18042"><span class="lineNum">   18042 </span>            : }</a>
+<a name="18043"><span class="lineNum">   18043 </span>            : #include &lt;cmath&gt;</a>
+<a name="18044"><span class="lineNum">   18044 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18045"><span class="lineNum">   18045 </span>            : </a>
+<a name="18046"><span class="lineNum">   18046 </span>            : </a>
+<a name="18047"><span class="lineNum">   18047 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18048"><span class="lineNum">   18048 </span>            : namespace PLMD{</a>
+<a name="18049"><span class="lineNum">   18049 </span>            : namespace lapack{</a>
+<a name="18050"><span class="lineNum">   18050 </span>            : using namespace blas;</a>
+<a name="18051"><span class="lineNum">   18051 </span>            : void</a>
+<a name="18052"><span class="lineNum">   18052 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slae2,SLAE2)(float *a, </span></a>
+<a name="18053"><span class="lineNum">   18053 </span>            :        float *b,</a>
+<a name="18054"><span class="lineNum">   18054 </span>            :        float *c__, </a>
+<a name="18055"><span class="lineNum">   18055 </span>            :        float *rt1, </a>
+<a name="18056"><span class="lineNum">   18056 </span>            :        float *rt2)</a>
+<a name="18057"><span class="lineNum">   18057 </span>            : {</a>
+<a name="18058"><span class="lineNum">   18058 </span>            :     float d__1;</a>
+<a name="18059"><span class="lineNum">   18059 </span>            :     float ab, df, tb, sm, rt, adf, acmn, acmx;</a>
+<a name="18060"><span class="lineNum">   18060 </span>            : </a>
+<a name="18061"><span class="lineNum">   18061 </span>            : </a>
+<a name="18062"><span class="lineNum">   18062 </span><span class="lineNoCov">          0 :     sm = *a + *c__;</span></a>
+<a name="18063"><span class="lineNum">   18063 </span><span class="lineNoCov">          0 :     df = *a - *c__;</span></a>
+<a name="18064"><span class="lineNum">   18064 </span>            :     adf = std::abs(df);</a>
+<a name="18065"><span class="lineNum">   18065 </span><span class="lineNoCov">          0 :     tb = *b + *b;</span></a>
+<a name="18066"><span class="lineNum">   18066 </span>            :     ab = std::abs(tb);</a>
+<a name="18067"><span class="lineNum">   18067 </span><span class="lineNoCov">          0 :     if (std::abs(*a) &gt; std::abs(*c__)) {</span></a>
+<a name="18068"><span class="lineNum">   18068 </span>            :         acmx = *a;</a>
+<a name="18069"><span class="lineNum">   18069 </span>            :         acmn = *c__;</a>
+<a name="18070"><span class="lineNum">   18070 </span>            :     } else {</a>
+<a name="18071"><span class="lineNum">   18071 </span>            :         acmx = *c__;</a>
+<a name="18072"><span class="lineNum">   18072 </span>            :         acmn = *a;</a>
+<a name="18073"><span class="lineNum">   18073 </span>            :     }</a>
+<a name="18074"><span class="lineNum">   18074 </span><span class="lineNoCov">          0 :     if (adf &gt; ab) {</span></a>
+<a name="18075"><span class="lineNum">   18075 </span><span class="lineNoCov">          0 :         d__1 = ab / adf;</span></a>
+<a name="18076"><span class="lineNum">   18076 </span><span class="lineNoCov">          0 :         rt = adf *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="18077"><span class="lineNum">   18077 </span><span class="lineNoCov">          0 :     } else if (adf &lt; ab) {</span></a>
+<a name="18078"><span class="lineNum">   18078 </span><span class="lineNoCov">          0 :         d__1 = adf / ab;</span></a>
+<a name="18079"><span class="lineNum">   18079 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="18080"><span class="lineNum">   18080 </span>            :     } else {</a>
+<a name="18081"><span class="lineNum">   18081 </span>            : </a>
+<a name="18082"><span class="lineNum">   18082 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(2.);</span></a>
+<a name="18083"><span class="lineNum">   18083 </span>            :     }</a>
+<a name="18084"><span class="lineNum">   18084 </span><span class="lineNoCov">          0 :     if (sm &lt; 0.) {</span></a>
+<a name="18085"><span class="lineNum">   18085 </span><span class="lineNoCov">          0 :         *rt1 = (sm - rt) * .5;</span></a>
+<a name="18086"><span class="lineNum">   18086 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="18087"><span class="lineNum">   18087 </span><span class="lineNoCov">          0 :     } else if (sm &gt; 0.) {</span></a>
+<a name="18088"><span class="lineNum">   18088 </span><span class="lineNoCov">          0 :         *rt1 = (sm + rt) * .5;</span></a>
+<a name="18089"><span class="lineNum">   18089 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="18090"><span class="lineNum">   18090 </span>            :     } else {</a>
+<a name="18091"><span class="lineNum">   18091 </span><span class="lineNoCov">          0 :         *rt1 = rt * .5;</span></a>
+<a name="18092"><span class="lineNum">   18092 </span><span class="lineNoCov">          0 :         *rt2 = rt * -.5;</span></a>
+<a name="18093"><span class="lineNum">   18093 </span>            :     }</a>
+<a name="18094"><span class="lineNum">   18094 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="18095"><span class="lineNum">   18095 </span>            : </a>
+<a name="18096"><span class="lineNum">   18096 </span>            : }</a>
+<a name="18097"><span class="lineNum">   18097 </span>            : </a>
+<a name="18098"><span class="lineNum">   18098 </span>            : </a>
+<a name="18099"><span class="lineNum">   18099 </span>            : }</a>
+<a name="18100"><span class="lineNum">   18100 </span>            : }</a>
+<a name="18101"><span class="lineNum">   18101 </span>            : #include &lt;cmath&gt;</a>
+<a name="18102"><span class="lineNum">   18102 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18103"><span class="lineNum">   18103 </span>            : </a>
+<a name="18104"><span class="lineNum">   18104 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18105"><span class="lineNum">   18105 </span>            : namespace PLMD{</a>
+<a name="18106"><span class="lineNum">   18106 </span>            : namespace lapack{</a>
+<a name="18107"><span class="lineNum">   18107 </span>            : using namespace blas;</a>
+<a name="18108"><span class="lineNum">   18108 </span>            : void</a>
+<a name="18109"><span class="lineNum">   18109 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slaebz,SLAEBZ)(int *ijob,</span></a>
+<a name="18110"><span class="lineNum">   18110 </span>            :         int *nitmax,</a>
+<a name="18111"><span class="lineNum">   18111 </span>            :         int *n, </a>
+<a name="18112"><span class="lineNum">   18112 </span>            :         int *mmax,</a>
+<a name="18113"><span class="lineNum">   18113 </span>            :         int *minp,</a>
+<a name="18114"><span class="lineNum">   18114 </span>            :         int *nbmin,</a>
+<a name="18115"><span class="lineNum">   18115 </span>            :         float *abstol, </a>
+<a name="18116"><span class="lineNum">   18116 </span>            :         float *reltol, </a>
+<a name="18117"><span class="lineNum">   18117 </span>            :         float *pivmin, </a>
+<a name="18118"><span class="lineNum">   18118 </span>            :         float *d__,</a>
+<a name="18119"><span class="lineNum">   18119 </span>            :         float *e,</a>
+<a name="18120"><span class="lineNum">   18120 </span>            :         float *e2, </a>
+<a name="18121"><span class="lineNum">   18121 </span>            :         int *nval,</a>
+<a name="18122"><span class="lineNum">   18122 </span>            :         float *ab, </a>
+<a name="18123"><span class="lineNum">   18123 </span>            :         float *c__, </a>
+<a name="18124"><span class="lineNum">   18124 </span>            :         int *mout, </a>
+<a name="18125"><span class="lineNum">   18125 </span>            :         int *nab,</a>
+<a name="18126"><span class="lineNum">   18126 </span>            :         float *work,</a>
+<a name="18127"><span class="lineNum">   18127 </span>            :         int *iwork, </a>
+<a name="18128"><span class="lineNum">   18128 </span>            :         int *info)</a>
+<a name="18129"><span class="lineNum">   18129 </span>            : {</a>
+<a name="18130"><span class="lineNum">   18130 </span>            :     int nab_dim1, nab_offset, ab_dim1, ab_offset, i__1, i__2, i__3, i__4, </a>
+<a name="18131"><span class="lineNum">   18131 </span>            :             i__5, i__6;</a>
+<a name="18132"><span class="lineNum">   18132 </span>            :     float d__1, d__2, d__3, d__4;</a>
+<a name="18133"><span class="lineNum">   18133 </span>            : </a>
+<a name="18134"><span class="lineNum">   18134 </span>            :     int j, kf, ji, kl, jp, jit;</a>
+<a name="18135"><span class="lineNum">   18135 </span>            :     float tmp1, tmp2;</a>
+<a name="18136"><span class="lineNum">   18136 </span>            :     int itmp1, itmp2, kfnew, klnew;</a>
+<a name="18137"><span class="lineNum">   18137 </span>            : </a>
+<a name="18138"><span class="lineNum">   18138 </span><span class="lineNoCov">          0 :     nab_dim1 = *mmax;</span></a>
+<a name="18139"><span class="lineNum">   18139 </span><span class="lineNoCov">          0 :     nab_offset = 1 + nab_dim1;</span></a>
+<a name="18140"><span class="lineNum">   18140 </span><span class="lineNoCov">          0 :     nab -= nab_offset;</span></a>
+<a name="18141"><span class="lineNum">   18141 </span>            :     ab_dim1 = *mmax;</a>
+<a name="18142"><span class="lineNum">   18142 </span>            :     ab_offset = 1 + ab_dim1;</a>
+<a name="18143"><span class="lineNum">   18143 </span><span class="lineNoCov">          0 :     ab -= ab_offset;</span></a>
+<a name="18144"><span class="lineNum">   18144 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="18145"><span class="lineNum">   18145 </span>            :     --e;</a>
+<a name="18146"><span class="lineNum">   18146 </span><span class="lineNoCov">          0 :     --e2;</span></a>
+<a name="18147"><span class="lineNum">   18147 </span><span class="lineNoCov">          0 :     --nval;</span></a>
+<a name="18148"><span class="lineNum">   18148 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="18149"><span class="lineNum">   18149 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="18150"><span class="lineNum">   18150 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="18151"><span class="lineNum">   18151 </span>            : </a>
+<a name="18152"><span class="lineNum">   18152 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="18153"><span class="lineNum">   18153 </span><span class="lineNoCov">          0 :     if (*ijob &lt; 1 || *ijob &gt; 3) {</span></a>
+<a name="18154"><span class="lineNum">   18154 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="18155"><span class="lineNum">   18155 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="18156"><span class="lineNum">   18156 </span>            :     }</a>
+<a name="18157"><span class="lineNum">   18157 </span>            : </a>
+<a name="18158"><span class="lineNum">   18158 </span><span class="lineNoCov">          0 :     if (*ijob == 1) {</span></a>
+<a name="18159"><span class="lineNum">   18159 </span>            : </a>
+<a name="18160"><span class="lineNum">   18160 </span><span class="lineNoCov">          0 :         *mout = 0;</span></a>
+<a name="18161"><span class="lineNum">   18161 </span>            : </a>
+<a name="18162"><span class="lineNum">   18162 </span><span class="lineNoCov">          0 :         i__1 = *minp;</span></a>
+<a name="18163"><span class="lineNum">   18163 </span><span class="lineNoCov">          0 :         for (ji = 1; ji &lt;= i__1; ++ji) {</span></a>
+<a name="18164"><span class="lineNum">   18164 </span><span class="lineNoCov">          0 :             for (jp = 1; jp &lt;= 2; ++jp) {</span></a>
+<a name="18165"><span class="lineNum">   18165 </span><span class="lineNoCov">          0 :                 tmp1 = d__[1] - ab[ji + jp * ab_dim1];</span></a>
+<a name="18166"><span class="lineNum">   18166 </span><span class="lineNoCov">          0 :                 if (std::abs(tmp1) &lt; *pivmin) {</span></a>
+<a name="18167"><span class="lineNum">   18167 </span><span class="lineNoCov">          0 :                     tmp1 = -(*pivmin);</span></a>
+<a name="18168"><span class="lineNum">   18168 </span>            :                 }</a>
+<a name="18169"><span class="lineNum">   18169 </span><span class="lineNoCov">          0 :                 nab[ji + jp * nab_dim1] = 0;</span></a>
+<a name="18170"><span class="lineNum">   18170 </span><span class="lineNoCov">          0 :                 if (tmp1 &lt;= 0.) {</span></a>
+<a name="18171"><span class="lineNum">   18171 </span><span class="lineNoCov">          0 :                     nab[ji + jp * nab_dim1] = 1;</span></a>
+<a name="18172"><span class="lineNum">   18172 </span>            :                 }</a>
+<a name="18173"><span class="lineNum">   18173 </span>            : </a>
+<a name="18174"><span class="lineNum">   18174 </span><span class="lineNoCov">          0 :                 i__2 = *n;</span></a>
+<a name="18175"><span class="lineNum">   18175 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="18176"><span class="lineNum">   18176 </span><span class="lineNoCov">          0 :                     tmp1 = d__[j] - e2[j - 1] / tmp1 - ab[ji + jp * ab_dim1];</span></a>
+<a name="18177"><span class="lineNum">   18177 </span><span class="lineNoCov">          0 :                     if (std::abs(tmp1) &lt; *pivmin) {</span></a>
+<a name="18178"><span class="lineNum">   18178 </span><span class="lineNoCov">          0 :                         tmp1 = -(*pivmin);</span></a>
+<a name="18179"><span class="lineNum">   18179 </span>            :                     }</a>
+<a name="18180"><span class="lineNum">   18180 </span><span class="lineNoCov">          0 :                     if (tmp1 &lt;= 0.) {</span></a>
+<a name="18181"><span class="lineNum">   18181 </span><span class="lineNoCov">          0 :                         ++nab[ji + jp * nab_dim1];</span></a>
+<a name="18182"><span class="lineNum">   18182 </span>            :                     }</a>
+<a name="18183"><span class="lineNum">   18183 </span>            :                 }</a>
+<a name="18184"><span class="lineNum">   18184 </span>            :             }</a>
+<a name="18185"><span class="lineNum">   18185 </span><span class="lineNoCov">          0 :             *mout = *mout + nab[ji + (nab_dim1 &lt;&lt; 1)] - nab[ji + nab_dim1];</span></a>
+<a name="18186"><span class="lineNum">   18186 </span>            :         }</a>
+<a name="18187"><span class="lineNum">   18187 </span>            :         return;</a>
+<a name="18188"><span class="lineNum">   18188 </span>            :     }</a>
+<a name="18189"><span class="lineNum">   18189 </span>            : </a>
+<a name="18190"><span class="lineNum">   18190 </span>            :     kf = 1;</a>
+<a name="18191"><span class="lineNum">   18191 </span><span class="lineNoCov">          0 :     kl = *minp;</span></a>
+<a name="18192"><span class="lineNum">   18192 </span>            : </a>
+<a name="18193"><span class="lineNum">   18193 </span><span class="lineNoCov">          0 :     if (*ijob == 2) {</span></a>
+<a name="18194"><span class="lineNum">   18194 </span>            :         i__1 = *minp;</a>
+<a name="18195"><span class="lineNum">   18195 </span><span class="lineNoCov">          0 :         for (ji = 1; ji &lt;= i__1; ++ji) {</span></a>
+<a name="18196"><span class="lineNum">   18196 </span><span class="lineNoCov">          0 :             c__[ji] = (ab[ji + ab_dim1] + ab[ji + (ab_dim1 &lt;&lt; 1)]) * .5;</span></a>
+<a name="18197"><span class="lineNum">   18197 </span>            :         }</a>
+<a name="18198"><span class="lineNum">   18198 </span>            :     }</a>
+<a name="18199"><span class="lineNum">   18199 </span>            : </a>
+<a name="18200"><span class="lineNum">   18200 </span><span class="lineNoCov">          0 :     i__1 = *nitmax;</span></a>
+<a name="18201"><span class="lineNum">   18201 </span><span class="lineNoCov">          0 :     for (jit = 1; jit &lt;= i__1; ++jit) {</span></a>
+<a name="18202"><span class="lineNum">   18202 </span>            : </a>
+<a name="18203"><span class="lineNum">   18203 </span><span class="lineNoCov">          0 :         if (kl - kf + 1 &gt;= *nbmin &amp;&amp; *nbmin &gt; 0) {</span></a>
+<a name="18204"><span class="lineNum">   18204 </span>            : </a>
+<a name="18205"><span class="lineNum">   18205 </span>            :             i__2 = kl;</a>
+<a name="18206"><span class="lineNum">   18206 </span><span class="lineNoCov">          0 :             for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="18207"><span class="lineNum">   18207 </span>            : </a>
+<a name="18208"><span class="lineNum">   18208 </span><span class="lineNoCov">          0 :                 work[ji] = d__[1] - c__[ji];</span></a>
+<a name="18209"><span class="lineNum">   18209 </span><span class="lineNoCov">          0 :                 iwork[ji] = 0;</span></a>
+<a name="18210"><span class="lineNum">   18210 </span><span class="lineNoCov">          0 :                 if (work[ji] &lt;= *pivmin) {</span></a>
+<a name="18211"><span class="lineNum">   18211 </span><span class="lineNoCov">          0 :                     iwork[ji] = 1;</span></a>
+<a name="18212"><span class="lineNum">   18212 </span><span class="lineNoCov">          0 :                     d__1 = work[ji], d__2 = -(*pivmin);</span></a>
+<a name="18213"><span class="lineNum">   18213 </span><span class="lineNoCov">          0 :                     work[ji] = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="18214"><span class="lineNum">   18214 </span>            :                 }</a>
+<a name="18215"><span class="lineNum">   18215 </span>            : </a>
+<a name="18216"><span class="lineNum">   18216 </span><span class="lineNoCov">          0 :                 i__3 = *n;</span></a>
+<a name="18217"><span class="lineNum">   18217 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__3; ++j) {</span></a>
+<a name="18218"><span class="lineNum">   18218 </span><span class="lineNoCov">          0 :                     work[ji] = d__[j] - e2[j - 1] / work[ji] - c__[ji];</span></a>
+<a name="18219"><span class="lineNum">   18219 </span><span class="lineNoCov">          0 :                     if (work[ji] &lt;= *pivmin) {</span></a>
+<a name="18220"><span class="lineNum">   18220 </span><span class="lineNoCov">          0 :                         ++iwork[ji];</span></a>
+<a name="18221"><span class="lineNum">   18221 </span><span class="lineNoCov">          0 :                         d__1 = work[ji], d__2 = -(*pivmin);</span></a>
+<a name="18222"><span class="lineNum">   18222 </span><span class="lineNoCov">          0 :                         work[ji] = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="18223"><span class="lineNum">   18223 </span>            :                     }</a>
+<a name="18224"><span class="lineNum">   18224 </span>            :                 }</a>
+<a name="18225"><span class="lineNum">   18225 </span>            :             }</a>
+<a name="18226"><span class="lineNum">   18226 </span>            : </a>
+<a name="18227"><span class="lineNum">   18227 </span><span class="lineNoCov">          0 :             if (*ijob &lt;= 2) {</span></a>
+<a name="18228"><span class="lineNum">   18228 </span>            : </a>
+<a name="18229"><span class="lineNum">   18229 </span>            :                 klnew = kl;</a>
+<a name="18230"><span class="lineNum">   18230 </span>            :                 i__2 = kl;</a>
+<a name="18231"><span class="lineNum">   18231 </span><span class="lineNoCov">          0 :                 for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="18232"><span class="lineNum">   18232 </span>            : </a>
+<a name="18233"><span class="lineNum">   18233 </span><span class="lineNoCov">          0 :                   i__5 = nab[ji + nab_dim1];</span></a>
+<a name="18234"><span class="lineNum">   18234 </span><span class="lineNoCov">          0 :                   i__6 = iwork[ji];</span></a>
+<a name="18235"><span class="lineNum">   18235 </span><span class="lineNoCov">          0 :                   i__3 = nab[ji + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="18236"><span class="lineNum">   18236 </span>            :                   i__4 = (i__5&gt;i__6) ? i__5 : i__6;</a>
+<a name="18237"><span class="lineNum">   18237 </span><span class="lineNoCov">          0 :                     iwork[ji] = (i__3&lt;i__4) ? i__3 : i__4;</span></a>
+<a name="18238"><span class="lineNum">   18238 </span>            : </a>
+<a name="18239"><span class="lineNum">   18239 </span><span class="lineNoCov">          0 :                     if (iwork[ji] == nab[ji + (nab_dim1 &lt;&lt; 1)]) {</span></a>
+<a name="18240"><span class="lineNum">   18240 </span>            : </a>
+<a name="18241"><span class="lineNum">   18241 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = c__[ji];</span></a>
+<a name="18242"><span class="lineNum">   18242 </span>            : </a>
+<a name="18243"><span class="lineNum">   18243 </span><span class="lineNoCov">          0 :                     } else if (iwork[ji] == nab[ji + nab_dim1]) {</span></a>
+<a name="18244"><span class="lineNum">   18244 </span>            : </a>
+<a name="18245"><span class="lineNum">   18245 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = c__[ji];</span></a>
+<a name="18246"><span class="lineNum">   18246 </span>            :                     } else {</a>
+<a name="18247"><span class="lineNum">   18247 </span><span class="lineNoCov">          0 :                         ++klnew;</span></a>
+<a name="18248"><span class="lineNum">   18248 </span><span class="lineNoCov">          0 :                         if (klnew &lt;= *mmax) {</span></a>
+<a name="18249"><span class="lineNum">   18249 </span>            : </a>
+<a name="18250"><span class="lineNum">   18250 </span><span class="lineNoCov">          0 :                             ab[klnew + (ab_dim1 &lt;&lt; 1)] = ab[ji + (ab_dim1 &lt;&lt; </span></a>
+<a name="18251"><span class="lineNum">   18251 </span><span class="lineNoCov">          0 :                                     1)];</span></a>
+<a name="18252"><span class="lineNum">   18252 </span><span class="lineNoCov">          0 :                             nab[klnew + (nab_dim1 &lt;&lt; 1)] = nab[ji + (nab_dim1 </span></a>
+<a name="18253"><span class="lineNum">   18253 </span><span class="lineNoCov">          0 :                                     &lt;&lt; 1)];</span></a>
+<a name="18254"><span class="lineNum">   18254 </span><span class="lineNoCov">          0 :                             ab[klnew + ab_dim1] = c__[ji];</span></a>
+<a name="18255"><span class="lineNum">   18255 </span><span class="lineNoCov">          0 :                             nab[klnew + nab_dim1] = iwork[ji];</span></a>
+<a name="18256"><span class="lineNum">   18256 </span><span class="lineNoCov">          0 :                             ab[ji + (ab_dim1 &lt;&lt; 1)] = c__[ji];</span></a>
+<a name="18257"><span class="lineNum">   18257 </span><span class="lineNoCov">          0 :                             nab[ji + (nab_dim1 &lt;&lt; 1)] = iwork[ji];</span></a>
+<a name="18258"><span class="lineNum">   18258 </span>            :                         } else {</a>
+<a name="18259"><span class="lineNum">   18259 </span><span class="lineNoCov">          0 :                             *info = *mmax + 1;</span></a>
+<a name="18260"><span class="lineNum">   18260 </span>            :                         }</a>
+<a name="18261"><span class="lineNum">   18261 </span>            :                     }</a>
+<a name="18262"><span class="lineNum">   18262 </span>            :                 }</a>
+<a name="18263"><span class="lineNum">   18263 </span><span class="lineNoCov">          0 :                 if (*info != 0) {</span></a>
+<a name="18264"><span class="lineNum">   18264 </span>            :                     return;</a>
+<a name="18265"><span class="lineNum">   18265 </span>            :                 }</a>
+<a name="18266"><span class="lineNum">   18266 </span>            :                 kl = klnew;</a>
+<a name="18267"><span class="lineNum">   18267 </span>            :             } else {</a>
+<a name="18268"><span class="lineNum">   18268 </span>            : </a>
+<a name="18269"><span class="lineNum">   18269 </span>            :                 i__2 = kl;</a>
+<a name="18270"><span class="lineNum">   18270 </span><span class="lineNoCov">          0 :                 for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="18271"><span class="lineNum">   18271 </span><span class="lineNoCov">          0 :                     if (iwork[ji] &lt;= nval[ji]) {</span></a>
+<a name="18272"><span class="lineNum">   18272 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = c__[ji];</span></a>
+<a name="18273"><span class="lineNum">   18273 </span><span class="lineNoCov">          0 :                         nab[ji + nab_dim1] = iwork[ji];</span></a>
+<a name="18274"><span class="lineNum">   18274 </span>            :                     }</a>
+<a name="18275"><span class="lineNum">   18275 </span><span class="lineNoCov">          0 :                     if (iwork[ji] &gt;= nval[ji]) {</span></a>
+<a name="18276"><span class="lineNum">   18276 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = c__[ji];</span></a>
+<a name="18277"><span class="lineNum">   18277 </span><span class="lineNoCov">          0 :                         nab[ji + (nab_dim1 &lt;&lt; 1)] = iwork[ji];</span></a>
+<a name="18278"><span class="lineNum">   18278 </span>            :                     }</a>
+<a name="18279"><span class="lineNum">   18279 </span>            :                 }</a>
+<a name="18280"><span class="lineNum">   18280 </span>            :             }</a>
+<a name="18281"><span class="lineNum">   18281 </span>            : </a>
+<a name="18282"><span class="lineNum">   18282 </span>            :         } else {</a>
+<a name="18283"><span class="lineNum">   18283 </span>            : </a>
+<a name="18284"><span class="lineNum">   18284 </span>            :             klnew = kl;</a>
+<a name="18285"><span class="lineNum">   18285 </span>            :             i__2 = kl;</a>
+<a name="18286"><span class="lineNum">   18286 </span><span class="lineNoCov">          0 :             for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="18287"><span class="lineNum">   18287 </span>            : </a>
+<a name="18288"><span class="lineNum">   18288 </span><span class="lineNoCov">          0 :                 tmp1 = c__[ji];</span></a>
+<a name="18289"><span class="lineNum">   18289 </span><span class="lineNoCov">          0 :                 tmp2 = d__[1] - tmp1;</span></a>
+<a name="18290"><span class="lineNum">   18290 </span>            :                 itmp1 = 0;</a>
+<a name="18291"><span class="lineNum">   18291 </span><span class="lineNoCov">          0 :                 if (tmp2 &lt;= *pivmin) {</span></a>
+<a name="18292"><span class="lineNum">   18292 </span>            :                     itmp1 = 1;</a>
+<a name="18293"><span class="lineNum">   18293 </span><span class="lineNoCov">          0 :                     d__1 = tmp2, d__2 = -(*pivmin);</span></a>
+<a name="18294"><span class="lineNum">   18294 </span><span class="lineNoCov">          0 :                     tmp2 = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="18295"><span class="lineNum">   18295 </span>            :                 }</a>
+<a name="18296"><span class="lineNum">   18296 </span>            : </a>
+<a name="18297"><span class="lineNum">   18297 </span><span class="lineNoCov">          0 :                 i__3 = *n;</span></a>
+<a name="18298"><span class="lineNum">   18298 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__3; ++j) {</span></a>
+<a name="18299"><span class="lineNum">   18299 </span><span class="lineNoCov">          0 :                     tmp2 = d__[j] - e2[j - 1] / tmp2 - tmp1;</span></a>
+<a name="18300"><span class="lineNum">   18300 </span><span class="lineNoCov">          0 :                     if (tmp2 &lt;= *pivmin) {</span></a>
+<a name="18301"><span class="lineNum">   18301 </span><span class="lineNoCov">          0 :                         ++itmp1;</span></a>
+<a name="18302"><span class="lineNum">   18302 </span><span class="lineNoCov">          0 :                         d__1 = tmp2, d__2 = -(*pivmin);</span></a>
+<a name="18303"><span class="lineNum">   18303 </span><span class="lineNoCov">          0 :                         tmp2 = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="18304"><span class="lineNum">   18304 </span>            :                     }</a>
+<a name="18305"><span class="lineNum">   18305 </span>            :                 }</a>
+<a name="18306"><span class="lineNum">   18306 </span>            : </a>
+<a name="18307"><span class="lineNum">   18307 </span><span class="lineNoCov">          0 :                 if (*ijob &lt;= 2) {</span></a>
+<a name="18308"><span class="lineNum">   18308 </span>            : </a>
+<a name="18309"><span class="lineNum">   18309 </span><span class="lineNoCov">          0 :                     i__5 = nab[ji + nab_dim1];</span></a>
+<a name="18310"><span class="lineNum">   18310 </span><span class="lineNoCov">          0 :                     i__3 = nab[ji + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="18311"><span class="lineNum">   18311 </span>            :                     i__4 = (i__5&gt;itmp1) ? i__5 : itmp1;</a>
+<a name="18312"><span class="lineNum">   18312 </span>            :                     itmp1 = (i__3&lt;i__4) ? i__3 : i__4;</a>
+<a name="18313"><span class="lineNum">   18313 </span>            : </a>
+<a name="18314"><span class="lineNum">   18314 </span><span class="lineNoCov">          0 :                     if (itmp1 == nab[ji + (nab_dim1 &lt;&lt; 1)]) {</span></a>
+<a name="18315"><span class="lineNum">   18315 </span>            : </a>
+<a name="18316"><span class="lineNum">   18316 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = tmp1;</span></a>
+<a name="18317"><span class="lineNum">   18317 </span>            : </a>
+<a name="18318"><span class="lineNum">   18318 </span><span class="lineNoCov">          0 :                     } else if (itmp1 == nab[ji + nab_dim1]) {</span></a>
+<a name="18319"><span class="lineNum">   18319 </span>            : </a>
+<a name="18320"><span class="lineNum">   18320 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = tmp1;</span></a>
+<a name="18321"><span class="lineNum">   18321 </span><span class="lineNoCov">          0 :                     } else if (klnew &lt; *mmax) {</span></a>
+<a name="18322"><span class="lineNum">   18322 </span>            : </a>
+<a name="18323"><span class="lineNum">   18323 </span><span class="lineNoCov">          0 :                         ++klnew;</span></a>
+<a name="18324"><span class="lineNum">   18324 </span><span class="lineNoCov">          0 :                         ab[klnew + (ab_dim1 &lt;&lt; 1)] = ab[ji + (ab_dim1 &lt;&lt; 1)];</span></a>
+<a name="18325"><span class="lineNum">   18325 </span><span class="lineNoCov">          0 :                         nab[klnew + (nab_dim1 &lt;&lt; 1)] = nab[ji + (nab_dim1 &lt;&lt; </span></a>
+<a name="18326"><span class="lineNum">   18326 </span><span class="lineNoCov">          0 :                                 1)];</span></a>
+<a name="18327"><span class="lineNum">   18327 </span><span class="lineNoCov">          0 :                         ab[klnew + ab_dim1] = tmp1;</span></a>
+<a name="18328"><span class="lineNum">   18328 </span><span class="lineNoCov">          0 :                         nab[klnew + nab_dim1] = itmp1;</span></a>
+<a name="18329"><span class="lineNum">   18329 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = tmp1;</span></a>
+<a name="18330"><span class="lineNum">   18330 </span><span class="lineNoCov">          0 :                         nab[ji + (nab_dim1 &lt;&lt; 1)] = itmp1;</span></a>
+<a name="18331"><span class="lineNum">   18331 </span>            :                     } else {</a>
+<a name="18332"><span class="lineNum">   18332 </span><span class="lineNoCov">          0 :                         *info = *mmax + 1;</span></a>
+<a name="18333"><span class="lineNum">   18333 </span><span class="lineNoCov">          0 :                         return;</span></a>
+<a name="18334"><span class="lineNum">   18334 </span>            :                     }</a>
+<a name="18335"><span class="lineNum">   18335 </span>            :                 } else {</a>
+<a name="18336"><span class="lineNum">   18336 </span>            : </a>
+<a name="18337"><span class="lineNum">   18337 </span><span class="lineNoCov">          0 :                     if (itmp1 &lt;= nval[ji]) {</span></a>
+<a name="18338"><span class="lineNum">   18338 </span><span class="lineNoCov">          0 :                         ab[ji + ab_dim1] = tmp1;</span></a>
+<a name="18339"><span class="lineNum">   18339 </span><span class="lineNoCov">          0 :                         nab[ji + nab_dim1] = itmp1;</span></a>
+<a name="18340"><span class="lineNum">   18340 </span>            :                     }</a>
+<a name="18341"><span class="lineNum">   18341 </span><span class="lineNoCov">          0 :                     if (itmp1 &gt;= nval[ji]) {</span></a>
+<a name="18342"><span class="lineNum">   18342 </span><span class="lineNoCov">          0 :                         ab[ji + (ab_dim1 &lt;&lt; 1)] = tmp1;</span></a>
+<a name="18343"><span class="lineNum">   18343 </span><span class="lineNoCov">          0 :                         nab[ji + (nab_dim1 &lt;&lt; 1)] = itmp1;</span></a>
+<a name="18344"><span class="lineNum">   18344 </span>            :                     }</a>
+<a name="18345"><span class="lineNum">   18345 </span>            :                 }</a>
+<a name="18346"><span class="lineNum">   18346 </span>            :             }</a>
+<a name="18347"><span class="lineNum">   18347 </span>            :             kl = klnew;</a>
+<a name="18348"><span class="lineNum">   18348 </span>            : </a>
+<a name="18349"><span class="lineNum">   18349 </span>            :         }</a>
+<a name="18350"><span class="lineNum">   18350 </span>            : </a>
+<a name="18351"><span class="lineNum">   18351 </span>            :         kfnew = kf;</a>
+<a name="18352"><span class="lineNum">   18352 </span>            :         i__2 = kl;</a>
+<a name="18353"><span class="lineNum">   18353 </span><span class="lineNoCov">          0 :         for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="18354"><span class="lineNum">   18354 </span><span class="lineNoCov">          0 :             tmp1 = std::abs(ab[ji + (ab_dim1 &lt;&lt; 1)] - ab[ji + ab_dim1]);</span></a>
+<a name="18355"><span class="lineNum">   18355 </span>            :             d__3 = std::abs(ab[ji + (ab_dim1 &lt;&lt; 1)]);</a>
+<a name="18356"><span class="lineNum">   18356 </span>            :             d__4 = std::abs(ab[ji + ab_dim1]);</a>
+<a name="18357"><span class="lineNum">   18357 </span><span class="lineNoCov">          0 :             tmp2 = (d__3&gt;d__4) ? d__3 : d__4;</span></a>
+<a name="18358"><span class="lineNum">   18358 </span><span class="lineNoCov">          0 :             d__1 = (*abstol&gt;*pivmin) ? *abstol : *pivmin;</span></a>
+<a name="18359"><span class="lineNum">   18359 </span><span class="lineNoCov">          0 :             d__2 = *reltol * tmp2;</span></a>
+<a name="18360"><span class="lineNum">   18360 </span><span class="lineNoCov">          0 :             if (tmp1 &lt; ((d__1&gt;d__2) ? d__1 : d__2) || nab[ji + nab_dim1] &gt;= nab[ji + (</span></a>
+<a name="18361"><span class="lineNum">   18361 </span><span class="lineNoCov">          0 :                     nab_dim1 &lt;&lt; 1)]) {</span></a>
+<a name="18362"><span class="lineNum">   18362 </span>            : </a>
+<a name="18363"><span class="lineNum">   18363 </span><span class="lineNoCov">          0 :                 if (ji &gt; kfnew) {</span></a>
+<a name="18364"><span class="lineNum">   18364 </span>            :                     tmp1 = ab[ji + ab_dim1];</a>
+<a name="18365"><span class="lineNum">   18365 </span>            :                     tmp2 = ab[ji + (ab_dim1 &lt;&lt; 1)];</a>
+<a name="18366"><span class="lineNum">   18366 </span><span class="lineNoCov">          0 :                     itmp1 = nab[ji + nab_dim1];</span></a>
+<a name="18367"><span class="lineNum">   18367 </span><span class="lineNoCov">          0 :                     itmp2 = nab[ji + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="18368"><span class="lineNum">   18368 </span><span class="lineNoCov">          0 :                     ab[ji + ab_dim1] = ab[kfnew + ab_dim1];</span></a>
+<a name="18369"><span class="lineNum">   18369 </span><span class="lineNoCov">          0 :                     ab[ji + (ab_dim1 &lt;&lt; 1)] = ab[kfnew + (ab_dim1 &lt;&lt; 1)];</span></a>
+<a name="18370"><span class="lineNum">   18370 </span><span class="lineNoCov">          0 :                     nab[ji + nab_dim1] = nab[kfnew + nab_dim1];</span></a>
+<a name="18371"><span class="lineNum">   18371 </span><span class="lineNoCov">          0 :                     nab[ji + (nab_dim1 &lt;&lt; 1)] = nab[kfnew + (nab_dim1 &lt;&lt; 1)];</span></a>
+<a name="18372"><span class="lineNum">   18372 </span><span class="lineNoCov">          0 :                     ab[kfnew + ab_dim1] = tmp1;</span></a>
+<a name="18373"><span class="lineNum">   18373 </span><span class="lineNoCov">          0 :                     ab[kfnew + (ab_dim1 &lt;&lt; 1)] = tmp2;</span></a>
+<a name="18374"><span class="lineNum">   18374 </span><span class="lineNoCov">          0 :                     nab[kfnew + nab_dim1] = itmp1;</span></a>
+<a name="18375"><span class="lineNum">   18375 </span><span class="lineNoCov">          0 :                     nab[kfnew + (nab_dim1 &lt;&lt; 1)] = itmp2;</span></a>
+<a name="18376"><span class="lineNum">   18376 </span><span class="lineNoCov">          0 :                     if (*ijob == 3) {</span></a>
+<a name="18377"><span class="lineNum">   18377 </span><span class="lineNoCov">          0 :                         itmp1 = nval[ji];</span></a>
+<a name="18378"><span class="lineNum">   18378 </span><span class="lineNoCov">          0 :                         nval[ji] = nval[kfnew];</span></a>
+<a name="18379"><span class="lineNum">   18379 </span><span class="lineNoCov">          0 :                         nval[kfnew] = itmp1;</span></a>
+<a name="18380"><span class="lineNum">   18380 </span>            :                     }</a>
+<a name="18381"><span class="lineNum">   18381 </span>            :                 }</a>
+<a name="18382"><span class="lineNum">   18382 </span><span class="lineNoCov">          0 :                 ++kfnew;</span></a>
+<a name="18383"><span class="lineNum">   18383 </span>            :             }</a>
+<a name="18384"><span class="lineNum">   18384 </span>            :         }</a>
+<a name="18385"><span class="lineNum">   18385 </span>            :         kf = kfnew;</a>
+<a name="18386"><span class="lineNum">   18386 </span>            : </a>
+<a name="18387"><span class="lineNum">   18387 </span>            :         i__2 = kl;</a>
+<a name="18388"><span class="lineNum">   18388 </span><span class="lineNoCov">          0 :         for (ji = kf; ji &lt;= i__2; ++ji) {</span></a>
+<a name="18389"><span class="lineNum">   18389 </span><span class="lineNoCov">          0 :             c__[ji] = (ab[ji + ab_dim1] + ab[ji + (ab_dim1 &lt;&lt; 1)]) * .5;</span></a>
+<a name="18390"><span class="lineNum">   18390 </span>            :         }</a>
+<a name="18391"><span class="lineNum">   18391 </span>            : </a>
+<a name="18392"><span class="lineNum">   18392 </span><span class="lineNoCov">          0 :         if (kf &gt; kl) {</span></a>
+<a name="18393"><span class="lineNum">   18393 </span>            :             break;</a>
+<a name="18394"><span class="lineNum">   18394 </span>            :         }</a>
+<a name="18395"><span class="lineNum">   18395 </span>            :     }</a>
+<a name="18396"><span class="lineNum">   18396 </span>            : </a>
+<a name="18397"><span class="lineNum">   18397 </span><span class="lineNoCov">          0 :     i__1 = kl + 1 - kf;</span></a>
+<a name="18398"><span class="lineNum">   18398 </span><span class="lineNoCov">          0 :     if(i__1&gt;0)</span></a>
+<a name="18399"><span class="lineNum">   18399 </span><span class="lineNoCov">          0 :       *info = i__1;</span></a>
+<a name="18400"><span class="lineNum">   18400 </span>            : </a>
+<a name="18401"><span class="lineNum">   18401 </span><span class="lineNoCov">          0 :     *mout = kl;</span></a>
+<a name="18402"><span class="lineNum">   18402 </span>            : </a>
+<a name="18403"><span class="lineNum">   18403 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="18404"><span class="lineNum">   18404 </span>            : </a>
+<a name="18405"><span class="lineNum">   18405 </span>            : }</a>
+<a name="18406"><span class="lineNum">   18406 </span>            : </a>
+<a name="18407"><span class="lineNum">   18407 </span>            : </a>
+<a name="18408"><span class="lineNum">   18408 </span>            : }</a>
+<a name="18409"><span class="lineNum">   18409 </span>            : }</a>
+<a name="18410"><span class="lineNum">   18410 </span>            : #include &lt;cmath&gt;</a>
+<a name="18411"><span class="lineNum">   18411 </span>            : </a>
+<a name="18412"><span class="lineNum">   18412 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18413"><span class="lineNum">   18413 </span>            : </a>
+<a name="18414"><span class="lineNum">   18414 </span>            : #include &quot;real.h&quot;</a>
+<a name="18415"><span class="lineNum">   18415 </span>            : </a>
+<a name="18416"><span class="lineNum">   18416 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18417"><span class="lineNum">   18417 </span>            : namespace PLMD{</a>
+<a name="18418"><span class="lineNum">   18418 </span>            : namespace lapack{</a>
+<a name="18419"><span class="lineNum">   18419 </span>            : using namespace blas;</a>
+<a name="18420"><span class="lineNum">   18420 </span>            : void</a>
+<a name="18421"><span class="lineNum">   18421 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slaed6,SLAED6)(int *kniter, </span></a>
+<a name="18422"><span class="lineNum">   18422 </span>            :                         int *orgati, </a>
+<a name="18423"><span class="lineNum">   18423 </span>            :                         float *rho, </a>
+<a name="18424"><span class="lineNum">   18424 </span>            :                         float *d__,</a>
+<a name="18425"><span class="lineNum">   18425 </span>            :                         float *z__, </a>
+<a name="18426"><span class="lineNum">   18426 </span>            :                         float *finit, </a>
+<a name="18427"><span class="lineNum">   18427 </span>            :                         float *tau, </a>
+<a name="18428"><span class="lineNum">   18428 </span>            :                         int *info)</a>
+<a name="18429"><span class="lineNum">   18429 </span>            : {</a>
+<a name="18430"><span class="lineNum">   18430 </span>            :     int i__1;</a>
+<a name="18431"><span class="lineNum">   18431 </span>            :     float r__1, r__2, r__3, r__4;</a>
+<a name="18432"><span class="lineNum">   18432 </span>            : </a>
+<a name="18433"><span class="lineNum">   18433 </span>            :     float a, b, c__, f;</a>
+<a name="18434"><span class="lineNum">   18434 </span>            :     int i__;</a>
+<a name="18435"><span class="lineNum">   18435 </span>            :     float fc, df, ddf, eta, eps, base;</a>
+<a name="18436"><span class="lineNum">   18436 </span>            :     int iter;</a>
+<a name="18437"><span class="lineNum">   18437 </span>            :     float temp, temp1, temp2, temp3, temp4;</a>
+<a name="18438"><span class="lineNum">   18438 </span>            :     int scale;</a>
+<a name="18439"><span class="lineNum">   18439 </span>            :     int niter;</a>
+<a name="18440"><span class="lineNum">   18440 </span>            :     float small1, small2, sminv1, sminv2, dscale[3], sclfac;</a>
+<a name="18441"><span class="lineNum">   18441 </span>            :     float zscale[3], erretm;</a>
+<a name="18442"><span class="lineNum">   18442 </span>            :     float safemin;</a>
+<a name="18443"><span class="lineNum">   18443 </span>            :     float sclinv = 0;</a>
+<a name="18444"><span class="lineNum">   18444 </span>            :     </a>
+<a name="18445"><span class="lineNum">   18445 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="18446"><span class="lineNum">   18446 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="18447"><span class="lineNum">   18447 </span>            : </a>
+<a name="18448"><span class="lineNum">   18448 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="18449"><span class="lineNum">   18449 </span>            : </a>
+<a name="18450"><span class="lineNum">   18450 </span>            :     niter = 1;</a>
+<a name="18451"><span class="lineNum">   18451 </span><span class="lineNoCov">          0 :     *tau = 0.f;</span></a>
+<a name="18452"><span class="lineNum">   18452 </span><span class="lineNoCov">          0 :     if (*kniter == 2) {</span></a>
+<a name="18453"><span class="lineNum">   18453 </span><span class="lineNoCov">          0 :         if (*orgati) {</span></a>
+<a name="18454"><span class="lineNum">   18454 </span><span class="lineNoCov">          0 :             temp = (d__[3] - d__[2]) / 2.f;</span></a>
+<a name="18455"><span class="lineNum">   18455 </span><span class="lineNoCov">          0 :             c__ = *rho + z__[1] / (d__[1] - d__[2] - temp);</span></a>
+<a name="18456"><span class="lineNum">   18456 </span><span class="lineNoCov">          0 :             a = c__ * (d__[2] + d__[3]) + z__[2] + z__[3];</span></a>
+<a name="18457"><span class="lineNum">   18457 </span><span class="lineNoCov">          0 :             b = c__ * d__[2] * d__[3] + z__[2] * d__[3] + z__[3] * d__[2];</span></a>
+<a name="18458"><span class="lineNum">   18458 </span>            :         } else {</a>
+<a name="18459"><span class="lineNum">   18459 </span><span class="lineNoCov">          0 :             temp = (d__[1] - d__[2]) / 2.f;</span></a>
+<a name="18460"><span class="lineNum">   18460 </span><span class="lineNoCov">          0 :             c__ = *rho + z__[3] / (d__[3] - d__[2] - temp);</span></a>
+<a name="18461"><span class="lineNum">   18461 </span><span class="lineNoCov">          0 :             a = c__ * (d__[1] + d__[2]) + z__[1] + z__[2];</span></a>
+<a name="18462"><span class="lineNum">   18462 </span><span class="lineNoCov">          0 :             b = c__ * d__[1] * d__[2] + z__[1] * d__[2] + z__[2] * d__[1];</span></a>
+<a name="18463"><span class="lineNum">   18463 </span>            :         }</a>
+<a name="18464"><span class="lineNum">   18464 </span><span class="lineNoCov">          0 :         r__1 = std::abs(a), r__2 = std::abs(b), r__1 = ((r__1&gt;r__2)? r__1:r__2), r__2 = std::abs(c__);</span></a>
+<a name="18465"><span class="lineNum">   18465 </span><span class="lineNoCov">          0 :         temp = (r__1&gt;r__2) ? r__1 : r__2;</span></a>
+<a name="18466"><span class="lineNum">   18466 </span><span class="lineNoCov">          0 :         a /= temp;</span></a>
+<a name="18467"><span class="lineNum">   18467 </span><span class="lineNoCov">          0 :         b /= temp;</span></a>
+<a name="18468"><span class="lineNum">   18468 </span><span class="lineNoCov">          0 :         c__ /= temp;</span></a>
+<a name="18469"><span class="lineNum">   18469 </span><span class="lineNoCov">          0 :         if (c__ == 0.f) {</span></a>
+<a name="18470"><span class="lineNum">   18470 </span><span class="lineNoCov">          0 :             *tau = b / a;</span></a>
+<a name="18471"><span class="lineNum">   18471 </span><span class="lineNoCov">          0 :         } else if (a &lt;= 0.f) {</span></a>
+<a name="18472"><span class="lineNum">   18472 </span><span class="lineNoCov">          0 :             *tau = (a -  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs(r__1)))) / (</span></a>
+<a name="18473"><span class="lineNum">   18473 </span><span class="lineNoCov">          0 :                     c__ * 2.f);</span></a>
+<a name="18474"><span class="lineNum">   18474 </span>            :         } else {</a>
+<a name="18475"><span class="lineNum">   18475 </span><span class="lineNoCov">          0 :             *tau = b * 2.f / (a +  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs(r__1))));</span></a>
+<a name="18476"><span class="lineNum">   18476 </span>            :         }</a>
+<a name="18477"><span class="lineNum">   18477 </span>            : </a>
+<a name="18478"><span class="lineNum">   18478 </span><span class="lineNoCov">          0 :         temp = *rho + z__[1] / (d__[1] - *tau) + z__[2] / (d__[2] - *tau) + </span></a>
+<a name="18479"><span class="lineNum">   18479 </span><span class="lineNoCov">          0 :                 z__[3] / (d__[3] - *tau);</span></a>
+<a name="18480"><span class="lineNum">   18480 </span><span class="lineNoCov">          0 :         if (std::abs(*finit) &lt;= std::abs(temp)) {</span></a>
+<a name="18481"><span class="lineNum">   18481 </span><span class="lineNoCov">          0 :             *tau = 0.f;</span></a>
+<a name="18482"><span class="lineNum">   18482 </span>            :         }</a>
+<a name="18483"><span class="lineNum">   18483 </span>            :     }</a>
+<a name="18484"><span class="lineNum">   18484 </span>            : </a>
+<a name="18485"><span class="lineNum">   18485 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="18486"><span class="lineNum">   18486 </span>            :     base = 2;</a>
+<a name="18487"><span class="lineNum">   18487 </span>            :     safemin = PLUMED_GMX_FLOAT_MIN*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="18488"><span class="lineNum">   18488 </span>            :     i__1 = static_cast&lt;int&gt;(std::log(safemin) / std::log(base) / 3.f);</a>
+<a name="18489"><span class="lineNum">   18489 </span>            :     small1 = std::pow(base, static_cast&lt;float&gt;(i__1));</a>
+<a name="18490"><span class="lineNum">   18490 </span>            :     sminv1 = 1.f / small1;</a>
+<a name="18491"><span class="lineNum">   18491 </span>            :     small2 = small1 * small1;</a>
+<a name="18492"><span class="lineNum">   18492 </span>            :     sminv2 = sminv1 * sminv1;</a>
+<a name="18493"><span class="lineNum">   18493 </span>            : </a>
+<a name="18494"><span class="lineNum">   18494 </span><span class="lineNoCov">          0 :     if (*orgati) {</span></a>
+<a name="18495"><span class="lineNum">   18495 </span><span class="lineNoCov">          0 :         r__3 = (r__1 = d__[2] - *tau, std::abs(r__1)), r__4 = (r__2 = d__[3] - *</span></a>
+<a name="18496"><span class="lineNum">   18496 </span>            :                 tau, std::abs(r__2));</a>
+<a name="18497"><span class="lineNum">   18497 </span><span class="lineNoCov">          0 :         temp = (r__3&lt;r__4) ? r__3 : r__4;</span></a>
+<a name="18498"><span class="lineNum">   18498 </span>            :     } else {</a>
+<a name="18499"><span class="lineNum">   18499 </span><span class="lineNoCov">          0 :         r__3 = (r__1 = d__[1] - *tau, std::abs(r__1)), r__4 = (r__2 = d__[2] - *</span></a>
+<a name="18500"><span class="lineNum">   18500 </span>            :                 tau, std::abs(r__2));</a>
+<a name="18501"><span class="lineNum">   18501 </span><span class="lineNoCov">          0 :         temp = (r__3&lt;r__4) ? r__3 : r__4;</span></a>
+<a name="18502"><span class="lineNum">   18502 </span>            :     }</a>
+<a name="18503"><span class="lineNum">   18503 </span>            :     scale = 0;</a>
+<a name="18504"><span class="lineNum">   18504 </span><span class="lineNoCov">          0 :     if (temp &lt;= small1) {</span></a>
+<a name="18505"><span class="lineNum">   18505 </span>            :         scale = 1;</a>
+<a name="18506"><span class="lineNum">   18506 </span><span class="lineNoCov">          0 :         if (temp &lt;= small2) {</span></a>
+<a name="18507"><span class="lineNum">   18507 </span>            : </a>
+<a name="18508"><span class="lineNum">   18508 </span>            :             sclfac = sminv2;</a>
+<a name="18509"><span class="lineNum">   18509 </span>            :             sclinv = small2;</a>
+<a name="18510"><span class="lineNum">   18510 </span>            :         } else {</a>
+<a name="18511"><span class="lineNum">   18511 </span>            : </a>
+<a name="18512"><span class="lineNum">   18512 </span>            :             sclfac = sminv1;</a>
+<a name="18513"><span class="lineNum">   18513 </span>            :             sclinv = small1;</a>
+<a name="18514"><span class="lineNum">   18514 </span>            : </a>
+<a name="18515"><span class="lineNum">   18515 </span>            :         }</a>
+<a name="18516"><span class="lineNum">   18516 </span>            : </a>
+<a name="18517"><span class="lineNum">   18517 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="18518"><span class="lineNum">   18518 </span><span class="lineNoCov">          0 :             dscale[i__ - 1] = d__[i__] * sclfac;</span></a>
+<a name="18519"><span class="lineNum">   18519 </span><span class="lineNoCov">          0 :             zscale[i__ - 1] = z__[i__] * sclfac;</span></a>
+<a name="18520"><span class="lineNum">   18520 </span>            :         }</a>
+<a name="18521"><span class="lineNum">   18521 </span><span class="lineNoCov">          0 :         *tau *= sclfac;</span></a>
+<a name="18522"><span class="lineNum">   18522 </span>            :     } else {</a>
+<a name="18523"><span class="lineNum">   18523 </span>            : </a>
+<a name="18524"><span class="lineNum">   18524 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="18525"><span class="lineNum">   18525 </span><span class="lineNoCov">          0 :             dscale[i__ - 1] = d__[i__];</span></a>
+<a name="18526"><span class="lineNum">   18526 </span><span class="lineNoCov">          0 :             zscale[i__ - 1] = z__[i__];</span></a>
+<a name="18527"><span class="lineNum">   18527 </span>            :         }</a>
+<a name="18528"><span class="lineNum">   18528 </span>            :     }</a>
+<a name="18529"><span class="lineNum">   18529 </span>            :     fc = 0.f;</a>
+<a name="18530"><span class="lineNum">   18530 </span>            :     df = 0.f;</a>
+<a name="18531"><span class="lineNum">   18531 </span>            :     ddf = 0.f;</a>
+<a name="18532"><span class="lineNum">   18532 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="18533"><span class="lineNum">   18533 </span><span class="lineNoCov">          0 :         temp = 1.f / (dscale[i__ - 1] - *tau);</span></a>
+<a name="18534"><span class="lineNum">   18534 </span><span class="lineNoCov">          0 :         temp1 = zscale[i__ - 1] * temp;</span></a>
+<a name="18535"><span class="lineNum">   18535 </span><span class="lineNoCov">          0 :         temp2 = temp1 * temp;</span></a>
+<a name="18536"><span class="lineNum">   18536 </span><span class="lineNoCov">          0 :         temp3 = temp2 * temp;</span></a>
+<a name="18537"><span class="lineNum">   18537 </span><span class="lineNoCov">          0 :         fc += temp1 / dscale[i__ - 1];</span></a>
+<a name="18538"><span class="lineNum">   18538 </span><span class="lineNoCov">          0 :         df += temp2;</span></a>
+<a name="18539"><span class="lineNum">   18539 </span><span class="lineNoCov">          0 :         ddf += temp3;</span></a>
+<a name="18540"><span class="lineNum">   18540 </span>            :     }</a>
+<a name="18541"><span class="lineNum">   18541 </span><span class="lineNoCov">          0 :     f = *finit + *tau * fc;</span></a>
+<a name="18542"><span class="lineNum">   18542 </span>            : </a>
+<a name="18543"><span class="lineNum">   18543 </span><span class="lineNoCov">          0 :     if (std::abs(f) &lt;= 0.f) {</span></a>
+<a name="18544"><span class="lineNum">   18544 </span><span class="lineNoCov">          0 :         goto L60;</span></a>
+<a name="18545"><span class="lineNum">   18545 </span>            :     }</a>
+<a name="18546"><span class="lineNum">   18546 </span>            :     iter = niter + 1;</a>
+<a name="18547"><span class="lineNum">   18547 </span><span class="lineNoCov">          0 :     for (niter = iter; niter &lt;= 20; ++niter) {</span></a>
+<a name="18548"><span class="lineNum">   18548 </span><span class="lineNoCov">          0 :         if (*orgati) {</span></a>
+<a name="18549"><span class="lineNum">   18549 </span><span class="lineNoCov">          0 :             temp1 = dscale[1] - *tau;</span></a>
+<a name="18550"><span class="lineNum">   18550 </span><span class="lineNoCov">          0 :             temp2 = dscale[2] - *tau;</span></a>
+<a name="18551"><span class="lineNum">   18551 </span>            :         } else {</a>
+<a name="18552"><span class="lineNum">   18552 </span><span class="lineNoCov">          0 :             temp1 = dscale[0] - *tau;</span></a>
+<a name="18553"><span class="lineNum">   18553 </span><span class="lineNoCov">          0 :             temp2 = dscale[1] - *tau;</span></a>
+<a name="18554"><span class="lineNum">   18554 </span>            :         }</a>
+<a name="18555"><span class="lineNum">   18555 </span><span class="lineNoCov">          0 :         a = (temp1 + temp2) * f - temp1 * temp2 * df;</span></a>
+<a name="18556"><span class="lineNum">   18556 </span><span class="lineNoCov">          0 :         b = temp1 * temp2 * f;</span></a>
+<a name="18557"><span class="lineNum">   18557 </span><span class="lineNoCov">          0 :         c__ = f - (temp1 + temp2) * df + temp1 * temp2 * ddf;</span></a>
+<a name="18558"><span class="lineNum">   18558 </span><span class="lineNoCov">          0 :         r__1 = std::abs(a), r__2 = std::abs(b), r__1 = ((r__1&gt;r__2)? r__1:r__2), r__2 = std::abs(c__);</span></a>
+<a name="18559"><span class="lineNum">   18559 </span><span class="lineNoCov">          0 :         temp = (r__1&gt;r__2) ? r__1 : r__2;</span></a>
+<a name="18560"><span class="lineNum">   18560 </span><span class="lineNoCov">          0 :         a /= temp;</span></a>
+<a name="18561"><span class="lineNum">   18561 </span><span class="lineNoCov">          0 :         b /= temp;</span></a>
+<a name="18562"><span class="lineNum">   18562 </span><span class="lineNoCov">          0 :         c__ /= temp;</span></a>
+<a name="18563"><span class="lineNum">   18563 </span><span class="lineNoCov">          0 :         if (c__ == 0.f) {</span></a>
+<a name="18564"><span class="lineNum">   18564 </span><span class="lineNoCov">          0 :             eta = b / a;</span></a>
+<a name="18565"><span class="lineNum">   18565 </span><span class="lineNoCov">          0 :         } else if (a &lt;= 0.f) {</span></a>
+<a name="18566"><span class="lineNum">   18566 </span><span class="lineNoCov">          0 :             eta = (a -  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs(r__1)))) / ( c__ * 2.f);</span></a>
+<a name="18567"><span class="lineNum">   18567 </span>            :         } else {</a>
+<a name="18568"><span class="lineNum">   18568 </span><span class="lineNoCov">          0 :             eta = b * 2.f / (a +  std::sqrt((r__1 = a * a - b * 4.f * c__, std::abs( r__1))));</span></a>
+<a name="18569"><span class="lineNum">   18569 </span>            :         }</a>
+<a name="18570"><span class="lineNum">   18570 </span><span class="lineNoCov">          0 :         if (f * eta &gt;= 0.f) {</span></a>
+<a name="18571"><span class="lineNum">   18571 </span><span class="lineNoCov">          0 :             eta = -f / df;</span></a>
+<a name="18572"><span class="lineNum">   18572 </span>            :         }</a>
+<a name="18573"><span class="lineNum">   18573 </span><span class="lineNoCov">          0 :         temp = eta + *tau;</span></a>
+<a name="18574"><span class="lineNum">   18574 </span><span class="lineNoCov">          0 :         if (*orgati) {</span></a>
+<a name="18575"><span class="lineNum">   18575 </span><span class="lineNoCov">          0 :             if (eta &gt; 0.f &amp;&amp; temp &gt;= dscale[2]) {</span></a>
+<a name="18576"><span class="lineNum">   18576 </span><span class="lineNoCov">          0 :                 eta = (dscale[2] - *tau) / 2.f;</span></a>
+<a name="18577"><span class="lineNum">   18577 </span>            :             }</a>
+<a name="18578"><span class="lineNum">   18578 </span>            : </a>
+<a name="18579"><span class="lineNum">   18579 </span><span class="lineNoCov">          0 :             if (eta &lt; 0.f &amp;&amp; temp &lt;= dscale[1]) {</span></a>
+<a name="18580"><span class="lineNum">   18580 </span><span class="lineNoCov">          0 :                 eta = (dscale[1] - *tau) / 2.f;</span></a>
+<a name="18581"><span class="lineNum">   18581 </span>            :             }</a>
+<a name="18582"><span class="lineNum">   18582 </span>            :         } else {</a>
+<a name="18583"><span class="lineNum">   18583 </span><span class="lineNoCov">          0 :             if (eta &gt; 0.f &amp;&amp; temp &gt;= dscale[1]) {</span></a>
+<a name="18584"><span class="lineNum">   18584 </span><span class="lineNoCov">          0 :                 eta = (dscale[1] - *tau) / 2.f;</span></a>
+<a name="18585"><span class="lineNum">   18585 </span>            :             }</a>
+<a name="18586"><span class="lineNum">   18586 </span><span class="lineNoCov">          0 :             if (eta &lt; 0.f &amp;&amp; temp &lt;= dscale[0]) {</span></a>
+<a name="18587"><span class="lineNum">   18587 </span><span class="lineNoCov">          0 :                 eta = (dscale[0] - *tau) / 2.f;</span></a>
+<a name="18588"><span class="lineNum">   18588 </span>            :             }</a>
+<a name="18589"><span class="lineNum">   18589 </span>            :         }</a>
+<a name="18590"><span class="lineNum">   18590 </span><span class="lineNoCov">          0 :         *tau += eta;</span></a>
+<a name="18591"><span class="lineNum">   18591 </span>            :         fc = 0.f;</a>
+<a name="18592"><span class="lineNum">   18592 </span>            :         erretm = 0.f;</a>
+<a name="18593"><span class="lineNum">   18593 </span>            :         df = 0.f;</a>
+<a name="18594"><span class="lineNum">   18594 </span>            :         ddf = 0.f;</a>
+<a name="18595"><span class="lineNum">   18595 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= 3; ++i__) {</span></a>
+<a name="18596"><span class="lineNum">   18596 </span><span class="lineNoCov">          0 :             temp = 1.f / (dscale[i__ - 1] - *tau);</span></a>
+<a name="18597"><span class="lineNum">   18597 </span><span class="lineNoCov">          0 :             temp1 = zscale[i__ - 1] * temp;</span></a>
+<a name="18598"><span class="lineNum">   18598 </span><span class="lineNoCov">          0 :             temp2 = temp1 * temp;</span></a>
+<a name="18599"><span class="lineNum">   18599 </span><span class="lineNoCov">          0 :             temp3 = temp2 * temp;</span></a>
+<a name="18600"><span class="lineNum">   18600 </span><span class="lineNoCov">          0 :             temp4 = temp1 / dscale[i__ - 1];</span></a>
+<a name="18601"><span class="lineNum">   18601 </span><span class="lineNoCov">          0 :             fc += temp4;</span></a>
+<a name="18602"><span class="lineNum">   18602 </span><span class="lineNoCov">          0 :             erretm += std::abs(temp4);</span></a>
+<a name="18603"><span class="lineNum">   18603 </span><span class="lineNoCov">          0 :             df += temp2;</span></a>
+<a name="18604"><span class="lineNum">   18604 </span><span class="lineNoCov">          0 :             ddf += temp3;</span></a>
+<a name="18605"><span class="lineNum">   18605 </span>            :         }</a>
+<a name="18606"><span class="lineNum">   18606 </span><span class="lineNoCov">          0 :         f = *finit + *tau * fc;</span></a>
+<a name="18607"><span class="lineNum">   18607 </span><span class="lineNoCov">          0 :         erretm = (std::abs(*finit) + std::abs(*tau) * erretm) * 8.f + std::abs(*tau) * df;</span></a>
+<a name="18608"><span class="lineNum">   18608 </span><span class="lineNoCov">          0 :         if (std::abs(f) &lt;= eps * erretm) {</span></a>
+<a name="18609"><span class="lineNum">   18609 </span><span class="lineNoCov">          0 :             goto L60;</span></a>
+<a name="18610"><span class="lineNum">   18610 </span>            :         }</a>
+<a name="18611"><span class="lineNum">   18611 </span>            :     }</a>
+<a name="18612"><span class="lineNum">   18612 </span><span class="lineNoCov">          0 :     *info = 1;</span></a>
+<a name="18613"><span class="lineNum">   18613 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="18614"><span class="lineNum">   18614 </span><span class="lineNoCov">          0 :     if (scale) {</span></a>
+<a name="18615"><span class="lineNum">   18615 </span><span class="lineNoCov">          0 :         *tau *= sclinv;</span></a>
+<a name="18616"><span class="lineNum">   18616 </span>            :     }</a>
+<a name="18617"><span class="lineNum">   18617 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="18618"><span class="lineNum">   18618 </span>            : } </a>
+<a name="18619"><span class="lineNum">   18619 </span>            : </a>
+<a name="18620"><span class="lineNum">   18620 </span>            : </a>
+<a name="18621"><span class="lineNum">   18621 </span>            : }</a>
+<a name="18622"><span class="lineNum">   18622 </span>            : }</a>
+<a name="18623"><span class="lineNum">   18623 </span>            : #include &lt;cmath&gt;</a>
+<a name="18624"><span class="lineNum">   18624 </span>            : #include &quot;real.h&quot;</a>
+<a name="18625"><span class="lineNum">   18625 </span>            : </a>
+<a name="18626"><span class="lineNum">   18626 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18627"><span class="lineNum">   18627 </span>            : </a>
+<a name="18628"><span class="lineNum">   18628 </span>            : </a>
+<a name="18629"><span class="lineNum">   18629 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18630"><span class="lineNum">   18630 </span>            : namespace PLMD{</a>
+<a name="18631"><span class="lineNum">   18631 </span>            : namespace lapack{</a>
+<a name="18632"><span class="lineNum">   18632 </span>            : using namespace blas;</a>
+<a name="18633"><span class="lineNum">   18633 </span>            : void</a>
+<a name="18634"><span class="lineNum">   18634 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slaev2,SLAEV2)(float *   a, </span></a>
+<a name="18635"><span class="lineNum">   18635 </span>            :         float *   b, </a>
+<a name="18636"><span class="lineNum">   18636 </span>            :         float *   c__, </a>
+<a name="18637"><span class="lineNum">   18637 </span>            :         float *   rt1, </a>
+<a name="18638"><span class="lineNum">   18638 </span>            :         float *   rt2, </a>
+<a name="18639"><span class="lineNum">   18639 </span>            :         float *   cs1, </a>
+<a name="18640"><span class="lineNum">   18640 </span>            :         float *   sn1)</a>
+<a name="18641"><span class="lineNum">   18641 </span>            : {</a>
+<a name="18642"><span class="lineNum">   18642 </span>            :     float d__1;</a>
+<a name="18643"><span class="lineNum">   18643 </span>            : </a>
+<a name="18644"><span class="lineNum">   18644 </span>            :     float ab, df, cs, ct, tb, sm, tn, rt, adf, acs;</a>
+<a name="18645"><span class="lineNum">   18645 </span>            :     int sgn1, sgn2;</a>
+<a name="18646"><span class="lineNum">   18646 </span>            :     float acmn, acmx;</a>
+<a name="18647"><span class="lineNum">   18647 </span>            : </a>
+<a name="18648"><span class="lineNum">   18648 </span><span class="lineNoCov">          0 :     sm = *a + *c__;</span></a>
+<a name="18649"><span class="lineNum">   18649 </span><span class="lineNoCov">          0 :     df = *a - *c__;</span></a>
+<a name="18650"><span class="lineNum">   18650 </span>            :     adf = std::abs(df);</a>
+<a name="18651"><span class="lineNum">   18651 </span><span class="lineNoCov">          0 :     tb = *b + *b;</span></a>
+<a name="18652"><span class="lineNum">   18652 </span>            :     ab = std::abs(tb);</a>
+<a name="18653"><span class="lineNum">   18653 </span><span class="lineNoCov">          0 :     if (std::abs(*a) &gt; std::abs(*c__)) {</span></a>
+<a name="18654"><span class="lineNum">   18654 </span>            :         acmx = *a;</a>
+<a name="18655"><span class="lineNum">   18655 </span>            :         acmn = *c__;</a>
+<a name="18656"><span class="lineNum">   18656 </span>            :     } else {</a>
+<a name="18657"><span class="lineNum">   18657 </span>            :         acmx = *c__;</a>
+<a name="18658"><span class="lineNum">   18658 </span>            :         acmn = *a;</a>
+<a name="18659"><span class="lineNum">   18659 </span>            :     }</a>
+<a name="18660"><span class="lineNum">   18660 </span><span class="lineNoCov">          0 :     if (adf &gt; ab) {</span></a>
+<a name="18661"><span class="lineNum">   18661 </span><span class="lineNoCov">          0 :         d__1 = ab / adf;</span></a>
+<a name="18662"><span class="lineNum">   18662 </span><span class="lineNoCov">          0 :         rt = adf *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="18663"><span class="lineNum">   18663 </span><span class="lineNoCov">          0 :     } else if (adf &lt; ab) {</span></a>
+<a name="18664"><span class="lineNum">   18664 </span><span class="lineNoCov">          0 :         d__1 = adf / ab;</span></a>
+<a name="18665"><span class="lineNum">   18665 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(d__1 * d__1 + 1.);</span></a>
+<a name="18666"><span class="lineNum">   18666 </span>            :     } else {</a>
+<a name="18667"><span class="lineNum">   18667 </span>            : </a>
+<a name="18668"><span class="lineNum">   18668 </span><span class="lineNoCov">          0 :         rt = ab *  std::sqrt(2.);</span></a>
+<a name="18669"><span class="lineNum">   18669 </span>            :     }</a>
+<a name="18670"><span class="lineNum">   18670 </span><span class="lineNoCov">          0 :     if (sm &lt; 0.) {</span></a>
+<a name="18671"><span class="lineNum">   18671 </span><span class="lineNoCov">          0 :         *rt1 = (sm - rt) * .5;</span></a>
+<a name="18672"><span class="lineNum">   18672 </span>            :         sgn1 = -1;</a>
+<a name="18673"><span class="lineNum">   18673 </span>            : </a>
+<a name="18674"><span class="lineNum">   18674 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="18675"><span class="lineNum">   18675 </span><span class="lineNoCov">          0 :     } else if (sm &gt; 0.) {</span></a>
+<a name="18676"><span class="lineNum">   18676 </span><span class="lineNoCov">          0 :         *rt1 = (sm + rt) * .5;</span></a>
+<a name="18677"><span class="lineNum">   18677 </span>            :         sgn1 = 1;</a>
+<a name="18678"><span class="lineNum">   18678 </span><span class="lineNoCov">          0 :         *rt2 = acmx / *rt1 * acmn - *b / *rt1 * *b;</span></a>
+<a name="18679"><span class="lineNum">   18679 </span>            :     } else {</a>
+<a name="18680"><span class="lineNum">   18680 </span><span class="lineNoCov">          0 :         *rt1 = rt * .5;</span></a>
+<a name="18681"><span class="lineNum">   18681 </span><span class="lineNoCov">          0 :         *rt2 = rt * -.5;</span></a>
+<a name="18682"><span class="lineNum">   18682 </span>            :         sgn1 = 1;</a>
+<a name="18683"><span class="lineNum">   18683 </span>            :     }</a>
+<a name="18684"><span class="lineNum">   18684 </span><span class="lineNoCov">          0 :     if (df &gt;= 0.) {</span></a>
+<a name="18685"><span class="lineNum">   18685 </span><span class="lineNoCov">          0 :         cs = df + rt;</span></a>
+<a name="18686"><span class="lineNum">   18686 </span>            :         sgn2 = 1;</a>
+<a name="18687"><span class="lineNum">   18687 </span>            :     } else {</a>
+<a name="18688"><span class="lineNum">   18688 </span><span class="lineNoCov">          0 :         cs = df - rt;</span></a>
+<a name="18689"><span class="lineNum">   18689 </span>            :         sgn2 = -1;</a>
+<a name="18690"><span class="lineNum">   18690 </span>            :     }</a>
+<a name="18691"><span class="lineNum">   18691 </span>            :     acs = std::abs(cs);</a>
+<a name="18692"><span class="lineNum">   18692 </span><span class="lineNoCov">          0 :     if (acs &gt; ab) {</span></a>
+<a name="18693"><span class="lineNum">   18693 </span><span class="lineNoCov">          0 :         ct = -tb / cs;</span></a>
+<a name="18694"><span class="lineNum">   18694 </span><span class="lineNoCov">          0 :         *sn1 = 1. /  std::sqrt(ct * ct + 1.);</span></a>
+<a name="18695"><span class="lineNum">   18695 </span><span class="lineNoCov">          0 :         *cs1 = ct * *sn1;</span></a>
+<a name="18696"><span class="lineNum">   18696 </span>            :     } else {</a>
+<a name="18697"><span class="lineNum">   18697 </span><span class="lineNoCov">          0 :         if (std::abs(ab)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="18698"><span class="lineNum">   18698 </span><span class="lineNoCov">          0 :             *cs1 = 1.;</span></a>
+<a name="18699"><span class="lineNum">   18699 </span><span class="lineNoCov">          0 :             *sn1 = 0.;</span></a>
+<a name="18700"><span class="lineNum">   18700 </span>            :         } else {</a>
+<a name="18701"><span class="lineNum">   18701 </span><span class="lineNoCov">          0 :             tn = -cs / tb;</span></a>
+<a name="18702"><span class="lineNum">   18702 </span><span class="lineNoCov">          0 :             *cs1 = 1. /  std::sqrt(tn * tn + 1.);</span></a>
+<a name="18703"><span class="lineNum">   18703 </span><span class="lineNoCov">          0 :             *sn1 = tn * *cs1;</span></a>
+<a name="18704"><span class="lineNum">   18704 </span>            :         }</a>
+<a name="18705"><span class="lineNum">   18705 </span>            :     }</a>
+<a name="18706"><span class="lineNum">   18706 </span><span class="lineNoCov">          0 :     if (sgn1 == sgn2) {</span></a>
+<a name="18707"><span class="lineNum">   18707 </span><span class="lineNoCov">          0 :         tn = *cs1;</span></a>
+<a name="18708"><span class="lineNum">   18708 </span><span class="lineNoCov">          0 :         *cs1 = -(*sn1);</span></a>
+<a name="18709"><span class="lineNum">   18709 </span><span class="lineNoCov">          0 :         *sn1 = tn;</span></a>
+<a name="18710"><span class="lineNum">   18710 </span>            :     }</a>
+<a name="18711"><span class="lineNum">   18711 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="18712"><span class="lineNum">   18712 </span>            : </a>
+<a name="18713"><span class="lineNum">   18713 </span>            : }</a>
+<a name="18714"><span class="lineNum">   18714 </span>            : </a>
+<a name="18715"><span class="lineNum">   18715 </span>            : </a>
+<a name="18716"><span class="lineNum">   18716 </span>            : }</a>
+<a name="18717"><span class="lineNum">   18717 </span>            : }</a>
+<a name="18718"><span class="lineNum">   18718 </span>            : #include &lt;cmath&gt;</a>
+<a name="18719"><span class="lineNum">   18719 </span>            : #include &quot;real.h&quot;</a>
+<a name="18720"><span class="lineNum">   18720 </span>            : </a>
+<a name="18721"><span class="lineNum">   18721 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18722"><span class="lineNum">   18722 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="18723"><span class="lineNum">   18723 </span>            : </a>
+<a name="18724"><span class="lineNum">   18724 </span>            : </a>
+<a name="18725"><span class="lineNum">   18725 </span>            : </a>
+<a name="18726"><span class="lineNum">   18726 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18727"><span class="lineNum">   18727 </span>            : namespace PLMD{</a>
+<a name="18728"><span class="lineNum">   18728 </span>            : namespace lapack{</a>
+<a name="18729"><span class="lineNum">   18729 </span>            : using namespace blas;</a>
+<a name="18730"><span class="lineNum">   18730 </span>            : void</a>
+<a name="18731"><span class="lineNum">   18731 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slagtf,SLAGTF)(int *n, </span></a>
+<a name="18732"><span class="lineNum">   18732 </span>            :         float *a, </a>
+<a name="18733"><span class="lineNum">   18733 </span>            :         float *lambda, </a>
+<a name="18734"><span class="lineNum">   18734 </span>            :         float *b, </a>
+<a name="18735"><span class="lineNum">   18735 </span>            :         float *c__, </a>
+<a name="18736"><span class="lineNum">   18736 </span>            :         float *tol, </a>
+<a name="18737"><span class="lineNum">   18737 </span>            :         float *d__, </a>
+<a name="18738"><span class="lineNum">   18738 </span>            :         int *in, </a>
+<a name="18739"><span class="lineNum">   18739 </span>            :         int *info)</a>
+<a name="18740"><span class="lineNum">   18740 </span>            : {</a>
+<a name="18741"><span class="lineNum">   18741 </span>            :     int i__1;</a>
+<a name="18742"><span class="lineNum">   18742 </span>            : </a>
+<a name="18743"><span class="lineNum">   18743 </span>            :     int k;</a>
+<a name="18744"><span class="lineNum">   18744 </span>            :     float tl, eps, piv1, piv2, temp, mult, scale1, scale2;</a>
+<a name="18745"><span class="lineNum">   18745 </span>            : </a>
+<a name="18746"><span class="lineNum">   18746 </span><span class="lineNoCov">          0 :     --in;</span></a>
+<a name="18747"><span class="lineNum">   18747 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="18748"><span class="lineNum">   18748 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="18749"><span class="lineNum">   18749 </span><span class="lineNoCov">          0 :     --b;</span></a>
+<a name="18750"><span class="lineNum">   18750 </span><span class="lineNoCov">          0 :     --a;</span></a>
+<a name="18751"><span class="lineNum">   18751 </span>            : </a>
+<a name="18752"><span class="lineNum">   18752 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="18753"><span class="lineNum">   18753 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="18754"><span class="lineNum">   18754 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="18755"><span class="lineNum">   18755 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="18756"><span class="lineNum">   18756 </span>            :     }</a>
+<a name="18757"><span class="lineNum">   18757 </span>            : </a>
+<a name="18758"><span class="lineNum">   18758 </span><span class="lineNoCov">          0 :     if (*n == 0) </span></a>
+<a name="18759"><span class="lineNum">   18759 </span>            :         return;</a>
+<a name="18760"><span class="lineNum">   18760 </span>            :     </a>
+<a name="18761"><span class="lineNum">   18761 </span><span class="lineNoCov">          0 :     a[1] -= *lambda;</span></a>
+<a name="18762"><span class="lineNum">   18762 </span><span class="lineNoCov">          0 :     in[*n] = 0;</span></a>
+<a name="18763"><span class="lineNum">   18763 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="18764"><span class="lineNum">   18764 </span><span class="lineNoCov">          0 :         if (std::abs(a[1])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="18765"><span class="lineNum">   18765 </span><span class="lineNoCov">          0 :             in[1] = 1;</span></a>
+<a name="18766"><span class="lineNum">   18766 </span>            :         }</a>
+<a name="18767"><span class="lineNum">   18767 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="18768"><span class="lineNum">   18768 </span>            :     }</a>
+<a name="18769"><span class="lineNum">   18769 </span>            : </a>
+<a name="18770"><span class="lineNum">   18770 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="18771"><span class="lineNum">   18771 </span>            : </a>
+<a name="18772"><span class="lineNum">   18772 </span><span class="lineNoCov">          0 :     tl = (*tol&gt;eps) ? *tol : eps;</span></a>
+<a name="18773"><span class="lineNum">   18773 </span><span class="lineNoCov">          0 :     scale1 = std::abs(a[1]) + std::abs(b[1]);</span></a>
+<a name="18774"><span class="lineNum">   18774 </span>            :     i__1 = *n - 1;</a>
+<a name="18775"><span class="lineNum">   18775 </span><span class="lineNoCov">          0 :     for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="18776"><span class="lineNum">   18776 </span><span class="lineNoCov">          0 :         a[k + 1] -= *lambda;</span></a>
+<a name="18777"><span class="lineNum">   18777 </span><span class="lineNoCov">          0 :         scale2 = std::abs(c__[k]) + std::abs(a[k + 1]);</span></a>
+<a name="18778"><span class="lineNum">   18778 </span><span class="lineNoCov">          0 :         if (k &lt; *n - 1) {</span></a>
+<a name="18779"><span class="lineNum">   18779 </span><span class="lineNoCov">          0 :             scale2 += std::abs(b[k + 1]);</span></a>
+<a name="18780"><span class="lineNum">   18780 </span>            :         }</a>
+<a name="18781"><span class="lineNum">   18781 </span><span class="lineNoCov">          0 :         if (std::abs(a[k])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="18782"><span class="lineNum">   18782 </span>            :             piv1 = 0.;</a>
+<a name="18783"><span class="lineNum">   18783 </span>            :         } else {</a>
+<a name="18784"><span class="lineNum">   18784 </span><span class="lineNoCov">          0 :             piv1 = std::abs(a[k]) / scale1;</span></a>
+<a name="18785"><span class="lineNum">   18785 </span>            :         }</a>
+<a name="18786"><span class="lineNum">   18786 </span><span class="lineNoCov">          0 :         if (std::abs(c__[k])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="18787"><span class="lineNum">   18787 </span><span class="lineNoCov">          0 :             in[k] = 0;</span></a>
+<a name="18788"><span class="lineNum">   18788 </span>            :             piv2 = 0.;</a>
+<a name="18789"><span class="lineNum">   18789 </span>            :             scale1 = scale2;</a>
+<a name="18790"><span class="lineNum">   18790 </span><span class="lineNoCov">          0 :             if (k &lt; *n - 1) {</span></a>
+<a name="18791"><span class="lineNum">   18791 </span><span class="lineNoCov">          0 :                 d__[k] = 0.;</span></a>
+<a name="18792"><span class="lineNum">   18792 </span>            :             }</a>
+<a name="18793"><span class="lineNum">   18793 </span>            :         } else {</a>
+<a name="18794"><span class="lineNum">   18794 </span><span class="lineNoCov">          0 :             piv2 = std::abs(c__[k]) / scale2;</span></a>
+<a name="18795"><span class="lineNum">   18795 </span><span class="lineNoCov">          0 :             if (piv2 &lt;= piv1) {</span></a>
+<a name="18796"><span class="lineNum">   18796 </span><span class="lineNoCov">          0 :                 in[k] = 0;</span></a>
+<a name="18797"><span class="lineNum">   18797 </span>            :                 scale1 = scale2;</a>
+<a name="18798"><span class="lineNum">   18798 </span><span class="lineNoCov">          0 :                 c__[k] /= a[k];</span></a>
+<a name="18799"><span class="lineNum">   18799 </span><span class="lineNoCov">          0 :                 a[k + 1] -= c__[k] * b[k];</span></a>
+<a name="18800"><span class="lineNum">   18800 </span><span class="lineNoCov">          0 :                 if (k &lt; *n - 1) {</span></a>
+<a name="18801"><span class="lineNum">   18801 </span><span class="lineNoCov">          0 :                     d__[k] = 0.;</span></a>
+<a name="18802"><span class="lineNum">   18802 </span>            :                 }</a>
+<a name="18803"><span class="lineNum">   18803 </span>            :             } else {</a>
+<a name="18804"><span class="lineNum">   18804 </span><span class="lineNoCov">          0 :                 in[k] = 1;</span></a>
+<a name="18805"><span class="lineNum">   18805 </span><span class="lineNoCov">          0 :                 mult = a[k] / c__[k];</span></a>
+<a name="18806"><span class="lineNum">   18806 </span><span class="lineNoCov">          0 :                 a[k] = c__[k];</span></a>
+<a name="18807"><span class="lineNum">   18807 </span><span class="lineNoCov">          0 :                 temp = a[k + 1];</span></a>
+<a name="18808"><span class="lineNum">   18808 </span><span class="lineNoCov">          0 :                 a[k + 1] = b[k] - mult * temp;</span></a>
+<a name="18809"><span class="lineNum">   18809 </span><span class="lineNoCov">          0 :                 if (k &lt; *n - 1) {</span></a>
+<a name="18810"><span class="lineNum">   18810 </span><span class="lineNoCov">          0 :                     d__[k] = b[k + 1];</span></a>
+<a name="18811"><span class="lineNum">   18811 </span><span class="lineNoCov">          0 :                     b[k + 1] = -mult * d__[k];</span></a>
+<a name="18812"><span class="lineNum">   18812 </span>            :                 }</a>
+<a name="18813"><span class="lineNum">   18813 </span><span class="lineNoCov">          0 :                 b[k] = temp;</span></a>
+<a name="18814"><span class="lineNum">   18814 </span><span class="lineNoCov">          0 :                 c__[k] = mult;</span></a>
+<a name="18815"><span class="lineNum">   18815 </span>            :             }</a>
+<a name="18816"><span class="lineNum">   18816 </span>            :         }</a>
+<a name="18817"><span class="lineNum">   18817 </span><span class="lineNoCov">          0 :         if (((piv1&gt;piv2) ? piv1 : piv2) &lt;= tl &amp;&amp; in[*n] == 0) {</span></a>
+<a name="18818"><span class="lineNum">   18818 </span><span class="lineNoCov">          0 :             in[*n] = k;</span></a>
+<a name="18819"><span class="lineNum">   18819 </span>            :         }</a>
+<a name="18820"><span class="lineNum">   18820 </span>            :     }</a>
+<a name="18821"><span class="lineNum">   18821 </span><span class="lineNoCov">          0 :     if (std::abs(a[*n]) &lt;= scale1 * tl &amp;&amp; in[*n] == 0) {</span></a>
+<a name="18822"><span class="lineNum">   18822 </span><span class="lineNoCov">          0 :         in[*n] = *n;</span></a>
+<a name="18823"><span class="lineNum">   18823 </span>            :     }</a>
+<a name="18824"><span class="lineNum">   18824 </span>            : </a>
+<a name="18825"><span class="lineNum">   18825 </span>            :     return;</a>
+<a name="18826"><span class="lineNum">   18826 </span>            : </a>
+<a name="18827"><span class="lineNum">   18827 </span>            : }</a>
+<a name="18828"><span class="lineNum">   18828 </span>            : </a>
+<a name="18829"><span class="lineNum">   18829 </span>            : </a>
+<a name="18830"><span class="lineNum">   18830 </span>            : }</a>
+<a name="18831"><span class="lineNum">   18831 </span>            : }</a>
+<a name="18832"><span class="lineNum">   18832 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="18833"><span class="lineNum">   18833 </span>            : #include &lt;cmath&gt;</a>
+<a name="18834"><span class="lineNum">   18834 </span>            : #include &quot;real.h&quot;</a>
+<a name="18835"><span class="lineNum">   18835 </span>            : </a>
+<a name="18836"><span class="lineNum">   18836 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="18837"><span class="lineNum">   18837 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="18838"><span class="lineNum">   18838 </span>            : </a>
+<a name="18839"><span class="lineNum">   18839 </span>            : </a>
+<a name="18840"><span class="lineNum">   18840 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="18841"><span class="lineNum">   18841 </span>            : namespace PLMD{</a>
+<a name="18842"><span class="lineNum">   18842 </span>            : namespace lapack{</a>
+<a name="18843"><span class="lineNum">   18843 </span>            : using namespace blas;</a>
+<a name="18844"><span class="lineNum">   18844 </span>            : void</a>
+<a name="18845"><span class="lineNum">   18845 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slagts,SLAGTS)(int *job, </span></a>
+<a name="18846"><span class="lineNum">   18846 </span>            :         int *n, </a>
+<a name="18847"><span class="lineNum">   18847 </span>            :         float *a, </a>
+<a name="18848"><span class="lineNum">   18848 </span>            :         float *b, </a>
+<a name="18849"><span class="lineNum">   18849 </span>            :         float *c__, </a>
+<a name="18850"><span class="lineNum">   18850 </span>            :         float *d__, </a>
+<a name="18851"><span class="lineNum">   18851 </span>            :         int *in, </a>
+<a name="18852"><span class="lineNum">   18852 </span>            :         float *y, </a>
+<a name="18853"><span class="lineNum">   18853 </span>            :         float *tol, </a>
+<a name="18854"><span class="lineNum">   18854 </span>            :         int *info)</a>
+<a name="18855"><span class="lineNum">   18855 </span>            : {</a>
+<a name="18856"><span class="lineNum">   18856 </span>            :     int i__1;</a>
+<a name="18857"><span class="lineNum">   18857 </span>            :     float d__1, d__2, d__4, d__5;</a>
+<a name="18858"><span class="lineNum">   18858 </span>            : </a>
+<a name="18859"><span class="lineNum">   18859 </span>            :     int k;</a>
+<a name="18860"><span class="lineNum">   18860 </span>            :     float ak, eps, temp, pert, absak, sfmin;</a>
+<a name="18861"><span class="lineNum">   18861 </span>            :     float bignum,minval;</a>
+<a name="18862"><span class="lineNum">   18862 </span><span class="lineNoCov">          0 :     --y;</span></a>
+<a name="18863"><span class="lineNum">   18863 </span><span class="lineNoCov">          0 :     --in;</span></a>
+<a name="18864"><span class="lineNum">   18864 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="18865"><span class="lineNum">   18865 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="18866"><span class="lineNum">   18866 </span><span class="lineNoCov">          0 :     --b;</span></a>
+<a name="18867"><span class="lineNum">   18867 </span><span class="lineNoCov">          0 :     --a;</span></a>
+<a name="18868"><span class="lineNum">   18868 </span>            : </a>
+<a name="18869"><span class="lineNum">   18869 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="18870"><span class="lineNum">   18870 </span><span class="lineNoCov">          0 :     if (abs(*job) &gt; 2 || *job == 0) {</span></a>
+<a name="18871"><span class="lineNum">   18871 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="18872"><span class="lineNum">   18872 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="18873"><span class="lineNum">   18873 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="18874"><span class="lineNum">   18874 </span>            :     }</a>
+<a name="18875"><span class="lineNum">   18875 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="18876"><span class="lineNum">   18876 </span>            :         return;</a>
+<a name="18877"><span class="lineNum">   18877 </span>            :     }</a>
+<a name="18878"><span class="lineNum">   18878 </span>            : </a>
+<a name="18879"><span class="lineNum">   18879 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="18880"><span class="lineNum">   18880 </span>            :         return;</a>
+<a name="18881"><span class="lineNum">   18881 </span>            :     }</a>
+<a name="18882"><span class="lineNum">   18882 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="18883"><span class="lineNum">   18883 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="18884"><span class="lineNum">   18884 </span>            :     sfmin = minval / eps;</a>
+<a name="18885"><span class="lineNum">   18885 </span>            : </a>
+<a name="18886"><span class="lineNum">   18886 </span>            :     bignum = 1. / sfmin;</a>
+<a name="18887"><span class="lineNum">   18887 </span>            : </a>
+<a name="18888"><span class="lineNum">   18888 </span><span class="lineNoCov">          0 :     if (*job &lt; 0) {</span></a>
+<a name="18889"><span class="lineNum">   18889 </span><span class="lineNoCov">          0 :         if (*tol &lt;= 0.) {</span></a>
+<a name="18890"><span class="lineNum">   18890 </span><span class="lineNoCov">          0 :             *tol = std::abs(a[1]);</span></a>
+<a name="18891"><span class="lineNum">   18891 </span><span class="lineNoCov">          0 :             if (*n &gt; 1) {</span></a>
+<a name="18892"><span class="lineNum">   18892 </span>            :                 d__1 = *tol;</a>
+<a name="18893"><span class="lineNum">   18893 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(a[2]);</span></a>
+<a name="18894"><span class="lineNum">   18894 </span><span class="lineNoCov">          0 :                 d__1 = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="18895"><span class="lineNum">   18895 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(b[1]);</span></a>
+<a name="18896"><span class="lineNum">   18896 </span><span class="lineNoCov">          0 :                 *tol = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="18897"><span class="lineNum">   18897 </span>            :             }</a>
+<a name="18898"><span class="lineNum">   18898 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="18899"><span class="lineNum">   18899 </span><span class="lineNoCov">          0 :             for (k = 3; k &lt;= i__1; ++k) {</span></a>
+<a name="18900"><span class="lineNum">   18900 </span><span class="lineNoCov">          0 :               d__4 = *tol;</span></a>
+<a name="18901"><span class="lineNum">   18901 </span><span class="lineNoCov">          0 :               d__5 = std::abs(a[k]);</span></a>
+<a name="18902"><span class="lineNum">   18902 </span><span class="lineNoCov">          0 :               d__4 = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="18903"><span class="lineNum">   18903 </span><span class="lineNoCov">          0 :               d__5 = std::abs(b[k - 1]);</span></a>
+<a name="18904"><span class="lineNum">   18904 </span><span class="lineNoCov">          0 :               d__4 = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="18905"><span class="lineNum">   18905 </span><span class="lineNoCov">          0 :               d__5 = std::abs(d__[k - 2]);</span></a>
+<a name="18906"><span class="lineNum">   18906 </span><span class="lineNoCov">          0 :               *tol = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="18907"><span class="lineNum">   18907 </span>            :             }</a>
+<a name="18908"><span class="lineNum">   18908 </span><span class="lineNoCov">          0 :             *tol *= eps;</span></a>
+<a name="18909"><span class="lineNum">   18909 </span><span class="lineNoCov">          0 :             if (std::abs(*tol)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="18910"><span class="lineNum">   18910 </span><span class="lineNoCov">          0 :                 *tol = eps;</span></a>
+<a name="18911"><span class="lineNum">   18911 </span>            :             }</a>
+<a name="18912"><span class="lineNum">   18912 </span>            :         }</a>
+<a name="18913"><span class="lineNum">   18913 </span>            :     }</a>
+<a name="18914"><span class="lineNum">   18914 </span>            : </a>
+<a name="18915"><span class="lineNum">   18915 </span><span class="lineNoCov">          0 :     if (1 == abs(*job)) {</span></a>
+<a name="18916"><span class="lineNum">   18916 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="18917"><span class="lineNum">   18917 </span><span class="lineNoCov">          0 :         for (k = 2; k &lt;= i__1; ++k) {</span></a>
+<a name="18918"><span class="lineNum">   18918 </span><span class="lineNoCov">          0 :             if (in[k - 1] == 0) {</span></a>
+<a name="18919"><span class="lineNum">   18919 </span><span class="lineNoCov">          0 :                 y[k] -= c__[k - 1] * y[k - 1];</span></a>
+<a name="18920"><span class="lineNum">   18920 </span>            :             } else {</a>
+<a name="18921"><span class="lineNum">   18921 </span><span class="lineNoCov">          0 :                 temp = y[k - 1];</span></a>
+<a name="18922"><span class="lineNum">   18922 </span><span class="lineNoCov">          0 :                 y[k - 1] = y[k];</span></a>
+<a name="18923"><span class="lineNum">   18923 </span><span class="lineNoCov">          0 :                 y[k] = temp - c__[k - 1] * y[k];</span></a>
+<a name="18924"><span class="lineNum">   18924 </span>            :             }</a>
+<a name="18925"><span class="lineNum">   18925 </span>            :         }</a>
+<a name="18926"><span class="lineNum">   18926 </span><span class="lineNoCov">          0 :         if (*job == 1) {</span></a>
+<a name="18927"><span class="lineNum">   18927 </span><span class="lineNoCov">          0 :             for (k = *n; k &gt;= 1; --k) {</span></a>
+<a name="18928"><span class="lineNum">   18928 </span><span class="lineNoCov">          0 :                 if (k &lt;= *n - 2) {</span></a>
+<a name="18929"><span class="lineNum">   18929 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1] - d__[k] * y[k + 2];</span></a>
+<a name="18930"><span class="lineNum">   18930 </span><span class="lineNoCov">          0 :                 } else if (k == *n - 1) {</span></a>
+<a name="18931"><span class="lineNum">   18931 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1];</span></a>
+<a name="18932"><span class="lineNum">   18932 </span>            :                 } else {</a>
+<a name="18933"><span class="lineNum">   18933 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="18934"><span class="lineNum">   18934 </span>            :                 }</a>
+<a name="18935"><span class="lineNum">   18935 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="18936"><span class="lineNum">   18936 </span>            :                 absak = std::abs(ak);</a>
+<a name="18937"><span class="lineNum">   18937 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="18938"><span class="lineNum">   18938 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="18939"><span class="lineNum">   18939 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_FLOAT_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="18940"><span class="lineNum">   18940 </span><span class="lineNoCov">          0 :                             *info = k;</span></a>
+<a name="18941"><span class="lineNum">   18941 </span><span class="lineNoCov">          0 :                             return;</span></a>
+<a name="18942"><span class="lineNum">   18942 </span>            :                         } else {</a>
+<a name="18943"><span class="lineNum">   18943 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="18944"><span class="lineNum">   18944 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="18945"><span class="lineNum">   18945 </span>            :                         }</a>
+<a name="18946"><span class="lineNum">   18946 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="18947"><span class="lineNum">   18947 </span><span class="lineNoCov">          0 :                         *info = k;</span></a>
+<a name="18948"><span class="lineNum">   18948 </span><span class="lineNoCov">          0 :                         return;</span></a>
+<a name="18949"><span class="lineNum">   18949 </span>            :                     }</a>
+<a name="18950"><span class="lineNum">   18950 </span>            :                 }</a>
+<a name="18951"><span class="lineNum">   18951 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="18952"><span class="lineNum">   18952 </span>            :             }</a>
+<a name="18953"><span class="lineNum">   18953 </span>            :         } else {</a>
+<a name="18954"><span class="lineNum">   18954 </span><span class="lineNoCov">          0 :             for (k = *n; k &gt;= 1; --k) {</span></a>
+<a name="18955"><span class="lineNum">   18955 </span><span class="lineNoCov">          0 :                 if (k + 2 &lt;= *n) {</span></a>
+<a name="18956"><span class="lineNum">   18956 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1] - d__[k] * y[k + 2];</span></a>
+<a name="18957"><span class="lineNum">   18957 </span><span class="lineNoCov">          0 :                 } else if (k + 1 == *n) {</span></a>
+<a name="18958"><span class="lineNum">   18958 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k] * y[k + 1];</span></a>
+<a name="18959"><span class="lineNum">   18959 </span>            :                 } else {</a>
+<a name="18960"><span class="lineNum">   18960 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="18961"><span class="lineNum">   18961 </span>            :                 }</a>
+<a name="18962"><span class="lineNum">   18962 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="18963"><span class="lineNum">   18963 </span>            : </a>
+<a name="18964"><span class="lineNum">   18964 </span><span class="lineNoCov">          0 :                 pert = *tol;</span></a>
+<a name="18965"><span class="lineNum">   18965 </span><span class="lineNoCov">          0 :                 if(ak&lt;0)</span></a>
+<a name="18966"><span class="lineNum">   18966 </span><span class="lineNoCov">          0 :                   pert *= -1.0;</span></a>
+<a name="18967"><span class="lineNum">   18967 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="18968"><span class="lineNum">   18968 </span>            :                 absak = std::abs(ak);</a>
+<a name="18969"><span class="lineNum">   18969 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="18970"><span class="lineNum">   18970 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="18971"><span class="lineNum">   18971 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_FLOAT_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="18972"><span class="lineNum">   18972 </span><span class="lineNoCov">          0 :                             ak += pert;</span></a>
+<a name="18973"><span class="lineNum">   18973 </span><span class="lineNoCov">          0 :                             pert *= 2;</span></a>
+<a name="18974"><span class="lineNum">   18974 </span><span class="lineNoCov">          0 :                             goto L40;</span></a>
+<a name="18975"><span class="lineNum">   18975 </span>            :                         } else {</a>
+<a name="18976"><span class="lineNum">   18976 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="18977"><span class="lineNum">   18977 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="18978"><span class="lineNum">   18978 </span>            :                         }</a>
+<a name="18979"><span class="lineNum">   18979 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="18980"><span class="lineNum">   18980 </span><span class="lineNoCov">          0 :                         ak += pert;</span></a>
+<a name="18981"><span class="lineNum">   18981 </span><span class="lineNoCov">          0 :                         pert *= 2;</span></a>
+<a name="18982"><span class="lineNum">   18982 </span><span class="lineNoCov">          0 :                         goto L40;</span></a>
+<a name="18983"><span class="lineNum">   18983 </span>            :                     }</a>
+<a name="18984"><span class="lineNum">   18984 </span>            :                 }</a>
+<a name="18985"><span class="lineNum">   18985 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="18986"><span class="lineNum">   18986 </span>            :             }</a>
+<a name="18987"><span class="lineNum">   18987 </span>            :         }</a>
+<a name="18988"><span class="lineNum">   18988 </span>            :     } else {</a>
+<a name="18989"><span class="lineNum">   18989 </span>            : </a>
+<a name="18990"><span class="lineNum">   18990 </span><span class="lineNoCov">          0 :         if (*job == 2) {</span></a>
+<a name="18991"><span class="lineNum">   18991 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="18992"><span class="lineNum">   18992 </span><span class="lineNoCov">          0 :             for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="18993"><span class="lineNum">   18993 </span><span class="lineNoCov">          0 :                 if (k &gt;= 3) {</span></a>
+<a name="18994"><span class="lineNum">   18994 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1] - d__[k - 2] * y[k - 2];</span></a>
+<a name="18995"><span class="lineNum">   18995 </span><span class="lineNoCov">          0 :                 } else if (k == 2) {</span></a>
+<a name="18996"><span class="lineNum">   18996 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1];</span></a>
+<a name="18997"><span class="lineNum">   18997 </span>            :                 } else {</a>
+<a name="18998"><span class="lineNum">   18998 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="18999"><span class="lineNum">   18999 </span>            :                 }</a>
+<a name="19000"><span class="lineNum">   19000 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="19001"><span class="lineNum">   19001 </span>            :                 absak = std::abs(ak);</a>
+<a name="19002"><span class="lineNum">   19002 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="19003"><span class="lineNum">   19003 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="19004"><span class="lineNum">   19004 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_FLOAT_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="19005"><span class="lineNum">   19005 </span><span class="lineNoCov">          0 :                             *info = k;</span></a>
+<a name="19006"><span class="lineNum">   19006 </span><span class="lineNoCov">          0 :                             return;</span></a>
+<a name="19007"><span class="lineNum">   19007 </span>            :                         } else {</a>
+<a name="19008"><span class="lineNum">   19008 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="19009"><span class="lineNum">   19009 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="19010"><span class="lineNum">   19010 </span>            :                         }</a>
+<a name="19011"><span class="lineNum">   19011 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="19012"><span class="lineNum">   19012 </span><span class="lineNoCov">          0 :                         *info = k;</span></a>
+<a name="19013"><span class="lineNum">   19013 </span><span class="lineNoCov">          0 :                         return;</span></a>
+<a name="19014"><span class="lineNum">   19014 </span>            :                     }</a>
+<a name="19015"><span class="lineNum">   19015 </span>            :                 }</a>
+<a name="19016"><span class="lineNum">   19016 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="19017"><span class="lineNum">   19017 </span>            :             }</a>
+<a name="19018"><span class="lineNum">   19018 </span>            :         } else {</a>
+<a name="19019"><span class="lineNum">   19019 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19020"><span class="lineNum">   19020 </span><span class="lineNoCov">          0 :             for (k = 1; k &lt;= i__1; ++k) {</span></a>
+<a name="19021"><span class="lineNum">   19021 </span><span class="lineNoCov">          0 :                 if (k &gt;= 3) {</span></a>
+<a name="19022"><span class="lineNum">   19022 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1] - d__[k - 2] * y[k - 2];</span></a>
+<a name="19023"><span class="lineNum">   19023 </span><span class="lineNoCov">          0 :                 } else if (k == 2) {</span></a>
+<a name="19024"><span class="lineNum">   19024 </span><span class="lineNoCov">          0 :                     temp = y[k] - b[k - 1] * y[k - 1];</span></a>
+<a name="19025"><span class="lineNum">   19025 </span>            :                 } else {</a>
+<a name="19026"><span class="lineNum">   19026 </span><span class="lineNoCov">          0 :                     temp = y[k];</span></a>
+<a name="19027"><span class="lineNum">   19027 </span>            :                 }</a>
+<a name="19028"><span class="lineNum">   19028 </span><span class="lineNoCov">          0 :                 ak = a[k];</span></a>
+<a name="19029"><span class="lineNum">   19029 </span>            : </a>
+<a name="19030"><span class="lineNum">   19030 </span><span class="lineNoCov">          0 :                 pert = *tol;</span></a>
+<a name="19031"><span class="lineNum">   19031 </span><span class="lineNoCov">          0 :                 if(ak&lt;0)</span></a>
+<a name="19032"><span class="lineNum">   19032 </span><span class="lineNoCov">          0 :                   pert *= -1.0;</span></a>
+<a name="19033"><span class="lineNum">   19033 </span>            : </a>
+<a name="19034"><span class="lineNum">   19034 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="19035"><span class="lineNum">   19035 </span>            :                 absak = std::abs(ak);</a>
+<a name="19036"><span class="lineNum">   19036 </span><span class="lineNoCov">          0 :                 if (absak &lt; 1.) {</span></a>
+<a name="19037"><span class="lineNum">   19037 </span><span class="lineNoCov">          0 :                     if (absak &lt; sfmin) {</span></a>
+<a name="19038"><span class="lineNum">   19038 </span><span class="lineNoCov">          0 :                         if (std::abs(absak)&lt;PLUMED_GMX_FLOAT_MIN || std::abs(temp) * sfmin &gt; absak) {</span></a>
+<a name="19039"><span class="lineNum">   19039 </span><span class="lineNoCov">          0 :                             ak += pert;</span></a>
+<a name="19040"><span class="lineNum">   19040 </span><span class="lineNoCov">          0 :                             pert *= 2;</span></a>
+<a name="19041"><span class="lineNum">   19041 </span><span class="lineNoCov">          0 :                             goto L70;</span></a>
+<a name="19042"><span class="lineNum">   19042 </span>            :                         } else {</a>
+<a name="19043"><span class="lineNum">   19043 </span><span class="lineNoCov">          0 :                             temp *= bignum;</span></a>
+<a name="19044"><span class="lineNum">   19044 </span><span class="lineNoCov">          0 :                             ak *= bignum;</span></a>
+<a name="19045"><span class="lineNum">   19045 </span>            :                         }</a>
+<a name="19046"><span class="lineNum">   19046 </span><span class="lineNoCov">          0 :                     } else if (std::abs(temp) &gt; absak * bignum) {</span></a>
+<a name="19047"><span class="lineNum">   19047 </span><span class="lineNoCov">          0 :                         ak += pert;</span></a>
+<a name="19048"><span class="lineNum">   19048 </span><span class="lineNoCov">          0 :                         pert *= 2;</span></a>
+<a name="19049"><span class="lineNum">   19049 </span><span class="lineNoCov">          0 :                         goto L70;</span></a>
+<a name="19050"><span class="lineNum">   19050 </span>            :                     }</a>
+<a name="19051"><span class="lineNum">   19051 </span>            :                 }</a>
+<a name="19052"><span class="lineNum">   19052 </span><span class="lineNoCov">          0 :                 y[k] = temp / ak;</span></a>
+<a name="19053"><span class="lineNum">   19053 </span>            :             }</a>
+<a name="19054"><span class="lineNum">   19054 </span>            :         }</a>
+<a name="19055"><span class="lineNum">   19055 </span>            : </a>
+<a name="19056"><span class="lineNum">   19056 </span><span class="lineNoCov">          0 :         for (k = *n; k &gt;= 2; --k) {</span></a>
+<a name="19057"><span class="lineNum">   19057 </span><span class="lineNoCov">          0 :             if (in[k - 1] == 0) {</span></a>
+<a name="19058"><span class="lineNum">   19058 </span><span class="lineNoCov">          0 :                 y[k - 1] -= c__[k - 1] * y[k];</span></a>
+<a name="19059"><span class="lineNum">   19059 </span>            :             } else {</a>
+<a name="19060"><span class="lineNum">   19060 </span><span class="lineNoCov">          0 :                 temp = y[k - 1];</span></a>
+<a name="19061"><span class="lineNum">   19061 </span><span class="lineNoCov">          0 :                 y[k - 1] = y[k];</span></a>
+<a name="19062"><span class="lineNum">   19062 </span><span class="lineNoCov">          0 :                 y[k] = temp - c__[k - 1] * y[k];</span></a>
+<a name="19063"><span class="lineNum">   19063 </span>            :             }</a>
+<a name="19064"><span class="lineNum">   19064 </span>            :         }</a>
+<a name="19065"><span class="lineNum">   19065 </span>            :     }</a>
+<a name="19066"><span class="lineNum">   19066 </span>            : </a>
+<a name="19067"><span class="lineNum">   19067 </span>            :     return;</a>
+<a name="19068"><span class="lineNum">   19068 </span>            : }</a>
+<a name="19069"><span class="lineNum">   19069 </span>            : </a>
+<a name="19070"><span class="lineNum">   19070 </span>            : </a>
+<a name="19071"><span class="lineNum">   19071 </span>            : }</a>
+<a name="19072"><span class="lineNum">   19072 </span>            : }</a>
+<a name="19073"><span class="lineNum">   19073 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19074"><span class="lineNum">   19074 </span>            : </a>
+<a name="19075"><span class="lineNum">   19075 </span>            : </a>
+<a name="19076"><span class="lineNum">   19076 </span>            : /* LAPACK */</a>
+<a name="19077"><span class="lineNum">   19077 </span>            : </a>
+<a name="19078"><span class="lineNum">   19078 </span>            : </a>
+<a name="19079"><span class="lineNum">   19079 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19080"><span class="lineNum">   19080 </span>            : namespace PLMD{</a>
+<a name="19081"><span class="lineNum">   19081 </span>            : namespace lapack{</a>
+<a name="19082"><span class="lineNum">   19082 </span>            : using namespace blas;</a>
+<a name="19083"><span class="lineNum">   19083 </span>            : void</a>
+<a name="19084"><span class="lineNum">   19084 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slamrg,SLAMRG)(int *n1,</span></a>
+<a name="19085"><span class="lineNum">   19085 </span>            :                         int *n2,</a>
+<a name="19086"><span class="lineNum">   19086 </span>            :                         float *a,</a>
+<a name="19087"><span class="lineNum">   19087 </span>            :                         int *dtrd1,</a>
+<a name="19088"><span class="lineNum">   19088 </span>            :                         int *dtrd2,</a>
+<a name="19089"><span class="lineNum">   19089 </span>            :                         int *index)</a>
+<a name="19090"><span class="lineNum">   19090 </span>            : {</a>
+<a name="19091"><span class="lineNum">   19091 </span><span class="lineNoCov">          0 :   int n1sv = *n1;</span></a>
+<a name="19092"><span class="lineNum">   19092 </span><span class="lineNoCov">          0 :   int n2sv = *n2;</span></a>
+<a name="19093"><span class="lineNum">   19093 </span>            :   int i,ind1,ind2;</a>
+<a name="19094"><span class="lineNum">   19094 </span>            : </a>
+<a name="19095"><span class="lineNum">   19095 </span><span class="lineNoCov">          0 :   if(*dtrd1&gt;0)</span></a>
+<a name="19096"><span class="lineNum">   19096 </span>            :     ind1 = 0;</a>
+<a name="19097"><span class="lineNum">   19097 </span>            :   else</a>
+<a name="19098"><span class="lineNum">   19098 </span><span class="lineNoCov">          0 :     ind1 = *n1-1;</span></a>
+<a name="19099"><span class="lineNum">   19099 </span>            : </a>
+<a name="19100"><span class="lineNum">   19100 </span><span class="lineNoCov">          0 :   if(*dtrd2&gt;0)</span></a>
+<a name="19101"><span class="lineNum">   19101 </span>            :     ind2 = *n1;</a>
+<a name="19102"><span class="lineNum">   19102 </span>            :   else</a>
+<a name="19103"><span class="lineNum">   19103 </span><span class="lineNoCov">          0 :     ind2 = *n1+*n2-1;</span></a>
+<a name="19104"><span class="lineNum">   19104 </span>            : </a>
+<a name="19105"><span class="lineNum">   19105 </span>            :   i = 0;</a>
+<a name="19106"><span class="lineNum">   19106 </span>            :   </a>
+<a name="19107"><span class="lineNum">   19107 </span><span class="lineNoCov">          0 :   while(n1sv&gt;0 &amp;&amp; n2sv&gt;0) {</span></a>
+<a name="19108"><span class="lineNum">   19108 </span><span class="lineNoCov">          0 :     if(a[ind1]&lt;=a[ind2]) {</span></a>
+<a name="19109"><span class="lineNum">   19109 </span><span class="lineNoCov">          0 :       index[i] = ind1 + 1;</span></a>
+<a name="19110"><span class="lineNum">   19110 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="19111"><span class="lineNum">   19111 </span><span class="lineNoCov">          0 :       ind1 += *dtrd1;</span></a>
+<a name="19112"><span class="lineNum">   19112 </span><span class="lineNoCov">          0 :       n1sv--;</span></a>
+<a name="19113"><span class="lineNum">   19113 </span>            :     } else {</a>
+<a name="19114"><span class="lineNum">   19114 </span><span class="lineNoCov">          0 :       index[i] = ind2 + 1;</span></a>
+<a name="19115"><span class="lineNum">   19115 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="19116"><span class="lineNum">   19116 </span><span class="lineNoCov">          0 :       ind2 += *dtrd2;</span></a>
+<a name="19117"><span class="lineNum">   19117 </span><span class="lineNoCov">          0 :       n2sv--;</span></a>
+<a name="19118"><span class="lineNum">   19118 </span>            :     }</a>
+<a name="19119"><span class="lineNum">   19119 </span>            :   }</a>
+<a name="19120"><span class="lineNum">   19120 </span>            : </a>
+<a name="19121"><span class="lineNum">   19121 </span><span class="lineNoCov">          0 :   if(n1sv==0) {</span></a>
+<a name="19122"><span class="lineNum">   19122 </span><span class="lineNoCov">          0 :     for(n1sv=1;n1sv&lt;=n2sv;n1sv++) {</span></a>
+<a name="19123"><span class="lineNum">   19123 </span><span class="lineNoCov">          0 :       index[i] = ind2 + 1;</span></a>
+<a name="19124"><span class="lineNum">   19124 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="19125"><span class="lineNum">   19125 </span><span class="lineNoCov">          0 :       ind2 += *dtrd2;</span></a>
+<a name="19126"><span class="lineNum">   19126 </span>            :     } </a>
+<a name="19127"><span class="lineNum">   19127 </span>            :   } else {</a>
+<a name="19128"><span class="lineNum">   19128 </span><span class="lineNoCov">          0 :     for(n2sv=1;n2sv&lt;=n1sv;n2sv++) {</span></a>
+<a name="19129"><span class="lineNum">   19129 </span><span class="lineNoCov">          0 :       index[i] = ind1 + 1;</span></a>
+<a name="19130"><span class="lineNum">   19130 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="19131"><span class="lineNum">   19131 </span><span class="lineNoCov">          0 :       ind1 += *dtrd1;</span></a>
+<a name="19132"><span class="lineNum">   19132 </span>            :     } </a>
+<a name="19133"><span class="lineNum">   19133 </span>            :   }</a>
+<a name="19134"><span class="lineNum">   19134 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="19135"><span class="lineNum">   19135 </span>            : }</a>
+<a name="19136"><span class="lineNum">   19136 </span>            : }</a>
+<a name="19137"><span class="lineNum">   19137 </span>            : }</a>
+<a name="19138"><span class="lineNum">   19138 </span>            : #include &lt;cctype&gt;</a>
+<a name="19139"><span class="lineNum">   19139 </span>            : #include &lt;cmath&gt;</a>
+<a name="19140"><span class="lineNum">   19140 </span>            : </a>
+<a name="19141"><span class="lineNum">   19141 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19142"><span class="lineNum">   19142 </span>            : </a>
+<a name="19143"><span class="lineNum">   19143 </span>            : </a>
+<a name="19144"><span class="lineNum">   19144 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19145"><span class="lineNum">   19145 </span>            : namespace PLMD{</a>
+<a name="19146"><span class="lineNum">   19146 </span>            : namespace lapack{</a>
+<a name="19147"><span class="lineNum">   19147 </span>            : using namespace blas;</a>
+<a name="19148"><span class="lineNum">   19148 </span>            : float</a>
+<a name="19149"><span class="lineNum">   19149 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slange,SLANGE)(const char *norm,</span></a>
+<a name="19150"><span class="lineNum">   19150 </span>            :         int *m,</a>
+<a name="19151"><span class="lineNum">   19151 </span>            :         int *n,</a>
+<a name="19152"><span class="lineNum">   19152 </span>            :         float *a,</a>
+<a name="19153"><span class="lineNum">   19153 </span>            :         int *lda,</a>
+<a name="19154"><span class="lineNum">   19154 </span>            :         float *work)</a>
+<a name="19155"><span class="lineNum">   19155 </span>            : {</a>
+<a name="19156"><span class="lineNum">   19156 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*norm);</span></a>
+<a name="19157"><span class="lineNum">   19157 </span>            :   float dtemp,sum,max,val,scale;</a>
+<a name="19158"><span class="lineNum">   19158 </span>            :   int i,j;</a>
+<a name="19159"><span class="lineNum">   19159 </span>            : </a>
+<a name="19160"><span class="lineNum">   19160 </span><span class="lineNoCov">          0 :   switch(ch) {</span></a>
+<a name="19161"><span class="lineNum">   19161 </span>            :   case 'M':</a>
+<a name="19162"><span class="lineNum">   19162 </span>            :     max = 0.0;</a>
+<a name="19163"><span class="lineNum">   19163 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++)</span></a>
+<a name="19164"><span class="lineNum">   19164 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++) {</span></a>
+<a name="19165"><span class="lineNum">   19165 </span><span class="lineNoCov">          0 :         dtemp = std::abs(a[j*(*lda)+i]);</span></a>
+<a name="19166"><span class="lineNum">   19166 </span><span class="lineNoCov">          0 :         if(dtemp&gt;max)</span></a>
+<a name="19167"><span class="lineNum">   19167 </span>            :           max = dtemp;</a>
+<a name="19168"><span class="lineNum">   19168 </span>            :       }</a>
+<a name="19169"><span class="lineNum">   19169 </span>            :     val = max;</a>
+<a name="19170"><span class="lineNum">   19170 </span>            :     break;</a>
+<a name="19171"><span class="lineNum">   19171 </span>            : </a>
+<a name="19172"><span class="lineNum">   19172 </span>            :   case 'O':</a>
+<a name="19173"><span class="lineNum">   19173 </span>            :   case '1':</a>
+<a name="19174"><span class="lineNum">   19174 </span>            :     max = 0.0;</a>
+<a name="19175"><span class="lineNum">   19175 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="19176"><span class="lineNum">   19176 </span><span class="lineNoCov">          0 :       sum = 0.0;</span></a>
+<a name="19177"><span class="lineNum">   19177 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++) </span></a>
+<a name="19178"><span class="lineNum">   19178 </span><span class="lineNoCov">          0 :         sum += std::abs(a[j*(*lda)+i]);</span></a>
+<a name="19179"><span class="lineNum">   19179 </span><span class="lineNoCov">          0 :       if(sum&gt;max)</span></a>
+<a name="19180"><span class="lineNum">   19180 </span>            :         max = sum;</a>
+<a name="19181"><span class="lineNum">   19181 </span>            :     }</a>
+<a name="19182"><span class="lineNum">   19182 </span>            :     val = max;</a>
+<a name="19183"><span class="lineNum">   19183 </span>            :     break;</a>
+<a name="19184"><span class="lineNum">   19184 </span>            : </a>
+<a name="19185"><span class="lineNum">   19185 </span><span class="lineNoCov">          0 :   case 'I':</span></a>
+<a name="19186"><span class="lineNum">   19186 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*m;i++)</span></a>
+<a name="19187"><span class="lineNum">   19187 </span><span class="lineNoCov">          0 :       work[i] = 0.0;</span></a>
+<a name="19188"><span class="lineNum">   19188 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++)</span></a>
+<a name="19189"><span class="lineNum">   19189 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++)</span></a>
+<a name="19190"><span class="lineNum">   19190 </span><span class="lineNoCov">          0 :         work[i] += std::abs(a[j*(*lda)+i]);</span></a>
+<a name="19191"><span class="lineNum">   19191 </span>            :     max = 0;</a>
+<a name="19192"><span class="lineNum">   19192 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*m;i++)</span></a>
+<a name="19193"><span class="lineNum">   19193 </span><span class="lineNoCov">          0 :       if(work[i]&gt;max)</span></a>
+<a name="19194"><span class="lineNum">   19194 </span>            :         max=work[i];</a>
+<a name="19195"><span class="lineNum">   19195 </span>            :     val = max;</a>
+<a name="19196"><span class="lineNum">   19196 </span>            :     break;</a>
+<a name="19197"><span class="lineNum">   19197 </span>            : </a>
+<a name="19198"><span class="lineNum">   19198 </span><span class="lineNoCov">          0 :   case 'F':</span></a>
+<a name="19199"><span class="lineNum">   19199 </span>            :   case 'E':</a>
+<a name="19200"><span class="lineNum">   19200 </span><span class="lineNoCov">          0 :     scale = 0.0;</span></a>
+<a name="19201"><span class="lineNum">   19201 </span><span class="lineNoCov">          0 :     sum   = 1.0;</span></a>
+<a name="19202"><span class="lineNum">   19202 </span><span class="lineNoCov">          0 :     i = 1;</span></a>
+<a name="19203"><span class="lineNum">   19203 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) </span></a>
+<a name="19204"><span class="lineNum">   19204 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(m,&amp;(a[j*(*lda)+0]),&amp;i,&amp;scale,&amp;sum);</span></a>
+<a name="19205"><span class="lineNum">   19205 </span><span class="lineNoCov">          0 :     val = scale* std::sqrt(sum);</span></a>
+<a name="19206"><span class="lineNum">   19206 </span><span class="lineNoCov">          0 :     break;</span></a>
+<a name="19207"><span class="lineNum">   19207 </span>            : </a>
+<a name="19208"><span class="lineNum">   19208 </span>            :   default:</a>
+<a name="19209"><span class="lineNum">   19209 </span>            :     val = 0.0;</a>
+<a name="19210"><span class="lineNum">   19210 </span>            :     break;</a>
+<a name="19211"><span class="lineNum">   19211 </span>            :   }</a>
+<a name="19212"><span class="lineNum">   19212 </span><span class="lineNoCov">          0 :   return val;</span></a>
+<a name="19213"><span class="lineNum">   19213 </span>            : }</a>
+<a name="19214"><span class="lineNum">   19214 </span>            : }</a>
+<a name="19215"><span class="lineNum">   19215 </span>            : }</a>
+<a name="19216"><span class="lineNum">   19216 </span>            : #include &lt;cctype&gt;</a>
+<a name="19217"><span class="lineNum">   19217 </span>            : #include &lt;cmath&gt;</a>
+<a name="19218"><span class="lineNum">   19218 </span>            : </a>
+<a name="19219"><span class="lineNum">   19219 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19220"><span class="lineNum">   19220 </span>            : </a>
+<a name="19221"><span class="lineNum">   19221 </span>            : </a>
+<a name="19222"><span class="lineNum">   19222 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19223"><span class="lineNum">   19223 </span>            : namespace PLMD{</a>
+<a name="19224"><span class="lineNum">   19224 </span>            : namespace lapack{</a>
+<a name="19225"><span class="lineNum">   19225 </span>            : using namespace blas;</a>
+<a name="19226"><span class="lineNum">   19226 </span>            : float</a>
+<a name="19227"><span class="lineNum">   19227 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slanst,SLANST)(const char *norm,</span></a>
+<a name="19228"><span class="lineNum">   19228 </span>            :         int *n,</a>
+<a name="19229"><span class="lineNum">   19229 </span>            :         float *d,</a>
+<a name="19230"><span class="lineNum">   19230 </span>            :         float *e)</a>
+<a name="19231"><span class="lineNum">   19231 </span>            : {</a>
+<a name="19232"><span class="lineNum">   19232 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*norm);</span></a>
+<a name="19233"><span class="lineNum">   19233 </span>            :   float dtemp,max,val,scale,sum;</a>
+<a name="19234"><span class="lineNum">   19234 </span>            :   int i,j;</a>
+<a name="19235"><span class="lineNum">   19235 </span>            : </a>
+<a name="19236"><span class="lineNum">   19236 </span>            : </a>
+<a name="19237"><span class="lineNum">   19237 </span><span class="lineNoCov">          0 :   if(*n&lt;=0)</span></a>
+<a name="19238"><span class="lineNum">   19238 </span>            :     return 0.0;</a>
+<a name="19239"><span class="lineNum">   19239 </span>            :   </a>
+<a name="19240"><span class="lineNum">   19240 </span><span class="lineNoCov">          0 :   switch(ch) {</span></a>
+<a name="19241"><span class="lineNum">   19241 </span><span class="lineNoCov">          0 :   case 'M':</span></a>
+<a name="19242"><span class="lineNum">   19242 </span><span class="lineNoCov">          0 :     max = std::abs(d[*n-1]);</span></a>
+<a name="19243"><span class="lineNum">   19243 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;(*n-1);i++) {</span></a>
+<a name="19244"><span class="lineNum">   19244 </span><span class="lineNoCov">          0 :         dtemp = std::abs(d[i]);</span></a>
+<a name="19245"><span class="lineNum">   19245 </span><span class="lineNoCov">          0 :         if(dtemp&gt;max)</span></a>
+<a name="19246"><span class="lineNum">   19246 </span>            :           max = dtemp;</a>
+<a name="19247"><span class="lineNum">   19247 </span><span class="lineNoCov">          0 :         dtemp = std::abs(e[i]);</span></a>
+<a name="19248"><span class="lineNum">   19248 </span><span class="lineNoCov">          0 :         if(dtemp&gt;max)</span></a>
+<a name="19249"><span class="lineNum">   19249 </span>            :           max = dtemp;</a>
+<a name="19250"><span class="lineNum">   19250 </span>            :       }</a>
+<a name="19251"><span class="lineNum">   19251 </span>            :     val = max;</a>
+<a name="19252"><span class="lineNum">   19252 </span>            :     break;</a>
+<a name="19253"><span class="lineNum">   19253 </span>            :     </a>
+<a name="19254"><span class="lineNum">   19254 </span><span class="lineNoCov">          0 :   case 'O':</span></a>
+<a name="19255"><span class="lineNum">   19255 </span>            :   case '1':</a>
+<a name="19256"><span class="lineNum">   19256 </span>            :   case 'I':</a>
+<a name="19257"><span class="lineNum">   19257 </span>            : </a>
+<a name="19258"><span class="lineNum">   19258 </span><span class="lineNoCov">          0 :     if(*n==1)</span></a>
+<a name="19259"><span class="lineNum">   19259 </span><span class="lineNoCov">          0 :       val = std::abs(d[0]);</span></a>
+<a name="19260"><span class="lineNum">   19260 </span>            :     else {</a>
+<a name="19261"><span class="lineNum">   19261 </span><span class="lineNoCov">          0 :       max = std::abs(d[0]) + std::abs(e[0]);</span></a>
+<a name="19262"><span class="lineNum">   19262 </span><span class="lineNoCov">          0 :       dtemp = std::abs(e[*n-2]) + std::abs(d[*n-1]);</span></a>
+<a name="19263"><span class="lineNum">   19263 </span><span class="lineNoCov">          0 :       if(dtemp&gt;max)</span></a>
+<a name="19264"><span class="lineNum">   19264 </span>            :         max = dtemp;</a>
+<a name="19265"><span class="lineNum">   19265 </span><span class="lineNoCov">          0 :       for(i=1;i&lt;(*n-1);i++) {</span></a>
+<a name="19266"><span class="lineNum">   19266 </span><span class="lineNoCov">          0 :         dtemp = std::abs(d[i]) + std::abs(e[i]) + std::abs(e[i-1]);</span></a>
+<a name="19267"><span class="lineNum">   19267 </span><span class="lineNoCov">          0 :         if(dtemp&gt;max)</span></a>
+<a name="19268"><span class="lineNum">   19268 </span>            :           max = dtemp;</a>
+<a name="19269"><span class="lineNum">   19269 </span>            :       }</a>
+<a name="19270"><span class="lineNum">   19270 </span>            :       val = max;</a>
+<a name="19271"><span class="lineNum">   19271 </span>            :     }</a>
+<a name="19272"><span class="lineNum">   19272 </span>            :     break;</a>
+<a name="19273"><span class="lineNum">   19273 </span>            : </a>
+<a name="19274"><span class="lineNum">   19274 </span><span class="lineNoCov">          0 :   case 'F':</span></a>
+<a name="19275"><span class="lineNum">   19275 </span>            :   case 'E':</a>
+<a name="19276"><span class="lineNum">   19276 </span><span class="lineNoCov">          0 :     scale = 0.0;</span></a>
+<a name="19277"><span class="lineNum">   19277 </span><span class="lineNoCov">          0 :     sum   = 1.0;</span></a>
+<a name="19278"><span class="lineNum">   19278 </span><span class="lineNoCov">          0 :     i = *n-1;</span></a>
+<a name="19279"><span class="lineNum">   19279 </span><span class="lineNoCov">          0 :     j = 1;</span></a>
+<a name="19280"><span class="lineNum">   19280 </span><span class="lineNoCov">          0 :     if(*n&gt;1) {</span></a>
+<a name="19281"><span class="lineNum">   19281 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(&amp;i,e,&amp;j,&amp;scale,&amp;sum);</span></a>
+<a name="19282"><span class="lineNum">   19282 </span><span class="lineNoCov">          0 :       sum *= 2;</span></a>
+<a name="19283"><span class="lineNum">   19283 </span>            :     }</a>
+<a name="19284"><span class="lineNum">   19284 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(n,d,&amp;j,&amp;scale,&amp;sum);</span></a>
+<a name="19285"><span class="lineNum">   19285 </span><span class="lineNoCov">          0 :     val = scale *  std::sqrt(sum);</span></a>
+<a name="19286"><span class="lineNum">   19286 </span><span class="lineNoCov">          0 :     break;</span></a>
+<a name="19287"><span class="lineNum">   19287 </span>            :     </a>
+<a name="19288"><span class="lineNum">   19288 </span>            :   default:</a>
+<a name="19289"><span class="lineNum">   19289 </span>            :     val = 0.0;</a>
+<a name="19290"><span class="lineNum">   19290 </span>            :     break;</a>
+<a name="19291"><span class="lineNum">   19291 </span>            :   }</a>
+<a name="19292"><span class="lineNum">   19292 </span>            :   return val;</a>
+<a name="19293"><span class="lineNum">   19293 </span>            : }</a>
+<a name="19294"><span class="lineNum">   19294 </span>            : }</a>
+<a name="19295"><span class="lineNum">   19295 </span>            : }</a>
+<a name="19296"><span class="lineNum">   19296 </span>            : #include &lt;cmath&gt;</a>
+<a name="19297"><span class="lineNum">   19297 </span>            : </a>
+<a name="19298"><span class="lineNum">   19298 </span>            : </a>
+<a name="19299"><span class="lineNum">   19299 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19300"><span class="lineNum">   19300 </span>            : </a>
+<a name="19301"><span class="lineNum">   19301 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19302"><span class="lineNum">   19302 </span>            : namespace PLMD{</a>
+<a name="19303"><span class="lineNum">   19303 </span>            : namespace lapack{</a>
+<a name="19304"><span class="lineNum">   19304 </span>            : using namespace blas;</a>
+<a name="19305"><span class="lineNum">   19305 </span>            : float </a>
+<a name="19306"><span class="lineNum">   19306 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slansy,SLANSY)(const char *norm, const char *uplo, int *n, float *a, int </span></a>
+<a name="19307"><span class="lineNum">   19307 </span>            :         *lda, float *work)</a>
+<a name="19308"><span class="lineNum">   19308 </span>            : {</a>
+<a name="19309"><span class="lineNum">   19309 </span>            :     /* System generated locals */</a>
+<a name="19310"><span class="lineNum">   19310 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="19311"><span class="lineNum">   19311 </span>            :     float ret_val, d__1, d__2, d__3;</a>
+<a name="19312"><span class="lineNum">   19312 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="19313"><span class="lineNum">   19313 </span>            : </a>
+<a name="19314"><span class="lineNum">   19314 </span>            :     /* Local variables */</a>
+<a name="19315"><span class="lineNum">   19315 </span>            :     int i__, j;</a>
+<a name="19316"><span class="lineNum">   19316 </span>            :     float sum, absa, scale;</a>
+<a name="19317"><span class="lineNum">   19317 </span>            :     float value =0.0;</a>
+<a name="19318"><span class="lineNum">   19318 </span>            : </a>
+<a name="19319"><span class="lineNum">   19319 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="19320"><span class="lineNum">   19320 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="19321"><span class="lineNum">   19321 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="19322"><span class="lineNum">   19322 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="19323"><span class="lineNum">   19323 </span>            : </a>
+<a name="19324"><span class="lineNum">   19324 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="19325"><span class="lineNum">   19325 </span>            :         value = 0.;</a>
+<a name="19326"><span class="lineNum">   19326 </span><span class="lineNoCov">          0 :     } else if (*norm=='M' || *norm=='m') {</span></a>
+<a name="19327"><span class="lineNum">   19327 </span>            : </a>
+<a name="19328"><span class="lineNum">   19328 </span>            :         value = 0.;</a>
+<a name="19329"><span class="lineNum">   19329 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="19330"><span class="lineNum">   19330 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19331"><span class="lineNum">   19331 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19332"><span class="lineNum">   19332 </span>            :                 i__2 = j;</a>
+<a name="19333"><span class="lineNum">   19333 </span><span class="lineNoCov">          0 :                 for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19334"><span class="lineNum">   19334 </span>            :                   d__2 = value;</a>
+<a name="19335"><span class="lineNum">   19335 </span><span class="lineNoCov">          0 :                   d__3 = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="19336"><span class="lineNum">   19336 </span><span class="lineNoCov">          0 :                   value = (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="19337"><span class="lineNum">   19337 </span>            :                 }</a>
+<a name="19338"><span class="lineNum">   19338 </span>            :             }</a>
+<a name="19339"><span class="lineNum">   19339 </span>            :         } else {</a>
+<a name="19340"><span class="lineNum">   19340 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19341"><span class="lineNum">   19341 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19342"><span class="lineNum">   19342 </span>            :                 i__2 = *n;</a>
+<a name="19343"><span class="lineNum">   19343 </span><span class="lineNoCov">          0 :                 for (i__ = j; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19344"><span class="lineNum">   19344 </span>            :                   d__2 = value;</a>
+<a name="19345"><span class="lineNum">   19345 </span><span class="lineNoCov">          0 :                   d__3 = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="19346"><span class="lineNum">   19346 </span><span class="lineNoCov">          0 :                     value =  (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="19347"><span class="lineNum">   19347 </span>            :                 }</a>
+<a name="19348"><span class="lineNum">   19348 </span>            :             }</a>
+<a name="19349"><span class="lineNum">   19349 </span>            :         }</a>
+<a name="19350"><span class="lineNum">   19350 </span><span class="lineNoCov">          0 :     } else if (*norm=='I' || *norm=='i' || *norm=='O' || *norm=='o' || *norm=='1') {</span></a>
+<a name="19351"><span class="lineNum">   19351 </span>            : </a>
+<a name="19352"><span class="lineNum">   19352 </span>            :         value = 0.;</a>
+<a name="19353"><span class="lineNum">   19353 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="19354"><span class="lineNum">   19354 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19355"><span class="lineNum">   19355 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19356"><span class="lineNum">   19356 </span><span class="lineNoCov">          0 :                 sum = 0.;</span></a>
+<a name="19357"><span class="lineNum">   19357 </span><span class="lineNoCov">          0 :                 i__2 = j - 1;</span></a>
+<a name="19358"><span class="lineNum">   19358 </span><span class="lineNoCov">          0 :                 for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19359"><span class="lineNum">   19359 </span><span class="lineNoCov">          0 :                     absa = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="19360"><span class="lineNum">   19360 </span><span class="lineNoCov">          0 :                     sum += absa;</span></a>
+<a name="19361"><span class="lineNum">   19361 </span><span class="lineNoCov">          0 :                     work[i__] += absa;</span></a>
+<a name="19362"><span class="lineNum">   19362 </span>            :                 }</a>
+<a name="19363"><span class="lineNum">   19363 </span><span class="lineNoCov">          0 :                 work[j] = sum + std::abs(a[j + j * a_dim1]);</span></a>
+<a name="19364"><span class="lineNum">   19364 </span>            :             }</a>
+<a name="19365"><span class="lineNum">   19365 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19366"><span class="lineNum">   19366 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19367"><span class="lineNum">   19367 </span><span class="lineNoCov">          0 :                 d__1 = value, d__2 = work[i__];</span></a>
+<a name="19368"><span class="lineNum">   19368 </span><span class="lineNoCov">          0 :                 value =  (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="19369"><span class="lineNum">   19369 </span>            :             }</a>
+<a name="19370"><span class="lineNum">   19370 </span>            :         } else {</a>
+<a name="19371"><span class="lineNum">   19371 </span>            :             i__1 = *n;</a>
+<a name="19372"><span class="lineNum">   19372 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19373"><span class="lineNum">   19373 </span><span class="lineNoCov">          0 :                 work[i__] = 0.;</span></a>
+<a name="19374"><span class="lineNum">   19374 </span>            :             }</a>
+<a name="19375"><span class="lineNum">   19375 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19376"><span class="lineNum">   19376 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19377"><span class="lineNum">   19377 </span><span class="lineNoCov">          0 :                 sum = work[j] + std::abs(a[j + j * a_dim1]);</span></a>
+<a name="19378"><span class="lineNum">   19378 </span><span class="lineNoCov">          0 :                 i__2 = *n;</span></a>
+<a name="19379"><span class="lineNum">   19379 </span><span class="lineNoCov">          0 :                 for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19380"><span class="lineNum">   19380 </span><span class="lineNoCov">          0 :                     absa = std::abs(a[i__ + j * a_dim1]);</span></a>
+<a name="19381"><span class="lineNum">   19381 </span><span class="lineNoCov">          0 :                     sum += absa;</span></a>
+<a name="19382"><span class="lineNum">   19382 </span><span class="lineNoCov">          0 :                     work[i__] += absa;</span></a>
+<a name="19383"><span class="lineNum">   19383 </span>            :                 }</a>
+<a name="19384"><span class="lineNum">   19384 </span><span class="lineNoCov">          0 :                 if(sum&gt;value)</span></a>
+<a name="19385"><span class="lineNum">   19385 </span>            :                   value = sum;</a>
+<a name="19386"><span class="lineNum">   19386 </span>            :             }</a>
+<a name="19387"><span class="lineNum">   19387 </span>            :         }</a>
+<a name="19388"><span class="lineNum">   19388 </span>            :     } else if (*norm=='F' || *norm=='f' || *norm=='E' || *norm=='e') {</a>
+<a name="19389"><span class="lineNum">   19389 </span>            : </a>
+<a name="19390"><span class="lineNum">   19390 </span><span class="lineNoCov">          0 :         scale = 0.;</span></a>
+<a name="19391"><span class="lineNum">   19391 </span><span class="lineNoCov">          0 :         sum = 1.;</span></a>
+<a name="19392"><span class="lineNum">   19392 </span><span class="lineNoCov">          0 :         if (*uplo=='U' || *uplo=='u') {</span></a>
+<a name="19393"><span class="lineNum">   19393 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="19394"><span class="lineNum">   19394 </span><span class="lineNoCov">          0 :             for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="19395"><span class="lineNum">   19395 </span><span class="lineNoCov">          0 :                 i__2 = j - 1;</span></a>
+<a name="19396"><span class="lineNum">   19396 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(&amp;i__2, &amp;a[j * a_dim1 + 1], &amp;c__1, &amp;scale, &amp;sum);</span></a>
+<a name="19397"><span class="lineNum">   19397 </span>            :             }</a>
+<a name="19398"><span class="lineNum">   19398 </span>            :         } else {</a>
+<a name="19399"><span class="lineNum">   19399 </span><span class="lineNoCov">          0 :             i__1 = *n - 1;</span></a>
+<a name="19400"><span class="lineNum">   19400 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19401"><span class="lineNum">   19401 </span><span class="lineNoCov">          0 :                 i__2 = *n - j;</span></a>
+<a name="19402"><span class="lineNum">   19402 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(&amp;i__2, &amp;a[j + 1 + j * a_dim1], &amp;c__1, &amp;scale, &amp;sum);</span></a>
+<a name="19403"><span class="lineNum">   19403 </span>            :             }</a>
+<a name="19404"><span class="lineNum">   19404 </span>            :         }</a>
+<a name="19405"><span class="lineNum">   19405 </span><span class="lineNoCov">          0 :         sum *= 2;</span></a>
+<a name="19406"><span class="lineNum">   19406 </span><span class="lineNoCov">          0 :         i__1 = *lda + 1;</span></a>
+<a name="19407"><span class="lineNum">   19407 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(n, &amp;a[a_offset], &amp;i__1, &amp;scale, &amp;sum);</span></a>
+<a name="19408"><span class="lineNum">   19408 </span><span class="lineNoCov">          0 :         value = scale *  std::sqrt(sum);</span></a>
+<a name="19409"><span class="lineNum">   19409 </span>            :     }</a>
+<a name="19410"><span class="lineNum">   19410 </span>            : </a>
+<a name="19411"><span class="lineNum">   19411 </span>            :     ret_val = value;</a>
+<a name="19412"><span class="lineNum">   19412 </span><span class="lineNoCov">          0 :     return ret_val;</span></a>
+<a name="19413"><span class="lineNum">   19413 </span>            : }</a>
+<a name="19414"><span class="lineNum">   19414 </span>            : </a>
+<a name="19415"><span class="lineNum">   19415 </span>            : </a>
+<a name="19416"><span class="lineNum">   19416 </span>            : }</a>
+<a name="19417"><span class="lineNum">   19417 </span>            : }</a>
+<a name="19418"><span class="lineNum">   19418 </span>            : #include &lt;cmath&gt;</a>
+<a name="19419"><span class="lineNum">   19419 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19420"><span class="lineNum">   19420 </span>            : </a>
+<a name="19421"><span class="lineNum">   19421 </span>            : #include &quot;real.h&quot;</a>
+<a name="19422"><span class="lineNum">   19422 </span>            : </a>
+<a name="19423"><span class="lineNum">   19423 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19424"><span class="lineNum">   19424 </span>            : namespace PLMD{</a>
+<a name="19425"><span class="lineNum">   19425 </span>            : namespace lapack{</a>
+<a name="19426"><span class="lineNum">   19426 </span>            : using namespace blas;</a>
+<a name="19427"><span class="lineNum">   19427 </span>            : float</a>
+<a name="19428"><span class="lineNum">   19428 </span><span class="lineCov">          1 : PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(float * x, float * y)</span></a>
+<a name="19429"><span class="lineNum">   19429 </span>            : {</a>
+<a name="19430"><span class="lineNum">   19430 </span>            :   float xabs,yabs;</a>
+<a name="19431"><span class="lineNum">   19431 </span>            :   float w,z;</a>
+<a name="19432"><span class="lineNum">   19432 </span>            : </a>
+<a name="19433"><span class="lineNum">   19433 </span><span class="lineCov">          1 :   xabs = std::abs(*x);</span></a>
+<a name="19434"><span class="lineNum">   19434 </span><span class="lineCov">          1 :   yabs = std::abs(*y);</span></a>
+<a name="19435"><span class="lineNum">   19435 </span>            :   </a>
+<a name="19436"><span class="lineNum">   19436 </span><span class="lineCov">          1 :   if(xabs&gt;yabs) {</span></a>
+<a name="19437"><span class="lineNum">   19437 </span>            :     w = xabs;</a>
+<a name="19438"><span class="lineNum">   19438 </span>            :     z = yabs;</a>
+<a name="19439"><span class="lineNum">   19439 </span>            :   } else {</a>
+<a name="19440"><span class="lineNum">   19440 </span>            :     w = yabs;</a>
+<a name="19441"><span class="lineNum">   19441 </span>            :     z = xabs;</a>
+<a name="19442"><span class="lineNum">   19442 </span>            :   }</a>
+<a name="19443"><span class="lineNum">   19443 </span>            : </a>
+<a name="19444"><span class="lineNum">   19444 </span><span class="lineCov">          1 :   if( std::abs(z)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="19445"><span class="lineNum">   19445 </span>            :     return w;</a>
+<a name="19446"><span class="lineNum">   19446 </span>            :   else {</a>
+<a name="19447"><span class="lineNum">   19447 </span><span class="lineCov">          1 :     z = z/w;</span></a>
+<a name="19448"><span class="lineNum">   19448 </span><span class="lineCov">          1 :     return w* std::sqrt(1.0+z*z);</span></a>
+<a name="19449"><span class="lineNum">   19449 </span>            :   }</a>
+<a name="19450"><span class="lineNum">   19450 </span>            : }</a>
+<a name="19451"><span class="lineNum">   19451 </span>            :   </a>
+<a name="19452"><span class="lineNum">   19452 </span>            : }</a>
+<a name="19453"><span class="lineNum">   19453 </span>            : }</a>
+<a name="19454"><span class="lineNum">   19454 </span>            : #include &lt;cmath&gt;</a>
+<a name="19455"><span class="lineNum">   19455 </span>            : </a>
+<a name="19456"><span class="lineNum">   19456 </span>            : #include &quot;real.h&quot;</a>
+<a name="19457"><span class="lineNum">   19457 </span>            : </a>
+<a name="19458"><span class="lineNum">   19458 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19459"><span class="lineNum">   19459 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="19460"><span class="lineNum">   19460 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19461"><span class="lineNum">   19461 </span>            : namespace PLMD{</a>
+<a name="19462"><span class="lineNum">   19462 </span>            : namespace lapack{</a>
+<a name="19463"><span class="lineNum">   19463 </span>            : using namespace blas;</a>
+<a name="19464"><span class="lineNum">   19464 </span>            : </a>
+<a name="19465"><span class="lineNum">   19465 </span><span class="lineNoCov">          0 : void PLUMED_BLAS_F77_FUNC(slar1vx,SLAR1VX)(int *n, </span></a>
+<a name="19466"><span class="lineNum">   19466 </span>            :               int *b1, </a>
+<a name="19467"><span class="lineNum">   19467 </span>            :               int *bn,</a>
+<a name="19468"><span class="lineNum">   19468 </span>            :               float *sigma, </a>
+<a name="19469"><span class="lineNum">   19469 </span>            :               float *d__, </a>
+<a name="19470"><span class="lineNum">   19470 </span>            :               float *l, </a>
+<a name="19471"><span class="lineNum">   19471 </span>            :               float *ld, </a>
+<a name="19472"><span class="lineNum">   19472 </span>            :               float *lld, </a>
+<a name="19473"><span class="lineNum">   19473 </span>            :               float *eval, </a>
+<a name="19474"><span class="lineNum">   19474 </span>            :               float *gersch, </a>
+<a name="19475"><span class="lineNum">   19475 </span>            :               float *z__, </a>
+<a name="19476"><span class="lineNum">   19476 </span>            :               float *ztz, </a>
+<a name="19477"><span class="lineNum">   19477 </span>            :               float *mingma, </a>
+<a name="19478"><span class="lineNum">   19478 </span>            :               int *r__, </a>
+<a name="19479"><span class="lineNum">   19479 </span>            :               int *isuppz, </a>
+<a name="19480"><span class="lineNum">   19480 </span>            :               float *work)</a>
+<a name="19481"><span class="lineNum">   19481 </span>            : {</a>
+<a name="19482"><span class="lineNum">   19482 </span>            :     int i__1;</a>
+<a name="19483"><span class="lineNum">   19483 </span>            : </a>
+<a name="19484"><span class="lineNum">   19484 </span>            :     int i__, j;</a>
+<a name="19485"><span class="lineNum">   19485 </span>            :     float s;</a>
+<a name="19486"><span class="lineNum">   19486 </span>            :     int r1, r2;</a>
+<a name="19487"><span class="lineNum">   19487 </span>            :     int to;</a>
+<a name="19488"><span class="lineNum">   19488 </span>            :     float eps, tmp;</a>
+<a name="19489"><span class="lineNum">   19489 </span>            :     int indp, inds, from;</a>
+<a name="19490"><span class="lineNum">   19490 </span>            :     float dplus;</a>
+<a name="19491"><span class="lineNum">   19491 </span>            :     int sawnan;</a>
+<a name="19492"><span class="lineNum">   19492 </span>            :     int indumn;</a>
+<a name="19493"><span class="lineNum">   19493 </span>            :     float dminus;</a>
+<a name="19494"><span class="lineNum">   19494 </span>            : </a>
+<a name="19495"><span class="lineNum">   19495 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="19496"><span class="lineNum">   19496 </span>            :     --isuppz;</a>
+<a name="19497"><span class="lineNum">   19497 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="19498"><span class="lineNum">   19498 </span><span class="lineNoCov">          0 :     --gersch;</span></a>
+<a name="19499"><span class="lineNum">   19499 </span><span class="lineNoCov">          0 :     --lld;</span></a>
+<a name="19500"><span class="lineNum">   19500 </span><span class="lineNoCov">          0 :     --ld;</span></a>
+<a name="19501"><span class="lineNum">   19501 </span><span class="lineNoCov">          0 :     --l;</span></a>
+<a name="19502"><span class="lineNum">   19502 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="19503"><span class="lineNum">   19503 </span>            : </a>
+<a name="19504"><span class="lineNum">   19504 </span>            :     /* Function Body */</a>
+<a name="19505"><span class="lineNum">   19505 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="19506"><span class="lineNum">   19506 </span><span class="lineNoCov">          0 :     if (*r__ == 0) {</span></a>
+<a name="19507"><span class="lineNum">   19507 </span>            : </a>
+<a name="19508"><span class="lineNum">   19508 </span><span class="lineNoCov">          0 :         r1 = *b1;</span></a>
+<a name="19509"><span class="lineNum">   19509 </span><span class="lineNoCov">          0 :         r2 = *bn;</span></a>
+<a name="19510"><span class="lineNum">   19510 </span>            :         i__1 = *bn;</a>
+<a name="19511"><span class="lineNum">   19511 </span><span class="lineNoCov">          0 :         for (i__ = *b1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19512"><span class="lineNum">   19512 </span><span class="lineNoCov">          0 :             if (*eval &gt;= gersch[(i__ &lt;&lt; 1) - 1] &amp;&amp; *eval &lt;= gersch[i__ * 2]) {</span></a>
+<a name="19513"><span class="lineNum">   19513 </span>            :                 r1 = i__;</a>
+<a name="19514"><span class="lineNum">   19514 </span><span class="lineNoCov">          0 :                 goto L20;</span></a>
+<a name="19515"><span class="lineNum">   19515 </span>            :             }</a>
+<a name="19516"><span class="lineNum">   19516 </span>            :         }</a>
+<a name="19517"><span class="lineNum">   19517 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="19518"><span class="lineNum">   19518 </span>            : L20:</a>
+<a name="19519"><span class="lineNum">   19519 </span>            :         i__1 = *b1;</a>
+<a name="19520"><span class="lineNum">   19520 </span><span class="lineNoCov">          0 :         for (i__ = *bn; i__ &gt;= i__1; --i__) {</span></a>
+<a name="19521"><span class="lineNum">   19521 </span><span class="lineNoCov">          0 :             if (*eval &gt;= gersch[(i__ &lt;&lt; 1) - 1] &amp;&amp; *eval &lt;= gersch[i__ * 2]) {</span></a>
+<a name="19522"><span class="lineNum">   19522 </span>            :                 r2 = i__;</a>
+<a name="19523"><span class="lineNum">   19523 </span><span class="lineNoCov">          0 :                 goto L40;</span></a>
+<a name="19524"><span class="lineNum">   19524 </span>            :             }</a>
+<a name="19525"><span class="lineNum">   19525 </span>            :         }</a>
+<a name="19526"><span class="lineNum">   19526 </span>            :     } else {</a>
+<a name="19527"><span class="lineNum">   19527 </span>            :         r1 = *r__;</a>
+<a name="19528"><span class="lineNum">   19528 </span>            :         r2 = *r__;</a>
+<a name="19529"><span class="lineNum">   19529 </span>            :     }</a>
+<a name="19530"><span class="lineNum">   19530 </span>            : </a>
+<a name="19531"><span class="lineNum">   19531 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="19532"><span class="lineNum">   19532 </span><span class="lineNoCov">          0 :     indumn = *n;</span></a>
+<a name="19533"><span class="lineNum">   19533 </span><span class="lineNoCov">          0 :     inds = (*n &lt;&lt; 1) + 1;</span></a>
+<a name="19534"><span class="lineNum">   19534 </span><span class="lineNoCov">          0 :     indp = *n * 3 + 1;</span></a>
+<a name="19535"><span class="lineNum">   19535 </span>            :     sawnan = 0;</a>
+<a name="19536"><span class="lineNum">   19536 </span>            : </a>
+<a name="19537"><span class="lineNum">   19537 </span><span class="lineNoCov">          0 :     if (*b1 == 1) {</span></a>
+<a name="19538"><span class="lineNum">   19538 </span><span class="lineNoCov">          0 :         work[inds] = 0.;</span></a>
+<a name="19539"><span class="lineNum">   19539 </span>            :     } else {</a>
+<a name="19540"><span class="lineNum">   19540 </span><span class="lineNoCov">          0 :         work[inds] = lld[*b1 - 1];</span></a>
+<a name="19541"><span class="lineNum">   19541 </span>            :     }</a>
+<a name="19542"><span class="lineNum">   19542 </span><span class="lineNoCov">          0 :     s = work[inds] - *sigma;</span></a>
+<a name="19543"><span class="lineNum">   19543 </span>            :     i__1 = r2 - 1;</a>
+<a name="19544"><span class="lineNum">   19544 </span><span class="lineNoCov">          0 :     for (i__ = *b1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19545"><span class="lineNum">   19545 </span><span class="lineNoCov">          0 :         dplus = d__[i__] + s;</span></a>
+<a name="19546"><span class="lineNum">   19546 </span><span class="lineNoCov">          0 :         work[i__] = ld[i__] / dplus;</span></a>
+<a name="19547"><span class="lineNum">   19547 </span><span class="lineNoCov">          0 :         work[inds + i__] = s * work[i__] * l[i__];</span></a>
+<a name="19548"><span class="lineNum">   19548 </span><span class="lineNoCov">          0 :         s = work[inds + i__] - *sigma;</span></a>
+<a name="19549"><span class="lineNum">   19549 </span>            :     }</a>
+<a name="19550"><span class="lineNum">   19550 </span>            : </a>
+<a name="19551"><span class="lineNum">   19551 </span><span class="lineNoCov">          0 :     if (std::isnan(s)) {</span></a>
+<a name="19552"><span class="lineNum">   19552 </span>            : </a>
+<a name="19553"><span class="lineNum">   19553 </span>            :         sawnan = 1;</a>
+<a name="19554"><span class="lineNum">   19554 </span><span class="lineNoCov">          0 :         j = *b1 + 1;</span></a>
+<a name="19555"><span class="lineNum">   19555 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="19556"><span class="lineNum">   19556 </span><span class="lineNoCov">          0 :     if (!std::isnan(work[inds + j])) {</span></a>
+<a name="19557"><span class="lineNum">   19557 </span><span class="lineNoCov">          0 :             ++j;</span></a>
+<a name="19558"><span class="lineNum">   19558 </span><span class="lineNoCov">          0 :             goto L60;</span></a>
+<a name="19559"><span class="lineNum">   19559 </span>            :         }</a>
+<a name="19560"><span class="lineNum">   19560 </span><span class="lineNoCov">          0 :         work[inds + j] = lld[j];</span></a>
+<a name="19561"><span class="lineNum">   19561 </span><span class="lineNoCov">          0 :         s = work[inds + j] - *sigma;</span></a>
+<a name="19562"><span class="lineNum">   19562 </span>            :         i__1 = r2 - 1;</a>
+<a name="19563"><span class="lineNum">   19563 </span><span class="lineNoCov">          0 :         for (i__ = j + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19564"><span class="lineNum">   19564 </span><span class="lineNoCov">          0 :             dplus = d__[i__] + s;</span></a>
+<a name="19565"><span class="lineNum">   19565 </span><span class="lineNoCov">          0 :             work[i__] = ld[i__] / dplus;</span></a>
+<a name="19566"><span class="lineNum">   19566 </span><span class="lineNoCov">          0 :             if (std::abs(work[i__])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19567"><span class="lineNum">   19567 </span><span class="lineNoCov">          0 :                 work[inds + i__] = lld[i__];</span></a>
+<a name="19568"><span class="lineNum">   19568 </span>            :             } else {</a>
+<a name="19569"><span class="lineNum">   19569 </span><span class="lineNoCov">          0 :                 work[inds + i__] = s * work[i__] * l[i__];</span></a>
+<a name="19570"><span class="lineNum">   19570 </span>            :             }</a>
+<a name="19571"><span class="lineNum">   19571 </span><span class="lineNoCov">          0 :             s = work[inds + i__] - *sigma;</span></a>
+<a name="19572"><span class="lineNum">   19572 </span>            :         }</a>
+<a name="19573"><span class="lineNum">   19573 </span>            :     }</a>
+<a name="19574"><span class="lineNum">   19574 </span>            : </a>
+<a name="19575"><span class="lineNum">   19575 </span><span class="lineNoCov">          0 :     work[indp + *bn - 1] = d__[*bn] - *sigma;</span></a>
+<a name="19576"><span class="lineNum">   19576 </span>            :     i__1 = r1;</a>
+<a name="19577"><span class="lineNum">   19577 </span><span class="lineNoCov">          0 :     for (i__ = *bn - 1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="19578"><span class="lineNum">   19578 </span><span class="lineNoCov">          0 :         dminus = lld[i__] + work[indp + i__];</span></a>
+<a name="19579"><span class="lineNum">   19579 </span><span class="lineNoCov">          0 :         tmp = d__[i__] / dminus;</span></a>
+<a name="19580"><span class="lineNum">   19580 </span><span class="lineNoCov">          0 :         work[indumn + i__] = l[i__] * tmp;</span></a>
+<a name="19581"><span class="lineNum">   19581 </span><span class="lineNoCov">          0 :         work[indp + i__ - 1] = work[indp + i__] * tmp - *sigma;</span></a>
+<a name="19582"><span class="lineNum">   19582 </span>            :     }</a>
+<a name="19583"><span class="lineNum">   19583 </span><span class="lineNoCov">          0 :     tmp = work[indp + r1 - 1];</span></a>
+<a name="19584"><span class="lineNum">   19584 </span><span class="lineNoCov">          0 :     if (std::isnan(tmp)) {</span></a>
+<a name="19585"><span class="lineNum">   19585 </span>            : </a>
+<a name="19586"><span class="lineNum">   19586 </span>            :         sawnan = 1;</a>
+<a name="19587"><span class="lineNum">   19587 </span><span class="lineNoCov">          0 :         j = *bn - 3;</span></a>
+<a name="19588"><span class="lineNum">   19588 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="19589"><span class="lineNum">   19589 </span><span class="lineNoCov">          0 :     if (!std::isnan(work[indp + j])) {</span></a>
+<a name="19590"><span class="lineNum">   19590 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="19591"><span class="lineNum">   19591 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="19592"><span class="lineNum">   19592 </span>            :         }</a>
+<a name="19593"><span class="lineNum">   19593 </span><span class="lineNoCov">          0 :         work[indp + j] = d__[j + 1] - *sigma;</span></a>
+<a name="19594"><span class="lineNum">   19594 </span>            :         i__1 = r1;</a>
+<a name="19595"><span class="lineNum">   19595 </span><span class="lineNoCov">          0 :         for (i__ = j; i__ &gt;= i__1; --i__) {</span></a>
+<a name="19596"><span class="lineNum">   19596 </span><span class="lineNoCov">          0 :             dminus = lld[i__] + work[indp + i__];</span></a>
+<a name="19597"><span class="lineNum">   19597 </span><span class="lineNoCov">          0 :             tmp = d__[i__] / dminus;</span></a>
+<a name="19598"><span class="lineNum">   19598 </span><span class="lineNoCov">          0 :             work[indumn + i__] = l[i__] * tmp;</span></a>
+<a name="19599"><span class="lineNum">   19599 </span><span class="lineNoCov">          0 :             if (std::abs(tmp)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19600"><span class="lineNum">   19600 </span><span class="lineNoCov">          0 :                 work[indp + i__ - 1] = d__[i__] - *sigma;</span></a>
+<a name="19601"><span class="lineNum">   19601 </span>            :             } else {</a>
+<a name="19602"><span class="lineNum">   19602 </span><span class="lineNoCov">          0 :                 work[indp + i__ - 1] = work[indp + i__] * tmp - *sigma;</span></a>
+<a name="19603"><span class="lineNum">   19603 </span>            :             }</a>
+<a name="19604"><span class="lineNum">   19604 </span>            :         }</a>
+<a name="19605"><span class="lineNum">   19605 </span>            :     }</a>
+<a name="19606"><span class="lineNum">   19606 </span>            : </a>
+<a name="19607"><span class="lineNum">   19607 </span><span class="lineNoCov">          0 :     *mingma = work[inds + r1 - 1] + work[indp + r1 - 1];</span></a>
+<a name="19608"><span class="lineNum">   19608 </span><span class="lineNoCov">          0 :     if (std::abs(*mingma)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19609"><span class="lineNum">   19609 </span><span class="lineNoCov">          0 :         *mingma = eps * work[inds + r1 - 1];</span></a>
+<a name="19610"><span class="lineNum">   19610 </span>            :     }</a>
+<a name="19611"><span class="lineNum">   19611 </span><span class="lineNoCov">          0 :     *r__ = r1;</span></a>
+<a name="19612"><span class="lineNum">   19612 </span>            :     i__1 = r2 - 1;</a>
+<a name="19613"><span class="lineNum">   19613 </span><span class="lineNoCov">          0 :     for (i__ = r1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19614"><span class="lineNum">   19614 </span><span class="lineNoCov">          0 :         tmp = work[inds + i__] + work[indp + i__];</span></a>
+<a name="19615"><span class="lineNum">   19615 </span><span class="lineNoCov">          0 :         if (std::abs(tmp)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19616"><span class="lineNum">   19616 </span><span class="lineNoCov">          0 :             tmp = eps * work[inds + i__];</span></a>
+<a name="19617"><span class="lineNum">   19617 </span>            :         }</a>
+<a name="19618"><span class="lineNum">   19618 </span><span class="lineNoCov">          0 :         if (std::abs(tmp) &lt; std::abs(*mingma)) {</span></a>
+<a name="19619"><span class="lineNum">   19619 </span><span class="lineNoCov">          0 :             *mingma = tmp;</span></a>
+<a name="19620"><span class="lineNum">   19620 </span><span class="lineNoCov">          0 :             *r__ = i__ + 1;</span></a>
+<a name="19621"><span class="lineNum">   19621 </span>            :         }</a>
+<a name="19622"><span class="lineNum">   19622 </span>            :     }</a>
+<a name="19623"><span class="lineNum">   19623 </span>            : </a>
+<a name="19624"><span class="lineNum">   19624 </span><span class="lineNoCov">          0 :     isuppz[1] = *b1;</span></a>
+<a name="19625"><span class="lineNum">   19625 </span><span class="lineNoCov">          0 :     isuppz[2] = *bn;</span></a>
+<a name="19626"><span class="lineNum">   19626 </span><span class="lineNoCov">          0 :     z__[*r__] = 1.;</span></a>
+<a name="19627"><span class="lineNum">   19627 </span><span class="lineNoCov">          0 :     *ztz = 1.;</span></a>
+<a name="19628"><span class="lineNum">   19628 </span><span class="lineNoCov">          0 :     if (! sawnan) {</span></a>
+<a name="19629"><span class="lineNum">   19629 </span><span class="lineNoCov">          0 :         from = *r__ - 1;</span></a>
+<a name="19630"><span class="lineNum">   19630 </span><span class="lineNoCov">          0 :         i__1 = *r__ - 32;</span></a>
+<a name="19631"><span class="lineNum">   19631 </span><span class="lineNoCov">          0 :         to = (i__1&gt;(*b1)) ? i__1 : (*b1);</span></a>
+<a name="19632"><span class="lineNum">   19632 </span>            : L120:</a>
+<a name="19633"><span class="lineNum">   19633 </span><span class="lineNoCov">          0 :         if (from &gt;= *b1) {</span></a>
+<a name="19634"><span class="lineNum">   19634 </span>            :             i__1 = to;</a>
+<a name="19635"><span class="lineNum">   19635 </span><span class="lineNoCov">          0 :             for (i__ = from; i__ &gt;= i__1; --i__) {</span></a>
+<a name="19636"><span class="lineNum">   19636 </span><span class="lineNoCov">          0 :                 z__[i__] = -(work[i__] * z__[i__ + 1]);</span></a>
+<a name="19637"><span class="lineNum">   19637 </span><span class="lineNoCov">          0 :                 *ztz += z__[i__] * z__[i__];</span></a>
+<a name="19638"><span class="lineNum">   19638 </span>            :             }</a>
+<a name="19639"><span class="lineNum">   19639 </span><span class="lineNoCov">          0 :             if (std::abs(z__[to]) &lt;= eps &amp;&amp; std::abs(z__[to + 1]) &lt;= eps) {</span></a>
+<a name="19640"><span class="lineNum">   19640 </span><span class="lineNoCov">          0 :                 isuppz[1] = to + 2;</span></a>
+<a name="19641"><span class="lineNum">   19641 </span>            :             } else {</a>
+<a name="19642"><span class="lineNum">   19642 </span><span class="lineNoCov">          0 :                 from = to - 1;</span></a>
+<a name="19643"><span class="lineNum">   19643 </span><span class="lineNoCov">          0 :                 i__1 = to - 32;</span></a>
+<a name="19644"><span class="lineNum">   19644 </span><span class="lineNoCov">          0 :                 to = (i__1&gt;*b1) ? i__1 : *b1;</span></a>
+<a name="19645"><span class="lineNum">   19645 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="19646"><span class="lineNum">   19646 </span>            :             }</a>
+<a name="19647"><span class="lineNum">   19647 </span>            :         }</a>
+<a name="19648"><span class="lineNum">   19648 </span><span class="lineNoCov">          0 :         from = *r__ + 1;</span></a>
+<a name="19649"><span class="lineNum">   19649 </span><span class="lineNoCov">          0 :         i__1 = *r__ + 32;</span></a>
+<a name="19650"><span class="lineNum">   19650 </span><span class="lineNoCov">          0 :         to = (i__1&lt;*bn) ? i__1 : *bn;</span></a>
+<a name="19651"><span class="lineNum">   19651 </span>            : L140:</a>
+<a name="19652"><span class="lineNum">   19652 </span><span class="lineNoCov">          0 :         if (from &lt;= *bn) {</span></a>
+<a name="19653"><span class="lineNum">   19653 </span>            :             i__1 = to;</a>
+<a name="19654"><span class="lineNum">   19654 </span><span class="lineNoCov">          0 :             for (i__ = from; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19655"><span class="lineNum">   19655 </span><span class="lineNoCov">          0 :                 z__[i__] = -(work[indumn + i__ - 1] * z__[i__ - 1]);</span></a>
+<a name="19656"><span class="lineNum">   19656 </span><span class="lineNoCov">          0 :                 *ztz += z__[i__] * z__[i__];</span></a>
+<a name="19657"><span class="lineNum">   19657 </span>            :             }</a>
+<a name="19658"><span class="lineNum">   19658 </span><span class="lineNoCov">          0 :             if (std::abs(z__[to]) &lt;= eps &amp;&amp; std::abs(z__[to - 1]) &lt;= eps) {</span></a>
+<a name="19659"><span class="lineNum">   19659 </span><span class="lineNoCov">          0 :                 isuppz[2] = to - 2;</span></a>
+<a name="19660"><span class="lineNum">   19660 </span>            :             } else {</a>
+<a name="19661"><span class="lineNum">   19661 </span><span class="lineNoCov">          0 :                 from = to + 1;</span></a>
+<a name="19662"><span class="lineNum">   19662 </span><span class="lineNoCov">          0 :                 i__1 = to + 32;</span></a>
+<a name="19663"><span class="lineNum">   19663 </span><span class="lineNoCov">          0 :                 to = (i__1&lt;*bn) ? i__1 : *bn;</span></a>
+<a name="19664"><span class="lineNum">   19664 </span><span class="lineNoCov">          0 :                 goto L140;</span></a>
+<a name="19665"><span class="lineNum">   19665 </span>            :             }</a>
+<a name="19666"><span class="lineNum">   19666 </span>            :         }</a>
+<a name="19667"><span class="lineNum">   19667 </span>            :     } else {</a>
+<a name="19668"><span class="lineNum">   19668 </span><span class="lineNoCov">          0 :         i__1 = *b1;</span></a>
+<a name="19669"><span class="lineNum">   19669 </span><span class="lineNoCov">          0 :         for (i__ = *r__ - 1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="19670"><span class="lineNum">   19670 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__ + 1])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19671"><span class="lineNum">   19671 </span><span class="lineNoCov">          0 :                 z__[i__] = -(ld[i__ + 1] / ld[i__]) * z__[i__ + 2];</span></a>
+<a name="19672"><span class="lineNum">   19672 </span>            :             } else {</a>
+<a name="19673"><span class="lineNum">   19673 </span><span class="lineNoCov">          0 :                 z__[i__] = -(work[i__] * z__[i__ + 1]);</span></a>
+<a name="19674"><span class="lineNum">   19674 </span>            :             }</a>
+<a name="19675"><span class="lineNum">   19675 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__]) &lt;= eps &amp;&amp; std::abs(z__[i__ + 1]) &lt;= eps) {</span></a>
+<a name="19676"><span class="lineNum">   19676 </span><span class="lineNoCov">          0 :                 isuppz[1] = i__ + 2;</span></a>
+<a name="19677"><span class="lineNum">   19677 </span><span class="lineNoCov">          0 :                 goto L170;</span></a>
+<a name="19678"><span class="lineNum">   19678 </span>            :             }</a>
+<a name="19679"><span class="lineNum">   19679 </span><span class="lineNoCov">          0 :             *ztz += z__[i__] * z__[i__];</span></a>
+<a name="19680"><span class="lineNum">   19680 </span>            :         }</a>
+<a name="19681"><span class="lineNum">   19681 </span><span class="lineNoCov">          0 : L170:</span></a>
+<a name="19682"><span class="lineNum">   19682 </span><span class="lineNoCov">          0 :         i__1 = *bn - 1;</span></a>
+<a name="19683"><span class="lineNum">   19683 </span><span class="lineNoCov">          0 :         for (i__ = *r__; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="19684"><span class="lineNum">   19684 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19685"><span class="lineNum">   19685 </span><span class="lineNoCov">          0 :                 z__[i__ + 1] = -(ld[i__ - 1] / ld[i__]) * z__[i__ - 1];</span></a>
+<a name="19686"><span class="lineNum">   19686 </span>            :             } else {</a>
+<a name="19687"><span class="lineNum">   19687 </span><span class="lineNoCov">          0 :                 z__[i__ + 1] = -(work[indumn + i__] * z__[i__]);</span></a>
+<a name="19688"><span class="lineNum">   19688 </span>            :             }</a>
+<a name="19689"><span class="lineNum">   19689 </span><span class="lineNoCov">          0 :             if (std::abs(z__[i__]) &lt;= eps &amp;&amp; std::abs(z__[i__ + 1]) &lt;= eps) {</span></a>
+<a name="19690"><span class="lineNum">   19690 </span><span class="lineNoCov">          0 :                 isuppz[2] = i__ - 1;</span></a>
+<a name="19691"><span class="lineNum">   19691 </span><span class="lineNoCov">          0 :                 break;</span></a>
+<a name="19692"><span class="lineNum">   19692 </span>            :             }</a>
+<a name="19693"><span class="lineNum">   19693 </span><span class="lineNoCov">          0 :             *ztz += z__[i__ + 1] * z__[i__ + 1];</span></a>
+<a name="19694"><span class="lineNum">   19694 </span>            :         }</a>
+<a name="19695"><span class="lineNum">   19695 </span>            :     }</a>
+<a name="19696"><span class="lineNum">   19696 </span>            : </a>
+<a name="19697"><span class="lineNum">   19697 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="19698"><span class="lineNum">   19698 </span>            : </a>
+<a name="19699"><span class="lineNum">   19699 </span>            : }</a>
+<a name="19700"><span class="lineNum">   19700 </span>            : </a>
+<a name="19701"><span class="lineNum">   19701 </span>            : </a>
+<a name="19702"><span class="lineNum">   19702 </span>            : }</a>
+<a name="19703"><span class="lineNum">   19703 </span>            : }</a>
+<a name="19704"><span class="lineNum">   19704 </span>            : #include &lt;cctype&gt;</a>
+<a name="19705"><span class="lineNum">   19705 </span>            : #include &lt;cmath&gt;</a>
+<a name="19706"><span class="lineNum">   19706 </span>            : </a>
+<a name="19707"><span class="lineNum">   19707 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19708"><span class="lineNum">   19708 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19709"><span class="lineNum">   19709 </span>            : </a>
+<a name="19710"><span class="lineNum">   19710 </span>            : #include &quot;real.h&quot;</a>
+<a name="19711"><span class="lineNum">   19711 </span>            : </a>
+<a name="19712"><span class="lineNum">   19712 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19713"><span class="lineNum">   19713 </span>            : namespace PLMD{</a>
+<a name="19714"><span class="lineNum">   19714 </span>            : namespace lapack{</a>
+<a name="19715"><span class="lineNum">   19715 </span>            : using namespace blas;</a>
+<a name="19716"><span class="lineNum">   19716 </span>            : void</a>
+<a name="19717"><span class="lineNum">   19717 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarf,SLARF)(const char *side,</span></a>
+<a name="19718"><span class="lineNum">   19718 </span>            :        int *m,</a>
+<a name="19719"><span class="lineNum">   19719 </span>            :        int *n,</a>
+<a name="19720"><span class="lineNum">   19720 </span>            :        float *v,</a>
+<a name="19721"><span class="lineNum">   19721 </span>            :        int *incv,</a>
+<a name="19722"><span class="lineNum">   19722 </span>            :        float *tau,</a>
+<a name="19723"><span class="lineNum">   19723 </span>            :        float *c,</a>
+<a name="19724"><span class="lineNum">   19724 </span>            :        int *ldc,</a>
+<a name="19725"><span class="lineNum">   19725 </span>            :        float *work)</a>
+<a name="19726"><span class="lineNum">   19726 </span>            : {</a>
+<a name="19727"><span class="lineNum">   19727 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*side);</span></a>
+<a name="19728"><span class="lineNum">   19728 </span><span class="lineNoCov">          0 :   float one = 1.0;</span></a>
+<a name="19729"><span class="lineNum">   19729 </span><span class="lineNoCov">          0 :   float zero = 0.0;</span></a>
+<a name="19730"><span class="lineNum">   19730 </span><span class="lineNoCov">          0 :   float minustau = -(*tau);</span></a>
+<a name="19731"><span class="lineNum">   19731 </span><span class="lineNoCov">          0 :   int i1 = 1;</span></a>
+<a name="19732"><span class="lineNum">   19732 </span>            : </a>
+<a name="19733"><span class="lineNum">   19733 </span>            : </a>
+<a name="19734"><span class="lineNum">   19734 </span><span class="lineNoCov">          0 :   if(ch=='L') {</span></a>
+<a name="19735"><span class="lineNum">   19735 </span><span class="lineNoCov">          0 :     if(std::abs(*tau)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19736"><span class="lineNum">   19736 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;T&quot;,m,n,&amp;one,c,ldc,v,incv,&amp;zero,work,&amp;i1);</span></a>
+<a name="19737"><span class="lineNum">   19737 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sger,SGER)(m,n,&amp;minustau,v,incv,work,&amp;i1,c,ldc);</span></a>
+<a name="19738"><span class="lineNum">   19738 </span>            :     }</a>
+<a name="19739"><span class="lineNum">   19739 </span>            :   } else {</a>
+<a name="19740"><span class="lineNum">   19740 </span><span class="lineNoCov">          0 :     if(std::abs(*tau)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="19741"><span class="lineNum">   19741 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,m,n,&amp;one,c,ldc,v,incv,&amp;zero,work,&amp;i1);</span></a>
+<a name="19742"><span class="lineNum">   19742 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sger,SGER)(m,n,&amp;minustau,work,&amp;i1,v,incv,c,ldc);</span></a>
+<a name="19743"><span class="lineNum">   19743 </span>            :     }</a>
+<a name="19744"><span class="lineNum">   19744 </span>            :   }</a>
+<a name="19745"><span class="lineNum">   19745 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="19746"><span class="lineNum">   19746 </span>            : }</a>
+<a name="19747"><span class="lineNum">   19747 </span>            : }</a>
+<a name="19748"><span class="lineNum">   19748 </span>            : }</a>
+<a name="19749"><span class="lineNum">   19749 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19750"><span class="lineNum">   19750 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="19751"><span class="lineNum">   19751 </span>            : </a>
+<a name="19752"><span class="lineNum">   19752 </span>            : </a>
+<a name="19753"><span class="lineNum">   19753 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="19754"><span class="lineNum">   19754 </span>            : namespace PLMD{</a>
+<a name="19755"><span class="lineNum">   19755 </span>            : namespace lapack{</a>
+<a name="19756"><span class="lineNum">   19756 </span>            : using namespace blas;</a>
+<a name="19757"><span class="lineNum">   19757 </span>            : void </a>
+<a name="19758"><span class="lineNum">   19758 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(const char *side, </span></a>
+<a name="19759"><span class="lineNum">   19759 </span>            :         const char *trans, </a>
+<a name="19760"><span class="lineNum">   19760 </span>            :         const char *direct, </a>
+<a name="19761"><span class="lineNum">   19761 </span>            :         const char *storev, </a>
+<a name="19762"><span class="lineNum">   19762 </span>            :         int *m, </a>
+<a name="19763"><span class="lineNum">   19763 </span>            :         int *n, </a>
+<a name="19764"><span class="lineNum">   19764 </span>            :         int *k, </a>
+<a name="19765"><span class="lineNum">   19765 </span>            :         float *v, </a>
+<a name="19766"><span class="lineNum">   19766 </span>            :         int *ldv, </a>
+<a name="19767"><span class="lineNum">   19767 </span>            :         float *t, </a>
+<a name="19768"><span class="lineNum">   19768 </span>            :         int *ldt, </a>
+<a name="19769"><span class="lineNum">   19769 </span>            :         float *c__,</a>
+<a name="19770"><span class="lineNum">   19770 </span>            :         int *ldc, </a>
+<a name="19771"><span class="lineNum">   19771 </span>            :         float *work, </a>
+<a name="19772"><span class="lineNum">   19772 </span>            :         int *ldwork)</a>
+<a name="19773"><span class="lineNum">   19773 </span>            : {</a>
+<a name="19774"><span class="lineNum">   19774 </span>            :     int c_dim1, c_offset, t_dim1, t_offset, v_dim1, v_offset, work_dim1, </a>
+<a name="19775"><span class="lineNum">   19775 </span>            :             work_offset, i__1, i__2;</a>
+<a name="19776"><span class="lineNum">   19776 </span>            : </a>
+<a name="19777"><span class="lineNum">   19777 </span>            :     int i__, j;</a>
+<a name="19778"><span class="lineNum">   19778 </span>            :     char transt[1];</a>
+<a name="19779"><span class="lineNum">   19779 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="19780"><span class="lineNum">   19780 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="19781"><span class="lineNum">   19781 </span><span class="lineNoCov">          0 :     float minusone = -1.0;</span></a>
+<a name="19782"><span class="lineNum">   19782 </span>            : </a>
+<a name="19783"><span class="lineNum">   19783 </span><span class="lineNoCov">          0 :     v_dim1 = *ldv;</span></a>
+<a name="19784"><span class="lineNum">   19784 </span><span class="lineNoCov">          0 :     v_offset = 1 + v_dim1;</span></a>
+<a name="19785"><span class="lineNum">   19785 </span><span class="lineNoCov">          0 :     v -= v_offset;</span></a>
+<a name="19786"><span class="lineNum">   19786 </span>            :     t_dim1 = *ldt;</a>
+<a name="19787"><span class="lineNum">   19787 </span>            :     t_offset = 1 + t_dim1;</a>
+<a name="19788"><span class="lineNum">   19788 </span>            :     t -= t_offset;</a>
+<a name="19789"><span class="lineNum">   19789 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="19790"><span class="lineNum">   19790 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="19791"><span class="lineNum">   19791 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="19792"><span class="lineNum">   19792 </span><span class="lineNoCov">          0 :     work_dim1 = *ldwork;</span></a>
+<a name="19793"><span class="lineNum">   19793 </span><span class="lineNoCov">          0 :     work_offset = 1 + work_dim1;</span></a>
+<a name="19794"><span class="lineNum">   19794 </span><span class="lineNoCov">          0 :     work -= work_offset;</span></a>
+<a name="19795"><span class="lineNum">   19795 </span>            : </a>
+<a name="19796"><span class="lineNum">   19796 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0 || *n &lt;= 0) {</span></a>
+<a name="19797"><span class="lineNum">   19797 </span>            :         return;</a>
+<a name="19798"><span class="lineNum">   19798 </span>            :     }</a>
+<a name="19799"><span class="lineNum">   19799 </span><span class="lineNoCov">          0 :     if (*trans=='N' || *trans=='n') {</span></a>
+<a name="19800"><span class="lineNum">   19800 </span><span class="lineNoCov">          0 :       *(unsigned char *)transt = 'T';</span></a>
+<a name="19801"><span class="lineNum">   19801 </span>            :     } else {</a>
+<a name="19802"><span class="lineNum">   19802 </span><span class="lineNoCov">          0 :         *(unsigned char *)transt = 'N';</span></a>
+<a name="19803"><span class="lineNum">   19803 </span>            :     }</a>
+<a name="19804"><span class="lineNum">   19804 </span>            :     </a>
+<a name="19805"><span class="lineNum">   19805 </span><span class="lineNoCov">          0 :     if (*storev=='C' || *storev=='c') {</span></a>
+<a name="19806"><span class="lineNum">   19806 </span>            : </a>
+<a name="19807"><span class="lineNum">   19807 </span><span class="lineNoCov">          0 :         if (*direct=='F' || *direct=='f') {</span></a>
+<a name="19808"><span class="lineNum">   19808 </span><span class="lineNoCov">          0 :           if (*side=='l' || *side=='L') {</span></a>
+<a name="19809"><span class="lineNum">   19809 </span>            : </a>
+<a name="19810"><span class="lineNum">   19810 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19811"><span class="lineNum">   19811 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19812"><span class="lineNum">   19812 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;c__[j + c_dim1], ldc, &amp;work[j * work_dim1 + 1],</span></a>
+<a name="19813"><span class="lineNum">   19813 </span>            :                              &amp;c__1);</a>
+<a name="19814"><span class="lineNum">   19814 </span>            :                 }</a>
+<a name="19815"><span class="lineNum">   19815 </span>            : </a>
+<a name="19816"><span class="lineNum">   19816 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="19817"><span class="lineNum">   19817 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="19818"><span class="lineNum">   19818 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="19819"><span class="lineNum">   19819 </span>            : </a>
+<a name="19820"><span class="lineNum">   19820 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="19821"><span class="lineNum">   19821 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;Transpose&quot;, &quot;No transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="19822"><span class="lineNum">   19822 </span><span class="lineNoCov">          0 :                             c__[*k + 1 + c_dim1], ldc, &amp;v[*k + 1 + v_dim1], </span></a>
+<a name="19823"><span class="lineNum">   19823 </span>            :                             ldv, &amp;one, &amp;work[work_offset], ldwork);</a>
+<a name="19824"><span class="lineNum">   19824 </span>            :                 }</a>
+<a name="19825"><span class="lineNum">   19825 </span>            : </a>
+<a name="19826"><span class="lineNum">   19826 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="19827"><span class="lineNum">   19827 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="19828"><span class="lineNum">   19828 </span>            : </a>
+<a name="19829"><span class="lineNum">   19829 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="19830"><span class="lineNum">   19830 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="19831"><span class="lineNum">   19831 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;</span></a>
+<a name="19832"><span class="lineNum">   19832 </span><span class="lineNoCov">          0 :                             v[*k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="19833"><span class="lineNum">   19833 </span><span class="lineNoCov">          0 :                             ldwork, &amp;one, &amp;c__[*k + 1 + c_dim1], ldc);</span></a>
+<a name="19834"><span class="lineNum">   19834 </span>            :                 }</a>
+<a name="19835"><span class="lineNum">   19835 </span>            : </a>
+<a name="19836"><span class="lineNum">   19836 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="19837"><span class="lineNum">   19837 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="19838"><span class="lineNum">   19838 </span>            : </a>
+<a name="19839"><span class="lineNum">   19839 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19840"><span class="lineNum">   19840 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19841"><span class="lineNum">   19841 </span><span class="lineNoCov">          0 :                     i__2 = *n;</span></a>
+<a name="19842"><span class="lineNum">   19842 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19843"><span class="lineNum">   19843 </span><span class="lineNoCov">          0 :                         c__[j + i__ * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="19844"><span class="lineNum">   19844 </span>            :                     }</a>
+<a name="19845"><span class="lineNum">   19845 </span>            :                 }</a>
+<a name="19846"><span class="lineNum">   19846 </span>            : </a>
+<a name="19847"><span class="lineNum">   19847 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="19848"><span class="lineNum">   19848 </span>            : </a>
+<a name="19849"><span class="lineNum">   19849 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19850"><span class="lineNum">   19850 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19851"><span class="lineNum">   19851 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(m, &amp;c__[j * c_dim1 + 1], &amp;c__1, &amp;work[j * </span></a>
+<a name="19852"><span class="lineNum">   19852 </span><span class="lineNoCov">          0 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="19853"><span class="lineNum">   19853 </span>            :                 }</a>
+<a name="19854"><span class="lineNum">   19854 </span>            : </a>
+<a name="19855"><span class="lineNum">   19855 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="19856"><span class="lineNum">   19856 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="19857"><span class="lineNum">   19857 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="19858"><span class="lineNum">   19858 </span>            : </a>
+<a name="19859"><span class="lineNum">   19859 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="19860"><span class="lineNum">   19860 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, k, &amp;i__1, &amp;</span></a>
+<a name="19861"><span class="lineNum">   19861 </span><span class="lineNoCov">          0 :                             one, &amp;c__[(*k + 1) * c_dim1 + 1], ldc, &amp;v[*k + </span></a>
+<a name="19862"><span class="lineNum">   19862 </span><span class="lineNoCov">          0 :                             1 + v_dim1], ldv, &amp;one, &amp;work[work_offset], </span></a>
+<a name="19863"><span class="lineNum">   19863 </span>            :                             ldwork);</a>
+<a name="19864"><span class="lineNum">   19864 </span>            :                 }</a>
+<a name="19865"><span class="lineNum">   19865 </span>            : </a>
+<a name="19866"><span class="lineNum">   19866 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="19867"><span class="lineNum">   19867 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="19868"><span class="lineNum">   19868 </span>            : </a>
+<a name="19869"><span class="lineNum">   19869 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="19870"><span class="lineNum">   19870 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="19871"><span class="lineNum">   19871 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, &amp;i__1, k, &amp;minusone, &amp;</span></a>
+<a name="19872"><span class="lineNum">   19872 </span><span class="lineNoCov">          0 :                             work[work_offset], ldwork, &amp;v[*k + 1 + v_dim1], </span></a>
+<a name="19873"><span class="lineNum">   19873 </span><span class="lineNoCov">          0 :                             ldv, &amp;one, &amp;c__[(*k + 1) * c_dim1 + 1], ldc);</span></a>
+<a name="19874"><span class="lineNum">   19874 </span>            :                 }</a>
+<a name="19875"><span class="lineNum">   19875 </span>            : </a>
+<a name="19876"><span class="lineNum">   19876 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="19877"><span class="lineNum">   19877 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="19878"><span class="lineNum">   19878 </span>            : </a>
+<a name="19879"><span class="lineNum">   19879 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19880"><span class="lineNum">   19880 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19881"><span class="lineNum">   19881 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="19882"><span class="lineNum">   19882 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19883"><span class="lineNum">   19883 </span><span class="lineNoCov">          0 :                         c__[i__ + j * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="19884"><span class="lineNum">   19884 </span>            :                     }</a>
+<a name="19885"><span class="lineNum">   19885 </span>            :                 }</a>
+<a name="19886"><span class="lineNum">   19886 </span>            :             }</a>
+<a name="19887"><span class="lineNum">   19887 </span>            : </a>
+<a name="19888"><span class="lineNum">   19888 </span>            :         } else {</a>
+<a name="19889"><span class="lineNum">   19889 </span>            : </a>
+<a name="19890"><span class="lineNum">   19890 </span><span class="lineNoCov">          0 :           if (*side=='l' || *side=='L') {</span></a>
+<a name="19891"><span class="lineNum">   19891 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19892"><span class="lineNum">   19892 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19893"><span class="lineNum">   19893 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;c__[*m - *k + j + c_dim1], ldc, &amp;work[j * </span></a>
+<a name="19894"><span class="lineNum">   19894 </span><span class="lineNoCov">          0 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="19895"><span class="lineNum">   19895 </span>            :                 }</a>
+<a name="19896"><span class="lineNum">   19896 </span>            : </a>
+<a name="19897"><span class="lineNum">   19897 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="19898"><span class="lineNum">   19898 </span><span class="lineNoCov">          0 :                          &amp;v[*m - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="19899"><span class="lineNum">   19899 </span>            :                         ldwork);</a>
+<a name="19900"><span class="lineNum">   19900 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="19901"><span class="lineNum">   19901 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="19902"><span class="lineNum">   19902 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;Transpose&quot;, &quot;No transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="19903"><span class="lineNum">   19903 </span>            :                             c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;one, &amp;</a>
+<a name="19904"><span class="lineNum">   19904 </span>            :                             work[work_offset], ldwork);</a>
+<a name="19905"><span class="lineNum">   19905 </span>            :                 }</a>
+<a name="19906"><span class="lineNum">   19906 </span>            : </a>
+<a name="19907"><span class="lineNum">   19907 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="19908"><span class="lineNum">   19908 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="19909"><span class="lineNum">   19909 </span>            : </a>
+<a name="19910"><span class="lineNum">   19910 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="19911"><span class="lineNum">   19911 </span>            : </a>
+<a name="19912"><span class="lineNum">   19912 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="19913"><span class="lineNum">   19913 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;</span></a>
+<a name="19914"><span class="lineNum">   19914 </span>            :                             v[v_offset], ldv, &amp;work[work_offset], ldwork, &amp;</a>
+<a name="19915"><span class="lineNum">   19915 </span>            :                             one, &amp;c__[c_offset], ldc)</a>
+<a name="19916"><span class="lineNum">   19916 </span>            :                             ;</a>
+<a name="19917"><span class="lineNum">   19917 </span>            :                 }</a>
+<a name="19918"><span class="lineNum">   19918 </span>            : </a>
+<a name="19919"><span class="lineNum">   19919 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="19920"><span class="lineNum">   19920 </span><span class="lineNoCov">          0 :                         v[*m - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="19921"><span class="lineNum">   19921 </span>            :                         ldwork);</a>
+<a name="19922"><span class="lineNum">   19922 </span>            : </a>
+<a name="19923"><span class="lineNum">   19923 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19924"><span class="lineNum">   19924 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19925"><span class="lineNum">   19925 </span><span class="lineNoCov">          0 :                     i__2 = *n;</span></a>
+<a name="19926"><span class="lineNum">   19926 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19927"><span class="lineNum">   19927 </span><span class="lineNoCov">          0 :                         c__[*m - *k + j + i__ * c_dim1] -= work[i__ + j * </span></a>
+<a name="19928"><span class="lineNum">   19928 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="19929"><span class="lineNum">   19929 </span>            :                     }</a>
+<a name="19930"><span class="lineNum">   19930 </span>            :                 }</a>
+<a name="19931"><span class="lineNum">   19931 </span>            : </a>
+<a name="19932"><span class="lineNum">   19932 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="19933"><span class="lineNum">   19933 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19934"><span class="lineNum">   19934 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19935"><span class="lineNum">   19935 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(m, &amp;c__[(*n - *k + j) * c_dim1 + 1], &amp;c__1, &amp;work[</span></a>
+<a name="19936"><span class="lineNum">   19936 </span><span class="lineNoCov">          0 :                             j * work_dim1 + 1], &amp;c__1);</span></a>
+<a name="19937"><span class="lineNum">   19937 </span>            :                 }</a>
+<a name="19938"><span class="lineNum">   19938 </span>            : </a>
+<a name="19939"><span class="lineNum">   19939 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="19940"><span class="lineNum">   19940 </span><span class="lineNoCov">          0 :                          &amp;v[*n - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="19941"><span class="lineNum">   19941 </span>            :                         ldwork);</a>
+<a name="19942"><span class="lineNum">   19942 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="19943"><span class="lineNum">   19943 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="19944"><span class="lineNum">   19944 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, k, &amp;i__1, &amp;</span></a>
+<a name="19945"><span class="lineNum">   19945 </span>            :                             one, &amp;c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;</a>
+<a name="19946"><span class="lineNum">   19946 </span>            :                             one, &amp;work[work_offset], ldwork);</a>
+<a name="19947"><span class="lineNum">   19947 </span>            :                 }</a>
+<a name="19948"><span class="lineNum">   19948 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="19949"><span class="lineNum">   19949 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="19950"><span class="lineNum">   19950 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="19951"><span class="lineNum">   19951 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="19952"><span class="lineNum">   19952 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, &amp;i__1, k, &amp;minusone, &amp;</span></a>
+<a name="19953"><span class="lineNum">   19953 </span>            :                             work[work_offset], ldwork, &amp;v[v_offset], ldv, &amp;</a>
+<a name="19954"><span class="lineNum">   19954 </span>            :                             one, &amp;c__[c_offset], ldc)</a>
+<a name="19955"><span class="lineNum">   19955 </span>            :                             ;</a>
+<a name="19956"><span class="lineNum">   19956 </span>            :                 }</a>
+<a name="19957"><span class="lineNum">   19957 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="19958"><span class="lineNum">   19958 </span><span class="lineNoCov">          0 :                         v[*n - *k + 1 + v_dim1], ldv, &amp;work[work_offset], </span></a>
+<a name="19959"><span class="lineNum">   19959 </span>            :                         ldwork);</a>
+<a name="19960"><span class="lineNum">   19960 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19961"><span class="lineNum">   19961 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19962"><span class="lineNum">   19962 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="19963"><span class="lineNum">   19963 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="19964"><span class="lineNum">   19964 </span><span class="lineNoCov">          0 :                         c__[i__ + (*n - *k + j) * c_dim1] -= work[i__ + j * </span></a>
+<a name="19965"><span class="lineNum">   19965 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="19966"><span class="lineNum">   19966 </span>            :                     }</a>
+<a name="19967"><span class="lineNum">   19967 </span>            :                 }</a>
+<a name="19968"><span class="lineNum">   19968 </span>            :             }</a>
+<a name="19969"><span class="lineNum">   19969 </span>            :         }</a>
+<a name="19970"><span class="lineNum">   19970 </span>            : </a>
+<a name="19971"><span class="lineNum">   19971 </span><span class="lineNoCov">          0 :     } else  if (*storev=='r' || *storev=='R') {</span></a>
+<a name="19972"><span class="lineNum">   19972 </span><span class="lineNoCov">          0 :       if (*direct=='F' || *direct=='f') {</span></a>
+<a name="19973"><span class="lineNum">   19973 </span><span class="lineNoCov">          0 :           if (*side=='l' || *side=='L') {</span></a>
+<a name="19974"><span class="lineNum">   19974 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="19975"><span class="lineNum">   19975 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="19976"><span class="lineNum">   19976 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;c__[j + c_dim1], ldc, &amp;work[j * work_dim1 + 1],</span></a>
+<a name="19977"><span class="lineNum">   19977 </span>            :                              &amp;c__1);</a>
+<a name="19978"><span class="lineNum">   19978 </span>            :                 }</a>
+<a name="19979"><span class="lineNum">   19979 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="19980"><span class="lineNum">   19980 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="19981"><span class="lineNum">   19981 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="19982"><span class="lineNum">   19982 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="19983"><span class="lineNum">   19983 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="19984"><span class="lineNum">   19984 </span><span class="lineNoCov">          0 :                             c__[*k + 1 + c_dim1], ldc, &amp;v[(*k + 1) * v_dim1 + </span></a>
+<a name="19985"><span class="lineNum">   19985 </span><span class="lineNoCov">          0 :                             1], ldv, &amp;one, &amp;work[work_offset], ldwork);</span></a>
+<a name="19986"><span class="lineNum">   19986 </span>            :                 }</a>
+<a name="19987"><span class="lineNum">   19987 </span>            : </a>
+<a name="19988"><span class="lineNum">   19988 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="19989"><span class="lineNum">   19989 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="19990"><span class="lineNum">   19990 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="19991"><span class="lineNum">   19991 </span>            : </a>
+<a name="19992"><span class="lineNum">   19992 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="19993"><span class="lineNum">   19993 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;v[(</span></a>
+<a name="19994"><span class="lineNum">   19994 </span><span class="lineNoCov">          0 :                             *k + 1) * v_dim1 + 1], ldv, &amp;work[work_offset], </span></a>
+<a name="19995"><span class="lineNum">   19995 </span><span class="lineNoCov">          0 :                             ldwork, &amp;one, &amp;c__[*k + 1 + c_dim1], ldc);</span></a>
+<a name="19996"><span class="lineNum">   19996 </span>            :                 }</a>
+<a name="19997"><span class="lineNum">   19997 </span>            : </a>
+<a name="19998"><span class="lineNum">   19998 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="19999"><span class="lineNum">   19999 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="20000"><span class="lineNum">   20000 </span>            : </a>
+<a name="20001"><span class="lineNum">   20001 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20002"><span class="lineNum">   20002 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20003"><span class="lineNum">   20003 </span><span class="lineNoCov">          0 :                     i__2 = *n;</span></a>
+<a name="20004"><span class="lineNum">   20004 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20005"><span class="lineNum">   20005 </span><span class="lineNoCov">          0 :                         c__[j + i__ * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="20006"><span class="lineNum">   20006 </span>            :                     }</a>
+<a name="20007"><span class="lineNum">   20007 </span>            :                 }</a>
+<a name="20008"><span class="lineNum">   20008 </span>            : </a>
+<a name="20009"><span class="lineNum">   20009 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="20010"><span class="lineNum">   20010 </span>            : </a>
+<a name="20011"><span class="lineNum">   20011 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20012"><span class="lineNum">   20012 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20013"><span class="lineNum">   20013 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(m, &amp;c__[j * c_dim1 + 1], &amp;c__1, &amp;work[j * </span></a>
+<a name="20014"><span class="lineNum">   20014 </span><span class="lineNoCov">          0 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="20015"><span class="lineNum">   20015 </span>            :                 }</a>
+<a name="20016"><span class="lineNum">   20016 </span>            : </a>
+<a name="20017"><span class="lineNum">   20017 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="20018"><span class="lineNum">   20018 </span>            :                         v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="20019"><span class="lineNum">   20019 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="20020"><span class="lineNum">   20020 </span>            : </a>
+<a name="20021"><span class="lineNum">   20021 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="20022"><span class="lineNum">   20022 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="20023"><span class="lineNum">   20023 </span><span class="lineNoCov">          0 :                             c__[(*k + 1) * c_dim1 + 1], ldc, &amp;v[(*k + 1) * </span></a>
+<a name="20024"><span class="lineNum">   20024 </span><span class="lineNoCov">          0 :                             v_dim1 + 1], ldv, &amp;one, &amp;work[work_offset], </span></a>
+<a name="20025"><span class="lineNum">   20025 </span>            :                             ldwork);</a>
+<a name="20026"><span class="lineNum">   20026 </span>            :                 }</a>
+<a name="20027"><span class="lineNum">   20027 </span>            : </a>
+<a name="20028"><span class="lineNum">   20028 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="20029"><span class="lineNum">   20029 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="20030"><span class="lineNum">   20030 </span>            : </a>
+<a name="20031"><span class="lineNum">   20031 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="20032"><span class="lineNum">   20032 </span>            : </a>
+<a name="20033"><span class="lineNum">   20033 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="20034"><span class="lineNum">   20034 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, &amp;i__1, k, &amp;</span></a>
+<a name="20035"><span class="lineNum">   20035 </span><span class="lineNoCov">          0 :                             minusone, &amp;work[work_offset], ldwork, &amp;v[(*k + 1) * </span></a>
+<a name="20036"><span class="lineNum">   20036 </span><span class="lineNoCov">          0 :                             v_dim1 + 1], ldv, &amp;one, &amp;c__[(*k + 1) * c_dim1 </span></a>
+<a name="20037"><span class="lineNum">   20037 </span><span class="lineNoCov">          0 :                             + 1], ldc);</span></a>
+<a name="20038"><span class="lineNum">   20038 </span>            :                 }</a>
+<a name="20039"><span class="lineNum">   20039 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="20040"><span class="lineNum">   20040 </span>            :                          &amp;v[v_offset], ldv, &amp;work[work_offset], ldwork);</a>
+<a name="20041"><span class="lineNum">   20041 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20042"><span class="lineNum">   20042 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20043"><span class="lineNum">   20043 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="20044"><span class="lineNum">   20044 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20045"><span class="lineNum">   20045 </span><span class="lineNoCov">          0 :                         c__[i__ + j * c_dim1] -= work[i__ + j * work_dim1];</span></a>
+<a name="20046"><span class="lineNum">   20046 </span>            :                     }</a>
+<a name="20047"><span class="lineNum">   20047 </span>            :                 }</a>
+<a name="20048"><span class="lineNum">   20048 </span>            : </a>
+<a name="20049"><span class="lineNum">   20049 </span>            :             }</a>
+<a name="20050"><span class="lineNum">   20050 </span>            : </a>
+<a name="20051"><span class="lineNum">   20051 </span>            :         } else {</a>
+<a name="20052"><span class="lineNum">   20052 </span>            : </a>
+<a name="20053"><span class="lineNum">   20053 </span><span class="lineNoCov">          0 :             if (*side=='l' || *side=='L') {</span></a>
+<a name="20054"><span class="lineNum">   20054 </span>            : </a>
+<a name="20055"><span class="lineNum">   20055 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20056"><span class="lineNum">   20056 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20057"><span class="lineNum">   20057 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;c__[*m - *k + j + c_dim1], ldc, &amp;work[j * </span></a>
+<a name="20058"><span class="lineNum">   20058 </span><span class="lineNoCov">          0 :                             work_dim1 + 1], &amp;c__1);</span></a>
+<a name="20059"><span class="lineNum">   20059 </span>            :                 }</a>
+<a name="20060"><span class="lineNum">   20060 </span>            : </a>
+<a name="20061"><span class="lineNum">   20061 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, n, k, &amp;one, &amp;</span></a>
+<a name="20062"><span class="lineNum">   20062 </span><span class="lineNoCov">          0 :                         v[(*m - *k + 1) * v_dim1 + 1], ldv, &amp;work[work_offset]</span></a>
+<a name="20063"><span class="lineNum">   20063 </span>            :                         , ldwork);</a>
+<a name="20064"><span class="lineNum">   20064 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="20065"><span class="lineNum">   20065 </span>            : </a>
+<a name="20066"><span class="lineNum">   20066 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="20067"><span class="lineNum">   20067 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, n, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="20068"><span class="lineNum">   20068 </span>            :                             c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;one, &amp;</a>
+<a name="20069"><span class="lineNum">   20069 </span>            :                             work[work_offset], ldwork);</a>
+<a name="20070"><span class="lineNum">   20070 </span>            :                 }</a>
+<a name="20071"><span class="lineNum">   20071 </span>            : </a>
+<a name="20072"><span class="lineNum">   20072 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, transt, &quot;Non-unit&quot;, n, k, &amp;one, &amp;t[</span></a>
+<a name="20073"><span class="lineNum">   20073 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="20074"><span class="lineNum">   20074 </span>            : </a>
+<a name="20075"><span class="lineNum">   20075 </span><span class="lineNoCov">          0 :                 if (*m &gt; *k) {</span></a>
+<a name="20076"><span class="lineNum">   20076 </span>            : </a>
+<a name="20077"><span class="lineNum">   20077 </span><span class="lineNoCov">          0 :                     i__1 = *m - *k;</span></a>
+<a name="20078"><span class="lineNum">   20078 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;Transpose&quot;, &quot;Transpose&quot;, &amp;i__1, n, k, &amp;minusone, &amp;v[</span></a>
+<a name="20079"><span class="lineNum">   20079 </span>            :                             v_offset], ldv, &amp;work[work_offset], ldwork, &amp;</a>
+<a name="20080"><span class="lineNum">   20080 </span>            :                             one, &amp;c__[c_offset], ldc);</a>
+<a name="20081"><span class="lineNum">   20081 </span>            :                 }</a>
+<a name="20082"><span class="lineNum">   20082 </span>            : </a>
+<a name="20083"><span class="lineNum">   20083 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, n, k, &amp;one,</span></a>
+<a name="20084"><span class="lineNum">   20084 </span><span class="lineNoCov">          0 :                          &amp;v[(*m - *k + 1) * v_dim1 + 1], ldv, &amp;work[</span></a>
+<a name="20085"><span class="lineNum">   20085 </span>            :                         work_offset], ldwork);</a>
+<a name="20086"><span class="lineNum">   20086 </span>            : </a>
+<a name="20087"><span class="lineNum">   20087 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20088"><span class="lineNum">   20088 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20089"><span class="lineNum">   20089 </span><span class="lineNoCov">          0 :                     i__2 = *n;</span></a>
+<a name="20090"><span class="lineNum">   20090 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20091"><span class="lineNum">   20091 </span><span class="lineNoCov">          0 :                         c__[*m - *k + j + i__ * c_dim1] -= work[i__ + j * </span></a>
+<a name="20092"><span class="lineNum">   20092 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="20093"><span class="lineNum">   20093 </span>            :                     }</a>
+<a name="20094"><span class="lineNum">   20094 </span>            :                 }</a>
+<a name="20095"><span class="lineNum">   20095 </span>            : </a>
+<a name="20096"><span class="lineNum">   20096 </span><span class="lineNoCov">          0 :             } else if (*side=='r' || *side=='R') {</span></a>
+<a name="20097"><span class="lineNum">   20097 </span>            : </a>
+<a name="20098"><span class="lineNum">   20098 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20099"><span class="lineNum">   20099 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20100"><span class="lineNum">   20100 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(m, &amp;c__[(*n - *k + j) * c_dim1 + 1], &amp;c__1, &amp;work[</span></a>
+<a name="20101"><span class="lineNum">   20101 </span><span class="lineNoCov">          0 :                             j * work_dim1 + 1], &amp;c__1);</span></a>
+<a name="20102"><span class="lineNum">   20102 </span>            :                 }</a>
+<a name="20103"><span class="lineNum">   20103 </span>            : </a>
+<a name="20104"><span class="lineNum">   20104 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;Transpose&quot;, &quot;Unit&quot;, m, k, &amp;one, &amp;</span></a>
+<a name="20105"><span class="lineNum">   20105 </span><span class="lineNoCov">          0 :                         v[(*n - *k + 1) * v_dim1 + 1], ldv, &amp;work[work_offset]</span></a>
+<a name="20106"><span class="lineNum">   20106 </span>            :                         , ldwork);</a>
+<a name="20107"><span class="lineNum">   20107 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="20108"><span class="lineNum">   20108 </span>            : </a>
+<a name="20109"><span class="lineNum">   20109 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="20110"><span class="lineNum">   20110 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;Transpose&quot;, m, k, &amp;i__1, &amp;one, &amp;</span></a>
+<a name="20111"><span class="lineNum">   20111 </span>            :                             c__[c_offset], ldc, &amp;v[v_offset], ldv, &amp;one, &amp;</a>
+<a name="20112"><span class="lineNum">   20112 </span>            :                             work[work_offset], ldwork);</a>
+<a name="20113"><span class="lineNum">   20113 </span>            :                 }</a>
+<a name="20114"><span class="lineNum">   20114 </span>            : </a>
+<a name="20115"><span class="lineNum">   20115 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, trans, &quot;Non-unit&quot;, m, k, &amp;one, &amp;t[</span></a>
+<a name="20116"><span class="lineNum">   20116 </span>            :                         t_offset], ldt, &amp;work[work_offset], ldwork);</a>
+<a name="20117"><span class="lineNum">   20117 </span>            : </a>
+<a name="20118"><span class="lineNum">   20118 </span><span class="lineNoCov">          0 :                 if (*n &gt; *k) {</span></a>
+<a name="20119"><span class="lineNum">   20119 </span>            : </a>
+<a name="20120"><span class="lineNum">   20120 </span><span class="lineNoCov">          0 :                     i__1 = *n - *k;</span></a>
+<a name="20121"><span class="lineNum">   20121 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;No transpose&quot;, &quot;No transpose&quot;, m, &amp;i__1, k, &amp;</span></a>
+<a name="20122"><span class="lineNum">   20122 </span>            :                             minusone, &amp;work[work_offset], ldwork, &amp;v[v_offset], </a>
+<a name="20123"><span class="lineNum">   20123 </span>            :                             ldv, &amp;one, &amp;c__[c_offset], ldc);</a>
+<a name="20124"><span class="lineNum">   20124 </span>            :                 }</a>
+<a name="20125"><span class="lineNum">   20125 </span>            : </a>
+<a name="20126"><span class="lineNum">   20126 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, &quot;Unit&quot;, m, k, &amp;one,</span></a>
+<a name="20127"><span class="lineNum">   20127 </span><span class="lineNoCov">          0 :                          &amp;v[(*n - *k + 1) * v_dim1 + 1], ldv, &amp;work[</span></a>
+<a name="20128"><span class="lineNum">   20128 </span>            :                         work_offset], ldwork);</a>
+<a name="20129"><span class="lineNum">   20129 </span>            : </a>
+<a name="20130"><span class="lineNum">   20130 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20131"><span class="lineNum">   20131 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20132"><span class="lineNum">   20132 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="20133"><span class="lineNum">   20133 </span><span class="lineNoCov">          0 :                     for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20134"><span class="lineNum">   20134 </span><span class="lineNoCov">          0 :                         c__[i__ + (*n - *k + j) * c_dim1] -= work[i__ + j * </span></a>
+<a name="20135"><span class="lineNum">   20135 </span><span class="lineNoCov">          0 :                                 work_dim1];</span></a>
+<a name="20136"><span class="lineNum">   20136 </span>            :                     }</a>
+<a name="20137"><span class="lineNum">   20137 </span>            :                 }</a>
+<a name="20138"><span class="lineNum">   20138 </span>            : </a>
+<a name="20139"><span class="lineNum">   20139 </span>            :             }</a>
+<a name="20140"><span class="lineNum">   20140 </span>            : </a>
+<a name="20141"><span class="lineNum">   20141 </span>            :         }</a>
+<a name="20142"><span class="lineNum">   20142 </span>            :     }</a>
+<a name="20143"><span class="lineNum">   20143 </span>            : </a>
+<a name="20144"><span class="lineNum">   20144 </span>            :     return;</a>
+<a name="20145"><span class="lineNum">   20145 </span>            : </a>
+<a name="20146"><span class="lineNum">   20146 </span>            : </a>
+<a name="20147"><span class="lineNum">   20147 </span>            : }</a>
+<a name="20148"><span class="lineNum">   20148 </span>            : </a>
+<a name="20149"><span class="lineNum">   20149 </span>            : }</a>
+<a name="20150"><span class="lineNum">   20150 </span>            : }</a>
+<a name="20151"><span class="lineNum">   20151 </span>            : #include &lt;cmath&gt;</a>
+<a name="20152"><span class="lineNum">   20152 </span>            : #include &quot;real.h&quot;</a>
+<a name="20153"><span class="lineNum">   20153 </span>            : </a>
+<a name="20154"><span class="lineNum">   20154 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20155"><span class="lineNum">   20155 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="20156"><span class="lineNum">   20156 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="20157"><span class="lineNum">   20157 </span>            : </a>
+<a name="20158"><span class="lineNum">   20158 </span>            : </a>
+<a name="20159"><span class="lineNum">   20159 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20160"><span class="lineNum">   20160 </span>            : namespace PLMD{</a>
+<a name="20161"><span class="lineNum">   20161 </span>            : namespace lapack{</a>
+<a name="20162"><span class="lineNum">   20162 </span>            : using namespace blas;</a>
+<a name="20163"><span class="lineNum">   20163 </span>            : void</a>
+<a name="20164"><span class="lineNum">   20164 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(int   *n,</span></a>
+<a name="20165"><span class="lineNum">   20165 </span>            :                         float *alpha,</a>
+<a name="20166"><span class="lineNum">   20166 </span>            :                         float *x,</a>
+<a name="20167"><span class="lineNum">   20167 </span>            :                         int    *incx,</a>
+<a name="20168"><span class="lineNum">   20168 </span>            :                         float *tau)</a>
+<a name="20169"><span class="lineNum">   20169 </span>            : {</a>
+<a name="20170"><span class="lineNum">   20170 </span>            :   float xnorm,t;</a>
+<a name="20171"><span class="lineNum">   20171 </span>            :   int    ti1,knt,j;</a>
+<a name="20172"><span class="lineNum">   20172 </span>            :   float minval,safmin,rsafmn,beta;</a>
+<a name="20173"><span class="lineNum">   20173 </span>            : </a>
+<a name="20174"><span class="lineNum">   20174 </span><span class="lineNoCov">          0 :   if(*n&lt;=1) {</span></a>
+<a name="20175"><span class="lineNum">   20175 </span><span class="lineNoCov">          0 :     *tau = 0;</span></a>
+<a name="20176"><span class="lineNum">   20176 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="20177"><span class="lineNum">   20177 </span>            :   }</a>
+<a name="20178"><span class="lineNum">   20178 </span>            : </a>
+<a name="20179"><span class="lineNum">   20179 </span><span class="lineNoCov">          0 :   ti1 = *n-1;</span></a>
+<a name="20180"><span class="lineNum">   20180 </span>            : </a>
+<a name="20181"><span class="lineNum">   20181 </span><span class="lineNoCov">          0 :   xnorm = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(&amp;ti1,x,incx);</span></a>
+<a name="20182"><span class="lineNum">   20182 </span>            : </a>
+<a name="20183"><span class="lineNum">   20183 </span><span class="lineNoCov">          0 :   if(std::abs(xnorm)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="20184"><span class="lineNum">   20184 </span><span class="lineNoCov">          0 :     *tau = 0.0;</span></a>
+<a name="20185"><span class="lineNum">   20185 </span>            :   } else {</a>
+<a name="20186"><span class="lineNum">   20186 </span>            : </a>
+<a name="20187"><span class="lineNum">   20187 </span><span class="lineNoCov">          0 :     t = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(alpha,&amp;xnorm);</span></a>
+<a name="20188"><span class="lineNum">   20188 </span>            : </a>
+<a name="20189"><span class="lineNum">   20189 </span><span class="lineNoCov">          0 :     if(*alpha&lt;0)</span></a>
+<a name="20190"><span class="lineNum">   20190 </span>            :       beta = t;</a>
+<a name="20191"><span class="lineNum">   20191 </span>            :     else</a>
+<a name="20192"><span class="lineNum">   20192 </span><span class="lineNoCov">          0 :       beta = -t;</span></a>
+<a name="20193"><span class="lineNum">   20193 </span>            : </a>
+<a name="20194"><span class="lineNum">   20194 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="20195"><span class="lineNum">   20195 </span>            :     </a>
+<a name="20196"><span class="lineNum">   20196 </span>            :     safmin = minval*(1.0+PLUMED_GMX_FLOAT_EPS) / PLUMED_GMX_FLOAT_EPS;</a>
+<a name="20197"><span class="lineNum">   20197 </span>            : </a>
+<a name="20198"><span class="lineNum">   20198 </span>            :         </a>
+<a name="20199"><span class="lineNum">   20199 </span><span class="lineNoCov">          0 :     if(std::abs(beta)&lt;safmin) {</span></a>
+<a name="20200"><span class="lineNum">   20200 </span>            : </a>
+<a name="20201"><span class="lineNum">   20201 </span>            :       knt = 0;</a>
+<a name="20202"><span class="lineNum">   20202 </span><span class="lineNoCov">          0 :       rsafmn = 1.0 / safmin;</span></a>
+<a name="20203"><span class="lineNum">   20203 </span>            :       </a>
+<a name="20204"><span class="lineNum">   20204 </span><span class="lineNoCov">          0 :       while(std::abs(beta)&lt;safmin) {</span></a>
+<a name="20205"><span class="lineNum">   20205 </span><span class="lineNoCov">          0 :         knt++;</span></a>
+<a name="20206"><span class="lineNum">   20206 </span><span class="lineNoCov">          0 :         ti1 = *n-1;</span></a>
+<a name="20207"><span class="lineNum">   20207 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;ti1,&amp;rsafmn,x,incx);</span></a>
+<a name="20208"><span class="lineNum">   20208 </span><span class="lineNoCov">          0 :         beta *= rsafmn;</span></a>
+<a name="20209"><span class="lineNum">   20209 </span><span class="lineNoCov">          0 :         *alpha *= rsafmn;</span></a>
+<a name="20210"><span class="lineNum">   20210 </span>            :       }</a>
+<a name="20211"><span class="lineNum">   20211 </span>            :       </a>
+<a name="20212"><span class="lineNum">   20212 </span>            :       /* safmin &lt;= beta &lt;= 1 now */</a>
+<a name="20213"><span class="lineNum">   20213 </span><span class="lineNoCov">          0 :       ti1 = *n-1;</span></a>
+<a name="20214"><span class="lineNum">   20214 </span><span class="lineNoCov">          0 :       xnorm = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(&amp;ti1,x,incx);</span></a>
+<a name="20215"><span class="lineNum">   20215 </span><span class="lineNoCov">          0 :       t = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(alpha,&amp;xnorm);</span></a>
+<a name="20216"><span class="lineNum">   20216 </span>            :       </a>
+<a name="20217"><span class="lineNum">   20217 </span><span class="lineNoCov">          0 :       if(*alpha&lt;0)</span></a>
+<a name="20218"><span class="lineNum">   20218 </span>            :         beta = t;</a>
+<a name="20219"><span class="lineNum">   20219 </span>            :       else</a>
+<a name="20220"><span class="lineNum">   20220 </span><span class="lineNoCov">          0 :         beta = -t;</span></a>
+<a name="20221"><span class="lineNum">   20221 </span>            :       </a>
+<a name="20222"><span class="lineNum">   20222 </span><span class="lineNoCov">          0 :       *tau = (beta-*alpha)/beta;</span></a>
+<a name="20223"><span class="lineNum">   20223 </span>            : </a>
+<a name="20224"><span class="lineNum">   20224 </span><span class="lineNoCov">          0 :       ti1= *n-1;</span></a>
+<a name="20225"><span class="lineNum">   20225 </span><span class="lineNoCov">          0 :       t = 1.0/(*alpha-beta);</span></a>
+<a name="20226"><span class="lineNum">   20226 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;ti1,&amp;t,x,incx);</span></a>
+<a name="20227"><span class="lineNum">   20227 </span>            :    </a>
+<a name="20228"><span class="lineNum">   20228 </span><span class="lineNoCov">          0 :       *alpha = beta;</span></a>
+<a name="20229"><span class="lineNum">   20229 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;knt;j++)</span></a>
+<a name="20230"><span class="lineNum">   20230 </span><span class="lineNoCov">          0 :         *alpha *= safmin;</span></a>
+<a name="20231"><span class="lineNum">   20231 </span>            :     } else {</a>
+<a name="20232"><span class="lineNum">   20232 </span><span class="lineNoCov">          0 :       *tau = (beta-*alpha)/beta;</span></a>
+<a name="20233"><span class="lineNum">   20233 </span><span class="lineNoCov">          0 :       ti1= *n-1;</span></a>
+<a name="20234"><span class="lineNum">   20234 </span><span class="lineNoCov">          0 :       t = 1.0/(*alpha-beta);</span></a>
+<a name="20235"><span class="lineNum">   20235 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;ti1,&amp;t,x,incx);</span></a>
+<a name="20236"><span class="lineNum">   20236 </span><span class="lineNoCov">          0 :       *alpha = beta;</span></a>
+<a name="20237"><span class="lineNum">   20237 </span>            :     }</a>
+<a name="20238"><span class="lineNum">   20238 </span>            :   }</a>
+<a name="20239"><span class="lineNum">   20239 </span>            :    </a>
+<a name="20240"><span class="lineNum">   20240 </span>            :   return;</a>
+<a name="20241"><span class="lineNum">   20241 </span>            : }</a>
+<a name="20242"><span class="lineNum">   20242 </span>            : }</a>
+<a name="20243"><span class="lineNum">   20243 </span>            : }</a>
+<a name="20244"><span class="lineNum">   20244 </span>            : #include &lt;cmath&gt;</a>
+<a name="20245"><span class="lineNum">   20245 </span>            : #include &quot;real.h&quot;</a>
+<a name="20246"><span class="lineNum">   20246 </span>            : </a>
+<a name="20247"><span class="lineNum">   20247 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20248"><span class="lineNum">   20248 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="20249"><span class="lineNum">   20249 </span>            : </a>
+<a name="20250"><span class="lineNum">   20250 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20251"><span class="lineNum">   20251 </span>            : namespace PLMD{</a>
+<a name="20252"><span class="lineNum">   20252 </span>            : namespace lapack{</a>
+<a name="20253"><span class="lineNum">   20253 </span>            : using namespace blas;</a>
+<a name="20254"><span class="lineNum">   20254 </span>            : void </a>
+<a name="20255"><span class="lineNum">   20255 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(const char *direct, </span></a>
+<a name="20256"><span class="lineNum">   20256 </span>            :         const char *storev, </a>
+<a name="20257"><span class="lineNum">   20257 </span>            :         int *n, </a>
+<a name="20258"><span class="lineNum">   20258 </span>            :         int *k, </a>
+<a name="20259"><span class="lineNum">   20259 </span>            :         float *v, </a>
+<a name="20260"><span class="lineNum">   20260 </span>            :         int *ldv, </a>
+<a name="20261"><span class="lineNum">   20261 </span>            :         float *tau, </a>
+<a name="20262"><span class="lineNum">   20262 </span>            :         float *t, </a>
+<a name="20263"><span class="lineNum">   20263 </span>            :         int *ldt)</a>
+<a name="20264"><span class="lineNum">   20264 </span>            : {</a>
+<a name="20265"><span class="lineNum">   20265 </span>            :     /* System generated locals */</a>
+<a name="20266"><span class="lineNum">   20266 </span>            :     int t_dim1, t_offset, v_dim1, v_offset, i__1, i__2, i__3;</a>
+<a name="20267"><span class="lineNum">   20267 </span>            :     float d__1;</a>
+<a name="20268"><span class="lineNum">   20268 </span>            : </a>
+<a name="20269"><span class="lineNum">   20269 </span>            :     /* Local variables */</a>
+<a name="20270"><span class="lineNum">   20270 </span>            :     int i__, j;</a>
+<a name="20271"><span class="lineNum">   20271 </span>            :     float vii;</a>
+<a name="20272"><span class="lineNum">   20272 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="20273"><span class="lineNum">   20273 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="20274"><span class="lineNum">   20274 </span>            : </a>
+<a name="20275"><span class="lineNum">   20275 </span><span class="lineNoCov">          0 :     v_dim1 = *ldv;</span></a>
+<a name="20276"><span class="lineNum">   20276 </span><span class="lineNoCov">          0 :     v_offset = 1 + v_dim1;</span></a>
+<a name="20277"><span class="lineNum">   20277 </span><span class="lineNoCov">          0 :     v -= v_offset;</span></a>
+<a name="20278"><span class="lineNum">   20278 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="20279"><span class="lineNum">   20279 </span><span class="lineNoCov">          0 :     t_dim1 = *ldt;</span></a>
+<a name="20280"><span class="lineNum">   20280 </span><span class="lineNoCov">          0 :     t_offset = 1 + t_dim1;</span></a>
+<a name="20281"><span class="lineNum">   20281 </span><span class="lineNoCov">          0 :     t -= t_offset;</span></a>
+<a name="20282"><span class="lineNum">   20282 </span>            : </a>
+<a name="20283"><span class="lineNum">   20283 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="20284"><span class="lineNum">   20284 </span>            :         return;</a>
+<a name="20285"><span class="lineNum">   20285 </span>            :     }</a>
+<a name="20286"><span class="lineNum">   20286 </span>            : </a>
+<a name="20287"><span class="lineNum">   20287 </span><span class="lineNoCov">          0 :     if (*direct=='F' || *direct=='f') {</span></a>
+<a name="20288"><span class="lineNum">   20288 </span><span class="lineNoCov">          0 :         i__1 = *k;</span></a>
+<a name="20289"><span class="lineNum">   20289 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="20290"><span class="lineNum">   20290 </span><span class="lineNoCov">          0 :             if (std::abs(tau[i__])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="20291"><span class="lineNum">   20291 </span>            : </a>
+<a name="20292"><span class="lineNum">   20292 </span><span class="lineNoCov">          0 :                 i__2 = i__;</span></a>
+<a name="20293"><span class="lineNum">   20293 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="20294"><span class="lineNum">   20294 </span><span class="lineNoCov">          0 :                     t[j + i__ * t_dim1] = 0.;</span></a>
+<a name="20295"><span class="lineNum">   20295 </span>            :                 }</a>
+<a name="20296"><span class="lineNum">   20296 </span>            :             } else {</a>
+<a name="20297"><span class="lineNum">   20297 </span>            : </a>
+<a name="20298"><span class="lineNum">   20298 </span><span class="lineNoCov">          0 :                 vii = v[i__ + i__ * v_dim1];</span></a>
+<a name="20299"><span class="lineNum">   20299 </span><span class="lineNoCov">          0 :                 v[i__ + i__ * v_dim1] = 1.;</span></a>
+<a name="20300"><span class="lineNum">   20300 </span><span class="lineNoCov">          0 :                 if (*storev=='C' || *storev=='c') {</span></a>
+<a name="20301"><span class="lineNum">   20301 </span>            : </a>
+<a name="20302"><span class="lineNum">   20302 </span><span class="lineNoCov">          0 :                     i__2 = *n - i__ + 1;</span></a>
+<a name="20303"><span class="lineNum">   20303 </span><span class="lineNoCov">          0 :                     i__3 = i__ - 1;</span></a>
+<a name="20304"><span class="lineNum">   20304 </span><span class="lineNoCov">          0 :                     d__1 = -tau[i__];</span></a>
+<a name="20305"><span class="lineNum">   20305 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__2, &amp;i__3, &amp;d__1, &amp;v[i__ + v_dim1],</span></a>
+<a name="20306"><span class="lineNum">   20306 </span>            :                              ldv, &amp;v[i__ + i__ * v_dim1], &amp;c__1, &amp;zero, &amp;t[</a>
+<a name="20307"><span class="lineNum">   20307 </span><span class="lineNoCov">          0 :                             i__ * t_dim1 + 1], &amp;c__1);</span></a>
+<a name="20308"><span class="lineNum">   20308 </span>            :                 } else {</a>
+<a name="20309"><span class="lineNum">   20309 </span>            : </a>
+<a name="20310"><span class="lineNum">   20310 </span><span class="lineNoCov">          0 :                     i__2 = i__ - 1;</span></a>
+<a name="20311"><span class="lineNum">   20311 </span><span class="lineNoCov">          0 :                     i__3 = *n - i__ + 1;</span></a>
+<a name="20312"><span class="lineNum">   20312 </span><span class="lineNoCov">          0 :                     d__1 = -tau[i__];</span></a>
+<a name="20313"><span class="lineNum">   20313 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__2, &amp;i__3, &amp;d__1, &amp;v[i__ * </span></a>
+<a name="20314"><span class="lineNum">   20314 </span><span class="lineNoCov">          0 :                             v_dim1 + 1], ldv, &amp;v[i__ + i__ * v_dim1], ldv, &amp;</span></a>
+<a name="20315"><span class="lineNum">   20315 </span><span class="lineNoCov">          0 :                             zero, &amp;t[i__ * t_dim1 + 1], &amp;c__1);</span></a>
+<a name="20316"><span class="lineNum">   20316 </span>            :                 }</a>
+<a name="20317"><span class="lineNum">   20317 </span><span class="lineNoCov">          0 :                 v[i__ + i__ * v_dim1] = vii;</span></a>
+<a name="20318"><span class="lineNum">   20318 </span>            : </a>
+<a name="20319"><span class="lineNum">   20319 </span>            : </a>
+<a name="20320"><span class="lineNum">   20320 </span><span class="lineNoCov">          0 :                 i__2 = i__ - 1;</span></a>
+<a name="20321"><span class="lineNum">   20321 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmv,STRMV)(&quot;Upper&quot;, &quot;No transpose&quot;, &quot;Non-unit&quot;, &amp;i__2, &amp;t[</span></a>
+<a name="20322"><span class="lineNum">   20322 </span><span class="lineNoCov">          0 :                         t_offset], ldt, &amp;t[i__ * t_dim1 + 1], &amp;c__1);</span></a>
+<a name="20323"><span class="lineNum">   20323 </span><span class="lineNoCov">          0 :                 t[i__ + i__ * t_dim1] = tau[i__];</span></a>
+<a name="20324"><span class="lineNum">   20324 </span>            :             }</a>
+<a name="20325"><span class="lineNum">   20325 </span>            :         }</a>
+<a name="20326"><span class="lineNum">   20326 </span>            :     } else {</a>
+<a name="20327"><span class="lineNum">   20327 </span><span class="lineNoCov">          0 :         for (i__ = *k; i__ &gt;= 1; --i__) {</span></a>
+<a name="20328"><span class="lineNum">   20328 </span><span class="lineNoCov">          0 :             if (std::abs(tau[i__])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="20329"><span class="lineNum">   20329 </span>            : </a>
+<a name="20330"><span class="lineNum">   20330 </span><span class="lineNoCov">          0 :                 i__1 = *k;</span></a>
+<a name="20331"><span class="lineNum">   20331 </span><span class="lineNoCov">          0 :                 for (j = i__; j &lt;= i__1; ++j) {</span></a>
+<a name="20332"><span class="lineNum">   20332 </span><span class="lineNoCov">          0 :                     t[j + i__ * t_dim1] = 0.;</span></a>
+<a name="20333"><span class="lineNum">   20333 </span>            :                 }</a>
+<a name="20334"><span class="lineNum">   20334 </span>            :             } else {</a>
+<a name="20335"><span class="lineNum">   20335 </span>            : </a>
+<a name="20336"><span class="lineNum">   20336 </span><span class="lineNoCov">          0 :                 if (i__ &lt; *k) {</span></a>
+<a name="20337"><span class="lineNum">   20337 </span><span class="lineNoCov">          0 :                     if (*storev=='C' || *storev=='c') {</span></a>
+<a name="20338"><span class="lineNum">   20338 </span><span class="lineNoCov">          0 :                         vii = v[*n - *k + i__ + i__ * v_dim1];</span></a>
+<a name="20339"><span class="lineNum">   20339 </span><span class="lineNoCov">          0 :                         v[*n - *k + i__ + i__ * v_dim1] = 1.;</span></a>
+<a name="20340"><span class="lineNum">   20340 </span>            : </a>
+<a name="20341"><span class="lineNum">   20341 </span><span class="lineNoCov">          0 :                         i__1 = *n - *k + i__;</span></a>
+<a name="20342"><span class="lineNum">   20342 </span><span class="lineNoCov">          0 :                         i__2 = *k - i__;</span></a>
+<a name="20343"><span class="lineNum">   20343 </span><span class="lineNoCov">          0 :                         d__1 = -tau[i__];</span></a>
+<a name="20344"><span class="lineNum">   20344 </span><span class="lineNoCov">          0 :                         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;Transpose&quot;, &amp;i__1, &amp;i__2, &amp;d__1, &amp;v[(i__ + 1) </span></a>
+<a name="20345"><span class="lineNum">   20345 </span><span class="lineNoCov">          0 :                                 * v_dim1 + 1], ldv, &amp;v[i__ * v_dim1 + 1], &amp;</span></a>
+<a name="20346"><span class="lineNum">   20346 </span><span class="lineNoCov">          0 :                                 c__1, &amp;zero, &amp;t[i__ + 1 + i__ * t_dim1], &amp;</span></a>
+<a name="20347"><span class="lineNum">   20347 </span>            :                                 c__1);</a>
+<a name="20348"><span class="lineNum">   20348 </span><span class="lineNoCov">          0 :                         v[*n - *k + i__ + i__ * v_dim1] = vii;</span></a>
+<a name="20349"><span class="lineNum">   20349 </span>            :                     } else {</a>
+<a name="20350"><span class="lineNum">   20350 </span><span class="lineNoCov">          0 :                         vii = v[i__ + (*n - *k + i__) * v_dim1];</span></a>
+<a name="20351"><span class="lineNum">   20351 </span><span class="lineNoCov">          0 :                         v[i__ + (*n - *k + i__) * v_dim1] = 1.;</span></a>
+<a name="20352"><span class="lineNum">   20352 </span>            : </a>
+<a name="20353"><span class="lineNum">   20353 </span><span class="lineNoCov">          0 :                         i__1 = *k - i__;</span></a>
+<a name="20354"><span class="lineNum">   20354 </span><span class="lineNoCov">          0 :                         i__2 = *n - *k + i__;</span></a>
+<a name="20355"><span class="lineNum">   20355 </span><span class="lineNoCov">          0 :                         d__1 = -tau[i__];</span></a>
+<a name="20356"><span class="lineNum">   20356 </span><span class="lineNoCov">          0 :                         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;No transpose&quot;, &amp;i__1, &amp;i__2, &amp;d__1, &amp;v[i__ + </span></a>
+<a name="20357"><span class="lineNum">   20357 </span><span class="lineNoCov">          0 :                                 1 + v_dim1], ldv, &amp;v[i__ + v_dim1], ldv, &amp;</span></a>
+<a name="20358"><span class="lineNum">   20358 </span><span class="lineNoCov">          0 :                                 zero, &amp;t[i__ + 1 + i__ * t_dim1], &amp;c__1);</span></a>
+<a name="20359"><span class="lineNum">   20359 </span><span class="lineNoCov">          0 :                         v[i__ + (*n - *k + i__) * v_dim1] = vii;</span></a>
+<a name="20360"><span class="lineNum">   20360 </span>            :                     }</a>
+<a name="20361"><span class="lineNum">   20361 </span>            : </a>
+<a name="20362"><span class="lineNum">   20362 </span><span class="lineNoCov">          0 :                     i__1 = *k - i__;</span></a>
+<a name="20363"><span class="lineNum">   20363 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(strmv,STRMV)(&quot;Lower&quot;, &quot;No transpose&quot;, &quot;Non-unit&quot;, &amp;i__1, &amp;t[i__ </span></a>
+<a name="20364"><span class="lineNum">   20364 </span><span class="lineNoCov">          0 :                             + 1 + (i__ + 1) * t_dim1], ldt, &amp;t[i__ + 1 + i__ *</span></a>
+<a name="20365"><span class="lineNum">   20365 </span><span class="lineNoCov">          0 :                              t_dim1], &amp;c__1)</span></a>
+<a name="20366"><span class="lineNum">   20366 </span>            :                             ;</a>
+<a name="20367"><span class="lineNum">   20367 </span>            :                 }</a>
+<a name="20368"><span class="lineNum">   20368 </span><span class="lineNoCov">          0 :                 t[i__ + i__ * t_dim1] = tau[i__];</span></a>
+<a name="20369"><span class="lineNum">   20369 </span>            :             }</a>
+<a name="20370"><span class="lineNum">   20370 </span>            :         }</a>
+<a name="20371"><span class="lineNum">   20371 </span>            :     }</a>
+<a name="20372"><span class="lineNum">   20372 </span>            :     return;</a>
+<a name="20373"><span class="lineNum">   20373 </span>            : </a>
+<a name="20374"><span class="lineNum">   20374 </span>            : </a>
+<a name="20375"><span class="lineNum">   20375 </span>            : }</a>
+<a name="20376"><span class="lineNum">   20376 </span>            : }</a>
+<a name="20377"><span class="lineNum">   20377 </span>            : }</a>
+<a name="20378"><span class="lineNum">   20378 </span>            : #include &lt;cmath&gt;</a>
+<a name="20379"><span class="lineNum">   20379 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="20380"><span class="lineNum">   20380 </span>            : </a>
+<a name="20381"><span class="lineNum">   20381 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20382"><span class="lineNum">   20382 </span>            : namespace PLMD{</a>
+<a name="20383"><span class="lineNum">   20383 </span>            : namespace lapack{</a>
+<a name="20384"><span class="lineNum">   20384 </span>            : using namespace blas;</a>
+<a name="20385"><span class="lineNum">   20385 </span>            : void</a>
+<a name="20386"><span class="lineNum">   20386 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarnv,SLARNV)(int *idist, </span></a>
+<a name="20387"><span class="lineNum">   20387 </span>            :         int *iseed, </a>
+<a name="20388"><span class="lineNum">   20388 </span>            :         int *n, </a>
+<a name="20389"><span class="lineNum">   20389 </span>            :         float *x)</a>
+<a name="20390"><span class="lineNum">   20390 </span>            : {</a>
+<a name="20391"><span class="lineNum">   20391 </span>            :     int i__1, i__2, i__3;</a>
+<a name="20392"><span class="lineNum">   20392 </span>            : </a>
+<a name="20393"><span class="lineNum">   20393 </span>            :     int i__;</a>
+<a name="20394"><span class="lineNum">   20394 </span>            :     float u[128];</a>
+<a name="20395"><span class="lineNum">   20395 </span>            :     int il, iv, il2;</a>
+<a name="20396"><span class="lineNum">   20396 </span>            : </a>
+<a name="20397"><span class="lineNum">   20397 </span><span class="lineNoCov">          0 :     --x;</span></a>
+<a name="20398"><span class="lineNum">   20398 </span>            :     --iseed;</a>
+<a name="20399"><span class="lineNum">   20399 </span>            : </a>
+<a name="20400"><span class="lineNum">   20400 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="20401"><span class="lineNum">   20401 </span><span class="lineNoCov">          0 :     for (iv = 1; iv &lt;= i__1; iv += 64) {</span></a>
+<a name="20402"><span class="lineNum">   20402 </span><span class="lineNoCov">          0 :         i__2 = 64, i__3 = *n - iv + 1;</span></a>
+<a name="20403"><span class="lineNum">   20403 </span>            :         il = (i__2&lt;i__3) ? i__2 : i__3;</a>
+<a name="20404"><span class="lineNum">   20404 </span><span class="lineNoCov">          0 :         if (*idist == 3) {</span></a>
+<a name="20405"><span class="lineNum">   20405 </span><span class="lineNoCov">          0 :             il2 = il &lt;&lt; 1;</span></a>
+<a name="20406"><span class="lineNum">   20406 </span>            :         } else {</a>
+<a name="20407"><span class="lineNum">   20407 </span><span class="lineNoCov">          0 :             il2 = il;</span></a>
+<a name="20408"><span class="lineNum">   20408 </span>            :         }</a>
+<a name="20409"><span class="lineNum">   20409 </span>            : </a>
+<a name="20410"><span class="lineNum">   20410 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaruv,SLARUV)(&amp;iseed[1], &amp;il2, u);</span></a>
+<a name="20411"><span class="lineNum">   20411 </span>            : </a>
+<a name="20412"><span class="lineNum">   20412 </span><span class="lineNoCov">          0 :         if (*idist == 1) {</span></a>
+<a name="20413"><span class="lineNum">   20413 </span>            : </a>
+<a name="20414"><span class="lineNum">   20414 </span>            :             i__2 = il;</a>
+<a name="20415"><span class="lineNum">   20415 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20416"><span class="lineNum">   20416 </span><span class="lineNoCov">          0 :                 x[iv + i__ - 1] = u[i__ - 1];</span></a>
+<a name="20417"><span class="lineNum">   20417 </span>            :             }</a>
+<a name="20418"><span class="lineNum">   20418 </span><span class="lineNoCov">          0 :         } else if (*idist == 2) {</span></a>
+<a name="20419"><span class="lineNum">   20419 </span>            : </a>
+<a name="20420"><span class="lineNum">   20420 </span>            :             i__2 = il;</a>
+<a name="20421"><span class="lineNum">   20421 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20422"><span class="lineNum">   20422 </span><span class="lineNoCov">          0 :                 x[iv + i__ - 1] = u[i__ - 1] * 2. - 1.;</span></a>
+<a name="20423"><span class="lineNum">   20423 </span>            :             }</a>
+<a name="20424"><span class="lineNum">   20424 </span><span class="lineNoCov">          0 :         } else if (*idist == 3) {</span></a>
+<a name="20425"><span class="lineNum">   20425 </span>            : </a>
+<a name="20426"><span class="lineNum">   20426 </span>            :             i__2 = il;</a>
+<a name="20427"><span class="lineNum">   20427 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20428"><span class="lineNum">   20428 </span><span class="lineNoCov">          0 :                 x[iv + i__ - 1] =  std::sqrt(std::log(u[(i__ &lt;&lt; 1) - 2]) * -2.) * </span></a>
+<a name="20429"><span class="lineNum">   20429 </span><span class="lineNoCov">          0 :                   std::cos(u[(i__ &lt;&lt; 1) - 1] * (float)6.2831853071795864769252867663);</span></a>
+<a name="20430"><span class="lineNum">   20430 </span>            :             }</a>
+<a name="20431"><span class="lineNum">   20431 </span>            :         }</a>
+<a name="20432"><span class="lineNum">   20432 </span>            :     }</a>
+<a name="20433"><span class="lineNum">   20433 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="20434"><span class="lineNum">   20434 </span>            : </a>
+<a name="20435"><span class="lineNum">   20435 </span>            : }</a>
+<a name="20436"><span class="lineNum">   20436 </span>            : }</a>
+<a name="20437"><span class="lineNum">   20437 </span>            : }</a>
+<a name="20438"><span class="lineNum">   20438 </span>            : #include &lt;cmath&gt;</a>
+<a name="20439"><span class="lineNum">   20439 </span>            : </a>
+<a name="20440"><span class="lineNum">   20440 </span>            : #include &quot;real.h&quot;</a>
+<a name="20441"><span class="lineNum">   20441 </span>            : </a>
+<a name="20442"><span class="lineNum">   20442 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="20443"><span class="lineNum">   20443 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="20444"><span class="lineNum">   20444 </span>            : </a>
+<a name="20445"><span class="lineNum">   20445 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20446"><span class="lineNum">   20446 </span>            : namespace PLMD{</a>
+<a name="20447"><span class="lineNum">   20447 </span>            : namespace lapack{</a>
+<a name="20448"><span class="lineNum">   20448 </span>            : using namespace blas;</a>
+<a name="20449"><span class="lineNum">   20449 </span>            : void</a>
+<a name="20450"><span class="lineNum">   20450 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarrbx,SLARRBX)(int *n, </span></a>
+<a name="20451"><span class="lineNum">   20451 </span>            :          float *d__, </a>
+<a name="20452"><span class="lineNum">   20452 </span>            :          float *l, </a>
+<a name="20453"><span class="lineNum">   20453 </span>            :          float *ld, </a>
+<a name="20454"><span class="lineNum">   20454 </span>            :          float *lld, </a>
+<a name="20455"><span class="lineNum">   20455 </span>            :          int *ifirst, </a>
+<a name="20456"><span class="lineNum">   20456 </span>            :          int *ilast, </a>
+<a name="20457"><span class="lineNum">   20457 </span>            :          float *rtol1, </a>
+<a name="20458"><span class="lineNum">   20458 </span>            :          float *rtol2, </a>
+<a name="20459"><span class="lineNum">   20459 </span>            :          int *offset, </a>
+<a name="20460"><span class="lineNum">   20460 </span>            :          float *w, </a>
+<a name="20461"><span class="lineNum">   20461 </span>            :          float *wgap, </a>
+<a name="20462"><span class="lineNum">   20462 </span>            :          float *werr, </a>
+<a name="20463"><span class="lineNum">   20463 </span>            :          float *work,</a>
+<a name="20464"><span class="lineNum">   20464 </span>            :          int *iwork, </a>
+<a name="20465"><span class="lineNum">   20465 </span>            :          int *info)</a>
+<a name="20466"><span class="lineNum">   20466 </span>            : {</a>
+<a name="20467"><span class="lineNum">   20467 </span>            :     int i__1, i__2, i__3;</a>
+<a name="20468"><span class="lineNum">   20468 </span>            :     float d__1, d__2;</a>
+<a name="20469"><span class="lineNum">   20469 </span>            : </a>
+<a name="20470"><span class="lineNum">   20470 </span>            :     int i__, j, k, p;</a>
+<a name="20471"><span class="lineNum">   20471 </span>            :     float s;</a>
+<a name="20472"><span class="lineNum">   20472 </span>            :     int i1, i2, ii, kk;</a>
+<a name="20473"><span class="lineNum">   20473 </span>            :     float fac, gap, mid;</a>
+<a name="20474"><span class="lineNum">   20474 </span>            :     int cnt;</a>
+<a name="20475"><span class="lineNum">   20475 </span>            :     float tmp, left;</a>
+<a name="20476"><span class="lineNum">   20476 </span>            :     int nint, prev, next, nleft;</a>
+<a name="20477"><span class="lineNum">   20477 </span>            :     float right, width, dplus;</a>
+<a name="20478"><span class="lineNum">   20478 </span>            :     int nright, olnint;</a>
+<a name="20479"><span class="lineNum">   20479 </span>            :     k = 0;</a>
+<a name="20480"><span class="lineNum">   20480 </span>            :     right = 0.0;</a>
+<a name="20481"><span class="lineNum">   20481 </span>            : </a>
+<a name="20482"><span class="lineNum">   20482 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="20483"><span class="lineNum">   20483 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="20484"><span class="lineNum">   20484 </span><span class="lineNoCov">          0 :     --werr;</span></a>
+<a name="20485"><span class="lineNum">   20485 </span><span class="lineNoCov">          0 :     --wgap;</span></a>
+<a name="20486"><span class="lineNum">   20486 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="20487"><span class="lineNum">   20487 </span><span class="lineNoCov">          0 :     --lld;</span></a>
+<a name="20488"><span class="lineNum">   20488 </span>            :     --ld;</a>
+<a name="20489"><span class="lineNum">   20489 </span>            :     --l;</a>
+<a name="20490"><span class="lineNum">   20490 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="20491"><span class="lineNum">   20491 </span>            : </a>
+<a name="20492"><span class="lineNum">   20492 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="20493"><span class="lineNum">   20493 </span><span class="lineNoCov">          0 :     i__1 = *n &lt;&lt; 1;</span></a>
+<a name="20494"><span class="lineNum">   20494 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="20495"><span class="lineNum">   20495 </span><span class="lineNoCov">          0 :         iwork[i__] = 0;</span></a>
+<a name="20496"><span class="lineNum">   20496 </span>            :     }</a>
+<a name="20497"><span class="lineNum">   20497 </span><span class="lineNoCov">          0 :     i1 = *ifirst;</span></a>
+<a name="20498"><span class="lineNum">   20498 </span>            :     i2 = *ifirst;</a>
+<a name="20499"><span class="lineNum">   20499 </span>            :     prev = 0;</a>
+<a name="20500"><span class="lineNum">   20500 </span><span class="lineNoCov">          0 :     i__1 = *ilast;</span></a>
+<a name="20501"><span class="lineNum">   20501 </span><span class="lineNoCov">          0 :     for (i__ = *ifirst; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="20502"><span class="lineNum">   20502 </span><span class="lineNoCov">          0 :         k = i__ &lt;&lt; 1;</span></a>
+<a name="20503"><span class="lineNum">   20503 </span><span class="lineNoCov">          0 :         iwork[k - 1] = 1;</span></a>
+<a name="20504"><span class="lineNum">   20504 </span>            :         i2 = i__;</a>
+<a name="20505"><span class="lineNum">   20505 </span>            :     }</a>
+<a name="20506"><span class="lineNum">   20506 </span>            : </a>
+<a name="20507"><span class="lineNum">   20507 </span>            :     i__ = i1;</a>
+<a name="20508"><span class="lineNum">   20508 </span>            :     nint = 0;</a>
+<a name="20509"><span class="lineNum">   20509 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="20510"><span class="lineNum">   20510 </span><span class="lineNoCov">          0 :     if (i__ &lt;= i2) {</span></a>
+<a name="20511"><span class="lineNum">   20511 </span><span class="lineNoCov">          0 :         ii = i__ - *offset;</span></a>
+<a name="20512"><span class="lineNum">   20512 </span><span class="lineNoCov">          0 :         if (iwork[(i__ &lt;&lt; 1) - 1] == 1) {</span></a>
+<a name="20513"><span class="lineNum">   20513 </span>            :             fac = 1.;</a>
+<a name="20514"><span class="lineNum">   20514 </span><span class="lineNoCov">          0 :             left = w[ii] - werr[ii];</span></a>
+<a name="20515"><span class="lineNum">   20515 </span>            : </a>
+<a name="20516"><span class="lineNum">   20516 </span>            : </a>
+<a name="20517"><span class="lineNum">   20517 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="20518"><span class="lineNum">   20518 </span><span class="lineNoCov">          0 :             if (i__ &gt; i1 &amp;&amp; left &lt;= right) {</span></a>
+<a name="20519"><span class="lineNum">   20519 </span>            :                 left = right;</a>
+<a name="20520"><span class="lineNum">   20520 </span><span class="lineNoCov">          0 :                 cnt = i__ - 1;</span></a>
+<a name="20521"><span class="lineNum">   20521 </span>            :             } else {</a>
+<a name="20522"><span class="lineNum">   20522 </span><span class="lineNoCov">          0 :                 s = -left;</span></a>
+<a name="20523"><span class="lineNum">   20523 </span>            :                 cnt = 0;</a>
+<a name="20524"><span class="lineNum">   20524 </span><span class="lineNoCov">          0 :                 i__1 = *n - 1;</span></a>
+<a name="20525"><span class="lineNum">   20525 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20526"><span class="lineNum">   20526 </span><span class="lineNoCov">          0 :                     dplus = d__[j] + s;</span></a>
+<a name="20527"><span class="lineNum">   20527 </span><span class="lineNoCov">          0 :                     s = s * lld[j] / dplus - left;</span></a>
+<a name="20528"><span class="lineNum">   20528 </span><span class="lineNoCov">          0 :                     if (dplus &lt; 0.) {</span></a>
+<a name="20529"><span class="lineNum">   20529 </span><span class="lineNoCov">          0 :                         ++cnt;</span></a>
+<a name="20530"><span class="lineNum">   20530 </span>            :                     }</a>
+<a name="20531"><span class="lineNum">   20531 </span>            :                 }</a>
+<a name="20532"><span class="lineNum">   20532 </span><span class="lineNoCov">          0 :                 dplus = d__[*n] + s;</span></a>
+<a name="20533"><span class="lineNum">   20533 </span><span class="lineNoCov">          0 :                 if (dplus &lt; 0.) {</span></a>
+<a name="20534"><span class="lineNum">   20534 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="20535"><span class="lineNum">   20535 </span>            :                 }</a>
+<a name="20536"><span class="lineNum">   20536 </span><span class="lineNoCov">          0 :                 if (std::isnan(s)) {</span></a>
+<a name="20537"><span class="lineNum">   20537 </span>            : </a>
+<a name="20538"><span class="lineNum">   20538 </span>            :                     cnt = 0;</a>
+<a name="20539"><span class="lineNum">   20539 </span>            :                     s = -left;</a>
+<a name="20540"><span class="lineNum">   20540 </span>            :                     i__1 = *n - 1;</a>
+<a name="20541"><span class="lineNum">   20541 </span><span class="lineNoCov">          0 :                     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20542"><span class="lineNum">   20542 </span><span class="lineNoCov">          0 :                         dplus = d__[j] + s;</span></a>
+<a name="20543"><span class="lineNum">   20543 </span><span class="lineNoCov">          0 :                         if (dplus &lt; 0.) {</span></a>
+<a name="20544"><span class="lineNum">   20544 </span><span class="lineNoCov">          0 :                             ++cnt;</span></a>
+<a name="20545"><span class="lineNum">   20545 </span>            :                         }</a>
+<a name="20546"><span class="lineNum">   20546 </span><span class="lineNoCov">          0 :                         tmp = lld[j] / dplus;</span></a>
+<a name="20547"><span class="lineNum">   20547 </span><span class="lineNoCov">          0 :                         if (std::abs(tmp)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="20548"><span class="lineNum">   20548 </span><span class="lineNoCov">          0 :                             s = lld[j] - left;</span></a>
+<a name="20549"><span class="lineNum">   20549 </span>            :                         } else {</a>
+<a name="20550"><span class="lineNum">   20550 </span><span class="lineNoCov">          0 :                             s = s * tmp - left;</span></a>
+<a name="20551"><span class="lineNum">   20551 </span>            :                         }</a>
+<a name="20552"><span class="lineNum">   20552 </span>            :                     }</a>
+<a name="20553"><span class="lineNum">   20553 </span><span class="lineNoCov">          0 :                     dplus = d__[*n] + s;</span></a>
+<a name="20554"><span class="lineNum">   20554 </span><span class="lineNoCov">          0 :                     if (dplus &lt; 0.) {</span></a>
+<a name="20555"><span class="lineNum">   20555 </span><span class="lineNoCov">          0 :                         ++cnt;</span></a>
+<a name="20556"><span class="lineNum">   20556 </span>            :                     }</a>
+<a name="20557"><span class="lineNum">   20557 </span>            :                 }</a>
+<a name="20558"><span class="lineNum">   20558 </span><span class="lineNoCov">          0 :                 if (cnt &gt; i__ - 1) {</span></a>
+<a name="20559"><span class="lineNum">   20559 </span><span class="lineNoCov">          0 :                     left -= werr[ii] * fac;</span></a>
+<a name="20560"><span class="lineNum">   20560 </span><span class="lineNoCov">          0 :                     fac *= 2.;</span></a>
+<a name="20561"><span class="lineNum">   20561 </span><span class="lineNoCov">          0 :                     goto L40;</span></a>
+<a name="20562"><span class="lineNum">   20562 </span>            :                 }</a>
+<a name="20563"><span class="lineNum">   20563 </span>            :             }</a>
+<a name="20564"><span class="lineNum">   20564 </span><span class="lineNoCov">          0 :             nleft = cnt + 1;</span></a>
+<a name="20565"><span class="lineNum">   20565 </span>            :             i1 = (i1&lt;nleft) ? i1 : nleft;</a>
+<a name="20566"><span class="lineNum">   20566 </span>            :             fac = 1.;</a>
+<a name="20567"><span class="lineNum">   20567 </span><span class="lineNoCov">          0 :             right = w[ii] + werr[ii];</span></a>
+<a name="20568"><span class="lineNum">   20568 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="20569"><span class="lineNum">   20569 </span><span class="lineNoCov">          0 :             s = -right;</span></a>
+<a name="20570"><span class="lineNum">   20570 </span>            :             cnt = 0;</a>
+<a name="20571"><span class="lineNum">   20571 </span><span class="lineNoCov">          0 :             i__1 = *n - 1;</span></a>
+<a name="20572"><span class="lineNum">   20572 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20573"><span class="lineNum">   20573 </span><span class="lineNoCov">          0 :                 dplus = d__[j] + s;</span></a>
+<a name="20574"><span class="lineNum">   20574 </span><span class="lineNoCov">          0 :                 s = s * lld[j] / dplus - right;</span></a>
+<a name="20575"><span class="lineNum">   20575 </span><span class="lineNoCov">          0 :                 if (dplus &lt; 0.) {</span></a>
+<a name="20576"><span class="lineNum">   20576 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="20577"><span class="lineNum">   20577 </span>            :                 }</a>
+<a name="20578"><span class="lineNum">   20578 </span>            :             }</a>
+<a name="20579"><span class="lineNum">   20579 </span><span class="lineNoCov">          0 :             dplus = d__[*n] + s;</span></a>
+<a name="20580"><span class="lineNum">   20580 </span><span class="lineNoCov">          0 :             if (dplus &lt; 0.) {</span></a>
+<a name="20581"><span class="lineNum">   20581 </span><span class="lineNoCov">          0 :                 ++cnt;</span></a>
+<a name="20582"><span class="lineNum">   20582 </span>            :             }</a>
+<a name="20583"><span class="lineNum">   20583 </span><span class="lineNoCov">          0 :             if (std::isnan(s)) {</span></a>
+<a name="20584"><span class="lineNum">   20584 </span>            : </a>
+<a name="20585"><span class="lineNum">   20585 </span>            :                 cnt = 0;</a>
+<a name="20586"><span class="lineNum">   20586 </span>            :                 s = -right;</a>
+<a name="20587"><span class="lineNum">   20587 </span>            :                 i__1 = *n - 1;</a>
+<a name="20588"><span class="lineNum">   20588 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="20589"><span class="lineNum">   20589 </span><span class="lineNoCov">          0 :                     dplus = d__[j] + s;</span></a>
+<a name="20590"><span class="lineNum">   20590 </span><span class="lineNoCov">          0 :                     if (dplus &lt; 0.) {</span></a>
+<a name="20591"><span class="lineNum">   20591 </span><span class="lineNoCov">          0 :                         ++cnt;</span></a>
+<a name="20592"><span class="lineNum">   20592 </span>            :                     }</a>
+<a name="20593"><span class="lineNum">   20593 </span><span class="lineNoCov">          0 :                     tmp = lld[j] / dplus;</span></a>
+<a name="20594"><span class="lineNum">   20594 </span><span class="lineNoCov">          0 :                     if (std::abs(tmp)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="20595"><span class="lineNum">   20595 </span><span class="lineNoCov">          0 :                         s = lld[j] - right;</span></a>
+<a name="20596"><span class="lineNum">   20596 </span>            :                     } else {</a>
+<a name="20597"><span class="lineNum">   20597 </span><span class="lineNoCov">          0 :                         s = s * tmp - right;</span></a>
+<a name="20598"><span class="lineNum">   20598 </span>            :                     }</a>
+<a name="20599"><span class="lineNum">   20599 </span>            :                 }</a>
+<a name="20600"><span class="lineNum">   20600 </span><span class="lineNoCov">          0 :                 dplus = d__[*n] + s;</span></a>
+<a name="20601"><span class="lineNum">   20601 </span><span class="lineNoCov">          0 :                 if (dplus &lt; 0.) {</span></a>
+<a name="20602"><span class="lineNum">   20602 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="20603"><span class="lineNum">   20603 </span>            :                 }</a>
+<a name="20604"><span class="lineNum">   20604 </span>            :             }</a>
+<a name="20605"><span class="lineNum">   20605 </span><span class="lineNoCov">          0 :             if (cnt &lt; i__) {</span></a>
+<a name="20606"><span class="lineNum">   20606 </span><span class="lineNoCov">          0 :                 right += werr[ii] * fac;</span></a>
+<a name="20607"><span class="lineNum">   20607 </span><span class="lineNoCov">          0 :                 fac *= 2.;</span></a>
+<a name="20608"><span class="lineNum">   20608 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="20609"><span class="lineNum">   20609 </span>            :             }</a>
+<a name="20610"><span class="lineNum">   20610 </span>            :             cnt = (cnt&lt;i2) ? cnt : i2;</a>
+<a name="20611"><span class="lineNum">   20611 </span><span class="lineNoCov">          0 :             ++nint;</span></a>
+<a name="20612"><span class="lineNum">   20612 </span><span class="lineNoCov">          0 :             k = nleft &lt;&lt; 1;</span></a>
+<a name="20613"><span class="lineNum">   20613 </span><span class="lineNoCov">          0 :             work[k - 1] = left;</span></a>
+<a name="20614"><span class="lineNum">   20614 </span><span class="lineNoCov">          0 :             work[k] = right;</span></a>
+<a name="20615"><span class="lineNum">   20615 </span><span class="lineNoCov">          0 :             i__ = cnt + 1;</span></a>
+<a name="20616"><span class="lineNum">   20616 </span><span class="lineNoCov">          0 :             iwork[k - 1] = i__;</span></a>
+<a name="20617"><span class="lineNum">   20617 </span><span class="lineNoCov">          0 :             iwork[k] = cnt;</span></a>
+<a name="20618"><span class="lineNum">   20618 </span><span class="lineNoCov">          0 :             if (prev != nleft - 1) {</span></a>
+<a name="20619"><span class="lineNum">   20619 </span><span class="lineNoCov">          0 :                 work[k - 2] = left;</span></a>
+<a name="20620"><span class="lineNum">   20620 </span>            :             }</a>
+<a name="20621"><span class="lineNum">   20621 </span>            :             prev = nleft;</a>
+<a name="20622"><span class="lineNum">   20622 </span>            :         } else {</a>
+<a name="20623"><span class="lineNum">   20623 </span><span class="lineNoCov">          0 :             right = work[i__ * 2];</span></a>
+<a name="20624"><span class="lineNum">   20624 </span>            : </a>
+<a name="20625"><span class="lineNum">   20625 </span><span class="lineNoCov">          0 :             ++iwork[k - 1];</span></a>
+<a name="20626"><span class="lineNum">   20626 </span>            :             prev = i__;</a>
+<a name="20627"><span class="lineNum">   20627 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="20628"><span class="lineNum">   20628 </span>            :         }</a>
+<a name="20629"><span class="lineNum">   20629 </span><span class="lineNoCov">          0 :         goto L30;</span></a>
+<a name="20630"><span class="lineNum">   20630 </span>            :     }</a>
+<a name="20631"><span class="lineNum">   20631 </span><span class="lineNoCov">          0 :     if (i__ &lt;= *n &amp;&amp; iwork[(i__ &lt;&lt; 1) - 1] != -1) {</span></a>
+<a name="20632"><span class="lineNum">   20632 </span><span class="lineNoCov">          0 :         work[(i__ &lt;&lt; 1) - 1] = work[prev * 2];</span></a>
+<a name="20633"><span class="lineNum">   20633 </span>            :     }</a>
+<a name="20634"><span class="lineNum">   20634 </span>            : </a>
+<a name="20635"><span class="lineNum">   20635 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="20636"><span class="lineNum">   20636 </span><span class="lineNoCov">          0 :     prev = i1 - 1;</span></a>
+<a name="20637"><span class="lineNum">   20637 </span>            :     olnint = nint;</a>
+<a name="20638"><span class="lineNum">   20638 </span>            :     i__ = i1;</a>
+<a name="20639"><span class="lineNum">   20639 </span>            :     i__1 = olnint;</a>
+<a name="20640"><span class="lineNum">   20640 </span><span class="lineNoCov">          0 :     for (p = 1; p &lt;= i__1; ++p) {</span></a>
+<a name="20641"><span class="lineNum">   20641 </span><span class="lineNoCov">          0 :         k = i__ &lt;&lt; 1;</span></a>
+<a name="20642"><span class="lineNum">   20642 </span><span class="lineNoCov">          0 :         left = work[k - 1];</span></a>
+<a name="20643"><span class="lineNum">   20643 </span><span class="lineNoCov">          0 :         right = work[k];</span></a>
+<a name="20644"><span class="lineNum">   20644 </span><span class="lineNoCov">          0 :         next = iwork[k - 1];</span></a>
+<a name="20645"><span class="lineNum">   20645 </span><span class="lineNoCov">          0 :         nright = iwork[k];</span></a>
+<a name="20646"><span class="lineNum">   20646 </span><span class="lineNoCov">          0 :         mid = (left + right) * .5;</span></a>
+<a name="20647"><span class="lineNum">   20647 </span><span class="lineNoCov">          0 :         width = right - mid;</span></a>
+<a name="20648"><span class="lineNum">   20648 </span>            :         d__1 = std::abs(left);</a>
+<a name="20649"><span class="lineNum">   20649 </span>            :         d__2 = std::abs(right);</a>
+<a name="20650"><span class="lineNum">   20650 </span><span class="lineNoCov">          0 :         tmp = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="20651"><span class="lineNum">   20651 </span>            : </a>
+<a name="20652"><span class="lineNum">   20652 </span>            :         gap = 0.;</a>
+<a name="20653"><span class="lineNum">   20653 </span><span class="lineNoCov">          0 :         if (i__ == nright) {</span></a>
+<a name="20654"><span class="lineNum">   20654 </span><span class="lineNoCov">          0 :             if (prev &gt; 0 &amp;&amp; next &lt;= *n) {</span></a>
+<a name="20655"><span class="lineNum">   20655 </span><span class="lineNoCov">          0 :                 d__1 = left - work[k - 2], d__2 = work[k + 1] - right;</span></a>
+<a name="20656"><span class="lineNum">   20656 </span><span class="lineNoCov">          0 :                 gap = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="20657"><span class="lineNum">   20657 </span><span class="lineNoCov">          0 :             } else if (prev &gt; 0) {</span></a>
+<a name="20658"><span class="lineNum">   20658 </span><span class="lineNoCov">          0 :                 gap = left - work[k - 2];</span></a>
+<a name="20659"><span class="lineNum">   20659 </span><span class="lineNoCov">          0 :             } else if (next &lt;= *n) {</span></a>
+<a name="20660"><span class="lineNum">   20660 </span><span class="lineNoCov">          0 :                 gap = work[k + 1] - right;</span></a>
+<a name="20661"><span class="lineNum">   20661 </span>            :             }</a>
+<a name="20662"><span class="lineNum">   20662 </span>            :         }</a>
+<a name="20663"><span class="lineNum">   20663 </span><span class="lineNoCov">          0 :         d__1 = *rtol1 * gap, d__2 = *rtol2 * tmp;</span></a>
+<a name="20664"><span class="lineNum">   20664 </span><span class="lineNoCov">          0 :         if (width &lt; ((d__1&gt;d__2) ? d__1 : d__2)) {</span></a>
+<a name="20665"><span class="lineNum">   20665 </span><span class="lineNoCov">          0 :             --nint;</span></a>
+<a name="20666"><span class="lineNum">   20666 </span><span class="lineNoCov">          0 :             iwork[k - 1] = 0;</span></a>
+<a name="20667"><span class="lineNum">   20667 </span>            :             kk = k;</a>
+<a name="20668"><span class="lineNum">   20668 </span>            :             i__2 = nright;</a>
+<a name="20669"><span class="lineNum">   20669 </span><span class="lineNoCov">          0 :             for (j = i__ + 1; j &lt;= i__2; ++j) {</span></a>
+<a name="20670"><span class="lineNum">   20670 </span><span class="lineNoCov">          0 :                 kk += 2;</span></a>
+<a name="20671"><span class="lineNum">   20671 </span><span class="lineNoCov">          0 :                 iwork[kk - 1] = 0;</span></a>
+<a name="20672"><span class="lineNum">   20672 </span><span class="lineNoCov">          0 :                 work[kk - 1] = left;</span></a>
+<a name="20673"><span class="lineNum">   20673 </span><span class="lineNoCov">          0 :                 work[kk] = right;</span></a>
+<a name="20674"><span class="lineNum">   20674 </span><span class="lineNoCov">          0 :                 wgap[j - 1 - *offset] = 0.;</span></a>
+<a name="20675"><span class="lineNum">   20675 </span>            :             }</a>
+<a name="20676"><span class="lineNum">   20676 </span><span class="lineNoCov">          0 :             if (i1 == i__) {</span></a>
+<a name="20677"><span class="lineNum">   20677 </span>            :                 i1 = next;</a>
+<a name="20678"><span class="lineNum">   20678 </span>            :             } else {</a>
+<a name="20679"><span class="lineNum">   20679 </span><span class="lineNoCov">          0 :                 iwork[(prev &lt;&lt; 1) - 1] = next;</span></a>
+<a name="20680"><span class="lineNum">   20680 </span>            :             }</a>
+<a name="20681"><span class="lineNum">   20681 </span>            :             i__ = next;</a>
+<a name="20682"><span class="lineNum">   20682 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="20683"><span class="lineNum">   20683 </span>            :         }</a>
+<a name="20684"><span class="lineNum">   20684 </span>            :         prev = i__;</a>
+<a name="20685"><span class="lineNum">   20685 </span>            : </a>
+<a name="20686"><span class="lineNum">   20686 </span><span class="lineNoCov">          0 :         s = -mid;</span></a>
+<a name="20687"><span class="lineNum">   20687 </span>            :         cnt = 0;</a>
+<a name="20688"><span class="lineNum">   20688 </span><span class="lineNoCov">          0 :         i__2 = *n - 1;</span></a>
+<a name="20689"><span class="lineNum">   20689 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="20690"><span class="lineNum">   20690 </span><span class="lineNoCov">          0 :             dplus = d__[j] + s;</span></a>
+<a name="20691"><span class="lineNum">   20691 </span><span class="lineNoCov">          0 :             s = s * lld[j] / dplus - mid;</span></a>
+<a name="20692"><span class="lineNum">   20692 </span><span class="lineNoCov">          0 :             if (dplus &lt; 0.) {</span></a>
+<a name="20693"><span class="lineNum">   20693 </span><span class="lineNoCov">          0 :                 ++cnt;</span></a>
+<a name="20694"><span class="lineNum">   20694 </span>            :             }</a>
+<a name="20695"><span class="lineNum">   20695 </span>            :         }</a>
+<a name="20696"><span class="lineNum">   20696 </span><span class="lineNoCov">          0 :         dplus = d__[*n] + s;</span></a>
+<a name="20697"><span class="lineNum">   20697 </span><span class="lineNoCov">          0 :         if (dplus &lt; 0.) {</span></a>
+<a name="20698"><span class="lineNum">   20698 </span><span class="lineNoCov">          0 :             ++cnt;</span></a>
+<a name="20699"><span class="lineNum">   20699 </span>            :         }</a>
+<a name="20700"><span class="lineNum">   20700 </span><span class="lineNoCov">          0 :         if (std::isnan(s)) {</span></a>
+<a name="20701"><span class="lineNum">   20701 </span>            :             cnt = 0;</a>
+<a name="20702"><span class="lineNum">   20702 </span>            :             s = -mid;</a>
+<a name="20703"><span class="lineNum">   20703 </span>            :             i__2 = *n - 1;</a>
+<a name="20704"><span class="lineNum">   20704 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="20705"><span class="lineNum">   20705 </span><span class="lineNoCov">          0 :                 dplus = d__[j] + s;</span></a>
+<a name="20706"><span class="lineNum">   20706 </span><span class="lineNoCov">          0 :                 if (dplus &lt; 0.) {</span></a>
+<a name="20707"><span class="lineNum">   20707 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="20708"><span class="lineNum">   20708 </span>            :                 }</a>
+<a name="20709"><span class="lineNum">   20709 </span><span class="lineNoCov">          0 :                 tmp = lld[j] / dplus;</span></a>
+<a name="20710"><span class="lineNum">   20710 </span><span class="lineNoCov">          0 :                 if (std::abs(tmp)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="20711"><span class="lineNum">   20711 </span><span class="lineNoCov">          0 :                     s = lld[j] - mid;</span></a>
+<a name="20712"><span class="lineNum">   20712 </span>            :                 } else {</a>
+<a name="20713"><span class="lineNum">   20713 </span><span class="lineNoCov">          0 :                     s = s * tmp - mid;</span></a>
+<a name="20714"><span class="lineNum">   20714 </span>            :                 }</a>
+<a name="20715"><span class="lineNum">   20715 </span>            :             }</a>
+<a name="20716"><span class="lineNum">   20716 </span><span class="lineNoCov">          0 :             dplus = d__[*n] + s;</span></a>
+<a name="20717"><span class="lineNum">   20717 </span><span class="lineNoCov">          0 :             if (dplus &lt; 0.) {</span></a>
+<a name="20718"><span class="lineNum">   20718 </span><span class="lineNoCov">          0 :                 ++cnt;</span></a>
+<a name="20719"><span class="lineNum">   20719 </span>            :             }</a>
+<a name="20720"><span class="lineNum">   20720 </span>            :         }</a>
+<a name="20721"><span class="lineNum">   20721 </span><span class="lineNoCov">          0 :         i__2 = i__ - 1, i__3 = (nright&lt;cnt) ? nright : cnt;</span></a>
+<a name="20722"><span class="lineNum">   20722 </span>            :         cnt = (i__2&gt;i__3) ? i__2 : i__3;</a>
+<a name="20723"><span class="lineNum">   20723 </span><span class="lineNoCov">          0 :         if (cnt == i__ - 1) {</span></a>
+<a name="20724"><span class="lineNum">   20724 </span><span class="lineNoCov">          0 :             work[k - 1] = mid;</span></a>
+<a name="20725"><span class="lineNum">   20725 </span><span class="lineNoCov">          0 :         } else if (cnt == nright) {</span></a>
+<a name="20726"><span class="lineNum">   20726 </span><span class="lineNoCov">          0 :             work[k] = mid;</span></a>
+<a name="20727"><span class="lineNum">   20727 </span>            :         } else {</a>
+<a name="20728"><span class="lineNum">   20728 </span><span class="lineNoCov">          0 :             iwork[k] = cnt;</span></a>
+<a name="20729"><span class="lineNum">   20729 </span><span class="lineNoCov">          0 :             ++cnt;</span></a>
+<a name="20730"><span class="lineNum">   20730 </span><span class="lineNoCov">          0 :             iwork[k - 1] = cnt;</span></a>
+<a name="20731"><span class="lineNum">   20731 </span><span class="lineNoCov">          0 :             kk = cnt &lt;&lt; 1;</span></a>
+<a name="20732"><span class="lineNum">   20732 </span><span class="lineNoCov">          0 :             iwork[kk - 1] = next;</span></a>
+<a name="20733"><span class="lineNum">   20733 </span><span class="lineNoCov">          0 :             iwork[kk] = nright;</span></a>
+<a name="20734"><span class="lineNum">   20734 </span><span class="lineNoCov">          0 :             work[k] = mid;</span></a>
+<a name="20735"><span class="lineNum">   20735 </span><span class="lineNoCov">          0 :             work[kk - 1] = mid;</span></a>
+<a name="20736"><span class="lineNum">   20736 </span><span class="lineNoCov">          0 :             work[kk] = right;</span></a>
+<a name="20737"><span class="lineNum">   20737 </span>            :             prev = cnt;</a>
+<a name="20738"><span class="lineNum">   20738 </span><span class="lineNoCov">          0 :             if (cnt - 1 &gt; i__) {</span></a>
+<a name="20739"><span class="lineNum">   20739 </span><span class="lineNoCov">          0 :                 work[kk - 2] = mid;</span></a>
+<a name="20740"><span class="lineNum">   20740 </span>            :             }</a>
+<a name="20741"><span class="lineNum">   20741 </span><span class="lineNoCov">          0 :             if (cnt &gt; *ifirst &amp;&amp; cnt &lt;= *ilast) {</span></a>
+<a name="20742"><span class="lineNum">   20742 </span><span class="lineNoCov">          0 :                 ++nint;</span></a>
+<a name="20743"><span class="lineNum">   20743 </span><span class="lineNoCov">          0 :             } else if (cnt &lt;= *ifirst) {</span></a>
+<a name="20744"><span class="lineNum">   20744 </span>            :                 i1 = cnt;</a>
+<a name="20745"><span class="lineNum">   20745 </span>            :             }</a>
+<a name="20746"><span class="lineNum">   20746 </span>            :         }</a>
+<a name="20747"><span class="lineNum">   20747 </span>            :         i__ = next;</a>
+<a name="20748"><span class="lineNum">   20748 </span>            :     }</a>
+<a name="20749"><span class="lineNum">   20749 </span><span class="lineNoCov">          0 :     if (nint &gt; 0) {</span></a>
+<a name="20750"><span class="lineNum">   20750 </span><span class="lineNoCov">          0 :         goto L80;</span></a>
+<a name="20751"><span class="lineNum">   20751 </span>            :     }</a>
+<a name="20752"><span class="lineNum">   20752 </span><span class="lineNoCov">          0 :     i__1 = *ilast;</span></a>
+<a name="20753"><span class="lineNum">   20753 </span><span class="lineNoCov">          0 :     for (i__ = *ifirst; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="20754"><span class="lineNum">   20754 </span><span class="lineNoCov">          0 :         k = i__ &lt;&lt; 1;</span></a>
+<a name="20755"><span class="lineNum">   20755 </span><span class="lineNoCov">          0 :         ii = i__ - *offset;</span></a>
+<a name="20756"><span class="lineNum">   20756 </span><span class="lineNoCov">          0 :         if (iwork[k - 1] != -1) {</span></a>
+<a name="20757"><span class="lineNum">   20757 </span><span class="lineNoCov">          0 :             w[ii] = (work[k - 1] + work[k]) * .5;</span></a>
+<a name="20758"><span class="lineNum">   20758 </span><span class="lineNoCov">          0 :             werr[ii] = work[k] - w[ii];</span></a>
+<a name="20759"><span class="lineNum">   20759 </span><span class="lineNoCov">          0 :             if (i__ != *ilast) {</span></a>
+<a name="20760"><span class="lineNum">   20760 </span><span class="lineNoCov">          0 :                 wgap[ii] = work[k + 1] - work[k];</span></a>
+<a name="20761"><span class="lineNum">   20761 </span>            :             }</a>
+<a name="20762"><span class="lineNum">   20762 </span>            :         }</a>
+<a name="20763"><span class="lineNum">   20763 </span>            :     }</a>
+<a name="20764"><span class="lineNum">   20764 </span>            : </a>
+<a name="20765"><span class="lineNum">   20765 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="20766"><span class="lineNum">   20766 </span>            : </a>
+<a name="20767"><span class="lineNum">   20767 </span>            : } </a>
+<a name="20768"><span class="lineNum">   20768 </span>            : }</a>
+<a name="20769"><span class="lineNum">   20769 </span>            : }</a>
+<a name="20770"><span class="lineNum">   20770 </span>            : #include &lt;cctype&gt;</a>
+<a name="20771"><span class="lineNum">   20771 </span>            : #include &lt;cmath&gt;</a>
+<a name="20772"><span class="lineNum">   20772 </span>            : </a>
+<a name="20773"><span class="lineNum">   20773 </span>            : #include &quot;real.h&quot;</a>
+<a name="20774"><span class="lineNum">   20774 </span>            : </a>
+<a name="20775"><span class="lineNum">   20775 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20776"><span class="lineNum">   20776 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="20777"><span class="lineNum">   20777 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="20778"><span class="lineNum">   20778 </span>            : </a>
+<a name="20779"><span class="lineNum">   20779 </span>            : </a>
+<a name="20780"><span class="lineNum">   20780 </span>            : </a>
+<a name="20781"><span class="lineNum">   20781 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="20782"><span class="lineNum">   20782 </span>            : namespace PLMD{</a>
+<a name="20783"><span class="lineNum">   20783 </span>            : namespace lapack{</a>
+<a name="20784"><span class="lineNum">   20784 </span>            : using namespace blas;</a>
+<a name="20785"><span class="lineNum">   20785 </span>            : void</a>
+<a name="20786"><span class="lineNum">   20786 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarrex,SLARREX)(const char *range,</span></a>
+<a name="20787"><span class="lineNum">   20787 </span>            :          int *n, </a>
+<a name="20788"><span class="lineNum">   20788 </span>            :          float *vl, </a>
+<a name="20789"><span class="lineNum">   20789 </span>            :          float *vu, </a>
+<a name="20790"><span class="lineNum">   20790 </span>            :          int *il, </a>
+<a name="20791"><span class="lineNum">   20791 </span>            :          int *iu, </a>
+<a name="20792"><span class="lineNum">   20792 </span>            :          float *d__, </a>
+<a name="20793"><span class="lineNum">   20793 </span>            :          float *e, </a>
+<a name="20794"><span class="lineNum">   20794 </span>            :          float *tol, </a>
+<a name="20795"><span class="lineNum">   20795 </span>            :          int *nsplit, </a>
+<a name="20796"><span class="lineNum">   20796 </span>            :          int *isplit, </a>
+<a name="20797"><span class="lineNum">   20797 </span>            :          int *m, </a>
+<a name="20798"><span class="lineNum">   20798 </span>            :          float *w, </a>
+<a name="20799"><span class="lineNum">   20799 </span>            :          int *iblock, </a>
+<a name="20800"><span class="lineNum">   20800 </span>            :          int *indexw, </a>
+<a name="20801"><span class="lineNum">   20801 </span>            :          float *gersch, </a>
+<a name="20802"><span class="lineNum">   20802 </span>            :          float *work,</a>
+<a name="20803"><span class="lineNum">   20803 </span>            :          int *iwork, </a>
+<a name="20804"><span class="lineNum">   20804 </span>            :          int *info)</a>
+<a name="20805"><span class="lineNum">   20805 </span>            : {</a>
+<a name="20806"><span class="lineNum">   20806 </span>            :     int i__1, i__2, i__3;</a>
+<a name="20807"><span class="lineNum">   20807 </span>            :     float d__1, d__2;</a>
+<a name="20808"><span class="lineNum">   20808 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="20809"><span class="lineNum">   20809 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="20810"><span class="lineNum">   20810 </span>            : </a>
+<a name="20811"><span class="lineNum">   20811 </span>            :     int i__, j, k;</a>
+<a name="20812"><span class="lineNum">   20812 </span>            :     float s, gl;</a>
+<a name="20813"><span class="lineNum">   20813 </span>            :     int in;</a>
+<a name="20814"><span class="lineNum">   20814 </span>            :     float gu;</a>
+<a name="20815"><span class="lineNum">   20815 </span>            :     int cnt;</a>
+<a name="20816"><span class="lineNum">   20816 </span>            :     float eps, tau, nrm, tmp, vvl, vvu, offd;</a>
+<a name="20817"><span class="lineNum">   20817 </span>            :     int iend, jblk, till, itmp;</a>
+<a name="20818"><span class="lineNum">   20818 </span>            :     float rtol, delta, sigma;</a>
+<a name="20819"><span class="lineNum">   20819 </span>            :     int iinfo;</a>
+<a name="20820"><span class="lineNum">   20820 </span>            :     float width;</a>
+<a name="20821"><span class="lineNum">   20821 </span>            :     int ibegin;</a>
+<a name="20822"><span class="lineNum">   20822 </span>            :     int irange;</a>
+<a name="20823"><span class="lineNum">   20823 </span>            :     float sgndef;</a>
+<a name="20824"><span class="lineNum">   20824 </span>            :     int maxcnt;</a>
+<a name="20825"><span class="lineNum">   20825 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="20826"><span class="lineNum">   20826 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="20827"><span class="lineNum">   20827 </span><span class="lineNoCov">          0 :     --gersch;</span></a>
+<a name="20828"><span class="lineNum">   20828 </span><span class="lineNoCov">          0 :     --indexw;</span></a>
+<a name="20829"><span class="lineNum">   20829 </span><span class="lineNoCov">          0 :     --iblock;</span></a>
+<a name="20830"><span class="lineNum">   20830 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="20831"><span class="lineNum">   20831 </span><span class="lineNoCov">          0 :     --isplit;</span></a>
+<a name="20832"><span class="lineNum">   20832 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="20833"><span class="lineNum">   20833 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="20834"><span class="lineNum">   20834 </span>            : </a>
+<a name="20835"><span class="lineNum">   20835 </span>            :     sigma = 0;</a>
+<a name="20836"><span class="lineNum">   20836 </span>            :     irange = 0;</a>
+<a name="20837"><span class="lineNum">   20837 </span>            :     sgndef = 0;</a>
+<a name="20838"><span class="lineNum">   20838 </span>            :     maxcnt = 0;</a>
+<a name="20839"><span class="lineNum">   20839 </span>            : </a>
+<a name="20840"><span class="lineNum">   20840 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="20841"><span class="lineNum">   20841 </span>            : </a>
+<a name="20842"><span class="lineNum">   20842 </span><span class="lineNoCov">          0 :     if (*range=='A' || *range=='a')</span></a>
+<a name="20843"><span class="lineNum">   20843 </span>            :         irange = 1;</a>
+<a name="20844"><span class="lineNum">   20844 </span><span class="lineNoCov">          0 :     else if (*range=='V' || *range=='v')</span></a>
+<a name="20845"><span class="lineNum">   20845 </span>            :         irange = 2;</a>
+<a name="20846"><span class="lineNum">   20846 </span><span class="lineNoCov">          0 :     else if (*range=='I' || *range=='i')</span></a>
+<a name="20847"><span class="lineNum">   20847 </span>            :         irange = 3;</a>
+<a name="20848"><span class="lineNum">   20848 </span>            :     </a>
+<a name="20849"><span class="lineNum">   20849 </span>            : </a>
+<a name="20850"><span class="lineNum">   20850 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="20851"><span class="lineNum">   20851 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="20852"><span class="lineNum">   20852 </span>            : </a>
+<a name="20853"><span class="lineNum">   20853 </span><span class="lineNoCov">          0 :     *nsplit = 1;</span></a>
+<a name="20854"><span class="lineNum">   20854 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="20855"><span class="lineNum">   20855 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="20856"><span class="lineNum">   20856 </span><span class="lineNoCov">          0 :         if (std::abs(e[i__]) &lt;= *tol) {</span></a>
+<a name="20857"><span class="lineNum">   20857 </span><span class="lineNoCov">          0 :             isplit[*nsplit] = i__;</span></a>
+<a name="20858"><span class="lineNum">   20858 </span><span class="lineNoCov">          0 :             ++(*nsplit);</span></a>
+<a name="20859"><span class="lineNum">   20859 </span>            :         }</a>
+<a name="20860"><span class="lineNum">   20860 </span>            :     }</a>
+<a name="20861"><span class="lineNum">   20861 </span><span class="lineNoCov">          0 :     isplit[*nsplit] = *n;</span></a>
+<a name="20862"><span class="lineNum">   20862 </span>            : </a>
+<a name="20863"><span class="lineNum">   20863 </span>            :     ibegin = 1;</a>
+<a name="20864"><span class="lineNum">   20864 </span><span class="lineNoCov">          0 :     i__1 = *nsplit;</span></a>
+<a name="20865"><span class="lineNum">   20865 </span><span class="lineNoCov">          0 :     for (jblk = 1; jblk &lt;= i__1; ++jblk) {</span></a>
+<a name="20866"><span class="lineNum">   20866 </span><span class="lineNoCov">          0 :         iend = isplit[jblk];</span></a>
+<a name="20867"><span class="lineNum">   20867 </span><span class="lineNoCov">          0 :         if (ibegin == iend) {</span></a>
+<a name="20868"><span class="lineNum">   20868 </span><span class="lineNoCov">          0 :             ++(*m);</span></a>
+<a name="20869"><span class="lineNum">   20869 </span><span class="lineNoCov">          0 :             w[*m] = d__[ibegin];</span></a>
+<a name="20870"><span class="lineNum">   20870 </span><span class="lineNoCov">          0 :             iblock[*m] = jblk;</span></a>
+<a name="20871"><span class="lineNum">   20871 </span><span class="lineNoCov">          0 :             indexw[*m] = 1;</span></a>
+<a name="20872"><span class="lineNum">   20872 </span><span class="lineNoCov">          0 :             e[iend] = 0.;</span></a>
+<a name="20873"><span class="lineNum">   20873 </span><span class="lineNoCov">          0 :             ibegin = iend + 1;</span></a>
+<a name="20874"><span class="lineNum">   20874 </span><span class="lineNoCov">          0 :             goto L170;</span></a>
+<a name="20875"><span class="lineNum">   20875 </span>            :         }</a>
+<a name="20876"><span class="lineNum">   20876 </span><span class="lineNoCov">          0 :         in = iend - ibegin + 1;</span></a>
+<a name="20877"><span class="lineNum">   20877 </span>            : </a>
+<a name="20878"><span class="lineNum">   20878 </span><span class="lineNoCov">          0 :         gl = d__[ibegin] - std::abs(e[ibegin]);</span></a>
+<a name="20879"><span class="lineNum">   20879 </span><span class="lineNoCov">          0 :         gu = d__[ibegin] + std::abs(e[ibegin]);</span></a>
+<a name="20880"><span class="lineNum">   20880 </span><span class="lineNoCov">          0 :         gersch[(ibegin &lt;&lt; 1) - 1] = gl;</span></a>
+<a name="20881"><span class="lineNum">   20881 </span><span class="lineNoCov">          0 :         gersch[ibegin * 2] = gu;</span></a>
+<a name="20882"><span class="lineNum">   20882 </span><span class="lineNoCov">          0 :         gersch[(iend &lt;&lt; 1) - 1] = d__[iend] - std::abs(e[iend - 1]);</span></a>
+<a name="20883"><span class="lineNum">   20883 </span><span class="lineNoCov">          0 :         gersch[iend * 2] = d__[iend] + std::abs(e[iend - 1]);</span></a>
+<a name="20884"><span class="lineNum">   20884 </span><span class="lineNoCov">          0 :         d__1 = gersch[(iend &lt;&lt; 1) - 1];</span></a>
+<a name="20885"><span class="lineNum">   20885 </span><span class="lineNoCov">          0 :         gl = (d__1&lt;gl) ? d__1 : gl;</span></a>
+<a name="20886"><span class="lineNum">   20886 </span>            :         d__1 = gersch[iend * 2];</a>
+<a name="20887"><span class="lineNum">   20887 </span><span class="lineNoCov">          0 :         gu = (d__1&gt;gu) ? d__1 : gu;</span></a>
+<a name="20888"><span class="lineNum">   20888 </span><span class="lineNoCov">          0 :         i__2 = iend - 1;</span></a>
+<a name="20889"><span class="lineNum">   20889 </span><span class="lineNoCov">          0 :         for (i__ = ibegin + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20890"><span class="lineNum">   20890 </span><span class="lineNoCov">          0 :             offd = std::abs(e[i__ - 1]) + std::abs(e[i__]);</span></a>
+<a name="20891"><span class="lineNum">   20891 </span><span class="lineNoCov">          0 :             gersch[(i__ &lt;&lt; 1) - 1] = d__[i__] - offd;</span></a>
+<a name="20892"><span class="lineNum">   20892 </span>            :             d__1 = gersch[(i__ &lt;&lt; 1) - 1];</a>
+<a name="20893"><span class="lineNum">   20893 </span><span class="lineNoCov">          0 :             gl = (d__1&lt;gl) ? d__1 : gl;</span></a>
+<a name="20894"><span class="lineNum">   20894 </span><span class="lineNoCov">          0 :             gersch[i__ * 2] = d__[i__] + offd;</span></a>
+<a name="20895"><span class="lineNum">   20895 </span>            :             d__1 = gersch[i__ * 2];</a>
+<a name="20896"><span class="lineNum">   20896 </span><span class="lineNoCov">          0 :             gu = (d__1&gt;gu) ? d__1 : gu;</span></a>
+<a name="20897"><span class="lineNum">   20897 </span>            :         }</a>
+<a name="20898"><span class="lineNum">   20898 </span>            :         d__1 = std::abs(gl), d__2 = std::abs(gu);</a>
+<a name="20899"><span class="lineNum">   20899 </span><span class="lineNoCov">          0 :         nrm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="20900"><span class="lineNum">   20900 </span>            : </a>
+<a name="20901"><span class="lineNum">   20901 </span><span class="lineNoCov">          0 :         width = gu - gl;</span></a>
+<a name="20902"><span class="lineNum">   20902 </span>            :         i__2 = iend - 1;</a>
+<a name="20903"><span class="lineNum">   20903 </span><span class="lineNoCov">          0 :         for (i__ = ibegin; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20904"><span class="lineNum">   20904 </span><span class="lineNoCov">          0 :             work[i__] = e[i__] * e[i__];</span></a>
+<a name="20905"><span class="lineNum">   20905 </span>            :         }</a>
+<a name="20906"><span class="lineNum">   20906 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= 2; ++j) {</span></a>
+<a name="20907"><span class="lineNum">   20907 </span><span class="lineNoCov">          0 :             if (j == 1) {</span></a>
+<a name="20908"><span class="lineNum">   20908 </span><span class="lineNoCov">          0 :                 tau = gl + width * .25;</span></a>
+<a name="20909"><span class="lineNum">   20909 </span>            :             } else {</a>
+<a name="20910"><span class="lineNum">   20910 </span><span class="lineNoCov">          0 :                 tau = gu - width * .25;</span></a>
+<a name="20911"><span class="lineNum">   20911 </span>            :             }</a>
+<a name="20912"><span class="lineNum">   20912 </span><span class="lineNoCov">          0 :             tmp = d__[ibegin] - tau;</span></a>
+<a name="20913"><span class="lineNum">   20913 </span><span class="lineNoCov">          0 :             if (tmp &lt; 0.) {</span></a>
+<a name="20914"><span class="lineNum">   20914 </span><span class="lineNoCov">          0 :                 cnt = 1;</span></a>
+<a name="20915"><span class="lineNum">   20915 </span>            :             } else {</a>
+<a name="20916"><span class="lineNum">   20916 </span><span class="lineNoCov">          0 :                 cnt = 0;</span></a>
+<a name="20917"><span class="lineNum">   20917 </span>            :             }</a>
+<a name="20918"><span class="lineNum">   20918 </span><span class="lineNoCov">          0 :             i__2 = iend;</span></a>
+<a name="20919"><span class="lineNum">   20919 </span><span class="lineNoCov">          0 :             for (i__ = ibegin + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20920"><span class="lineNum">   20920 </span><span class="lineNoCov">          0 :                 tmp = d__[i__] - tau - work[i__ - 1] / tmp;</span></a>
+<a name="20921"><span class="lineNum">   20921 </span><span class="lineNoCov">          0 :                 if (tmp &lt; 0.) {</span></a>
+<a name="20922"><span class="lineNum">   20922 </span><span class="lineNoCov">          0 :                     ++cnt;</span></a>
+<a name="20923"><span class="lineNum">   20923 </span>            :                 }</a>
+<a name="20924"><span class="lineNum">   20924 </span>            :             }</a>
+<a name="20925"><span class="lineNum">   20925 </span><span class="lineNoCov">          0 :             if (cnt == 0) {</span></a>
+<a name="20926"><span class="lineNum">   20926 </span>            :                 gl = tau;</a>
+<a name="20927"><span class="lineNum">   20927 </span><span class="lineNoCov">          0 :             } else if (cnt == in) {</span></a>
+<a name="20928"><span class="lineNum">   20928 </span>            :                 gu = tau;</a>
+<a name="20929"><span class="lineNum">   20929 </span>            :             }</a>
+<a name="20930"><span class="lineNum">   20930 </span><span class="lineNoCov">          0 :             if (j == 1) {</span></a>
+<a name="20931"><span class="lineNum">   20931 </span>            :                 maxcnt = cnt;</a>
+<a name="20932"><span class="lineNum">   20932 </span>            :                 sigma = gl;</a>
+<a name="20933"><span class="lineNum">   20933 </span>            :                 sgndef = 1.;</a>
+<a name="20934"><span class="lineNum">   20934 </span>            :             } else {</a>
+<a name="20935"><span class="lineNum">   20935 </span><span class="lineNoCov">          0 :                 if (in - cnt &gt; maxcnt) {</span></a>
+<a name="20936"><span class="lineNum">   20936 </span>            :                     sigma = gu;</a>
+<a name="20937"><span class="lineNum">   20937 </span>            :                     sgndef = -1.;</a>
+<a name="20938"><span class="lineNum">   20938 </span>            :                 }</a>
+<a name="20939"><span class="lineNum">   20939 </span>            :             }</a>
+<a name="20940"><span class="lineNum">   20940 </span>            :         }</a>
+<a name="20941"><span class="lineNum">   20941 </span>            : </a>
+<a name="20942"><span class="lineNum">   20942 </span><span class="lineNoCov">          0 :         work[in * 3] = 1.;</span></a>
+<a name="20943"><span class="lineNum">   20943 </span>            :         delta = eps;</a>
+<a name="20944"><span class="lineNum">   20944 </span><span class="lineNoCov">          0 :         tau = sgndef * nrm;</span></a>
+<a name="20945"><span class="lineNum">   20945 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="20946"><span class="lineNum">   20946 </span><span class="lineNoCov">          0 :         sigma -= delta * tau;</span></a>
+<a name="20947"><span class="lineNum">   20947 </span><span class="lineNoCov">          0 :         work[1] = d__[ibegin] - sigma;</span></a>
+<a name="20948"><span class="lineNum">   20948 </span>            :         j = ibegin;</a>
+<a name="20949"><span class="lineNum">   20949 </span><span class="lineNoCov">          0 :         i__2 = in - 1;</span></a>
+<a name="20950"><span class="lineNum">   20950 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20951"><span class="lineNum">   20951 </span><span class="lineNoCov">          0 :             work[(in &lt;&lt; 1) + i__] = 1. / work[i__];</span></a>
+<a name="20952"><span class="lineNum">   20952 </span><span class="lineNoCov">          0 :             tmp = e[j] * work[(in &lt;&lt; 1) + i__];</span></a>
+<a name="20953"><span class="lineNum">   20953 </span><span class="lineNoCov">          0 :             work[i__ + 1] = d__[j + 1] - sigma - tmp * e[j];</span></a>
+<a name="20954"><span class="lineNum">   20954 </span><span class="lineNoCov">          0 :             work[in + i__] = tmp;</span></a>
+<a name="20955"><span class="lineNum">   20955 </span><span class="lineNoCov">          0 :             ++j;</span></a>
+<a name="20956"><span class="lineNum">   20956 </span>            :         }</a>
+<a name="20957"><span class="lineNum">   20957 </span><span class="lineNoCov">          0 :         for (i__ = in; i__ &gt;= 1; --i__) {</span></a>
+<a name="20958"><span class="lineNum">   20958 </span><span class="lineNoCov">          0 :             tmp = sgndef * work[i__];</span></a>
+<a name="20959"><span class="lineNum">   20959 </span><span class="lineNoCov">          0 :             if (tmp &lt; 0. || std::abs(work[(in &lt;&lt; 1) + i__])&lt;PLUMED_GMX_FLOAT_MIN || std::isnan(tmp)) {</span></a>
+<a name="20960"><span class="lineNum">   20960 </span><span class="lineNoCov">          0 :                 delta *= 2.;</span></a>
+<a name="20961"><span class="lineNum">   20961 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="20962"><span class="lineNum">   20962 </span>            :             }</a>
+<a name="20963"><span class="lineNum">   20963 </span>            :         }</a>
+<a name="20964"><span class="lineNum">   20964 </span>            : </a>
+<a name="20965"><span class="lineNum">   20965 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;in, &amp;work[1], &amp;c__1, &amp;d__[ibegin], &amp;c__1);</span></a>
+<a name="20966"><span class="lineNum">   20966 </span><span class="lineNoCov">          0 :         i__2 = in - 1;</span></a>
+<a name="20967"><span class="lineNum">   20967 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__2, &amp;work[in + 1], &amp;c__1, &amp;e[ibegin], &amp;c__1);</span></a>
+<a name="20968"><span class="lineNum">   20968 </span><span class="lineNoCov">          0 :         i__2 = in - 1;</span></a>
+<a name="20969"><span class="lineNum">   20969 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="20970"><span class="lineNum">   20970 </span><span class="lineNoCov">          0 :             work[in * 3 + i__] = work[i__] * work[in + i__];</span></a>
+<a name="20971"><span class="lineNum">   20971 </span><span class="lineNoCov">          0 :             work[(in &lt;&lt; 2) + i__] = work[in * 3 + i__] * work[in + i__];</span></a>
+<a name="20972"><span class="lineNum">   20972 </span>            :         }</a>
+<a name="20973"><span class="lineNum">   20973 </span><span class="lineNoCov">          0 :         if (sgndef &gt; 0.) {</span></a>
+<a name="20974"><span class="lineNum">   20974 </span><span class="lineNoCov">          0 :             cnt = 1;</span></a>
+<a name="20975"><span class="lineNum">   20975 </span><span class="lineNoCov">          0 :             work[1] = (gl + gu) / 2. - sigma;</span></a>
+<a name="20976"><span class="lineNum">   20976 </span><span class="lineNoCov">          0 :             work[in + 1] = 0.;</span></a>
+<a name="20977"><span class="lineNum">   20977 </span><span class="lineNoCov">          0 :             work[(in &lt;&lt; 1) + 1] = (gu - gl) / 2.;</span></a>
+<a name="20978"><span class="lineNum">   20978 </span>            :         } else {</a>
+<a name="20979"><span class="lineNum">   20979 </span><span class="lineNoCov">          0 :             cnt = in;</span></a>
+<a name="20980"><span class="lineNum">   20980 </span><span class="lineNoCov">          0 :             work[in] = (gl + gu) / 2. - sigma;</span></a>
+<a name="20981"><span class="lineNum">   20981 </span><span class="lineNoCov">          0 :             work[in * 2] = 0.;</span></a>
+<a name="20982"><span class="lineNum">   20982 </span><span class="lineNoCov">          0 :             work[in * 3] = (gu - gl) / 2.;</span></a>
+<a name="20983"><span class="lineNum">   20983 </span>            :         }</a>
+<a name="20984"><span class="lineNum">   20984 </span><span class="lineNoCov">          0 :         rtol = eps * 4.;</span></a>
+<a name="20985"><span class="lineNum">   20985 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarrbx,SLARRBX)(&amp;in, &amp;d__[ibegin], &amp;e[ibegin], &amp;work[in * 3 + 1], &amp;work[(in &lt;&lt;</span></a>
+<a name="20986"><span class="lineNum">   20986 </span><span class="lineNoCov">          0 :                  2) + 1], &amp;cnt, &amp;cnt, &amp;rtol, &amp;rtol, &amp;c__0, &amp;work[1], &amp;work[in </span></a>
+<a name="20987"><span class="lineNum">   20987 </span><span class="lineNoCov">          0 :                 + 1], &amp;work[(in &lt;&lt; 1) + 1], &amp;work[in * 5 + 1], &amp;iwork[1], &amp;</span></a>
+<a name="20988"><span class="lineNum">   20988 </span>            :                 iinfo);</a>
+<a name="20989"><span class="lineNum">   20989 </span><span class="lineNoCov">          0 :         if (sgndef &gt; 0.) {</span></a>
+<a name="20990"><span class="lineNum">   20990 </span><span class="lineNoCov">          0 :             tau = work[1] - work[(in &lt;&lt; 1) + 1];</span></a>
+<a name="20991"><span class="lineNum">   20991 </span>            :         } else {</a>
+<a name="20992"><span class="lineNum">   20992 </span><span class="lineNoCov">          0 :             tau = work[in] + work[in * 3];</span></a>
+<a name="20993"><span class="lineNum">   20993 </span>            :         }</a>
+<a name="20994"><span class="lineNum">   20994 </span>            : </a>
+<a name="20995"><span class="lineNum">   20995 </span><span class="lineNoCov">          0 :         work[in * 3] = 1.;</span></a>
+<a name="20996"><span class="lineNum">   20996 </span>            :         delta = eps * 2.;</a>
+<a name="20997"><span class="lineNum">   20997 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="20998"><span class="lineNum">   20998 </span><span class="lineNoCov">          0 :         tau *= 1. - delta;</span></a>
+<a name="20999"><span class="lineNum">   20999 </span>            : </a>
+<a name="21000"><span class="lineNum">   21000 </span><span class="lineNoCov">          0 :         s = -tau;</span></a>
+<a name="21001"><span class="lineNum">   21001 </span>            :         j = ibegin;</a>
+<a name="21002"><span class="lineNum">   21002 </span><span class="lineNoCov">          0 :         i__2 = in - 1;</span></a>
+<a name="21003"><span class="lineNum">   21003 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21004"><span class="lineNum">   21004 </span><span class="lineNoCov">          0 :             work[i__] = d__[j] + s;</span></a>
+<a name="21005"><span class="lineNum">   21005 </span><span class="lineNoCov">          0 :             work[(in &lt;&lt; 1) + i__] = 1. / work[i__];</span></a>
+<a name="21006"><span class="lineNum">   21006 </span><span class="lineNoCov">          0 :             work[in + i__] = e[j] * d__[j] * work[(in &lt;&lt; 1) + i__];</span></a>
+<a name="21007"><span class="lineNum">   21007 </span><span class="lineNoCov">          0 :             s = s * work[in + i__] * e[j] - tau;</span></a>
+<a name="21008"><span class="lineNum">   21008 </span><span class="lineNoCov">          0 :             ++j;</span></a>
+<a name="21009"><span class="lineNum">   21009 </span>            :         }</a>
+<a name="21010"><span class="lineNum">   21010 </span><span class="lineNoCov">          0 :         work[in] = d__[iend] + s;</span></a>
+<a name="21011"><span class="lineNum">   21011 </span>            : </a>
+<a name="21012"><span class="lineNum">   21012 </span><span class="lineNoCov">          0 :         for (i__ = in; i__ &gt;= 1; --i__) {</span></a>
+<a name="21013"><span class="lineNum">   21013 </span><span class="lineNoCov">          0 :             tmp = sgndef * work[i__];</span></a>
+<a name="21014"><span class="lineNum">   21014 </span><span class="lineNoCov">          0 :             if (tmp &lt; 0. || std::abs(work[(in &lt;&lt; 1) + i__])&lt;PLUMED_GMX_FLOAT_MIN || std::isnan(tmp)) {</span></a>
+<a name="21015"><span class="lineNum">   21015 </span><span class="lineNoCov">          0 :                 delta *= 2.;</span></a>
+<a name="21016"><span class="lineNum">   21016 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="21017"><span class="lineNum">   21017 </span>            :             }</a>
+<a name="21018"><span class="lineNum">   21018 </span>            :         }</a>
+<a name="21019"><span class="lineNum">   21019 </span>            : </a>
+<a name="21020"><span class="lineNum">   21020 </span><span class="lineNoCov">          0 :         sigma += tau;</span></a>
+<a name="21021"><span class="lineNum">   21021 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;in, &amp;work[1], &amp;c__1, &amp;d__[ibegin], &amp;c__1);</span></a>
+<a name="21022"><span class="lineNum">   21022 </span><span class="lineNoCov">          0 :         i__2 = in - 1;</span></a>
+<a name="21023"><span class="lineNum">   21023 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__2, &amp;work[in + 1], &amp;c__1, &amp;e[ibegin], &amp;c__1);</span></a>
+<a name="21024"><span class="lineNum">   21024 </span><span class="lineNoCov">          0 :         e[iend] = sigma;</span></a>
+<a name="21025"><span class="lineNum">   21025 </span><span class="lineNoCov">          0 :         tmp = (float) in * 4. * eps * (std::abs(sigma) + std::abs(tau));</span></a>
+<a name="21026"><span class="lineNum">   21026 </span>            :         i__2 = iend;</a>
+<a name="21027"><span class="lineNum">   21027 </span><span class="lineNoCov">          0 :         for (i__ = ibegin; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21028"><span class="lineNum">   21028 </span><span class="lineNoCov">          0 :             gersch[(i__ &lt;&lt; 1) - 1] = gersch[(i__ &lt;&lt; 1) - 1] - sigma - tmp;</span></a>
+<a name="21029"><span class="lineNum">   21029 </span><span class="lineNoCov">          0 :             gersch[i__ * 2] = gersch[i__ * 2] - sigma + tmp;</span></a>
+<a name="21030"><span class="lineNum">   21030 </span>            :         }</a>
+<a name="21031"><span class="lineNum">   21031 </span>            : </a>
+<a name="21032"><span class="lineNum">   21032 </span>            :         j = ibegin;</a>
+<a name="21033"><span class="lineNum">   21033 </span><span class="lineNoCov">          0 :         i__2 = in - 1;</span></a>
+<a name="21034"><span class="lineNum">   21034 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21035"><span class="lineNum">   21035 </span><span class="lineNoCov">          0 :             work[(i__ &lt;&lt; 1) - 1] = std::abs(d__[j]);</span></a>
+<a name="21036"><span class="lineNum">   21036 </span><span class="lineNoCov">          0 :             work[i__ * 2] = e[j] * e[j] * work[(i__ &lt;&lt; 1) - 1];</span></a>
+<a name="21037"><span class="lineNum">   21037 </span><span class="lineNoCov">          0 :             ++j;</span></a>
+<a name="21038"><span class="lineNum">   21038 </span>            :         }</a>
+<a name="21039"><span class="lineNum">   21039 </span><span class="lineNoCov">          0 :         work[(in &lt;&lt; 1) - 1] = std::abs(d__[iend]);</span></a>
+<a name="21040"><span class="lineNum">   21040 </span>            : </a>
+<a name="21041"><span class="lineNum">   21041 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasq2,SLASQ2)(&amp;in, &amp;work[1], info);</span></a>
+<a name="21042"><span class="lineNum">   21042 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="21043"><span class="lineNum">   21043 </span>            :             return;</a>
+<a name="21044"><span class="lineNum">   21044 </span>            :         }</a>
+<a name="21045"><span class="lineNum">   21045 </span>            : </a>
+<a name="21046"><span class="lineNum">   21046 </span><span class="lineNoCov">          0 :         if (sgndef &gt; 0.) {</span></a>
+<a name="21047"><span class="lineNum">   21047 </span><span class="lineNoCov">          0 :             i__2 = in;</span></a>
+<a name="21048"><span class="lineNum">   21048 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21049"><span class="lineNum">   21049 </span><span class="lineNoCov">          0 :                 ++(*m);</span></a>
+<a name="21050"><span class="lineNum">   21050 </span><span class="lineNoCov">          0 :                 w[*m] = work[in - i__ + 1];</span></a>
+<a name="21051"><span class="lineNum">   21051 </span><span class="lineNoCov">          0 :                 iblock[*m] = jblk;</span></a>
+<a name="21052"><span class="lineNum">   21052 </span><span class="lineNoCov">          0 :                 indexw[*m] = i__;</span></a>
+<a name="21053"><span class="lineNum">   21053 </span>            :             }</a>
+<a name="21054"><span class="lineNum">   21054 </span>            :         } else {</a>
+<a name="21055"><span class="lineNum">   21055 </span><span class="lineNoCov">          0 :             i__2 = in;</span></a>
+<a name="21056"><span class="lineNum">   21056 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21057"><span class="lineNum">   21057 </span><span class="lineNoCov">          0 :                 ++(*m);</span></a>
+<a name="21058"><span class="lineNum">   21058 </span><span class="lineNoCov">          0 :                 w[*m] = -work[i__];</span></a>
+<a name="21059"><span class="lineNum">   21059 </span><span class="lineNoCov">          0 :                 iblock[*m] = jblk;</span></a>
+<a name="21060"><span class="lineNum">   21060 </span><span class="lineNoCov">          0 :                 indexw[*m] = i__;</span></a>
+<a name="21061"><span class="lineNum">   21061 </span>            :             }</a>
+<a name="21062"><span class="lineNum">   21062 </span>            :         }</a>
+<a name="21063"><span class="lineNum">   21063 </span><span class="lineNoCov">          0 :         ibegin = iend + 1;</span></a>
+<a name="21064"><span class="lineNum">   21064 </span><span class="lineNoCov">          0 : L170:</span></a>
+<a name="21065"><span class="lineNum">   21065 </span>            :         ;</a>
+<a name="21066"><span class="lineNum">   21066 </span>            :     }</a>
+<a name="21067"><span class="lineNum">   21067 </span><span class="lineNoCov">          0 :     if (irange == 2) {</span></a>
+<a name="21068"><span class="lineNum">   21068 </span><span class="lineNoCov">          0 :         *m = 0;</span></a>
+<a name="21069"><span class="lineNum">   21069 </span>            :         ibegin = 1;</a>
+<a name="21070"><span class="lineNum">   21070 </span><span class="lineNoCov">          0 :         i__1 = *nsplit;</span></a>
+<a name="21071"><span class="lineNum">   21071 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21072"><span class="lineNum">   21072 </span><span class="lineNoCov">          0 :             iend = isplit[i__];</span></a>
+<a name="21073"><span class="lineNum">   21073 </span><span class="lineNoCov">          0 :             vvl = *vl - e[iend];</span></a>
+<a name="21074"><span class="lineNum">   21074 </span><span class="lineNoCov">          0 :             vvu = *vu - e[iend];</span></a>
+<a name="21075"><span class="lineNum">   21075 </span><span class="lineNoCov">          0 :             i__2 = iend;</span></a>
+<a name="21076"><span class="lineNum">   21076 </span><span class="lineNoCov">          0 :             for (j = ibegin; j &lt;= i__2; ++j) {</span></a>
+<a name="21077"><span class="lineNum">   21077 </span><span class="lineNoCov">          0 :                 if (vvl &lt;= w[j] &amp;&amp; w[j] &lt;= vvu) {</span></a>
+<a name="21078"><span class="lineNum">   21078 </span><span class="lineNoCov">          0 :                     ++(*m);</span></a>
+<a name="21079"><span class="lineNum">   21079 </span><span class="lineNoCov">          0 :                     w[*m] = w[j];</span></a>
+<a name="21080"><span class="lineNum">   21080 </span><span class="lineNoCov">          0 :                     iblock[*m] = i__;</span></a>
+<a name="21081"><span class="lineNum">   21081 </span><span class="lineNoCov">          0 :                     indexw[*m] = j - ibegin + 1;</span></a>
+<a name="21082"><span class="lineNum">   21082 </span>            :                 }</a>
+<a name="21083"><span class="lineNum">   21083 </span>            :             }</a>
+<a name="21084"><span class="lineNum">   21084 </span><span class="lineNoCov">          0 :             ibegin = iend + 1;</span></a>
+<a name="21085"><span class="lineNum">   21085 </span>            :         }</a>
+<a name="21086"><span class="lineNum">   21086 </span><span class="lineNoCov">          0 :     } else if (irange == 3) {</span></a>
+<a name="21087"><span class="lineNum">   21087 </span><span class="lineNoCov">          0 :         *m = *iu - *il + 1;</span></a>
+<a name="21088"><span class="lineNum">   21088 </span><span class="lineNoCov">          0 :         if (*nsplit == 1) {</span></a>
+<a name="21089"><span class="lineNum">   21089 </span>            :             i__1 = *m;</a>
+<a name="21090"><span class="lineNum">   21090 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21091"><span class="lineNum">   21091 </span><span class="lineNoCov">          0 :                 w[i__] = w[*il + i__ - 1];</span></a>
+<a name="21092"><span class="lineNum">   21092 </span><span class="lineNoCov">          0 :                 indexw[i__] = *il + i__ - 1;</span></a>
+<a name="21093"><span class="lineNum">   21093 </span>            :             }</a>
+<a name="21094"><span class="lineNum">   21094 </span>            :         } else {</a>
+<a name="21095"><span class="lineNum">   21095 </span>            :             ibegin = 1;</a>
+<a name="21096"><span class="lineNum">   21096 </span>            :             i__1 = *nsplit;</a>
+<a name="21097"><span class="lineNum">   21097 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21098"><span class="lineNum">   21098 </span><span class="lineNoCov">          0 :                 iend = isplit[i__];</span></a>
+<a name="21099"><span class="lineNum">   21099 </span><span class="lineNoCov">          0 :                 i__2 = iend;</span></a>
+<a name="21100"><span class="lineNum">   21100 </span><span class="lineNoCov">          0 :                 for (j = ibegin; j &lt;= i__2; ++j) {</span></a>
+<a name="21101"><span class="lineNum">   21101 </span><span class="lineNoCov">          0 :                     work[j] = w[j] + e[iend];</span></a>
+<a name="21102"><span class="lineNum">   21102 </span>            :                 }</a>
+<a name="21103"><span class="lineNum">   21103 </span><span class="lineNoCov">          0 :                 ibegin = iend + 1;</span></a>
+<a name="21104"><span class="lineNum">   21104 </span>            :             }</a>
+<a name="21105"><span class="lineNum">   21105 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="21106"><span class="lineNum">   21106 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21107"><span class="lineNum">   21107 </span><span class="lineNoCov">          0 :                 iwork[i__] = i__;</span></a>
+<a name="21108"><span class="lineNum">   21108 </span><span class="lineNoCov">          0 :                 iwork[*n + i__] = iblock[i__];</span></a>
+<a name="21109"><span class="lineNum">   21109 </span>            :             }</a>
+<a name="21110"><span class="lineNum">   21110 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasrt2,SLASRT2)(&quot;I&quot;, n, &amp;work[1], &amp;iwork[1], &amp;iinfo);</span></a>
+<a name="21111"><span class="lineNum">   21111 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="21112"><span class="lineNum">   21112 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21113"><span class="lineNum">   21113 </span><span class="lineNoCov">          0 :                 itmp = iwork[*il + i__ - 1];</span></a>
+<a name="21114"><span class="lineNum">   21114 </span><span class="lineNoCov">          0 :                 work[i__] = w[itmp];</span></a>
+<a name="21115"><span class="lineNum">   21115 </span><span class="lineNoCov">          0 :                 iblock[i__] = iwork[*n + itmp];</span></a>
+<a name="21116"><span class="lineNum">   21116 </span>            :             }</a>
+<a name="21117"><span class="lineNum">   21117 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="21118"><span class="lineNum">   21118 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21119"><span class="lineNum">   21119 </span><span class="lineNoCov">          0 :                 iwork[*n + i__] = iwork[*il + i__ - 1];</span></a>
+<a name="21120"><span class="lineNum">   21120 </span><span class="lineNoCov">          0 :                 iwork[i__] = i__;</span></a>
+<a name="21121"><span class="lineNum">   21121 </span>            :             }</a>
+<a name="21122"><span class="lineNum">   21122 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(ilasrt2,ILASRT2)(&quot;I&quot;, m, &amp;iblock[1], &amp;iwork[1], &amp;iinfo);</span></a>
+<a name="21123"><span class="lineNum">   21123 </span>            :             j = 1;</a>
+<a name="21124"><span class="lineNum">   21124 </span><span class="lineNoCov">          0 :             itmp = iblock[j];</span></a>
+<a name="21125"><span class="lineNum">   21125 </span><span class="lineNoCov">          0 :             cnt = iwork[*n + iwork[j]];</span></a>
+<a name="21126"><span class="lineNum">   21126 </span><span class="lineNoCov">          0 :             if (itmp == 1) {</span></a>
+<a name="21127"><span class="lineNum">   21127 </span>            :                 ibegin = 1;</a>
+<a name="21128"><span class="lineNum">   21128 </span>            :             } else {</a>
+<a name="21129"><span class="lineNum">   21129 </span><span class="lineNoCov">          0 :                 ibegin = isplit[itmp - 1] + 1;</span></a>
+<a name="21130"><span class="lineNum">   21130 </span>            :             }</a>
+<a name="21131"><span class="lineNum">   21131 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="21132"><span class="lineNum">   21132 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21133"><span class="lineNum">   21133 </span><span class="lineNoCov">          0 :                 w[i__] = work[iwork[i__]];</span></a>
+<a name="21134"><span class="lineNum">   21134 </span><span class="lineNoCov">          0 :                 if (iblock[i__] != itmp || i__ == *m) {</span></a>
+<a name="21135"><span class="lineNum">   21135 </span><span class="lineNoCov">          0 :                     if (iblock[i__] == itmp) {</span></a>
+<a name="21136"><span class="lineNum">   21136 </span><span class="lineNoCov">          0 :                         till = *m;</span></a>
+<a name="21137"><span class="lineNum">   21137 </span>            :                     } else {</a>
+<a name="21138"><span class="lineNum">   21138 </span><span class="lineNoCov">          0 :                         till = i__ - 1;</span></a>
+<a name="21139"><span class="lineNum">   21139 </span>            :                     }</a>
+<a name="21140"><span class="lineNum">   21140 </span><span class="lineNoCov">          0 :                     i__2 = till - j + 1;</span></a>
+<a name="21141"><span class="lineNum">   21141 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(&quot;I&quot;, &amp;i__2, &amp;w[j], &amp;iinfo);</span></a>
+<a name="21142"><span class="lineNum">   21142 </span><span class="lineNoCov">          0 :                     cnt = cnt - ibegin + 1;</span></a>
+<a name="21143"><span class="lineNum">   21143 </span><span class="lineNoCov">          0 :                     i__2 = till;</span></a>
+<a name="21144"><span class="lineNum">   21144 </span><span class="lineNoCov">          0 :                     for (k = j; k &lt;= i__2; ++k) {</span></a>
+<a name="21145"><span class="lineNum">   21145 </span><span class="lineNoCov">          0 :                         indexw[k] = cnt + k - j;</span></a>
+<a name="21146"><span class="lineNum">   21146 </span>            :                     }</a>
+<a name="21147"><span class="lineNum">   21147 </span>            :                     j = i__;</a>
+<a name="21148"><span class="lineNum">   21148 </span><span class="lineNoCov">          0 :                     itmp = iblock[j];</span></a>
+<a name="21149"><span class="lineNum">   21149 </span><span class="lineNoCov">          0 :                     cnt = iwork[*n + iwork[j]];</span></a>
+<a name="21150"><span class="lineNum">   21150 </span><span class="lineNoCov">          0 :                     ibegin = isplit[itmp - 1] + 1;</span></a>
+<a name="21151"><span class="lineNum">   21151 </span><span class="lineNoCov">          0 :                     if (i__ == *m &amp;&amp; till &lt; *m) {</span></a>
+<a name="21152"><span class="lineNum">   21152 </span><span class="lineNoCov">          0 :                         indexw[*m] = cnt - ibegin + 1;</span></a>
+<a name="21153"><span class="lineNum">   21153 </span>            :                     }</a>
+<a name="21154"><span class="lineNum">   21154 </span>            :                 } else {</a>
+<a name="21155"><span class="lineNum">   21155 </span><span class="lineNoCov">          0 :                     i__2 = cnt, i__3 = iwork[*n + iwork[i__]];</span></a>
+<a name="21156"><span class="lineNum">   21156 </span><span class="lineNoCov">          0 :                     cnt = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="21157"><span class="lineNum">   21157 </span>            :                 }</a>
+<a name="21158"><span class="lineNum">   21158 </span>            :             }</a>
+<a name="21159"><span class="lineNum">   21159 </span>            :         }</a>
+<a name="21160"><span class="lineNum">   21160 </span>            :     }</a>
+<a name="21161"><span class="lineNum">   21161 </span>            : </a>
+<a name="21162"><span class="lineNum">   21162 </span>            :     return;</a>
+<a name="21163"><span class="lineNum">   21163 </span>            : </a>
+<a name="21164"><span class="lineNum">   21164 </span>            : }</a>
+<a name="21165"><span class="lineNum">   21165 </span>            : </a>
+<a name="21166"><span class="lineNum">   21166 </span>            : </a>
+<a name="21167"><span class="lineNum">   21167 </span>            : }</a>
+<a name="21168"><span class="lineNum">   21168 </span>            : }</a>
+<a name="21169"><span class="lineNum">   21169 </span>            : #include &lt;cmath&gt;</a>
+<a name="21170"><span class="lineNum">   21170 </span>            : </a>
+<a name="21171"><span class="lineNum">   21171 </span>            : #include &quot;real.h&quot;</a>
+<a name="21172"><span class="lineNum">   21172 </span>            : </a>
+<a name="21173"><span class="lineNum">   21173 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21174"><span class="lineNum">   21174 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="21175"><span class="lineNum">   21175 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="21176"><span class="lineNum">   21176 </span>            : </a>
+<a name="21177"><span class="lineNum">   21177 </span>            : </a>
+<a name="21178"><span class="lineNum">   21178 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21179"><span class="lineNum">   21179 </span>            : namespace PLMD{</a>
+<a name="21180"><span class="lineNum">   21180 </span>            : namespace lapack{</a>
+<a name="21181"><span class="lineNum">   21181 </span>            : using namespace blas;</a>
+<a name="21182"><span class="lineNum">   21182 </span>            : void</a>
+<a name="21183"><span class="lineNum">   21183 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarrfx,SLARRFX)(int *n, </span></a>
+<a name="21184"><span class="lineNum">   21184 </span>            :         float *d__, </a>
+<a name="21185"><span class="lineNum">   21185 </span>            :         float *l, </a>
+<a name="21186"><span class="lineNum">   21186 </span>            :         float *ld, </a>
+<a name="21187"><span class="lineNum">   21187 </span>            :         float *lld, </a>
+<a name="21188"><span class="lineNum">   21188 </span>            :         int *ifirst, </a>
+<a name="21189"><span class="lineNum">   21189 </span>            :         int *ilast, </a>
+<a name="21190"><span class="lineNum">   21190 </span>            :         float *w, </a>
+<a name="21191"><span class="lineNum">   21191 </span>            :         float *sigma, </a>
+<a name="21192"><span class="lineNum">   21192 </span>            :         float *dplus, </a>
+<a name="21193"><span class="lineNum">   21193 </span>            :         float *lplus, </a>
+<a name="21194"><span class="lineNum">   21194 </span>            :         float *work,</a>
+<a name="21195"><span class="lineNum">   21195 </span>            :         int *info)</a>
+<a name="21196"><span class="lineNum">   21196 </span>            : {</a>
+<a name="21197"><span class="lineNum">   21197 </span><span class="lineNoCov">          0 :     int i1 = 1;</span></a>
+<a name="21198"><span class="lineNum">   21198 </span>            :     int i__1;</a>
+<a name="21199"><span class="lineNum">   21199 </span>            :     float d__2, d__3;</a>
+<a name="21200"><span class="lineNum">   21200 </span>            : </a>
+<a name="21201"><span class="lineNum">   21201 </span>            :     int i__;</a>
+<a name="21202"><span class="lineNum">   21202 </span>            :     float s, eps, tmp, dmax1, dmax2, delta;</a>
+<a name="21203"><span class="lineNum">   21203 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="21204"><span class="lineNum">   21204 </span><span class="lineNoCov">          0 :     --lplus;</span></a>
+<a name="21205"><span class="lineNum">   21205 </span><span class="lineNoCov">          0 :     --dplus;</span></a>
+<a name="21206"><span class="lineNum">   21206 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="21207"><span class="lineNum">   21207 </span>            :     --lld;</a>
+<a name="21208"><span class="lineNum">   21208 </span><span class="lineNoCov">          0 :     --ld;</span></a>
+<a name="21209"><span class="lineNum">   21209 </span><span class="lineNoCov">          0 :     --l;</span></a>
+<a name="21210"><span class="lineNum">   21210 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="21211"><span class="lineNum">   21211 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="21212"><span class="lineNum">   21212 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="21213"><span class="lineNum">   21213 </span><span class="lineNoCov">          0 :     *sigma = w[*ifirst];</span></a>
+<a name="21214"><span class="lineNum">   21214 </span>            :     delta = eps * 2.;</a>
+<a name="21215"><span class="lineNum">   21215 </span>            : </a>
+<a name="21216"><span class="lineNum">   21216 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="21217"><span class="lineNum">   21217 </span><span class="lineNoCov">          0 :     s = -(*sigma);</span></a>
+<a name="21218"><span class="lineNum">   21218 </span><span class="lineNoCov">          0 :     dplus[1] = d__[1] + s;</span></a>
+<a name="21219"><span class="lineNum">   21219 </span>            :     dmax1 = std::abs(dplus[1]);</a>
+<a name="21220"><span class="lineNum">   21220 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="21221"><span class="lineNum">   21221 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21222"><span class="lineNum">   21222 </span><span class="lineNoCov">          0 :         lplus[i__] = ld[i__] / dplus[i__];</span></a>
+<a name="21223"><span class="lineNum">   21223 </span><span class="lineNoCov">          0 :         s = s * lplus[i__] * l[i__] - *sigma;</span></a>
+<a name="21224"><span class="lineNum">   21224 </span><span class="lineNoCov">          0 :         dplus[i__ + 1] = d__[i__ + 1] + s;</span></a>
+<a name="21225"><span class="lineNum">   21225 </span>            :         d__2 = dmax1, d__3 = std::abs(dplus[i__ + 1]);</a>
+<a name="21226"><span class="lineNum">   21226 </span><span class="lineNoCov">          0 :         dmax1 = (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="21227"><span class="lineNum">   21227 </span>            :     }</a>
+<a name="21228"><span class="lineNum">   21228 </span><span class="lineNoCov">          0 :     if (std::isnan(dmax1)) {</span></a>
+<a name="21229"><span class="lineNum">   21229 </span><span class="lineNoCov">          0 :         *sigma -= std::abs(*sigma) * delta;</span></a>
+<a name="21230"><span class="lineNum">   21230 </span><span class="lineNoCov">          0 :         delta *= 2.;</span></a>
+<a name="21231"><span class="lineNum">   21231 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="21232"><span class="lineNum">   21232 </span>            :     }</a>
+<a name="21233"><span class="lineNum">   21233 </span>            : </a>
+<a name="21234"><span class="lineNum">   21234 </span><span class="lineNoCov">          0 :     tmp = w[*ilast];</span></a>
+<a name="21235"><span class="lineNum">   21235 </span>            :     delta = eps * 2.;</a>
+<a name="21236"><span class="lineNum">   21236 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="21237"><span class="lineNum">   21237 </span><span class="lineNoCov">          0 :     s = -tmp;</span></a>
+<a name="21238"><span class="lineNum">   21238 </span><span class="lineNoCov">          0 :     work[1] = d__[1] + s;</span></a>
+<a name="21239"><span class="lineNum">   21239 </span>            :     dmax2 = std::abs(work[1]);</a>
+<a name="21240"><span class="lineNum">   21240 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="21241"><span class="lineNum">   21241 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21242"><span class="lineNum">   21242 </span><span class="lineNoCov">          0 :         work[*n + i__] = ld[i__] / work[i__];</span></a>
+<a name="21243"><span class="lineNum">   21243 </span><span class="lineNoCov">          0 :         s = s * work[*n + i__] * l[i__] - tmp;</span></a>
+<a name="21244"><span class="lineNum">   21244 </span><span class="lineNoCov">          0 :         work[i__ + 1] = d__[i__ + 1] + s;</span></a>
+<a name="21245"><span class="lineNum">   21245 </span>            :         d__2 = dmax2, d__3 = std::abs(work[i__ + 1]);</a>
+<a name="21246"><span class="lineNum">   21246 </span><span class="lineNoCov">          0 :         dmax2 = (d__2&gt;d__3) ? d__2 : d__3;</span></a>
+<a name="21247"><span class="lineNum">   21247 </span>            :     }</a>
+<a name="21248"><span class="lineNum">   21248 </span><span class="lineNoCov">          0 :     if (std::isnan(dmax2)) {</span></a>
+<a name="21249"><span class="lineNum">   21249 </span><span class="lineNoCov">          0 :         tmp += std::abs(tmp) * delta;</span></a>
+<a name="21250"><span class="lineNum">   21250 </span><span class="lineNoCov">          0 :         delta *= 2.;</span></a>
+<a name="21251"><span class="lineNum">   21251 </span><span class="lineNoCov">          0 :         goto L30;</span></a>
+<a name="21252"><span class="lineNum">   21252 </span>            :     }</a>
+<a name="21253"><span class="lineNum">   21253 </span><span class="lineNoCov">          0 :     if (dmax2 &lt; dmax1) {</span></a>
+<a name="21254"><span class="lineNum">   21254 </span><span class="lineNoCov">          0 :         *sigma = tmp;</span></a>
+<a name="21255"><span class="lineNum">   21255 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;work[1], &amp;i1, &amp;dplus[1], &amp;i1);</span></a>
+<a name="21256"><span class="lineNum">   21256 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="21257"><span class="lineNum">   21257 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;work[*n + 1], &amp;i1, &amp;lplus[1], &amp;i1);</span></a>
+<a name="21258"><span class="lineNum">   21258 </span>            :     }</a>
+<a name="21259"><span class="lineNum">   21259 </span>            : </a>
+<a name="21260"><span class="lineNum">   21260 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="21261"><span class="lineNum">   21261 </span>            : }</a>
+<a name="21262"><span class="lineNum">   21262 </span>            : }</a>
+<a name="21263"><span class="lineNum">   21263 </span>            : }</a>
+<a name="21264"><span class="lineNum">   21264 </span>            : #include &lt;cmath&gt;</a>
+<a name="21265"><span class="lineNum">   21265 </span>            : </a>
+<a name="21266"><span class="lineNum">   21266 </span>            : #include &quot;real.h&quot;</a>
+<a name="21267"><span class="lineNum">   21267 </span>            : </a>
+<a name="21268"><span class="lineNum">   21268 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21269"><span class="lineNum">   21269 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="21270"><span class="lineNum">   21270 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="21271"><span class="lineNum">   21271 </span>            : </a>
+<a name="21272"><span class="lineNum">   21272 </span>            : </a>
+<a name="21273"><span class="lineNum">   21273 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21274"><span class="lineNum">   21274 </span>            : namespace PLMD{</a>
+<a name="21275"><span class="lineNum">   21275 </span>            : namespace lapack{</a>
+<a name="21276"><span class="lineNum">   21276 </span>            : using namespace blas;</a>
+<a name="21277"><span class="lineNum">   21277 </span>            : void</a>
+<a name="21278"><span class="lineNum">   21278 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slarrvx,SLARRVX)(int *n, </span></a>
+<a name="21279"><span class="lineNum">   21279 </span>            :         float *d__, </a>
+<a name="21280"><span class="lineNum">   21280 </span>            :         float *l, </a>
+<a name="21281"><span class="lineNum">   21281 </span>            :         int *isplit,</a>
+<a name="21282"><span class="lineNum">   21282 </span>            :         int *m, </a>
+<a name="21283"><span class="lineNum">   21283 </span>            :         float *w,</a>
+<a name="21284"><span class="lineNum">   21284 </span>            :         int *iblock, </a>
+<a name="21285"><span class="lineNum">   21285 </span>            :         int *indexw, </a>
+<a name="21286"><span class="lineNum">   21286 </span>            :         float *gersch, </a>
+<a name="21287"><span class="lineNum">   21287 </span>            :         float *tol, </a>
+<a name="21288"><span class="lineNum">   21288 </span>            :         float *z__, </a>
+<a name="21289"><span class="lineNum">   21289 </span>            :         int *ldz, </a>
+<a name="21290"><span class="lineNum">   21290 </span>            :         int *isuppz, </a>
+<a name="21291"><span class="lineNum">   21291 </span>            :         float *work, </a>
+<a name="21292"><span class="lineNum">   21292 </span>            :         int *iwork, </a>
+<a name="21293"><span class="lineNum">   21293 </span>            :         int *info)</a>
+<a name="21294"><span class="lineNum">   21294 </span>            : {</a>
+<a name="21295"><span class="lineNum">   21295 </span>            :     int z_dim1, z_offset, i__1, i__2, i__3, i__4, i__5, i__6;</a>
+<a name="21296"><span class="lineNum">   21296 </span>            :     float d__1, d__2;</a>
+<a name="21297"><span class="lineNum">   21297 </span><span class="lineNoCov">          0 :     float c_b5 = 0.;</span></a>
+<a name="21298"><span class="lineNum">   21298 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="21299"><span class="lineNum">   21299 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="21300"><span class="lineNum">   21300 </span>            : </a>
+<a name="21301"><span class="lineNum">   21301 </span>            :     int i__, j, k, p, q;</a>
+<a name="21302"><span class="lineNum">   21302 </span>            :     int im, in;</a>
+<a name="21303"><span class="lineNum">   21303 </span>            :     float gap, eps, tmp;</a>
+<a name="21304"><span class="lineNum">   21304 </span>            :     int zto;</a>
+<a name="21305"><span class="lineNum">   21305 </span>            :     float ztz;</a>
+<a name="21306"><span class="lineNum">   21306 </span>            :     int iend, jblk;</a>
+<a name="21307"><span class="lineNum">   21307 </span>            :     int wend, iter, temp[1], ktot;</a>
+<a name="21308"><span class="lineNum">   21308 </span>            :     int itmp1, itmp2;</a>
+<a name="21309"><span class="lineNum">   21309 </span>            :     int indld;</a>
+<a name="21310"><span class="lineNum">   21310 </span>            :     float sigma;</a>
+<a name="21311"><span class="lineNum">   21311 </span>            :     int ndone, iinfo, iindr;</a>
+<a name="21312"><span class="lineNum">   21312 </span>            :     float resid;</a>
+<a name="21313"><span class="lineNum">   21313 </span>            :     int nomgs;</a>
+<a name="21314"><span class="lineNum">   21314 </span>            :     int nclus;</a>
+<a name="21315"><span class="lineNum">   21315 </span>            :     int zfrom, iindc1, iindc2;</a>
+<a name="21316"><span class="lineNum">   21316 </span>            :     float lambda;</a>
+<a name="21317"><span class="lineNum">   21317 </span>            :     int ibegin;</a>
+<a name="21318"><span class="lineNum">   21318 </span>            :     int indgap, indlld;</a>
+<a name="21319"><span class="lineNum">   21319 </span>            :     float mingma;</a>
+<a name="21320"><span class="lineNum">   21320 </span>            :     int oldien, oldncl, wbegin;</a>
+<a name="21321"><span class="lineNum">   21321 </span>            :     float relgap;</a>
+<a name="21322"><span class="lineNum">   21322 </span>            :     int oldcls;</a>
+<a name="21323"><span class="lineNum">   21323 </span>            :     int ndepth, inderr, iindwk;</a>
+<a name="21324"><span class="lineNum">   21324 </span>            :     int newcls, oldfst;</a>
+<a name="21325"><span class="lineNum">   21325 </span>            :     float minrgp=0.0;</a>
+<a name="21326"><span class="lineNum">   21326 </span>            :     int indwrk, oldlst;</a>
+<a name="21327"><span class="lineNum">   21327 </span>            :     float reltol;</a>
+<a name="21328"><span class="lineNum">   21328 </span>            :     int newfrs, newftt, parity;</a>
+<a name="21329"><span class="lineNum">   21329 </span>            :     float mgstol, nrminv, rqcorr;</a>
+<a name="21330"><span class="lineNum">   21330 </span>            :     int newlst, newsiz;</a>
+<a name="21331"><span class="lineNum">   21331 </span>            : </a>
+<a name="21332"><span class="lineNum">   21332 </span>            : </a>
+<a name="21333"><span class="lineNum">   21333 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="21334"><span class="lineNum">   21334 </span><span class="lineNoCov">          0 :     --l;</span></a>
+<a name="21335"><span class="lineNum">   21335 </span>            :     --isplit;</a>
+<a name="21336"><span class="lineNum">   21336 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="21337"><span class="lineNum">   21337 </span><span class="lineNoCov">          0 :     --iblock;</span></a>
+<a name="21338"><span class="lineNum">   21338 </span><span class="lineNoCov">          0 :     --indexw;</span></a>
+<a name="21339"><span class="lineNum">   21339 </span>            :     --gersch;</a>
+<a name="21340"><span class="lineNum">   21340 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="21341"><span class="lineNum">   21341 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="21342"><span class="lineNum">   21342 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="21343"><span class="lineNum">   21343 </span><span class="lineNoCov">          0 :     --isuppz;</span></a>
+<a name="21344"><span class="lineNum">   21344 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="21345"><span class="lineNum">   21345 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="21346"><span class="lineNum">   21346 </span>            : </a>
+<a name="21347"><span class="lineNum">   21347 </span><span class="lineNoCov">          0 :     inderr = *n;</span></a>
+<a name="21348"><span class="lineNum">   21348 </span><span class="lineNoCov">          0 :     indld = *n &lt;&lt; 1;</span></a>
+<a name="21349"><span class="lineNum">   21349 </span><span class="lineNoCov">          0 :     indlld = *n * 3;</span></a>
+<a name="21350"><span class="lineNum">   21350 </span><span class="lineNoCov">          0 :     indgap = *n &lt;&lt; 2;</span></a>
+<a name="21351"><span class="lineNum">   21351 </span><span class="lineNoCov">          0 :     indwrk = *n * 5 + 1;</span></a>
+<a name="21352"><span class="lineNum">   21352 </span>            : </a>
+<a name="21353"><span class="lineNum">   21353 </span>            :     iindr = *n;</a>
+<a name="21354"><span class="lineNum">   21354 </span>            :     iindc1 = *n &lt;&lt; 1;</a>
+<a name="21355"><span class="lineNum">   21355 </span>            :     iindc2 = *n * 3;</a>
+<a name="21356"><span class="lineNum">   21356 </span><span class="lineNoCov">          0 :     iindwk = (*n &lt;&lt; 2) + 1;</span></a>
+<a name="21357"><span class="lineNum">   21357 </span>            : </a>
+<a name="21358"><span class="lineNum">   21358 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="21359"><span class="lineNum">   21359 </span>            : </a>
+<a name="21360"><span class="lineNum">   21360 </span>            :     i__1 = *n &lt;&lt; 1;</a>
+<a name="21361"><span class="lineNum">   21361 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21362"><span class="lineNum">   21362 </span><span class="lineNoCov">          0 :         iwork[i__] = 0;</span></a>
+<a name="21363"><span class="lineNum">   21363 </span>            :     }</a>
+<a name="21364"><span class="lineNum">   21364 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;Full&quot;, n, m, &amp;c_b5, &amp;c_b5, &amp;z__[z_offset], ldz);</span></a>
+<a name="21365"><span class="lineNum">   21365 </span>            :     mgstol = eps * 100.;</a>
+<a name="21366"><span class="lineNum">   21366 </span>            : </a>
+<a name="21367"><span class="lineNum">   21367 </span>            :     ibegin = 1;</a>
+<a name="21368"><span class="lineNum">   21368 </span>            :     wbegin = 1;</a>
+<a name="21369"><span class="lineNum">   21369 </span><span class="lineNoCov">          0 :     i__1 = iblock[*m];</span></a>
+<a name="21370"><span class="lineNum">   21370 </span><span class="lineNoCov">          0 :     for (jblk = 1; jblk &lt;= i__1; ++jblk) {</span></a>
+<a name="21371"><span class="lineNum">   21371 </span><span class="lineNoCov">          0 :         iend = isplit[jblk];</span></a>
+<a name="21372"><span class="lineNum">   21372 </span>            : </a>
+<a name="21373"><span class="lineNum">   21373 </span><span class="lineNoCov">          0 :         wend = wbegin - 1;</span></a>
+<a name="21374"><span class="lineNum">   21374 </span><span class="lineNoCov">          0 : L171:</span></a>
+<a name="21375"><span class="lineNum">   21375 </span><span class="lineNoCov">          0 :         if (wend &lt; *m) {</span></a>
+<a name="21376"><span class="lineNum">   21376 </span><span class="lineNoCov">          0 :             if (iblock[wend + 1] == jblk) {</span></a>
+<a name="21377"><span class="lineNum">   21377 </span><span class="lineNoCov">          0 :                 ++wend;</span></a>
+<a name="21378"><span class="lineNum">   21378 </span><span class="lineNoCov">          0 :                 goto L171;</span></a>
+<a name="21379"><span class="lineNum">   21379 </span>            :             }</a>
+<a name="21380"><span class="lineNum">   21380 </span>            :         }</a>
+<a name="21381"><span class="lineNum">   21381 </span><span class="lineNoCov">          0 :         if (wend &lt; wbegin) {</span></a>
+<a name="21382"><span class="lineNum">   21382 </span><span class="lineNoCov">          0 :             ibegin = iend + 1;</span></a>
+<a name="21383"><span class="lineNum">   21383 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="21384"><span class="lineNum">   21384 </span>            :         }</a>
+<a name="21385"><span class="lineNum">   21385 </span>            : </a>
+<a name="21386"><span class="lineNum">   21386 </span><span class="lineNoCov">          0 :         if (ibegin == iend) {</span></a>
+<a name="21387"><span class="lineNum">   21387 </span><span class="lineNoCov">          0 :             z__[ibegin + wbegin * z_dim1] = 1.;</span></a>
+<a name="21388"><span class="lineNum">   21388 </span><span class="lineNoCov">          0 :             isuppz[(wbegin &lt;&lt; 1) - 1] = ibegin;</span></a>
+<a name="21389"><span class="lineNum">   21389 </span><span class="lineNoCov">          0 :             isuppz[wbegin * 2] = ibegin;</span></a>
+<a name="21390"><span class="lineNum">   21390 </span><span class="lineNoCov">          0 :             ibegin = iend + 1;</span></a>
+<a name="21391"><span class="lineNum">   21391 </span><span class="lineNoCov">          0 :             wbegin = wend + 1;</span></a>
+<a name="21392"><span class="lineNum">   21392 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="21393"><span class="lineNum">   21393 </span>            :         }</a>
+<a name="21394"><span class="lineNum">   21394 </span><span class="lineNoCov">          0 :         oldien = ibegin - 1;</span></a>
+<a name="21395"><span class="lineNum">   21395 </span><span class="lineNoCov">          0 :         in = iend - oldien;</span></a>
+<a name="21396"><span class="lineNum">   21396 </span><span class="lineNoCov">          0 :         d__1 = .001, d__2 = 1. / (float) in;</span></a>
+<a name="21397"><span class="lineNum">   21397 </span><span class="lineNoCov">          0 :         reltol = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="21398"><span class="lineNum">   21398 </span><span class="lineNoCov">          0 :         im = wend - wbegin + 1;</span></a>
+<a name="21399"><span class="lineNum">   21399 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;im, &amp;w[wbegin], &amp;c__1, &amp;work[1], &amp;c__1);</span></a>
+<a name="21400"><span class="lineNum">   21400 </span><span class="lineNoCov">          0 :         i__2 = im - 1;</span></a>
+<a name="21401"><span class="lineNum">   21401 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21402"><span class="lineNum">   21402 </span><span class="lineNoCov">          0 :             work[inderr + i__] = eps * std::abs(work[i__]);</span></a>
+<a name="21403"><span class="lineNum">   21403 </span><span class="lineNoCov">          0 :             work[indgap + i__] = work[i__ + 1] - work[i__];</span></a>
+<a name="21404"><span class="lineNum">   21404 </span>            :         }</a>
+<a name="21405"><span class="lineNum">   21405 </span><span class="lineNoCov">          0 :         work[inderr + im] = eps * std::abs(work[im]);</span></a>
+<a name="21406"><span class="lineNum">   21406 </span><span class="lineNoCov">          0 :         d__2 = std::abs(work[im]);</span></a>
+<a name="21407"><span class="lineNum">   21407 </span><span class="lineNoCov">          0 :         work[indgap + im] = (d__2&gt;eps) ? d__2 : eps;</span></a>
+<a name="21408"><span class="lineNum">   21408 </span>            :         ndone = 0;</a>
+<a name="21409"><span class="lineNum">   21409 </span>            : </a>
+<a name="21410"><span class="lineNum">   21410 </span>            :         ndepth = 0;</a>
+<a name="21411"><span class="lineNum">   21411 </span>            :         parity = 1;</a>
+<a name="21412"><span class="lineNum">   21412 </span>            :         nclus = 1;</a>
+<a name="21413"><span class="lineNum">   21413 </span><span class="lineNoCov">          0 :         iwork[iindc1 + 1] = 1;</span></a>
+<a name="21414"><span class="lineNum">   21414 </span><span class="lineNoCov">          0 :         iwork[iindc1 + 2] = im;</span></a>
+<a name="21415"><span class="lineNum">   21415 </span>            : </a>
+<a name="21416"><span class="lineNum">   21416 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="21417"><span class="lineNum">   21417 </span><span class="lineNoCov">          0 :         if (ndone &lt; im) {</span></a>
+<a name="21418"><span class="lineNum">   21418 </span>            :             oldncl = nclus;</a>
+<a name="21419"><span class="lineNum">   21419 </span>            :             nclus = 0;</a>
+<a name="21420"><span class="lineNum">   21420 </span><span class="lineNoCov">          0 :             parity = 1 - parity;</span></a>
+<a name="21421"><span class="lineNum">   21421 </span><span class="lineNoCov">          0 :             if (parity == 0) {</span></a>
+<a name="21422"><span class="lineNum">   21422 </span>            :                 oldcls = iindc1;</a>
+<a name="21423"><span class="lineNum">   21423 </span>            :                 newcls = iindc2;</a>
+<a name="21424"><span class="lineNum">   21424 </span>            :             } else {</a>
+<a name="21425"><span class="lineNum">   21425 </span>            :                 oldcls = iindc2;</a>
+<a name="21426"><span class="lineNum">   21426 </span>            :                 newcls = iindc1;</a>
+<a name="21427"><span class="lineNum">   21427 </span>            :             }</a>
+<a name="21428"><span class="lineNum">   21428 </span>            :             i__2 = oldncl;</a>
+<a name="21429"><span class="lineNum">   21429 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21430"><span class="lineNum">   21430 </span>            : </a>
+<a name="21431"><span class="lineNum">   21431 </span><span class="lineNoCov">          0 :                 j = oldcls + (i__ &lt;&lt; 1);</span></a>
+<a name="21432"><span class="lineNum">   21432 </span><span class="lineNoCov">          0 :                 oldfst = iwork[j - 1];</span></a>
+<a name="21433"><span class="lineNum">   21433 </span><span class="lineNoCov">          0 :                 oldlst = iwork[j];</span></a>
+<a name="21434"><span class="lineNum">   21434 </span><span class="lineNoCov">          0 :                 if (ndepth &gt; 0) {</span></a>
+<a name="21435"><span class="lineNum">   21435 </span><span class="lineNoCov">          0 :                     j = wbegin + oldfst - 1;</span></a>
+<a name="21436"><span class="lineNum">   21436 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;in, &amp;z__[ibegin + j * z_dim1], &amp;c__1, &amp;d__[ibegin]</span></a>
+<a name="21437"><span class="lineNum">   21437 </span>            :                             , &amp;c__1);</a>
+<a name="21438"><span class="lineNum">   21438 </span><span class="lineNoCov">          0 :                     i__3 = in - 1;</span></a>
+<a name="21439"><span class="lineNum">   21439 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__3, &amp;z__[ibegin + (j + 1) * z_dim1], &amp;c__1, &amp;l[</span></a>
+<a name="21440"><span class="lineNum">   21440 </span>            :                             ibegin], &amp;c__1);</a>
+<a name="21441"><span class="lineNum">   21441 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;Full&quot;, &amp;in, &amp;c__2, &amp;c_b5, &amp;c_b5, &amp;z__[ibegin + j </span></a>
+<a name="21442"><span class="lineNum">   21442 </span>            :                             * z_dim1], ldz);</a>
+<a name="21443"><span class="lineNum">   21443 </span>            :                 }</a>
+<a name="21444"><span class="lineNum">   21444 </span>            :                 k = ibegin;</a>
+<a name="21445"><span class="lineNum">   21445 </span><span class="lineNoCov">          0 :                 i__3 = in - 1;</span></a>
+<a name="21446"><span class="lineNum">   21446 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__3; ++j) {</span></a>
+<a name="21447"><span class="lineNum">   21447 </span><span class="lineNoCov">          0 :                     tmp = d__[k] * l[k];</span></a>
+<a name="21448"><span class="lineNum">   21448 </span><span class="lineNoCov">          0 :                     work[indld + j] = tmp;</span></a>
+<a name="21449"><span class="lineNum">   21449 </span><span class="lineNoCov">          0 :                     work[indlld + j] = tmp * l[k];</span></a>
+<a name="21450"><span class="lineNum">   21450 </span><span class="lineNoCov">          0 :                     ++k;</span></a>
+<a name="21451"><span class="lineNum">   21451 </span>            :                 }</a>
+<a name="21452"><span class="lineNum">   21452 </span><span class="lineNoCov">          0 :                 if (ndepth &gt; 0) {</span></a>
+<a name="21453"><span class="lineNum">   21453 </span>            : </a>
+<a name="21454"><span class="lineNum">   21454 </span><span class="lineNoCov">          0 :                     p = indexw[wbegin - 1 + oldfst];</span></a>
+<a name="21455"><span class="lineNum">   21455 </span><span class="lineNoCov">          0 :                     q = indexw[wbegin - 1 + oldlst];</span></a>
+<a name="21456"><span class="lineNum">   21456 </span><span class="lineNoCov">          0 :                     d__1 = eps * 4.;</span></a>
+<a name="21457"><span class="lineNum">   21457 </span><span class="lineNoCov">          0 :                     i__3 = p - oldfst;</span></a>
+<a name="21458"><span class="lineNum">   21458 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(slarrbx,SLARRBX)(&amp;in, &amp;d__[ibegin], &amp;l[ibegin], &amp;work[indld + 1], &amp;</span></a>
+<a name="21459"><span class="lineNum">   21459 </span><span class="lineNoCov">          0 :                             work[indlld + 1], &amp;p, &amp;q, &amp;reltol, &amp;d__1, &amp;i__3, &amp;</span></a>
+<a name="21460"><span class="lineNum">   21460 </span><span class="lineNoCov">          0 :                             work[1], &amp;work[indgap + 1], &amp;work[inderr + 1], &amp;</span></a>
+<a name="21461"><span class="lineNum">   21461 </span><span class="lineNoCov">          0 :                             work[indwrk + in], &amp;iwork[iindwk], &amp;iinfo);</span></a>
+<a name="21462"><span class="lineNum">   21462 </span>            :                 }</a>
+<a name="21463"><span class="lineNum">   21463 </span><span class="lineNoCov">          0 :                 newfrs = oldfst;</span></a>
+<a name="21464"><span class="lineNum">   21464 </span><span class="lineNoCov">          0 :                 i__3 = oldlst;</span></a>
+<a name="21465"><span class="lineNum">   21465 </span><span class="lineNoCov">          0 :                 for (j = oldfst; j &lt;= i__3; ++j) {</span></a>
+<a name="21466"><span class="lineNum">   21466 </span><span class="lineNoCov">          0 :                     if (j == oldlst || work[indgap + j] &gt;= </span></a>
+<a name="21467"><span class="lineNum">   21467 </span><span class="lineNoCov">          0 :                         reltol * std::abs(work[j])) {</span></a>
+<a name="21468"><span class="lineNum">   21468 </span><span class="lineNoCov">          0 :                         newlst = j;</span></a>
+<a name="21469"><span class="lineNum">   21469 </span>            :                     } else {</a>
+<a name="21470"><span class="lineNum">   21470 </span>            : </a>
+<a name="21471"><span class="lineNum">   21471 </span><span class="lineNoCov">          0 :                         relgap = work[indgap + j] / std::abs(work[j]);</span></a>
+<a name="21472"><span class="lineNum">   21472 </span><span class="lineNoCov">          0 :                         if (j == newfrs) {</span></a>
+<a name="21473"><span class="lineNum">   21473 </span>            :                             minrgp = relgap;</a>
+<a name="21474"><span class="lineNum">   21474 </span>            :                         } else {</a>
+<a name="21475"><span class="lineNum">   21475 </span><span class="lineNoCov">          0 :                             minrgp = (minrgp&lt;relgap) ? minrgp : relgap;</span></a>
+<a name="21476"><span class="lineNum">   21476 </span>            :                         }</a>
+<a name="21477"><span class="lineNum">   21477 </span><span class="lineNoCov">          0 :                         continue;</span></a>
+<a name="21478"><span class="lineNum">   21478 </span>            :                     }</a>
+<a name="21479"><span class="lineNum">   21479 </span><span class="lineNoCov">          0 :                     newsiz = newlst - newfrs + 1;</span></a>
+<a name="21480"><span class="lineNum">   21480 </span><span class="lineNoCov">          0 :                     newftt = wbegin + newfrs - 1;</span></a>
+<a name="21481"><span class="lineNum">   21481 </span><span class="lineNoCov">          0 :                     nomgs = newsiz == 1 || newsiz &gt; 1 || minrgp &lt; mgstol;</span></a>
+<a name="21482"><span class="lineNum">   21482 </span><span class="lineNoCov">          0 :                     if (newsiz &gt; 1 &amp;&amp; nomgs) {</span></a>
+<a name="21483"><span class="lineNum">   21483 </span>            : </a>
+<a name="21484"><span class="lineNum">   21484 </span><span class="lineNoCov">          0 :                         PLUMED_BLAS_F77_FUNC(slarrfx,SLARRFX)(&amp;in, &amp;d__[ibegin], &amp;l[ibegin], &amp;work[indld + </span></a>
+<a name="21485"><span class="lineNum">   21485 </span><span class="lineNoCov">          0 :                                 1], &amp;work[indlld + 1], &amp;newfrs, &amp;newlst, &amp;</span></a>
+<a name="21486"><span class="lineNum">   21486 </span><span class="lineNoCov">          0 :                                 work[1], &amp;sigma, &amp;z__[ibegin + newftt * </span></a>
+<a name="21487"><span class="lineNum">   21487 </span><span class="lineNoCov">          0 :                                 z_dim1], &amp;z__[ibegin + (newftt + 1) * z_dim1],</span></a>
+<a name="21488"><span class="lineNum">   21488 </span><span class="lineNoCov">          0 :                                  &amp;work[indwrk], info);</span></a>
+<a name="21489"><span class="lineNum">   21489 </span><span class="lineNoCov">          0 :                         if (*info == 0) {</span></a>
+<a name="21490"><span class="lineNum">   21490 </span><span class="lineNoCov">          0 :                             tmp = eps * std::abs(sigma);</span></a>
+<a name="21491"><span class="lineNum">   21491 </span><span class="lineNoCov">          0 :                             i__4 = newlst;</span></a>
+<a name="21492"><span class="lineNum">   21492 </span><span class="lineNoCov">          0 :                             for (k = newfrs; k &lt;= i__4; ++k) {</span></a>
+<a name="21493"><span class="lineNum">   21493 </span><span class="lineNoCov">          0 :                                 work[k] -= sigma;</span></a>
+<a name="21494"><span class="lineNum">   21494 </span><span class="lineNoCov">          0 :                                 d__1 = work[indgap + k];</span></a>
+<a name="21495"><span class="lineNum">   21495 </span><span class="lineNoCov">          0 :                                 work[indgap + k] = (d__1&gt;tmp) ? d__1 : tmp;</span></a>
+<a name="21496"><span class="lineNum">   21496 </span><span class="lineNoCov">          0 :                                 work[inderr + k] += tmp;</span></a>
+<a name="21497"><span class="lineNum">   21497 </span>            :                             }</a>
+<a name="21498"><span class="lineNum">   21498 </span><span class="lineNoCov">          0 :                             ++nclus;</span></a>
+<a name="21499"><span class="lineNum">   21499 </span><span class="lineNoCov">          0 :                             k = newcls + (nclus &lt;&lt; 1);</span></a>
+<a name="21500"><span class="lineNum">   21500 </span><span class="lineNoCov">          0 :                             iwork[k - 1] = newfrs;</span></a>
+<a name="21501"><span class="lineNum">   21501 </span><span class="lineNoCov">          0 :                             iwork[k] = newlst;</span></a>
+<a name="21502"><span class="lineNum">   21502 </span>            :                         } else {</a>
+<a name="21503"><span class="lineNum">   21503 </span><span class="lineNoCov">          0 :                             *info = 0;</span></a>
+<a name="21504"><span class="lineNum">   21504 </span><span class="lineNoCov">          0 :                             if (minrgp &lt; mgstol) {</span></a>
+<a name="21505"><span class="lineNum">   21505 </span>            : </a>
+<a name="21506"><span class="lineNum">   21506 </span><span class="lineNoCov">          0 :                                 work[indwrk] = d__[ibegin];</span></a>
+<a name="21507"><span class="lineNum">   21507 </span><span class="lineNoCov">          0 :                                 i__4 = in - 1;</span></a>
+<a name="21508"><span class="lineNum">   21508 </span><span class="lineNoCov">          0 :                                 for (k = 1; k &lt;= i__4; ++k) {</span></a>
+<a name="21509"><span class="lineNum">   21509 </span><span class="lineNoCov">          0 :                                     work[indwrk + k] = d__[ibegin + k] + work[</span></a>
+<a name="21510"><span class="lineNum">   21510 </span><span class="lineNoCov">          0 :                                             indlld + k];</span></a>
+<a name="21511"><span class="lineNum">   21511 </span>            :                                 }</a>
+<a name="21512"><span class="lineNum">   21512 </span><span class="lineNoCov">          0 :                                 i__4 = newsiz;</span></a>
+<a name="21513"><span class="lineNum">   21513 </span><span class="lineNoCov">          0 :                                 for (k = 1; k &lt;= i__4; ++k) {</span></a>
+<a name="21514"><span class="lineNum">   21514 </span><span class="lineNoCov">          0 :                                     iwork[iindwk + k - 1] = 1;</span></a>
+<a name="21515"><span class="lineNum">   21515 </span>            :                                 }</a>
+<a name="21516"><span class="lineNum">   21516 </span><span class="lineNoCov">          0 :                                 i__4 = newlst;</span></a>
+<a name="21517"><span class="lineNum">   21517 </span><span class="lineNoCov">          0 :                                 for (k = newfrs; k &lt;= i__4; ++k) {</span></a>
+<a name="21518"><span class="lineNum">   21518 </span><span class="lineNoCov">          0 :                                     isuppz[2*(oldien + k) - 1] = 1;</span></a>
+<a name="21519"><span class="lineNum">   21519 </span><span class="lineNoCov">          0 :                                     isuppz[(oldien + k) * 2] = in;</span></a>
+<a name="21520"><span class="lineNum">   21520 </span>            :                                 }</a>
+<a name="21521"><span class="lineNum">   21521 </span><span class="lineNoCov">          0 :                                 temp[0] = in;</span></a>
+<a name="21522"><span class="lineNum">   21522 </span><span class="lineNoCov">          0 :                                 PLUMED_BLAS_F77_FUNC(sstein,SSTEIN)(&amp;in, &amp;work[indwrk], &amp;work[indld + 1], </span></a>
+<a name="21523"><span class="lineNum">   21523 </span><span class="lineNoCov">          0 :                                         &amp;newsiz, &amp;work[newfrs], &amp;iwork[iindwk]</span></a>
+<a name="21524"><span class="lineNum">   21524 </span>            :                                         , temp, &amp;z__[ibegin + newftt * z_dim1]</a>
+<a name="21525"><span class="lineNum">   21525 </span><span class="lineNoCov">          0 :                                         , ldz, &amp;work[indwrk + in], &amp;iwork[</span></a>
+<a name="21526"><span class="lineNum">   21526 </span><span class="lineNoCov">          0 :                                         iindwk + in], &amp;iwork[iindwk + (in*2)], &amp;iinfo);</span></a>
+<a name="21527"><span class="lineNum">   21527 </span><span class="lineNoCov">          0 :                                 if (iinfo != 0) {</span></a>
+<a name="21528"><span class="lineNum">   21528 </span><span class="lineNoCov">          0 :                                     *info = 2;</span></a>
+<a name="21529"><span class="lineNum">   21529 </span><span class="lineNoCov">          0 :                                     return;</span></a>
+<a name="21530"><span class="lineNum">   21530 </span>            :                                 }</a>
+<a name="21531"><span class="lineNum">   21531 </span><span class="lineNoCov">          0 :                                 ndone += newsiz;</span></a>
+<a name="21532"><span class="lineNum">   21532 </span>            :                             }</a>
+<a name="21533"><span class="lineNum">   21533 </span>            :                         }</a>
+<a name="21534"><span class="lineNum">   21534 </span>            :                     } else {</a>
+<a name="21535"><span class="lineNum">   21535 </span>            :                         ktot = newftt;</a>
+<a name="21536"><span class="lineNum">   21536 </span>            :                         i__4 = newlst;</a>
+<a name="21537"><span class="lineNum">   21537 </span><span class="lineNoCov">          0 :                         for (k = newfrs; k &lt;= i__4; ++k) {</span></a>
+<a name="21538"><span class="lineNum">   21538 </span>            :                             iter = 0;</a>
+<a name="21539"><span class="lineNum">   21539 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="21540"><span class="lineNum">   21540 </span><span class="lineNoCov">          0 :                             lambda = work[k];</span></a>
+<a name="21541"><span class="lineNum">   21541 </span>            : </a>
+<a name="21542"><span class="lineNum">   21542 </span><span class="lineNoCov">          0 :                             PLUMED_BLAS_F77_FUNC(slar1vx,SLAR1VX)(&amp;in, &amp;c__1, &amp;in, &amp;lambda, &amp;d__[ibegin], &amp;</span></a>
+<a name="21543"><span class="lineNum">   21543 </span><span class="lineNoCov">          0 :                                     l[ibegin], &amp;work[indld + 1], &amp;work[indlld </span></a>
+<a name="21544"><span class="lineNum">   21544 </span><span class="lineNoCov">          0 :                                     + 1], &amp;w[wbegin + k - 1], &amp;gersch[(oldien </span></a>
+<a name="21545"><span class="lineNum">   21545 </span><span class="lineNoCov">          0 :                                     &lt;&lt; 1) + 1], &amp;z__[ibegin + ktot * z_dim1], </span></a>
+<a name="21546"><span class="lineNum">   21546 </span><span class="lineNoCov">          0 :                                     &amp;ztz, &amp;mingma, &amp;iwork[iindr + ktot], &amp;</span></a>
+<a name="21547"><span class="lineNum">   21547 </span><span class="lineNoCov">          0 :                                     isuppz[(ktot &lt;&lt; 1) - 1], &amp;work[indwrk]);</span></a>
+<a name="21548"><span class="lineNum">   21548 </span><span class="lineNoCov">          0 :                             tmp = 1. / ztz;</span></a>
+<a name="21549"><span class="lineNum">   21549 </span><span class="lineNoCov">          0 :                             nrminv =  std::sqrt(tmp);</span></a>
+<a name="21550"><span class="lineNum">   21550 </span><span class="lineNoCov">          0 :                             resid = std::abs(mingma) * nrminv;</span></a>
+<a name="21551"><span class="lineNum">   21551 </span><span class="lineNoCov">          0 :                             rqcorr = mingma * tmp;</span></a>
+<a name="21552"><span class="lineNum">   21552 </span><span class="lineNoCov">          0 :                             if (k == in) {</span></a>
+<a name="21553"><span class="lineNum">   21553 </span><span class="lineNoCov">          0 :                                 gap = work[indgap + k - 1];</span></a>
+<a name="21554"><span class="lineNum">   21554 </span><span class="lineNoCov">          0 :                             } else if (k == 1) {</span></a>
+<a name="21555"><span class="lineNum">   21555 </span><span class="lineNoCov">          0 :                                 gap = work[indgap + k];</span></a>
+<a name="21556"><span class="lineNum">   21556 </span>            :                             } else {</a>
+<a name="21557"><span class="lineNum">   21557 </span><span class="lineNoCov">          0 :                                 d__1 = work[indgap + k - 1], d__2 = work[</span></a>
+<a name="21558"><span class="lineNum">   21558 </span><span class="lineNoCov">          0 :                                         indgap + k];</span></a>
+<a name="21559"><span class="lineNum">   21559 </span><span class="lineNoCov">          0 :                                 gap = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="21560"><span class="lineNum">   21560 </span>            :                             }</a>
+<a name="21561"><span class="lineNum">   21561 </span><span class="lineNoCov">          0 :                             ++iter;</span></a>
+<a name="21562"><span class="lineNum">   21562 </span><span class="lineNoCov">          0 :                             if (resid &gt; *tol * gap &amp;&amp; std::abs(rqcorr) &gt; eps * 4. *</span></a>
+<a name="21563"><span class="lineNum">   21563 </span><span class="lineNoCov">          0 :                                      std::abs(lambda)) {</span></a>
+<a name="21564"><span class="lineNum">   21564 </span><span class="lineNoCov">          0 :                                 work[k] = lambda + rqcorr;</span></a>
+<a name="21565"><span class="lineNum">   21565 </span><span class="lineNoCov">          0 :                                 if (iter &lt; 8) {</span></a>
+<a name="21566"><span class="lineNum">   21566 </span><span class="lineNoCov">          0 :                                     goto L90;</span></a>
+<a name="21567"><span class="lineNum">   21567 </span>            :                                 }</a>
+<a name="21568"><span class="lineNum">   21568 </span>            :                             }</a>
+<a name="21569"><span class="lineNum">   21569 </span><span class="lineNoCov">          0 :                             iwork[ktot] = 1;</span></a>
+<a name="21570"><span class="lineNum">   21570 </span><span class="lineNoCov">          0 :                             if (newsiz == 1) {</span></a>
+<a name="21571"><span class="lineNum">   21571 </span><span class="lineNoCov">          0 :                                 ++ndone;</span></a>
+<a name="21572"><span class="lineNum">   21572 </span>            :                             }</a>
+<a name="21573"><span class="lineNum">   21573 </span><span class="lineNoCov">          0 :                             zfrom = isuppz[(ktot &lt;&lt; 1) - 1];</span></a>
+<a name="21574"><span class="lineNum">   21574 </span><span class="lineNoCov">          0 :                             zto = isuppz[ktot * 2];</span></a>
+<a name="21575"><span class="lineNum">   21575 </span><span class="lineNoCov">          0 :                             i__5 = zto - zfrom + 1;</span></a>
+<a name="21576"><span class="lineNum">   21576 </span><span class="lineNoCov">          0 :                             PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__5, &amp;nrminv, &amp;z__[ibegin + zfrom - 1 + </span></a>
+<a name="21577"><span class="lineNum">   21577 </span><span class="lineNoCov">          0 :                                     ktot * z_dim1], &amp;c__1);</span></a>
+<a name="21578"><span class="lineNum">   21578 </span><span class="lineNoCov">          0 :                             ++ktot;</span></a>
+<a name="21579"><span class="lineNum">   21579 </span>            :                         }</a>
+<a name="21580"><span class="lineNum">   21580 </span><span class="lineNoCov">          0 :                         if (newsiz &gt; 1) {</span></a>
+<a name="21581"><span class="lineNum">   21581 </span><span class="lineNoCov">          0 :                             itmp1 = isuppz[(newftt &lt;&lt; 1) - 1];</span></a>
+<a name="21582"><span class="lineNum">   21582 </span><span class="lineNoCov">          0 :                             itmp2 = isuppz[newftt * 2];</span></a>
+<a name="21583"><span class="lineNum">   21583 </span><span class="lineNoCov">          0 :                             ktot = oldien + newlst;</span></a>
+<a name="21584"><span class="lineNum">   21584 </span>            :                             i__4 = ktot;</a>
+<a name="21585"><span class="lineNum">   21585 </span><span class="lineNoCov">          0 :                             for (p = newftt + 1; p &lt;= i__4; ++p) {</span></a>
+<a name="21586"><span class="lineNum">   21586 </span><span class="lineNoCov">          0 :                                 i__5 = p - 1;</span></a>
+<a name="21587"><span class="lineNum">   21587 </span><span class="lineNoCov">          0 :                                 for (q = newftt; q &lt;= i__5; ++q) {</span></a>
+<a name="21588"><span class="lineNum">   21588 </span><span class="lineNoCov">          0 :                                     tmp = -PLUMED_BLAS_F77_FUNC(sdot,SDOT)(&amp;in, &amp;z__[ibegin + p * </span></a>
+<a name="21589"><span class="lineNum">   21589 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1, &amp;z__[ibegin + q * </span></a>
+<a name="21590"><span class="lineNum">   21590 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1);</span></a>
+<a name="21591"><span class="lineNum">   21591 </span><span class="lineNoCov">          0 :                                     PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(&amp;in, &amp;tmp, &amp;z__[ibegin + q * </span></a>
+<a name="21592"><span class="lineNum">   21592 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1, &amp;z__[ibegin + p * </span></a>
+<a name="21593"><span class="lineNum">   21593 </span><span class="lineNoCov">          0 :                                             z_dim1], &amp;c__1);</span></a>
+<a name="21594"><span class="lineNum">   21594 </span>            :                                 }</a>
+<a name="21595"><span class="lineNum">   21595 </span><span class="lineNoCov">          0 :                                 tmp = 1. / PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(&amp;in, &amp;z__[ibegin + p * </span></a>
+<a name="21596"><span class="lineNum">   21596 </span><span class="lineNoCov">          0 :                                         z_dim1], &amp;c__1);</span></a>
+<a name="21597"><span class="lineNum">   21597 </span><span class="lineNoCov">          0 :                                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;in, &amp;tmp, &amp;z__[ibegin + p * z_dim1], &amp;</span></a>
+<a name="21598"><span class="lineNum">   21598 </span>            :                                         c__1);</a>
+<a name="21599"><span class="lineNum">   21599 </span><span class="lineNoCov">          0 :                                 i__5 = itmp1, i__6 = isuppz[(p &lt;&lt; 1) - 1];</span></a>
+<a name="21600"><span class="lineNum">   21600 </span>            :                                 itmp1 = (i__5&lt;i__6) ? i__5 : i__6;</a>
+<a name="21601"><span class="lineNum">   21601 </span><span class="lineNoCov">          0 :                                 i__5 = itmp2, i__6 = isuppz[p * 2];</span></a>
+<a name="21602"><span class="lineNum">   21602 </span>            :                                 itmp2 = (i__5&gt;i__6) ? i__5 : i__6;</a>
+<a name="21603"><span class="lineNum">   21603 </span>            :                             }</a>
+<a name="21604"><span class="lineNum">   21604 </span>            :                             i__4 = ktot;</a>
+<a name="21605"><span class="lineNum">   21605 </span><span class="lineNoCov">          0 :                             for (p = newftt; p &lt;= i__4; ++p) {</span></a>
+<a name="21606"><span class="lineNum">   21606 </span><span class="lineNoCov">          0 :                                 isuppz[(p &lt;&lt; 1) - 1] = itmp1;</span></a>
+<a name="21607"><span class="lineNum">   21607 </span><span class="lineNoCov">          0 :                                 isuppz[p * 2] = itmp2;</span></a>
+<a name="21608"><span class="lineNum">   21608 </span>            :                             }</a>
+<a name="21609"><span class="lineNum">   21609 </span><span class="lineNoCov">          0 :                             ndone += newsiz;</span></a>
+<a name="21610"><span class="lineNum">   21610 </span>            :                         }</a>
+<a name="21611"><span class="lineNum">   21611 </span>            :                     }</a>
+<a name="21612"><span class="lineNum">   21612 </span><span class="lineNoCov">          0 :                     newfrs = j + 1;</span></a>
+<a name="21613"><span class="lineNum">   21613 </span>            :                 }</a>
+<a name="21614"><span class="lineNum">   21614 </span>            :             }</a>
+<a name="21615"><span class="lineNum">   21615 </span><span class="lineNoCov">          0 :             ++ndepth;</span></a>
+<a name="21616"><span class="lineNum">   21616 </span><span class="lineNoCov">          0 :             goto L40;</span></a>
+<a name="21617"><span class="lineNum">   21617 </span>            :         }</a>
+<a name="21618"><span class="lineNum">   21618 </span><span class="lineNoCov">          0 :         j = wbegin &lt;&lt; 1;</span></a>
+<a name="21619"><span class="lineNum">   21619 </span>            :         i__2 = wend;</a>
+<a name="21620"><span class="lineNum">   21620 </span><span class="lineNoCov">          0 :         for (i__ = wbegin; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="21621"><span class="lineNum">   21621 </span><span class="lineNoCov">          0 :             isuppz[j - 1] += oldien;</span></a>
+<a name="21622"><span class="lineNum">   21622 </span><span class="lineNoCov">          0 :             isuppz[j] += oldien;</span></a>
+<a name="21623"><span class="lineNum">   21623 </span><span class="lineNoCov">          0 :             j += 2;</span></a>
+<a name="21624"><span class="lineNum">   21624 </span>            : </a>
+<a name="21625"><span class="lineNum">   21625 </span>            :         }</a>
+<a name="21626"><span class="lineNum">   21626 </span><span class="lineNoCov">          0 :         ibegin = iend + 1;</span></a>
+<a name="21627"><span class="lineNum">   21627 </span><span class="lineNoCov">          0 :         wbegin = wend + 1;</span></a>
+<a name="21628"><span class="lineNum">   21628 </span>            :     }</a>
+<a name="21629"><span class="lineNum">   21629 </span>            : </a>
+<a name="21630"><span class="lineNum">   21630 </span>            :     return;</a>
+<a name="21631"><span class="lineNum">   21631 </span>            : </a>
+<a name="21632"><span class="lineNum">   21632 </span>            : } </a>
+<a name="21633"><span class="lineNum">   21633 </span>            : }</a>
+<a name="21634"><span class="lineNum">   21634 </span>            : }</a>
+<a name="21635"><span class="lineNum">   21635 </span>            : #include &lt;cmath&gt;</a>
+<a name="21636"><span class="lineNum">   21636 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="21637"><span class="lineNum">   21637 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="21638"><span class="lineNum">   21638 </span>            : </a>
+<a name="21639"><span class="lineNum">   21639 </span>            : #include &quot;real.h&quot;</a>
+<a name="21640"><span class="lineNum">   21640 </span>            : </a>
+<a name="21641"><span class="lineNum">   21641 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21642"><span class="lineNum">   21642 </span>            : namespace PLMD{</a>
+<a name="21643"><span class="lineNum">   21643 </span>            : namespace lapack{</a>
+<a name="21644"><span class="lineNum">   21644 </span>            : using namespace blas;</a>
+<a name="21645"><span class="lineNum">   21645 </span>            : void</a>
+<a name="21646"><span class="lineNum">   21646 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(float *f,</span></a>
+<a name="21647"><span class="lineNum">   21647 </span>            :         float *g,</a>
+<a name="21648"><span class="lineNum">   21648 </span>            :         float *cs,</a>
+<a name="21649"><span class="lineNum">   21649 </span>            :         float *sn,</a>
+<a name="21650"><span class="lineNum">   21650 </span>            :         float *r)</a>
+<a name="21651"><span class="lineNum">   21651 </span>            : {</a>
+<a name="21652"><span class="lineNum">   21652 </span>            :   float minval,safemin, safemin2, safemx2, eps;</a>
+<a name="21653"><span class="lineNum">   21653 </span>            :   float f1,g1,f1a,g1a,scale;</a>
+<a name="21654"><span class="lineNum">   21654 </span>            :   int i,n,count;</a>
+<a name="21655"><span class="lineNum">   21655 </span>            : </a>
+<a name="21656"><span class="lineNum">   21656 </span>            :   eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="21657"><span class="lineNum">   21657 </span>            :   minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="21658"><span class="lineNum">   21658 </span>            :   safemin = minval*(1.0+eps);</a>
+<a name="21659"><span class="lineNum">   21659 </span>            :   n = static_cast&lt;int&gt;(0.5*std::log( safemin/eps ) / std::log(2.0));</a>
+<a name="21660"><span class="lineNum">   21660 </span>            :   safemin2 = std::pow(static_cast&lt;float&gt;(2.0),static_cast&lt;float&gt;(n));</a>
+<a name="21661"><span class="lineNum">   21661 </span>            : </a>
+<a name="21662"><span class="lineNum">   21662 </span>            :   safemx2 = 1.0 / safemin2;</a>
+<a name="21663"><span class="lineNum">   21663 </span>            : </a>
+<a name="21664"><span class="lineNum">   21664 </span><span class="lineNoCov">          0 :   if(std::abs(*g)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="21665"><span class="lineNum">   21665 </span><span class="lineNoCov">          0 :     *cs = 1.0;</span></a>
+<a name="21666"><span class="lineNum">   21666 </span><span class="lineNoCov">          0 :     *sn = 0.0;</span></a>
+<a name="21667"><span class="lineNum">   21667 </span><span class="lineNoCov">          0 :     *r = *f;</span></a>
+<a name="21668"><span class="lineNum">   21668 </span><span class="lineNoCov">          0 :   } else if (std::abs(*f)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="21669"><span class="lineNum">   21669 </span><span class="lineNoCov">          0 :     *cs = 0.0;</span></a>
+<a name="21670"><span class="lineNum">   21670 </span><span class="lineNoCov">          0 :     *sn = 1.0;</span></a>
+<a name="21671"><span class="lineNum">   21671 </span><span class="lineNoCov">          0 :     *r = *g;</span></a>
+<a name="21672"><span class="lineNum">   21672 </span>            :   } else {</a>
+<a name="21673"><span class="lineNum">   21673 </span>            :     f1 = *f;</a>
+<a name="21674"><span class="lineNum">   21674 </span>            :     g1 = *g;</a>
+<a name="21675"><span class="lineNum">   21675 </span>            :     f1a = std::abs(f1);</a>
+<a name="21676"><span class="lineNum">   21676 </span>            :     g1a = std::abs(g1);</a>
+<a name="21677"><span class="lineNum">   21677 </span><span class="lineNoCov">          0 :     scale = (f1a &gt; g1a) ? f1a : g1a;</span></a>
+<a name="21678"><span class="lineNum">   21678 </span><span class="lineNoCov">          0 :     if(scale &gt;= safemx2) {</span></a>
+<a name="21679"><span class="lineNum">   21679 </span>            :       count = 0;</a>
+<a name="21680"><span class="lineNum">   21680 </span><span class="lineNoCov">          0 :       while(scale &gt;= safemx2) {</span></a>
+<a name="21681"><span class="lineNum">   21681 </span><span class="lineNoCov">          0 :         count++;</span></a>
+<a name="21682"><span class="lineNum">   21682 </span><span class="lineNoCov">          0 :         f1 *= safemin2;</span></a>
+<a name="21683"><span class="lineNum">   21683 </span><span class="lineNoCov">          0 :         g1 *= safemin2;</span></a>
+<a name="21684"><span class="lineNum">   21684 </span>            :         f1a = std::abs(f1);</a>
+<a name="21685"><span class="lineNum">   21685 </span>            :         g1a = std::abs(g1);</a>
+<a name="21686"><span class="lineNum">   21686 </span><span class="lineNoCov">          0 :         scale = (f1a &gt; g1a) ? f1a : g1a;</span></a>
+<a name="21687"><span class="lineNum">   21687 </span>            :       }</a>
+<a name="21688"><span class="lineNum">   21688 </span><span class="lineNoCov">          0 :       *r =  std::sqrt(f1*f1 + g1*g1);</span></a>
+<a name="21689"><span class="lineNum">   21689 </span><span class="lineNoCov">          0 :       *cs = f1 / *r;</span></a>
+<a name="21690"><span class="lineNum">   21690 </span><span class="lineNoCov">          0 :       *sn = g1 / *r;</span></a>
+<a name="21691"><span class="lineNum">   21691 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;count;i++)</span></a>
+<a name="21692"><span class="lineNum">   21692 </span><span class="lineNoCov">          0 :         *r *= safemx2;</span></a>
+<a name="21693"><span class="lineNum">   21693 </span><span class="lineNoCov">          0 :     } else if (scale&lt;=safemin2) {</span></a>
+<a name="21694"><span class="lineNum">   21694 </span>            :       count = 0;</a>
+<a name="21695"><span class="lineNum">   21695 </span><span class="lineNoCov">          0 :       while(scale &lt;= safemin2) {</span></a>
+<a name="21696"><span class="lineNum">   21696 </span><span class="lineNoCov">          0 :         count++;</span></a>
+<a name="21697"><span class="lineNum">   21697 </span><span class="lineNoCov">          0 :         f1 *= safemx2;</span></a>
+<a name="21698"><span class="lineNum">   21698 </span><span class="lineNoCov">          0 :         g1 *= safemx2;</span></a>
+<a name="21699"><span class="lineNum">   21699 </span>            :         f1a = std::abs(f1);</a>
+<a name="21700"><span class="lineNum">   21700 </span>            :         g1a = std::abs(g1);</a>
+<a name="21701"><span class="lineNum">   21701 </span><span class="lineNoCov">          0 :         scale = (f1a &gt; g1a) ? f1a : g1a;</span></a>
+<a name="21702"><span class="lineNum">   21702 </span>            :       }</a>
+<a name="21703"><span class="lineNum">   21703 </span><span class="lineNoCov">          0 :       *r =  std::sqrt(f1*f1 + g1*g1);</span></a>
+<a name="21704"><span class="lineNum">   21704 </span><span class="lineNoCov">          0 :       *cs = f1 / *r;</span></a>
+<a name="21705"><span class="lineNum">   21705 </span><span class="lineNoCov">          0 :       *sn = g1 / *r;</span></a>
+<a name="21706"><span class="lineNum">   21706 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;count;i++)</span></a>
+<a name="21707"><span class="lineNum">   21707 </span><span class="lineNoCov">          0 :         *r *= safemin2;</span></a>
+<a name="21708"><span class="lineNum">   21708 </span>            :     } else {</a>
+<a name="21709"><span class="lineNum">   21709 </span><span class="lineNoCov">          0 :       *r =  std::sqrt(f1*f1 + g1*g1);</span></a>
+<a name="21710"><span class="lineNum">   21710 </span><span class="lineNoCov">          0 :       *cs = f1 / *r;</span></a>
+<a name="21711"><span class="lineNum">   21711 </span><span class="lineNoCov">          0 :       *sn = g1 / *r;</span></a>
+<a name="21712"><span class="lineNum">   21712 </span>            :     }</a>
+<a name="21713"><span class="lineNum">   21713 </span><span class="lineNoCov">          0 :     if(std::abs(*f)&gt;std::abs(*g) &amp;&amp; *cs&lt;0.0) {</span></a>
+<a name="21714"><span class="lineNum">   21714 </span><span class="lineNoCov">          0 :       *cs *= -1.0;</span></a>
+<a name="21715"><span class="lineNum">   21715 </span><span class="lineNoCov">          0 :       *sn *= -1.0;</span></a>
+<a name="21716"><span class="lineNum">   21716 </span><span class="lineNoCov">          0 :       *r  *= -1.0;</span></a>
+<a name="21717"><span class="lineNum">   21717 </span>            :     }</a>
+<a name="21718"><span class="lineNum">   21718 </span>            :   }</a>
+<a name="21719"><span class="lineNum">   21719 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="21720"><span class="lineNum">   21720 </span>            : }</a>
+<a name="21721"><span class="lineNum">   21721 </span>            :       </a>
+<a name="21722"><span class="lineNum">   21722 </span>            : }</a>
+<a name="21723"><span class="lineNum">   21723 </span>            : }</a>
+<a name="21724"><span class="lineNum">   21724 </span>            : #include &lt;cmath&gt;</a>
+<a name="21725"><span class="lineNum">   21725 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="21726"><span class="lineNum">   21726 </span>            : </a>
+<a name="21727"><span class="lineNum">   21727 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21728"><span class="lineNum">   21728 </span>            : namespace PLMD{</a>
+<a name="21729"><span class="lineNum">   21729 </span>            : namespace lapack{</a>
+<a name="21730"><span class="lineNum">   21730 </span>            : using namespace blas;</a>
+<a name="21731"><span class="lineNum">   21731 </span>            : void</a>
+<a name="21732"><span class="lineNum">   21732 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slaruv,SLARUV)(int *iseed, int *n, float *x)</span></a>
+<a name="21733"><span class="lineNum">   21733 </span>            : {</a>
+<a name="21734"><span class="lineNum">   21734 </span>            :   const int</a>
+<a name="21735"><span class="lineNum">   21735 </span><span class="lineNoCov">          0 :     mm[512] = {</span></a>
+<a name="21736"><span class="lineNum">   21736 </span>            :       494,2637,255,2008,1253,</a>
+<a name="21737"><span class="lineNum">   21737 </span>            :       3344,4084,1739,3143,3468,688,1657,1238,3166,1292,3422,1270,2016,</a>
+<a name="21738"><span class="lineNum">   21738 </span>            :       154,2862,697,1706,491,931,1444,444,3577,3944,2184,1661,3482,657,</a>
+<a name="21739"><span class="lineNum">   21739 </span>            :       3023,3618,1267,1828,164,3798,3087,2400,2870,3876,1905,1593,1797,</a>
+<a name="21740"><span class="lineNum">   21740 </span>            :       1234,3460,328,2861,1950,617,2070,3331,769,1558,2412,2800,189,287,</a>
+<a name="21741"><span class="lineNum">   21741 </span>            :       2045,1227,2838,209,2770,3654,3993,192,2253,3491,2889,2857,2094,</a>
+<a name="21742"><span class="lineNum">   21742 </span>            :       1818,688,1407,634,3231,815,3524,1914,516,164,303,2144,3480,119,</a>
+<a name="21743"><span class="lineNum">   21743 </span>            :       3357,837,2826,2332,2089,3780,1700,3712,150,2000,3375,1621,3090,</a>
+<a name="21744"><span class="lineNum">   21744 </span>            :       3765,1149,3146,33,3082,2741,359,3316,1749,185,2784,2202,2199,1364,</a>
+<a name="21745"><span class="lineNum">   21745 </span>            :       1244,2020,3160,2785,2772,1217,1822,1245,2252,3904,2774,997,2573,</a>
+<a name="21746"><span class="lineNum">   21746 </span>            :       1148,545,322,789,1440,752,2859,123,1848,643,2405,2638,2344,46,</a>
+<a name="21747"><span class="lineNum">   21747 </span>            :       3814,913,3649,339,3808,822,2832,3078,3633,2970,637,2249,2081,4019,</a>
+<a name="21748"><span class="lineNum">   21748 </span>            :       1478,242,481,2075,4058,622,3376,812,234,641,4005,1122,3135,2640,</a>
+<a name="21749"><span class="lineNum">   21749 </span>            :       2302,40,1832,2247,2034,2637,1287,1691,496,1597,2394,2584,1843,336,</a>
+<a name="21750"><span class="lineNum">   21750 </span>            :       1472,2407,433,2096,1761,2810,566,442,41,1238,1086,603,840,3168,</a>
+<a name="21751"><span class="lineNum">   21751 </span>            :       1499,1084,3438,2408,1589,2391,288,26,512,1456,171,1677,2657,2270,</a>
+<a name="21752"><span class="lineNum">   21752 </span>            :       2587,2961,1970,1817,676,1410,3723,2803,3185,184,663,499,3784,1631,</a>
+<a name="21753"><span class="lineNum">   21753 </span>            :       1925,3912,1398,1349,1441,2224,2411,1907,3192,2786,382,37,759,2948,</a>
+<a name="21754"><span class="lineNum">   21754 </span>            :       1862,3802,2423,2051,2295,1332,1832,2405,3638,3661,327,3660,716,</a>
+<a name="21755"><span class="lineNum">   21755 </span>            :       1842,3987,1368,1848,2366,2508,3754,1766,3572,2893,307,1297,3966,</a>
+<a name="21756"><span class="lineNum">   21756 </span>            :       758,2598,3406,2922,1038,2934,2091,2451,1580,1958,2055,1507,1078,</a>
+<a name="21757"><span class="lineNum">   21757 </span>            :       3273,17,854,2916,3971,2889,3831,2621,1541,893,736,3992,787,2125,</a>
+<a name="21758"><span class="lineNum">   21758 </span>            :       2364,2460,257,1574,3912,1216,3248,3401,2124,2762,149,2245,166,466,</a>
+<a name="21759"><span class="lineNum">   21759 </span>            :       4018,1399,190,2879,153,2320,18,712,2159,2318,2091,3443,1510,449,</a>
+<a name="21760"><span class="lineNum">   21760 </span>            :       1956,2201,3137,3399,1321,2271,3667,2703,629,2365,2431,1113,3922,</a>
+<a name="21761"><span class="lineNum">   21761 </span>            :       2554,184,2099,3228,4012,1921,3452,3901,572,3309,3171,817,3039,</a>
+<a name="21762"><span class="lineNum">   21762 </span>            :       1696,1256,3715,2077,3019,1497,1101,717,51,981,1978,1813,3881,76,</a>
+<a name="21763"><span class="lineNum">   21763 </span>            :       3846,3694,1682,124,1660,3997,479,1141,886,3514,1301,3604,1888,</a>
+<a name="21764"><span class="lineNum">   21764 </span>            :       1836,1990,2058,692,1194,20,3285,2046,2107,3508,3525,3801,2549,</a>
+<a name="21765"><span class="lineNum">   21765 </span>            :       1145,2253,305,3301,1065,3133,2913,3285,1241,1197,3729,2501,1673,</a>
+<a name="21766"><span class="lineNum">   21766 </span>            :       541,2753,949,2361,1165,4081,2725,3305,3069,3617,3733,409,2157,</a>
+<a name="21767"><span class="lineNum">   21767 </span>            :       1361,3973,1865,2525,1409,3445,3577,77,3761,2149,1449,3005,225,85,</a>
+<a name="21768"><span class="lineNum">   21768 </span>            :       3673,3117,3089,1349,2057,413,65,1845,697,3085,3441,1573,3689,2941,</a>
+<a name="21769"><span class="lineNum">   21769 </span>            :       929,533,2841,4077,721,2821,2249,2397,2817,245,1913,1997,3121,997,</a>
+<a name="21770"><span class="lineNum">   21770 </span>            :       1833,2877,1633,981,2009,941,2449,197,2441,285,1473,2741,3129,909,</a>
+<a name="21771"><span class="lineNum">   21771 </span>            :       2801,421,4073,2813,2337,1429,1177,1901,81,1669,2633,2269,129,1141,</a>
+<a name="21772"><span class="lineNum">   21772 </span>            :       249,3917,2481,3941,2217,2749,3041,1877,345,2861,1809,3141,2825,</a>
+<a name="21773"><span class="lineNum">   21773 </span>            :       157,2881,3637,1465,2829,2161,3365,361,2685,3745,2325,3609,3821,</a>
+<a name="21774"><span class="lineNum">   21774 </span>            :       3537,517,3017,2141,1537 </a>
+<a name="21775"><span class="lineNum">   21775 </span>            :     };</a>
+<a name="21776"><span class="lineNum">   21776 </span>            : </a>
+<a name="21777"><span class="lineNum">   21777 </span>            :     int i__1;</a>
+<a name="21778"><span class="lineNum">   21778 </span>            : </a>
+<a name="21779"><span class="lineNum">   21779 </span>            :     int i__, i1, i2, i3, i4, it1, it2, it3, it4;</a>
+<a name="21780"><span class="lineNum">   21780 </span>            : </a>
+<a name="21781"><span class="lineNum">   21781 </span>            : </a>
+<a name="21782"><span class="lineNum">   21782 </span>            :     --iseed;</a>
+<a name="21783"><span class="lineNum">   21783 </span>            :     --x;</a>
+<a name="21784"><span class="lineNum">   21784 </span>            : </a>
+<a name="21785"><span class="lineNum">   21785 </span>            :     it1 = it2 = it3 = it4 = 0;</a>
+<a name="21786"><span class="lineNum">   21786 </span>            : </a>
+<a name="21787"><span class="lineNum">   21787 </span><span class="lineNoCov">          0 :     i1 = iseed[1];</span></a>
+<a name="21788"><span class="lineNum">   21788 </span><span class="lineNoCov">          0 :     i2 = iseed[2];</span></a>
+<a name="21789"><span class="lineNum">   21789 </span><span class="lineNoCov">          0 :     i3 = iseed[3];</span></a>
+<a name="21790"><span class="lineNum">   21790 </span><span class="lineNoCov">          0 :     i4 = iseed[4];</span></a>
+<a name="21791"><span class="lineNum">   21791 </span>            : </a>
+<a name="21792"><span class="lineNum">   21792 </span><span class="lineNoCov">          0 :     i__1 = (*n&lt;128) ? *n : 128;</span></a>
+<a name="21793"><span class="lineNum">   21793 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="21794"><span class="lineNum">   21794 </span>            : </a>
+<a name="21795"><span class="lineNum">   21795 </span><span class="lineNoCov">          0 :         it4 = i4 * mm[i__ + 383];</span></a>
+<a name="21796"><span class="lineNum">   21796 </span><span class="lineNoCov">          0 :         it3 = it4 / 4096;</span></a>
+<a name="21797"><span class="lineNum">   21797 </span><span class="lineNoCov">          0 :         it4 -= it3 &lt;&lt; 12;</span></a>
+<a name="21798"><span class="lineNum">   21798 </span><span class="lineNoCov">          0 :         it3 = it3 + i3 * mm[i__ + 383] + i4 * mm[i__ + 255];</span></a>
+<a name="21799"><span class="lineNum">   21799 </span><span class="lineNoCov">          0 :         it2 = it3 / 4096;</span></a>
+<a name="21800"><span class="lineNum">   21800 </span><span class="lineNoCov">          0 :         it3 -= it2 &lt;&lt; 12;</span></a>
+<a name="21801"><span class="lineNum">   21801 </span><span class="lineNoCov">          0 :         it2 = it2 + i2 * mm[i__ + 383] + i3 * mm[i__ + 255] + </span></a>
+<a name="21802"><span class="lineNum">   21802 </span><span class="lineNoCov">          0 :           i4 * mm[i__ + 127];</span></a>
+<a name="21803"><span class="lineNum">   21803 </span><span class="lineNoCov">          0 :         it1 = it2 / 4096;</span></a>
+<a name="21804"><span class="lineNum">   21804 </span><span class="lineNoCov">          0 :         it2 -= it1 &lt;&lt; 12;</span></a>
+<a name="21805"><span class="lineNum">   21805 </span><span class="lineNoCov">          0 :         it1 = it1 + i1 * mm[i__ + 383] + i2 * mm[i__ + 255] + </span></a>
+<a name="21806"><span class="lineNum">   21806 </span><span class="lineNoCov">          0 :           i3 * mm[i__ + 127] + i4 * mm[i__ - 1];</span></a>
+<a name="21807"><span class="lineNum">   21807 </span><span class="lineNoCov">          0 :         it1 %= 4096;</span></a>
+<a name="21808"><span class="lineNum">   21808 </span>            : </a>
+<a name="21809"><span class="lineNum">   21809 </span><span class="lineNoCov">          0 :         x[i__] = ((float) it1 + ((float) it2 + ((float) it3 + (</span></a>
+<a name="21810"><span class="lineNum">   21810 </span><span class="lineNoCov">          0 :                 float) it4 * 2.44140625e-4) * 2.44140625e-4) * </span></a>
+<a name="21811"><span class="lineNum">   21811 </span><span class="lineNoCov">          0 :                 2.44140625e-4) * 2.44140625e-4;</span></a>
+<a name="21812"><span class="lineNum">   21812 </span>            :     }</a>
+<a name="21813"><span class="lineNum">   21813 </span>            : </a>
+<a name="21814"><span class="lineNum">   21814 </span><span class="lineNoCov">          0 :     iseed[1] = it1;</span></a>
+<a name="21815"><span class="lineNum">   21815 </span><span class="lineNoCov">          0 :     iseed[2] = it2;</span></a>
+<a name="21816"><span class="lineNum">   21816 </span><span class="lineNoCov">          0 :     iseed[3] = it3;</span></a>
+<a name="21817"><span class="lineNum">   21817 </span><span class="lineNoCov">          0 :     iseed[4] = it4;</span></a>
+<a name="21818"><span class="lineNum">   21818 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="21819"><span class="lineNum">   21819 </span>            : </a>
+<a name="21820"><span class="lineNum">   21820 </span>            : } </a>
+<a name="21821"><span class="lineNum">   21821 </span>            : }</a>
+<a name="21822"><span class="lineNum">   21822 </span>            : }</a>
+<a name="21823"><span class="lineNum">   21823 </span>            : #include &lt;cmath&gt;</a>
+<a name="21824"><span class="lineNum">   21824 </span>            : #include &quot;real.h&quot;</a>
+<a name="21825"><span class="lineNum">   21825 </span>            : </a>
+<a name="21826"><span class="lineNum">   21826 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="21827"><span class="lineNum">   21827 </span>            : </a>
+<a name="21828"><span class="lineNum">   21828 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21829"><span class="lineNum">   21829 </span>            : namespace PLMD{</a>
+<a name="21830"><span class="lineNum">   21830 </span>            : namespace lapack{</a>
+<a name="21831"><span class="lineNum">   21831 </span>            : using namespace blas;</a>
+<a name="21832"><span class="lineNum">   21832 </span>            : void</a>
+<a name="21833"><span class="lineNum">   21833 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slas2,SLAS2)(float *f,</span></a>
+<a name="21834"><span class="lineNum">   21834 </span>            :        float *g,</a>
+<a name="21835"><span class="lineNum">   21835 </span>            :        float *h,</a>
+<a name="21836"><span class="lineNum">   21836 </span>            :        float *ssmin,</a>
+<a name="21837"><span class="lineNum">   21837 </span>            :        float *ssmax)</a>
+<a name="21838"><span class="lineNum">   21838 </span>            : {</a>
+<a name="21839"><span class="lineNum">   21839 </span><span class="lineNoCov">          0 :   float fa = std::abs(*f);</span></a>
+<a name="21840"><span class="lineNum">   21840 </span><span class="lineNoCov">          0 :   float ga = std::abs(*g);</span></a>
+<a name="21841"><span class="lineNum">   21841 </span><span class="lineNoCov">          0 :   float ha = std::abs(*h);</span></a>
+<a name="21842"><span class="lineNum">   21842 </span>            :   float fhmin,fhmax,tmax,tmin,tmp1,tmp2;</a>
+<a name="21843"><span class="lineNum">   21843 </span>            :   float as,at,au,c;</a>
+<a name="21844"><span class="lineNum">   21844 </span>            : </a>
+<a name="21845"><span class="lineNum">   21845 </span><span class="lineNoCov">          0 :   fhmin = (fa&lt;ha) ? fa : ha;</span></a>
+<a name="21846"><span class="lineNum">   21846 </span><span class="lineNoCov">          0 :   fhmax = (fa&gt;ha) ? fa : ha;</span></a>
+<a name="21847"><span class="lineNum">   21847 </span>            :   </a>
+<a name="21848"><span class="lineNum">   21848 </span><span class="lineNoCov">          0 :   if(std::abs(fhmin)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="21849"><span class="lineNum">   21849 </span><span class="lineNoCov">          0 :     *ssmin = 0.0;</span></a>
+<a name="21850"><span class="lineNum">   21850 </span><span class="lineNoCov">          0 :     if(std::abs(fhmax)&lt;PLUMED_GMX_FLOAT_MIN) </span></a>
+<a name="21851"><span class="lineNum">   21851 </span><span class="lineNoCov">          0 :       *ssmax = ga;</span></a>
+<a name="21852"><span class="lineNum">   21852 </span>            :     else {</a>
+<a name="21853"><span class="lineNum">   21853 </span><span class="lineNoCov">          0 :       tmax = (fhmax&gt;ga) ? fhmax : ga;</span></a>
+<a name="21854"><span class="lineNum">   21854 </span><span class="lineNoCov">          0 :       tmin = (fhmax&lt;ga) ? fhmax : ga;</span></a>
+<a name="21855"><span class="lineNum">   21855 </span><span class="lineNoCov">          0 :       tmp1 = tmin / tmax;</span></a>
+<a name="21856"><span class="lineNum">   21856 </span><span class="lineNoCov">          0 :       tmp1 = tmp1 * tmp1;</span></a>
+<a name="21857"><span class="lineNum">   21857 </span><span class="lineNoCov">          0 :       *ssmax = tmax* std::sqrt(1.0 + tmp1);</span></a>
+<a name="21858"><span class="lineNum">   21858 </span>            :     }</a>
+<a name="21859"><span class="lineNum">   21859 </span>            :   } else {</a>
+<a name="21860"><span class="lineNum">   21860 </span><span class="lineNoCov">          0 :     if(ga&lt;fhmax) {</span></a>
+<a name="21861"><span class="lineNum">   21861 </span><span class="lineNoCov">          0 :       as = 1.0 + fhmin / fhmax;</span></a>
+<a name="21862"><span class="lineNum">   21862 </span><span class="lineNoCov">          0 :       at = (fhmax-fhmin) / fhmax;</span></a>
+<a name="21863"><span class="lineNum">   21863 </span><span class="lineNoCov">          0 :       au = (ga/fhmax);</span></a>
+<a name="21864"><span class="lineNum">   21864 </span><span class="lineNoCov">          0 :       au = au * au;</span></a>
+<a name="21865"><span class="lineNum">   21865 </span><span class="lineNoCov">          0 :       c = 2.0 / (  std::sqrt(as*as+au) + std::sqrt(at*at+au) );</span></a>
+<a name="21866"><span class="lineNum">   21866 </span><span class="lineNoCov">          0 :       *ssmin = fhmin * c;</span></a>
+<a name="21867"><span class="lineNum">   21867 </span><span class="lineNoCov">          0 :       *ssmax = fhmax / c;</span></a>
+<a name="21868"><span class="lineNum">   21868 </span>            :     } else {</a>
+<a name="21869"><span class="lineNum">   21869 </span><span class="lineNoCov">          0 :       au = fhmax / ga;</span></a>
+<a name="21870"><span class="lineNum">   21870 </span><span class="lineNoCov">          0 :       if(std::abs(au)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="21871"><span class="lineNum">   21871 </span><span class="lineNoCov">          0 :         *ssmin = (fhmin*fhmax)/ga;</span></a>
+<a name="21872"><span class="lineNum">   21872 </span><span class="lineNoCov">          0 :         *ssmax = ga;</span></a>
+<a name="21873"><span class="lineNum">   21873 </span>            :       } else {</a>
+<a name="21874"><span class="lineNum">   21874 </span><span class="lineNoCov">          0 :         as = 1.0 + fhmin / fhmax;</span></a>
+<a name="21875"><span class="lineNum">   21875 </span><span class="lineNoCov">          0 :         at = (fhmax-fhmin)/fhmax;</span></a>
+<a name="21876"><span class="lineNum">   21876 </span><span class="lineNoCov">          0 :         tmp1 = as*au;</span></a>
+<a name="21877"><span class="lineNum">   21877 </span><span class="lineNoCov">          0 :         tmp2 = at*au;</span></a>
+<a name="21878"><span class="lineNum">   21878 </span><span class="lineNoCov">          0 :         c = 1.0 / (  std::sqrt(1.0+tmp1*tmp1) + std::sqrt(1.0+tmp2*tmp2));</span></a>
+<a name="21879"><span class="lineNum">   21879 </span><span class="lineNoCov">          0 :         *ssmin = (fhmin*c)*au;</span></a>
+<a name="21880"><span class="lineNum">   21880 </span><span class="lineNoCov">          0 :         *ssmin = *ssmin + *ssmin;</span></a>
+<a name="21881"><span class="lineNum">   21881 </span><span class="lineNoCov">          0 :         *ssmax = ga / (c+c);</span></a>
+<a name="21882"><span class="lineNum">   21882 </span>            :       }</a>
+<a name="21883"><span class="lineNum">   21883 </span>            :     }</a>
+<a name="21884"><span class="lineNum">   21884 </span>            :   }</a>
+<a name="21885"><span class="lineNum">   21885 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="21886"><span class="lineNum">   21886 </span>            : }</a>
+<a name="21887"><span class="lineNum">   21887 </span>            : }</a>
+<a name="21888"><span class="lineNum">   21888 </span>            : }</a>
+<a name="21889"><span class="lineNum">   21889 </span>            : #include &lt;cctype&gt;</a>
+<a name="21890"><span class="lineNum">   21890 </span>            : #include &lt;cmath&gt;</a>
+<a name="21891"><span class="lineNum">   21891 </span>            : #include &quot;real.h&quot;</a>
+<a name="21892"><span class="lineNum">   21892 </span>            : </a>
+<a name="21893"><span class="lineNum">   21893 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="21894"><span class="lineNum">   21894 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="21895"><span class="lineNum">   21895 </span>            : </a>
+<a name="21896"><span class="lineNum">   21896 </span>            : </a>
+<a name="21897"><span class="lineNum">   21897 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="21898"><span class="lineNum">   21898 </span>            : namespace PLMD{</a>
+<a name="21899"><span class="lineNum">   21899 </span>            : namespace lapack{</a>
+<a name="21900"><span class="lineNum">   21900 </span>            : using namespace blas;</a>
+<a name="21901"><span class="lineNum">   21901 </span>            : void</a>
+<a name="21902"><span class="lineNum">   21902 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(const char *type,</span></a>
+<a name="21903"><span class="lineNum">   21903 </span>            :                         int *kl,</a>
+<a name="21904"><span class="lineNum">   21904 </span>            :                         int *ku,</a>
+<a name="21905"><span class="lineNum">   21905 </span>            :                         float *cfrom,</a>
+<a name="21906"><span class="lineNum">   21906 </span>            :                         float *cto,</a>
+<a name="21907"><span class="lineNum">   21907 </span>            :                         int *m,</a>
+<a name="21908"><span class="lineNum">   21908 </span>            :                         int *n,</a>
+<a name="21909"><span class="lineNum">   21909 </span>            :                         float *a,</a>
+<a name="21910"><span class="lineNum">   21910 </span>            :                         int *lda,</a>
+<a name="21911"><span class="lineNum">   21911 </span>            :                         int *info)</a>
+<a name="21912"><span class="lineNum">   21912 </span>            : {</a>
+<a name="21913"><span class="lineNum">   21913 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*type);</span></a>
+<a name="21914"><span class="lineNum">   21914 </span>            :   int i,j,k,l,k1,k2,k3,k4;</a>
+<a name="21915"><span class="lineNum">   21915 </span>            :   int done=0;</a>
+<a name="21916"><span class="lineNum">   21916 </span>            :   float minval,smlnum,bignum;</a>
+<a name="21917"><span class="lineNum">   21917 </span>            :   float cfromc, ctoc, cfrom1, cto1, mul;</a>
+<a name="21918"><span class="lineNum">   21918 </span>            : </a>
+<a name="21919"><span class="lineNum">   21919 </span><span class="lineNoCov">          0 :   if(*n&lt;=0 || *m&lt;=0)</span></a>
+<a name="21920"><span class="lineNum">   21920 </span>            :     return;</a>
+<a name="21921"><span class="lineNum">   21921 </span>            : </a>
+<a name="21922"><span class="lineNum">   21922 </span>            :   minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="21923"><span class="lineNum">   21923 </span>            :   smlnum = minval / PLUMED_GMX_FLOAT_EPS;</a>
+<a name="21924"><span class="lineNum">   21924 </span>            :   bignum = 1.0 / smlnum;</a>
+<a name="21925"><span class="lineNum">   21925 </span>            : </a>
+<a name="21926"><span class="lineNum">   21926 </span><span class="lineNoCov">          0 :   cfromc = *cfrom;</span></a>
+<a name="21927"><span class="lineNum">   21927 </span><span class="lineNoCov">          0 :   ctoc   = *cto;</span></a>
+<a name="21928"><span class="lineNum">   21928 </span>            : </a>
+<a name="21929"><span class="lineNum">   21929 </span><span class="lineNoCov">          0 :   while(!done) {</span></a>
+<a name="21930"><span class="lineNum">   21930 </span>            :     </a>
+<a name="21931"><span class="lineNum">   21931 </span><span class="lineNoCov">          0 :     cfrom1 = cfromc * smlnum;</span></a>
+<a name="21932"><span class="lineNum">   21932 </span><span class="lineNoCov">          0 :     cto1   = ctoc / bignum;</span></a>
+<a name="21933"><span class="lineNum">   21933 </span>            : </a>
+<a name="21934"><span class="lineNum">   21934 </span><span class="lineNoCov">          0 :     if(std::abs(cfrom1)&gt;std::abs(ctoc) &amp;&amp; std::abs(ctoc)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="21935"><span class="lineNum">   21935 </span>            :       mul = smlnum;</a>
+<a name="21936"><span class="lineNum">   21936 </span>            :       done = 0;</a>
+<a name="21937"><span class="lineNum">   21937 </span>            :       cfromc = cfrom1;</a>
+<a name="21938"><span class="lineNum">   21938 </span><span class="lineNoCov">          0 :     } else if(std::abs(cto1)&gt;std::abs(cfromc)) {</span></a>
+<a name="21939"><span class="lineNum">   21939 </span>            :       mul = bignum;</a>
+<a name="21940"><span class="lineNum">   21940 </span>            :       done = 0;</a>
+<a name="21941"><span class="lineNum">   21941 </span>            :       ctoc = cto1;</a>
+<a name="21942"><span class="lineNum">   21942 </span>            :     } else {</a>
+<a name="21943"><span class="lineNum">   21943 </span><span class="lineNoCov">          0 :       mul = ctoc / cfromc;</span></a>
+<a name="21944"><span class="lineNum">   21944 </span>            :       done = 1;</a>
+<a name="21945"><span class="lineNum">   21945 </span>            :     }</a>
+<a name="21946"><span class="lineNum">   21946 </span>            : </a>
+<a name="21947"><span class="lineNum">   21947 </span><span class="lineNoCov">          0 :     switch(ch) {</span></a>
+<a name="21948"><span class="lineNum">   21948 </span>            :     case 'G': </a>
+<a name="21949"><span class="lineNum">   21949 </span>            :       /* Full matrix */</a>
+<a name="21950"><span class="lineNum">   21950 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++)</span></a>
+<a name="21951"><span class="lineNum">   21951 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;*m;i++)</span></a>
+<a name="21952"><span class="lineNum">   21952 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="21953"><span class="lineNum">   21953 </span>            :       break;</a>
+<a name="21954"><span class="lineNum">   21954 </span>            : </a>
+<a name="21955"><span class="lineNum">   21955 </span>            :     case 'L': </a>
+<a name="21956"><span class="lineNum">   21956 </span>            :       /* Lower triangular matrix */</a>
+<a name="21957"><span class="lineNum">   21957 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++)</span></a>
+<a name="21958"><span class="lineNum">   21958 </span><span class="lineNoCov">          0 :         for(i=j;i&lt;*m;i++)</span></a>
+<a name="21959"><span class="lineNum">   21959 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="21960"><span class="lineNum">   21960 </span>            :       break;</a>
+<a name="21961"><span class="lineNum">   21961 </span>            : </a>
+<a name="21962"><span class="lineNum">   21962 </span>            :     case 'U': </a>
+<a name="21963"><span class="lineNum">   21963 </span>            :       /* Upper triangular matrix */</a>
+<a name="21964"><span class="lineNum">   21964 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="21965"><span class="lineNum">   21965 </span><span class="lineNoCov">          0 :         k = (j &lt; (*m-1)) ? j : (*m-1);</span></a>
+<a name="21966"><span class="lineNum">   21966 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;=k;i++)</span></a>
+<a name="21967"><span class="lineNum">   21967 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="21968"><span class="lineNum">   21968 </span>            :       }</a>
+<a name="21969"><span class="lineNum">   21969 </span>            :       break;</a>
+<a name="21970"><span class="lineNum">   21970 </span>            : </a>
+<a name="21971"><span class="lineNum">   21971 </span>            :     case 'H': </a>
+<a name="21972"><span class="lineNum">   21972 </span>            :       /* Upper Hessenberg matrix */</a>
+<a name="21973"><span class="lineNum">   21973 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="21974"><span class="lineNum">   21974 </span><span class="lineNoCov">          0 :         k = ((j+1) &lt; (*m-1)) ? (j+1) : (*m-1);</span></a>
+<a name="21975"><span class="lineNum">   21975 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;=k;i++)</span></a>
+<a name="21976"><span class="lineNum">   21976 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="21977"><span class="lineNum">   21977 </span>            :       }</a>
+<a name="21978"><span class="lineNum">   21978 </span>            :       break;</a>
+<a name="21979"><span class="lineNum">   21979 </span>            : </a>
+<a name="21980"><span class="lineNum">   21980 </span><span class="lineNoCov">          0 :     case 'B': </span></a>
+<a name="21981"><span class="lineNum">   21981 </span>            :       /* Symmetric band matrix, lower bandwidth KL, upper KU,</a>
+<a name="21982"><span class="lineNum">   21982 </span>            :        * only the lower half stored.</a>
+<a name="21983"><span class="lineNum">   21983 </span>            :        */</a>
+<a name="21984"><span class="lineNum">   21984 </span><span class="lineNoCov">          0 :       k3 = *kl;</span></a>
+<a name="21985"><span class="lineNum">   21985 </span><span class="lineNoCov">          0 :       k4 = *n - 1;</span></a>
+<a name="21986"><span class="lineNum">   21986 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="21987"><span class="lineNum">   21987 </span><span class="lineNoCov">          0 :         k = (k3 &lt; (k4-j)) ? k3 : (k4-j);</span></a>
+<a name="21988"><span class="lineNum">   21988 </span><span class="lineNoCov">          0 :         for(i=0;i&lt;=k;i++)</span></a>
+<a name="21989"><span class="lineNum">   21989 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="21990"><span class="lineNum">   21990 </span>            :       }</a>
+<a name="21991"><span class="lineNum">   21991 </span>            :       break;</a>
+<a name="21992"><span class="lineNum">   21992 </span>            : </a>
+<a name="21993"><span class="lineNum">   21993 </span><span class="lineNoCov">          0 :     case 'Q': </span></a>
+<a name="21994"><span class="lineNum">   21994 </span>            :       /* Symmetric band matrix, lower bandwidth KL, upper KU,</a>
+<a name="21995"><span class="lineNum">   21995 </span>            :        * only the upper half stored.</a>
+<a name="21996"><span class="lineNum">   21996 </span>            :        */</a>
+<a name="21997"><span class="lineNum">   21997 </span><span class="lineNoCov">          0 :       k1 = *ku;</span></a>
+<a name="21998"><span class="lineNum">   21998 </span>            :       k3 = *ku;</a>
+<a name="21999"><span class="lineNum">   21999 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="22000"><span class="lineNum">   22000 </span><span class="lineNoCov">          0 :         k = ((k1-j) &gt; 0) ? (k1-j) : 0;</span></a>
+<a name="22001"><span class="lineNum">   22001 </span><span class="lineNoCov">          0 :         for(i=k;i&lt;=k3;i++)</span></a>
+<a name="22002"><span class="lineNum">   22002 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="22003"><span class="lineNum">   22003 </span>            :       }</a>
+<a name="22004"><span class="lineNum">   22004 </span>            :       break;</a>
+<a name="22005"><span class="lineNum">   22005 </span>            : </a>
+<a name="22006"><span class="lineNum">   22006 </span><span class="lineNoCov">          0 :     case 'Z': </span></a>
+<a name="22007"><span class="lineNum">   22007 </span>            :       /* Band matrix, lower bandwidth KL, upper KU. */</a>
+<a name="22008"><span class="lineNum">   22008 </span>            : </a>
+<a name="22009"><span class="lineNum">   22009 </span><span class="lineNoCov">          0 :       k1 = *kl + *ku;</span></a>
+<a name="22010"><span class="lineNum">   22010 </span>            :       k2 = *kl;</a>
+<a name="22011"><span class="lineNum">   22011 </span><span class="lineNoCov">          0 :       k3 = 2*(*kl) + *ku;</span></a>
+<a name="22012"><span class="lineNum">   22012 </span><span class="lineNoCov">          0 :       k4 = *kl + *ku - 1 + *m;</span></a>
+<a name="22013"><span class="lineNum">   22013 </span><span class="lineNoCov">          0 :       for(j=0;j&lt;*n;j++) {</span></a>
+<a name="22014"><span class="lineNum">   22014 </span><span class="lineNoCov">          0 :         k = ((k1-j) &gt; k2) ? (k1-j) : k2;</span></a>
+<a name="22015"><span class="lineNum">   22015 </span><span class="lineNoCov">          0 :         l = (k3 &lt; (k4-j)) ? k3 : (k4-j);</span></a>
+<a name="22016"><span class="lineNum">   22016 </span><span class="lineNoCov">          0 :         for(i=k;i&lt;=l;i++)</span></a>
+<a name="22017"><span class="lineNum">   22017 </span><span class="lineNoCov">          0 :           a[j*(*lda)+i] *= mul;</span></a>
+<a name="22018"><span class="lineNum">   22018 </span>            :       }</a>
+<a name="22019"><span class="lineNum">   22019 </span>            :       break;</a>
+<a name="22020"><span class="lineNum">   22020 </span>            : </a>
+<a name="22021"><span class="lineNum">   22021 </span><span class="lineNoCov">          0 :     default:</span></a>
+<a name="22022"><span class="lineNum">   22022 </span><span class="lineNoCov">          0 :       *info = -1;</span></a>
+<a name="22023"><span class="lineNum">   22023 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="22024"><span class="lineNum">   22024 </span>            :     }</a>
+<a name="22025"><span class="lineNum">   22025 </span>            :   } /* finished */</a>
+<a name="22026"><span class="lineNum">   22026 </span>            : </a>
+<a name="22027"><span class="lineNum">   22027 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="22028"><span class="lineNum">   22028 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="22029"><span class="lineNum">   22029 </span>            : }</a>
+<a name="22030"><span class="lineNum">   22030 </span>            : }</a>
+<a name="22031"><span class="lineNum">   22031 </span>            : }</a>
+<a name="22032"><span class="lineNum">   22032 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="22033"><span class="lineNum">   22033 </span>            : </a>
+<a name="22034"><span class="lineNum">   22034 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22035"><span class="lineNum">   22035 </span>            : namespace PLMD{</a>
+<a name="22036"><span class="lineNum">   22036 </span>            : namespace lapack{</a>
+<a name="22037"><span class="lineNum">   22037 </span>            : using namespace blas;</a>
+<a name="22038"><span class="lineNum">   22038 </span>            : void </a>
+<a name="22039"><span class="lineNum">   22039 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd0,SLASD0)(int *n, </span></a>
+<a name="22040"><span class="lineNum">   22040 </span>            :         int *sqre, </a>
+<a name="22041"><span class="lineNum">   22041 </span>            :         float *d__, </a>
+<a name="22042"><span class="lineNum">   22042 </span>            :         float *e, </a>
+<a name="22043"><span class="lineNum">   22043 </span>            :         float *u, </a>
+<a name="22044"><span class="lineNum">   22044 </span>            :         int *ldu, </a>
+<a name="22045"><span class="lineNum">   22045 </span>            :         float *vt, </a>
+<a name="22046"><span class="lineNum">   22046 </span>            :         int *ldvt,</a>
+<a name="22047"><span class="lineNum">   22047 </span>            :         int *smlsiz, </a>
+<a name="22048"><span class="lineNum">   22048 </span>            :         int *iwork,</a>
+<a name="22049"><span class="lineNum">   22049 </span>            :         float *work, </a>
+<a name="22050"><span class="lineNum">   22050 </span>            :         int *info)</a>
+<a name="22051"><span class="lineNum">   22051 </span>            : {</a>
+<a name="22052"><span class="lineNum">   22052 </span>            :     int u_dim1, u_offset, vt_dim1, vt_offset, i__1, i__2;</a>
+<a name="22053"><span class="lineNum">   22053 </span>            : </a>
+<a name="22054"><span class="lineNum">   22054 </span>            :     int i__, j, m, i1, ic, lf, nd, ll, nl, nr, im1, ncc, nlf, nrf, </a>
+<a name="22055"><span class="lineNum">   22055 </span>            :             iwk, lvl, ndb1, nlp1, nrp1;</a>
+<a name="22056"><span class="lineNum">   22056 </span>            :     float beta;</a>
+<a name="22057"><span class="lineNum">   22057 </span>            :     int idxq, nlvl;</a>
+<a name="22058"><span class="lineNum">   22058 </span>            :     float alpha;</a>
+<a name="22059"><span class="lineNum">   22059 </span>            :     int inode, ndiml, idxqc, ndimr, itemp, sqrei;</a>
+<a name="22060"><span class="lineNum">   22060 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="22061"><span class="lineNum">   22061 </span>            : </a>
+<a name="22062"><span class="lineNum">   22062 </span>            : </a>
+<a name="22063"><span class="lineNum">   22063 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="22064"><span class="lineNum">   22064 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="22065"><span class="lineNum">   22065 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="22066"><span class="lineNum">   22066 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="22067"><span class="lineNum">   22067 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="22068"><span class="lineNum">   22068 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="22069"><span class="lineNum">   22069 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="22070"><span class="lineNum">   22070 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="22071"><span class="lineNum">   22071 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="22072"><span class="lineNum">   22072 </span>            :     --work;</a>
+<a name="22073"><span class="lineNum">   22073 </span>            : </a>
+<a name="22074"><span class="lineNum">   22074 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="22075"><span class="lineNum">   22075 </span>            : </a>
+<a name="22076"><span class="lineNum">   22076 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="22077"><span class="lineNum">   22077 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="22078"><span class="lineNum">   22078 </span><span class="lineNoCov">          0 :     } else if (*sqre &lt; 0 || *sqre &gt; 1) {</span></a>
+<a name="22079"><span class="lineNum">   22079 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="22080"><span class="lineNum">   22080 </span>            :     }</a>
+<a name="22081"><span class="lineNum">   22081 </span>            : </a>
+<a name="22082"><span class="lineNum">   22082 </span><span class="lineNoCov">          0 :     m = *n + *sqre;</span></a>
+<a name="22083"><span class="lineNum">   22083 </span>            : </a>
+<a name="22084"><span class="lineNum">   22084 </span><span class="lineNoCov">          0 :     if (*ldu &lt; *n) {</span></a>
+<a name="22085"><span class="lineNum">   22085 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="22086"><span class="lineNum">   22086 </span><span class="lineNoCov">          0 :     } else if (*ldvt &lt; m) {</span></a>
+<a name="22087"><span class="lineNum">   22087 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="22088"><span class="lineNum">   22088 </span><span class="lineNoCov">          0 :     } else if (*smlsiz &lt; 3) {</span></a>
+<a name="22089"><span class="lineNum">   22089 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="22090"><span class="lineNum">   22090 </span>            :     }</a>
+<a name="22091"><span class="lineNum">   22091 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="22092"><span class="lineNum">   22092 </span>            :         return;</a>
+<a name="22093"><span class="lineNum">   22093 </span>            :     }</a>
+<a name="22094"><span class="lineNum">   22094 </span>            : </a>
+<a name="22095"><span class="lineNum">   22095 </span><span class="lineNoCov">          0 :     if (*n &lt;= *smlsiz) {</span></a>
+<a name="22096"><span class="lineNum">   22096 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, sqre, n, &amp;m, n, &amp;c__0, &amp;d__[1], &amp;e[1], &amp;vt[vt_offset], </span></a>
+<a name="22097"><span class="lineNum">   22097 </span>            :                 ldvt, &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;work[1], info);</a>
+<a name="22098"><span class="lineNum">   22098 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="22099"><span class="lineNum">   22099 </span>            :     }</a>
+<a name="22100"><span class="lineNum">   22100 </span>            : </a>
+<a name="22101"><span class="lineNum">   22101 </span>            :     inode = 1;</a>
+<a name="22102"><span class="lineNum">   22102 </span><span class="lineNoCov">          0 :     ndiml = inode + *n;</span></a>
+<a name="22103"><span class="lineNum">   22103 </span><span class="lineNoCov">          0 :     ndimr = ndiml + *n;</span></a>
+<a name="22104"><span class="lineNum">   22104 </span><span class="lineNoCov">          0 :     idxq = ndimr + *n;</span></a>
+<a name="22105"><span class="lineNum">   22105 </span><span class="lineNoCov">          0 :     iwk = idxq + *n;</span></a>
+<a name="22106"><span class="lineNum">   22106 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasdt,SLASDT)(n, &amp;nlvl, &amp;nd, &amp;iwork[inode], &amp;iwork[ndiml], &amp;iwork[ndimr], </span></a>
+<a name="22107"><span class="lineNum">   22107 </span>            :             smlsiz);</a>
+<a name="22108"><span class="lineNum">   22108 </span>            : </a>
+<a name="22109"><span class="lineNum">   22109 </span><span class="lineNoCov">          0 :     ndb1 = (nd + 1) / 2;</span></a>
+<a name="22110"><span class="lineNum">   22110 </span><span class="lineNoCov">          0 :     ncc = 0;</span></a>
+<a name="22111"><span class="lineNum">   22111 </span>            :     i__1 = nd;</a>
+<a name="22112"><span class="lineNum">   22112 </span><span class="lineNoCov">          0 :     for (i__ = ndb1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22113"><span class="lineNum">   22113 </span>            : </a>
+<a name="22114"><span class="lineNum">   22114 </span><span class="lineNoCov">          0 :         i1 = i__ - 1;</span></a>
+<a name="22115"><span class="lineNum">   22115 </span><span class="lineNoCov">          0 :         ic = iwork[inode + i1];</span></a>
+<a name="22116"><span class="lineNum">   22116 </span><span class="lineNoCov">          0 :         nl = iwork[ndiml + i1];</span></a>
+<a name="22117"><span class="lineNum">   22117 </span><span class="lineNoCov">          0 :         nlp1 = nl + 1;</span></a>
+<a name="22118"><span class="lineNum">   22118 </span><span class="lineNoCov">          0 :         nr = iwork[ndimr + i1];</span></a>
+<a name="22119"><span class="lineNum">   22119 </span><span class="lineNoCov">          0 :         nrp1 = nr + 1;</span></a>
+<a name="22120"><span class="lineNum">   22120 </span><span class="lineNoCov">          0 :         nlf = ic - nl;</span></a>
+<a name="22121"><span class="lineNum">   22121 </span><span class="lineNoCov">          0 :         nrf = ic + 1;</span></a>
+<a name="22122"><span class="lineNum">   22122 </span><span class="lineNoCov">          0 :         sqrei = 1;</span></a>
+<a name="22123"><span class="lineNum">   22123 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nl, &amp;nlp1, &amp;nl, &amp;ncc, &amp;d__[nlf], &amp;e[nlf], &amp;vt[</span></a>
+<a name="22124"><span class="lineNum">   22124 </span><span class="lineNoCov">          0 :                 nlf + nlf * vt_dim1], ldvt, &amp;u[nlf + nlf * u_dim1], ldu, &amp;u[</span></a>
+<a name="22125"><span class="lineNum">   22125 </span><span class="lineNoCov">          0 :                 nlf + nlf * u_dim1], ldu, &amp;work[1], info);</span></a>
+<a name="22126"><span class="lineNum">   22126 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="22127"><span class="lineNum">   22127 </span>            :             return;</a>
+<a name="22128"><span class="lineNum">   22128 </span>            :         }</a>
+<a name="22129"><span class="lineNum">   22129 </span><span class="lineNoCov">          0 :         itemp = idxq + nlf - 2;</span></a>
+<a name="22130"><span class="lineNum">   22130 </span><span class="lineNoCov">          0 :         i__2 = nl;</span></a>
+<a name="22131"><span class="lineNum">   22131 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="22132"><span class="lineNum">   22132 </span><span class="lineNoCov">          0 :             iwork[itemp + j] = j;</span></a>
+<a name="22133"><span class="lineNum">   22133 </span>            :         }</a>
+<a name="22134"><span class="lineNum">   22134 </span><span class="lineNoCov">          0 :         if (i__ == nd) {</span></a>
+<a name="22135"><span class="lineNum">   22135 </span><span class="lineNoCov">          0 :             sqrei = *sqre;</span></a>
+<a name="22136"><span class="lineNum">   22136 </span>            :         } else {</a>
+<a name="22137"><span class="lineNum">   22137 </span><span class="lineNoCov">          0 :             sqrei = 1;</span></a>
+<a name="22138"><span class="lineNum">   22138 </span>            :         }</a>
+<a name="22139"><span class="lineNum">   22139 </span><span class="lineNoCov">          0 :         nrp1 = nr + sqrei;</span></a>
+<a name="22140"><span class="lineNum">   22140 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nr, &amp;nrp1, &amp;nr, &amp;ncc, &amp;d__[nrf], &amp;e[nrf], &amp;vt[</span></a>
+<a name="22141"><span class="lineNum">   22141 </span><span class="lineNoCov">          0 :                 nrf + nrf * vt_dim1], ldvt, &amp;u[nrf + nrf * u_dim1], ldu, &amp;u[</span></a>
+<a name="22142"><span class="lineNum">   22142 </span><span class="lineNoCov">          0 :                 nrf + nrf * u_dim1], ldu, &amp;work[1], info);</span></a>
+<a name="22143"><span class="lineNum">   22143 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="22144"><span class="lineNum">   22144 </span>            :             return;</a>
+<a name="22145"><span class="lineNum">   22145 </span>            :         }</a>
+<a name="22146"><span class="lineNum">   22146 </span><span class="lineNoCov">          0 :         itemp = idxq + ic;</span></a>
+<a name="22147"><span class="lineNum">   22147 </span><span class="lineNoCov">          0 :         i__2 = nr;</span></a>
+<a name="22148"><span class="lineNum">   22148 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="22149"><span class="lineNum">   22149 </span><span class="lineNoCov">          0 :             iwork[itemp + j - 1] = j;</span></a>
+<a name="22150"><span class="lineNum">   22150 </span>            :         }</a>
+<a name="22151"><span class="lineNum">   22151 </span>            :     }</a>
+<a name="22152"><span class="lineNum">   22152 </span>            : </a>
+<a name="22153"><span class="lineNum">   22153 </span><span class="lineNoCov">          0 :     for (lvl = nlvl; lvl &gt;= 1; --lvl) {</span></a>
+<a name="22154"><span class="lineNum">   22154 </span>            : </a>
+<a name="22155"><span class="lineNum">   22155 </span><span class="lineNoCov">          0 :         if (lvl == 1) {</span></a>
+<a name="22156"><span class="lineNum">   22156 </span>            :             lf = 1;</a>
+<a name="22157"><span class="lineNum">   22157 </span>            :             ll = 1;</a>
+<a name="22158"><span class="lineNum">   22158 </span>            :         } else {</a>
+<a name="22159"><span class="lineNum">   22159 </span><span class="lineNoCov">          0 :             i__1 = lvl - 1;</span></a>
+<a name="22160"><span class="lineNum">   22160 </span><span class="lineNoCov">          0 :             lf = (1 &lt;&lt; i__1);</span></a>
+<a name="22161"><span class="lineNum">   22161 </span><span class="lineNoCov">          0 :             ll = (lf &lt;&lt; 1) - 1;</span></a>
+<a name="22162"><span class="lineNum">   22162 </span>            :         }</a>
+<a name="22163"><span class="lineNum">   22163 </span>            :         i__1 = ll;</a>
+<a name="22164"><span class="lineNum">   22164 </span><span class="lineNoCov">          0 :         for (i__ = lf; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22165"><span class="lineNum">   22165 </span><span class="lineNoCov">          0 :             im1 = i__ - 1;</span></a>
+<a name="22166"><span class="lineNum">   22166 </span><span class="lineNoCov">          0 :             ic = iwork[inode + im1];</span></a>
+<a name="22167"><span class="lineNum">   22167 </span><span class="lineNoCov">          0 :             nl = iwork[ndiml + im1];</span></a>
+<a name="22168"><span class="lineNum">   22168 </span><span class="lineNoCov">          0 :             nr = iwork[ndimr + im1];</span></a>
+<a name="22169"><span class="lineNum">   22169 </span><span class="lineNoCov">          0 :             nlf = ic - nl;</span></a>
+<a name="22170"><span class="lineNum">   22170 </span><span class="lineNoCov">          0 :             if (*sqre == 0 &amp;&amp; i__ == ll) {</span></a>
+<a name="22171"><span class="lineNum">   22171 </span><span class="lineNoCov">          0 :                 sqrei = *sqre;</span></a>
+<a name="22172"><span class="lineNum">   22172 </span>            :             } else {</a>
+<a name="22173"><span class="lineNum">   22173 </span><span class="lineNoCov">          0 :                 sqrei = 1;</span></a>
+<a name="22174"><span class="lineNum">   22174 </span>            :             }</a>
+<a name="22175"><span class="lineNum">   22175 </span><span class="lineNoCov">          0 :             idxqc = idxq + nlf - 1;</span></a>
+<a name="22176"><span class="lineNum">   22176 </span><span class="lineNoCov">          0 :             alpha = d__[ic];</span></a>
+<a name="22177"><span class="lineNum">   22177 </span><span class="lineNoCov">          0 :             beta = e[ic];</span></a>
+<a name="22178"><span class="lineNum">   22178 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasd1,SLASD1)(&amp;nl, &amp;nr, &amp;sqrei, &amp;d__[nlf], &amp;alpha, &amp;beta, &amp;u[nlf + nlf *</span></a>
+<a name="22179"><span class="lineNum">   22179 </span><span class="lineNoCov">          0 :                      u_dim1], ldu, &amp;vt[nlf + nlf * vt_dim1], ldvt, &amp;iwork[</span></a>
+<a name="22180"><span class="lineNum">   22180 </span><span class="lineNoCov">          0 :                     idxqc], &amp;iwork[iwk], &amp;work[1], info);</span></a>
+<a name="22181"><span class="lineNum">   22181 </span><span class="lineNoCov">          0 :             if (*info != 0) {</span></a>
+<a name="22182"><span class="lineNum">   22182 </span>            :                 return;</a>
+<a name="22183"><span class="lineNum">   22183 </span>            :             }</a>
+<a name="22184"><span class="lineNum">   22184 </span>            :         }</a>
+<a name="22185"><span class="lineNum">   22185 </span>            :     }</a>
+<a name="22186"><span class="lineNum">   22186 </span>            : </a>
+<a name="22187"><span class="lineNum">   22187 </span>            :     return;</a>
+<a name="22188"><span class="lineNum">   22188 </span>            : </a>
+<a name="22189"><span class="lineNum">   22189 </span>            : }</a>
+<a name="22190"><span class="lineNum">   22190 </span>            : }</a>
+<a name="22191"><span class="lineNum">   22191 </span>            : }</a>
+<a name="22192"><span class="lineNum">   22192 </span>            : #include &lt;cmath&gt;</a>
+<a name="22193"><span class="lineNum">   22193 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="22194"><span class="lineNum">   22194 </span>            : </a>
+<a name="22195"><span class="lineNum">   22195 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22196"><span class="lineNum">   22196 </span>            : namespace PLMD{</a>
+<a name="22197"><span class="lineNum">   22197 </span>            : namespace lapack{</a>
+<a name="22198"><span class="lineNum">   22198 </span>            : using namespace blas;</a>
+<a name="22199"><span class="lineNum">   22199 </span>            : void </a>
+<a name="22200"><span class="lineNum">   22200 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd1,SLASD1)(int *nl, </span></a>
+<a name="22201"><span class="lineNum">   22201 </span>            :         int *nr, </a>
+<a name="22202"><span class="lineNum">   22202 </span>            :         int *sqre, </a>
+<a name="22203"><span class="lineNum">   22203 </span>            :         float *d__, </a>
+<a name="22204"><span class="lineNum">   22204 </span>            :         float *alpha, </a>
+<a name="22205"><span class="lineNum">   22205 </span>            :         float *beta, </a>
+<a name="22206"><span class="lineNum">   22206 </span>            :         float *u, </a>
+<a name="22207"><span class="lineNum">   22207 </span>            :         int *ldu, </a>
+<a name="22208"><span class="lineNum">   22208 </span>            :         float *vt, </a>
+<a name="22209"><span class="lineNum">   22209 </span>            :         int *ldvt, </a>
+<a name="22210"><span class="lineNum">   22210 </span>            :         int *idxq, </a>
+<a name="22211"><span class="lineNum">   22211 </span>            :         int *iwork, </a>
+<a name="22212"><span class="lineNum">   22212 </span>            :         float *work, </a>
+<a name="22213"><span class="lineNum">   22213 </span>            :         int *info)</a>
+<a name="22214"><span class="lineNum">   22214 </span>            : {</a>
+<a name="22215"><span class="lineNum">   22215 </span>            :     int u_dim1, u_offset, vt_dim1, vt_offset, i__1;</a>
+<a name="22216"><span class="lineNum">   22216 </span>            :     float d__1, d__2;</a>
+<a name="22217"><span class="lineNum">   22217 </span>            : </a>
+<a name="22218"><span class="lineNum">   22218 </span>            :     int i__, k, m, n, n1, n2, iq, iz, iu2, ldq, idx, ldu2, ivt2, </a>
+<a name="22219"><span class="lineNum">   22219 </span>            :             idxc, idxp, ldvt2;</a>
+<a name="22220"><span class="lineNum">   22220 </span>            :     int isigma;</a>
+<a name="22221"><span class="lineNum">   22221 </span>            :     float orgnrm;</a>
+<a name="22222"><span class="lineNum">   22222 </span>            :     int coltyp;</a>
+<a name="22223"><span class="lineNum">   22223 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="22224"><span class="lineNum">   22224 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="22225"><span class="lineNum">   22225 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="22226"><span class="lineNum">   22226 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="22227"><span class="lineNum">   22227 </span>            : </a>
+<a name="22228"><span class="lineNum">   22228 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="22229"><span class="lineNum">   22229 </span>            :     u_dim1 = *ldu;</a>
+<a name="22230"><span class="lineNum">   22230 </span>            :     u_offset = 1 + u_dim1;</a>
+<a name="22231"><span class="lineNum">   22231 </span>            :     u -= u_offset;</a>
+<a name="22232"><span class="lineNum">   22232 </span>            :     vt_dim1 = *ldvt;</a>
+<a name="22233"><span class="lineNum">   22233 </span>            :     vt_offset = 1 + vt_dim1;</a>
+<a name="22234"><span class="lineNum">   22234 </span>            :     vt -= vt_offset;</a>
+<a name="22235"><span class="lineNum">   22235 </span>            :     --idxq;</a>
+<a name="22236"><span class="lineNum">   22236 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="22237"><span class="lineNum">   22237 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="22238"><span class="lineNum">   22238 </span>            : </a>
+<a name="22239"><span class="lineNum">   22239 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="22240"><span class="lineNum">   22240 </span>            : </a>
+<a name="22241"><span class="lineNum">   22241 </span><span class="lineNoCov">          0 :     if (*nl &lt; 1) {</span></a>
+<a name="22242"><span class="lineNum">   22242 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="22243"><span class="lineNum">   22243 </span><span class="lineNoCov">          0 :     } else if (*nr &lt; 1) {</span></a>
+<a name="22244"><span class="lineNum">   22244 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="22245"><span class="lineNum">   22245 </span><span class="lineNoCov">          0 :     } else if (*sqre &lt; 0 || *sqre &gt; 1) {</span></a>
+<a name="22246"><span class="lineNum">   22246 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="22247"><span class="lineNum">   22247 </span>            :     }</a>
+<a name="22248"><span class="lineNum">   22248 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="22249"><span class="lineNum">   22249 </span>            :         return;</a>
+<a name="22250"><span class="lineNum">   22250 </span>            :     }</a>
+<a name="22251"><span class="lineNum">   22251 </span>            : </a>
+<a name="22252"><span class="lineNum">   22252 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="22253"><span class="lineNum">   22253 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="22254"><span class="lineNum">   22254 </span>            : </a>
+<a name="22255"><span class="lineNum">   22255 </span>            : </a>
+<a name="22256"><span class="lineNum">   22256 </span><span class="lineNoCov">          0 :     ldu2 = n;</span></a>
+<a name="22257"><span class="lineNum">   22257 </span><span class="lineNoCov">          0 :     ldvt2 = m;</span></a>
+<a name="22258"><span class="lineNum">   22258 </span>            : </a>
+<a name="22259"><span class="lineNum">   22259 </span>            :     iz = 1;</a>
+<a name="22260"><span class="lineNum">   22260 </span><span class="lineNoCov">          0 :     isigma = iz + m;</span></a>
+<a name="22261"><span class="lineNum">   22261 </span><span class="lineNoCov">          0 :     iu2 = isigma + n;</span></a>
+<a name="22262"><span class="lineNum">   22262 </span><span class="lineNoCov">          0 :     ivt2 = iu2 + ldu2 * n;</span></a>
+<a name="22263"><span class="lineNum">   22263 </span><span class="lineNoCov">          0 :     iq = ivt2 + ldvt2 * m;</span></a>
+<a name="22264"><span class="lineNum">   22264 </span>            : </a>
+<a name="22265"><span class="lineNum">   22265 </span>            :     idx = 1;</a>
+<a name="22266"><span class="lineNum">   22266 </span><span class="lineNoCov">          0 :     idxc = idx + n;</span></a>
+<a name="22267"><span class="lineNum">   22267 </span><span class="lineNoCov">          0 :     coltyp = idxc + n;</span></a>
+<a name="22268"><span class="lineNum">   22268 </span><span class="lineNoCov">          0 :     idxp = coltyp + n;</span></a>
+<a name="22269"><span class="lineNum">   22269 </span>            : </a>
+<a name="22270"><span class="lineNum">   22270 </span><span class="lineNoCov">          0 :     d__1 = std::abs(*alpha);</span></a>
+<a name="22271"><span class="lineNum">   22271 </span><span class="lineNoCov">          0 :     d__2 = std::abs(*beta);</span></a>
+<a name="22272"><span class="lineNum">   22272 </span><span class="lineNoCov">          0 :     orgnrm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="22273"><span class="lineNum">   22273 </span><span class="lineNoCov">          0 :     d__[*nl + 1] = 0.;</span></a>
+<a name="22274"><span class="lineNum">   22274 </span>            :     i__1 = n;</a>
+<a name="22275"><span class="lineNum">   22275 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22276"><span class="lineNum">   22276 </span><span class="lineNoCov">          0 :         if (std::abs(d__[i__]) &gt; orgnrm) {</span></a>
+<a name="22277"><span class="lineNum">   22277 </span><span class="lineNoCov">          0 :             orgnrm = std::abs(d__[i__]);</span></a>
+<a name="22278"><span class="lineNum">   22278 </span>            :         }</a>
+<a name="22279"><span class="lineNum">   22279 </span>            :     }</a>
+<a name="22280"><span class="lineNum">   22280 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;orgnrm, &amp;one, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="22281"><span class="lineNum">   22281 </span><span class="lineNoCov">          0 :     *alpha /= orgnrm;</span></a>
+<a name="22282"><span class="lineNum">   22282 </span><span class="lineNoCov">          0 :     *beta /= orgnrm;</span></a>
+<a name="22283"><span class="lineNum">   22283 </span>            : </a>
+<a name="22284"><span class="lineNum">   22284 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasd2,SLASD2)(nl, nr, sqre, &amp;k, &amp;d__[1], &amp;work[iz], alpha, beta, &amp;u[u_offset], </span></a>
+<a name="22285"><span class="lineNum">   22285 </span><span class="lineNoCov">          0 :             ldu, &amp;vt[vt_offset], ldvt, &amp;work[isigma], &amp;work[iu2], &amp;ldu2, &amp;</span></a>
+<a name="22286"><span class="lineNum">   22286 </span><span class="lineNoCov">          0 :             work[ivt2], &amp;ldvt2, &amp;iwork[idxp], &amp;iwork[idx], &amp;iwork[idxc], &amp;</span></a>
+<a name="22287"><span class="lineNum">   22287 </span><span class="lineNoCov">          0 :             idxq[1], &amp;iwork[coltyp], info);</span></a>
+<a name="22288"><span class="lineNum">   22288 </span>            : </a>
+<a name="22289"><span class="lineNum">   22289 </span><span class="lineNoCov">          0 :     ldq = k;</span></a>
+<a name="22290"><span class="lineNum">   22290 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasd3,SLASD3)(nl, nr, sqre, &amp;k, &amp;d__[1], &amp;work[iq], &amp;ldq, &amp;work[isigma], &amp;u[</span></a>
+<a name="22291"><span class="lineNum">   22291 </span>            :             u_offset], ldu, &amp;work[iu2], &amp;ldu2, &amp;vt[vt_offset], ldvt, &amp;work[</a>
+<a name="22292"><span class="lineNum">   22292 </span>            :             ivt2], &amp;ldvt2, &amp;iwork[idxc], &amp;iwork[coltyp], &amp;work[iz], info);</a>
+<a name="22293"><span class="lineNum">   22293 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="22294"><span class="lineNum">   22294 </span>            :         return;</a>
+<a name="22295"><span class="lineNum">   22295 </span>            :     }</a>
+<a name="22296"><span class="lineNum">   22296 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;one, &amp;orgnrm, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="22297"><span class="lineNum">   22297 </span>            : </a>
+<a name="22298"><span class="lineNum">   22298 </span><span class="lineNoCov">          0 :     n1 = k;</span></a>
+<a name="22299"><span class="lineNum">   22299 </span><span class="lineNoCov">          0 :     n2 = n - k;</span></a>
+<a name="22300"><span class="lineNum">   22300 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slamrg,SLAMRG)(&amp;n1, &amp;n2, &amp;d__[1], &amp;c__1, &amp;c_n1, &amp;idxq[1]);</span></a>
+<a name="22301"><span class="lineNum">   22301 </span>            : </a>
+<a name="22302"><span class="lineNum">   22302 </span>            :     return;</a>
+<a name="22303"><span class="lineNum">   22303 </span>            : </a>
+<a name="22304"><span class="lineNum">   22304 </span>            : }</a>
+<a name="22305"><span class="lineNum">   22305 </span>            : }</a>
+<a name="22306"><span class="lineNum">   22306 </span>            : }</a>
+<a name="22307"><span class="lineNum">   22307 </span>            : #include &lt;cmath&gt;</a>
+<a name="22308"><span class="lineNum">   22308 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22309"><span class="lineNum">   22309 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="22310"><span class="lineNum">   22310 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="22311"><span class="lineNum">   22311 </span>            : </a>
+<a name="22312"><span class="lineNum">   22312 </span>            : #include &quot;real.h&quot;</a>
+<a name="22313"><span class="lineNum">   22313 </span>            : </a>
+<a name="22314"><span class="lineNum">   22314 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22315"><span class="lineNum">   22315 </span>            : namespace PLMD{</a>
+<a name="22316"><span class="lineNum">   22316 </span>            : namespace lapack{</a>
+<a name="22317"><span class="lineNum">   22317 </span>            : using namespace blas;</a>
+<a name="22318"><span class="lineNum">   22318 </span>            : void </a>
+<a name="22319"><span class="lineNum">   22319 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd2,SLASD2)(int *nl, </span></a>
+<a name="22320"><span class="lineNum">   22320 </span>            :                         int *nr, </a>
+<a name="22321"><span class="lineNum">   22321 </span>            :                         int *sqre, </a>
+<a name="22322"><span class="lineNum">   22322 </span>            :                         int *k, </a>
+<a name="22323"><span class="lineNum">   22323 </span>            :                         float *d__, </a>
+<a name="22324"><span class="lineNum">   22324 </span>            :                         float *z__, </a>
+<a name="22325"><span class="lineNum">   22325 </span>            :                         float *alpha, </a>
+<a name="22326"><span class="lineNum">   22326 </span>            :                         float *beta, </a>
+<a name="22327"><span class="lineNum">   22327 </span>            :                         float *u, </a>
+<a name="22328"><span class="lineNum">   22328 </span>            :                         int *ldu, </a>
+<a name="22329"><span class="lineNum">   22329 </span>            :                         float *vt, </a>
+<a name="22330"><span class="lineNum">   22330 </span>            :                         int *ldvt, </a>
+<a name="22331"><span class="lineNum">   22331 </span>            :                         float *dsigma, </a>
+<a name="22332"><span class="lineNum">   22332 </span>            :                         float *u2, </a>
+<a name="22333"><span class="lineNum">   22333 </span>            :                         int *ldu2, </a>
+<a name="22334"><span class="lineNum">   22334 </span>            :                         float *vt2, </a>
+<a name="22335"><span class="lineNum">   22335 </span>            :                         int *ldvt2, </a>
+<a name="22336"><span class="lineNum">   22336 </span>            :                         int *idxp, </a>
+<a name="22337"><span class="lineNum">   22337 </span>            :                         int *idx, </a>
+<a name="22338"><span class="lineNum">   22338 </span>            :                         int *idxc, </a>
+<a name="22339"><span class="lineNum">   22339 </span>            :                         int *idxq, </a>
+<a name="22340"><span class="lineNum">   22340 </span>            :                         int *coltyp, </a>
+<a name="22341"><span class="lineNum">   22341 </span>            :                         int *info)</a>
+<a name="22342"><span class="lineNum">   22342 </span>            : {</a>
+<a name="22343"><span class="lineNum">   22343 </span>            :     int u_dim1, u_offset, u2_dim1, u2_offset, vt_dim1, vt_offset;</a>
+<a name="22344"><span class="lineNum">   22344 </span>            :     int vt2_dim1, vt2_offset, i__1;</a>
+<a name="22345"><span class="lineNum">   22345 </span>            :     float d__1, d__2;</a>
+<a name="22346"><span class="lineNum">   22346 </span>            : </a>
+<a name="22347"><span class="lineNum">   22347 </span>            :     float c__;</a>
+<a name="22348"><span class="lineNum">   22348 </span>            :     int i__, j, m, n;</a>
+<a name="22349"><span class="lineNum">   22349 </span>            :     float s;</a>
+<a name="22350"><span class="lineNum">   22350 </span>            :     int k2;</a>
+<a name="22351"><span class="lineNum">   22351 </span>            :     float z1;</a>
+<a name="22352"><span class="lineNum">   22352 </span>            :     int ct, jp;</a>
+<a name="22353"><span class="lineNum">   22353 </span>            :     float eps, tau, tol;</a>
+<a name="22354"><span class="lineNum">   22354 </span>            :     int psm[4], nlp1, nlp2, idxi, idxj;</a>
+<a name="22355"><span class="lineNum">   22355 </span>            :     int ctot[4], idxjp;</a>
+<a name="22356"><span class="lineNum">   22356 </span>            :     int jprev = 0;</a>
+<a name="22357"><span class="lineNum">   22357 </span>            :     float hlftol;</a>
+<a name="22358"><span class="lineNum">   22358 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="22359"><span class="lineNum">   22359 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="22360"><span class="lineNum">   22360 </span>            : </a>
+<a name="22361"><span class="lineNum">   22361 </span>            : </a>
+<a name="22362"><span class="lineNum">   22362 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="22363"><span class="lineNum">   22363 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="22364"><span class="lineNum">   22364 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="22365"><span class="lineNum">   22365 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="22366"><span class="lineNum">   22366 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="22367"><span class="lineNum">   22367 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="22368"><span class="lineNum">   22368 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="22369"><span class="lineNum">   22369 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="22370"><span class="lineNum">   22370 </span><span class="lineNoCov">          0 :     --dsigma;</span></a>
+<a name="22371"><span class="lineNum">   22371 </span><span class="lineNoCov">          0 :     u2_dim1 = *ldu2;</span></a>
+<a name="22372"><span class="lineNum">   22372 </span><span class="lineNoCov">          0 :     u2_offset = 1 + u2_dim1;</span></a>
+<a name="22373"><span class="lineNum">   22373 </span><span class="lineNoCov">          0 :     u2 -= u2_offset;</span></a>
+<a name="22374"><span class="lineNum">   22374 </span><span class="lineNoCov">          0 :     vt2_dim1 = *ldvt2;</span></a>
+<a name="22375"><span class="lineNum">   22375 </span><span class="lineNoCov">          0 :     vt2_offset = 1 + vt2_dim1;</span></a>
+<a name="22376"><span class="lineNum">   22376 </span><span class="lineNoCov">          0 :     vt2 -= vt2_offset;</span></a>
+<a name="22377"><span class="lineNum">   22377 </span><span class="lineNoCov">          0 :     --idxp;</span></a>
+<a name="22378"><span class="lineNum">   22378 </span><span class="lineNoCov">          0 :     --idx;</span></a>
+<a name="22379"><span class="lineNum">   22379 </span><span class="lineNoCov">          0 :     --idxc;</span></a>
+<a name="22380"><span class="lineNum">   22380 </span><span class="lineNoCov">          0 :     --idxq;</span></a>
+<a name="22381"><span class="lineNum">   22381 </span><span class="lineNoCov">          0 :     --coltyp;</span></a>
+<a name="22382"><span class="lineNum">   22382 </span>            : </a>
+<a name="22383"><span class="lineNum">   22383 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="22384"><span class="lineNum">   22384 </span>            : </a>
+<a name="22385"><span class="lineNum">   22385 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="22386"><span class="lineNum">   22386 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="22387"><span class="lineNum">   22387 </span>            : </a>
+<a name="22388"><span class="lineNum">   22388 </span><span class="lineNoCov">          0 :     nlp1 = *nl + 1;</span></a>
+<a name="22389"><span class="lineNum">   22389 </span><span class="lineNoCov">          0 :     nlp2 = *nl + 2;</span></a>
+<a name="22390"><span class="lineNum">   22390 </span>            : </a>
+<a name="22391"><span class="lineNum">   22391 </span><span class="lineNoCov">          0 :     z1 = *alpha * vt[nlp1 + nlp1 * vt_dim1];</span></a>
+<a name="22392"><span class="lineNum">   22392 </span><span class="lineNoCov">          0 :     z__[1] = z1;</span></a>
+<a name="22393"><span class="lineNum">   22393 </span><span class="lineNoCov">          0 :     for (i__ = *nl; i__ &gt;= 1; --i__) {</span></a>
+<a name="22394"><span class="lineNum">   22394 </span><span class="lineNoCov">          0 :         z__[i__ + 1] = *alpha * vt[i__ + nlp1 * vt_dim1];</span></a>
+<a name="22395"><span class="lineNum">   22395 </span><span class="lineNoCov">          0 :         d__[i__ + 1] = d__[i__];</span></a>
+<a name="22396"><span class="lineNum">   22396 </span><span class="lineNoCov">          0 :         idxq[i__ + 1] = idxq[i__] + 1;</span></a>
+<a name="22397"><span class="lineNum">   22397 </span>            :     }</a>
+<a name="22398"><span class="lineNum">   22398 </span>            : </a>
+<a name="22399"><span class="lineNum">   22399 </span>            :     i__1 = m;</a>
+<a name="22400"><span class="lineNum">   22400 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22401"><span class="lineNum">   22401 </span><span class="lineNoCov">          0 :         z__[i__] = *beta * vt[i__ + nlp2 * vt_dim1];</span></a>
+<a name="22402"><span class="lineNum">   22402 </span>            :     }</a>
+<a name="22403"><span class="lineNum">   22403 </span>            : </a>
+<a name="22404"><span class="lineNum">   22404 </span>            :     i__1 = nlp1;</a>
+<a name="22405"><span class="lineNum">   22405 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22406"><span class="lineNum">   22406 </span><span class="lineNoCov">          0 :         coltyp[i__] = 1;</span></a>
+<a name="22407"><span class="lineNum">   22407 </span>            :     }</a>
+<a name="22408"><span class="lineNum">   22408 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="22409"><span class="lineNum">   22409 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22410"><span class="lineNum">   22410 </span><span class="lineNoCov">          0 :         coltyp[i__] = 2;</span></a>
+<a name="22411"><span class="lineNum">   22411 </span>            :     }</a>
+<a name="22412"><span class="lineNum">   22412 </span>            : </a>
+<a name="22413"><span class="lineNum">   22413 </span>            :     i__1 = n;</a>
+<a name="22414"><span class="lineNum">   22414 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22415"><span class="lineNum">   22415 </span><span class="lineNoCov">          0 :         idxq[i__] += nlp1;</span></a>
+<a name="22416"><span class="lineNum">   22416 </span>            :     }</a>
+<a name="22417"><span class="lineNum">   22417 </span>            : </a>
+<a name="22418"><span class="lineNum">   22418 </span>            :     i__1 = n;</a>
+<a name="22419"><span class="lineNum">   22419 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22420"><span class="lineNum">   22420 </span><span class="lineNoCov">          0 :         dsigma[i__] = d__[idxq[i__]];</span></a>
+<a name="22421"><span class="lineNum">   22421 </span><span class="lineNoCov">          0 :         u2[i__ + u2_dim1] = z__[idxq[i__]];</span></a>
+<a name="22422"><span class="lineNum">   22422 </span><span class="lineNoCov">          0 :         idxc[i__] = coltyp[idxq[i__]];</span></a>
+<a name="22423"><span class="lineNum">   22423 </span>            :     }</a>
+<a name="22424"><span class="lineNum">   22424 </span>            : </a>
+<a name="22425"><span class="lineNum">   22425 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slamrg,SLAMRG)(nl, nr, &amp;dsigma[2], &amp;c__1, &amp;c__1, &amp;idx[2]);</span></a>
+<a name="22426"><span class="lineNum">   22426 </span>            : </a>
+<a name="22427"><span class="lineNum">   22427 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="22428"><span class="lineNum">   22428 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22429"><span class="lineNum">   22429 </span><span class="lineNoCov">          0 :         idxi = idx[i__] + 1;</span></a>
+<a name="22430"><span class="lineNum">   22430 </span><span class="lineNoCov">          0 :         d__[i__] = dsigma[idxi];</span></a>
+<a name="22431"><span class="lineNum">   22431 </span><span class="lineNoCov">          0 :         z__[i__] = u2[idxi + u2_dim1];</span></a>
+<a name="22432"><span class="lineNum">   22432 </span><span class="lineNoCov">          0 :         coltyp[i__] = idxc[idxi];</span></a>
+<a name="22433"><span class="lineNum">   22433 </span>            :     }</a>
+<a name="22434"><span class="lineNum">   22434 </span>            : </a>
+<a name="22435"><span class="lineNum">   22435 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="22436"><span class="lineNum">   22436 </span><span class="lineNoCov">          0 :     d__1 = std::abs(*alpha), d__2 = std::abs(*beta);</span></a>
+<a name="22437"><span class="lineNum">   22437 </span><span class="lineNoCov">          0 :     tol = (d__1 &gt; d__2) ? d__1 : d__2;</span></a>
+<a name="22438"><span class="lineNum">   22438 </span><span class="lineNoCov">          0 :     d__2 = std::abs(d__[n]);</span></a>
+<a name="22439"><span class="lineNum">   22439 </span><span class="lineNoCov">          0 :     tol = eps * 8. * ((d__2 &gt; tol) ? d__2 : tol);</span></a>
+<a name="22440"><span class="lineNum">   22440 </span>            : </a>
+<a name="22441"><span class="lineNum">   22441 </span><span class="lineNoCov">          0 :     *k = 1;</span></a>
+<a name="22442"><span class="lineNum">   22442 </span><span class="lineNoCov">          0 :     k2 = n + 1;</span></a>
+<a name="22443"><span class="lineNum">   22443 </span>            :     i__1 = n;</a>
+<a name="22444"><span class="lineNum">   22444 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="22445"><span class="lineNum">   22445 </span><span class="lineNoCov">          0 :         if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="22446"><span class="lineNum">   22446 </span>            : </a>
+<a name="22447"><span class="lineNum">   22447 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="22448"><span class="lineNum">   22448 </span><span class="lineNoCov">          0 :             idxp[k2] = j;</span></a>
+<a name="22449"><span class="lineNum">   22449 </span><span class="lineNoCov">          0 :             coltyp[j] = 4;</span></a>
+<a name="22450"><span class="lineNum">   22450 </span><span class="lineNoCov">          0 :             if (j == n) {</span></a>
+<a name="22451"><span class="lineNum">   22451 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="22452"><span class="lineNum">   22452 </span>            :             }</a>
+<a name="22453"><span class="lineNum">   22453 </span>            :         } else {</a>
+<a name="22454"><span class="lineNum">   22454 </span>            :             jprev = j;</a>
+<a name="22455"><span class="lineNum">   22455 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="22456"><span class="lineNum">   22456 </span>            :         }</a>
+<a name="22457"><span class="lineNum">   22457 </span>            :     }</a>
+<a name="22458"><span class="lineNum">   22458 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="22459"><span class="lineNum">   22459 </span>            :     j = jprev;</a>
+<a name="22460"><span class="lineNum">   22460 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="22461"><span class="lineNum">   22461 </span><span class="lineNoCov">          0 :     ++j;</span></a>
+<a name="22462"><span class="lineNum">   22462 </span><span class="lineNoCov">          0 :     if (j &gt; n) {</span></a>
+<a name="22463"><span class="lineNum">   22463 </span><span class="lineNoCov">          0 :         goto L110;</span></a>
+<a name="22464"><span class="lineNum">   22464 </span>            :     }</a>
+<a name="22465"><span class="lineNum">   22465 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="22466"><span class="lineNum">   22466 </span>            : </a>
+<a name="22467"><span class="lineNum">   22467 </span><span class="lineNoCov">          0 :         --k2;</span></a>
+<a name="22468"><span class="lineNum">   22468 </span><span class="lineNoCov">          0 :         idxp[k2] = j;</span></a>
+<a name="22469"><span class="lineNum">   22469 </span><span class="lineNoCov">          0 :         coltyp[j] = 4;</span></a>
+<a name="22470"><span class="lineNum">   22470 </span>            :     } else {</a>
+<a name="22471"><span class="lineNum">   22471 </span>            : </a>
+<a name="22472"><span class="lineNum">   22472 </span><span class="lineNoCov">          0 :         if (std::abs(d__[j] - d__[jprev]) &lt;= tol) {</span></a>
+<a name="22473"><span class="lineNum">   22473 </span>            : </a>
+<a name="22474"><span class="lineNum">   22474 </span><span class="lineNoCov">          0 :             s = z__[jprev];</span></a>
+<a name="22475"><span class="lineNum">   22475 </span><span class="lineNoCov">          0 :             c__ = z__[j];</span></a>
+<a name="22476"><span class="lineNum">   22476 </span>            : </a>
+<a name="22477"><span class="lineNum">   22477 </span><span class="lineNoCov">          0 :             tau = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;c__, &amp;s);</span></a>
+<a name="22478"><span class="lineNum">   22478 </span><span class="lineNoCov">          0 :             c__ /= tau;</span></a>
+<a name="22479"><span class="lineNum">   22479 </span><span class="lineNoCov">          0 :             s = -s / tau;</span></a>
+<a name="22480"><span class="lineNum">   22480 </span><span class="lineNoCov">          0 :             z__[j] = tau;</span></a>
+<a name="22481"><span class="lineNum">   22481 </span><span class="lineNoCov">          0 :             z__[jprev] = 0.;</span></a>
+<a name="22482"><span class="lineNum">   22482 </span>            : </a>
+<a name="22483"><span class="lineNum">   22483 </span><span class="lineNoCov">          0 :             idxjp = idxq[idx[jprev] + 1];</span></a>
+<a name="22484"><span class="lineNum">   22484 </span><span class="lineNoCov">          0 :             idxj = idxq[idx[j] + 1];</span></a>
+<a name="22485"><span class="lineNum">   22485 </span><span class="lineNoCov">          0 :             if (idxjp &lt;= nlp1) {</span></a>
+<a name="22486"><span class="lineNum">   22486 </span><span class="lineNoCov">          0 :                 --idxjp;</span></a>
+<a name="22487"><span class="lineNum">   22487 </span>            :             }</a>
+<a name="22488"><span class="lineNum">   22488 </span><span class="lineNoCov">          0 :             if (idxj &lt;= nlp1) {</span></a>
+<a name="22489"><span class="lineNum">   22489 </span><span class="lineNoCov">          0 :                 --idxj;</span></a>
+<a name="22490"><span class="lineNum">   22490 </span>            :             }</a>
+<a name="22491"><span class="lineNum">   22491 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(&amp;n, &amp;u[idxjp * u_dim1 + 1], &amp;c__1, &amp;u[idxj * u_dim1 + 1], &amp;</span></a>
+<a name="22492"><span class="lineNum">   22492 </span>            :                     c__1, &amp;c__, &amp;s);</a>
+<a name="22493"><span class="lineNum">   22493 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(&amp;m, &amp;vt[idxjp + vt_dim1], ldvt, &amp;vt[idxj + vt_dim1], ldvt, &amp;</span></a>
+<a name="22494"><span class="lineNum">   22494 </span>            :                     c__, &amp;s);</a>
+<a name="22495"><span class="lineNum">   22495 </span><span class="lineNoCov">          0 :             if (coltyp[j] != coltyp[jprev]) {</span></a>
+<a name="22496"><span class="lineNum">   22496 </span><span class="lineNoCov">          0 :                 coltyp[j] = 3;</span></a>
+<a name="22497"><span class="lineNum">   22497 </span>            :             }</a>
+<a name="22498"><span class="lineNum">   22498 </span><span class="lineNoCov">          0 :             coltyp[jprev] = 4;</span></a>
+<a name="22499"><span class="lineNum">   22499 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="22500"><span class="lineNum">   22500 </span><span class="lineNoCov">          0 :             idxp[k2] = jprev;</span></a>
+<a name="22501"><span class="lineNum">   22501 </span>            :             jprev = j;</a>
+<a name="22502"><span class="lineNum">   22502 </span>            :         } else {</a>
+<a name="22503"><span class="lineNum">   22503 </span><span class="lineNoCov">          0 :             ++(*k);</span></a>
+<a name="22504"><span class="lineNum">   22504 </span><span class="lineNoCov">          0 :             u2[*k + u2_dim1] = z__[jprev];</span></a>
+<a name="22505"><span class="lineNum">   22505 </span><span class="lineNoCov">          0 :             dsigma[*k] = d__[jprev];</span></a>
+<a name="22506"><span class="lineNum">   22506 </span><span class="lineNoCov">          0 :             idxp[*k] = jprev;</span></a>
+<a name="22507"><span class="lineNum">   22507 </span>            :             jprev = j;</a>
+<a name="22508"><span class="lineNum">   22508 </span>            :         }</a>
+<a name="22509"><span class="lineNum">   22509 </span>            :     }</a>
+<a name="22510"><span class="lineNum">   22510 </span><span class="lineNoCov">          0 :     goto L100;</span></a>
+<a name="22511"><span class="lineNum">   22511 </span>            : L110:</a>
+<a name="22512"><span class="lineNum">   22512 </span>            : </a>
+<a name="22513"><span class="lineNum">   22513 </span><span class="lineNoCov">          0 :     ++(*k);</span></a>
+<a name="22514"><span class="lineNum">   22514 </span><span class="lineNoCov">          0 :     u2[*k + u2_dim1] = z__[jprev];</span></a>
+<a name="22515"><span class="lineNum">   22515 </span><span class="lineNoCov">          0 :     dsigma[*k] = d__[jprev];</span></a>
+<a name="22516"><span class="lineNum">   22516 </span><span class="lineNoCov">          0 :     idxp[*k] = jprev;</span></a>
+<a name="22517"><span class="lineNum">   22517 </span>            : </a>
+<a name="22518"><span class="lineNum">   22518 </span>            : L120:</a>
+<a name="22519"><span class="lineNum">   22519 </span>            : </a>
+<a name="22520"><span class="lineNum">   22520 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= 4; ++j) {</span></a>
+<a name="22521"><span class="lineNum">   22521 </span><span class="lineNoCov">          0 :         ctot[j - 1] = 0;</span></a>
+<a name="22522"><span class="lineNum">   22522 </span>            :     }</a>
+<a name="22523"><span class="lineNum">   22523 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="22524"><span class="lineNum">   22524 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="22525"><span class="lineNum">   22525 </span><span class="lineNoCov">          0 :         ct = coltyp[j];</span></a>
+<a name="22526"><span class="lineNum">   22526 </span><span class="lineNoCov">          0 :         ++ctot[ct - 1];</span></a>
+<a name="22527"><span class="lineNum">   22527 </span>            :     }</a>
+<a name="22528"><span class="lineNum">   22528 </span>            : </a>
+<a name="22529"><span class="lineNum">   22529 </span><span class="lineNoCov">          0 :     psm[0] = 2;</span></a>
+<a name="22530"><span class="lineNum">   22530 </span><span class="lineNoCov">          0 :     psm[1] = ctot[0] + 2;</span></a>
+<a name="22531"><span class="lineNum">   22531 </span><span class="lineNoCov">          0 :     psm[2] = psm[1] + ctot[1];</span></a>
+<a name="22532"><span class="lineNum">   22532 </span><span class="lineNoCov">          0 :     psm[3] = psm[2] + ctot[2];</span></a>
+<a name="22533"><span class="lineNum">   22533 </span>            : </a>
+<a name="22534"><span class="lineNum">   22534 </span>            :     i__1 = n;</a>
+<a name="22535"><span class="lineNum">   22535 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="22536"><span class="lineNum">   22536 </span><span class="lineNoCov">          0 :         jp = idxp[j];</span></a>
+<a name="22537"><span class="lineNum">   22537 </span><span class="lineNoCov">          0 :         ct = coltyp[jp];</span></a>
+<a name="22538"><span class="lineNum">   22538 </span><span class="lineNoCov">          0 :         idxc[psm[ct - 1]] = j;</span></a>
+<a name="22539"><span class="lineNum">   22539 </span><span class="lineNoCov">          0 :         ++psm[ct - 1];</span></a>
+<a name="22540"><span class="lineNum">   22540 </span>            :     }</a>
+<a name="22541"><span class="lineNum">   22541 </span>            : </a>
+<a name="22542"><span class="lineNum">   22542 </span>            :     i__1 = n;</a>
+<a name="22543"><span class="lineNum">   22543 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="22544"><span class="lineNum">   22544 </span><span class="lineNoCov">          0 :         jp = idxp[j];</span></a>
+<a name="22545"><span class="lineNum">   22545 </span><span class="lineNoCov">          0 :         dsigma[j] = d__[jp];</span></a>
+<a name="22546"><span class="lineNum">   22546 </span><span class="lineNoCov">          0 :         idxj = idxq[idx[idxp[idxc[j]]] + 1];</span></a>
+<a name="22547"><span class="lineNum">   22547 </span><span class="lineNoCov">          0 :         if (idxj &lt;= nlp1) {</span></a>
+<a name="22548"><span class="lineNum">   22548 </span><span class="lineNoCov">          0 :             --idxj;</span></a>
+<a name="22549"><span class="lineNum">   22549 </span>            :         }</a>
+<a name="22550"><span class="lineNum">   22550 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;n, &amp;u[idxj * u_dim1 + 1], &amp;c__1, &amp;u2[j * u2_dim1 + 1], &amp;c__1);</span></a>
+<a name="22551"><span class="lineNum">   22551 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;m, &amp;vt[idxj + vt_dim1], ldvt, &amp;vt2[j + vt2_dim1], ldvt2);</span></a>
+<a name="22552"><span class="lineNum">   22552 </span>            :     }</a>
+<a name="22553"><span class="lineNum">   22553 </span>            : </a>
+<a name="22554"><span class="lineNum">   22554 </span><span class="lineNoCov">          0 :     dsigma[1] = 0.;</span></a>
+<a name="22555"><span class="lineNum">   22555 </span><span class="lineNoCov">          0 :     hlftol = tol / 2.;</span></a>
+<a name="22556"><span class="lineNum">   22556 </span><span class="lineNoCov">          0 :     if (std::abs(dsigma[2]) &lt;= hlftol) {</span></a>
+<a name="22557"><span class="lineNum">   22557 </span><span class="lineNoCov">          0 :         dsigma[2] = hlftol;</span></a>
+<a name="22558"><span class="lineNum">   22558 </span>            :     }</a>
+<a name="22559"><span class="lineNum">   22559 </span><span class="lineNoCov">          0 :     if (m &gt; n) {</span></a>
+<a name="22560"><span class="lineNum">   22560 </span><span class="lineNoCov">          0 :         z__[1] = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;z1, &amp;z__[m]);</span></a>
+<a name="22561"><span class="lineNum">   22561 </span><span class="lineNoCov">          0 :         if (z__[1] &lt;= tol) {</span></a>
+<a name="22562"><span class="lineNum">   22562 </span><span class="lineNoCov">          0 :             c__ = 1.;</span></a>
+<a name="22563"><span class="lineNum">   22563 </span><span class="lineNoCov">          0 :             s = 0.;</span></a>
+<a name="22564"><span class="lineNum">   22564 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="22565"><span class="lineNum">   22565 </span>            :         } else {</a>
+<a name="22566"><span class="lineNum">   22566 </span><span class="lineNoCov">          0 :             c__ = z1 / z__[1];</span></a>
+<a name="22567"><span class="lineNum">   22567 </span><span class="lineNoCov">          0 :             s = z__[m] / z__[1];</span></a>
+<a name="22568"><span class="lineNum">   22568 </span>            :         }</a>
+<a name="22569"><span class="lineNum">   22569 </span>            :     } else {</a>
+<a name="22570"><span class="lineNum">   22570 </span><span class="lineNoCov">          0 :         if (std::abs(z1) &lt;= tol) {</span></a>
+<a name="22571"><span class="lineNum">   22571 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="22572"><span class="lineNum">   22572 </span>            :         } else {</a>
+<a name="22573"><span class="lineNum">   22573 </span><span class="lineNoCov">          0 :             z__[1] = z1;</span></a>
+<a name="22574"><span class="lineNum">   22574 </span>            :         }</a>
+<a name="22575"><span class="lineNum">   22575 </span>            :     }</a>
+<a name="22576"><span class="lineNum">   22576 </span>            : </a>
+<a name="22577"><span class="lineNum">   22577 </span><span class="lineNoCov">          0 :     i__1 = *k - 1;</span></a>
+<a name="22578"><span class="lineNum">   22578 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;u2[u2_dim1 + 2], &amp;c__1, &amp;z__[2], &amp;c__1);</span></a>
+<a name="22579"><span class="lineNum">   22579 </span>            : </a>
+<a name="22580"><span class="lineNum">   22580 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;n, &amp;c__1, &amp;zero, &amp;zero, &amp;u2[u2_offset], ldu2);</span></a>
+<a name="22581"><span class="lineNum">   22581 </span><span class="lineNoCov">          0 :     u2[nlp1 + u2_dim1] = 1.;</span></a>
+<a name="22582"><span class="lineNum">   22582 </span><span class="lineNoCov">          0 :     if (m &gt; n) {</span></a>
+<a name="22583"><span class="lineNum">   22583 </span>            :         i__1 = nlp1;</a>
+<a name="22584"><span class="lineNum">   22584 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22585"><span class="lineNum">   22585 </span><span class="lineNoCov">          0 :             vt[m + i__ * vt_dim1] = -s * vt[nlp1 + i__ * vt_dim1];</span></a>
+<a name="22586"><span class="lineNum">   22586 </span><span class="lineNoCov">          0 :             vt2[i__ * vt2_dim1 + 1] = c__ * vt[nlp1 + i__ * vt_dim1];</span></a>
+<a name="22587"><span class="lineNum">   22587 </span>            :         }</a>
+<a name="22588"><span class="lineNum">   22588 </span><span class="lineNoCov">          0 :         i__1 = m;</span></a>
+<a name="22589"><span class="lineNum">   22589 </span><span class="lineNoCov">          0 :         for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22590"><span class="lineNum">   22590 </span><span class="lineNoCov">          0 :             vt2[i__ * vt2_dim1 + 1] = s * vt[m + i__ * vt_dim1];</span></a>
+<a name="22591"><span class="lineNum">   22591 </span><span class="lineNoCov">          0 :             vt[m + i__ * vt_dim1] = c__ * vt[m + i__ * vt_dim1];</span></a>
+<a name="22592"><span class="lineNum">   22592 </span>            :         }</a>
+<a name="22593"><span class="lineNum">   22593 </span>            :     } else {</a>
+<a name="22594"><span class="lineNum">   22594 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;m, &amp;vt[nlp1 + vt_dim1], ldvt, &amp;vt2[vt2_dim1 + 1], ldvt2);</span></a>
+<a name="22595"><span class="lineNum">   22595 </span>            :     }</a>
+<a name="22596"><span class="lineNum">   22596 </span><span class="lineNoCov">          0 :     if (m &gt; n) {</span></a>
+<a name="22597"><span class="lineNum">   22597 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;m, &amp;vt[m + vt_dim1], ldvt, &amp;vt2[m + vt2_dim1], ldvt2);</span></a>
+<a name="22598"><span class="lineNum">   22598 </span>            :     }</a>
+<a name="22599"><span class="lineNum">   22599 </span>            : </a>
+<a name="22600"><span class="lineNum">   22600 </span><span class="lineNoCov">          0 :     if (n &gt; *k) {</span></a>
+<a name="22601"><span class="lineNum">   22601 </span><span class="lineNoCov">          0 :         i__1 = n - *k;</span></a>
+<a name="22602"><span class="lineNum">   22602 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;dsigma[*k + 1], &amp;c__1, &amp;d__[*k + 1], &amp;c__1);</span></a>
+<a name="22603"><span class="lineNum">   22603 </span><span class="lineNoCov">          0 :         i__1 = n - *k;</span></a>
+<a name="22604"><span class="lineNum">   22604 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;A&quot;, &amp;n, &amp;i__1, &amp;u2[(*k + 1) * u2_dim1 + 1], ldu2, &amp;u[(*k + 1)</span></a>
+<a name="22605"><span class="lineNum">   22605 </span><span class="lineNoCov">          0 :                  * u_dim1 + 1], ldu);</span></a>
+<a name="22606"><span class="lineNum">   22606 </span><span class="lineNoCov">          0 :         i__1 = n - *k;</span></a>
+<a name="22607"><span class="lineNum">   22607 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;A&quot;, &amp;i__1, &amp;m, &amp;vt2[*k + 1 + vt2_dim1], ldvt2, &amp;vt[*k + 1 + </span></a>
+<a name="22608"><span class="lineNum">   22608 </span><span class="lineNoCov">          0 :                 vt_dim1], ldvt);</span></a>
+<a name="22609"><span class="lineNum">   22609 </span>            :     }</a>
+<a name="22610"><span class="lineNum">   22610 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= 4; ++j) {</span></a>
+<a name="22611"><span class="lineNum">   22611 </span><span class="lineNoCov">          0 :         coltyp[j] = ctot[j - 1];</span></a>
+<a name="22612"><span class="lineNum">   22612 </span>            :     }</a>
+<a name="22613"><span class="lineNum">   22613 </span>            : </a>
+<a name="22614"><span class="lineNum">   22614 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="22615"><span class="lineNum">   22615 </span>            : </a>
+<a name="22616"><span class="lineNum">   22616 </span>            : }</a>
+<a name="22617"><span class="lineNum">   22617 </span>            : </a>
+<a name="22618"><span class="lineNum">   22618 </span>            : </a>
+<a name="22619"><span class="lineNum">   22619 </span>            : }</a>
+<a name="22620"><span class="lineNum">   22620 </span>            : }</a>
+<a name="22621"><span class="lineNum">   22621 </span>            : #include &lt;cmath&gt;</a>
+<a name="22622"><span class="lineNum">   22622 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22623"><span class="lineNum">   22623 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="22624"><span class="lineNum">   22624 </span>            : </a>
+<a name="22625"><span class="lineNum">   22625 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22626"><span class="lineNum">   22626 </span>            : namespace PLMD{</a>
+<a name="22627"><span class="lineNum">   22627 </span>            : namespace lapack{</a>
+<a name="22628"><span class="lineNum">   22628 </span>            : using namespace blas;</a>
+<a name="22629"><span class="lineNum">   22629 </span>            : void </a>
+<a name="22630"><span class="lineNum">   22630 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd3,SLASD3)(int *nl, </span></a>
+<a name="22631"><span class="lineNum">   22631 </span>            :         int *nr,</a>
+<a name="22632"><span class="lineNum">   22632 </span>            :         int *sqre, </a>
+<a name="22633"><span class="lineNum">   22633 </span>            :         int *k, </a>
+<a name="22634"><span class="lineNum">   22634 </span>            :         float *d__, </a>
+<a name="22635"><span class="lineNum">   22635 </span>            :         float *q, </a>
+<a name="22636"><span class="lineNum">   22636 </span>            :         int *ldq, </a>
+<a name="22637"><span class="lineNum">   22637 </span>            :         float *dsigma, </a>
+<a name="22638"><span class="lineNum">   22638 </span>            :         float *u, </a>
+<a name="22639"><span class="lineNum">   22639 </span>            :         int *ldu, </a>
+<a name="22640"><span class="lineNum">   22640 </span>            :         float *u2, </a>
+<a name="22641"><span class="lineNum">   22641 </span>            :         int *ldu2, </a>
+<a name="22642"><span class="lineNum">   22642 </span>            :         float *vt, </a>
+<a name="22643"><span class="lineNum">   22643 </span>            :         int *ldvt, </a>
+<a name="22644"><span class="lineNum">   22644 </span>            :         float *vt2, </a>
+<a name="22645"><span class="lineNum">   22645 </span>            :         int *ldvt2, </a>
+<a name="22646"><span class="lineNum">   22646 </span>            :         int *idxc, </a>
+<a name="22647"><span class="lineNum">   22647 </span>            :         int *ctot, </a>
+<a name="22648"><span class="lineNum">   22648 </span>            :         float *z__, </a>
+<a name="22649"><span class="lineNum">   22649 </span>            :         int *info)</a>
+<a name="22650"><span class="lineNum">   22650 </span>            : {</a>
+<a name="22651"><span class="lineNum">   22651 </span>            :     int q_dim1, q_offset, u_dim1, u_offset, u2_dim1, u2_offset, vt_dim1, </a>
+<a name="22652"><span class="lineNum">   22652 </span>            :             vt_offset, vt2_dim1, vt2_offset, i__1, i__2;</a>
+<a name="22653"><span class="lineNum">   22653 </span>            :     float d__2;</a>
+<a name="22654"><span class="lineNum">   22654 </span>            : </a>
+<a name="22655"><span class="lineNum">   22655 </span>            :     int i__, j, m, n, jc;</a>
+<a name="22656"><span class="lineNum">   22656 </span>            :     float rho;</a>
+<a name="22657"><span class="lineNum">   22657 </span>            :     int nlp1, nlp2, nrp1;</a>
+<a name="22658"><span class="lineNum">   22658 </span>            :     float temp;</a>
+<a name="22659"><span class="lineNum">   22659 </span>            :     int ctemp;</a>
+<a name="22660"><span class="lineNum">   22660 </span>            :     int ktemp;</a>
+<a name="22661"><span class="lineNum">   22661 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="22662"><span class="lineNum">   22662 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="22663"><span class="lineNum">   22663 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="22664"><span class="lineNum">   22664 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="22665"><span class="lineNum">   22665 </span>            : </a>
+<a name="22666"><span class="lineNum">   22666 </span>            :     --d__;</a>
+<a name="22667"><span class="lineNum">   22667 </span><span class="lineNoCov">          0 :     q_dim1 = *ldq;</span></a>
+<a name="22668"><span class="lineNum">   22668 </span><span class="lineNoCov">          0 :     q_offset = 1 + q_dim1;</span></a>
+<a name="22669"><span class="lineNum">   22669 </span><span class="lineNoCov">          0 :     q -= q_offset;</span></a>
+<a name="22670"><span class="lineNum">   22670 </span><span class="lineNoCov">          0 :     --dsigma;</span></a>
+<a name="22671"><span class="lineNum">   22671 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="22672"><span class="lineNum">   22672 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="22673"><span class="lineNum">   22673 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="22674"><span class="lineNum">   22674 </span><span class="lineNoCov">          0 :     u2_dim1 = *ldu2;</span></a>
+<a name="22675"><span class="lineNum">   22675 </span><span class="lineNoCov">          0 :     u2_offset = 1 + u2_dim1;</span></a>
+<a name="22676"><span class="lineNum">   22676 </span><span class="lineNoCov">          0 :     u2 -= u2_offset;</span></a>
+<a name="22677"><span class="lineNum">   22677 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="22678"><span class="lineNum">   22678 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="22679"><span class="lineNum">   22679 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="22680"><span class="lineNum">   22680 </span><span class="lineNoCov">          0 :     vt2_dim1 = *ldvt2;</span></a>
+<a name="22681"><span class="lineNum">   22681 </span><span class="lineNoCov">          0 :     vt2_offset = 1 + vt2_dim1;</span></a>
+<a name="22682"><span class="lineNum">   22682 </span><span class="lineNoCov">          0 :     vt2 -= vt2_offset;</span></a>
+<a name="22683"><span class="lineNum">   22683 </span><span class="lineNoCov">          0 :     --idxc;</span></a>
+<a name="22684"><span class="lineNum">   22684 </span>            :     --ctot;</a>
+<a name="22685"><span class="lineNum">   22685 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="22686"><span class="lineNum">   22686 </span>            : </a>
+<a name="22687"><span class="lineNum">   22687 </span>            :     /* Function Body */</a>
+<a name="22688"><span class="lineNum">   22688 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="22689"><span class="lineNum">   22689 </span>            : </a>
+<a name="22690"><span class="lineNum">   22690 </span><span class="lineNoCov">          0 :     if (*nl &lt; 1) {</span></a>
+<a name="22691"><span class="lineNum">   22691 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="22692"><span class="lineNum">   22692 </span><span class="lineNoCov">          0 :     } else if (*nr &lt; 1) {</span></a>
+<a name="22693"><span class="lineNum">   22693 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="22694"><span class="lineNum">   22694 </span><span class="lineNoCov">          0 :     } else if (*sqre != 1 &amp;&amp; *sqre != 0) {</span></a>
+<a name="22695"><span class="lineNum">   22695 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="22696"><span class="lineNum">   22696 </span>            :     }</a>
+<a name="22697"><span class="lineNum">   22697 </span>            : </a>
+<a name="22698"><span class="lineNum">   22698 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="22699"><span class="lineNum">   22699 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="22700"><span class="lineNum">   22700 </span><span class="lineNoCov">          0 :     nlp1 = *nl + 1;</span></a>
+<a name="22701"><span class="lineNum">   22701 </span><span class="lineNoCov">          0 :     nlp2 = *nl + 2;</span></a>
+<a name="22702"><span class="lineNum">   22702 </span>            : </a>
+<a name="22703"><span class="lineNum">   22703 </span><span class="lineNoCov">          0 :     if (*k == 1) {</span></a>
+<a name="22704"><span class="lineNum">   22704 </span><span class="lineNoCov">          0 :         d__[1] = std::abs(z__[1]);</span></a>
+<a name="22705"><span class="lineNum">   22705 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;m, &amp;vt2[vt2_dim1 + 1], ldvt2, &amp;vt[vt_dim1 + 1], ldvt);</span></a>
+<a name="22706"><span class="lineNum">   22706 </span><span class="lineNoCov">          0 :         if (z__[1] &gt; 0.) {</span></a>
+<a name="22707"><span class="lineNum">   22707 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;n, &amp;u2[u2_dim1 + 1], &amp;c__1, &amp;u[u_dim1 + 1], &amp;c__1);</span></a>
+<a name="22708"><span class="lineNum">   22708 </span>            :         } else {</a>
+<a name="22709"><span class="lineNum">   22709 </span><span class="lineNoCov">          0 :             i__1 = n;</span></a>
+<a name="22710"><span class="lineNum">   22710 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22711"><span class="lineNum">   22711 </span><span class="lineNoCov">          0 :                 u[i__ + u_dim1] = -u2[i__ + u2_dim1];</span></a>
+<a name="22712"><span class="lineNum">   22712 </span>            :             }</a>
+<a name="22713"><span class="lineNum">   22713 </span>            :         }</a>
+<a name="22714"><span class="lineNum">   22714 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="22715"><span class="lineNum">   22715 </span>            :     }</a>
+<a name="22716"><span class="lineNum">   22716 </span>            : </a>
+<a name="22717"><span class="lineNum">   22717 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(k, &amp;z__[1], &amp;c__1, &amp;q[q_offset], &amp;c__1);</span></a>
+<a name="22718"><span class="lineNum">   22718 </span>            : </a>
+<a name="22719"><span class="lineNum">   22719 </span><span class="lineNoCov">          0 :     rho = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(k, &amp;z__[1], &amp;c__1);</span></a>
+<a name="22720"><span class="lineNum">   22720 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;rho, &amp;one, k, &amp;c__1, &amp;z__[1], k, info);</span></a>
+<a name="22721"><span class="lineNum">   22721 </span><span class="lineNoCov">          0 :     rho *= rho;</span></a>
+<a name="22722"><span class="lineNum">   22722 </span>            : </a>
+<a name="22723"><span class="lineNum">   22723 </span>            : </a>
+<a name="22724"><span class="lineNum">   22724 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="22725"><span class="lineNum">   22725 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="22726"><span class="lineNum">   22726 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasd4,SLASD4)(k, &amp;j, &amp;dsigma[1], &amp;z__[1], &amp;u[j * u_dim1 + 1], &amp;rho, &amp;d__[j],</span></a>
+<a name="22727"><span class="lineNum">   22727 </span><span class="lineNoCov">          0 :                  &amp;vt[j * vt_dim1 + 1], info);</span></a>
+<a name="22728"><span class="lineNum">   22728 </span>            : </a>
+<a name="22729"><span class="lineNum">   22729 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="22730"><span class="lineNum">   22730 </span>            :             return;</a>
+<a name="22731"><span class="lineNum">   22731 </span>            :         }</a>
+<a name="22732"><span class="lineNum">   22732 </span>            :     }</a>
+<a name="22733"><span class="lineNum">   22733 </span>            : </a>
+<a name="22734"><span class="lineNum">   22734 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="22735"><span class="lineNum">   22735 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22736"><span class="lineNum">   22736 </span><span class="lineNoCov">          0 :         z__[i__] = u[i__ + *k * u_dim1] * vt[i__ + *k * vt_dim1];</span></a>
+<a name="22737"><span class="lineNum">   22737 </span>            :         i__2 = i__ - 1;</a>
+<a name="22738"><span class="lineNum">   22738 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="22739"><span class="lineNum">   22739 </span><span class="lineNoCov">          0 :             z__[i__] *= u[i__ + j * u_dim1] * vt[i__ + j * vt_dim1] / (dsigma[</span></a>
+<a name="22740"><span class="lineNum">   22740 </span><span class="lineNoCov">          0 :                     i__] - dsigma[j]) / (dsigma[i__] + dsigma[j]);</span></a>
+<a name="22741"><span class="lineNum">   22741 </span>            :         }</a>
+<a name="22742"><span class="lineNum">   22742 </span><span class="lineNoCov">          0 :         i__2 = *k - 1;</span></a>
+<a name="22743"><span class="lineNum">   22743 </span><span class="lineNoCov">          0 :         for (j = i__; j &lt;= i__2; ++j) {</span></a>
+<a name="22744"><span class="lineNum">   22744 </span><span class="lineNoCov">          0 :             z__[i__] *= u[i__ + j * u_dim1] * vt[i__ + j * vt_dim1] / (dsigma[</span></a>
+<a name="22745"><span class="lineNum">   22745 </span><span class="lineNoCov">          0 :                     i__] - dsigma[j + 1]) / (dsigma[i__] + dsigma[j + 1]);</span></a>
+<a name="22746"><span class="lineNum">   22746 </span>            :         }</a>
+<a name="22747"><span class="lineNum">   22747 </span><span class="lineNoCov">          0 :         d__2 =  std::sqrt(std::abs(z__[i__]));</span></a>
+<a name="22748"><span class="lineNum">   22748 </span><span class="lineNoCov">          0 :         z__[i__] = (q[i__ + q_dim1] &gt; 0) ? d__2 : -d__2;</span></a>
+<a name="22749"><span class="lineNum">   22749 </span>            :     }</a>
+<a name="22750"><span class="lineNum">   22750 </span>            : </a>
+<a name="22751"><span class="lineNum">   22751 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="22752"><span class="lineNum">   22752 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22753"><span class="lineNum">   22753 </span><span class="lineNoCov">          0 :         vt[i__ * vt_dim1 + 1] = z__[1] / u[i__ * u_dim1 + 1] / vt[i__ * </span></a>
+<a name="22754"><span class="lineNum">   22754 </span><span class="lineNoCov">          0 :                 vt_dim1 + 1];</span></a>
+<a name="22755"><span class="lineNum">   22755 </span><span class="lineNoCov">          0 :         u[i__ * u_dim1 + 1] = -1.;</span></a>
+<a name="22756"><span class="lineNum">   22756 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="22757"><span class="lineNum">   22757 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="22758"><span class="lineNum">   22758 </span><span class="lineNoCov">          0 :             vt[j + i__ * vt_dim1] = z__[j] / u[j + i__ * u_dim1] / vt[j + i__ </span></a>
+<a name="22759"><span class="lineNum">   22759 </span><span class="lineNoCov">          0 :                     * vt_dim1];</span></a>
+<a name="22760"><span class="lineNum">   22760 </span><span class="lineNoCov">          0 :             u[j + i__ * u_dim1] = dsigma[j] * vt[j + i__ * vt_dim1];</span></a>
+<a name="22761"><span class="lineNum">   22761 </span>            :         }</a>
+<a name="22762"><span class="lineNum">   22762 </span><span class="lineNoCov">          0 :         temp = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(k, &amp;u[i__ * u_dim1 + 1], &amp;c__1);</span></a>
+<a name="22763"><span class="lineNum">   22763 </span><span class="lineNoCov">          0 :         q[i__ * q_dim1 + 1] = u[i__ * u_dim1 + 1] / temp;</span></a>
+<a name="22764"><span class="lineNum">   22764 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="22765"><span class="lineNum">   22765 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="22766"><span class="lineNum">   22766 </span><span class="lineNoCov">          0 :             jc = idxc[j];</span></a>
+<a name="22767"><span class="lineNum">   22767 </span><span class="lineNoCov">          0 :             q[j + i__ * q_dim1] = u[jc + i__ * u_dim1] / temp;</span></a>
+<a name="22768"><span class="lineNum">   22768 </span>            :         }</a>
+<a name="22769"><span class="lineNum">   22769 </span>            :     }</a>
+<a name="22770"><span class="lineNum">   22770 </span>            : </a>
+<a name="22771"><span class="lineNum">   22771 </span><span class="lineNoCov">          0 :     if (*k == 2) {</span></a>
+<a name="22772"><span class="lineNum">   22772 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, &amp;n, k, k, &amp;one, &amp;u2[u2_offset], ldu2, &amp;q[q_offset],</span></a>
+<a name="22773"><span class="lineNum">   22773 </span>            :                  ldq, &amp;zero, &amp;u[u_offset], ldu);</a>
+<a name="22774"><span class="lineNum">   22774 </span><span class="lineNoCov">          0 :         goto L100;</span></a>
+<a name="22775"><span class="lineNum">   22775 </span>            :     }</a>
+<a name="22776"><span class="lineNum">   22776 </span><span class="lineNoCov">          0 :     if (ctot[1] &gt; 0) {</span></a>
+<a name="22777"><span class="lineNum">   22777 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, nl, k, &amp;ctot[1], &amp;one, &amp;u2[(u2_dim1 &lt;&lt; 1) + 1], </span></a>
+<a name="22778"><span class="lineNum">   22778 </span><span class="lineNoCov">          0 :                 ldu2, &amp;q[q_dim1 + 2], ldq, &amp;zero, &amp;u[u_dim1 + 1], ldu);</span></a>
+<a name="22779"><span class="lineNum">   22779 </span><span class="lineNoCov">          0 :         if (ctot[3] &gt; 0) {</span></a>
+<a name="22780"><span class="lineNum">   22780 </span><span class="lineNoCov">          0 :             ktemp = ctot[1] + 2 + ctot[2];</span></a>
+<a name="22781"><span class="lineNum">   22781 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, nl, k, &amp;ctot[3], &amp;one, &amp;u2[ktemp * u2_dim1 + 1]</span></a>
+<a name="22782"><span class="lineNum">   22782 </span><span class="lineNoCov">          0 :                     , ldu2, &amp;q[ktemp + q_dim1], ldq, &amp;one, &amp;u[u_dim1 + 1], </span></a>
+<a name="22783"><span class="lineNum">   22783 </span>            :                     ldu);</a>
+<a name="22784"><span class="lineNum">   22784 </span>            :         }</a>
+<a name="22785"><span class="lineNum">   22785 </span><span class="lineNoCov">          0 :     } else if (ctot[3] &gt; 0) {</span></a>
+<a name="22786"><span class="lineNum">   22786 </span><span class="lineNoCov">          0 :         ktemp = ctot[1] + 2 + ctot[2];</span></a>
+<a name="22787"><span class="lineNum">   22787 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, nl, k, &amp;ctot[3], &amp;one, &amp;u2[ktemp * u2_dim1 + 1], </span></a>
+<a name="22788"><span class="lineNum">   22788 </span><span class="lineNoCov">          0 :                 ldu2, &amp;q[ktemp + q_dim1], ldq, &amp;zero, &amp;u[u_dim1 + 1], ldu);</span></a>
+<a name="22789"><span class="lineNum">   22789 </span>            :     } else {</a>
+<a name="22790"><span class="lineNum">   22790 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slacpy,SLACPY)(&quot;F&quot;, nl, k, &amp;u2[u2_offset], ldu2, &amp;u[u_offset], ldu);</span></a>
+<a name="22791"><span class="lineNum">   22791 </span>            :     }</a>
+<a name="22792"><span class="lineNum">   22792 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(k, &amp;q[q_dim1 + 1], ldq, &amp;u[nlp1 + u_dim1], ldu);</span></a>
+<a name="22793"><span class="lineNum">   22793 </span><span class="lineNoCov">          0 :     ktemp = ctot[1] + 2;</span></a>
+<a name="22794"><span class="lineNum">   22794 </span><span class="lineNoCov">          0 :     ctemp = ctot[2] + ctot[3];</span></a>
+<a name="22795"><span class="lineNum">   22795 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, nr, k, &amp;ctemp, &amp;one, &amp;u2[nlp2 + ktemp * u2_dim1], ldu2,</span></a>
+<a name="22796"><span class="lineNum">   22796 </span><span class="lineNoCov">          0 :              &amp;q[ktemp + q_dim1], ldq, &amp;zero, &amp;u[nlp2 + u_dim1], ldu);</span></a>
+<a name="22797"><span class="lineNum">   22797 </span>            : </a>
+<a name="22798"><span class="lineNum">   22798 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="22799"><span class="lineNum">   22799 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="22800"><span class="lineNum">   22800 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22801"><span class="lineNum">   22801 </span><span class="lineNoCov">          0 :         temp = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(k, &amp;vt[i__ * vt_dim1 + 1], &amp;c__1);</span></a>
+<a name="22802"><span class="lineNum">   22802 </span><span class="lineNoCov">          0 :         q[i__ + q_dim1] = vt[i__ * vt_dim1 + 1] / temp;</span></a>
+<a name="22803"><span class="lineNum">   22803 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="22804"><span class="lineNum">   22804 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__2; ++j) {</span></a>
+<a name="22805"><span class="lineNum">   22805 </span><span class="lineNoCov">          0 :             jc = idxc[j];</span></a>
+<a name="22806"><span class="lineNum">   22806 </span><span class="lineNoCov">          0 :             q[i__ + j * q_dim1] = vt[jc + i__ * vt_dim1] / temp;</span></a>
+<a name="22807"><span class="lineNum">   22807 </span>            :         }</a>
+<a name="22808"><span class="lineNum">   22808 </span>            :     }</a>
+<a name="22809"><span class="lineNum">   22809 </span>            : </a>
+<a name="22810"><span class="lineNum">   22810 </span><span class="lineNoCov">          0 :     if (*k == 2) {</span></a>
+<a name="22811"><span class="lineNum">   22811 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;m, k, &amp;one, &amp;q[q_offset], ldq, &amp;vt2[vt2_offset]</span></a>
+<a name="22812"><span class="lineNum">   22812 </span>            :                 , ldvt2, &amp;zero, &amp;vt[vt_offset], ldvt);</a>
+<a name="22813"><span class="lineNum">   22813 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="22814"><span class="lineNum">   22814 </span>            :     }</a>
+<a name="22815"><span class="lineNum">   22815 </span><span class="lineNoCov">          0 :     ktemp = ctot[1] + 1;</span></a>
+<a name="22816"><span class="lineNum">   22816 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;nlp1, &amp;ktemp, &amp;one, &amp;q[q_dim1 + 1], ldq, &amp;vt2[</span></a>
+<a name="22817"><span class="lineNum">   22817 </span><span class="lineNoCov">          0 :             vt2_dim1 + 1], ldvt2, &amp;zero, &amp;vt[vt_dim1 + 1], ldvt);</span></a>
+<a name="22818"><span class="lineNum">   22818 </span><span class="lineNoCov">          0 :     ktemp = ctot[1] + 2 + ctot[2];</span></a>
+<a name="22819"><span class="lineNum">   22819 </span><span class="lineNoCov">          0 :     if (ktemp &lt;= *ldvt2) {</span></a>
+<a name="22820"><span class="lineNum">   22820 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;nlp1, &amp;ctot[3], &amp;one, &amp;q[ktemp * q_dim1 + 1], </span></a>
+<a name="22821"><span class="lineNum">   22821 </span><span class="lineNoCov">          0 :                 ldq, &amp;vt2[ktemp + vt2_dim1], ldvt2, &amp;one, &amp;vt[vt_dim1 + 1], </span></a>
+<a name="22822"><span class="lineNum">   22822 </span>            :                 ldvt);</a>
+<a name="22823"><span class="lineNum">   22823 </span>            :     }</a>
+<a name="22824"><span class="lineNum">   22824 </span>            : </a>
+<a name="22825"><span class="lineNum">   22825 </span><span class="lineNoCov">          0 :     ktemp = ctot[1] + 1;</span></a>
+<a name="22826"><span class="lineNum">   22826 </span><span class="lineNoCov">          0 :     nrp1 = *nr + *sqre;</span></a>
+<a name="22827"><span class="lineNum">   22827 </span><span class="lineNoCov">          0 :     if (ktemp &gt; 1) {</span></a>
+<a name="22828"><span class="lineNum">   22828 </span><span class="lineNoCov">          0 :         i__1 = *k;</span></a>
+<a name="22829"><span class="lineNum">   22829 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22830"><span class="lineNum">   22830 </span><span class="lineNoCov">          0 :             q[i__ + ktemp * q_dim1] = q[i__ + q_dim1];</span></a>
+<a name="22831"><span class="lineNum">   22831 </span>            :         }</a>
+<a name="22832"><span class="lineNum">   22832 </span><span class="lineNoCov">          0 :         i__1 = m;</span></a>
+<a name="22833"><span class="lineNum">   22833 </span><span class="lineNoCov">          0 :         for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="22834"><span class="lineNum">   22834 </span><span class="lineNoCov">          0 :             vt2[ktemp + i__ * vt2_dim1] = vt2[i__ * vt2_dim1 + 1];</span></a>
+<a name="22835"><span class="lineNum">   22835 </span>            :         }</a>
+<a name="22836"><span class="lineNum">   22836 </span>            :     }</a>
+<a name="22837"><span class="lineNum">   22837 </span><span class="lineNoCov">          0 :     ctemp = ctot[2] + 1 + ctot[3];</span></a>
+<a name="22838"><span class="lineNum">   22838 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sgemm,SGEMM)(&quot;N&quot;, &quot;N&quot;, k, &amp;nrp1, &amp;ctemp, &amp;one, &amp;q[ktemp * q_dim1 + 1], ldq, &amp;</span></a>
+<a name="22839"><span class="lineNum">   22839 </span><span class="lineNoCov">          0 :             vt2[ktemp + nlp2 * vt2_dim1], ldvt2, &amp;zero, &amp;vt[nlp2 * vt_dim1 + </span></a>
+<a name="22840"><span class="lineNum">   22840 </span><span class="lineNoCov">          0 :             1], ldvt);</span></a>
+<a name="22841"><span class="lineNum">   22841 </span>            : </a>
+<a name="22842"><span class="lineNum">   22842 </span>            :     return;</a>
+<a name="22843"><span class="lineNum">   22843 </span>            : </a>
+<a name="22844"><span class="lineNum">   22844 </span>            : </a>
+<a name="22845"><span class="lineNum">   22845 </span>            : }</a>
+<a name="22846"><span class="lineNum">   22846 </span>            : </a>
+<a name="22847"><span class="lineNum">   22847 </span>            : </a>
+<a name="22848"><span class="lineNum">   22848 </span>            : }</a>
+<a name="22849"><span class="lineNum">   22849 </span>            : }</a>
+<a name="22850"><span class="lineNum">   22850 </span>            : #include &lt;cmath&gt;</a>
+<a name="22851"><span class="lineNum">   22851 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="22852"><span class="lineNum">   22852 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="22853"><span class="lineNum">   22853 </span>            : </a>
+<a name="22854"><span class="lineNum">   22854 </span>            : #include &quot;real.h&quot;</a>
+<a name="22855"><span class="lineNum">   22855 </span>            : </a>
+<a name="22856"><span class="lineNum">   22856 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="22857"><span class="lineNum">   22857 </span>            : namespace PLMD{</a>
+<a name="22858"><span class="lineNum">   22858 </span>            : namespace lapack{</a>
+<a name="22859"><span class="lineNum">   22859 </span>            : using namespace blas;</a>
+<a name="22860"><span class="lineNum">   22860 </span>            : void </a>
+<a name="22861"><span class="lineNum">   22861 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd4,SLASD4)(int *n, </span></a>
+<a name="22862"><span class="lineNum">   22862 </span>            :         int *i__, </a>
+<a name="22863"><span class="lineNum">   22863 </span>            :         float *d__, </a>
+<a name="22864"><span class="lineNum">   22864 </span>            :         float *z__, </a>
+<a name="22865"><span class="lineNum">   22865 </span>            :         float *delta, </a>
+<a name="22866"><span class="lineNum">   22866 </span>            :         float *rho, </a>
+<a name="22867"><span class="lineNum">   22867 </span>            :         float *sigma, </a>
+<a name="22868"><span class="lineNum">   22868 </span>            :         float *work, </a>
+<a name="22869"><span class="lineNum">   22869 </span>            :         int *info)</a>
+<a name="22870"><span class="lineNum">   22870 </span>            : {</a>
+<a name="22871"><span class="lineNum">   22871 </span>            :     int i__1;</a>
+<a name="22872"><span class="lineNum">   22872 </span>            :     float d__1;</a>
+<a name="22873"><span class="lineNum">   22873 </span>            : </a>
+<a name="22874"><span class="lineNum">   22874 </span>            :     float a, b, c__;</a>
+<a name="22875"><span class="lineNum">   22875 </span>            :     int j;</a>
+<a name="22876"><span class="lineNum">   22876 </span>            :     float w, dd[3];</a>
+<a name="22877"><span class="lineNum">   22877 </span>            :     int ii;</a>
+<a name="22878"><span class="lineNum">   22878 </span>            :     float dw, zz[3];</a>
+<a name="22879"><span class="lineNum">   22879 </span>            :     int ip1;</a>
+<a name="22880"><span class="lineNum">   22880 </span>            :     float eta, phi, eps, tau, psi;</a>
+<a name="22881"><span class="lineNum">   22881 </span>            :     int iim1, iip1;</a>
+<a name="22882"><span class="lineNum">   22882 </span>            :     float dphi, dpsi;</a>
+<a name="22883"><span class="lineNum">   22883 </span>            :     int iter;</a>
+<a name="22884"><span class="lineNum">   22884 </span>            :     float temp, prew, sg2lb, sg2ub, temp1, temp2, dtiim, delsq, </a>
+<a name="22885"><span class="lineNum">   22885 </span>            :             dtiip;</a>
+<a name="22886"><span class="lineNum">   22886 </span>            :     int niter;</a>
+<a name="22887"><span class="lineNum">   22887 </span>            :     float dtisq;</a>
+<a name="22888"><span class="lineNum">   22888 </span>            :     int swtch;</a>
+<a name="22889"><span class="lineNum">   22889 </span>            :     float dtnsq;</a>
+<a name="22890"><span class="lineNum">   22890 </span>            :     float delsq2, dtnsq1;</a>
+<a name="22891"><span class="lineNum">   22891 </span>            :     int swtch3;</a>
+<a name="22892"><span class="lineNum">   22892 </span>            :     int orgati;</a>
+<a name="22893"><span class="lineNum">   22893 </span>            :     float erretm, dtipsq, rhoinv;</a>
+<a name="22894"><span class="lineNum">   22894 </span>            : </a>
+<a name="22895"><span class="lineNum">   22895 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="22896"><span class="lineNum">   22896 </span><span class="lineNoCov">          0 :     --delta;</span></a>
+<a name="22897"><span class="lineNum">   22897 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="22898"><span class="lineNum">   22898 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="22899"><span class="lineNum">   22899 </span>            : </a>
+<a name="22900"><span class="lineNum">   22900 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="22901"><span class="lineNum">   22901 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="22902"><span class="lineNum">   22902 </span>            : </a>
+<a name="22903"><span class="lineNum">   22903 </span><span class="lineNoCov">          0 :         *sigma =  std::sqrt(d__[1] * d__[1] + *rho * z__[1] * z__[1]);</span></a>
+<a name="22904"><span class="lineNum">   22904 </span><span class="lineNoCov">          0 :         delta[1] = 1.;</span></a>
+<a name="22905"><span class="lineNum">   22905 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="22906"><span class="lineNum">   22906 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="22907"><span class="lineNum">   22907 </span>            :     }</a>
+<a name="22908"><span class="lineNum">   22908 </span><span class="lineNoCov">          0 :     if (*n == 2) {</span></a>
+<a name="22909"><span class="lineNum">   22909 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasd5,SLASD5)(i__, &amp;d__[1], &amp;z__[1], &amp;delta[1], rho, sigma, &amp;work[1]);</span></a>
+<a name="22910"><span class="lineNum">   22910 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="22911"><span class="lineNum">   22911 </span>            :     }</a>
+<a name="22912"><span class="lineNum">   22912 </span>            : </a>
+<a name="22913"><span class="lineNum">   22913 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="22914"><span class="lineNum">   22914 </span><span class="lineNoCov">          0 :     rhoinv = 1. / *rho;</span></a>
+<a name="22915"><span class="lineNum">   22915 </span>            : </a>
+<a name="22916"><span class="lineNum">   22916 </span><span class="lineNoCov">          0 :     if (*i__ == *n) {</span></a>
+<a name="22917"><span class="lineNum">   22917 </span>            : </a>
+<a name="22918"><span class="lineNum">   22918 </span><span class="lineNoCov">          0 :         ii = *n - 1;</span></a>
+<a name="22919"><span class="lineNum">   22919 </span><span class="lineNoCov">          0 :         niter = 1;</span></a>
+<a name="22920"><span class="lineNum">   22920 </span>            : </a>
+<a name="22921"><span class="lineNum">   22921 </span><span class="lineNoCov">          0 :         temp = *rho / 2.;</span></a>
+<a name="22922"><span class="lineNum">   22922 </span>            : </a>
+<a name="22923"><span class="lineNum">   22923 </span><span class="lineNoCov">          0 :         temp1 = temp / (d__[*n] +  std::sqrt(d__[*n] * d__[*n] + temp));</span></a>
+<a name="22924"><span class="lineNum">   22924 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="22925"><span class="lineNum">   22925 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="22926"><span class="lineNum">   22926 </span><span class="lineNoCov">          0 :             work[j] = d__[j] + d__[*n] + temp1;</span></a>
+<a name="22927"><span class="lineNum">   22927 </span><span class="lineNoCov">          0 :             delta[j] = d__[j] - d__[*n] - temp1;</span></a>
+<a name="22928"><span class="lineNum">   22928 </span>            :         }</a>
+<a name="22929"><span class="lineNum">   22929 </span>            : </a>
+<a name="22930"><span class="lineNum">   22930 </span>            :         psi = 0.;</a>
+<a name="22931"><span class="lineNum">   22931 </span><span class="lineNoCov">          0 :         i__1 = *n - 2;</span></a>
+<a name="22932"><span class="lineNum">   22932 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="22933"><span class="lineNum">   22933 </span><span class="lineNoCov">          0 :             psi += z__[j] * z__[j] / (delta[j] * work[j]);</span></a>
+<a name="22934"><span class="lineNum">   22934 </span>            :         }</a>
+<a name="22935"><span class="lineNum">   22935 </span>            : </a>
+<a name="22936"><span class="lineNum">   22936 </span><span class="lineNoCov">          0 :         c__ = rhoinv + psi;</span></a>
+<a name="22937"><span class="lineNum">   22937 </span><span class="lineNoCov">          0 :         w = c__ + z__[ii] * z__[ii] / (delta[ii] * work[ii]) + z__[*n] * z__[*</span></a>
+<a name="22938"><span class="lineNum">   22938 </span><span class="lineNoCov">          0 :                 n] / (delta[*n] * work[*n]);</span></a>
+<a name="22939"><span class="lineNum">   22939 </span>            : </a>
+<a name="22940"><span class="lineNum">   22940 </span><span class="lineNoCov">          0 :         if (w &lt;= 0.) {</span></a>
+<a name="22941"><span class="lineNum">   22941 </span><span class="lineNoCov">          0 :             temp1 =  std::sqrt(d__[*n] * d__[*n] + *rho);</span></a>
+<a name="22942"><span class="lineNum">   22942 </span><span class="lineNoCov">          0 :             temp = z__[*n - 1] * z__[*n - 1] / ((d__[*n - 1] + temp1) * (d__[*</span></a>
+<a name="22943"><span class="lineNum">   22943 </span><span class="lineNoCov">          0 :                     n] - d__[*n - 1] + *rho / (d__[*n] + temp1))) + z__[*n] * </span></a>
+<a name="22944"><span class="lineNum">   22944 </span><span class="lineNoCov">          0 :                     z__[*n] / *rho;</span></a>
+<a name="22945"><span class="lineNum">   22945 </span>            : </a>
+<a name="22946"><span class="lineNum">   22946 </span><span class="lineNoCov">          0 :             if (c__ &lt;= temp) {</span></a>
+<a name="22947"><span class="lineNum">   22947 </span>            :                 tau = *rho;</a>
+<a name="22948"><span class="lineNum">   22948 </span>            :             } else {</a>
+<a name="22949"><span class="lineNum">   22949 </span><span class="lineNoCov">          0 :                 delsq = (d__[*n] - d__[*n - 1]) * (d__[*n] + d__[*n - 1]);</span></a>
+<a name="22950"><span class="lineNum">   22950 </span><span class="lineNoCov">          0 :                 a = -c__ * delsq + z__[*n - 1] * z__[*n - 1] + z__[*n] * z__[*</span></a>
+<a name="22951"><span class="lineNum">   22951 </span>            :                         n];</a>
+<a name="22952"><span class="lineNum">   22952 </span><span class="lineNoCov">          0 :                 b = z__[*n] * z__[*n] * delsq;</span></a>
+<a name="22953"><span class="lineNum">   22953 </span><span class="lineNoCov">          0 :                 if (a &lt; 0.) {</span></a>
+<a name="22954"><span class="lineNum">   22954 </span><span class="lineNoCov">          0 :                     tau = b * 2. / ( std::sqrt(a * a + b * 4. * c__) - a);</span></a>
+<a name="22955"><span class="lineNum">   22955 </span>            :                 } else {</a>
+<a name="22956"><span class="lineNum">   22956 </span><span class="lineNoCov">          0 :                     tau = (a +  std::sqrt(a * a + b * 4. * c__)) / (c__ * 2.);</span></a>
+<a name="22957"><span class="lineNum">   22957 </span>            :                 }</a>
+<a name="22958"><span class="lineNum">   22958 </span>            :             }</a>
+<a name="22959"><span class="lineNum">   22959 </span>            : </a>
+<a name="22960"><span class="lineNum">   22960 </span>            :         } else {</a>
+<a name="22961"><span class="lineNum">   22961 </span><span class="lineNoCov">          0 :             delsq = (d__[*n] - d__[*n - 1]) * (d__[*n] + d__[*n - 1]);</span></a>
+<a name="22962"><span class="lineNum">   22962 </span><span class="lineNoCov">          0 :             a = -c__ * delsq + z__[*n - 1] * z__[*n - 1] + z__[*n] * z__[*n];</span></a>
+<a name="22963"><span class="lineNum">   22963 </span><span class="lineNoCov">          0 :             b = z__[*n] * z__[*n] * delsq;</span></a>
+<a name="22964"><span class="lineNum">   22964 </span>            : </a>
+<a name="22965"><span class="lineNum">   22965 </span><span class="lineNoCov">          0 :             if (a &lt; 0.) {</span></a>
+<a name="22966"><span class="lineNum">   22966 </span><span class="lineNoCov">          0 :                 tau = b * 2. / ( std::sqrt(a * a + b * 4. * c__) - a);</span></a>
+<a name="22967"><span class="lineNum">   22967 </span>            :             } else {</a>
+<a name="22968"><span class="lineNum">   22968 </span><span class="lineNoCov">          0 :                 tau = (a +  std::sqrt(a * a + b * 4. * c__)) / (c__ * 2.);</span></a>
+<a name="22969"><span class="lineNum">   22969 </span>            :             }</a>
+<a name="22970"><span class="lineNum">   22970 </span>            : </a>
+<a name="22971"><span class="lineNum">   22971 </span>            :         }</a>
+<a name="22972"><span class="lineNum">   22972 </span>            : </a>
+<a name="22973"><span class="lineNum">   22973 </span><span class="lineNoCov">          0 :         eta = tau / (d__[*n] +  std::sqrt(d__[*n] * d__[*n] + tau));</span></a>
+<a name="22974"><span class="lineNum">   22974 </span>            : </a>
+<a name="22975"><span class="lineNum">   22975 </span><span class="lineNoCov">          0 :         *sigma = d__[*n] + eta;</span></a>
+<a name="22976"><span class="lineNum">   22976 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="22977"><span class="lineNum">   22977 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="22978"><span class="lineNum">   22978 </span><span class="lineNoCov">          0 :             delta[j] = d__[j] - d__[*i__] - eta;</span></a>
+<a name="22979"><span class="lineNum">   22979 </span><span class="lineNoCov">          0 :             work[j] = d__[j] + d__[*i__] + eta;</span></a>
+<a name="22980"><span class="lineNum">   22980 </span>            :         }</a>
+<a name="22981"><span class="lineNum">   22981 </span>            : </a>
+<a name="22982"><span class="lineNum">   22982 </span>            :         dpsi = 0.;</a>
+<a name="22983"><span class="lineNum">   22983 </span>            :         psi = 0.;</a>
+<a name="22984"><span class="lineNum">   22984 </span>            :         erretm = 0.;</a>
+<a name="22985"><span class="lineNum">   22985 </span>            :         i__1 = ii;</a>
+<a name="22986"><span class="lineNum">   22986 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="22987"><span class="lineNum">   22987 </span><span class="lineNoCov">          0 :             temp = z__[j] / (delta[j] * work[j]);</span></a>
+<a name="22988"><span class="lineNum">   22988 </span><span class="lineNoCov">          0 :             psi += z__[j] * temp;</span></a>
+<a name="22989"><span class="lineNum">   22989 </span><span class="lineNoCov">          0 :             dpsi += temp * temp;</span></a>
+<a name="22990"><span class="lineNum">   22990 </span><span class="lineNoCov">          0 :             erretm += psi;</span></a>
+<a name="22991"><span class="lineNum">   22991 </span>            :         }</a>
+<a name="22992"><span class="lineNum">   22992 </span>            :         erretm = std::abs(erretm);</a>
+<a name="22993"><span class="lineNum">   22993 </span>            : </a>
+<a name="22994"><span class="lineNum">   22994 </span><span class="lineNoCov">          0 :         temp = z__[*n] / (delta[*n] * work[*n]);</span></a>
+<a name="22995"><span class="lineNum">   22995 </span><span class="lineNoCov">          0 :         phi = z__[*n] * temp;</span></a>
+<a name="22996"><span class="lineNum">   22996 </span><span class="lineNoCov">          0 :         dphi = temp * temp;</span></a>
+<a name="22997"><span class="lineNum">   22997 </span><span class="lineNoCov">          0 :         erretm = (-phi - psi) * 8. + erretm - phi + rhoinv + std::abs(tau) * (dpsi </span></a>
+<a name="22998"><span class="lineNum">   22998 </span><span class="lineNoCov">          0 :                 + dphi);</span></a>
+<a name="22999"><span class="lineNum">   22999 </span>            : </a>
+<a name="23000"><span class="lineNum">   23000 </span><span class="lineNoCov">          0 :         w = rhoinv + phi + psi;</span></a>
+<a name="23001"><span class="lineNum">   23001 </span>            : </a>
+<a name="23002"><span class="lineNum">   23002 </span><span class="lineNoCov">          0 :         if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="23003"><span class="lineNum">   23003 </span><span class="lineNoCov">          0 :             goto L240;</span></a>
+<a name="23004"><span class="lineNum">   23004 </span>            :         }</a>
+<a name="23005"><span class="lineNum">   23005 </span>            : </a>
+<a name="23006"><span class="lineNum">   23006 </span><span class="lineNoCov">          0 :         ++niter;</span></a>
+<a name="23007"><span class="lineNum">   23007 </span><span class="lineNoCov">          0 :         dtnsq1 = work[*n - 1] * delta[*n - 1];</span></a>
+<a name="23008"><span class="lineNum">   23008 </span>            :         dtnsq = work[*n] * delta[*n];</a>
+<a name="23009"><span class="lineNum">   23009 </span><span class="lineNoCov">          0 :         c__ = w - dtnsq1 * dpsi - dtnsq * dphi;</span></a>
+<a name="23010"><span class="lineNum">   23010 </span><span class="lineNoCov">          0 :         a = (dtnsq + dtnsq1) * w - dtnsq * dtnsq1 * (dpsi + dphi);</span></a>
+<a name="23011"><span class="lineNum">   23011 </span><span class="lineNoCov">          0 :         b = dtnsq * dtnsq1 * w;</span></a>
+<a name="23012"><span class="lineNum">   23012 </span><span class="lineNoCov">          0 :         if (c__ &lt; 0.) {</span></a>
+<a name="23013"><span class="lineNum">   23013 </span><span class="lineNoCov">          0 :             c__ = std::abs(c__);</span></a>
+<a name="23014"><span class="lineNum">   23014 </span>            :         }</a>
+<a name="23015"><span class="lineNum">   23015 </span><span class="lineNoCov">          0 :         if ( std::abs(c__)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="23016"><span class="lineNum">   23016 </span><span class="lineNoCov">          0 :             eta = *rho - *sigma * *sigma;</span></a>
+<a name="23017"><span class="lineNum">   23017 </span><span class="lineNoCov">          0 :         } else if (a &gt;= 0.) {</span></a>
+<a name="23018"><span class="lineNum">   23018 </span><span class="lineNoCov">          0 :             eta = (a +  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__  * 2.);</span></a>
+<a name="23019"><span class="lineNum">   23019 </span>            :         } else {</a>
+<a name="23020"><span class="lineNum">   23020 </span><span class="lineNoCov">          0 :           eta = b * 2. / (a -  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="23021"><span class="lineNum">   23021 </span>            :         }</a>
+<a name="23022"><span class="lineNum">   23022 </span>            : </a>
+<a name="23023"><span class="lineNum">   23023 </span><span class="lineNoCov">          0 :         if (w * eta &gt; 0.) {</span></a>
+<a name="23024"><span class="lineNum">   23024 </span><span class="lineNoCov">          0 :             eta = -w / (dpsi + dphi);</span></a>
+<a name="23025"><span class="lineNum">   23025 </span>            :         }</a>
+<a name="23026"><span class="lineNum">   23026 </span><span class="lineNoCov">          0 :         temp = eta - dtnsq;</span></a>
+<a name="23027"><span class="lineNum">   23027 </span><span class="lineNoCov">          0 :         if (temp &gt; *rho) {</span></a>
+<a name="23028"><span class="lineNum">   23028 </span><span class="lineNoCov">          0 :             eta = *rho + dtnsq;</span></a>
+<a name="23029"><span class="lineNum">   23029 </span>            :         }</a>
+<a name="23030"><span class="lineNum">   23030 </span>            : </a>
+<a name="23031"><span class="lineNum">   23031 </span><span class="lineNoCov">          0 :         tau += eta;</span></a>
+<a name="23032"><span class="lineNum">   23032 </span><span class="lineNoCov">          0 :         eta /= *sigma +  std::sqrt(eta + *sigma * *sigma);</span></a>
+<a name="23033"><span class="lineNum">   23033 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="23034"><span class="lineNum">   23034 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23035"><span class="lineNum">   23035 </span><span class="lineNoCov">          0 :             delta[j] -= eta;</span></a>
+<a name="23036"><span class="lineNum">   23036 </span><span class="lineNoCov">          0 :             work[j] += eta;</span></a>
+<a name="23037"><span class="lineNum">   23037 </span>            :         }</a>
+<a name="23038"><span class="lineNum">   23038 </span>            : </a>
+<a name="23039"><span class="lineNum">   23039 </span><span class="lineNoCov">          0 :         *sigma += eta;</span></a>
+<a name="23040"><span class="lineNum">   23040 </span>            : </a>
+<a name="23041"><span class="lineNum">   23041 </span>            :         dpsi = 0.;</a>
+<a name="23042"><span class="lineNum">   23042 </span>            :         psi = 0.;</a>
+<a name="23043"><span class="lineNum">   23043 </span>            :         erretm = 0.;</a>
+<a name="23044"><span class="lineNum">   23044 </span>            :         i__1 = ii;</a>
+<a name="23045"><span class="lineNum">   23045 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23046"><span class="lineNum">   23046 </span><span class="lineNoCov">          0 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23047"><span class="lineNum">   23047 </span><span class="lineNoCov">          0 :             psi += z__[j] * temp;</span></a>
+<a name="23048"><span class="lineNum">   23048 </span><span class="lineNoCov">          0 :             dpsi += temp * temp;</span></a>
+<a name="23049"><span class="lineNum">   23049 </span><span class="lineNoCov">          0 :             erretm += psi;</span></a>
+<a name="23050"><span class="lineNum">   23050 </span>            :         }</a>
+<a name="23051"><span class="lineNum">   23051 </span>            :         erretm = std::abs(erretm);</a>
+<a name="23052"><span class="lineNum">   23052 </span>            : </a>
+<a name="23053"><span class="lineNum">   23053 </span><span class="lineNoCov">          0 :         temp = z__[*n] / (work[*n] * delta[*n]);</span></a>
+<a name="23054"><span class="lineNum">   23054 </span><span class="lineNoCov">          0 :         phi = z__[*n] * temp;</span></a>
+<a name="23055"><span class="lineNum">   23055 </span><span class="lineNoCov">          0 :         dphi = temp * temp;</span></a>
+<a name="23056"><span class="lineNum">   23056 </span><span class="lineNoCov">          0 :         erretm = (-phi - psi) * 8. + erretm - phi + rhoinv + std::abs(tau) * (dpsi </span></a>
+<a name="23057"><span class="lineNum">   23057 </span><span class="lineNoCov">          0 :                 + dphi);</span></a>
+<a name="23058"><span class="lineNum">   23058 </span>            : </a>
+<a name="23059"><span class="lineNum">   23059 </span><span class="lineNoCov">          0 :         w = rhoinv + phi + psi;</span></a>
+<a name="23060"><span class="lineNum">   23060 </span>            : </a>
+<a name="23061"><span class="lineNum">   23061 </span>            :         iter = niter + 1;</a>
+<a name="23062"><span class="lineNum">   23062 </span>            : </a>
+<a name="23063"><span class="lineNum">   23063 </span><span class="lineNoCov">          0 :         for (niter = iter; niter &lt;= 20; ++niter) {</span></a>
+<a name="23064"><span class="lineNum">   23064 </span>            : </a>
+<a name="23065"><span class="lineNum">   23065 </span><span class="lineNoCov">          0 :             if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="23066"><span class="lineNum">   23066 </span><span class="lineNoCov">          0 :                 goto L240;</span></a>
+<a name="23067"><span class="lineNum">   23067 </span>            :             }</a>
+<a name="23068"><span class="lineNum">   23068 </span><span class="lineNoCov">          0 :             dtnsq1 = work[*n - 1] * delta[*n - 1];</span></a>
+<a name="23069"><span class="lineNum">   23069 </span><span class="lineNoCov">          0 :             dtnsq = work[*n] * delta[*n];</span></a>
+<a name="23070"><span class="lineNum">   23070 </span><span class="lineNoCov">          0 :             c__ = w - dtnsq1 * dpsi - dtnsq * dphi;</span></a>
+<a name="23071"><span class="lineNum">   23071 </span><span class="lineNoCov">          0 :             a = (dtnsq + dtnsq1) * w - dtnsq1 * dtnsq * (dpsi + dphi);</span></a>
+<a name="23072"><span class="lineNum">   23072 </span><span class="lineNoCov">          0 :             b = dtnsq1 * dtnsq * w;</span></a>
+<a name="23073"><span class="lineNum">   23073 </span><span class="lineNoCov">          0 :             if (a &gt;= 0.) {</span></a>
+<a name="23074"><span class="lineNum">   23074 </span><span class="lineNoCov">          0 :                 eta = (a +  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="23075"><span class="lineNum">   23075 </span>            :             } else {</a>
+<a name="23076"><span class="lineNum">   23076 </span><span class="lineNoCov">          0 :               eta = b * 2. / (a -  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="23077"><span class="lineNum">   23077 </span>            :             }</a>
+<a name="23078"><span class="lineNum">   23078 </span>            : </a>
+<a name="23079"><span class="lineNum">   23079 </span><span class="lineNoCov">          0 :             if (w * eta &gt; 0.) {</span></a>
+<a name="23080"><span class="lineNum">   23080 </span><span class="lineNoCov">          0 :                 eta = -w / (dpsi + dphi);</span></a>
+<a name="23081"><span class="lineNum">   23081 </span>            :             }</a>
+<a name="23082"><span class="lineNum">   23082 </span><span class="lineNoCov">          0 :             temp = eta - dtnsq;</span></a>
+<a name="23083"><span class="lineNum">   23083 </span><span class="lineNoCov">          0 :             if (temp &lt;= 0.) {</span></a>
+<a name="23084"><span class="lineNum">   23084 </span><span class="lineNoCov">          0 :                 eta /= 2.;</span></a>
+<a name="23085"><span class="lineNum">   23085 </span>            :             }</a>
+<a name="23086"><span class="lineNum">   23086 </span>            : </a>
+<a name="23087"><span class="lineNum">   23087 </span><span class="lineNoCov">          0 :             tau += eta;</span></a>
+<a name="23088"><span class="lineNum">   23088 </span><span class="lineNoCov">          0 :             eta /= *sigma +  std::sqrt(eta + *sigma * *sigma);</span></a>
+<a name="23089"><span class="lineNum">   23089 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="23090"><span class="lineNum">   23090 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23091"><span class="lineNum">   23091 </span><span class="lineNoCov">          0 :                 delta[j] -= eta;</span></a>
+<a name="23092"><span class="lineNum">   23092 </span><span class="lineNoCov">          0 :                 work[j] += eta;</span></a>
+<a name="23093"><span class="lineNum">   23093 </span>            :             }</a>
+<a name="23094"><span class="lineNum">   23094 </span>            : </a>
+<a name="23095"><span class="lineNum">   23095 </span><span class="lineNoCov">          0 :             *sigma += eta;</span></a>
+<a name="23096"><span class="lineNum">   23096 </span>            : </a>
+<a name="23097"><span class="lineNum">   23097 </span>            :             dpsi = 0.;</a>
+<a name="23098"><span class="lineNum">   23098 </span>            :             psi = 0.;</a>
+<a name="23099"><span class="lineNum">   23099 </span>            :             erretm = 0.;</a>
+<a name="23100"><span class="lineNum">   23100 </span>            :             i__1 = ii;</a>
+<a name="23101"><span class="lineNum">   23101 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23102"><span class="lineNum">   23102 </span><span class="lineNoCov">          0 :                 temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23103"><span class="lineNum">   23103 </span><span class="lineNoCov">          0 :                 psi += z__[j] * temp;</span></a>
+<a name="23104"><span class="lineNum">   23104 </span><span class="lineNoCov">          0 :                 dpsi += temp * temp;</span></a>
+<a name="23105"><span class="lineNum">   23105 </span><span class="lineNoCov">          0 :                 erretm += psi;</span></a>
+<a name="23106"><span class="lineNum">   23106 </span>            :             }</a>
+<a name="23107"><span class="lineNum">   23107 </span>            :             erretm = std::abs(erretm);</a>
+<a name="23108"><span class="lineNum">   23108 </span>            : </a>
+<a name="23109"><span class="lineNum">   23109 </span><span class="lineNoCov">          0 :             temp = z__[*n] / (work[*n] * delta[*n]);</span></a>
+<a name="23110"><span class="lineNum">   23110 </span><span class="lineNoCov">          0 :             phi = z__[*n] * temp;</span></a>
+<a name="23111"><span class="lineNum">   23111 </span><span class="lineNoCov">          0 :             dphi = temp * temp;</span></a>
+<a name="23112"><span class="lineNum">   23112 </span><span class="lineNoCov">          0 :             erretm = (-phi - psi) * 8. + erretm - phi + rhoinv + std::abs(tau) * (</span></a>
+<a name="23113"><span class="lineNum">   23113 </span><span class="lineNoCov">          0 :                     dpsi + dphi);</span></a>
+<a name="23114"><span class="lineNum">   23114 </span>            : </a>
+<a name="23115"><span class="lineNum">   23115 </span><span class="lineNoCov">          0 :             w = rhoinv + phi + psi;</span></a>
+<a name="23116"><span class="lineNum">   23116 </span>            :         }</a>
+<a name="23117"><span class="lineNum">   23117 </span>            : </a>
+<a name="23118"><span class="lineNum">   23118 </span><span class="lineNoCov">          0 :         *info = 1;</span></a>
+<a name="23119"><span class="lineNum">   23119 </span><span class="lineNoCov">          0 :         goto L240;</span></a>
+<a name="23120"><span class="lineNum">   23120 </span>            : </a>
+<a name="23121"><span class="lineNum">   23121 </span>            :     } else {</a>
+<a name="23122"><span class="lineNum">   23122 </span>            : </a>
+<a name="23123"><span class="lineNum">   23123 </span><span class="lineNoCov">          0 :         niter = 1;</span></a>
+<a name="23124"><span class="lineNum">   23124 </span><span class="lineNoCov">          0 :         ip1 = *i__ + 1;</span></a>
+<a name="23125"><span class="lineNum">   23125 </span>            : </a>
+<a name="23126"><span class="lineNum">   23126 </span><span class="lineNoCov">          0 :         delsq = (d__[ip1] - d__[*i__]) * (d__[ip1] + d__[*i__]);</span></a>
+<a name="23127"><span class="lineNum">   23127 </span><span class="lineNoCov">          0 :         delsq2 = delsq / 2.;</span></a>
+<a name="23128"><span class="lineNum">   23128 </span><span class="lineNoCov">          0 :         temp = delsq2 / (d__[*i__] +  std::sqrt(d__[*i__] * d__[*i__] + delsq2));</span></a>
+<a name="23129"><span class="lineNum">   23129 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="23130"><span class="lineNum">   23130 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23131"><span class="lineNum">   23131 </span><span class="lineNoCov">          0 :             work[j] = d__[j] + d__[*i__] + temp;</span></a>
+<a name="23132"><span class="lineNum">   23132 </span><span class="lineNoCov">          0 :             delta[j] = d__[j] - d__[*i__] - temp;</span></a>
+<a name="23133"><span class="lineNum">   23133 </span>            :         }</a>
+<a name="23134"><span class="lineNum">   23134 </span>            : </a>
+<a name="23135"><span class="lineNum">   23135 </span>            :         psi = 0.;</a>
+<a name="23136"><span class="lineNum">   23136 </span><span class="lineNoCov">          0 :         i__1 = *i__ - 1;</span></a>
+<a name="23137"><span class="lineNum">   23137 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23138"><span class="lineNum">   23138 </span><span class="lineNoCov">          0 :             psi += z__[j] * z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23139"><span class="lineNum">   23139 </span>            :         }</a>
+<a name="23140"><span class="lineNum">   23140 </span>            : </a>
+<a name="23141"><span class="lineNum">   23141 </span>            :         phi = 0.;</a>
+<a name="23142"><span class="lineNum">   23142 </span><span class="lineNoCov">          0 :         i__1 = *i__ + 2;</span></a>
+<a name="23143"><span class="lineNum">   23143 </span><span class="lineNoCov">          0 :         for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="23144"><span class="lineNum">   23144 </span><span class="lineNoCov">          0 :             phi += z__[j] * z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23145"><span class="lineNum">   23145 </span>            :         }</a>
+<a name="23146"><span class="lineNum">   23146 </span><span class="lineNoCov">          0 :         c__ = rhoinv + psi + phi;</span></a>
+<a name="23147"><span class="lineNum">   23147 </span><span class="lineNoCov">          0 :         w = c__ + z__[*i__] * z__[*i__] / (work[*i__] * delta[*i__]) + z__[</span></a>
+<a name="23148"><span class="lineNum">   23148 </span><span class="lineNoCov">          0 :                 ip1] * z__[ip1] / (work[ip1] * delta[ip1]);</span></a>
+<a name="23149"><span class="lineNum">   23149 </span>            : </a>
+<a name="23150"><span class="lineNum">   23150 </span><span class="lineNoCov">          0 :         if (w &gt; 0.) {</span></a>
+<a name="23151"><span class="lineNum">   23151 </span>            : </a>
+<a name="23152"><span class="lineNum">   23152 </span><span class="lineNoCov">          0 :             orgati = 1;</span></a>
+<a name="23153"><span class="lineNum">   23153 </span>            :             sg2lb = 0.;</a>
+<a name="23154"><span class="lineNum">   23154 </span>            :             sg2ub = delsq2;</a>
+<a name="23155"><span class="lineNum">   23155 </span><span class="lineNoCov">          0 :             a = c__ * delsq + z__[*i__] * z__[*i__] + z__[ip1] * z__[ip1];</span></a>
+<a name="23156"><span class="lineNum">   23156 </span><span class="lineNoCov">          0 :             b = z__[*i__] * z__[*i__] * delsq;</span></a>
+<a name="23157"><span class="lineNum">   23157 </span><span class="lineNoCov">          0 :             if (a &gt; 0.) {</span></a>
+<a name="23158"><span class="lineNum">   23158 </span><span class="lineNoCov">          0 :                 tau = b * 2. / (a +  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="23159"><span class="lineNum">   23159 </span>            :             } else {</a>
+<a name="23160"><span class="lineNum">   23160 </span><span class="lineNoCov">          0 :                 tau = (a -  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="23161"><span class="lineNum">   23161 </span>            :             }</a>
+<a name="23162"><span class="lineNum">   23162 </span><span class="lineNoCov">          0 :             eta = tau / (d__[*i__] +  std::sqrt(d__[*i__] * d__[*i__] + tau));</span></a>
+<a name="23163"><span class="lineNum">   23163 </span>            :         } else {</a>
+<a name="23164"><span class="lineNum">   23164 </span>            : </a>
+<a name="23165"><span class="lineNum">   23165 </span><span class="lineNoCov">          0 :             orgati = 0;</span></a>
+<a name="23166"><span class="lineNum">   23166 </span><span class="lineNoCov">          0 :             sg2lb = -delsq2;</span></a>
+<a name="23167"><span class="lineNum">   23167 </span>            :             sg2ub = 0.;</a>
+<a name="23168"><span class="lineNum">   23168 </span><span class="lineNoCov">          0 :             a = c__ * delsq - z__[*i__] * z__[*i__] - z__[ip1] * z__[ip1];</span></a>
+<a name="23169"><span class="lineNum">   23169 </span><span class="lineNoCov">          0 :             b = z__[ip1] * z__[ip1] * delsq;</span></a>
+<a name="23170"><span class="lineNum">   23170 </span><span class="lineNoCov">          0 :             if (a &lt; 0.) {</span></a>
+<a name="23171"><span class="lineNum">   23171 </span><span class="lineNoCov">          0 :                 tau = b * 2. / (a -  std::sqrt(std::abs(a * a + b * 4. * c__)));</span></a>
+<a name="23172"><span class="lineNum">   23172 </span>            :             } else {</a>
+<a name="23173"><span class="lineNum">   23173 </span><span class="lineNoCov">          0 :                 tau = -(a +  std::sqrt(std::abs(a * a + b * 4. * c__))) /       (c__ * 2.);</span></a>
+<a name="23174"><span class="lineNum">   23174 </span>            :             }</a>
+<a name="23175"><span class="lineNum">   23175 </span><span class="lineNoCov">          0 :             eta = tau / (d__[ip1] +  std::sqrt(std::abs(d__[ip1] * d__[ip1] + tau)));</span></a>
+<a name="23176"><span class="lineNum">   23176 </span>            :         }</a>
+<a name="23177"><span class="lineNum">   23177 </span>            : </a>
+<a name="23178"><span class="lineNum">   23178 </span><span class="lineNoCov">          0 :         if (orgati) {</span></a>
+<a name="23179"><span class="lineNum">   23179 </span><span class="lineNoCov">          0 :             ii = *i__;</span></a>
+<a name="23180"><span class="lineNum">   23180 </span><span class="lineNoCov">          0 :             *sigma = d__[*i__] + eta;</span></a>
+<a name="23181"><span class="lineNum">   23181 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="23182"><span class="lineNum">   23182 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23183"><span class="lineNum">   23183 </span><span class="lineNoCov">          0 :                 work[j] = d__[j] + d__[*i__] + eta;</span></a>
+<a name="23184"><span class="lineNum">   23184 </span><span class="lineNoCov">          0 :                 delta[j] = d__[j] - d__[*i__] - eta;</span></a>
+<a name="23185"><span class="lineNum">   23185 </span>            :             }</a>
+<a name="23186"><span class="lineNum">   23186 </span>            :         } else {</a>
+<a name="23187"><span class="lineNum">   23187 </span><span class="lineNoCov">          0 :             ii = *i__ + 1;</span></a>
+<a name="23188"><span class="lineNum">   23188 </span><span class="lineNoCov">          0 :             *sigma = d__[ip1] + eta;</span></a>
+<a name="23189"><span class="lineNum">   23189 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="23190"><span class="lineNum">   23190 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23191"><span class="lineNum">   23191 </span><span class="lineNoCov">          0 :                 work[j] = d__[j] + d__[ip1] + eta;</span></a>
+<a name="23192"><span class="lineNum">   23192 </span><span class="lineNoCov">          0 :                 delta[j] = d__[j] - d__[ip1] - eta;</span></a>
+<a name="23193"><span class="lineNum">   23193 </span>            :             }</a>
+<a name="23194"><span class="lineNum">   23194 </span>            :         }</a>
+<a name="23195"><span class="lineNum">   23195 </span><span class="lineNoCov">          0 :         iim1 = ii - 1;</span></a>
+<a name="23196"><span class="lineNum">   23196 </span><span class="lineNoCov">          0 :         iip1 = ii + 1;</span></a>
+<a name="23197"><span class="lineNum">   23197 </span>            : </a>
+<a name="23198"><span class="lineNum">   23198 </span>            :         dpsi = 0.;</a>
+<a name="23199"><span class="lineNum">   23199 </span>            :         psi = 0.;</a>
+<a name="23200"><span class="lineNum">   23200 </span>            :         erretm = 0.;</a>
+<a name="23201"><span class="lineNum">   23201 </span>            :         i__1 = iim1;</a>
+<a name="23202"><span class="lineNum">   23202 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23203"><span class="lineNum">   23203 </span><span class="lineNoCov">          0 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23204"><span class="lineNum">   23204 </span><span class="lineNoCov">          0 :             psi += z__[j] * temp;</span></a>
+<a name="23205"><span class="lineNum">   23205 </span><span class="lineNoCov">          0 :             dpsi += temp * temp;</span></a>
+<a name="23206"><span class="lineNum">   23206 </span><span class="lineNoCov">          0 :             erretm += psi;</span></a>
+<a name="23207"><span class="lineNum">   23207 </span>            :         }</a>
+<a name="23208"><span class="lineNum">   23208 </span>            :         erretm = std::abs(erretm);</a>
+<a name="23209"><span class="lineNum">   23209 </span>            : </a>
+<a name="23210"><span class="lineNum">   23210 </span>            :         dphi = 0.;</a>
+<a name="23211"><span class="lineNum">   23211 </span>            :         phi = 0.;</a>
+<a name="23212"><span class="lineNum">   23212 </span>            :         i__1 = iip1;</a>
+<a name="23213"><span class="lineNum">   23213 </span><span class="lineNoCov">          0 :         for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="23214"><span class="lineNum">   23214 </span><span class="lineNoCov">          0 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23215"><span class="lineNum">   23215 </span><span class="lineNoCov">          0 :             phi += z__[j] * temp;</span></a>
+<a name="23216"><span class="lineNum">   23216 </span><span class="lineNoCov">          0 :             dphi += temp * temp;</span></a>
+<a name="23217"><span class="lineNum">   23217 </span><span class="lineNoCov">          0 :             erretm += phi;</span></a>
+<a name="23218"><span class="lineNum">   23218 </span>            :         }</a>
+<a name="23219"><span class="lineNum">   23219 </span>            : </a>
+<a name="23220"><span class="lineNum">   23220 </span><span class="lineNoCov">          0 :         w = rhoinv + phi + psi;</span></a>
+<a name="23221"><span class="lineNum">   23221 </span>            : </a>
+<a name="23222"><span class="lineNum">   23222 </span>            :         swtch3 = 0;</a>
+<a name="23223"><span class="lineNum">   23223 </span><span class="lineNoCov">          0 :         if (orgati) {</span></a>
+<a name="23224"><span class="lineNum">   23224 </span><span class="lineNoCov">          0 :             if (w &lt; 0.) {</span></a>
+<a name="23225"><span class="lineNum">   23225 </span>            :                 swtch3 = 1;</a>
+<a name="23226"><span class="lineNum">   23226 </span>            :             }</a>
+<a name="23227"><span class="lineNum">   23227 </span>            :         } else {</a>
+<a name="23228"><span class="lineNum">   23228 </span><span class="lineNoCov">          0 :             if (w &gt; 0.) {</span></a>
+<a name="23229"><span class="lineNum">   23229 </span>            :                 swtch3 = 1;</a>
+<a name="23230"><span class="lineNum">   23230 </span>            :             }</a>
+<a name="23231"><span class="lineNum">   23231 </span>            :         }</a>
+<a name="23232"><span class="lineNum">   23232 </span><span class="lineNoCov">          0 :         if (ii == 1 || ii == *n) {</span></a>
+<a name="23233"><span class="lineNum">   23233 </span>            :             swtch3 = 0;</a>
+<a name="23234"><span class="lineNum">   23234 </span>            :         }</a>
+<a name="23235"><span class="lineNum">   23235 </span>            : </a>
+<a name="23236"><span class="lineNum">   23236 </span><span class="lineNoCov">          0 :         temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="23237"><span class="lineNum">   23237 </span><span class="lineNoCov">          0 :         dw = dpsi + dphi + temp * temp;</span></a>
+<a name="23238"><span class="lineNum">   23238 </span><span class="lineNoCov">          0 :         temp = z__[ii] * temp;</span></a>
+<a name="23239"><span class="lineNum">   23239 </span><span class="lineNoCov">          0 :         w += temp;</span></a>
+<a name="23240"><span class="lineNum">   23240 </span><span class="lineNoCov">          0 :         erretm = (phi - psi) * 8. + erretm + rhoinv * 2. + std::abs(temp) * 3. + </span></a>
+<a name="23241"><span class="lineNum">   23241 </span><span class="lineNoCov">          0 :                 std::abs(tau) * dw;</span></a>
+<a name="23242"><span class="lineNum">   23242 </span>            : </a>
+<a name="23243"><span class="lineNum">   23243 </span><span class="lineNoCov">          0 :         if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="23244"><span class="lineNum">   23244 </span><span class="lineNoCov">          0 :             goto L240;</span></a>
+<a name="23245"><span class="lineNum">   23245 </span>            :         }</a>
+<a name="23246"><span class="lineNum">   23246 </span>            : </a>
+<a name="23247"><span class="lineNum">   23247 </span><span class="lineNoCov">          0 :         if (w &lt;= 0.) {</span></a>
+<a name="23248"><span class="lineNum">   23248 </span><span class="lineNoCov">          0 :             sg2lb = (sg2lb &gt; tau) ? sg2lb : tau;</span></a>
+<a name="23249"><span class="lineNum">   23249 </span>            :         } else {</a>
+<a name="23250"><span class="lineNum">   23250 </span><span class="lineNoCov">          0 :             sg2ub = (sg2ub &lt; tau) ? sg2ub : tau;</span></a>
+<a name="23251"><span class="lineNum">   23251 </span>            :         }</a>
+<a name="23252"><span class="lineNum">   23252 </span>            : </a>
+<a name="23253"><span class="lineNum">   23253 </span><span class="lineNoCov">          0 :         ++niter;</span></a>
+<a name="23254"><span class="lineNum">   23254 </span><span class="lineNoCov">          0 :         if (! swtch3) {</span></a>
+<a name="23255"><span class="lineNum">   23255 </span><span class="lineNoCov">          0 :             dtipsq = work[ip1] * delta[ip1];</span></a>
+<a name="23256"><span class="lineNum">   23256 </span><span class="lineNoCov">          0 :             dtisq = work[*i__] * delta[*i__];</span></a>
+<a name="23257"><span class="lineNum">   23257 </span><span class="lineNoCov">          0 :             if (orgati) {</span></a>
+<a name="23258"><span class="lineNum">   23258 </span><span class="lineNoCov">          0 :                 d__1 = z__[*i__] / dtisq;</span></a>
+<a name="23259"><span class="lineNum">   23259 </span><span class="lineNoCov">          0 :                 c__ = w - dtipsq * dw + delsq * (d__1 * d__1);</span></a>
+<a name="23260"><span class="lineNum">   23260 </span>            :             } else {</a>
+<a name="23261"><span class="lineNum">   23261 </span><span class="lineNoCov">          0 :                 d__1 = z__[ip1] / dtipsq;</span></a>
+<a name="23262"><span class="lineNum">   23262 </span><span class="lineNoCov">          0 :                 c__ = w - dtisq * dw - delsq * (d__1 * d__1);</span></a>
+<a name="23263"><span class="lineNum">   23263 </span>            :             }</a>
+<a name="23264"><span class="lineNum">   23264 </span><span class="lineNoCov">          0 :             a = (dtipsq + dtisq) * w - dtipsq * dtisq * dw;</span></a>
+<a name="23265"><span class="lineNum">   23265 </span><span class="lineNoCov">          0 :             b = dtipsq * dtisq * w;</span></a>
+<a name="23266"><span class="lineNum">   23266 </span><span class="lineNoCov">          0 :             if ( std::abs(c__)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="23267"><span class="lineNum">   23267 </span><span class="lineNoCov">          0 :                 if ( std::abs(a)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="23268"><span class="lineNum">   23268 </span><span class="lineNoCov">          0 :                     if (orgati) {</span></a>
+<a name="23269"><span class="lineNum">   23269 </span><span class="lineNoCov">          0 :                         a = z__[*i__] * z__[*i__] + dtipsq * dtipsq * (dpsi + </span></a>
+<a name="23270"><span class="lineNum">   23270 </span>            :                                 dphi);</a>
+<a name="23271"><span class="lineNum">   23271 </span>            :                     } else {</a>
+<a name="23272"><span class="lineNum">   23272 </span><span class="lineNoCov">          0 :                         a = z__[ip1] * z__[ip1] + dtisq * dtisq * (dpsi + </span></a>
+<a name="23273"><span class="lineNum">   23273 </span>            :                                 dphi);</a>
+<a name="23274"><span class="lineNum">   23274 </span>            :                     }</a>
+<a name="23275"><span class="lineNum">   23275 </span>            :                 }</a>
+<a name="23276"><span class="lineNum">   23276 </span><span class="lineNoCov">          0 :                 eta = b / a;</span></a>
+<a name="23277"><span class="lineNum">   23277 </span><span class="lineNoCov">          0 :             } else if (a &lt;= 0.) {</span></a>
+<a name="23278"><span class="lineNum">   23278 </span><span class="lineNoCov">          0 :                 eta = (a -  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="23279"><span class="lineNum">   23279 </span>            :             } else {</a>
+<a name="23280"><span class="lineNum">   23280 </span><span class="lineNoCov">          0 :                 eta = b * 2. / (a +  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="23281"><span class="lineNum">   23281 </span>            :             }</a>
+<a name="23282"><span class="lineNum">   23282 </span>            :         } else {</a>
+<a name="23283"><span class="lineNum">   23283 </span>            : </a>
+<a name="23284"><span class="lineNum">   23284 </span><span class="lineNoCov">          0 :             dtiim = work[iim1] * delta[iim1];</span></a>
+<a name="23285"><span class="lineNum">   23285 </span><span class="lineNoCov">          0 :             dtiip = work[iip1] * delta[iip1];</span></a>
+<a name="23286"><span class="lineNum">   23286 </span><span class="lineNoCov">          0 :             temp = rhoinv + psi + phi;</span></a>
+<a name="23287"><span class="lineNum">   23287 </span><span class="lineNoCov">          0 :             if (orgati) {</span></a>
+<a name="23288"><span class="lineNum">   23288 </span><span class="lineNoCov">          0 :                 temp1 = z__[iim1] / dtiim;</span></a>
+<a name="23289"><span class="lineNum">   23289 </span><span class="lineNoCov">          0 :                 temp1 *= temp1;</span></a>
+<a name="23290"><span class="lineNum">   23290 </span><span class="lineNoCov">          0 :                 c__ = temp - dtiip * (dpsi + dphi) - (d__[iim1] - d__[iip1]) *</span></a>
+<a name="23291"><span class="lineNum">   23291 </span><span class="lineNoCov">          0 :                          (d__[iim1] + d__[iip1]) * temp1;</span></a>
+<a name="23292"><span class="lineNum">   23292 </span><span class="lineNoCov">          0 :                 zz[0] = z__[iim1] * z__[iim1];</span></a>
+<a name="23293"><span class="lineNum">   23293 </span><span class="lineNoCov">          0 :                 if (dpsi &lt; temp1) {</span></a>
+<a name="23294"><span class="lineNum">   23294 </span><span class="lineNoCov">          0 :                     zz[2] = dtiip * dtiip * dphi;</span></a>
+<a name="23295"><span class="lineNum">   23295 </span>            :                 } else {</a>
+<a name="23296"><span class="lineNum">   23296 </span><span class="lineNoCov">          0 :                     zz[2] = dtiip * dtiip * (dpsi - temp1 + dphi);</span></a>
+<a name="23297"><span class="lineNum">   23297 </span>            :                 }</a>
+<a name="23298"><span class="lineNum">   23298 </span>            :             } else {</a>
+<a name="23299"><span class="lineNum">   23299 </span><span class="lineNoCov">          0 :                 temp1 = z__[iip1] / dtiip;</span></a>
+<a name="23300"><span class="lineNum">   23300 </span><span class="lineNoCov">          0 :                 temp1 *= temp1;</span></a>
+<a name="23301"><span class="lineNum">   23301 </span><span class="lineNoCov">          0 :                 c__ = temp - dtiim * (dpsi + dphi) - (d__[iip1] - d__[iim1]) *</span></a>
+<a name="23302"><span class="lineNum">   23302 </span><span class="lineNoCov">          0 :                          (d__[iim1] + d__[iip1]) * temp1;</span></a>
+<a name="23303"><span class="lineNum">   23303 </span><span class="lineNoCov">          0 :                 if (dphi &lt; temp1) {</span></a>
+<a name="23304"><span class="lineNum">   23304 </span><span class="lineNoCov">          0 :                     zz[0] = dtiim * dtiim * dpsi;</span></a>
+<a name="23305"><span class="lineNum">   23305 </span>            :                 } else {</a>
+<a name="23306"><span class="lineNum">   23306 </span><span class="lineNoCov">          0 :                     zz[0] = dtiim * dtiim * (dpsi + (dphi - temp1));</span></a>
+<a name="23307"><span class="lineNum">   23307 </span>            :                 }</a>
+<a name="23308"><span class="lineNum">   23308 </span><span class="lineNoCov">          0 :                 zz[2] = z__[iip1] * z__[iip1];</span></a>
+<a name="23309"><span class="lineNum">   23309 </span>            :             }</a>
+<a name="23310"><span class="lineNum">   23310 </span><span class="lineNoCov">          0 :             zz[1] = z__[ii] * z__[ii];</span></a>
+<a name="23311"><span class="lineNum">   23311 </span><span class="lineNoCov">          0 :             dd[0] = dtiim;</span></a>
+<a name="23312"><span class="lineNum">   23312 </span><span class="lineNoCov">          0 :             dd[1] = delta[ii] * work[ii];</span></a>
+<a name="23313"><span class="lineNum">   23313 </span><span class="lineNoCov">          0 :             dd[2] = dtiip;</span></a>
+<a name="23314"><span class="lineNum">   23314 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaed6,SLAED6)(&amp;niter, &amp;orgati, &amp;c__, dd, zz, &amp;w, &amp;eta, info);</span></a>
+<a name="23315"><span class="lineNum">   23315 </span><span class="lineNoCov">          0 :             if (*info != 0) {</span></a>
+<a name="23316"><span class="lineNum">   23316 </span><span class="lineNoCov">          0 :                 goto L240;</span></a>
+<a name="23317"><span class="lineNum">   23317 </span>            :             }</a>
+<a name="23318"><span class="lineNum">   23318 </span>            :         }</a>
+<a name="23319"><span class="lineNum">   23319 </span>            : </a>
+<a name="23320"><span class="lineNum">   23320 </span><span class="lineNoCov">          0 :         if (w * eta &gt;= 0.) {</span></a>
+<a name="23321"><span class="lineNum">   23321 </span><span class="lineNoCov">          0 :             eta = -w / dw;</span></a>
+<a name="23322"><span class="lineNum">   23322 </span>            :         }</a>
+<a name="23323"><span class="lineNum">   23323 </span><span class="lineNoCov">          0 :         if (orgati) {</span></a>
+<a name="23324"><span class="lineNum">   23324 </span><span class="lineNoCov">          0 :             temp1 = work[*i__] * delta[*i__];</span></a>
+<a name="23325"><span class="lineNum">   23325 </span><span class="lineNoCov">          0 :             temp = eta - temp1;</span></a>
+<a name="23326"><span class="lineNum">   23326 </span>            :         } else {</a>
+<a name="23327"><span class="lineNum">   23327 </span><span class="lineNoCov">          0 :             temp1 = work[ip1] * delta[ip1];</span></a>
+<a name="23328"><span class="lineNum">   23328 </span><span class="lineNoCov">          0 :             temp = eta - temp1;</span></a>
+<a name="23329"><span class="lineNum">   23329 </span>            :         }</a>
+<a name="23330"><span class="lineNum">   23330 </span><span class="lineNoCov">          0 :         if (temp &gt; sg2ub || temp &lt; sg2lb) {</span></a>
+<a name="23331"><span class="lineNum">   23331 </span><span class="lineNoCov">          0 :             if (w &lt; 0.) {</span></a>
+<a name="23332"><span class="lineNum">   23332 </span><span class="lineNoCov">          0 :                 eta = (sg2ub - tau) / 2.;</span></a>
+<a name="23333"><span class="lineNum">   23333 </span>            :             } else {</a>
+<a name="23334"><span class="lineNum">   23334 </span><span class="lineNoCov">          0 :                 eta = (sg2lb - tau) / 2.;</span></a>
+<a name="23335"><span class="lineNum">   23335 </span>            :             }</a>
+<a name="23336"><span class="lineNum">   23336 </span>            :         }</a>
+<a name="23337"><span class="lineNum">   23337 </span>            : </a>
+<a name="23338"><span class="lineNum">   23338 </span><span class="lineNoCov">          0 :         tau += eta;</span></a>
+<a name="23339"><span class="lineNum">   23339 </span><span class="lineNoCov">          0 :         eta /= *sigma +  std::sqrt(*sigma * *sigma + eta);</span></a>
+<a name="23340"><span class="lineNum">   23340 </span>            : </a>
+<a name="23341"><span class="lineNum">   23341 </span>            :         prew = w;</a>
+<a name="23342"><span class="lineNum">   23342 </span>            : </a>
+<a name="23343"><span class="lineNum">   23343 </span><span class="lineNoCov">          0 :         *sigma += eta;</span></a>
+<a name="23344"><span class="lineNum">   23344 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="23345"><span class="lineNum">   23345 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23346"><span class="lineNum">   23346 </span><span class="lineNoCov">          0 :             work[j] += eta;</span></a>
+<a name="23347"><span class="lineNum">   23347 </span><span class="lineNoCov">          0 :             delta[j] -= eta;</span></a>
+<a name="23348"><span class="lineNum">   23348 </span>            :         }</a>
+<a name="23349"><span class="lineNum">   23349 </span>            : </a>
+<a name="23350"><span class="lineNum">   23350 </span>            :         dpsi = 0.;</a>
+<a name="23351"><span class="lineNum">   23351 </span>            :         psi = 0.;</a>
+<a name="23352"><span class="lineNum">   23352 </span>            :         erretm = 0.;</a>
+<a name="23353"><span class="lineNum">   23353 </span>            :         i__1 = iim1;</a>
+<a name="23354"><span class="lineNum">   23354 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23355"><span class="lineNum">   23355 </span><span class="lineNoCov">          0 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23356"><span class="lineNum">   23356 </span><span class="lineNoCov">          0 :             psi += z__[j] * temp;</span></a>
+<a name="23357"><span class="lineNum">   23357 </span><span class="lineNoCov">          0 :             dpsi += temp * temp;</span></a>
+<a name="23358"><span class="lineNum">   23358 </span><span class="lineNoCov">          0 :             erretm += psi;</span></a>
+<a name="23359"><span class="lineNum">   23359 </span>            :         }</a>
+<a name="23360"><span class="lineNum">   23360 </span>            :         erretm = std::abs(erretm);</a>
+<a name="23361"><span class="lineNum">   23361 </span>            : </a>
+<a name="23362"><span class="lineNum">   23362 </span>            :         dphi = 0.;</a>
+<a name="23363"><span class="lineNum">   23363 </span>            :         phi = 0.;</a>
+<a name="23364"><span class="lineNum">   23364 </span>            :         i__1 = iip1;</a>
+<a name="23365"><span class="lineNum">   23365 </span><span class="lineNoCov">          0 :         for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="23366"><span class="lineNum">   23366 </span><span class="lineNoCov">          0 :             temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23367"><span class="lineNum">   23367 </span><span class="lineNoCov">          0 :             phi += z__[j] * temp;</span></a>
+<a name="23368"><span class="lineNum">   23368 </span><span class="lineNoCov">          0 :             dphi += temp * temp;</span></a>
+<a name="23369"><span class="lineNum">   23369 </span><span class="lineNoCov">          0 :             erretm += phi;</span></a>
+<a name="23370"><span class="lineNum">   23370 </span>            :         }</a>
+<a name="23371"><span class="lineNum">   23371 </span>            : </a>
+<a name="23372"><span class="lineNum">   23372 </span><span class="lineNoCov">          0 :         temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="23373"><span class="lineNum">   23373 </span><span class="lineNoCov">          0 :         dw = dpsi + dphi + temp * temp;</span></a>
+<a name="23374"><span class="lineNum">   23374 </span><span class="lineNoCov">          0 :         temp = z__[ii] * temp;</span></a>
+<a name="23375"><span class="lineNum">   23375 </span><span class="lineNoCov">          0 :         w = rhoinv + phi + psi + temp;</span></a>
+<a name="23376"><span class="lineNum">   23376 </span><span class="lineNoCov">          0 :         erretm = (phi - psi) * 8. + erretm + rhoinv * 2. + std::abs(temp) * 3. + </span></a>
+<a name="23377"><span class="lineNum">   23377 </span><span class="lineNoCov">          0 :                 std::abs(tau) * dw;</span></a>
+<a name="23378"><span class="lineNum">   23378 </span>            : </a>
+<a name="23379"><span class="lineNum">   23379 </span><span class="lineNoCov">          0 :         if (w &lt;= 0.) {</span></a>
+<a name="23380"><span class="lineNum">   23380 </span><span class="lineNoCov">          0 :             sg2lb = (sg2lb &gt; tau) ? sg2lb : tau;</span></a>
+<a name="23381"><span class="lineNum">   23381 </span>            :         } else {</a>
+<a name="23382"><span class="lineNum">   23382 </span><span class="lineNoCov">          0 :             sg2ub = (sg2ub &lt; tau) ? sg2ub : tau;</span></a>
+<a name="23383"><span class="lineNum">   23383 </span>            :         }</a>
+<a name="23384"><span class="lineNum">   23384 </span>            : </a>
+<a name="23385"><span class="lineNum">   23385 </span>            :         swtch = 0;</a>
+<a name="23386"><span class="lineNum">   23386 </span><span class="lineNoCov">          0 :         if (orgati) {</span></a>
+<a name="23387"><span class="lineNum">   23387 </span><span class="lineNoCov">          0 :             if (-w &gt; std::abs(prew) / 10.) {</span></a>
+<a name="23388"><span class="lineNum">   23388 </span>            :                 swtch = 1;</a>
+<a name="23389"><span class="lineNum">   23389 </span>            :             }</a>
+<a name="23390"><span class="lineNum">   23390 </span>            :         } else {</a>
+<a name="23391"><span class="lineNum">   23391 </span><span class="lineNoCov">          0 :             if (w &gt; std::abs(prew) / 10.) {</span></a>
+<a name="23392"><span class="lineNum">   23392 </span>            :                 swtch = 1;</a>
+<a name="23393"><span class="lineNum">   23393 </span>            :             }</a>
+<a name="23394"><span class="lineNum">   23394 </span>            :         }</a>
+<a name="23395"><span class="lineNum">   23395 </span>            : </a>
+<a name="23396"><span class="lineNum">   23396 </span><span class="lineNoCov">          0 :         iter = niter + 1;</span></a>
+<a name="23397"><span class="lineNum">   23397 </span>            : </a>
+<a name="23398"><span class="lineNum">   23398 </span><span class="lineNoCov">          0 :         for (niter = iter; niter &lt;= 20; ++niter) {</span></a>
+<a name="23399"><span class="lineNum">   23399 </span>            : </a>
+<a name="23400"><span class="lineNum">   23400 </span><span class="lineNoCov">          0 :             if (std::abs(w) &lt;= eps * erretm) {</span></a>
+<a name="23401"><span class="lineNum">   23401 </span><span class="lineNoCov">          0 :                 goto L240;</span></a>
+<a name="23402"><span class="lineNum">   23402 </span>            :             }</a>
+<a name="23403"><span class="lineNum">   23403 </span>            : </a>
+<a name="23404"><span class="lineNum">   23404 </span><span class="lineNoCov">          0 :             if (! swtch3) {</span></a>
+<a name="23405"><span class="lineNum">   23405 </span><span class="lineNoCov">          0 :                 dtipsq = work[ip1] * delta[ip1];</span></a>
+<a name="23406"><span class="lineNum">   23406 </span><span class="lineNoCov">          0 :                 dtisq = work[*i__] * delta[*i__];</span></a>
+<a name="23407"><span class="lineNum">   23407 </span><span class="lineNoCov">          0 :                 if (! swtch) {</span></a>
+<a name="23408"><span class="lineNum">   23408 </span><span class="lineNoCov">          0 :                     if (orgati) {</span></a>
+<a name="23409"><span class="lineNum">   23409 </span><span class="lineNoCov">          0 :                         d__1 = z__[*i__] / dtisq;</span></a>
+<a name="23410"><span class="lineNum">   23410 </span><span class="lineNoCov">          0 :                         c__ = w - dtipsq * dw + delsq * (d__1 * d__1);</span></a>
+<a name="23411"><span class="lineNum">   23411 </span>            :                     } else {</a>
+<a name="23412"><span class="lineNum">   23412 </span><span class="lineNoCov">          0 :                         d__1 = z__[ip1] / dtipsq;</span></a>
+<a name="23413"><span class="lineNum">   23413 </span><span class="lineNoCov">          0 :                         c__ = w - dtisq * dw - delsq * (d__1 * d__1);</span></a>
+<a name="23414"><span class="lineNum">   23414 </span>            :                     }</a>
+<a name="23415"><span class="lineNum">   23415 </span>            :                 } else {</a>
+<a name="23416"><span class="lineNum">   23416 </span><span class="lineNoCov">          0 :                     temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="23417"><span class="lineNum">   23417 </span><span class="lineNoCov">          0 :                     if (orgati) {</span></a>
+<a name="23418"><span class="lineNum">   23418 </span><span class="lineNoCov">          0 :                         dpsi += temp * temp;</span></a>
+<a name="23419"><span class="lineNum">   23419 </span>            :                     } else {</a>
+<a name="23420"><span class="lineNum">   23420 </span><span class="lineNoCov">          0 :                         dphi += temp * temp;</span></a>
+<a name="23421"><span class="lineNum">   23421 </span>            :                     }</a>
+<a name="23422"><span class="lineNum">   23422 </span><span class="lineNoCov">          0 :                     c__ = w - dtisq * dpsi - dtipsq * dphi;</span></a>
+<a name="23423"><span class="lineNum">   23423 </span>            :                 }</a>
+<a name="23424"><span class="lineNum">   23424 </span><span class="lineNoCov">          0 :                 a = (dtipsq + dtisq) * w - dtipsq * dtisq * dw;</span></a>
+<a name="23425"><span class="lineNum">   23425 </span><span class="lineNoCov">          0 :                 b = dtipsq * dtisq * w;</span></a>
+<a name="23426"><span class="lineNum">   23426 </span><span class="lineNoCov">          0 :                 if (std::abs(c__)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="23427"><span class="lineNum">   23427 </span><span class="lineNoCov">          0 :                     if (std::abs(a)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="23428"><span class="lineNum">   23428 </span><span class="lineNoCov">          0 :                         if (! swtch) {</span></a>
+<a name="23429"><span class="lineNum">   23429 </span><span class="lineNoCov">          0 :                             if (orgati) {</span></a>
+<a name="23430"><span class="lineNum">   23430 </span><span class="lineNoCov">          0 :                                 a = z__[*i__] * z__[*i__] + dtipsq * dtipsq * </span></a>
+<a name="23431"><span class="lineNum">   23431 </span><span class="lineNoCov">          0 :                                         (dpsi + dphi);</span></a>
+<a name="23432"><span class="lineNum">   23432 </span>            :                             } else {</a>
+<a name="23433"><span class="lineNum">   23433 </span><span class="lineNoCov">          0 :                                 a = z__[ip1] * z__[ip1] + dtisq * dtisq * (</span></a>
+<a name="23434"><span class="lineNum">   23434 </span><span class="lineNoCov">          0 :                                         dpsi + dphi);</span></a>
+<a name="23435"><span class="lineNum">   23435 </span>            :                             }</a>
+<a name="23436"><span class="lineNum">   23436 </span>            :                         } else {</a>
+<a name="23437"><span class="lineNum">   23437 </span><span class="lineNoCov">          0 :                             a = dtisq * dtisq * dpsi + dtipsq * dtipsq * dphi;</span></a>
+<a name="23438"><span class="lineNum">   23438 </span>            :                         }</a>
+<a name="23439"><span class="lineNum">   23439 </span>            :                     }</a>
+<a name="23440"><span class="lineNum">   23440 </span><span class="lineNoCov">          0 :                     eta = b / a;</span></a>
+<a name="23441"><span class="lineNum">   23441 </span><span class="lineNoCov">          0 :                 } else if (a &lt;= 0.) {</span></a>
+<a name="23442"><span class="lineNum">   23442 </span><span class="lineNoCov">          0 :                   eta = (a -  std::sqrt(std::abs(a * a - b * 4. * c__))) / (c__ * 2.);</span></a>
+<a name="23443"><span class="lineNum">   23443 </span>            :                 } else {</a>
+<a name="23444"><span class="lineNum">   23444 </span><span class="lineNoCov">          0 :                   eta = b * 2. / (a +  std::sqrt(std::abs(a * a - b * 4. * c__)));</span></a>
+<a name="23445"><span class="lineNum">   23445 </span>            :                 }</a>
+<a name="23446"><span class="lineNum">   23446 </span>            :             } else {</a>
+<a name="23447"><span class="lineNum">   23447 </span>            : </a>
+<a name="23448"><span class="lineNum">   23448 </span><span class="lineNoCov">          0 :                 dtiim = work[iim1] * delta[iim1];</span></a>
+<a name="23449"><span class="lineNum">   23449 </span><span class="lineNoCov">          0 :                 dtiip = work[iip1] * delta[iip1];</span></a>
+<a name="23450"><span class="lineNum">   23450 </span><span class="lineNoCov">          0 :                 temp = rhoinv + psi + phi;</span></a>
+<a name="23451"><span class="lineNum">   23451 </span><span class="lineNoCov">          0 :                 if (swtch) {</span></a>
+<a name="23452"><span class="lineNum">   23452 </span><span class="lineNoCov">          0 :                     c__ = temp - dtiim * dpsi - dtiip * dphi;</span></a>
+<a name="23453"><span class="lineNum">   23453 </span><span class="lineNoCov">          0 :                     zz[0] = dtiim * dtiim * dpsi;</span></a>
+<a name="23454"><span class="lineNum">   23454 </span><span class="lineNoCov">          0 :                     zz[2] = dtiip * dtiip * dphi;</span></a>
+<a name="23455"><span class="lineNum">   23455 </span>            :                 } else {</a>
+<a name="23456"><span class="lineNum">   23456 </span><span class="lineNoCov">          0 :                     if (orgati) {</span></a>
+<a name="23457"><span class="lineNum">   23457 </span><span class="lineNoCov">          0 :                         temp1 = z__[iim1] / dtiim;</span></a>
+<a name="23458"><span class="lineNum">   23458 </span><span class="lineNoCov">          0 :                         temp1 *= temp1;</span></a>
+<a name="23459"><span class="lineNum">   23459 </span><span class="lineNoCov">          0 :                         temp2 = (d__[iim1] - d__[iip1]) * (d__[iim1] + d__[</span></a>
+<a name="23460"><span class="lineNum">   23460 </span>            :                                 iip1]) * temp1;</a>
+<a name="23461"><span class="lineNum">   23461 </span><span class="lineNoCov">          0 :                         c__ = temp - dtiip * (dpsi + dphi) - temp2;</span></a>
+<a name="23462"><span class="lineNum">   23462 </span><span class="lineNoCov">          0 :                         zz[0] = z__[iim1] * z__[iim1];</span></a>
+<a name="23463"><span class="lineNum">   23463 </span><span class="lineNoCov">          0 :                         if (dpsi &lt; temp1) {</span></a>
+<a name="23464"><span class="lineNum">   23464 </span><span class="lineNoCov">          0 :                             zz[2] = dtiip * dtiip * dphi;</span></a>
+<a name="23465"><span class="lineNum">   23465 </span>            :                         } else {</a>
+<a name="23466"><span class="lineNum">   23466 </span><span class="lineNoCov">          0 :                             zz[2] = dtiip * dtiip * (dpsi - temp1 + dphi);</span></a>
+<a name="23467"><span class="lineNum">   23467 </span>            :                         }</a>
+<a name="23468"><span class="lineNum">   23468 </span>            :                     } else {</a>
+<a name="23469"><span class="lineNum">   23469 </span><span class="lineNoCov">          0 :                         temp1 = z__[iip1] / dtiip;</span></a>
+<a name="23470"><span class="lineNum">   23470 </span><span class="lineNoCov">          0 :                         temp1 *= temp1;</span></a>
+<a name="23471"><span class="lineNum">   23471 </span><span class="lineNoCov">          0 :                         temp2 = (d__[iip1] - d__[iim1]) * (d__[iim1] + d__[</span></a>
+<a name="23472"><span class="lineNum">   23472 </span>            :                                 iip1]) * temp1;</a>
+<a name="23473"><span class="lineNum">   23473 </span><span class="lineNoCov">          0 :                         c__ = temp - dtiim * (dpsi + dphi) - temp2;</span></a>
+<a name="23474"><span class="lineNum">   23474 </span><span class="lineNoCov">          0 :                         if (dphi &lt; temp1) {</span></a>
+<a name="23475"><span class="lineNum">   23475 </span><span class="lineNoCov">          0 :                             zz[0] = dtiim * dtiim * dpsi;</span></a>
+<a name="23476"><span class="lineNum">   23476 </span>            :                         } else {</a>
+<a name="23477"><span class="lineNum">   23477 </span><span class="lineNoCov">          0 :                             zz[0] = dtiim * dtiim * (dpsi + (dphi - temp1));</span></a>
+<a name="23478"><span class="lineNum">   23478 </span>            :                         }</a>
+<a name="23479"><span class="lineNum">   23479 </span><span class="lineNoCov">          0 :                         zz[2] = z__[iip1] * z__[iip1];</span></a>
+<a name="23480"><span class="lineNum">   23480 </span>            :                     }</a>
+<a name="23481"><span class="lineNum">   23481 </span>            :                 }</a>
+<a name="23482"><span class="lineNum">   23482 </span><span class="lineNoCov">          0 :                 dd[0] = dtiim;</span></a>
+<a name="23483"><span class="lineNum">   23483 </span><span class="lineNoCov">          0 :                 dd[1] = delta[ii] * work[ii];</span></a>
+<a name="23484"><span class="lineNum">   23484 </span><span class="lineNoCov">          0 :                 dd[2] = dtiip;</span></a>
+<a name="23485"><span class="lineNum">   23485 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaed6,SLAED6)(&amp;niter, &amp;orgati, &amp;c__, dd, zz, &amp;w, &amp;eta, info);</span></a>
+<a name="23486"><span class="lineNum">   23486 </span><span class="lineNoCov">          0 :                 if (*info != 0) {</span></a>
+<a name="23487"><span class="lineNum">   23487 </span><span class="lineNoCov">          0 :                     goto L240;</span></a>
+<a name="23488"><span class="lineNum">   23488 </span>            :                 }</a>
+<a name="23489"><span class="lineNum">   23489 </span>            :             }</a>
+<a name="23490"><span class="lineNum">   23490 </span>            : </a>
+<a name="23491"><span class="lineNum">   23491 </span><span class="lineNoCov">          0 :             if (w * eta &gt;= 0.) {</span></a>
+<a name="23492"><span class="lineNum">   23492 </span><span class="lineNoCov">          0 :                 eta = -w / dw;</span></a>
+<a name="23493"><span class="lineNum">   23493 </span>            :             }</a>
+<a name="23494"><span class="lineNum">   23494 </span><span class="lineNoCov">          0 :             if (orgati) {</span></a>
+<a name="23495"><span class="lineNum">   23495 </span><span class="lineNoCov">          0 :                 temp1 = work[*i__] * delta[*i__];</span></a>
+<a name="23496"><span class="lineNum">   23496 </span><span class="lineNoCov">          0 :                 temp = eta - temp1;</span></a>
+<a name="23497"><span class="lineNum">   23497 </span>            :             } else {</a>
+<a name="23498"><span class="lineNum">   23498 </span><span class="lineNoCov">          0 :                 temp1 = work[ip1] * delta[ip1];</span></a>
+<a name="23499"><span class="lineNum">   23499 </span><span class="lineNoCov">          0 :                 temp = eta - temp1;</span></a>
+<a name="23500"><span class="lineNum">   23500 </span>            :             }</a>
+<a name="23501"><span class="lineNum">   23501 </span><span class="lineNoCov">          0 :             if (temp &gt; sg2ub || temp &lt; sg2lb) {</span></a>
+<a name="23502"><span class="lineNum">   23502 </span><span class="lineNoCov">          0 :                 if (w &lt; 0.) {</span></a>
+<a name="23503"><span class="lineNum">   23503 </span><span class="lineNoCov">          0 :                     eta = (sg2ub - tau) / 2.;</span></a>
+<a name="23504"><span class="lineNum">   23504 </span>            :                 } else {</a>
+<a name="23505"><span class="lineNum">   23505 </span><span class="lineNoCov">          0 :                     eta = (sg2lb - tau) / 2.;</span></a>
+<a name="23506"><span class="lineNum">   23506 </span>            :                 }</a>
+<a name="23507"><span class="lineNum">   23507 </span>            :             }</a>
+<a name="23508"><span class="lineNum">   23508 </span>            : </a>
+<a name="23509"><span class="lineNum">   23509 </span><span class="lineNoCov">          0 :             tau += eta;</span></a>
+<a name="23510"><span class="lineNum">   23510 </span><span class="lineNoCov">          0 :             eta /= *sigma +  std::sqrt(*sigma * *sigma + eta);</span></a>
+<a name="23511"><span class="lineNum">   23511 </span>            : </a>
+<a name="23512"><span class="lineNum">   23512 </span><span class="lineNoCov">          0 :             *sigma += eta;</span></a>
+<a name="23513"><span class="lineNum">   23513 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="23514"><span class="lineNum">   23514 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23515"><span class="lineNum">   23515 </span><span class="lineNoCov">          0 :                 work[j] += eta;</span></a>
+<a name="23516"><span class="lineNum">   23516 </span><span class="lineNoCov">          0 :                 delta[j] -= eta;</span></a>
+<a name="23517"><span class="lineNum">   23517 </span>            :             }</a>
+<a name="23518"><span class="lineNum">   23518 </span>            : </a>
+<a name="23519"><span class="lineNum">   23519 </span>            :             prew = w;</a>
+<a name="23520"><span class="lineNum">   23520 </span>            : </a>
+<a name="23521"><span class="lineNum">   23521 </span>            :             dpsi = 0.;</a>
+<a name="23522"><span class="lineNum">   23522 </span>            :             psi = 0.;</a>
+<a name="23523"><span class="lineNum">   23523 </span>            :             erretm = 0.;</a>
+<a name="23524"><span class="lineNum">   23524 </span>            :             i__1 = iim1;</a>
+<a name="23525"><span class="lineNum">   23525 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="23526"><span class="lineNum">   23526 </span><span class="lineNoCov">          0 :                 temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23527"><span class="lineNum">   23527 </span><span class="lineNoCov">          0 :                 psi += z__[j] * temp;</span></a>
+<a name="23528"><span class="lineNum">   23528 </span><span class="lineNoCov">          0 :                 dpsi += temp * temp;</span></a>
+<a name="23529"><span class="lineNum">   23529 </span><span class="lineNoCov">          0 :                 erretm += psi;</span></a>
+<a name="23530"><span class="lineNum">   23530 </span>            :             }</a>
+<a name="23531"><span class="lineNum">   23531 </span>            :             erretm = std::abs(erretm);</a>
+<a name="23532"><span class="lineNum">   23532 </span>            : </a>
+<a name="23533"><span class="lineNum">   23533 </span>            :             dphi = 0.;</a>
+<a name="23534"><span class="lineNum">   23534 </span>            :             phi = 0.;</a>
+<a name="23535"><span class="lineNum">   23535 </span>            :             i__1 = iip1;</a>
+<a name="23536"><span class="lineNum">   23536 </span><span class="lineNoCov">          0 :             for (j = *n; j &gt;= i__1; --j) {</span></a>
+<a name="23537"><span class="lineNum">   23537 </span><span class="lineNoCov">          0 :                 temp = z__[j] / (work[j] * delta[j]);</span></a>
+<a name="23538"><span class="lineNum">   23538 </span><span class="lineNoCov">          0 :                 phi += z__[j] * temp;</span></a>
+<a name="23539"><span class="lineNum">   23539 </span><span class="lineNoCov">          0 :                 dphi += temp * temp;</span></a>
+<a name="23540"><span class="lineNum">   23540 </span><span class="lineNoCov">          0 :                 erretm += phi;</span></a>
+<a name="23541"><span class="lineNum">   23541 </span>            :             }</a>
+<a name="23542"><span class="lineNum">   23542 </span>            : </a>
+<a name="23543"><span class="lineNum">   23543 </span><span class="lineNoCov">          0 :             temp = z__[ii] / (work[ii] * delta[ii]);</span></a>
+<a name="23544"><span class="lineNum">   23544 </span><span class="lineNoCov">          0 :             dw = dpsi + dphi + temp * temp;</span></a>
+<a name="23545"><span class="lineNum">   23545 </span><span class="lineNoCov">          0 :             temp = z__[ii] * temp;</span></a>
+<a name="23546"><span class="lineNum">   23546 </span><span class="lineNoCov">          0 :             w = rhoinv + phi + psi + temp;</span></a>
+<a name="23547"><span class="lineNum">   23547 </span><span class="lineNoCov">          0 :             erretm = (phi - psi) * 8. + erretm + rhoinv * 2. + std::abs(temp) * 3. </span></a>
+<a name="23548"><span class="lineNum">   23548 </span><span class="lineNoCov">          0 :                     + std::abs(tau) * dw;</span></a>
+<a name="23549"><span class="lineNum">   23549 </span><span class="lineNoCov">          0 :             if (w * prew &gt; 0. &amp;&amp; std::abs(w) &gt; std::abs(prew) / 10.) {</span></a>
+<a name="23550"><span class="lineNum">   23550 </span><span class="lineNoCov">          0 :                 swtch = ! swtch;</span></a>
+<a name="23551"><span class="lineNum">   23551 </span>            :             }</a>
+<a name="23552"><span class="lineNum">   23552 </span>            : </a>
+<a name="23553"><span class="lineNum">   23553 </span><span class="lineNoCov">          0 :             if (w &lt;= 0.) {</span></a>
+<a name="23554"><span class="lineNum">   23554 </span><span class="lineNoCov">          0 :                 sg2lb = (sg2lb &gt; tau) ? sg2lb : tau;</span></a>
+<a name="23555"><span class="lineNum">   23555 </span>            :             } else {</a>
+<a name="23556"><span class="lineNum">   23556 </span><span class="lineNoCov">          0 :                 sg2ub = (sg2ub &lt; tau) ? sg2ub : tau;</span></a>
+<a name="23557"><span class="lineNum">   23557 </span>            :             }</a>
+<a name="23558"><span class="lineNum">   23558 </span>            :         }</a>
+<a name="23559"><span class="lineNum">   23559 </span>            : </a>
+<a name="23560"><span class="lineNum">   23560 </span><span class="lineNoCov">          0 :         *info = 1;</span></a>
+<a name="23561"><span class="lineNum">   23561 </span>            : </a>
+<a name="23562"><span class="lineNum">   23562 </span>            :     }</a>
+<a name="23563"><span class="lineNum">   23563 </span>            : </a>
+<a name="23564"><span class="lineNum">   23564 </span><span class="lineNoCov">          0 : L240:</span></a>
+<a name="23565"><span class="lineNum">   23565 </span>            :     return;</a>
+<a name="23566"><span class="lineNum">   23566 </span>            : </a>
+<a name="23567"><span class="lineNum">   23567 </span>            : } </a>
+<a name="23568"><span class="lineNum">   23568 </span>            : }</a>
+<a name="23569"><span class="lineNum">   23569 </span>            : }</a>
+<a name="23570"><span class="lineNum">   23570 </span>            : #include &lt;cmath&gt;</a>
+<a name="23571"><span class="lineNum">   23571 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="23572"><span class="lineNum">   23572 </span>            : </a>
+<a name="23573"><span class="lineNum">   23573 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="23574"><span class="lineNum">   23574 </span>            : namespace PLMD{</a>
+<a name="23575"><span class="lineNum">   23575 </span>            : namespace lapack{</a>
+<a name="23576"><span class="lineNum">   23576 </span>            : using namespace blas;</a>
+<a name="23577"><span class="lineNum">   23577 </span>            : void </a>
+<a name="23578"><span class="lineNum">   23578 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd5,SLASD5)(int *i__, </span></a>
+<a name="23579"><span class="lineNum">   23579 </span>            :         float *d__, </a>
+<a name="23580"><span class="lineNum">   23580 </span>            :         float *z__, </a>
+<a name="23581"><span class="lineNum">   23581 </span>            :         float *delta, </a>
+<a name="23582"><span class="lineNum">   23582 </span>            :         float *rho, </a>
+<a name="23583"><span class="lineNum">   23583 </span>            :         float *dsigma, </a>
+<a name="23584"><span class="lineNum">   23584 </span>            :         float *work)</a>
+<a name="23585"><span class="lineNum">   23585 </span>            : {</a>
+<a name="23586"><span class="lineNum">   23586 </span>            :     float b, c__, w, del, tau, delsq;</a>
+<a name="23587"><span class="lineNum">   23587 </span>            : </a>
+<a name="23588"><span class="lineNum">   23588 </span>            :     --work;</a>
+<a name="23589"><span class="lineNum">   23589 </span>            :     --delta;</a>
+<a name="23590"><span class="lineNum">   23590 </span>            :     --z__;</a>
+<a name="23591"><span class="lineNum">   23591 </span>            :     --d__;</a>
+<a name="23592"><span class="lineNum">   23592 </span>            : </a>
+<a name="23593"><span class="lineNum">   23593 </span><span class="lineNoCov">          0 :     del = d__[2] - d__[1];</span></a>
+<a name="23594"><span class="lineNum">   23594 </span><span class="lineNoCov">          0 :     delsq = del * (d__[2] + d__[1]);</span></a>
+<a name="23595"><span class="lineNum">   23595 </span><span class="lineNoCov">          0 :     if (*i__ == 1) {</span></a>
+<a name="23596"><span class="lineNum">   23596 </span><span class="lineNoCov">          0 :         w = *rho * 4. * (z__[2] * z__[2] / (d__[1] + d__[2] * 3.) - z__[1] * </span></a>
+<a name="23597"><span class="lineNum">   23597 </span><span class="lineNoCov">          0 :                 z__[1] / (d__[1] * 3. + d__[2])) / del + 1.;</span></a>
+<a name="23598"><span class="lineNum">   23598 </span><span class="lineNoCov">          0 :         if (w &gt; 0.) {</span></a>
+<a name="23599"><span class="lineNum">   23599 </span><span class="lineNoCov">          0 :             b = delsq + *rho * (z__[1] * z__[1] + z__[2] * z__[2]);</span></a>
+<a name="23600"><span class="lineNum">   23600 </span><span class="lineNoCov">          0 :             c__ = *rho * z__[1] * z__[1] * delsq;</span></a>
+<a name="23601"><span class="lineNum">   23601 </span>            : </a>
+<a name="23602"><span class="lineNum">   23602 </span><span class="lineNoCov">          0 :             tau = c__ * 2. / (b +  std::sqrt(std::abs(b * b - c__ * 4.)));</span></a>
+<a name="23603"><span class="lineNum">   23603 </span>            : </a>
+<a name="23604"><span class="lineNum">   23604 </span><span class="lineNoCov">          0 :             tau /= d__[1] +  std::sqrt(d__[1] * d__[1] + tau);</span></a>
+<a name="23605"><span class="lineNum">   23605 </span><span class="lineNoCov">          0 :             *dsigma = d__[1] + tau;</span></a>
+<a name="23606"><span class="lineNum">   23606 </span><span class="lineNoCov">          0 :             delta[1] = -tau;</span></a>
+<a name="23607"><span class="lineNum">   23607 </span><span class="lineNoCov">          0 :             delta[2] = del - tau;</span></a>
+<a name="23608"><span class="lineNum">   23608 </span><span class="lineNoCov">          0 :             work[1] = d__[1] * 2. + tau;</span></a>
+<a name="23609"><span class="lineNum">   23609 </span><span class="lineNoCov">          0 :             work[2] = d__[1] + tau + d__[2];</span></a>
+<a name="23610"><span class="lineNum">   23610 </span>            :         } else {</a>
+<a name="23611"><span class="lineNum">   23611 </span><span class="lineNoCov">          0 :             b = -delsq + *rho * (z__[1] * z__[1] + z__[2] * z__[2]);</span></a>
+<a name="23612"><span class="lineNum">   23612 </span><span class="lineNoCov">          0 :             c__ = *rho * z__[2] * z__[2] * delsq;</span></a>
+<a name="23613"><span class="lineNum">   23613 </span>            : </a>
+<a name="23614"><span class="lineNum">   23614 </span><span class="lineNoCov">          0 :             if (b &gt; 0.) {</span></a>
+<a name="23615"><span class="lineNum">   23615 </span><span class="lineNoCov">          0 :                 tau = c__ * -2. / (b +  std::sqrt(b * b + c__ * 4.));</span></a>
+<a name="23616"><span class="lineNum">   23616 </span>            :             } else {</a>
+<a name="23617"><span class="lineNum">   23617 </span><span class="lineNoCov">          0 :                 tau = (b -  std::sqrt(b * b + c__ * 4.)) / 2.;</span></a>
+<a name="23618"><span class="lineNum">   23618 </span>            :             }</a>
+<a name="23619"><span class="lineNum">   23619 </span>            : </a>
+<a name="23620"><span class="lineNum">   23620 </span><span class="lineNoCov">          0 :             tau /= d__[2] +  std::sqrt(std::abs(d__[2] * d__[2] + tau));</span></a>
+<a name="23621"><span class="lineNum">   23621 </span><span class="lineNoCov">          0 :             *dsigma = d__[2] + tau;</span></a>
+<a name="23622"><span class="lineNum">   23622 </span><span class="lineNoCov">          0 :             delta[1] = -(del + tau);</span></a>
+<a name="23623"><span class="lineNum">   23623 </span><span class="lineNoCov">          0 :             delta[2] = -tau;</span></a>
+<a name="23624"><span class="lineNum">   23624 </span><span class="lineNoCov">          0 :             work[1] = d__[1] + tau + d__[2];</span></a>
+<a name="23625"><span class="lineNum">   23625 </span><span class="lineNoCov">          0 :             work[2] = d__[2] * 2. + tau;</span></a>
+<a name="23626"><span class="lineNum">   23626 </span>            :         }</a>
+<a name="23627"><span class="lineNum">   23627 </span>            :     } else {</a>
+<a name="23628"><span class="lineNum">   23628 </span>            : </a>
+<a name="23629"><span class="lineNum">   23629 </span><span class="lineNoCov">          0 :         b = -delsq + *rho * (z__[1] * z__[1] + z__[2] * z__[2]);</span></a>
+<a name="23630"><span class="lineNum">   23630 </span><span class="lineNoCov">          0 :         c__ = *rho * z__[2] * z__[2] * delsq;</span></a>
+<a name="23631"><span class="lineNum">   23631 </span>            : </a>
+<a name="23632"><span class="lineNum">   23632 </span><span class="lineNoCov">          0 :         if (b &gt; 0.) {</span></a>
+<a name="23633"><span class="lineNum">   23633 </span><span class="lineNoCov">          0 :             tau = (b +  std::sqrt(b * b + c__ * 4.)) / 2.;</span></a>
+<a name="23634"><span class="lineNum">   23634 </span>            :         } else {</a>
+<a name="23635"><span class="lineNum">   23635 </span><span class="lineNoCov">          0 :             tau = c__ * 2. / (-b +  std::sqrt(b * b + c__ * 4.));</span></a>
+<a name="23636"><span class="lineNum">   23636 </span>            :         }</a>
+<a name="23637"><span class="lineNum">   23637 </span><span class="lineNoCov">          0 :         tau /= d__[2] +  std::sqrt(d__[2] * d__[2] + tau);</span></a>
+<a name="23638"><span class="lineNum">   23638 </span><span class="lineNoCov">          0 :         *dsigma = d__[2] + tau;</span></a>
+<a name="23639"><span class="lineNum">   23639 </span><span class="lineNoCov">          0 :         delta[1] = -(del + tau);</span></a>
+<a name="23640"><span class="lineNum">   23640 </span><span class="lineNoCov">          0 :         delta[2] = -tau;</span></a>
+<a name="23641"><span class="lineNum">   23641 </span><span class="lineNoCov">          0 :         work[1] = d__[1] + tau + d__[2];</span></a>
+<a name="23642"><span class="lineNum">   23642 </span><span class="lineNoCov">          0 :         work[2] = d__[2] * 2. + tau;</span></a>
+<a name="23643"><span class="lineNum">   23643 </span>            :     }</a>
+<a name="23644"><span class="lineNum">   23644 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="23645"><span class="lineNum">   23645 </span>            : </a>
+<a name="23646"><span class="lineNum">   23646 </span>            : } </a>
+<a name="23647"><span class="lineNum">   23647 </span>            : }</a>
+<a name="23648"><span class="lineNum">   23648 </span>            : }</a>
+<a name="23649"><span class="lineNum">   23649 </span>            : #include &lt;cmath&gt;</a>
+<a name="23650"><span class="lineNum">   23650 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="23651"><span class="lineNum">   23651 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="23652"><span class="lineNum">   23652 </span>            : </a>
+<a name="23653"><span class="lineNum">   23653 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="23654"><span class="lineNum">   23654 </span>            : namespace PLMD{</a>
+<a name="23655"><span class="lineNum">   23655 </span>            : namespace lapack{</a>
+<a name="23656"><span class="lineNum">   23656 </span>            : using namespace blas;</a>
+<a name="23657"><span class="lineNum">   23657 </span>            : void </a>
+<a name="23658"><span class="lineNum">   23658 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd6,SLASD6)(int *icompq, </span></a>
+<a name="23659"><span class="lineNum">   23659 </span>            :         int *nl, </a>
+<a name="23660"><span class="lineNum">   23660 </span>            :         int *nr, </a>
+<a name="23661"><span class="lineNum">   23661 </span>            :         int *sqre, </a>
+<a name="23662"><span class="lineNum">   23662 </span>            :         float *d__, </a>
+<a name="23663"><span class="lineNum">   23663 </span>            :         float *vf, </a>
+<a name="23664"><span class="lineNum">   23664 </span>            :         float *vl, </a>
+<a name="23665"><span class="lineNum">   23665 </span>            :         float *alpha, </a>
+<a name="23666"><span class="lineNum">   23666 </span>            :         float *beta, </a>
+<a name="23667"><span class="lineNum">   23667 </span>            :         int *idxq, </a>
+<a name="23668"><span class="lineNum">   23668 </span>            :         int *perm, </a>
+<a name="23669"><span class="lineNum">   23669 </span>            :         int *givptr, </a>
+<a name="23670"><span class="lineNum">   23670 </span>            :         int *givcol, </a>
+<a name="23671"><span class="lineNum">   23671 </span>            :         int *ldgcol, </a>
+<a name="23672"><span class="lineNum">   23672 </span>            :         float *givnum,</a>
+<a name="23673"><span class="lineNum">   23673 </span>            :         int *ldgnum, </a>
+<a name="23674"><span class="lineNum">   23674 </span>            :         float *poles, </a>
+<a name="23675"><span class="lineNum">   23675 </span>            :         float *difl, </a>
+<a name="23676"><span class="lineNum">   23676 </span>            :         float *difr, </a>
+<a name="23677"><span class="lineNum">   23677 </span>            :         float *z__, </a>
+<a name="23678"><span class="lineNum">   23678 </span>            :         int *k, </a>
+<a name="23679"><span class="lineNum">   23679 </span>            :         float *c__, </a>
+<a name="23680"><span class="lineNum">   23680 </span>            :         float *s, </a>
+<a name="23681"><span class="lineNum">   23681 </span>            :         float *work, </a>
+<a name="23682"><span class="lineNum">   23682 </span>            :         int *iwork, </a>
+<a name="23683"><span class="lineNum">   23683 </span>            :         int *info)</a>
+<a name="23684"><span class="lineNum">   23684 </span>            : {</a>
+<a name="23685"><span class="lineNum">   23685 </span>            :     int givcol_dim1, givcol_offset, givnum_dim1, givnum_offset, </a>
+<a name="23686"><span class="lineNum">   23686 </span>            :             poles_dim1, poles_offset, i__1;</a>
+<a name="23687"><span class="lineNum">   23687 </span>            :     float d__1, d__2;</a>
+<a name="23688"><span class="lineNum">   23688 </span>            : </a>
+<a name="23689"><span class="lineNum">   23689 </span>            :     int i__, m, n, n1, n2, iw, idx, idxc, idxp, ivfw, ivlw;</a>
+<a name="23690"><span class="lineNum">   23690 </span>            :     int isigma;</a>
+<a name="23691"><span class="lineNum">   23691 </span>            :     float orgnrm;</a>
+<a name="23692"><span class="lineNum">   23692 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="23693"><span class="lineNum">   23693 </span><span class="lineNoCov">          0 :     float one = 1.0;</span></a>
+<a name="23694"><span class="lineNum">   23694 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="23695"><span class="lineNum">   23695 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="23696"><span class="lineNum">   23696 </span>            : </a>
+<a name="23697"><span class="lineNum">   23697 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="23698"><span class="lineNum">   23698 </span>            :     --vf;</a>
+<a name="23699"><span class="lineNum">   23699 </span>            :     --vl;</a>
+<a name="23700"><span class="lineNum">   23700 </span>            :     --idxq;</a>
+<a name="23701"><span class="lineNum">   23701 </span>            :     --perm;</a>
+<a name="23702"><span class="lineNum">   23702 </span>            :     givcol_dim1 = *ldgcol;</a>
+<a name="23703"><span class="lineNum">   23703 </span>            :     givcol_offset = 1 + givcol_dim1;</a>
+<a name="23704"><span class="lineNum">   23704 </span>            :     givcol -= givcol_offset;</a>
+<a name="23705"><span class="lineNum">   23705 </span><span class="lineNoCov">          0 :     poles_dim1 = *ldgnum;</span></a>
+<a name="23706"><span class="lineNum">   23706 </span><span class="lineNoCov">          0 :     poles_offset = 1 + poles_dim1;</span></a>
+<a name="23707"><span class="lineNum">   23707 </span><span class="lineNoCov">          0 :     poles -= poles_offset;</span></a>
+<a name="23708"><span class="lineNum">   23708 </span>            :     givnum_dim1 = *ldgnum;</a>
+<a name="23709"><span class="lineNum">   23709 </span>            :     givnum_offset = 1 + givnum_dim1;</a>
+<a name="23710"><span class="lineNum">   23710 </span>            :     givnum -= givnum_offset;</a>
+<a name="23711"><span class="lineNum">   23711 </span>            :     --difl;</a>
+<a name="23712"><span class="lineNum">   23712 </span>            :     --difr;</a>
+<a name="23713"><span class="lineNum">   23713 </span>            :     --z__;</a>
+<a name="23714"><span class="lineNum">   23714 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="23715"><span class="lineNum">   23715 </span>            :     --iwork;</a>
+<a name="23716"><span class="lineNum">   23716 </span>            : </a>
+<a name="23717"><span class="lineNum">   23717 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="23718"><span class="lineNum">   23718 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="23719"><span class="lineNum">   23719 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="23720"><span class="lineNum">   23720 </span>            : </a>
+<a name="23721"><span class="lineNum">   23721 </span>            :     isigma = 1;</a>
+<a name="23722"><span class="lineNum">   23722 </span><span class="lineNoCov">          0 :     iw = isigma + n;</span></a>
+<a name="23723"><span class="lineNum">   23723 </span><span class="lineNoCov">          0 :     ivfw = iw + m;</span></a>
+<a name="23724"><span class="lineNum">   23724 </span><span class="lineNoCov">          0 :     ivlw = ivfw + m;</span></a>
+<a name="23725"><span class="lineNum">   23725 </span>            : </a>
+<a name="23726"><span class="lineNum">   23726 </span>            :     idx = 1;</a>
+<a name="23727"><span class="lineNum">   23727 </span>            :     idxc = idx + n;</a>
+<a name="23728"><span class="lineNum">   23728 </span><span class="lineNoCov">          0 :     idxp = idxc + n;</span></a>
+<a name="23729"><span class="lineNum">   23729 </span>            : </a>
+<a name="23730"><span class="lineNum">   23730 </span><span class="lineNoCov">          0 :     d__1 = std::abs(*alpha); </span></a>
+<a name="23731"><span class="lineNum">   23731 </span><span class="lineNoCov">          0 :     d__2 = std::abs(*beta);</span></a>
+<a name="23732"><span class="lineNum">   23732 </span><span class="lineNoCov">          0 :     orgnrm = (d__1 &gt; d__2) ? d__1 : d__2;</span></a>
+<a name="23733"><span class="lineNum">   23733 </span><span class="lineNoCov">          0 :     d__[*nl + 1] = 0.;</span></a>
+<a name="23734"><span class="lineNum">   23734 </span>            :     i__1 = n;</a>
+<a name="23735"><span class="lineNum">   23735 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="23736"><span class="lineNum">   23736 </span><span class="lineNoCov">          0 :       d__1 = std::abs(d__[i__]);</span></a>
+<a name="23737"><span class="lineNum">   23737 </span><span class="lineNoCov">          0 :         if (d__1 &gt; orgnrm)</span></a>
+<a name="23738"><span class="lineNum">   23738 </span><span class="lineNoCov">          0 :             orgnrm = d__1;</span></a>
+<a name="23739"><span class="lineNum">   23739 </span>            :     }</a>
+<a name="23740"><span class="lineNum">   23740 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;orgnrm, &amp;one, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="23741"><span class="lineNum">   23741 </span><span class="lineNoCov">          0 :     *alpha /= orgnrm;</span></a>
+<a name="23742"><span class="lineNum">   23742 </span><span class="lineNoCov">          0 :     *beta /= orgnrm;</span></a>
+<a name="23743"><span class="lineNum">   23743 </span>            : </a>
+<a name="23744"><span class="lineNum">   23744 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasd7,SLASD7)(icompq, nl, nr, sqre, k, &amp;d__[1], &amp;z__[1], &amp;work[iw], &amp;vf[1], &amp;</span></a>
+<a name="23745"><span class="lineNum">   23745 </span><span class="lineNoCov">          0 :             work[ivfw], &amp;vl[1], &amp;work[ivlw], alpha, beta, &amp;work[isigma], &amp;</span></a>
+<a name="23746"><span class="lineNum">   23746 </span><span class="lineNoCov">          0 :             iwork[idx], &amp;iwork[idxp], &amp;idxq[1], &amp;perm[1], givptr, &amp;givcol[</span></a>
+<a name="23747"><span class="lineNum">   23747 </span>            :             givcol_offset], ldgcol, &amp;givnum[givnum_offset], ldgnum, c__, s, </a>
+<a name="23748"><span class="lineNum">   23748 </span>            :             info);</a>
+<a name="23749"><span class="lineNum">   23749 </span>            : </a>
+<a name="23750"><span class="lineNum">   23750 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasd8,SLASD8)(icompq, k, &amp;d__[1], &amp;z__[1], &amp;vf[1], &amp;vl[1], &amp;difl[1], &amp;difr[1], </span></a>
+<a name="23751"><span class="lineNum">   23751 </span>            :             ldgnum, &amp;work[isigma], &amp;work[iw], info);</a>
+<a name="23752"><span class="lineNum">   23752 </span>            : </a>
+<a name="23753"><span class="lineNum">   23753 </span><span class="lineNoCov">          0 :     if (*icompq == 1) {</span></a>
+<a name="23754"><span class="lineNum">   23754 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(k, &amp;d__[1], &amp;c__1, &amp;poles[poles_dim1 + 1], &amp;c__1);</span></a>
+<a name="23755"><span class="lineNum">   23755 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(k, &amp;work[isigma], &amp;c__1, &amp;poles[(poles_dim1 &lt;&lt; 1) + 1], &amp;c__1);</span></a>
+<a name="23756"><span class="lineNum">   23756 </span>            :     }</a>
+<a name="23757"><span class="lineNum">   23757 </span>            : </a>
+<a name="23758"><span class="lineNum">   23758 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;one, &amp;orgnrm, &amp;n, &amp;c__1, &amp;d__[1], &amp;n, info);</span></a>
+<a name="23759"><span class="lineNum">   23759 </span>            : </a>
+<a name="23760"><span class="lineNum">   23760 </span><span class="lineNoCov">          0 :     n1 = *k;</span></a>
+<a name="23761"><span class="lineNum">   23761 </span><span class="lineNoCov">          0 :     n2 = n - *k;</span></a>
+<a name="23762"><span class="lineNum">   23762 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slamrg,SLAMRG)(&amp;n1, &amp;n2, &amp;d__[1], &amp;c__1, &amp;c_n1, &amp;idxq[1]);</span></a>
+<a name="23763"><span class="lineNum">   23763 </span>            : </a>
+<a name="23764"><span class="lineNum">   23764 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="23765"><span class="lineNum">   23765 </span>            : </a>
+<a name="23766"><span class="lineNum">   23766 </span>            : }</a>
+<a name="23767"><span class="lineNum">   23767 </span>            : </a>
+<a name="23768"><span class="lineNum">   23768 </span>            : </a>
+<a name="23769"><span class="lineNum">   23769 </span>            : }</a>
+<a name="23770"><span class="lineNum">   23770 </span>            : }</a>
+<a name="23771"><span class="lineNum">   23771 </span>            : #include &lt;cmath&gt;</a>
+<a name="23772"><span class="lineNum">   23772 </span>            : #include &quot;real.h&quot;</a>
+<a name="23773"><span class="lineNum">   23773 </span>            : </a>
+<a name="23774"><span class="lineNum">   23774 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="23775"><span class="lineNum">   23775 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="23776"><span class="lineNum">   23776 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="23777"><span class="lineNum">   23777 </span>            : </a>
+<a name="23778"><span class="lineNum">   23778 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="23779"><span class="lineNum">   23779 </span>            : namespace PLMD{</a>
+<a name="23780"><span class="lineNum">   23780 </span>            : namespace lapack{</a>
+<a name="23781"><span class="lineNum">   23781 </span>            : using namespace blas;</a>
+<a name="23782"><span class="lineNum">   23782 </span>            : void </a>
+<a name="23783"><span class="lineNum">   23783 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd7,SLASD7)(int *icompq, </span></a>
+<a name="23784"><span class="lineNum">   23784 </span>            :         int *nl, </a>
+<a name="23785"><span class="lineNum">   23785 </span>            :         int *nr, </a>
+<a name="23786"><span class="lineNum">   23786 </span>            :         int *sqre, </a>
+<a name="23787"><span class="lineNum">   23787 </span>            :         int *k, </a>
+<a name="23788"><span class="lineNum">   23788 </span>            :         float *d__, </a>
+<a name="23789"><span class="lineNum">   23789 </span>            :         float *z__, </a>
+<a name="23790"><span class="lineNum">   23790 </span>            :         float *zw, </a>
+<a name="23791"><span class="lineNum">   23791 </span>            :         float *vf, </a>
+<a name="23792"><span class="lineNum">   23792 </span>            :         float *vfw,</a>
+<a name="23793"><span class="lineNum">   23793 </span>            :         float *vl, </a>
+<a name="23794"><span class="lineNum">   23794 </span>            :         float *vlw,</a>
+<a name="23795"><span class="lineNum">   23795 </span>            :         float *alpha, </a>
+<a name="23796"><span class="lineNum">   23796 </span>            :         float *beta,</a>
+<a name="23797"><span class="lineNum">   23797 </span>            :         float *dsigma, </a>
+<a name="23798"><span class="lineNum">   23798 </span>            :         int *idx, </a>
+<a name="23799"><span class="lineNum">   23799 </span>            :         int *idxp,</a>
+<a name="23800"><span class="lineNum">   23800 </span>            :         int *idxq, </a>
+<a name="23801"><span class="lineNum">   23801 </span>            :         int *perm, </a>
+<a name="23802"><span class="lineNum">   23802 </span>            :         int *givptr,</a>
+<a name="23803"><span class="lineNum">   23803 </span>            :         int *givcol, </a>
+<a name="23804"><span class="lineNum">   23804 </span>            :         int *ldgcol, </a>
+<a name="23805"><span class="lineNum">   23805 </span>            :         float *givnum,</a>
+<a name="23806"><span class="lineNum">   23806 </span>            :         int *ldgnum, </a>
+<a name="23807"><span class="lineNum">   23807 </span>            :         float *c__, </a>
+<a name="23808"><span class="lineNum">   23808 </span>            :         float *s, </a>
+<a name="23809"><span class="lineNum">   23809 </span>            :         int *info)</a>
+<a name="23810"><span class="lineNum">   23810 </span>            : {</a>
+<a name="23811"><span class="lineNum">   23811 </span>            :     int givcol_dim1, givcol_offset, givnum_dim1, givnum_offset, i__1;</a>
+<a name="23812"><span class="lineNum">   23812 </span>            :     float d__1, d__2;</a>
+<a name="23813"><span class="lineNum">   23813 </span>            : </a>
+<a name="23814"><span class="lineNum">   23814 </span>            :     int i__, j, m, n, k2;</a>
+<a name="23815"><span class="lineNum">   23815 </span>            :     float z1;</a>
+<a name="23816"><span class="lineNum">   23816 </span>            :     int jp;</a>
+<a name="23817"><span class="lineNum">   23817 </span>            :     float eps, tau, tol;</a>
+<a name="23818"><span class="lineNum">   23818 </span>            :     int nlp1, nlp2, idxi, idxj;</a>
+<a name="23819"><span class="lineNum">   23819 </span>            :     int idxjp;</a>
+<a name="23820"><span class="lineNum">   23820 </span>            :     int jprev = 0;</a>
+<a name="23821"><span class="lineNum">   23821 </span>            :     float hlftol;</a>
+<a name="23822"><span class="lineNum">   23822 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="23823"><span class="lineNum">   23823 </span>            : </a>
+<a name="23824"><span class="lineNum">   23824 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="23825"><span class="lineNum">   23825 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="23826"><span class="lineNum">   23826 </span><span class="lineNoCov">          0 :     --zw;</span></a>
+<a name="23827"><span class="lineNum">   23827 </span><span class="lineNoCov">          0 :     --vf;</span></a>
+<a name="23828"><span class="lineNum">   23828 </span><span class="lineNoCov">          0 :     --vfw;</span></a>
+<a name="23829"><span class="lineNum">   23829 </span><span class="lineNoCov">          0 :     --vl;</span></a>
+<a name="23830"><span class="lineNum">   23830 </span><span class="lineNoCov">          0 :     --vlw;</span></a>
+<a name="23831"><span class="lineNum">   23831 </span><span class="lineNoCov">          0 :     --dsigma;</span></a>
+<a name="23832"><span class="lineNum">   23832 </span><span class="lineNoCov">          0 :     --idx;</span></a>
+<a name="23833"><span class="lineNum">   23833 </span><span class="lineNoCov">          0 :     --idxp;</span></a>
+<a name="23834"><span class="lineNum">   23834 </span><span class="lineNoCov">          0 :     --idxq;</span></a>
+<a name="23835"><span class="lineNum">   23835 </span><span class="lineNoCov">          0 :     --perm;</span></a>
+<a name="23836"><span class="lineNum">   23836 </span><span class="lineNoCov">          0 :     givcol_dim1 = *ldgcol;</span></a>
+<a name="23837"><span class="lineNum">   23837 </span><span class="lineNoCov">          0 :     givcol_offset = 1 + givcol_dim1;</span></a>
+<a name="23838"><span class="lineNum">   23838 </span><span class="lineNoCov">          0 :     givcol -= givcol_offset;</span></a>
+<a name="23839"><span class="lineNum">   23839 </span><span class="lineNoCov">          0 :     givnum_dim1 = *ldgnum;</span></a>
+<a name="23840"><span class="lineNum">   23840 </span><span class="lineNoCov">          0 :     givnum_offset = 1 + givnum_dim1;</span></a>
+<a name="23841"><span class="lineNum">   23841 </span><span class="lineNoCov">          0 :     givnum -= givnum_offset;</span></a>
+<a name="23842"><span class="lineNum">   23842 </span>            : </a>
+<a name="23843"><span class="lineNum">   23843 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="23844"><span class="lineNum">   23844 </span><span class="lineNoCov">          0 :     n = *nl + *nr + 1;</span></a>
+<a name="23845"><span class="lineNum">   23845 </span><span class="lineNoCov">          0 :     m = n + *sqre;</span></a>
+<a name="23846"><span class="lineNum">   23846 </span>            : </a>
+<a name="23847"><span class="lineNum">   23847 </span><span class="lineNoCov">          0 :     nlp1 = *nl + 1;</span></a>
+<a name="23848"><span class="lineNum">   23848 </span><span class="lineNoCov">          0 :     nlp2 = *nl + 2;</span></a>
+<a name="23849"><span class="lineNum">   23849 </span><span class="lineNoCov">          0 :     if (*icompq == 1) {</span></a>
+<a name="23850"><span class="lineNum">   23850 </span><span class="lineNoCov">          0 :         *givptr = 0;</span></a>
+<a name="23851"><span class="lineNum">   23851 </span>            :     }</a>
+<a name="23852"><span class="lineNum">   23852 </span>            : </a>
+<a name="23853"><span class="lineNum">   23853 </span><span class="lineNoCov">          0 :     z1 = *alpha * vl[nlp1];</span></a>
+<a name="23854"><span class="lineNum">   23854 </span><span class="lineNoCov">          0 :     vl[nlp1] = 0.;</span></a>
+<a name="23855"><span class="lineNum">   23855 </span><span class="lineNoCov">          0 :     tau = vf[nlp1];</span></a>
+<a name="23856"><span class="lineNum">   23856 </span><span class="lineNoCov">          0 :     for (i__ = *nl; i__ &gt;= 1; --i__) {</span></a>
+<a name="23857"><span class="lineNum">   23857 </span><span class="lineNoCov">          0 :         z__[i__ + 1] = *alpha * vl[i__];</span></a>
+<a name="23858"><span class="lineNum">   23858 </span><span class="lineNoCov">          0 :         vl[i__] = 0.;</span></a>
+<a name="23859"><span class="lineNum">   23859 </span><span class="lineNoCov">          0 :         vf[i__ + 1] = vf[i__];</span></a>
+<a name="23860"><span class="lineNum">   23860 </span><span class="lineNoCov">          0 :         d__[i__ + 1] = d__[i__];</span></a>
+<a name="23861"><span class="lineNum">   23861 </span><span class="lineNoCov">          0 :         idxq[i__ + 1] = idxq[i__] + 1;</span></a>
+<a name="23862"><span class="lineNum">   23862 </span>            :     }</a>
+<a name="23863"><span class="lineNum">   23863 </span><span class="lineNoCov">          0 :     vf[1] = tau;</span></a>
+<a name="23864"><span class="lineNum">   23864 </span>            : </a>
+<a name="23865"><span class="lineNum">   23865 </span>            :     i__1 = m;</a>
+<a name="23866"><span class="lineNum">   23866 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="23867"><span class="lineNum">   23867 </span><span class="lineNoCov">          0 :         z__[i__] = *beta * vf[i__];</span></a>
+<a name="23868"><span class="lineNum">   23868 </span><span class="lineNoCov">          0 :         vf[i__] = 0.;</span></a>
+<a name="23869"><span class="lineNum">   23869 </span>            :     }</a>
+<a name="23870"><span class="lineNum">   23870 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="23871"><span class="lineNum">   23871 </span><span class="lineNoCov">          0 :     for (i__ = nlp2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="23872"><span class="lineNum">   23872 </span><span class="lineNoCov">          0 :         idxq[i__] += nlp1;</span></a>
+<a name="23873"><span class="lineNum">   23873 </span>            :     }</a>
+<a name="23874"><span class="lineNum">   23874 </span>            : </a>
+<a name="23875"><span class="lineNum">   23875 </span>            :     i__1 = n;</a>
+<a name="23876"><span class="lineNum">   23876 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="23877"><span class="lineNum">   23877 </span><span class="lineNoCov">          0 :         dsigma[i__] = d__[idxq[i__]];</span></a>
+<a name="23878"><span class="lineNum">   23878 </span><span class="lineNoCov">          0 :         zw[i__] = z__[idxq[i__]];</span></a>
+<a name="23879"><span class="lineNum">   23879 </span><span class="lineNoCov">          0 :         vfw[i__] = vf[idxq[i__]];</span></a>
+<a name="23880"><span class="lineNum">   23880 </span><span class="lineNoCov">          0 :         vlw[i__] = vl[idxq[i__]];</span></a>
+<a name="23881"><span class="lineNum">   23881 </span>            :     }</a>
+<a name="23882"><span class="lineNum">   23882 </span>            : </a>
+<a name="23883"><span class="lineNum">   23883 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slamrg,SLAMRG)(nl, nr, &amp;dsigma[2], &amp;c__1, &amp;c__1, &amp;idx[2]);</span></a>
+<a name="23884"><span class="lineNum">   23884 </span>            : </a>
+<a name="23885"><span class="lineNum">   23885 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="23886"><span class="lineNum">   23886 </span><span class="lineNoCov">          0 :     for (i__ = 2; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="23887"><span class="lineNum">   23887 </span><span class="lineNoCov">          0 :         idxi = idx[i__] + 1;</span></a>
+<a name="23888"><span class="lineNum">   23888 </span><span class="lineNoCov">          0 :         d__[i__] = dsigma[idxi];</span></a>
+<a name="23889"><span class="lineNum">   23889 </span><span class="lineNoCov">          0 :         z__[i__] = zw[idxi];</span></a>
+<a name="23890"><span class="lineNum">   23890 </span><span class="lineNoCov">          0 :         vf[i__] = vfw[idxi];</span></a>
+<a name="23891"><span class="lineNum">   23891 </span><span class="lineNoCov">          0 :         vl[i__] = vlw[idxi];</span></a>
+<a name="23892"><span class="lineNum">   23892 </span>            :     }</a>
+<a name="23893"><span class="lineNum">   23893 </span>            : </a>
+<a name="23894"><span class="lineNum">   23894 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="23895"><span class="lineNum">   23895 </span>            : </a>
+<a name="23896"><span class="lineNum">   23896 </span><span class="lineNoCov">          0 :     d__1 = std::abs(*alpha);</span></a>
+<a name="23897"><span class="lineNum">   23897 </span><span class="lineNoCov">          0 :     d__2 = std::abs(*beta);</span></a>
+<a name="23898"><span class="lineNum">   23898 </span><span class="lineNoCov">          0 :     tol = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="23899"><span class="lineNum">   23899 </span><span class="lineNoCov">          0 :     d__2 = std::abs(d__[n]);</span></a>
+<a name="23900"><span class="lineNum">   23900 </span><span class="lineNoCov">          0 :     tol = eps * 64. * ((d__2&gt;tol) ? d__2 : tol);</span></a>
+<a name="23901"><span class="lineNum">   23901 </span>            : </a>
+<a name="23902"><span class="lineNum">   23902 </span><span class="lineNoCov">          0 :     *k = 1;</span></a>
+<a name="23903"><span class="lineNum">   23903 </span><span class="lineNoCov">          0 :     k2 = n + 1;</span></a>
+<a name="23904"><span class="lineNum">   23904 </span>            :     i__1 = n;</a>
+<a name="23905"><span class="lineNum">   23905 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="23906"><span class="lineNum">   23906 </span><span class="lineNoCov">          0 :         if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="23907"><span class="lineNum">   23907 </span>            : </a>
+<a name="23908"><span class="lineNum">   23908 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="23909"><span class="lineNum">   23909 </span><span class="lineNoCov">          0 :             idxp[k2] = j;</span></a>
+<a name="23910"><span class="lineNum">   23910 </span><span class="lineNoCov">          0 :             if (j == n) {</span></a>
+<a name="23911"><span class="lineNum">   23911 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="23912"><span class="lineNum">   23912 </span>            :             }</a>
+<a name="23913"><span class="lineNum">   23913 </span>            :         } else {</a>
+<a name="23914"><span class="lineNum">   23914 </span>            :             jprev = j;</a>
+<a name="23915"><span class="lineNum">   23915 </span><span class="lineNoCov">          0 :             goto L70;</span></a>
+<a name="23916"><span class="lineNum">   23916 </span>            :         }</a>
+<a name="23917"><span class="lineNum">   23917 </span>            :     }</a>
+<a name="23918"><span class="lineNum">   23918 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="23919"><span class="lineNum">   23919 </span>            :     j = jprev;</a>
+<a name="23920"><span class="lineNum">   23920 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="23921"><span class="lineNum">   23921 </span><span class="lineNoCov">          0 :     ++j;</span></a>
+<a name="23922"><span class="lineNum">   23922 </span><span class="lineNoCov">          0 :     if (j &gt; n) {</span></a>
+<a name="23923"><span class="lineNum">   23923 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="23924"><span class="lineNum">   23924 </span>            :     }</a>
+<a name="23925"><span class="lineNum">   23925 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j]) &lt;= tol) {</span></a>
+<a name="23926"><span class="lineNum">   23926 </span>            : </a>
+<a name="23927"><span class="lineNum">   23927 </span><span class="lineNoCov">          0 :         --k2;</span></a>
+<a name="23928"><span class="lineNum">   23928 </span><span class="lineNoCov">          0 :         idxp[k2] = j;</span></a>
+<a name="23929"><span class="lineNum">   23929 </span>            :     } else {</a>
+<a name="23930"><span class="lineNum">   23930 </span>            : </a>
+<a name="23931"><span class="lineNum">   23931 </span><span class="lineNoCov">          0 :         if (std::abs(d__[j] - d__[jprev]) &lt;= tol) {</span></a>
+<a name="23932"><span class="lineNum">   23932 </span>            : </a>
+<a name="23933"><span class="lineNum">   23933 </span><span class="lineNoCov">          0 :             *s = z__[jprev];</span></a>
+<a name="23934"><span class="lineNum">   23934 </span><span class="lineNoCov">          0 :             *c__ = z__[j];</span></a>
+<a name="23935"><span class="lineNum">   23935 </span>            : </a>
+<a name="23936"><span class="lineNum">   23936 </span><span class="lineNoCov">          0 :             tau = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(c__, s);</span></a>
+<a name="23937"><span class="lineNum">   23937 </span><span class="lineNoCov">          0 :             z__[j] = tau;</span></a>
+<a name="23938"><span class="lineNum">   23938 </span><span class="lineNoCov">          0 :             z__[jprev] = 0.;</span></a>
+<a name="23939"><span class="lineNum">   23939 </span><span class="lineNoCov">          0 :             *c__ /= tau;</span></a>
+<a name="23940"><span class="lineNum">   23940 </span><span class="lineNoCov">          0 :             *s = -(*s) / tau;</span></a>
+<a name="23941"><span class="lineNum">   23941 </span>            : </a>
+<a name="23942"><span class="lineNum">   23942 </span>            : </a>
+<a name="23943"><span class="lineNum">   23943 </span><span class="lineNoCov">          0 :             if (*icompq == 1) {</span></a>
+<a name="23944"><span class="lineNum">   23944 </span><span class="lineNoCov">          0 :                 ++(*givptr);</span></a>
+<a name="23945"><span class="lineNum">   23945 </span><span class="lineNoCov">          0 :                 idxjp = idxq[idx[jprev] + 1];</span></a>
+<a name="23946"><span class="lineNum">   23946 </span><span class="lineNoCov">          0 :                 idxj = idxq[idx[j] + 1];</span></a>
+<a name="23947"><span class="lineNum">   23947 </span><span class="lineNoCov">          0 :                 if (idxjp &lt;= nlp1) {</span></a>
+<a name="23948"><span class="lineNum">   23948 </span><span class="lineNoCov">          0 :                     --idxjp;</span></a>
+<a name="23949"><span class="lineNum">   23949 </span>            :                 }</a>
+<a name="23950"><span class="lineNum">   23950 </span><span class="lineNoCov">          0 :                 if (idxj &lt;= nlp1) {</span></a>
+<a name="23951"><span class="lineNum">   23951 </span><span class="lineNoCov">          0 :                     --idxj;</span></a>
+<a name="23952"><span class="lineNum">   23952 </span>            :                 }</a>
+<a name="23953"><span class="lineNum">   23953 </span><span class="lineNoCov">          0 :                 givcol[*givptr + (givcol_dim1 &lt;&lt; 1)] = idxjp;</span></a>
+<a name="23954"><span class="lineNum">   23954 </span><span class="lineNoCov">          0 :                 givcol[*givptr + givcol_dim1] = idxj;</span></a>
+<a name="23955"><span class="lineNum">   23955 </span><span class="lineNoCov">          0 :                 givnum[*givptr + (givnum_dim1 &lt;&lt; 1)] = *c__;</span></a>
+<a name="23956"><span class="lineNum">   23956 </span><span class="lineNoCov">          0 :                 givnum[*givptr + givnum_dim1] = *s;</span></a>
+<a name="23957"><span class="lineNum">   23957 </span>            :             }</a>
+<a name="23958"><span class="lineNum">   23958 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(&amp;c__1, &amp;vf[jprev], &amp;c__1, &amp;vf[j], &amp;c__1, c__, s);</span></a>
+<a name="23959"><span class="lineNum">   23959 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(srot,SROT)(&amp;c__1, &amp;vl[jprev], &amp;c__1, &amp;vl[j], &amp;c__1, c__, s);</span></a>
+<a name="23960"><span class="lineNum">   23960 </span><span class="lineNoCov">          0 :             --k2;</span></a>
+<a name="23961"><span class="lineNum">   23961 </span><span class="lineNoCov">          0 :             idxp[k2] = jprev;</span></a>
+<a name="23962"><span class="lineNum">   23962 </span>            :             jprev = j;</a>
+<a name="23963"><span class="lineNum">   23963 </span>            :         } else {</a>
+<a name="23964"><span class="lineNum">   23964 </span><span class="lineNoCov">          0 :             ++(*k);</span></a>
+<a name="23965"><span class="lineNum">   23965 </span><span class="lineNoCov">          0 :             zw[*k] = z__[jprev];</span></a>
+<a name="23966"><span class="lineNum">   23966 </span><span class="lineNoCov">          0 :             dsigma[*k] = d__[jprev];</span></a>
+<a name="23967"><span class="lineNum">   23967 </span><span class="lineNoCov">          0 :             idxp[*k] = jprev;</span></a>
+<a name="23968"><span class="lineNum">   23968 </span>            :             jprev = j;</a>
+<a name="23969"><span class="lineNum">   23969 </span>            :         }</a>
+<a name="23970"><span class="lineNum">   23970 </span>            :     }</a>
+<a name="23971"><span class="lineNum">   23971 </span><span class="lineNoCov">          0 :     goto L80;</span></a>
+<a name="23972"><span class="lineNum">   23972 </span>            : L90:</a>
+<a name="23973"><span class="lineNum">   23973 </span>            : </a>
+<a name="23974"><span class="lineNum">   23974 </span><span class="lineNoCov">          0 :     ++(*k);</span></a>
+<a name="23975"><span class="lineNum">   23975 </span><span class="lineNoCov">          0 :     zw[*k] = z__[jprev];</span></a>
+<a name="23976"><span class="lineNum">   23976 </span><span class="lineNoCov">          0 :     dsigma[*k] = d__[jprev];</span></a>
+<a name="23977"><span class="lineNum">   23977 </span><span class="lineNoCov">          0 :     idxp[*k] = jprev;</span></a>
+<a name="23978"><span class="lineNum">   23978 </span>            : </a>
+<a name="23979"><span class="lineNum">   23979 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="23980"><span class="lineNum">   23980 </span>            : </a>
+<a name="23981"><span class="lineNum">   23981 </span><span class="lineNoCov">          0 :     i__1 = n;</span></a>
+<a name="23982"><span class="lineNum">   23982 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="23983"><span class="lineNum">   23983 </span><span class="lineNoCov">          0 :         jp = idxp[j];</span></a>
+<a name="23984"><span class="lineNum">   23984 </span><span class="lineNoCov">          0 :         dsigma[j] = d__[jp];</span></a>
+<a name="23985"><span class="lineNum">   23985 </span><span class="lineNoCov">          0 :         vfw[j] = vf[jp];</span></a>
+<a name="23986"><span class="lineNum">   23986 </span><span class="lineNoCov">          0 :         vlw[j] = vl[jp];</span></a>
+<a name="23987"><span class="lineNum">   23987 </span>            :     }</a>
+<a name="23988"><span class="lineNum">   23988 </span><span class="lineNoCov">          0 :     if (*icompq == 1) {</span></a>
+<a name="23989"><span class="lineNum">   23989 </span>            :         i__1 = n;</a>
+<a name="23990"><span class="lineNum">   23990 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="23991"><span class="lineNum">   23991 </span><span class="lineNoCov">          0 :             jp = idxp[j];</span></a>
+<a name="23992"><span class="lineNum">   23992 </span><span class="lineNoCov">          0 :             perm[j] = idxq[idx[jp] + 1];</span></a>
+<a name="23993"><span class="lineNum">   23993 </span><span class="lineNoCov">          0 :             if (perm[j] &lt;= nlp1) {</span></a>
+<a name="23994"><span class="lineNum">   23994 </span><span class="lineNoCov">          0 :                 --perm[j];</span></a>
+<a name="23995"><span class="lineNum">   23995 </span>            :             }</a>
+<a name="23996"><span class="lineNum">   23996 </span>            :         }</a>
+<a name="23997"><span class="lineNum">   23997 </span>            :     }</a>
+<a name="23998"><span class="lineNum">   23998 </span><span class="lineNoCov">          0 :     i__1 = n - *k;</span></a>
+<a name="23999"><span class="lineNum">   23999 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;dsigma[*k + 1], &amp;c__1, &amp;d__[*k + 1], &amp;c__1);</span></a>
+<a name="24000"><span class="lineNum">   24000 </span>            : </a>
+<a name="24001"><span class="lineNum">   24001 </span><span class="lineNoCov">          0 :     dsigma[1] = 0.;</span></a>
+<a name="24002"><span class="lineNum">   24002 </span><span class="lineNoCov">          0 :     hlftol = tol / 2.;</span></a>
+<a name="24003"><span class="lineNum">   24003 </span><span class="lineNoCov">          0 :     if (std::abs(dsigma[2]) &lt;= hlftol) {</span></a>
+<a name="24004"><span class="lineNum">   24004 </span><span class="lineNoCov">          0 :         dsigma[2] = hlftol;</span></a>
+<a name="24005"><span class="lineNum">   24005 </span>            :     }</a>
+<a name="24006"><span class="lineNum">   24006 </span><span class="lineNoCov">          0 :     if (m &gt; n) {</span></a>
+<a name="24007"><span class="lineNum">   24007 </span><span class="lineNoCov">          0 :         z__[1] = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;z1, &amp;z__[m]);</span></a>
+<a name="24008"><span class="lineNum">   24008 </span><span class="lineNoCov">          0 :         if (z__[1] &lt;= tol) {</span></a>
+<a name="24009"><span class="lineNum">   24009 </span><span class="lineNoCov">          0 :             *c__ = 1.;</span></a>
+<a name="24010"><span class="lineNum">   24010 </span><span class="lineNoCov">          0 :             *s = 0.;</span></a>
+<a name="24011"><span class="lineNum">   24011 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="24012"><span class="lineNum">   24012 </span>            :         } else {</a>
+<a name="24013"><span class="lineNum">   24013 </span><span class="lineNoCov">          0 :             *c__ = z1 / z__[1];</span></a>
+<a name="24014"><span class="lineNum">   24014 </span><span class="lineNoCov">          0 :             *s = -z__[m] / z__[1];</span></a>
+<a name="24015"><span class="lineNum">   24015 </span>            :         }</a>
+<a name="24016"><span class="lineNum">   24016 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(srot,SROT)(&amp;c__1, &amp;vf[m], &amp;c__1, &amp;vf[1], &amp;c__1, c__, s);</span></a>
+<a name="24017"><span class="lineNum">   24017 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(srot,SROT)(&amp;c__1, &amp;vl[m], &amp;c__1, &amp;vl[1], &amp;c__1, c__, s);</span></a>
+<a name="24018"><span class="lineNum">   24018 </span>            :     } else {</a>
+<a name="24019"><span class="lineNum">   24019 </span><span class="lineNoCov">          0 :         if (std::abs(z1) &lt;= tol) {</span></a>
+<a name="24020"><span class="lineNum">   24020 </span><span class="lineNoCov">          0 :             z__[1] = tol;</span></a>
+<a name="24021"><span class="lineNum">   24021 </span>            :         } else {</a>
+<a name="24022"><span class="lineNum">   24022 </span><span class="lineNoCov">          0 :             z__[1] = z1;</span></a>
+<a name="24023"><span class="lineNum">   24023 </span>            :         }</a>
+<a name="24024"><span class="lineNum">   24024 </span>            :     }</a>
+<a name="24025"><span class="lineNum">   24025 </span>            : </a>
+<a name="24026"><span class="lineNum">   24026 </span><span class="lineNoCov">          0 :     i__1 = *k - 1;</span></a>
+<a name="24027"><span class="lineNum">   24027 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;zw[2], &amp;c__1, &amp;z__[2], &amp;c__1);</span></a>
+<a name="24028"><span class="lineNum">   24028 </span><span class="lineNoCov">          0 :     i__1 = n - 1;</span></a>
+<a name="24029"><span class="lineNum">   24029 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;vfw[2], &amp;c__1, &amp;vf[2], &amp;c__1);</span></a>
+<a name="24030"><span class="lineNum">   24030 </span><span class="lineNoCov">          0 :     i__1 = n - 1;</span></a>
+<a name="24031"><span class="lineNum">   24031 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;vlw[2], &amp;c__1, &amp;vl[2], &amp;c__1);</span></a>
+<a name="24032"><span class="lineNum">   24032 </span>            : </a>
+<a name="24033"><span class="lineNum">   24033 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="24034"><span class="lineNum">   24034 </span>            : </a>
+<a name="24035"><span class="lineNum">   24035 </span>            : }</a>
+<a name="24036"><span class="lineNum">   24036 </span>            : </a>
+<a name="24037"><span class="lineNum">   24037 </span>            : </a>
+<a name="24038"><span class="lineNum">   24038 </span>            : }</a>
+<a name="24039"><span class="lineNum">   24039 </span>            : }</a>
+<a name="24040"><span class="lineNum">   24040 </span>            : #include &lt;cmath&gt;</a>
+<a name="24041"><span class="lineNum">   24041 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24042"><span class="lineNum">   24042 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24043"><span class="lineNum">   24043 </span>            : </a>
+<a name="24044"><span class="lineNum">   24044 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24045"><span class="lineNum">   24045 </span>            : namespace PLMD{</a>
+<a name="24046"><span class="lineNum">   24046 </span>            : namespace lapack{</a>
+<a name="24047"><span class="lineNum">   24047 </span>            : using namespace blas;</a>
+<a name="24048"><span class="lineNum">   24048 </span>            : void </a>
+<a name="24049"><span class="lineNum">   24049 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasd8,SLASD8)(int *icompq, </span></a>
+<a name="24050"><span class="lineNum">   24050 </span>            :         int *k, </a>
+<a name="24051"><span class="lineNum">   24051 </span>            :         float *d__, </a>
+<a name="24052"><span class="lineNum">   24052 </span>            :         float *z__, </a>
+<a name="24053"><span class="lineNum">   24053 </span>            :         float *vf, </a>
+<a name="24054"><span class="lineNum">   24054 </span>            :         float *vl, </a>
+<a name="24055"><span class="lineNum">   24055 </span>            :         float *difl, </a>
+<a name="24056"><span class="lineNum">   24056 </span>            :         float *difr, </a>
+<a name="24057"><span class="lineNum">   24057 </span>            :         int *lddifr, </a>
+<a name="24058"><span class="lineNum">   24058 </span>            :         float *dsigma, </a>
+<a name="24059"><span class="lineNum">   24059 </span>            :         float *work, </a>
+<a name="24060"><span class="lineNum">   24060 </span>            :         int *info)</a>
+<a name="24061"><span class="lineNum">   24061 </span>            : {</a>
+<a name="24062"><span class="lineNum">   24062 </span>            :     int difr_dim1, difr_offset, i__1, i__2;</a>
+<a name="24063"><span class="lineNum">   24063 </span>            :     float d__2;</a>
+<a name="24064"><span class="lineNum">   24064 </span>            : </a>
+<a name="24065"><span class="lineNum">   24065 </span>            :     int i__, j;</a>
+<a name="24066"><span class="lineNum">   24066 </span>            :     float dj, rho;</a>
+<a name="24067"><span class="lineNum">   24067 </span>            :     int iwk1, iwk2, iwk3;</a>
+<a name="24068"><span class="lineNum">   24068 </span>            :     float temp;</a>
+<a name="24069"><span class="lineNum">   24069 </span>            :     int iwk2i, iwk3i;</a>
+<a name="24070"><span class="lineNum">   24070 </span>            :     float diflj, difrj, dsigj;</a>
+<a name="24071"><span class="lineNum">   24071 </span>            :     float dsigjp;</a>
+<a name="24072"><span class="lineNum">   24072 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="24073"><span class="lineNum">   24073 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="24074"><span class="lineNum">   24074 </span><span class="lineNoCov">          0 :     float one = 1.;</span></a>
+<a name="24075"><span class="lineNum">   24075 </span>            : </a>
+<a name="24076"><span class="lineNum">   24076 </span>            :     /* avoid warnings on high gcc optimization levels */</a>
+<a name="24077"><span class="lineNum">   24077 </span>            :     difrj = dsigjp = 0;</a>
+<a name="24078"><span class="lineNum">   24078 </span>            : </a>
+<a name="24079"><span class="lineNum">   24079 </span><span class="lineNoCov">          0 :      --d__;</span></a>
+<a name="24080"><span class="lineNum">   24080 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="24081"><span class="lineNum">   24081 </span>            :     --vf;</a>
+<a name="24082"><span class="lineNum">   24082 </span>            :     --vl;</a>
+<a name="24083"><span class="lineNum">   24083 </span><span class="lineNoCov">          0 :     --difl;</span></a>
+<a name="24084"><span class="lineNum">   24084 </span><span class="lineNoCov">          0 :     difr_dim1 = *lddifr;</span></a>
+<a name="24085"><span class="lineNum">   24085 </span><span class="lineNoCov">          0 :     difr_offset = 1 + difr_dim1;</span></a>
+<a name="24086"><span class="lineNum">   24086 </span><span class="lineNoCov">          0 :     difr -= difr_offset;</span></a>
+<a name="24087"><span class="lineNum">   24087 </span><span class="lineNoCov">          0 :     --dsigma;</span></a>
+<a name="24088"><span class="lineNum">   24088 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="24089"><span class="lineNum">   24089 </span>            : </a>
+<a name="24090"><span class="lineNum">   24090 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="24091"><span class="lineNum">   24091 </span>            : </a>
+<a name="24092"><span class="lineNum">   24092 </span><span class="lineNoCov">          0 :     if (*k == 1) {</span></a>
+<a name="24093"><span class="lineNum">   24093 </span><span class="lineNoCov">          0 :         d__[1] = std::abs(z__[1]);</span></a>
+<a name="24094"><span class="lineNum">   24094 </span><span class="lineNoCov">          0 :         difl[1] = d__[1];</span></a>
+<a name="24095"><span class="lineNum">   24095 </span><span class="lineNoCov">          0 :         if (*icompq == 1) {</span></a>
+<a name="24096"><span class="lineNum">   24096 </span><span class="lineNoCov">          0 :             difl[2] = 1.;</span></a>
+<a name="24097"><span class="lineNum">   24097 </span><span class="lineNoCov">          0 :             difr[(difr_dim1 &lt;&lt; 1) + 1] = 1.;</span></a>
+<a name="24098"><span class="lineNum">   24098 </span>            :         }</a>
+<a name="24099"><span class="lineNum">   24099 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24100"><span class="lineNum">   24100 </span>            :     }</a>
+<a name="24101"><span class="lineNum">   24101 </span>            : </a>
+<a name="24102"><span class="lineNum">   24102 </span>            :     iwk1 = 1;</a>
+<a name="24103"><span class="lineNum">   24103 </span><span class="lineNoCov">          0 :     iwk2 = iwk1 + *k;</span></a>
+<a name="24104"><span class="lineNum">   24104 </span><span class="lineNoCov">          0 :     iwk3 = iwk2 + *k;</span></a>
+<a name="24105"><span class="lineNum">   24105 </span>            :     iwk2i = iwk2 - 1;</a>
+<a name="24106"><span class="lineNum">   24106 </span><span class="lineNoCov">          0 :     iwk3i = iwk3 - 1;</span></a>
+<a name="24107"><span class="lineNum">   24107 </span>            : </a>
+<a name="24108"><span class="lineNum">   24108 </span><span class="lineNoCov">          0 :     rho = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(k, &amp;z__[1], &amp;c__1);</span></a>
+<a name="24109"><span class="lineNum">   24109 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;rho, &amp;one, k, &amp;c__1, &amp;z__[1], k, info);</span></a>
+<a name="24110"><span class="lineNum">   24110 </span><span class="lineNoCov">          0 :     rho *= rho;</span></a>
+<a name="24111"><span class="lineNum">   24111 </span>            : </a>
+<a name="24112"><span class="lineNum">   24112 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, k, &amp;c__1, &amp;one, &amp;one, &amp;work[iwk3], k);</span></a>
+<a name="24113"><span class="lineNum">   24113 </span>            : </a>
+<a name="24114"><span class="lineNum">   24114 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="24115"><span class="lineNum">   24115 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="24116"><span class="lineNum">   24116 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasd4,SLASD4)(k, &amp;j, &amp;dsigma[1], &amp;z__[1], &amp;work[iwk1], &amp;rho, &amp;d__[j], &amp;work[</span></a>
+<a name="24117"><span class="lineNum">   24117 </span><span class="lineNoCov">          0 :                 iwk2], info);</span></a>
+<a name="24118"><span class="lineNum">   24118 </span>            : </a>
+<a name="24119"><span class="lineNum">   24119 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="24120"><span class="lineNum">   24120 </span>            :             return;</a>
+<a name="24121"><span class="lineNum">   24121 </span>            :         }</a>
+<a name="24122"><span class="lineNum">   24122 </span><span class="lineNoCov">          0 :         work[iwk3i + j] = work[iwk3i + j] * work[j] * work[iwk2i + j];</span></a>
+<a name="24123"><span class="lineNum">   24123 </span><span class="lineNoCov">          0 :         difl[j] = -work[j];</span></a>
+<a name="24124"><span class="lineNum">   24124 </span><span class="lineNoCov">          0 :         difr[j + difr_dim1] = -work[j + 1];</span></a>
+<a name="24125"><span class="lineNum">   24125 </span>            :         i__2 = j - 1;</a>
+<a name="24126"><span class="lineNum">   24126 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="24127"><span class="lineNum">   24127 </span><span class="lineNoCov">          0 :             work[iwk3i + i__] = work[iwk3i + i__] * work[i__] * work[iwk2i + </span></a>
+<a name="24128"><span class="lineNum">   24128 </span><span class="lineNoCov">          0 :                     i__] / (dsigma[i__] - dsigma[j]) / (dsigma[i__] + dsigma[</span></a>
+<a name="24129"><span class="lineNum">   24129 </span>            :                     j]);</a>
+<a name="24130"><span class="lineNum">   24130 </span>            :         }</a>
+<a name="24131"><span class="lineNum">   24131 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="24132"><span class="lineNum">   24132 </span><span class="lineNoCov">          0 :         for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="24133"><span class="lineNum">   24133 </span><span class="lineNoCov">          0 :             work[iwk3i + i__] = work[iwk3i + i__] * work[i__] * work[iwk2i + </span></a>
+<a name="24134"><span class="lineNum">   24134 </span><span class="lineNoCov">          0 :                     i__] / (dsigma[i__] - dsigma[j]) / (dsigma[i__] + dsigma[</span></a>
+<a name="24135"><span class="lineNum">   24135 </span>            :                     j]);</a>
+<a name="24136"><span class="lineNum">   24136 </span>            :         }</a>
+<a name="24137"><span class="lineNum">   24137 </span>            :     }</a>
+<a name="24138"><span class="lineNum">   24138 </span>            : </a>
+<a name="24139"><span class="lineNum">   24139 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="24140"><span class="lineNum">   24140 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="24141"><span class="lineNum">   24141 </span><span class="lineNoCov">          0 :         d__2 =  std::sqrt(std::abs(work[iwk3i + i__]));</span></a>
+<a name="24142"><span class="lineNum">   24142 </span><span class="lineNoCov">          0 :         z__[i__] = (z__[i__] &gt; 0) ? d__2 : -d__2;</span></a>
+<a name="24143"><span class="lineNum">   24143 </span>            :     }</a>
+<a name="24144"><span class="lineNum">   24144 </span>            : </a>
+<a name="24145"><span class="lineNum">   24145 </span><span class="lineNoCov">          0 :     i__1 = *k;</span></a>
+<a name="24146"><span class="lineNum">   24146 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="24147"><span class="lineNum">   24147 </span><span class="lineNoCov">          0 :         diflj = difl[j];</span></a>
+<a name="24148"><span class="lineNum">   24148 </span><span class="lineNoCov">          0 :         dj = d__[j];</span></a>
+<a name="24149"><span class="lineNum">   24149 </span><span class="lineNoCov">          0 :         dsigj = -dsigma[j];</span></a>
+<a name="24150"><span class="lineNum">   24150 </span><span class="lineNoCov">          0 :         if (j &lt; *k) {</span></a>
+<a name="24151"><span class="lineNum">   24151 </span><span class="lineNoCov">          0 :             difrj = -difr[j + difr_dim1];</span></a>
+<a name="24152"><span class="lineNum">   24152 </span><span class="lineNoCov">          0 :             dsigjp = -dsigma[j + 1];</span></a>
+<a name="24153"><span class="lineNum">   24153 </span>            :         }</a>
+<a name="24154"><span class="lineNum">   24154 </span><span class="lineNoCov">          0 :         work[j] = -z__[j] / diflj / (dsigma[j] + dj);</span></a>
+<a name="24155"><span class="lineNum">   24155 </span>            :         i__2 = j - 1;</a>
+<a name="24156"><span class="lineNum">   24156 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="24157"><span class="lineNum">   24157 </span><span class="lineNoCov">          0 :           work[i__] = z__[i__] / (dsigma[i__] + dsigj - diflj) / ( dsigma[i__] + dj);</span></a>
+<a name="24158"><span class="lineNum">   24158 </span>            :         }</a>
+<a name="24159"><span class="lineNum">   24159 </span><span class="lineNoCov">          0 :         i__2 = *k;</span></a>
+<a name="24160"><span class="lineNum">   24160 </span><span class="lineNoCov">          0 :         for (i__ = j + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="24161"><span class="lineNum">   24161 </span><span class="lineNoCov">          0 :             work[i__] = z__[i__] / (dsigma[i__] + dsigjp - difrj) / (dsigma[i__] + dj);</span></a>
+<a name="24162"><span class="lineNum">   24162 </span>            :         }</a>
+<a name="24163"><span class="lineNum">   24163 </span><span class="lineNoCov">          0 :         temp = PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(k, &amp;work[1], &amp;c__1);</span></a>
+<a name="24164"><span class="lineNum">   24164 </span><span class="lineNoCov">          0 :         work[iwk2i + j] = PLUMED_BLAS_F77_FUNC(sdot,SDOT)(k, &amp;work[1], &amp;c__1, &amp;vf[1], &amp;c__1) / temp;</span></a>
+<a name="24165"><span class="lineNum">   24165 </span><span class="lineNoCov">          0 :         work[iwk3i + j] = PLUMED_BLAS_F77_FUNC(sdot,SDOT)(k, &amp;work[1], &amp;c__1, &amp;vl[1], &amp;c__1) / temp;</span></a>
+<a name="24166"><span class="lineNum">   24166 </span><span class="lineNoCov">          0 :         if (*icompq == 1) {</span></a>
+<a name="24167"><span class="lineNum">   24167 </span><span class="lineNoCov">          0 :             difr[j + (difr_dim1 &lt;&lt; 1)] = temp;</span></a>
+<a name="24168"><span class="lineNum">   24168 </span>            :         }</a>
+<a name="24169"><span class="lineNum">   24169 </span>            :     }</a>
+<a name="24170"><span class="lineNum">   24170 </span>            : </a>
+<a name="24171"><span class="lineNum">   24171 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(k, &amp;work[iwk2], &amp;c__1, &amp;vf[1], &amp;c__1);</span></a>
+<a name="24172"><span class="lineNum">   24172 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(k, &amp;work[iwk3], &amp;c__1, &amp;vl[1], &amp;c__1);</span></a>
+<a name="24173"><span class="lineNum">   24173 </span>            : </a>
+<a name="24174"><span class="lineNum">   24174 </span>            :     return;</a>
+<a name="24175"><span class="lineNum">   24175 </span>            : </a>
+<a name="24176"><span class="lineNum">   24176 </span>            : } </a>
+<a name="24177"><span class="lineNum">   24177 </span>            : }</a>
+<a name="24178"><span class="lineNum">   24178 </span>            : }</a>
+<a name="24179"><span class="lineNum">   24179 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24180"><span class="lineNum">   24180 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24181"><span class="lineNum">   24181 </span>            : </a>
+<a name="24182"><span class="lineNum">   24182 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24183"><span class="lineNum">   24183 </span>            : namespace PLMD{</a>
+<a name="24184"><span class="lineNum">   24184 </span>            : namespace lapack{</a>
+<a name="24185"><span class="lineNum">   24185 </span>            : using namespace blas;</a>
+<a name="24186"><span class="lineNum">   24186 </span>            : void </a>
+<a name="24187"><span class="lineNum">   24187 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasda,SLASDA)(int *icompq, </span></a>
+<a name="24188"><span class="lineNum">   24188 </span>            :         int *smlsiz, </a>
+<a name="24189"><span class="lineNum">   24189 </span>            :         int *n, </a>
+<a name="24190"><span class="lineNum">   24190 </span>            :         int *sqre, </a>
+<a name="24191"><span class="lineNum">   24191 </span>            :         float *d__, </a>
+<a name="24192"><span class="lineNum">   24192 </span>            :         float *e, </a>
+<a name="24193"><span class="lineNum">   24193 </span>            :         float *u, </a>
+<a name="24194"><span class="lineNum">   24194 </span>            :         int *ldu, </a>
+<a name="24195"><span class="lineNum">   24195 </span>            :         float *vt, </a>
+<a name="24196"><span class="lineNum">   24196 </span>            :         int *k, </a>
+<a name="24197"><span class="lineNum">   24197 </span>            :         float *difl, </a>
+<a name="24198"><span class="lineNum">   24198 </span>            :         float *difr, </a>
+<a name="24199"><span class="lineNum">   24199 </span>            :         float *z__, </a>
+<a name="24200"><span class="lineNum">   24200 </span>            :         float *poles, </a>
+<a name="24201"><span class="lineNum">   24201 </span>            :         int *givptr, </a>
+<a name="24202"><span class="lineNum">   24202 </span>            :         int *givcol, </a>
+<a name="24203"><span class="lineNum">   24203 </span>            :         int *ldgcol, </a>
+<a name="24204"><span class="lineNum">   24204 </span>            :         int *perm, </a>
+<a name="24205"><span class="lineNum">   24205 </span>            :         float *givnum, </a>
+<a name="24206"><span class="lineNum">   24206 </span>            :         float *c__, </a>
+<a name="24207"><span class="lineNum">   24207 </span>            :         float *s, </a>
+<a name="24208"><span class="lineNum">   24208 </span>            :         float *work, </a>
+<a name="24209"><span class="lineNum">   24209 </span>            :         int *iwork, </a>
+<a name="24210"><span class="lineNum">   24210 </span>            :         int *info)</a>
+<a name="24211"><span class="lineNum">   24211 </span>            : {</a>
+<a name="24212"><span class="lineNum">   24212 </span>            :     int givcol_dim1, givcol_offset, perm_dim1, perm_offset, difl_dim1, </a>
+<a name="24213"><span class="lineNum">   24213 </span>            :             difl_offset, difr_dim1, difr_offset, givnum_dim1, givnum_offset, </a>
+<a name="24214"><span class="lineNum">   24214 </span>            :             poles_dim1, poles_offset, u_dim1, u_offset, vt_dim1, vt_offset, </a>
+<a name="24215"><span class="lineNum">   24215 </span>            :             z_dim1, z_offset, i__1, i__2;</a>
+<a name="24216"><span class="lineNum">   24216 </span>            : </a>
+<a name="24217"><span class="lineNum">   24217 </span>            :     int i__, j, m, i1, ic, lf, nd, ll, nl, vf, nr, vl, im1, ncc, </a>
+<a name="24218"><span class="lineNum">   24218 </span>            :             nlf, nrf, vfi, iwk, vli, lvl, nru, ndb1, nlp1, lvl2, nrp1;</a>
+<a name="24219"><span class="lineNum">   24219 </span>            :     float beta;</a>
+<a name="24220"><span class="lineNum">   24220 </span>            :     int idxq, nlvl;</a>
+<a name="24221"><span class="lineNum">   24221 </span>            :     float alpha;</a>
+<a name="24222"><span class="lineNum">   24222 </span>            :     int inode, ndiml, ndimr, idxqi, itemp;</a>
+<a name="24223"><span class="lineNum">   24223 </span>            :     int sqrei;</a>
+<a name="24224"><span class="lineNum">   24224 </span>            :     int nwork1, nwork2;</a>
+<a name="24225"><span class="lineNum">   24225 </span>            :     int smlszp;</a>
+<a name="24226"><span class="lineNum">   24226 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="24227"><span class="lineNum">   24227 </span><span class="lineNoCov">          0 :     float zero = 0.0;</span></a>
+<a name="24228"><span class="lineNum">   24228 </span><span class="lineNoCov">          0 :     float one = 1.;</span></a>
+<a name="24229"><span class="lineNum">   24229 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="24230"><span class="lineNum">   24230 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="24231"><span class="lineNum">   24231 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="24232"><span class="lineNum">   24232 </span><span class="lineNoCov">          0 :     givnum_dim1 = *ldu;</span></a>
+<a name="24233"><span class="lineNum">   24233 </span><span class="lineNoCov">          0 :     givnum_offset = 1 + givnum_dim1;</span></a>
+<a name="24234"><span class="lineNum">   24234 </span><span class="lineNoCov">          0 :     givnum -= givnum_offset;</span></a>
+<a name="24235"><span class="lineNum">   24235 </span>            :     poles_dim1 = *ldu;</a>
+<a name="24236"><span class="lineNum">   24236 </span>            :     poles_offset = 1 + poles_dim1;</a>
+<a name="24237"><span class="lineNum">   24237 </span>            :     poles -= poles_offset;</a>
+<a name="24238"><span class="lineNum">   24238 </span>            :     z_dim1 = *ldu;</a>
+<a name="24239"><span class="lineNum">   24239 </span>            :     z_offset = 1 + z_dim1;</a>
+<a name="24240"><span class="lineNum">   24240 </span>            :     z__ -= z_offset;</a>
+<a name="24241"><span class="lineNum">   24241 </span>            :     difr_dim1 = *ldu;</a>
+<a name="24242"><span class="lineNum">   24242 </span>            :     difr_offset = 1 + difr_dim1;</a>
+<a name="24243"><span class="lineNum">   24243 </span>            :     difr -= difr_offset;</a>
+<a name="24244"><span class="lineNum">   24244 </span>            :     difl_dim1 = *ldu;</a>
+<a name="24245"><span class="lineNum">   24245 </span>            :     difl_offset = 1 + difl_dim1;</a>
+<a name="24246"><span class="lineNum">   24246 </span>            :     difl -= difl_offset;</a>
+<a name="24247"><span class="lineNum">   24247 </span>            :     vt_dim1 = *ldu;</a>
+<a name="24248"><span class="lineNum">   24248 </span>            :     vt_offset = 1 + vt_dim1;</a>
+<a name="24249"><span class="lineNum">   24249 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="24250"><span class="lineNum">   24250 </span>            :     u_dim1 = *ldu;</a>
+<a name="24251"><span class="lineNum">   24251 </span>            :     u_offset = 1 + u_dim1;</a>
+<a name="24252"><span class="lineNum">   24252 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="24253"><span class="lineNum">   24253 </span>            :     --k;</a>
+<a name="24254"><span class="lineNum">   24254 </span>            :     --givptr;</a>
+<a name="24255"><span class="lineNum">   24255 </span><span class="lineNoCov">          0 :     perm_dim1 = *ldgcol;</span></a>
+<a name="24256"><span class="lineNum">   24256 </span><span class="lineNoCov">          0 :     perm_offset = 1 + perm_dim1;</span></a>
+<a name="24257"><span class="lineNum">   24257 </span><span class="lineNoCov">          0 :     perm -= perm_offset;</span></a>
+<a name="24258"><span class="lineNum">   24258 </span>            :     givcol_dim1 = *ldgcol;</a>
+<a name="24259"><span class="lineNum">   24259 </span>            :     givcol_offset = 1 + givcol_dim1;</a>
+<a name="24260"><span class="lineNum">   24260 </span>            :     givcol -= givcol_offset;</a>
+<a name="24261"><span class="lineNum">   24261 </span>            :     --c__;</a>
+<a name="24262"><span class="lineNum">   24262 </span>            :     --s;</a>
+<a name="24263"><span class="lineNum">   24263 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="24264"><span class="lineNum">   24264 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="24265"><span class="lineNum">   24265 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="24266"><span class="lineNum">   24266 </span>            : </a>
+<a name="24267"><span class="lineNum">   24267 </span><span class="lineNoCov">          0 :     m = *n + *sqre;</span></a>
+<a name="24268"><span class="lineNum">   24268 </span>            : </a>
+<a name="24269"><span class="lineNum">   24269 </span><span class="lineNoCov">          0 :     if (*n &lt;= *smlsiz) {</span></a>
+<a name="24270"><span class="lineNum">   24270 </span><span class="lineNoCov">          0 :         if (*icompq == 0) {</span></a>
+<a name="24271"><span class="lineNum">   24271 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, sqre, n, &amp;c__0, &amp;c__0, &amp;c__0, &amp;d__[1], &amp;e[1], &amp;vt[</span></a>
+<a name="24272"><span class="lineNum">   24272 </span>            :                     vt_offset], ldu, &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;</a>
+<a name="24273"><span class="lineNum">   24273 </span>            :                     work[1], info);</a>
+<a name="24274"><span class="lineNum">   24274 </span>            :         } else {</a>
+<a name="24275"><span class="lineNum">   24275 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, sqre, n, &amp;m, n, &amp;c__0, &amp;d__[1], &amp;e[1], &amp;vt[vt_offset]</span></a>
+<a name="24276"><span class="lineNum">   24276 </span>            :                     , ldu, &amp;u[u_offset], ldu, &amp;u[u_offset], ldu, &amp;work[1], </a>
+<a name="24277"><span class="lineNum">   24277 </span>            :                     info);</a>
+<a name="24278"><span class="lineNum">   24278 </span>            :         }</a>
+<a name="24279"><span class="lineNum">   24279 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24280"><span class="lineNum">   24280 </span>            :     }</a>
+<a name="24281"><span class="lineNum">   24281 </span>            : </a>
+<a name="24282"><span class="lineNum">   24282 </span>            :     inode = 1;</a>
+<a name="24283"><span class="lineNum">   24283 </span><span class="lineNoCov">          0 :     ndiml = inode + *n;</span></a>
+<a name="24284"><span class="lineNum">   24284 </span><span class="lineNoCov">          0 :     ndimr = ndiml + *n;</span></a>
+<a name="24285"><span class="lineNum">   24285 </span><span class="lineNoCov">          0 :     idxq = ndimr + *n;</span></a>
+<a name="24286"><span class="lineNum">   24286 </span><span class="lineNoCov">          0 :     iwk = idxq + *n;</span></a>
+<a name="24287"><span class="lineNum">   24287 </span>            : </a>
+<a name="24288"><span class="lineNum">   24288 </span><span class="lineNoCov">          0 :     ncc = 0;</span></a>
+<a name="24289"><span class="lineNum">   24289 </span><span class="lineNoCov">          0 :     nru = 0;</span></a>
+<a name="24290"><span class="lineNum">   24290 </span>            : </a>
+<a name="24291"><span class="lineNum">   24291 </span><span class="lineNoCov">          0 :     smlszp = *smlsiz + 1;</span></a>
+<a name="24292"><span class="lineNum">   24292 </span>            :     vf = 1;</a>
+<a name="24293"><span class="lineNum">   24293 </span><span class="lineNoCov">          0 :     vl = vf + m;</span></a>
+<a name="24294"><span class="lineNum">   24294 </span><span class="lineNoCov">          0 :     nwork1 = vl + m;</span></a>
+<a name="24295"><span class="lineNum">   24295 </span><span class="lineNoCov">          0 :     nwork2 = nwork1 + smlszp * smlszp;</span></a>
+<a name="24296"><span class="lineNum">   24296 </span>            : </a>
+<a name="24297"><span class="lineNum">   24297 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasdt,SLASDT)(n, &amp;nlvl, &amp;nd, &amp;iwork[inode], &amp;iwork[ndiml], &amp;iwork[ndimr], </span></a>
+<a name="24298"><span class="lineNum">   24298 </span>            :             smlsiz);</a>
+<a name="24299"><span class="lineNum">   24299 </span>            : </a>
+<a name="24300"><span class="lineNum">   24300 </span><span class="lineNoCov">          0 :     ndb1 = (nd + 1) / 2;</span></a>
+<a name="24301"><span class="lineNum">   24301 </span>            :     i__1 = nd;</a>
+<a name="24302"><span class="lineNum">   24302 </span><span class="lineNoCov">          0 :     for (i__ = ndb1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="24303"><span class="lineNum">   24303 </span><span class="lineNoCov">          0 :         i1 = i__ - 1;</span></a>
+<a name="24304"><span class="lineNum">   24304 </span><span class="lineNoCov">          0 :         ic = iwork[inode + i1];</span></a>
+<a name="24305"><span class="lineNum">   24305 </span><span class="lineNoCov">          0 :         nl = iwork[ndiml + i1];</span></a>
+<a name="24306"><span class="lineNum">   24306 </span><span class="lineNoCov">          0 :         nlp1 = nl + 1;</span></a>
+<a name="24307"><span class="lineNum">   24307 </span><span class="lineNoCov">          0 :         nr = iwork[ndimr + i1];</span></a>
+<a name="24308"><span class="lineNum">   24308 </span><span class="lineNoCov">          0 :         nlf = ic - nl;</span></a>
+<a name="24309"><span class="lineNum">   24309 </span><span class="lineNoCov">          0 :         nrf = ic + 1;</span></a>
+<a name="24310"><span class="lineNum">   24310 </span><span class="lineNoCov">          0 :         idxqi = idxq + nlf - 2;</span></a>
+<a name="24311"><span class="lineNum">   24311 </span>            :         vfi = vf + nlf - 1;</a>
+<a name="24312"><span class="lineNum">   24312 </span><span class="lineNoCov">          0 :         vli = vl + nlf - 1;</span></a>
+<a name="24313"><span class="lineNum">   24313 </span><span class="lineNoCov">          0 :         sqrei = 1;</span></a>
+<a name="24314"><span class="lineNum">   24314 </span><span class="lineNoCov">          0 :         if (*icompq == 0) {</span></a>
+<a name="24315"><span class="lineNum">   24315 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;nlp1, &amp;nlp1, &amp;zero, &amp;one, &amp;work[nwork1], &amp;smlszp);</span></a>
+<a name="24316"><span class="lineNum">   24316 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nl, &amp;nlp1, &amp;nru, &amp;ncc, &amp;d__[nlf], &amp;e[nlf], &amp;</span></a>
+<a name="24317"><span class="lineNum">   24317 </span>            :                     work[nwork1], &amp;smlszp, &amp;work[nwork2], &amp;nl, &amp;work[nwork2], </a>
+<a name="24318"><span class="lineNum">   24318 </span><span class="lineNoCov">          0 :                     &amp;nl, &amp;work[nwork2], info);</span></a>
+<a name="24319"><span class="lineNum">   24319 </span><span class="lineNoCov">          0 :             itemp = nwork1 + nl * smlszp;</span></a>
+<a name="24320"><span class="lineNum">   24320 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nlp1, &amp;work[nwork1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="24321"><span class="lineNum">   24321 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nlp1, &amp;work[itemp], &amp;c__1, &amp;work[vli], &amp;c__1);</span></a>
+<a name="24322"><span class="lineNum">   24322 </span>            :         } else {</a>
+<a name="24323"><span class="lineNum">   24323 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;nl, &amp;nl, &amp;zero, &amp;one, &amp;u[nlf + u_dim1], ldu);</span></a>
+<a name="24324"><span class="lineNum">   24324 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;nlp1, &amp;nlp1, &amp;zero, &amp;one, &amp;vt[nlf + vt_dim1], </span></a>
+<a name="24325"><span class="lineNum">   24325 </span>            :                     ldu);</a>
+<a name="24326"><span class="lineNum">   24326 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nl, &amp;nlp1, &amp;nl, &amp;ncc, &amp;d__[nlf], &amp;e[nlf], &amp;</span></a>
+<a name="24327"><span class="lineNum">   24327 </span>            :                     vt[nlf + vt_dim1], ldu, &amp;u[nlf + u_dim1], ldu, &amp;u[nlf + </a>
+<a name="24328"><span class="lineNum">   24328 </span><span class="lineNoCov">          0 :                     u_dim1], ldu, &amp;work[nwork1], info);</span></a>
+<a name="24329"><span class="lineNum">   24329 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nlp1, &amp;vt[nlf + vt_dim1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="24330"><span class="lineNum">   24330 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nlp1, &amp;vt[nlf + nlp1 * vt_dim1], &amp;c__1, &amp;work[vli], &amp;c__1)</span></a>
+<a name="24331"><span class="lineNum">   24331 </span>            :                     ;</a>
+<a name="24332"><span class="lineNum">   24332 </span>            :         }</a>
+<a name="24333"><span class="lineNum">   24333 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="24334"><span class="lineNum">   24334 </span>            :             return;</a>
+<a name="24335"><span class="lineNum">   24335 </span>            :         }</a>
+<a name="24336"><span class="lineNum">   24336 </span><span class="lineNoCov">          0 :         i__2 = nl;</span></a>
+<a name="24337"><span class="lineNum">   24337 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="24338"><span class="lineNum">   24338 </span><span class="lineNoCov">          0 :             iwork[idxqi + j] = j;</span></a>
+<a name="24339"><span class="lineNum">   24339 </span>            :         }</a>
+<a name="24340"><span class="lineNum">   24340 </span><span class="lineNoCov">          0 :         if (i__ == nd &amp;&amp; *sqre == 0) {</span></a>
+<a name="24341"><span class="lineNum">   24341 </span><span class="lineNoCov">          0 :             sqrei = 0;</span></a>
+<a name="24342"><span class="lineNum">   24342 </span>            :         } else {</a>
+<a name="24343"><span class="lineNum">   24343 </span><span class="lineNoCov">          0 :             sqrei = 1;</span></a>
+<a name="24344"><span class="lineNum">   24344 </span>            :         }</a>
+<a name="24345"><span class="lineNum">   24345 </span><span class="lineNoCov">          0 :         idxqi += nlp1;</span></a>
+<a name="24346"><span class="lineNum">   24346 </span><span class="lineNoCov">          0 :         vfi += nlp1;</span></a>
+<a name="24347"><span class="lineNum">   24347 </span><span class="lineNoCov">          0 :         vli += nlp1;</span></a>
+<a name="24348"><span class="lineNum">   24348 </span><span class="lineNoCov">          0 :         nrp1 = nr + sqrei;</span></a>
+<a name="24349"><span class="lineNum">   24349 </span><span class="lineNoCov">          0 :         if (*icompq == 0) {</span></a>
+<a name="24350"><span class="lineNum">   24350 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;nrp1, &amp;nrp1, &amp;zero, &amp;one, &amp;work[nwork1], &amp;smlszp);</span></a>
+<a name="24351"><span class="lineNum">   24351 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nr, &amp;nrp1, &amp;nru, &amp;ncc, &amp;d__[nrf], &amp;e[nrf], &amp;</span></a>
+<a name="24352"><span class="lineNum">   24352 </span>            :                     work[nwork1], &amp;smlszp, &amp;work[nwork2], &amp;nr, &amp;work[nwork2], </a>
+<a name="24353"><span class="lineNum">   24353 </span><span class="lineNoCov">          0 :                     &amp;nr, &amp;work[nwork2], info);</span></a>
+<a name="24354"><span class="lineNum">   24354 </span><span class="lineNoCov">          0 :             itemp = nwork1 + (nrp1 - 1) * smlszp;</span></a>
+<a name="24355"><span class="lineNum">   24355 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nrp1, &amp;work[nwork1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="24356"><span class="lineNum">   24356 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nrp1, &amp;work[itemp], &amp;c__1, &amp;work[vli], &amp;c__1);</span></a>
+<a name="24357"><span class="lineNum">   24357 </span>            :         } else {</a>
+<a name="24358"><span class="lineNum">   24358 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;nr, &amp;nr, &amp;zero, &amp;one, &amp;u[nrf + u_dim1], ldu);</span></a>
+<a name="24359"><span class="lineNum">   24359 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;A&quot;, &amp;nrp1, &amp;nrp1, &amp;zero, &amp;one, &amp;vt[nrf + vt_dim1], </span></a>
+<a name="24360"><span class="lineNum">   24360 </span>            :                     ldu);</a>
+<a name="24361"><span class="lineNum">   24361 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(&quot;U&quot;, &amp;sqrei, &amp;nr, &amp;nrp1, &amp;nr, &amp;ncc, &amp;d__[nrf], &amp;e[nrf], &amp;</span></a>
+<a name="24362"><span class="lineNum">   24362 </span>            :                     vt[nrf + vt_dim1], ldu, &amp;u[nrf + u_dim1], ldu, &amp;u[nrf + </a>
+<a name="24363"><span class="lineNum">   24363 </span><span class="lineNoCov">          0 :                     u_dim1], ldu, &amp;work[nwork1], info);</span></a>
+<a name="24364"><span class="lineNum">   24364 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nrp1, &amp;vt[nrf + vt_dim1], &amp;c__1, &amp;work[vfi], &amp;c__1);</span></a>
+<a name="24365"><span class="lineNum">   24365 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;nrp1, &amp;vt[nrf + nrp1 * vt_dim1], &amp;c__1, &amp;work[vli], &amp;c__1)</span></a>
+<a name="24366"><span class="lineNum">   24366 </span>            :                     ;</a>
+<a name="24367"><span class="lineNum">   24367 </span>            :         }</a>
+<a name="24368"><span class="lineNum">   24368 </span><span class="lineNoCov">          0 :         if (*info != 0) {</span></a>
+<a name="24369"><span class="lineNum">   24369 </span>            :             return;</a>
+<a name="24370"><span class="lineNum">   24370 </span>            :         }</a>
+<a name="24371"><span class="lineNum">   24371 </span><span class="lineNoCov">          0 :         i__2 = nr;</span></a>
+<a name="24372"><span class="lineNum">   24372 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="24373"><span class="lineNum">   24373 </span><span class="lineNoCov">          0 :             iwork[idxqi + j] = j;</span></a>
+<a name="24374"><span class="lineNum">   24374 </span>            :         }</a>
+<a name="24375"><span class="lineNum">   24375 </span>            :     }</a>
+<a name="24376"><span class="lineNum">   24376 </span>            : </a>
+<a name="24377"><span class="lineNum">   24377 </span><span class="lineNoCov">          0 :     j = (1 &lt;&lt; nlvl);</span></a>
+<a name="24378"><span class="lineNum">   24378 </span>            : </a>
+<a name="24379"><span class="lineNum">   24379 </span><span class="lineNoCov">          0 :     for (lvl = nlvl; lvl &gt;= 1; --lvl) {</span></a>
+<a name="24380"><span class="lineNum">   24380 </span><span class="lineNoCov">          0 :         lvl2 = (lvl &lt;&lt; 1) - 1;</span></a>
+<a name="24381"><span class="lineNum">   24381 </span>            : </a>
+<a name="24382"><span class="lineNum">   24382 </span><span class="lineNoCov">          0 :         if (lvl == 1) {</span></a>
+<a name="24383"><span class="lineNum">   24383 </span>            :             lf = 1;</a>
+<a name="24384"><span class="lineNum">   24384 </span>            :             ll = 1;</a>
+<a name="24385"><span class="lineNum">   24385 </span>            :         } else {</a>
+<a name="24386"><span class="lineNum">   24386 </span><span class="lineNoCov">          0 :             lf = (1 &lt;&lt; (lvl-1));</span></a>
+<a name="24387"><span class="lineNum">   24387 </span><span class="lineNoCov">          0 :             ll = (lf &lt;&lt; 1) - 1;</span></a>
+<a name="24388"><span class="lineNum">   24388 </span>            :         }</a>
+<a name="24389"><span class="lineNum">   24389 </span>            :         i__1 = ll;</a>
+<a name="24390"><span class="lineNum">   24390 </span><span class="lineNoCov">          0 :         for (i__ = lf; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="24391"><span class="lineNum">   24391 </span><span class="lineNoCov">          0 :             im1 = i__ - 1;</span></a>
+<a name="24392"><span class="lineNum">   24392 </span><span class="lineNoCov">          0 :             ic = iwork[inode + im1];</span></a>
+<a name="24393"><span class="lineNum">   24393 </span><span class="lineNoCov">          0 :             nl = iwork[ndiml + im1];</span></a>
+<a name="24394"><span class="lineNum">   24394 </span><span class="lineNoCov">          0 :             nr = iwork[ndimr + im1];</span></a>
+<a name="24395"><span class="lineNum">   24395 </span><span class="lineNoCov">          0 :             nlf = ic - nl;</span></a>
+<a name="24396"><span class="lineNum">   24396 </span><span class="lineNoCov">          0 :             if (i__ == ll) {</span></a>
+<a name="24397"><span class="lineNum">   24397 </span><span class="lineNoCov">          0 :                 sqrei = *sqre;</span></a>
+<a name="24398"><span class="lineNum">   24398 </span>            :             } else {</a>
+<a name="24399"><span class="lineNum">   24399 </span><span class="lineNoCov">          0 :                 sqrei = 1;</span></a>
+<a name="24400"><span class="lineNum">   24400 </span>            :             }</a>
+<a name="24401"><span class="lineNum">   24401 </span>            :             vfi = vf + nlf - 1;</a>
+<a name="24402"><span class="lineNum">   24402 </span><span class="lineNoCov">          0 :             vli = vl + nlf - 1;</span></a>
+<a name="24403"><span class="lineNum">   24403 </span><span class="lineNoCov">          0 :             idxqi = idxq + nlf - 1;</span></a>
+<a name="24404"><span class="lineNum">   24404 </span><span class="lineNoCov">          0 :             alpha = d__[ic];</span></a>
+<a name="24405"><span class="lineNum">   24405 </span><span class="lineNoCov">          0 :             beta = e[ic];</span></a>
+<a name="24406"><span class="lineNum">   24406 </span><span class="lineNoCov">          0 :             if (*icompq == 0) {</span></a>
+<a name="24407"><span class="lineNum">   24407 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasd6,SLASD6)(icompq, &amp;nl, &amp;nr, &amp;sqrei, &amp;d__[nlf], &amp;work[vfi], &amp;</span></a>
+<a name="24408"><span class="lineNum">   24408 </span><span class="lineNoCov">          0 :                         work[vli], &amp;alpha, &amp;beta, &amp;iwork[idxqi], &amp;perm[</span></a>
+<a name="24409"><span class="lineNum">   24409 </span>            :                         perm_offset], &amp;givptr[1], &amp;givcol[givcol_offset], </a>
+<a name="24410"><span class="lineNum">   24410 </span>            :                         ldgcol, &amp;givnum[givnum_offset], ldu, &amp;poles[</a>
+<a name="24411"><span class="lineNum">   24411 </span>            :                         poles_offset], &amp;difl[difl_offset], &amp;difr[difr_offset],</a>
+<a name="24412"><span class="lineNum">   24412 </span><span class="lineNoCov">          0 :                          &amp;z__[z_offset], &amp;k[1], &amp;c__[1], &amp;s[1], &amp;work[nwork1],</span></a>
+<a name="24413"><span class="lineNum">   24413 </span><span class="lineNoCov">          0 :                          &amp;iwork[iwk], info);</span></a>
+<a name="24414"><span class="lineNum">   24414 </span>            :             } else {</a>
+<a name="24415"><span class="lineNum">   24415 </span><span class="lineNoCov">          0 :                 --j;</span></a>
+<a name="24416"><span class="lineNum">   24416 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasd6,SLASD6)(icompq, &amp;nl, &amp;nr, &amp;sqrei, &amp;d__[nlf], &amp;work[vfi], &amp;</span></a>
+<a name="24417"><span class="lineNum">   24417 </span><span class="lineNoCov">          0 :                         work[vli], &amp;alpha, &amp;beta, &amp;iwork[idxqi], &amp;perm[nlf + </span></a>
+<a name="24418"><span class="lineNum">   24418 </span><span class="lineNoCov">          0 :                         lvl * perm_dim1], &amp;givptr[j], &amp;givcol[nlf + lvl2 * </span></a>
+<a name="24419"><span class="lineNum">   24419 </span>            :                         givcol_dim1], ldgcol, &amp;givnum[nlf + lvl2 * </a>
+<a name="24420"><span class="lineNum">   24420 </span>            :                         givnum_dim1], ldu, &amp;poles[nlf + lvl2 * poles_dim1], &amp;</a>
+<a name="24421"><span class="lineNum">   24421 </span><span class="lineNoCov">          0 :                         difl[nlf + lvl * difl_dim1], &amp;difr[nlf + lvl2 * </span></a>
+<a name="24422"><span class="lineNum">   24422 </span><span class="lineNoCov">          0 :                         difr_dim1], &amp;z__[nlf + lvl * z_dim1], &amp;k[j], &amp;c__[j], </span></a>
+<a name="24423"><span class="lineNum">   24423 </span><span class="lineNoCov">          0 :                         &amp;s[j], &amp;work[nwork1], &amp;iwork[iwk], info);</span></a>
+<a name="24424"><span class="lineNum">   24424 </span>            :             }</a>
+<a name="24425"><span class="lineNum">   24425 </span><span class="lineNoCov">          0 :             if (*info != 0) {</span></a>
+<a name="24426"><span class="lineNum">   24426 </span>            :                 return;</a>
+<a name="24427"><span class="lineNum">   24427 </span>            :             }</a>
+<a name="24428"><span class="lineNum">   24428 </span>            :         }</a>
+<a name="24429"><span class="lineNum">   24429 </span>            :     }</a>
+<a name="24430"><span class="lineNum">   24430 </span>            : </a>
+<a name="24431"><span class="lineNum">   24431 </span>            :     return;</a>
+<a name="24432"><span class="lineNum">   24432 </span>            : </a>
+<a name="24433"><span class="lineNum">   24433 </span>            : }</a>
+<a name="24434"><span class="lineNum">   24434 </span>            : </a>
+<a name="24435"><span class="lineNum">   24435 </span>            : </a>
+<a name="24436"><span class="lineNum">   24436 </span>            : }</a>
+<a name="24437"><span class="lineNum">   24437 </span>            : }</a>
+<a name="24438"><span class="lineNum">   24438 </span>            : #include &lt;cctype&gt;</a>
+<a name="24439"><span class="lineNum">   24439 </span>            : </a>
+<a name="24440"><span class="lineNum">   24440 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24441"><span class="lineNum">   24441 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24442"><span class="lineNum">   24442 </span>            : </a>
+<a name="24443"><span class="lineNum">   24443 </span>            : </a>
+<a name="24444"><span class="lineNum">   24444 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24445"><span class="lineNum">   24445 </span>            : namespace PLMD{</a>
+<a name="24446"><span class="lineNum">   24446 </span>            : namespace lapack{</a>
+<a name="24447"><span class="lineNum">   24447 </span>            : using namespace blas;</a>
+<a name="24448"><span class="lineNum">   24448 </span>            : void </a>
+<a name="24449"><span class="lineNum">   24449 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasdq,SLASDQ)(const char *uplo,</span></a>
+<a name="24450"><span class="lineNum">   24450 </span>            :                         int *sqre,</a>
+<a name="24451"><span class="lineNum">   24451 </span>            :                         int *n,</a>
+<a name="24452"><span class="lineNum">   24452 </span>            :                         int *ncvt,</a>
+<a name="24453"><span class="lineNum">   24453 </span>            :                         int *nru,</a>
+<a name="24454"><span class="lineNum">   24454 </span>            :                         int *ncc,</a>
+<a name="24455"><span class="lineNum">   24455 </span>            :                         float *d__,</a>
+<a name="24456"><span class="lineNum">   24456 </span>            :                         float *e, </a>
+<a name="24457"><span class="lineNum">   24457 </span>            :                         float *vt, </a>
+<a name="24458"><span class="lineNum">   24458 </span>            :                         int *ldvt, </a>
+<a name="24459"><span class="lineNum">   24459 </span>            :                         float *u,</a>
+<a name="24460"><span class="lineNum">   24460 </span>            :                         int *ldu, </a>
+<a name="24461"><span class="lineNum">   24461 </span>            :                         float *c__,</a>
+<a name="24462"><span class="lineNum">   24462 </span>            :                         int *ldc,</a>
+<a name="24463"><span class="lineNum">   24463 </span>            :                         float *work, </a>
+<a name="24464"><span class="lineNum">   24464 </span>            :                         int *info)</a>
+<a name="24465"><span class="lineNum">   24465 </span>            : {</a>
+<a name="24466"><span class="lineNum">   24466 </span><span class="lineNoCov">          0 :     const char xuplo=std::toupper(*uplo);</span></a>
+<a name="24467"><span class="lineNum">   24467 </span>            :     int c_dim1, c_offset, u_dim1, u_offset, vt_dim1, vt_offset, i__1, </a>
+<a name="24468"><span class="lineNum">   24468 </span>            :             i__2;</a>
+<a name="24469"><span class="lineNum">   24469 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="24470"><span class="lineNum">   24470 </span>            :     int itmp1,itmp2;</a>
+<a name="24471"><span class="lineNum">   24471 </span>            :     int i__, j;</a>
+<a name="24472"><span class="lineNum">   24472 </span>            :     float r__, cs, sn;</a>
+<a name="24473"><span class="lineNum">   24473 </span>            :     int np1, isub;</a>
+<a name="24474"><span class="lineNum">   24474 </span>            :     float smin;</a>
+<a name="24475"><span class="lineNum">   24475 </span>            :     int sqre1;</a>
+<a name="24476"><span class="lineNum">   24476 </span>            :     int iuplo;</a>
+<a name="24477"><span class="lineNum">   24477 </span>            :     int rotate;</a>
+<a name="24478"><span class="lineNum">   24478 </span>            : </a>
+<a name="24479"><span class="lineNum">   24479 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="24480"><span class="lineNum">   24480 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="24481"><span class="lineNum">   24481 </span><span class="lineNoCov">          0 :     vt_dim1 = *ldvt;</span></a>
+<a name="24482"><span class="lineNum">   24482 </span><span class="lineNoCov">          0 :     vt_offset = 1 + vt_dim1;</span></a>
+<a name="24483"><span class="lineNum">   24483 </span><span class="lineNoCov">          0 :     vt -= vt_offset;</span></a>
+<a name="24484"><span class="lineNum">   24484 </span><span class="lineNoCov">          0 :     u_dim1 = *ldu;</span></a>
+<a name="24485"><span class="lineNum">   24485 </span><span class="lineNoCov">          0 :     u_offset = 1 + u_dim1;</span></a>
+<a name="24486"><span class="lineNum">   24486 </span><span class="lineNoCov">          0 :     u -= u_offset;</span></a>
+<a name="24487"><span class="lineNum">   24487 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="24488"><span class="lineNum">   24488 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="24489"><span class="lineNum">   24489 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="24490"><span class="lineNum">   24490 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="24491"><span class="lineNum">   24491 </span>            : </a>
+<a name="24492"><span class="lineNum">   24492 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="24493"><span class="lineNum">   24493 </span>            :     iuplo = 0;</a>
+<a name="24494"><span class="lineNum">   24494 </span><span class="lineNoCov">          0 :     if (xuplo == 'U') {</span></a>
+<a name="24495"><span class="lineNum">   24495 </span>            :         iuplo = 1;</a>
+<a name="24496"><span class="lineNum">   24496 </span>            :     }</a>
+<a name="24497"><span class="lineNum">   24497 </span><span class="lineNoCov">          0 :     if (xuplo == 'L') {</span></a>
+<a name="24498"><span class="lineNum">   24498 </span>            :         iuplo = 2;</a>
+<a name="24499"><span class="lineNum">   24499 </span>            :     }</a>
+<a name="24500"><span class="lineNum">   24500 </span>            :     </a>
+<a name="24501"><span class="lineNum">   24501 </span><span class="lineNoCov">          0 :     itmp1 = (*n &gt; 1) ? *n : 1;</span></a>
+<a name="24502"><span class="lineNum">   24502 </span><span class="lineNoCov">          0 :     itmp2 = (*nru &gt; 1) ? *nru : 1;</span></a>
+<a name="24503"><span class="lineNum">   24503 </span><span class="lineNoCov">          0 :     if (iuplo == 0) {</span></a>
+<a name="24504"><span class="lineNum">   24504 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="24505"><span class="lineNum">   24505 </span><span class="lineNoCov">          0 :     } else if (*sqre &lt; 0 || *sqre &gt; 1) {</span></a>
+<a name="24506"><span class="lineNum">   24506 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="24507"><span class="lineNum">   24507 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="24508"><span class="lineNum">   24508 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="24509"><span class="lineNum">   24509 </span><span class="lineNoCov">          0 :     } else if (*ncvt &lt; 0) {</span></a>
+<a name="24510"><span class="lineNum">   24510 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="24511"><span class="lineNum">   24511 </span><span class="lineNoCov">          0 :     } else if (*nru &lt; 0) {</span></a>
+<a name="24512"><span class="lineNum">   24512 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="24513"><span class="lineNum">   24513 </span><span class="lineNoCov">          0 :     } else if (*ncc &lt; 0) {</span></a>
+<a name="24514"><span class="lineNum">   24514 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="24515"><span class="lineNum">   24515 </span><span class="lineNoCov">          0 :     } else if ( (*ncvt == 0 &amp;&amp; *ldvt &lt; 1) || (*ncvt &gt; 0 &amp;&amp; *ldvt &lt; itmp1)) {</span></a>
+<a name="24516"><span class="lineNum">   24516 </span><span class="lineNoCov">          0 :         *info = -10;</span></a>
+<a name="24517"><span class="lineNum">   24517 </span><span class="lineNoCov">          0 :     } else if (*ldu &lt; itmp2) {</span></a>
+<a name="24518"><span class="lineNum">   24518 </span><span class="lineNoCov">          0 :         *info = -12;</span></a>
+<a name="24519"><span class="lineNum">   24519 </span><span class="lineNoCov">          0 :     } else if ((*ncc == 0 &amp;&amp; *ldc &lt; 1) || (*ncc &gt; 0 &amp;&amp; *ldc &lt; itmp1)) {</span></a>
+<a name="24520"><span class="lineNum">   24520 </span><span class="lineNoCov">          0 :         *info = -14;</span></a>
+<a name="24521"><span class="lineNum">   24521 </span>            :     }</a>
+<a name="24522"><span class="lineNum">   24522 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="24523"><span class="lineNum">   24523 </span>            :         return;</a>
+<a name="24524"><span class="lineNum">   24524 </span>            :     }</a>
+<a name="24525"><span class="lineNum">   24525 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="24526"><span class="lineNum">   24526 </span>            :         return;</a>
+<a name="24527"><span class="lineNum">   24527 </span>            :     }</a>
+<a name="24528"><span class="lineNum">   24528 </span>            : </a>
+<a name="24529"><span class="lineNum">   24529 </span><span class="lineNoCov">          0 :     rotate = *ncvt &gt; 0 || *nru &gt; 0 || *ncc &gt; 0;</span></a>
+<a name="24530"><span class="lineNum">   24530 </span><span class="lineNoCov">          0 :     np1 = *n + 1;</span></a>
+<a name="24531"><span class="lineNum">   24531 </span><span class="lineNoCov">          0 :     sqre1 = *sqre;</span></a>
+<a name="24532"><span class="lineNum">   24532 </span>            : </a>
+<a name="24533"><span class="lineNum">   24533 </span><span class="lineNoCov">          0 :     if (iuplo == 1 &amp;&amp; sqre1 == 1) {</span></a>
+<a name="24534"><span class="lineNum">   24534 </span>            :         i__1 = *n - 1;</a>
+<a name="24535"><span class="lineNum">   24535 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="24536"><span class="lineNum">   24536 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="24537"><span class="lineNum">   24537 </span><span class="lineNoCov">          0 :             d__[i__] = r__;</span></a>
+<a name="24538"><span class="lineNum">   24538 </span><span class="lineNoCov">          0 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="24539"><span class="lineNum">   24539 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="24540"><span class="lineNum">   24540 </span><span class="lineNoCov">          0 :             if (rotate) {</span></a>
+<a name="24541"><span class="lineNum">   24541 </span><span class="lineNoCov">          0 :                 work[i__] = cs;</span></a>
+<a name="24542"><span class="lineNum">   24542 </span><span class="lineNoCov">          0 :                 work[*n + i__] = sn;</span></a>
+<a name="24543"><span class="lineNum">   24543 </span>            :             }</a>
+<a name="24544"><span class="lineNum">   24544 </span>            :         }</a>
+<a name="24545"><span class="lineNum">   24545 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;d__[*n], &amp;e[*n], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="24546"><span class="lineNum">   24546 </span><span class="lineNoCov">          0 :         d__[*n] = r__;</span></a>
+<a name="24547"><span class="lineNum">   24547 </span><span class="lineNoCov">          0 :         e[*n] = 0.f;</span></a>
+<a name="24548"><span class="lineNum">   24548 </span><span class="lineNoCov">          0 :         if (rotate) {</span></a>
+<a name="24549"><span class="lineNum">   24549 </span><span class="lineNoCov">          0 :             work[*n] = cs;</span></a>
+<a name="24550"><span class="lineNum">   24550 </span><span class="lineNoCov">          0 :             work[*n + *n] = sn;</span></a>
+<a name="24551"><span class="lineNum">   24551 </span>            :         }</a>
+<a name="24552"><span class="lineNum">   24552 </span>            :         iuplo = 2;</a>
+<a name="24553"><span class="lineNum">   24553 </span>            :         sqre1 = 0;</a>
+<a name="24554"><span class="lineNum">   24554 </span>            : </a>
+<a name="24555"><span class="lineNum">   24555 </span><span class="lineNoCov">          0 :         if (*ncvt &gt; 0) {</span></a>
+<a name="24556"><span class="lineNum">   24556 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;np1, ncvt, &amp;work[1], &amp;work[np1], &amp;vt[</span></a>
+<a name="24557"><span class="lineNum">   24557 </span>            :                     vt_offset], ldvt);</a>
+<a name="24558"><span class="lineNum">   24558 </span>            :         }</a>
+<a name="24559"><span class="lineNum">   24559 </span>            :     }</a>
+<a name="24560"><span class="lineNum">   24560 </span><span class="lineNoCov">          0 :     if (iuplo == 2) {</span></a>
+<a name="24561"><span class="lineNum">   24561 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="24562"><span class="lineNum">   24562 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="24563"><span class="lineNum">   24563 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;d__[i__], &amp;e[i__], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="24564"><span class="lineNum">   24564 </span><span class="lineNoCov">          0 :             d__[i__] = r__;</span></a>
+<a name="24565"><span class="lineNum">   24565 </span><span class="lineNoCov">          0 :             e[i__] = sn * d__[i__ + 1];</span></a>
+<a name="24566"><span class="lineNum">   24566 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = cs * d__[i__ + 1];</span></a>
+<a name="24567"><span class="lineNum">   24567 </span><span class="lineNoCov">          0 :             if (rotate) {</span></a>
+<a name="24568"><span class="lineNum">   24568 </span><span class="lineNoCov">          0 :                 work[i__] = cs;</span></a>
+<a name="24569"><span class="lineNum">   24569 </span><span class="lineNoCov">          0 :                 work[*n + i__] = sn;</span></a>
+<a name="24570"><span class="lineNum">   24570 </span>            :             }</a>
+<a name="24571"><span class="lineNum">   24571 </span>            :         }</a>
+<a name="24572"><span class="lineNum">   24572 </span>            : </a>
+<a name="24573"><span class="lineNum">   24573 </span><span class="lineNoCov">          0 :         if (sqre1 == 1) {</span></a>
+<a name="24574"><span class="lineNum">   24574 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;d__[*n], &amp;e[*n], &amp;cs, &amp;sn, &amp;r__);</span></a>
+<a name="24575"><span class="lineNum">   24575 </span><span class="lineNoCov">          0 :             d__[*n] = r__;</span></a>
+<a name="24576"><span class="lineNum">   24576 </span><span class="lineNoCov">          0 :             if (rotate) {</span></a>
+<a name="24577"><span class="lineNum">   24577 </span><span class="lineNoCov">          0 :                 work[*n] = cs;</span></a>
+<a name="24578"><span class="lineNum">   24578 </span><span class="lineNoCov">          0 :                 work[*n + *n] = sn;</span></a>
+<a name="24579"><span class="lineNum">   24579 </span>            :             }</a>
+<a name="24580"><span class="lineNum">   24580 </span>            :         }</a>
+<a name="24581"><span class="lineNum">   24581 </span><span class="lineNoCov">          0 :         if (*nru &gt; 0) {</span></a>
+<a name="24582"><span class="lineNum">   24582 </span><span class="lineNoCov">          0 :             if (sqre1 == 0) {</span></a>
+<a name="24583"><span class="lineNum">   24583 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, n, &amp;work[1], &amp;work[np1], &amp;u[</span></a>
+<a name="24584"><span class="lineNum">   24584 </span>            :                         u_offset], ldu);</a>
+<a name="24585"><span class="lineNum">   24585 </span>            :             } else {</a>
+<a name="24586"><span class="lineNum">   24586 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, nru, &amp;np1, &amp;work[1], &amp;work[np1], &amp;u[</span></a>
+<a name="24587"><span class="lineNum">   24587 </span>            :                         u_offset], ldu);</a>
+<a name="24588"><span class="lineNum">   24588 </span>            :             }</a>
+<a name="24589"><span class="lineNum">   24589 </span>            :         }</a>
+<a name="24590"><span class="lineNum">   24590 </span><span class="lineNoCov">          0 :         if (*ncc &gt; 0) {</span></a>
+<a name="24591"><span class="lineNum">   24591 </span><span class="lineNoCov">          0 :             if (sqre1 == 0) {</span></a>
+<a name="24592"><span class="lineNum">   24592 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, n, ncc, &amp;work[1], &amp;work[np1], &amp;c__[</span></a>
+<a name="24593"><span class="lineNum">   24593 </span>            :                         c_offset], ldc);</a>
+<a name="24594"><span class="lineNum">   24594 </span>            :             } else {</a>
+<a name="24595"><span class="lineNum">   24595 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;L&quot;, &quot;V&quot;, &quot;F&quot;, &amp;np1, ncc, &amp;work[1], &amp;work[np1], &amp;c__[</span></a>
+<a name="24596"><span class="lineNum">   24596 </span>            :                         c_offset], ldc);</a>
+<a name="24597"><span class="lineNum">   24597 </span>            :             }</a>
+<a name="24598"><span class="lineNum">   24598 </span>            :         }</a>
+<a name="24599"><span class="lineNum">   24599 </span>            :     }</a>
+<a name="24600"><span class="lineNum">   24600 </span>            : </a>
+<a name="24601"><span class="lineNum">   24601 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sbdsqr,SBDSQR)(&quot;U&quot;, n, ncvt, nru, ncc, &amp;d__[1], &amp;e[1], &amp;vt[vt_offset], ldvt, &amp;u[</span></a>
+<a name="24602"><span class="lineNum">   24602 </span>            :             u_offset], ldu, &amp;c__[c_offset], ldc, &amp;work[1], info);</a>
+<a name="24603"><span class="lineNum">   24603 </span>            : </a>
+<a name="24604"><span class="lineNum">   24604 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="24605"><span class="lineNum">   24605 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="24606"><span class="lineNum">   24606 </span>            : </a>
+<a name="24607"><span class="lineNum">   24607 </span>            :         isub = i__;</a>
+<a name="24608"><span class="lineNum">   24608 </span><span class="lineNoCov">          0 :         smin = d__[i__];</span></a>
+<a name="24609"><span class="lineNum">   24609 </span><span class="lineNoCov">          0 :         i__2 = *n;</span></a>
+<a name="24610"><span class="lineNum">   24610 </span><span class="lineNoCov">          0 :         for (j = i__ + 1; j &lt;= i__2; ++j) {</span></a>
+<a name="24611"><span class="lineNum">   24611 </span><span class="lineNoCov">          0 :             if (d__[j] &lt; smin) {</span></a>
+<a name="24612"><span class="lineNum">   24612 </span>            :                 isub = j;</a>
+<a name="24613"><span class="lineNum">   24613 </span>            :                 smin = d__[j];</a>
+<a name="24614"><span class="lineNum">   24614 </span>            :             }</a>
+<a name="24615"><span class="lineNum">   24615 </span>            :         }</a>
+<a name="24616"><span class="lineNum">   24616 </span><span class="lineNoCov">          0 :         if (isub != i__) {</span></a>
+<a name="24617"><span class="lineNum">   24617 </span><span class="lineNoCov">          0 :             d__[isub] = d__[i__];</span></a>
+<a name="24618"><span class="lineNum">   24618 </span><span class="lineNoCov">          0 :             d__[i__] = smin;</span></a>
+<a name="24619"><span class="lineNum">   24619 </span><span class="lineNoCov">          0 :             if (*ncvt &gt; 0) {</span></a>
+<a name="24620"><span class="lineNum">   24620 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(ncvt, &amp;vt[isub + vt_dim1], ldvt, &amp;vt[i__ + vt_dim1], </span></a>
+<a name="24621"><span class="lineNum">   24621 </span>            :                         ldvt);</a>
+<a name="24622"><span class="lineNum">   24622 </span>            :             }</a>
+<a name="24623"><span class="lineNum">   24623 </span><span class="lineNoCov">          0 :             if (*nru &gt; 0) {</span></a>
+<a name="24624"><span class="lineNum">   24624 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(nru, &amp;u[isub * u_dim1 + 1], &amp;c__1, &amp;u[i__ * u_dim1 + 1]</span></a>
+<a name="24625"><span class="lineNum">   24625 </span>            :                         , &amp;c__1);</a>
+<a name="24626"><span class="lineNum">   24626 </span>            :             }</a>
+<a name="24627"><span class="lineNum">   24627 </span><span class="lineNoCov">          0 :             if (*ncc &gt; 0) {</span></a>
+<a name="24628"><span class="lineNum">   24628 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(ncc, &amp;c__[isub + c_dim1], ldc, &amp;c__[i__ + c_dim1], ldc)</span></a>
+<a name="24629"><span class="lineNum">   24629 </span>            :                         ;</a>
+<a name="24630"><span class="lineNum">   24630 </span>            :             }</a>
+<a name="24631"><span class="lineNum">   24631 </span>            :         }</a>
+<a name="24632"><span class="lineNum">   24632 </span>            :     }</a>
+<a name="24633"><span class="lineNum">   24633 </span>            : </a>
+<a name="24634"><span class="lineNum">   24634 </span>            :     return;</a>
+<a name="24635"><span class="lineNum">   24635 </span>            : }</a>
+<a name="24636"><span class="lineNum">   24636 </span>            : </a>
+<a name="24637"><span class="lineNum">   24637 </span>            : </a>
+<a name="24638"><span class="lineNum">   24638 </span>            : }</a>
+<a name="24639"><span class="lineNum">   24639 </span>            : }</a>
+<a name="24640"><span class="lineNum">   24640 </span>            : #include &lt;cmath&gt;</a>
+<a name="24641"><span class="lineNum">   24641 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24642"><span class="lineNum">   24642 </span>            : </a>
+<a name="24643"><span class="lineNum">   24643 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24644"><span class="lineNum">   24644 </span>            : namespace PLMD{</a>
+<a name="24645"><span class="lineNum">   24645 </span>            : namespace lapack{</a>
+<a name="24646"><span class="lineNum">   24646 </span>            : using namespace blas;</a>
+<a name="24647"><span class="lineNum">   24647 </span>            : void</a>
+<a name="24648"><span class="lineNum">   24648 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasdt,SLASDT)(int *n,</span></a>
+<a name="24649"><span class="lineNum">   24649 </span>            :         int *lvl,</a>
+<a name="24650"><span class="lineNum">   24650 </span>            :         int *nd,</a>
+<a name="24651"><span class="lineNum">   24651 </span>            :         int *inode,</a>
+<a name="24652"><span class="lineNum">   24652 </span>            :         int *ndiml,</a>
+<a name="24653"><span class="lineNum">   24653 </span>            :         int *ndimr,</a>
+<a name="24654"><span class="lineNum">   24654 </span>            :         int *msub)</a>
+<a name="24655"><span class="lineNum">   24655 </span>            : {</a>
+<a name="24656"><span class="lineNum">   24656 </span><span class="lineNoCov">          0 :   int maxn = (*n &gt; 1) ? *n : 1;</span></a>
+<a name="24657"><span class="lineNum">   24657 </span>            :   float temp;</a>
+<a name="24658"><span class="lineNum">   24658 </span>            :   int i,il,ir,llst,nlvl,ncrnt;</a>
+<a name="24659"><span class="lineNum">   24659 </span>            : </a>
+<a name="24660"><span class="lineNum">   24660 </span><span class="lineNoCov">          0 :   temp = std::log( ((float) maxn) / ((float)(*msub+1))) / std::log(2.0);</span></a>
+<a name="24661"><span class="lineNum">   24661 </span>            :   </a>
+<a name="24662"><span class="lineNum">   24662 </span><span class="lineNoCov">          0 :   *lvl = 1 + (int) temp;</span></a>
+<a name="24663"><span class="lineNum">   24663 </span>            : </a>
+<a name="24664"><span class="lineNum">   24664 </span><span class="lineNoCov">          0 :   i = *n / 2;</span></a>
+<a name="24665"><span class="lineNum">   24665 </span><span class="lineNoCov">          0 :   inode[0] = i + 1;</span></a>
+<a name="24666"><span class="lineNum">   24666 </span><span class="lineNoCov">          0 :   ndiml[0] = i;</span></a>
+<a name="24667"><span class="lineNum">   24667 </span><span class="lineNoCov">          0 :   ndimr[0] = *n - i - 1;</span></a>
+<a name="24668"><span class="lineNum">   24668 </span>            :   il = -1;</a>
+<a name="24669"><span class="lineNum">   24669 </span>            :   ir = 0;</a>
+<a name="24670"><span class="lineNum">   24670 </span>            :   llst = 1;</a>
+<a name="24671"><span class="lineNum">   24671 </span>            : </a>
+<a name="24672"><span class="lineNum">   24672 </span><span class="lineNoCov">          0 :   for(nlvl=1;nlvl&lt;*lvl;nlvl++) {</span></a>
+<a name="24673"><span class="lineNum">   24673 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;llst;i++) {</span></a>
+<a name="24674"><span class="lineNum">   24674 </span><span class="lineNoCov">          0 :       il += 2;</span></a>
+<a name="24675"><span class="lineNum">   24675 </span><span class="lineNoCov">          0 :       ir += 2;</span></a>
+<a name="24676"><span class="lineNum">   24676 </span><span class="lineNoCov">          0 :       ncrnt = llst + i - 1;</span></a>
+<a name="24677"><span class="lineNum">   24677 </span><span class="lineNoCov">          0 :       ndiml[il] = ndiml[ncrnt] / 2;</span></a>
+<a name="24678"><span class="lineNum">   24678 </span><span class="lineNoCov">          0 :       ndimr[il] = ndiml[ncrnt] - ndiml[il] - 1;</span></a>
+<a name="24679"><span class="lineNum">   24679 </span><span class="lineNoCov">          0 :       inode[il] = inode[ncrnt] - ndimr[il] - 1;</span></a>
+<a name="24680"><span class="lineNum">   24680 </span><span class="lineNoCov">          0 :       ndiml[ir] = ndimr[ncrnt] / 2;</span></a>
+<a name="24681"><span class="lineNum">   24681 </span><span class="lineNoCov">          0 :       ndimr[ir] = ndimr[ncrnt] - ndiml[ir] - 1;</span></a>
+<a name="24682"><span class="lineNum">   24682 </span><span class="lineNoCov">          0 :       inode[ir] = inode[ncrnt] + ndiml[ir] + 1;</span></a>
+<a name="24683"><span class="lineNum">   24683 </span>            :     }</a>
+<a name="24684"><span class="lineNum">   24684 </span><span class="lineNoCov">          0 :     llst *= 2;</span></a>
+<a name="24685"><span class="lineNum">   24685 </span>            :   }</a>
+<a name="24686"><span class="lineNum">   24686 </span><span class="lineNoCov">          0 :   *nd = llst*2 - 1;</span></a>
+<a name="24687"><span class="lineNum">   24687 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="24688"><span class="lineNum">   24688 </span>            : }</a>
+<a name="24689"><span class="lineNum">   24689 </span>            : }</a>
+<a name="24690"><span class="lineNum">   24690 </span>            : }</a>
+<a name="24691"><span class="lineNum">   24691 </span>            : #include &lt;cctype&gt;</a>
+<a name="24692"><span class="lineNum">   24692 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24693"><span class="lineNum">   24693 </span>            : </a>
+<a name="24694"><span class="lineNum">   24694 </span>            : </a>
+<a name="24695"><span class="lineNum">   24695 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24696"><span class="lineNum">   24696 </span>            : namespace PLMD{</a>
+<a name="24697"><span class="lineNum">   24697 </span>            : namespace lapack{</a>
+<a name="24698"><span class="lineNum">   24698 </span>            : using namespace blas;</a>
+<a name="24699"><span class="lineNum">   24699 </span>            : void</a>
+<a name="24700"><span class="lineNum">   24700 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slaset,SLASET)(const char *uplo,</span></a>
+<a name="24701"><span class="lineNum">   24701 </span>            :         int *m,</a>
+<a name="24702"><span class="lineNum">   24702 </span>            :         int *n,</a>
+<a name="24703"><span class="lineNum">   24703 </span>            :         float *alpha,</a>
+<a name="24704"><span class="lineNum">   24704 </span>            :         float *beta,</a>
+<a name="24705"><span class="lineNum">   24705 </span>            :         float *a,</a>
+<a name="24706"><span class="lineNum">   24706 </span>            :         int *lda)</a>
+<a name="24707"><span class="lineNum">   24707 </span>            : {</a>
+<a name="24708"><span class="lineNum">   24708 </span>            :   int i,j,k;</a>
+<a name="24709"><span class="lineNum">   24709 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="24710"><span class="lineNum">   24710 </span>            : </a>
+<a name="24711"><span class="lineNum">   24711 </span><span class="lineNoCov">          0 :   if(ch=='U') {</span></a>
+<a name="24712"><span class="lineNum">   24712 </span><span class="lineNoCov">          0 :     for(j=1;j&lt;*n;j++) {</span></a>
+<a name="24713"><span class="lineNum">   24713 </span><span class="lineNoCov">          0 :       k = (j &lt; *m) ? j : *m;</span></a>
+<a name="24714"><span class="lineNum">   24714 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;k;i++)</span></a>
+<a name="24715"><span class="lineNum">   24715 </span><span class="lineNoCov">          0 :         a[j*(*lda)+i] = *alpha;</span></a>
+<a name="24716"><span class="lineNum">   24716 </span>            :     }</a>
+<a name="24717"><span class="lineNum">   24717 </span><span class="lineNoCov">          0 :   } else if(ch=='L') {</span></a>
+<a name="24718"><span class="lineNum">   24718 </span><span class="lineNoCov">          0 :     k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="24719"><span class="lineNum">   24719 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;k;j++) {</span></a>
+<a name="24720"><span class="lineNum">   24720 </span><span class="lineNoCov">          0 :       for(i=j+1;i&lt;*m;i++)</span></a>
+<a name="24721"><span class="lineNum">   24721 </span><span class="lineNoCov">          0 :         a[j*(*lda)+i] = *alpha;</span></a>
+<a name="24722"><span class="lineNum">   24722 </span>            :     }</a>
+<a name="24723"><span class="lineNum">   24723 </span>            :   } else {</a>
+<a name="24724"><span class="lineNum">   24724 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;*n;j++) {</span></a>
+<a name="24725"><span class="lineNum">   24725 </span><span class="lineNoCov">          0 :       for(i=0;i&lt;*m;i++)</span></a>
+<a name="24726"><span class="lineNum">   24726 </span><span class="lineNoCov">          0 :         a[j*(*lda)+i] = *alpha;</span></a>
+<a name="24727"><span class="lineNum">   24727 </span>            :     }    </a>
+<a name="24728"><span class="lineNum">   24728 </span>            :   }</a>
+<a name="24729"><span class="lineNum">   24729 </span>            : </a>
+<a name="24730"><span class="lineNum">   24730 </span><span class="lineNoCov">          0 :   k = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="24731"><span class="lineNum">   24731 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;k;i++)</span></a>
+<a name="24732"><span class="lineNum">   24732 </span><span class="lineNoCov">          0 :     a[i*(*lda)+i] = *beta;</span></a>
+<a name="24733"><span class="lineNum">   24733 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="24734"><span class="lineNum">   24734 </span>            : }</a>
+<a name="24735"><span class="lineNum">   24735 </span>            : }</a>
+<a name="24736"><span class="lineNum">   24736 </span>            : #include &lt;cmath&gt;</a>
+<a name="24737"><span class="lineNum">   24737 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24738"><span class="lineNum">   24738 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24739"><span class="lineNum">   24739 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="24740"><span class="lineNum">   24740 </span>            : </a>
+<a name="24741"><span class="lineNum">   24741 </span>            : #include &quot;real.h&quot;</a>
+<a name="24742"><span class="lineNum">   24742 </span>            : </a>
+<a name="24743"><span class="lineNum">   24743 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24744"><span class="lineNum">   24744 </span>            : namespace PLMD{</a>
+<a name="24745"><span class="lineNum">   24745 </span>            : namespace lapack{</a>
+<a name="24746"><span class="lineNum">   24746 </span>            : using namespace blas;</a>
+<a name="24747"><span class="lineNum">   24747 </span>            : void</a>
+<a name="24748"><span class="lineNum">   24748 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasq1,SLASQ1)(int *n,</span></a>
+<a name="24749"><span class="lineNum">   24749 </span>            :         float *d,</a>
+<a name="24750"><span class="lineNum">   24750 </span>            :         float *e,</a>
+<a name="24751"><span class="lineNum">   24751 </span>            :         float *work,</a>
+<a name="24752"><span class="lineNum">   24752 </span>            :         int *info)</a>
+<a name="24753"><span class="lineNum">   24753 </span>            : {</a>
+<a name="24754"><span class="lineNum">   24754 </span><span class="lineNoCov">          0 :   float sigmx = 0.0;</span></a>
+<a name="24755"><span class="lineNum">   24755 </span>            :   int i,j,k,iinfo;</a>
+<a name="24756"><span class="lineNum">   24756 </span>            :   float minval,safemin;</a>
+<a name="24757"><span class="lineNum">   24757 </span>            :   float dtemp,scale;</a>
+<a name="24758"><span class="lineNum">   24758 </span>            :   float eps;</a>
+<a name="24759"><span class="lineNum">   24759 </span>            : </a>
+<a name="24760"><span class="lineNum">   24760 </span>            :   eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="24761"><span class="lineNum">   24761 </span>            :   minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="24762"><span class="lineNum">   24762 </span>            :   safemin = minval*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="24763"><span class="lineNum">   24763 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="24764"><span class="lineNum">   24764 </span>            : </a>
+<a name="24765"><span class="lineNum">   24765 </span><span class="lineNoCov">          0 :   if(*n&lt;0) {</span></a>
+<a name="24766"><span class="lineNum">   24766 </span><span class="lineNoCov">          0 :     *info = -2;</span></a>
+<a name="24767"><span class="lineNum">   24767 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="24768"><span class="lineNum">   24768 </span>            :   }</a>
+<a name="24769"><span class="lineNum">   24769 </span>            :   </a>
+<a name="24770"><span class="lineNum">   24770 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;*n-1;i++) {</span></a>
+<a name="24771"><span class="lineNum">   24771 </span><span class="lineNoCov">          0 :     d[i] = std::abs(d[i]);</span></a>
+<a name="24772"><span class="lineNum">   24772 </span><span class="lineNoCov">          0 :     dtemp = std::abs(e[i]);</span></a>
+<a name="24773"><span class="lineNum">   24773 </span><span class="lineNoCov">          0 :     if(dtemp&gt;sigmx)</span></a>
+<a name="24774"><span class="lineNum">   24774 </span><span class="lineNoCov">          0 :       sigmx=dtemp;</span></a>
+<a name="24775"><span class="lineNum">   24775 </span>            :   }</a>
+<a name="24776"><span class="lineNum">   24776 </span><span class="lineNoCov">          0 :   d[*n-1] = std::abs(d[*n-1]);</span></a>
+<a name="24777"><span class="lineNum">   24777 </span>            :   </a>
+<a name="24778"><span class="lineNum">   24778 </span><span class="lineNoCov">          0 :   if(std::abs(sigmx)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="24779"><span class="lineNum">   24779 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(&quot;D&quot;,n,d,&amp;iinfo);</span></a>
+<a name="24780"><span class="lineNum">   24780 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="24781"><span class="lineNum">   24781 </span>            :   }</a>
+<a name="24782"><span class="lineNum">   24782 </span>            : </a>
+<a name="24783"><span class="lineNum">   24783 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;*n;i++) {</span></a>
+<a name="24784"><span class="lineNum">   24784 </span><span class="lineNoCov">          0 :     if(d[i]&gt;sigmx)</span></a>
+<a name="24785"><span class="lineNum">   24785 </span><span class="lineNoCov">          0 :       sigmx=d[i];</span></a>
+<a name="24786"><span class="lineNum">   24786 </span>            :   }</a>
+<a name="24787"><span class="lineNum">   24787 </span>            : </a>
+<a name="24788"><span class="lineNum">   24788 </span>            :   /* Copy d and e into work (z format) and scale.</a>
+<a name="24789"><span class="lineNum">   24789 </span>            :    * Squaring input data makes scaling by a power of the</a>
+<a name="24790"><span class="lineNum">   24790 </span>            :    * radix pointless.</a>
+<a name="24791"><span class="lineNum">   24791 </span>            :    */</a>
+<a name="24792"><span class="lineNum">   24792 </span><span class="lineNoCov">          0 :   scale =  std::sqrt(eps/safemin);</span></a>
+<a name="24793"><span class="lineNum">   24793 </span><span class="lineNoCov">          0 :   i = 1;</span></a>
+<a name="24794"><span class="lineNum">   24794 </span><span class="lineNoCov">          0 :   j = 2;</span></a>
+<a name="24795"><span class="lineNum">   24795 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n,d,&amp;i,work,&amp;j);</span></a>
+<a name="24796"><span class="lineNum">   24796 </span><span class="lineNoCov">          0 :   k = *n-1;</span></a>
+<a name="24797"><span class="lineNum">   24797 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;k,e,&amp;i,work+1,&amp;j);</span></a>
+<a name="24798"><span class="lineNum">   24798 </span><span class="lineNoCov">          0 :   i = 0;</span></a>
+<a name="24799"><span class="lineNum">   24799 </span><span class="lineNoCov">          0 :   j = 2*(*n)-1;</span></a>
+<a name="24800"><span class="lineNum">   24800 </span><span class="lineNoCov">          0 :   k = 1;</span></a>
+<a name="24801"><span class="lineNum">   24801 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;,&amp;i,&amp;i,&amp;sigmx,&amp;scale,&amp;j,&amp;k,work,&amp;j,&amp;iinfo);</span></a>
+<a name="24802"><span class="lineNum">   24802 </span>            : </a>
+<a name="24803"><span class="lineNum">   24803 </span>            : </a>
+<a name="24804"><span class="lineNum">   24804 </span>            :   /* Compute q and e elements */</a>
+<a name="24805"><span class="lineNum">   24805 </span><span class="lineNoCov">          0 :   for(i=0;i&lt;2*(*n)-1;i++)</span></a>
+<a name="24806"><span class="lineNum">   24806 </span><span class="lineNoCov">          0 :     work[i] = work[i]*work[i];</span></a>
+<a name="24807"><span class="lineNum">   24807 </span>            : </a>
+<a name="24808"><span class="lineNum">   24808 </span><span class="lineNoCov">          0 :   work[2*(*n)-1] = 0.0;</span></a>
+<a name="24809"><span class="lineNum">   24809 </span>            : </a>
+<a name="24810"><span class="lineNum">   24810 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(slasq2,SLASQ2)(n,work,info);</span></a>
+<a name="24811"><span class="lineNum">   24811 </span>            : </a>
+<a name="24812"><span class="lineNum">   24812 </span><span class="lineNoCov">          0 :   j = 0;</span></a>
+<a name="24813"><span class="lineNum">   24813 </span><span class="lineNoCov">          0 :   k = 1;</span></a>
+<a name="24814"><span class="lineNum">   24814 </span><span class="lineNoCov">          0 :   if(*info==0) {</span></a>
+<a name="24815"><span class="lineNum">   24815 </span><span class="lineNoCov">          0 :     for(i=0;i&lt;*n;i++)</span></a>
+<a name="24816"><span class="lineNum">   24816 </span><span class="lineNoCov">          0 :       d[i]= std::sqrt(work[i]);</span></a>
+<a name="24817"><span class="lineNum">   24817 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;,&amp;j,&amp;j,&amp;scale,&amp;sigmx,n,&amp;k,d,n,&amp;iinfo);</span></a>
+<a name="24818"><span class="lineNum">   24818 </span>            :   }</a>
+<a name="24819"><span class="lineNum">   24819 </span>            :   return;</a>
+<a name="24820"><span class="lineNum">   24820 </span>            : }</a>
+<a name="24821"><span class="lineNum">   24821 </span>            : }</a>
+<a name="24822"><span class="lineNum">   24822 </span>            : }</a>
+<a name="24823"><span class="lineNum">   24823 </span>            : #include &lt;cmath&gt;</a>
+<a name="24824"><span class="lineNum">   24824 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="24825"><span class="lineNum">   24825 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="24826"><span class="lineNum">   24826 </span>            : </a>
+<a name="24827"><span class="lineNum">   24827 </span>            : #include &quot;real.h&quot;</a>
+<a name="24828"><span class="lineNum">   24828 </span>            : </a>
+<a name="24829"><span class="lineNum">   24829 </span>            : #ifdef _MSC_VER</a>
+<a name="24830"><span class="lineNum">   24830 </span>            : #pragma warning(disable: 4723) /*division by zero - is used on purpose here*/</a>
+<a name="24831"><span class="lineNum">   24831 </span>            : #endif</a>
+<a name="24832"><span class="lineNum">   24832 </span>            : </a>
+<a name="24833"><span class="lineNum">   24833 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="24834"><span class="lineNum">   24834 </span>            : namespace PLMD{</a>
+<a name="24835"><span class="lineNum">   24835 </span>            : namespace lapack{</a>
+<a name="24836"><span class="lineNum">   24836 </span>            : using namespace blas;</a>
+<a name="24837"><span class="lineNum">   24837 </span>            : void </a>
+<a name="24838"><span class="lineNum">   24838 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasq2,SLASQ2)(int *n, </span></a>
+<a name="24839"><span class="lineNum">   24839 </span>            :                         float *z__, </a>
+<a name="24840"><span class="lineNum">   24840 </span>            :                         int *info)</a>
+<a name="24841"><span class="lineNum">   24841 </span>            : {</a>
+<a name="24842"><span class="lineNum">   24842 </span>            :     int i__1, i__2, i__3;</a>
+<a name="24843"><span class="lineNum">   24843 </span>            :     float d__1, d__2;</a>
+<a name="24844"><span class="lineNum">   24844 </span>            : </a>
+<a name="24845"><span class="lineNum">   24845 </span>            :     float d__, e;</a>
+<a name="24846"><span class="lineNum">   24846 </span>            :     int k;</a>
+<a name="24847"><span class="lineNum">   24847 </span>            :     float s, t;</a>
+<a name="24848"><span class="lineNum">   24848 </span>            :     int i0, i4, n0, pp;</a>
+<a name="24849"><span class="lineNum">   24849 </span>            :     float dee, eps, tol;</a>
+<a name="24850"><span class="lineNum">   24850 </span>            :     int ipn4;</a>
+<a name="24851"><span class="lineNum">   24851 </span>            :     float tol2;</a>
+<a name="24852"><span class="lineNum">   24852 </span>            :     int ieee;</a>
+<a name="24853"><span class="lineNum">   24853 </span>            :     int nbig;</a>
+<a name="24854"><span class="lineNum">   24854 </span>            :     float dmin__, emin, emax;</a>
+<a name="24855"><span class="lineNum">   24855 </span>            :     int kmin, ndiv, iter;</a>
+<a name="24856"><span class="lineNum">   24856 </span>            :     float qmin, temp, qmax, zmax;</a>
+<a name="24857"><span class="lineNum">   24857 </span>            :     int splt, nfail;</a>
+<a name="24858"><span class="lineNum">   24858 </span>            :     float desig, trace, sigma;</a>
+<a name="24859"><span class="lineNum">   24859 </span>            :     int iinfo;</a>
+<a name="24860"><span class="lineNum">   24860 </span>            :     float deemin;</a>
+<a name="24861"><span class="lineNum">   24861 </span>            :     int iwhila, iwhilb;</a>
+<a name="24862"><span class="lineNum">   24862 </span>            :     float oldemn, safmin, minval;</a>
+<a name="24863"><span class="lineNum">   24863 </span>            :     float posinf,neginf,negzro,newzro;</a>
+<a name="24864"><span class="lineNum">   24864 </span>            :     float zero = 0.0;</a>
+<a name="24865"><span class="lineNum">   24865 </span>            :     float one = 1.0;</a>
+<a name="24866"><span class="lineNum">   24866 </span>            : </a>
+<a name="24867"><span class="lineNum">   24867 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="24868"><span class="lineNum">   24868 </span>            : </a>
+<a name="24869"><span class="lineNum">   24869 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="24870"><span class="lineNum">   24870 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="24871"><span class="lineNum">   24871 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="24872"><span class="lineNum">   24872 </span>            :     safmin = minval*(1.0+eps);</a>
+<a name="24873"><span class="lineNum">   24873 </span>            : </a>
+<a name="24874"><span class="lineNum">   24874 </span>            :     tol = eps * 100.;</a>
+<a name="24875"><span class="lineNum">   24875 </span>            : </a>
+<a name="24876"><span class="lineNum">   24876 </span>            :     d__1 = tol;</a>
+<a name="24877"><span class="lineNum">   24877 </span>            :     tol2 = d__1 * d__1;</a>
+<a name="24878"><span class="lineNum">   24878 </span>            : </a>
+<a name="24879"><span class="lineNum">   24879 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="24880"><span class="lineNum">   24880 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="24881"><span class="lineNum">   24881 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24882"><span class="lineNum">   24882 </span><span class="lineNoCov">          0 :     } else if (*n == 0) {</span></a>
+<a name="24883"><span class="lineNum">   24883 </span>            :         return;</a>
+<a name="24884"><span class="lineNum">   24884 </span><span class="lineNoCov">          0 :     } else if (*n == 1) {</span></a>
+<a name="24885"><span class="lineNum">   24885 </span>            : </a>
+<a name="24886"><span class="lineNum">   24886 </span><span class="lineNoCov">          0 :         if (z__[1] &lt; 0.) {</span></a>
+<a name="24887"><span class="lineNum">   24887 </span><span class="lineNoCov">          0 :             *info = -201;</span></a>
+<a name="24888"><span class="lineNum">   24888 </span>            :         }</a>
+<a name="24889"><span class="lineNum">   24889 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24890"><span class="lineNum">   24890 </span><span class="lineNoCov">          0 :     } else if (*n == 2) {</span></a>
+<a name="24891"><span class="lineNum">   24891 </span>            : </a>
+<a name="24892"><span class="lineNum">   24892 </span><span class="lineNoCov">          0 :         if (z__[2] &lt; 0. || z__[3] &lt; 0.) {</span></a>
+<a name="24893"><span class="lineNum">   24893 </span><span class="lineNoCov">          0 :             *info = -2;</span></a>
+<a name="24894"><span class="lineNum">   24894 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="24895"><span class="lineNum">   24895 </span><span class="lineNoCov">          0 :         } else if (z__[3] &gt; z__[1]) {</span></a>
+<a name="24896"><span class="lineNum">   24896 </span>            :             d__ = z__[3];</a>
+<a name="24897"><span class="lineNum">   24897 </span><span class="lineNoCov">          0 :             z__[3] = z__[1];</span></a>
+<a name="24898"><span class="lineNum">   24898 </span><span class="lineNoCov">          0 :             z__[1] = d__;</span></a>
+<a name="24899"><span class="lineNum">   24899 </span>            :         }</a>
+<a name="24900"><span class="lineNum">   24900 </span><span class="lineNoCov">          0 :         z__[5] = z__[1] + z__[2] + z__[3];</span></a>
+<a name="24901"><span class="lineNum">   24901 </span><span class="lineNoCov">          0 :         if (z__[2] &gt; z__[3] * tol2) {</span></a>
+<a name="24902"><span class="lineNum">   24902 </span><span class="lineNoCov">          0 :             t = (z__[1] - z__[3] + z__[2]) * .5;</span></a>
+<a name="24903"><span class="lineNum">   24903 </span><span class="lineNoCov">          0 :             s = z__[3] * (z__[2] / t);</span></a>
+<a name="24904"><span class="lineNum">   24904 </span><span class="lineNoCov">          0 :             if (s &lt;= t) {</span></a>
+<a name="24905"><span class="lineNum">   24905 </span><span class="lineNoCov">          0 :                 s = z__[3] * (z__[2] / (t * ( std::sqrt(s / t + 1.) + 1.)));</span></a>
+<a name="24906"><span class="lineNum">   24906 </span>            :             } else {</a>
+<a name="24907"><span class="lineNum">   24907 </span><span class="lineNoCov">          0 :                 s = z__[3] * (z__[2] / (t +  std::sqrt(t) * std::sqrt(t + s)));</span></a>
+<a name="24908"><span class="lineNum">   24908 </span>            :             }</a>
+<a name="24909"><span class="lineNum">   24909 </span><span class="lineNoCov">          0 :             t = z__[1] + (s + z__[2]);</span></a>
+<a name="24910"><span class="lineNum">   24910 </span><span class="lineNoCov">          0 :             z__[3] *= z__[1] / t;</span></a>
+<a name="24911"><span class="lineNum">   24911 </span><span class="lineNoCov">          0 :             z__[1] = t;</span></a>
+<a name="24912"><span class="lineNum">   24912 </span>            :         }</a>
+<a name="24913"><span class="lineNum">   24913 </span><span class="lineNoCov">          0 :         z__[2] = z__[3];</span></a>
+<a name="24914"><span class="lineNum">   24914 </span><span class="lineNoCov">          0 :         z__[6] = z__[2] + z__[1];</span></a>
+<a name="24915"><span class="lineNum">   24915 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24916"><span class="lineNum">   24916 </span>            :     }</a>
+<a name="24917"><span class="lineNum">   24917 </span><span class="lineNoCov">          0 :     z__[*n * 2] = 0.;</span></a>
+<a name="24918"><span class="lineNum">   24918 </span><span class="lineNoCov">          0 :     emin = z__[2];</span></a>
+<a name="24919"><span class="lineNum">   24919 </span><span class="lineNoCov">          0 :     qmax = 0.;</span></a>
+<a name="24920"><span class="lineNum">   24920 </span>            :     zmax = 0.;</a>
+<a name="24921"><span class="lineNum">   24921 </span>            :     d__ = 0.;</a>
+<a name="24922"><span class="lineNum">   24922 </span>            :     e = 0.;</a>
+<a name="24923"><span class="lineNum">   24923 </span>            : </a>
+<a name="24924"><span class="lineNum">   24924 </span><span class="lineNoCov">          0 :     i__1 = 2*(*n - 1);</span></a>
+<a name="24925"><span class="lineNum">   24925 </span><span class="lineNoCov">          0 :     for (k = 1; k &lt;= i__1; k += 2) {</span></a>
+<a name="24926"><span class="lineNum">   24926 </span><span class="lineNoCov">          0 :         if (z__[k] &lt; 0.) {</span></a>
+<a name="24927"><span class="lineNum">   24927 </span><span class="lineNoCov">          0 :             *info = -(k + 200);</span></a>
+<a name="24928"><span class="lineNum">   24928 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="24929"><span class="lineNum">   24929 </span><span class="lineNoCov">          0 :         } else if (z__[k + 1] &lt; 0.) {</span></a>
+<a name="24930"><span class="lineNum">   24930 </span><span class="lineNoCov">          0 :             *info = -(k + 201);</span></a>
+<a name="24931"><span class="lineNum">   24931 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="24932"><span class="lineNum">   24932 </span>            :         }</a>
+<a name="24933"><span class="lineNum">   24933 </span><span class="lineNoCov">          0 :         d__ += z__[k];</span></a>
+<a name="24934"><span class="lineNum">   24934 </span><span class="lineNoCov">          0 :         e += z__[k + 1];</span></a>
+<a name="24935"><span class="lineNum">   24935 </span><span class="lineNoCov">          0 :         d__1 = qmax, d__2 = z__[k];</span></a>
+<a name="24936"><span class="lineNum">   24936 </span><span class="lineNoCov">          0 :         qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="24937"><span class="lineNum">   24937 </span>            :         d__1 = emin, d__2 = z__[k + 1];</a>
+<a name="24938"><span class="lineNum">   24938 </span><span class="lineNoCov">          0 :         emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="24939"><span class="lineNum">   24939 </span><span class="lineNoCov">          0 :         d__1 = (qmax&gt;zmax) ? qmax : zmax;</span></a>
+<a name="24940"><span class="lineNum">   24940 </span>            :         d__2 = z__[k + 1];</a>
+<a name="24941"><span class="lineNum">   24941 </span><span class="lineNoCov">          0 :         zmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="24942"><span class="lineNum">   24942 </span>            :     }</a>
+<a name="24943"><span class="lineNum">   24943 </span><span class="lineNoCov">          0 :     if (z__[(*n &lt;&lt; 1) - 1] &lt; 0.) {</span></a>
+<a name="24944"><span class="lineNum">   24944 </span><span class="lineNoCov">          0 :         *info = -((*n &lt;&lt; 1) + 199);</span></a>
+<a name="24945"><span class="lineNum">   24945 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24946"><span class="lineNum">   24946 </span>            :     }</a>
+<a name="24947"><span class="lineNum">   24947 </span><span class="lineNoCov">          0 :     d__ += z__[(*n &lt;&lt; 1) - 1];</span></a>
+<a name="24948"><span class="lineNum">   24948 </span><span class="lineNoCov">          0 :     d__1 = qmax, d__2 = z__[(*n &lt;&lt; 1) - 1];</span></a>
+<a name="24949"><span class="lineNum">   24949 </span><span class="lineNoCov">          0 :     qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="24950"><span class="lineNum">   24950 </span>            : </a>
+<a name="24951"><span class="lineNum">   24951 </span><span class="lineNoCov">          0 :     if (std::abs(e)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="24952"><span class="lineNum">   24952 </span>            :         i__1 = *n;</a>
+<a name="24953"><span class="lineNum">   24953 </span><span class="lineNoCov">          0 :         for (k = 2; k &lt;= i__1; ++k) {</span></a>
+<a name="24954"><span class="lineNum">   24954 </span><span class="lineNoCov">          0 :             z__[k] = z__[(k &lt;&lt; 1) - 1];</span></a>
+<a name="24955"><span class="lineNum">   24955 </span>            :         }</a>
+<a name="24956"><span class="lineNum">   24956 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(&quot;D&quot;, n, &amp;z__[1], &amp;iinfo);</span></a>
+<a name="24957"><span class="lineNum">   24957 </span><span class="lineNoCov">          0 :         z__[(*n &lt;&lt; 1) - 1] = d__;</span></a>
+<a name="24958"><span class="lineNum">   24958 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24959"><span class="lineNum">   24959 </span>            :     }</a>
+<a name="24960"><span class="lineNum">   24960 </span>            : </a>
+<a name="24961"><span class="lineNum">   24961 </span><span class="lineNoCov">          0 :     trace = d__ + e;</span></a>
+<a name="24962"><span class="lineNum">   24962 </span>            : </a>
+<a name="24963"><span class="lineNum">   24963 </span><span class="lineNoCov">          0 :     if (std::abs(trace)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="24964"><span class="lineNum">   24964 </span><span class="lineNoCov">          0 :         z__[(*n &lt;&lt; 1) - 1] = 0.;</span></a>
+<a name="24965"><span class="lineNum">   24965 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="24966"><span class="lineNum">   24966 </span>            :     }</a>
+<a name="24967"><span class="lineNum">   24967 </span>            : </a>
+<a name="24968"><span class="lineNum">   24968 </span><span class="lineNoCov">          0 :     ieee = 1;</span></a>
+<a name="24969"><span class="lineNum">   24969 </span><span class="lineNoCov">          0 :     posinf = one/zero;</span></a>
+<a name="24970"><span class="lineNum">   24970 </span><span class="lineNoCov">          0 :     if(posinf&lt;=1.0)</span></a>
+<a name="24971"><span class="lineNum">   24971 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24972"><span class="lineNum">   24972 </span>            :     neginf = -one/zero;</a>
+<a name="24973"><span class="lineNum">   24973 </span><span class="lineNoCov">          0 :     if(neginf&gt;=0.0)</span></a>
+<a name="24974"><span class="lineNum">   24974 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24975"><span class="lineNum">   24975 </span><span class="lineNoCov">          0 :     negzro = one/(neginf+one);</span></a>
+<a name="24976"><span class="lineNum">   24976 </span><span class="lineNoCov">          0 :     if(std::abs(negzro)&gt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="24977"><span class="lineNum">   24977 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24978"><span class="lineNum">   24978 </span><span class="lineNoCov">          0 :     neginf = one/negzro;</span></a>
+<a name="24979"><span class="lineNum">   24979 </span><span class="lineNoCov">          0 :     if(neginf&gt;=0)</span></a>
+<a name="24980"><span class="lineNum">   24980 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24981"><span class="lineNum">   24981 </span><span class="lineNoCov">          0 :     newzro = negzro + zero;</span></a>
+<a name="24982"><span class="lineNum">   24982 </span><span class="lineNoCov">          0 :     if(std::abs(newzro-zero)&gt;PLUMED_GMX_FLOAT_MIN)</span></a>
+<a name="24983"><span class="lineNum">   24983 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24984"><span class="lineNum">   24984 </span><span class="lineNoCov">          0 :     posinf = one /newzro;</span></a>
+<a name="24985"><span class="lineNum">   24985 </span><span class="lineNoCov">          0 :     if(posinf&lt;=one)</span></a>
+<a name="24986"><span class="lineNum">   24986 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24987"><span class="lineNum">   24987 </span><span class="lineNoCov">          0 :     neginf = neginf*posinf;</span></a>
+<a name="24988"><span class="lineNum">   24988 </span><span class="lineNoCov">          0 :     if(neginf&gt;=zero)</span></a>
+<a name="24989"><span class="lineNum">   24989 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24990"><span class="lineNum">   24990 </span><span class="lineNoCov">          0 :     posinf = posinf*posinf;</span></a>
+<a name="24991"><span class="lineNum">   24991 </span><span class="lineNoCov">          0 :     if(posinf&lt;=1.0)</span></a>
+<a name="24992"><span class="lineNum">   24992 </span><span class="lineNoCov">          0 :       ieee = 0;</span></a>
+<a name="24993"><span class="lineNum">   24993 </span>            : </a>
+<a name="24994"><span class="lineNum">   24994 </span><span class="lineNoCov">          0 :     for (k = *n &lt;&lt; 1; k &gt;= 2; k += -2) {</span></a>
+<a name="24995"><span class="lineNum">   24995 </span><span class="lineNoCov">          0 :         z__[k * 2] = 0.;</span></a>
+<a name="24996"><span class="lineNum">   24996 </span><span class="lineNoCov">          0 :         z__[(k &lt;&lt; 1) - 1] = z__[k];</span></a>
+<a name="24997"><span class="lineNum">   24997 </span><span class="lineNoCov">          0 :         z__[(k &lt;&lt; 1) - 2] = 0.;</span></a>
+<a name="24998"><span class="lineNum">   24998 </span><span class="lineNoCov">          0 :         z__[(k &lt;&lt; 1) - 3] = z__[k - 1];</span></a>
+<a name="24999"><span class="lineNum">   24999 </span>            :     }</a>
+<a name="25000"><span class="lineNum">   25000 </span>            : </a>
+<a name="25001"><span class="lineNum">   25001 </span><span class="lineNoCov">          0 :     i0 = 1;</span></a>
+<a name="25002"><span class="lineNum">   25002 </span><span class="lineNoCov">          0 :     n0 = *n;</span></a>
+<a name="25003"><span class="lineNum">   25003 </span>            : </a>
+<a name="25004"><span class="lineNum">   25004 </span><span class="lineNoCov">          0 :     if (z__[(i0 &lt;&lt; 2) - 3] * 1.5 &lt; z__[(n0 &lt;&lt; 2) - 3]) {</span></a>
+<a name="25005"><span class="lineNum">   25005 </span><span class="lineNoCov">          0 :         ipn4 = 4*(i0 + n0);</span></a>
+<a name="25006"><span class="lineNum">   25006 </span><span class="lineNoCov">          0 :         i__1 = 2*(i0 + n0 - 1);</span></a>
+<a name="25007"><span class="lineNum">   25007 </span><span class="lineNoCov">          0 :         for (i4 = i0 &lt;&lt; 2; i4 &lt;= i__1; i4 += 4) {</span></a>
+<a name="25008"><span class="lineNum">   25008 </span><span class="lineNoCov">          0 :             temp = z__[i4 - 3];</span></a>
+<a name="25009"><span class="lineNum">   25009 </span><span class="lineNoCov">          0 :             z__[i4 - 3] = z__[ipn4 - i4 - 3];</span></a>
+<a name="25010"><span class="lineNum">   25010 </span><span class="lineNoCov">          0 :             z__[ipn4 - i4 - 3] = temp;</span></a>
+<a name="25011"><span class="lineNum">   25011 </span><span class="lineNoCov">          0 :             temp = z__[i4 - 1];</span></a>
+<a name="25012"><span class="lineNum">   25012 </span><span class="lineNoCov">          0 :             z__[i4 - 1] = z__[ipn4 - i4 - 5];</span></a>
+<a name="25013"><span class="lineNum">   25013 </span><span class="lineNoCov">          0 :             z__[ipn4 - i4 - 5] = temp;</span></a>
+<a name="25014"><span class="lineNum">   25014 </span>            :         }</a>
+<a name="25015"><span class="lineNum">   25015 </span>            :     }</a>
+<a name="25016"><span class="lineNum">   25016 </span>            : </a>
+<a name="25017"><span class="lineNum">   25017 </span><span class="lineNoCov">          0 :     pp = 0;</span></a>
+<a name="25018"><span class="lineNum">   25018 </span>            : </a>
+<a name="25019"><span class="lineNum">   25019 </span><span class="lineNoCov">          0 :     for (k = 1; k &lt;= 2; ++k) {</span></a>
+<a name="25020"><span class="lineNum">   25020 </span>            : </a>
+<a name="25021"><span class="lineNum">   25021 </span><span class="lineNoCov">          0 :         d__ = z__[(n0 &lt;&lt; 2) + pp - 3];</span></a>
+<a name="25022"><span class="lineNum">   25022 </span><span class="lineNoCov">          0 :         i__1 = (i0 &lt;&lt; 2) + pp;</span></a>
+<a name="25023"><span class="lineNum">   25023 </span><span class="lineNoCov">          0 :         for (i4 = 4*(n0 - 1) + pp; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="25024"><span class="lineNum">   25024 </span><span class="lineNoCov">          0 :             if (z__[i4 - 1] &lt;= tol2 * d__) {</span></a>
+<a name="25025"><span class="lineNum">   25025 </span><span class="lineNoCov">          0 :                 z__[i4 - 1] = -0.;</span></a>
+<a name="25026"><span class="lineNum">   25026 </span><span class="lineNoCov">          0 :                 d__ = z__[i4 - 3];</span></a>
+<a name="25027"><span class="lineNum">   25027 </span>            :             } else {</a>
+<a name="25028"><span class="lineNum">   25028 </span><span class="lineNoCov">          0 :                 d__ = z__[i4 - 3] * (d__ / (d__ + z__[i4 - 1]));</span></a>
+<a name="25029"><span class="lineNum">   25029 </span>            :             }</a>
+<a name="25030"><span class="lineNum">   25030 </span>            :         }</a>
+<a name="25031"><span class="lineNum">   25031 </span>            : </a>
+<a name="25032"><span class="lineNum">   25032 </span><span class="lineNoCov">          0 :         emin = z__[(i0 &lt;&lt; 2) + pp + 1];</span></a>
+<a name="25033"><span class="lineNum">   25033 </span><span class="lineNoCov">          0 :         d__ = z__[(i0 &lt;&lt; 2) + pp - 3];</span></a>
+<a name="25034"><span class="lineNum">   25034 </span>            :         i__1 = 4*(n0 - 1) + pp;</a>
+<a name="25035"><span class="lineNum">   25035 </span><span class="lineNoCov">          0 :         for (i4 = (i0 &lt;&lt; 2) + pp; i4 &lt;= i__1; i4 += 4) {</span></a>
+<a name="25036"><span class="lineNum">   25036 </span><span class="lineNoCov">          0 :             z__[i4 - (pp &lt;&lt; 1) - 2] = d__ + z__[i4 - 1];</span></a>
+<a name="25037"><span class="lineNum">   25037 </span><span class="lineNoCov">          0 :             if (z__[i4 - 1] &lt;= tol2 * d__) {</span></a>
+<a name="25038"><span class="lineNum">   25038 </span><span class="lineNoCov">          0 :                 z__[i4 - 1] = -0.;</span></a>
+<a name="25039"><span class="lineNum">   25039 </span><span class="lineNoCov">          0 :                 z__[i4 - (pp &lt;&lt; 1) - 2] = d__;</span></a>
+<a name="25040"><span class="lineNum">   25040 </span><span class="lineNoCov">          0 :                 z__[i4 - (pp &lt;&lt; 1)] = 0.;</span></a>
+<a name="25041"><span class="lineNum">   25041 </span><span class="lineNoCov">          0 :                 d__ = z__[i4 + 1];</span></a>
+<a name="25042"><span class="lineNum">   25042 </span><span class="lineNoCov">          0 :             } else if (safmin * z__[i4 + 1] &lt; z__[i4 - (pp &lt;&lt; 1) - 2] &amp;&amp; </span></a>
+<a name="25043"><span class="lineNum">   25043 </span><span class="lineNoCov">          0 :                     safmin * z__[i4 - (pp &lt;&lt; 1) - 2] &lt; z__[i4 + 1]) {</span></a>
+<a name="25044"><span class="lineNum">   25044 </span><span class="lineNoCov">          0 :                 temp = z__[i4 + 1] / z__[i4 - (pp &lt;&lt; 1) - 2];</span></a>
+<a name="25045"><span class="lineNum">   25045 </span><span class="lineNoCov">          0 :                 z__[i4 - (pp &lt;&lt; 1)] = z__[i4 - 1] * temp;</span></a>
+<a name="25046"><span class="lineNum">   25046 </span><span class="lineNoCov">          0 :                 d__ *= temp;</span></a>
+<a name="25047"><span class="lineNum">   25047 </span>            :             } else {</a>
+<a name="25048"><span class="lineNum">   25048 </span><span class="lineNoCov">          0 :                 z__[i4 - (pp &lt;&lt; 1)] = z__[i4 + 1] * (z__[i4 - 1] / z__[i4 - (</span></a>
+<a name="25049"><span class="lineNum">   25049 </span>            :                         pp &lt;&lt; 1) - 2]);</a>
+<a name="25050"><span class="lineNum">   25050 </span><span class="lineNoCov">          0 :                 d__ = z__[i4 + 1] * (d__ / z__[i4 - (pp &lt;&lt; 1) - 2]);</span></a>
+<a name="25051"><span class="lineNum">   25051 </span>            :             }</a>
+<a name="25052"><span class="lineNum">   25052 </span><span class="lineNoCov">          0 :             d__1 = emin, d__2 = z__[i4 - (pp &lt;&lt; 1)];</span></a>
+<a name="25053"><span class="lineNum">   25053 </span><span class="lineNoCov">          0 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25054"><span class="lineNum">   25054 </span>            :         }</a>
+<a name="25055"><span class="lineNum">   25055 </span><span class="lineNoCov">          0 :         z__[(n0 &lt;&lt; 2) - pp - 2] = d__;</span></a>
+<a name="25056"><span class="lineNum">   25056 </span>            : </a>
+<a name="25057"><span class="lineNum">   25057 </span>            : </a>
+<a name="25058"><span class="lineNum">   25058 </span><span class="lineNoCov">          0 :         qmax = z__[(i0 &lt;&lt; 2) - pp - 2];</span></a>
+<a name="25059"><span class="lineNum">   25059 </span><span class="lineNoCov">          0 :         i__1 = (n0 &lt;&lt; 2) - pp - 2;</span></a>
+<a name="25060"><span class="lineNum">   25060 </span><span class="lineNoCov">          0 :         for (i4 = (i0 &lt;&lt; 2) - pp + 2; i4 &lt;= i__1; i4 += 4) {</span></a>
+<a name="25061"><span class="lineNum">   25061 </span><span class="lineNoCov">          0 :             d__1 = qmax, d__2 = z__[i4];</span></a>
+<a name="25062"><span class="lineNum">   25062 </span><span class="lineNoCov">          0 :             qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25063"><span class="lineNum">   25063 </span>            :         }</a>
+<a name="25064"><span class="lineNum">   25064 </span>            : </a>
+<a name="25065"><span class="lineNum">   25065 </span><span class="lineNoCov">          0 :         pp = 1 - pp;</span></a>
+<a name="25066"><span class="lineNum">   25066 </span>            :     }</a>
+<a name="25067"><span class="lineNum">   25067 </span>            : </a>
+<a name="25068"><span class="lineNum">   25068 </span><span class="lineNoCov">          0 :     iter = 2;</span></a>
+<a name="25069"><span class="lineNum">   25069 </span><span class="lineNoCov">          0 :     nfail = 0;</span></a>
+<a name="25070"><span class="lineNum">   25070 </span><span class="lineNoCov">          0 :     ndiv = 2*(n0 - i0);</span></a>
+<a name="25071"><span class="lineNum">   25071 </span>            : </a>
+<a name="25072"><span class="lineNum">   25072 </span><span class="lineNoCov">          0 :     i__1 = *n + 1;</span></a>
+<a name="25073"><span class="lineNum">   25073 </span><span class="lineNoCov">          0 :     for (iwhila = 1; iwhila &lt;= i__1; ++iwhila) {</span></a>
+<a name="25074"><span class="lineNum">   25074 </span><span class="lineNoCov">          0 :         if (n0 &lt; 1) {</span></a>
+<a name="25075"><span class="lineNum">   25075 </span><span class="lineNoCov">          0 :             goto L170;</span></a>
+<a name="25076"><span class="lineNum">   25076 </span>            :         }</a>
+<a name="25077"><span class="lineNum">   25077 </span>            : </a>
+<a name="25078"><span class="lineNum">   25078 </span><span class="lineNoCov">          0 :         desig = 0.;</span></a>
+<a name="25079"><span class="lineNum">   25079 </span><span class="lineNoCov">          0 :         if (n0 == *n) {</span></a>
+<a name="25080"><span class="lineNum">   25080 </span><span class="lineNoCov">          0 :             sigma = 0.;</span></a>
+<a name="25081"><span class="lineNum">   25081 </span>            :         } else {</a>
+<a name="25082"><span class="lineNum">   25082 </span><span class="lineNoCov">          0 :             sigma = -z__[(n0 &lt;&lt; 2) - 1];</span></a>
+<a name="25083"><span class="lineNum">   25083 </span>            :         }</a>
+<a name="25084"><span class="lineNum">   25084 </span><span class="lineNoCov">          0 :         if (sigma &lt; 0.) {</span></a>
+<a name="25085"><span class="lineNum">   25085 </span><span class="lineNoCov">          0 :             *info = 1;</span></a>
+<a name="25086"><span class="lineNum">   25086 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="25087"><span class="lineNum">   25087 </span>            :         }</a>
+<a name="25088"><span class="lineNum">   25088 </span>            : </a>
+<a name="25089"><span class="lineNum">   25089 </span>            :         emax = 0.;</a>
+<a name="25090"><span class="lineNum">   25090 </span><span class="lineNoCov">          0 :         if (n0 &gt; i0) {</span></a>
+<a name="25091"><span class="lineNum">   25091 </span><span class="lineNoCov">          0 :             emin = std::abs(z__[(n0 &lt;&lt; 2) - 5]);</span></a>
+<a name="25092"><span class="lineNum">   25092 </span>            :         } else {</a>
+<a name="25093"><span class="lineNum">   25093 </span>            :             emin = 0.;</a>
+<a name="25094"><span class="lineNum">   25094 </span>            :         }</a>
+<a name="25095"><span class="lineNum">   25095 </span><span class="lineNoCov">          0 :         qmin = z__[(n0 &lt;&lt; 2) - 3];</span></a>
+<a name="25096"><span class="lineNum">   25096 </span><span class="lineNoCov">          0 :         qmax = qmin;</span></a>
+<a name="25097"><span class="lineNum">   25097 </span><span class="lineNoCov">          0 :         for (i4 = n0 &lt;&lt; 2; i4 &gt;= 8; i4 += -4) {</span></a>
+<a name="25098"><span class="lineNum">   25098 </span><span class="lineNoCov">          0 :             if (z__[i4 - 5] &lt;= 0.) {</span></a>
+<a name="25099"><span class="lineNum">   25099 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="25100"><span class="lineNum">   25100 </span>            :             }</a>
+<a name="25101"><span class="lineNum">   25101 </span><span class="lineNoCov">          0 :             if (qmin &gt;= emax * 4.) {</span></a>
+<a name="25102"><span class="lineNum">   25102 </span><span class="lineNoCov">          0 :                 d__1 = qmin, d__2 = z__[i4 - 3];</span></a>
+<a name="25103"><span class="lineNum">   25103 </span><span class="lineNoCov">          0 :                 qmin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25104"><span class="lineNum">   25104 </span>            :                 d__1 = emax, d__2 = z__[i4 - 5];</a>
+<a name="25105"><span class="lineNum">   25105 </span><span class="lineNoCov">          0 :                 emax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25106"><span class="lineNum">   25106 </span>            :             }</a>
+<a name="25107"><span class="lineNum">   25107 </span><span class="lineNoCov">          0 :             d__1 = qmax, d__2 = z__[i4 - 7] + z__[i4 - 5];</span></a>
+<a name="25108"><span class="lineNum">   25108 </span><span class="lineNoCov">          0 :             qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25109"><span class="lineNum">   25109 </span>            :             d__1 = emin, d__2 = z__[i4 - 5];</a>
+<a name="25110"><span class="lineNum">   25110 </span><span class="lineNoCov">          0 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25111"><span class="lineNum">   25111 </span>            :         }</a>
+<a name="25112"><span class="lineNum">   25112 </span>            :         i4 = 4;</a>
+<a name="25113"><span class="lineNum">   25113 </span>            : </a>
+<a name="25114"><span class="lineNum">   25114 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="25115"><span class="lineNum">   25115 </span><span class="lineNoCov">          0 :         i0 = i4 / 4;</span></a>
+<a name="25116"><span class="lineNum">   25116 </span><span class="lineNoCov">          0 :         pp = 0;</span></a>
+<a name="25117"><span class="lineNum">   25117 </span>            : </a>
+<a name="25118"><span class="lineNum">   25118 </span><span class="lineNoCov">          0 :         if (n0 - i0 &gt; 1) {</span></a>
+<a name="25119"><span class="lineNum">   25119 </span><span class="lineNoCov">          0 :             dee = z__[(i0 &lt;&lt; 2) - 3];</span></a>
+<a name="25120"><span class="lineNum">   25120 </span>            :             deemin = dee;</a>
+<a name="25121"><span class="lineNum">   25121 </span>            :             kmin = i0;</a>
+<a name="25122"><span class="lineNum">   25122 </span><span class="lineNoCov">          0 :             i__2 = (n0 &lt;&lt; 2) - 3;</span></a>
+<a name="25123"><span class="lineNum">   25123 </span><span class="lineNoCov">          0 :             for (i4 = (i0 &lt;&lt; 2) - 3; i4 &lt;= i__2; i4 += 4) {</span></a>
+<a name="25124"><span class="lineNum">   25124 </span><span class="lineNoCov">          0 :                 dee = z__[i4] * (dee / (dee + z__[i4 - 2]));</span></a>
+<a name="25125"><span class="lineNum">   25125 </span><span class="lineNoCov">          0 :                 if (dee &lt;= deemin) {</span></a>
+<a name="25126"><span class="lineNum">   25126 </span>            :                     deemin = dee;</a>
+<a name="25127"><span class="lineNum">   25127 </span><span class="lineNoCov">          0 :                     kmin = (i4 + 3) / 4;</span></a>
+<a name="25128"><span class="lineNum">   25128 </span>            :                 }</a>
+<a name="25129"><span class="lineNum">   25129 </span>            :             }</a>
+<a name="25130"><span class="lineNum">   25130 </span><span class="lineNoCov">          0 :             if (2*(kmin - i0) &lt; n0 - kmin &amp;&amp; deemin &lt;= z__[(n0 &lt;&lt; 2) - 3] * </span></a>
+<a name="25131"><span class="lineNum">   25131 </span>            :                     .5) {</a>
+<a name="25132"><span class="lineNum">   25132 </span><span class="lineNoCov">          0 :                 ipn4 = 4*(i0 + n0);</span></a>
+<a name="25133"><span class="lineNum">   25133 </span><span class="lineNoCov">          0 :                 pp = 2;</span></a>
+<a name="25134"><span class="lineNum">   25134 </span><span class="lineNoCov">          0 :                 i__2 = 2*(i0 + n0 - 1);</span></a>
+<a name="25135"><span class="lineNum">   25135 </span><span class="lineNoCov">          0 :                 for (i4 = i0 &lt;&lt; 2; i4 &lt;= i__2; i4 += 4) {</span></a>
+<a name="25136"><span class="lineNum">   25136 </span><span class="lineNoCov">          0 :                     temp = z__[i4 - 3];</span></a>
+<a name="25137"><span class="lineNum">   25137 </span><span class="lineNoCov">          0 :                     z__[i4 - 3] = z__[ipn4 - i4 - 3];</span></a>
+<a name="25138"><span class="lineNum">   25138 </span><span class="lineNoCov">          0 :                     z__[ipn4 - i4 - 3] = temp;</span></a>
+<a name="25139"><span class="lineNum">   25139 </span><span class="lineNoCov">          0 :                     temp = z__[i4 - 2];</span></a>
+<a name="25140"><span class="lineNum">   25140 </span><span class="lineNoCov">          0 :                     z__[i4 - 2] = z__[ipn4 - i4 - 2];</span></a>
+<a name="25141"><span class="lineNum">   25141 </span><span class="lineNoCov">          0 :                     z__[ipn4 - i4 - 2] = temp;</span></a>
+<a name="25142"><span class="lineNum">   25142 </span><span class="lineNoCov">          0 :                     temp = z__[i4 - 1];</span></a>
+<a name="25143"><span class="lineNum">   25143 </span><span class="lineNoCov">          0 :                     z__[i4 - 1] = z__[ipn4 - i4 - 5];</span></a>
+<a name="25144"><span class="lineNum">   25144 </span><span class="lineNoCov">          0 :                     z__[ipn4 - i4 - 5] = temp;</span></a>
+<a name="25145"><span class="lineNum">   25145 </span><span class="lineNoCov">          0 :                     temp = z__[i4];</span></a>
+<a name="25146"><span class="lineNum">   25146 </span><span class="lineNoCov">          0 :                     z__[i4] = z__[ipn4 - i4 - 4];</span></a>
+<a name="25147"><span class="lineNum">   25147 </span><span class="lineNoCov">          0 :                     z__[ipn4 - i4 - 4] = temp;</span></a>
+<a name="25148"><span class="lineNum">   25148 </span>            :                 }</a>
+<a name="25149"><span class="lineNum">   25149 </span>            :             }</a>
+<a name="25150"><span class="lineNum">   25150 </span>            :         }</a>
+<a name="25151"><span class="lineNum">   25151 </span>            : </a>
+<a name="25152"><span class="lineNum">   25152 </span>            : </a>
+<a name="25153"><span class="lineNum">   25153 </span><span class="lineNoCov">          0 :         d__1 = 0., d__2 = qmin -  std::sqrt(qmin) * 2. * std::sqrt(emax);</span></a>
+<a name="25154"><span class="lineNum">   25154 </span><span class="lineNoCov">          0 :         dmin__ = -((d__1&gt;d__2) ? d__1 : d__2);</span></a>
+<a name="25155"><span class="lineNum">   25155 </span>            : </a>
+<a name="25156"><span class="lineNum">   25156 </span><span class="lineNoCov">          0 :         nbig = (n0 - i0 + 1) * 30;</span></a>
+<a name="25157"><span class="lineNum">   25157 </span>            :         i__2 = nbig;</a>
+<a name="25158"><span class="lineNum">   25158 </span><span class="lineNoCov">          0 :         for (iwhilb = 1; iwhilb &lt;= i__2; ++iwhilb) {</span></a>
+<a name="25159"><span class="lineNum">   25159 </span><span class="lineNoCov">          0 :             if (i0 &gt; n0) {</span></a>
+<a name="25160"><span class="lineNum">   25160 </span><span class="lineNoCov">          0 :                 goto L150;</span></a>
+<a name="25161"><span class="lineNum">   25161 </span>            :             }</a>
+<a name="25162"><span class="lineNum">   25162 </span>            : </a>
+<a name="25163"><span class="lineNum">   25163 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasq3,SLASQ3)(&amp;i0, &amp;n0, &amp;z__[1], &amp;pp, &amp;dmin__, &amp;sigma, &amp;desig, &amp;qmax, &amp;</span></a>
+<a name="25164"><span class="lineNum">   25164 </span>            :                     nfail, &amp;iter, &amp;ndiv, &amp;ieee);</a>
+<a name="25165"><span class="lineNum">   25165 </span>            : </a>
+<a name="25166"><span class="lineNum">   25166 </span><span class="lineNoCov">          0 :             pp = 1 - pp;</span></a>
+<a name="25167"><span class="lineNum">   25167 </span>            : </a>
+<a name="25168"><span class="lineNum">   25168 </span><span class="lineNoCov">          0 :             if (pp == 0 &amp;&amp; n0 - i0 &gt;= 3) {</span></a>
+<a name="25169"><span class="lineNum">   25169 </span><span class="lineNoCov">          0 :                 if (z__[n0 * 4] &lt;= tol2 * qmax || z__[(n0 &lt;&lt; 2) - 1] &lt;= tol2 *</span></a>
+<a name="25170"><span class="lineNum">   25170 </span>            :                          sigma) {</a>
+<a name="25171"><span class="lineNum">   25171 </span><span class="lineNoCov">          0 :                     splt = i0 - 1;</span></a>
+<a name="25172"><span class="lineNum">   25172 </span><span class="lineNoCov">          0 :                     qmax = z__[(i0 &lt;&lt; 2) - 3];</span></a>
+<a name="25173"><span class="lineNum">   25173 </span><span class="lineNoCov">          0 :                     emin = z__[(i0 &lt;&lt; 2) - 1];</span></a>
+<a name="25174"><span class="lineNum">   25174 </span><span class="lineNoCov">          0 :                     oldemn = z__[i0 * 4];</span></a>
+<a name="25175"><span class="lineNum">   25175 </span><span class="lineNoCov">          0 :                     i__3 = 4*(n0 - 3);</span></a>
+<a name="25176"><span class="lineNum">   25176 </span><span class="lineNoCov">          0 :                     for (i4 = i0 &lt;&lt; 2; i4 &lt;= i__3; i4 += 4) {</span></a>
+<a name="25177"><span class="lineNum">   25177 </span><span class="lineNoCov">          0 :                         if (z__[i4] &lt;= tol2 * z__[i4 - 3] || z__[i4 - 1] &lt;= </span></a>
+<a name="25178"><span class="lineNum">   25178 </span><span class="lineNoCov">          0 :                                 tol2 * sigma) {</span></a>
+<a name="25179"><span class="lineNum">   25179 </span><span class="lineNoCov">          0 :                             z__[i4 - 1] = -sigma;</span></a>
+<a name="25180"><span class="lineNum">   25180 </span><span class="lineNoCov">          0 :                             splt = i4 / 4;</span></a>
+<a name="25181"><span class="lineNum">   25181 </span><span class="lineNoCov">          0 :                             qmax = 0.;</span></a>
+<a name="25182"><span class="lineNum">   25182 </span><span class="lineNoCov">          0 :                             emin = z__[i4 + 3];</span></a>
+<a name="25183"><span class="lineNum">   25183 </span><span class="lineNoCov">          0 :                             oldemn = z__[i4 + 4];</span></a>
+<a name="25184"><span class="lineNum">   25184 </span>            :                         } else {</a>
+<a name="25185"><span class="lineNum">   25185 </span><span class="lineNoCov">          0 :                             d__1 = qmax, d__2 = z__[i4 + 1];</span></a>
+<a name="25186"><span class="lineNum">   25186 </span><span class="lineNoCov">          0 :                             qmax = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25187"><span class="lineNum">   25187 </span>            :                             d__1 = emin, d__2 = z__[i4 - 1];</a>
+<a name="25188"><span class="lineNum">   25188 </span><span class="lineNoCov">          0 :                             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25189"><span class="lineNum">   25189 </span>            :                             d__1 = oldemn, d__2 = z__[i4];</a>
+<a name="25190"><span class="lineNum">   25190 </span><span class="lineNoCov">          0 :                             oldemn = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25191"><span class="lineNum">   25191 </span>            :                         }</a>
+<a name="25192"><span class="lineNum">   25192 </span>            :                     }</a>
+<a name="25193"><span class="lineNum">   25193 </span><span class="lineNoCov">          0 :                     z__[(n0 &lt;&lt; 2) - 1] = emin;</span></a>
+<a name="25194"><span class="lineNum">   25194 </span><span class="lineNoCov">          0 :                     z__[n0 * 4] = oldemn;</span></a>
+<a name="25195"><span class="lineNum">   25195 </span><span class="lineNoCov">          0 :                     i0 = splt + 1;</span></a>
+<a name="25196"><span class="lineNum">   25196 </span>            :                 }</a>
+<a name="25197"><span class="lineNum">   25197 </span>            :             }</a>
+<a name="25198"><span class="lineNum">   25198 </span>            :         }</a>
+<a name="25199"><span class="lineNum">   25199 </span>            : </a>
+<a name="25200"><span class="lineNum">   25200 </span><span class="lineNoCov">          0 :         *info = 2;</span></a>
+<a name="25201"><span class="lineNum">   25201 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="25202"><span class="lineNum">   25202 </span>            : </a>
+<a name="25203"><span class="lineNum">   25203 </span>            : L150:</a>
+<a name="25204"><span class="lineNum">   25204 </span>            :         ;</a>
+<a name="25205"><span class="lineNum">   25205 </span>            :     }</a>
+<a name="25206"><span class="lineNum">   25206 </span>            : </a>
+<a name="25207"><span class="lineNum">   25207 </span><span class="lineNoCov">          0 :     *info = 3;</span></a>
+<a name="25208"><span class="lineNum">   25208 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="25209"><span class="lineNum">   25209 </span>            : </a>
+<a name="25210"><span class="lineNum">   25210 </span>            : </a>
+<a name="25211"><span class="lineNum">   25211 </span>            : L170:</a>
+<a name="25212"><span class="lineNum">   25212 </span>            : </a>
+<a name="25213"><span class="lineNum">   25213 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="25214"><span class="lineNum">   25214 </span><span class="lineNoCov">          0 :     for (k = 2; k &lt;= i__1; ++k) {</span></a>
+<a name="25215"><span class="lineNum">   25215 </span><span class="lineNoCov">          0 :         z__[k] = z__[(k &lt;&lt; 2) - 3];</span></a>
+<a name="25216"><span class="lineNum">   25216 </span>            :     }</a>
+<a name="25217"><span class="lineNum">   25217 </span>            : </a>
+<a name="25218"><span class="lineNum">   25218 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(&quot;D&quot;, n, &amp;z__[1], &amp;iinfo);</span></a>
+<a name="25219"><span class="lineNum">   25219 </span>            : </a>
+<a name="25220"><span class="lineNum">   25220 </span>            :     e = 0.;</a>
+<a name="25221"><span class="lineNum">   25221 </span><span class="lineNoCov">          0 :     for (k = *n; k &gt;= 1; --k) {</span></a>
+<a name="25222"><span class="lineNum">   25222 </span><span class="lineNoCov">          0 :         e += z__[k];</span></a>
+<a name="25223"><span class="lineNum">   25223 </span>            :     }</a>
+<a name="25224"><span class="lineNum">   25224 </span>            : </a>
+<a name="25225"><span class="lineNum">   25225 </span>            : </a>
+<a name="25226"><span class="lineNum">   25226 </span><span class="lineNoCov">          0 :     z__[(*n &lt;&lt; 1) + 1] = trace;</span></a>
+<a name="25227"><span class="lineNum">   25227 </span><span class="lineNoCov">          0 :     z__[(*n &lt;&lt; 1) + 2] = e;</span></a>
+<a name="25228"><span class="lineNum">   25228 </span><span class="lineNoCov">          0 :     z__[(*n &lt;&lt; 1) + 3] = (float) iter;</span></a>
+<a name="25229"><span class="lineNum">   25229 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="25230"><span class="lineNum">   25230 </span><span class="lineNoCov">          0 :     z__[(*n &lt;&lt; 1) + 4] = (float) ndiv / (float) (i__1 * i__1);</span></a>
+<a name="25231"><span class="lineNum">   25231 </span><span class="lineNoCov">          0 :     z__[(*n &lt;&lt; 1) + 5] = nfail * 100. / (float) iter;</span></a>
+<a name="25232"><span class="lineNum">   25232 </span>            : </a>
+<a name="25233"><span class="lineNum">   25233 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="25234"><span class="lineNum">   25234 </span>            : </a>
+<a name="25235"><span class="lineNum">   25235 </span>            : }</a>
+<a name="25236"><span class="lineNum">   25236 </span>            : </a>
+<a name="25237"><span class="lineNum">   25237 </span>            : </a>
+<a name="25238"><span class="lineNum">   25238 </span>            : </a>
+<a name="25239"><span class="lineNum">   25239 </span>            : }</a>
+<a name="25240"><span class="lineNum">   25240 </span>            : }</a>
+<a name="25241"><span class="lineNum">   25241 </span>            : #include &lt;cmath&gt;</a>
+<a name="25242"><span class="lineNum">   25242 </span>            : #include &quot;real.h&quot;</a>
+<a name="25243"><span class="lineNum">   25243 </span>            : </a>
+<a name="25244"><span class="lineNum">   25244 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="25245"><span class="lineNum">   25245 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="25246"><span class="lineNum">   25246 </span>            : </a>
+<a name="25247"><span class="lineNum">   25247 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="25248"><span class="lineNum">   25248 </span>            : namespace PLMD{</a>
+<a name="25249"><span class="lineNum">   25249 </span>            : namespace lapack{</a>
+<a name="25250"><span class="lineNum">   25250 </span>            : using namespace blas;</a>
+<a name="25251"><span class="lineNum">   25251 </span>            : void</a>
+<a name="25252"><span class="lineNum">   25252 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasq3,SLASQ3)(int *i0, </span></a>
+<a name="25253"><span class="lineNum">   25253 </span>            :                         int *n0, </a>
+<a name="25254"><span class="lineNum">   25254 </span>            :                         float *z__, </a>
+<a name="25255"><span class="lineNum">   25255 </span>            :                         int *pp, </a>
+<a name="25256"><span class="lineNum">   25256 </span>            :                         float *dmin__, </a>
+<a name="25257"><span class="lineNum">   25257 </span>            :                         float *sigma,</a>
+<a name="25258"><span class="lineNum">   25258 </span>            :                         float *desig,</a>
+<a name="25259"><span class="lineNum">   25259 </span>            :                         float *qmax, </a>
+<a name="25260"><span class="lineNum">   25260 </span>            :                         int *nfail, </a>
+<a name="25261"><span class="lineNum">   25261 </span>            :                         int *iter, </a>
+<a name="25262"><span class="lineNum">   25262 </span>            :                         int *ndiv, </a>
+<a name="25263"><span class="lineNum">   25263 </span>            :         int *ieee)</a>
+<a name="25264"><span class="lineNum">   25264 </span>            : {</a>
+<a name="25265"><span class="lineNum">   25265 </span>            : </a>
+<a name="25266"><span class="lineNum">   25266 </span><span class="lineNoCov">          0 :     int ttype = 0;</span></a>
+<a name="25267"><span class="lineNum">   25267 </span><span class="lineNoCov">          0 :     float dmin1 = 0.;</span></a>
+<a name="25268"><span class="lineNum">   25268 </span><span class="lineNoCov">          0 :     float dmin2 = 0.;</span></a>
+<a name="25269"><span class="lineNum">   25269 </span><span class="lineNoCov">          0 :     float dn = 0.;</span></a>
+<a name="25270"><span class="lineNum">   25270 </span><span class="lineNoCov">          0 :     float dn1 = 0.;</span></a>
+<a name="25271"><span class="lineNum">   25271 </span><span class="lineNoCov">          0 :     float dn2 = 0.;</span></a>
+<a name="25272"><span class="lineNum">   25272 </span><span class="lineNoCov">          0 :     float tau = 0.;</span></a>
+<a name="25273"><span class="lineNum">   25273 </span>            : </a>
+<a name="25274"><span class="lineNum">   25274 </span>            :     int i__1;</a>
+<a name="25275"><span class="lineNum">   25275 </span>            :     float d__1, d__2;</a>
+<a name="25276"><span class="lineNum">   25276 </span>            :     float s, t;</a>
+<a name="25277"><span class="lineNum">   25277 </span>            :     int j4, nn;</a>
+<a name="25278"><span class="lineNum">   25278 </span>            :     float eps, tol;</a>
+<a name="25279"><span class="lineNum">   25279 </span>            :     int n0in, ipn4;</a>
+<a name="25280"><span class="lineNum">   25280 </span>            :     float tol2, temp;</a>
+<a name="25281"><span class="lineNum">   25281 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="25282"><span class="lineNum">   25282 </span>            : </a>
+<a name="25283"><span class="lineNum">   25283 </span><span class="lineNoCov">          0 :     n0in = *n0;</span></a>
+<a name="25284"><span class="lineNum">   25284 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="25285"><span class="lineNum">   25285 </span>            :     tol = eps * 100.;</a>
+<a name="25286"><span class="lineNum">   25286 </span>            :     d__1 = tol;</a>
+<a name="25287"><span class="lineNum">   25287 </span>            :     tol2 = d__1 * d__1;</a>
+<a name="25288"><span class="lineNum">   25288 </span>            : </a>
+<a name="25289"><span class="lineNum">   25289 </span>            : </a>
+<a name="25290"><span class="lineNum">   25290 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="25291"><span class="lineNum">   25291 </span>            : </a>
+<a name="25292"><span class="lineNum">   25292 </span><span class="lineNoCov">          0 :     if (*n0 &lt; *i0) {</span></a>
+<a name="25293"><span class="lineNum">   25293 </span>            :         return;</a>
+<a name="25294"><span class="lineNum">   25294 </span>            :     }</a>
+<a name="25295"><span class="lineNum">   25295 </span><span class="lineNoCov">          0 :     if (*n0 == *i0) {</span></a>
+<a name="25296"><span class="lineNum">   25296 </span><span class="lineNoCov">          0 :         goto L20;</span></a>
+<a name="25297"><span class="lineNum">   25297 </span>            :     }</a>
+<a name="25298"><span class="lineNum">   25298 </span><span class="lineNoCov">          0 :     nn = (*n0 &lt;&lt; 2) + *pp;</span></a>
+<a name="25299"><span class="lineNum">   25299 </span><span class="lineNoCov">          0 :     if (*n0 == *i0 + 1) {</span></a>
+<a name="25300"><span class="lineNum">   25300 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="25301"><span class="lineNum">   25301 </span>            :     }</a>
+<a name="25302"><span class="lineNum">   25302 </span>            : </a>
+<a name="25303"><span class="lineNum">   25303 </span><span class="lineNoCov">          0 :     if (z__[nn - 5] &gt; tol2 * (*sigma + z__[nn - 3]) &amp;&amp; z__[nn - (*pp &lt;&lt; 1) - </span></a>
+<a name="25304"><span class="lineNum">   25304 </span><span class="lineNoCov">          0 :             4] &gt; tol2 * z__[nn - 7]) {</span></a>
+<a name="25305"><span class="lineNum">   25305 </span><span class="lineNoCov">          0 :         goto L30;</span></a>
+<a name="25306"><span class="lineNum">   25306 </span>            :     }</a>
+<a name="25307"><span class="lineNum">   25307 </span>            : </a>
+<a name="25308"><span class="lineNum">   25308 </span><span class="lineNoCov">          0 : L20:</span></a>
+<a name="25309"><span class="lineNum">   25309 </span>            : </a>
+<a name="25310"><span class="lineNum">   25310 </span><span class="lineNoCov">          0 :     z__[(*n0 &lt;&lt; 2) - 3] = z__[(*n0 &lt;&lt; 2) + *pp - 3] + *sigma;</span></a>
+<a name="25311"><span class="lineNum">   25311 </span><span class="lineNoCov">          0 :     --(*n0);</span></a>
+<a name="25312"><span class="lineNum">   25312 </span><span class="lineNoCov">          0 :     goto L10;</span></a>
+<a name="25313"><span class="lineNum">   25313 </span>            : </a>
+<a name="25314"><span class="lineNum">   25314 </span>            : L30:</a>
+<a name="25315"><span class="lineNum">   25315 </span>            : </a>
+<a name="25316"><span class="lineNum">   25316 </span><span class="lineNoCov">          0 :     if (z__[nn - 9] &gt; tol2 * *sigma &amp;&amp; z__[nn - (*pp &lt;&lt; 1) - 8] &gt; tol2 * z__[</span></a>
+<a name="25317"><span class="lineNum">   25317 </span><span class="lineNoCov">          0 :             nn - 11]) {</span></a>
+<a name="25318"><span class="lineNum">   25318 </span><span class="lineNoCov">          0 :         goto L50;</span></a>
+<a name="25319"><span class="lineNum">   25319 </span>            :     }</a>
+<a name="25320"><span class="lineNum">   25320 </span>            : </a>
+<a name="25321"><span class="lineNum">   25321 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="25322"><span class="lineNum">   25322 </span>            : </a>
+<a name="25323"><span class="lineNum">   25323 </span><span class="lineNoCov">          0 :     if (z__[nn - 3] &gt; z__[nn - 7]) {</span></a>
+<a name="25324"><span class="lineNum">   25324 </span>            :         s = z__[nn - 3];</a>
+<a name="25325"><span class="lineNum">   25325 </span><span class="lineNoCov">          0 :         z__[nn - 3] = z__[nn - 7];</span></a>
+<a name="25326"><span class="lineNum">   25326 </span><span class="lineNoCov">          0 :         z__[nn - 7] = s;</span></a>
+<a name="25327"><span class="lineNum">   25327 </span>            :     }</a>
+<a name="25328"><span class="lineNum">   25328 </span><span class="lineNoCov">          0 :     if (z__[nn - 5] &gt; z__[nn - 3] * tol2) {</span></a>
+<a name="25329"><span class="lineNum">   25329 </span><span class="lineNoCov">          0 :         t = (z__[nn - 7] - z__[nn - 3] + z__[nn - 5]) * .5;</span></a>
+<a name="25330"><span class="lineNum">   25330 </span><span class="lineNoCov">          0 :         s = z__[nn - 3] * (z__[nn - 5] / t);</span></a>
+<a name="25331"><span class="lineNum">   25331 </span><span class="lineNoCov">          0 :         if (s &lt;= t) {</span></a>
+<a name="25332"><span class="lineNum">   25332 </span><span class="lineNoCov">          0 :             s = z__[nn - 3] * (z__[nn - 5] / (t * ( std::sqrt(s / t + 1.) + 1.)));</span></a>
+<a name="25333"><span class="lineNum">   25333 </span>            :         } else {</a>
+<a name="25334"><span class="lineNum">   25334 </span><span class="lineNoCov">          0 :             s = z__[nn - 3] * (z__[nn - 5] / (t +  std::sqrt(t) * std::sqrt(t + s)));</span></a>
+<a name="25335"><span class="lineNum">   25335 </span>            :         }</a>
+<a name="25336"><span class="lineNum">   25336 </span><span class="lineNoCov">          0 :         t = z__[nn - 7] + (s + z__[nn - 5]);</span></a>
+<a name="25337"><span class="lineNum">   25337 </span><span class="lineNoCov">          0 :         z__[nn - 3] *= z__[nn - 7] / t;</span></a>
+<a name="25338"><span class="lineNum">   25338 </span><span class="lineNoCov">          0 :         z__[nn - 7] = t;</span></a>
+<a name="25339"><span class="lineNum">   25339 </span>            :     }</a>
+<a name="25340"><span class="lineNum">   25340 </span><span class="lineNoCov">          0 :     z__[(*n0 &lt;&lt; 2) - 7] = z__[nn - 7] + *sigma;</span></a>
+<a name="25341"><span class="lineNum">   25341 </span><span class="lineNoCov">          0 :     z__[(*n0 &lt;&lt; 2) - 3] = z__[nn - 3] + *sigma;</span></a>
+<a name="25342"><span class="lineNum">   25342 </span><span class="lineNoCov">          0 :     *n0 += -2;</span></a>
+<a name="25343"><span class="lineNum">   25343 </span><span class="lineNoCov">          0 :     goto L10;</span></a>
+<a name="25344"><span class="lineNum">   25344 </span>            : </a>
+<a name="25345"><span class="lineNum">   25345 </span>            : L50:</a>
+<a name="25346"><span class="lineNum">   25346 </span><span class="lineNoCov">          0 :     if (*pp == 2) {</span></a>
+<a name="25347"><span class="lineNum">   25347 </span><span class="lineNoCov">          0 :         *pp = 0;</span></a>
+<a name="25348"><span class="lineNum">   25348 </span>            :     }</a>
+<a name="25349"><span class="lineNum">   25349 </span>            : </a>
+<a name="25350"><span class="lineNum">   25350 </span><span class="lineNoCov">          0 :     if (*dmin__ &lt;= 0. || *n0 &lt; n0in) {</span></a>
+<a name="25351"><span class="lineNum">   25351 </span><span class="lineNoCov">          0 :         if (z__[(*i0 &lt;&lt; 2) + *pp - 3] * 1.5 &lt; z__[(*n0 &lt;&lt; 2) + *pp - 3]) {</span></a>
+<a name="25352"><span class="lineNum">   25352 </span><span class="lineNoCov">          0 :             ipn4 = 4*(*i0 + *n0);</span></a>
+<a name="25353"><span class="lineNum">   25353 </span><span class="lineNoCov">          0 :             i__1 = 2*(*i0 + *n0 - 1);</span></a>
+<a name="25354"><span class="lineNum">   25354 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25355"><span class="lineNum">   25355 </span><span class="lineNoCov">          0 :                 temp = z__[j4 - 3];</span></a>
+<a name="25356"><span class="lineNum">   25356 </span><span class="lineNoCov">          0 :                 z__[j4 - 3] = z__[ipn4 - j4 - 3];</span></a>
+<a name="25357"><span class="lineNum">   25357 </span><span class="lineNoCov">          0 :                 z__[ipn4 - j4 - 3] = temp;</span></a>
+<a name="25358"><span class="lineNum">   25358 </span><span class="lineNoCov">          0 :                 temp = z__[j4 - 2];</span></a>
+<a name="25359"><span class="lineNum">   25359 </span><span class="lineNoCov">          0 :                 z__[j4 - 2] = z__[ipn4 - j4 - 2];</span></a>
+<a name="25360"><span class="lineNum">   25360 </span><span class="lineNoCov">          0 :                 z__[ipn4 - j4 - 2] = temp;</span></a>
+<a name="25361"><span class="lineNum">   25361 </span><span class="lineNoCov">          0 :                 temp = z__[j4 - 1];</span></a>
+<a name="25362"><span class="lineNum">   25362 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = z__[ipn4 - j4 - 5];</span></a>
+<a name="25363"><span class="lineNum">   25363 </span><span class="lineNoCov">          0 :                 z__[ipn4 - j4 - 5] = temp;</span></a>
+<a name="25364"><span class="lineNum">   25364 </span><span class="lineNoCov">          0 :                 temp = z__[j4];</span></a>
+<a name="25365"><span class="lineNum">   25365 </span><span class="lineNoCov">          0 :                 z__[j4] = z__[ipn4 - j4 - 4];</span></a>
+<a name="25366"><span class="lineNum">   25366 </span><span class="lineNoCov">          0 :                 z__[ipn4 - j4 - 4] = temp;</span></a>
+<a name="25367"><span class="lineNum">   25367 </span>            :             }</a>
+<a name="25368"><span class="lineNum">   25368 </span><span class="lineNoCov">          0 :             if (*n0 - *i0 &lt;= 4) {</span></a>
+<a name="25369"><span class="lineNum">   25369 </span><span class="lineNoCov">          0 :                 z__[(*n0 &lt;&lt; 2) + *pp - 1] = z__[(*i0 &lt;&lt; 2) + *pp - 1];</span></a>
+<a name="25370"><span class="lineNum">   25370 </span><span class="lineNoCov">          0 :                 z__[(*n0 &lt;&lt; 2) - *pp] = z__[(*i0 &lt;&lt; 2) - *pp];</span></a>
+<a name="25371"><span class="lineNum">   25371 </span>            :             }</a>
+<a name="25372"><span class="lineNum">   25372 </span><span class="lineNoCov">          0 :             d__1 = dmin2, d__2 = z__[(*n0 &lt;&lt; 2) + *pp - 1];</span></a>
+<a name="25373"><span class="lineNum">   25373 </span><span class="lineNoCov">          0 :             dmin2 = ((d__1&lt;d__2) ? d__1 : d__2);</span></a>
+<a name="25374"><span class="lineNum">   25374 </span><span class="lineNoCov">          0 :             d__1 = z__[(*n0 &lt;&lt; 2) + *pp - 1], d__2 = z__[(*i0 &lt;&lt; 2) + *pp - 1]</span></a>
+<a name="25375"><span class="lineNum">   25375 </span><span class="lineNoCov">          0 :                     , d__1 = ((d__1&lt;d__2) ? d__1 : d__2), d__2 = z__[(*i0 &lt;&lt; 2) + *pp + 3];</span></a>
+<a name="25376"><span class="lineNum">   25376 </span><span class="lineNoCov">          0 :             z__[(*n0 &lt;&lt; 2) + *pp - 1] = ((d__1&lt;d__2) ? d__1 : d__2);</span></a>
+<a name="25377"><span class="lineNum">   25377 </span><span class="lineNoCov">          0 :             d__1 = z__[(*n0 &lt;&lt; 2) - *pp], d__2 = z__[(*i0 &lt;&lt; 2) - *pp], d__1 =</span></a>
+<a name="25378"><span class="lineNum">   25378 </span><span class="lineNoCov">          0 :                      ((d__1&lt;d__2) ? d__1 : d__2), d__2 = z__[(*i0 &lt;&lt; 2) - *pp + 4];</span></a>
+<a name="25379"><span class="lineNum">   25379 </span><span class="lineNoCov">          0 :             z__[(*n0 &lt;&lt; 2) - *pp] = ((d__1&lt;d__2) ? d__1 : d__2);</span></a>
+<a name="25380"><span class="lineNum">   25380 </span><span class="lineNoCov">          0 :             d__1 = *qmax;</span></a>
+<a name="25381"><span class="lineNum">   25381 </span><span class="lineNoCov">          0 :             d__2 = z__[(*i0 &lt;&lt; 2) + *pp - 3];</span></a>
+<a name="25382"><span class="lineNum">   25382 </span><span class="lineNoCov">          0 :             d__1 = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25383"><span class="lineNum">   25383 </span><span class="lineNoCov">          0 :             d__2 = z__[(*i0 &lt;&lt; 2) + *pp + 1];</span></a>
+<a name="25384"><span class="lineNum">   25384 </span><span class="lineNoCov">          0 :             *qmax = ((d__1&gt;d__2) ? d__1 : d__2);</span></a>
+<a name="25385"><span class="lineNum">   25385 </span><span class="lineNoCov">          0 :             *dmin__ = -0.;</span></a>
+<a name="25386"><span class="lineNum">   25386 </span>            :         }</a>
+<a name="25387"><span class="lineNum">   25387 </span>            :     }</a>
+<a name="25388"><span class="lineNum">   25388 </span>            : </a>
+<a name="25389"><span class="lineNum">   25389 </span>            : </a>
+<a name="25390"><span class="lineNum">   25390 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasq4,SLASQ4)(i0, n0, &amp;z__[1], pp, &amp;n0in, dmin__, &amp;dmin1, &amp;dmin2, &amp;dn, &amp;dn1, &amp;</span></a>
+<a name="25391"><span class="lineNum">   25391 </span>            :             dn2, &amp;tau, &amp;ttype);</a>
+<a name="25392"><span class="lineNum">   25392 </span>            : </a>
+<a name="25393"><span class="lineNum">   25393 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="25394"><span class="lineNum">   25394 </span>            : </a>
+<a name="25395"><span class="lineNum">   25395 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasq5,SLASQ5)(i0, n0, &amp;z__[1], pp, &amp;tau, dmin__, &amp;dmin1, &amp;dmin2, &amp;dn, &amp;dn1, &amp;</span></a>
+<a name="25396"><span class="lineNum">   25396 </span>            :             dn2, ieee);</a>
+<a name="25397"><span class="lineNum">   25397 </span>            : </a>
+<a name="25398"><span class="lineNum">   25398 </span><span class="lineNoCov">          0 :     *ndiv += *n0 - *i0 + 2;</span></a>
+<a name="25399"><span class="lineNum">   25399 </span><span class="lineNoCov">          0 :     ++(*iter);</span></a>
+<a name="25400"><span class="lineNum">   25400 </span>            : </a>
+<a name="25401"><span class="lineNum">   25401 </span><span class="lineNoCov">          0 :     if (*dmin__ &gt;= 0. &amp;&amp; dmin1 &gt; 0.) {</span></a>
+<a name="25402"><span class="lineNum">   25402 </span>            : </a>
+<a name="25403"><span class="lineNum">   25403 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="25404"><span class="lineNum">   25404 </span>            : </a>
+<a name="25405"><span class="lineNum">   25405 </span><span class="lineNoCov">          0 :     } else if (*dmin__ &lt; 0. &amp;&amp; dmin1 &gt; 0. &amp;&amp; z__[4*(*n0 - 1) - *pp] &lt; tol *</span></a>
+<a name="25406"><span class="lineNum">   25406 </span><span class="lineNoCov">          0 :              (*sigma + dn1) &amp;&amp; std::abs(dn) &lt; tol * *sigma) {</span></a>
+<a name="25407"><span class="lineNum">   25407 </span>            : </a>
+<a name="25408"><span class="lineNum">   25408 </span><span class="lineNoCov">          0 :         z__[4*(*n0 - 1) - *pp + 2] = 0.;</span></a>
+<a name="25409"><span class="lineNum">   25409 </span><span class="lineNoCov">          0 :         *dmin__ = 0.;</span></a>
+<a name="25410"><span class="lineNum">   25410 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="25411"><span class="lineNum">   25411 </span><span class="lineNoCov">          0 :     } else if (*dmin__ &lt; 0.) {</span></a>
+<a name="25412"><span class="lineNum">   25412 </span>            : </a>
+<a name="25413"><span class="lineNum">   25413 </span><span class="lineNoCov">          0 :         ++(*nfail);</span></a>
+<a name="25414"><span class="lineNum">   25414 </span><span class="lineNoCov">          0 :         if (ttype &lt; -22) {</span></a>
+<a name="25415"><span class="lineNum">   25415 </span>            : </a>
+<a name="25416"><span class="lineNum">   25416 </span><span class="lineNoCov">          0 :             tau = 0.;</span></a>
+<a name="25417"><span class="lineNum">   25417 </span><span class="lineNoCov">          0 :         } else if (dmin1 &gt; 0.) {</span></a>
+<a name="25418"><span class="lineNum">   25418 </span>            : </a>
+<a name="25419"><span class="lineNum">   25419 </span><span class="lineNoCov">          0 :             tau = (tau + *dmin__) * (1. - eps * 2.);</span></a>
+<a name="25420"><span class="lineNum">   25420 </span><span class="lineNoCov">          0 :             ttype += -11;</span></a>
+<a name="25421"><span class="lineNum">   25421 </span>            :         } else {</a>
+<a name="25422"><span class="lineNum">   25422 </span>            : </a>
+<a name="25423"><span class="lineNum">   25423 </span><span class="lineNoCov">          0 :             tau *= .25;</span></a>
+<a name="25424"><span class="lineNum">   25424 </span><span class="lineNoCov">          0 :             ttype += -12;</span></a>
+<a name="25425"><span class="lineNum">   25425 </span>            :         }</a>
+<a name="25426"><span class="lineNum">   25426 </span><span class="lineNoCov">          0 :         goto L70;</span></a>
+<a name="25427"><span class="lineNum">   25427 </span>            :     }</a>
+<a name="25428"><span class="lineNum">   25428 </span>            :     else {</a>
+<a name="25429"><span class="lineNum">   25429 </span>            :         </a>
+<a name="25430"><span class="lineNum">   25430 </span><span class="lineNoCov">          0 :         goto L80;</span></a>
+<a name="25431"><span class="lineNum">   25431 </span>            :     }</a>
+<a name="25432"><span class="lineNum">   25432 </span>            : </a>
+<a name="25433"><span class="lineNum">   25433 </span>            : L80:</a>
+<a name="25434"><span class="lineNum">   25434 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slasq6,SLASQ6)(i0, n0, &amp;z__[1], pp, dmin__, &amp;dmin1, &amp;dmin2, &amp;dn, &amp;dn1, &amp;dn2);</span></a>
+<a name="25435"><span class="lineNum">   25435 </span><span class="lineNoCov">          0 :     *ndiv += *n0 - *i0 + 2;</span></a>
+<a name="25436"><span class="lineNum">   25436 </span><span class="lineNoCov">          0 :     ++(*iter);</span></a>
+<a name="25437"><span class="lineNum">   25437 </span><span class="lineNoCov">          0 :     tau = 0.;</span></a>
+<a name="25438"><span class="lineNum">   25438 </span>            : </a>
+<a name="25439"><span class="lineNum">   25439 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="25440"><span class="lineNum">   25440 </span><span class="lineNoCov">          0 :     if (tau &lt; *sigma) {</span></a>
+<a name="25441"><span class="lineNum">   25441 </span><span class="lineNoCov">          0 :         *desig += tau;</span></a>
+<a name="25442"><span class="lineNum">   25442 </span><span class="lineNoCov">          0 :         t = *sigma + *desig;</span></a>
+<a name="25443"><span class="lineNum">   25443 </span><span class="lineNoCov">          0 :         *desig -= t - *sigma;</span></a>
+<a name="25444"><span class="lineNum">   25444 </span>            :     } else {</a>
+<a name="25445"><span class="lineNum">   25445 </span><span class="lineNoCov">          0 :         t = *sigma + tau;</span></a>
+<a name="25446"><span class="lineNum">   25446 </span><span class="lineNoCov">          0 :         *desig = *sigma - (t - tau) + *desig;</span></a>
+<a name="25447"><span class="lineNum">   25447 </span>            :     }</a>
+<a name="25448"><span class="lineNum">   25448 </span><span class="lineNoCov">          0 :     *sigma = t;</span></a>
+<a name="25449"><span class="lineNum">   25449 </span>            : </a>
+<a name="25450"><span class="lineNum">   25450 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="25451"><span class="lineNum">   25451 </span>            : }</a>
+<a name="25452"><span class="lineNum">   25452 </span>            : }</a>
+<a name="25453"><span class="lineNum">   25453 </span>            : }</a>
+<a name="25454"><span class="lineNum">   25454 </span>            : #include &lt;cmath&gt;</a>
+<a name="25455"><span class="lineNum">   25455 </span>            : #include &quot;real.h&quot;</a>
+<a name="25456"><span class="lineNum">   25456 </span>            : </a>
+<a name="25457"><span class="lineNum">   25457 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="25458"><span class="lineNum">   25458 </span>            : </a>
+<a name="25459"><span class="lineNum">   25459 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="25460"><span class="lineNum">   25460 </span>            : namespace PLMD{</a>
+<a name="25461"><span class="lineNum">   25461 </span>            : namespace lapack{</a>
+<a name="25462"><span class="lineNum">   25462 </span>            : using namespace blas;</a>
+<a name="25463"><span class="lineNum">   25463 </span>            : void </a>
+<a name="25464"><span class="lineNum">   25464 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasq4,SLASQ4)(int *i0, </span></a>
+<a name="25465"><span class="lineNum">   25465 </span>            :         int *n0, </a>
+<a name="25466"><span class="lineNum">   25466 </span>            :         float *z__, </a>
+<a name="25467"><span class="lineNum">   25467 </span>            :         int *pp, </a>
+<a name="25468"><span class="lineNum">   25468 </span>            :         int *n0in, </a>
+<a name="25469"><span class="lineNum">   25469 </span>            :         float *dmin__, </a>
+<a name="25470"><span class="lineNum">   25470 </span>            :         float *dmin1, </a>
+<a name="25471"><span class="lineNum">   25471 </span>            :         float *dmin2, </a>
+<a name="25472"><span class="lineNum">   25472 </span>            :         float *dn, </a>
+<a name="25473"><span class="lineNum">   25473 </span>            :         float *dn1, </a>
+<a name="25474"><span class="lineNum">   25474 </span>            :         float *dn2, </a>
+<a name="25475"><span class="lineNum">   25475 </span>            :         float *tau, </a>
+<a name="25476"><span class="lineNum">   25476 </span>            :         int *ttype)</a>
+<a name="25477"><span class="lineNum">   25477 </span>            : {</a>
+<a name="25478"><span class="lineNum">   25478 </span>            :     float g = 0.;</a>
+<a name="25479"><span class="lineNum">   25479 </span>            :     int i__1;</a>
+<a name="25480"><span class="lineNum">   25480 </span>            :     float d__1, d__2;</a>
+<a name="25481"><span class="lineNum">   25481 </span>            : </a>
+<a name="25482"><span class="lineNum">   25482 </span>            :     float s, a2, b1, b2;</a>
+<a name="25483"><span class="lineNum">   25483 </span>            :     int i4, nn, np;</a>
+<a name="25484"><span class="lineNum">   25484 </span>            :     float gam, gap1, gap2;</a>
+<a name="25485"><span class="lineNum">   25485 </span>            : </a>
+<a name="25486"><span class="lineNum">   25486 </span>            : </a>
+<a name="25487"><span class="lineNum">   25487 </span><span class="lineNoCov">          0 :     if (*dmin__ &lt;= 0.) {</span></a>
+<a name="25488"><span class="lineNum">   25488 </span><span class="lineNoCov">          0 :         *tau = -(*dmin__);</span></a>
+<a name="25489"><span class="lineNum">   25489 </span><span class="lineNoCov">          0 :         *ttype = -1;</span></a>
+<a name="25490"><span class="lineNum">   25490 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="25491"><span class="lineNum">   25491 </span>            :     }</a>
+<a name="25492"><span class="lineNum">   25492 </span>            : </a>
+<a name="25493"><span class="lineNum">   25493 </span>            :     s = 0.0;</a>
+<a name="25494"><span class="lineNum">   25494 </span>            : </a>
+<a name="25495"><span class="lineNum">   25495 </span><span class="lineNoCov">          0 :     nn = (*n0 &lt;&lt; 2) + *pp;</span></a>
+<a name="25496"><span class="lineNum">   25496 </span><span class="lineNoCov">          0 :     if (*n0in == *n0) {</span></a>
+<a name="25497"><span class="lineNum">   25497 </span>            : </a>
+<a name="25498"><span class="lineNum">   25498 </span><span class="lineNoCov">          0 :         if ( std::abs(*dmin__ - *dn)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin__ + *dn) ||</span></a>
+<a name="25499"><span class="lineNum">   25499 </span><span class="lineNoCov">          0 :          std::abs(*dmin__ - *dn1)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin__ + *dn1)) {</span></a>
+<a name="25500"><span class="lineNum">   25500 </span>            : </a>
+<a name="25501"><span class="lineNum">   25501 </span><span class="lineNoCov">          0 :             b1 =  std::sqrt(z__[nn - 3]) * std::sqrt(z__[nn - 5]);</span></a>
+<a name="25502"><span class="lineNum">   25502 </span><span class="lineNoCov">          0 :             b2 =  std::sqrt(z__[nn - 7]) * std::sqrt(z__[nn - 9]);</span></a>
+<a name="25503"><span class="lineNum">   25503 </span><span class="lineNoCov">          0 :             a2 = z__[nn - 7] + z__[nn - 5];</span></a>
+<a name="25504"><span class="lineNum">   25504 </span>            : </a>
+<a name="25505"><span class="lineNum">   25505 </span><span class="lineNoCov">          0 :         if ( std::abs(*dmin__ - *dn)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin__ + *dn) &amp;&amp;</span></a>
+<a name="25506"><span class="lineNum">   25506 </span><span class="lineNoCov">          0 :              std::abs(*dmin1 - *dn1)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin1 + *dn1)) {</span></a>
+<a name="25507"><span class="lineNum">   25507 </span>            : </a>
+<a name="25508"><span class="lineNum">   25508 </span><span class="lineNoCov">          0 :             gap2 = *dmin2 - a2 - *dmin2 * .25;</span></a>
+<a name="25509"><span class="lineNum">   25509 </span><span class="lineNoCov">          0 :                 if (gap2 &gt; 0. &amp;&amp; gap2 &gt; b2) {</span></a>
+<a name="25510"><span class="lineNum">   25510 </span><span class="lineNoCov">          0 :                     gap1 = a2 - *dn - b2 / gap2 * b2;</span></a>
+<a name="25511"><span class="lineNum">   25511 </span>            :                 } else {</a>
+<a name="25512"><span class="lineNum">   25512 </span><span class="lineNoCov">          0 :                     gap1 = a2 - *dn - (b1 + b2);</span></a>
+<a name="25513"><span class="lineNum">   25513 </span>            :                 }</a>
+<a name="25514"><span class="lineNum">   25514 </span><span class="lineNoCov">          0 :                 if (gap1 &gt; 0. &amp;&amp; gap1 &gt; b1) {</span></a>
+<a name="25515"><span class="lineNum">   25515 </span><span class="lineNoCov">          0 :                     d__1 = *dn - b1 / gap1 * b1, d__2 = *dmin__ * .5;</span></a>
+<a name="25516"><span class="lineNum">   25516 </span><span class="lineNoCov">          0 :                     s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25517"><span class="lineNum">   25517 </span><span class="lineNoCov">          0 :                     *ttype = -2;</span></a>
+<a name="25518"><span class="lineNum">   25518 </span>            :                 } else {</a>
+<a name="25519"><span class="lineNum">   25519 </span>            :                     s = 0.;</a>
+<a name="25520"><span class="lineNum">   25520 </span><span class="lineNoCov">          0 :                     if (*dn &gt; b1) {</span></a>
+<a name="25521"><span class="lineNum">   25521 </span><span class="lineNoCov">          0 :                         s = *dn - b1;</span></a>
+<a name="25522"><span class="lineNum">   25522 </span>            :                     }</a>
+<a name="25523"><span class="lineNum">   25523 </span><span class="lineNoCov">          0 :                     if (a2 &gt; b1 + b2) {</span></a>
+<a name="25524"><span class="lineNum">   25524 </span><span class="lineNoCov">          0 :                         d__1 = s, d__2 = a2 - (b1 + b2);</span></a>
+<a name="25525"><span class="lineNum">   25525 </span><span class="lineNoCov">          0 :                         s = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25526"><span class="lineNum">   25526 </span>            :                     }</a>
+<a name="25527"><span class="lineNum">   25527 </span><span class="lineNoCov">          0 :                     d__1 = s, d__2 = *dmin__ * .333;</span></a>
+<a name="25528"><span class="lineNum">   25528 </span><span class="lineNoCov">          0 :                     s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25529"><span class="lineNum">   25529 </span><span class="lineNoCov">          0 :                     *ttype = -3;</span></a>
+<a name="25530"><span class="lineNum">   25530 </span>            :                 }</a>
+<a name="25531"><span class="lineNum">   25531 </span>            :             } else {</a>
+<a name="25532"><span class="lineNum">   25532 </span>            : </a>
+<a name="25533"><span class="lineNum">   25533 </span>            : </a>
+<a name="25534"><span class="lineNum">   25534 </span><span class="lineNoCov">          0 :                 *ttype = -4;</span></a>
+<a name="25535"><span class="lineNum">   25535 </span><span class="lineNoCov">          0 :                 s = *dmin__ * .25;</span></a>
+<a name="25536"><span class="lineNum">   25536 </span><span class="lineNoCov">          0 :                 if (std::abs(*dmin__ - *dn)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin__ + *dn)) {</span></a>
+<a name="25537"><span class="lineNum">   25537 </span>            :                     gam = *dn;</a>
+<a name="25538"><span class="lineNum">   25538 </span>            :                     a2 = 0.;</a>
+<a name="25539"><span class="lineNum">   25539 </span><span class="lineNoCov">          0 :                     if (z__[nn - 5] &gt; z__[nn - 7]) {</span></a>
+<a name="25540"><span class="lineNum">   25540 </span>            :                         return;</a>
+<a name="25541"><span class="lineNum">   25541 </span>            :                     }</a>
+<a name="25542"><span class="lineNum">   25542 </span><span class="lineNoCov">          0 :                     b2 = z__[nn - 5] / z__[nn - 7];</span></a>
+<a name="25543"><span class="lineNum">   25543 </span><span class="lineNoCov">          0 :                     np = nn - 9;</span></a>
+<a name="25544"><span class="lineNum">   25544 </span>            :                 } else {</a>
+<a name="25545"><span class="lineNum">   25545 </span><span class="lineNoCov">          0 :                     np = nn - (*pp &lt;&lt; 1);</span></a>
+<a name="25546"><span class="lineNum">   25546 </span><span class="lineNoCov">          0 :                     gam = *dn1;</span></a>
+<a name="25547"><span class="lineNum">   25547 </span><span class="lineNoCov">          0 :                     if (z__[np - 4] &gt; z__[np - 2]) {</span></a>
+<a name="25548"><span class="lineNum">   25548 </span>            :                         return;</a>
+<a name="25549"><span class="lineNum">   25549 </span>            :                     }</a>
+<a name="25550"><span class="lineNum">   25550 </span><span class="lineNoCov">          0 :                     a2 = z__[np - 4] / z__[np - 2];</span></a>
+<a name="25551"><span class="lineNum">   25551 </span><span class="lineNoCov">          0 :                     if (z__[nn - 9] &gt; z__[nn - 11]) {</span></a>
+<a name="25552"><span class="lineNum">   25552 </span>            :                         return;</a>
+<a name="25553"><span class="lineNum">   25553 </span>            :                     }</a>
+<a name="25554"><span class="lineNum">   25554 </span><span class="lineNoCov">          0 :                     b2 = z__[nn - 9] / z__[nn - 11];</span></a>
+<a name="25555"><span class="lineNum">   25555 </span><span class="lineNoCov">          0 :                     np = nn - 13;</span></a>
+<a name="25556"><span class="lineNum">   25556 </span>            :                 }</a>
+<a name="25557"><span class="lineNum">   25557 </span>            : </a>
+<a name="25558"><span class="lineNum">   25558 </span>            : </a>
+<a name="25559"><span class="lineNum">   25559 </span><span class="lineNoCov">          0 :                 a2 += b2;</span></a>
+<a name="25560"><span class="lineNum">   25560 </span><span class="lineNoCov">          0 :                 i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="25561"><span class="lineNum">   25561 </span><span class="lineNoCov">          0 :                 for (i4 = np; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="25562"><span class="lineNum">   25562 </span><span class="lineNoCov">          0 :                     if (std::abs(b2)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25563"><span class="lineNum">   25563 </span><span class="lineNoCov">          0 :                         goto L20;</span></a>
+<a name="25564"><span class="lineNum">   25564 </span>            :                     }</a>
+<a name="25565"><span class="lineNum">   25565 </span>            :                     b1 = b2;</a>
+<a name="25566"><span class="lineNum">   25566 </span><span class="lineNoCov">          0 :                     if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="25567"><span class="lineNum">   25567 </span>            :                         return;</a>
+<a name="25568"><span class="lineNum">   25568 </span>            :                     }</a>
+<a name="25569"><span class="lineNum">   25569 </span><span class="lineNoCov">          0 :                     b2 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="25570"><span class="lineNum">   25570 </span><span class="lineNoCov">          0 :                     a2 += b2;</span></a>
+<a name="25571"><span class="lineNum">   25571 </span><span class="lineNoCov">          0 :                     if (((b2&gt;b1) ? b2 : b1) * 100. &lt; a2 || .563 &lt; a2) {</span></a>
+<a name="25572"><span class="lineNum">   25572 </span><span class="lineNoCov">          0 :                         goto L20;</span></a>
+<a name="25573"><span class="lineNum">   25573 </span>            :                     }</a>
+<a name="25574"><span class="lineNum">   25574 </span>            :                 }</a>
+<a name="25575"><span class="lineNum">   25575 </span><span class="lineNoCov">          0 : L20:</span></a>
+<a name="25576"><span class="lineNum">   25576 </span><span class="lineNoCov">          0 :                 a2 *= 1.05;</span></a>
+<a name="25577"><span class="lineNum">   25577 </span>            : </a>
+<a name="25578"><span class="lineNum">   25578 </span>            : </a>
+<a name="25579"><span class="lineNum">   25579 </span><span class="lineNoCov">          0 :                 if (a2 &lt; .563) {</span></a>
+<a name="25580"><span class="lineNum">   25580 </span><span class="lineNoCov">          0 :                     s = gam * (1. -  std::sqrt(a2)) / (a2 + 1.);</span></a>
+<a name="25581"><span class="lineNum">   25581 </span>            :                 }</a>
+<a name="25582"><span class="lineNum">   25582 </span>            :             }</a>
+<a name="25583"><span class="lineNum">   25583 </span><span class="lineNoCov">          0 :         } else if (std::abs(*dmin__ - *dn2)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin__ + *dn2)) {</span></a>
+<a name="25584"><span class="lineNum">   25584 </span>            : </a>
+<a name="25585"><span class="lineNum">   25585 </span><span class="lineNoCov">          0 :             *ttype = -5;</span></a>
+<a name="25586"><span class="lineNum">   25586 </span><span class="lineNoCov">          0 :             s = *dmin__ * .25;</span></a>
+<a name="25587"><span class="lineNum">   25587 </span>            : </a>
+<a name="25588"><span class="lineNum">   25588 </span><span class="lineNoCov">          0 :             np = nn - (*pp &lt;&lt; 1);</span></a>
+<a name="25589"><span class="lineNum">   25589 </span><span class="lineNoCov">          0 :             b1 = z__[np - 2];</span></a>
+<a name="25590"><span class="lineNum">   25590 </span><span class="lineNoCov">          0 :             b2 = z__[np - 6];</span></a>
+<a name="25591"><span class="lineNum">   25591 </span><span class="lineNoCov">          0 :             gam = *dn2;</span></a>
+<a name="25592"><span class="lineNum">   25592 </span><span class="lineNoCov">          0 :             if (z__[np - 8] &gt; b2 || z__[np - 4] &gt; b1) {</span></a>
+<a name="25593"><span class="lineNum">   25593 </span>            :                 return;</a>
+<a name="25594"><span class="lineNum">   25594 </span>            :             }</a>
+<a name="25595"><span class="lineNum">   25595 </span><span class="lineNoCov">          0 :             a2 = z__[np - 8] / b2 * (z__[np - 4] / b1 + 1.);</span></a>
+<a name="25596"><span class="lineNum">   25596 </span>            : </a>
+<a name="25597"><span class="lineNum">   25597 </span>            : </a>
+<a name="25598"><span class="lineNum">   25598 </span><span class="lineNoCov">          0 :             if (*n0 - *i0 &gt; 2) {</span></a>
+<a name="25599"><span class="lineNum">   25599 </span><span class="lineNoCov">          0 :                 b2 = z__[nn - 13] / z__[nn - 15];</span></a>
+<a name="25600"><span class="lineNum">   25600 </span><span class="lineNoCov">          0 :                 a2 += b2;</span></a>
+<a name="25601"><span class="lineNum">   25601 </span><span class="lineNoCov">          0 :                 i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="25602"><span class="lineNum">   25602 </span><span class="lineNoCov">          0 :                 for (i4 = nn - 17; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="25603"><span class="lineNum">   25603 </span><span class="lineNoCov">          0 :                     if (std::abs(b2)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25604"><span class="lineNum">   25604 </span><span class="lineNoCov">          0 :                         goto L40;</span></a>
+<a name="25605"><span class="lineNum">   25605 </span>            :                     }</a>
+<a name="25606"><span class="lineNum">   25606 </span>            :                     b1 = b2;</a>
+<a name="25607"><span class="lineNum">   25607 </span><span class="lineNoCov">          0 :                     if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="25608"><span class="lineNum">   25608 </span>            :                         return;</a>
+<a name="25609"><span class="lineNum">   25609 </span>            :                     }</a>
+<a name="25610"><span class="lineNum">   25610 </span><span class="lineNoCov">          0 :                     b2 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="25611"><span class="lineNum">   25611 </span><span class="lineNoCov">          0 :                     a2 += b2;</span></a>
+<a name="25612"><span class="lineNum">   25612 </span><span class="lineNoCov">          0 :                     if (((b2&gt;b1) ? b2 : b1) * 100. &lt; a2 || .563 &lt; a2) {</span></a>
+<a name="25613"><span class="lineNum">   25613 </span><span class="lineNoCov">          0 :                         goto L40;</span></a>
+<a name="25614"><span class="lineNum">   25614 </span>            :                     }</a>
+<a name="25615"><span class="lineNum">   25615 </span>            :                 }</a>
+<a name="25616"><span class="lineNum">   25616 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="25617"><span class="lineNum">   25617 </span><span class="lineNoCov">          0 :                 a2 *= 1.05;</span></a>
+<a name="25618"><span class="lineNum">   25618 </span>            :             }</a>
+<a name="25619"><span class="lineNum">   25619 </span>            : </a>
+<a name="25620"><span class="lineNum">   25620 </span><span class="lineNoCov">          0 :             if (a2 &lt; .563) {</span></a>
+<a name="25621"><span class="lineNum">   25621 </span><span class="lineNoCov">          0 :                 s = gam * (1. -  std::sqrt(a2)) / (a2 + 1.);</span></a>
+<a name="25622"><span class="lineNum">   25622 </span>            :             }</a>
+<a name="25623"><span class="lineNum">   25623 </span>            :         } else {</a>
+<a name="25624"><span class="lineNum">   25624 </span>            : </a>
+<a name="25625"><span class="lineNum">   25625 </span><span class="lineNoCov">          0 :             if (*ttype == -6) {</span></a>
+<a name="25626"><span class="lineNum">   25626 </span>            :                 g += (1. - g) * .333;</a>
+<a name="25627"><span class="lineNum">   25627 </span><span class="lineNoCov">          0 :             } else if (*ttype == -18) {</span></a>
+<a name="25628"><span class="lineNum">   25628 </span>            :                 g = .083250000000000005;</a>
+<a name="25629"><span class="lineNum">   25629 </span>            :             } else {</a>
+<a name="25630"><span class="lineNum">   25630 </span>            :                 g = .25;</a>
+<a name="25631"><span class="lineNum">   25631 </span>            :             }</a>
+<a name="25632"><span class="lineNum">   25632 </span><span class="lineNoCov">          0 :             s = g * *dmin__;</span></a>
+<a name="25633"><span class="lineNum">   25633 </span><span class="lineNoCov">          0 :             *ttype = -6;</span></a>
+<a name="25634"><span class="lineNum">   25634 </span>            :         }</a>
+<a name="25635"><span class="lineNum">   25635 </span>            : </a>
+<a name="25636"><span class="lineNum">   25636 </span><span class="lineNoCov">          0 :     } else if (*n0in == *n0 + 1) {</span></a>
+<a name="25637"><span class="lineNum">   25637 </span>            : </a>
+<a name="25638"><span class="lineNum">   25638 </span><span class="lineNoCov">          0 :         if ( std::abs(*dmin1 - *dn1)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin1 + *dn1) &amp;&amp;</span></a>
+<a name="25639"><span class="lineNum">   25639 </span><span class="lineNoCov">          0 :              std::abs(*dmin2 - *dn2)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin2 + *dn2)) {</span></a>
+<a name="25640"><span class="lineNum">   25640 </span>            : </a>
+<a name="25641"><span class="lineNum">   25641 </span><span class="lineNoCov">          0 :             *ttype = -7;</span></a>
+<a name="25642"><span class="lineNum">   25642 </span><span class="lineNoCov">          0 :             s = *dmin1 * .333;</span></a>
+<a name="25643"><span class="lineNum">   25643 </span><span class="lineNoCov">          0 :             if (z__[nn - 5] &gt; z__[nn - 7]) {</span></a>
+<a name="25644"><span class="lineNum">   25644 </span>            :                 return;</a>
+<a name="25645"><span class="lineNum">   25645 </span>            :             }</a>
+<a name="25646"><span class="lineNum">   25646 </span><span class="lineNoCov">          0 :             b1 = z__[nn - 5] / z__[nn - 7];</span></a>
+<a name="25647"><span class="lineNum">   25647 </span>            :             b2 = b1;</a>
+<a name="25648"><span class="lineNum">   25648 </span><span class="lineNoCov">          0 :             if (std::abs(b2)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25649"><span class="lineNum">   25649 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="25650"><span class="lineNum">   25650 </span>            :             }</a>
+<a name="25651"><span class="lineNum">   25651 </span><span class="lineNoCov">          0 :             i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="25652"><span class="lineNum">   25652 </span><span class="lineNoCov">          0 :             for (i4 = (*n0 &lt;&lt; 2) - 9 + *pp; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="25653"><span class="lineNum">   25653 </span>            :                 a2 = b1;</a>
+<a name="25654"><span class="lineNum">   25654 </span><span class="lineNoCov">          0 :                 if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="25655"><span class="lineNum">   25655 </span>            :                     return;</a>
+<a name="25656"><span class="lineNum">   25656 </span>            :                 }</a>
+<a name="25657"><span class="lineNum">   25657 </span><span class="lineNoCov">          0 :                 b1 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="25658"><span class="lineNum">   25658 </span><span class="lineNoCov">          0 :                 b2 += b1;</span></a>
+<a name="25659"><span class="lineNum">   25659 </span><span class="lineNoCov">          0 :                 if (((a2&gt;b1) ? a2 : b1) * 100. &lt; b2) {</span></a>
+<a name="25660"><span class="lineNum">   25660 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="25661"><span class="lineNum">   25661 </span>            :                 }</a>
+<a name="25662"><span class="lineNum">   25662 </span>            :             }</a>
+<a name="25663"><span class="lineNum">   25663 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="25664"><span class="lineNum">   25664 </span><span class="lineNoCov">          0 :             b2 =  std::sqrt(b2 * 1.05);</span></a>
+<a name="25665"><span class="lineNum">   25665 </span>            :             d__1 = b2;</a>
+<a name="25666"><span class="lineNum">   25666 </span><span class="lineNoCov">          0 :             a2 = *dmin1 / (d__1 * d__1 + 1.);</span></a>
+<a name="25667"><span class="lineNum">   25667 </span><span class="lineNoCov">          0 :             gap2 = *dmin2 * .5 - a2;</span></a>
+<a name="25668"><span class="lineNum">   25668 </span><span class="lineNoCov">          0 :             if (gap2 &gt; 0. &amp;&amp; gap2 &gt; b2 * a2) {</span></a>
+<a name="25669"><span class="lineNum">   25669 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - a2 * 1.01 * (b2 / gap2) * b2);</span></a>
+<a name="25670"><span class="lineNum">   25670 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25671"><span class="lineNum">   25671 </span>            :             } else {</a>
+<a name="25672"><span class="lineNum">   25672 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - b2 * 1.01);</span></a>
+<a name="25673"><span class="lineNum">   25673 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25674"><span class="lineNum">   25674 </span><span class="lineNoCov">          0 :                 *ttype = -8;</span></a>
+<a name="25675"><span class="lineNum">   25675 </span>            :             }</a>
+<a name="25676"><span class="lineNum">   25676 </span>            :         } else {</a>
+<a name="25677"><span class="lineNum">   25677 </span>            : </a>
+<a name="25678"><span class="lineNum">   25678 </span><span class="lineNoCov">          0 :             s = *dmin1 * .25;</span></a>
+<a name="25679"><span class="lineNum">   25679 </span><span class="lineNoCov">          0 :             if (std::abs(*dmin1 - *dn1)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin1 + *dn1)) {</span></a>
+<a name="25680"><span class="lineNum">   25680 </span><span class="lineNoCov">          0 :                 s = *dmin1 * .5;</span></a>
+<a name="25681"><span class="lineNum">   25681 </span>            :             }</a>
+<a name="25682"><span class="lineNum">   25682 </span><span class="lineNoCov">          0 :             *ttype = -9;</span></a>
+<a name="25683"><span class="lineNum">   25683 </span>            :         }</a>
+<a name="25684"><span class="lineNum">   25684 </span>            : </a>
+<a name="25685"><span class="lineNum">   25685 </span><span class="lineNoCov">          0 :     } else if (*n0in == *n0 + 2) {</span></a>
+<a name="25686"><span class="lineNum">   25686 </span>            : </a>
+<a name="25687"><span class="lineNum">   25687 </span><span class="lineNoCov">          0 :         if (std::abs(*dmin2 - *dn2)&lt;PLUMED_GMX_FLOAT_EPS*std::abs(*dmin2 + *dn2) &amp;&amp;</span></a>
+<a name="25688"><span class="lineNum">   25688 </span><span class="lineNoCov">          0 :         z__[nn - 5] * 2. &lt; z__[nn - 7]) {</span></a>
+<a name="25689"><span class="lineNum">   25689 </span><span class="lineNoCov">          0 :             *ttype = -10;</span></a>
+<a name="25690"><span class="lineNum">   25690 </span><span class="lineNoCov">          0 :             s = *dmin2 * .333;</span></a>
+<a name="25691"><span class="lineNum">   25691 </span><span class="lineNoCov">          0 :             if (z__[nn - 5] &gt; z__[nn - 7]) {</span></a>
+<a name="25692"><span class="lineNum">   25692 </span>            :                 return;</a>
+<a name="25693"><span class="lineNum">   25693 </span>            :             }</a>
+<a name="25694"><span class="lineNum">   25694 </span><span class="lineNoCov">          0 :             b1 = z__[nn - 5] / z__[nn - 7];</span></a>
+<a name="25695"><span class="lineNum">   25695 </span>            :             b2 = b1;</a>
+<a name="25696"><span class="lineNum">   25696 </span><span class="lineNoCov">          0 :             if (std::abs(b2)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25697"><span class="lineNum">   25697 </span><span class="lineNoCov">          0 :                 goto L80;</span></a>
+<a name="25698"><span class="lineNum">   25698 </span>            :             }</a>
+<a name="25699"><span class="lineNum">   25699 </span><span class="lineNoCov">          0 :             i__1 = (*i0 &lt;&lt; 2) - 1 + *pp;</span></a>
+<a name="25700"><span class="lineNum">   25700 </span><span class="lineNoCov">          0 :             for (i4 = (*n0 &lt;&lt; 2) - 9 + *pp; i4 &gt;= i__1; i4 += -4) {</span></a>
+<a name="25701"><span class="lineNum">   25701 </span><span class="lineNoCov">          0 :                 if (z__[i4] &gt; z__[i4 - 2]) {</span></a>
+<a name="25702"><span class="lineNum">   25702 </span>            :                     return;</a>
+<a name="25703"><span class="lineNum">   25703 </span>            :                 }</a>
+<a name="25704"><span class="lineNum">   25704 </span><span class="lineNoCov">          0 :                 b1 *= z__[i4] / z__[i4 - 2];</span></a>
+<a name="25705"><span class="lineNum">   25705 </span><span class="lineNoCov">          0 :                 b2 += b1;</span></a>
+<a name="25706"><span class="lineNum">   25706 </span><span class="lineNoCov">          0 :                 if (b1 * 100. &lt; b2) {</span></a>
+<a name="25707"><span class="lineNum">   25707 </span><span class="lineNoCov">          0 :                     goto L80;</span></a>
+<a name="25708"><span class="lineNum">   25708 </span>            :                 }</a>
+<a name="25709"><span class="lineNum">   25709 </span>            :             }</a>
+<a name="25710"><span class="lineNum">   25710 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="25711"><span class="lineNum">   25711 </span><span class="lineNoCov">          0 :             b2 =  std::sqrt(b2 * 1.05);</span></a>
+<a name="25712"><span class="lineNum">   25712 </span>            :             d__1 = b2;</a>
+<a name="25713"><span class="lineNum">   25713 </span><span class="lineNoCov">          0 :             a2 = *dmin2 / (d__1 * d__1 + 1.);</span></a>
+<a name="25714"><span class="lineNum">   25714 </span><span class="lineNoCov">          0 :             gap2 = z__[nn - 7] + z__[nn - 9] -  std::sqrt(z__[nn - 11]) * std::sqrt(z__[</span></a>
+<a name="25715"><span class="lineNum">   25715 </span>            :                     nn - 9]) - a2;</a>
+<a name="25716"><span class="lineNum">   25716 </span><span class="lineNoCov">          0 :             if (gap2 &gt; 0. &amp;&amp; gap2 &gt; b2 * a2) {</span></a>
+<a name="25717"><span class="lineNum">   25717 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - a2 * 1.01 * (b2 / gap2) * b2);</span></a>
+<a name="25718"><span class="lineNum">   25718 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25719"><span class="lineNum">   25719 </span>            :             } else {</a>
+<a name="25720"><span class="lineNum">   25720 </span><span class="lineNoCov">          0 :                 d__1 = s, d__2 = a2 * (1. - b2 * 1.01);</span></a>
+<a name="25721"><span class="lineNum">   25721 </span><span class="lineNoCov">          0 :                 s = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="25722"><span class="lineNum">   25722 </span>            :             }</a>
+<a name="25723"><span class="lineNum">   25723 </span>            :         } else {</a>
+<a name="25724"><span class="lineNum">   25724 </span><span class="lineNoCov">          0 :             s = *dmin2 * .25;</span></a>
+<a name="25725"><span class="lineNum">   25725 </span><span class="lineNoCov">          0 :             *ttype = -11;</span></a>
+<a name="25726"><span class="lineNum">   25726 </span>            :         }</a>
+<a name="25727"><span class="lineNum">   25727 </span><span class="lineNoCov">          0 :     } else if (*n0in &gt; *n0 + 2) {</span></a>
+<a name="25728"><span class="lineNum">   25728 </span>            : </a>
+<a name="25729"><span class="lineNum">   25729 </span>            :         s = 0.;</a>
+<a name="25730"><span class="lineNum">   25730 </span><span class="lineNoCov">          0 :         *ttype = -12;</span></a>
+<a name="25731"><span class="lineNum">   25731 </span>            :     }</a>
+<a name="25732"><span class="lineNum">   25732 </span>            : </a>
+<a name="25733"><span class="lineNum">   25733 </span><span class="lineNoCov">          0 :     *tau = s;</span></a>
+<a name="25734"><span class="lineNum">   25734 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="25735"><span class="lineNum">   25735 </span>            : </a>
+<a name="25736"><span class="lineNum">   25736 </span>            : }</a>
+<a name="25737"><span class="lineNum">   25737 </span>            : </a>
+<a name="25738"><span class="lineNum">   25738 </span>            : </a>
+<a name="25739"><span class="lineNum">   25739 </span>            : }</a>
+<a name="25740"><span class="lineNum">   25740 </span>            : }</a>
+<a name="25741"><span class="lineNum">   25741 </span>            : #include &lt;cmath&gt;</a>
+<a name="25742"><span class="lineNum">   25742 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="25743"><span class="lineNum">   25743 </span>            : </a>
+<a name="25744"><span class="lineNum">   25744 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="25745"><span class="lineNum">   25745 </span>            : namespace PLMD{</a>
+<a name="25746"><span class="lineNum">   25746 </span>            : namespace lapack{</a>
+<a name="25747"><span class="lineNum">   25747 </span>            : using namespace blas;</a>
+<a name="25748"><span class="lineNum">   25748 </span>            : void</a>
+<a name="25749"><span class="lineNum">   25749 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasq5,SLASQ5)(int *i0, </span></a>
+<a name="25750"><span class="lineNum">   25750 </span>            :         int *n0,</a>
+<a name="25751"><span class="lineNum">   25751 </span>            :         float *z__, </a>
+<a name="25752"><span class="lineNum">   25752 </span>            :         int *pp, </a>
+<a name="25753"><span class="lineNum">   25753 </span>            :         float *tau,</a>
+<a name="25754"><span class="lineNum">   25754 </span>            :         float *dmin__, </a>
+<a name="25755"><span class="lineNum">   25755 </span>            :         float *dmin1, </a>
+<a name="25756"><span class="lineNum">   25756 </span>            :         float *dmin2, </a>
+<a name="25757"><span class="lineNum">   25757 </span>            :         float *dn,</a>
+<a name="25758"><span class="lineNum">   25758 </span>            :         float *dnm1, </a>
+<a name="25759"><span class="lineNum">   25759 </span>            :         float *dnm2,</a>
+<a name="25760"><span class="lineNum">   25760 </span>            :         int *ieee)</a>
+<a name="25761"><span class="lineNum">   25761 </span>            : {</a>
+<a name="25762"><span class="lineNum">   25762 </span>            :     int i__1;</a>
+<a name="25763"><span class="lineNum">   25763 </span>            :     float d__1, d__2;</a>
+<a name="25764"><span class="lineNum">   25764 </span>            : </a>
+<a name="25765"><span class="lineNum">   25765 </span>            :     float d__;</a>
+<a name="25766"><span class="lineNum">   25766 </span>            :     int j4, j4p2;</a>
+<a name="25767"><span class="lineNum">   25767 </span>            :     float emin, temp;</a>
+<a name="25768"><span class="lineNum">   25768 </span>            : </a>
+<a name="25769"><span class="lineNum">   25769 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="25770"><span class="lineNum">   25770 </span>            : </a>
+<a name="25771"><span class="lineNum">   25771 </span><span class="lineNoCov">          0 :     if (*n0 - *i0 - 1 &lt;= 0) {</span></a>
+<a name="25772"><span class="lineNum">   25772 </span>            :         return;</a>
+<a name="25773"><span class="lineNum">   25773 </span>            :     }</a>
+<a name="25774"><span class="lineNum">   25774 </span>            : </a>
+<a name="25775"><span class="lineNum">   25775 </span><span class="lineNoCov">          0 :     j4 = (*i0 &lt;&lt; 2) + *pp - 3;</span></a>
+<a name="25776"><span class="lineNum">   25776 </span><span class="lineNoCov">          0 :     emin = z__[j4 + 4];</span></a>
+<a name="25777"><span class="lineNum">   25777 </span><span class="lineNoCov">          0 :     d__ = z__[j4] - *tau;</span></a>
+<a name="25778"><span class="lineNum">   25778 </span><span class="lineNoCov">          0 :     *dmin__ = d__;</span></a>
+<a name="25779"><span class="lineNum">   25779 </span><span class="lineNoCov">          0 :     *dmin1 = -z__[j4];</span></a>
+<a name="25780"><span class="lineNum">   25780 </span>            : </a>
+<a name="25781"><span class="lineNum">   25781 </span><span class="lineNoCov">          0 :     if (*ieee) {</span></a>
+<a name="25782"><span class="lineNum">   25782 </span>            : </a>
+<a name="25783"><span class="lineNum">   25783 </span><span class="lineNoCov">          0 :         if (*pp == 0) {</span></a>
+<a name="25784"><span class="lineNum">   25784 </span><span class="lineNoCov">          0 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="25785"><span class="lineNum">   25785 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25786"><span class="lineNum">   25786 </span><span class="lineNoCov">          0 :                 z__[j4 - 2] = d__ + z__[j4 - 1];</span></a>
+<a name="25787"><span class="lineNum">   25787 </span><span class="lineNoCov">          0 :                 temp = z__[j4 + 1] / z__[j4 - 2];</span></a>
+<a name="25788"><span class="lineNum">   25788 </span><span class="lineNoCov">          0 :                 d__ = d__ * temp - *tau;</span></a>
+<a name="25789"><span class="lineNum">   25789 </span><span class="lineNoCov">          0 :                 if(d__&lt;*dmin__)</span></a>
+<a name="25790"><span class="lineNum">   25790 </span><span class="lineNoCov">          0 :                   *dmin__ = d__;</span></a>
+<a name="25791"><span class="lineNum">   25791 </span><span class="lineNoCov">          0 :                 z__[j4] = z__[j4 - 1] * temp;</span></a>
+<a name="25792"><span class="lineNum">   25792 </span>            :                 d__1 = z__[j4];</a>
+<a name="25793"><span class="lineNum">   25793 </span><span class="lineNoCov">          0 :                 if(d__1&lt;emin)</span></a>
+<a name="25794"><span class="lineNum">   25794 </span>            :                   emin = d__1;</a>
+<a name="25795"><span class="lineNum">   25795 </span>            :             }</a>
+<a name="25796"><span class="lineNum">   25796 </span>            :         } else {</a>
+<a name="25797"><span class="lineNum">   25797 </span><span class="lineNoCov">          0 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="25798"><span class="lineNum">   25798 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25799"><span class="lineNum">   25799 </span><span class="lineNoCov">          0 :                 z__[j4 - 3] = d__ + z__[j4];</span></a>
+<a name="25800"><span class="lineNum">   25800 </span><span class="lineNoCov">          0 :                 temp = z__[j4 + 2] / z__[j4 - 3];</span></a>
+<a name="25801"><span class="lineNum">   25801 </span><span class="lineNoCov">          0 :                 d__ = d__ * temp - *tau;</span></a>
+<a name="25802"><span class="lineNum">   25802 </span><span class="lineNoCov">          0 :                 if(d__&lt;*dmin__)</span></a>
+<a name="25803"><span class="lineNum">   25803 </span><span class="lineNoCov">          0 :                   *dmin__ = d__;</span></a>
+<a name="25804"><span class="lineNum">   25804 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = z__[j4] * temp;</span></a>
+<a name="25805"><span class="lineNum">   25805 </span>            :                 d__1 = z__[j4 - 1];</a>
+<a name="25806"><span class="lineNum">   25806 </span><span class="lineNoCov">          0 :                 if(d__1&lt;emin)</span></a>
+<a name="25807"><span class="lineNum">   25807 </span>            :                   emin = d__1;</a>
+<a name="25808"><span class="lineNum">   25808 </span>            :             }</a>
+<a name="25809"><span class="lineNum">   25809 </span>            :         }</a>
+<a name="25810"><span class="lineNum">   25810 </span>            : </a>
+<a name="25811"><span class="lineNum">   25811 </span><span class="lineNoCov">          0 :         *dnm2 = d__;</span></a>
+<a name="25812"><span class="lineNum">   25812 </span><span class="lineNoCov">          0 :         *dmin2 = *dmin__;</span></a>
+<a name="25813"><span class="lineNum">   25813 </span><span class="lineNoCov">          0 :         j4 = 4*(*n0 - 2) - *pp;</span></a>
+<a name="25814"><span class="lineNum">   25814 </span><span class="lineNoCov">          0 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="25815"><span class="lineNum">   25815 </span><span class="lineNoCov">          0 :         z__[j4 - 2] = *dnm2 + z__[j4p2];</span></a>
+<a name="25816"><span class="lineNum">   25816 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="25817"><span class="lineNum">   25817 </span><span class="lineNoCov">          0 :         *dnm1 = z__[j4p2 + 2] * (*dnm2 / z__[j4 - 2]) - *tau;</span></a>
+<a name="25818"><span class="lineNum">   25818 </span><span class="lineNoCov">          0 :         if(*dnm1&lt;*dmin__)</span></a>
+<a name="25819"><span class="lineNum">   25819 </span><span class="lineNoCov">          0 :           *dmin__ = *dnm1;</span></a>
+<a name="25820"><span class="lineNum">   25820 </span>            : </a>
+<a name="25821"><span class="lineNum">   25821 </span><span class="lineNoCov">          0 :         *dmin1 = *dmin__;</span></a>
+<a name="25822"><span class="lineNum">   25822 </span><span class="lineNoCov">          0 :         j4 += 4;</span></a>
+<a name="25823"><span class="lineNum">   25823 </span><span class="lineNoCov">          0 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="25824"><span class="lineNum">   25824 </span><span class="lineNoCov">          0 :         z__[j4 - 2] = *dnm1 + z__[j4p2];</span></a>
+<a name="25825"><span class="lineNum">   25825 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="25826"><span class="lineNum">   25826 </span><span class="lineNoCov">          0 :         *dn = z__[j4p2 + 2] * (*dnm1 / z__[j4 - 2]) - *tau;</span></a>
+<a name="25827"><span class="lineNum">   25827 </span><span class="lineNoCov">          0 :         if(*dn&lt;*dmin__)</span></a>
+<a name="25828"><span class="lineNum">   25828 </span><span class="lineNoCov">          0 :           *dmin__ = *dn;</span></a>
+<a name="25829"><span class="lineNum">   25829 </span>            : </a>
+<a name="25830"><span class="lineNum">   25830 </span>            :     } else {</a>
+<a name="25831"><span class="lineNum">   25831 </span>            : </a>
+<a name="25832"><span class="lineNum">   25832 </span><span class="lineNoCov">          0 :         if (*pp == 0) {</span></a>
+<a name="25833"><span class="lineNum">   25833 </span><span class="lineNoCov">          0 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="25834"><span class="lineNum">   25834 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25835"><span class="lineNum">   25835 </span><span class="lineNoCov">          0 :                 z__[j4 - 2] = d__ + z__[j4 - 1];</span></a>
+<a name="25836"><span class="lineNum">   25836 </span><span class="lineNoCov">          0 :                 if (d__ &lt; 0.) {</span></a>
+<a name="25837"><span class="lineNum">   25837 </span>            :                     return;</a>
+<a name="25838"><span class="lineNum">   25838 </span>            :                 } else {</a>
+<a name="25839"><span class="lineNum">   25839 </span><span class="lineNoCov">          0 :                     z__[j4] = z__[j4 + 1] * (z__[j4 - 1] / z__[j4 - 2]);</span></a>
+<a name="25840"><span class="lineNum">   25840 </span><span class="lineNoCov">          0 :                     d__ = z__[j4 + 1] * (d__ / z__[j4 - 2]) - *tau;</span></a>
+<a name="25841"><span class="lineNum">   25841 </span>            :                 }</a>
+<a name="25842"><span class="lineNum">   25842 </span><span class="lineNoCov">          0 :                 if(d__&lt;*dmin__)</span></a>
+<a name="25843"><span class="lineNum">   25843 </span><span class="lineNoCov">          0 :                   *dmin__ = d__;</span></a>
+<a name="25844"><span class="lineNum">   25844 </span><span class="lineNoCov">          0 :                 d__1 = emin, d__2 = z__[j4];</span></a>
+<a name="25845"><span class="lineNum">   25845 </span><span class="lineNoCov">          0 :                 emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25846"><span class="lineNum">   25846 </span>            :             }</a>
+<a name="25847"><span class="lineNum">   25847 </span>            :         } else {</a>
+<a name="25848"><span class="lineNum">   25848 </span><span class="lineNoCov">          0 :             i__1 = 4*(*n0 - 3);</span></a>
+<a name="25849"><span class="lineNum">   25849 </span><span class="lineNoCov">          0 :             for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25850"><span class="lineNum">   25850 </span><span class="lineNoCov">          0 :                 z__[j4 - 3] = d__ + z__[j4];</span></a>
+<a name="25851"><span class="lineNum">   25851 </span><span class="lineNoCov">          0 :                 if (d__ &lt; 0.) {</span></a>
+<a name="25852"><span class="lineNum">   25852 </span>            :                     return;</a>
+<a name="25853"><span class="lineNum">   25853 </span>            :                 } else {</a>
+<a name="25854"><span class="lineNum">   25854 </span><span class="lineNoCov">          0 :                     z__[j4 - 1] = z__[j4 + 2] * (z__[j4] / z__[j4 - 3]);</span></a>
+<a name="25855"><span class="lineNum">   25855 </span><span class="lineNoCov">          0 :                     d__ = z__[j4 + 2] * (d__ / z__[j4 - 3]) - *tau;</span></a>
+<a name="25856"><span class="lineNum">   25856 </span>            :                 }</a>
+<a name="25857"><span class="lineNum">   25857 </span><span class="lineNoCov">          0 :                 if(d__&lt;*dmin__)</span></a>
+<a name="25858"><span class="lineNum">   25858 </span><span class="lineNoCov">          0 :                   *dmin__ = d__;</span></a>
+<a name="25859"><span class="lineNum">   25859 </span><span class="lineNoCov">          0 :                 d__1 = emin, d__2 = z__[j4 - 1];</span></a>
+<a name="25860"><span class="lineNum">   25860 </span><span class="lineNoCov">          0 :                 emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25861"><span class="lineNum">   25861 </span>            :             }</a>
+<a name="25862"><span class="lineNum">   25862 </span>            :         }</a>
+<a name="25863"><span class="lineNum">   25863 </span>            : </a>
+<a name="25864"><span class="lineNum">   25864 </span><span class="lineNoCov">          0 :         *dnm2 = d__;</span></a>
+<a name="25865"><span class="lineNum">   25865 </span><span class="lineNoCov">          0 :         *dmin2 = *dmin__;</span></a>
+<a name="25866"><span class="lineNum">   25866 </span><span class="lineNoCov">          0 :         j4 = 4*(*n0 - 2) - *pp;</span></a>
+<a name="25867"><span class="lineNum">   25867 </span><span class="lineNoCov">          0 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="25868"><span class="lineNum">   25868 </span><span class="lineNoCov">          0 :         z__[j4 - 2] = *dnm2 + z__[j4p2];</span></a>
+<a name="25869"><span class="lineNum">   25869 </span><span class="lineNoCov">          0 :         if (*dnm2 &lt; 0.) {</span></a>
+<a name="25870"><span class="lineNum">   25870 </span>            :             return;</a>
+<a name="25871"><span class="lineNum">   25871 </span>            :         } else {</a>
+<a name="25872"><span class="lineNum">   25872 </span><span class="lineNoCov">          0 :             z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="25873"><span class="lineNum">   25873 </span><span class="lineNoCov">          0 :             *dnm1 = z__[j4p2 + 2] * (*dnm2 / z__[j4 - 2]) - *tau;</span></a>
+<a name="25874"><span class="lineNum">   25874 </span>            :         }</a>
+<a name="25875"><span class="lineNum">   25875 </span><span class="lineNoCov">          0 :         if(*dnm1&lt;*dmin__)</span></a>
+<a name="25876"><span class="lineNum">   25876 </span><span class="lineNoCov">          0 :           *dmin__ = *dnm1;</span></a>
+<a name="25877"><span class="lineNum">   25877 </span>            : </a>
+<a name="25878"><span class="lineNum">   25878 </span><span class="lineNoCov">          0 :         *dmin1 = *dmin__;</span></a>
+<a name="25879"><span class="lineNum">   25879 </span><span class="lineNoCov">          0 :         j4 += 4;</span></a>
+<a name="25880"><span class="lineNum">   25880 </span><span class="lineNoCov">          0 :         j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="25881"><span class="lineNum">   25881 </span><span class="lineNoCov">          0 :         z__[j4 - 2] = *dnm1 + z__[j4p2];</span></a>
+<a name="25882"><span class="lineNum">   25882 </span><span class="lineNoCov">          0 :         if (*dnm1 &lt; 0.) {</span></a>
+<a name="25883"><span class="lineNum">   25883 </span>            :             return;</a>
+<a name="25884"><span class="lineNum">   25884 </span>            :         } else {</a>
+<a name="25885"><span class="lineNum">   25885 </span><span class="lineNoCov">          0 :             z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="25886"><span class="lineNum">   25886 </span><span class="lineNoCov">          0 :             *dn = z__[j4p2 + 2] * (*dnm1 / z__[j4 - 2]) - *tau;</span></a>
+<a name="25887"><span class="lineNum">   25887 </span>            :         }</a>
+<a name="25888"><span class="lineNum">   25888 </span><span class="lineNoCov">          0 :         if(*dn&lt;*dmin__)</span></a>
+<a name="25889"><span class="lineNum">   25889 </span><span class="lineNoCov">          0 :           *dmin__ = *dn;</span></a>
+<a name="25890"><span class="lineNum">   25890 </span>            : </a>
+<a name="25891"><span class="lineNum">   25891 </span>            :     }</a>
+<a name="25892"><span class="lineNum">   25892 </span>            : </a>
+<a name="25893"><span class="lineNum">   25893 </span><span class="lineNoCov">          0 :     z__[j4 + 2] = *dn;</span></a>
+<a name="25894"><span class="lineNum">   25894 </span><span class="lineNoCov">          0 :     z__[(*n0 &lt;&lt; 2) - *pp] = emin;</span></a>
+<a name="25895"><span class="lineNum">   25895 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="25896"><span class="lineNum">   25896 </span>            : </a>
+<a name="25897"><span class="lineNum">   25897 </span>            : }</a>
+<a name="25898"><span class="lineNum">   25898 </span>            : </a>
+<a name="25899"><span class="lineNum">   25899 </span>            : }</a>
+<a name="25900"><span class="lineNum">   25900 </span>            : }</a>
+<a name="25901"><span class="lineNum">   25901 </span>            : #include &lt;cmath&gt;</a>
+<a name="25902"><span class="lineNum">   25902 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="25903"><span class="lineNum">   25903 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="25904"><span class="lineNum">   25904 </span>            : </a>
+<a name="25905"><span class="lineNum">   25905 </span>            : #include &quot;real.h&quot;</a>
+<a name="25906"><span class="lineNum">   25906 </span>            : </a>
+<a name="25907"><span class="lineNum">   25907 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="25908"><span class="lineNum">   25908 </span>            : namespace PLMD{</a>
+<a name="25909"><span class="lineNum">   25909 </span>            : namespace lapack{</a>
+<a name="25910"><span class="lineNum">   25910 </span>            : using namespace blas;</a>
+<a name="25911"><span class="lineNum">   25911 </span>            : void </a>
+<a name="25912"><span class="lineNum">   25912 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasq6,SLASQ6)(int *i0, </span></a>
+<a name="25913"><span class="lineNum">   25913 </span>            :         int *n0, </a>
+<a name="25914"><span class="lineNum">   25914 </span>            :         float *z__, </a>
+<a name="25915"><span class="lineNum">   25915 </span>            :         int *pp, </a>
+<a name="25916"><span class="lineNum">   25916 </span>            :         float *dmin__, </a>
+<a name="25917"><span class="lineNum">   25917 </span>            :         float *dmin1, </a>
+<a name="25918"><span class="lineNum">   25918 </span>            :         float *dmin2,</a>
+<a name="25919"><span class="lineNum">   25919 </span>            :         float *dn, </a>
+<a name="25920"><span class="lineNum">   25920 </span>            :         float *dnm1, </a>
+<a name="25921"><span class="lineNum">   25921 </span>            :         float *dnm2)</a>
+<a name="25922"><span class="lineNum">   25922 </span>            : {</a>
+<a name="25923"><span class="lineNum">   25923 </span>            :     int i__1;</a>
+<a name="25924"><span class="lineNum">   25924 </span>            :     float d__1, d__2;</a>
+<a name="25925"><span class="lineNum">   25925 </span>            : </a>
+<a name="25926"><span class="lineNum">   25926 </span>            :     /* Local variables */</a>
+<a name="25927"><span class="lineNum">   25927 </span>            :     float d__;</a>
+<a name="25928"><span class="lineNum">   25928 </span>            :     int j4, j4p2;</a>
+<a name="25929"><span class="lineNum">   25929 </span>            :     float emin, temp;</a>
+<a name="25930"><span class="lineNum">   25930 </span>            :     const float safemin = PLUMED_GMX_FLOAT_MIN*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="25931"><span class="lineNum">   25931 </span>            : </a>
+<a name="25932"><span class="lineNum">   25932 </span><span class="lineNoCov">          0 :     --z__;</span></a>
+<a name="25933"><span class="lineNum">   25933 </span>            : </a>
+<a name="25934"><span class="lineNum">   25934 </span><span class="lineNoCov">          0 :     if (*n0 - *i0 - 1 &lt;= 0) {</span></a>
+<a name="25935"><span class="lineNum">   25935 </span>            :         return;</a>
+<a name="25936"><span class="lineNum">   25936 </span>            :     }</a>
+<a name="25937"><span class="lineNum">   25937 </span>            : </a>
+<a name="25938"><span class="lineNum">   25938 </span><span class="lineNoCov">          0 :     j4 = (*i0 &lt;&lt; 2) + *pp - 3;</span></a>
+<a name="25939"><span class="lineNum">   25939 </span><span class="lineNoCov">          0 :     emin = z__[j4 + 4];</span></a>
+<a name="25940"><span class="lineNum">   25940 </span><span class="lineNoCov">          0 :     d__ = z__[j4];</span></a>
+<a name="25941"><span class="lineNum">   25941 </span><span class="lineNoCov">          0 :     *dmin__ = d__;</span></a>
+<a name="25942"><span class="lineNum">   25942 </span>            : </a>
+<a name="25943"><span class="lineNum">   25943 </span><span class="lineNoCov">          0 :     if (*pp == 0) {</span></a>
+<a name="25944"><span class="lineNum">   25944 </span><span class="lineNoCov">          0 :         i__1 = 4*(*n0 - 3);</span></a>
+<a name="25945"><span class="lineNum">   25945 </span><span class="lineNoCov">          0 :         for (j4 = *i0*4; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25946"><span class="lineNum">   25946 </span><span class="lineNoCov">          0 :             z__[j4 - 2] = d__ + z__[j4 - 1];</span></a>
+<a name="25947"><span class="lineNum">   25947 </span><span class="lineNoCov">          0 :             if (std::abs(z__[j4 - 2])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25948"><span class="lineNum">   25948 </span><span class="lineNoCov">          0 :                 z__[j4] = 0.;</span></a>
+<a name="25949"><span class="lineNum">   25949 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 1];</span></a>
+<a name="25950"><span class="lineNum">   25950 </span><span class="lineNoCov">          0 :                 *dmin__ = d__;</span></a>
+<a name="25951"><span class="lineNum">   25951 </span>            :                 emin = 0.;</a>
+<a name="25952"><span class="lineNum">   25952 </span><span class="lineNoCov">          0 :             } else if (safemin * z__[j4 + 1] &lt; z__[j4 - 2] &amp;&amp; safemin * z__[j4 </span></a>
+<a name="25953"><span class="lineNum">   25953 </span>            :                     - 2] &lt; z__[j4 + 1]) {</a>
+<a name="25954"><span class="lineNum">   25954 </span><span class="lineNoCov">          0 :                 temp = z__[j4 + 1] / z__[j4 - 2];</span></a>
+<a name="25955"><span class="lineNum">   25955 </span><span class="lineNoCov">          0 :                 z__[j4] = z__[j4 - 1] * temp;</span></a>
+<a name="25956"><span class="lineNum">   25956 </span><span class="lineNoCov">          0 :                 d__ *= temp;</span></a>
+<a name="25957"><span class="lineNum">   25957 </span>            :             } else {</a>
+<a name="25958"><span class="lineNum">   25958 </span><span class="lineNoCov">          0 :                 z__[j4] = z__[j4 + 1] * (z__[j4 - 1] / z__[j4 - 2]);</span></a>
+<a name="25959"><span class="lineNum">   25959 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 1] * (d__ / z__[j4 - 2]);</span></a>
+<a name="25960"><span class="lineNum">   25960 </span>            :             }</a>
+<a name="25961"><span class="lineNum">   25961 </span><span class="lineNoCov">          0 :             if(d__&lt;*dmin__)</span></a>
+<a name="25962"><span class="lineNum">   25962 </span><span class="lineNoCov">          0 :               *dmin__ = d__;</span></a>
+<a name="25963"><span class="lineNum">   25963 </span>            : </a>
+<a name="25964"><span class="lineNum">   25964 </span><span class="lineNoCov">          0 :             d__1 = emin, d__2 = z__[j4];</span></a>
+<a name="25965"><span class="lineNum">   25965 </span><span class="lineNoCov">          0 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25966"><span class="lineNum">   25966 </span>            :         }</a>
+<a name="25967"><span class="lineNum">   25967 </span>            :     } else {</a>
+<a name="25968"><span class="lineNum">   25968 </span><span class="lineNoCov">          0 :         i__1 = 4*(*n0 - 3);</span></a>
+<a name="25969"><span class="lineNum">   25969 </span><span class="lineNoCov">          0 :         for (j4 = *i0 &lt;&lt; 2; j4 &lt;= i__1; j4 += 4) {</span></a>
+<a name="25970"><span class="lineNum">   25970 </span><span class="lineNoCov">          0 :             z__[j4 - 3] = d__ + z__[j4];</span></a>
+<a name="25971"><span class="lineNum">   25971 </span><span class="lineNoCov">          0 :             if (std::abs(z__[j4 - 3])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25972"><span class="lineNum">   25972 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = 0.;</span></a>
+<a name="25973"><span class="lineNum">   25973 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 2];</span></a>
+<a name="25974"><span class="lineNum">   25974 </span><span class="lineNoCov">          0 :                 *dmin__ = d__;</span></a>
+<a name="25975"><span class="lineNum">   25975 </span>            :                 emin = 0.;</a>
+<a name="25976"><span class="lineNum">   25976 </span><span class="lineNoCov">          0 :             } else if (safemin * z__[j4 + 2] &lt; z__[j4 - 3] &amp;&amp; safemin * z__[j4 </span></a>
+<a name="25977"><span class="lineNum">   25977 </span>            :                     - 3] &lt; z__[j4 + 2]) {</a>
+<a name="25978"><span class="lineNum">   25978 </span><span class="lineNoCov">          0 :                 temp = z__[j4 + 2] / z__[j4 - 3];</span></a>
+<a name="25979"><span class="lineNum">   25979 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = z__[j4] * temp;</span></a>
+<a name="25980"><span class="lineNum">   25980 </span><span class="lineNoCov">          0 :                 d__ *= temp;</span></a>
+<a name="25981"><span class="lineNum">   25981 </span>            :             } else {</a>
+<a name="25982"><span class="lineNum">   25982 </span><span class="lineNoCov">          0 :                 z__[j4 - 1] = z__[j4 + 2] * (z__[j4] / z__[j4 - 3]);</span></a>
+<a name="25983"><span class="lineNum">   25983 </span><span class="lineNoCov">          0 :                 d__ = z__[j4 + 2] * (d__ / z__[j4 - 3]);</span></a>
+<a name="25984"><span class="lineNum">   25984 </span>            :             }</a>
+<a name="25985"><span class="lineNum">   25985 </span><span class="lineNoCov">          0 :             if(d__&lt;*dmin__)</span></a>
+<a name="25986"><span class="lineNum">   25986 </span><span class="lineNoCov">          0 :               *dmin__ = d__;</span></a>
+<a name="25987"><span class="lineNum">   25987 </span><span class="lineNoCov">          0 :             d__1 = emin, d__2 = z__[j4 - 1];</span></a>
+<a name="25988"><span class="lineNum">   25988 </span><span class="lineNoCov">          0 :             emin = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="25989"><span class="lineNum">   25989 </span>            :         }</a>
+<a name="25990"><span class="lineNum">   25990 </span>            :     }</a>
+<a name="25991"><span class="lineNum">   25991 </span>            : </a>
+<a name="25992"><span class="lineNum">   25992 </span><span class="lineNoCov">          0 :     *dnm2 = d__;</span></a>
+<a name="25993"><span class="lineNum">   25993 </span><span class="lineNoCov">          0 :     *dmin2 = *dmin__;</span></a>
+<a name="25994"><span class="lineNum">   25994 </span><span class="lineNoCov">          0 :     j4 = 4*(*n0 - 2) - *pp;</span></a>
+<a name="25995"><span class="lineNum">   25995 </span><span class="lineNoCov">          0 :     j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="25996"><span class="lineNum">   25996 </span><span class="lineNoCov">          0 :     z__[j4 - 2] = *dnm2 + z__[j4p2];</span></a>
+<a name="25997"><span class="lineNum">   25997 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j4 - 2])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="25998"><span class="lineNum">   25998 </span><span class="lineNoCov">          0 :         z__[j4] = 0.;</span></a>
+<a name="25999"><span class="lineNum">   25999 </span><span class="lineNoCov">          0 :         *dnm1 = z__[j4p2 + 2];</span></a>
+<a name="26000"><span class="lineNum">   26000 </span><span class="lineNoCov">          0 :         *dmin__ = *dnm1;</span></a>
+<a name="26001"><span class="lineNum">   26001 </span>            :         emin = 0.;</a>
+<a name="26002"><span class="lineNum">   26002 </span><span class="lineNoCov">          0 :     } else if (safemin * z__[j4p2 + 2] &lt; z__[j4 - 2] &amp;&amp; safemin * z__[j4 - 2] &lt; </span></a>
+<a name="26003"><span class="lineNum">   26003 </span>            :             z__[j4p2 + 2]) {</a>
+<a name="26004"><span class="lineNum">   26004 </span><span class="lineNoCov">          0 :         temp = z__[j4p2 + 2] / z__[j4 - 2];</span></a>
+<a name="26005"><span class="lineNum">   26005 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2] * temp;</span></a>
+<a name="26006"><span class="lineNum">   26006 </span><span class="lineNoCov">          0 :         *dnm1 = *dnm2 * temp;</span></a>
+<a name="26007"><span class="lineNum">   26007 </span>            :     } else {</a>
+<a name="26008"><span class="lineNum">   26008 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="26009"><span class="lineNum">   26009 </span><span class="lineNoCov">          0 :         *dnm1 = z__[j4p2 + 2] * (*dnm2 / z__[j4 - 2]);</span></a>
+<a name="26010"><span class="lineNum">   26010 </span>            :     }</a>
+<a name="26011"><span class="lineNum">   26011 </span><span class="lineNoCov">          0 :     if(*dnm1&lt;*dmin__)</span></a>
+<a name="26012"><span class="lineNum">   26012 </span><span class="lineNoCov">          0 :       *dmin__ = *dnm1;</span></a>
+<a name="26013"><span class="lineNum">   26013 </span>            : </a>
+<a name="26014"><span class="lineNum">   26014 </span><span class="lineNoCov">          0 :     *dmin1 = *dmin__;</span></a>
+<a name="26015"><span class="lineNum">   26015 </span><span class="lineNoCov">          0 :     j4 += 4;</span></a>
+<a name="26016"><span class="lineNum">   26016 </span><span class="lineNoCov">          0 :     j4p2 = j4 + (*pp &lt;&lt; 1) - 1;</span></a>
+<a name="26017"><span class="lineNum">   26017 </span><span class="lineNoCov">          0 :     z__[j4 - 2] = *dnm1 + z__[j4p2];</span></a>
+<a name="26018"><span class="lineNum">   26018 </span><span class="lineNoCov">          0 :     if (std::abs(z__[j4 - 2])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26019"><span class="lineNum">   26019 </span><span class="lineNoCov">          0 :         z__[j4] = 0.;</span></a>
+<a name="26020"><span class="lineNum">   26020 </span><span class="lineNoCov">          0 :         *dn = z__[j4p2 + 2];</span></a>
+<a name="26021"><span class="lineNum">   26021 </span><span class="lineNoCov">          0 :         *dmin__ = *dn;</span></a>
+<a name="26022"><span class="lineNum">   26022 </span>            :         emin = 0.;</a>
+<a name="26023"><span class="lineNum">   26023 </span><span class="lineNoCov">          0 :     } else if (safemin * z__[j4p2 + 2] &lt; z__[j4 - 2] &amp;&amp; safemin * z__[j4 - 2] &lt; </span></a>
+<a name="26024"><span class="lineNum">   26024 </span>            :             z__[j4p2 + 2]) {</a>
+<a name="26025"><span class="lineNum">   26025 </span><span class="lineNoCov">          0 :         temp = z__[j4p2 + 2] / z__[j4 - 2];</span></a>
+<a name="26026"><span class="lineNum">   26026 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2] * temp;</span></a>
+<a name="26027"><span class="lineNum">   26027 </span><span class="lineNoCov">          0 :         *dn = *dnm1 * temp;</span></a>
+<a name="26028"><span class="lineNum">   26028 </span>            :     } else {</a>
+<a name="26029"><span class="lineNum">   26029 </span><span class="lineNoCov">          0 :         z__[j4] = z__[j4p2 + 2] * (z__[j4p2] / z__[j4 - 2]);</span></a>
+<a name="26030"><span class="lineNum">   26030 </span><span class="lineNoCov">          0 :         *dn = z__[j4p2 + 2] * (*dnm1 / z__[j4 - 2]);</span></a>
+<a name="26031"><span class="lineNum">   26031 </span>            :     }</a>
+<a name="26032"><span class="lineNum">   26032 </span><span class="lineNoCov">          0 :     if(*dn&lt;*dmin__)</span></a>
+<a name="26033"><span class="lineNum">   26033 </span><span class="lineNoCov">          0 :       *dmin__ = *dn;</span></a>
+<a name="26034"><span class="lineNum">   26034 </span>            : </a>
+<a name="26035"><span class="lineNum">   26035 </span><span class="lineNoCov">          0 :     z__[j4 + 2] = *dn;</span></a>
+<a name="26036"><span class="lineNum">   26036 </span><span class="lineNoCov">          0 :     z__[(*n0 &lt;&lt; 2) - *pp] = emin;</span></a>
+<a name="26037"><span class="lineNum">   26037 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="26038"><span class="lineNum">   26038 </span>            : </a>
+<a name="26039"><span class="lineNum">   26039 </span>            : </a>
+<a name="26040"><span class="lineNum">   26040 </span>            : } </a>
+<a name="26041"><span class="lineNum">   26041 </span>            : }</a>
+<a name="26042"><span class="lineNum">   26042 </span>            : }</a>
+<a name="26043"><span class="lineNum">   26043 </span>            : #include &lt;cmath&gt;</a>
+<a name="26044"><span class="lineNum">   26044 </span>            : </a>
+<a name="26045"><span class="lineNum">   26045 </span>            : #include &quot;real.h&quot;</a>
+<a name="26046"><span class="lineNum">   26046 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26047"><span class="lineNum">   26047 </span>            : </a>
+<a name="26048"><span class="lineNum">   26048 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26049"><span class="lineNum">   26049 </span>            : namespace PLMD{</a>
+<a name="26050"><span class="lineNum">   26050 </span>            : namespace lapack{</a>
+<a name="26051"><span class="lineNum">   26051 </span>            : using namespace blas;</a>
+<a name="26052"><span class="lineNum">   26052 </span>            : void </a>
+<a name="26053"><span class="lineNum">   26053 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasr,SLASR)(const char *side, </span></a>
+<a name="26054"><span class="lineNum">   26054 </span>            :        const char *pivot, </a>
+<a name="26055"><span class="lineNum">   26055 </span>            :        const char *direct, </a>
+<a name="26056"><span class="lineNum">   26056 </span>            :        int *m,</a>
+<a name="26057"><span class="lineNum">   26057 </span>            :        int *n, </a>
+<a name="26058"><span class="lineNum">   26058 </span>            :        float *c__, </a>
+<a name="26059"><span class="lineNum">   26059 </span>            :        float *s, </a>
+<a name="26060"><span class="lineNum">   26060 </span>            :        float *a, </a>
+<a name="26061"><span class="lineNum">   26061 </span>            :        int *lda)</a>
+<a name="26062"><span class="lineNum">   26062 </span>            : {</a>
+<a name="26063"><span class="lineNum">   26063 </span>            :     /* System generated locals */</a>
+<a name="26064"><span class="lineNum">   26064 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="26065"><span class="lineNum">   26065 </span>            : </a>
+<a name="26066"><span class="lineNum">   26066 </span>            :     /* Local variables */</a>
+<a name="26067"><span class="lineNum">   26067 </span>            :     int i__, j;</a>
+<a name="26068"><span class="lineNum">   26068 </span>            :     float temp;</a>
+<a name="26069"><span class="lineNum">   26069 </span>            :     float ctemp, stemp;</a>
+<a name="26070"><span class="lineNum">   26070 </span>            : </a>
+<a name="26071"><span class="lineNum">   26071 </span><span class="lineNoCov">          0 :     --c__;</span></a>
+<a name="26072"><span class="lineNum">   26072 </span><span class="lineNoCov">          0 :     --s;</span></a>
+<a name="26073"><span class="lineNum">   26073 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="26074"><span class="lineNum">   26074 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="26075"><span class="lineNum">   26075 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="26076"><span class="lineNum">   26076 </span>            : </a>
+<a name="26077"><span class="lineNum">   26077 </span>            :     /* Function Body */</a>
+<a name="26078"><span class="lineNum">   26078 </span>            : </a>
+<a name="26079"><span class="lineNum">   26079 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0) {</span></a>
+<a name="26080"><span class="lineNum">   26080 </span>            :         return;</a>
+<a name="26081"><span class="lineNum">   26081 </span>            :     }</a>
+<a name="26082"><span class="lineNum">   26082 </span><span class="lineNoCov">          0 :     if (*side=='L' || *side=='l') {</span></a>
+<a name="26083"><span class="lineNum">   26083 </span>            : </a>
+<a name="26084"><span class="lineNum">   26084 </span><span class="lineNoCov">          0 :         if (*pivot=='V' || *pivot=='v') {</span></a>
+<a name="26085"><span class="lineNum">   26085 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="26086"><span class="lineNum">   26086 </span>            :                 i__1 = *m - 1;</a>
+<a name="26087"><span class="lineNum">   26087 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="26088"><span class="lineNum">   26088 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26089"><span class="lineNum">   26089 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26090"><span class="lineNum">   26090 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26091"><span class="lineNum">   26091 </span><span class="lineNoCov">          0 :                         i__2 = *n;</span></a>
+<a name="26092"><span class="lineNum">   26092 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="26093"><span class="lineNum">   26093 </span><span class="lineNoCov">          0 :                             temp = a[j + 1 + i__ * a_dim1];</span></a>
+<a name="26094"><span class="lineNum">   26094 </span><span class="lineNoCov">          0 :                             a[j + 1 + i__ * a_dim1] = ctemp * temp - stemp * </span></a>
+<a name="26095"><span class="lineNum">   26095 </span><span class="lineNoCov">          0 :                                     a[j + i__ * a_dim1];</span></a>
+<a name="26096"><span class="lineNum">   26096 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = stemp * temp + ctemp * a[j </span></a>
+<a name="26097"><span class="lineNum">   26097 </span><span class="lineNoCov">          0 :                                     + i__ * a_dim1];</span></a>
+<a name="26098"><span class="lineNum">   26098 </span>            :                         }</a>
+<a name="26099"><span class="lineNum">   26099 </span>            :                     }</a>
+<a name="26100"><span class="lineNum">   26100 </span>            :                 }</a>
+<a name="26101"><span class="lineNum">   26101 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="26102"><span class="lineNum">   26102 </span><span class="lineNoCov">          0 :                 for (j = *m - 1; j &gt;= 1; --j) {</span></a>
+<a name="26103"><span class="lineNum">   26103 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26104"><span class="lineNum">   26104 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26105"><span class="lineNum">   26105 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26106"><span class="lineNum">   26106 </span><span class="lineNoCov">          0 :                         i__1 = *n;</span></a>
+<a name="26107"><span class="lineNum">   26107 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26108"><span class="lineNum">   26108 </span><span class="lineNoCov">          0 :                             temp = a[j + 1 + i__ * a_dim1];</span></a>
+<a name="26109"><span class="lineNum">   26109 </span><span class="lineNoCov">          0 :                             a[j + 1 + i__ * a_dim1] = ctemp * temp - stemp * </span></a>
+<a name="26110"><span class="lineNum">   26110 </span><span class="lineNoCov">          0 :                                     a[j + i__ * a_dim1];</span></a>
+<a name="26111"><span class="lineNum">   26111 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = stemp * temp + ctemp * a[j </span></a>
+<a name="26112"><span class="lineNum">   26112 </span><span class="lineNoCov">          0 :                                     + i__ * a_dim1];</span></a>
+<a name="26113"><span class="lineNum">   26113 </span>            :                         }</a>
+<a name="26114"><span class="lineNum">   26114 </span>            :                     }</a>
+<a name="26115"><span class="lineNum">   26115 </span>            :                 }</a>
+<a name="26116"><span class="lineNum">   26116 </span>            :             }</a>
+<a name="26117"><span class="lineNum">   26117 </span><span class="lineNoCov">          0 :         } else if (*pivot=='T' || *pivot=='t') {</span></a>
+<a name="26118"><span class="lineNum">   26118 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="26119"><span class="lineNum">   26119 </span>            :                 i__1 = *m;</a>
+<a name="26120"><span class="lineNum">   26120 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="26121"><span class="lineNum">   26121 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="26122"><span class="lineNum">   26122 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="26123"><span class="lineNum">   26123 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26124"><span class="lineNum">   26124 </span><span class="lineNoCov">          0 :                         i__2 = *n;</span></a>
+<a name="26125"><span class="lineNum">   26125 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="26126"><span class="lineNum">   26126 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="26127"><span class="lineNum">   26127 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="26128"><span class="lineNum">   26128 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="26129"><span class="lineNum">   26129 </span><span class="lineNoCov">          0 :                             a[i__ * a_dim1 + 1] = stemp * temp + ctemp * a[</span></a>
+<a name="26130"><span class="lineNum">   26130 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="26131"><span class="lineNum">   26131 </span>            :                         }</a>
+<a name="26132"><span class="lineNum">   26132 </span>            :                     }</a>
+<a name="26133"><span class="lineNum">   26133 </span>            :                 }</a>
+<a name="26134"><span class="lineNum">   26134 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="26135"><span class="lineNum">   26135 </span><span class="lineNoCov">          0 :                 for (j = *m; j &gt;= 2; --j) {</span></a>
+<a name="26136"><span class="lineNum">   26136 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="26137"><span class="lineNum">   26137 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="26138"><span class="lineNum">   26138 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26139"><span class="lineNum">   26139 </span><span class="lineNoCov">          0 :                         i__1 = *n;</span></a>
+<a name="26140"><span class="lineNum">   26140 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26141"><span class="lineNum">   26141 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="26142"><span class="lineNum">   26142 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="26143"><span class="lineNum">   26143 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="26144"><span class="lineNum">   26144 </span><span class="lineNoCov">          0 :                             a[i__ * a_dim1 + 1] = stemp * temp + ctemp * a[</span></a>
+<a name="26145"><span class="lineNum">   26145 </span><span class="lineNoCov">          0 :                                     i__ * a_dim1 + 1];</span></a>
+<a name="26146"><span class="lineNum">   26146 </span>            :                         }</a>
+<a name="26147"><span class="lineNum">   26147 </span>            :                     }</a>
+<a name="26148"><span class="lineNum">   26148 </span>            :                 }</a>
+<a name="26149"><span class="lineNum">   26149 </span>            :             }</a>
+<a name="26150"><span class="lineNum">   26150 </span><span class="lineNoCov">          0 :         } else if (*pivot=='B' || *pivot=='b') {</span></a>
+<a name="26151"><span class="lineNum">   26151 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="26152"><span class="lineNum">   26152 </span>            :                 i__1 = *m - 1;</a>
+<a name="26153"><span class="lineNum">   26153 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="26154"><span class="lineNum">   26154 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26155"><span class="lineNum">   26155 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26156"><span class="lineNum">   26156 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26157"><span class="lineNum">   26157 </span><span class="lineNoCov">          0 :                         i__2 = *n;</span></a>
+<a name="26158"><span class="lineNum">   26158 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="26159"><span class="lineNum">   26159 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="26160"><span class="lineNum">   26160 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = stemp * a[*m + i__ * a_dim1]</span></a>
+<a name="26161"><span class="lineNum">   26161 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="26162"><span class="lineNum">   26162 </span><span class="lineNoCov">          0 :                             a[*m + i__ * a_dim1] = ctemp * a[*m + i__ * </span></a>
+<a name="26163"><span class="lineNum">   26163 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="26164"><span class="lineNum">   26164 </span>            :                         }</a>
+<a name="26165"><span class="lineNum">   26165 </span>            :                     }</a>
+<a name="26166"><span class="lineNum">   26166 </span>            :                 }</a>
+<a name="26167"><span class="lineNum">   26167 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="26168"><span class="lineNum">   26168 </span><span class="lineNoCov">          0 :                 for (j = *m - 1; j &gt;= 1; --j) {</span></a>
+<a name="26169"><span class="lineNum">   26169 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26170"><span class="lineNum">   26170 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26171"><span class="lineNum">   26171 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26172"><span class="lineNum">   26172 </span><span class="lineNoCov">          0 :                         i__1 = *n;</span></a>
+<a name="26173"><span class="lineNum">   26173 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26174"><span class="lineNum">   26174 </span><span class="lineNoCov">          0 :                             temp = a[j + i__ * a_dim1];</span></a>
+<a name="26175"><span class="lineNum">   26175 </span><span class="lineNoCov">          0 :                             a[j + i__ * a_dim1] = stemp * a[*m + i__ * a_dim1]</span></a>
+<a name="26176"><span class="lineNum">   26176 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="26177"><span class="lineNum">   26177 </span><span class="lineNoCov">          0 :                             a[*m + i__ * a_dim1] = ctemp * a[*m + i__ * </span></a>
+<a name="26178"><span class="lineNum">   26178 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="26179"><span class="lineNum">   26179 </span>            :                         }</a>
+<a name="26180"><span class="lineNum">   26180 </span>            :                     }</a>
+<a name="26181"><span class="lineNum">   26181 </span>            :                 }</a>
+<a name="26182"><span class="lineNum">   26182 </span>            :             }</a>
+<a name="26183"><span class="lineNum">   26183 </span>            :         }</a>
+<a name="26184"><span class="lineNum">   26184 </span><span class="lineNoCov">          0 :     } else if (*side=='R' || *side=='r') {</span></a>
+<a name="26185"><span class="lineNum">   26185 </span>            : </a>
+<a name="26186"><span class="lineNum">   26186 </span><span class="lineNoCov">          0 :         if (*pivot=='V' || *pivot=='v') {</span></a>
+<a name="26187"><span class="lineNum">   26187 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="26188"><span class="lineNum">   26188 </span>            :                 i__1 = *n - 1;</a>
+<a name="26189"><span class="lineNum">   26189 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="26190"><span class="lineNum">   26190 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26191"><span class="lineNum">   26191 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26192"><span class="lineNum">   26192 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26193"><span class="lineNum">   26193 </span><span class="lineNoCov">          0 :                         i__2 = *m;</span></a>
+<a name="26194"><span class="lineNum">   26194 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="26195"><span class="lineNum">   26195 </span><span class="lineNoCov">          0 :                             temp = a[i__ + (j + 1) * a_dim1];</span></a>
+<a name="26196"><span class="lineNum">   26196 </span><span class="lineNoCov">          0 :                             a[i__ + (j + 1) * a_dim1] = ctemp * temp - stemp *</span></a>
+<a name="26197"><span class="lineNum">   26197 </span><span class="lineNoCov">          0 :                                      a[i__ + j * a_dim1];</span></a>
+<a name="26198"><span class="lineNum">   26198 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = stemp * temp + ctemp * a[</span></a>
+<a name="26199"><span class="lineNum">   26199 </span><span class="lineNoCov">          0 :                                     i__ + j * a_dim1];</span></a>
+<a name="26200"><span class="lineNum">   26200 </span>            :                         }</a>
+<a name="26201"><span class="lineNum">   26201 </span>            :                     }</a>
+<a name="26202"><span class="lineNum">   26202 </span>            :                 }</a>
+<a name="26203"><span class="lineNum">   26203 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="26204"><span class="lineNum">   26204 </span><span class="lineNoCov">          0 :                 for (j = *n - 1; j &gt;= 1; --j) {</span></a>
+<a name="26205"><span class="lineNum">   26205 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26206"><span class="lineNum">   26206 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26207"><span class="lineNum">   26207 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26208"><span class="lineNum">   26208 </span><span class="lineNoCov">          0 :                         i__1 = *m;</span></a>
+<a name="26209"><span class="lineNum">   26209 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26210"><span class="lineNum">   26210 </span><span class="lineNoCov">          0 :                             temp = a[i__ + (j + 1) * a_dim1];</span></a>
+<a name="26211"><span class="lineNum">   26211 </span><span class="lineNoCov">          0 :                             a[i__ + (j + 1) * a_dim1] = ctemp * temp - stemp *</span></a>
+<a name="26212"><span class="lineNum">   26212 </span><span class="lineNoCov">          0 :                                      a[i__ + j * a_dim1];</span></a>
+<a name="26213"><span class="lineNum">   26213 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = stemp * temp + ctemp * a[</span></a>
+<a name="26214"><span class="lineNum">   26214 </span><span class="lineNoCov">          0 :                                     i__ + j * a_dim1];</span></a>
+<a name="26215"><span class="lineNum">   26215 </span>            :                         }</a>
+<a name="26216"><span class="lineNum">   26216 </span>            :                     }</a>
+<a name="26217"><span class="lineNum">   26217 </span>            :                 }</a>
+<a name="26218"><span class="lineNum">   26218 </span>            :             }</a>
+<a name="26219"><span class="lineNum">   26219 </span><span class="lineNoCov">          0 :         } else if (*pivot=='T' || *pivot=='t') {</span></a>
+<a name="26220"><span class="lineNum">   26220 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="26221"><span class="lineNum">   26221 </span>            :                 i__1 = *n;</a>
+<a name="26222"><span class="lineNum">   26222 </span><span class="lineNoCov">          0 :                 for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="26223"><span class="lineNum">   26223 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="26224"><span class="lineNum">   26224 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="26225"><span class="lineNum">   26225 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26226"><span class="lineNum">   26226 </span><span class="lineNoCov">          0 :                         i__2 = *m;</span></a>
+<a name="26227"><span class="lineNum">   26227 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="26228"><span class="lineNum">   26228 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="26229"><span class="lineNum">   26229 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="26230"><span class="lineNum">   26230 </span><span class="lineNoCov">          0 :                                     i__ + a_dim1];</span></a>
+<a name="26231"><span class="lineNum">   26231 </span><span class="lineNoCov">          0 :                             a[i__ + a_dim1] = stemp * temp + ctemp * a[i__ + </span></a>
+<a name="26232"><span class="lineNum">   26232 </span><span class="lineNoCov">          0 :                                     a_dim1];</span></a>
+<a name="26233"><span class="lineNum">   26233 </span>            :                         }</a>
+<a name="26234"><span class="lineNum">   26234 </span>            :                     }</a>
+<a name="26235"><span class="lineNum">   26235 </span>            :                 }</a>
+<a name="26236"><span class="lineNum">   26236 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="26237"><span class="lineNum">   26237 </span><span class="lineNoCov">          0 :                 for (j = *n; j &gt;= 2; --j) {</span></a>
+<a name="26238"><span class="lineNum">   26238 </span><span class="lineNoCov">          0 :                     ctemp = c__[j - 1];</span></a>
+<a name="26239"><span class="lineNum">   26239 </span><span class="lineNoCov">          0 :                     stemp = s[j - 1];</span></a>
+<a name="26240"><span class="lineNum">   26240 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26241"><span class="lineNum">   26241 </span><span class="lineNoCov">          0 :                         i__1 = *m;</span></a>
+<a name="26242"><span class="lineNum">   26242 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26243"><span class="lineNum">   26243 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="26244"><span class="lineNum">   26244 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = ctemp * temp - stemp * a[</span></a>
+<a name="26245"><span class="lineNum">   26245 </span><span class="lineNoCov">          0 :                                     i__ + a_dim1];</span></a>
+<a name="26246"><span class="lineNum">   26246 </span><span class="lineNoCov">          0 :                             a[i__ + a_dim1] = stemp * temp + ctemp * a[i__ + </span></a>
+<a name="26247"><span class="lineNum">   26247 </span><span class="lineNoCov">          0 :                                     a_dim1];</span></a>
+<a name="26248"><span class="lineNum">   26248 </span>            :                         }</a>
+<a name="26249"><span class="lineNum">   26249 </span>            :                     }</a>
+<a name="26250"><span class="lineNum">   26250 </span>            :                 }</a>
+<a name="26251"><span class="lineNum">   26251 </span>            :             }</a>
+<a name="26252"><span class="lineNum">   26252 </span><span class="lineNoCov">          0 :         } else if (*pivot=='B' || *pivot=='b') {</span></a>
+<a name="26253"><span class="lineNum">   26253 </span><span class="lineNoCov">          0 :             if (*direct=='F' || *direct=='f') {</span></a>
+<a name="26254"><span class="lineNum">   26254 </span>            :                 i__1 = *n - 1;</a>
+<a name="26255"><span class="lineNum">   26255 </span><span class="lineNoCov">          0 :                 for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="26256"><span class="lineNum">   26256 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26257"><span class="lineNum">   26257 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26258"><span class="lineNum">   26258 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26259"><span class="lineNum">   26259 </span><span class="lineNoCov">          0 :                         i__2 = *m;</span></a>
+<a name="26260"><span class="lineNum">   26260 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="26261"><span class="lineNum">   26261 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="26262"><span class="lineNum">   26262 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = stemp * a[i__ + *n * a_dim1]</span></a>
+<a name="26263"><span class="lineNum">   26263 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="26264"><span class="lineNum">   26264 </span><span class="lineNoCov">          0 :                             a[i__ + *n * a_dim1] = ctemp * a[i__ + *n * </span></a>
+<a name="26265"><span class="lineNum">   26265 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="26266"><span class="lineNum">   26266 </span>            :                         }</a>
+<a name="26267"><span class="lineNum">   26267 </span>            :                     }</a>
+<a name="26268"><span class="lineNum">   26268 </span>            :                 }</a>
+<a name="26269"><span class="lineNum">   26269 </span><span class="lineNoCov">          0 :             } else if (*direct=='B' || *direct=='b') {</span></a>
+<a name="26270"><span class="lineNum">   26270 </span><span class="lineNoCov">          0 :                 for (j = *n - 1; j &gt;= 1; --j) {</span></a>
+<a name="26271"><span class="lineNum">   26271 </span><span class="lineNoCov">          0 :                     ctemp = c__[j];</span></a>
+<a name="26272"><span class="lineNum">   26272 </span><span class="lineNoCov">          0 :                     stemp = s[j];</span></a>
+<a name="26273"><span class="lineNum">   26273 </span><span class="lineNoCov">          0 :                     if (std::abs(ctemp-1.0)&gt;PLUMED_GMX_FLOAT_EPS || std::abs(stemp)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26274"><span class="lineNum">   26274 </span><span class="lineNoCov">          0 :                         i__1 = *m;</span></a>
+<a name="26275"><span class="lineNum">   26275 </span><span class="lineNoCov">          0 :                         for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26276"><span class="lineNum">   26276 </span><span class="lineNoCov">          0 :                             temp = a[i__ + j * a_dim1];</span></a>
+<a name="26277"><span class="lineNum">   26277 </span><span class="lineNoCov">          0 :                             a[i__ + j * a_dim1] = stemp * a[i__ + *n * a_dim1]</span></a>
+<a name="26278"><span class="lineNum">   26278 </span><span class="lineNoCov">          0 :                                      + ctemp * temp;</span></a>
+<a name="26279"><span class="lineNum">   26279 </span><span class="lineNoCov">          0 :                             a[i__ + *n * a_dim1] = ctemp * a[i__ + *n * </span></a>
+<a name="26280"><span class="lineNum">   26280 </span><span class="lineNoCov">          0 :                                     a_dim1] - stemp * temp;</span></a>
+<a name="26281"><span class="lineNum">   26281 </span>            :                         }</a>
+<a name="26282"><span class="lineNum">   26282 </span>            :                     }</a>
+<a name="26283"><span class="lineNum">   26283 </span>            :                 }</a>
+<a name="26284"><span class="lineNum">   26284 </span>            :             }</a>
+<a name="26285"><span class="lineNum">   26285 </span>            :         }</a>
+<a name="26286"><span class="lineNum">   26286 </span>            :     }</a>
+<a name="26287"><span class="lineNum">   26287 </span>            : </a>
+<a name="26288"><span class="lineNum">   26288 </span>            :     return;</a>
+<a name="26289"><span class="lineNum">   26289 </span>            : </a>
+<a name="26290"><span class="lineNum">   26290 </span>            : }</a>
+<a name="26291"><span class="lineNum">   26291 </span>            : </a>
+<a name="26292"><span class="lineNum">   26292 </span>            : </a>
+<a name="26293"><span class="lineNum">   26293 </span>            : }</a>
+<a name="26294"><span class="lineNum">   26294 </span>            : }</a>
+<a name="26295"><span class="lineNum">   26295 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26296"><span class="lineNum">   26296 </span>            : </a>
+<a name="26297"><span class="lineNum">   26297 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26298"><span class="lineNum">   26298 </span>            : namespace PLMD{</a>
+<a name="26299"><span class="lineNum">   26299 </span>            : namespace lapack{</a>
+<a name="26300"><span class="lineNum">   26300 </span>            : using namespace blas;</a>
+<a name="26301"><span class="lineNum">   26301 </span>            : void </a>
+<a name="26302"><span class="lineNum">   26302 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(const char *id, </span></a>
+<a name="26303"><span class="lineNum">   26303 </span>            :         int *n, </a>
+<a name="26304"><span class="lineNum">   26304 </span>            :         float *d__, </a>
+<a name="26305"><span class="lineNum">   26305 </span>            :         int *info)</a>
+<a name="26306"><span class="lineNum">   26306 </span>            : {</a>
+<a name="26307"><span class="lineNum">   26307 </span>            :     int i__1, i__2;</a>
+<a name="26308"><span class="lineNum">   26308 </span>            : </a>
+<a name="26309"><span class="lineNum">   26309 </span>            :     int i__, j;</a>
+<a name="26310"><span class="lineNum">   26310 </span>            :     float d1, d2, d3;</a>
+<a name="26311"><span class="lineNum">   26311 </span>            :     int dir;</a>
+<a name="26312"><span class="lineNum">   26312 </span>            :     float tmp;</a>
+<a name="26313"><span class="lineNum">   26313 </span>            :     int endd;</a>
+<a name="26314"><span class="lineNum">   26314 </span>            :     int stack[64];</a>
+<a name="26315"><span class="lineNum">   26315 </span>            :     float dmnmx;</a>
+<a name="26316"><span class="lineNum">   26316 </span>            :     int start;</a>
+<a name="26317"><span class="lineNum">   26317 </span>            :     int stkpnt;</a>
+<a name="26318"><span class="lineNum">   26318 </span>            : </a>
+<a name="26319"><span class="lineNum">   26319 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="26320"><span class="lineNum">   26320 </span>            : </a>
+<a name="26321"><span class="lineNum">   26321 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="26322"><span class="lineNum">   26322 </span>            :     dir = -1;</a>
+<a name="26323"><span class="lineNum">   26323 </span><span class="lineNoCov">          0 :     if (*id=='D' || *id=='d') </span></a>
+<a name="26324"><span class="lineNum">   26324 </span>            :         dir = 0;</a>
+<a name="26325"><span class="lineNum">   26325 </span><span class="lineNoCov">          0 :     else if (*id=='I' || *id=='i') </span></a>
+<a name="26326"><span class="lineNum">   26326 </span>            :         dir = 1;</a>
+<a name="26327"><span class="lineNum">   26327 </span>            :    </a>
+<a name="26328"><span class="lineNum">   26328 </span>            :     if (dir == -1) {</a>
+<a name="26329"><span class="lineNum">   26329 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="26330"><span class="lineNum">   26330 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="26331"><span class="lineNum">   26331 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="26332"><span class="lineNum">   26332 </span>            :     }</a>
+<a name="26333"><span class="lineNum">   26333 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="26334"><span class="lineNum">   26334 </span>            :         return;</a>
+<a name="26335"><span class="lineNum">   26335 </span>            :     }</a>
+<a name="26336"><span class="lineNum">   26336 </span><span class="lineNoCov">          0 :     if (*n &lt;= 1) {</span></a>
+<a name="26337"><span class="lineNum">   26337 </span>            :         return;</a>
+<a name="26338"><span class="lineNum">   26338 </span>            :     }</a>
+<a name="26339"><span class="lineNum">   26339 </span>            : </a>
+<a name="26340"><span class="lineNum">   26340 </span>            :     stkpnt = 1;</a>
+<a name="26341"><span class="lineNum">   26341 </span><span class="lineNoCov">          0 :     stack[0] = 1;</span></a>
+<a name="26342"><span class="lineNum">   26342 </span><span class="lineNoCov">          0 :     stack[1] = *n;</span></a>
+<a name="26343"><span class="lineNum">   26343 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="26344"><span class="lineNum">   26344 </span><span class="lineNoCov">          0 :     start = stack[(stkpnt &lt;&lt; 1) - 2];</span></a>
+<a name="26345"><span class="lineNum">   26345 </span><span class="lineNoCov">          0 :     endd = stack[(stkpnt &lt;&lt; 1) - 1];</span></a>
+<a name="26346"><span class="lineNum">   26346 </span><span class="lineNoCov">          0 :     --stkpnt;</span></a>
+<a name="26347"><span class="lineNum">   26347 </span><span class="lineNoCov">          0 :     if (endd - start &lt;= 20 &amp;&amp; endd - start &gt; 0) {</span></a>
+<a name="26348"><span class="lineNum">   26348 </span>            : </a>
+<a name="26349"><span class="lineNum">   26349 </span>            : </a>
+<a name="26350"><span class="lineNum">   26350 </span><span class="lineNoCov">          0 :         if (dir == 0) {</span></a>
+<a name="26351"><span class="lineNum">   26351 </span>            : </a>
+<a name="26352"><span class="lineNum">   26352 </span>            :             i__1 = endd;</a>
+<a name="26353"><span class="lineNum">   26353 </span><span class="lineNoCov">          0 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26354"><span class="lineNum">   26354 </span>            :                 i__2 = start + 1;</a>
+<a name="26355"><span class="lineNum">   26355 </span><span class="lineNoCov">          0 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="26356"><span class="lineNum">   26356 </span><span class="lineNoCov">          0 :                     if (d__[j] &gt; d__[j - 1]) {</span></a>
+<a name="26357"><span class="lineNum">   26357 </span>            :                         dmnmx = d__[j];</a>
+<a name="26358"><span class="lineNum">   26358 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="26359"><span class="lineNum">   26359 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="26360"><span class="lineNum">   26360 </span>            :                     } else {</a>
+<a name="26361"><span class="lineNum">   26361 </span><span class="lineNoCov">          0 :                         goto L30;</span></a>
+<a name="26362"><span class="lineNum">   26362 </span>            :                     }</a>
+<a name="26363"><span class="lineNum">   26363 </span>            :                 }</a>
+<a name="26364"><span class="lineNum">   26364 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="26365"><span class="lineNum">   26365 </span>            :                 ;</a>
+<a name="26366"><span class="lineNum">   26366 </span>            :             }</a>
+<a name="26367"><span class="lineNum">   26367 </span>            : </a>
+<a name="26368"><span class="lineNum">   26368 </span>            :         } else {</a>
+<a name="26369"><span class="lineNum">   26369 </span>            : </a>
+<a name="26370"><span class="lineNum">   26370 </span>            :             i__1 = endd;</a>
+<a name="26371"><span class="lineNum">   26371 </span><span class="lineNoCov">          0 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26372"><span class="lineNum">   26372 </span>            :                 i__2 = start + 1;</a>
+<a name="26373"><span class="lineNum">   26373 </span><span class="lineNoCov">          0 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="26374"><span class="lineNum">   26374 </span><span class="lineNoCov">          0 :                     if (d__[j] &lt; d__[j - 1]) {</span></a>
+<a name="26375"><span class="lineNum">   26375 </span>            :                         dmnmx = d__[j];</a>
+<a name="26376"><span class="lineNum">   26376 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="26377"><span class="lineNum">   26377 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="26378"><span class="lineNum">   26378 </span>            :                     } else {</a>
+<a name="26379"><span class="lineNum">   26379 </span><span class="lineNoCov">          0 :                         goto L50;</span></a>
+<a name="26380"><span class="lineNum">   26380 </span>            :                     }</a>
+<a name="26381"><span class="lineNum">   26381 </span>            :                 }</a>
+<a name="26382"><span class="lineNum">   26382 </span><span class="lineNoCov">          0 : L50:</span></a>
+<a name="26383"><span class="lineNum">   26383 </span>            :                 ;</a>
+<a name="26384"><span class="lineNum">   26384 </span>            :             }</a>
+<a name="26385"><span class="lineNum">   26385 </span>            : </a>
+<a name="26386"><span class="lineNum">   26386 </span>            :         }</a>
+<a name="26387"><span class="lineNum">   26387 </span>            : </a>
+<a name="26388"><span class="lineNum">   26388 </span><span class="lineNoCov">          0 :     } else if (endd - start &gt; 20) {</span></a>
+<a name="26389"><span class="lineNum">   26389 </span>            : </a>
+<a name="26390"><span class="lineNum">   26390 </span><span class="lineNoCov">          0 :         d1 = d__[start];</span></a>
+<a name="26391"><span class="lineNum">   26391 </span><span class="lineNoCov">          0 :         d2 = d__[endd];</span></a>
+<a name="26392"><span class="lineNum">   26392 </span><span class="lineNoCov">          0 :         i__ = (start + endd) / 2;</span></a>
+<a name="26393"><span class="lineNum">   26393 </span><span class="lineNoCov">          0 :         d3 = d__[i__];</span></a>
+<a name="26394"><span class="lineNum">   26394 </span><span class="lineNoCov">          0 :         if (d1 &lt; d2) {</span></a>
+<a name="26395"><span class="lineNum">   26395 </span><span class="lineNoCov">          0 :             if (d3 &lt; d1) {</span></a>
+<a name="26396"><span class="lineNum">   26396 </span>            :                 dmnmx = d1;</a>
+<a name="26397"><span class="lineNum">   26397 </span><span class="lineNoCov">          0 :             } else if (d3 &lt; d2) {</span></a>
+<a name="26398"><span class="lineNum">   26398 </span>            :                 dmnmx = d3;</a>
+<a name="26399"><span class="lineNum">   26399 </span>            :             } else {</a>
+<a name="26400"><span class="lineNum">   26400 </span>            :                 dmnmx = d2;</a>
+<a name="26401"><span class="lineNum">   26401 </span>            :             }</a>
+<a name="26402"><span class="lineNum">   26402 </span>            :         } else {</a>
+<a name="26403"><span class="lineNum">   26403 </span><span class="lineNoCov">          0 :             if (d3 &lt; d2) {</span></a>
+<a name="26404"><span class="lineNum">   26404 </span>            :                 dmnmx = d2;</a>
+<a name="26405"><span class="lineNum">   26405 </span><span class="lineNoCov">          0 :             } else if (d3 &lt; d1) {</span></a>
+<a name="26406"><span class="lineNum">   26406 </span>            :                 dmnmx = d3;</a>
+<a name="26407"><span class="lineNum">   26407 </span>            :             } else {</a>
+<a name="26408"><span class="lineNum">   26408 </span>            :                 dmnmx = d1;</a>
+<a name="26409"><span class="lineNum">   26409 </span>            :             }</a>
+<a name="26410"><span class="lineNum">   26410 </span>            :         }</a>
+<a name="26411"><span class="lineNum">   26411 </span>            : </a>
+<a name="26412"><span class="lineNum">   26412 </span><span class="lineNoCov">          0 :         if (dir == 0) {</span></a>
+<a name="26413"><span class="lineNum">   26413 </span>            : </a>
+<a name="26414"><span class="lineNum">   26414 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="26415"><span class="lineNum">   26415 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="26416"><span class="lineNum">   26416 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="26417"><span class="lineNum">   26417 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="26418"><span class="lineNum">   26418 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="26419"><span class="lineNum">   26419 </span><span class="lineNoCov">          0 :             if (d__[j] &lt; dmnmx) {</span></a>
+<a name="26420"><span class="lineNum">   26420 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="26421"><span class="lineNum">   26421 </span>            :             }</a>
+<a name="26422"><span class="lineNum">   26422 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="26423"><span class="lineNum">   26423 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="26424"><span class="lineNum">   26424 </span><span class="lineNoCov">          0 :             if (d__[i__] &gt; dmnmx) {</span></a>
+<a name="26425"><span class="lineNum">   26425 </span><span class="lineNoCov">          0 :                 goto L80;</span></a>
+<a name="26426"><span class="lineNum">   26426 </span>            :             }</a>
+<a name="26427"><span class="lineNum">   26427 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="26428"><span class="lineNum">   26428 </span>            :                 tmp = d__[i__];</a>
+<a name="26429"><span class="lineNum">   26429 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="26430"><span class="lineNum">   26430 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="26431"><span class="lineNum">   26431 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="26432"><span class="lineNum">   26432 </span>            :             }</a>
+<a name="26433"><span class="lineNum">   26433 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="26434"><span class="lineNum">   26434 </span>            :                 ++stkpnt;</a>
+<a name="26435"><span class="lineNum">   26435 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="26436"><span class="lineNum">   26436 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26437"><span class="lineNum">   26437 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26438"><span class="lineNum">   26438 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26439"><span class="lineNum">   26439 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26440"><span class="lineNum">   26440 </span>            :             } else {</a>
+<a name="26441"><span class="lineNum">   26441 </span>            :                 ++stkpnt;</a>
+<a name="26442"><span class="lineNum">   26442 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26443"><span class="lineNum">   26443 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26444"><span class="lineNum">   26444 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26445"><span class="lineNum">   26445 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="26446"><span class="lineNum">   26446 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26447"><span class="lineNum">   26447 </span>            :             }</a>
+<a name="26448"><span class="lineNum">   26448 </span>            :         } else {</a>
+<a name="26449"><span class="lineNum">   26449 </span>            : </a>
+<a name="26450"><span class="lineNum">   26450 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="26451"><span class="lineNum">   26451 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="26452"><span class="lineNum">   26452 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="26453"><span class="lineNum">   26453 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="26454"><span class="lineNum">   26454 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="26455"><span class="lineNum">   26455 </span><span class="lineNoCov">          0 :             if (d__[j] &gt; dmnmx) {</span></a>
+<a name="26456"><span class="lineNum">   26456 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="26457"><span class="lineNum">   26457 </span>            :             }</a>
+<a name="26458"><span class="lineNum">   26458 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="26459"><span class="lineNum">   26459 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="26460"><span class="lineNum">   26460 </span><span class="lineNoCov">          0 :             if (d__[i__] &lt; dmnmx) {</span></a>
+<a name="26461"><span class="lineNum">   26461 </span><span class="lineNoCov">          0 :                 goto L110;</span></a>
+<a name="26462"><span class="lineNum">   26462 </span>            :             }</a>
+<a name="26463"><span class="lineNum">   26463 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="26464"><span class="lineNum">   26464 </span>            :                 tmp = d__[i__];</a>
+<a name="26465"><span class="lineNum">   26465 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="26466"><span class="lineNum">   26466 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="26467"><span class="lineNum">   26467 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="26468"><span class="lineNum">   26468 </span>            :             }</a>
+<a name="26469"><span class="lineNum">   26469 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="26470"><span class="lineNum">   26470 </span>            :                 ++stkpnt;</a>
+<a name="26471"><span class="lineNum">   26471 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="26472"><span class="lineNum">   26472 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26473"><span class="lineNum">   26473 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26474"><span class="lineNum">   26474 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26475"><span class="lineNum">   26475 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26476"><span class="lineNum">   26476 </span>            :             } else {</a>
+<a name="26477"><span class="lineNum">   26477 </span>            :                 ++stkpnt;</a>
+<a name="26478"><span class="lineNum">   26478 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26479"><span class="lineNum">   26479 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26480"><span class="lineNum">   26480 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26481"><span class="lineNum">   26481 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="26482"><span class="lineNum">   26482 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26483"><span class="lineNum">   26483 </span>            :             }</a>
+<a name="26484"><span class="lineNum">   26484 </span>            :         }</a>
+<a name="26485"><span class="lineNum">   26485 </span>            :     }</a>
+<a name="26486"><span class="lineNum">   26486 </span><span class="lineNoCov">          0 :     if (stkpnt &gt; 0) {</span></a>
+<a name="26487"><span class="lineNum">   26487 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="26488"><span class="lineNum">   26488 </span>            :     }</a>
+<a name="26489"><span class="lineNum">   26489 </span>            :     return;</a>
+<a name="26490"><span class="lineNum">   26490 </span>            : </a>
+<a name="26491"><span class="lineNum">   26491 </span>            : }</a>
+<a name="26492"><span class="lineNum">   26492 </span>            : }</a>
+<a name="26493"><span class="lineNum">   26493 </span>            : }</a>
+<a name="26494"><span class="lineNum">   26494 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26495"><span class="lineNum">   26495 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26496"><span class="lineNum">   26496 </span>            : namespace PLMD{</a>
+<a name="26497"><span class="lineNum">   26497 </span>            : namespace lapack{</a>
+<a name="26498"><span class="lineNum">   26498 </span>            : using namespace blas;</a>
+<a name="26499"><span class="lineNum">   26499 </span>            : </a>
+<a name="26500"><span class="lineNum">   26500 </span><span class="lineNoCov">          0 : void PLUMED_BLAS_F77_FUNC(slasrt2,SLASRT2)(const char *id, </span></a>
+<a name="26501"><span class="lineNum">   26501 </span>            :               int *n, </a>
+<a name="26502"><span class="lineNum">   26502 </span>            :               float *d__, </a>
+<a name="26503"><span class="lineNum">   26503 </span>            :               int * key, </a>
+<a name="26504"><span class="lineNum">   26504 </span>            :               int *info)</a>
+<a name="26505"><span class="lineNum">   26505 </span>            : {</a>
+<a name="26506"><span class="lineNum">   26506 </span>            :     int i__1, i__2;</a>
+<a name="26507"><span class="lineNum">   26507 </span>            : </a>
+<a name="26508"><span class="lineNum">   26508 </span>            :     int i__, j;</a>
+<a name="26509"><span class="lineNum">   26509 </span>            :     float d1, d2, d3;</a>
+<a name="26510"><span class="lineNum">   26510 </span>            :     int dir;</a>
+<a name="26511"><span class="lineNum">   26511 </span>            :     float tmp;</a>
+<a name="26512"><span class="lineNum">   26512 </span>            :     int endd;</a>
+<a name="26513"><span class="lineNum">   26513 </span>            :     int stack[64];</a>
+<a name="26514"><span class="lineNum">   26514 </span>            :     float dmnmx;</a>
+<a name="26515"><span class="lineNum">   26515 </span>            :     int start;</a>
+<a name="26516"><span class="lineNum">   26516 </span>            :     int tmpkey, stkpnt;</a>
+<a name="26517"><span class="lineNum">   26517 </span>            : </a>
+<a name="26518"><span class="lineNum">   26518 </span><span class="lineNoCov">          0 :     --key;</span></a>
+<a name="26519"><span class="lineNum">   26519 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="26520"><span class="lineNum">   26520 </span>            : </a>
+<a name="26521"><span class="lineNum">   26521 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="26522"><span class="lineNum">   26522 </span>            :     dir = -1;</a>
+<a name="26523"><span class="lineNum">   26523 </span><span class="lineNoCov">          0 :     if (*id=='D' || *id=='d')</span></a>
+<a name="26524"><span class="lineNum">   26524 </span>            :         dir = 0;</a>
+<a name="26525"><span class="lineNum">   26525 </span><span class="lineNoCov">          0 :     else if (*id=='I' || *id=='i')</span></a>
+<a name="26526"><span class="lineNum">   26526 </span>            :         dir = 1;</a>
+<a name="26527"><span class="lineNum">   26527 </span>            :     </a>
+<a name="26528"><span class="lineNum">   26528 </span>            :     if (dir == -1) {</a>
+<a name="26529"><span class="lineNum">   26529 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="26530"><span class="lineNum">   26530 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="26531"><span class="lineNum">   26531 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="26532"><span class="lineNum">   26532 </span>            :     }</a>
+<a name="26533"><span class="lineNum">   26533 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="26534"><span class="lineNum">   26534 </span>            :         return;</a>
+<a name="26535"><span class="lineNum">   26535 </span>            :     }</a>
+<a name="26536"><span class="lineNum">   26536 </span>            : </a>
+<a name="26537"><span class="lineNum">   26537 </span><span class="lineNoCov">          0 :     if (*n &lt;= 1) {</span></a>
+<a name="26538"><span class="lineNum">   26538 </span>            :         return;</a>
+<a name="26539"><span class="lineNum">   26539 </span>            :     }</a>
+<a name="26540"><span class="lineNum">   26540 </span>            : </a>
+<a name="26541"><span class="lineNum">   26541 </span>            :     stkpnt = 1;</a>
+<a name="26542"><span class="lineNum">   26542 </span><span class="lineNoCov">          0 :     stack[0] = 1;</span></a>
+<a name="26543"><span class="lineNum">   26543 </span><span class="lineNoCov">          0 :     stack[1] = *n;</span></a>
+<a name="26544"><span class="lineNum">   26544 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="26545"><span class="lineNum">   26545 </span><span class="lineNoCov">          0 :     start = stack[(stkpnt &lt;&lt; 1) - 2];</span></a>
+<a name="26546"><span class="lineNum">   26546 </span><span class="lineNoCov">          0 :     endd = stack[(stkpnt &lt;&lt; 1) - 1];</span></a>
+<a name="26547"><span class="lineNum">   26547 </span><span class="lineNoCov">          0 :     --stkpnt;</span></a>
+<a name="26548"><span class="lineNum">   26548 </span><span class="lineNoCov">          0 :     if (endd - start &gt; 0) {</span></a>
+<a name="26549"><span class="lineNum">   26549 </span>            : </a>
+<a name="26550"><span class="lineNum">   26550 </span><span class="lineNoCov">          0 :         if (dir == 0) {</span></a>
+<a name="26551"><span class="lineNum">   26551 </span>            : </a>
+<a name="26552"><span class="lineNum">   26552 </span>            :             i__1 = endd;</a>
+<a name="26553"><span class="lineNum">   26553 </span><span class="lineNoCov">          0 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26554"><span class="lineNum">   26554 </span>            :                 i__2 = start + 1;</a>
+<a name="26555"><span class="lineNum">   26555 </span><span class="lineNoCov">          0 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="26556"><span class="lineNum">   26556 </span><span class="lineNoCov">          0 :                     if (d__[j] &gt; d__[j - 1]) {</span></a>
+<a name="26557"><span class="lineNum">   26557 </span>            :                         dmnmx = d__[j];</a>
+<a name="26558"><span class="lineNum">   26558 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="26559"><span class="lineNum">   26559 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="26560"><span class="lineNum">   26560 </span><span class="lineNoCov">          0 :                         tmpkey = key[j];</span></a>
+<a name="26561"><span class="lineNum">   26561 </span><span class="lineNoCov">          0 :                         key[j] = key[j - 1];</span></a>
+<a name="26562"><span class="lineNum">   26562 </span><span class="lineNoCov">          0 :                         key[j - 1] = tmpkey;</span></a>
+<a name="26563"><span class="lineNum">   26563 </span>            :                     } else {</a>
+<a name="26564"><span class="lineNum">   26564 </span>            :                         break;</a>
+<a name="26565"><span class="lineNum">   26565 </span>            :                     }</a>
+<a name="26566"><span class="lineNum">   26566 </span>            :                 }</a>
+<a name="26567"><span class="lineNum">   26567 </span>            :             }</a>
+<a name="26568"><span class="lineNum">   26568 </span>            : </a>
+<a name="26569"><span class="lineNum">   26569 </span>            :         } else {</a>
+<a name="26570"><span class="lineNum">   26570 </span>            : </a>
+<a name="26571"><span class="lineNum">   26571 </span>            :             i__1 = endd;</a>
+<a name="26572"><span class="lineNum">   26572 </span><span class="lineNoCov">          0 :             for (i__ = start + 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="26573"><span class="lineNum">   26573 </span>            :                 i__2 = start + 1;</a>
+<a name="26574"><span class="lineNum">   26574 </span><span class="lineNoCov">          0 :                 for (j = i__; j &gt;= i__2; --j) {</span></a>
+<a name="26575"><span class="lineNum">   26575 </span><span class="lineNoCov">          0 :                     if (d__[j] &lt; d__[j - 1]) {</span></a>
+<a name="26576"><span class="lineNum">   26576 </span>            :                         dmnmx = d__[j];</a>
+<a name="26577"><span class="lineNum">   26577 </span><span class="lineNoCov">          0 :                         d__[j] = d__[j - 1];</span></a>
+<a name="26578"><span class="lineNum">   26578 </span><span class="lineNoCov">          0 :                         d__[j - 1] = dmnmx;</span></a>
+<a name="26579"><span class="lineNum">   26579 </span><span class="lineNoCov">          0 :                         tmpkey = key[j];</span></a>
+<a name="26580"><span class="lineNum">   26580 </span><span class="lineNoCov">          0 :                         key[j] = key[j - 1];</span></a>
+<a name="26581"><span class="lineNum">   26581 </span><span class="lineNoCov">          0 :                         key[j - 1] = tmpkey;</span></a>
+<a name="26582"><span class="lineNum">   26582 </span>            :                     } else {</a>
+<a name="26583"><span class="lineNum">   26583 </span>            :                         break;</a>
+<a name="26584"><span class="lineNum">   26584 </span>            :                     }</a>
+<a name="26585"><span class="lineNum">   26585 </span>            :                 }</a>
+<a name="26586"><span class="lineNum">   26586 </span>            :             }</a>
+<a name="26587"><span class="lineNum">   26587 </span>            : </a>
+<a name="26588"><span class="lineNum">   26588 </span>            :         }</a>
+<a name="26589"><span class="lineNum">   26589 </span>            : </a>
+<a name="26590"><span class="lineNum">   26590 </span><span class="lineNoCov">          0 :     } else if (endd - start &gt; 20) {</span></a>
+<a name="26591"><span class="lineNum">   26591 </span>            : </a>
+<a name="26592"><span class="lineNum">   26592 </span><span class="lineNoCov">          0 :         d1 = d__[start];</span></a>
+<a name="26593"><span class="lineNum">   26593 </span><span class="lineNoCov">          0 :         d2 = d__[endd];</span></a>
+<a name="26594"><span class="lineNum">   26594 </span><span class="lineNoCov">          0 :         i__ = (start + endd) / 2;</span></a>
+<a name="26595"><span class="lineNum">   26595 </span><span class="lineNoCov">          0 :         d3 = d__[i__];</span></a>
+<a name="26596"><span class="lineNum">   26596 </span><span class="lineNoCov">          0 :         if (d1 &lt; d2) {</span></a>
+<a name="26597"><span class="lineNum">   26597 </span><span class="lineNoCov">          0 :             if (d3 &lt; d1) {</span></a>
+<a name="26598"><span class="lineNum">   26598 </span>            :                 dmnmx = d1;</a>
+<a name="26599"><span class="lineNum">   26599 </span><span class="lineNoCov">          0 :             } else if (d3 &lt; d2) {</span></a>
+<a name="26600"><span class="lineNum">   26600 </span>            :                 dmnmx = d3;</a>
+<a name="26601"><span class="lineNum">   26601 </span>            :             } else {</a>
+<a name="26602"><span class="lineNum">   26602 </span>            :                 dmnmx = d2;</a>
+<a name="26603"><span class="lineNum">   26603 </span>            :             }</a>
+<a name="26604"><span class="lineNum">   26604 </span>            :         } else {</a>
+<a name="26605"><span class="lineNum">   26605 </span><span class="lineNoCov">          0 :             if (d3 &lt; d2) {</span></a>
+<a name="26606"><span class="lineNum">   26606 </span>            :                 dmnmx = d2;</a>
+<a name="26607"><span class="lineNum">   26607 </span><span class="lineNoCov">          0 :             } else if (d3 &lt; d1) {</span></a>
+<a name="26608"><span class="lineNum">   26608 </span>            :                 dmnmx = d3;</a>
+<a name="26609"><span class="lineNum">   26609 </span>            :             } else {</a>
+<a name="26610"><span class="lineNum">   26610 </span>            :                 dmnmx = d1;</a>
+<a name="26611"><span class="lineNum">   26611 </span>            :             }</a>
+<a name="26612"><span class="lineNum">   26612 </span>            :         }</a>
+<a name="26613"><span class="lineNum">   26613 </span>            : </a>
+<a name="26614"><span class="lineNum">   26614 </span><span class="lineNoCov">          0 :         if (dir == 0) {</span></a>
+<a name="26615"><span class="lineNum">   26615 </span>            : </a>
+<a name="26616"><span class="lineNum">   26616 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="26617"><span class="lineNum">   26617 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="26618"><span class="lineNum">   26618 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="26619"><span class="lineNum">   26619 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="26620"><span class="lineNum">   26620 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="26621"><span class="lineNum">   26621 </span><span class="lineNoCov">          0 :             if (d__[j] &lt; dmnmx) {</span></a>
+<a name="26622"><span class="lineNum">   26622 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="26623"><span class="lineNum">   26623 </span>            :             }</a>
+<a name="26624"><span class="lineNum">   26624 </span><span class="lineNoCov">          0 : L80:</span></a>
+<a name="26625"><span class="lineNum">   26625 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="26626"><span class="lineNum">   26626 </span><span class="lineNoCov">          0 :             if (d__[i__] &gt; dmnmx) {</span></a>
+<a name="26627"><span class="lineNum">   26627 </span><span class="lineNoCov">          0 :                 goto L80;</span></a>
+<a name="26628"><span class="lineNum">   26628 </span>            :             }</a>
+<a name="26629"><span class="lineNum">   26629 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="26630"><span class="lineNum">   26630 </span>            :                 tmp = d__[i__];</a>
+<a name="26631"><span class="lineNum">   26631 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="26632"><span class="lineNum">   26632 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="26633"><span class="lineNum">   26633 </span><span class="lineNoCov">          0 :                 tmpkey = key[j];</span></a>
+<a name="26634"><span class="lineNum">   26634 </span><span class="lineNoCov">          0 :                 key[j] = key[i__];</span></a>
+<a name="26635"><span class="lineNum">   26635 </span><span class="lineNoCov">          0 :                 key[i__] = tmpkey;</span></a>
+<a name="26636"><span class="lineNum">   26636 </span><span class="lineNoCov">          0 :                 goto L60;</span></a>
+<a name="26637"><span class="lineNum">   26637 </span>            :             }</a>
+<a name="26638"><span class="lineNum">   26638 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="26639"><span class="lineNum">   26639 </span>            :                 ++stkpnt;</a>
+<a name="26640"><span class="lineNum">   26640 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="26641"><span class="lineNum">   26641 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26642"><span class="lineNum">   26642 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26643"><span class="lineNum">   26643 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26644"><span class="lineNum">   26644 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26645"><span class="lineNum">   26645 </span>            :             } else {</a>
+<a name="26646"><span class="lineNum">   26646 </span>            :                 ++stkpnt;</a>
+<a name="26647"><span class="lineNum">   26647 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26648"><span class="lineNum">   26648 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26649"><span class="lineNum">   26649 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26650"><span class="lineNum">   26650 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="26651"><span class="lineNum">   26651 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26652"><span class="lineNum">   26652 </span>            :             }</a>
+<a name="26653"><span class="lineNum">   26653 </span>            :         } else {</a>
+<a name="26654"><span class="lineNum">   26654 </span>            : </a>
+<a name="26655"><span class="lineNum">   26655 </span><span class="lineNoCov">          0 :             i__ = start - 1;</span></a>
+<a name="26656"><span class="lineNum">   26656 </span><span class="lineNoCov">          0 :             j = endd + 1;</span></a>
+<a name="26657"><span class="lineNum">   26657 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="26658"><span class="lineNum">   26658 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="26659"><span class="lineNum">   26659 </span><span class="lineNoCov">          0 :             --j;</span></a>
+<a name="26660"><span class="lineNum">   26660 </span><span class="lineNoCov">          0 :             if (d__[j] &gt; dmnmx) {</span></a>
+<a name="26661"><span class="lineNum">   26661 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="26662"><span class="lineNum">   26662 </span>            :             }</a>
+<a name="26663"><span class="lineNum">   26663 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="26664"><span class="lineNum">   26664 </span><span class="lineNoCov">          0 :             ++i__;</span></a>
+<a name="26665"><span class="lineNum">   26665 </span><span class="lineNoCov">          0 :             if (d__[i__] &lt; dmnmx) {</span></a>
+<a name="26666"><span class="lineNum">   26666 </span><span class="lineNoCov">          0 :                 goto L110;</span></a>
+<a name="26667"><span class="lineNum">   26667 </span>            :             }</a>
+<a name="26668"><span class="lineNum">   26668 </span><span class="lineNoCov">          0 :             if (i__ &lt; j) {</span></a>
+<a name="26669"><span class="lineNum">   26669 </span>            :                 tmp = d__[i__];</a>
+<a name="26670"><span class="lineNum">   26670 </span><span class="lineNoCov">          0 :                 d__[i__] = d__[j];</span></a>
+<a name="26671"><span class="lineNum">   26671 </span><span class="lineNoCov">          0 :                 d__[j] = tmp;</span></a>
+<a name="26672"><span class="lineNum">   26672 </span><span class="lineNoCov">          0 :                 tmpkey = key[j];</span></a>
+<a name="26673"><span class="lineNum">   26673 </span><span class="lineNoCov">          0 :                 key[j] = key[i__];</span></a>
+<a name="26674"><span class="lineNum">   26674 </span><span class="lineNoCov">          0 :                 key[i__] = tmpkey;</span></a>
+<a name="26675"><span class="lineNum">   26675 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="26676"><span class="lineNum">   26676 </span>            :             }</a>
+<a name="26677"><span class="lineNum">   26677 </span><span class="lineNoCov">          0 :             if (j - start &gt; endd - j - 1) {</span></a>
+<a name="26678"><span class="lineNum">   26678 </span>            :                 ++stkpnt;</a>
+<a name="26679"><span class="lineNum">   26679 </span>            :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</a>
+<a name="26680"><span class="lineNum">   26680 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26681"><span class="lineNum">   26681 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26682"><span class="lineNum">   26682 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26683"><span class="lineNum">   26683 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26684"><span class="lineNum">   26684 </span>            :             } else {</a>
+<a name="26685"><span class="lineNum">   26685 </span>            :                 ++stkpnt;</a>
+<a name="26686"><span class="lineNum">   26686 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = j + 1;</span></a>
+<a name="26687"><span class="lineNum">   26687 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = endd;</span></a>
+<a name="26688"><span class="lineNum">   26688 </span><span class="lineNoCov">          0 :                 ++stkpnt;</span></a>
+<a name="26689"><span class="lineNum">   26689 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 2] = start;</span></a>
+<a name="26690"><span class="lineNum">   26690 </span><span class="lineNoCov">          0 :                 stack[(stkpnt &lt;&lt; 1) - 1] = j;</span></a>
+<a name="26691"><span class="lineNum">   26691 </span>            :             }</a>
+<a name="26692"><span class="lineNum">   26692 </span>            :         }</a>
+<a name="26693"><span class="lineNum">   26693 </span>            :     }</a>
+<a name="26694"><span class="lineNum">   26694 </span><span class="lineNoCov">          0 :     if (stkpnt &gt; 0) {</span></a>
+<a name="26695"><span class="lineNum">   26695 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="26696"><span class="lineNum">   26696 </span>            :     }</a>
+<a name="26697"><span class="lineNum">   26697 </span>            : </a>
+<a name="26698"><span class="lineNum">   26698 </span>            :     return;</a>
+<a name="26699"><span class="lineNum">   26699 </span>            : }</a>
+<a name="26700"><span class="lineNum">   26700 </span>            : }</a>
+<a name="26701"><span class="lineNum">   26701 </span>            : }</a>
+<a name="26702"><span class="lineNum">   26702 </span>            : #include &lt;cmath&gt;</a>
+<a name="26703"><span class="lineNum">   26703 </span>            : #include &quot;real.h&quot;</a>
+<a name="26704"><span class="lineNum">   26704 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26705"><span class="lineNum">   26705 </span>            : </a>
+<a name="26706"><span class="lineNum">   26706 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26707"><span class="lineNum">   26707 </span>            : namespace PLMD{</a>
+<a name="26708"><span class="lineNum">   26708 </span>            : namespace lapack{</a>
+<a name="26709"><span class="lineNum">   26709 </span>            : using namespace blas;</a>
+<a name="26710"><span class="lineNum">   26710 </span>            : void</a>
+<a name="26711"><span class="lineNum">   26711 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slassq,SLASSQ)(int *n,</span></a>
+<a name="26712"><span class="lineNum">   26712 </span>            :                         float *x,</a>
+<a name="26713"><span class="lineNum">   26713 </span>            :                         int *incx,</a>
+<a name="26714"><span class="lineNum">   26714 </span>            :                         float *scale,</a>
+<a name="26715"><span class="lineNum">   26715 </span>            :                         float *sumsq)</a>
+<a name="26716"><span class="lineNum">   26716 </span>            : {</a>
+<a name="26717"><span class="lineNum">   26717 </span>            :   int ix;</a>
+<a name="26718"><span class="lineNum">   26718 </span>            :   float absxi,t;</a>
+<a name="26719"><span class="lineNum">   26719 </span>            : </a>
+<a name="26720"><span class="lineNum">   26720 </span><span class="lineNoCov">          0 :   if(*n&gt;0) {</span></a>
+<a name="26721"><span class="lineNum">   26721 </span><span class="lineNoCov">          0 :     for(ix=0;ix&lt;=(*n-1)*(*incx);ix+=*incx) {</span></a>
+<a name="26722"><span class="lineNum">   26722 </span><span class="lineNoCov">          0 :       if(std::abs(x[ix])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26723"><span class="lineNum">   26723 </span>            :         absxi = std::abs(x[ix]);</a>
+<a name="26724"><span class="lineNum">   26724 </span><span class="lineNoCov">          0 :         if(*scale&lt;absxi) {</span></a>
+<a name="26725"><span class="lineNum">   26725 </span><span class="lineNoCov">          0 :           t = *scale/absxi;</span></a>
+<a name="26726"><span class="lineNum">   26726 </span><span class="lineNoCov">          0 :           t = t*t;</span></a>
+<a name="26727"><span class="lineNum">   26727 </span><span class="lineNoCov">          0 :           *sumsq = 1.0 + (*sumsq)*t;</span></a>
+<a name="26728"><span class="lineNum">   26728 </span><span class="lineNoCov">          0 :           *scale = absxi;</span></a>
+<a name="26729"><span class="lineNum">   26729 </span>            :         } else {</a>
+<a name="26730"><span class="lineNum">   26730 </span><span class="lineNoCov">          0 :           t = absxi/(*scale);</span></a>
+<a name="26731"><span class="lineNum">   26731 </span><span class="lineNoCov">          0 :           *sumsq += t*t;</span></a>
+<a name="26732"><span class="lineNum">   26732 </span>            :         }</a>
+<a name="26733"><span class="lineNum">   26733 </span>            :       }</a>
+<a name="26734"><span class="lineNum">   26734 </span>            :     }</a>
+<a name="26735"><span class="lineNum">   26735 </span>            :   }</a>
+<a name="26736"><span class="lineNum">   26736 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="26737"><span class="lineNum">   26737 </span>            : }</a>
+<a name="26738"><span class="lineNum">   26738 </span>            : }</a>
+<a name="26739"><span class="lineNum">   26739 </span>            : }</a>
+<a name="26740"><span class="lineNum">   26740 </span>            : #include &lt;cmath&gt;</a>
+<a name="26741"><span class="lineNum">   26741 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26742"><span class="lineNum">   26742 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="26743"><span class="lineNum">   26743 </span>            : </a>
+<a name="26744"><span class="lineNum">   26744 </span>            : #include &quot;real.h&quot;</a>
+<a name="26745"><span class="lineNum">   26745 </span>            : </a>
+<a name="26746"><span class="lineNum">   26746 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26747"><span class="lineNum">   26747 </span>            : namespace PLMD{</a>
+<a name="26748"><span class="lineNum">   26748 </span>            : namespace lapack{</a>
+<a name="26749"><span class="lineNum">   26749 </span>            : using namespace blas;</a>
+<a name="26750"><span class="lineNum">   26750 </span>            : void </a>
+<a name="26751"><span class="lineNum">   26751 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slasv2,SLASV2)(float *f, </span></a>
+<a name="26752"><span class="lineNum">   26752 </span>            :                         float *g, </a>
+<a name="26753"><span class="lineNum">   26753 </span>            :                         float *h__, </a>
+<a name="26754"><span class="lineNum">   26754 </span>            :                         float *ssmin, </a>
+<a name="26755"><span class="lineNum">   26755 </span>            :                         float *ssmax, </a>
+<a name="26756"><span class="lineNum">   26756 </span>            :                         float *snr, </a>
+<a name="26757"><span class="lineNum">   26757 </span>            :                         float *csr, </a>
+<a name="26758"><span class="lineNum">   26758 </span>            :                         float *snl, </a>
+<a name="26759"><span class="lineNum">   26759 </span>            :                         float *csl)</a>
+<a name="26760"><span class="lineNum">   26760 </span>            : {</a>
+<a name="26761"><span class="lineNum">   26761 </span>            :     float d__1;</a>
+<a name="26762"><span class="lineNum">   26762 </span>            : </a>
+<a name="26763"><span class="lineNum">   26763 </span>            :     float a, d__, l, m, r__, s, t, fa, ga, ha, ft, gt, ht, mm, tt,</a>
+<a name="26764"><span class="lineNum">   26764 </span>            :              clt, crt, slt, srt;</a>
+<a name="26765"><span class="lineNum">   26765 </span>            :     int pmax;</a>
+<a name="26766"><span class="lineNum">   26766 </span>            :     float temp;</a>
+<a name="26767"><span class="lineNum">   26767 </span>            :     int swap;</a>
+<a name="26768"><span class="lineNum">   26768 </span>            :     float tsign=1.0;</a>
+<a name="26769"><span class="lineNum">   26769 </span>            :     int gasmal;</a>
+<a name="26770"><span class="lineNum">   26770 </span>            : </a>
+<a name="26771"><span class="lineNum">   26771 </span><span class="lineNoCov">          0 :     ft = *f;</span></a>
+<a name="26772"><span class="lineNum">   26772 </span>            :     fa = std::abs(ft);</a>
+<a name="26773"><span class="lineNum">   26773 </span><span class="lineNoCov">          0 :     ht = *h__;</span></a>
+<a name="26774"><span class="lineNum">   26774 </span>            :     ha = std::abs(*h__);</a>
+<a name="26775"><span class="lineNum">   26775 </span>            : </a>
+<a name="26776"><span class="lineNum">   26776 </span>            :     pmax = 1;</a>
+<a name="26777"><span class="lineNum">   26777 </span>            :     swap = ha &gt; fa;</a>
+<a name="26778"><span class="lineNum">   26778 </span><span class="lineNoCov">          0 :     if (swap) {</span></a>
+<a name="26779"><span class="lineNum">   26779 </span>            :         pmax = 3;</a>
+<a name="26780"><span class="lineNum">   26780 </span>            :         temp = ft;</a>
+<a name="26781"><span class="lineNum">   26781 </span>            :         ft = ht;</a>
+<a name="26782"><span class="lineNum">   26782 </span>            :         ht = temp;</a>
+<a name="26783"><span class="lineNum">   26783 </span>            :         temp = fa;</a>
+<a name="26784"><span class="lineNum">   26784 </span>            :         fa = ha;</a>
+<a name="26785"><span class="lineNum">   26785 </span>            :         ha = temp;</a>
+<a name="26786"><span class="lineNum">   26786 </span>            : </a>
+<a name="26787"><span class="lineNum">   26787 </span>            :     }</a>
+<a name="26788"><span class="lineNum">   26788 </span><span class="lineNoCov">          0 :     gt = *g;</span></a>
+<a name="26789"><span class="lineNum">   26789 </span>            :     ga = std::abs(gt);</a>
+<a name="26790"><span class="lineNum">   26790 </span><span class="lineNoCov">          0 :     if (std::abs(ga)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26791"><span class="lineNum">   26791 </span>            : </a>
+<a name="26792"><span class="lineNum">   26792 </span><span class="lineNoCov">          0 :         *ssmin = ha;</span></a>
+<a name="26793"><span class="lineNum">   26793 </span><span class="lineNoCov">          0 :         *ssmax = fa;</span></a>
+<a name="26794"><span class="lineNum">   26794 </span>            :         clt = 1.;</a>
+<a name="26795"><span class="lineNum">   26795 </span>            :         crt = 1.;</a>
+<a name="26796"><span class="lineNum">   26796 </span>            :         slt = 0.;</a>
+<a name="26797"><span class="lineNum">   26797 </span>            :         srt = 0.;</a>
+<a name="26798"><span class="lineNum">   26798 </span>            :     } else {</a>
+<a name="26799"><span class="lineNum">   26799 </span>            :         gasmal = 1;</a>
+<a name="26800"><span class="lineNum">   26800 </span><span class="lineNoCov">          0 :         if (ga &gt; fa) {</span></a>
+<a name="26801"><span class="lineNum">   26801 </span>            :             pmax = 2;</a>
+<a name="26802"><span class="lineNum">   26802 </span><span class="lineNoCov">          0 :             if (fa / ga &lt; PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="26803"><span class="lineNum">   26803 </span>            : </a>
+<a name="26804"><span class="lineNum">   26804 </span>            :                 gasmal = 0;</a>
+<a name="26805"><span class="lineNum">   26805 </span><span class="lineNoCov">          0 :                 *ssmax = ga;</span></a>
+<a name="26806"><span class="lineNum">   26806 </span><span class="lineNoCov">          0 :                 if (ha &gt; 1.) {</span></a>
+<a name="26807"><span class="lineNum">   26807 </span><span class="lineNoCov">          0 :                     *ssmin = fa / (ga / ha);</span></a>
+<a name="26808"><span class="lineNum">   26808 </span>            :                 } else {</a>
+<a name="26809"><span class="lineNum">   26809 </span><span class="lineNoCov">          0 :                     *ssmin = fa / ga * ha;</span></a>
+<a name="26810"><span class="lineNum">   26810 </span>            :                 }</a>
+<a name="26811"><span class="lineNum">   26811 </span>            :                 clt = 1.;</a>
+<a name="26812"><span class="lineNum">   26812 </span><span class="lineNoCov">          0 :                 slt = ht / gt;</span></a>
+<a name="26813"><span class="lineNum">   26813 </span>            :                 srt = 1.;</a>
+<a name="26814"><span class="lineNum">   26814 </span><span class="lineNoCov">          0 :                 crt = ft / gt;</span></a>
+<a name="26815"><span class="lineNum">   26815 </span>            :             }</a>
+<a name="26816"><span class="lineNum">   26816 </span>            :         }</a>
+<a name="26817"><span class="lineNum">   26817 </span><span class="lineNoCov">          0 :         if (gasmal) {</span></a>
+<a name="26818"><span class="lineNum">   26818 </span>            : </a>
+<a name="26819"><span class="lineNum">   26819 </span><span class="lineNoCov">          0 :             d__ = fa - ha;</span></a>
+<a name="26820"><span class="lineNum">   26820 </span><span class="lineNoCov">          0 :             if ( std::abs( fa - d__ )&lt;PLUMED_GMX_FLOAT_EPS*std::abs( fa + d__ )) {</span></a>
+<a name="26821"><span class="lineNum">   26821 </span>            :                 l = 1.;</a>
+<a name="26822"><span class="lineNum">   26822 </span>            :             } else {</a>
+<a name="26823"><span class="lineNum">   26823 </span><span class="lineNoCov">          0 :                 l = d__ / fa;</span></a>
+<a name="26824"><span class="lineNum">   26824 </span>            :             }</a>
+<a name="26825"><span class="lineNum">   26825 </span>            : </a>
+<a name="26826"><span class="lineNum">   26826 </span><span class="lineNoCov">          0 :             m = gt / ft;</span></a>
+<a name="26827"><span class="lineNum">   26827 </span><span class="lineNoCov">          0 :             t = 2. - l;</span></a>
+<a name="26828"><span class="lineNum">   26828 </span>            : </a>
+<a name="26829"><span class="lineNum">   26829 </span><span class="lineNoCov">          0 :             mm = m * m;</span></a>
+<a name="26830"><span class="lineNum">   26830 </span><span class="lineNoCov">          0 :             tt = t * t;</span></a>
+<a name="26831"><span class="lineNum">   26831 </span><span class="lineNoCov">          0 :             s =  std::sqrt(tt + mm);</span></a>
+<a name="26832"><span class="lineNum">   26832 </span>            : </a>
+<a name="26833"><span class="lineNum">   26833 </span><span class="lineNoCov">          0 :             if ( std::abs(l)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26834"><span class="lineNum">   26834 </span>            :                 r__ = std::abs(m);</a>
+<a name="26835"><span class="lineNum">   26835 </span>            :             } else {</a>
+<a name="26836"><span class="lineNum">   26836 </span><span class="lineNoCov">          0 :                 r__ =  std::sqrt(l * l + mm);</span></a>
+<a name="26837"><span class="lineNum">   26837 </span>            :             }</a>
+<a name="26838"><span class="lineNum">   26838 </span><span class="lineNoCov">          0 :             a = (s + r__) * .5;</span></a>
+<a name="26839"><span class="lineNum">   26839 </span>            : </a>
+<a name="26840"><span class="lineNum">   26840 </span><span class="lineNoCov">          0 :             *ssmin = ha / a;</span></a>
+<a name="26841"><span class="lineNum">   26841 </span><span class="lineNoCov">          0 :             *ssmax = fa * a;</span></a>
+<a name="26842"><span class="lineNum">   26842 </span><span class="lineNoCov">          0 :             if ( std::abs(mm)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26843"><span class="lineNum">   26843 </span>            : </a>
+<a name="26844"><span class="lineNum">   26844 </span><span class="lineNoCov">          0 :                 if (std::abs(l)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="26845"><span class="lineNum">   26845 </span><span class="lineNoCov">          0 :                     t = ( (ft&gt;0) ? 2.0 : -2.0) * ( (gt&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="26846"><span class="lineNum">   26846 </span>            :                 } else {</a>
+<a name="26847"><span class="lineNum">   26847 </span><span class="lineNoCov">          0 :                     t = gt / ( (ft&gt;0) ? d__ : -d__) + m / t;</span></a>
+<a name="26848"><span class="lineNum">   26848 </span>            :                 }</a>
+<a name="26849"><span class="lineNum">   26849 </span>            :             } else {</a>
+<a name="26850"><span class="lineNum">   26850 </span><span class="lineNoCov">          0 :                 t = (m / (s + t) + m / (r__ + l)) * (a + 1.);</span></a>
+<a name="26851"><span class="lineNum">   26851 </span>            :             }</a>
+<a name="26852"><span class="lineNum">   26852 </span><span class="lineNoCov">          0 :             l =  std::sqrt(t * t + 4.);</span></a>
+<a name="26853"><span class="lineNum">   26853 </span><span class="lineNoCov">          0 :             crt = 2. / l;</span></a>
+<a name="26854"><span class="lineNum">   26854 </span><span class="lineNoCov">          0 :             srt = t / l;</span></a>
+<a name="26855"><span class="lineNum">   26855 </span><span class="lineNoCov">          0 :             clt = (crt + srt * m) / a;</span></a>
+<a name="26856"><span class="lineNum">   26856 </span><span class="lineNoCov">          0 :             slt = ht / ft * srt / a;</span></a>
+<a name="26857"><span class="lineNum">   26857 </span>            :         }</a>
+<a name="26858"><span class="lineNum">   26858 </span>            :     }</a>
+<a name="26859"><span class="lineNum">   26859 </span><span class="lineNoCov">          0 :     if (swap) {</span></a>
+<a name="26860"><span class="lineNum">   26860 </span><span class="lineNoCov">          0 :         *csl = srt;</span></a>
+<a name="26861"><span class="lineNum">   26861 </span><span class="lineNoCov">          0 :         *snl = crt;</span></a>
+<a name="26862"><span class="lineNum">   26862 </span><span class="lineNoCov">          0 :         *csr = slt;</span></a>
+<a name="26863"><span class="lineNum">   26863 </span><span class="lineNoCov">          0 :         *snr = clt;</span></a>
+<a name="26864"><span class="lineNum">   26864 </span>            :     } else {</a>
+<a name="26865"><span class="lineNum">   26865 </span><span class="lineNoCov">          0 :         *csl = clt;</span></a>
+<a name="26866"><span class="lineNum">   26866 </span><span class="lineNoCov">          0 :         *snl = slt;</span></a>
+<a name="26867"><span class="lineNum">   26867 </span><span class="lineNoCov">          0 :         *csr = crt;</span></a>
+<a name="26868"><span class="lineNum">   26868 </span><span class="lineNoCov">          0 :         *snr = srt;</span></a>
+<a name="26869"><span class="lineNum">   26869 </span>            :     }</a>
+<a name="26870"><span class="lineNum">   26870 </span>            : </a>
+<a name="26871"><span class="lineNum">   26871 </span><span class="lineNoCov">          0 :     if (pmax == 1) {</span></a>
+<a name="26872"><span class="lineNum">   26872 </span><span class="lineNoCov">          0 :         tsign = ( (*csr&gt;0) ? 1.0 : -1.0) * ( (*csl&gt;0) ? 1.0 : -1.0) * ( (*f&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="26873"><span class="lineNum">   26873 </span>            :     }</a>
+<a name="26874"><span class="lineNum">   26874 </span><span class="lineNoCov">          0 :     if (pmax == 2) {</span></a>
+<a name="26875"><span class="lineNum">   26875 </span><span class="lineNoCov">          0 :         tsign = ( (*snr&gt;0) ? 1.0 : -1.0) * ( (*csl&gt;0) ? 1.0 : -1.0) * ( (*g&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="26876"><span class="lineNum">   26876 </span>            :     }</a>
+<a name="26877"><span class="lineNum">   26877 </span><span class="lineNoCov">          0 :     if (pmax == 3) {</span></a>
+<a name="26878"><span class="lineNum">   26878 </span><span class="lineNoCov">          0 :         tsign = ( (*snr&gt;0) ? 1.0 : -1.0) * ( (*snl&gt;0) ? 1.0 : -1.0) * ( (*h__&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="26879"><span class="lineNum">   26879 </span>            :     }</a>
+<a name="26880"><span class="lineNum">   26880 </span><span class="lineNoCov">          0 :     if(tsign&lt;0)</span></a>
+<a name="26881"><span class="lineNum">   26881 </span><span class="lineNoCov">          0 :       *ssmax *= -1.0;</span></a>
+<a name="26882"><span class="lineNum">   26882 </span><span class="lineNoCov">          0 :     d__1 = tsign * ( (*f&gt;0) ? 1.0 : -1.0) * ( (*h__&gt;0) ? 1.0 : -1.0);</span></a>
+<a name="26883"><span class="lineNum">   26883 </span><span class="lineNoCov">          0 :     if(d__1&lt;0)</span></a>
+<a name="26884"><span class="lineNum">   26884 </span><span class="lineNoCov">          0 :       *ssmin *= -1.0;</span></a>
+<a name="26885"><span class="lineNum">   26885 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="26886"><span class="lineNum">   26886 </span>            : </a>
+<a name="26887"><span class="lineNum">   26887 </span>            : }</a>
+<a name="26888"><span class="lineNum">   26888 </span>            : }</a>
+<a name="26889"><span class="lineNum">   26889 </span>            : }</a>
+<a name="26890"><span class="lineNum">   26890 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26891"><span class="lineNum">   26891 </span>            : </a>
+<a name="26892"><span class="lineNum">   26892 </span>            : /* LAPACK */</a>
+<a name="26893"><span class="lineNum">   26893 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26894"><span class="lineNum">   26894 </span>            : namespace PLMD{</a>
+<a name="26895"><span class="lineNum">   26895 </span>            : namespace lapack{</a>
+<a name="26896"><span class="lineNum">   26896 </span>            : using namespace blas;</a>
+<a name="26897"><span class="lineNum">   26897 </span>            : void</a>
+<a name="26898"><span class="lineNum">   26898 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slaswp,SLASWP)(int *n,</span></a>
+<a name="26899"><span class="lineNum">   26899 </span>            :         float *a,</a>
+<a name="26900"><span class="lineNum">   26900 </span>            :         int *lda,</a>
+<a name="26901"><span class="lineNum">   26901 </span>            :         int *k1,</a>
+<a name="26902"><span class="lineNum">   26902 </span>            :         int *k2,</a>
+<a name="26903"><span class="lineNum">   26903 </span>            :         int *ipiv,</a>
+<a name="26904"><span class="lineNum">   26904 </span>            :         int *incx)</a>
+<a name="26905"><span class="lineNum">   26905 </span>            : {</a>
+<a name="26906"><span class="lineNum">   26906 </span>            :   int ix0,i1,i2,inc,n32;</a>
+<a name="26907"><span class="lineNum">   26907 </span>            :   int ix,i,j,ip,k;</a>
+<a name="26908"><span class="lineNum">   26908 </span>            :   float temp;</a>
+<a name="26909"><span class="lineNum">   26909 </span>            : </a>
+<a name="26910"><span class="lineNum">   26910 </span><span class="lineNoCov">          0 :   if(*incx&gt;0) {</span></a>
+<a name="26911"><span class="lineNum">   26911 </span><span class="lineNoCov">          0 :     ix0 = *k1 - 1;</span></a>
+<a name="26912"><span class="lineNum">   26912 </span>            :     i1 = *k1 - 1;</a>
+<a name="26913"><span class="lineNum">   26913 </span><span class="lineNoCov">          0 :     i2 = *k2;</span></a>
+<a name="26914"><span class="lineNum">   26914 </span>            :     inc = 1;</a>
+<a name="26915"><span class="lineNum">   26915 </span><span class="lineNoCov">          0 :   } else if(*incx&lt;0) {</span></a>
+<a name="26916"><span class="lineNum">   26916 </span><span class="lineNoCov">          0 :     ix0 = *incx * (1- *k2);</span></a>
+<a name="26917"><span class="lineNum">   26917 </span><span class="lineNoCov">          0 :     i1 = *k2 - 1;</span></a>
+<a name="26918"><span class="lineNum">   26918 </span><span class="lineNoCov">          0 :     i2 = *k1;</span></a>
+<a name="26919"><span class="lineNum">   26919 </span>            :     inc = -1;</a>
+<a name="26920"><span class="lineNum">   26920 </span>            :   } else</a>
+<a name="26921"><span class="lineNum">   26921 </span>            :     return;</a>
+<a name="26922"><span class="lineNum">   26922 </span>            : </a>
+<a name="26923"><span class="lineNum">   26923 </span><span class="lineNoCov">          0 :   n32 = *n / 32;</span></a>
+<a name="26924"><span class="lineNum">   26924 </span>            :   </a>
+<a name="26925"><span class="lineNum">   26925 </span><span class="lineNoCov">          0 :   n32 *= 32;</span></a>
+<a name="26926"><span class="lineNum">   26926 </span>            : </a>
+<a name="26927"><span class="lineNum">   26927 </span>            : </a>
+<a name="26928"><span class="lineNum">   26928 </span><span class="lineNoCov">          0 :   if(n32!=0) {</span></a>
+<a name="26929"><span class="lineNum">   26929 </span><span class="lineNoCov">          0 :     for(j=0;j&lt;n32;j+=32) {</span></a>
+<a name="26930"><span class="lineNum">   26930 </span>            :       ix = ix0;</a>
+<a name="26931"><span class="lineNum">   26931 </span><span class="lineNoCov">          0 :       for(i=i1;i&lt;i2;i+=inc,ix+=*incx) {</span></a>
+<a name="26932"><span class="lineNum">   26932 </span><span class="lineNoCov">          0 :         ip = ipiv[ix] - 1;</span></a>
+<a name="26933"><span class="lineNum">   26933 </span><span class="lineNoCov">          0 :         if(ip != i) {</span></a>
+<a name="26934"><span class="lineNum">   26934 </span><span class="lineNoCov">          0 :           for(k=j;k&lt;j+32;k++) {</span></a>
+<a name="26935"><span class="lineNum">   26935 </span><span class="lineNoCov">          0 :             temp = a[(k)*(*lda)+i];</span></a>
+<a name="26936"><span class="lineNum">   26936 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+i] = a[(k)*(*lda)+ip];</span></a>
+<a name="26937"><span class="lineNum">   26937 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+ip] = temp;</span></a>
+<a name="26938"><span class="lineNum">   26938 </span>            :           }</a>
+<a name="26939"><span class="lineNum">   26939 </span>            :         }</a>
+<a name="26940"><span class="lineNum">   26940 </span>            :       }</a>
+<a name="26941"><span class="lineNum">   26941 </span>            :     }</a>
+<a name="26942"><span class="lineNum">   26942 </span>            :   }</a>
+<a name="26943"><span class="lineNum">   26943 </span><span class="lineNoCov">          0 :   if(n32!=*n) {</span></a>
+<a name="26944"><span class="lineNum">   26944 </span>            :     ix = ix0;</a>
+<a name="26945"><span class="lineNum">   26945 </span><span class="lineNoCov">          0 :     for(i=i1;i&lt;i2;i+=inc,ix+=*incx) {</span></a>
+<a name="26946"><span class="lineNum">   26946 </span><span class="lineNoCov">          0 :       ip = ipiv[ix] - 1;</span></a>
+<a name="26947"><span class="lineNum">   26947 </span><span class="lineNoCov">          0 :       if(ip != i) {</span></a>
+<a name="26948"><span class="lineNum">   26948 </span><span class="lineNoCov">          0 :         for(k=n32;k&lt;*n;k++) {</span></a>
+<a name="26949"><span class="lineNum">   26949 </span><span class="lineNoCov">          0 :             temp = a[(k)*(*lda)+i];</span></a>
+<a name="26950"><span class="lineNum">   26950 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+i] = a[(k)*(*lda)+ip];</span></a>
+<a name="26951"><span class="lineNum">   26951 </span><span class="lineNoCov">          0 :             a[(k)*(*lda)+ip] = temp;</span></a>
+<a name="26952"><span class="lineNum">   26952 </span>            :         }</a>
+<a name="26953"><span class="lineNum">   26953 </span>            :       }</a>
+<a name="26954"><span class="lineNum">   26954 </span>            :     }</a>
+<a name="26955"><span class="lineNum">   26955 </span>            :   }</a>
+<a name="26956"><span class="lineNum">   26956 </span>            :   return;</a>
+<a name="26957"><span class="lineNum">   26957 </span>            : }</a>
+<a name="26958"><span class="lineNum">   26958 </span>            : }</a>
+<a name="26959"><span class="lineNum">   26959 </span>            : }</a>
+<a name="26960"><span class="lineNum">   26960 </span>            : #include &lt;cctype&gt;</a>
+<a name="26961"><span class="lineNum">   26961 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26962"><span class="lineNum">   26962 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="26963"><span class="lineNum">   26963 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="26964"><span class="lineNum">   26964 </span>            : </a>
+<a name="26965"><span class="lineNum">   26965 </span>            : </a>
+<a name="26966"><span class="lineNum">   26966 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="26967"><span class="lineNum">   26967 </span>            : namespace PLMD{</a>
+<a name="26968"><span class="lineNum">   26968 </span>            : namespace lapack{</a>
+<a name="26969"><span class="lineNum">   26969 </span>            : using namespace blas;</a>
+<a name="26970"><span class="lineNum">   26970 </span>            : void</a>
+<a name="26971"><span class="lineNum">   26971 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(slatrd,SLATRD)(const char *  uplo,</span></a>
+<a name="26972"><span class="lineNum">   26972 </span>            :        int  *   n,</a>
+<a name="26973"><span class="lineNum">   26973 </span>            :        int  *   nb,</a>
+<a name="26974"><span class="lineNum">   26974 </span>            :        float * a,</a>
+<a name="26975"><span class="lineNum">   26975 </span>            :        int *    lda,</a>
+<a name="26976"><span class="lineNum">   26976 </span>            :        float * e,</a>
+<a name="26977"><span class="lineNum">   26977 </span>            :        float * tau,</a>
+<a name="26978"><span class="lineNum">   26978 </span>            :        float * w,</a>
+<a name="26979"><span class="lineNum">   26979 </span>            :        int *    ldw)</a>
+<a name="26980"><span class="lineNum">   26980 </span>            : {</a>
+<a name="26981"><span class="lineNum">   26981 </span>            :   int i,iw;</a>
+<a name="26982"><span class="lineNum">   26982 </span>            :   int ti1,ti2,ti3;</a>
+<a name="26983"><span class="lineNum">   26983 </span>            :   float one,zero,minusone,alpha;</a>
+<a name="26984"><span class="lineNum">   26984 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="26985"><span class="lineNum">   26985 </span>            : </a>
+<a name="26986"><span class="lineNum">   26986 </span><span class="lineNoCov">          0 :   one=1.0;</span></a>
+<a name="26987"><span class="lineNum">   26987 </span><span class="lineNoCov">          0 :   minusone=-1.0;</span></a>
+<a name="26988"><span class="lineNum">   26988 </span><span class="lineNoCov">          0 :   zero=0.0;</span></a>
+<a name="26989"><span class="lineNum">   26989 </span>            : </a>
+<a name="26990"><span class="lineNum">   26990 </span><span class="lineNoCov">          0 :   if(*n&lt;=0)</span></a>
+<a name="26991"><span class="lineNum">   26991 </span>            :     return;</a>
+<a name="26992"><span class="lineNum">   26992 </span>            : </a>
+<a name="26993"><span class="lineNum">   26993 </span><span class="lineNoCov">          0 :   if(ch=='U') {</span></a>
+<a name="26994"><span class="lineNum">   26994 </span><span class="lineNoCov">          0 :     for(i=*n;i&gt;=(*n-*nb+1);i--) {</span></a>
+<a name="26995"><span class="lineNum">   26995 </span><span class="lineNoCov">          0 :       iw = i -*n + *nb;</span></a>
+<a name="26996"><span class="lineNum">   26996 </span>            :       </a>
+<a name="26997"><span class="lineNum">   26997 </span><span class="lineNoCov">          0 :       if(i&lt;*n) {</span></a>
+<a name="26998"><span class="lineNum">   26998 </span><span class="lineNoCov">          0 :         ti1 = *n-i;</span></a>
+<a name="26999"><span class="lineNum">   26999 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="27000"><span class="lineNum">   27000 </span>            :         /* BLAS */</a>
+<a name="27001"><span class="lineNum">   27001 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;i,&amp;ti1,&amp;minusone, &amp;(a[ i*(*lda) + 0]),lda,&amp;(w[iw*(*ldw)+(i-1)]),</span></a>
+<a name="27002"><span class="lineNum">   27002 </span><span class="lineNoCov">          0 :                ldw,&amp;one, &amp;(a[ (i-1)*(*lda) + 0]), &amp;ti2);</span></a>
+<a name="27003"><span class="lineNum">   27003 </span>            :         /* BLAS */</a>
+<a name="27004"><span class="lineNum">   27004 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;i,&amp;ti1,&amp;minusone, &amp;(w[ iw*(*ldw) + 0]),ldw,&amp;(a[i*(*lda)+(i-1)]),</span></a>
+<a name="27005"><span class="lineNum">   27005 </span><span class="lineNoCov">          0 :                lda,&amp;one, &amp;(a[ (i-1)*(*lda) + 0]), &amp;ti2);</span></a>
+<a name="27006"><span class="lineNum">   27006 </span>            :       }</a>
+<a name="27007"><span class="lineNum">   27007 </span>            : </a>
+<a name="27008"><span class="lineNum">   27008 </span><span class="lineNoCov">          0 :       if(i&gt;1) {</span></a>
+<a name="27009"><span class="lineNum">   27009 </span>            :         /*  Generate elementary reflector H(i) to annihilate</a>
+<a name="27010"><span class="lineNum">   27010 </span>            :          *              A(1:i-2,i) </a>
+<a name="27011"><span class="lineNum">   27011 </span>            :          */</a>
+<a name="27012"><span class="lineNum">   27012 </span><span class="lineNoCov">          0 :         ti1 = i-1;</span></a>
+<a name="27013"><span class="lineNum">   27013 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="27014"><span class="lineNum">   27014 </span>            : </a>
+<a name="27015"><span class="lineNum">   27015 </span>            :         /* LAPACK */</a>
+<a name="27016"><span class="lineNum">   27016 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;ti1,&amp;(a[(i-1)*(*lda)+(i-2)]),&amp;(a[(i-1)*(*lda)+0]),&amp;ti2,&amp;(tau[i-2]));</span></a>
+<a name="27017"><span class="lineNum">   27017 </span>            :       </a>
+<a name="27018"><span class="lineNum">   27018 </span><span class="lineNoCov">          0 :         e[i-2] = a[(i-1)*(*lda)+(i-2)];</span></a>
+<a name="27019"><span class="lineNum">   27019 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i-2)] = 1.0;</span></a>
+<a name="27020"><span class="lineNum">   27020 </span>            : </a>
+<a name="27021"><span class="lineNum">   27021 </span>            :         /* Compute W(1:i-1,i) */</a>
+<a name="27022"><span class="lineNum">   27022 </span><span class="lineNoCov">          0 :         ti1 = i-1;</span></a>
+<a name="27023"><span class="lineNum">   27023 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="27024"><span class="lineNum">   27024 </span>            : </a>
+<a name="27025"><span class="lineNum">   27025 </span>            :         /* BLAS */</a>
+<a name="27026"><span class="lineNum">   27026 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)(&quot;U&quot;,&amp;ti1,&amp;one,a,lda,&amp;(a[(i-1)*(*lda)+0]),&amp;ti2,&amp;zero,</span></a>
+<a name="27027"><span class="lineNum">   27027 </span><span class="lineNoCov">          0 :                &amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2);</span></a>
+<a name="27028"><span class="lineNum">   27028 </span><span class="lineNoCov">          0 :         if(i&lt;*n) {</span></a>
+<a name="27029"><span class="lineNum">   27029 </span><span class="lineNoCov">          0 :           ti1 = i-1;</span></a>
+<a name="27030"><span class="lineNum">   27030 </span><span class="lineNoCov">          0 :           ti2 = *n-i;</span></a>
+<a name="27031"><span class="lineNum">   27031 </span><span class="lineNoCov">          0 :           ti3 = 1;</span></a>
+<a name="27032"><span class="lineNum">   27032 </span>            :           /* BLAS */</a>
+<a name="27033"><span class="lineNum">   27033 </span><span class="lineNoCov">          0 :           PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(w[iw*(*ldw)+0]),ldw,&amp;(a[(i-1)*(*lda)+0]),&amp;ti3,</span></a>
+<a name="27034"><span class="lineNum">   27034 </span><span class="lineNoCov">          0 :                  &amp;zero,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="27035"><span class="lineNum">   27035 </span>            :         </a>
+<a name="27036"><span class="lineNum">   27036 </span>            :           /* BLAS */</a>
+<a name="27037"><span class="lineNum">   27037 </span><span class="lineNoCov">          0 :           PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(a[i*(*lda)+0]),lda,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3,</span></a>
+<a name="27038"><span class="lineNum">   27038 </span><span class="lineNoCov">          0 :                  &amp;one,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="27039"><span class="lineNum">   27039 </span>            :         </a>
+<a name="27040"><span class="lineNum">   27040 </span>            :           /* BLAS */</a>
+<a name="27041"><span class="lineNum">   27041 </span><span class="lineNoCov">          0 :           PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(a[i*(*lda)+0]),lda,&amp;(a[(i-1)*(*lda)+0]),&amp;ti3,</span></a>
+<a name="27042"><span class="lineNum">   27042 </span><span class="lineNoCov">          0 :                  &amp;zero,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="27043"><span class="lineNum">   27043 </span>            :         </a>
+<a name="27044"><span class="lineNum">   27044 </span>            :           /* BLAS */</a>
+<a name="27045"><span class="lineNum">   27045 </span><span class="lineNoCov">          0 :           PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(w[iw*(*ldw)+0]),ldw,&amp;(w[(iw-1)*(*ldw)+i]),&amp;ti3,</span></a>
+<a name="27046"><span class="lineNum">   27046 </span><span class="lineNoCov">          0 :                  &amp;one,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="27047"><span class="lineNum">   27047 </span>            :         }</a>
+<a name="27048"><span class="lineNum">   27048 </span>            :       </a>
+<a name="27049"><span class="lineNum">   27049 </span><span class="lineNoCov">          0 :         ti1 = i-1;</span></a>
+<a name="27050"><span class="lineNum">   27050 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="27051"><span class="lineNum">   27051 </span>            :         /* BLAS */</a>
+<a name="27052"><span class="lineNum">   27052 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;ti1,&amp;(tau[i-2]),&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2);</span></a>
+<a name="27053"><span class="lineNum">   27053 </span>            :       </a>
+<a name="27054"><span class="lineNum">   27054 </span><span class="lineNoCov">          0 :         alpha = -0.5*tau[i-2]*PLUMED_BLAS_F77_FUNC(sdot,SDOT)(&amp;ti1,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2,</span></a>
+<a name="27055"><span class="lineNum">   27055 </span><span class="lineNoCov">          0 :                                     &amp;(a[(i-1)*(*lda)+0]),&amp;ti2);</span></a>
+<a name="27056"><span class="lineNum">   27056 </span>            :       </a>
+<a name="27057"><span class="lineNum">   27057 </span>            :         /* BLAS */</a>
+<a name="27058"><span class="lineNum">   27058 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(&amp;ti1,&amp;alpha,&amp;(a[(i-1)*(*lda)+0]),&amp;ti2,&amp;(w[(iw-1)*(*ldw)+0]),&amp;ti2);</span></a>
+<a name="27059"><span class="lineNum">   27059 </span>            : </a>
+<a name="27060"><span class="lineNum">   27060 </span>            :       }</a>
+<a name="27061"><span class="lineNum">   27061 </span>            :     }</a>
+<a name="27062"><span class="lineNum">   27062 </span>            :   } else {</a>
+<a name="27063"><span class="lineNum">   27063 </span>            :     /* lower */</a>
+<a name="27064"><span class="lineNum">   27064 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;=*nb;i++) {</span></a>
+<a name="27065"><span class="lineNum">   27065 </span>            : </a>
+<a name="27066"><span class="lineNum">   27066 </span><span class="lineNoCov">          0 :       ti1 = *n-i+1;</span></a>
+<a name="27067"><span class="lineNum">   27067 </span><span class="lineNoCov">          0 :       ti2 = i-1;</span></a>
+<a name="27068"><span class="lineNum">   27068 </span><span class="lineNoCov">          0 :       ti3 = 1;</span></a>
+<a name="27069"><span class="lineNum">   27069 </span>            :       /* BLAS */</a>
+<a name="27070"><span class="lineNum">   27070 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone, &amp;(a[ i-1 ]),lda,&amp;(w[ i-1 ]),</span></a>
+<a name="27071"><span class="lineNum">   27071 </span><span class="lineNoCov">          0 :                ldw,&amp;one, &amp;(a[ (i-1)*(*lda) + (i-1)]), &amp;ti3);</span></a>
+<a name="27072"><span class="lineNum">   27072 </span>            :       /* BLAS */</a>
+<a name="27073"><span class="lineNum">   27073 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone, &amp;(w[ i-1 ]),ldw,&amp;(a[ i-1 ]),</span></a>
+<a name="27074"><span class="lineNum">   27074 </span><span class="lineNoCov">          0 :                lda,&amp;one, &amp;(a[ (i-1)*(*lda) + (i-1)]), &amp;ti3);</span></a>
+<a name="27075"><span class="lineNum">   27075 </span>            : </a>
+<a name="27076"><span class="lineNum">   27076 </span><span class="lineNoCov">          0 :       if(i&lt;*n) {</span></a>
+<a name="27077"><span class="lineNum">   27077 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="27078"><span class="lineNum">   27078 </span><span class="lineNoCov">          0 :         ti2 = (*n &lt; i+2 ) ? *n : (i+2);</span></a>
+<a name="27079"><span class="lineNum">   27079 </span><span class="lineNoCov">          0 :         ti3 = 1;</span></a>
+<a name="27080"><span class="lineNum">   27080 </span>            :         /* LAPACK */</a>
+<a name="27081"><span class="lineNum">   27081 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;ti1,&amp;(a[(i-1)*(*lda)+(i)]),&amp;(a[(i-1)*(*lda)+(ti2-1)]),&amp;ti3,&amp;(tau[i-1]));</span></a>
+<a name="27082"><span class="lineNum">   27082 </span><span class="lineNoCov">          0 :         e[i-1] = a[(i-1)*(*lda)+(i)];</span></a>
+<a name="27083"><span class="lineNum">   27083 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i)] = 1.0;</span></a>
+<a name="27084"><span class="lineNum">   27084 </span>            :         </a>
+<a name="27085"><span class="lineNum">   27085 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="27086"><span class="lineNum">   27086 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="27087"><span class="lineNum">   27087 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)(&quot;L&quot;,&amp;ti1,&amp;one,&amp;(a[i*(*lda)+i]),lda,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2,</span></a>
+<a name="27088"><span class="lineNum">   27088 </span><span class="lineNoCov">          0 :                &amp;zero,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti2);</span></a>
+<a name="27089"><span class="lineNum">   27089 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="27090"><span class="lineNum">   27090 </span><span class="lineNoCov">          0 :         ti2 = i-1;</span></a>
+<a name="27091"><span class="lineNum">   27091 </span><span class="lineNoCov">          0 :         ti3 = 1;</span></a>
+<a name="27092"><span class="lineNum">   27092 </span>            :         /* BLAS */</a>
+<a name="27093"><span class="lineNum">   27093 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(w[ i ]),ldw,&amp;(a[(i-1)*(*lda)+i]),&amp;ti3,</span></a>
+<a name="27094"><span class="lineNum">   27094 </span><span class="lineNoCov">          0 :                &amp;zero,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="27095"><span class="lineNum">   27095 </span>            :         </a>
+<a name="27096"><span class="lineNum">   27096 </span>            :         /* BLAS */</a>
+<a name="27097"><span class="lineNum">   27097 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(a[ i ]),lda,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3,</span></a>
+<a name="27098"><span class="lineNum">   27098 </span><span class="lineNoCov">          0 :                &amp;one,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="27099"><span class="lineNum">   27099 </span>            :         </a>
+<a name="27100"><span class="lineNum">   27100 </span>            :         /* BLAS */</a>
+<a name="27101"><span class="lineNum">   27101 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;T&quot;,&amp;ti1,&amp;ti2,&amp;one,&amp;(a[ i ]),lda,&amp;(a[(i-1)*(*lda)+i]),&amp;ti3,</span></a>
+<a name="27102"><span class="lineNum">   27102 </span><span class="lineNoCov">          0 :                &amp;zero,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3);</span></a>
+<a name="27103"><span class="lineNum">   27103 </span>            :         </a>
+<a name="27104"><span class="lineNum">   27104 </span>            :         /* BLAS */</a>
+<a name="27105"><span class="lineNum">   27105 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sgemv,SGEMV)(&quot;N&quot;,&amp;ti1,&amp;ti2,&amp;minusone,&amp;(w[ i ]),ldw,&amp;(w[(i-1)*(*ldw)+0]),&amp;ti3,</span></a>
+<a name="27106"><span class="lineNum">   27106 </span><span class="lineNoCov">          0 :                &amp;one,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="27107"><span class="lineNum">   27107 </span>            : </a>
+<a name="27108"><span class="lineNum">   27108 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;ti1,&amp;(tau[i-1]),&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="27109"><span class="lineNum">   27109 </span><span class="lineNoCov">          0 :         alpha = -0.5*tau[i-1]*PLUMED_BLAS_F77_FUNC(sdot,SDOT)(&amp;ti1,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3,</span></a>
+<a name="27110"><span class="lineNum">   27110 </span><span class="lineNoCov">          0 :                                    &amp;(a[(i-1)*(*lda)+i]),&amp;ti3);</span></a>
+<a name="27111"><span class="lineNum">   27111 </span>            :         </a>
+<a name="27112"><span class="lineNum">   27112 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(&amp;ti1,&amp;alpha,&amp;(a[(i-1)*(*lda)+i]),&amp;ti3,&amp;(w[(i-1)*(*ldw)+i]),&amp;ti3);</span></a>
+<a name="27113"><span class="lineNum">   27113 </span>            :       }</a>
+<a name="27114"><span class="lineNum">   27114 </span>            :     }</a>
+<a name="27115"><span class="lineNum">   27115 </span>            :   }</a>
+<a name="27116"><span class="lineNum">   27116 </span>            :   return;</a>
+<a name="27117"><span class="lineNum">   27117 </span>            : }</a>
+<a name="27118"><span class="lineNum">   27118 </span>            :         </a>
+<a name="27119"><span class="lineNum">   27119 </span>            : </a>
+<a name="27120"><span class="lineNum">   27120 </span>            : </a>
+<a name="27121"><span class="lineNum">   27121 </span>            :   </a>
+<a name="27122"><span class="lineNum">   27122 </span>            : }</a>
+<a name="27123"><span class="lineNum">   27123 </span>            : }</a>
+<a name="27124"><span class="lineNum">   27124 </span>            : #include &lt;cmath&gt;</a>
+<a name="27125"><span class="lineNum">   27125 </span>            : </a>
+<a name="27126"><span class="lineNum">   27126 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27127"><span class="lineNum">   27127 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27128"><span class="lineNum">   27128 </span>            : </a>
+<a name="27129"><span class="lineNum">   27129 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27130"><span class="lineNum">   27130 </span>            : namespace PLMD{</a>
+<a name="27131"><span class="lineNum">   27131 </span>            : namespace lapack{</a>
+<a name="27132"><span class="lineNum">   27132 </span>            : using namespace blas;</a>
+<a name="27133"><span class="lineNum">   27133 </span>            : void </a>
+<a name="27134"><span class="lineNum">   27134 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorg2r,SORG2R)(int *m, </span></a>
+<a name="27135"><span class="lineNum">   27135 </span>            :                         int *n,</a>
+<a name="27136"><span class="lineNum">   27136 </span>            :                         int *k, </a>
+<a name="27137"><span class="lineNum">   27137 </span>            :                         float *a, </a>
+<a name="27138"><span class="lineNum">   27138 </span>            :                         int *lda,</a>
+<a name="27139"><span class="lineNum">   27139 </span>            :                         float *tau,</a>
+<a name="27140"><span class="lineNum">   27140 </span>            :                         float *work,</a>
+<a name="27141"><span class="lineNum">   27141 </span>            :                         int *info)</a>
+<a name="27142"><span class="lineNum">   27142 </span>            : {</a>
+<a name="27143"><span class="lineNum">   27143 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="27144"><span class="lineNum">   27144 </span>            :     float r__1;</a>
+<a name="27145"><span class="lineNum">   27145 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="27146"><span class="lineNum">   27146 </span>            : </a>
+<a name="27147"><span class="lineNum">   27147 </span>            :     int i__, j, l;</a>
+<a name="27148"><span class="lineNum">   27148 </span>            : </a>
+<a name="27149"><span class="lineNum">   27149 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27150"><span class="lineNum">   27150 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27151"><span class="lineNum">   27151 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27152"><span class="lineNum">   27152 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="27153"><span class="lineNum">   27153 </span>            :     --work;</a>
+<a name="27154"><span class="lineNum">   27154 </span>            : </a>
+<a name="27155"><span class="lineNum">   27155 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27156"><span class="lineNum">   27156 </span>            : </a>
+<a name="27157"><span class="lineNum">   27157 </span><span class="lineNoCov">          0 :     if (*n &lt;= 0) {</span></a>
+<a name="27158"><span class="lineNum">   27158 </span>            :         return;</a>
+<a name="27159"><span class="lineNum">   27159 </span>            :     }</a>
+<a name="27160"><span class="lineNum">   27160 </span>            : </a>
+<a name="27161"><span class="lineNum">   27161 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="27162"><span class="lineNum">   27162 </span><span class="lineNoCov">          0 :     for (j = *k + 1; j &lt;= i__1; ++j) {</span></a>
+<a name="27163"><span class="lineNum">   27163 </span><span class="lineNoCov">          0 :         i__2 = *m;</span></a>
+<a name="27164"><span class="lineNum">   27164 </span><span class="lineNoCov">          0 :         for (l = 1; l &lt;= i__2; ++l) {</span></a>
+<a name="27165"><span class="lineNum">   27165 </span><span class="lineNoCov">          0 :             a[l + j * a_dim1] = 0.0;</span></a>
+<a name="27166"><span class="lineNum">   27166 </span>            :         }</a>
+<a name="27167"><span class="lineNum">   27167 </span><span class="lineNoCov">          0 :         a[j + j * a_dim1] = 1.0;</span></a>
+<a name="27168"><span class="lineNum">   27168 </span>            :     }</a>
+<a name="27169"><span class="lineNum">   27169 </span><span class="lineNoCov">          0 :     for (i__ = *k; i__ &gt;= 1; --i__) {</span></a>
+<a name="27170"><span class="lineNum">   27170 </span><span class="lineNoCov">          0 :         if (i__ &lt; *n) {</span></a>
+<a name="27171"><span class="lineNum">   27171 </span><span class="lineNoCov">          0 :             a[i__ + i__ * a_dim1] = 1.0;</span></a>
+<a name="27172"><span class="lineNum">   27172 </span><span class="lineNoCov">          0 :             i__1 = *m - i__ + 1;</span></a>
+<a name="27173"><span class="lineNum">   27173 </span><span class="lineNoCov">          0 :             i__2 = *n - i__;</span></a>
+<a name="27174"><span class="lineNum">   27174 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;L&quot;, &amp;i__1, &amp;i__2, &amp;a[i__ + i__ * a_dim1], &amp;c__1, </span></a>
+<a name="27175"><span class="lineNum">   27175 </span><span class="lineNoCov">          0 :                               &amp;tau[i__], &amp;a[i__ + (i__ + 1) * a_dim1], lda, &amp;work[1]);</span></a>
+<a name="27176"><span class="lineNum">   27176 </span>            :         }</a>
+<a name="27177"><span class="lineNum">   27177 </span><span class="lineNoCov">          0 :         if (i__ &lt; *m) {</span></a>
+<a name="27178"><span class="lineNum">   27178 </span><span class="lineNoCov">          0 :             i__1 = *m - i__;</span></a>
+<a name="27179"><span class="lineNum">   27179 </span><span class="lineNoCov">          0 :             r__1 = -tau[i__];</span></a>
+<a name="27180"><span class="lineNum">   27180 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__1, &amp;r__1, &amp;a[i__ + 1 + i__ * a_dim1], &amp;c__1);</span></a>
+<a name="27181"><span class="lineNum">   27181 </span>            :         }</a>
+<a name="27182"><span class="lineNum">   27182 </span><span class="lineNoCov">          0 :         a[i__ + i__ * a_dim1] = 1.0 - tau[i__];</span></a>
+<a name="27183"><span class="lineNum">   27183 </span><span class="lineNoCov">          0 :         i__1 = i__ - 1;</span></a>
+<a name="27184"><span class="lineNum">   27184 </span><span class="lineNoCov">          0 :         for (l = 1; l &lt;= i__1; ++l) {</span></a>
+<a name="27185"><span class="lineNum">   27185 </span><span class="lineNoCov">          0 :             a[l + i__ * a_dim1] = 0.0;</span></a>
+<a name="27186"><span class="lineNum">   27186 </span>            :         }</a>
+<a name="27187"><span class="lineNum">   27187 </span>            :     }</a>
+<a name="27188"><span class="lineNum">   27188 </span>            :     return;</a>
+<a name="27189"><span class="lineNum">   27189 </span>            : </a>
+<a name="27190"><span class="lineNum">   27190 </span>            : }</a>
+<a name="27191"><span class="lineNum">   27191 </span>            : </a>
+<a name="27192"><span class="lineNum">   27192 </span>            : </a>
+<a name="27193"><span class="lineNum">   27193 </span>            : }</a>
+<a name="27194"><span class="lineNum">   27194 </span>            : }</a>
+<a name="27195"><span class="lineNum">   27195 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27196"><span class="lineNum">   27196 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="27197"><span class="lineNum">   27197 </span>            : </a>
+<a name="27198"><span class="lineNum">   27198 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27199"><span class="lineNum">   27199 </span>            : namespace PLMD{</a>
+<a name="27200"><span class="lineNum">   27200 </span>            : namespace lapack{</a>
+<a name="27201"><span class="lineNum">   27201 </span>            : using namespace blas;</a>
+<a name="27202"><span class="lineNum">   27202 </span>            : void</a>
+<a name="27203"><span class="lineNum">   27203 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorgbr,SORGBR)(const char *vect,</span></a>
+<a name="27204"><span class="lineNum">   27204 </span>            :         int *m,</a>
+<a name="27205"><span class="lineNum">   27205 </span>            :         int *n,</a>
+<a name="27206"><span class="lineNum">   27206 </span>            :         int *k,</a>
+<a name="27207"><span class="lineNum">   27207 </span>            :         float *a,</a>
+<a name="27208"><span class="lineNum">   27208 </span>            :         int *lda,</a>
+<a name="27209"><span class="lineNum">   27209 </span>            :         float *tau,</a>
+<a name="27210"><span class="lineNum">   27210 </span>            :         float *work,</a>
+<a name="27211"><span class="lineNum">   27211 </span>            :         int *lwork,</a>
+<a name="27212"><span class="lineNum">   27212 </span>            :         int *info)</a>
+<a name="27213"><span class="lineNum">   27213 </span>            : {</a>
+<a name="27214"><span class="lineNum">   27214 </span>            :   int wantq,iinfo,j,i,i1,wrksz;</a>
+<a name="27215"><span class="lineNum">   27215 </span><span class="lineNoCov">          0 :   int mn = (*m &lt; *n) ? *m : *n;</span></a>
+<a name="27216"><span class="lineNum">   27216 </span>            : </a>
+<a name="27217"><span class="lineNum">   27217 </span><span class="lineNoCov">          0 :   wantq = (*vect=='Q' || *vect=='q');</span></a>
+<a name="27218"><span class="lineNum">   27218 </span>            : </a>
+<a name="27219"><span class="lineNum">   27219 </span><span class="lineNoCov">          0 :   *info = 0;</span></a>
+<a name="27220"><span class="lineNum">   27220 </span><span class="lineNoCov">          0 :   wrksz = mn*DORGBR_BLOCKSIZE;</span></a>
+<a name="27221"><span class="lineNum">   27221 </span><span class="lineNoCov">          0 :   if(*lwork==-1) {</span></a>
+<a name="27222"><span class="lineNum">   27222 </span><span class="lineNoCov">          0 :     work[0] = wrksz;</span></a>
+<a name="27223"><span class="lineNum">   27223 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="27224"><span class="lineNum">   27224 </span>            :   }</a>
+<a name="27225"><span class="lineNum">   27225 </span>            :   </a>
+<a name="27226"><span class="lineNum">   27226 </span><span class="lineNoCov">          0 :   if(*m==0 || *n==0)</span></a>
+<a name="27227"><span class="lineNum">   27227 </span>            :     return;</a>
+<a name="27228"><span class="lineNum">   27228 </span>            : </a>
+<a name="27229"><span class="lineNum">   27229 </span><span class="lineNoCov">          0 :   if(wantq) {</span></a>
+<a name="27230"><span class="lineNum">   27230 </span><span class="lineNoCov">          0 :     if(*m&gt;=*k)</span></a>
+<a name="27231"><span class="lineNum">   27231 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sorgqr,SORGQR)(m,n,k,a,lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="27232"><span class="lineNum">   27232 </span>            :     else {</a>
+<a name="27233"><span class="lineNum">   27233 </span><span class="lineNoCov">          0 :       for(j=*m;j&gt;=2;j--) {</span></a>
+<a name="27234"><span class="lineNum">   27234 </span><span class="lineNoCov">          0 :         a[(j-1)*(*lda)+0] = 0.0;</span></a>
+<a name="27235"><span class="lineNum">   27235 </span><span class="lineNoCov">          0 :         for(i=j+1;i&lt;=*m;i++)</span></a>
+<a name="27236"><span class="lineNum">   27236 </span><span class="lineNoCov">          0 :           a[(j-1)*(*lda)+(i-1)] = a[(j-2)*(*lda)+(i-1)]; </span></a>
+<a name="27237"><span class="lineNum">   27237 </span>            :       }</a>
+<a name="27238"><span class="lineNum">   27238 </span><span class="lineNoCov">          0 :       a[0] = 1.0;</span></a>
+<a name="27239"><span class="lineNum">   27239 </span><span class="lineNoCov">          0 :       for(i=2;i&lt;=*m;i++)</span></a>
+<a name="27240"><span class="lineNum">   27240 </span><span class="lineNoCov">          0 :         a[i-1] = 0.0;</span></a>
+<a name="27241"><span class="lineNum">   27241 </span><span class="lineNoCov">          0 :       if(*m&gt;1) {</span></a>
+<a name="27242"><span class="lineNum">   27242 </span><span class="lineNoCov">          0 :         i1 = *m-1;</span></a>
+<a name="27243"><span class="lineNum">   27243 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorgqr,SORGQR)(&amp;i1,&amp;i1,&amp;i1,&amp;(a[*lda+1]),lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="27244"><span class="lineNum">   27244 </span>            :       }</a>
+<a name="27245"><span class="lineNum">   27245 </span>            :     }</a>
+<a name="27246"><span class="lineNum">   27246 </span>            :   } else {</a>
+<a name="27247"><span class="lineNum">   27247 </span><span class="lineNoCov">          0 :     if(*k&lt;*n)</span></a>
+<a name="27248"><span class="lineNum">   27248 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sorglq,SORGLQ)(m,n,k,a,lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="27249"><span class="lineNum">   27249 </span>            :     else {</a>
+<a name="27250"><span class="lineNum">   27250 </span><span class="lineNoCov">          0 :       a[0] = 1.0;</span></a>
+<a name="27251"><span class="lineNum">   27251 </span><span class="lineNoCov">          0 :       for(i=2;i&lt;=*m;i++)</span></a>
+<a name="27252"><span class="lineNum">   27252 </span><span class="lineNoCov">          0 :         a[i-1] = 0.0;</span></a>
+<a name="27253"><span class="lineNum">   27253 </span><span class="lineNoCov">          0 :       for(j=2;j&lt;=*n;j++) {</span></a>
+<a name="27254"><span class="lineNum">   27254 </span><span class="lineNoCov">          0 :         for(i=j-1;i&gt;=2;i--)</span></a>
+<a name="27255"><span class="lineNum">   27255 </span><span class="lineNoCov">          0 :           a[(j-1)*(*lda)+(i-1)] = a[(j-1)*(*lda)+(i-2)]; </span></a>
+<a name="27256"><span class="lineNum">   27256 </span><span class="lineNoCov">          0 :         a[(j-1)*(*lda)+0] = 0.0;</span></a>
+<a name="27257"><span class="lineNum">   27257 </span>            :       }</a>
+<a name="27258"><span class="lineNum">   27258 </span><span class="lineNoCov">          0 :       if(*n&gt;1) {</span></a>
+<a name="27259"><span class="lineNum">   27259 </span><span class="lineNoCov">          0 :         i1 = *n-1;</span></a>
+<a name="27260"><span class="lineNum">   27260 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorglq,SORGLQ)(&amp;i1,&amp;i1,&amp;i1,&amp;(a[*lda+1]),lda,tau,work,lwork,&amp;iinfo);</span></a>
+<a name="27261"><span class="lineNum">   27261 </span>            :       }</a>
+<a name="27262"><span class="lineNum">   27262 </span>            :     }</a>
+<a name="27263"><span class="lineNum">   27263 </span>            :   }</a>
+<a name="27264"><span class="lineNum">   27264 </span><span class="lineNoCov">          0 :   work[0] = wrksz;</span></a>
+<a name="27265"><span class="lineNum">   27265 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="27266"><span class="lineNum">   27266 </span>            : }</a>
+<a name="27267"><span class="lineNum">   27267 </span>            :  </a>
+<a name="27268"><span class="lineNum">   27268 </span>            : }</a>
+<a name="27269"><span class="lineNum">   27269 </span>            : }</a>
+<a name="27270"><span class="lineNum">   27270 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27271"><span class="lineNum">   27271 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27272"><span class="lineNum">   27272 </span>            : </a>
+<a name="27273"><span class="lineNum">   27273 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27274"><span class="lineNum">   27274 </span>            : namespace PLMD{</a>
+<a name="27275"><span class="lineNum">   27275 </span>            : namespace lapack{</a>
+<a name="27276"><span class="lineNum">   27276 </span>            : using namespace blas;</a>
+<a name="27277"><span class="lineNum">   27277 </span>            : void</a>
+<a name="27278"><span class="lineNum">   27278 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorgl2,SORGL2)(int *m,</span></a>
+<a name="27279"><span class="lineNum">   27279 </span>            :                         int *n, </a>
+<a name="27280"><span class="lineNum">   27280 </span>            :                         int *k, </a>
+<a name="27281"><span class="lineNum">   27281 </span>            :                         float *a, </a>
+<a name="27282"><span class="lineNum">   27282 </span>            :                         int *lda, </a>
+<a name="27283"><span class="lineNum">   27283 </span>            :                         float *tau, </a>
+<a name="27284"><span class="lineNum">   27284 </span>            :                         float *work, </a>
+<a name="27285"><span class="lineNum">   27285 </span>            :                         int *info)</a>
+<a name="27286"><span class="lineNum">   27286 </span>            : {</a>
+<a name="27287"><span class="lineNum">   27287 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="27288"><span class="lineNum">   27288 </span>            :     float r__1;</a>
+<a name="27289"><span class="lineNum">   27289 </span>            : </a>
+<a name="27290"><span class="lineNum">   27290 </span>            :     int i__, j, l;</a>
+<a name="27291"><span class="lineNum">   27291 </span>            : </a>
+<a name="27292"><span class="lineNum">   27292 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27293"><span class="lineNum">   27293 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27294"><span class="lineNum">   27294 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27295"><span class="lineNum">   27295 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="27296"><span class="lineNum">   27296 </span>            :     --work;</a>
+<a name="27297"><span class="lineNum">   27297 </span>            : </a>
+<a name="27298"><span class="lineNum">   27298 </span><span class="lineNoCov">          0 :     i__ = (*m &gt; 1) ? *m : 1;</span></a>
+<a name="27299"><span class="lineNum">   27299 </span>            :     </a>
+<a name="27300"><span class="lineNum">   27300 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27301"><span class="lineNum">   27301 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="27302"><span class="lineNum">   27302 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="27303"><span class="lineNum">   27303 </span><span class="lineNoCov">          0 :     } else if (*n &lt; *m) {</span></a>
+<a name="27304"><span class="lineNum">   27304 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="27305"><span class="lineNum">   27305 </span><span class="lineNoCov">          0 :     } else if (*k &lt; 0 || *k &gt; *m) {</span></a>
+<a name="27306"><span class="lineNum">   27306 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="27307"><span class="lineNum">   27307 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; i__) {</span></a>
+<a name="27308"><span class="lineNum">   27308 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="27309"><span class="lineNum">   27309 </span>            :     }</a>
+<a name="27310"><span class="lineNum">   27310 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="27311"><span class="lineNum">   27311 </span>            :         return;</a>
+<a name="27312"><span class="lineNum">   27312 </span>            :     }</a>
+<a name="27313"><span class="lineNum">   27313 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0) {</span></a>
+<a name="27314"><span class="lineNum">   27314 </span>            :         return;</a>
+<a name="27315"><span class="lineNum">   27315 </span>            :     }</a>
+<a name="27316"><span class="lineNum">   27316 </span>            : </a>
+<a name="27317"><span class="lineNum">   27317 </span><span class="lineNoCov">          0 :     if (*k &lt; *m) {</span></a>
+<a name="27318"><span class="lineNum">   27318 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="27319"><span class="lineNum">   27319 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="27320"><span class="lineNum">   27320 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="27321"><span class="lineNum">   27321 </span><span class="lineNoCov">          0 :             for (l = *k + 1; l &lt;= i__2; ++l) {</span></a>
+<a name="27322"><span class="lineNum">   27322 </span><span class="lineNoCov">          0 :                 a[l + j * a_dim1] = 0.0;</span></a>
+<a name="27323"><span class="lineNum">   27323 </span>            :             }</a>
+<a name="27324"><span class="lineNum">   27324 </span><span class="lineNoCov">          0 :             if (j &gt; *k &amp;&amp; j &lt;= *m) {</span></a>
+<a name="27325"><span class="lineNum">   27325 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = 1.0;</span></a>
+<a name="27326"><span class="lineNum">   27326 </span>            :             }</a>
+<a name="27327"><span class="lineNum">   27327 </span>            :         }</a>
+<a name="27328"><span class="lineNum">   27328 </span>            :     }</a>
+<a name="27329"><span class="lineNum">   27329 </span>            : </a>
+<a name="27330"><span class="lineNum">   27330 </span><span class="lineNoCov">          0 :     for (i__ = *k; i__ &gt;= 1; --i__) {</span></a>
+<a name="27331"><span class="lineNum">   27331 </span><span class="lineNoCov">          0 :         if (i__ &lt; *n) {</span></a>
+<a name="27332"><span class="lineNum">   27332 </span><span class="lineNoCov">          0 :             if (i__ &lt; *m) {</span></a>
+<a name="27333"><span class="lineNum">   27333 </span><span class="lineNoCov">          0 :                 a[i__ + i__ * a_dim1] = 1.0;</span></a>
+<a name="27334"><span class="lineNum">   27334 </span><span class="lineNoCov">          0 :                 i__1 = *m - i__;</span></a>
+<a name="27335"><span class="lineNum">   27335 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__ + 1;</span></a>
+<a name="27336"><span class="lineNum">   27336 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarf,SLARF)(&quot;R&quot;, &amp;i__1, &amp;i__2, &amp;a[i__ + i__ * a_dim1], lda, </span></a>
+<a name="27337"><span class="lineNum">   27337 </span><span class="lineNoCov">          0 :                &amp;tau[i__], &amp;a[i__ + 1 + i__ * a_dim1], lda, &amp;work[1]);</span></a>
+<a name="27338"><span class="lineNum">   27338 </span>            :             }</a>
+<a name="27339"><span class="lineNum">   27339 </span><span class="lineNoCov">          0 :             i__1 = *n - i__;</span></a>
+<a name="27340"><span class="lineNum">   27340 </span><span class="lineNoCov">          0 :             r__1 = -tau[i__];</span></a>
+<a name="27341"><span class="lineNum">   27341 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__1, &amp;r__1, &amp;a[i__ + (i__ + 1) * a_dim1], lda);</span></a>
+<a name="27342"><span class="lineNum">   27342 </span>            :         }</a>
+<a name="27343"><span class="lineNum">   27343 </span><span class="lineNoCov">          0 :         a[i__ + i__ * a_dim1] = 1.0 - tau[i__];</span></a>
+<a name="27344"><span class="lineNum">   27344 </span><span class="lineNoCov">          0 :         i__1 = i__ - 1;</span></a>
+<a name="27345"><span class="lineNum">   27345 </span><span class="lineNoCov">          0 :         for (l = 1; l &lt;= i__1; ++l) {</span></a>
+<a name="27346"><span class="lineNum">   27346 </span><span class="lineNoCov">          0 :             a[i__ + l * a_dim1] = 0.0;</span></a>
+<a name="27347"><span class="lineNum">   27347 </span>            :         }</a>
+<a name="27348"><span class="lineNum">   27348 </span>            :     }</a>
+<a name="27349"><span class="lineNum">   27349 </span>            :     return;</a>
+<a name="27350"><span class="lineNum">   27350 </span>            : </a>
+<a name="27351"><span class="lineNum">   27351 </span>            : }</a>
+<a name="27352"><span class="lineNum">   27352 </span>            : </a>
+<a name="27353"><span class="lineNum">   27353 </span>            : </a>
+<a name="27354"><span class="lineNum">   27354 </span>            : </a>
+<a name="27355"><span class="lineNum">   27355 </span>            : }</a>
+<a name="27356"><span class="lineNum">   27356 </span>            : }</a>
+<a name="27357"><span class="lineNum">   27357 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27358"><span class="lineNum">   27358 </span>            : </a>
+<a name="27359"><span class="lineNum">   27359 </span>            : #define SORGLQ_BLOCKSIZE    32</a>
+<a name="27360"><span class="lineNum">   27360 </span>            : #define SORGLQ_MINBLOCKSIZE 2</a>
+<a name="27361"><span class="lineNum">   27361 </span>            : #define SORGLQ_CROSSOVER    128</a>
+<a name="27362"><span class="lineNum">   27362 </span>            : </a>
+<a name="27363"><span class="lineNum">   27363 </span>            : </a>
+<a name="27364"><span class="lineNum">   27364 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27365"><span class="lineNum">   27365 </span>            : namespace PLMD{</a>
+<a name="27366"><span class="lineNum">   27366 </span>            : namespace lapack{</a>
+<a name="27367"><span class="lineNum">   27367 </span>            : using namespace blas;</a>
+<a name="27368"><span class="lineNum">   27368 </span>            : void </a>
+<a name="27369"><span class="lineNum">   27369 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorglq,SORGLQ)(int *m, </span></a>
+<a name="27370"><span class="lineNum">   27370 </span>            :         int *n, </a>
+<a name="27371"><span class="lineNum">   27371 </span>            :         int *k, </a>
+<a name="27372"><span class="lineNum">   27372 </span>            :         float *a, </a>
+<a name="27373"><span class="lineNum">   27373 </span>            :         int *lda, </a>
+<a name="27374"><span class="lineNum">   27374 </span>            :         float *tau, </a>
+<a name="27375"><span class="lineNum">   27375 </span>            :         float *work, </a>
+<a name="27376"><span class="lineNum">   27376 </span>            :         int *lwork, </a>
+<a name="27377"><span class="lineNum">   27377 </span>            :         int *info)</a>
+<a name="27378"><span class="lineNum">   27378 </span>            : {</a>
+<a name="27379"><span class="lineNum">   27379 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="27380"><span class="lineNum">   27380 </span>            : </a>
+<a name="27381"><span class="lineNum">   27381 </span>            :     int i__, j, l, ib, nb, ki, kk, nx, iws, nbmin, iinfo;</a>
+<a name="27382"><span class="lineNum">   27382 </span>            : </a>
+<a name="27383"><span class="lineNum">   27383 </span>            :     int ldwork, lwkopt;</a>
+<a name="27384"><span class="lineNum">   27384 </span>            :     int lquery;</a>
+<a name="27385"><span class="lineNum">   27385 </span>            :     </a>
+<a name="27386"><span class="lineNum">   27386 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27387"><span class="lineNum">   27387 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27388"><span class="lineNum">   27388 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27389"><span class="lineNum">   27389 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="27390"><span class="lineNum">   27390 </span>            :     --work;</a>
+<a name="27391"><span class="lineNum">   27391 </span>            : </a>
+<a name="27392"><span class="lineNum">   27392 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27393"><span class="lineNum">   27393 </span>            :     ki = 0;</a>
+<a name="27394"><span class="lineNum">   27394 </span>            :     nb = SORGLQ_BLOCKSIZE;</a>
+<a name="27395"><span class="lineNum">   27395 </span><span class="lineNoCov">          0 :     lwkopt = (*m) * nb;</span></a>
+<a name="27396"><span class="lineNum">   27396 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="27397"><span class="lineNum">   27397 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="27398"><span class="lineNum">   27398 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="27399"><span class="lineNum">   27399 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="27400"><span class="lineNum">   27400 </span><span class="lineNoCov">          0 :     } else if (*n &lt; *m) {</span></a>
+<a name="27401"><span class="lineNum">   27401 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="27402"><span class="lineNum">   27402 </span><span class="lineNoCov">          0 :     } else if (*k &lt; 0 || *k &gt; *m) {</span></a>
+<a name="27403"><span class="lineNum">   27403 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="27404"><span class="lineNum">   27404 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; (*m)) {</span></a>
+<a name="27405"><span class="lineNum">   27405 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="27406"><span class="lineNum">   27406 </span><span class="lineNoCov">          0 :     } else if (*lwork &lt; (*m) &amp;&amp; ! lquery) {</span></a>
+<a name="27407"><span class="lineNum">   27407 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="27408"><span class="lineNum">   27408 </span>            :     }</a>
+<a name="27409"><span class="lineNum">   27409 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="27410"><span class="lineNum">   27410 </span>            :         i__1 = -(*info);</a>
+<a name="27411"><span class="lineNum">   27411 </span>            :         return;</a>
+<a name="27412"><span class="lineNum">   27412 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="27413"><span class="lineNum">   27413 </span>            :         return;</a>
+<a name="27414"><span class="lineNum">   27414 </span>            :     }</a>
+<a name="27415"><span class="lineNum">   27415 </span>            : </a>
+<a name="27416"><span class="lineNum">   27416 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0) {</span></a>
+<a name="27417"><span class="lineNum">   27417 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="27418"><span class="lineNum">   27418 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="27419"><span class="lineNum">   27419 </span>            :     }</a>
+<a name="27420"><span class="lineNum">   27420 </span>            : </a>
+<a name="27421"><span class="lineNum">   27421 </span>            :     nbmin = 2;</a>
+<a name="27422"><span class="lineNum">   27422 </span>            :     nx = 0;</a>
+<a name="27423"><span class="lineNum">   27423 </span>            :     iws = *m;</a>
+<a name="27424"><span class="lineNum">   27424 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="27425"><span class="lineNum">   27425 </span>            : </a>
+<a name="27426"><span class="lineNum">   27426 </span>            :         nx = SORGLQ_CROSSOVER;</a>
+<a name="27427"><span class="lineNum">   27427 </span><span class="lineNoCov">          0 :         if (nx &lt; *k) {</span></a>
+<a name="27428"><span class="lineNum">   27428 </span>            : </a>
+<a name="27429"><span class="lineNum">   27429 </span><span class="lineNoCov">          0 :             ldwork = *m;</span></a>
+<a name="27430"><span class="lineNum">   27430 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="27431"><span class="lineNum">   27431 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="27432"><span class="lineNum">   27432 </span>            : </a>
+<a name="27433"><span class="lineNum">   27433 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="27434"><span class="lineNum">   27434 </span>            :                 nbmin = SORGLQ_MINBLOCKSIZE;</a>
+<a name="27435"><span class="lineNum">   27435 </span>            :             }</a>
+<a name="27436"><span class="lineNum">   27436 </span>            :         }</a>
+<a name="27437"><span class="lineNum">   27437 </span>            :     }</a>
+<a name="27438"><span class="lineNum">   27438 </span>            : </a>
+<a name="27439"><span class="lineNum">   27439 </span><span class="lineNoCov">          0 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; *k &amp;&amp; nx &lt; *k) {</span></a>
+<a name="27440"><span class="lineNum">   27440 </span>            : </a>
+<a name="27441"><span class="lineNum">   27441 </span><span class="lineNoCov">          0 :         ki = (*k - nx - 1) / nb * nb;</span></a>
+<a name="27442"><span class="lineNum">   27442 </span><span class="lineNoCov">          0 :         i__1 = *k, i__2 = ki + nb;</span></a>
+<a name="27443"><span class="lineNum">   27443 </span>            :         kk = (i__1&lt;i__2) ? i__1 : i__2;</a>
+<a name="27444"><span class="lineNum">   27444 </span>            : </a>
+<a name="27445"><span class="lineNum">   27445 </span><span class="lineNoCov">          0 :         i__1 = kk;</span></a>
+<a name="27446"><span class="lineNum">   27446 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="27447"><span class="lineNum">   27447 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="27448"><span class="lineNum">   27448 </span><span class="lineNoCov">          0 :             for (i__ = kk + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="27449"><span class="lineNum">   27449 </span><span class="lineNoCov">          0 :                 a[i__ + j * a_dim1] = 0.;</span></a>
+<a name="27450"><span class="lineNum">   27450 </span>            :             }</a>
+<a name="27451"><span class="lineNum">   27451 </span>            :         }</a>
+<a name="27452"><span class="lineNum">   27452 </span>            :     } else {</a>
+<a name="27453"><span class="lineNum">   27453 </span>            :         kk = 0;</a>
+<a name="27454"><span class="lineNum">   27454 </span>            :     }</a>
+<a name="27455"><span class="lineNum">   27455 </span><span class="lineNoCov">          0 :     if (kk &lt; *m) {</span></a>
+<a name="27456"><span class="lineNum">   27456 </span><span class="lineNoCov">          0 :         i__1 = *m - kk;</span></a>
+<a name="27457"><span class="lineNum">   27457 </span><span class="lineNoCov">          0 :         i__2 = *n - kk;</span></a>
+<a name="27458"><span class="lineNum">   27458 </span><span class="lineNoCov">          0 :         i__3 = *k - kk;</span></a>
+<a name="27459"><span class="lineNum">   27459 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorgl2,SORGL2)(&amp;i__1, &amp;i__2, &amp;i__3, &amp;a[kk + 1 + (kk + 1) * a_dim1], lda, &amp;</span></a>
+<a name="27460"><span class="lineNum">   27460 </span><span class="lineNoCov">          0 :                 tau[kk + 1], &amp;work[1], &amp;iinfo);</span></a>
+<a name="27461"><span class="lineNum">   27461 </span>            :     }</a>
+<a name="27462"><span class="lineNum">   27462 </span>            : </a>
+<a name="27463"><span class="lineNum">   27463 </span><span class="lineNoCov">          0 :     if (kk &gt; 0) {</span></a>
+<a name="27464"><span class="lineNum">   27464 </span>            : </a>
+<a name="27465"><span class="lineNum">   27465 </span><span class="lineNoCov">          0 :         i__1 = -nb;</span></a>
+<a name="27466"><span class="lineNum">   27466 </span><span class="lineNoCov">          0 :         for (i__ = ki + 1; i__1 &lt; 0 ? i__ &gt;= 1 : i__ &lt;= 1; i__ += i__1) {</span></a>
+<a name="27467"><span class="lineNum">   27467 </span><span class="lineNoCov">          0 :             i__2 = nb, i__3 = *k - i__ + 1;</span></a>
+<a name="27468"><span class="lineNum">   27468 </span><span class="lineNoCov">          0 :             ib = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="27469"><span class="lineNum">   27469 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *m) {</span></a>
+<a name="27470"><span class="lineNum">   27470 </span>            : </a>
+<a name="27471"><span class="lineNum">   27471 </span><span class="lineNoCov">          0 :                 i__2 = *n - i__ + 1;</span></a>
+<a name="27472"><span class="lineNum">   27472 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__2, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="27473"><span class="lineNum">   27473 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</span></a>
+<a name="27474"><span class="lineNum">   27474 </span>            : </a>
+<a name="27475"><span class="lineNum">   27475 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ - ib + 1;</span></a>
+<a name="27476"><span class="lineNum">   27476 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ + 1;</span></a>
+<a name="27477"><span class="lineNum">   27477 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(&quot;Right&quot;, &quot;Transpose&quot;, &quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__2, &amp;</span></a>
+<a name="27478"><span class="lineNum">   27478 </span>            :                         i__3, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[1], &amp;</a>
+<a name="27479"><span class="lineNum">   27479 </span><span class="lineNoCov">          0 :                         ldwork, &amp;a[i__ + ib + i__ * a_dim1], lda, &amp;work[ib + </span></a>
+<a name="27480"><span class="lineNum">   27480 </span><span class="lineNoCov">          0 :                         1], &amp;ldwork);</span></a>
+<a name="27481"><span class="lineNum">   27481 </span>            :             }</a>
+<a name="27482"><span class="lineNum">   27482 </span>            : </a>
+<a name="27483"><span class="lineNum">   27483 </span><span class="lineNoCov">          0 :             i__2 = *n - i__ + 1;</span></a>
+<a name="27484"><span class="lineNum">   27484 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sorgl2,SORGL2)(&amp;ib, &amp;i__2, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;</span></a>
+<a name="27485"><span class="lineNum">   27485 </span>            :                     work[1], &amp;iinfo);</a>
+<a name="27486"><span class="lineNum">   27486 </span>            : </a>
+<a name="27487"><span class="lineNum">   27487 </span><span class="lineNoCov">          0 :             i__2 = i__ - 1;</span></a>
+<a name="27488"><span class="lineNum">   27488 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="27489"><span class="lineNum">   27489 </span><span class="lineNoCov">          0 :                 i__3 = i__ + ib - 1;</span></a>
+<a name="27490"><span class="lineNum">   27490 </span><span class="lineNoCov">          0 :                 for (l = i__; l &lt;= i__3; ++l) {</span></a>
+<a name="27491"><span class="lineNum">   27491 </span><span class="lineNoCov">          0 :                     a[l + j * a_dim1] = 0.;</span></a>
+<a name="27492"><span class="lineNum">   27492 </span>            :                 }</a>
+<a name="27493"><span class="lineNum">   27493 </span>            :             }</a>
+<a name="27494"><span class="lineNum">   27494 </span>            :         }</a>
+<a name="27495"><span class="lineNum">   27495 </span>            :     }</a>
+<a name="27496"><span class="lineNum">   27496 </span>            : </a>
+<a name="27497"><span class="lineNum">   27497 </span><span class="lineNoCov">          0 :     work[1] = (float) iws;</span></a>
+<a name="27498"><span class="lineNum">   27498 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="27499"><span class="lineNum">   27499 </span>            : </a>
+<a name="27500"><span class="lineNum">   27500 </span>            : }</a>
+<a name="27501"><span class="lineNum">   27501 </span>            : </a>
+<a name="27502"><span class="lineNum">   27502 </span>            : </a>
+<a name="27503"><span class="lineNum">   27503 </span>            : }</a>
+<a name="27504"><span class="lineNum">   27504 </span>            : }</a>
+<a name="27505"><span class="lineNum">   27505 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27506"><span class="lineNum">   27506 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="27507"><span class="lineNum">   27507 </span>            : </a>
+<a name="27508"><span class="lineNum">   27508 </span>            : </a>
+<a name="27509"><span class="lineNum">   27509 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27510"><span class="lineNum">   27510 </span>            : namespace PLMD{</a>
+<a name="27511"><span class="lineNum">   27511 </span>            : namespace lapack{</a>
+<a name="27512"><span class="lineNum">   27512 </span>            : using namespace blas;</a>
+<a name="27513"><span class="lineNum">   27513 </span>            : void </a>
+<a name="27514"><span class="lineNum">   27514 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorgqr,SORGQR)(int *m, </span></a>
+<a name="27515"><span class="lineNum">   27515 </span>            :         int *n, </a>
+<a name="27516"><span class="lineNum">   27516 </span>            :         int *k, </a>
+<a name="27517"><span class="lineNum">   27517 </span>            :         float *a, </a>
+<a name="27518"><span class="lineNum">   27518 </span>            :         int *lda, </a>
+<a name="27519"><span class="lineNum">   27519 </span>            :         float *tau, </a>
+<a name="27520"><span class="lineNum">   27520 </span>            :         float *work, </a>
+<a name="27521"><span class="lineNum">   27521 </span>            :         int *lwork, </a>
+<a name="27522"><span class="lineNum">   27522 </span>            :         int *info)</a>
+<a name="27523"><span class="lineNum">   27523 </span>            : {</a>
+<a name="27524"><span class="lineNum">   27524 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="27525"><span class="lineNum">   27525 </span>            : </a>
+<a name="27526"><span class="lineNum">   27526 </span>            :     int i__, j, l, ib, nb, ki, kk, nx, iws, nbmin, iinfo;</a>
+<a name="27527"><span class="lineNum">   27527 </span>            :     int ldwork, lwkopt;</a>
+<a name="27528"><span class="lineNum">   27528 </span>            :     int lquery;</a>
+<a name="27529"><span class="lineNum">   27529 </span>            :  </a>
+<a name="27530"><span class="lineNum">   27530 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27531"><span class="lineNum">   27531 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27532"><span class="lineNum">   27532 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27533"><span class="lineNum">   27533 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="27534"><span class="lineNum">   27534 </span>            :     --work;</a>
+<a name="27535"><span class="lineNum">   27535 </span>            : </a>
+<a name="27536"><span class="lineNum">   27536 </span>            :     ki = 0;</a>
+<a name="27537"><span class="lineNum">   27537 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27538"><span class="lineNum">   27538 </span>            :     nb = DORGQR_BLOCKSIZE;</a>
+<a name="27539"><span class="lineNum">   27539 </span><span class="lineNoCov">          0 :     lwkopt = (*n) * nb;</span></a>
+<a name="27540"><span class="lineNum">   27540 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="27541"><span class="lineNum">   27541 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="27542"><span class="lineNum">   27542 </span><span class="lineNoCov">          0 :     if (*m &lt; 0) {</span></a>
+<a name="27543"><span class="lineNum">   27543 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="27544"><span class="lineNum">   27544 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0 || *n &gt; *m) {</span></a>
+<a name="27545"><span class="lineNum">   27545 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="27546"><span class="lineNum">   27546 </span><span class="lineNoCov">          0 :     } else if (*k &lt; 0 || *k &gt; *n) {</span></a>
+<a name="27547"><span class="lineNum">   27547 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="27548"><span class="lineNum">   27548 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; (*m)) {</span></a>
+<a name="27549"><span class="lineNum">   27549 </span><span class="lineNoCov">          0 :         *info = -5;</span></a>
+<a name="27550"><span class="lineNum">   27550 </span><span class="lineNoCov">          0 :     } else if (*lwork &lt; (*n) &amp;&amp; ! lquery) {</span></a>
+<a name="27551"><span class="lineNum">   27551 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="27552"><span class="lineNum">   27552 </span>            :     }</a>
+<a name="27553"><span class="lineNum">   27553 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="27554"><span class="lineNum">   27554 </span>            :         i__1 = -(*info);</a>
+<a name="27555"><span class="lineNum">   27555 </span>            :         return;</a>
+<a name="27556"><span class="lineNum">   27556 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="27557"><span class="lineNum">   27557 </span>            :         return;</a>
+<a name="27558"><span class="lineNum">   27558 </span>            :     }</a>
+<a name="27559"><span class="lineNum">   27559 </span>            : </a>
+<a name="27560"><span class="lineNum">   27560 </span><span class="lineNoCov">          0 :     if (*n &lt;= 0) {</span></a>
+<a name="27561"><span class="lineNum">   27561 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="27562"><span class="lineNum">   27562 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="27563"><span class="lineNum">   27563 </span>            :     }</a>
+<a name="27564"><span class="lineNum">   27564 </span>            : </a>
+<a name="27565"><span class="lineNum">   27565 </span>            :     nbmin = 2;</a>
+<a name="27566"><span class="lineNum">   27566 </span>            :     nx = 0;</a>
+<a name="27567"><span class="lineNum">   27567 </span>            :     iws = *n;</a>
+<a name="27568"><span class="lineNum">   27568 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="27569"><span class="lineNum">   27569 </span>            : </a>
+<a name="27570"><span class="lineNum">   27570 </span>            :         nx = DORGQR_CROSSOVER;</a>
+<a name="27571"><span class="lineNum">   27571 </span><span class="lineNoCov">          0 :         if (nx &lt; *k) {</span></a>
+<a name="27572"><span class="lineNum">   27572 </span>            : </a>
+<a name="27573"><span class="lineNum">   27573 </span><span class="lineNoCov">          0 :             ldwork = *n;</span></a>
+<a name="27574"><span class="lineNum">   27574 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="27575"><span class="lineNum">   27575 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="27576"><span class="lineNum">   27576 </span>            : </a>
+<a name="27577"><span class="lineNum">   27577 </span><span class="lineNoCov">          0 :                 nb = *lwork / ldwork;</span></a>
+<a name="27578"><span class="lineNum">   27578 </span>            :                 nbmin = DORGQR_MINBLOCKSIZE;</a>
+<a name="27579"><span class="lineNum">   27579 </span>            :             }</a>
+<a name="27580"><span class="lineNum">   27580 </span>            :         }</a>
+<a name="27581"><span class="lineNum">   27581 </span>            :     }</a>
+<a name="27582"><span class="lineNum">   27582 </span>            : </a>
+<a name="27583"><span class="lineNum">   27583 </span><span class="lineNoCov">          0 :     if (nb &gt;= nbmin &amp;&amp; nb &lt; *k &amp;&amp; nx &lt; *k) {</span></a>
+<a name="27584"><span class="lineNum">   27584 </span>            : </a>
+<a name="27585"><span class="lineNum">   27585 </span><span class="lineNoCov">          0 :         ki = (*k - nx - 1) / nb * nb;</span></a>
+<a name="27586"><span class="lineNum">   27586 </span><span class="lineNoCov">          0 :         i__1 = *k, i__2 = ki + nb;</span></a>
+<a name="27587"><span class="lineNum">   27587 </span>            :         kk = (i__1&lt;i__2) ? i__1 : i__2;</a>
+<a name="27588"><span class="lineNum">   27588 </span>            : </a>
+<a name="27589"><span class="lineNum">   27589 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="27590"><span class="lineNum">   27590 </span><span class="lineNoCov">          0 :         for (j = kk + 1; j &lt;= i__1; ++j) {</span></a>
+<a name="27591"><span class="lineNum">   27591 </span><span class="lineNoCov">          0 :             i__2 = kk;</span></a>
+<a name="27592"><span class="lineNum">   27592 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="27593"><span class="lineNum">   27593 </span><span class="lineNoCov">          0 :                 a[i__ + j * a_dim1] = 0.;</span></a>
+<a name="27594"><span class="lineNum">   27594 </span>            :             }</a>
+<a name="27595"><span class="lineNum">   27595 </span>            :         }</a>
+<a name="27596"><span class="lineNum">   27596 </span>            :     } else {</a>
+<a name="27597"><span class="lineNum">   27597 </span>            :         kk = 0;</a>
+<a name="27598"><span class="lineNum">   27598 </span>            :     }</a>
+<a name="27599"><span class="lineNum">   27599 </span>            : </a>
+<a name="27600"><span class="lineNum">   27600 </span><span class="lineNoCov">          0 :     if (kk &lt; *n) {</span></a>
+<a name="27601"><span class="lineNum">   27601 </span><span class="lineNoCov">          0 :         i__1 = *m - kk;</span></a>
+<a name="27602"><span class="lineNum">   27602 </span><span class="lineNoCov">          0 :         i__2 = *n - kk;</span></a>
+<a name="27603"><span class="lineNum">   27603 </span><span class="lineNoCov">          0 :         i__3 = *k - kk;</span></a>
+<a name="27604"><span class="lineNum">   27604 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorg2r,SORG2R)(&amp;i__1, &amp;i__2, &amp;i__3, &amp;a[kk + 1 + (kk + 1) * a_dim1], lda, &amp;</span></a>
+<a name="27605"><span class="lineNum">   27605 </span><span class="lineNoCov">          0 :                 tau[kk + 1], &amp;work[1], &amp;iinfo);</span></a>
+<a name="27606"><span class="lineNum">   27606 </span>            :     }</a>
+<a name="27607"><span class="lineNum">   27607 </span>            : </a>
+<a name="27608"><span class="lineNum">   27608 </span><span class="lineNoCov">          0 :     if (kk &gt; 0) {</span></a>
+<a name="27609"><span class="lineNum">   27609 </span>            : </a>
+<a name="27610"><span class="lineNum">   27610 </span><span class="lineNoCov">          0 :         i__1 = -nb;</span></a>
+<a name="27611"><span class="lineNum">   27611 </span><span class="lineNoCov">          0 :         for (i__ = ki + 1; i__1 &lt; 0 ? i__ &gt;= 1 : i__ &lt;= 1; i__ += i__1) {</span></a>
+<a name="27612"><span class="lineNum">   27612 </span><span class="lineNoCov">          0 :             i__2 = nb, i__3 = *k - i__ + 1;</span></a>
+<a name="27613"><span class="lineNum">   27613 </span><span class="lineNoCov">          0 :             ib = (i__2&lt;i__3) ? i__2 : i__3;</span></a>
+<a name="27614"><span class="lineNum">   27614 </span><span class="lineNoCov">          0 :             if (i__ + ib &lt;= *n) {</span></a>
+<a name="27615"><span class="lineNum">   27615 </span>            : </a>
+<a name="27616"><span class="lineNum">   27616 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="27617"><span class="lineNum">   27617 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__2, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="27618"><span class="lineNum">   27618 </span><span class="lineNoCov">          0 :                         a_dim1], lda, &amp;tau[i__], &amp;work[1], &amp;ldwork);</span></a>
+<a name="27619"><span class="lineNum">   27619 </span>            : </a>
+<a name="27620"><span class="lineNum">   27620 </span><span class="lineNoCov">          0 :                 i__2 = *m - i__ + 1;</span></a>
+<a name="27621"><span class="lineNum">   27621 </span><span class="lineNoCov">          0 :                 i__3 = *n - i__ - ib + 1;</span></a>
+<a name="27622"><span class="lineNum">   27622 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(&quot;Left&quot;, &quot;No transpose&quot;, &quot;Forward&quot;, &quot;Columnwise&quot;, &amp;</span></a>
+<a name="27623"><span class="lineNum">   27623 </span>            :                         i__2, &amp;i__3, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;work[</a>
+<a name="27624"><span class="lineNum">   27624 </span><span class="lineNoCov">          0 :                         1], &amp;ldwork, &amp;a[i__ + (i__ + ib) * a_dim1], lda, &amp;</span></a>
+<a name="27625"><span class="lineNum">   27625 </span><span class="lineNoCov">          0 :                         work[ib + 1], &amp;ldwork);</span></a>
+<a name="27626"><span class="lineNum">   27626 </span>            :             }</a>
+<a name="27627"><span class="lineNum">   27627 </span>            : </a>
+<a name="27628"><span class="lineNum">   27628 </span><span class="lineNoCov">          0 :             i__2 = *m - i__ + 1;</span></a>
+<a name="27629"><span class="lineNum">   27629 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sorg2r,SORG2R)(&amp;i__2, &amp;ib, &amp;ib, &amp;a[i__ + i__ * a_dim1], lda, &amp;tau[i__], &amp;</span></a>
+<a name="27630"><span class="lineNum">   27630 </span>            :                     work[1], &amp;iinfo);</a>
+<a name="27631"><span class="lineNum">   27631 </span>            : </a>
+<a name="27632"><span class="lineNum">   27632 </span><span class="lineNoCov">          0 :             i__2 = i__ + ib - 1;</span></a>
+<a name="27633"><span class="lineNum">   27633 </span><span class="lineNoCov">          0 :             for (j = i__; j &lt;= i__2; ++j) {</span></a>
+<a name="27634"><span class="lineNum">   27634 </span><span class="lineNoCov">          0 :                 i__3 = i__ - 1;</span></a>
+<a name="27635"><span class="lineNum">   27635 </span><span class="lineNoCov">          0 :                 for (l = 1; l &lt;= i__3; ++l) {</span></a>
+<a name="27636"><span class="lineNum">   27636 </span><span class="lineNoCov">          0 :                     a[l + j * a_dim1] = 0.;</span></a>
+<a name="27637"><span class="lineNum">   27637 </span>            :                 }</a>
+<a name="27638"><span class="lineNum">   27638 </span>            :             }</a>
+<a name="27639"><span class="lineNum">   27639 </span>            :         }</a>
+<a name="27640"><span class="lineNum">   27640 </span>            :     }</a>
+<a name="27641"><span class="lineNum">   27641 </span>            : </a>
+<a name="27642"><span class="lineNum">   27642 </span><span class="lineNoCov">          0 :     work[1] = (float) iws;</span></a>
+<a name="27643"><span class="lineNum">   27643 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="27644"><span class="lineNum">   27644 </span>            : </a>
+<a name="27645"><span class="lineNum">   27645 </span>            : } </a>
+<a name="27646"><span class="lineNum">   27646 </span>            : }</a>
+<a name="27647"><span class="lineNum">   27647 </span>            : }</a>
+<a name="27648"><span class="lineNum">   27648 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27649"><span class="lineNum">   27649 </span>            : </a>
+<a name="27650"><span class="lineNum">   27650 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27651"><span class="lineNum">   27651 </span>            : namespace PLMD{</a>
+<a name="27652"><span class="lineNum">   27652 </span>            : namespace lapack{</a>
+<a name="27653"><span class="lineNum">   27653 </span>            : using namespace blas;</a>
+<a name="27654"><span class="lineNum">   27654 </span>            : void</a>
+<a name="27655"><span class="lineNum">   27655 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorm2l,SORM2L)(const char *side, </span></a>
+<a name="27656"><span class="lineNum">   27656 </span>            :         const char *trans, </a>
+<a name="27657"><span class="lineNum">   27657 </span>            :         int *m, </a>
+<a name="27658"><span class="lineNum">   27658 </span>            :         int *n, </a>
+<a name="27659"><span class="lineNum">   27659 </span>            :         int *k, </a>
+<a name="27660"><span class="lineNum">   27660 </span>            :         float *a,</a>
+<a name="27661"><span class="lineNum">   27661 </span>            :         int *lda, </a>
+<a name="27662"><span class="lineNum">   27662 </span>            :         float *tau,</a>
+<a name="27663"><span class="lineNum">   27663 </span>            :         float *c__,</a>
+<a name="27664"><span class="lineNum">   27664 </span>            :         int *ldc, </a>
+<a name="27665"><span class="lineNum">   27665 </span>            :         float *work, </a>
+<a name="27666"><span class="lineNum">   27666 </span>            :         int *info)</a>
+<a name="27667"><span class="lineNum">   27667 </span>            : {</a>
+<a name="27668"><span class="lineNum">   27668 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2;</a>
+<a name="27669"><span class="lineNum">   27669 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="27670"><span class="lineNum">   27670 </span>            : </a>
+<a name="27671"><span class="lineNum">   27671 </span>            :     int i__, i1, i2, i3, mi, ni, nq;</a>
+<a name="27672"><span class="lineNum">   27672 </span>            :     float aii;</a>
+<a name="27673"><span class="lineNum">   27673 </span>            :     int left;</a>
+<a name="27674"><span class="lineNum">   27674 </span>            :     int notran;</a>
+<a name="27675"><span class="lineNum">   27675 </span>            : </a>
+<a name="27676"><span class="lineNum">   27676 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27677"><span class="lineNum">   27677 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27678"><span class="lineNum">   27678 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27679"><span class="lineNum">   27679 </span>            :     --tau;</a>
+<a name="27680"><span class="lineNum">   27680 </span>            :     c_dim1 = *ldc;</a>
+<a name="27681"><span class="lineNum">   27681 </span>            :     c_offset = 1 + c_dim1;</a>
+<a name="27682"><span class="lineNum">   27682 </span>            :     c__ -= c_offset;</a>
+<a name="27683"><span class="lineNum">   27683 </span>            :     --work;</a>
+<a name="27684"><span class="lineNum">   27684 </span>            : </a>
+<a name="27685"><span class="lineNum">   27685 </span>            :     /* Function Body */</a>
+<a name="27686"><span class="lineNum">   27686 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27687"><span class="lineNum">   27687 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="27688"><span class="lineNum">   27688 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="27689"><span class="lineNum">   27689 </span>            : </a>
+<a name="27690"><span class="lineNum">   27690 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="27691"><span class="lineNum">   27691 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="27692"><span class="lineNum">   27692 </span>            :     } else {</a>
+<a name="27693"><span class="lineNum">   27693 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="27694"><span class="lineNum">   27694 </span>            :     }</a>
+<a name="27695"><span class="lineNum">   27695 </span>            :     if (*info != 0) {</a>
+<a name="27696"><span class="lineNum">   27696 </span>            :         return;</a>
+<a name="27697"><span class="lineNum">   27697 </span>            :     }</a>
+<a name="27698"><span class="lineNum">   27698 </span>            : </a>
+<a name="27699"><span class="lineNum">   27699 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="27700"><span class="lineNum">   27700 </span>            :         return;</a>
+<a name="27701"><span class="lineNum">   27701 </span>            :     }</a>
+<a name="27702"><span class="lineNum">   27702 </span>            : </a>
+<a name="27703"><span class="lineNum">   27703 </span><span class="lineNoCov">          0 :     if ((left &amp;&amp; notran) || (! left &amp;&amp; ! notran)) {</span></a>
+<a name="27704"><span class="lineNum">   27704 </span>            :         i1 = 1;</a>
+<a name="27705"><span class="lineNum">   27705 </span>            :         i2 = *k;</a>
+<a name="27706"><span class="lineNum">   27706 </span>            :         i3 = 1;</a>
+<a name="27707"><span class="lineNum">   27707 </span>            :     } else {</a>
+<a name="27708"><span class="lineNum">   27708 </span>            :         i1 = *k;</a>
+<a name="27709"><span class="lineNum">   27709 </span>            :         i2 = 1;</a>
+<a name="27710"><span class="lineNum">   27710 </span>            :         i3 = -1;</a>
+<a name="27711"><span class="lineNum">   27711 </span>            :     }</a>
+<a name="27712"><span class="lineNum">   27712 </span>            : </a>
+<a name="27713"><span class="lineNum">   27713 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="27714"><span class="lineNum">   27714 </span><span class="lineNoCov">          0 :         ni = *n;</span></a>
+<a name="27715"><span class="lineNum">   27715 </span>            :     } else {</a>
+<a name="27716"><span class="lineNum">   27716 </span><span class="lineNoCov">          0 :         mi = *m;</span></a>
+<a name="27717"><span class="lineNum">   27717 </span>            :     }</a>
+<a name="27718"><span class="lineNum">   27718 </span>            : </a>
+<a name="27719"><span class="lineNum">   27719 </span>            :     i__1 = i2;</a>
+<a name="27720"><span class="lineNum">   27720 </span>            :     i__2 = i3;</a>
+<a name="27721"><span class="lineNum">   27721 </span><span class="lineNoCov">          0 :     for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="27722"><span class="lineNum">   27722 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="27723"><span class="lineNum">   27723 </span>            : </a>
+<a name="27724"><span class="lineNum">   27724 </span><span class="lineNoCov">          0 :             mi = *m - *k + i__;</span></a>
+<a name="27725"><span class="lineNum">   27725 </span>            :         } else {</a>
+<a name="27726"><span class="lineNum">   27726 </span>            : </a>
+<a name="27727"><span class="lineNum">   27727 </span><span class="lineNoCov">          0 :             ni = *n - *k + i__;</span></a>
+<a name="27728"><span class="lineNum">   27728 </span>            :         }</a>
+<a name="27729"><span class="lineNum">   27729 </span>            : </a>
+<a name="27730"><span class="lineNum">   27730 </span><span class="lineNoCov">          0 :         aii = a[nq - *k + i__ + i__ * a_dim1];</span></a>
+<a name="27731"><span class="lineNum">   27731 </span><span class="lineNoCov">          0 :         a[nq - *k + i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="27732"><span class="lineNum">   27732 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarf,SLARF)(side, &amp;mi, &amp;ni, &amp;a[i__ * a_dim1 + 1], &amp;c__1, &amp;tau[i__], &amp;c__[</span></a>
+<a name="27733"><span class="lineNum">   27733 </span>            :                 c_offset], ldc, &amp;work[1]);</a>
+<a name="27734"><span class="lineNum">   27734 </span><span class="lineNoCov">          0 :         a[nq - *k + i__ + i__ * a_dim1] = aii;</span></a>
+<a name="27735"><span class="lineNum">   27735 </span>            :     }</a>
+<a name="27736"><span class="lineNum">   27736 </span>            :     return;</a>
+<a name="27737"><span class="lineNum">   27737 </span>            : }</a>
+<a name="27738"><span class="lineNum">   27738 </span>            : }</a>
+<a name="27739"><span class="lineNum">   27739 </span>            : }</a>
+<a name="27740"><span class="lineNum">   27740 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27741"><span class="lineNum">   27741 </span>            : </a>
+<a name="27742"><span class="lineNum">   27742 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27743"><span class="lineNum">   27743 </span>            : namespace PLMD{</a>
+<a name="27744"><span class="lineNum">   27744 </span>            : namespace lapack{</a>
+<a name="27745"><span class="lineNum">   27745 </span>            : using namespace blas;</a>
+<a name="27746"><span class="lineNum">   27746 </span>            : void </a>
+<a name="27747"><span class="lineNum">   27747 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorm2r,SORM2R)(const char *side, </span></a>
+<a name="27748"><span class="lineNum">   27748 </span>            :         const char *trans, </a>
+<a name="27749"><span class="lineNum">   27749 </span>            :         int *m, </a>
+<a name="27750"><span class="lineNum">   27750 </span>            :         int *n, </a>
+<a name="27751"><span class="lineNum">   27751 </span>            :         int *k, </a>
+<a name="27752"><span class="lineNum">   27752 </span>            :         float *a, </a>
+<a name="27753"><span class="lineNum">   27753 </span>            :         int *lda, </a>
+<a name="27754"><span class="lineNum">   27754 </span>            :         float *tau, </a>
+<a name="27755"><span class="lineNum">   27755 </span>            :         float *c__, </a>
+<a name="27756"><span class="lineNum">   27756 </span>            :         int *ldc, </a>
+<a name="27757"><span class="lineNum">   27757 </span>            :         float *work, </a>
+<a name="27758"><span class="lineNum">   27758 </span>            :         int *info)</a>
+<a name="27759"><span class="lineNum">   27759 </span>            : {</a>
+<a name="27760"><span class="lineNum">   27760 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2;</a>
+<a name="27761"><span class="lineNum">   27761 </span>            : </a>
+<a name="27762"><span class="lineNum">   27762 </span>            :     int i__, i1, i2, i3, ic, jc, mi, ni;</a>
+<a name="27763"><span class="lineNum">   27763 </span>            :     float aii;</a>
+<a name="27764"><span class="lineNum">   27764 </span>            :     int left;</a>
+<a name="27765"><span class="lineNum">   27765 </span>            :     int notran;</a>
+<a name="27766"><span class="lineNum">   27766 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="27767"><span class="lineNum">   27767 </span>            : </a>
+<a name="27768"><span class="lineNum">   27768 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27769"><span class="lineNum">   27769 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27770"><span class="lineNum">   27770 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27771"><span class="lineNum">   27771 </span>            :     --tau;</a>
+<a name="27772"><span class="lineNum">   27772 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="27773"><span class="lineNum">   27773 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="27774"><span class="lineNum">   27774 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="27775"><span class="lineNum">   27775 </span>            :     --work;</a>
+<a name="27776"><span class="lineNum">   27776 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27777"><span class="lineNum">   27777 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="27778"><span class="lineNum">   27778 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="27779"><span class="lineNum">   27779 </span>            : </a>
+<a name="27780"><span class="lineNum">   27780 </span>            :     ic = jc = 0;</a>
+<a name="27781"><span class="lineNum">   27781 </span>            : </a>
+<a name="27782"><span class="lineNum">   27782 </span><span class="lineNoCov">          0 :     if (*m &lt;= 0 || *n &lt;= 0 || *k &lt;= 0) {</span></a>
+<a name="27783"><span class="lineNum">   27783 </span>            :         return;</a>
+<a name="27784"><span class="lineNum">   27784 </span>            :     }</a>
+<a name="27785"><span class="lineNum">   27785 </span>            : </a>
+<a name="27786"><span class="lineNum">   27786 </span><span class="lineNoCov">          0 :     if ((left &amp;&amp; !notran) || (!left &amp;&amp; notran)) {</span></a>
+<a name="27787"><span class="lineNum">   27787 </span>            :         i1 = 1;</a>
+<a name="27788"><span class="lineNum">   27788 </span>            :         i2 = *k;</a>
+<a name="27789"><span class="lineNum">   27789 </span>            :         i3 = 1;</a>
+<a name="27790"><span class="lineNum">   27790 </span>            :     } else {</a>
+<a name="27791"><span class="lineNum">   27791 </span>            :         i1 = *k;</a>
+<a name="27792"><span class="lineNum">   27792 </span>            :         i2 = 1;</a>
+<a name="27793"><span class="lineNum">   27793 </span>            :         i3 = -1;</a>
+<a name="27794"><span class="lineNum">   27794 </span>            :     }</a>
+<a name="27795"><span class="lineNum">   27795 </span>            : </a>
+<a name="27796"><span class="lineNum">   27796 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="27797"><span class="lineNum">   27797 </span><span class="lineNoCov">          0 :         ni = *n;</span></a>
+<a name="27798"><span class="lineNum">   27798 </span>            :         jc = 1;</a>
+<a name="27799"><span class="lineNum">   27799 </span>            :     } else {</a>
+<a name="27800"><span class="lineNum">   27800 </span><span class="lineNoCov">          0 :         mi = *m;</span></a>
+<a name="27801"><span class="lineNum">   27801 </span>            :         ic = 1;</a>
+<a name="27802"><span class="lineNum">   27802 </span>            :     }</a>
+<a name="27803"><span class="lineNum">   27803 </span>            : </a>
+<a name="27804"><span class="lineNum">   27804 </span>            :     i__1 = i2;</a>
+<a name="27805"><span class="lineNum">   27805 </span>            :     i__2 = i3;</a>
+<a name="27806"><span class="lineNum">   27806 </span><span class="lineNoCov">          0 :     for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="27807"><span class="lineNum">   27807 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="27808"><span class="lineNum">   27808 </span>            : </a>
+<a name="27809"><span class="lineNum">   27809 </span><span class="lineNoCov">          0 :             mi = *m - i__ + 1;</span></a>
+<a name="27810"><span class="lineNum">   27810 </span>            :             ic = i__;</a>
+<a name="27811"><span class="lineNum">   27811 </span>            :         } else {</a>
+<a name="27812"><span class="lineNum">   27812 </span>            : </a>
+<a name="27813"><span class="lineNum">   27813 </span><span class="lineNoCov">          0 :             ni = *n - i__ + 1;</span></a>
+<a name="27814"><span class="lineNum">   27814 </span>            :             jc = i__;</a>
+<a name="27815"><span class="lineNum">   27815 </span>            :         }</a>
+<a name="27816"><span class="lineNum">   27816 </span>            : </a>
+<a name="27817"><span class="lineNum">   27817 </span>            : </a>
+<a name="27818"><span class="lineNum">   27818 </span><span class="lineNoCov">          0 :         aii = a[i__ + i__ * a_dim1];</span></a>
+<a name="27819"><span class="lineNum">   27819 </span><span class="lineNoCov">          0 :         a[i__ + i__ * a_dim1] = 1.;</span></a>
+<a name="27820"><span class="lineNum">   27820 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarf,SLARF)(side, &amp;mi, &amp;ni, &amp;a[i__ + i__ * a_dim1], &amp;c__1, &amp;tau[i__], &amp;c__[</span></a>
+<a name="27821"><span class="lineNum">   27821 </span><span class="lineNoCov">          0 :                 ic + jc * c_dim1], ldc, &amp;work[1]);</span></a>
+<a name="27822"><span class="lineNum">   27822 </span><span class="lineNoCov">          0 :         a[i__ + i__ * a_dim1] = aii;</span></a>
+<a name="27823"><span class="lineNum">   27823 </span>            :     }</a>
+<a name="27824"><span class="lineNum">   27824 </span>            :     return;</a>
+<a name="27825"><span class="lineNum">   27825 </span>            : </a>
+<a name="27826"><span class="lineNum">   27826 </span>            : } </a>
+<a name="27827"><span class="lineNum">   27827 </span>            : }</a>
+<a name="27828"><span class="lineNum">   27828 </span>            : }</a>
+<a name="27829"><span class="lineNum">   27829 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27830"><span class="lineNum">   27830 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="27831"><span class="lineNum">   27831 </span>            : </a>
+<a name="27832"><span class="lineNum">   27832 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27833"><span class="lineNum">   27833 </span>            : namespace PLMD{</a>
+<a name="27834"><span class="lineNum">   27834 </span>            : namespace lapack{</a>
+<a name="27835"><span class="lineNum">   27835 </span>            : using namespace blas;</a>
+<a name="27836"><span class="lineNum">   27836 </span>            : void </a>
+<a name="27837"><span class="lineNum">   27837 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sormbr,SORMBR)(const char *vect, </span></a>
+<a name="27838"><span class="lineNum">   27838 </span>            :         const char *side, </a>
+<a name="27839"><span class="lineNum">   27839 </span>            :         const char *trans, </a>
+<a name="27840"><span class="lineNum">   27840 </span>            :         int *m, </a>
+<a name="27841"><span class="lineNum">   27841 </span>            :         int *n, </a>
+<a name="27842"><span class="lineNum">   27842 </span>            :         int *k, </a>
+<a name="27843"><span class="lineNum">   27843 </span>            :         float *a, </a>
+<a name="27844"><span class="lineNum">   27844 </span>            :         int *lda, </a>
+<a name="27845"><span class="lineNum">   27845 </span>            :         float *tau, </a>
+<a name="27846"><span class="lineNum">   27846 </span>            :         float *c__, </a>
+<a name="27847"><span class="lineNum">   27847 </span>            :         int *ldc, </a>
+<a name="27848"><span class="lineNum">   27848 </span>            :         float *work, </a>
+<a name="27849"><span class="lineNum">   27849 </span>            :         int *lwork, </a>
+<a name="27850"><span class="lineNum">   27850 </span>            :         int *info)</a>
+<a name="27851"><span class="lineNum">   27851 </span>            : {</a>
+<a name="27852"><span class="lineNum">   27852 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1;</a>
+<a name="27853"><span class="lineNum">   27853 </span>            :  </a>
+<a name="27854"><span class="lineNum">   27854 </span>            : </a>
+<a name="27855"><span class="lineNum">   27855 </span>            :     int i1, i2, nb, mi, ni, nq, nw;</a>
+<a name="27856"><span class="lineNum">   27856 </span>            :     int left;</a>
+<a name="27857"><span class="lineNum">   27857 </span>            :     int iinfo;</a>
+<a name="27858"><span class="lineNum">   27858 </span>            :     int notran;</a>
+<a name="27859"><span class="lineNum">   27859 </span>            :     int applyq;</a>
+<a name="27860"><span class="lineNum">   27860 </span>            :     char transt[1];</a>
+<a name="27861"><span class="lineNum">   27861 </span>            :     int lwkopt;</a>
+<a name="27862"><span class="lineNum">   27862 </span>            :     int lquery;</a>
+<a name="27863"><span class="lineNum">   27863 </span>            : </a>
+<a name="27864"><span class="lineNum">   27864 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="27865"><span class="lineNum">   27865 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="27866"><span class="lineNum">   27866 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="27867"><span class="lineNum">   27867 </span>            :     --tau;</a>
+<a name="27868"><span class="lineNum">   27868 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="27869"><span class="lineNum">   27869 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="27870"><span class="lineNum">   27870 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="27871"><span class="lineNum">   27871 </span>            :     --work;</a>
+<a name="27872"><span class="lineNum">   27872 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="27873"><span class="lineNum">   27873 </span><span class="lineNoCov">          0 :     applyq = (*vect=='Q' || *vect=='q');</span></a>
+<a name="27874"><span class="lineNum">   27874 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="27875"><span class="lineNum">   27875 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="27876"><span class="lineNum">   27876 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="27877"><span class="lineNum">   27877 </span>            : </a>
+<a name="27878"><span class="lineNum">   27878 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="27879"><span class="lineNum">   27879 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="27880"><span class="lineNum">   27880 </span><span class="lineNoCov">          0 :         nw = *n;</span></a>
+<a name="27881"><span class="lineNum">   27881 </span>            :     } else {</a>
+<a name="27882"><span class="lineNum">   27882 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="27883"><span class="lineNum">   27883 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="27884"><span class="lineNum">   27884 </span>            :     }</a>
+<a name="27885"><span class="lineNum">   27885 </span>            : </a>
+<a name="27886"><span class="lineNum">   27886 </span>            :     nb = DORMQR_BLOCKSIZE;</a>
+<a name="27887"><span class="lineNum">   27887 </span><span class="lineNoCov">          0 :     lwkopt = nw * nb;</span></a>
+<a name="27888"><span class="lineNum">   27888 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="27889"><span class="lineNum">   27889 </span>            :     </a>
+<a name="27890"><span class="lineNum">   27890 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="27891"><span class="lineNum">   27891 </span>            :         i__1 = -(*info);</a>
+<a name="27892"><span class="lineNum">   27892 </span>            :         return;</a>
+<a name="27893"><span class="lineNum">   27893 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="27894"><span class="lineNum">   27894 </span>            :         return;</a>
+<a name="27895"><span class="lineNum">   27895 </span>            :     }</a>
+<a name="27896"><span class="lineNum">   27896 </span>            : </a>
+<a name="27897"><span class="lineNum">   27897 </span><span class="lineNoCov">          0 :     work[1] = 1.;</span></a>
+<a name="27898"><span class="lineNum">   27898 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0) {</span></a>
+<a name="27899"><span class="lineNum">   27899 </span>            :         return;</a>
+<a name="27900"><span class="lineNum">   27900 </span>            :     }</a>
+<a name="27901"><span class="lineNum">   27901 </span>            : </a>
+<a name="27902"><span class="lineNum">   27902 </span><span class="lineNoCov">          0 :     if (applyq) {</span></a>
+<a name="27903"><span class="lineNum">   27903 </span>            : </a>
+<a name="27904"><span class="lineNum">   27904 </span><span class="lineNoCov">          0 :         if (nq &gt;= *k) {</span></a>
+<a name="27905"><span class="lineNum">   27905 </span>            : </a>
+<a name="27906"><span class="lineNum">   27906 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sormqr,SORMQR)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="27907"><span class="lineNum">   27907 </span>            :                     c_offset], ldc, &amp;work[1], lwork, &amp;iinfo);</a>
+<a name="27908"><span class="lineNum">   27908 </span><span class="lineNoCov">          0 :         } else if (nq &gt; 1) {</span></a>
+<a name="27909"><span class="lineNum">   27909 </span>            : </a>
+<a name="27910"><span class="lineNum">   27910 </span><span class="lineNoCov">          0 :             if (left) {</span></a>
+<a name="27911"><span class="lineNum">   27911 </span><span class="lineNoCov">          0 :                 mi = *m - 1;</span></a>
+<a name="27912"><span class="lineNum">   27912 </span><span class="lineNoCov">          0 :                 ni = *n;</span></a>
+<a name="27913"><span class="lineNum">   27913 </span>            :                 i1 = 2;</a>
+<a name="27914"><span class="lineNum">   27914 </span>            :                 i2 = 1;</a>
+<a name="27915"><span class="lineNum">   27915 </span>            :             } else {</a>
+<a name="27916"><span class="lineNum">   27916 </span><span class="lineNoCov">          0 :                 mi = *m;</span></a>
+<a name="27917"><span class="lineNum">   27917 </span><span class="lineNoCov">          0 :                 ni = *n - 1;</span></a>
+<a name="27918"><span class="lineNum">   27918 </span>            :                 i1 = 1;</a>
+<a name="27919"><span class="lineNum">   27919 </span>            :                 i2 = 2;</a>
+<a name="27920"><span class="lineNum">   27920 </span>            :             }</a>
+<a name="27921"><span class="lineNum">   27921 </span><span class="lineNoCov">          0 :             i__1 = nq - 1;</span></a>
+<a name="27922"><span class="lineNum">   27922 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sormqr,SORMQR)(side, trans, &amp;mi, &amp;ni, &amp;i__1, &amp;a[a_dim1 + 2], lda, &amp;tau[1]</span></a>
+<a name="27923"><span class="lineNum">   27923 </span><span class="lineNoCov">          0 :                     , &amp;c__[i1 + i2 * c_dim1], ldc, &amp;work[1], lwork, &amp;iinfo);</span></a>
+<a name="27924"><span class="lineNum">   27924 </span>            :         }</a>
+<a name="27925"><span class="lineNum">   27925 </span>            :     } else {</a>
+<a name="27926"><span class="lineNum">   27926 </span>            : </a>
+<a name="27927"><span class="lineNum">   27927 </span><span class="lineNoCov">          0 :         if (notran) {</span></a>
+<a name="27928"><span class="lineNum">   27928 </span><span class="lineNoCov">          0 :             *(unsigned char *)transt = 'T';</span></a>
+<a name="27929"><span class="lineNum">   27929 </span>            :         } else {</a>
+<a name="27930"><span class="lineNum">   27930 </span><span class="lineNoCov">          0 :             *(unsigned char *)transt = 'N';</span></a>
+<a name="27931"><span class="lineNum">   27931 </span>            :         }</a>
+<a name="27932"><span class="lineNum">   27932 </span><span class="lineNoCov">          0 :         if (nq &gt; *k) {</span></a>
+<a name="27933"><span class="lineNum">   27933 </span>            : </a>
+<a name="27934"><span class="lineNum">   27934 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sormlq,SORMLQ)(side, transt, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="27935"><span class="lineNum">   27935 </span>            :                     c_offset], ldc, &amp;work[1], lwork, &amp;iinfo);</a>
+<a name="27936"><span class="lineNum">   27936 </span><span class="lineNoCov">          0 :         } else if (nq &gt; 1) {</span></a>
+<a name="27937"><span class="lineNum">   27937 </span>            : </a>
+<a name="27938"><span class="lineNum">   27938 </span><span class="lineNoCov">          0 :             if (left) {</span></a>
+<a name="27939"><span class="lineNum">   27939 </span><span class="lineNoCov">          0 :                 mi = *m - 1;</span></a>
+<a name="27940"><span class="lineNum">   27940 </span><span class="lineNoCov">          0 :                 ni = *n;</span></a>
+<a name="27941"><span class="lineNum">   27941 </span>            :                 i1 = 2;</a>
+<a name="27942"><span class="lineNum">   27942 </span>            :                 i2 = 1;</a>
+<a name="27943"><span class="lineNum">   27943 </span>            :             } else {</a>
+<a name="27944"><span class="lineNum">   27944 </span><span class="lineNoCov">          0 :                 mi = *m;</span></a>
+<a name="27945"><span class="lineNum">   27945 </span><span class="lineNoCov">          0 :                 ni = *n - 1;</span></a>
+<a name="27946"><span class="lineNum">   27946 </span>            :                 i1 = 1;</a>
+<a name="27947"><span class="lineNum">   27947 </span>            :                 i2 = 2;</a>
+<a name="27948"><span class="lineNum">   27948 </span>            :             }</a>
+<a name="27949"><span class="lineNum">   27949 </span><span class="lineNoCov">          0 :             i__1 = nq - 1;</span></a>
+<a name="27950"><span class="lineNum">   27950 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sormlq,SORMLQ)(side, transt, &amp;mi, &amp;ni, &amp;i__1, &amp;a[(a_dim1 &lt;&lt; 1) + 1], lda,</span></a>
+<a name="27951"><span class="lineNum">   27951 </span><span class="lineNoCov">          0 :                      &amp;tau[1], &amp;c__[i1 + i2 * c_dim1], ldc, &amp;work[1], lwork, &amp;</span></a>
+<a name="27952"><span class="lineNum">   27952 </span>            :                     iinfo);</a>
+<a name="27953"><span class="lineNum">   27953 </span>            :         }</a>
+<a name="27954"><span class="lineNum">   27954 </span>            :     }</a>
+<a name="27955"><span class="lineNum">   27955 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="27956"><span class="lineNum">   27956 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="27957"><span class="lineNum">   27957 </span>            : </a>
+<a name="27958"><span class="lineNum">   27958 </span>            : </a>
+<a name="27959"><span class="lineNum">   27959 </span>            : }</a>
+<a name="27960"><span class="lineNum">   27960 </span>            : </a>
+<a name="27961"><span class="lineNum">   27961 </span>            : </a>
+<a name="27962"><span class="lineNum">   27962 </span>            : }</a>
+<a name="27963"><span class="lineNum">   27963 </span>            : }</a>
+<a name="27964"><span class="lineNum">   27964 </span>            : #include &lt;cctype&gt;</a>
+<a name="27965"><span class="lineNum">   27965 </span>            : #include &quot;real.h&quot;</a>
+<a name="27966"><span class="lineNum">   27966 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="27967"><span class="lineNum">   27967 </span>            : </a>
+<a name="27968"><span class="lineNum">   27968 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="27969"><span class="lineNum">   27969 </span>            : namespace PLMD{</a>
+<a name="27970"><span class="lineNum">   27970 </span>            : namespace lapack{</a>
+<a name="27971"><span class="lineNum">   27971 </span>            : using namespace blas;</a>
+<a name="27972"><span class="lineNum">   27972 </span>            : void</a>
+<a name="27973"><span class="lineNum">   27973 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sorml2,SORML2)(const char *side,</span></a>
+<a name="27974"><span class="lineNum">   27974 </span>            :                         const char *trans,</a>
+<a name="27975"><span class="lineNum">   27975 </span>            :                         int *m,</a>
+<a name="27976"><span class="lineNum">   27976 </span>            :                         int *n,</a>
+<a name="27977"><span class="lineNum">   27977 </span>            :                         int *k,</a>
+<a name="27978"><span class="lineNum">   27978 </span>            :                         float *a,</a>
+<a name="27979"><span class="lineNum">   27979 </span>            :                         int *lda,</a>
+<a name="27980"><span class="lineNum">   27980 </span>            :                         float *tau,</a>
+<a name="27981"><span class="lineNum">   27981 </span>            :                         float *c,</a>
+<a name="27982"><span class="lineNum">   27982 </span>            :                         int *ldc,</a>
+<a name="27983"><span class="lineNum">   27983 </span>            :                         float *work,</a>
+<a name="27984"><span class="lineNum">   27984 </span>            :                         int *info)</a>
+<a name="27985"><span class="lineNum">   27985 </span>            : {</a>
+<a name="27986"><span class="lineNum">   27986 </span><span class="lineNoCov">          0 :   const char xside=std::toupper(*side);</span></a>
+<a name="27987"><span class="lineNum">   27987 </span><span class="lineNoCov">          0 :   const char xtrans=std::toupper(*trans);</span></a>
+<a name="27988"><span class="lineNum">   27988 </span>            :   int i,i1,i2,i3,ni,mi,ic,jc;</a>
+<a name="27989"><span class="lineNum">   27989 </span>            :   float aii;</a>
+<a name="27990"><span class="lineNum">   27990 </span>            : </a>
+<a name="27991"><span class="lineNum">   27991 </span><span class="lineNoCov">          0 :   if(*m&lt;=0 || *n&lt;=0 || *k&lt;=0)</span></a>
+<a name="27992"><span class="lineNum">   27992 </span>            :     return;</a>
+<a name="27993"><span class="lineNum">   27993 </span>            : </a>
+<a name="27994"><span class="lineNum">   27994 </span>            :   ic = jc = 0;</a>
+<a name="27995"><span class="lineNum">   27995 </span>            : </a>
+<a name="27996"><span class="lineNum">   27996 </span><span class="lineNoCov">          0 :   if((xside=='L' &amp;&amp; xtrans=='N') || (xside!='L' &amp;&amp; xtrans!='N')) {</span></a>
+<a name="27997"><span class="lineNum">   27997 </span>            :     i1 = 0;</a>
+<a name="27998"><span class="lineNum">   27998 </span>            :     i2 = *k;</a>
+<a name="27999"><span class="lineNum">   27999 </span>            :     i3 = 1;</a>
+<a name="28000"><span class="lineNum">   28000 </span>            :   } else {</a>
+<a name="28001"><span class="lineNum">   28001 </span><span class="lineNoCov">          0 :     i1 = *k-1;</span></a>
+<a name="28002"><span class="lineNum">   28002 </span>            :     i2 = -1;</a>
+<a name="28003"><span class="lineNum">   28003 </span>            :     i3 = -1;</a>
+<a name="28004"><span class="lineNum">   28004 </span>            :   }</a>
+<a name="28005"><span class="lineNum">   28005 </span>            :   </a>
+<a name="28006"><span class="lineNum">   28006 </span><span class="lineNoCov">          0 :   if(xside=='L') {</span></a>
+<a name="28007"><span class="lineNum">   28007 </span><span class="lineNoCov">          0 :     ni = *n;</span></a>
+<a name="28008"><span class="lineNum">   28008 </span>            :     jc = 0;</a>
+<a name="28009"><span class="lineNum">   28009 </span>            :   } else {</a>
+<a name="28010"><span class="lineNum">   28010 </span><span class="lineNoCov">          0 :     mi = *m;</span></a>
+<a name="28011"><span class="lineNum">   28011 </span>            :     ic = 0;</a>
+<a name="28012"><span class="lineNum">   28012 </span>            :   }</a>
+<a name="28013"><span class="lineNum">   28013 </span>            : </a>
+<a name="28014"><span class="lineNum">   28014 </span><span class="lineNoCov">          0 :   for(i=i1;i!=i2;i+=i3) {</span></a>
+<a name="28015"><span class="lineNum">   28015 </span><span class="lineNoCov">          0 :     if(xside=='L') {</span></a>
+<a name="28016"><span class="lineNum">   28016 </span><span class="lineNoCov">          0 :       mi = *m - i;</span></a>
+<a name="28017"><span class="lineNum">   28017 </span>            :       ic = i;</a>
+<a name="28018"><span class="lineNum">   28018 </span>            :     } else {</a>
+<a name="28019"><span class="lineNum">   28019 </span><span class="lineNoCov">          0 :       ni = *n - i;</span></a>
+<a name="28020"><span class="lineNum">   28020 </span>            :       jc = i;</a>
+<a name="28021"><span class="lineNum">   28021 </span>            :     }</a>
+<a name="28022"><span class="lineNum">   28022 </span><span class="lineNoCov">          0 :     aii = a[i*(*lda)+i];</span></a>
+<a name="28023"><span class="lineNum">   28023 </span><span class="lineNoCov">          0 :     a[i*(*lda)+i] = 1.0;</span></a>
+<a name="28024"><span class="lineNum">   28024 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slarf,SLARF)(side,&amp;mi,&amp;ni,&amp;(a[i*(*lda)+i]),lda,tau+i,</span></a>
+<a name="28025"><span class="lineNum">   28025 </span><span class="lineNoCov">          0 :            &amp;(c[jc*(*ldc)+ic]),ldc,work);</span></a>
+<a name="28026"><span class="lineNum">   28026 </span><span class="lineNoCov">          0 :     a[i*(*lda)+i] = aii;</span></a>
+<a name="28027"><span class="lineNum">   28027 </span>            :   }</a>
+<a name="28028"><span class="lineNum">   28028 </span>            :   return;</a>
+<a name="28029"><span class="lineNum">   28029 </span>            : }</a>
+<a name="28030"><span class="lineNum">   28030 </span>            :              </a>
+<a name="28031"><span class="lineNum">   28031 </span>            : }</a>
+<a name="28032"><span class="lineNum">   28032 </span>            : }</a>
+<a name="28033"><span class="lineNum">   28033 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="28034"><span class="lineNum">   28034 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="28035"><span class="lineNum">   28035 </span>            : </a>
+<a name="28036"><span class="lineNum">   28036 </span>            : </a>
+<a name="28037"><span class="lineNum">   28037 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="28038"><span class="lineNum">   28038 </span>            : namespace PLMD{</a>
+<a name="28039"><span class="lineNum">   28039 </span>            : namespace lapack{</a>
+<a name="28040"><span class="lineNum">   28040 </span>            : using namespace blas;</a>
+<a name="28041"><span class="lineNum">   28041 </span>            : void </a>
+<a name="28042"><span class="lineNum">   28042 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sormlq,SORMLQ)(const char *side, </span></a>
+<a name="28043"><span class="lineNum">   28043 </span>            :         const char *trans,</a>
+<a name="28044"><span class="lineNum">   28044 </span>            :         int *m, </a>
+<a name="28045"><span class="lineNum">   28045 </span>            :         int *n, </a>
+<a name="28046"><span class="lineNum">   28046 </span>            :         int *k,</a>
+<a name="28047"><span class="lineNum">   28047 </span>            :         float *a,</a>
+<a name="28048"><span class="lineNum">   28048 </span>            :         int *lda, </a>
+<a name="28049"><span class="lineNum">   28049 </span>            :         float *tau, </a>
+<a name="28050"><span class="lineNum">   28050 </span>            :         float *c__, </a>
+<a name="28051"><span class="lineNum">   28051 </span>            :         int *ldc, </a>
+<a name="28052"><span class="lineNum">   28052 </span>            :         float *work, </a>
+<a name="28053"><span class="lineNum">   28053 </span>            :         int *lwork, </a>
+<a name="28054"><span class="lineNum">   28054 </span>            :         int *info)</a>
+<a name="28055"><span class="lineNum">   28055 </span>            : {</a>
+<a name="28056"><span class="lineNum">   28056 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2, i__4, </a>
+<a name="28057"><span class="lineNum">   28057 </span>            :             i__5;</a>
+<a name="28058"><span class="lineNum">   28058 </span>            :   </a>
+<a name="28059"><span class="lineNum">   28059 </span>            : </a>
+<a name="28060"><span class="lineNum">   28060 </span>            :     int i__;</a>
+<a name="28061"><span class="lineNum">   28061 </span>            :     float t[4160]       /* was [65][64] */;</a>
+<a name="28062"><span class="lineNum">   28062 </span>            :     int i1, i2, i3, ib, ic, jc, nb, mi, ni, nq, nw, iws;</a>
+<a name="28063"><span class="lineNum">   28063 </span>            :     int left;</a>
+<a name="28064"><span class="lineNum">   28064 </span>            :     int nbmin, iinfo;</a>
+<a name="28065"><span class="lineNum">   28065 </span>            :     int notran;</a>
+<a name="28066"><span class="lineNum">   28066 </span>            :     int ldwork;</a>
+<a name="28067"><span class="lineNum">   28067 </span>            :     char transt[1];</a>
+<a name="28068"><span class="lineNum">   28068 </span>            :     int lwkopt;</a>
+<a name="28069"><span class="lineNum">   28069 </span>            :     int lquery;</a>
+<a name="28070"><span class="lineNum">   28070 </span><span class="lineNoCov">          0 :     int ldt = 65;</span></a>
+<a name="28071"><span class="lineNum">   28071 </span>            : </a>
+<a name="28072"><span class="lineNum">   28072 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="28073"><span class="lineNum">   28073 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="28074"><span class="lineNum">   28074 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="28075"><span class="lineNum">   28075 </span>            :     --tau;</a>
+<a name="28076"><span class="lineNum">   28076 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="28077"><span class="lineNum">   28077 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="28078"><span class="lineNum">   28078 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="28079"><span class="lineNum">   28079 </span>            :     --work;</a>
+<a name="28080"><span class="lineNum">   28080 </span>            : </a>
+<a name="28081"><span class="lineNum">   28081 </span>            :     ic = jc = 0;</a>
+<a name="28082"><span class="lineNum">   28082 </span>            : </a>
+<a name="28083"><span class="lineNum">   28083 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28084"><span class="lineNum">   28084 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="28085"><span class="lineNum">   28085 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="28086"><span class="lineNum">   28086 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="28087"><span class="lineNum">   28087 </span>            : </a>
+<a name="28088"><span class="lineNum">   28088 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="28089"><span class="lineNum">   28089 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="28090"><span class="lineNum">   28090 </span><span class="lineNoCov">          0 :         nw = *n;</span></a>
+<a name="28091"><span class="lineNum">   28091 </span>            :     } else {</a>
+<a name="28092"><span class="lineNum">   28092 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="28093"><span class="lineNum">   28093 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="28094"><span class="lineNum">   28094 </span>            :     }</a>
+<a name="28095"><span class="lineNum">   28095 </span>            : </a>
+<a name="28096"><span class="lineNum">   28096 </span>            :     nb = DORMLQ_BLOCKSIZE;</a>
+<a name="28097"><span class="lineNum">   28097 </span><span class="lineNoCov">          0 :     lwkopt = nw * nb;</span></a>
+<a name="28098"><span class="lineNum">   28098 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28099"><span class="lineNum">   28099 </span>            :     </a>
+<a name="28100"><span class="lineNum">   28100 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="28101"><span class="lineNum">   28101 </span>            :         return;</a>
+<a name="28102"><span class="lineNum">   28102 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="28103"><span class="lineNum">   28103 </span>            :         return;</a>
+<a name="28104"><span class="lineNum">   28104 </span>            :     }</a>
+<a name="28105"><span class="lineNum">   28105 </span>            : </a>
+<a name="28106"><span class="lineNum">   28106 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="28107"><span class="lineNum">   28107 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="28108"><span class="lineNum">   28108 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="28109"><span class="lineNum">   28109 </span>            :     }</a>
+<a name="28110"><span class="lineNum">   28110 </span>            : </a>
+<a name="28111"><span class="lineNum">   28111 </span>            :     nbmin = 2;</a>
+<a name="28112"><span class="lineNum">   28112 </span><span class="lineNoCov">          0 :     ldwork = nw;</span></a>
+<a name="28113"><span class="lineNum">   28113 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="28114"><span class="lineNum">   28114 </span>            :         iws = nw * nb;</a>
+<a name="28115"><span class="lineNum">   28115 </span><span class="lineNoCov">          0 :         if (*lwork &lt; iws) {</span></a>
+<a name="28116"><span class="lineNum">   28116 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="28117"><span class="lineNum">   28117 </span>            :             nbmin = DORMLQ_MINBLOCKSIZE;</a>
+<a name="28118"><span class="lineNum">   28118 </span>            :         }</a>
+<a name="28119"><span class="lineNum">   28119 </span>            :     }</a>
+<a name="28120"><span class="lineNum">   28120 </span>            : </a>
+<a name="28121"><span class="lineNum">   28121 </span><span class="lineNoCov">          0 :     if (nb &lt; nbmin || nb &gt;= *k) {</span></a>
+<a name="28122"><span class="lineNum">   28122 </span>            : </a>
+<a name="28123"><span class="lineNum">   28123 </span>            : </a>
+<a name="28124"><span class="lineNum">   28124 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorml2,SORML2)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="28125"><span class="lineNum">   28125 </span>            :                 c_offset], ldc, &amp;work[1], &amp;iinfo);</a>
+<a name="28126"><span class="lineNum">   28126 </span>            :     } else {</a>
+<a name="28127"><span class="lineNum">   28127 </span>            : </a>
+<a name="28128"><span class="lineNum">   28128 </span><span class="lineNoCov">          0 :         if ((left &amp;&amp; notran) || (!left &amp;&amp; !notran)) {</span></a>
+<a name="28129"><span class="lineNum">   28129 </span>            :             i1 = 1;</a>
+<a name="28130"><span class="lineNum">   28130 </span>            :             i2 = *k;</a>
+<a name="28131"><span class="lineNum">   28131 </span>            :             i3 = nb;</a>
+<a name="28132"><span class="lineNum">   28132 </span>            :         } else {</a>
+<a name="28133"><span class="lineNum">   28133 </span><span class="lineNoCov">          0 :             i1 = (*k - 1) / nb * nb + 1;</span></a>
+<a name="28134"><span class="lineNum">   28134 </span>            :             i2 = 1;</a>
+<a name="28135"><span class="lineNum">   28135 </span><span class="lineNoCov">          0 :             i3 = -nb;</span></a>
+<a name="28136"><span class="lineNum">   28136 </span>            :         }</a>
+<a name="28137"><span class="lineNum">   28137 </span>            : </a>
+<a name="28138"><span class="lineNum">   28138 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="28139"><span class="lineNum">   28139 </span><span class="lineNoCov">          0 :             ni = *n;</span></a>
+<a name="28140"><span class="lineNum">   28140 </span>            :             jc = 1;</a>
+<a name="28141"><span class="lineNum">   28141 </span>            :         } else {</a>
+<a name="28142"><span class="lineNum">   28142 </span><span class="lineNoCov">          0 :             mi = *m;</span></a>
+<a name="28143"><span class="lineNum">   28143 </span>            :             ic = 1;</a>
+<a name="28144"><span class="lineNum">   28144 </span>            :         }</a>
+<a name="28145"><span class="lineNum">   28145 </span>            : </a>
+<a name="28146"><span class="lineNum">   28146 </span><span class="lineNoCov">          0 :         if (notran) {</span></a>
+<a name="28147"><span class="lineNum">   28147 </span><span class="lineNoCov">          0 :             *(unsigned char *)transt = 'T';</span></a>
+<a name="28148"><span class="lineNum">   28148 </span>            :         } else {</a>
+<a name="28149"><span class="lineNum">   28149 </span><span class="lineNoCov">          0 :             *(unsigned char *)transt = 'N';</span></a>
+<a name="28150"><span class="lineNum">   28150 </span>            :         }</a>
+<a name="28151"><span class="lineNum">   28151 </span>            : </a>
+<a name="28152"><span class="lineNum">   28152 </span>            :         i__1 = i2;</a>
+<a name="28153"><span class="lineNum">   28153 </span>            :         i__2 = i3;</a>
+<a name="28154"><span class="lineNum">   28154 </span><span class="lineNoCov">          0 :         for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="28155"><span class="lineNum">   28155 </span><span class="lineNoCov">          0 :             i__4 = nb, i__5 = *k - i__ + 1;</span></a>
+<a name="28156"><span class="lineNum">   28156 </span><span class="lineNoCov">          0 :             ib = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="28157"><span class="lineNum">   28157 </span>            : </a>
+<a name="28158"><span class="lineNum">   28158 </span><span class="lineNoCov">          0 :             i__4 = nq - i__ + 1;</span></a>
+<a name="28159"><span class="lineNum">   28159 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Forward&quot;, &quot;Rowwise&quot;, &amp;i__4, &amp;ib, &amp;a[i__ + i__ * a_dim1], </span></a>
+<a name="28160"><span class="lineNum">   28160 </span><span class="lineNoCov">          0 :                     lda, &amp;tau[i__], t, &amp;ldt);</span></a>
+<a name="28161"><span class="lineNum">   28161 </span><span class="lineNoCov">          0 :             if (left) {</span></a>
+<a name="28162"><span class="lineNum">   28162 </span>            : </a>
+<a name="28163"><span class="lineNum">   28163 </span><span class="lineNoCov">          0 :                 mi = *m - i__ + 1;</span></a>
+<a name="28164"><span class="lineNum">   28164 </span>            :                 ic = i__;</a>
+<a name="28165"><span class="lineNum">   28165 </span>            :             } else {</a>
+<a name="28166"><span class="lineNum">   28166 </span>            : </a>
+<a name="28167"><span class="lineNum">   28167 </span><span class="lineNoCov">          0 :                 ni = *n - i__ + 1;</span></a>
+<a name="28168"><span class="lineNum">   28168 </span>            :                 jc = i__;</a>
+<a name="28169"><span class="lineNum">   28169 </span>            :             }</a>
+<a name="28170"><span class="lineNum">   28170 </span>            : </a>
+<a name="28171"><span class="lineNum">   28171 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(side, transt, &quot;Forward&quot;, &quot;Rowwise&quot;, &amp;mi, &amp;ni, &amp;ib, &amp;a[i__ </span></a>
+<a name="28172"><span class="lineNum">   28172 </span><span class="lineNoCov">          0 :                     + i__ * a_dim1], lda, t, &amp;ldt, &amp;c__[ic + jc * c_dim1], </span></a>
+<a name="28173"><span class="lineNum">   28173 </span>            :                     ldc, &amp;work[1], &amp;ldwork);</a>
+<a name="28174"><span class="lineNum">   28174 </span>            :         }</a>
+<a name="28175"><span class="lineNum">   28175 </span>            :     }</a>
+<a name="28176"><span class="lineNum">   28176 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28177"><span class="lineNum">   28177 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="28178"><span class="lineNum">   28178 </span>            : </a>
+<a name="28179"><span class="lineNum">   28179 </span>            : }</a>
+<a name="28180"><span class="lineNum">   28180 </span>            : </a>
+<a name="28181"><span class="lineNum">   28181 </span>            : </a>
+<a name="28182"><span class="lineNum">   28182 </span>            : }</a>
+<a name="28183"><span class="lineNum">   28183 </span>            : }</a>
+<a name="28184"><span class="lineNum">   28184 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="28185"><span class="lineNum">   28185 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="28186"><span class="lineNum">   28186 </span>            : </a>
+<a name="28187"><span class="lineNum">   28187 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="28188"><span class="lineNum">   28188 </span>            : namespace PLMD{</a>
+<a name="28189"><span class="lineNum">   28189 </span>            : namespace lapack{</a>
+<a name="28190"><span class="lineNum">   28190 </span>            : using namespace blas;</a>
+<a name="28191"><span class="lineNum">   28191 </span>            : void</a>
+<a name="28192"><span class="lineNum">   28192 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sormql,SORMQL)(const char *side, const char *trans, int *m, int *n, </span></a>
+<a name="28193"><span class="lineNum">   28193 </span>            :         int *k, float *a, int *lda, float *tau, float *</a>
+<a name="28194"><span class="lineNum">   28194 </span>            :         c__, int *ldc, float *work, int *lwork, int *info)</a>
+<a name="28195"><span class="lineNum">   28195 </span>            : {</a>
+<a name="28196"><span class="lineNum">   28196 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2, i__4, i__5;</a>
+<a name="28197"><span class="lineNum">   28197 </span><span class="lineNoCov">          0 :     int c__65 = 65;</span></a>
+<a name="28198"><span class="lineNum">   28198 </span>            : </a>
+<a name="28199"><span class="lineNum">   28199 </span>            :     int i__;</a>
+<a name="28200"><span class="lineNum">   28200 </span>            :     float t[4160];</a>
+<a name="28201"><span class="lineNum">   28201 </span>            :     int i1, i2, i3, ib, nb, mi, ni, nq, nw, iws;</a>
+<a name="28202"><span class="lineNum">   28202 </span>            :     int left;</a>
+<a name="28203"><span class="lineNum">   28203 </span>            :     int nbmin, iinfo;</a>
+<a name="28204"><span class="lineNum">   28204 </span>            :     int notran;</a>
+<a name="28205"><span class="lineNum">   28205 </span>            :     int ldwork, lwkopt;</a>
+<a name="28206"><span class="lineNum">   28206 </span>            :     int lquery;</a>
+<a name="28207"><span class="lineNum">   28207 </span>            : </a>
+<a name="28208"><span class="lineNum">   28208 </span>            : </a>
+<a name="28209"><span class="lineNum">   28209 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="28210"><span class="lineNum">   28210 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="28211"><span class="lineNum">   28211 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="28212"><span class="lineNum">   28212 </span>            :     --tau;</a>
+<a name="28213"><span class="lineNum">   28213 </span>            :     c_dim1 = *ldc;</a>
+<a name="28214"><span class="lineNum">   28214 </span>            :     c_offset = 1 + c_dim1;</a>
+<a name="28215"><span class="lineNum">   28215 </span>            :     c__ -= c_offset;</a>
+<a name="28216"><span class="lineNum">   28216 </span>            :     --work;</a>
+<a name="28217"><span class="lineNum">   28217 </span>            : </a>
+<a name="28218"><span class="lineNum">   28218 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28219"><span class="lineNum">   28219 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="28220"><span class="lineNum">   28220 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="28221"><span class="lineNum">   28221 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="28222"><span class="lineNum">   28222 </span>            : </a>
+<a name="28223"><span class="lineNum">   28223 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="28224"><span class="lineNum">   28224 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="28225"><span class="lineNum">   28225 </span><span class="lineNoCov">          0 :         nw = *n;</span></a>
+<a name="28226"><span class="lineNum">   28226 </span>            :     } else {</a>
+<a name="28227"><span class="lineNum">   28227 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="28228"><span class="lineNum">   28228 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="28229"><span class="lineNum">   28229 </span>            :     }</a>
+<a name="28230"><span class="lineNum">   28230 </span>            : </a>
+<a name="28231"><span class="lineNum">   28231 </span>            :     nb = DORMQL_BLOCKSIZE;</a>
+<a name="28232"><span class="lineNum">   28232 </span><span class="lineNoCov">          0 :     lwkopt = nw * nb;</span></a>
+<a name="28233"><span class="lineNum">   28233 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28234"><span class="lineNum">   28234 </span>            :     </a>
+<a name="28235"><span class="lineNum">   28235 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="28236"><span class="lineNum">   28236 </span>            :         return;</a>
+<a name="28237"><span class="lineNum">   28237 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="28238"><span class="lineNum">   28238 </span>            :         return;</a>
+<a name="28239"><span class="lineNum">   28239 </span>            :     }</a>
+<a name="28240"><span class="lineNum">   28240 </span>            : </a>
+<a name="28241"><span class="lineNum">   28241 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="28242"><span class="lineNum">   28242 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="28243"><span class="lineNum">   28243 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="28244"><span class="lineNum">   28244 </span>            :     }</a>
+<a name="28245"><span class="lineNum">   28245 </span>            : </a>
+<a name="28246"><span class="lineNum">   28246 </span>            :     nbmin = 2;</a>
+<a name="28247"><span class="lineNum">   28247 </span><span class="lineNoCov">          0 :     ldwork = nw;</span></a>
+<a name="28248"><span class="lineNum">   28248 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="28249"><span class="lineNum">   28249 </span>            :         iws = nw * nb;</a>
+<a name="28250"><span class="lineNum">   28250 </span><span class="lineNoCov">          0 :         if (*lwork &lt; iws) {</span></a>
+<a name="28251"><span class="lineNum">   28251 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="28252"><span class="lineNum">   28252 </span>            :             nbmin = DORMQL_MINBLOCKSIZE;</a>
+<a name="28253"><span class="lineNum">   28253 </span>            :         }</a>
+<a name="28254"><span class="lineNum">   28254 </span>            :     }</a>
+<a name="28255"><span class="lineNum">   28255 </span>            : </a>
+<a name="28256"><span class="lineNum">   28256 </span><span class="lineNoCov">          0 :     if (nb &lt; nbmin || nb &gt;= *k) {</span></a>
+<a name="28257"><span class="lineNum">   28257 </span>            : </a>
+<a name="28258"><span class="lineNum">   28258 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorm2l,SORM2L)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="28259"><span class="lineNum">   28259 </span>            :                 c_offset], ldc, &amp;work[1], &amp;iinfo);</a>
+<a name="28260"><span class="lineNum">   28260 </span>            :     } else {</a>
+<a name="28261"><span class="lineNum">   28261 </span>            : </a>
+<a name="28262"><span class="lineNum">   28262 </span><span class="lineNoCov">          0 :         if ((left &amp;&amp; notran) || (! left &amp;&amp; ! notran)) {</span></a>
+<a name="28263"><span class="lineNum">   28263 </span>            :             i1 = 1;</a>
+<a name="28264"><span class="lineNum">   28264 </span>            :             i2 = *k;</a>
+<a name="28265"><span class="lineNum">   28265 </span>            :             i3 = nb;</a>
+<a name="28266"><span class="lineNum">   28266 </span>            :         } else {</a>
+<a name="28267"><span class="lineNum">   28267 </span><span class="lineNoCov">          0 :             i1 = (*k - 1) / nb * nb + 1;</span></a>
+<a name="28268"><span class="lineNum">   28268 </span>            :             i2 = 1;</a>
+<a name="28269"><span class="lineNum">   28269 </span><span class="lineNoCov">          0 :             i3 = -nb;</span></a>
+<a name="28270"><span class="lineNum">   28270 </span>            :         }</a>
+<a name="28271"><span class="lineNum">   28271 </span>            : </a>
+<a name="28272"><span class="lineNum">   28272 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="28273"><span class="lineNum">   28273 </span><span class="lineNoCov">          0 :             ni = *n;</span></a>
+<a name="28274"><span class="lineNum">   28274 </span>            :         } else {</a>
+<a name="28275"><span class="lineNum">   28275 </span><span class="lineNoCov">          0 :             mi = *m;</span></a>
+<a name="28276"><span class="lineNum">   28276 </span>            :         }</a>
+<a name="28277"><span class="lineNum">   28277 </span>            : </a>
+<a name="28278"><span class="lineNum">   28278 </span>            :         i__1 = i2;</a>
+<a name="28279"><span class="lineNum">   28279 </span>            :         i__2 = i3;</a>
+<a name="28280"><span class="lineNum">   28280 </span><span class="lineNoCov">          0 :         for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="28281"><span class="lineNum">   28281 </span><span class="lineNoCov">          0 :             i__4 = nb, i__5 = *k - i__ + 1;</span></a>
+<a name="28282"><span class="lineNum">   28282 </span><span class="lineNoCov">          0 :             ib = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="28283"><span class="lineNum">   28283 </span>            : </a>
+<a name="28284"><span class="lineNum">   28284 </span><span class="lineNoCov">          0 :             i__4 = nq - *k + i__ + ib - 1;</span></a>
+<a name="28285"><span class="lineNum">   28285 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Backward&quot;, &quot;Columnwise&quot;, &amp;i__4, &amp;ib, &amp;a[i__ * a_dim1 + 1]</span></a>
+<a name="28286"><span class="lineNum">   28286 </span><span class="lineNoCov">          0 :                     , lda, &amp;tau[i__], t, &amp;c__65);</span></a>
+<a name="28287"><span class="lineNum">   28287 </span><span class="lineNoCov">          0 :             if (left) {</span></a>
+<a name="28288"><span class="lineNum">   28288 </span>            : </a>
+<a name="28289"><span class="lineNum">   28289 </span><span class="lineNoCov">          0 :                 mi = *m - *k + i__ + ib - 1;</span></a>
+<a name="28290"><span class="lineNum">   28290 </span>            :             } else {</a>
+<a name="28291"><span class="lineNum">   28291 </span>            : </a>
+<a name="28292"><span class="lineNum">   28292 </span><span class="lineNoCov">          0 :                 ni = *n - *k + i__ + ib - 1;</span></a>
+<a name="28293"><span class="lineNum">   28293 </span>            :             }</a>
+<a name="28294"><span class="lineNum">   28294 </span>            : </a>
+<a name="28295"><span class="lineNum">   28295 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(side, trans, &quot;Backward&quot;, &quot;Columnwise&quot;, &amp;mi, &amp;ni, &amp;ib, &amp;a[</span></a>
+<a name="28296"><span class="lineNum">   28296 </span>            :                     i__ * a_dim1 + 1], lda, t, &amp;c__65, &amp;c__[c_offset], ldc, &amp;</a>
+<a name="28297"><span class="lineNum">   28297 </span>            :                     work[1], &amp;ldwork);</a>
+<a name="28298"><span class="lineNum">   28298 </span>            :         }</a>
+<a name="28299"><span class="lineNum">   28299 </span>            :     }</a>
+<a name="28300"><span class="lineNum">   28300 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28301"><span class="lineNum">   28301 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="28302"><span class="lineNum">   28302 </span>            : </a>
+<a name="28303"><span class="lineNum">   28303 </span>            : }</a>
+<a name="28304"><span class="lineNum">   28304 </span>            : </a>
+<a name="28305"><span class="lineNum">   28305 </span>            : </a>
+<a name="28306"><span class="lineNum">   28306 </span>            : }</a>
+<a name="28307"><span class="lineNum">   28307 </span>            : }</a>
+<a name="28308"><span class="lineNum">   28308 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="28309"><span class="lineNum">   28309 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="28310"><span class="lineNum">   28310 </span>            : </a>
+<a name="28311"><span class="lineNum">   28311 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="28312"><span class="lineNum">   28312 </span>            : namespace PLMD{</a>
+<a name="28313"><span class="lineNum">   28313 </span>            : namespace lapack{</a>
+<a name="28314"><span class="lineNum">   28314 </span>            : using namespace blas;</a>
+<a name="28315"><span class="lineNum">   28315 </span>            : void </a>
+<a name="28316"><span class="lineNum">   28316 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sormqr,SORMQR)(const char *side, </span></a>
+<a name="28317"><span class="lineNum">   28317 </span>            :         const char *trans, </a>
+<a name="28318"><span class="lineNum">   28318 </span>            :         int *m, </a>
+<a name="28319"><span class="lineNum">   28319 </span>            :         int *n, </a>
+<a name="28320"><span class="lineNum">   28320 </span>            :         int *k, </a>
+<a name="28321"><span class="lineNum">   28321 </span>            :         float *a, </a>
+<a name="28322"><span class="lineNum">   28322 </span>            :         int *lda, </a>
+<a name="28323"><span class="lineNum">   28323 </span>            :         float *tau, </a>
+<a name="28324"><span class="lineNum">   28324 </span>            :         float *c__, </a>
+<a name="28325"><span class="lineNum">   28325 </span>            :         int *ldc, </a>
+<a name="28326"><span class="lineNum">   28326 </span>            :         float *work, </a>
+<a name="28327"><span class="lineNum">   28327 </span>            :         int *lwork, </a>
+<a name="28328"><span class="lineNum">   28328 </span>            :         int *info)</a>
+<a name="28329"><span class="lineNum">   28329 </span>            : {</a>
+<a name="28330"><span class="lineNum">   28330 </span>            :    int a_dim1, a_offset, c_dim1, c_offset, i__1, i__2, i__4, i__5;</a>
+<a name="28331"><span class="lineNum">   28331 </span>            : </a>
+<a name="28332"><span class="lineNum">   28332 </span>            :     int i__;</a>
+<a name="28333"><span class="lineNum">   28333 </span>            :     float t[4160];</a>
+<a name="28334"><span class="lineNum">   28334 </span>            :     int i1, i2, i3, ib, ic, jc, nb, mi, ni, nq, nw, iws;</a>
+<a name="28335"><span class="lineNum">   28335 </span>            :     int left;</a>
+<a name="28336"><span class="lineNum">   28336 </span>            :     int nbmin, iinfo;</a>
+<a name="28337"><span class="lineNum">   28337 </span>            :     int notran;</a>
+<a name="28338"><span class="lineNum">   28338 </span>            :     int ldwork, lwkopt;</a>
+<a name="28339"><span class="lineNum">   28339 </span>            :     int lquery;</a>
+<a name="28340"><span class="lineNum">   28340 </span><span class="lineNoCov">          0 :     int ldt = 65;</span></a>
+<a name="28341"><span class="lineNum">   28341 </span>            : </a>
+<a name="28342"><span class="lineNum">   28342 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="28343"><span class="lineNum">   28343 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="28344"><span class="lineNum">   28344 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="28345"><span class="lineNum">   28345 </span>            :     --tau;</a>
+<a name="28346"><span class="lineNum">   28346 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="28347"><span class="lineNum">   28347 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="28348"><span class="lineNum">   28348 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="28349"><span class="lineNum">   28349 </span>            :     --work;</a>
+<a name="28350"><span class="lineNum">   28350 </span>            : </a>
+<a name="28351"><span class="lineNum">   28351 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28352"><span class="lineNum">   28352 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="28353"><span class="lineNum">   28353 </span><span class="lineNoCov">          0 :     notran = (*trans=='N' || *trans=='n');</span></a>
+<a name="28354"><span class="lineNum">   28354 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="28355"><span class="lineNum">   28355 </span>            : </a>
+<a name="28356"><span class="lineNum">   28356 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="28357"><span class="lineNum">   28357 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="28358"><span class="lineNum">   28358 </span><span class="lineNoCov">          0 :         nw = *n;</span></a>
+<a name="28359"><span class="lineNum">   28359 </span>            :     } else {</a>
+<a name="28360"><span class="lineNum">   28360 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="28361"><span class="lineNum">   28361 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="28362"><span class="lineNum">   28362 </span>            :     }</a>
+<a name="28363"><span class="lineNum">   28363 </span>            : </a>
+<a name="28364"><span class="lineNum">   28364 </span>            :      ic = jc = 0;</a>
+<a name="28365"><span class="lineNum">   28365 </span>            :      nb = DORMQR_BLOCKSIZE;</a>
+<a name="28366"><span class="lineNum">   28366 </span><span class="lineNoCov">          0 :      lwkopt = nw * nb;</span></a>
+<a name="28367"><span class="lineNum">   28367 </span><span class="lineNoCov">          0 :      work[1] = (float) lwkopt;</span></a>
+<a name="28368"><span class="lineNum">   28368 </span>            : </a>
+<a name="28369"><span class="lineNum">   28369 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="28370"><span class="lineNum">   28370 </span>            :         return;</a>
+<a name="28371"><span class="lineNum">   28371 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="28372"><span class="lineNum">   28372 </span>            :       return;</a>
+<a name="28373"><span class="lineNum">   28373 </span>            :     }</a>
+<a name="28374"><span class="lineNum">   28374 </span>            : </a>
+<a name="28375"><span class="lineNum">   28375 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0 || *k == 0) {</span></a>
+<a name="28376"><span class="lineNum">   28376 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="28377"><span class="lineNum">   28377 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="28378"><span class="lineNum">   28378 </span>            :     }</a>
+<a name="28379"><span class="lineNum">   28379 </span>            : </a>
+<a name="28380"><span class="lineNum">   28380 </span>            :     nbmin = 2;</a>
+<a name="28381"><span class="lineNum">   28381 </span><span class="lineNoCov">          0 :     ldwork = nw;</span></a>
+<a name="28382"><span class="lineNum">   28382 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *k) {</span></a>
+<a name="28383"><span class="lineNum">   28383 </span>            :         iws = nw * nb;</a>
+<a name="28384"><span class="lineNum">   28384 </span><span class="lineNoCov">          0 :         if (*lwork &lt; iws) {</span></a>
+<a name="28385"><span class="lineNum">   28385 </span><span class="lineNoCov">          0 :             nb = *lwork / ldwork;</span></a>
+<a name="28386"><span class="lineNum">   28386 </span>            :             nbmin = DORMQR_MINBLOCKSIZE;</a>
+<a name="28387"><span class="lineNum">   28387 </span>            :         }</a>
+<a name="28388"><span class="lineNum">   28388 </span>            :     }</a>
+<a name="28389"><span class="lineNum">   28389 </span>            : </a>
+<a name="28390"><span class="lineNum">   28390 </span><span class="lineNoCov">          0 :     if (nb &lt; nbmin || nb &gt;= *k) {</span></a>
+<a name="28391"><span class="lineNum">   28391 </span>            : </a>
+<a name="28392"><span class="lineNum">   28392 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sorm2r,SORM2R)(side, trans, m, n, k, &amp;a[a_offset], lda, &amp;tau[1], &amp;c__[</span></a>
+<a name="28393"><span class="lineNum">   28393 </span>            :                 c_offset], ldc, &amp;work[1], &amp;iinfo);</a>
+<a name="28394"><span class="lineNum">   28394 </span>            :     } else {</a>
+<a name="28395"><span class="lineNum">   28395 </span>            : </a>
+<a name="28396"><span class="lineNum">   28396 </span><span class="lineNoCov">          0 :         if ((left &amp;&amp; !notran) || (!left &amp;&amp; notran)) {</span></a>
+<a name="28397"><span class="lineNum">   28397 </span>            :             i1 = 1;</a>
+<a name="28398"><span class="lineNum">   28398 </span>            :             i2 = *k;</a>
+<a name="28399"><span class="lineNum">   28399 </span>            :             i3 = nb;</a>
+<a name="28400"><span class="lineNum">   28400 </span>            :         } else {</a>
+<a name="28401"><span class="lineNum">   28401 </span><span class="lineNoCov">          0 :             i1 = (*k - 1) / nb * nb + 1;</span></a>
+<a name="28402"><span class="lineNum">   28402 </span>            :             i2 = 1;</a>
+<a name="28403"><span class="lineNum">   28403 </span><span class="lineNoCov">          0 :             i3 = -nb;</span></a>
+<a name="28404"><span class="lineNum">   28404 </span>            :         }</a>
+<a name="28405"><span class="lineNum">   28405 </span>            : </a>
+<a name="28406"><span class="lineNum">   28406 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="28407"><span class="lineNum">   28407 </span><span class="lineNoCov">          0 :             ni = *n;</span></a>
+<a name="28408"><span class="lineNum">   28408 </span>            :             jc = 1;</a>
+<a name="28409"><span class="lineNum">   28409 </span>            :         } else {</a>
+<a name="28410"><span class="lineNum">   28410 </span><span class="lineNoCov">          0 :             mi = *m;</span></a>
+<a name="28411"><span class="lineNum">   28411 </span>            :             ic = 1;</a>
+<a name="28412"><span class="lineNum">   28412 </span>            :         }</a>
+<a name="28413"><span class="lineNum">   28413 </span>            : </a>
+<a name="28414"><span class="lineNum">   28414 </span>            :         i__1 = i2;</a>
+<a name="28415"><span class="lineNum">   28415 </span>            :         i__2 = i3;</a>
+<a name="28416"><span class="lineNum">   28416 </span><span class="lineNoCov">          0 :         for (i__ = i1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += i__2) {</span></a>
+<a name="28417"><span class="lineNum">   28417 </span><span class="lineNoCov">          0 :             i__4 = nb, i__5 = *k - i__ + 1;</span></a>
+<a name="28418"><span class="lineNum">   28418 </span><span class="lineNoCov">          0 :             ib = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="28419"><span class="lineNum">   28419 </span>            : </a>
+<a name="28420"><span class="lineNum">   28420 </span><span class="lineNoCov">          0 :             i__4 = nq - i__ + 1;</span></a>
+<a name="28421"><span class="lineNum">   28421 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarft,SLARFT)(&quot;Forward&quot;, &quot;Columnwise&quot;, &amp;i__4, &amp;ib, &amp;a[i__ + i__ * </span></a>
+<a name="28422"><span class="lineNum">   28422 </span><span class="lineNoCov">          0 :                     a_dim1], lda, &amp;tau[i__], t, &amp;ldt);</span></a>
+<a name="28423"><span class="lineNum">   28423 </span><span class="lineNoCov">          0 :             if (left) {</span></a>
+<a name="28424"><span class="lineNum">   28424 </span>            : </a>
+<a name="28425"><span class="lineNum">   28425 </span><span class="lineNoCov">          0 :                 mi = *m - i__ + 1;</span></a>
+<a name="28426"><span class="lineNum">   28426 </span>            :                 ic = i__;</a>
+<a name="28427"><span class="lineNum">   28427 </span>            :             } else {</a>
+<a name="28428"><span class="lineNum">   28428 </span><span class="lineNoCov">          0 :                 ni = *n - i__ + 1;</span></a>
+<a name="28429"><span class="lineNum">   28429 </span>            :                 jc = i__;</a>
+<a name="28430"><span class="lineNum">   28430 </span>            :             }</a>
+<a name="28431"><span class="lineNum">   28431 </span>            : </a>
+<a name="28432"><span class="lineNum">   28432 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarfb,SLARFB)(side, trans, &quot;Forward&quot;, &quot;Columnwise&quot;, &amp;mi, &amp;ni, &amp;ib, &amp;a[</span></a>
+<a name="28433"><span class="lineNum">   28433 </span><span class="lineNoCov">          0 :                     i__ + i__ * a_dim1], lda, t, &amp;ldt, &amp;c__[ic + jc * </span></a>
+<a name="28434"><span class="lineNum">   28434 </span>            :                     c_dim1], ldc, &amp;work[1], &amp;ldwork);</a>
+<a name="28435"><span class="lineNum">   28435 </span>            :         }</a>
+<a name="28436"><span class="lineNum">   28436 </span>            :     }</a>
+<a name="28437"><span class="lineNum">   28437 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28438"><span class="lineNum">   28438 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="28439"><span class="lineNum">   28439 </span>            : </a>
+<a name="28440"><span class="lineNum">   28440 </span>            : </a>
+<a name="28441"><span class="lineNum">   28441 </span>            : }</a>
+<a name="28442"><span class="lineNum">   28442 </span>            : </a>
+<a name="28443"><span class="lineNum">   28443 </span>            : </a>
+<a name="28444"><span class="lineNum">   28444 </span>            : }</a>
+<a name="28445"><span class="lineNum">   28445 </span>            : }</a>
+<a name="28446"><span class="lineNum">   28446 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="28447"><span class="lineNum">   28447 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="28448"><span class="lineNum">   28448 </span>            : </a>
+<a name="28449"><span class="lineNum">   28449 </span>            : </a>
+<a name="28450"><span class="lineNum">   28450 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="28451"><span class="lineNum">   28451 </span>            : namespace PLMD{</a>
+<a name="28452"><span class="lineNum">   28452 </span>            : namespace lapack{</a>
+<a name="28453"><span class="lineNum">   28453 </span>            : using namespace blas;</a>
+<a name="28454"><span class="lineNum">   28454 </span>            : void</a>
+<a name="28455"><span class="lineNum">   28455 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sormtr,SORMTR)(const char *side, </span></a>
+<a name="28456"><span class="lineNum">   28456 </span>            :         const char *uplo,</a>
+<a name="28457"><span class="lineNum">   28457 </span>            :         const char *trans, </a>
+<a name="28458"><span class="lineNum">   28458 </span>            :         int *m, </a>
+<a name="28459"><span class="lineNum">   28459 </span>            :         int *n,</a>
+<a name="28460"><span class="lineNum">   28460 </span>            :         float *a, </a>
+<a name="28461"><span class="lineNum">   28461 </span>            :         int *lda, </a>
+<a name="28462"><span class="lineNum">   28462 </span>            :         float *tau, </a>
+<a name="28463"><span class="lineNum">   28463 </span>            :         float *c__, </a>
+<a name="28464"><span class="lineNum">   28464 </span>            :         int *ldc,</a>
+<a name="28465"><span class="lineNum">   28465 </span>            :         float *work, </a>
+<a name="28466"><span class="lineNum">   28466 </span>            :         int *lwork, </a>
+<a name="28467"><span class="lineNum">   28467 </span>            :         int *info)</a>
+<a name="28468"><span class="lineNum">   28468 </span>            : {</a>
+<a name="28469"><span class="lineNum">   28469 </span>            :     int a_dim1, a_offset, c_dim1, c_offset, i__2;</a>
+<a name="28470"><span class="lineNum">   28470 </span>            : </a>
+<a name="28471"><span class="lineNum">   28471 </span>            :     int i1, i2, nb, mi, ni, nq, nw;</a>
+<a name="28472"><span class="lineNum">   28472 </span>            :     int left;</a>
+<a name="28473"><span class="lineNum">   28473 </span>            :     int iinfo;</a>
+<a name="28474"><span class="lineNum">   28474 </span>            :     int upper;</a>
+<a name="28475"><span class="lineNum">   28475 </span>            :     int lwkopt;</a>
+<a name="28476"><span class="lineNum">   28476 </span>            :     int lquery;</a>
+<a name="28477"><span class="lineNum">   28477 </span>            : </a>
+<a name="28478"><span class="lineNum">   28478 </span>            : </a>
+<a name="28479"><span class="lineNum">   28479 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="28480"><span class="lineNum">   28480 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="28481"><span class="lineNum">   28481 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="28482"><span class="lineNum">   28482 </span>            :     --tau;</a>
+<a name="28483"><span class="lineNum">   28483 </span><span class="lineNoCov">          0 :     c_dim1 = *ldc;</span></a>
+<a name="28484"><span class="lineNum">   28484 </span><span class="lineNoCov">          0 :     c_offset = 1 + c_dim1;</span></a>
+<a name="28485"><span class="lineNum">   28485 </span><span class="lineNoCov">          0 :     c__ -= c_offset;</span></a>
+<a name="28486"><span class="lineNum">   28486 </span>            :     --work;</a>
+<a name="28487"><span class="lineNum">   28487 </span>            : </a>
+<a name="28488"><span class="lineNum">   28488 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28489"><span class="lineNum">   28489 </span><span class="lineNoCov">          0 :     left = (*side=='L' || *side=='l');</span></a>
+<a name="28490"><span class="lineNum">   28490 </span><span class="lineNoCov">          0 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="28491"><span class="lineNum">   28491 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1;</span></a>
+<a name="28492"><span class="lineNum">   28492 </span>            : </a>
+<a name="28493"><span class="lineNum">   28493 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="28494"><span class="lineNum">   28494 </span><span class="lineNoCov">          0 :         nq = *m;</span></a>
+<a name="28495"><span class="lineNum">   28495 </span><span class="lineNoCov">          0 :         nw = *n;</span></a>
+<a name="28496"><span class="lineNum">   28496 </span>            :     } else {</a>
+<a name="28497"><span class="lineNum">   28497 </span><span class="lineNoCov">          0 :         nq = *n;</span></a>
+<a name="28498"><span class="lineNum">   28498 </span><span class="lineNoCov">          0 :         nw = *m;</span></a>
+<a name="28499"><span class="lineNum">   28499 </span>            :     }</a>
+<a name="28500"><span class="lineNum">   28500 </span>            : </a>
+<a name="28501"><span class="lineNum">   28501 </span>            : </a>
+<a name="28502"><span class="lineNum">   28502 </span>            :     nb = DORMQL_BLOCKSIZE;</a>
+<a name="28503"><span class="lineNum">   28503 </span><span class="lineNoCov">          0 :     lwkopt = nw * nb;</span></a>
+<a name="28504"><span class="lineNum">   28504 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28505"><span class="lineNum">   28505 </span>            :     </a>
+<a name="28506"><span class="lineNum">   28506 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="28507"><span class="lineNum">   28507 </span>            :         i__2 = -(*info);</a>
+<a name="28508"><span class="lineNum">   28508 </span>            :         return;</a>
+<a name="28509"><span class="lineNum">   28509 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="28510"><span class="lineNum">   28510 </span>            :         return;</a>
+<a name="28511"><span class="lineNum">   28511 </span>            :     }</a>
+<a name="28512"><span class="lineNum">   28512 </span>            : </a>
+<a name="28513"><span class="lineNum">   28513 </span><span class="lineNoCov">          0 :     if (*m == 0 || *n == 0 || nq == 1) {</span></a>
+<a name="28514"><span class="lineNum">   28514 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="28515"><span class="lineNum">   28515 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="28516"><span class="lineNum">   28516 </span>            :     }</a>
+<a name="28517"><span class="lineNum">   28517 </span>            : </a>
+<a name="28518"><span class="lineNum">   28518 </span><span class="lineNoCov">          0 :     if (left) {</span></a>
+<a name="28519"><span class="lineNum">   28519 </span><span class="lineNoCov">          0 :         mi = *m - 1;</span></a>
+<a name="28520"><span class="lineNum">   28520 </span><span class="lineNoCov">          0 :         ni = *n;</span></a>
+<a name="28521"><span class="lineNum">   28521 </span>            :     } else {</a>
+<a name="28522"><span class="lineNum">   28522 </span><span class="lineNoCov">          0 :         mi = *m;</span></a>
+<a name="28523"><span class="lineNum">   28523 </span><span class="lineNoCov">          0 :         ni = *n - 1;</span></a>
+<a name="28524"><span class="lineNum">   28524 </span>            :     }</a>
+<a name="28525"><span class="lineNum">   28525 </span>            : </a>
+<a name="28526"><span class="lineNum">   28526 </span><span class="lineNoCov">          0 :     if (upper) {</span></a>
+<a name="28527"><span class="lineNum">   28527 </span><span class="lineNoCov">          0 :         i__2 = nq - 1;</span></a>
+<a name="28528"><span class="lineNum">   28528 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sormql,SORMQL)(side, trans, &amp;mi, &amp;ni, &amp;i__2, &amp;a[(a_dim1 &lt;&lt; 1) + 1], lda, &amp;</span></a>
+<a name="28529"><span class="lineNum">   28529 </span>            :                 tau[1], &amp;c__[c_offset], ldc, &amp;work[1], lwork, &amp;iinfo);</a>
+<a name="28530"><span class="lineNum">   28530 </span>            :     } else {</a>
+<a name="28531"><span class="lineNum">   28531 </span><span class="lineNoCov">          0 :         if (left) {</span></a>
+<a name="28532"><span class="lineNum">   28532 </span>            :             i1 = 2;</a>
+<a name="28533"><span class="lineNum">   28533 </span>            :             i2 = 1;</a>
+<a name="28534"><span class="lineNum">   28534 </span>            :         } else {</a>
+<a name="28535"><span class="lineNum">   28535 </span>            :             i1 = 1;</a>
+<a name="28536"><span class="lineNum">   28536 </span>            :             i2 = 2;</a>
+<a name="28537"><span class="lineNum">   28537 </span>            :         }</a>
+<a name="28538"><span class="lineNum">   28538 </span><span class="lineNoCov">          0 :         i__2 = nq - 1;</span></a>
+<a name="28539"><span class="lineNum">   28539 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sormqr,SORMQR)(side, trans, &amp;mi, &amp;ni, &amp;i__2, &amp;a[a_dim1 + 2], lda, &amp;tau[1], &amp;</span></a>
+<a name="28540"><span class="lineNum">   28540 </span><span class="lineNoCov">          0 :                 c__[i1 + i2 * c_dim1], ldc, &amp;work[1], lwork, &amp;iinfo);</span></a>
+<a name="28541"><span class="lineNum">   28541 </span>            :     }</a>
+<a name="28542"><span class="lineNum">   28542 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="28543"><span class="lineNum">   28543 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="28544"><span class="lineNum">   28544 </span>            : </a>
+<a name="28545"><span class="lineNum">   28545 </span>            : }</a>
+<a name="28546"><span class="lineNum">   28546 </span>            : </a>
+<a name="28547"><span class="lineNum">   28547 </span>            : </a>
+<a name="28548"><span class="lineNum">   28548 </span>            : }</a>
+<a name="28549"><span class="lineNum">   28549 </span>            : }</a>
+<a name="28550"><span class="lineNum">   28550 </span>            : #include &lt;cmath&gt;</a>
+<a name="28551"><span class="lineNum">   28551 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="28552"><span class="lineNum">   28552 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="28553"><span class="lineNum">   28553 </span>            : </a>
+<a name="28554"><span class="lineNum">   28554 </span>            : #include &quot;real.h&quot;</a>
+<a name="28555"><span class="lineNum">   28555 </span>            : </a>
+<a name="28556"><span class="lineNum">   28556 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="28557"><span class="lineNum">   28557 </span>            : namespace PLMD{</a>
+<a name="28558"><span class="lineNum">   28558 </span>            : namespace lapack{</a>
+<a name="28559"><span class="lineNum">   28559 </span>            : using namespace blas;</a>
+<a name="28560"><span class="lineNum">   28560 </span>            : void</a>
+<a name="28561"><span class="lineNum">   28561 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sstebz,SSTEBZ)(const char *range, </span></a>
+<a name="28562"><span class="lineNum">   28562 </span>            :                         const char *order,</a>
+<a name="28563"><span class="lineNum">   28563 </span>            :                         int *n,</a>
+<a name="28564"><span class="lineNum">   28564 </span>            :                         float *vl, </a>
+<a name="28565"><span class="lineNum">   28565 </span>            :                         float *vu, </a>
+<a name="28566"><span class="lineNum">   28566 </span>            :                         int *il,</a>
+<a name="28567"><span class="lineNum">   28567 </span>            :                         int *iu,</a>
+<a name="28568"><span class="lineNum">   28568 </span>            :                         float *abstol, </a>
+<a name="28569"><span class="lineNum">   28569 </span>            :                         float *d__,</a>
+<a name="28570"><span class="lineNum">   28570 </span>            :                         float *e,</a>
+<a name="28571"><span class="lineNum">   28571 </span>            :                         int *m, </a>
+<a name="28572"><span class="lineNum">   28572 </span>            :                         int *nsplit, </a>
+<a name="28573"><span class="lineNum">   28573 </span>            :                         float *w,</a>
+<a name="28574"><span class="lineNum">   28574 </span>            :                         int *iblock,</a>
+<a name="28575"><span class="lineNum">   28575 </span>            :                         int *isplit,</a>
+<a name="28576"><span class="lineNum">   28576 </span>            :                         float *work, </a>
+<a name="28577"><span class="lineNum">   28577 </span>            :                         int *iwork, </a>
+<a name="28578"><span class="lineNum">   28578 </span>            :                         int *info)</a>
+<a name="28579"><span class="lineNum">   28579 </span>            : {</a>
+<a name="28580"><span class="lineNum">   28580 </span>            :     int i__1, i__2, i__3;</a>
+<a name="28581"><span class="lineNum">   28581 </span>            :     float d__1, d__2, d__3, d__4, d__5;</a>
+<a name="28582"><span class="lineNum">   28582 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="28583"><span class="lineNum">   28583 </span><span class="lineNoCov">          0 :     int c__3 = 3;</span></a>
+<a name="28584"><span class="lineNum">   28584 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="28585"><span class="lineNum">   28585 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="28586"><span class="lineNum">   28586 </span>            : </a>
+<a name="28587"><span class="lineNum">   28587 </span>            :     int j, ib, jb, ie, je, nb;</a>
+<a name="28588"><span class="lineNum">   28588 </span>            :     float gl;</a>
+<a name="28589"><span class="lineNum">   28589 </span>            :     int im, in;</a>
+<a name="28590"><span class="lineNum">   28590 </span>            :     float gu;</a>
+<a name="28591"><span class="lineNum">   28591 </span>            :     int iw;</a>
+<a name="28592"><span class="lineNum">   28592 </span>            :     float wl, wu;</a>
+<a name="28593"><span class="lineNum">   28593 </span>            :     int nwl;</a>
+<a name="28594"><span class="lineNum">   28594 </span>            :     float ulp, wlu, wul;</a>
+<a name="28595"><span class="lineNum">   28595 </span>            :     int nwu;</a>
+<a name="28596"><span class="lineNum">   28596 </span>            :     float tmp1, tmp2;</a>
+<a name="28597"><span class="lineNum">   28597 </span>            :     int iend, ioff, iout, itmp1, jdisc;</a>
+<a name="28598"><span class="lineNum">   28598 </span>            :     int iinfo;</a>
+<a name="28599"><span class="lineNum">   28599 </span>            :     float atoli;</a>
+<a name="28600"><span class="lineNum">   28600 </span>            :     int iwoff;</a>
+<a name="28601"><span class="lineNum">   28601 </span>            :     float bnorm;</a>
+<a name="28602"><span class="lineNum">   28602 </span>            :     int itmax;</a>
+<a name="28603"><span class="lineNum">   28603 </span>            :     float wkill, rtoli, tnorm;</a>
+<a name="28604"><span class="lineNum">   28604 </span>            :     int ibegin;</a>
+<a name="28605"><span class="lineNum">   28605 </span>            :     int irange, idiscl;</a>
+<a name="28606"><span class="lineNum">   28606 </span>            :     int idumma[1];</a>
+<a name="28607"><span class="lineNum">   28607 </span>            :     int idiscu, iorder;</a>
+<a name="28608"><span class="lineNum">   28608 </span>            :     int ncnvrg;</a>
+<a name="28609"><span class="lineNum">   28609 </span>            :     float pivmin;</a>
+<a name="28610"><span class="lineNum">   28610 </span>            :     int toofew;</a>
+<a name="28611"><span class="lineNum">   28611 </span>            :     const float safemn = PLUMED_GMX_FLOAT_MIN*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="28612"><span class="lineNum">   28612 </span>            : </a>
+<a name="28613"><span class="lineNum">   28613 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="28614"><span class="lineNum">   28614 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="28615"><span class="lineNum">   28615 </span><span class="lineNoCov">          0 :     --isplit;</span></a>
+<a name="28616"><span class="lineNum">   28616 </span><span class="lineNoCov">          0 :     --iblock;</span></a>
+<a name="28617"><span class="lineNum">   28617 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="28618"><span class="lineNum">   28618 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="28619"><span class="lineNum">   28619 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="28620"><span class="lineNum">   28620 </span>            : </a>
+<a name="28621"><span class="lineNum">   28621 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28622"><span class="lineNum">   28622 </span>            : </a>
+<a name="28623"><span class="lineNum">   28623 </span><span class="lineNoCov">          0 :     if (*range=='A' || *range=='a') {</span></a>
+<a name="28624"><span class="lineNum">   28624 </span>            :         irange = 1;</a>
+<a name="28625"><span class="lineNum">   28625 </span><span class="lineNoCov">          0 :     } else if (*range=='V' || *range=='v') {</span></a>
+<a name="28626"><span class="lineNum">   28626 </span>            :         irange = 2;</a>
+<a name="28627"><span class="lineNum">   28627 </span>            :     } else if (*range=='I' || *range=='i') {</a>
+<a name="28628"><span class="lineNum">   28628 </span>            :         irange = 3;</a>
+<a name="28629"><span class="lineNum">   28629 </span>            :     } else {</a>
+<a name="28630"><span class="lineNum">   28630 </span>            :         irange = 0;</a>
+<a name="28631"><span class="lineNum">   28631 </span>            :     }</a>
+<a name="28632"><span class="lineNum">   28632 </span>            : </a>
+<a name="28633"><span class="lineNum">   28633 </span><span class="lineNoCov">          0 :     if (*order=='B' || *order=='b') {</span></a>
+<a name="28634"><span class="lineNum">   28634 </span>            :         iorder = 2;</a>
+<a name="28635"><span class="lineNum">   28635 </span><span class="lineNoCov">          0 :     } else if (*order=='E' || *order=='e') {</span></a>
+<a name="28636"><span class="lineNum">   28636 </span>            :         iorder = 1;</a>
+<a name="28637"><span class="lineNum">   28637 </span>            :     } else {</a>
+<a name="28638"><span class="lineNum">   28638 </span>            :         iorder = 0;</a>
+<a name="28639"><span class="lineNum">   28639 </span>            :     }</a>
+<a name="28640"><span class="lineNum">   28640 </span>            : </a>
+<a name="28641"><span class="lineNum">   28641 </span><span class="lineNoCov">          0 :     if (irange &lt;= 0) {</span></a>
+<a name="28642"><span class="lineNum">   28642 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="28643"><span class="lineNum">   28643 </span><span class="lineNoCov">          0 :     } else if (iorder &lt;= 0) {</span></a>
+<a name="28644"><span class="lineNum">   28644 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="28645"><span class="lineNum">   28645 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="28646"><span class="lineNum">   28646 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="28647"><span class="lineNum">   28647 </span><span class="lineNoCov">          0 :     } else if (irange == 2) {</span></a>
+<a name="28648"><span class="lineNum">   28648 </span><span class="lineNoCov">          0 :         if (*vl &gt;= *vu) {</span></a>
+<a name="28649"><span class="lineNum">   28649 </span><span class="lineNoCov">          0 :             *info = -5;</span></a>
+<a name="28650"><span class="lineNum">   28650 </span>            :         }</a>
+<a name="28651"><span class="lineNum">   28651 </span><span class="lineNoCov">          0 :     } else if (irange == 3 &amp;&amp; (*il &lt; 1 || *il &gt; (*n))) {</span></a>
+<a name="28652"><span class="lineNum">   28652 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="28653"><span class="lineNum">   28653 </span><span class="lineNoCov">          0 :     } else if (irange == 3 &amp;&amp; (*iu &lt; ((*n&lt;*il) ? *n : *il) || *iu &gt; *n)) {</span></a>
+<a name="28654"><span class="lineNum">   28654 </span><span class="lineNoCov">          0 :         *info = -7;</span></a>
+<a name="28655"><span class="lineNum">   28655 </span>            :     }</a>
+<a name="28656"><span class="lineNum">   28656 </span>            : </a>
+<a name="28657"><span class="lineNum">   28657 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="28658"><span class="lineNum">   28658 </span>            :         return;</a>
+<a name="28659"><span class="lineNum">   28659 </span>            :     }</a>
+<a name="28660"><span class="lineNum">   28660 </span>            : </a>
+<a name="28661"><span class="lineNum">   28661 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28662"><span class="lineNum">   28662 </span>            :     ncnvrg = 0;</a>
+<a name="28663"><span class="lineNum">   28663 </span>            :     toofew = 0;</a>
+<a name="28664"><span class="lineNum">   28664 </span>            : </a>
+<a name="28665"><span class="lineNum">   28665 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="28666"><span class="lineNum">   28666 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="28667"><span class="lineNum">   28667 </span>            :         return;</a>
+<a name="28668"><span class="lineNum">   28668 </span>            :     }</a>
+<a name="28669"><span class="lineNum">   28669 </span>            : </a>
+<a name="28670"><span class="lineNum">   28670 </span><span class="lineNoCov">          0 :     if (irange == 3 &amp;&amp; *il == 1 &amp;&amp; *iu == *n) {</span></a>
+<a name="28671"><span class="lineNum">   28671 </span>            :         irange = 1;</a>
+<a name="28672"><span class="lineNum">   28672 </span>            :     }</a>
+<a name="28673"><span class="lineNum">   28673 </span>            : </a>
+<a name="28674"><span class="lineNum">   28674 </span>            :     ulp = 2*PLUMED_GMX_FLOAT_EPS;</a>
+<a name="28675"><span class="lineNum">   28675 </span><span class="lineNoCov">          0 :     rtoli = ulp * 2.;</span></a>
+<a name="28676"><span class="lineNum">   28676 </span>            :     nb = DSTEBZ_BLOCKSIZE;</a>
+<a name="28677"><span class="lineNum">   28677 </span>            :     // cppcheck-suppress knownConditionTrueFalse</a>
+<a name="28678"><span class="lineNum">   28678 </span>            :     if (nb &lt;= 1) {</a>
+<a name="28679"><span class="lineNum">   28679 </span><span class="lineNoCov">          0 :         nb = 0;</span></a>
+<a name="28680"><span class="lineNum">   28680 </span>            :     }</a>
+<a name="28681"><span class="lineNum">   28681 </span>            : </a>
+<a name="28682"><span class="lineNum">   28682 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="28683"><span class="lineNum">   28683 </span><span class="lineNoCov">          0 :         *nsplit = 1;</span></a>
+<a name="28684"><span class="lineNum">   28684 </span><span class="lineNoCov">          0 :         isplit[1] = 1;</span></a>
+<a name="28685"><span class="lineNum">   28685 </span><span class="lineNoCov">          0 :         if (irange == 2 &amp;&amp; (*vl &gt;= d__[1] || *vu &lt; d__[1])) {</span></a>
+<a name="28686"><span class="lineNum">   28686 </span><span class="lineNoCov">          0 :             *m = 0;</span></a>
+<a name="28687"><span class="lineNum">   28687 </span>            :         } else {</a>
+<a name="28688"><span class="lineNum">   28688 </span><span class="lineNoCov">          0 :             w[1] = d__[1];</span></a>
+<a name="28689"><span class="lineNum">   28689 </span><span class="lineNoCov">          0 :             iblock[1] = 1;</span></a>
+<a name="28690"><span class="lineNum">   28690 </span><span class="lineNoCov">          0 :             *m = 1;</span></a>
+<a name="28691"><span class="lineNum">   28691 </span>            :         }</a>
+<a name="28692"><span class="lineNum">   28692 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="28693"><span class="lineNum">   28693 </span>            :     }</a>
+<a name="28694"><span class="lineNum">   28694 </span>            : </a>
+<a name="28695"><span class="lineNum">   28695 </span><span class="lineNoCov">          0 :     *nsplit = 1;</span></a>
+<a name="28696"><span class="lineNum">   28696 </span><span class="lineNoCov">          0 :     work[*n] = 0.;</span></a>
+<a name="28697"><span class="lineNum">   28697 </span><span class="lineNoCov">          0 :     pivmin = 1.;</span></a>
+<a name="28698"><span class="lineNum">   28698 </span><span class="lineNoCov">          0 :     i__1 = *n;</span></a>
+<a name="28699"><span class="lineNum">   28699 </span><span class="lineNoCov">          0 :     for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="28700"><span class="lineNum">   28700 </span><span class="lineNoCov">          0 :         d__1 = e[j - 1];</span></a>
+<a name="28701"><span class="lineNum">   28701 </span><span class="lineNoCov">          0 :         tmp1 = d__1 * d__1;</span></a>
+<a name="28702"><span class="lineNum">   28702 </span>            :         d__2 = ulp;</a>
+<a name="28703"><span class="lineNum">   28703 </span><span class="lineNoCov">          0 :         if (std::abs(d__[j] * d__[j - 1]) * (d__2 * d__2) + safemn </span></a>
+<a name="28704"><span class="lineNum">   28704 </span>            :                 &gt; tmp1) {</a>
+<a name="28705"><span class="lineNum">   28705 </span><span class="lineNoCov">          0 :             isplit[*nsplit] = j - 1;</span></a>
+<a name="28706"><span class="lineNum">   28706 </span><span class="lineNoCov">          0 :             ++(*nsplit);</span></a>
+<a name="28707"><span class="lineNum">   28707 </span><span class="lineNoCov">          0 :             work[j - 1] = 0.;</span></a>
+<a name="28708"><span class="lineNum">   28708 </span>            :         } else {</a>
+<a name="28709"><span class="lineNum">   28709 </span><span class="lineNoCov">          0 :             work[j - 1] = tmp1;</span></a>
+<a name="28710"><span class="lineNum">   28710 </span><span class="lineNoCov">          0 :             pivmin = (pivmin&gt;tmp1) ? pivmin : tmp1;</span></a>
+<a name="28711"><span class="lineNum">   28711 </span>            :         }</a>
+<a name="28712"><span class="lineNum">   28712 </span>            :     }</a>
+<a name="28713"><span class="lineNum">   28713 </span><span class="lineNoCov">          0 :     isplit[*nsplit] = *n;</span></a>
+<a name="28714"><span class="lineNum">   28714 </span><span class="lineNoCov">          0 :     pivmin *= safemn;</span></a>
+<a name="28715"><span class="lineNum">   28715 </span>            : </a>
+<a name="28716"><span class="lineNum">   28716 </span><span class="lineNoCov">          0 :     if (irange == 3) {</span></a>
+<a name="28717"><span class="lineNum">   28717 </span>            : </a>
+<a name="28718"><span class="lineNum">   28718 </span><span class="lineNoCov">          0 :         gu = d__[1];</span></a>
+<a name="28719"><span class="lineNum">   28719 </span>            :         gl = d__[1];</a>
+<a name="28720"><span class="lineNum">   28720 </span>            :         tmp1 = 0.;</a>
+<a name="28721"><span class="lineNum">   28721 </span>            : </a>
+<a name="28722"><span class="lineNum">   28722 </span>            :         i__1 = *n - 1;</a>
+<a name="28723"><span class="lineNum">   28723 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="28724"><span class="lineNum">   28724 </span><span class="lineNoCov">          0 :             tmp2 =  std::sqrt(work[j]);</span></a>
+<a name="28725"><span class="lineNum">   28725 </span><span class="lineNoCov">          0 :             d__1 = gu, d__2 = d__[j] + tmp1 + tmp2;</span></a>
+<a name="28726"><span class="lineNum">   28726 </span><span class="lineNoCov">          0 :             gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="28727"><span class="lineNum">   28727 </span><span class="lineNoCov">          0 :             d__1 = gl, d__2 = d__[j] - tmp1 - tmp2;</span></a>
+<a name="28728"><span class="lineNum">   28728 </span><span class="lineNoCov">          0 :             gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="28729"><span class="lineNum">   28729 </span>            :             tmp1 = tmp2;</a>
+<a name="28730"><span class="lineNum">   28730 </span>            :         }</a>
+<a name="28731"><span class="lineNum">   28731 </span>            : </a>
+<a name="28732"><span class="lineNum">   28732 </span><span class="lineNoCov">          0 :         d__1 = gu, d__2 = d__[*n] + tmp1;</span></a>
+<a name="28733"><span class="lineNum">   28733 </span><span class="lineNoCov">          0 :         gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="28734"><span class="lineNum">   28734 </span><span class="lineNoCov">          0 :         d__1 = gl, d__2 = d__[*n] - tmp1;</span></a>
+<a name="28735"><span class="lineNum">   28735 </span><span class="lineNoCov">          0 :         gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="28736"><span class="lineNum">   28736 </span>            :         d__1 = std::abs(gl);</a>
+<a name="28737"><span class="lineNum">   28737 </span>            :         d__2 = std::abs(gu);</a>
+<a name="28738"><span class="lineNum">   28738 </span><span class="lineNoCov">          0 :         tnorm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="28739"><span class="lineNum">   28739 </span><span class="lineNoCov">          0 :         gl = gl - tnorm * 2. * ulp * *n - pivmin * 4.;</span></a>
+<a name="28740"><span class="lineNum">   28740 </span><span class="lineNoCov">          0 :         gu = gu + tnorm * 2. * ulp * *n + pivmin * 2.;</span></a>
+<a name="28741"><span class="lineNum">   28741 </span>            : </a>
+<a name="28742"><span class="lineNum">   28742 </span><span class="lineNoCov">          0 :         itmax = (int) ((std::log(tnorm + pivmin) - std::log(pivmin)) / std::log(2.)) + 2;</span></a>
+<a name="28743"><span class="lineNum">   28743 </span><span class="lineNoCov">          0 :         if (*abstol &lt;= 0.) {</span></a>
+<a name="28744"><span class="lineNum">   28744 </span><span class="lineNoCov">          0 :             atoli = ulp * tnorm;</span></a>
+<a name="28745"><span class="lineNum">   28745 </span>            :         } else {</a>
+<a name="28746"><span class="lineNum">   28746 </span><span class="lineNoCov">          0 :             atoli = *abstol;</span></a>
+<a name="28747"><span class="lineNum">   28747 </span>            :         }</a>
+<a name="28748"><span class="lineNum">   28748 </span>            : </a>
+<a name="28749"><span class="lineNum">   28749 </span><span class="lineNoCov">          0 :         work[*n + 1] = gl;</span></a>
+<a name="28750"><span class="lineNum">   28750 </span><span class="lineNoCov">          0 :         work[*n + 2] = gl;</span></a>
+<a name="28751"><span class="lineNum">   28751 </span><span class="lineNoCov">          0 :         work[*n + 3] = gu;</span></a>
+<a name="28752"><span class="lineNum">   28752 </span><span class="lineNoCov">          0 :         work[*n + 4] = gu;</span></a>
+<a name="28753"><span class="lineNum">   28753 </span><span class="lineNoCov">          0 :         work[*n + 5] = gl;</span></a>
+<a name="28754"><span class="lineNum">   28754 </span><span class="lineNoCov">          0 :         work[*n + 6] = gu;</span></a>
+<a name="28755"><span class="lineNum">   28755 </span><span class="lineNoCov">          0 :         iwork[1] = -1;</span></a>
+<a name="28756"><span class="lineNum">   28756 </span><span class="lineNoCov">          0 :         iwork[2] = -1;</span></a>
+<a name="28757"><span class="lineNum">   28757 </span><span class="lineNoCov">          0 :         iwork[3] = *n + 1;</span></a>
+<a name="28758"><span class="lineNum">   28758 </span><span class="lineNoCov">          0 :         iwork[4] = *n + 1;</span></a>
+<a name="28759"><span class="lineNum">   28759 </span><span class="lineNoCov">          0 :         iwork[5] = *il - 1;</span></a>
+<a name="28760"><span class="lineNum">   28760 </span><span class="lineNoCov">          0 :         iwork[6] = *iu;</span></a>
+<a name="28761"><span class="lineNum">   28761 </span>            : </a>
+<a name="28762"><span class="lineNum">   28762 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaebz,SLAEBZ)(&amp;c__3, &amp;itmax, n, &amp;c__2, &amp;c__2, &amp;nb, &amp;atoli, &amp;rtoli, &amp;pivmin, </span></a>
+<a name="28763"><span class="lineNum">   28763 </span><span class="lineNoCov">          0 :                 &amp;d__[1], &amp;e[1], &amp;work[1], &amp;iwork[5], &amp;work[*n + 1], &amp;work[*n </span></a>
+<a name="28764"><span class="lineNum">   28764 </span><span class="lineNoCov">          0 :                 + 5], &amp;iout, &amp;iwork[1], &amp;w[1], &amp;iblock[1], &amp;iinfo);</span></a>
+<a name="28765"><span class="lineNum">   28765 </span>            : </a>
+<a name="28766"><span class="lineNum">   28766 </span><span class="lineNoCov">          0 :         if (iwork[6] == *iu) {</span></a>
+<a name="28767"><span class="lineNum">   28767 </span><span class="lineNoCov">          0 :             wl = work[*n + 1];</span></a>
+<a name="28768"><span class="lineNum">   28768 </span><span class="lineNoCov">          0 :             wlu = work[*n + 3];</span></a>
+<a name="28769"><span class="lineNum">   28769 </span><span class="lineNoCov">          0 :             nwl = iwork[1];</span></a>
+<a name="28770"><span class="lineNum">   28770 </span><span class="lineNoCov">          0 :             wu = work[*n + 4];</span></a>
+<a name="28771"><span class="lineNum">   28771 </span><span class="lineNoCov">          0 :             wul = work[*n + 2];</span></a>
+<a name="28772"><span class="lineNum">   28772 </span><span class="lineNoCov">          0 :             nwu = iwork[4];</span></a>
+<a name="28773"><span class="lineNum">   28773 </span>            :         } else {</a>
+<a name="28774"><span class="lineNum">   28774 </span><span class="lineNoCov">          0 :             wl = work[*n + 2];</span></a>
+<a name="28775"><span class="lineNum">   28775 </span><span class="lineNoCov">          0 :             wlu = work[*n + 4];</span></a>
+<a name="28776"><span class="lineNum">   28776 </span><span class="lineNoCov">          0 :             nwl = iwork[2];</span></a>
+<a name="28777"><span class="lineNum">   28777 </span><span class="lineNoCov">          0 :             wu = work[*n + 3];</span></a>
+<a name="28778"><span class="lineNum">   28778 </span><span class="lineNoCov">          0 :             wul = work[*n + 1];</span></a>
+<a name="28779"><span class="lineNum">   28779 </span><span class="lineNoCov">          0 :             nwu = iwork[3];</span></a>
+<a name="28780"><span class="lineNum">   28780 </span>            :         }</a>
+<a name="28781"><span class="lineNum">   28781 </span>            : </a>
+<a name="28782"><span class="lineNum">   28782 </span><span class="lineNoCov">          0 :         if (nwl &lt; 0 || nwl &gt;= *n || nwu &lt; 1 || nwu &gt; *n) {</span></a>
+<a name="28783"><span class="lineNum">   28783 </span><span class="lineNoCov">          0 :             *info = 4;</span></a>
+<a name="28784"><span class="lineNum">   28784 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="28785"><span class="lineNum">   28785 </span>            :         }</a>
+<a name="28786"><span class="lineNum">   28786 </span>            :     } else {</a>
+<a name="28787"><span class="lineNum">   28787 </span>            : </a>
+<a name="28788"><span class="lineNum">   28788 </span>            : </a>
+<a name="28789"><span class="lineNum">   28789 </span>            :       /* avoid warnings for high gcc optimization */</a>
+<a name="28790"><span class="lineNum">   28790 </span>            :       wlu = wul = 1.0;</a>
+<a name="28791"><span class="lineNum">   28791 </span>            : </a>
+<a name="28792"><span class="lineNum">   28792 </span><span class="lineNoCov">          0 :         d__3 = std::abs(d__[1]) + std::abs(e[1]);</span></a>
+<a name="28793"><span class="lineNum">   28793 </span><span class="lineNoCov">          0 :         d__4 = std::abs(d__[*n]) + std::abs(e[*n - 1]);</span></a>
+<a name="28794"><span class="lineNum">   28794 </span><span class="lineNoCov">          0 :         tnorm = (d__3&gt;d__4) ? d__3 : d__4;</span></a>
+<a name="28795"><span class="lineNum">   28795 </span>            : </a>
+<a name="28796"><span class="lineNum">   28796 </span>            :         i__1 = *n - 1;</a>
+<a name="28797"><span class="lineNum">   28797 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="28798"><span class="lineNum">   28798 </span>            :             d__4 = tnorm;</a>
+<a name="28799"><span class="lineNum">   28799 </span><span class="lineNoCov">          0 :             d__5 = std::abs(d__[j]) + std::abs(e[j - 1]) + std::abs(e[j]);</span></a>
+<a name="28800"><span class="lineNum">   28800 </span><span class="lineNoCov">          0 :             tnorm = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="28801"><span class="lineNum">   28801 </span>            :         }</a>
+<a name="28802"><span class="lineNum">   28802 </span>            : </a>
+<a name="28803"><span class="lineNum">   28803 </span><span class="lineNoCov">          0 :         if (*abstol &lt;= 0.) {</span></a>
+<a name="28804"><span class="lineNum">   28804 </span><span class="lineNoCov">          0 :             atoli = ulp * tnorm;</span></a>
+<a name="28805"><span class="lineNum">   28805 </span>            :         } else {</a>
+<a name="28806"><span class="lineNum">   28806 </span><span class="lineNoCov">          0 :             atoli = *abstol;</span></a>
+<a name="28807"><span class="lineNum">   28807 </span>            :         }</a>
+<a name="28808"><span class="lineNum">   28808 </span>            : </a>
+<a name="28809"><span class="lineNum">   28809 </span><span class="lineNoCov">          0 :         if (irange == 2) {</span></a>
+<a name="28810"><span class="lineNum">   28810 </span><span class="lineNoCov">          0 :             wl = *vl;</span></a>
+<a name="28811"><span class="lineNum">   28811 </span><span class="lineNoCov">          0 :             wu = *vu;</span></a>
+<a name="28812"><span class="lineNum">   28812 </span>            :         } else {</a>
+<a name="28813"><span class="lineNum">   28813 </span>            :             wl = 0.;</a>
+<a name="28814"><span class="lineNum">   28814 </span>            :             wu = 0.;</a>
+<a name="28815"><span class="lineNum">   28815 </span>            :         }</a>
+<a name="28816"><span class="lineNum">   28816 </span>            :     }</a>
+<a name="28817"><span class="lineNum">   28817 </span>            : </a>
+<a name="28818"><span class="lineNum">   28818 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="28819"><span class="lineNum">   28819 </span>            :     iend = 0;</a>
+<a name="28820"><span class="lineNum">   28820 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="28821"><span class="lineNum">   28821 </span>            :     nwl = 0;</a>
+<a name="28822"><span class="lineNum">   28822 </span>            :     nwu = 0;</a>
+<a name="28823"><span class="lineNum">   28823 </span>            : </a>
+<a name="28824"><span class="lineNum">   28824 </span><span class="lineNoCov">          0 :     i__1 = *nsplit;</span></a>
+<a name="28825"><span class="lineNum">   28825 </span><span class="lineNoCov">          0 :     for (jb = 1; jb &lt;= i__1; ++jb) {</span></a>
+<a name="28826"><span class="lineNum">   28826 </span>            :         ioff = iend;</a>
+<a name="28827"><span class="lineNum">   28827 </span><span class="lineNoCov">          0 :         ibegin = ioff + 1;</span></a>
+<a name="28828"><span class="lineNum">   28828 </span><span class="lineNoCov">          0 :         iend = isplit[jb];</span></a>
+<a name="28829"><span class="lineNum">   28829 </span><span class="lineNoCov">          0 :         in = iend - ioff;</span></a>
+<a name="28830"><span class="lineNum">   28830 </span>            : </a>
+<a name="28831"><span class="lineNum">   28831 </span><span class="lineNoCov">          0 :         if (in == 1) {</span></a>
+<a name="28832"><span class="lineNum">   28832 </span>            : </a>
+<a name="28833"><span class="lineNum">   28833 </span><span class="lineNoCov">          0 :             if (irange == 1 || wl &gt;= d__[ibegin] - pivmin) {</span></a>
+<a name="28834"><span class="lineNum">   28834 </span><span class="lineNoCov">          0 :                 ++nwl;</span></a>
+<a name="28835"><span class="lineNum">   28835 </span>            :             }</a>
+<a name="28836"><span class="lineNum">   28836 </span><span class="lineNoCov">          0 :             if (irange == 1 || wu &gt;= d__[ibegin] - pivmin) {</span></a>
+<a name="28837"><span class="lineNum">   28837 </span><span class="lineNoCov">          0 :                 ++nwu;</span></a>
+<a name="28838"><span class="lineNum">   28838 </span>            :             }</a>
+<a name="28839"><span class="lineNum">   28839 </span><span class="lineNoCov">          0 :             if (irange == 1 || ((wl &lt; d__[ibegin] - pivmin) &amp;&amp; (wu &gt;= d__[ibegin] - pivmin))) {</span></a>
+<a name="28840"><span class="lineNum">   28840 </span><span class="lineNoCov">          0 :                 ++(*m);</span></a>
+<a name="28841"><span class="lineNum">   28841 </span><span class="lineNoCov">          0 :                 w[*m] = d__[ibegin];</span></a>
+<a name="28842"><span class="lineNum">   28842 </span><span class="lineNoCov">          0 :                 iblock[*m] = jb;</span></a>
+<a name="28843"><span class="lineNum">   28843 </span>            :             }</a>
+<a name="28844"><span class="lineNum">   28844 </span>            :         } else {</a>
+<a name="28845"><span class="lineNum">   28845 </span>            : </a>
+<a name="28846"><span class="lineNum">   28846 </span><span class="lineNoCov">          0 :             gu = d__[ibegin];</span></a>
+<a name="28847"><span class="lineNum">   28847 </span>            :             gl = d__[ibegin];</a>
+<a name="28848"><span class="lineNum">   28848 </span>            :             tmp1 = 0.;</a>
+<a name="28849"><span class="lineNum">   28849 </span>            : </a>
+<a name="28850"><span class="lineNum">   28850 </span>            :             i__2 = iend - 1;</a>
+<a name="28851"><span class="lineNum">   28851 </span><span class="lineNoCov">          0 :             for (j = ibegin; j &lt;= i__2; ++j) {</span></a>
+<a name="28852"><span class="lineNum">   28852 </span><span class="lineNoCov">          0 :                 tmp2 = std::abs(e[j]);</span></a>
+<a name="28853"><span class="lineNum">   28853 </span><span class="lineNoCov">          0 :                 d__1 = gu, d__2 = d__[j] + tmp1 + tmp2;</span></a>
+<a name="28854"><span class="lineNum">   28854 </span><span class="lineNoCov">          0 :                 gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="28855"><span class="lineNum">   28855 </span><span class="lineNoCov">          0 :                 d__1 = gl, d__2 = d__[j] - tmp1 - tmp2;</span></a>
+<a name="28856"><span class="lineNum">   28856 </span><span class="lineNoCov">          0 :                 gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="28857"><span class="lineNum">   28857 </span>            :                 tmp1 = tmp2;</a>
+<a name="28858"><span class="lineNum">   28858 </span>            :             }</a>
+<a name="28859"><span class="lineNum">   28859 </span>            : </a>
+<a name="28860"><span class="lineNum">   28860 </span><span class="lineNoCov">          0 :             d__1 = gu, d__2 = d__[iend] + tmp1;</span></a>
+<a name="28861"><span class="lineNum">   28861 </span><span class="lineNoCov">          0 :             gu = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="28862"><span class="lineNum">   28862 </span><span class="lineNoCov">          0 :             d__1 = gl, d__2 = d__[iend] - tmp1;</span></a>
+<a name="28863"><span class="lineNum">   28863 </span><span class="lineNoCov">          0 :             gl = (d__1&lt;d__2) ? d__1 : d__2;</span></a>
+<a name="28864"><span class="lineNum">   28864 </span>            :             d__1 = std::abs(gl);</a>
+<a name="28865"><span class="lineNum">   28865 </span>            :             d__2 = std::abs(gu);</a>
+<a name="28866"><span class="lineNum">   28866 </span><span class="lineNoCov">          0 :             bnorm = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="28867"><span class="lineNum">   28867 </span><span class="lineNoCov">          0 :             gl = gl - bnorm * 2. * ulp * in - pivmin * 2.;</span></a>
+<a name="28868"><span class="lineNum">   28868 </span><span class="lineNoCov">          0 :             gu = gu + bnorm * 2. * ulp * in + pivmin * 2.;</span></a>
+<a name="28869"><span class="lineNum">   28869 </span>            : </a>
+<a name="28870"><span class="lineNum">   28870 </span><span class="lineNoCov">          0 :             if (*abstol &lt;= 0.) {</span></a>
+<a name="28871"><span class="lineNum">   28871 </span>            :                 d__1 = std::abs(gl);</a>
+<a name="28872"><span class="lineNum">   28872 </span>            :                 d__2 = std::abs(gu);</a>
+<a name="28873"><span class="lineNum">   28873 </span><span class="lineNoCov">          0 :                 atoli = ulp * ((d__1&gt;d__2) ? d__1 : d__2);</span></a>
+<a name="28874"><span class="lineNum">   28874 </span>            :             } else {</a>
+<a name="28875"><span class="lineNum">   28875 </span><span class="lineNoCov">          0 :                 atoli = *abstol;</span></a>
+<a name="28876"><span class="lineNum">   28876 </span>            :             }</a>
+<a name="28877"><span class="lineNum">   28877 </span>            : </a>
+<a name="28878"><span class="lineNum">   28878 </span><span class="lineNoCov">          0 :             if (irange &gt; 1) {</span></a>
+<a name="28879"><span class="lineNum">   28879 </span><span class="lineNoCov">          0 :                 if (gu &lt; wl) {</span></a>
+<a name="28880"><span class="lineNum">   28880 </span><span class="lineNoCov">          0 :                     nwl += in;</span></a>
+<a name="28881"><span class="lineNum">   28881 </span><span class="lineNoCov">          0 :                     nwu += in;</span></a>
+<a name="28882"><span class="lineNum">   28882 </span>            :                 }</a>
+<a name="28883"><span class="lineNum">   28883 </span>            :                 gl = (gl&gt;wl) ? gl : wl;</a>
+<a name="28884"><span class="lineNum">   28884 </span>            :                 gu = (gu&lt;wu) ? gu : wu;</a>
+<a name="28885"><span class="lineNum">   28885 </span>            :                 if (gl &gt;= gu) {</a>
+<a name="28886"><span class="lineNum">   28886 </span>            :                 }</a>
+<a name="28887"><span class="lineNum">   28887 </span><span class="lineNoCov">          0 :                 continue;</span></a>
+<a name="28888"><span class="lineNum">   28888 </span>            :             }</a>
+<a name="28889"><span class="lineNum">   28889 </span>            : </a>
+<a name="28890"><span class="lineNum">   28890 </span><span class="lineNoCov">          0 :             work[*n + 1] = gl;</span></a>
+<a name="28891"><span class="lineNum">   28891 </span><span class="lineNoCov">          0 :             work[*n + in + 1] = gu;</span></a>
+<a name="28892"><span class="lineNum">   28892 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaebz,SLAEBZ)(&amp;c__1, &amp;c__0, &amp;in, &amp;in, &amp;c__1, &amp;nb, &amp;atoli, &amp;rtoli, &amp;</span></a>
+<a name="28893"><span class="lineNum">   28893 </span>            :                     pivmin, &amp;d__[ibegin], &amp;e[ibegin], &amp;work[ibegin], idumma, &amp;</a>
+<a name="28894"><span class="lineNum">   28894 </span><span class="lineNoCov">          0 :                     work[*n + 1], &amp;work[*n + (in &lt;&lt; 1) + 1], &amp;im, &amp;iwork[1], &amp;</span></a>
+<a name="28895"><span class="lineNum">   28895 </span><span class="lineNoCov">          0 :                     w[*m + 1], &amp;iblock[*m + 1], &amp;iinfo);</span></a>
+<a name="28896"><span class="lineNum">   28896 </span>            : </a>
+<a name="28897"><span class="lineNum">   28897 </span><span class="lineNoCov">          0 :             nwl += iwork[1];</span></a>
+<a name="28898"><span class="lineNum">   28898 </span><span class="lineNoCov">          0 :             nwu += iwork[in + 1];</span></a>
+<a name="28899"><span class="lineNum">   28899 </span><span class="lineNoCov">          0 :             iwoff = *m - iwork[1];</span></a>
+<a name="28900"><span class="lineNum">   28900 </span>            : </a>
+<a name="28901"><span class="lineNum">   28901 </span><span class="lineNoCov">          0 :             itmax = (int) ((log(gu - gl + pivmin) - log(pivmin)) / log(2.)</span></a>
+<a name="28902"><span class="lineNum">   28902 </span><span class="lineNoCov">          0 :                     ) + 2;</span></a>
+<a name="28903"><span class="lineNum">   28903 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slaebz,SLAEBZ)(&amp;c__2, &amp;itmax, &amp;in, &amp;in, &amp;c__1, &amp;nb, &amp;atoli, &amp;rtoli, &amp;</span></a>
+<a name="28904"><span class="lineNum">   28904 </span>            :                     pivmin, &amp;d__[ibegin], &amp;e[ibegin], &amp;work[ibegin], idumma, &amp;</a>
+<a name="28905"><span class="lineNum">   28905 </span><span class="lineNoCov">          0 :                     work[*n + 1], &amp;work[*n + (in &lt;&lt; 1) + 1], &amp;iout, &amp;iwork[1],</span></a>
+<a name="28906"><span class="lineNum">   28906 </span><span class="lineNoCov">          0 :                      &amp;w[*m + 1], &amp;iblock[*m + 1], &amp;iinfo);</span></a>
+<a name="28907"><span class="lineNum">   28907 </span>            : </a>
+<a name="28908"><span class="lineNum">   28908 </span><span class="lineNoCov">          0 :             i__2 = iout;</span></a>
+<a name="28909"><span class="lineNum">   28909 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__2; ++j) {</span></a>
+<a name="28910"><span class="lineNum">   28910 </span><span class="lineNoCov">          0 :                 tmp1 = (work[j + *n] + work[j + in + *n]) * .5;</span></a>
+<a name="28911"><span class="lineNum">   28911 </span>            : </a>
+<a name="28912"><span class="lineNum">   28912 </span><span class="lineNoCov">          0 :                 if (j &gt; iout - iinfo) {</span></a>
+<a name="28913"><span class="lineNum">   28913 </span>            :                     ncnvrg = 1;</a>
+<a name="28914"><span class="lineNum">   28914 </span><span class="lineNoCov">          0 :                     ib = -jb;</span></a>
+<a name="28915"><span class="lineNum">   28915 </span>            :                 } else {</a>
+<a name="28916"><span class="lineNum">   28916 </span>            :                     ib = jb;</a>
+<a name="28917"><span class="lineNum">   28917 </span>            :                 }</a>
+<a name="28918"><span class="lineNum">   28918 </span><span class="lineNoCov">          0 :                 i__3 = iwork[j + in] + iwoff;</span></a>
+<a name="28919"><span class="lineNum">   28919 </span><span class="lineNoCov">          0 :                 for (je = iwork[j] + 1 + iwoff; je &lt;= i__3; ++je) {</span></a>
+<a name="28920"><span class="lineNum">   28920 </span><span class="lineNoCov">          0 :                     w[je] = tmp1;</span></a>
+<a name="28921"><span class="lineNum">   28921 </span><span class="lineNoCov">          0 :                     iblock[je] = ib;</span></a>
+<a name="28922"><span class="lineNum">   28922 </span>            :                 }</a>
+<a name="28923"><span class="lineNum">   28923 </span>            :             }</a>
+<a name="28924"><span class="lineNum">   28924 </span>            : </a>
+<a name="28925"><span class="lineNum">   28925 </span><span class="lineNoCov">          0 :             *m += im;</span></a>
+<a name="28926"><span class="lineNum">   28926 </span>            :         }</a>
+<a name="28927"><span class="lineNum">   28927 </span>            :     }</a>
+<a name="28928"><span class="lineNum">   28928 </span>            : </a>
+<a name="28929"><span class="lineNum">   28929 </span><span class="lineNoCov">          0 :     if (irange == 3) {</span></a>
+<a name="28930"><span class="lineNum">   28930 </span><span class="lineNoCov">          0 :         im = 0;</span></a>
+<a name="28931"><span class="lineNum">   28931 </span><span class="lineNoCov">          0 :         idiscl = *il - 1 - nwl;</span></a>
+<a name="28932"><span class="lineNum">   28932 </span><span class="lineNoCov">          0 :         idiscu = nwu - *iu;</span></a>
+<a name="28933"><span class="lineNum">   28933 </span>            : </a>
+<a name="28934"><span class="lineNum">   28934 </span><span class="lineNoCov">          0 :         if (idiscl &gt; 0 || idiscu &gt; 0) {</span></a>
+<a name="28935"><span class="lineNum">   28935 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="28936"><span class="lineNum">   28936 </span><span class="lineNoCov">          0 :             for (je = 1; je &lt;= i__1; ++je) {</span></a>
+<a name="28937"><span class="lineNum">   28937 </span><span class="lineNoCov">          0 :                 if (w[je] &lt;= wlu &amp;&amp; idiscl &gt; 0) {</span></a>
+<a name="28938"><span class="lineNum">   28938 </span><span class="lineNoCov">          0 :                     --idiscl;</span></a>
+<a name="28939"><span class="lineNum">   28939 </span><span class="lineNoCov">          0 :                 } else if (w[je] &gt;= wul &amp;&amp; idiscu &gt; 0) {</span></a>
+<a name="28940"><span class="lineNum">   28940 </span><span class="lineNoCov">          0 :                     --idiscu;</span></a>
+<a name="28941"><span class="lineNum">   28941 </span>            :                 } else {</a>
+<a name="28942"><span class="lineNum">   28942 </span><span class="lineNoCov">          0 :                     ++im;</span></a>
+<a name="28943"><span class="lineNum">   28943 </span><span class="lineNoCov">          0 :                     w[im] = w[je];</span></a>
+<a name="28944"><span class="lineNum">   28944 </span><span class="lineNoCov">          0 :                     iblock[im] = iblock[je];</span></a>
+<a name="28945"><span class="lineNum">   28945 </span>            :                 }</a>
+<a name="28946"><span class="lineNum">   28946 </span>            :             }</a>
+<a name="28947"><span class="lineNum">   28947 </span><span class="lineNoCov">          0 :             *m = im;</span></a>
+<a name="28948"><span class="lineNum">   28948 </span>            :         }</a>
+<a name="28949"><span class="lineNum">   28949 </span><span class="lineNoCov">          0 :         if (idiscl &gt; 0 || idiscu &gt; 0) {</span></a>
+<a name="28950"><span class="lineNum">   28950 </span>            : </a>
+<a name="28951"><span class="lineNum">   28951 </span><span class="lineNoCov">          0 :             if (idiscl &gt; 0) {</span></a>
+<a name="28952"><span class="lineNum">   28952 </span>            :                 wkill = wu;</a>
+<a name="28953"><span class="lineNum">   28953 </span>            :                 i__1 = idiscl;</a>
+<a name="28954"><span class="lineNum">   28954 </span><span class="lineNoCov">          0 :                 for (jdisc = 1; jdisc &lt;= i__1; ++jdisc) {</span></a>
+<a name="28955"><span class="lineNum">   28955 </span>            :                     iw = 0;</a>
+<a name="28956"><span class="lineNum">   28956 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="28957"><span class="lineNum">   28957 </span><span class="lineNoCov">          0 :                     for (je = 1; je &lt;= i__2; ++je) {</span></a>
+<a name="28958"><span class="lineNum">   28958 </span><span class="lineNoCov">          0 :                         if (iblock[je] != 0 &amp;&amp; (w[je] &lt; wkill || iw == 0)) {</span></a>
+<a name="28959"><span class="lineNum">   28959 </span>            :                             iw = je;</a>
+<a name="28960"><span class="lineNum">   28960 </span>            :                             wkill = w[je];</a>
+<a name="28961"><span class="lineNum">   28961 </span>            :                         }</a>
+<a name="28962"><span class="lineNum">   28962 </span>            :                     }</a>
+<a name="28963"><span class="lineNum">   28963 </span><span class="lineNoCov">          0 :                     iblock[iw] = 0;</span></a>
+<a name="28964"><span class="lineNum">   28964 </span>            :                 }</a>
+<a name="28965"><span class="lineNum">   28965 </span>            :             }</a>
+<a name="28966"><span class="lineNum">   28966 </span><span class="lineNoCov">          0 :             if (idiscu &gt; 0) {</span></a>
+<a name="28967"><span class="lineNum">   28967 </span>            : </a>
+<a name="28968"><span class="lineNum">   28968 </span>            :                 wkill = wl;</a>
+<a name="28969"><span class="lineNum">   28969 </span>            :                 i__1 = idiscu;</a>
+<a name="28970"><span class="lineNum">   28970 </span><span class="lineNoCov">          0 :                 for (jdisc = 1; jdisc &lt;= i__1; ++jdisc) {</span></a>
+<a name="28971"><span class="lineNum">   28971 </span>            :                     iw = 0;</a>
+<a name="28972"><span class="lineNum">   28972 </span><span class="lineNoCov">          0 :                     i__2 = *m;</span></a>
+<a name="28973"><span class="lineNum">   28973 </span><span class="lineNoCov">          0 :                     for (je = 1; je &lt;= i__2; ++je) {</span></a>
+<a name="28974"><span class="lineNum">   28974 </span><span class="lineNoCov">          0 :                         if (iblock[je] != 0 &amp;&amp; (w[je] &gt; wkill || iw == 0)) {</span></a>
+<a name="28975"><span class="lineNum">   28975 </span>            :                             iw = je;</a>
+<a name="28976"><span class="lineNum">   28976 </span>            :                             wkill = w[je];</a>
+<a name="28977"><span class="lineNum">   28977 </span>            :                         }</a>
+<a name="28978"><span class="lineNum">   28978 </span>            :                     }</a>
+<a name="28979"><span class="lineNum">   28979 </span><span class="lineNoCov">          0 :                     iblock[iw] = 0;</span></a>
+<a name="28980"><span class="lineNum">   28980 </span>            :                 }</a>
+<a name="28981"><span class="lineNum">   28981 </span>            :             }</a>
+<a name="28982"><span class="lineNum">   28982 </span><span class="lineNoCov">          0 :             im = 0;</span></a>
+<a name="28983"><span class="lineNum">   28983 </span><span class="lineNoCov">          0 :             i__1 = *m;</span></a>
+<a name="28984"><span class="lineNum">   28984 </span><span class="lineNoCov">          0 :             for (je = 1; je &lt;= i__1; ++je) {</span></a>
+<a name="28985"><span class="lineNum">   28985 </span><span class="lineNoCov">          0 :                 if (iblock[je] != 0) {</span></a>
+<a name="28986"><span class="lineNum">   28986 </span><span class="lineNoCov">          0 :                     ++im;</span></a>
+<a name="28987"><span class="lineNum">   28987 </span><span class="lineNoCov">          0 :                     w[im] = w[je];</span></a>
+<a name="28988"><span class="lineNum">   28988 </span><span class="lineNoCov">          0 :                     iblock[im] = iblock[je];</span></a>
+<a name="28989"><span class="lineNum">   28989 </span>            :                 }</a>
+<a name="28990"><span class="lineNum">   28990 </span>            :             }</a>
+<a name="28991"><span class="lineNum">   28991 </span><span class="lineNoCov">          0 :             *m = im;</span></a>
+<a name="28992"><span class="lineNum">   28992 </span>            :         }</a>
+<a name="28993"><span class="lineNum">   28993 </span><span class="lineNoCov">          0 :         if (idiscl &lt; 0 || idiscu &lt; 0) {</span></a>
+<a name="28994"><span class="lineNum">   28994 </span>            :             toofew = 1;</a>
+<a name="28995"><span class="lineNum">   28995 </span>            :         }</a>
+<a name="28996"><span class="lineNum">   28996 </span>            :     }</a>
+<a name="28997"><span class="lineNum">   28997 </span>            : </a>
+<a name="28998"><span class="lineNum">   28998 </span><span class="lineNoCov">          0 :     if (iorder == 1 &amp;&amp; *nsplit &gt; 1) {</span></a>
+<a name="28999"><span class="lineNum">   28999 </span><span class="lineNoCov">          0 :         i__1 = *m - 1;</span></a>
+<a name="29000"><span class="lineNum">   29000 </span><span class="lineNoCov">          0 :         for (je = 1; je &lt;= i__1; ++je) {</span></a>
+<a name="29001"><span class="lineNum">   29001 </span>            :             ie = 0;</a>
+<a name="29002"><span class="lineNum">   29002 </span><span class="lineNoCov">          0 :             tmp1 = w[je];</span></a>
+<a name="29003"><span class="lineNum">   29003 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="29004"><span class="lineNum">   29004 </span><span class="lineNoCov">          0 :             for (j = je + 1; j &lt;= i__2; ++j) {</span></a>
+<a name="29005"><span class="lineNum">   29005 </span><span class="lineNoCov">          0 :                 if (w[j] &lt; tmp1) {</span></a>
+<a name="29006"><span class="lineNum">   29006 </span>            :                     ie = j;</a>
+<a name="29007"><span class="lineNum">   29007 </span>            :                     tmp1 = w[j];</a>
+<a name="29008"><span class="lineNum">   29008 </span>            :                 }</a>
+<a name="29009"><span class="lineNum">   29009 </span>            :             }</a>
+<a name="29010"><span class="lineNum">   29010 </span>            : </a>
+<a name="29011"><span class="lineNum">   29011 </span><span class="lineNoCov">          0 :             if (ie != 0) {</span></a>
+<a name="29012"><span class="lineNum">   29012 </span><span class="lineNoCov">          0 :                 itmp1 = iblock[ie];</span></a>
+<a name="29013"><span class="lineNum">   29013 </span><span class="lineNoCov">          0 :                 w[ie] = w[je];</span></a>
+<a name="29014"><span class="lineNum">   29014 </span><span class="lineNoCov">          0 :                 iblock[ie] = iblock[je];</span></a>
+<a name="29015"><span class="lineNum">   29015 </span><span class="lineNoCov">          0 :                 w[je] = tmp1;</span></a>
+<a name="29016"><span class="lineNum">   29016 </span><span class="lineNoCov">          0 :                 iblock[je] = itmp1;</span></a>
+<a name="29017"><span class="lineNum">   29017 </span>            :             }</a>
+<a name="29018"><span class="lineNum">   29018 </span>            :         }</a>
+<a name="29019"><span class="lineNum">   29019 </span>            :     }</a>
+<a name="29020"><span class="lineNum">   29020 </span>            : </a>
+<a name="29021"><span class="lineNum">   29021 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="29022"><span class="lineNum">   29022 </span><span class="lineNoCov">          0 :     if (ncnvrg) {</span></a>
+<a name="29023"><span class="lineNum">   29023 </span><span class="lineNoCov">          0 :         ++(*info);</span></a>
+<a name="29024"><span class="lineNum">   29024 </span>            :     }</a>
+<a name="29025"><span class="lineNum">   29025 </span><span class="lineNoCov">          0 :     if (toofew) {</span></a>
+<a name="29026"><span class="lineNum">   29026 </span><span class="lineNoCov">          0 :         *info += 2;</span></a>
+<a name="29027"><span class="lineNum">   29027 </span>            :     }</a>
+<a name="29028"><span class="lineNum">   29028 </span>            :     return;</a>
+<a name="29029"><span class="lineNum">   29029 </span>            : </a>
+<a name="29030"><span class="lineNum">   29030 </span>            : }</a>
+<a name="29031"><span class="lineNum">   29031 </span>            : </a>
+<a name="29032"><span class="lineNum">   29032 </span>            : </a>
+<a name="29033"><span class="lineNum">   29033 </span>            : }</a>
+<a name="29034"><span class="lineNum">   29034 </span>            : }</a>
+<a name="29035"><span class="lineNum">   29035 </span>            : #include &lt;cmath&gt;</a>
+<a name="29036"><span class="lineNum">   29036 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29037"><span class="lineNum">   29037 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="29038"><span class="lineNum">   29038 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="29039"><span class="lineNum">   29039 </span>            : </a>
+<a name="29040"><span class="lineNum">   29040 </span>            : #include &quot;real.h&quot;</a>
+<a name="29041"><span class="lineNum">   29041 </span>            : </a>
+<a name="29042"><span class="lineNum">   29042 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29043"><span class="lineNum">   29043 </span>            : namespace PLMD{</a>
+<a name="29044"><span class="lineNum">   29044 </span>            : namespace lapack{</a>
+<a name="29045"><span class="lineNum">   29045 </span>            : using namespace blas;</a>
+<a name="29046"><span class="lineNum">   29046 </span>            : void</a>
+<a name="29047"><span class="lineNum">   29047 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sstegr,SSTEGR)(const char *jobz, </span></a>
+<a name="29048"><span class="lineNum">   29048 </span>            :         const char *range, </a>
+<a name="29049"><span class="lineNum">   29049 </span>            :         int *n, </a>
+<a name="29050"><span class="lineNum">   29050 </span>            :         float *d__, </a>
+<a name="29051"><span class="lineNum">   29051 </span>            :         float *e, </a>
+<a name="29052"><span class="lineNum">   29052 </span>            :         float *vl, </a>
+<a name="29053"><span class="lineNum">   29053 </span>            :         float *vu, </a>
+<a name="29054"><span class="lineNum">   29054 </span>            :         int *il, </a>
+<a name="29055"><span class="lineNum">   29055 </span>            :         int *iu, </a>
+<a name="29056"><span class="lineNum">   29056 </span>            :         float *abstol, </a>
+<a name="29057"><span class="lineNum">   29057 </span>            :         int *m, </a>
+<a name="29058"><span class="lineNum">   29058 </span>            :         float *w, </a>
+<a name="29059"><span class="lineNum">   29059 </span>            :         float *z__, </a>
+<a name="29060"><span class="lineNum">   29060 </span>            :         int *ldz, </a>
+<a name="29061"><span class="lineNum">   29061 </span>            :         int *isuppz,</a>
+<a name="29062"><span class="lineNum">   29062 </span>            :         float *work, </a>
+<a name="29063"><span class="lineNum">   29063 </span>            :         int *lwork, </a>
+<a name="29064"><span class="lineNum">   29064 </span>            :         int *iwork, </a>
+<a name="29065"><span class="lineNum">   29065 </span>            :         int *liwork, </a>
+<a name="29066"><span class="lineNum">   29066 </span>            :         int *info)</a>
+<a name="29067"><span class="lineNum">   29067 </span>            : {</a>
+<a name="29068"><span class="lineNum">   29068 </span>            :     int z_dim1, z_offset, i__1, i__2;</a>
+<a name="29069"><span class="lineNum">   29069 </span>            :     float d__1, d__2;</a>
+<a name="29070"><span class="lineNum">   29070 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="29071"><span class="lineNum">   29071 </span>            : </a>
+<a name="29072"><span class="lineNum">   29072 </span>            :     int i__, j;</a>
+<a name="29073"><span class="lineNum">   29073 </span>            :     int jj;</a>
+<a name="29074"><span class="lineNum">   29074 </span>            :     float eps, tol, tmp, rmin, rmax;</a>
+<a name="29075"><span class="lineNum">   29075 </span>            :     int itmp;</a>
+<a name="29076"><span class="lineNum">   29076 </span>            :     float tnrm;</a>
+<a name="29077"><span class="lineNum">   29077 </span>            :     float scale;</a>
+<a name="29078"><span class="lineNum">   29078 </span>            :     int iinfo, iindw;</a>
+<a name="29079"><span class="lineNum">   29079 </span>            :     int lwmin;</a>
+<a name="29080"><span class="lineNum">   29080 </span>            :     int wantz;</a>
+<a name="29081"><span class="lineNum">   29081 </span>            :     int iindbl;</a>
+<a name="29082"><span class="lineNum">   29082 </span>            :     int valeig,alleig,indeig;</a>
+<a name="29083"><span class="lineNum">   29083 </span>            :     float safmin,minval;</a>
+<a name="29084"><span class="lineNum">   29084 </span>            :     float bignum;</a>
+<a name="29085"><span class="lineNum">   29085 </span>            :     int iindwk, indgrs;</a>
+<a name="29086"><span class="lineNum">   29086 </span>            :     float thresh;</a>
+<a name="29087"><span class="lineNum">   29087 </span>            :     int iinspl, indwrk, liwmin, nsplit;</a>
+<a name="29088"><span class="lineNum">   29088 </span>            :     float smlnum;</a>
+<a name="29089"><span class="lineNum">   29089 </span>            :     int lquery;</a>
+<a name="29090"><span class="lineNum">   29090 </span>            : </a>
+<a name="29091"><span class="lineNum">   29091 </span>            : </a>
+<a name="29092"><span class="lineNum">   29092 </span>            :     --d__;</a>
+<a name="29093"><span class="lineNum">   29093 </span>            :     --e;</a>
+<a name="29094"><span class="lineNum">   29094 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="29095"><span class="lineNum">   29095 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="29096"><span class="lineNum">   29096 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="29097"><span class="lineNum">   29097 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="29098"><span class="lineNum">   29098 </span><span class="lineNoCov">          0 :     --isuppz;</span></a>
+<a name="29099"><span class="lineNum">   29099 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="29100"><span class="lineNum">   29100 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="29101"><span class="lineNum">   29101 </span>            : </a>
+<a name="29102"><span class="lineNum">   29102 </span><span class="lineNoCov">          0 :     wantz = (*jobz=='V' || *jobz=='v');</span></a>
+<a name="29103"><span class="lineNum">   29103 </span><span class="lineNoCov">          0 :     alleig = (*range=='A' || *range=='a');</span></a>
+<a name="29104"><span class="lineNum">   29104 </span><span class="lineNoCov">          0 :     valeig = (*range=='V' || *range=='v');</span></a>
+<a name="29105"><span class="lineNum">   29105 </span><span class="lineNoCov">          0 :     indeig = (*range=='I' || *range=='i');</span></a>
+<a name="29106"><span class="lineNum">   29106 </span>            : </a>
+<a name="29107"><span class="lineNum">   29107 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1 || *liwork == -1;</span></a>
+<a name="29108"><span class="lineNum">   29108 </span><span class="lineNoCov">          0 :     lwmin = *n * 17;</span></a>
+<a name="29109"><span class="lineNum">   29109 </span><span class="lineNoCov">          0 :     liwmin = *n * 10;</span></a>
+<a name="29110"><span class="lineNum">   29110 </span>            : </a>
+<a name="29111"><span class="lineNum">   29111 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="29112"><span class="lineNum">   29112 </span><span class="lineNoCov">          0 :     if (! (wantz || (*jobz=='N' || *jobz=='n'))) {</span></a>
+<a name="29113"><span class="lineNum">   29113 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="29114"><span class="lineNum">   29114 </span><span class="lineNoCov">          0 :     } else if (! (alleig || valeig || indeig)) {</span></a>
+<a name="29115"><span class="lineNum">   29115 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="29116"><span class="lineNum">   29116 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="29117"><span class="lineNum">   29117 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="29118"><span class="lineNum">   29118 </span><span class="lineNoCov">          0 :     } else if (valeig &amp;&amp; *n &gt; 0 &amp;&amp; *vu &lt;= *vl) {</span></a>
+<a name="29119"><span class="lineNum">   29119 </span><span class="lineNoCov">          0 :         *info = -7;</span></a>
+<a name="29120"><span class="lineNum">   29120 </span><span class="lineNoCov">          0 :     } else if (indeig &amp;&amp; (*il &lt; 1 || *il &gt; *n)) {</span></a>
+<a name="29121"><span class="lineNum">   29121 </span><span class="lineNoCov">          0 :         *info = -8;</span></a>
+<a name="29122"><span class="lineNum">   29122 </span><span class="lineNoCov">          0 :     } else if (indeig &amp;&amp; (*iu &lt; *il || *iu &gt; *n)) {</span></a>
+<a name="29123"><span class="lineNum">   29123 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="29124"><span class="lineNum">   29124 </span><span class="lineNoCov">          0 :     } else if (*ldz &lt; 1 || (wantz &amp;&amp; *ldz &lt; *n)) {</span></a>
+<a name="29125"><span class="lineNum">   29125 </span><span class="lineNoCov">          0 :         *info = -14;</span></a>
+<a name="29126"><span class="lineNum">   29126 </span><span class="lineNoCov">          0 :     } else if (*lwork &lt; lwmin &amp;&amp; ! lquery) {</span></a>
+<a name="29127"><span class="lineNum">   29127 </span><span class="lineNoCov">          0 :         *info = -17;</span></a>
+<a name="29128"><span class="lineNum">   29128 </span><span class="lineNoCov">          0 :     } else if (*liwork &lt; liwmin &amp;&amp; ! lquery) {</span></a>
+<a name="29129"><span class="lineNum">   29129 </span><span class="lineNoCov">          0 :         *info = -19;</span></a>
+<a name="29130"><span class="lineNum">   29130 </span>            :     }</a>
+<a name="29131"><span class="lineNum">   29131 </span><span class="lineNoCov">          0 :     if (*info == 0) {</span></a>
+<a name="29132"><span class="lineNum">   29132 </span><span class="lineNoCov">          0 :         work[1] = (float) lwmin;</span></a>
+<a name="29133"><span class="lineNum">   29133 </span><span class="lineNoCov">          0 :         iwork[1] = liwmin;</span></a>
+<a name="29134"><span class="lineNum">   29134 </span>            :     }</a>
+<a name="29135"><span class="lineNum">   29135 </span>            : </a>
+<a name="29136"><span class="lineNum">   29136 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="29137"><span class="lineNum">   29137 </span>            :         i__1 = -(*info);</a>
+<a name="29138"><span class="lineNum">   29138 </span>            :         return;</a>
+<a name="29139"><span class="lineNum">   29139 </span><span class="lineNoCov">          0 :     } else if (lquery) {</span></a>
+<a name="29140"><span class="lineNum">   29140 </span>            :         return;</a>
+<a name="29141"><span class="lineNum">   29141 </span>            :     }</a>
+<a name="29142"><span class="lineNum">   29142 </span>            : </a>
+<a name="29143"><span class="lineNum">   29143 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="29144"><span class="lineNum">   29144 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="29145"><span class="lineNum">   29145 </span>            :         return;</a>
+<a name="29146"><span class="lineNum">   29146 </span>            :     }</a>
+<a name="29147"><span class="lineNum">   29147 </span>            : </a>
+<a name="29148"><span class="lineNum">   29148 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="29149"><span class="lineNum">   29149 </span><span class="lineNoCov">          0 :         if (alleig || indeig) {</span></a>
+<a name="29150"><span class="lineNum">   29150 </span><span class="lineNoCov">          0 :             *m = 1;</span></a>
+<a name="29151"><span class="lineNum">   29151 </span><span class="lineNoCov">          0 :             w[1] = d__[1];</span></a>
+<a name="29152"><span class="lineNum">   29152 </span>            :         } else {</a>
+<a name="29153"><span class="lineNum">   29153 </span><span class="lineNoCov">          0 :             if (*vl &lt; d__[1] &amp;&amp; *vu &gt;= d__[1]) {</span></a>
+<a name="29154"><span class="lineNum">   29154 </span><span class="lineNoCov">          0 :                 *m = 1;</span></a>
+<a name="29155"><span class="lineNum">   29155 </span><span class="lineNoCov">          0 :                 w[1] = d__[1];</span></a>
+<a name="29156"><span class="lineNum">   29156 </span>            :             }</a>
+<a name="29157"><span class="lineNum">   29157 </span>            :         }</a>
+<a name="29158"><span class="lineNum">   29158 </span><span class="lineNoCov">          0 :         if (wantz) {</span></a>
+<a name="29159"><span class="lineNum">   29159 </span><span class="lineNoCov">          0 :             z__[z_dim1 + 1] = 1.;</span></a>
+<a name="29160"><span class="lineNum">   29160 </span>            :         }</a>
+<a name="29161"><span class="lineNum">   29161 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="29162"><span class="lineNum">   29162 </span>            :     }</a>
+<a name="29163"><span class="lineNum">   29163 </span>            : </a>
+<a name="29164"><span class="lineNum">   29164 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="29165"><span class="lineNum">   29165 </span>            :     safmin = minval*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="29166"><span class="lineNum">   29166 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="29167"><span class="lineNum">   29167 </span>            :     smlnum = safmin / eps;</a>
+<a name="29168"><span class="lineNum">   29168 </span>            :     bignum = 1. / smlnum;</a>
+<a name="29169"><span class="lineNum">   29169 </span>            :     rmin =  std::sqrt(smlnum);</a>
+<a name="29170"><span class="lineNum">   29170 </span><span class="lineNoCov">          0 :     d__1 =  std::sqrt(bignum), d__2 = 1. / std::sqrt(sqrt(safmin));</span></a>
+<a name="29171"><span class="lineNum">   29171 </span>            :     rmax = (d__1&lt;d__2) ? d__1 : d__2;</a>
+<a name="29172"><span class="lineNum">   29172 </span><span class="lineNoCov">          0 :     scale = 1.;</span></a>
+<a name="29173"><span class="lineNum">   29173 </span><span class="lineNoCov">          0 :     tnrm = PLUMED_BLAS_F77_FUNC(slanst,SLANST)(&quot;M&quot;, n, &amp;d__[1], &amp;e[1]);</span></a>
+<a name="29174"><span class="lineNum">   29174 </span><span class="lineNoCov">          0 :     if (tnrm &gt; 0. &amp;&amp; tnrm &lt; rmin) {</span></a>
+<a name="29175"><span class="lineNum">   29175 </span><span class="lineNoCov">          0 :         scale = rmin / tnrm;</span></a>
+<a name="29176"><span class="lineNum">   29176 </span><span class="lineNoCov">          0 :     } else if (tnrm &gt; rmax) {</span></a>
+<a name="29177"><span class="lineNum">   29177 </span><span class="lineNoCov">          0 :         scale = rmax / tnrm;</span></a>
+<a name="29178"><span class="lineNum">   29178 </span>            :     }</a>
+<a name="29179"><span class="lineNum">   29179 </span><span class="lineNoCov">          0 :     if ( std::abs(scale-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="29180"><span class="lineNum">   29180 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(n, &amp;scale, &amp;d__[1], &amp;c__1);</span></a>
+<a name="29181"><span class="lineNum">   29181 </span><span class="lineNoCov">          0 :         i__1 = *n - 1;</span></a>
+<a name="29182"><span class="lineNum">   29182 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__1, &amp;scale, &amp;e[1], &amp;c__1);</span></a>
+<a name="29183"><span class="lineNum">   29183 </span><span class="lineNoCov">          0 :         tnrm *= scale;</span></a>
+<a name="29184"><span class="lineNum">   29184 </span>            :     }</a>
+<a name="29185"><span class="lineNum">   29185 </span>            :     indgrs = 1;</a>
+<a name="29186"><span class="lineNum">   29186 </span><span class="lineNoCov">          0 :     indwrk = (*n &lt;&lt; 1) + 1;</span></a>
+<a name="29187"><span class="lineNum">   29187 </span>            : </a>
+<a name="29188"><span class="lineNum">   29188 </span>            :     iinspl = 1;</a>
+<a name="29189"><span class="lineNum">   29189 </span><span class="lineNoCov">          0 :     iindbl = *n + 1;</span></a>
+<a name="29190"><span class="lineNum">   29190 </span>            :     iindw = (*n &lt;&lt; 1) + 1;</a>
+<a name="29191"><span class="lineNum">   29191 </span><span class="lineNoCov">          0 :     iindwk = *n * 3 + 1;</span></a>
+<a name="29192"><span class="lineNum">   29192 </span>            : </a>
+<a name="29193"><span class="lineNum">   29193 </span><span class="lineNoCov">          0 :     thresh = eps * tnrm;</span></a>
+<a name="29194"><span class="lineNum">   29194 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(slarrex,SLARREX)(range, n, vl, vu, il, iu, &amp;d__[1], &amp;e[1], &amp;thresh, &amp;nsplit, &amp;</span></a>
+<a name="29195"><span class="lineNum">   29195 </span><span class="lineNoCov">          0 :             iwork[iinspl], m, &amp;w[1], &amp;iwork[iindbl], &amp;iwork[iindw], &amp;work[</span></a>
+<a name="29196"><span class="lineNum">   29196 </span><span class="lineNoCov">          0 :             indgrs], &amp;work[indwrk], &amp;iwork[iindwk], &amp;iinfo);</span></a>
+<a name="29197"><span class="lineNum">   29197 </span>            :     </a>
+<a name="29198"><span class="lineNum">   29198 </span><span class="lineNoCov">          0 :     if (iinfo != 0) {</span></a>
+<a name="29199"><span class="lineNum">   29199 </span><span class="lineNoCov">          0 :         *info = 1;</span></a>
+<a name="29200"><span class="lineNum">   29200 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="29201"><span class="lineNum">   29201 </span>            :     }</a>
+<a name="29202"><span class="lineNum">   29202 </span>            : </a>
+<a name="29203"><span class="lineNum">   29203 </span><span class="lineNoCov">          0 :     if (wantz) {</span></a>
+<a name="29204"><span class="lineNum">   29204 </span><span class="lineNoCov">          0 :         d__1 = *abstol, d__2 = (float) (*n) * eps;</span></a>
+<a name="29205"><span class="lineNum">   29205 </span><span class="lineNoCov">          0 :         tol = (d__1&gt;d__2) ? d__1 : d__2;</span></a>
+<a name="29206"><span class="lineNum">   29206 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slarrvx,SLARRVX)(n, &amp;d__[1], &amp;e[1], &amp;iwork[iinspl], m, &amp;w[1], &amp;iwork[iindbl], &amp;</span></a>
+<a name="29207"><span class="lineNum">   29207 </span>            :                 iwork[iindw], &amp;work[indgrs], &amp;tol, &amp;z__[z_offset], ldz, &amp;</a>
+<a name="29208"><span class="lineNum">   29208 </span>            :                 isuppz[1], &amp;work[indwrk], &amp;iwork[iindwk], &amp;iinfo);</a>
+<a name="29209"><span class="lineNum">   29209 </span><span class="lineNoCov">          0 :         if (iinfo != 0) {</span></a>
+<a name="29210"><span class="lineNum">   29210 </span><span class="lineNoCov">          0 :             *info = 2;</span></a>
+<a name="29211"><span class="lineNum">   29211 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="29212"><span class="lineNum">   29212 </span>            :         }</a>
+<a name="29213"><span class="lineNum">   29213 </span>            :     }</a>
+<a name="29214"><span class="lineNum">   29214 </span>            : </a>
+<a name="29215"><span class="lineNum">   29215 </span><span class="lineNoCov">          0 :     i__1 = *m;</span></a>
+<a name="29216"><span class="lineNum">   29216 </span><span class="lineNoCov">          0 :     for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="29217"><span class="lineNum">   29217 </span><span class="lineNoCov">          0 :         itmp = iwork[iindbl + j - 1];</span></a>
+<a name="29218"><span class="lineNum">   29218 </span><span class="lineNoCov">          0 :         w[j] += e[iwork[iinspl + itmp - 1]];</span></a>
+<a name="29219"><span class="lineNum">   29219 </span>            :     } </a>
+<a name="29220"><span class="lineNum">   29220 </span>            : </a>
+<a name="29221"><span class="lineNum">   29221 </span><span class="lineNoCov">          0 :     if (std::abs(scale-1.0)&gt;PLUMED_GMX_FLOAT_EPS) {</span></a>
+<a name="29222"><span class="lineNum">   29222 </span><span class="lineNoCov">          0 :         d__1 = 1. / scale;</span></a>
+<a name="29223"><span class="lineNum">   29223 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(m, &amp;d__1, &amp;w[1], &amp;c__1);</span></a>
+<a name="29224"><span class="lineNum">   29224 </span>            :     }</a>
+<a name="29225"><span class="lineNum">   29225 </span><span class="lineNoCov">          0 :     if (nsplit &gt; 1) {</span></a>
+<a name="29226"><span class="lineNum">   29226 </span><span class="lineNoCov">          0 :         i__1 = *m - 1;</span></a>
+<a name="29227"><span class="lineNum">   29227 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="29228"><span class="lineNum">   29228 </span>            :             i__ = 0;</a>
+<a name="29229"><span class="lineNum">   29229 </span><span class="lineNoCov">          0 :             tmp = w[j];</span></a>
+<a name="29230"><span class="lineNum">   29230 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="29231"><span class="lineNum">   29231 </span><span class="lineNoCov">          0 :             for (jj = j + 1; jj &lt;= i__2; ++jj) {</span></a>
+<a name="29232"><span class="lineNum">   29232 </span><span class="lineNoCov">          0 :                 if (w[jj] &lt; tmp) {</span></a>
+<a name="29233"><span class="lineNum">   29233 </span>            :                     i__ = jj;</a>
+<a name="29234"><span class="lineNum">   29234 </span>            :                     tmp = w[jj];</a>
+<a name="29235"><span class="lineNum">   29235 </span>            :                 }</a>
+<a name="29236"><span class="lineNum">   29236 </span>            :             }</a>
+<a name="29237"><span class="lineNum">   29237 </span><span class="lineNoCov">          0 :             if (i__ != 0) {</span></a>
+<a name="29238"><span class="lineNum">   29238 </span><span class="lineNoCov">          0 :                 w[i__] = w[j];</span></a>
+<a name="29239"><span class="lineNum">   29239 </span><span class="lineNoCov">          0 :                 w[j] = tmp;</span></a>
+<a name="29240"><span class="lineNum">   29240 </span><span class="lineNoCov">          0 :                 if (wantz) {</span></a>
+<a name="29241"><span class="lineNum">   29241 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n, &amp;z__[i__ * z_dim1 + 1], &amp;c__1, &amp;z__[j * z_dim1 </span></a>
+<a name="29242"><span class="lineNum">   29242 </span><span class="lineNoCov">          0 :                             + 1], &amp;c__1);</span></a>
+<a name="29243"><span class="lineNum">   29243 </span><span class="lineNoCov">          0 :                     itmp = isuppz[(i__ &lt;&lt; 1) - 1];</span></a>
+<a name="29244"><span class="lineNum">   29244 </span><span class="lineNoCov">          0 :                     isuppz[(i__ &lt;&lt; 1) - 1] = isuppz[(j &lt;&lt; 1) - 1];</span></a>
+<a name="29245"><span class="lineNum">   29245 </span><span class="lineNoCov">          0 :                     isuppz[(j &lt;&lt; 1) - 1] = itmp;</span></a>
+<a name="29246"><span class="lineNum">   29246 </span><span class="lineNoCov">          0 :                     itmp = isuppz[i__ * 2];</span></a>
+<a name="29247"><span class="lineNum">   29247 </span><span class="lineNoCov">          0 :                     isuppz[i__ * 2] = isuppz[j * 2];</span></a>
+<a name="29248"><span class="lineNum">   29248 </span><span class="lineNoCov">          0 :                     isuppz[j * 2] = itmp;</span></a>
+<a name="29249"><span class="lineNum">   29249 </span>            :                 }</a>
+<a name="29250"><span class="lineNum">   29250 </span>            :             }</a>
+<a name="29251"><span class="lineNum">   29251 </span>            :         }</a>
+<a name="29252"><span class="lineNum">   29252 </span>            :     }</a>
+<a name="29253"><span class="lineNum">   29253 </span>            : </a>
+<a name="29254"><span class="lineNum">   29254 </span><span class="lineNoCov">          0 :     work[1] = (float) lwmin;</span></a>
+<a name="29255"><span class="lineNum">   29255 </span><span class="lineNoCov">          0 :     iwork[1] = liwmin;</span></a>
+<a name="29256"><span class="lineNum">   29256 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="29257"><span class="lineNum">   29257 </span>            : </a>
+<a name="29258"><span class="lineNum">   29258 </span>            : } </a>
+<a name="29259"><span class="lineNum">   29259 </span>            : }</a>
+<a name="29260"><span class="lineNum">   29260 </span>            : }</a>
+<a name="29261"><span class="lineNum">   29261 </span>            : #include &lt;cmath&gt;</a>
+<a name="29262"><span class="lineNum">   29262 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29263"><span class="lineNum">   29263 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="29264"><span class="lineNum">   29264 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="29265"><span class="lineNum">   29265 </span>            : </a>
+<a name="29266"><span class="lineNum">   29266 </span>            : #include &quot;real.h&quot;</a>
+<a name="29267"><span class="lineNum">   29267 </span>            : </a>
+<a name="29268"><span class="lineNum">   29268 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29269"><span class="lineNum">   29269 </span>            : namespace PLMD{</a>
+<a name="29270"><span class="lineNum">   29270 </span>            : namespace lapack{</a>
+<a name="29271"><span class="lineNum">   29271 </span>            : using namespace blas;</a>
+<a name="29272"><span class="lineNum">   29272 </span>            : void</a>
+<a name="29273"><span class="lineNum">   29273 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sstein,SSTEIN)(int *n, </span></a>
+<a name="29274"><span class="lineNum">   29274 </span>            :         float *d__, </a>
+<a name="29275"><span class="lineNum">   29275 </span>            :         float *e, </a>
+<a name="29276"><span class="lineNum">   29276 </span>            :         int *m, </a>
+<a name="29277"><span class="lineNum">   29277 </span>            :         float *w, </a>
+<a name="29278"><span class="lineNum">   29278 </span>            :         int *iblock,</a>
+<a name="29279"><span class="lineNum">   29279 </span>            :         int *isplit, </a>
+<a name="29280"><span class="lineNum">   29280 </span>            :         float *z__,</a>
+<a name="29281"><span class="lineNum">   29281 </span>            :         int *ldz, </a>
+<a name="29282"><span class="lineNum">   29282 </span>            :         float *work,</a>
+<a name="29283"><span class="lineNum">   29283 </span>            :         int *iwork, </a>
+<a name="29284"><span class="lineNum">   29284 </span>            :         int *ifail,</a>
+<a name="29285"><span class="lineNum">   29285 </span>            :         int *info)</a>
+<a name="29286"><span class="lineNum">   29286 </span>            : {</a>
+<a name="29287"><span class="lineNum">   29287 </span>            :     int z_dim1, z_offset, i__1, i__2, i__3;</a>
+<a name="29288"><span class="lineNum">   29288 </span>            :     float d__2, d__3, d__4, d__5;</a>
+<a name="29289"><span class="lineNum">   29289 </span>            : </a>
+<a name="29290"><span class="lineNum">   29290 </span>            :     int i__, j, b1, j1, bn;</a>
+<a name="29291"><span class="lineNum">   29291 </span>            :     float xj, scl, eps, sep, nrm, tol;</a>
+<a name="29292"><span class="lineNum">   29292 </span>            :     int its;</a>
+<a name="29293"><span class="lineNum">   29293 </span>            :     float xjm, ztr, eps1;</a>
+<a name="29294"><span class="lineNum">   29294 </span>            :     int jblk, nblk;</a>
+<a name="29295"><span class="lineNum">   29295 </span>            :     int jmax;</a>
+<a name="29296"><span class="lineNum">   29296 </span>            : </a>
+<a name="29297"><span class="lineNum">   29297 </span>            :     int iseed[4], gpind, iinfo;</a>
+<a name="29298"><span class="lineNum">   29298 </span>            :     float ortol;</a>
+<a name="29299"><span class="lineNum">   29299 </span>            :     int indrv1, indrv2, indrv3, indrv4, indrv5;</a>
+<a name="29300"><span class="lineNum">   29300 </span>            :     int nrmchk;</a>
+<a name="29301"><span class="lineNum">   29301 </span>            :     int blksiz;</a>
+<a name="29302"><span class="lineNum">   29302 </span>            :     float onenrm, dtpcrt, pertol;</a>
+<a name="29303"><span class="lineNum">   29303 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="29304"><span class="lineNum">   29304 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="29305"><span class="lineNum">   29305 </span><span class="lineNoCov">          0 :     int c_n1 = -1;</span></a>
+<a name="29306"><span class="lineNum">   29306 </span>            : </a>
+<a name="29307"><span class="lineNum">   29307 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="29308"><span class="lineNum">   29308 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="29309"><span class="lineNum">   29309 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="29310"><span class="lineNum">   29310 </span><span class="lineNoCov">          0 :     --iblock;</span></a>
+<a name="29311"><span class="lineNum">   29311 </span><span class="lineNoCov">          0 :     --isplit;</span></a>
+<a name="29312"><span class="lineNum">   29312 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="29313"><span class="lineNum">   29313 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="29314"><span class="lineNum">   29314 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="29315"><span class="lineNum">   29315 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="29316"><span class="lineNum">   29316 </span>            :     --iwork;</a>
+<a name="29317"><span class="lineNum">   29317 </span><span class="lineNoCov">          0 :     --ifail;</span></a>
+<a name="29318"><span class="lineNum">   29318 </span>            : </a>
+<a name="29319"><span class="lineNum">   29319 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="29320"><span class="lineNum">   29320 </span>            : </a>
+<a name="29321"><span class="lineNum">   29321 </span>            :     xjm = 0.0;</a>
+<a name="29322"><span class="lineNum">   29322 </span><span class="lineNoCov">          0 :     i__1 = *m;</span></a>
+<a name="29323"><span class="lineNum">   29323 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="29324"><span class="lineNum">   29324 </span><span class="lineNoCov">          0 :         ifail[i__] = 0;</span></a>
+<a name="29325"><span class="lineNum">   29325 </span>            :     }</a>
+<a name="29326"><span class="lineNum">   29326 </span>            : </a>
+<a name="29327"><span class="lineNum">   29327 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="29328"><span class="lineNum">   29328 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="29329"><span class="lineNum">   29329 </span><span class="lineNoCov">          0 :     } else if (*m &lt; 0 || *m &gt; *n) {</span></a>
+<a name="29330"><span class="lineNum">   29330 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="29331"><span class="lineNum">   29331 </span><span class="lineNoCov">          0 :     } else if (*ldz &lt; (*n)) {</span></a>
+<a name="29332"><span class="lineNum">   29332 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="29333"><span class="lineNum">   29333 </span>            :     } else {</a>
+<a name="29334"><span class="lineNum">   29334 </span>            :         i__1 = *m;</a>
+<a name="29335"><span class="lineNum">   29335 </span><span class="lineNoCov">          0 :         for (j = 2; j &lt;= i__1; ++j) {</span></a>
+<a name="29336"><span class="lineNum">   29336 </span><span class="lineNoCov">          0 :             if (iblock[j] &lt; iblock[j - 1]) {</span></a>
+<a name="29337"><span class="lineNum">   29337 </span><span class="lineNoCov">          0 :                 *info = -6;</span></a>
+<a name="29338"><span class="lineNum">   29338 </span><span class="lineNoCov">          0 :                 break;</span></a>
+<a name="29339"><span class="lineNum">   29339 </span>            :             }</a>
+<a name="29340"><span class="lineNum">   29340 </span><span class="lineNoCov">          0 :             if (iblock[j] == iblock[j - 1] &amp;&amp; w[j] &lt; w[j - 1]) {</span></a>
+<a name="29341"><span class="lineNum">   29341 </span><span class="lineNoCov">          0 :                 *info = -5;</span></a>
+<a name="29342"><span class="lineNum">   29342 </span><span class="lineNoCov">          0 :                 break;</span></a>
+<a name="29343"><span class="lineNum">   29343 </span>            :             }</a>
+<a name="29344"><span class="lineNum">   29344 </span>            :         }</a>
+<a name="29345"><span class="lineNum">   29345 </span>            :     }</a>
+<a name="29346"><span class="lineNum">   29346 </span>            : </a>
+<a name="29347"><span class="lineNum">   29347 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="29348"><span class="lineNum">   29348 </span>            :         return;</a>
+<a name="29349"><span class="lineNum">   29349 </span>            :     }</a>
+<a name="29350"><span class="lineNum">   29350 </span>            : </a>
+<a name="29351"><span class="lineNum">   29351 </span><span class="lineNoCov">          0 :     if (*n == 0 || *m == 0) {</span></a>
+<a name="29352"><span class="lineNum">   29352 </span>            :         return;</a>
+<a name="29353"><span class="lineNum">   29353 </span><span class="lineNoCov">          0 :     } else if (*n == 1) {</span></a>
+<a name="29354"><span class="lineNum">   29354 </span><span class="lineNoCov">          0 :         z__[z_dim1 + 1] = 1.;</span></a>
+<a name="29355"><span class="lineNum">   29355 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="29356"><span class="lineNum">   29356 </span>            :     }</a>
+<a name="29357"><span class="lineNum">   29357 </span>            : </a>
+<a name="29358"><span class="lineNum">   29358 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="29359"><span class="lineNum">   29359 </span>            : </a>
+<a name="29360"><span class="lineNum">   29360 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= 4; ++i__) {</span></a>
+<a name="29361"><span class="lineNum">   29361 </span><span class="lineNoCov">          0 :         iseed[i__ - 1] = 1;</span></a>
+<a name="29362"><span class="lineNum">   29362 </span>            :     }</a>
+<a name="29363"><span class="lineNum">   29363 </span>            : </a>
+<a name="29364"><span class="lineNum">   29364 </span>            :     indrv1 = 0;</a>
+<a name="29365"><span class="lineNum">   29365 </span>            :     indrv2 = indrv1 + *n;</a>
+<a name="29366"><span class="lineNum">   29366 </span><span class="lineNoCov">          0 :     indrv3 = indrv2 + *n;</span></a>
+<a name="29367"><span class="lineNum">   29367 </span><span class="lineNoCov">          0 :     indrv4 = indrv3 + *n;</span></a>
+<a name="29368"><span class="lineNum">   29368 </span><span class="lineNoCov">          0 :     indrv5 = indrv4 + *n;</span></a>
+<a name="29369"><span class="lineNum">   29369 </span>            : </a>
+<a name="29370"><span class="lineNum">   29370 </span>            :     j1 = 1;</a>
+<a name="29371"><span class="lineNum">   29371 </span><span class="lineNoCov">          0 :     i__1 = iblock[*m];</span></a>
+<a name="29372"><span class="lineNum">   29372 </span><span class="lineNoCov">          0 :     for (nblk = 1; nblk &lt;= i__1; ++nblk) {</span></a>
+<a name="29373"><span class="lineNum">   29373 </span>            : </a>
+<a name="29374"><span class="lineNum">   29374 </span><span class="lineNoCov">          0 :         if (nblk == 1) {</span></a>
+<a name="29375"><span class="lineNum">   29375 </span>            :             b1 = 1;</a>
+<a name="29376"><span class="lineNum">   29376 </span>            :         } else {</a>
+<a name="29377"><span class="lineNum">   29377 </span><span class="lineNoCov">          0 :             b1 = isplit[nblk - 1] + 1;</span></a>
+<a name="29378"><span class="lineNum">   29378 </span>            :         }</a>
+<a name="29379"><span class="lineNum">   29379 </span><span class="lineNoCov">          0 :         bn = isplit[nblk];</span></a>
+<a name="29380"><span class="lineNum">   29380 </span><span class="lineNoCov">          0 :         blksiz = bn - b1 + 1;</span></a>
+<a name="29381"><span class="lineNum">   29381 </span><span class="lineNoCov">          0 :         if (blksiz == 1) {</span></a>
+<a name="29382"><span class="lineNum">   29382 </span><span class="lineNoCov">          0 :             continue;</span></a>
+<a name="29383"><span class="lineNum">   29383 </span>            :         }</a>
+<a name="29384"><span class="lineNum">   29384 </span>            :         gpind = b1;</a>
+<a name="29385"><span class="lineNum">   29385 </span>            : </a>
+<a name="29386"><span class="lineNum">   29386 </span><span class="lineNoCov">          0 :         onenrm = std::abs(d__[b1]) + std::abs(e[b1]);</span></a>
+<a name="29387"><span class="lineNum">   29387 </span>            :         d__3 = onenrm;</a>
+<a name="29388"><span class="lineNum">   29388 </span><span class="lineNoCov">          0 :         d__4 = std::abs(d__[bn]) + std::abs(e[bn - 1]);</span></a>
+<a name="29389"><span class="lineNum">   29389 </span><span class="lineNoCov">          0 :         onenrm = (d__3&gt;d__4) ? d__3 : d__4;</span></a>
+<a name="29390"><span class="lineNum">   29390 </span>            :         i__2 = bn - 1;</a>
+<a name="29391"><span class="lineNum">   29391 </span><span class="lineNoCov">          0 :         for (i__ = b1 + 1; i__ &lt;= i__2; ++i__) {</span></a>
+<a name="29392"><span class="lineNum">   29392 </span>            :           d__4 = onenrm;</a>
+<a name="29393"><span class="lineNum">   29393 </span><span class="lineNoCov">          0 :           d__5 = std::abs(d__[i__]) + std::abs(e[i__ - 1]) + std::abs(e[i__]);</span></a>
+<a name="29394"><span class="lineNum">   29394 </span><span class="lineNoCov">          0 :             onenrm = (d__4&gt;d__5) ? d__4 : d__5;</span></a>
+<a name="29395"><span class="lineNum">   29395 </span>            :         }</a>
+<a name="29396"><span class="lineNum">   29396 </span><span class="lineNoCov">          0 :         ortol = onenrm * .001;</span></a>
+<a name="29397"><span class="lineNum">   29397 </span>            : </a>
+<a name="29398"><span class="lineNum">   29398 </span><span class="lineNoCov">          0 :         dtpcrt =  std::sqrt(.1 / blksiz);</span></a>
+<a name="29399"><span class="lineNum">   29399 </span>            : </a>
+<a name="29400"><span class="lineNum">   29400 </span>            :         jblk = 0;</a>
+<a name="29401"><span class="lineNum">   29401 </span><span class="lineNoCov">          0 :         i__2 = *m;</span></a>
+<a name="29402"><span class="lineNum">   29402 </span><span class="lineNoCov">          0 :         for (j = j1; j &lt;= i__2; ++j) {</span></a>
+<a name="29403"><span class="lineNum">   29403 </span><span class="lineNoCov">          0 :             if (iblock[j] != nblk) {</span></a>
+<a name="29404"><span class="lineNum">   29404 </span>            :                 j1 = j;</a>
+<a name="29405"><span class="lineNum">   29405 </span>            :                 break;</a>
+<a name="29406"><span class="lineNum">   29406 </span>            :             }</a>
+<a name="29407"><span class="lineNum">   29407 </span><span class="lineNoCov">          0 :             ++jblk;</span></a>
+<a name="29408"><span class="lineNum">   29408 </span><span class="lineNoCov">          0 :             xj = w[j];</span></a>
+<a name="29409"><span class="lineNum">   29409 </span>            : </a>
+<a name="29410"><span class="lineNum">   29410 </span><span class="lineNoCov">          0 :             if (blksiz == 1) {</span></a>
+<a name="29411"><span class="lineNum">   29411 </span><span class="lineNoCov">          0 :                 work[indrv1 + 1] = 1.;</span></a>
+<a name="29412"><span class="lineNum">   29412 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="29413"><span class="lineNum">   29413 </span>            :             }</a>
+<a name="29414"><span class="lineNum">   29414 </span>            : </a>
+<a name="29415"><span class="lineNum">   29415 </span><span class="lineNoCov">          0 :             if (jblk &gt; 1) {</span></a>
+<a name="29416"><span class="lineNum">   29416 </span><span class="lineNoCov">          0 :                 eps1 = std::abs(eps * xj);</span></a>
+<a name="29417"><span class="lineNum">   29417 </span><span class="lineNoCov">          0 :                 pertol = eps1 * 10.;</span></a>
+<a name="29418"><span class="lineNum">   29418 </span><span class="lineNoCov">          0 :                 sep = xj - xjm;</span></a>
+<a name="29419"><span class="lineNum">   29419 </span><span class="lineNoCov">          0 :                 if (sep &lt; pertol) {</span></a>
+<a name="29420"><span class="lineNum">   29420 </span><span class="lineNoCov">          0 :                     xj = xjm + pertol;</span></a>
+<a name="29421"><span class="lineNum">   29421 </span>            :                 }</a>
+<a name="29422"><span class="lineNum">   29422 </span>            :             }</a>
+<a name="29423"><span class="lineNum">   29423 </span>            : </a>
+<a name="29424"><span class="lineNum">   29424 </span>            :             its = 0;</a>
+<a name="29425"><span class="lineNum">   29425 </span>            :             nrmchk = 0;</a>
+<a name="29426"><span class="lineNum">   29426 </span>            : </a>
+<a name="29427"><span class="lineNum">   29427 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slarnv,SLARNV)(&amp;c__2, iseed, &amp;blksiz, &amp;work[indrv1 + 1]);</span></a>
+<a name="29428"><span class="lineNum">   29428 </span>            : </a>
+<a name="29429"><span class="lineNum">   29429 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;blksiz, &amp;d__[b1], &amp;c__1, &amp;work[indrv4 + 1], &amp;c__1);</span></a>
+<a name="29430"><span class="lineNum">   29430 </span><span class="lineNoCov">          0 :             i__3 = blksiz - 1;</span></a>
+<a name="29431"><span class="lineNum">   29431 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__3, &amp;e[b1], &amp;c__1, &amp;work[indrv2 + 2], &amp;c__1);</span></a>
+<a name="29432"><span class="lineNum">   29432 </span><span class="lineNoCov">          0 :             i__3 = blksiz - 1;</span></a>
+<a name="29433"><span class="lineNum">   29433 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__3, &amp;e[b1], &amp;c__1, &amp;work[indrv3 + 1], &amp;c__1);</span></a>
+<a name="29434"><span class="lineNum">   29434 </span>            : </a>
+<a name="29435"><span class="lineNum">   29435 </span><span class="lineNoCov">          0 :             tol = 0.;</span></a>
+<a name="29436"><span class="lineNum">   29436 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slagtf,SLAGTF)(&amp;blksiz, &amp;work[indrv4 + 1], &amp;xj, &amp;work[indrv2 + 2], &amp;work[</span></a>
+<a name="29437"><span class="lineNum">   29437 </span><span class="lineNoCov">          0 :                     indrv3 + 1], &amp;tol, &amp;work[indrv5 + 1], &amp;iwork[1], &amp;iinfo);</span></a>
+<a name="29438"><span class="lineNum">   29438 </span>            : </a>
+<a name="29439"><span class="lineNum">   29439 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="29440"><span class="lineNum">   29440 </span><span class="lineNoCov">          0 :             ++its;</span></a>
+<a name="29441"><span class="lineNum">   29441 </span><span class="lineNoCov">          0 :             if (its &gt; 5) {</span></a>
+<a name="29442"><span class="lineNum">   29442 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="29443"><span class="lineNum">   29443 </span>            :             }</a>
+<a name="29444"><span class="lineNum">   29444 </span>            : </a>
+<a name="29445"><span class="lineNum">   29445 </span>            :             d__2 = eps;</a>
+<a name="29446"><span class="lineNum">   29446 </span><span class="lineNoCov">          0 :             d__3 = std::abs(work[indrv4 + blksiz]);</span></a>
+<a name="29447"><span class="lineNum">   29447 </span><span class="lineNoCov">          0 :             scl = blksiz * onenrm * ((d__2&gt;d__3) ? d__2 : d__3) / PLUMED_BLAS_F77_FUNC(sasum,SASUM)(&amp;blksiz, &amp;work[</span></a>
+<a name="29448"><span class="lineNum">   29448 </span>            :                     indrv1 + 1], &amp;c__1);</a>
+<a name="29449"><span class="lineNum">   29449 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;blksiz, &amp;scl, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="29450"><span class="lineNum">   29450 </span>            : </a>
+<a name="29451"><span class="lineNum">   29451 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slagts,SLAGTS)(&amp;c_n1, &amp;blksiz, &amp;work[indrv4 + 1], &amp;work[indrv2 + 2], &amp;</span></a>
+<a name="29452"><span class="lineNum">   29452 </span>            :                     work[indrv3 + 1], &amp;work[indrv5 + 1], &amp;iwork[1], &amp;work[</a>
+<a name="29453"><span class="lineNum">   29453 </span>            :                     indrv1 + 1], &amp;tol, &amp;iinfo);</a>
+<a name="29454"><span class="lineNum">   29454 </span>            : </a>
+<a name="29455"><span class="lineNum">   29455 </span><span class="lineNoCov">          0 :             if (jblk == 1) {</span></a>
+<a name="29456"><span class="lineNum">   29456 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="29457"><span class="lineNum">   29457 </span>            :             }</a>
+<a name="29458"><span class="lineNum">   29458 </span><span class="lineNoCov">          0 :             if (std::abs(xj - xjm) &gt; ortol) {</span></a>
+<a name="29459"><span class="lineNum">   29459 </span>            :                 gpind = j;</a>
+<a name="29460"><span class="lineNum">   29460 </span>            :             }</a>
+<a name="29461"><span class="lineNum">   29461 </span><span class="lineNoCov">          0 :             if (gpind != j) {</span></a>
+<a name="29462"><span class="lineNum">   29462 </span><span class="lineNoCov">          0 :                 i__3 = j - 1;</span></a>
+<a name="29463"><span class="lineNum">   29463 </span><span class="lineNoCov">          0 :                 for (i__ = gpind; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="29464"><span class="lineNum">   29464 </span><span class="lineNoCov">          0 :                     ztr = -PLUMED_BLAS_F77_FUNC(sdot,SDOT)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1, &amp;z__[b1 + </span></a>
+<a name="29465"><span class="lineNum">   29465 </span><span class="lineNoCov">          0 :                             i__ * z_dim1], &amp;c__1);</span></a>
+<a name="29466"><span class="lineNum">   29466 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(&amp;blksiz, &amp;ztr, &amp;z__[b1 + i__ * z_dim1], &amp;c__1, &amp;</span></a>
+<a name="29467"><span class="lineNum">   29467 </span>            :                             work[indrv1 + 1], &amp;c__1);</a>
+<a name="29468"><span class="lineNum">   29468 </span>            :                 }</a>
+<a name="29469"><span class="lineNum">   29469 </span>            :             }</a>
+<a name="29470"><span class="lineNum">   29470 </span>            : </a>
+<a name="29471"><span class="lineNum">   29471 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="29472"><span class="lineNum">   29472 </span><span class="lineNoCov">          0 :             jmax = PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="29473"><span class="lineNum">   29473 </span><span class="lineNoCov">          0 :             nrm = std::abs(work[indrv1 + jmax]);</span></a>
+<a name="29474"><span class="lineNum">   29474 </span>            : </a>
+<a name="29475"><span class="lineNum">   29475 </span><span class="lineNoCov">          0 :             if (nrm &lt; dtpcrt) {</span></a>
+<a name="29476"><span class="lineNum">   29476 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="29477"><span class="lineNum">   29477 </span>            :             }</a>
+<a name="29478"><span class="lineNum">   29478 </span><span class="lineNoCov">          0 :             ++nrmchk;</span></a>
+<a name="29479"><span class="lineNum">   29479 </span><span class="lineNoCov">          0 :             if (nrmchk &lt; 3) {</span></a>
+<a name="29480"><span class="lineNum">   29480 </span><span class="lineNoCov">          0 :                 goto L70;</span></a>
+<a name="29481"><span class="lineNum">   29481 </span>            :             }</a>
+<a name="29482"><span class="lineNum">   29482 </span>            : </a>
+<a name="29483"><span class="lineNum">   29483 </span><span class="lineNoCov">          0 :             goto L110;</span></a>
+<a name="29484"><span class="lineNum">   29484 </span>            : </a>
+<a name="29485"><span class="lineNum">   29485 </span>            : L100:</a>
+<a name="29486"><span class="lineNum">   29486 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="29487"><span class="lineNum">   29487 </span><span class="lineNoCov">          0 :             ifail[*info] = j;</span></a>
+<a name="29488"><span class="lineNum">   29488 </span>            : </a>
+<a name="29489"><span class="lineNum">   29489 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="29490"><span class="lineNum">   29490 </span><span class="lineNoCov">          0 :             scl = 1. / PLUMED_BLAS_F77_FUNC(snrm2,SNRM2)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="29491"><span class="lineNum">   29491 </span><span class="lineNoCov">          0 :             jmax = PLUMED_BLAS_F77_FUNC(isamax,ISAMAX)(&amp;blksiz, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="29492"><span class="lineNum">   29492 </span><span class="lineNoCov">          0 :             if (work[indrv1 + jmax] &lt; 0.) {</span></a>
+<a name="29493"><span class="lineNum">   29493 </span><span class="lineNoCov">          0 :                 scl = -scl;</span></a>
+<a name="29494"><span class="lineNum">   29494 </span>            :             }</a>
+<a name="29495"><span class="lineNum">   29495 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;blksiz, &amp;scl, &amp;work[indrv1 + 1], &amp;c__1);</span></a>
+<a name="29496"><span class="lineNum">   29496 </span><span class="lineNoCov">          0 : L120:</span></a>
+<a name="29497"><span class="lineNum">   29497 </span><span class="lineNoCov">          0 :             i__3 = *n;</span></a>
+<a name="29498"><span class="lineNum">   29498 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="29499"><span class="lineNum">   29499 </span><span class="lineNoCov">          0 :                 z__[i__ + j * z_dim1] = 0.;</span></a>
+<a name="29500"><span class="lineNum">   29500 </span>            :             }</a>
+<a name="29501"><span class="lineNum">   29501 </span><span class="lineNoCov">          0 :             i__3 = blksiz;</span></a>
+<a name="29502"><span class="lineNum">   29502 </span><span class="lineNoCov">          0 :             for (i__ = 1; i__ &lt;= i__3; ++i__) {</span></a>
+<a name="29503"><span class="lineNum">   29503 </span><span class="lineNoCov">          0 :                 z__[b1 + i__ - 1 + j * z_dim1] = work[indrv1 + i__];</span></a>
+<a name="29504"><span class="lineNum">   29504 </span>            :             }</a>
+<a name="29505"><span class="lineNum">   29505 </span>            : </a>
+<a name="29506"><span class="lineNum">   29506 </span><span class="lineNoCov">          0 :             xjm = xj;</span></a>
+<a name="29507"><span class="lineNum">   29507 </span>            :         }</a>
+<a name="29508"><span class="lineNum">   29508 </span>            :     }</a>
+<a name="29509"><span class="lineNum">   29509 </span>            : </a>
+<a name="29510"><span class="lineNum">   29510 </span>            :     return;</a>
+<a name="29511"><span class="lineNum">   29511 </span>            : </a>
+<a name="29512"><span class="lineNum">   29512 </span>            : }</a>
+<a name="29513"><span class="lineNum">   29513 </span>            : </a>
+<a name="29514"><span class="lineNum">   29514 </span>            : </a>
+<a name="29515"><span class="lineNum">   29515 </span>            : }</a>
+<a name="29516"><span class="lineNum">   29516 </span>            : }</a>
+<a name="29517"><span class="lineNum">   29517 </span>            : #include &lt;cmath&gt;</a>
+<a name="29518"><span class="lineNum">   29518 </span>            : #include &quot;real.h&quot;</a>
+<a name="29519"><span class="lineNum">   29519 </span>            : </a>
+<a name="29520"><span class="lineNum">   29520 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29521"><span class="lineNum">   29521 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="29522"><span class="lineNum">   29522 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="29523"><span class="lineNum">   29523 </span>            : </a>
+<a name="29524"><span class="lineNum">   29524 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29525"><span class="lineNum">   29525 </span>            : namespace PLMD{</a>
+<a name="29526"><span class="lineNum">   29526 </span>            : namespace lapack{</a>
+<a name="29527"><span class="lineNum">   29527 </span>            : using namespace blas;</a>
+<a name="29528"><span class="lineNum">   29528 </span>            : void</a>
+<a name="29529"><span class="lineNum">   29529 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssteqr,SSTEQR)(const char *    compz, </span></a>
+<a name="29530"><span class="lineNum">   29530 </span>            :                         int *     n, </a>
+<a name="29531"><span class="lineNum">   29531 </span>            :                         float *  d__, </a>
+<a name="29532"><span class="lineNum">   29532 </span>            :                         float *  e, </a>
+<a name="29533"><span class="lineNum">   29533 </span>            :                         float *  z__, </a>
+<a name="29534"><span class="lineNum">   29534 </span>            :                         int *     ldz, </a>
+<a name="29535"><span class="lineNum">   29535 </span>            :                         float *  work, </a>
+<a name="29536"><span class="lineNum">   29536 </span>            :                         int *     info)</a>
+<a name="29537"><span class="lineNum">   29537 </span>            : {</a>
+<a name="29538"><span class="lineNum">   29538 </span><span class="lineNoCov">          0 :     float c_b9 = 0.;</span></a>
+<a name="29539"><span class="lineNum">   29539 </span><span class="lineNoCov">          0 :     float c_b10 = 1.;</span></a>
+<a name="29540"><span class="lineNum">   29540 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="29541"><span class="lineNum">   29541 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="29542"><span class="lineNum">   29542 </span><span class="lineNoCov">          0 :     int c__2 = 2;</span></a>
+<a name="29543"><span class="lineNum">   29543 </span>            :     int z_dim1, z_offset, i__1, i__2;</a>
+<a name="29544"><span class="lineNum">   29544 </span>            :     float d__1, d__2;</a>
+<a name="29545"><span class="lineNum">   29545 </span>            : </a>
+<a name="29546"><span class="lineNum">   29546 </span>            :     float b, c__, f, g;</a>
+<a name="29547"><span class="lineNum">   29547 </span>            :     int i__, j, k, l, m;</a>
+<a name="29548"><span class="lineNum">   29548 </span>            :     float p, r__, s;</a>
+<a name="29549"><span class="lineNum">   29549 </span>            :     int l1, ii, mm, lm1, mm1, nm1;</a>
+<a name="29550"><span class="lineNum">   29550 </span>            :     float rt1, rt2, eps;</a>
+<a name="29551"><span class="lineNum">   29551 </span>            :     int lsv;</a>
+<a name="29552"><span class="lineNum">   29552 </span>            :     float tst, eps2;</a>
+<a name="29553"><span class="lineNum">   29553 </span>            :     int lend, jtot;</a>
+<a name="29554"><span class="lineNum">   29554 </span>            :     float anorm;</a>
+<a name="29555"><span class="lineNum">   29555 </span>            :     int lendm1, lendp1;</a>
+<a name="29556"><span class="lineNum">   29556 </span>            :     int iscale;</a>
+<a name="29557"><span class="lineNum">   29557 </span>            :     float safmin,minval;</a>
+<a name="29558"><span class="lineNum">   29558 </span>            :     float safmax;</a>
+<a name="29559"><span class="lineNum">   29559 </span>            :     int lendsv;</a>
+<a name="29560"><span class="lineNum">   29560 </span>            :     float ssfmin;</a>
+<a name="29561"><span class="lineNum">   29561 </span>            :     int nmaxit, icompz;</a>
+<a name="29562"><span class="lineNum">   29562 </span>            :     float ssfmax;</a>
+<a name="29563"><span class="lineNum">   29563 </span>            : </a>
+<a name="29564"><span class="lineNum">   29564 </span>            : </a>
+<a name="29565"><span class="lineNum">   29565 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="29566"><span class="lineNum">   29566 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="29567"><span class="lineNum">   29567 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="29568"><span class="lineNum">   29568 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="29569"><span class="lineNum">   29569 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="29570"><span class="lineNum">   29570 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="29571"><span class="lineNum">   29571 </span>            : </a>
+<a name="29572"><span class="lineNum">   29572 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="29573"><span class="lineNum">   29573 </span>            : </a>
+<a name="29574"><span class="lineNum">   29574 </span><span class="lineNoCov">          0 :     if (*compz=='N' || *compz=='n') {</span></a>
+<a name="29575"><span class="lineNum">   29575 </span>            :         icompz = 0;</a>
+<a name="29576"><span class="lineNum">   29576 </span><span class="lineNoCov">          0 :     } else if (*compz=='V' || *compz=='v') {</span></a>
+<a name="29577"><span class="lineNum">   29577 </span>            :         icompz = 1;</a>
+<a name="29578"><span class="lineNum">   29578 </span>            :     } else if (*compz=='I' || *compz=='i') {</a>
+<a name="29579"><span class="lineNum">   29579 </span>            :         icompz = 2;</a>
+<a name="29580"><span class="lineNum">   29580 </span>            :     } else {</a>
+<a name="29581"><span class="lineNum">   29581 </span>            :         icompz = -1;</a>
+<a name="29582"><span class="lineNum">   29582 </span>            :     }</a>
+<a name="29583"><span class="lineNum">   29583 </span>            :     if (icompz &lt; 0) {</a>
+<a name="29584"><span class="lineNum">   29584 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="29585"><span class="lineNum">   29585 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="29586"><span class="lineNum">   29586 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="29587"><span class="lineNum">   29587 </span><span class="lineNoCov">          0 :     } else if (*ldz &lt; 1 || (icompz &gt; 0 &amp;&amp; *ldz &lt; ((*n&gt;1) ? *n : 1))) {</span></a>
+<a name="29588"><span class="lineNum">   29588 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="29589"><span class="lineNum">   29589 </span>            :     }</a>
+<a name="29590"><span class="lineNum">   29590 </span><span class="lineNoCov">          0 :     if (*info != 0) {</span></a>
+<a name="29591"><span class="lineNum">   29591 </span>            :         return;</a>
+<a name="29592"><span class="lineNum">   29592 </span>            :     }</a>
+<a name="29593"><span class="lineNum">   29593 </span>            : </a>
+<a name="29594"><span class="lineNum">   29594 </span>            : </a>
+<a name="29595"><span class="lineNum">   29595 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="29596"><span class="lineNum">   29596 </span>            :         return;</a>
+<a name="29597"><span class="lineNum">   29597 </span>            :     }</a>
+<a name="29598"><span class="lineNum">   29598 </span>            : </a>
+<a name="29599"><span class="lineNum">   29599 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="29600"><span class="lineNum">   29600 </span><span class="lineNoCov">          0 :         if (icompz == 2) {</span></a>
+<a name="29601"><span class="lineNum">   29601 </span><span class="lineNoCov">          0 :             z__[z_dim1 + 1] = 1.;</span></a>
+<a name="29602"><span class="lineNum">   29602 </span>            :         }</a>
+<a name="29603"><span class="lineNum">   29603 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="29604"><span class="lineNum">   29604 </span>            :     }</a>
+<a name="29605"><span class="lineNum">   29605 </span>            : </a>
+<a name="29606"><span class="lineNum">   29606 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="29607"><span class="lineNum">   29607 </span>            :     d__1 = eps;</a>
+<a name="29608"><span class="lineNum">   29608 </span>            :     eps2 = d__1 * d__1;</a>
+<a name="29609"><span class="lineNum">   29609 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="29610"><span class="lineNum">   29610 </span>            :     safmin = minval*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="29611"><span class="lineNum">   29611 </span>            : </a>
+<a name="29612"><span class="lineNum">   29612 </span>            :     safmax = 1. / safmin;</a>
+<a name="29613"><span class="lineNum">   29613 </span><span class="lineNoCov">          0 :     ssfmax =  std::sqrt(safmax) / 3.;</span></a>
+<a name="29614"><span class="lineNum">   29614 </span><span class="lineNoCov">          0 :     ssfmin =  std::sqrt(safmin) / eps2;</span></a>
+<a name="29615"><span class="lineNum">   29615 </span>            : </a>
+<a name="29616"><span class="lineNum">   29616 </span><span class="lineNoCov">          0 :     if (icompz == 2) {</span></a>
+<a name="29617"><span class="lineNum">   29617 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slaset,SLASET)(&quot;Full&quot;, n, n, &amp;c_b9, &amp;c_b10, &amp;z__[z_offset], ldz);</span></a>
+<a name="29618"><span class="lineNum">   29618 </span>            :     }</a>
+<a name="29619"><span class="lineNum">   29619 </span>            : </a>
+<a name="29620"><span class="lineNum">   29620 </span><span class="lineNoCov">          0 :     nmaxit = *n * 30;</span></a>
+<a name="29621"><span class="lineNum">   29621 </span>            :     jtot = 0;</a>
+<a name="29622"><span class="lineNum">   29622 </span>            : </a>
+<a name="29623"><span class="lineNum">   29623 </span>            :     l1 = 1;</a>
+<a name="29624"><span class="lineNum">   29624 </span><span class="lineNoCov">          0 :     nm1 = *n - 1;</span></a>
+<a name="29625"><span class="lineNum">   29625 </span>            : </a>
+<a name="29626"><span class="lineNum">   29626 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="29627"><span class="lineNum">   29627 </span><span class="lineNoCov">          0 :     if (l1 &gt; *n) {</span></a>
+<a name="29628"><span class="lineNum">   29628 </span><span class="lineNoCov">          0 :         goto L160;</span></a>
+<a name="29629"><span class="lineNum">   29629 </span>            :     }</a>
+<a name="29630"><span class="lineNum">   29630 </span><span class="lineNoCov">          0 :     if (l1 &gt; 1) {</span></a>
+<a name="29631"><span class="lineNum">   29631 </span><span class="lineNoCov">          0 :         e[l1 - 1] = 0.;</span></a>
+<a name="29632"><span class="lineNum">   29632 </span>            :     }</a>
+<a name="29633"><span class="lineNum">   29633 </span><span class="lineNoCov">          0 :     if (l1 &lt;= nm1) {</span></a>
+<a name="29634"><span class="lineNum">   29634 </span><span class="lineNoCov">          0 :         i__1 = nm1;</span></a>
+<a name="29635"><span class="lineNum">   29635 </span><span class="lineNoCov">          0 :         for (m = l1; m &lt;= i__1; ++m) {</span></a>
+<a name="29636"><span class="lineNum">   29636 </span><span class="lineNoCov">          0 :             tst = std::abs(e[m]);</span></a>
+<a name="29637"><span class="lineNum">   29637 </span><span class="lineNoCov">          0 :             if (std::abs(tst)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="29638"><span class="lineNum">   29638 </span><span class="lineNoCov">          0 :                 goto L30;</span></a>
+<a name="29639"><span class="lineNum">   29639 </span>            :             }</a>
+<a name="29640"><span class="lineNum">   29640 </span><span class="lineNoCov">          0 :             if (tst &lt;=  std::sqrt(std::abs(d__[m])) * std::sqrt(std::abs(d__[m + 1])) * eps) {</span></a>
+<a name="29641"><span class="lineNum">   29641 </span><span class="lineNoCov">          0 :                 e[m] = 0.;</span></a>
+<a name="29642"><span class="lineNum">   29642 </span><span class="lineNoCov">          0 :                 goto L30;</span></a>
+<a name="29643"><span class="lineNum">   29643 </span>            :             }</a>
+<a name="29644"><span class="lineNum">   29644 </span>            :         }</a>
+<a name="29645"><span class="lineNum">   29645 </span>            :     }</a>
+<a name="29646"><span class="lineNum">   29646 </span><span class="lineNoCov">          0 :     m = *n;</span></a>
+<a name="29647"><span class="lineNum">   29647 </span>            : </a>
+<a name="29648"><span class="lineNum">   29648 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="29649"><span class="lineNum">   29649 </span>            :     l = l1;</a>
+<a name="29650"><span class="lineNum">   29650 </span>            :     lsv = l;</a>
+<a name="29651"><span class="lineNum">   29651 </span>            :     lend = m;</a>
+<a name="29652"><span class="lineNum">   29652 </span>            :     lendsv = lend;</a>
+<a name="29653"><span class="lineNum">   29653 </span><span class="lineNoCov">          0 :     l1 = m + 1;</span></a>
+<a name="29654"><span class="lineNum">   29654 </span><span class="lineNoCov">          0 :     if (lend == l) {</span></a>
+<a name="29655"><span class="lineNum">   29655 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="29656"><span class="lineNum">   29656 </span>            :     }</a>
+<a name="29657"><span class="lineNum">   29657 </span>            : </a>
+<a name="29658"><span class="lineNum">   29658 </span><span class="lineNoCov">          0 :     i__1 = lend - l + 1;</span></a>
+<a name="29659"><span class="lineNum">   29659 </span><span class="lineNoCov">          0 :     anorm = PLUMED_BLAS_F77_FUNC(slanst,SLANST)(&quot;I&quot;, &amp;i__1, &amp;d__[l], &amp;e[l]);</span></a>
+<a name="29660"><span class="lineNum">   29660 </span>            :     iscale = 0;</a>
+<a name="29661"><span class="lineNum">   29661 </span><span class="lineNoCov">          0 :     if (std::abs(anorm)&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="29662"><span class="lineNum">   29662 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="29663"><span class="lineNum">   29663 </span>            :     }</a>
+<a name="29664"><span class="lineNum">   29664 </span><span class="lineNoCov">          0 :     if (anorm &gt; ssfmax) {</span></a>
+<a name="29665"><span class="lineNum">   29665 </span>            :         iscale = 1;</a>
+<a name="29666"><span class="lineNum">   29666 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="29667"><span class="lineNum">   29667 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="29668"><span class="lineNum">   29668 </span>            :                 info);</a>
+<a name="29669"><span class="lineNum">   29669 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="29670"><span class="lineNum">   29670 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="29671"><span class="lineNum">   29671 </span>            :                 info);</a>
+<a name="29672"><span class="lineNum">   29672 </span><span class="lineNoCov">          0 :     } else if (anorm &lt; ssfmin) {</span></a>
+<a name="29673"><span class="lineNum">   29673 </span>            :         iscale = 2;</a>
+<a name="29674"><span class="lineNum">   29674 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="29675"><span class="lineNum">   29675 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="29676"><span class="lineNum">   29676 </span>            :                 info);</a>
+<a name="29677"><span class="lineNum">   29677 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="29678"><span class="lineNum">   29678 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="29679"><span class="lineNum">   29679 </span>            :                 info);</a>
+<a name="29680"><span class="lineNum">   29680 </span>            :     }</a>
+<a name="29681"><span class="lineNum">   29681 </span>            : </a>
+<a name="29682"><span class="lineNum">   29682 </span><span class="lineNoCov">          0 :     if (std::abs(d__[lend]) &lt; std::abs(d__[l])) {</span></a>
+<a name="29683"><span class="lineNum">   29683 </span>            :         lend = lsv;</a>
+<a name="29684"><span class="lineNum">   29684 </span>            :         l = lendsv;</a>
+<a name="29685"><span class="lineNum">   29685 </span>            :     }</a>
+<a name="29686"><span class="lineNum">   29686 </span>            : </a>
+<a name="29687"><span class="lineNum">   29687 </span><span class="lineNoCov">          0 :     if (lend &gt; l) {</span></a>
+<a name="29688"><span class="lineNum">   29688 </span>            : </a>
+<a name="29689"><span class="lineNum">   29689 </span><span class="lineNoCov">          0 : L40:</span></a>
+<a name="29690"><span class="lineNum">   29690 </span><span class="lineNoCov">          0 :         if (l != lend) {</span></a>
+<a name="29691"><span class="lineNum">   29691 </span><span class="lineNoCov">          0 :             lendm1 = lend - 1;</span></a>
+<a name="29692"><span class="lineNum">   29692 </span><span class="lineNoCov">          0 :             i__1 = lendm1;</span></a>
+<a name="29693"><span class="lineNum">   29693 </span><span class="lineNoCov">          0 :             for (m = l; m &lt;= i__1; ++m) {</span></a>
+<a name="29694"><span class="lineNum">   29694 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(e[m]);</span></a>
+<a name="29695"><span class="lineNum">   29695 </span><span class="lineNoCov">          0 :                 tst = d__2 * d__2;</span></a>
+<a name="29696"><span class="lineNum">   29696 </span><span class="lineNoCov">          0 :                 if (tst &lt;= eps2 * std::abs(d__[m]) * std::abs(d__[m+ 1]) + safmin) {</span></a>
+<a name="29697"><span class="lineNum">   29697 </span><span class="lineNoCov">          0 :                     goto L60;</span></a>
+<a name="29698"><span class="lineNum">   29698 </span>            :                 }</a>
+<a name="29699"><span class="lineNum">   29699 </span>            :             }</a>
+<a name="29700"><span class="lineNum">   29700 </span>            :         }</a>
+<a name="29701"><span class="lineNum">   29701 </span>            : </a>
+<a name="29702"><span class="lineNum">   29702 </span>            :         m = lend;</a>
+<a name="29703"><span class="lineNum">   29703 </span>            : </a>
+<a name="29704"><span class="lineNum">   29704 </span><span class="lineNoCov">          0 : L60:</span></a>
+<a name="29705"><span class="lineNum">   29705 </span><span class="lineNoCov">          0 :         if (m &lt; lend) {</span></a>
+<a name="29706"><span class="lineNum">   29706 </span><span class="lineNoCov">          0 :             e[m] = 0.;</span></a>
+<a name="29707"><span class="lineNum">   29707 </span>            :         }</a>
+<a name="29708"><span class="lineNum">   29708 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="29709"><span class="lineNum">   29709 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="29710"><span class="lineNum">   29710 </span><span class="lineNoCov">          0 :             goto L80;</span></a>
+<a name="29711"><span class="lineNum">   29711 </span>            :         }</a>
+<a name="29712"><span class="lineNum">   29712 </span>            : </a>
+<a name="29713"><span class="lineNum">   29713 </span><span class="lineNoCov">          0 :         if (m == l + 1) {</span></a>
+<a name="29714"><span class="lineNum">   29714 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="29715"><span class="lineNum">   29715 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaev2,SLAEV2)(&amp;d__[l], &amp;e[l], &amp;d__[l + 1], &amp;rt1, &amp;rt2, &amp;c__, &amp;s);</span></a>
+<a name="29716"><span class="lineNum">   29716 </span><span class="lineNoCov">          0 :                 work[l] = c__;</span></a>
+<a name="29717"><span class="lineNum">   29717 </span><span class="lineNoCov">          0 :                 work[*n - 1 + l] = s;</span></a>
+<a name="29718"><span class="lineNum">   29718 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, n, &amp;c__2, &amp;work[l], &amp;work[*n - 1 + l], &amp;</span></a>
+<a name="29719"><span class="lineNum">   29719 </span><span class="lineNoCov">          0 :                         z__[l * z_dim1 + 1], ldz);</span></a>
+<a name="29720"><span class="lineNum">   29720 </span>            :             } else {</a>
+<a name="29721"><span class="lineNum">   29721 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slae2,SLAE2)(&amp;d__[l], &amp;e[l], &amp;d__[l + 1], &amp;rt1, &amp;rt2);</span></a>
+<a name="29722"><span class="lineNum">   29722 </span>            :             }</a>
+<a name="29723"><span class="lineNum">   29723 </span><span class="lineNoCov">          0 :             d__[l] = rt1;</span></a>
+<a name="29724"><span class="lineNum">   29724 </span><span class="lineNoCov">          0 :             d__[l + 1] = rt2;</span></a>
+<a name="29725"><span class="lineNum">   29725 </span><span class="lineNoCov">          0 :             e[l] = 0.;</span></a>
+<a name="29726"><span class="lineNum">   29726 </span><span class="lineNoCov">          0 :             l += 2;</span></a>
+<a name="29727"><span class="lineNum">   29727 </span><span class="lineNoCov">          0 :             if (l &lt;= lend) {</span></a>
+<a name="29728"><span class="lineNum">   29728 </span><span class="lineNoCov">          0 :                 goto L40;</span></a>
+<a name="29729"><span class="lineNum">   29729 </span>            :             }</a>
+<a name="29730"><span class="lineNum">   29730 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="29731"><span class="lineNum">   29731 </span>            :         }</a>
+<a name="29732"><span class="lineNum">   29732 </span>            : </a>
+<a name="29733"><span class="lineNum">   29733 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="29734"><span class="lineNum">   29734 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="29735"><span class="lineNum">   29735 </span>            :         }</a>
+<a name="29736"><span class="lineNum">   29736 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="29737"><span class="lineNum">   29737 </span>            : </a>
+<a name="29738"><span class="lineNum">   29738 </span><span class="lineNoCov">          0 :         g = (d__[l + 1] - p) / (e[l] * 2.);</span></a>
+<a name="29739"><span class="lineNum">   29739 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;g, &amp;c_b10);</span></a>
+<a name="29740"><span class="lineNum">   29740 </span><span class="lineNoCov">          0 :         g = d__[m] - p + e[l] / (g + ( (g&gt;0) ? r__ : -r__ ) );</span></a>
+<a name="29741"><span class="lineNum">   29741 </span>            : </a>
+<a name="29742"><span class="lineNum">   29742 </span><span class="lineNoCov">          0 :         s = 1.;</span></a>
+<a name="29743"><span class="lineNum">   29743 </span><span class="lineNoCov">          0 :         c__ = 1.;</span></a>
+<a name="29744"><span class="lineNum">   29744 </span>            :         p = 0.;</a>
+<a name="29745"><span class="lineNum">   29745 </span>            : </a>
+<a name="29746"><span class="lineNum">   29746 </span><span class="lineNoCov">          0 :         mm1 = m - 1;</span></a>
+<a name="29747"><span class="lineNum">   29747 </span><span class="lineNoCov">          0 :         i__1 = l;</span></a>
+<a name="29748"><span class="lineNum">   29748 </span><span class="lineNoCov">          0 :         for (i__ = mm1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="29749"><span class="lineNum">   29749 </span><span class="lineNoCov">          0 :             f = s * e[i__];</span></a>
+<a name="29750"><span class="lineNum">   29750 </span><span class="lineNoCov">          0 :             b = c__ * e[i__];</span></a>
+<a name="29751"><span class="lineNum">   29751 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;g, &amp;f, &amp;c__, &amp;s, &amp;r__);</span></a>
+<a name="29752"><span class="lineNum">   29752 </span><span class="lineNoCov">          0 :             if (i__ != m - 1) {</span></a>
+<a name="29753"><span class="lineNum">   29753 </span><span class="lineNoCov">          0 :                 e[i__ + 1] = r__;</span></a>
+<a name="29754"><span class="lineNum">   29754 </span>            :             }</a>
+<a name="29755"><span class="lineNum">   29755 </span><span class="lineNoCov">          0 :             g = d__[i__ + 1] - p;</span></a>
+<a name="29756"><span class="lineNum">   29756 </span><span class="lineNoCov">          0 :             r__ = (d__[i__] - g) * s + c__ * 2. * b;</span></a>
+<a name="29757"><span class="lineNum">   29757 </span><span class="lineNoCov">          0 :             p = s * r__;</span></a>
+<a name="29758"><span class="lineNum">   29758 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = g + p;</span></a>
+<a name="29759"><span class="lineNum">   29759 </span><span class="lineNoCov">          0 :             g = c__ * r__ - b;</span></a>
+<a name="29760"><span class="lineNum">   29760 </span>            : </a>
+<a name="29761"><span class="lineNum">   29761 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="29762"><span class="lineNum">   29762 </span><span class="lineNoCov">          0 :                 work[i__] = c__;</span></a>
+<a name="29763"><span class="lineNum">   29763 </span><span class="lineNoCov">          0 :                 work[*n - 1 + i__] = -s;</span></a>
+<a name="29764"><span class="lineNum">   29764 </span>            :             }</a>
+<a name="29765"><span class="lineNum">   29765 </span>            :         }</a>
+<a name="29766"><span class="lineNum">   29766 </span>            : </a>
+<a name="29767"><span class="lineNum">   29767 </span><span class="lineNoCov">          0 :         if (icompz &gt; 0) {</span></a>
+<a name="29768"><span class="lineNum">   29768 </span><span class="lineNoCov">          0 :             mm = m - l + 1;</span></a>
+<a name="29769"><span class="lineNum">   29769 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;B&quot;, n, &amp;mm, &amp;work[l], &amp;work[*n - 1 + l], &amp;z__[l </span></a>
+<a name="29770"><span class="lineNum">   29770 </span><span class="lineNoCov">          0 :                     * z_dim1 + 1], ldz);</span></a>
+<a name="29771"><span class="lineNum">   29771 </span>            :         }</a>
+<a name="29772"><span class="lineNum">   29772 </span>            : </a>
+<a name="29773"><span class="lineNum">   29773 </span><span class="lineNoCov">          0 :         d__[l] -= p;</span></a>
+<a name="29774"><span class="lineNum">   29774 </span><span class="lineNoCov">          0 :         e[l] = g;</span></a>
+<a name="29775"><span class="lineNum">   29775 </span><span class="lineNoCov">          0 :         goto L40;</span></a>
+<a name="29776"><span class="lineNum">   29776 </span>            : </a>
+<a name="29777"><span class="lineNum">   29777 </span>            : L80:</a>
+<a name="29778"><span class="lineNum">   29778 </span>            :         d__[l] = p;</a>
+<a name="29779"><span class="lineNum">   29779 </span>            : </a>
+<a name="29780"><span class="lineNum">   29780 </span><span class="lineNoCov">          0 :         ++l;</span></a>
+<a name="29781"><span class="lineNum">   29781 </span><span class="lineNoCov">          0 :         if (l &lt;= lend) {</span></a>
+<a name="29782"><span class="lineNum">   29782 </span><span class="lineNoCov">          0 :             goto L40;</span></a>
+<a name="29783"><span class="lineNum">   29783 </span>            :         }</a>
+<a name="29784"><span class="lineNum">   29784 </span><span class="lineNoCov">          0 :         goto L140;</span></a>
+<a name="29785"><span class="lineNum">   29785 </span>            : </a>
+<a name="29786"><span class="lineNum">   29786 </span>            :     } else {</a>
+<a name="29787"><span class="lineNum">   29787 </span>            : </a>
+<a name="29788"><span class="lineNum">   29788 </span><span class="lineNoCov">          0 : L90:</span></a>
+<a name="29789"><span class="lineNum">   29789 </span><span class="lineNoCov">          0 :         if (l != lend) {</span></a>
+<a name="29790"><span class="lineNum">   29790 </span><span class="lineNoCov">          0 :             lendp1 = lend + 1;</span></a>
+<a name="29791"><span class="lineNum">   29791 </span><span class="lineNoCov">          0 :             i__1 = lendp1;</span></a>
+<a name="29792"><span class="lineNum">   29792 </span><span class="lineNoCov">          0 :             for (m = l; m &gt;= i__1; --m) {</span></a>
+<a name="29793"><span class="lineNum">   29793 </span><span class="lineNoCov">          0 :                 d__2 = std::abs(e[m - 1]);</span></a>
+<a name="29794"><span class="lineNum">   29794 </span><span class="lineNoCov">          0 :                 tst = d__2 * d__2;</span></a>
+<a name="29795"><span class="lineNum">   29795 </span><span class="lineNoCov">          0 :                 if (tst &lt;= eps2 * std::abs(d__[m]) * std::abs(d__[m- 1]) + safmin) {</span></a>
+<a name="29796"><span class="lineNum">   29796 </span><span class="lineNoCov">          0 :                     goto L110;</span></a>
+<a name="29797"><span class="lineNum">   29797 </span>            :                 }</a>
+<a name="29798"><span class="lineNum">   29798 </span>            :             }</a>
+<a name="29799"><span class="lineNum">   29799 </span>            :         }</a>
+<a name="29800"><span class="lineNum">   29800 </span>            : </a>
+<a name="29801"><span class="lineNum">   29801 </span>            :         m = lend;</a>
+<a name="29802"><span class="lineNum">   29802 </span>            : </a>
+<a name="29803"><span class="lineNum">   29803 </span><span class="lineNoCov">          0 : L110:</span></a>
+<a name="29804"><span class="lineNum">   29804 </span><span class="lineNoCov">          0 :         if (m &gt; lend) {</span></a>
+<a name="29805"><span class="lineNum">   29805 </span><span class="lineNoCov">          0 :             e[m - 1] = 0.;</span></a>
+<a name="29806"><span class="lineNum">   29806 </span>            :         }</a>
+<a name="29807"><span class="lineNum">   29807 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="29808"><span class="lineNum">   29808 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="29809"><span class="lineNum">   29809 </span><span class="lineNoCov">          0 :             goto L130;</span></a>
+<a name="29810"><span class="lineNum">   29810 </span>            :         }</a>
+<a name="29811"><span class="lineNum">   29811 </span><span class="lineNoCov">          0 :         if (m == l - 1) {</span></a>
+<a name="29812"><span class="lineNum">   29812 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="29813"><span class="lineNum">   29813 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slaev2,SLAEV2)(&amp;d__[l - 1], &amp;e[l - 1], &amp;d__[l], &amp;rt1, &amp;rt2, &amp;c__, &amp;s)</span></a>
+<a name="29814"><span class="lineNum">   29814 </span>            :                         ;</a>
+<a name="29815"><span class="lineNum">   29815 </span><span class="lineNoCov">          0 :                 work[m] = c__;</span></a>
+<a name="29816"><span class="lineNum">   29816 </span><span class="lineNoCov">          0 :                 work[*n - 1 + m] = s;</span></a>
+<a name="29817"><span class="lineNum">   29817 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, n, &amp;c__2, &amp;work[m], &amp;work[*n - 1 + m], &amp;</span></a>
+<a name="29818"><span class="lineNum">   29818 </span><span class="lineNoCov">          0 :                         z__[(l - 1) * z_dim1 + 1], ldz);</span></a>
+<a name="29819"><span class="lineNum">   29819 </span>            :             } else {</a>
+<a name="29820"><span class="lineNum">   29820 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(slae2,SLAE2)(&amp;d__[l - 1], &amp;e[l - 1], &amp;d__[l], &amp;rt1, &amp;rt2);</span></a>
+<a name="29821"><span class="lineNum">   29821 </span>            :             }</a>
+<a name="29822"><span class="lineNum">   29822 </span><span class="lineNoCov">          0 :             d__[l - 1] = rt1;</span></a>
+<a name="29823"><span class="lineNum">   29823 </span><span class="lineNoCov">          0 :             d__[l] = rt2;</span></a>
+<a name="29824"><span class="lineNum">   29824 </span><span class="lineNoCov">          0 :             e[l - 1] = 0.;</span></a>
+<a name="29825"><span class="lineNum">   29825 </span><span class="lineNoCov">          0 :             l += -2;</span></a>
+<a name="29826"><span class="lineNum">   29826 </span><span class="lineNoCov">          0 :             if (l &gt;= lend) {</span></a>
+<a name="29827"><span class="lineNum">   29827 </span><span class="lineNoCov">          0 :                 goto L90;</span></a>
+<a name="29828"><span class="lineNum">   29828 </span>            :             }</a>
+<a name="29829"><span class="lineNum">   29829 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="29830"><span class="lineNum">   29830 </span>            :         }</a>
+<a name="29831"><span class="lineNum">   29831 </span>            : </a>
+<a name="29832"><span class="lineNum">   29832 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="29833"><span class="lineNum">   29833 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="29834"><span class="lineNum">   29834 </span>            :         }</a>
+<a name="29835"><span class="lineNum">   29835 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="29836"><span class="lineNum">   29836 </span>            : </a>
+<a name="29837"><span class="lineNum">   29837 </span><span class="lineNoCov">          0 :         g = (d__[l - 1] - p) / (e[l - 1] * 2.);</span></a>
+<a name="29838"><span class="lineNum">   29838 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;g, &amp;c_b10);</span></a>
+<a name="29839"><span class="lineNum">   29839 </span><span class="lineNoCov">          0 :         g = d__[m] - p + e[l - 1] / (g + ( (g&gt;0) ? r__ : -r__ ));</span></a>
+<a name="29840"><span class="lineNum">   29840 </span>            : </a>
+<a name="29841"><span class="lineNum">   29841 </span><span class="lineNoCov">          0 :         s = 1.;</span></a>
+<a name="29842"><span class="lineNum">   29842 </span><span class="lineNoCov">          0 :         c__ = 1.;</span></a>
+<a name="29843"><span class="lineNum">   29843 </span>            :         p = 0.;</a>
+<a name="29844"><span class="lineNum">   29844 </span>            : </a>
+<a name="29845"><span class="lineNum">   29845 </span>            :         lm1 = l - 1;</a>
+<a name="29846"><span class="lineNum">   29846 </span><span class="lineNoCov">          0 :         i__1 = lm1;</span></a>
+<a name="29847"><span class="lineNum">   29847 </span><span class="lineNoCov">          0 :         for (i__ = m; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="29848"><span class="lineNum">   29848 </span><span class="lineNoCov">          0 :             f = s * e[i__];</span></a>
+<a name="29849"><span class="lineNum">   29849 </span><span class="lineNoCov">          0 :             b = c__ * e[i__];</span></a>
+<a name="29850"><span class="lineNum">   29850 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slartg,SLARTG)(&amp;g, &amp;f, &amp;c__, &amp;s, &amp;r__);</span></a>
+<a name="29851"><span class="lineNum">   29851 </span><span class="lineNoCov">          0 :             if (i__ != m) {</span></a>
+<a name="29852"><span class="lineNum">   29852 </span><span class="lineNoCov">          0 :                 e[i__ - 1] = r__;</span></a>
+<a name="29853"><span class="lineNum">   29853 </span>            :             }</a>
+<a name="29854"><span class="lineNum">   29854 </span><span class="lineNoCov">          0 :             g = d__[i__] - p;</span></a>
+<a name="29855"><span class="lineNum">   29855 </span><span class="lineNoCov">          0 :             r__ = (d__[i__ + 1] - g) * s + c__ * 2. * b;</span></a>
+<a name="29856"><span class="lineNum">   29856 </span><span class="lineNoCov">          0 :             p = s * r__;</span></a>
+<a name="29857"><span class="lineNum">   29857 </span><span class="lineNoCov">          0 :             d__[i__] = g + p;</span></a>
+<a name="29858"><span class="lineNum">   29858 </span><span class="lineNoCov">          0 :             g = c__ * r__ - b;</span></a>
+<a name="29859"><span class="lineNum">   29859 </span>            : </a>
+<a name="29860"><span class="lineNum">   29860 </span><span class="lineNoCov">          0 :             if (icompz &gt; 0) {</span></a>
+<a name="29861"><span class="lineNum">   29861 </span><span class="lineNoCov">          0 :                 work[i__] = c__;</span></a>
+<a name="29862"><span class="lineNum">   29862 </span><span class="lineNoCov">          0 :                 work[*n - 1 + i__] = s;</span></a>
+<a name="29863"><span class="lineNum">   29863 </span>            :             }</a>
+<a name="29864"><span class="lineNum">   29864 </span>            :         }</a>
+<a name="29865"><span class="lineNum">   29865 </span>            : </a>
+<a name="29866"><span class="lineNum">   29866 </span><span class="lineNoCov">          0 :         if (icompz &gt; 0) {</span></a>
+<a name="29867"><span class="lineNum">   29867 </span><span class="lineNoCov">          0 :             mm = l - m + 1;</span></a>
+<a name="29868"><span class="lineNum">   29868 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slasr,SLASR)(&quot;R&quot;, &quot;V&quot;, &quot;F&quot;, n, &amp;mm, &amp;work[m], &amp;work[*n - 1 + m], &amp;z__[m </span></a>
+<a name="29869"><span class="lineNum">   29869 </span><span class="lineNoCov">          0 :                     * z_dim1 + 1], ldz);</span></a>
+<a name="29870"><span class="lineNum">   29870 </span>            :         }</a>
+<a name="29871"><span class="lineNum">   29871 </span>            : </a>
+<a name="29872"><span class="lineNum">   29872 </span><span class="lineNoCov">          0 :         d__[l] -= p;</span></a>
+<a name="29873"><span class="lineNum">   29873 </span><span class="lineNoCov">          0 :         e[lm1] = g;</span></a>
+<a name="29874"><span class="lineNum">   29874 </span><span class="lineNoCov">          0 :         goto L90;</span></a>
+<a name="29875"><span class="lineNum">   29875 </span>            : </a>
+<a name="29876"><span class="lineNum">   29876 </span>            : L130:</a>
+<a name="29877"><span class="lineNum">   29877 </span>            :         d__[l] = p;</a>
+<a name="29878"><span class="lineNum">   29878 </span>            : </a>
+<a name="29879"><span class="lineNum">   29879 </span><span class="lineNoCov">          0 :         --l;</span></a>
+<a name="29880"><span class="lineNum">   29880 </span><span class="lineNoCov">          0 :         if (l &gt;= lend) {</span></a>
+<a name="29881"><span class="lineNum">   29881 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="29882"><span class="lineNum">   29882 </span>            :         }</a>
+<a name="29883"><span class="lineNum">   29883 </span><span class="lineNoCov">          0 :         goto L140;</span></a>
+<a name="29884"><span class="lineNum">   29884 </span>            : </a>
+<a name="29885"><span class="lineNum">   29885 </span>            :     }</a>
+<a name="29886"><span class="lineNum">   29886 </span>            : </a>
+<a name="29887"><span class="lineNum">   29887 </span><span class="lineNoCov">          0 : L140:</span></a>
+<a name="29888"><span class="lineNum">   29888 </span><span class="lineNoCov">          0 :     if (iscale == 1) {</span></a>
+<a name="29889"><span class="lineNum">   29889 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="29890"><span class="lineNum">   29890 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmax, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="29891"><span class="lineNum">   29891 </span>            :                 n, info);</a>
+<a name="29892"><span class="lineNum">   29892 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv;</span></a>
+<a name="29893"><span class="lineNum">   29893 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmax, &amp;anorm, &amp;i__1, &amp;c__1, &amp;e[lsv], n, </span></a>
+<a name="29894"><span class="lineNum">   29894 </span>            :                 info);</a>
+<a name="29895"><span class="lineNum">   29895 </span><span class="lineNoCov">          0 :     } else if (iscale == 2) {</span></a>
+<a name="29896"><span class="lineNum">   29896 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="29897"><span class="lineNum">   29897 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmin, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="29898"><span class="lineNum">   29898 </span>            :                 n, info);</a>
+<a name="29899"><span class="lineNum">   29899 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv;</span></a>
+<a name="29900"><span class="lineNum">   29900 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmin, &amp;anorm, &amp;i__1, &amp;c__1, &amp;e[lsv], n, </span></a>
+<a name="29901"><span class="lineNum">   29901 </span>            :                 info);</a>
+<a name="29902"><span class="lineNum">   29902 </span>            :     }</a>
+<a name="29903"><span class="lineNum">   29903 </span>            : </a>
+<a name="29904"><span class="lineNum">   29904 </span><span class="lineNoCov">          0 :     if (jtot &lt; nmaxit) {</span></a>
+<a name="29905"><span class="lineNum">   29905 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="29906"><span class="lineNum">   29906 </span>            :     }</a>
+<a name="29907"><span class="lineNum">   29907 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="29908"><span class="lineNum">   29908 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="29909"><span class="lineNum">   29909 </span><span class="lineNoCov">          0 :         if (std::abs(e[i__])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="29910"><span class="lineNum">   29910 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="29911"><span class="lineNum">   29911 </span>            :         }</a>
+<a name="29912"><span class="lineNum">   29912 </span>            :     }</a>
+<a name="29913"><span class="lineNum">   29913 </span><span class="lineNoCov">          0 :     goto L190;</span></a>
+<a name="29914"><span class="lineNum">   29914 </span>            : </a>
+<a name="29915"><span class="lineNum">   29915 </span>            : L160:</a>
+<a name="29916"><span class="lineNum">   29916 </span><span class="lineNoCov">          0 :     if (icompz == 0) {</span></a>
+<a name="29917"><span class="lineNum">   29917 </span>            : </a>
+<a name="29918"><span class="lineNum">   29918 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(&quot;I&quot;, n, &amp;d__[1], info);</span></a>
+<a name="29919"><span class="lineNum">   29919 </span>            : </a>
+<a name="29920"><span class="lineNum">   29920 </span>            :     } else {</a>
+<a name="29921"><span class="lineNum">   29921 </span>            : </a>
+<a name="29922"><span class="lineNum">   29922 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="29923"><span class="lineNum">   29923 </span><span class="lineNoCov">          0 :         for (ii = 2; ii &lt;= i__1; ++ii) {</span></a>
+<a name="29924"><span class="lineNum">   29924 </span><span class="lineNoCov">          0 :             i__ = ii - 1;</span></a>
+<a name="29925"><span class="lineNum">   29925 </span>            :             k = i__;</a>
+<a name="29926"><span class="lineNum">   29926 </span><span class="lineNoCov">          0 :             p = d__[i__];</span></a>
+<a name="29927"><span class="lineNum">   29927 </span><span class="lineNoCov">          0 :             i__2 = *n;</span></a>
+<a name="29928"><span class="lineNum">   29928 </span><span class="lineNoCov">          0 :             for (j = ii; j &lt;= i__2; ++j) {</span></a>
+<a name="29929"><span class="lineNum">   29929 </span><span class="lineNoCov">          0 :                 if (d__[j] &lt; p) {</span></a>
+<a name="29930"><span class="lineNum">   29930 </span>            :                     k = j;</a>
+<a name="29931"><span class="lineNum">   29931 </span>            :                     p = d__[j];</a>
+<a name="29932"><span class="lineNum">   29932 </span>            :                 }</a>
+<a name="29933"><span class="lineNum">   29933 </span>            :             }</a>
+<a name="29934"><span class="lineNum">   29934 </span><span class="lineNoCov">          0 :             if (k != i__) {</span></a>
+<a name="29935"><span class="lineNum">   29935 </span><span class="lineNoCov">          0 :                 d__[k] = d__[i__];</span></a>
+<a name="29936"><span class="lineNum">   29936 </span><span class="lineNoCov">          0 :                 d__[i__] = p;</span></a>
+<a name="29937"><span class="lineNum">   29937 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n, &amp;z__[i__ * z_dim1 + 1], &amp;c__1, &amp;z__[k * z_dim1 + 1],</span></a>
+<a name="29938"><span class="lineNum">   29938 </span>            :                          &amp;c__1);</a>
+<a name="29939"><span class="lineNum">   29939 </span>            :             }</a>
+<a name="29940"><span class="lineNum">   29940 </span>            :         }</a>
+<a name="29941"><span class="lineNum">   29941 </span>            :     }</a>
+<a name="29942"><span class="lineNum">   29942 </span>            : </a>
+<a name="29943"><span class="lineNum">   29943 </span><span class="lineNoCov">          0 : L190:</span></a>
+<a name="29944"><span class="lineNum">   29944 </span>            :     return;</a>
+<a name="29945"><span class="lineNum">   29945 </span>            : }</a>
+<a name="29946"><span class="lineNum">   29946 </span>            : </a>
+<a name="29947"><span class="lineNum">   29947 </span>            : </a>
+<a name="29948"><span class="lineNum">   29948 </span>            : }</a>
+<a name="29949"><span class="lineNum">   29949 </span>            : }</a>
+<a name="29950"><span class="lineNum">   29950 </span>            : #include &lt;cmath&gt;</a>
+<a name="29951"><span class="lineNum">   29951 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="29952"><span class="lineNum">   29952 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="29953"><span class="lineNum">   29953 </span>            : </a>
+<a name="29954"><span class="lineNum">   29954 </span>            : #include &quot;real.h&quot;</a>
+<a name="29955"><span class="lineNum">   29955 </span>            : </a>
+<a name="29956"><span class="lineNum">   29956 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="29957"><span class="lineNum">   29957 </span>            : namespace PLMD{</a>
+<a name="29958"><span class="lineNum">   29958 </span>            : namespace lapack{</a>
+<a name="29959"><span class="lineNum">   29959 </span>            : using namespace blas;</a>
+<a name="29960"><span class="lineNum">   29960 </span>            : void</a>
+<a name="29961"><span class="lineNum">   29961 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssterf,SSTERF)(int *n, </span></a>
+<a name="29962"><span class="lineNum">   29962 </span>            :         float *d__, </a>
+<a name="29963"><span class="lineNum">   29963 </span>            :         float *e, </a>
+<a name="29964"><span class="lineNum">   29964 </span>            :         int *info)</a>
+<a name="29965"><span class="lineNum">   29965 </span>            : {</a>
+<a name="29966"><span class="lineNum">   29966 </span>            :     int i__1;</a>
+<a name="29967"><span class="lineNum">   29967 </span>            :     float d__1;</a>
+<a name="29968"><span class="lineNum">   29968 </span>            : </a>
+<a name="29969"><span class="lineNum">   29969 </span>            :     float c__;</a>
+<a name="29970"><span class="lineNum">   29970 </span>            :     int i__, l, m;</a>
+<a name="29971"><span class="lineNum">   29971 </span>            :     float p, r__, s;</a>
+<a name="29972"><span class="lineNum">   29972 </span>            :     int l1;</a>
+<a name="29973"><span class="lineNum">   29973 </span>            :     float bb, rt1, rt2, eps, rte;</a>
+<a name="29974"><span class="lineNum">   29974 </span>            :     int lsv;</a>
+<a name="29975"><span class="lineNum">   29975 </span>            :     float eps2, oldc;</a>
+<a name="29976"><span class="lineNum">   29976 </span>            :     int lend, jtot;</a>
+<a name="29977"><span class="lineNum">   29977 </span>            :     float gamma, alpha, sigma, anorm;</a>
+<a name="29978"><span class="lineNum">   29978 </span>            :       int iscale;</a>
+<a name="29979"><span class="lineNum">   29979 </span>            :     float oldgam;</a>
+<a name="29980"><span class="lineNum">   29980 </span>            :     float safmax;</a>
+<a name="29981"><span class="lineNum">   29981 </span>            :     int lendsv;</a>
+<a name="29982"><span class="lineNum">   29982 </span>            :     float ssfmin;</a>
+<a name="29983"><span class="lineNum">   29983 </span>            :     int nmaxit;</a>
+<a name="29984"><span class="lineNum">   29984 </span>            :     float ssfmax;</a>
+<a name="29985"><span class="lineNum">   29985 </span><span class="lineNoCov">          0 :     int c__0 = 0;</span></a>
+<a name="29986"><span class="lineNum">   29986 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="29987"><span class="lineNum">   29987 </span><span class="lineNoCov">          0 :     float c_b32 = 1.;</span></a>
+<a name="29988"><span class="lineNum">   29988 </span>            :     const float safmin = PLUMED_GMX_FLOAT_MIN*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="29989"><span class="lineNum">   29989 </span>            : </a>
+<a name="29990"><span class="lineNum">   29990 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="29991"><span class="lineNum">   29991 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="29992"><span class="lineNum">   29992 </span>            : </a>
+<a name="29993"><span class="lineNum">   29993 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="29994"><span class="lineNum">   29994 </span>            : </a>
+<a name="29995"><span class="lineNum">   29995 </span><span class="lineNoCov">          0 :     if (*n &lt; 0) {</span></a>
+<a name="29996"><span class="lineNum">   29996 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="29997"><span class="lineNum">   29997 </span>            :         i__1 = -(*info);</a>
+<a name="29998"><span class="lineNum">   29998 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="29999"><span class="lineNum">   29999 </span>            :     }</a>
+<a name="30000"><span class="lineNum">   30000 </span><span class="lineNoCov">          0 :     if (*n &lt;= 1) {</span></a>
+<a name="30001"><span class="lineNum">   30001 </span>            :         return;</a>
+<a name="30002"><span class="lineNum">   30002 </span>            :     }</a>
+<a name="30003"><span class="lineNum">   30003 </span>            : </a>
+<a name="30004"><span class="lineNum">   30004 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="30005"><span class="lineNum">   30005 </span>            :     d__1 = eps;</a>
+<a name="30006"><span class="lineNum">   30006 </span>            :     eps2 = d__1 * d__1;</a>
+<a name="30007"><span class="lineNum">   30007 </span>            :     safmax = 1. / safmin;</a>
+<a name="30008"><span class="lineNum">   30008 </span><span class="lineNoCov">          0 :     ssfmax =  std::sqrt(safmax) / 3.;</span></a>
+<a name="30009"><span class="lineNum">   30009 </span><span class="lineNoCov">          0 :     ssfmin =  std::sqrt(safmin) / eps2;</span></a>
+<a name="30010"><span class="lineNum">   30010 </span>            : </a>
+<a name="30011"><span class="lineNum">   30011 </span><span class="lineNoCov">          0 :     nmaxit = *n * 30;</span></a>
+<a name="30012"><span class="lineNum">   30012 </span><span class="lineNoCov">          0 :     sigma = 0.;</span></a>
+<a name="30013"><span class="lineNum">   30013 </span>            :     jtot = 0;</a>
+<a name="30014"><span class="lineNum">   30014 </span>            : </a>
+<a name="30015"><span class="lineNum">   30015 </span>            :     l1 = 1;</a>
+<a name="30016"><span class="lineNum">   30016 </span>            : </a>
+<a name="30017"><span class="lineNum">   30017 </span><span class="lineNoCov">          0 : L10:</span></a>
+<a name="30018"><span class="lineNum">   30018 </span><span class="lineNoCov">          0 :     if (l1 &gt; *n) {</span></a>
+<a name="30019"><span class="lineNum">   30019 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slasrt,SLASRT)(&quot;I&quot;, n, &amp;d__[1], info);</span></a>
+<a name="30020"><span class="lineNum">   30020 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="30021"><span class="lineNum">   30021 </span>            :     }</a>
+<a name="30022"><span class="lineNum">   30022 </span><span class="lineNoCov">          0 :     if (l1 &gt; 1) {</span></a>
+<a name="30023"><span class="lineNum">   30023 </span><span class="lineNoCov">          0 :         e[l1 - 1] = 0.;</span></a>
+<a name="30024"><span class="lineNum">   30024 </span>            :     }</a>
+<a name="30025"><span class="lineNum">   30025 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="30026"><span class="lineNum">   30026 </span><span class="lineNoCov">          0 :     for (m = l1; m &lt;= i__1; ++m) {</span></a>
+<a name="30027"><span class="lineNum">   30027 </span><span class="lineNoCov">          0 :         if (std::abs(e[m]) &lt;=  std::sqrt(std::abs(d__[m])) * </span></a>
+<a name="30028"><span class="lineNum">   30028 </span><span class="lineNoCov">          0 :                  std::sqrt(std::abs(d__[m + 1])) * eps) {</span></a>
+<a name="30029"><span class="lineNum">   30029 </span><span class="lineNoCov">          0 :             e[m] = 0.;</span></a>
+<a name="30030"><span class="lineNum">   30030 </span><span class="lineNoCov">          0 :             goto L30;</span></a>
+<a name="30031"><span class="lineNum">   30031 </span>            :         }</a>
+<a name="30032"><span class="lineNum">   30032 </span>            :     }</a>
+<a name="30033"><span class="lineNum">   30033 </span><span class="lineNoCov">          0 :     m = *n;</span></a>
+<a name="30034"><span class="lineNum">   30034 </span>            : </a>
+<a name="30035"><span class="lineNum">   30035 </span><span class="lineNoCov">          0 : L30:</span></a>
+<a name="30036"><span class="lineNum">   30036 </span>            :     l = l1;</a>
+<a name="30037"><span class="lineNum">   30037 </span>            :     lsv = l;</a>
+<a name="30038"><span class="lineNum">   30038 </span>            :     lend = m;</a>
+<a name="30039"><span class="lineNum">   30039 </span>            :     lendsv = lend;</a>
+<a name="30040"><span class="lineNum">   30040 </span><span class="lineNoCov">          0 :     l1 = m + 1;</span></a>
+<a name="30041"><span class="lineNum">   30041 </span><span class="lineNoCov">          0 :     if (lend == l) {</span></a>
+<a name="30042"><span class="lineNum">   30042 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="30043"><span class="lineNum">   30043 </span>            :     }</a>
+<a name="30044"><span class="lineNum">   30044 </span>            : </a>
+<a name="30045"><span class="lineNum">   30045 </span><span class="lineNoCov">          0 :     i__1 = lend - l + 1;</span></a>
+<a name="30046"><span class="lineNum">   30046 </span><span class="lineNoCov">          0 :     anorm = PLUMED_BLAS_F77_FUNC(slanst,SLANST)(&quot;I&quot;, &amp;i__1, &amp;d__[l], &amp;e[l]);</span></a>
+<a name="30047"><span class="lineNum">   30047 </span>            :     iscale = 0;</a>
+<a name="30048"><span class="lineNum">   30048 </span><span class="lineNoCov">          0 :     if (anorm &gt; ssfmax) {</span></a>
+<a name="30049"><span class="lineNum">   30049 </span>            :         iscale = 1;</a>
+<a name="30050"><span class="lineNum">   30050 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="30051"><span class="lineNum">   30051 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="30052"><span class="lineNum">   30052 </span>            :                 info);</a>
+<a name="30053"><span class="lineNum">   30053 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="30054"><span class="lineNum">   30054 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmax, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="30055"><span class="lineNum">   30055 </span>            :                 info);</a>
+<a name="30056"><span class="lineNum">   30056 </span><span class="lineNoCov">          0 :     } else if (anorm &lt; ssfmin) {</span></a>
+<a name="30057"><span class="lineNum">   30057 </span>            :         iscale = 2;</a>
+<a name="30058"><span class="lineNum">   30058 </span><span class="lineNoCov">          0 :         i__1 = lend - l + 1;</span></a>
+<a name="30059"><span class="lineNum">   30059 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;d__[l], n, </span></a>
+<a name="30060"><span class="lineNum">   30060 </span>            :                 info);</a>
+<a name="30061"><span class="lineNum">   30061 </span><span class="lineNoCov">          0 :         i__1 = lend - l;</span></a>
+<a name="30062"><span class="lineNum">   30062 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;anorm, &amp;ssfmin, &amp;i__1, &amp;c__1, &amp;e[l], n, </span></a>
+<a name="30063"><span class="lineNum">   30063 </span>            :                 info);</a>
+<a name="30064"><span class="lineNum">   30064 </span>            :     }</a>
+<a name="30065"><span class="lineNum">   30065 </span>            : </a>
+<a name="30066"><span class="lineNum">   30066 </span><span class="lineNoCov">          0 :     i__1 = lend - 1;</span></a>
+<a name="30067"><span class="lineNum">   30067 </span><span class="lineNoCov">          0 :     for (i__ = l; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="30068"><span class="lineNum">   30068 </span><span class="lineNoCov">          0 :         d__1 = e[i__];</span></a>
+<a name="30069"><span class="lineNum">   30069 </span><span class="lineNoCov">          0 :         e[i__] = d__1 * d__1;</span></a>
+<a name="30070"><span class="lineNum">   30070 </span>            :     }</a>
+<a name="30071"><span class="lineNum">   30071 </span>            : </a>
+<a name="30072"><span class="lineNum">   30072 </span><span class="lineNoCov">          0 :     if (std::abs(d__[lend]) &lt; std::abs(d__[l])) {</span></a>
+<a name="30073"><span class="lineNum">   30073 </span>            :         lend = lsv;</a>
+<a name="30074"><span class="lineNum">   30074 </span>            :         l = lendsv;</a>
+<a name="30075"><span class="lineNum">   30075 </span>            :     }</a>
+<a name="30076"><span class="lineNum">   30076 </span>            : </a>
+<a name="30077"><span class="lineNum">   30077 </span><span class="lineNoCov">          0 :     if (lend &gt;= l) {</span></a>
+<a name="30078"><span class="lineNum">   30078 </span>            : </a>
+<a name="30079"><span class="lineNum">   30079 </span><span class="lineNoCov">          0 : L50:</span></a>
+<a name="30080"><span class="lineNum">   30080 </span><span class="lineNoCov">          0 :         if (l != lend) {</span></a>
+<a name="30081"><span class="lineNum">   30081 </span><span class="lineNoCov">          0 :             i__1 = lend - 1;</span></a>
+<a name="30082"><span class="lineNum">   30082 </span><span class="lineNoCov">          0 :             for (m = l; m &lt;= i__1; ++m) {</span></a>
+<a name="30083"><span class="lineNum">   30083 </span><span class="lineNoCov">          0 :                 if (std::abs(e[m]) &lt;= eps2 * std::abs(d__[m] * d__[m + 1])) {</span></a>
+<a name="30084"><span class="lineNum">   30084 </span><span class="lineNoCov">          0 :                     goto L70;</span></a>
+<a name="30085"><span class="lineNum">   30085 </span>            :                 }</a>
+<a name="30086"><span class="lineNum">   30086 </span>            :             }</a>
+<a name="30087"><span class="lineNum">   30087 </span>            :         }</a>
+<a name="30088"><span class="lineNum">   30088 </span>            :         m = lend;</a>
+<a name="30089"><span class="lineNum">   30089 </span>            : </a>
+<a name="30090"><span class="lineNum">   30090 </span><span class="lineNoCov">          0 : L70:</span></a>
+<a name="30091"><span class="lineNum">   30091 </span><span class="lineNoCov">          0 :         if (m &lt; lend) {</span></a>
+<a name="30092"><span class="lineNum">   30092 </span><span class="lineNoCov">          0 :             e[m] = 0.;</span></a>
+<a name="30093"><span class="lineNum">   30093 </span>            :         }</a>
+<a name="30094"><span class="lineNum">   30094 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="30095"><span class="lineNum">   30095 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="30096"><span class="lineNum">   30096 </span><span class="lineNoCov">          0 :             goto L90;</span></a>
+<a name="30097"><span class="lineNum">   30097 </span>            :         }</a>
+<a name="30098"><span class="lineNum">   30098 </span><span class="lineNoCov">          0 :         if (m == l + 1) {</span></a>
+<a name="30099"><span class="lineNum">   30099 </span><span class="lineNoCov">          0 :             rte =  std::sqrt(e[l]);</span></a>
+<a name="30100"><span class="lineNum">   30100 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slae2,SLAE2)(&amp;d__[l], &amp;rte, &amp;d__[l + 1], &amp;rt1, &amp;rt2);</span></a>
+<a name="30101"><span class="lineNum">   30101 </span><span class="lineNoCov">          0 :             d__[l] = rt1;</span></a>
+<a name="30102"><span class="lineNum">   30102 </span><span class="lineNoCov">          0 :             d__[l + 1] = rt2;</span></a>
+<a name="30103"><span class="lineNum">   30103 </span><span class="lineNoCov">          0 :             e[l] = 0.;</span></a>
+<a name="30104"><span class="lineNum">   30104 </span><span class="lineNoCov">          0 :             l += 2;</span></a>
+<a name="30105"><span class="lineNum">   30105 </span><span class="lineNoCov">          0 :             if (l &lt;= lend) {</span></a>
+<a name="30106"><span class="lineNum">   30106 </span><span class="lineNoCov">          0 :                 goto L50;</span></a>
+<a name="30107"><span class="lineNum">   30107 </span>            :             }</a>
+<a name="30108"><span class="lineNum">   30108 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="30109"><span class="lineNum">   30109 </span>            :         }</a>
+<a name="30110"><span class="lineNum">   30110 </span>            : </a>
+<a name="30111"><span class="lineNum">   30111 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="30112"><span class="lineNum">   30112 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="30113"><span class="lineNum">   30113 </span>            :         }</a>
+<a name="30114"><span class="lineNum">   30114 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="30115"><span class="lineNum">   30115 </span>            : </a>
+<a name="30116"><span class="lineNum">   30116 </span><span class="lineNoCov">          0 :         rte =  std::sqrt(e[l]);</span></a>
+<a name="30117"><span class="lineNum">   30117 </span><span class="lineNoCov">          0 :         sigma = (d__[l + 1] - p) / (rte * 2.);</span></a>
+<a name="30118"><span class="lineNum">   30118 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;sigma, &amp;c_b32);</span></a>
+<a name="30119"><span class="lineNum">   30119 </span><span class="lineNoCov">          0 :         sigma = p - rte / (sigma + ( (sigma&gt;0) ? r__ : -r__));</span></a>
+<a name="30120"><span class="lineNum">   30120 </span>            : </a>
+<a name="30121"><span class="lineNum">   30121 </span>            :         c__ = 1.;</a>
+<a name="30122"><span class="lineNum">   30122 </span>            :         s = 0.;</a>
+<a name="30123"><span class="lineNum">   30123 </span><span class="lineNoCov">          0 :         gamma = d__[m] - sigma;</span></a>
+<a name="30124"><span class="lineNum">   30124 </span><span class="lineNoCov">          0 :         p = gamma * gamma;</span></a>
+<a name="30125"><span class="lineNum">   30125 </span>            : </a>
+<a name="30126"><span class="lineNum">   30126 </span><span class="lineNoCov">          0 :         i__1 = l;</span></a>
+<a name="30127"><span class="lineNum">   30127 </span><span class="lineNoCov">          0 :         for (i__ = m - 1; i__ &gt;= i__1; --i__) {</span></a>
+<a name="30128"><span class="lineNum">   30128 </span><span class="lineNoCov">          0 :             bb = e[i__];</span></a>
+<a name="30129"><span class="lineNum">   30129 </span><span class="lineNoCov">          0 :             r__ = p + bb;</span></a>
+<a name="30130"><span class="lineNum">   30130 </span><span class="lineNoCov">          0 :             if (i__ != m - 1) {</span></a>
+<a name="30131"><span class="lineNum">   30131 </span><span class="lineNoCov">          0 :                 e[i__ + 1] = s * r__;</span></a>
+<a name="30132"><span class="lineNum">   30132 </span>            :             }</a>
+<a name="30133"><span class="lineNum">   30133 </span>            :             oldc = c__;</a>
+<a name="30134"><span class="lineNum">   30134 </span><span class="lineNoCov">          0 :             c__ = p / r__;</span></a>
+<a name="30135"><span class="lineNum">   30135 </span><span class="lineNoCov">          0 :             s = bb / r__;</span></a>
+<a name="30136"><span class="lineNum">   30136 </span>            :             oldgam = gamma;</a>
+<a name="30137"><span class="lineNum">   30137 </span><span class="lineNoCov">          0 :             alpha = d__[i__];</span></a>
+<a name="30138"><span class="lineNum">   30138 </span><span class="lineNoCov">          0 :             gamma = c__ * (alpha - sigma) - s * oldgam;</span></a>
+<a name="30139"><span class="lineNum">   30139 </span><span class="lineNoCov">          0 :             d__[i__ + 1] = oldgam + (alpha - gamma);</span></a>
+<a name="30140"><span class="lineNum">   30140 </span><span class="lineNoCov">          0 :             if (std::abs(c__)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="30141"><span class="lineNum">   30141 </span><span class="lineNoCov">          0 :                 p = gamma * gamma / c__;</span></a>
+<a name="30142"><span class="lineNum">   30142 </span>            :             } else {</a>
+<a name="30143"><span class="lineNum">   30143 </span><span class="lineNoCov">          0 :                 p = oldc * bb;</span></a>
+<a name="30144"><span class="lineNum">   30144 </span>            :             }</a>
+<a name="30145"><span class="lineNum">   30145 </span>            :         }</a>
+<a name="30146"><span class="lineNum">   30146 </span>            : </a>
+<a name="30147"><span class="lineNum">   30147 </span><span class="lineNoCov">          0 :         e[l] = s * p;</span></a>
+<a name="30148"><span class="lineNum">   30148 </span><span class="lineNoCov">          0 :         d__[l] = sigma + gamma;</span></a>
+<a name="30149"><span class="lineNum">   30149 </span><span class="lineNoCov">          0 :         goto L50;</span></a>
+<a name="30150"><span class="lineNum">   30150 </span>            : </a>
+<a name="30151"><span class="lineNum">   30151 </span>            : L90:</a>
+<a name="30152"><span class="lineNum">   30152 </span>            :         d__[l] = p;</a>
+<a name="30153"><span class="lineNum">   30153 </span>            : </a>
+<a name="30154"><span class="lineNum">   30154 </span><span class="lineNoCov">          0 :         ++l;</span></a>
+<a name="30155"><span class="lineNum">   30155 </span><span class="lineNoCov">          0 :         if (l &lt;= lend) {</span></a>
+<a name="30156"><span class="lineNum">   30156 </span><span class="lineNoCov">          0 :             goto L50;</span></a>
+<a name="30157"><span class="lineNum">   30157 </span>            :         }</a>
+<a name="30158"><span class="lineNum">   30158 </span><span class="lineNoCov">          0 :         goto L150;</span></a>
+<a name="30159"><span class="lineNum">   30159 </span>            : </a>
+<a name="30160"><span class="lineNum">   30160 </span>            :     } else {</a>
+<a name="30161"><span class="lineNum">   30161 </span>            : </a>
+<a name="30162"><span class="lineNum">   30162 </span><span class="lineNoCov">          0 : L100:</span></a>
+<a name="30163"><span class="lineNum">   30163 </span><span class="lineNoCov">          0 :         i__1 = lend + 1;</span></a>
+<a name="30164"><span class="lineNum">   30164 </span><span class="lineNoCov">          0 :         for (m = l; m &gt;= i__1; --m) {</span></a>
+<a name="30165"><span class="lineNum">   30165 </span><span class="lineNoCov">          0 :             if (std::abs(e[m - 1]) &lt;= eps2 * std::abs(d__[m] * d__[m - 1])) {</span></a>
+<a name="30166"><span class="lineNum">   30166 </span><span class="lineNoCov">          0 :                 goto L120;</span></a>
+<a name="30167"><span class="lineNum">   30167 </span>            :             }</a>
+<a name="30168"><span class="lineNum">   30168 </span>            :         }</a>
+<a name="30169"><span class="lineNum">   30169 </span>            :         m = lend;</a>
+<a name="30170"><span class="lineNum">   30170 </span>            : </a>
+<a name="30171"><span class="lineNum">   30171 </span><span class="lineNoCov">          0 : L120:</span></a>
+<a name="30172"><span class="lineNum">   30172 </span><span class="lineNoCov">          0 :         if (m &gt; lend) {</span></a>
+<a name="30173"><span class="lineNum">   30173 </span><span class="lineNoCov">          0 :             e[m - 1] = 0.;</span></a>
+<a name="30174"><span class="lineNum">   30174 </span>            :         }</a>
+<a name="30175"><span class="lineNum">   30175 </span><span class="lineNoCov">          0 :         p = d__[l];</span></a>
+<a name="30176"><span class="lineNum">   30176 </span><span class="lineNoCov">          0 :         if (m == l) {</span></a>
+<a name="30177"><span class="lineNum">   30177 </span><span class="lineNoCov">          0 :             goto L140;</span></a>
+<a name="30178"><span class="lineNum">   30178 </span>            :         }</a>
+<a name="30179"><span class="lineNum">   30179 </span>            : </a>
+<a name="30180"><span class="lineNum">   30180 </span><span class="lineNoCov">          0 :         if (m == l - 1) {</span></a>
+<a name="30181"><span class="lineNum">   30181 </span><span class="lineNoCov">          0 :             rte =  std::sqrt(e[l - 1]);</span></a>
+<a name="30182"><span class="lineNum">   30182 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slae2,SLAE2)(&amp;d__[l], &amp;rte, &amp;d__[l - 1], &amp;rt1, &amp;rt2);</span></a>
+<a name="30183"><span class="lineNum">   30183 </span><span class="lineNoCov">          0 :             d__[l] = rt1;</span></a>
+<a name="30184"><span class="lineNum">   30184 </span><span class="lineNoCov">          0 :             d__[l - 1] = rt2;</span></a>
+<a name="30185"><span class="lineNum">   30185 </span><span class="lineNoCov">          0 :             e[l - 1] = 0.;</span></a>
+<a name="30186"><span class="lineNum">   30186 </span><span class="lineNoCov">          0 :             l += -2;</span></a>
+<a name="30187"><span class="lineNum">   30187 </span><span class="lineNoCov">          0 :             if (l &gt;= lend) {</span></a>
+<a name="30188"><span class="lineNum">   30188 </span><span class="lineNoCov">          0 :                 goto L100;</span></a>
+<a name="30189"><span class="lineNum">   30189 </span>            :             }</a>
+<a name="30190"><span class="lineNum">   30190 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="30191"><span class="lineNum">   30191 </span>            :         }</a>
+<a name="30192"><span class="lineNum">   30192 </span>            : </a>
+<a name="30193"><span class="lineNum">   30193 </span><span class="lineNoCov">          0 :         if (jtot == nmaxit) {</span></a>
+<a name="30194"><span class="lineNum">   30194 </span><span class="lineNoCov">          0 :             goto L150;</span></a>
+<a name="30195"><span class="lineNum">   30195 </span>            :         }</a>
+<a name="30196"><span class="lineNum">   30196 </span><span class="lineNoCov">          0 :         ++jtot;</span></a>
+<a name="30197"><span class="lineNum">   30197 </span>            : </a>
+<a name="30198"><span class="lineNum">   30198 </span><span class="lineNoCov">          0 :         rte =  std::sqrt(e[l - 1]);</span></a>
+<a name="30199"><span class="lineNum">   30199 </span><span class="lineNoCov">          0 :         sigma = (d__[l - 1] - p) / (rte * 2.);</span></a>
+<a name="30200"><span class="lineNum">   30200 </span><span class="lineNoCov">          0 :         r__ = PLUMED_BLAS_F77_FUNC(slapy2,SLAPY2)(&amp;sigma, &amp;c_b32);</span></a>
+<a name="30201"><span class="lineNum">   30201 </span><span class="lineNoCov">          0 :         sigma = p - rte / (sigma + ( (sigma&gt;0) ? r__ : -r__));</span></a>
+<a name="30202"><span class="lineNum">   30202 </span>            : </a>
+<a name="30203"><span class="lineNum">   30203 </span>            :         c__ = 1.;</a>
+<a name="30204"><span class="lineNum">   30204 </span>            :         s = 0.;</a>
+<a name="30205"><span class="lineNum">   30205 </span><span class="lineNoCov">          0 :         gamma = d__[m] - sigma;</span></a>
+<a name="30206"><span class="lineNum">   30206 </span><span class="lineNoCov">          0 :         p = gamma * gamma;</span></a>
+<a name="30207"><span class="lineNum">   30207 </span>            : </a>
+<a name="30208"><span class="lineNum">   30208 </span><span class="lineNoCov">          0 :         i__1 = l - 1;</span></a>
+<a name="30209"><span class="lineNum">   30209 </span><span class="lineNoCov">          0 :         for (i__ = m; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="30210"><span class="lineNum">   30210 </span><span class="lineNoCov">          0 :             bb = e[i__];</span></a>
+<a name="30211"><span class="lineNum">   30211 </span><span class="lineNoCov">          0 :             r__ = p + bb;</span></a>
+<a name="30212"><span class="lineNum">   30212 </span><span class="lineNoCov">          0 :             if (i__ != m) {</span></a>
+<a name="30213"><span class="lineNum">   30213 </span><span class="lineNoCov">          0 :                 e[i__ - 1] = s * r__;</span></a>
+<a name="30214"><span class="lineNum">   30214 </span>            :             }</a>
+<a name="30215"><span class="lineNum">   30215 </span>            :             oldc = c__;</a>
+<a name="30216"><span class="lineNum">   30216 </span><span class="lineNoCov">          0 :             c__ = p / r__;</span></a>
+<a name="30217"><span class="lineNum">   30217 </span><span class="lineNoCov">          0 :             s = bb / r__;</span></a>
+<a name="30218"><span class="lineNum">   30218 </span>            :             oldgam = gamma;</a>
+<a name="30219"><span class="lineNum">   30219 </span><span class="lineNoCov">          0 :             alpha = d__[i__ + 1];</span></a>
+<a name="30220"><span class="lineNum">   30220 </span><span class="lineNoCov">          0 :             gamma = c__ * (alpha - sigma) - s * oldgam;</span></a>
+<a name="30221"><span class="lineNum">   30221 </span><span class="lineNoCov">          0 :             d__[i__] = oldgam + (alpha - gamma);</span></a>
+<a name="30222"><span class="lineNum">   30222 </span><span class="lineNoCov">          0 :             if (std::abs(c__)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="30223"><span class="lineNum">   30223 </span><span class="lineNoCov">          0 :                 p = gamma * gamma / c__;</span></a>
+<a name="30224"><span class="lineNum">   30224 </span>            :             } else {</a>
+<a name="30225"><span class="lineNum">   30225 </span><span class="lineNoCov">          0 :                 p = oldc * bb;</span></a>
+<a name="30226"><span class="lineNum">   30226 </span>            :             }</a>
+<a name="30227"><span class="lineNum">   30227 </span>            :         }</a>
+<a name="30228"><span class="lineNum">   30228 </span>            : </a>
+<a name="30229"><span class="lineNum">   30229 </span><span class="lineNoCov">          0 :         e[l - 1] = s * p;</span></a>
+<a name="30230"><span class="lineNum">   30230 </span><span class="lineNoCov">          0 :         d__[l] = sigma + gamma;</span></a>
+<a name="30231"><span class="lineNum">   30231 </span><span class="lineNoCov">          0 :         goto L100;</span></a>
+<a name="30232"><span class="lineNum">   30232 </span>            : </a>
+<a name="30233"><span class="lineNum">   30233 </span>            : L140:</a>
+<a name="30234"><span class="lineNum">   30234 </span>            :         d__[l] = p;</a>
+<a name="30235"><span class="lineNum">   30235 </span>            : </a>
+<a name="30236"><span class="lineNum">   30236 </span><span class="lineNoCov">          0 :         --l;</span></a>
+<a name="30237"><span class="lineNum">   30237 </span><span class="lineNoCov">          0 :         if (l &gt;= lend) {</span></a>
+<a name="30238"><span class="lineNum">   30238 </span><span class="lineNoCov">          0 :             goto L100;</span></a>
+<a name="30239"><span class="lineNum">   30239 </span>            :         }</a>
+<a name="30240"><span class="lineNum">   30240 </span><span class="lineNoCov">          0 :         goto L150;</span></a>
+<a name="30241"><span class="lineNum">   30241 </span>            : </a>
+<a name="30242"><span class="lineNum">   30242 </span>            :     }</a>
+<a name="30243"><span class="lineNum">   30243 </span>            : </a>
+<a name="30244"><span class="lineNum">   30244 </span><span class="lineNoCov">          0 : L150:</span></a>
+<a name="30245"><span class="lineNum">   30245 </span><span class="lineNoCov">          0 :     if (iscale == 1) {</span></a>
+<a name="30246"><span class="lineNum">   30246 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="30247"><span class="lineNum">   30247 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmax, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="30248"><span class="lineNum">   30248 </span>            :                 n, info);</a>
+<a name="30249"><span class="lineNum">   30249 </span>            :     }</a>
+<a name="30250"><span class="lineNum">   30250 </span><span class="lineNoCov">          0 :     if (iscale == 2) {</span></a>
+<a name="30251"><span class="lineNum">   30251 </span><span class="lineNoCov">          0 :         i__1 = lendsv - lsv + 1;</span></a>
+<a name="30252"><span class="lineNum">   30252 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(slascl,SLASCL)(&quot;G&quot;, &amp;c__0, &amp;c__0, &amp;ssfmin, &amp;anorm, &amp;i__1, &amp;c__1, &amp;d__[lsv], </span></a>
+<a name="30253"><span class="lineNum">   30253 </span>            :                 n, info);</a>
+<a name="30254"><span class="lineNum">   30254 </span>            :     }</a>
+<a name="30255"><span class="lineNum">   30255 </span>            : </a>
+<a name="30256"><span class="lineNum">   30256 </span><span class="lineNoCov">          0 :     if (jtot &lt; nmaxit) {</span></a>
+<a name="30257"><span class="lineNum">   30257 </span><span class="lineNoCov">          0 :         goto L10;</span></a>
+<a name="30258"><span class="lineNum">   30258 </span>            :     }</a>
+<a name="30259"><span class="lineNum">   30259 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="30260"><span class="lineNum">   30260 </span><span class="lineNoCov">          0 :     for (i__ = 1; i__ &lt;= i__1; ++i__) {</span></a>
+<a name="30261"><span class="lineNum">   30261 </span><span class="lineNoCov">          0 :         if (std::abs(e[i__])&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="30262"><span class="lineNum">   30262 </span><span class="lineNoCov">          0 :             ++(*info);</span></a>
+<a name="30263"><span class="lineNum">   30263 </span>            :         }</a>
+<a name="30264"><span class="lineNum">   30264 </span>            :     }</a>
+<a name="30265"><span class="lineNum">   30265 </span>            :     return;</a>
+<a name="30266"><span class="lineNum">   30266 </span>            : }</a>
+<a name="30267"><span class="lineNum">   30267 </span>            : </a>
+<a name="30268"><span class="lineNum">   30268 </span>            : </a>
+<a name="30269"><span class="lineNum">   30269 </span>            : }</a>
+<a name="30270"><span class="lineNum">   30270 </span>            : }</a>
+<a name="30271"><span class="lineNum">   30271 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="30272"><span class="lineNum">   30272 </span>            : </a>
+<a name="30273"><span class="lineNum">   30273 </span>            : </a>
+<a name="30274"><span class="lineNum">   30274 </span>            : /* Normally, SSTEVR is the LAPACK wrapper which calls one</a>
+<a name="30275"><span class="lineNum">   30275 </span>            :  * of the eigenvalue methods. However, our code includes a</a>
+<a name="30276"><span class="lineNum">   30276 </span>            :  * version of SSTEGR which is never than LAPACK 3.0 and can</a>
+<a name="30277"><span class="lineNum">   30277 </span>            :  * handle requests for a subset of eigenvalues/vectors too,</a>
+<a name="30278"><span class="lineNum">   30278 </span>            :  * and it should not need to call SSTEIN.</a>
+<a name="30279"><span class="lineNum">   30279 </span>            :  * Just in case somebody has a faster version in their lapack</a>
+<a name="30280"><span class="lineNum">   30280 </span>            :  * library we still call the driver routine, but in our own</a>
+<a name="30281"><span class="lineNum">   30281 </span>            :  * case this is just a wrapper to sstegr.</a>
+<a name="30282"><span class="lineNum">   30282 </span>            :  */</a>
+<a name="30283"><span class="lineNum">   30283 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30284"><span class="lineNum">   30284 </span>            : namespace PLMD{</a>
+<a name="30285"><span class="lineNum">   30285 </span>            : namespace lapack{</a>
+<a name="30286"><span class="lineNum">   30286 </span>            : using namespace blas;</a>
+<a name="30287"><span class="lineNum">   30287 </span>            : void</a>
+<a name="30288"><span class="lineNum">   30288 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(sstevr,SSTEVR)(const char *jobz, </span></a>
+<a name="30289"><span class="lineNum">   30289 </span>            :                         const char *range,</a>
+<a name="30290"><span class="lineNum">   30290 </span>            :                         int *n,</a>
+<a name="30291"><span class="lineNum">   30291 </span>            :                         float *d,</a>
+<a name="30292"><span class="lineNum">   30292 </span>            :                         float *e,</a>
+<a name="30293"><span class="lineNum">   30293 </span>            :                         float *vl, </a>
+<a name="30294"><span class="lineNum">   30294 </span>            :                         float *vu,</a>
+<a name="30295"><span class="lineNum">   30295 </span>            :                         int *il, </a>
+<a name="30296"><span class="lineNum">   30296 </span>            :                         int *iu, </a>
+<a name="30297"><span class="lineNum">   30297 </span>            :                         float *abstol,</a>
+<a name="30298"><span class="lineNum">   30298 </span>            :                         int *m,</a>
+<a name="30299"><span class="lineNum">   30299 </span>            :                         float *w, </a>
+<a name="30300"><span class="lineNum">   30300 </span>            :                         float *z,</a>
+<a name="30301"><span class="lineNum">   30301 </span>            :                         int *ldz,</a>
+<a name="30302"><span class="lineNum">   30302 </span>            :                         int *isuppz, </a>
+<a name="30303"><span class="lineNum">   30303 </span>            :                         float *work, </a>
+<a name="30304"><span class="lineNum">   30304 </span>            :                         int *lwork, </a>
+<a name="30305"><span class="lineNum">   30305 </span>            :                         int *iwork,</a>
+<a name="30306"><span class="lineNum">   30306 </span>            :                         int *liwork, </a>
+<a name="30307"><span class="lineNum">   30307 </span>            :                         int *info)</a>
+<a name="30308"><span class="lineNum">   30308 </span>            : {</a>
+<a name="30309"><span class="lineNum">   30309 </span><span class="lineNoCov">          0 :   PLUMED_BLAS_F77_FUNC(sstegr,SSTEGR)(jobz, range, n, d, e, vl, vu, il, iu, abstol, m, w,</span></a>
+<a name="30310"><span class="lineNum">   30310 </span>            :           z, ldz, isuppz, work, lwork, iwork, liwork, info);</a>
+<a name="30311"><span class="lineNum">   30311 </span>            :   </a>
+<a name="30312"><span class="lineNum">   30312 </span>            : </a>
+<a name="30313"><span class="lineNum">   30313 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="30314"><span class="lineNum">   30314 </span>            : </a>
+<a name="30315"><span class="lineNum">   30315 </span>            : }</a>
+<a name="30316"><span class="lineNum">   30316 </span>            : </a>
+<a name="30317"><span class="lineNum">   30317 </span>            : </a>
+<a name="30318"><span class="lineNum">   30318 </span>            : }</a>
+<a name="30319"><span class="lineNum">   30319 </span>            : }</a>
+<a name="30320"><span class="lineNum">   30320 </span>            : #include &lt;cmath&gt;</a>
+<a name="30321"><span class="lineNum">   30321 </span>            : </a>
+<a name="30322"><span class="lineNum">   30322 </span>            : #include &quot;real.h&quot;</a>
+<a name="30323"><span class="lineNum">   30323 </span>            : </a>
+<a name="30324"><span class="lineNum">   30324 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30325"><span class="lineNum">   30325 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="30326"><span class="lineNum">   30326 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="30327"><span class="lineNum">   30327 </span>            : </a>
+<a name="30328"><span class="lineNum">   30328 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30329"><span class="lineNum">   30329 </span>            : namespace PLMD{</a>
+<a name="30330"><span class="lineNum">   30330 </span>            : namespace lapack{</a>
+<a name="30331"><span class="lineNum">   30331 </span>            : using namespace blas;</a>
+<a name="30332"><span class="lineNum">   30332 </span>            : void</a>
+<a name="30333"><span class="lineNum">   30333 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssyevr,SSYEVR)(const char *jobz, const char *range, const char *uplo, int *n, </span></a>
+<a name="30334"><span class="lineNum">   30334 </span>            :         float *a, int *lda, float *vl, float *vu, int *</a>
+<a name="30335"><span class="lineNum">   30335 </span>            :         il, int *iu, float *abstol, int *m, float *w, </a>
+<a name="30336"><span class="lineNum">   30336 </span>            :         float *z__, int *ldz, int *isuppz, float *work, </a>
+<a name="30337"><span class="lineNum">   30337 </span>            :         int *lwork, int *iwork, int *liwork, int *info)</a>
+<a name="30338"><span class="lineNum">   30338 </span>            : {</a>
+<a name="30339"><span class="lineNum">   30339 </span>            :     /* System generated locals */</a>
+<a name="30340"><span class="lineNum">   30340 </span>            :     int a_dim1, a_offset, z_dim1, z_offset, i__1, i__2;</a>
+<a name="30341"><span class="lineNum">   30341 </span>            :     float d__1, d__2;</a>
+<a name="30342"><span class="lineNum">   30342 </span>            : </a>
+<a name="30343"><span class="lineNum">   30343 </span>            :     /* Local variables */</a>
+<a name="30344"><span class="lineNum">   30344 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="30345"><span class="lineNum">   30345 </span>            :     int i__, j, nb, jj;</a>
+<a name="30346"><span class="lineNum">   30346 </span>            :     float eps, tmp1;</a>
+<a name="30347"><span class="lineNum">   30347 </span>            :     int indd, inde;</a>
+<a name="30348"><span class="lineNum">   30348 </span>            :     float anrm;</a>
+<a name="30349"><span class="lineNum">   30349 </span>            :     int imax;</a>
+<a name="30350"><span class="lineNum">   30350 </span>            :     float rmin, rmax;</a>
+<a name="30351"><span class="lineNum">   30351 </span>            :     int itmp1, inddd, indee;</a>
+<a name="30352"><span class="lineNum">   30352 </span>            :     float sigma;</a>
+<a name="30353"><span class="lineNum">   30353 </span>            :     int iinfo;</a>
+<a name="30354"><span class="lineNum">   30354 </span>            :     int indwk;</a>
+<a name="30355"><span class="lineNum">   30355 </span>            :     int lwmin;</a>
+<a name="30356"><span class="lineNum">   30356 </span>            :     int lower, wantz;</a>
+<a name="30357"><span class="lineNum">   30357 </span>            :     int alleig, indeig;</a>
+<a name="30358"><span class="lineNum">   30358 </span>            :     int iscale, indibl, indifl;</a>
+<a name="30359"><span class="lineNum">   30359 </span>            :     int valeig;</a>
+<a name="30360"><span class="lineNum">   30360 </span>            :     float safmin,minval;</a>
+<a name="30361"><span class="lineNum">   30361 </span>            :     float bignum;</a>
+<a name="30362"><span class="lineNum">   30362 </span>            :     int indtau;</a>
+<a name="30363"><span class="lineNum">   30363 </span>            :     int indwkn;</a>
+<a name="30364"><span class="lineNum">   30364 </span>            :     int liwmin;</a>
+<a name="30365"><span class="lineNum">   30365 </span>            :     int llwrkn, llwork;</a>
+<a name="30366"><span class="lineNum">   30366 </span>            :     float smlnum;</a>
+<a name="30367"><span class="lineNum">   30367 </span>            :     int lwkopt;</a>
+<a name="30368"><span class="lineNum">   30368 </span>            :     int lquery;</a>
+<a name="30369"><span class="lineNum">   30369 </span>            :     </a>
+<a name="30370"><span class="lineNum">   30370 </span>            :     /* Parameter adjustments */</a>
+<a name="30371"><span class="lineNum">   30371 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="30372"><span class="lineNum">   30372 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="30373"><span class="lineNum">   30373 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="30374"><span class="lineNum">   30374 </span><span class="lineNoCov">          0 :     --w;</span></a>
+<a name="30375"><span class="lineNum">   30375 </span><span class="lineNoCov">          0 :     z_dim1 = *ldz;</span></a>
+<a name="30376"><span class="lineNum">   30376 </span><span class="lineNoCov">          0 :     z_offset = 1 + z_dim1;</span></a>
+<a name="30377"><span class="lineNum">   30377 </span><span class="lineNoCov">          0 :     z__ -= z_offset;</span></a>
+<a name="30378"><span class="lineNum">   30378 </span>            :     --isuppz;</a>
+<a name="30379"><span class="lineNum">   30379 </span><span class="lineNoCov">          0 :     --work;</span></a>
+<a name="30380"><span class="lineNum">   30380 </span><span class="lineNoCov">          0 :     --iwork;</span></a>
+<a name="30381"><span class="lineNum">   30381 </span>            : </a>
+<a name="30382"><span class="lineNum">   30382 </span><span class="lineNoCov">          0 :     lower = (*uplo=='L' || *uplo=='l');</span></a>
+<a name="30383"><span class="lineNum">   30383 </span><span class="lineNoCov">          0 :     wantz = (*jobz=='V' || *jobz=='v');</span></a>
+<a name="30384"><span class="lineNum">   30384 </span><span class="lineNoCov">          0 :     alleig = (*range=='A' || *range=='a');</span></a>
+<a name="30385"><span class="lineNum">   30385 </span><span class="lineNoCov">          0 :     valeig = (*range=='V' || *range=='v');</span></a>
+<a name="30386"><span class="lineNum">   30386 </span><span class="lineNoCov">          0 :     indeig = (*range=='I' || *range=='i');</span></a>
+<a name="30387"><span class="lineNum">   30387 </span>            : </a>
+<a name="30388"><span class="lineNum">   30388 </span>            :     indibl = 0;</a>
+<a name="30389"><span class="lineNum">   30389 </span><span class="lineNoCov">          0 :     lquery = *lwork == -1 || *liwork == -1;</span></a>
+<a name="30390"><span class="lineNum">   30390 </span>            : </a>
+<a name="30391"><span class="lineNum">   30391 </span>            :     i__1 = 1;</a>
+<a name="30392"><span class="lineNum">   30392 </span><span class="lineNoCov">          0 :     i__2 = *n * 26;</span></a>
+<a name="30393"><span class="lineNum">   30393 </span>            : </a>
+<a name="30394"><span class="lineNum">   30394 </span><span class="lineNoCov">          0 :     if(*n&gt;0) </span></a>
+<a name="30395"><span class="lineNum">   30395 </span>            :       lwmin = *n * 26;</a>
+<a name="30396"><span class="lineNum">   30396 </span>            :     else</a>
+<a name="30397"><span class="lineNum">   30397 </span>            :       lwmin = 1;</a>
+<a name="30398"><span class="lineNum">   30398 </span>            : </a>
+<a name="30399"><span class="lineNum">   30399 </span><span class="lineNoCov">          0 :     if(*n&gt;0) </span></a>
+<a name="30400"><span class="lineNum">   30400 </span><span class="lineNoCov">          0 :       liwmin = *n * 10;</span></a>
+<a name="30401"><span class="lineNum">   30401 </span>            :     else</a>
+<a name="30402"><span class="lineNum">   30402 </span>            :       liwmin = 1;</a>
+<a name="30403"><span class="lineNum">   30403 </span>            : </a>
+<a name="30404"><span class="lineNum">   30404 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="30405"><span class="lineNum">   30405 </span><span class="lineNoCov">          0 :     if (! (wantz || (*jobz=='N' || *jobz=='n'))) {</span></a>
+<a name="30406"><span class="lineNum">   30406 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="30407"><span class="lineNum">   30407 </span><span class="lineNoCov">          0 :     } else if (! (alleig || valeig || indeig)) {</span></a>
+<a name="30408"><span class="lineNum">   30408 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="30409"><span class="lineNum">   30409 </span><span class="lineNoCov">          0 :     } else if (! (lower || (*uplo=='U' || *uplo=='u'))) {</span></a>
+<a name="30410"><span class="lineNum">   30410 </span><span class="lineNoCov">          0 :         *info = -3;</span></a>
+<a name="30411"><span class="lineNum">   30411 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="30412"><span class="lineNum">   30412 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="30413"><span class="lineNum">   30413 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; ((*n&gt;1) ? *n : 1) ) {</span></a>
+<a name="30414"><span class="lineNum">   30414 </span><span class="lineNoCov">          0 :         *info = -6;</span></a>
+<a name="30415"><span class="lineNum">   30415 </span>            :     } else {</a>
+<a name="30416"><span class="lineNum">   30416 </span><span class="lineNoCov">          0 :         if (valeig) {</span></a>
+<a name="30417"><span class="lineNum">   30417 </span><span class="lineNoCov">          0 :             if (*n &gt; 0 &amp;&amp; *vu &lt;= *vl) {</span></a>
+<a name="30418"><span class="lineNum">   30418 </span><span class="lineNoCov">          0 :                 *info = -8;</span></a>
+<a name="30419"><span class="lineNum">   30419 </span>            :             }</a>
+<a name="30420"><span class="lineNum">   30420 </span><span class="lineNoCov">          0 :         } else if (indeig) {</span></a>
+<a name="30421"><span class="lineNum">   30421 </span><span class="lineNoCov">          0 :           if (*il &lt; 1 || *il &gt; ((*n&gt;1) ? *n : 1)) {</span></a>
+<a name="30422"><span class="lineNum">   30422 </span><span class="lineNoCov">          0 :                 *info = -9;</span></a>
+<a name="30423"><span class="lineNum">   30423 </span><span class="lineNoCov">          0 :             } else if (*iu &lt; ((*n&lt;*il) ? *n : *il) || *iu &gt; *n) {</span></a>
+<a name="30424"><span class="lineNum">   30424 </span><span class="lineNoCov">          0 :                 *info = -10;</span></a>
+<a name="30425"><span class="lineNum">   30425 </span>            :             }</a>
+<a name="30426"><span class="lineNum">   30426 </span>            :         }</a>
+<a name="30427"><span class="lineNum">   30427 </span>            :     }</a>
+<a name="30428"><span class="lineNum">   30428 </span><span class="lineNoCov">          0 :     if (*info == 0) {</span></a>
+<a name="30429"><span class="lineNum">   30429 </span><span class="lineNoCov">          0 :       if (*ldz &lt; 1 || (wantz &amp;&amp; *ldz &lt; *n)) {</span></a>
+<a name="30430"><span class="lineNum">   30430 </span><span class="lineNoCov">          0 :             *info = -15;</span></a>
+<a name="30431"><span class="lineNum">   30431 </span><span class="lineNoCov">          0 :         } else if (*lwork &lt; lwmin &amp;&amp; ! lquery) {</span></a>
+<a name="30432"><span class="lineNum">   30432 </span><span class="lineNoCov">          0 :             *info = -18;</span></a>
+<a name="30433"><span class="lineNum">   30433 </span><span class="lineNoCov">          0 :         } else if (*liwork &lt; liwmin &amp;&amp; ! lquery) {</span></a>
+<a name="30434"><span class="lineNum">   30434 </span><span class="lineNoCov">          0 :             *info = -20;</span></a>
+<a name="30435"><span class="lineNum">   30435 </span>            :         }</a>
+<a name="30436"><span class="lineNum">   30436 </span>            :     }</a>
+<a name="30437"><span class="lineNum">   30437 </span>            : </a>
+<a name="30438"><span class="lineNum">   30438 </span><span class="lineNoCov">          0 :     if (*info == 0) {</span></a>
+<a name="30439"><span class="lineNum">   30439 </span>            :       nb = 32;</a>
+<a name="30440"><span class="lineNum">   30440 </span>            :       /* Computing MAX */</a>
+<a name="30441"><span class="lineNum">   30441 </span><span class="lineNoCov">          0 :       i__1 = (nb + 1) * *n;</span></a>
+<a name="30442"><span class="lineNum">   30442 </span>            :       lwkopt = (i__1&gt;lwmin) ? i__1 : lwmin;</a>
+<a name="30443"><span class="lineNum">   30443 </span><span class="lineNoCov">          0 :       work[1] = (float) lwkopt;</span></a>
+<a name="30444"><span class="lineNum">   30444 </span><span class="lineNoCov">          0 :       iwork[1] = liwmin;</span></a>
+<a name="30445"><span class="lineNum">   30445 </span>            :     } else </a>
+<a name="30446"><span class="lineNum">   30446 </span>            :       return;</a>
+<a name="30447"><span class="lineNum">   30447 </span>            : </a>
+<a name="30448"><span class="lineNum">   30448 </span><span class="lineNoCov">          0 :     if (lquery) </span></a>
+<a name="30449"><span class="lineNum">   30449 </span>            :         return;</a>
+<a name="30450"><span class="lineNum">   30450 </span>            :     </a>
+<a name="30451"><span class="lineNum">   30451 </span><span class="lineNoCov">          0 :     *m = 0;</span></a>
+<a name="30452"><span class="lineNum">   30452 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="30453"><span class="lineNum">   30453 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="30454"><span class="lineNum">   30454 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="30455"><span class="lineNum">   30455 </span>            :     }</a>
+<a name="30456"><span class="lineNum">   30456 </span>            : </a>
+<a name="30457"><span class="lineNum">   30457 </span><span class="lineNoCov">          0 :     if (*n == 1) {</span></a>
+<a name="30458"><span class="lineNum">   30458 </span><span class="lineNoCov">          0 :         work[1] = 7.;</span></a>
+<a name="30459"><span class="lineNum">   30459 </span><span class="lineNoCov">          0 :         if (alleig || indeig) {</span></a>
+<a name="30460"><span class="lineNum">   30460 </span><span class="lineNoCov">          0 :             *m = 1;</span></a>
+<a name="30461"><span class="lineNum">   30461 </span><span class="lineNoCov">          0 :             w[1] = a[a_dim1 + 1];</span></a>
+<a name="30462"><span class="lineNum">   30462 </span>            :         } else {</a>
+<a name="30463"><span class="lineNum">   30463 </span><span class="lineNoCov">          0 :             if (*vl &lt; a[a_dim1 + 1] &amp;&amp; *vu &gt;= a[a_dim1 + 1]) {</span></a>
+<a name="30464"><span class="lineNum">   30464 </span><span class="lineNoCov">          0 :                 *m = 1;</span></a>
+<a name="30465"><span class="lineNum">   30465 </span><span class="lineNoCov">          0 :                 w[1] = a[a_dim1 + 1];</span></a>
+<a name="30466"><span class="lineNum">   30466 </span>            :             }</a>
+<a name="30467"><span class="lineNum">   30467 </span>            :         }</a>
+<a name="30468"><span class="lineNum">   30468 </span><span class="lineNoCov">          0 :         if (wantz) {</span></a>
+<a name="30469"><span class="lineNum">   30469 </span><span class="lineNoCov">          0 :             z__[z_dim1 + 1] = 1.;</span></a>
+<a name="30470"><span class="lineNum">   30470 </span>            :         }</a>
+<a name="30471"><span class="lineNum">   30471 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="30472"><span class="lineNum">   30472 </span>            :     }</a>
+<a name="30473"><span class="lineNum">   30473 </span>            :     minval = PLUMED_GMX_FLOAT_MIN;</a>
+<a name="30474"><span class="lineNum">   30474 </span>            :     safmin = minval*(1.0+PLUMED_GMX_FLOAT_EPS);</a>
+<a name="30475"><span class="lineNum">   30475 </span>            :     eps = PLUMED_GMX_FLOAT_EPS;</a>
+<a name="30476"><span class="lineNum">   30476 </span>            : </a>
+<a name="30477"><span class="lineNum">   30477 </span>            :     smlnum = safmin / eps;</a>
+<a name="30478"><span class="lineNum">   30478 </span>            :     bignum = 1. / smlnum;</a>
+<a name="30479"><span class="lineNum">   30479 </span>            :     rmin =  std::sqrt(smlnum);</a>
+<a name="30480"><span class="lineNum">   30480 </span>            : </a>
+<a name="30481"><span class="lineNum">   30481 </span><span class="lineNoCov">          0 :     d__1 =  std::sqrt(bignum), d__2 = 1. / std::sqrt(sqrt(safmin));</span></a>
+<a name="30482"><span class="lineNum">   30482 </span>            :     rmax = (d__1&lt;d__2) ? d__1 : d__2;</a>
+<a name="30483"><span class="lineNum">   30483 </span>            : </a>
+<a name="30484"><span class="lineNum">   30484 </span>            :     iscale = 0;</a>
+<a name="30485"><span class="lineNum">   30485 </span><span class="lineNoCov">          0 :     anrm = PLUMED_BLAS_F77_FUNC(slansy,SLANSY)(&quot;M&quot;, uplo, n, &amp;a[a_offset], lda, &amp;work[1]);</span></a>
+<a name="30486"><span class="lineNum">   30486 </span><span class="lineNoCov">          0 :     if (anrm &gt; 0. &amp;&amp; anrm &lt; rmin) {</span></a>
+<a name="30487"><span class="lineNum">   30487 </span>            :         iscale = 1;</a>
+<a name="30488"><span class="lineNum">   30488 </span><span class="lineNoCov">          0 :         sigma = rmin / anrm;</span></a>
+<a name="30489"><span class="lineNum">   30489 </span><span class="lineNoCov">          0 :     } else if (anrm &gt; rmax) {</span></a>
+<a name="30490"><span class="lineNum">   30490 </span>            :         iscale = 1;</a>
+<a name="30491"><span class="lineNum">   30491 </span><span class="lineNoCov">          0 :         sigma = rmax / anrm; </span></a>
+<a name="30492"><span class="lineNum">   30492 </span>            :     }</a>
+<a name="30493"><span class="lineNum">   30493 </span>            :     if (iscale == 1) {</a>
+<a name="30494"><span class="lineNum">   30494 </span><span class="lineNoCov">          0 :         if (lower) {</span></a>
+<a name="30495"><span class="lineNum">   30495 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="30496"><span class="lineNum">   30496 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="30497"><span class="lineNum">   30497 </span><span class="lineNoCov">          0 :                 i__2 = *n - j + 1;</span></a>
+<a name="30498"><span class="lineNum">   30498 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__2, &amp;sigma, &amp;a[j + j * a_dim1], &amp;c__1);</span></a>
+<a name="30499"><span class="lineNum">   30499 </span>            :             }</a>
+<a name="30500"><span class="lineNum">   30500 </span>            :         } else {</a>
+<a name="30501"><span class="lineNum">   30501 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="30502"><span class="lineNum">   30502 </span><span class="lineNoCov">          0 :             for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="30503"><span class="lineNum">   30503 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;j, &amp;sigma, &amp;a[j * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="30504"><span class="lineNum">   30504 </span>            : </a>
+<a name="30505"><span class="lineNum">   30505 </span>            :             }</a>
+<a name="30506"><span class="lineNum">   30506 </span>            :         }</a>
+<a name="30507"><span class="lineNum">   30507 </span>            :     }</a>
+<a name="30508"><span class="lineNum">   30508 </span>            : </a>
+<a name="30509"><span class="lineNum">   30509 </span>            :     indtau = 1;</a>
+<a name="30510"><span class="lineNum">   30510 </span><span class="lineNoCov">          0 :     inde = indtau + *n;</span></a>
+<a name="30511"><span class="lineNum">   30511 </span><span class="lineNoCov">          0 :     indd = inde + *n;</span></a>
+<a name="30512"><span class="lineNum">   30512 </span><span class="lineNoCov">          0 :     indee = indd + *n;</span></a>
+<a name="30513"><span class="lineNum">   30513 </span><span class="lineNoCov">          0 :     inddd = indee + *n;</span></a>
+<a name="30514"><span class="lineNum">   30514 </span><span class="lineNoCov">          0 :     indifl = inddd + *n;</span></a>
+<a name="30515"><span class="lineNum">   30515 </span><span class="lineNoCov">          0 :     indwk = indifl + *n;</span></a>
+<a name="30516"><span class="lineNum">   30516 </span><span class="lineNoCov">          0 :     llwork = *lwork - indwk + 1;</span></a>
+<a name="30517"><span class="lineNum">   30517 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(ssytrd,SSYTRD)(uplo, n, &amp;a[a_offset], lda, &amp;work[indd], &amp;work[inde], &amp;work[</span></a>
+<a name="30518"><span class="lineNum">   30518 </span><span class="lineNoCov">          0 :             indtau], &amp;work[indwk], &amp;llwork, &amp;iinfo);</span></a>
+<a name="30519"><span class="lineNum">   30519 </span>            : </a>
+<a name="30520"><span class="lineNum">   30520 </span><span class="lineNoCov">          0 :     i__1 = *n - 1;</span></a>
+<a name="30521"><span class="lineNum">   30521 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(&amp;i__1, &amp;work[inde], &amp;c__1, &amp;work[indee], &amp;c__1);</span></a>
+<a name="30522"><span class="lineNum">   30522 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(scopy,SCOPY)(n, &amp;work[indd], &amp;c__1, &amp;work[inddd], &amp;c__1);</span></a>
+<a name="30523"><span class="lineNum">   30523 </span>            : </a>
+<a name="30524"><span class="lineNum">   30524 </span><span class="lineNoCov">          0 :     PLUMED_BLAS_F77_FUNC(sstegr,SSTEGR)(jobz, range, n, &amp;work[inddd], &amp;work[indee], vl, vu, il, iu, </span></a>
+<a name="30525"><span class="lineNum">   30525 </span>            :             abstol, m, &amp;w[1], &amp;z__[z_offset], ldz, &amp;isuppz[1], </a>
+<a name="30526"><span class="lineNum">   30526 </span>            :             &amp;work[indwk], lwork, &amp;iwork[1], liwork, info);</a>
+<a name="30527"><span class="lineNum">   30527 </span><span class="lineNoCov">          0 :     if (wantz &amp;&amp; *info == 0) {</span></a>
+<a name="30528"><span class="lineNum">   30528 </span>            :       indwkn = inde;</a>
+<a name="30529"><span class="lineNum">   30529 </span><span class="lineNoCov">          0 :       llwrkn = *lwork - indwkn + 1;</span></a>
+<a name="30530"><span class="lineNum">   30530 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(sormtr,SORMTR)(&quot;L&quot;, uplo, &quot;N&quot;, n, m, &amp;a[a_offset], lda, &amp;work[indtau]</span></a>
+<a name="30531"><span class="lineNum">   30531 </span>            :               , &amp;z__[z_offset], ldz, &amp;work[indwkn], &amp;llwrkn, &amp;iinfo);</a>
+<a name="30532"><span class="lineNum">   30532 </span>            :     }</a>
+<a name="30533"><span class="lineNum">   30533 </span>            : </a>
+<a name="30534"><span class="lineNum">   30534 </span><span class="lineNoCov">          0 :     if (*info != 0) </span></a>
+<a name="30535"><span class="lineNum">   30535 </span>            :       return;</a>
+<a name="30536"><span class="lineNum">   30536 </span>            : </a>
+<a name="30537"><span class="lineNum">   30537 </span><span class="lineNoCov">          0 :     if (iscale == 1) {</span></a>
+<a name="30538"><span class="lineNum">   30538 </span>            :         if (*info == 0) {</a>
+<a name="30539"><span class="lineNum">   30539 </span><span class="lineNoCov">          0 :             imax = *m;</span></a>
+<a name="30540"><span class="lineNum">   30540 </span>            :         } else {</a>
+<a name="30541"><span class="lineNum">   30541 </span>            :             imax = *info - 1;</a>
+<a name="30542"><span class="lineNum">   30542 </span>            :         }</a>
+<a name="30543"><span class="lineNum">   30543 </span><span class="lineNoCov">          0 :         d__1 = 1. / sigma;</span></a>
+<a name="30544"><span class="lineNum">   30544 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;imax, &amp;d__1, &amp;w[1], &amp;c__1);</span></a>
+<a name="30545"><span class="lineNum">   30545 </span>            :     }</a>
+<a name="30546"><span class="lineNum">   30546 </span>            : </a>
+<a name="30547"><span class="lineNum">   30547 </span><span class="lineNoCov">          0 :     if (wantz) {</span></a>
+<a name="30548"><span class="lineNum">   30548 </span><span class="lineNoCov">          0 :         i__1 = *m - 1;</span></a>
+<a name="30549"><span class="lineNum">   30549 </span>            :         </a>
+<a name="30550"><span class="lineNum">   30550 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="30551"><span class="lineNum">   30551 </span>            :             i__ = 0;</a>
+<a name="30552"><span class="lineNum">   30552 </span><span class="lineNoCov">          0 :             tmp1 = w[j];</span></a>
+<a name="30553"><span class="lineNum">   30553 </span><span class="lineNoCov">          0 :             i__2 = *m;</span></a>
+<a name="30554"><span class="lineNum">   30554 </span><span class="lineNoCov">          0 :             for (jj = j + 1; jj &lt;= i__2; ++jj) {</span></a>
+<a name="30555"><span class="lineNum">   30555 </span><span class="lineNoCov">          0 :                 if (w[jj] &lt; tmp1) {</span></a>
+<a name="30556"><span class="lineNum">   30556 </span>            :                     i__ = jj;</a>
+<a name="30557"><span class="lineNum">   30557 </span>            :                     tmp1 = w[jj];</a>
+<a name="30558"><span class="lineNum">   30558 </span>            :                 }</a>
+<a name="30559"><span class="lineNum">   30559 </span>            :             }</a>
+<a name="30560"><span class="lineNum">   30560 </span>            : </a>
+<a name="30561"><span class="lineNum">   30561 </span><span class="lineNoCov">          0 :             if (i__ != 0) {</span></a>
+<a name="30562"><span class="lineNum">   30562 </span><span class="lineNoCov">          0 :                 itmp1 = iwork[indibl + i__ - 1];</span></a>
+<a name="30563"><span class="lineNum">   30563 </span><span class="lineNoCov">          0 :                 w[i__] = w[j];</span></a>
+<a name="30564"><span class="lineNum">   30564 </span><span class="lineNoCov">          0 :                 iwork[indibl + i__ - 1] = iwork[indibl + j - 1];</span></a>
+<a name="30565"><span class="lineNum">   30565 </span><span class="lineNoCov">          0 :                 w[j] = tmp1;</span></a>
+<a name="30566"><span class="lineNum">   30566 </span><span class="lineNoCov">          0 :                 iwork[indibl + j - 1] = itmp1;</span></a>
+<a name="30567"><span class="lineNum">   30567 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sswap,SSWAP)(n, &amp;z__[i__ * z_dim1 + 1], &amp;c__1, &amp;z__[j * z_dim1 + 1],</span></a>
+<a name="30568"><span class="lineNum">   30568 </span>            :                          &amp;c__1);</a>
+<a name="30569"><span class="lineNum">   30569 </span>            :             }</a>
+<a name="30570"><span class="lineNum">   30570 </span>            :         }</a>
+<a name="30571"><span class="lineNum">   30571 </span>            :     }</a>
+<a name="30572"><span class="lineNum">   30572 </span>            : </a>
+<a name="30573"><span class="lineNum">   30573 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="30574"><span class="lineNum">   30574 </span><span class="lineNoCov">          0 :     iwork[1] = liwmin;</span></a>
+<a name="30575"><span class="lineNum">   30575 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="30576"><span class="lineNum">   30576 </span>            : </a>
+<a name="30577"><span class="lineNum">   30577 </span>            : }</a>
+<a name="30578"><span class="lineNum">   30578 </span>            : }</a>
+<a name="30579"><span class="lineNum">   30579 </span>            : }</a>
+<a name="30580"><span class="lineNum">   30580 </span>            : #include &lt;cctype&gt;</a>
+<a name="30581"><span class="lineNum">   30581 </span>            : #include &lt;cmath&gt;</a>
+<a name="30582"><span class="lineNum">   30582 </span>            : </a>
+<a name="30583"><span class="lineNum">   30583 </span>            : #include &quot;real.h&quot;</a>
+<a name="30584"><span class="lineNum">   30584 </span>            : </a>
+<a name="30585"><span class="lineNum">   30585 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30586"><span class="lineNum">   30586 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="30587"><span class="lineNum">   30587 </span>            : </a>
+<a name="30588"><span class="lineNum">   30588 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30589"><span class="lineNum">   30589 </span>            : namespace PLMD{</a>
+<a name="30590"><span class="lineNum">   30590 </span>            : namespace lapack{</a>
+<a name="30591"><span class="lineNum">   30591 </span>            : using namespace blas;</a>
+<a name="30592"><span class="lineNum">   30592 </span>            : void</a>
+<a name="30593"><span class="lineNum">   30593 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssytd2,SSYTD2)(const char *    uplo,</span></a>
+<a name="30594"><span class="lineNum">   30594 </span>            :         int *     n,</a>
+<a name="30595"><span class="lineNum">   30595 </span>            :         float *  a,</a>
+<a name="30596"><span class="lineNum">   30596 </span>            :         int *     lda,</a>
+<a name="30597"><span class="lineNum">   30597 </span>            :         float *  d,</a>
+<a name="30598"><span class="lineNum">   30598 </span>            :         float *  e,</a>
+<a name="30599"><span class="lineNum">   30599 </span>            :         float *  tau,</a>
+<a name="30600"><span class="lineNum">   30600 </span>            :     int *     info)</a>
+<a name="30601"><span class="lineNum">   30601 </span>            : {</a>
+<a name="30602"><span class="lineNum">   30602 </span>            :   float minusone,zero;</a>
+<a name="30603"><span class="lineNum">   30603 </span>            :   float taui,alpha,tmp;</a>
+<a name="30604"><span class="lineNum">   30604 </span>            :   int ti1,ti2,ti3,i;</a>
+<a name="30605"><span class="lineNum">   30605 </span><span class="lineNoCov">          0 :   const char ch=std::toupper(*uplo);</span></a>
+<a name="30606"><span class="lineNum">   30606 </span>            : </a>
+<a name="30607"><span class="lineNum">   30607 </span><span class="lineNoCov">          0 :   zero = 0.0;</span></a>
+<a name="30608"><span class="lineNum">   30608 </span><span class="lineNoCov">          0 :   minusone = -1.0;</span></a>
+<a name="30609"><span class="lineNum">   30609 </span>            : </a>
+<a name="30610"><span class="lineNum">   30610 </span><span class="lineNoCov">          0 :   if(*n&lt;=0)</span></a>
+<a name="30611"><span class="lineNum">   30611 </span>            :     return;</a>
+<a name="30612"><span class="lineNum">   30612 </span>            : </a>
+<a name="30613"><span class="lineNum">   30613 </span><span class="lineNoCov">          0 :   if(ch=='U') {</span></a>
+<a name="30614"><span class="lineNum">   30614 </span><span class="lineNoCov">          0 :     for(i=*n-1;i&gt;=1;i--) {</span></a>
+<a name="30615"><span class="lineNum">   30615 </span>            : </a>
+<a name="30616"><span class="lineNum">   30616 </span><span class="lineNoCov">          0 :       ti1 = 1;</span></a>
+<a name="30617"><span class="lineNum">   30617 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;i,&amp;(a[i*(*lda)+(i-1)]),&amp;(a[i*(*lda)+0]),&amp;ti1,&amp;taui);</span></a>
+<a name="30618"><span class="lineNum">   30618 </span><span class="lineNoCov">          0 :       e[i-1] = a[i*(*lda) + (i-1)];</span></a>
+<a name="30619"><span class="lineNum">   30619 </span><span class="lineNoCov">          0 :       if(std::abs(taui)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="30620"><span class="lineNum">   30620 </span><span class="lineNoCov">          0 :         a[i*(*lda)+(i-1)] = 1.0;</span></a>
+<a name="30621"><span class="lineNum">   30621 </span>            :       </a>
+<a name="30622"><span class="lineNum">   30622 </span><span class="lineNoCov">          0 :         ti1 = 1;</span></a>
+<a name="30623"><span class="lineNum">   30623 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)(&quot;U&quot;,&amp;i,&amp;taui,a,lda,&amp;(a[i*(*lda)+0]),&amp;ti1,&amp;zero,tau,&amp;ti1);</span></a>
+<a name="30624"><span class="lineNum">   30624 </span>            : </a>
+<a name="30625"><span class="lineNum">   30625 </span><span class="lineNoCov">          0 :         tmp = PLUMED_BLAS_F77_FUNC(sdot,SDOT)(&amp;i,tau,&amp;ti1,&amp;(a[i*(*lda)+0]),&amp;ti1);</span></a>
+<a name="30626"><span class="lineNum">   30626 </span>            : </a>
+<a name="30627"><span class="lineNum">   30627 </span><span class="lineNoCov">          0 :         alpha = -0.5*taui*tmp;</span></a>
+<a name="30628"><span class="lineNum">   30628 </span>            : </a>
+<a name="30629"><span class="lineNum">   30629 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(&amp;i,&amp;alpha,&amp;(a[i*(*lda)+0]),&amp;ti1,tau,&amp;ti1);</span></a>
+<a name="30630"><span class="lineNum">   30630 </span>            : </a>
+<a name="30631"><span class="lineNum">   30631 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssyr2,SSYR2)(&quot;U&quot;,&amp;i,&amp;minusone,&amp;(a[i*(*lda)+0]),&amp;ti1,tau,&amp;ti1,a,lda);</span></a>
+<a name="30632"><span class="lineNum">   30632 </span>            : </a>
+<a name="30633"><span class="lineNum">   30633 </span><span class="lineNoCov">          0 :         a[i*(*lda)+(i-1)] = e[i-1]; </span></a>
+<a name="30634"><span class="lineNum">   30634 </span>            : </a>
+<a name="30635"><span class="lineNum">   30635 </span>            :       }</a>
+<a name="30636"><span class="lineNum">   30636 </span><span class="lineNoCov">          0 :       d[i] = a[i*(*lda)+i];</span></a>
+<a name="30637"><span class="lineNum">   30637 </span><span class="lineNoCov">          0 :       tau[i-1] = taui;</span></a>
+<a name="30638"><span class="lineNum">   30638 </span>            :     }</a>
+<a name="30639"><span class="lineNum">   30639 </span><span class="lineNoCov">          0 :     d[0] = a[0];</span></a>
+<a name="30640"><span class="lineNum">   30640 </span>            :     </a>
+<a name="30641"><span class="lineNum">   30641 </span>            :   } else {</a>
+<a name="30642"><span class="lineNum">   30642 </span>            :     /* lower */</a>
+<a name="30643"><span class="lineNum">   30643 </span>            : </a>
+<a name="30644"><span class="lineNum">   30644 </span><span class="lineNoCov">          0 :     for(i=1;i&lt;*n;i++) {</span></a>
+<a name="30645"><span class="lineNum">   30645 </span>            : </a>
+<a name="30646"><span class="lineNum">   30646 </span><span class="lineNoCov">          0 :       ti1 = *n - i;</span></a>
+<a name="30647"><span class="lineNum">   30647 </span><span class="lineNoCov">          0 :       ti2 = ( *n &lt; i+2) ? *n : i+2;</span></a>
+<a name="30648"><span class="lineNum">   30648 </span><span class="lineNoCov">          0 :       ti3 = 1;</span></a>
+<a name="30649"><span class="lineNum">   30649 </span><span class="lineNoCov">          0 :       PLUMED_BLAS_F77_FUNC(slarfg,SLARFG)(&amp;ti1,&amp;(a[(i-1)*(*lda)+(i)]),&amp;(a[(i-1)*(*lda)+ti2-1]),&amp;ti3,&amp;taui);</span></a>
+<a name="30650"><span class="lineNum">   30650 </span>            : </a>
+<a name="30651"><span class="lineNum">   30651 </span><span class="lineNoCov">          0 :       e[i-1] = a[(i-1)*(*lda) + (i)];</span></a>
+<a name="30652"><span class="lineNum">   30652 </span>            : </a>
+<a name="30653"><span class="lineNum">   30653 </span><span class="lineNoCov">          0 :       if(std::abs(taui)&gt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="30654"><span class="lineNum">   30654 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i)] = 1.0;</span></a>
+<a name="30655"><span class="lineNum">   30655 </span>            :       </a>
+<a name="30656"><span class="lineNum">   30656 </span><span class="lineNoCov">          0 :         ti1 = *n - i;</span></a>
+<a name="30657"><span class="lineNum">   30657 </span><span class="lineNoCov">          0 :         ti2 = 1;</span></a>
+<a name="30658"><span class="lineNum">   30658 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssymv,SSYMV)(uplo,&amp;ti1,&amp;taui,&amp;(a[i*(*lda)+i]),lda,&amp;(a[(i-1)*(*lda)+i]),</span></a>
+<a name="30659"><span class="lineNum">   30659 </span>            :                &amp;ti2,&amp;zero,&amp;(tau[i-1]),&amp;ti2);</a>
+<a name="30660"><span class="lineNum">   30660 </span>            :         </a>
+<a name="30661"><span class="lineNum">   30661 </span><span class="lineNoCov">          0 :         tmp = PLUMED_BLAS_F77_FUNC(sdot,SDOT)(&amp;ti1,&amp;(tau[i-1]),&amp;ti2,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2);</span></a>
+<a name="30662"><span class="lineNum">   30662 </span>            : </a>
+<a name="30663"><span class="lineNum">   30663 </span><span class="lineNoCov">          0 :         alpha = -0.5*taui*tmp;</span></a>
+<a name="30664"><span class="lineNum">   30664 </span>            : </a>
+<a name="30665"><span class="lineNum">   30665 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(saxpy,SAXPY)(&amp;ti1,&amp;alpha,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2,&amp;(tau[i-1]),&amp;ti2);</span></a>
+<a name="30666"><span class="lineNum">   30666 </span>            : </a>
+<a name="30667"><span class="lineNum">   30667 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssyr2,SSYR2)(uplo,&amp;ti1,&amp;minusone,&amp;(a[(i-1)*(*lda)+i]),&amp;ti2,&amp;(tau[i-1]),&amp;ti2,</span></a>
+<a name="30668"><span class="lineNum">   30668 </span><span class="lineNoCov">          0 :                &amp;(a[(i)*(*lda)+i]),lda);</span></a>
+<a name="30669"><span class="lineNum">   30669 </span>            : </a>
+<a name="30670"><span class="lineNum">   30670 </span><span class="lineNoCov">          0 :         a[(i-1)*(*lda)+(i)] = e[i-1]; </span></a>
+<a name="30671"><span class="lineNum">   30671 </span>            : </a>
+<a name="30672"><span class="lineNum">   30672 </span>            :       }</a>
+<a name="30673"><span class="lineNum">   30673 </span><span class="lineNoCov">          0 :       d[i-1] = a[(i-1)*(*lda)+i-1];</span></a>
+<a name="30674"><span class="lineNum">   30674 </span><span class="lineNoCov">          0 :       tau[i-1] = taui;</span></a>
+<a name="30675"><span class="lineNum">   30675 </span>            :     }</a>
+<a name="30676"><span class="lineNum">   30676 </span><span class="lineNoCov">          0 :     d[*n-1] = a[(*n-1)*(*lda)+(*n-1)];</span></a>
+<a name="30677"><span class="lineNum">   30677 </span>            :  </a>
+<a name="30678"><span class="lineNum">   30678 </span>            :   }</a>
+<a name="30679"><span class="lineNum">   30679 </span>            :   return;</a>
+<a name="30680"><span class="lineNum">   30680 </span>            : }</a>
+<a name="30681"><span class="lineNum">   30681 </span>            : }</a>
+<a name="30682"><span class="lineNum">   30682 </span>            : }</a>
+<a name="30683"><span class="lineNum">   30683 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30684"><span class="lineNum">   30684 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="30685"><span class="lineNum">   30685 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="30686"><span class="lineNum">   30686 </span>            : </a>
+<a name="30687"><span class="lineNum">   30687 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30688"><span class="lineNum">   30688 </span>            : namespace PLMD{</a>
+<a name="30689"><span class="lineNum">   30689 </span>            : namespace lapack{</a>
+<a name="30690"><span class="lineNum">   30690 </span>            : using namespace blas;</a>
+<a name="30691"><span class="lineNum">   30691 </span>            : void</a>
+<a name="30692"><span class="lineNum">   30692 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(ssytrd,SSYTRD)(const char *uplo, int *n, float *a, int *</span></a>
+<a name="30693"><span class="lineNum">   30693 </span>            :         lda, float *d__, float *e, float *tau, float *</a>
+<a name="30694"><span class="lineNum">   30694 </span>            :         work, int *lwork, int *info)</a>
+<a name="30695"><span class="lineNum">   30695 </span>            : {</a>
+<a name="30696"><span class="lineNum">   30696 </span>            :     /* System generated locals */</a>
+<a name="30697"><span class="lineNum">   30697 </span>            :     int a_dim1, a_offset, i__1, i__2, i__3;</a>
+<a name="30698"><span class="lineNum">   30698 </span>            : </a>
+<a name="30699"><span class="lineNum">   30699 </span>            :     /* Local variables */</a>
+<a name="30700"><span class="lineNum">   30700 </span>            :     int i__, j, nb, kk, nx, iws;</a>
+<a name="30701"><span class="lineNum">   30701 </span>            :     int nbmin, iinfo;</a>
+<a name="30702"><span class="lineNum">   30702 </span>            :     int upper;</a>
+<a name="30703"><span class="lineNum">   30703 </span>            :     int ldwork, lwkopt;</a>
+<a name="30704"><span class="lineNum">   30704 </span>            :     int lquery;</a>
+<a name="30705"><span class="lineNum">   30705 </span><span class="lineNoCov">          0 :     float c_b22 = -1.;</span></a>
+<a name="30706"><span class="lineNum">   30706 </span><span class="lineNoCov">          0 :     float c_b23 = 1.;</span></a>
+<a name="30707"><span class="lineNum">   30707 </span>            : </a>
+<a name="30708"><span class="lineNum">   30708 </span>            : </a>
+<a name="30709"><span class="lineNum">   30709 </span>            :     /* Parameter adjustments */</a>
+<a name="30710"><span class="lineNum">   30710 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="30711"><span class="lineNum">   30711 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="30712"><span class="lineNum">   30712 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="30713"><span class="lineNum">   30713 </span><span class="lineNoCov">          0 :     --d__;</span></a>
+<a name="30714"><span class="lineNum">   30714 </span><span class="lineNoCov">          0 :     --e;</span></a>
+<a name="30715"><span class="lineNum">   30715 </span><span class="lineNoCov">          0 :     --tau;</span></a>
+<a name="30716"><span class="lineNum">   30716 </span>            :     --work;</a>
+<a name="30717"><span class="lineNum">   30717 </span>            : </a>
+<a name="30718"><span class="lineNum">   30718 </span>            :     /* Function Body */</a>
+<a name="30719"><span class="lineNum">   30719 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="30720"><span class="lineNum">   30720 </span><span class="lineNoCov">          0 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="30721"><span class="lineNum">   30721 </span><span class="lineNoCov">          0 :     lquery = (*lwork == -1);</span></a>
+<a name="30722"><span class="lineNum">   30722 </span>            : </a>
+<a name="30723"><span class="lineNum">   30723 </span><span class="lineNoCov">          0 :     if (! upper &amp;&amp; ! (*uplo=='L' || *uplo=='l')) {</span></a>
+<a name="30724"><span class="lineNum">   30724 </span><span class="lineNoCov">          0 :         *info = -1;</span></a>
+<a name="30725"><span class="lineNum">   30725 </span><span class="lineNoCov">          0 :     } else if (*n &lt; 0) {</span></a>
+<a name="30726"><span class="lineNum">   30726 </span><span class="lineNoCov">          0 :         *info = -2;</span></a>
+<a name="30727"><span class="lineNum">   30727 </span><span class="lineNoCov">          0 :     } else if (*lda &lt; ((1&gt;*n) ? 1 : *n)) {</span></a>
+<a name="30728"><span class="lineNum">   30728 </span><span class="lineNoCov">          0 :         *info = -4;</span></a>
+<a name="30729"><span class="lineNum">   30729 </span><span class="lineNoCov">          0 :     } else if (*lwork &lt; 1 &amp;&amp; ! lquery) {</span></a>
+<a name="30730"><span class="lineNum">   30730 </span><span class="lineNoCov">          0 :         *info = -9;</span></a>
+<a name="30731"><span class="lineNum">   30731 </span>            :     }</a>
+<a name="30732"><span class="lineNum">   30732 </span>            : </a>
+<a name="30733"><span class="lineNum">   30733 </span><span class="lineNoCov">          0 :     if (*info == 0) {</span></a>
+<a name="30734"><span class="lineNum">   30734 </span>            : </a>
+<a name="30735"><span class="lineNum">   30735 </span><span class="lineNoCov">          0 :       nb = DSYTRD_BLOCKSIZE;</span></a>
+<a name="30736"><span class="lineNum">   30736 </span><span class="lineNoCov">          0 :       lwkopt = *n * nb;</span></a>
+<a name="30737"><span class="lineNum">   30737 </span><span class="lineNoCov">          0 :       work[1] = (float) lwkopt;</span></a>
+<a name="30738"><span class="lineNum">   30738 </span>            :     } else</a>
+<a name="30739"><span class="lineNum">   30739 </span>            :       return;</a>
+<a name="30740"><span class="lineNum">   30740 </span>            : </a>
+<a name="30741"><span class="lineNum">   30741 </span><span class="lineNoCov">          0 :     if (lquery) </span></a>
+<a name="30742"><span class="lineNum">   30742 </span>            :       return;</a>
+<a name="30743"><span class="lineNum">   30743 </span>            :   </a>
+<a name="30744"><span class="lineNum">   30744 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="30745"><span class="lineNum">   30745 </span><span class="lineNoCov">          0 :         work[1] = 1.;</span></a>
+<a name="30746"><span class="lineNum">   30746 </span><span class="lineNoCov">          0 :         return;</span></a>
+<a name="30747"><span class="lineNum">   30747 </span>            :     }</a>
+<a name="30748"><span class="lineNum">   30748 </span>            : </a>
+<a name="30749"><span class="lineNum">   30749 </span>            :     nx = *n;</a>
+<a name="30750"><span class="lineNum">   30750 </span><span class="lineNoCov">          0 :     if (nb &gt; 1 &amp;&amp; nb &lt; *n) {</span></a>
+<a name="30751"><span class="lineNum">   30751 </span>            : </a>
+<a name="30752"><span class="lineNum">   30752 </span>            :         nx = DSYTRD_CROSSOVER;</a>
+<a name="30753"><span class="lineNum">   30753 </span><span class="lineNoCov">          0 :         if (nx &lt; *n) {</span></a>
+<a name="30754"><span class="lineNum">   30754 </span>            : </a>
+<a name="30755"><span class="lineNum">   30755 </span><span class="lineNoCov">          0 :             ldwork = *n;</span></a>
+<a name="30756"><span class="lineNum">   30756 </span><span class="lineNoCov">          0 :             iws = ldwork * nb;</span></a>
+<a name="30757"><span class="lineNum">   30757 </span><span class="lineNoCov">          0 :             if (*lwork &lt; iws) {</span></a>
+<a name="30758"><span class="lineNum">   30758 </span>            : </a>
+<a name="30759"><span class="lineNum">   30759 </span><span class="lineNoCov">          0 :                 i__1 = *lwork / ldwork;</span></a>
+<a name="30760"><span class="lineNum">   30760 </span><span class="lineNoCov">          0 :                 nb = (i__1&gt;1) ? i__1 : 1;</span></a>
+<a name="30761"><span class="lineNum">   30761 </span>            :                 nbmin = DSYTRD_MINBLOCKSIZE;</a>
+<a name="30762"><span class="lineNum">   30762 </span><span class="lineNoCov">          0 :                 if (nb &lt; nbmin) {</span></a>
+<a name="30763"><span class="lineNum">   30763 </span>            :                     nx = *n;</a>
+<a name="30764"><span class="lineNum">   30764 </span>            :                 }</a>
+<a name="30765"><span class="lineNum">   30765 </span>            :             }</a>
+<a name="30766"><span class="lineNum">   30766 </span>            :         } else {</a>
+<a name="30767"><span class="lineNum">   30767 </span>            :             nx = *n;</a>
+<a name="30768"><span class="lineNum">   30768 </span>            :         }</a>
+<a name="30769"><span class="lineNum">   30769 </span>            :     } else {</a>
+<a name="30770"><span class="lineNum">   30770 </span><span class="lineNoCov">          0 :         nb = 1;</span></a>
+<a name="30771"><span class="lineNum">   30771 </span>            :     }</a>
+<a name="30772"><span class="lineNum">   30772 </span>            : </a>
+<a name="30773"><span class="lineNum">   30773 </span><span class="lineNoCov">          0 :     if (upper) {</span></a>
+<a name="30774"><span class="lineNum">   30774 </span>            : </a>
+<a name="30775"><span class="lineNum">   30775 </span><span class="lineNoCov">          0 :         kk = *n - (*n - nx + nb - 1) / nb * nb;</span></a>
+<a name="30776"><span class="lineNum">   30776 </span><span class="lineNoCov">          0 :         i__1 = kk + 1;</span></a>
+<a name="30777"><span class="lineNum">   30777 </span>            :         i__2 = -nb;</a>
+<a name="30778"><span class="lineNum">   30778 </span><span class="lineNoCov">          0 :         for (i__ = *n - nb + 1; i__2 &lt; 0 ? i__ &gt;= i__1 : i__ &lt;= i__1; i__ += </span></a>
+<a name="30779"><span class="lineNum">   30779 </span>            :                 i__2) {</a>
+<a name="30780"><span class="lineNum">   30780 </span>            : </a>
+<a name="30781"><span class="lineNum">   30781 </span><span class="lineNoCov">          0 :             i__3 = i__ + nb - 1;</span></a>
+<a name="30782"><span class="lineNum">   30782 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slatrd,SLATRD)(uplo, &amp;i__3, &amp;nb, &amp;a[a_offset], lda, &amp;e[1], &amp;tau[1], &amp;</span></a>
+<a name="30783"><span class="lineNum">   30783 </span>            :                     work[1], &amp;ldwork);</a>
+<a name="30784"><span class="lineNum">   30784 </span>            : </a>
+<a name="30785"><span class="lineNum">   30785 </span><span class="lineNoCov">          0 :             i__3 = i__ - 1;</span></a>
+<a name="30786"><span class="lineNum">   30786 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(ssyr2k,SSYR2K)(uplo, &quot;No transpose&quot;, &amp;i__3, &amp;nb, &amp;c_b22, &amp;a[i__ * a_dim1 </span></a>
+<a name="30787"><span class="lineNum">   30787 </span><span class="lineNoCov">          0 :                     + 1], lda, &amp;work[1], &amp;ldwork, &amp;c_b23, &amp;a[a_offset], lda);</span></a>
+<a name="30788"><span class="lineNum">   30788 </span>            : </a>
+<a name="30789"><span class="lineNum">   30789 </span><span class="lineNoCov">          0 :             i__3 = i__ + nb - 1;</span></a>
+<a name="30790"><span class="lineNum">   30790 </span><span class="lineNoCov">          0 :             for (j = i__; j &lt;= i__3; ++j) {</span></a>
+<a name="30791"><span class="lineNum">   30791 </span><span class="lineNoCov">          0 :                 a[j - 1 + j * a_dim1] = e[j - 1];</span></a>
+<a name="30792"><span class="lineNum">   30792 </span><span class="lineNoCov">          0 :                 d__[j] = a[j + j * a_dim1];</span></a>
+<a name="30793"><span class="lineNum">   30793 </span>            : </a>
+<a name="30794"><span class="lineNum">   30794 </span>            :             }</a>
+<a name="30795"><span class="lineNum">   30795 </span>            : </a>
+<a name="30796"><span class="lineNum">   30796 </span>            :         }</a>
+<a name="30797"><span class="lineNum">   30797 </span>            : </a>
+<a name="30798"><span class="lineNum">   30798 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssytd2,SSYTD2)(uplo, &amp;kk, &amp;a[a_offset], lda, &amp;d__[1], &amp;e[1], &amp;tau[1], &amp;iinfo);</span></a>
+<a name="30799"><span class="lineNum">   30799 </span>            :     } else {</a>
+<a name="30800"><span class="lineNum">   30800 </span>            : </a>
+<a name="30801"><span class="lineNum">   30801 </span><span class="lineNoCov">          0 :         i__2 = *n - nx;</span></a>
+<a name="30802"><span class="lineNum">   30802 </span><span class="lineNoCov">          0 :         i__1 = nb;</span></a>
+<a name="30803"><span class="lineNum">   30803 </span><span class="lineNoCov">          0 :         for (i__ = 1; i__1 &lt; 0 ? i__ &gt;= i__2 : i__ &lt;= i__2; i__ += i__1) {</span></a>
+<a name="30804"><span class="lineNum">   30804 </span>            : </a>
+<a name="30805"><span class="lineNum">   30805 </span>            : </a>
+<a name="30806"><span class="lineNum">   30806 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ + 1;</span></a>
+<a name="30807"><span class="lineNum">   30807 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(slatrd,SLATRD)(uplo, &amp;i__3, &amp;nb, &amp;a[i__ + i__ * a_dim1], lda, &amp;e[i__], &amp;</span></a>
+<a name="30808"><span class="lineNum">   30808 </span><span class="lineNoCov">          0 :                     tau[i__], &amp;work[1], &amp;ldwork);</span></a>
+<a name="30809"><span class="lineNum">   30809 </span>            : </a>
+<a name="30810"><span class="lineNum">   30810 </span><span class="lineNoCov">          0 :             i__3 = *n - i__ - nb + 1;</span></a>
+<a name="30811"><span class="lineNum">   30811 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(ssyr2k,SSYR2K)(uplo, &quot;No transpose&quot;, &amp;i__3, &amp;nb, &amp;c_b22, &amp;a[i__ + nb + </span></a>
+<a name="30812"><span class="lineNum">   30812 </span><span class="lineNoCov">          0 :                     i__ * a_dim1], lda, &amp;work[nb + 1], &amp;ldwork, &amp;c_b23, &amp;a[</span></a>
+<a name="30813"><span class="lineNum">   30813 </span><span class="lineNoCov">          0 :                     i__ + nb + (i__ + nb) * a_dim1], lda);</span></a>
+<a name="30814"><span class="lineNum">   30814 </span>            : </a>
+<a name="30815"><span class="lineNum">   30815 </span>            : </a>
+<a name="30816"><span class="lineNum">   30816 </span><span class="lineNoCov">          0 :             i__3 = i__ + nb - 1;</span></a>
+<a name="30817"><span class="lineNum">   30817 </span><span class="lineNoCov">          0 :             for (j = i__; j &lt;= i__3; ++j) {</span></a>
+<a name="30818"><span class="lineNum">   30818 </span><span class="lineNoCov">          0 :                 a[j + 1 + j * a_dim1] = e[j];</span></a>
+<a name="30819"><span class="lineNum">   30819 </span><span class="lineNoCov">          0 :                 d__[j] = a[j + j * a_dim1];</span></a>
+<a name="30820"><span class="lineNum">   30820 </span>            : </a>
+<a name="30821"><span class="lineNum">   30821 </span>            :             }</a>
+<a name="30822"><span class="lineNum">   30822 </span>            : </a>
+<a name="30823"><span class="lineNum">   30823 </span>            :         }</a>
+<a name="30824"><span class="lineNum">   30824 </span>            : </a>
+<a name="30825"><span class="lineNum">   30825 </span>            : </a>
+<a name="30826"><span class="lineNum">   30826 </span><span class="lineNoCov">          0 :         i__1 = *n - i__ + 1;</span></a>
+<a name="30827"><span class="lineNum">   30827 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(ssytd2,SSYTD2)(uplo, &amp;i__1, &amp;a[i__ + i__ * a_dim1], lda, &amp;d__[i__], &amp;e[i__], </span></a>
+<a name="30828"><span class="lineNum">   30828 </span><span class="lineNoCov">          0 :                 &amp;tau[i__], &amp;iinfo);</span></a>
+<a name="30829"><span class="lineNum">   30829 </span>            :     }</a>
+<a name="30830"><span class="lineNum">   30830 </span>            : </a>
+<a name="30831"><span class="lineNum">   30831 </span><span class="lineNoCov">          0 :     work[1] = (float) lwkopt;</span></a>
+<a name="30832"><span class="lineNum">   30832 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="30833"><span class="lineNum">   30833 </span>            : </a>
+<a name="30834"><span class="lineNum">   30834 </span>            : }</a>
+<a name="30835"><span class="lineNum">   30835 </span>            : </a>
+<a name="30836"><span class="lineNum">   30836 </span>            : </a>
+<a name="30837"><span class="lineNum">   30837 </span>            : }</a>
+<a name="30838"><span class="lineNum">   30838 </span>            : }</a>
+<a name="30839"><span class="lineNum">   30839 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30840"><span class="lineNum">   30840 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="30841"><span class="lineNum">   30841 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="30842"><span class="lineNum">   30842 </span>            : </a>
+<a name="30843"><span class="lineNum">   30843 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30844"><span class="lineNum">   30844 </span>            : namespace PLMD{</a>
+<a name="30845"><span class="lineNum">   30845 </span>            : namespace lapack{</a>
+<a name="30846"><span class="lineNum">   30846 </span>            : using namespace blas;</a>
+<a name="30847"><span class="lineNum">   30847 </span>            : void</a>
+<a name="30848"><span class="lineNum">   30848 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(strti2,STRTI2)(const char *uplo,</span></a>
+<a name="30849"><span class="lineNum">   30849 </span>            :         const char *diag, </a>
+<a name="30850"><span class="lineNum">   30850 </span>            :         int *n, </a>
+<a name="30851"><span class="lineNum">   30851 </span>            :         float *a,</a>
+<a name="30852"><span class="lineNum">   30852 </span>            :         int *lda,</a>
+<a name="30853"><span class="lineNum">   30853 </span>            :         int *info)</a>
+<a name="30854"><span class="lineNum">   30854 </span>            : {</a>
+<a name="30855"><span class="lineNum">   30855 </span>            :     int a_dim1, a_offset, i__1, i__2;</a>
+<a name="30856"><span class="lineNum">   30856 </span>            : </a>
+<a name="30857"><span class="lineNum">   30857 </span>            :     int j;</a>
+<a name="30858"><span class="lineNum">   30858 </span>            :     float ajj;</a>
+<a name="30859"><span class="lineNum">   30859 </span>            :     int upper, nounit;</a>
+<a name="30860"><span class="lineNum">   30860 </span><span class="lineNoCov">          0 :     int c__1 = 1;</span></a>
+<a name="30861"><span class="lineNum">   30861 </span>            : </a>
+<a name="30862"><span class="lineNum">   30862 </span>            : </a>
+<a name="30863"><span class="lineNum">   30863 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="30864"><span class="lineNum">   30864 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="30865"><span class="lineNum">   30865 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="30866"><span class="lineNum">   30866 </span>            : </a>
+<a name="30867"><span class="lineNum">   30867 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="30868"><span class="lineNum">   30868 </span><span class="lineNoCov">          0 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="30869"><span class="lineNum">   30869 </span><span class="lineNoCov">          0 :     nounit = (*diag=='N' || *diag=='n');</span></a>
+<a name="30870"><span class="lineNum">   30870 </span>            : </a>
+<a name="30871"><span class="lineNum">   30871 </span>            :     if (*info != 0) {</a>
+<a name="30872"><span class="lineNum">   30872 </span>            :         i__1 = -(*info);</a>
+<a name="30873"><span class="lineNum">   30873 </span>            :         return;</a>
+<a name="30874"><span class="lineNum">   30874 </span>            :     }</a>
+<a name="30875"><span class="lineNum">   30875 </span>            : </a>
+<a name="30876"><span class="lineNum">   30876 </span><span class="lineNoCov">          0 :     if (upper) {</span></a>
+<a name="30877"><span class="lineNum">   30877 </span>            : </a>
+<a name="30878"><span class="lineNum">   30878 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="30879"><span class="lineNum">   30879 </span><span class="lineNoCov">          0 :         for (j = 1; j &lt;= i__1; ++j) {</span></a>
+<a name="30880"><span class="lineNum">   30880 </span><span class="lineNoCov">          0 :             if (nounit) {</span></a>
+<a name="30881"><span class="lineNum">   30881 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = 1. / a[j + j * a_dim1];</span></a>
+<a name="30882"><span class="lineNum">   30882 </span><span class="lineNoCov">          0 :                 ajj = -a[j + j * a_dim1];</span></a>
+<a name="30883"><span class="lineNum">   30883 </span>            :             } else {</a>
+<a name="30884"><span class="lineNum">   30884 </span><span class="lineNoCov">          0 :                 ajj = -1.;</span></a>
+<a name="30885"><span class="lineNum">   30885 </span>            :             }</a>
+<a name="30886"><span class="lineNum">   30886 </span>            : </a>
+<a name="30887"><span class="lineNum">   30887 </span><span class="lineNoCov">          0 :             i__2 = j - 1;</span></a>
+<a name="30888"><span class="lineNum">   30888 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(strmv,STRMV)(&quot;Upper&quot;, &quot;No transpose&quot;, diag, &amp;i__2, &amp;a[a_offset], lda, &amp;</span></a>
+<a name="30889"><span class="lineNum">   30889 </span><span class="lineNoCov">          0 :                     a[j * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="30890"><span class="lineNum">   30890 </span><span class="lineNoCov">          0 :             i__2 = j - 1;</span></a>
+<a name="30891"><span class="lineNum">   30891 </span><span class="lineNoCov">          0 :             PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__2, &amp;ajj, &amp;a[j * a_dim1 + 1], &amp;c__1);</span></a>
+<a name="30892"><span class="lineNum">   30892 </span>            :         }</a>
+<a name="30893"><span class="lineNum">   30893 </span>            :     } else {</a>
+<a name="30894"><span class="lineNum">   30894 </span>            : </a>
+<a name="30895"><span class="lineNum">   30895 </span><span class="lineNoCov">          0 :         for (j = *n; j &gt;= 1; --j) {</span></a>
+<a name="30896"><span class="lineNum">   30896 </span><span class="lineNoCov">          0 :             if (nounit) {</span></a>
+<a name="30897"><span class="lineNum">   30897 </span><span class="lineNoCov">          0 :                 a[j + j * a_dim1] = 1. / a[j + j * a_dim1];</span></a>
+<a name="30898"><span class="lineNum">   30898 </span><span class="lineNoCov">          0 :                 ajj = -a[j + j * a_dim1];</span></a>
+<a name="30899"><span class="lineNum">   30899 </span>            :             } else {</a>
+<a name="30900"><span class="lineNum">   30900 </span><span class="lineNoCov">          0 :                 ajj = -1.;</span></a>
+<a name="30901"><span class="lineNum">   30901 </span>            :             }</a>
+<a name="30902"><span class="lineNum">   30902 </span><span class="lineNoCov">          0 :             if (j &lt; *n) {</span></a>
+<a name="30903"><span class="lineNum">   30903 </span>            : </a>
+<a name="30904"><span class="lineNum">   30904 </span><span class="lineNoCov">          0 :                 i__1 = *n - j;</span></a>
+<a name="30905"><span class="lineNum">   30905 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmv,STRMV)(&quot;Lower&quot;, &quot;No transpose&quot;, diag, &amp;i__1, &amp;a[j + 1 + (j + </span></a>
+<a name="30906"><span class="lineNum">   30906 </span><span class="lineNoCov">          0 :                         1) * a_dim1], lda, &amp;a[j + 1 + j * a_dim1], &amp;c__1);</span></a>
+<a name="30907"><span class="lineNum">   30907 </span><span class="lineNoCov">          0 :                 i__1 = *n - j;</span></a>
+<a name="30908"><span class="lineNum">   30908 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(sscal,SSCAL)(&amp;i__1, &amp;ajj, &amp;a[j + 1 + j * a_dim1], &amp;c__1);</span></a>
+<a name="30909"><span class="lineNum">   30909 </span>            :             }</a>
+<a name="30910"><span class="lineNum">   30910 </span>            :         }</a>
+<a name="30911"><span class="lineNum">   30911 </span>            :     }</a>
+<a name="30912"><span class="lineNum">   30912 </span>            :     return;</a>
+<a name="30913"><span class="lineNum">   30913 </span>            : }</a>
+<a name="30914"><span class="lineNum">   30914 </span>            : }</a>
+<a name="30915"><span class="lineNum">   30915 </span>            : }</a>
+<a name="30916"><span class="lineNum">   30916 </span>            : #include &lt;cmath&gt;</a>
+<a name="30917"><span class="lineNum">   30917 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30918"><span class="lineNum">   30918 </span>            : #include &quot;lapack.h&quot;</a>
+<a name="30919"><span class="lineNum">   30919 </span>            : #include &quot;lapack_limits.h&quot;</a>
+<a name="30920"><span class="lineNum">   30920 </span>            : </a>
+<a name="30921"><span class="lineNum">   30921 </span>            : #include &quot;real.h&quot;</a>
+<a name="30922"><span class="lineNum">   30922 </span>            : </a>
+<a name="30923"><span class="lineNum">   30923 </span>            : #include &quot;blas/blas.h&quot;</a>
+<a name="30924"><span class="lineNum">   30924 </span>            : namespace PLMD{</a>
+<a name="30925"><span class="lineNum">   30925 </span>            : namespace lapack{</a>
+<a name="30926"><span class="lineNum">   30926 </span>            : using namespace blas;</a>
+<a name="30927"><span class="lineNum">   30927 </span>            : void</a>
+<a name="30928"><span class="lineNum">   30928 </span><span class="lineNoCov">          0 : PLUMED_BLAS_F77_FUNC(strtri,STRTRI)(const char *uplo,</span></a>
+<a name="30929"><span class="lineNum">   30929 </span>            :         const char *diag, </a>
+<a name="30930"><span class="lineNum">   30930 </span>            :         int *n,</a>
+<a name="30931"><span class="lineNum">   30931 </span>            :         float *a, </a>
+<a name="30932"><span class="lineNum">   30932 </span>            :         int *lda,</a>
+<a name="30933"><span class="lineNum">   30933 </span>            :         int *info)</a>
+<a name="30934"><span class="lineNum">   30934 </span>            : {</a>
+<a name="30935"><span class="lineNum">   30935 </span>            :     int a_dim1, a_offset, i__1, i__3, i__4, i__5;</a>
+<a name="30936"><span class="lineNum">   30936 </span>            :     int j, jb, nb, nn;</a>
+<a name="30937"><span class="lineNum">   30937 </span><span class="lineNoCov">          0 :     float c_b18 = 1.;</span></a>
+<a name="30938"><span class="lineNum">   30938 </span><span class="lineNoCov">          0 :     float c_b22 = -1.;</span></a>
+<a name="30939"><span class="lineNum">   30939 </span>            : </a>
+<a name="30940"><span class="lineNum">   30940 </span>            :     int upper;</a>
+<a name="30941"><span class="lineNum">   30941 </span>            :     int nounit;</a>
+<a name="30942"><span class="lineNum">   30942 </span>            : </a>
+<a name="30943"><span class="lineNum">   30943 </span><span class="lineNoCov">          0 :     a_dim1 = *lda;</span></a>
+<a name="30944"><span class="lineNum">   30944 </span><span class="lineNoCov">          0 :     a_offset = 1 + a_dim1;</span></a>
+<a name="30945"><span class="lineNum">   30945 </span><span class="lineNoCov">          0 :     a -= a_offset;</span></a>
+<a name="30946"><span class="lineNum">   30946 </span>            : </a>
+<a name="30947"><span class="lineNum">   30947 </span><span class="lineNoCov">          0 :     *info = 0;</span></a>
+<a name="30948"><span class="lineNum">   30948 </span><span class="lineNoCov">          0 :     upper = (*uplo=='U' || *uplo=='u');</span></a>
+<a name="30949"><span class="lineNum">   30949 </span><span class="lineNoCov">          0 :     nounit = (*diag=='N' || *diag=='n');</span></a>
+<a name="30950"><span class="lineNum">   30950 </span>            : </a>
+<a name="30951"><span class="lineNum">   30951 </span>            :     if (*info != 0) {</a>
+<a name="30952"><span class="lineNum">   30952 </span>            :         i__1 = -(*info);</a>
+<a name="30953"><span class="lineNum">   30953 </span>            :         return;</a>
+<a name="30954"><span class="lineNum">   30954 </span>            :     }</a>
+<a name="30955"><span class="lineNum">   30955 </span>            : </a>
+<a name="30956"><span class="lineNum">   30956 </span><span class="lineNoCov">          0 :     if (*n == 0) {</span></a>
+<a name="30957"><span class="lineNum">   30957 </span>            :         return;</a>
+<a name="30958"><span class="lineNum">   30958 </span>            :     }</a>
+<a name="30959"><span class="lineNum">   30959 </span>            : </a>
+<a name="30960"><span class="lineNum">   30960 </span><span class="lineNoCov">          0 :     if (nounit) {</span></a>
+<a name="30961"><span class="lineNum">   30961 </span><span class="lineNoCov">          0 :         i__1 = *n;</span></a>
+<a name="30962"><span class="lineNum">   30962 </span><span class="lineNoCov">          0 :         for (*info = 1; *info &lt;= i__1; ++(*info)) {</span></a>
+<a name="30963"><span class="lineNum">   30963 </span><span class="lineNoCov">          0 :             if (std::abs(a[*info + *info * a_dim1])&lt;PLUMED_GMX_FLOAT_MIN) {</span></a>
+<a name="30964"><span class="lineNum">   30964 </span>            :                 return;</a>
+<a name="30965"><span class="lineNum">   30965 </span>            :             }</a>
+<a name="30966"><span class="lineNum">   30966 </span>            :         }</a>
+<a name="30967"><span class="lineNum">   30967 </span><span class="lineNoCov">          0 :         *info = 0;</span></a>
+<a name="30968"><span class="lineNum">   30968 </span>            :     }</a>
+<a name="30969"><span class="lineNum">   30969 </span>            : </a>
+<a name="30970"><span class="lineNum">   30970 </span>            :     nb = DTRTRI_BLOCKSIZE;</a>
+<a name="30971"><span class="lineNum">   30971 </span><span class="lineNoCov">          0 :     if (nb &lt;= 1 || nb &gt;= *n) {</span></a>
+<a name="30972"><span class="lineNum">   30972 </span>            : </a>
+<a name="30973"><span class="lineNum">   30973 </span><span class="lineNoCov">          0 :         PLUMED_BLAS_F77_FUNC(strti2,STRTI2)(uplo, diag, n, &amp;a[a_offset], lda, info);</span></a>
+<a name="30974"><span class="lineNum">   30974 </span>            :     } else {</a>
+<a name="30975"><span class="lineNum">   30975 </span>            : </a>
+<a name="30976"><span class="lineNum">   30976 </span><span class="lineNoCov">          0 :         if (upper) {</span></a>
+<a name="30977"><span class="lineNum">   30977 </span>            : </a>
+<a name="30978"><span class="lineNum">   30978 </span><span class="lineNoCov">          0 :             i__1 = *n;</span></a>
+<a name="30979"><span class="lineNum">   30979 </span>            :             i__3 = nb;</a>
+<a name="30980"><span class="lineNum">   30980 </span><span class="lineNoCov">          0 :             for (j = 1; i__3 &lt; 0 ? j &gt;= i__1 : j &lt;= i__1; j += i__3) {</span></a>
+<a name="30981"><span class="lineNum">   30981 </span><span class="lineNoCov">          0 :                 i__4 = nb, i__5 = *n - j + 1;</span></a>
+<a name="30982"><span class="lineNum">   30982 </span><span class="lineNoCov">          0 :                 jb = (i__4&lt;i__5) ? i__4 : i__5;</span></a>
+<a name="30983"><span class="lineNum">   30983 </span>            : </a>
+<a name="30984"><span class="lineNum">   30984 </span><span class="lineNoCov">          0 :                 i__4 = j - 1;</span></a>
+<a name="30985"><span class="lineNum">   30985 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Left&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, diag, &amp;i__4, &amp;jb, &amp;</span></a>
+<a name="30986"><span class="lineNum">   30986 </span><span class="lineNoCov">          0 :                         c_b18, &amp;a[a_offset], lda, &amp;a[j * a_dim1 + 1], lda);</span></a>
+<a name="30987"><span class="lineNum">   30987 </span><span class="lineNoCov">          0 :                 i__4 = j - 1;</span></a>
+<a name="30988"><span class="lineNum">   30988 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Right&quot;, &quot;Upper&quot;, &quot;No transpose&quot;, diag, &amp;i__4, &amp;jb, &amp;</span></a>
+<a name="30989"><span class="lineNum">   30989 </span><span class="lineNoCov">          0 :                         c_b22, &amp;a[j + j * a_dim1], lda, &amp;a[j * a_dim1 + 1], </span></a>
+<a name="30990"><span class="lineNum">   30990 </span>            :                         lda);</a>
+<a name="30991"><span class="lineNum">   30991 </span>            : </a>
+<a name="30992"><span class="lineNum">   30992 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strti2,STRTI2)(&quot;Upper&quot;, diag, &amp;jb, &amp;a[j + j * a_dim1], lda, info);</span></a>
+<a name="30993"><span class="lineNum">   30993 </span>            :             }</a>
+<a name="30994"><span class="lineNum">   30994 </span>            :         } else {</a>
+<a name="30995"><span class="lineNum">   30995 </span>            : </a>
+<a name="30996"><span class="lineNum">   30996 </span><span class="lineNoCov">          0 :             nn = (*n - 1) / nb * nb + 1;</span></a>
+<a name="30997"><span class="lineNum">   30997 </span>            :             i__3 = -nb;</a>
+<a name="30998"><span class="lineNum">   30998 </span><span class="lineNoCov">          0 :             for (j = nn; i__3 &lt; 0 ? j &gt;= 1 : j &lt;= 1; j += i__3) {</span></a>
+<a name="30999"><span class="lineNum">   30999 </span><span class="lineNoCov">          0 :                 i__1 = nb, i__4 = *n - j + 1;</span></a>
+<a name="31000"><span class="lineNum">   31000 </span><span class="lineNoCov">          0 :                 jb = (i__1&lt;i__4) ? i__1 : i__4;</span></a>
+<a name="31001"><span class="lineNum">   31001 </span><span class="lineNoCov">          0 :                 if (j + jb &lt;= *n) {</span></a>
+<a name="31002"><span class="lineNum">   31002 </span>            : </a>
+<a name="31003"><span class="lineNum">   31003 </span><span class="lineNoCov">          0 :                     i__1 = *n - j - jb + 1;</span></a>
+<a name="31004"><span class="lineNum">   31004 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(strmm,STRMM)(&quot;Left&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, diag, &amp;i__1, &amp;jb, </span></a>
+<a name="31005"><span class="lineNum">   31005 </span><span class="lineNoCov">          0 :                             &amp;c_b18, &amp;a[j + jb + (j + jb) * a_dim1], lda, &amp;a[j </span></a>
+<a name="31006"><span class="lineNum">   31006 </span><span class="lineNoCov">          0 :                             + jb + j * a_dim1], lda);</span></a>
+<a name="31007"><span class="lineNum">   31007 </span><span class="lineNoCov">          0 :                     i__1 = *n - j - jb + 1;</span></a>
+<a name="31008"><span class="lineNum">   31008 </span><span class="lineNoCov">          0 :                     PLUMED_BLAS_F77_FUNC(strsm,STRSM)(&quot;Right&quot;, &quot;Lower&quot;, &quot;No transpose&quot;, diag, &amp;i__1, &amp;jb,</span></a>
+<a name="31009"><span class="lineNum">   31009 </span><span class="lineNoCov">          0 :                              &amp;c_b22, &amp;a[j + j * a_dim1], lda, &amp;a[j + jb + j * </span></a>
+<a name="31010"><span class="lineNum">   31010 </span><span class="lineNoCov">          0 :                             a_dim1], lda);</span></a>
+<a name="31011"><span class="lineNum">   31011 </span>            :                 }</a>
+<a name="31012"><span class="lineNum">   31012 </span>            : </a>
+<a name="31013"><span class="lineNum">   31013 </span><span class="lineNoCov">          0 :                 PLUMED_BLAS_F77_FUNC(strti2,STRTI2)(&quot;Lower&quot;, diag, &amp;jb, &amp;a[j + j * a_dim1], lda, info);</span></a>
+<a name="31014"><span class="lineNum">   31014 </span>            :             }</a>
+<a name="31015"><span class="lineNum">   31015 </span>            :         }</a>
+<a name="31016"><span class="lineNum">   31016 </span>            :     }</a>
+<a name="31017"><span class="lineNum">   31017 </span>            :     return;</a>
+<a name="31018"><span class="lineNum">   31018 </span>            : }</a>
+<a name="31019"><span class="lineNum">   31019 </span>            : </a>
+<a name="31020"><span class="lineNum">   31020 </span>            : </a>
+<a name="31021"><span class="lineNum">   31021 </span>            : }</a>
+<a name="31022"><span class="lineNum">   31022 </span>            : }</a>
+<a name="31023"><span class="lineNum">   31023 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/CompiledExpression.cpp.func-sort-c.html b/coverage-libs/lepton/CompiledExpression.cpp.func-sort-c.html
new file mode 100644
index 0000000000..bd9e7b5658
--- /dev/null
+++ b/coverage-libs/lepton/CompiledExpression.cpp.func-sort-c.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/CompiledExpression.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - CompiledExpression.cpp<span style="font-size: 80%;"> (<a href="CompiledExpression.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">224</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CompiledExpression.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#130">_ZN4PLMD6lepton18CompiledExpressionC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#497">_ZN4PLMDL18generateTwoArgCallERNS_6asmjit11X86CompilerERNS0_6X86XmmES4_S4_PFdddE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#79">_ZZN4PLMD6lepton9useAsmJitEvENKUlvE_clEv</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#197">_ZNK4PLMD6lepton18CompiledExpression12getVariablesB5cxx11Ev</a></td>
+              <td class="coverFnHi">526</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#211">_ZN4PLMD6lepton18CompiledExpression20setVariableLocationsERSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPdSt4lessIS8_ESaISt4pairIKS8_S9_EEE</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#110">_ZN4PLMD6lepton18CompiledExpressionC2ERKNS0_16ParsedExpressionE</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#134">_ZN4PLMD6lepton18CompiledExpressionaSERKS1_</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#107">_ZN4PLMD6lepton18CompiledExpressionC2Ev</a></td>
+              <td class="coverFnHi">1164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#489">_ZN4PLMDL21generateSingleArgCallERNS_6asmjit11X86CompilerERNS0_6X86XmmES4_PFddE</a></td>
+              <td class="coverFnHi">1426</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#265">_ZN4PLMD6lepton18CompiledExpression15generateJitCodeEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#94">_ZN4PLMD6lepton16AsmJitRuntimePtrC2Ev</a></td>
+              <td class="coverFnHi">2300</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#100">_ZN4PLMD6lepton16AsmJitRuntimePtrD2Ev</a></td>
+              <td class="coverFnHi">2300</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#124">_ZN4PLMD6lepton18CompiledExpressionD2Ev</a></td>
+              <td class="coverFnHi">2300</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#201">_ZN4PLMD6lepton18CompiledExpression20getVariableReferenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#77">_ZN4PLMD6lepton9useAsmJitEv</a></td>
+              <td class="coverFnHi">5877</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#148">_ZN4PLMD6lepton18CompiledExpression17compileExpressionERKNS0_18ExpressionTreeNodeERSt6vectorISt4pairIS2_iESaIS7_EE</a></td>
+              <td class="coverFnHi">8589</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#190">_ZN4PLMD6lepton18CompiledExpression13findTempIndexERKNS0_18ExpressionTreeNodeERSt6vectorISt4pairIS2_iESaIS7_EE</a></td>
+              <td class="coverFnHi">16042</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#257">_ZN4PLMDL17evaluateOperationEPNS_6lepton9OperationEPd</a></td>
+              <td class="coverFnHi">10695248</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#233">_ZNK4PLMD6lepton18CompiledExpression8evaluateEv</a></td>
+              <td class="coverFnHi">12901536</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/CompiledExpression.cpp.func.html b/coverage-libs/lepton/CompiledExpression.cpp.func.html
new file mode 100644
index 0000000000..f2d36f3dda
--- /dev/null
+++ b/coverage-libs/lepton/CompiledExpression.cpp.func.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/CompiledExpression.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - CompiledExpression.cpp<span style="font-size: 80%;"> (<a href="CompiledExpression.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">224</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CompiledExpression.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#94">_ZN4PLMD6lepton16AsmJitRuntimePtrC2Ev</a></td>
+              <td class="coverFnHi">2300</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#100">_ZN4PLMD6lepton16AsmJitRuntimePtrD2Ev</a></td>
+              <td class="coverFnHi">2300</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#190">_ZN4PLMD6lepton18CompiledExpression13findTempIndexERKNS0_18ExpressionTreeNodeERSt6vectorISt4pairIS2_iESaIS7_EE</a></td>
+              <td class="coverFnHi">16042</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#265">_ZN4PLMD6lepton18CompiledExpression15generateJitCodeEv</a></td>
+              <td class="coverFnHi">1948</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#148">_ZN4PLMD6lepton18CompiledExpression17compileExpressionERKNS0_18ExpressionTreeNodeERSt6vectorISt4pairIS2_iESaIS7_EE</a></td>
+              <td class="coverFnHi">8589</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#201">_ZN4PLMD6lepton18CompiledExpression20getVariableReferenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#211">_ZN4PLMD6lepton18CompiledExpression20setVariableLocationsERSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPdSt4lessIS8_ESaISt4pairIKS8_S9_EEE</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#110">_ZN4PLMD6lepton18CompiledExpressionC2ERKNS0_16ParsedExpressionE</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#130">_ZN4PLMD6lepton18CompiledExpressionC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#107">_ZN4PLMD6lepton18CompiledExpressionC2Ev</a></td>
+              <td class="coverFnHi">1164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#124">_ZN4PLMD6lepton18CompiledExpressionD2Ev</a></td>
+              <td class="coverFnHi">2300</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#134">_ZN4PLMD6lepton18CompiledExpressionaSERKS1_</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#77">_ZN4PLMD6lepton9useAsmJitEv</a></td>
+              <td class="coverFnHi">5877</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#257">_ZN4PLMDL17evaluateOperationEPNS_6lepton9OperationEPd</a></td>
+              <td class="coverFnHi">10695248</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#497">_ZN4PLMDL18generateTwoArgCallERNS_6asmjit11X86CompilerERNS0_6X86XmmES4_S4_PFdddE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#489">_ZN4PLMDL21generateSingleArgCallERNS_6asmjit11X86CompilerERNS0_6X86XmmES4_PFddE</a></td>
+              <td class="coverFnHi">1426</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#197">_ZNK4PLMD6lepton18CompiledExpression12getVariablesB5cxx11Ev</a></td>
+              <td class="coverFnHi">526</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#233">_ZNK4PLMD6lepton18CompiledExpression8evaluateEv</a></td>
+              <td class="coverFnHi">12901536</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CompiledExpression.cpp.gcov.html#79">_ZZN4PLMD6lepton9useAsmJitEvENKUlvE_clEv</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/CompiledExpression.cpp.gcov.html b/coverage-libs/lepton/CompiledExpression.cpp.gcov.html
new file mode 100644
index 0000000000..d20ff9f429
--- /dev/null
+++ b/coverage-libs/lepton/CompiledExpression.cpp.gcov.html
@@ -0,0 +1,585 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/CompiledExpression.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - CompiledExpression.cpp<span style="font-size: 80%;"> (source / <a href="CompiledExpression.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">224</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  *                                   lepton                                   *</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *                                                                            *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Portions copyright (c) 2013-2019 Stanford University and the Authors.      *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Contributors:                                                              *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *                                                                            *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *                                                                            *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &quot;CompiledExpression.h&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &quot;Operation.h&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;ParsedExpression.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="68"><span class="lineNum">      68 </span>            :     #include &quot;asmjit/asmjit.h&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            : #endif</a>
+<a name="70"><span class="lineNum">      70 </span>            : #include &lt;utility&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : namespace PLMD {</a>
+<a name="73"><span class="lineNum">      73 </span>            : using namespace lepton;</a>
+<a name="74"><span class="lineNum">      74 </span>            : using namespace std;</a>
+<a name="75"><span class="lineNum">      75 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="76"><span class="lineNum">      76 </span>            :     using namespace asmjit;</a>
+<a name="77"><span class="lineNum">      77 </span>            : #endif</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       5877 : bool lepton::useAsmJit() {</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         71 :   static const bool use=[](){</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         71 :     if(auto s=std::getenv(&quot;PLUMED_USE_ASMJIT&quot;)) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          2 :       auto ss=std::string(s);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :       if(ss==&quot;yes&quot;) return true;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          1 :       if(ss==&quot;no&quot;) return false;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :       throw Exception(&quot;PLUMED_USE_ASMJIT variable is set to &quot; + ss + &quot;; should be yes or no&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :     }</a>
+<a name="88"><span class="lineNum">      88 </span>            :     return true; // by default use asmjit</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       5877 :   }();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       5877 :   return use;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : #else</a>
+<a name="92"><span class="lineNum">      92 </span>            :   return false;</a>
+<a name="93"><span class="lineNum">      93 </span>            : #endif</a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       2300 : AsmJitRuntimePtr::AsmJitRuntimePtr()</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       2300 :   : ptr(useAsmJit()?new asmjit::JitRuntime:nullptr)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : #endif</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       2300 : {}</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       2300 : AsmJitRuntimePtr::~AsmJitRuntimePtr()</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       2300 :   if(useAsmJit()) delete static_cast&lt;asmjit::JitRuntime*&gt;(ptr);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : #endif</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       2300 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1164 : CompiledExpression::CompiledExpression() : jitCode(NULL) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       1164 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1136 : CompiledExpression::CompiledExpression(const ParsedExpression&amp; expression) : jitCode(NULL) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1136 :     ParsedExpression expr = expression.optimize(); // Just in case it wasn't already optimized.</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     vector&lt;pair&lt;ExpressionTreeNode, int&gt; &gt; temps;</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1136 :     compileExpression(expr.getRootNode(), temps);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     int maxArguments = 1;</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       6805 :     for (int i = 0; i &lt; (int) operation.size(); i++)</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       5669 :         if (operation[i]-&gt;getNumArguments() &gt; maxArguments)</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        623 :             maxArguments = operation[i]-&gt;getNumArguments();</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1136 :     argValues.resize(maxArguments);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       1136 :     if(useAsmJit()) generateJitCode();</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : #endif</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       2272 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       2300 : CompiledExpression::~CompiledExpression() {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      13638 :     for (int i = 0; i &lt; (int) operation.size(); i++)</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      11338 :         if (operation[i] != NULL)</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      11338 :             delete operation[i];</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       4600 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 : CompiledExpression::CompiledExpression(const CompiledExpression&amp; expression) : jitCode(NULL) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     *this = expression;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1136 : CompiledExpression&amp; CompiledExpression::operator=(const CompiledExpression&amp; expression) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1136 :     arguments = expression.arguments;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       1136 :     target = expression.target;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     variableIndices = expression.variableIndices;</a>
+<a name="140"><span class="lineNum">     140 </span>            :     variableNames = expression.variableNames;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1136 :     workspace.resize(expression.workspace.size());</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       1136 :     argValues.resize(expression.argValues.size());</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1136 :     operation.resize(expression.operation.size());</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       6805 :     for (int i = 0; i &lt; (int) operation.size(); i++)</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       5669 :         operation[i] = expression.operation[i]-&gt;clone();</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1136 :     setVariableLocations(variablePointers);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1136 :     return *this;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       8589 : void CompiledExpression::compileExpression(const ExpressionTreeNode&amp; node, vector&lt;pair&lt;ExpressionTreeNode, int&gt; &gt;&amp; temps) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       8589 :     if (findTempIndex(node, temps) != -1)</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1767 :         return; // We have already processed a node identical to this one.</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     </a>
+<a name="154"><span class="lineNum">     154 </span>            :     // Process the child nodes.</a>
+<a name="155"><span class="lineNum">     155 </span>            :     </a>
+<a name="156"><span class="lineNum">     156 </span>            :     vector&lt;int&gt; args;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      14275 :     for (int i = 0; i &lt; node.getChildren().size(); i++) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       7453 :         compileExpression(node.getChildren()[i], temps);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       7453 :         args.push_back(findTempIndex(node.getChildren()[i], temps));</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span>            :     </a>
+<a name="162"><span class="lineNum">     162 </span>            :     // Process this node.</a>
+<a name="163"><span class="lineNum">     163 </span>            :     </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       6822 :     if (node.getOperation().getId() == Operation::VARIABLE) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       1153 :         variableIndices[node.getOperation().getName()] = (int) workspace.size();</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       2306 :         variableNames.insert(node.getOperation().getName());</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :     }</a>
+<a name="168"><span class="lineNum">     168 </span>            :     else {</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       5669 :         int stepIndex = (int) arguments.size();</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       5669 :         arguments.push_back(vector&lt;int&gt;());</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       5669 :         target.push_back((int) workspace.size());</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       5669 :         operation.push_back(node.getOperation().clone());</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       5669 :         if (args.size() == 0)</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        247 :             arguments[stepIndex].push_back(0); // The value won't actually be used.  We just need something there.</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :         else {</a>
+<a name="176"><span class="lineNum">     176 </span>            :             // If the arguments are sequential, we can just pass a pointer to the first one.</a>
+<a name="177"><span class="lineNum">     177 </span>            :             </a>
+<a name="178"><span class="lineNum">     178 </span>            :             bool sequential = true;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       7453 :             for (int i = 1; i &lt; args.size(); i++)</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       2031 :                 if (args[i] != args[i-1]+1)</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :                     sequential = false;</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       5422 :             if (sequential)</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       4198 :                 arguments[stepIndex].push_back(args[0]);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :             else</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       1224 :                 arguments[stepIndex] = args;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :         }</a>
+<a name="187"><span class="lineNum">     187 </span>            :     }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       6822 :     temps.push_back(make_pair(node, (int) workspace.size()));</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       6822 :     workspace.push_back(0.0);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      16042 : int CompiledExpression::findTempIndex(const ExpressionTreeNode&amp; node, vector&lt;pair&lt;ExpressionTreeNode, int&gt; &gt;&amp; temps) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      64196 :     for (int i = 0; i &lt; (int) temps.size(); i++)</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      57374 :         if (temps[i].first == node)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :             return i;</a>
+<a name="196"><span class="lineNum">     196 </span>            :     return -1;</a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        526 : const set&lt;string&gt;&amp; CompiledExpression::getVariables() const {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        526 :     return variableNames;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       3743 : double&amp; CompiledExpression::getVariableReference(const string&amp; name) {</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :     map&lt;string, double*&gt;::iterator pointer = variablePointers.find(name);</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       3743 :     if (pointer != variablePointers.end())</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :         return *pointer-&gt;second;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     map&lt;string, int&gt;::iterator index = variableIndices.find(name);</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       3743 :     if (index == variableIndices.end())</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1100 :         throw Exception(&quot;getVariableReference: Unknown variable '&quot;+name+&quot;'&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       3193 :     return workspace[index-&gt;second];</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1136 : void CompiledExpression::setVariableLocations(map&lt;string, double*&gt;&amp; variableLocations) {</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   variablePointers = variableLocations;</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1136 :   static const bool asmjit=useAsmJit();</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1136 :   if(asmjit) {</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="218"><span class="lineNum">     218 </span>            :     // Rebuild the JIT code.</a>
+<a name="219"><span class="lineNum">     219 </span>            :     </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        974 :     if (workspace.size() &gt; 0)</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        974 :         generateJitCode();</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : #endif</a>
+<a name="223"><span class="lineNum">     223 </span>            :   } else {</a>
+<a name="224"><span class="lineNum">     224 </span>            :     // Make a list of all variables we will need to copy before evaluating the expression.</a>
+<a name="225"><span class="lineNum">     225 </span>            :     </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        162 :     variablesToCopy.clear();</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        292 :     for (map&lt;string, int&gt;::const_iterator iter = variableIndices.begin(); iter != variableIndices.end(); ++iter) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        130 :         map&lt;string, double*&gt;::iterator pointer = variablePointers.find(iter-&gt;first);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        130 :         if (pointer != variablePointers.end())</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :             variablesToCopy.push_back(make_pair(&amp;workspace[iter-&gt;second], pointer-&gt;second));</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     }</a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       1136 : }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">   12901536 : double CompiledExpression::evaluate() const {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">   12901536 :     static const bool asmjit=useAsmJit();</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">   12901536 :     if(asmjit) return ((double (*)()) jitCode)();</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : #endif</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      16362 :     for (int i = 0; i &lt; variablesToCopy.size(); i++)</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :         *variablesToCopy[i].first = *variablesToCopy[i].second;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :     // Loop over the operations and evaluate each one.</a>
+<a name="244"><span class="lineNum">     244 </span>            :     </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      49288 :     for (int step = 0; step &lt; operation.size(); step++) {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :         const vector&lt;int&gt;&amp; args = arguments[step];</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      32926 :         if (args.size() == 1)</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">      30098 :             workspace[target[step]] = operation[step]-&gt;evaluate(&amp;workspace[args[0]], dummyVariables);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :         else {</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       8888 :             for (int i = 0; i &lt; args.size(); i++)</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       6060 :                 argValues[i] = workspace[args[i]];</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       2828 :             workspace[target[step]] = operation[step]-&gt;evaluate(&amp;argValues[0], dummyVariables);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :         }</a>
+<a name="254"><span class="lineNum">     254 </span>            :     }</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">      16362 :     return workspace[workspace.size()-1];</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : }</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : #ifdef __PLUMED_HAS_ASMJIT</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">   10695248 : static double evaluateOperation(Operation* op, double* args) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">   10695248 :     static map&lt;string, double&gt; dummyVariables;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">   10695248 :     return op-&gt;evaluate(args, dummyVariables);</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : static void generateSingleArgCall(X86Compiler&amp; c, X86Xmm&amp; dest, X86Xmm&amp; arg, double (*function)(double));</a>
+<a name="265"><span class="lineNum">     265 </span>            : static void generateTwoArgCall(X86Compiler&amp; c, X86Xmm&amp; dest, X86Xmm&amp; arg1, X86Xmm&amp; arg2, double (*function)(double, double));</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       1948 : void CompiledExpression::generateJitCode() {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       1948 :     CodeHolder code;</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     auto &amp; runtime(*static_cast&lt;asmjit::JitRuntime*&gt;(runtimeptr.get()));</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       1948 :     code.init(runtime.getCodeInfo());</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       1948 :     X86Compiler c(&amp;code);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       1948 :     c.addFunc(FuncSignature0&lt;double&gt;());</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       1948 :     vector&lt;X86Xmm&gt; workspaceVar(workspace.size());</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      14680 :     for (int i = 0; i &lt; (int) workspaceVar.size(); i++)</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      12732 :         workspaceVar[i] = c.newXmmSd();</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     X86Gp argsPointer = c.newIntPtr();</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       1948 :     c.mov(argsPointer, imm_ptr(&amp;argValues[0]));</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     </a>
+<a name="279"><span class="lineNum">     279 </span>            :     // Load the arguments into variables.</a>
+<a name="280"><span class="lineNum">     280 </span>            :     </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       3994 :     for (set&lt;string&gt;::const_iterator iter = variableNames.begin(); iter != variableNames.end(); ++iter) {</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :         map&lt;string, int&gt;::iterator index = variableIndices.find(*iter);</a>
+<a name="283"><span class="lineNum">     283 </span>            :         X86Gp variablePointer = c.newIntPtr();</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       4092 :         c.mov(variablePointer, imm_ptr(&amp;getVariableReference(index-&gt;first)));</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       2046 :         c.movsd(workspaceVar[index-&gt;second], x86::ptr(variablePointer, 0, 0));</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :     }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :     // Make a list of all constants that will be needed for evaluation.</a>
+<a name="289"><span class="lineNum">     289 </span>            :     </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       1948 :     vector&lt;int&gt; operationConstantIndex(operation.size(), -1);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">      12634 :     for (int step = 0; step &lt; (int) operation.size(); step++) {</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :         // Find the constant value (if any) used by this operation.</a>
+<a name="293"><span class="lineNum">     293 </span>            :         </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      10686 :         Operation&amp; op = *operation[step];</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :         double value;</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">      10686 :         if (op.getId() == Operation::CONSTANT)</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">        346 :             value = dynamic_cast&lt;Operation::Constant&amp;&gt;(op).getValue();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">      10340 :         else if (op.getId() == Operation::ADD_CONSTANT)</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        846 :             value = dynamic_cast&lt;Operation::AddConstant&amp;&gt;(op).getValue();</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       9494 :         else if (op.getId() == Operation::MULTIPLY_CONSTANT)</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       2884 :             value = dynamic_cast&lt;Operation::MultiplyConstant&amp;&gt;(op).getValue();</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       6610 :         else if (op.getId() == Operation::RECIPROCAL)</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        148 :             value = 1.0;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       6462 :         else if (op.getId() == Operation::STEP)</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         74 :             value = 1.0;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       6388 :         else if (op.getId() == Operation::DELTA)</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         40 :             value = 1.0/0.0;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       6348 :         else if (op.getId() == Operation::NANDELTA)</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          6 :             value = std::numeric_limits&lt;double&gt;::quiet_NaN();</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :         else</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       6342 :             continue;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :         </a>
+<a name="313"><span class="lineNum">     313 </span>            :         // See if we already have a variable for this constant.</a>
+<a name="314"><span class="lineNum">     314 </span>            :         </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       9234 :         for (int i = 0; i &lt; (int) constants.size(); i++)</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       5446 :             if (value == constants[i]) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        556 :                 operationConstantIndex[step] = i;</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        556 :                 break;</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :             }</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       4344 :         if (operationConstantIndex[step] == -1) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       3788 :             operationConstantIndex[step] = constants.size();</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       3788 :             constants.push_back(value);</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :         }</a>
+<a name="324"><span class="lineNum">     324 </span>            :     }</a>
+<a name="325"><span class="lineNum">     325 </span>            :     </a>
+<a name="326"><span class="lineNum">     326 </span>            :     // Load constants into variables.</a>
+<a name="327"><span class="lineNum">     327 </span>            :     </a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       1948 :     vector&lt;X86Xmm&gt; constantVar(constants.size());</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       1948 :     if (constants.size() &gt; 0) {</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :         X86Gp constantsPointer = c.newIntPtr();</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       1626 :         c.mov(constantsPointer, imm_ptr(&amp;constants[0]));</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       5414 :         for (int i = 0; i &lt; (int) constants.size(); i++) {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       3788 :             constantVar[i] = c.newXmmSd();</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       3788 :             c.movsd(constantVar[i], x86::ptr(constantsPointer, 8*i, 0));</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :         }</a>
+<a name="336"><span class="lineNum">     336 </span>            :     }</a>
+<a name="337"><span class="lineNum">     337 </span>            :     </a>
+<a name="338"><span class="lineNum">     338 </span>            :     // Evaluate the operations.</a>
+<a name="339"><span class="lineNum">     339 </span>            :     </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      12634 :     for (int step = 0; step &lt; (int) operation.size(); step++) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      10686 :         Operation&amp; op = *operation[step];</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">      10686 :         vector&lt;int&gt; args = arguments[step];</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">      10686 :         if (args.size() == 1) {</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :             // One or more sequential arguments.  Fill out the list.</a>
+<a name="345"><span class="lineNum">     345 </span>            :             </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">       9822 :             for (int i = 1; i &lt; op.getNumArguments(); i++)</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       1528 :                 args.push_back(args[0]+i);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :         }</a>
+<a name="349"><span class="lineNum">     349 </span>            :         </a>
+<a name="350"><span class="lineNum">     350 </span>            :         // Generate instructions to execute this operation.</a>
+<a name="351"><span class="lineNum">     351 </span>            :         </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">      10686 :         switch (op.getId()) {</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        346 :             case Operation::CONSTANT:</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        346 :                 c.movsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      10476 :                 break;</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :             case Operation::ADD:</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       1140 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">       1140 :                 c.addsd(workspaceVar[target[step]], workspaceVar[args[1]]);</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :                 break;</a>
+<a name="360"><span class="lineNum">     360 </span>            :             case Operation::SUBTRACT:</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        862 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        862 :                 c.subsd(workspaceVar[target[step]], workspaceVar[args[1]]);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :                 break;</a>
+<a name="364"><span class="lineNum">     364 </span>            :             case Operation::MULTIPLY:</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">       1736 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       1736 :                 c.mulsd(workspaceVar[target[step]], workspaceVar[args[1]]);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :                 break;</a>
+<a name="368"><span class="lineNum">     368 </span>            :             case Operation::DIVIDE:</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        122 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        122 :                 c.divsd(workspaceVar[target[step]], workspaceVar[args[1]]);</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :                 break;</a>
+<a name="372"><span class="lineNum">     372 </span>            :             case Operation::POWER:</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          4 :                 generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], pow);</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :                 break;</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        128 :             case Operation::NEGATE:</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        128 :                 c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        128 :                 c.subsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :                 break;</a>
+<a name="379"><span class="lineNum">     379 </span>            :             case Operation::SQRT:</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        126 :                 c.sqrtsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :                 break;</a>
+<a name="382"><span class="lineNum">     382 </span>            :             case Operation::EXP:</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         56 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], exp);</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :                 break;</a>
+<a name="385"><span class="lineNum">     385 </span>            :             case Operation::LOG:</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], log);</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :                 break;</a>
+<a name="388"><span class="lineNum">     388 </span>            :             case Operation::SIN:</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        508 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sin);</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :                 break;</a>
+<a name="391"><span class="lineNum">     391 </span>            :             case Operation::COS:</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        800 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], cos);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :                 break;</a>
+<a name="394"><span class="lineNum">     394 </span>            :             case Operation::TAN:</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          4 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tan);</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :                 break;</a>
+<a name="397"><span class="lineNum">     397 </span>            :             case Operation::ASIN:</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], asin);</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :                 break;</a>
+<a name="400"><span class="lineNum">     400 </span>            :             case Operation::ACOS:</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], acos);</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :                 break;</a>
+<a name="403"><span class="lineNum">     403 </span>            :             case Operation::ATAN:</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atan);</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :                 break;</a>
+<a name="406"><span class="lineNum">     406 </span>            :             case Operation::ATAN2:</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          8 :                 generateTwoArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], workspaceVar[args[1]], atan2);</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :                 break;</a>
+<a name="409"><span class="lineNum">     409 </span>            :             case Operation::SINH:</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">          4 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], sinh);</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :                 break;</a>
+<a name="412"><span class="lineNum">     412 </span>            :             case Operation::COSH:</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          4 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], cosh);</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :                 break;</a>
+<a name="415"><span class="lineNum">     415 </span>            :             case Operation::TANH:</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          6 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], tanh);</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :                 break;</a>
+<a name="418"><span class="lineNum">     418 </span>            :             case Operation::ASINH:</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], asinh);</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :                 break;</a>
+<a name="421"><span class="lineNum">     421 </span>            :             case Operation::ACOSH:</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], acosh);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :                 break;</a>
+<a name="424"><span class="lineNum">     424 </span>            :             case Operation::ATANH:</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], atanh);</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :                 break;</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         74 :             case Operation::STEP:</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         74 :                 c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         74 :                 c.cmpsd(workspaceVar[target[step]], workspaceVar[args[0]], imm(18)); // Comparison mode is _CMP_LE_OQ = 18</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         74 :                 c.andps(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :                 break;</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         40 :             case Operation::DELTA:</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         40 :                 c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         40 :                 c.cmpsd(workspaceVar[target[step]], workspaceVar[args[0]], imm(16)); // Comparison mode is _CMP_EQ_OS = 16</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         40 :                 c.andps(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :                 break;</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          6 :             case Operation::NANDELTA:</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          6 :                 c.xorps(workspaceVar[target[step]], workspaceVar[target[step]]);</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          6 :                 c.cmpsd(workspaceVar[target[step]], workspaceVar[args[0]], imm(16)); // Comparison mode is _CMP_EQ_OS = 16</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          6 :                 c.andps(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :                 break;</a>
+<a name="442"><span class="lineNum">     442 </span>            :             case Operation::SQUARE:</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">        514 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">        514 :                 c.mulsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :                 break;</a>
+<a name="446"><span class="lineNum">     446 </span>            :             case Operation::CUBE:</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         66 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         66 :                 c.mulsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         66 :                 c.mulsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :                 break;</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        148 :             case Operation::RECIPROCAL:</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">        148 :                 c.movsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">        148 :                 c.divsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :                 break;</a>
+<a name="455"><span class="lineNum">     455 </span>            :             case Operation::ADD_CONSTANT:</a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        846 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        846 :                 c.addsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :                 break;</a>
+<a name="459"><span class="lineNum">     459 </span>            :             case Operation::MULTIPLY_CONSTANT:</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">       2884 :                 c.movsd(workspaceVar[target[step]], workspaceVar[args[0]]);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">       2884 :                 c.mulsd(workspaceVar[target[step]], constantVar[operationConstantIndex[step]]);</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :                 break;</a>
+<a name="463"><span class="lineNum">     463 </span>            :             case Operation::ABS:</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         26 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], fabs);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :                 break;</a>
+<a name="466"><span class="lineNum">     466 </span>            :             case Operation::FLOOR:</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], floor);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :                 break;</a>
+<a name="469"><span class="lineNum">     469 </span>            :             case Operation::CEIL:</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          2 :                 generateSingleArgCall(c, workspaceVar[target[step]], workspaceVar[args[0]], ceil);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :                 break;</a>
+<a name="472"><span class="lineNum">     472 </span>            :             default:</a>
+<a name="473"><span class="lineNum">     473 </span>            :                 // Just invoke evaluateOperation().</a>
+<a name="474"><span class="lineNum">     474 </span>            :                 </a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">        476 :                 for (int i = 0; i &lt; (int) args.size(); i++)</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">        266 :                     c.movsd(x86::ptr(argsPointer, 8*i, 0), workspaceVar[args[i]]);</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :                 X86Gp fn = c.newIntPtr();</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        210 :                 c.mov(fn, imm_ptr((void*) evaluateOperation));</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        210 :                 CCFuncCall* call = c.call(fn, FuncSignature2&lt;double, Operation*, double*&gt;());</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">        210 :                 call-&gt;setArg(0, imm_ptr(&amp;op));</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">        210 :                 call-&gt;setArg(1, imm_ptr(&amp;argValues[0]));</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">        210 :                 call-&gt;setRet(0, workspaceVar[target[step]]);</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :         }</a>
+<a name="484"><span class="lineNum">     484 </span>            :     }</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">       1948 :     c.ret(workspaceVar[workspace.size()-1]);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">       1948 :     c.endFunc();</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">       1948 :     c.finalize();</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">       1948 :     runtime.add(&amp;jitCode, &amp;code);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">       1948 : }</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">       1426 : void generateSingleArgCall(X86Compiler&amp; c, X86Xmm&amp; dest, X86Xmm&amp; arg, double (*function)(double)) {</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :     X86Gp fn = c.newIntPtr();</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">       1426 :     c.mov(fn, imm_ptr((void*) function));</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">       1426 :     CCFuncCall* call = c.call(fn, FuncSignature1&lt;double, double&gt;());</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     call-&gt;setArg(0, arg);</a>
+<a name="496"><span class="lineNum">     496 </span>            :     call-&gt;setRet(0, dest);</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">       1426 : }</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         12 : void generateTwoArgCall(X86Compiler&amp; c, X86Xmm&amp; dest, X86Xmm&amp; arg1, X86Xmm&amp; arg2, double (*function)(double, double)) {</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :     X86Gp fn = c.newIntPtr();</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         12 :     c.mov(fn, imm_ptr((void*) function));</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         24 :     CCFuncCall* call = c.call(fn, FuncSignature2&lt;double, double, double&gt;());</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :     call-&gt;setArg(0, arg1);</a>
+<a name="504"><span class="lineNum">     504 </span>            :     call-&gt;setArg(1, arg2);</a>
+<a name="505"><span class="lineNum">     505 </span>            :     call-&gt;setRet(0, dest);</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         12 : }</span></a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span>            : #endif</a>
+<a name="509"><span class="lineNum">     509 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/CompiledExpression.h.func-sort-c.html b/coverage-libs/lepton/CompiledExpression.h.func-sort-c.html
new file mode 100644
index 0000000000..c9be23f7e2
--- /dev/null
+++ b/coverage-libs/lepton/CompiledExpression.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/CompiledExpression.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - CompiledExpression.h<span style="font-size: 80%;"> (<a href="CompiledExpression.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CompiledExpression.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/CompiledExpression.h.func.html b/coverage-libs/lepton/CompiledExpression.h.func.html
new file mode 100644
index 0000000000..2b24c2096e
--- /dev/null
+++ b/coverage-libs/lepton/CompiledExpression.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/CompiledExpression.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - CompiledExpression.h<span style="font-size: 80%;"> (<a href="CompiledExpression.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CompiledExpression.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/CompiledExpression.h.gcov.html b/coverage-libs/lepton/CompiledExpression.h.gcov.html
new file mode 100644
index 0000000000..a672c9198b
--- /dev/null
+++ b/coverage-libs/lepton/CompiledExpression.h.gcov.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/CompiledExpression.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - CompiledExpression.h<span style="font-size: 80%;"> (source / <a href="CompiledExpression.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : #ifndef __PLUMED_lepton_CompiledExpression_h</a>
+<a name="34"><span class="lineNum">      34 </span>            : #define __PLUMED_lepton_CompiledExpression_h</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  *                                   lepton                                   *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *                                                                            *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * Portions copyright (c) 2013-2019 Stanford University and the Authors.      *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * Contributors:                                                              *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  *                                                                            *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *                                                                            *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="63"><span class="lineNum">      63 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="64"><span class="lineNum">      64 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="65"><span class="lineNum">      65 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;ExpressionTreeNode.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &quot;windowsIncludes.h&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            : #include &lt;map&gt;</a>
+<a name="70"><span class="lineNum">      70 </span>            : #include &lt;set&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            : #include &lt;string&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : #include &lt;utility&gt;</a>
+<a name="73"><span class="lineNum">      73 </span>            : #include &lt;vector&gt;</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : namespace PLMD {</a>
+<a name="76"><span class="lineNum">      76 </span>            : namespace lepton {</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : bool useAsmJit();</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : // Utility class.</a>
+<a name="81"><span class="lineNum">      81 </span>            : // Implement an unique pointer to asmjit::JitRuntime.</a>
+<a name="82"><span class="lineNum">      82 </span>            : // Needed to decouple asmjit header file from this one.</a>
+<a name="83"><span class="lineNum">      83 </span>            : class AsmJitRuntimePtr {</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// if ASMJIT is not defined, just set the pointer to null</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void* ptr=nullptr;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// constructor</a>
+<a name="88"><span class="lineNum">      88 </span>            :   AsmJitRuntimePtr();</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// destructor</a>
+<a name="90"><span class="lineNum">      90 </span>            :   ~AsmJitRuntimePtr();</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// deleted copy constructor</a>
+<a name="92"><span class="lineNum">      92 </span>            :   AsmJitRuntimePtr(const AsmJitRuntimePtr&amp;) = delete;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// deleted assignment</a>
+<a name="94"><span class="lineNum">      94 </span>            :   AsmJitRuntimePtr &amp; operator=(const AsmJitRuntimePtr&amp;) = delete;</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// get the pointer</a>
+<a name="96"><span class="lineNum">      96 </span>            :   void* get() {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1948 :     return ptr;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span>            : };</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : class Operation;</a>
+<a name="102"><span class="lineNum">     102 </span>            : class ParsedExpression;</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : /**</a>
+<a name="105"><span class="lineNum">     105 </span>            :  * A CompiledExpression is a highly optimized representation of an expression for cases when you want to evaluate</a>
+<a name="106"><span class="lineNum">     106 </span>            :  * it many times as quickly as possible.  You should treat it as an opaque object; none of the internal representation</a>
+<a name="107"><span class="lineNum">     107 </span>            :  * is visible.</a>
+<a name="108"><span class="lineNum">     108 </span>            :  * </a>
+<a name="109"><span class="lineNum">     109 </span>            :  * A CompiledExpression is created by calling createCompiledExpression() on a ParsedExpression.</a>
+<a name="110"><span class="lineNum">     110 </span>            :  * </a>
+<a name="111"><span class="lineNum">     111 </span>            :  * WARNING: CompiledExpression is NOT thread safe.  You should never access a CompiledExpression from two threads at</a>
+<a name="112"><span class="lineNum">     112 </span>            :  * the same time.</a>
+<a name="113"><span class="lineNum">     113 </span>            :  */</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : class LEPTON_EXPORT CompiledExpression {</a>
+<a name="116"><span class="lineNum">     116 </span>            : public:</a>
+<a name="117"><span class="lineNum">     117 </span>            :     CompiledExpression();</a>
+<a name="118"><span class="lineNum">     118 </span>            :     CompiledExpression(const CompiledExpression&amp; expression);</a>
+<a name="119"><span class="lineNum">     119 </span>            :     ~CompiledExpression();</a>
+<a name="120"><span class="lineNum">     120 </span>            :     CompiledExpression&amp; operator=(const CompiledExpression&amp; expression);</a>
+<a name="121"><span class="lineNum">     121 </span>            :     /**</a>
+<a name="122"><span class="lineNum">     122 </span>            :      * Get the names of all variables used by this expression.</a>
+<a name="123"><span class="lineNum">     123 </span>            :      */</a>
+<a name="124"><span class="lineNum">     124 </span>            :     const std::set&lt;std::string&gt;&amp; getVariables() const;</a>
+<a name="125"><span class="lineNum">     125 </span>            :     /**</a>
+<a name="126"><span class="lineNum">     126 </span>            :      * Get a reference to the memory location where the value of a particular variable is stored.  This can be used</a>
+<a name="127"><span class="lineNum">     127 </span>            :      * to set the value of the variable before calling evaluate().</a>
+<a name="128"><span class="lineNum">     128 </span>            :      */</a>
+<a name="129"><span class="lineNum">     129 </span>            :     double&amp; getVariableReference(const std::string&amp; name);</a>
+<a name="130"><span class="lineNum">     130 </span>            :     /**</a>
+<a name="131"><span class="lineNum">     131 </span>            :      * You can optionally specify the memory locations from which the values of variables should be read.</a>
+<a name="132"><span class="lineNum">     132 </span>            :      * This is useful, for example, when several expressions all use the same variable.  You can then set</a>
+<a name="133"><span class="lineNum">     133 </span>            :      * the value of that variable in one place, and it will be seen by all of them.</a>
+<a name="134"><span class="lineNum">     134 </span>            :      */</a>
+<a name="135"><span class="lineNum">     135 </span>            :     void setVariableLocations(std::map&lt;std::string, double*&gt;&amp; variableLocations);</a>
+<a name="136"><span class="lineNum">     136 </span>            :     /**</a>
+<a name="137"><span class="lineNum">     137 </span>            :      * Evaluate the expression.  The values of all variables should have been set before calling this.</a>
+<a name="138"><span class="lineNum">     138 </span>            :      */</a>
+<a name="139"><span class="lineNum">     139 </span>            :     double evaluate() const;</a>
+<a name="140"><span class="lineNum">     140 </span>            : private:</a>
+<a name="141"><span class="lineNum">     141 </span>            :     friend class ParsedExpression;</a>
+<a name="142"><span class="lineNum">     142 </span>            :     CompiledExpression(const ParsedExpression&amp; expression);</a>
+<a name="143"><span class="lineNum">     143 </span>            :     void compileExpression(const ExpressionTreeNode&amp; node, std::vector&lt;std::pair&lt;ExpressionTreeNode, int&gt; &gt;&amp; temps);</a>
+<a name="144"><span class="lineNum">     144 </span>            :     int findTempIndex(const ExpressionTreeNode&amp; node, std::vector&lt;std::pair&lt;ExpressionTreeNode, int&gt; &gt;&amp; temps);</a>
+<a name="145"><span class="lineNum">     145 </span>            :     std::map&lt;std::string, double*&gt; variablePointers;</a>
+<a name="146"><span class="lineNum">     146 </span>            :     std::vector&lt;std::pair&lt;double*, double*&gt; &gt; variablesToCopy;</a>
+<a name="147"><span class="lineNum">     147 </span>            :     std::vector&lt;std::vector&lt;int&gt; &gt; arguments;</a>
+<a name="148"><span class="lineNum">     148 </span>            :     std::vector&lt;int&gt; target;</a>
+<a name="149"><span class="lineNum">     149 </span>            :     std::vector&lt;Operation*&gt; operation;</a>
+<a name="150"><span class="lineNum">     150 </span>            :     std::map&lt;std::string, int&gt; variableIndices;</a>
+<a name="151"><span class="lineNum">     151 </span>            :     std::set&lt;std::string&gt; variableNames;</a>
+<a name="152"><span class="lineNum">     152 </span>            :     mutable std::vector&lt;double&gt; workspace;</a>
+<a name="153"><span class="lineNum">     153 </span>            :     mutable std::vector&lt;double&gt; argValues;</a>
+<a name="154"><span class="lineNum">     154 </span>            :     std::map&lt;std::string, double&gt; dummyVariables;</a>
+<a name="155"><span class="lineNum">     155 </span>            :     void* jitCode;</a>
+<a name="156"><span class="lineNum">     156 </span>            :     void generateJitCode();</a>
+<a name="157"><span class="lineNum">     157 </span>            :     std::vector&lt;double&gt; constants;</a>
+<a name="158"><span class="lineNum">     158 </span>            :     AsmJitRuntimePtr runtimeptr;</a>
+<a name="159"><span class="lineNum">     159 </span>            : };</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : } // namespace lepton</a>
+<a name="162"><span class="lineNum">     162 </span>            : } // namespace PLMD</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : #endif /*LEPTON_COMPILED_EXPRESSION_H_*/</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Exception.h.func-sort-c.html b/coverage-libs/lepton/Exception.h.func-sort-c.html
new file mode 100644
index 0000000000..2d6060adf9
--- /dev/null
+++ b/coverage-libs/lepton/Exception.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Exception.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Exception.h<span style="font-size: 80%;"> (<a href="Exception.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Exception.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#79">_ZN4PLMD6lepton9ExceptionD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#81">_ZNK4PLMD6lepton9Exception4whatEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#77">_ZN4PLMD6lepton9ExceptionC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">611</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#79">_ZN4PLMD6lepton9ExceptionD2Ev</a></td>
+              <td class="coverFnHi">611</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Exception.h.func.html b/coverage-libs/lepton/Exception.h.func.html
new file mode 100644
index 0000000000..81b213e766
--- /dev/null
+++ b/coverage-libs/lepton/Exception.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Exception.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Exception.h<span style="font-size: 80%;"> (<a href="Exception.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Exception.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#77">_ZN4PLMD6lepton9ExceptionC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">611</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#79">_ZN4PLMD6lepton9ExceptionD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#79">_ZN4PLMD6lepton9ExceptionD2Ev</a></td>
+              <td class="coverFnHi">611</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#81">_ZNK4PLMD6lepton9Exception4whatEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Exception.h.gcov.html b/coverage-libs/lepton/Exception.h.gcov.html
new file mode 100644
index 0000000000..9f58a1a5f4
--- /dev/null
+++ b/coverage-libs/lepton/Exception.h.gcov.html
@@ -0,0 +1,169 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Exception.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Exception.h<span style="font-size: 80%;"> (source / <a href="Exception.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : #ifndef __PLUMED_lepton_Exception_h</a>
+<a name="34"><span class="lineNum">      34 </span>            : #define __PLUMED_lepton_Exception_h</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  *                                   lepton                                   *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *                                                                            *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * Portions copyright (c) 2009 Stanford University and the Authors.           *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * Contributors:                                                              *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  *                                                                            *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *                                                                            *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="63"><span class="lineNum">      63 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="64"><span class="lineNum">      64 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="65"><span class="lineNum">      65 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &lt;exception&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &lt;string&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace PLMD {</a>
+<a name="71"><span class="lineNum">      71 </span>            : namespace lepton {</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : /**</a>
+<a name="74"><span class="lineNum">      74 </span>            :  * This class is used for all exceptions thrown by lepton.</a>
+<a name="75"><span class="lineNum">      75 </span>            :  */</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : class Exception : public std::exception {</a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        611 :     Exception(const std::string&amp; message) : message(message) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        611 :     }</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        611 :     ~Exception() throw() {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        611 :     }</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         20 :     const char* what() const throw() {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         20 :         return message.c_str();</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :     }</a>
+<a name="86"><span class="lineNum">      86 </span>            : private:</a>
+<a name="87"><span class="lineNum">      87 </span>            :     std::string message;</a>
+<a name="88"><span class="lineNum">      88 </span>            : };</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : } // namespace lepton</a>
+<a name="91"><span class="lineNum">      91 </span>            : } // namespace PLMD</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : #endif /*LEPTON_EXCEPTION_H_*/</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ExpressionProgram.cpp.func-sort-c.html b/coverage-libs/lepton/ExpressionProgram.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3690d6d0ab
--- /dev/null
+++ b/coverage-libs/lepton/ExpressionProgram.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ExpressionProgram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ExpressionProgram.cpp<span style="font-size: 80%;"> (<a href="ExpressionProgram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExpressionProgram.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#104">_ZN4PLMD6lepton17ExpressionProgram12buildProgramERKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#118">_ZN4PLMD6lepton17ExpressionProgram12setOperationEiPNS0_9OperationE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#73">_ZN4PLMD6lepton17ExpressionProgramC2ERKNS0_16ParsedExpressionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#91">_ZN4PLMD6lepton17ExpressionProgramC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#70">_ZN4PLMD6lepton17ExpressionProgramC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#86">_ZN4PLMD6lepton17ExpressionProgramD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#95">_ZN4PLMD6lepton17ExpressionProgramaSERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#114">_ZNK4PLMD6lepton17ExpressionProgram12getOperationEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#123">_ZNK4PLMD6lepton17ExpressionProgram12getStackSizeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#110">_ZNK4PLMD6lepton17ExpressionProgram16getNumOperationsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#131">_ZNK4PLMD6lepton17ExpressionProgram8evaluateERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS8_ESaISt4pairIKS8_dEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#127">_ZNK4PLMD6lepton17ExpressionProgram8evaluateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ExpressionProgram.cpp.func.html b/coverage-libs/lepton/ExpressionProgram.cpp.func.html
new file mode 100644
index 0000000000..13bc6a1fda
--- /dev/null
+++ b/coverage-libs/lepton/ExpressionProgram.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ExpressionProgram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ExpressionProgram.cpp<span style="font-size: 80%;"> (<a href="ExpressionProgram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExpressionProgram.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#104">_ZN4PLMD6lepton17ExpressionProgram12buildProgramERKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#118">_ZN4PLMD6lepton17ExpressionProgram12setOperationEiPNS0_9OperationE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#73">_ZN4PLMD6lepton17ExpressionProgramC2ERKNS0_16ParsedExpressionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#91">_ZN4PLMD6lepton17ExpressionProgramC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#70">_ZN4PLMD6lepton17ExpressionProgramC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#86">_ZN4PLMD6lepton17ExpressionProgramD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#95">_ZN4PLMD6lepton17ExpressionProgramaSERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#114">_ZNK4PLMD6lepton17ExpressionProgram12getOperationEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#123">_ZNK4PLMD6lepton17ExpressionProgram12getStackSizeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#110">_ZNK4PLMD6lepton17ExpressionProgram16getNumOperationsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#131">_ZNK4PLMD6lepton17ExpressionProgram8evaluateERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS8_ESaISt4pairIKS8_dEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionProgram.cpp.gcov.html#127">_ZNK4PLMD6lepton17ExpressionProgram8evaluateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ExpressionProgram.cpp.gcov.html b/coverage-libs/lepton/ExpressionProgram.cpp.gcov.html
new file mode 100644
index 0000000000..a97a22555c
--- /dev/null
+++ b/coverage-libs/lepton/ExpressionProgram.cpp.gcov.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ExpressionProgram.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ExpressionProgram.cpp<span style="font-size: 80%;"> (source / <a href="ExpressionProgram.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  *                                   lepton                                   *</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *                                                                            *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Portions copyright (c) 2009-2018 Stanford University and the Authors.      *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Contributors:                                                              *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *                                                                            *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *                                                                            *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &quot;ExpressionProgram.h&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &quot;Operation.h&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;ParsedExpression.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : namespace PLMD {</a>
+<a name="69"><span class="lineNum">      69 </span>            : using namespace lepton;</a>
+<a name="70"><span class="lineNum">      70 </span>            : using namespace std;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 : ExpressionProgram::ExpressionProgram() : maxArgs(0), stackSize(0) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 : ExpressionProgram::ExpressionProgram(const ParsedExpression&amp; expression) : maxArgs(0), stackSize(0) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :     buildProgram(expression.getRootNode());</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     int currentStackSize = 0;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     for (int i = 0; i &lt; (int) operations.size(); i++) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :         int args = operations[i]-&gt;getNumArguments();</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :         if (args &gt; maxArgs)</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :             maxArgs = args;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :         currentStackSize += 1-args;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :         if (currentStackSize &gt; stackSize)</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :             stackSize = currentStackSize;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :     }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 : ExpressionProgram::~ExpressionProgram() {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     for (int i = 0; i &lt; (int) operations.size(); i++)</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :         delete operations[i];</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : ExpressionProgram::ExpressionProgram(const ExpressionProgram&amp; program) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     *this = program;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 : ExpressionProgram&amp; ExpressionProgram::operator=(const ExpressionProgram&amp; program) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     maxArgs = program.maxArgs;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     stackSize = program.stackSize;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     operations.resize(program.operations.size());</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :     for (int i = 0; i &lt; (int) operations.size(); i++)</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :         operations[i] = program.operations[i]-&gt;clone();</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     return *this;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 : void ExpressionProgram::buildProgram(const ExpressionTreeNode&amp; node) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     for (int i = (int) node.getChildren().size()-1; i &gt;= 0; i--)</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :         buildProgram(node.getChildren()[i]);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     operations.push_back(node.getOperation().clone());</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 : int ExpressionProgram::getNumOperations() const {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :     return (int) operations.size();</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 : const Operation&amp; ExpressionProgram::getOperation(int index) const {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     return *operations[index];</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 : void ExpressionProgram::setOperation(int index, Operation* operation) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     delete operations[index];</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     operations[index] = operation;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 : int ExpressionProgram::getStackSize() const {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     return stackSize;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 : double ExpressionProgram::evaluate() const {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     return evaluate(map&lt;string, double&gt;());</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 : double ExpressionProgram::evaluate(const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     vector&lt;double&gt; stack(stackSize+1);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     int stackPointer = stackSize;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     for (int i = 0; i &lt; (int) operations.size(); i++) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :         int numArgs = operations[i]-&gt;getNumArguments();</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :         double result = operations[i]-&gt;evaluate(&amp;stack[stackPointer], variables);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :         stackPointer += numArgs-1;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :         stack[stackPointer] = result;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     return stack[stackSize-1];</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ExpressionTreeNode.cpp.func-sort-c.html b/coverage-libs/lepton/ExpressionTreeNode.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b8350f56fd
--- /dev/null
+++ b/coverage-libs/lepton/ExpressionTreeNode.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ExpressionTreeNode.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ExpressionTreeNode.cpp<span style="font-size: 80%;"> (<a href="ExpressionTreeNode.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExpressionTreeNode.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#83">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationERKS1_</a></td>
+              <td class="coverFnHi">4104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#76">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationERKS1_S5_</a></td>
+              <td class="coverFnHi">8433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#97">_ZN4PLMD6lepton18ExpressionTreeNodeC2EOS1_</a></td>
+              <td class="coverFnHi">31689</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#71">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationERKSt6vectorIS1_SaIS1_EE</a></td>
+              <td class="coverFnHi">57700</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#130">_ZN4PLMD6lepton18ExpressionTreeNodeaSERKS1_</a></td>
+              <td class="coverFnHi">64603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#156">_ZNK4PLMD6lepton18ExpressionTreeNode10assignTagsERSt6vectorIPKS1_SaIS4_EE</a></td>
+              <td class="coverFnHi">79706</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#126">_ZNK4PLMD6lepton18ExpressionTreeNodeeqERKS1_</a></td>
+              <td class="coverFnHi">86035</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#110">_ZNK4PLMD6lepton18ExpressionTreeNodeneERKS1_</a></td>
+              <td class="coverFnHi">119413</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#89">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationE</a></td>
+              <td class="coverFnHi">2021173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#138">_ZN4PLMD6lepton18ExpressionTreeNodeaSEOS1_</a></td>
+              <td class="coverFnHi">2094661</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#102">_ZN4PLMD6lepton18ExpressionTreeNodeC2Ev</a></td>
+              <td class="coverFnHi">2136840</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#94">_ZN4PLMD6lepton18ExpressionTreeNodeC2ERKS1_</a></td>
+              <td class="coverFnHi">2753562</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#148">_ZNK4PLMD6lepton18ExpressionTreeNode12getOperationEv</a></td>
+              <td class="coverFnHi">4894636</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#152">_ZNK4PLMD6lepton18ExpressionTreeNode11getChildrenEv</a></td>
+              <td class="coverFnHi">5837189</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#105">_ZN4PLMD6lepton18ExpressionTreeNodeD2Ev</a></td>
+              <td class="coverFnHi">7013501</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ExpressionTreeNode.cpp.func.html b/coverage-libs/lepton/ExpressionTreeNode.cpp.func.html
new file mode 100644
index 0000000000..ce5a3b9e21
--- /dev/null
+++ b/coverage-libs/lepton/ExpressionTreeNode.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ExpressionTreeNode.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ExpressionTreeNode.cpp<span style="font-size: 80%;"> (<a href="ExpressionTreeNode.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExpressionTreeNode.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#97">_ZN4PLMD6lepton18ExpressionTreeNodeC2EOS1_</a></td>
+              <td class="coverFnHi">31689</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#89">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationE</a></td>
+              <td class="coverFnHi">2021173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#83">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationERKS1_</a></td>
+              <td class="coverFnHi">4104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#76">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationERKS1_S5_</a></td>
+              <td class="coverFnHi">8433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#71">_ZN4PLMD6lepton18ExpressionTreeNodeC2EPNS0_9OperationERKSt6vectorIS1_SaIS1_EE</a></td>
+              <td class="coverFnHi">57700</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#94">_ZN4PLMD6lepton18ExpressionTreeNodeC2ERKS1_</a></td>
+              <td class="coverFnHi">2753562</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#102">_ZN4PLMD6lepton18ExpressionTreeNodeC2Ev</a></td>
+              <td class="coverFnHi">2136840</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#105">_ZN4PLMD6lepton18ExpressionTreeNodeD2Ev</a></td>
+              <td class="coverFnHi">7013501</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#138">_ZN4PLMD6lepton18ExpressionTreeNodeaSEOS1_</a></td>
+              <td class="coverFnHi">2094661</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#130">_ZN4PLMD6lepton18ExpressionTreeNodeaSERKS1_</a></td>
+              <td class="coverFnHi">64603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#156">_ZNK4PLMD6lepton18ExpressionTreeNode10assignTagsERSt6vectorIPKS1_SaIS4_EE</a></td>
+              <td class="coverFnHi">79706</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#152">_ZNK4PLMD6lepton18ExpressionTreeNode11getChildrenEv</a></td>
+              <td class="coverFnHi">5837189</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#148">_ZNK4PLMD6lepton18ExpressionTreeNode12getOperationEv</a></td>
+              <td class="coverFnHi">4894636</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#126">_ZNK4PLMD6lepton18ExpressionTreeNodeeqERKS1_</a></td>
+              <td class="coverFnHi">86035</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpressionTreeNode.cpp.gcov.html#110">_ZNK4PLMD6lepton18ExpressionTreeNodeneERKS1_</a></td>
+              <td class="coverFnHi">119413</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ExpressionTreeNode.cpp.gcov.html b/coverage-libs/lepton/ExpressionTreeNode.cpp.gcov.html
new file mode 100644
index 0000000000..79d85678f9
--- /dev/null
+++ b/coverage-libs/lepton/ExpressionTreeNode.cpp.gcov.html
@@ -0,0 +1,263 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ExpressionTreeNode.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ExpressionTreeNode.cpp<span style="font-size: 80%;"> (source / <a href="ExpressionTreeNode.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  *                                   lepton                                   *</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *                                                                            *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Portions copyright (c) 2009-2021 Stanford University and the Authors.      *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Contributors:                                                              *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *                                                                            *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *                                                                            *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &quot;ExpressionTreeNode.h&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;Operation.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &lt;utility&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace PLMD {</a>
+<a name="70"><span class="lineNum">      70 </span>            : using namespace lepton;</a>
+<a name="71"><span class="lineNum">      71 </span>            : using namespace std;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      57700 : ExpressionTreeNode::ExpressionTreeNode(Operation* operation, const vector&lt;ExpressionTreeNode&gt;&amp; children) : operation(operation), children(children) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      57700 :     if (operation-&gt;getNumArguments() != children.size())</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :         throw Exception(&quot;wrong number of arguments to function: &quot;+operation-&gt;getName());</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      57700 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       8433 : ExpressionTreeNode::ExpressionTreeNode(Operation* operation, const ExpressionTreeNode&amp; child1, const ExpressionTreeNode&amp; child2) : operation(operation) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       8433 :     children.push_back(child1);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       8433 :     children.push_back(child2);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       8433 :     if (operation-&gt;getNumArguments() != children.size())</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :         throw Exception(&quot;wrong number of arguments to function: &quot;+operation-&gt;getName());</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       8433 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       4104 : ExpressionTreeNode::ExpressionTreeNode(Operation* operation, const ExpressionTreeNode&amp; child) : operation(operation) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       4104 :     children.push_back(child);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       4104 :     if (operation-&gt;getNumArguments() != children.size())</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :         throw Exception(&quot;wrong number of arguments to function: &quot;+operation-&gt;getName());</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       4104 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    2021173 : ExpressionTreeNode::ExpressionTreeNode(Operation* operation) : operation(operation) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    2021173 :     if (operation-&gt;getNumArguments() != children.size())</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :         throw Exception(&quot;wrong number of arguments to function: &quot;+operation-&gt;getName());</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    2021173 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    2753562 : ExpressionTreeNode::ExpressionTreeNode(const ExpressionTreeNode&amp; node) : operation(node.operation == NULL ? NULL : node.operation-&gt;clone()), children(node.getChildren()) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    2753562 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      31689 : ExpressionTreeNode::ExpressionTreeNode(ExpressionTreeNode&amp;&amp; node) : operation(node.operation), children(move(node.children)) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      31689 :     node.operation = NULL;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     node.children.clear();</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      31689 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">    2136840 : ExpressionTreeNode::ExpressionTreeNode() : operation(NULL) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">    2136840 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    7013501 : ExpressionTreeNode::~ExpressionTreeNode() {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">    7013501 :     if (operation != NULL)</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">    4887083 :         delete operation;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">    7013501 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     119413 : bool ExpressionTreeNode::operator!=(const ExpressionTreeNode&amp; node) const {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">     119413 :     if (node.getOperation() != getOperation())</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :         return true;</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      61697 :     if (getOperation().isSymmetric() &amp;&amp; getChildren().size() == 2) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       9882 :         if (getChildren()[0] == node.getChildren()[0] &amp;&amp; getChildren()[1] == node.getChildren()[1])</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :             return false;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       3556 :         if (getChildren()[0] == node.getChildren()[1] &amp;&amp; getChildren()[1] == node.getChildren()[0])</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :             return false;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       3556 :         return true;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      82904 :     for (int i = 0; i &lt; (int) getChildren().size(); i++)</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      33378 :         if (getChildren()[i] != node.getChildren()[i])</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :             return true;</a>
+<a name="125"><span class="lineNum">     125 </span>            :     return false;</a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      86035 : bool ExpressionTreeNode::operator==(const ExpressionTreeNode&amp; node) const {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      86035 :     return !(*this != node);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      64603 : ExpressionTreeNode&amp; ExpressionTreeNode::operator=(const ExpressionTreeNode&amp; node) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      64603 :     if (operation != NULL)</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      11673 :         delete operation;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      64603 :     operation = node.getOperation().clone();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      64603 :     children = node.getChildren();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      64603 :     return *this;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">    2094661 : ExpressionTreeNode&amp; ExpressionTreeNode::operator=(ExpressionTreeNode&amp;&amp; node) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">    2094661 :     if (operation != NULL)</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      10819 :         delete operation;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">    2094661 :     operation = node.operation;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">    2094661 :     children = move(node.children);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">    2094661 :     node.operation = NULL;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     node.children.clear();</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">    2094661 :     return *this;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">    4894636 : const Operation&amp; ExpressionTreeNode::getOperation() const {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">    4894636 :     return *operation;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    5837189 : const vector&lt;ExpressionTreeNode&gt;&amp; ExpressionTreeNode::getChildren() const {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">    5837189 :     return children;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      79706 : void ExpressionTreeNode::assignTags(vector&lt;const ExpressionTreeNode*&gt;&amp; examples) const {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     // Assign tag values to all nodes in a tree, such that two nodes have the same</a>
+<a name="160"><span class="lineNum">     160 </span>            :     // tag if and only if they (and all their children) are equal.  This is used to</a>
+<a name="161"><span class="lineNum">     161 </span>            :     // optimize other operations.</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      79706 :     int numTags = examples.size();</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     153265 :     for (const ExpressionTreeNode&amp; child : getChildren())</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      73559 :         child.assignTags(examples);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      79706 :     if (numTags == examples.size()) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :         // All the children matched existing tags, so possibly this node does too.</a>
+<a name="168"><span class="lineNum">     168 </span>            :         </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     226626 :         for (int i = 0; i &lt; examples.size(); i++) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     206772 :             const ExpressionTreeNode&amp; example = *examples[i];</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     206772 :             bool matches = (getChildren().size() == example.getChildren().size() &amp;&amp; getOperation() == example.getOperation());</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     232773 :             for (int j = 0; matches &amp;&amp; j &lt; getChildren().size(); j++)</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      26001 :                 if (getChildren()[j].tag != example.getChildren()[j].tag)</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :                     matches = false;</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     206772 :             if (matches) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      30735 :                 tag = i;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      30735 :                 return;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :             }</a>
+<a name="179"><span class="lineNum">     179 </span>            :         }</a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span>            :     </a>
+<a name="182"><span class="lineNum">     182 </span>            :     // This node does not match any previous node, so assign a new tag.</a>
+<a name="183"><span class="lineNum">     183 </span>            :     </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      48971 :     tag = examples.size();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">      48971 :     examples.push_back(this);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Operation.cpp.func-sort-c.html b/coverage-libs/lepton/Operation.cpp.func-sort-c.html
new file mode 100644
index 0000000000..93ab82df89
--- /dev/null
+++ b/coverage-libs/lepton/Operation.cpp.func-sort-c.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Operation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Operation.cpp<span style="font-size: 80%;"> (<a href="Operation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">267</td>
+            <td class="headerCovTableEntry">315</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Operation.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Operation.cpp.gcov.html#407">_ZNK4PLMD6lepton9Operation11AddConstant13differentiateERKSt6vectorINS0_18ExpressionTreeNodeESaIS4_EES8_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage-libs/lepton/Operation.cpp.func.html b/coverage-libs/lepton/Operation.cpp.func.html
new file mode 100644
index 0000000000..28d8dec833
--- /dev/null
+++ b/coverage-libs/lepton/Operation.cpp.func.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Operation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Operation.cpp<span style="font-size: 80%;"> (<a href="Operation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">267</td>
+            <td class="headerCovTableEntry">315</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Operation.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">4762</td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
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+</html>
diff --git a/coverage-libs/lepton/Operation.cpp.gcov.html b/coverage-libs/lepton/Operation.cpp.gcov.html
new file mode 100644
index 0000000000..c57ff236fa
--- /dev/null
+++ b/coverage-libs/lepton/Operation.cpp.gcov.html
@@ -0,0 +1,746 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Operation.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Operation.cpp<span style="font-size: 80%;"> (source / <a href="Operation.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">267</td>
+            <td class="headerCovTableEntry">315</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="35"><span class="lineNum">      35 </span>            :  *                                   lepton                                   *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *                                                                            *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Portions copyright (c) 2009-2021 Stanford University and the Authors.      *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * Contributors:                                                              *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  *                                                                            *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *                                                                            *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  *                                                                            *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="63"><span class="lineNum">      63 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &quot;Operation.h&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;ExpressionTreeNode.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;MSVC_erfc.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace PLMD {</a>
+<a name="70"><span class="lineNum">      70 </span>            : using namespace lepton;</a>
+<a name="71"><span class="lineNum">      71 </span>            : using namespace std;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       4762 : static bool isZero(const ExpressionTreeNode&amp; node) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       4762 :     if (node.getOperation().getId() != Operation::CONSTANT)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :         return false;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       2791 :     return dynamic_cast&lt;const Operation::Constant&amp;&gt;(node.getOperation()).getValue() == 0.0;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        202 : double Operation::Erf::evaluate(double* args, const map&lt;string, double&gt;&amp; variables) const {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        202 :     return erf(args[0]);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        202 : double Operation::Erfc::evaluate(double* args, const map&lt;string, double&gt;&amp; variables) const {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        202 :     return erfc(args[0]);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1114 : ExpressionTreeNode Operation::Constant::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1114 :     return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1120 : ExpressionTreeNode Operation::Variable::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1120 :     if (variable == name)</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        595 :         return ExpressionTreeNode(new Operation::Constant(1.0));</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        525 :     return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 : ExpressionTreeNode Operation::Custom::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     if (function-&gt;getNumArguments() == 0)</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     ExpressionTreeNode result;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     bool foundTerm = false;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :     for (int i = 0; i &lt; getNumArguments(); i++) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :         if (!isZero(childDerivs[i])) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :             if (foundTerm)</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :                 result = ExpressionTreeNode(new Operation::Add(),</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :                                             result,</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :                                             ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Custom(*this, i), children), childDerivs[i]));</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :             else {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :                 result = ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::Custom(*this, i), children), childDerivs[i]);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :                 foundTerm = true;</a>
+<a name="111"><span class="lineNum">     111 </span>            :             }</a>
+<a name="112"><span class="lineNum">     112 </span>            :         }</a>
+<a name="113"><span class="lineNum">     113 </span>            :     }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     if (foundTerm)</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :         return result;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        577 : ExpressionTreeNode Operation::Add::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        577 :     if (isZero(childDerivs[0]))</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        124 :         return childDerivs[1];</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        453 :     if (isZero(childDerivs[1]))</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        360 :         return childDerivs[0];</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         93 :     return ExpressionTreeNode(new Operation::Add(), childDerivs[0], childDerivs[1]);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        340 : ExpressionTreeNode Operation::Subtract::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        340 :     if (isZero(childDerivs[0])) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         75 :         if (isZero(childDerivs[1]))</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         60 :             return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         15 :         return ExpressionTreeNode(new Operation::Negate(), childDerivs[1]);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     }</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        265 :     if (isZero(childDerivs[1]))</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         66 :         return childDerivs[0];</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        199 :     return ExpressionTreeNode(new Operation::Subtract(), childDerivs[0], childDerivs[1]);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       1226 : ExpressionTreeNode Operation::Multiply::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       1226 :     if (isZero(childDerivs[0])) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        902 :         if (isZero(childDerivs[1]))</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        313 :             return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        589 :         return ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1]);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        324 :     if (isZero(childDerivs[1]))</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         26 :         return ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        298 :     return ExpressionTreeNode(new Operation::Add(),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        596 :                               ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1]),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        894 :                               ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]));</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        128 : ExpressionTreeNode Operation::Divide::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        128 :     ExpressionTreeNode subexp;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        128 :     if (isZero(childDerivs[0])) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         99 :         if (isZero(childDerivs[1]))</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         68 :             return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         31 :         subexp = ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1]));</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     }</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         29 :     else if (isZero(childDerivs[1]))</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         16 :         subexp = ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     else</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         26 :         subexp = ExpressionTreeNode(new Operation::Subtract(),</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         26 :                                                  ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]),</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         39 :                                                  ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1]));</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         60 :     return ExpressionTreeNode(new Operation::Divide(), subexp, ExpressionTreeNode(new Operation::Square(), children[1]));</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        128 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        111 : ExpressionTreeNode Operation::Power::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        111 :     return ExpressionTreeNode(new Operation::Add(),</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        222 :                               ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        222 :                                                  ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :                                                                     children[1],</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        222 :                                                                     ExpressionTreeNode(new Operation::Power(),</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        222 :                                                                                        children[0], ExpressionTreeNode(new Operation::AddConstant(-1.0), children[1]))),</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :                                                  childDerivs[0]),</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        222 :                               ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        222 :                                                  ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        222 :                                                                     ExpressionTreeNode(new Operation::Log(), children[0]),</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        222 :                                                                     ExpressionTreeNode(new Operation::Power(), children[0], children[1])),</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        222 :                                                  childDerivs[1]));</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         11 : ExpressionTreeNode Operation::Negate::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         11 :     if (isZero(childDerivs[0]))</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          3 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          8 :     return ExpressionTreeNode(new Operation::Negate(), childDerivs[0]);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         41 : ExpressionTreeNode Operation::Sqrt::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         41 :     if (isZero(childDerivs[0]))</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         41 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         82 :                               ExpressionTreeNode(new Operation::MultiplyConstant(0.5),</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         82 :                                                  ExpressionTreeNode(new Operation::Reciprocal(),</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         82 :                                                                     ExpressionTreeNode(new Operation::Sqrt(), children[0]))),</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         41 :                               childDerivs[0]);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          3 : ExpressionTreeNode Operation::Exp::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          3 :     if (isZero(childDerivs[0]))</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          3 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          6 :                               ExpressionTreeNode(new Operation::Exp(), children[0]),</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          3 :                               childDerivs[0]);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Log::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Reciprocal(), children[0]),</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         56 : ExpressionTreeNode Operation::Sin::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         56 :     if (isZero(childDerivs[0]))</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          2 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         54 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        108 :                               ExpressionTreeNode(new Operation::Cos(), children[0]),</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         54 :                               childDerivs[0]);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        198 : ExpressionTreeNode Operation::Cos::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        198 :     if (isZero(childDerivs[0]))</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        198 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        396 :                               ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        396 :                                                  ExpressionTreeNode(new Operation::Sin(), children[0])),</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        198 :                               childDerivs[0]);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Sec::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Sec(), children[0]),</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Tan(), children[0])),</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : }</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Csc::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Csc(), children[0]),</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Cot(), children[0]))),</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : }</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Tan::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Square(),</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Sec(), children[0])),</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Cot::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Square(),</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Csc(), children[0]))),</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Asin::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Reciprocal(),</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Sqrt(),</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Subtract(),</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          4 :                                                                                        ExpressionTreeNode(new Operation::Constant(1.0)),</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          4 :                                                                                        ExpressionTreeNode(new Operation::Square(), children[0])))),</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : }</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Acos::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Reciprocal(),</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Sqrt(),</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          4 :                                                                                        ExpressionTreeNode(new Operation::Subtract(),</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          4 :                                                                                                           ExpressionTreeNode(new Operation::Constant(1.0)),</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          4 :                                                                                                           ExpressionTreeNode(new Operation::Square(), children[0]))))),</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : }</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Atan::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Reciprocal(),</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::AddConstant(1.0),</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Square(), children[0]))),</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : }</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          8 : ExpressionTreeNode Operation::Atan2::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          8 :     return ExpressionTreeNode(new Operation::Divide(),</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         16 :                               ExpressionTreeNode(new Operation::Subtract(),</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         16 :                                                  ExpressionTreeNode(new Operation::Multiply(), children[1], childDerivs[0]),</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         16 :                                                  ExpressionTreeNode(new Operation::Multiply(), children[0], childDerivs[1])),</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         16 :                               ExpressionTreeNode(new Operation::Add(),</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         16 :                                                  ExpressionTreeNode(new Operation::Square(), children[0]),</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         24 :                                                  ExpressionTreeNode(new Operation::Square(), children[1])));</span></a>
+<a name="314"><span class="lineNum">     314 </span>            : }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Sinh::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Cosh(),</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :                                                  children[0]),</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : }</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Cosh::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Sinh(),</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :                                                  children[0]),</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : }</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Tanh::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Subtract(),</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Constant(1.0)),</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Square(),</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Tanh(), children[0]))),</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Erf::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Constant(2.0/sqrt(M_PI))),</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Exp(),</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          4 :                                                                                        ExpressionTreeNode(new Operation::Square(), children[0])))),</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Erfc::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Constant(-2.0/sqrt(M_PI))),</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Exp(),</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          4 :                                                                                        ExpressionTreeNode(new Operation::Square(), children[0])))),</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         13 : ExpressionTreeNode Operation::Step::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         13 :     return ExpressionTreeNode(new Operation::Delta(),children[0]);</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : }</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Delta::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Nandelta(), children[0]);</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : }</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Nandelta::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Nandelta(), children[0]);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            : }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Square::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::MultiplyConstant(2.0),</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :                                                  children[0]),</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="388"><span class="lineNum">     388 </span>            : }</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Cube::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::MultiplyConstant(3.0),</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Square(), children[0])),</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            : }</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Reciprocal::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          2 :     if (isZero(childDerivs[0]))</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          4 :                               ExpressionTreeNode(new Operation::Negate(),</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          4 :                                                  ExpressionTreeNode(new Operation::Reciprocal(),</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          4 :                                                                     ExpressionTreeNode(new Operation::Square(), children[0]))),</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          2 :                               childDerivs[0]);</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : }</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 : ExpressionTreeNode Operation::AddConstant::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :     return childDerivs[0];</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : }</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 : ExpressionTreeNode Operation::MultiplyConstant::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :     if (isZero(childDerivs[0]))</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :     return ExpressionTreeNode(new Operation::MultiplyConstant(value),</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :                               childDerivs[0]);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            : }</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 : ExpressionTreeNode Operation::PowerConstant::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :     if (isZero(childDerivs[0]))</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :                               ExpressionTreeNode(new Operation::MultiplyConstant(value),</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :                                                  ExpressionTreeNode(new Operation::PowerConstant(value-1),</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :                                                                     children[0])),</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :                               childDerivs[0]);</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : }</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          4 : ExpressionTreeNode Operation::Min::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">          4 :     ExpressionTreeNode step(new Operation::Step(),</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">          8 :                             ExpressionTreeNode(new Operation::Subtract(), children[0], children[1]));</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         20 :     return ExpressionTreeNode(new Operation::Select(), {step, childDerivs[1], childDerivs[0]});</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          4 : }</span></a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          4 : ExpressionTreeNode Operation::Max::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          4 :     ExpressionTreeNode step(new Operation::Step(),</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          8 :                             ExpressionTreeNode(new Operation::Subtract(), children[0], children[1]));</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         20 :     return ExpressionTreeNode(new Operation::Select(), {step, childDerivs[0], childDerivs[1]});</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          4 : }</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          3 : ExpressionTreeNode Operation::Abs::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          3 :     if (isZero(childDerivs[0]))</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :         return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          3 :     ExpressionTreeNode step(new Operation::Step(), children[0]);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          3 :     return ExpressionTreeNode(new Operation::Multiply(),</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :                               childDerivs[0],</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          6 :                               ExpressionTreeNode(new Operation::AddConstant(-1),</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          9 :                                                  ExpressionTreeNode(new Operation::MultiplyConstant(2), step)));</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          3 : }</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Floor::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Ceil::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          2 :     return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         12 : ExpressionTreeNode Operation::Select::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :     vector&lt;ExpressionTreeNode&gt; derivChildren;</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         12 :     derivChildren.push_back(children[0]);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         12 :     derivChildren.push_back(childDerivs[1]);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         12 :     derivChildren.push_back(childDerivs[2]);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         24 :     return ExpressionTreeNode(new Operation::Select(), derivChildren);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         12 : }</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            : #define LEPTON_CONST(x) ExpressionTreeNode(new Operation::Constant(x))</a>
+<a name="469"><span class="lineNum">     469 </span>            : #define LEPTON_OP1(name,x) ExpressionTreeNode(new Operation::name(),x)</a>
+<a name="470"><span class="lineNum">     470 </span>            : #define LEPTON_OP2(name,x,y) ExpressionTreeNode(new Operation::name(),x,y)</a>
+<a name="471"><span class="lineNum">     471 </span>            : #define LEPTON_ADD_CONST(x,y) ExpressionTreeNode(new Operation::AddConstant(x),y)</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Acot::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="474"><span class="lineNum">     474 </span>            :     return</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">          2 :       LEPTON_OP2(Multiply,</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :         LEPTON_OP1(Negate,</a>
+<a name="477"><span class="lineNum">     477 </span>            :           LEPTON_OP1(Reciprocal,</a>
+<a name="478"><span class="lineNum">     478 </span>            :             LEPTON_ADD_CONST(1.0,</a>
+<a name="479"><span class="lineNum">     479 </span>            :               LEPTON_OP1(Square,children[0])</a>
+<a name="480"><span class="lineNum">     480 </span>            :             )</a>
+<a name="481"><span class="lineNum">     481 </span>            :           )</a>
+<a name="482"><span class="lineNum">     482 </span>            :         ),</a>
+<a name="483"><span class="lineNum">     483 </span>            :         childDerivs[0]</a>
+<a name="484"><span class="lineNum">     484 </span>            :       );</a>
+<a name="485"><span class="lineNum">     485 </span>            : }</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Asec::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :     return</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          2 :       LEPTON_OP2(Multiply,</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :         LEPTON_OP1(Reciprocal,</a>
+<a name="491"><span class="lineNum">     491 </span>            :           LEPTON_OP2(Multiply,</a>
+<a name="492"><span class="lineNum">     492 </span>            :             LEPTON_OP1(Abs,children[0]),</a>
+<a name="493"><span class="lineNum">     493 </span>            :             LEPTON_OP1(Sqrt,</a>
+<a name="494"><span class="lineNum">     494 </span>            :               LEPTON_OP2(Subtract,</a>
+<a name="495"><span class="lineNum">     495 </span>            :                 LEPTON_OP1(Square,children[0]),</a>
+<a name="496"><span class="lineNum">     496 </span>            :                 LEPTON_CONST(1.0)</a>
+<a name="497"><span class="lineNum">     497 </span>            :               )</a>
+<a name="498"><span class="lineNum">     498 </span>            :             )</a>
+<a name="499"><span class="lineNum">     499 </span>            :           )</a>
+<a name="500"><span class="lineNum">     500 </span>            :         ),</a>
+<a name="501"><span class="lineNum">     501 </span>            :         childDerivs[0]</a>
+<a name="502"><span class="lineNum">     502 </span>            :       );</a>
+<a name="503"><span class="lineNum">     503 </span>            : }</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Acsc::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     return</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :       LEPTON_OP1(Negate,</a>
+<a name="509"><span class="lineNum">     509 </span>            :         LEPTON_OP1(Reciprocal,</a>
+<a name="510"><span class="lineNum">     510 </span>            :           LEPTON_OP2(Multiply,</a>
+<a name="511"><span class="lineNum">     511 </span>            :             LEPTON_OP1(Abs,children[0]),</a>
+<a name="512"><span class="lineNum">     512 </span>            :             LEPTON_OP1(Sqrt,</a>
+<a name="513"><span class="lineNum">     513 </span>            :               LEPTON_OP2(Subtract,</a>
+<a name="514"><span class="lineNum">     514 </span>            :                 LEPTON_OP1(Square,children[0]),</a>
+<a name="515"><span class="lineNum">     515 </span>            :                 LEPTON_CONST(1.0)</a>
+<a name="516"><span class="lineNum">     516 </span>            :               )</a>
+<a name="517"><span class="lineNum">     517 </span>            :             )</a>
+<a name="518"><span class="lineNum">     518 </span>            :           )</a>
+<a name="519"><span class="lineNum">     519 </span>            :         )</a>
+<a name="520"><span class="lineNum">     520 </span>            :       ),</a>
+<a name="521"><span class="lineNum">     521 </span>            :       childDerivs[0]</a>
+<a name="522"><span class="lineNum">     522 </span>            :     );</a>
+<a name="523"><span class="lineNum">     523 </span>            : }</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Coth::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :     return</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :       LEPTON_OP2(Subtract,</a>
+<a name="529"><span class="lineNum">     529 </span>            :         LEPTON_CONST(1.0),</a>
+<a name="530"><span class="lineNum">     530 </span>            :         LEPTON_OP1(Square,</a>
+<a name="531"><span class="lineNum">     531 </span>            :           LEPTON_OP1(Coth,children[0])</a>
+<a name="532"><span class="lineNum">     532 </span>            :         )</a>
+<a name="533"><span class="lineNum">     533 </span>            :       ),</a>
+<a name="534"><span class="lineNum">     534 </span>            :       childDerivs[0]</a>
+<a name="535"><span class="lineNum">     535 </span>            :     );</a>
+<a name="536"><span class="lineNum">     536 </span>            : }</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Sech::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :     return</a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :       LEPTON_OP1(Negate,</a>
+<a name="542"><span class="lineNum">     542 </span>            :         LEPTON_OP2(Multiply,</a>
+<a name="543"><span class="lineNum">     543 </span>            :           LEPTON_OP1(Tanh,children[0]),</a>
+<a name="544"><span class="lineNum">     544 </span>            :           LEPTON_OP1(Sech,children[0])</a>
+<a name="545"><span class="lineNum">     545 </span>            :         )</a>
+<a name="546"><span class="lineNum">     546 </span>            :       ),</a>
+<a name="547"><span class="lineNum">     547 </span>            :       childDerivs[0]</a>
+<a name="548"><span class="lineNum">     548 </span>            :     );</a>
+<a name="549"><span class="lineNum">     549 </span>            : }</a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Csch::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :     return</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :       LEPTON_OP1(Negate,</a>
+<a name="555"><span class="lineNum">     555 </span>            :         LEPTON_OP2(Multiply,</a>
+<a name="556"><span class="lineNum">     556 </span>            :           LEPTON_OP1(Coth,children[0]),</a>
+<a name="557"><span class="lineNum">     557 </span>            :           LEPTON_OP1(Csch,children[0])</a>
+<a name="558"><span class="lineNum">     558 </span>            :         )</a>
+<a name="559"><span class="lineNum">     559 </span>            :       ),</a>
+<a name="560"><span class="lineNum">     560 </span>            :       childDerivs[0]</a>
+<a name="561"><span class="lineNum">     561 </span>            :     );</a>
+<a name="562"><span class="lineNum">     562 </span>            : }</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Acosh::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :     return</a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :       LEPTON_OP1(Reciprocal,</a>
+<a name="568"><span class="lineNum">     568 </span>            :         LEPTON_OP1(Sqrt,</a>
+<a name="569"><span class="lineNum">     569 </span>            :           LEPTON_OP2(Subtract,</a>
+<a name="570"><span class="lineNum">     570 </span>            :             LEPTON_OP1(Square,children[0]),</a>
+<a name="571"><span class="lineNum">     571 </span>            :             LEPTON_CONST(1.0)</a>
+<a name="572"><span class="lineNum">     572 </span>            :           )</a>
+<a name="573"><span class="lineNum">     573 </span>            :         )</a>
+<a name="574"><span class="lineNum">     574 </span>            :       ),</a>
+<a name="575"><span class="lineNum">     575 </span>            :       childDerivs[0]</a>
+<a name="576"><span class="lineNum">     576 </span>            :     );</a>
+<a name="577"><span class="lineNum">     577 </span>            : }</a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Atanh::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :     return</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :       LEPTON_OP1(Reciprocal,</a>
+<a name="583"><span class="lineNum">     583 </span>            :         LEPTON_OP2(Subtract,</a>
+<a name="584"><span class="lineNum">     584 </span>            :           LEPTON_CONST(1.0),</a>
+<a name="585"><span class="lineNum">     585 </span>            :           LEPTON_OP1(Square,children[0])</a>
+<a name="586"><span class="lineNum">     586 </span>            :         )</a>
+<a name="587"><span class="lineNum">     587 </span>            :       ),</a>
+<a name="588"><span class="lineNum">     588 </span>            :       childDerivs[0]</a>
+<a name="589"><span class="lineNum">     589 </span>            :     );</a>
+<a name="590"><span class="lineNum">     590 </span>            : }</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Asinh::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="593"><span class="lineNum">     593 </span>            :     return</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :       LEPTON_OP1(Reciprocal,</a>
+<a name="596"><span class="lineNum">     596 </span>            :         LEPTON_OP1(Sqrt,</a>
+<a name="597"><span class="lineNum">     597 </span>            :           LEPTON_ADD_CONST(1.0,</a>
+<a name="598"><span class="lineNum">     598 </span>            :             LEPTON_OP1(Square,children[0])</a>
+<a name="599"><span class="lineNum">     599 </span>            :           )</a>
+<a name="600"><span class="lineNum">     600 </span>            :         )</a>
+<a name="601"><span class="lineNum">     601 </span>            :       ),</a>
+<a name="602"><span class="lineNum">     602 </span>            :       childDerivs[0]</a>
+<a name="603"><span class="lineNum">     603 </span>            :     );</a>
+<a name="604"><span class="lineNum">     604 </span>            : }</a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Acoth::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :     return</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="609"><span class="lineNum">     609 </span>            :       LEPTON_OP1(Reciprocal,</a>
+<a name="610"><span class="lineNum">     610 </span>            :         LEPTON_OP2(Subtract,</a>
+<a name="611"><span class="lineNum">     611 </span>            :           LEPTON_CONST(1.0),</a>
+<a name="612"><span class="lineNum">     612 </span>            :           LEPTON_OP1(Square,children[0])</a>
+<a name="613"><span class="lineNum">     613 </span>            :         )</a>
+<a name="614"><span class="lineNum">     614 </span>            :       ),</a>
+<a name="615"><span class="lineNum">     615 </span>            :       childDerivs[0]</a>
+<a name="616"><span class="lineNum">     616 </span>            :     );</a>
+<a name="617"><span class="lineNum">     617 </span>            : }</a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Asech::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="620"><span class="lineNum">     620 </span>            :     return</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :       LEPTON_OP1(Negate,</a>
+<a name="623"><span class="lineNum">     623 </span>            :         LEPTON_OP1(Reciprocal,</a>
+<a name="624"><span class="lineNum">     624 </span>            :           LEPTON_OP2(Multiply,</a>
+<a name="625"><span class="lineNum">     625 </span>            :             children[0],</a>
+<a name="626"><span class="lineNum">     626 </span>            :             LEPTON_OP2(Multiply,</a>
+<a name="627"><span class="lineNum">     627 </span>            :               LEPTON_ADD_CONST(1.0,</a>
+<a name="628"><span class="lineNum">     628 </span>            :                 children[0]</a>
+<a name="629"><span class="lineNum">     629 </span>            :               ),</a>
+<a name="630"><span class="lineNum">     630 </span>            :               LEPTON_OP1(Sqrt,</a>
+<a name="631"><span class="lineNum">     631 </span>            :                 LEPTON_OP2(Divide,</a>
+<a name="632"><span class="lineNum">     632 </span>            :                   LEPTON_OP2(Subtract,</a>
+<a name="633"><span class="lineNum">     633 </span>            :                     LEPTON_CONST(1.0),</a>
+<a name="634"><span class="lineNum">     634 </span>            :                     children[0]</a>
+<a name="635"><span class="lineNum">     635 </span>            :                   ),</a>
+<a name="636"><span class="lineNum">     636 </span>            :                   LEPTON_ADD_CONST(1.0,</a>
+<a name="637"><span class="lineNum">     637 </span>            :                     children[0]</a>
+<a name="638"><span class="lineNum">     638 </span>            :                   )</a>
+<a name="639"><span class="lineNum">     639 </span>            :                 )</a>
+<a name="640"><span class="lineNum">     640 </span>            :               )</a>
+<a name="641"><span class="lineNum">     641 </span>            :             )</a>
+<a name="642"><span class="lineNum">     642 </span>            :           )</a>
+<a name="643"><span class="lineNum">     643 </span>            :         )</a>
+<a name="644"><span class="lineNum">     644 </span>            :       ),</a>
+<a name="645"><span class="lineNum">     645 </span>            :       childDerivs[0]</a>
+<a name="646"><span class="lineNum">     646 </span>            :     );</a>
+<a name="647"><span class="lineNum">     647 </span>            : }</a>
+<a name="648"><span class="lineNum">     648 </span>            : </a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          2 : ExpressionTreeNode Operation::Acsch::differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const {</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :     return</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          2 :     LEPTON_OP2(Multiply,</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :       LEPTON_OP1(Negate,</a>
+<a name="653"><span class="lineNum">     653 </span>            :         LEPTON_OP1(Reciprocal,</a>
+<a name="654"><span class="lineNum">     654 </span>            :           LEPTON_OP2(Multiply,</a>
+<a name="655"><span class="lineNum">     655 </span>            :             LEPTON_OP1(Square,children[0]),</a>
+<a name="656"><span class="lineNum">     656 </span>            :             LEPTON_OP1(Sqrt,</a>
+<a name="657"><span class="lineNum">     657 </span>            :               LEPTON_ADD_CONST(1.0,</a>
+<a name="658"><span class="lineNum">     658 </span>            :                 LEPTON_OP1(Reciprocal,</a>
+<a name="659"><span class="lineNum">     659 </span>            :                   LEPTON_OP1(Square,children[0])</a>
+<a name="660"><span class="lineNum">     660 </span>            :                 )</a>
+<a name="661"><span class="lineNum">     661 </span>            :               )</a>
+<a name="662"><span class="lineNum">     662 </span>            :             )</a>
+<a name="663"><span class="lineNum">     663 </span>            :           )</a>
+<a name="664"><span class="lineNum">     664 </span>            :         )</a>
+<a name="665"><span class="lineNum">     665 </span>            :       ),</a>
+<a name="666"><span class="lineNum">     666 </span>            :       childDerivs[0]</a>
+<a name="667"><span class="lineNum">     667 </span>            :     );</a>
+<a name="668"><span class="lineNum">     668 </span>            : }</a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Operation.h.func-sort-c.html b/coverage-libs/lepton/Operation.h.func-sort-c.html
new file mode 100644
index 0000000000..a2284a6729
--- /dev/null
+++ b/coverage-libs/lepton/Operation.h.func-sort-c.html
@@ -0,0 +1,1232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Operation.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Operation.h<span style="font-size: 80%;"> (<a href="Operation.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">530</td>
+            <td class="headerCovTableEntry">556</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">280</td>
+            <td class="headerCovTableEntry">290</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Operation.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Operation.h.gcov.html#274">_ZN4PLMD6lepton9Operation6CustomC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_14CustomFunctionE</a></td>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage-libs/lepton/Operation.h.func.html b/coverage-libs/lepton/Operation.h.func.html
new file mode 100644
index 0000000000..2d3e8b00fe
--- /dev/null
+++ b/coverage-libs/lepton/Operation.h.func.html
@@ -0,0 +1,1232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Operation.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Operation.h<span style="font-size: 80%;"> (<a href="Operation.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">530</td>
+            <td class="headerCovTableEntry">556</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">280</td>
+            <td class="headerCovTableEntry">290</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Operation.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">9142</td>
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+    <tr>
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+              <td class="coverFnHi">9018</td>
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+    <tr>
+              <td class="coverFn"><a href="Operation.h.gcov.html#257">_ZNK4PLMD6lepton9Operation8Variable8evaluateEPdRKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISA_ESaISt4pairIKSA_dEEE</a></td>
+              <td class="coverFnHi">30</td>
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+    <tr>
+              <td class="coverFn"><a href="Operation.h.gcov.html#264">_ZNK4PLMD6lepton9Operation8VariableneERKS1_</a></td>
+              <td class="coverFnHi">45589</td>
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+              <td class="coverFn"><a href="Operation.h.gcov.html#149">_ZNK4PLMD6lepton9OperationeqERKS1_</a></td>
+              <td class="coverFnHi">105194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Operation.h.gcov.html#146">_ZNK4PLMD6lepton9OperationneERKS1_</a></td>
+              <td class="coverFnHi">101640</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Operation.h.gcov.html b/coverage-libs/lepton/Operation.h.gcov.html
new file mode 100644
index 0000000000..0dcee3918c
--- /dev/null
+++ b/coverage-libs/lepton/Operation.h.gcov.html
@@ -0,0 +1,1378 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Operation.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Operation.h<span style="font-size: 80%;"> (source / <a href="Operation.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">530</td>
+            <td class="headerCovTableEntry">556</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">280</td>
+            <td class="headerCovTableEntry">290</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : #ifndef __PLUMED_lepton_Operation_h</a>
+<a name="34"><span class="lineNum">      34 </span>            : #define __PLUMED_lepton_Operation_h</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  *                                   lepton                                   *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *                                                                            *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * Contributors:                                                              *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  *                                                                            *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *                                                                            *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="63"><span class="lineNum">      63 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="64"><span class="lineNum">      64 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="65"><span class="lineNum">      65 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;windowsIncludes.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &quot;CustomFunction.h&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            : #include &lt;cmath&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            : #include &lt;map&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : #include &lt;string&gt;</a>
+<a name="73"><span class="lineNum">      73 </span>            : #include &lt;vector&gt;</a>
+<a name="74"><span class="lineNum">      74 </span>            : #include &lt;sstream&gt;</a>
+<a name="75"><span class="lineNum">      75 </span>            : #include &lt;algorithm&gt;</a>
+<a name="76"><span class="lineNum">      76 </span>            : #include &lt;limits&gt;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : namespace PLMD {</a>
+<a name="79"><span class="lineNum">      79 </span>            : namespace lepton {</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class ExpressionTreeNode;</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : /**</a>
+<a name="84"><span class="lineNum">      84 </span>            :  * An Operation represents a single step in the evaluation of an expression, such as a function,</a>
+<a name="85"><span class="lineNum">      85 </span>            :  * an operator, or a constant value.  Each Operation takes some number of values as arguments</a>
+<a name="86"><span class="lineNum">      86 </span>            :  * and produces a single value.</a>
+<a name="87"><span class="lineNum">      87 </span>            :  *</a>
+<a name="88"><span class="lineNum">      88 </span>            :  * This is an abstract class with subclasses for specific operations.</a>
+<a name="89"><span class="lineNum">      89 </span>            :  */</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : class LEPTON_EXPORT Operation {</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            :     virtual ~Operation() {</a>
+<a name="94"><span class="lineNum">      94 </span>            :     }</a>
+<a name="95"><span class="lineNum">      95 </span>            :     /**</a>
+<a name="96"><span class="lineNum">      96 </span>            :      * This enumeration lists all Operation subclasses.  This is provided so that switch statements</a>
+<a name="97"><span class="lineNum">      97 </span>            :      * can be used when processing or analyzing parsed expressions.</a>
+<a name="98"><span class="lineNum">      98 </span>            :      */</a>
+<a name="99"><span class="lineNum">      99 </span>            :     enum Id {CONSTANT, VARIABLE, CUSTOM, ADD, SUBTRACT, MULTIPLY, DIVIDE, POWER, NEGATE, SQRT, EXP, LOG,</a>
+<a name="100"><span class="lineNum">     100 </span>            :              SIN, COS, SEC, CSC, TAN, COT, ASIN, ACOS, ATAN, ATAN2, SINH, COSH, TANH, ERF, ERFC, STEP, DELTA, NANDELTA, SQUARE, CUBE, RECIPROCAL,</a>
+<a name="101"><span class="lineNum">     101 </span>            :              ADD_CONSTANT, MULTIPLY_CONSTANT, POWER_CONSTANT, MIN, MAX, ABS, FLOOR, CEIL, SELECT,</a>
+<a name="102"><span class="lineNum">     102 </span>            :              ACOT, ASEC, ACSC, COTH, SECH, CSCH, ASINH, ACOSH, ATANH, ACOTH, ASECH, ACSCH};</a>
+<a name="103"><span class="lineNum">     103 </span>            :     /**</a>
+<a name="104"><span class="lineNum">     104 </span>            :      * Get the name of this Operation.</a>
+<a name="105"><span class="lineNum">     105 </span>            :      */</a>
+<a name="106"><span class="lineNum">     106 </span>            :     virtual std::string getName() const = 0;</a>
+<a name="107"><span class="lineNum">     107 </span>            :     /**</a>
+<a name="108"><span class="lineNum">     108 </span>            :      * Get this Operation's ID.</a>
+<a name="109"><span class="lineNum">     109 </span>            :      */</a>
+<a name="110"><span class="lineNum">     110 </span>            :     virtual Id getId() const = 0;</a>
+<a name="111"><span class="lineNum">     111 </span>            :     /**</a>
+<a name="112"><span class="lineNum">     112 </span>            :      * Get the number of arguments this operation expects.</a>
+<a name="113"><span class="lineNum">     113 </span>            :      */</a>
+<a name="114"><span class="lineNum">     114 </span>            :     virtual int getNumArguments() const = 0;</a>
+<a name="115"><span class="lineNum">     115 </span>            :     /**</a>
+<a name="116"><span class="lineNum">     116 </span>            :      * Create a clone of this Operation.</a>
+<a name="117"><span class="lineNum">     117 </span>            :      */</a>
+<a name="118"><span class="lineNum">     118 </span>            :     virtual Operation* clone() const = 0;</a>
+<a name="119"><span class="lineNum">     119 </span>            :     /**</a>
+<a name="120"><span class="lineNum">     120 </span>            :      * Perform the computation represented by this operation.</a>
+<a name="121"><span class="lineNum">     121 </span>            :      *</a>
+<a name="122"><span class="lineNum">     122 </span>            :      * @param args        the array of arguments</a>
+<a name="123"><span class="lineNum">     123 </span>            :      * @param variables   a map containing the values of all variables</a>
+<a name="124"><span class="lineNum">     124 </span>            :      * @return the result of performing the computation.</a>
+<a name="125"><span class="lineNum">     125 </span>            :      */</a>
+<a name="126"><span class="lineNum">     126 </span>            :     virtual double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const = 0;</a>
+<a name="127"><span class="lineNum">     127 </span>            :     /**</a>
+<a name="128"><span class="lineNum">     128 </span>            :      * Return an ExpressionTreeNode which represents the analytic derivative of this Operation with respect to a variable.</a>
+<a name="129"><span class="lineNum">     129 </span>            :      *</a>
+<a name="130"><span class="lineNum">     130 </span>            :      * @param children     the child nodes</a>
+<a name="131"><span class="lineNum">     131 </span>            :      * @param childDerivs  the derivatives of the child nodes with respect to the variable</a>
+<a name="132"><span class="lineNum">     132 </span>            :      * @param variable     the variable with respect to which the derivate should be taken</a>
+<a name="133"><span class="lineNum">     133 </span>            :      */</a>
+<a name="134"><span class="lineNum">     134 </span>            :     virtual ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const = 0;</a>
+<a name="135"><span class="lineNum">     135 </span>            :     /**</a>
+<a name="136"><span class="lineNum">     136 </span>            :      * Get whether this operation should be displayed with infix notation.</a>
+<a name="137"><span class="lineNum">     137 </span>            :      */</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      15950 :     virtual bool isInfixOperator() const {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      15950 :         return false;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            :     /**</a>
+<a name="142"><span class="lineNum">     142 </span>            :      * Get whether this is a symmetric binary operation, such that exchanging its arguments</a>
+<a name="143"><span class="lineNum">     143 </span>            :      * does not affect the result.</a>
+<a name="144"><span class="lineNum">     144 </span>            :      */</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      51815 :     virtual bool isSymmetric() const {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      51815 :         return false;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">     101640 :     virtual bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">     101640 :         return op.getId() != getId();</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">     105194 :     virtual bool operator==(const Operation&amp; op) const {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     105194 :         return !(*this != op);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     }</a>
+<a name="154"><span class="lineNum">     154 </span>            :     class Constant;</a>
+<a name="155"><span class="lineNum">     155 </span>            :     class Variable;</a>
+<a name="156"><span class="lineNum">     156 </span>            :     class Custom;</a>
+<a name="157"><span class="lineNum">     157 </span>            :     class Add;</a>
+<a name="158"><span class="lineNum">     158 </span>            :     class Subtract;</a>
+<a name="159"><span class="lineNum">     159 </span>            :     class Multiply;</a>
+<a name="160"><span class="lineNum">     160 </span>            :     class Divide;</a>
+<a name="161"><span class="lineNum">     161 </span>            :     class Power;</a>
+<a name="162"><span class="lineNum">     162 </span>            :     class Negate;</a>
+<a name="163"><span class="lineNum">     163 </span>            :     class Sqrt;</a>
+<a name="164"><span class="lineNum">     164 </span>            :     class Exp;</a>
+<a name="165"><span class="lineNum">     165 </span>            :     class Log;</a>
+<a name="166"><span class="lineNum">     166 </span>            :     class Sin;</a>
+<a name="167"><span class="lineNum">     167 </span>            :     class Cos;</a>
+<a name="168"><span class="lineNum">     168 </span>            :     class Sec;</a>
+<a name="169"><span class="lineNum">     169 </span>            :     class Csc;</a>
+<a name="170"><span class="lineNum">     170 </span>            :     class Tan;</a>
+<a name="171"><span class="lineNum">     171 </span>            :     class Cot;</a>
+<a name="172"><span class="lineNum">     172 </span>            :     class Asin;</a>
+<a name="173"><span class="lineNum">     173 </span>            :     class Acos;</a>
+<a name="174"><span class="lineNum">     174 </span>            :     class Atan;</a>
+<a name="175"><span class="lineNum">     175 </span>            :     class Atan2;</a>
+<a name="176"><span class="lineNum">     176 </span>            :     class Sinh;</a>
+<a name="177"><span class="lineNum">     177 </span>            :     class Cosh;</a>
+<a name="178"><span class="lineNum">     178 </span>            :     class Tanh;</a>
+<a name="179"><span class="lineNum">     179 </span>            :     class Erf;</a>
+<a name="180"><span class="lineNum">     180 </span>            :     class Erfc;</a>
+<a name="181"><span class="lineNum">     181 </span>            :     class Step;</a>
+<a name="182"><span class="lineNum">     182 </span>            :     class Delta;</a>
+<a name="183"><span class="lineNum">     183 </span>            :     class Nandelta;</a>
+<a name="184"><span class="lineNum">     184 </span>            :     class Square;</a>
+<a name="185"><span class="lineNum">     185 </span>            :     class Cube;</a>
+<a name="186"><span class="lineNum">     186 </span>            :     class Reciprocal;</a>
+<a name="187"><span class="lineNum">     187 </span>            :     class AddConstant;</a>
+<a name="188"><span class="lineNum">     188 </span>            :     class MultiplyConstant;</a>
+<a name="189"><span class="lineNum">     189 </span>            :     class PowerConstant;</a>
+<a name="190"><span class="lineNum">     190 </span>            :     class Min;</a>
+<a name="191"><span class="lineNum">     191 </span>            :     class Max;</a>
+<a name="192"><span class="lineNum">     192 </span>            :     class Abs;</a>
+<a name="193"><span class="lineNum">     193 </span>            :     class Floor;</a>
+<a name="194"><span class="lineNum">     194 </span>            :     class Ceil;</a>
+<a name="195"><span class="lineNum">     195 </span>            :     class Select;</a>
+<a name="196"><span class="lineNum">     196 </span>            :     class Acot;</a>
+<a name="197"><span class="lineNum">     197 </span>            :     class Asec;</a>
+<a name="198"><span class="lineNum">     198 </span>            :     class Acsc;</a>
+<a name="199"><span class="lineNum">     199 </span>            :     class Coth;</a>
+<a name="200"><span class="lineNum">     200 </span>            :     class Sech;</a>
+<a name="201"><span class="lineNum">     201 </span>            :     class Csch;</a>
+<a name="202"><span class="lineNum">     202 </span>            :     class Asinh;</a>
+<a name="203"><span class="lineNum">     203 </span>            :     class Acosh;</a>
+<a name="204"><span class="lineNum">     204 </span>            :     class Atanh;</a>
+<a name="205"><span class="lineNum">     205 </span>            :     class Acoth;</a>
+<a name="206"><span class="lineNum">     206 </span>            :     class Asech;</a>
+<a name="207"><span class="lineNum">     207 </span>            :     class Acsch;</a>
+<a name="208"><span class="lineNum">     208 </span>            : };</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : class LEPTON_EXPORT Operation::Constant : public Operation {</a>
+<a name="211"><span class="lineNum">     211 </span>            : public:</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">    2017868 :     Constant(double value) : value(value) {</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        243 :     std::string getName() const {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        243 :         std::stringstream name;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        243 :         name &lt;&lt; value;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        243 :         return name.str();</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        243 :     }</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      27219 :     Id getId() const {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      27219 :         return CONSTANT;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">    2029059 :     int getNumArguments() const {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">    2029059 :         return 0;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :     }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">    2145791 :     Operation* clone() const {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">    2145791 :         return new Constant(value);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">    2019547 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">    2019547 :         return value;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="232"><span class="lineNum">     232 </span>            :     double getValue() const {</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       6457 :         return value;</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     }</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      31550 :     bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      31550 :         const Constant* o = dynamic_cast&lt;const Constant*&gt;(&amp;op);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      31550 :         return (o == NULL || o-&gt;value != value);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :     }</a>
+<a name="239"><span class="lineNum">     239 </span>            : private:</a>
+<a name="240"><span class="lineNum">     240 </span>            :     double value;</a>
+<a name="241"><span class="lineNum">     241 </span>            : };</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : class LEPTON_EXPORT Operation::Variable : public Operation {</a>
+<a name="244"><span class="lineNum">     244 </span>            : public:</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">     243504 :     Variable(const std::string&amp; name) : name(name) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">     243504 :     }</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       9018 :     std::string getName() const {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       9018 :         return name;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :     }</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      30578 :     Id getId() const {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">      30578 :         return VARIABLE;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       9142 :     int getNumArguments() const {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       9142 :         return 0;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">     240199 :     Operation* clone() const {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">     480398 :         return new Variable(name);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :     }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         30 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         30 :         std::map&lt;std::string, double&gt;::const_iterator iter = variables.find(name);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         30 :         if (iter == variables.end())</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         44 :             throw Exception(&quot;No value specified for variable &quot;+name);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          8 :         return iter-&gt;second;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :     }</a>
+<a name="265"><span class="lineNum">     265 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">      45589 :     bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">      45589 :         const Variable* o = dynamic_cast&lt;const Variable*&gt;(&amp;op);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      45589 :         return (o == NULL || o-&gt;name != name);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     }</a>
+<a name="270"><span class="lineNum">     270 </span>            : private:</a>
+<a name="271"><span class="lineNum">     271 </span>            :     std::string name;</a>
+<a name="272"><span class="lineNum">     272 </span>            : };</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : class LEPTON_EXPORT Operation::Custom : public Operation {</a>
+<a name="275"><span class="lineNum">     275 </span>            : public:</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     Custom(const std::string&amp; name, CustomFunction* function) : name(name), function(function), isDerivative(false), derivOrder(function-&gt;getNumArguments(), 0) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     Custom(const std::string&amp; name, CustomFunction* function, const std::vector&lt;int&gt;&amp; derivOrder) : name(name), function(function), isDerivative(false), derivOrder(derivOrder) {</a>
+<a name="279"><span class="lineNum">     279 </span>            :         for (int order : derivOrder)</a>
+<a name="280"><span class="lineNum">     280 </span>            :             if (order != 0)</a>
+<a name="281"><span class="lineNum">     281 </span>            :                 isDerivative = true;</a>
+<a name="282"><span class="lineNum">     282 </span>            :     }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :     Custom(const Custom&amp; base, int derivIndex) : name(base.name), function(base.function-&gt;clone()), isDerivative(true), derivOrder(base.derivOrder) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :         derivOrder[derivIndex]++;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :     ~Custom() {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :         delete function;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :     std::string getName() const {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :         return name;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :     }</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     Id getId() const {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :         return CUSTOM;</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :     }</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     int getNumArguments() const {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :         return function-&gt;getNumArguments();</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :     }</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :     Operation* clone() const {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :         Custom* clone = new Custom(name, function-&gt;clone());</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :         clone-&gt;isDerivative = isDerivative;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :         clone-&gt;derivOrder = derivOrder;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :         return clone;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :         if (isDerivative)</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 :             return function-&gt;evaluateDerivative(args, &amp;derivOrder[0]);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :         return function-&gt;evaluate(args);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :     }</a>
+<a name="309"><span class="lineNum">     309 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="310"><span class="lineNum">     310 </span>            :     const std::vector&lt;int&gt;&amp; getDerivOrder() const {</a>
+<a name="311"><span class="lineNum">     311 </span>            :         return derivOrder;</a>
+<a name="312"><span class="lineNum">     312 </span>            :     }</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :         const Custom* o = dynamic_cast&lt;const Custom*&gt;(&amp;op);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :         return (o == NULL || o-&gt;name != name || o-&gt;isDerivative != isDerivative || o-&gt;derivOrder != derivOrder);</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :     }</a>
+<a name="317"><span class="lineNum">     317 </span>            : private:</a>
+<a name="318"><span class="lineNum">     318 </span>            :     std::string name;</a>
+<a name="319"><span class="lineNum">     319 </span>            :     CustomFunction* function;</a>
+<a name="320"><span class="lineNum">     320 </span>            :     bool isDerivative;</a>
+<a name="321"><span class="lineNum">     321 </span>            :     std::vector&lt;int&gt; derivOrder;</a>
+<a name="322"><span class="lineNum">     322 </span>            : };</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : class LEPTON_EXPORT Operation::Add : public Operation {</a>
+<a name="325"><span class="lineNum">     325 </span>            : public:</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       1593 :     Add() {</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     }</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        614 :     std::string getName() const {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        614 :         return &quot;+&quot;;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">      40244 :     Id getId() const {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      40244 :         return ADD;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       7429 :     int getNumArguments() const {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">       7429 :         return 2;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :     }</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      41274 :     Operation* clone() const {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      41274 :         return new Add();</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :     }</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">        413 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        413 :         return args[0]+args[1];</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :     }</a>
+<a name="343"><span class="lineNum">     343 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        614 :     bool isInfixOperator() const {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        614 :         return true;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :     }</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       3592 :     bool isSymmetric() const {</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       3592 :         return true;</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :     }</a>
+<a name="350"><span class="lineNum">     350 </span>            : };</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            : class LEPTON_EXPORT Operation::Subtract : public Operation {</a>
+<a name="353"><span class="lineNum">     353 </span>            : public:</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">       1134 :     Subtract() {</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :     }</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        431 :     std::string getName() const {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        431 :         return &quot;-&quot;;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :     }</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">      25401 :     Id getId() const {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">      25401 :         return SUBTRACT;</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :     }</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       6657 :     int getNumArguments() const {</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       6657 :         return 2;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :     }</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">      31327 :     Operation* clone() const {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">      31327 :         return new Subtract();</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :     }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">       1284 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">       1284 :         return args[0]-args[1];</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :     }</a>
+<a name="371"><span class="lineNum">     371 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        431 :     bool isInfixOperator() const {</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        431 :         return true;</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :     }</a>
+<a name="375"><span class="lineNum">     375 </span>            : };</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : class LEPTON_EXPORT Operation::Multiply : public Operation {</a>
+<a name="378"><span class="lineNum">     378 </span>            : public:</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">       4712 :     Multiply() {</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :     }</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        838 :     std::string getName() const {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        838 :         return &quot;*&quot;;</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     }</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">      83355 :     Id getId() const {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      83355 :         return MULTIPLY;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :     }</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">      18815 :     int getNumArguments() const {</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">      18815 :         return 2;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :     }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">     115826 :     Operation* clone() const {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">     115826 :         return new Multiply();</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :     }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       1441 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       1441 :         return args[0]*args[1];</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :     }</a>
+<a name="396"><span class="lineNum">     396 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        838 :     bool isInfixOperator() const {</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        838 :         return true;</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :     }</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       6290 :     bool isSymmetric() const {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       6290 :         return true;</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :     }</a>
+<a name="403"><span class="lineNum">     403 </span>            : };</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            : class LEPTON_EXPORT Operation::Divide : public Operation {</a>
+<a name="406"><span class="lineNum">     406 </span>            : public:</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">        554 :     Divide() {</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :     }</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         50 :     std::string getName() const {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         50 :         return &quot;/&quot;;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :     }</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">       5521 :     Id getId() const {</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">       5521 :         return DIVIDE;</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :     }</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">       1721 :     int getNumArguments() const {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       1721 :         return 2;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :     }</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">      11742 :     Operation* clone() const {</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      11742 :         return new Divide();</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :     }</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        668 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        668 :         return args[0]/args[1];</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :     }</a>
+<a name="424"><span class="lineNum">     424 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         50 :     bool isInfixOperator() const {</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         50 :         return true;</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :     }</a>
+<a name="428"><span class="lineNum">     428 </span>            : };</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span>            : class LEPTON_EXPORT Operation::Power : public Operation {</a>
+<a name="431"><span class="lineNum">     431 </span>            : public:</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        440 :     Power() {</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :     }</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          4 :         return &quot;^&quot;;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :     }</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">       4509 :     Id getId() const {</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">       4509 :         return POWER;</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     }</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">       1168 :     int getNumArguments() const {</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">       1168 :         return 2;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :     }</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">       9169 :     Operation* clone() const {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">       9169 :         return new Power();</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :     }</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        204 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        204 :         return std::pow(args[0], args[1]);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :     }</a>
+<a name="449"><span class="lineNum">     449 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          4 :     bool isInfixOperator() const {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">          4 :         return true;</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :     }</a>
+<a name="453"><span class="lineNum">     453 </span>            : };</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            : class LEPTON_EXPORT Operation::Negate : public Operation {</a>
+<a name="456"><span class="lineNum">     456 </span>            : public:</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        357 :     Negate() {</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :     }</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         70 :     std::string getName() const {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         70 :         return &quot;-&quot;;</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :     }</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">      12854 :     Id getId() const {</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">      12854 :         return NEGATE;</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :     }</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">       2336 :     int getNumArguments() const {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">       2336 :         return 1;</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :     }</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">      23162 :     Operation* clone() const {</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">      23162 :         return new Negate();</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :     }</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">       1439 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">       1439 :         return -args[0];</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :     }</a>
+<a name="474"><span class="lineNum">     474 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="475"><span class="lineNum">     475 </span>            : };</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span>            : class LEPTON_EXPORT Operation::Sqrt : public Operation {</a>
+<a name="478"><span class="lineNum">     478 </span>            : public:</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        122 :     Sqrt() {</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :     }</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         83 :     std::string getName() const {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         83 :         return &quot;sqrt&quot;;</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :     }</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">       4653 :     Id getId() const {</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">       4653 :         return SQRT;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :     }</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        797 :     int getNumArguments() const {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">        797 :         return 1;</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :     }</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">       5491 :     Operation* clone() const {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">       5491 :         return new Sqrt();</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :     }</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">       1111 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">       1111 :         return std::sqrt(args[0]);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     }</a>
+<a name="496"><span class="lineNum">     496 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="497"><span class="lineNum">     497 </span>            : };</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            : class LEPTON_EXPORT Operation::Exp : public Operation {</a>
+<a name="500"><span class="lineNum">     500 </span>            : public:</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         34 :     Exp() {</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :     }</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         28 :     std::string getName() const {</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         28 :         return &quot;exp&quot;;</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     }</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">       1495 :     Id getId() const {</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">       1495 :         return EXP;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :     }</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">        308 :     int getNumArguments() const {</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">        308 :         return 1;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :     }</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">        924 :     Operation* clone() const {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">        924 :         return new Exp();</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :     }</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        405 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        405 :         return std::exp(args[0]);</span></a>
+<a name="517"><span class="lineNum">     517 </span>            :     }</a>
+<a name="518"><span class="lineNum">     518 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="519"><span class="lineNum">     519 </span>            : };</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            : class LEPTON_EXPORT Operation::Log : public Operation {</a>
+<a name="522"><span class="lineNum">     522 </span>            : public:</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">        116 :     Log() {</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :     }</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">          2 :         return &quot;log&quot;;</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :     }</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">       1832 :     Id getId() const {</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">       1832 :         return LOG;</span></a>
+<a name="530"><span class="lineNum">     530 </span>            :     }</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">        442 :     int getNumArguments() const {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        442 :         return 1;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :     }</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">       3637 :     Operation* clone() const {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">       3637 :         return new Log();</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :     }</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">        108 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">        108 :         return std::log(args[0]);</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :     }</a>
+<a name="540"><span class="lineNum">     540 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="541"><span class="lineNum">     541 </span>            : };</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            : class LEPTON_EXPORT Operation::Sin : public Operation {</a>
+<a name="544"><span class="lineNum">     544 </span>            : public:</a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">        315 :     Sin() {</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :     }</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">        734 :     std::string getName() const {</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        734 :         return &quot;sin&quot;;</span></a>
+<a name="549"><span class="lineNum">     549 </span>            :     }</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">      49117 :     Id getId() const {</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">      49117 :         return SIN;</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :     }</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">       3286 :     int getNumArguments() const {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">       3286 :         return 1;</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :     }</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">      52638 :     Operation* clone() const {</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">      52638 :         return new Sin();</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :     }</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">        206 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">        206 :         return std::sin(args[0]);</span></a>
+<a name="561"><span class="lineNum">     561 </span>            :     }</a>
+<a name="562"><span class="lineNum">     562 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="563"><span class="lineNum">     563 </span>            : };</a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span>            : class LEPTON_EXPORT Operation::Cos : public Operation {</a>
+<a name="566"><span class="lineNum">     566 </span>            : public:</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">       1319 :     Cos() {</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :     }</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">       1118 :     std::string getName() const {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">       1118 :         return &quot;cos&quot;;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :     }</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">      64872 :     Id getId() const {</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">      64872 :         return COS;</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :     }</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">       5835 :     int getNumArguments() const {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">       5835 :         return 1;</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :     }</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">      76543 :     Operation* clone() const {</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">      76543 :         return new Cos();</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :     }</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">        204 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">        204 :         return std::cos(args[0]);</span></a>
+<a name="583"><span class="lineNum">     583 </span>            :     }</a>
+<a name="584"><span class="lineNum">     584 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="585"><span class="lineNum">     585 </span>            : };</a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span>            : class LEPTON_EXPORT Operation::Sec : public Operation {</a>
+<a name="588"><span class="lineNum">     588 </span>            : public:</a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">          8 :     Sec() {</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :     }</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">          6 :     std::string getName() const {</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">          6 :         return &quot;sec&quot;;</span></a>
+<a name="593"><span class="lineNum">     593 </span>            :     }</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">        214 :     Id getId() const {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">        214 :         return SEC;</span></a>
+<a name="596"><span class="lineNum">     596 </span>            :     }</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">         54 :     int getNumArguments() const {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         54 :         return 1;</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :     }</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">        184 :     Operation* clone() const {</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">        184 :         return new Sec();</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :     }</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">        606 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        606 :         return 1.0/std::cos(args[0]);</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :     }</a>
+<a name="606"><span class="lineNum">     606 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="607"><span class="lineNum">     607 </span>            : };</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            : class LEPTON_EXPORT Operation::Csc : public Operation {</a>
+<a name="610"><span class="lineNum">     610 </span>            : public:</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">          8 :     Csc() {</span></a>
+<a name="612"><span class="lineNum">     612 </span>            :     }</a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">          6 :     std::string getName() const {</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">          6 :         return &quot;csc&quot;;</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :     }</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">        224 :     Id getId() const {</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">        224 :         return CSC;</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :     }</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         54 :     int getNumArguments() const {</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         54 :         return 1;</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :     }</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        240 :     Operation* clone() const {</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        240 :         return new Csc();</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :     }</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">        606 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        606 :         return 1.0/std::sin(args[0]);</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :     }</a>
+<a name="628"><span class="lineNum">     628 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="629"><span class="lineNum">     629 </span>            : };</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            : class LEPTON_EXPORT Operation::Tan : public Operation {</a>
+<a name="632"><span class="lineNum">     632 </span>            : public:</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">          6 :     Tan() {</span></a>
+<a name="634"><span class="lineNum">     634 </span>            :     }</a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">          4 :         return &quot;tan&quot;;</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :     }</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">        140 :     Id getId() const {</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">        140 :         return TAN;</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :     }</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">         36 :     int getNumArguments() const {</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">         36 :         return 1;</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :     }</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">        104 :     Operation* clone() const {</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">        104 :         return new Tan();</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :     }</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">        202 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">        202 :         return std::tan(args[0]);</span></a>
+<a name="649"><span class="lineNum">     649 </span>            :     }</a>
+<a name="650"><span class="lineNum">     650 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="651"><span class="lineNum">     651 </span>            : };</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            : class LEPTON_EXPORT Operation::Cot : public Operation {</a>
+<a name="654"><span class="lineNum">     654 </span>            : public:</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">          6 :     Cot() {</span></a>
+<a name="656"><span class="lineNum">     656 </span>            :     }</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">          4 :         return &quot;cot&quot;;</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :     }</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">        146 :     Id getId() const {</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">        146 :         return COT;</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :     }</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         36 :     int getNumArguments() const {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         36 :         return 1;</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :     }</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">        134 :     Operation* clone() const {</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">        134 :         return new Cot();</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :     }</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">        404 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">        404 :         return 1.0/std::tan(args[0]);</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :     }</a>
+<a name="672"><span class="lineNum">     672 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="673"><span class="lineNum">     673 </span>            : };</a>
+<a name="674"><span class="lineNum">     674 </span>            : </a>
+<a name="675"><span class="lineNum">     675 </span>            : class LEPTON_EXPORT Operation::Asin : public Operation {</a>
+<a name="676"><span class="lineNum">     676 </span>            : public:</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         38 :     Asin() {</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :     }</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">          2 :         return &quot;asin&quot;;</span></a>
+<a name="681"><span class="lineNum">     681 </span>            :     }</a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         46 :     Id getId() const {</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">         46 :         return ASIN;</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :     }</a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">         20 :     int getNumArguments() const {</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         20 :         return 1;</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :     }</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         34 :     Operation* clone() const {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">         34 :         return new Asin();</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :     }</a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">        101 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">        101 :         return std::asin(args[0]);</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :     }</a>
+<a name="694"><span class="lineNum">     694 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="695"><span class="lineNum">     695 </span>            : };</a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span>            : class LEPTON_EXPORT Operation::Acos : public Operation {</a>
+<a name="698"><span class="lineNum">     698 </span>            : public:</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         38 :     Acos() {</span></a>
+<a name="700"><span class="lineNum">     700 </span>            :     }</a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">          2 :         return &quot;acos&quot;;</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :     }</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">         46 :     Id getId() const {</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         46 :         return ACOS;</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :     }</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         20 :     int getNumArguments() const {</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">         20 :         return 1;</span></a>
+<a name="709"><span class="lineNum">     709 </span>            :     }</a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">         34 :     Operation* clone() const {</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">         34 :         return new Acos();</span></a>
+<a name="712"><span class="lineNum">     712 </span>            :     }</a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">        101 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">        101 :         return std::acos(args[0]);</span></a>
+<a name="715"><span class="lineNum">     715 </span>            :     }</a>
+<a name="716"><span class="lineNum">     716 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="717"><span class="lineNum">     717 </span>            : };</a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            : class LEPTON_EXPORT Operation::Atan : public Operation {</a>
+<a name="720"><span class="lineNum">     720 </span>            : public:</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">         38 :     Atan() {</span></a>
+<a name="722"><span class="lineNum">     722 </span>            :     }</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">          2 :         return &quot;atan&quot;;</span></a>
+<a name="725"><span class="lineNum">     725 </span>            :     }</a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">         46 :     Id getId() const {</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">         46 :         return ATAN;</span></a>
+<a name="728"><span class="lineNum">     728 </span>            :     }</a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">         20 :     int getNumArguments() const {</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">         20 :         return 1;</span></a>
+<a name="731"><span class="lineNum">     731 </span>            :     }</a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">         34 :     Operation* clone() const {</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">         34 :         return new Atan();</span></a>
+<a name="734"><span class="lineNum">     734 </span>            :     }</a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">        101 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">        101 :         return std::atan(args[0]);</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :     }</a>
+<a name="738"><span class="lineNum">     738 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="739"><span class="lineNum">     739 </span>            : };</a>
+<a name="740"><span class="lineNum">     740 </span>            : </a>
+<a name="741"><span class="lineNum">     741 </span>            : class LEPTON_EXPORT Operation::Atan2 : public Operation {</a>
+<a name="742"><span class="lineNum">     742 </span>            : public:</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">        136 :     Atan2() {</span></a>
+<a name="744"><span class="lineNum">     744 </span>            :     }</a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">          8 :     std::string getName() const {</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">          8 :         return &quot;atan2&quot;;</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :     }</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">        160 :     Id getId() const {</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">        160 :         return ATAN2;</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :     }</a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">         88 :     int getNumArguments() const {</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">         88 :         return 2;</span></a>
+<a name="753"><span class="lineNum">     753 </span>            :     }</a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">        120 :     Operation* clone() const {</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">        120 :         return new Atan2();</span></a>
+<a name="756"><span class="lineNum">     756 </span>            :     }</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">        404 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">        404 :         return std::atan2(args[0], args[1]);</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :     }</a>
+<a name="760"><span class="lineNum">     760 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="761"><span class="lineNum">     761 </span>            : };</a>
+<a name="762"><span class="lineNum">     762 </span>            : </a>
+<a name="763"><span class="lineNum">     763 </span>            : class LEPTON_EXPORT Operation::Sinh : public Operation {</a>
+<a name="764"><span class="lineNum">     764 </span>            : public:</a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">          6 :     Sinh() {</span></a>
+<a name="766"><span class="lineNum">     766 </span>            :     }</a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">          4 :         return &quot;sinh&quot;;</span></a>
+<a name="769"><span class="lineNum">     769 </span>            :     }</a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">         88 :     Id getId() const {</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">         88 :         return SINH;</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :     }</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">         36 :     int getNumArguments() const {</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">         36 :         return 1;</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :     }</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">         78 :     Operation* clone() const {</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">         78 :         return new Sinh();</span></a>
+<a name="778"><span class="lineNum">     778 </span>            :     }</a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">        202 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">        202 :         return std::sinh(args[0]);</span></a>
+<a name="781"><span class="lineNum">     781 </span>            :     }</a>
+<a name="782"><span class="lineNum">     782 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="783"><span class="lineNum">     783 </span>            : };</a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            : class LEPTON_EXPORT Operation::Cosh : public Operation {</a>
+<a name="786"><span class="lineNum">     786 </span>            : public:</a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">          6 :     Cosh() {</span></a>
+<a name="788"><span class="lineNum">     788 </span>            :     }</a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">          4 :         return &quot;cosh&quot;;</span></a>
+<a name="791"><span class="lineNum">     791 </span>            :     }</a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">         88 :     Id getId() const {</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">         88 :         return COSH;</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :     }</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">         36 :     int getNumArguments() const {</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">         36 :         return 1;</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :     }</a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">         78 :     Operation* clone() const {</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">         78 :         return new Cosh();</span></a>
+<a name="800"><span class="lineNum">     800 </span>            :     }</a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">        202 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">        202 :         return std::cosh(args[0]);</span></a>
+<a name="803"><span class="lineNum">     803 </span>            :     }</a>
+<a name="804"><span class="lineNum">     804 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="805"><span class="lineNum">     805 </span>            : };</a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span>            : class LEPTON_EXPORT Operation::Tanh : public Operation {</a>
+<a name="808"><span class="lineNum">     808 </span>            : public:</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">          8 :     Tanh() {</span></a>
+<a name="810"><span class="lineNum">     810 </span>            :     }</a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">          6 :     std::string getName() const {</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">          6 :         return &quot;tanh&quot;;</span></a>
+<a name="813"><span class="lineNum">     813 </span>            :     }</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">        228 :     Id getId() const {</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">        228 :         return TANH;</span></a>
+<a name="816"><span class="lineNum">     816 </span>            :     }</a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">         54 :     int getNumArguments() const {</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">         54 :         return 1;</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :     }</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">        242 :     Operation* clone() const {</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">        242 :         return new Tanh();</span></a>
+<a name="822"><span class="lineNum">     822 </span>            :     }</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">        303 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        303 :         return std::tanh(args[0]);</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="827"><span class="lineNum">     827 </span>            : };</a>
+<a name="828"><span class="lineNum">     828 </span>            : </a>
+<a name="829"><span class="lineNum">     829 </span>            : class LEPTON_EXPORT Operation::Erf : public Operation {</a>
+<a name="830"><span class="lineNum">     830 </span>            : public:</a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">         34 :     Erf() {</span></a>
+<a name="832"><span class="lineNum">     832 </span>            :     }</a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">          2 :         return &quot;erf&quot;;</span></a>
+<a name="835"><span class="lineNum">     835 </span>            :     }</a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">         40 :     Id getId() const {</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">         40 :         return ERF;</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :     }</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">         18 :     int getNumArguments() const {</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">         18 :         return 1;</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :     }</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">         30 :     Operation* clone() const {</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         30 :         return new Erf();</span></a>
+<a name="844"><span class="lineNum">     844 </span>            :     }</a>
+<a name="845"><span class="lineNum">     845 </span>            :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const;</a>
+<a name="846"><span class="lineNum">     846 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="847"><span class="lineNum">     847 </span>            : };</a>
+<a name="848"><span class="lineNum">     848 </span>            : </a>
+<a name="849"><span class="lineNum">     849 </span>            : class LEPTON_EXPORT Operation::Erfc : public Operation {</a>
+<a name="850"><span class="lineNum">     850 </span>            : public:</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">         34 :     Erfc() {</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :     }</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">          2 :         return &quot;erfc&quot;;</span></a>
+<a name="855"><span class="lineNum">     855 </span>            :     }</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">         40 :     Id getId() const {</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">         40 :         return ERFC;</span></a>
+<a name="858"><span class="lineNum">     858 </span>            :     }</a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">         18 :     int getNumArguments() const {</span></a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">         18 :         return 1;</span></a>
+<a name="861"><span class="lineNum">     861 </span>            :     }</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">         30 :     Operation* clone() const {</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">         30 :         return new Erfc();</span></a>
+<a name="864"><span class="lineNum">     864 </span>            :     }</a>
+<a name="865"><span class="lineNum">     865 </span>            :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const;</a>
+<a name="866"><span class="lineNum">     866 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="867"><span class="lineNum">     867 </span>            : };</a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span>            : class LEPTON_EXPORT Operation::Step : public Operation {</a>
+<a name="870"><span class="lineNum">     870 </span>            : public:</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">         39 :     Step() {</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :     }</a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">         17 :     std::string getName() const {</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">         17 :         return &quot;step&quot;;</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :     }</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">       4261 :     Id getId() const {</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">       4261 :         return STEP;</span></a>
+<a name="878"><span class="lineNum">     878 </span>            :     }</a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">        361 :     int getNumArguments() const {</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">        361 :         return 1;</span></a>
+<a name="881"><span class="lineNum">     881 </span>            :     }</a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">       2422 :     Operation* clone() const {</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">       2422 :         return new Step();</span></a>
+<a name="884"><span class="lineNum">     884 </span>            :     }</a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">        606 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">        606 :         return (args[0] &gt;= 0.0 ? 1.0 : 0.0);</span></a>
+<a name="887"><span class="lineNum">     887 </span>            :     }</a>
+<a name="888"><span class="lineNum">     888 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="889"><span class="lineNum">     889 </span>            : };</a>
+<a name="890"><span class="lineNum">     890 </span>            : </a>
+<a name="891"><span class="lineNum">     891 </span>            : class LEPTON_EXPORT Operation::Delta : public Operation {</a>
+<a name="892"><span class="lineNum">     892 </span>            : public:</a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">         17 :     Delta() {</span></a>
+<a name="894"><span class="lineNum">     894 </span>            :     }</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">          8 :     std::string getName() const {</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">          8 :         return &quot;delta&quot;;</span></a>
+<a name="897"><span class="lineNum">     897 </span>            :     }</a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">       2395 :     Id getId() const {</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">       2395 :         return DELTA;</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :     }</a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">        182 :     int getNumArguments() const {</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">        182 :         return 1;</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :     }</a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">       1107 :     Operation* clone() const {</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">       1107 :         return new Delta();</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :     }</a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">        202 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">        202 :         return (args[0] == 0.0 ? 1.0/0.0 : 0.0);</span></a>
+<a name="909"><span class="lineNum">     909 </span>            :     }</a>
+<a name="910"><span class="lineNum">     910 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="911"><span class="lineNum">     911 </span>            : };</a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span>            : class LEPTON_EXPORT Operation::Nandelta : public Operation {</a>
+<a name="914"><span class="lineNum">     914 </span>            : public:</a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">          8 :     Nandelta() {</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :     }</a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">          6 :     std::string getName() const {</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">          6 :         return &quot;nandelta&quot;;</span></a>
+<a name="919"><span class="lineNum">     919 </span>            :     }</a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">        120 :     Id getId() const {</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">        120 :         return NANDELTA;</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :     }</a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">         50 :     int getNumArguments() const {</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">         50 :         return 1;</span></a>
+<a name="925"><span class="lineNum">     925 </span>            :     }</a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">         90 :     Operation* clone() const {</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">         90 :         return new Nandelta();</span></a>
+<a name="928"><span class="lineNum">     928 </span>            :     }</a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">        303 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">        303 :         return (args[0] == 0.0 ? std::numeric_limits&lt;double&gt;::quiet_NaN() : 0.0);</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :     }</a>
+<a name="932"><span class="lineNum">     932 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="933"><span class="lineNum">     933 </span>            : };</a>
+<a name="934"><span class="lineNum">     934 </span>            : </a>
+<a name="935"><span class="lineNum">     935 </span>            : class LEPTON_EXPORT Operation::Square : public Operation {</a>
+<a name="936"><span class="lineNum">     936 </span>            : public:</a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">        378 :     Square() {</span></a>
+<a name="938"><span class="lineNum">     938 </span>            :     }</a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">        374 :     std::string getName() const {</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">        374 :         return &quot;square&quot;;</span></a>
+<a name="941"><span class="lineNum">     941 </span>            :     }</a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">      19443 :     Id getId() const {</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">      19443 :         return SQUARE;</span></a>
+<a name="944"><span class="lineNum">     944 </span>            :     }</a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">       2333 :     int getNumArguments() const {</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">       2333 :         return 1;</span></a>
+<a name="947"><span class="lineNum">     947 </span>            :     }</a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">      20360 :     Operation* clone() const {</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">      20360 :         return new Square();</span></a>
+<a name="950"><span class="lineNum">     950 </span>            :     }</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">       3155 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">       3155 :         return args[0]*args[0];</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :     }</a>
+<a name="954"><span class="lineNum">     954 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="955"><span class="lineNum">     955 </span>            : };</a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            : class LEPTON_EXPORT Operation::Cube : public Operation {</a>
+<a name="958"><span class="lineNum">     958 </span>            : public:</a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">       1107 :     Cube() {</span></a>
+<a name="960"><span class="lineNum">     960 </span>            :     }</a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">         23 :     std::string getName() const {</span></a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">         23 :         return &quot;cube&quot;;</span></a>
+<a name="963"><span class="lineNum">     963 </span>            :     }</a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">       1405 :     Id getId() const {</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">       1405 :         return CUBE;</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :     }</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">        256 :     int getNumArguments() const {</span></a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">        256 :         return 1;</span></a>
+<a name="969"><span class="lineNum">     969 </span>            :     }</a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">       1055 :     Operation* clone() const {</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">       1055 :         return new Cube();</span></a>
+<a name="972"><span class="lineNum">     972 </span>            :     }</a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">        202 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">        202 :         return args[0]*args[0]*args[0];</span></a>
+<a name="975"><span class="lineNum">     975 </span>            :     }</a>
+<a name="976"><span class="lineNum">     976 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="977"><span class="lineNum">     977 </span>            : };</a>
+<a name="978"><span class="lineNum">     978 </span>            : </a>
+<a name="979"><span class="lineNum">     979 </span>            : class LEPTON_EXPORT Operation::Reciprocal : public Operation {</a>
+<a name="980"><span class="lineNum">     980 </span>            : public:</a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">         93 :     Reciprocal() {</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :     }</a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">         81 :     std::string getName() const {</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">         81 :         return &quot;recip&quot;;</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :     }</a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">       4059 :     Id getId() const {</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">       4059 :         return RECIPROCAL;</span></a>
+<a name="988"><span class="lineNum">     988 </span>            :     }</a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">        834 :     int getNumArguments() const {</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">        834 :         return 1;</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :     }</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">       4372 :     Operation* clone() const {</span></a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">       4372 :         return new Reciprocal();</span></a>
+<a name="994"><span class="lineNum">     994 </span>            :     }</a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">       2121 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">       2121 :         return 1.0/args[0];</span></a>
+<a name="997"><span class="lineNum">     997 </span>            :     }</a>
+<a name="998"><span class="lineNum">     998 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="999"><span class="lineNum">     999 </span>            : };</a>
+<a name="1000"><span class="lineNum">    1000 </span>            : </a>
+<a name="1001"><span class="lineNum">    1001 </span>            : class LEPTON_EXPORT Operation::AddConstant : public Operation {</a>
+<a name="1002"><span class="lineNum">    1002 </span>            : public:</a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">        534 :     AddConstant(double value) : value(value) {</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :     }</a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">        792 :     std::string getName() const {</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">        792 :         std::stringstream name;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">        792 :         name &lt;&lt; value &lt;&lt; &quot;+&quot;;</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineCov">        792 :         return name.str();</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">        792 :     }</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">      11904 :     Id getId() const {</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">      11904 :         return ADD_CONSTANT;</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :     }</a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">       3461 :     int getNumArguments() const {</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">       3461 :         return 1;</span></a>
+<a name="1015"><span class="lineNum">    1015 </span>            :     }</a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">      37127 :     Operation* clone() const {</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">      37127 :         return new AddConstant(value);</span></a>
+<a name="1018"><span class="lineNum">    1018 </span>            :     }</a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">       2705 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">       2705 :         return args[0]+value;</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            :     }</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :     double getValue() const {</a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">        846 :         return value;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :     }</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">      10039 :     bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">      10039 :         const AddConstant* o = dynamic_cast&lt;const AddConstant*&gt;(&amp;op);</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">      10039 :         return (o == NULL || o-&gt;value != value);</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            :     }</a>
+<a name="1030"><span class="lineNum">    1030 </span>            : private:</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :     double value;</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : };</a>
+<a name="1033"><span class="lineNum">    1033 </span>            : </a>
+<a name="1034"><span class="lineNum">    1034 </span>            : class LEPTON_EXPORT Operation::MultiplyConstant : public Operation {</a>
+<a name="1035"><span class="lineNum">    1035 </span>            : public:</a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">       2135 :     MultiplyConstant(double value) : value(value) {</span></a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     }</a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">       1412 :     std::string getName() const {</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">       1412 :         std::stringstream name;</span></a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">       1412 :         name &lt;&lt; value &lt;&lt; &quot;*&quot;;</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">       1412 :         return name.str();</span></a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">       1412 :     }</span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">      54125 :     Id getId() const {</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">      54125 :         return MULTIPLY_CONSTANT;</span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     }</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">      11256 :     int getNumArguments() const {</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">      11256 :         return 1;</span></a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     }</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">      55327 :     Operation* clone() const {</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">      55327 :         return new MultiplyConstant(value);</span></a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     }</a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">       2626 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">       2626 :         return args[0]*value;</span></a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     }</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :     double getValue() const {</a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">       3550 :         return value;</span></a>
+<a name="1058"><span class="lineNum">    1058 </span>            :     }</a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">      35217 :     bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">      35217 :         const MultiplyConstant* o = dynamic_cast&lt;const MultiplyConstant*&gt;(&amp;op);</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">      35217 :         return (o == NULL || o-&gt;value != value);</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     }</a>
+<a name="1063"><span class="lineNum">    1063 </span>            : private:</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     double value;</a>
+<a name="1065"><span class="lineNum">    1065 </span>            : };</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : </a>
+<a name="1067"><span class="lineNum">    1067 </span>            : class LEPTON_EXPORT Operation::PowerConstant : public Operation {</a>
+<a name="1068"><span class="lineNum">    1068 </span>            : public:</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">       2298 :     PowerConstant(double value) : value(value) {</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">       2298 :         intValue = (int) value;</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         69 :         isIntPower = (intValue == value);</span></a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     }</a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">         37 :     std::string getName() const {</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">         37 :         std::stringstream name;</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">         37 :         name &lt;&lt; &quot;^&quot; &lt;&lt; value;</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">         37 :         return name.str();</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">         37 :     }</span></a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">       2047 :     Id getId() const {</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">       2047 :         return POWER_CONSTANT;</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     }</a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">        454 :     int getNumArguments() const {</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">        454 :         return 1;</span></a>
+<a name="1083"><span class="lineNum">    1083 </span>            :     }</a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">       2229 :     Operation* clone() const {</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">       2229 :         return new PowerConstant(value);</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            :     }</a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">   10691410 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">   10691410 :         if (isIntPower) {</span></a>
+<a name="1089"><span class="lineNum">    1089 </span>            :             // Integer powers can be computed much more quickly by repeated multiplication.</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :             </a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">   10687191 :             int exponent = intValue;</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">   10687191 :             double base = args[0];</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">   10687191 :             if (exponent &lt; 0) {</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineCov">        804 :                 exponent = -exponent;</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">        804 :                 base = 1.0/base;</span></a>
+<a name="1096"><span class="lineNum">    1096 </span>            :             }</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :             double result = 1.0;</a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">   42750671 :             while (exponent != 0) {</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">   32063480 :                 if ((exponent&amp;1) == 1)</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">   23423887 :                     result *= base;</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">   32063480 :                 base *= base;</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">   32063480 :                 exponent = exponent&gt;&gt;1;</span></a>
+<a name="1103"><span class="lineNum">    1103 </span>            :            }</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :            return result;</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :         }</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :         else</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">       4219 :         return std::pow(args[0], value);</span></a>
+<a name="1108"><span class="lineNum">    1108 </span>            :     }</a>
+<a name="1109"><span class="lineNum">    1109 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :     double getValue() const {</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :         return value;</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :     }</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">        572 :     bool operator!=(const Operation&amp; op) const {</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">        572 :         const PowerConstant* o = dynamic_cast&lt;const PowerConstant*&gt;(&amp;op);</span></a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">        572 :         return (o == NULL || o-&gt;value != value);</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            :     }</a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineCov">         74 :     bool isInfixOperator() const {</span></a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">         74 :         return true;</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :     }</a>
+<a name="1120"><span class="lineNum">    1120 </span>            : private:</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     double value;</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     int intValue;</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :     bool isIntPower;</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : };</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : </a>
+<a name="1126"><span class="lineNum">    1126 </span>            : class LEPTON_EXPORT Operation::Min : public Operation {</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : public:</a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">         68 :     Min() {</span></a>
+<a name="1129"><span class="lineNum">    1129 </span>            :     }</a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">          4 :         return &quot;min&quot;;</span></a>
+<a name="1132"><span class="lineNum">    1132 </span>            :     }</a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">         80 :     Id getId() const {</span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">         80 :         return MIN;</span></a>
+<a name="1135"><span class="lineNum">    1135 </span>            :     }</a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">         44 :     int getNumArguments() const {</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">         44 :         return 2;</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     }</a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">         60 :     Operation* clone() const {</span></a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineCov">         60 :         return new Min();</span></a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     }</a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">        404 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1143"><span class="lineNum">    1143 </span>            :         // parens around (std::min) are workaround for horrible microsoft max/min macro trouble</a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">        404 :         return (std::min)(args[0], args[1]);</span></a>
+<a name="1145"><span class="lineNum">    1145 </span>            :     }</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1147"><span class="lineNum">    1147 </span>            : };</a>
+<a name="1148"><span class="lineNum">    1148 </span>            : </a>
+<a name="1149"><span class="lineNum">    1149 </span>            : class LEPTON_EXPORT Operation::Max : public Operation {</a>
+<a name="1150"><span class="lineNum">    1150 </span>            : public:</a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">         68 :     Max() {</span></a>
+<a name="1152"><span class="lineNum">    1152 </span>            :     }</a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineCov">          4 :     std::string getName() const {</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">          4 :         return &quot;max&quot;;</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :     }</a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">         80 :     Id getId() const {</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">         80 :         return MAX;</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :     }</a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineCov">         44 :     int getNumArguments() const {</span></a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">         44 :         return 2;</span></a>
+<a name="1161"><span class="lineNum">    1161 </span>            :     }</a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">         60 :     Operation* clone() const {</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">         60 :         return new Max();</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     }</a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">        404 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            :         // parens around (std::min) are workaround for horrible microsoft max/min macro trouble</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">        404 :         return (std::max)(args[0], args[1]);</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :     }</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1170"><span class="lineNum">    1170 </span>            : };</a>
+<a name="1171"><span class="lineNum">    1171 </span>            : </a>
+<a name="1172"><span class="lineNum">    1172 </span>            : class LEPTON_EXPORT Operation::Abs : public Operation {</a>
+<a name="1173"><span class="lineNum">    1173 </span>            : public:</a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineCov">         21 :     Abs() {</span></a>
+<a name="1175"><span class="lineNum">    1175 </span>            :     }</a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">         18 :     std::string getName() const {</span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">         18 :         return &quot;abs&quot;;</span></a>
+<a name="1178"><span class="lineNum">    1178 </span>            :     }</a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineCov">        846 :     Id getId() const {</span></a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineCov">        846 :         return ABS;</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            :     }</a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">        160 :     int getNumArguments() const {</span></a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineCov">        160 :         return 1;</span></a>
+<a name="1184"><span class="lineNum">    1184 </span>            :     }</a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">        976 :     Operation* clone() const {</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineCov">        976 :         return new Abs();</span></a>
+<a name="1187"><span class="lineNum">    1187 </span>            :     }</a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">        505 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">        505 :         return std::abs(args[0]);</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     }</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1192"><span class="lineNum">    1192 </span>            : };</a>
+<a name="1193"><span class="lineNum">    1193 </span>            : </a>
+<a name="1194"><span class="lineNum">    1194 </span>            : class LEPTON_EXPORT Operation::Floor : public Operation {</a>
+<a name="1195"><span class="lineNum">    1195 </span>            : public:</a>
+<a name="1196"><span class="lineNum">    1196 </span>            : </a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineCov">         34 :     Floor() {</span></a>
+<a name="1198"><span class="lineNum">    1198 </span>            :     }</a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineCov">          2 :         return &quot;floor&quot;;</span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            :     }</a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineCov">         40 :     Id getId() const {</span></a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineCov">         40 :         return FLOOR;</span></a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     }</a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">         18 :     int getNumArguments() const {</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">         18 :         return 1;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            :     }</a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">         30 :     Operation* clone() const {</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">         30 :         return new Floor();</span></a>
+<a name="1210"><span class="lineNum">    1210 </span>            :     }</a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineCov">        101 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineCov">        101 :         return std::floor(args[0]);</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            :     }</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1215"><span class="lineNum">    1215 </span>            : };</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span>            : class LEPTON_EXPORT Operation::Ceil : public Operation {</a>
+<a name="1218"><span class="lineNum">    1218 </span>            : public:</a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">         34 :     Ceil() {</span></a>
+<a name="1220"><span class="lineNum">    1220 </span>            :     }</a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineCov">          2 :     std::string getName() const {</span></a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">          2 :         return &quot;ceil&quot;;</span></a>
+<a name="1223"><span class="lineNum">    1223 </span>            :     }</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">         40 :     Id getId() const {</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">         40 :         return CEIL;</span></a>
+<a name="1226"><span class="lineNum">    1226 </span>            :     }</a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">         18 :     int getNumArguments() const {</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">         18 :         return 1;</span></a>
+<a name="1229"><span class="lineNum">    1229 </span>            :     }</a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineCov">         30 :     Operation* clone() const {</span></a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">         30 :         return new Ceil();</span></a>
+<a name="1232"><span class="lineNum">    1232 </span>            :     }</a>
+<a name="1233"><span class="lineNum">    1233 </span><span class="lineCov">        101 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">        101 :         return std::ceil(args[0]);</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            :     }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1237"><span class="lineNum">    1237 </span>            : };</a>
+<a name="1238"><span class="lineNum">    1238 </span>            : </a>
+<a name="1239"><span class="lineNum">    1239 </span>            : class LEPTON_EXPORT Operation::Select : public Operation {</a>
+<a name="1240"><span class="lineNum">    1240 </span>            : public:</a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineCov">         44 :     Select() {</span></a>
+<a name="1242"><span class="lineNum">    1242 </span>            :     }</a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">         24 :     std::string getName() const {</span></a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">         24 :         return &quot;select&quot;;</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :     }</a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">        516 :     Id getId() const {</span></a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">        516 :         return SELECT;</span></a>
+<a name="1248"><span class="lineNum">    1248 </span>            :     }</a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">        280 :     int getNumArguments() const {</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">        280 :         return 3;</span></a>
+<a name="1251"><span class="lineNum">    1251 </span>            :     }</a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineCov">        400 :     Operation* clone() const {</span></a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineCov">        400 :         return new Select();</span></a>
+<a name="1254"><span class="lineNum">    1254 </span>            :     }</a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineCov">       2432 :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const {</span></a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineCov">       2432 :         return (args[0] != 0.0 ? args[1] : args[2]);</span></a>
+<a name="1257"><span class="lineNum">    1257 </span>            :     }</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const;</a>
+<a name="1259"><span class="lineNum">    1259 </span>            : };</a>
+<a name="1260"><span class="lineNum">    1260 </span>            : </a>
+<a name="1261"><span class="lineNum">    1261 </span>            : #define LEPTON_CLASS_OPERATION(Name,name,NAME,nargs,impl) \</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : class LEPTON_EXPORT Operation::Name : public Operation { \</a>
+<a name="1263"><span class="lineNum">    1263 </span>            : public: \</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :     Name() { \</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :     } \</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :     std::string getName() const { \</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :         return #name; \</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :     } \</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :     Id getId() const { \</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :         return NAME; \</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :     } \</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :     int getNumArguments() const { \</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :         return nargs; \</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :     } \</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :     Operation* clone() const { \</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :         return new Name(); \</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :     } \</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :     double evaluate(double* args, const std::map&lt;std::string, double&gt;&amp; variables) const { \</a>
+<a name="1279"><span class="lineNum">    1279 </span>            :         return impl; \</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :     } \</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :     ExpressionTreeNode differentiate(const std::vector&lt;ExpressionTreeNode&gt;&amp; children, const std::vector&lt;ExpressionTreeNode&gt;&amp; childDerivs, const std::string&amp; variable) const; \</a>
+<a name="1282"><span class="lineNum">    1282 </span>            : }</a>
+<a name="1283"><span class="lineNum">    1283 </span>            : </a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">        296 : LEPTON_CLASS_OPERATION(Acot,acot,ACOT,1,std::atan(1.0/args[0]));</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineCov">        296 : LEPTON_CLASS_OPERATION(Asec,asec,ASEC,1,std::acos(1.0/args[0]));</span></a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineCov">        296 : LEPTON_CLASS_OPERATION(Acsc,acsc,ACSC,1,std::asin(1.0/args[0]));</span></a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineCov">       1144 : LEPTON_CLASS_OPERATION(Coth,coth,ACOT,1,1.0/std::tanh(args[0]));</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">        730 : LEPTON_CLASS_OPERATION(Sech,sech,SECH,1,1.0/std::cosh(args[0]));</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineCov">        730 : LEPTON_CLASS_OPERATION(Csch,csch,CSCH,1,1.0/std::sinh(args[0]));</span></a>
+<a name="1290"><span class="lineNum">    1290 </span>            : </a>
+<a name="1291"><span class="lineNum">    1291 </span><span class="lineCov">        195 : LEPTON_CLASS_OPERATION(Asinh,asinh,ASINH,1,std::asinh(args[0]));</span></a>
+<a name="1292"><span class="lineNum">    1292 </span><span class="lineCov">        195 : LEPTON_CLASS_OPERATION(Acosh,acosh,ACOSH,1,std::acosh(args[0]));</span></a>
+<a name="1293"><span class="lineNum">    1293 </span><span class="lineCov">        195 : LEPTON_CLASS_OPERATION(Atanh,atanh,ATANH,1,std::atanh(args[0]));</span></a>
+<a name="1294"><span class="lineNum">    1294 </span>            : </a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineCov">        296 : LEPTON_CLASS_OPERATION(Acoth,acoth,ACOTH,1,0.5*std::log((args[0]+1.0)/(args[0]-1.0)));</span></a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineCov">        296 : LEPTON_CLASS_OPERATION(Asech,asech,ASECH,1,std::log(std::sqrt(1.0/args[0]-1.0)*std::sqrt(1.0/args[0]+1.0)+1.0/args[0]));</span></a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineCov">        296 : LEPTON_CLASS_OPERATION(Acsch,acsch,ACSCH,1,std::log(1.0/args[0]+std::sqrt(1.0/(args[0]*args[0])+1.0)));</span></a>
+<a name="1298"><span class="lineNum">    1298 </span>            : </a>
+<a name="1299"><span class="lineNum">    1299 </span>            : } // namespace lepton</a>
+<a name="1300"><span class="lineNum">    1300 </span>            : } // namespace PLMD</a>
+<a name="1301"><span class="lineNum">    1301 </span>            : </a>
+<a name="1302"><span class="lineNum">    1302 </span>            : #endif /*LEPTON_OPERATION_H_*/</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ParsedExpression.cpp.func-sort-c.html b/coverage-libs/lepton/ParsedExpression.cpp.func-sort-c.html
new file mode 100644
index 0000000000..442eb49d9a
--- /dev/null
+++ b/coverage-libs/lepton/ParsedExpression.cpp.func-sort-c.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ParsedExpression.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ParsedExpression.cpp<span style="font-size: 80%;"> (<a href="ParsedExpression.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">221</td>
+            <td class="headerCovTableEntry">257</td>
+            <td class="headerCovTableEntryMed">86.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">76.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ParsedExpression.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#411">_ZN4PLMD6lepton16ParsedExpression19renameNodeVariablesERKNS0_18ExpressionTreeNodeERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESB_St4lessISB_ESaISt4pairIKSB_SB_EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#73">_ZN4PLMD6lepton16ParsedExpressionC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#399">_ZNK4PLMD6lepton16ParsedExpression13createProgramEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#407">_ZNK4PLMD6lepton16ParsedExpression15renameVariablesERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_ESaISt4pairIKS8_S8_EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#85">_ZNK4PLMD6lepton16ParsedExpression8evaluateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#369">_ZNK4PLMD6lepton16ParsedExpression13differentiateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">597</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#445">_ZN4PLMD6leptonlsERSoRKNS0_16ParsedExpressionE</a></td>
+              <td class="coverFnHi">1088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#119">_ZNK4PLMD6lepton16ParsedExpression8optimizeERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS8_ESaISt4pairIKS8_dEEE</a></td>
+              <td class="coverFnHi">1112</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#403">_ZNK4PLMD6lepton16ParsedExpression24createCompiledExpressionEv</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#101">_ZNK4PLMD6lepton16ParsedExpression8optimizeEv</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#392">_ZN4PLMD6lepton16ParsedExpression16getConstantValueERKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnHi">3320</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#376">_ZN4PLMD6lepton16ParsedExpression13differentiateERKNS0_18ExpressionTreeNodeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt3mapIiS2_St4lessIiESaISt4pairIKiS2_EEE</a></td>
+              <td class="coverFnHi">5818</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#423">_ZN4PLMD6leptonlsERSoRKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnHi">9949</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#137">_ZN4PLMD6lepton16ParsedExpression20preevaluateVariablesERKNS0_18ExpressionTreeNodeERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISB_ESaISt4pairIKSB_dEEE</a></td>
+              <td class="coverFnHi">19812</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#151">_ZN4PLMD6lepton16ParsedExpression34precalculateConstantSubexpressionsERKNS0_18ExpressionTreeNodeERSt3mapIiS2_St4lessIiESaISt4pairIKiS2_EEE</a></td>
+              <td class="coverFnHi">22789</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#173">_ZN4PLMD6lepton16ParsedExpression27substituteSimplerExpressionERKNS0_18ExpressionTreeNodeERSt3mapIiS2_St4lessIiESaISt4pairIKiS2_EEE</a></td>
+              <td class="coverFnHi">25877</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#388">_ZN4PLMD6lepton16ParsedExpression10isConstantERKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnHi">29780</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#89">_ZNK4PLMD6lepton16ParsedExpression8evaluateERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS8_ESaISt4pairIKS8_dEEE</a></td>
+              <td class="coverFnHi">2008077</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#76">_ZN4PLMD6lepton16ParsedExpressionC2ERKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnHi">2012034</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#93">_ZN4PLMD6lepton16ParsedExpression8evaluateERKNS0_18ExpressionTreeNodeERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessISB_ESaISt4pairIKSB_dEEE</a></td>
+              <td class="coverFnHi">2012733</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#79">_ZNK4PLMD6lepton16ParsedExpression11getRootNodeEv</a></td>
+              <td class="coverFnHi">2013743</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ParsedExpression.cpp.func.html b/coverage-libs/lepton/ParsedExpression.cpp.func.html
new file mode 100644
index 0000000000..978c67ee7b
--- /dev/null
+++ b/coverage-libs/lepton/ParsedExpression.cpp.func.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ParsedExpression.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ParsedExpression.cpp<span style="font-size: 80%;"> (<a href="ParsedExpression.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">221</td>
+            <td class="headerCovTableEntry">257</td>
+            <td class="headerCovTableEntryMed">86.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">76.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ParsedExpression.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFnHi">5818</td>
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+              <td class="coverFnHi">19812</td>
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+    <tr>
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+              <td class="coverFnHi">2012733</td>
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+              <td class="coverFnHi">2012034</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#73">_ZN4PLMD6lepton16ParsedExpressionC2Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
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+              <td class="coverFnHi">1088</td>
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+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#423">_ZN4PLMD6leptonlsERSoRKNS0_18ExpressionTreeNodeE</a></td>
+              <td class="coverFnHi">9949</td>
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+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#79">_ZNK4PLMD6lepton16ParsedExpression11getRootNodeEv</a></td>
+              <td class="coverFnHi">2013743</td>
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+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#399">_ZNK4PLMD6lepton16ParsedExpression13createProgramEv</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#369">_ZNK4PLMD6lepton16ParsedExpression13differentiateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">597</td>
+            </tr>
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+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#407">_ZNK4PLMD6lepton16ParsedExpression15renameVariablesERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_St4lessIS8_ESaISt4pairIKS8_S8_EEE</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#403">_ZNK4PLMD6lepton16ParsedExpression24createCompiledExpressionEv</a></td>
+              <td class="coverFnHi">1136</td>
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+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#89">_ZNK4PLMD6lepton16ParsedExpression8evaluateERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS8_ESaISt4pairIKS8_dEEE</a></td>
+              <td class="coverFnHi">2008077</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#85">_ZNK4PLMD6lepton16ParsedExpression8evaluateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#119">_ZNK4PLMD6lepton16ParsedExpression8optimizeERKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdSt4lessIS8_ESaISt4pairIKS8_dEEE</a></td>
+              <td class="coverFnHi">1112</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParsedExpression.cpp.gcov.html#101">_ZNK4PLMD6lepton16ParsedExpression8optimizeEv</a></td>
+              <td class="coverFnHi">1136</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ParsedExpression.cpp.gcov.html b/coverage-libs/lepton/ParsedExpression.cpp.gcov.html
new file mode 100644
index 0000000000..b70915936e
--- /dev/null
+++ b/coverage-libs/lepton/ParsedExpression.cpp.gcov.html
@@ -0,0 +1,527 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ParsedExpression.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ParsedExpression.cpp<span style="font-size: 80%;"> (source / <a href="ParsedExpression.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">221</td>
+            <td class="headerCovTableEntry">257</td>
+            <td class="headerCovTableEntryMed">86.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">76.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  *                                   lepton                                   *</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *                                                                            *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Portions copyright (c) 2009-2021 Stanford University and the Authors.      *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Contributors:                                                              *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *                                                                            *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *                                                                            *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &quot;ParsedExpression.h&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &quot;CompiledExpression.h&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;ExpressionProgram.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;Operation.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &lt;limits&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            : #include &lt;vector&gt;</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : namespace PLMD {</a>
+<a name="72"><span class="lineNum">      72 </span>            : using namespace lepton;</a>
+<a name="73"><span class="lineNum">      73 </span>            : using namespace std;</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 : ParsedExpression::ParsedExpression() : rootNode(ExpressionTreeNode()) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    2012034 : ParsedExpression::ParsedExpression(const ExpressionTreeNode&amp; rootNode) : rootNode(rootNode) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">    2012034 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">    2013743 : const ExpressionTreeNode&amp; ParsedExpression::getRootNode() const {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">    2013743 :     if (&amp;rootNode.getOperation() == NULL)</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :         throw Exception(&quot;Illegal call to an initialized ParsedExpression&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    2013743 :     return rootNode;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 : double ParsedExpression::evaluate() const {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     return evaluate(getRootNode(), map&lt;string, double&gt;());</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    2008077 : double ParsedExpression::evaluate(const map&lt;string, double&gt;&amp; variables) const {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    2008077 :     return evaluate(getRootNode(), variables);</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    2012733 : double ParsedExpression::evaluate(const ExpressionTreeNode&amp; node, const map&lt;string, double&gt;&amp; variables) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    2012733 :     int numArgs = (int) node.getChildren().size();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    4024836 :     vector&lt;double&gt; args(max(numArgs, 1));</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">    2013849 :     for (int i = 0; i &lt; numArgs; i++)</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1121 :         args[i] = evaluate(node.getChildren()[i], variables);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">    4025434 :     return node.getOperation().evaluate(&amp;args[0], variables);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1136 : ParsedExpression ParsedExpression::optimize() const {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1136 :     ExpressionTreeNode result = getRootNode();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :     vector&lt;const ExpressionTreeNode*&gt; examples;</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1136 :     result.assignTags(examples);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     map&lt;int, ExpressionTreeNode&gt; nodeCache;</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1136 :     result = precalculateConstantSubexpressions(result, nodeCache);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     while (true) {</a>
+<a name="110"><span class="lineNum">     110 </span>            :         examples.clear();</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1136 :         result.assignTags(examples);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :         nodeCache.clear();</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1136 :         ExpressionTreeNode simplified = substituteSimplerExpression(result, nodeCache);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1136 :         if (simplified == result)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :             break;</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :         result = simplified;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       1136 :     }</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       2272 :     return ParsedExpression(result);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1136 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       1112 : ParsedExpression ParsedExpression::optimize(const map&lt;string, double&gt;&amp; variables) const {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       1112 :     ExpressionTreeNode result = preevaluateVariables(getRootNode(), variables);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     vector&lt;const ExpressionTreeNode*&gt; examples;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       1112 :     result.assignTags(examples);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     map&lt;int, ExpressionTreeNode&gt; nodeCache;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       1112 :     result = precalculateConstantSubexpressions(result, nodeCache);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     while (true) {</a>
+<a name="128"><span class="lineNum">     128 </span>            :         examples.clear();</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       2166 :         result.assignTags(examples);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :         nodeCache.clear();</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       2166 :         ExpressionTreeNode simplified = substituteSimplerExpression(result, nodeCache);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       2166 :         if (simplified == result)</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :             break;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1054 :         result = simplified;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       2166 :     }</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       2224 :     return ParsedExpression(result);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1112 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      19812 : ExpressionTreeNode ParsedExpression::preevaluateVariables(const ExpressionTreeNode&amp; node, const map&lt;string, double&gt;&amp; variables) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      19812 :     if (node.getOperation().getId() == Operation::VARIABLE) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       3866 :         const Operation::Variable&amp; var = dynamic_cast&lt;const Operation::Variable&amp;&gt;(node.getOperation());</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       7732 :         map&lt;string, double&gt;::const_iterator iter = variables.find(var.getName());</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       3866 :         if (iter == variables.end())</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       3460 :             return node;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        406 :         return ExpressionTreeNode(new Operation::Constant(iter-&gt;second));</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      15946 :     vector&lt;ExpressionTreeNode&gt; children(node.getChildren().size());</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      34646 :     for (int i = 0; i &lt; (int) children.size(); i++)</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      18700 :         children[i] = preevaluateVariables(node.getChildren()[i], variables);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      15946 :     return ExpressionTreeNode(node.getOperation().clone(), children);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      15946 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      22789 : ExpressionTreeNode ParsedExpression::precalculateConstantSubexpressions(const ExpressionTreeNode&amp; node, map&lt;int, ExpressionTreeNode&gt;&amp; nodeCache) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      22789 :     auto cached = nodeCache.find(node.tag);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      22789 :     if (cached != nodeCache.end())</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       4728 :         return cached-&gt;second;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      18061 :     vector&lt;ExpressionTreeNode&gt; children(node.getChildren().size());</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      38602 :     for (int i = 0; i &lt; (int) children.size(); i++)</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      20541 :         children[i] = precalculateConstantSubexpressions(node.getChildren()[i], nodeCache);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      18061 :     ExpressionTreeNode result = ExpressionTreeNode(node.getOperation().clone(), children);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">      18061 :     if (node.getOperation().getId() == Operation::VARIABLE || node.getOperation().getId() == Operation::CUSTOM) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       2326 :         nodeCache[node.tag] = result;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       2326 :         return result;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      18370 :     for (int i = 0; i &lt; (int) children.size(); i++)</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      14835 :         if (children[i].getOperation().getId() != Operation::CONSTANT) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      12200 :             nodeCache[node.tag] = result;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      12200 :             return result;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :         }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       3535 :     result = ExpressionTreeNode(new Operation::Constant(evaluate(result, map&lt;string, double&gt;())));</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       3535 :     nodeCache[node.tag] = result;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       3535 :     return result;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      18061 : }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      25877 : ExpressionTreeNode ParsedExpression::substituteSimplerExpression(const ExpressionTreeNode&amp; node, map&lt;int, ExpressionTreeNode&gt;&amp; nodeCache) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      25877 :     vector&lt;ExpressionTreeNode&gt; children(node.getChildren().size());</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      55709 :     for (int i = 0; i &lt; (int) children.size(); i++) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">      29832 :         const ExpressionTreeNode&amp; child = node.getChildren()[i];</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      29832 :         auto cached = nodeCache.find(child.tag);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      29832 :         if (cached == nodeCache.end()) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      22575 :             children[i] = substituteSimplerExpression(child, nodeCache);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      22575 :             nodeCache[child.tag] = children[i];</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :         }</a>
+<a name="184"><span class="lineNum">     184 </span>            :         else</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       7257 :             children[i] = cached-&gt;second;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     }</a>
+<a name="187"><span class="lineNum">     187 </span>            :     </a>
+<a name="188"><span class="lineNum">     188 </span>            :     // Collect some info on constant expressions in children</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      25877 :     bool first_const = children.size() &gt; 0 &amp;&amp; isConstant(children[0]); // is first child constant?</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      25877 :     bool second_const = children.size() &gt; 1 &amp;&amp; isConstant(children[1]); ; // is second child constant?   </span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     double first, second; // if yes, value of first and second child</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      25877 :     if (first_const)</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       1699 :         first = getConstantValue(children[0]);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      25877 :     if (second_const)</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1621 :         second = getConstantValue(children[1]);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      25877 :     switch (node.getOperation().getId()) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       2410 :         case Operation::ADD:</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :         {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       2410 :             if (first_const) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         74 :                 if (first == 0.0) { // Add 0</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         54 :                     return children[1];</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :                 } else { // Add a constant</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         20 :                     return ExpressionTreeNode(new Operation::AddConstant(first), children[1]);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :                 }</a>
+<a name="206"><span class="lineNum">     206 </span>            :             }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       2336 :             if (second_const) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        354 :                 if (second == 0.0) { // Add 0</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        104 :                     return children[0];</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :                 } else { // Add a constant</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        250 :                     return ExpressionTreeNode(new Operation::AddConstant(second), children[0]);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :                 }</a>
+<a name="213"><span class="lineNum">     213 </span>            :             }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1982 :             if (children[1].getOperation().getId() == Operation::NEGATE) // a+(-b) = a-b</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Subtract(), children[0], children[1].getChildren()[0]);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1980 :             if (children[0].getOperation().getId() == Operation::NEGATE) // (-a)+b = b-a</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Subtract(), children[1], children[0].getChildren()[0]);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :             break;</a>
+<a name="219"><span class="lineNum">     219 </span>            :         }</a>
+<a name="220"><span class="lineNum">     220 </span>            :         case Operation::SUBTRACT:</a>
+<a name="221"><span class="lineNum">     221 </span>            :         {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       1649 :             if (children[0] == children[1])</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Constant(0.0)); // Subtracting anything from itself is 0</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       1647 :             if (first_const) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         84 :                 if (first == 0.0) // Subtract from 0</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          4 :                     return ExpressionTreeNode(new Operation::Negate(), children[1]);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :             }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       1643 :             if (second_const) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        143 :                 if (second == 0.0) { // Subtract 0</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          5 :                     return children[0];</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :                 } else { // Subtract a constant</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        138 :                     return ExpressionTreeNode(new Operation::AddConstant(-second), children[0]);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :                 }</a>
+<a name="234"><span class="lineNum">     234 </span>            :             }</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       1500 :             if (children[1].getOperation().getId() == Operation::NEGATE) // a-(-b) = a+b</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Add(), children[0], children[1].getChildren()[0]);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :             break;</a>
+<a name="238"><span class="lineNum">     238 </span>            :         }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       5421 :         case Operation::MULTIPLY:</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :         {   </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       5421 :             if ((first_const &amp;&amp; first == 0.0) || (second_const &amp;&amp; second == 0.0)) // Multiply by 0</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        182 :                 return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       5239 :             if (first_const &amp;&amp; first == 1.0) // Multiply by 1</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         18 :                 return children[1];</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       5221 :             if (second_const &amp;&amp; second == 1.0) // Multiply by 1</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        489 :                 return children[0];</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       4732 :             if (first_const) { // Multiply by a constant</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       1388 :                 if (children[1].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         24 :                     return ExpressionTreeNode(new Operation::MultiplyConstant(first*dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[1].getOperation())-&gt;getValue()), children[1].getChildren()[0]);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       1364 :                 return ExpressionTreeNode(new Operation::MultiplyConstant(first), children[1]);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :             }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       3344 :             if (second_const) { // Multiply by a constant</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         23 :                 if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          1 :                     return ExpressionTreeNode(new Operation::MultiplyConstant(second*dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[0].getOperation())-&gt;getValue()), children[0].getChildren()[0]);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         22 :                 return ExpressionTreeNode(new Operation::MultiplyConstant(second), children[0]);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :             }</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       3321 :             if (children[0].getOperation().getId() == Operation::NEGATE &amp;&amp; children[1].getOperation().getId() == Operation::NEGATE) // The two negations cancel</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Multiply(), children[0].getChildren()[0], children[1].getChildren()[0]);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       3321 :             if (children[0].getOperation().getId() == Operation::NEGATE &amp;&amp; children[1].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Negate the constant</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Multiply(), children[0].getChildren()[0], ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[1].getOperation())-&gt;getValue()), children[1].getChildren()[0]));</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       3321 :             if (children[1].getOperation().getId() == Operation::NEGATE &amp;&amp; children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Negate the constant</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        192 :                 return ExpressionTreeNode(new Operation::Multiply(), ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[0].getOperation())-&gt;getValue()), children[0].getChildren()[0]), children[1].getChildren()[0]);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       3129 :             if (children[0].getOperation().getId() == Operation::NEGATE) // Pull the negation out so it can possibly be optimized further</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Multiply(), children[0].getChildren()[0], children[1]));</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       3127 :             if (children[1].getOperation().getId() == Operation::NEGATE) // Pull the negation out so it can possibly be optimized further</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Multiply(), children[0], children[1].getChildren()[0]));</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       3127 :             if (children[1].getOperation().getId() == Operation::RECIPROCAL) // a*(1/b) = a/b</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Divide(), children[0], children[1].getChildren()[0]);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       3127 :             if (children[0].getOperation().getId() == Operation::RECIPROCAL) // (1/a)*b = b/a</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Divide(), children[1], children[0].getChildren()[0]);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       3125 :             if (children[0] == children[1])</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        134 :                 return ExpressionTreeNode(new Operation::Square(), children[0]); // x*x = square(x)</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       2991 :             if (children[0].getOperation().getId() == Operation::SQUARE &amp;&amp; children[0].getChildren()[0] == children[1])</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Cube(), children[1]); // x*x*x = cube(x)</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       2989 :             if (children[1].getOperation().getId() == Operation::SQUARE &amp;&amp; children[1].getChildren()[0] == children[0])</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Cube(), children[0]); // x*x*x = cube(x)</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :             break;</a>
+<a name="278"><span class="lineNum">     278 </span>            :         }</a>
+<a name="279"><span class="lineNum">     279 </span>            :         case Operation::DIVIDE:</a>
+<a name="280"><span class="lineNum">     280 </span>            :         {</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        243 :             if (children[0] == children[1])</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Constant(1.0)); // Dividing anything from itself is 0</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        241 :             if (first_const &amp;&amp; first == 0.0) // 0 divided by something</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          6 :                 return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        235 :             if (first_const &amp;&amp; first == 1.0) // 1 divided by something</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         18 :                 return ExpressionTreeNode(new Operation::Reciprocal(), children[1]);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        217 :             if (second_const &amp;&amp; second == 1.0) // Divide by 1</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :                 return children[0];</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        217 :             if (second_const) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         35 :                 if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine a multiply and a divide into one multiply</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :                     return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[0].getOperation())-&gt;getValue()/second), children[0].getChildren()[0]);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         35 :                 return ExpressionTreeNode(new Operation::MultiplyConstant(1.0/second), children[0]); // Replace a divide with a multiply</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :             }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        182 :             if (children[0].getOperation().getId() == Operation::NEGATE &amp;&amp; children[1].getOperation().getId() == Operation::NEGATE) // The two negations cancel</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Divide(), children[0].getChildren()[0], children[1].getChildren()[0]);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        182 :             if (children[1].getOperation().getId() == Operation::NEGATE &amp;&amp; children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Negate the constant</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Divide(), ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[0].getOperation())-&gt;getValue()), children[0].getChildren()[0]), children[1].getChildren()[0]);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">        182 :             if (children[0].getOperation().getId() == Operation::NEGATE) // Pull the negation out so it can possibly be optimized further</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         22 :                 return ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Divide(), children[0].getChildren()[0], children[1]));</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">        160 :             if (children[1].getOperation().getId() == Operation::NEGATE) // Pull the negation out so it can possibly be optimized further</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Negate(), ExpressionTreeNode(new Operation::Divide(), children[0], children[1].getChildren()[0]));</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        160 :             if (children[1].getOperation().getId() == Operation::RECIPROCAL) // a/(1/b) = a*b</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          2 :                 return ExpressionTreeNode(new Operation::Multiply(), children[0], children[1].getChildren()[0]);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :             break;</a>
+<a name="305"><span class="lineNum">     305 </span>            :         }</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        329 :         case Operation::POWER:</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :         {</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">        329 :             if (first_const &amp;&amp; first == 0.0) // 0 to any power is 0</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          6 :                 return ExpressionTreeNode(new Operation::Constant(0.0));</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        323 :             if (first_const &amp;&amp; first == 1.0) // 1 to any power is 1</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          6 :                 return ExpressionTreeNode(new Operation::Constant(1.0));</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        317 :             if (second_const) { // Constant exponent</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        305 :                 if (second == 0.0) // x^0 = 1</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :                     return ExpressionTreeNode(new Operation::Constant(1.0));</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        305 :                 if (second == 1.0) // x^1 = x</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         59 :                     return children[0];</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        246 :                 if (second == -1.0) // x^-1 = recip(x)</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :                     return ExpressionTreeNode(new Operation::Reciprocal(), children[0]);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        246 :                 if (second == 2.0) // x^2 = square(x)</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        124 :                     return ExpressionTreeNode(new Operation::Square(), children[0]);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        122 :                 if (second == 3.0) // x^3 = cube(x)</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         46 :                     return ExpressionTreeNode(new Operation::Cube(), children[0]);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         76 :                 if (second == 0.5) // x^0.5 = sqrt(x)</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          7 :                     return ExpressionTreeNode(new Operation::Sqrt(), children[0]);</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :                 // Constant power</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         69 :                 return ExpressionTreeNode(new Operation::PowerConstant(second), children[0]);</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :             }</a>
+<a name="328"><span class="lineNum">     328 </span>            :             break;</a>
+<a name="329"><span class="lineNum">     329 </span>            :         }</a>
+<a name="330"><span class="lineNum">     330 </span>            :         case Operation::NEGATE:</a>
+<a name="331"><span class="lineNum">     331 </span>            :         {</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        640 :             if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine a multiply and a negate into a single multiply</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         10 :                 return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[0].getOperation())-&gt;getValue()), children[0].getChildren()[0]);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">        630 :             if (first_const) // Negate a constant</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Constant(-first));</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        630 :             if (children[0].getOperation().getId() == Operation::NEGATE) // The two negations cancel</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :                 return children[0].getChildren()[0];</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :             break;</a>
+<a name="339"><span class="lineNum">     339 </span>            :         }</a>
+<a name="340"><span class="lineNum">     340 </span>            :         case Operation::MULTIPLY_CONSTANT:</a>
+<a name="341"><span class="lineNum">     341 </span>            :         {</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       3644 :             if (children[0].getOperation().getId() == Operation::MULTIPLY_CONSTANT) // Combine two multiplies into a single one</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::MultiplyConstant(dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;node.getOperation())-&gt;getValue()*dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;children[0].getOperation())-&gt;getValue()), children[0].getChildren()[0]);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">       3644 :             if (first_const) // Multiply two constants</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :                 return ExpressionTreeNode(new Operation::Constant(dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;node.getOperation())-&gt;getValue()*getConstantValue(children[0])));</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">       3644 :             if (children[0].getOperation().getId() == Operation::NEGATE) // Combine a multiply and a negate into a single multiply</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">        439 :                 return ExpressionTreeNode(new Operation::MultiplyConstant(-dynamic_cast&lt;const Operation::MultiplyConstant*&gt;(&amp;node.getOperation())-&gt;getValue()), children[0].getChildren()[0]);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :             break;</a>
+<a name="349"><span class="lineNum">     349 </span>            :         }</a>
+<a name="350"><span class="lineNum">     350 </span>            :         case Operation::SQRT:</a>
+<a name="351"><span class="lineNum">     351 </span>            :         {</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        221 :             if (children[0].getOperation().getId() == Operation::SQUARE) // sqrt(square(x)) = abs(x)</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          4 :                 return ExpressionTreeNode(new Operation::Abs(), children[0].getChildren()[0]);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :         }</a>
+<a name="355"><span class="lineNum">     355 </span>            :         case Operation::SQUARE:</a>
+<a name="356"><span class="lineNum">     356 </span>            :         {</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        875 :             if (children[0].getOperation().getId() == Operation::SQRT) // square(sqrt(x)) = x</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         27 :                 return children[0].getChildren()[0];</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :         }</a>
+<a name="360"><span class="lineNum">     360 </span>            :         default:</a>
+<a name="361"><span class="lineNum">     361 </span>            :         {</a>
+<a name="362"><span class="lineNum">     362 </span>            :             // If operation ID is not one of the above,</a>
+<a name="363"><span class="lineNum">     363 </span>            :             // we don't substitute a simpler expression.</a>
+<a name="364"><span class="lineNum">     364 </span>            :             break;</a>
+<a name="365"><span class="lineNum">     365 </span>            :         }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :     }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">      21980 :     return ExpressionTreeNode(node.getOperation().clone(), children);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">      25877 : }</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        597 : ParsedExpression ParsedExpression::differentiate(const string&amp; variable) const {</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :     vector&lt;const ExpressionTreeNode*&gt; examples;</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        597 :     getRootNode().assignTags(examples);</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :     map&lt;int, ExpressionTreeNode&gt; nodeCache;</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">       1194 :     return differentiate(getRootNode(), variable, nodeCache);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">       5818 : ExpressionTreeNode ParsedExpression::differentiate(const ExpressionTreeNode&amp; node, const string&amp; variable, map&lt;int, ExpressionTreeNode&gt;&amp; nodeCache) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">       5818 :     auto cached = nodeCache.find(node.tag);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">       5818 :     if (cached != nodeCache.end())</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        785 :         return cached-&gt;second;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       5033 :     vector&lt;ExpressionTreeNode&gt; childDerivs(node.getChildren().size());</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">      10254 :     for (int i = 0; i &lt; (int) childDerivs.size(); i++)</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       5221 :         childDerivs[i] = differentiate(node.getChildren()[i], variable, nodeCache);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       5033 :     ExpressionTreeNode result = node.getOperation().differentiate(node.getChildren(), childDerivs, variable);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       5033 :     nodeCache[node.tag] = result;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       5033 :     return result;</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       5033 : }</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      29780 : bool ParsedExpression::isConstant(const ExpressionTreeNode&amp; node) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">      29780 :     return (node.getOperation().getId() == Operation::CONSTANT);</span></a>
+<a name="392"><span class="lineNum">     392 </span>            : }</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       3320 : double ParsedExpression::getConstantValue(const ExpressionTreeNode&amp; node) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       3320 :     if (node.getOperation().getId() != Operation::CONSTANT) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :         throw Exception(&quot;getConstantValue called on a non-constant ExpressionNode&quot;);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :     }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       3320 :     return dynamic_cast&lt;const Operation::Constant&amp;&gt;(node.getOperation()).getValue();</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : }</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 : ExpressionProgram ParsedExpression::createProgram() const {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :     return ExpressionProgram(*this);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            : }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       1136 : CompiledExpression ParsedExpression::createCompiledExpression() const {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">       1136 :     return CompiledExpression(*this);</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : }</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 : ParsedExpression ParsedExpression::renameVariables(const map&lt;string, string&gt;&amp; replacements) const {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :     return ParsedExpression(renameNodeVariables(getRootNode(), replacements));</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : }</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 : ExpressionTreeNode ParsedExpression::renameNodeVariables(const ExpressionTreeNode&amp; node, const map&lt;string, string&gt;&amp; replacements) {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :     if (node.getOperation().getId() == Operation::VARIABLE) {</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :         map&lt;string, string&gt;::const_iterator replace = replacements.find(node.getOperation().getName());</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :         if (replace != replacements.end())</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :             return ExpressionTreeNode(new Operation::Variable(replace-&gt;second));</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :     }</a>
+<a name="419"><span class="lineNum">     419 </span>            :     vector&lt;ExpressionTreeNode&gt; children;</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :     for (int i = 0; i &lt; (int) node.getChildren().size(); i++)</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :         children.push_back(renameNodeVariables(node.getChildren()[i], replacements));</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :     return ExpressionTreeNode(node.getOperation().clone(), children);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">       9949 : ostream&amp; lepton::operator&lt;&lt;(ostream&amp; out, const ExpressionTreeNode&amp; node) {</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">       9949 :     if (node.getOperation().isInfixOperator() &amp;&amp; node.getChildren().size() == 2) {</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">       5811 :         out &lt;&lt; &quot;(&quot; &lt;&lt; node.getChildren()[0] &lt;&lt; &quot;)&quot; &lt;&lt; node.getOperation().getName() &lt;&lt; &quot;(&quot; &lt;&lt; node.getChildren()[1] &lt;&lt; &quot;)&quot;;</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :     }</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       8012 :     else if (node.getOperation().isInfixOperator() &amp;&amp; node.getChildren().size() == 1) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         74 :         out &lt;&lt; &quot;(&quot; &lt;&lt; node.getChildren()[0] &lt;&lt; &quot;)&quot; &lt;&lt; node.getOperation().getName();</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :     }</a>
+<a name="432"><span class="lineNum">     432 </span>            :     else {</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">       7975 :         out &lt;&lt; node.getOperation().getName();</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">       7975 :         if (node.getChildren().size() &gt; 0) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">       4886 :             out &lt;&lt; &quot;(&quot;;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">       9836 :             for (int i = 0; i &lt; (int) node.getChildren().size(); i++) {</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">       4950 :                 if (i &gt; 0)</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">         64 :                     out &lt;&lt; &quot;, &quot;;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">       4950 :                 out &lt;&lt; node.getChildren()[i];</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :             }</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">       4886 :             out &lt;&lt; &quot;)&quot;;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :         }</a>
+<a name="443"><span class="lineNum">     443 </span>            :     }</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">       9949 :     return out;</span></a>
+<a name="445"><span class="lineNum">     445 </span>            : }</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">       1088 : ostream&amp; lepton::operator&lt;&lt;(ostream&amp; out, const ParsedExpression&amp; exp) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">       1088 :     out &lt;&lt; exp.getRootNode();</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">       1088 :     return out;</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : }</a>
+<a name="451"><span class="lineNum">     451 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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index 0000000000..6b566cf920
--- /dev/null
+++ b/coverage-libs/lepton/ParsedExpression.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ParsedExpression.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ParsedExpression.h<span style="font-size: 80%;"> (<a href="ParsedExpression.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ParsedExpression.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ParsedExpression.h.func.html b/coverage-libs/lepton/ParsedExpression.h.func.html
new file mode 100644
index 0000000000..a1c1705809
--- /dev/null
+++ b/coverage-libs/lepton/ParsedExpression.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ParsedExpression.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ParsedExpression.h<span style="font-size: 80%;"> (<a href="ParsedExpression.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ParsedExpression.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/ParsedExpression.h.gcov.html b/coverage-libs/lepton/ParsedExpression.h.gcov.html
new file mode 100644
index 0000000000..ad28b23941
--- /dev/null
+++ b/coverage-libs/lepton/ParsedExpression.h.gcov.html
@@ -0,0 +1,241 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/ParsedExpression.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - ParsedExpression.h<span style="font-size: 80%;"> (source / <a href="ParsedExpression.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : #ifndef __PLUMED_lepton_ParsedExpression_h</a>
+<a name="34"><span class="lineNum">      34 </span>            : #define __PLUMED_lepton_ParsedExpression_h</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  *                                   lepton                                   *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *                                                                            *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * Portions copyright (c) 2009=2021 Stanford University and the Authors.      *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * Contributors:                                                              *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  *                                                                            *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *                                                                            *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="63"><span class="lineNum">      63 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="64"><span class="lineNum">      64 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="65"><span class="lineNum">      65 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;ExpressionTreeNode.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &quot;windowsIncludes.h&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            : #include &lt;map&gt;</a>
+<a name="70"><span class="lineNum">      70 </span>            : #include &lt;string&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : namespace PLMD {</a>
+<a name="73"><span class="lineNum">      73 </span>            : namespace lepton {</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : class CompiledExpression;</a>
+<a name="76"><span class="lineNum">      76 </span>            : class ExpressionProgram;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : /**</a>
+<a name="79"><span class="lineNum">      79 </span>            :  * This class represents the result of parsing an expression.  It provides methods for working with the</a>
+<a name="80"><span class="lineNum">      80 </span>            :  * expression in various ways, such as evaluating it, getting the tree representation of the expresson, etc.</a>
+<a name="81"><span class="lineNum">      81 </span>            :  */</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    2011426 : class LEPTON_EXPORT ParsedExpression {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :     /**</a>
+<a name="86"><span class="lineNum">      86 </span>            :      * Create an uninitialized ParsedExpression.  This exists so that ParsedExpressions can be put in STL containers.</a>
+<a name="87"><span class="lineNum">      87 </span>            :      * Doing anything with it will produce an exception.</a>
+<a name="88"><span class="lineNum">      88 </span>            :      */</a>
+<a name="89"><span class="lineNum">      89 </span>            :     ParsedExpression();</a>
+<a name="90"><span class="lineNum">      90 </span>            :     /**</a>
+<a name="91"><span class="lineNum">      91 </span>            :      * Create a ParsedExpression.  Normally you will not call this directly.  Instead, use the Parser class</a>
+<a name="92"><span class="lineNum">      92 </span>            :      * to parse expression.</a>
+<a name="93"><span class="lineNum">      93 </span>            :      */</a>
+<a name="94"><span class="lineNum">      94 </span>            :     ParsedExpression(const ExpressionTreeNode&amp; rootNode);</a>
+<a name="95"><span class="lineNum">      95 </span>            :     /**</a>
+<a name="96"><span class="lineNum">      96 </span>            :      * Get the root node of the expression's abstract syntax tree.</a>
+<a name="97"><span class="lineNum">      97 </span>            :      */</a>
+<a name="98"><span class="lineNum">      98 </span>            :     const ExpressionTreeNode&amp; getRootNode() const;</a>
+<a name="99"><span class="lineNum">      99 </span>            :     /**</a>
+<a name="100"><span class="lineNum">     100 </span>            :      * Evaluate the expression.  If the expression involves any variables, this method will throw an exception.</a>
+<a name="101"><span class="lineNum">     101 </span>            :      */</a>
+<a name="102"><span class="lineNum">     102 </span>            :     double evaluate() const;</a>
+<a name="103"><span class="lineNum">     103 </span>            :     /**</a>
+<a name="104"><span class="lineNum">     104 </span>            :      * Evaluate the expression.</a>
+<a name="105"><span class="lineNum">     105 </span>            :      *</a>
+<a name="106"><span class="lineNum">     106 </span>            :      * @param variables    a map specifying the values of all variables that appear in the expression.  If any</a>
+<a name="107"><span class="lineNum">     107 </span>            :      *                     variable appears in the expression but is not included in this map, an exception</a>
+<a name="108"><span class="lineNum">     108 </span>            :      *                     will be thrown.</a>
+<a name="109"><span class="lineNum">     109 </span>            :      */</a>
+<a name="110"><span class="lineNum">     110 </span>            :     double evaluate(const std::map&lt;std::string, double&gt;&amp; variables) const;</a>
+<a name="111"><span class="lineNum">     111 </span>            :     /**</a>
+<a name="112"><span class="lineNum">     112 </span>            :      * Create a new ParsedExpression which produces the same result as this one, but is faster to evaluate.</a>
+<a name="113"><span class="lineNum">     113 </span>            :      */</a>
+<a name="114"><span class="lineNum">     114 </span>            :     ParsedExpression optimize() const;</a>
+<a name="115"><span class="lineNum">     115 </span>            :     /**</a>
+<a name="116"><span class="lineNum">     116 </span>            :      * Create a new ParsedExpression which produces the same result as this one, but is faster to evaluate.</a>
+<a name="117"><span class="lineNum">     117 </span>            :      *</a>
+<a name="118"><span class="lineNum">     118 </span>            :      * @param variables    a map specifying values for a subset of variables that appear in the expression.</a>
+<a name="119"><span class="lineNum">     119 </span>            :      *                     All occurrences of these variables in the expression are replaced with the values</a>
+<a name="120"><span class="lineNum">     120 </span>            :      *                     specified.</a>
+<a name="121"><span class="lineNum">     121 </span>            :      */</a>
+<a name="122"><span class="lineNum">     122 </span>            :     ParsedExpression optimize(const std::map&lt;std::string, double&gt;&amp; variables) const;</a>
+<a name="123"><span class="lineNum">     123 </span>            :     /**</a>
+<a name="124"><span class="lineNum">     124 </span>            :      * Create a new ParsedExpression which is the analytic derivative of this expression with respect to a</a>
+<a name="125"><span class="lineNum">     125 </span>            :      * particular variable.</a>
+<a name="126"><span class="lineNum">     126 </span>            :      *</a>
+<a name="127"><span class="lineNum">     127 </span>            :      * @param variable     the variable with respect to which the derivate should be taken</a>
+<a name="128"><span class="lineNum">     128 </span>            :      */</a>
+<a name="129"><span class="lineNum">     129 </span>            :     ParsedExpression differentiate(const std::string&amp; variable) const;</a>
+<a name="130"><span class="lineNum">     130 </span>            :     /**</a>
+<a name="131"><span class="lineNum">     131 </span>            :      * Create an ExpressionProgram that represents the same calculation as this expression.</a>
+<a name="132"><span class="lineNum">     132 </span>            :      */</a>
+<a name="133"><span class="lineNum">     133 </span>            :     ExpressionProgram createProgram() const;</a>
+<a name="134"><span class="lineNum">     134 </span>            :     /**</a>
+<a name="135"><span class="lineNum">     135 </span>            :      * Create a CompiledExpression that represents the same calculation as this expression.</a>
+<a name="136"><span class="lineNum">     136 </span>            :      */</a>
+<a name="137"><span class="lineNum">     137 </span>            :     CompiledExpression createCompiledExpression() const;</a>
+<a name="138"><span class="lineNum">     138 </span>            :     /**</a>
+<a name="139"><span class="lineNum">     139 </span>            :      * Create a new ParsedExpression which is identical to this one, except that the names of some</a>
+<a name="140"><span class="lineNum">     140 </span>            :      * variables have been changed.</a>
+<a name="141"><span class="lineNum">     141 </span>            :      *</a>
+<a name="142"><span class="lineNum">     142 </span>            :      * @param replacements    a map whose keys are the names of variables, and whose values are the</a>
+<a name="143"><span class="lineNum">     143 </span>            :      *                        new names to replace them with</a>
+<a name="144"><span class="lineNum">     144 </span>            :      */</a>
+<a name="145"><span class="lineNum">     145 </span>            :     ParsedExpression renameVariables(const std::map&lt;std::string, std::string&gt;&amp; replacements) const;</a>
+<a name="146"><span class="lineNum">     146 </span>            : private:</a>
+<a name="147"><span class="lineNum">     147 </span>            :     static double evaluate(const ExpressionTreeNode&amp; node, const std::map&lt;std::string, double&gt;&amp; variables);</a>
+<a name="148"><span class="lineNum">     148 </span>            :     static ExpressionTreeNode preevaluateVariables(const ExpressionTreeNode&amp; node, const std::map&lt;std::string, double&gt;&amp; variables);</a>
+<a name="149"><span class="lineNum">     149 </span>            :     static ExpressionTreeNode precalculateConstantSubexpressions(const ExpressionTreeNode&amp; node, std::map&lt;int, ExpressionTreeNode&gt;&amp; nodeCache);</a>
+<a name="150"><span class="lineNum">     150 </span>            :     static ExpressionTreeNode substituteSimplerExpression(const ExpressionTreeNode&amp; node, std::map&lt;int, ExpressionTreeNode&gt;&amp; nodeCache);</a>
+<a name="151"><span class="lineNum">     151 </span>            :     static ExpressionTreeNode differentiate(const ExpressionTreeNode&amp; node, const std::string&amp; variable, std::map&lt;int, ExpressionTreeNode&gt;&amp; nodeCache);</a>
+<a name="152"><span class="lineNum">     152 </span>            :     static bool isConstant(const ExpressionTreeNode&amp; node);</a>
+<a name="153"><span class="lineNum">     153 </span>            :     static double getConstantValue(const ExpressionTreeNode&amp; node);</a>
+<a name="154"><span class="lineNum">     154 </span>            :     static ExpressionTreeNode renameNodeVariables(const ExpressionTreeNode&amp; node, const std::map&lt;std::string, std::string&gt;&amp; replacements);</a>
+<a name="155"><span class="lineNum">     155 </span>            :     ExpressionTreeNode rootNode;</a>
+<a name="156"><span class="lineNum">     156 </span>            : };</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : LEPTON_EXPORT std::ostream&amp; operator&lt;&lt;(std::ostream&amp; out, const ExpressionTreeNode&amp; node);</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : LEPTON_EXPORT std::ostream&amp; operator&lt;&lt;(std::ostream&amp; out, const ParsedExpression&amp; exp);</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : } // namespace lepton</a>
+<a name="163"><span class="lineNum">     163 </span>            : } // namespace PLMD</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : #endif /*LEPTON_PARSED_EXPRESSION_H_*/</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Parser.cpp.func-sort-c.html b/coverage-libs/lepton/Parser.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a71de139a0
--- /dev/null
+++ b/coverage-libs/lepton/Parser.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Parser.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Parser.cpp<span style="font-size: 80%;"> (<a href="Parser.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">275</td>
+            <td class="headerCovTableEntry">298</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Parser.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#122">_ZN4PLMD6lepton6Parser4trimERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#357">_ZZN4PLMD6lepton6Parser20getFunctionOperationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS7_PNS0_14CustomFunctionESt4lessIS7_ESaISt4pairIS8_SC_EEEENKUlvE_clEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#355">_ZN4PLMD6lepton6Parser20getFunctionOperationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS7_PNS0_14CustomFunctionESt4lessIS7_ESaISt4pairIS8_SC_EEE</a></td>
+              <td class="coverFnHi">1693</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#338">_ZN4PLMD6lepton6Parser20getOperatorOperationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">5036</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#83">_ZN4PLMD6lepton9ConstantsB5cxx11Ev</a></td>
+              <td class="coverFnHi">2009189</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#203">_ZN4PLMD6lepton6Parser5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2009208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#207">_ZN4PLMD6lepton6Parser5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS7_PNS0_14CustomFunctionESt4lessIS7_ESaISt4pairIS8_SC_EEE</a></td>
+              <td class="coverFnHi">2009208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#191">_ZN4PLMD6lepton6Parser8tokenizeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2009212</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#254">_ZN4PLMD6lepton6Parser15parsePrecedenceERKSt6vectorINS0_10ParseTokenESaIS3_EERiRKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_14CustomFunctionESt4lessISF_ESaISt4pairIKSF_SH_EEERKS9_ISF_NS0_18ExpressionTreeNodeESJ_SaISK_ISL_SR_EEEi</a></td>
+              <td class="coverFnHi">2016749</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#135">_ZN4PLMD6lepton6Parser12getNextTokenERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi</a></td>
+              <td class="coverFnHi">2024272</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Parser.cpp.func.html b/coverage-libs/lepton/Parser.cpp.func.html
new file mode 100644
index 0000000000..64c1b06d9c
--- /dev/null
+++ b/coverage-libs/lepton/Parser.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Parser.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Parser.cpp<span style="font-size: 80%;"> (<a href="Parser.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">275</td>
+            <td class="headerCovTableEntry">298</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Parser.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#135">_ZN4PLMD6lepton6Parser12getNextTokenERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi</a></td>
+              <td class="coverFnHi">2024272</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#254">_ZN4PLMD6lepton6Parser15parsePrecedenceERKSt6vectorINS0_10ParseTokenESaIS3_EERiRKSt3mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPNS0_14CustomFunctionESt4lessISF_ESaISt4pairIKSF_SH_EEERKS9_ISF_NS0_18ExpressionTreeNodeESJ_SaISK_ISL_SR_EEEi</a></td>
+              <td class="coverFnHi">2016749</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#355">_ZN4PLMD6lepton6Parser20getFunctionOperationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS7_PNS0_14CustomFunctionESt4lessIS7_ESaISt4pairIS8_SC_EEE</a></td>
+              <td class="coverFnHi">1693</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#338">_ZN4PLMD6lepton6Parser20getOperatorOperationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">5036</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#122">_ZN4PLMD6lepton6Parser4trimERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#203">_ZN4PLMD6lepton6Parser5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2009208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#207">_ZN4PLMD6lepton6Parser5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS7_PNS0_14CustomFunctionESt4lessIS7_ESaISt4pairIS8_SC_EEE</a></td>
+              <td class="coverFnHi">2009208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#191">_ZN4PLMD6lepton6Parser8tokenizeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2009212</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#83">_ZN4PLMD6lepton9ConstantsB5cxx11Ev</a></td>
+              <td class="coverFnHi">2009189</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Parser.cpp.gcov.html#357">_ZZN4PLMD6lepton6Parser20getFunctionOperationERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt3mapIS7_PNS0_14CustomFunctionESt4lessIS7_ESaISt4pairIS8_SC_EEEENKUlvE_clEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/Parser.cpp.gcov.html b/coverage-libs/lepton/Parser.cpp.gcov.html
new file mode 100644
index 0000000000..ededc22145
--- /dev/null
+++ b/coverage-libs/lepton/Parser.cpp.gcov.html
@@ -0,0 +1,584 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton/Parser.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">lepton</a> - Parser.cpp<span style="font-size: 80%;"> (source / <a href="Parser.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">275</td>
+            <td class="headerCovTableEntry">298</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="3"><span class="lineNum">       3 </span>            :  *                                   Lepton                                   *</a>
+<a name="4"><span class="lineNum">       4 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="5"><span class="lineNum">       5 </span>            :  * This is part of the Lepton expression parser originating from              *</a>
+<a name="6"><span class="lineNum">       6 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="7"><span class="lineNum">       7 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="8"><span class="lineNum">       8 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="9"><span class="lineNum">       9 </span>            :  *                                                                            *</a>
+<a name="10"><span class="lineNum">      10 </span>            :  * Portions copyright (c) 2013-2016 Stanford University and the Authors.      *</a>
+<a name="11"><span class="lineNum">      11 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="12"><span class="lineNum">      12 </span>            :  * Contributors:                                                              *</a>
+<a name="13"><span class="lineNum">      13 </span>            :  *                                                                            *</a>
+<a name="14"><span class="lineNum">      14 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="15"><span class="lineNum">      15 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="16"><span class="lineNum">      16 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="17"><span class="lineNum">      17 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="18"><span class="lineNum">      18 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="19"><span class="lineNum">      19 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="20"><span class="lineNum">      20 </span>            :  *                                                                            *</a>
+<a name="21"><span class="lineNum">      21 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="22"><span class="lineNum">      22 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="23"><span class="lineNum">      23 </span>            :  *                                                                            *</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="27"><span class="lineNum">      27 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="32"><span class="lineNum">      32 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="33"><span class="lineNum">      33 </span>            : /* -------------------------------------------------------------------------- *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  *                                   lepton                                   *</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * -------------------------------------------------------------------------- *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * This is part of the lepton expression parser originating from              *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Simbios, the NIH National Center for Physics-Based Simulation of           *</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * Biological Structures at Stanford, funded under the NIH Roadmap for        *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * Medical Research, grant U54 GM072970. See https://simtk.org.               *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *                                                                            *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Portions copyright (c) 2009-2019 Stanford University and the Authors.      *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * Authors: Peter Eastman                                                     *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Contributors:                                                              *</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *                                                                            *</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * Permission is hereby granted, free of charge, to any person obtaining a    *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * copy of this software and associated documentation files (the &quot;Software&quot;), *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * to deal in the Software without restriction, including without limitation  *</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * the rights to use, copy, modify, merge, publish, distribute, sublicense,   *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * and/or sell copies of the Software, and to permit persons to whom the      *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * Software is furnished to do so, subject to the following conditions:       *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *                                                                            *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * The above copyright notice and this permission notice shall be included in *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * all copies or substantial portions of the Software.                        *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *                                                                            *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,   *</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL    *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * THE AUTHORS, CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM,    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR      *</a>
+<a name="60"><span class="lineNum">      60 </span>            :  * OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE  *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  * USE OR OTHER DEALINGS IN THE SOFTWARE.                                     *</a>
+<a name="62"><span class="lineNum">      62 </span>            :  * -------------------------------------------------------------------------- */</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &quot;Parser.h&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &quot;CustomFunction.h&quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;ExpressionTreeNode.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &quot;Operation.h&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            : #include &quot;ParsedExpression.h&quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            : #include &lt;cctype&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            : #include &lt;iostream&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : namespace PLMD {</a>
+<a name="74"><span class="lineNum">      74 </span>            : using namespace lepton;</a>
+<a name="75"><span class="lineNum">      75 </span>            : using namespace std;</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : namespace lepton {</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : static const string Digits = &quot;0123456789&quot;;</a>
+<a name="80"><span class="lineNum">      80 </span>            : static const string Operators = &quot;+-*/^&quot;;</a>
+<a name="81"><span class="lineNum">      81 </span>            : static const bool LeftAssociative[] = {true, true, true, true, false};</a>
+<a name="82"><span class="lineNum">      82 </span>            : static const int Precedence[] = {0, 0, 1, 1, 3};</a>
+<a name="83"><span class="lineNum">      83 </span>            : static const Operation::Id OperationId[] = {Operation::ADD, Operation::SUBTRACT, Operation::MULTIPLY, Operation::DIVIDE, Operation::POWER};</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    2009189 : const std::map&lt;std::string, double&gt; &amp; Constants() {</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   static const std::map&lt;std::string, double&gt; constants = {</a>
+<a name="87"><span class="lineNum">      87 </span>            :   {&quot;e&quot;, std::exp(1.0)},</a>
+<a name="88"><span class="lineNum">      88 </span>            :   {&quot;log2e&quot;, 1.0/std::log(2.0)},</a>
+<a name="89"><span class="lineNum">      89 </span>            :   {&quot;log10e&quot;, 1.0/std::log(10.0)},</a>
+<a name="90"><span class="lineNum">      90 </span>            :   {&quot;ln2&quot;, std::log(2.0)},</a>
+<a name="91"><span class="lineNum">      91 </span>            :   {&quot;ln10&quot;, std::log(10.0)},</a>
+<a name="92"><span class="lineNum">      92 </span>            :   {&quot;pi&quot;, 3.14159265358979323844},</a>
+<a name="93"><span class="lineNum">      93 </span>            :   {&quot;pi_2&quot;, 3.14159265358979323844*0.5},</a>
+<a name="94"><span class="lineNum">      94 </span>            :   {&quot;pi_4&quot;, 3.14159265358979323844*0.25},</a>
+<a name="95"><span class="lineNum">      95 </span>            : //  {&quot;1_pi&quot;, 1.0/pi},</a>
+<a name="96"><span class="lineNum">      96 </span>            : //  {&quot;2_pi&quot;, 2.0/pi},</a>
+<a name="97"><span class="lineNum">      97 </span>            : //  {&quot;2_sqrtpi&quot;, 2.0/std::sqrt(pi)},</a>
+<a name="98"><span class="lineNum">      98 </span>            :   {&quot;sqrt2&quot;, std::sqrt(2.0)},</a>
+<a name="99"><span class="lineNum">      99 </span>            :   {&quot;sqrt1_2&quot;, std::sqrt(0.5)}</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">    2010223 :   };</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">    2009189 :   return constants;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    6111977 : class lepton::ParseToken {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : public:</a>
+<a name="109"><span class="lineNum">     109 </span>            :     enum Type {Number, Operator, Variable, Function, LeftParen, RightParen, Comma, Whitespace};</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">    2024272 :     ParseToken(string text, Type type) : text(text), type(type) {</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :     }</a>
+<a name="113"><span class="lineNum">     113 </span>            :     const string&amp; getText() const {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         15 :         return text;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     }</a>
+<a name="116"><span class="lineNum">     116 </span>            :     Type getType() const {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      13167 :         return type;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :     }</a>
+<a name="119"><span class="lineNum">     119 </span>            : private:</a>
+<a name="120"><span class="lineNum">     120 </span>            :     string text;</a>
+<a name="121"><span class="lineNum">     121 </span>            :     Type type;</a>
+<a name="122"><span class="lineNum">     122 </span>            : };</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 : string Parser::trim(const string&amp; expression) {</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     // Remove leading and trailing spaces.</a>
+<a name="126"><span class="lineNum">     126 </span>            :     </a>
+<a name="127"><span class="lineNum">     127 </span>            :     int start, end;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         12 :     for (start = 0; start &lt; (int) expression.size() &amp;&amp; isspace(expression[start]); start++)</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :         ;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :     for (end = (int) expression.size()-1; end &gt; start &amp;&amp; isspace(expression[end]); end--)</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :         ;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          8 :     if (start == end &amp;&amp; isspace(expression[end]))</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :         return &quot;&quot;;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          8 :     return expression.substr(start, end-start+1);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">    2024272 : ParseToken Parser::getNextToken(const string&amp; expression, int start) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">    2024272 :     char c = expression[start];</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">    2024272 :     if (c == '(')</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1350 :         return ParseToken(&quot;(&quot;, ParseToken::LeftParen);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">    2023597 :     if (c == ')')</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       4736 :         return ParseToken(&quot;)&quot;, ParseToken::RightParen);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">    2021229 :     if (c == ',')</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        160 :         return ParseToken(&quot;,&quot;, ParseToken::Comma);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">    2021149 :     if (Operators.find(c) != string::npos)</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       5089 :         return ParseToken(string(1, c), ParseToken::Operator);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">    2016060 :     if (isspace(c)) {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :         // White space</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         28 :         for (int pos = start+1; pos &lt; (int) expression.size(); pos++) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         21 :             if (!isspace(expression[pos]))</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         42 :                 return ParseToken(expression.substr(start, pos-start), ParseToken::Whitespace);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :         }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         14 :         return ParseToken(expression.substr(start, string::npos), ParseToken::Whitespace);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">    2016032 :     if (c == '.' || Digits.find(c) != string::npos) {</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :         // A number</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    2011015 :         bool foundDecimal = (c == '.');</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :         bool foundExp = false;</a>
+<a name="161"><span class="lineNum">     161 </span>            :         int pos;</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">   20090528 :         for (pos = start+1; pos &lt; (int) expression.size(); pos++) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">   18082169 :             c = expression[pos];</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">   18082169 :             if (Digits.find(c) != string::npos)</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">   16069233 :                 continue;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">    2012936 :             if (c == '.' &amp;&amp; !foundDecimal) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :                 foundDecimal = true;</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">    2010276 :                 continue;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :             }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       2660 :             if ((c == 'e' || c == 'E') &amp;&amp; !foundExp) {</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :                 foundExp = true;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 :                 if (pos &lt; (int) expression.size()-1 &amp;&amp; (expression[pos+1] == '-' || expression[pos+1] == '+'))</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :                     pos++;</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          4 :                 continue;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :             }</a>
+<a name="176"><span class="lineNum">     176 </span>            :             break;</a>
+<a name="177"><span class="lineNum">     177 </span>            :         }</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    4022030 :         return ParseToken(expression.substr(start, pos-start), ParseToken::Number);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :     }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :     // A variable, function, or left parenthesis</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      14882 :     for (int pos = start; pos &lt; (int) expression.size(); pos++) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      14659 :         c = expression[pos];</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">      14659 :         if (c == '(')</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       3386 :             return ParseToken(expression.substr(start, pos-start+1), ParseToken::Function);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      12966 :         if (Operators.find(c) != string::npos || c == ',' || c == ')' || isspace(c))</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       6202 :             return ParseToken(expression.substr(start, pos-start), ParseToken::Variable);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     }</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        446 :     return ParseToken(expression.substr(start, string::npos), ParseToken::Variable);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">    2009212 : vector&lt;ParseToken&gt; Parser::tokenize(const string&amp; expression) {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     vector&lt;ParseToken&gt; tokens;</a>
+<a name="195"><span class="lineNum">     195 </span>            :     int pos = 0;</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">    4033484 :     while (pos &lt; (int) expression.size()) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">    2024272 :         ParseToken token = getNextToken(expression, pos);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">    2024272 :         if (token.getType() != ParseToken::Whitespace)</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">    2024244 :             tokens.push_back(token);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">    2024272 :         pos += (int) token.getText().size();</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :     }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">    2009212 :     return tokens;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">    2009208 : ParsedExpression Parser::parse(const string&amp; expression) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">    4018397 :     return parse(expression, map&lt;string, CustomFunction*&gt;());</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    2009208 : ParsedExpression Parser::parse(const string&amp; expression, const map&lt;string, CustomFunction*&gt;&amp; customFunctions) {</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     try {</a>
+<a name="211"><span class="lineNum">     211 </span>            :         // First split the expression into subexpressions.</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">    2009208 :         string primaryExpression = expression;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :         vector&lt;string&gt; subexpressions;</a>
+<a name="215"><span class="lineNum">     215 </span>            :         while (true) {</a>
+<a name="216"><span class="lineNum">     216 </span>            :             string::size_type pos = primaryExpression.find_last_of(';');</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">    2009212 :             if (pos == string::npos)</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :                 break;</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          8 :             string sub = trim(primaryExpression.substr(pos+1));</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          4 :             if (sub.size() &gt; 0)</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          4 :                 subexpressions.push_back(sub);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          8 :             primaryExpression = primaryExpression.substr(0, pos);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          4 :         }</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :         // Parse the subexpressions.</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :         map&lt;string, ExpressionTreeNode&gt; subexpDefs;</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">    2009212 :         for (int i = 0; i &lt; (int) subexpressions.size(); i++) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          4 :             string::size_type equalsPos = subexpressions[i].find('=');</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          4 :             if (equalsPos == string::npos)</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :                 throw Exception(&quot;subexpression does not specify a name&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         27 :             string name = trim(subexpressions[i].substr(0, equalsPos));</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          4 :             if (name.size() == 0)</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :                 throw Exception(&quot;subexpression does not specify a name&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          4 :             vector&lt;ParseToken&gt; tokens = tokenize(subexpressions[i].substr(equalsPos+1));</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          4 :             int pos = 0;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          4 :             subexpDefs[name] = parsePrecedence(tokens, pos, customFunctions, subexpDefs, 0);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          4 :             if (pos != tokens.size())</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :                 throw Exception(&quot;unexpected text at end of subexpression: &quot;+tokens[pos].getText());</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          4 :         }</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :         // Now parse the primary expression.</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">    2009208 :         vector&lt;ParseToken&gt; tokens = tokenize(primaryExpression);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    2009208 :         int pos = 0;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">    2009208 :         ExpressionTreeNode result = parsePrecedence(tokens, pos, customFunctions, subexpDefs, 0);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">    2009204 :         if (pos != tokens.size())</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         30 :             throw Exception(&quot;unexpected text at end of expression: &quot;+tokens[pos].getText());</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">    4018378 :         return ParsedExpression(result);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">    4018431 :     }</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         19 :     catch (Exception&amp; ex) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         38 :         throw Exception(&quot;Parse error in expression \&quot;&quot;+expression+&quot;\&quot;: &quot;+ex.what());</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         19 :     }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">    2016749 : ExpressionTreeNode Parser::parsePrecedence(const vector&lt;ParseToken&gt;&amp; tokens, int&amp; pos, const map&lt;string, CustomFunction*&gt;&amp; customFunctions,</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :             const map&lt;string, ExpressionTreeNode&gt;&amp; subexpressionDefs, int precedence) {</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">    2016749 :     if (pos == tokens.size())</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          8 :         throw Exception(&quot;unexpected end of expression&quot;);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :     // Parse the next value (number, variable, function, parenthesized expression)</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :     ParseToken token = tokens[pos];</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">    2016745 :     ExpressionTreeNode result;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">    2016745 :     if (token.getType() == ParseToken::Number) {</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :         double value;</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">    4022030 :         stringstream(token.getText()) &gt;&gt; value;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">    2011015 :         result = ExpressionTreeNode(new Operation::Constant(value));</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">    2011015 :         pos++;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       5730 :     else if (token.getType() == ParseToken::Variable) {</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :         map&lt;string, ExpressionTreeNode&gt;::const_iterator subexp = subexpressionDefs.find(token.getText());</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       3309 :         if (subexp == subexpressionDefs.end()) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       3305 :             Operation* op = new Operation::Variable(token.getText());</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       3305 :             result = ExpressionTreeNode(op);</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :         }</a>
+<a name="277"><span class="lineNum">     277 </span>            :         else</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          4 :             result = subexp-&gt;second;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       3309 :         pos++;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :     }</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       2421 :     else if (token.getType() == ParseToken::LeftParen) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        675 :         pos++;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        675 :         result = parsePrecedence(tokens, pos, customFunctions, subexpressionDefs, 0);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        675 :         if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen)</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :             throw Exception(&quot;unbalanced parentheses&quot;);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">        675 :         pos++;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :     }</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       1746 :     else if (token.getType() == ParseToken::Function) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       1693 :         pos++;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :         vector&lt;ExpressionTreeNode&gt; args;</a>
+<a name="291"><span class="lineNum">     291 </span>            :         bool moreArgs;</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       1773 :         do {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       3546 :             args.push_back(parsePrecedence(tokens, pos, customFunctions, subexpressionDefs, 0));</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       1773 :             moreArgs = (pos &lt; (int) tokens.size() &amp;&amp; tokens[pos].getType() == ParseToken::Comma);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :             if (moreArgs)</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         80 :                 pos++;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :         } while (moreArgs);</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1693 :         if (pos == tokens.size() || tokens[pos].getType() != ParseToken::RightParen)</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :             throw Exception(&quot;unbalanced parentheses&quot;);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1693 :         pos++;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       1693 :         Operation* op = getFunctionOperation(token.getText(), customFunctions);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :         try {</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       1693 :             result = ExpressionTreeNode(op, args);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :         }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :         catch (...) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 :             delete op;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :             throw;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1693 :     }</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        106 :     else if (token.getType() == ParseToken::Operator &amp;&amp; token.getText() == &quot;-&quot;) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         53 :         pos++;</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         53 :         ExpressionTreeNode toNegate = parsePrecedence(tokens, pos, customFunctions, subexpressionDefs, 2);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         53 :         result = ExpressionTreeNode(new Operation::Negate(), toNegate);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         53 :     }</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :     else</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :         throw Exception(&quot;unexpected token: &quot;+token.getText());</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :     // Now deal with the next binary operator.</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">    2021781 :     while (pos &lt; (int) tokens.size() &amp;&amp; tokens[pos].getType() == ParseToken::Operator) {</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :         token = tokens[pos];</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       7336 :         int opIndex = (int) Operators.find(token.getText());</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       7336 :         int opPrecedence = Precedence[opIndex];</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">       7336 :         if (opPrecedence &lt; precedence)</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       2300 :             return result;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       5036 :         pos++;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">       5036 :         ExpressionTreeNode arg = parsePrecedence(tokens, pos, customFunctions, subexpressionDefs, LeftAssociative[opIndex] ? opPrecedence+1 : opPrecedence);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       5036 :         Operation* op = getOperatorOperation(token.getText());</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :         try {</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       5036 :             result = ExpressionTreeNode(op, result, arg);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :         }</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :         catch (...) {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :             delete op;</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :             throw;</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       5036 :     }</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     return result;</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       5036 : Operation* Parser::getOperatorOperation(const std::string&amp; name) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       5036 :     switch (OperationId[Operators.find(name)]) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       1081 :         case Operation::ADD:</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">       1081 :             return new Operation::Add();</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        882 :         case Operation::SUBTRACT:</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        882 :             return new Operation::Subtract();</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">       2395 :         case Operation::MULTIPLY:</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       2395 :             return new Operation::Multiply();</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        460 :         case Operation::DIVIDE:</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        460 :             return new Operation::Divide();</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        218 :         case Operation::POWER:</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        218 :             return new Operation::Power();</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :         default:</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :             throw Exception(&quot;unknown operator&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :     }</a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       1693 : Operation* Parser::getFunctionOperation(const std::string&amp; name, const map&lt;string, CustomFunction*&gt;&amp; customFunctions) {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         40 :     const static map&lt;string, Operation::Id&gt; opMap = []() {</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :         map&lt;string, Operation::Id&gt; opMap;</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         40 :         opMap[&quot;sqrt&quot;] = Operation::SQRT;</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         40 :         opMap[&quot;exp&quot;] = Operation::EXP;</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         40 :         opMap[&quot;log&quot;] = Operation::LOG;</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         40 :         opMap[&quot;sin&quot;] = Operation::SIN;</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         40 :         opMap[&quot;cos&quot;] = Operation::COS;</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         40 :         opMap[&quot;sec&quot;] = Operation::SEC;</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         40 :         opMap[&quot;csc&quot;] = Operation::CSC;</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         40 :         opMap[&quot;tan&quot;] = Operation::TAN;</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         40 :         opMap[&quot;cot&quot;] = Operation::COT;</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         40 :         opMap[&quot;asin&quot;] = Operation::ASIN;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         40 :         opMap[&quot;acos&quot;] = Operation::ACOS;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         40 :         opMap[&quot;atan&quot;] = Operation::ATAN;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         40 :         opMap[&quot;atan2&quot;] = Operation::ATAN2;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         40 :         opMap[&quot;sinh&quot;] = Operation::SINH;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         40 :         opMap[&quot;cosh&quot;] = Operation::COSH;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         40 :         opMap[&quot;tanh&quot;] = Operation::TANH;</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         40 :         opMap[&quot;erf&quot;] = Operation::ERF;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         40 :         opMap[&quot;erfc&quot;] = Operation::ERFC;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         40 :         opMap[&quot;step&quot;] = Operation::STEP;</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         40 :         opMap[&quot;delta&quot;] = Operation::DELTA;</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         40 :         opMap[&quot;nandelta&quot;] = Operation::NANDELTA;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         40 :         opMap[&quot;square&quot;] = Operation::SQUARE;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         40 :         opMap[&quot;cube&quot;] = Operation::CUBE;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         40 :         opMap[&quot;recip&quot;] = Operation::RECIPROCAL;</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         40 :         opMap[&quot;min&quot;] = Operation::MIN;</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         40 :         opMap[&quot;max&quot;] = Operation::MAX;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         40 :         opMap[&quot;abs&quot;] = Operation::ABS;</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         40 :         opMap[&quot;floor&quot;] = Operation::FLOOR;</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         40 :         opMap[&quot;ceil&quot;] = Operation::CEIL;</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         40 :         opMap[&quot;select&quot;] = Operation::SELECT;</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         40 :         opMap[&quot;acot&quot;] = Operation::ACOT;</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         40 :         opMap[&quot;asec&quot;] = Operation::ASEC;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         40 :         opMap[&quot;acsc&quot;] = Operation::ACSC;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         40 :         opMap[&quot;coth&quot;] = Operation::COTH;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         40 :         opMap[&quot;sech&quot;] = Operation::SECH;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         40 :         opMap[&quot;csch&quot;] = Operation::CSCH;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         40 :         opMap[&quot;asinh&quot;] = Operation::ASINH;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         40 :         opMap[&quot;acosh&quot;] = Operation::ACOSH;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         40 :         opMap[&quot;atanh&quot;] = Operation::ATANH;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         40 :         opMap[&quot;acoth&quot;] = Operation::ACOTH;</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         40 :         opMap[&quot;asech&quot;] = Operation::ASECH;</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         40 :         opMap[&quot;acsch&quot;] = Operation::ACSCH;</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         40 :         opMap[&quot;atan2&quot;] = Operation::ATAN2;</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         40 :         return opMap;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       1693 :     }();</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">       1693 :     string trimmed = name.substr(0, name.size()-1);</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :     // First check custom functions.</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :     map&lt;string, CustomFunction*&gt;::const_iterator custom = customFunctions.find(trimmed);</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       1693 :     if (custom != customFunctions.end())</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :         return new Operation::Custom(trimmed, custom-&gt;second-&gt;clone());</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :     // Now try standard functions.</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            :     map&lt;string, Operation::Id&gt;::const_iterator iter = opMap.find(trimmed);</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">       1693 :     if (iter == opMap.end())</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :         throw Exception(&quot;unknown function: &quot;+trimmed);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">       1693 :     switch (iter-&gt;second) {</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         58 :         case Operation::SQRT:</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         58 :             return new Operation::Sqrt();</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         27 :         case Operation::EXP:</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         27 :             return new Operation::Exp();</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          5 :         case Operation::LOG:</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          5 :             return new Operation::Log();</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">        117 :         case Operation::SIN:</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">        117 :             return new Operation::Sin();</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">       1265 :         case Operation::COS:</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       1265 :             return new Operation::Cos();</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          4 :         case Operation::SEC:</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">          4 :             return new Operation::Sec();</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">          4 :         case Operation::CSC:</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">          4 :             return new Operation::Csc();</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          4 :         case Operation::TAN:</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          4 :             return new Operation::Tan();</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          4 :         case Operation::COT:</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          4 :             return new Operation::Cot();</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          4 :         case Operation::ASIN:</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          4 :             return new Operation::Asin();</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          4 :         case Operation::ACOS:</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          4 :             return new Operation::Acos();</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          4 :         case Operation::ATAN:</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          4 :             return new Operation::Atan();</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         16 :         case Operation::ATAN2:</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         16 :             return new Operation::Atan2();</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          4 :         case Operation::SINH:</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          4 :             return new Operation::Sinh();</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          4 :         case Operation::COSH:</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          4 :             return new Operation::Cosh();</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          4 :         case Operation::TANH:</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">          4 :             return new Operation::Tanh();</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          4 :         case Operation::ERF:</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">          4 :             return new Operation::Erf();</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          4 :         case Operation::ERFC:</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          4 :             return new Operation::Erfc();</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">         28 :         case Operation::STEP:</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         28 :             return new Operation::Step();</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          4 :         case Operation::DELTA:</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          4 :             return new Operation::Delta();</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          4 :         case Operation::NANDELTA:</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          4 :             return new Operation::Nandelta();</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          4 :         case Operation::SQUARE:</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          4 :             return new Operation::Square();</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">          4 :         case Operation::CUBE:</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          4 :             return new Operation::Cube();</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          4 :         case Operation::RECIPROCAL:</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          4 :             return new Operation::Reciprocal();</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          8 :         case Operation::MIN:</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          8 :             return new Operation::Min();</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          8 :         case Operation::MAX:</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          8 :             return new Operation::Max();</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         13 :         case Operation::ABS:</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         13 :             return new Operation::Abs();</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          4 :         case Operation::FLOOR:</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">          4 :             return new Operation::Floor();</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          4 :         case Operation::CEIL:</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          4 :             return new Operation::Ceil();</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         24 :         case Operation::SELECT:</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         24 :             return new Operation::Select();</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          4 :         case Operation::ACOT:</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          4 :             return new Operation::Acot();</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          4 :         case Operation::ASEC:</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          4 :             return new Operation::Asec();</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          4 :         case Operation::ACSC:</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          4 :             return new Operation::Acsc();</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          4 :         case Operation::COTH:</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          4 :             return new Operation::Coth();</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          4 :         case Operation::SECH:</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          4 :             return new Operation::Sech();</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          4 :         case Operation::CSCH:</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          4 :             return new Operation::Csch();</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          4 :         case Operation::ASINH:</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          4 :             return new Operation::Asinh();</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          4 :         case Operation::ACOSH:</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          4 :             return new Operation::Acosh();</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          4 :         case Operation::ATANH:</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          4 :             return new Operation::Atanh();</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          4 :         case Operation::ACOTH:</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          4 :             return new Operation::Acoth();</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          4 :         case Operation::ASECH:</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          4 :             return new Operation::Asech();</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          4 :         case Operation::ACSCH:</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          4 :             return new Operation::Acsch();</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :         default:</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :             throw Exception(&quot;unknown function&quot;);</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     }</a>
+<a name="507"><span class="lineNum">     507 </span>            : }</a>
+<a name="508"><span class="lineNum">     508 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/index-sort-f.html b/coverage-libs/lepton/index-sort-f.html
new file mode 100644
index 0000000000..7b0692d8c2
--- /dev/null
+++ b/coverage-libs/lepton/index-sort-f.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - lepton</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1593</td>
+            <td class="headerCovTableEntry">1789</td>
+            <td class="headerCovTableEntryMed">89.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">395</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpressionProgram.cpp.gcov.html">ExpressionProgram.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 52</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.h.gcov.html">Exception.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParsedExpression.cpp.gcov.html">ParsedExpression.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.0%"><img src="../snow.png" width=14 height=10 alt="86.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.0&nbsp;%</td>
+      <td class="coverNumMed">221 / 257</td>
+      <td class="coverPerMed">76.2&nbsp;%</td>
+      <td class="coverNumMed">16 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Operation.cpp.gcov.html">Operation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">267 / 315</td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 57</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CompiledExpression.cpp.gcov.html">CompiledExpression.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">224 / 231</td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">18 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Operation.h.gcov.html">Operation.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.3%"><img src="../snow.png" width=5 height=10 alt="95.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.3&nbsp;%</td>
+      <td class="coverNumHi">530 / 556</td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">280 / 290</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParsedExpression.h.gcov.html">ParsedExpression.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CompiledExpression.h.gcov.html">CompiledExpression.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Parser.cpp.gcov.html">Parser.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">275 / 298</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpressionTreeNode.cpp.gcov.html">ExpressionTreeNode.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">68 / 72</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/index-sort-l.html b/coverage-libs/lepton/index-sort-l.html
new file mode 100644
index 0000000000..6dd52f90d8
--- /dev/null
+++ b/coverage-libs/lepton/index-sort-l.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - lepton</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1593</td>
+            <td class="headerCovTableEntry">1789</td>
+            <td class="headerCovTableEntryMed">89.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">395</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpressionProgram.cpp.gcov.html">ExpressionProgram.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 52</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Operation.cpp.gcov.html">Operation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">267 / 315</td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 57</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParsedExpression.cpp.gcov.html">ParsedExpression.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.0%"><img src="../snow.png" width=14 height=10 alt="86.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.0&nbsp;%</td>
+      <td class="coverNumMed">221 / 257</td>
+      <td class="coverPerMed">76.2&nbsp;%</td>
+      <td class="coverNumMed">16 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Parser.cpp.gcov.html">Parser.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">275 / 298</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpressionTreeNode.cpp.gcov.html">ExpressionTreeNode.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">68 / 72</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Operation.h.gcov.html">Operation.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.3%"><img src="../snow.png" width=5 height=10 alt="95.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.3&nbsp;%</td>
+      <td class="coverNumHi">530 / 556</td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">280 / 290</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CompiledExpression.cpp.gcov.html">CompiledExpression.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">224 / 231</td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">18 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParsedExpression.h.gcov.html">ParsedExpression.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CompiledExpression.h.gcov.html">CompiledExpression.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.h.gcov.html">Exception.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/lepton/index.html b/coverage-libs/lepton/index.html
new file mode 100644
index 0000000000..121dc0aec9
--- /dev/null
+++ b/coverage-libs/lepton/index.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - lepton</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - lepton</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1593</td>
+            <td class="headerCovTableEntry">1789</td>
+            <td class="headerCovTableEntryMed">89.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">395</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CompiledExpression.cpp.gcov.html">CompiledExpression.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">224 / 231</td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">18 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CompiledExpression.h.gcov.html">CompiledExpression.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.h.gcov.html">Exception.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpressionProgram.cpp.gcov.html">ExpressionProgram.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 52</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpressionTreeNode.cpp.gcov.html">ExpressionTreeNode.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">68 / 72</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Operation.cpp.gcov.html">Operation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">267 / 315</td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 57</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Operation.h.gcov.html">Operation.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.3%"><img src="../snow.png" width=5 height=10 alt="95.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.3&nbsp;%</td>
+      <td class="coverNumHi">530 / 556</td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">280 / 290</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParsedExpression.cpp.gcov.html">ParsedExpression.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.0%"><img src="../snow.png" width=14 height=10 alt="86.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.0&nbsp;%</td>
+      <td class="coverNumMed">221 / 257</td>
+      <td class="coverPerMed">76.2&nbsp;%</td>
+      <td class="coverNumMed">16 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParsedExpression.h.gcov.html">ParsedExpression.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Parser.cpp.gcov.html">Parser.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">275 / 298</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/Gromacs.h.func-sort-c.html b/coverage-libs/molfile/Gromacs.h.func-sort-c.html
new file mode 100644
index 0000000000..2558e4c232
--- /dev/null
+++ b/coverage-libs/molfile/Gromacs.h.func-sort-c.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/Gromacs.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - Gromacs.h<span style="font-size: 80%;"> (<a href="Gromacs.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">342</td>
+            <td class="headerCovTableEntry">750</td>
+            <td class="headerCovTableEntryLo">45.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">61.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  </table>
+  <br>
+
+</body>
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diff --git a/coverage-libs/molfile/Gromacs.h.func.html b/coverage-libs/molfile/Gromacs.h.func.html
new file mode 100644
index 0000000000..7c5ebbe3eb
--- /dev/null
+++ b/coverage-libs/molfile/Gromacs.h.func.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/Gromacs.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - Gromacs.h<span style="font-size: 80%;"> (<a href="Gromacs.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">342</td>
+            <td class="headerCovTableEntry">750</td>
+            <td class="headerCovTableEntryLo">45.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">61.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
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+    <tr>
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+    <tr>
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+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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index 0000000000..b2573f2f2b
--- /dev/null
+++ b/coverage-libs/molfile/Gromacs.h.gcov.html
@@ -0,0 +1,2089 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/Gromacs.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - Gromacs.h<span style="font-size: 80%;"> (source / <a href="Gromacs.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">342</td>
+            <td class="headerCovTableEntry">750</td>
+            <td class="headerCovTableEntryLo">45.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">61.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifndef __PLUMED_molfile_Gromacs_h</a>
+<a name="38"><span class="lineNum">      38 </span>            : #define __PLUMED_molfile_Gromacs_h</a>
+<a name="39"><span class="lineNum">      39 </span>            : /***************************************************************************</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                        University of Illinois</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr                         All Rights Reserved</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *cr</a>
+<a name="45"><span class="lineNum">      45 </span>            :  ***************************************************************************/</a>
+<a name="46"><span class="lineNum">      46 </span>            : /***************************************************************************</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * RCS INFORMATION:</a>
+<a name="48"><span class="lineNum">      48 </span>            :  *      $RCSfile: Gromacs.h,v $</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $Revision: 1.36 $       $Date: 2020/01/09 16:21:28 $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  ***************************************************************************/</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : /*</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * GROMACS file format reader for VMD</a>
+<a name="55"><span class="lineNum">      55 </span>            :  *</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * This code provides a high level I/O library for reading</a>
+<a name="57"><span class="lineNum">      57 </span>            :  * and writing the following file formats:</a>
+<a name="58"><span class="lineNum">      58 </span>            :  *      gro     GROMACS format or trajectory</a>
+<a name="59"><span class="lineNum">      59 </span>            :  *      g96     GROMOS-96 format or trajectory</a>
+<a name="60"><span class="lineNum">      60 </span>            :  *      trj     Trajectory - x, v and f (binary, full precision)</a>
+<a name="61"><span class="lineNum">      61 </span>            :  *      trr     Trajectory - x, v and f (binary, full precision, portable)</a>
+<a name="62"><span class="lineNum">      62 </span>            :  *      xtc     Trajectory - x only (compressed, portable, any precision)</a>
+<a name="63"><span class="lineNum">      63 </span>            :  *      top</a>
+<a name="64"><span class="lineNum">      64 </span>            :  * Currently supported: gro trj trr g96 [xtc]</a>
+<a name="65"><span class="lineNum">      65 </span>            :  *</a>
+<a name="66"><span class="lineNum">      66 </span>            :  * TODO list</a>
+<a name="67"><span class="lineNum">      67 </span>            :  *   o  velocities are ignored because VMD doesn't use them, but some other </a>
+<a name="68"><span class="lineNum">      68 </span>            :  *      program might ...</a>
+<a name="69"><span class="lineNum">      69 </span>            :  *   o  gro_rec() assumes positions in .gro files are nanometers and</a>
+<a name="70"><span class="lineNum">      70 </span>            :  *      converts to angstroms, whereas they really could be any unit</a>
+<a name="71"><span class="lineNum">      71 </span>            :  */</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : #ifndef GROMACS_H</a>
+<a name="74"><span class="lineNum">      74 </span>            : #define GROMACS_H</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : #include &lt;math.h&gt;</a>
+<a name="77"><span class="lineNum">      77 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="78"><span class="lineNum">      78 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="79"><span class="lineNum">      79 </span>            : #include &lt;string.h&gt;</a>
+<a name="80"><span class="lineNum">      80 </span>            : #include &lt;ctype.h&gt;</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : #if defined(_AIX)</a>
+<a name="83"><span class="lineNum">      83 </span>            : #include &lt;strings.h&gt;</a>
+<a name="84"><span class="lineNum">      84 </span>            : #endif</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : #include &quot;endianswap.h&quot;</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : namespace PLMD{</a>
+<a name="89"><span class="lineNum">      89 </span>            : namespace molfile{</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : #if defined(WIN32) || defined(WIN64)</a>
+<a name="92"><span class="lineNum">      92 </span>            : #define strcasecmp stricmp</a>
+<a name="93"><span class="lineNum">      93 </span>            : #endif</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : #ifndef M_PI_2</a>
+<a name="96"><span class="lineNum">      96 </span>            : #define M_PI_2 1.57079632679489661922</a>
+<a name="97"><span class="lineNum">      97 </span>            : #endif</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : // Error codes for mdio_errno</a>
+<a name="100"><span class="lineNum">     100 </span>            : #define MDIO_SUCCESS            0</a>
+<a name="101"><span class="lineNum">     101 </span>            : #define MDIO_BADFORMAT          1</a>
+<a name="102"><span class="lineNum">     102 </span>            : #define MDIO_EOF                2</a>
+<a name="103"><span class="lineNum">     103 </span>            : #define MDIO_BADPARAMS          3</a>
+<a name="104"><span class="lineNum">     104 </span>            : #define MDIO_IOERROR            4</a>
+<a name="105"><span class="lineNum">     105 </span>            : #define MDIO_BADPRECISION       5</a>
+<a name="106"><span class="lineNum">     106 </span>            : #define MDIO_BADMALLOC          6</a>
+<a name="107"><span class="lineNum">     107 </span>            : #define MDIO_CANTOPEN           7</a>
+<a name="108"><span class="lineNum">     108 </span>            : #define MDIO_BADEXTENSION       8</a>
+<a name="109"><span class="lineNum">     109 </span>            : #define MDIO_UNKNOWNFMT         9</a>
+<a name="110"><span class="lineNum">     110 </span>            : #define MDIO_CANTCLOSE          10</a>
+<a name="111"><span class="lineNum">     111 </span>            : #define MDIO_WRONGFORMAT        11</a>
+<a name="112"><span class="lineNum">     112 </span>            : #define MDIO_SIZEERROR          12</a>
+<a name="113"><span class="lineNum">     113 </span>            : #define MDIO_UNKNOWNERROR       1000</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : #define MDIO_READ       0</a>
+<a name="116"><span class="lineNum">     116 </span>            : #define MDIO_WRITE      1</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : #define MDIO_MAX_ERRVAL         11</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : // Format extensions</a>
+<a name="121"><span class="lineNum">     121 </span>            : const char *mdio_fmtexts[] = {</a>
+<a name="122"><span class="lineNum">     122 </span>            :     &quot;&quot;,</a>
+<a name="123"><span class="lineNum">     123 </span>            :     &quot;.gro&quot;,</a>
+<a name="124"><span class="lineNum">     124 </span>            :     &quot;.trr&quot;,</a>
+<a name="125"><span class="lineNum">     125 </span>            :     &quot;.g96&quot;,</a>
+<a name="126"><span class="lineNum">     126 </span>            :     &quot;.trj&quot;,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     &quot;.xtc&quot;,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     NULL</a>
+<a name="129"><span class="lineNum">     129 </span>            : };</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : static int mdio_errcode;        // Last error code</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : #define TRX_MAGIC       1993    // Magic number for .trX files</a>
+<a name="135"><span class="lineNum">     135 </span>            : #define XTC_MAGIC       1995    // Magic number for .xtc files</a>
+<a name="136"><span class="lineNum">     136 </span>            : #define MAX_GRO_LINE    500     // Maximum line length of .gro files</a>
+<a name="137"><span class="lineNum">     137 </span>            : #define MAX_G96_LINE    500     // Maximum line length of .g96 files</a>
+<a name="138"><span class="lineNum">     138 </span>            : #define MAX_TRX_TITLE   80      // Maximum length of a title in .trX</a>
+<a name="139"><span class="lineNum">     139 </span>            : #define MAX_MDIO_TITLE  80      // Maximum supported title length</a>
+<a name="140"><span class="lineNum">     140 </span>            : #define ANGS_PER_NM     10      // Unit conversion factor</a>
+<a name="141"><span class="lineNum">     141 </span>            : #define ANGS2_PER_NM2   100     // Unit conversion factor</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : // All the supported file types and their respective extensions</a>
+<a name="145"><span class="lineNum">     145 </span>            : #define MDFMT_GRO               1</a>
+<a name="146"><span class="lineNum">     146 </span>            : #define MDFMT_TRR               2</a>
+<a name="147"><span class="lineNum">     147 </span>            : #define MDFMT_G96               3</a>
+<a name="148"><span class="lineNum">     148 </span>            : #define MDFMT_TRJ               4</a>
+<a name="149"><span class="lineNum">     149 </span>            : #define MDFMT_XTC               5</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : // A structure to hold .trX file format header information. This</a>
+<a name="153"><span class="lineNum">     153 </span>            : // is an optional member of the md_file structure that is used</a>
+<a name="154"><span class="lineNum">     154 </span>            : // when .trX files are being dealt with.</a>
+<a name="155"><span class="lineNum">     155 </span>            : typedef struct {</a>
+<a name="156"><span class="lineNum">     156 </span>            :         int version;            // File version number</a>
+<a name="157"><span class="lineNum">     157 </span>            :         char title[MAX_TRX_TITLE + 1];  // File title</a>
+<a name="158"><span class="lineNum">     158 </span>            :         int ir_size;</a>
+<a name="159"><span class="lineNum">     159 </span>            :         int e_size;</a>
+<a name="160"><span class="lineNum">     160 </span>            :         int box_size;</a>
+<a name="161"><span class="lineNum">     161 </span>            :         int vir_size;</a>
+<a name="162"><span class="lineNum">     162 </span>            :         int pres_size;</a>
+<a name="163"><span class="lineNum">     163 </span>            :         int top_size;</a>
+<a name="164"><span class="lineNum">     164 </span>            :         int sym_size;</a>
+<a name="165"><span class="lineNum">     165 </span>            :         int x_size;             // Positions of atoms</a>
+<a name="166"><span class="lineNum">     166 </span>            :         int v_size;             // Velocities of atoms</a>
+<a name="167"><span class="lineNum">     167 </span>            :         int f_size;</a>
+<a name="168"><span class="lineNum">     168 </span>            :         int natoms;             // Number of atoms in the system</a>
+<a name="169"><span class="lineNum">     169 </span>            :         int step;</a>
+<a name="170"><span class="lineNum">     170 </span>            :         int nre;</a>
+<a name="171"><span class="lineNum">     171 </span>            :         float t;</a>
+<a name="172"><span class="lineNum">     172 </span>            :         float lambda;</a>
+<a name="173"><span class="lineNum">     173 </span>            : } trx_hdr;</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : // A generic i/o structure that contains information about the</a>
+<a name="177"><span class="lineNum">     177 </span>            : // file itself and the input/output state</a>
+<a name="178"><span class="lineNum">     178 </span>            : typedef struct {</a>
+<a name="179"><span class="lineNum">     179 </span>            :         FILE *  f;      // Pointer to the file</a>
+<a name="180"><span class="lineNum">     180 </span>            :         int     fmt;    // The file format</a>
+<a name="181"><span class="lineNum">     181 </span>            :         int     prec;   // Real number precision</a>
+<a name="182"><span class="lineNum">     182 </span>            :         int     rev;    // Reverse endiannism?</a>
+<a name="183"><span class="lineNum">     183 </span>            :         trx_hdr * trx;  // Trx files require a great deal more</a>
+<a name="184"><span class="lineNum">     184 </span>            :                         // header data to be stored.</a>
+<a name="185"><span class="lineNum">     185 </span>            : } md_file;</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : // A format-independent structure to hold header data from files</a>
+<a name="189"><span class="lineNum">     189 </span>            : typedef struct {</a>
+<a name="190"><span class="lineNum">     190 </span>            :         char title[MAX_MDIO_TITLE + 1];</a>
+<a name="191"><span class="lineNum">     191 </span>            :         int natoms;</a>
+<a name="192"><span class="lineNum">     192 </span>            :         float timeval;</a>
+<a name="193"><span class="lineNum">     193 </span>            : } md_header;</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : // A format-independent structure to hold unit cell data</a>
+<a name="197"><span class="lineNum">     197 </span>            : typedef struct {</a>
+<a name="198"><span class="lineNum">     198 </span>            :   float A, B, C, alpha, beta, gamma;</a>
+<a name="199"><span class="lineNum">     199 </span>            : } md_box;</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : // Timestep information</a>
+<a name="203"><span class="lineNum">     203 </span>            : typedef struct {</a>
+<a name="204"><span class="lineNum">     204 </span>            :         float *pos;     // Position array (3 * natoms)</a>
+<a name="205"><span class="lineNum">     205 </span>            :         //float *vel;   // Velocity array ** (VMD doesn't use this) **</a>
+<a name="206"><span class="lineNum">     206 </span>            :         //float *f;     // Force array ** (VMD doesn't use this) **</a>
+<a name="207"><span class="lineNum">     207 </span>            :         //float *box;   // Computational box ** (VMD doesn't use this) **</a>
+<a name="208"><span class="lineNum">     208 </span>            :         int natoms;     // Number of atoms</a>
+<a name="209"><span class="lineNum">     209 </span>            :         int step;       // Simulation step</a>
+<a name="210"><span class="lineNum">     210 </span>            :         float time;     // Time of simulation</a>
+<a name="211"><span class="lineNum">     211 </span>            :   md_box *box;</a>
+<a name="212"><span class="lineNum">     212 </span>            : } md_ts;</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : // Atom information</a>
+<a name="216"><span class="lineNum">     216 </span>            : typedef struct {</a>
+<a name="217"><span class="lineNum">     217 </span>            :         char resid[7];          // Residue index number</a>
+<a name="218"><span class="lineNum">     218 </span>            :         char resname[7];        // Residue name</a>
+<a name="219"><span class="lineNum">     219 </span>            :         int atomnum;            // Atom index number</a>
+<a name="220"><span class="lineNum">     220 </span>            :         char atomname[7];       // Atom name</a>
+<a name="221"><span class="lineNum">     221 </span>            :         float pos[3];           // Position array (3 * natoms)</a>
+<a name="222"><span class="lineNum">     222 </span>            :         //float vel[3]; // Velocity array ** (VMD doesn't use this) **</a>
+<a name="223"><span class="lineNum">     223 </span>            : } md_atom;</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : // Open a molecular dynamics file. The second parameter specifies</a>
+<a name="227"><span class="lineNum">     227 </span>            : // the format of the file. If it is zero, the format is determined</a>
+<a name="228"><span class="lineNum">     228 </span>            : // from the file extension. the third argument (if given) decides</a>
+<a name="229"><span class="lineNum">     229 </span>            : // whether to read (==0) or to write (!= 0).</a>
+<a name="230"><span class="lineNum">     230 </span>            : // using a default argument set to read for backward compatibility.</a>
+<a name="231"><span class="lineNum">     231 </span>            : static md_file *mdio_open(const char *, const int, const int=MDIO_READ);</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : // Closes a molecular dynamics file.</a>
+<a name="234"><span class="lineNum">     234 </span>            : static int mdio_close(md_file *);</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : // Format-independent file I/O routines</a>
+<a name="238"><span class="lineNum">     238 </span>            : static int mdio_header(md_file *, md_header *);</a>
+<a name="239"><span class="lineNum">     239 </span>            : static int mdio_timestep(md_file *, md_ts *);</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : // .gro file functions</a>
+<a name="243"><span class="lineNum">     243 </span>            : static int gro_header(md_file *, char *, int, float *, int *, int = 1);</a>
+<a name="244"><span class="lineNum">     244 </span>            : static int gro_rec(md_file *, md_atom *);</a>
+<a name="245"><span class="lineNum">     245 </span>            : static int gro_timestep(md_file *, md_ts *);</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : // .trX file functions</a>
+<a name="249"><span class="lineNum">     249 </span>            : static int trx_header(md_file *, int = 0);</a>
+<a name="250"><span class="lineNum">     250 </span>            : static int trx_int(md_file *, int *);</a>
+<a name="251"><span class="lineNum">     251 </span>            : static int trx_real(md_file *, float *);</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : static int trx_rvector(md_file *, float *);</a>
+<a name="254"><span class="lineNum">     254 </span>            : static int trx_string(md_file *, char *, int);</a>
+<a name="255"><span class="lineNum">     255 </span>            : static int trx_timestep(md_file *, md_ts *);</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : // .g96 file functions</a>
+<a name="258"><span class="lineNum">     258 </span>            : static int g96_header(md_file *, char *, int, float *);</a>
+<a name="259"><span class="lineNum">     259 </span>            : static int g96_timestep(md_file *, md_ts *);</a>
+<a name="260"><span class="lineNum">     260 </span>            : static int g96_rec(md_file *, md_atom *);</a>
+<a name="261"><span class="lineNum">     261 </span>            : static int g96_countatoms(md_file *);</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : // .xtc file functions</a>
+<a name="265"><span class="lineNum">     265 </span>            : static int xtc_int(md_file *, int *);</a>
+<a name="266"><span class="lineNum">     266 </span>            : static int xtc_float(md_file *, float *);</a>
+<a name="267"><span class="lineNum">     267 </span>            : /* </a>
+<a name="268"><span class="lineNum">     268 </span>            : static int xtc_receivebits(int *, int);</a>
+<a name="269"><span class="lineNum">     269 </span>            : static void xtc_receiveints(int *, int, int, const unsigned *, int *);</a>
+<a name="270"><span class="lineNum">     270 </span>            : */</a>
+<a name="271"><span class="lineNum">     271 </span>            : static int xtc_timestep(md_file *, md_ts *);</a>
+<a name="272"><span class="lineNum">     272 </span>            : static int xtc_3dfcoord(md_file *, float *, int *, float *);</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : // Error reporting functions</a>
+<a name="276"><span class="lineNum">     276 </span>            : static int mdio_errno(void);</a>
+<a name="277"><span class="lineNum">     277 </span>            : static const char *mdio_errmsg(int);</a>
+<a name="278"><span class="lineNum">     278 </span>            : static int mdio_seterror(int);</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : // Miscellaneous functions</a>
+<a name="282"><span class="lineNum">     282 </span>            : static int strip_white(char *);</a>
+<a name="283"><span class="lineNum">     283 </span>            : static int mdio_readline(md_file *, char *, int, int = 1);</a>
+<a name="284"><span class="lineNum">     284 </span>            : static int mdio_tsfree(md_ts *, int = 0);</a>
+<a name="285"><span class="lineNum">     285 </span>            : static int mdio_readbox(md_box *, float *, float *, float *);</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : static int xtc_receivebits(int *, int);</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : // Error descriptions for mdio_errno</a>
+<a name="292"><span class="lineNum">     292 </span>            : static const char *mdio_errdescs[] = {</a>
+<a name="293"><span class="lineNum">     293 </span>            :         &quot;no error&quot;,</a>
+<a name="294"><span class="lineNum">     294 </span>            :         &quot;file does not match format&quot;,</a>
+<a name="295"><span class="lineNum">     295 </span>            :         &quot;unexpected end-of-file reached&quot;,</a>
+<a name="296"><span class="lineNum">     296 </span>            :         &quot;function called with bad parameters&quot;,</a>
+<a name="297"><span class="lineNum">     297 </span>            :         &quot;file i/o error&quot;,</a>
+<a name="298"><span class="lineNum">     298 </span>            :         &quot;unsupported precision&quot;,</a>
+<a name="299"><span class="lineNum">     299 </span>            :         &quot;out of memory&quot;,</a>
+<a name="300"><span class="lineNum">     300 </span>            :         &quot;cannot open file&quot;,</a>
+<a name="301"><span class="lineNum">     301 </span>            :         &quot;bad file extension&quot;,</a>
+<a name="302"><span class="lineNum">     302 </span>            :         &quot;unknown file format&quot;,</a>
+<a name="303"><span class="lineNum">     303 </span>            :         &quot;cannot close file&quot;,</a>
+<a name="304"><span class="lineNum">     304 </span>            :         &quot;wrong file format for this function&quot;,</a>
+<a name="305"><span class="lineNum">     305 </span>            :         &quot;binary i/o error: sizeof(int) != 4&quot;,</a>
+<a name="306"><span class="lineNum">     306 </span>            :         NULL</a>
+<a name="307"><span class="lineNum">     307 </span>            : };</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : /*! \fn static inline bool host_is_little_endian(void)</a>
+<a name="310"><span class="lineNum">     310 </span>            :  * detect endiannes of host machine. returns true on little endian machines. */</a>
+<a name="311"><span class="lineNum">     311 </span>            : static inline int host_is_little_endian(void) </a>
+<a name="312"><span class="lineNum">     312 </span>            : {</a>
+<a name="313"><span class="lineNum">     313 </span>            :   const union { unsigned char c[4]; unsigned int i; } </a>
+<a name="314"><span class="lineNum">     314 </span>            :   fixed = { { 0x10 , 0x20 , 0x40 , 0x80 } };</a>
+<a name="315"><span class="lineNum">     315 </span>            :   const unsigned int i = 0x80402010U;</a>
+<a name="316"><span class="lineNum">     316 </span>            :         </a>
+<a name="317"><span class="lineNum">     317 </span>            :   if (fixed.i == i) {</a>
+<a name="318"><span class="lineNum">     318 </span>            :     return 1;</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            :   return 0;</a>
+<a name="321"><span class="lineNum">     321 </span>            : }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            : // Open a molecular dynamics file. The second parameter specifies</a>
+<a name="326"><span class="lineNum">     326 </span>            : // the format of the file. If it is zero, the format is determined</a>
+<a name="327"><span class="lineNum">     327 </span>            : // from the file extension.</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        195 : md_file *mdio_open(const char *fn, const int fmt, const int rw) {</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :         md_file *mf;</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        195 :         if (!fn) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :                 mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :                 return NULL;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :         }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :         // Allocate memory</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        195 :         mf = (md_file *) malloc(sizeof(md_file));</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        195 :         if (!mf) {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :                 mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :                 return NULL;</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :         }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :         // Zero out the structure</a>
+<a name="344"><span class="lineNum">     344 </span>            :         memset(mf, 0, sizeof(md_file));</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            :         // Determine the file type from the extension</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">        195 :         if (!fmt) {</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :                 char *p;</a>
+<a name="349"><span class="lineNum">     349 </span>            :                 int n;</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :                 // Seek to the extension part of the filename</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :                 for (p = (char *) &amp;fn[strlen(fn) - 1]; *p != '.' &amp;&amp; p &gt; fn; p--);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :                 if (p == fn) {</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :                         free(mf);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 :                         mdio_seterror(MDIO_BADEXTENSION);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :                         return NULL;</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :                 }</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            :                 // Check the extension against known extensions</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :                 for (n = 1; mdio_fmtexts[n]; n++)</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :                         if (!strcasecmp(p, mdio_fmtexts[n])) break;</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            :                 // If !mdio_fmtexts[n], we failed (unknown ext)</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :                 if (!mdio_fmtexts[n]) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :                         free(mf);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :                         mdio_seterror(MDIO_UNKNOWNFMT);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :                         return NULL;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :                 }</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span>            :                 // All set</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :                 mf-&gt;fmt = n;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :         }</a>
+<a name="373"><span class="lineNum">     373 </span>            :         else {</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        195 :                 mf-&gt;fmt = fmt;</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :         }</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            :         // Differentiate between binary and ascii files. Also,</a>
+<a name="378"><span class="lineNum">     378 </span>            :         // .trX files need a header information structure allocated.</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        195 :         switch (mf-&gt;fmt) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     case MDFMT_GRO:</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :         case MDFMT_G96: /* fallthrough */</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :         if (rw) </span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :             mf-&gt;f = fopen(fn, &quot;wt&quot;);</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :         else</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :             mf-&gt;f = fopen(fn, &quot;rt&quot;);</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            :                 break;</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">          5 :         case MDFMT_TRR:</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :         case MDFMT_TRJ: /* fallthrough */</a>
+<a name="390"><span class="lineNum">     390 </span>            :                 // Allocate the trx header data struct</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          5 :                 mf-&gt;trx = (trx_hdr *) malloc(sizeof(trx_hdr));</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          5 :                 if (!mf-&gt;trx) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :                         free(mf);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :                         mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :                         return NULL;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :                 }</a>
+<a name="397"><span class="lineNum">     397 </span>            :                 memset(mf-&gt;trx, 0, sizeof(trx_hdr));</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        195 :         case MDFMT_XTC:  /* fallthrough */</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :                 // Finally, open the file</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        195 :         if (rw)</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :             mf-&gt;f = fopen(fn, &quot;wb&quot;);</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :         else</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">        195 :             mf-&gt;f = fopen(fn, &quot;rb&quot;);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            :                 break;</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineNoCov">          0 :         default:</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :                 free(mf);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :                 mdio_seterror(MDIO_UNKNOWNFMT);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :                 return NULL;</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :         }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            :         // Check for opening error</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">        195 :         if (!mf-&gt;f) {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :                 if (mf-&gt;trx) free(mf-&gt;trx);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :                 free(mf);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :                 mdio_seterror(MDIO_CANTOPEN);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :                 return NULL;</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :         }</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :         // File is opened, we're all set!</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        195 :         mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        195 :         return mf;</span></a>
+<a name="423"><span class="lineNum">     423 </span>            : }</a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            : // Closes a molecular dynamics file.</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">        195 : static int mdio_close(md_file *mf) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">        195 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        195 :         if (fclose(mf-&gt;f) == EOF) return mdio_seterror(MDIO_CANTCLOSE);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :         // Free the dynamically allocated memory</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        195 :         if (mf-&gt;trx) free(mf-&gt;trx);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        195 :         free(mf);</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">        195 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : }</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span>            : // Returns the last error code reported by any of the mdio functions</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        195 : static int mdio_errno(void) {</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">        195 :         return mdio_errcode;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : }</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span>            : // Returns a textual message regarding an mdio error code</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 : static const char *mdio_errmsg(int n) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineNoCov">          0 :         if (n &lt; 0 || n &gt; MDIO_MAX_ERRVAL) return (char *) &quot;unknown error&quot;;</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :         else return mdio_errdescs[n];</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : }</a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            : // Sets the error code and returns an appropriate return value</a>
+<a name="453"><span class="lineNum">     453 </span>            : // for the calling function to return to its parent</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">    2419581 : static int mdio_seterror(int code) {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">    2419581 :         mdio_errcode = code;</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">    2419581 :         return code ? -1 : 0;</span></a>
+<a name="457"><span class="lineNum">     457 </span>            : }</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            : // Reads a line from the text file, strips leading/trailing whitespace</a>
+<a name="461"><span class="lineNum">     461 </span>            : // and newline, checks for errors, and returns the number of characters</a>
+<a name="462"><span class="lineNum">     462 </span>            : // in the string on success or -1 on error.</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 : static int mdio_readline(md_file *mf, char *buf, int n, int strip) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :         if (!buf || n &lt; 1 || !mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span>            :         // Read the line</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :         fgets(buf, n, mf-&gt;f);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span>            :         // End of file reached?</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 :         if (feof(mf-&gt;f)) return mdio_seterror(MDIO_EOF);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :         // File I/O error?</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :         if (ferror(mf-&gt;f)) return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            :         // comment line?</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :         if (buf[0] == '#') return mdio_readline(mf,buf,n,strip);</span></a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span>            :         // Strip whitespace</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :         if (strip) strip_white(buf);</span></a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :         return strlen(buf);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            : }</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            : // Strips leading and trailing whitespace from a string. Tabs,</a>
+<a name="486"><span class="lineNum">     486 </span>            : // spaces, newlines and carriage returns are stripped. Example:</a>
+<a name="487"><span class="lineNum">     487 </span>            : // &quot;\n   hello\t \r&quot; becomes &quot;hello&quot;.</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 : static int strip_white(char *buf) {</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :         int i, j, k;</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            :         // Protect against NULL pointer</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :         if (!buf) return -1;</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :         if (!strlen(buf)) return -1;</span></a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :         // Kill trailing whitespace first</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :         for (i = strlen(buf) - 1;</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :              buf[i] == ' ' || buf[i] == '\t' ||</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :              buf[i] == '\n' || buf[i] == '\r';</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :              i--)</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :                 buf[i] = 0;</span></a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            :         // Skip past leading whitespace</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :         for (i = 0; buf[i] == ' ' || buf[i] == '\t' ||</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :              buf[i] == '\n' || buf[i] == '\r'; i++);</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :         if (i) {</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :                 k = 0;</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :                 for (j = i; buf[j]; j++)</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineNoCov">          0 :                         buf[k++] = buf[j];</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :                 buf[k] = 0;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :         }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :         return strlen(buf);</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : </a>
+<a name="516"><span class="lineNum">     516 </span>            : // Frees the memory allocated in a ts structure. The holderror</a>
+<a name="517"><span class="lineNum">     517 </span>            : // parameter defaults to zero. Programs that are calling this</a>
+<a name="518"><span class="lineNum">     518 </span>            : // function because of an error reported by another function should</a>
+<a name="519"><span class="lineNum">     519 </span>            : // set holderror so that mdio_tsfree() does not overwrite the error</a>
+<a name="520"><span class="lineNum">     520 </span>            : // code with mdio_seterror().</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">      18257 : static int mdio_tsfree(md_ts *ts, int holderror) {</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">      18257 :         if (!ts) {</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :                 if (holderror) return -1;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :                 else return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :         }</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">      18257 :         if (ts-&gt;pos &amp;&amp; ts-&gt;natoms &gt; 0) free(ts-&gt;pos);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">      18257 :   if (ts-&gt;box) free(ts-&gt;box);</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">      18257 :         if (holderror) return -1;</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">      18257 :         else return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="533"><span class="lineNum">     533 </span>            : }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span>            : // Converts box basis vectors to A, B, C, alpha, beta, and gamma.  </a>
+<a name="537"><span class="lineNum">     537 </span>            : // Stores values in md_box struct, which should be allocated before calling</a>
+<a name="538"><span class="lineNum">     538 </span>            : // this function.</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">      18257 : static int mdio_readbox(md_box *box, float *x, float *y, float *z) {</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :   float A, B, C;</a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">      18257 :   if (!box) {</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :   }</a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span>            :   // A, B, C are the lengths of the x, y, z vectors, respectively</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">      18257 :   A = sqrt( x[0]*x[0] + x[1]*x[1] + x[2]*x[2] ) * ANGS_PER_NM;</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">      18257 :   B = sqrt( y[0]*y[0] + y[1]*y[1] + y[2]*y[2] ) * ANGS_PER_NM;</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">      18257 :   C = sqrt( z[0]*z[0] + z[1]*z[1] + z[2]*z[2] ) * ANGS_PER_NM;</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">      18257 :   if ((A&lt;=0) || (B&lt;=0) || (C&lt;=0)) {</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :     /* Use zero-length box size and set angles to 90. */</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :     box-&gt;A = box-&gt;B = box-&gt;C = 0;</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :     box-&gt;alpha = box-&gt;beta = box-&gt;gamma = 90;</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :   } else {</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">      18257 :     box-&gt;A = A;</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">      18257 :     box-&gt;B = B;</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">      18257 :     box-&gt;C = C;</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   </a>
+<a name="559"><span class="lineNum">     559 </span>            :     // gamma, beta, alpha are the angles between the x &amp; y, x &amp; z, y &amp; z</a>
+<a name="560"><span class="lineNum">     560 </span>            :     // vectors, respectively</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">      18257 :     box-&gt;gamma = acos( (x[0]*y[0]+x[1]*y[1]+x[2]*y[2])*ANGS2_PER_NM2/(A*B) ) * 90.0/M_PI_2;</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">      18257 :     box-&gt;beta = acos( (x[0]*z[0]+x[1]*z[1]+x[2]*z[2])*ANGS2_PER_NM2/(A*C) ) * 90.0/M_PI_2;</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">      18257 :     box-&gt;alpha = acos( (y[0]*z[0]+y[1]*z[1]+y[2]*z[2])*ANGS2_PER_NM2/(B*C) ) * 90.0/M_PI_2; </span></a>
+<a name="564"><span class="lineNum">     564 </span>            :   }</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">      18257 :   return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : }</a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span>            : // Reads the header of a file (format independent)</a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">        195 : static int mdio_header(md_file *mf, md_header *mdh) {</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :         int n;</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">        195 :         if (!mf || !mdh) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        195 :         if (!mf-&gt;f) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        195 :         switch (mf-&gt;fmt) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :         case MDFMT_GRO:</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :                 if (gro_header(mf, mdh-&gt;title, MAX_MDIO_TITLE,</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :                 &amp;mdh-&gt;timeval, &amp;mdh-&gt;natoms, 1) &lt; 0)</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :                 return 0;</a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">          5 :         case MDFMT_TRR: </span></a>
+<a name="583"><span class="lineNum">     583 </span>            :         case MDFMT_TRJ: /* fallthrough */</a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">          5 :                 if (trx_header(mf, 1) &lt; 0) return -1;</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">          5 :                 mdh-&gt;natoms = mf-&gt;trx-&gt;natoms;</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">          5 :                 mdh-&gt;timeval = (float) mf-&gt;trx-&gt;t;</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">          5 :                 strncpy(mdh-&gt;title, mf-&gt;trx-&gt;title, MAX_MDIO_TITLE);</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">          5 :                 return 0;</span></a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :         case MDFMT_G96:</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :                 if (g96_header(mf, mdh-&gt;title, MAX_MDIO_TITLE,</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :                 &amp;mdh-&gt;timeval) &lt; 0) return -1;</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 :                 mdh-&gt;natoms = -1;</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            :         case MDFMT_XTC:</a>
+<a name="597"><span class="lineNum">     597 </span>            :                 memset(mdh, 0, sizeof(md_header));</a>
+<a name="598"><span class="lineNum">     598 </span>            :                 // Check magic number</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">        190 :                 if (xtc_int(mf, &amp;n) &lt; 0) return -1;</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">        190 :                 if (n != XTC_MAGIC) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span>            :                 // Get number of atoms</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">        190 :                 if (xtc_int(mf, &amp;n) &lt; 0) return -1;</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        190 :                 mdh-&gt;natoms = n;</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        190 :                 rewind(mf-&gt;f);</span></a>
+<a name="606"><span class="lineNum">     606 </span>            :                 return 0;</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :         default:</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_UNKNOWNFMT);</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :         }</a>
+<a name="611"><span class="lineNum">     611 </span>            : }</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            : // Reads in a timestep from a file (format independent)</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">      18452 : static int mdio_timestep(md_file *mf, md_ts *ts) {</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">      18452 :         if (!mf || !ts) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">      18452 :         if (!mf-&gt;f) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">      18452 :         switch (mf-&gt;fmt) {</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :         case MDFMT_GRO:</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :                 return gro_timestep(mf, ts);</span></a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        155 :         case MDFMT_TRR:</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :         case MDFMT_TRJ: /* fallthrough */</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">        155 :                 return trx_timestep(mf, ts);</span></a>
+<a name="626"><span class="lineNum">     626 </span>            : </a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :         case MDFMT_G96:</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :                 return g96_timestep(mf, ts);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">      18297 :         case MDFMT_XTC:</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">      18297 :                 return xtc_timestep(mf, ts);</span></a>
+<a name="632"><span class="lineNum">     632 </span>            : </a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineNoCov">          0 :         default:</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_UNKNOWNFMT);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :         }</a>
+<a name="636"><span class="lineNum">     636 </span>            : }</a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 : static int g96_header(md_file *mf, char *title, int titlelen, float *timeval) {</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :         char buf[MAX_G96_LINE + 1];</a>
+<a name="642"><span class="lineNum">     642 </span>            :         char *p;</a>
+<a name="643"><span class="lineNum">     643 </span>            : </a>
+<a name="644"><span class="lineNum">     644 </span>            :         // Check parameters</a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            :         // The header consists of blocks. The title block</a>
+<a name="648"><span class="lineNum">     648 </span>            :         // is mandatory, and a TIMESTEP block is optional.</a>
+<a name="649"><span class="lineNum">     649 </span>            :         // Example:</a>
+<a name="650"><span class="lineNum">     650 </span>            :         //</a>
+<a name="651"><span class="lineNum">     651 </span>            :         // TITLE</a>
+<a name="652"><span class="lineNum">     652 </span>            :         // Generated by trjconv :  t=  90.00000</a>
+<a name="653"><span class="lineNum">     653 </span>            :         // more title info</a>
+<a name="654"><span class="lineNum">     654 </span>            :         // .</a>
+<a name="655"><span class="lineNum">     655 </span>            :         // .</a>
+<a name="656"><span class="lineNum">     656 </span>            :         // .</a>
+<a name="657"><span class="lineNum">     657 </span>            :         // END</a>
+<a name="658"><span class="lineNum">     658 </span>            :         // .</a>
+<a name="659"><span class="lineNum">     659 </span>            :         // .</a>
+<a name="660"><span class="lineNum">     660 </span>            :         // .</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :         if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :         if (strcasecmp(buf, &quot;TITLE&quot;)) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="664"><span class="lineNum">     664 </span>            : </a>
+<a name="665"><span class="lineNum">     665 </span>            :         // Read in the title itself</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :         if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="667"><span class="lineNum">     667 </span>            : </a>
+<a name="668"><span class="lineNum">     668 </span>            :         // The timevalue can be included in the title string</a>
+<a name="669"><span class="lineNum">     669 </span>            :         // after a &quot;t=&quot; prefix.</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :         if ((p = (char *) strstr(buf, &quot;t=&quot;))) {</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :                 char *q = p;</a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :                 *(q--) = 0;</span></a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :                 // Skip the `t=' and strip whitespace from</a>
+<a name="675"><span class="lineNum">     675 </span>            :                 // the resulting strings</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :                 p += 2;</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :                 strip_white(p);</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :                 strip_white(buf);</span></a>
+<a name="679"><span class="lineNum">     679 </span>            : </a>
+<a name="680"><span class="lineNum">     680 </span>            :                 // Grab the timevalue from the title string</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :                 if (timeval) *timeval = (float) atof(p);</span></a>
+<a name="682"><span class="lineNum">     682 </span>            :         }</a>
+<a name="683"><span class="lineNum">     683 </span>            :         else {</a>
+<a name="684"><span class="lineNum">     684 </span>            :                 // No timevalue - just copy the string and strip</a>
+<a name="685"><span class="lineNum">     685 </span>            :                 // any leading/trailing whitespace</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :                 if (timeval) *timeval = 0;</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :                 strip_white(buf);</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :         }</a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span>            :         // Copy the title string</a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :         if (title &amp;&amp; titlelen) strncpy(title, buf, titlelen);</span></a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :         // Now ignore subsequent title lines and get the END string</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :         while (strcasecmp(buf, &quot;END&quot;))</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="696"><span class="lineNum">     696 </span>            : </a>
+<a name="697"><span class="lineNum">     697 </span>            :         // Done!</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="699"><span class="lineNum">     699 </span>            : }</a>
+<a name="700"><span class="lineNum">     700 </span>            : </a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            : // Used to determine the number of atoms in a g96 file, because</a>
+<a name="703"><span class="lineNum">     703 </span>            : // VMD needs to know this for some reason.</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineNoCov">          0 : static int g96_countatoms(md_file *mf) {</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :         char buf[MAX_G96_LINE + 1];</a>
+<a name="706"><span class="lineNum">     706 </span>            :         int natoms;</a>
+<a name="707"><span class="lineNum">     707 </span>            :         int n;</a>
+<a name="708"><span class="lineNum">     708 </span>            :         long fpos;</a>
+<a name="709"><span class="lineNum">     709 </span>            :         float lastf;</a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineNoCov">          0 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :         fpos = ftell(mf-&gt;f);</span></a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            :         natoms = 0;</a>
+<a name="716"><span class="lineNum">     716 </span>            :         for (;;) {</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1, 0) &lt; 0)</span></a>
+<a name="718"><span class="lineNum">     718 </span>            :                         break;</a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :                 n = sscanf(buf, &quot;%*6c%*6c%*6c%*6c %*f %*f %f&quot;, &amp;lastf);</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineNoCov">          0 :                 if (n == 1) natoms++;</span></a>
+<a name="721"><span class="lineNum">     721 </span>            :                 else {</a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineNoCov">          0 :                         strip_white(buf);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :                         if (!strcasecmp(buf, &quot;END&quot;)) break;</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :                 }</a>
+<a name="725"><span class="lineNum">     725 </span>            :         }</a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :         fseek(mf-&gt;f, fpos, SEEK_SET);</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :         return natoms;</span></a>
+<a name="729"><span class="lineNum">     729 </span>            : }</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span>            : </a>
+<a name="732"><span class="lineNum">     732 </span>            : // Reads an atom line from the G96 file</a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineNoCov">          0 : static int g96_rec(md_file *mf, md_atom *ma) {</span></a>
+<a name="734"><span class="lineNum">     734 </span>            :         char buf[MAX_G96_LINE + 1];</a>
+<a name="735"><span class="lineNum">     735 </span>            :         char atomnum[7];</a>
+<a name="736"><span class="lineNum">     736 </span>            :         int n;</a>
+<a name="737"><span class="lineNum">     737 </span>            : </a>
+<a name="738"><span class="lineNum">     738 </span>            :         // Check parameters</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :         if (!mf || !ma) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="740"><span class="lineNum">     740 </span>            : </a>
+<a name="741"><span class="lineNum">     741 </span>            :         // Read in a line, assuming it is an atom line</a>
+<a name="742"><span class="lineNum">     742 </span>            :         do {</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1, 0) &lt; 0) return -1;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :         } while (buf[0] == '#' || strlen(buf) == 0);</span></a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 :         n = sscanf(buf, &quot;%6c%6c%6c%6c %f %f %f&quot;,</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineNoCov">          0 :                 ma-&gt;resid, ma-&gt;resname, ma-&gt;atomname, atomnum,</span></a>
+<a name="748"><span class="lineNum">     748 </span>            :                 &amp;ma-&gt;pos[0], &amp;ma-&gt;pos[1], &amp;ma-&gt;pos[2]);</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineNoCov">          0 :         if (n == 7) {</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :                 atomnum[6] = 0;</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineNoCov">          0 :                 ma-&gt;resid[6] = 0;</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineNoCov">          0 :                 ma-&gt;resname[6] = 0;</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :                 ma-&gt;atomname[6] = 0;</span></a>
+<a name="754"><span class="lineNum">     754 </span>            : </a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :                 strip_white(atomnum);</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineNoCov">          0 :                 strip_white(ma-&gt;resid);</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 :                 strip_white(ma-&gt;resname);</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :                 strip_white(ma-&gt;atomname);</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineNoCov">          0 :                 ma-&gt;atomnum = atoi(atomnum);</span></a>
+<a name="761"><span class="lineNum">     761 </span>            : </a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :                 ma-&gt;pos[0] *= ANGS_PER_NM;</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineNoCov">          0 :                 ma-&gt;pos[1] *= ANGS_PER_NM;</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineNoCov">          0 :                 ma-&gt;pos[2] *= ANGS_PER_NM;</span></a>
+<a name="765"><span class="lineNum">     765 </span>            : </a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="767"><span class="lineNum">     767 </span>            :         }</a>
+<a name="768"><span class="lineNum">     768 </span>            : </a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="770"><span class="lineNum">     770 </span>            : }</a>
+<a name="771"><span class="lineNum">     771 </span>            : </a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            : // Reads a timestep from a G96 file and stores the data in</a>
+<a name="774"><span class="lineNum">     774 </span>            : // the generic md_ts structure. Returns 0 on success or a</a>
+<a name="775"><span class="lineNum">     775 </span>            : // negative number on error and sets mdio_errcode.</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineNoCov">          0 : static int g96_timestep(md_file *mf, md_ts *ts) {</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :         char            buf[MAX_G96_LINE + 1];</a>
+<a name="778"><span class="lineNum">     778 </span>            :         char            stripbuf[MAX_G96_LINE + 1];</a>
+<a name="779"><span class="lineNum">     779 </span>            :         float           pos[3], x[3], y[3], z[3], *currAtom;</a>
+<a name="780"><span class="lineNum">     780 </span>            :         long            fpos;</a>
+<a name="781"><span class="lineNum">     781 </span>            :         int             n, i, boxItems;</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            :         // Check parameters</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineNoCov">          0 :         if (!mf || !ts) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="785"><span class="lineNum">     785 </span>            : </a>
+<a name="786"><span class="lineNum">     786 </span>            :   // Allocate data space for the timestep, using the number of atoms</a>
+<a name="787"><span class="lineNum">     787 </span>            :   // determined by open_g96_read().</a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineNoCov">          0 :         ts-&gt;pos = (float *) malloc(sizeof(float) * 3 * ts-&gt;natoms);</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineNoCov">          0 :         if (!ts-&gt;pos) {</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="791"><span class="lineNum">     791 </span>            :         }</a>
+<a name="792"><span class="lineNum">     792 </span>            :   currAtom = ts-&gt;pos;</a>
+<a name="793"><span class="lineNum">     793 </span>            : </a>
+<a name="794"><span class="lineNum">     794 </span>            :         // The timesteps follow the header in a fixed block</a>
+<a name="795"><span class="lineNum">     795 </span>            :         // format:</a>
+<a name="796"><span class="lineNum">     796 </span>            :         //</a>
+<a name="797"><span class="lineNum">     797 </span>            :         // TIMESTEP</a>
+<a name="798"><span class="lineNum">     798 </span>            :         //         &lt;step number&gt; &lt;time value&gt;</a>
+<a name="799"><span class="lineNum">     799 </span>            :         // END</a>
+<a name="800"><span class="lineNum">     800 </span>            :         // POSITIONRED</a>
+<a name="801"><span class="lineNum">     801 </span>            :         //     &lt;x float&gt; &lt;y float&gt; &lt;z float&gt;</a>
+<a name="802"><span class="lineNum">     802 </span>            :         //     .         .         .</a>
+<a name="803"><span class="lineNum">     803 </span>            :         //     .         .         .</a>
+<a name="804"><span class="lineNum">     804 </span>            :         //     .         .         .</a>
+<a name="805"><span class="lineNum">     805 </span>            :         // END</a>
+<a name="806"><span class="lineNum">     806 </span>            :         // VELOCITYRED</a>
+<a name="807"><span class="lineNum">     807 </span>            :         //     &lt;x float&gt; &lt;y float&gt; &lt;z float&gt;</a>
+<a name="808"><span class="lineNum">     808 </span>            :         //     .         .         .</a>
+<a name="809"><span class="lineNum">     809 </span>            :         //     .         .         .</a>
+<a name="810"><span class="lineNum">     810 </span>            :         //     .         .         .</a>
+<a name="811"><span class="lineNum">     811 </span>            :         // END</a>
+<a name="812"><span class="lineNum">     812 </span>            :         // BOX</a>
+<a name="813"><span class="lineNum">     813 </span>            :         //     &lt;x float&gt; &lt;y float&gt; &lt;z float&gt;</a>
+<a name="814"><span class="lineNum">     814 </span>            :         // END</a>
+<a name="815"><span class="lineNum">     815 </span>            :         //</a>
+<a name="816"><span class="lineNum">     816 </span>            :         // -----</a>
+<a name="817"><span class="lineNum">     817 </span>            :         //</a>
+<a name="818"><span class="lineNum">     818 </span>            :         // The TIMESTEP, VELOCITY and BOX blocks are optional.</a>
+<a name="819"><span class="lineNum">     819 </span>            :         // Floats are written in 15.9 precision.</a>
+<a name="820"><span class="lineNum">     820 </span>            :         //</a>
+<a name="821"><span class="lineNum">     821 </span>            :         // Reference: GROMACS 2.0 user manual</a>
+<a name="822"><span class="lineNum">     822 </span>            :         //            http://rugmd4.chem.rug.nl/~gmx/online2.0/g96.html</a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span>            :         // First, look for an (optional) title block and skip it</a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineNoCov">          0 :         if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="826"><span class="lineNum">     826 </span>            : </a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineNoCov">          0 :   if (!strcasecmp(buf, &quot;TITLE&quot;)) {</span></a>
+<a name="828"><span class="lineNum">     828 </span>            :     // skip over the text until we reach 'END'</a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineNoCov">          0 :     while (strcasecmp(buf, &quot;END&quot;)) {</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineNoCov">          0 :       if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :     }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            :     // Read in the next line</a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineNoCov">          0 :     if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="835"><span class="lineNum">     835 </span>            :   }</a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            :         // Next, look for a timestep block</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineNoCov">          0 :         if (!strcasecmp(buf, &quot;TIMESTEP&quot;)) {</span></a>
+<a name="839"><span class="lineNum">     839 </span>            :                 // Read in the value line</a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="841"><span class="lineNum">     841 </span>            : </a>
+<a name="842"><span class="lineNum">     842 </span>            :                 // Extract the time value and the timestep index</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineNoCov">          0 :                 n = sscanf(buf, &quot;%d %f&quot;, &amp;ts-&gt;step, &amp;ts-&gt;time);</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineNoCov">          0 :                 if (n != 2) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span>            :                 // Read the &quot;END&quot; line</a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineNoCov">          0 :                 if (strcasecmp(buf, &quot;END&quot;))</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="850"><span class="lineNum">     850 </span>            : </a>
+<a name="851"><span class="lineNum">     851 </span>            :                 // Read in the next line</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="853"><span class="lineNum">     853 </span>            :         }</a>
+<a name="854"><span class="lineNum">     854 </span>            :         else {</a>
+<a name="855"><span class="lineNum">     855 </span>            :                 // No timestep specified -- set to zero</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :                 ts-&gt;step = 0;</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineNoCov">          0 :                 ts-&gt;time = 0;</span></a>
+<a name="858"><span class="lineNum">     858 </span>            :         }</a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :         // At this point a POSITION or POSITIONRED block</a>
+<a name="861"><span class="lineNum">     861 </span>            :         // is REQUIRED by the format</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineNoCov">          0 :         if (!strcasecmp(buf, &quot;POSITIONRED&quot;)) {</span></a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span>            :     // So now we read in some atoms</a>
+<a name="865"><span class="lineNum">     865 </span>            :     i = 0;</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineNoCov">          0 :                 while (i &lt; ts-&gt;natoms) {</span></a>
+<a name="867"><span class="lineNum">     867 </span>            :                         // Read in an atom</a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineNoCov">          0 :                         if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :                                 return -1;</a>
+<a name="870"><span class="lineNum">     870 </span>            :  </a>
+<a name="871"><span class="lineNum">     871 </span>            :       // We shouldn't reach the end yet</a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineNoCov">          0 :       if (!strcasecmp(buf, &quot;END&quot;))</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="874"><span class="lineNum">     874 </span>            : </a>
+<a name="875"><span class="lineNum">     875 </span>            :                         // Get the x,y,z coordinates</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineNoCov">          0 :                         n = sscanf(buf, &quot;%f %f %f&quot;, &amp;pos[0], &amp;pos[1], &amp;pos[2]);</span></a>
+<a name="877"><span class="lineNum">     877 </span>            :       </a>
+<a name="878"><span class="lineNum">     878 </span>            :       // Ignore improperly formatted lines</a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineNoCov">          0 :                         if (n == 3) {</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :                                 pos[0] *= ANGS_PER_NM;</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineNoCov">          0 :                                 pos[1] *= ANGS_PER_NM;</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineNoCov">          0 :                                 pos[2] *= ANGS_PER_NM;</span></a>
+<a name="883"><span class="lineNum">     883 </span>            : </a>
+<a name="884"><span class="lineNum">     884 </span>            :                                 // Copy the atom data into the array</a>
+<a name="885"><span class="lineNum">     885 </span>            :                                 memcpy(currAtom, pos, sizeof(float) * 3);</a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineNoCov">          0 :         currAtom += 3;</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :         i++;</span></a>
+<a name="888"><span class="lineNum">     888 </span>            :                         }</a>
+<a name="889"><span class="lineNum">     889 </span>            :                 }</a>
+<a name="890"><span class="lineNum">     890 </span>            :         }</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineNoCov">          0 :         else if (!strcasecmp(buf, &quot;POSITION&quot;) || !strcasecmp(buf, &quot;REFPOSITION&quot;)) {</span></a>
+<a name="892"><span class="lineNum">     892 </span>            :                 /*</a>
+<a name="893"><span class="lineNum">     893 </span>            :                 char resnum[7];</a>
+<a name="894"><span class="lineNum">     894 </span>            :                 char resname[7];</a>
+<a name="895"><span class="lineNum">     895 </span>            :                 char atomname[7];</a>
+<a name="896"><span class="lineNum">     896 </span>            :                 char atomnum[7];</a>
+<a name="897"><span class="lineNum">     897 </span>            :                 */</a>
+<a name="898"><span class="lineNum">     898 </span>            : </a>
+<a name="899"><span class="lineNum">     899 </span>            :                 // So now we read in some atoms</a>
+<a name="900"><span class="lineNum">     900 </span>            :     i = 0;</a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineNoCov">          0 :                 while (i &lt; ts-&gt;natoms) {</span></a>
+<a name="902"><span class="lineNum">     902 </span>            :                         // Read in the first line</a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineNoCov">          0 :                         if (mdio_readline(mf, buf, MAX_G96_LINE + 1, 0) &lt; 0)</span></a>
+<a name="904"><span class="lineNum">     904 </span>            :                                 return -1;</a>
+<a name="905"><span class="lineNum">     905 </span>            :  </a>
+<a name="906"><span class="lineNum">     906 </span>            :       // We shouldn't reach the end yet</a>
+<a name="907"><span class="lineNum">     907 </span>            :       strcpy(stripbuf, buf);</a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineNoCov">          0 :       strip_white(stripbuf); </span></a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineNoCov">          0 :       if (!strcasecmp(stripbuf, &quot;END&quot;))</span></a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="911"><span class="lineNum">     911 </span>            : </a>
+<a name="912"><span class="lineNum">     912 </span>            :                         // Get the x,y,z coordinates and name data</a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineNoCov">          0 :                         n = sscanf(buf, &quot;%*6c%*6c%*6c%*6c %f %f %f&quot;,</span></a>
+<a name="914"><span class="lineNum">     914 </span>            :                                 &amp;pos[0], &amp;pos[1], &amp;pos[2]);</a>
+<a name="915"><span class="lineNum">     915 </span>            : </a>
+<a name="916"><span class="lineNum">     916 </span>            :       // Ignore improperly formatted lines</a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineNoCov">          0 :                         if (n == 3) {</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineNoCov">          0 :                                 pos[0] *= ANGS_PER_NM;</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :                                 pos[1] *= ANGS_PER_NM;</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :                                 pos[2] *= ANGS_PER_NM;</span></a>
+<a name="921"><span class="lineNum">     921 </span>            : </a>
+<a name="922"><span class="lineNum">     922 </span>            :                                 // Copy the atom data into the linked list item</a>
+<a name="923"><span class="lineNum">     923 </span>            :                                 memcpy(currAtom, pos, sizeof(float) * 3);</a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineNoCov">          0 :                                 currAtom += 3;</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineNoCov">          0 :         i++;</span></a>
+<a name="926"><span class="lineNum">     926 </span>            :                         }</a>
+<a name="927"><span class="lineNum">     927 </span>            :                 }</a>
+<a name="928"><span class="lineNum">     928 </span>            :         }</a>
+<a name="929"><span class="lineNum">     929 </span>            :         else {</a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :         }</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span>            :   // Read the END keyword</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :   if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="935"><span class="lineNum">     935 </span>            :     return -1;</a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 :   if (strcasecmp(buf, &quot;END&quot;))</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="938"><span class="lineNum">     938 </span>            : </a>
+<a name="939"><span class="lineNum">     939 </span>            :         // ... another problem: there may or may not be a VELOCITY</a>
+<a name="940"><span class="lineNum">     940 </span>            :         // block or a BOX block, so we need to read one line beyond</a>
+<a name="941"><span class="lineNum">     941 </span>            :         // the POSITION block to determine this. If neither VEL. nor</a>
+<a name="942"><span class="lineNum">     942 </span>            :         // BOX are present we've read a line too far and infringed</a>
+<a name="943"><span class="lineNum">     943 </span>            :         // on the next timestep, so we need to keep track of the</a>
+<a name="944"><span class="lineNum">     944 </span>            :         // position now for a possible fseek() later to backtrack.</a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineNoCov">          0 :         fpos = ftell(mf-&gt;f);</span></a>
+<a name="946"><span class="lineNum">     946 </span>            : </a>
+<a name="947"><span class="lineNum">     947 </span>            :         // Now we must read in the velocities and the box, if present</a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineNoCov">          0 :         if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) {</span></a>
+<a name="949"><span class="lineNum">     949 </span>            :     // It's okay if we end the file here; any other errors need to be</a>
+<a name="950"><span class="lineNum">     950 </span>            :     // reported.</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineNoCov">          0 :     if (mdio_errcode == MDIO_EOF) </span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :     else </a>
+<a name="954"><span class="lineNum">     954 </span>            :       return -1;</a>
+<a name="955"><span class="lineNum">     955 </span>            :   }</a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            :         // Is there a velocity block present ?</a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineNoCov">          0 :         if (!strcasecmp(buf, &quot;VELOCITY&quot;) || !strcasecmp(buf, &quot;VELOCITYRED&quot;)) {</span></a>
+<a name="959"><span class="lineNum">     959 </span>            :                 // Ignore all the coordinates - VMD doesn't use them</a>
+<a name="960"><span class="lineNum">     960 </span>            :                 for (;;) {</a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineNoCov">          0 :                         if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :                                 return -1;</a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineNoCov">          0 :                         if (!strcasecmp(buf, &quot;END&quot;)) break;</span></a>
+<a name="964"><span class="lineNum">     964 </span>            :                 }</a>
+<a name="965"><span class="lineNum">     965 </span>            : </a>
+<a name="966"><span class="lineNum">     966 </span>            :                 // Again, record our position because we may need</a>
+<a name="967"><span class="lineNum">     967 </span>            :                 // to fseek here later if we read too far.</a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineNoCov">          0 :                 fpos = ftell(mf-&gt;f);</span></a>
+<a name="969"><span class="lineNum">     969 </span>            : </a>
+<a name="970"><span class="lineNum">     970 </span>            :                 // Go ahead and read the next line.</a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="972"><span class="lineNum">     972 </span>            :         }</a>
+<a name="973"><span class="lineNum">     973 </span>            : </a>
+<a name="974"><span class="lineNum">     974 </span>            :         // Is there a box present ?</a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineNoCov">          0 :         if (!strcasecmp(buf, &quot;BOX&quot;)) {</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineNoCov">          0 :     boxItems = sscanf(buf, &quot; %f %f %f %f %f %f %f %f %f&quot;, </span></a>
+<a name="978"><span class="lineNum">     978 </span>            :                &amp;x[0], &amp;y[1], &amp;z[2], &amp;x[1], &amp;x[2], &amp;y[0], &amp;y[2], &amp;z[0], &amp;z[1]);</a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineNoCov">          0 :     if (boxItems == 3) {</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :       x[1] = x[2] = 0;</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 :       y[0] = y[2] = 0;</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineNoCov">          0 :       z[0] = z[1] = 0;</span></a>
+<a name="983"><span class="lineNum">     983 </span>            :     }</a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineNoCov">          0 :     else if (boxItems != 9) </span></a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span>            :     // Allocate the box and convert the vectors.</a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineNoCov">          0 :     ts-&gt;box = (md_box *) malloc(sizeof(md_box));</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineNoCov">          0 :     if (mdio_readbox(ts-&gt;box, x, y, z) &lt; 0) {</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineNoCov">          0 :       free(ts-&gt;box);</span></a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineNoCov">          0 :       ts-&gt;box = NULL;</span></a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="993"><span class="lineNum">     993 </span>            :     }</a>
+<a name="994"><span class="lineNum">     994 </span>            : </a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineNoCov">          0 :                 if (mdio_readline(mf, buf, MAX_G96_LINE + 1) &lt; 0) {</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineNoCov">          0 :       free(ts-&gt;box);</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineNoCov">          0 :       ts-&gt;box = NULL;</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineNoCov">          0 :       return -1;</span></a>
+<a name="999"><span class="lineNum">     999 </span>            :     }</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineNoCov">          0 :                 if (strcasecmp(buf, &quot;END&quot;)) {</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineNoCov">          0 :       free(ts-&gt;box);</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineNoCov">          0 :       ts-&gt;box = NULL;</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :     }</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :         }</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :         else {</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :                 // We have read too far, so fseek back to the</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :                 // last known safe position so we don't return</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :                 // with the file pointer set infringing on the</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :                 // next timestep data.</a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineNoCov">          0 :                 fseek(mf-&gt;f, fpos, SEEK_SET);</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :         }</a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span>            :         // We're done!</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            : }</a>
+<a name="1017"><span class="lineNum">    1017 </span>            : </a>
+<a name="1018"><span class="lineNum">    1018 </span>            : </a>
+<a name="1019"><span class="lineNum">    1019 </span>            : // Attempts to read header data from a GROMACS structure file</a>
+<a name="1020"><span class="lineNum">    1020 </span>            : // The GROMACS header format is as follows (fixed, 2 lines ASCII):</a>
+<a name="1021"><span class="lineNum">    1021 </span>            : // &lt;title&gt; [ n= &lt;timevalue&gt; ]</a>
+<a name="1022"><span class="lineNum">    1022 </span>            : //     &lt;num atoms&gt;</a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineNoCov">          0 : static int gro_header(md_file *mf, char *title, int titlelen, float *timeval,</span></a>
+<a name="1024"><span class="lineNum">    1024 </span>            :                int *natoms, int rewind) {</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   char buf[MAX_GRO_LINE + 1];</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :   long fpos;</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :   char *p;</a>
+<a name="1028"><span class="lineNum">    1028 </span>            : </a>
+<a name="1029"><span class="lineNum">    1029 </span>            :   // Check parameters</a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineNoCov">          0 :   if (!mf)</span></a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1032"><span class="lineNum">    1032 </span>            : </a>
+<a name="1033"><span class="lineNum">    1033 </span>            :   // Get the current file position for rewinding later</a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineNoCov">          0 :   fpos = ftell(mf-&gt;f);</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            : </a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   // The header consists of 2 lines - get the first line</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineNoCov">          0 :   if (mdio_readline(mf, buf, MAX_GRO_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="1038"><span class="lineNum">    1038 </span>            : </a>
+<a name="1039"><span class="lineNum">    1039 </span>            :   // The timevalue can be included in the title string</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   // after a &quot;t=&quot; prefix.</a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineNoCov">          0 :   if ((p = (char *) strstr(buf, &quot;t=&quot;))) {</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     char *q = p;</a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineNoCov">          0 :     *(q--) = 0;</span></a>
+<a name="1044"><span class="lineNum">    1044 </span>            : </a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     // Skip the `t=' and strip whitespace from</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :     // the resulting strings</a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineNoCov">          0 :     p += 2;</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineNoCov">          0 :     strip_white(p);</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineNoCov">          0 :     strip_white(buf);</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            : </a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     // Grab the timevalue from the title string</a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineNoCov">          0 :     if (timeval) *timeval = (float) atof(p);</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   } else {</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     // No timevalue - just copy the string</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineNoCov">          0 :     if (timeval) *timeval = 0;</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            :   }</a>
+<a name="1057"><span class="lineNum">    1057 </span>            : </a>
+<a name="1058"><span class="lineNum">    1058 </span>            :   // Copy the title string</a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineNoCov">          0 :   if (title &amp;&amp; titlelen) strncpy(title, buf, titlelen);</span></a>
+<a name="1060"><span class="lineNum">    1060 </span>            : </a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   // Get the second line and grab the number of atoms</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineNoCov">          0 :   if (mdio_readline(mf, buf, MAX_GRO_LINE + 1) &lt; 0) return -1;</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            : </a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   // Store the number of atoms</a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineNoCov">          0 :   if (natoms &amp;&amp; (!(*natoms = atoi(buf))))</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1067"><span class="lineNum">    1067 </span>            : </a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   // Now we rewind the file so that subsequent calls to</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :   // gro_timestep() will succeed. gro_timestep() requires</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :   // the header to be at the current file pointer.</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineNoCov">          0 :   if (rewind)</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineNoCov">          0 :     fseek(mf-&gt;f, fpos, SEEK_SET);</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            : </a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   return 0; // Done!</a>
+<a name="1075"><span class="lineNum">    1075 </span>            : }</a>
+<a name="1076"><span class="lineNum">    1076 </span>            : </a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span>            : // Reads one atom record from a GROMACS file. Returns GMX_SUCCESS</a>
+<a name="1079"><span class="lineNum">    1079 </span>            : // on success or a negative number on error.</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : //</a>
+<a name="1081"><span class="lineNum">    1081 </span>            : // Record format (one line, fixed):</a>
+<a name="1082"><span class="lineNum">    1082 </span>            : //    rrrrrRRRRRaaaaaAAAAA &lt;x pos&gt; &lt;y pos&gt; &lt;z pos&gt; &lt;x vel&gt; &lt;y vel&gt; &lt;z vel&gt;</a>
+<a name="1083"><span class="lineNum">    1083 </span>            : //</a>
+<a name="1084"><span class="lineNum">    1084 </span>            : //    r = residue number</a>
+<a name="1085"><span class="lineNum">    1085 </span>            : //    R = residue name</a>
+<a name="1086"><span class="lineNum">    1086 </span>            : //    a = atom name</a>
+<a name="1087"><span class="lineNum">    1087 </span>            : //    A = atom number</a>
+<a name="1088"><span class="lineNum">    1088 </span>            : //</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 : static int gro_rec(md_file *mf, md_atom *ma) {</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   char buf[MAX_GRO_LINE + 1];</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   char atomnum[6];</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   char xposc[12], yposc[12], zposc[12];</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   int n;</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineNoCov">          0 :   if (!mf)</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1097"><span class="lineNum">    1097 </span>            : </a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   do {</a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineNoCov">          0 :     if (mdio_readline(mf, buf, MAX_GRO_LINE + 1, 0) &lt; 0)</span></a>
+<a name="1100"><span class="lineNum">    1100 </span>            :       return -1;</a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineNoCov">          0 :   } while (buf[0] == '#' || !strlen(buf));</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            : </a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   // Read in the fields</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineNoCov">          0 :   n = sscanf(buf, &quot;%5c%5c%5c%5c%8c%8c%8c&quot;, </span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineNoCov">          0 :              ma-&gt;resid, ma-&gt;resname, ma-&gt;atomname, atomnum, </span></a>
+<a name="1106"><span class="lineNum">    1106 </span>            :              xposc, yposc, zposc);</a>
+<a name="1107"><span class="lineNum">    1107 </span>            : </a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineNoCov">          0 :   if (n != 7)</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1110"><span class="lineNum">    1110 </span>            : </a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   // Null terminate the strings</a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineNoCov">          0 :   ma-&gt;resname[5] = 0;</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineNoCov">          0 :   ma-&gt;atomname[5] = 0;</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineNoCov">          0 :   ma-&gt;resid[5] = 0;</span></a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineNoCov">          0 :   atomnum[5] = 0;</span></a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineNoCov">          0 :   xposc[8] = 0;</span></a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineNoCov">          0 :   yposc[8] = 0;</span></a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineNoCov">          0 :   zposc[8] = 0;</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :  </a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineNoCov">          0 :   if ((sscanf(xposc, &quot;%f&quot;, &amp;ma-&gt;pos[0]) != 1) ||</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineNoCov">          0 :       (sscanf(yposc, &quot;%f&quot;, &amp;ma-&gt;pos[1]) != 1) ||</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineNoCov">          0 :       (sscanf(zposc, &quot;%f&quot;, &amp;ma-&gt;pos[2]) != 1)) {</span></a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   }</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : </a>
+<a name="1126"><span class="lineNum">    1126 </span>            :   // Convert strings to numbers</a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineNoCov">          0 :   strip_white(atomnum);</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineNoCov">          0 :   ma-&gt;atomnum = atoi(atomnum);</span></a>
+<a name="1129"><span class="lineNum">    1129 </span>            : </a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   // Convert nanometers to angstroms</a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineNoCov">          0 :   ma-&gt;pos[0] *= ANGS_PER_NM;</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineNoCov">          0 :   ma-&gt;pos[1] *= ANGS_PER_NM;</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineNoCov">          0 :   ma-&gt;pos[2] *= ANGS_PER_NM;</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            : </a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   // Strip leading and trailing whitespace</a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineNoCov">          0 :   strip_white(ma-&gt;atomname);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineNoCov">          0 :   strip_white(ma-&gt;resname);</span></a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineNoCov">          0 :   strip_white(ma-&gt;resid);</span></a>
+<a name="1139"><span class="lineNum">    1139 </span>            : </a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineNoCov">          0 :   return 0;</span></a>
+<a name="1141"><span class="lineNum">    1141 </span>            : }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            : </a>
+<a name="1143"><span class="lineNum">    1143 </span>            : </a>
+<a name="1144"><span class="lineNum">    1144 </span>            : // Reads in a timestep from a .gro file. Ignores the data</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : // not needed for a timestep, so is a little faster than</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : // calling gro_rec() for each atom. Also reads in the</a>
+<a name="1147"><span class="lineNum">    1147 </span>            : // header block.</a>
+<a name="1148"><span class="lineNum">    1148 </span>            : //</a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineNoCov">          0 : static int gro_timestep(md_file *mf, md_ts *ts) {</span></a>
+<a name="1150"><span class="lineNum">    1150 </span>            :         char buf[MAX_GRO_LINE + 1];</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :         long coord;</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :         int i, n, boxItems;</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   float x[3], y[3], z[3];</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :   char xposc[12], yposc[12], zposc[12];</a>
+<a name="1155"><span class="lineNum">    1155 </span>            : </a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineNoCov">          0 :   if (!mf || !ts) </span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            : </a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineNoCov">          0 :   if (gro_header(mf, NULL, 0, &amp;ts-&gt;time, &amp;ts-&gt;natoms, 0) &lt; 0)</span></a>
+<a name="1160"><span class="lineNum">    1160 </span>            :     return -1;</a>
+<a name="1161"><span class="lineNum">    1161 </span>            : </a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineNoCov">          0 :   ts-&gt;pos = (float *) malloc(3 * sizeof(float) * ts-&gt;natoms);</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineNoCov">          0 :   if (!ts-&gt;pos)</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            : </a>
+<a name="1166"><span class="lineNum">    1166 </span>            :   coord = 0;</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineNoCov">          0 :   for (i = 0; i &lt; ts-&gt;natoms; i++) {</span></a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineNoCov">          0 :     if (mdio_readline(mf, buf, MAX_GRO_LINE + 1, 0) &lt; 0) {</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :       free(ts-&gt;pos);</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineNoCov">          0 :       return -1;</span></a>
+<a name="1171"><span class="lineNum">    1171 </span>            :     }</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :         </a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineNoCov">          0 :     n = sscanf(buf, &quot;%*5c%*5c%*5c%*5c%8c%8c%8c&quot;, xposc, yposc, zposc);</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineNoCov">          0 :     if (n != 3) </span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1176"><span class="lineNum">    1176 </span>            : </a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 :     if ((sscanf(xposc, &quot;%f&quot;, &amp;ts-&gt;pos[coord    ]) != 1) ||</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineNoCov">          0 :         (sscanf(yposc, &quot;%f&quot;, &amp;ts-&gt;pos[coord + 1]) != 1) ||</span></a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineNoCov">          0 :         (sscanf(zposc, &quot;%f&quot;, &amp;ts-&gt;pos[coord + 2]) != 1)) {</span></a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            :     }</a>
+<a name="1182"><span class="lineNum">    1182 </span>            : </a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineNoCov">          0 :     ts-&gt;pos[coord    ] *= ANGS_PER_NM;</span></a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineNoCov">          0 :     ts-&gt;pos[coord + 1] *= ANGS_PER_NM;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineNoCov">          0 :     ts-&gt;pos[coord + 2] *= ANGS_PER_NM;</span></a>
+<a name="1186"><span class="lineNum">    1186 </span>            : </a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineNoCov">          0 :     coord += 3;</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :   }</a>
+<a name="1189"><span class="lineNum">    1189 </span>            : </a>
+<a name="1190"><span class="lineNum">    1190 </span>            :   // Read the box, stored as three vectors representing its edges</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :   if (mdio_readline(mf, buf, MAX_GRO_LINE + 1, 0) &lt; 0) {</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :     free(ts-&gt;pos);</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineNoCov">          0 :     return -1;</span></a>
+<a name="1194"><span class="lineNum">    1194 </span>            :   }</a>
+<a name="1195"><span class="lineNum">    1195 </span>            : </a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineNoCov">          0 :   boxItems = sscanf(buf, &quot; %f %f %f %f %f %f %f %f %f&quot;, </span></a>
+<a name="1197"><span class="lineNum">    1197 </span>            :              &amp;x[0], &amp;y[1], &amp;z[2], &amp;x[1], &amp;x[2], &amp;y[0], &amp;y[2], &amp;z[0], &amp;z[1]);</a>
+<a name="1198"><span class="lineNum">    1198 </span>            : </a>
+<a name="1199"><span class="lineNum">    1199 </span>            :   // File may only include three scalars for the box information -- if</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :   // that's the case, the box is orthoganal.</a>
+<a name="1201"><span class="lineNum">    1201 </span><span class="lineNoCov">          0 :   if (boxItems == 3) {</span></a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineNoCov">          0 :     x[1] = x[2] = 0;</span></a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineNoCov">          0 :     y[0] = y[2] = 0;</span></a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineNoCov">          0 :     z[0] = z[1] = 0;</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineNoCov">          0 :   } else if (boxItems != 9) {</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :     free(ts-&gt;pos);</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineNoCov">          0 :     return -1;</span></a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   }</a>
+<a name="1209"><span class="lineNum">    1209 </span>            : </a>
+<a name="1210"><span class="lineNum">    1210 </span>            :   // Allocate the box and convert the vectors.</a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineNoCov">          0 :   ts-&gt;box = (md_box *) malloc(sizeof(md_box));</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineNoCov">          0 :   if (mdio_readbox(ts-&gt;box, x, y, z) &lt; 0) {</span></a>
+<a name="1213"><span class="lineNum">    1213 </span><span class="lineNoCov">          0 :     free(ts-&gt;pos);</span></a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineNoCov">          0 :     free(ts-&gt;box);</span></a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineNoCov">          0 :     ts-&gt;box = NULL;</span></a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineNoCov">          0 :     return -1;</span></a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   }</a>
+<a name="1218"><span class="lineNum">    1218 </span>            : </a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   return 0;</a>
+<a name="1220"><span class="lineNum">    1220 </span>            : }</a>
+<a name="1221"><span class="lineNum">    1221 </span>            : </a>
+<a name="1222"><span class="lineNum">    1222 </span>            : </a>
+<a name="1223"><span class="lineNum">    1223 </span>            : // Attempts to read header data from a .trX trajectory file</a>
+<a name="1224"><span class="lineNum">    1224 </span>            : //</a>
+<a name="1225"><span class="lineNum">    1225 </span>            : // The .trX header format is as follows:</a>
+<a name="1226"><span class="lineNum">    1226 </span>            : //</a>
+<a name="1227"><span class="lineNum">    1227 </span>            : //      4 bytes         - magic number (0x07C9)</a>
+<a name="1228"><span class="lineNum">    1228 </span>            : //      ...</a>
+<a name="1229"><span class="lineNum">    1229 </span>            : //</a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineCov">        160 : static int trx_header(md_file *mf, int rewind) {</span></a>
+<a name="1231"><span class="lineNum">    1231 </span>            :         int magic;</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :         trx_hdr *hdr;</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :         long fpos;</a>
+<a name="1234"><span class="lineNum">    1234 </span>            : </a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineCov">        160 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1236"><span class="lineNum">    1236 </span>            : </a>
+<a name="1237"><span class="lineNum">    1237 </span>            :         // In case we need to rewind</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">        160 :         fpos = ftell(mf-&gt;f);</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            : </a>
+<a name="1240"><span class="lineNum">    1240 </span>            :         // We need to store some data to the trX header data</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :         // structure inside the md_file structure</a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineCov">        160 :         hdr = mf-&gt;trx;</span></a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">        160 :         if (!mf-&gt;trx) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            : </a>
+<a name="1245"><span class="lineNum">    1245 </span>            :         // Read the magic number</a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">        160 :         if (trx_int(mf, &amp;magic) &lt; 0) return -1;</span></a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">        155 :         if (magic != TRX_MAGIC) {</span></a>
+<a name="1248"><span class="lineNum">    1248 </span>            :                 // Try reverse endianism</a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">          5 :                 swap4_aligned(&amp;magic, 1);</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">          5 :                 if (magic != TRX_MAGIC) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1251"><span class="lineNum">    1251 </span>            : </a>
+<a name="1252"><span class="lineNum">    1252 </span>            :                 // Enable byte swapping (actually works, too!)</a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineCov">          5 :                 mf-&gt;rev = 1;</span></a>
+<a name="1254"><span class="lineNum">    1254 </span>            :         }</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : </a>
+<a name="1256"><span class="lineNum">    1256 </span>            :         // Read the version number. </a>
+<a name="1257"><span class="lineNum">    1257 </span>            :         // XXX. this is not the version number, but the storage size</a>
+<a name="1258"><span class="lineNum">    1258 </span>            :         // of the following XDR encoded string.</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :         // the 'title' string is in fact the version identifier.</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :         // since VMD does not use any of that, it does no harm,</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :         // but is should still be fixed occasionally. AK 2005/01/08.</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">        155 :         if(mf-&gt;fmt!=MDFMT_TRJ) {</span></a>
+<a name="1264"><span class="lineNum">    1264 </span>            :                 // It appears that TRJ files either don't contain a version</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :                 // number or don't have a length-delimiter on the string,</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :                 // whereas TRR files do contain both.  Thus, with TRJ, we just</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :                 // assume that the version number is the string length and </a>
+<a name="1268"><span class="lineNum">    1268 </span>            :                 // just hope for the best. -- WLD 2006/07/09</a>
+<a name="1269"><span class="lineNum">    1269 </span><span class="lineCov">        155 :                 if (trx_int(mf, &amp;hdr-&gt;version) &lt; 0) return -1;</span></a>
+<a name="1270"><span class="lineNum">    1270 </span>            :         }</a>
+<a name="1271"><span class="lineNum">    1271 </span>            : </a>
+<a name="1272"><span class="lineNum">    1272 </span>            :         // Read in the title string</a>
+<a name="1273"><span class="lineNum">    1273 </span><span class="lineCov">        155 :         if (trx_string(mf, hdr-&gt;title, MAX_TRX_TITLE) &lt; 0)</span></a>
+<a name="1274"><span class="lineNum">    1274 </span>            :                 return -1;</a>
+<a name="1275"><span class="lineNum">    1275 </span>            : </a>
+<a name="1276"><span class="lineNum">    1276 </span>            :         // Read in some size data</a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;ir_size) &lt; 0) return -1;</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;e_size) &lt; 0) return -1;</span></a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;box_size) &lt; 0) return -1;</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;vir_size) &lt; 0) return -1;</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;pres_size) &lt; 0) return -1;</span></a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;top_size) &lt; 0) return -1;</span></a>
+<a name="1283"><span class="lineNum">    1283 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;sym_size) &lt; 0) return -1;</span></a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;x_size) &lt; 0) return -1;</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;v_size) &lt; 0) return -1;</span></a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;f_size) &lt; 0) return -1;</span></a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;natoms) &lt; 0) return -1;</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;step) &lt; 0) return -1;</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;hdr-&gt;nre) &lt; 0) return -1;</span></a>
+<a name="1290"><span class="lineNum">    1290 </span>            : </a>
+<a name="1291"><span class="lineNum">    1291 </span>            :         // Make sure there are atoms...</a>
+<a name="1292"><span class="lineNum">    1292 </span><span class="lineCov">        155 :         if (!hdr-&gt;natoms) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1293"><span class="lineNum">    1293 </span>            : </a>
+<a name="1294"><span class="lineNum">    1294 </span>            :         // Try to determine precision (float? double?)</a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineCov">        155 :         if (hdr-&gt;x_size) mf-&gt;prec = hdr-&gt;x_size / (hdr-&gt;natoms * 3);</span></a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineNoCov">          0 :         else if (hdr-&gt;v_size) mf-&gt;prec = hdr-&gt;v_size / (hdr-&gt;natoms * 3);</span></a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineNoCov">          0 :         else if (hdr-&gt;f_size) mf-&gt;prec = hdr-&gt;f_size / (hdr-&gt;natoms * 3);</span></a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineNoCov">          0 :         else return mdio_seterror(MDIO_BADPRECISION);</span></a>
+<a name="1299"><span class="lineNum">    1299 </span>            : </a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">        155 :         if (mf-&gt;prec != sizeof(float) &amp;&amp; mf-&gt;prec != sizeof(double)) {</span></a>
+<a name="1301"><span class="lineNum">    1301 </span>            :                 // We have no data types this size! The</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :                 // file must've been generated on another</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :                 // platform</a>
+<a name="1304"><span class="lineNum">    1304 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_BADPRECISION);</span></a>
+<a name="1305"><span class="lineNum">    1305 </span>            :         }</a>
+<a name="1306"><span class="lineNum">    1306 </span>            : </a>
+<a name="1307"><span class="lineNum">    1307 </span>            :         // Read in timestep and lambda</a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">        155 :         if (trx_real(mf, &amp;hdr-&gt;t) &lt; 0) return -1;</span></a>
+<a name="1309"><span class="lineNum">    1309 </span><span class="lineCov">        155 :         if (trx_real(mf, &amp;hdr-&gt;lambda) &lt; 0) return -1;</span></a>
+<a name="1310"><span class="lineNum">    1310 </span>            : </a>
+<a name="1311"><span class="lineNum">    1311 </span>            :         // Rewind if necessary</a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">        155 :         if (rewind) fseek(mf-&gt;f, fpos, SEEK_SET);</span></a>
+<a name="1313"><span class="lineNum">    1313 </span>            : </a>
+<a name="1314"><span class="lineNum">    1314 </span>            :         return 0;</a>
+<a name="1315"><span class="lineNum">    1315 </span>            : }</a>
+<a name="1316"><span class="lineNum">    1316 </span>            : </a>
+<a name="1317"><span class="lineNum">    1317 </span>            : </a>
+<a name="1318"><span class="lineNum">    1318 </span>            : // Reads in an integer and stores it in y. Returns GMX_SUCCESS</a>
+<a name="1319"><span class="lineNum">    1319 </span>            : // on success or a negative number on error.</a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">       2485 : static int trx_int(md_file *mf, int *y) {</span></a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">       2485 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1322"><span class="lineNum">    1322 </span>            : </a>
+<a name="1323"><span class="lineNum">    1323 </span>            :         // sanity check.</a>
+<a name="1324"><span class="lineNum">    1324 </span>            :         if (sizeof(int) != 4) return mdio_seterror(MDIO_SIZEERROR);</a>
+<a name="1325"><span class="lineNum">    1325 </span>            : </a>
+<a name="1326"><span class="lineNum">    1326 </span><span class="lineCov">       2485 :         if (y) {</span></a>
+<a name="1327"><span class="lineNum">    1327 </span><span class="lineCov">       4970 :                 if (fread(y, 4, 1, mf-&gt;f) != 1)</span></a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineCov">          5 :                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineCov">       2480 :                 if (mf-&gt;rev) swap4_aligned(y, 1);</span></a>
+<a name="1330"><span class="lineNum">    1330 </span>            :         }</a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineNoCov">          0 :         else if (fseek(mf-&gt;f, 4, SEEK_CUR) != 0)</span></a>
+<a name="1332"><span class="lineNum">    1332 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1333"><span class="lineNum">    1333 </span>            : </a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">       2480 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            : }</a>
+<a name="1336"><span class="lineNum">    1336 </span>            : </a>
+<a name="1337"><span class="lineNum">    1337 </span>            : </a>
+<a name="1338"><span class="lineNum">    1338 </span>            : // Reads in either a float or a double, depending on the</a>
+<a name="1339"><span class="lineNum">    1339 </span>            : // precision, and stores that number in y. Returns</a>
+<a name="1340"><span class="lineNum">    1340 </span>            : // GMX_SUCCESS on success or a negative number on error.</a>
+<a name="1341"><span class="lineNum">    1341 </span><span class="lineCov">    1458760 : static int trx_real(md_file *mf, float *y) {</span></a>
+<a name="1342"><span class="lineNum">    1342 </span>            :         double x;</a>
+<a name="1343"><span class="lineNum">    1343 </span>            : </a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineCov">    1458760 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1345"><span class="lineNum">    1345 </span>            : </a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineCov">    1458760 :         switch (mf-&gt;prec) {</span></a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">    1458760 :                 case sizeof(float):</span></a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineCov">    1458760 :                         if (!y) {</span></a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineNoCov">          0 :                                 if (fseek(mf-&gt;f, mf-&gt;prec, SEEK_CUR) != 0)</span></a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineNoCov">          0 :                                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1351"><span class="lineNum">    1351 </span>            :                         } else {</a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">    2917520 :                                 if (fread(y, mf-&gt;prec, 1, mf-&gt;f) != 1)</span></a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineNoCov">          0 :                                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineCov">    1458760 :                                 if (mf-&gt;rev) swap4_aligned(y, 1);</span></a>
+<a name="1355"><span class="lineNum">    1355 </span>            :                         }</a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineCov">    1458760 :                         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1357"><span class="lineNum">    1357 </span>            : </a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineNoCov">          0 :                 case sizeof(double):</span></a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineNoCov">          0 :                         if (!y) {</span></a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineNoCov">          0 :                                 if (fseek(mf-&gt;f, mf-&gt;prec, SEEK_CUR) != 0)</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineNoCov">          0 :                                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1362"><span class="lineNum">    1362 </span>            :                         } else {</a>
+<a name="1363"><span class="lineNum">    1363 </span><span class="lineNoCov">          0 :                                 if (fread(&amp;x, mf-&gt;prec, 1, mf-&gt;f) != 1)</span></a>
+<a name="1364"><span class="lineNum">    1364 </span><span class="lineNoCov">          0 :                                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineNoCov">          0 :                                 if (mf-&gt;rev) swap8_aligned(&amp;x, 1);</span></a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineNoCov">          0 :                                 *y = (float) x;</span></a>
+<a name="1367"><span class="lineNum">    1367 </span>            :                         }</a>
+<a name="1368"><span class="lineNum">    1368 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1369"><span class="lineNum">    1369 </span>            : </a>
+<a name="1370"><span class="lineNum">    1370 </span><span class="lineNoCov">          0 :                 default:</span></a>
+<a name="1371"><span class="lineNum">    1371 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_BADPRECISION);</span></a>
+<a name="1372"><span class="lineNum">    1372 </span>            :         }</a>
+<a name="1373"><span class="lineNum">    1373 </span>            : </a>
+<a name="1374"><span class="lineNum">    1374 </span>            : }</a>
+<a name="1375"><span class="lineNum">    1375 </span>            : </a>
+<a name="1376"><span class="lineNum">    1376 </span>            : </a>
+<a name="1377"><span class="lineNum">    1377 </span>            : // Reads in a real-valued vector (taking precision into account).</a>
+<a name="1378"><span class="lineNum">    1378 </span>            : // Stores the vector in vec, and returns GMX_SUCCESS on success</a>
+<a name="1379"><span class="lineNum">    1379 </span>            : // or a negative number on error.</a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">     486150 : static int trx_rvector(md_file *mf, float *vec) {</span></a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineCov">     486150 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1382"><span class="lineNum">    1382 </span>            : </a>
+<a name="1383"><span class="lineNum">    1383 </span><span class="lineCov">     486150 :         if (!vec) {</span></a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineNoCov">          0 :                 if (trx_real(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineNoCov">          0 :                 if (trx_real(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineNoCov">          0 :                 if (trx_real(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineNoCov">          0 :                 return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1388"><span class="lineNum">    1388 </span>            :         } else {</a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineCov">     486150 :                 if (trx_real(mf, &amp;vec[0]) &lt; 0) return -1;</span></a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineCov">     486150 :                 if (trx_real(mf, &amp;vec[1]) &lt; 0) return -1;</span></a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineCov">     486150 :                 if (trx_real(mf, &amp;vec[2]) &lt; 0) return -1;</span></a>
+<a name="1392"><span class="lineNum">    1392 </span><span class="lineCov">     486150 :                 return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1393"><span class="lineNum">    1393 </span>            :         }</a>
+<a name="1394"><span class="lineNum">    1394 </span>            : }</a>
+<a name="1395"><span class="lineNum">    1395 </span>            : </a>
+<a name="1396"><span class="lineNum">    1396 </span>            : </a>
+<a name="1397"><span class="lineNum">    1397 </span>            : // Reads in a string by first reading an integer containing the</a>
+<a name="1398"><span class="lineNum">    1398 </span>            : // string's length, then reading in the string itself and storing</a>
+<a name="1399"><span class="lineNum">    1399 </span>            : // it in str. If the length is greater than max, it is truncated</a>
+<a name="1400"><span class="lineNum">    1400 </span>            : // and the rest of the string is skipped in the file. Returns the</a>
+<a name="1401"><span class="lineNum">    1401 </span>            : // length of the string on success or a negative number on error.</a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">        155 : static int trx_string(md_file *mf, char *str, int max) {</span></a>
+<a name="1403"><span class="lineNum">    1403 </span>            :         int size;</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :   size_t ssize;</a>
+<a name="1405"><span class="lineNum">    1405 </span>            : </a>
+<a name="1406"><span class="lineNum">    1406 </span><span class="lineCov">        155 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1407"><span class="lineNum">    1407 </span>            : </a>
+<a name="1408"><span class="lineNum">    1408 </span><span class="lineCov">        155 :         if (trx_int(mf, &amp;size) &lt; 0) return -1;</span></a>
+<a name="1409"><span class="lineNum">    1409 </span><span class="lineCov">        155 :   ssize = (size_t)size;</span></a>
+<a name="1410"><span class="lineNum">    1410 </span>            : </a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineCov">        155 :         if (str &amp;&amp; size &lt;= max) {</span></a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">        310 :                 if (fread(str, 1, size, mf-&gt;f) != ssize)</span></a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineCov">        155 :                 str[size] = 0;</span></a>
+<a name="1415"><span class="lineNum">    1415 </span><span class="lineCov">        155 :                 return size;</span></a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineNoCov">          0 :         } else if (str) {</span></a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineNoCov">          0 :                 if (fread(str, 1, max, mf-&gt;f) != ssize)</span></a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1419"><span class="lineNum">    1419 </span><span class="lineNoCov">          0 :                 if (fseek(mf-&gt;f, size - max, SEEK_CUR) != 0)</span></a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1421"><span class="lineNum">    1421 </span><span class="lineNoCov">          0 :                 str[max] = 0;</span></a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineNoCov">          0 :                 return max;</span></a>
+<a name="1423"><span class="lineNum">    1423 </span>            :         } else {</a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineNoCov">          0 :                 if (fseek(mf-&gt;f, size, SEEK_CUR) != 0)</span></a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineNoCov">          0 :                         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1426"><span class="lineNum">    1426 </span>            :                 return 0;</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :         }</a>
+<a name="1428"><span class="lineNum">    1428 </span>            : }</a>
+<a name="1429"><span class="lineNum">    1429 </span>            : </a>
+<a name="1430"><span class="lineNum">    1430 </span>            : </a>
+<a name="1431"><span class="lineNum">    1431 </span>            : // Reads in a timestep frame from the .trX file and returns the</a>
+<a name="1432"><span class="lineNum">    1432 </span>            : // data in a timestep structure. Returns NULL on error.</a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineCov">        155 : static int trx_timestep(md_file *mf, md_ts *ts) {</span></a>
+<a name="1434"><span class="lineNum">    1434 </span>            :   int i;</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :   float x[3], y[3], z[3];</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :   trx_hdr *hdr;</a>
+<a name="1437"><span class="lineNum">    1437 </span>            : </a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineCov">        155 :   if (!mf || !ts) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineCov">        155 :   if (mf-&gt;fmt != MDFMT_TRJ &amp;&amp; mf-&gt;fmt != MDFMT_TRR)</span></a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_WRONGFORMAT);</span></a>
+<a name="1441"><span class="lineNum">    1441 </span>            : </a>
+<a name="1442"><span class="lineNum">    1442 </span>            :   // Read the header</a>
+<a name="1443"><span class="lineNum">    1443 </span><span class="lineCov">        155 :   if (trx_header(mf) &lt; 0) return -1;</span></a>
+<a name="1444"><span class="lineNum">    1444 </span>            : </a>
+<a name="1445"><span class="lineNum">    1445 </span>            :   // We need some data from the trX header</a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineCov">        150 :   hdr = mf-&gt;trx;</span></a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineCov">        150 :   if (!hdr) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1448"><span class="lineNum">    1448 </span>            : </a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineCov">        150 :   if (hdr-&gt;box_size) { // XXX need to check value of box_size!!</span></a>
+<a name="1450"><span class="lineNum">    1450 </span><span class="lineCov">        150 :     if (trx_rvector(mf, x) &lt; 0) return -1;</span></a>
+<a name="1451"><span class="lineNum">    1451 </span><span class="lineCov">        150 :     if (trx_rvector(mf, y) &lt; 0) return -1;</span></a>
+<a name="1452"><span class="lineNum">    1452 </span><span class="lineCov">        150 :     if (trx_rvector(mf, z) &lt; 0) return -1;</span></a>
+<a name="1453"><span class="lineNum">    1453 </span>            : </a>
+<a name="1454"><span class="lineNum">    1454 </span>            :     // Allocate the box and convert the vectors.</a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineCov">        150 :     ts-&gt;box = (md_box *) malloc(sizeof(md_box));</span></a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineCov">        150 :     if (mdio_readbox(ts-&gt;box, x, y, z) &lt; 0) {</span></a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineNoCov">          0 :       free(ts-&gt;box);</span></a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineNoCov">          0 :       ts-&gt;box = NULL;</span></a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineNoCov">          0 :       return -1;</span></a>
+<a name="1460"><span class="lineNum">    1460 </span>            :     }</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :   }</a>
+<a name="1462"><span class="lineNum">    1462 </span>            : </a>
+<a name="1463"><span class="lineNum">    1463 </span><span class="lineCov">        150 :   if (hdr-&gt;vir_size) {</span></a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineNoCov">          0 :     if (trx_rvector(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineNoCov">          0 :     if (trx_rvector(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1466"><span class="lineNum">    1466 </span><span class="lineNoCov">          0 :     if (trx_rvector(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1467"><span class="lineNum">    1467 </span>            :   }</a>
+<a name="1468"><span class="lineNum">    1468 </span>            : </a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineCov">        150 :   if (hdr-&gt;pres_size) {</span></a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineNoCov">          0 :     if (trx_rvector(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineNoCov">          0 :     if (trx_rvector(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineNoCov">          0 :     if (trx_rvector(mf, NULL) &lt; 0) return -1;</span></a>
+<a name="1473"><span class="lineNum">    1473 </span>            :   }</a>
+<a name="1474"><span class="lineNum">    1474 </span>            : </a>
+<a name="1475"><span class="lineNum">    1475 </span><span class="lineCov">        150 :   if (hdr-&gt;x_size) {</span></a>
+<a name="1476"><span class="lineNum">    1476 </span><span class="lineCov">        150 :     ts-&gt;pos = (float *) malloc(sizeof(float) * 3 * hdr-&gt;natoms);</span></a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">        150 :     if (!ts-&gt;pos) </span></a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1479"><span class="lineNum">    1479 </span>            : </a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">        150 :     ts-&gt;natoms = hdr-&gt;natoms;</span></a>
+<a name="1481"><span class="lineNum">    1481 </span><span class="lineCov">     485850 :     for (i = 0; i &lt; hdr-&gt;natoms; i++) {</span></a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineCov">     485700 :       if (trx_rvector(mf, &amp;ts-&gt;pos[i * 3]) &lt; 0) {</span></a>
+<a name="1483"><span class="lineNum">    1483 </span><span class="lineNoCov">          0 :         mdio_tsfree(ts, 1);</span></a>
+<a name="1484"><span class="lineNum">    1484 </span><span class="lineNoCov">          0 :         return -1;</span></a>
+<a name="1485"><span class="lineNum">    1485 </span>            :       }</a>
+<a name="1486"><span class="lineNum">    1486 </span>            : </a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineCov">     485700 :       ts-&gt;pos[i * 3    ] *= ANGS_PER_NM;</span></a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineCov">     485700 :       ts-&gt;pos[i * 3 + 1] *= ANGS_PER_NM;</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineCov">     485700 :       ts-&gt;pos[i * 3 + 2] *= ANGS_PER_NM;</span></a>
+<a name="1490"><span class="lineNum">    1490 </span>            :     }</a>
+<a name="1491"><span class="lineNum">    1491 </span>            :   }</a>
+<a name="1492"><span class="lineNum">    1492 </span>            : </a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineCov">        150 :   if (hdr-&gt;v_size) {</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; hdr-&gt;natoms; i++) {</span></a>
+<a name="1495"><span class="lineNum">    1495 </span><span class="lineNoCov">          0 :       if (trx_rvector(mf, NULL) &lt; 0) {</span></a>
+<a name="1496"><span class="lineNum">    1496 </span><span class="lineNoCov">          0 :         mdio_tsfree(ts, 1);</span></a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineNoCov">          0 :         return -1;</span></a>
+<a name="1498"><span class="lineNum">    1498 </span>            :       }</a>
+<a name="1499"><span class="lineNum">    1499 </span>            :     }</a>
+<a name="1500"><span class="lineNum">    1500 </span>            :   }</a>
+<a name="1501"><span class="lineNum">    1501 </span>            : </a>
+<a name="1502"><span class="lineNum">    1502 </span><span class="lineCov">        150 :   if (hdr-&gt;f_size) {</span></a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineNoCov">          0 :     for (i = 0; i &lt; hdr-&gt;natoms; i++) {</span></a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineNoCov">          0 :       if (trx_rvector(mf, NULL) &lt; 0) {</span></a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineNoCov">          0 :         mdio_tsfree(ts, 1);</span></a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineNoCov">          0 :         return -1;</span></a>
+<a name="1507"><span class="lineNum">    1507 </span>            :       }</a>
+<a name="1508"><span class="lineNum">    1508 </span>            :     }</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :   }</a>
+<a name="1510"><span class="lineNum">    1510 </span>            : </a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineCov">        150 :   return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1512"><span class="lineNum">    1512 </span>            : }</a>
+<a name="1513"><span class="lineNum">    1513 </span>            : </a>
+<a name="1514"><span class="lineNum">    1514 </span>            : </a>
+<a name="1515"><span class="lineNum">    1515 </span>            : // writes an int in big endian. Returns GMX_SUCCESS</a>
+<a name="1516"><span class="lineNum">    1516 </span>            : // on success or a negative number on error.</a>
+<a name="1517"><span class="lineNum">    1517 </span><span class="lineNoCov">          0 : static int put_trx_int(md_file *mf, int y) {</span></a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineNoCov">          0 :       if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1519"><span class="lineNum">    1519 </span>            : </a>
+<a name="1520"><span class="lineNum">    1520 </span>            :       // sanity check.</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :       if (sizeof(int) != 4) return mdio_seterror(MDIO_SIZEERROR);</a>
+<a name="1522"><span class="lineNum">    1522 </span>            : </a>
+<a name="1523"><span class="lineNum">    1523 </span><span class="lineNoCov">          0 :       if (mf-&gt;rev) swap4_aligned(&amp;y, 1);</span></a>
+<a name="1524"><span class="lineNum">    1524 </span><span class="lineNoCov">          0 :       if (fwrite(&amp;y, 4, 1, mf-&gt;f) != 1)</span></a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineNoCov">          0 :     return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1526"><span class="lineNum">    1526 </span>            : </a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineNoCov">          0 :   return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1528"><span class="lineNum">    1528 </span>            : }</a>
+<a name="1529"><span class="lineNum">    1529 </span>            : </a>
+<a name="1530"><span class="lineNum">    1530 </span>            : // writes a real in big-endian. Returns GMX_SUCCESS</a>
+<a name="1531"><span class="lineNum">    1531 </span>            : // on success or a negative number on error.</a>
+<a name="1532"><span class="lineNum">    1532 </span><span class="lineNoCov">          0 : static int put_trx_real(md_file *mf, float y) {</span></a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineNoCov">          0 :       if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1534"><span class="lineNum">    1534 </span>            : </a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineNoCov">          0 :       if (mf-&gt;rev) swap4_aligned(&amp;y, 1);</span></a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineNoCov">          0 :       if (fwrite(&amp;y, 4, 1, mf-&gt;f) != 1)</span></a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1538"><span class="lineNum">    1538 </span>            : </a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineNoCov">          0 :       return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1540"><span class="lineNum">    1540 </span>            : }</a>
+<a name="1541"><span class="lineNum">    1541 </span>            : </a>
+<a name="1542"><span class="lineNum">    1542 </span>            : </a>
+<a name="1543"><span class="lineNum">    1543 </span>            : // writes an xdr encoded string. Returns GMX_SUCCESS</a>
+<a name="1544"><span class="lineNum">    1544 </span>            : // on success or a negative number on error.</a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineNoCov">          0 : static int put_trx_string(md_file *mf, const char *s) {</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineNoCov">          0 :         if (!mf || !s) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1547"><span class="lineNum">    1547 </span>            :         </a>
+<a name="1548"><span class="lineNum">    1548 </span>            :         // write: size of object, string length, string data</a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineNoCov">          0 :         size_t len = strlen(s);</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineNoCov">          0 :         if ( put_trx_int(mf, len+1)</span></a>
+<a name="1551"><span class="lineNum">    1551 </span><span class="lineNoCov">          0 :              || put_trx_int(mf, len)</span></a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineNoCov">          0 :              || (fwrite(s, len, 1, mf-&gt;f) != 1))</span></a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineNoCov">          0 :           return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1554"><span class="lineNum">    1554 </span>            : </a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineNoCov">          0 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1556"><span class="lineNum">    1556 </span>            : }</a>
+<a name="1557"><span class="lineNum">    1557 </span>            : </a>
+<a name="1558"><span class="lineNum">    1558 </span>            : </a>
+<a name="1559"><span class="lineNum">    1559 </span>            : // xtc_int() - reads an integer from an xtc file</a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineCov">     217846 : static int xtc_int(md_file *mf, int *i) {</span></a>
+<a name="1561"><span class="lineNum">    1561 </span>            :         unsigned char c[4];</a>
+<a name="1562"><span class="lineNum">    1562 </span>            : </a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineCov">     217846 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1564"><span class="lineNum">    1564 </span>            :         // sanity check.</a>
+<a name="1565"><span class="lineNum">    1565 </span>            :         if (sizeof(int) != 4) return mdio_seterror(MDIO_SIZEERROR);</a>
+<a name="1566"><span class="lineNum">    1566 </span>            : </a>
+<a name="1567"><span class="lineNum">    1567 </span><span class="lineCov">     217846 :         if (fread(c, 1, 4, mf-&gt;f) != 4) {</span></a>
+<a name="1568"><span class="lineNum">    1568 </span><span class="lineCov">        190 :                 if (feof(mf-&gt;f)) return mdio_seterror(MDIO_EOF);</span></a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineNoCov">          0 :                 else if (ferror(mf-&gt;f)) return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineNoCov">          0 :                 else return mdio_seterror(MDIO_UNKNOWNERROR);</span></a>
+<a name="1571"><span class="lineNum">    1571 </span>            :         }</a>
+<a name="1572"><span class="lineNum">    1572 </span>            : </a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineCov">     217656 :         if (i) *i = c[3] + (c[2] &lt;&lt; 8) + (c[1] &lt;&lt; 16) + (c[0] &lt;&lt; 24);</span></a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineCov">     217656 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            : }</a>
+<a name="1576"><span class="lineNum">    1576 </span>            : </a>
+<a name="1577"><span class="lineNum">    1577 </span>            : </a>
+<a name="1578"><span class="lineNum">    1578 </span>            : // xtc_float() - reads a float from an xtc file</a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineCov">     199179 : static int xtc_float(md_file *mf, float *f) {</span></a>
+<a name="1580"><span class="lineNum">    1580 </span>            :         unsigned char c[4];</a>
+<a name="1581"><span class="lineNum">    1581 </span>            :         int i;</a>
+<a name="1582"><span class="lineNum">    1582 </span>            : </a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineCov">     199179 :         if (!mf) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1584"><span class="lineNum">    1584 </span>            : </a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineCov">     199179 :         if (fread(c, 1, 4, mf-&gt;f) != 4) {</span></a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineNoCov">          0 :                 if (feof(mf-&gt;f)) return mdio_seterror(MDIO_EOF);</span></a>
+<a name="1587"><span class="lineNum">    1587 </span><span class="lineNoCov">          0 :                 else if (ferror(mf-&gt;f)) return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineNoCov">          0 :                 else return mdio_seterror(MDIO_UNKNOWNERROR);</span></a>
+<a name="1589"><span class="lineNum">    1589 </span>            :         }</a>
+<a name="1590"><span class="lineNum">    1590 </span>            : </a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineCov">     199179 :         if (f) {</span></a>
+<a name="1592"><span class="lineNum">    1592 </span>            :                 // By reading the number in as an integer and then</a>
+<a name="1593"><span class="lineNum">    1593 </span>            :                 // copying it to a floating point number we can</a>
+<a name="1594"><span class="lineNum">    1594 </span>            :                 // ensure proper endianness</a>
+<a name="1595"><span class="lineNum">    1595 </span><span class="lineCov">     199179 :                 i = c[3] + (c[2] &lt;&lt; 8) + (c[1] &lt;&lt; 16) + (c[0] &lt;&lt; 24);</span></a>
+<a name="1596"><span class="lineNum">    1596 </span>            :                 memcpy(f, &amp;i, 4);</a>
+<a name="1597"><span class="lineNum">    1597 </span>            :         }</a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineCov">     199179 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1599"><span class="lineNum">    1599 </span>            : }</a>
+<a name="1600"><span class="lineNum">    1600 </span>            : </a>
+<a name="1601"><span class="lineNum">    1601 </span>            : </a>
+<a name="1602"><span class="lineNum">    1602 </span>            : // xtc_data() - reads a specific amount of data from an xtc</a>
+<a name="1603"><span class="lineNum">    1603 </span>            : // file using the xdr format.</a>
+<a name="1604"><span class="lineNum">    1604 </span><span class="lineCov">      18106 : static int xtc_data(md_file *mf, char *buf, int len) {</span></a>
+<a name="1605"><span class="lineNum">    1605 </span><span class="lineCov">      18106 :         if (!mf || len &lt; 1) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">      18106 :   size_t slen = (size_t)len;</span></a>
+<a name="1607"><span class="lineNum">    1607 </span><span class="lineCov">      18106 :         if (buf) {</span></a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineCov">      36212 :                 if (fread(buf, 1, slen, mf-&gt;f) != slen) {</span></a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineNoCov">          0 :                         if (feof(mf-&gt;f)) return mdio_seterror(MDIO_EOF);</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineNoCov">          0 :                         if (ferror(mf-&gt;f)) return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineNoCov">          0 :                         else return mdio_seterror(MDIO_UNKNOWNERROR);</span></a>
+<a name="1612"><span class="lineNum">    1612 </span>            :                 }</a>
+<a name="1613"><span class="lineNum">    1613 </span><span class="lineCov">      18106 :                 if (len % 4) {</span></a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineCov">      14011 :                         if (fseek(mf-&gt;f, 4 - (len % 4), SEEK_CUR)) {</span></a>
+<a name="1615"><span class="lineNum">    1615 </span><span class="lineNoCov">          0 :                                 if (feof(mf-&gt;f)) return mdio_seterror(MDIO_EOF);</span></a>
+<a name="1616"><span class="lineNum">    1616 </span><span class="lineNoCov">          0 :                                 if (ferror(mf-&gt;f)) return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1617"><span class="lineNum">    1617 </span><span class="lineNoCov">          0 :                                 else return mdio_seterror(MDIO_UNKNOWNERROR);</span></a>
+<a name="1618"><span class="lineNum">    1618 </span>            :                         }</a>
+<a name="1619"><span class="lineNum">    1619 </span>            :                 }</a>
+<a name="1620"><span class="lineNum">    1620 </span>            :         }</a>
+<a name="1621"><span class="lineNum">    1621 </span>            :         else {</a>
+<a name="1622"><span class="lineNum">    1622 </span>            :                 int newlen;</a>
+<a name="1623"><span class="lineNum">    1623 </span>            :                 newlen = len;</a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineNoCov">          0 :                 if (len % 4) newlen += (4 - (len % 4));</span></a>
+<a name="1625"><span class="lineNum">    1625 </span><span class="lineNoCov">          0 :                 if (fseek(mf-&gt;f, newlen, SEEK_CUR)) {</span></a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineNoCov">          0 :                         if (feof(mf-&gt;f)) return mdio_seterror(MDIO_EOF);</span></a>
+<a name="1627"><span class="lineNum">    1627 </span><span class="lineNoCov">          0 :                         if (ferror(mf-&gt;f)) return mdio_seterror(MDIO_IOERROR);</span></a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineNoCov">          0 :                         else return mdio_seterror(MDIO_UNKNOWNERROR);</span></a>
+<a name="1629"><span class="lineNum">    1629 </span>            :                 }</a>
+<a name="1630"><span class="lineNum">    1630 </span>            :         }</a>
+<a name="1631"><span class="lineNum">    1631 </span>            :         return len;</a>
+<a name="1632"><span class="lineNum">    1632 </span>            : }</a>
+<a name="1633"><span class="lineNum">    1633 </span>            : </a>
+<a name="1634"><span class="lineNum">    1634 </span>            : </a>
+<a name="1635"><span class="lineNum">    1635 </span>            : // xtc_timestep() - reads a timestep from an .xtc file.</a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineCov">      18297 : static int xtc_timestep(md_file *mf, md_ts *ts) {</span></a>
+<a name="1637"><span class="lineNum">    1637 </span>            :         int n;</a>
+<a name="1638"><span class="lineNum">    1638 </span>            :         float f, x[3], y[3], z[3];</a>
+<a name="1639"><span class="lineNum">    1639 </span>            : </a>
+<a name="1640"><span class="lineNum">    1640 </span><span class="lineCov">      18297 :         int size = 0; // explicitly initialized to zero.</span></a>
+<a name="1641"><span class="lineNum">    1641 </span>            :         float precision;</a>
+<a name="1642"><span class="lineNum">    1642 </span>            : </a>
+<a name="1643"><span class="lineNum">    1643 </span><span class="lineCov">      18297 :         if (!mf || !ts) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineCov">      18297 :         if (!mf-&gt;f) return mdio_seterror(MDIO_BADPARAMS);</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineCov">      18297 :         if (mf-&gt;fmt != MDFMT_XTC) return mdio_seterror(MDIO_WRONGFORMAT);</span></a>
+<a name="1646"><span class="lineNum">    1646 </span>            : </a>
+<a name="1647"><span class="lineNum">    1647 </span>            :         // Check magic number</a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">      18297 :         if (xtc_int(mf, &amp;n) &lt; 0) return -1;</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">      18107 :         if (n != XTC_MAGIC) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1650"><span class="lineNum">    1650 </span>            : </a>
+<a name="1651"><span class="lineNum">    1651 </span>            :         // Get number of atoms</a>
+<a name="1652"><span class="lineNum">    1652 </span><span class="lineCov">      18107 :         if (xtc_int(mf, &amp;n) &lt; 0) return -1;</span></a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineCov">      18107 :         ts-&gt;natoms = n;</span></a>
+<a name="1654"><span class="lineNum">    1654 </span>            : </a>
+<a name="1655"><span class="lineNum">    1655 </span>            :         // Get the simulation step</a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineCov">      18107 :         if (xtc_int(mf, &amp;n) &lt; 0) return -1;</span></a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">      18107 :         ts-&gt;step = n;</span></a>
+<a name="1658"><span class="lineNum">    1658 </span>            : </a>
+<a name="1659"><span class="lineNum">    1659 </span>            :         // Get the time value</a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">      18107 :         if (xtc_float(mf, &amp;f) &lt; 0) return -1;</span></a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineCov">      18107 :         ts-&gt;time = f;</span></a>
+<a name="1662"><span class="lineNum">    1662 </span>            : </a>
+<a name="1663"><span class="lineNum">    1663 </span>            :         // Read the basis vectors of the box</a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">      36214 :   if ( (xtc_float(mf, &amp;x[0]) &lt; 0) ||</span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">      36214 :        (xtc_float(mf, &amp;x[1]) &lt; 0) ||</span></a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineCov">      36214 :        (xtc_float(mf, &amp;x[2]) &lt; 0) ||</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineCov">      36214 :        (xtc_float(mf, &amp;y[0]) &lt; 0) ||</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">      36214 :        (xtc_float(mf, &amp;y[1]) &lt; 0) ||</span></a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineCov">      36214 :        (xtc_float(mf, &amp;y[2]) &lt; 0) ||</span></a>
+<a name="1670"><span class="lineNum">    1670 </span><span class="lineCov">      36214 :        (xtc_float(mf, &amp;z[0]) &lt; 0) ||</span></a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineCov">      54321 :        (xtc_float(mf, &amp;z[1]) &lt; 0) ||</span></a>
+<a name="1672"><span class="lineNum">    1672 </span><span class="lineCov">      18107 :        (xtc_float(mf, &amp;z[2]) &lt; 0) )</span></a>
+<a name="1673"><span class="lineNum">    1673 </span><span class="lineNoCov">          0 :     return -1;</span></a>
+<a name="1674"><span class="lineNum">    1674 </span>            :   // Allocate the box and convert the vectors.</a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineCov">      18107 :   ts-&gt;box = (md_box *) malloc(sizeof(md_box));</span></a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineCov">      18107 :   if (mdio_readbox(ts-&gt;box, x, y, z) &lt; 0) {</span></a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineNoCov">          0 :     free(ts-&gt;box);</span></a>
+<a name="1678"><span class="lineNum">    1678 </span><span class="lineNoCov">          0 :     ts-&gt;box = NULL;</span></a>
+<a name="1679"><span class="lineNum">    1679 </span><span class="lineNoCov">          0 :     return -1;</span></a>
+<a name="1680"><span class="lineNum">    1680 </span>            :   }</a>
+<a name="1681"><span class="lineNum">    1681 </span>            : </a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineCov">      18107 :         ts-&gt;pos = (float *) malloc(sizeof(float) * 3 * ts-&gt;natoms);</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineCov">      18107 :         if (!ts-&gt;pos) return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineCov">      18107 :         n = xtc_3dfcoord(mf, ts-&gt;pos, &amp;size, &amp;precision);</span></a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineCov">      18107 :         if (n &lt; 0) return -1;</span></a>
+<a name="1686"><span class="lineNum">    1686 </span>            : </a>
+<a name="1687"><span class="lineNum">    1687 </span>            :         /* Now we're left with the job of scaling... */</a>
+<a name="1688"><span class="lineNum">    1688 </span><span class="lineCov">   60583244 :         for (n = 0; n &lt; ts-&gt;natoms * 3; n++)</span></a>
+<a name="1689"><span class="lineNum">    1689 </span><span class="lineCov">   60565137 :                 ts-&gt;pos[n] *= ANGS_PER_NM;</span></a>
+<a name="1690"><span class="lineNum">    1690 </span>            : </a>
+<a name="1691"><span class="lineNum">    1691 </span><span class="lineCov">      18107 :         return mdio_seterror(MDIO_SUCCESS);</span></a>
+<a name="1692"><span class="lineNum">    1692 </span>            : }</a>
+<a name="1693"><span class="lineNum">    1693 </span>            : </a>
+<a name="1694"><span class="lineNum">    1694 </span>            : </a>
+<a name="1695"><span class="lineNum">    1695 </span>            : ///////////////////////////////////////////////////////////////////////</a>
+<a name="1696"><span class="lineNum">    1696 </span>            : // This algorithm is an implementation of the 3dfcoord algorithm</a>
+<a name="1697"><span class="lineNum">    1697 </span>            : // written by Frans van Hoesel (hoesel@chem.rug.nl) as part of the</a>
+<a name="1698"><span class="lineNum">    1698 </span>            : // Europort project in 1995.</a>
+<a name="1699"><span class="lineNum">    1699 </span>            : ///////////////////////////////////////////////////////////////////////</a>
+<a name="1700"><span class="lineNum">    1700 </span>            : </a>
+<a name="1701"><span class="lineNum">    1701 </span>            : // integer table used in decompression</a>
+<a name="1702"><span class="lineNum">    1702 </span>            : static int xtc_magicints[] = {</a>
+<a name="1703"><span class="lineNum">    1703 </span>            :         0, 0, 0, 0, 0, 0, 0, 0, 0,8, 10, 12, 16, 20, 25, 32, 40, 50, 64,</a>
+<a name="1704"><span class="lineNum">    1704 </span>            :         80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,</a>
+<a name="1705"><span class="lineNum">    1705 </span>            :         1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003, 16384,</a>
+<a name="1706"><span class="lineNum">    1706 </span>            :         20642, 26007, 32768, 41285, 52015, 65536, 82570, 104031, 131072,</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :         165140, 208063, 262144, 330280, 416127, 524287, 660561, 832255,</a>
+<a name="1708"><span class="lineNum">    1708 </span>            :         1048576, 1321122, 1664510, 2097152, 2642245, 3329021, 4194304,</a>
+<a name="1709"><span class="lineNum">    1709 </span>            :         5284491, 6658042, 8388607, 10568983, 13316085, 16777216 };</a>
+<a name="1710"><span class="lineNum">    1710 </span>            : </a>
+<a name="1711"><span class="lineNum">    1711 </span>            : #define FIRSTIDX 9</a>
+<a name="1712"><span class="lineNum">    1712 </span>            : /* note that magicints[FIRSTIDX-1] == 0 */</a>
+<a name="1713"><span class="lineNum">    1713 </span>            : #define LASTIDX (sizeof(xtc_magicints) / sizeof(*xtc_magicints))</a>
+<a name="1714"><span class="lineNum">    1714 </span>            : </a>
+<a name="1715"><span class="lineNum">    1715 </span>            : </a>
+<a name="1716"><span class="lineNum">    1716 </span>            : // returns the number of bits in the binary expansion of</a>
+<a name="1717"><span class="lineNum">    1717 </span>            : // the given integer.</a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineNoCov">          0 : static int xtc_sizeofint(int size) {</span></a>
+<a name="1719"><span class="lineNum">    1719 </span>            :         unsigned int num = 1;</a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineNoCov">          0 :   unsigned int ssize = (unsigned int)size;</span></a>
+<a name="1721"><span class="lineNum">    1721 </span>            :         int nbits = 0;</a>
+<a name="1722"><span class="lineNum">    1722 </span>            : </a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineNoCov">          0 :         while (ssize &gt;= num &amp;&amp; nbits &lt; 32) {</span></a>
+<a name="1724"><span class="lineNum">    1724 </span><span class="lineNoCov">          0 :                 nbits++;</span></a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineNoCov">          0 :                 num &lt;&lt;= 1;</span></a>
+<a name="1726"><span class="lineNum">    1726 </span>            :         }</a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineNoCov">          0 :         return nbits;</span></a>
+<a name="1728"><span class="lineNum">    1728 </span>            : }</a>
+<a name="1729"><span class="lineNum">    1729 </span>            : </a>
+<a name="1730"><span class="lineNum">    1730 </span>            : // calculates the number of bits a set of integers, when compressed,</a>
+<a name="1731"><span class="lineNum">    1731 </span>            : // will take up.</a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineCov">      18106 : static int xtc_sizeofints(int nints, unsigned int *sizes) {</span></a>
+<a name="1733"><span class="lineNum">    1733 </span>            :         int i;</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :   unsigned int num;</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :         unsigned int nbytes, nbits, bytes[32], bytecnt, tmp;</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :         nbytes = 1;</a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineCov">      18106 :         bytes[0] = 1;</span></a>
+<a name="1738"><span class="lineNum">    1738 </span>            :         nbits = 0;</a>
+<a name="1739"><span class="lineNum">    1739 </span><span class="lineCov">      72424 :         for (i=0; i &lt; nints; i++) {  </span></a>
+<a name="1740"><span class="lineNum">    1740 </span>            :                 tmp = 0;</a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineCov">     171242 :                 for (bytecnt = 0; bytecnt &lt; nbytes; bytecnt++) {</span></a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineCov">     116924 :                         tmp = bytes[bytecnt] * sizes[i] + tmp;</span></a>
+<a name="1743"><span class="lineNum">    1743 </span><span class="lineCov">     116924 :                         bytes[bytecnt] = tmp &amp; 0xff;</span></a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineCov">     116924 :                         tmp &gt;&gt;= 8;</span></a>
+<a name="1745"><span class="lineNum">    1745 </span>            :                 }</a>
+<a name="1746"><span class="lineNum">    1746 </span><span class="lineCov">     119604 :                 while (tmp != 0) {</span></a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineCov">      65286 :                         bytes[bytecnt++] = tmp &amp; 0xff;</span></a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineCov">      65286 :                         tmp &gt;&gt;= 8;</span></a>
+<a name="1749"><span class="lineNum">    1749 </span>            :                 }</a>
+<a name="1750"><span class="lineNum">    1750 </span>            :                 nbytes = bytecnt;</a>
+<a name="1751"><span class="lineNum">    1751 </span>            :         }</a>
+<a name="1752"><span class="lineNum">    1752 </span>            :         num = 1;</a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineCov">      18106 :         nbytes--;</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineCov">     110165 :         while (bytes[nbytes] &gt;= num) {</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineCov">      92059 :                 nbits++;</span></a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineCov">      92059 :                 num *= 2;</span></a>
+<a name="1757"><span class="lineNum">    1757 </span>            :         }</a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineCov">      18106 :         return nbits + nbytes * 8;</span></a>
+<a name="1759"><span class="lineNum">    1759 </span>            : }</a>
+<a name="1760"><span class="lineNum">    1760 </span>            : </a>
+<a name="1761"><span class="lineNum">    1761 </span>            : // reads bits from a buffer.    </a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineCov">   90001066 : static int xtc_receivebits(int *buf, int nbits) {</span></a>
+<a name="1763"><span class="lineNum">    1763 </span>            :         int cnt, num; </a>
+<a name="1764"><span class="lineNum">    1764 </span>            :         unsigned int lastbits, lastbyte;</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :         unsigned char * cbuf;</a>
+<a name="1766"><span class="lineNum">    1766 </span><span class="lineCov">   90001066 :         int mask = (1 &lt;&lt; nbits) -1;</span></a>
+<a name="1767"><span class="lineNum">    1767 </span>            : </a>
+<a name="1768"><span class="lineNum">    1768 </span><span class="lineCov">   90001066 :         cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);</span></a>
+<a name="1769"><span class="lineNum">    1769 </span><span class="lineCov">   90001066 :         cnt = buf[0];</span></a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineCov">   90001066 :         lastbits = (unsigned int) buf[1];</span></a>
+<a name="1771"><span class="lineNum">    1771 </span><span class="lineCov">   90001066 :         lastbyte = (unsigned int) buf[2];</span></a>
+<a name="1772"><span class="lineNum">    1772 </span>            : </a>
+<a name="1773"><span class="lineNum">    1773 </span>            :         num = 0;</a>
+<a name="1774"><span class="lineNum">    1774 </span><span class="lineCov">  154222343 :         while (nbits &gt;= 8) {</span></a>
+<a name="1775"><span class="lineNum">    1775 </span><span class="lineCov">   64221277 :                 lastbyte = ( lastbyte &lt;&lt; 8 ) | cbuf[cnt++];</span></a>
+<a name="1776"><span class="lineNum">    1776 </span><span class="lineCov">   64221277 :                 num |=  (lastbyte &gt;&gt; lastbits) &lt;&lt; (nbits - 8);</span></a>
+<a name="1777"><span class="lineNum">    1777 </span>            :                 nbits -=8;</a>
+<a name="1778"><span class="lineNum">    1778 </span>            :         }</a>
+<a name="1779"><span class="lineNum">    1779 </span><span class="lineCov">   90001066 :         if (nbits &gt; 0) {</span></a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineCov">   25779789 :                 if (lastbits &lt; (unsigned int)nbits) {</span></a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineCov">   13251584 :                         lastbits += 8;</span></a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineCov">   13251584 :                         lastbyte = (lastbyte &lt;&lt; 8) | cbuf[cnt++];</span></a>
+<a name="1783"><span class="lineNum">    1783 </span>            :                 }</a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineCov">   25779789 :                 lastbits -= nbits;</span></a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineCov">   25779789 :                 num |= (lastbyte &gt;&gt; lastbits) &amp; ((1 &lt;&lt; nbits) -1);</span></a>
+<a name="1786"><span class="lineNum">    1786 </span>            :         }</a>
+<a name="1787"><span class="lineNum">    1787 </span><span class="lineCov">   90001066 :         num &amp;= mask;</span></a>
+<a name="1788"><span class="lineNum">    1788 </span><span class="lineCov">   90001066 :         buf[0] = cnt;</span></a>
+<a name="1789"><span class="lineNum">    1789 </span><span class="lineCov">   90001066 :         buf[1] = lastbits;</span></a>
+<a name="1790"><span class="lineNum">    1790 </span><span class="lineCov">   90001066 :         buf[2] = lastbyte;</span></a>
+<a name="1791"><span class="lineNum">    1791 </span><span class="lineCov">   90001066 :         return num; </span></a>
+<a name="1792"><span class="lineNum">    1792 </span>            : }</a>
+<a name="1793"><span class="lineNum">    1793 </span>            : </a>
+<a name="1794"><span class="lineNum">    1794 </span>            : // decompresses small integers from the buffer</a>
+<a name="1795"><span class="lineNum">    1795 </span>            : // sizes parameter has to be non-zero to prevent divide-by-zero</a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineCov">   20188378 : static void xtc_receiveints(int *buf, const int nints, int nbits,</span></a>
+<a name="1797"><span class="lineNum">    1797 </span>            :                         unsigned int *sizes, int *nums) {</a>
+<a name="1798"><span class="lineNum">    1798 </span>            :         int bytes[32];</a>
+<a name="1799"><span class="lineNum">    1799 </span>            :         int i, j, nbytes, p, num;</a>
+<a name="1800"><span class="lineNum">    1800 </span>            : </a>
+<a name="1801"><span class="lineNum">    1801 </span><span class="lineCov">   20188378 :         bytes[1] = bytes[2] = bytes[3] = 0;</span></a>
+<a name="1802"><span class="lineNum">    1802 </span>            :         nbytes = 0;</a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineCov">   83939932 :         while (nbits &gt; 8) {</span></a>
+<a name="1804"><span class="lineNum">    1804 </span><span class="lineCov">   63751554 :                 bytes[nbytes++] = xtc_receivebits(buf, 8);</span></a>
+<a name="1805"><span class="lineNum">    1805 </span><span class="lineCov">   63751554 :                 nbits -= 8;</span></a>
+<a name="1806"><span class="lineNum">    1806 </span>            :         }</a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineCov">   20188378 :         if (nbits &gt; 0) {</span></a>
+<a name="1808"><span class="lineNum">    1808 </span><span class="lineCov">   20188378 :                 bytes[nbytes++] = xtc_receivebits(buf, nbits);</span></a>
+<a name="1809"><span class="lineNum">    1809 </span>            :         }</a>
+<a name="1810"><span class="lineNum">    1810 </span><span class="lineCov">   60565134 :         for (i = nints-1; i &gt; 0; i--) {</span></a>
+<a name="1811"><span class="lineNum">    1811 </span>            :                 num = 0;</a>
+<a name="1812"><span class="lineNum">    1812 </span><span class="lineCov">  208256620 :                 for (j = nbytes-1; j &gt;=0; j--) {</span></a>
+<a name="1813"><span class="lineNum">    1813 </span><span class="lineCov">  167879864 :                         num = (num &lt;&lt; 8) | bytes[j];</span></a>
+<a name="1814"><span class="lineNum">    1814 </span><span class="lineCov">  167879864 :                         p = num / sizes[i];</span></a>
+<a name="1815"><span class="lineNum">    1815 </span><span class="lineCov">  167879864 :                         bytes[j] = p;</span></a>
+<a name="1816"><span class="lineNum">    1816 </span><span class="lineCov">  167879864 :                         num = num - p * sizes[i];</span></a>
+<a name="1817"><span class="lineNum">    1817 </span>            :                 }</a>
+<a name="1818"><span class="lineNum">    1818 </span><span class="lineCov">   40376756 :                 nums[i] = num;</span></a>
+<a name="1819"><span class="lineNum">    1819 </span>            :         }</a>
+<a name="1820"><span class="lineNum">    1820 </span><span class="lineCov">   20188378 :         nums[0] = bytes[0] | (bytes[1] &lt;&lt; 8) | (bytes[2] &lt;&lt; 16) | (bytes[3] &lt;&lt; 24);</span></a>
+<a name="1821"><span class="lineNum">    1821 </span><span class="lineCov">   20188378 : }</span></a>
+<a name="1822"><span class="lineNum">    1822 </span>            : </a>
+<a name="1823"><span class="lineNum">    1823 </span>            : // function that actually reads and writes compressed coordinates    </a>
+<a name="1824"><span class="lineNum">    1824 </span><span class="lineCov">      18107 : static int xtc_3dfcoord(md_file *mf, float *fp, int *size, float *precision) {</span></a>
+<a name="1825"><span class="lineNum">    1825 </span>            :         static int *ip = NULL;</a>
+<a name="1826"><span class="lineNum">    1826 </span>            :         static int oldsize;</a>
+<a name="1827"><span class="lineNum">    1827 </span>            :         static int *buf;</a>
+<a name="1828"><span class="lineNum">    1828 </span>            : </a>
+<a name="1829"><span class="lineNum">    1829 </span>            :         int minint[3], maxint[3], *lip;</a>
+<a name="1830"><span class="lineNum">    1830 </span>            :         int smallidx;</a>
+<a name="1831"><span class="lineNum">    1831 </span>            :         unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3;</a>
+<a name="1832"><span class="lineNum">    1832 </span>            :         int flag, k;</a>
+<a name="1833"><span class="lineNum">    1833 </span>            :         int small, smaller, i, is_smaller, run;</a>
+<a name="1834"><span class="lineNum">    1834 </span>            :         float *lfp;</a>
+<a name="1835"><span class="lineNum">    1835 </span>            :         int tmp, *thiscoord,  prevcoord[3];</a>
+<a name="1836"><span class="lineNum">    1836 </span>            : </a>
+<a name="1837"><span class="lineNum">    1837 </span>            :         int bufsize, lsize;</a>
+<a name="1838"><span class="lineNum">    1838 </span>            :         unsigned int bitsize;</a>
+<a name="1839"><span class="lineNum">    1839 </span>            :         float inv_precision;</a>
+<a name="1840"><span class="lineNum">    1840 </span>            : </a>
+<a name="1841"><span class="lineNum">    1841 </span>            :         /* avoid uninitialized data compiler warnings */</a>
+<a name="1842"><span class="lineNum">    1842 </span>            :         bitsizeint[0] = 0;</a>
+<a name="1843"><span class="lineNum">    1843 </span>            :         bitsizeint[1] = 0;</a>
+<a name="1844"><span class="lineNum">    1844 </span>            :         bitsizeint[2] = 0;</a>
+<a name="1845"><span class="lineNum">    1845 </span>            : </a>
+<a name="1846"><span class="lineNum">    1846 </span><span class="lineCov">      18107 :         if (xtc_int(mf, &amp;lsize) &lt; 0) return -1;</span></a>
+<a name="1847"><span class="lineNum">    1847 </span>            : </a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineCov">      18107 :         if (*size != 0 &amp;&amp; lsize != *size) return mdio_seterror(MDIO_BADFORMAT);</span></a>
+<a name="1849"><span class="lineNum">    1849 </span>            : </a>
+<a name="1850"><span class="lineNum">    1850 </span><span class="lineCov">      18107 :         *size = lsize;</span></a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineCov">      18107 :         size3 = *size * 3;</span></a>
+<a name="1852"><span class="lineNum">    1852 </span><span class="lineCov">      18107 :         if (*size &lt;= 9) {</span></a>
+<a name="1853"><span class="lineNum">    1853 </span><span class="lineCov">          2 :                 for (i = 0; i &lt; *size; i++) {</span></a>
+<a name="1854"><span class="lineNum">    1854 </span><span class="lineCov">          1 :                         if (xtc_float(mf, fp + (3 * i)) &lt; 0) return -1;</span></a>
+<a name="1855"><span class="lineNum">    1855 </span><span class="lineCov">          1 :                         if (xtc_float(mf, fp + (3 * i) + 1) &lt; 0) return -1;</span></a>
+<a name="1856"><span class="lineNum">    1856 </span><span class="lineCov">          1 :                         if (xtc_float(mf, fp + (3 * i) + 2) &lt; 0) return -1;</span></a>
+<a name="1857"><span class="lineNum">    1857 </span>            :                 }</a>
+<a name="1858"><span class="lineNum">    1858 </span>            :                 return *size;</a>
+<a name="1859"><span class="lineNum">    1859 </span>            :         }</a>
+<a name="1860"><span class="lineNum">    1860 </span><span class="lineCov">      18106 :         xtc_float(mf, precision);</span></a>
+<a name="1861"><span class="lineNum">    1861 </span><span class="lineCov">      18106 :         if (ip == NULL) {</span></a>
+<a name="1862"><span class="lineNum">    1862 </span><span class="lineCov">        110 :                 ip = (int *)malloc(size3 * sizeof(*ip));</span></a>
+<a name="1863"><span class="lineNum">    1863 </span><span class="lineCov">        110 :                 if (ip == NULL) return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1864"><span class="lineNum">    1864 </span><span class="lineCov">        110 :                 bufsize = (int) (size3 * 1.2);</span></a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineCov">        110 :                 buf = (int *)malloc(bufsize * sizeof(*buf));</span></a>
+<a name="1866"><span class="lineNum">    1866 </span><span class="lineCov">        110 :                 if (buf == NULL) return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1867"><span class="lineNum">    1867 </span><span class="lineCov">        110 :                 oldsize = *size;</span></a>
+<a name="1868"><span class="lineNum">    1868 </span><span class="lineCov">      17996 :         } else if (*size &gt; oldsize) {</span></a>
+<a name="1869"><span class="lineNum">    1869 </span><span class="lineNoCov">          0 :                 ip = (int *)realloc(ip, size3 * sizeof(*ip));</span></a>
+<a name="1870"><span class="lineNum">    1870 </span><span class="lineNoCov">          0 :                 if (ip == NULL) return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1871"><span class="lineNum">    1871 </span><span class="lineNoCov">          0 :                 bufsize = (int) (size3 * 1.2);</span></a>
+<a name="1872"><span class="lineNum">    1872 </span><span class="lineNoCov">          0 :                 buf = (int *)realloc(buf, bufsize * sizeof(*buf));</span></a>
+<a name="1873"><span class="lineNum">    1873 </span><span class="lineNoCov">          0 :                 if (buf == NULL) return mdio_seterror(MDIO_BADMALLOC);</span></a>
+<a name="1874"><span class="lineNum">    1874 </span><span class="lineNoCov">          0 :                 oldsize = *size;</span></a>
+<a name="1875"><span class="lineNum">    1875 </span>            :         }</a>
+<a name="1876"><span class="lineNum">    1876 </span><span class="lineCov">      18106 :         buf[0] = buf[1] = buf[2] = 0;</span></a>
+<a name="1877"><span class="lineNum">    1877 </span>            : </a>
+<a name="1878"><span class="lineNum">    1878 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;(minint[0]));</span></a>
+<a name="1879"><span class="lineNum">    1879 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;(minint[1]));</span></a>
+<a name="1880"><span class="lineNum">    1880 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;(minint[2]));</span></a>
+<a name="1881"><span class="lineNum">    1881 </span>            : </a>
+<a name="1882"><span class="lineNum">    1882 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;(maxint[0]));</span></a>
+<a name="1883"><span class="lineNum">    1883 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;(maxint[1]));</span></a>
+<a name="1884"><span class="lineNum">    1884 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;(maxint[2]));</span></a>
+<a name="1885"><span class="lineNum">    1885 </span>            :                 </a>
+<a name="1886"><span class="lineNum">    1886 </span><span class="lineCov">      18106 :         sizeint[0] = maxint[0] - minint[0]+1;</span></a>
+<a name="1887"><span class="lineNum">    1887 </span><span class="lineCov">      18106 :         sizeint[1] = maxint[1] - minint[1]+1;</span></a>
+<a name="1888"><span class="lineNum">    1888 </span><span class="lineCov">      18106 :         sizeint[2] = maxint[2] - minint[2]+1;</span></a>
+<a name="1889"><span class="lineNum">    1889 </span>            :         </a>
+<a name="1890"><span class="lineNum">    1890 </span>            :         /* check if one of the sizes is to big to be multiplied */</a>
+<a name="1891"><span class="lineNum">    1891 </span><span class="lineCov">      18106 :         if ((sizeint[0] | sizeint[1] | sizeint[2] ) &gt; 0xffffff) {</span></a>
+<a name="1892"><span class="lineNum">    1892 </span><span class="lineNoCov">          0 :                 bitsizeint[0] = xtc_sizeofint(sizeint[0]);</span></a>
+<a name="1893"><span class="lineNum">    1893 </span><span class="lineNoCov">          0 :                 bitsizeint[1] = xtc_sizeofint(sizeint[1]);</span></a>
+<a name="1894"><span class="lineNum">    1894 </span><span class="lineNoCov">          0 :                 bitsizeint[2] = xtc_sizeofint(sizeint[2]);</span></a>
+<a name="1895"><span class="lineNum">    1895 </span>            :                 bitsize = 0; /* flag the use of large sizes */</a>
+<a name="1896"><span class="lineNum">    1896 </span>            :         } else {</a>
+<a name="1897"><span class="lineNum">    1897 </span><span class="lineCov">      18106 :                 bitsize = xtc_sizeofints(3, sizeint);</span></a>
+<a name="1898"><span class="lineNum">    1898 </span>            :         }</a>
+<a name="1899"><span class="lineNum">    1899 </span>            : </a>
+<a name="1900"><span class="lineNum">    1900 </span><span class="lineCov">      18106 :         xtc_int(mf, &amp;smallidx);</span></a>
+<a name="1901"><span class="lineNum">    1901 </span><span class="lineCov">      18106 :         smaller = xtc_magicints[FIRSTIDX &gt; smallidx - 1 ? FIRSTIDX : smallidx - 1] / 2;</span></a>
+<a name="1902"><span class="lineNum">    1902 </span><span class="lineCov">      18106 :         small = xtc_magicints[smallidx] / 2;</span></a>
+<a name="1903"><span class="lineNum">    1903 </span><span class="lineCov">      18106 :         sizesmall[0] = sizesmall[1] = sizesmall[2] = xtc_magicints[smallidx];</span></a>
+<a name="1904"><span class="lineNum">    1904 </span>            : </a>
+<a name="1905"><span class="lineNum">    1905 </span>            :         /* check for zero values that would yield corrupted data */</a>
+<a name="1906"><span class="lineNum">    1906 </span><span class="lineCov">      18106 :         if ( !sizesmall[0] || !sizesmall[1] || !sizesmall[2] ) {</span></a>
+<a name="1907"><span class="lineNum">    1907 </span>            :                 printf(&quot;XTC corrupted, sizesmall==0 (case 1)\n&quot;);</a>
+<a name="1908"><span class="lineNum">    1908 </span><span class="lineNoCov">          0 :                 return -1;</span></a>
+<a name="1909"><span class="lineNum">    1909 </span>            :         }</a>
+<a name="1910"><span class="lineNum">    1910 </span>            : </a>
+<a name="1911"><span class="lineNum">    1911 </span>            : </a>
+<a name="1912"><span class="lineNum">    1912 </span>            :         /* buf[0] holds the length in bytes */</a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineCov">      18106 :         if (xtc_int(mf, &amp;(buf[0])) &lt; 0) return -1;</span></a>
+<a name="1914"><span class="lineNum">    1914 </span>            : </a>
+<a name="1915"><span class="lineNum">    1915 </span><span class="lineCov">      18106 :         if (xtc_data(mf, (char *) &amp;buf[3], (int) buf[0]) &lt; 0) return -1;</span></a>
+<a name="1916"><span class="lineNum">    1916 </span>            : </a>
+<a name="1917"><span class="lineNum">    1917 </span><span class="lineCov">      18106 :         buf[0] = buf[1] = buf[2] = 0;</span></a>
+<a name="1918"><span class="lineNum">    1918 </span>            : </a>
+<a name="1919"><span class="lineNum">    1919 </span>            :         lfp = fp;</a>
+<a name="1920"><span class="lineNum">    1920 </span><span class="lineCov">      18106 :         inv_precision = 1.0f / (*precision);</span></a>
+<a name="1921"><span class="lineNum">    1921 </span>            :         run = 0;</a>
+<a name="1922"><span class="lineNum">    1922 </span>            :         i = 0;</a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineCov">      18106 :         lip = ip;</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineCov">    3521140 :         while (i &lt; lsize) {</span></a>
+<a name="1925"><span class="lineNum">    1925 </span><span class="lineCov">    3503034 :                 thiscoord = (int *)(lip) + i * 3;</span></a>
+<a name="1926"><span class="lineNum">    1926 </span>            : </a>
+<a name="1927"><span class="lineNum">    1927 </span><span class="lineCov">    3503034 :                 if (bitsize == 0) {</span></a>
+<a name="1928"><span class="lineNum">    1928 </span><span class="lineNoCov">          0 :                         thiscoord[0] = xtc_receivebits(buf, bitsizeint[0]);</span></a>
+<a name="1929"><span class="lineNum">    1929 </span><span class="lineNoCov">          0 :                         thiscoord[1] = xtc_receivebits(buf, bitsizeint[1]);</span></a>
+<a name="1930"><span class="lineNum">    1930 </span><span class="lineNoCov">          0 :                         thiscoord[2] = xtc_receivebits(buf, bitsizeint[2]);</span></a>
+<a name="1931"><span class="lineNum">    1931 </span>            :                 } else {</a>
+<a name="1932"><span class="lineNum">    1932 </span><span class="lineCov">    3503034 :                         xtc_receiveints(buf, 3, bitsize, sizeint, thiscoord);</span></a>
+<a name="1933"><span class="lineNum">    1933 </span>            :                 }</a>
+<a name="1934"><span class="lineNum">    1934 </span>            : </a>
+<a name="1935"><span class="lineNum">    1935 </span><span class="lineCov">    3503034 :                 i++;</span></a>
+<a name="1936"><span class="lineNum">    1936 </span><span class="lineCov">    3503034 :                 thiscoord[0] += minint[0];</span></a>
+<a name="1937"><span class="lineNum">    1937 </span><span class="lineCov">    3503034 :                 thiscoord[1] += minint[1];</span></a>
+<a name="1938"><span class="lineNum">    1938 </span><span class="lineCov">    3503034 :                 thiscoord[2] += minint[2];</span></a>
+<a name="1939"><span class="lineNum">    1939 </span>            : </a>
+<a name="1940"><span class="lineNum">    1940 </span>            :                 prevcoord[0] = thiscoord[0];</a>
+<a name="1941"><span class="lineNum">    1941 </span>            :                 prevcoord[1] = thiscoord[1];</a>
+<a name="1942"><span class="lineNum">    1942 </span>            :                 prevcoord[2] = thiscoord[2];</a>
+<a name="1943"><span class="lineNum">    1943 </span>            :  </a>
+<a name="1944"><span class="lineNum">    1944 </span>            : </a>
+<a name="1945"><span class="lineNum">    1945 </span><span class="lineCov">    3503034 :                 flag = xtc_receivebits(buf, 1);</span></a>
+<a name="1946"><span class="lineNum">    1946 </span>            :                 is_smaller = 0;</a>
+<a name="1947"><span class="lineNum">    1947 </span><span class="lineCov">    3503034 :                 if (flag == 1) {</span></a>
+<a name="1948"><span class="lineNum">    1948 </span><span class="lineCov">    2558100 :                         run = xtc_receivebits(buf, 5);</span></a>
+<a name="1949"><span class="lineNum">    1949 </span><span class="lineCov">    2558100 :                         is_smaller = run % 3;</span></a>
+<a name="1950"><span class="lineNum">    1950 </span><span class="lineCov">    2558100 :                         run -= is_smaller;</span></a>
+<a name="1951"><span class="lineNum">    1951 </span><span class="lineCov">    2558100 :                         is_smaller--;</span></a>
+<a name="1952"><span class="lineNum">    1952 </span>            :                 }</a>
+<a name="1953"><span class="lineNum">    1953 </span><span class="lineCov">    3503034 :                 if (run &gt; 0) {</span></a>
+<a name="1954"><span class="lineNum">    1954 </span><span class="lineCov">    2772470 :                         thiscoord += 3;</span></a>
+<a name="1955"><span class="lineNum">    1955 </span><span class="lineCov">   19457814 :                         for (k = 0; k &lt; run; k+=3) {</span></a>
+<a name="1956"><span class="lineNum">    1956 </span><span class="lineCov">   16685344 :                                 xtc_receiveints(buf, 3, smallidx, sizesmall, thiscoord);</span></a>
+<a name="1957"><span class="lineNum">    1957 </span><span class="lineCov">   16685344 :                                 i++;</span></a>
+<a name="1958"><span class="lineNum">    1958 </span><span class="lineCov">   16685344 :                                 thiscoord[0] += prevcoord[0] - small;</span></a>
+<a name="1959"><span class="lineNum">    1959 </span><span class="lineCov">   16685344 :                                 thiscoord[1] += prevcoord[1] - small;</span></a>
+<a name="1960"><span class="lineNum">    1960 </span><span class="lineCov">   16685344 :                                 thiscoord[2] += prevcoord[2] - small;</span></a>
+<a name="1961"><span class="lineNum">    1961 </span><span class="lineCov">   16685344 :                                 if (k == 0) {</span></a>
+<a name="1962"><span class="lineNum">    1962 </span>            :                                         /* interchange first with second atom for better</a>
+<a name="1963"><span class="lineNum">    1963 </span>            :                                          * compression of water molecules</a>
+<a name="1964"><span class="lineNum">    1964 </span>            :                                          */</a>
+<a name="1965"><span class="lineNum">    1965 </span><span class="lineCov">    2772470 :                                         tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];</span></a>
+<a name="1966"><span class="lineNum">    1966 </span>            :                                         prevcoord[0] = tmp;</a>
+<a name="1967"><span class="lineNum">    1967 </span><span class="lineCov">    2772470 :                                         tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];</span></a>
+<a name="1968"><span class="lineNum">    1968 </span>            :                                         prevcoord[1] = tmp;</a>
+<a name="1969"><span class="lineNum">    1969 </span><span class="lineCov">    2772470 :                                         tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];</span></a>
+<a name="1970"><span class="lineNum">    1970 </span>            :                                         prevcoord[2] = tmp;</a>
+<a name="1971"><span class="lineNum">    1971 </span><span class="lineCov">    2772470 :                                         *lfp++ = prevcoord[0] * inv_precision;</span></a>
+<a name="1972"><span class="lineNum">    1972 </span><span class="lineCov">    2772470 :                                         *lfp++ = prevcoord[1] * inv_precision;</span></a>
+<a name="1973"><span class="lineNum">    1973 </span><span class="lineCov">    2772470 :                                         *lfp++ = prevcoord[2] * inv_precision;</span></a>
+<a name="1974"><span class="lineNum">    1974 </span>            : </a>
+<a name="1975"><span class="lineNum">    1975 </span><span class="lineCov">    2772470 :                                         if ( !sizesmall[0] || !sizesmall[1] || !sizesmall[2] ) {</span></a>
+<a name="1976"><span class="lineNum">    1976 </span>            :                                                 printf(&quot;XTC corrupted, sizesmall==0 (case 2)\n&quot;);</a>
+<a name="1977"><span class="lineNum">    1977 </span><span class="lineNoCov">          0 :                                                 return -1;</span></a>
+<a name="1978"><span class="lineNum">    1978 </span>            :                                         }</a>
+<a name="1979"><span class="lineNum">    1979 </span>            : </a>
+<a name="1980"><span class="lineNum">    1980 </span>            :                                 } else {</a>
+<a name="1981"><span class="lineNum">    1981 </span>            :                                         prevcoord[0] = thiscoord[0];</a>
+<a name="1982"><span class="lineNum">    1982 </span>            :                                         prevcoord[1] = thiscoord[1];</a>
+<a name="1983"><span class="lineNum">    1983 </span>            :                                         prevcoord[2] = thiscoord[2];</a>
+<a name="1984"><span class="lineNum">    1984 </span>            :                                 }</a>
+<a name="1985"><span class="lineNum">    1985 </span><span class="lineCov">   16685344 :                                 *lfp++ = thiscoord[0] * inv_precision;</span></a>
+<a name="1986"><span class="lineNum">    1986 </span><span class="lineCov">   16685344 :                                 *lfp++ = thiscoord[1] * inv_precision;</span></a>
+<a name="1987"><span class="lineNum">    1987 </span><span class="lineCov">   16685344 :                                 *lfp++ = thiscoord[2] * inv_precision;</span></a>
+<a name="1988"><span class="lineNum">    1988 </span>            :                         }</a>
+<a name="1989"><span class="lineNum">    1989 </span>            :                 } else {</a>
+<a name="1990"><span class="lineNum">    1990 </span><span class="lineCov">     730564 :                         *lfp++ = thiscoord[0] * inv_precision;</span></a>
+<a name="1991"><span class="lineNum">    1991 </span><span class="lineCov">     730564 :                         *lfp++ = thiscoord[1] * inv_precision;</span></a>
+<a name="1992"><span class="lineNum">    1992 </span><span class="lineCov">     730564 :                         *lfp++ = thiscoord[2] * inv_precision;          </span></a>
+<a name="1993"><span class="lineNum">    1993 </span>            :                 }</a>
+<a name="1994"><span class="lineNum">    1994 </span><span class="lineCov">    3503034 :                 smallidx += is_smaller;</span></a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineCov">    3503034 :                 if (is_smaller &lt; 0) {</span></a>
+<a name="1996"><span class="lineNum">    1996 </span>            :                         small = smaller;</a>
+<a name="1997"><span class="lineNum">    1997 </span><span class="lineCov">     969122 :                         if (smallidx &gt; FIRSTIDX) {</span></a>
+<a name="1998"><span class="lineNum">    1998 </span><span class="lineCov">     969122 :                                 smaller = xtc_magicints[smallidx - 1] /2;</span></a>
+<a name="1999"><span class="lineNum">    1999 </span>            :                         } else {</a>
+<a name="2000"><span class="lineNum">    2000 </span>            :                                 smaller = 0;</a>
+<a name="2001"><span class="lineNum">    2001 </span>            :                         }</a>
+<a name="2002"><span class="lineNum">    2002 </span><span class="lineCov">    2533912 :                 } else if (is_smaller &gt; 0) {</span></a>
+<a name="2003"><span class="lineNum">    2003 </span>            :                         smaller = small;</a>
+<a name="2004"><span class="lineNum">    2004 </span><span class="lineCov">    1092856 :                         small = xtc_magicints[smallidx] / 2;</span></a>
+<a name="2005"><span class="lineNum">    2005 </span>            :                 }</a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineCov">    3503034 :                 sizesmall[0] = sizesmall[1] = sizesmall[2] = xtc_magicints[smallidx] ;</span></a>
+<a name="2007"><span class="lineNum">    2007 </span>            :         }</a>
+<a name="2008"><span class="lineNum">    2008 </span>            :         return 1;</a>
+<a name="2009"><span class="lineNum">    2009 </span>            : }</a>
+<a name="2010"><span class="lineNum">    2010 </span>            : }</a>
+<a name="2011"><span class="lineNum">    2011 </span>            : }</a>
+<a name="2012"><span class="lineNum">    2012 </span>            : #endif</a>
+<a name="2013"><span class="lineNum">    2013 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/crdplugin.cpp.func-sort-c.html b/coverage-libs/molfile/crdplugin.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ca5e1504a1
--- /dev/null
+++ b/coverage-libs/molfile/crdplugin.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/crdplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - crdplugin.cpp<span style="font-size: 80%;"> (<a href="crdplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryLo">64.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="crdplugin.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#254">_ZN4PLMD7molfile22molfile_crdplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#169">_ZN4PLMD7molfileL14open_crd_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#212">_ZN4PLMD7molfileL15close_crd_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#188">_ZN4PLMD7molfileL18write_crd_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#77">_ZN4PLMD7molfileL13open_crd_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#163">_ZN4PLMD7molfileL14close_crd_readEPv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#107">_ZN4PLMD7molfileL17read_crd_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#223">_ZN4PLMD7molfile22molfile_crdplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#248">_ZN4PLMD7molfile26molfile_crdplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/crdplugin.cpp.func.html b/coverage-libs/molfile/crdplugin.cpp.func.html
new file mode 100644
index 0000000000..cb4c0b1def
--- /dev/null
+++ b/coverage-libs/molfile/crdplugin.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/crdplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - crdplugin.cpp<span style="font-size: 80%;"> (<a href="crdplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryLo">64.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="crdplugin.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#254">_ZN4PLMD7molfile22molfile_crdplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#223">_ZN4PLMD7molfile22molfile_crdplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#248">_ZN4PLMD7molfile26molfile_crdplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#77">_ZN4PLMD7molfileL13open_crd_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#163">_ZN4PLMD7molfileL14close_crd_readEPv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#169">_ZN4PLMD7molfileL14open_crd_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#212">_ZN4PLMD7molfileL15close_crd_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#107">_ZN4PLMD7molfileL17read_crd_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="crdplugin.cpp.gcov.html#188">_ZN4PLMD7molfileL18write_crd_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/crdplugin.cpp.gcov.html b/coverage-libs/molfile/crdplugin.cpp.gcov.html
new file mode 100644
index 0000000000..ac1fb73c1f
--- /dev/null
+++ b/coverage-libs/molfile/crdplugin.cpp.gcov.html
@@ -0,0 +1,338 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/crdplugin.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - crdplugin.cpp<span style="font-size: 80%;"> (source / <a href="crdplugin.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryLo">64.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #if defined(__PLUMED_HAS_MOLFILE_PLUGINS) &amp;&amp; ! defined(__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS)</a>
+<a name="38"><span class="lineNum">      38 </span>            : /***************************************************************************</a>
+<a name="39"><span class="lineNum">      39 </span>            :  *cr</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr            (C) Copyright 1995-2009 The Board of Trustees of the</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr                        University of Illinois</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                         All Rights Reserved</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr</a>
+<a name="44"><span class="lineNum">      44 </span>            :  ***************************************************************************/</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : /***************************************************************************</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * RCS INFORMATION:</a>
+<a name="48"><span class="lineNum">      48 </span>            :  *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *      $RCSfile: crdplugin.c,v $</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $Revision: 1.39 $       $Date: 2013/04/13 03:29:48 $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  ***************************************************************************/</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : /*</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * TODO: This plugin should probably be merged with the 'rst7' plugin, since</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *       the differences between them are minor, and there's no logical reason</a>
+<a name="58"><span class="lineNum">      58 </span>            :  *       for them to be implemented completely independently as they are now.</a>
+<a name="59"><span class="lineNum">      59 </span>            :  *       The major differences in formatting are in regard to the 6F12.7 (rst7)</a>
+<a name="60"><span class="lineNum">      60 </span>            :  *       versus 10F8.3 (crd) ascii floating point conversion modes. </a>
+<a name="61"><span class="lineNum">      61 </span>            :  */</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : #include &quot;largefiles.h&quot;   /* platform dependent 64-bit file I/O defines */</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &lt;string.h&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &quot;molfile_plugin.h&quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace PLMD{</a>
+<a name="71"><span class="lineNum">      71 </span>            : namespace molfile{</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : typedef struct {</a>
+<a name="74"><span class="lineNum">      74 </span>            :   FILE *file;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   int has_box;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   int numatoms;</a>
+<a name="77"><span class="lineNum">      77 </span>            : } crddata;</a>
+<a name="78"><span class="lineNum">      78 </span>            :  </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          2 : static void *open_crd_read(const char *filename, const char *filetype, </span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     int *natoms) {</a>
+<a name="81"><span class="lineNum">      81 </span>            :  </a>
+<a name="82"><span class="lineNum">      82 </span>            :   FILE *fd;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   crddata *data;</a>
+<a name="84"><span class="lineNum">      84 </span>            :  </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 :   fd = fopen(filename, &quot;rb&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :   if (!fd) return NULL;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   </a>
+<a name="88"><span class="lineNum">      88 </span>            :   /* first line is title, so skip past it */</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        162 :   while (getc(fd) != '\n');</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   /* </a>
+<a name="92"><span class="lineNum">      92 </span>            :    * CRD's don't store the number of atoms in the timestep, so we assume that</a>
+<a name="93"><span class="lineNum">      93 </span>            :    * the application will determine this for us.  </a>
+<a name="94"><span class="lineNum">      94 </span>            :    */</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   data = (crddata *)malloc(sizeof(crddata));</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   data-&gt;file = fd;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   *natoms = MOLFILE_NUMATOMS_UNKNOWN;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   /* filetype &quot;crd&quot; has no box; filetype &quot;crdbox&quot; does. */</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   data-&gt;has_box = strcmp(filetype, &quot;crd&quot;); </span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   return data;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : /*</a>
+<a name="104"><span class="lineNum">     104 </span>            :  * CRD files with box info are indistinguishable from regular CRD's.  </a>
+<a name="105"><span class="lineNum">     105 </span>            :  * We regard CRD's with box info as a different file format.</a>
+<a name="106"><span class="lineNum">     106 </span>            :  * CRD's don't tell how many atoms there are in each frame.  We therefore</a>
+<a name="107"><span class="lineNum">     107 </span>            :  * rely on the numatoms field in the molfile_timestep_t parameter.</a>
+<a name="108"><span class="lineNum">     108 </span>            :  */</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          5 : static int read_crd_timestep(void *mydata, int natoms, molfile_timestep_t *ts) {</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   crddata *crd = (crddata *)mydata;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   int i, j;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   float x, y, z;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   float a, b, c;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   /* Read in the atom coordinates */</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      21382 :   for (i=0; i&lt;natoms; i++) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      21379 :     j = fscanf(crd-&gt;file, &quot;%f %f %f&quot;, &amp;x, &amp;y, &amp;z);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      21379 :     if (j == EOF) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       return MOLFILE_ERROR;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      21377 :     } else if (j &lt;= 0) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       fprintf(stderr, &quot;Problem reading CRD file\n&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :     /* only save coords if we're given a valid ts pointer */ </a>
+<a name="126"><span class="lineNum">     126 </span>            :     /* otherwise assume that VMD wants us to skip it.     */</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      21377 :     if (ts != NULL) {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      21377 :       ts-&gt;coords[3*i  ] = x;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      21377 :       ts-&gt;coords[3*i+1] = y;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      21377 :       ts-&gt;coords[3*i+2] = z;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     }</a>
+<a name="132"><span class="lineNum">     132 </span>            :   }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   /* Read the PBC box info. */</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 :   if (crd-&gt;has_box) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :     j = fscanf(crd-&gt;file, &quot;%f %f %f&quot;, &amp;a, &amp;b, &amp;c);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :     if (j == EOF) {</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :       printf(&quot;EOF in box\n&quot;);</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :     } else if (j &lt;= 0) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :       printf(&quot;Problem reading box part of CRD file, scanf returned %d\n&quot;,j);</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :     /* only save coords if we're given a valid ts pointer */ </a>
+<a name="147"><span class="lineNum">     147 </span>            :     /* otherwise assume that VMD wants us to skip it.     */</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :     if (ts != NULL) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :       ts-&gt;A = a;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :       ts-&gt;B = b;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          2 :       ts-&gt;C = c;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :       /* XXX periodic cell angles are only stored in the PARM file */</a>
+<a name="154"><span class="lineNum">     154 </span>            :       /* we should probably retrieve these from the already-loaded */</a>
+<a name="155"><span class="lineNum">     155 </span>            :       /* molecule when possible.                                   */</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :       ts-&gt;alpha = 90.0;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :       ts-&gt;beta  = 90.0;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          2 :       ts-&gt;gamma = 90.0;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            :     </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 : static void close_crd_read(void *mydata) {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   crddata *crd = (crddata *)mydata;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   fclose(crd-&gt;file);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          2 :   free(crd);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 : }</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 : static void *open_crd_write(const char *path, const char *filetype,</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     int natoms) {</a>
+<a name="173"><span class="lineNum">     173 </span>            :   crddata *crd;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   FILE *fd;</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :   fd = fopen(path, &quot;wb&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   if (!fd) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;Could not open file %s for writing\n&quot;, path);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   }</a>
+<a name="181"><span class="lineNum">     181 </span>            :   fprintf(fd, &quot;TITLE : Created by VMD with %d atoms\n&quot;, natoms);</a>
+<a name="182"><span class="lineNum">     182 </span>            :   </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   crd = (crddata *)malloc(sizeof(crddata));</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :   crd-&gt;file = fd;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   crd-&gt;numatoms = natoms;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   crd-&gt;has_box = strcmp(filetype, &quot;crd&quot;); </span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   return crd;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : }    </a>
+<a name="189"><span class="lineNum">     189 </span>            :   </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 : static int write_crd_timestep(void *v, const molfile_timestep_t *ts) {</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   crddata *crd = (crddata *)v;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   int i;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   int lfdone=0;</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   const int ndata = crd-&gt;numatoms * 3;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;ndata; i++) {</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     lfdone = 0;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :     fprintf(crd-&gt;file, &quot;%8.3f&quot;, ts-&gt;coords[i]);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :     if ((i+1) % 10 == 0) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :       fprintf(crd-&gt;file, &quot;\n&quot;); </span></a>
+<a name="201"><span class="lineNum">     201 </span>            :       lfdone = 1;</a>
+<a name="202"><span class="lineNum">     202 </span>            :     }</a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   if (!lfdone)</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :     fprintf(crd-&gt;file, &quot;\n&quot;); </span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :   if (crd-&gt;has_box) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     fprintf (crd-&gt;file, &quot;%8.3f%8.3f%8.3f\n&quot;, ts-&gt;A, ts-&gt;B, ts-&gt;C);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 : static void close_crd_write(void *v) {</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   crddata *crd = (crddata *)v;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   fclose(crd-&gt;file);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   free(crd);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : /* registration stuff */</a>
+<a name="221"><span class="lineNum">     221 </span>            :     </a>
+<a name="222"><span class="lineNum">     222 </span>            : static molfile_plugin_t plugin;</a>
+<a name="223"><span class="lineNum">     223 </span>            : static molfile_plugin_t crdboxplugin;</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_init(void) { </span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   memset(&amp;plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       8336 :   plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       8336 :   plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       8336 :   plugin.name = &quot;crd&quot;;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       8336 :   plugin.prettyname = &quot;AMBER Coordinates&quot;;</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       8336 :   plugin.author = &quot;Justin Gullingsrud, John Stone&quot;;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   plugin.majorv = 0;</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       8336 :   plugin.minorv = 9;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       8336 :   plugin.is_reentrant = VMDPLUGIN_THREADSAFE;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       8336 :   plugin.filename_extension = &quot;mdcrd,crd&quot;;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       8336 :   plugin.open_file_read = open_crd_read;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       8336 :   plugin.read_next_timestep = read_crd_timestep;</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       8336 :   plugin.close_file_read = close_crd_read;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       8336 :   plugin.open_file_write = open_crd_write;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       8336 :   plugin.write_timestep = write_crd_timestep;</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       8336 :   plugin.close_file_write = close_crd_write;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   memcpy(&amp;crdboxplugin, &amp;plugin, sizeof(molfile_plugin_t));</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">       8336 :   crdboxplugin.name = &quot;crdbox&quot;;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       8336 :   crdboxplugin.prettyname = &quot;AMBER Coordinates with Periodic Box&quot;;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       8336 :   return VMDPLUGIN_SUCCESS; </span></a>
+<a name="248"><span class="lineNum">     248 </span>            : }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;plugin);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;crdboxplugin);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       8336 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 : VMDPLUGIN_API int VMDPLUGIN_fini(void) { return VMDPLUGIN_SUCCESS; }</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : }</a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : #endif</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/dcdplugin.cpp.func-sort-c.html b/coverage-libs/molfile/dcdplugin.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e29e1c03a2
--- /dev/null
+++ b/coverage-libs/molfile/dcdplugin.cpp.func-sort-c.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/dcdplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - dcdplugin.cpp<span style="font-size: 80%;"> (<a href="dcdplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntry">461</td>
+            <td class="headerCovTableEntryLo">43.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">52.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="dcdplugin.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1240">_ZN4PLMD7molfile22molfile_dcdplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#736">_ZN4PLMD7molfileL12skip_dcdstepEiiii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#775">_ZN4PLMD7molfileL13write_dcdstepEiiiiPKfS2_S2_PKdi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1106">_ZN4PLMD7molfileL14open_dcd_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#158">_ZN4PLMD7molfileL14print_dcderrorEPKci</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1164">_ZN4PLMD7molfileL14write_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#822">_ZN4PLMD7molfileL15write_dcdheaderEiPKciiidii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1200">_ZN4PLMD7molfileL16close_file_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#505">_ZN4PLMD7molfileL16read_fixed_atomsEiiiPKiiPKfPfS5_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#903">_ZN4PLMD7molfileL13open_dcd_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#897">_ZN4PLMD7molfileL14close_dcd_readEPiPf</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#194">_ZN4PLMD7molfileL14read_dcdheaderEiPiS1_S1_S1_PdS1_PS1_PPfS1_S1_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1095">_ZN4PLMD7molfileL15close_file_readEPv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#579">_ZN4PLMD7molfileL12read_dcdstepEiiPfS1_S1_S1_iiPiS1_ii</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#542">_ZN4PLMD7molfileL16read_charmm_4dimEiii</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#472">_ZN4PLMD7molfileL22read_charmm_extrablockEiiiPf</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1014">_ZN4PLMD7molfileL18read_next_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1215">_ZN4PLMD7molfile22molfile_dcdplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1235">_ZN4PLMD7molfile26molfile_dcdplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/dcdplugin.cpp.func.html b/coverage-libs/molfile/dcdplugin.cpp.func.html
new file mode 100644
index 0000000000..1c67463bc6
--- /dev/null
+++ b/coverage-libs/molfile/dcdplugin.cpp.func.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/dcdplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - dcdplugin.cpp<span style="font-size: 80%;"> (<a href="dcdplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntry">461</td>
+            <td class="headerCovTableEntryLo">43.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">52.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="dcdplugin.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1240">_ZN4PLMD7molfile22molfile_dcdplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1215">_ZN4PLMD7molfile22molfile_dcdplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1235">_ZN4PLMD7molfile26molfile_dcdplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#579">_ZN4PLMD7molfileL12read_dcdstepEiiPfS1_S1_S1_iiPiS1_ii</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#736">_ZN4PLMD7molfileL12skip_dcdstepEiiii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#903">_ZN4PLMD7molfileL13open_dcd_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#775">_ZN4PLMD7molfileL13write_dcdstepEiiiiPKfS2_S2_PKdi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#897">_ZN4PLMD7molfileL14close_dcd_readEPiPf</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1106">_ZN4PLMD7molfileL14open_dcd_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#158">_ZN4PLMD7molfileL14print_dcderrorEPKci</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#194">_ZN4PLMD7molfileL14read_dcdheaderEiPiS1_S1_S1_PdS1_PS1_PPfS1_S1_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1164">_ZN4PLMD7molfileL14write_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1095">_ZN4PLMD7molfileL15close_file_readEPv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#822">_ZN4PLMD7molfileL15write_dcdheaderEiPKciiidii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1200">_ZN4PLMD7molfileL16close_file_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#542">_ZN4PLMD7molfileL16read_charmm_4dimEiii</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#505">_ZN4PLMD7molfileL16read_fixed_atomsEiiiPKiiPKfPfS5_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#1014">_ZN4PLMD7molfileL18read_next_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="dcdplugin.cpp.gcov.html#472">_ZN4PLMD7molfileL22read_charmm_extrablockEiiiPf</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/dcdplugin.cpp.gcov.html b/coverage-libs/molfile/dcdplugin.cpp.gcov.html
new file mode 100644
index 0000000000..3bc8cf7f64
--- /dev/null
+++ b/coverage-libs/molfile/dcdplugin.cpp.gcov.html
@@ -0,0 +1,1393 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/dcdplugin.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - dcdplugin.cpp<span style="font-size: 80%;"> (source / <a href="dcdplugin.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntry">461</td>
+            <td class="headerCovTableEntryLo">43.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">52.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #if defined(__PLUMED_HAS_MOLFILE_PLUGINS) &amp;&amp; ! defined(__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS)</a>
+<a name="38"><span class="lineNum">      38 </span>            : /***************************************************************************</a>
+<a name="39"><span class="lineNum">      39 </span>            :  *cr                                                                       </a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the           </a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr                        University of Illinois                       </a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                         All Rights Reserved                        </a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr                                                                   </a>
+<a name="44"><span class="lineNum">      44 </span>            :  ***************************************************************************/</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : /***************************************************************************</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * RCS INFORMATION:</a>
+<a name="48"><span class="lineNum">      48 </span>            :  *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *      $RCSfile: dcdplugin.c,v $</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $Revision: 1.88 $       $Date: 2020/12/17 17:14:07 $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  ***************************************************************************</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * DESCRIPTION:</a>
+<a name="55"><span class="lineNum">      55 </span>            :  *   Code for reading and writing CHARMM, NAMD, and X-PLOR format </a>
+<a name="56"><span class="lineNum">      56 </span>            :  *   molecular dynamic trajectory files.</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * TODO:</a>
+<a name="59"><span class="lineNum">      59 </span>            :  *   Integrate improvements from the NAMD source tree</a>
+<a name="60"><span class="lineNum">      60 </span>            :  *    - NAMD's writer code has better type-correctness for the sizes</a>
+<a name="61"><span class="lineNum">      61 </span>            :  *      of &quot;int&quot;.  NAMD uses &quot;int32&quot; explicitly, which is required on</a>
+<a name="62"><span class="lineNum">      62 </span>            :  *      machines like the T3E.  VMD's version of the code doesn't do that</a>
+<a name="63"><span class="lineNum">      63 </span>            :  *      presently.</a>
+<a name="64"><span class="lineNum">      64 </span>            :  *</a>
+<a name="65"><span class="lineNum">      65 </span>            :  *  Try various alternative I/O API options:</a>
+<a name="66"><span class="lineNum">      66 </span>            :  *   - use mmap(), with read-once flags</a>
+<a name="67"><span class="lineNum">      67 </span>            :  *   - use O_DIRECT open mode on new revs of Linux kernel </a>
+<a name="68"><span class="lineNum">      68 </span>            :  *   - use directio() call on a file descriptor to enable on Solaris</a>
+<a name="69"><span class="lineNum">      69 </span>            :  *   - use aio_open()/read()/write()</a>
+<a name="70"><span class="lineNum">      70 </span>            :  *   - use readv/writev() etc.</a>
+<a name="71"><span class="lineNum">      71 </span>            :  *</a>
+<a name="72"><span class="lineNum">      72 </span>            :  *  Standalone test binary compilation flags:</a>
+<a name="73"><span class="lineNum">      73 </span>            :  *  cc -fast -xarch=v9a -I../../include -DTEST_DCDPLUGIN dcdplugin.c \</a>
+<a name="74"><span class="lineNum">      74 </span>            :  *    -o ~/bin/readdcd -lm</a>
+<a name="75"><span class="lineNum">      75 </span>            :  *</a>
+<a name="76"><span class="lineNum">      76 </span>            :  *  Profiling flags:</a>
+<a name="77"><span class="lineNum">      77 </span>            :  *  cc -xpg -fast -xarch=v9a -g -I../../include -DTEST_DCDPLUGIN dcdplugin.c \</a>
+<a name="78"><span class="lineNum">      78 </span>            :  *    -o ~/bin/readdcd -lm</a>
+<a name="79"><span class="lineNum">      79 </span>            :  *</a>
+<a name="80"><span class="lineNum">      80 </span>            :  ***************************************************************************/</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : #include &quot;largefiles.h&quot;   /* platform dependent 64-bit file I/O defines */</a>
+<a name="83"><span class="lineNum">      83 </span>            : #include &quot;fastio.h&quot;       /* must come before others, for O_DIRECT...   */</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="86"><span class="lineNum">      86 </span>            : #include &lt;sys/stat.h&gt;</a>
+<a name="87"><span class="lineNum">      87 </span>            : #include &lt;sys/types.h&gt;</a>
+<a name="88"><span class="lineNum">      88 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="89"><span class="lineNum">      89 </span>            : #include &lt;stddef.h&gt;</a>
+<a name="90"><span class="lineNum">      90 </span>            : #include &lt;string.h&gt;</a>
+<a name="91"><span class="lineNum">      91 </span>            : #include &lt;math.h&gt;</a>
+<a name="92"><span class="lineNum">      92 </span>            : #include &lt;time.h&gt;</a>
+<a name="93"><span class="lineNum">      93 </span>            : #include &quot;endianswap.h&quot;</a>
+<a name="94"><span class="lineNum">      94 </span>            : #include &quot;molfile_plugin.h&quot;</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : namespace PLMD{</a>
+<a name="97"><span class="lineNum">      97 </span>            : namespace molfile{</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : #ifndef M_PI_2</a>
+<a name="100"><span class="lineNum">     100 </span>            : #define M_PI_2 1.57079632679489661922</a>
+<a name="101"><span class="lineNum">     101 </span>            : #endif</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : #define RECSCALE32BIT 1</a>
+<a name="104"><span class="lineNum">     104 </span>            : #define RECSCALE64BIT 2</a>
+<a name="105"><span class="lineNum">     105 </span>            : #define RECSCALEMAX   2</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : typedef struct {</a>
+<a name="108"><span class="lineNum">     108 </span>            :   fio_fd fd;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   int natoms;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   int nsets;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   int setsread;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   int istart;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   int nsavc;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   double delta;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   int nfixed;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   float *x, *y, *z;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   int *freeind;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   float *fixedcoords;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   int reverse;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   int charmm;  </a>
+<a name="121"><span class="lineNum">     121 </span>            :   int first;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   int with_unitcell;</a>
+<a name="123"><span class="lineNum">     123 </span>            : } dcdhandle;</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : /* Define error codes that may be returned by the DCD routines */</a>
+<a name="126"><span class="lineNum">     126 </span>            : #define DCD_SUCCESS      0  /* No problems                     */</a>
+<a name="127"><span class="lineNum">     127 </span>            : #define DCD_EOF         -1  /* Normal EOF                      */</a>
+<a name="128"><span class="lineNum">     128 </span>            : #define DCD_DNE         -2  /* DCD file does not exist         */</a>
+<a name="129"><span class="lineNum">     129 </span>            : #define DCD_OPENFAILED  -3  /* Open of DCD file failed         */</a>
+<a name="130"><span class="lineNum">     130 </span>            : #define DCD_BADREAD     -4  /* read call on DCD file failed    */</a>
+<a name="131"><span class="lineNum">     131 </span>            : #define DCD_BADEOF      -5  /* premature EOF found in DCD file */</a>
+<a name="132"><span class="lineNum">     132 </span>            : #define DCD_BADFORMAT   -6  /* format of DCD file is wrong     */</a>
+<a name="133"><span class="lineNum">     133 </span>            : #define DCD_FILEEXISTS  -7  /* output file already exists      */</a>
+<a name="134"><span class="lineNum">     134 </span>            : #define DCD_BADMALLOC   -8  /* malloc failed                   */</a>
+<a name="135"><span class="lineNum">     135 </span>            : #define DCD_BADWRITE    -9  /* write call on DCD file failed   */</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : /* Define feature flags for this DCD file */</a>
+<a name="138"><span class="lineNum">     138 </span>            : #define DCD_IS_XPLOR        0x00</a>
+<a name="139"><span class="lineNum">     139 </span>            : #define DCD_IS_CHARMM       0x01</a>
+<a name="140"><span class="lineNum">     140 </span>            : #define DCD_HAS_4DIMS       0x02</a>
+<a name="141"><span class="lineNum">     141 </span>            : #define DCD_HAS_EXTRA_BLOCK 0x04</a>
+<a name="142"><span class="lineNum">     142 </span>            : #define DCD_HAS_64BIT_REC   0x08</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : /* defines used by write_dcdstep */</a>
+<a name="145"><span class="lineNum">     145 </span>            : #define NFILE_POS 8L</a>
+<a name="146"><span class="lineNum">     146 </span>            : #define NSTEP_POS 20L</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : /* READ Macro to make porting easier */</a>
+<a name="149"><span class="lineNum">     149 </span>            : #define READ(fd, buf, size)  fio_fread(((void *) buf), (size), 1, (fd))</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : /* WRITE Macro to make porting easier */</a>
+<a name="152"><span class="lineNum">     152 </span>            : #define WRITE(fd, buf, size) fio_fwrite(((void *) buf), (size), 1, (fd))</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : /* XXX This is broken - fread never returns -1 */</a>
+<a name="155"><span class="lineNum">     155 </span>            : #define CHECK_FREAD(X, msg) if (X==-1) { return(DCD_BADREAD); }</a>
+<a name="156"><span class="lineNum">     156 </span>            : #define CHECK_FEOF(X, msg)  if (X==0)  { return(DCD_BADEOF); }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : /* print DCD error in a human readable way */</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 : static void print_dcderror(const char *func, int errcode) {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   const char *errstr;</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   switch (errcode) {</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     case DCD_EOF:         errstr = &quot;end of file&quot;; break;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     case DCD_DNE:         errstr = &quot;file not found&quot;; break;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     case DCD_OPENFAILED:  errstr = &quot;file open failed&quot;; break;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     case DCD_BADREAD:     errstr = &quot;error during read&quot;; break;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     case DCD_BADEOF:      errstr = &quot;premature end of file&quot;; break;</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     case DCD_BADFORMAT:   errstr = &quot;corruption or unrecognized file structure&quot;; break;</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     case DCD_FILEEXISTS:  errstr = &quot;output file already exists&quot;; break;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :     case DCD_BADMALLOC:   errstr = &quot;memory allocation failed&quot;; break;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :     case DCD_BADWRITE:    errstr = &quot;error during write&quot;; break;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     case DCD_SUCCESS:     </span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     default:</a>
+<a name="175"><span class="lineNum">     175 </span>            :       errstr = &quot;no error&quot;;</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   } </a>
+<a name="178"><span class="lineNum">     178 </span>            :   printf(&quot;dcdplugin) %s: %s\n&quot;, func, errstr); </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : /*</a>
+<a name="183"><span class="lineNum">     183 </span>            :  * Read the header information from a dcd file.</a>
+<a name="184"><span class="lineNum">     184 </span>            :  * Input: fd - a file struct opened for binary reading.</a>
+<a name="185"><span class="lineNum">     185 </span>            :  * Output: 0 on success, negative error code on failure.</a>
+<a name="186"><span class="lineNum">     186 </span>            :  * Side effects: *natoms set to number of atoms per frame</a>
+<a name="187"><span class="lineNum">     187 </span>            :  *               *nsets set to number of frames in dcd file</a>
+<a name="188"><span class="lineNum">     188 </span>            :  *               *istart set to starting timestep of dcd file</a>
+<a name="189"><span class="lineNum">     189 </span>            :  *               *nsavc set to timesteps between dcd saves</a>
+<a name="190"><span class="lineNum">     190 </span>            :  *               *delta set to value of trajectory timestep</a>
+<a name="191"><span class="lineNum">     191 </span>            :  *               *nfixed set to number of fixed atoms </a>
+<a name="192"><span class="lineNum">     192 </span>            :  *               *freeind may be set to heap-allocated space</a>
+<a name="193"><span class="lineNum">     193 </span>            :  *               *reverse set to one if reverse-endian, zero if not.</a>
+<a name="194"><span class="lineNum">     194 </span>            :  *               *charmm set to internal code for handling charmm data.</a>
+<a name="195"><span class="lineNum">     195 </span>            :  */</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          1 : static int read_dcdheader(fio_fd fd, int *N, int *NSET, int *ISTART, </span></a>
+<a name="197"><span class="lineNum">     197 </span>            :                    int *NSAVC, double *DELTA, int *NAMNF, </a>
+<a name="198"><span class="lineNum">     198 </span>            :                    int **FREEINDEXES, float **fixedcoords, int *reverseEndian, </a>
+<a name="199"><span class="lineNum">     199 </span>            :                    int *charmm)</a>
+<a name="200"><span class="lineNum">     200 </span>            : {</a>
+<a name="201"><span class="lineNum">     201 </span>            :   unsigned int input_integer[2];  /* buffer space */</a>
+<a name="202"><span class="lineNum">     202 </span>            :   int i, ret_val, rec_scale;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   char hdrbuf[84];    /* char buffer used to store header */</a>
+<a name="204"><span class="lineNum">     204 </span>            :   int NTITLE;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   int dcdcordmagic;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   int hugefile = 0;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   char *corp = (char *) &amp;dcdcordmagic;</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   /* coordinate dcd file magic string 'CORD' */</a>
+<a name="210"><span class="lineNum">     210 </span>            :   corp[0] = 'C';</a>
+<a name="211"><span class="lineNum">     211 </span>            :   corp[1] = 'O';</a>
+<a name="212"><span class="lineNum">     212 </span>            :   corp[2] = 'R';</a>
+<a name="213"><span class="lineNum">     213 </span>            :   corp[3] = 'D';</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   /* First thing in the file should be an 84.</a>
+<a name="216"><span class="lineNum">     216 </span>            :    * some 64-bit compiles have a 64-bit record length indicator,</a>
+<a name="217"><span class="lineNum">     217 </span>            :    * so we have to read two ints and check in a more complicated </a>
+<a name="218"><span class="lineNum">     218 </span>            :    * way. :-( */</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          1 :   ret_val = READ(fd, input_integer, 2*sizeof(unsigned int));</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;reading first int from dcd file&quot;);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;reading first int from dcd file&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   /* Check magic number in file header and determine byte order*/</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          1 :   if ((input_integer[0]+input_integer[1]) == 84) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     *reverseEndian=0;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :     rec_scale=RECSCALE64BIT;</a>
+<a name="227"><span class="lineNum">     227 </span>            :     printf(&quot;dcdplugin) detected CHARMM -i8 64-bit DCD file of native endianness\n&quot;);</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          1 :   } else if (input_integer[0] == 84 &amp;&amp; input_integer[1] == dcdcordmagic) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          1 :     *reverseEndian=0;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     rec_scale=RECSCALE32BIT;</a>
+<a name="231"><span class="lineNum">     231 </span>            :     printf(&quot;dcdplugin) detected standard 32-bit DCD file of native endianness\n&quot;);</a>
+<a name="232"><span class="lineNum">     232 </span>            :   } else {</a>
+<a name="233"><span class="lineNum">     233 </span>            :     /* now try reverse endian */</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :     swap4_aligned(input_integer, 2); /* will have to unswap magic if 32-bit */</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :     if ((input_integer[0]+input_integer[1]) == 84) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :       *reverseEndian=1;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :       rec_scale=RECSCALE64BIT;</a>
+<a name="238"><span class="lineNum">     238 </span>            :       printf(&quot;dcdplugin) detected CHARMM -i8 64-bit DCD file of opposite endianness\n&quot;);</a>
+<a name="239"><span class="lineNum">     239 </span>            :     } else {</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :       swap4_aligned(&amp;input_integer[1], 1); /* unswap magic (see above) */</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :       if (input_integer[0] == 84 &amp;&amp; input_integer[1] == dcdcordmagic) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :         *reverseEndian=1;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :         rec_scale=RECSCALE32BIT;</a>
+<a name="244"><span class="lineNum">     244 </span>            :         printf(&quot;dcdplugin) detected standard 32-bit DCD file of opposite endianness\n&quot;);</a>
+<a name="245"><span class="lineNum">     245 </span>            :       } else {</a>
+<a name="246"><span class="lineNum">     246 </span>            :         /* not simply reversed endianism or -i8, something rather more evil */</a>
+<a name="247"><span class="lineNum">     247 </span>            :         printf(&quot;dcdplugin) unrecognized DCD header:\n&quot;);</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :         printf(&quot;dcdplugin)   [0]: %10d  [1]: %10d\n&quot;, input_integer[0], input_integer[1]);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :         printf(&quot;dcdplugin)   [0]: 0x%08x  [1]: 0x%08x\n&quot;, input_integer[0], input_integer[1]);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :         return DCD_BADFORMAT;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :       }</a>
+<a name="253"><span class="lineNum">     253 </span>            :     }</a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            :   /* check for magic string, in case of long record markers */</a>
+<a name="257"><span class="lineNum">     257 </span>            :   if (rec_scale == RECSCALE64BIT) { </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :     ret_val = READ(fd, input_integer, sizeof(unsigned int));</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     if (input_integer[0] != dcdcordmagic) {</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :       printf(&quot;dcdplugin) failed to find CORD magic in CHARMM -i8 64-bit DCD file\n&quot;);</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :       return DCD_BADFORMAT;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :     }</a>
+<a name="263"><span class="lineNum">     263 </span>            :   }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   /* Buffer the entire header for random access */</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          1 :   ret_val = READ(fd, hdrbuf, 80);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;buffering header&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;buffering header&quot;);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   /* CHARMm-genereate DCD files set the last integer in the     */</a>
+<a name="271"><span class="lineNum">     271 </span>            :   /* header, which is unused by X-PLOR, to its version number.  */</a>
+<a name="272"><span class="lineNum">     272 </span>            :   /* Checking if this is nonzero tells us this is a CHARMm file */</a>
+<a name="273"><span class="lineNum">     273 </span>            :   /* and to look for other CHARMm flags.                        */</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          1 :   if (*((int *) (hdrbuf + 76)) != 0) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          1 :     (*charmm) = DCD_IS_CHARMM;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          1 :     if (*((int *) (hdrbuf + 40)) != 0)</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          1 :       (*charmm) |= DCD_HAS_EXTRA_BLOCK;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          1 :     if (*((int *) (hdrbuf + 44)) == 1)</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :       (*charmm) |= DCD_HAS_4DIMS;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          1 :     if (rec_scale == RECSCALE64BIT)</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :       (*charmm) |= DCD_HAS_64BIT_REC;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   </a>
+<a name="285"><span class="lineNum">     285 </span>            :   } else {</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :     (*charmm) = DCD_IS_XPLOR; /* must be an X-PLOR format DCD file */</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :   }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          1 :   if (*charmm &amp; DCD_IS_CHARMM) {</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :     /* CHARMM and NAMD versions 2.1b1 and later */</a>
+<a name="291"><span class="lineNum">     291 </span>            :     printf(&quot;dcdplugin) CHARMM format DCD file (also NAMD 2.1 and later)\n&quot;);</a>
+<a name="292"><span class="lineNum">     292 </span>            :   } else {</a>
+<a name="293"><span class="lineNum">     293 </span>            :     /* CHARMM and NAMD versions prior to 2.1b1  */</a>
+<a name="294"><span class="lineNum">     294 </span>            :     printf(&quot;dcdplugin) X-PLOR format DCD file (also NAMD 2.0 and earlier)\n&quot;);</a>
+<a name="295"><span class="lineNum">     295 </span>            :   }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            :   /* Store the number of sets of coordinates (NSET) */</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          1 :   (*NSET) = *((int *) (hdrbuf));</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_unaligned(NSET, 1);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   /* Store ISTART, the starting timestep */</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          1 :   (*ISTART) = *((int *) (hdrbuf + 4));</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_unaligned(ISTART, 1);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            :   /* Store NSAVC, the number of timesteps between dcd saves */</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          1 :   (*NSAVC) = *((int *) (hdrbuf + 8));</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_unaligned(NSAVC, 1);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :   /* Store NAMNF, the number of fixed atoms */</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          1 :   (*NAMNF) = *((int *) (hdrbuf + 32));</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_unaligned(NAMNF, 1);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   /* Read in the timestep, DELTA */</a>
+<a name="314"><span class="lineNum">     314 </span>            :   /* Note: DELTA is stored as a double with X-PLOR but as a float with CHARMm */</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          1 :   if ((*charmm) &amp; DCD_IS_CHARMM) {</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :     float ftmp;</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          1 :     ftmp = *((float *)(hdrbuf+36)); /* is this safe on Alpha? */</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          1 :     if (*reverseEndian)</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :       swap4_aligned(&amp;ftmp, 1);</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          1 :     *DELTA = (double)ftmp;</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   } else {</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     (*DELTA) = *((double *)(hdrbuf + 36));</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :     if (*reverseEndian) swap8_unaligned(DELTA, 1);</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :   }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            :   /* Get the end size of the first block */</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          1 :   ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;reading second 84 from dcd file&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;reading second 84 from dcd file&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          1 :   if (rec_scale == RECSCALE64BIT) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :     if ((input_integer[0]+input_integer[1]) != 84) {</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :       return DCD_BADFORMAT;</a>
+<a name="336"><span class="lineNum">     336 </span>            :     }</a>
+<a name="337"><span class="lineNum">     337 </span>            :   } else {</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          1 :     if (input_integer[0] != 84) {</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :       return DCD_BADFORMAT;</a>
+<a name="340"><span class="lineNum">     340 </span>            :     }</a>
+<a name="341"><span class="lineNum">     341 </span>            :   }</a>
+<a name="342"><span class="lineNum">     342 </span>            :   </a>
+<a name="343"><span class="lineNum">     343 </span>            :   /* Read in the size of the next block */</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          1 :   input_integer[1] = 0;</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          1 :   ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;reading size of title block&quot;);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;reading size of title block&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          1 :   if ((((input_integer[0]+input_integer[1])-4) % 80) == 0) {</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :     /* Read NTITLE, the number of 80 character title strings there are */</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          1 :     ret_val = READ(fd, &amp;NTITLE, sizeof(int));</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          1 :     CHECK_FREAD(ret_val, &quot;reading NTITLE&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          1 :     CHECK_FEOF(ret_val, &quot;reading NTITLE&quot;);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          1 :     if (*reverseEndian) swap4_aligned(&amp;NTITLE, 1);</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          1 :     if (NTITLE &lt; 0) {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :       printf(&quot;dcdplugin) WARNING: Bogus NTITLE value: %d (hex: %08x)\n&quot;, </a>
+<a name="359"><span class="lineNum">     359 </span>            :              NTITLE, NTITLE);</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :       return DCD_BADFORMAT;</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :     }</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          1 :     if (NTITLE &gt; 1000) {</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :       printf(&quot;dcdplugin) WARNING: Bogus NTITLE value: %d (hex: %08x)\n&quot;, </a>
+<a name="365"><span class="lineNum">     365 </span>            :              NTITLE, NTITLE);</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :       if (NTITLE == 1095062083) {</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :         printf(&quot;dcdplugin) WARNING: Broken Vega ZZ 2.4.0 DCD file detected\n&quot;);</a>
+<a name="368"><span class="lineNum">     368 </span>            :         printf(&quot;dcdplugin) Assuming 2 title lines, good luck...\n&quot;);</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :         NTITLE = 2;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :       } else {</a>
+<a name="371"><span class="lineNum">     371 </span>            :         printf(&quot;dcdplugin) Assuming zero title lines, good luck...\n&quot;);</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :         NTITLE = 0;</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :       }</a>
+<a name="374"><span class="lineNum">     374 </span>            :     }</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          3 :     for (i=0; i&lt;NTITLE; i++) {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          2 :       fio_fseek(fd, 80, FIO_SEEK_CUR);</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :       CHECK_FEOF(ret_val, &quot;reading TITLE&quot;);</a>
+<a name="379"><span class="lineNum">     379 </span>            :     }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            :     /* Get the ending size for this block */</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          1 :     ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          1 :     CHECK_FREAD(ret_val, &quot;reading size of title block&quot;);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          1 :     CHECK_FEOF(ret_val, &quot;reading size of title block&quot;);</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :   } else {</a>
+<a name="386"><span class="lineNum">     386 </span>            :     return DCD_BADFORMAT;</a>
+<a name="387"><span class="lineNum">     387 </span>            :   }</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            :   /* Read in an integer '4' */</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">          1 :   input_integer[1] = 0;</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          1 :   ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   </a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;reading a '4'&quot;);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;reading a '4'&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          1 :   if ((input_integer[0]+input_integer[1]) != 4) {</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :     return DCD_BADFORMAT;</a>
+<a name="399"><span class="lineNum">     399 </span>            :   }</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :   /* Read in the number of atoms */</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          1 :   ret_val = READ(fd, N, sizeof(int));</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;reading number of atoms&quot;);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;reading number of atoms&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_aligned(N, 1);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          1 :   if (*N &gt; (1L&lt;&lt;30)) {</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :     hugefile=1;</a>
+<a name="409"><span class="lineNum">     409 </span>            :     printf(&quot;dcdplugin) ***\n&quot;);</a>
+<a name="410"><span class="lineNum">     410 </span>            :     printf(&quot;dcdplugin) *** Trajectory contains over 2^30 atoms.\n&quot;);</a>
+<a name="411"><span class="lineNum">     411 </span>            :     printf(&quot;dcdplugin) *** Huge file integer wraparound handling enabled.\n&quot;);</a>
+<a name="412"><span class="lineNum">     412 </span>            :     printf(&quot;dcdplugin) ***\n&quot;);</a>
+<a name="413"><span class="lineNum">     413 </span>            :   }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            :   /* Read in an integer '4' */</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          1 :   input_integer[1] = 0;</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">          1 :   ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          1 :   CHECK_FREAD(ret_val, &quot;reading a '4'&quot;);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          1 :   CHECK_FEOF(ret_val, &quot;reading a '4'&quot;);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          1 :   if (*reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          1 :   if ((input_integer[0]+input_integer[1]) != 4) {</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :     return DCD_BADFORMAT;</a>
+<a name="424"><span class="lineNum">     424 </span>            :   }</a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          1 :   *FREEINDEXES = NULL;</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          1 :   *fixedcoords = NULL;</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          1 :   if (*NAMNF != 0) {</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :     (*FREEINDEXES) = (int *) calloc((((ptrdiff_t)(*N))-(*NAMNF)), sizeof(int));</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :     if (*FREEINDEXES == NULL)</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :       return DCD_BADMALLOC;</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :     *fixedcoords = (float *) calloc(((ptrdiff_t)(*N))*4L - (*NAMNF), sizeof(float));</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     if (*fixedcoords == NULL)</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :       return DCD_BADMALLOC;</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            :     /* Read in index array size */</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :     input_integer[1]=0;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :     ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :     CHECK_FREAD(ret_val, &quot;reading size of index array&quot;);</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :     CHECK_FEOF(ret_val, &quot;reading size of index array&quot;);</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :     if (*reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            :     /* when we have more then 2^30 atoms, tests like this one */</a>
+<a name="445"><span class="lineNum">     445 </span>            :     /* are no longer meaningful and have to be bypassed...    */</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     if (!hugefile &amp;&amp; ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4L)) {</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :       return DCD_BADFORMAT;</a>
+<a name="448"><span class="lineNum">     448 </span>            :     }</a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :     ret_val = READ(fd, (*FREEINDEXES), ((ptrdiff_t) ((*N)-(*NAMNF)))*sizeof(int));</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :     CHECK_FREAD(ret_val, &quot;reading size of index array&quot;);</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :     CHECK_FEOF(ret_val, &quot;reading size of index array&quot;);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :     if (*reverseEndian)</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :       swap4_aligned((*FREEINDEXES), ((*N)-(*NAMNF)));</span></a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :     input_integer[1]=0;</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 :     ret_val = READ(fd, input_integer, rec_scale*sizeof(int));</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineNoCov">          0 :     CHECK_FREAD(ret_val, &quot;reading size of index array&quot;);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :     CHECK_FEOF(ret_val, &quot;reading size of index array&quot;);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :     if (*reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            :     /* when we have more then 2^30 atoms, tests like this one */</a>
+<a name="464"><span class="lineNum">     464 </span>            :     /* are no longer meaningful and have to be bypassed...    */</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 :     if (!hugefile &amp;&amp; ((input_integer[0]+input_integer[1]) != ((*N)-(*NAMNF))*4L)) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :       return DCD_BADFORMAT;</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :     }</a>
+<a name="468"><span class="lineNum">     468 </span>            :   }</a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            :   return DCD_SUCCESS;</a>
+<a name="471"><span class="lineNum">     471 </span>            : }</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         21 : static int read_charmm_extrablock(fio_fd fd, int charmm, int reverseEndian,</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :                                   float *unitcell) {</a>
+<a name="476"><span class="lineNum">     476 </span>            :   int i, input_integer[2], rec_scale;</a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         21 :   if (charmm &amp; DCD_HAS_64BIT_REC) {</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :     rec_scale = RECSCALE64BIT;</a>
+<a name="480"><span class="lineNum">     480 </span>            :   } else {</a>
+<a name="481"><span class="lineNum">     481 </span>            :     rec_scale = RECSCALE32BIT;</a>
+<a name="482"><span class="lineNum">     482 </span>            :   }</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         21 :   if ((charmm &amp; DCD_IS_CHARMM) &amp;&amp; (charmm &amp; DCD_HAS_EXTRA_BLOCK)) {</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :     /* Leading integer must be 48 */</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         21 :     input_integer[1] = 0;</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">         21 :     if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale)</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :       return DCD_BADREAD; </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         21 :     if (reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         21 :     if ((input_integer[0]+input_integer[1]) == 48) {</span></a>
+<a name="491"><span class="lineNum">     491 </span>            :       double tmp[6];</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         21 :       if (fio_fread(tmp, 48, 1, fd) != 1) return DCD_BADREAD;</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         21 :       if (reverseEndian) </span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :         swap8_aligned(tmp, 6);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">        147 :       for (i=0; i&lt;6; i++) unitcell[i] = (float)tmp[i];</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :     } else {</a>
+<a name="497"><span class="lineNum">     497 </span>            :       /* unrecognized block, just skip it */</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :       if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :     }</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         21 :     if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD; </span></a>
+<a name="501"><span class="lineNum">     501 </span>            :   } </a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            :   return DCD_SUCCESS;</a>
+<a name="504"><span class="lineNum">     504 </span>            : }</a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 : static int read_fixed_atoms(fio_fd fd, int N, int num_free, const int *indexes,</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :                             int reverseEndian, const float *fixedcoords, </a>
+<a name="509"><span class="lineNum">     509 </span>            :                             float *freeatoms, float *pos, int charmm) {</a>
+<a name="510"><span class="lineNum">     510 </span>            :   int i, input_integer[2], rec_scale;</a>
+<a name="511"><span class="lineNum">     511 </span>            :   </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :   if(charmm &amp; DCD_HAS_64BIT_REC) {</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :     rec_scale=RECSCALE64BIT;</a>
+<a name="514"><span class="lineNum">     514 </span>            :   } else {</a>
+<a name="515"><span class="lineNum">     515 </span>            :     rec_scale=RECSCALE32BIT;</a>
+<a name="516"><span class="lineNum">     516 </span>            :   }</a>
+<a name="517"><span class="lineNum">     517 </span>            :   </a>
+<a name="518"><span class="lineNum">     518 </span>            :   /* Read leading integer */</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :   input_integer[1]=0;</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :   if (reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 :   if ((input_integer[0]+input_integer[1]) != 4L*num_free) return DCD_BADFORMAT;</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :   </a>
+<a name="524"><span class="lineNum">     524 </span>            :   /* Read free atom coordinates */</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :   if (fio_fread(freeatoms, 4L*num_free, 1, fd) != 1) return DCD_BADREAD;</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   if (reverseEndian)</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :     swap4_aligned(freeatoms, num_free);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span>            :   /* Copy fixed and free atom coordinates into position buffer */</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :   memcpy(pos, fixedcoords, 4L*N);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;num_free; i++)</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :     pos[indexes[i]-1] = freeatoms[i];</span></a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            :   /* Read trailing integer */ </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :   input_integer[1]=0;</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :   if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :   if (reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :   if ((input_integer[0]+input_integer[1]) != 4L*num_free) return DCD_BADFORMAT;</span></a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span>            :   return DCD_SUCCESS;</a>
+<a name="541"><span class="lineNum">     541 </span>            : }</a>
+<a name="542"><span class="lineNum">     542 </span>            :  </a>
+<a name="543"><span class="lineNum">     543 </span>            :  </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         21 : static int read_charmm_4dim(fio_fd fd, int charmm, int reverseEndian) {</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :   int input_integer[2], rec_scale;</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         21 :   if (charmm &amp; DCD_HAS_64BIT_REC) {</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :     rec_scale=RECSCALE64BIT;</a>
+<a name="549"><span class="lineNum">     549 </span>            :   } else {</a>
+<a name="550"><span class="lineNum">     550 </span>            :     rec_scale=RECSCALE32BIT;</a>
+<a name="551"><span class="lineNum">     551 </span>            :   }</a>
+<a name="552"><span class="lineNum">     552 </span>            :     </a>
+<a name="553"><span class="lineNum">     553 </span>            :   /* If this is a CHARMm file and contains a 4th dimension block, */</a>
+<a name="554"><span class="lineNum">     554 </span>            :   /* we must skip past it to avoid problems                       */</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         21 :   if ((charmm &amp; DCD_IS_CHARMM) &amp;&amp; (charmm &amp; DCD_HAS_4DIMS)) {</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineNoCov">          0 :     input_integer[1]=0;</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :     if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;  </span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineNoCov">          0 :     if (reverseEndian) swap4_aligned(input_integer, rec_scale);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :     if (fio_fseek(fd, (input_integer[0]+input_integer[1]), FIO_SEEK_CUR)) return DCD_BADREAD;</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineNoCov">          0 :     if (fio_fread(input_integer, sizeof(int), rec_scale, fd) != rec_scale) return DCD_BADREAD;  </span></a>
+<a name="561"><span class="lineNum">     561 </span>            :   }</a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span>            :   return DCD_SUCCESS;</a>
+<a name="564"><span class="lineNum">     564 </span>            : }</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            : /* </a>
+<a name="568"><span class="lineNum">     568 </span>            :  * Read a dcd timestep from a dcd file</a>
+<a name="569"><span class="lineNum">     569 </span>            :  * Input: fd - a file struct opened for binary reading, from which the </a>
+<a name="570"><span class="lineNum">     570 </span>            :  *             header information has already been read.</a>
+<a name="571"><span class="lineNum">     571 </span>            :  *        natoms, nfixed, first, *freeind, reverse, charmm - the corresponding </a>
+<a name="572"><span class="lineNum">     572 </span>            :  *             items as set by read_dcdheader</a>
+<a name="573"><span class="lineNum">     573 </span>            :  *        first - true if this is the first frame we are reading.</a>
+<a name="574"><span class="lineNum">     574 </span>            :  *        x, y, z: space for natoms each of floats.</a>
+<a name="575"><span class="lineNum">     575 </span>            :  *        unitcell - space for six floats to hold the unit cell data.  </a>
+<a name="576"><span class="lineNum">     576 </span>            :  *                   Not set if no unit cell data is present.</a>
+<a name="577"><span class="lineNum">     577 </span>            :  * Output: 0 on success, negative error code on failure.</a>
+<a name="578"><span class="lineNum">     578 </span>            :  * Side effects: x, y, z contain the coordinates for the timestep read.</a>
+<a name="579"><span class="lineNum">     579 </span>            :  *               unitcell holds unit cell data if present.</a>
+<a name="580"><span class="lineNum">     580 </span>            :  */</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         21 : static int read_dcdstep(fio_fd fd, int N, float *X, float *Y, float *Z, </span></a>
+<a name="582"><span class="lineNum">     582 </span>            :                         float *unitcell, int num_fixed,</a>
+<a name="583"><span class="lineNum">     583 </span>            :                         int first, int *indexes, float *fixedcoords, </a>
+<a name="584"><span class="lineNum">     584 </span>            :                         int reverseEndian, int charmm) {</a>
+<a name="585"><span class="lineNum">     585 </span>            :   int ret_val;    /* Return value from read */</a>
+<a name="586"><span class="lineNum">     586 </span>            :   ptrdiff_t rec_scale;</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         21 :   int hugefile = (N &gt; (1L&lt;&lt;30)) ? 1 : 0;</span></a>
+<a name="588"><span class="lineNum">     588 </span>            :   int check_reclen = 1; /* Enable Fortran record length value safety checks */</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span>            :   /* Fortran record length checks disabled for huge files or user request */</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         21 :   if (hugefile || (getenv(&quot;VMDDCDNOCHECKRECLEN&quot;) != NULL))</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :     check_reclen = 0;</a>
+<a name="593"><span class="lineNum">     593 </span>            :  </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         21 :   if (charmm &amp; DCD_HAS_64BIT_REC) {</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :     rec_scale=RECSCALE64BIT;</a>
+<a name="596"><span class="lineNum">     596 </span>            :   } else {</a>
+<a name="597"><span class="lineNum">     597 </span>            :     rec_scale=RECSCALE32BIT;</a>
+<a name="598"><span class="lineNum">     598 </span>            :   }</a>
+<a name="599"><span class="lineNum">     599 </span>            :   </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         21 :   if ((num_fixed==0) || first) {</span></a>
+<a name="601"><span class="lineNum">     601 </span>            :     /* temp storage for reading formatting info */</a>
+<a name="602"><span class="lineNum">     602 </span>            :     /* note: has to be max size we'll ever use  */</a>
+<a name="603"><span class="lineNum">     603 </span>            :     int tmpbuf[6L*RECSCALEMAX]; </a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span>            :     fio_iovec iov[7];   /* I/O vector for fio_readv() call          */</a>
+<a name="606"><span class="lineNum">     606 </span>            :     int i;</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span>            :     /* if there are no fixed atoms or this is the first timestep read */</a>
+<a name="609"><span class="lineNum">     609 </span>            :     /* then we read all coordinates normally.                         */</a>
+<a name="610"><span class="lineNum">     610 </span>            : </a>
+<a name="611"><span class="lineNum">     611 </span>            :     /* read the charmm periodic cell information */</a>
+<a name="612"><span class="lineNum">     612 </span>            :     /* XXX this too should be read together with the other items in a */</a>
+<a name="613"><span class="lineNum">     613 </span>            :     /*     single fio_readv() call in order to prevent lots of extra  */</a>
+<a name="614"><span class="lineNum">     614 </span>            :     /*     kernel/user context switches.                              */</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         21 :     ret_val = read_charmm_extrablock(fd, charmm, reverseEndian, unitcell);</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         21 :     if (ret_val) return ret_val;</span></a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span>            :     /* setup the I/O vector for the call to fio_readv() */</a>
+<a name="619"><span class="lineNum">     619 </span>            :     iov[0].iov_base = (fio_caddr_t) &amp;tmpbuf[0]; /* read format integer    */</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         21 :     iov[0].iov_len  = rec_scale*sizeof(int);</span></a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span>            :     iov[1].iov_base = (fio_caddr_t) X;          /* read X coordinates     */</a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         21 :     iov[1].iov_len  = sizeof(float)*N;</span></a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         21 :     iov[2].iov_base = (fio_caddr_t) &amp;tmpbuf[1*rec_scale]; /* read 2 format integers */</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         21 :     iov[2].iov_len  = rec_scale*sizeof(int) * 2L;</span></a>
+<a name="627"><span class="lineNum">     627 </span>            : </a>
+<a name="628"><span class="lineNum">     628 </span>            :     iov[3].iov_base = (fio_caddr_t) Y;          /* read Y coordinates     */</a>
+<a name="629"><span class="lineNum">     629 </span>            :     iov[3].iov_len  = sizeof(float)*N;</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         21 :     iov[4].iov_base = (fio_caddr_t) &amp;tmpbuf[3L*rec_scale]; /* read 2 format integers */</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :     iov[4].iov_len  = rec_scale*sizeof(int) * 2L;</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :     iov[5].iov_base = (fio_caddr_t) Z;          /* read Y coordinates     */</a>
+<a name="635"><span class="lineNum">     635 </span>            :     iov[5].iov_len  = sizeof(float)*N;</a>
+<a name="636"><span class="lineNum">     636 </span>            : </a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">         21 :     iov[6].iov_base = (fio_caddr_t) &amp;tmpbuf[5L*rec_scale]; /* read format integer    */</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :     iov[6].iov_len  = rec_scale*sizeof(int);</a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span>            : #if 1</a>
+<a name="641"><span class="lineNum">     641 </span>            :     /* Use fall-back code instead of readv():                            */</a>
+<a name="642"><span class="lineNum">     642 </span>            :     /*  Some platforms implement readv() as user level code in libc,     */</a>
+<a name="643"><span class="lineNum">     643 </span>            :     /*  and due to POSIX atomicity requirements for readv()/writev(),    */</a>
+<a name="644"><span class="lineNum">     644 </span>            :     /*  they may copy data to internal temp buffers, which can kill      */</a>
+<a name="645"><span class="lineNum">     645 </span>            :     /*  performance, and in cases when doing single I/O ops on large,    */</a>
+<a name="646"><span class="lineNum">     646 </span>            :     /*  buffers, e.g. &gt; 2GB, can fail with shorts reads or writes...     */</a>
+<a name="647"><span class="lineNum">     647 </span>            :     /*  On such platforms it is best to avoid using readv()/writev()...  */</a>
+<a name="648"><span class="lineNum">     648 </span>            :     {</a>
+<a name="649"><span class="lineNum">     649 </span>            :       int readcnt = 0;</a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         21 :       readcnt =  fio_fread(iov[0].iov_base, iov[0].iov_len, 1, fd);</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         21 :       readcnt += fio_fread(iov[1].iov_base, iov[1].iov_len, 1, fd);</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         21 :       readcnt += fio_fread(iov[2].iov_base, iov[2].iov_len, 1, fd);</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">         21 :       readcnt += fio_fread(iov[3].iov_base, iov[3].iov_len, 1, fd);</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">         21 :       readcnt += fio_fread(iov[4].iov_base, iov[4].iov_len, 1, fd);</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         21 :       readcnt += fio_fread(iov[5].iov_base, iov[5].iov_len, 1, fd);</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">         21 :       readcnt += fio_fread(iov[6].iov_base, iov[6].iov_len, 1, fd);</span></a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span>            :       /* if all records read correctly, then the reads are okay */</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">         21 :       if (readcnt != 7)</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :         return DCD_BADREAD;</a>
+<a name="661"><span class="lineNum">     661 </span>            :     }</a>
+<a name="662"><span class="lineNum">     662 </span>            : #else</a>
+<a name="663"><span class="lineNum">     663 </span>            :     /* check number of bytes actually read            */</a>
+<a name="664"><span class="lineNum">     664 </span>            :     if (fio_readv(fd, &amp;iov[0], 7) != ((fio_size_t) (rec_scale*6L*sizeof(int) + 3L*N*sizeof(float))))</a>
+<a name="665"><span class="lineNum">     665 </span>            :       return DCD_BADREAD;</a>
+<a name="666"><span class="lineNum">     666 </span>            : #endif</a>
+<a name="667"><span class="lineNum">     667 </span>            : </a>
+<a name="668"><span class="lineNum">     668 </span>            :     /* convert endianism if necessary */</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">         21 :     if (reverseEndian) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :       swap4_aligned(&amp;tmpbuf[0], rec_scale*6L);</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :       swap4_aligned(X, N);</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :       swap4_aligned(Y, N);</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :       swap4_aligned(Z, N);</span></a>
+<a name="674"><span class="lineNum">     674 </span>            :     }</a>
+<a name="675"><span class="lineNum">     675 </span>            : </a>
+<a name="676"><span class="lineNum">     676 </span>            :     /* when we have more then 2^30 atoms, tests like this one */</a>
+<a name="677"><span class="lineNum">     677 </span>            :     /* are no longer meaningful and have to be bypassed...    */</a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         21 :     if (check_reclen) {</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :       /* double-check the fortran format size values for safety */</a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         21 :       if (rec_scale == 1) {</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">        147 :         for (i=0; i&lt;6; i++) {</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">        126 :           if (tmpbuf[i] != sizeof(float)*N) return DCD_BADFORMAT;</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :         }</a>
+<a name="684"><span class="lineNum">     684 </span>            :       } else {</a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :         for (i=0; i&lt;6; i++) {</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :           if ((tmpbuf[2L*i]+tmpbuf[2L*i+1L]) != sizeof(float)*N) return DCD_BADFORMAT;</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :         }</a>
+<a name="688"><span class="lineNum">     688 </span>            :       }</a>
+<a name="689"><span class="lineNum">     689 </span>            :     }</a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span>            :     /* copy fixed atom coordinates into fixedcoords array if this was the */</a>
+<a name="692"><span class="lineNum">     692 </span>            :     /* first timestep, to be used from now on.  We just copy all atoms.   */</a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">         21 :     if (num_fixed &amp;&amp; first) {</span></a>
+<a name="694"><span class="lineNum">     694 </span>            :       memcpy(fixedcoords, X, N*sizeof(float));</a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :       memcpy(fixedcoords+N, Y, N*sizeof(float));</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :       memcpy(fixedcoords+2L*N, Z, N*sizeof(float));</span></a>
+<a name="697"><span class="lineNum">     697 </span>            :     }</a>
+<a name="698"><span class="lineNum">     698 </span>            : </a>
+<a name="699"><span class="lineNum">     699 </span>            :     /* read in the optional charmm 4th array */</a>
+<a name="700"><span class="lineNum">     700 </span>            :     /* XXX this too should be read together with the other items in a */</a>
+<a name="701"><span class="lineNum">     701 </span>            :     /*     single fio_readv() call in order to prevent lots of extra  */</a>
+<a name="702"><span class="lineNum">     702 </span>            :     /*     kernel/user context switches.                              */</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         21 :     ret_val = read_charmm_4dim(fd, charmm, reverseEndian);</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">         21 :     if (ret_val) return ret_val;</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :   } else {</a>
+<a name="706"><span class="lineNum">     706 </span>            :     /* if there are fixed atoms, and this isn't the first frame, then we */</a>
+<a name="707"><span class="lineNum">     707 </span>            :     /* only read in the non-fixed atoms for all subsequent timesteps.    */</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :     ret_val = read_charmm_extrablock(fd, charmm, reverseEndian, unitcell);</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :     if (ret_val) return ret_val;</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :     ret_val = read_fixed_atoms(fd, N, N-num_fixed, indexes, reverseEndian,</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineNoCov">          0 :                                fixedcoords, fixedcoords+3L*N, X, charmm);</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :     if (ret_val) return ret_val;</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :     ret_val = read_fixed_atoms(fd, N, N-num_fixed, indexes, reverseEndian,</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :                                fixedcoords+N, fixedcoords+3L*N, Y, charmm);</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :     if (ret_val) return ret_val;</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineNoCov">          0 :     ret_val = read_fixed_atoms(fd, N, N-num_fixed, indexes, reverseEndian,</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :                                fixedcoords+2*N, fixedcoords+3L*N, Z, charmm);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineNoCov">          0 :     if (ret_val) return ret_val;</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :     ret_val = read_charmm_4dim(fd, charmm, reverseEndian);</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineNoCov">          0 :     if (ret_val) return ret_val;</span></a>
+<a name="721"><span class="lineNum">     721 </span>            :   }</a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            :   return DCD_SUCCESS;</a>
+<a name="724"><span class="lineNum">     724 </span>            : }</a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span>            : /* </a>
+<a name="728"><span class="lineNum">     728 </span>            :  * Skip past a timestep.  If there are fixed atoms, this cannot be used with</a>
+<a name="729"><span class="lineNum">     729 </span>            :  * the first timestep.  </a>
+<a name="730"><span class="lineNum">     730 </span>            :  * Input: fd - a file struct from which the header has already been read</a>
+<a name="731"><span class="lineNum">     731 </span>            :  *        natoms - number of atoms per timestep</a>
+<a name="732"><span class="lineNum">     732 </span>            :  *        nfixed - number of fixed atoms</a>
+<a name="733"><span class="lineNum">     733 </span>            :  *        charmm - charmm flags as returned by read_dcdheader</a>
+<a name="734"><span class="lineNum">     734 </span>            :  * Output: 0 on success, negative error code on failure.</a>
+<a name="735"><span class="lineNum">     735 </span>            :  * Side effects: One timestep will be skipped; fd will be positioned at the</a>
+<a name="736"><span class="lineNum">     736 </span>            :  *               next timestep.</a>
+<a name="737"><span class="lineNum">     737 </span>            :  */</a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 : static int skip_dcdstep(fio_fd fd, int natoms, int nfixed, int charmm) {</span></a>
+<a name="739"><span class="lineNum">     739 </span>            :   ptrdiff_t seekoffset = 0;</a>
+<a name="740"><span class="lineNum">     740 </span>            :   ptrdiff_t rec_scale;</a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineNoCov">          0 :   if (charmm &amp; DCD_HAS_64BIT_REC) {</span></a>
+<a name="743"><span class="lineNum">     743 </span>            :     rec_scale=RECSCALE64BIT;</a>
+<a name="744"><span class="lineNum">     744 </span>            :   } else {</a>
+<a name="745"><span class="lineNum">     745 </span>            :     rec_scale=RECSCALE32BIT;</a>
+<a name="746"><span class="lineNum">     746 </span>            :   }</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span>            :   /* Skip charmm extra block */</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineNoCov">          0 :   if ((charmm &amp; DCD_IS_CHARMM) &amp;&amp; (charmm &amp; DCD_HAS_EXTRA_BLOCK)) {</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :     seekoffset += 4L*rec_scale + 48L + 4L*rec_scale;</span></a>
+<a name="751"><span class="lineNum">     751 </span>            :   }</a>
+<a name="752"><span class="lineNum">     752 </span>            : </a>
+<a name="753"><span class="lineNum">     753 </span>            :   /* For each atom set, seek past an int, the free atoms, and another int. */</a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineNoCov">          0 :   seekoffset += 3L * (2L*rec_scale + natoms - nfixed) * 4L;</span></a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span>            :   /* Assume that charmm 4th dim is the same size as the other three. */</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 :   if ((charmm &amp; DCD_IS_CHARMM) &amp;&amp; (charmm &amp; DCD_HAS_4DIMS)) {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :     seekoffset += (2L*rec_scale + natoms - nfixed) * 4L;</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :   }</a>
+<a name="760"><span class="lineNum">     760 </span>            :  </a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineNoCov">          0 :   if (fio_fseek(fd, seekoffset, FIO_SEEK_CUR)) return DCD_BADEOF;</span></a>
+<a name="762"><span class="lineNum">     762 </span>            : </a>
+<a name="763"><span class="lineNum">     763 </span>            :   return DCD_SUCCESS;</a>
+<a name="764"><span class="lineNum">     764 </span>            : }</a>
+<a name="765"><span class="lineNum">     765 </span>            : </a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            : /* </a>
+<a name="768"><span class="lineNum">     768 </span>            :  * Write a timestep to a dcd file</a>
+<a name="769"><span class="lineNum">     769 </span>            :  * Input: fd - a file struct for which a dcd header has already been written</a>
+<a name="770"><span class="lineNum">     770 </span>            :  *       curframe: Count of frames written to this file, starting with 1.</a>
+<a name="771"><span class="lineNum">     771 </span>            :  *        curstep: Count of timesteps elapsed = istart + curframe * nsavc.</a>
+<a name="772"><span class="lineNum">     772 </span>            :  *         natoms: number of elements in x, y, z arrays</a>
+<a name="773"><span class="lineNum">     773 </span>            :  *        x, y, z: pointers to atom coordinates</a>
+<a name="774"><span class="lineNum">     774 </span>            :  * Output: 0 on success, negative error code on failure.</a>
+<a name="775"><span class="lineNum">     775 </span>            :  * Side effects: coordinates are written to the dcd file.</a>
+<a name="776"><span class="lineNum">     776 </span>            :  */</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineNoCov">          0 : static int write_dcdstep(fio_fd fd, int curframe, int curstep, int N, </span></a>
+<a name="778"><span class="lineNum">     778 </span>            :                   const float *X, const float *Y, const float *Z, </a>
+<a name="779"><span class="lineNum">     779 </span>            :                   const double *unitcell, int charmm) {</a>
+<a name="780"><span class="lineNum">     780 </span>            :   int out_integer;</a>
+<a name="781"><span class="lineNum">     781 </span>            : </a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineNoCov">          0 :   if (charmm) {</span></a>
+<a name="783"><span class="lineNum">     783 </span>            :     /* write out optional unit cell */</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineNoCov">          0 :     if (unitcell != NULL) {</span></a>
+<a name="785"><span class="lineNum">     785 </span>            :       out_integer = 48; /* 48 bytes (6 floats) */</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineNoCov">          0 :       fio_write_int32(fd, out_integer);</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineNoCov">          0 :       WRITE(fd, unitcell, out_integer);</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineNoCov">          0 :       fio_write_int32(fd, out_integer);</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :     }</a>
+<a name="790"><span class="lineNum">     790 </span>            :   }</a>
+<a name="791"><span class="lineNum">     791 </span>            : </a>
+<a name="792"><span class="lineNum">     792 </span>            :   /* write out coordinates */</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineNoCov">          0 :   out_integer = N*4; /* N*4 bytes per X/Y/Z array (N floats per array) */</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, out_integer);</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineNoCov">          0 :   if (fio_fwrite((void *) X, out_integer, 1, fd) != 1) return DCD_BADWRITE;</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, out_integer);</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, out_integer);</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 :   if (fio_fwrite((void *) Y, out_integer, 1, fd) != 1) return DCD_BADWRITE;</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, out_integer);</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, out_integer);</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineNoCov">          0 :   if (fio_fwrite((void *) Z, out_integer, 1, fd) != 1) return DCD_BADWRITE;</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, out_integer);</span></a>
+<a name="803"><span class="lineNum">     803 </span>            : </a>
+<a name="804"><span class="lineNum">     804 </span>            :   /* update the DCD header information */</a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineNoCov">          0 :   fio_fseek(fd, NFILE_POS, FIO_SEEK_SET);</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, curframe);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineNoCov">          0 :   fio_fseek(fd, NSTEP_POS, FIO_SEEK_SET);</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, curstep);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineNoCov">          0 :   fio_fseek(fd, 0, FIO_SEEK_END);</span></a>
+<a name="810"><span class="lineNum">     810 </span>            : </a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineNoCov">          0 :   return DCD_SUCCESS;</span></a>
+<a name="812"><span class="lineNum">     812 </span>            : }</a>
+<a name="813"><span class="lineNum">     813 </span>            : </a>
+<a name="814"><span class="lineNum">     814 </span>            : </a>
+<a name="815"><span class="lineNum">     815 </span>            : /*</a>
+<a name="816"><span class="lineNum">     816 </span>            :  * Write a header for a new dcd file</a>
+<a name="817"><span class="lineNum">     817 </span>            :  * Input: fd - file struct opened for binary writing</a>
+<a name="818"><span class="lineNum">     818 </span>            :  *        remarks - string to be put in the remarks section of the header.  </a>
+<a name="819"><span class="lineNum">     819 </span>            :  *                  The string will be truncated to 70 characters.</a>
+<a name="820"><span class="lineNum">     820 </span>            :  *        natoms, istart, nsavc, delta - see comments in read_dcdheader</a>
+<a name="821"><span class="lineNum">     821 </span>            :  * Output: 0 on success, negative error code on failure.</a>
+<a name="822"><span class="lineNum">     822 </span>            :  * Side effects: Header information is written to the dcd file.</a>
+<a name="823"><span class="lineNum">     823 </span>            :  */</a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineNoCov">          0 : static int write_dcdheader(fio_fd fd, const char *remarks, int N, </span></a>
+<a name="825"><span class="lineNum">     825 </span>            :                     int ISTART, int NSAVC, double DELTA, int with_unitcell,</a>
+<a name="826"><span class="lineNum">     826 </span>            :                     int charmm) {</a>
+<a name="827"><span class="lineNum">     827 </span>            :   int out_integer;</a>
+<a name="828"><span class="lineNum">     828 </span>            :   float out_float;</a>
+<a name="829"><span class="lineNum">     829 </span>            :   char title_string[200];</a>
+<a name="830"><span class="lineNum">     830 </span>            :   time_t cur_time;</a>
+<a name="831"><span class="lineNum">     831 </span>            :   struct tm *tmbuf;</a>
+<a name="832"><span class="lineNum">     832 </span>            :   char time_str[81];</a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineNoCov">          0 :   out_integer = 84;</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineNoCov">          0 :   WRITE(fd, (char *) &amp; out_integer, sizeof(int));</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :   strcpy(title_string, &quot;CORD&quot;);</a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineNoCov">          0 :   WRITE(fd, title_string, 4);</span></a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);      /* Number of frames in file, none written yet   */</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, ISTART); /* Starting timestep                            */</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, NSAVC);  /* Timesteps between frames written to the file */</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);      /* Number of timesteps in simulation            */</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);      /* NAMD writes NSTEP or ISTART - NSAVC here?    */</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineNoCov">          0 :   if (charmm) {</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineNoCov">          0 :     out_float = DELTA;</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :     WRITE(fd, (char *) &amp;out_float, sizeof(float));</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineNoCov">          0 :     if (with_unitcell) {</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineNoCov">          0 :       fio_write_int32(fd, 1);</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :     } else {</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :       fio_write_int32(fd, 0);</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :     }</a>
+<a name="855"><span class="lineNum">     855 </span>            :   } else {</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :     WRITE(fd, (char *) &amp;DELTA, sizeof(double));</span></a>
+<a name="857"><span class="lineNum">     857 </span>            :   }</a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 0);</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineNoCov">          0 :   if (charmm) {</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineNoCov">          0 :     fio_write_int32(fd, 24); /* Pretend to be CHARMM version 24 */</span></a>
+<a name="868"><span class="lineNum">     868 </span>            :   } else {</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineNoCov">          0 :     fio_write_int32(fd, 0);</span></a>
+<a name="870"><span class="lineNum">     870 </span>            :   }</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 84);</span></a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 164);</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 2);</span></a>
+<a name="874"><span class="lineNum">     874 </span>            : </a>
+<a name="875"><span class="lineNum">     875 </span>            :   strncpy(title_string, remarks, 80);</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineNoCov">          0 :   title_string[79] = '\0';</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineNoCov">          0 :   WRITE(fd, title_string, 80);</span></a>
+<a name="878"><span class="lineNum">     878 </span>            : </a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineNoCov">          0 :   cur_time=time(NULL);</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :   tmbuf=localtime(&amp;cur_time);</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineNoCov">          0 :   strftime(time_str, 80, &quot;REMARKS Created %d %B, %Y at %R&quot;, tmbuf);</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineNoCov">          0 :   WRITE(fd, time_str, 80);</span></a>
+<a name="883"><span class="lineNum">     883 </span>            : </a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 164);</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 4);</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, N);</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :   fio_write_int32(fd, 4);</span></a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineNoCov">          0 :   return DCD_SUCCESS;</span></a>
+<a name="890"><span class="lineNum">     890 </span>            : }</a>
+<a name="891"><span class="lineNum">     891 </span>            : </a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            : /*</a>
+<a name="894"><span class="lineNum">     894 </span>            :  * clean up dcd data</a>
+<a name="895"><span class="lineNum">     895 </span>            :  * Input: nfixed, freeind - elements as returned by read_dcdheader</a>
+<a name="896"><span class="lineNum">     896 </span>            :  * Output: None</a>
+<a name="897"><span class="lineNum">     897 </span>            :  * Side effects: Space pointed to by freeind is freed if necessary.</a>
+<a name="898"><span class="lineNum">     898 </span>            :  */</a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">          1 : static void close_dcd_read(int *indexes, float *fixedcoords) {</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">          1 :   free(indexes);</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">          1 :   free(fixedcoords);</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">          1 : }</span></a>
+<a name="903"><span class="lineNum">     903 </span>            : </a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">          1 : static void *open_dcd_read(const char *path, const char *filetype, </span></a>
+<a name="906"><span class="lineNum">     906 </span>            :     int *natoms) {</a>
+<a name="907"><span class="lineNum">     907 </span>            :   dcdhandle *dcd;</a>
+<a name="908"><span class="lineNum">     908 </span>            :   fio_fd fd;</a>
+<a name="909"><span class="lineNum">     909 </span>            :   int rc;</a>
+<a name="910"><span class="lineNum">     910 </span>            :   struct stat stbuf;</a>
+<a name="911"><span class="lineNum">     911 </span>            : </a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">          1 :   if (!path) return NULL;</span></a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span>            : #if !(defined(_MSC_VER) &amp;&amp; defined(FASTIO_NATIVEWIN32))</a>
+<a name="915"><span class="lineNum">     915 </span>            :   /* See if the file exists, and get its size */</a>
+<a name="916"><span class="lineNum">     916 </span>            :   memset(&amp;stbuf, 0, sizeof(struct stat));</a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">          1 :   if (stat(path, &amp;stbuf)) {</span></a>
+<a name="918"><span class="lineNum">     918 </span>            :     printf(&quot;dcdplugin) Could not access file '%s'.\n&quot;, path);</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="920"><span class="lineNum">     920 </span>            :   }</a>
+<a name="921"><span class="lineNum">     921 </span>            : #endif</a>
+<a name="922"><span class="lineNum">     922 </span>            : </a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">          1 :   if (fio_open(path, FIO_READ, &amp;fd) &lt; 0) {</span></a>
+<a name="924"><span class="lineNum">     924 </span>            :     printf(&quot;dcdplugin) Could not open file '%s' for reading.\n&quot;, path);</a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="926"><span class="lineNum">     926 </span>            :   }</a>
+<a name="927"><span class="lineNum">     927 </span>            : </a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">          1 :   dcd = (dcdhandle *)malloc(sizeof(dcdhandle));</span></a>
+<a name="929"><span class="lineNum">     929 </span>            :   memset(dcd, 0, sizeof(dcdhandle));</a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">          1 :   dcd-&gt;fd = fd;</span></a>
+<a name="931"><span class="lineNum">     931 </span>            : </a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">          1 :   if ((rc = read_dcdheader(dcd-&gt;fd, &amp;dcd-&gt;natoms, &amp;dcd-&gt;nsets, &amp;dcd-&gt;istart, </span></a>
+<a name="933"><span class="lineNum">     933 </span>            :          &amp;dcd-&gt;nsavc, &amp;dcd-&gt;delta, &amp;dcd-&gt;nfixed, &amp;dcd-&gt;freeind, </a>
+<a name="934"><span class="lineNum">     934 </span>            :          &amp;dcd-&gt;fixedcoords, &amp;dcd-&gt;reverse, &amp;dcd-&gt;charmm))) {</a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineNoCov">          0 :     print_dcderror(&quot;read_dcdheader&quot;, rc);</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 :     fio_fclose(dcd-&gt;fd);</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineNoCov">          0 :     free(dcd);</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="939"><span class="lineNum">     939 </span>            :   }</a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span>            :   /*</a>
+<a name="942"><span class="lineNum">     942 </span>            :    * Check that the file is big enough to really hold the number of sets</a>
+<a name="943"><span class="lineNum">     943 </span>            :    * it claims to have.  Then we'll use nsets to keep track of where EOF</a>
+<a name="944"><span class="lineNum">     944 </span>            :    * should be.</a>
+<a name="945"><span class="lineNum">     945 </span>            :    */</a>
+<a name="946"><span class="lineNum">     946 </span>            :   {</a>
+<a name="947"><span class="lineNum">     947 </span>            :     fio_size_t ndims, firstframesize, framesize, extrablocksize;</a>
+<a name="948"><span class="lineNum">     948 </span>            :     fio_size_t trjsize, filesize, curpos;</a>
+<a name="949"><span class="lineNum">     949 </span>            :     int newnsets;</a>
+<a name="950"><span class="lineNum">     950 </span>            : </a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">          1 :     extrablocksize = dcd-&gt;charmm &amp; DCD_HAS_EXTRA_BLOCK ? 48 + 8 : 0;</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">          1 :     ndims = dcd-&gt;charmm &amp; DCD_HAS_4DIMS ? 4 : 3;</span></a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">          1 :     firstframesize = (dcd-&gt;natoms+2) * ndims * sizeof(float) + extrablocksize;</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">          1 :     framesize = (dcd-&gt;natoms-dcd-&gt;nfixed+2) * ndims * sizeof(float) </span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">          1 :       + extrablocksize;</span></a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            :     /* </a>
+<a name="958"><span class="lineNum">     958 </span>            :      * It's safe to use ftell, even though ftell returns a long, because the </a>
+<a name="959"><span class="lineNum">     959 </span>            :      * header size is &lt; 4GB.</a>
+<a name="960"><span class="lineNum">     960 </span>            :      */</a>
+<a name="961"><span class="lineNum">     961 </span>            : </a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">          1 :     curpos = fio_ftell(dcd-&gt;fd); /* save current offset (end of header) */</span></a>
+<a name="963"><span class="lineNum">     963 </span>            : </a>
+<a name="964"><span class="lineNum">     964 </span>            : #if defined(_MSC_VER) &amp;&amp; defined(FASTIO_NATIVEWIN32)</a>
+<a name="965"><span class="lineNum">     965 </span>            :     /* the stat() call is not 64-bit savvy on Windows             */</a>
+<a name="966"><span class="lineNum">     966 </span>            :     /* so we have to use the fastio fseek/ftell routines for this */</a>
+<a name="967"><span class="lineNum">     967 </span>            :     /* until we add a portable filesize routine for this purpose  */</a>
+<a name="968"><span class="lineNum">     968 </span>            :     fio_fseek(dcd-&gt;fd, 0, FIO_SEEK_END);       /* seek to end of file */</a>
+<a name="969"><span class="lineNum">     969 </span>            :     filesize = fio_ftell(dcd-&gt;fd);</a>
+<a name="970"><span class="lineNum">     970 </span>            :     fio_fseek(dcd-&gt;fd, curpos, FIO_SEEK_SET);  /* return to end of header */</a>
+<a name="971"><span class="lineNum">     971 </span>            : #else</a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">          1 :     filesize = stbuf.st_size; /* this works ok on Unix machines */</span></a>
+<a name="973"><span class="lineNum">     973 </span>            : #endif</a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">          1 :     trjsize = filesize - curpos - firstframesize;</span></a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">          1 :     if (trjsize &lt; 0) {</span></a>
+<a name="976"><span class="lineNum">     976 </span>            :       printf(&quot;dcdplugin) file '%s' appears to contain no timesteps.\n&quot;, path);</a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineNoCov">          0 :       fio_fclose(dcd-&gt;fd);</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineNoCov">          0 :       free(dcd);</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineNoCov">          0 :       return NULL;</span></a>
+<a name="980"><span class="lineNum">     980 </span>            :     }</a>
+<a name="981"><span class="lineNum">     981 </span>            : </a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">          1 :     newnsets = trjsize / framesize + 1;</span></a>
+<a name="983"><span class="lineNum">     983 </span>            : </a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">          1 :     if (dcd-&gt;nsets &gt; 0 &amp;&amp; newnsets != dcd-&gt;nsets) {</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :       printf(&quot;dcdplugin) Warning: DCD header claims %d frames, but \n&quot;</a>
+<a name="986"><span class="lineNum">     986 </span>            :              &quot;dcdplugin) file size (%ld) indicates there are actually \n&quot;</a>
+<a name="987"><span class="lineNum">     987 </span>            :              &quot;%d frames of size (%ld)\n&quot;, </a>
+<a name="988"><span class="lineNum">     988 </span>            :              dcd-&gt;nsets, trjsize, newnsets, framesize);</a>
+<a name="989"><span class="lineNum">     989 </span>            :     }</a>
+<a name="990"><span class="lineNum">     990 </span>            : </a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">          1 :     dcd-&gt;nsets = newnsets; </span></a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">          1 :     dcd-&gt;setsread = 0;</span></a>
+<a name="993"><span class="lineNum">     993 </span>            :   }</a>
+<a name="994"><span class="lineNum">     994 </span>            : </a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">          1 :   dcd-&gt;first = 1;</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">          1 :   dcd-&gt;x = (float *)malloc(dcd-&gt;natoms * sizeof(float));</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">          1 :   dcd-&gt;y = (float *)malloc(dcd-&gt;natoms * sizeof(float));</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">          1 :   dcd-&gt;z = (float *)malloc(dcd-&gt;natoms * sizeof(float));</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">          1 :   if (!dcd-&gt;x || !dcd-&gt;y || !dcd-&gt;z) {</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            :     printf(&quot;dcdplugin) Unable to allocate space for %d atoms.\n&quot;, dcd-&gt;natoms);</a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineNoCov">          0 :     if (dcd-&gt;x)</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineNoCov">          0 :       free(dcd-&gt;x);</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineNoCov">          0 :     if (dcd-&gt;y)</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineNoCov">          0 :       free(dcd-&gt;y);</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineNoCov">          0 :     if (dcd-&gt;z)</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineNoCov">          0 :       free(dcd-&gt;z);</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :     fio_fclose(dcd-&gt;fd);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineNoCov">          0 :     free(dcd);</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   }</a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">          1 :   *natoms = dcd-&gt;natoms;</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">          1 :   return dcd;</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            : }</a>
+<a name="1014"><span class="lineNum">    1014 </span>            : </a>
+<a name="1015"><span class="lineNum">    1015 </span>            : </a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">         22 : static int read_next_timestep(void *v, int natoms, molfile_timestep_t *ts) {</span></a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   dcdhandle *dcd;</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :   int i, j, rc;</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   float unitcell[6];</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">         22 :   unitcell[0] = unitcell[2] = unitcell[5] = 0.0f;</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">         22 :   unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;</span></a>
+<a name="1022"><span class="lineNum">    1022 </span>            :   dcd = (dcdhandle *)v;</a>
+<a name="1023"><span class="lineNum">    1023 </span>            : </a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   /* Check for EOF here; that way all EOF's encountered later must be errors */</a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineCov">         22 :   if (dcd-&gt;setsread == dcd-&gt;nsets) return MOLFILE_EOF;</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">         21 :   dcd-&gt;setsread++;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">         21 :   if (!ts) {</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineNoCov">          0 :     if (dcd-&gt;first &amp;&amp; dcd-&gt;nfixed) {</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            :       /* We can't just skip it because we need the fixed atom coordinates */</a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineNoCov">          0 :       rc = read_dcdstep(dcd-&gt;fd, dcd-&gt;natoms, dcd-&gt;x, dcd-&gt;y, dcd-&gt;z, </span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :           unitcell, dcd-&gt;nfixed, dcd-&gt;first, dcd-&gt;freeind, dcd-&gt;fixedcoords, </a>
+<a name="1032"><span class="lineNum">    1032 </span>            :              dcd-&gt;reverse, dcd-&gt;charmm);</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineNoCov">          0 :       dcd-&gt;first = 0;</span></a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineNoCov">          0 :       return rc; /* XXX this needs to be updated */</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     }</a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineNoCov">          0 :     dcd-&gt;first = 0;</span></a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     /* XXX this needs to be changed */</a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineNoCov">          0 :     return skip_dcdstep(dcd-&gt;fd, dcd-&gt;natoms, dcd-&gt;nfixed, dcd-&gt;charmm);</span></a>
+<a name="1039"><span class="lineNum">    1039 </span>            :   }</a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">         21 :   rc = read_dcdstep(dcd-&gt;fd, dcd-&gt;natoms, dcd-&gt;x, dcd-&gt;y, dcd-&gt;z, unitcell,</span></a>
+<a name="1041"><span class="lineNum">    1041 </span>            :              dcd-&gt;nfixed, dcd-&gt;first, dcd-&gt;freeind, dcd-&gt;fixedcoords, </a>
+<a name="1042"><span class="lineNum">    1042 </span>            :              dcd-&gt;reverse, dcd-&gt;charmm);</a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">         21 :   dcd-&gt;first = 0;</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">         21 :   if (rc &lt; 0) {  </span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineNoCov">          0 :     print_dcderror(&quot;read_dcdstep&quot;, rc);</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineNoCov">          0 :     return MOLFILE_ERROR;</span></a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   }</a>
+<a name="1048"><span class="lineNum">    1048 </span>            : </a>
+<a name="1049"><span class="lineNum">    1049 </span>            :   /* copy timestep data from plugin-local buffers to VMD's buffer */</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   /* XXX </a>
+<a name="1051"><span class="lineNum">    1051 </span>            :    *   This code is still the root of all evil.  Just doing this extra copy</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :    *   cuts the I/O rate of the DCD reader from 728 MB/sec down to</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :    *   394 MB/sec when reading from a ram filesystem.  </a>
+<a name="1054"><span class="lineNum">    1054 </span>            :    *   For a physical disk filesystem, the I/O rate goes from </a>
+<a name="1055"><span class="lineNum">    1055 </span>            :    *   187 MB/sec down to 122 MB/sec.  Clearly this extra copy has to go.</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :    */</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :   {</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">         21 :     int natoms = dcd-&gt;natoms;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">         21 :     float *nts = ts-&gt;coords;</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">         21 :     const float *bufx = dcd-&gt;x;</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">         21 :     const float *bufy = dcd-&gt;y;</span></a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">         21 :     const float *bufz = dcd-&gt;z;</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            : </a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">        483 :     for (i=0, j=0; i&lt;natoms; i++, j+=3) {</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">        462 :       nts[j    ] = bufx[i];</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">        462 :       nts[j + 1] = bufy[i];</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">        462 :       nts[j + 2] = bufz[i];</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     }</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :   }</a>
+<a name="1070"><span class="lineNum">    1070 </span>            : </a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         21 :   ts-&gt;A = unitcell[0];</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         21 :   ts-&gt;B = unitcell[2];</span></a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">         21 :   ts-&gt;C = unitcell[5];</span></a>
+<a name="1074"><span class="lineNum">    1074 </span>            : </a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">         21 :   if (unitcell[1] &gt;= -1.0 &amp;&amp; unitcell[1] &lt;= 1.0 &amp;&amp;</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">         21 :       unitcell[3] &gt;= -1.0 &amp;&amp; unitcell[3] &lt;= 1.0 &amp;&amp;</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">         21 :       unitcell[4] &gt;= -1.0 &amp;&amp; unitcell[4] &lt;= 1.0) {</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     /* This file was generated by CHARMM, or by NAMD &gt; 2.5, with the angle */</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     /* cosines of the periodic cell angles written to the DCD file.        */ </a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     /* This formulation improves rounding behavior for orthogonal cells    */</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     /* so that the angles end up at precisely 90 degrees, unlike acos().   */</a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">         21 :     ts-&gt;alpha = 90.0 - asin(unitcell[4]) * 90.0 / M_PI_2; /* cosBC */</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">         21 :     ts-&gt;beta  = 90.0 - asin(unitcell[3]) * 90.0 / M_PI_2; /* cosAC */</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">         21 :     ts-&gt;gamma = 90.0 - asin(unitcell[1]) * 90.0 / M_PI_2; /* cosAB */</span></a>
+<a name="1085"><span class="lineNum">    1085 </span>            :   } else {</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :     /* This file was likely generated by NAMD 2.5 and the periodic cell    */</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :     /* angles are specified in degrees rather than angle cosines.          */</a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineNoCov">          0 :     ts-&gt;alpha = unitcell[4]; /* angle between B and C */</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :     ts-&gt;beta  = unitcell[3]; /* angle between A and C */</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineNoCov">          0 :     ts-&gt;gamma = unitcell[1]; /* angle between A and B */</span></a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   }</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :  </a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : }</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :  </a>
+<a name="1096"><span class="lineNum">    1096 </span>            : </a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">          1 : static void close_file_read(void *v) {</span></a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   dcdhandle *dcd = (dcdhandle *)v;</a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">          1 :   close_dcd_read(dcd-&gt;freeind, dcd-&gt;fixedcoords);</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">          1 :   fio_fclose(dcd-&gt;fd);</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">          1 :   free(dcd-&gt;x);</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">          1 :   free(dcd-&gt;y);</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">          1 :   free(dcd-&gt;z);</span></a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">          1 :   free(dcd); </span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">          1 : }</span></a>
+<a name="1106"><span class="lineNum">    1106 </span>            : </a>
+<a name="1107"><span class="lineNum">    1107 </span>            : </a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineNoCov">          0 : static void *open_dcd_write(const char *path, const char *filetype, </span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            :     int natoms) {</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   dcdhandle *dcd;</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   fio_fd fd;</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   int rc;</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :   int istart, nsavc;</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :   double delta;</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   int with_unitcell;</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :   int charmm;</a>
+<a name="1117"><span class="lineNum">    1117 </span>            : </a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineNoCov">          0 :   if (fio_open(path, FIO_WRITE, &amp;fd) &lt; 0) {</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :     printf(&quot;dcdplugin) Could not open file '%s' for writing\n&quot;, path);</a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="1121"><span class="lineNum">    1121 </span>            :   }</a>
+<a name="1122"><span class="lineNum">    1122 </span>            : </a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineNoCov">          0 :   dcd = (dcdhandle *)malloc(sizeof(dcdhandle));</span></a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   memset(dcd, 0, sizeof(dcdhandle));</a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineNoCov">          0 :   dcd-&gt;fd = fd;</span></a>
+<a name="1126"><span class="lineNum">    1126 </span>            : </a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   istart = 0;             /* starting timestep of DCD file                  */</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   nsavc = 1;              /* number of timesteps between written DCD frames */</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   delta = 1.0;            /* length of a timestep                           */</a>
+<a name="1130"><span class="lineNum">    1130 </span>            : </a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineNoCov">          0 :   if (getenv(&quot;VMDDCDWRITEXPLORFORMAT&quot;) != NULL) {</span></a>
+<a name="1132"><span class="lineNum">    1132 </span>            :     with_unitcell = 0;      /* no unit cell info */</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     charmm = DCD_IS_XPLOR;  /* X-PLOR format */</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     printf(&quot;dcdplugin) WARNING: Writing DCD file in X-PLOR format, \n&quot;);</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :     printf(&quot;dcdplugin) WARNING: unit cell information will be lost!\n&quot;);</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :   } else {</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :     with_unitcell = 1;      /* contains unit cell infor (Charmm format) */</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     charmm = DCD_IS_CHARMM; /* charmm-formatted DCD file                */ </a>
+<a name="1139"><span class="lineNum">    1139 </span>            :     if (with_unitcell) </a>
+<a name="1140"><span class="lineNum">    1140 </span>            :       charmm |= DCD_HAS_EXTRA_BLOCK;</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :  </a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineNoCov">          0 :   rc = write_dcdheader(dcd-&gt;fd, &quot;Created by DCD plugin&quot;, natoms, </span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            :                        istart, nsavc, delta, with_unitcell, charmm);</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : </a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineNoCov">          0 :   if (rc &lt; 0) {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineNoCov">          0 :     print_dcderror(&quot;write_dcdheader&quot;, rc);</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineNoCov">          0 :     fio_fclose(dcd-&gt;fd);</span></a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineNoCov">          0 :     free(dcd);</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   }</a>
+<a name="1152"><span class="lineNum">    1152 </span>            : </a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineNoCov">          0 :   dcd-&gt;natoms = natoms;</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineNoCov">          0 :   dcd-&gt;nsets = 0;</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineNoCov">          0 :   dcd-&gt;istart = istart;</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineNoCov">          0 :   dcd-&gt;nsavc = nsavc;</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineNoCov">          0 :   dcd-&gt;with_unitcell = with_unitcell;</span></a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineNoCov">          0 :   dcd-&gt;charmm = charmm;</span></a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineNoCov">          0 :   dcd-&gt;x = (float *)malloc(natoms * sizeof(float));</span></a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineNoCov">          0 :   dcd-&gt;y = (float *)malloc(natoms * sizeof(float));</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineNoCov">          0 :   dcd-&gt;z = (float *)malloc(natoms * sizeof(float));</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineNoCov">          0 :   return dcd;</span></a>
+<a name="1163"><span class="lineNum">    1163 </span>            : }</a>
+<a name="1164"><span class="lineNum">    1164 </span>            : </a>
+<a name="1165"><span class="lineNum">    1165 </span>            : </a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineNoCov">          0 : static int write_timestep(void *v, const molfile_timestep_t *ts) { </span></a>
+<a name="1167"><span class="lineNum">    1167 </span>            :   dcdhandle *dcd = (dcdhandle *)v;</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :   int i, rc, curstep;</a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :   float *pos = ts-&gt;coords;</span></a>
+<a name="1170"><span class="lineNum">    1170 </span>            :   double unitcell[6];</a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :   unitcell[0] = unitcell[2] = unitcell[5] = 0.0f;</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :   unitcell[1] = unitcell[3] = unitcell[4] = 90.0f;</span></a>
+<a name="1173"><span class="lineNum">    1173 </span>            : </a>
+<a name="1174"><span class="lineNum">    1174 </span>            :   /* copy atom coords into separate X/Y/Z arrays for writing */</a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;dcd-&gt;natoms; i++) {</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineNoCov">          0 :     dcd-&gt;x[i] = *(pos++); </span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 :     dcd-&gt;y[i] = *(pos++); </span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineNoCov">          0 :     dcd-&gt;z[i] = *(pos++); </span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            :   }</a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :   dcd-&gt;nsets++;</span></a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineNoCov">          0 :   curstep = dcd-&gt;istart + dcd-&gt;nsets * dcd-&gt;nsavc;</span></a>
+<a name="1182"><span class="lineNum">    1182 </span>            : </a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineNoCov">          0 :   unitcell[0] = ts-&gt;A;</span></a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineNoCov">          0 :   unitcell[2] = ts-&gt;B;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineNoCov">          0 :   unitcell[5] = ts-&gt;C;</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineNoCov">          0 :   unitcell[1] = sin((M_PI_2 / 90.0) * (90.0 - ts-&gt;gamma)); /* cosAB */</span></a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineNoCov">          0 :   unitcell[3] = sin((M_PI_2 / 90.0) * (90.0 - ts-&gt;beta));  /* cosAC */</span></a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineNoCov">          0 :   unitcell[4] = sin((M_PI_2 / 90.0) * (90.0 - ts-&gt;alpha)); /* cosBC */</span></a>
+<a name="1189"><span class="lineNum">    1189 </span>            : </a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineNoCov">          0 :   rc = write_dcdstep(dcd-&gt;fd, dcd-&gt;nsets, curstep, dcd-&gt;natoms, </span></a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :                      dcd-&gt;x, dcd-&gt;y, dcd-&gt;z,</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :                      dcd-&gt;with_unitcell ? unitcell : NULL,</span></a>
+<a name="1193"><span class="lineNum">    1193 </span>            :                      dcd-&gt;charmm);</a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineNoCov">          0 :   if (rc &lt; 0) {</span></a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineNoCov">          0 :     print_dcderror(&quot;write_dcdstep&quot;, rc);</span></a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineNoCov">          0 :     return MOLFILE_ERROR;</span></a>
+<a name="1197"><span class="lineNum">    1197 </span>            :   }</a>
+<a name="1198"><span class="lineNum">    1198 </span>            : </a>
+<a name="1199"><span class="lineNum">    1199 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="1200"><span class="lineNum">    1200 </span>            : }</a>
+<a name="1201"><span class="lineNum">    1201 </span>            : </a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineNoCov">          0 : static void close_file_write(void *v) {</span></a>
+<a name="1203"><span class="lineNum">    1203 </span>            :   dcdhandle *dcd = (dcdhandle *)v;</a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineNoCov">          0 :   fio_fclose(dcd-&gt;fd);</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineNoCov">          0 :   free(dcd-&gt;x);</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :   free(dcd-&gt;y);</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineNoCov">          0 :   free(dcd-&gt;z);</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineNoCov">          0 :   free(dcd);</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1210"><span class="lineNum">    1210 </span>            : </a>
+<a name="1211"><span class="lineNum">    1211 </span>            : </a>
+<a name="1212"><span class="lineNum">    1212 </span>            : /*</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :  * Initialization stuff here</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :  */</a>
+<a name="1215"><span class="lineNum">    1215 </span>            : static molfile_plugin_t plugin;</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_init() {</span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   memset(&amp;plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">       8336 :   plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">       8336 :   plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineCov">       8336 :   plugin.name = &quot;dcd&quot;;</span></a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">       8336 :   plugin.prettyname = &quot;CHARMM,NAMD,XPLOR DCD Trajectory&quot;;</span></a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">       8336 :   plugin.author = &quot;Axel Kohlmeyer, Justin Gullingsrud, John Stone&quot;;</span></a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">       8336 :   plugin.majorv = 1;</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">       8336 :   plugin.minorv = 18;</span></a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">       8336 :   plugin.is_reentrant = VMDPLUGIN_THREADSAFE;</span></a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">       8336 :   plugin.filename_extension = &quot;dcd&quot;;</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">       8336 :   plugin.open_file_read = open_dcd_read;</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">       8336 :   plugin.read_next_timestep = read_next_timestep;</span></a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineCov">       8336 :   plugin.close_file_read = close_file_read;</span></a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">       8336 :   plugin.open_file_write = open_dcd_write;</span></a>
+<a name="1232"><span class="lineNum">    1232 </span><span class="lineCov">       8336 :   plugin.write_timestep = write_timestep;</span></a>
+<a name="1233"><span class="lineNum">    1233 </span><span class="lineCov">       8336 :   plugin.close_file_write = close_file_write;</span></a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">       8336 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            : }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            : </a>
+<a name="1237"><span class="lineNum">    1237 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {</span></a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;plugin);</span></a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineCov">       8336 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            : }</a>
+<a name="1241"><span class="lineNum">    1241 </span>            : </a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineNoCov">          0 : VMDPLUGIN_API int VMDPLUGIN_fini() {</span></a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineNoCov">          0 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            : }</a>
+<a name="1245"><span class="lineNum">    1245 </span>            : </a>
+<a name="1246"><span class="lineNum">    1246 </span>            : }</a>
+<a name="1247"><span class="lineNum">    1247 </span>            : }</a>
+<a name="1248"><span class="lineNum">    1248 </span>            : </a>
+<a name="1249"><span class="lineNum">    1249 </span>            :   </a>
+<a name="1250"><span class="lineNum">    1250 </span>            : #ifdef TEST_DCDPLUGIN</a>
+<a name="1251"><span class="lineNum">    1251 </span>            : </a>
+<a name="1252"><span class="lineNum">    1252 </span>            : #include &lt;sys/time.h&gt;</a>
+<a name="1253"><span class="lineNum">    1253 </span>            : </a>
+<a name="1254"><span class="lineNum">    1254 </span>            : /* get the time of day from the system clock, and store it (in seconds) */</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : double time_of_day(void) {</a>
+<a name="1256"><span class="lineNum">    1256 </span>            : #if defined(_MSC_VER)</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :   double t;</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : </a>
+<a name="1259"><span class="lineNum">    1259 </span>            :   t = GetTickCount();</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   t = t / 1000.0;</a>
+<a name="1261"><span class="lineNum">    1261 </span>            : </a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   return t;</a>
+<a name="1263"><span class="lineNum">    1263 </span>            : #else</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :   struct timeval tm;</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :   struct timezone tz;</a>
+<a name="1266"><span class="lineNum">    1266 </span>            : </a>
+<a name="1267"><span class="lineNum">    1267 </span>            :   gettimeofday(&amp;tm, &amp;tz);</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :   return((double)(tm.tv_sec) + (double)(tm.tv_usec)/1000000.0);</a>
+<a name="1269"><span class="lineNum">    1269 </span>            : #endif</a>
+<a name="1270"><span class="lineNum">    1270 </span>            : }</a>
+<a name="1271"><span class="lineNum">    1271 </span>            : </a>
+<a name="1272"><span class="lineNum">    1272 </span>            : int main(int argc, char *argv[]) {</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   molfile_timestep_t timestep;</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :   void *v;</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :   dcdhandle *dcd;</a>
+<a name="1276"><span class="lineNum">    1276 </span>            :   int i, natoms;</a>
+<a name="1277"><span class="lineNum">    1277 </span>            :   float sizeMB =0.0, totalMB = 0.0;</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :   double starttime, endtime, totaltime = 0.0;</a>
+<a name="1279"><span class="lineNum">    1279 </span>            : </a>
+<a name="1280"><span class="lineNum">    1280 </span>            :   while (--argc) {</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :     ++argv; </a>
+<a name="1282"><span class="lineNum">    1282 </span>            :     natoms = 0;</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :     v = open_dcd_read(*argv, &quot;dcd&quot;, &amp;natoms);</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :     if (!v) {</a>
+<a name="1285"><span class="lineNum">    1285 </span>            :       fprintf(stderr, &quot;main) open_dcd_read failed for file %s\n&quot;, *argv);</a>
+<a name="1286"><span class="lineNum">    1286 </span>            :       return 1;</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :     }</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :     dcd = (dcdhandle *)v;</a>
+<a name="1289"><span class="lineNum">    1289 </span>            :     sizeMB = ((natoms * 3.0) * dcd-&gt;nsets * 4.0) / (1024.0 * 1024.0);</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :     totalMB += sizeMB; </a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     printf(&quot;main) file: %s\n&quot;, *argv);</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :     printf(&quot;  %d atoms, %d frames, size: %6.1fMB\n&quot;, natoms, dcd-&gt;nsets, sizeMB);</a>
+<a name="1293"><span class="lineNum">    1293 </span>            : </a>
+<a name="1294"><span class="lineNum">    1294 </span>            :     starttime = time_of_day();</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :     timestep.coords = (float *)malloc(3*sizeof(float)*natoms);</a>
+<a name="1296"><span class="lineNum">    1296 </span>            :     for (i=0; i&lt;dcd-&gt;nsets; i++) {</a>
+<a name="1297"><span class="lineNum">    1297 </span>            :       int rc = read_next_timestep(v, natoms, &amp;timestep);</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :       if (rc) {</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :         fprintf(stderr, &quot;error in read_next_timestep on frame %d\n&quot;, i);</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :         return 1;</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :       }</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :     }</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :     endtime = time_of_day();</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :     close_file_read(v);</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :     totaltime += endtime - starttime;</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :     printf(&quot;  Time: %5.1f seconds\n&quot;, endtime - starttime);</a>
+<a name="1307"><span class="lineNum">    1307 </span>            :     printf(&quot;  Speed: %5.1f MB/sec, %5.1f timesteps/sec\n&quot;, sizeMB / (endtime - starttime), (dcd-&gt;nsets / (endtime - starttime)));</a>
+<a name="1308"><span class="lineNum">    1308 </span>            :   }</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :   printf(&quot;Overall Size: %6.1f MB\n&quot;, totalMB);</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   printf(&quot;Overall Time: %6.1f seconds\n&quot;, totaltime);</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :   printf(&quot;Overall Speed: %5.1f MB/sec\n&quot;, totalMB / totaltime);</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :   return 0;</a>
+<a name="1313"><span class="lineNum">    1313 </span>            : }</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :       </a>
+<a name="1315"><span class="lineNum">    1315 </span>            : #endif</a>
+<a name="1316"><span class="lineNum">    1316 </span>            : </a>
+<a name="1317"><span class="lineNum">    1317 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/endianswap.h.func-sort-c.html b/coverage-libs/molfile/endianswap.h.func-sort-c.html
new file mode 100644
index 0000000000..a190c55a92
--- /dev/null
+++ b/coverage-libs/molfile/endianswap.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/endianswap.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - endianswap.h<span style="font-size: 80%;"> (<a href="endianswap.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryLo">12.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="endianswap.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#164">_ZN4PLMD7molfileL13swap8_alignedEPvl</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#86">_ZN4PLMD7molfileL15swap4_unalignedEPvl</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#105">_ZN4PLMD7molfileL15swap8_unalignedEPvl</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#150">_ZN4PLMD7molfileL13swap4_alignedEPvl</a></td>
+              <td class="coverFnHi">1461240</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/endianswap.h.func.html b/coverage-libs/molfile/endianswap.h.func.html
new file mode 100644
index 0000000000..f4ea889c48
--- /dev/null
+++ b/coverage-libs/molfile/endianswap.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/endianswap.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - endianswap.h<span style="font-size: 80%;"> (<a href="endianswap.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryLo">12.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="endianswap.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#150">_ZN4PLMD7molfileL13swap4_alignedEPvl</a></td>
+              <td class="coverFnHi">1461240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#164">_ZN4PLMD7molfileL13swap8_alignedEPvl</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#86">_ZN4PLMD7molfileL15swap4_unalignedEPvl</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="endianswap.h.gcov.html#105">_ZN4PLMD7molfileL15swap8_unalignedEPvl</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/endianswap.h.gcov.html b/coverage-libs/molfile/endianswap.h.gcov.html
new file mode 100644
index 0000000000..1a79c0900b
--- /dev/null
+++ b/coverage-libs/molfile/endianswap.h.gcov.html
@@ -0,0 +1,293 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/endianswap.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - endianswap.h<span style="font-size: 80%;"> (source / <a href="endianswap.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryLo">12.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifndef __PLUMED_molfile_endianswap_h</a>
+<a name="38"><span class="lineNum">      38 </span>            : #define __PLUMED_molfile_endianswap_h</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD{</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace molfile{</a>
+<a name="41"><span class="lineNum">      41 </span>            : /***************************************************************************</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *cr                        University of Illinois</a>
+<a name="45"><span class="lineNum">      45 </span>            :  *cr                         All Rights Reserved</a>
+<a name="46"><span class="lineNum">      46 </span>            :  *cr</a>
+<a name="47"><span class="lineNum">      47 </span>            :  ***************************************************************************/</a>
+<a name="48"><span class="lineNum">      48 </span>            : /***************************************************************************</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * RCS INFORMATION:</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $RCSfile: endianswap.h,v $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="53"><span class="lineNum">      53 </span>            :  *      $Revision: 1.8 $       $Date: 2020/10/21 18:03:15 $</a>
+<a name="54"><span class="lineNum">      54 </span>            :  *</a>
+<a name="55"><span class="lineNum">      55 </span>            :  ***************************************************************************</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * DESCRIPTION:</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *   Byte swapping routines used in various plugins</a>
+<a name="58"><span class="lineNum">      58 </span>            :  *   There are two versions of each routine, one that's safe to use in</a>
+<a name="59"><span class="lineNum">      59 </span>            :  *   all cases (but is slow) and one that is only safe to use on memory </a>
+<a name="60"><span class="lineNum">      60 </span>            :  *   addresses that are aligned to the word size that's being byte-swapped</a>
+<a name="61"><span class="lineNum">      61 </span>            :  *   but are much much much faster.  Use the aligned versions of these</a>
+<a name="62"><span class="lineNum">      62 </span>            :  *   routines whenever possible.  The 'ndata' length count parameters and</a>
+<a name="63"><span class="lineNum">      63 </span>            :  *   internal loops should be safe to use on huge memory arrays on 64-bit</a>
+<a name="64"><span class="lineNum">      64 </span>            :  *   machines.</a>
+<a name="65"><span class="lineNum">      65 </span>            :  *</a>
+<a name="66"><span class="lineNum">      66 </span>            :  ***************************************************************************/</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : #ifndef ENDIAN_SWAP_H</a>
+<a name="69"><span class="lineNum">      69 </span>            : #define ENDIAN_SWAP_H</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : #include &lt;stddef.h&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : /* works on unaligned 2-byte quantities */</a>
+<a name="74"><span class="lineNum">      74 </span>            : static void swap2_unaligned(void *v, ptrdiff_t ndata) {</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ptrdiff_t i;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   char * dataptr = (char *) v;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   char tmp;</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   for (i = 0; i &lt; ndata-1; i += 2) {</a>
+<a name="80"><span class="lineNum">      80 </span>            :     tmp = dataptr[i];</a>
+<a name="81"><span class="lineNum">      81 </span>            :     dataptr[i] = dataptr[i+1];</a>
+<a name="82"><span class="lineNum">      82 </span>            :     dataptr[i+1] = tmp;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : /* works on unaligned 4-byte quantities */</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 : static void swap4_unaligned(void *v, ptrdiff_t ndata) {</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   ptrdiff_t i;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   char *dataptr;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   char tmp;</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   dataptr = (char *) v; </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;ndata; i++) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     tmp = dataptr[0];</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     dataptr[0] = dataptr[3];</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     dataptr[3] = tmp;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     tmp = dataptr[1];</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     dataptr[1] = dataptr[2];</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     dataptr[2] = tmp;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :     dataptr += 4;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : /* works on unaligned 8-byte quantities */</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 : static void swap8_unaligned(void *v, ptrdiff_t ndata) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   char *data = (char *) v;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ptrdiff_t i;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   char byteArray[8];</a>
+<a name="111"><span class="lineNum">     111 </span>            :   char *bytePointer;</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;ndata; i++) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     bytePointer = data + (i&lt;&lt;3);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     byteArray[0]  =  *bytePointer;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     byteArray[1]  =  *(bytePointer+1);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     byteArray[2]  =  *(bytePointer+2);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     byteArray[3]  =  *(bytePointer+3);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     byteArray[4]  =  *(bytePointer+4);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     byteArray[5]  =  *(bytePointer+5);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     byteArray[6]  =  *(bytePointer+6);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     byteArray[7]  =  *(bytePointer+7);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     *bytePointer     = byteArray[7];</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     *(bytePointer+1) = byteArray[6];</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     *(bytePointer+2) = byteArray[5];</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     *(bytePointer+3) = byteArray[4];</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :     *(bytePointer+4) = byteArray[3];</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     *(bytePointer+5) = byteArray[2];</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     *(bytePointer+6) = byteArray[1];</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     *(bytePointer+7) = byteArray[0];</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   }</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : /* Only works with aligned 2-byte quantities, will cause a bus error */</a>
+<a name="137"><span class="lineNum">     137 </span>            : /* on some platforms if used on unaligned data.                      */</a>
+<a name="138"><span class="lineNum">     138 </span>            : static void swap2_aligned(void *v, ptrdiff_t ndata) {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   short *data = (short *) v;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   ptrdiff_t i;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   short *N; </a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   for (i=0; i&lt;ndata; i++) {</a>
+<a name="144"><span class="lineNum">     144 </span>            :     N = data + i;</a>
+<a name="145"><span class="lineNum">     145 </span>            :     *N=(((*N&gt;&gt;8)&amp;0xff) | ((*N&amp;0xff)&lt;&lt;8));  </a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : /* Only works with aligned 4-byte quantities, will cause a bus error */</a>
+<a name="151"><span class="lineNum">     151 </span>            : /* on some platforms if used on unaligned data.                      */</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">    1461240 : static void swap4_aligned(void *v, ptrdiff_t ndata) {</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   int *data = (int *) v;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   ptrdiff_t i;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   int *N;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">    2922480 :   for (i=0; i&lt;ndata; i++) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">    1461240 :     N = data + i;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">    1461240 :     *N=(((*N&gt;&gt;24)&amp;0xff) | ((*N&amp;0xff)&lt;&lt;24) | </span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    1461240 :         ((*N&gt;&gt;8)&amp;0xff00) | ((*N&amp;0xff00)&lt;&lt;8));</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    1461240 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : /* Only works with aligned 8-byte quantities, will cause a bus error */</a>
+<a name="165"><span class="lineNum">     165 </span>            : /* on some platforms if used on unaligned data.                      */</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 : static void swap8_aligned(void *v, ptrdiff_t ndata) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   /* Use int* internally to prevent bugs caused by some compilers */</a>
+<a name="168"><span class="lineNum">     168 </span>            :   /* and hardware that would potentially load data into an FP reg */</a>
+<a name="169"><span class="lineNum">     169 </span>            :   /* and hose everything, such as the old &quot;jmemcpy()&quot; bug in NAMD */</a>
+<a name="170"><span class="lineNum">     170 </span>            :   int *data = (int *) v;  </a>
+<a name="171"><span class="lineNum">     171 </span>            :   ptrdiff_t i;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   int *N; </a>
+<a name="173"><span class="lineNum">     173 </span>            :   int t0, t1;</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;ndata; i++) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     N = data + (i&lt;&lt;1);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     t0 = N[0];</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     t0=(((t0&gt;&gt;24)&amp;0xff) | ((t0&amp;0xff)&lt;&lt;24) | </span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :         ((t0&gt;&gt;8)&amp;0xff00) | ((t0&amp;0xff00)&lt;&lt;8));</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     t1 = N[1];</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     t1=(((t1&gt;&gt;24)&amp;0xff) | ((t1&amp;0xff)&lt;&lt;24) | </span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :         ((t1&gt;&gt;8)&amp;0xff00) | ((t1&amp;0xff00)&lt;&lt;8));</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     N[0] = t1; </span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     N[1] = t0; </span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : #if 0</a>
+<a name="191"><span class="lineNum">     191 </span>            : /* Other implementations that might be faster in some cases */</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : /* swaps the endianism of an eight byte word. */</a>
+<a name="194"><span class="lineNum">     194 </span>            : void mdio_swap8(double *i) {</a>
+<a name="195"><span class="lineNum">     195 </span>            :         char c;</a>
+<a name="196"><span class="lineNum">     196 </span>            :         char *n;</a>
+<a name="197"><span class="lineNum">     197 </span>            :         n = (char *) i;</a>
+<a name="198"><span class="lineNum">     198 </span>            :         c = n[0];</a>
+<a name="199"><span class="lineNum">     199 </span>            :         n[0] = n[7];</a>
+<a name="200"><span class="lineNum">     200 </span>            :         n[7] = c;</a>
+<a name="201"><span class="lineNum">     201 </span>            :         c = n[1];</a>
+<a name="202"><span class="lineNum">     202 </span>            :         n[1] = n[6];</a>
+<a name="203"><span class="lineNum">     203 </span>            :         n[6] = c;</a>
+<a name="204"><span class="lineNum">     204 </span>            :         c = n[2];</a>
+<a name="205"><span class="lineNum">     205 </span>            :         n[2] = n[5];</a>
+<a name="206"><span class="lineNum">     206 </span>            :         n[5] = c;</a>
+<a name="207"><span class="lineNum">     207 </span>            :         c = n[3];</a>
+<a name="208"><span class="lineNum">     208 </span>            :         n[3] = n[4];</a>
+<a name="209"><span class="lineNum">     209 </span>            :         n[4] = c;</a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            : #endif</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : #endif</a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+<a name="217"><span class="lineNum">     217 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/fastio.h.func-sort-c.html b/coverage-libs/molfile/fastio.h.func-sort-c.html
new file mode 100644
index 0000000000..d1d696cb8c
--- /dev/null
+++ b/coverage-libs/molfile/fastio.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/fastio.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - fastio.h<span style="font-size: 80%;"> (<a href="fastio.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryLo">55.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="fastio.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#588">_ZN4PLMD7molfileL10fio_fwriteEPvlli</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#666">_ZN4PLMD7molfileL15fio_write_int32Eii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#465">_ZN4PLMD7molfileL10fio_fcloseEi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#437">_ZN4PLMD7molfileL8fio_openEPKciPi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#651">_ZN4PLMD7molfileL9fio_ftellEi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#644">_ZN4PLMD7molfileL9fio_fseekEili</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#469">_ZN4PLMD7molfileL9fio_freadEPvlli</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/fastio.h.func.html b/coverage-libs/molfile/fastio.h.func.html
new file mode 100644
index 0000000000..c85f0d3a4b
--- /dev/null
+++ b/coverage-libs/molfile/fastio.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/fastio.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - fastio.h<span style="font-size: 80%;"> (<a href="fastio.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryLo">55.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="fastio.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#465">_ZN4PLMD7molfileL10fio_fcloseEi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#588">_ZN4PLMD7molfileL10fio_fwriteEPvlli</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#666">_ZN4PLMD7molfileL15fio_write_int32Eii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#437">_ZN4PLMD7molfileL8fio_openEPKciPi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#469">_ZN4PLMD7molfileL9fio_freadEPvlli</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#644">_ZN4PLMD7molfileL9fio_fseekEili</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="fastio.h.gcov.html#651">_ZN4PLMD7molfileL9fio_ftellEi</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/fastio.h.gcov.html b/coverage-libs/molfile/fastio.h.gcov.html
new file mode 100644
index 0000000000..ecbbf67458
--- /dev/null
+++ b/coverage-libs/molfile/fastio.h.gcov.html
@@ -0,0 +1,759 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/fastio.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - fastio.h<span style="font-size: 80%;"> (source / <a href="fastio.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryLo">55.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifndef __PLUMED_molfile_fastio_h</a>
+<a name="38"><span class="lineNum">      38 </span>            : #define __PLUMED_molfile_fastio_h</a>
+<a name="39"><span class="lineNum">      39 </span>            : /***************************************************************************</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                        University of Illinois</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr                         All Rights Reserved</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *cr</a>
+<a name="45"><span class="lineNum">      45 </span>            :  ***************************************************************************/</a>
+<a name="46"><span class="lineNum">      46 </span>            : /***************************************************************************</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * RCS INFORMATION:</a>
+<a name="48"><span class="lineNum">      48 </span>            :  *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *      $RCSfile: fastio.h,v $</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $Revision: 1.34 $       $Date: 2016/11/28 05:01:53 $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  ***************************************************************************</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * DESCRIPTION:</a>
+<a name="55"><span class="lineNum">      55 </span>            :  *   This is a simple abstraction layer for system-dependent I/O calls</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * that allow plugins to do binary I/O using the fastest possible method.</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *</a>
+<a name="58"><span class="lineNum">      58 </span>            :  * This code is intended for use by binary trajectory reader plugins that</a>
+<a name="59"><span class="lineNum">      59 </span>            :  * work with multi-gigabyte data sets, reading only binary data.</a>
+<a name="60"><span class="lineNum">      60 </span>            :  *</a>
+<a name="61"><span class="lineNum">      61 </span>            :  ***************************************************************************/</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : #define FIO_READ    0x01</a>
+<a name="64"><span class="lineNum">      64 </span>            : #define FIO_WRITE   0x02</a>
+<a name="65"><span class="lineNum">      65 </span>            : #define FIO_DIRECT  0x04 /* emulate Unix O_DIRECT flag */</a>
+<a name="66"><span class="lineNum">      66 </span>            :  </a>
+<a name="67"><span class="lineNum">      67 </span>            : /* Compiling on windows */</a>
+<a name="68"><span class="lineNum">      68 </span>            : #if defined(_MSC_VER) || defined(__MINGW32__)</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : #if 1 </a>
+<a name="71"><span class="lineNum">      71 </span>            : /* use native Windows I/O calls */</a>
+<a name="72"><span class="lineNum">      72 </span>            : #define FASTIO_NATIVEWIN32 1</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="75"><span class="lineNum">      75 </span>            : #include &lt;string.h&gt;</a>
+<a name="76"><span class="lineNum">      76 </span>            : #include &lt;windows.h&gt;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : namespace PLMD{</a>
+<a name="79"><span class="lineNum">      79 </span>            : namespace molfile{</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : typedef HANDLE fio_fd;</a>
+<a name="82"><span class="lineNum">      82 </span>            : typedef LONGLONG fio_size_t;</a>
+<a name="83"><span class="lineNum">      83 </span>            : typedef void * fio_caddr_t;</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : typedef struct {</a>
+<a name="86"><span class="lineNum">      86 </span>            :   fio_caddr_t iov_base;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   int iov_len;</a>
+<a name="88"><span class="lineNum">      88 </span>            : } fio_iovec;</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : #define FIO_SEEK_CUR  FILE_CURRENT</a>
+<a name="92"><span class="lineNum">      92 </span>            : #define FIO_SEEK_SET  FILE_BEGIN</a>
+<a name="93"><span class="lineNum">      93 </span>            : #define FIO_SEEK_END  FILE_END</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : static int fio_win32convertfilename(const char *filename, char *newfilename, int maxlen) {</a>
+<a name="96"><span class="lineNum">      96 </span>            :   int i;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   int len=strlen(filename);</a>
+<a name="98"><span class="lineNum">      98 </span>            :  </a>
+<a name="99"><span class="lineNum">      99 </span>            :   if ((len + 1) &gt;= maxlen)</a>
+<a name="100"><span class="lineNum">     100 </span>            :     return -1;</a>
+<a name="101"><span class="lineNum">     101 </span>            :    </a>
+<a name="102"><span class="lineNum">     102 </span>            :   for (i=0; i&lt;len; i++) {</a>
+<a name="103"><span class="lineNum">     103 </span>            :     if (filename[i] == '/')</a>
+<a name="104"><span class="lineNum">     104 </span>            :       newfilename[i] = '\\';</a>
+<a name="105"><span class="lineNum">     105 </span>            :     else</a>
+<a name="106"><span class="lineNum">     106 </span>            :       newfilename[i] = filename[i];</a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span>            :   newfilename[len] = '\0'; /* NUL terminate the string */</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   return 0;</a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : static int fio_open(const char *filename, int mode, fio_fd *fd) {</a>
+<a name="114"><span class="lineNum">     114 </span>            :   HANDLE fp;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   char winfilename[8192];</a>
+<a name="116"><span class="lineNum">     116 </span>            :   DWORD access;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   DWORD sharing;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   LPSECURITY_ATTRIBUTES security;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   DWORD createmode;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   DWORD flags;</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   if (fio_win32convertfilename(filename, winfilename, sizeof(winfilename)))</a>
+<a name="123"><span class="lineNum">     123 </span>            :     return -1;  </a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   access = 0;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   if (mode &amp; FIO_READ)</a>
+<a name="127"><span class="lineNum">     127 </span>            :     access |= GENERIC_READ;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   if (mode &amp; FIO_WRITE)</a>
+<a name="129"><span class="lineNum">     129 </span>            :     access |= GENERIC_WRITE;</a>
+<a name="130"><span class="lineNum">     130 </span>            : #if 0</a>
+<a name="131"><span class="lineNum">     131 </span>            :   access = FILE_ALL_ACCESS; /* XXX hack if above modes fail */</a>
+<a name="132"><span class="lineNum">     132 </span>            : #endif</a>
+<a name="133"><span class="lineNum">     133 </span>            : #if 1</a>
+<a name="134"><span class="lineNum">     134 </span>            :   if (mode &amp; FIO_DIRECT)</a>
+<a name="135"><span class="lineNum">     135 </span>            :     flags = FILE_FLAG_NO_BUFFERING;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   else</a>
+<a name="137"><span class="lineNum">     137 </span>            :     flags = FILE_ATTRIBUTE_NORMAL;</a>
+<a name="138"><span class="lineNum">     138 </span>            : #else</a>
+<a name="139"><span class="lineNum">     139 </span>            :   if (mode &amp; FIO_DIRECT)</a>
+<a name="140"><span class="lineNum">     140 </span>            :     return -1; /* not supported yet */</a>
+<a name="141"><span class="lineNum">     141 </span>            : #endif</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   sharing = 0;       /* disallow sharing with other processes  */</a>
+<a name="144"><span class="lineNum">     144 </span>            :   security = NULL;   /* child processes don't inherit anything */</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   /* since we never append, blow away anything that's already there */</a>
+<a name="147"><span class="lineNum">     147 </span>            :   if (mode &amp; FIO_WRITE)</a>
+<a name="148"><span class="lineNum">     148 </span>            :     createmode = CREATE_ALWAYS;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   else </a>
+<a name="150"><span class="lineNum">     150 </span>            :     createmode = OPEN_EXISTING;</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   fp = CreateFile(winfilename, access, sharing, security, </a>
+<a name="153"><span class="lineNum">     153 </span>            :                   createmode, flags, NULL);</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   if (fp == NULL) {</a>
+<a name="156"><span class="lineNum">     156 </span>            :     return -1;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   } else {</a>
+<a name="158"><span class="lineNum">     158 </span>            :     *fd = fp;</a>
+<a name="159"><span class="lineNum">     159 </span>            :     return 0;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : static int fio_fclose(fio_fd fd) {</a>
+<a name="165"><span class="lineNum">     165 </span>            :   BOOL rc;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   rc = CloseHandle(fd);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   if (rc) </a>
+<a name="168"><span class="lineNum">     168 </span>            :     return 0;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   else </a>
+<a name="170"><span class="lineNum">     170 </span>            :     return -1;</a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : static fio_size_t fio_fread(void *ptr, fio_size_t size, </a>
+<a name="174"><span class="lineNum">     174 </span>            :                             fio_size_t nitems, fio_fd fd) {</a>
+<a name="175"><span class="lineNum">     175 </span>            :   BOOL rc;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   DWORD len;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   DWORD readlen;</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   len = size * nitems;</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   rc = ReadFile(fd, ptr, len, &amp;readlen, NULL);</a>
+<a name="182"><span class="lineNum">     182 </span>            :   if (rc) {</a>
+<a name="183"><span class="lineNum">     183 </span>            :     if (readlen == len)</a>
+<a name="184"><span class="lineNum">     184 </span>            :       return nitems;</a>
+<a name="185"><span class="lineNum">     185 </span>            :     else </a>
+<a name="186"><span class="lineNum">     186 </span>            :       return 0;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   } else {</a>
+<a name="188"><span class="lineNum">     188 </span>            :     return 0;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {</a>
+<a name="193"><span class="lineNum">     193 </span>            :   int i;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   fio_size_t len = 0; </a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   for (i=0; i&lt;iovcnt; i++) {</a>
+<a name="197"><span class="lineNum">     197 </span>            :     fio_size_t rc = fio_fread(iov[i].iov_base, iov[i].iov_len, 1, fd);</a>
+<a name="198"><span class="lineNum">     198 </span>            :     if (rc != 1)</a>
+<a name="199"><span class="lineNum">     199 </span>            :       break;</a>
+<a name="200"><span class="lineNum">     200 </span>            :     len += iov[i].iov_len;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   return len;</a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : static fio_size_t fio_fwrite(void *ptr, fio_size_t size, </a>
+<a name="207"><span class="lineNum">     207 </span>            :                              fio_size_t nitems, fio_fd fd) {</a>
+<a name="208"><span class="lineNum">     208 </span>            :   BOOL rc;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   DWORD len;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   DWORD writelen;</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   len = size * nitems; </a>
+<a name="213"><span class="lineNum">     213 </span>            :  </a>
+<a name="214"><span class="lineNum">     214 </span>            :   rc = WriteFile(fd, ptr, len, &amp;writelen, NULL);</a>
+<a name="215"><span class="lineNum">     215 </span>            :   if (rc) {</a>
+<a name="216"><span class="lineNum">     216 </span>            :     if (writelen == len)</a>
+<a name="217"><span class="lineNum">     217 </span>            :       return nitems;</a>
+<a name="218"><span class="lineNum">     218 </span>            :     else</a>
+<a name="219"><span class="lineNum">     219 </span>            :       return 0;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   } else {</a>
+<a name="221"><span class="lineNum">     221 </span>            :     return 0;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span>            : }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {</a>
+<a name="226"><span class="lineNum">     226 </span>            : #if 1</a>
+<a name="227"><span class="lineNum">     227 </span>            :   /* code that works with older MSVC6 compilers */</a>
+<a name="228"><span class="lineNum">     228 </span>            :   LONGLONG finaloffset;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   LARGE_INTEGER bigint;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   LARGE_INTEGER finalint;</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :   bigint.QuadPart = offset;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   finalint = bigint;      /* set the high part, which will be overwritten */</a>
+<a name="234"><span class="lineNum">     234 </span>            :   finalint.LowPart = SetFilePointer(fd, bigint.LowPart, &amp;finalint.HighPart, whence);</a>
+<a name="235"><span class="lineNum">     235 </span>            :   if (finalint.LowPart == -1) {</a>
+<a name="236"><span class="lineNum">     236 </span>            :     /* if (finalint.LowPart == INVALID_SET_FILE_POINTER) { */</a>
+<a name="237"><span class="lineNum">     237 </span>            :     /* INVALID_SET_FILE_POINTER is a possible &quot;ok&quot; low order result when */</a>
+<a name="238"><span class="lineNum">     238 </span>            :     /* working with 64-bit offsets, so we have to also check the system  */</a>
+<a name="239"><span class="lineNum">     239 </span>            :     /* error value for this thread to be sure */</a>
+<a name="240"><span class="lineNum">     240 </span>            :     if (GetLastError() != ERROR_SUCCESS) {</a>
+<a name="241"><span class="lineNum">     241 </span>            :       return -1;</a>
+<a name="242"><span class="lineNum">     242 </span>            :     }</a>
+<a name="243"><span class="lineNum">     243 </span>            :   } </a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   finaloffset = finalint.QuadPart;</a>
+<a name="246"><span class="lineNum">     246 </span>            :   return 0;</a>
+<a name="247"><span class="lineNum">     247 </span>            : #else</a>
+<a name="248"><span class="lineNum">     248 </span>            :   BOOL rc;</a>
+<a name="249"><span class="lineNum">     249 </span>            :   LONGLONG finaloffset;</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :   /* SetFilePointerEx() only exists with new .NET compilers */</a>
+<a name="252"><span class="lineNum">     252 </span>            :   rc = SetFilePointerEx(fd, offset, &amp;finaloffset, whence);</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   if (rc) </a>
+<a name="255"><span class="lineNum">     255 </span>            :     return 0;</a>
+<a name="256"><span class="lineNum">     256 </span>            :   else</a>
+<a name="257"><span class="lineNum">     257 </span>            :     return -1;</a>
+<a name="258"><span class="lineNum">     258 </span>            : #endif</a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : static fio_size_t fio_ftell(fio_fd fd) {</a>
+<a name="262"><span class="lineNum">     262 </span>            :   /* code that works with older MSVC6 compilers */</a>
+<a name="263"><span class="lineNum">     263 </span>            :   LONGLONG finaloffset;</a>
+<a name="264"><span class="lineNum">     264 </span>            :   LARGE_INTEGER bigint;</a>
+<a name="265"><span class="lineNum">     265 </span>            :   LARGE_INTEGER finalint;</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            :   bigint.QuadPart = 0;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   finalint = bigint;      /* set the high part, which will be overwritten */</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   finalint.LowPart = SetFilePointer(fd, bigint.LowPart, &amp;finalint.HighPart, FILE_CURRENT);</a>
+<a name="271"><span class="lineNum">     271 </span>            :   if (finalint.LowPart == -1) {</a>
+<a name="272"><span class="lineNum">     272 </span>            :     /* if (finalint.LowPart == INVALID_SET_FILE_POINTER) { */</a>
+<a name="273"><span class="lineNum">     273 </span>            :     /* INVALID_SET_FILE_POINTER is a possible &quot;ok&quot; low order result when */</a>
+<a name="274"><span class="lineNum">     274 </span>            :     /* working with 64-bit offsets, so we have to also check the system  */</a>
+<a name="275"><span class="lineNum">     275 </span>            :     /* error value for this thread to be sure */</a>
+<a name="276"><span class="lineNum">     276 </span>            :     if (GetLastError() != ERROR_SUCCESS) {</a>
+<a name="277"><span class="lineNum">     277 </span>            :       return -1;</a>
+<a name="278"><span class="lineNum">     278 </span>            :     }</a>
+<a name="279"><span class="lineNum">     279 </span>            :   }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            :   finaloffset = finalint.QuadPart;</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            :   return finaloffset;</a>
+<a name="284"><span class="lineNum">     284 </span>            : }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : #else</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : /* Version for machines with plain old ANSI C  */</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="292"><span class="lineNum">     292 </span>            : #include &lt;string.h&gt;</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : typedef FILE * fio_fd;</a>
+<a name="295"><span class="lineNum">     295 </span>            : typedef size_t fio_size_t;  /* MSVC doesn't uinversally support ssize_t */</a>
+<a name="296"><span class="lineNum">     296 </span>            : typedef void * fio_caddr_t; /* MSVC doesn't universally support caddr_t */</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : typedef struct {</a>
+<a name="299"><span class="lineNum">     299 </span>            :   fio_caddr_t iov_base;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   int iov_len;</a>
+<a name="301"><span class="lineNum">     301 </span>            : } fio_iovec;</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : #define FIO_SEEK_CUR SEEK_CUR</a>
+<a name="304"><span class="lineNum">     304 </span>            : #define FIO_SEEK_SET SEEK_SET</a>
+<a name="305"><span class="lineNum">     305 </span>            : #define FIO_SEEK_END SEEK_END</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : static int fio_open(const char *filename, int mode, fio_fd *fd) {</a>
+<a name="308"><span class="lineNum">     308 </span>            :   char * modestr;</a>
+<a name="309"><span class="lineNum">     309 </span>            :   FILE *fp;</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :   if (mode &amp; FIO_READ) </a>
+<a name="312"><span class="lineNum">     312 </span>            :     modestr = &quot;rb&quot;;</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :   if (mode &amp; FIO_WRITE) </a>
+<a name="315"><span class="lineNum">     315 </span>            :     modestr = &quot;wb&quot;;</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :   if (mode &amp; FIO_DIRECT)</a>
+<a name="318"><span class="lineNum">     318 </span>            :     return -1; /* not supported yet */</a>
+<a name="319"><span class="lineNum">     319 </span>            :  </a>
+<a name="320"><span class="lineNum">     320 </span>            :   fp = fopen(filename, modestr);</a>
+<a name="321"><span class="lineNum">     321 </span>            :   if (fp == NULL) {</a>
+<a name="322"><span class="lineNum">     322 </span>            :     return -1;</a>
+<a name="323"><span class="lineNum">     323 </span>            :   } else {</a>
+<a name="324"><span class="lineNum">     324 </span>            :     *fd = fp;</a>
+<a name="325"><span class="lineNum">     325 </span>            :     return 0;</a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span>            : }</a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            : static int fio_fclose(fio_fd fd) {</a>
+<a name="330"><span class="lineNum">     330 </span>            :   return fclose(fd);</a>
+<a name="331"><span class="lineNum">     331 </span>            : }</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            : static fio_size_t fio_fread(void *ptr, fio_size_t size, </a>
+<a name="334"><span class="lineNum">     334 </span>            :                             fio_size_t nitems, fio_fd fd) {</a>
+<a name="335"><span class="lineNum">     335 </span>            :   return fread(ptr, size, nitems, fd);</a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {</a>
+<a name="339"><span class="lineNum">     339 </span>            :   int i;</a>
+<a name="340"><span class="lineNum">     340 </span>            :   fio_size_t len = 0; </a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            :   for (i=0; i&lt;iovcnt; i++) {</a>
+<a name="343"><span class="lineNum">     343 </span>            :     fio_size_t rc = fread(iov[i].iov_base, iov[i].iov_len, 1, fd);</a>
+<a name="344"><span class="lineNum">     344 </span>            :     if (rc != 1)</a>
+<a name="345"><span class="lineNum">     345 </span>            :       break;</a>
+<a name="346"><span class="lineNum">     346 </span>            :     len += iov[i].iov_len;</a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :   return len;</a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            : static fio_size_t fio_fwrite(void *ptr, fio_size_t size, </a>
+<a name="353"><span class="lineNum">     353 </span>            :                              fio_size_t nitems, fio_fd fd) {</a>
+<a name="354"><span class="lineNum">     354 </span>            :   return fwrite(ptr, size, nitems, fd);</a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {</a>
+<a name="358"><span class="lineNum">     358 </span>            :   return fseek(fd, offset, whence);</a>
+<a name="359"><span class="lineNum">     359 </span>            : }</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : static fio_size_t fio_ftell(fio_fd fd) {</a>
+<a name="362"><span class="lineNum">     362 </span>            :   return ftell(fd);</a>
+<a name="363"><span class="lineNum">     363 </span>            : }</a>
+<a name="364"><span class="lineNum">     364 </span>            : #endif /* plain ANSI C */</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            : }</a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : #else </a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span>            : /* Version for UNIX machines */</a>
+<a name="372"><span class="lineNum">     372 </span>            : #if defined(__linux)</a>
+<a name="373"><span class="lineNum">     373 </span>            : #ifndef _GNU_SOURCE</a>
+<a name="374"><span class="lineNum">     374 </span>            : #define _GNU_SOURCE            /* required for O_DIRECT */</a>
+<a name="375"><span class="lineNum">     375 </span>            : #endif</a>
+<a name="376"><span class="lineNum">     376 </span>            : #endif</a>
+<a name="377"><span class="lineNum">     377 </span>            : #include &lt;unistd.h&gt;</a>
+<a name="378"><span class="lineNum">     378 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="379"><span class="lineNum">     379 </span>            : #include &lt;sys/types.h&gt;</a>
+<a name="380"><span class="lineNum">     380 </span>            : #include &lt;sys/stat.h&gt;</a>
+<a name="381"><span class="lineNum">     381 </span>            : #include &lt;fcntl.h&gt;</a>
+<a name="382"><span class="lineNum">     382 </span>            : #include &lt;string.h&gt;</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            : namespace PLMD{</a>
+<a name="385"><span class="lineNum">     385 </span>            : namespace molfile{</a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            : typedef int fio_fd;</a>
+<a name="388"><span class="lineNum">     388 </span>            : typedef off_t fio_size_t;      /* off_t is 64-bits with LFS builds */</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            : /*</a>
+<a name="391"><span class="lineNum">     391 </span>            :  * Enable use of kernel readv() if available and reliable</a>
+<a name="392"><span class="lineNum">     392 </span>            :  *</a>
+<a name="393"><span class="lineNum">     393 </span>            :  * Note: Some Linux implementations incorporate readv() code in libc </a>
+<a name="394"><span class="lineNum">     394 </span>            :  * that does userspace copying of I/O vectors to internal temporary</a>
+<a name="395"><span class="lineNum">     395 </span>            :  * buffers in order to meet the atomicity requirements of the POSIX standard.</a>
+<a name="396"><span class="lineNum">     396 </span>            :  * Such copies make the use of vectorized I/O APIs much less useful for</a>
+<a name="397"><span class="lineNum">     397 </span>            :  * large trajectory files because the internal buffer allocations can fail</a>
+<a name="398"><span class="lineNum">     398 </span>            :  * badly when performing large aggregate I/O operations.  It may be that</a>
+<a name="399"><span class="lineNum">     399 </span>            :  * other implementations of vector I/O have similar problems, and in these</a>
+<a name="400"><span class="lineNum">     400 </span>            :  * cases it is probably best not to use it at all, and to fall back to </a>
+<a name="401"><span class="lineNum">     401 </span>            :  * non-vectorized I/O APIs to avoid such extra copies.</a>
+<a name="402"><span class="lineNum">     402 </span>            :  */</a>
+<a name="403"><span class="lineNum">     403 </span>            : #if defined(__sun) || defined(__APPLE_CC__) || defined(__linux)</a>
+<a name="404"><span class="lineNum">     404 </span>            : #define USE_KERNEL_READV 1</a>
+<a name="405"><span class="lineNum">     405 </span>            : #endif</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            : typedef void * fio_caddr_t;</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            : #if defined(USE_KERNEL_READV)</a>
+<a name="413"><span class="lineNum">     413 </span>            : #include &lt;errno.h&gt;</a>
+<a name="414"><span class="lineNum">     414 </span>            : #include &lt;sys/uio.h&gt;</a>
+<a name="415"><span class="lineNum">     415 </span>            : namespace PLMD{</a>
+<a name="416"><span class="lineNum">     416 </span>            : namespace molfile{</a>
+<a name="417"><span class="lineNum">     417 </span>            : typedef struct iovec fio_iovec;</a>
+<a name="418"><span class="lineNum">     418 </span>            : }</a>
+<a name="419"><span class="lineNum">     419 </span>            : }</a>
+<a name="420"><span class="lineNum">     420 </span>            : #else</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            : namespace PLMD{</a>
+<a name="423"><span class="lineNum">     423 </span>            : namespace molfile{</a>
+<a name="424"><span class="lineNum">     424 </span>            : typedef struct {</a>
+<a name="425"><span class="lineNum">     425 </span>            :   fio_caddr_t iov_base;</a>
+<a name="426"><span class="lineNum">     426 </span>            :   int iov_len;</a>
+<a name="427"><span class="lineNum">     427 </span>            : } fio_iovec;</a>
+<a name="428"><span class="lineNum">     428 </span>            : }</a>
+<a name="429"><span class="lineNum">     429 </span>            : }</a>
+<a name="430"><span class="lineNum">     430 </span>            : #endif</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            : #define FIO_SEEK_CUR SEEK_CUR</a>
+<a name="433"><span class="lineNum">     433 </span>            : #define FIO_SEEK_SET SEEK_SET</a>
+<a name="434"><span class="lineNum">     434 </span>            : #define FIO_SEEK_END SEEK_END</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            : namespace PLMD{</a>
+<a name="437"><span class="lineNum">     437 </span>            : namespace molfile{</a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          1 : static int fio_open(const char *filename, int mode, fio_fd *fd) {</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   int nfd;</a>
+<a name="441"><span class="lineNum">     441 </span>            :   int oflag = 0;</a>
+<a name="442"><span class="lineNum">     442 </span>            :   </a>
+<a name="443"><span class="lineNum">     443 </span>            :   if (mode &amp; FIO_READ) </a>
+<a name="444"><span class="lineNum">     444 </span>            :     oflag = O_RDONLY;</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          1 :   if (mode &amp; FIO_WRITE) </span></a>
+<a name="447"><span class="lineNum">     447 </span>            :     oflag = O_WRONLY | O_CREAT | O_TRUNC;</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            : #if defined(__linux)</a>
+<a name="450"><span class="lineNum">     450 </span>            :   /* enable direct I/O, requires block-aligned buffers and I/O sizes */</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">          1 :   if (mode &amp; FIO_DIRECT)</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :     oflag |= O_DIRECT;</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : #else</a>
+<a name="454"><span class="lineNum">     454 </span>            :   if (mode &amp; FIO_DIRECT)</a>
+<a name="455"><span class="lineNum">     455 </span>            :     return -1; /* not supported yet */</a>
+<a name="456"><span class="lineNum">     456 </span>            : #endif</a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span>            :   nfd = open(filename, oflag, 0666);</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          1 :   if (nfd &lt; 0) {</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :     return -1;</a>
+<a name="461"><span class="lineNum">     461 </span>            :   } else {</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          1 :     *fd = nfd;</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          1 :     return 0;</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :   }</a>
+<a name="465"><span class="lineNum">     465 </span>            : }</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          1 : static int fio_fclose(fio_fd fd) {</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          1 :   return close(fd);</span></a>
+<a name="469"><span class="lineNum">     469 </span>            : }</a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">        219 : static fio_size_t fio_fread(void *ptr, fio_size_t size, </span></a>
+<a name="472"><span class="lineNum">     472 </span>            :                             fio_size_t nitems, fio_fd fd) {</a>
+<a name="473"><span class="lineNum">     473 </span>            :   fio_size_t i;</a>
+<a name="474"><span class="lineNum">     474 </span>            :   fio_size_t len = 0; </a>
+<a name="475"><span class="lineNum">     475 </span>            :   fio_size_t cnt = 0;</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span>            : #if 1</a>
+<a name="478"><span class="lineNum">     478 </span>            :   /*</a>
+<a name="479"><span class="lineNum">     479 </span>            :    * On Linux individual calls to read() can end up doing short reads when</a>
+<a name="480"><span class="lineNum">     480 </span>            :    * reading more than 2GB in a single read call, even on 64-bit machines.  </a>
+<a name="481"><span class="lineNum">     481 </span>            :    * For large structures, e.g. 240M-atoms or larger, we have to use a loop</a>
+<a name="482"><span class="lineNum">     482 </span>            :    * to continue reading into the memory buffer until completion.</a>
+<a name="483"><span class="lineNum">     483 </span>            :    */ </a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        438 :   for (i=0; i&lt;nitems; i++) {</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :     fio_size_t szleft = size;</a>
+<a name="486"><span class="lineNum">     486 </span>            :     fio_size_t rc = 0;</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        438 :     for (szleft=size; szleft &gt; 0; szleft -= rc) {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">        219 :       rc = read(fd, ((char*) ptr) + (cnt*size) + (size-szleft), szleft);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">        219 :        if (rc == 0) {</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :           return cnt;  /* end of file scenario */</a>
+<a name="491"><span class="lineNum">     491 </span>            :        }</a>
+<a name="492"><span class="lineNum">     492 </span>            : //      if (rc != szleft) {</a>
+<a name="493"><span class="lineNum">     493 </span>            : //        printf(&quot;fio_fread(): rc %ld  sz: %ld\n&quot;, rc, szleft);</a>
+<a name="494"><span class="lineNum">     494 </span>            : //      }</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">        219 :       if (rc &lt; 0) {</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :         printf(&quot;fio_fread(): rc %ld  sz: %ld\n&quot;, rc, size);</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :         perror(&quot;  perror fio_fread(): &quot;);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :       }</a>
+<a name="500"><span class="lineNum">     500 </span>            :     }</a>
+<a name="501"><span class="lineNum">     501 </span>            :     len += rc;</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        219 :     cnt++;</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   }</a>
+<a name="504"><span class="lineNum">     504 </span>            : #else</a>
+<a name="505"><span class="lineNum">     505 </span>            :   for (i=0; i&lt;nitems; i++) {</a>
+<a name="506"><span class="lineNum">     506 </span>            :     fio_size_t rc = read(fd, (void*) (((char *) ptr) + (cnt * size)), size);</a>
+<a name="507"><span class="lineNum">     507 </span>            :     if (rc != size) {</a>
+<a name="508"><span class="lineNum">     508 </span>            : //      printf(&quot;fio_fread(): rc %ld  sz: %ld\n&quot;, rc, size);</a>
+<a name="509"><span class="lineNum">     509 </span>            : //      perror(&quot;  perror fio_fread(): &quot;);</a>
+<a name="510"><span class="lineNum">     510 </span>            :       break;</a>
+<a name="511"><span class="lineNum">     511 </span>            :     }</a>
+<a name="512"><span class="lineNum">     512 </span>            :     len += rc;</a>
+<a name="513"><span class="lineNum">     513 </span>            :     cnt++;</a>
+<a name="514"><span class="lineNum">     514 </span>            :   }</a>
+<a name="515"><span class="lineNum">     515 </span>            : #endif</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span>            :   return cnt;</a>
+<a name="518"><span class="lineNum">     518 </span>            : }</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            : static fio_size_t fio_readv(fio_fd fd, const fio_iovec * iov, int iovcnt) {</a>
+<a name="521"><span class="lineNum">     521 </span>            :   fio_size_t len;</a>
+<a name="522"><span class="lineNum">     522 </span>            :   int i;</a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            : #if 0</a>
+<a name="525"><span class="lineNum">     525 </span>            :   fio_size_t tlen;</a>
+<a name="526"><span class="lineNum">     526 </span>            :   for (tlen=0,i=0; i&lt;iovcnt; i++) {</a>
+<a name="527"><span class="lineNum">     527 </span>            :     tlen += iov[i].iov_len;</a>
+<a name="528"><span class="lineNum">     528 </span>            :   }</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : #if defined(USE_KERNEL_READV)</a>
+<a name="531"><span class="lineNum">     531 </span>            :   len = readv(fd, iov, iovcnt);</a>
+<a name="532"><span class="lineNum">     532 </span>            :   if (len != tlen) {</a>
+<a name="533"><span class="lineNum">     533 </span>            :     printf(&quot;fio_readv(): readv() rc: %ld  sz: %ld\n&quot;, len, tlen);</a>
+<a name="534"><span class="lineNum">     534 </span>            :     printf(&quot;fio_readv(): readv() errno %d\n&quot;, errno);</a>
+<a name="535"><span class="lineNum">     535 </span>            :   }</a>
+<a name="536"><span class="lineNum">     536 </span>            : </a>
+<a name="537"><span class="lineNum">     537 </span>            :   if ((len &lt; 0 &amp;&amp; errno == ENOSYS) ||</a>
+<a name="538"><span class="lineNum">     538 </span>            :       (len != tlen &amp;&amp; errno == EINVAL)) </a>
+<a name="539"><span class="lineNum">     539 </span>            : #endif</a>
+<a name="540"><span class="lineNum">     540 </span>            :   {</a>
+<a name="541"><span class="lineNum">     541 </span>            :     /* XXX this loop doesn't meet the atomicity requirements of</a>
+<a name="542"><span class="lineNum">     542 </span>            :      *     real POSIX readv(), since we don't need that feature </a>
+<a name="543"><span class="lineNum">     543 </span>            :      */</a>
+<a name="544"><span class="lineNum">     544 </span>            :     len = 0; </a>
+<a name="545"><span class="lineNum">     545 </span>            :     for (i=0; i&lt;iovcnt; i++) {</a>
+<a name="546"><span class="lineNum">     546 </span>            :       void *ptr = iov[i].iov_base;</a>
+<a name="547"><span class="lineNum">     547 </span>            :       fio_size_t sz = iov[i].iov_len;</a>
+<a name="548"><span class="lineNum">     548 </span>            :       fio_size_t szleft = sz;</a>
+<a name="549"><span class="lineNum">     549 </span>            :       fio_size_t rc=0;</a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span>            :       for (szleft=sz; szleft &gt; 0; szleft -= rc) {</a>
+<a name="552"><span class="lineNum">     552 </span>            :         rc = read(fd, ((char*) ptr)+(sz-szleft), szleft);</a>
+<a name="553"><span class="lineNum">     553 </span>            :         if (rc == 0) {</a>
+<a name="554"><span class="lineNum">     554 </span>            :           return len;  /* end of file scenario */</a>
+<a name="555"><span class="lineNum">     555 </span>            :         }</a>
+<a name="556"><span class="lineNum">     556 </span>            :         if (rc != szleft) {</a>
+<a name="557"><span class="lineNum">     557 </span>            :           printf(&quot;fio_readv(): read() rc %ld  sz: %ld\n&quot;, rc, szleft);</a>
+<a name="558"><span class="lineNum">     558 </span>            :         }</a>
+<a name="559"><span class="lineNum">     559 </span>            :         if (rc &lt; 0) {</a>
+<a name="560"><span class="lineNum">     560 </span>            :           printf(&quot;fio_readv(): read() rc %ld  sz: %ld\n&quot;, rc, szleft);</a>
+<a name="561"><span class="lineNum">     561 </span>            :           perror(&quot;  perror fio_readv(): &quot;);</a>
+<a name="562"><span class="lineNum">     562 </span>            :           break;</a>
+<a name="563"><span class="lineNum">     563 </span>            :         }</a>
+<a name="564"><span class="lineNum">     564 </span>            :       }</a>
+<a name="565"><span class="lineNum">     565 </span>            :       len += iov[i].iov_len;</a>
+<a name="566"><span class="lineNum">     566 </span>            :     }</a>
+<a name="567"><span class="lineNum">     567 </span>            :   }</a>
+<a name="568"><span class="lineNum">     568 </span>            : #else</a>
+<a name="569"><span class="lineNum">     569 </span>            : #if defined(USE_KERNEL_READV)</a>
+<a name="570"><span class="lineNum">     570 </span>            :   len = readv(fd, iov, iovcnt);</a>
+<a name="571"><span class="lineNum">     571 </span>            :   if (len &lt; 0 &amp;&amp; errno == ENOSYS)</a>
+<a name="572"><span class="lineNum">     572 </span>            : #endif</a>
+<a name="573"><span class="lineNum">     573 </span>            :   {</a>
+<a name="574"><span class="lineNum">     574 </span>            :     /* XXX this loop doesn't meet the atomicity requirements of</a>
+<a name="575"><span class="lineNum">     575 </span>            :      *     real POSIX readv(), since we don't need that feature </a>
+<a name="576"><span class="lineNum">     576 </span>            :      */</a>
+<a name="577"><span class="lineNum">     577 </span>            :     len = 0; </a>
+<a name="578"><span class="lineNum">     578 </span>            :     for (i=0; i&lt;iovcnt; i++) {</a>
+<a name="579"><span class="lineNum">     579 </span>            :       fio_size_t rc = read(fd, iov[i].iov_base, iov[i].iov_len);</a>
+<a name="580"><span class="lineNum">     580 </span>            :       if (rc != iov[i].iov_len)</a>
+<a name="581"><span class="lineNum">     581 </span>            :         break;</a>
+<a name="582"><span class="lineNum">     582 </span>            :       len += iov[i].iov_len;</a>
+<a name="583"><span class="lineNum">     583 </span>            :     }</a>
+<a name="584"><span class="lineNum">     584 </span>            :   }</a>
+<a name="585"><span class="lineNum">     585 </span>            : #endif</a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span>            :   return len;</a>
+<a name="588"><span class="lineNum">     588 </span>            : }</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 : static fio_size_t fio_fwrite(void *ptr, fio_size_t size, </span></a>
+<a name="591"><span class="lineNum">     591 </span>            :                              fio_size_t nitems, fio_fd fd) {</a>
+<a name="592"><span class="lineNum">     592 </span>            :   fio_size_t i;</a>
+<a name="593"><span class="lineNum">     593 </span>            :   fio_size_t len = 0; </a>
+<a name="594"><span class="lineNum">     594 </span>            :   fio_size_t cnt = 0;</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            : #if 1</a>
+<a name="597"><span class="lineNum">     597 </span>            :   /*</a>
+<a name="598"><span class="lineNum">     598 </span>            :    * On Linux individual calls to write() can end up doing short writes when</a>
+<a name="599"><span class="lineNum">     599 </span>            :    * writing more than 2GB in a single write call, even on 64-bit machines.  </a>
+<a name="600"><span class="lineNum">     600 </span>            :    * For large structures, e.g. 240M-atoms or larger, we have to use a loop</a>
+<a name="601"><span class="lineNum">     601 </span>            :    * to continue writing the memory buffer until completion.</a>
+<a name="602"><span class="lineNum">     602 </span>            :    */ </a>
+<a name="603"><span class="lineNum">     603 </span>            :   int writecalls=0;</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;nitems; i++) {</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :     fio_size_t szleft = size;</a>
+<a name="606"><span class="lineNum">     606 </span>            :     fio_size_t rc = 0;</a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :     for (szleft=size; szleft &gt; 0; szleft -= rc) {</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :       fio_size_t writesz = szleft;</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            : #if 0</a>
+<a name="611"><span class="lineNum">     611 </span>            :       /* On some kernel versions write calls beyond 2GB may not do */</a>
+<a name="612"><span class="lineNum">     612 </span>            :       /* a partial write and may just return an error immediately. */</a>
+<a name="613"><span class="lineNum">     613 </span>            :       /* Clamp maximum write size to 1GB per write call.           */</a>
+<a name="614"><span class="lineNum">     614 </span>            :       if (writesz &gt; (1024L * 1024L * 1024L))</a>
+<a name="615"><span class="lineNum">     615 </span>            :         writesz = (1024L * 1024L * 1024L);</a>
+<a name="616"><span class="lineNum">     616 </span>            : #endif</a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :       writecalls++;</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :       rc = write(fd, ((char*) ptr)+(size-szleft), writesz);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :       if (rc &lt; 0) {</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :         printf(&quot;fio_fwrite(): rc %ld  sz: %ld  szleft: %ld  calls: %d\n&quot;, </a>
+<a name="622"><span class="lineNum">     622 </span>            :                rc, size, szleft, writecalls);</a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineNoCov">          0 :         perror(&quot;  perror fio_fwrite(): &quot;);</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineNoCov">          0 :         return cnt;</span></a>
+<a name="625"><span class="lineNum">     625 </span>            :       }</a>
+<a name="626"><span class="lineNum">     626 </span>            :     }</a>
+<a name="627"><span class="lineNum">     627 </span>            :     len += rc;</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :     cnt++;</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :   }</a>
+<a name="630"><span class="lineNum">     630 </span>            : #else</a>
+<a name="631"><span class="lineNum">     631 </span>            :   for (i=0; i&lt;nitems; i++) {</a>
+<a name="632"><span class="lineNum">     632 </span>            :     fio_size_t rc = write(fd, ptr, size);</a>
+<a name="633"><span class="lineNum">     633 </span>            :     if (rc != size) {</a>
+<a name="634"><span class="lineNum">     634 </span>            :       printf(&quot;fio_fwrite(): rc %ld  sz: %ld\n&quot;, rc, size);</a>
+<a name="635"><span class="lineNum">     635 </span>            :       perror(&quot;  perror fio_fwrite(): &quot;);</a>
+<a name="636"><span class="lineNum">     636 </span>            :       break;</a>
+<a name="637"><span class="lineNum">     637 </span>            :     }</a>
+<a name="638"><span class="lineNum">     638 </span>            :     len += rc;</a>
+<a name="639"><span class="lineNum">     639 </span>            :     cnt++;</a>
+<a name="640"><span class="lineNum">     640 </span>            :   }</a>
+<a name="641"><span class="lineNum">     641 </span>            : #endif</a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span>            :   return cnt;</a>
+<a name="644"><span class="lineNum">     644 </span>            : }</a>
+<a name="645"><span class="lineNum">     645 </span>            : </a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">          2 : static fio_size_t fio_fseek(fio_fd fd, fio_size_t offset, int whence) {</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          2 :  if (lseek(fd, offset, whence) &gt;= 0)</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :    return 0;  /* success (emulate behavior of fseek) */</a>
+<a name="649"><span class="lineNum">     649 </span>            :  else </a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineNoCov">          0 :    return -1; /* failure (emulate behavior of fseek) */</span></a>
+<a name="651"><span class="lineNum">     651 </span>            : }</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">          1 : static fio_size_t fio_ftell(fio_fd fd) {</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">          1 :   return lseek(fd, 0, SEEK_CUR);</span></a>
+<a name="655"><span class="lineNum">     655 </span>            : }</a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            : }</a>
+<a name="658"><span class="lineNum">     658 </span>            : }</a>
+<a name="659"><span class="lineNum">     659 </span>            : </a>
+<a name="660"><span class="lineNum">     660 </span>            : #endif</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span>            : namespace PLMD{</a>
+<a name="663"><span class="lineNum">     663 </span>            : namespace molfile{</a>
+<a name="664"><span class="lineNum">     664 </span>            : </a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span>            : /* higher level routines that are OS independent */</a>
+<a name="667"><span class="lineNum">     667 </span>            : </a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 : static int fio_write_int32(fio_fd fd, int i) {</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :   return (fio_fwrite(&amp;i, 4, 1, fd) != 1);</span></a>
+<a name="670"><span class="lineNum">     670 </span>            : }</a>
+<a name="671"><span class="lineNum">     671 </span>            : </a>
+<a name="672"><span class="lineNum">     672 </span>            : static int fio_read_int32(fio_fd fd, int *i) {</a>
+<a name="673"><span class="lineNum">     673 </span>            :   return (fio_fread(i, 4, 1, fd) != 1);</a>
+<a name="674"><span class="lineNum">     674 </span>            : }</a>
+<a name="675"><span class="lineNum">     675 </span>            : </a>
+<a name="676"><span class="lineNum">     676 </span>            : static int fio_write_str(fio_fd fd, const char *str) {</a>
+<a name="677"><span class="lineNum">     677 </span>            :   int len = strlen(str);</a>
+<a name="678"><span class="lineNum">     678 </span>            :   return (fio_fwrite((void *) str, len, 1, fd) != 1);</a>
+<a name="679"><span class="lineNum">     679 </span>            : }</a>
+<a name="680"><span class="lineNum">     680 </span>            : </a>
+<a name="681"><span class="lineNum">     681 </span>            : }</a>
+<a name="682"><span class="lineNum">     682 </span>            : }</a>
+<a name="683"><span class="lineNum">     683 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/gromacsplugin.cpp.func-sort-c.html b/coverage-libs/molfile/gromacsplugin.cpp.func-sort-c.html
new file mode 100644
index 0000000000..56a702067a
--- /dev/null
+++ b/coverage-libs/molfile/gromacsplugin.cpp.func-sort-c.html
@@ -0,0 +1,164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/gromacsplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - gromacsplugin.cpp<span style="font-size: 80%;"> (<a href="gromacsplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntry">360</td>
+            <td class="headerCovTableEntryLo">29.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">21.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="gromacsplugin.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#779">_ZN4PLMD7molfile26molfile_gromacsplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#304">_ZN4PLMD7molfileL13open_g96_readEPKcS2_Pi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#107">_ZN4PLMD7molfileL13open_gro_readEPKcS2_Pi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#463">_ZN4PLMD7molfileL14close_g96_readEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#204">_ZN4PLMD7molfileL14close_gro_readEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#212">_ZN4PLMD7molfileL14open_gro_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#559">_ZN4PLMD7molfileL14open_trr_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#295">_ZN4PLMD7molfileL15close_gro_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#661">_ZN4PLMD7molfileL15close_trr_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#439">_ZN4PLMD7molfileL17read_g96_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#181">_ZN4PLMD7molfileL17read_gro_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#354">_ZN4PLMD7molfileL18read_g96_structureEPvPiPNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#141">_ZN4PLMD7molfileL18read_gro_structureEPvPiPNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#247">_ZN4PLMD7molfileL18write_gro_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#592">_ZN4PLMD7molfileL18write_trr_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#236">_ZN4PLMD7molfileL19write_gro_structureEPviPKNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#175">_ZN4PLMD7molfileL26read_gro_molecule_metadataEPvPPNS0_18molfile_metadata_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#87">_ZN4PLMD7molfileL27convert_vmd_box_for_writingEPKNS0_18molfile_timestep_tEPfS4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#474">_ZN4PLMD7molfileL13open_trr_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#552">_ZN4PLMD7molfileL14close_trr_readEPv</a></td>
+              <td class="coverFnHi">195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#681">_ZN4PLMD7molfile26molfile_gromacsplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#770">_ZN4PLMD7molfile30molfile_gromacsplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#511">_ZN4PLMD7molfileL17read_trr_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">18452</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/gromacsplugin.cpp.func.html b/coverage-libs/molfile/gromacsplugin.cpp.func.html
new file mode 100644
index 0000000000..f3e31b7cdd
--- /dev/null
+++ b/coverage-libs/molfile/gromacsplugin.cpp.func.html
@@ -0,0 +1,164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/gromacsplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - gromacsplugin.cpp<span style="font-size: 80%;"> (<a href="gromacsplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntry">360</td>
+            <td class="headerCovTableEntryLo">29.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">21.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="gromacsplugin.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#779">_ZN4PLMD7molfile26molfile_gromacsplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#681">_ZN4PLMD7molfile26molfile_gromacsplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#770">_ZN4PLMD7molfile30molfile_gromacsplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#304">_ZN4PLMD7molfileL13open_g96_readEPKcS2_Pi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#107">_ZN4PLMD7molfileL13open_gro_readEPKcS2_Pi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#474">_ZN4PLMD7molfileL13open_trr_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#463">_ZN4PLMD7molfileL14close_g96_readEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#204">_ZN4PLMD7molfileL14close_gro_readEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#552">_ZN4PLMD7molfileL14close_trr_readEPv</a></td>
+              <td class="coverFnHi">195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#212">_ZN4PLMD7molfileL14open_gro_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#559">_ZN4PLMD7molfileL14open_trr_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#295">_ZN4PLMD7molfileL15close_gro_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#661">_ZN4PLMD7molfileL15close_trr_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#439">_ZN4PLMD7molfileL17read_g96_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#181">_ZN4PLMD7molfileL17read_gro_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#511">_ZN4PLMD7molfileL17read_trr_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">18452</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#354">_ZN4PLMD7molfileL18read_g96_structureEPvPiPNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#141">_ZN4PLMD7molfileL18read_gro_structureEPvPiPNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#247">_ZN4PLMD7molfileL18write_gro_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#592">_ZN4PLMD7molfileL18write_trr_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#236">_ZN4PLMD7molfileL19write_gro_structureEPviPKNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#175">_ZN4PLMD7molfileL26read_gro_molecule_metadataEPvPPNS0_18molfile_metadata_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="gromacsplugin.cpp.gcov.html#87">_ZN4PLMD7molfileL27convert_vmd_box_for_writingEPKNS0_18molfile_timestep_tEPfS4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/gromacsplugin.cpp.gcov.html b/coverage-libs/molfile/gromacsplugin.cpp.gcov.html
new file mode 100644
index 0000000000..0bdd89cd49
--- /dev/null
+++ b/coverage-libs/molfile/gromacsplugin.cpp.gcov.html
@@ -0,0 +1,936 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/gromacsplugin.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - gromacsplugin.cpp<span style="font-size: 80%;"> (source / <a href="gromacsplugin.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntry">360</td>
+            <td class="headerCovTableEntryLo">29.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">21.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #if defined(__PLUMED_HAS_MOLFILE_PLUGINS) &amp;&amp; ! defined(__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS)</a>
+<a name="38"><span class="lineNum">      38 </span>            : /***************************************************************************</a>
+<a name="39"><span class="lineNum">      39 </span>            :  *cr</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr                        University of Illinois</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                         All Rights Reserved</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr</a>
+<a name="44"><span class="lineNum">      44 </span>            :  ***************************************************************************/</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : /***************************************************************************</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * RCS INFORMATION:</a>
+<a name="48"><span class="lineNum">      48 </span>            :  *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *      $RCSfile: gromacsplugin.C,v $</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $Revision: 1.54 $       $Date: 2017/05/20 05:37:53 $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  ***************************************************************************/</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : #include &quot;largefiles.h&quot;   /* platform dependent 64-bit file I/O defines */</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &lt;math.h&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="59"><span class="lineNum">      59 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="60"><span class="lineNum">      60 </span>            : #include &lt;string.h&gt;</a>
+<a name="61"><span class="lineNum">      61 </span>            : #include &lt;ctype.h&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &quot;Gromacs.h&quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            : #include &quot;molfile_plugin.h&quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : #if defined(_AIX)</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &lt;strings.h&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #endif</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace PLMD{</a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace molfile{</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : #ifndef M_PI</a>
+<a name="73"><span class="lineNum">      73 </span>            : #define M_PI           3.14159265358979323846</a>
+<a name="74"><span class="lineNum">      74 </span>            : #endif</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : #if defined(WIN32) || defined(WIN64)</a>
+<a name="77"><span class="lineNum">      77 </span>            : #define strcasecmp stricmp</a>
+<a name="78"><span class="lineNum">      78 </span>            : #endif</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : typedef struct {</a>
+<a name="81"><span class="lineNum">      81 </span>            :   md_file *mf;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   int natoms;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   int step;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   float timeval;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   molfile_atom_t *atomlist;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   molfile_metadata_t *meta;</a>
+<a name="87"><span class="lineNum">      87 </span>            : } gmxdata;</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 : static void convert_vmd_box_for_writing(const molfile_timestep_t *ts, float *x, float *y, float *z)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : {</a>
+<a name="91"><span class="lineNum">      91 </span>            : //     const float sa = sin((double)ts-&gt;alpha/180.0*M_PI);</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     const float ca = cos((double)ts-&gt;alpha/180.0*M_PI);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     const float cb = cos((double)ts-&gt;beta/180.0*M_PI);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     const float cg = cos((double)ts-&gt;gamma/180.0*M_PI);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     const float sg = sin((double)ts-&gt;gamma/180.0*M_PI);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     x[0] = ts-&gt;A / ANGS_PER_NM;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     y[0] = 0.0;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     z[0] = 0.0;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     x[1] = ts-&gt;B*cg / ANGS_PER_NM; // ts-&gt;B*ca when writing trr?!</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :     y[1] = ts-&gt;B*sg / ANGS_PER_NM; // ts-&gt;B*sa when writing trr?!</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :     z[1] = 0.0;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     x[2] = ts-&gt;C*cb / ANGS_PER_NM;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     y[2] = (ts-&gt;C / ANGS_PER_NM)*(ca - cb*cg)/sg;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     z[2] = (ts-&gt;C / ANGS_PER_NM)*sqrt((double)(1.0 + 2.0*ca*cb*cg</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :                                - ca*ca - cb*cb - cg*cg)/(1.0 - cg*cg));</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 : static void *open_gro_read(const char *filename, const char *,</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     int *natoms) {</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :     md_file *mf;</a>
+<a name="113"><span class="lineNum">     113 </span>            :     md_header mdh;</a>
+<a name="114"><span class="lineNum">     114 </span>            :     gmxdata *gmx;</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     mf = mdio_open(filename, MDFMT_GRO);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     if (!mf) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot open file '%s', %s\n&quot;,</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :     // read in the header data (careful not to rewind!)</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     if (gro_header(mf, mdh.title, MAX_MDIO_TITLE,</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     &amp;mdh.timeval, &amp;mdh.natoms, 0) &lt; 0) {</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot read header fromm '%s', %s\n&quot;,</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="128"><span class="lineNum">     128 </span>            :             // XXX should free the file handle...</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :     }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     *natoms = mdh.natoms;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     gmx = new gmxdata;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     memset(gmx,0,sizeof(gmxdata));</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     gmx-&gt;mf = mf;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     gmx-&gt;natoms = mdh.natoms;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     gmx-&gt;meta = new molfile_metadata_t;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     memset(gmx-&gt;meta,0,sizeof(molfile_metadata_t));</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     strncpy(gmx-&gt;meta-&gt;title, mdh.title, 80);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     gmx-&gt;timeval = mdh.timeval;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     return gmx;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : static int read_gro_structure(void *mydata, int *optflags,</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     molfile_atom_t *atoms) {</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   md_atom ma;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   char buf[MAX_GRO_LINE + 1];</a>
+<a name="148"><span class="lineNum">     148 </span>            :   gmxdata *gmx = (gmxdata *)mydata;</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   *optflags = MOLFILE_NOOPTIONS; // no optional data</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   // read in each atom and add it into the molecule</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   for (int i = 0; i &lt; gmx-&gt;natoms; i++) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :     molfile_atom_t *atom = atoms+i;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     if (gro_rec(gmx-&gt;mf, &amp;ma) &lt; 0) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :       fprintf(stderr, &quot;gromacsplugin) Error reading atom %d from file, %s\n&quot;,</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :               i+1, mdio_errmsg(mdio_errno()));</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     strcpy(atom-&gt;name, ma.atomname);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     strcpy(atom-&gt;type, ma.atomname);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     strcpy(atom-&gt;resname, ma.resname);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     atom-&gt;resid = atoi(ma.resid);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     atom-&gt;chain[0] = '\0';</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     atom-&gt;segid[0] = '\0';</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :   if (mdio_readline(gmx-&gt;mf, buf, MAX_GRO_LINE + 1, 0) &lt; 0) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;gromacsplugin) Warning, error reading box, %s\n&quot;,</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :             mdio_errmsg(mdio_errno()));</a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   rewind(gmx-&gt;mf-&gt;f);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 : static int read_gro_molecule_metadata(void *v, molfile_metadata_t **metadata) {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   *metadata = gmx-&gt;meta;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 : static int read_gro_timestep(void *v, int natoms, molfile_timestep_t *ts) {</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   md_ts mdts;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   memset(&amp;mdts, 0, sizeof(md_ts));</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   mdts.natoms = natoms;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   if (mdio_timestep(gmx-&gt;mf, &amp;mdts) &lt; 0)</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :     return MOLFILE_ERROR;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :   if (ts) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     memcpy(ts-&gt;coords, mdts.pos, 3 * sizeof(float) * gmx-&gt;natoms);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     if (mdts.box) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :       ts-&gt;A = mdts.box-&gt;A;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :       ts-&gt;B = mdts.box-&gt;B;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       ts-&gt;C = mdts.box-&gt;C;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :       ts-&gt;alpha = mdts.box-&gt;alpha;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :       ts-&gt;beta = mdts.box-&gt;beta;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :       ts-&gt;gamma = mdts.box-&gt;gamma;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   mdio_tsfree(&amp;mdts);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 : static void close_gro_read(void *v) {</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :   mdio_close(gmx-&gt;mf);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :   delete gmx-&gt;meta;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   delete gmx;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : // open file for writing</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 : static void *open_gro_write(const char *filename, const char *filetype,</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :     int natoms) {</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :     md_file *mf;</a>
+<a name="218"><span class="lineNum">     218 </span>            :     gmxdata *gmx;</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :     mf = mdio_open(filename, MDFMT_GRO, MDIO_WRITE);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     if (!mf) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot open file '%s', %s\n&quot;,</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     gmx = new gmxdata;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     memset(gmx,0,sizeof(gmxdata));</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     gmx-&gt;mf = mf;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     gmx-&gt;natoms = natoms;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     gmx-&gt;step   = 0;</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     gmx-&gt;meta = new molfile_metadata_t;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     memset(gmx-&gt;meta,0,sizeof(molfile_metadata_t));</a>
+<a name="233"><span class="lineNum">     233 </span>            :     gmx-&gt;meta-&gt;title[0] = '\0';</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :     return gmx;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 : static int write_gro_structure(void *v, int optflags,</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :     const molfile_atom_t *atoms) {</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :   int natoms = gmx-&gt;natoms;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   gmx-&gt;atomlist = (molfile_atom_t *)malloc(natoms*sizeof(molfile_atom_t));</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   memcpy(gmx-&gt;atomlist, atoms, natoms*sizeof(molfile_atom_t));</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 : static int write_gro_timestep(void *v, const molfile_timestep_t *ts) {</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="251"><span class="lineNum">     251 </span>            :   const molfile_atom_t *atom;</a>
+<a name="252"><span class="lineNum">     252 </span>            :   const float *pos, *vel;</a>
+<a name="253"><span class="lineNum">     253 </span>            :   float x[3], y[3], z[3];</a>
+<a name="254"><span class="lineNum">     254 </span>            :   int i;</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   if (gmx-&gt;natoms == 0)</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :     return MOLFILE_SUCCESS;</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :   atom = gmx-&gt;atomlist;</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :   pos = ts-&gt;coords;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   vel = ts-&gt;velocities;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   /* The title cannot be written */</a>
+<a name="264"><span class="lineNum">     264 </span>            : /*  fprintf(gmx-&gt;mf-&gt;f, &quot;%s&quot;, gmx-&gt;meta-&gt;title);*/</a>
+<a name="265"><span class="lineNum">     265 </span>            :   /* Write a dummy title instead */</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :   fprintf(gmx-&gt;mf-&gt;f, &quot;generated by VMD&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : #if vmdplugin_ABIVERSION &gt; 10</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :   fprintf(gmx-&gt;mf-&gt;f, &quot;, t= %f&quot;, ts-&gt;physical_time);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : #endif</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :   fprintf(gmx-&gt;mf-&gt;f, &quot;\n&quot;);</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :   fprintf(gmx-&gt;mf-&gt;f, &quot;%d\n&quot;, gmx-&gt;natoms);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;gmx-&gt;natoms; i++)</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :   {</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :      fprintf(gmx-&gt;mf-&gt;f, &quot;%5d%-5s%5s%5d%8.3f%8.3f%8.3f&quot;,</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :              atom-&gt;resid, atom-&gt;resname, atom-&gt;name,</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :              (i+1) % 100000, // GRO format only supports indices up to 99999</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :                              // but since GROMACS ignores indices, modular</a>
+<a name="279"><span class="lineNum">     279 </span>            :                              // arithmetic prevents formatting problems for </a>
+<a name="280"><span class="lineNum">     280 </span>            :                              // very large structures</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :              pos[0] / ANGS_PER_NM, pos[1] / ANGS_PER_NM, pos[2] / ANGS_PER_NM);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :      if(vel)</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :      {</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :          fprintf(gmx-&gt;mf-&gt;f, &quot;%8.4f%8.4f%8.4f&quot;, vel[0] / ANGS_PER_NM, vel[1] / ANGS_PER_NM, vel[2] / ANGS_PER_NM);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :          vel += 3;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :      }</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :      fprintf(gmx-&gt;mf-&gt;f, &quot;\n&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :      ++atom;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :      pos += 3;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   convert_vmd_box_for_writing(ts, x, y, z);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   fprintf(gmx-&gt;mf-&gt;f, &quot;%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f%10.5f\n&quot;, x[0], y[1], z[2], y[0], z[0], x[1], z[1], x[2], y[2]);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 : static void close_gro_write(void *v) {</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :   mdio_close(gmx-&gt;mf);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   free(gmx-&gt;atomlist);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :   delete gmx-&gt;meta;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :   delete gmx;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 : static void *open_g96_read(const char *filename, const char *,</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :     int *natoms) {</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :     md_file *mf;</a>
+<a name="310"><span class="lineNum">     310 </span>            :     md_header mdh;</a>
+<a name="311"><span class="lineNum">     311 </span>            :     char gbuf[MAX_G96_LINE + 1];</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     mf = mdio_open(filename, MDFMT_G96);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :     if (!mf) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot open file '%s', %s\n&quot;,</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :         // read in the header data</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :         if (g96_header(mf, mdh.title, MAX_MDIO_TITLE, &amp;mdh.timeval) &lt; 0) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :             fprintf(stderr, &quot;gromacsplugin) Cannot read header from '%s', %s\n&quot;,</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :                     filename, mdio_errmsg(mdio_errno()));</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :             return NULL;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :         }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            :         // First, look for a timestep block</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :         if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :             fprintf(stderr, &quot;gromacsplugin) Cannot read header from '%s', %s\n&quot;,</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :                     filename, mdio_errmsg(mdio_errno()));</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :             return NULL;</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :         }</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :         if (!strcasecmp(gbuf, &quot;TIMESTEP&quot;)) {</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :             // Read in the value line and the END line, and the next</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :             if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0 ||</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :                 mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0 ||</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :                 mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :               fprintf(stderr, &quot;gromacsplugin) Cannot read header from '%s', %s\n&quot;,</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :                       filename, mdio_errmsg(mdio_errno()));</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :               return NULL;</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :             }</a>
+<a name="342"><span class="lineNum">     342 </span>            :         }</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :         if (strcasecmp(gbuf, &quot;POSITION&quot;) &amp;&amp; strcasecmp(gbuf, &quot;REFPOSITION&quot;)) {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :           fprintf(stderr, &quot;gromacsplugin) No structure information in file %s\n&quot;, filename);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :           return NULL;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :         }</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :         *natoms = g96_countatoms(mf);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :         gmxdata *gmx = new gmxdata;</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :         memset(gmx,0,sizeof(gmxdata));</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :         gmx-&gt;mf = mf;</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :         gmx-&gt;natoms = *natoms; </span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :         return gmx;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 : static int read_g96_structure(void *mydata, int *optflags,</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :     molfile_atom_t *atoms) {</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            :     char gbuf[MAX_G96_LINE + 1];</a>
+<a name="360"><span class="lineNum">     360 </span>            :     gmxdata *gmx = (gmxdata *)mydata;</a>
+<a name="361"><span class="lineNum">     361 </span>            :     md_atom ma;</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :     md_file *mf = gmx-&gt;mf;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :     *optflags = MOLFILE_NOOPTIONS; // no optional data</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :         for (int i = 0; i &lt; gmx-&gt;natoms; i++) {</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :             molfile_atom_t *atom = atoms+i;</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :             if (g96_rec(mf, &amp;ma) &lt; 0) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :                 fprintf(stderr, &quot;gromacsplugin) Error reading atom %d from file, %s\n&quot;,</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :                   i+1, mdio_errmsg(mdio_errno()));</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :                 return MOLFILE_ERROR;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :             }</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :             strcpy(atom-&gt;name, ma.atomname);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :             strcpy(atom-&gt;type, ma.atomname);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :             strcpy(atom-&gt;resname, ma.resname);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :             atom-&gt;resid = atoi(ma.resid);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :             atom-&gt;chain[0] = '\0';</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :             atom-&gt;segid[0] = '\0';</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :         }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :         if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :             fprintf(stderr, &quot;gromacsplugin) Warning, error reading END record, %s\n&quot;,</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :                 mdio_errmsg(mdio_errno()));</a>
+<a name="384"><span class="lineNum">     384 </span>            :         }</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            :             // ... another problem: there may or may not be a VELOCITY</a>
+<a name="387"><span class="lineNum">     387 </span>            :             // block or a BOX block, so we need to read one line beyond</a>
+<a name="388"><span class="lineNum">     388 </span>            :             // the POSITION block to determine this. If neither VEL. nor</a>
+<a name="389"><span class="lineNum">     389 </span>            :             // BOX are present we've read a line too far and infringed</a>
+<a name="390"><span class="lineNum">     390 </span>            :             // on the next timestep, so we need to keep track of the</a>
+<a name="391"><span class="lineNum">     391 </span>            :             // position now for a possible fseek() later to backtrack.</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :             long fpos = ftell(mf-&gt;f);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            :             // Now we must read in the velocities and the box, if present</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :             if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &gt;= 0) {</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :                 // Is there a velocity block present ?</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :                 if (!strcasecmp(gbuf, &quot;VELOCITY&quot;) || !strcasecmp(gbuf, &quot;VELOCITYRED&quot;)) {</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :                         // Ignore all the coordinates - VMD doesn't use them</a>
+<a name="400"><span class="lineNum">     400 </span>            :                         for (;;) {</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :                                 if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :                                         return MOLFILE_ERROR;</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :                                 if (!strcasecmp(gbuf, &quot;END&quot;)) break;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :                         }</a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            :                         // Again, record our position because we may need</a>
+<a name="407"><span class="lineNum">     407 </span>            :                         // to fseek here later if we read too far.</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :                         fpos = ftell(mf-&gt;f);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :                         // Go ahead and read the next line.</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :                         if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :                     return MOLFILE_ERROR;</a>
+<a name="413"><span class="lineNum">     413 </span>            :                 }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            :                 // Is there a box present ?</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :                 if (!strcasecmp(gbuf, &quot;BOX&quot;)) {</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :                         // Ignore the box coordinates at this time.</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :                         if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :                     return MOLFILE_ERROR;</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :                         if (mdio_readline(mf, gbuf, MAX_G96_LINE + 1) &lt; 0)</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :                     return MOLFILE_ERROR;</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :                         if (strcasecmp(gbuf, &quot;END&quot;))</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :                     return MOLFILE_ERROR;</a>
+<a name="424"><span class="lineNum">     424 </span>            :                 }</a>
+<a name="425"><span class="lineNum">     425 </span>            :                 else {</a>
+<a name="426"><span class="lineNum">     426 </span>            :                         // We have read too far, so fseek back to the</a>
+<a name="427"><span class="lineNum">     427 </span>            :                         // last known safe position so we don't return</a>
+<a name="428"><span class="lineNum">     428 </span>            :                         // with the file pointer set infringing on the</a>
+<a name="429"><span class="lineNum">     429 </span>            :                         // next timestep data.</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :                         fseek(mf-&gt;f, fpos, SEEK_SET);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :                 }</a>
+<a name="432"><span class="lineNum">     432 </span>            :         }</a>
+<a name="433"><span class="lineNum">     433 </span>            :         else {</a>
+<a name="434"><span class="lineNum">     434 </span>            :             // Go ahead and rewind for good measure</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :             fseek(mf-&gt;f, fpos, SEEK_SET);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :         }</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :         rewind(mf-&gt;f);</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :         return MOLFILE_SUCCESS;</a>
+<a name="439"><span class="lineNum">     439 </span>            : }</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 : static int read_g96_timestep(void *v, int natoms, molfile_timestep_t *ts) {</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="444"><span class="lineNum">     444 </span>            :   md_ts mdts;</a>
+<a name="445"><span class="lineNum">     445 </span>            :   memset(&amp;mdts, 0, sizeof(md_ts));</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :   mdts.natoms = natoms;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :   if (mdio_timestep(gmx-&gt;mf, &amp;mdts) &lt; 0)</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :     return MOLFILE_ERROR;</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :   if (ts) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :     memcpy(ts-&gt;coords, mdts.pos, 3 * sizeof(float) * gmx-&gt;natoms);</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :     if (mdts.box) {</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :       ts-&gt;A = mdts.box-&gt;A;</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :       ts-&gt;B = mdts.box-&gt;B;</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :       ts-&gt;C = mdts.box-&gt;C;</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :       ts-&gt;alpha = mdts.box-&gt;alpha;</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :       ts-&gt;beta = mdts.box-&gt;beta;</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 :       ts-&gt;gamma = mdts.box-&gt;gamma;</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :     }</a>
+<a name="460"><span class="lineNum">     460 </span>            :   }</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :   mdio_tsfree(&amp;mdts);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="463"><span class="lineNum">     463 </span>            : }</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 : static void close_g96_read(void *v) {</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :   mdio_close(gmx-&gt;mf);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :   delete gmx;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            : //</a>
+<a name="473"><span class="lineNum">     473 </span>            : // TRR and XTC files</a>
+<a name="474"><span class="lineNum">     474 </span>            : //</a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">        195 : static void *open_trr_read(const char *filename, const char *filetype,</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :     int *natoms) {</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            :     md_file *mf;</a>
+<a name="480"><span class="lineNum">     480 </span>            :     md_header mdh;</a>
+<a name="481"><span class="lineNum">     481 </span>            :     gmxdata *gmx;</a>
+<a name="482"><span class="lineNum">     482 </span>            :     int format;</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        195 :     if (!strcmp(filetype, &quot;trr&quot;))</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :       format = MDFMT_TRR;</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">        190 :     else if (!strcmp(filetype, &quot;trj&quot;))</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :       format = MDFMT_TRJ;</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">        190 :     else if (!strcmp(filetype, &quot;xtc&quot;))</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :       format = MDFMT_XTC;</a>
+<a name="490"><span class="lineNum">     490 </span>            :     else</a>
+<a name="491"><span class="lineNum">     491 </span>            :       return NULL;</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        195 :     mf = mdio_open(filename, format);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        195 :     if (!mf) {</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot open file '%s', %s\n&quot;,</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :     }</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        195 :     if (mdio_header(mf, &amp;mdh) &lt; 0) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :         mdio_close(mf);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot read header fromm '%s', %s\n&quot;,</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :     }</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        195 :     *natoms = mdh.natoms;</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        195 :     gmx = new gmxdata;</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :     memset(gmx,0,sizeof(gmxdata));</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">        195 :     gmx-&gt;mf = mf;</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">        195 :     gmx-&gt;natoms = mdh.natoms;</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">        195 :     return gmx;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            : }</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">      18452 : static int read_trr_timestep(void *v, int natoms, molfile_timestep_t *ts) {</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="515"><span class="lineNum">     515 </span>            :   md_ts mdts;</a>
+<a name="516"><span class="lineNum">     516 </span>            :   memset(&amp;mdts, 0, sizeof(md_ts));</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">      18452 :   mdts.natoms = natoms;</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">      18452 :   if (mdio_timestep(gmx-&gt;mf, &amp;mdts) &lt; 0) {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">        195 :     if (mdio_errno() == MDIO_EOF || mdio_errno() == MDIO_IOERROR) {</span></a>
+<a name="521"><span class="lineNum">     521 </span>            :       // XXX Lame, why does mdio treat IOERROR like EOF?</a>
+<a name="522"><span class="lineNum">     522 </span>            :       return MOLFILE_ERROR;</a>
+<a name="523"><span class="lineNum">     523 </span>            :     }</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;gromacsplugin) Error reading timestep, %s\n&quot;,</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :             mdio_errmsg(mdio_errno()));</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :     return MOLFILE_ERROR;</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :   }</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">      18257 :   if (mdts.natoms != gmx-&gt;natoms) {</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;gromacsplugin) Timestep in file contains wrong number of atoms\n&quot;);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;gromacsplugin) Found %d, expected %d\n&quot;, mdts.natoms, gmx-&gt;natoms);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :     mdio_tsfree(&amp;mdts);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :     return MOLFILE_ERROR;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">      18257 :   if (ts) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">      18257 :     if (mdts.pos) </span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">      18257 :       memcpy(ts-&gt;coords, mdts.pos, 3 * sizeof(float) * gmx-&gt;natoms);</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :     else </a>
+<a name="539"><span class="lineNum">     539 </span>            :       printf(&quot;gromacsplugin) Warning: skipping empty timestep!\n&quot;);</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">      18257 :     if (mdts.box) {</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">      18257 :       ts-&gt;A = mdts.box-&gt;A;</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">      18257 :       ts-&gt;B = mdts.box-&gt;B;</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">      18257 :       ts-&gt;C = mdts.box-&gt;C;</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">      18257 :       ts-&gt;alpha = mdts.box-&gt;alpha;</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">      18257 :       ts-&gt;beta = mdts.box-&gt;beta;</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">      18257 :       ts-&gt;gamma = mdts.box-&gt;gamma;</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :     }</a>
+<a name="549"><span class="lineNum">     549 </span>            :   }</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">      18257 :   mdio_tsfree(&amp;mdts);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">      18257 :   return MOLFILE_SUCCESS;</span></a>
+<a name="552"><span class="lineNum">     552 </span>            : }</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">        195 : static void close_trr_read(void *v) {</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">        195 :   mdio_close(gmx-&gt;mf);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        195 :   delete gmx;</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">        195 : }</span></a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span>            : // open file for writing</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 : static void *open_trr_write(const char *filename, const char *filetype,</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :     int natoms) {</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :     md_file *mf;</a>
+<a name="565"><span class="lineNum">     565 </span>            :     gmxdata *gmx;</a>
+<a name="566"><span class="lineNum">     566 </span>            :     int format;</a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineNoCov">          0 :     if (!strcmp(filetype, &quot;trr&quot;))</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :       format = MDFMT_TRR;</a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :     else if (!strcmp(filetype, &quot;xtc&quot;))</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :       format = MDFMT_XTC;</a>
+<a name="572"><span class="lineNum">     572 </span>            :     else</a>
+<a name="573"><span class="lineNum">     573 </span>            :       return NULL;</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :     mf = mdio_open(filename, format, MDIO_WRITE);</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :     if (!mf) {</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :         fprintf(stderr, &quot;gromacsplugin) Cannot open file '%s', %s\n&quot;,</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :                 filename, mdio_errmsg(mdio_errno()));</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineNoCov">          0 :         return NULL;</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :     }</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :     gmx = new gmxdata;</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :     memset(gmx,0,sizeof(gmxdata));</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :     gmx-&gt;mf = mf;</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineNoCov">          0 :     gmx-&gt;natoms = natoms;</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :     // set some parameters for the output stream:</a>
+<a name="586"><span class="lineNum">     586 </span>            :     // start at step 0, convert to big-endian, write single precision.</a>
+<a name="587"><span class="lineNum">     587 </span>            :     gmx-&gt;step   = 0;</a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :     gmx-&gt;mf-&gt;rev = host_is_little_endian();</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :     gmx-&gt;mf-&gt;prec = sizeof(float);</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :     return gmx;</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : }</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span>            : // write a trr timestep. the file format has a header with each record</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 : static int write_trr_timestep(void *mydata, const molfile_timestep_t *ts)</span></a>
+<a name="595"><span class="lineNum">     595 </span>            : {</a>
+<a name="596"><span class="lineNum">     596 </span>            :   const float nm=0.1;</a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span>            :   gmxdata *gmx = (gmxdata *)mydata;</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span>            :   // determine and write header from structure info.</a>
+<a name="601"><span class="lineNum">     601 </span>            :   // write trr header. XXX: move this to Gromacs.h ??</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :   if (gmx-&gt;mf-&gt;fmt == MDFMT_TRR) {</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :     int i;</a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 :     if ( put_trx_int(gmx-&gt;mf, TRX_MAGIC)            // ID</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :          || put_trx_string(gmx-&gt;mf, &quot;GMX_trn_file&quot;) // version</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // ir_size (ignored)</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // e_size (ignored)</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 9*sizeof(float))   // box</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // vir_size (ignored)</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // pres_size (ignored)</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // top_size (ignored)</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // sym_size (ignored)</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 3*sizeof(float)*gmx-&gt;natoms) // coordinates</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // no velocities</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // no forces</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, gmx-&gt;natoms)       // number of atoms</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, gmx-&gt;step)         // current step number</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :          || put_trx_int(gmx-&gt;mf, 0)                 // nre (ignored)</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :          || put_trx_real(gmx-&gt;mf, 0.1*gmx-&gt;step)    // current time. (dummy value: 0.1)</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :          || put_trx_real(gmx-&gt;mf, 0.0))             // current lambda</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            :     // set up box according to the VMD unitcell conventions.</a>
+<a name="625"><span class="lineNum">     625 </span>            :     // the a-vector is collinear with the x-axis and</a>
+<a name="626"><span class="lineNum">     626 </span>            :     // the b-vector is in the xy-plane.</a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :     const float sa = sin((double)ts-&gt;alpha/180.0*M_PI);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :     const float ca = cos((double)ts-&gt;alpha/180.0*M_PI);</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :     const float cb = cos((double)ts-&gt;beta/180.0*M_PI);</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :     const float cg = cos((double)ts-&gt;gamma/180.0*M_PI);</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :     const float sg = sin((double)ts-&gt;gamma/180.0*M_PI);</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :     float box[9];</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineNoCov">          0 :     box[0] = ts-&gt;A;    box[1] = 0.0;      box[2] = 0.0;</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :     box[3] = ts-&gt;B*ca; box[4] = ts-&gt;B*sa; box[5] = 0.0;</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineNoCov">          0 :     box[6] = ts-&gt;C*cb; box[7] = ts-&gt;C*(ca - cb*cg)/sg;</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :     box[8] = ts-&gt;C*sqrt((double)(1.0 + 2.0*ca*cb*cg</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :                                  - ca*ca - cb*cb - cg*cg)/(1.0 - cg*cg));</span></a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;9; ++i) {</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :       if (put_trx_real(gmx-&gt;mf, box[i]*nm))</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :         return MOLFILE_ERROR;</a>
+<a name="642"><span class="lineNum">     642 </span>            :     }</a>
+<a name="643"><span class="lineNum">     643 </span>            : #ifdef TEST_TRR_PLUGIN</a>
+<a name="644"><span class="lineNum">     644 </span>            :     fprintf(stderr, &quot;gromacsplugin) box is:\n %f %f %f\n %f %f %f\n %f %f %f\n\n&quot;,</a>
+<a name="645"><span class="lineNum">     645 </span>            :             box[0], box[1], box[2], box[3], box[4], box[5], box[6], box[7], box[8]);</a>
+<a name="646"><span class="lineNum">     646 </span>            : #endif</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            :     // write coordinates</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;(3*gmx-&gt;natoms); ++i) {</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineNoCov">          0 :       if (put_trx_real(gmx-&gt;mf, ts-&gt;coords[i]*nm))</span></a>
+<a name="651"><span class="lineNum">     651 </span>            :         return MOLFILE_ERROR;</a>
+<a name="652"><span class="lineNum">     652 </span>            :     }</a>
+<a name="653"><span class="lineNum">     653 </span>            :   } else {</a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;gromacsplugin) only .trr is supported for writing\n&quot;);</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineNoCov">          0 :     return MOLFILE_ERROR;</span></a>
+<a name="656"><span class="lineNum">     656 </span>            :   }</a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 :   ++ gmx-&gt;step;</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :   }</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 : static void close_trr_write(void *v) {</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :   gmxdata *gmx = (gmxdata *)v;</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineNoCov">          0 :   mdio_close(gmx-&gt;mf);</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :   delete gmx;</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="668"><span class="lineNum">     668 </span>            : </a>
+<a name="669"><span class="lineNum">     669 </span>            : #define GROMACS_PLUGIN_MAJOR_VERSION 1</a>
+<a name="670"><span class="lineNum">     670 </span>            : #define GROMACS_PLUGIN_MINOR_VERSION 3 </a>
+<a name="671"><span class="lineNum">     671 </span>            : </a>
+<a name="672"><span class="lineNum">     672 </span>            : //</a>
+<a name="673"><span class="lineNum">     673 </span>            : // plugin registration stuff below</a>
+<a name="674"><span class="lineNum">     674 </span>            : //</a>
+<a name="675"><span class="lineNum">     675 </span>            : </a>
+<a name="676"><span class="lineNum">     676 </span>            : static molfile_plugin_t gro_plugin;</a>
+<a name="677"><span class="lineNum">     677 </span>            : static molfile_plugin_t g96_plugin;</a>
+<a name="678"><span class="lineNum">     678 </span>            : static molfile_plugin_t trr_plugin;</a>
+<a name="679"><span class="lineNum">     679 </span>            : static molfile_plugin_t xtc_plugin;</a>
+<a name="680"><span class="lineNum">     680 </span>            : static molfile_plugin_t trj_plugin;</a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span>            : </a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_init() {</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :   // GRO plugin init</a>
+<a name="685"><span class="lineNum">     685 </span>            :   memset(&amp;gro_plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">       8336 :   gro_plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">       8336 :   gro_plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">       8336 :   gro_plugin.name = &quot;gro&quot;;</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">       8336 :   gro_plugin.prettyname = &quot;Gromacs GRO&quot;;</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">       8336 :   gro_plugin.author = &quot;David Norris, Justin Gullingsrud, Magnus Lundborg&quot;;</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">       8336 :   gro_plugin.majorv = GROMACS_PLUGIN_MAJOR_VERSION;</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">       8336 :   gro_plugin.minorv = GROMACS_PLUGIN_MINOR_VERSION;</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :   gro_plugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">       8336 :   gro_plugin.filename_extension = &quot;gro&quot;;</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">       8336 :   gro_plugin.open_file_read = open_gro_read;</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">       8336 :   gro_plugin.read_structure = read_gro_structure;</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">       8336 :   gro_plugin.read_next_timestep = read_gro_timestep;</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">       8336 :   gro_plugin.close_file_read = close_gro_read;</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">       8336 :   gro_plugin.open_file_write = open_gro_write;</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">       8336 :   gro_plugin.write_structure = write_gro_structure;</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">       8336 :   gro_plugin.write_timestep = write_gro_timestep;</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">       8336 :   gro_plugin.close_file_write = close_gro_write;</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">       8336 :   gro_plugin.read_molecule_metadata = read_gro_molecule_metadata;</span></a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span>            :   // G96 plugin init</a>
+<a name="706"><span class="lineNum">     706 </span>            :   memset(&amp;g96_plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">       8336 :   g96_plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">       8336 :   g96_plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">       8336 :   g96_plugin.name = &quot;g96&quot;;</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">       8336 :   g96_plugin.prettyname = &quot;Gromacs g96&quot;;</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">       8336 :   g96_plugin.author = &quot;David Norris, Justin Gullingsrud&quot;;</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">       8336 :   g96_plugin.majorv = GROMACS_PLUGIN_MAJOR_VERSION;</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">       8336 :   g96_plugin.minorv = GROMACS_PLUGIN_MINOR_VERSION;</span></a>
+<a name="714"><span class="lineNum">     714 </span>            :   g96_plugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">       8336 :   g96_plugin.filename_extension = &quot;g96&quot;;</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">       8336 :   g96_plugin.open_file_read = open_g96_read;</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">       8336 :   g96_plugin.read_structure = read_g96_structure;</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">       8336 :   g96_plugin.read_next_timestep = read_g96_timestep;</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">       8336 :   g96_plugin.close_file_read = close_g96_read;</span></a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span>            :   // TRR plugin</a>
+<a name="722"><span class="lineNum">     722 </span>            :   memset(&amp;trr_plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">       8336 :   trr_plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">       8336 :   trr_plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">       8336 :   trr_plugin.name = &quot;trr&quot;;</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">       8336 :   trr_plugin.prettyname = &quot;Gromacs TRR Trajectory&quot;;</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">       8336 :   trr_plugin.author = &quot;David Norris, Justin Gullingsrud, Axel Kohlmeyer&quot;;</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">       8336 :   trr_plugin.majorv = GROMACS_PLUGIN_MAJOR_VERSION;</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">       8336 :   trr_plugin.minorv = GROMACS_PLUGIN_MINOR_VERSION;</span></a>
+<a name="730"><span class="lineNum">     730 </span>            :   trr_plugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;</a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">       8336 :   trr_plugin.filename_extension = &quot;trr&quot;;</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">       8336 :   trr_plugin.open_file_read = open_trr_read;</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">       8336 :   trr_plugin.read_next_timestep = read_trr_timestep;</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">       8336 :   trr_plugin.close_file_read = close_trr_read;</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">       8336 :   trr_plugin.open_file_write = open_trr_write;</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">       8336 :   trr_plugin.write_timestep = write_trr_timestep;</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">       8336 :   trr_plugin.close_file_write = close_trr_write;</span></a>
+<a name="738"><span class="lineNum">     738 </span>            : </a>
+<a name="739"><span class="lineNum">     739 </span>            :   // XTC plugin </a>
+<a name="740"><span class="lineNum">     740 </span>            :   memset(&amp;xtc_plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">       8336 :   xtc_plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">       8336 :   xtc_plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">       8336 :   xtc_plugin.name = &quot;xtc&quot;;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">       8336 :   xtc_plugin.prettyname = &quot;Gromacs XTC Compressed Trajectory&quot;;</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">       8336 :   xtc_plugin.author = &quot;David Norris, Justin Gullingsrud&quot;;</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">       8336 :   xtc_plugin.majorv = GROMACS_PLUGIN_MAJOR_VERSION;</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">       8336 :   xtc_plugin.minorv = GROMACS_PLUGIN_MINOR_VERSION;</span></a>
+<a name="748"><span class="lineNum">     748 </span>            :   xtc_plugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">       8336 :   xtc_plugin.filename_extension = &quot;xtc&quot;;</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">       8336 :   xtc_plugin.open_file_read = open_trr_read;</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">       8336 :   xtc_plugin.read_next_timestep = read_trr_timestep;</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">       8336 :   xtc_plugin.close_file_read = close_trr_read;</span></a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span>            :   // TRJ plugin</a>
+<a name="755"><span class="lineNum">     755 </span>            :   memset(&amp;trj_plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">       8336 :   trj_plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">       8336 :   trj_plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">       8336 :   trj_plugin.name = &quot;trj&quot;;</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">       8336 :   trj_plugin.prettyname = &quot;Gromacs TRJ Trajectory&quot;;</span></a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">       8336 :   trj_plugin.author = &quot;David Norris, Justin Gullingsrud&quot;;</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">       8336 :   trj_plugin.majorv = GROMACS_PLUGIN_MAJOR_VERSION;</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">       8336 :   trj_plugin.minorv = GROMACS_PLUGIN_MINOR_VERSION;</span></a>
+<a name="763"><span class="lineNum">     763 </span>            :   trj_plugin.is_reentrant = VMDPLUGIN_THREADUNSAFE;</a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">       8336 :   trj_plugin.filename_extension = &quot;trj&quot;;</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">       8336 :   trj_plugin.open_file_read = open_trr_read;</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">       8336 :   trj_plugin.read_next_timestep = read_trr_timestep;</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       8336 :   trj_plugin.close_file_read = close_trr_read;</span></a>
+<a name="768"><span class="lineNum">     768 </span>            : </a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">       8336 :   return 0;</span></a>
+<a name="770"><span class="lineNum">     770 </span>            : }</a>
+<a name="771"><span class="lineNum">     771 </span>            : </a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;gro_plugin);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;g96_plugin);</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;trr_plugin);</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;trj_plugin);</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;xtc_plugin);</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">       8336 :   return 0;</span></a>
+<a name="779"><span class="lineNum">     779 </span>            : }</a>
+<a name="780"><span class="lineNum">     780 </span>            : </a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineNoCov">          0 : VMDPLUGIN_API int VMDPLUGIN_fini() {</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineNoCov">          0 :   return 0;</span></a>
+<a name="783"><span class="lineNum">     783 </span>            : }</a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            : }</a>
+<a name="786"><span class="lineNum">     786 </span>            : }</a>
+<a name="787"><span class="lineNum">     787 </span>            : </a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span>            : #ifdef TEST_G96_PLUGIN</a>
+<a name="790"><span class="lineNum">     790 </span>            : </a>
+<a name="791"><span class="lineNum">     791 </span>            : int main(int argc, char *argv[]) {</a>
+<a name="792"><span class="lineNum">     792 </span>            :   int natoms;</a>
+<a name="793"><span class="lineNum">     793 </span>            : </a>
+<a name="794"><span class="lineNum">     794 </span>            :   molfile_timestep_t timestep;</a>
+<a name="795"><span class="lineNum">     795 </span>            :   void *v;</a>
+<a name="796"><span class="lineNum">     796 </span>            :   int i;</a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span>            :   if (argc &lt; 2) return 1;</a>
+<a name="799"><span class="lineNum">     799 </span>            :   while (--argc) {</a>
+<a name="800"><span class="lineNum">     800 </span>            :     ++argv;</a>
+<a name="801"><span class="lineNum">     801 </span>            :     v = open_g96_read(*argv, &quot;g96&quot;, &amp;natoms);</a>
+<a name="802"><span class="lineNum">     802 </span>            :     if (!v) {</a>
+<a name="803"><span class="lineNum">     803 </span>            :       fprintf(stderr, &quot;open_g96_read failed for file %s\n&quot;, *argv);</a>
+<a name="804"><span class="lineNum">     804 </span>            :       return 1;</a>
+<a name="805"><span class="lineNum">     805 </span>            :     }</a>
+<a name="806"><span class="lineNum">     806 </span>            :     timestep.coords = (float *)malloc(3*sizeof(float)*natoms);</a>
+<a name="807"><span class="lineNum">     807 </span>            :     i = 0;</a>
+<a name="808"><span class="lineNum">     808 </span>            :     while(!read_g96_timestep(v, natoms, &amp;timestep)) {</a>
+<a name="809"><span class="lineNum">     809 </span>            :       ++i;</a>
+<a name="810"><span class="lineNum">     810 </span>            :     }</a>
+<a name="811"><span class="lineNum">     811 </span>            :     fprintf(stderr, &quot;ended read_g96_timestep on step %d\n&quot;, i);</a>
+<a name="812"><span class="lineNum">     812 </span>            :     free(timestep.coords);</a>
+<a name="813"><span class="lineNum">     813 </span>            :     close_g96_read(v);</a>
+<a name="814"><span class="lineNum">     814 </span>            :   }</a>
+<a name="815"><span class="lineNum">     815 </span>            :   return 0;</a>
+<a name="816"><span class="lineNum">     816 </span>            : }</a>
+<a name="817"><span class="lineNum">     817 </span>            : </a>
+<a name="818"><span class="lineNum">     818 </span>            : #endif</a>
+<a name="819"><span class="lineNum">     819 </span>            : </a>
+<a name="820"><span class="lineNum">     820 </span>            : #ifdef TEST_TRR_PLUGIN</a>
+<a name="821"><span class="lineNum">     821 </span>            : </a>
+<a name="822"><span class="lineNum">     822 </span>            : int main(int argc, char *argv[]) {</a>
+<a name="823"><span class="lineNum">     823 </span>            :   int natoms;</a>
+<a name="824"><span class="lineNum">     824 </span>            : </a>
+<a name="825"><span class="lineNum">     825 </span>            :   molfile_timestep_t timestep;</a>
+<a name="826"><span class="lineNum">     826 </span>            :   void *v, *w;</a>
+<a name="827"><span class="lineNum">     827 </span>            :   int i;</a>
+<a name="828"><span class="lineNum">     828 </span>            : </a>
+<a name="829"><span class="lineNum">     829 </span>            :   if (argc != 3) return 1;</a>
+<a name="830"><span class="lineNum">     830 </span>            :   v = open_trr_read(argv[1], &quot;trr&quot;, &amp;natoms);</a>
+<a name="831"><span class="lineNum">     831 </span>            :   if (!v) {</a>
+<a name="832"><span class="lineNum">     832 </span>            :     fprintf(stderr, &quot;open_trr_read failed for file %s\n&quot;, argv[1]);</a>
+<a name="833"><span class="lineNum">     833 </span>            :     return 1;</a>
+<a name="834"><span class="lineNum">     834 </span>            :   }</a>
+<a name="835"><span class="lineNum">     835 </span>            :   timestep.coords = (float *)malloc(3*sizeof(float)*natoms);</a>
+<a name="836"><span class="lineNum">     836 </span>            :   w = open_trr_write(argv[2], &quot;trr&quot;, natoms);</a>
+<a name="837"><span class="lineNum">     837 </span>            :   if (!w) {</a>
+<a name="838"><span class="lineNum">     838 </span>            :     fprintf(stderr, &quot;open_trr_write failed for file %s\n&quot;, argv[2]);</a>
+<a name="839"><span class="lineNum">     839 </span>            :     return 1;</a>
+<a name="840"><span class="lineNum">     840 </span>            :   }</a>
+<a name="841"><span class="lineNum">     841 </span>            : </a>
+<a name="842"><span class="lineNum">     842 </span>            :   i = 0;</a>
+<a name="843"><span class="lineNum">     843 </span>            :   while(!read_trr_timestep(v, natoms, &amp;timestep)) {</a>
+<a name="844"><span class="lineNum">     844 </span>            :     ++i;</a>
+<a name="845"><span class="lineNum">     845 </span>            :     if (write_trr_timestep(w, &amp;timestep)) {</a>
+<a name="846"><span class="lineNum">     846 </span>            :       fprintf(stderr, &quot;write error\n&quot;);</a>
+<a name="847"><span class="lineNum">     847 </span>            :       return 1;</a>
+<a name="848"><span class="lineNum">     848 </span>            :     }</a>
+<a name="849"><span class="lineNum">     849 </span>            :   }</a>
+<a name="850"><span class="lineNum">     850 </span>            : </a>
+<a name="851"><span class="lineNum">     851 </span>            :   fprintf(stderr, &quot;ended read_trr_timestep on step %d\n&quot;, i);</a>
+<a name="852"><span class="lineNum">     852 </span>            :   free(timestep.coords);</a>
+<a name="853"><span class="lineNum">     853 </span>            :   close_trr_read(v);</a>
+<a name="854"><span class="lineNum">     854 </span>            :   close_trr_write(w);</a>
+<a name="855"><span class="lineNum">     855 </span>            :   return 0;</a>
+<a name="856"><span class="lineNum">     856 </span>            : }</a>
+<a name="857"><span class="lineNum">     857 </span>            : </a>
+<a name="858"><span class="lineNum">     858 </span>            : #endif</a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/index-sort-f.html b/coverage-libs/molfile/index-sort-f.html
new file mode 100644
index 0000000000..79fa67dd72
--- /dev/null
+++ b/coverage-libs/molfile/index-sort-f.html
@@ -0,0 +1,173 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - molfile</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">861</td>
+            <td class="headerCovTableEntry">2104</td>
+            <td class="headerCovTableEntryLo">40.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">124</td>
+            <td class="headerCovTableEntryLo">45.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="periodic_table.h.gcov.html">periodic_table.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 20</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="gromacsplugin.cpp.gcov.html">gromacsplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=30 height=10 alt="29.7%"><img src="../snow.png" width=70 height=10 alt="29.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">29.7&nbsp;%</td>
+      <td class="coverNumLo">107 / 360</td>
+      <td class="coverPerLo">21.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 23</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="endianswap.h.gcov.html">endianswap.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="12.5%"><img src="../snow.png" width=88 height=10 alt="12.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">12.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 48</td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pdbplugin.cpp.gcov.html">pdbplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=41 height=10 alt="41.2%"><img src="../snow.png" width=59 height=10 alt="41.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">41.2&nbsp;%</td>
+      <td class="coverNumLo">87 / 211</td>
+      <td class="coverPerLo">35.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="readpdb.h.gcov.html">readpdb.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="32.6%"><img src="../snow.png" width=67 height=10 alt="32.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">32.6&nbsp;%</td>
+      <td class="coverNumLo">44 / 135</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="dcdplugin.cpp.gcov.html">dcdplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=44 height=10 alt="43.6%"><img src="../snow.png" width=56 height=10 alt="43.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">43.6&nbsp;%</td>
+      <td class="coverNumLo">201 / 461</td>
+      <td class="coverPerLo">52.6&nbsp;%</td>
+      <td class="coverNumLo">10 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="crdplugin.cpp.gcov.html">crdplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=65 height=10 alt="64.7%"><img src="../snow.png" width=35 height=10 alt="64.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">64.7&nbsp;%</td>
+      <td class="coverNumLo">55 / 85</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gromacs.h.gcov.html">Gromacs.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.6%"><img src="../snow.png" width=54 height=10 alt="45.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.6&nbsp;%</td>
+      <td class="coverNumLo">342 / 750</td>
+      <td class="coverPerLo">61.1&nbsp;%</td>
+      <td class="coverNumLo">22 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="fastio.h.gcov.html">fastio.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=56 height=10 alt="55.9%"><img src="../snow.png" width=44 height=10 alt="55.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.9&nbsp;%</td>
+      <td class="coverNumLo">19 / 34</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/index-sort-l.html b/coverage-libs/molfile/index-sort-l.html
new file mode 100644
index 0000000000..a817699836
--- /dev/null
+++ b/coverage-libs/molfile/index-sort-l.html
@@ -0,0 +1,173 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - molfile</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">861</td>
+            <td class="headerCovTableEntry">2104</td>
+            <td class="headerCovTableEntryLo">40.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">124</td>
+            <td class="headerCovTableEntryLo">45.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="periodic_table.h.gcov.html">periodic_table.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 20</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="endianswap.h.gcov.html">endianswap.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="12.5%"><img src="../snow.png" width=88 height=10 alt="12.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">12.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 48</td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="gromacsplugin.cpp.gcov.html">gromacsplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=30 height=10 alt="29.7%"><img src="../snow.png" width=70 height=10 alt="29.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">29.7&nbsp;%</td>
+      <td class="coverNumLo">107 / 360</td>
+      <td class="coverPerLo">21.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 23</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="readpdb.h.gcov.html">readpdb.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="32.6%"><img src="../snow.png" width=67 height=10 alt="32.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">32.6&nbsp;%</td>
+      <td class="coverNumLo">44 / 135</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pdbplugin.cpp.gcov.html">pdbplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=41 height=10 alt="41.2%"><img src="../snow.png" width=59 height=10 alt="41.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">41.2&nbsp;%</td>
+      <td class="coverNumLo">87 / 211</td>
+      <td class="coverPerLo">35.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="dcdplugin.cpp.gcov.html">dcdplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=44 height=10 alt="43.6%"><img src="../snow.png" width=56 height=10 alt="43.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">43.6&nbsp;%</td>
+      <td class="coverNumLo">201 / 461</td>
+      <td class="coverPerLo">52.6&nbsp;%</td>
+      <td class="coverNumLo">10 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gromacs.h.gcov.html">Gromacs.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.6%"><img src="../snow.png" width=54 height=10 alt="45.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.6&nbsp;%</td>
+      <td class="coverNumLo">342 / 750</td>
+      <td class="coverPerLo">61.1&nbsp;%</td>
+      <td class="coverNumLo">22 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="fastio.h.gcov.html">fastio.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=56 height=10 alt="55.9%"><img src="../snow.png" width=44 height=10 alt="55.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.9&nbsp;%</td>
+      <td class="coverNumLo">19 / 34</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="crdplugin.cpp.gcov.html">crdplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=65 height=10 alt="64.7%"><img src="../snow.png" width=35 height=10 alt="64.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">64.7&nbsp;%</td>
+      <td class="coverNumLo">55 / 85</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/index.html b/coverage-libs/molfile/index.html
new file mode 100644
index 0000000000..04192bada0
--- /dev/null
+++ b/coverage-libs/molfile/index.html
@@ -0,0 +1,173 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - molfile</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">861</td>
+            <td class="headerCovTableEntry">2104</td>
+            <td class="headerCovTableEntryLo">40.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">124</td>
+            <td class="headerCovTableEntryLo">45.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gromacs.h.gcov.html">Gromacs.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.6%"><img src="../snow.png" width=54 height=10 alt="45.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.6&nbsp;%</td>
+      <td class="coverNumLo">342 / 750</td>
+      <td class="coverPerLo">61.1&nbsp;%</td>
+      <td class="coverNumLo">22 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="crdplugin.cpp.gcov.html">crdplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=65 height=10 alt="64.7%"><img src="../snow.png" width=35 height=10 alt="64.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">64.7&nbsp;%</td>
+      <td class="coverNumLo">55 / 85</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="dcdplugin.cpp.gcov.html">dcdplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=44 height=10 alt="43.6%"><img src="../snow.png" width=56 height=10 alt="43.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">43.6&nbsp;%</td>
+      <td class="coverNumLo">201 / 461</td>
+      <td class="coverPerLo">52.6&nbsp;%</td>
+      <td class="coverNumLo">10 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="endianswap.h.gcov.html">endianswap.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="12.5%"><img src="../snow.png" width=88 height=10 alt="12.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">12.5&nbsp;%</td>
+      <td class="coverNumLo">6 / 48</td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="fastio.h.gcov.html">fastio.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=56 height=10 alt="55.9%"><img src="../snow.png" width=44 height=10 alt="55.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.9&nbsp;%</td>
+      <td class="coverNumLo">19 / 34</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="gromacsplugin.cpp.gcov.html">gromacsplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=30 height=10 alt="29.7%"><img src="../snow.png" width=70 height=10 alt="29.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">29.7&nbsp;%</td>
+      <td class="coverNumLo">107 / 360</td>
+      <td class="coverPerLo">21.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 23</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pdbplugin.cpp.gcov.html">pdbplugin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=41 height=10 alt="41.2%"><img src="../snow.png" width=59 height=10 alt="41.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">41.2&nbsp;%</td>
+      <td class="coverNumLo">87 / 211</td>
+      <td class="coverPerLo">35.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="periodic_table.h.gcov.html">periodic_table.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 20</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="readpdb.h.gcov.html">readpdb.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="32.6%"><img src="../snow.png" width=67 height=10 alt="32.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">32.6&nbsp;%</td>
+      <td class="coverNumLo">44 / 135</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/pdbplugin.cpp.func-sort-c.html b/coverage-libs/molfile/pdbplugin.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1923d59ee6
--- /dev/null
+++ b/coverage-libs/molfile/pdbplugin.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/pdbplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - pdbplugin.cpp<span style="font-size: 80%;"> (<a href="pdbplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntry">211</td>
+            <td class="headerCovTableEntryLo">41.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">35.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="pdbplugin.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#639">_ZN4PLMD7molfile22molfile_pdbplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#236">_ZN4PLMD7molfileL10read_bondsEPvPiPS2_S3_PPfS3_S2_PPPc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#526">_ZN4PLMD7molfileL12write_cryst1EP8_IO_FILEPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#532">_ZN4PLMD7molfileL14write_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#332">_ZN4PLMD7molfileL15open_file_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#350">_ZN4PLMD7molfileL15write_structureEPviPKNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#591">_ZN4PLMD7molfileL16close_file_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#164">_ZN4PLMD7molfileL18read_pdb_structureEPvPiPNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#598">_ZN4PLMD7molfileL22read_molecule_metadataEPvPPNS0_18molfile_metadata_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#85">_ZN4PLMD7molfileL13open_pdb_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#319">_ZN4PLMD7molfileL14close_pdb_readEPv</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#277">_ZN4PLMD7molfileL18read_next_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#610">_ZN4PLMD7molfile22molfile_pdbplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#634">_ZN4PLMD7molfile26molfile_pdbplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/pdbplugin.cpp.func.html b/coverage-libs/molfile/pdbplugin.cpp.func.html
new file mode 100644
index 0000000000..4c2b96d2c5
--- /dev/null
+++ b/coverage-libs/molfile/pdbplugin.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/pdbplugin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - pdbplugin.cpp<span style="font-size: 80%;"> (<a href="pdbplugin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntry">211</td>
+            <td class="headerCovTableEntryLo">41.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">35.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="pdbplugin.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#639">_ZN4PLMD7molfile22molfile_pdbplugin_finiEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#610">_ZN4PLMD7molfile22molfile_pdbplugin_initEv</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#634">_ZN4PLMD7molfile26molfile_pdbplugin_registerEPvPFiS1_PNS0_11vmdplugin_tEE</a></td>
+              <td class="coverFnHi">8336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#236">_ZN4PLMD7molfileL10read_bondsEPvPiPS2_S3_PPfS3_S2_PPPc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#526">_ZN4PLMD7molfileL12write_cryst1EP8_IO_FILEPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#85">_ZN4PLMD7molfileL13open_pdb_readEPKcS2_Pi</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#319">_ZN4PLMD7molfileL14close_pdb_readEPv</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#532">_ZN4PLMD7molfileL14write_timestepEPvPKNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#332">_ZN4PLMD7molfileL15open_file_writeEPKcS2_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#350">_ZN4PLMD7molfileL15write_structureEPviPKNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#591">_ZN4PLMD7molfileL16close_file_writeEPv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#277">_ZN4PLMD7molfileL18read_next_timestepEPviPNS0_18molfile_timestep_tE</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#164">_ZN4PLMD7molfileL18read_pdb_structureEPvPiPNS0_14molfile_atom_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pdbplugin.cpp.gcov.html#598">_ZN4PLMD7molfileL22read_molecule_metadataEPvPPNS0_18molfile_metadata_tE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/pdbplugin.cpp.gcov.html b/coverage-libs/molfile/pdbplugin.cpp.gcov.html
new file mode 100644
index 0000000000..32ab986429
--- /dev/null
+++ b/coverage-libs/molfile/pdbplugin.cpp.gcov.html
@@ -0,0 +1,724 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/pdbplugin.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - pdbplugin.cpp<span style="font-size: 80%;"> (source / <a href="pdbplugin.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntry">211</td>
+            <td class="headerCovTableEntryLo">41.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">35.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #if defined(__PLUMED_HAS_MOLFILE_PLUGINS) &amp;&amp; ! defined(__PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS)</a>
+<a name="38"><span class="lineNum">      38 </span>            : /***************************************************************************</a>
+<a name="39"><span class="lineNum">      39 </span>            :  *cr</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr                        University of Illinois</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                         All Rights Reserved</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr</a>
+<a name="44"><span class="lineNum">      44 </span>            :  ***************************************************************************/</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : /***************************************************************************</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * RCS INFORMATION:</a>
+<a name="48"><span class="lineNum">      48 </span>            :  *</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *      $RCSfile: pdbplugin.c,v $</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $Revision: 1.73 $       $Date: 2016/11/28 05:01:54 $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *</a>
+<a name="53"><span class="lineNum">      53 </span>            :  ***************************************************************************/</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : /*</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * PDB file format specifications:</a>
+<a name="57"><span class="lineNum">      57 </span>            :  *   http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html</a>
+<a name="58"><span class="lineNum">      58 </span>            :  */</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : #include &quot;largefiles.h&quot;   /* platform dependent 64-bit file I/O defines */</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &quot;molfile_plugin.h&quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            : #include &quot;readpdb.h&quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &quot;periodic_table.h&quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &lt;string.h&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace PLMD{</a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace molfile{</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : /*</a>
+<a name="73"><span class="lineNum">      73 </span>            :  * API functions start here</a>
+<a name="74"><span class="lineNum">      74 </span>            :  */</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : typedef struct {</a>
+<a name="77"><span class="lineNum">      77 </span>            :   FILE *fd;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   int first_frame;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   int natoms;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   molfile_atom_t *atomlist;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   molfile_metadata_t *meta;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   int nconect;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   int nbonds, maxbnum;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   int *from, *to, *idxmap;</a>
+<a name="85"><span class="lineNum">      85 </span>            : } pdbdata;</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         49 : static void *open_pdb_read(const char *filepath, const char *filetype, </span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     int *natoms) {</a>
+<a name="89"><span class="lineNum">      89 </span>            :   FILE *fd;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   pdbdata *pdb;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   char pdbstr[PDB_BUFFER_LENGTH];</a>
+<a name="92"><span class="lineNum">      92 </span>            :   int indx, nconect;</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         49 :   fd = fopen(filepath, &quot;r&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         49 :   if (!fd) </span></a>
+<a name="96"><span class="lineNum">      96 </span>            :     return NULL;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         49 :   pdb = (pdbdata *)malloc(sizeof(pdbdata));</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         49 :   pdb-&gt;fd = fd;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         49 :   pdb-&gt;meta = (molfile_metadata_t *) malloc(sizeof(molfile_metadata_t));</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   memset(pdb-&gt;meta, 0, sizeof(molfile_metadata_t));</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   pdb-&gt;meta-&gt;remarklen = 0;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   pdb-&gt;meta-&gt;remarks = NULL;</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         49 :   *natoms=0;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   nconect=0;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   do {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     101357 :     indx = read_pdb_record(pdb-&gt;fd, pdbstr);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     101357 :     if (indx == PDB_ATOM) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">     101142 :       *natoms += 1;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        215 :     } else if (indx == PDB_CONECT) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :       nconect++;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        215 :     } else if (indx == PDB_HEADER) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :       get_pdb_header(pdbstr, pdb-&gt;meta-&gt;accession, pdb-&gt;meta-&gt;date, NULL);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :       if (strlen(pdb-&gt;meta-&gt;accession) &gt; 0) </span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :         strcpy(pdb-&gt;meta-&gt;database, &quot;PDB&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        215 :     } else if (indx == PDB_REMARK || indx == PDB_CONECT || indx == PDB_UNKNOWN) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        136 :       int len=strlen(pdbstr);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        136 :       int newlen = len + pdb-&gt;meta-&gt;remarklen;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        136 :       char *newstr=(char*)realloc(pdb-&gt;meta-&gt;remarks, newlen + 1);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        136 :       if (newstr != NULL) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        136 :         pdb-&gt;meta-&gt;remarks = newstr;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        136 :         pdb-&gt;meta-&gt;remarks[pdb-&gt;meta-&gt;remarklen] = '\0';</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        136 :         memcpy(pdb-&gt;meta-&gt;remarks + pdb-&gt;meta-&gt;remarklen, pdbstr, len);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        136 :         pdb-&gt;meta-&gt;remarks[newlen] = '\0';</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        136 :         pdb-&gt;meta-&gt;remarklen = newlen;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :       }</a>
+<a name="129"><span class="lineNum">     129 </span>            :     }</a>
+<a name="130"><span class="lineNum">     130 </span>            :  </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     101357 :   } while (indx != PDB_END &amp;&amp; indx != PDB_EOF);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   /* If no atoms were found, this is probably not a PDB file! */</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         49 :   if (!*natoms) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;PDB file '%s' contains no atoms.\n&quot;, filepath);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     if (pdb-&gt;meta-&gt;remarks != NULL)</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :       free(pdb-&gt;meta-&gt;remarks);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     if (pdb-&gt;meta != NULL)</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :       free(pdb-&gt;meta);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     free(pdb);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         49 :   rewind(pdb-&gt;fd); /* if ok, rewind file and prepare to parse it for real */</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         49 :   pdb-&gt;natoms = *natoms;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         49 :   pdb-&gt;nconect = nconect;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         49 :   pdb-&gt;nbonds = 0;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         49 :   pdb-&gt;maxbnum = 0;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         49 :   pdb-&gt;from = NULL;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         49 :   pdb-&gt;to = NULL;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         49 :   pdb-&gt;idxmap = NULL;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         49 :   pdb-&gt;atomlist = NULL;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : #if defined(VMDUSECONECTRECORDS)</a>
+<a name="155"><span class="lineNum">     155 </span>            :   /* allocate atom index translation table if we have 99,999 atoms or less */</a>
+<a name="156"><span class="lineNum">     156 </span>            :   /* and we have conect records to process                                 */</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         49 :   if (pdb-&gt;natoms &lt; 100000 &amp;&amp; pdb-&gt;nconect &gt; 0) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     pdb-&gt;idxmap = (int *) malloc(100000 * sizeof(int));</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     memset(pdb-&gt;idxmap, 0, 100000 * sizeof(int));</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : #endif</a>
+<a name="162"><span class="lineNum">     162 </span>            :  </a>
+<a name="163"><span class="lineNum">     163 </span>            :   return pdb; </a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 : static int read_pdb_structure(void *mydata, int *optflags, </span></a>
+<a name="167"><span class="lineNum">     167 </span>            :     molfile_atom_t *atoms) { </a>
+<a name="168"><span class="lineNum">     168 </span>            :   pdbdata *pdb = (pdbdata *)mydata;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   molfile_atom_t *atom;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   char pdbrec[PDB_BUFFER_LENGTH];</a>
+<a name="171"><span class="lineNum">     171 </span>            :   int i, rectype, atomserial, pteidx;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   char ridstr[8];</a>
+<a name="173"><span class="lineNum">     173 </span>            :   char elementsymbol[3];</a>
+<a name="174"><span class="lineNum">     174 </span>            :   int badptecount = 0;</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :   long fpos = ftell(pdb-&gt;fd);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   *optflags = MOLFILE_INSERTION | MOLFILE_OCCUPANCY | MOLFILE_BFACTOR |</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :               MOLFILE_ALTLOC | MOLFILE_ATOMICNUMBER | MOLFILE_BONDSSPECIAL;</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   i = 0;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   do {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     rectype = read_pdb_record(pdb-&gt;fd, pdbrec);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     switch (rectype) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :     case PDB_ATOM:</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :       atom = atoms+i;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :       get_pdb_fields(pdbrec, strlen(pdbrec), &amp;atomserial, </span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :           atom-&gt;name, atom-&gt;resname, atom-&gt;chain, atom-&gt;segid, </span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :           ridstr, atom-&gt;insertion, atom-&gt;altloc, elementsymbol,</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :           NULL, NULL, NULL, &amp;atom-&gt;occupancy, &amp;atom-&gt;bfactor);</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :       if (pdb-&gt;idxmap != NULL &amp;&amp; atomserial &lt; 100000) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :         pdb-&gt;idxmap[atomserial] = i; /* record new serial number translation */ </span></a>
+<a name="193"><span class="lineNum">     193 </span>            :       }</a>
+<a name="194"><span class="lineNum">     194 </span>            :  </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :       atom-&gt;resid = atoi(ridstr);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :       /* determine atomic number from the element symbol */</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :       pteidx = get_pte_idx_from_string(elementsymbol);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :       atom-&gt;atomicnumber = pteidx;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :       if (pteidx != 0) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :         atom-&gt;mass = get_pte_mass(pteidx);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :         atom-&gt;radius = get_pte_vdw_radius(pteidx);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       } else {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :         badptecount++; /* unrecognized element */</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :       }</a>
+<a name="206"><span class="lineNum">     206 </span>            :  </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :       strcpy(atom-&gt;type, atom-&gt;name);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :       i++;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :     case PDB_CONECT:</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :       /* only read CONECT records for structures where we know they can */</a>
+<a name="213"><span class="lineNum">     213 </span>            :       /* be valid for all of the atoms in the structure                 */</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :       if (pdb-&gt;idxmap != NULL) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :         get_pdb_conect(pdbrec, pdb-&gt;natoms, pdb-&gt;idxmap, </span></a>
+<a name="216"><span class="lineNum">     216 </span>            :                        &amp;pdb-&gt;maxbnum, &amp;pdb-&gt;nbonds, &amp;pdb-&gt;from, &amp;pdb-&gt;to);</a>
+<a name="217"><span class="lineNum">     217 </span>            :       }</a>
+<a name="218"><span class="lineNum">     218 </span>            :       break;</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :     default:</a>
+<a name="221"><span class="lineNum">     221 </span>            :       /* other record types are ignored in the structure callback */</a>
+<a name="222"><span class="lineNum">     222 </span>            :       /* and are dealt with in the timestep callback or elsewhere */</a>
+<a name="223"><span class="lineNum">     223 </span>            :       break;</a>
+<a name="224"><span class="lineNum">     224 </span>            :     }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :   } while (rectype != PDB_END &amp;&amp; rectype != PDB_EOF);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   fseek(pdb-&gt;fd, fpos, SEEK_SET);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :   /* if all atoms are recognized, set the mass and radius flags too,  */</a>
+<a name="230"><span class="lineNum">     230 </span>            :   /* otherwise let VMD guess these for itself using it's own methods  */</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   if (badptecount == 0) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     *optflags |= MOLFILE_MASS | MOLFILE_RADIUS;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 : static int read_bonds(void *v, int *nbonds, int **fromptr, int **toptr, </span></a>
+<a name="239"><span class="lineNum">     239 </span>            :                       float ** bondorder,int **bondtype, </a>
+<a name="240"><span class="lineNum">     240 </span>            :                       int *nbondtypes, char ***bondtypename) {</a>
+<a name="241"><span class="lineNum">     241 </span>            :   pdbdata *pdb = (pdbdata *)v;</a>
+<a name="242"><span class="lineNum">     242 </span>            :   </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   *nbonds = 0;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :   *fromptr = NULL;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :   *toptr = NULL;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   *bondorder = NULL; /* PDB files don't have bond order information */</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :   *bondtype = NULL;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   *nbondtypes = 0;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   *bondtypename = NULL;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : /* The newest plugin API allows us to return CONECT records as </a>
+<a name="252"><span class="lineNum">     252 </span>            :  * additional bonds above and beyond what the distance search returns.</a>
+<a name="253"><span class="lineNum">     253 </span>            :  * Without that feature, we otherwise have to check completeness and</a>
+<a name="254"><span class="lineNum">     254 </span>            :  * ignore them if they don't look to be fully specified for this molecule */</a>
+<a name="255"><span class="lineNum">     255 </span>            : #if !defined(MOLFILE_BONDSSPECIAL)</a>
+<a name="256"><span class="lineNum">     256 </span>            :   if (pdb-&gt;natoms &gt;= 100000) {</a>
+<a name="257"><span class="lineNum">     257 </span>            :     printf(&quot;pdbplugin) Warning: more than 99,999 atoms, ignored CONECT records\n&quot;);</a>
+<a name="258"><span class="lineNum">     258 </span>            :     return MOLFILE_SUCCESS;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   } else if (((float) pdb-&gt;nconect / (float) pdb-&gt;natoms) &lt;= 0.85) {</a>
+<a name="260"><span class="lineNum">     260 </span>            :     printf(&quot;pdbplugin) Warning: Probable incomplete bond structure specified,\n&quot;);</a>
+<a name="261"><span class="lineNum">     261 </span>            :     printf(&quot;pdbplugin)          ignoring CONECT records\n&quot;);</a>
+<a name="262"><span class="lineNum">     262 </span>            :     return MOLFILE_SUCCESS;</a>
+<a name="263"><span class="lineNum">     263 </span>            :   } else if (pdb-&gt;nconect == 0) {</a>
+<a name="264"><span class="lineNum">     264 </span>            :     return MOLFILE_SUCCESS;</a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span>            : #endif</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :   *nbonds = pdb-&gt;nbonds;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :   *fromptr = pdb-&gt;from;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :   *toptr = pdb-&gt;to;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : }</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : /* </a>
+<a name="277"><span class="lineNum">     277 </span>            :  * </a>
+<a name="278"><span class="lineNum">     278 </span>            :  */</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        109 : static int read_next_timestep(void *v, int natoms, molfile_timestep_t *ts) {</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   pdbdata *pdb = (pdbdata *)v;</a>
+<a name="281"><span class="lineNum">     281 </span>            :   char pdbstr[PDB_BUFFER_LENGTH];</a>
+<a name="282"><span class="lineNum">     282 </span>            :   int indx, i;</a>
+<a name="283"><span class="lineNum">     283 </span>            :   float *x, *y, *z;</a>
+<a name="284"><span class="lineNum">     284 </span>            :   float occup, bfac;</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        109 :   if (pdb-&gt;natoms == 0) </span></a>
+<a name="286"><span class="lineNum">     286 </span>            :     return MOLFILE_ERROR; /* EOF */</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        109 :   if (ts) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        109 :     x = ts-&gt;coords;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        109 :     y = x+1;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        109 :     z = x+2;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :   } else {</a>
+<a name="292"><span class="lineNum">     292 </span>            :     x = y = z = 0;</a>
+<a name="293"><span class="lineNum">     293 </span>            :   } </a>
+<a name="294"><span class="lineNum">     294 </span>            :   i = 0;</a>
+<a name="295"><span class="lineNum">     295 </span>            :   do {</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">     105533 :     indx = read_pdb_record(pdb-&gt;fd, pdbstr);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     105533 :     if((indx == PDB_END || indx == PDB_EOF) &amp;&amp; (i &lt; pdb-&gt;natoms)) {</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :       return MOLFILE_ERROR;</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">     105484 :     } else if(indx == PDB_ATOM) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">     105240 :       if(i++ &gt;= pdb-&gt;natoms) {</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :         break;      </a>
+<a name="302"><span class="lineNum">     302 </span>            :       }</a>
+<a name="303"><span class="lineNum">     303 </span>            :       /* just get the coordinates, and store them */</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     105240 :       if (ts) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     105240 :         get_pdb_coordinates(pdbstr, x, y, z, &amp;occup, &amp;bfac);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">     105240 :         x += 3;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">     105240 :         y += 3;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">     105240 :         z += 3;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :       } </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        244 :     } else if (indx == PDB_CRYST1) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         32 :       if (ts) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         32 :         get_pdb_cryst1(pdbstr, &amp;ts-&gt;alpha, &amp;ts-&gt;beta, &amp;ts-&gt;gamma,</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :                                &amp;ts-&gt;A, &amp;ts-&gt;B, &amp;ts-&gt;C);</a>
+<a name="314"><span class="lineNum">     314 </span>            :       }</a>
+<a name="315"><span class="lineNum">     315 </span>            :     }</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">     105484 :   } while(!(indx == PDB_END || indx == PDB_EOF));</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         49 : static void close_pdb_read(void *v) { </span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   pdbdata *pdb = (pdbdata *)v;</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         49 :   if (pdb-&gt;fd != NULL)</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         49 :     fclose(pdb-&gt;fd);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         49 :   if (pdb-&gt;idxmap != NULL)</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :     free(pdb-&gt;idxmap);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         49 :   if (pdb-&gt;meta-&gt;remarks != NULL)</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         38 :     free(pdb-&gt;meta-&gt;remarks);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         49 :   if (pdb-&gt;meta != NULL) </span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         49 :     free(pdb-&gt;meta);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         49 :   free(pdb);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         49 : }</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 : static void *open_file_write(const char *path, const char *filetype, </span></a>
+<a name="335"><span class="lineNum">     335 </span>            :     int natoms) {</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            :   FILE *fd;</a>
+<a name="338"><span class="lineNum">     338 </span>            :   pdbdata *pdb;</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :   fd = fopen(path, &quot;w&quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :   if (!fd) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :     fprintf(stderr, &quot;Unable to open file %s for writing\n&quot;, path);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :     return NULL;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :   pdb = (pdbdata *)malloc(sizeof(pdbdata));</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   pdb-&gt;fd = fd;</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   pdb-&gt;natoms = natoms; </span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :   pdb-&gt;atomlist = NULL;</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :   pdb-&gt;first_frame = 1;</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   return pdb;</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+<a name="351"><span class="lineNum">     351 </span>            :  </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 : static int write_structure(void *v, int optflags, </span></a>
+<a name="353"><span class="lineNum">     353 </span>            :     const molfile_atom_t *atoms) {</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :   int i;</a>
+<a name="356"><span class="lineNum">     356 </span>            :   pdbdata *pdb = (pdbdata *)v;</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :   int natoms = pdb-&gt;natoms;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   pdb-&gt;atomlist = (molfile_atom_t *)malloc(natoms*sizeof(molfile_atom_t));</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :   memcpy(pdb-&gt;atomlist, atoms, natoms*sizeof(molfile_atom_t));</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            :   /* If occ, bfactor, and insertion aren't given, we assign defaultvalues. */</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :   if (!(optflags &amp; MOLFILE_OCCUPANCY)) {</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;natoms; i++) pdb-&gt;atomlist[i].occupancy = 0.0f;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   }</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :   if (!(optflags &amp; MOLFILE_BFACTOR)) {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;natoms; i++) pdb-&gt;atomlist[i].bfactor= 0.0f;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :   }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :   if (!(optflags &amp; MOLFILE_INSERTION)) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;natoms; i++) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :       pdb-&gt;atomlist[i].insertion[0] =' ';</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :       pdb-&gt;atomlist[i].insertion[1] ='\0';</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :     }</a>
+<a name="373"><span class="lineNum">     373 </span>            :   }</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :   if (!(optflags &amp; MOLFILE_ALTLOC)) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;natoms; i++) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :       pdb-&gt;atomlist[i].altloc[0]=' ';</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :       pdb-&gt;atomlist[i].altloc[1]='\0';</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :     }</a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :   if (!(optflags &amp; MOLFILE_ATOMICNUMBER)) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :     for (i=0; i&lt;natoms; i++) pdb-&gt;atomlist[i].atomicnumber = 0;</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   }</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            :   /* TODO: put bonds into CONECT records? */</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : }</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            : /* SEQRES records look like this:</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            : COLUMNS        DATA TYPE       FIELD         DEFINITION</a>
+<a name="391"><span class="lineNum">     391 </span>            : ---------------------------------------------------------------------------------</a>
+<a name="392"><span class="lineNum">     392 </span>            :  1 -  6        Record name     &quot;SEQRES&quot;</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            :  9 - 10        Integer         serNum        Serial number of the SEQRES record</a>
+<a name="395"><span class="lineNum">     395 </span>            :                                              for the current chain.  Starts at 1</a>
+<a name="396"><span class="lineNum">     396 </span>            :                                              and increments by one each line.</a>
+<a name="397"><span class="lineNum">     397 </span>            :                                              Reset to 1 for each chain.</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : 12             Character       chainID       Chain identifier.  This may be any</a>
+<a name="400"><span class="lineNum">     400 </span>            :                                              single legal character, including a</a>
+<a name="401"><span class="lineNum">     401 </span>            :                                              blank which is used if there is</a>
+<a name="402"><span class="lineNum">     402 </span>            :                                              only one chain.</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            : 14 - 17        Integer         numRes        Number of residues in the chain.</a>
+<a name="405"><span class="lineNum">     405 </span>            :                                              This value is repeated on every</a>
+<a name="406"><span class="lineNum">     406 </span>            :                                              record.</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : 20 - 22        Residue name    resName       Residue name.</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            : 24 - 26        Residue name    resName       Residue name.</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            : ... and so forth out to 68-70, for a total of 13 in each line (except possibly</a>
+<a name="413"><span class="lineNum">     413 </span>            : the last.</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            : source:</a>
+<a name="416"><span class="lineNum">     416 </span>            : http://www.rcsb.org/pdb/file_formats/pdb/pdbguide2.2/part_35.html</a>
+<a name="417"><span class="lineNum">     417 </span>            : */</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span>            : /*</a>
+<a name="420"><span class="lineNum">     420 </span>            :  * However, we don't use them right now because of several issues that</a>
+<a name="421"><span class="lineNum">     421 </span>            :  * can't presently be resolved satisfactorily in VMD:</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span>            : According to the RCSB, SEQRES records have to contain all residues, not</a>
+<a name="424"><span class="lineNum">     424 </span>            : just those in the structure, which means VMD will usually produce incorrect</a>
+<a name="425"><span class="lineNum">     425 </span>            : output and there's nothing we can do about it.  The RCSB actually specifies</a>
+<a name="426"><span class="lineNum">     426 </span>            : that all residues in the chain have to present in the SEQRES records, even</a>
+<a name="427"><span class="lineNum">     427 </span>            : if they're not in the structure.</a>
+<a name="428"><span class="lineNum">     428 </span>            :   </a>
+<a name="429"><span class="lineNum">     429 </span>            : We can never know which residues to output.  Our current system of outputting   </a>
+<a name="430"><span class="lineNum">     430 </span>            : everything is just terrible when you have 20,000 waters in your system; we</a>
+<a name="431"><span class="lineNum">     431 </span>            : have to fix this immediately.  We could almost get away with making a hash</a>
+<a name="432"><span class="lineNum">     432 </span>            : table of the names of protein and nucleic acid residues and only write chains</a>
+<a name="433"><span class="lineNum">     433 </span>            : containing those residues.  However, there's this little snippet from the</a>
+<a name="434"><span class="lineNum">     434 </span>            : specification:</a>
+<a name="435"><span class="lineNum">     435 </span>            :   </a>
+<a name="436"><span class="lineNum">     436 </span>            : * Heterogens which are integrated into the backbone of the chain are listed</a>
+<a name="437"><span class="lineNum">     437 </span>            :   as being part of the chain and are included in the SEQRES records for</a>
+<a name="438"><span class="lineNum">     438 </span>            :   that chain.</a>
+<a name="439"><span class="lineNum">     439 </span>            :   </a>
+<a name="440"><span class="lineNum">     440 </span>            : That means that we can never know what might appear in the sequence unless we</a>
+<a name="441"><span class="lineNum">     441 </span>            : also read HET records and keep track of them in VMD as well.  We shouldn't </a>
+<a name="442"><span class="lineNum">     442 </span>            : get people depending on such fallible SEQRES records.</a>
+<a name="443"><span class="lineNum">     443 </span>            :   </a>
+<a name="444"><span class="lineNum">     444 </span>            : And of course, there's the fact that no other program that we know of besides   </a>
+<a name="445"><span class="lineNum">     445 </span>            : CE needs these SEQRES records.</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span>            :  * Uncomment the write_seqres line in write_timestep to turn them back on.</a>
+<a name="448"><span class="lineNum">     448 </span>            :  */</a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            : #if 0</a>
+<a name="452"><span class="lineNum">     452 </span>            : static void write_seqres(FILE * fd, int natoms, const molfile_atom_t *atomlist) {</a>
+<a name="453"><span class="lineNum">     453 </span>            :   int i=0;</a>
+<a name="454"><span class="lineNum">     454 </span>            :   while (i &lt; natoms) {</a>
+<a name="455"><span class="lineNum">     455 </span>            :     int k, serNum;</a>
+<a name="456"><span class="lineNum">     456 </span>            :     int j = i;</a>
+<a name="457"><span class="lineNum">     457 </span>            :     int ires, nres = 1;</a>
+<a name="458"><span class="lineNum">     458 </span>            :     int resid = atomlist[i].resid;</a>
+<a name="459"><span class="lineNum">     459 </span>            :     /* Count up the number of residues in the chain */</a>
+<a name="460"><span class="lineNum">     460 </span>            :     const char *chain = atomlist[i].chain;</a>
+<a name="461"><span class="lineNum">     461 </span>            :     while (j &lt; natoms &amp;&amp; !strcmp(chain, atomlist[j].chain)) {</a>
+<a name="462"><span class="lineNum">     462 </span>            :       if (resid != atomlist[j].resid) {</a>
+<a name="463"><span class="lineNum">     463 </span>            :         nres++;</a>
+<a name="464"><span class="lineNum">     464 </span>            :         resid = atomlist[j].resid;</a>
+<a name="465"><span class="lineNum">     465 </span>            :       }</a>
+<a name="466"><span class="lineNum">     466 </span>            :       j++;</a>
+<a name="467"><span class="lineNum">     467 </span>            :     }</a>
+<a name="468"><span class="lineNum">     468 </span>            :     /* There are nres residues in the chain, from atoms i to j. */</a>
+<a name="469"><span class="lineNum">     469 </span>            :     serNum = 1;</a>
+<a name="470"><span class="lineNum">     470 </span>            :     ires = 1;</a>
+<a name="471"><span class="lineNum">     471 </span>            :     resid = atomlist[i].resid;</a>
+<a name="472"><span class="lineNum">     472 </span>            :     fprintf(fd, &quot;SEQRES  %2d %c %4d  &quot;,  serNum, chain[0], nres);</a>
+<a name="473"><span class="lineNum">     473 </span>            :     serNum = 2;</a>
+<a name="474"><span class="lineNum">     474 </span>            :     fprintf(fd, &quot;%3s &quot;, atomlist[i].resname);</a>
+<a name="475"><span class="lineNum">     475 </span>            :     for (k=i; k&lt;j; k++) {</a>
+<a name="476"><span class="lineNum">     476 </span>            :       if (resid != atomlist[k].resid) {</a>
+<a name="477"><span class="lineNum">     477 </span>            :         resid = atomlist[k].resid;</a>
+<a name="478"><span class="lineNum">     478 </span>            :         if (!(ires % 13)) {</a>
+<a name="479"><span class="lineNum">     479 </span>            :           fprintf(fd, &quot;\nSEQRES  %2d %c %4d  &quot;,  serNum, chain[0], nres);</a>
+<a name="480"><span class="lineNum">     480 </span>            :           serNum++;</a>
+<a name="481"><span class="lineNum">     481 </span>            :         }</a>
+<a name="482"><span class="lineNum">     482 </span>            :         fprintf(fd, &quot;%3s &quot;, atomlist[k].resname);</a>
+<a name="483"><span class="lineNum">     483 </span>            :         ires++;</a>
+<a name="484"><span class="lineNum">     484 </span>            :       }</a>
+<a name="485"><span class="lineNum">     485 </span>            :     }</a>
+<a name="486"><span class="lineNum">     486 </span>            :     i = j;</a>
+<a name="487"><span class="lineNum">     487 </span>            :     fprintf(fd, &quot;\n&quot;);</a>
+<a name="488"><span class="lineNum">     488 </span>            :   }</a>
+<a name="489"><span class="lineNum">     489 </span>            : }</a>
+<a name="490"><span class="lineNum">     490 </span>            : #endif</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            : /*</a>
+<a name="493"><span class="lineNum">     493 </span>            : CRYST1 records look like this:</a>
+<a name="494"><span class="lineNum">     494 </span>            : The CRYST1 record presents the unit cell parameters, space group, and Z value. If the structure was not determined by crystallographic means, CRYST1 simply defines a unit cube. </a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span>            : Record Format </a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            : COLUMNS       DATA TYPE      FIELD         DEFINITION</a>
+<a name="500"><span class="lineNum">     500 </span>            : -------------------------------------------------------------</a>
+<a name="501"><span class="lineNum">     501 </span>            :  1 -  6       Record name    &quot;CRYST1&quot;</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            :  7 - 15       Real(9.3)      a             a (Angstroms).</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            : 16 - 24       Real(9.3)      b             b (Angstroms).</a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span>            : 25 - 33       Real(9.3)      c             c (Angstroms).</a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            : 34 - 40       Real(7.2)      alpha         alpha (degrees).</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            : 41 - 47       Real(7.2)      beta          beta (degrees).</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span>            : 48 - 54       Real(7.2)      gamma         gamma (degrees).</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : 56 - 66       LString        sGroup        Space group.</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span>            : 67 - 70       Integer        z             Z value.</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span>            : * If the coordinate entry describes a structure determined by a technique</a>
+<a name="520"><span class="lineNum">     520 </span>            : other than crystallography, CRYST1 contains a = b = c = 1.0, alpha =</a>
+<a name="521"><span class="lineNum">     521 </span>            : beta = gamma = 90 degrees, space group = P 1, and Z = 1.</a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span>            : We will use &quot;P 1&quot; and &quot;1&quot; for space group and z value, as recommended, but</a>
+<a name="524"><span class="lineNum">     524 </span>            : we'll populate the other fields with the unit cell information we do have.</a>
+<a name="525"><span class="lineNum">     525 </span>            : </a>
+<a name="526"><span class="lineNum">     526 </span>            : */</a>
+<a name="527"><span class="lineNum">     527 </span>            :   </a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 : static void write_cryst1(FILE *fd, const molfile_timestep_t *ts) {</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :   fprintf(fd, &quot;CRYST1%9.3f%9.3f%9.3f%7.2f%7.2f%7.2f P 1           1\n&quot;, </span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :     ts-&gt;A, ts-&gt;B, ts-&gt;C, ts-&gt;alpha, ts-&gt;beta, ts-&gt;gamma);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 : static int write_timestep(void *v, const molfile_timestep_t *ts) {</span></a>
+<a name="535"><span class="lineNum">     535 </span>            :   pdbdata *pdb = (pdbdata *)v; </a>
+<a name="536"><span class="lineNum">     536 </span>            :   const molfile_atom_t *atom;</a>
+<a name="537"><span class="lineNum">     537 </span>            :   const float *pos;</a>
+<a name="538"><span class="lineNum">     538 </span>            :   int i;</a>
+<a name="539"><span class="lineNum">     539 </span>            :   char elementsymbol[3];</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :   if (pdb-&gt;natoms == 0)</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :     return MOLFILE_SUCCESS;</a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :   if (pdb-&gt;first_frame) {</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :     /* Turn off SEQRES writing for now; see comments above.</a>
+<a name="546"><span class="lineNum">     546 </span>            :     write_seqres(pdb-&gt;fd, pdb-&gt;natoms, pdb-&gt;atomlist);</a>
+<a name="547"><span class="lineNum">     547 </span>            :     */</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineNoCov">          0 :     write_cryst1(pdb-&gt;fd, ts);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :     pdb-&gt;first_frame = 0;</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :   }</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :   atom = pdb-&gt;atomlist;</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :   pos = ts-&gt;coords;</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;pdb-&gt;natoms; i++) {</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :     /*</a>
+<a name="555"><span class="lineNum">     555 </span>            :      * The 8.3 format for position, occupancy, and bfactor permits values </a>
+<a name="556"><span class="lineNum">     556 </span>            :      * only in the range of -999.9994 to 9999.9994 (so that they round</a>
+<a name="557"><span class="lineNum">     557 </span>            :      * to the range [-999.999, 9999.999]).  If values fall outside of that</a>
+<a name="558"><span class="lineNum">     558 </span>            :      * range, fail and emit an error message rather than generate a</a>
+<a name="559"><span class="lineNum">     559 </span>            :      * misformatted PDB file.</a>
+<a name="560"><span class="lineNum">     560 </span>            :      */</a>
+<a name="561"><span class="lineNum">     561 </span>            : #define PDBBAD(x) ((x) &lt; -999.9994f || (x) &gt; 9999.9994f)</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :     if (PDBBAD(pos[0]) || PDBBAD(pos[1]) || PDBBAD(pos[2]) ||</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineNoCov">          0 :                 PDBBAD(atom-&gt;occupancy) || PDBBAD(atom-&gt;bfactor)) {</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :             fprintf(stderr, &quot;PDB WRITE ERROR: Position, occupancy, or b-factor (beta) for atom %d\n&quot;, i);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :       fprintf(stderr, &quot;                 cannot be written in PDB format.\n&quot;);</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineNoCov">          0 :       fprintf(stderr, &quot;                 File will be truncated.\n&quot;);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :     }</a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span>            :     /* check the atomicnumber and format the atomic element symbol string */</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineNoCov">          0 :     strcpy(elementsymbol, (atom-&gt;atomicnumber &lt; 1) ? &quot;  &quot; : get_pte_label(atom-&gt;atomicnumber));</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineNoCov">          0 :     elementsymbol[0] = toupper(elementsymbol[0]);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :     elementsymbol[1] = toupper(elementsymbol[1]);</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :  </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :     if (!write_raw_pdb_record(pdb-&gt;fd,  </span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :         &quot;ATOM  &quot;, i+1, atom-&gt;name, atom-&gt;resname, atom-&gt;resid, </span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :         atom-&gt;insertion, atom-&gt;altloc, elementsymbol,</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :         pos[0], pos[1], pos[2], </a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineNoCov">          0 :         atom-&gt;occupancy, atom-&gt;bfactor, atom-&gt;chain, atom-&gt;segid)) {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :       fprintf(stderr, </span></a>
+<a name="581"><span class="lineNum">     581 </span>            :           &quot;PDB: Error encountered writing atom %d; file may be incomplete.\n&quot;,</a>
+<a name="582"><span class="lineNum">     582 </span>            :           i+1);</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :       return MOLFILE_ERROR;</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :     }</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineNoCov">          0 :     ++atom;</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 :     pos += 3;</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :   }</a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :   fprintf(pdb-&gt;fd, &quot;END\n&quot;);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span>            :   return MOLFILE_SUCCESS;</a>
+<a name="591"><span class="lineNum">     591 </span>            : }</a>
+<a name="592"><span class="lineNum">     592 </span>            :  </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 : static void close_file_write(void *v) {</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :   pdbdata *pdb = (pdbdata *)v; </a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineNoCov">          0 :   fclose(pdb-&gt;fd);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :   free(pdb-&gt;atomlist);</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :   free(pdb);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 : static int read_molecule_metadata(void *v, molfile_metadata_t **metadata) {</span></a>
+<a name="601"><span class="lineNum">     601 </span>            :   pdbdata *pdb = (pdbdata *)v; </a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :   *metadata = pdb-&gt;meta;</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :   return MOLFILE_SUCCESS;</span></a>
+<a name="604"><span class="lineNum">     604 </span>            : }</a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            : /*</a>
+<a name="607"><span class="lineNum">     607 </span>            :  * Initialization stuff down here</a>
+<a name="608"><span class="lineNum">     608 </span>            :  */</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            : static molfile_plugin_t plugin;</a>
+<a name="611"><span class="lineNum">     611 </span>            :  </a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_init() {</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :   memset(&amp;plugin, 0, sizeof(molfile_plugin_t));</a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">       8336 :   plugin.abiversion = vmdplugin_ABIVERSION;</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">       8336 :   plugin.type = MOLFILE_PLUGIN_TYPE;</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">       8336 :   plugin.name = &quot;pdb&quot;;</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">       8336 :   plugin.prettyname = &quot;PDB&quot;;</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">       8336 :   plugin.author = &quot;Justin Gullingsrud, John Stone&quot;;</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">       8336 :   plugin.majorv = 1;</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">       8336 :   plugin.minorv = 16;</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">       8336 :   plugin.is_reentrant = VMDPLUGIN_THREADSAFE;</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">       8336 :   plugin.filename_extension = &quot;pdb,ent&quot;;</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">       8336 :   plugin.open_file_read = open_pdb_read;</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">       8336 :   plugin.read_structure = read_pdb_structure;</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">       8336 :   plugin.read_bonds = read_bonds;</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">       8336 :   plugin.read_next_timestep = read_next_timestep;</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">       8336 :   plugin.close_file_read = close_pdb_read;</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">       8336 :   plugin.open_file_write = open_file_write;</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">       8336 :   plugin.write_structure = write_structure;</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">       8336 :   plugin.write_timestep = write_timestep;</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">       8336 :   plugin.close_file_write = close_file_write;</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">       8336 :   plugin.read_molecule_metadata = read_molecule_metadata;</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">       8336 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="634"><span class="lineNum">     634 </span>            : }</a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       8336 : VMDPLUGIN_API int VMDPLUGIN_register(void *v, vmdplugin_register_cb cb) {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">       8336 :   (*cb)(v, (vmdplugin_t *)&amp;plugin);</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">       8336 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="639"><span class="lineNum">     639 </span>            : }</a>
+<a name="640"><span class="lineNum">     640 </span>            : </a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 : VMDPLUGIN_API int VMDPLUGIN_fini() {</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="643"><span class="lineNum">     643 </span>            : }</a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span>            : }</a>
+<a name="646"><span class="lineNum">     646 </span>            : }</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/periodic_table.h.func-sort-c.html b/coverage-libs/molfile/periodic_table.h.func-sort-c.html
new file mode 100644
index 0000000000..751c7c28ed
--- /dev/null
+++ b/coverage-libs/molfile/periodic_table.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/periodic_table.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - periodic_table.h<span style="font-size: 80%;"> (<a href="periodic_table.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="periodic_table.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#140">_ZN4PLMD7molfileL12get_pte_massEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#133">_ZN4PLMD7molfileL13get_pte_labelEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#147">_ZN4PLMD7molfileL18get_pte_vdw_radiusEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#198">_ZN4PLMD7molfileL23get_pte_idx_from_stringEPKc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/periodic_table.h.func.html b/coverage-libs/molfile/periodic_table.h.func.html
new file mode 100644
index 0000000000..7db94e7056
--- /dev/null
+++ b/coverage-libs/molfile/periodic_table.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/periodic_table.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - periodic_table.h<span style="font-size: 80%;"> (<a href="periodic_table.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="periodic_table.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#140">_ZN4PLMD7molfileL12get_pte_massEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#133">_ZN4PLMD7molfileL13get_pte_labelEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#147">_ZN4PLMD7molfileL18get_pte_vdw_radiusEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="periodic_table.h.gcov.html#198">_ZN4PLMD7molfileL23get_pte_idx_from_stringEPKc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/periodic_table.h.gcov.html b/coverage-libs/molfile/periodic_table.h.gcov.html
new file mode 100644
index 0000000000..d5789052ae
--- /dev/null
+++ b/coverage-libs/molfile/periodic_table.h.gcov.html
@@ -0,0 +1,324 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/periodic_table.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - periodic_table.h<span style="font-size: 80%;"> (source / <a href="periodic_table.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifndef __PLUMED_molfile_periodic_table_h</a>
+<a name="38"><span class="lineNum">      38 </span>            : #define __PLUMED_molfile_periodic_table_h</a>
+<a name="39"><span class="lineNum">      39 </span>            : /***************************************************************************</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * RCS INFORMATION:</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *      $RCSfile: periodic_table.h,v $</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *      $Revision: 1.12 $       $Date: 2009/01/21 17:45:41 $</a>
+<a name="45"><span class="lineNum">      45 </span>            :  *</a>
+<a name="46"><span class="lineNum">      46 </span>            :  ***************************************************************************/</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : /*</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * periodic table of elements and helper functions to convert</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * ordinal numbers to labels and back.</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * all tables and functions are declared static, so that it</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * can be safely included by all plugins that may need it.</a>
+<a name="53"><span class="lineNum">      53 </span>            :  *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * 2002-2009 akohlmey@cmm.chem.upenn.edu, vmd@ks.uiuc.edu</a>
+<a name="55"><span class="lineNum">      55 </span>            :  */</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &lt;string.h&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : #include &lt;ctype.h&gt;</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : namespace PLMD{</a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace molfile{</a>
+<a name="62"><span class="lineNum">      62 </span>            : /* periodic table of elements for translation of ordinal to atom type */</a>
+<a name="63"><span class="lineNum">      63 </span>            : static const char *pte_label[] = { </a>
+<a name="64"><span class="lineNum">      64 </span>            :     &quot;X&quot;,  &quot;H&quot;,  &quot;He&quot;, &quot;Li&quot;, &quot;Be&quot;, &quot;B&quot;,  &quot;C&quot;,  &quot;N&quot;,  &quot;O&quot;,  &quot;F&quot;,  &quot;Ne&quot;,</a>
+<a name="65"><span class="lineNum">      65 </span>            :     &quot;Na&quot;, &quot;Mg&quot;, &quot;Al&quot;, &quot;Si&quot;, &quot;P&quot; , &quot;S&quot;,  &quot;Cl&quot;, &quot;Ar&quot;, &quot;K&quot;,  &quot;Ca&quot;, &quot;Sc&quot;,</a>
+<a name="66"><span class="lineNum">      66 </span>            :     &quot;Ti&quot;, &quot;V&quot;,  &quot;Cr&quot;, &quot;Mn&quot;, &quot;Fe&quot;, &quot;Co&quot;, &quot;Ni&quot;, &quot;Cu&quot;, &quot;Zn&quot;, &quot;Ga&quot;, &quot;Ge&quot;, </a>
+<a name="67"><span class="lineNum">      67 </span>            :     &quot;As&quot;, &quot;Se&quot;, &quot;Br&quot;, &quot;Kr&quot;, &quot;Rb&quot;, &quot;Sr&quot;, &quot;Y&quot;,  &quot;Zr&quot;, &quot;Nb&quot;, &quot;Mo&quot;, &quot;Tc&quot;,</a>
+<a name="68"><span class="lineNum">      68 </span>            :     &quot;Ru&quot;, &quot;Rh&quot;, &quot;Pd&quot;, &quot;Ag&quot;, &quot;Cd&quot;, &quot;In&quot;, &quot;Sn&quot;, &quot;Sb&quot;, &quot;Te&quot;, &quot;I&quot;,  &quot;Xe&quot;,</a>
+<a name="69"><span class="lineNum">      69 </span>            :     &quot;Cs&quot;, &quot;Ba&quot;, &quot;La&quot;, &quot;Ce&quot;, &quot;Pr&quot;, &quot;Nd&quot;, &quot;Pm&quot;, &quot;Sm&quot;, &quot;Eu&quot;, &quot;Gd&quot;, &quot;Tb&quot;,</a>
+<a name="70"><span class="lineNum">      70 </span>            :     &quot;Dy&quot;, &quot;Ho&quot;, &quot;Er&quot;, &quot;Tm&quot;, &quot;Yb&quot;, &quot;Lu&quot;, &quot;Hf&quot;, &quot;Ta&quot;, &quot;W&quot;,  &quot;Re&quot;, &quot;Os&quot;,</a>
+<a name="71"><span class="lineNum">      71 </span>            :     &quot;Ir&quot;, &quot;Pt&quot;, &quot;Au&quot;, &quot;Hg&quot;, &quot;Tl&quot;, &quot;Pb&quot;, &quot;Bi&quot;, &quot;Po&quot;, &quot;At&quot;, &quot;Rn&quot;, &quot;Fr&quot;,</a>
+<a name="72"><span class="lineNum">      72 </span>            :     &quot;Ra&quot;, &quot;Ac&quot;, &quot;Th&quot;, &quot;Pa&quot;, &quot;U&quot;,  &quot;Np&quot;, &quot;Pu&quot;, &quot;Am&quot;, &quot;Cm&quot;, &quot;Bk&quot;, &quot;Cf&quot;,</a>
+<a name="73"><span class="lineNum">      73 </span>            :     &quot;Es&quot;, &quot;Fm&quot;, &quot;Md&quot;, &quot;No&quot;, &quot;Lr&quot;, &quot;Rf&quot;, &quot;Db&quot;, &quot;Sg&quot;, &quot;Bh&quot;, &quot;Hs&quot;, &quot;Mt&quot;,</a>
+<a name="74"><span class="lineNum">      74 </span>            :     &quot;Ds&quot;, &quot;Rg&quot;</a>
+<a name="75"><span class="lineNum">      75 </span>            : };</a>
+<a name="76"><span class="lineNum">      76 </span>            : static const int nr_pte_entries = sizeof(pte_label) / sizeof(char *);</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : /* corresponding table of masses. */</a>
+<a name="79"><span class="lineNum">      79 </span>            : static const float pte_mass[] = { </a>
+<a name="80"><span class="lineNum">      80 </span>            :     /* X  */ 0.00000, 1.00794, 4.00260, 6.941, 9.012182, 10.811,  </a>
+<a name="81"><span class="lineNum">      81 </span>            :     /* C  */ 12.0107, 14.0067, 15.9994, 18.9984032, 20.1797, </a>
+<a name="82"><span class="lineNum">      82 </span>            :     /* Na */ 22.989770, 24.3050, 26.981538, 28.0855, 30.973761,</a>
+<a name="83"><span class="lineNum">      83 </span>            :     /* S  */ 32.065, 35.453, 39.948, 39.0983, 40.078, 44.955910,</a>
+<a name="84"><span class="lineNum">      84 </span>            :     /* Ti */ 47.867, 50.9415, 51.9961, 54.938049, 55.845, 58.9332,</a>
+<a name="85"><span class="lineNum">      85 </span>            :     /* Ni */ 58.6934, 63.546, 65.409, 69.723, 72.64, 74.92160, </a>
+<a name="86"><span class="lineNum">      86 </span>            :     /* Se */ 78.96, 79.904, 83.798, 85.4678, 87.62, 88.90585, </a>
+<a name="87"><span class="lineNum">      87 </span>            :     /* Zr */ 91.224, 92.90638, 95.94, 98.0, 101.07, 102.90550,</a>
+<a name="88"><span class="lineNum">      88 </span>            :     /* Pd */ 106.42, 107.8682, 112.411, 114.818, 118.710, 121.760, </a>
+<a name="89"><span class="lineNum">      89 </span>            :     /* Te */ 127.60, 126.90447, 131.293, 132.90545, 137.327, </a>
+<a name="90"><span class="lineNum">      90 </span>            :     /* La */ 138.9055, 140.116, 140.90765, 144.24, 145.0, 150.36,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     /* Eu */ 151.964, 157.25, 158.92534, 162.500, 164.93032, </a>
+<a name="92"><span class="lineNum">      92 </span>            :     /* Er */ 167.259, 168.93421, 173.04, 174.967, 178.49, 180.9479,</a>
+<a name="93"><span class="lineNum">      93 </span>            :     /* W  */ 183.84, 186.207, 190.23, 192.217, 195.078, 196.96655, </a>
+<a name="94"><span class="lineNum">      94 </span>            :     /* Hg */ 200.59, 204.3833, 207.2, 208.98038, 209.0, 210.0, 222.0, </a>
+<a name="95"><span class="lineNum">      95 </span>            :     /* Fr */ 223.0, 226.0, 227.0, 232.0381, 231.03588, 238.02891,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     /* Np */ 237.0, 244.0, 243.0, 247.0, 247.0, 251.0, 252.0, 257.0,</a>
+<a name="97"><span class="lineNum">      97 </span>            :     /* Md */ 258.0, 259.0, 262.0, 261.0, 262.0, 266.0, 264.0, 269.0,</a>
+<a name="98"><span class="lineNum">      98 </span>            :     /* Mt */ 268.0, 271.0, 272.0</a>
+<a name="99"><span class="lineNum">      99 </span>            : };</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : /*</a>
+<a name="102"><span class="lineNum">     102 </span>            :  * corresponding table of VDW radii.</a>
+<a name="103"><span class="lineNum">     103 </span>            :  * van der Waals radii are taken from A. Bondi, </a>
+<a name="104"><span class="lineNum">     104 </span>            :  * J. Phys. Chem., 68, 441 - 452, 1964, </a>
+<a name="105"><span class="lineNum">     105 </span>            :  * except the value for H, which is taken from R.S. Rowland &amp; R. Taylor, </a>
+<a name="106"><span class="lineNum">     106 </span>            :  * J.Phys.Chem., 100, 7384 - 7391, 1996. Radii that are not available in </a>
+<a name="107"><span class="lineNum">     107 </span>            :  * either of these publications have RvdW = 2.00 Å.</a>
+<a name="108"><span class="lineNum">     108 </span>            :  * The radii for Ions (Na, K, Cl, Ca, Mg, and Cs are based on the CHARMM27 </a>
+<a name="109"><span class="lineNum">     109 </span>            :  * Rmin/2 parameters for (SOD, POT, CLA, CAL, MG, CES) by default.</a>
+<a name="110"><span class="lineNum">     110 </span>            :  */</a>
+<a name="111"><span class="lineNum">     111 </span>            : static const float pte_vdw_radius[] = { </a>
+<a name="112"><span class="lineNum">     112 </span>            :     /* X  */ 1.5, 1.2, 1.4, 1.82, 2.0, 2.0,  </a>
+<a name="113"><span class="lineNum">     113 </span>            :     /* C  */ 1.7, 1.55, 1.52, 1.47, 1.54, </a>
+<a name="114"><span class="lineNum">     114 </span>            :     /* Na */ 1.36, 1.18, 2.0, 2.1, 1.8,</a>
+<a name="115"><span class="lineNum">     115 </span>            :     /* S  */ 1.8, 2.27, 1.88, 1.76, 1.37, 2.0,</a>
+<a name="116"><span class="lineNum">     116 </span>            :     /* Ti */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="117"><span class="lineNum">     117 </span>            :     /* Ni */ 1.63, 1.4, 1.39, 1.07, 2.0, 1.85,</a>
+<a name="118"><span class="lineNum">     118 </span>            :     /* Se */ 1.9, 1.85, 2.02, 2.0, 2.0, 2.0, </a>
+<a name="119"><span class="lineNum">     119 </span>            :     /* Zr */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="120"><span class="lineNum">     120 </span>            :     /* Pd */ 1.63, 1.72, 1.58, 1.93, 2.17, 2.0, </a>
+<a name="121"><span class="lineNum">     121 </span>            :     /* Te */ 2.06, 1.98, 2.16, 2.1, 2.0,</a>
+<a name="122"><span class="lineNum">     122 </span>            :     /* La */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="123"><span class="lineNum">     123 </span>            :     /* Eu */ 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="124"><span class="lineNum">     124 </span>            :     /* Er */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="125"><span class="lineNum">     125 </span>            :     /* W  */ 2.0, 2.0, 2.0, 2.0, 1.72, 1.66,</a>
+<a name="126"><span class="lineNum">     126 </span>            :     /* Hg */ 1.55, 1.96, 2.02, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     /* Fr */ 2.0, 2.0, 2.0, 2.0, 2.0, 1.86,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     /* Np */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="129"><span class="lineNum">     129 </span>            :     /* Md */ 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0, 2.0,</a>
+<a name="130"><span class="lineNum">     130 </span>            :     /* Mt */ 2.0, 2.0, 2.0</a>
+<a name="131"><span class="lineNum">     131 </span>            : };</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : /* lookup functions */</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 : static const char *get_pte_label(const int idx)</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     if ((idx &lt; 1) || (idx &gt;= nr_pte_entries)) return pte_label[0];</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     return pte_label[idx];</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 : static float get_pte_mass(const int idx)</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :     if ((idx &lt; 1) || (idx &gt;= nr_pte_entries)) return pte_mass[0];</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     return pte_mass[idx];</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 : static float get_pte_vdw_radius(const int idx)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : {</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     if ((idx &lt; 1) || (idx &gt;= nr_pte_entries)) return pte_vdw_radius[0];</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : #if 1</a>
+<a name="154"><span class="lineNum">     154 </span>            :     /* Replace with Hydrogen radius with an &quot;all-atom&quot; radius */</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     if (idx == 1)</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :       return 1.0;    /* H  */</a>
+<a name="157"><span class="lineNum">     157 </span>            : #else</a>
+<a name="158"><span class="lineNum">     158 </span>            :     /* Replace with old VMD atom radii values */</a>
+<a name="159"><span class="lineNum">     159 </span>            :     switch (idx) {</a>
+<a name="160"><span class="lineNum">     160 </span>            :       case  1: return 1.0;    /* H  */</a>
+<a name="161"><span class="lineNum">     161 </span>            :       case  6: return 1.5;    /* C  */</a>
+<a name="162"><span class="lineNum">     162 </span>            :       case  7: return 1.4;    /* N  */</a>
+<a name="163"><span class="lineNum">     163 </span>            :       case  8: return 1.3;    /* O  */</a>
+<a name="164"><span class="lineNum">     164 </span>            :       case  9: return 1.2;    /* F  */</a>
+<a name="165"><span class="lineNum">     165 </span>            :       case 15: return 1.5;    /* P  */</a>
+<a name="166"><span class="lineNum">     166 </span>            :       case 16: return 1.9;    /* S  */ </a>
+<a name="167"><span class="lineNum">     167 </span>            :     }</a>
+<a name="168"><span class="lineNum">     168 </span>            : #endif</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     return pte_vdw_radius[idx];</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : static int get_pte_idx(const char *label)</a>
+<a name="174"><span class="lineNum">     174 </span>            : {</a>
+<a name="175"><span class="lineNum">     175 </span>            :     int i;</a>
+<a name="176"><span class="lineNum">     176 </span>            :     char atom[3];</a>
+<a name="177"><span class="lineNum">     177 </span>            :     </a>
+<a name="178"><span class="lineNum">     178 </span>            :     /* zap string */</a>
+<a name="179"><span class="lineNum">     179 </span>            :     atom[0] = (char) 0;</a>
+<a name="180"><span class="lineNum">     180 </span>            :     atom[1] = (char) 0;</a>
+<a name="181"><span class="lineNum">     181 </span>            :     atom[2] = (char) 0;</a>
+<a name="182"><span class="lineNum">     182 </span>            :     /* if we don't have a null-pointer, there must be at least two </a>
+<a name="183"><span class="lineNum">     183 </span>            :      * chars, which is all we need. we convert to the capitalization </a>
+<a name="184"><span class="lineNum">     184 </span>            :      * convention of the table above during assignment. */</a>
+<a name="185"><span class="lineNum">     185 </span>            :     if (label != NULL) {</a>
+<a name="186"><span class="lineNum">     186 </span>            :         atom[0] = (char) toupper((int) label[0]);</a>
+<a name="187"><span class="lineNum">     187 </span>            :         atom[1] = (char) tolower((int) label[1]);</a>
+<a name="188"><span class="lineNum">     188 </span>            :     }</a>
+<a name="189"><span class="lineNum">     189 </span>            :     /* discard numbers in atom label */</a>
+<a name="190"><span class="lineNum">     190 </span>            :     if (isdigit(atom[1])) atom[1] = (char) 0;</a>
+<a name="191"><span class="lineNum">     191 </span>            :     </a>
+<a name="192"><span class="lineNum">     192 </span>            :     for (i=0; i &lt; nr_pte_entries; ++i) {</a>
+<a name="193"><span class="lineNum">     193 </span>            :         if ( (pte_label[i][0] == atom[0])</a>
+<a name="194"><span class="lineNum">     194 </span>            :              &amp;&amp; (pte_label[i][1] == atom[1]) ) return i;</a>
+<a name="195"><span class="lineNum">     195 </span>            :     }</a>
+<a name="196"><span class="lineNum">     196 </span>            :     </a>
+<a name="197"><span class="lineNum">     197 </span>            :     return 0;</a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 : static int get_pte_idx_from_string(const char *label) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   int i, ind;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   char atom[3];</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   if (label != NULL) {</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     /* zap string */</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :     atom[0] = atom[1] = atom[2] = '\0';</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     for (ind=0,i=0; (ind&lt;2) &amp;&amp; (label[i]!='\0'); i++) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       if (label[i] != ' ') {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :         atom[ind] = toupper(label[i]);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :         ind++;</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :       }</a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     if (ind &lt; 1)</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :       return 0; /* no non-whitespace characters */</a>
+<a name="217"><span class="lineNum">     217 </span>            :  </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :     for (i=0; i &lt; nr_pte_entries; ++i) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :       if ((toupper(pte_label[i][0]) == atom[0]) &amp;&amp; (toupper(pte_label[i][1]) == atom[1])) </span></a>
+<a name="220"><span class="lineNum">     220 </span>            :         return i;</a>
+<a name="221"><span class="lineNum">     221 </span>            :     }</a>
+<a name="222"><span class="lineNum">     222 </span>            :   }  </a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   return 0;</a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            : #if 0</a>
+<a name="228"><span class="lineNum">     228 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : int main() {</a>
+<a name="231"><span class="lineNum">     231 </span>            :   int i;</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :   printf(&quot;Periodic table check/dump\n&quot;);</a>
+<a name="234"><span class="lineNum">     234 </span>            :   printf(&quot;  Table contains data for %d elements\n&quot;, nr_pte_entries);</a>
+<a name="235"><span class="lineNum">     235 </span>            :   printf(&quot;   Mass table size check: %d\n&quot;, sizeof(pte_mass) / sizeof(float));</a>
+<a name="236"><span class="lineNum">     236 </span>            :   printf(&quot;    VDW table size check: %d\n&quot;, sizeof(pte_vdw_radius) / sizeof(float));</a>
+<a name="237"><span class="lineNum">     237 </span>            :   printf(&quot;\n&quot;);</a>
+<a name="238"><span class="lineNum">     238 </span>            :   printf(&quot;Symbol Num    Mass   rVDW\n&quot;);</a>
+<a name="239"><span class="lineNum">     239 </span>            :   for (i=0; i&lt;nr_pte_entries; i++) {</a>
+<a name="240"><span class="lineNum">     240 </span>            :     printf(&quot;   %-2s  %3d  %6.2f  %4.2f\n&quot;,</a>
+<a name="241"><span class="lineNum">     241 </span>            :       get_pte_label(i), i, get_pte_mass(i), get_pte_vdw_radius(i));</a>
+<a name="242"><span class="lineNum">     242 </span>            :   } </a>
+<a name="243"><span class="lineNum">     243 </span>            :   return 0;</a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+<a name="245"><span class="lineNum">     245 </span>            : #endif</a>
+<a name="246"><span class="lineNum">     246 </span>            : }</a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/readpdb.h.func-sort-c.html b/coverage-libs/molfile/readpdb.h.func-sort-c.html
new file mode 100644
index 0000000000..060384934d
--- /dev/null
+++ b/coverage-libs/molfile/readpdb.h.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/readpdb.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - readpdb.h<span style="font-size: 80%;"> (<a href="readpdb.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryLo">32.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="readpdb.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#246">_ZN4PLMD7molfileL14get_pdb_conectEPKciPiS3_S3_PS3_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#323">_ZN4PLMD7molfileL14get_pdb_fieldsEPKciPiPcS4_S4_S4_S4_S4_S4_S4_PfS5_S5_S5_S5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#226">_ZN4PLMD7molfileL14get_pdb_headerEPKcPcS3_S3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#387">_ZN4PLMD7molfileL20write_raw_pdb_recordEP8_IO_FILEPKciS4_S4_iS4_S4_S4_fffffS4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#210">_ZN4PLMD7molfileL23adjust_pdb_field_stringEPc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#152">_ZN4PLMD7molfileL14get_pdb_cryst1EPKcPfS3_S3_S3_S3_S3_</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#176">_ZN4PLMD7molfileL19get_pdb_coordinatesEPKcPfS3_S3_S3_S3_</a></td>
+              <td class="coverFnHi">105240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#78">_ZN4PLMD7molfileL15read_pdb_recordEP8_IO_FILEPc</a></td>
+              <td class="coverFnHi">206890</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/readpdb.h.func.html b/coverage-libs/molfile/readpdb.h.func.html
new file mode 100644
index 0000000000..667000e0f9
--- /dev/null
+++ b/coverage-libs/molfile/readpdb.h.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/readpdb.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - readpdb.h<span style="font-size: 80%;"> (<a href="readpdb.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryLo">32.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="readpdb.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#246">_ZN4PLMD7molfileL14get_pdb_conectEPKciPiS3_S3_PS3_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#152">_ZN4PLMD7molfileL14get_pdb_cryst1EPKcPfS3_S3_S3_S3_S3_</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#323">_ZN4PLMD7molfileL14get_pdb_fieldsEPKciPiPcS4_S4_S4_S4_S4_S4_S4_PfS5_S5_S5_S5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#226">_ZN4PLMD7molfileL14get_pdb_headerEPKcPcS3_S3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#78">_ZN4PLMD7molfileL15read_pdb_recordEP8_IO_FILEPc</a></td>
+              <td class="coverFnHi">206890</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#176">_ZN4PLMD7molfileL19get_pdb_coordinatesEPKcPfS3_S3_S3_S3_</a></td>
+              <td class="coverFnHi">105240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#387">_ZN4PLMD7molfileL20write_raw_pdb_recordEP8_IO_FILEPKciS4_S4_iS4_S4_S4_fffffS4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="readpdb.h.gcov.html#210">_ZN4PLMD7molfileL23adjust_pdb_field_stringEPc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/molfile/readpdb.h.gcov.html b/coverage-libs/molfile/readpdb.h.gcov.html
new file mode 100644
index 0000000000..b06ce139a1
--- /dev/null
+++ b/coverage-libs/molfile/readpdb.h.gcov.html
@@ -0,0 +1,523 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - molfile/readpdb.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">molfile</a> - readpdb.h<span style="font-size: 80%;"> (source / <a href="readpdb.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryLo">32.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : University of Illinois Open Source License</a>
+<a name="3"><span class="lineNum">       3 </span>            : Copyright 2003 Theoretical and Computational Biophysics Group, </a>
+<a name="4"><span class="lineNum">       4 </span>            : All rights reserved.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Developed by:           Theoretical and Computational Biophysics Group</a>
+<a name="7"><span class="lineNum">       7 </span>            :                         University of Illinois at Urbana-Champaign</a>
+<a name="8"><span class="lineNum">       8 </span>            :                         http://www.ks.uiuc.edu/</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy of</a>
+<a name="11"><span class="lineNum">      11 </span>            : this software and associated documentation files (the Software), to deal with </a>
+<a name="12"><span class="lineNum">      12 </span>            : the Software without restriction, including without limitation the rights to </a>
+<a name="13"><span class="lineNum">      13 </span>            : use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies </a>
+<a name="14"><span class="lineNum">      14 </span>            : of the Software, and to permit persons to whom the Software is furnished to </a>
+<a name="15"><span class="lineNum">      15 </span>            : do so, subject to the following conditions:</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : Redistributions of source code must retain the above copyright notice, </a>
+<a name="18"><span class="lineNum">      18 </span>            : this list of conditions and the following disclaimers.</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : Redistributions in binary form must reproduce the above copyright notice, </a>
+<a name="21"><span class="lineNum">      21 </span>            : this list of conditions and the following disclaimers in the documentation </a>
+<a name="22"><span class="lineNum">      22 </span>            : and/or other materials provided with the distribution.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : Neither the names of Theoretical and Computational Biophysics Group, </a>
+<a name="25"><span class="lineNum">      25 </span>            : University of Illinois at Urbana-Champaign, nor the names of its contributors </a>
+<a name="26"><span class="lineNum">      26 </span>            : may be used to endorse or promote products derived from this Software without </a>
+<a name="27"><span class="lineNum">      27 </span>            : specific prior written permission.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : THE SOFTWARE IS PROVIDED AS IS, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR </a>
+<a name="30"><span class="lineNum">      30 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, </a>
+<a name="31"><span class="lineNum">      31 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT.  IN NO EVENT SHALL </a>
+<a name="32"><span class="lineNum">      32 </span>            : THE CONTRIBUTORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR </a>
+<a name="33"><span class="lineNum">      33 </span>            : OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, </a>
+<a name="34"><span class="lineNum">      34 </span>            : ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR </a>
+<a name="35"><span class="lineNum">      35 </span>            : OTHER DEALINGS WITH THE SOFTWARE.</a>
+<a name="36"><span class="lineNum">      36 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifndef __PLUMED_molfile_readpdb_h</a>
+<a name="38"><span class="lineNum">      38 </span>            : #define __PLUMED_molfile_readpdb_h</a>
+<a name="39"><span class="lineNum">      39 </span>            : /***************************************************************************</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *cr</a>
+<a name="41"><span class="lineNum">      41 </span>            :  *cr            (C) Copyright 1995-2016 The Board of Trustees of the</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *cr                        University of Illinois</a>
+<a name="43"><span class="lineNum">      43 </span>            :  *cr                         All Rights Reserved</a>
+<a name="44"><span class="lineNum">      44 </span>            :  *cr</a>
+<a name="45"><span class="lineNum">      45 </span>            :  ***************************************************************************/</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : /***************************************************************************</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * RCS INFORMATION:</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *      $RCSfile: readpdb.h,v $</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *      $Author: johns $       $Locker:  $             $State: Exp $</a>
+<a name="52"><span class="lineNum">      52 </span>            :  *      $Revision: 1.43 $       $Date: 2016/11/28 05:01:54 $</a>
+<a name="53"><span class="lineNum">      53 </span>            :  *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  ***************************************************************************/</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : #ifndef READ_PDB_H</a>
+<a name="57"><span class="lineNum">      57 </span>            : #define READ_PDB_H</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="60"><span class="lineNum">      60 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="61"><span class="lineNum">      61 </span>            : #include &lt;string.h&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : namespace PLMD{</a>
+<a name="64"><span class="lineNum">      64 </span>            : namespace molfile{</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : #define PDB_RECORD_LENGTH   80   /* actual record size */</a>
+<a name="67"><span class="lineNum">      67 </span>            : #define PDB_BUFFER_LENGTH   83   /* size need to buffer + CR, LF, and NUL */</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : #define VMDUSECONECTRECORDS 1</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : /*  record type defines */</a>
+<a name="72"><span class="lineNum">      72 </span>            : enum {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   PDB_HEADER, PDB_REMARK, PDB_ATOM, PDB_CONECT, PDB_UNKNOWN, PDB_END, PDB_EOF, PDB_CRYST1</a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : /* read the next record from the specified pdb file, and put the string found</a>
+<a name="77"><span class="lineNum">      77 </span>            :    in the given string pointer (the caller must provide adequate (81 chars)</a>
+<a name="78"><span class="lineNum">      78 </span>            :    buffer space); return the type of record found</a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     206890 : static int read_pdb_record(FILE *f, char *retStr) {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   int ch;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   char inbuf[PDB_BUFFER_LENGTH]; /* space for line + cr + lf + NUL */</a>
+<a name="83"><span class="lineNum">      83 </span>            :   int recType = PDB_UNKNOWN;</a>
+<a name="84"><span class="lineNum">      84 </span>            :  </a>
+<a name="85"><span class="lineNum">      85 </span>            :   /* XXX This PDB record reading code breaks with files that use</a>
+<a name="86"><span class="lineNum">      86 </span>            :    * Mac or DOS style line breaks with ctrl-M characters.  We need</a>
+<a name="87"><span class="lineNum">      87 </span>            :    * to replace the use of fgets() and comparisons against \n with</a>
+<a name="88"><span class="lineNum">      88 </span>            :    * code that properly handles the other cases.</a>
+<a name="89"><span class="lineNum">      89 </span>            :    */</a>
+<a name="90"><span class="lineNum">      90 </span>            :  </a>
+<a name="91"><span class="lineNum">      91 </span>            :   /* read the next line, including any ending cr/lf char */</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">     206890 :   if (inbuf != fgets(inbuf, PDB_RECORD_LENGTH + 2, f)) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         49 :     retStr[0] = '\0';</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :     recType = PDB_EOF;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   } else {</a>
+<a name="96"><span class="lineNum">      96 </span>            : #if 0</a>
+<a name="97"><span class="lineNum">      97 </span>            :     /* XXX disabled this code since \n chars are desirable in remarks */</a>
+<a name="98"><span class="lineNum">      98 </span>            :     /* and to make the behavior consistent with webpdbplugin          */</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :     /* remove the newline character, if there is one */</a>
+<a name="101"><span class="lineNum">     101 </span>            :     if (inbuf[strlen(inbuf)-1] == '\n')</a>
+<a name="102"><span class="lineNum">     102 </span>            :       inbuf[strlen(inbuf)-1] = '\0';</a>
+<a name="103"><span class="lineNum">     103 </span>            : #endif</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :     /* atom records are the most common */</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">     206841 :     if (!strncmp(inbuf, &quot;ATOM &quot;,  5) || !strncmp(inbuf, &quot;HETATM&quot;, 6)) {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :       /* Note that by only comparing 5 chars for &quot;ATOM &quot; rather than 6,     */</a>
+<a name="108"><span class="lineNum">     108 </span>            :       /* we allow PDB files containing &gt; 99,999 atoms generated by AMBER    */</a>
+<a name="109"><span class="lineNum">     109 </span>            :       /* to load which would otherwise fail.  Not needed for HETATM since   */</a>
+<a name="110"><span class="lineNum">     110 </span>            :       /* those aren't going to show up in files produced for/by MD engines. */</a>
+<a name="111"><span class="lineNum">     111 </span>            :       recType = PDB_ATOM;</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        459 :     } else if (!strncmp(inbuf, &quot;CONECT&quot;, 6)) {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :       recType = PDB_CONECT;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        459 :     } else if (!strncmp(inbuf, &quot;REMARK&quot;, 6)) {</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :       recType = PDB_REMARK;</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        369 :     } else if (!strncmp(inbuf, &quot;CRYST1&quot;, 6)) {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :       recType = PDB_CRYST1;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        307 :     } else if (!strncmp(inbuf, &quot;HEADER&quot;, 6)) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       recType = PDB_HEADER;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        307 :     } else if (!strncmp(inbuf, &quot;END&quot;, 3)) {  /* very permissive */</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :       /* XXX we treat any &quot;ENDxxx&quot; record as an end, to simplify testing */</a>
+<a name="122"><span class="lineNum">     122 </span>            :       /*     since we don't remove trailing '\n' chars                   */</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :       /* the only two legal END records are &quot;END   &quot; and &quot;ENDMDL&quot; */</a>
+<a name="125"><span class="lineNum">     125 </span>            :       recType = PDB_END;</a>
+<a name="126"><span class="lineNum">     126 </span>            :     } </a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : #if 0</a>
+<a name="129"><span class="lineNum">     129 </span>            :     /* XXX disable record type checking for now */</a>
+<a name="130"><span class="lineNum">     130 </span>            :     if (recType == PDB_ATOM || </a>
+<a name="131"><span class="lineNum">     131 </span>            :         recType == PDB_CONECT || </a>
+<a name="132"><span class="lineNum">     132 </span>            :         recType == PDB_REMARK || </a>
+<a name="133"><span class="lineNum">     133 </span>            :         recType == PDB_HEADER || </a>
+<a name="134"><span class="lineNum">     134 </span>            :         recType == PDB_CRYST1) {</a>
+<a name="135"><span class="lineNum">     135 </span>            :       strcpy(retStr, inbuf);</a>
+<a name="136"><span class="lineNum">     136 </span>            :     } else {</a>
+<a name="137"><span class="lineNum">     137 </span>            :       retStr[0] = '\0';</a>
+<a name="138"><span class="lineNum">     138 </span>            :     }</a>
+<a name="139"><span class="lineNum">     139 </span>            : #else</a>
+<a name="140"><span class="lineNum">     140 </span>            :     strcpy(retStr, inbuf);</a>
+<a name="141"><span class="lineNum">     141 </span>            : #endif</a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   /* read the '\r', if there was one */</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">     206890 :   ch = fgetc(f);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">     206890 :   if (ch != '\r')</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">     206890 :     ungetc(ch, f);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">     206890 :   return recType;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : /* Extract the alpha/beta/gamma a/b/c unit cell info from a CRYST1 record */</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         32 : static void get_pdb_cryst1(const char *record, </span></a>
+<a name="155"><span class="lineNum">     155 </span>            :                            float *alpha, float *beta, float *gamma, </a>
+<a name="156"><span class="lineNum">     156 </span>            :                            float *a, float *b, float *c) {</a>
+<a name="157"><span class="lineNum">     157 </span>            :   char tmp[PDB_RECORD_LENGTH+3]; /* space for line + cr + lf + NUL */</a>
+<a name="158"><span class="lineNum">     158 </span>            :   char ch, *s;</a>
+<a name="159"><span class="lineNum">     159 </span>            :   memset(tmp, 0, sizeof(tmp));</a>
+<a name="160"><span class="lineNum">     160 </span>            :   strncpy(tmp, record, PDB_RECORD_LENGTH);</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         32 :   s = tmp+6 ;          ch = tmp[15]; tmp[15] = 0;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         32 :   *a = (float) atof(s);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         32 :   s = tmp+15; *s = ch; ch = tmp[24]; tmp[24] = 0;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         32 :   *b = (float) atof(s);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         32 :   s = tmp+24; *s = ch; ch = tmp[33]; tmp[33] = 0;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         32 :   *c = (float) atof(s);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         32 :   s = tmp+33; *s = ch; ch = tmp[40]; tmp[40] = 0;</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         32 :   *alpha = (float) atof(s);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         32 :   s = tmp+40; *s = ch; ch = tmp[47]; tmp[47] = 0;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         32 :   *beta = (float) atof(s);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         32 :   s = tmp+47; *s = ch; ch = tmp[54]; tmp[54] = 0;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         32 :   *gamma = (float) atof(s);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         32 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : /* Extract the x,y,z coords, occupancy, and beta from an ATOM record */</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     105240 : static void get_pdb_coordinates(const char *record, </span></a>
+<a name="179"><span class="lineNum">     179 </span>            :                                 float *x, float *y, float *z,</a>
+<a name="180"><span class="lineNum">     180 </span>            :                                 float *occup, float *beta) {</a>
+<a name="181"><span class="lineNum">     181 </span>            :   char numstr[50]; /* store all fields in one array to save memset calls */</a>
+<a name="182"><span class="lineNum">     182 </span>            :   memset(numstr, 0, sizeof(numstr));</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     105240 :   if (x != NULL) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">     105240 :     strncpy(numstr, record + 30, 8);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     105240 :     *x = (float) atof(numstr);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">     105240 :   if (y != NULL) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">     105240 :     strncpy(numstr+10, record + 38, 8);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     105240 :     *y = (float) atof(numstr+10);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     105240 :   if (z != NULL) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     105240 :     strncpy(numstr+20, record + 46, 8);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     105240 :     *z = (float) atof(numstr+20);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     105240 :   if (occup != NULL) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">     105240 :     strncpy(numstr+30, record + 54, 6);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     105240 :     *occup = (float) atof(numstr+30);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     105240 :   if (beta != NULL) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     105240 :     strncpy(numstr+40, record + 60, 6);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">     105240 :     *beta = (float) atof(numstr+40);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     105240 : }</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : /* remove leading and trailing spaces from PDB fields */</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 : static void adjust_pdb_field_string(char *field) {</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   int i, len;</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   len = strlen(field);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   while (len &gt; 0 &amp;&amp; field[len-1] == ' ') {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :     field[len-1] = '\0';</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :     len--;</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :   while (len &gt; 0 &amp;&amp; field[0] == ' ') {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :     for (i=0; i &lt; len; i++)</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :       field[i] = field[i+1];</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :     len--;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   }</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 : static void get_pdb_header(const char *record, char *pdbcode, char *date,</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :                            char *classification) {</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :   if (date != NULL) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     strncpy(date, record + 50, 9);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     date[9] = '\0';</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   if (classification != NULL) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :     strncpy(classification, record + 10, 40);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :     classification[40] = '\0';</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :   if (pdbcode != NULL) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :     strncpy(pdbcode, record + 62, 4);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :     pdbcode[4] = '\0';</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :     adjust_pdb_field_string(pdbcode); /* remove spaces from accession code */</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   }</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 : static void get_pdb_conect(const char *record, int natoms, int *idxmap,</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :                            int *maxbnum, int *nbonds, int **from, int **to) {</a>
+<a name="250"><span class="lineNum">     250 </span>            :   int bondto[11], numbonds, i;</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :   int reclen = strlen(record);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :   for (numbonds=0, i=0; i&lt;11; i++) {</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :     char bondstr[6];</a>
+<a name="255"><span class="lineNum">     255 </span>            :     const int fieldwidth = 5;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :     int start = 6 + i*fieldwidth;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :     int end = start + fieldwidth;</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     if (end &gt;= reclen)</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :       break;</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :     memcpy(bondstr, record + start, fieldwidth);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :     bondstr[5] = '\0';</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :     if (sscanf(bondstr, &quot;%d&quot;, &amp;bondto[numbonds]) &lt; 0)</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :       break;</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :     numbonds++; </span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   }</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :   for (i=0; i&lt;numbonds; i++) {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     /* only add one bond per pair, PDBs list them redundantly */ </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :     if (bondto[i] &gt; bondto[0]) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :       int newnbonds = *nbonds + 1; /* add a new bond */</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :       /* allocate more bondlist space if necessary */</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :       if (newnbonds &gt;= *maxbnum) {</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :         int newmax;</a>
+<a name="277"><span class="lineNum">     277 </span>            :         int *newfromlist, *newtolist;</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :         newmax = (newnbonds + 11) * 1.25;</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :         newfromlist = (int *) realloc(*from, newmax * sizeof(int));</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :         newtolist = (int *) realloc(*to, newmax * sizeof(int));</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :         if (newfromlist != NULL || newtolist != NULL) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :           *maxbnum = newmax;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :           *from = newfromlist;</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :           *to = newtolist;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :         } else {</a>
+<a name="288"><span class="lineNum">     288 </span>            :           printf(&quot;readpdb) failed to allocate memory for bondlists\n&quot;);</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :           return; /* abort */</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :         }</a>
+<a name="291"><span class="lineNum">     291 </span>            :       }</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :       *nbonds = newnbonds;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :       (*from)[newnbonds-1] = idxmap[bondto[0]] + 1;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :       (*to)[newnbonds-1] = idxmap[bondto[i]] + 1;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :     }</a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span>            : }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : /* ATOM field format according to PDB standard v2.2</a>
+<a name="301"><span class="lineNum">     301 </span>            :   COLUMNS        DATA TYPE       FIELD         DEFINITION</a>
+<a name="302"><span class="lineNum">     302 </span>            : ---------------------------------------------------------------------------------</a>
+<a name="303"><span class="lineNum">     303 </span>            :  1 -  6        Record name     &quot;ATOM  &quot;</a>
+<a name="304"><span class="lineNum">     304 </span>            :  7 - 11        Integer         serial        Atom serial number.</a>
+<a name="305"><span class="lineNum">     305 </span>            : 13 - 16        Atom            name          Atom name.</a>
+<a name="306"><span class="lineNum">     306 </span>            : 17             Character       altLoc        Alternate location indicator.</a>
+<a name="307"><span class="lineNum">     307 </span>            : 18 - 20        Residue name    resName       Residue name.</a>
+<a name="308"><span class="lineNum">     308 </span>            : 22             Character       chainID       Chain identifier.</a>
+<a name="309"><span class="lineNum">     309 </span>            : 23 - 26        Integer         resSeq        Residue sequence number.</a>
+<a name="310"><span class="lineNum">     310 </span>            : 27             AChar           iCode         Code for insertion of residues.</a>
+<a name="311"><span class="lineNum">     311 </span>            : 31 - 38        Real(8.3)       x             Orthogonal coordinates for X in Angstroms.</a>
+<a name="312"><span class="lineNum">     312 </span>            : 39 - 46        Real(8.3)       y             Orthogonal coordinates for Y in Angstroms.</a>
+<a name="313"><span class="lineNum">     313 </span>            : 47 - 54        Real(8.3)       z             Orthogonal coordinates for Z in Angstroms.</a>
+<a name="314"><span class="lineNum">     314 </span>            : 55 - 60        Real(6.2)       occupancy     Occupancy.</a>
+<a name="315"><span class="lineNum">     315 </span>            : 61 - 66        Real(6.2)       tempFactor    Temperature factor.</a>
+<a name="316"><span class="lineNum">     316 </span>            : 73 - 76        LString(4)      segID         Segment identifier, left-justified.</a>
+<a name="317"><span class="lineNum">     317 </span>            : 77 - 78        LString(2)      element       Element symbol, right-justified.</a>
+<a name="318"><span class="lineNum">     318 </span>            : 79 - 80        LString(2)      charge        Charge on the atom.</a>
+<a name="319"><span class="lineNum">     319 </span>            :  */</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : /* Break a pdb ATOM record into its fields.  The user must provide the</a>
+<a name="322"><span class="lineNum">     322 </span>            :    necessary space to store the atom name, residue name, and segment name.</a>
+<a name="323"><span class="lineNum">     323 </span>            :    Character strings will be null-terminated.</a>
+<a name="324"><span class="lineNum">     324 </span>            : */</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 : static void get_pdb_fields(const char *record, int reclength, int *serial,</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :                            char *name, char *resname, char *chain, </a>
+<a name="327"><span class="lineNum">     327 </span>            :                            char *segname, char *resid, char *insertion, </a>
+<a name="328"><span class="lineNum">     328 </span>            :                            char *altloc, char *elementsymbol,</a>
+<a name="329"><span class="lineNum">     329 </span>            :                            float *x, float *y, float *z, </a>
+<a name="330"><span class="lineNum">     330 </span>            :                            float *occup, float *beta) {</a>
+<a name="331"><span class="lineNum">     331 </span>            :   char serialbuf[6];</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   /* get atom serial number */</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :   strncpy(serialbuf, record + 6, 5);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :   serialbuf[5] = '\0';</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :   *serial = 0;</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :   sscanf(serialbuf, &quot;%5d&quot;, serial);</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   </a>
+<a name="339"><span class="lineNum">     339 </span>            :   /* get atom name */</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :   strncpy(name, record + 12, 4);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :   name[4] = '\0';</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :   adjust_pdb_field_string(name); /* remove spaces from the name */</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :   /* get alternate location identifier */</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   strncpy(altloc, record + 16, 1);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   altloc[1] = '\0';</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            :   /* get residue name */</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   strncpy(resname, record + 17, 4);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :   resname[4] = '\0';</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :   adjust_pdb_field_string(resname); /* remove spaces from the resname */</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            :   /* get chain name */</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :   chain[0] = record[21];</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 :   chain[1] = '\0';</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   /* get residue id number */</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   strncpy(resid, record + 22, 4);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :   resid[4] = '\0';</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :   adjust_pdb_field_string(resid); /* remove spaces from the resid */</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   /* get the insertion code */</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   insertion[0] = record[26];</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :   insertion[1] = '\0';</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            :   /* get x, y, and z coordinates */</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :   get_pdb_coordinates(record, x, y, z, occup, beta);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            :   /* get segment name */</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :   if (reclength &gt;= 73) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :     strncpy(segname, record + 72, 4);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     segname[4] = '\0';</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :     adjust_pdb_field_string(segname); /* remove spaces from the segname */</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :   } else {</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :     segname[0] = '\0';</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :   /* get the atomic element symbol */</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   if (reclength &gt;= 77) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     strncpy(elementsymbol, record + 76, 2);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :     elementsymbol[2] = '\0';</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   } else {</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :     elementsymbol[0] = '\0';</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 : }  </span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            : /* Write PDB data to given file descriptor; return success. */</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 : static int write_raw_pdb_record(FILE *fd, const char *recordname,</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :     int index,const char *atomname, const char *resname,int resid, </a>
+<a name="391"><span class="lineNum">     391 </span>            :     const char *insertion, const char *altloc, const char *elementsymbol,</a>
+<a name="392"><span class="lineNum">     392 </span>            :     float x, float y, float z, float occ, float beta, </a>
+<a name="393"><span class="lineNum">     393 </span>            :     const char *chain, const char *segname) {</a>
+<a name="394"><span class="lineNum">     394 </span>            :   int rc;</a>
+<a name="395"><span class="lineNum">     395 </span>            :   char indexbuf[32];</a>
+<a name="396"><span class="lineNum">     396 </span>            :   char residbuf[32];</a>
+<a name="397"><span class="lineNum">     397 </span>            :   char segnamebuf[5];</a>
+<a name="398"><span class="lineNum">     398 </span>            :   char resnamebuf[5];</a>
+<a name="399"><span class="lineNum">     399 </span>            :   char altlocchar;</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            :   /* XXX                                                          */</a>
+<a name="402"><span class="lineNum">     402 </span>            :   /* if the atom or residue indices exceed the legal PDB spec, we */</a>
+<a name="403"><span class="lineNum">     403 </span>            :   /* start emitting asterisks or hexadecimal strings rather than  */</a>
+<a name="404"><span class="lineNum">     404 </span>            :   /* aborting.  This is not really legal, but is an accepted hack */</a>
+<a name="405"><span class="lineNum">     405 </span>            :   /* among various other programs that deal with large PDB files  */</a>
+<a name="406"><span class="lineNum">     406 </span>            :   /* If we run out of hexadecimal indices, then we just print     */</a>
+<a name="407"><span class="lineNum">     407 </span>            :   /* asterisks.                                                   */</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :   if (index &lt; 100000) {</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     snprintf(indexbuf, 32, &quot;%5d&quot;, index);</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :   } else if (index &lt; 1048576) {</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :     snprintf(indexbuf, 32, &quot;%05x&quot;, index);</a>
+<a name="412"><span class="lineNum">     412 </span>            :   } else {</a>
+<a name="413"><span class="lineNum">     413 </span>            :     snprintf(indexbuf, 32, &quot;*****&quot;);</a>
+<a name="414"><span class="lineNum">     414 </span>            :   }</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :   if (resid &lt; 10000) {</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :     snprintf(residbuf, 32, &quot;%4d&quot;, resid);</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :   } else if (resid &lt; 65536) {</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :     snprintf(residbuf, 32, &quot;%04x&quot;, resid);</a>
+<a name="420"><span class="lineNum">     420 </span>            :   } else { </a>
+<a name="421"><span class="lineNum">     421 </span>            :     snprintf(residbuf, 32, &quot;****&quot;);</a>
+<a name="422"><span class="lineNum">     422 </span>            :   }</a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :   altlocchar = altloc[0];</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :   if (altlocchar == '\0') {</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     altlocchar = ' ';</a>
+<a name="427"><span class="lineNum">     427 </span>            :   }</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            :   /* make sure the segname or resname do not overflow the format */ </a>
+<a name="430"><span class="lineNum">     430 </span>            :   strncpy(segnamebuf,segname,4);</a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :   segnamebuf[4] = '\0';</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :   strncpy(resnamebuf,resname,4);</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :   resnamebuf[4] = '\0';</span></a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :  </a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :   rc = fprintf(fd,</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :          &quot;%-6s%5s %4s%c%-4s%c%4s%c   %8.3f%8.3f%8.3f%6.2f%6.2f      %-4s%2s\n&quot;,</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :          recordname, indexbuf, atomname, altlocchar, resnamebuf, chain[0], </span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :          residbuf, insertion[0], x, y, z, occ, beta, segnamebuf, elementsymbol);</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :   return (rc &gt; 0);</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : }</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            : }</a>
+<a name="445"><span class="lineNum">     445 </span>            : }</a>
+<a name="446"><span class="lineNum">     446 </span>            : #endif</a>
+<a name="447"><span class="lineNum">     447 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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index 0000000000000000000000000000000000000000..2cdae107fceec6e7f02ac7acb4a34a82a540caa5
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+++ b/coverage-libs/xdrfile/index-sort-f.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - xdrfile</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">563</td>
+            <td class="headerCovTableEntry">1166</td>
+            <td class="headerCovTableEntryLo">48.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryLo">46.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile.cpp.gcov.html">xdrfile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.8%"><img src="../snow.png" width=54 height=10 alt="45.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.8&nbsp;%</td>
+      <td class="coverNumLo">432 / 943</td>
+      <td class="coverPerLo">38.3&nbsp;%</td>
+      <td class="coverNumLo">31 / 81</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile_xtc.cpp.gcov.html">xdrfile_xtc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">27 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile_trr.cpp.gcov.html">xdrfile_trr.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.7%"><img src="../snow.png" width=45 height=10 alt="54.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.7&nbsp;%</td>
+      <td class="coverNumLo">104 / 190</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/index-sort-l.html b/coverage-libs/xdrfile/index-sort-l.html
new file mode 100644
index 0000000000..4baa7caa69
--- /dev/null
+++ b/coverage-libs/xdrfile/index-sort-l.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - xdrfile</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">563</td>
+            <td class="headerCovTableEntry">1166</td>
+            <td class="headerCovTableEntryLo">48.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryLo">46.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile.cpp.gcov.html">xdrfile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.8%"><img src="../snow.png" width=54 height=10 alt="45.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.8&nbsp;%</td>
+      <td class="coverNumLo">432 / 943</td>
+      <td class="coverPerLo">38.3&nbsp;%</td>
+      <td class="coverNumLo">31 / 81</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile_trr.cpp.gcov.html">xdrfile_trr.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.7%"><img src="../snow.png" width=45 height=10 alt="54.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.7&nbsp;%</td>
+      <td class="coverNumLo">104 / 190</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile_xtc.cpp.gcov.html">xdrfile_xtc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">27 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/index.html b/coverage-libs/xdrfile/index.html
new file mode 100644
index 0000000000..d544481d8f
--- /dev/null
+++ b/coverage-libs/xdrfile/index.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - xdrfile</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">563</td>
+            <td class="headerCovTableEntry">1166</td>
+            <td class="headerCovTableEntryLo">48.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryLo">46.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile.cpp.gcov.html">xdrfile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=46 height=10 alt="45.8%"><img src="../snow.png" width=54 height=10 alt="45.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">45.8&nbsp;%</td>
+      <td class="coverNumLo">432 / 943</td>
+      <td class="coverPerLo">38.3&nbsp;%</td>
+      <td class="coverNumLo">31 / 81</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile_trr.cpp.gcov.html">xdrfile_trr.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="54.7%"><img src="../snow.png" width=45 height=10 alt="54.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">54.7&nbsp;%</td>
+      <td class="coverNumLo">104 / 190</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="xdrfile_xtc.cpp.gcov.html">xdrfile_xtc.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">27 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile.cpp.func-sort-c.html b/coverage-libs/xdrfile/xdrfile.cpp.func-sort-c.html
new file mode 100644
index 0000000000..34fabdf9c4
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile.cpp.func-sort-c.html
@@ -0,0 +1,396 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile.cpp<span style="font-size: 80%;"> (<a href="xdrfile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">432</td>
+            <td class="headerCovTableEntry">943</td>
+            <td class="headerCovTableEntryLo">45.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntryLo">38.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="xdrfile.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1879">_ZN4PLMD7xdrfile10xdrrshort_EPiPsS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1867">_ZN4PLMD7xdrfile10xdrruchar_EPiPhS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1885">_ZN4PLMD7xdrfile10xdrwshort_EPiPsS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1873">_ZN4PLMD7xdrfile10xdrwuchar_EPiPhS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1915">_ZN4PLMD7xdrfile11xdrrdouble_EPiPdS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1997">_ZN4PLMD7xdrfile11xdrropaque_EPiPcS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1903">_ZN4PLMD7xdrfile11xdrrsingle_EPiPfS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1957">_ZN4PLMD7xdrfile11xdrrstring_EPiPcS1_i</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1891">_ZN4PLMD7xdrfile11xdrrushort_EPiPtS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile.cpp.gcov.html#1921">_ZN4PLMD7xdrfile11xdrwdouble_EPiPdS1_S1_</a></td>
+              <td class="coverFnLo">0</td>
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diff --git a/coverage-libs/xdrfile/xdrfile.cpp.func.html b/coverage-libs/xdrfile/xdrfile.cpp.func.html
new file mode 100644
index 0000000000..238bc1732c
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile.cpp.func.html
@@ -0,0 +1,396 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
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+<body>
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+          <tr>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile.cpp.gcov.html b/coverage-libs/xdrfile/xdrfile.cpp.gcov.html
new file mode 100644
index 0000000000..6ed9872514
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile.cpp.gcov.html
@@ -0,0 +1,2724 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile.cpp<span style="font-size: 80%;"> (source / <a href="xdrfile.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">432</td>
+            <td class="headerCovTableEntry">943</td>
+            <td class="headerCovTableEntryLo">45.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntryLo">38.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2009-2014, Erik Lindahl &amp; David van der Spoel</a>
+<a name="3"><span class="lineNum">       3 </span>            : All rights reserved.</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            : Redistribution and use in source and binary forms, with or without</a>
+<a name="6"><span class="lineNum">       6 </span>            : modification, are permitted provided that the following conditions are met:</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : 1. Redistributions of source code must retain the above copyright notice, this</a>
+<a name="9"><span class="lineNum">       9 </span>            : list of conditions and the following disclaimer.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            : 2. Redistributions in binary form must reproduce the above copyright notice,</a>
+<a name="12"><span class="lineNum">      12 </span>            : this list of conditions and the following disclaimer in the documentation</a>
+<a name="13"><span class="lineNum">      13 </span>            : and/or other materials provided with the distribution.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            : THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</a>
+<a name="16"><span class="lineNum">      16 </span>            : AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</a>
+<a name="17"><span class="lineNum">      17 </span>            : IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</a>
+<a name="18"><span class="lineNum">      18 </span>            : DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</a>
+<a name="19"><span class="lineNum">      19 </span>            : FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</a>
+<a name="20"><span class="lineNum">      20 </span>            : DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</a>
+<a name="21"><span class="lineNum">      21 </span>            : SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</a>
+<a name="22"><span class="lineNum">      22 </span>            : CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</a>
+<a name="23"><span class="lineNum">      23 </span>            : OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</a>
+<a name="24"><span class="lineNum">      24 </span>            : OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</a>
+<a name="25"><span class="lineNum">      25 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="26"><span class="lineNum">      26 </span>            : /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- </a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * $Id$</a>
+<a name="29"><span class="lineNum">      29 </span>            :  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-</a>
+<a name="31"><span class="lineNum">      31 </span>            :  *</a>
+<a name="32"><span class="lineNum">      32 </span>            :  * $Id$</a>
+<a name="33"><span class="lineNum">      33 </span>            :  *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  * Copyright (c) 2009-2014, Erik Lindahl &amp; David van der Spoel</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * All rights reserved.</a>
+<a name="36"><span class="lineNum">      36 </span>            :  *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Redistribution and use in source and binary forms, with or without</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * modification, are permitted provided that the following conditions are met:</a>
+<a name="39"><span class="lineNum">      39 </span>            :  *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * 1. Redistributions of source code must retain the above copyright notice, this</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * list of conditions and the following disclaimer.</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * 2. Redistributions in binary form must reproduce the above copyright notice,</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * this list of conditions and the following disclaimer in the documentation</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * and/or other materials provided with the distribution.</a>
+<a name="46"><span class="lineNum">      46 </span>            :  *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</a>
+<a name="57"><span class="lineNum">      57 </span>            :  */</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : /* Get HAVE_RPC_XDR_H, F77_FUNC from config.h if available */</a>
+<a name="60"><span class="lineNum">      60 </span>            : #ifdef HAVE_CONFIG_H</a>
+<a name="61"><span class="lineNum">      61 </span>            : #include &lt;config.h&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : #endif</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="65"><span class="lineNum">      65 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &lt;string.h&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &lt;math.h&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : #include &lt;limits.h&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : #define _FILE_OFFSET_BITS  64</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : /* get fixed-width types if we are using ANSI C99 */</a>
+<a name="73"><span class="lineNum">      73 </span>            : #ifdef HAVE_STDINT_H</a>
+<a name="74"><span class="lineNum">      74 </span>            : #  include &lt;stdint.h&gt;</a>
+<a name="75"><span class="lineNum">      75 </span>            : #elif (defined HAVE_INTTYPES_H)</a>
+<a name="76"><span class="lineNum">      76 </span>            : #  include &lt;inttypes.h&gt;</a>
+<a name="77"><span class="lineNum">      77 </span>            : #endif</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : #ifdef HAVE_RPC_XDR_H</a>
+<a name="81"><span class="lineNum">      81 </span>            : #  include &lt;rpc/rpc.h&gt;</a>
+<a name="82"><span class="lineNum">      82 </span>            : #  include &lt;rpc/xdr.h&gt;</a>
+<a name="83"><span class="lineNum">      83 </span>            : #endif</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : #include &quot;xdrfile.h&quot;</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : /* Default FORTRAN name mangling is: lower case name, append underscore */</a>
+<a name="88"><span class="lineNum">      88 </span>            : #ifndef F77_FUNC</a>
+<a name="89"><span class="lineNum">      89 </span>            : #define F77_FUNC(name,NAME) name ## _</a>
+<a name="90"><span class="lineNum">      90 </span>            : #endif</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : namespace PLMD</a>
+<a name="93"><span class="lineNum">      93 </span>            : {</a>
+<a name="94"><span class="lineNum">      94 </span>            : namespace xdrfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : {</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :  const char *exdr_message[exdrNR] = {</a>
+<a name="98"><span class="lineNum">      98 </span>            :         &quot;OK&quot;, </a>
+<a name="99"><span class="lineNum">      99 </span>            :         &quot;Header&quot;,</a>
+<a name="100"><span class="lineNum">     100 </span>            :         &quot;String&quot;, </a>
+<a name="101"><span class="lineNum">     101 </span>            :         &quot;Double&quot;,</a>
+<a name="102"><span class="lineNum">     102 </span>            :         &quot;Integer&quot;,</a>
+<a name="103"><span class="lineNum">     103 </span>            :         &quot;Float&quot;,</a>
+<a name="104"><span class="lineNum">     104 </span>            :         &quot;Unsigned integer&quot;,</a>
+<a name="105"><span class="lineNum">     105 </span>            :         &quot;Compressed 3D coordinate&quot;,</a>
+<a name="106"><span class="lineNum">     106 </span>            :         &quot;Closing file&quot;,</a>
+<a name="107"><span class="lineNum">     107 </span>            :         &quot;Magic number&quot;,</a>
+<a name="108"><span class="lineNum">     108 </span>            :         &quot;Not enough memory&quot;,</a>
+<a name="109"><span class="lineNum">     109 </span>            :         &quot;End of file&quot;,</a>
+<a name="110"><span class="lineNum">     110 </span>            :         &quot;File not found&quot; </a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : /*</a>
+<a name="114"><span class="lineNum">     114 </span>            :  * Declare our own XDR routines statically if no libraries are present.</a>
+<a name="115"><span class="lineNum">     115 </span>            :  * Actual implementation is at the end of this file.</a>
+<a name="116"><span class="lineNum">     116 </span>            :  *</a>
+<a name="117"><span class="lineNum">     117 </span>            :  * We don't want the low-level XDR implementation as part of the Gromacs</a>
+<a name="118"><span class="lineNum">     118 </span>            :  * documentation, so skip it for doxygen too...</a>
+<a name="119"><span class="lineNum">     119 </span>            :  */</a>
+<a name="120"><span class="lineNum">     120 </span>            : #if (!defined HAVE_RPC_XDR_H &amp;&amp; !defined DOXYGEN)</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : enum xdr_op</a>
+<a name="123"><span class="lineNum">     123 </span>            : {</a>
+<a name="124"><span class="lineNum">     124 </span>            :         XDR_ENCODE = 0,</a>
+<a name="125"><span class="lineNum">     125 </span>            :         XDR_DECODE = 1,</a>
+<a name="126"><span class="lineNum">     126 </span>            :         XDR_FREE   = 2</a>
+<a name="127"><span class="lineNum">     127 </span>            : };</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : /* We need integer types that are guaranteed to be 4 bytes wide.</a>
+<a name="131"><span class="lineNum">     131 </span>            :  * If ANSI C99 headers were included they are already defined</a>
+<a name="132"><span class="lineNum">     132 </span>            :  * as int32_t and uint32_t. Check, and if not define them ourselves.</a>
+<a name="133"><span class="lineNum">     133 </span>            :  * Since it is just our workaround for missing ANSI C99 types, avoid adding</a>
+<a name="134"><span class="lineNum">     134 </span>            :  * it to the doxygen documentation.</a>
+<a name="135"><span class="lineNum">     135 </span>            :  */</a>
+<a name="136"><span class="lineNum">     136 </span>            : #if !(defined INT32_MAX || defined DOXYGEN)</a>
+<a name="137"><span class="lineNum">     137 </span>            : #    if (INT_MAX == 2147483647)</a>
+<a name="138"><span class="lineNum">     138 </span>            : #        define int32_t int</a>
+<a name="139"><span class="lineNum">     139 </span>            : #        define uint32_t unsigned int</a>
+<a name="140"><span class="lineNum">     140 </span>            : #        define INT32_MAX 2147483647</a>
+<a name="141"><span class="lineNum">     141 </span>            : #    elif (LONG_MAX == 2147483647)</a>
+<a name="142"><span class="lineNum">     142 </span>            : #        define int32_t long</a>
+<a name="143"><span class="lineNum">     143 </span>            : #        define uint32_t unsigned long</a>
+<a name="144"><span class="lineNum">     144 </span>            : #        define INT32_MAX 2147483647L</a>
+<a name="145"><span class="lineNum">     145 </span>            : #    else</a>
+<a name="146"><span class="lineNum">     146 </span>            : #        error ERROR: No 32 bit wide integer type found!</a>
+<a name="147"><span class="lineNum">     147 </span>            : #        error Use system XDR libraries instead, or update xdrfile.c</a>
+<a name="148"><span class="lineNum">     148 </span>            : #    endif</a>
+<a name="149"><span class="lineNum">     149 </span>            : #endif</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : typedef struct XDR XDR;</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : struct XDR</a>
+<a name="154"><span class="lineNum">     154 </span>            : {</a>
+<a name="155"><span class="lineNum">     155 </span>            :         enum xdr_op x_op;               </a>
+<a name="156"><span class="lineNum">     156 </span>            :         struct xdr_ops</a>
+<a name="157"><span class="lineNum">     157 </span>            :         {</a>
+<a name="158"><span class="lineNum">     158 </span>            :                 int (*x_getlong) (XDR *__xdrs, int32_t *__lp);</a>
+<a name="159"><span class="lineNum">     159 </span>            :                 int (*x_putlong) (XDR *__xdrs, int32_t *__lp);</a>
+<a name="160"><span class="lineNum">     160 </span>            :                 int (*x_getbytes) (XDR *__xdrs, char *__addr, unsigned int __len);</a>
+<a name="161"><span class="lineNum">     161 </span>            :                 int (*x_putbytes) (XDR *__xdrs, char *__addr, unsigned int __len);</a>
+<a name="162"><span class="lineNum">     162 </span>            :                 /* two next routines are not 64-bit IO safe - don't use! */</a>
+<a name="163"><span class="lineNum">     163 </span>            :                 unsigned int (*x_getpostn) (XDR *__xdrs); </a>
+<a name="164"><span class="lineNum">     164 </span>            :                 int (*x_setpostn) (XDR *__xdrs, unsigned int __pos);</a>
+<a name="165"><span class="lineNum">     165 </span>            :                 void (*x_destroy) (XDR *__xdrs); </a>
+<a name="166"><span class="lineNum">     166 </span>            :         } </a>
+<a name="167"><span class="lineNum">     167 </span>            :     *x_ops;         </a>
+<a name="168"><span class="lineNum">     168 </span>            :         char *x_private;</a>
+<a name="169"><span class="lineNum">     169 </span>            : };</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : static int  xdr_char        (XDR *xdrs, char *ip);</a>
+<a name="172"><span class="lineNum">     172 </span>            : static int  xdr_u_char      (XDR *xdrs, unsigned char *ip);</a>
+<a name="173"><span class="lineNum">     173 </span>            : static int  xdr_short       (XDR *xdrs, short *ip);</a>
+<a name="174"><span class="lineNum">     174 </span>            : static int  xdr_u_short     (XDR *xdrs, unsigned short *ip);</a>
+<a name="175"><span class="lineNum">     175 </span>            : static int  xdr_int         (XDR *xdrs, int *ip);</a>
+<a name="176"><span class="lineNum">     176 </span>            : static int  xdr_u_int       (XDR *xdrs, unsigned int *ip);</a>
+<a name="177"><span class="lineNum">     177 </span>            : static int  xdr_float       (XDR *xdrs, float *ip);</a>
+<a name="178"><span class="lineNum">     178 </span>            : static int  xdr_double      (XDR *xdrs, double *ip);</a>
+<a name="179"><span class="lineNum">     179 </span>            : static int  xdr_string      (XDR *xdrs, char **ip, unsigned int maxsize);</a>
+<a name="180"><span class="lineNum">     180 </span>            : static int  xdr_opaque      (XDR *xdrs, char *cp, unsigned int cnt);</a>
+<a name="181"><span class="lineNum">     181 </span>            : static void xdrstdio_create (XDR *xdrs, FILE *fp, enum xdr_op xop);</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : #define xdr_getpos(xdrs)                                \</a>
+<a name="184"><span class="lineNum">     184 </span>            :         (*(xdrs)-&gt;x_ops-&gt;x_getpostn)(xdrs)</a>
+<a name="185"><span class="lineNum">     185 </span>            : #define xdr_setpos(xdrs, pos)                           \</a>
+<a name="186"><span class="lineNum">     186 </span>            :         (*(xdrs)-&gt;x_ops-&gt;x_setpostn)(xdrs, pos)</a>
+<a name="187"><span class="lineNum">     187 </span>            : #define xdr_destroy(xdrs)                                       \</a>
+<a name="188"><span class="lineNum">     188 </span>            :         do {                                                    \</a>
+<a name="189"><span class="lineNum">     189 </span>            :                 if ((xdrs)-&gt;x_ops-&gt;x_destroy)                   \</a>
+<a name="190"><span class="lineNum">     190 </span>            :                         (*(xdrs)-&gt;x_ops-&gt;x_destroy)(xdrs);      \</a>
+<a name="191"><span class="lineNum">     191 </span>            :         } while (0)</a>
+<a name="192"><span class="lineNum">     192 </span>            : #endif /* end of our own XDR declarations */</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : /** Contents of the abstract XDRFILE data structure.</a>
+<a name="199"><span class="lineNum">     199 </span>            :  *</a>
+<a name="200"><span class="lineNum">     200 </span>            :  *  @internal</a>
+<a name="201"><span class="lineNum">     201 </span>            :  * </a>
+<a name="202"><span class="lineNum">     202 </span>            :  *  This structure is used to provide an XDR file interface that is</a>
+<a name="203"><span class="lineNum">     203 </span>            :  *  virtual identical to the standard UNIX fopen/fread/fwrite/fclose.</a>
+<a name="204"><span class="lineNum">     204 </span>            :  */</a>
+<a name="205"><span class="lineNum">     205 </span>            : struct XDRFILE </a>
+<a name="206"><span class="lineNum">     206 </span>            : { </a>
+<a name="207"><span class="lineNum">     207 </span>            :     FILE *   fp;       /**&lt; pointer to standard C library file handle */</a>
+<a name="208"><span class="lineNum">     208 </span>            :     XDR *    xdr;      /**&lt; pointer to corresponding XDR handle       */</a>
+<a name="209"><span class="lineNum">     209 </span>            :     char     mode;     /**&lt; r=read, w=write, a=append                 */</a>
+<a name="210"><span class="lineNum">     210 </span>            :     int *    buf1;     /**&lt; Buffer for internal use                   */</a>
+<a name="211"><span class="lineNum">     211 </span>            :     int      buf1size; /**&lt; Current allocated length of buf1          */    </a>
+<a name="212"><span class="lineNum">     212 </span>            :     int *    buf2;     /**&lt; Buffer for internal use                   */</a>
+<a name="213"><span class="lineNum">     213 </span>            :     int      buf2size; /**&lt; Current allocated length of buf2          */ </a>
+<a name="214"><span class="lineNum">     214 </span>            : };</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            : /*************************************************************</a>
+<a name="220"><span class="lineNum">     220 </span>            :  * Implementation of higher-level routines to read/write     * </a>
+<a name="221"><span class="lineNum">     221 </span>            :  * portable data based on the XDR standard. These should be  *</a>
+<a name="222"><span class="lineNum">     222 </span>            :  * called from C - see further down for Fortran77 wrappers.  *</a>
+<a name="223"><span class="lineNum">     223 </span>            :  *************************************************************/</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : XDRFILE *</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         20 : xdrfile_open(const char *path, const char *mode)</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : {</a>
+<a name="228"><span class="lineNum">     228 </span>            :         char newmode[5];</a>
+<a name="229"><span class="lineNum">     229 </span>            :         enum xdr_op xdrmode;</a>
+<a name="230"><span class="lineNum">     230 </span>            :         XDRFILE *xfp;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   </a>
+<a name="232"><span class="lineNum">     232 </span>            :         /* make sure XDR files are opened in binary mode... */</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         20 :         if(*mode=='w' || *mode=='W') </span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     {</a>
+<a name="235"><span class="lineNum">     235 </span>            :                 snprintf(newmode,5,&quot;wb+&quot;);</a>
+<a name="236"><span class="lineNum">     236 </span>            :                 xdrmode=XDR_ENCODE;</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         10 :         } else if(*mode == 'a' || *mode == 'A') </span></a>
+<a name="238"><span class="lineNum">     238 </span>            :     {</a>
+<a name="239"><span class="lineNum">     239 </span>            :                 snprintf(newmode,5,&quot;ab+&quot;);</a>
+<a name="240"><span class="lineNum">     240 </span>            :                 xdrmode = XDR_ENCODE;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         10 :         } else if(*mode == 'r' || *mode == 'R')</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     {</a>
+<a name="243"><span class="lineNum">     243 </span>            :                 snprintf(newmode,5,&quot;rb&quot;);</a>
+<a name="244"><span class="lineNum">     244 </span>            :                 xdrmode = XDR_DECODE;</a>
+<a name="245"><span class="lineNum">     245 </span>            :         } else /* cannot determine mode */</a>
+<a name="246"><span class="lineNum">     246 </span>            :                 return NULL;</a>
+<a name="247"><span class="lineNum">     247 </span>            :   </a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         20 :         if((xfp=(XDRFILE *)malloc(sizeof(XDRFILE)))==NULL)</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :                 return NULL;</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         20 :         if((xfp-&gt;fp=fopen(path,newmode))==NULL)</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     {</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :                 free(xfp);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :                 return NULL;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :         }</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         20 :         if((xfp-&gt;xdr=(XDR *)malloc(sizeof(XDR)))==NULL) </span></a>
+<a name="256"><span class="lineNum">     256 </span>            :     {</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :                 fclose(xfp-&gt;fp);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :                 free(xfp);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :                 return NULL;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :         }</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         20 :         xfp-&gt;mode=*mode;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         20 :         xdrstdio_create((XDR *)(xfp-&gt;xdr),xfp-&gt;fp,xdrmode);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         20 :         xfp-&gt;buf1 = xfp-&gt;buf2 = NULL;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         20 :         xfp-&gt;buf1size = xfp-&gt;buf2size = 0;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         20 :         return xfp;</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : int </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         20 : xdrfile_close(XDRFILE *xfp)</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : {</a>
+<a name="271"><span class="lineNum">     271 </span>            :         int ret=exdrCLOSE;</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         20 :         if(xfp) </span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     {</a>
+<a name="274"><span class="lineNum">     274 </span>            :                 /* flush and destroy XDR stream */</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         20 :                 if(xfp-&gt;xdr)</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         20 :                         xdr_destroy((XDR *)(xfp-&gt;xdr));</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         20 :                 free(xfp-&gt;xdr);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :                 /* close the file */</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         20 :                 ret=fclose(xfp-&gt;fp);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         20 :                 if(xfp-&gt;buf1size)</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          7 :                         free(xfp-&gt;buf1);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         20 :                 if(xfp-&gt;buf2size)</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          7 :                         free(xfp-&gt;buf2);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         20 :                 free(xfp);</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :         }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         20 :         return ret; /* return 0 if ok */</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : int </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       1448 : xdrfile_read_int(int *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="293"><span class="lineNum">     293 </span>            : {</a>
+<a name="294"><span class="lineNum">     294 </span>            :         int i=0;</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       3005 :         while(i&lt;ndata &amp;&amp; xdr_int((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1557 :                 i++;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1448 :         return i;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : int </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        620 : xdrfile_write_int(int *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="305"><span class="lineNum">     305 </span>            : {</a>
+<a name="306"><span class="lineNum">     306 </span>            :         int i=0;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   </a>
+<a name="308"><span class="lineNum">     308 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1478 :         while(i&lt;ndata &amp;&amp; xdr_int((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        858 :                 i++;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        620 :         return i;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : }</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            : int </a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 : xdrfile_read_uint(unsigned int *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="317"><span class="lineNum">     317 </span>            : {</a>
+<a name="318"><span class="lineNum">     318 </span>            :         int i=0;</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_u_int((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   </a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            : int </a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 : xdrfile_write_uint(unsigned int *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="329"><span class="lineNum">     329 </span>            : {</a>
+<a name="330"><span class="lineNum">     330 </span>            :         int i=0;</a>
+<a name="331"><span class="lineNum">     331 </span>            :   </a>
+<a name="332"><span class="lineNum">     332 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_u_int((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : int </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 : xdrfile_read_char(char *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="340"><span class="lineNum">     340 </span>            : {</a>
+<a name="341"><span class="lineNum">     341 </span>            :         int i=0;</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_char((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :   </a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : }</a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : int </a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 : xdrfile_write_char(char *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="352"><span class="lineNum">     352 </span>            : {</a>
+<a name="353"><span class="lineNum">     353 </span>            :         int i=0;</a>
+<a name="354"><span class="lineNum">     354 </span>            :   </a>
+<a name="355"><span class="lineNum">     355 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_char((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="359"><span class="lineNum">     359 </span>            : }</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            : int </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 : xdrfile_read_uchar(unsigned char *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="364"><span class="lineNum">     364 </span>            : {</a>
+<a name="365"><span class="lineNum">     365 </span>            :         int i=0;</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_u_char((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : }</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : int </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 : xdrfile_write_uchar(unsigned char *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="376"><span class="lineNum">     376 </span>            : {</a>
+<a name="377"><span class="lineNum">     377 </span>            :         int i=0;</a>
+<a name="378"><span class="lineNum">     378 </span>            :   </a>
+<a name="379"><span class="lineNum">     379 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_u_char((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : }</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            : int </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 : xdrfile_read_short(short *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="387"><span class="lineNum">     387 </span>            : {</a>
+<a name="388"><span class="lineNum">     388 </span>            :         int i=0;</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_short((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : }</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            : int </a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 : xdrfile_write_short(short *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="399"><span class="lineNum">     399 </span>            : {</a>
+<a name="400"><span class="lineNum">     400 </span>            :         int i=0;</a>
+<a name="401"><span class="lineNum">     401 </span>            :   </a>
+<a name="402"><span class="lineNum">     402 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_short((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            : int </a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 : xdrfile_read_ushort(unsigned short *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="411"><span class="lineNum">     411 </span>            : {</a>
+<a name="412"><span class="lineNum">     412 </span>            :         int i=0;</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_u_short((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :   </a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : }</a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            : int </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 : xdrfile_write_ushort(unsigned short *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="423"><span class="lineNum">     423 </span>            : {</a>
+<a name="424"><span class="lineNum">     424 </span>            :         int i=0;</a>
+<a name="425"><span class="lineNum">     425 </span>            :   </a>
+<a name="426"><span class="lineNum">     426 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_u_short((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="430"><span class="lineNum">     430 </span>            : }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            : int </a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        470 : xdrfile_read_float(float *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="434"><span class="lineNum">     434 </span>            : {</a>
+<a name="435"><span class="lineNum">     435 </span>            :         int i=0;</a>
+<a name="436"><span class="lineNum">     436 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">      11832 :         while(i&lt;ndata &amp;&amp; xdr_float((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">      11362 :                 i++;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">        470 :         return i;</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : }</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            : int </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">        174 : xdrfile_write_float(float *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="444"><span class="lineNum">     444 </span>            : {</a>
+<a name="445"><span class="lineNum">     445 </span>            :         int i=0;</a>
+<a name="446"><span class="lineNum">     446 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        336 :         while(i&lt;ndata &amp;&amp; xdr_float((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        162 :                 i++;</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">        174 :         return i;</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : }</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            : int </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 : xdrfile_read_double(double *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="454"><span class="lineNum">     454 </span>            : {</a>
+<a name="455"><span class="lineNum">     455 </span>            :         int i=0;</a>
+<a name="456"><span class="lineNum">     456 </span>            :         /* read write is encoded in the XDR struct */</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_double((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="460"><span class="lineNum">     460 </span>            : }</a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            : int </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 : xdrfile_write_double(double *ptr, int ndata, XDRFILE* xfp) </span></a>
+<a name="464"><span class="lineNum">     464 </span>            : {</a>
+<a name="465"><span class="lineNum">     465 </span>            :         int i=0;</a>
+<a name="466"><span class="lineNum">     466 </span>            :         /* read write is encoded in the XDR struct */  </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :         while(i&lt;ndata &amp;&amp; xdr_double((XDR *)(xfp-&gt;xdr),ptr+i))</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :         return i;</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : }</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            : int</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         39 : xdrfile_read_string(char *ptr, int maxlen, XDRFILE* xfp)</span></a>
+<a name="474"><span class="lineNum">     474 </span>            : {</a>
+<a name="475"><span class="lineNum">     475 </span>            :         int i;</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         39 :         if(xdr_string((XDR *)(xfp-&gt;xdr),&amp;ptr,maxlen)) {</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :                 i=0;</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        507 :                 while(i&lt;maxlen &amp;&amp; ptr[i]!=0)</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        468 :                         i++;</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         39 :                 if(i==maxlen)</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :                         return maxlen;</a>
+<a name="482"><span class="lineNum">     482 </span>            :                 else</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         39 :                         return i+1;</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :         } else</a>
+<a name="485"><span class="lineNum">     485 </span>            :                 return 0;</a>
+<a name="486"><span class="lineNum">     486 </span>            : }</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            : int</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         48 : xdrfile_write_string(char *ptr, XDRFILE* xfp)</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : {</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">         48 :         int len=strlen(ptr)+1;</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :   </a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         48 :         if(xdr_string((XDR *)(xfp-&gt;xdr),&amp;ptr,len)) </span></a>
+<a name="494"><span class="lineNum">     494 </span>            :                 return len;</a>
+<a name="495"><span class="lineNum">     495 </span>            :         else</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : }</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            : int</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         28 : xdrfile_read_opaque(char *ptr, int cnt, XDRFILE* xfp)</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : {</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         28 :         if(xdr_opaque((XDR *)(xfp-&gt;xdr),ptr,cnt))</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :                 return cnt;</a>
+<a name="505"><span class="lineNum">     505 </span>            :         else </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="507"><span class="lineNum">     507 </span>            : }</a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : int</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         60 : xdrfile_write_opaque(char *ptr, int cnt, XDRFILE* xfp)</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : {</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         60 :         if(xdr_opaque((XDR *)(xfp-&gt;xdr),ptr,cnt))</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :                 return cnt;</a>
+<a name="515"><span class="lineNum">     515 </span>            :         else</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : }</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            : /* Internal support routines for reading/writing compressed coordinates </a>
+<a name="521"><span class="lineNum">     521 </span>            :  * sizeofint - calculate smallest number of bits necessary</a>
+<a name="522"><span class="lineNum">     522 </span>            :  * to represent a certain integer.</a>
+<a name="523"><span class="lineNum">     523 </span>            :  */</a>
+<a name="524"><span class="lineNum">     524 </span>            : static int </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 : sizeofint(int size) {</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :     unsigned int num = 1;</a>
+<a name="527"><span class="lineNum">     527 </span>            :     int num_of_bits = 0;</a>
+<a name="528"><span class="lineNum">     528 </span>            :     </a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :     while (size &gt;= num &amp;&amp; num_of_bits &lt; 32) </span></a>
+<a name="530"><span class="lineNum">     530 </span>            :     {</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :                 num_of_bits++;</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :                 num &lt;&lt;= 1;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :     }</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :     return num_of_bits;</span></a>
+<a name="535"><span class="lineNum">     535 </span>            : }</a>
+<a name="536"><span class="lineNum">     536 </span>            : </a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            : /*</a>
+<a name="539"><span class="lineNum">     539 </span>            :  * sizeofints - calculate 'bitsize' of compressed ints</a>
+<a name="540"><span class="lineNum">     540 </span>            :  *</a>
+<a name="541"><span class="lineNum">     541 </span>            :  * given a number of small unsigned integers and the maximum value</a>
+<a name="542"><span class="lineNum">     542 </span>            :  * return the number of bits needed to read or write them with the</a>
+<a name="543"><span class="lineNum">     543 </span>            :  * routines encodeints/decodeints. You need this parameter when</a>
+<a name="544"><span class="lineNum">     544 </span>            :  * calling those routines. </a>
+<a name="545"><span class="lineNum">     545 </span>            :  * (However, in some cases we can just use the variable 'smallidx' </a>
+<a name="546"><span class="lineNum">     546 </span>            :  * which is the exact number of bits, and them we dont need to call</a>
+<a name="547"><span class="lineNum">     547 </span>            :  * this routine).</a>
+<a name="548"><span class="lineNum">     548 </span>            :  */</a>
+<a name="549"><span class="lineNum">     549 </span>            : static int </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         88 : sizeofints(int num_of_ints, unsigned int sizes[]) </span></a>
+<a name="551"><span class="lineNum">     551 </span>            : {</a>
+<a name="552"><span class="lineNum">     552 </span>            :     int i, num;</a>
+<a name="553"><span class="lineNum">     553 </span>            :     unsigned int num_of_bytes, num_of_bits, bytes[32], bytecnt, tmp;</a>
+<a name="554"><span class="lineNum">     554 </span>            :     num_of_bytes = 1;</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         88 :     bytes[0] = 1;</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :     num_of_bits = 0;</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        352 :     for (i=0; i &lt; num_of_ints; i++)</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :     {   </a>
+<a name="559"><span class="lineNum">     559 </span>            :                 tmp = 0;</a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">        876 :                 for (bytecnt = 0; bytecnt &lt; num_of_bytes; bytecnt++)</span></a>
+<a name="561"><span class="lineNum">     561 </span>            :         {</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">        612 :                         tmp = bytes[bytecnt] * sizes[i] + tmp;</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">        612 :                         bytes[bytecnt] = tmp &amp; 0xff;</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">        612 :                         tmp &gt;&gt;= 8;</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :                 }</a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">        612 :                 while (tmp != 0) </span></a>
+<a name="567"><span class="lineNum">     567 </span>            :         {</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">        348 :                         bytes[bytecnt++] = tmp &amp; 0xff;</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">        348 :                         tmp &gt;&gt;= 8;</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :                 }</a>
+<a name="571"><span class="lineNum">     571 </span>            :                 num_of_bytes = bytecnt;</a>
+<a name="572"><span class="lineNum">     572 </span>            :     }</a>
+<a name="573"><span class="lineNum">     573 </span>            :     num = 1;</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         88 :     num_of_bytes--;</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        497 :     while (bytes[num_of_bytes] &gt;= num) </span></a>
+<a name="576"><span class="lineNum">     576 </span>            :     {</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        409 :                 num_of_bits++;</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">        409 :                 num *= 2;</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :     }</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         88 :     return num_of_bits + num_of_bytes * 8;</span></a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span>            : }</a>
+<a name="583"><span class="lineNum">     583 </span>            :     </a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span>            : /*</a>
+<a name="586"><span class="lineNum">     586 </span>            :  * encodebits - encode num into buf using the specified number of bits</a>
+<a name="587"><span class="lineNum">     587 </span>            :  *</a>
+<a name="588"><span class="lineNum">     588 </span>            :  * This routines appends the value of num to the bits already present in</a>
+<a name="589"><span class="lineNum">     589 </span>            :  * the array buf. You need to give it the number of bits to use and you had</a>
+<a name="590"><span class="lineNum">     590 </span>            :  * better make sure that this number of bits is enough to hold the value.</a>
+<a name="591"><span class="lineNum">     591 </span>            :  * Num must also be positive.</a>
+<a name="592"><span class="lineNum">     592 </span>            :  */</a>
+<a name="593"><span class="lineNum">     593 </span>            : static void </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">      21991 : encodebits(int buf[], int num_of_bits, int num) </span></a>
+<a name="595"><span class="lineNum">     595 </span>            : {</a>
+<a name="596"><span class="lineNum">     596 </span>            :     </a>
+<a name="597"><span class="lineNum">     597 </span>            :     unsigned int cnt, lastbyte;</a>
+<a name="598"><span class="lineNum">     598 </span>            :     int lastbits;</a>
+<a name="599"><span class="lineNum">     599 </span>            :     unsigned char * cbuf;</a>
+<a name="600"><span class="lineNum">     600 </span>            :     </a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">      21991 :     cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">      21991 :     cnt = (unsigned int) buf[0];</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">      21991 :     lastbits = buf[1];</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">      21991 :     lastbyte =(unsigned int) buf[2];</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">      38553 :     while (num_of_bits &gt;= 8)</span></a>
+<a name="606"><span class="lineNum">     606 </span>            :     {</a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">      16562 :                 lastbyte = (lastbyte &lt;&lt; 8) | ((num &gt;&gt; (num_of_bits -8)) /* &amp; 0xff*/);</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">      16562 :                 cbuf[cnt++] = lastbyte &gt;&gt; lastbits;</span></a>
+<a name="609"><span class="lineNum">     609 </span>            :                 num_of_bits -= 8;</a>
+<a name="610"><span class="lineNum">     610 </span>            :     }</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">      21991 :     if (num_of_bits &gt; 0)</span></a>
+<a name="612"><span class="lineNum">     612 </span>            :     {</a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       4729 :                 lastbyte = (lastbyte &lt;&lt; num_of_bits) | num;</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">       4729 :                 lastbits += num_of_bits;</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">       4729 :                 if (lastbits &gt;= 8) </span></a>
+<a name="616"><span class="lineNum">     616 </span>            :         {</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">       1916 :                         lastbits -= 8;</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">       1916 :                         cbuf[cnt++] = lastbyte &gt;&gt; lastbits;</span></a>
+<a name="619"><span class="lineNum">     619 </span>            :                 }</a>
+<a name="620"><span class="lineNum">     620 </span>            :     }</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">      21991 :     buf[0] = cnt;</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">      21991 :     buf[1] = lastbits;</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">      21991 :     buf[2] = lastbyte;</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">      21991 :     if (lastbits&gt;0) </span></a>
+<a name="625"><span class="lineNum">     625 </span>            :     {</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">      19395 :                 cbuf[cnt] = lastbyte &lt;&lt; (8 - lastbits);</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :     }</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">      21991 : }</span></a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            : /*</a>
+<a name="631"><span class="lineNum">     631 </span>            :  * encodeints - encode a small set of small integers in compressed format</a>
+<a name="632"><span class="lineNum">     632 </span>            :  *</a>
+<a name="633"><span class="lineNum">     633 </span>            :  * this routine is used internally by xdr3dfcoord, to encode a set of</a>
+<a name="634"><span class="lineNum">     634 </span>            :  * small integers to the buffer for writing to a file.</a>
+<a name="635"><span class="lineNum">     635 </span>            :  * Multiplication with fixed (specified maximum) sizes is used to get</a>
+<a name="636"><span class="lineNum">     636 </span>            :  * to one big, multibyte integer. Allthough the routine could be</a>
+<a name="637"><span class="lineNum">     637 </span>            :  * modified to handle sizes bigger than 16777216, or more than just</a>
+<a name="638"><span class="lineNum">     638 </span>            :  * a few integers, this is not done because the gain in compression</a>
+<a name="639"><span class="lineNum">     639 </span>            :  * isn't worth the effort. Note that overflowing the multiplication</a>
+<a name="640"><span class="lineNum">     640 </span>            :  * or the byte buffer (32 bytes) is unchecked and whould cause bad results.</a>
+<a name="641"><span class="lineNum">     641 </span>            :  * THese things are checked in the calling routines, so make sure not</a>
+<a name="642"><span class="lineNum">     642 </span>            :  * to remove those checks...</a>
+<a name="643"><span class="lineNum">     643 </span>            :  */</a>
+<a name="644"><span class="lineNum">     644 </span>            :  </a>
+<a name="645"><span class="lineNum">     645 </span>            : static void </a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">       3960 : encodeints(int buf[], int num_of_ints, int num_of_bits,</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :                    unsigned int sizes[], unsigned int nums[]) </a>
+<a name="648"><span class="lineNum">     648 </span>            : {</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span>            :     int i;</a>
+<a name="651"><span class="lineNum">     651 </span>            :     unsigned int bytes[32], num_of_bytes, bytecnt, tmp;</a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">       3960 :     tmp = nums[0];</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :     num_of_bytes = 0;</a>
+<a name="655"><span class="lineNum">     655 </span>            :     do </a>
+<a name="656"><span class="lineNum">     656 </span>            :     {</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">       7242 :                 bytes[num_of_bytes++] = tmp &amp; 0xff;</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">       7242 :                 tmp &gt;&gt;= 8;</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       7242 :     } while (tmp != 0);</span></a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">      11880 :     for (i = 1; i &lt; num_of_ints; i++) </span></a>
+<a name="662"><span class="lineNum">     662 </span>            :     {</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">       7920 :                 if (nums[i] &gt;= sizes[i])</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :         {</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;major breakdown in encodeints - num %u doesn't &quot;</span></a>
+<a name="666"><span class="lineNum">     666 </span>            :                                         &quot;match size %u\n&quot;, nums[i], sizes[i]);</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :                         abort();</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :                 }</a>
+<a name="669"><span class="lineNum">     669 </span>            :                 /* use one step multiply */    </a>
+<a name="670"><span class="lineNum">     670 </span>            :                 tmp = nums[i];</a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">      28600 :                 for (bytecnt = 0; bytecnt &lt; num_of_bytes; bytecnt++) </span></a>
+<a name="672"><span class="lineNum">     672 </span>            :         {</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">      20680 :                         tmp = bytes[bytecnt] * sizes[i] + tmp;</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">      20680 :                         bytes[bytecnt] = tmp &amp; 0xff;</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">      20680 :                         tmp &gt;&gt;= 8;</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :                 }</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">      20013 :                 while (tmp != 0)</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :         {</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">      12093 :                         bytes[bytecnt++] = tmp &amp; 0xff;</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">      12093 :                         tmp &gt;&gt;= 8;</span></a>
+<a name="681"><span class="lineNum">     681 </span>            :                 }</a>
+<a name="682"><span class="lineNum">     682 </span>            :                 num_of_bytes = bytecnt;</a>
+<a name="683"><span class="lineNum">     683 </span>            :     }</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">       3960 :     if (num_of_bits &gt;= num_of_bytes * 8) </span></a>
+<a name="685"><span class="lineNum">     685 </span>            :     {</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">       7225 :                 for (i = 0; i &lt; num_of_bytes; i++) </span></a>
+<a name="687"><span class="lineNum">     687 </span>            :         {</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">       6040 :                         encodebits(buf, 8, bytes[i]);</span></a>
+<a name="689"><span class="lineNum">     689 </span>            :                 }</a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">       1185 :                 encodebits(buf, num_of_bits - num_of_bytes * 8, 0);</span></a>
+<a name="691"><span class="lineNum">     691 </span>            :     } </a>
+<a name="692"><span class="lineNum">     692 </span>            :     else</a>
+<a name="693"><span class="lineNum">     693 </span>            :     {</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">      13295 :                 for (i = 0; i &lt; num_of_bytes-1; i++)</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :         {</a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">      10520 :                         encodebits(buf, 8, bytes[i]);</span></a>
+<a name="697"><span class="lineNum">     697 </span>            :                 }</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">       2775 :                 encodebits(buf, num_of_bits- (num_of_bytes -1) * 8, bytes[i]);</span></a>
+<a name="699"><span class="lineNum">     699 </span>            :     }</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">       3960 : }</span></a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span>            : /*</a>
+<a name="704"><span class="lineNum">     704 </span>            :  * decodebits - decode number from buf using specified number of bits</a>
+<a name="705"><span class="lineNum">     705 </span>            :  * </a>
+<a name="706"><span class="lineNum">     706 </span>            :  * extract the number of bits from the array buf and construct an integer</a>
+<a name="707"><span class="lineNum">     707 </span>            :  * from it. Return that value.</a>
+<a name="708"><span class="lineNum">     708 </span>            :  *</a>
+<a name="709"><span class="lineNum">     709 </span>            :  */</a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            : static int </a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">      14579 : decodebits(int buf[], int num_of_bits) </span></a>
+<a name="713"><span class="lineNum">     713 </span>            : {</a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            :     int cnt, num; </a>
+<a name="716"><span class="lineNum">     716 </span>            :     unsigned int lastbits, lastbyte;</a>
+<a name="717"><span class="lineNum">     717 </span>            :     unsigned char * cbuf;</a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">      14579 :     int mask = (1 &lt;&lt; num_of_bits) -1;</span></a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">      14579 :     cbuf = ((unsigned char *)buf) + 3 * sizeof(*buf);</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">      14579 :     cnt = buf[0];</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">      14579 :     lastbits = (unsigned int) buf[1];</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">      14579 :     lastbyte = (unsigned int) buf[2];</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :     </a>
+<a name="725"><span class="lineNum">     725 </span>            :     num = 0;</a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">      26636 :     while (num_of_bits &gt;= 8)</span></a>
+<a name="727"><span class="lineNum">     727 </span>            :     {</a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">      12057 :                 lastbyte = ( lastbyte &lt;&lt; 8 ) | cbuf[cnt++];</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">      12057 :                 num |=  (lastbyte &gt;&gt; lastbits) &lt;&lt; (num_of_bits - 8);</span></a>
+<a name="730"><span class="lineNum">     730 </span>            :                 num_of_bits -=8;</a>
+<a name="731"><span class="lineNum">     731 </span>            :     }</a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">      14579 :     if (num_of_bits &gt; 0) </span></a>
+<a name="733"><span class="lineNum">     733 </span>            :     {</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">       2522 :                 if (lastbits &lt; num_of_bits) </span></a>
+<a name="735"><span class="lineNum">     735 </span>            :         {</a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">        998 :                         lastbits += 8;</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">        998 :                         lastbyte = (lastbyte &lt;&lt; 8) | cbuf[cnt++];</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :                 }</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">       2522 :                 lastbits -= num_of_bits;</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">       2522 :                 num |= (lastbyte &gt;&gt; lastbits) &amp; ((1 &lt;&lt; num_of_bits) -1);</span></a>
+<a name="741"><span class="lineNum">     741 </span>            :     }</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">      14579 :     num &amp;= mask;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">      14579 :     buf[0] = cnt;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">      14579 :     buf[1] = lastbits;</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">      14579 :     buf[2] = lastbyte;</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">      14579 :     return num; </span></a>
+<a name="747"><span class="lineNum">     747 </span>            : }</a>
+<a name="748"><span class="lineNum">     748 </span>            : </a>
+<a name="749"><span class="lineNum">     749 </span>            : /*</a>
+<a name="750"><span class="lineNum">     750 </span>            :  * decodeints - decode 'small' integers from the buf array</a>
+<a name="751"><span class="lineNum">     751 </span>            :  *</a>
+<a name="752"><span class="lineNum">     752 </span>            :  * this routine is the inverse from encodeints() and decodes the small integers</a>
+<a name="753"><span class="lineNum">     753 </span>            :  * written to buf by calculating the remainder and doing divisions with</a>
+<a name="754"><span class="lineNum">     754 </span>            :  * the given sizes[]. You need to specify the total number of bits to be</a>
+<a name="755"><span class="lineNum">     755 </span>            :  * used from buf in num_of_bits.</a>
+<a name="756"><span class="lineNum">     756 </span>            :  *</a>
+<a name="757"><span class="lineNum">     757 </span>            :  */</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            : static void </a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">       1936 : decodeints(int buf[], int num_of_ints, int num_of_bits,</span></a>
+<a name="761"><span class="lineNum">     761 </span>            :                    unsigned int sizes[], int nums[])</a>
+<a name="762"><span class="lineNum">     762 </span>            : {</a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span>            :         int bytes[32];</a>
+<a name="765"><span class="lineNum">     765 </span>            :         int i, j, num_of_bytes, p, num;</a>
+<a name="766"><span class="lineNum">     766 </span>            :   </a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       1936 :         bytes[1] = bytes[2] = bytes[3] = 0;</span></a>
+<a name="768"><span class="lineNum">     768 </span>            :         num_of_bytes = 0;</a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">      13916 :         while (num_of_bits &gt; 8)</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :     {</a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">      11980 :                 bytes[num_of_bytes++] = decodebits(buf, 8);</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">      11980 :                 num_of_bits -= 8;</span></a>
+<a name="773"><span class="lineNum">     773 </span>            :         }</a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">       1936 :         if (num_of_bits &gt; 0)</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :     {</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">       1936 :                 bytes[num_of_bytes++] = decodebits(buf, num_of_bits);</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :         }</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">       5808 :         for (i = num_of_ints-1; i &gt; 0; i--) </span></a>
+<a name="779"><span class="lineNum">     779 </span>            :     {</a>
+<a name="780"><span class="lineNum">     780 </span>            :                 num = 0;</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">      31704 :                 for (j = num_of_bytes-1; j &gt;=0; j--) </span></a>
+<a name="782"><span class="lineNum">     782 </span>            :         {</a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">      27832 :                         num = (num &lt;&lt; 8) | bytes[j];</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">      27832 :                         p = num / sizes[i];</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">      27832 :                         bytes[j] = p;</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">      27832 :                         num = num - p * sizes[i];</span></a>
+<a name="787"><span class="lineNum">     787 </span>            :                 }</a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">       3872 :                 nums[i] = num;</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :         }</a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">       1936 :         nums[0] = bytes[0] | (bytes[1] &lt;&lt; 8) | (bytes[2] &lt;&lt; 16) | (bytes[3] &lt;&lt; 24);</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">       1936 : }</span></a>
+<a name="792"><span class="lineNum">     792 </span>            :     </a>
+<a name="793"><span class="lineNum">     793 </span>            : </a>
+<a name="794"><span class="lineNum">     794 </span>            : static const int magicints[] = </a>
+<a name="795"><span class="lineNum">     795 </span>            : {</a>
+<a name="796"><span class="lineNum">     796 </span>            :     0, 0, 0, 0, 0, 0, 0, 0, 0, 8, 10, 12, 16, 20, 25, 32, 40, 50, 64,</a>
+<a name="797"><span class="lineNum">     797 </span>            :     80, 101, 128, 161, 203, 256, 322, 406, 512, 645, 812, 1024, 1290,</a>
+<a name="798"><span class="lineNum">     798 </span>            :     1625, 2048, 2580, 3250, 4096, 5060, 6501, 8192, 10321, 13003, </a>
+<a name="799"><span class="lineNum">     799 </span>            :     16384, 20642, 26007, 32768, 41285, 52015, 65536,82570, 104031, </a>
+<a name="800"><span class="lineNum">     800 </span>            :     131072, 165140, 208063, 262144, 330280, 416127, 524287, 660561, </a>
+<a name="801"><span class="lineNum">     801 </span>            :     832255, 1048576, 1321122, 1664510, 2097152, 2642245, 3329021, </a>
+<a name="802"><span class="lineNum">     802 </span>            :     4194304, 5284491, 6658042, 8388607, 10568983, 13316085, 16777216 </a>
+<a name="803"><span class="lineNum">     803 </span>            : };</a>
+<a name="804"><span class="lineNum">     804 </span>            : </a>
+<a name="805"><span class="lineNum">     805 </span>            : #define FIRSTIDX 9</a>
+<a name="806"><span class="lineNum">     806 </span>            : /* note that magicints[FIRSTIDX-1] == 0 */</a>
+<a name="807"><span class="lineNum">     807 </span>            : #define LASTIDX (sizeof(magicints) / sizeof(*magicints))</a>
+<a name="808"><span class="lineNum">     808 </span>            : </a>
+<a name="809"><span class="lineNum">     809 </span>            : /* Compressed coordinate routines - modified from the original</a>
+<a name="810"><span class="lineNum">     810 </span>            :  * implementation by Frans v. Hoesel to make them threadsafe.</a>
+<a name="811"><span class="lineNum">     811 </span>            :  */</a>
+<a name="812"><span class="lineNum">     812 </span>            : int</a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         28 : xdrfile_decompress_coord_float(float     *ptr,</span></a>
+<a name="814"><span class="lineNum">     814 </span>            :                                                            int       *size,</a>
+<a name="815"><span class="lineNum">     815 </span>            :                                                            float     *precision,</a>
+<a name="816"><span class="lineNum">     816 </span>            :                                                            XDRFILE*   xfp)</a>
+<a name="817"><span class="lineNum">     817 </span>            : {</a>
+<a name="818"><span class="lineNum">     818 </span>            :         int minint[3], maxint[3], *lip;</a>
+<a name="819"><span class="lineNum">     819 </span>            :         int smallidx, minidx, maxidx;</a>
+<a name="820"><span class="lineNum">     820 </span>            :         unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3;</a>
+<a name="821"><span class="lineNum">     821 </span>            :         int k, *buf1, *buf2, lsize, flag;</a>
+<a name="822"><span class="lineNum">     822 </span>            :         int smallnum, smaller, larger, i, is_smaller, run;</a>
+<a name="823"><span class="lineNum">     823 </span>            :         float *lfp, inv_precision;</a>
+<a name="824"><span class="lineNum">     824 </span>            :         int tmp, *thiscoord,  prevcoord[3];</a>
+<a name="825"><span class="lineNum">     825 </span>            :         unsigned int bitsize;</a>
+<a name="826"><span class="lineNum">     826 </span>            :   </a>
+<a name="827"><span class="lineNum">     827 </span>            :     bitsizeint[0] = 0;</a>
+<a name="828"><span class="lineNum">     828 </span>            :     bitsizeint[1] = 0;</a>
+<a name="829"><span class="lineNum">     829 </span>            :     bitsizeint[2] = 0;</a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">         28 :         if(xfp==NULL || ptr==NULL)</span></a>
+<a name="832"><span class="lineNum">     832 </span>            :                 return -1;</a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">         28 :         tmp=xdrfile_read_int(&amp;lsize,1,xfp);</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">         28 :         if(tmp==0)</span></a>
+<a name="835"><span class="lineNum">     835 </span>            :                 return -1; /* return if we could not read size */</a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">         28 :         if (*size &lt; lsize) </span></a>
+<a name="837"><span class="lineNum">     837 </span>            :     {</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineNoCov">          0 :                 fprintf(stderr, &quot;Requested to decompress %d coords, file contains %d\n&quot;,</span></a>
+<a name="839"><span class="lineNum">     839 </span>            :                                 *size, lsize);</a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineNoCov">          0 :                 return -1;</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :         }</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">         28 :         *size = lsize;</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         28 :         size3 = *size * 3;</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">         28 :         if(size3&gt;xfp-&gt;buf1size) </span></a>
+<a name="845"><span class="lineNum">     845 </span>            :     {</a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">          2 :                 if((xfp-&gt;buf1=(int *)malloc(sizeof(int)*size3))==NULL) </span></a>
+<a name="847"><span class="lineNum">     847 </span>            :         {</a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for decompressing coordinates.\n&quot;);</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :                         return -1; </span></a>
+<a name="850"><span class="lineNum">     850 </span>            :                 }</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">          2 :                 xfp-&gt;buf1size=size3;</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">          2 :                 xfp-&gt;buf2size=size3*1.2;</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">          2 :                 if((xfp-&gt;buf2=(int *)malloc(sizeof(int)*xfp-&gt;buf2size))==NULL)</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :         {</a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for decompressing coordinates.\n&quot;);</span></a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="857"><span class="lineNum">     857 </span>            :                 }</a>
+<a name="858"><span class="lineNum">     858 </span>            :         }</a>
+<a name="859"><span class="lineNum">     859 </span>            :         /* Dont bother with compression for three atoms or less */</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">         28 :         if(*size&lt;=9) </span></a>
+<a name="861"><span class="lineNum">     861 </span>            :     {</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineNoCov">          0 :                 return xdrfile_read_float(ptr,size3,xfp)/3;</span></a>
+<a name="863"><span class="lineNum">     863 </span>            :                 /* return number of coords, not floats */</a>
+<a name="864"><span class="lineNum">     864 </span>            :         }</a>
+<a name="865"><span class="lineNum">     865 </span>            :         /* Compression-time if we got here. Read precision first */</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">         28 :         xdrfile_read_float(precision,1,xfp);</span></a>
+<a name="867"><span class="lineNum">     867 </span>            :   </a>
+<a name="868"><span class="lineNum">     868 </span>            :         /* avoid repeated pointer dereferencing. */</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">         28 :         buf1=xfp-&gt;buf1; </span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">         28 :         buf2=xfp-&gt;buf2;</span></a>
+<a name="871"><span class="lineNum">     871 </span>            :         /* buf2[0-2] are special and do not contain actual data */</a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">         28 :         buf2[0] = buf2[1] = buf2[2] = 0;</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">         28 :         xdrfile_read_int(minint,3,xfp);</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">         28 :         xdrfile_read_int(maxint,3,xfp);</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :   </a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">         28 :         sizeint[0] = maxint[0] - minint[0]+1;</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">         28 :         sizeint[1] = maxint[1] - minint[1]+1;</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">         28 :         sizeint[2] = maxint[2] - minint[2]+1;</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :         </a>
+<a name="880"><span class="lineNum">     880 </span>            :         /* check if one of the sizes is to big to be multiplied */</a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">         28 :         if ((sizeint[0] | sizeint[1] | sizeint[2] ) &gt; 0xffffff)</span></a>
+<a name="882"><span class="lineNum">     882 </span>            :     {</a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineNoCov">          0 :                 bitsizeint[0] = sizeofint(sizeint[0]);</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineNoCov">          0 :                 bitsizeint[1] = sizeofint(sizeint[1]);</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineNoCov">          0 :                 bitsizeint[2] = sizeofint(sizeint[2]);</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :                 bitsize = 0; /* flag the use of large sizes */</a>
+<a name="887"><span class="lineNum">     887 </span>            :         }</a>
+<a name="888"><span class="lineNum">     888 </span>            :     else </a>
+<a name="889"><span class="lineNum">     889 </span>            :     {</a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">         28 :                 bitsize = sizeofints(3, sizeint);</span></a>
+<a name="891"><span class="lineNum">     891 </span>            :         }</a>
+<a name="892"><span class="lineNum">     892 </span>            :         </a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">         28 :         if (xdrfile_read_int(&amp;smallidx,1,xfp) == 0) </span></a>
+<a name="894"><span class="lineNum">     894 </span>            :                 return 0; /* not sure what has happened here or why we return... */</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">         28 :         tmp=smallidx+8;</span></a>
+<a name="896"><span class="lineNum">     896 </span>            :         maxidx = (LASTIDX&lt;tmp) ? LASTIDX : tmp;</a>
+<a name="897"><span class="lineNum">     897 </span>            :         minidx = maxidx - 8; /* often this equal smallidx */</a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">         28 :         tmp = smallidx-1;</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">         28 :         tmp = (FIRSTIDX&gt;tmp) ? FIRSTIDX : tmp;</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">         28 :         smaller = magicints[tmp] / 2;</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">         28 :         smallnum = magicints[smallidx] / 2;</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">         28 :         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :         larger = magicints[maxidx];</a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span>            :         /* buf2[0] holds the length in bytes */</a>
+<a name="906"><span class="lineNum">     906 </span>            :   </a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">         28 :         if (xdrfile_read_int(buf2,1,xfp) == 0)</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :                 return 0;</a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">         28 :         if (xdrfile_read_opaque((char *)&amp;(buf2[3]),(unsigned int)buf2[0],xfp) == 0)</span></a>
+<a name="910"><span class="lineNum">     910 </span>            :                 return 0;</a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">         28 :         buf2[0] = buf2[1] = buf2[2] = 0;</span></a>
+<a name="912"><span class="lineNum">     912 </span>            :   </a>
+<a name="913"><span class="lineNum">     913 </span>            :         lfp = ptr;</a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         28 :         inv_precision = 1.0 / * precision;</span></a>
+<a name="915"><span class="lineNum">     915 </span>            :         run = 0;</a>
+<a name="916"><span class="lineNum">     916 </span>            :         i = 0;</a>
+<a name="917"><span class="lineNum">     917 </span>            :         lip = buf1;</a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">        387 :         while ( i &lt; lsize ) </span></a>
+<a name="919"><span class="lineNum">     919 </span>            :     {</a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">        359 :                 thiscoord = (int *)(lip) + i * 3;</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :     </a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">        359 :                 if (bitsize == 0) </span></a>
+<a name="923"><span class="lineNum">     923 </span>            :         {</a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineNoCov">          0 :                         thiscoord[0] = decodebits(buf2, bitsizeint[0]);</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineNoCov">          0 :                         thiscoord[1] = decodebits(buf2, bitsizeint[1]);</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineNoCov">          0 :                         thiscoord[2] = decodebits(buf2, bitsizeint[2]);</span></a>
+<a name="927"><span class="lineNum">     927 </span>            :                 }</a>
+<a name="928"><span class="lineNum">     928 </span>            :         else</a>
+<a name="929"><span class="lineNum">     929 </span>            :         {</a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">        359 :                         decodeints(buf2, 3, bitsize, sizeint, thiscoord);</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :                 }</a>
+<a name="932"><span class="lineNum">     932 </span>            :     </a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">        359 :                 i++;</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">        359 :                 thiscoord[0] += minint[0];</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">        359 :                 thiscoord[1] += minint[1];</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">        359 :                 thiscoord[2] += minint[2];</span></a>
+<a name="937"><span class="lineNum">     937 </span>            :     </a>
+<a name="938"><span class="lineNum">     938 </span>            :                 prevcoord[0] = thiscoord[0];</a>
+<a name="939"><span class="lineNum">     939 </span>            :                 prevcoord[1] = thiscoord[1];</a>
+<a name="940"><span class="lineNum">     940 </span>            :                 prevcoord[2] = thiscoord[2];</a>
+<a name="941"><span class="lineNum">     941 </span>            :     </a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">        359 :                 flag = decodebits(buf2, 1);</span></a>
+<a name="943"><span class="lineNum">     943 </span>            :                 is_smaller = 0;</a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">        359 :                 if (flag == 1) </span></a>
+<a name="945"><span class="lineNum">     945 </span>            :         {</a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">        304 :                         run = decodebits(buf2, 5);</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">        304 :                         is_smaller = run % 3;</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">        304 :                         run -= is_smaller;</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">        304 :                         is_smaller--;</span></a>
+<a name="950"><span class="lineNum">     950 </span>            :                 }</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">        359 :                 if (run &gt; 0)</span></a>
+<a name="952"><span class="lineNum">     952 </span>            :         {</a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">        241 :                         thiscoord += 3;</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">       1818 :                         for (k = 0; k &lt; run; k+=3) </span></a>
+<a name="955"><span class="lineNum">     955 </span>            :             {</a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">       1577 :                                 decodeints(buf2, 3, smallidx, sizesmall, thiscoord);</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">       1577 :                                 i++;</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">       1577 :                                 thiscoord[0] += prevcoord[0] - smallnum;</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">       1577 :                                 thiscoord[1] += prevcoord[1] - smallnum;</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">       1577 :                                 thiscoord[2] += prevcoord[2] - smallnum;</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">       1577 :                                 if (k == 0) {</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :                                         /* interchange first with second atom for better</a>
+<a name="963"><span class="lineNum">     963 </span>            :                                          * compression of water molecules</a>
+<a name="964"><span class="lineNum">     964 </span>            :                                          */</a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">        241 :                                         tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :                                         prevcoord[0] = tmp;</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">        241 :                                         tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];</span></a>
+<a name="968"><span class="lineNum">     968 </span>            :                                         prevcoord[1] = tmp;</a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">        241 :                                         tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];</span></a>
+<a name="970"><span class="lineNum">     970 </span>            :                                         prevcoord[2] = tmp;</a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">        241 :                                         *lfp++ = prevcoord[0] * inv_precision;</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">        241 :                                         *lfp++ = prevcoord[1] * inv_precision;</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">        241 :                                         *lfp++ = prevcoord[2] * inv_precision;</span></a>
+<a name="974"><span class="lineNum">     974 </span>            :                                 } else {</a>
+<a name="975"><span class="lineNum">     975 </span>            :                                         prevcoord[0] = thiscoord[0];</a>
+<a name="976"><span class="lineNum">     976 </span>            :                                         prevcoord[1] = thiscoord[1];</a>
+<a name="977"><span class="lineNum">     977 </span>            :                                         prevcoord[2] = thiscoord[2];</a>
+<a name="978"><span class="lineNum">     978 </span>            :                                 }</a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">       1577 :                                 *lfp++ = thiscoord[0] * inv_precision;</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">       1577 :                                 *lfp++ = thiscoord[1] * inv_precision;</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">       1577 :                                 *lfp++ = thiscoord[2] * inv_precision;</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :                         }</a>
+<a name="983"><span class="lineNum">     983 </span>            :                 } </a>
+<a name="984"><span class="lineNum">     984 </span>            :         else</a>
+<a name="985"><span class="lineNum">     985 </span>            :         {</a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">        118 :                         *lfp++ = thiscoord[0] * inv_precision;</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">        118 :                         *lfp++ = thiscoord[1] * inv_precision;</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">        118 :                         *lfp++ = thiscoord[2] * inv_precision;          </span></a>
+<a name="989"><span class="lineNum">     989 </span>            :                 }</a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">        359 :                 smallidx += is_smaller;</span></a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">        359 :                 if (is_smaller &lt; 0) </span></a>
+<a name="992"><span class="lineNum">     992 </span>            :         {</a>
+<a name="993"><span class="lineNum">     993 </span>            :                         smallnum = smaller;</a>
+<a name="994"><span class="lineNum">     994 </span>            :             </a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">         38 :                         if (smallidx &gt; FIRSTIDX) </span></a>
+<a name="996"><span class="lineNum">     996 </span>            :             {</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">         38 :                                 smaller = magicints[smallidx - 1] /2;</span></a>
+<a name="998"><span class="lineNum">     998 </span>            :                         } </a>
+<a name="999"><span class="lineNum">     999 </span>            :             else </a>
+<a name="1000"><span class="lineNum">    1000 </span>            :             {</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :                                 smaller = 0;</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :                         }</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :                 } </a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">        321 :         else if (is_smaller &gt; 0)</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            :         {</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :                         smaller = smallnum;</a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">        230 :                         smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            :                 }</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">        359 :                 sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            :         }</a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">         28 :         return *size;</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            : }</a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span>            : int</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">         72 : xdrfile_compress_coord_float(float   *ptr,</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            :                                                          int      size,</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :                                                          float    precision,</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :                                                          XDRFILE* xfp)</a>
+<a name="1019"><span class="lineNum">    1019 </span>            : {</a>
+<a name="1020"><span class="lineNum">    1020 </span>            :         int minint[3], maxint[3], mindiff, *lip, diff;</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :         int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :         int minidx, maxidx;</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :         unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :         int k, *buf1, *buf2;</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :         int smallnum, smaller, larger, i, j, is_small, is_smaller, run, prevrun;</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :         float *lfp, lf;</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :         int tmp, tmpsum, *thiscoord,  prevcoord[3];</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :         unsigned int tmpcoord[30];</a>
+<a name="1029"><span class="lineNum">    1029 </span>            :         int errval=1;</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :         unsigned int bitsize;</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   </a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">         72 :         if(xfp==NULL)</span></a>
+<a name="1033"><span class="lineNum">    1033 </span>            :                 return -1;</a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">         72 :         size3=3*size;</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     </a>
+<a name="1036"><span class="lineNum">    1036 </span>            :     bitsizeint[0] = 0;</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :     bitsizeint[1] = 0;</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :     bitsizeint[2] = 0;</a>
+<a name="1039"><span class="lineNum">    1039 </span>            : </a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">         72 :         if(size3&gt;xfp-&gt;buf1size)</span></a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     {</a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">          5 :                 if((xfp-&gt;buf1=(int *)malloc(sizeof(int)*size3))==NULL) </span></a>
+<a name="1043"><span class="lineNum">    1043 </span>            :         {</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for compressing coordinates.\n&quot;);</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="1046"><span class="lineNum">    1046 </span>            :                 }</a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">          5 :                 xfp-&gt;buf1size=size3;</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">          5 :                 xfp-&gt;buf2size=size3*1.2;</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">          5 :                 if((xfp-&gt;buf2=(int *)malloc(sizeof(int)*xfp-&gt;buf2size))==NULL)</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :         {</a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for compressing coordinates.\n&quot;);</span></a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            :                 }</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :         }</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">         72 :         if(xdrfile_write_int(&amp;size,1,xfp)==0)</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            :                 return -1; /* return if we could not write size */</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :         /* Dont bother with compression for three atoms or less */</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">         72 :         if(size&lt;=9) </span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :     {</a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">         12 :                 return xdrfile_write_float(ptr,size3,xfp)/3;</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            :                 /* return number of coords, not floats */</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :         }</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :         /* Compression-time if we got here. Write precision first */</a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">         60 :         if (precision &lt;= 0)</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineNoCov">          0 :                 precision = 1000;</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">         60 :         xdrfile_write_float(&amp;precision,1,xfp);</span></a>
+<a name="1067"><span class="lineNum">    1067 </span>            :         /* avoid repeated pointer dereferencing. */</a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">         60 :         buf1=xfp-&gt;buf1; </span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">         60 :         buf2=xfp-&gt;buf2;</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            :         /* buf2[0-2] are special and do not contain actual data */</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         60 :         buf2[0] = buf2[1] = buf2[2] = 0;</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         60 :         minint[0] = minint[1] = minint[2] = INT_MAX;</span></a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">         60 :         maxint[0] = maxint[1] = maxint[2] = INT_MIN;</span></a>
+<a name="1074"><span class="lineNum">    1074 </span>            :         prevrun = -1;</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :         lfp = ptr;</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :         lip = buf1;</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :         mindiff = INT_MAX;</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :         oldlint1 = oldlint2 = oldlint3 = 0;</a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">       4020 :         while(lfp &lt; ptr + size3 )</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     {</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :                 /* find nearest integer */</a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">       3960 :                 if (*lfp &gt;= 0.0)</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">         35 :                         lf = *lfp * precision + 0.5;</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :                 else</a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">       3925 :                         lf = *lfp * precision - 0.5;</span></a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">       3960 :                 if (fabs(lf) &gt; INT_MAX-2) </span></a>
+<a name="1087"><span class="lineNum">    1087 </span>            :         {</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :                         /* scaling would cause overflow */</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Internal overflow compressing coordinates.\n&quot;);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :                         errval=0;</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :                 }</a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">       3960 :                 lint1 = lf;</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">       3960 :                 if (lint1 &lt; minint[0]) minint[0] = lint1;</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineCov">       3960 :                 if (lint1 &gt; maxint[0]) maxint[0] = lint1;</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">       3960 :                 *lip++ = lint1;</span></a>
+<a name="1096"><span class="lineNum">    1096 </span>            :                 lfp++;</a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">       3960 :                 if (*lfp &gt;= 0.0)</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">          4 :                         lf = *lfp * precision + 0.5;</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            :                 else</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">       3956 :                         lf = *lfp * precision - 0.5;</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">       3960 :                 if (fabs(lf) &gt; INT_MAX-2)</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            :         {</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :                         /* scaling would cause overflow */</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Internal overflow compressing coordinates.\n&quot;);</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            :                         errval=0;</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :                 }</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">       3960 :                 lint2 = lf;</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">       3960 :                 if (lint2 &lt; minint[1]) minint[1] = lint2;</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineCov">       3960 :                 if (lint2 &gt; maxint[1]) maxint[1] = lint2;</span></a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">       3960 :                 *lip++ = lint2;</span></a>
+<a name="1111"><span class="lineNum">    1111 </span>            :                 lfp++;</a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineCov">       3960 :                 if (*lfp &gt;= 0.0)</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">       3960 :                         lf = *lfp * precision + 0.5;</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            :                 else</a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineNoCov">          0 :                         lf = *lfp * precision - 0.5;</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            :                 if (fabs(lf) &gt; INT_MAX-2) </a>
+<a name="1117"><span class="lineNum">    1117 </span>            :         {</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :                         errval=0;      </a>
+<a name="1119"><span class="lineNum">    1119 </span>            :                 }</a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">       3960 :                 lint3 = lf;</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">       3960 :                 if (lint3 &lt; minint[2]) minint[2] = lint3;</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">       3960 :                 if (lint3 &gt; maxint[2]) maxint[2] = lint3;</span></a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">       3960 :                 *lip++ = lint3;</span></a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">       3960 :                 lfp++;</span></a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">       3960 :                 diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">       3960 :                 if (diff &lt; mindiff &amp;&amp; lfp &gt; ptr + 3)</span></a>
+<a name="1127"><span class="lineNum">    1127 </span>            :                         mindiff = diff;</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :                 oldlint1 = lint1;</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :                 oldlint2 = lint2;</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :                 oldlint3 = lint3;</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :         }  </a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">         60 :         xdrfile_write_int(minint,3,xfp);</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">         60 :         xdrfile_write_int(maxint,3,xfp);</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   </a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">         60 :         if ((float)maxint[0] - (float)minint[0] &gt;= INT_MAX-2 ||</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">         60 :                 (float)maxint[1] - (float)minint[1] &gt;= INT_MAX-2 ||</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">         60 :                 (float)maxint[2] - (float)minint[2] &gt;= INT_MAX-2) {</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :                 /* turning value in unsigned by subtracting minint</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :                  * would cause overflow</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :                  */</a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineNoCov">          0 :                 fprintf(stderr,&quot;Internal overflow compressing coordinates.\n&quot;);</span></a>
+<a name="1142"><span class="lineNum">    1142 </span>            :                 errval=0;</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :         }</a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">         60 :         sizeint[0] = maxint[0] - minint[0]+1;</span></a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineCov">         60 :         sizeint[1] = maxint[1] - minint[1]+1;</span></a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">         60 :         sizeint[2] = maxint[2] - minint[2]+1;</span></a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   </a>
+<a name="1148"><span class="lineNum">    1148 </span>            :         /* check if one of the sizes is to big to be multiplied */</a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">         60 :         if ((sizeint[0] | sizeint[1] | sizeint[2] ) &gt; 0xffffff)</span></a>
+<a name="1150"><span class="lineNum">    1150 </span>            :     {</a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineNoCov">          0 :                 bitsizeint[0] = sizeofint(sizeint[0]);</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineNoCov">          0 :                 bitsizeint[1] = sizeofint(sizeint[1]);</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineNoCov">          0 :                 bitsizeint[2] = sizeofint(sizeint[2]);</span></a>
+<a name="1154"><span class="lineNum">    1154 </span>            :                 bitsize = 0; /* flag the use of large sizes */</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :         }</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     else</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :     {</a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">         60 :                 bitsize = sizeofints(3, sizeint);</span></a>
+<a name="1159"><span class="lineNum">    1159 </span>            :         }</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :         lip = buf1;</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :         luip = (unsigned int *) buf1;</a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">         60 :         smallidx = FIRSTIDX;</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">       1046 :         while (smallidx &lt; LASTIDX &amp;&amp; magicints[smallidx] &lt; mindiff)</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     {</a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">        986 :                 smallidx++;</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            :         }</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">         60 :         xdrfile_write_int(&amp;smallidx,1,xfp);</span></a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineCov">         60 :         tmp=smallidx+8;</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">         60 :         maxidx = (LASTIDX&lt;tmp) ? LASTIDX : tmp;</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">         60 :         minidx = maxidx - 8; /* often this equal smallidx */</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineCov">         60 :         tmp=smallidx-1;</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineCov">         60 :         tmp= (FIRSTIDX&gt;tmp) ? FIRSTIDX : tmp;</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineCov">         60 :         smaller = magicints[tmp] / 2;</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineCov">         60 :         smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineCov">         60 :         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">         60 :         larger = magicints[maxidx] / 2;</span></a>
+<a name="1177"><span class="lineNum">    1177 </span>            :         i = 0;</a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">        814 :         while (i &lt; size) </span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            :     {</a>
+<a name="1180"><span class="lineNum">    1180 </span>            :                 is_small = 0;</a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineCov">        754 :                 thiscoord = (int *)(luip) + i * 3;</span></a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">        754 :                 if (smallidx &lt; maxidx &amp;&amp; i &gt;= 1 &amp;&amp;</span></a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineCov">        531 :                         abs(thiscoord[0] - prevcoord[0]) &lt; larger &amp;&amp;</span></a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineCov">        531 :                         abs(thiscoord[1] - prevcoord[1]) &lt; larger &amp;&amp;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">        531 :                         abs(thiscoord[2] - prevcoord[2]) &lt; larger) {</span></a>
+<a name="1186"><span class="lineNum">    1186 </span>            :                         is_smaller = 1;</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :                 } </a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">        223 :         else if (smallidx &gt; minidx) </span></a>
+<a name="1189"><span class="lineNum">    1189 </span>            :         {</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :                         is_smaller = -1;</a>
+<a name="1191"><span class="lineNum">    1191 </span>            :                 }</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :         else</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :         {</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :                         is_smaller = 0;</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :                 }</a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineCov">        754 :                 if (i + 1 &lt; size) </span></a>
+<a name="1197"><span class="lineNum">    1197 </span>            :         {</a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineCov">        738 :                         if (abs(thiscoord[0] - thiscoord[3]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineCov">        651 :                                 abs(thiscoord[1] - thiscoord[4]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineCov">        580 :                                 abs(thiscoord[2] - thiscoord[5]) &lt; smallnum) </span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            :             {</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :                                 /* interchange first with second atom for better</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :                                  * compression of water molecules</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :                                  */</a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">        532 :                                 tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">        532 :                                 thiscoord[3] = tmp;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">        532 :                                 tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">        532 :                                 thiscoord[4] = tmp;</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">        532 :                                 tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">        532 :                                 thiscoord[5] = tmp;</span></a>
+<a name="1211"><span class="lineNum">    1211 </span>            :                                 is_small = 1;</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :                         } </a>
+<a name="1213"><span class="lineNum">    1213 </span>            :                 }</a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineCov">        754 :                 tmpcoord[0] = thiscoord[0] - minint[0];</span></a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineCov">        754 :                 tmpcoord[1] = thiscoord[1] - minint[1];</span></a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineCov">        754 :                 tmpcoord[2] = thiscoord[2] - minint[2];</span></a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">        754 :                 if (bitsize == 0) </span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            :         {</a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineNoCov">          0 :                         encodebits(buf2, bitsizeint[0], tmpcoord[0]);</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineNoCov">          0 :                         encodebits(buf2, bitsizeint[1], tmpcoord[1]);</span></a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineNoCov">          0 :                         encodebits(buf2, bitsizeint[2], tmpcoord[2]);</span></a>
+<a name="1222"><span class="lineNum">    1222 </span>            :                 } </a>
+<a name="1223"><span class="lineNum">    1223 </span>            :         else</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :         {</a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">        754 :                         encodeints(buf2, 3, bitsize, sizeint, tmpcoord);</span></a>
+<a name="1226"><span class="lineNum">    1226 </span>            :                 }</a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">        754 :                 prevcoord[0] = thiscoord[0];</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">        754 :                 prevcoord[1] = thiscoord[1];</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">        754 :                 prevcoord[2] = thiscoord[2];</span></a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineCov">        754 :                 thiscoord = thiscoord + 3;</span></a>
+<a name="1231"><span class="lineNum">    1231 </span>            :                 i++;</a>
+<a name="1232"><span class="lineNum">    1232 </span>            : </a>
+<a name="1233"><span class="lineNum">    1233 </span>            :                 run = 0;</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">        754 :                 if (is_small == 0 &amp;&amp; is_smaller == -1)</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            :                         is_smaller = 0;</a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineCov">       3960 :                 while (is_small &amp;&amp; run &lt; 8*3)</span></a>
+<a name="1237"><span class="lineNum">    1237 </span>            :         {</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :                         tmpsum=0;</a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineCov">      12824 :                         for(j=0;j&lt;3;j++) </span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            :             {</a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineCov">       9618 :                                 tmp=thiscoord[j] - prevcoord[j];</span></a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineCov">       9618 :                                 tmpsum+=tmp*tmp;</span></a>
+<a name="1243"><span class="lineNum">    1243 </span>            :                         }</a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">       3206 :                         if (is_smaller == -1 &amp;&amp; tmpsum &gt;= smaller * smaller)</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :             {</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :                                 is_smaller = 0;</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :                         }</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :       </a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">       3206 :                         tmpcoord[run++] = thiscoord[0] - prevcoord[0] + smallnum;</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">       3206 :                         tmpcoord[run++] = thiscoord[1] - prevcoord[1] + smallnum;</span></a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineCov">       3206 :                         tmpcoord[run++] = thiscoord[2] - prevcoord[2] + smallnum;</span></a>
+<a name="1252"><span class="lineNum">    1252 </span>            :       </a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineCov">       3206 :                         prevcoord[0] = thiscoord[0];</span></a>
+<a name="1254"><span class="lineNum">    1254 </span><span class="lineCov">       3206 :                         prevcoord[1] = thiscoord[1];</span></a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineCov">       3206 :                         prevcoord[2] = thiscoord[2];</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            :       </a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">       3206 :                         i++;</span></a>
+<a name="1258"><span class="lineNum">    1258 </span><span class="lineCov">       3206 :                         thiscoord = thiscoord + 3;</span></a>
+<a name="1259"><span class="lineNum">    1259 </span>            :                         is_small = 0;</a>
+<a name="1260"><span class="lineNum">    1260 </span><span class="lineCov">       3206 :                         if (i &lt; size &amp;&amp;</span></a>
+<a name="1261"><span class="lineNum">    1261 </span><span class="lineCov">       3162 :                                 abs(thiscoord[0] - prevcoord[0]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineCov">       3083 :                                 abs(thiscoord[1] - prevcoord[1]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">       3027 :                                 abs(thiscoord[2] - prevcoord[2]) &lt; smallnum)</span></a>
+<a name="1264"><span class="lineNum">    1264 </span>            :             {</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :                                 is_small = 1;</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :                         }</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :                 }</a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineCov">        754 :                 if (run != prevrun || is_smaller != 0) </span></a>
+<a name="1269"><span class="lineNum">    1269 </span>            :         {</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :                         prevrun = run;</a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">        717 :                         encodebits(buf2, 1, 1); /* flag the change in run-length */</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineCov">        717 :                         encodebits(buf2, 5, run+is_smaller+1);</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :                 } </a>
+<a name="1274"><span class="lineNum">    1274 </span>            :         else </a>
+<a name="1275"><span class="lineNum">    1275 </span>            :         {</a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">         37 :                         encodebits(buf2, 1, 0); /* flag the fact that runlength did not change */</span></a>
+<a name="1277"><span class="lineNum">    1277 </span>            :                 }</a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">       3960 :                 for (k=0; k &lt; run; k+=3) </span></a>
+<a name="1279"><span class="lineNum">    1279 </span>            :         {</a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">       3206 :                         encodeints(buf2, 3, smallidx, sizesmall, &amp;tmpcoord[k]);     </span></a>
+<a name="1281"><span class="lineNum">    1281 </span>            :                 }</a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineCov">        754 :                 if (is_smaller != 0) </span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            :         {</a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">        652 :                         smallidx += is_smaller;</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineCov">        652 :                         if (is_smaller &lt; 0) </span></a>
+<a name="1286"><span class="lineNum">    1286 </span>            :             {</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :                                 smallnum = smaller;</a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">        121 :                                 smaller = magicints[smallidx-1] / 2;</span></a>
+<a name="1289"><span class="lineNum">    1289 </span>            :                         } </a>
+<a name="1290"><span class="lineNum">    1290 </span>            :             else </a>
+<a name="1291"><span class="lineNum">    1291 </span>            :             {</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :                                 smaller = smallnum;</a>
+<a name="1293"><span class="lineNum">    1293 </span><span class="lineCov">        531 :                                 smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1294"><span class="lineNum">    1294 </span>            :                         }</a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineCov">        652 :                         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];</span></a>
+<a name="1296"><span class="lineNum">    1296 </span>            :                 }   </a>
+<a name="1297"><span class="lineNum">    1297 </span>            :         }</a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineCov">         60 :         if (buf2[1] != 0) buf2[0]++;</span></a>
+<a name="1299"><span class="lineNum">    1299 </span><span class="lineCov">         60 :         xdrfile_write_int(buf2,1,xfp); /* buf2[0] holds the length in bytes */</span></a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">         60 :         tmp=xdrfile_write_opaque((char *)&amp;(buf2[3]),(unsigned int)buf2[0],xfp);</span></a>
+<a name="1301"><span class="lineNum">    1301 </span><span class="lineCov">         60 :         if(tmp==(unsigned int)buf2[0])</span></a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineCov">         60 :                 return size;</span></a>
+<a name="1303"><span class="lineNum">    1303 </span>            :         else</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :                 return -1;</a>
+<a name="1305"><span class="lineNum">    1305 </span>            : }</a>
+<a name="1306"><span class="lineNum">    1306 </span>            : </a>
+<a name="1307"><span class="lineNum">    1307 </span>            : </a>
+<a name="1308"><span class="lineNum">    1308 </span>            : int</a>
+<a name="1309"><span class="lineNum">    1309 </span><span class="lineNoCov">          0 : xdrfile_decompress_coord_double(double     *ptr, </span></a>
+<a name="1310"><span class="lineNum">    1310 </span>            :                                                                 int        *size,</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :                                                                 double     *precision,</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :                                                                 XDRFILE*   xfp)</a>
+<a name="1313"><span class="lineNum">    1313 </span>            : {</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :         int minint[3], maxint[3], *lip;</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :         int smallidx, minidx, maxidx;</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :         unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3;</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :         int k, *buf1, *buf2, lsize, flag;</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :         int smallnum, smaller, larger, i, is_smaller, run;</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :         double *lfp, inv_precision;</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :         float float_prec, tmpdata[30];</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :         int tmp, *thiscoord,  prevcoord[3];</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :         unsigned int bitsize;</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :   </a>
+<a name="1324"><span class="lineNum">    1324 </span>            :     bitsizeint[0] = 0;</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :     bitsizeint[1] = 0;</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :     bitsizeint[2] = 0;</a>
+<a name="1327"><span class="lineNum">    1327 </span>            : </a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineNoCov">          0 :         if(xfp==NULL || ptr==NULL)</span></a>
+<a name="1329"><span class="lineNum">    1329 </span>            :                 return -1;</a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineNoCov">          0 :         tmp=xdrfile_read_int(&amp;lsize,1,xfp);</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineNoCov">          0 :         if(tmp==0)</span></a>
+<a name="1332"><span class="lineNum">    1332 </span>            :                 return -1; /* return if we could not read size */</a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineNoCov">          0 :         if (*size &lt; lsize) </span></a>
+<a name="1334"><span class="lineNum">    1334 </span>            :     {</a>
+<a name="1335"><span class="lineNum">    1335 </span><span class="lineNoCov">          0 :                 fprintf(stderr, &quot;Requested to decompress %d coords, file contains %d\n&quot;,</span></a>
+<a name="1336"><span class="lineNum">    1336 </span>            :                                 *size, lsize);</a>
+<a name="1337"><span class="lineNum">    1337 </span><span class="lineNoCov">          0 :                 return -1;</span></a>
+<a name="1338"><span class="lineNum">    1338 </span>            :         }</a>
+<a name="1339"><span class="lineNum">    1339 </span><span class="lineNoCov">          0 :         *size = lsize;</span></a>
+<a name="1340"><span class="lineNum">    1340 </span><span class="lineNoCov">          0 :         size3 = *size * 3;</span></a>
+<a name="1341"><span class="lineNum">    1341 </span><span class="lineNoCov">          0 :         if(size3&gt;xfp-&gt;buf1size) </span></a>
+<a name="1342"><span class="lineNum">    1342 </span>            :     {</a>
+<a name="1343"><span class="lineNum">    1343 </span><span class="lineNoCov">          0 :                 if((xfp-&gt;buf1=(int *)malloc(sizeof(int)*size3))==NULL) </span></a>
+<a name="1344"><span class="lineNum">    1344 </span>            :         {</a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for decompression coordinates.\n&quot;);</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineNoCov">          0 :                         return -1; </span></a>
+<a name="1347"><span class="lineNum">    1347 </span>            :                 }</a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineNoCov">          0 :                 xfp-&gt;buf1size=size3;</span></a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineNoCov">          0 :                 xfp-&gt;buf2size=size3*1.2;</span></a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineNoCov">          0 :                 if((xfp-&gt;buf2=(int *)malloc(sizeof(int)*xfp-&gt;buf2size))==NULL)</span></a>
+<a name="1351"><span class="lineNum">    1351 </span>            :         {</a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for decompressing coordinates.\n&quot;);</span></a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="1354"><span class="lineNum">    1354 </span>            :                 }</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :         }</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :         /* Dont bother with compression for three atoms or less */</a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineNoCov">          0 :         if(*size&lt;=9)</span></a>
+<a name="1358"><span class="lineNum">    1358 </span>            :     {</a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineNoCov">          0 :                 tmp=xdrfile_read_float(tmpdata,size3,xfp);</span></a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineNoCov">          0 :                 for(i=0;i&lt;9*3;i++)</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineNoCov">          0 :                         ptr[i]=tmpdata[i];</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineNoCov">          0 :                 return tmp/3;</span></a>
+<a name="1363"><span class="lineNum">    1363 </span>            :                 /* return number of coords, not floats */</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :         }</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :         /* Compression-time if we got here. Read precision first */</a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineNoCov">          0 :         xdrfile_read_float(&amp;float_prec,1,xfp);</span></a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineNoCov">          0 :         *precision=float_prec;</span></a>
+<a name="1368"><span class="lineNum">    1368 </span>            :         /* avoid repeated pointer dereferencing. */</a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineNoCov">          0 :         buf1=xfp-&gt;buf1; </span></a>
+<a name="1370"><span class="lineNum">    1370 </span><span class="lineNoCov">          0 :         buf2=xfp-&gt;buf2;</span></a>
+<a name="1371"><span class="lineNum">    1371 </span>            :         /* buf2[0-2] are special and do not contain actual data */</a>
+<a name="1372"><span class="lineNum">    1372 </span><span class="lineNoCov">          0 :         buf2[0] = buf2[1] = buf2[2] = 0;</span></a>
+<a name="1373"><span class="lineNum">    1373 </span><span class="lineNoCov">          0 :         xdrfile_read_int(minint,3,xfp);</span></a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineNoCov">          0 :         xdrfile_read_int(maxint,3,xfp);</span></a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   </a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineNoCov">          0 :         sizeint[0] = maxint[0] - minint[0]+1;</span></a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineNoCov">          0 :         sizeint[1] = maxint[1] - minint[1]+1;</span></a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineNoCov">          0 :         sizeint[2] = maxint[2] - minint[2]+1;</span></a>
+<a name="1379"><span class="lineNum">    1379 </span>            :         </a>
+<a name="1380"><span class="lineNum">    1380 </span>            :         /* check if one of the sizes is to big to be multiplied */</a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineNoCov">          0 :         if ((sizeint[0] | sizeint[1] | sizeint[2] ) &gt; 0xffffff)</span></a>
+<a name="1382"><span class="lineNum">    1382 </span>            :     {</a>
+<a name="1383"><span class="lineNum">    1383 </span><span class="lineNoCov">          0 :                 bitsizeint[0] = sizeofint(sizeint[0]);</span></a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineNoCov">          0 :                 bitsizeint[1] = sizeofint(sizeint[1]);</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineNoCov">          0 :                 bitsizeint[2] = sizeofint(sizeint[2]);</span></a>
+<a name="1386"><span class="lineNum">    1386 </span>            :                 bitsize = 0; /* flag the use of large sizes */</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :         }</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :     else </a>
+<a name="1389"><span class="lineNum">    1389 </span>            :     {</a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineNoCov">          0 :                 bitsize = sizeofints(3, sizeint);</span></a>
+<a name="1391"><span class="lineNum">    1391 </span>            :         }</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :         </a>
+<a name="1393"><span class="lineNum">    1393 </span><span class="lineNoCov">          0 :         if (xdrfile_read_int(&amp;smallidx,1,xfp) == 0) </span></a>
+<a name="1394"><span class="lineNum">    1394 </span>            :                 return 0;</a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineNoCov">          0 :         tmp=smallidx+8;</span></a>
+<a name="1396"><span class="lineNum">    1396 </span>            :         maxidx = (LASTIDX&lt;tmp) ? LASTIDX : tmp;</a>
+<a name="1397"><span class="lineNum">    1397 </span>            :         minidx = maxidx - 8; /* often this equal smallidx */</a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineNoCov">          0 :         tmp = smallidx-1;</span></a>
+<a name="1399"><span class="lineNum">    1399 </span><span class="lineNoCov">          0 :         tmp = (FIRSTIDX&gt;tmp) ? FIRSTIDX : tmp;</span></a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineNoCov">          0 :         smaller = magicints[tmp] / 2;</span></a>
+<a name="1401"><span class="lineNum">    1401 </span><span class="lineNoCov">          0 :         smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineNoCov">          0 :         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;</span></a>
+<a name="1403"><span class="lineNum">    1403 </span>            :         larger = magicints[maxidx];</a>
+<a name="1404"><span class="lineNum">    1404 </span>            : </a>
+<a name="1405"><span class="lineNum">    1405 </span>            :         /* buf2[0] holds the length in bytes */</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :   </a>
+<a name="1407"><span class="lineNum">    1407 </span><span class="lineNoCov">          0 :         if (xdrfile_read_int(buf2,1,xfp) == 0)</span></a>
+<a name="1408"><span class="lineNum">    1408 </span>            :                 return 0;</a>
+<a name="1409"><span class="lineNum">    1409 </span><span class="lineNoCov">          0 :         if (xdrfile_read_opaque((char *)&amp;(buf2[3]),(unsigned int)buf2[0],xfp) == 0)</span></a>
+<a name="1410"><span class="lineNum">    1410 </span>            :                 return 0;</a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineNoCov">          0 :         buf2[0] = buf2[1] = buf2[2] = 0;</span></a>
+<a name="1412"><span class="lineNum">    1412 </span>            :   </a>
+<a name="1413"><span class="lineNum">    1413 </span>            :         lfp = ptr;</a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineNoCov">          0 :         inv_precision = 1.0 / * precision;</span></a>
+<a name="1415"><span class="lineNum">    1415 </span>            :         run = 0;</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :         i = 0;</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :         lip = buf1;</a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineNoCov">          0 :         while ( i &lt; lsize ) </span></a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     {</a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineNoCov">          0 :                 thiscoord = (int *)(lip) + i * 3;</span></a>
+<a name="1421"><span class="lineNum">    1421 </span>            :     </a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineNoCov">          0 :                 if (bitsize == 0) </span></a>
+<a name="1423"><span class="lineNum">    1423 </span>            :         {</a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineNoCov">          0 :                         thiscoord[0] = decodebits(buf2, bitsizeint[0]);</span></a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineNoCov">          0 :                         thiscoord[1] = decodebits(buf2, bitsizeint[1]);</span></a>
+<a name="1426"><span class="lineNum">    1426 </span><span class="lineNoCov">          0 :                         thiscoord[2] = decodebits(buf2, bitsizeint[2]);</span></a>
+<a name="1427"><span class="lineNum">    1427 </span>            :                 } else {</a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineNoCov">          0 :                         decodeints(buf2, 3, bitsize, sizeint, thiscoord);</span></a>
+<a name="1429"><span class="lineNum">    1429 </span>            :                 }</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :     </a>
+<a name="1431"><span class="lineNum">    1431 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="1432"><span class="lineNum">    1432 </span><span class="lineNoCov">          0 :                 thiscoord[0] += minint[0];</span></a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineNoCov">          0 :                 thiscoord[1] += minint[1];</span></a>
+<a name="1434"><span class="lineNum">    1434 </span><span class="lineNoCov">          0 :                 thiscoord[2] += minint[2];</span></a>
+<a name="1435"><span class="lineNum">    1435 </span>            :     </a>
+<a name="1436"><span class="lineNum">    1436 </span>            :                 prevcoord[0] = thiscoord[0];</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :                 prevcoord[1] = thiscoord[1];</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :                 prevcoord[2] = thiscoord[2];</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :     </a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineNoCov">          0 :                 flag = decodebits(buf2, 1);</span></a>
+<a name="1441"><span class="lineNum">    1441 </span>            :                 is_smaller = 0;</a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineNoCov">          0 :                 if (flag == 1) </span></a>
+<a name="1443"><span class="lineNum">    1443 </span>            :         {</a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineNoCov">          0 :                         run = decodebits(buf2, 5);</span></a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineNoCov">          0 :                         is_smaller = run % 3;</span></a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineNoCov">          0 :                         run -= is_smaller;</span></a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineNoCov">          0 :                         is_smaller--;</span></a>
+<a name="1448"><span class="lineNum">    1448 </span>            :                 }</a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineNoCov">          0 :                 if (run &gt; 0) </span></a>
+<a name="1450"><span class="lineNum">    1450 </span>            :         {</a>
+<a name="1451"><span class="lineNum">    1451 </span><span class="lineNoCov">          0 :                         thiscoord += 3;</span></a>
+<a name="1452"><span class="lineNum">    1452 </span><span class="lineNoCov">          0 :                         for (k = 0; k &lt; run; k+=3) </span></a>
+<a name="1453"><span class="lineNum">    1453 </span>            :             {</a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineNoCov">          0 :                                 decodeints(buf2, 3, smallidx, sizesmall, thiscoord);</span></a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineNoCov">          0 :                                 i++;</span></a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineNoCov">          0 :                                 thiscoord[0] += prevcoord[0] - smallnum;</span></a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineNoCov">          0 :                                 thiscoord[1] += prevcoord[1] - smallnum;</span></a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineNoCov">          0 :                                 thiscoord[2] += prevcoord[2] - smallnum;</span></a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineNoCov">          0 :                                 if (k == 0)</span></a>
+<a name="1460"><span class="lineNum">    1460 </span>            :                 {</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :                                         /* interchange first with second atom for better</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :                                          * compression of water molecules</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :                                          */</a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineNoCov">          0 :                                         tmp = thiscoord[0]; thiscoord[0] = prevcoord[0];</span></a>
+<a name="1465"><span class="lineNum">    1465 </span>            :                                         prevcoord[0] = tmp;</a>
+<a name="1466"><span class="lineNum">    1466 </span><span class="lineNoCov">          0 :                                         tmp = thiscoord[1]; thiscoord[1] = prevcoord[1];</span></a>
+<a name="1467"><span class="lineNum">    1467 </span>            :                                         prevcoord[1] = tmp;</a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineNoCov">          0 :                                         tmp = thiscoord[2]; thiscoord[2] = prevcoord[2];</span></a>
+<a name="1469"><span class="lineNum">    1469 </span>            :                                         prevcoord[2] = tmp;</a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineNoCov">          0 :                                         *lfp++ = prevcoord[0] * inv_precision;</span></a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineNoCov">          0 :                                         *lfp++ = prevcoord[1] * inv_precision;</span></a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineNoCov">          0 :                                         *lfp++ = prevcoord[2] * inv_precision;</span></a>
+<a name="1473"><span class="lineNum">    1473 </span>            :                                 }</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :                 else </a>
+<a name="1475"><span class="lineNum">    1475 </span>            :                 {</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :                                         prevcoord[0] = thiscoord[0];</a>
+<a name="1477"><span class="lineNum">    1477 </span>            :                                         prevcoord[1] = thiscoord[1];</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :                                         prevcoord[2] = thiscoord[2];</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :                                 }</a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineNoCov">          0 :                                 *lfp++ = thiscoord[0] * inv_precision;</span></a>
+<a name="1481"><span class="lineNum">    1481 </span><span class="lineNoCov">          0 :                                 *lfp++ = thiscoord[1] * inv_precision;</span></a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineNoCov">          0 :                                 *lfp++ = thiscoord[2] * inv_precision;</span></a>
+<a name="1483"><span class="lineNum">    1483 </span>            :                         }</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :                 } else {</a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineNoCov">          0 :                         *lfp++ = thiscoord[0] * inv_precision;</span></a>
+<a name="1486"><span class="lineNum">    1486 </span><span class="lineNoCov">          0 :                         *lfp++ = thiscoord[1] * inv_precision;</span></a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineNoCov">          0 :                         *lfp++ = thiscoord[2] * inv_precision;          </span></a>
+<a name="1488"><span class="lineNum">    1488 </span>            :                 }</a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineNoCov">          0 :                 smallidx += is_smaller;</span></a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineNoCov">          0 :                 if (is_smaller &lt; 0) {</span></a>
+<a name="1491"><span class="lineNum">    1491 </span>            :                         smallnum = smaller;</a>
+<a name="1492"><span class="lineNum">    1492 </span><span class="lineNoCov">          0 :                         if (smallidx &gt; FIRSTIDX) {</span></a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineNoCov">          0 :                                 smaller = magicints[smallidx - 1] /2;</span></a>
+<a name="1494"><span class="lineNum">    1494 </span>            :                         } else {</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :                                 smaller = 0;</a>
+<a name="1496"><span class="lineNum">    1496 </span>            :                         }</a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineNoCov">          0 :                 } else if (is_smaller &gt; 0) {</span></a>
+<a name="1498"><span class="lineNum">    1498 </span>            :                         smaller = smallnum;</a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineNoCov">          0 :                         smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1500"><span class="lineNum">    1500 </span>            :                 }</a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineNoCov">          0 :                 sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx] ;</span></a>
+<a name="1502"><span class="lineNum">    1502 </span>            :         }</a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineNoCov">          0 :         return *size;</span></a>
+<a name="1504"><span class="lineNum">    1504 </span>            : }</a>
+<a name="1505"><span class="lineNum">    1505 </span>            : </a>
+<a name="1506"><span class="lineNum">    1506 </span>            : int</a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineNoCov">          0 : xdrfile_compress_coord_double(double   *ptr,</span></a>
+<a name="1508"><span class="lineNum">    1508 </span>            :                                                           int      size,</a>
+<a name="1509"><span class="lineNum">    1509 </span>            :                                                           double    precision,</a>
+<a name="1510"><span class="lineNum">    1510 </span>            :                                                           XDRFILE* xfp)</a>
+<a name="1511"><span class="lineNum">    1511 </span>            : {</a>
+<a name="1512"><span class="lineNum">    1512 </span>            :         int minint[3], maxint[3], mindiff, *lip, diff;</a>
+<a name="1513"><span class="lineNum">    1513 </span>            :         int lint1, lint2, lint3, oldlint1, oldlint2, oldlint3, smallidx;</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :         int minidx, maxidx;</a>
+<a name="1515"><span class="lineNum">    1515 </span>            :         unsigned sizeint[3], sizesmall[3], bitsizeint[3], size3, *luip;</a>
+<a name="1516"><span class="lineNum">    1516 </span>            :         int k, *buf1, *buf2;</a>
+<a name="1517"><span class="lineNum">    1517 </span>            :         int smallnum, smaller, larger, i, j, is_small, is_smaller, run, prevrun;</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :         double *lfp;</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :         float float_prec, lf,tmpdata[30];</a>
+<a name="1520"><span class="lineNum">    1520 </span>            :         int tmp, tmpsum, *thiscoord,  prevcoord[3];</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :         unsigned int tmpcoord[30];</a>
+<a name="1522"><span class="lineNum">    1522 </span>            :         int errval=1;</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :         unsigned int bitsize;</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :   </a>
+<a name="1525"><span class="lineNum">    1525 </span>            :     bitsizeint[0] = 0;</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :     bitsizeint[1] = 0;</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :     bitsizeint[2] = 0;</a>
+<a name="1528"><span class="lineNum">    1528 </span>            : </a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineNoCov">          0 :         if(xfp==NULL)</span></a>
+<a name="1530"><span class="lineNum">    1530 </span>            :                 return -1;</a>
+<a name="1531"><span class="lineNum">    1531 </span><span class="lineNoCov">          0 :         size3=3*size;</span></a>
+<a name="1532"><span class="lineNum">    1532 </span><span class="lineNoCov">          0 :         if(size3&gt;xfp-&gt;buf1size) {</span></a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineNoCov">          0 :                 if((xfp-&gt;buf1=(int *)malloc(sizeof(int)*size3))==NULL) {</span></a>
+<a name="1534"><span class="lineNum">    1534 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for compressing coordinates.\n&quot;);</span></a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="1536"><span class="lineNum">    1536 </span>            :                 }</a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineNoCov">          0 :                 xfp-&gt;buf1size=size3;</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineNoCov">          0 :                 xfp-&gt;buf2size=size3*1.2;</span></a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineNoCov">          0 :                 if((xfp-&gt;buf2=(int *)malloc(sizeof(int)*xfp-&gt;buf2size))==NULL) {</span></a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Cannot allocate memory for compressing coordinates.\n&quot;);</span></a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineNoCov">          0 :                         return -1;</span></a>
+<a name="1542"><span class="lineNum">    1542 </span>            :                 }</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :         }</a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineNoCov">          0 :         if(xdrfile_write_int(&amp;size,1,xfp)==0)</span></a>
+<a name="1545"><span class="lineNum">    1545 </span>            :                 return -1; /* return if we could not write size */</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :         /* Dont bother with compression for three atoms or less */</a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineNoCov">          0 :         if(size&lt;=9) {</span></a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineNoCov">          0 :                 for(i=0;i&lt;9*3;i++)</span></a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineNoCov">          0 :                         tmpdata[i]=ptr[i];</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineNoCov">          0 :                 return xdrfile_write_float(tmpdata,size3,xfp)/3;</span></a>
+<a name="1551"><span class="lineNum">    1551 </span>            :                 /* return number of coords, not floats */</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :         }</a>
+<a name="1553"><span class="lineNum">    1553 </span>            :         /* Compression-time if we got here. Write precision first */</a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineNoCov">          0 :         if (precision &lt;= 0)</span></a>
+<a name="1555"><span class="lineNum">    1555 </span>            :                 precision = 1000;</a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineNoCov">          0 :         float_prec=precision;</span></a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineNoCov">          0 :         xdrfile_write_float(&amp;float_prec,1,xfp);</span></a>
+<a name="1558"><span class="lineNum">    1558 </span>            :         /* avoid repeated pointer dereferencing. */</a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineNoCov">          0 :         buf1=xfp-&gt;buf1; </span></a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineNoCov">          0 :         buf2=xfp-&gt;buf2;</span></a>
+<a name="1561"><span class="lineNum">    1561 </span>            :         /* buf2[0-2] are special and do not contain actual data */</a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineNoCov">          0 :         buf2[0] = buf2[1] = buf2[2] = 0;</span></a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineNoCov">          0 :         minint[0] = minint[1] = minint[2] = INT_MAX;</span></a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineNoCov">          0 :         maxint[0] = maxint[1] = maxint[2] = INT_MIN;</span></a>
+<a name="1565"><span class="lineNum">    1565 </span>            :         prevrun = -1;</a>
+<a name="1566"><span class="lineNum">    1566 </span>            :         lfp = ptr;</a>
+<a name="1567"><span class="lineNum">    1567 </span>            :         lip = buf1;</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :         mindiff = INT_MAX;</a>
+<a name="1569"><span class="lineNum">    1569 </span>            :         oldlint1 = oldlint2 = oldlint3 = 0;</a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineNoCov">          0 :         while(lfp &lt; ptr + size3 ) {</span></a>
+<a name="1571"><span class="lineNum">    1571 </span>            :                 /* find nearest integer */</a>
+<a name="1572"><span class="lineNum">    1572 </span><span class="lineNoCov">          0 :                 if (*lfp &gt;= 0.0)</span></a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineNoCov">          0 :                         lf = (float)*lfp * float_prec + 0.5;</span></a>
+<a name="1574"><span class="lineNum">    1574 </span>            :                 else</a>
+<a name="1575"><span class="lineNum">    1575 </span><span class="lineNoCov">          0 :                         lf = (float)*lfp * float_prec - 0.5;</span></a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineNoCov">          0 :                 if (fabs(lf) &gt; INT_MAX-2) {</span></a>
+<a name="1577"><span class="lineNum">    1577 </span>            :                         /* scaling would cause overflow */</a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Internal overflow compressing coordinates.\n&quot;);</span></a>
+<a name="1579"><span class="lineNum">    1579 </span>            :                         errval=0;</a>
+<a name="1580"><span class="lineNum">    1580 </span>            :                 }</a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineNoCov">          0 :                 lint1 = lf;</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineNoCov">          0 :                 if (lint1 &lt; minint[0]) minint[0] = lint1;</span></a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineNoCov">          0 :                 if (lint1 &gt; maxint[0]) maxint[0] = lint1;</span></a>
+<a name="1584"><span class="lineNum">    1584 </span><span class="lineNoCov">          0 :                 *lip++ = lint1;</span></a>
+<a name="1585"><span class="lineNum">    1585 </span>            :                 lfp++;</a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineNoCov">          0 :                 if (*lfp &gt;= 0.0)</span></a>
+<a name="1587"><span class="lineNum">    1587 </span><span class="lineNoCov">          0 :                         lf = (float)*lfp * float_prec + 0.5;</span></a>
+<a name="1588"><span class="lineNum">    1588 </span>            :                 else</a>
+<a name="1589"><span class="lineNum">    1589 </span><span class="lineNoCov">          0 :                         lf = (float)*lfp * float_prec - 0.5;</span></a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineNoCov">          0 :                 if (fabs(lf) &gt; INT_MAX-2) {</span></a>
+<a name="1591"><span class="lineNum">    1591 </span>            :                         /* scaling would cause overflow */</a>
+<a name="1592"><span class="lineNum">    1592 </span><span class="lineNoCov">          0 :                         fprintf(stderr,&quot;Internal overflow compressing coordinates.\n&quot;);</span></a>
+<a name="1593"><span class="lineNum">    1593 </span>            :                         errval=0;</a>
+<a name="1594"><span class="lineNum">    1594 </span>            :                 }</a>
+<a name="1595"><span class="lineNum">    1595 </span><span class="lineNoCov">          0 :                 lint2 = lf;</span></a>
+<a name="1596"><span class="lineNum">    1596 </span><span class="lineNoCov">          0 :                 if (lint2 &lt; minint[1]) minint[1] = lint2;</span></a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineNoCov">          0 :                 if (lint2 &gt; maxint[1]) maxint[1] = lint2;</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineNoCov">          0 :                 *lip++ = lint2;</span></a>
+<a name="1599"><span class="lineNum">    1599 </span>            :                 lfp++;</a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineNoCov">          0 :                 if (*lfp &gt;= 0.0)</span></a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineNoCov">          0 :                         lf = (float)*lfp * float_prec + 0.5;</span></a>
+<a name="1602"><span class="lineNum">    1602 </span>            :                 else</a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineNoCov">          0 :                         lf = (float)*lfp * float_prec - 0.5;</span></a>
+<a name="1604"><span class="lineNum">    1604 </span>            :                 if (fabs(lf) &gt; INT_MAX-2) {</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :                         errval=0;      </a>
+<a name="1606"><span class="lineNum">    1606 </span>            :                 }</a>
+<a name="1607"><span class="lineNum">    1607 </span><span class="lineNoCov">          0 :                 lint3 = lf;</span></a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineNoCov">          0 :                 if (lint3 &lt; minint[2]) minint[2] = lint3;</span></a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineNoCov">          0 :                 if (lint3 &gt; maxint[2]) maxint[2] = lint3;</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineNoCov">          0 :                 *lip++ = lint3;</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineNoCov">          0 :                 lfp++;</span></a>
+<a name="1612"><span class="lineNum">    1612 </span><span class="lineNoCov">          0 :                 diff = abs(oldlint1-lint1)+abs(oldlint2-lint2)+abs(oldlint3-lint3);</span></a>
+<a name="1613"><span class="lineNum">    1613 </span><span class="lineNoCov">          0 :                 if (diff &lt; mindiff &amp;&amp; lfp &gt; ptr + 3)</span></a>
+<a name="1614"><span class="lineNum">    1614 </span>            :                         mindiff = diff;</a>
+<a name="1615"><span class="lineNum">    1615 </span>            :                 oldlint1 = lint1;</a>
+<a name="1616"><span class="lineNum">    1616 </span>            :                 oldlint2 = lint2;</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :                 oldlint3 = lint3;</a>
+<a name="1618"><span class="lineNum">    1618 </span>            :         }  </a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineNoCov">          0 :         xdrfile_write_int(minint,3,xfp);</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineNoCov">          0 :         xdrfile_write_int(maxint,3,xfp);</span></a>
+<a name="1621"><span class="lineNum">    1621 </span>            :   </a>
+<a name="1622"><span class="lineNum">    1622 </span><span class="lineNoCov">          0 :         if ((float)maxint[0] - (float)minint[0] &gt;= INT_MAX-2 ||</span></a>
+<a name="1623"><span class="lineNum">    1623 </span><span class="lineNoCov">          0 :                 (float)maxint[1] - (float)minint[1] &gt;= INT_MAX-2 ||</span></a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineNoCov">          0 :                 (float)maxint[2] - (float)minint[2] &gt;= INT_MAX-2) {</span></a>
+<a name="1625"><span class="lineNum">    1625 </span>            :                 /* turning value in unsigned by subtracting minint</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :                  * would cause overflow</a>
+<a name="1627"><span class="lineNum">    1627 </span>            :                  */</a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineNoCov">          0 :                 fprintf(stderr,&quot;Internal overflow compressing coordinates.\n&quot;);</span></a>
+<a name="1629"><span class="lineNum">    1629 </span>            :                 errval=0;</a>
+<a name="1630"><span class="lineNum">    1630 </span>            :         }</a>
+<a name="1631"><span class="lineNum">    1631 </span><span class="lineNoCov">          0 :         sizeint[0] = maxint[0] - minint[0]+1;</span></a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineNoCov">          0 :         sizeint[1] = maxint[1] - minint[1]+1;</span></a>
+<a name="1633"><span class="lineNum">    1633 </span><span class="lineNoCov">          0 :         sizeint[2] = maxint[2] - minint[2]+1;</span></a>
+<a name="1634"><span class="lineNum">    1634 </span>            :   </a>
+<a name="1635"><span class="lineNum">    1635 </span>            :         /* check if one of the sizes is to big to be multiplied */</a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineNoCov">          0 :         if ((sizeint[0] | sizeint[1] | sizeint[2] ) &gt; 0xffffff) {</span></a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineNoCov">          0 :                 bitsizeint[0] = sizeofint(sizeint[0]);</span></a>
+<a name="1638"><span class="lineNum">    1638 </span><span class="lineNoCov">          0 :                 bitsizeint[1] = sizeofint(sizeint[1]);</span></a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineNoCov">          0 :                 bitsizeint[2] = sizeofint(sizeint[2]);</span></a>
+<a name="1640"><span class="lineNum">    1640 </span>            :                 bitsize = 0; /* flag the use of large sizes */</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :         } else {</a>
+<a name="1642"><span class="lineNum">    1642 </span><span class="lineNoCov">          0 :                 bitsize = sizeofints(3, sizeint);</span></a>
+<a name="1643"><span class="lineNum">    1643 </span>            :         }</a>
+<a name="1644"><span class="lineNum">    1644 </span>            :         lip = buf1;</a>
+<a name="1645"><span class="lineNum">    1645 </span>            :         luip = (unsigned int *) buf1;</a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineNoCov">          0 :         smallidx = FIRSTIDX;</span></a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineNoCov">          0 :         while (smallidx &lt; LASTIDX &amp;&amp; magicints[smallidx] &lt; mindiff) {</span></a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineNoCov">          0 :                 smallidx++;</span></a>
+<a name="1649"><span class="lineNum">    1649 </span>            :         }</a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineNoCov">          0 :         xdrfile_write_int(&amp;smallidx,1,xfp);</span></a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineNoCov">          0 :         tmp=smallidx+8;</span></a>
+<a name="1652"><span class="lineNum">    1652 </span><span class="lineNoCov">          0 :         maxidx = (LASTIDX&lt;tmp) ? LASTIDX : tmp;</span></a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineNoCov">          0 :         minidx = maxidx - 8; /* often this equal smallidx */</span></a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineNoCov">          0 :         tmp=smallidx-1;</span></a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineNoCov">          0 :         tmp= (FIRSTIDX&gt;tmp) ? FIRSTIDX : tmp;</span></a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineNoCov">          0 :         smaller = magicints[tmp] / 2;</span></a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineNoCov">          0 :         smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1658"><span class="lineNum">    1658 </span><span class="lineNoCov">          0 :         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];</span></a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineNoCov">          0 :         larger = magicints[maxidx] / 2;</span></a>
+<a name="1660"><span class="lineNum">    1660 </span>            :         i = 0;</a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineNoCov">          0 :         while (i &lt; size) {</span></a>
+<a name="1662"><span class="lineNum">    1662 </span>            :                 is_small = 0;</a>
+<a name="1663"><span class="lineNum">    1663 </span><span class="lineNoCov">          0 :                 thiscoord = (int *)(luip) + i * 3;</span></a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineNoCov">          0 :                 if (smallidx &lt; maxidx &amp;&amp; i &gt;= 1 &amp;&amp;</span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineNoCov">          0 :                         abs(thiscoord[0] - prevcoord[0]) &lt; larger &amp;&amp;</span></a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineNoCov">          0 :                         abs(thiscoord[1] - prevcoord[1]) &lt; larger &amp;&amp;</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineNoCov">          0 :                         abs(thiscoord[2] - prevcoord[2]) &lt; larger) {</span></a>
+<a name="1668"><span class="lineNum">    1668 </span>            :                         is_smaller = 1;</a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineNoCov">          0 :                 } else if (smallidx &gt; minidx) {</span></a>
+<a name="1670"><span class="lineNum">    1670 </span>            :                         is_smaller = -1;</a>
+<a name="1671"><span class="lineNum">    1671 </span>            :                 } else {</a>
+<a name="1672"><span class="lineNum">    1672 </span>            :                         is_smaller = 0;</a>
+<a name="1673"><span class="lineNum">    1673 </span>            :                 }</a>
+<a name="1674"><span class="lineNum">    1674 </span><span class="lineNoCov">          0 :                 if (i + 1 &lt; size) {</span></a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineNoCov">          0 :                         if (abs(thiscoord[0] - thiscoord[3]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineNoCov">          0 :                                 abs(thiscoord[1] - thiscoord[4]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineNoCov">          0 :                                 abs(thiscoord[2] - thiscoord[5]) &lt; smallnum) {</span></a>
+<a name="1678"><span class="lineNum">    1678 </span>            :                                 /* interchange first with second atom for better</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :                                  * compression of water molecules</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :                                  */</a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineNoCov">          0 :                                 tmp = thiscoord[0]; thiscoord[0] = thiscoord[3];</span></a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineNoCov">          0 :                                 thiscoord[3] = tmp;</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineNoCov">          0 :                                 tmp = thiscoord[1]; thiscoord[1] = thiscoord[4];</span></a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineNoCov">          0 :                                 thiscoord[4] = tmp;</span></a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineNoCov">          0 :                                 tmp = thiscoord[2]; thiscoord[2] = thiscoord[5];</span></a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineNoCov">          0 :                                 thiscoord[5] = tmp;</span></a>
+<a name="1687"><span class="lineNum">    1687 </span>            :                                 is_small = 1;</a>
+<a name="1688"><span class="lineNum">    1688 </span>            :                         } </a>
+<a name="1689"><span class="lineNum">    1689 </span>            :                 }</a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineNoCov">          0 :                 tmpcoord[0] = thiscoord[0] - minint[0];</span></a>
+<a name="1691"><span class="lineNum">    1691 </span><span class="lineNoCov">          0 :                 tmpcoord[1] = thiscoord[1] - minint[1];</span></a>
+<a name="1692"><span class="lineNum">    1692 </span><span class="lineNoCov">          0 :                 tmpcoord[2] = thiscoord[2] - minint[2];</span></a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineNoCov">          0 :                 if (bitsize == 0) {</span></a>
+<a name="1694"><span class="lineNum">    1694 </span><span class="lineNoCov">          0 :                         encodebits(buf2, bitsizeint[0], tmpcoord[0]);</span></a>
+<a name="1695"><span class="lineNum">    1695 </span><span class="lineNoCov">          0 :                         encodebits(buf2, bitsizeint[1], tmpcoord[1]);</span></a>
+<a name="1696"><span class="lineNum">    1696 </span><span class="lineNoCov">          0 :                         encodebits(buf2, bitsizeint[2], tmpcoord[2]);</span></a>
+<a name="1697"><span class="lineNum">    1697 </span>            :                 } else {</a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineNoCov">          0 :                         encodeints(buf2, 3, bitsize, sizeint, tmpcoord);</span></a>
+<a name="1699"><span class="lineNum">    1699 </span>            :                 }</a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineNoCov">          0 :                 prevcoord[0] = thiscoord[0];</span></a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineNoCov">          0 :                 prevcoord[1] = thiscoord[1];</span></a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineNoCov">          0 :                 prevcoord[2] = thiscoord[2];</span></a>
+<a name="1703"><span class="lineNum">    1703 </span><span class="lineNoCov">          0 :                 thiscoord = thiscoord + 3;</span></a>
+<a name="1704"><span class="lineNum">    1704 </span>            :                 i++;</a>
+<a name="1705"><span class="lineNum">    1705 </span>            : </a>
+<a name="1706"><span class="lineNum">    1706 </span>            :                 run = 0;</a>
+<a name="1707"><span class="lineNum">    1707 </span><span class="lineNoCov">          0 :                 if (is_small == 0 &amp;&amp; is_smaller == -1)</span></a>
+<a name="1708"><span class="lineNum">    1708 </span>            :                         is_smaller = 0;</a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineNoCov">          0 :                 while (is_small &amp;&amp; run &lt; 8*3) {</span></a>
+<a name="1710"><span class="lineNum">    1710 </span>            :                         tmpsum=0;</a>
+<a name="1711"><span class="lineNum">    1711 </span><span class="lineNoCov">          0 :                         for(j=0;j&lt;3;j++) {</span></a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineNoCov">          0 :                                 tmp=thiscoord[j] - prevcoord[j];</span></a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineNoCov">          0 :                                 tmpsum+=tmp*tmp;</span></a>
+<a name="1714"><span class="lineNum">    1714 </span>            :                         }</a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineNoCov">          0 :                         if (is_smaller == -1 &amp;&amp; tmpsum &gt;= smaller * smaller) {</span></a>
+<a name="1716"><span class="lineNum">    1716 </span>            :                                 is_smaller = 0;</a>
+<a name="1717"><span class="lineNum">    1717 </span>            :                         }</a>
+<a name="1718"><span class="lineNum">    1718 </span>            :       </a>
+<a name="1719"><span class="lineNum">    1719 </span><span class="lineNoCov">          0 :                         tmpcoord[run++] = thiscoord[0] - prevcoord[0] + smallnum;</span></a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineNoCov">          0 :                         tmpcoord[run++] = thiscoord[1] - prevcoord[1] + smallnum;</span></a>
+<a name="1721"><span class="lineNum">    1721 </span><span class="lineNoCov">          0 :                         tmpcoord[run++] = thiscoord[2] - prevcoord[2] + smallnum;</span></a>
+<a name="1722"><span class="lineNum">    1722 </span>            :       </a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineNoCov">          0 :                         prevcoord[0] = thiscoord[0];</span></a>
+<a name="1724"><span class="lineNum">    1724 </span><span class="lineNoCov">          0 :                         prevcoord[1] = thiscoord[1];</span></a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineNoCov">          0 :                         prevcoord[2] = thiscoord[2];</span></a>
+<a name="1726"><span class="lineNum">    1726 </span>            :       </a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineNoCov">          0 :                         i++;</span></a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineNoCov">          0 :                         thiscoord = thiscoord + 3;</span></a>
+<a name="1729"><span class="lineNum">    1729 </span>            :                         is_small = 0;</a>
+<a name="1730"><span class="lineNum">    1730 </span><span class="lineNoCov">          0 :                         if (i &lt; size &amp;&amp;</span></a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineNoCov">          0 :                                 abs(thiscoord[0] - prevcoord[0]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineNoCov">          0 :                                 abs(thiscoord[1] - prevcoord[1]) &lt; smallnum &amp;&amp;</span></a>
+<a name="1733"><span class="lineNum">    1733 </span><span class="lineNoCov">          0 :                                 abs(thiscoord[2] - prevcoord[2]) &lt; smallnum) {</span></a>
+<a name="1734"><span class="lineNum">    1734 </span>            :                                 is_small = 1;</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :                         }</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :                 }</a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineNoCov">          0 :                 if (run != prevrun || is_smaller != 0) {</span></a>
+<a name="1738"><span class="lineNum">    1738 </span>            :                         prevrun = run;</a>
+<a name="1739"><span class="lineNum">    1739 </span><span class="lineNoCov">          0 :                         encodebits(buf2, 1, 1); /* flag the change in run-length */</span></a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineNoCov">          0 :                         encodebits(buf2, 5, run+is_smaller+1);</span></a>
+<a name="1741"><span class="lineNum">    1741 </span>            :                 } else {</a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineNoCov">          0 :                         encodebits(buf2, 1, 0); /* flag the fact that runlength did not change */</span></a>
+<a name="1743"><span class="lineNum">    1743 </span>            :                 }</a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineNoCov">          0 :                 for (k=0; k &lt; run; k+=3) {</span></a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineNoCov">          0 :                         encodeints(buf2, 3, smallidx, sizesmall, &amp;tmpcoord[k]);     </span></a>
+<a name="1746"><span class="lineNum">    1746 </span>            :                 }</a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineNoCov">          0 :                 if (is_smaller != 0) {</span></a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineNoCov">          0 :                         smallidx += is_smaller;</span></a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineNoCov">          0 :                         if (is_smaller &lt; 0) {</span></a>
+<a name="1750"><span class="lineNum">    1750 </span>            :                                 smallnum = smaller;</a>
+<a name="1751"><span class="lineNum">    1751 </span><span class="lineNoCov">          0 :                                 smaller = magicints[smallidx-1] / 2;</span></a>
+<a name="1752"><span class="lineNum">    1752 </span>            :                         } else {</a>
+<a name="1753"><span class="lineNum">    1753 </span>            :                                 smaller = smallnum;</a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineNoCov">          0 :                                 smallnum = magicints[smallidx] / 2;</span></a>
+<a name="1755"><span class="lineNum">    1755 </span>            :                         }</a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineNoCov">          0 :                         sizesmall[0] = sizesmall[1] = sizesmall[2] = magicints[smallidx];</span></a>
+<a name="1757"><span class="lineNum">    1757 </span>            :                 }   </a>
+<a name="1758"><span class="lineNum">    1758 </span>            :         }</a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineNoCov">          0 :         if (buf2[1] != 0) buf2[0]++;</span></a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineNoCov">          0 :         xdrfile_write_int(buf2,1,xfp); /* buf2[0] holds the length in bytes */</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineNoCov">          0 :         tmp=xdrfile_write_opaque((char *)&amp;(buf2[3]),(unsigned int)buf2[0],xfp);</span></a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineNoCov">          0 :         if(tmp==(unsigned int)buf2[0])</span></a>
+<a name="1763"><span class="lineNum">    1763 </span><span class="lineNoCov">          0 :                 return size;</span></a>
+<a name="1764"><span class="lineNum">    1764 </span>            :         else</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :                 return -1; </a>
+<a name="1766"><span class="lineNum">    1766 </span>            : }</a>
+<a name="1767"><span class="lineNum">    1767 </span>            : </a>
+<a name="1768"><span class="lineNum">    1768 </span>            : </a>
+<a name="1769"><span class="lineNum">    1769 </span>            : /* Dont try do document Fortran interface, since</a>
+<a name="1770"><span class="lineNum">    1770 </span>            :  * Doxygen barfs at the F77_FUNC macro </a>
+<a name="1771"><span class="lineNum">    1771 </span>            :  */</a>
+<a name="1772"><span class="lineNum">    1772 </span>            : #ifndef DOXYGEN </a>
+<a name="1773"><span class="lineNum">    1773 </span>            : </a>
+<a name="1774"><span class="lineNum">    1774 </span>            : /*************************************************************</a>
+<a name="1775"><span class="lineNum">    1775 </span>            :  * Fortran77 interface for reading/writing portable data     *</a>
+<a name="1776"><span class="lineNum">    1776 </span>            :  * The routine are not threadsafe when called from Fortran   *</a>
+<a name="1777"><span class="lineNum">    1777 </span>            :  * (as they are when called from C) unless you compile with  *</a>
+<a name="1778"><span class="lineNum">    1778 </span>            :  * this file with posix thread support.                      *</a>
+<a name="1779"><span class="lineNum">    1779 </span>            :  * Note that these are not multithread-safe.                 * </a>
+<a name="1780"><span class="lineNum">    1780 </span>            :  *************************************************************/</a>
+<a name="1781"><span class="lineNum">    1781 </span>            : #define MAX_FORTRAN_XDR 1024</a>
+<a name="1782"><span class="lineNum">    1782 </span>            : static XDRFILE *f77xdr[MAX_FORTRAN_XDR]; /* array of file handles */</a>
+<a name="1783"><span class="lineNum">    1783 </span>            : static int      f77init = 1;             /* zero array first time */</a>
+<a name="1784"><span class="lineNum">    1784 </span>            : </a>
+<a name="1785"><span class="lineNum">    1785 </span>            : /* internal to this file: C&lt;--&gt;Fortran string conversion */</a>
+<a name="1786"><span class="lineNum">    1786 </span>            : static int ftocstr(char *dest, int dest_len, char *src, int src_len);</a>
+<a name="1787"><span class="lineNum">    1787 </span>            : static int ctofstr(char *dest, int dest_len, char *src);</a>
+<a name="1788"><span class="lineNum">    1788 </span>            : </a>
+<a name="1789"><span class="lineNum">    1789 </span>            : </a>
+<a name="1790"><span class="lineNum">    1790 </span>            : void</a>
+<a name="1791"><span class="lineNum">    1791 </span><span class="lineNoCov">          0 : F77_FUNC(xdropen,XDROPEN)(int *fid, char *filename, char *mode,</span></a>
+<a name="1792"><span class="lineNum">    1792 </span>            :                                                   int fn_len, int mode_len)</a>
+<a name="1793"><span class="lineNum">    1793 </span>            : {</a>
+<a name="1794"><span class="lineNum">    1794 </span>            :         char cfilename[512];</a>
+<a name="1795"><span class="lineNum">    1795 </span>            :         char cmode[5];</a>
+<a name="1796"><span class="lineNum">    1796 </span>            :         int i;</a>
+<a name="1797"><span class="lineNum">    1797 </span>            :   </a>
+<a name="1798"><span class="lineNum">    1798 </span>            :         /* zero array at first invocation */</a>
+<a name="1799"><span class="lineNum">    1799 </span><span class="lineNoCov">          0 :         if(f77init) {</span></a>
+<a name="1800"><span class="lineNum">    1800 </span><span class="lineNoCov">          0 :                 for(i=0;i&lt;MAX_FORTRAN_XDR;i++)</span></a>
+<a name="1801"><span class="lineNum">    1801 </span><span class="lineNoCov">          0 :                         f77xdr[i]=NULL;</span></a>
+<a name="1802"><span class="lineNum">    1802 </span><span class="lineNoCov">          0 :                 f77init=0;</span></a>
+<a name="1803"><span class="lineNum">    1803 </span>            :         }</a>
+<a name="1804"><span class="lineNum">    1804 </span>            :         i=0;</a>
+<a name="1805"><span class="lineNum">    1805 </span>            :   </a>
+<a name="1806"><span class="lineNum">    1806 </span>            :         /* nf77xdr is always smaller or equal to MAX_FORTRAN_XDR */</a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineNoCov">          0 :         while(i&lt;MAX_FORTRAN_XDR &amp;&amp; f77xdr[i]!=NULL)</span></a>
+<a name="1808"><span class="lineNum">    1808 </span><span class="lineNoCov">          0 :                 i++;</span></a>
+<a name="1809"><span class="lineNum">    1809 </span><span class="lineNoCov">          0 :         if(i==MAX_FORTRAN_XDR) {</span></a>
+<a name="1810"><span class="lineNum">    1810 </span><span class="lineNoCov">          0 :                 *fid = -1;</span></a>
+<a name="1811"><span class="lineNum">    1811 </span><span class="lineNoCov">          0 :         } else if (ftocstr(cfilename, sizeof(cfilename), filename, fn_len)) {</span></a>
+<a name="1812"><span class="lineNum">    1812 </span><span class="lineNoCov">          0 :                 *fid = -1;</span></a>
+<a name="1813"><span class="lineNum">    1813 </span><span class="lineNoCov">          0 :         } else if (ftocstr(cmode, sizeof(cmode), mode,mode_len)) {</span></a>
+<a name="1814"><span class="lineNum">    1814 </span><span class="lineNoCov">          0 :                 *fid = -1;</span></a>
+<a name="1815"><span class="lineNum">    1815 </span>            :         } else {</a>
+<a name="1816"><span class="lineNum">    1816 </span><span class="lineNoCov">          0 :                 f77xdr[i]=xdrfile_open(cfilename,cmode);</span></a>
+<a name="1817"><span class="lineNum">    1817 </span>            :                 /* return the index in the array as a fortran file handle */</a>
+<a name="1818"><span class="lineNum">    1818 </span><span class="lineNoCov">          0 :                 *fid=i; </span></a>
+<a name="1819"><span class="lineNum">    1819 </span>            :         }</a>
+<a name="1820"><span class="lineNum">    1820 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1821"><span class="lineNum">    1821 </span>            : </a>
+<a name="1822"><span class="lineNum">    1822 </span>            : void</a>
+<a name="1823"><span class="lineNum">    1823 </span><span class="lineNoCov">          0 : F77_FUNC(xdrclose,XDRCLOSE)(int *fid)</span></a>
+<a name="1824"><span class="lineNum">    1824 </span>            : {</a>
+<a name="1825"><span class="lineNum">    1825 </span>            :     /* first close it */</a>
+<a name="1826"><span class="lineNum">    1826 </span><span class="lineNoCov">          0 :     xdrfile_close(f77xdr[*fid]);</span></a>
+<a name="1827"><span class="lineNum">    1827 </span>            :     /* the remove it from file handle list */</a>
+<a name="1828"><span class="lineNum">    1828 </span><span class="lineNoCov">          0 :     f77xdr[*fid]=NULL;</span></a>
+<a name="1829"><span class="lineNum">    1829 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1830"><span class="lineNum">    1830 </span>            : </a>
+<a name="1831"><span class="lineNum">    1831 </span>            : </a>
+<a name="1832"><span class="lineNum">    1832 </span>            : void</a>
+<a name="1833"><span class="lineNum">    1833 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrint,XDRRINT)(int *fid, int *data, int *ndata, int *ret)</span></a>
+<a name="1834"><span class="lineNum">    1834 </span>            : {</a>
+<a name="1835"><span class="lineNum">    1835 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_int(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1836"><span class="lineNum">    1836 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1837"><span class="lineNum">    1837 </span>            : </a>
+<a name="1838"><span class="lineNum">    1838 </span>            : void</a>
+<a name="1839"><span class="lineNum">    1839 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwint,XDRWINT)(int *fid, int *data, int *ndata, int *ret)</span></a>
+<a name="1840"><span class="lineNum">    1840 </span>            : {</a>
+<a name="1841"><span class="lineNum">    1841 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_int(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1842"><span class="lineNum">    1842 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1843"><span class="lineNum">    1843 </span>            : </a>
+<a name="1844"><span class="lineNum">    1844 </span>            : void</a>
+<a name="1845"><span class="lineNum">    1845 </span><span class="lineNoCov">          0 : F77_FUNC(xdrruint,XDRRUINT)(int *fid, unsigned int *data, int *ndata, int *ret)</span></a>
+<a name="1846"><span class="lineNum">    1846 </span>            : {</a>
+<a name="1847"><span class="lineNum">    1847 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_uint(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1849"><span class="lineNum">    1849 </span>            : </a>
+<a name="1850"><span class="lineNum">    1850 </span>            : void</a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwuint,XDRWUINT)(int *fid, unsigned int *data, int *ndata, int *ret)</span></a>
+<a name="1852"><span class="lineNum">    1852 </span>            : {</a>
+<a name="1853"><span class="lineNum">    1853 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_uint(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1854"><span class="lineNum">    1854 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1855"><span class="lineNum">    1855 </span>            : </a>
+<a name="1856"><span class="lineNum">    1856 </span>            : void</a>
+<a name="1857"><span class="lineNum">    1857 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrchar,XDRRCHAR)(int *fid, char *ip, int *ndata, int *ret)</span></a>
+<a name="1858"><span class="lineNum">    1858 </span>            : {</a>
+<a name="1859"><span class="lineNum">    1859 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_char(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1860"><span class="lineNum">    1860 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1861"><span class="lineNum">    1861 </span>            : </a>
+<a name="1862"><span class="lineNum">    1862 </span>            : void</a>
+<a name="1863"><span class="lineNum">    1863 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwchar,XDRWCHAR)(int *fid, char *ip, int *ndata, int *ret)</span></a>
+<a name="1864"><span class="lineNum">    1864 </span>            : {</a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_char(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1866"><span class="lineNum">    1866 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1867"><span class="lineNum">    1867 </span>            : </a>
+<a name="1868"><span class="lineNum">    1868 </span>            : void</a>
+<a name="1869"><span class="lineNum">    1869 </span><span class="lineNoCov">          0 : F77_FUNC(xdrruchar,XDRRUCHAR)(int *fid, unsigned char *ip, int *ndata, int *ret)</span></a>
+<a name="1870"><span class="lineNum">    1870 </span>            : {</a>
+<a name="1871"><span class="lineNum">    1871 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_uchar(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1872"><span class="lineNum">    1872 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1873"><span class="lineNum">    1873 </span>            : </a>
+<a name="1874"><span class="lineNum">    1874 </span>            : void</a>
+<a name="1875"><span class="lineNum">    1875 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwuchar,XDRWUCHAR)(int *fid, unsigned char *ip, int *ndata, int *ret)</span></a>
+<a name="1876"><span class="lineNum">    1876 </span>            : {</a>
+<a name="1877"><span class="lineNum">    1877 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_uchar(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1878"><span class="lineNum">    1878 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1879"><span class="lineNum">    1879 </span>            : </a>
+<a name="1880"><span class="lineNum">    1880 </span>            : void</a>
+<a name="1881"><span class="lineNum">    1881 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrshort,XDRRSHORT)(int *fid, short *ip, int *ndata, int *ret)</span></a>
+<a name="1882"><span class="lineNum">    1882 </span>            : {</a>
+<a name="1883"><span class="lineNum">    1883 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_short(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1884"><span class="lineNum">    1884 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1885"><span class="lineNum">    1885 </span>            : </a>
+<a name="1886"><span class="lineNum">    1886 </span>            : void</a>
+<a name="1887"><span class="lineNum">    1887 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwshort,XDRWSHORT)(int *fid, short *ip, int *ndata, int *ret)</span></a>
+<a name="1888"><span class="lineNum">    1888 </span>            : {</a>
+<a name="1889"><span class="lineNum">    1889 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_short(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1890"><span class="lineNum">    1890 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1891"><span class="lineNum">    1891 </span>            : </a>
+<a name="1892"><span class="lineNum">    1892 </span>            : void</a>
+<a name="1893"><span class="lineNum">    1893 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrushort,XDRRUSHORT)(int *fid, unsigned short *ip, int *ndata, int *ret)</span></a>
+<a name="1894"><span class="lineNum">    1894 </span>            : {</a>
+<a name="1895"><span class="lineNum">    1895 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_ushort(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1896"><span class="lineNum">    1896 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1897"><span class="lineNum">    1897 </span>            : </a>
+<a name="1898"><span class="lineNum">    1898 </span>            : void</a>
+<a name="1899"><span class="lineNum">    1899 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwushort,XDRWUSHORT)(int *fid, unsigned short *ip, int *ndata, int *ret)</span></a>
+<a name="1900"><span class="lineNum">    1900 </span>            : {</a>
+<a name="1901"><span class="lineNum">    1901 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_ushort(ip,*ndata,f77xdr[*fid]);</span></a>
+<a name="1902"><span class="lineNum">    1902 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1903"><span class="lineNum">    1903 </span>            : </a>
+<a name="1904"><span class="lineNum">    1904 </span>            : void</a>
+<a name="1905"><span class="lineNum">    1905 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrsingle,XDRRSINGLE)(int *fid, float *data, int *ndata, int *ret)</span></a>
+<a name="1906"><span class="lineNum">    1906 </span>            : {</a>
+<a name="1907"><span class="lineNum">    1907 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_float(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1908"><span class="lineNum">    1908 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1909"><span class="lineNum">    1909 </span>            : </a>
+<a name="1910"><span class="lineNum">    1910 </span>            : void</a>
+<a name="1911"><span class="lineNum">    1911 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwsingle,XDRWSINGLE)(int *fid, float *data, int *ndata, int *ret)</span></a>
+<a name="1912"><span class="lineNum">    1912 </span>            : {</a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_float(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1914"><span class="lineNum">    1914 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1915"><span class="lineNum">    1915 </span>            : </a>
+<a name="1916"><span class="lineNum">    1916 </span>            : void</a>
+<a name="1917"><span class="lineNum">    1917 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrdouble,XDRRDOUBLE)(int *fid, double *data, int *ndata, int *ret)</span></a>
+<a name="1918"><span class="lineNum">    1918 </span>            : {</a>
+<a name="1919"><span class="lineNum">    1919 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_double(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1920"><span class="lineNum">    1920 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1921"><span class="lineNum">    1921 </span>            : </a>
+<a name="1922"><span class="lineNum">    1922 </span>            : void</a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwdouble,XDRWDOUBLE)(int *fid, double *data, int *ndata, int *ret)</span></a>
+<a name="1924"><span class="lineNum">    1924 </span>            : {</a>
+<a name="1925"><span class="lineNum">    1925 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_double(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="1926"><span class="lineNum">    1926 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1927"><span class="lineNum">    1927 </span>            : </a>
+<a name="1928"><span class="lineNum">    1928 </span><span class="lineNoCov">          0 : static int ftocstr(char *dest, int destlen, char *src, int srclen)</span></a>
+<a name="1929"><span class="lineNum">    1929 </span>            : {</a>
+<a name="1930"><span class="lineNum">    1930 </span>            :     char *p;</a>
+<a name="1931"><span class="lineNum">    1931 </span>            : </a>
+<a name="1932"><span class="lineNum">    1932 </span><span class="lineNoCov">          0 :     p = src + srclen;</span></a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineNoCov">          0 :     while ( --p &gt;= src &amp;&amp; *p == ' ' );</span></a>
+<a name="1934"><span class="lineNum">    1934 </span><span class="lineNoCov">          0 :     srclen = p - src + 1;</span></a>
+<a name="1935"><span class="lineNum">    1935 </span>            :     destlen--;</a>
+<a name="1936"><span class="lineNum">    1936 </span><span class="lineNoCov">          0 :     dest[0] = 0;</span></a>
+<a name="1937"><span class="lineNum">    1937 </span><span class="lineNoCov">          0 :     if (srclen &gt; destlen)</span></a>
+<a name="1938"><span class="lineNum">    1938 </span>            :                 return 1;</a>
+<a name="1939"><span class="lineNum">    1939 </span><span class="lineNoCov">          0 :     while (srclen--)</span></a>
+<a name="1940"><span class="lineNum">    1940 </span><span class="lineNoCov">          0 :                 (*dest++ = *src++);</span></a>
+<a name="1941"><span class="lineNum">    1941 </span><span class="lineNoCov">          0 :     *dest = '\0';</span></a>
+<a name="1942"><span class="lineNum">    1942 </span><span class="lineNoCov">          0 :     return 0;</span></a>
+<a name="1943"><span class="lineNum">    1943 </span>            : }</a>
+<a name="1944"><span class="lineNum">    1944 </span>            : </a>
+<a name="1945"><span class="lineNum">    1945 </span>            : </a>
+<a name="1946"><span class="lineNum">    1946 </span><span class="lineNoCov">          0 : static int ctofstr(char *dest, int destlen, char *src)</span></a>
+<a name="1947"><span class="lineNum">    1947 </span>            : {</a>
+<a name="1948"><span class="lineNum">    1948 </span><span class="lineNoCov">          0 :     while (destlen &amp;&amp; *src) {</span></a>
+<a name="1949"><span class="lineNum">    1949 </span><span class="lineNoCov">          0 :         *dest++ = *src++;</span></a>
+<a name="1950"><span class="lineNum">    1950 </span><span class="lineNoCov">          0 :         destlen--;</span></a>
+<a name="1951"><span class="lineNum">    1951 </span>            :     }</a>
+<a name="1952"><span class="lineNum">    1952 </span><span class="lineNoCov">          0 :     while (destlen--)</span></a>
+<a name="1953"><span class="lineNum">    1953 </span><span class="lineNoCov">          0 :         *dest++ = ' ';</span></a>
+<a name="1954"><span class="lineNum">    1954 </span><span class="lineNoCov">          0 :     return 0;</span></a>
+<a name="1955"><span class="lineNum">    1955 </span>            : }</a>
+<a name="1956"><span class="lineNum">    1956 </span>            : </a>
+<a name="1957"><span class="lineNum">    1957 </span>            : </a>
+<a name="1958"><span class="lineNum">    1958 </span>            : void</a>
+<a name="1959"><span class="lineNum">    1959 </span><span class="lineNoCov">          0 : F77_FUNC(xdrrstring,XDRRSTRING)(int *fid, char *str, int *ret, int len)</span></a>
+<a name="1960"><span class="lineNum">    1960 </span>            : {</a>
+<a name="1961"><span class="lineNum">    1961 </span>            :         char *cstr;</a>
+<a name="1962"><span class="lineNum">    1962 </span>            :   </a>
+<a name="1963"><span class="lineNum">    1963 </span><span class="lineNoCov">          0 :         if((cstr=(char*)malloc((len+1)*sizeof(char)))==NULL) {</span></a>
+<a name="1964"><span class="lineNum">    1964 </span><span class="lineNoCov">          0 :                 *ret = 0;</span></a>
+<a name="1965"><span class="lineNum">    1965 </span><span class="lineNoCov">          0 :                 return;</span></a>
+<a name="1966"><span class="lineNum">    1966 </span>            :         }</a>
+<a name="1967"><span class="lineNum">    1967 </span><span class="lineNoCov">          0 :         if (ftocstr(cstr, len+1, str, len)) {</span></a>
+<a name="1968"><span class="lineNum">    1968 </span><span class="lineNoCov">          0 :                 *ret = 0;</span></a>
+<a name="1969"><span class="lineNum">    1969 </span><span class="lineNoCov">          0 :                 free(cstr);</span></a>
+<a name="1970"><span class="lineNum">    1970 </span><span class="lineNoCov">          0 :                 return;</span></a>
+<a name="1971"><span class="lineNum">    1971 </span>            :         }</a>
+<a name="1972"><span class="lineNum">    1972 </span>            :   </a>
+<a name="1973"><span class="lineNum">    1973 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_string(cstr, len+1,f77xdr[*fid]);</span></a>
+<a name="1974"><span class="lineNum">    1974 </span><span class="lineNoCov">          0 :         ctofstr( str, len , cstr);</span></a>
+<a name="1975"><span class="lineNum">    1975 </span><span class="lineNoCov">          0 :         free(cstr);</span></a>
+<a name="1976"><span class="lineNum">    1976 </span>            : }</a>
+<a name="1977"><span class="lineNum">    1977 </span>            : </a>
+<a name="1978"><span class="lineNum">    1978 </span>            : void</a>
+<a name="1979"><span class="lineNum">    1979 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwstring,XDRWSTRING)(int *fid, char *str, int *ret, int len)</span></a>
+<a name="1980"><span class="lineNum">    1980 </span>            : {</a>
+<a name="1981"><span class="lineNum">    1981 </span>            :         char *cstr;</a>
+<a name="1982"><span class="lineNum">    1982 </span>            :   </a>
+<a name="1983"><span class="lineNum">    1983 </span><span class="lineNoCov">          0 :         if((cstr=(char*)malloc((len+1)*sizeof(char)))==NULL) {</span></a>
+<a name="1984"><span class="lineNum">    1984 </span><span class="lineNoCov">          0 :                 *ret = 0;</span></a>
+<a name="1985"><span class="lineNum">    1985 </span><span class="lineNoCov">          0 :                 return;</span></a>
+<a name="1986"><span class="lineNum">    1986 </span>            :         }</a>
+<a name="1987"><span class="lineNum">    1987 </span><span class="lineNoCov">          0 :         if (ftocstr(cstr, len+1, str, len)) {</span></a>
+<a name="1988"><span class="lineNum">    1988 </span><span class="lineNoCov">          0 :                 *ret = 0;</span></a>
+<a name="1989"><span class="lineNum">    1989 </span><span class="lineNoCov">          0 :                 free(cstr);</span></a>
+<a name="1990"><span class="lineNum">    1990 </span><span class="lineNoCov">          0 :                 return;</span></a>
+<a name="1991"><span class="lineNum">    1991 </span>            :         }</a>
+<a name="1992"><span class="lineNum">    1992 </span>            :   </a>
+<a name="1993"><span class="lineNum">    1993 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_string(cstr, f77xdr[*fid]);</span></a>
+<a name="1994"><span class="lineNum">    1994 </span><span class="lineNoCov">          0 :         ctofstr( str, len , cstr);</span></a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineNoCov">          0 :         free(cstr);</span></a>
+<a name="1996"><span class="lineNum">    1996 </span>            : }</a>
+<a name="1997"><span class="lineNum">    1997 </span>            : </a>
+<a name="1998"><span class="lineNum">    1998 </span>            : void</a>
+<a name="1999"><span class="lineNum">    1999 </span><span class="lineNoCov">          0 : F77_FUNC(xdrropaque,XDRROPAQUE)(int *fid, char *data, int *ndata, int *ret)</span></a>
+<a name="2000"><span class="lineNum">    2000 </span>            : {</a>
+<a name="2001"><span class="lineNum">    2001 </span><span class="lineNoCov">          0 :         *ret = xdrfile_read_opaque(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="2002"><span class="lineNum">    2002 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="2003"><span class="lineNum">    2003 </span>            : </a>
+<a name="2004"><span class="lineNum">    2004 </span>            : void</a>
+<a name="2005"><span class="lineNum">    2005 </span><span class="lineNoCov">          0 : F77_FUNC(xdrwopaque,XDRWOPAQUE)(int *fid, char *data, int *ndata, int *ret)</span></a>
+<a name="2006"><span class="lineNum">    2006 </span>            : {</a>
+<a name="2007"><span class="lineNum">    2007 </span><span class="lineNoCov">          0 :         *ret = xdrfile_write_opaque(data,*ndata,f77xdr[*fid]);</span></a>
+<a name="2008"><span class="lineNum">    2008 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="2009"><span class="lineNum">    2009 </span>            : </a>
+<a name="2010"><span class="lineNum">    2010 </span>            : </a>
+<a name="2011"><span class="lineNum">    2011 </span>            : /* Write single-precision compressed 3d coordinates */</a>
+<a name="2012"><span class="lineNum">    2012 </span>            : void</a>
+<a name="2013"><span class="lineNum">    2013 </span><span class="lineNoCov">          0 : F77_FUNC(xdrccs,XDRCCS)(int *fid, float *data, int *ncoord, </span></a>
+<a name="2014"><span class="lineNum">    2014 </span>            :                                                 float *precision, int *ret)</a>
+<a name="2015"><span class="lineNum">    2015 </span>            : {</a>
+<a name="2016"><span class="lineNum">    2016 </span><span class="lineNoCov">          0 :     *ret = xdrfile_compress_coord_float(data,*ncoord,*precision,f77xdr[*fid]);</span></a>
+<a name="2017"><span class="lineNum">    2017 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="2018"><span class="lineNum">    2018 </span>            : </a>
+<a name="2019"><span class="lineNum">    2019 </span>            : </a>
+<a name="2020"><span class="lineNum">    2020 </span>            : /* Read single-precision compressed 3d coordinates */</a>
+<a name="2021"><span class="lineNum">    2021 </span>            : void</a>
+<a name="2022"><span class="lineNum">    2022 </span><span class="lineNoCov">          0 : F77_FUNC(xdrdcs,XDRDCS)(int *fid, float *data, int *ncoord, </span></a>
+<a name="2023"><span class="lineNum">    2023 </span>            :                                                 float *precision, int *ret)</a>
+<a name="2024"><span class="lineNum">    2024 </span>            : {</a>
+<a name="2025"><span class="lineNum">    2025 </span><span class="lineNoCov">          0 :         *ret = xdrfile_decompress_coord_float(data,ncoord,precision,f77xdr[*fid]);</span></a>
+<a name="2026"><span class="lineNum">    2026 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="2027"><span class="lineNum">    2027 </span>            : </a>
+<a name="2028"><span class="lineNum">    2028 </span>            : </a>
+<a name="2029"><span class="lineNum">    2029 </span>            : /* Write compressed 3d coordinates from double precision data */</a>
+<a name="2030"><span class="lineNum">    2030 </span>            : void</a>
+<a name="2031"><span class="lineNum">    2031 </span><span class="lineNoCov">          0 : F77_FUNC(xdrccd,XDRCCD)(int *fid, double *data, int *ncoord, </span></a>
+<a name="2032"><span class="lineNum">    2032 </span>            :                                                 double *precision, int *ret)</a>
+<a name="2033"><span class="lineNum">    2033 </span>            : {</a>
+<a name="2034"><span class="lineNum">    2034 </span><span class="lineNoCov">          0 :         *ret = xdrfile_compress_coord_double(data,*ncoord,*precision,f77xdr[*fid]);</span></a>
+<a name="2035"><span class="lineNum">    2035 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="2036"><span class="lineNum">    2036 </span>            : </a>
+<a name="2037"><span class="lineNum">    2037 </span>            : /* Read compressed 3d coordinates into double precision data */</a>
+<a name="2038"><span class="lineNum">    2038 </span>            : void</a>
+<a name="2039"><span class="lineNum">    2039 </span><span class="lineNoCov">          0 : F77_FUNC(xddcd,XDRDCD)(int *fid, double *data, int *ncoord, </span></a>
+<a name="2040"><span class="lineNum">    2040 </span>            :                                            double *precision, int *ret)</a>
+<a name="2041"><span class="lineNum">    2041 </span>            : {</a>
+<a name="2042"><span class="lineNum">    2042 </span><span class="lineNoCov">          0 :     *ret = xdrfile_decompress_coord_double(data,ncoord,precision,f77xdr[*fid]);</span></a>
+<a name="2043"><span class="lineNum">    2043 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="2044"><span class="lineNum">    2044 </span>            : </a>
+<a name="2045"><span class="lineNum">    2045 </span>            : </a>
+<a name="2046"><span class="lineNum">    2046 </span>            : </a>
+<a name="2047"><span class="lineNum">    2047 </span>            : </a>
+<a name="2048"><span class="lineNum">    2048 </span>            : </a>
+<a name="2049"><span class="lineNum">    2049 </span>            : </a>
+<a name="2050"><span class="lineNum">    2050 </span>            : </a>
+<a name="2051"><span class="lineNum">    2051 </span>            : #endif /* DOXYGEN */</a>
+<a name="2052"><span class="lineNum">    2052 </span>            : </a>
+<a name="2053"><span class="lineNum">    2053 </span>            : /*************************************************************</a>
+<a name="2054"><span class="lineNum">    2054 </span>            :  * End of higher-level routines - dont change things below!  *</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :  *************************************************************/</a>
+<a name="2056"><span class="lineNum">    2056 </span>            : </a>
+<a name="2057"><span class="lineNum">    2057 </span>            : </a>
+<a name="2058"><span class="lineNum">    2058 </span>            : </a>
+<a name="2059"><span class="lineNum">    2059 </span>            : </a>
+<a name="2060"><span class="lineNum">    2060 </span>            : </a>
+<a name="2061"><span class="lineNum">    2061 </span>            : </a>
+<a name="2062"><span class="lineNum">    2062 </span>            : </a>
+<a name="2063"><span class="lineNum">    2063 </span>            : </a>
+<a name="2064"><span class="lineNum">    2064 </span>            : </a>
+<a name="2065"><span class="lineNum">    2065 </span>            : </a>
+<a name="2066"><span class="lineNum">    2066 </span>            : </a>
+<a name="2067"><span class="lineNum">    2067 </span>            : </a>
+<a name="2068"><span class="lineNum">    2068 </span>            : </a>
+<a name="2069"><span class="lineNum">    2069 </span>            : </a>
+<a name="2070"><span class="lineNum">    2070 </span>            : </a>
+<a name="2071"><span class="lineNum">    2071 </span>            : </a>
+<a name="2072"><span class="lineNum">    2072 </span>            : </a>
+<a name="2073"><span class="lineNum">    2073 </span>            : </a>
+<a name="2074"><span class="lineNum">    2074 </span>            : </a>
+<a name="2075"><span class="lineNum">    2075 </span>            : </a>
+<a name="2076"><span class="lineNum">    2076 </span>            : /*************************************************************</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :  * The rest of this file contains our own implementation     *</a>
+<a name="2078"><span class="lineNum">    2078 </span>            :  * of the XDR calls in case you are compiling without them.  *</a>
+<a name="2079"><span class="lineNum">    2079 </span>            :  * You do NOT want to change things here since it would make *</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :  * things incompatible with the standard RPC/XDR routines.   *</a>
+<a name="2081"><span class="lineNum">    2081 </span>            :  *************************************************************/</a>
+<a name="2082"><span class="lineNum">    2082 </span>            : #ifndef HAVE_RPC_XDR_H</a>
+<a name="2083"><span class="lineNum">    2083 </span>            : </a>
+<a name="2084"><span class="lineNum">    2084 </span>            : /*</a>
+<a name="2085"><span class="lineNum">    2085 </span>            :  * What follows is a modified version of the Sun XDR code. For reference</a>
+<a name="2086"><span class="lineNum">    2086 </span>            :  * we include their copyright and license:</a>
+<a name="2087"><span class="lineNum">    2087 </span>            :  * </a>
+<a name="2088"><span class="lineNum">    2088 </span>            :  * Sun RPC is a product of Sun Microsystems, Inc. and is provided for</a>
+<a name="2089"><span class="lineNum">    2089 </span>            :  * unrestricted use provided that this legend is included on all tape</a>
+<a name="2090"><span class="lineNum">    2090 </span>            :  * media and as a part of the software program in whole or part.  Users</a>
+<a name="2091"><span class="lineNum">    2091 </span>            :  * may copy or modify Sun RPC without charge, but are not authorized</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :  * to license or distribute it to anyone else except as part of a product or</a>
+<a name="2093"><span class="lineNum">    2093 </span>            :  * program developed by the user.</a>
+<a name="2094"><span class="lineNum">    2094 </span>            :  *</a>
+<a name="2095"><span class="lineNum">    2095 </span>            :  * SUN RPC IS PROVIDED AS IS WITH NO WARRANTIES OF ANY KIND INCLUDING THE</a>
+<a name="2096"><span class="lineNum">    2096 </span>            :  * WARRANTIES OF DESIGN, MERCHANTIBILITY AND FITNESS FOR A PARTICULAR</a>
+<a name="2097"><span class="lineNum">    2097 </span>            :  * PURPOSE, OR ARISING FROM A COURSE OF DEALING, USAGE OR TRADE PRACTICE.</a>
+<a name="2098"><span class="lineNum">    2098 </span>            :  *</a>
+<a name="2099"><span class="lineNum">    2099 </span>            :  * Sun RPC is provided with no support and without any obligation on the</a>
+<a name="2100"><span class="lineNum">    2100 </span>            :  * part of Sun Microsystems, Inc. to assist in its use, correction,</a>
+<a name="2101"><span class="lineNum">    2101 </span>            :  * modification or enhancement.</a>
+<a name="2102"><span class="lineNum">    2102 </span>            :  *</a>
+<a name="2103"><span class="lineNum">    2103 </span>            :  * SUN MICROSYSTEMS, INC. SHALL HAVE NO LIABILITY WITH RESPECT TO THE</a>
+<a name="2104"><span class="lineNum">    2104 </span>            :  * INFRINGEMENT OF COPYRIGHTS, TRADE SECRETS OR ANY PATENTS BY SUN RPC</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :  * OR ANY PART THEREOF.</a>
+<a name="2106"><span class="lineNum">    2106 </span>            :  *</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :  * In no event will Sun Microsystems, Inc. be liable for any lost revenue</a>
+<a name="2108"><span class="lineNum">    2108 </span>            :  * or profits or other special, indirect and consequential damages, even if</a>
+<a name="2109"><span class="lineNum">    2109 </span>            :  * Sun has been advised of the possibility of such damages.</a>
+<a name="2110"><span class="lineNum">    2110 </span>            :  *</a>
+<a name="2111"><span class="lineNum">    2111 </span>            :  * Sun Microsystems, Inc.</a>
+<a name="2112"><span class="lineNum">    2112 </span>            :  * 2550 Garcia Avenue</a>
+<a name="2113"><span class="lineNum">    2113 </span>            :  * Mountain View, California  94043</a>
+<a name="2114"><span class="lineNum">    2114 </span>            :  */</a>
+<a name="2115"><span class="lineNum">    2115 </span>            : </a>
+<a name="2116"><span class="lineNum">    2116 </span>            : /* INT_MAX is defined in limits.h according to ANSI C */</a>
+<a name="2117"><span class="lineNum">    2117 </span>            : #if (INT_MAX &gt; 2147483647)</a>
+<a name="2118"><span class="lineNum">    2118 </span>            : #    error Error: Cannot use builtin XDR support when size of int</a>
+<a name="2119"><span class="lineNum">    2119 </span>            : #    error is larger than 4 bytes. Use your system XDR libraries </a>
+<a name="2120"><span class="lineNum">    2120 </span>            : #    error instead, or modify the source code in xdrfile.c</a>
+<a name="2121"><span class="lineNum">    2121 </span>            : #endif /* Check for 4 byte int type */</a>
+<a name="2122"><span class="lineNum">    2122 </span>            : </a>
+<a name="2123"><span class="lineNum">    2123 </span>            : </a>
+<a name="2124"><span class="lineNum">    2124 </span>            : </a>
+<a name="2125"><span class="lineNum">    2125 </span>            : </a>
+<a name="2126"><span class="lineNum">    2126 </span>            : </a>
+<a name="2127"><span class="lineNum">    2127 </span>            : typedef int (*xdrproc_t) (XDR *, void *,...);</a>
+<a name="2128"><span class="lineNum">    2128 </span>            : </a>
+<a name="2129"><span class="lineNum">    2129 </span>            : #define xdr_getlong(xdrs, longp)                        \</a>
+<a name="2130"><span class="lineNum">    2130 </span>            :         (*(xdrs)-&gt;x_ops-&gt;x_getlong)(xdrs, longp)</a>
+<a name="2131"><span class="lineNum">    2131 </span>            : #define xdr_putlong(xdrs, longp)                        \</a>
+<a name="2132"><span class="lineNum">    2132 </span>            :         (*(xdrs)-&gt;x_ops-&gt;x_putlong)(xdrs, longp)</a>
+<a name="2133"><span class="lineNum">    2133 </span>            : #define xdr_getbytes(xdrs, addr, len)                   \</a>
+<a name="2134"><span class="lineNum">    2134 </span>            :         (*(xdrs)-&gt;x_ops-&gt;x_getbytes)(xdrs, addr, len)</a>
+<a name="2135"><span class="lineNum">    2135 </span>            : #define xdr_putbytes(xdrs, addr, len)                   \</a>
+<a name="2136"><span class="lineNum">    2136 </span>            :         (*(xdrs)-&gt;x_ops-&gt;x_putbytes)(xdrs, addr, len)</a>
+<a name="2137"><span class="lineNum">    2137 </span>            : </a>
+<a name="2138"><span class="lineNum">    2138 </span>            : #define BYTES_PER_XDR_UNIT 4 </a>
+<a name="2139"><span class="lineNum">    2139 </span>            : static char xdr_zero[BYTES_PER_XDR_UNIT] = {0, 0, 0, 0};</a>
+<a name="2140"><span class="lineNum">    2140 </span>            : </a>
+<a name="2141"><span class="lineNum">    2141 </span>            : static int32_t</a>
+<a name="2142"><span class="lineNum">    2142 </span><span class="lineCov">      14026 : xdr_swapbytes(int32_t x)</span></a>
+<a name="2143"><span class="lineNum">    2143 </span>            : {</a>
+<a name="2144"><span class="lineNum">    2144 </span>            :         int32_t y,i;</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :         char *px=(char *)&amp;x;</a>
+<a name="2146"><span class="lineNum">    2146 </span>            :         char *py=(char *)&amp;y;</a>
+<a name="2147"><span class="lineNum">    2147 </span>            :   </a>
+<a name="2148"><span class="lineNum">    2148 </span><span class="lineCov">      70130 :         for(i=0;i&lt;4;i++)</span></a>
+<a name="2149"><span class="lineNum">    2149 </span><span class="lineCov">      56104 :                 py[i]=px[3-i];</span></a>
+<a name="2150"><span class="lineNum">    2150 </span>            :   </a>
+<a name="2151"><span class="lineNum">    2151 </span><span class="lineCov">      14026 :         return y;</span></a>
+<a name="2152"><span class="lineNum">    2152 </span>            : }</a>
+<a name="2153"><span class="lineNum">    2153 </span>            : </a>
+<a name="2154"><span class="lineNum">    2154 </span>            : static int32_t</a>
+<a name="2155"><span class="lineNum">    2155 </span><span class="lineCov">       9972 : xdr_htonl(int32_t x)</span></a>
+<a name="2156"><span class="lineNum">    2156 </span>            : {</a>
+<a name="2157"><span class="lineNum">    2157 </span>            :         int s=0x1234;</a>
+<a name="2158"><span class="lineNum">    2158 </span>            :         if( *((char *)&amp;s)==(char)0x34) {</a>
+<a name="2159"><span class="lineNum">    2159 </span>            :                 /* smallendian,swap bytes */</a>
+<a name="2160"><span class="lineNum">    2160 </span><span class="lineCov">       9972 :                 return xdr_swapbytes(x);</span></a>
+<a name="2161"><span class="lineNum">    2161 </span>            :         } else {</a>
+<a name="2162"><span class="lineNum">    2162 </span>            :                 /* bigendian, do nothing */</a>
+<a name="2163"><span class="lineNum">    2163 </span>            :                 return x;</a>
+<a name="2164"><span class="lineNum">    2164 </span>            :         }</a>
+<a name="2165"><span class="lineNum">    2165 </span>            : }</a>
+<a name="2166"><span class="lineNum">    2166 </span>            : </a>
+<a name="2167"><span class="lineNum">    2167 </span>            : static int32_t</a>
+<a name="2168"><span class="lineNum">    2168 </span><span class="lineCov">       4054 : xdr_ntohl(int x)</span></a>
+<a name="2169"><span class="lineNum">    2169 </span>            : {</a>
+<a name="2170"><span class="lineNum">    2170 </span>            :         int s=0x1234;</a>
+<a name="2171"><span class="lineNum">    2171 </span>            :         if( *((char *)&amp;s)==(char)0x34) {</a>
+<a name="2172"><span class="lineNum">    2172 </span>            :                 /* smallendian, swap bytes */</a>
+<a name="2173"><span class="lineNum">    2173 </span><span class="lineCov">       4054 :                 return xdr_swapbytes(x);</span></a>
+<a name="2174"><span class="lineNum">    2174 </span>            :         } else {</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :                 /* bigendian, do nothing */</a>
+<a name="2176"><span class="lineNum">    2176 </span>            :                 return x;</a>
+<a name="2177"><span class="lineNum">    2177 </span>            :         }</a>
+<a name="2178"><span class="lineNum">    2178 </span>            : }</a>
+<a name="2179"><span class="lineNum">    2179 </span>            : </a>
+<a name="2180"><span class="lineNum">    2180 </span>            : static int</a>
+<a name="2181"><span class="lineNum">    2181 </span><span class="lineCov">       2420 : xdr_int (XDR *xdrs, int *ip)</span></a>
+<a name="2182"><span class="lineNum">    2182 </span>            : {</a>
+<a name="2183"><span class="lineNum">    2183 </span>            :         int32_t i32;</a>
+<a name="2184"><span class="lineNum">    2184 </span>            : </a>
+<a name="2185"><span class="lineNum">    2185 </span><span class="lineCov">       2420 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2186"><span class="lineNum">    2186 </span>            :                 {</a>
+<a name="2187"><span class="lineNum">    2187 </span><span class="lineCov">       1488 :                 case XDR_ENCODE:</span></a>
+<a name="2188"><span class="lineNum">    2188 </span><span class="lineCov">       1488 :                         i32 = (int32_t) *ip;</span></a>
+<a name="2189"><span class="lineNum">    2189 </span><span class="lineCov">       1488 :                         return xdr_putlong (xdrs, &amp;i32);</span></a>
+<a name="2190"><span class="lineNum">    2190 </span>            : </a>
+<a name="2191"><span class="lineNum">    2191 </span><span class="lineCov">        932 :                 case XDR_DECODE:</span></a>
+<a name="2192"><span class="lineNum">    2192 </span><span class="lineCov">        932 :                         if (!xdr_getlong (xdrs, &amp;i32))</span></a>
+<a name="2193"><span class="lineNum">    2193 </span>            :                                 {</a>
+<a name="2194"><span class="lineNum">    2194 </span>            :                                         return 0;</a>
+<a name="2195"><span class="lineNum">    2195 </span>            :                                 }</a>
+<a name="2196"><span class="lineNum">    2196 </span><span class="lineCov">        927 :                         *ip = (int) i32;</span></a>
+<a name="2197"><span class="lineNum">    2197 </span>            :                 case XDR_FREE:</a>
+<a name="2198"><span class="lineNum">    2198 </span>            :                         return 1;</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :                 }</a>
+<a name="2200"><span class="lineNum">    2200 </span>            :         return 0;</a>
+<a name="2201"><span class="lineNum">    2201 </span>            : }</a>
+<a name="2202"><span class="lineNum">    2202 </span>            : </a>
+<a name="2203"><span class="lineNum">    2203 </span>            : static int</a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineCov">         87 : xdr_u_int (XDR *xdrs, unsigned int *up)</span></a>
+<a name="2205"><span class="lineNum">    2205 </span>            : {</a>
+<a name="2206"><span class="lineNum">    2206 </span>            :         uint32_t ui32;</a>
+<a name="2207"><span class="lineNum">    2207 </span>            : </a>
+<a name="2208"><span class="lineNum">    2208 </span><span class="lineCov">         87 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2209"><span class="lineNum">    2209 </span>            :                 {</a>
+<a name="2210"><span class="lineNum">    2210 </span><span class="lineCov">         48 :                 case XDR_ENCODE:</span></a>
+<a name="2211"><span class="lineNum">    2211 </span><span class="lineCov">         48 :                         ui32 = (uint32_t) * up;</span></a>
+<a name="2212"><span class="lineNum">    2212 </span><span class="lineCov">         48 :                         return xdr_putlong (xdrs, (int32_t *)&amp;ui32);</span></a>
+<a name="2213"><span class="lineNum">    2213 </span>            : </a>
+<a name="2214"><span class="lineNum">    2214 </span><span class="lineCov">         39 :                 case XDR_DECODE:</span></a>
+<a name="2215"><span class="lineNum">    2215 </span><span class="lineCov">         39 :                         if (!xdr_getlong (xdrs, (int32_t *)&amp;ui32))</span></a>
+<a name="2216"><span class="lineNum">    2216 </span>            :                                 {</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :                                         return 0;</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :                                 }</a>
+<a name="2219"><span class="lineNum">    2219 </span><span class="lineCov">         39 :                         *up = (uint32_t) ui32;</span></a>
+<a name="2220"><span class="lineNum">    2220 </span>            :                 case XDR_FREE:</a>
+<a name="2221"><span class="lineNum">    2221 </span>            :                         return 1;</a>
+<a name="2222"><span class="lineNum">    2222 </span>            :                 }</a>
+<a name="2223"><span class="lineNum">    2223 </span>            :         return 0;</a>
+<a name="2224"><span class="lineNum">    2224 </span>            : }</a>
+<a name="2225"><span class="lineNum">    2225 </span>            : </a>
+<a name="2226"><span class="lineNum">    2226 </span>            : static int</a>
+<a name="2227"><span class="lineNum">    2227 </span><span class="lineNoCov">          0 : xdr_short (XDR *xdrs, short *sp)</span></a>
+<a name="2228"><span class="lineNum">    2228 </span>            : {</a>
+<a name="2229"><span class="lineNum">    2229 </span>            :         int32_t i32;</a>
+<a name="2230"><span class="lineNum">    2230 </span>            : </a>
+<a name="2231"><span class="lineNum">    2231 </span><span class="lineNoCov">          0 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2232"><span class="lineNum">    2232 </span>            :                 {</a>
+<a name="2233"><span class="lineNum">    2233 </span><span class="lineNoCov">          0 :                 case XDR_ENCODE:</span></a>
+<a name="2234"><span class="lineNum">    2234 </span><span class="lineNoCov">          0 :                         i32 = (int32_t) *sp;</span></a>
+<a name="2235"><span class="lineNum">    2235 </span><span class="lineNoCov">          0 :                         return xdr_putlong (xdrs, &amp;i32);</span></a>
+<a name="2236"><span class="lineNum">    2236 </span>            : </a>
+<a name="2237"><span class="lineNum">    2237 </span><span class="lineNoCov">          0 :                 case XDR_DECODE:</span></a>
+<a name="2238"><span class="lineNum">    2238 </span><span class="lineNoCov">          0 :                         if (!xdr_getlong (xdrs, &amp;i32))</span></a>
+<a name="2239"><span class="lineNum">    2239 </span>            :                                 {</a>
+<a name="2240"><span class="lineNum">    2240 </span>            :                                         return 0;</a>
+<a name="2241"><span class="lineNum">    2241 </span>            :                                 }</a>
+<a name="2242"><span class="lineNum">    2242 </span><span class="lineNoCov">          0 :                         *sp = (short) i32;</span></a>
+<a name="2243"><span class="lineNum">    2243 </span><span class="lineNoCov">          0 :                         return 1;</span></a>
+<a name="2244"><span class="lineNum">    2244 </span>            : </a>
+<a name="2245"><span class="lineNum">    2245 </span>            :                 case XDR_FREE:</a>
+<a name="2246"><span class="lineNum">    2246 </span>            :                         return 1;</a>
+<a name="2247"><span class="lineNum">    2247 </span>            :                 }</a>
+<a name="2248"><span class="lineNum">    2248 </span><span class="lineNoCov">          0 :         return 0;</span></a>
+<a name="2249"><span class="lineNum">    2249 </span>            : }</a>
+<a name="2250"><span class="lineNum">    2250 </span>            : </a>
+<a name="2251"><span class="lineNum">    2251 </span>            : static int</a>
+<a name="2252"><span class="lineNum">    2252 </span><span class="lineNoCov">          0 : xdr_u_short (XDR *xdrs, unsigned short *sp)</span></a>
+<a name="2253"><span class="lineNum">    2253 </span>            : {</a>
+<a name="2254"><span class="lineNum">    2254 </span>            :         uint32_t ui32;</a>
+<a name="2255"><span class="lineNum">    2255 </span>            : </a>
+<a name="2256"><span class="lineNum">    2256 </span><span class="lineNoCov">          0 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2257"><span class="lineNum">    2257 </span>            :                 {</a>
+<a name="2258"><span class="lineNum">    2258 </span><span class="lineNoCov">          0 :                 case XDR_ENCODE:</span></a>
+<a name="2259"><span class="lineNum">    2259 </span><span class="lineNoCov">          0 :                         ui32 = (uint32_t) *sp;</span></a>
+<a name="2260"><span class="lineNum">    2260 </span><span class="lineNoCov">          0 :                         return xdr_putlong (xdrs, (int32_t *)&amp;ui32);</span></a>
+<a name="2261"><span class="lineNum">    2261 </span>            : </a>
+<a name="2262"><span class="lineNum">    2262 </span><span class="lineNoCov">          0 :                 case XDR_DECODE:</span></a>
+<a name="2263"><span class="lineNum">    2263 </span><span class="lineNoCov">          0 :                         if (!xdr_getlong (xdrs, (int32_t *)&amp;ui32))</span></a>
+<a name="2264"><span class="lineNum">    2264 </span>            :                                 {</a>
+<a name="2265"><span class="lineNum">    2265 </span>            :                                         return 0;</a>
+<a name="2266"><span class="lineNum">    2266 </span>            :                                 }</a>
+<a name="2267"><span class="lineNum">    2267 </span><span class="lineNoCov">          0 :                         *sp = (unsigned short) ui32;</span></a>
+<a name="2268"><span class="lineNum">    2268 </span><span class="lineNoCov">          0 :                         return 1;</span></a>
+<a name="2269"><span class="lineNum">    2269 </span>            : </a>
+<a name="2270"><span class="lineNum">    2270 </span>            :                 case XDR_FREE:</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :                         return 1;</a>
+<a name="2272"><span class="lineNum">    2272 </span>            :                 }</a>
+<a name="2273"><span class="lineNum">    2273 </span><span class="lineNoCov">          0 :         return 0;</span></a>
+<a name="2274"><span class="lineNum">    2274 </span>            : }</a>
+<a name="2275"><span class="lineNum">    2275 </span>            : </a>
+<a name="2276"><span class="lineNum">    2276 </span>            : static int</a>
+<a name="2277"><span class="lineNum">    2277 </span><span class="lineNoCov">          0 : xdr_char (XDR *xdrs, char *cp)</span></a>
+<a name="2278"><span class="lineNum">    2278 </span>            : {</a>
+<a name="2279"><span class="lineNum">    2279 </span>            :         int i;</a>
+<a name="2280"><span class="lineNum">    2280 </span>            : </a>
+<a name="2281"><span class="lineNum">    2281 </span><span class="lineNoCov">          0 :         i = (*cp);</span></a>
+<a name="2282"><span class="lineNum">    2282 </span><span class="lineNoCov">          0 :         if (!xdr_int (xdrs, &amp;i))</span></a>
+<a name="2283"><span class="lineNum">    2283 </span>            :                 {</a>
+<a name="2284"><span class="lineNum">    2284 </span>            :                         return 0;</a>
+<a name="2285"><span class="lineNum">    2285 </span>            :                 }</a>
+<a name="2286"><span class="lineNum">    2286 </span><span class="lineNoCov">          0 :         *cp = i;</span></a>
+<a name="2287"><span class="lineNum">    2287 </span><span class="lineNoCov">          0 :         return 1;</span></a>
+<a name="2288"><span class="lineNum">    2288 </span>            : }</a>
+<a name="2289"><span class="lineNum">    2289 </span>            : </a>
+<a name="2290"><span class="lineNum">    2290 </span>            : static int</a>
+<a name="2291"><span class="lineNum">    2291 </span><span class="lineNoCov">          0 : xdr_u_char (XDR *xdrs, unsigned char *cp)</span></a>
+<a name="2292"><span class="lineNum">    2292 </span>            : {</a>
+<a name="2293"><span class="lineNum">    2293 </span>            :         unsigned int u;</a>
+<a name="2294"><span class="lineNum">    2294 </span>            : </a>
+<a name="2295"><span class="lineNum">    2295 </span><span class="lineNoCov">          0 :         u = (*cp);</span></a>
+<a name="2296"><span class="lineNum">    2296 </span><span class="lineNoCov">          0 :         if (!xdr_u_int (xdrs, &amp;u))</span></a>
+<a name="2297"><span class="lineNum">    2297 </span>            :                 {</a>
+<a name="2298"><span class="lineNum">    2298 </span>            :                         return 0;</a>
+<a name="2299"><span class="lineNum">    2299 </span>            :                 }</a>
+<a name="2300"><span class="lineNum">    2300 </span><span class="lineNoCov">          0 :         *cp = u;</span></a>
+<a name="2301"><span class="lineNum">    2301 </span><span class="lineNoCov">          0 :         return 1;</span></a>
+<a name="2302"><span class="lineNum">    2302 </span>            : }</a>
+<a name="2303"><span class="lineNum">    2303 </span>            : </a>
+<a name="2304"><span class="lineNum">    2304 </span>            : /*</a>
+<a name="2305"><span class="lineNum">    2305 </span>            :  * XDR opaque data</a>
+<a name="2306"><span class="lineNum">    2306 </span>            :  * Allows the specification of a fixed size sequence of opaque bytes.</a>
+<a name="2307"><span class="lineNum">    2307 </span>            :  * cp points to the opaque object and cnt gives the byte length.</a>
+<a name="2308"><span class="lineNum">    2308 </span>            :  */</a>
+<a name="2309"><span class="lineNum">    2309 </span>            : static int</a>
+<a name="2310"><span class="lineNum">    2310 </span><span class="lineCov">        175 : xdr_opaque (XDR *xdrs, char *cp, unsigned int cnt)</span></a>
+<a name="2311"><span class="lineNum">    2311 </span>            : {</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :         unsigned int rndup;</a>
+<a name="2313"><span class="lineNum">    2313 </span>            :         static char crud[BYTES_PER_XDR_UNIT];</a>
+<a name="2314"><span class="lineNum">    2314 </span>            : </a>
+<a name="2315"><span class="lineNum">    2315 </span>            :         /*</a>
+<a name="2316"><span class="lineNum">    2316 </span>            :          * if no data we are done</a>
+<a name="2317"><span class="lineNum">    2317 </span>            :          */</a>
+<a name="2318"><span class="lineNum">    2318 </span><span class="lineCov">        175 :         if (cnt == 0)</span></a>
+<a name="2319"><span class="lineNum">    2319 </span>            :                 return 1;</a>
+<a name="2320"><span class="lineNum">    2320 </span>            : </a>
+<a name="2321"><span class="lineNum">    2321 </span>            :         /*</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :          * round byte count to full xdr units</a>
+<a name="2323"><span class="lineNum">    2323 </span>            :          */</a>
+<a name="2324"><span class="lineNum">    2324 </span><span class="lineCov">        175 :         rndup = cnt % BYTES_PER_XDR_UNIT;</span></a>
+<a name="2325"><span class="lineNum">    2325 </span><span class="lineCov">        175 :         if (rndup &gt; 0)</span></a>
+<a name="2326"><span class="lineNum">    2326 </span><span class="lineCov">         61 :                 rndup = BYTES_PER_XDR_UNIT - rndup;</span></a>
+<a name="2327"><span class="lineNum">    2327 </span>            : </a>
+<a name="2328"><span class="lineNum">    2328 </span><span class="lineCov">        175 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2329"><span class="lineNum">    2329 </span>            :                 {</a>
+<a name="2330"><span class="lineNum">    2330 </span><span class="lineCov">         67 :                 case XDR_DECODE:</span></a>
+<a name="2331"><span class="lineNum">    2331 </span><span class="lineCov">         67 :                         if (!xdr_getbytes (xdrs, cp, cnt))</span></a>
+<a name="2332"><span class="lineNum">    2332 </span>            :                                 {</a>
+<a name="2333"><span class="lineNum">    2333 </span>            :                                         return 0;</a>
+<a name="2334"><span class="lineNum">    2334 </span>            :                                 }</a>
+<a name="2335"><span class="lineNum">    2335 </span><span class="lineCov">         67 :                         if (rndup == 0)</span></a>
+<a name="2336"><span class="lineNum">    2336 </span>            :                                 return 1;</a>
+<a name="2337"><span class="lineNum">    2337 </span><span class="lineCov">         22 :                         return xdr_getbytes (xdrs, (char *)crud, rndup);</span></a>
+<a name="2338"><span class="lineNum">    2338 </span>            : </a>
+<a name="2339"><span class="lineNum">    2339 </span><span class="lineCov">        108 :                 case XDR_ENCODE:</span></a>
+<a name="2340"><span class="lineNum">    2340 </span><span class="lineCov">        108 :                         if (!xdr_putbytes (xdrs, cp, cnt))</span></a>
+<a name="2341"><span class="lineNum">    2341 </span>            :                                 {</a>
+<a name="2342"><span class="lineNum">    2342 </span>            :                                         return 0;</a>
+<a name="2343"><span class="lineNum">    2343 </span>            :                                 }</a>
+<a name="2344"><span class="lineNum">    2344 </span><span class="lineCov">        108 :                         if (rndup == 0)</span></a>
+<a name="2345"><span class="lineNum">    2345 </span>            :                                 return 1;</a>
+<a name="2346"><span class="lineNum">    2346 </span><span class="lineCov">         39 :                         return xdr_putbytes (xdrs, xdr_zero, rndup);</span></a>
+<a name="2347"><span class="lineNum">    2347 </span>            : </a>
+<a name="2348"><span class="lineNum">    2348 </span>            :                 case XDR_FREE:</a>
+<a name="2349"><span class="lineNum">    2349 </span>            :                         return 1;</a>
+<a name="2350"><span class="lineNum">    2350 </span>            :                 }</a>
+<a name="2351"><span class="lineNum">    2351 </span>            : #undef BYTES_PER_XDR_UNIT</a>
+<a name="2352"><span class="lineNum">    2352 </span><span class="lineNoCov">          0 :         return 0;</span></a>
+<a name="2353"><span class="lineNum">    2353 </span>            : }</a>
+<a name="2354"><span class="lineNum">    2354 </span>            : </a>
+<a name="2355"><span class="lineNum">    2355 </span>            : </a>
+<a name="2356"><span class="lineNum">    2356 </span>            : /*</a>
+<a name="2357"><span class="lineNum">    2357 </span>            :  * XDR null terminated ASCII strings</a>
+<a name="2358"><span class="lineNum">    2358 </span>            :  */</a>
+<a name="2359"><span class="lineNum">    2359 </span>            : static int</a>
+<a name="2360"><span class="lineNum">    2360 </span><span class="lineCov">         87 : xdr_string (XDR *xdrs, char **cpp, unsigned int maxsize)</span></a>
+<a name="2361"><span class="lineNum">    2361 </span>            : {</a>
+<a name="2362"><span class="lineNum">    2362 </span><span class="lineCov">         87 :         char *sp = *cpp;        /* sp is the actual string pointer */</span></a>
+<a name="2363"><span class="lineNum">    2363 </span>            :         unsigned int size;</a>
+<a name="2364"><span class="lineNum">    2364 </span>            :         unsigned int nodesize;</a>
+<a name="2365"><span class="lineNum">    2365 </span>            : </a>
+<a name="2366"><span class="lineNum">    2366 </span>            :         /*</a>
+<a name="2367"><span class="lineNum">    2367 </span>            :          * first deal with the length since xdr strings are counted-strings</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :          */</a>
+<a name="2369"><span class="lineNum">    2369 </span><span class="lineCov">         87 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2370"><span class="lineNum">    2370 </span>            :                 {</a>
+<a name="2371"><span class="lineNum">    2371 </span><span class="lineNoCov">          0 :                 case XDR_FREE:</span></a>
+<a name="2372"><span class="lineNum">    2372 </span><span class="lineNoCov">          0 :                         if (sp == NULL)</span></a>
+<a name="2373"><span class="lineNum">    2373 </span>            :                                 {</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :                                         return 1;               /* already free */</a>
+<a name="2375"><span class="lineNum">    2375 </span>            :                                 }</a>
+<a name="2376"><span class="lineNum">    2376 </span>            :                         /* fall through... */</a>
+<a name="2377"><span class="lineNum">    2377 </span>            :                 case XDR_ENCODE:</a>
+<a name="2378"><span class="lineNum">    2378 </span><span class="lineCov">         48 :                         if (sp == NULL)</span></a>
+<a name="2379"><span class="lineNum">    2379 </span>            :                                 return 0;</a>
+<a name="2380"><span class="lineNum">    2380 </span><span class="lineCov">         48 :                         size = strlen (sp);</span></a>
+<a name="2381"><span class="lineNum">    2381 </span><span class="lineCov">         48 :                         break;</span></a>
+<a name="2382"><span class="lineNum">    2382 </span>            :                 case XDR_DECODE:</a>
+<a name="2383"><span class="lineNum">    2383 </span>            :                         break;</a>
+<a name="2384"><span class="lineNum">    2384 </span>            :                 }</a>
+<a name="2385"><span class="lineNum">    2385 </span><span class="lineCov">         87 :         if (!xdr_u_int (xdrs, &amp;size))</span></a>
+<a name="2386"><span class="lineNum">    2386 </span>            :                 {</a>
+<a name="2387"><span class="lineNum">    2387 </span>            :                         return 0;</a>
+<a name="2388"><span class="lineNum">    2388 </span>            :                 }</a>
+<a name="2389"><span class="lineNum">    2389 </span><span class="lineCov">         87 :         if (size &gt; maxsize)</span></a>
+<a name="2390"><span class="lineNum">    2390 </span>            :                 {</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :                         return 0;</a>
+<a name="2392"><span class="lineNum">    2392 </span>            :                 }</a>
+<a name="2393"><span class="lineNum">    2393 </span><span class="lineCov">         87 :         nodesize = size + 1;</span></a>
+<a name="2394"><span class="lineNum">    2394 </span>            : </a>
+<a name="2395"><span class="lineNum">    2395 </span>            :         /*</a>
+<a name="2396"><span class="lineNum">    2396 </span>            :          * now deal with the actual bytes</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :          */</a>
+<a name="2398"><span class="lineNum">    2398 </span><span class="lineCov">         87 :         switch (xdrs-&gt;x_op)</span></a>
+<a name="2399"><span class="lineNum">    2399 </span>            :                 {</a>
+<a name="2400"><span class="lineNum">    2400 </span><span class="lineCov">         39 :                 case XDR_DECODE:</span></a>
+<a name="2401"><span class="lineNum">    2401 </span><span class="lineCov">         39 :                         if (nodesize == 0)</span></a>
+<a name="2402"><span class="lineNum">    2402 </span>            :                                 {</a>
+<a name="2403"><span class="lineNum">    2403 </span>            :                                         return 1;</a>
+<a name="2404"><span class="lineNum">    2404 </span>            :                                 }</a>
+<a name="2405"><span class="lineNum">    2405 </span><span class="lineCov">         39 :                         if (sp == NULL)</span></a>
+<a name="2406"><span class="lineNum">    2406 </span><span class="lineNoCov">          0 :                                 *cpp = sp = (char *) malloc (nodesize);</span></a>
+<a name="2407"><span class="lineNum">    2407 </span><span class="lineCov">         39 :                         if (sp == NULL)</span></a>
+<a name="2408"><span class="lineNum">    2408 </span>            :                                 {</a>
+<a name="2409"><span class="lineNum">    2409 </span><span class="lineNoCov">          0 :                                         (void) fputs (&quot;xdr_string: out of memory\n&quot;, stderr);</span></a>
+<a name="2410"><span class="lineNum">    2410 </span><span class="lineNoCov">          0 :                                         return 0;</span></a>
+<a name="2411"><span class="lineNum">    2411 </span>            :                                 }</a>
+<a name="2412"><span class="lineNum">    2412 </span><span class="lineCov">         39 :                         sp[size] = 0;</span></a>
+<a name="2413"><span class="lineNum">    2413 </span>            :                         /* fall into ... */</a>
+<a name="2414"><span class="lineNum">    2414 </span>            : </a>
+<a name="2415"><span class="lineNum">    2415 </span><span class="lineCov">         87 :                 case XDR_ENCODE:</span></a>
+<a name="2416"><span class="lineNum">    2416 </span><span class="lineCov">         87 :                         return xdr_opaque (xdrs, sp, size);</span></a>
+<a name="2417"><span class="lineNum">    2417 </span>            : </a>
+<a name="2418"><span class="lineNum">    2418 </span><span class="lineNoCov">          0 :                 case XDR_FREE:</span></a>
+<a name="2419"><span class="lineNum">    2419 </span><span class="lineNoCov">          0 :                         free (sp);</span></a>
+<a name="2420"><span class="lineNum">    2420 </span><span class="lineNoCov">          0 :                         *cpp = NULL;</span></a>
+<a name="2421"><span class="lineNum">    2421 </span><span class="lineNoCov">          0 :                         return 1;</span></a>
+<a name="2422"><span class="lineNum">    2422 </span>            :                 }</a>
+<a name="2423"><span class="lineNum">    2423 </span>            :         return 0;</a>
+<a name="2424"><span class="lineNum">    2424 </span>            : }</a>
+<a name="2425"><span class="lineNum">    2425 </span>            : </a>
+<a name="2426"><span class="lineNum">    2426 </span>            : </a>
+<a name="2427"><span class="lineNum">    2427 </span>            : </a>
+<a name="2428"><span class="lineNum">    2428 </span>            : /* Floating-point stuff */</a>
+<a name="2429"><span class="lineNum">    2429 </span>            : </a>
+<a name="2430"><span class="lineNum">    2430 </span>            : static int</a>
+<a name="2431"><span class="lineNum">    2431 </span><span class="lineCov">      11524 : xdr_float(XDR *xdrs, float *fp)</span></a>
+<a name="2432"><span class="lineNum">    2432 </span>            : {</a>
+<a name="2433"><span class="lineNum">    2433 </span><span class="lineCov">      11524 :         switch (xdrs-&gt;x_op) {</span></a>
+<a name="2434"><span class="lineNum">    2434 </span>            : </a>
+<a name="2435"><span class="lineNum">    2435 </span>            :         case XDR_ENCODE:</a>
+<a name="2436"><span class="lineNum">    2436 </span>            :                 if (sizeof(float) == sizeof(int32_t))</a>
+<a name="2437"><span class="lineNum">    2437 </span><span class="lineCov">       8436 :                         return (xdr_putlong(xdrs, (int32_t *) (void*) fp));</span></a>
+<a name="2438"><span class="lineNum">    2438 </span>            :                 else if (sizeof(float) == sizeof(int)) {</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :                         int32_t tmp = *(int *) (void*) fp;</a>
+<a name="2440"><span class="lineNum">    2440 </span>            :                         return (xdr_putlong(xdrs, &amp;tmp));</a>
+<a name="2441"><span class="lineNum">    2441 </span>            :                 }</a>
+<a name="2442"><span class="lineNum">    2442 </span>            :                 break;</a>
+<a name="2443"><span class="lineNum">    2443 </span>            : </a>
+<a name="2444"><span class="lineNum">    2444 </span>            :         case XDR_DECODE:</a>
+<a name="2445"><span class="lineNum">    2445 </span>            :                 if (sizeof(float) == sizeof(int32_t))</a>
+<a name="2446"><span class="lineNum">    2446 </span><span class="lineCov">       3088 :                         return (xdr_getlong(xdrs, (int32_t *) (void*) fp));</span></a>
+<a name="2447"><span class="lineNum">    2447 </span>            :                 else if (sizeof(float) == sizeof(int)) {</a>
+<a name="2448"><span class="lineNum">    2448 </span>            :                         int32_t tmp;</a>
+<a name="2449"><span class="lineNum">    2449 </span>            :                         if (xdr_getlong(xdrs, &amp;tmp)) {</a>
+<a name="2450"><span class="lineNum">    2450 </span>            :                                 *(int *) (void*)fp = tmp;</a>
+<a name="2451"><span class="lineNum">    2451 </span>            :                                 return (1);</a>
+<a name="2452"><span class="lineNum">    2452 </span>            :                         }</a>
+<a name="2453"><span class="lineNum">    2453 </span>            :                 }</a>
+<a name="2454"><span class="lineNum">    2454 </span>            :                 break;</a>
+<a name="2455"><span class="lineNum">    2455 </span>            : </a>
+<a name="2456"><span class="lineNum">    2456 </span>            :         case XDR_FREE:</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :                 return (1);</a>
+<a name="2458"><span class="lineNum">    2458 </span>            :         }</a>
+<a name="2459"><span class="lineNum">    2459 </span><span class="lineNoCov">          0 :         return (0);</span></a>
+<a name="2460"><span class="lineNum">    2460 </span>            : }</a>
+<a name="2461"><span class="lineNum">    2461 </span>            : </a>
+<a name="2462"><span class="lineNum">    2462 </span>            : </a>
+<a name="2463"><span class="lineNum">    2463 </span>            : static int</a>
+<a name="2464"><span class="lineNum">    2464 </span><span class="lineNoCov">          0 : xdr_double(XDR *xdrs, double *dp)</span></a>
+<a name="2465"><span class="lineNum">    2465 </span>            : {</a>
+<a name="2466"><span class="lineNum">    2466 </span>            :     /* Gromacs detects floating-point stuff at compile time, which is faster */</a>
+<a name="2467"><span class="lineNum">    2467 </span>            : #ifdef GROMACS</a>
+<a name="2468"><span class="lineNum">    2468 </span>            : #  ifndef FLOAT_FORMAT_IEEE754 </a>
+<a name="2469"><span class="lineNum">    2469 </span>            : #    error non-IEEE floating point system, or you defined GROMACS yourself...</a>
+<a name="2470"><span class="lineNum">    2470 </span>            : #  endif</a>
+<a name="2471"><span class="lineNum">    2471 </span>            :     int LSW;</a>
+<a name="2472"><span class="lineNum">    2472 </span>            : #  ifdef IEEE754_BIG_ENDIAN_WORD_ORDER </a>
+<a name="2473"><span class="lineNum">    2473 </span>            :     int LSW=1;</a>
+<a name="2474"><span class="lineNum">    2474 </span>            : #  else</a>
+<a name="2475"><span class="lineNum">    2475 </span>            :     int LSW=0;</a>
+<a name="2476"><span class="lineNum">    2476 </span>            : #  endif /* Big endian word order */</a>
+<a name="2477"><span class="lineNum">    2477 </span>            : #else </a>
+<a name="2478"><span class="lineNum">    2478 </span>            :     /* Outside Gromacs we rely on dynamic detection of FP order. */</a>
+<a name="2479"><span class="lineNum">    2479 </span>            :     int LSW; /* Least significant fp word */</a>
+<a name="2480"><span class="lineNum">    2480 </span>            : </a>
+<a name="2481"><span class="lineNum">    2481 </span>            :     double x=0.987654321; /* Just a number */</a>
+<a name="2482"><span class="lineNum">    2482 </span>            :     unsigned char ix = *((char *)&amp;x);</a>
+<a name="2483"><span class="lineNum">    2483 </span>            :     </a>
+<a name="2484"><span class="lineNum">    2484 </span>            :     /* Possible representations in IEEE double precision: </a>
+<a name="2485"><span class="lineNum">    2485 </span>            :      * (S=small endian, B=big endian)</a>
+<a name="2486"><span class="lineNum">    2486 </span>            :      *  </a>
+<a name="2487"><span class="lineNum">    2487 </span>            :      * Byte order, Word order, Hex</a>
+<a name="2488"><span class="lineNum">    2488 </span>            :      *     S           S       b8 56 0e 3c dd 9a ef 3f    </a>
+<a name="2489"><span class="lineNum">    2489 </span>            :      *     B           S       3c 0e 56 b8 3f ef 9a dd</a>
+<a name="2490"><span class="lineNum">    2490 </span>            :      *     S           B       dd 9a ef 3f b8 56 0e 3c</a>
+<a name="2491"><span class="lineNum">    2491 </span>            :      *     B           B       3f ef 9a dd 3c 0e 56 b8</a>
+<a name="2492"><span class="lineNum">    2492 </span>            :      */ </a>
+<a name="2493"><span class="lineNum">    2493 </span>            :     if(ix==0xdd || ix==0x3f)</a>
+<a name="2494"><span class="lineNum">    2494 </span>            :                 LSW=1;  /* Big endian word order */</a>
+<a name="2495"><span class="lineNum">    2495 </span>            :     else if(ix==0xb8 || ix==0x3c)</a>
+<a name="2496"><span class="lineNum">    2496 </span>            :                 LSW=0;  /* Small endian word order */</a>
+<a name="2497"><span class="lineNum">    2497 </span>            :     else { /* Catch strange errors */</a>
+<a name="2498"><span class="lineNum">    2498 </span>            :                 fprintf(stderr,&quot;Cannot detect floating-point word order.\n&quot;</a>
+<a name="2499"><span class="lineNum">    2499 </span>            :                                 &quot;Do you have a non-IEEE system?\n&quot;</a>
+<a name="2500"><span class="lineNum">    2500 </span>            :                                 &quot;Use system XDR libraries or fix xdr_double().\n&quot;);</a>
+<a name="2501"><span class="lineNum">    2501 </span>            :                 abort();</a>
+<a name="2502"><span class="lineNum">    2502 </span>            :     }</a>
+<a name="2503"><span class="lineNum">    2503 </span>            : #endif /* end of dynamic detection of fp word order */</a>
+<a name="2504"><span class="lineNum">    2504 </span>            : </a>
+<a name="2505"><span class="lineNum">    2505 </span><span class="lineNoCov">          0 :         switch (xdrs-&gt;x_op) {</span></a>
+<a name="2506"><span class="lineNum">    2506 </span>            :     </a>
+<a name="2507"><span class="lineNum">    2507 </span>            :         case XDR_ENCODE:</a>
+<a name="2508"><span class="lineNum">    2508 </span>            :                 if (2*sizeof(int32_t) == sizeof(double)) {</a>
+<a name="2509"><span class="lineNum">    2509 </span>            :                         int32_t *lp = (int32_t *) (void*) dp;</a>
+<a name="2510"><span class="lineNum">    2510 </span><span class="lineNoCov">          0 :                         return (xdr_putlong(xdrs, lp+!LSW) &amp;&amp;</span></a>
+<a name="2511"><span class="lineNum">    2511 </span><span class="lineNoCov">          0 :                                         xdr_putlong(xdrs, lp+LSW));</span></a>
+<a name="2512"><span class="lineNum">    2512 </span>            :                 } else if (2*sizeof(int) == sizeof(double)) {</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :                         int *ip = (int *) (void*) dp;</a>
+<a name="2514"><span class="lineNum">    2514 </span>            :                         int32_t tmp[2];</a>
+<a name="2515"><span class="lineNum">    2515 </span>            :                         tmp[0] = ip[!LSW];</a>
+<a name="2516"><span class="lineNum">    2516 </span>            :                         tmp[1] = ip[LSW];</a>
+<a name="2517"><span class="lineNum">    2517 </span>            :                         return (xdr_putlong(xdrs, tmp) &amp;&amp;</a>
+<a name="2518"><span class="lineNum">    2518 </span>            :                                         xdr_putlong(xdrs, tmp+1));</a>
+<a name="2519"><span class="lineNum">    2519 </span>            :                 }</a>
+<a name="2520"><span class="lineNum">    2520 </span>            :                 break;</a>
+<a name="2521"><span class="lineNum">    2521 </span>            :     </a>
+<a name="2522"><span class="lineNum">    2522 </span>            :         case XDR_DECODE:</a>
+<a name="2523"><span class="lineNum">    2523 </span>            :                 if (2*sizeof(int32_t) == sizeof(double)) {</a>
+<a name="2524"><span class="lineNum">    2524 </span>            :                         int32_t *lp = (int32_t *) (void*) dp;</a>
+<a name="2525"><span class="lineNum">    2525 </span><span class="lineNoCov">          0 :                         return (xdr_getlong(xdrs, lp+!LSW) &amp;&amp;</span></a>
+<a name="2526"><span class="lineNum">    2526 </span><span class="lineNoCov">          0 :                                         xdr_getlong(xdrs, lp+LSW));</span></a>
+<a name="2527"><span class="lineNum">    2527 </span>            :                 } else if (2*sizeof(int) == sizeof(double)) {</a>
+<a name="2528"><span class="lineNum">    2528 </span>            :                         int *ip = (int *) (void*) dp;</a>
+<a name="2529"><span class="lineNum">    2529 </span>            :                         int32_t tmp[2];</a>
+<a name="2530"><span class="lineNum">    2530 </span>            :                         if (xdr_getlong(xdrs, tmp+!LSW) &amp;&amp;</a>
+<a name="2531"><span class="lineNum">    2531 </span>            :                                 xdr_getlong(xdrs, tmp+LSW)) {</a>
+<a name="2532"><span class="lineNum">    2532 </span>            :                                 ip[0] = tmp[0];</a>
+<a name="2533"><span class="lineNum">    2533 </span>            :                                 ip[1] = tmp[1];</a>
+<a name="2534"><span class="lineNum">    2534 </span>            :                                 return (1);</a>
+<a name="2535"><span class="lineNum">    2535 </span>            :                         }</a>
+<a name="2536"><span class="lineNum">    2536 </span>            :                 }</a>
+<a name="2537"><span class="lineNum">    2537 </span>            :                 break;</a>
+<a name="2538"><span class="lineNum">    2538 </span>            :     </a>
+<a name="2539"><span class="lineNum">    2539 </span>            :         case XDR_FREE:</a>
+<a name="2540"><span class="lineNum">    2540 </span>            :                 return (1);</a>
+<a name="2541"><span class="lineNum">    2541 </span>            :         }</a>
+<a name="2542"><span class="lineNum">    2542 </span><span class="lineNoCov">          0 :         return (0);</span></a>
+<a name="2543"><span class="lineNum">    2543 </span>            : }</a>
+<a name="2544"><span class="lineNum">    2544 </span>            : </a>
+<a name="2545"><span class="lineNum">    2545 </span>            : </a>
+<a name="2546"><span class="lineNum">    2546 </span>            : static int xdrstdio_getlong (XDR *, int32_t *);</a>
+<a name="2547"><span class="lineNum">    2547 </span>            : static int xdrstdio_putlong (XDR *, int32_t *);</a>
+<a name="2548"><span class="lineNum">    2548 </span>            : static int xdrstdio_getbytes (XDR *, char *, unsigned int);</a>
+<a name="2549"><span class="lineNum">    2549 </span>            : static int xdrstdio_putbytes (XDR *, char *, unsigned int);</a>
+<a name="2550"><span class="lineNum">    2550 </span>            : static unsigned int xdrstdio_getpos (XDR *);</a>
+<a name="2551"><span class="lineNum">    2551 </span>            : static int xdrstdio_setpos (XDR *, unsigned int);</a>
+<a name="2552"><span class="lineNum">    2552 </span>            : static void xdrstdio_destroy (XDR *);</a>
+<a name="2553"><span class="lineNum">    2553 </span>            : </a>
+<a name="2554"><span class="lineNum">    2554 </span>            : /*</a>
+<a name="2555"><span class="lineNum">    2555 </span>            :  * Ops vector for stdio type XDR</a>
+<a name="2556"><span class="lineNum">    2556 </span>            :  */</a>
+<a name="2557"><span class="lineNum">    2557 </span>            : static const XDR::xdr_ops xdrstdio_ops =</a>
+<a name="2558"><span class="lineNum">    2558 </span>            :         {</a>
+<a name="2559"><span class="lineNum">    2559 </span>            :                 xdrstdio_getlong,               /* deserialize a long int */</a>
+<a name="2560"><span class="lineNum">    2560 </span>            :                 xdrstdio_putlong,               /* serialize a long int */</a>
+<a name="2561"><span class="lineNum">    2561 </span>            :                 xdrstdio_getbytes,              /* deserialize counted bytes */</a>
+<a name="2562"><span class="lineNum">    2562 </span>            :                 xdrstdio_putbytes,      /* serialize counted bytes */</a>
+<a name="2563"><span class="lineNum">    2563 </span>            :                 xdrstdio_getpos,                /* get offset in the stream */</a>
+<a name="2564"><span class="lineNum">    2564 </span>            :                 xdrstdio_setpos,                /* set offset in the stream */</a>
+<a name="2565"><span class="lineNum">    2565 </span>            :                 xdrstdio_destroy,               /* destroy stream */</a>
+<a name="2566"><span class="lineNum">    2566 </span>            :         };</a>
+<a name="2567"><span class="lineNum">    2567 </span>            : </a>
+<a name="2568"><span class="lineNum">    2568 </span>            : /*</a>
+<a name="2569"><span class="lineNum">    2569 </span>            :  * Initialize a stdio xdr stream.</a>
+<a name="2570"><span class="lineNum">    2570 </span>            :  * Sets the xdr stream handle xdrs for use on the stream file.</a>
+<a name="2571"><span class="lineNum">    2571 </span>            :  * Operation flag is set to op.</a>
+<a name="2572"><span class="lineNum">    2572 </span>            :  */</a>
+<a name="2573"><span class="lineNum">    2573 </span>            : static void</a>
+<a name="2574"><span class="lineNum">    2574 </span><span class="lineCov">         20 : xdrstdio_create (XDR *xdrs, FILE *file, enum xdr_op op)</span></a>
+<a name="2575"><span class="lineNum">    2575 </span>            : {</a>
+<a name="2576"><span class="lineNum">    2576 </span><span class="lineCov">         20 :         xdrs-&gt;x_op = op;</span></a>
+<a name="2577"><span class="lineNum">    2577 </span>            : </a>
+<a name="2578"><span class="lineNum">    2578 </span><span class="lineCov">         20 :         xdrs-&gt;x_ops = (XDR::xdr_ops *) &amp;xdrstdio_ops;</span></a>
+<a name="2579"><span class="lineNum">    2579 </span><span class="lineCov">         20 :         xdrs-&gt;x_private = (char *) file;</span></a>
+<a name="2580"><span class="lineNum">    2580 </span><span class="lineCov">         20 : }</span></a>
+<a name="2581"><span class="lineNum">    2581 </span>            : </a>
+<a name="2582"><span class="lineNum">    2582 </span>            : /*</a>
+<a name="2583"><span class="lineNum">    2583 </span>            :  * Destroy a stdio xdr stream.</a>
+<a name="2584"><span class="lineNum">    2584 </span>            :  * Cleans up the xdr stream handle xdrs previously set up by xdrstdio_create.</a>
+<a name="2585"><span class="lineNum">    2585 </span>            :  */</a>
+<a name="2586"><span class="lineNum">    2586 </span>            : static void</a>
+<a name="2587"><span class="lineNum">    2587 </span><span class="lineCov">         20 : xdrstdio_destroy (XDR *xdrs)</span></a>
+<a name="2588"><span class="lineNum">    2588 </span>            : {</a>
+<a name="2589"><span class="lineNum">    2589 </span><span class="lineCov">         20 :         (void) fflush ((FILE *) xdrs-&gt;x_private);</span></a>
+<a name="2590"><span class="lineNum">    2590 </span>            :         /* xx should we close the file ?? */</a>
+<a name="2591"><span class="lineNum">    2591 </span><span class="lineCov">         20 : }</span></a>
+<a name="2592"><span class="lineNum">    2592 </span>            : </a>
+<a name="2593"><span class="lineNum">    2593 </span>            : static int</a>
+<a name="2594"><span class="lineNum">    2594 </span><span class="lineCov">       4059 : xdrstdio_getlong (XDR *xdrs, int32_t *lp)</span></a>
+<a name="2595"><span class="lineNum">    2595 </span>            : {</a>
+<a name="2596"><span class="lineNum">    2596 </span>            :         int32_t mycopy;</a>
+<a name="2597"><span class="lineNum">    2597 </span>            : </a>
+<a name="2598"><span class="lineNum">    2598 </span><span class="lineCov">       4059 :         if (fread ((char *) &amp; mycopy, 4, 1, (FILE *) xdrs-&gt;x_private) != 1)</span></a>
+<a name="2599"><span class="lineNum">    2599 </span>            :                 return 0;</a>
+<a name="2600"><span class="lineNum">    2600 </span><span class="lineCov">       4054 :         *lp = (int32_t) xdr_ntohl (mycopy);</span></a>
+<a name="2601"><span class="lineNum">    2601 </span><span class="lineCov">       4054 :         return 1;</span></a>
+<a name="2602"><span class="lineNum">    2602 </span>            : }</a>
+<a name="2603"><span class="lineNum">    2603 </span>            : </a>
+<a name="2604"><span class="lineNum">    2604 </span>            : static int</a>
+<a name="2605"><span class="lineNum">    2605 </span><span class="lineCov">       9972 : xdrstdio_putlong (XDR *xdrs, int32_t *lp)</span></a>
+<a name="2606"><span class="lineNum">    2606 </span>            : {</a>
+<a name="2607"><span class="lineNum">    2607 </span><span class="lineCov">       9972 :         int32_t mycopy = xdr_htonl (*lp);</span></a>
+<a name="2608"><span class="lineNum">    2608 </span>            :         lp = &amp;mycopy;</a>
+<a name="2609"><span class="lineNum">    2609 </span><span class="lineCov">       9972 :         if (fwrite ((char *) lp, 4, 1, (FILE *) xdrs-&gt;x_private) != 1)</span></a>
+<a name="2610"><span class="lineNum">    2610 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="2611"><span class="lineNum">    2611 </span>            :         return 1;</a>
+<a name="2612"><span class="lineNum">    2612 </span>            : }</a>
+<a name="2613"><span class="lineNum">    2613 </span>            : </a>
+<a name="2614"><span class="lineNum">    2614 </span>            : static int</a>
+<a name="2615"><span class="lineNum">    2615 </span><span class="lineCov">         89 : xdrstdio_getbytes (XDR *xdrs, char *addr, unsigned int len)</span></a>
+<a name="2616"><span class="lineNum">    2616 </span>            : {</a>
+<a name="2617"><span class="lineNum">    2617 </span><span class="lineCov">        178 :         if ((len != 0) &amp;&amp; (fread (addr, (int) len, 1,</span></a>
+<a name="2618"><span class="lineNum">    2618 </span><span class="lineCov">         89 :                                                           (FILE *) xdrs-&gt;x_private) != 1))</span></a>
+<a name="2619"><span class="lineNum">    2619 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="2620"><span class="lineNum">    2620 </span>            :         return 1;</a>
+<a name="2621"><span class="lineNum">    2621 </span>            : }</a>
+<a name="2622"><span class="lineNum">    2622 </span>            : </a>
+<a name="2623"><span class="lineNum">    2623 </span>            : static int</a>
+<a name="2624"><span class="lineNum">    2624 </span><span class="lineCov">        147 : xdrstdio_putbytes (XDR *xdrs, char *addr, unsigned int len)</span></a>
+<a name="2625"><span class="lineNum">    2625 </span>            : {</a>
+<a name="2626"><span class="lineNum">    2626 </span><span class="lineCov">        294 :         if ((len != 0) &amp;&amp; (fwrite (addr, (int) len, 1,</span></a>
+<a name="2627"><span class="lineNum">    2627 </span><span class="lineCov">        147 :                                                            (FILE *) xdrs-&gt;x_private) != 1)) </span></a>
+<a name="2628"><span class="lineNum">    2628 </span><span class="lineNoCov">          0 :                 return 0;</span></a>
+<a name="2629"><span class="lineNum">    2629 </span>            :         return 1;</a>
+<a name="2630"><span class="lineNum">    2630 </span>            : }</a>
+<a name="2631"><span class="lineNum">    2631 </span>            : </a>
+<a name="2632"><span class="lineNum">    2632 </span>            : /* 32 bit fileseek operations */</a>
+<a name="2633"><span class="lineNum">    2633 </span>            : static unsigned int</a>
+<a name="2634"><span class="lineNum">    2634 </span><span class="lineNoCov">          0 : xdrstdio_getpos (XDR *xdrs)</span></a>
+<a name="2635"><span class="lineNum">    2635 </span>            : {</a>
+<a name="2636"><span class="lineNum">    2636 </span><span class="lineNoCov">          0 :         return (unsigned int) ftell ((FILE *) xdrs-&gt;x_private);</span></a>
+<a name="2637"><span class="lineNum">    2637 </span>            : }</a>
+<a name="2638"><span class="lineNum">    2638 </span>            : </a>
+<a name="2639"><span class="lineNum">    2639 </span>            : static int</a>
+<a name="2640"><span class="lineNum">    2640 </span><span class="lineNoCov">          0 : xdrstdio_setpos (XDR *xdrs, unsigned int pos)</span></a>
+<a name="2641"><span class="lineNum">    2641 </span>            : {</a>
+<a name="2642"><span class="lineNum">    2642 </span><span class="lineNoCov">          0 :         return fseek ((FILE *) xdrs-&gt;x_private, pos, 0) &lt; 0 ? 0 : 1;</span></a>
+<a name="2643"><span class="lineNum">    2643 </span>            : }</a>
+<a name="2644"><span class="lineNum">    2644 </span>            : </a>
+<a name="2645"><span class="lineNum">    2645 </span>            : #endif /* HAVE_RPC_XDR_H not defined */</a>
+<a name="2646"><span class="lineNum">    2646 </span>            : </a>
+<a name="2647"><span class="lineNum">    2647 </span>            : }</a>
+<a name="2648"><span class="lineNum">    2648 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile_trr.cpp.func-sort-c.html b/coverage-libs/xdrfile/xdrfile_trr.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ae81828cf1
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile_trr.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile_trr.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile_trr.cpp<span style="font-size: 80%;"> (<a href="xdrfile_trr.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntryLo">54.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="xdrfile_trr.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#496">_ZN4PLMD7xdrfile15read_trr_natomsEPcPi</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#519">_ZN4PLMD7xdrfile8read_trrEPNS0_7XDRFILEEiPiPfS4_PA3_fS6_S6_S6_</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#513">_ZN4PLMD7xdrfile9write_trrEPNS0_7XDRFILEEiiffPA3_fS4_S4_S4_</a></td>
+              <td class="coverFnHi">48</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#200">_ZN4PLMD7xdrfileL7do_htrnEPNS0_7XDRFILEEiPNS0_11t_trnheaderEPA3_fS6_S6_S6_</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#97">_ZN4PLMD7xdrfileL10nFloatSizeEPNS0_11t_trnheaderEPi</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#453">_ZN4PLMD7xdrfileL6do_trnEPNS0_7XDRFILEEiPiPfS4_PA3_fS3_S6_S6_S6_</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#120">_ZN4PLMD7xdrfileL12do_trnheaderEPNS0_7XDRFILEEiPNS0_11t_trnheaderE</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile_trr.cpp.func.html b/coverage-libs/xdrfile/xdrfile_trr.cpp.func.html
new file mode 100644
index 0000000000..e86f10de0d
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile_trr.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile_trr.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile_trr.cpp<span style="font-size: 80%;"> (<a href="xdrfile_trr.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntryLo">54.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="xdrfile_trr.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#496">_ZN4PLMD7xdrfile15read_trr_natomsEPcPi</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#519">_ZN4PLMD7xdrfile8read_trrEPNS0_7XDRFILEEiPiPfS4_PA3_fS6_S6_S6_</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#513">_ZN4PLMD7xdrfile9write_trrEPNS0_7XDRFILEEiiffPA3_fS4_S4_S4_</a></td>
+              <td class="coverFnHi">48</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#97">_ZN4PLMD7xdrfileL10nFloatSizeEPNS0_11t_trnheaderEPi</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#120">_ZN4PLMD7xdrfileL12do_trnheaderEPNS0_7XDRFILEEiPNS0_11t_trnheaderE</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#453">_ZN4PLMD7xdrfileL6do_trnEPNS0_7XDRFILEEiPiPfS4_PA3_fS3_S6_S6_S6_</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_trr.cpp.gcov.html#200">_ZN4PLMD7xdrfileL7do_htrnEPNS0_7XDRFILEEiPNS0_11t_trnheaderEPA3_fS6_S6_S6_</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile_trr.cpp.gcov.html b/coverage-libs/xdrfile/xdrfile_trr.cpp.gcov.html
new file mode 100644
index 0000000000..60d67dd290
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile_trr.cpp.gcov.html
@@ -0,0 +1,605 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile_trr.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile_trr.cpp<span style="font-size: 80%;"> (source / <a href="xdrfile_trr.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntryLo">54.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2009-2014, Erik Lindahl &amp; David van der Spoel</a>
+<a name="3"><span class="lineNum">       3 </span>            : All rights reserved.</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            : Redistribution and use in source and binary forms, with or without</a>
+<a name="6"><span class="lineNum">       6 </span>            : modification, are permitted provided that the following conditions are met:</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : 1. Redistributions of source code must retain the above copyright notice, this</a>
+<a name="9"><span class="lineNum">       9 </span>            : list of conditions and the following disclaimer.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            : 2. Redistributions in binary form must reproduce the above copyright notice,</a>
+<a name="12"><span class="lineNum">      12 </span>            : this list of conditions and the following disclaimer in the documentation</a>
+<a name="13"><span class="lineNum">      13 </span>            : and/or other materials provided with the distribution.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            : THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</a>
+<a name="16"><span class="lineNum">      16 </span>            : AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</a>
+<a name="17"><span class="lineNum">      17 </span>            : IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</a>
+<a name="18"><span class="lineNum">      18 </span>            : DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</a>
+<a name="19"><span class="lineNum">      19 </span>            : FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</a>
+<a name="20"><span class="lineNum">      20 </span>            : DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</a>
+<a name="21"><span class="lineNum">      21 </span>            : SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</a>
+<a name="22"><span class="lineNum">      22 </span>            : CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</a>
+<a name="23"><span class="lineNum">      23 </span>            : OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</a>
+<a name="24"><span class="lineNum">      24 </span>            : OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</a>
+<a name="25"><span class="lineNum">      25 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="26"><span class="lineNum">      26 </span>            : /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- </a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * $Id$</a>
+<a name="29"><span class="lineNum">      29 </span>            :  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*-</a>
+<a name="31"><span class="lineNum">      31 </span>            :  *</a>
+<a name="32"><span class="lineNum">      32 </span>            :  * $Id$</a>
+<a name="33"><span class="lineNum">      33 </span>            :  *</a>
+<a name="34"><span class="lineNum">      34 </span>            :  * Copyright (c) 2009-2014, Erik Lindahl &amp; David van der Spoel</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * All rights reserved.</a>
+<a name="36"><span class="lineNum">      36 </span>            :  *</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * Redistribution and use in source and binary forms, with or without</a>
+<a name="38"><span class="lineNum">      38 </span>            :  * modification, are permitted provided that the following conditions are met:</a>
+<a name="39"><span class="lineNum">      39 </span>            :  *</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * 1. Redistributions of source code must retain the above copyright notice, this</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * list of conditions and the following disclaimer.</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * 2. Redistributions in binary form must reproduce the above copyright notice,</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * this list of conditions and the following disclaimer in the documentation</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * and/or other materials provided with the distribution.</a>
+<a name="46"><span class="lineNum">      46 </span>            :  *</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</a>
+<a name="53"><span class="lineNum">      53 </span>            :  * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</a>
+<a name="55"><span class="lineNum">      55 </span>            :  * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</a>
+<a name="56"><span class="lineNum">      56 </span>            :  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</a>
+<a name="57"><span class="lineNum">      57 </span>            :  */</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="60"><span class="lineNum">      60 </span>            : #include &lt;string.h&gt;</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : #ifdef HAVE_CONFIG_H</a>
+<a name="63"><span class="lineNum">      63 </span>            : #include &quot;config.h&quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            : #endif</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : #include &quot;xdrfile.h&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            : #include &quot;xdrfile_trr.h&quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : #define BUFSIZE         128</a>
+<a name="70"><span class="lineNum">      70 </span>            : #define GROMACS_MAGIC   1993</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : namespace PLMD {</a>
+<a name="73"><span class="lineNum">      73 </span>            : namespace xdrfile {</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : typedef struct          /* This struct describes the order and the      */</a>
+<a name="76"><span class="lineNum">      76 </span>            : /* sizes of the structs in a trjfile, sizes are given in bytes. */</a>
+<a name="77"><span class="lineNum">      77 </span>            : {</a>
+<a name="78"><span class="lineNum">      78 </span>            :     mybool  bDouble;        /* Double precision?                            */</a>
+<a name="79"><span class="lineNum">      79 </span>            :     int ir_size;        /* Backward compatibility                       */</a>
+<a name="80"><span class="lineNum">      80 </span>            :     int e_size;         /* Backward compatibility                       */</a>
+<a name="81"><span class="lineNum">      81 </span>            :     int box_size;       /* Non zero if a box is present                 */</a>
+<a name="82"><span class="lineNum">      82 </span>            :     int   vir_size;       /* Backward compatibility                     */</a>
+<a name="83"><span class="lineNum">      83 </span>            :     int   pres_size;      /* Backward compatibility                     */</a>
+<a name="84"><span class="lineNum">      84 </span>            :     int top_size;       /* Backward compatibility                       */</a>
+<a name="85"><span class="lineNum">      85 </span>            :     int sym_size;       /* Backward compatibility                       */</a>
+<a name="86"><span class="lineNum">      86 </span>            :     int x_size;         /* Non zero if coordinates are present          */</a>
+<a name="87"><span class="lineNum">      87 </span>            :     int v_size;         /* Non zero if velocities are present           */</a>
+<a name="88"><span class="lineNum">      88 </span>            :     int f_size;         /* Non zero if forces are present               */</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :     int natoms;         /* The total number of atoms                    */</a>
+<a name="91"><span class="lineNum">      91 </span>            :     int step;           /* Current step number                          */</a>
+<a name="92"><span class="lineNum">      92 </span>            :     int nre;            /* Backward compatibility                       */</a>
+<a name="93"><span class="lineNum">      93 </span>            :     float       tf;             /* Current time                                 */</a>
+<a name="94"><span class="lineNum">      94 </span>            :     float       lambdaf;                /* Current value of lambda                      */</a>
+<a name="95"><span class="lineNum">      95 </span>            :     double      td;             /* Current time                                 */</a>
+<a name="96"><span class="lineNum">      96 </span>            :     double      lambdad;                /* Current value of lambda                      */</a>
+<a name="97"><span class="lineNum">      97 </span>            : } t_trnheader;</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         87 : static int nFloatSize(t_trnheader *sh,int *nflsz)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : {</a>
+<a name="101"><span class="lineNum">     101 </span>            :     int nflsize=0;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         87 :     if (sh-&gt;box_size)</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         87 :         nflsize = sh-&gt;box_size/(DIM*DIM);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     else if (sh-&gt;x_size)</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :         nflsize = sh-&gt;x_size/(sh-&gt;natoms*DIM);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     else if (sh-&gt;v_size)</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :         nflsize = sh-&gt;v_size/(sh-&gt;natoms*DIM);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     else if (sh-&gt;f_size)</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :         nflsize = sh-&gt;f_size/(sh-&gt;natoms*DIM);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     else </a>
+<a name="112"><span class="lineNum">     112 </span>            :         return exdrHEADER;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         87 :     if (((nflsize != sizeof(float)) &amp;&amp; (nflsize != sizeof(double))))</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :         return exdrHEADER;</a>
+<a name="116"><span class="lineNum">     116 </span>            :       </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         87 :     *nflsz = nflsize;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         87 :     return exdrOK;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         90 : static int do_trnheader(XDRFILE *xd,mybool bRead,t_trnheader *sh)</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : {</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         90 :         int magic=GROMACS_MAGIC;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :         int nflsz,slen,result;</a>
+<a name="126"><span class="lineNum">     126 </span>            :         const char *version = &quot;GMX_trn_file&quot;;</a>
+<a name="127"><span class="lineNum">     127 </span>            :         char buf[BUFSIZE];</a>
+<a name="128"><span class="lineNum">     128 </span>            :   </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         90 :         if (xdrfile_read_int(&amp;magic,1,xd) != 1)</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :                 return exdrINT;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         87 :         if (bRead) </span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         39 :         if (xdrfile_read_int(&amp;slen,1,xd) != 1)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :             return exdrINT;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         39 :         if (slen != strlen(version)+1)</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :             return exdrSTRING;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         39 :         if (xdrfile_read_string(buf,BUFSIZE,xd) &lt;= 0)</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :             return exdrSTRING;</a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            :         else </a>
+<a name="142"><span class="lineNum">     142 </span>            :     {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         48 :         slen = strlen(version)+1;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         48 :         if (xdrfile_read_int(&amp;slen,1,xd) != 1)</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :             return exdrINT;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         48 :         if (xdrfile_write_string(const_cast&lt;char*&gt;(version),xd) != (strlen(version)+1) )</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :             return exdrSTRING;</a>
+<a name="148"><span class="lineNum">     148 </span>            :     }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;ir_size,1,xd) != 1)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :                 return exdrINT;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;e_size,1,xd) != 1)</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :                 return exdrINT;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;box_size,1,xd) != 1)</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :                 return exdrINT;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;vir_size,1,xd) != 1)</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :                 return exdrINT;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;pres_size,1,xd) != 1)</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :                 return exdrINT;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;top_size,1,xd) != 1)</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :                 return exdrINT;</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;sym_size,1,xd) != 1)</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :                 return exdrINT;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;x_size,1,xd) != 1)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :                 return exdrINT;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;v_size,1,xd) != 1)</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :                 return exdrINT;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;f_size,1,xd) != 1)</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :                 return exdrINT;</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;natoms,1,xd) != 1)</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :                 return exdrINT;</a>
+<a name="171"><span class="lineNum">     171 </span>            :         </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         87 :         if ((result = nFloatSize(sh,&amp;nflsz)) != exdrOK)</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :                 return result;</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         87 :         sh-&gt;bDouble = (nflsz == sizeof(double));</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :         </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;step,1,xd) != 1)</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :                 return exdrINT;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         87 :         if (xdrfile_read_int(&amp;sh-&gt;nre,1,xd) != 1)</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :                 return exdrINT;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         87 :         if (sh-&gt;bDouble) </span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :         if (xdrfile_read_double(&amp;sh-&gt;td,1,xd) != 1)</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :             return exdrDOUBLE;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :         sh-&gt;tf = sh-&gt;td;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :         if (xdrfile_read_double(&amp;sh-&gt;lambdad,1,xd) != 1)</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :             return exdrDOUBLE;</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :         sh-&gt;lambdaf = sh-&gt;lambdad;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     }</a>
+<a name="189"><span class="lineNum">     189 </span>            :         else </a>
+<a name="190"><span class="lineNum">     190 </span>            :     {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         87 :         if (xdrfile_read_float(&amp;sh-&gt;tf,1,xd) != 1)</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :             return exdrFLOAT;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         87 :         sh-&gt;td = sh-&gt;tf;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         87 :         if (xdrfile_read_float(&amp;sh-&gt;lambdaf,1,xd) != 1)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :             return exdrFLOAT;</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         87 :         sh-&gt;lambdad = sh-&gt;lambdaf;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            :   </a>
+<a name="199"><span class="lineNum">     199 </span>            :     return exdrOK;</a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         84 : static int do_htrn(XDRFILE *xd,mybool bRead,t_trnheader *sh,</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :                                    matrix box,rvec *x,rvec *v,rvec *f)</a>
+<a name="204"><span class="lineNum">     204 </span>            : {</a>
+<a name="205"><span class="lineNum">     205 </span>            :         double pvd[DIM*DIM];</a>
+<a name="206"><span class="lineNum">     206 </span>            :         double *dx=NULL;</a>
+<a name="207"><span class="lineNum">     207 </span>            :         float  pvf[DIM*DIM];</a>
+<a name="208"><span class="lineNum">     208 </span>            :         float  *fx=NULL;</a>
+<a name="209"><span class="lineNum">     209 </span>            :         int    i,j;</a>
+<a name="210"><span class="lineNum">     210 </span>            :         </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         84 :         if (sh-&gt;bDouble) </span></a>
+<a name="212"><span class="lineNum">     212 </span>            :         {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :                 if (sh-&gt;box_size != 0) </span></a>
+<a name="214"><span class="lineNum">     214 </span>            :         {</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :             if (!bRead) </span></a>
+<a name="216"><span class="lineNum">     216 </span>            :             {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;DIM); i++)</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :                         if (NULL != box)</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :                         {</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :                             pvd[i*DIM+j] = box[i][j];</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :                         }</a>
+<a name="223"><span class="lineNum">     223 </span>            :             }</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :             if (xdrfile_read_double(pvd,DIM*DIM,xd) == DIM*DIM) </span></a>
+<a name="225"><span class="lineNum">     225 </span>            :             {</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;DIM); i++)</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :                         if (NULL != box)</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :                         {</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :                             box[i][j] = pvd[i*DIM+j];</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :                         }</a>
+<a name="232"><span class="lineNum">     232 </span>            :             }</a>
+<a name="233"><span class="lineNum">     233 </span>            :             else</a>
+<a name="234"><span class="lineNum">     234 </span>            :                 return exdrDOUBLE;</a>
+<a name="235"><span class="lineNum">     235 </span>            :         }</a>
+<a name="236"><span class="lineNum">     236 </span>            :                         </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :                 if (sh-&gt;vir_size != 0) </span></a>
+<a name="238"><span class="lineNum">     238 </span>            :         {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :             if (xdrfile_read_double(pvd,DIM*DIM,xd) != DIM*DIM) </span></a>
+<a name="240"><span class="lineNum">     240 </span>            :                 return exdrDOUBLE;</a>
+<a name="241"><span class="lineNum">     241 </span>            :         }</a>
+<a name="242"><span class="lineNum">     242 </span>            :                 </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :                 if (sh-&gt;pres_size!= 0) </span></a>
+<a name="244"><span class="lineNum">     244 </span>            :         {</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :             if (xdrfile_read_double(pvd,DIM*DIM,xd) != DIM*DIM) </span></a>
+<a name="246"><span class="lineNum">     246 </span>            :                 return exdrDOUBLE;</a>
+<a name="247"><span class="lineNum">     247 </span>            :         }</a>
+<a name="248"><span class="lineNum">     248 </span>            :                 </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :                 if ((sh-&gt;x_size != 0) || (sh-&gt;v_size != 0) || (sh-&gt;f_size != 0)) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :                         dx = (double *)calloc(sh-&gt;natoms*DIM,sizeof(dx[0]));</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :                         if (NULL == dx)</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :                                 return exdrNOMEM;</a>
+<a name="253"><span class="lineNum">     253 </span>            :                 }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :                 if (sh-&gt;x_size   != 0) </span></a>
+<a name="255"><span class="lineNum">     255 </span>            :         {</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :             if (!bRead) </span></a>
+<a name="257"><span class="lineNum">     257 </span>            :             {</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :                         if (NULL != x)</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :                         {</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :                             dx[i*DIM+j] = x[i][j];</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :                         }</a>
+<a name="264"><span class="lineNum">     264 </span>            :             }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :             if (xdrfile_read_double(dx,sh-&gt;natoms*DIM,xd) == sh-&gt;natoms*DIM)</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :             {</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :                 if (bRead) </span></a>
+<a name="268"><span class="lineNum">     268 </span>            :                 {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :                     for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :                         for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :                             if (NULL != x)</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :                             {</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :                                 x[i][j] = dx[i*DIM+j];</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :                             }</a>
+<a name="275"><span class="lineNum">     275 </span>            :                 }</a>
+<a name="276"><span class="lineNum">     276 </span>            :             }</a>
+<a name="277"><span class="lineNum">     277 </span>            :             else</a>
+<a name="278"><span class="lineNum">     278 </span>            :                 return exdrDOUBLE;</a>
+<a name="279"><span class="lineNum">     279 </span>            :         }</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :                 if (sh-&gt;v_size   != 0) </span></a>
+<a name="281"><span class="lineNum">     281 </span>            :         {</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :             if (!bRead) </span></a>
+<a name="283"><span class="lineNum">     283 </span>            :             {</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :                         if (NULL != x)</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :                         {</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :                             dx[i*DIM+j] = v[i][j];</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :                         }</a>
+<a name="290"><span class="lineNum">     290 </span>            :             }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :             if (xdrfile_read_double(dx,sh-&gt;natoms*DIM,xd) == sh-&gt;natoms*DIM)</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :             {</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :                         if (NULL != v)</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :                         {</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :                             v[i][j] = dx[i*DIM+j];</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :                         }</a>
+<a name="299"><span class="lineNum">     299 </span>            :             }</a>
+<a name="300"><span class="lineNum">     300 </span>            :             else</a>
+<a name="301"><span class="lineNum">     301 </span>            :                 return exdrDOUBLE;</a>
+<a name="302"><span class="lineNum">     302 </span>            :         }</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :                 if (sh-&gt;f_size   != 0) </span></a>
+<a name="304"><span class="lineNum">     304 </span>            :         {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :             if (!bRead) </span></a>
+<a name="306"><span class="lineNum">     306 </span>            :             {</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :                         if (NULL != x)</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :                         {</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :                             dx[i*DIM+j] = f[i][j];</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :                         }</a>
+<a name="313"><span class="lineNum">     313 </span>            :             }</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :             if (xdrfile_read_double(dx,sh-&gt;natoms*DIM,xd) == sh-&gt;natoms*DIM)</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :             {</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :                 {</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :                     {</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :                         if (NULL != f)</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :                         {</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :                             f[i][j] = dx[i*DIM+j];</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :                         }</a>
+<a name="324"><span class="lineNum">     324 </span>            :                     }</a>
+<a name="325"><span class="lineNum">     325 </span>            :                 }</a>
+<a name="326"><span class="lineNum">     326 </span>            :             }</a>
+<a name="327"><span class="lineNum">     327 </span>            :             else</a>
+<a name="328"><span class="lineNum">     328 </span>            :                 return exdrDOUBLE;</a>
+<a name="329"><span class="lineNum">     329 </span>            :         }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :                 if ((sh-&gt;x_size != 0) || (sh-&gt;v_size != 0) || (sh-&gt;f_size != 0)) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :                         free(dx);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :                 }</a>
+<a name="333"><span class="lineNum">     333 </span>            :         }</a>
+<a name="334"><span class="lineNum">     334 </span>            :         else</a>
+<a name="335"><span class="lineNum">     335 </span>            :                 /* Float */</a>
+<a name="336"><span class="lineNum">     336 </span>            :         {</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         84 :                 if (sh-&gt;box_size != 0) </span></a>
+<a name="338"><span class="lineNum">     338 </span>            :         {</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         84 :             if (!bRead) </span></a>
+<a name="340"><span class="lineNum">     340 </span>            :             {</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        192 :                 for(i=0; (i&lt;DIM); i++)</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">        576 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">        432 :                         if (NULL != box)</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :                         {</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        432 :                             pvf[i*DIM+j] = box[i][j];</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :                         }</a>
+<a name="347"><span class="lineNum">     347 </span>            :             }</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         84 :             if (xdrfile_read_float(pvf,DIM*DIM,xd) == DIM*DIM) </span></a>
+<a name="349"><span class="lineNum">     349 </span>            :             {</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        336 :                 for(i=0; (i&lt;DIM); i++)</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :                 {</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       1008 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :                     {</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        756 :                         if (NULL != box)</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :                         {</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        756 :                             box[i][j] = pvf[i*DIM+j];</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :                         }</a>
+<a name="358"><span class="lineNum">     358 </span>            :                     }</a>
+<a name="359"><span class="lineNum">     359 </span>            :                 }</a>
+<a name="360"><span class="lineNum">     360 </span>            :             }</a>
+<a name="361"><span class="lineNum">     361 </span>            :             else</a>
+<a name="362"><span class="lineNum">     362 </span>            :                 return exdrFLOAT;</a>
+<a name="363"><span class="lineNum">     363 </span>            :         }</a>
+<a name="364"><span class="lineNum">     364 </span>            :                         </a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         84 :                 if (sh-&gt;vir_size != 0) </span></a>
+<a name="366"><span class="lineNum">     366 </span>            :         {</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :             if (xdrfile_read_float(pvf,DIM*DIM,xd) != DIM*DIM) </span></a>
+<a name="368"><span class="lineNum">     368 </span>            :                 return exdrFLOAT;</a>
+<a name="369"><span class="lineNum">     369 </span>            :         }</a>
+<a name="370"><span class="lineNum">     370 </span>            :                 </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         84 :                 if (sh-&gt;pres_size!= 0) </span></a>
+<a name="372"><span class="lineNum">     372 </span>            :         {</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :             if (xdrfile_read_float(pvf,DIM*DIM,xd) != DIM*DIM) </span></a>
+<a name="374"><span class="lineNum">     374 </span>            :                 return exdrFLOAT;</a>
+<a name="375"><span class="lineNum">     375 </span>            :         }</a>
+<a name="376"><span class="lineNum">     376 </span>            :                 </a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         84 :                 if ((sh-&gt;x_size != 0) || (sh-&gt;v_size != 0) || (sh-&gt;f_size != 0)) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         84 :                         fx = (float *)calloc(sh-&gt;natoms*DIM,sizeof(fx[0]));</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         84 :                         if (NULL == fx)</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :                                 return exdrNOMEM;</a>
+<a name="381"><span class="lineNum">     381 </span>            :                 }</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         84 :                 if (sh-&gt;x_size   != 0) </span></a>
+<a name="383"><span class="lineNum">     383 </span>            :         {</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         84 :             if (!bRead) </span></a>
+<a name="385"><span class="lineNum">     385 </span>            :             {</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       2424 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       9504 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       7128 :                         if (NULL != x)</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :                         {</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">       7128 :                             fx[i*DIM+j] = x[i][j];</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :                         }</a>
+<a name="392"><span class="lineNum">     392 </span>            :             }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         84 :             if (xdrfile_read_float(fx,sh-&gt;natoms*DIM,xd) == sh-&gt;natoms*DIM)</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :             {</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         84 :                 if (bRead) </span></a>
+<a name="396"><span class="lineNum">     396 </span>            :                 {</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        828 :                     for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       3168 :                         for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       2376 :                             if (NULL != x)</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       2376 :                                 x[i][j] = fx[i*DIM+j];</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :                 }</a>
+<a name="402"><span class="lineNum">     402 </span>            :             }</a>
+<a name="403"><span class="lineNum">     403 </span>            :             else</a>
+<a name="404"><span class="lineNum">     404 </span>            :                 return exdrFLOAT;</a>
+<a name="405"><span class="lineNum">     405 </span>            :         }</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         84 :                 if (sh-&gt;v_size   != 0) </span></a>
+<a name="407"><span class="lineNum">     407 </span>            :         {</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :             if (!bRead) </span></a>
+<a name="409"><span class="lineNum">     409 </span>            :             {</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :                         if (NULL != x)</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :                         {</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :                             fx[i*DIM+j] = v[i][j];</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :                         }</a>
+<a name="416"><span class="lineNum">     416 </span>            :             }</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :             if (xdrfile_read_float(fx,sh-&gt;natoms*DIM,xd) == sh-&gt;natoms*DIM)</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :             {</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :                         if (NULL != v)</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :                             v[i][j] = fx[i*DIM+j];</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :             }</a>
+<a name="424"><span class="lineNum">     424 </span>            :             else</a>
+<a name="425"><span class="lineNum">     425 </span>            :                 return exdrFLOAT;</a>
+<a name="426"><span class="lineNum">     426 </span>            :         }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         84 :                 if (sh-&gt;f_size   != 0) </span></a>
+<a name="428"><span class="lineNum">     428 </span>            :         {</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :            if (!bRead) </span></a>
+<a name="430"><span class="lineNum">     430 </span>            :             {</a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :                         if (NULL != x)</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :                         {</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :                             fx[i*DIM+j] = f[i][j];</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :                         }</a>
+<a name="437"><span class="lineNum">     437 </span>            :             }</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :              if (xdrfile_read_float(fx,sh-&gt;natoms*DIM,xd) == sh-&gt;natoms*DIM)</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :             {</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :                 for(i=0; (i&lt;sh-&gt;natoms); i++)</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :                     for(j=0; (j&lt;DIM); j++)</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :                         if (NULL != f)</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :                             f[i][j] = fx[i*DIM+j];</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :             }</a>
+<a name="445"><span class="lineNum">     445 </span>            :             else</a>
+<a name="446"><span class="lineNum">     446 </span>            :                 return exdrFLOAT;</a>
+<a name="447"><span class="lineNum">     447 </span>            :         }</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         84 :                 if ((sh-&gt;x_size != 0) || (sh-&gt;v_size != 0) || (sh-&gt;f_size != 0)) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         84 :                         free(fx);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :                 }</a>
+<a name="451"><span class="lineNum">     451 </span>            :         }</a>
+<a name="452"><span class="lineNum">     452 </span>            :         return exdrOK;</a>
+<a name="453"><span class="lineNum">     453 </span>            : }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         87 : static int do_trn(XDRFILE *xd,mybool bRead,int *step,float *t,float *lambda,</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :                                   matrix box,int *natoms,rvec *x,rvec *v,rvec *f)</a>
+<a name="457"><span class="lineNum">     457 </span>            : {</a>
+<a name="458"><span class="lineNum">     458 </span>            :     t_trnheader *sh;</a>
+<a name="459"><span class="lineNum">     459 </span>            :     int result;</a>
+<a name="460"><span class="lineNum">     460 </span>            :   </a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         87 :     sh = (t_trnheader *)calloc(1,sizeof(*sh));</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :   </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         87 :     if (!bRead) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         48 :         sh-&gt;box_size = (NULL != box) ? sizeof(matrix):0;</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         48 :         sh-&gt;x_size   = ((NULL != x) ? (*natoms*sizeof(x[0])):0);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         48 :         sh-&gt;v_size   = ((NULL != v) ? (*natoms*sizeof(v[0])):0);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         48 :         sh-&gt;f_size   = ((NULL != f) ? (*natoms*sizeof(f[0])):0);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         48 :         sh-&gt;natoms = *natoms;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         48 :         sh-&gt;step   = *step;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         48 :         sh-&gt;nre    = 0;</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         48 :         sh-&gt;td      = *t;</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         48 :         sh-&gt;lambdad = *lambda;</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         48 :         sh-&gt;tf      = *t;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         48 :         sh-&gt;lambdaf = *lambda;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :     }</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         87 :     if ((result = do_trnheader(xd,bRead,sh)) != exdrOK)</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :         return result;</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         84 :     if (bRead) {</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         36 :         *natoms = sh-&gt;natoms;</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         36 :         *step   = sh-&gt;step;</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         36 :         *t      = sh-&gt;td;</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         36 :         *lambda = sh-&gt;lambdad;</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :     }</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         84 :     if ((result = do_htrn(xd,bRead,sh,box,x,v,f)) != exdrOK)</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :         return result;</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">         84 :     free(sh);</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         84 :     return exdrOK;</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : }</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            : /************************************************************</a>
+<a name="493"><span class="lineNum">     493 </span>            :  *</a>
+<a name="494"><span class="lineNum">     494 </span>            :  *  The following routines are the exported ones</a>
+<a name="495"><span class="lineNum">     495 </span>            :  *</a>
+<a name="496"><span class="lineNum">     496 </span>            :  ************************************************************/</a>
+<a name="497"><span class="lineNum">     497 </span>            :  </a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          3 : int read_trr_natoms(char *fn,int *natoms)</span></a>
+<a name="499"><span class="lineNum">     499 </span>            : {</a>
+<a name="500"><span class="lineNum">     500 </span>            :         XDRFILE *xd;</a>
+<a name="501"><span class="lineNum">     501 </span>            :         t_trnheader sh;</a>
+<a name="502"><span class="lineNum">     502 </span>            :         int  result;</a>
+<a name="503"><span class="lineNum">     503 </span>            :         </a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          3 :         xd = xdrfile_open(fn,&quot;r&quot;);</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          3 :         if (NULL == xd)</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :                 return exdrFILENOTFOUND;</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          3 :         if ((result = do_trnheader(xd,1,&amp;sh)) != exdrOK)</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :                 return result;</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          3 :         xdrfile_close(xd);</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">          3 :         *natoms = sh.natoms;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :         </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">          3 :         return exdrOK;</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         48 : int write_trr(XDRFILE *xd,int natoms,int step,float t,float lambda,</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :                           matrix box,rvec *x,rvec *v,rvec *f)</a>
+<a name="517"><span class="lineNum">     517 </span>            : {</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         48 :         return do_trn(xd,0,&amp;step,&amp;t,&amp;lambda,box,&amp;natoms,x,v,f);</span></a>
+<a name="519"><span class="lineNum">     519 </span>            : }</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         39 : int read_trr(XDRFILE *xd,int natoms,int *step,float *t,float *lambda,</span></a>
+<a name="522"><span class="lineNum">     522 </span>            :                          matrix box,rvec *x,rvec *v,rvec *f)</a>
+<a name="523"><span class="lineNum">     523 </span>            : {</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         39 :         return do_trn(xd,1,step,t,lambda,box,&amp;natoms,x,v,f);</span></a>
+<a name="525"><span class="lineNum">     525 </span>            : }</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            : }</a>
+<a name="528"><span class="lineNum">     528 </span>            : }</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile_xtc.cpp.func-sort-c.html b/coverage-libs/xdrfile/xdrfile_xtc.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7e5965933d
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile_xtc.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile_xtc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile_xtc.cpp<span style="font-size: 80%;"> (<a href="xdrfile_xtc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="xdrfile_xtc.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#116">_ZN4PLMD7xdrfile15read_xtc_natomsEPcPi</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#131">_ZN4PLMD7xdrfile8read_xtcEPNS0_7XDRFILEEiPiPfPA3_fS6_S4_</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#147">_ZN4PLMD7xdrfile9write_xtcEPNS0_7XDRFILEEiifPA3_fS4_f</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#89">_ZN4PLMD7xdrfileL9xtc_coordEPNS0_7XDRFILEEPiPA3_fS5_Pfi</a></td>
+              <td class="coverFnHi">100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#64">_ZN4PLMD7xdrfileL10xtc_headerEPNS0_7XDRFILEEPiS3_Pfi</a></td>
+              <td class="coverFnHi">104</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile_xtc.cpp.func.html b/coverage-libs/xdrfile/xdrfile_xtc.cpp.func.html
new file mode 100644
index 0000000000..747586db43
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile_xtc.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile_xtc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile_xtc.cpp<span style="font-size: 80%;"> (<a href="xdrfile_xtc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="xdrfile_xtc.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#116">_ZN4PLMD7xdrfile15read_xtc_natomsEPcPi</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#131">_ZN4PLMD7xdrfile8read_xtcEPNS0_7XDRFILEEiPiPfPA3_fS6_S4_</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#147">_ZN4PLMD7xdrfile9write_xtcEPNS0_7XDRFILEEiifPA3_fS4_f</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#64">_ZN4PLMD7xdrfileL10xtc_headerEPNS0_7XDRFILEEPiS3_Pfi</a></td>
+              <td class="coverFnHi">104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="xdrfile_xtc.cpp.gcov.html#89">_ZN4PLMD7xdrfileL9xtc_coordEPNS0_7XDRFILEEPiPA3_fS5_Pfi</a></td>
+              <td class="coverFnHi">100</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage-libs/xdrfile/xdrfile_xtc.cpp.gcov.html b/coverage-libs/xdrfile/xdrfile_xtc.cpp.gcov.html
new file mode 100644
index 0000000000..2a098fded9
--- /dev/null
+++ b/coverage-libs/xdrfile/xdrfile_xtc.cpp.gcov.html
@@ -0,0 +1,241 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage (other modules) - xdrfile/xdrfile_xtc.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">xdrfile</a> - xdrfile_xtc.cpp<span style="font-size: 80%;"> (source / <a href="xdrfile_xtc.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage (other modules)</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:16</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2009-2014, Erik Lindahl &amp; David van der Spoel</a>
+<a name="3"><span class="lineNum">       3 </span>            : All rights reserved.</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            : Redistribution and use in source and binary forms, with or without</a>
+<a name="6"><span class="lineNum">       6 </span>            : modification, are permitted provided that the following conditions are met:</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : 1. Redistributions of source code must retain the above copyright notice, this</a>
+<a name="9"><span class="lineNum">       9 </span>            : list of conditions and the following disclaimer.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            : 2. Redistributions in binary form must reproduce the above copyright notice,</a>
+<a name="12"><span class="lineNum">      12 </span>            : this list of conditions and the following disclaimer in the documentation</a>
+<a name="13"><span class="lineNum">      13 </span>            : and/or other materials provided with the distribution.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            : THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</a>
+<a name="16"><span class="lineNum">      16 </span>            : AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</a>
+<a name="17"><span class="lineNum">      17 </span>            : IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</a>
+<a name="18"><span class="lineNum">      18 </span>            : DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</a>
+<a name="19"><span class="lineNum">      19 </span>            : FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</a>
+<a name="20"><span class="lineNum">      20 </span>            : DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</a>
+<a name="21"><span class="lineNum">      21 </span>            : SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</a>
+<a name="22"><span class="lineNum">      22 </span>            : CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</a>
+<a name="23"><span class="lineNum">      23 </span>            : OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</a>
+<a name="24"><span class="lineNum">      24 </span>            : OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</a>
+<a name="25"><span class="lineNum">      25 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="26"><span class="lineNum">      26 </span>            : /* -*- mode: c; tab-width: 4; indent-tabs-mode: t; c-basic-offset: 4 -*- </a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * $Id$</a>
+<a name="29"><span class="lineNum">      29 </span>            :  *</a>
+<a name="30"><span class="lineNum">      30 </span>            :  * Copyright (c) 2009-2014, Erik Lindahl &amp; David van der Spoel</a>
+<a name="31"><span class="lineNum">      31 </span>            :  * All rights reserved.</a>
+<a name="32"><span class="lineNum">      32 </span>            :  *</a>
+<a name="33"><span class="lineNum">      33 </span>            :  * Redistribution and use in source and binary forms, with or without</a>
+<a name="34"><span class="lineNum">      34 </span>            :  * modification, are permitted provided that the following conditions are met:</a>
+<a name="35"><span class="lineNum">      35 </span>            :  *</a>
+<a name="36"><span class="lineNum">      36 </span>            :  * 1. Redistributions of source code must retain the above copyright notice, this</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * list of conditions and the following disclaimer.</a>
+<a name="38"><span class="lineNum">      38 </span>            :  *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * 2. Redistributions in binary form must reproduce the above copyright notice,</a>
+<a name="40"><span class="lineNum">      40 </span>            :  * this list of conditions and the following disclaimer in the documentation</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * and/or other materials provided with the distribution.</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS &quot;AS IS&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE</a>
+<a name="46"><span class="lineNum">      46 </span>            :  * DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE</a>
+<a name="47"><span class="lineNum">      47 </span>            :  * FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR</a>
+<a name="49"><span class="lineNum">      49 </span>            :  * SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,</a>
+<a name="51"><span class="lineNum">      51 </span>            :  * OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.</a>
+<a name="53"><span class="lineNum">      53 </span>            :  */</a>
+<a name="54"><span class="lineNum">      54 </span>            :  </a>
+<a name="55"><span class="lineNum">      55 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="56"><span class="lineNum">      56 </span>            : #include &quot;xdrfile.h&quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &quot;xdrfile_xtc.h&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :         </a>
+<a name="59"><span class="lineNum">      59 </span>            : #define MAGIC 1995</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace PLMD {</a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace xdrfile {</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : enum { FALSE, TRUE };</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        104 : static int xtc_header(XDRFILE *xd,int *natoms,int *step,float *time,mybool bRead)</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : {</a>
+<a name="68"><span class="lineNum">      68 </span>            :         int result,magic,n=1;</a>
+<a name="69"><span class="lineNum">      69 </span>            :         </a>
+<a name="70"><span class="lineNum">      70 </span>            :         /* Note: read is same as write. He he he */</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        104 :         magic  = MAGIC;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        104 :         if ((result = xdrfile_write_int(&amp;magic,n,xd)) != n)</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :                 {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          2 :                         if (bRead)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :                                 return exdrENDOFFILE;</a>
+<a name="76"><span class="lineNum">      76 </span>            :                         else</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :                                 return exdrINT;</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :                 }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        102 :         if (magic != MAGIC)</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :                 return exdrMAGIC;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        102 :         if ((result = xdrfile_write_int(natoms,n,xd)) != n)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :                 return exdrINT;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        102 :         if ((result = xdrfile_write_int(step,n,xd)) != n)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :                 return exdrINT;</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        102 :         if ((result = xdrfile_write_float(time,n,xd)) != n)</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :                 return exdrFLOAT;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :         </a>
+<a name="88"><span class="lineNum">      88 </span>            :         return exdrOK;</a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        100 : static int xtc_coord(XDRFILE *xd,int *natoms,matrix box,rvec *x,float *prec,</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :                                          mybool bRead)</a>
+<a name="93"><span class="lineNum">      93 </span>            : {</a>
+<a name="94"><span class="lineNum">      94 </span>            :         int i,j,result;</a>
+<a name="95"><span class="lineNum">      95 </span>            :     </a>
+<a name="96"><span class="lineNum">      96 </span>            :         /* box */</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        100 :         result = xdrfile_read_float(box[0],DIM*DIM,xd);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        100 :         if (DIM*DIM != result)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :                 return exdrFLOAT;</a>
+<a name="100"><span class="lineNum">     100 </span>            :         else </a>
+<a name="101"><span class="lineNum">     101 </span>            :                 {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        100 :                         if (bRead)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :                                 {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         28 :                                         result = xdrfile_decompress_coord_float(x[0],natoms,prec,xd); </span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         28 :                                         if (result != *natoms)</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :                                                 return exdr3DX;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :                                 }</a>
+<a name="108"><span class="lineNum">     108 </span>            :                         else</a>
+<a name="109"><span class="lineNum">     109 </span>            :                                 {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         72 :                                         result = xdrfile_compress_coord_float(x[0],*natoms,*prec,xd); </span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         72 :                                         if (result != *natoms)</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :                                                 return exdr3DX;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :                                 }</a>
+<a name="114"><span class="lineNum">     114 </span>            :                 }</a>
+<a name="115"><span class="lineNum">     115 </span>            :         return exdrOK;</a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 : int read_xtc_natoms(char *fn,int *natoms)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : {</a>
+<a name="120"><span class="lineNum">     120 </span>            :         XDRFILE *xd;</a>
+<a name="121"><span class="lineNum">     121 </span>            :         int step,result;</a>
+<a name="122"><span class="lineNum">     122 </span>            :         float time;</a>
+<a name="123"><span class="lineNum">     123 </span>            :         </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :         xd = xdrfile_open(fn,&quot;r&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :         if (NULL == xd)</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :                 return exdrFILENOTFOUND;</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :         result = xtc_header(xd,natoms,&amp;step,&amp;time,TRUE);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          2 :         xdrfile_close(xd);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :         </a>
+<a name="130"><span class="lineNum">     130 </span>            :         return result;</a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         30 : int read_xtc(XDRFILE *xd,</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :                          int natoms,int *step,float *time,</a>
+<a name="135"><span class="lineNum">     135 </span>            :                          matrix box,rvec *x,float *prec)</a>
+<a name="136"><span class="lineNum">     136 </span>            : /* Read subsequent frames */</a>
+<a name="137"><span class="lineNum">     137 </span>            : {</a>
+<a name="138"><span class="lineNum">     138 </span>            :         int result;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         30 :         if ((result = xtc_header(xd,&amp;natoms,step,time,TRUE)) != exdrOK)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :                 return result;</a>
+<a name="142"><span class="lineNum">     142 </span>            :           </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         28 :         if ((result = xtc_coord(xd,&amp;natoms,box,x,prec,1)) != exdrOK)</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :                 return result;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   </a>
+<a name="146"><span class="lineNum">     146 </span>            :         return exdrOK;</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         72 : int write_xtc(XDRFILE *xd,</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :                           int natoms,int step,float time,</a>
+<a name="151"><span class="lineNum">     151 </span>            :                           matrix box,rvec *x,float prec)</a>
+<a name="152"><span class="lineNum">     152 </span>            : /* Write a frame to xtc file */</a>
+<a name="153"><span class="lineNum">     153 </span>            : {</a>
+<a name="154"><span class="lineNum">     154 </span>            :         int result;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         72 :         if ((result = xtc_header(xd,&amp;natoms,&amp;step,&amp;time,FALSE)) != exdrOK)</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :                 return result;</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         72 :         if ((result = xtc_coord(xd,&amp;natoms,box,x,&amp;prec,0)) != exdrOK)</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :                 return result;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   </a>
+<a name="162"><span class="lineNum">     162 </span>            :         return exdrOK;</a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ActionWithInputMatrix.cpp.func-sort-c.html b/coverage/adjmat/ActionWithInputMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..18bdc96290
--- /dev/null
+++ b/coverage/adjmat/ActionWithInputMatrix.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ActionWithInputMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ActionWithInputMatrix.cpp<span style="font-size: 80%;"> (<a href="ActionWithInputMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithInputMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#36">_ZN4PLMD6adjmat21ActionWithInputMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#142">_ZNK4PLMD6adjmat21ActionWithInputMatrix18getBaseMultiColvarERKj</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#36">_ZN4PLMD6adjmat21ActionWithInputMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#137">_ZNK4PLMD6adjmat21ActionWithInputMatrix23getNumberOfAtomsInGroupERKj</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#30">_ZN4PLMD6adjmat21ActionWithInputMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#126">_ZNK4PLMD6adjmat21ActionWithInputMatrix20getNumberOfNodeTypesEv</a></td>
+              <td class="coverFnHi">66</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#73">_ZNK4PLMD6adjmat21ActionWithInputMatrix29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">504</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#98">_ZNK4PLMD6adjmat21ActionWithInputMatrix24addConnectionDerivativesERKjS3_RNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">1440</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#109">_ZNK4PLMD6adjmat21ActionWithInputMatrix19getInputDerivativesERKjRKbRKNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">1679</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#86">_ZNK4PLMD6adjmat21ActionWithInputMatrix12getInputDataERKjRKbRKNS_11multicolvar13AtomValuePackERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#132">_ZNK4PLMD6adjmat21ActionWithInputMatrix21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">2181</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#61">_ZN4PLMD6adjmat21ActionWithInputMatrix22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">13250</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#77">_ZNK4PLMD6adjmat21ActionWithInputMatrix23retrieveConnectionValueERKjS3_RSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">46452</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#147">_ZNK4PLMD6adjmat21ActionWithInputMatrix29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnHi">54763</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#69">_ZNK4PLMD6adjmat21ActionWithInputMatrix18getAdjacencyVesselEv</a></td>
+              <td class="coverFnHi">78058</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#65">_ZNK4PLMD6adjmat21ActionWithInputMatrix16getNumberOfNodesEv</a></td>
+              <td class="coverFnHi">16261547</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ActionWithInputMatrix.cpp.func.html b/coverage/adjmat/ActionWithInputMatrix.cpp.func.html
new file mode 100644
index 0000000000..9efb51137a
--- /dev/null
+++ b/coverage/adjmat/ActionWithInputMatrix.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ActionWithInputMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ActionWithInputMatrix.cpp<span style="font-size: 80%;"> (<a href="ActionWithInputMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithInputMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#30">_ZN4PLMD6adjmat21ActionWithInputMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#61">_ZN4PLMD6adjmat21ActionWithInputMatrix22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">13250</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#36">_ZN4PLMD6adjmat21ActionWithInputMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#36">_ZN4PLMD6adjmat21ActionWithInputMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#86">_ZNK4PLMD6adjmat21ActionWithInputMatrix12getInputDataERKjRKbRKNS_11multicolvar13AtomValuePackERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#65">_ZNK4PLMD6adjmat21ActionWithInputMatrix16getNumberOfNodesEv</a></td>
+              <td class="coverFnHi">16261547</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#69">_ZNK4PLMD6adjmat21ActionWithInputMatrix18getAdjacencyVesselEv</a></td>
+              <td class="coverFnHi">78058</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#142">_ZNK4PLMD6adjmat21ActionWithInputMatrix18getBaseMultiColvarERKj</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#109">_ZNK4PLMD6adjmat21ActionWithInputMatrix19getInputDerivativesERKjRKbRKNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">1679</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#126">_ZNK4PLMD6adjmat21ActionWithInputMatrix20getNumberOfNodeTypesEv</a></td>
+              <td class="coverFnHi">66</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#132">_ZNK4PLMD6adjmat21ActionWithInputMatrix21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">2181</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#137">_ZNK4PLMD6adjmat21ActionWithInputMatrix23getNumberOfAtomsInGroupERKj</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#77">_ZNK4PLMD6adjmat21ActionWithInputMatrix23retrieveConnectionValueERKjS3_RSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">46452</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#98">_ZNK4PLMD6adjmat21ActionWithInputMatrix24addConnectionDerivativesERKjS3_RNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">1440</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#73">_ZNK4PLMD6adjmat21ActionWithInputMatrix29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">504</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.cpp.gcov.html#147">_ZNK4PLMD6adjmat21ActionWithInputMatrix29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnHi">54763</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ActionWithInputMatrix.cpp.gcov.html b/coverage/adjmat/ActionWithInputMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..59d22e383e
--- /dev/null
+++ b/coverage/adjmat/ActionWithInputMatrix.cpp.gcov.html
@@ -0,0 +1,230 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ActionWithInputMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ActionWithInputMatrix.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithInputMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithInputMatrix.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace adjmat {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         37 : void ActionWithInputMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         37 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         74 :   keys.add(&quot;compulsory&quot;,&quot;MATRIX&quot;,&quot;the action that calculates the adjacency matrix vessel we would like to analyze&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         37 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         27 : ActionWithInputMatrix::ActionWithInputMatrix(const ActionOptions&amp; ao):</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   Action(ao),</a>
+<a name="40"><span class="lineNum">      40 </span>            :   MultiColvarBase(ao),</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         27 :   mymatrix(NULL)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         27 :   matsums=true;</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         54 :   if( keywords.exists(&quot;MATRIX&quot;) ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :     std::vector&lt;AtomNumber&gt; fake_atoms;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         50 :     if( !parseMultiColvarAtomList(&quot;MATRIX&quot;,-1,fake_atoms ) ) error(&quot;unable to interpret input matrix&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         25 :     if( mybasemulticolvars.size()!=1 ) error(&quot;should be exactly one matrix input&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            :     // Retrieve the adjacency matrix of interest</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         25 :     for(unsigned i=0; i&lt;mybasemulticolvars[0]-&gt;getNumberOfVessels(); ++i) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         25 :       mymatrix = dynamic_cast&lt;AdjacencyMatrixVessel*&gt;( mybasemulticolvars[0]-&gt;getPntrToVessel(i) );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         25 :       if( mymatrix ) break ;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :     }</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         25 :     if( !mymatrix ) error( mybasemulticolvars[0]-&gt;getLabel() + &quot; does not calculate an adjacency matrix&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         25 :     atom_lab.resize(0); unsigned nnodes; // Delete all the atom labels that have been created</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         25 :     if( mymatrix-&gt;undirectedGraph() ) nnodes = (mymatrix-&gt;function)-&gt;ablocks[0].size();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          2 :     else nnodes = (mymatrix-&gt;function)-&gt;ablocks[0].size() + (mymatrix-&gt;function)-&gt;ablocks[1].size();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       6816 :     for(unsigned i=0; i&lt;nnodes; ++i) atom_lab.push_back( std::pair&lt;unsigned,unsigned&gt;( 1, i ) );</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         27 : }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      13250 : unsigned ActionWithInputMatrix::getNumberOfDerivatives() {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      13250 :   return (mymatrix-&gt;function)-&gt;getNumberOfDerivatives();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">   16261547 : unsigned ActionWithInputMatrix::getNumberOfNodes() const {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">   16261547 :   return (mymatrix-&gt;function)-&gt;ablocks[0].size();</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      78058 : AdjacencyMatrixVessel* ActionWithInputMatrix::getAdjacencyVessel() const {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      78058 :   return mymatrix;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        504 : AtomNumber ActionWithInputMatrix::getAbsoluteIndexOfCentralAtom(const unsigned&amp; i) const {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        504 :   return (mymatrix-&gt;function)-&gt;getAbsoluteIndexOfCentralAtom(i);</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      46452 : double ActionWithInputMatrix::retrieveConnectionValue( const unsigned&amp; i, const unsigned&amp; j, std::vector&lt;double&gt;&amp; vals ) const {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      46452 :   if( !mymatrix-&gt;matrixElementIsActive( i, j ) ) return 0;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      25360 :   unsigned myelem = mymatrix-&gt;getStoreIndexFromMatrixIndices( i, j );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   // unsigned vi; double df;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      25360 :   mymatrix-&gt;retrieveValueWithIndex( myelem, false, vals );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      25360 :   return vals[0]*vals[1];       // (mymatrix-&gt;function)-&gt;transformStoredValues( vals, vi, df );</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       2004 : void ActionWithInputMatrix::getInputData( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms, std::vector&lt;double&gt;&amp; orient0 ) const {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       2004 :   if( (mymatrix-&gt;function)-&gt;mybasemulticolvars.size()==0  ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        305 :     std::vector&lt;double&gt; tvals( mymatrix-&gt;getNumberOfComponents() ); orient0.assign(orient0.size(),0);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      38263 :     for(unsigned i=0; i&lt;mymatrix-&gt;getNumberOfColumns(); ++i) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      37958 :       if( mymatrix-&gt;undirectedGraph() &amp;&amp; ind==i ) continue;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      37678 :       orient0[1]+=retrieveConnectionValue( ind, i, tvals );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :     }</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        305 :     orient0[0]=1.0; return;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1699 :   (mymatrix-&gt;function)-&gt;getInputData( ind, normed, myatoms, orient0 );</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1440 : void ActionWithInputMatrix::addConnectionDerivatives( const unsigned&amp; i, const unsigned&amp; j, MultiValue&amp; myvals, MultiValue&amp; myvout ) const {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1440 :   if( !mymatrix-&gt;matrixElementIsActive( i, j ) ) return;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       1440 :   unsigned myelem = mymatrix-&gt;getStoreIndexFromMatrixIndices( i, j );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   // Get derivatives and add</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1440 :   mymatrix-&gt;retrieveDerivatives( myelem, false, myvals );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      31086 :   for(unsigned jd=0; jd&lt;myvals.getNumberActive(); ++jd) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      29646 :     unsigned ider=myvals.getActiveIndex(jd);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      29646 :     myvout.addDerivative( 1, ider, myvals.getDerivative( 1, ider ) );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1679 : MultiValue&amp; ActionWithInputMatrix::getInputDerivatives( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1679 :   if( (mymatrix-&gt;function)-&gt;mybasemulticolvars.size()==0  ) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         90 :     MultiValue&amp; myder=mymatrix-&gt;getTemporyMultiValue(0);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         90 :     if( myder.getNumberOfValues()!=2 || myder.getNumberOfDerivatives()!=(mymatrix-&gt;function)-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          3 :       myder.resize( 2, (mymatrix-&gt;function)-&gt;getNumberOfDerivatives() );</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         90 :     myder.clearAll();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         90 :     MultiValue myvals( (mymatrix-&gt;function)-&gt;getNumberOfQuantities(), (mymatrix-&gt;function)-&gt;getNumberOfDerivatives() );</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        885 :     for(unsigned i=0; i&lt;mymatrix-&gt;getNumberOfColumns(); ++i) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        795 :       if( mymatrix-&gt;undirectedGraph() &amp;&amp; ind==i ) continue;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        730 :       addConnectionDerivatives( ind, i, myvals, myder );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     }</a>
+<a name="123"><span class="lineNum">     123 </span>            :     myder.updateDynamicList(); return myder;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         90 :   }</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       1589 :   return (mymatrix-&gt;function)-&gt;getInputDerivatives( ind, normed, myatoms );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         66 : unsigned ActionWithInputMatrix::getNumberOfNodeTypes() const {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         66 :   unsigned size = (mymatrix-&gt;function)-&gt;mybasemulticolvars.size();</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   if( size==0 ) return 1;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   return size;</a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       2181 : unsigned ActionWithInputMatrix::getNumberOfQuantities() const {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       2181 :   if( (mymatrix-&gt;function)-&gt;mybasemulticolvars.size()==0 ) return 2;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       2082 :   return (mymatrix-&gt;function)-&gt;mybasemulticolvars[0]-&gt;getNumberOfQuantities();</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         34 : unsigned ActionWithInputMatrix::getNumberOfAtomsInGroup( const unsigned&amp; igrp ) const {</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   plumed_dbg_assert( igrp&lt;(mymatrix-&gt;function)-&gt;mybasemulticolvars.size() );</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         34 :   return (mymatrix-&gt;function)-&gt;mybasemulticolvars[igrp]-&gt;getFullNumberOfTasks();</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          7 : multicolvar::MultiColvarBase* ActionWithInputMatrix::getBaseMultiColvar( const unsigned&amp; igrp ) const {</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   plumed_dbg_assert( igrp&lt;(mymatrix-&gt;function)-&gt;mybasemulticolvars.size() );</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          7 :   return (mymatrix-&gt;function)-&gt;mybasemulticolvars[igrp];</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      54763 : Vector ActionWithInputMatrix::getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      54763 :   return (getAdjacencyVessel()-&gt;function)-&gt;getPositionOfAtomForLinkCells( iatom );</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ActionWithInputMatrix.h.func-sort-c.html b/coverage/adjmat/ActionWithInputMatrix.h.func-sort-c.html
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+  <title>LCOV - plumed test coverage - adjmat/ActionWithInputMatrix.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ActionWithInputMatrix.h<span style="font-size: 80%;"> (<a href="ActionWithInputMatrix.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithInputMatrix.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.h.gcov.html#63">_ZNK4PLMD6adjmat21ActionWithInputMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.h.gcov.html#58">_ZN4PLMD6adjmat21ActionWithInputMatrix10isPeriodicEv</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ActionWithInputMatrix.h.func.html b/coverage/adjmat/ActionWithInputMatrix.h.func.html
new file mode 100644
index 0000000000..e05df659b7
--- /dev/null
+++ b/coverage/adjmat/ActionWithInputMatrix.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ActionWithInputMatrix.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ActionWithInputMatrix.h<span style="font-size: 80%;"> (<a href="ActionWithInputMatrix.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithInputMatrix.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.h.gcov.html#58">_ZN4PLMD6adjmat21ActionWithInputMatrix10isPeriodicEv</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputMatrix.h.gcov.html#63">_ZNK4PLMD6adjmat21ActionWithInputMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ActionWithInputMatrix.h.gcov.html b/coverage/adjmat/ActionWithInputMatrix.h.gcov.html
new file mode 100644
index 0000000000..f12dcf8e2c
--- /dev/null
+++ b/coverage/adjmat/ActionWithInputMatrix.h.gcov.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ActionWithInputMatrix.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ActionWithInputMatrix.h<span style="font-size: 80%;"> (source / <a href="ActionWithInputMatrix.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_adjmat_ActionWithInputMatrix_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_adjmat_ActionWithInputMatrix_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace adjmat {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class AdjacencyMatrixVessel;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class ActionWithInputMatrix : public multicolvar::MultiColvarBase {</a>
+<a name="35"><span class="lineNum">      35 </span>            : protected:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// The vessel that holds the adjacency matrix</a>
+<a name="37"><span class="lineNum">      37 </span>            :   AdjacencyMatrixVessel* mymatrix;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Get number of base multicolvar types</a>
+<a name="39"><span class="lineNum">      39 </span>            :   unsigned getNumberOfNodeTypes() const ;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Get number of atoms in each base multicolvar</a>
+<a name="41"><span class="lineNum">      41 </span>            :   unsigned getNumberOfAtomsInGroup( const unsigned&amp; igrp ) const ;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Get a pointer to the igrp th base multicolvar</a>
+<a name="43"><span class="lineNum">      43 </span>            :   multicolvar::MultiColvarBase* getBaseMultiColvar( const unsigned&amp; igrp ) const ;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   explicit ActionWithInputMatrix(const ActionOptions&amp;);</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Retrieve the vessel that holds the adjacency matrix</a>
+<a name="48"><span class="lineNum">      48 </span>            :   AdjacencyMatrixVessel* getAdjacencyVessel() const ;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Retrieve the value of the connection</a>
+<a name="50"><span class="lineNum">      50 </span>            :   double retrieveConnectionValue( const unsigned&amp; i, const unsigned&amp; j, std::vector&lt;double&gt;&amp; vals ) const ;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Get the vector for task ind</a>
+<a name="52"><span class="lineNum">      52 </span>            :   void getInputData( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms, std::vector&lt;double&gt;&amp; orient0 ) const override;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Add the derivatives on a connection</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void addConnectionDerivatives( const unsigned&amp; i, const unsigned&amp; j, MultiValue&amp; myvals, MultiValue&amp; myvout ) const ;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Get vector derivatives</a>
+<a name="56"><span class="lineNum">      56 </span>            :   MultiValue&amp; getInputDerivatives( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="58"><span class="lineNum">      58 </span>            : ///  Get the number of rows/cols in the adjacency matrix vessel</a>
+<a name="59"><span class="lineNum">      59 </span>            :   virtual unsigned getNumberOfNodes() const;</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         80 :   bool isPeriodic() override { return false; }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="62"><span class="lineNum">      62 </span>            : ///</a>
+<a name="63"><span class="lineNum">      63 </span>            :   AtomNumber getAbsoluteIndexOfCentralAtom(const unsigned&amp; i) const override;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// No loop over tasks for ActionWithInputMatrix</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override { plumed_error(); }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : ///</a>
+<a name="67"><span class="lineNum">      67 </span>            :   Vector getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const override;</a>
+<a name="68"><span class="lineNum">      68 </span>            : };</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixBase.cpp.func-sort-c.html b/coverage/adjmat/AdjacencyMatrixBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..225e742d61
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixBase.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixBase.cpp<span style="font-size: 80%;"> (<a href="AdjacencyMatrixBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryMed">85.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AdjacencyMatrixBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#185">_ZN4PLMD6adjmat19AdjacencyMatrixBase24recalculateMatrixElementERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#35">_ZN4PLMD6adjmat19AdjacencyMatrixBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#173">_ZN4PLMD6adjmat19AdjacencyMatrixBase25readMaxThreeSpeciesMatrixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_S9_S9_RKb</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#168">_ZN4PLMD6adjmat19AdjacencyMatrixBase23readMaxTwoSpeciesMatrixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_S9_RKb</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#147">_ZN4PLMD6adjmat19AdjacencyMatrixBase17finishMatrixSetupERKbRKSt6vectorINS_10AtomNumberESaIS5_EE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#35">_ZN4PLMD6adjmat19AdjacencyMatrixBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#107">_ZNK4PLMD6adjmat19AdjacencyMatrixBase22retrieveTypeDimensionsERjS2_S2_</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#30">_ZN4PLMD6adjmat19AdjacencyMatrixBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#45">_ZN4PLMD6adjmat19AdjacencyMatrixBase27parseConnectionDescriptionsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKbRKj</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#101">_ZNK4PLMD6adjmat19AdjacencyMatrixBase20getNumberOfNodeTypesEv</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#91">_ZNK4PLMD6adjmat19AdjacencyMatrixBase21getSizeOfInputVectorsEv</a></td>
+              <td class="coverFnHi">5807</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixBase.cpp.func.html b/coverage/adjmat/AdjacencyMatrixBase.cpp.func.html
new file mode 100644
index 0000000000..abd8375377
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixBase.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixBase.cpp<span style="font-size: 80%;"> (<a href="AdjacencyMatrixBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryMed">85.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AdjacencyMatrixBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#30">_ZN4PLMD6adjmat19AdjacencyMatrixBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#147">_ZN4PLMD6adjmat19AdjacencyMatrixBase17finishMatrixSetupERKbRKSt6vectorINS_10AtomNumberESaIS5_EE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#168">_ZN4PLMD6adjmat19AdjacencyMatrixBase23readMaxTwoSpeciesMatrixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_S9_RKb</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#185">_ZN4PLMD6adjmat19AdjacencyMatrixBase24recalculateMatrixElementERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#173">_ZN4PLMD6adjmat19AdjacencyMatrixBase25readMaxThreeSpeciesMatrixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_S9_S9_RKb</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#45">_ZN4PLMD6adjmat19AdjacencyMatrixBase27parseConnectionDescriptionsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKbRKj</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#35">_ZN4PLMD6adjmat19AdjacencyMatrixBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#35">_ZN4PLMD6adjmat19AdjacencyMatrixBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#101">_ZNK4PLMD6adjmat19AdjacencyMatrixBase20getNumberOfNodeTypesEv</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#91">_ZNK4PLMD6adjmat19AdjacencyMatrixBase21getSizeOfInputVectorsEv</a></td>
+              <td class="coverFnHi">5807</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.cpp.gcov.html#107">_ZNK4PLMD6adjmat19AdjacencyMatrixBase22retrieveTypeDimensionsERjS2_S2_</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixBase.cpp.gcov.html b/coverage/adjmat/AdjacencyMatrixBase.cpp.gcov.html
new file mode 100644
index 0000000000..9c9a7c7316
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixBase.cpp.gcov.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixBase.cpp<span style="font-size: 80%;"> (source / <a href="AdjacencyMatrixBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryMed">85.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/BridgedMultiColvarFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/CatomPack.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace adjmat {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         35 : void AdjacencyMatrixBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         35 :   multicolvar::MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         70 :   keys.remove(&quot;LOWMEM&quot;); keys.use(&quot;HIGHMEM&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         35 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         23 : AdjacencyMatrixBase::AdjacencyMatrixBase(const ActionOptions&amp; ao):</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   Action(ao),</a>
+<a name="39"><span class="lineNum">      39 </span>            :   MultiColvarBase(ao),</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         23 :   connect_id(0),</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         23 :   no_third_dim_accum(true),</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         23 :   mat(NULL)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         46 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Tribello, Giberti, Sosso, Salvalaglio and Parrinello, J. Chem. Theory Comput. 13, 1317 (2017)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         23 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         46 : void AdjacencyMatrixBase::parseConnectionDescriptions( const std::string&amp; key, const bool&amp; multiple, const unsigned&amp; nrow_t ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         46 :   if( getNumberOfNodeTypes()==1 || (getNumberOfNodeTypes()==2 &amp;&amp; nrow_t==1) ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :     std::vector&lt;std::string&gt; sw;</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         45 :     if( !multiple ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         44 :       sw.resize(1); parse(key,sw[0]);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         44 :       if(sw[0].length()==0) error(&quot;could not find &quot; + key + &quot; keyword&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :     } else {</a>
+<a name="54"><span class="lineNum">      54 </span>            :       std::string input;</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          2 :       for(int i=1;; i++) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          3 :         if( !parseNumbered(key, i, input ) ) break;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          2 :         sw.push_back( input );</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :       }</a>
+<a name="59"><span class="lineNum">      59 </span>            :     }</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         45 :     setupConnector( connect_id, 0, 0, sw );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         45 :   } else {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :     if( multiple ) error(&quot;keyword &quot; + key + &quot; does not work with multiple input strings&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     unsigned nr, nc;</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          1 :     if( nrow_t==0 ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          1 :       nr=nc=getNumberOfNodeTypes();</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :     } else {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :       nr=nrow_t; nc = getNumberOfNodeTypes() - nr;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     }</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;nr; ++i) {</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :       // Retrieve the base number</a>
+<a name="71"><span class="lineNum">      71 </span>            :       unsigned ibase;</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          2 :       if( nc&lt;10 ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 :         ibase=(i+1)*10;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :       } else if ( nc&lt;100 ) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :         ibase=(i+1)*100;</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :       } else {</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :         error(&quot;wow this is an error I never would have expected&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :       }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          5 :       for(unsigned j=i; j&lt;nc; ++j) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          3 :         std::vector&lt;std::string&gt; sw(1); parseNumbered(key,ibase+j+1,sw[0]);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          3 :         if(sw[0].length()==0) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :           std::string num; Tools::convert(ibase+j+1,num);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :           error(&quot;could not find &quot; + key + num + &quot; keyword. Need one &quot; + key + &quot; keyword for each distinct base-multicolvar-pair type&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :         }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          3 :         setupConnector( connect_id, i, j, sw );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 :       }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     }</a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         46 :   connect_id++;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         46 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       5807 : unsigned AdjacencyMatrixBase::getSizeOfInputVectors() const {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       5807 :   if( mybasemulticolvars.size()==0 ) return 2;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       5807 :   unsigned nq = mybasemulticolvars[0]-&gt;getNumberOfQuantities();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       5807 :   for(unsigned i=1; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     if( mybasemulticolvars[i]-&gt;getNumberOfQuantities()!=nq ) error(&quot;mismatch between vectors in base colvars&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span>            :   return nq;</a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        132 : unsigned AdjacencyMatrixBase::getNumberOfNodeTypes() const {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        132 :   unsigned size=mybasemulticolvars.size();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   if( size==0 ) return 1;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   return size;</a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         24 : void AdjacencyMatrixBase::retrieveTypeDimensions( unsigned&amp; nrows, unsigned&amp; ncols, unsigned&amp; ntype ) const {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         24 :   bool allsame=(ablocks[0].size()==ablocks[1].size());</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         24 :   if( allsame ) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       6952 :     for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       6929 :       if( ablocks[0][i]!=ablocks[1][i] ) allsame=false;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     }</a>
+<a name="115"><span class="lineNum">     115 </span>            :   }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         24 :   if( allsame ) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         23 :     std::vector&lt;unsigned&gt; types(1); types[0]=atom_lab[ablocks[0][0]].first;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       6929 :     for(unsigned i=1; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :       bool found = false;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       6913 :       for(unsigned j=0; j&lt;types.size(); ++j) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       6912 :         if( atom_lab[ablocks[0][i]].first==types[j] ) { found=true; break; }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :       }</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       6906 :       if( !found ) types.push_back( atom_lab[ablocks[0][i]].first );</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     }</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         23 :     ntype=0; nrows=ncols=types.size();</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   } else {</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          1 :     std::vector&lt;unsigned&gt; types(1); types[0]=atom_lab[ablocks[0][0]].first;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          5 :     for(unsigned i=1; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :       bool found = false;</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 :       for(unsigned j=0; j&lt;types.size(); ++j) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          4 :         if( atom_lab[ablocks[0][i]].first==types[j] ) { found=true; break; }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :       }</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 :       if( !found ) types.push_back( atom_lab[ablocks[0][i]].first );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :     }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :     nrows=ntype=types.size();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         11 :     for(unsigned i=0; i&lt;ablocks[1].size(); ++i) {</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :       bool found = false;</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         10 :       for(unsigned j=0; j&lt;types.size(); ++j) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         10 :         if( atom_lab[ablocks[1][i]].first==types[j] ) { found=true; break; }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :       }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         10 :       if( !found ) types.push_back( atom_lab[ablocks[1][i]].first );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :     if( types.size()==nrows ) { ntype=0; ncols=1; plumed_assert( types.size()==1 &amp;&amp; atom_lab[ablocks[0][0]].first==0 ); }</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     else ncols = types.size() - ntype;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         24 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         23 : void AdjacencyMatrixBase::finishMatrixSetup( const bool&amp; symmetric, const std::vector&lt;AtomNumber&gt;&amp; all_atoms ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   std::string param;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         23 :   if( symmetric &amp;&amp; ablocks[0].size()==ablocks[1].size() ) param=&quot;SYMMETRIC&quot;;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         23 :   if( !symmetric ) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :     bool usehbonds=( ablocks[0].size()==ablocks[1].size() );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :     if( usehbonds ) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        138 :       for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        134 :         if( ablocks[0][i]!=ablocks[1][i] ) { usehbonds = false; break; }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       }</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :       if( usehbonds ) param=&quot;HBONDS&quot;;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         46 :   vesselbase::VesselOptions da(&quot;&quot;,&quot;&quot;,0,param,this);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         23 :   Keywords keys; AdjacencyMatrixVessel::registerKeywords( keys );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         23 :   vesselbase::VesselOptions da2(da,keys);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         23 :   auto ves=Tools::make_unique&lt;AdjacencyMatrixVessel&gt;(da2);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         23 :   addVessel( std::move( ves ) );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         23 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         46 : }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         13 : void AdjacencyMatrixBase::readMaxTwoSpeciesMatrix( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, const bool&amp; symmetric ) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         13 :   std::vector&lt;AtomNumber&gt; all_atoms; readTwoGroups( key0, key1, key2, all_atoms );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         13 :   finishMatrixSetup( symmetric, all_atoms );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         13 : }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         10 : void AdjacencyMatrixBase::readMaxThreeSpeciesMatrix( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, const std::string&amp; keym, const bool&amp; symmetric ) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         10 :   std::vector&lt;AtomNumber&gt; all_atoms; readGroupKeywords( key0, key1, key2, keym, true, symmetric, all_atoms );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         10 :   finishMatrixSetup( symmetric, all_atoms );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         10 : }</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : // Maybe put this back GAT to check that it is returning an atom number that is one of the nodes</a>
+<a name="181"><span class="lineNum">     181 </span>            : // and not a hydrogen if we are doing HBPAMM</a>
+<a name="182"><span class="lineNum">     182 </span>            : // AtomNumber AdjacencyMatrixBase::getAbsoluteIndexOfCentralAtom(const unsigned&amp; i) const {</a>
+<a name="183"><span class="lineNum">     183 </span>            : //   plumed_dbg_assert( i&lt;myinputdata.getFullNumberOfBaseTasks() );</a>
+<a name="184"><span class="lineNum">     184 </span>            : //   return myinputdata.getAtomicIndex( i );</a>
+<a name="185"><span class="lineNum">     185 </span>            : // }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 : void AdjacencyMatrixBase::recalculateMatrixElement( const unsigned&amp; myelem, MultiValue&amp; myvals ) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; myatoms; decodeIndexToAtoms( getTaskCode( myelem ), myatoms );</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   unsigned i=myatoms[0], j=myatoms[1];</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   for(unsigned k=bookeeping(i,j).first; k&lt;bookeeping(i,j).second; ++k) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     if( !taskIsCurrentlyActive(k) ) continue;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     performTask( k, getTaskCode(k), myvals );  // This may not accumulate as we would like  GAT</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixBase.h.func-sort-c.html b/coverage/adjmat/AdjacencyMatrixBase.h.func-sort-c.html
new file mode 100644
index 0000000000..b00d68098b
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixBase.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixBase.h<span style="font-size: 80%;"> (<a href="AdjacencyMatrixBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AdjacencyMatrixBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.h.gcov.html#74">_ZN4PLMD6adjmat19AdjacencyMatrixBase10isPeriodicEv</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.h.gcov.html#92">_ZNK4PLMD6adjmat19AdjacencyMatrixBase29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">504</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixBase.h.func.html b/coverage/adjmat/AdjacencyMatrixBase.h.func.html
new file mode 100644
index 0000000000..c95d7a3ff2
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixBase.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixBase.h<span style="font-size: 80%;"> (<a href="AdjacencyMatrixBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AdjacencyMatrixBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.h.gcov.html#74">_ZN4PLMD6adjmat19AdjacencyMatrixBase10isPeriodicEv</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixBase.h.gcov.html#92">_ZNK4PLMD6adjmat19AdjacencyMatrixBase29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">504</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixBase.h.gcov.html b/coverage/adjmat/AdjacencyMatrixBase.h.gcov.html
new file mode 100644
index 0000000000..133782b4d8
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixBase.h.gcov.html
@@ -0,0 +1,181 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixBase.h<span style="font-size: 80%;"> (source / <a href="AdjacencyMatrixBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_adjmat_AdjacencyMatrixBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_adjmat_AdjacencyMatrixBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace adjmat {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class AdjacencyMatrixBase : public multicolvar::MultiColvarBase {</a>
+<a name="32"><span class="lineNum">      32 </span>            :   friend class AdjacencyMatrixVessel;</a>
+<a name="33"><span class="lineNum">      33 </span>            :   friend class ActionWithInputMatrix;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   friend class MatrixColumnSums;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   friend class MatrixRowSums;</a>
+<a name="36"><span class="lineNum">      36 </span>            : private:</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Used for read in of multiple connection descriptors</a>
+<a name="38"><span class="lineNum">      38 </span>            :   unsigned connect_id;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Do we need to separate out the tasks for the third atoms</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool no_third_dim_accum;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// This is the vessel that stores the adjacency matrix</a>
+<a name="42"><span class="lineNum">      42 </span>            :   AdjacencyMatrixVessel* mat;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// This is used within AdjacencyMatrixVessel to recalculate matrix elements</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// which is useful when we are operating with lowmem</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void recalculateMatrixElement( const unsigned&amp; myelem, MultiValue&amp; myvals );</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Finish the setup of the matrix</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void finishMatrixSetup( const bool&amp; symmetric, const std::vector&lt;AtomNumber&gt;&amp; all_atoms );</a>
+<a name="48"><span class="lineNum">      48 </span>            : protected:</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Read in a matrix involving a maximum of two species</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void readMaxTwoSpeciesMatrix( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, const bool&amp; symmetric );</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Read in a matrix involving a maximum of three species</a>
+<a name="52"><span class="lineNum">      52 </span>            :   void readMaxThreeSpeciesMatrix( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, const std::string&amp; keym, const bool&amp; symmetric );</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Get the dimensions of the matrix of types</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void retrieveTypeDimensions( unsigned&amp; nrows, unsigned&amp; ncols, unsigned&amp; ntype ) const ;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Retrieve the vessel that holds the adjacency matrix</a>
+<a name="56"><span class="lineNum">      56 </span>            :   AdjacencyMatrixVessel* getAdjacencyVessel();</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Put the indices of the matrix elements in current atoms</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void setMatrixIndexesForTask( const unsigned&amp; ii );</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Add derivatives to a matrix element</a>
+<a name="60"><span class="lineNum">      60 </span>            :   void addDerivativesOnMatrixElement( const unsigned&amp; ielem, const unsigned&amp; jrow, const double&amp; df, Matrix&lt;double&gt;&amp; der );</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Read in the information on the connectors</a>
+<a name="62"><span class="lineNum">      62 </span>            :   void parseConnectionDescriptions( const std::string&amp; key, const bool&amp; multiple, const unsigned&amp; nrow_t );</a>
+<a name="63"><span class="lineNum">      63 </span>            : protected:</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Get the number of nodes of different types</a>
+<a name="65"><span class="lineNum">      65 </span>            :   unsigned getNumberOfNodeTypes() const ;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Get the size of the vectors that were stored in the base colvars</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned getSizeOfInputVectors() const ;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Return the group this atom is a part of</a>
+<a name="69"><span class="lineNum">      69 </span>            :   unsigned getBaseColvarNumber( const unsigned&amp; ) const ;</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   explicit AdjacencyMatrixBase(const ActionOptions&amp;);</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Create the connection object</a>
+<a name="74"><span class="lineNum">      74 </span>            :   virtual void setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) = 0;</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// None of these things are allowed</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         25 :   bool isPeriodic() { return false; }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   Vector getCentralAtom() { plumed_merror(&quot;cannot find central atoms for adjacency matrix actions&quot;); }</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Get the atom number</a>
+<a name="79"><span class="lineNum">      79 </span>            :   AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned&amp; i ) const ;</a>
+<a name="80"><span class="lineNum">      80 </span>            : };</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : inline</a>
+<a name="83"><span class="lineNum">      83 </span>            : AdjacencyMatrixVessel* AdjacencyMatrixBase::getAdjacencyVessel() {</a>
+<a name="84"><span class="lineNum">      84 </span>            :   return mat;</a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : inline</a>
+<a name="88"><span class="lineNum">      88 </span>            : unsigned AdjacencyMatrixBase::getBaseColvarNumber( const unsigned&amp; inum ) const {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">  224925223 :   if( atom_lab[inum].first&gt;0 ) return atom_lab[inum].first-1;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   return 0;</a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : inline</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        504 : AtomNumber AdjacencyMatrixBase::getAbsoluteIndexOfCentralAtom( const unsigned&amp; iatom ) const {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        504 :   if( atom_lab[iatom].first&gt;0 ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        156 :     unsigned mmc=atom_lab[ iatom ].first - 1;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        156 :     return mybasemulticolvars[mmc]-&gt;getAbsoluteIndexOfCentralAtom( atom_lab[iatom].second );</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        348 :   return ActionAtomistic::getAbsoluteIndex( atom_lab[iatom].second );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixVessel.cpp.func-sort-c.html b/coverage/adjmat/AdjacencyMatrixVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..be04f4b373
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixVessel.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixVessel.cpp<span style="font-size: 80%;"> (<a href="AdjacencyMatrixVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">91.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AdjacencyMatrixVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#137">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel17nodesAreConnectedERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#122">_ZN4PLMD6adjmat21AdjacencyMatrixVessel16retrieveEdgeListERjRSt6vectorISt4pairIjjESaIS5_EE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#146">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel22getCutoffForConnectionEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#85">_ZN4PLMD6adjmat21AdjacencyMatrixVessel14retrieveMatrixERNS_11DynamicListIjEERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#75">_ZN4PLMD6adjmat21AdjacencyMatrixVessel15getMatrixActionEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#27">_ZN4PLMD6adjmat21AdjacencyMatrixVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#33">_ZN4PLMD6adjmat21AdjacencyMatrixVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#100">_ZN4PLMD6adjmat21AdjacencyMatrixVessel22retrieveAdjacencyListsERSt6vectorIjSaIjEERNS_6MatrixIjEE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#44">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel11isSymmetricEv</a></td>
+              <td class="coverFnHi">775</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#52">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel15getNumberOfRowsEv</a></td>
+              <td class="coverFnHi">1596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#79">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel16getMatrixIndicesERKjRjS4_</a></td>
+              <td class="coverFnHi">24491</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#56">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel18getNumberOfColumnsEv</a></td>
+              <td class="coverFnHi">39153</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#60">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel21matrixElementIsActiveERKjS3_</a></td>
+              <td class="coverFnHi">47892</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#48">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel15undirectedGraphEv</a></td>
+              <td class="coverFnHi">72251</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#64">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel30getStoreIndexFromMatrixIndicesERKjS3_</a></td>
+              <td class="coverFnHi">74692</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixVessel.cpp.func.html b/coverage/adjmat/AdjacencyMatrixVessel.cpp.func.html
new file mode 100644
index 0000000000..143ecb72b1
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixVessel.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixVessel.cpp<span style="font-size: 80%;"> (<a href="AdjacencyMatrixVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">91.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AdjacencyMatrixVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#85">_ZN4PLMD6adjmat21AdjacencyMatrixVessel14retrieveMatrixERNS_11DynamicListIjEERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#75">_ZN4PLMD6adjmat21AdjacencyMatrixVessel15getMatrixActionEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#27">_ZN4PLMD6adjmat21AdjacencyMatrixVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#122">_ZN4PLMD6adjmat21AdjacencyMatrixVessel16retrieveEdgeListERjRSt6vectorISt4pairIjjESaIS5_EE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#100">_ZN4PLMD6adjmat21AdjacencyMatrixVessel22retrieveAdjacencyListsERSt6vectorIjSaIjEERNS_6MatrixIjEE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#33">_ZN4PLMD6adjmat21AdjacencyMatrixVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#44">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel11isSymmetricEv</a></td>
+              <td class="coverFnHi">775</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#52">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel15getNumberOfRowsEv</a></td>
+              <td class="coverFnHi">1596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#48">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel15undirectedGraphEv</a></td>
+              <td class="coverFnHi">72251</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#79">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel16getMatrixIndicesERKjRjS4_</a></td>
+              <td class="coverFnHi">24491</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#137">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel17nodesAreConnectedERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#56">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel18getNumberOfColumnsEv</a></td>
+              <td class="coverFnHi">39153</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#60">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel21matrixElementIsActiveERKjS3_</a></td>
+              <td class="coverFnHi">47892</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#146">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel22getCutoffForConnectionEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdjacencyMatrixVessel.cpp.gcov.html#64">_ZNK4PLMD6adjmat21AdjacencyMatrixVessel30getStoreIndexFromMatrixIndicesERKjS3_</a></td>
+              <td class="coverFnHi">74692</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AdjacencyMatrixVessel.cpp.gcov.html b/coverage/adjmat/AdjacencyMatrixVessel.cpp.gcov.html
new file mode 100644
index 0000000000..6080386c07
--- /dev/null
+++ b/coverage/adjmat/AdjacencyMatrixVessel.cpp.gcov.html
@@ -0,0 +1,230 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AdjacencyMatrixVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AdjacencyMatrixVessel.cpp<span style="font-size: 80%;"> (source / <a href="AdjacencyMatrixVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">91.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace adjmat {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         23 : void AdjacencyMatrixVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         23 :   StoreDataVessel::registerKeywords(keys);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         46 :   keys.addFlag(&quot;SYMMETRIC&quot;,false,&quot;is the matrix symmetric&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         46 :   keys.addFlag(&quot;HBONDS&quot;,false,&quot;can we think of the matrix as a undirected graph&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         23 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         23 : AdjacencyMatrixVessel::AdjacencyMatrixVessel( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         23 :   StoreDataVessel(da)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         23 :   function=dynamic_cast&lt;AdjacencyMatrixBase*&gt;( getAction() );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         23 :   plumed_assert( function );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         46 :   parseFlag(&quot;SYMMETRIC&quot;,symmetric); parseFlag(&quot;HBONDS&quot;,hbonds);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         23 :   if( symmetric &amp;&amp; hbonds ) error(&quot;matrix should be either symmetric or hbonds&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         23 :   if( symmetric &amp;&amp; function-&gt;ablocks[0].size()!=function-&gt;ablocks[1].size() ) error(&quot;matrix is supposed to be symmetric but nrows!=ncols&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         23 :   if( hbonds &amp;&amp;  function-&gt;ablocks[0].size()!=function-&gt;ablocks[1].size() ) error(&quot;matrix is supposed to be hbonds but nrows!=ncols&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         23 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        775 : bool AdjacencyMatrixVessel::isSymmetric() const {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        775 :   return symmetric;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      72251 : bool AdjacencyMatrixVessel::undirectedGraph() const {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      72251 :   return ( symmetric || hbonds );</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : }</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1596 : unsigned AdjacencyMatrixVessel::getNumberOfRows() const {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1596 :   return function-&gt;ablocks[0].size();</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      39153 : unsigned AdjacencyMatrixVessel::getNumberOfColumns() const {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      39153 :   return function-&gt;ablocks[1].size();</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : }</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      47892 : bool AdjacencyMatrixVessel::matrixElementIsActive( const unsigned&amp; ielem, const unsigned&amp; jelem ) const {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      47892 :   return StoreDataVessel::storedValueIsActive( getStoreIndexFromMatrixIndices( ielem, jelem ) );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      74692 : unsigned AdjacencyMatrixVessel::getStoreIndexFromMatrixIndices( const unsigned&amp; ielem, const unsigned&amp; jelem ) const {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      74692 :   if( !symmetric &amp;&amp; !hbonds ) return (function-&gt;ablocks[1].size())*ielem + jelem;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      72692 :   if( !symmetric ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :     plumed_dbg_assert( ielem!=jelem );</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      32256 :     if( jelem&lt;ielem ) return (function-&gt;ablocks[1].size()-1)*ielem + jelem;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      16128 :     return (function-&gt;ablocks[1].size()-1)*ielem + jelem - 1;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   }</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      40436 :   if( ielem&gt;jelem ) return 0.5*ielem*(ielem-1)+jelem;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      17363 :   return 0.5*jelem*(jelem-1) + ielem;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         17 : AdjacencyMatrixBase* AdjacencyMatrixVessel::getMatrixAction() {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         17 :   return function;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      24491 : void AdjacencyMatrixVessel::getMatrixIndices( const unsigned&amp; code, unsigned&amp; i, unsigned&amp; j ) const {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      24491 :   std::vector&lt;unsigned&gt; myatoms; function-&gt;decodeIndexToAtoms( function-&gt;getTaskCode(code), myatoms );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      24491 :   i=myatoms[0]; j=myatoms[1];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      24491 :   if( !undirectedGraph() ) j -= function-&gt;ablocks[0].size(); // Have to remove number of columns as returns number in ablocks[1]</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      24491 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         17 : void AdjacencyMatrixVessel::retrieveMatrix( DynamicList&lt;unsigned&gt;&amp; myactive_elements, Matrix&lt;double&gt;&amp; mymatrix ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         17 :   myactive_elements.deactivateAll(); std::vector&lt;double&gt; vals( getNumberOfComponents() );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1564 :   for(unsigned i=0; i&lt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1547 :     retrieveSequentialValue( i, false, vals );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1547 :     if( vals[0]&lt;epsilon ) continue ;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       1547 :     myactive_elements.activate(i);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1547 :     unsigned j, k; getMatrixIndices( function-&gt;getPositionInFullTaskList(i), k, j );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1547 :     if( symmetric ) mymatrix(k,j)=mymatrix(j,k)=vals[0]*vals[1];</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     else mymatrix(k,j)=vals[0]*vals[1];</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         17 :   myactive_elements.updateActiveMembers();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         17 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         24 : void AdjacencyMatrixVessel::retrieveAdjacencyLists( std::vector&lt;unsigned&gt;&amp; nneigh, Matrix&lt;unsigned&gt;&amp; adj_list ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   plumed_dbg_assert( undirectedGraph() );</a>
+<a name="104"><span class="lineNum">     104 </span>            :   // Currently everything has zero neighbors</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       8217 :   for(unsigned i=0; i&lt;nneigh.size(); ++i) nneigh[i]=0;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   // And set up the adjacency list</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         24 :   std::vector&lt;double&gt; myvals( getNumberOfComponents() );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     214258 :   for(unsigned i=0; i&lt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     // Check if atoms are connected</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">     214234 :     retrieveSequentialValue( i, false, myvals );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     214234 :     if( myvals[0]&lt;epsilon || myvals[1]&lt;epsilon ) continue ;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      15013 :     unsigned j, k; getMatrixIndices( function-&gt;getPositionInFullTaskList(i), k, j );</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      15013 :     if( nneigh[j]&gt;=adj_list.ncols() || nneigh[k]&gt;=adj_list.ncols() ) error(&quot;adjacency lists are not large enough, increase maxconnections&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     // Store if atoms are connected</a>
+<a name="118"><span class="lineNum">     118 </span>            :     // unsigned j, k; getMatrixIndices( i, k, j );</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      15013 :     adj_list(k,nneigh[k])=j; nneigh[k]++;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      15013 :     adj_list(j,nneigh[j])=k; nneigh[j]++;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         24 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          4 : void AdjacencyMatrixVessel::retrieveEdgeList( unsigned&amp; nedge, std::vector&lt;std::pair&lt;unsigned,unsigned&gt; &gt;&amp; edge_list ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          4 :   plumed_dbg_assert( undirectedGraph() ); nedge=0;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; myvals( getNumberOfComponents() );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          4 :   if( getNumberOfStoredValues()&gt;edge_list.size() ) error(&quot;adjacency lists are not large enough, increase maxconnections&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     124576 :   for(unsigned i=0; i&lt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :     // Check if atoms are connected</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     124572 :     retrieveSequentialValue( i, false, myvals );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     124572 :     if( myvals[0]&lt;epsilon || myvals[1]&lt;epsilon ) continue ;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       6384 :     getMatrixIndices( function-&gt;getPositionInFullTaskList(i), edge_list[nedge].first, edge_list[nedge].second );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       6384 :     nedge++;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 : bool AdjacencyMatrixVessel::nodesAreConnected( const unsigned&amp; iatom, const unsigned&amp; jatom ) const {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   if( !matrixElementIsActive( iatom, jatom ) ) return false;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   unsigned ind=getStoreIndexFromMatrixIndices( iatom, jatom );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; myvals( getNumberOfComponents() );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   retrieveValueWithIndex( ind, false, myvals );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   return ( myvals[0]&gt;epsilon &amp;&amp; myvals[1]&gt;epsilon );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          8 : double AdjacencyMatrixVessel::getCutoffForConnection() const {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          8 :   return function-&gt;getLinkCellCutoff();</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AlignedMatrixBase.cpp.func-sort-c.html b/coverage/adjmat/AlignedMatrixBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7d6879516d
--- /dev/null
+++ b/coverage/adjmat/AlignedMatrixBase.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AlignedMatrixBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AlignedMatrixBase.cpp<span style="font-size: 80%;"> (<a href="AlignedMatrixBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AlignedMatrixBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#46">_ZN4PLMD6adjmat17AlignedMatrixBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#46">_ZN4PLMD6adjmat17AlignedMatrixBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#71">_ZN4PLMD6adjmat17AlignedMatrixBase14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#28">_ZN4PLMD6adjmat17AlignedMatrixBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#89">_ZNK4PLMD6adjmat17AlignedMatrixBase7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">5806</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#83">_ZNK4PLMD6adjmat17AlignedMatrixBase15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">57063</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AlignedMatrixBase.cpp.func.html b/coverage/adjmat/AlignedMatrixBase.cpp.func.html
new file mode 100644
index 0000000000..62806a9de3
--- /dev/null
+++ b/coverage/adjmat/AlignedMatrixBase.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AlignedMatrixBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AlignedMatrixBase.cpp<span style="font-size: 80%;"> (<a href="AlignedMatrixBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AlignedMatrixBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#71">_ZN4PLMD6adjmat17AlignedMatrixBase14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#28">_ZN4PLMD6adjmat17AlignedMatrixBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#46">_ZN4PLMD6adjmat17AlignedMatrixBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#46">_ZN4PLMD6adjmat17AlignedMatrixBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#83">_ZNK4PLMD6adjmat17AlignedMatrixBase15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">57063</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlignedMatrixBase.cpp.gcov.html#89">_ZNK4PLMD6adjmat17AlignedMatrixBase7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">5806</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/AlignedMatrixBase.cpp.gcov.html b/coverage/adjmat/AlignedMatrixBase.cpp.gcov.html
new file mode 100644
index 0000000000..b192ee67ec
--- /dev/null
+++ b/coverage/adjmat/AlignedMatrixBase.cpp.gcov.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/AlignedMatrixBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - AlignedMatrixBase.cpp<span style="font-size: 80%;"> (source / <a href="AlignedMatrixBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AlignedMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace adjmat {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">          5 : void AlignedMatrixBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          5 :   AdjacencyMatrixBase::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         10 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;The list of molecules for which you would like to calculate the contact matrix.  The molecules involved must &quot;</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :            &quot;have an orientation so your list will be a list of the labels of \\ref mcolv or \\ref multicolvarfunction &quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            :            &quot;as PLUMED calculates the orientations of molecules within these operations.  Please note also that the majority &quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            :            &quot;of \\ref mcolv and \\ref multicolvarfunction do not calculate a molecular orientation.&quot;);</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         10 :   keys.add(&quot;atoms-1&quot;,&quot;ATOMSA&quot;,&quot;The list of molecules that you would like to use for the rows of the contact matrix.  The molecules involved must &quot;</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :            &quot;have an orientation so your list will be a list of the labels of \\ref mcolv or \\ref multicolvarfunction &quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            :            &quot;as PLUMED calculates the orientations of molecules within these operations.  Please note also that the majority &quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            :            &quot;of \\ref mcolv and \\ref multicolvarfunction do not calculate a molecular orientation.&quot;);</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         10 :   keys.add(&quot;atoms-1&quot;,&quot;ATOMSB&quot;,&quot;The list of molecules that you would like to use for the columns of the contact matrix.  The molecules involved must &quot;</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :            &quot;have an orientation so your list will be a list of the labels of \\ref mcolv or \\ref multicolvarfunction &quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            :            &quot;as PLUMED calculates the orientations of molecules within these operations.  Please note also that the majority &quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            :            &quot;of \\ref mcolv and \\ref multicolvarfunction do not calculate a molecular orientation.&quot;);</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         10 :   keys.add(&quot;numbered&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available.&quot;);</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          5 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 : AlignedMatrixBase::AlignedMatrixBase( const ActionOptions&amp; ao ):</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   Action(ao),</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :   AdjacencyMatrixBase(ao)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : {</a>
+<a name="52"><span class="lineNum">      52 </span>            :   // Read in the atomic positions</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          2 :   readMaxTwoSpeciesMatrix( &quot;ATOMS&quot;, &quot;ATOMSA&quot;, &quot;ATOMSB&quot;, true );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          1 :   unsigned nrows, ncols; retrieveTypeDimensions( nrows, ncols, ncol_t );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          1 :   if( mybasemulticolvars.size()==0 ) error(&quot;cannot use atom indices as input to this variable / input was not specified&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          1 :   if( getSizeOfInputVectors()&lt;3 ) error(&quot;base multicolvars do not calculate an orientation&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   // Read in the switching function</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          1 :   switchingFunction.resize( nrows, ncols );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          2 :   parseConnectionDescriptions(&quot;SWITCH&quot;,false,ncol_t);</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   // Find the largest sf cutoff</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :   double sfmax=switchingFunction(0,0).get_dmax();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;getNumberOfNodeTypes(); ++i) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          2 :     for(unsigned j=0; j&lt;getNumberOfNodeTypes(); ++j) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          1 :       double tsf=switchingFunction(i,j).get_dmax();</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          1 :       if( tsf&gt;sfmax ) sfmax=tsf;</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     }</a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // And set the link cell cutoff</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          1 :   setLinkCellCutoff( sfmax );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 : void AlignedMatrixBase::setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          2 :   plumed_assert( id&lt;2 );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          2 :   if( id==0 ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          1 :     plumed_assert( desc.size()==1 ); std::string errors; switchingFunction(j,i).set(desc[0],errors);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          1 :     if( errors.length()!=0 ) error(&quot;problem reading switching function in SWITCH keywrd description &quot; + errors);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :     if( j!=i) switchingFunction(i,j).set(desc[0],errors);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          2 :     log.printf(&quot;  %u th and %u th multicolvar groups must be within %s\n&quot;,i+1,j+1,(switchingFunction(i,j).description()).c_str() );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          1 :   } else if( id==1 ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          1 :     readOrientationConnector( i, j, desc );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          2 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      57063 : double AlignedMatrixBase::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      57063 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     171189 :   if( distance.modulo2()&lt;switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) )-ncol_t ).get_dmax2() ) return 1.0;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   return 0.0;</a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       5806 : double AlignedMatrixBase::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       5806 :   unsigned ncomp=getSizeOfInputVectors(); Vector ddistance;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       5806 :   std::vector&lt;double&gt; orient0(ncomp), orient1(ncomp), dorient0(ncomp), dorient1(ncomp);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       5806 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       5806 :   getInputData( 0, true, myatoms, orient0 ); getInputData( 1, true, myatoms, orient1 );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      17418 :   double f_dot = computeVectorFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) )-ncol_t,</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :                                         distance, orient0, orient1, ddistance, dorient0, dorient1 );</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   // Retrieve the weight of the connection</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      11612 :   double dfunc, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) )-ncol_t ).calculate( distance.modulo(), dfunc );</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       5806 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 1, 0, (-dfunc)*f_dot*distance - sw*ddistance, myatoms );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 1, 1, (+dfunc)*f_dot*distance + sw*ddistance, myatoms );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) - sw*extProduct( distance, ddistance ) );</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :     // Add derivatives of orientation</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     for(unsigned k=2; k&lt;orient0.size(); ++k) { dorient0[k]*=sw; dorient1[k]*=sw; }</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     mergeInputDerivatives( 1, 2, orient0.size(), 0, dorient0, getInputDerivatives( 0, true, myatoms ), myatoms );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     mergeInputDerivatives( 1, 2, orient1.size(), 1, dorient1, getInputDerivatives( 1, true, myatoms ), myatoms );</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      11612 :   return sw*f_dot;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterAnalysisBase.cpp.func-sort-c.html b/coverage/adjmat/ClusterAnalysisBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b5ec1fa264
--- /dev/null
+++ b/coverage/adjmat/ClusterAnalysisBase.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterAnalysisBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterAnalysisBase.cpp<span style="font-size: 80%;"> (<a href="ClusterAnalysisBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterAnalysisBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#30">_ZN4PLMD6adjmat19ClusterAnalysisBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#99">_ZNK4PLMD6adjmat19ClusterAnalysisBase12areConnectedERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#95">_ZNK4PLMD6adjmat19ClusterAnalysisBase22getCutoffForConnectionEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#79">_ZNK4PLMD6adjmat19ClusterAnalysisBase12nodeIsActiveERKj</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#67">_ZNK4PLMD6adjmat19ClusterAnalysisBase19getNumberOfClustersEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#50">_ZN4PLMD6adjmat19ClusterAnalysisBase17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#71">_ZN4PLMD6adjmat19ClusterAnalysisBase10isPeriodicEv</a></td>
+              <td class="coverFnHi">11</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#30">_ZN4PLMD6adjmat19ClusterAnalysisBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#25">_ZN4PLMD6adjmat19ClusterAnalysisBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#75">_ZNK4PLMD6adjmat19ClusterAnalysisBase22retrieveAtomsInClusterERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">66</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#87">_ZNK4PLMD6adjmat19ClusterAnalysisBase26getNodePropertyDerivativesERKjRNS_10MultiValueE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#83">_ZNK4PLMD6adjmat19ClusterAnalysisBase19getPropertiesOfNodeERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1801</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#91">_ZNK4PLMD6adjmat19ClusterAnalysisBase29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnHi">1975</td>
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+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#59">_ZNK4PLMD6adjmat19ClusterAnalysisBase21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">2073</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#63">_ZNK4PLMD6adjmat19ClusterAnalysisBase16getNumberOfNodesEv</a></td>
+              <td class="coverFnHi">15981876</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterAnalysisBase.cpp.func.html b/coverage/adjmat/ClusterAnalysisBase.cpp.func.html
new file mode 100644
index 0000000000..a1a2e1d0f6
--- /dev/null
+++ b/coverage/adjmat/ClusterAnalysisBase.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterAnalysisBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterAnalysisBase.cpp<span style="font-size: 80%;"> (<a href="ClusterAnalysisBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterAnalysisBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#71">_ZN4PLMD6adjmat19ClusterAnalysisBase10isPeriodicEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#25">_ZN4PLMD6adjmat19ClusterAnalysisBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#50">_ZN4PLMD6adjmat19ClusterAnalysisBase17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#30">_ZN4PLMD6adjmat19ClusterAnalysisBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#30">_ZN4PLMD6adjmat19ClusterAnalysisBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#99">_ZNK4PLMD6adjmat19ClusterAnalysisBase12areConnectedERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#79">_ZNK4PLMD6adjmat19ClusterAnalysisBase12nodeIsActiveERKj</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#63">_ZNK4PLMD6adjmat19ClusterAnalysisBase16getNumberOfNodesEv</a></td>
+              <td class="coverFnHi">15981876</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#67">_ZNK4PLMD6adjmat19ClusterAnalysisBase19getNumberOfClustersEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#83">_ZNK4PLMD6adjmat19ClusterAnalysisBase19getPropertiesOfNodeERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1801</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#59">_ZNK4PLMD6adjmat19ClusterAnalysisBase21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">2073</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#95">_ZNK4PLMD6adjmat19ClusterAnalysisBase22getCutoffForConnectionEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#75">_ZNK4PLMD6adjmat19ClusterAnalysisBase22retrieveAtomsInClusterERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">66</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#87">_ZNK4PLMD6adjmat19ClusterAnalysisBase26getNodePropertyDerivativesERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">1604</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.cpp.gcov.html#91">_ZNK4PLMD6adjmat19ClusterAnalysisBase29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnHi">1975</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterAnalysisBase.cpp.gcov.html b/coverage/adjmat/ClusterAnalysisBase.cpp.gcov.html
new file mode 100644
index 0000000000..153c72d4c7
--- /dev/null
+++ b/coverage/adjmat/ClusterAnalysisBase.cpp.gcov.html
@@ -0,0 +1,182 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterAnalysisBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterAnalysisBase.cpp<span style="font-size: 80%;"> (source / <a href="ClusterAnalysisBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusterAnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace adjmat {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         62 : void ClusterAnalysisBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         62 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        124 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTERS&quot;,&quot;the label of the action that does the clustering&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         62 : }</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         54 : ClusterAnalysisBase::ClusterAnalysisBase(const ActionOptions&amp; ao):</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :   Action(ao),</a>
+<a name="34"><span class="lineNum">      34 </span>            :   MultiColvarBase(ao),</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        108 :   myfvals(0,0),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         54 :   myfatoms( myfvals, this ),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         54 :   myclusters(NULL)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span>            :   // This makes these colvars behave appropriately with dump and analysis</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         54 :   matsums=usespecies=true; std::vector&lt;AtomNumber&gt; fake_atoms;</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   // Find what action we are taking the clusters from</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        108 :   if( !parseMultiColvarAtomList(&quot;CLUSTERS&quot;,-1,fake_atoms ) ) error(&quot;unable to interpret input CLUSTERS&quot; );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         54 :   if( mybasemulticolvars.size()!=1 ) error(&quot;should be exactly one multicolvar input&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         54 :   atom_lab.resize(0); myclusters = dynamic_cast&lt;ClusteringBase*&gt;( mybasemulticolvars[0] );</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         54 :   if( !myclusters ) error(&quot;input label is not that of a DFS object&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   // Setup the atom pack</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         54 :   myfatoms.setNumberOfAtoms( myclusters-&gt;getNumberOfNodes() );</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         54 :   myfvals.getIndices().resize( myclusters-&gt;getNumberOfNodes() );</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      33703 :   for(unsigned i=0; i&lt;myclusters-&gt;getNumberOfNodes(); ++i) myfatoms.setAtomIndex( i, i );</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         54 : }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          8 : void ClusterAnalysisBase::turnOnDerivatives() {</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   // Check for dubious vessels</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         18 :   for(unsigned i=0; i&lt;getNumberOfVessels(); ++i) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         20 :     if( getPntrToVessel(i)-&gt;getName()==&quot;MEAN&quot; ) error(&quot;MEAN of cluster is not differentiable&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         20 :     if( getPntrToVessel(i)-&gt;getName()==&quot;VMEAN&quot; ) error(&quot;VMEAN of cluster is not differentiable&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          8 :   MultiColvarBase::turnOnDerivatives();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          8 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       2073 : unsigned ClusterAnalysisBase::getNumberOfQuantities() const {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       2073 :   return myclusters-&gt;getNumberOfQuantities();</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">   15981876 : unsigned ClusterAnalysisBase::getNumberOfNodes() const {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">   15981876 :   return myclusters-&gt;getNumberOfNodes();</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          4 : unsigned ClusterAnalysisBase::getNumberOfClusters() const {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          4 :   return myclusters-&gt;getNumberOfClusters();</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         11 : bool ClusterAnalysisBase::isPeriodic() {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         11 :   return mybasemulticolvars[0]-&gt;isPeriodic();</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         66 : void ClusterAnalysisBase::retrieveAtomsInCluster( const unsigned&amp; clust, std::vector&lt;unsigned&gt;&amp; myatoms ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         66 :   myclusters-&gt;retrieveAtomsInCluster( clust, myatoms );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         66 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          1 : bool ClusterAnalysisBase::nodeIsActive( const unsigned&amp; ind ) const {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 :   return myclusters-&gt;isCurrentlyActive( ind );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1801 : void ClusterAnalysisBase::getPropertiesOfNode( const unsigned&amp; ind, std::vector&lt;double&gt;&amp; vals ) const {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1801 :   myclusters-&gt;getInputData( ind, false, myfatoms, vals );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1801 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1604 : void ClusterAnalysisBase::getNodePropertyDerivatives( const unsigned&amp; ind, MultiValue&amp; myvals ) const {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1604 :   myvals=myclusters-&gt;getInputDerivatives( ind, false, myfatoms );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1604 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       1975 : Vector ClusterAnalysisBase::getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1975 :   return myclusters-&gt;getPositionOfAtomForLinkCells( iatom );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 : double ClusterAnalysisBase::getCutoffForConnection() const {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   return myclusters-&gt;getCutoffForConnection();</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : bool ClusterAnalysisBase::areConnected( const unsigned&amp; ind1, const unsigned&amp; ind2 ) const {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   return myclusters-&gt;areConnected( ind1, ind2 );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterAnalysisBase.h.func-sort-c.html b/coverage/adjmat/ClusterAnalysisBase.h.func-sort-c.html
new file mode 100644
index 0000000000..dd1120d791
--- /dev/null
+++ b/coverage/adjmat/ClusterAnalysisBase.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterAnalysisBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterAnalysisBase.h<span style="font-size: 80%;"> (<a href="ClusterAnalysisBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterAnalysisBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.h.gcov.html#51">_ZNK4PLMD6adjmat19ClusterAnalysisBase7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterAnalysisBase.h.func.html b/coverage/adjmat/ClusterAnalysisBase.h.func.html
new file mode 100644
index 0000000000..4355d00309
--- /dev/null
+++ b/coverage/adjmat/ClusterAnalysisBase.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterAnalysisBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterAnalysisBase.h<span style="font-size: 80%;"> (<a href="ClusterAnalysisBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterAnalysisBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterAnalysisBase.h.gcov.html#51">_ZNK4PLMD6adjmat19ClusterAnalysisBase7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterAnalysisBase.h.gcov.html b/coverage/adjmat/ClusterAnalysisBase.h.gcov.html
new file mode 100644
index 0000000000..795b8336fa
--- /dev/null
+++ b/coverage/adjmat/ClusterAnalysisBase.h.gcov.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterAnalysisBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterAnalysisBase.h<span style="font-size: 80%;"> (source / <a href="ClusterAnalysisBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_adjmat_ClusterAnalysisBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_adjmat_ClusterAnalysisBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ClusteringBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace adjmat {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class ClusterAnalysisBase : public multicolvar::MultiColvarBase {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   MultiValue myfvals;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   multicolvar::AtomValuePack myfatoms;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   ClusteringBase* myclusters;</a>
+<a name="36"><span class="lineNum">      36 </span>            : protected:</a>
+<a name="37"><span class="lineNum">      37 </span>            :   unsigned getNumberOfNodes() const ;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   unsigned getNumberOfClusters() const ;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void retrieveAtomsInCluster( const unsigned&amp; clust, std::vector&lt;unsigned&gt;&amp; myatoms ) const ;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool nodeIsActive( const unsigned&amp; ind ) const ;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double getCutoffForConnection() const ;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   bool areConnected( const unsigned&amp; ind1, const unsigned&amp; ind2 ) const ;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void getPropertiesOfNode( const unsigned&amp; ind, std::vector&lt;double&gt;&amp; vals ) const ;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void getNodePropertyDerivatives( const unsigned&amp; ind, MultiValue&amp; myvals ) const ;</a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit ClusterAnalysisBase(const ActionOptions&amp;);</a>
+<a name="48"><span class="lineNum">      48 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   bool isPeriodic() override;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void turnOnDerivatives() override;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   void setupActiveTaskSet( std::vector&lt;unsigned&gt;&amp; active_tasks, const std::string&amp; input_label ) {}</a>
+<a name="52"><span class="lineNum">      52 </span>            :   Vector getPositionOfAtomForLinkCells( const unsigned&amp; ) const override;</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override { plumed_error(); }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : #endif</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterDiameter.cpp.func-sort-c.html b/coverage/adjmat/ClusterDiameter.cpp.func-sort-c.html
new file mode 100644
index 0000000000..abfae80e60
--- /dev/null
+++ b/coverage/adjmat/ClusterDiameter.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterDiameter.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterDiameter.cpp<span style="font-size: 80%;"> (<a href="ClusterDiameter.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">93.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterDiameter.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#103">_ZN4PLMD6adjmat15ClusterDiameter17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#85">_ZN4PLMD6adjmat15ClusterDiameterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#78">_ZN4PLMD6adjmat12_GLOBAL__N_127ClusterDiameterRegisterMe806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#107">_ZN4PLMD6adjmat15ClusterDiameter9calculateEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#85">_ZN4PLMD6adjmat15ClusterDiameterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#80">_ZN4PLMD6adjmat15ClusterDiameter16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#120">_ZNK4PLMD6adjmat15ClusterDiameter11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">2016</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#78">_ZN4PLMD6adjmat12_GLOBAL__N_127ClusterDiameterRegisterMe80C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#78">_ZN4PLMD6adjmat12_GLOBAL__N_127ClusterDiameterRegisterMe80D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterDiameter.cpp.func.html b/coverage/adjmat/ClusterDiameter.cpp.func.html
new file mode 100644
index 0000000000..0a72a5cb88
--- /dev/null
+++ b/coverage/adjmat/ClusterDiameter.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterDiameter.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterDiameter.cpp<span style="font-size: 80%;"> (<a href="ClusterDiameter.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">93.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterDiameter.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#78">_ZN4PLMD6adjmat12_GLOBAL__N_127ClusterDiameterRegisterMe806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#78">_ZN4PLMD6adjmat12_GLOBAL__N_127ClusterDiameterRegisterMe80C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#78">_ZN4PLMD6adjmat12_GLOBAL__N_127ClusterDiameterRegisterMe80D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#80">_ZN4PLMD6adjmat15ClusterDiameter16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#103">_ZN4PLMD6adjmat15ClusterDiameter17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#107">_ZN4PLMD6adjmat15ClusterDiameter9calculateEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#85">_ZN4PLMD6adjmat15ClusterDiameterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#85">_ZN4PLMD6adjmat15ClusterDiameterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDiameter.cpp.gcov.html#120">_ZNK4PLMD6adjmat15ClusterDiameter11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">2016</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterDiameter.cpp.gcov.html b/coverage/adjmat/ClusterDiameter.cpp.gcov.html
new file mode 100644
index 0000000000..e9f6aecd64
--- /dev/null
+++ b/coverage/adjmat/ClusterDiameter.cpp.gcov.html
@@ -0,0 +1,206 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterDiameter.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterDiameter.cpp<span style="font-size: 80%;"> (source / <a href="ClusterDiameter.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">93.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusterAnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC CONCOMP CLUSTER_DIAMETER</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Print out the diameter of one of the connected components</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="30"><span class="lineNum">      30 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="31"><span class="lineNum">      31 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  When analyzing these matrix</a>
+<a name="32"><span class="lineNum">      32 </span>            : we can treat them as a graph and find connected components using some clustering algorithm.  This action is used in tandem with this form of analysis</a>
+<a name="33"><span class="lineNum">      33 </span>            : to output the largest of the distances between the pairs of atoms that are connected together in a particular connected component.  It is important to</a>
+<a name="34"><span class="lineNum">      34 </span>            : note that the quantity that is output by this action cannot be differentiated.  As such it cannot be used as a collective variable in a biased simulation.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is greater</a>
+<a name="39"><span class="lineNum">      39 </span>            : than 2.0 and if they are within 6.0 nm of each other.  Depth first search clustering is used to find the connected components in this matrix.  The distance</a>
+<a name="40"><span class="lineNum">      40 </span>            : between every pair of atoms that are within the largest of the clusters found is then calculated and the largest of these distances is output to a file named</a>
+<a name="41"><span class="lineNum">      41 </span>            : colvar.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \plumedfile</a>
+<a name="44"><span class="lineNum">      44 </span>            : # Calculate coordination numbers</a>
+<a name="45"><span class="lineNum">      45 </span>            : c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="46"><span class="lineNum">      46 </span>            : # Select coordination numbers that are more than 2.0</a>
+<a name="47"><span class="lineNum">      47 </span>            : cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM</a>
+<a name="48"><span class="lineNum">      48 </span>            : # Build a contact matrix</a>
+<a name="49"><span class="lineNum">      49 </span>            : mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="50"><span class="lineNum">      50 </span>            : # Find largest cluster</a>
+<a name="51"><span class="lineNum">      51 </span>            : dfs: DFSCLUSTERING MATRIX=mat</a>
+<a name="52"><span class="lineNum">      52 </span>            : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1</a>
+<a name="53"><span class="lineNum">      53 </span>            : dia: CLUSTER_DIAMETER CLUSTERS=dfs CLUSTER=1</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=dia FILE=colvar</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : */</a>
+<a name="58"><span class="lineNum">      58 </span>            : //+ENDPLUMEDOC</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : namespace PLMD {</a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace adjmat {</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : class ClusterDiameter : public ClusterAnalysisBase {</a>
+<a name="64"><span class="lineNum">      64 </span>            : private:</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// The cluster we are looking for</a>
+<a name="66"><span class="lineNum">      66 </span>            :   unsigned clustr;</a>
+<a name="67"><span class="lineNum">      67 </span>            : public:</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Create manual</a>
+<a name="69"><span class="lineNum">      69 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Constructor</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit ClusterDiameter(const ActionOptions&amp;);</a>
+<a name="72"><span class="lineNum">      72 </span>            : ///</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void calculate() override;</a>
+<a name="74"><span class="lineNum">      74 </span>            : ///</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="76"><span class="lineNum">      76 </span>            : ///</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void turnOnDerivatives() override;</a>
+<a name="78"><span class="lineNum">      78 </span>            : };</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ClusterDiameter,&quot;CLUSTER_DIAMETER&quot;)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 : void ClusterDiameter::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   ClusterAnalysisBase::registerKeywords( keys );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTER&quot;,&quot;1&quot;,&quot;which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on.&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 : ClusterDiameter::ClusterDiameter(const ActionOptions&amp;ao):</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   Action(ao),</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 :   ClusterAnalysisBase(ao)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : {</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // Find out which cluster we want</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 :   parse(&quot;CLUSTER&quot;,clustr);</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   if( clustr&lt;1 ) error(&quot;cannot look for a cluster larger than the largest cluster&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   if( clustr&gt;getNumberOfNodes() ) error(&quot;cluster selected is invalid - too few atoms in system&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Create the task list</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       3994 :   for(unsigned  i=0; i&lt;getNumberOfNodes(); ++i) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">    7972024 :     for(unsigned j=0; j&lt;getNumberOfNodes(); ++j) addTaskToList( i*getNumberOfNodes() + j );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span>            :   // Now create a highest vessel</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :   addVessel(&quot;HIGHEST&quot;, &quot;&quot;, -1); std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          2 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 : void ClusterDiameter::turnOnDerivatives() {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   error(&quot;cannot calculate derivatives of cluster radius.  This quantity is not differentiable&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 : void ClusterDiameter::calculate() {</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Retrieve the atoms in the largest cluster</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :   std::vector&lt;unsigned&gt; myatoms; retrieveAtomsInCluster( clustr, myatoms );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   // Activate the relevant tasks</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   deactivateAllTasks();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        128 :   for(unsigned i=1; i&lt;myatoms.size(); ++i) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4158 :     for(unsigned j=0; j&lt;i; ++j) taskFlags[ myatoms[i]*getNumberOfNodes() + myatoms[j] ] = 1;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   lockContributors();</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   // Now do the calculation</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 :   runAllTasks();</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 : }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       2016 : void ClusterDiameter::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       2016 :   unsigned iatom=std::floor(current/getNumberOfNodes()), jatom = current - iatom*getNumberOfNodes();</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       2016 :   Vector distance=getSeparation( getPosition(iatom), getPosition(jatom) );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       2016 :   double dd = distance.modulo();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   myvals.setValue( 0, 1.0 ); myvals.setValue( 1, dd );</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       2016 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterDistribution.cpp.func-sort-c.html b/coverage/adjmat/ClusterDistribution.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7bf2a1f10d
--- /dev/null
+++ b/coverage/adjmat/ClusterDistribution.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterDistribution.cpp<span style="font-size: 80%;"> (<a href="ClusterDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryMed">87.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterDistribution.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#92">_ZN4PLMD6adjmat19ClusterDistributionC2ERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#113">_ZN4PLMD6adjmat19ClusterDistribution9calculateEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#92">_ZN4PLMD6adjmat19ClusterDistributionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#83">_ZN4PLMD6adjmat19ClusterDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#123">_ZNK4PLMD6adjmat19ClusterDistribution11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_131ClusterDistributionRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_131ClusterDistributionRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterDistribution.cpp.func.html b/coverage/adjmat/ClusterDistribution.cpp.func.html
new file mode 100644
index 0000000000..d56640f7c1
--- /dev/null
+++ b/coverage/adjmat/ClusterDistribution.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterDistribution.cpp<span style="font-size: 80%;"> (<a href="ClusterDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryMed">87.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterDistribution.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_131ClusterDistributionRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_131ClusterDistributionRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_131ClusterDistributionRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#83">_ZN4PLMD6adjmat19ClusterDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#113">_ZN4PLMD6adjmat19ClusterDistribution9calculateEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#92">_ZN4PLMD6adjmat19ClusterDistributionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#92">_ZN4PLMD6adjmat19ClusterDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterDistribution.cpp.gcov.html#123">_ZNK4PLMD6adjmat19ClusterDistribution11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterDistribution.cpp.gcov.html b/coverage/adjmat/ClusterDistribution.cpp.gcov.html
new file mode 100644
index 0000000000..44aefbfbf5
--- /dev/null
+++ b/coverage/adjmat/ClusterDistribution.cpp.gcov.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterDistribution.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterDistribution.cpp<span style="font-size: 80%;"> (source / <a href="ClusterDistribution.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryMed">87.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusterAnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC CONCOMP CLUSTER_DISTRIBUTION</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Calculate functions of the distribution of properties in your connected components.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : This collective variable was developed for looking at nucleation phenomena, where you are</a>
+<a name="32"><span class="lineNum">      32 </span>            : interested in using studying the behavior of atoms in small aggregates or nuclei.  In these sorts of</a>
+<a name="33"><span class="lineNum">      33 </span>            : problems you might be interested in the distribution of the sizes of the clusters in your system.</a>
+<a name="34"><span class="lineNum">      34 </span>            : A detailed description of this CV can be found in \cite tribello-clustering.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The input provided below calculates the local q6 Steinhardt parameter on each atom.  The coordination number</a>
+<a name="39"><span class="lineNum">      39 </span>            : that atoms with a high value for the local q6 Steinhardt parameter have with other atoms that have a high</a>
+<a name="40"><span class="lineNum">      40 </span>            : value for the local q6 Steinhardt parameter is then computed.  A contact matrix is then computed that measures</a>
+<a name="41"><span class="lineNum">      41 </span>            : whether atoms atoms \f$i\f$ and \f$j\f$ have a high value for this coordination number and if they are within</a>
+<a name="42"><span class="lineNum">      42 </span>            : 3.6 nm of each other.  The connected components of this matrix are then found using a depth first clustering</a>
+<a name="43"><span class="lineNum">      43 </span>            : algorithm on the corresponding graph. The number of components in this graph that contain more than 27 atoms is then computed.</a>
+<a name="44"><span class="lineNum">      44 </span>            : As discussed in \cite tribello-clustering an input similar to this one was used to analyze the formation of a polycrystal of GeTe from amorphous</a>
+<a name="45"><span class="lineNum">      45 </span>            : GeTe.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \plumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : q6: Q6 SPECIES=1-300 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM</a>
+<a name="49"><span class="lineNum">      49 </span>            : lq6: LOCAL_Q6 SPECIES=q6 SWITCH={GAUSSIAN D_0=5.29 R_0=0.01 D_MAX=5.3} LOWMEM</a>
+<a name="50"><span class="lineNum">      50 </span>            : flq6: MFILTER_MORE DATA=lq6 SWITCH={GAUSSIAN D_0=0.19 R_0=0.01 D_MAX=0.2}</a>
+<a name="51"><span class="lineNum">      51 </span>            : cc: COORDINATIONNUMBER SPECIES=flq6 SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}</a>
+<a name="52"><span class="lineNum">      52 </span>            : fcc: MFILTER_MORE DATA=cc SWITCH={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0}</a>
+<a name="53"><span class="lineNum">      53 </span>            : mat: CONTACT_MATRIX ATOMS=fcc SWITCH={GAUSSIAN D_0=3.59 R_0=0.01 D_MAX=3.6}</a>
+<a name="54"><span class="lineNum">      54 </span>            : dfs: DFSCLUSTERING MATRIX=mat</a>
+<a name="55"><span class="lineNum">      55 </span>            : nclust: CLUSTER_DISTRIBUTION CLUSTERS=dfs TRANSFORM={GAUSSIAN D_0=5.99 R_0=0.01 D_MAX=6.0} MORE_THAN={GAUSSIAN D_0=26.99 R_0=0.01 D_MAX=27}</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=nclust.* FILE=colvar</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : */</a>
+<a name="60"><span class="lineNum">      60 </span>            : //+ENDPLUMEDOC</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace PLMD {</a>
+<a name="63"><span class="lineNum">      63 </span>            : namespace adjmat {</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : class ClusterDistribution : public ClusterAnalysisBase {</a>
+<a name="66"><span class="lineNum">      66 </span>            : private:</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned nderivatives;</a>
+<a name="68"><span class="lineNum">      68 </span>            : ///</a>
+<a name="69"><span class="lineNum">      69 </span>            :   bool use_switch, inverse;</a>
+<a name="70"><span class="lineNum">      70 </span>            : //</a>
+<a name="71"><span class="lineNum">      71 </span>            :   SwitchingFunction sf;</a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Create manual</a>
+<a name="74"><span class="lineNum">      74 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Constructor</a>
+<a name="76"><span class="lineNum">      76 </span>            :   explicit ClusterDistribution(const ActionOptions&amp;);</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Do the calculation</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void calculate() override;</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// We can use ActionWithVessel to run all the calculation</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(ClusterDistribution,&quot;CLUSTER_DISTRIBUTION&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          3 : void ClusterDistribution::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          3 :   ClusterAnalysisBase::registerKeywords( keys );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;TRANSFORM&quot;,&quot;none&quot;,&quot;the switching function to use to convert the crystallinity parameter to a number between zero and one&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          6 :   keys.addFlag(&quot;INVERSE_TRANSFORM&quot;,false,&quot;when TRANSFORM appears alone the input symmetry functions, \\f$x\\f$ are transformed used \\f$1-s(x)\\f$ &quot;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :                &quot;where \\f$s(x)\\f$ is a switching function.  When this option is used you instead transform using \\f$s(x)\\f$ only.&quot;);</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          9 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;BETWEEN&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         12 :   keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          3 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 : ClusterDistribution::ClusterDistribution(const ActionOptions&amp;ao):</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   Action(ao),</a>
+<a name="96"><span class="lineNum">      96 </span>            :   ClusterAnalysisBase(ao),</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          1 :   nderivatives(0)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : {</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          1 :   use_switch=false;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   std::string input, errors; parse(&quot;TRANSFORM&quot;,input);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :   if( input!=&quot;none&quot; ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :     use_switch=true; sf.set( input, errors );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          1 :   parseFlag(&quot;INVERSE_TRANSFORM&quot;,inverse);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :   if( inverse &amp;&amp; !use_switch ) error(&quot;INVERSE_TRANSFORM option was specified but no TRANSOFRM switching function was given&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          7 :   for(unsigned i=0; i&lt;getNumberOfNodes(); ++i) addTaskToList(i);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   // And now finish the setup of everything in the base</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          1 :   std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          1 : void ClusterDistribution::calculate() {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   // Activate the relevant tasks</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :   nderivatives = getNumberOfDerivatives();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   deactivateAllTasks();</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;getNumberOfClusters(); ++i) taskFlags[i]=1;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          1 :   lockContributors();</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   // Now do the calculation</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 :   runAllTasks();</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 : void ClusterDistribution::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          3 :   std::vector&lt;unsigned&gt; myatoms; retrieveAtomsInCluster( current+1, myatoms );</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   // This deals with filters</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          3 :   if( myatoms.size()==1 &amp;&amp; !nodeIsActive(myatoms[0]) ) return ;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; vals( getNumberOfQuantities() );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          3 :   MultiValue tvals( getNumberOfQuantities(), nderivatives );</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   // And this builds everything for this particular atom</a>
+<a name="134"><span class="lineNum">     134 </span>            :   double vv, df, tval=0;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          9 :   for(unsigned j=0; j&lt;myatoms.size(); ++j) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          6 :     unsigned i=myatoms[j];</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :     getPropertiesOfNode( i, vals );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          6 :     if( use_switch &amp;&amp; !inverse ) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :       vv = 1.0 - sf.calculate( vals[1], df );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       tval += vals[0]*vv; df=-df*vals[1];</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          6 :     } else if( use_switch ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :       vv = sf.calculate( vals[1], df );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :       tval += vals[0]*vv; df=df*vals[1];</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     } else {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          6 :       tval += vals[0]*vals[1]; df=1.; vv=vals[1];</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          6 :     if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          6 :       getNodePropertyDerivatives( i, tvals );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        168 :       for(unsigned k=0; k&lt;tvals.getNumberActive(); ++k) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        162 :         unsigned kat=tvals.getActiveIndex(k);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        162 :         myvals.addDerivative( 1, kat, vals[0]*df*tvals.getDerivative(1,kat) + vv*tvals.getDerivative(0,kat) );</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :       }</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          6 :       tvals.clearAll();</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     }</a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            :   myvals.setValue( 0, 1.0 ); myvals.setValue( 1, tval );</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterProperties.cpp.func-sort-c.html b/coverage/adjmat/ClusterProperties.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fa17a1d9f9
--- /dev/null
+++ b/coverage/adjmat/ClusterProperties.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterProperties.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterProperties.cpp<span style="font-size: 80%;"> (<a href="ClusterProperties.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterProperties.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#84">_ZN4PLMD6adjmat17ClusterPropertiesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#72">_ZN4PLMD6adjmat12_GLOBAL__N_129ClusterPropertiesRegisterMe746createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#84">_ZN4PLMD6adjmat17ClusterPropertiesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#74">_ZN4PLMD6adjmat17ClusterProperties16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#101">_ZN4PLMD6adjmat17ClusterProperties9calculateEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#112">_ZNK4PLMD6adjmat17ClusterProperties11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">1795</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#72">_ZN4PLMD6adjmat12_GLOBAL__N_129ClusterPropertiesRegisterMe74C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#72">_ZN4PLMD6adjmat12_GLOBAL__N_129ClusterPropertiesRegisterMe74D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterProperties.cpp.func.html b/coverage/adjmat/ClusterProperties.cpp.func.html
new file mode 100644
index 0000000000..b52c1f0e47
--- /dev/null
+++ b/coverage/adjmat/ClusterProperties.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterProperties.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterProperties.cpp<span style="font-size: 80%;"> (<a href="ClusterProperties.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterProperties.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#72">_ZN4PLMD6adjmat12_GLOBAL__N_129ClusterPropertiesRegisterMe746createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#72">_ZN4PLMD6adjmat12_GLOBAL__N_129ClusterPropertiesRegisterMe74C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#72">_ZN4PLMD6adjmat12_GLOBAL__N_129ClusterPropertiesRegisterMe74D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#74">_ZN4PLMD6adjmat17ClusterProperties16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#101">_ZN4PLMD6adjmat17ClusterProperties9calculateEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#84">_ZN4PLMD6adjmat17ClusterPropertiesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#84">_ZN4PLMD6adjmat17ClusterPropertiesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterProperties.cpp.gcov.html#112">_ZNK4PLMD6adjmat17ClusterProperties11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">1795</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterProperties.cpp.gcov.html b/coverage/adjmat/ClusterProperties.cpp.gcov.html
new file mode 100644
index 0000000000..ebabb42ee5
--- /dev/null
+++ b/coverage/adjmat/ClusterProperties.cpp.gcov.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterProperties.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterProperties.cpp<span style="font-size: 80%;"> (source / <a href="ClusterProperties.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusterAnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC CONCOMP CLUSTER_PROPERTIES</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate properties of the distribution of some quantities that are part of a connected component</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : This collective variable was developed for looking at nucleation phenomena, where you are</a>
+<a name="31"><span class="lineNum">      31 </span>            : interested in using studying the behavior of atoms in small aggregates or nuclei.  In these sorts of</a>
+<a name="32"><span class="lineNum">      32 </span>            : problems you might be interested in the degree the atoms in a nucleus have adopted their crystalline</a>
+<a name="33"><span class="lineNum">      33 </span>            : structure or (in the case of heterogeneous nucleation of a solute from a solvent) you might be</a>
+<a name="34"><span class="lineNum">      34 </span>            : interested in how many atoms are present in the largest cluster \cite tribello-clustering.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The input below calculates the coordination numbers of atoms 1-100 and then computes the an adjacency</a>
+<a name="39"><span class="lineNum">      39 </span>            : matrix whose elements measures whether atoms \f$i\f$ and \f$j\f$ are within 0.55 nm of each other.  The action</a>
+<a name="40"><span class="lineNum">      40 </span>            : labelled dfs then treats the elements of this matrix as zero or ones and thus thinks of the matrix as defining</a>
+<a name="41"><span class="lineNum">      41 </span>            : a graph.  This dfs action then finds the largest connected component in this graph.  The sum of the coordination</a>
+<a name="42"><span class="lineNum">      42 </span>            : numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar</a>
+<a name="43"><span class="lineNum">      43 </span>            : file.  The way this input can be used is described in detail in \cite tribello-clustering.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55} LOWMEM</a>
+<a name="47"><span class="lineNum">      47 </span>            : cm: CONTACT_MATRIX ATOMS=lq  SWITCH={CUBIC D_0=0.45  D_MAX=0.55}</a>
+<a name="48"><span class="lineNum">      48 </span>            : dfs: DFSCLUSTERING MATRIX=cm</a>
+<a name="49"><span class="lineNum">      49 </span>            : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM</a>
+<a name="50"><span class="lineNum">      50 </span>            : PRINT ARG=clust1.* FILE=colvar</a>
+<a name="51"><span class="lineNum">      51 </span>            : \endplumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : */</a>
+<a name="54"><span class="lineNum">      54 </span>            : //+ENDPLUMEDOC</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : namespace PLMD {</a>
+<a name="57"><span class="lineNum">      57 </span>            : namespace adjmat {</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : class ClusterProperties : public ClusterAnalysisBase {</a>
+<a name="60"><span class="lineNum">      60 </span>            : private:</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// The cluster we are looking for</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned clustr;</a>
+<a name="63"><span class="lineNum">      63 </span>            : public:</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Create manual</a>
+<a name="65"><span class="lineNum">      65 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Constructor</a>
+<a name="67"><span class="lineNum">      67 </span>            :   explicit ClusterProperties(const ActionOptions&amp;);</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Do the calculation</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void calculate() override;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// We can use ActionWithVessel to run all the calculation</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="72"><span class="lineNum">      72 </span>            : };</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      12558 : PLUMED_REGISTER_ACTION(ClusterProperties,&quot;CLUSTER_PROPERTIES&quot;)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         29 : void ClusterProperties::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         29 :   ClusterAnalysisBase::registerKeywords( keys );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         58 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTER&quot;,&quot;1&quot;,&quot;which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on.&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         87 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         87 :   if( keys.reserved(&quot;VMEAN&quot;) ) keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         87 :   if( keys.reserved(&quot;VSUM&quot;) ) keys.use(&quot;VSUM&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        116 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;); keys.use(&quot;ALT_MIN&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        145 :   keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;SUM&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         29 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         27 : ClusterProperties::ClusterProperties(const ActionOptions&amp;ao):</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   Action(ao),</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         27 :   ClusterAnalysisBase(ao)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Find out which cluster we want</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         27 :   parse(&quot;CLUSTER&quot;,clustr);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         27 :   if( clustr&lt;1 ) error(&quot;cannot look for a cluster larger than the largest cluster&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         27 :   if( clustr&gt;getNumberOfNodes() ) error(&quot;cluster selected is invalid - too few atoms in system&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      18214 :   for(unsigned i=0; i&lt;getNumberOfNodes(); ++i) addTaskToList(i);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   // And now finish the setup of everything in the base</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         27 :   std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         27 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         34 : void ClusterProperties::calculate() {</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   // Retrieve the atoms in the largest cluster</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         34 :   std::vector&lt;unsigned&gt; myatoms; retrieveAtomsInCluster( clustr, myatoms );</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   // Activate the relevant tasks</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         34 :   deactivateAllTasks();</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1373 :   for(unsigned i=0; i&lt;myatoms.size(); ++i) taskFlags[myatoms[i]]=1;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         34 :   lockContributors();</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Now do the calculation</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         34 :   runAllTasks();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         34 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1795 : void ClusterProperties::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1795 :   std::vector&lt;double&gt; vals( myvals.getNumberOfValues() ); getPropertiesOfNode( current, vals );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       1795 :   if( !doNotCalculateDerivatives() ) getNodePropertyDerivatives( current, myvals );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       5385 :   for(unsigned k=0; k&lt;vals.size(); ++k) myvals.setValue( k, vals[k] );</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1795 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterSize.cpp.func-sort-c.html b/coverage/adjmat/ClusterSize.cpp.func-sort-c.html
new file mode 100644
index 0000000000..581e51972e
--- /dev/null
+++ b/coverage/adjmat/ClusterSize.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterSize.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterSize.cpp<span style="font-size: 80%;"> (<a href="ClusterSize.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">85.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterSize.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#101">_ZN4PLMD6adjmat11ClusterSize17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#84">_ZN4PLMD6adjmat11ClusterSizeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#72">_ZNK4PLMD6adjmat11ClusterSize11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#84">_ZN4PLMD6adjmat11ClusterSizeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#77">_ZN4PLMD6adjmat12_GLOBAL__N_123ClusterSizeRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#79">_ZN4PLMD6adjmat11ClusterSize16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#105">_ZN4PLMD6adjmat11ClusterSize9calculateEv</a></td>
+              <td class="coverFnHi">27</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#77">_ZN4PLMD6adjmat12_GLOBAL__N_123ClusterSizeRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#77">_ZN4PLMD6adjmat12_GLOBAL__N_123ClusterSizeRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterSize.cpp.func.html b/coverage/adjmat/ClusterSize.cpp.func.html
new file mode 100644
index 0000000000..cff91f004c
--- /dev/null
+++ b/coverage/adjmat/ClusterSize.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterSize.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterSize.cpp<span style="font-size: 80%;"> (<a href="ClusterSize.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">85.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterSize.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#79">_ZN4PLMD6adjmat11ClusterSize16registerKeywordsERNS_8KeywordsE</a></td>
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+    <tr>
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+    <tr>
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+    <tr>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#77">_ZN4PLMD6adjmat12_GLOBAL__N_123ClusterSizeRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#77">_ZN4PLMD6adjmat12_GLOBAL__N_123ClusterSizeRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#77">_ZN4PLMD6adjmat12_GLOBAL__N_123ClusterSizeRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterSize.cpp.gcov.html#72">_ZNK4PLMD6adjmat11ClusterSize11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterSize.cpp.gcov.html b/coverage/adjmat/ClusterSize.cpp.gcov.html
new file mode 100644
index 0000000000..32990c7189
--- /dev/null
+++ b/coverage/adjmat/ClusterSize.cpp.gcov.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterSize.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterSize.cpp<span style="font-size: 80%;"> (source / <a href="ClusterSize.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">85.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusterAnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC CONCOMP CLUSTER_NATOMS</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Gives the number of atoms in the connected component</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="30"><span class="lineNum">      30 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="31"><span class="lineNum">      31 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  When analyzing these matrix</a>
+<a name="32"><span class="lineNum">      32 </span>            : we can treat them as a graph and find connected components using some clustering algorithm.  This action is used in tandem with this form of analysis</a>
+<a name="33"><span class="lineNum">      33 </span>            : to output the number of atoms that are connected together in a particular connected component.  It is important to note that the quantity that is</a>
+<a name="34"><span class="lineNum">      34 </span>            : output by this action cannot be differentiated.  As such it cannot be used as a collective variable in a biased simulation.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is greater</a>
+<a name="39"><span class="lineNum">      39 </span>            : than 2.0 and if they are within 6.0 nm of each other.  Depth first search clustering is used to find the connected components in this matrix and then</a>
+<a name="40"><span class="lineNum">      40 </span>            : the number of atoms in the largest cluster is found.  This quantity is then output to a file called colvar</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : # Calculate coordination numbers</a>
+<a name="44"><span class="lineNum">      44 </span>            : c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="45"><span class="lineNum">      45 </span>            : # Select coordination numbers that are more than 2.0</a>
+<a name="46"><span class="lineNum">      46 </span>            : cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM</a>
+<a name="47"><span class="lineNum">      47 </span>            : # Build a contact matrix</a>
+<a name="48"><span class="lineNum">      48 </span>            : mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="49"><span class="lineNum">      49 </span>            : # Find largest cluster</a>
+<a name="50"><span class="lineNum">      50 </span>            : dfs: DFSCLUSTERING MATRIX=mat</a>
+<a name="51"><span class="lineNum">      51 </span>            : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1</a>
+<a name="52"><span class="lineNum">      52 </span>            : nat: CLUSTER_NATOMS CLUSTERS=dfs CLUSTER=1</a>
+<a name="53"><span class="lineNum">      53 </span>            : PRINT ARG=nat FILE=COLVAR</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endplumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : */</a>
+<a name="57"><span class="lineNum">      57 </span>            : //+ENDPLUMEDOC</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : namespace PLMD {</a>
+<a name="60"><span class="lineNum">      60 </span>            : namespace adjmat {</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : class ClusterSize : public ClusterAnalysisBase {</a>
+<a name="63"><span class="lineNum">      63 </span>            : private:</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// The cluster we are looking for</a>
+<a name="65"><span class="lineNum">      65 </span>            :   unsigned clustr;</a>
+<a name="66"><span class="lineNum">      66 </span>            : public:</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Create manual</a>
+<a name="68"><span class="lineNum">      68 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Constructor</a>
+<a name="70"><span class="lineNum">      70 </span>            :   explicit ClusterSize(const ActionOptions&amp;);</a>
+<a name="71"><span class="lineNum">      71 </span>            : ///</a>
+<a name="72"><span class="lineNum">      72 </span>            :   void calculate() override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : ///</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const override { plumed_error(); }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : ///</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void turnOnDerivatives() override;</a>
+<a name="77"><span class="lineNum">      77 </span>            : };</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      12552 : PLUMED_REGISTER_ACTION(ClusterSize,&quot;CLUSTER_NATOMS&quot;)</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         26 : void ClusterSize::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         26 :   ClusterAnalysisBase::registerKeywords( keys );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         52 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTER&quot;,&quot;1&quot;,&quot;which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on.&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         26 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         24 : ClusterSize::ClusterSize(const ActionOptions&amp;ao):</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   Action(ao),</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         24 :   ClusterAnalysisBase(ao)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Find out which cluster we want</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         24 :   parse(&quot;CLUSTER&quot;,clustr);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         24 :   if( clustr&lt;1 ) error(&quot;cannot look for a cluster larger than the largest cluster&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         24 :   if( clustr&gt;getNumberOfNodes() ) error(&quot;cluster selected is invalid - too few atoms in system&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Create all tasks by copying those from underlying DFS object (which is actually MultiColvar)</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      11488 :   for(unsigned i=0; i&lt;getNumberOfNodes(); ++i) addTaskToList(i);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   // And now finish the setup of everything in the base</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         24 :   std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         24 :   addValue(); setNotPeriodic();</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         24 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 : void ClusterSize::turnOnDerivatives() {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   error(&quot;cannot calculate derivatives of number of atoms in cluster.  This quantity is not differentiable&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         27 : void ClusterSize::calculate() {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Retrieve the atoms in the largest cluster</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         27 :   std::vector&lt;unsigned&gt; myatoms; retrieveAtomsInCluster( clustr, myatoms ); setValue( myatoms.size() );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         27 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterWithSurface.cpp.func-sort-c.html b/coverage/adjmat/ClusterWithSurface.cpp.func-sort-c.html
new file mode 100644
index 0000000000..879534a735
--- /dev/null
+++ b/coverage/adjmat/ClusterWithSurface.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterWithSurface.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterWithSurface.cpp<span style="font-size: 80%;"> (<a href="ClusterWithSurface.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">86.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusterWithSurface.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#106">_ZN4PLMD6adjmat18ClusterWithSurfaceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#139">_ZNK4PLMD6adjmat18ClusterWithSurface12getInputDataERKjRKbRKNS_11multicolvar13AtomValuePackERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#143">_ZNK4PLMD6adjmat18ClusterWithSurface19getInputDerivativesERKjRKbRKNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#186">_ZNK4PLMD6adjmat18ClusterWithSurface29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#96">_ZN4PLMD6adjmat12_GLOBAL__N_130ClusterWithSurfaceRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#89">_ZN4PLMD6adjmat18ClusterWithSurface17performClusteringEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#106">_ZN4PLMD6adjmat18ClusterWithSurfaceC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#151">_ZNK4PLMD6adjmat18ClusterWithSurface22getCutoffForConnectionEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#98">_ZN4PLMD6adjmat18ClusterWithSurface16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#127">_ZN4PLMD6adjmat18ClusterWithSurface22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#157">_ZNK4PLMD6adjmat18ClusterWithSurface22retrieveAtomsInClusterERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#135">_ZNK4PLMD6adjmat18ClusterWithSurface29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#96">_ZN4PLMD6adjmat12_GLOBAL__N_130ClusterWithSurfaceRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#96">_ZN4PLMD6adjmat12_GLOBAL__N_130ClusterWithSurfaceRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#131">_ZNK4PLMD6adjmat18ClusterWithSurface16getNumberOfNodesEv</a></td>
+              <td class="coverFnHi">16155834</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterWithSurface.cpp.func.html b/coverage/adjmat/ClusterWithSurface.cpp.func.html
new file mode 100644
index 0000000000..3fc3facf48
--- /dev/null
+++ b/coverage/adjmat/ClusterWithSurface.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterWithSurface.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterWithSurface.cpp<span style="font-size: 80%;"> (<a href="ClusterWithSurface.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">86.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusterWithSurface.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#96">_ZN4PLMD6adjmat12_GLOBAL__N_130ClusterWithSurfaceRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#96">_ZN4PLMD6adjmat12_GLOBAL__N_130ClusterWithSurfaceRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#96">_ZN4PLMD6adjmat12_GLOBAL__N_130ClusterWithSurfaceRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#98">_ZN4PLMD6adjmat18ClusterWithSurface16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#89">_ZN4PLMD6adjmat18ClusterWithSurface17performClusteringEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#127">_ZN4PLMD6adjmat18ClusterWithSurface22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#106">_ZN4PLMD6adjmat18ClusterWithSurfaceC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#106">_ZN4PLMD6adjmat18ClusterWithSurfaceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#139">_ZNK4PLMD6adjmat18ClusterWithSurface12getInputDataERKjRKbRKNS_11multicolvar13AtomValuePackERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#131">_ZNK4PLMD6adjmat18ClusterWithSurface16getNumberOfNodesEv</a></td>
+              <td class="coverFnHi">16155834</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#143">_ZNK4PLMD6adjmat18ClusterWithSurface19getInputDerivativesERKjRKbRKNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#147">_ZNK4PLMD6adjmat18ClusterWithSurface21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#151">_ZNK4PLMD6adjmat18ClusterWithSurface22getCutoffForConnectionEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#157">_ZNK4PLMD6adjmat18ClusterWithSurface22retrieveAtomsInClusterERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#135">_ZNK4PLMD6adjmat18ClusterWithSurface29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusterWithSurface.cpp.gcov.html#186">_ZNK4PLMD6adjmat18ClusterWithSurface29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusterWithSurface.cpp.gcov.html b/coverage/adjmat/ClusterWithSurface.cpp.gcov.html
new file mode 100644
index 0000000000..ccf1056846
--- /dev/null
+++ b/coverage/adjmat/ClusterWithSurface.cpp.gcov.html
@@ -0,0 +1,269 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusterWithSurface.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusterWithSurface.cpp<span style="font-size: 80%;"> (source / <a href="ClusterWithSurface.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">86.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusteringBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC MATRIXF CLUSTER_WITHSURFACE</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Take a connected component that was found using a clustering algorithm and create a new cluster that contains those atoms that are in the cluster together with those atoms that are within a certain cutoff of the cluster.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="32"><span class="lineNum">      32 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="33"><span class="lineNum">      33 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  When analyzing these matrix</a>
+<a name="34"><span class="lineNum">      34 </span>            : we can treat them as a graph and find connected components using some clustering algorithm.  This action is used in tandem with this form of analysis</a>
+<a name="35"><span class="lineNum">      35 </span>            : and takes one of the connected components that was found during this analysis and creates a new cluster that includes all the atoms within the</a>
+<a name="36"><span class="lineNum">      36 </span>            : connected component that was found together that were within a certain cutoff distance of the atoms in the connected component.  This form of analysis</a>
+<a name="37"><span class="lineNum">      37 </span>            : has been used successfully in the forward flux sampling simulations described in this paper \cite gab-ice-kaolinite</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The following input uses PLUMED to calculate a adjacency matrix that connects a pair of atoms if they both have a coordination number that is less</a>
+<a name="42"><span class="lineNum">      42 </span>            : than 13.5 and if they are within 0.38 nm of each other.  Depth first search clustering is used to find the connected components in this matrix.  The</a>
+<a name="43"><span class="lineNum">      43 </span>            : number of atoms with indices that are between 1 and 1996 and that are either in the second largest cluster or that are within within 0.3 nm of one of the</a>
+<a name="44"><span class="lineNum">      44 </span>            : atoms within the the second largest cluster are then counted and this number of atoms is output to a file called size.  In addition the indices of the atoms</a>
+<a name="45"><span class="lineNum">      45 </span>            : that were counted are output to a file called dfs2.dat.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \plumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}</a>
+<a name="49"><span class="lineNum">      49 </span>            : cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}</a>
+<a name="50"><span class="lineNum">      50 </span>            : mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}</a>
+<a name="51"><span class="lineNum">      51 </span>            : dfs: DFSCLUSTERING MATRIX=mat</a>
+<a name="52"><span class="lineNum">      52 </span>            : clust2a: CLUSTER_WITHSURFACE CLUSTERS=dfs RCUT_SURF=0.3</a>
+<a name="53"><span class="lineNum">      53 </span>            : size2a: CLUSTER_NATOMS CLUSTERS=clust2a CLUSTER=2</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=size2a FILE=size FMT=%8.4f</a>
+<a name="55"><span class="lineNum">      55 </span>            : OUTPUT_CLUSTER CLUSTERS=clust2a CLUSTER=2 FILE=dfs2.dat</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : */</a>
+<a name="60"><span class="lineNum">      60 </span>            : //+ENDPLUMEDOC</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace PLMD {</a>
+<a name="63"><span class="lineNum">      63 </span>            : namespace adjmat {</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : class ClusterWithSurface : public ClusteringBase {</a>
+<a name="66"><span class="lineNum">      66 </span>            : private:</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// The clusters that we are adding surface atoms to</a>
+<a name="68"><span class="lineNum">      68 </span>            :   ClusteringBase* myclusters;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// The cutoff for surface atoms</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double rcut_surf2;</a>
+<a name="71"><span class="lineNum">      71 </span>            : public:</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Create manual</a>
+<a name="73"><span class="lineNum">      73 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Constructor</a>
+<a name="75"><span class="lineNum">      75 </span>            :   explicit ClusterWithSurface(const ActionOptions&amp;);</a>
+<a name="76"><span class="lineNum">      76 </span>            : ///</a>
+<a name="77"><span class="lineNum">      77 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="78"><span class="lineNum">      78 </span>            : ///</a>
+<a name="79"><span class="lineNum">      79 </span>            :   unsigned getNumberOfNodes() const override;</a>
+<a name="80"><span class="lineNum">      80 </span>            : ///</a>
+<a name="81"><span class="lineNum">      81 </span>            :   AtomNumber getAbsoluteIndexOfCentralAtom(const unsigned&amp; i) const override;</a>
+<a name="82"><span class="lineNum">      82 </span>            : ///</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void retrieveAtomsInCluster( const unsigned&amp; clust, std::vector&lt;unsigned&gt;&amp; myatoms ) const override;</a>
+<a name="84"><span class="lineNum">      84 </span>            : ///</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void getInputData( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms, std::vector&lt;double&gt;&amp; orient0 ) const override;</a>
+<a name="86"><span class="lineNum">      86 </span>            : ///</a>
+<a name="87"><span class="lineNum">      87 </span>            :   MultiValue&amp; getInputDerivatives( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="88"><span class="lineNum">      88 </span>            : ///</a>
+<a name="89"><span class="lineNum">      89 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// Do the calculation</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   void performClustering() override {};</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : ///</a>
+<a name="93"><span class="lineNum">      93 </span>            :   double  getCutoffForConnection() const override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : ///</a>
+<a name="95"><span class="lineNum">      95 </span>            :   Vector getPositionOfAtomForLinkCells( const unsigned&amp; taskIndex ) const override;</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ClusterWithSurface,&quot;CLUSTER_WITHSURFACE&quot;)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          4 : void ClusterWithSurface::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :   ClusteringBase::registerKeywords( keys );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :   keys.remove(&quot;MATRIX&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTERS&quot;,&quot;the label of the action that does the clustering&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;RCUT_SURF&quot;,&quot;you also have the option to find the atoms on the surface of the cluster.  An atom must be within this distance of one of the atoms &quot;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :            &quot;of the cluster in order to be considered a surface atom&quot;);</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 : ClusterWithSurface::ClusterWithSurface(const ActionOptions&amp;ao):</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   Action(ao),</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   ClusteringBase(ao)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : {</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;AtomNumber&gt; fake_atoms;</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 :   if( !parseMultiColvarAtomList(&quot;CLUSTERS&quot;,-1,fake_atoms ) ) error(&quot;unable to find CLUSTERS input&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :   if( mybasemulticolvars.size()!=1 ) error(&quot;should be exactly one multicolvar input&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   // Retrieve the adjacency matrix of interest</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   atom_lab.resize(0); myclusters = dynamic_cast&lt;ClusteringBase*&gt;( mybasemulticolvars[0] );</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   if( !myclusters ) error( mybasemulticolvars[0]-&gt;getLabel() + &quot; does not calculate clusters&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   // Setup switching function for surface atoms</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   double rcut_surf; parse(&quot;RCUT_SURF&quot;,rcut_surf);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   if( rcut_surf&gt;0 ) log.printf(&quot;  counting surface atoms that are within %f of the cluster atoms \n&quot;,rcut_surf);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :   rcut_surf2=rcut_surf*rcut_surf;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   // And now finish the setup of everything in the base</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 :   setupMultiColvarBase( fake_atoms );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          4 : unsigned ClusterWithSurface::getNumberOfDerivatives() {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          4 :   return myclusters-&gt;getNumberOfDerivatives();</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">   16155834 : unsigned ClusterWithSurface::getNumberOfNodes() const {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">   16155834 :   return myclusters-&gt;getNumberOfNodes();</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        128 : AtomNumber ClusterWithSurface::getAbsoluteIndexOfCentralAtom(const unsigned&amp; i) const {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        128 :   return myclusters-&gt;getAbsoluteIndexOfCentralAtom(i);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : void ClusterWithSurface::getInputData( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms, std::vector&lt;double&gt;&amp; orient0 ) const {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   myclusters-&gt;getInputData( ind, normed, myatoms, orient0 );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 : MultiValue&amp; ClusterWithSurface::getInputDerivatives( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :   return myclusters-&gt;getInputDerivatives( ind, normed, myatoms );</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         14 : unsigned ClusterWithSurface::getNumberOfQuantities() const {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         14 :   return myclusters-&gt;getNumberOfQuantities();</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 : double  ClusterWithSurface::getCutoffForConnection() const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          2 :   double tcut = myclusters-&gt;getCutoffForConnection();</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   if( tcut&gt;std::sqrt(rcut_surf2) ) return tcut;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   return std::sqrt(rcut_surf2);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          6 : void ClusterWithSurface::retrieveAtomsInCluster( const unsigned&amp; clust, std::vector&lt;unsigned&gt;&amp; myatoms ) const {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          6 :   std::vector&lt;unsigned&gt; tmpat; myclusters-&gt;retrieveAtomsInCluster( clust, tmpat );</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Prevent double counting</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          6 :   std::vector&lt;bool&gt; incluster( getNumberOfNodes(), false );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         90 :   for(unsigned i=0; i&lt;tmpat.size(); ++i) incluster[tmpat[i]]=true;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   // Find the atoms in the the clusters</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          6 :   std::vector&lt;bool&gt; surface_atom( getNumberOfNodes(), false );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         90 :   for(unsigned i=0; i&lt;tmpat.size(); ++i) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     167748 :     for(unsigned j=0; j&lt;getNumberOfNodes(); ++j) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     167664 :       if( incluster[j] ) continue;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     166488 :       double dist2=getSeparation( getPosition(tmpat[i]), getPosition(j) ).modulo2();</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     166488 :       if( dist2&lt;rcut_surf2 ) { surface_atom[j]=true; }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     }</a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            :   unsigned nsurf_at=0;</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      11982 :   for(unsigned j=0; j&lt;getNumberOfNodes(); ++j) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      11976 :     if( surface_atom[j] ) nsurf_at++;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          6 :   myatoms.resize( nsurf_at + tmpat.size() );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         90 :   for(unsigned i=0; i&lt;tmpat.size(); ++i) myatoms[i]=tmpat[i];</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          6 :   unsigned nn=tmpat.size();</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      11982 :   for(unsigned j=0; j&lt;getNumberOfNodes(); ++j) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      11976 :     if( surface_atom[j] ) { myatoms[nn]=j; nn++; }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          6 :   plumed_assert( nn==myatoms.size() );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          6 : }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 : Vector ClusterWithSurface::getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   return myclusters-&gt;getPositionOfAtomForLinkCells( iatom );</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusteringBase.cpp.func-sort-c.html b/coverage/adjmat/ClusteringBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ce70bafc7d
--- /dev/null
+++ b/coverage/adjmat/ClusteringBase.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusteringBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusteringBase.cpp<span style="font-size: 80%;"> (<a href="ClusteringBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusteringBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#31">_ZN4PLMD6adjmat14ClusteringBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#72">_ZNK4PLMD6adjmat14ClusteringBase12areConnectedERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#46">_ZN4PLMD6adjmat14ClusteringBase17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#76">_ZNK4PLMD6adjmat14ClusteringBase22getCutoffForConnectionEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#31">_ZN4PLMD6adjmat14ClusteringBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#27">_ZN4PLMD6adjmat14ClusteringBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#56">_ZN4PLMD6adjmat14ClusteringBase9calculateEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#65">_ZNK4PLMD6adjmat14ClusteringBase22retrieveAtomsInClusterERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusteringBase.cpp.func.html b/coverage/adjmat/ClusteringBase.cpp.func.html
new file mode 100644
index 0000000000..bed1c3f831
--- /dev/null
+++ b/coverage/adjmat/ClusteringBase.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusteringBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusteringBase.cpp<span style="font-size: 80%;"> (<a href="ClusteringBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusteringBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#27">_ZN4PLMD6adjmat14ClusteringBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#46">_ZN4PLMD6adjmat14ClusteringBase17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#56">_ZN4PLMD6adjmat14ClusteringBase9calculateEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#31">_ZN4PLMD6adjmat14ClusteringBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#31">_ZN4PLMD6adjmat14ClusteringBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#72">_ZNK4PLMD6adjmat14ClusteringBase12areConnectedERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#76">_ZNK4PLMD6adjmat14ClusteringBase22getCutoffForConnectionEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.cpp.gcov.html#65">_ZNK4PLMD6adjmat14ClusteringBase22retrieveAtomsInClusterERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusteringBase.cpp.gcov.html b/coverage/adjmat/ClusteringBase.cpp.gcov.html
new file mode 100644
index 0000000000..72a846f7ac
--- /dev/null
+++ b/coverage/adjmat/ClusteringBase.cpp.gcov.html
@@ -0,0 +1,159 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusteringBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusteringBase.cpp<span style="font-size: 80%;"> (source / <a href="ClusteringBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusteringBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace adjmat {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         21 : void ClusteringBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         21 :   ActionWithInputMatrix::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         21 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         17 : ClusteringBase::ClusteringBase(const ActionOptions&amp;ao):</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   Action(ao),</a>
+<a name="35"><span class="lineNum">      35 </span>            :   ActionWithInputMatrix(ao),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         17 :   number_of_cluster(-1)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         17 :   if( getAdjacencyVessel() ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         15 :     cluster_sizes.resize(getNumberOfNodes()); which_cluster.resize(getNumberOfNodes());</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         15 :     if( getNumberOfNodeTypes()!=1 ) error(&quot;should only be running clustering with one base multicolvar in function&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         15 :     if( !getAdjacencyVessel()-&gt;undirectedGraph() ) error(&quot;input contact matrix is incompatible with clustering&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   }</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         34 :   if( keywords.exists(&quot;MATRIX&quot;) ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         15 :     std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   }</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         17 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          8 : void ClusteringBase::turnOnDerivatives() {</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   // Check base multicolvar isn't density probably other things shouldn't be allowed here as well</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          8 :   if( (getAdjacencyVessel()-&gt;getMatrixAction())-&gt;getNumberOfBaseMultiColvars()&gt;0 ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          7 :     if( getBaseMultiColvar(0)-&gt;isDensity() ) error(&quot;DFS clustering cannot be differentiated if base multicolvar is DENSITY&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   }</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            :   // Ensure that derivatives are turned on in base classes</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          8 :   ActionWithInputMatrix::turnOnDerivatives();</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          8 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         26 : void ClusteringBase::calculate() {</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   // All the clusters have zero size initially</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       8219 :   for(unsigned i=0; i&lt;cluster_sizes.size(); ++i) { cluster_sizes[i].first=0; cluster_sizes[i].second=i; }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   // Do the clustering bit</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         26 :   performClustering();</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   // Order the clusters in the system by size (this returns ascending order )</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         26 :   std::sort( cluster_sizes.begin(), cluster_sizes.end() );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         26 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         74 : void ClusteringBase::retrieveAtomsInCluster( const unsigned&amp; clust, std::vector&lt;unsigned&gt;&amp; myatoms ) const {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         74 :   unsigned n=0; myatoms.resize( cluster_sizes[cluster_sizes.size() - clust].first );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      45287 :   for(unsigned i=0; i&lt;getNumberOfNodes(); ++i) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      45213 :     if( which_cluster[i]==cluster_sizes[cluster_sizes.size() - clust].second ) { myatoms[n]=i; n++; }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   }</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         74 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 : bool ClusteringBase::areConnected( const unsigned&amp; iatom, const unsigned&amp; jatom ) const {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   return getAdjacencyVessel()-&gt;nodesAreConnected( iatom, jatom );</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          8 : double ClusteringBase::getCutoffForConnection() const {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          8 :   return getAdjacencyVessel()-&gt;getCutoffForConnection();</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusteringBase.h.func-sort-c.html b/coverage/adjmat/ClusteringBase.h.func-sort-c.html
new file mode 100644
index 0000000000..5695bb4a68
--- /dev/null
+++ b/coverage/adjmat/ClusteringBase.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusteringBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusteringBase.h<span style="font-size: 80%;"> (<a href="ClusteringBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ClusteringBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.h.gcov.html#55">_ZN4PLMD6adjmat14ClusteringBase5applyEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusteringBase.h.func.html b/coverage/adjmat/ClusteringBase.h.func.html
new file mode 100644
index 0000000000..f802f186af
--- /dev/null
+++ b/coverage/adjmat/ClusteringBase.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusteringBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusteringBase.h<span style="font-size: 80%;"> (<a href="ClusteringBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ClusteringBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ClusteringBase.h.gcov.html#55">_ZN4PLMD6adjmat14ClusteringBase5applyEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ClusteringBase.h.gcov.html b/coverage/adjmat/ClusteringBase.h.gcov.html
new file mode 100644
index 0000000000..98821b44ad
--- /dev/null
+++ b/coverage/adjmat/ClusteringBase.h.gcov.html
@@ -0,0 +1,146 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ClusteringBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ClusteringBase.h<span style="font-size: 80%;"> (source / <a href="ClusteringBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_adjmat_ClusteringBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_adjmat_ClusteringBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionWithInputMatrix.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace adjmat {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class ClusteringBase : public ActionWithInputMatrix {</a>
+<a name="32"><span class="lineNum">      32 </span>            : protected:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// Vector that stores the sizes of the current set of clusters</a>
+<a name="34"><span class="lineNum">      34 </span>            :   std::vector&lt; std::pair&lt;unsigned,unsigned&gt; &gt; cluster_sizes;</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// Used to identify the cluster we are working on</a>
+<a name="36"><span class="lineNum">      36 </span>            :   int number_of_cluster;</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Vector that identifies the cluster each atom belongs to</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::vector&lt;unsigned&gt; which_cluster;</a>
+<a name="39"><span class="lineNum">      39 </span>            : public:</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Create manual</a>
+<a name="41"><span class="lineNum">      41 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Constructor</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit ClusteringBase(const ActionOptions&amp;);</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// This checks whether derivatives can be computed given the base multicolvar</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void turnOnDerivatives() override;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Are these two atoms connected</a>
+<a name="47"><span class="lineNum">      47 </span>            :   bool areConnected( const unsigned&amp; iatom, const unsigned&amp; jatom ) const ;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Do the calculation</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void calculate() override;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Do the clustering</a>
+<a name="51"><span class="lineNum">      51 </span>            :   virtual void performClustering()=0;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Get the number of clusters that have been found</a>
+<a name="53"><span class="lineNum">      53 </span>            :   unsigned getNumberOfClusters() const ;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Get the atoms in one of the clusters</a>
+<a name="55"><span class="lineNum">      55 </span>            :   virtual void retrieveAtomsInCluster( const unsigned&amp; clust, std::vector&lt;unsigned&gt;&amp; myatoms ) const ;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Do nothing for apply here</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         26 :   void apply() override {}</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Get the cutoff</a>
+<a name="59"><span class="lineNum">      59 </span>            :   virtual double getCutoffForConnection() const ;</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : inline</a>
+<a name="63"><span class="lineNum">      63 </span>            : unsigned ClusteringBase::getNumberOfClusters() const {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :   return number_of_cluster + 1;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ContactAlignedMatrix.cpp.func-sort-c.html b/coverage/adjmat/ContactAlignedMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e682bddebe
--- /dev/null
+++ b/coverage/adjmat/ContactAlignedMatrix.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ContactAlignedMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ContactAlignedMatrix.cpp<span style="font-size: 80%;"> (<a href="ContactAlignedMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryLo">22.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ContactAlignedMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#85">_ZN4PLMD6adjmat12_GLOBAL__N_132ContactAlignedMatrixRegisterMe876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#101">_ZN4PLMD6adjmat20ContactAlignedMatrix24readOrientationConnectorERKjS3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#92">_ZN4PLMD6adjmat20ContactAlignedMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#92">_ZN4PLMD6adjmat20ContactAlignedMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#107">_ZNK4PLMD6adjmat20ContactAlignedMatrix21computeVectorFunctionERKjS3_RKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#87">_ZN4PLMD6adjmat20ContactAlignedMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#85">_ZN4PLMD6adjmat12_GLOBAL__N_132ContactAlignedMatrixRegisterMe87C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#85">_ZN4PLMD6adjmat12_GLOBAL__N_132ContactAlignedMatrixRegisterMe87D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ContactAlignedMatrix.cpp.func.html b/coverage/adjmat/ContactAlignedMatrix.cpp.func.html
new file mode 100644
index 0000000000..a32f2a46a6
--- /dev/null
+++ b/coverage/adjmat/ContactAlignedMatrix.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ContactAlignedMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ContactAlignedMatrix.cpp<span style="font-size: 80%;"> (<a href="ContactAlignedMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryLo">22.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ContactAlignedMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#85">_ZN4PLMD6adjmat12_GLOBAL__N_132ContactAlignedMatrixRegisterMe876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#85">_ZN4PLMD6adjmat12_GLOBAL__N_132ContactAlignedMatrixRegisterMe87C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#85">_ZN4PLMD6adjmat12_GLOBAL__N_132ContactAlignedMatrixRegisterMe87D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#87">_ZN4PLMD6adjmat20ContactAlignedMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#101">_ZN4PLMD6adjmat20ContactAlignedMatrix24readOrientationConnectorERKjS3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#92">_ZN4PLMD6adjmat20ContactAlignedMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#92">_ZN4PLMD6adjmat20ContactAlignedMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactAlignedMatrix.cpp.gcov.html#107">_ZNK4PLMD6adjmat20ContactAlignedMatrix21computeVectorFunctionERKjS3_RKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ContactAlignedMatrix.cpp.gcov.html b/coverage/adjmat/ContactAlignedMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..2b47697031
--- /dev/null
+++ b/coverage/adjmat/ContactAlignedMatrix.cpp.gcov.html
@@ -0,0 +1,199 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ContactAlignedMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ContactAlignedMatrix.cpp<span style="font-size: 80%;"> (source / <a href="ContactAlignedMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryLo">22.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AlignedMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MATRIX ALIGNED_MATRIX</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Adjacency matrix in which two molecule are adjacent if they are within a certain cutoff and if they have the same orientation.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="31"><span class="lineNum">      31 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="32"><span class="lineNum">      32 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  These matrices can then be further</a>
+<a name="33"><span class="lineNum">      33 </span>            : analyzed using a number of other algorithms as is detailed in \cite tribello-clustering.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : For this action the elements of the adjacency matrix are calculated using:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : a_{ij} = \sigma_1( |\mathbf{r}_{ij}| ) \sigma_2( \mathbf{v}_i . \mathbf{v}_j )</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : This form of adjacency matrix can only be used if the input species are objects that lie at a point in space and that have an orientation, \f$\mathbf{v}\f$.</a>
+<a name="42"><span class="lineNum">      42 </span>            : These orientations might represent the</a>
+<a name="43"><span class="lineNum">      43 </span>            : orientation of a molecule, which could be calculated using \ref MOLECULES or \ref PLANES, or it might be the complex vectors calculated using the</a>
+<a name="44"><span class="lineNum">      44 </span>            : Steinhardt parameters \ref Q3, \ref Q4 or \ref Q6.  In the expression above \f$\mathbf{r}_{ij}\f$ is the vector connecting the points in space</a>
+<a name="45"><span class="lineNum">      45 </span>            : where objects \f$i\f$ and \f$j\f$ find themselves and \f$\sigma_1\f$ is a \ref switchingfunction that acts upon the magnitude of this vector.</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f$\sigma_2\f$ is a second \ref switchingfunction that acts on the dot product of the directors of the vectors that define the orientations of</a>
+<a name="47"><span class="lineNum">      47 </span>            : objects \f$i\f$ and \f$j\f$.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The example input below is necessarily but gives you an idea of what can be achieved using this action.</a>
+<a name="52"><span class="lineNum">      52 </span>            : The orientations and positions of four molecules are defined using the \ref MOLECULES action as the position of the</a>
+<a name="53"><span class="lineNum">      53 </span>            : centers of mass of the two atoms specified and the direction of the vector connecting the two atoms that were specified.</a>
+<a name="54"><span class="lineNum">      54 </span>            : A \f$4 \times 4\f$ matrix is then computed using the formula above.  The \f$ij\f$-element of this matrix tells us whether</a>
+<a name="55"><span class="lineNum">      55 </span>            : or not atoms \f$i\f$ and \f$j\f$ are within 0.1 nm of each other and whether or not the dot-product of their orientation vectors</a>
+<a name="56"><span class="lineNum">      56 </span>            : is greater than 0.5.  The sum of the rows of this matrix are then computed.  The sums of the \f$i\f$th row of this matrix tells us how</a>
+<a name="57"><span class="lineNum">      57 </span>            : many of the molecules that are within the first coordination sphere of molecule \f$i\f$ have an orientation that is similar to that of</a>
+<a name="58"><span class="lineNum">      58 </span>            : molecule \f$i\f$.  We thus calculate the number of these &quot;coordination numbers&quot; that are greater than 1.0 and output this quantity to a file.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8</a>
+<a name="62"><span class="lineNum">      62 </span>            : mat: ALIGNED_MATRIX ATOMS=m1 SWITCH={RATIONAL R_0=0.1} ORIENTATION_SWITCH={RATIONAL R_0=0.1 D_MAX=0.5}</a>
+<a name="63"><span class="lineNum">      63 </span>            : row: ROWSUMS MATRIX=mat MORE_THAN={RATIONAL D_0=1.0 R_0=0.1}</a>
+<a name="64"><span class="lineNum">      64 </span>            : PRINT ARG=row.* FILE=colvar</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endplumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : //+ENDPLUMEDOC</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace PLMD {</a>
+<a name="71"><span class="lineNum">      71 </span>            : namespace adjmat {</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : class ContactAlignedMatrix : public AlignedMatrixBase {</a>
+<a name="74"><span class="lineNum">      74 </span>            : private:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   Matrix&lt;SwitchingFunction&gt; sf;</a>
+<a name="76"><span class="lineNum">      76 </span>            : public:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   ///</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ///</a>
+<a name="80"><span class="lineNum">      80 </span>            :   explicit ContactAlignedMatrix(const ActionOptions&amp;);</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void readOrientationConnector( const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   double computeVectorFunction( const unsigned&amp; iv, const unsigned&amp; jv,</a>
+<a name="83"><span class="lineNum">      83 </span>            :                                 const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="84"><span class="lineNum">      84 </span>            :                                 Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const override;</a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(ContactAlignedMatrix,&quot;ALIGNED_MATRIX&quot;)</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 : void ContactAlignedMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          2 :   AlignedMatrixBase::registerKeywords( keys );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 :   keys.add(&quot;numbered&quot;,&quot;ORIENTATION_SWITCH&quot;,&quot;A switching function that transforms the dot product of the input vectors.&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 : ContactAlignedMatrix::ContactAlignedMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   Action(ao),</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   AlignedMatrixBase(ao)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : {</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   unsigned nrows, ncols, ig; retrieveTypeDimensions( nrows, ncols, ig );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   sf.resize( nrows, ncols );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   parseConnectionDescriptions(&quot;ORIENTATION_SWITCH&quot;,false,0);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 : void ContactAlignedMatrix::readOrientationConnector( const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   plumed_assert( desc.size()==1 ); std::string errors; sf(j,i).set(desc[0],errors);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   if( j!=i ) sf(i,j).set(desc[0],errors);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   log.printf(&quot;  vectors in %u th and %u th groups must have a dot product that is greater than %s \n&quot;,i+1,j+1,(sf(i,j).description()).c_str() );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 : double ContactAlignedMatrix::computeVectorFunction( const unsigned&amp; iv, const unsigned&amp; jv,</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="111"><span class="lineNum">     111 </span>            :     Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   double dot_df, dot=0; dconn.zero();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   for(unsigned k=2; k&lt;vec1.size(); ++k) dot+=vec1[k]*vec2[k];</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   double f_dot = sf(iv,jv).calculate( dot, dot_df );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   for(unsigned k=2; k&lt;vec1.size(); ++k) { dvec1[k]=dot_df*vec2[k]; dvec2[k]=dot_df*vec1[k]; }</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :   return f_dot;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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new file mode 100644
index 0000000000..cfb6ae35f7
--- /dev/null
+++ b/coverage/adjmat/ContactMatrix.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ContactMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ContactMatrix.cpp<span style="font-size: 80%;"> (<a href="ContactMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ContactMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat13ContactMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_125ContactMatrixRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat13ContactMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#120">_ZN4PLMD6adjmat13ContactMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#83">_ZN4PLMD6adjmat13ContactMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_125ContactMatrixRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_125ContactMatrixRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#133">_ZNK4PLMD6adjmat13ContactMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">28888</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#127">_ZNK4PLMD6adjmat13ContactMatrix15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">55746</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ContactMatrix.cpp.func.html b/coverage/adjmat/ContactMatrix.cpp.func.html
new file mode 100644
index 0000000000..8dc30bce31
--- /dev/null
+++ b/coverage/adjmat/ContactMatrix.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ContactMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ContactMatrix.cpp<span style="font-size: 80%;"> (<a href="ContactMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ContactMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_125ContactMatrixRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_125ContactMatrixRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#81">_ZN4PLMD6adjmat12_GLOBAL__N_125ContactMatrixRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#120">_ZN4PLMD6adjmat13ContactMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#83">_ZN4PLMD6adjmat13ContactMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat13ContactMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat13ContactMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#127">_ZNK4PLMD6adjmat13ContactMatrix15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">55746</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMatrix.cpp.gcov.html#133">_ZNK4PLMD6adjmat13ContactMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">28888</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/ContactMatrix.cpp.gcov.html b/coverage/adjmat/ContactMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..b53665672c
--- /dev/null
+++ b/coverage/adjmat/ContactMatrix.cpp.gcov.html
@@ -0,0 +1,226 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/ContactMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - ContactMatrix.cpp<span style="font-size: 80%;"> (source / <a href="ContactMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC MATRIX CONTACT_MATRIX</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Adjacency matrix in which two atoms are adjacent if they are within a certain cutoff.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="33"><span class="lineNum">      33 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="34"><span class="lineNum">      34 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  These matrices can then be further</a>
+<a name="35"><span class="lineNum">      35 </span>            : analyzed using a number of other algorithms as is detailed in \cite tribello-clustering.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : For this action the elements of the contact matrix are calculated using:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            :  a_{ij} = \sigma( |\mathbf{r}_{ij}| )</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where \f$|\mathbf{r}_{ij}|\f$ is the magnitude of the vector connecting atoms \f$i\f$ and \f$j\f$ and where \f$\sigma\f$ is a \ref switchingfunction.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The input shown below calculates a \f$6 \times 6\f$ matrix whose elements are equal to one if atom \f$i\f$ and atom \f$j\f$ are within 0.3 nm</a>
+<a name="48"><span class="lineNum">      48 </span>            : of each other and which is zero otherwise.  The columns in this matrix are then summed so as to give the coordination number for each atom.</a>
+<a name="49"><span class="lineNum">      49 </span>            : The final quantity output in the colvar file is thus the average coordination number.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : mat: CONTACT_MATRIX ATOMS=1-6 SWITCH={EXP D_0=0.2 R_0=0.1 D_MAX=0.66}</a>
+<a name="53"><span class="lineNum">      53 </span>            : COLUMNSUMS MATRIX=mat MEAN LABEL=csums</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=csums.* FILE=colvar</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : */</a>
+<a name="58"><span class="lineNum">      58 </span>            : //+ENDPLUMEDOC</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace PLMD {</a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace adjmat {</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : class ContactMatrix : public AdjacencyMatrixBase {</a>
+<a name="65"><span class="lineNum">      65 </span>            : private:</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Number of types that are in rows</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned ncol_t;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// switching function</a>
+<a name="69"><span class="lineNum">      69 </span>            :   Matrix&lt;SwitchingFunction&gt; switchingFunction;</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Create manual</a>
+<a name="72"><span class="lineNum">      72 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Constructor</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit ContactMatrix(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Create the ith, ith switching function</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) override;</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// This actually calculates the value of the contact function</a>
+<a name="78"><span class="lineNum">      78 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// This does nothing</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(ContactMatrix,&quot;CONTACT_MATRIX&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         14 : void ContactMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         14 :   AdjacencyMatrixBase::registerKeywords( keys );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         28 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;The list of atoms for which you would like to calculate the contact matrix.  The atoms involved must be specified &quot;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="89"><span class="lineNum">      89 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="90"><span class="lineNum">      90 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="91"><span class="lineNum">      91 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         28 :   keys.add(&quot;numbered&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;);</a>
+<a name="94"><span class="lineNum">      94 </span>            : // I added these keywords so I can test the results I get for column and row sums against output from COORDINATIONNUMBERS</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// These  should never be used in production as I think they will be much slower than COORDINATIONNUMBERS</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         42 :   keys.add(&quot;hidden&quot;,&quot;ATOMSA&quot;,&quot;&quot;); keys.add(&quot;hidden&quot;,&quot;ATOMSB&quot;,&quot;&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         14 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         12 : ContactMatrix::ContactMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   Action(ao),</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         12 :   AdjacencyMatrixBase(ao)</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : {</a>
+<a name="103"><span class="lineNum">     103 </span>            :   // Read in the atoms and setup the matrix</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         24 :   readMaxTwoSpeciesMatrix( &quot;ATOMS&quot;, &quot;ATOMSA&quot;, &quot;ATOMSB&quot;, true );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         12 :   unsigned nrows, ncols; retrieveTypeDimensions( nrows, ncols, ncol_t );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :   switchingFunction.resize( nrows, ncols );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   // Read in the switching functions</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         24 :   parseConnectionDescriptions(&quot;SWITCH&quot;,false,ncol_t);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Find the largest sf cutoff</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         12 :   double sfmax=switchingFunction(0,0).get_dmax();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;switchingFunction.nrows(); ++i) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         28 :     for(unsigned j=0; j&lt;switchingFunction.ncols(); ++j) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         15 :       double tsf=switchingFunction(i,j).get_dmax();</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         15 :       if( tsf&gt;sfmax ) sfmax=tsf;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   // And set the link cell cutoff</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         12 :   setLinkCellCutoff( sfmax );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         12 : }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         14 : void ContactMatrix::setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         14 :   plumed_assert( id==0 &amp;&amp; desc.size()==1 ); std::string errors; switchingFunction(j,i).set(desc[0],errors);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         14 :   if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         14 :   if( j!=i) switchingFunction(i,j).set(desc[0],errors);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         28 :   log.printf(&quot;  %u th and %u th multicolvar groups must be within %s\n&quot;,i+1,j+1,(switchingFunction(i,j).description()).c_str() );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         14 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      55746 : double ContactMatrix::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      55746 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     166288 :   if( distance.modulo2()&lt;switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).get_dmax2() ) return 1.0;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   return 0.0;</a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      28888 : double ContactMatrix::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      28888 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   double dfunc;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      57301 :   double sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) - ncol_t ).calculate( distance.modulo(), dfunc );</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      28888 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      28654 :     addAtomDerivatives( 1, 0, (-dfunc)*distance, myatoms );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      28654 :     addAtomDerivatives( 1, 1, (+dfunc)*distance, myatoms );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      28654 :     myatoms.addBoxDerivatives( 1, (-dfunc)*Tensor(distance,distance) );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      28888 :   return sw;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/DFSClustering.cpp.func-sort-c.html b/coverage/adjmat/DFSClustering.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b82adddaa9
--- /dev/null
+++ b/coverage/adjmat/DFSClustering.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/DFSClustering.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - DFSClustering.cpp<span style="font-size: 80%;"> (<a href="DFSClustering.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DFSClustering.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#102">_ZN4PLMD6adjmat13DFSClusteringC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#92">_ZN4PLMD6adjmat12_GLOBAL__N_125DFSClusteringRegisterMe946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#102">_ZN4PLMD6adjmat13DFSClusteringC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#94">_ZN4PLMD6adjmat13DFSClustering16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#117">_ZN4PLMD6adjmat13DFSClustering17performClusteringEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#92">_ZN4PLMD6adjmat12_GLOBAL__N_125DFSClusteringRegisterMe94C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#92">_ZN4PLMD6adjmat12_GLOBAL__N_125DFSClusteringRegisterMe94D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#143">_ZN4PLMD6adjmat13DFSClustering7exploreERKj</a></td>
+              <td class="coverFnHi">8193</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/DFSClustering.cpp.func.html b/coverage/adjmat/DFSClustering.cpp.func.html
new file mode 100644
index 0000000000..339659304f
--- /dev/null
+++ b/coverage/adjmat/DFSClustering.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/DFSClustering.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - DFSClustering.cpp<span style="font-size: 80%;"> (<a href="DFSClustering.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DFSClustering.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#92">_ZN4PLMD6adjmat12_GLOBAL__N_125DFSClusteringRegisterMe946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#92">_ZN4PLMD6adjmat12_GLOBAL__N_125DFSClusteringRegisterMe94C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#92">_ZN4PLMD6adjmat12_GLOBAL__N_125DFSClusteringRegisterMe94D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#94">_ZN4PLMD6adjmat13DFSClustering16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#117">_ZN4PLMD6adjmat13DFSClustering17performClusteringEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#143">_ZN4PLMD6adjmat13DFSClustering7exploreERKj</a></td>
+              <td class="coverFnHi">8193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#102">_ZN4PLMD6adjmat13DFSClusteringC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DFSClustering.cpp.gcov.html#102">_ZN4PLMD6adjmat13DFSClusteringC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/DFSClustering.cpp.gcov.html b/coverage/adjmat/DFSClustering.cpp.gcov.html
new file mode 100644
index 0000000000..0c05f217c0
--- /dev/null
+++ b/coverage/adjmat/DFSClustering.cpp.gcov.html
@@ -0,0 +1,237 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/DFSClustering.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - DFSClustering.cpp<span style="font-size: 80%;"> (source / <a href="DFSClustering.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusteringBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #ifdef __PLUMED_HAS_BOOST_GRAPH</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;boost/graph/adjacency_list.hpp&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;boost/graph/connected_components.hpp&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;boost/graph/graph_utility.hpp&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #endif</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC MATRIXF DFSCLUSTERING</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Find the connected components of the matrix using the depth first search clustering algorithm.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="37"><span class="lineNum">      37 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="38"><span class="lineNum">      38 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  As detailed in \cite tribello-clustering</a>
+<a name="39"><span class="lineNum">      39 </span>            : these matrices provide a representation of a graph and can thus can be analyzed using tools from graph theory.  This particular action performs</a>
+<a name="40"><span class="lineNum">      40 </span>            : a depth first search clustering to find the connected components of this graph.  You can read more about depth first search here:</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : https://en.wikipedia.org/wiki/Depth-first_search</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This action is useful if you are looking at a phenomenon such as nucleation where the aim is to detect the sizes of the crystalline nuclei that have formed</a>
+<a name="45"><span class="lineNum">      45 </span>            : in your simulation cell.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \par Examples</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The input below calculates the coordination numbers of atoms 1-100 and then computes the an adjacency</a>
+<a name="50"><span class="lineNum">      50 </span>            : matrix whose elements measures whether atoms \f$i\f$ and \f$j\f$ are within 0.55 nm of each other.  The action</a>
+<a name="51"><span class="lineNum">      51 </span>            : labelled dfs then treats the elements of this matrix as zero or ones and thus thinks of the matrix as defining</a>
+<a name="52"><span class="lineNum">      52 </span>            : a graph.  This dfs action then finds the largest connected component in this graph.  The sum of the coordination</a>
+<a name="53"><span class="lineNum">      53 </span>            : numbers for the atoms in this largest connected component are then computed and this quantity is output to a colvar</a>
+<a name="54"><span class="lineNum">      54 </span>            : file.  The way this input can be used is described in detail in \cite tribello-clustering.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : lq: COORDINATIONNUMBER SPECIES=1-100 SWITCH={CUBIC D_0=0.45  D_MAX=0.55} LOWMEM</a>
+<a name="58"><span class="lineNum">      58 </span>            : cm: CONTACT_MATRIX ATOMS=lq  SWITCH={CUBIC D_0=0.45  D_MAX=0.55}</a>
+<a name="59"><span class="lineNum">      59 </span>            : dfs: DFSCLUSTERING MATRIX=cm</a>
+<a name="60"><span class="lineNum">      60 </span>            : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1 SUM</a>
+<a name="61"><span class="lineNum">      61 </span>            : PRINT ARG=clust1.* FILE=colvar</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : */</a>
+<a name="65"><span class="lineNum">      65 </span>            : //+ENDPLUMEDOC</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : namespace PLMD {</a>
+<a name="68"><span class="lineNum">      68 </span>            : namespace adjmat {</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : class DFSClustering : public ClusteringBase {</a>
+<a name="71"><span class="lineNum">      71 </span>            : private:</a>
+<a name="72"><span class="lineNum">      72 </span>            : #ifdef __PLUMED_HAS_BOOST_GRAPH</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// The list of edges in the graph</a>
+<a name="74"><span class="lineNum">      74 </span>            :   std::vector&lt;std::pair&lt;unsigned,unsigned&gt; &gt; edge_list;</a>
+<a name="75"><span class="lineNum">      75 </span>            : #else</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// The number of neighbors each atom has</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;unsigned&gt; nneigh;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// The adjacency list</a>
+<a name="79"><span class="lineNum">      79 </span>            :   Matrix&lt;unsigned&gt; adj_list;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// The color that tells us whether a node has been visited</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;unsigned&gt; color;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// The recursive function at the heart of this method</a>
+<a name="83"><span class="lineNum">      83 </span>            :   int explore( const unsigned&amp; index );</a>
+<a name="84"><span class="lineNum">      84 </span>            : #endif</a>
+<a name="85"><span class="lineNum">      85 </span>            : public:</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Create manual</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Constructor</a>
+<a name="89"><span class="lineNum">      89 </span>            :   explicit DFSClustering(const ActionOptions&amp;);</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// Do the clustering</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void performClustering() override;</a>
+<a name="92"><span class="lineNum">      92 </span>            : };</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      12534 : PLUMED_REGISTER_ACTION(DFSClustering,&quot;DFSCLUSTERING&quot;)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         17 : void DFSClustering::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         17 :   ClusteringBase::registerKeywords( keys );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         34 :   keys.add(&quot;compulsory&quot;,&quot;MAXCONNECT&quot;,&quot;0&quot;,&quot;maximum number of connections that can be formed by any given node in the graph. &quot;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :            &quot;By default this is set equal to zero and the number of connections is set equal to the number &quot;</a>
+<a name="100"><span class="lineNum">     100 </span>            :            &quot;of nodes.  You only really need to set this if you are working with a very large system and &quot;</a>
+<a name="101"><span class="lineNum">     101 </span>            :            &quot;memory is at a premium&quot;);</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         17 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         15 : DFSClustering::DFSClustering(const ActionOptions&amp;ao):</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   Action(ao),</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         15 :   ClusteringBase(ao)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         15 :   unsigned maxconnections; parse(&quot;MAXCONNECT&quot;,maxconnections);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : #ifdef __PLUMED_HAS_BOOST_GRAPH</a>
+<a name="110"><span class="lineNum">     110 </span>            :   if( maxconnections&gt;0 ) edge_list.resize( getNumberOfNodes()*maxconnections );</a>
+<a name="111"><span class="lineNum">     111 </span>            :   else edge_list.resize(0.5*getNumberOfNodes()*(getNumberOfNodes()-1));</a>
+<a name="112"><span class="lineNum">     112 </span>            : #else</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         15 :   nneigh.resize( getNumberOfNodes() ); color.resize(getNumberOfNodes());</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         15 :   if( maxconnections&gt;0 ) adj_list.resize(getNumberOfNodes(),maxconnections);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         15 :   else adj_list.resize(getNumberOfNodes(),getNumberOfNodes());</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : #endif</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         15 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         24 : void DFSClustering::performClustering() {</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : #ifdef __PLUMED_HAS_BOOST_GRAPH</a>
+<a name="121"><span class="lineNum">     121 </span>            :   // Get the list of edges</a>
+<a name="122"><span class="lineNum">     122 </span>            :   unsigned nedges=0; getAdjacencyVessel()-&gt;retrieveEdgeList( nedges, edge_list );</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   // Build the graph using boost</a>
+<a name="125"><span class="lineNum">     125 </span>            :   boost::adjacency_list&lt;boost::vecS,boost::vecS,boost::undirectedS&gt; sg(&amp;edge_list[0],&amp;edge_list[nedges],getNumberOfNodes());</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // Find the connected components using boost (-1 here for compatibility with non-boost version)</a>
+<a name="128"><span class="lineNum">     128 </span>            :   number_of_cluster=boost::connected_components(sg,&amp;which_cluster[0]) - 1;</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :   // And work out the size of each cluster</a>
+<a name="131"><span class="lineNum">     131 </span>            :   for(unsigned i=0; i&lt;which_cluster.size(); ++i) cluster_sizes[which_cluster[i]].first++;</a>
+<a name="132"><span class="lineNum">     132 </span>            : #else</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // Get the adjacency matrix</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         24 :   getAdjacencyVessel()-&gt;retrieveAdjacencyLists( nneigh, adj_list );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Perform clustering</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         24 :   number_of_cluster=-1; color.assign(color.size(),0);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       8217 :   for(unsigned i=0; i&lt;getNumberOfNodes(); ++i) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       8193 :     if( color[i]==0 ) { number_of_cluster++; color[i]=explore(i); }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span>            : #endif</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         24 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : #ifndef __PLUMED_HAS_BOOST_GRAPH</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       8193 : int DFSClustering::explore( const unsigned&amp; index ) {</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       8193 :   color[index]=1;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      38219 :   for(unsigned i=0; i&lt;nneigh[index]; ++i) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      30026 :     unsigned j=adj_list(index,i);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      30026 :     if( color[j]==0 ) color[j]=explore(j);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   // Count the size of the cluster</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       8193 :   cluster_sizes[number_of_cluster].first++;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       8193 :   which_cluster[index] = number_of_cluster;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       8193 :   return color[index];</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : #endif</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : }</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/DumpGraph.cpp.func-sort-c.html b/coverage/adjmat/DumpGraph.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7dfb0e7982
--- /dev/null
+++ b/coverage/adjmat/DumpGraph.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/DumpGraph.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - DumpGraph.cpp<span style="font-size: 80%;"> (<a href="DumpGraph.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpGraph.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#75">_ZN4PLMD6adjmat9DumpGraphC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#61">_ZN4PLMD6adjmat12_GLOBAL__N_121DumpGraphRegisterMe636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#56">_ZN4PLMD6adjmat9DumpGraph5applyEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#98">_ZN4PLMD6adjmat9DumpGraph6updateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#55">_ZN4PLMD6adjmat9DumpGraph9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#75">_ZN4PLMD6adjmat9DumpGraphC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#63">_ZN4PLMD6adjmat9DumpGraph16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#61">_ZN4PLMD6adjmat12_GLOBAL__N_121DumpGraphRegisterMe63C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#61">_ZN4PLMD6adjmat12_GLOBAL__N_121DumpGraphRegisterMe63D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
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diff --git a/coverage/adjmat/DumpGraph.cpp.func.html b/coverage/adjmat/DumpGraph.cpp.func.html
new file mode 100644
index 0000000000..e44d9986a0
--- /dev/null
+++ b/coverage/adjmat/DumpGraph.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/DumpGraph.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - DumpGraph.cpp<span style="font-size: 80%;"> (<a href="DumpGraph.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpGraph.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#61">_ZN4PLMD6adjmat12_GLOBAL__N_121DumpGraphRegisterMe636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#61">_ZN4PLMD6adjmat12_GLOBAL__N_121DumpGraphRegisterMe63C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#61">_ZN4PLMD6adjmat12_GLOBAL__N_121DumpGraphRegisterMe63D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#63">_ZN4PLMD6adjmat9DumpGraph16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#56">_ZN4PLMD6adjmat9DumpGraph5applyEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#98">_ZN4PLMD6adjmat9DumpGraph6updateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#55">_ZN4PLMD6adjmat9DumpGraph9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#75">_ZN4PLMD6adjmat9DumpGraphC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGraph.cpp.gcov.html#75">_ZN4PLMD6adjmat9DumpGraphC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/DumpGraph.cpp.gcov.html b/coverage/adjmat/DumpGraph.cpp.gcov.html
new file mode 100644
index 0000000000..65c68df184
--- /dev/null
+++ b/coverage/adjmat/DumpGraph.cpp.gcov.html
@@ -0,0 +1,190 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/DumpGraph.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - DumpGraph.cpp<span style="font-size: 80%;"> (source / <a href="DumpGraph.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace adjmat {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC CONCOMP DUMPGRAPH</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Write out the connectivity of the nodes in the graph in dot format.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : */</a>
+<a name="40"><span class="lineNum">      40 </span>            : //+ENDPLUMEDOC</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : class DumpGraph : public ActionPilot {</a>
+<a name="44"><span class="lineNum">      44 </span>            : private:</a>
+<a name="45"><span class="lineNum">      45 </span>            : ///</a>
+<a name="46"><span class="lineNum">      46 </span>            :   size_t maxconnections;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// The vessel that contains the graph</a>
+<a name="48"><span class="lineNum">      48 </span>            :   AdjacencyMatrixVessel* mymatrix;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// The name of the file on which we are outputting the graph</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string filename;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Create manual</a>
+<a name="53"><span class="lineNum">      53 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Constructor</a>
+<a name="55"><span class="lineNum">      55 </span>            :   explicit DumpGraph( const ActionOptions&amp; );</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Calculate and apply do nothing</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          4 :   void calculate() override {};</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :   void apply() override {};</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Update will do the output</a>
+<a name="60"><span class="lineNum">      60 </span>            :   void update() override;</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(DumpGraph,&quot;DUMPGRAPH&quot;)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          6 : void DumpGraph::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          6 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;MATRIX&quot;,&quot;the action that calculates the adjacency matrix vessel we would like to analyze&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which you would like to output the graph&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output the data&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;MAXCONNECT&quot;,&quot;0&quot;,&quot;maximum number of connections that can be formed by any given node in the graph. &quot;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :            &quot;By default this is set equal to zero and the number of connections is set equal to the number &quot;</a>
+<a name="72"><span class="lineNum">      72 </span>            :            &quot;of nodes.  You only really need to set this if you are working with a very large system and &quot;</a>
+<a name="73"><span class="lineNum">      73 </span>            :            &quot;memory is at a premium&quot;);</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          6 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          4 : DumpGraph::DumpGraph( const ActionOptions&amp; ao):</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   Action(ao),</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ActionPilot(ao),</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          4 :   mymatrix(NULL)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :   parse(&quot;MAXCONNECT&quot;,maxconnections); std::string mstring; parse(&quot;MATRIX&quot;,mstring);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   AdjacencyMatrixBase* mm = plumed.getActionSet().selectWithLabel&lt;AdjacencyMatrixBase*&gt;( mstring );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 :   if( !mm ) error(&quot;found no action in set with label &quot; + mstring + &quot; that calculates matrix&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :   log.printf(&quot;  printing graph for matrix calculated by action %s\n&quot;, mm-&gt;getLabel().c_str() );</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   // Retrieve the adjacency matrix of interest</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;mm-&gt;getNumberOfVessels(); ++i) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          4 :     mymatrix = dynamic_cast&lt;AdjacencyMatrixVessel*&gt;( mm-&gt;getPntrToVessel(i) );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          4 :     if( mymatrix ) break ;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          4 :   if( !mymatrix ) error( mm-&gt;getLabel() + &quot; does not calculate an adjacency matrix&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          4 :   if( !mymatrix-&gt;isSymmetric() ) error(&quot;input contact matrix must be symmetric&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          4 :   if( maxconnections==0 ) maxconnections=mymatrix-&gt;getNumberOfRows();</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 :   parse(&quot;FILE&quot;,filename);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          4 :   log.printf(&quot;  printing graph to file named %s \n&quot;,filename.c_str() );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          4 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          4 : void DumpGraph::update() {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :   OFile ofile; ofile.link(*this); ofile.setBackupString(&quot;graph&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :   ofile.open( filename ); ofile.printf(&quot;graph G { \n&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   // Print all nodes</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1336 :   for(unsigned i=0; i&lt;mymatrix-&gt;getNumberOfRows(); ++i) ofile.printf(&quot;%u [label=\&quot;%u\&quot;];\n&quot;,i,i);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Now retrieve connectivitives</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 :   unsigned nedge; std::vector&lt;std::pair&lt;unsigned,unsigned&gt; &gt; edge_list( mymatrix-&gt;getNumberOfRows()*maxconnections );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          4 :   mymatrix-&gt;retrieveEdgeList( nedge, edge_list );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       6388 :   for(unsigned i=0; i&lt;nedge; ++i) ofile.printf(&quot;%u -- %u \n&quot;, edge_list[i].first, edge_list[i].second );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   ofile.printf(&quot;} \n&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          4 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/HbondMatrix.cpp.func-sort-c.html b/coverage/adjmat/HbondMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c5e0f134a8
--- /dev/null
+++ b/coverage/adjmat/HbondMatrix.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/HbondMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - HbondMatrix.cpp<span style="font-size: 80%;"> (<a href="HbondMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HbondMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#136">_ZN4PLMD6adjmat11HBondMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#136">_ZN4PLMD6adjmat11HBondMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#105">_ZN4PLMD6adjmat12_GLOBAL__N_124HBondMatrixRegisterMe1076createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#107">_ZN4PLMD6adjmat11HBondMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#159">_ZN4PLMD6adjmat11HBondMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#179">_ZNK4PLMD6adjmat11HBondMatrix15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">4038</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#188">_ZNK4PLMD6adjmat11HBondMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">4038</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#105">_ZN4PLMD6adjmat12_GLOBAL__N_124HBondMatrixRegisterMe107C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#105">_ZN4PLMD6adjmat12_GLOBAL__N_124HBondMatrixRegisterMe107D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#208">_ZNK4PLMD6adjmat11HBondMatrix17calculateForThreeERKjS3_S3_RKNS_13VectorGenericILj3EEERKdS9_RNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">516132</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/HbondMatrix.cpp.func.html b/coverage/adjmat/HbondMatrix.cpp.func.html
new file mode 100644
index 0000000000..fdb2c9906d
--- /dev/null
+++ b/coverage/adjmat/HbondMatrix.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/HbondMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
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+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - HbondMatrix.cpp<span style="font-size: 80%;"> (<a href="HbondMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HbondMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#159">_ZN4PLMD6adjmat11HBondMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#107">_ZN4PLMD6adjmat11HBondMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#136">_ZN4PLMD6adjmat11HBondMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#136">_ZN4PLMD6adjmat11HBondMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#105">_ZN4PLMD6adjmat12_GLOBAL__N_124HBondMatrixRegisterMe1076createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#105">_ZN4PLMD6adjmat12_GLOBAL__N_124HBondMatrixRegisterMe107C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#105">_ZN4PLMD6adjmat12_GLOBAL__N_124HBondMatrixRegisterMe107D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#179">_ZNK4PLMD6adjmat11HBondMatrix15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">4038</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#208">_ZNK4PLMD6adjmat11HBondMatrix17calculateForThreeERKjS3_S3_RKNS_13VectorGenericILj3EEERKdS9_RNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">516132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HbondMatrix.cpp.gcov.html#188">_ZNK4PLMD6adjmat11HBondMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">4038</td>
+            </tr>
+  </table>
+  <br>
+  </center>
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+</html>
diff --git a/coverage/adjmat/HbondMatrix.cpp.gcov.html b/coverage/adjmat/HbondMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..f01acdd3d8
--- /dev/null
+++ b/coverage/adjmat/HbondMatrix.cpp.gcov.html
@@ -0,0 +1,308 @@
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+<body>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - HbondMatrix.cpp<span style="font-size: 80%;"> (source / <a href="HbondMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Angle.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC MATRIX HBOND_MATRIX</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Adjacency matrix in which two atoms are adjacent if there is a hydrogen bond between them.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="35"><span class="lineNum">      35 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="36"><span class="lineNum">      36 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  These matrices can then be further</a>
+<a name="37"><span class="lineNum">      37 </span>            : analyzed using a number of other algorithms as is detailed in \cite tribello-clustering.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : For this action the elements of the adjacency matrix are calculated using:</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : a_{ij} = \sigma_{oo}( |\mathbf{r}_{ij}| ) \sum_{k=1}^N \sigma_{oh}( |\mathbf{r}_{ik}| ) \sigma_{\theta}( \theta_{kij} )</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : This expression was derived by thinking about how to detect if there is a hydrogen bond between atoms \f$i\f$ and \f$j\f$.  The notion is that</a>
+<a name="46"><span class="lineNum">      46 </span>            : if the hydrogen bond is present atoms \f$i\f$ and \f$j\f$ should be within a certain cutoff distance.  In addition, there should be a hydrogen</a>
+<a name="47"><span class="lineNum">      47 </span>            : within a certain cutoff distance of atom \f$i\f$ and this hydrogen should lie on or close to the vector connecting atoms \f$i\f$ and \f$j\f$.</a>
+<a name="48"><span class="lineNum">      48 </span>            : As such \f$\sigma_{oo}( |\mathbf{r}_{ij}| )\f$ is a \ref switchingfunction that acts on the modulus of the vector connecting atom \f$i\f$ to atom</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f$j\f$.  The sum over \f$k\f$ then runs over all the hydrogen atoms that are specified using using HYDROGEN keyword.  \f$\sigma_{oh}(|\mathbf{r}_{ik}|)\f$</a>
+<a name="50"><span class="lineNum">      50 </span>            : is a \ref switchingfunction that acts on the modulus of the vector connecting atom \f$i\f$ to atom \f$k\f$ and \f$\sigma_{\theta}(\theta_{kij})\f$</a>
+<a name="51"><span class="lineNum">      51 </span>            : is a \ref switchingfunction that acts on the angle between the vector connecting atoms \f$i\f$ and \f$j\f$ and the vector connecting atoms \f$i\f$ and</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f$k\f$.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : It is important to note that hydrogen bonds, unlike regular bonds, are asymmetric. In other words, the hydrogen atom does not sit at the</a>
+<a name="55"><span class="lineNum">      55 </span>            : mid point between the two other atoms in this three-center bond.  As a result of this adjacency matrices calculated using \ref HBOND_MATRIX are not</a>
+<a name="56"><span class="lineNum">      56 </span>            : symmetric like those calculated by \ref CONTACT_MATRIX.  One consequence of this fact is that the quantities found by performing \ref ROWSUMS and</a>
+<a name="57"><span class="lineNum">      57 </span>            : \ref COLUMNSUMS on a square \ref HBOND_MATRIX are not the same as they would be if you performed \ref ROWSUMS and</a>
+<a name="58"><span class="lineNum">      58 </span>            : \ref COLUMNSUMS on a square \ref CONTACT_MATRIX.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \par Examples</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The following input can be used to analyze the number of hydrogen bonds each of the oxygen atoms in a box of water participates in.  Each</a>
+<a name="63"><span class="lineNum">      63 </span>            : water molecule can participate in a hydrogen bond in one of two ways.  It can either donate one of its hydrogen atom to the neighboring oxygen or</a>
+<a name="64"><span class="lineNum">      64 </span>            : it can accept a bond between the hydrogen of a neighboring water molecule and its own oxygen.  The input below allows you to output information</a>
+<a name="65"><span class="lineNum">      65 </span>            : on the number of hydrogen bonds each of the water molecules donates and accepts.  This information is output in two xyz files which each contain</a>
+<a name="66"><span class="lineNum">      66 </span>            : five columns of data.  The first four of these columns are a label for the atom and the x, y and z position of the oxygen.  The last column is then</a>
+<a name="67"><span class="lineNum">      67 </span>            : the number of accepted/donated hydrogen bonds.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : mat: HBOND_MATRIX ATOMS=1-192:3 HYDROGENS=2-192:3,3-192:3 SWITCH={RATIONAL R_0=3.20} HSWITCH={RATIONAL R_0=2.30} ASWITCH={RATIONAL R_0=0.167pi} SUM</a>
+<a name="71"><span class="lineNum">      71 </span>            : rsums: ROWSUMS MATRIX=mat MEAN</a>
+<a name="72"><span class="lineNum">      72 </span>            : csums: COLUMNSUMS MATRIX=mat MEAN</a>
+<a name="73"><span class="lineNum">      73 </span>            : DUMPMULTICOLVAR DATA=rsums FILE=donors.xyz</a>
+<a name="74"><span class="lineNum">      74 </span>            : DUMPMULTICOLVAR DATA=csums FILE=acceptors.xyz</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : namespace PLMD {</a>
+<a name="82"><span class="lineNum">      82 </span>            : namespace adjmat {</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : class HBondMatrix : public AdjacencyMatrixBase {</a>
+<a name="85"><span class="lineNum">      85 </span>            : private:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   unsigned ndonor_types;</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// switching function</a>
+<a name="88"><span class="lineNum">      88 </span>            :   Matrix&lt;SwitchingFunction&gt; distanceOOSwitch;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   Matrix&lt;SwitchingFunction&gt; distanceOHSwitch;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   Matrix&lt;SwitchingFunction&gt; angleSwitch;</a>
+<a name="91"><span class="lineNum">      91 </span>            : public:</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Create manual</a>
+<a name="93"><span class="lineNum">      93 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Constructor</a>
+<a name="95"><span class="lineNum">      95 </span>            :   explicit HBondMatrix(const ActionOptions&amp;);</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// Create the ith, ith switching function</a>
+<a name="97"><span class="lineNum">      97 </span>            :   void setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) override;</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// This actually calculates the value of the contact function</a>
+<a name="99"><span class="lineNum">      99 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// This does nothing</a>
+<a name="101"><span class="lineNum">     101 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="102"><span class="lineNum">     102 </span>            : ///</a>
+<a name="103"><span class="lineNum">     103 </span>            :   double calculateForThree( const unsigned&amp; iat, const unsigned&amp; ano, const unsigned&amp; dno, const Vector&amp; ood,</a>
+<a name="104"><span class="lineNum">     104 </span>            :                             const double&amp; ood_df, const double&amp; ood_sw, multicolvar::AtomValuePack&amp; myatoms ) const;</a>
+<a name="105"><span class="lineNum">     105 </span>            : };</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(HBondMatrix,&quot;HBOND_MATRIX&quot;)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 : void HBondMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          4 :   AdjacencyMatrixBase::registerKeywords( keys );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;The list of atoms which can be part of a hydrogen bond.  When this command is used the set of atoms that can donate a &quot;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :            &quot;hydrogen bond is assumed to be the same as the set of atoms that can form hydrogen bonds.  The atoms involved must be specified &quot;</a>
+<a name="113"><span class="lineNum">     113 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="114"><span class="lineNum">     114 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="115"><span class="lineNum">     115 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="116"><span class="lineNum">     116 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;HYDROGENS&quot;,&quot;The list of hydrogen atoms that can form part of a hydrogen bond.  The atoms must be specified using a comma separated list, &quot;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :            &quot;an index range or by using a \\ref GROUP.  A list of hydrogen atoms is always required even if you specify the other atoms using &quot;</a>
+<a name="119"><span class="lineNum">     119 </span>            :            &quot;DONORS and ACCEPTORS as described below.&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;DONORS&quot;,&quot;The list of atoms which can donate a hydrogen bond.  The atoms involved must be specified &quot;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="122"><span class="lineNum">     122 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="123"><span class="lineNum">     123 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="124"><span class="lineNum">     124 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;ACCEPTORS&quot;,&quot;The list of atoms which can accept a hydrogen bond.  The atoms involved must be specified &quot;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="127"><span class="lineNum">     127 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="128"><span class="lineNum">     128 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;SWITCH&quot;,&quot;The \\ref switchingfunction that specifies how close a pair of atoms must be together for there to be a hydrogen bond between them&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;HSWITCH&quot;,&quot;The \\ref switchingfunction that specifies how close the hydrogen must be to the donor atom of the hydrogen bond for it to be &quot;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :            &quot;considered a hydrogen bond&quot;);</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;ASWITCH&quot;,&quot;A \\ref switchingfunction that is used to specify what the angle between the vector connecting the donor atom to the acceptor atom and &quot;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :            &quot;the vector connecting the donor atom to the hydrogen must be in order for it considered to be a hydrogen bond&quot;);</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   keys.use(&quot;SUM&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 : HBondMatrix::HBondMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   Action(ao),</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   AdjacencyMatrixBase(ao)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : {</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :   readMaxThreeSpeciesMatrix( &quot;ATOMS&quot;, &quot;DONORS&quot;, &quot;ACCEPTORS&quot;, &quot;HYDROGENS&quot;, false );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 :   unsigned nrows, ncols; retrieveTypeDimensions( nrows, ncols, ndonor_types );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   distanceOOSwitch.resize( nrows, ncols ); distanceOHSwitch.resize( nrows, ncols ); angleSwitch.resize( nrows, ncols );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :   parseConnectionDescriptions(&quot;SWITCH&quot;,false,ndonor_types);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 :   parseConnectionDescriptions(&quot;HSWITCH&quot;,false,ndonor_types);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 :   parseConnectionDescriptions(&quot;ASWITCH&quot;,false,ndonor_types);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   // Find the largest sf cutoff</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :   double sfmax=distanceOOSwitch(0,0).get_dmax();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;getNumberOfNodeTypes(); ++i) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :     for(unsigned j=0; j&lt;getNumberOfNodeTypes(); ++j) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :       double tsf=distanceOOSwitch(i,j).get_dmax();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          2 :       if( tsf&gt;sfmax ) sfmax=tsf;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            :   // Set the link cell cutoff</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          2 :   setLinkCellCutoff( sfmax );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          6 : void HBondMatrix::setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          6 :   plumed_assert( id&lt;3 &amp;&amp; desc.size()==1 );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          6 :   if( id==0 ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 :     std::string errors; distanceOOSwitch(j,i).set(desc[0],errors);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :     if( j!=i) distanceOOSwitch(i,j).set(desc[0],errors);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          4 :     log.printf(&quot;  atoms of type %u and %u must be within %s\n&quot;,i+1,j+1,(distanceOOSwitch(i,j).description()).c_str() );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          4 :   } else if( id==1 ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :     std::string errors; distanceOHSwitch(j,i).set(desc[0],errors);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :     if( j!=i) distanceOHSwitch(i,j).set(desc[0],errors);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 :     log.printf(&quot;  for atoms of type %u and %u the OH distance must be less than %s \n&quot;,i+1,j+1,(distanceOHSwitch(i,j).description()).c_str() );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :   } else if( id==2 ) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :     std::string errors; angleSwitch(j,i).set(desc[0],errors);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :     if( j!=i) angleSwitch(i,j).set(desc[0],errors);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 :     log.printf(&quot;  for atoms of type %u and %u the OOH angle must be less than %s \n&quot;,i+1,j+1,(angleSwitch(i,j).description()).c_str() );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          6 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       4038 : double HBondMatrix::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   // Ensure we skip diagonal elements of square matrix</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       4038 :   if( myatoms.getIndex(0)==myatoms.getIndex(1) ) return 0.0;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       4038 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       8076 :   if( distance.modulo2()&lt;distanceOOSwitch( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax2() ) return 1.0;</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   return 0.0;</a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       4038 : double HBondMatrix::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       4038 :   Vector ood = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double ood_l = ood.modulo(); // acceptor - donor</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   double ood_df, ood_sw=distanceOOSwitch( getBaseColvarNumber( myatoms.getIndex(0) ),</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       4038 :                                           getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( ood_l, ood_df );</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            :   // Get the base colvar numbers</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       4038 :   unsigned ano, dno = getBaseColvarNumber( myatoms.getIndex(0) );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       8076 :   if( ndonor_types==0 ) ano = getBaseColvarNumber( myatoms.getIndex(1) );</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :   else ano = getBaseColvarNumber( myatoms.getIndex(1) ) - ndonor_types;</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   double value=0;</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       4038 :   if( myatoms.getNumberOfAtoms()&gt;3 ) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     520170 :     for(unsigned i=2; i&lt;myatoms.getNumberOfAtoms(); ++i) value+=calculateForThree( i, ano, dno, ood, ood_df, ood_sw,  myatoms );</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   } else {</a>
+<a name="204"><span class="lineNum">     204 </span>            :     plumed_dbg_assert( myatoms.getNumberOfAtoms()==3 );</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :     value=calculateForThree( 2, ano, dno, ood, ood_df, ood_sw, myatoms );</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       4038 :   return value;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     516132 : double HBondMatrix::calculateForThree( const unsigned&amp; iat, const unsigned&amp; ano, const unsigned&amp; dno, const Vector&amp; ood,</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :                                        const double&amp; ood_df, const double&amp; ood_sw, multicolvar::AtomValuePack&amp; myatoms ) const {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     516132 :   Vector ohd=getSeparation( myatoms.getPosition(0), myatoms.getPosition(iat) ); double ohd_l=ohd.modulo();</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   double ohd_df, ohd_sw=distanceOHSwitch( getBaseColvarNumber( myatoms.getIndex(0) ),</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">     516132 :                                           getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( ohd_l, ohd_df );</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     516132 :   Angle a; Vector ood_adf, ohd_adf; double angle=a.compute( ood, ohd, ood_adf, ohd_adf );</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   double angle_df, angle_sw=angleSwitch( getBaseColvarNumber( myatoms.getIndex(0) ),</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     516132 :                                          getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( angle, angle_df );</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     516132 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         36 :     addAtomDerivatives( 1, 0, angle_sw*ohd_sw*(-ood_df)*ood + angle_sw*ood_sw*(-ohd_df)*ohd + ood_sw*ohd_sw*angle_df*angle*(-ood_adf-ohd_adf), myatoms );</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         36 :     addAtomDerivatives( 1, 1, angle_sw*ohd_sw*(+ood_df)*ood + ood_sw*ohd_sw*angle_df*angle*ood_adf, myatoms );</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         36 :     addAtomDerivatives( 1, iat, angle_sw*ood_sw*(+ohd_df)*ohd + ood_sw*ohd_sw*angle_df*angle*ohd_adf, myatoms );</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         72 :     myatoms.addBoxDerivatives( 1, angle_sw*ohd_sw*(-ood_df)*Tensor(ood,ood) + angle_sw*ood_sw*(-ohd_df)*Tensor(ohd,ohd)</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        108 :                                -ood_sw*ohd_sw*angle_df*angle*(Tensor(ood,ood_adf)+Tensor(ohd,ohd_adf)) );</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">     516132 :   return ood_sw*ohd_sw*angle_sw;</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/MatrixColumnSums.cpp.func-sort-c.html b/coverage/adjmat/MatrixColumnSums.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e2c36c5df2
--- /dev/null
+++ b/coverage/adjmat/MatrixColumnSums.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/MatrixColumnSums.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - MatrixColumnSums.cpp<span style="font-size: 80%;"> (<a href="MatrixColumnSums.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MatrixColumnSums.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#82">_ZN4PLMD6adjmat16MatrixColumnSumsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_128MatrixColumnSumsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#82">_ZN4PLMD6adjmat16MatrixColumnSumsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#75">_ZN4PLMD6adjmat16MatrixColumnSums16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#100">_ZNK4PLMD6adjmat16MatrixColumnSums7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">238</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_128MatrixColumnSumsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_128MatrixColumnSumsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
+</html>
diff --git a/coverage/adjmat/MatrixColumnSums.cpp.func.html b/coverage/adjmat/MatrixColumnSums.cpp.func.html
new file mode 100644
index 0000000000..b10f7611a7
--- /dev/null
+++ b/coverage/adjmat/MatrixColumnSums.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/MatrixColumnSums.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - MatrixColumnSums.cpp<span style="font-size: 80%;"> (<a href="MatrixColumnSums.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
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+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MatrixColumnSums.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_128MatrixColumnSumsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_128MatrixColumnSumsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_128MatrixColumnSumsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#75">_ZN4PLMD6adjmat16MatrixColumnSums16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#82">_ZN4PLMD6adjmat16MatrixColumnSumsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#82">_ZN4PLMD6adjmat16MatrixColumnSumsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixColumnSums.cpp.gcov.html#100">_ZNK4PLMD6adjmat16MatrixColumnSums7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">238</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/MatrixColumnSums.cpp.gcov.html b/coverage/adjmat/MatrixColumnSums.cpp.gcov.html
new file mode 100644
index 0000000000..25883a17b8
--- /dev/null
+++ b/coverage/adjmat/MatrixColumnSums.cpp.gcov.html
@@ -0,0 +1,198 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/MatrixColumnSums.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - MatrixColumnSums.cpp<span style="font-size: 80%;"> (source / <a href="MatrixColumnSums.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithInputMatrix.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC MATRIXF COLUMNSUMS</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Sum the columns of a contact matrix</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="35"><span class="lineNum">      35 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="36"><span class="lineNum">      36 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  This action allows you to calculate</a>
+<a name="37"><span class="lineNum">      37 </span>            : the sum of the columns in this adjacency matrix and to then calculate further functions of these quantities.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The first instruction in the following input file tells PLUMED to compute a \f$10 \times 10\f$ matrix in which the \f$ij\f$-element</a>
+<a name="42"><span class="lineNum">      42 </span>            : tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other.  The numbers in each of this rows are then added together</a>
+<a name="43"><span class="lineNum">      43 </span>            : and the average value is computed.  As such the following input provides an alternative method for calculating the coordination numbers</a>
+<a name="44"><span class="lineNum">      44 </span>            : of atoms 1 to 10.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}</a>
+<a name="48"><span class="lineNum">      48 </span>            : rsums: COLUMNSUMS MATRIX=mat MEAN</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=rsums.* FILE=colvar</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following input demonstrates another way that an average coordination number can be computed.  This input calculates the number of atoms</a>
+<a name="53"><span class="lineNum">      53 </span>            : with indices between 1 and 5 that are within the first coordination spheres of each of the atoms within indices between 6 and 15.  The average</a>
+<a name="54"><span class="lineNum">      54 </span>            : coordination number is then calculated from these fifteen coordination numbers and this quantity is output to a file.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}</a>
+<a name="58"><span class="lineNum">      58 </span>            : rsums: COLUMNSUMS MATRIX=mat2 MEAN</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=rsums.* FILE=colvar</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : */</a>
+<a name="63"><span class="lineNum">      63 </span>            : //+ENDPLUMEDOC</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : namespace PLMD {</a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace adjmat {</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class MatrixColumnSums : public ActionWithInputMatrix {</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit MatrixColumnSums(const ActionOptions&amp;);</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double compute( const unsigned&amp; tinded, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(MatrixColumnSums,&quot;COLUMNSUMS&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          7 : void MatrixColumnSums::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          7 :   ActionWithInputMatrix::registerKeywords( keys );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         21 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         28 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         28 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          7 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          5 : MatrixColumnSums::MatrixColumnSums(const ActionOptions&amp; ao):</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Action(ao),</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          5 :   ActionWithInputMatrix(ao)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          5 :   if( (mymatrix-&gt;getMatrixAction())-&gt;mybasemulticolvars.size()&gt;0 ) error(&quot;matrix row sums should only be calculated when inputs are atoms&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   // Setup the tasks</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          5 :   unsigned ncols = mymatrix-&gt;getNumberOfColumns();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          5 :   ablocks.resize(1); ablocks[0].resize( ncols );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        155 :   for(unsigned i=0; i&lt;ncols; ++i) addTaskToList( i );</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   // Set the positions - this is only used when getting positions for central atoms</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          5 :   if( mymatrix-&gt;undirectedGraph() ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        144 :     for(unsigned i=0; i&lt;ncols; ++i) ablocks[0][i]=i;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   } else {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         11 :     for(unsigned i=0; i&lt;ncols; ++i) ablocks[0][i]=mymatrix-&gt;getNumberOfRows() + i;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          5 :   std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          5 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        238 : double MatrixColumnSums::compute( const unsigned&amp; tinded, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        238 :   double sum=0.0; std::vector&lt;double&gt; tvals( mymatrix-&gt;getNumberOfComponents() );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        238 :   unsigned nrows = mymatrix-&gt;getNumberOfRows();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       9200 :   for(unsigned i=0; i&lt;nrows; ++i) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       8962 :     if( mymatrix-&gt;undirectedGraph() &amp;&amp; tinded==i ) continue;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       8774 :     sum+=retrieveConnectionValue( i, tinded, tvals );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        238 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        110 :     MultiValue myvals( mymatrix-&gt;getNumberOfComponents(), myatoms.getNumberOfDerivatives() );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :     MultiValue&amp; myvout=myatoms.getUnderlyingMultiValue();</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        880 :     for(unsigned i=0; i&lt;nrows; ++i) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        770 :       if( mymatrix-&gt;isSymmetric() &amp;&amp; tinded==i ) continue ;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        710 :       addConnectionDerivatives( i, tinded, myvals, myvout );</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        110 :   }</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        238 :   return sum;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/MatrixRowSums.cpp.func-sort-c.html b/coverage/adjmat/MatrixRowSums.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8a6ead4329
--- /dev/null
+++ b/coverage/adjmat/MatrixRowSums.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/MatrixRowSums.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - MatrixRowSums.cpp<span style="font-size: 80%;"> (<a href="MatrixRowSums.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MatrixRowSums.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#82">_ZN4PLMD6adjmat13MatrixRowSumsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_125MatrixRowSumsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#82">_ZN4PLMD6adjmat13MatrixRowSumsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#75">_ZN4PLMD6adjmat13MatrixRowSums16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#94">_ZNK4PLMD6adjmat13MatrixRowSums7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">203</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_125MatrixRowSumsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_125MatrixRowSumsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/MatrixRowSums.cpp.func.html b/coverage/adjmat/MatrixRowSums.cpp.func.html
new file mode 100644
index 0000000000..2b85aefcfe
--- /dev/null
+++ b/coverage/adjmat/MatrixRowSums.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/MatrixRowSums.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - MatrixRowSums.cpp<span style="font-size: 80%;"> (<a href="MatrixRowSums.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MatrixRowSums.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_125MatrixRowSumsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_125MatrixRowSumsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#73">_ZN4PLMD6adjmat12_GLOBAL__N_125MatrixRowSumsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#75">_ZN4PLMD6adjmat13MatrixRowSums16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#82">_ZN4PLMD6adjmat13MatrixRowSumsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#82">_ZN4PLMD6adjmat13MatrixRowSumsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixRowSums.cpp.gcov.html#94">_ZNK4PLMD6adjmat13MatrixRowSums7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">203</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/MatrixRowSums.cpp.gcov.html b/coverage/adjmat/MatrixRowSums.cpp.gcov.html
new file mode 100644
index 0000000000..d5b1718283
--- /dev/null
+++ b/coverage/adjmat/MatrixRowSums.cpp.gcov.html
@@ -0,0 +1,184 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/MatrixRowSums.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - MatrixRowSums.cpp<span style="font-size: 80%;"> (source / <a href="MatrixRowSums.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithInputMatrix.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC MATRIXF ROWSUMS</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Sum the rows of a adjacency matrix.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : As discussed in the section of the manual on \ref contactmatrix a useful tool for developing complex collective variables is the notion of the</a>
+<a name="35"><span class="lineNum">      35 </span>            : so called adjacency matrix.  An adjacency matrix is an \f$N \times N\f$ matrix in which the \f$i\f$th, \f$j\f$th element tells you whether</a>
+<a name="36"><span class="lineNum">      36 </span>            : or not the \f$i\f$th and \f$j\f$th atoms/molecules from a set of \f$N\f$ atoms/molecules are adjacent or not.  This action allows you to calculate</a>
+<a name="37"><span class="lineNum">      37 </span>            : the sum of the rows in this adjacency matrix and to then calculate further functions of these quantities.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The first instruction in the following input file tells PLUMED to compute a \f$10 \times 10\f$ matrix in which the \f$ij\f$-element</a>
+<a name="42"><span class="lineNum">      42 </span>            : tells you whether atoms \f$i\f$ and \f$j\f$ are within 1.0 nm of each other.  The numbers in each of this rows are then added together</a>
+<a name="43"><span class="lineNum">      43 </span>            : and the average value is computed.  As such the following input provides an alternative method for calculating the coordination numbers</a>
+<a name="44"><span class="lineNum">      44 </span>            : of atoms 1 to 10.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : mat: CONTACT_MATRIX ATOMS=1-10 SWITCH={RATIONAL R_0=1.0}</a>
+<a name="48"><span class="lineNum">      48 </span>            : rsums: ROWSUMS MATRIX=mat MEAN</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=rsums.* FILE=colvar</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following input demonstrates another way that an average coordination number can be computed.  This input calculates the number of atoms</a>
+<a name="53"><span class="lineNum">      53 </span>            : with indices between 6 and 15 that are within the first coordination spheres of each of the atoms within indices between 1 and 5.  The average</a>
+<a name="54"><span class="lineNum">      54 </span>            : coordination number is then calculated from these five coordination numbers and this quantity is output to a file.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : mat2: CONTACT_MATRIX ATOMSA=1-5 ATOMSB=6-15 SWITCH={RATIONAL R_0=1.0}</a>
+<a name="58"><span class="lineNum">      58 </span>            : rsums: ROWSUMS MATRIX=mat2 MEAN</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=rsums.* FILE=colvar</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : */</a>
+<a name="63"><span class="lineNum">      63 </span>            : //+ENDPLUMEDOC</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : namespace PLMD {</a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace adjmat {</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class MatrixRowSums : public ActionWithInputMatrix {</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit MatrixRowSums(const ActionOptions&amp;);</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double compute( const unsigned&amp; tinded, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(MatrixRowSums,&quot;ROWSUMS&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          6 : void MatrixRowSums::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          6 :   ActionWithInputMatrix::registerKeywords( keys );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         18 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         24 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         24 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          6 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 : MatrixRowSums::MatrixRowSums(const ActionOptions&amp; ao):</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Action(ao),</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          4 :   ActionWithInputMatrix(ao)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          4 :   if( (mymatrix-&gt;getMatrixAction())-&gt;mybasemulticolvars.size()&gt;0 ) warning(&quot;matrix row may be problematic when inputs are not atoms&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   // Setup the tasks</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          4 :   unsigned nrows = mymatrix-&gt;getNumberOfRows();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 :   ablocks.resize(1); ablocks[0].resize( nrows );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        147 :   for(unsigned i=0; i&lt;nrows; ++i) { ablocks[0][i]=i; addTaskToList( i ); }</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          4 :   std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          4 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        203 : double MatrixRowSums::compute( const unsigned&amp; tinded, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        203 :   std::vector&lt;double&gt; tvals( mymatrix-&gt;getNumberOfComponents() );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        203 :   getInputData( tinded, false, myatoms, tvals ); double fval=tvals[1];</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        203 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         75 :     tvals.assign( tvals.size(), 0 ); tvals[1]=1.0;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         75 :     mergeInputDerivatives( 1, 1, 2, tinded, tvals, getInputDerivatives( tinded, false, myatoms ), myatoms );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        203 :   return fval;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/OutputCluster.cpp.func-sort-c.html b/coverage/adjmat/OutputCluster.cpp.func-sort-c.html
new file mode 100644
index 0000000000..60756fb07a
--- /dev/null
+++ b/coverage/adjmat/OutputCluster.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/OutputCluster.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - OutputCluster.cpp<span style="font-size: 80%;"> (<a href="OutputCluster.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntryLo">47.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputCluster.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#215">_ZN4PLMD6adjmat13OutputCluster11explore_dfsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#204">_ZN4PLMD6adjmat13OutputCluster7exploreERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#101">_ZN4PLMD6adjmat13OutputClusterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#87">_ZN4PLMD6adjmat12_GLOBAL__N_125OutputClusterRegisterMe896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#83">_ZN4PLMD6adjmat13OutputCluster5applyEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#134">_ZN4PLMD6adjmat13OutputCluster6updateEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#82">_ZN4PLMD6adjmat13OutputCluster9calculateEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#101">_ZN4PLMD6adjmat13OutputClusterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#89">_ZN4PLMD6adjmat13OutputCluster16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#87">_ZN4PLMD6adjmat12_GLOBAL__N_125OutputClusterRegisterMe89C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#87">_ZN4PLMD6adjmat12_GLOBAL__N_125OutputClusterRegisterMe89D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/OutputCluster.cpp.func.html b/coverage/adjmat/OutputCluster.cpp.func.html
new file mode 100644
index 0000000000..f61208343e
--- /dev/null
+++ b/coverage/adjmat/OutputCluster.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/OutputCluster.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - OutputCluster.cpp<span style="font-size: 80%;"> (<a href="OutputCluster.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntryLo">47.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputCluster.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#87">_ZN4PLMD6adjmat12_GLOBAL__N_125OutputClusterRegisterMe896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#87">_ZN4PLMD6adjmat12_GLOBAL__N_125OutputClusterRegisterMe89C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#87">_ZN4PLMD6adjmat12_GLOBAL__N_125OutputClusterRegisterMe89D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#215">_ZN4PLMD6adjmat13OutputCluster11explore_dfsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#89">_ZN4PLMD6adjmat13OutputCluster16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#83">_ZN4PLMD6adjmat13OutputCluster5applyEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#134">_ZN4PLMD6adjmat13OutputCluster6updateEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#204">_ZN4PLMD6adjmat13OutputCluster7exploreERKjS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#82">_ZN4PLMD6adjmat13OutputCluster9calculateEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#101">_ZN4PLMD6adjmat13OutputClusterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputCluster.cpp.gcov.html#101">_ZN4PLMD6adjmat13OutputClusterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/OutputCluster.cpp.gcov.html b/coverage/adjmat/OutputCluster.cpp.gcov.html
new file mode 100644
index 0000000000..abfb29b755
--- /dev/null
+++ b/coverage/adjmat/OutputCluster.cpp.gcov.html
@@ -0,0 +1,309 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/OutputCluster.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - OutputCluster.cpp<span style="font-size: 80%;"> (source / <a href="OutputCluster.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntryLo">47.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ClusteringBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC CONCOMP OUTPUT_CLUSTER</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Output the indices of the atoms in one of the clusters identified by a clustering object</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This action provides one way of getting output from a \ref DFSCLUSTERING calculation.</a>
+<a name="34"><span class="lineNum">      34 </span>            : The output in question here is either</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : - a file that contains a list of the atom indices that form part of one of the clusters that was identified using \ref DFSCLUSTERING</a>
+<a name="37"><span class="lineNum">      37 </span>            : - an xyz file containing the positions of the atoms in one of the the clusters that was identified using \ref DFSCLUSTERING</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Notice also that if you choose to output an xyz file you can ask PLUMED to try to reconstruct the cluster</a>
+<a name="40"><span class="lineNum">      40 </span>            : taking the periodic boundary conditions into account by using the MAKE_WHOLE flag.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : The input shown below identifies those atoms with a coordination number less than 13</a>
+<a name="45"><span class="lineNum">      45 </span>            : and then constructs a contact matrix that describes the connectivity between the atoms</a>
+<a name="46"><span class="lineNum">      46 </span>            : that satisfy this criteria.  The DFS algorithm is then used to find the connected components</a>
+<a name="47"><span class="lineNum">      47 </span>            : in this matrix and the indices of the atoms in the largest connected component are then output</a>
+<a name="48"><span class="lineNum">      48 </span>            : to a file.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \plumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : c1: COORDINATIONNUMBER SPECIES=1-1996 SWITCH={CUBIC D_0=0.34 D_MAX=0.38}</a>
+<a name="52"><span class="lineNum">      52 </span>            : cf: MFILTER_LESS DATA=c1 SWITCH={CUBIC D_0=13 D_MAX=13.5}</a>
+<a name="53"><span class="lineNum">      53 </span>            : mat: CONTACT_MATRIX ATOMS=cf SWITCH={CUBIC D_0=0.34 D_MAX=0.38}</a>
+<a name="54"><span class="lineNum">      54 </span>            : dfs: DFSCLUSTERING MATRIX=mat</a>
+<a name="55"><span class="lineNum">      55 </span>            : OUTPUT_CLUSTER CLUSTERS=dfs CLUSTER=1 FILE=dfs.dat</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace PLMD {</a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace adjmat {</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : class OutputCluster : public ActionPilot {</a>
+<a name="65"><span class="lineNum">      65 </span>            : private:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   bool makewhole, output_xyz;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   OFile ofile;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   ClusteringBase* myclusters;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double rcut2;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   unsigned clustr, maxdepth, maxgoes;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;bool&gt; visited;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;unsigned&gt; myatoms;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;Vector&gt; atomsin;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   std::vector&lt;unsigned&gt; nneigh;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   Matrix&lt;unsigned&gt; adj_list;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   int number_of_cluster;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt; std::pair&lt;unsigned,unsigned&gt; &gt; cluster_sizes;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::vector&lt;unsigned&gt; which_cluster;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   bool explore_dfs( const unsigned&amp; index );</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void explore( const unsigned&amp; index, const unsigned&amp; depth );</a>
+<a name="81"><span class="lineNum">      81 </span>            : public:</a>
+<a name="82"><span class="lineNum">      82 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="83"><span class="lineNum">      83 </span>            :   explicit OutputCluster(const ActionOptions&amp;);</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   void calculate() override {}</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          8 :   void apply() override {}</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   void update() override;</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(OutputCluster,&quot;OUTPUT_CLUSTER&quot;)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         10 : void OutputCluster::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         10 :   Action::registerKeywords( keys );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         10 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTERS&quot;,&quot;the action that performed the clustering&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTER&quot;,&quot;1&quot;,&quot;which cluster would you like to look at 1 is the largest cluster, 2 is the second largest, 3 is the the third largest and so on&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which you would like to output the atoms in the cluster&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output the details of the cluster&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;MAXDEPTH&quot;,&quot;6&quot;,&quot;maximum depth for searches over paths to reconstruct clusters for PBC&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;MAXGOES&quot;,&quot;200&quot;,&quot;number of times to run searches to reconstruct clusters&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         20 :   keys.addFlag(&quot;MAKE_WHOLE&quot;,false,&quot;reconstruct the clusters and remove all periodic boundary conditions.&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         10 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          8 : OutputCluster::OutputCluster(const ActionOptions&amp; ao):</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   Action(ao),</a>
+<a name="105"><span class="lineNum">     105 </span>            :   ActionPilot(ao),</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          8 :   myclusters(NULL)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : {</a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Setup output file</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         16 :   ofile.link(*this); std::string file; parse(&quot;FILE&quot;,file);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          8 :   if( file.length()==0 ) error(&quot;output file name was not specified&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   // Search for xyz extension</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 :   output_xyz=false;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          8 :   if( file.find(&quot;.&quot;)!=std::string::npos ) {</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     std::size_t dot=file.find_first_of('.');</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         16 :     if( file.substr(dot+1)==&quot;xyz&quot; ) output_xyz=true;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          8 :   ofile.open(file); log.printf(&quot;  on file %s \n&quot;,file.c_str());</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         24 :   parseFlag(&quot;MAKE_WHOLE&quot;,makewhole); parse(&quot;MAXDEPTH&quot;,maxdepth); parse(&quot;MAXGOES&quot;,maxgoes);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          8 :   if( makewhole &amp;&amp; !output_xyz) error(&quot;MAKE_WHOLE flag is not compatible with output of non-xyz files&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   // Find what action we are taking the clusters from</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          8 :   std::vector&lt;std::string&gt; matname(1); parse(&quot;CLUSTERS&quot;,matname[0]);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 :   myclusters = plumed.getActionSet().selectWithLabel&lt;ClusteringBase*&gt;( matname[0] );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   if( !myclusters ) error( matname[0] + &quot; does not calculate perform a clustering of the atomic positions&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   // N.B. the +0.3 is a fudge factor.  Reconstrucing PBC doesnt work without this GAT</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          8 :   addDependency( myclusters ); double rcut=myclusters-&gt;getCutoffForConnection() + 0.3; rcut2=rcut*rcut;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :   // Read in the cluster we are calculating</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :   parse(&quot;CLUSTER&quot;,clustr);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          8 :   if( clustr&lt;1 ) error(&quot;cannot look for a cluster larger than the largest cluster&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          8 :   if( clustr&gt;myclusters-&gt;getNumberOfNodes() ) error(&quot;cluster selected is invalid - too few atoms in system&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   log.printf(&quot;  outputting atoms in %u th largest cluster found by %s \n&quot;,clustr,matname[0].c_str() );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         16 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 : void OutputCluster::update() {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          8 :   myclusters-&gt;retrieveAtomsInCluster( clustr, myatoms );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          8 :   if( output_xyz ) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     ofile.printf(&quot;%u \n&quot;,static_cast&lt;unsigned&gt;(myatoms.size()));</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     ofile.printf(&quot;atoms in %u th largest cluster \n&quot;,clustr );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     if( makewhole ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :       // Retrieve the atom positions</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :       atomsin.resize( myatoms.size() );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;myatoms.size(); ++i) atomsin[i]=myclusters-&gt;getPositionOfAtomForLinkCells( myatoms[i] );</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :       // Build a connectivity matrix neglecting the pbc</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :       nneigh.resize( myatoms.size(), 0 ); adj_list.resize( myatoms.size(), myatoms.size() );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :       for(unsigned i=1; i&lt;myatoms.size(); ++i) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :           if( delta( atomsin[i], atomsin[j] ).modulo2()&lt;=rcut2 ) { adj_list(i,nneigh[i])=j; adj_list(j,nneigh[j])=i; nneigh[i]++; nneigh[j]++; }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :         }</a>
+<a name="151"><span class="lineNum">     151 </span>            :       }</a>
+<a name="152"><span class="lineNum">     152 </span>            :       // Use DFS to find the largest cluster not broken by PBC</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :       number_of_cluster=-1; visited.resize( myatoms.size(), false );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :       cluster_sizes.resize( myatoms.size() ); which_cluster.resize( myatoms.size() );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;cluster_sizes.size(); ++i) { cluster_sizes[i].first=0; cluster_sizes[i].second=i; }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;myatoms.size(); ++i) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :         if( !visited[i] ) { number_of_cluster++; visited[i]=explore_dfs(i); }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :       }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :       std::sort( cluster_sizes.begin(), cluster_sizes.end() );</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :       // Now set visited so that only those atoms in largest cluster will be start points for PBCing</a>
+<a name="163"><span class="lineNum">     163 </span>            :       visited.assign( visited.size(), false );</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;myatoms.size(); ++i) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :         if( which_cluster[i]==cluster_sizes[cluster_sizes.size()-1].second ) visited[i]=true;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :       }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :       // Now retrieve the original connectivity matrix (including pbc)</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       nneigh.assign( nneigh.size(), 0 );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :       for(unsigned i=1; i&lt;myatoms.size(); ++i) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :           if( myclusters-&gt;areConnected( myatoms[i], myatoms[j] ) ) { adj_list(i,nneigh[i])=j; adj_list(j,nneigh[j])=i; nneigh[i]++; nneigh[j]++; }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :         }</a>
+<a name="174"><span class="lineNum">     174 </span>            :       }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :       // Now find broken bonds and run iterative deepening depth first search to reconstruct</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :       for(unsigned jj=0; jj&lt;maxgoes; ++jj) {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;myatoms.size(); ++j) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :           if( !visited[j] ) continue;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :           for(unsigned k=0; k&lt;nneigh[j]; ++k) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :             if( delta( atomsin[j],atomsin[adj_list(j,k)] ).modulo2()&gt;rcut2 ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :               visited[j]=true;</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :               for(unsigned depth=0; depth&lt;=maxdepth; ++depth) explore( j, depth );</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :             }</a>
+<a name="187"><span class="lineNum">     187 </span>            :           }</a>
+<a name="188"><span class="lineNum">     188 </span>            :         }</a>
+<a name="189"><span class="lineNum">     189 </span>            :       }</a>
+<a name="190"><span class="lineNum">     190 </span>            :       // And print final positions</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;myatoms.size(); ++i) ofile.printf( &quot;X %f %f %f \n&quot;, atomsin[i][0], atomsin[i][1], atomsin[i][2] );</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     } else {</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;myatoms.size(); ++i) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :         Vector pos=myclusters-&gt;getPositionOfAtomForLinkCells( myatoms[i] );</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :         ofile.printf( &quot;X %f %f %f \n&quot;, pos[0], pos[1], pos[2] );</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       }</a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            :   } else {</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          8 :     ofile.printf(&quot;CLUSTERING RESULTS AT TIME %f : NUMBER OF ATOMS IN %u TH LARGEST CLUSTER EQUALS %u \n&quot;,getTime(),clustr,static_cast&lt;unsigned&gt;(myatoms.size()) );</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          8 :     ofile.printf(&quot;INDICES OF ATOMS : &quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        512 :     for(unsigned i=0; i&lt;myatoms.size(); ++i) ofile.printf(&quot;%d &quot;,(myclusters-&gt;getAbsoluteIndexOfCentralAtom(myatoms[i])).index());</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          8 :     ofile.printf(&quot;\n&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          8 : }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 : void OutputCluster::explore( const unsigned&amp; index, const unsigned&amp; depth ) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :   if( depth==0 ) return ;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;nneigh[index]; ++i) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :     unsigned j=adj_list(index,i); visited[j]=true;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :     Vector svec=myclusters-&gt;pbcDistance( atomsin[index], atomsin[j] );</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :     atomsin[j] = atomsin[index] + svec;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :     explore( j, depth-1 );</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 : bool OutputCluster::explore_dfs( const unsigned&amp; index ) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :   visited[index]=true;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;nneigh[index]; ++i) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :     unsigned j=adj_list(index,i);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     if( !visited[j] ) visited[j]=explore_dfs(j);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   // Count the size of the cluster</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :   cluster_sizes[number_of_cluster].first++;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :   which_cluster[index] = number_of_cluster;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   return visited[index];</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/SMACMatrix.cpp.func-sort-c.html b/coverage/adjmat/SMACMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2797455460
--- /dev/null
+++ b/coverage/adjmat/SMACMatrix.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/SMACMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - SMACMatrix.cpp<span style="font-size: 80%;"> (<a href="SMACMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SMACMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#100">_ZN4PLMD6adjmat10SMACMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#108">_ZN4PLMD6adjmat10SMACMatrix24readOrientationConnectorERKjS3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#100">_ZN4PLMD6adjmat10SMACMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#93">_ZN4PLMD6adjmat12_GLOBAL__N_122SMACMatrixRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#95">_ZN4PLMD6adjmat10SMACMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#93">_ZN4PLMD6adjmat12_GLOBAL__N_122SMACMatrixRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#93">_ZN4PLMD6adjmat12_GLOBAL__N_122SMACMatrixRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#117">_ZNK4PLMD6adjmat10SMACMatrix21computeVectorFunctionERKjS3_RKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnHi">5806</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/SMACMatrix.cpp.func.html b/coverage/adjmat/SMACMatrix.cpp.func.html
new file mode 100644
index 0000000000..606bdf7dd9
--- /dev/null
+++ b/coverage/adjmat/SMACMatrix.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/SMACMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - SMACMatrix.cpp<span style="font-size: 80%;"> (<a href="SMACMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SMACMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#95">_ZN4PLMD6adjmat10SMACMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#108">_ZN4PLMD6adjmat10SMACMatrix24readOrientationConnectorERKjS3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#100">_ZN4PLMD6adjmat10SMACMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#100">_ZN4PLMD6adjmat10SMACMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#93">_ZN4PLMD6adjmat12_GLOBAL__N_122SMACMatrixRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#93">_ZN4PLMD6adjmat12_GLOBAL__N_122SMACMatrixRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#93">_ZN4PLMD6adjmat12_GLOBAL__N_122SMACMatrixRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACMatrix.cpp.gcov.html#117">_ZNK4PLMD6adjmat10SMACMatrix21computeVectorFunctionERKjS3_RKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnHi">5806</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/SMACMatrix.cpp.gcov.html b/coverage/adjmat/SMACMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..5a7c38e2b8
--- /dev/null
+++ b/coverage/adjmat/SMACMatrix.cpp.gcov.html
@@ -0,0 +1,231 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/SMACMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - SMACMatrix.cpp<span style="font-size: 80%;"> (source / <a href="SMACMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AlignedMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC MATRIX SMAC_MATRIX</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Adjacency matrix in which two molecules are adjacent if they are within a certain cutoff and if the angle between them is within certain ranges.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : In this case the elements of the adjacency matrix are calculated using:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : A_{ij} = \sigma(r_{ij}) \sum_n K_n(\theta_{ij})</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : In this expression \f$r_{ij}\f$ is the distance between molecule \f$i\f$ and molecule \f$j\f$ and \f$\sigma(r_{ij}\f$ is a</a>
+<a name="39"><span class="lineNum">      39 </span>            : \ref switchingfunction that acts on this distance.  The $K_n functions are \ref kernelfunctions that take the torsion angle, \f$\theta_{ij}\f$, between the</a>
+<a name="40"><span class="lineNum">      40 </span>            : internal orientation vectors for molecules \f$i\f$ and \f$j\f$ as input.  These kernel functions should be set so that they are</a>
+<a name="41"><span class="lineNum">      41 </span>            : equal to one when the relative orientation of the molecules are as they are in the solid and equal to zero otherwise.</a>
+<a name="42"><span class="lineNum">      42 </span>            : As the above matrix element is a product of functions it is only equal to one when the centers of mass of molecules \f$i\f$ and\f$j\f$</a>
+<a name="43"><span class="lineNum">      43 </span>            : are with a certain distance of each other and when the molecules are aligned in some desirable way.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : In the following example an adjacency matrix is constructed in which the \f$(i,j)\f$ element is equal to one if</a>
+<a name="48"><span class="lineNum">      48 </span>            : molecules \f$i\f$ and \f$j\f$ are within 6 angstroms of each other and if the torsional angle between the orientations</a>
+<a name="49"><span class="lineNum">      49 </span>            : of these molecules is close to 0 or \f$\pi\f$.  The various connected components of this matrix are determined using the</a>
+<a name="50"><span class="lineNum">      50 </span>            : \ref DFSCLUSTERING algorithm and then the size of the largest cluster of connects molecules is output to a colvar file</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : UNITS LENGTH=A</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : MOLECULES ...</a>
+<a name="56"><span class="lineNum">      56 </span>            : MOL1=1,2,1</a>
+<a name="57"><span class="lineNum">      57 </span>            : MOL2=5,6,5</a>
+<a name="58"><span class="lineNum">      58 </span>            : MOL3=9,10,9</a>
+<a name="59"><span class="lineNum">      59 </span>            : MOL4=13,14,13</a>
+<a name="60"><span class="lineNum">      60 </span>            : MOL5=17,18,17</a>
+<a name="61"><span class="lineNum">      61 </span>            : LABEL=m1</a>
+<a name="62"><span class="lineNum">      62 </span>            : ... MOLECULES</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : SMAC_MATRIX ...</a>
+<a name="65"><span class="lineNum">      65 </span>            :    ATOMS=m1 SWITCH={RATIONAL D_0=5.99 R_0=0.1 D_MAX=6.0}</a>
+<a name="66"><span class="lineNum">      66 </span>            :    KERNEL1={TRIANGULAR CENTER=0 SIGMA=1.0} KERNEL2={TRIANGULAR CENTER=pi SIGMA=0.6}</a>
+<a name="67"><span class="lineNum">      67 </span>            :    LABEL=smac</a>
+<a name="68"><span class="lineNum">      68 </span>            : ... SMAC_MATRIX</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : dfs1: DFSCLUSTERING MATRIX=smac</a>
+<a name="71"><span class="lineNum">      71 </span>            : cc2: CLUSTER_NATOMS CLUSTERS=dfs1 CLUSTER=1</a>
+<a name="72"><span class="lineNum">      72 </span>            : PRINT ARG=cc2 FILE=colvar</a>
+<a name="73"><span class="lineNum">      73 </span>            : \endplumedfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : namespace PLMD {</a>
+<a name="79"><span class="lineNum">      79 </span>            : namespace adjmat {</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class SMACMatrix : public AlignedMatrixBase {</a>
+<a name="82"><span class="lineNum">      82 </span>            : private:</a>
+<a name="83"><span class="lineNum">      83 </span>            :   Matrix&lt;std::vector&lt;KernelFunctions&gt; &gt; kernels;</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ///</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ///</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit SMACMatrix(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void readOrientationConnector( const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) override;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double computeVectorFunction( const unsigned&amp; iv, const unsigned&amp; jv,</a>
+<a name="91"><span class="lineNum">      91 </span>            :                                 const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="92"><span class="lineNum">      92 </span>            :                                 Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const override;</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(SMACMatrix,&quot;SMAC_MATRIX&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          3 : void SMACMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          3 :   AlignedMatrixBase::registerKeywords( keys );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 :   keys.add(&quot;numbered&quot;,&quot;KERNEL&quot;,&quot;The various kernels that are used to determine whether or not the molecules are aligned&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          3 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 : SMACMatrix::SMACMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   Action(ao),</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          1 :   AlignedMatrixBase(ao)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :   unsigned nrows, ncols, ig; retrieveTypeDimensions( nrows, ncols, ig );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   kernels.resize( nrows, ncols ); parseConnectionDescriptions(&quot;KERNEL&quot;,true,0);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          1 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 : void SMACMatrix::readOrientationConnector( const unsigned&amp; iv, const unsigned&amp; jv, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          3 :   for(int i=0; i&lt;desc.size(); i++) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :     KernelFunctions mykernel( desc[i] );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :     kernels(iv,jv).push_back( mykernel );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :     if( jv!=iv ) kernels(jv,iv).push_back( mykernel );</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   }</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :   if( kernels(iv,jv).size()==0 ) error(&quot;no kernels defined&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       5806 : double SMACMatrix::computeVectorFunction( const unsigned&amp; iv, const unsigned&amp; jv,</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="121"><span class="lineNum">     121 </span>            :     Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const {</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       5806 :   unsigned nvectors = ( vec1.size() - 2 ) / 3; plumed_assert( (vec1.size()-2)%3==0 );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       5806 :   std::vector&lt;Vector&gt; dv1(nvectors), dv2(nvectors), tdconn(nvectors); Torsion t; std::vector&lt;Vector&gt; v1(nvectors), v2(nvectors);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; pos;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      11612 :   for(unsigned i=0; i&lt;nvectors; ++i) { pos.emplace_back( Tools::make_unique&lt;Value&gt;() ); pos[i]-&gt;setDomain( &quot;-pi&quot;, &quot;pi&quot; ); }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      11612 :   for(unsigned j=0; j&lt;nvectors; ++j) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      23224 :     for(unsigned k=0; k&lt;3; ++k) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      17418 :       v1[j][k]=vec1[2+3*j+k]; v2[j][k]=vec2[2+3*j+k];</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       5806 :     double angle = t.compute( v1[j], conn, v2[j], dv1[j], tdconn[j], dv2[j] );</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     pos[j]-&gt;set( angle );</a>
+<a name="134"><span class="lineNum">     134 </span>            :   }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       5806 :   double ans=0; std::vector&lt;double&gt; deriv( nvectors ), df( nvectors, 0 );</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       5806 :   auto pos_ptr=Tools::unique2raw(pos);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      17418 :   for(unsigned i=0; i&lt;kernels(iv,jv).size(); ++i) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      11612 :     ans += kernels(iv,jv)[i].evaluate( pos_ptr, deriv );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      23224 :     for(unsigned j=0; j&lt;nvectors; ++j) df[j] += deriv[j];</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      11612 :   dconn.zero(); for(unsigned j=0; j&lt;nvectors; ++j) dconn += df[j]*tdconn[j];</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      11612 :   for(unsigned j=0; j&lt;nvectors; ++j) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      23224 :     for(unsigned k=0; k&lt;3; ++k) { dvec1[2+3*j+k]=df[j]*dv1[j][k]; dvec2[2+3*j+k]=df[j]*dv2[j][k]; }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       5806 :   return ans;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       5806 : }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/Sprint.cpp.func-sort-c.html b/coverage/adjmat/Sprint.cpp.func-sort-c.html
new file mode 100644
index 0000000000..51a9a95637
--- /dev/null
+++ b/coverage/adjmat/Sprint.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/Sprint.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - Sprint.cpp<span style="font-size: 80%;"> (<a href="Sprint.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Sprint.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#116">_ZN4PLMD6adjmat6SprintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#106">_ZN4PLMD6adjmat12_GLOBAL__N_119SprintRegisterMe1086createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#116">_ZN4PLMD6adjmat6SprintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#108">_ZN4PLMD6adjmat6Sprint16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#212">_ZN4PLMD6adjmat6Sprint5applyEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#149">_ZN4PLMD6adjmat6Sprint9calculateEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#106">_ZN4PLMD6adjmat12_GLOBAL__N_119SprintRegisterMe108C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#106">_ZN4PLMD6adjmat12_GLOBAL__N_119SprintRegisterMe108D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/Sprint.cpp.func.html b/coverage/adjmat/Sprint.cpp.func.html
new file mode 100644
index 0000000000..3806afe588
--- /dev/null
+++ b/coverage/adjmat/Sprint.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/Sprint.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - Sprint.cpp<span style="font-size: 80%;"> (<a href="Sprint.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Sprint.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#106">_ZN4PLMD6adjmat12_GLOBAL__N_119SprintRegisterMe1086createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#106">_ZN4PLMD6adjmat12_GLOBAL__N_119SprintRegisterMe108C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#106">_ZN4PLMD6adjmat12_GLOBAL__N_119SprintRegisterMe108D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#108">_ZN4PLMD6adjmat6Sprint16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#212">_ZN4PLMD6adjmat6Sprint5applyEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#149">_ZN4PLMD6adjmat6Sprint9calculateEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#116">_ZN4PLMD6adjmat6SprintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sprint.cpp.gcov.html#116">_ZN4PLMD6adjmat6SprintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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new file mode 100644
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+  <title>LCOV - plumed test coverage - adjmat/Sprint.cpp</title>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - Sprint.cpp<span style="font-size: 80%;"> (source / <a href="Sprint.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithInputMatrix.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AdjacencyMatrixVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MATRIXF SPRINT</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate SPRINT topological variables from an adjacency matrix.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : The SPRINT topological variables are calculated from the largest eigenvalue, \f$\lambda\f$ of</a>
+<a name="31"><span class="lineNum">      31 </span>            : an \f$n\times n\f$ adjacency matrix and its corresponding eigenvector, \f$\mathbf{V}\f$, using:</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \f[</a>
+<a name="34"><span class="lineNum">      34 </span>            : s_i = \sqrt{n} \lambda v_i</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f]</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : You can use different quantities to measure whether or not two given atoms/molecules are</a>
+<a name="38"><span class="lineNum">      38 </span>            : adjacent or not in the adjacency matrix.  The simplest measure of adjacency is is whether</a>
+<a name="39"><span class="lineNum">      39 </span>            : two atoms/molecules are within some cutoff of each other.  Further complexity can be added by</a>
+<a name="40"><span class="lineNum">      40 </span>            : insisting that two molecules are adjacent if they are within a certain distance of each</a>
+<a name="41"><span class="lineNum">      41 </span>            : other and if they have similar orientations.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of Lennard-Jones</a>
+<a name="46"><span class="lineNum">      46 </span>            : atoms and prints their values to a file.  In this input the SPRINT coordinates are calculated</a>
+<a name="47"><span class="lineNum">      47 </span>            : in the manner described in \cite Pietrucci2011 so two atoms are adjacent if they are within a cutoff:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : DENSITY SPECIES=1-7 LABEL=d1</a>
+<a name="51"><span class="lineNum">      51 </span>            : CONTACT_MATRIX ATOMS=d1 SWITCH={RATIONAL R_0=0.1} LABEL=mat</a>
+<a name="52"><span class="lineNum">      52 </span>            : SPRINT MATRIX=mat LABEL=ss</a>
+<a name="53"><span class="lineNum">      53 </span>            : PRINT ARG=ss.* FILE=colvar</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endplumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : This example input calculates the 14 SPRINT coordinates for a molecule composed of 7 hydrogen and</a>
+<a name="57"><span class="lineNum">      57 </span>            : 7 carbon atoms.  Once again two atoms are adjacent if they are within a cutoff:</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \plumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : DENSITY SPECIES=1-7 LABEL=c</a>
+<a name="61"><span class="lineNum">      61 </span>            : DENSITY SPECIES=8-14 LABEL=h</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : CONTACT_MATRIX ...</a>
+<a name="64"><span class="lineNum">      64 </span>            :   ATOMS=c,h</a>
+<a name="65"><span class="lineNum">      65 </span>            :   SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}</a>
+<a name="66"><span class="lineNum">      66 </span>            :   SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}</a>
+<a name="67"><span class="lineNum">      67 </span>            :   SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}</a>
+<a name="68"><span class="lineNum">      68 </span>            :   LABEL=mat</a>
+<a name="69"><span class="lineNum">      69 </span>            : ... CONTACT_MATRIX</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : SPRINT MATRIX=mat LABEL=ss</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : PRINT ARG=ss.* FILE=colvar</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : */</a>
+<a name="77"><span class="lineNum">      77 </span>            : //+ENDPLUMEDOC</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : namespace PLMD {</a>
+<a name="81"><span class="lineNum">      81 </span>            : namespace adjmat {</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : class Sprint : public ActionWithInputMatrix {</a>
+<a name="84"><span class="lineNum">      84 </span>            : private:</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Square root of number of atoms</a>
+<a name="86"><span class="lineNum">      86 </span>            :   double sqrtn;</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Vector that stores eigenvalues</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;double&gt; eigvals;</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// This is used to speed up the calculation of derivatives</a>
+<a name="90"><span class="lineNum">      90 </span>            :   DynamicList&lt;unsigned&gt; active_elements;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Vector that stores max eigenvector</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt; std::pair&lt;double,int&gt; &gt; maxeig;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Adjacency matrix</a>
+<a name="94"><span class="lineNum">      94 </span>            :   Matrix&lt;double&gt; thematrix;</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Matrix that stores eigenvectors</a>
+<a name="96"><span class="lineNum">      96 </span>            :   Matrix&lt;double&gt; eigenvecs;</a>
+<a name="97"><span class="lineNum">      97 </span>            : public:</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Create manual</a>
+<a name="99"><span class="lineNum">      99 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Constructor</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit Sprint(const ActionOptions&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// Do the matrix calculation</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void calculate() override;</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// Sprint needs its only apply routine as it creates values</a>
+<a name="105"><span class="lineNum">     105 </span>            :   void apply() override;</a>
+<a name="106"><span class="lineNum">     106 </span>            : };</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Sprint,&quot;SPRINT&quot;)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 : void Sprint::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          3 :   ActionWithInputMatrix::registerKeywords( keys );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 :   componentsAreNotOptional(keys);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;coord&quot;,&quot;default&quot;,&quot;all \\f$n\\f$ sprint coordinates are calculated and then stored in increasing order. &quot;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :                           &quot;the smallest sprint coordinate will be labeled &lt;em&gt;label&lt;/em&gt;.coord-0, &quot;</a>
+<a name="115"><span class="lineNum">     115 </span>            :                           &quot;the second smallest will be labelled &lt;em&gt;label&lt;/em&gt;.coord-1 and so on&quot;);</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          3 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 : Sprint::Sprint(const ActionOptions&amp;ao):</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   Action(ao),</a>
+<a name="120"><span class="lineNum">     120 </span>            :   ActionWithInputMatrix(ao),</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          1 :   eigvals( getNumberOfNodes() ),</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 :   maxeig( getNumberOfNodes() ),</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :   thematrix( getNumberOfNodes(), getNumberOfNodes() ),</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 :   eigenvecs( getNumberOfNodes(), getNumberOfNodes() )</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : {</a>
+<a name="126"><span class="lineNum">     126 </span>            :   // Check on setup</a>
+<a name="127"><span class="lineNum">     127 </span>            :   // if( getNumberOfVessels()!=1 ) error(&quot;there should be no vessel keywords&quot;);</a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Check for bad colvar input ( we  are going to get rid of this because we are going to have input adjacency matrix in future )</a>
+<a name="129"><span class="lineNum">     129 </span>            :   // for(unsigned i=0;i&lt;getNumberOfAtomGroups();++i){</a>
+<a name="130"><span class="lineNum">     130 </span>            :   //    /// Check me GAT</a>
+<a name="131"><span class="lineNum">     131 </span>            :   //    // if( !getBaseMultiColvar(i)-&gt;hasDifferentiableOrientation() ) error(&quot;cannot use multicolvar of type &quot; + getBaseMultiColvar(i)-&gt;getName() );</a>
+<a name="132"><span class="lineNum">     132 </span>            :   // }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   if( !getAdjacencyVessel()-&gt;isSymmetric() ) error(&quot;input contact matrix is not symmetric&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   std::vector&lt;AtomNumber&gt; fake_atoms; setupMultiColvarBase( fake_atoms );</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            :   // Create all the values</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   sqrtn = std::sqrt( static_cast&lt;double&gt;( getNumberOfNodes() ) );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;getNumberOfNodes(); ++i) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         14 :     std::string num; Tools::convert(i,num);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         14 :     addComponentWithDerivatives(&quot;coord-&quot;+num);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;coord-&quot;+num);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         14 :     getPntrToComponent(i)-&gt;resizeDerivatives( getNumberOfDerivatives() );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Setup the dynamic list to hold all the tasks</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 :   unsigned ntriangle = 0.5*getNumberOfNodes()*(getNumberOfNodes()-1);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         92 :   for(unsigned i=0; i&lt;ntriangle; ++i) active_elements.addIndexToList( i );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 : }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         17 : void Sprint::calculate() {</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   // Get the adjacency matrix</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         17 :   getAdjacencyVessel()-&gt;retrieveMatrix( active_elements, thematrix );</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   // Diagonalize it</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         17 :   diagMat( thematrix, eigvals, eigenvecs );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Get the maximum eigevalue</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         17 :   double lambda = eigvals[ getNumberOfNodes()-1 ];</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   // Get the corresponding eigenvector</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        255 :   for(unsigned j=0; j&lt;maxeig.size(); ++j) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        238 :     maxeig[j].first = std::fabs( eigenvecs( getNumberOfNodes()-1, j ) );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        238 :     maxeig[j].second = j;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     // Must make all components of principle eigenvector +ve</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        238 :     eigenvecs( getNumberOfNodes()-1, j ) = maxeig[j].first;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   // Reorder each block of eigevectors</a>
+<a name="167"><span class="lineNum">     167 </span>            :   unsigned startnum=0;</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         51 :   for(unsigned j=0; j&lt;getNumberOfNodeTypes(); ++j) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         34 :     unsigned nthis = getNumberOfAtomsInGroup(j);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     // Sort into ascending order</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         34 :     std::sort( maxeig.begin() + startnum, maxeig.begin() + startnum + nthis );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     // Used so we can do sorting in blocks</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         34 :     startnum += nthis;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            :   // Set the sprint coordinates</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        255 :   for(int icomp=0; icomp&lt;getNumberOfComponents(); ++icomp) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        238 :     getPntrToComponent(icomp)-&gt;set( sqrtn*lambda*maxeig[icomp].first );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   // Parallelism</a>
+<a name="181"><span class="lineNum">     181 </span>            :   unsigned rank, stride;</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         17 :   if( serialCalculation() ) { stride=1; rank=0; }</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         17 :   else { rank=comm.Get_rank(); stride=comm.Get_size(); }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   // Derivatives</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         17 :   MultiValue myvals( 2, getNumberOfDerivatives() );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         17 :   Matrix&lt;double&gt; mymat_ders( getNumberOfComponents(), getNumberOfDerivatives() );</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   // std::vector&lt;unsigned&gt; catoms(2);</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         17 :   unsigned nval = getNumberOfNodes(); mymat_ders=0;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       1564 :   for(unsigned i=rank; i&lt;active_elements.getNumberActive(); i+=stride) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1547 :     unsigned j, k; getAdjacencyVessel()-&gt;getMatrixIndices( active_elements[i], j, k );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1547 :     double tmp1 = 2 * eigenvecs(nval-1,j)*eigenvecs(nval-1,k);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      23205 :     for(int icomp=0; icomp&lt;getNumberOfComponents(); ++icomp) {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :       double tmp2 = 0.;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     303212 :       for(unsigned n=0; n&lt;nval-1; ++n) { // Need care on following line</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     281554 :         tmp2 += eigenvecs(n,maxeig[icomp].second) * ( eigenvecs(n,j)*eigenvecs(nval-1,k) + eigenvecs(n,k)*eigenvecs(nval-1,j) ) / ( lambda - eigvals[n] );</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :       }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      21658 :       double prefactor=sqrtn*( tmp1*maxeig[icomp].first + tmp2*lambda );</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      21658 :       getAdjacencyVessel()-&gt;retrieveDerivatives( active_elements[i], false, myvals );</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">     346528 :       for(unsigned jd=0; jd&lt;myvals.getNumberActive(); ++jd) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :         unsigned ider=myvals.getActiveIndex(jd);</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     324870 :         mymat_ders( icomp, ider ) += prefactor*myvals.getDerivative( 1, ider );</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       }</a>
+<a name="204"><span class="lineNum">     204 </span>            :     }</a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         17 :   if( !serialCalculation() ) comm.Sum( mymat_ders );</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        255 :   for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        238 :     Value* val=getPntrToComponent(j);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      12376 :     for(unsigned i=0; i&lt;getNumberOfDerivatives(); ++i) val-&gt;addDerivative( i, mymat_ders(j,i) );</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         17 : }</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         17 : void Sprint::apply() {</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   std::vector&lt;Vector&gt;&amp;   f(modifyForces());</a>
+<a name="216"><span class="lineNum">     216 </span>            :   Tensor&amp;           v(modifyVirial());</a>
+<a name="217"><span class="lineNum">     217 </span>            :   unsigned          nat=getNumberOfAtoms();</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         17 :   std::vector&lt;double&gt; forces( 3*getNumberOfAtoms() + 9 );</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        255 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        238 :     if( getPntrToComponent(i)-&gt;applyForce( forces ) ) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;nat; ++j) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :         f[j][0]+=forces[3*j+0];</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :         f[j][1]+=forces[3*j+1];</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :         f[j][2]+=forces[3*j+2];</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :       }</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       v(0,0)+=forces[3*nat+0];</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :       v(0,1)+=forces[3*nat+1];</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       v(0,2)+=forces[3*nat+2];</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :       v(1,0)+=forces[3*nat+3];</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :       v(1,1)+=forces[3*nat+4];</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :       v(1,2)+=forces[3*nat+5];</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :       v(2,0)+=forces[3*nat+6];</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :       v(2,1)+=forces[3*nat+7];</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :       v(2,2)+=forces[3*nat+8];</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :     }</a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         17 : }</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/TopologyMatrix.cpp.func-sort-c.html b/coverage/adjmat/TopologyMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ad8810282e
--- /dev/null
+++ b/coverage/adjmat/TopologyMatrix.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/TopologyMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - TopologyMatrix.cpp<span style="font-size: 80%;"> (<a href="TopologyMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TopologyMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat14TopologyMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#76">_ZN4PLMD6adjmat12_GLOBAL__N_126TopologyMatrixRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat14TopologyMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#78">_ZN4PLMD6adjmat14TopologyMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#164">_ZN4PLMD6adjmat14TopologyMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#160">_ZNK4PLMD6adjmat14TopologyMatrix21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#76">_ZN4PLMD6adjmat12_GLOBAL__N_126TopologyMatrixRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#76">_ZN4PLMD6adjmat12_GLOBAL__N_126TopologyMatrixRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#194">_ZNK4PLMD6adjmat14TopologyMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">9616</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#188">_ZNK4PLMD6adjmat14TopologyMatrix15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">31203</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#240">_ZNK4PLMD6adjmat14TopologyMatrix22calculateForThreeAtomsERKjRKNS_13VectorGenericILj3EEERKdRNS_13HistogramBeadERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">117917799</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/TopologyMatrix.cpp.func.html b/coverage/adjmat/TopologyMatrix.cpp.func.html
new file mode 100644
index 0000000000..d18546d8b5
--- /dev/null
+++ b/coverage/adjmat/TopologyMatrix.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/TopologyMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - TopologyMatrix.cpp<span style="font-size: 80%;"> (<a href="TopologyMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TopologyMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#76">_ZN4PLMD6adjmat12_GLOBAL__N_126TopologyMatrixRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#76">_ZN4PLMD6adjmat12_GLOBAL__N_126TopologyMatrixRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#76">_ZN4PLMD6adjmat12_GLOBAL__N_126TopologyMatrixRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#164">_ZN4PLMD6adjmat14TopologyMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#78">_ZN4PLMD6adjmat14TopologyMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat14TopologyMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#97">_ZN4PLMD6adjmat14TopologyMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#188">_ZNK4PLMD6adjmat14TopologyMatrix15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">31203</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#160">_ZNK4PLMD6adjmat14TopologyMatrix21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#240">_ZNK4PLMD6adjmat14TopologyMatrix22calculateForThreeAtomsERKjRKNS_13VectorGenericILj3EEERKdRNS_13HistogramBeadERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">117917799</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TopologyMatrix.cpp.gcov.html#194">_ZNK4PLMD6adjmat14TopologyMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">9616</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/TopologyMatrix.cpp.gcov.html b/coverage/adjmat/TopologyMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..4faab5bbe6
--- /dev/null
+++ b/coverage/adjmat/TopologyMatrix.cpp.gcov.html
@@ -0,0 +1,400 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat/TopologyMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">adjmat</a> - TopologyMatrix.cpp<span style="font-size: 80%;"> (source / <a href="TopologyMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AdjacencyMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC MATRIX TOPOLOGY_MATRIX</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Adjacency matrix in which two atoms are adjacent if they are connected topologically</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \par Examples</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : */</a>
+<a name="37"><span class="lineNum">      37 </span>            : //+ENDPLUMEDOC</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace adjmat {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class TopologyMatrix : public AdjacencyMatrixBase {</a>
+<a name="43"><span class="lineNum">      43 </span>            : private:</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// The width to use for the kernel density estimation and the</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// sizes of the bins to be used in kernel density estimation</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double sigma;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::string kerneltype;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// The maximum number of bins that will be used</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// This is calculated based on the dmax of the switching functions</a>
+<a name="50"><span class="lineNum">      50 </span>            :   unsigned maxbins;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// The volume of the cells</a>
+<a name="52"><span class="lineNum">      52 </span>            :   Matrix&lt;double&gt; cell_volume;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// switching function</a>
+<a name="54"><span class="lineNum">      54 </span>            :   Matrix&lt;SwitchingFunction&gt; switchingFunction;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   Matrix&lt;SwitchingFunction&gt; cylinder_sw;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   Matrix&lt;SwitchingFunction&gt; low_sf;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   double beadrad, lsfmax;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   Matrix&lt;double&gt; binw_mat;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   SwitchingFunction threshold_switch;</a>
+<a name="60"><span class="lineNum">      60 </span>            : public:</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Create manual</a>
+<a name="62"><span class="lineNum">      62 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Constructor</a>
+<a name="64"><span class="lineNum">      64 </span>            :   explicit TopologyMatrix(const ActionOptions&amp;);</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Get the number of quantities that we must compute</a>
+<a name="66"><span class="lineNum">      66 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Create the ith, ith switching function</a>
+<a name="68"><span class="lineNum">      68 </span>            :   void setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) override;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// This actually calculates the value of the contact function</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// This does nothing</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Calculate the contribution from one of the atoms in the third element of the pack</a>
+<a name="74"><span class="lineNum">      74 </span>            :   void calculateForThreeAtoms( const unsigned&amp; iat, const Vector&amp; d1, const double&amp; d1_len,</a>
+<a name="75"><span class="lineNum">      75 </span>            :                                HistogramBead&amp; bead, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : };</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(TopologyMatrix,&quot;TOPOLOGY_MATRIX&quot;)</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 : void TopologyMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   AdjacencyMatrixBase::registerKeywords( keys );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         16 :   keys.add(&quot;atoms&quot;,&quot;NODES&quot;,&quot;The list of atoms for which you would like to calculate the contact matrix.  The atoms involved must be specified &quot;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="84"><span class="lineNum">      84 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="85"><span class="lineNum">      85 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="86"><span class="lineNum">      86 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         16 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available.&quot;);</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;RADIUS&quot;,&quot;&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;CYLINDER_SWITCH&quot;,&quot;a switching function on the distance from the center of the cylinder&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;BIN_SIZE&quot;,&quot;the size to use for the bins&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;DENSITY_THRESHOLD&quot;,&quot;&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;the width of the function to be used for kernel density estimation&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;KERNEL&quot;,&quot;gaussian&quot;,&quot;the type of kernel function to be used&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         16 :   keys.add(&quot;hidden&quot;,&quot;FAKE&quot;,&quot;&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          8 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 : TopologyMatrix::TopologyMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   Action(ao),</a>
+<a name="101"><span class="lineNum">     101 </span>            :   AdjacencyMatrixBase(ao),</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         12 :   maxbins(0)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         12 :   readMaxThreeSpeciesMatrix(&quot;NODES&quot;, &quot;FAKE&quot;, &quot;FAKE&quot;, &quot;ATOMS&quot;, true );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 :   unsigned nrows, ncols, ndonor_types; retrieveTypeDimensions( nrows, ncols, ndonor_types );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          6 :   switchingFunction.resize( nrows, ncols ); parseConnectionDescriptions(&quot;SWITCH&quot;,false,ndonor_types);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          6 :   cylinder_sw.resize( nrows, ncols ); parseConnectionDescriptions(&quot;RADIUS&quot;,false,ndonor_types);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          6 :   low_sf.resize( nrows, ncols ); parseConnectionDescriptions(&quot;CYLINDER_SWITCH&quot;,false,ndonor_types);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          6 :   binw_mat.resize( nrows, ncols ); cell_volume.resize( nrows, ncols );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          6 :   parseConnectionDescriptions(&quot;BIN_SIZE&quot;,false,ndonor_types);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   // Read in stuff for grid</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         18 :   parse(&quot;SIGMA&quot;,sigma); parse(&quot;KERNEL&quot;,kerneltype);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   // Read in threshold for density cutoff</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          6 :   std::string errors, thresh_sw_str; parse(&quot;DENSITY_THRESHOLD&quot;,thresh_sw_str);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          6 :   threshold_switch.set(thresh_sw_str, errors );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          6 :   if( errors.length()&gt;0 ) error(&quot;errors in DENSITY_THRESHOLD switching function : &quot; + errors );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          6 :   log.printf(&quot;  threshold on density of atoms in cylinder equals %s\n&quot;,threshold_switch.description().c_str() );</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;getNumberOfNodeTypes(); ++i) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         12 :     for(unsigned j=0; j&lt;getNumberOfNodeTypes(); ++j) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 :       double r=cylinder_sw(i,j).get_d0() + cylinder_sw(i,j).get_r0();</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          6 :       cell_volume(i,j)=binw_mat(i,j)*pi*r*r;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     }</a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   // Find the largest sf cutoff</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          6 :   lsfmax=low_sf(0,0).get_dmax();</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   double sfmax=switchingFunction(0,0).get_dmax();</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          6 :   double rfmax=cylinder_sw(0,0).get_dmax();</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;getNumberOfNodeTypes(); ++i) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         12 :     for(unsigned j=0; j&lt;getNumberOfNodeTypes(); ++j) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          6 :       double tsf=switchingFunction(i,j).get_dmax();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          6 :       if( tsf&gt;sfmax ) sfmax=tsf;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          6 :       double rsf=cylinder_sw(i,j).get_dmax();</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          6 :       if( rsf&gt;rfmax ) rfmax=rsf;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          6 :       double lsf=low_sf(i,j).get_dmax();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :       if( lsf&gt;lsfmax ) lsfmax=lsf;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :     }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   // Get the width of the bead</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          6 :   HistogramBead bead; bead.isNotPeriodic();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          6 :   bead.setKernelType( kerneltype ); bead.set( 0.0, 1.0, sigma );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          6 :   beadrad = bead.getCutoff();</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   // Set the link cell cutoff</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          6 :   log.printf(&quot;  setting cutoff %f \n&quot;, sfmax );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          6 :   setLinkCellCutoff( sfmax, std::numeric_limits&lt;double&gt;::max() );</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   double maxsize=0;</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;getNumberOfNodeTypes(); ++i) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         12 :     for(unsigned j=0; j&lt;getNumberOfNodeTypes(); ++j) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          6 :       if( binw_mat(i,j)&gt;maxsize ) maxsize=binw_mat(i,j);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     }</a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span>            :   // Set the maximum number of bins that we will need to compute</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          6 :   maxbins = std::floor( sfmax / maxsize ) + 1;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   // Need to resize functions again here to ensure that vector sizes</a>
+<a name="158"><span class="lineNum">     158 </span>            :   // are set correctly in AdjacencyMatrixVessel</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          6 :   resizeFunctions();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          6 : }</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        100 : unsigned TopologyMatrix::getNumberOfQuantities() const {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        100 :   return maxbins+3;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         24 : void TopologyMatrix::setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         24 :   plumed_assert( id&lt;4 );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         24 :   if( id==0 ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          6 :     std::string errors; switchingFunction(j,i).set(desc[0],errors);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          6 :     if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          6 :     if( j!=i) switchingFunction(i,j).set(desc[0],errors);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         12 :     log.printf(&quot;  %u th and %u th multicolvar groups must be within %s\n&quot;,i+1,j+1,(switchingFunction(i,j).description()).c_str() );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         18 :   } else if( id==1 ) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          6 :     std::string errors; cylinder_sw(j,i).set(desc[0],errors);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          6 :     if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          6 :     if( j!=i) cylinder_sw(i,j).set(desc[0],errors);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         12 :     log.printf(&quot;  there must be not atoms within the cylinder connections atoms of multicolvar groups %u th and %u th.  This cylinder has radius %s \n&quot;,i+1,j+1,(cylinder_sw(i,j).description()).c_str() );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         12 :   } else if( id==2 ) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          6 :     std::string errors; low_sf(j,i).set(desc[0],errors);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          6 :     if( errors.length()!=0 ) error(&quot;problem reading switching function description &quot; + errors);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          6 :     if( j!=i ) low_sf(i,j).set(desc[0],errors);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         12 :     log.printf(&quot;  %u th and %u th multicolvar groups must be further apart than %s\n&quot;,i+1,j+1,(low_sf(j,i).description()).c_str() );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          6 :   } else if( id==3 ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          6 :     Tools::convert( desc[0], binw_mat(j,i) );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          6 :     if( i!=j ) binw_mat(i,j)=binw_mat(j,i);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          6 :     log.printf(&quot;  cylinder for %u th and %u th multicolvar groups is split into bins of length %f \n&quot;,i,j,binw_mat(i,j) );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         24 : }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      31203 : double TopologyMatrix::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      31203 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      62406 :   if( distance.modulo2()&lt;switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax2() ) return 1.0;</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   return 0.0;</a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       9616 : double TopologyMatrix::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       9616 :   HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( kerneltype );</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Initialise to zero density on all bins</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      48200 :   for(unsigned bin=0; bin&lt;maxbins; ++bin) myatoms.setValue(bin+1,0);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   // Calculate whether or not atoms 1 and 2 are within cutoff (can use delta here as pbc are done in atom setup)</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       9616 :   Vector d1 = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double d1_len = d1.modulo();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       9616 :   d1 = d1 / d1_len;  // Convert vector into director</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       9616 :   AtomNumber a1 = myatoms.getAbsoluteIndex( 0 );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       9616 :   AtomNumber a2 = myatoms.getAbsoluteIndex( 1 );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">  117927415 :   for(unsigned i=2; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">  117917799 :     AtomNumber a3 = myatoms.getAbsoluteIndex( i );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">  117917799 :     if( a3!=a1 &amp;&amp; a3!=a2 ) calculateForThreeAtoms( i, d1, d1_len, bead, myatoms );</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span>            :   // std::vector&lt;double&gt; binvals( 1+maxbins ); for(unsigned i=1;i&lt;maxbins;++i) binvals[i]=myatoms.getValue(i);</a>
+<a name="211"><span class="lineNum">     211 </span>            :   // unsigned ii; double fdf;</a>
+<a name="212"><span class="lineNum">     212 </span>            :   //std::cout&lt;&lt;&quot;HELLO DENSITY &quot;&lt;&lt;myatoms.getIndex(0)&lt;&lt;&quot; &quot;&lt;&lt;myatoms.getIndex(1)&lt;&lt;&quot; &quot;&lt;&lt;transformStoredValues( binvals, ii, fdf )&lt;&lt;std::endl;</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   // Now find the element for which the density is maximal</a>
+<a name="215"><span class="lineNum">     215 </span>            :   unsigned vout=2; double max=myatoms.getValue( 2 );</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      38584 :   for(unsigned i=3; i&lt;myatoms.getUnderlyingMultiValue().getNumberOfValues()-1; ++i) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      28968 :     if( myatoms.getValue(i)&gt;max ) { max=myatoms.getValue(i); vout=i; }</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // Calculate value and derivative of switching function between atoms 1 and 2</a>
+<a name="220"><span class="lineNum">     220 </span>            :   double dfuncl, sw = switchingFunction( getBaseColvarNumber( myatoms.getIndex(0) ),</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       9616 :                                          getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( d1_len, dfuncl );</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   // Transform the density</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       9616 :   double df, tsw = threshold_switch.calculate( max, df );</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       9616 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     // Factor of d1_len is required here because d1 is normalized</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         60 :     d1 *= d1_len;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         60 :     addAtomDerivatives( 2+maxbins, 0, -dfuncl*d1, myatoms );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         60 :     addAtomDerivatives( 2+maxbins, 1, dfuncl*d1, myatoms );</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         60 :     myatoms.addBoxDerivatives( 2+maxbins, (-dfuncl)*Tensor(d1,d1) );</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     // Update active atoms so that next bit works</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         60 :     updateActiveAtoms( myatoms );</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     // Now finish caclulation of derivatives</a>
+<a name="233"><span class="lineNum">     233 </span>            :     MultiValue&amp; myvals=myatoms.getUnderlyingMultiValue();</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      13029 :     for(unsigned jd=0; jd&lt;myvals.getNumberActive(); ++jd) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      12969 :       unsigned ider=myvals.getActiveIndex(jd);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      12969 :       myvals.addDerivative( 1, ider, sw*df*max*myvals.getDerivative( vout, ider ) + tsw*myvals.getDerivative( 2+maxbins, ider ) );</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     }</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       9616 :   return sw*tsw;</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">  117917799 : void TopologyMatrix::calculateForThreeAtoms( const unsigned&amp; iat, const Vector&amp; d1, const double&amp; d1_len,</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     HistogramBead&amp; bead, multicolvar::AtomValuePack&amp; myatoms ) const {</a>
+<a name="244"><span class="lineNum">     244 </span>            :   // Calculate if there are atoms in the cylinder (can use delta here as pbc are done in atom setup)</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">  117917799 :   Vector d2 = getSeparation( myatoms.getPosition(0), myatoms.getPosition(iat) );</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   // Now calculate projection of d2 on d1</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">  117917799 :   double proj=dotProduct(d2,d1);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   // This tells us if we are outside the end of the cylinder</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">  117917799 :   double excess = proj - d1_len;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   // Return if we are outside of the cylinder as calculated based on excess</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">  175974631 :   if( excess&gt;low_sf( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax() ) return;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :   // Find the length of the cylinder</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">   81802351 :   double binw = binw_mat( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) );</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">   81802351 :   double lcylinder = (std::floor( d1_len / binw ) + 1)*binw;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :   // Return if the projection is outside the length of interest</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">   81802351 :   if( proj&lt;-bead.getCutoff() || proj&gt;(lcylinder+bead.getCutoff()) ) return;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // Calculate the excess swiching function</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">   23745519 :   double edf, eval = low_sf( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).calculate( excess, edf );</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   // Calculate the projection on the perpendicular distance from the center of the tube</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">   23745519 :   double cm = d2.modulo2() - proj*proj;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   // Now calculate the density in the cylinder</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">   23745519 :   if( cm&lt;cylinder_sw( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) ).get_dmax2() ) {</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     double dfuncr, val = cylinder_sw( getBaseColvarNumber( myatoms.getIndex(0) ),</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">     104467 :                                       getBaseColvarNumber( myatoms.getIndex(1) ) ).calculateSqr( cm, dfuncr );</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">     104467 :     double cellv = cell_volume( getBaseColvarNumber( myatoms.getIndex(0) ), getBaseColvarNumber( myatoms.getIndex(1) ) );</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">     104467 :     Vector dc1, dc2, dc3, dd1, dd2, dd3, de1, de2, de3;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">     104467 :     if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       4023 :       Tensor d1_a1;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :       // Derivative of director connecting atom1 - atom2 wrt the position of atom 1</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       4023 :       d1_a1(0,0) = ( -(d1[1]*d1[1]+d1[2]*d1[2])/d1_len );   // dx/dx</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       4023 :       d1_a1(0,1) = (  d1[0]*d1[1]/d1_len );                 // dx/dy</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       4023 :       d1_a1(0,2) = (  d1[0]*d1[2]/d1_len );                 // dx/dz</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       4023 :       d1_a1(1,0) = (  d1[1]*d1[0]/d1_len );                 // dy/dx</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       4023 :       d1_a1(1,1) = ( -(d1[0]*d1[0]+d1[2]*d1[2])/d1_len );   // dy/dy</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       4023 :       d1_a1(1,2) = (  d1[1]*d1[2]/d1_len );</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       4023 :       d1_a1(2,0) = (  d1[2]*d1[0]/d1_len );</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       4023 :       d1_a1(2,1) = (  d1[2]*d1[1]/d1_len );</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       4023 :       d1_a1(2,2) = ( -(d1[1]*d1[1]+d1[0]*d1[0])/d1_len );</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :       // Calculate derivatives of dot product</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       4023 :       dd1 = matmul(d2, d1_a1) - d1;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       4023 :       dd2 = matmul(d2, -d1_a1);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       4023 :       dd3 = d1;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :       // Calculate derivatives of cross product</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       4023 :       dc1 = dfuncr*( -d2 - proj*dd1 );</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       4023 :       dc2 = dfuncr*( -proj*dd2 );</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       4023 :       dc3 = dfuncr*( d2 - proj*dd3 );</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            :       // Calculate derivatives of excess</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       4023 :       de1 = edf*excess*( dd1 + d1 );</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       4023 :       de2 = edf*excess*( dd2 - d1 );</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       4023 :       de3 = edf*excess*dd3;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :     }</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">     104467 :     Vector pos1 = myatoms.getPosition(0) + d1_len*d1;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">     104467 :     Vector pos2 = myatoms.getPosition(0) + d2;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">     104467 :     Vector g1derivf,g2derivf,lderivf; Tensor vir;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">     530381 :     for(unsigned bin=0; bin&lt;maxbins; ++bin) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">     425914 :       bead.set( bin*binw, (bin+1)*binw, sigma );</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">     425914 :       if( proj&lt;(bin*binw-bead.getCutoff()) || proj&gt;binw*(bin+1)+bead.getCutoff() ) continue;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     132418 :       double der, contr=bead.calculateWithCutoff( proj, der ) / cellv; der /= cellv;</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     132418 :       myatoms.addValue( 2+bin, contr*val*eval );</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">     132418 :       if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       5835 :         g1derivf=contr*eval*dc1 + val*eval*der*dd1 + contr*val*de1;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       5835 :         addAtomDerivatives( 2+bin, 0, g1derivf, myatoms );</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">       5835 :         g2derivf=contr*eval*dc2 + val*eval*der*dd2 + contr*val*de2;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       5835 :         addAtomDerivatives( 2+bin, 1, g2derivf, myatoms );</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       5835 :         lderivf=contr*eval*dc3 + val*eval*der*dd3 + contr*val*de3;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       5835 :         addAtomDerivatives( 2+bin, iat, lderivf, myatoms );</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :         // Virial</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       5835 :         vir = -Tensor( myatoms.getPosition(0), g1derivf ) - Tensor( pos1, g2derivf ) - Tensor( pos2, lderivf );</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       5835 :         myatoms.addBoxDerivatives( 2+bin, vir );</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :       }</a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            : }</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : }</a>
+<a name="323"><span class="lineNum">     323 </span>            : }</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - adjmat</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1038</td>
+            <td class="headerCovTableEntry">1171</td>
+            <td class="headerCovTableEntryMed">88.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">183</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterAnalysisBase.h.gcov.html">ClusterAnalysisBase.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactAlignedMatrix.cpp.gcov.html">ContactAlignedMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="22.7%"><img src="../snow.png" width=77 height=10 alt="22.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 22</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputMatrix.h.gcov.html">ActionWithInputMatrix.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterSize.cpp.gcov.html">ClusterSize.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.0%"><img src="../snow.png" width=15 height=10 alt="85.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 20</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputCluster.cpp.gcov.html">OutputCluster.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=47 height=10 alt="47.1%"><img src="../snow.png" width=53 height=10 alt="47.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">47.1&nbsp;%</td>
+      <td class="coverNumLo">41 / 87</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusteringBase.cpp.gcov.html">ClusteringBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterWithSurface.cpp.gcov.html">ClusterWithSurface.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.0%"><img src="../snow.png" width=14 height=10 alt="86.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.0&nbsp;%</td>
+      <td class="coverNumMed">49 / 57</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterDiameter.cpp.gcov.html">ClusterDiameter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.1%"><img src="../snow.png" width=7 height=10 alt="93.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.1&nbsp;%</td>
+      <td class="coverNumHi">27 / 29</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterAnalysisBase.cpp.gcov.html">ClusterAnalysisBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">44 / 48</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixBase.cpp.gcov.html">AdjacencyMatrixBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.1%"><img src="../snow.png" width=15 height=10 alt="85.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.1&nbsp;%</td>
+      <td class="coverNumMed">86 / 101</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlignedMatrixBase.cpp.gcov.html">AlignedMatrixBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.0%"><img src="../snow.png" width=12 height=10 alt="88.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">44 / 50</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixColumnSums.cpp.gcov.html">MatrixColumnSums.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixRowSums.cpp.gcov.html">MatrixRowSums.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterDistribution.cpp.gcov.html">ClusterDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.8%"><img src="../snow.png" width=12 height=10 alt="87.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.8&nbsp;%</td>
+      <td class="coverNumMed">43 / 49</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterProperties.cpp.gcov.html">ClusterProperties.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DFSClustering.cpp.gcov.html">DFSClustering.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMACMatrix.cpp.gcov.html">SMACMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sprint.cpp.gcov.html">Sprint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.4%"><img src="../snow.png" width=18 height=10 alt="82.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">61 / 74</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpGraph.cpp.gcov.html">DumpGraph.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactMatrix.cpp.gcov.html">ContactMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HbondMatrix.cpp.gcov.html">HbondMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">69 / 71</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TopologyMatrix.cpp.gcov.html">TopologyMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">156 / 156</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixVessel.cpp.gcov.html">AdjacencyMatrixVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.0%"><img src="../snow.png" width=9 height=10 alt="91.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.0&nbsp;%</td>
+      <td class="coverNumHi">71 / 78</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputMatrix.cpp.gcov.html">ActionWithInputMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">70 / 70</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusteringBase.h.gcov.html">ClusteringBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixBase.h.gcov.html">AdjacencyMatrixBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/index-sort-l.html b/coverage/adjmat/index-sort-l.html
new file mode 100644
index 0000000000..e7775db5a9
--- /dev/null
+++ b/coverage/adjmat/index-sort-l.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - adjmat</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1038</td>
+            <td class="headerCovTableEntry">1171</td>
+            <td class="headerCovTableEntryMed">88.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">183</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterAnalysisBase.h.gcov.html">ClusterAnalysisBase.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactAlignedMatrix.cpp.gcov.html">ContactAlignedMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="22.7%"><img src="../snow.png" width=77 height=10 alt="22.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 22</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputCluster.cpp.gcov.html">OutputCluster.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=47 height=10 alt="47.1%"><img src="../snow.png" width=53 height=10 alt="47.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">47.1&nbsp;%</td>
+      <td class="coverNumLo">41 / 87</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputMatrix.h.gcov.html">ActionWithInputMatrix.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sprint.cpp.gcov.html">Sprint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.4%"><img src="../snow.png" width=18 height=10 alt="82.4%"></td></tr></table>
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+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">61 / 74</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterSize.cpp.gcov.html">ClusterSize.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.0%"><img src="../snow.png" width=15 height=10 alt="85.0%"></td></tr></table>
+      </td>
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+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixBase.cpp.gcov.html">AdjacencyMatrixBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.1%"><img src="../snow.png" width=15 height=10 alt="85.1%"></td></tr></table>
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+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterWithSurface.cpp.gcov.html">ClusterWithSurface.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.0%"><img src="../snow.png" width=14 height=10 alt="86.0%"></td></tr></table>
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+      <td class="coverNumMed">49 / 57</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterDistribution.cpp.gcov.html">ClusterDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.8%"><img src="../snow.png" width=12 height=10 alt="87.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.8&nbsp;%</td>
+      <td class="coverNumMed">43 / 49</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlignedMatrixBase.cpp.gcov.html">AlignedMatrixBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.0%"><img src="../snow.png" width=12 height=10 alt="88.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">44 / 50</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixVessel.cpp.gcov.html">AdjacencyMatrixVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.0%"><img src="../snow.png" width=9 height=10 alt="91.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.0&nbsp;%</td>
+      <td class="coverNumHi">71 / 78</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterAnalysisBase.cpp.gcov.html">ClusterAnalysisBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">44 / 48</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterDiameter.cpp.gcov.html">ClusterDiameter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.1%"><img src="../snow.png" width=7 height=10 alt="93.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.1&nbsp;%</td>
+      <td class="coverNumHi">27 / 29</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusteringBase.cpp.gcov.html">ClusteringBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HbondMatrix.cpp.gcov.html">HbondMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">69 / 71</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusteringBase.h.gcov.html">ClusteringBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixBase.h.gcov.html">AdjacencyMatrixBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixRowSums.cpp.gcov.html">MatrixRowSums.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DFSClustering.cpp.gcov.html">DFSClustering.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterProperties.cpp.gcov.html">ClusterProperties.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixColumnSums.cpp.gcov.html">MatrixColumnSums.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpGraph.cpp.gcov.html">DumpGraph.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMACMatrix.cpp.gcov.html">SMACMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactMatrix.cpp.gcov.html">ContactMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputMatrix.cpp.gcov.html">ActionWithInputMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">70 / 70</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TopologyMatrix.cpp.gcov.html">TopologyMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">156 / 156</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/adjmat/index.html b/coverage/adjmat/index.html
new file mode 100644
index 0000000000..e6f094c3e9
--- /dev/null
+++ b/coverage/adjmat/index.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - adjmat</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - adjmat</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1038</td>
+            <td class="headerCovTableEntry">1171</td>
+            <td class="headerCovTableEntryMed">88.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">183</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputMatrix.cpp.gcov.html">ActionWithInputMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">70 / 70</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputMatrix.h.gcov.html">ActionWithInputMatrix.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixBase.cpp.gcov.html">AdjacencyMatrixBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.1%"><img src="../snow.png" width=15 height=10 alt="85.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.1&nbsp;%</td>
+      <td class="coverNumMed">86 / 101</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixBase.h.gcov.html">AdjacencyMatrixBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdjacencyMatrixVessel.cpp.gcov.html">AdjacencyMatrixVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.0%"><img src="../snow.png" width=9 height=10 alt="91.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.0&nbsp;%</td>
+      <td class="coverNumHi">71 / 78</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlignedMatrixBase.cpp.gcov.html">AlignedMatrixBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.0%"><img src="../snow.png" width=12 height=10 alt="88.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">44 / 50</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
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+      <td class="coverBar" align="center">
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+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">44 / 48</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterAnalysisBase.h.gcov.html">ClusterAnalysisBase.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
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+      <td class="coverPerLo">0.0&nbsp;%</td>
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+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterDiameter.cpp.gcov.html">ClusterDiameter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.1%"><img src="../snow.png" width=7 height=10 alt="93.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.1&nbsp;%</td>
+      <td class="coverNumHi">27 / 29</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterDistribution.cpp.gcov.html">ClusterDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.8%"><img src="../snow.png" width=12 height=10 alt="87.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.8&nbsp;%</td>
+      <td class="coverNumMed">43 / 49</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterProperties.cpp.gcov.html">ClusterProperties.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterSize.cpp.gcov.html">ClusterSize.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.0%"><img src="../snow.png" width=15 height=10 alt="85.0%"></td></tr></table>
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+      <td class="coverNumMed">17 / 20</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClusterWithSurface.cpp.gcov.html">ClusterWithSurface.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.0%"><img src="../snow.png" width=14 height=10 alt="86.0%"></td></tr></table>
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+      <td class="coverFile"><a href="ClusteringBase.cpp.gcov.html">ClusteringBase.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverNumHi">29 / 31</td>
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+      <td class="coverNumMed">6 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="ClusteringBase.h.gcov.html">ClusteringBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
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+    <tr>
+      <td class="coverFile"><a href="ContactAlignedMatrix.cpp.gcov.html">ContactAlignedMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="22.7%"><img src="../snow.png" width=77 height=10 alt="22.7%"></td></tr></table>
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+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="ContactMatrix.cpp.gcov.html">ContactMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DFSClustering.cpp.gcov.html">DFSClustering.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpGraph.cpp.gcov.html">DumpGraph.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HbondMatrix.cpp.gcov.html">HbondMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">69 / 71</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixColumnSums.cpp.gcov.html">MatrixColumnSums.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixRowSums.cpp.gcov.html">MatrixRowSums.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputCluster.cpp.gcov.html">OutputCluster.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=47 height=10 alt="47.1%"><img src="../snow.png" width=53 height=10 alt="47.1%"></td></tr></table>
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+      <td class="coverPerLo">47.1&nbsp;%</td>
+      <td class="coverNumLo">41 / 87</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
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+    <tr>
+      <td class="coverFile"><a href="SMACMatrix.cpp.gcov.html">SMACMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
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+      <td class="coverNumMed">7 / 8</td>
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+      <td class="coverFile"><a href="Sprint.cpp.gcov.html">Sprint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.4%"><img src="../snow.png" width=18 height=10 alt="82.4%"></td></tr></table>
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+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">61 / 74</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
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+    <tr>
+      <td class="coverFile"><a href="TopologyMatrix.cpp.gcov.html">TopologyMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/analysis/AnalysisBase.cpp.func-sort-c.html b/coverage/analysis/AnalysisBase.cpp.func-sort-c.html
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+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AnalysisBase.cpp<span style="font-size: 80%;"> (<a href="AnalysisBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AnalysisBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#36">_ZN4PLMD8analysis12AnalysisBaseC1ERKNS_13ActionOptionsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#68">_ZN4PLMD8analysis12AnalysisBase6updateEv</a></td>
+              <td class="coverFnHi">39</td>
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+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#58">_ZN4PLMD8analysis12AnalysisBase16getArgumentNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">50</td>
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+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#74">_ZN4PLMD8analysis12AnalysisBase12runFinalJobsEv</a></td>
+              <td class="coverFnHi">107</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#36">_ZN4PLMD8analysis12AnalysisBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">109</td>
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+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#28">_ZN4PLMD8analysis12AnalysisBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">149</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
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new file mode 100644
index 0000000000..59cf70eab2
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+++ b/coverage/analysis/AnalysisBase.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AnalysisBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AnalysisBase.cpp<span style="font-size: 80%;"> (<a href="AnalysisBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
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+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
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+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AnalysisBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#74">_ZN4PLMD8analysis12AnalysisBase12runFinalJobsEv</a></td>
+              <td class="coverFnHi">107</td>
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+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#58">_ZN4PLMD8analysis12AnalysisBase16getArgumentNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#28">_ZN4PLMD8analysis12AnalysisBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">149</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#68">_ZN4PLMD8analysis12AnalysisBase6updateEv</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#36">_ZN4PLMD8analysis12AnalysisBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.cpp.gcov.html#36">_ZN4PLMD8analysis12AnalysisBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AnalysisBase.cpp.gcov.html b/coverage/analysis/AnalysisBase.cpp.gcov.html
new file mode 100644
index 0000000000..f1ff8cecf8
--- /dev/null
+++ b/coverage/analysis/AnalysisBase.cpp.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AnalysisBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AnalysisBase.cpp<span style="font-size: 80%;"> (source / <a href="AnalysisBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ReadAnalysisFrames.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace analysis {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        149 : void AnalysisBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        149 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        149 :   ActionWithValue::registerKeywords( keys ); ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        149 :   ActionWithArguments::registerKeywords( keys ); keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        447 :   ActionWithVessel::registerKeywords( keys ); keys.remove(&quot;TOL&quot;); keys.reset_style(&quot;TIMINGS&quot;,&quot;hidden&quot;); keys.isAnalysis();</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        298 :   keys.add(&quot;atoms-2&quot;,&quot;USE_OUTPUT_DATA_FROM&quot;,&quot;use the output of the analysis performed by this object as input to your new analysis object&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        149 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        109 : AnalysisBase::AnalysisBase(const ActionOptions&amp;ao):</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   Action(ao),</a>
+<a name="40"><span class="lineNum">      40 </span>            :   ActionPilot(ao),</a>
+<a name="41"><span class="lineNum">      41 </span>            :   ActionWithValue(ao),</a>
+<a name="42"><span class="lineNum">      42 </span>            :   ActionAtomistic(ao),</a>
+<a name="43"><span class="lineNum">      43 </span>            :   ActionWithArguments(ao),</a>
+<a name="44"><span class="lineNum">      44 </span>            :   ActionWithVessel(ao),</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        109 :   my_input_data(NULL)</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : {</a>
+<a name="47"><span class="lineNum">      47 </span>            :   // We have an if statement here so that this doesn't break with READ_DISSIMILARITIES</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        218 :   if( keywords.exists(&quot;USE_OUTPUT_DATA_FROM&quot;) ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         78 :     std::string datastr; parse(&quot;USE_OUTPUT_DATA_FROM&quot;,datastr);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        156 :     if( keywords.style(&quot;USE_OUTPUT_DATA_FROM&quot;,&quot;atoms&quot;) &amp;&amp; datastr.length()==0 ) error(&quot;input analysis action was not specified use USE_OUTPUT_DATA_FROM&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         78 :     if( datastr.length()&gt;0 ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         77 :       my_input_data=plumed.getActionSet().selectWithLabel&lt;AnalysisBase*&gt;( datastr );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         77 :       log.printf(&quot;  performing analysis on output from %s \n&quot;,datastr.c_str() );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         77 :       if( !my_input_data ) error(&quot;could not find analysis action named &quot; + datastr );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         77 :       addDependency( my_input_data );</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :     }</a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        109 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         50 : std::vector&lt;std::string&gt; AnalysisBase::getArgumentNames() {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         50 :   std::vector&lt;Value*&gt; arg_p( getArgumentList() );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         50 :   std::vector&lt;std::string&gt; argn( arg_p.size() );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        124 :   for(unsigned i=0; i&lt;arg_p.size(); ++i) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         74 :     plumed_assert( i&lt;argn.size() &amp;&amp; i&lt;arg_p.size() );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         74 :     argn[i]=arg_p[i]-&gt;getName();</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   }</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         50 :   return argn;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         39 : void AnalysisBase::update() {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         39 :   if( getStep()==0 || ( getStride()&gt;0 &amp;&amp; !onStep() ) ) return;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   // And do the analysis</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         30 :   performAnalysis();</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        107 : void AnalysisBase::runFinalJobs() {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        107 :   if( getStride()&gt;0 ) return;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         69 :   performAnalysis();</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AnalysisBase.h.func-sort-c.html b/coverage/analysis/AnalysisBase.h.func-sort-c.html
new file mode 100644
index 0000000000..9148ee0c8a
--- /dev/null
+++ b/coverage/analysis/AnalysisBase.h.func-sort-c.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AnalysisBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AnalysisBase.h<span style="font-size: 80%;"> (<a href="AnalysisBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">68.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AnalysisBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#90">_ZN4PLMD8analysis12AnalysisBase10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#91">_ZN4PLMD8analysis12AnalysisBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#92">_ZN4PLMD8analysis12AnalysisBase29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#136">_ZNK4PLMD8analysis12AnalysisBase11usingMemoryEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#126">_ZNK4PLMD8analysis12AnalysisBase13getMetricNameB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#141">_ZNK4PLMD8analysis12AnalysisBase16getNormalizationEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#166">_ZNK4PLMD8analysis12AnalysisBase14getAtomIndexesEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#156">_ZN4PLMD8analysis12AnalysisBase15getArgumentListEv</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#171">_ZNK4PLMD8analysis12AnalysisBase27getDissimilarityInstructionB5cxx11Ev</a></td>
+              <td class="coverFnHi">841</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#146">_ZNK4PLMD8analysis12AnalysisBase22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnHi">848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#104">_ZN4PLMD8analysis12AnalysisBase12lockRequestsEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#110">_ZN4PLMD8analysis12AnalysisBase14unlockRequestsEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#95">_ZN4PLMD8analysis12AnalysisBase5applyEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#94">_ZN4PLMD8analysis12AnalysisBase9calculateEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#116">_ZNK4PLMD8analysis12AnalysisBase21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">360092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#121">_ZNK4PLMD8analysis12AnalysisBase23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnHi">375002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#161">_ZN4PLMD8analysis12AnalysisBase13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">522156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#151">_ZN4PLMD8analysis12AnalysisBase16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">659376</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#131">_ZN4PLMD8analysis12AnalysisBase9getWeightERKj</a></td>
+              <td class="coverFnHi">40113999</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AnalysisBase.h.func.html b/coverage/analysis/AnalysisBase.h.func.html
new file mode 100644
index 0000000000..959001f6fd
--- /dev/null
+++ b/coverage/analysis/AnalysisBase.h.func.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AnalysisBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AnalysisBase.h<span style="font-size: 80%;"> (<a href="AnalysisBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">68.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AnalysisBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#90">_ZN4PLMD8analysis12AnalysisBase10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#104">_ZN4PLMD8analysis12AnalysisBase12lockRequestsEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#161">_ZN4PLMD8analysis12AnalysisBase13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">522156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#110">_ZN4PLMD8analysis12AnalysisBase14unlockRequestsEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#156">_ZN4PLMD8analysis12AnalysisBase15getArgumentListEv</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#151">_ZN4PLMD8analysis12AnalysisBase16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">659376</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#91">_ZN4PLMD8analysis12AnalysisBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#92">_ZN4PLMD8analysis12AnalysisBase29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#95">_ZN4PLMD8analysis12AnalysisBase5applyEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#94">_ZN4PLMD8analysis12AnalysisBase9calculateEv</a></td>
+              <td class="coverFnHi">7546</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#131">_ZN4PLMD8analysis12AnalysisBase9getWeightERKj</a></td>
+              <td class="coverFnHi">40113999</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#136">_ZNK4PLMD8analysis12AnalysisBase11usingMemoryEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#126">_ZNK4PLMD8analysis12AnalysisBase13getMetricNameB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#166">_ZNK4PLMD8analysis12AnalysisBase14getAtomIndexesEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#141">_ZNK4PLMD8analysis12AnalysisBase16getNormalizationEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#116">_ZNK4PLMD8analysis12AnalysisBase21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">360092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#146">_ZNK4PLMD8analysis12AnalysisBase22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnHi">848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#121">_ZNK4PLMD8analysis12AnalysisBase23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnHi">375002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AnalysisBase.h.gcov.html#171">_ZNK4PLMD8analysis12AnalysisBase27getDissimilarityInstructionB5cxx11Ev</a></td>
+              <td class="coverFnHi">841</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AnalysisBase.h.gcov.html b/coverage/analysis/AnalysisBase.h.gcov.html
new file mode 100644
index 0000000000..725524a57b
--- /dev/null
+++ b/coverage/analysis/AnalysisBase.h.gcov.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AnalysisBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AnalysisBase.h<span style="font-size: 80%;"> (source / <a href="AnalysisBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">68.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_analysis_AnalysisBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_analysis_AnalysisBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;DataCollectionObject.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class ReferenceConfiguration;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace analysis {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : /**</a>
+<a name="39"><span class="lineNum">      39 </span>            : \ingroup INHERIT</a>
+<a name="40"><span class="lineNum">      40 </span>            : This is the abstract base class to use for implementing new methods for analyzing the trajectory. You can find</a>
+<a name="41"><span class="lineNum">      41 </span>            : \ref AddingAnAnalysis &quot;information&quot; on how to use it to implement new analysis methods here.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : */</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : class AnalysisBase :</a>
+<a name="46"><span class="lineNum">      46 </span>            :   public ActionPilot,</a>
+<a name="47"><span class="lineNum">      47 </span>            :   public ActionWithValue,</a>
+<a name="48"><span class="lineNum">      48 </span>            :   public ActionAtomistic,</a>
+<a name="49"><span class="lineNum">      49 </span>            :   public ActionWithArguments,</a>
+<a name="50"><span class="lineNum">      50 </span>            :   public vesselbase::ActionWithVessel</a>
+<a name="51"><span class="lineNum">      51 </span>            : {</a>
+<a name="52"><span class="lineNum">      52 </span>            :   friend class ReselectLandmarks;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   friend class ReadDissimilarityMatrix;</a>
+<a name="54"><span class="lineNum">      54 </span>            : protected:</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// The Analysis action that we are reusing data from</a>
+<a name="56"><span class="lineNum">      56 </span>            :   AnalysisBase* my_input_data;</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="59"><span class="lineNum">      59 </span>            :   explicit AnalysisBase(const ActionOptions&amp;);</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// These are required because we inherit from both ActionAtomistic and ActionWithArguments</a>
+<a name="61"><span class="lineNum">      61 </span>            :   void lockRequests() override;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   void unlockRequests() override;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Return the number of data points</a>
+<a name="64"><span class="lineNum">      64 </span>            :   virtual unsigned getNumberOfDataPoints() const ;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Return the index of the data point in the base class</a>
+<a name="66"><span class="lineNum">      66 </span>            :   virtual unsigned getDataPointIndexInBase( const unsigned&amp; idata ) const ;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Return the weight of the ith point</a>
+<a name="68"><span class="lineNum">      68 </span>            :   virtual double getWeight( const unsigned&amp; idata );</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Get the name of the metric that is being used</a>
+<a name="70"><span class="lineNum">      70 </span>            :   virtual std::string getMetricName() const ;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Are we using memory in this calculation this affects the weights of points</a>
+<a name="72"><span class="lineNum">      72 </span>            :   virtual bool usingMemory() const ;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Return the normalisation constant for the calculation</a>
+<a name="74"><span class="lineNum">      74 </span>            :   virtual double getNormalization() const ;</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Ensures that dissimilarities were set somewhere</a>
+<a name="76"><span class="lineNum">      76 </span>            :   virtual bool dissimilaritiesWereSet() const ;</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Get the information on how dissimilarities were calculated for output PDB</a>
+<a name="78"><span class="lineNum">      78 </span>            :   virtual std::string getDissimilarityInstruction() const ;</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// Get the squared dissimilarity between two reference configurations</a>
+<a name="80"><span class="lineNum">      80 </span>            :   virtual double getDissimilarity( const unsigned&amp; i, const unsigned&amp; j );</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Get the indices of the atoms that have been stored</a>
+<a name="82"><span class="lineNum">      82 </span>            :   virtual const std::vector&lt;AtomNumber&gt;&amp; getAtomIndexes() const ;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Overwrite getArguments so we get arguments from underlying class</a>
+<a name="84"><span class="lineNum">      84 </span>            :   virtual std::vector&lt;Value*&gt; getArgumentList();</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Get the list of argument names in the base</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;std::string&gt; getArgumentNames();</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Get a reference configuration (in dimensionality reduction this returns the projection)</a>
+<a name="88"><span class="lineNum">      88 </span>            :   virtual DataCollectionObject&amp; getStoredData( const unsigned&amp; idata, const bool&amp; calcdist );</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// This actually performs the analysis</a>
+<a name="90"><span class="lineNum">      90 </span>            :   virtual void performAnalysis()=0;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// These overwrite things from inherited classes (this is a bit of a fudge)</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { plumed_error(); }</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   unsigned getNumberOfDerivatives() override { plumed_error(); }</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override { plumed_error(); }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Calculate and apply do nothing all analysis is done during update step</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       7546 :   void calculate() override {}</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       7546 :   void apply() override {}</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : /// This will call the analysis to be performed</a>
+<a name="99"><span class="lineNum">      99 </span>            :   void update() override;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// This calls the analysis to be performed in the final step of the calculation</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// i.e. when use_all_data is true</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void runFinalJobs() override;</a>
+<a name="103"><span class="lineNum">     103 </span>            : };</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : inline</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       7546 : void AnalysisBase::lockRequests() {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   ActionAtomistic::lockRequests();</a>
+<a name="108"><span class="lineNum">     108 </span>            :   ActionWithArguments::lockRequests();</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       7546 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : inline</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       7546 : void AnalysisBase::unlockRequests() {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   ActionAtomistic::unlockRequests();</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ActionWithArguments::unlockRequests();</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       7546 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : inline</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     360092 : unsigned AnalysisBase::getNumberOfDataPoints() const {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     360137 :   return my_input_data-&gt;getNumberOfDataPoints();</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : inline</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     375002 : unsigned AnalysisBase::getDataPointIndexInBase( const unsigned&amp; idata ) const {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     500004 :   return my_input_data-&gt;getDataPointIndexInBase( idata );</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : inline</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 : std::string AnalysisBase::getMetricName() const {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :   return my_input_data-&gt;getMetricName();</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : inline</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">   40113999 : double AnalysisBase::getWeight( const unsigned&amp; idata ) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">   40113999 :   return my_input_data-&gt;getWeight( idata );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : inline</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 : bool AnalysisBase::usingMemory() const {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   return my_input_data-&gt;usingMemory();</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : inline</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : double AnalysisBase::getNormalization() const {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   return my_input_data-&gt;getNormalization();</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : inline</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        848 : bool AnalysisBase::dissimilaritiesWereSet() const {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        877 :   return my_input_data-&gt;dissimilaritiesWereSet();</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : inline</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">     659376 : double AnalysisBase::getDissimilarity( const unsigned&amp; i, const unsigned&amp; j ) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     721705 :   return my_input_data-&gt;getDissimilarity( i, j );</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : inline</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         22 : std::vector&lt;Value*&gt; AnalysisBase::getArgumentList() {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         24 :   return my_input_data-&gt;getArgumentList();</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : inline</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     522156 : DataCollectionObject&amp; AnalysisBase::getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     526340 :   return my_input_data-&gt;getStoredData( idata, calcdist );</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : inline</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         14 : const std::vector&lt;AtomNumber&gt;&amp; AnalysisBase::getAtomIndexes() const {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         14 :   return my_input_data-&gt;getAtomIndexes();</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : inline</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        841 : std::string AnalysisBase::getDissimilarityInstruction() const {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        841 :   return my_input_data-&gt;getDissimilarityInstruction();</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Average.cpp.func-sort-c.html b/coverage/analysis/Average.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7f26012826
--- /dev/null
+++ b/coverage/analysis/Average.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Average.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Average.cpp<span style="font-size: 80%;"> (<a href="Average.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Average.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#100">_ZN4PLMD8analysis7Average10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#112">_ZN4PLMD8analysis7AverageC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#101">_ZNK4PLMD8analysis7Average11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#138">_ZNK4PLMD8analysis7Average17accumulateAverageERNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#105">_ZN4PLMD8analysis12_GLOBAL__N_120AverageRegisterMe1076createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#112">_ZN4PLMD8analysis7AverageC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#107">_ZN4PLMD8analysis7Average16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#143">_ZN4PLMD8analysis7Average15finishAveragingEv</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#134">_ZN4PLMD8analysis7Average17performOperationsERKb</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#97">_ZN4PLMD8analysis7Average5applyEv</a></td>
+              <td class="coverFnHi">1025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#96">_ZN4PLMD8analysis7Average9calculateEv</a></td>
+              <td class="coverFnHi">1025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#105">_ZN4PLMD8analysis12_GLOBAL__N_120AverageRegisterMe107C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#105">_ZN4PLMD8analysis12_GLOBAL__N_120AverageRegisterMe107D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Average.cpp.func.html b/coverage/analysis/Average.cpp.func.html
new file mode 100644
index 0000000000..6b2ccdf638
--- /dev/null
+++ b/coverage/analysis/Average.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Average.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Average.cpp<span style="font-size: 80%;"> (<a href="Average.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Average.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#105">_ZN4PLMD8analysis12_GLOBAL__N_120AverageRegisterMe1076createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#105">_ZN4PLMD8analysis12_GLOBAL__N_120AverageRegisterMe107C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#105">_ZN4PLMD8analysis12_GLOBAL__N_120AverageRegisterMe107D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#100">_ZN4PLMD8analysis7Average10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#143">_ZN4PLMD8analysis7Average15finishAveragingEv</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#107">_ZN4PLMD8analysis7Average16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#134">_ZN4PLMD8analysis7Average17performOperationsERKb</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#97">_ZN4PLMD8analysis7Average5applyEv</a></td>
+              <td class="coverFnHi">1025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#96">_ZN4PLMD8analysis7Average9calculateEv</a></td>
+              <td class="coverFnHi">1025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#112">_ZN4PLMD8analysis7AverageC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#112">_ZN4PLMD8analysis7AverageC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#101">_ZNK4PLMD8analysis7Average11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Average.cpp.gcov.html#138">_ZNK4PLMD8analysis7Average17accumulateAverageERNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Average.cpp.gcov.html b/coverage/analysis/Average.cpp.gcov.html
new file mode 100644
index 0000000000..e856c53e93
--- /dev/null
+++ b/coverage/analysis/Average.cpp.gcov.html
@@ -0,0 +1,226 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Average.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Average.cpp<span style="font-size: 80%;"> (source / <a href="Average.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;vesselbase/ActionWithAveraging.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AverageVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC GRIDCALC AVERAGE</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate the ensemble average of a collective variable</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : The ensemble average for a non-periodic, collective variable, \f$s\f$ is given by the following expression:</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            : \langle s \rangle = \frac{ \sum_{t'=0}^t w(t') s(t') }{ \sum_{t'=0}^t w(t') }</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : Here the sum runs over a the trajectory and \f$s(t')\f$ is used to denote the value of the collective variable</a>
+<a name="37"><span class="lineNum">      37 </span>            : at time \f$t'\f$.  The final quantity evaluated is a weighted</a>
+<a name="38"><span class="lineNum">      38 </span>            : average as the weights, \f$w(t')\f$, allow us to negate the effect any bias might have on the region of phase space</a>
+<a name="39"><span class="lineNum">      39 </span>            : sampled by the system.  This is discussed in the section of the manual on \ref Analysis.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : When the variable is periodic (e.g. \ref TORSION) and has a value, \f$s\f$, in \f$a \le s \le b\f$ the ensemble average is evaluated using:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : \langle s \rangle = a + \frac{b - a}{2\pi} \arctan \left[ \frac{ \sum_{t'=0}^t w(t') \sin\left( \frac{2\pi [s(t')-a]}{b - a} \right) }{ \sum_{t'=0}^t w(t') \cos\left( \frac{2\pi [s(t')-a]}{b - a} \right) } \right]</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \par Examples</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The following example calculates the ensemble average for the distance between atoms 1 and 2</a>
+<a name="50"><span class="lineNum">      50 </span>            : and output this to a file called COLVAR.  In this example it is assumed that no bias is acting</a>
+<a name="51"><span class="lineNum">      51 </span>            : on the system and that the weights, \f$w(t')\f$ in the formulas above can thus all be set equal</a>
+<a name="52"><span class="lineNum">      52 </span>            : to one.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="56"><span class="lineNum">      56 </span>            : d1a: AVERAGE ARG=d1</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=d1a FILE=colvar STRIDE=100</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following example calculates the ensemble average for the torsional angle involving atoms 1, 2, 3 and 4.</a>
+<a name="61"><span class="lineNum">      61 </span>            : At variance with the previous example this quantity is periodic so the second formula in the above introduction</a>
+<a name="62"><span class="lineNum">      62 </span>            : is used to calculate the average.  Furthermore, by using the CLEAR keyword we have specified that block averages</a>
+<a name="63"><span class="lineNum">      63 </span>            : are to be calculated.  Consequently, after 100 steps all the information acquired thus far in the simulation is</a>
+<a name="64"><span class="lineNum">      64 </span>            : forgotten and the process of averaging is begun again.  The quantities output in the colvar file are thus the</a>
+<a name="65"><span class="lineNum">      65 </span>            : block averages taken over the first 100 frames of the trajectory, the block average over the second 100 frames</a>
+<a name="66"><span class="lineNum">      66 </span>            : of trajectory and so on.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : t1: TORSION ATOMS=1,2,3,4</a>
+<a name="70"><span class="lineNum">      70 </span>            : t1a: AVERAGE ARG=t1 CLEAR=100</a>
+<a name="71"><span class="lineNum">      71 </span>            : PRINT ARG=t1a FILE=colvar STRIDE=100</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : This third example incorporates a bias.  Notice that the effect the bias has on the ensemble average is removed by taking</a>
+<a name="75"><span class="lineNum">      75 </span>            : advantage of the \ref REWEIGHT_BIAS method.  The final ensemble averages output to the file are thus block ensemble averages for the</a>
+<a name="76"><span class="lineNum">      76 </span>            : unbiased canonical ensemble at a temperature of 300 K.</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : t1: TORSION ATOMS=1,2,3,4</a>
+<a name="80"><span class="lineNum">      80 </span>            : RESTRAINT ARG=t1 AT=pi KAPPA=100.</a>
+<a name="81"><span class="lineNum">      81 </span>            : ww: REWEIGHT_BIAS TEMP=300</a>
+<a name="82"><span class="lineNum">      82 </span>            : t1a: AVERAGE ARG=t1 LOGWEIGHTS=ww CLEAR=100</a>
+<a name="83"><span class="lineNum">      83 </span>            : PRINT ARG=t1a FILE=colvar STRIDE=100</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endplumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : */</a>
+<a name="87"><span class="lineNum">      87 </span>            : //+ENDPLUMEDOC</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : namespace PLMD {</a>
+<a name="90"><span class="lineNum">      90 </span>            : namespace analysis {</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : class Average : public vesselbase::ActionWithAveraging {</a>
+<a name="93"><span class="lineNum">      93 </span>            : private:</a>
+<a name="94"><span class="lineNum">      94 </span>            :   AverageVessel* myaverage;</a>
+<a name="95"><span class="lineNum">      95 </span>            : public:</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="97"><span class="lineNum">      97 </span>            :   explicit Average( const ActionOptions&amp; );</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1025 :   void calculate() override {}</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1025 :   void apply() override {}</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   void performOperations( const bool&amp; from_update ) override;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void finishAveraging() override;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   void accumulateAverage( MultiValue&amp; myvals ) const override;</a>
+<a name="105"><span class="lineNum">     105 </span>            : };</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(Average,&quot;AVERAGE&quot;)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          5 : void Average::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          5 :   vesselbase::ActionWithAveraging::registerKeywords( keys ); keys.use(&quot;ARG&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         10 :   keys.remove(&quot;SERIAL&quot;); keys.remove(&quot;LOWMEM&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          5 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 : Average::Average( const ActionOptions&amp; ao ):</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   Action(ao),</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          3 :   ActionWithAveraging(ao)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          3 :   addValue(); // Create a value so that we can output the average</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          3 :   if( getNumberOfArguments()!=1 ) error(&quot;only one quantity can be averaged at a time&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::string instring;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          3 :   if( getPntrToArgument(0)-&gt;isPeriodic() ) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 :     std::string min, max; getPntrToArgument(0)-&gt;getDomain(min,max);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :     instring = &quot;PERIODIC=&quot; + min + &quot;,&quot; + max; setPeriodic( min, max );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   } else {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :     setNotPeriodic();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span>            :   // Create a vessel to hold the average</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   vesselbase::VesselOptions da(&quot;myaverage&quot;,&quot;&quot;,-1,instring,this);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :   Keywords keys; AverageVessel::registerKeywords( keys );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          3 :   vesselbase::VesselOptions dar( da, keys );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          3 :   auto average=Tools::make_unique&lt;AverageVessel&gt;(dar);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          3 :   myaverage = average.get();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          3 :   setAveragingAction( std::move(average), false );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          6 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1022 : void Average::performOperations( const bool&amp; from_update ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1022 :   myaverage-&gt;accumulate( cweight, getArgument(0) );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       1022 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 : void Average::accumulateAverage( MultiValue&amp; myvals ) const {</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   plumed_dbg_assert( myvals.getNumberOfValues()==3 );</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   myaverage-&gt;accumulate( myvals.get(0), myvals.get(1) );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1022 : void Average::finishAveraging() {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1022 :   setValue( myaverage-&gt;getAverage() );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1022 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AverageVessel.cpp.func-sort-c.html b/coverage/analysis/AverageVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9b973a29d7
--- /dev/null
+++ b/coverage/analysis/AverageVessel.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AverageVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AverageVessel.cpp<span style="font-size: 80%;"> (<a href="AverageVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AverageVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#56">_ZNK4PLMD8analysis13AverageVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#25">_ZN4PLMD8analysis13AverageVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#37">_ZN4PLMD8analysis13AverageVessel6resizeEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#30">_ZN4PLMD8analysis13AverageVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#43">_ZN4PLMD8analysis13AverageVessel10accumulateERKdS3_</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#51">_ZNK4PLMD8analysis13AverageVessel10getAverageEv</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AverageVessel.cpp.func.html b/coverage/analysis/AverageVessel.cpp.func.html
new file mode 100644
index 0000000000..20752d2f7b
--- /dev/null
+++ b/coverage/analysis/AverageVessel.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AverageVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AverageVessel.cpp<span style="font-size: 80%;"> (<a href="AverageVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AverageVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#43">_ZN4PLMD8analysis13AverageVessel10accumulateERKdS3_</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#25">_ZN4PLMD8analysis13AverageVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#37">_ZN4PLMD8analysis13AverageVessel6resizeEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#30">_ZN4PLMD8analysis13AverageVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#51">_ZNK4PLMD8analysis13AverageVessel10getAverageEv</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.cpp.gcov.html#56">_ZNK4PLMD8analysis13AverageVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AverageVessel.cpp.gcov.html b/coverage/analysis/AverageVessel.cpp.gcov.html
new file mode 100644
index 0000000000..872d2e7bd9
--- /dev/null
+++ b/coverage/analysis/AverageVessel.cpp.gcov.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AverageVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AverageVessel.cpp<span style="font-size: 80%;"> (source / <a href="AverageVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AverageVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace analysis {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">          3 : void AverageVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          3 :   vesselbase::AveragingVessel::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;PERIODIC&quot;,&quot;is the quantity being averaged periodic and what is its domain&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">          3 : }</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          3 : AverageVessel::AverageVessel( const vesselbase::VesselOptions&amp; da):</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          3 :   AveragingVessel(da)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          6 :   parseVector(&quot;PERIODIC&quot;,domain);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          3 :   plumed_assert( domain.size()==2 || domain.size()==0 );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          3 : }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          3 : void AverageVessel::resize() {</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   resizeBuffer(0);</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          3 :   if( domain.size()==2 ) setDataSize(2);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          2 :   else setDataSize(1);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          3 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1022 : void AverageVessel::accumulate( const double&amp; weight, const double&amp; val ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1022 :   if( domain.size()==2 ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :     // Average with Berry Phase</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         11 :     double tval = 2*pi*( val - domain[0] ) / ( domain[1] - domain[0] );</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         11 :     addDataElement( 0, weight*std::sin(tval) ); addDataElement( 1, weight*std::cos(tval) );</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1011 :   } else addDataElement( 0, weight*val );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1022 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       1022 : double AverageVessel::getAverage() const {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1022 :   if( domain.size()==2 ) return domain[0] + (( domain[1] - domain[0] )*std::atan2( getDataElement(0), getDataElement(1) ) / (2*pi));</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1011 :   return getDataElement(0);</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 : void AverageVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : }</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AverageVessel.h.func-sort-c.html b/coverage/analysis/AverageVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..b322daaa76
--- /dev/null
+++ b/coverage/analysis/AverageVessel.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AverageVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AverageVessel.h<span style="font-size: 80%;"> (<a href="AverageVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AverageVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.h.gcov.html#40">_ZN4PLMD8analysis13AverageVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AverageVessel.h.func.html b/coverage/analysis/AverageVessel.h.func.html
new file mode 100644
index 0000000000..46ba7e1a0b
--- /dev/null
+++ b/coverage/analysis/AverageVessel.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AverageVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AverageVessel.h<span style="font-size: 80%;"> (<a href="AverageVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AverageVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageVessel.h.gcov.html#40">_ZN4PLMD8analysis13AverageVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/AverageVessel.h.gcov.html b/coverage/analysis/AverageVessel.h.gcov.html
new file mode 100644
index 0000000000..6196ad4887
--- /dev/null
+++ b/coverage/analysis/AverageVessel.h.gcov.html
@@ -0,0 +1,127 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/AverageVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - AverageVessel.h<span style="font-size: 80%;"> (source / <a href="AverageVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_analysis_AverageVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_analysis_AverageVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/AveragingVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace analysis {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class AverageVessel : public vesselbase::AveragingVessel {</a>
+<a name="31"><span class="lineNum">      31 </span>            : private:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   std::vector&lt;double&gt; domain;</a>
+<a name="33"><span class="lineNum">      33 </span>            : public:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   /// keywords</a>
+<a name="35"><span class="lineNum">      35 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Constructor</a>
+<a name="37"><span class="lineNum">      37 </span>            :   explicit AverageVessel( const vesselbase::VesselOptions&amp; );</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Set the size of the data vessel</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void resize() override;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// This does nothing</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const override;</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          3 :   std::string description() override { return &quot;&quot;; }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Accumulate the average</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void accumulate( const double&amp; weight, const double&amp; val );</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Get the average value</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double getAverage() const ;</a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Committor.cpp.func-sort-c.html b/coverage/analysis/Committor.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7ebe447cec
--- /dev/null
+++ b/coverage/analysis/Committor.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Committor.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Committor.cpp<span style="font-size: 80%;"> (<a href="Committor.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Committor.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#91">_ZN4PLMD8analysis9CommittorC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#75">_ZN4PLMD8analysis12_GLOBAL__N_121CommittorRegisterMe776createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#91">_ZN4PLMD8analysis9CommittorC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#77">_ZN4PLMD8analysis9Committor16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#72">_ZN4PLMD8analysis9Committor5applyEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#141">_ZN4PLMD8analysis9Committor9calculateEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#75">_ZN4PLMD8analysis12_GLOBAL__N_121CommittorRegisterMe77C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#75">_ZN4PLMD8analysis12_GLOBAL__N_121CommittorRegisterMe77D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Committor.cpp.func.html b/coverage/analysis/Committor.cpp.func.html
new file mode 100644
index 0000000000..7467861ee0
--- /dev/null
+++ b/coverage/analysis/Committor.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Committor.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Committor.cpp<span style="font-size: 80%;"> (<a href="Committor.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Committor.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#75">_ZN4PLMD8analysis12_GLOBAL__N_121CommittorRegisterMe776createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#75">_ZN4PLMD8analysis12_GLOBAL__N_121CommittorRegisterMe77C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#75">_ZN4PLMD8analysis12_GLOBAL__N_121CommittorRegisterMe77D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#77">_ZN4PLMD8analysis9Committor16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#72">_ZN4PLMD8analysis9Committor5applyEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#141">_ZN4PLMD8analysis9Committor9calculateEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#91">_ZN4PLMD8analysis9CommittorC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Committor.cpp.gcov.html#91">_ZN4PLMD8analysis9CommittorC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Committor.cpp.gcov.html b/coverage/analysis/Committor.cpp.gcov.html
new file mode 100644
index 0000000000..da05f3fb8a
--- /dev/null
+++ b/coverage/analysis/Committor.cpp.gcov.html
@@ -0,0 +1,267 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Committor.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Committor.cpp<span style="font-size: 80%;"> (source / <a href="Committor.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace analysis {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC PRINTANALYSIS COMMITTOR</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Does a committor analysis.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \par Examples</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The following input monitors two torsional angles during a simulation,</a>
+<a name="38"><span class="lineNum">      38 </span>            : defines two basins (A and B) as a function of the two torsion angles and</a>
+<a name="39"><span class="lineNum">      39 </span>            : stops the simulation when it falls in one of the two. In the log</a>
+<a name="40"><span class="lineNum">      40 </span>            : file will be shown the latest values for the CVs and the basin reached.</a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="43"><span class="lineNum">      43 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="44"><span class="lineNum">      44 </span>            : COMMITTOR ...</a>
+<a name="45"><span class="lineNum">      45 </span>            :   ARG=r1,r2</a>
+<a name="46"><span class="lineNum">      46 </span>            :   STRIDE=10</a>
+<a name="47"><span class="lineNum">      47 </span>            :   BASIN_LL1=0.15,0.20</a>
+<a name="48"><span class="lineNum">      48 </span>            :   BASIN_UL1=0.25,0.40</a>
+<a name="49"><span class="lineNum">      49 </span>            :   BASIN_LL2=-0.25,-0.40</a>
+<a name="50"><span class="lineNum">      50 </span>            :   BASIN_UL2=-0.15,-0.20</a>
+<a name="51"><span class="lineNum">      51 </span>            : ... COMMITTOR</a>
+<a name="52"><span class="lineNum">      52 </span>            : \endplumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : */</a>
+<a name="55"><span class="lineNum">      55 </span>            : //+ENDPLUMEDOC</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : class Committor :</a>
+<a name="58"><span class="lineNum">      58 </span>            :   public ActionPilot,</a>
+<a name="59"><span class="lineNum">      59 </span>            :   public ActionWithArguments</a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span>            : private:</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::string file;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   OFile ofile;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::string fmt;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; lowerlimits;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; upperlimits;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned nbasins;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   unsigned basin;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   bool doNotStop;</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   explicit Committor(const ActionOptions&amp;ao);</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void calculate() override;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         30 :   void apply() override {}</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : };</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(Committor,&quot;COMMITTOR&quot;)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         11 : void Committor::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         11 :   Action::registerKeywords(keys);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         11 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         11 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         11 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         22 :   keys.add(&quot;numbered&quot;, &quot;BASIN_LL&quot;,&quot;List of lower limits for basin #&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         22 :   keys.add(&quot;numbered&quot;, &quot;BASIN_UL&quot;,&quot;List of upper limits for basin #&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         33 :   keys.reset_style(&quot;BASIN_LL&quot;,&quot;compulsory&quot;); keys.reset_style(&quot;BASIN_UL&quot;,&quot;compulsory&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the CVs are analyzed&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output the reached basin&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format that should be used to output real numbers&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         22 :   keys.addFlag(&quot;NOSTOP&quot;,false,&quot;if true do not stop the simulation when reaching a basin but just keep track of it&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         11 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          9 : Committor::Committor(const ActionOptions&amp;ao):</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   Action(ao),</a>
+<a name="95"><span class="lineNum">      95 </span>            :   ActionPilot(ao),</a>
+<a name="96"><span class="lineNum">      96 </span>            :   ActionWithArguments(ao),</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          9 :   fmt(&quot;%f&quot;),</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   basin(0),</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         18 :   doNotStop(false)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          9 :   ofile.link(*this);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         18 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          9 :   if(file.length()&gt;0) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          2 :     ofile.open(file);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 :     log.printf(&quot;  on file %s\n&quot;,file.c_str());</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   } else {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          7 :     log.printf(&quot;  on plumed log file\n&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          7 :     ofile.link(log);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          9 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          9 :   fmt=&quot; &quot;+fmt;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          9 :   log.printf(&quot;  with format %s\n&quot;,fmt.c_str());</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         13 :   for(unsigned b=1;; ++b ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     std::vector&lt;double&gt; tmpl, tmpu;</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         22 :     parseNumberedVector(&quot;BASIN_LL&quot;, b, tmpl );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         44 :     parseNumberedVector(&quot;BASIN_UL&quot;, b, tmpu );</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         22 :     if( tmpl.empty() &amp;&amp; tmpu.empty() ) break;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         13 :     if( tmpl.size()!=getNumberOfArguments()) error(&quot;Wrong number of values for BASIN_LL: they should be equal to the number of arguments&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         13 :     if( tmpu.size()!=getNumberOfArguments()) error(&quot;Wrong number of values for BASIN_UL: they should be equal to the number of arguments&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         13 :     lowerlimits.push_back(tmpl);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         13 :     upperlimits.push_back(tmpu);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         13 :     nbasins=b;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         13 :   }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          9 :   parseFlag(&quot;NOSTOP&quot;, doNotStop);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         22 :   for(unsigned b=0; b&lt;nbasins; b++) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         13 :     log.printf(&quot;  BASIN %u definition:\n&quot;, b+1);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         32 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         19 :       if(lowerlimits[b][i]&gt;upperlimits[b][i]) error(&quot;COMMITTOR: UPPER bounds must always be greater than LOWER bounds&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         19 :       log.printf(&quot; %f - %f\n&quot;, lowerlimits[b][i], upperlimits[b][i]);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :     }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         13 :     if(doNotStop) log.printf(&quot; COMMITOR will keep track of the visited basins without stopping the simulations\n&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         20 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) ofile.setupPrintValue( getPntrToArgument(i) );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          9 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         30 : void Committor::calculate() {</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::vector&lt;unsigned&gt; inbasin;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         30 :   inbasin.assign (nbasins,1);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   // check if current configuration belongs to a basin</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        106 :   for(unsigned b=0; b&lt;nbasins; ++b) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        221 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        145 :       if(getArgument(i)&gt;lowerlimits[b][i]&amp;&amp;getArgument(i)&lt;upperlimits[b][i]) {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :         inbasin[b]*=1;</a>
+<a name="152"><span class="lineNum">     152 </span>            :       } else {</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         80 :         inbasin[b]*=0;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :       }</a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            :   // check in which basin we are if any and if this is the same or a new one</a>
+<a name="159"><span class="lineNum">     159 </span>            :   bool inonebasin = false;</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         71 :   for(unsigned b=0; b&lt;nbasins; ++b) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         61 :     if(inbasin[b]==1) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         20 :       if(basin!=(b+1)) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         15 :         basin = b+1;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         15 :         ofile.fmtField(&quot; %f&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         15 :         ofile.printField(&quot;time&quot;,getTime());</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         38 :         for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         23 :           ofile.fmtField(fmt);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         23 :           ofile.printField( getPntrToArgument(i), getArgument(i) );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :         }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         15 :         ofile.printField(&quot;basin&quot;, static_cast&lt;int&gt; (b+1));</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         15 :         ofile.printField();</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :       }</a>
+<a name="173"><span class="lineNum">     173 </span>            :       inonebasin = true;</a>
+<a name="174"><span class="lineNum">     174 </span>            :       break;</a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         10 :   if(!inonebasin) basin = 0;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   // then check if the simulation should be stopped</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         30 :   if(inonebasin&amp;&amp;(!doNotStop)) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          8 :     std::string num; Tools::convert( basin, num );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          8 :     std::string str = &quot;COMMITTED TO BASIN &quot; + num;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          8 :     ofile.addConstantField(str);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          8 :     ofile.printField();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          8 :     ofile.flush();</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          8 :     plumed.stop();</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         30 : }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/DataCollectionObject.cpp.func-sort-c.html b/coverage/analysis/DataCollectionObject.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c84c25178a
--- /dev/null
+++ b/coverage/analysis/DataCollectionObject.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/DataCollectionObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - DataCollectionObject.cpp<span style="font-size: 80%;"> (<a href="DataCollectionObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DataCollectionObject.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#32">_ZN4PLMD8analysis20DataCollectionObject16setAtomPositionsERKSt6vectorINS_13VectorGenericILj3EEESaIS4_EE</a></td>
+              <td class="coverFnHi">7556</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#26">_ZN4PLMD8analysis20DataCollectionObject30setAtomNumbersAndArgumentNamesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorINS_10AtomNumberESaISB_EERKSA_IS7_SaIS7_EE</a></td>
+              <td class="coverFnHi">7556</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#37">_ZN4PLMD8analysis20DataCollectionObject11setArgumentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKd</a></td>
+              <td class="coverFnHi">16321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#43">_ZN4PLMD8analysis20DataCollectionObject17transferDataToPDBERNS_3PDBE</a></td>
+              <td class="coverFnHi">522438</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/DataCollectionObject.cpp.func.html b/coverage/analysis/DataCollectionObject.cpp.func.html
new file mode 100644
index 0000000000..f371e54c26
--- /dev/null
+++ b/coverage/analysis/DataCollectionObject.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/DataCollectionObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - DataCollectionObject.cpp<span style="font-size: 80%;"> (<a href="DataCollectionObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DataCollectionObject.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#37">_ZN4PLMD8analysis20DataCollectionObject11setArgumentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKd</a></td>
+              <td class="coverFnHi">16321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#32">_ZN4PLMD8analysis20DataCollectionObject16setAtomPositionsERKSt6vectorINS_13VectorGenericILj3EEESaIS4_EE</a></td>
+              <td class="coverFnHi">7556</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#43">_ZN4PLMD8analysis20DataCollectionObject17transferDataToPDBERNS_3PDBE</a></td>
+              <td class="coverFnHi">522438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.cpp.gcov.html#26">_ZN4PLMD8analysis20DataCollectionObject30setAtomNumbersAndArgumentNamesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorINS_10AtomNumberESaISB_EERKSA_IS7_SaIS7_EE</a></td>
+              <td class="coverFnHi">7556</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/DataCollectionObject.cpp.gcov.html b/coverage/analysis/DataCollectionObject.cpp.gcov.html
new file mode 100644
index 0000000000..f74d7247f9
--- /dev/null
+++ b/coverage/analysis/DataCollectionObject.cpp.gcov.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/DataCollectionObject.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - DataCollectionObject.cpp<span style="font-size: 80%;"> (source / <a href="DataCollectionObject.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DataCollectionObject.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace analysis {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">       7556 : void DataCollectionObject::setAtomNumbersAndArgumentNames( const std::string&amp; action_label, const std::vector&lt;AtomNumber&gt;&amp; ind, const std::vector&lt;std::string&gt;&amp; arg_names ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       7556 :   myaction=action_label; indices.resize( ind.size() ); positions.resize( indices.size() );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">      21193 :   for(unsigned i=0; i&lt;ind.size(); ++i) indices[i]=ind[i];</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">      16583 :   for(unsigned i=0; i&lt;arg_names.size(); ++i) args.insert( std::pair&lt;std::string,double&gt;( arg_names[i], 0.0 ) );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">       7556 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       7556 : void DataCollectionObject::setAtomPositions( const std::vector&lt;Vector&gt;&amp; pos ) {</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   plumed_dbg_assert( pos.size()==positions.size() &amp;&amp; pos.size()==indices.size() );</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">      21193 :   for(unsigned i=0; i&lt;positions.size(); ++i) positions[i]=pos[i];</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       7556 : }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">      16321 : void DataCollectionObject::setArgument( const std::string&amp; name, const double&amp; value ) {</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   std::map&lt;std::string,double&gt;::iterator it = args.find(name);</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      16321 :   if( it!=args.end() ) it-&gt;second = value;</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       6694 :   else args.insert( std::pair&lt;std::string,double&gt;( name, value ) );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      16321 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">     522438 : bool DataCollectionObject::transferDataToPDB( PDB&amp; mypdb ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   // Check if PDB contains argument names</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">     522438 :   std::vector&lt;std::string&gt; pdb_args( mypdb.getArgumentNames() );</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   // Now set the argument values</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::map&lt;std::string,double&gt;::iterator it;</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    2024164 :   for(unsigned i=0; i&lt;pdb_args.size(); ++i) {</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :     it=args.find( pdb_args[i] );</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">    1501726 :     if( it==args.end() ) return false;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">    1501726 :     mypdb.setArgumentValue( pdb_args[i], it-&gt;second );</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   }</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // Now set the atomic positions</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     522438 :   std::vector&lt;AtomNumber&gt; pdb_pos( mypdb.getAtomNumbers() );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">     522438 :   if( pdb_pos.size()==positions.size() ) mypdb.setAtomPositions( positions );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      29720 :   else if( pdb_pos.size()&gt;0 ) plumed_merror(&quot;This feature is currently not ready&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   return true;</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">     522438 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/DataCollectionObject.h.func-sort-c.html b/coverage/analysis/DataCollectionObject.h.func-sort-c.html
new file mode 100644
index 0000000000..b16b97db5d
--- /dev/null
+++ b/coverage/analysis/DataCollectionObject.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/DataCollectionObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - DataCollectionObject.h<span style="font-size: 80%;"> (<a href="DataCollectionObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DataCollectionObject.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.h.gcov.html#66">_ZNK4PLMD8analysis20DataCollectionObject16getArgumentValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">6517</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/DataCollectionObject.h.func.html b/coverage/analysis/DataCollectionObject.h.func.html
new file mode 100644
index 0000000000..4d77185d40
--- /dev/null
+++ b/coverage/analysis/DataCollectionObject.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/DataCollectionObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - DataCollectionObject.h<span style="font-size: 80%;"> (<a href="DataCollectionObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DataCollectionObject.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataCollectionObject.h.gcov.html#66">_ZNK4PLMD8analysis20DataCollectionObject16getArgumentValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">6517</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/DataCollectionObject.h.gcov.html b/coverage/analysis/DataCollectionObject.h.gcov.html
new file mode 100644
index 0000000000..d34316b1f5
--- /dev/null
+++ b/coverage/analysis/DataCollectionObject.h.gcov.html
@@ -0,0 +1,155 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/DataCollectionObject.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - DataCollectionObject.h<span style="font-size: 80%;"> (source / <a href="DataCollectionObject.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_analysis_DataCollectionObject_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_analysis_DataCollectionObject_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;map&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class PDB;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace analysis {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class DataCollectionObject {</a>
+<a name="37"><span class="lineNum">      37 </span>            :   friend class ReadAnalysisFrames;</a>
+<a name="38"><span class="lineNum">      38 </span>            : private:</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// The label of the action in which the data is stored</a>
+<a name="40"><span class="lineNum">      40 </span>            :   std::string myaction;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// The list of atom numbers that are stored in the object</a>
+<a name="42"><span class="lineNum">      42 </span>            :   std::vector&lt;AtomNumber&gt; indices;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// The list of atomic positions</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::vector&lt;Vector&gt; positions;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// The map containing the arguments that we are storing</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::map&lt;std::string,double&gt; args;</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Set the names and atom numbers</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void setAtomNumbersAndArgumentNames( const std::string&amp; action_label, const std::vector&lt;AtomNumber&gt;&amp; ind, const std::vector&lt;std::string&gt;&amp; arg_names );</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Set the positions of all the atoms</a>
+<a name="51"><span class="lineNum">      51 </span>            :   void setAtomPositions( const std::vector&lt;Vector&gt;&amp; pos );</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Set the value of one of the arguments</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void setArgument( const std::string&amp; name, const double&amp; value );</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Return one of the atomic positions</a>
+<a name="55"><span class="lineNum">      55 </span>            :   Vector getAtomPosition( const AtomNumber&amp; ind ) const ;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Get the value of one of the arguments</a>
+<a name="57"><span class="lineNum">      57 </span>            :   double getArgumentValue( const std::string&amp; name ) const ;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Transfer the data inside the object to a PDB object</a>
+<a name="59"><span class="lineNum">      59 </span>            :   bool transferDataToPDB( PDB&amp; mypdb );</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : inline</a>
+<a name="63"><span class="lineNum">      63 </span>            : Vector DataCollectionObject::getAtomPosition( const AtomNumber&amp; ind ) const {</a>
+<a name="64"><span class="lineNum">      64 </span>            :   return positions[ind.index()];</a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : inline</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       6517 : double DataCollectionObject::getArgumentValue( const std::string&amp; name ) const {</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::map&lt;std::string,double&gt;::const_iterator it = args.find(name);</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       6517 :   if( it != args.end() ) return it-&gt;second;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       2106 :   std::size_t dot=name.find_first_of('.'); std::string a=name.substr(0,dot);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       4212 :   if( a==myaction ) return args.find( name.substr(dot+1) )-&gt;second;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   else plumed_merror(&quot;could not find required data in collection object&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/EuclideanDissimilarityMatrix.cpp.func-sort-c.html b/coverage/analysis/EuclideanDissimilarityMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..95a644df4a
--- /dev/null
+++ b/coverage/analysis/EuclideanDissimilarityMatrix.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/EuclideanDissimilarityMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - EuclideanDissimilarityMatrix.cpp<span style="font-size: 80%;"> (<a href="EuclideanDissimilarityMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EuclideanDissimilarityMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#66">_ZN4PLMD8analysis28EuclideanDissimilarityMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#55">_ZNK4PLMD8analysis28EuclideanDissimilarityMatrix11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_140EuclideanDissimilarityMatrixRegisterMe606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#66">_ZN4PLMD8analysis28EuclideanDissimilarityMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#60">_ZN4PLMD8analysis28EuclideanDissimilarityMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#114">_ZN4PLMD8analysis28EuclideanDissimilarityMatrix15performAnalysisEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#121">_ZNK4PLMD8analysis28EuclideanDissimilarityMatrix27getDissimilarityInstructionB5cxx11Ev</a></td>
+              <td class="coverFnHi">413</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#49">_ZNK4PLMD8analysis28EuclideanDissimilarityMatrix22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnHi">436</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_140EuclideanDissimilarityMatrixRegisterMe60C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_140EuclideanDissimilarityMatrixRegisterMe60D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#125">_ZN4PLMD8analysis28EuclideanDissimilarityMatrix16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">611659</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/EuclideanDissimilarityMatrix.cpp.func.html b/coverage/analysis/EuclideanDissimilarityMatrix.cpp.func.html
new file mode 100644
index 0000000000..ade5719639
--- /dev/null
+++ b/coverage/analysis/EuclideanDissimilarityMatrix.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/EuclideanDissimilarityMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - EuclideanDissimilarityMatrix.cpp<span style="font-size: 80%;"> (<a href="EuclideanDissimilarityMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EuclideanDissimilarityMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_140EuclideanDissimilarityMatrixRegisterMe606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_140EuclideanDissimilarityMatrixRegisterMe60C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_140EuclideanDissimilarityMatrixRegisterMe60D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#114">_ZN4PLMD8analysis28EuclideanDissimilarityMatrix15performAnalysisEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#125">_ZN4PLMD8analysis28EuclideanDissimilarityMatrix16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">611659</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#60">_ZN4PLMD8analysis28EuclideanDissimilarityMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#66">_ZN4PLMD8analysis28EuclideanDissimilarityMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#55">_ZNK4PLMD8analysis28EuclideanDissimilarityMatrix11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#49">_ZNK4PLMD8analysis28EuclideanDissimilarityMatrix22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnHi">436</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html#121">_ZNK4PLMD8analysis28EuclideanDissimilarityMatrix27getDissimilarityInstructionB5cxx11Ev</a></td>
+              <td class="coverFnHi">413</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/EuclideanDissimilarityMatrix.cpp.gcov.html b/coverage/analysis/EuclideanDissimilarityMatrix.cpp.gcov.html
new file mode 100644
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+++ b/coverage/analysis/EuclideanDissimilarityMatrix.cpp.gcov.html
@@ -0,0 +1,222 @@
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+  <title>LCOV - plumed test coverage - analysis/EuclideanDissimilarityMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - EuclideanDissimilarityMatrix.cpp<span style="font-size: 80%;"> (source / <a href="EuclideanDissimilarityMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC ANALYSIS EUCLIDEAN_DISSIMILARITIES</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate the matrix of dissimilarities between a trajectory of atomic configurations.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : */</a>
+<a name="35"><span class="lineNum">      35 </span>            : //+ENDPLUMEDOC</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace analysis {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class EuclideanDissimilarityMatrix : public AnalysisBase {</a>
+<a name="41"><span class="lineNum">      41 </span>            : private:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   PDB mypdb;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::string mtype;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   Matrix&lt;double&gt; dissimilarities;</a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit EuclideanDissimilarityMatrix( const ActionOptions&amp; ao );</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Do the analysis</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void performAnalysis() override;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// This ensures that classes that use this data know that dissimilarities were set</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        436 :   bool dissimilaritiesWereSet() const override { return true; }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Get information on how to calculate dissimilarities</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::string getDissimilarityInstruction() const override;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Get the squared dissimilarity between two reference configurations</a>
+<a name="55"><span class="lineNum">      55 </span>            :   double getDissimilarity( const unsigned&amp; i, const unsigned&amp; j ) override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// This is just to deal with ActionWithVessel</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      12530 : PLUMED_REGISTER_ACTION(EuclideanDissimilarityMatrix,&quot;EUCLIDEAN_DISSIMILARITIES&quot;)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         15 : void EuclideanDissimilarityMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         45 :   AnalysisBase::registerKeywords( keys ); keys.use(&quot;ARG&quot;); keys.reset_style(&quot;ARG&quot;,&quot;optional&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         30 :   keys.add(&quot;compulsory&quot;,&quot;METRIC&quot;,&quot;EUCLIDEAN&quot;,&quot;the method that you are going to use to measure the distances between points&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         30 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the list of atoms that you are going to use in the measure of distance that you are using&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         15 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         13 : EuclideanDissimilarityMatrix::EuclideanDissimilarityMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   Action(ao),</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         13 :   AnalysisBase(ao)</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : {</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         26 :   parse(&quot;METRIC&quot;,mtype); std::vector&lt;AtomNumber&gt; atoms;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         13 :   if( my_input_data-&gt;getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 :     parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          3 :     if( atoms.size()!=0 ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :       mypdb.setAtomNumbers( atoms );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :         bool found=false;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;my_input_data-&gt;getAtomIndexes().size(); ++j) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :           if( my_input_data-&gt;getAtomIndexes()[j]==atoms[i] ) { found=true; break; }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :         }</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :         if( !found ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :           std::string num; Tools::convert( atoms[i].serial(), num );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :           error(&quot;atom number &quot; + num + &quot; is not stored in any action that has been input&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :         }</a>
+<a name="86"><span class="lineNum">      86 </span>            :       }</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :       mypdb.addBlockEnd( atoms.size() );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          3 :     } else if( getNumberOfArguments()==0 ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 :       mypdb.setAtomNumbers( my_input_data-&gt;getAtomIndexes() );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          1 :       mypdb.addBlockEnd( my_input_data-&gt;getAtomIndexes().size() );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          1 :       if( mtype==&quot;EUCLIDEAN&quot; ) mtype=&quot;OPTIMAL&quot;;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :     }</a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         13 :   log.printf(&quot;  measuring distances using %s metric \n&quot;,mtype.c_str() );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         13 :   if( my_input_data-&gt;getArgumentNames().size()&gt;0 ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         12 :     if( getNumberOfArguments()==0 &amp;&amp; atoms.size()==0 ) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         10 :       std::vector&lt;std::string&gt; argnames( my_input_data-&gt;getArgumentNames() );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         10 :       mypdb.setArgumentNames( argnames ); requestArguments( my_input_data-&gt;getArgumentList() );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         10 :     } else {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :       std::vector&lt;Value*&gt; myargs( getArguments() );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          2 :       std::vector&lt;std::string&gt; inargnames( my_input_data-&gt;getArgumentNames() );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          2 :       std::vector&lt;std::string&gt; argnames( myargs.size() );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;myargs.size(); ++i) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          4 :         argnames[i]=myargs[i]-&gt;getName();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :         bool found=false;</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          6 :         for(unsigned j=0; j&lt;inargnames.size(); ++j) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          6 :           if( argnames[i]==inargnames[j] ) { found=true; break; }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :         }</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :         if( !found ) error(&quot;input named &quot; + my_input_data-&gt;getLabel() + &quot; does not store/calculate quantity named &quot; + argnames[i] );</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :       }</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :       mypdb.setArgumentNames( argnames ); requestArguments( myargs );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :     }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         13 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         20 : void EuclideanDissimilarityMatrix::performAnalysis() {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   // Resize dissimilarities matrix and set all elements to zero</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         20 :   if( !usingLowMem() ) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         20 :     dissimilarities.resize( getNumberOfDataPoints(), getNumberOfDataPoints() ); dissimilarities=0;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         20 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        413 : std::string EuclideanDissimilarityMatrix::getDissimilarityInstruction() const {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        413 :   return &quot;TYPE=&quot; + mtype;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     611659 : double EuclideanDissimilarityMatrix::getDissimilarity( const unsigned&amp; iframe, const unsigned&amp; jframe ) {</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   plumed_dbg_assert( iframe&lt;getNumberOfDataPoints() &amp;&amp; jframe&lt;getNumberOfDataPoints() );</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     611659 :   if( !usingLowMem() ) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     611659 :     if( dissimilarities(iframe,jframe)&gt;0. ) { return dissimilarities(iframe,jframe); }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     256165 :   if( iframe!=jframe ) {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     double dd;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     255613 :     getStoredData( iframe, true ).transferDataToPDB( mypdb );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">     255613 :     auto myref1=metricRegister().create&lt;ReferenceConfiguration&gt;(mtype, mypdb);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     255613 :     getStoredData( jframe, true ).transferDataToPDB( mypdb );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">     255613 :     auto myref2=metricRegister().create&lt;ReferenceConfiguration&gt;(mtype, mypdb);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">     255613 :     if( !usingLowMem() ) dd=dissimilarities(iframe,jframe) = dissimilarities(jframe,iframe) = distance( getPbc(), getArguments(), myref1.get(), myref2.get(), true );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     else dd=distance( getPbc(), getArguments(), myref1.get(), myref2.get(), true );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     return dd;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">     255613 :   }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   return 0.0;</a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/FarthestPointSampling.cpp.func-sort-c.html b/coverage/analysis/FarthestPointSampling.cpp.func-sort-c.html
new file mode 100644
index 0000000000..56986abc97
--- /dev/null
+++ b/coverage/analysis/FarthestPointSampling.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/FarthestPointSampling.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - FarthestPointSampling.cpp<span style="font-size: 80%;"> (<a href="FarthestPointSampling.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FarthestPointSampling.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#52">_ZN4PLMD8analysis21FarthestPointSamplingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_133FarthestPointSamplingRegisterMe476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#60">_ZN4PLMD8analysis21FarthestPointSampling15selectLandmarksEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#52">_ZN4PLMD8analysis21FarthestPointSamplingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#47">_ZN4PLMD8analysis21FarthestPointSampling16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_133FarthestPointSamplingRegisterMe47C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_133FarthestPointSamplingRegisterMe47D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/FarthestPointSampling.cpp.func.html b/coverage/analysis/FarthestPointSampling.cpp.func.html
new file mode 100644
index 0000000000..94875cf6a2
--- /dev/null
+++ b/coverage/analysis/FarthestPointSampling.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/FarthestPointSampling.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - FarthestPointSampling.cpp<span style="font-size: 80%;"> (<a href="FarthestPointSampling.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FarthestPointSampling.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_133FarthestPointSamplingRegisterMe476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_133FarthestPointSamplingRegisterMe47C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_133FarthestPointSamplingRegisterMe47D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#60">_ZN4PLMD8analysis21FarthestPointSampling15selectLandmarksEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#47">_ZN4PLMD8analysis21FarthestPointSampling16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#52">_ZN4PLMD8analysis21FarthestPointSamplingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FarthestPointSampling.cpp.gcov.html#52">_ZN4PLMD8analysis21FarthestPointSamplingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/FarthestPointSampling.cpp.gcov.html b/coverage/analysis/FarthestPointSampling.cpp.gcov.html
new file mode 100644
index 0000000000..b20ce430ee
--- /dev/null
+++ b/coverage/analysis/FarthestPointSampling.cpp.gcov.html
@@ -0,0 +1,167 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/FarthestPointSampling.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - FarthestPointSampling.cpp<span style="font-size: 80%;"> (source / <a href="FarthestPointSampling.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LandmarkSelectionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC LANDMARKS LANDMARK_SELECT_FPS</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Select a set of landmarks using farthest point sampling.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \par Examples</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : //+ENDPLUMEDOC</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace analysis {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class FarthestPointSampling : public LandmarkSelectionBase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   unsigned seed;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit FarthestPointSampling( const ActionOptions&amp; ao );</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void selectLandmarks() override;</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FarthestPointSampling,&quot;LANDMARK_SELECT_FPS&quot;)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          3 : void FarthestPointSampling::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          3 :   LandmarkSelectionBase::registerKeywords(keys);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;SEED&quot;,&quot;1234&quot;,&quot;a random number seed&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          3 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          1 : FarthestPointSampling::FarthestPointSampling( const ActionOptions&amp; ao ):</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   Action(ao),</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          1 :   LandmarkSelectionBase(ao)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          1 :   if( !dissimilaritiesWereSet() ) error(&quot;dissimilarities have not been calcualted in input action&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          1 :   parse(&quot;SEED&quot;,seed);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          1 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 : void FarthestPointSampling::selectLandmarks() {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          1 :   std::vector&lt;unsigned&gt; landmarks( getNumberOfDataPoints() );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   // Select first point at random</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          1 :   Random random; random.setSeed(-seed); double rand=random.RandU01();</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          1 :   landmarks[0] = std::floor( my_input_data-&gt;getNumberOfDataPoints()*rand );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          1 :   selectFrame( landmarks[0] );</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Now find distance to all other points (N.B. We can use squared distances here for speed)</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 :   Matrix&lt;double&gt; distances( getNumberOfDataPoints(), my_input_data-&gt;getNumberOfDataPoints() );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         14 :   for(unsigned i=0; i&lt;my_input_data-&gt;getNumberOfDataPoints(); ++i) distances(0,i) = my_input_data-&gt;getDissimilarity( landmarks[0], i );</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   // Now find all other landmarks</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          3 :   for(unsigned i=1; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :     // Find point that has the largest minimum distance from the landmarks selected thus far</a>
+<a name="77"><span class="lineNum">      77 </span>            :     double maxd=0;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         28 :     for(unsigned j=0; j&lt;my_input_data-&gt;getNumberOfDataPoints(); ++j) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         26 :       double mind=distances(0,j);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         39 :       for(unsigned k=1; k&lt;i; ++k) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         13 :         if( distances(k,j)&lt;mind ) { mind=distances(k,j); }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :       }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         26 :       if( mind&gt;maxd ) { maxd=mind; landmarks[i]=j; }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :     }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 :     selectFrame( landmarks[i] );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         28 :     for(unsigned k=0; k&lt;my_input_data-&gt;getNumberOfDataPoints(); ++k) distances(i,k) = my_input_data-&gt;getDissimilarity( landmarks[i], k );</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          1 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Histogram.cpp.func-sort-c.html b/coverage/analysis/Histogram.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1855e9fc76
--- /dev/null
+++ b/coverage/analysis/Histogram.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Histogram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Histogram.cpp<span style="font-size: 80%;"> (<a href="Histogram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">203</td>
+            <td class="headerCovTableEntry">208</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Histogram.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#214">_ZN4PLMD8analysis9Histogram10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#235">_ZN4PLMD8analysis9HistogramC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#411">_ZN4PLMD8analysis9Histogram17performOperationsERKb</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#339">_ZN4PLMD8analysis9Histogram17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#221">_ZN4PLMD8analysis12_GLOBAL__N_122HistogramRegisterMe2236createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#235">_ZN4PLMD8analysis9HistogramC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#223">_ZN4PLMD8analysis9Histogram16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">36</td>
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+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#374">_ZN4PLMD8analysis9Histogram19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">115</td>
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+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#213">_ZNK4PLMD8analysis9Histogram10threadSafeEv</a></td>
+              <td class="coverFnHi">121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#504">_ZN4PLMD8analysis9Histogram5applyEv</a></td>
+              <td class="coverFnHi">133</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#413">_ZN4PLMD8analysis9Histogram15finishAveragingEv</a></td>
+              <td class="coverFnHi">135</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#368">_ZNK4PLMD8analysis9Histogram21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">462</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#359">_ZN4PLMD8analysis9Histogram22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#221">_ZN4PLMD8analysis12_GLOBAL__N_122HistogramRegisterMe223C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#221">_ZN4PLMD8analysis12_GLOBAL__N_122HistogramRegisterMe223D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#417">_ZNK4PLMD8analysis9Histogram7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">15404</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Histogram.cpp.func.html b/coverage/analysis/Histogram.cpp.func.html
new file mode 100644
index 0000000000..c8031c8316
--- /dev/null
+++ b/coverage/analysis/Histogram.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Histogram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Histogram.cpp<span style="font-size: 80%;"> (<a href="Histogram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">203</td>
+            <td class="headerCovTableEntry">208</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Histogram.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#221">_ZN4PLMD8analysis12_GLOBAL__N_122HistogramRegisterMe2236createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#221">_ZN4PLMD8analysis12_GLOBAL__N_122HistogramRegisterMe223C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#221">_ZN4PLMD8analysis12_GLOBAL__N_122HistogramRegisterMe223D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#214">_ZN4PLMD8analysis9Histogram10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#413">_ZN4PLMD8analysis9Histogram15finishAveragingEv</a></td>
+              <td class="coverFnHi">135</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#223">_ZN4PLMD8analysis9Histogram16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#411">_ZN4PLMD8analysis9Histogram17performOperationsERKb</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#339">_ZN4PLMD8analysis9Histogram17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#374">_ZN4PLMD8analysis9Histogram19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">115</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#359">_ZN4PLMD8analysis9Histogram22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#504">_ZN4PLMD8analysis9Histogram5applyEv</a></td>
+              <td class="coverFnHi">133</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#235">_ZN4PLMD8analysis9HistogramC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#235">_ZN4PLMD8analysis9HistogramC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#213">_ZNK4PLMD8analysis9Histogram10threadSafeEv</a></td>
+              <td class="coverFnHi">121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#368">_ZNK4PLMD8analysis9Histogram21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">462</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#417">_ZNK4PLMD8analysis9Histogram7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">15404</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/Histogram.cpp.gcov.html b/coverage/analysis/Histogram.cpp.gcov.html
new file mode 100644
index 0000000000..59a6ce419f
--- /dev/null
+++ b/coverage/analysis/Histogram.cpp.gcov.html
@@ -0,0 +1,610 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/Histogram.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - Histogram.cpp<span style="font-size: 80%;"> (source / <a href="Histogram.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">203</td>
+            <td class="headerCovTableEntry">208</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;gridtools/ActionWithGrid.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;vesselbase/StoreDataVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace analysis {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC GRIDCALC HISTOGRAM</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Accumulate the average probability density along a few CVs from a trajectory.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : When using this method it is supposed that you have some collective variable \f$\zeta\f$ that</a>
+<a name="39"><span class="lineNum">      39 </span>            : gives a reasonable description of some physical or chemical phenomenon.  As an example of what we</a>
+<a name="40"><span class="lineNum">      40 </span>            : mean by this suppose you wish to examine the following SN2 reaction:</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            :  \textrm{OH}^- + \textrm{CH}_3Cl  \rightarrow \textrm{CH}_3OH + \textrm{Cl}^-</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : The distance between the chlorine atom and the carbon is an excellent collective variable, \f$\zeta\f$,</a>
+<a name="47"><span class="lineNum">      47 </span>            : in this case because this distance is short for the reactant, \f$\textrm{CH}_3Cl\f$, because the carbon</a>
+<a name="48"><span class="lineNum">      48 </span>            : and chlorine are chemically bonded, and because it is long for the product state when these two atoms are</a>
+<a name="49"><span class="lineNum">      49 </span>            : not chemically bonded.  We thus might want to accumulate the probability density, \f$P(\zeta)\f$, as a function of this distance</a>
+<a name="50"><span class="lineNum">      50 </span>            : as this will provide us with information about the overall likelihood of the reaction.   Furthermore, the</a>
+<a name="51"><span class="lineNum">      51 </span>            : free energy, \f$F(\zeta)\f$, is related to this probability density via:</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \f[</a>
+<a name="54"><span class="lineNum">      54 </span>            : F(\zeta) = - k_B T \ln P(\zeta)</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f]</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : Accumulating these probability densities is precisely what this Action can be used to do.  Furthermore, the conversion</a>
+<a name="58"><span class="lineNum">      58 </span>            : of the histogram to the free energy can be achieved by using the method \ref CONVERT_TO_FES.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : We calculate histograms within PLUMED using a method known as kernel density estimation, which you can read more about here:</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : https://en.wikipedia.org/wiki/Kernel_density_estimation</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : In PLUMED the value of \f$\zeta\f$ at each discrete instant in time in the trajectory is accumulated.  A kernel, \f$K(\zeta-\zeta(t'),\sigma)\f$,</a>
+<a name="65"><span class="lineNum">      65 </span>            : centered at the current value, \f$\zeta(t)\f$, of this quantity is generated with a bandwidth \f$\sigma\f$, which</a>
+<a name="66"><span class="lineNum">      66 </span>            : is set by the user.  These kernels are then used to accumulate the ensemble average for the probability density:</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \f[</a>
+<a name="69"><span class="lineNum">      69 </span>            : \langle P(\zeta) \rangle = \frac{ \sum_{t'=0}^t w(t') K(\zeta-\zeta(t'),\sigma) }{ \sum_{t'=0}^t w(t') }</a>
+<a name="70"><span class="lineNum">      70 </span>            : \f]</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : Here the sums run over a portion of the trajectory specified by the user.  The final quantity evaluated is a weighted</a>
+<a name="73"><span class="lineNum">      73 </span>            : average as the weights, \f$w(t')\f$, allow us to negate the effect any bias might have on the region of phase space</a>
+<a name="74"><span class="lineNum">      74 </span>            : sampled by the system.  This is discussed in the section of the manual on \ref Analysis.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : A discrete analogue of kernel density estimation can also be used.  In this analogue the kernels in the above formula</a>
+<a name="77"><span class="lineNum">      77 </span>            : are replaced by Dirac delta functions.   When this method is used the final function calculated is no longer a probability</a>
+<a name="78"><span class="lineNum">      78 </span>            : density - it is instead a probability mass function as each element of the function tells you the value of an integral</a>
+<a name="79"><span class="lineNum">      79 </span>            : between two points on your grid rather than the value of a (continuous) function on a grid.</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : Additional material and examples can be also found in the tutorials \ref lugano-1.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \par A note on block averaging and errors</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : Some particularly important</a>
+<a name="86"><span class="lineNum">      86 </span>            : issues related to the convergence of histograms and the estimation of error bars around the ensemble averages you calculate are covered in \ref trieste-2.</a>
+<a name="87"><span class="lineNum">      87 </span>            : The technique for estimating error bars that is known as block averaging is introduced in this tutorial.  The essence of this technique is that</a>
+<a name="88"><span class="lineNum">      88 </span>            : the trajectory is split into a set of blocks and separate ensemble averages are calculated from each separate block of data.  If \f$\{A_i\}\f$ is</a>
+<a name="89"><span class="lineNum">      89 </span>            : the set of \f$N\f$ block averages that are obtained from this technique then the final error bar is calculated as:</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \f[</a>
+<a name="92"><span class="lineNum">      92 </span>            : \textrm{error} = \sqrt{ \frac{1}{N} \frac{1}{N-1} \sum_{i=1}^N (A_i^2 - \langle A \rangle )^2 } \qquad \textrm{where} \qquad \langle A \rangle = \frac{1}{N} \sum_{i=1}^N A_i</a>
+<a name="93"><span class="lineNum">      93 </span>            : \f]</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : If the simulation is biased and reweighting is performed then life is a little more complex as each of the block averages should be calculated as a</a>
+<a name="96"><span class="lineNum">      96 </span>            : weighted average.  Furthermore, the weights should be taken into account when the final ensemble and error bars are calculated.  As such the error should be:</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : \f[</a>
+<a name="99"><span class="lineNum">      99 </span>            : \textrm{error} = \sqrt{ \frac{1}{N} \frac{\sum_{i=1}^N W_i }{\sum_{i=1}^N W_i - \sum_{i=1}^N W_i^2 / \sum_{i=1}^N W_i} \sum_{i=1}^N W_i (A_i^2 - \langle A \rangle )^2 }</a>
+<a name="100"><span class="lineNum">     100 </span>            : \f]</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : where \f$W_i\f$ is the sum of all the weights for the \f$i\f$th block of data.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : If we wish to calculate a normalized histogram we must calculate ensemble averages from our biased simulation using:</a>
+<a name="105"><span class="lineNum">     105 </span>            : \f[</a>
+<a name="106"><span class="lineNum">     106 </span>            :  \langle H(x) \rangle = \frac{\sum_{t=1}^M w_t K( x - x_t,\sigma) }{\sum_{t=1}^M w_t}</a>
+<a name="107"><span class="lineNum">     107 </span>            : \f]</a>
+<a name="108"><span class="lineNum">     108 </span>            : where the sums runs over the trajectory, \f$w_t\f$ is the weight of the \f$t\f$th trajectory frame, \f$x_t\f$ is the value of the CV for the \f$t\f$th</a>
+<a name="109"><span class="lineNum">     109 </span>            : trajectory frame and \f$K\f$ is a kernel function centered on \f$x_t\f$ with bandwidth \f$\sigma\f$.  The quantity that is evaluated is the value of the</a>
+<a name="110"><span class="lineNum">     110 </span>            : normalized histogram at point \f$x\f$.  The following ensemble average will be calculated if you use the NORMALIZATION=true option in HISTOGRAM.</a>
+<a name="111"><span class="lineNum">     111 </span>            : If the ensemble average is calculated in this way we must calculate the associated error bars from our block averages using the second of the expressions</a>
+<a name="112"><span class="lineNum">     112 </span>            : above.</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : A number of works have shown that when biased simulations are performed it is often better to calculate an estimate of the histogram that is not normalized using:</a>
+<a name="115"><span class="lineNum">     115 </span>            : \f[</a>
+<a name="116"><span class="lineNum">     116 </span>            : \langle H(x) \rangle = \frac{1}{M} \sum_{t=1}^M w_t K( x - x_t,\sigma)</a>
+<a name="117"><span class="lineNum">     117 </span>            : \f]</a>
+<a name="118"><span class="lineNum">     118 </span>            : instead of the expression above.  As such this is what is done by default in HISTOGRAM or if the NORMALIZATION=ndata option is used.</a>
+<a name="119"><span class="lineNum">     119 </span>            : When the histogram is calculated in this second way the first of the two formula above can be used when calculating error bars from</a>
+<a name="120"><span class="lineNum">     120 </span>            : block averages.</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : \par Examples</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="125"><span class="lineNum">     125 </span>            : and outputs a continuous histogram as a function of them at the end of the simulation.</a>
+<a name="126"><span class="lineNum">     126 </span>            : \plumedfile</a>
+<a name="127"><span class="lineNum">     127 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="128"><span class="lineNum">     128 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="129"><span class="lineNum">     129 </span>            : HISTOGRAM ...</a>
+<a name="130"><span class="lineNum">     130 </span>            :   ARG=r1,r2</a>
+<a name="131"><span class="lineNum">     131 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="132"><span class="lineNum">     132 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="133"><span class="lineNum">     133 </span>            :   GRID_BIN=200,200</a>
+<a name="134"><span class="lineNum">     134 </span>            :   BANDWIDTH=0.05,0.05</a>
+<a name="135"><span class="lineNum">     135 </span>            :   LABEL=hh</a>
+<a name="136"><span class="lineNum">     136 </span>            : ... HISTOGRAM</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : DUMPGRID GRID=hh FILE=histo</a>
+<a name="139"><span class="lineNum">     139 </span>            : \endplumedfile</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="142"><span class="lineNum">     142 </span>            : and outputs a discrete histogram as a function of them at the end of the simulation.</a>
+<a name="143"><span class="lineNum">     143 </span>            : \plumedfile</a>
+<a name="144"><span class="lineNum">     144 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="145"><span class="lineNum">     145 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="146"><span class="lineNum">     146 </span>            : HISTOGRAM ...</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ARG=r1,r2</a>
+<a name="148"><span class="lineNum">     148 </span>            :   KERNEL=DISCRETE</a>
+<a name="149"><span class="lineNum">     149 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="150"><span class="lineNum">     150 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="151"><span class="lineNum">     151 </span>            :   GRID_BIN=200,200</a>
+<a name="152"><span class="lineNum">     152 </span>            :   LABEL=hh</a>
+<a name="153"><span class="lineNum">     153 </span>            : ... HISTOGRAM</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : DUMPGRID GRID=hh FILE=histo</a>
+<a name="156"><span class="lineNum">     156 </span>            : \endplumedfile</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="159"><span class="lineNum">     159 </span>            : and outputs the histogram accumulated thus far every 100000 steps.</a>
+<a name="160"><span class="lineNum">     160 </span>            : \plumedfile</a>
+<a name="161"><span class="lineNum">     161 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="162"><span class="lineNum">     162 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="163"><span class="lineNum">     163 </span>            : HISTOGRAM ...</a>
+<a name="164"><span class="lineNum">     164 </span>            :   ARG=r1,r2</a>
+<a name="165"><span class="lineNum">     165 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="166"><span class="lineNum">     166 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="167"><span class="lineNum">     167 </span>            :   GRID_BIN=200,200</a>
+<a name="168"><span class="lineNum">     168 </span>            :   BANDWIDTH=0.05,0.05</a>
+<a name="169"><span class="lineNum">     169 </span>            :   LABEL=hh</a>
+<a name="170"><span class="lineNum">     170 </span>            : ... HISTOGRAM</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : DUMPGRID GRID=hh FILE=histo STRIDE=100000</a>
+<a name="173"><span class="lineNum">     173 </span>            : \endplumedfile</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="176"><span class="lineNum">     176 </span>            : and outputs a separate histogram for each 100000 steps worth of trajectory.</a>
+<a name="177"><span class="lineNum">     177 </span>            : Notice how the CLEAR keyword is used here and how it is not used in the</a>
+<a name="178"><span class="lineNum">     178 </span>            : previous example.</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : \plumedfile</a>
+<a name="181"><span class="lineNum">     181 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="182"><span class="lineNum">     182 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="183"><span class="lineNum">     183 </span>            : HISTOGRAM ...</a>
+<a name="184"><span class="lineNum">     184 </span>            :   ARG=r1,r2 CLEAR=100000</a>
+<a name="185"><span class="lineNum">     185 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="186"><span class="lineNum">     186 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="187"><span class="lineNum">     187 </span>            :   GRID_BIN=200,200</a>
+<a name="188"><span class="lineNum">     188 </span>            :   BANDWIDTH=0.05,0.05</a>
+<a name="189"><span class="lineNum">     189 </span>            :   LABEL=hh</a>
+<a name="190"><span class="lineNum">     190 </span>            : ... HISTOGRAM</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : DUMPGRID GRID=hh FILE=histo STRIDE=100000</a>
+<a name="193"><span class="lineNum">     193 </span>            : \endplumedfile</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : */</a>
+<a name="196"><span class="lineNum">     196 </span>            : //+ENDPLUMEDOC</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : class Histogram : public gridtools::ActionWithGrid {</a>
+<a name="199"><span class="lineNum">     199 </span>            : private:</a>
+<a name="200"><span class="lineNum">     200 </span>            :   double ww;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   bool in_apply, mvectors;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   std::unique_ptr&lt;KernelFunctions&gt; kernel;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   std::vector&lt;double&gt; forcesToApply, finalForces;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   std::vector&lt;vesselbase::ActionWithVessel*&gt; myvessels;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   std::vector&lt;vesselbase::StoreDataVessel*&gt; stashes;</a>
+<a name="206"><span class="lineNum">     206 </span>            : // this is a plain pointer since this object is now owned</a>
+<a name="207"><span class="lineNum">     207 </span>            :   gridtools::HistogramOnGrid* myhist;</a>
+<a name="208"><span class="lineNum">     208 </span>            : public:</a>
+<a name="209"><span class="lineNum">     209 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="210"><span class="lineNum">     210 </span>            :   explicit Histogram(const ActionOptions&amp;ao);</a>
+<a name="211"><span class="lineNum">     211 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="212"><span class="lineNum">     212 </span>            :   void prepareForAveraging() override;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   void performOperations( const bool&amp; from_update ) override;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   void finishAveraging() override;</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        121 :   bool threadSafe() const override { return !in_apply; }</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   void turnOnDerivatives() override;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   void compute( const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   void apply() override;</a>
+<a name="221"><span class="lineNum">     221 </span>            : };</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      12572 : PLUMED_REGISTER_ACTION(Histogram,&quot;HISTOGRAM&quot;)</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         36 : void Histogram::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         72 :   gridtools::ActionWithGrid::registerKeywords( keys ); keys.use(&quot;ARG&quot;); keys.remove(&quot;NORMALIZATION&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         72 :   keys.add(&quot;compulsory&quot;,&quot;NORMALIZATION&quot;,&quot;ndata&quot;,&quot;This controls how the data is normalized it can be set equal to true, false or ndata.  See above for an explanation&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         72 :   keys.add(&quot;optional&quot;,&quot;DATA&quot;,&quot;input data from action with vessel and compute histogram&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         72 :   keys.add(&quot;optional&quot;,&quot;VECTORS&quot;,&quot;input three dimensional vectors for computing histogram&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         72 :   keys.add(&quot;compulsory&quot;,&quot;GRID_MIN&quot;,&quot;the lower bounds for the grid&quot;);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         72 :   keys.add(&quot;compulsory&quot;,&quot;GRID_MAX&quot;,&quot;the upper bounds for the grid&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         72 :   keys.add(&quot;optional&quot;,&quot;GRID_BIN&quot;,&quot;the number of bins for the grid&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         72 :   keys.add(&quot;optional&quot;,&quot;GRID_SPACING&quot;,&quot;the approximate grid spacing (to be used as an alternative or together with GRID_BIN)&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         72 :   keys.use(&quot;UPDATE_FROM&quot;); keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         36 : }</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         34 : Histogram::Histogram(const ActionOptions&amp;ao):</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   Action(ao),</a>
+<a name="239"><span class="lineNum">     239 </span>            :   ActionWithGrid(ao),</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         34 :   ww(0.0),</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         34 :   in_apply(false),</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         34 :   mvectors(false)</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : {</a>
+<a name="244"><span class="lineNum">     244 </span>            :   // Read in arguments</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         34 :   if( getNumberOfArguments()==0 ) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         16 :     std::string vlab; parse(&quot;VECTORS&quot;,vlab);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          8 :     if( vlab.length()&gt;0 ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          2 :       ActionWithVessel* myv = plumed.getActionSet().selectWithLabel&lt;ActionWithVessel*&gt;( vlab );</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          2 :       if( !myv ) error(&quot;action labelled &quot; + vlab + &quot; does not exist or is not an ActionWithVessel&quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :       myvessels.push_back( myv ); stashes.push_back( myv-&gt;buildDataStashes( NULL ) );</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          2 :       addDependency( myv ); mvectors=true;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 :       if( myv-&gt;getNumberOfQuantities()!=5 ) error(&quot;can only compute histograms for three dimensional vectors&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          2 :       log.printf(&quot;  for vector quantities calculated by %s \n&quot;, vlab.c_str() );</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :     } else {</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         12 :       std::vector&lt;std::string&gt; mlab; parseVector(&quot;DATA&quot;,mlab);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          6 :       if( mlab.size()&gt;0 ) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         16 :         for(unsigned i=0; i&lt;mlab.size(); ++i) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         10 :           ActionWithVessel* myv = plumed.getActionSet().selectWithLabel&lt;ActionWithVessel*&gt;( mlab[i] );</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         10 :           if( !myv ) error(&quot;action labelled &quot; + mlab[i] + &quot; does not exist or is not an ActionWithVessel&quot;);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         10 :           myvessels.push_back( myv ); stashes.push_back( myv-&gt;buildDataStashes( NULL ) );</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :           // log.printf(&quot;  for all base quantities calculated by %s \n&quot;,myvessel-&gt;getLabel().c_str() );</a>
+<a name="262"><span class="lineNum">     262 </span>            :           // Add the dependency</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         10 :           addDependency( myv );</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :         }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          6 :         unsigned nvals = myvessels[0]-&gt;getFullNumberOfTasks();</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         10 :         for(unsigned i=1; i&lt;mlab.size(); ++i) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          4 :           if( nvals!=myvessels[i]-&gt;getFullNumberOfTasks() ) error(&quot;mismatched number of quantities calculated by actions input to histogram&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :         }</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          6 :         log.printf(&quot;  for all base quantities calculated by %s &quot;, myvessels[0]-&gt;getLabel().c_str() );</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         10 :         for(unsigned i=1; i&lt;mlab.size(); ++i) log.printf(&quot;, %s \n&quot;, myvessels[i]-&gt;getLabel().c_str() );</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          6 :         log.printf(&quot;\n&quot;);</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :       } else {</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :         error(&quot;input data is missing use ARG/VECTORS/DATA&quot;);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :       }</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          6 :     }</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :   }</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   // Read stuff for grid</a>
+<a name="279"><span class="lineNum">     279 </span>            :   unsigned narg = getNumberOfArguments();</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         34 :   if( myvessels.size()&gt;0 ) narg=myvessels.size();</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   // Input of name and labels</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         34 :   std::string vstring=&quot;COMPONENTS=&quot; + getLabel();</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         34 :   if( mvectors ) {</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :     vstring += &quot; COORDINATES=x,y,z PBC=F,F,F&quot;;</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         32 :   } else if( myvessels.size()&gt;0 ) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          6 :     vstring += &quot; COORDINATES=&quot; + myvessels[0]-&gt;getLabel();</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         10 :     for(unsigned i=1; i&lt;myvessels.size(); ++i) vstring +=&quot;,&quot; + myvessels[i]-&gt;getLabel();</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     // Input for PBC</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          6 :     if( myvessels[0]-&gt;isPeriodic() ) vstring+=&quot; PBC=T&quot;;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :     else vstring+=&quot; PBC=F&quot;;</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         10 :     for(unsigned i=1; i&lt;myvessels.size(); ++i) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          4 :       if( myvessels[i]-&gt;isPeriodic() ) vstring+=&quot;,T&quot;;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :       else vstring+=&quot;,F&quot;;</a>
+<a name="294"><span class="lineNum">     294 </span>            :     }</a>
+<a name="295"><span class="lineNum">     295 </span>            :   } else {</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         26 :     vstring += &quot; COORDINATES=&quot; + getPntrToArgument(0)-&gt;getName();</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         35 :     for(unsigned i=1; i&lt;getNumberOfArguments(); ++i) vstring += &quot;,&quot; + getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     // Input for PBC</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         26 :     if( getPntrToArgument(0)-&gt;isPeriodic() ) vstring+=&quot; PBC=T&quot;;</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     else vstring+=&quot; PBC=F&quot;;</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         35 :     for(unsigned i=1; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          9 :       if( getPntrToArgument(i)-&gt;isPeriodic() ) vstring+=&quot;,T&quot;;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :       else vstring+=&quot;,F&quot;;</a>
+<a name="304"><span class="lineNum">     304 </span>            :     }</a>
+<a name="305"><span class="lineNum">     305 </span>            :   }</a>
+<a name="306"><span class="lineNum">     306 </span>            :   // And create the grid</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         34 :   auto grid=createGrid( &quot;histogram&quot;, vstring );</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :   // notice that createGrid also sets mygrid=grid.get()</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         68 :   if( mygrid-&gt;getType()==&quot;flat&quot; ) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         32 :     if( mvectors ) error(&quot;computing histogram for three dimensional vectors but grid is not of fibonacci type - use CONCENTRATION&quot;);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         32 :     std::vector&lt;std::string&gt; gmin( narg ), gmax( narg );</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         96 :     parseVector(&quot;GRID_MIN&quot;,gmin); parseVector(&quot;GRID_MAX&quot;,gmax);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         64 :     std::vector&lt;unsigned&gt; nbin; parseVector(&quot;GRID_BIN&quot;,nbin);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         64 :     std::vector&lt;double&gt; gspacing; parseVector(&quot;GRID_SPACING&quot;,gspacing);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         32 :     if( nbin.size()!=narg &amp;&amp; gspacing.size()!=narg ) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :       error(&quot;GRID_BIN or GRID_SPACING must be set&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     }</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         32 :     mygrid-&gt;setBounds( gmin, gmax, nbin, gspacing );</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         32 :   } else {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :     std::vector&lt;unsigned&gt; nbin; parseVector(&quot;GRID_BIN&quot;,nbin);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          2 :     if( nbin.size()!=1 ) error(&quot;should only be one index for number of bins with spherical grid&quot;);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          4 :     if( mygrid-&gt;getType()==&quot;fibonacci&quot; ) mygrid-&gt;setupFibonacciGrid( nbin[0] );</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   }</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         34 :   myhist = dynamic_cast&lt;gridtools::HistogramOnGrid*&gt;( mygrid );</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         34 :   plumed_assert( myhist );</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         34 :   if( myvessels.size()&gt;0 ) {</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     // Create a task list</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         72 :     for(unsigned i=0; i&lt;myvessels[0]-&gt;getFullNumberOfTasks(); ++i) addTaskToList(i);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          8 :     setAveragingAction( std::move(grid), true );</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :   } else if( storeThenAverage() ) {</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          7 :     setAveragingAction( std::move(grid), true );</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :   } else {</a>
+<a name="333"><span class="lineNum">     333 </span>            :     // Create a task list</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       9256 :     for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) addTaskToList(i);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         19 :     myhist-&gt;addOneKernelEachTimeOnly();</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         19 :     setAveragingAction( std::move(grid), myhist-&gt;noDiscreteKernels() );</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   }</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         34 :   checkRead();</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         68 : }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          8 : void Histogram::turnOnDerivatives() {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          8 :   ActionWithGrid::turnOnDerivatives();</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms, tmp_atoms;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         20 :   for(unsigned i=0; i&lt;myvessels.size(); ++i) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         12 :     multicolvar::MultiColvarBase* mbase=dynamic_cast&lt;multicolvar::MultiColvarBase*&gt;( myvessels[i] );</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         12 :     if( !mbase ) error(&quot;do not know how to get histogram derivatives for actions of type &quot; + myvessels[i]-&gt;getName() );</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         12 :     tmp_atoms = mbase-&gt;getAbsoluteIndexes();</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        482 :     for(unsigned j=0; j&lt;tmp_atoms.size(); ++j) all_atoms.push_back( tmp_atoms[j] );</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :     // Make a tempory multi value so we can avoid vector resizing</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         12 :     stashes[i]-&gt;resizeTemporyMultiValues( 1 );</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :   }</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          8 :   ActionAtomistic::requestAtoms( all_atoms );</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          8 :   finalForces.resize( 3*all_atoms.size() + 9 );</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          8 :   forcesToApply.resize( 3*all_atoms.size() + 9*myvessels.size() );</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :   // And make sure we still have the dependencies which are cleared by requestAtoms</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         20 :   for(unsigned i=0; i&lt;myvessels.size(); ++i) addDependency( myvessels[i] );</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   // And resize the histogram so that we have a place to store the forces</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          8 :   in_apply=true; mygrid-&gt;resize(); in_apply=false;</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          8 : }</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        728 : unsigned Histogram::getNumberOfDerivatives() {</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        728 :   if( in_apply ) {</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :     unsigned nder=0;</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        540 :     for(unsigned i=0; i&lt;myvessels.size(); ++i) nder += myvessels[i]-&gt;getNumberOfDerivatives();</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :     return nder;</a>
+<a name="366"><span class="lineNum">     366 </span>            :   }</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        506 :   return getNumberOfArguments();</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : }</a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        462 : unsigned Histogram::getNumberOfQuantities() const {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        462 :   if( mvectors ) return myvessels[0]-&gt;getNumberOfQuantities();</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        416 :   else if( myvessels.size()&gt;0 ) return myvessels.size()+2;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        294 :   return ActionWithAveraging::getNumberOfQuantities();</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : }</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        115 : void Histogram::prepareForAveraging() {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        115 :   if( myvessels.size()&gt;0 ) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         36 :     deactivateAllTasks(); double norm=0;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        332 :     for(unsigned i=0; i&lt;stashes[0]-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        296 :       std::vector&lt;double&gt; cvals( myvessels[0]-&gt;getNumberOfQuantities() );</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        296 :       stashes[0]-&gt;retrieveSequentialValue( i, false, cvals );</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        296 :       unsigned itask=myvessels[0]-&gt;getActiveTask(i); double tnorm = cvals[0];</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        444 :       for(unsigned j=1; j&lt;myvessels.size(); ++j) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        148 :         if( myvessels[j]-&gt;getActiveTask(i)!=itask ) error(&quot;mismatched task identities in histogram suggests histogram is meaningless&quot;);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        148 :         if( cvals.size()!=myvessels[j]-&gt;getNumberOfQuantities() ) cvals.resize( myvessels[j]-&gt;getNumberOfQuantities() );</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        148 :         stashes[j]-&gt;retrieveSequentialValue( i, false, cvals ); tnorm *= cvals[0];</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :       }</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        296 :       norm += tnorm; taskFlags[i]=1;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :     }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         36 :     lockContributors();</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     // Sort out normalization of histogram</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         36 :     if( !noNormalization() ) ww = cweight / norm;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          5 :     else ww = cweight;</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :   } else if( !storeThenAverage() ) {</a>
+<a name="395"><span class="lineNum">     395 </span>            :     // Now fetch the kernel and the active points</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         72 :     std::vector&lt;double&gt; point( getNumberOfArguments() );</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        180 :     for(unsigned i=0; i&lt;point.size(); ++i) point[i]=getArgument(i);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         72 :     unsigned num_neigh; std::vector&lt;unsigned&gt; neighbors(1);</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">        144 :     kernel=myhist-&gt;getKernelAndNeighbors( point, num_neigh, neighbors );</span></a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         72 :     if( num_neigh&gt;1 ) {</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :       // Activate relevant tasks</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         67 :       deactivateAllTasks();</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">      14975 :       for(unsigned i=0; i&lt;num_neigh; ++i) taskFlags[neighbors[i]]=1;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         67 :       lockContributors();</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :     } else {</a>
+<a name="407"><span class="lineNum">     407 </span>            :       // This is used when we are not doing kernel density evaluation</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          5 :       mygrid-&gt;addToGridElement( neighbors[0], 0, cweight );</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     }</a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        115 : }</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          5 : void Histogram::performOperations( const bool&amp; from_update ) { if( myvessels.size()==0 ) plumed_dbg_assert( !myhist-&gt;noDiscreteKernels() ); }</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        135 : void Histogram::finishAveraging() {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        135 :   if( myvessels.size()==0 ) kernel.reset();</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">        135 : }</span></a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      15404 : void Histogram::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      15404 :   if( mvectors ) {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        140 :     std::vector&lt;double&gt; cvals( myvessels[0]-&gt;getNumberOfQuantities() );</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        140 :     stashes[0]-&gt;retrieveSequentialValue( current, true, cvals );</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        560 :     for(unsigned i=2; i&lt;myvessels[0]-&gt;getNumberOfQuantities(); ++i) myvals.setValue( i-1, cvals[i] );</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        140 :     myvals.setValue( 0, cvals[0] ); myvals.setValue( myvessels[0]-&gt;getNumberOfQuantities() - 1, ww );</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">        140 :     if( in_apply ) {</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         50 :       MultiValue&amp; tmpval = stashes[0]-&gt;getTemporyMultiValue(0);</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         99 :       if( tmpval.getNumberOfValues()!=myvessels[0]-&gt;getNumberOfQuantities() ||</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         49 :           tmpval.getNumberOfDerivatives()!=myvessels[0]-&gt;getNumberOfDerivatives() )</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          1 :         tmpval.resize( myvessels[0]-&gt;getNumberOfQuantities(), myvessels[0]-&gt;getNumberOfDerivatives() );</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         50 :       stashes[0]-&gt;retrieveDerivatives( stashes[0]-&gt;getTrueIndex(current), true, tmpval );</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        350 :       for(unsigned j=0; j&lt;tmpval.getNumberActive(); ++j) {</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        300 :         unsigned jder=tmpval.getActiveIndex(j); myvals.addDerivative( 0, jder, tmpval.getDerivative(0, jder) );</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">       1200 :         for(unsigned i=2; i&lt;myvessels[0]-&gt;getNumberOfQuantities(); ++i) myvals.addDerivative( i-1, jder, tmpval.getDerivative(i, jder) );</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :       }</a>
+<a name="435"><span class="lineNum">     435 </span>            :       myvals.updateDynamicList();</a>
+<a name="436"><span class="lineNum">     436 </span>            :     }</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">      15264 :   } else if( myvessels.size()&gt;0 ) {</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">        356 :     std::vector&lt;double&gt; cvals( myvessels[0]-&gt;getNumberOfQuantities() );</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">        356 :     stashes[0]-&gt;retrieveSequentialValue( current, false, cvals );</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        356 :     unsigned derbase=0; double totweight=cvals[0], tnorm = cvals[0]; myvals.setValue( 1, cvals[1] );</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :     // Get the derivatives as well if we are in apply</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">        356 :     if( in_apply ) {</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :       // This bit gets the total weight</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">        150 :       double weight0 = cvals[0];  // Store the current weight</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        250 :       for(unsigned j=1; j&lt;myvessels.size(); ++j) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        100 :         stashes[j]-&gt;retrieveSequentialValue( current, false, cvals ); totweight *= cvals[0];</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :       }</a>
+<a name="448"><span class="lineNum">     448 </span>            :       // And this bit the derivatives</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">        150 :       MultiValue&amp; tmpval = stashes[0]-&gt;getTemporyMultiValue(0);</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">        297 :       if( tmpval.getNumberOfValues()!=myvessels[0]-&gt;getNumberOfQuantities() ||</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        147 :           tmpval.getNumberOfDerivatives()!=myvessels[0]-&gt;getNumberOfDerivatives() )</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          3 :         tmpval.resize( myvessels[0]-&gt;getNumberOfQuantities(), myvessels[0]-&gt;getNumberOfDerivatives() );</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">        150 :       stashes[0]-&gt;retrieveDerivatives( stashes[0]-&gt;getTrueIndex(current), false, tmpval );</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">      31590 :       for(unsigned j=0; j&lt;tmpval.getNumberActive(); ++j) {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">      31440 :         unsigned jder=tmpval.getActiveIndex(j);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">      31440 :         myvals.addDerivative( 1, jder, tmpval.getDerivative(1,jder) );</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">      31440 :         myvals.addDerivative( 0, jder, (totweight/weight0)*tmpval.getDerivative(0,jder) );</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :       }</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        150 :       derbase = myvessels[0]-&gt;getNumberOfDerivatives();</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :     }</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">        604 :     for(unsigned i=1; i&lt;myvessels.size(); ++i) {</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">        248 :       if( cvals.size()!=myvessels[i]-&gt;getNumberOfQuantities() ) cvals.resize( myvessels[i]-&gt;getNumberOfQuantities() );</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">        248 :       stashes[i]-&gt;retrieveSequentialValue( current, false, cvals );</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        248 :       tnorm *= cvals[0]; myvals.setValue( 1+i, cvals[1] );</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :       // Get the derivatives as well if we are in apply</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">        248 :       if( in_apply ) {</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">        100 :         MultiValue&amp; tmpval = stashes[0]-&gt;getTemporyMultiValue(0);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">        200 :         if( tmpval.getNumberOfValues()!=myvessels[0]-&gt;getNumberOfQuantities() ||</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        100 :             tmpval.getNumberOfDerivatives()!=myvessels[0]-&gt;getNumberOfDerivatives() )</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 :           tmpval.resize( myvessels[0]-&gt;getNumberOfQuantities(), myvessels[0]-&gt;getNumberOfDerivatives() );</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">        100 :         stashes[i]-&gt;retrieveDerivatives( stashes[i]-&gt;getTrueIndex(current), false, tmpval );</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">       1090 :         for(unsigned j=0; j&lt;tmpval.getNumberActive(); ++j) {</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :           unsigned jder=tmpval.getActiveIndex(j);</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        990 :           myvals.addDerivative( 1+i, derbase+jder, tmpval.getDerivative(1,jder) );</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">        990 :           myvals.addDerivative( 0, derbase+jder, (totweight/cvals[0])*tmpval.getDerivative(0,jder) );</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :         }</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">        100 :         derbase += myvessels[i]-&gt;getNumberOfDerivatives();</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :       }</a>
+<a name="479"><span class="lineNum">     479 </span>            :     }</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">        356 :     myvals.setValue( 0, tnorm ); myvals.setValue( 1+myvessels.size(), ww );</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">        356 :     if( in_apply ) myvals.updateDynamicList();</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   } else {</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">      14908 :     plumed_assert( !in_apply );</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">      14908 :     std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; vv( myhist-&gt;getVectorOfValues() );</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">      14908 :     std::vector&lt;double&gt; val( getNumberOfArguments() ), der( getNumberOfArguments() );</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :     // Retrieve the location of the grid point at which we are evaluating the kernel</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">      14908 :     mygrid-&gt;getGridPointCoordinates( current, val );</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">      14908 :     if( kernel ) {</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">      54492 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) vv[i]-&gt;set( val[i] );</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :       // Evaluate the histogram at the relevant grid point and set the values</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">      29816 :       double vvh = kernel-&gt;evaluate( Tools::unique2raw(vv), der,true); myvals.setValue( 1, vvh );</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :     } else {</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;normalisation of vectors does not work with arguments and spherical grids&quot;);</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :       // Evalulate dot product</a>
+<a name="495"><span class="lineNum">     495 </span>            :       double dot=0; for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) { dot+=val[j]*getArgument(j); der[j]=val[j]; }</a>
+<a name="496"><span class="lineNum">     496 </span>            :       // Von misses distribution for concentration parameter</a>
+<a name="497"><span class="lineNum">     497 </span>            :       double newval = (myhist-&gt;von_misses_norm)*std::exp( (myhist-&gt;von_misses_concentration)*dot ); myvals.setValue( 1, newval );</a>
+<a name="498"><span class="lineNum">     498 </span>            :       // And final derivatives</a>
+<a name="499"><span class="lineNum">     499 </span>            :       for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) der[j] *= (myhist-&gt;von_misses_concentration)*newval;</a>
+<a name="500"><span class="lineNum">     500 </span>            :     }</a>
+<a name="501"><span class="lineNum">     501 </span>            :     // Set the derivatives and delete the vector of values</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">      54492 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) { myvals.setDerivative( 1, i, der[i] ); }</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">      14908 :   }</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">      15404 : }</span></a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        133 : void Histogram::apply() {</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        133 :   if( !myhist-&gt;wasForced() ) return ;</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         20 :   in_apply=true;</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :   // Run the loop to calculate the forces</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">         20 :   runAllTasks(); finishAveraging();</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   // We now need to retrieve the buffer and set the forces on the atoms</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         20 :   myhist-&gt;applyForce( forcesToApply );</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :   // Now make the forces make sense for the virial</a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         20 :   unsigned fbase=0, tbase=0, vbase = getNumberOfDerivatives() - myvessels.size()*9;</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        200 :   for(unsigned i=vbase; i&lt;vbase+9; ++i) finalForces[i]=0.0;</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         50 :   for(unsigned i=0; i&lt;myvessels.size(); ++i) {</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">       3555 :     for(unsigned j=0; j&lt;myvessels[i]-&gt;getNumberOfDerivatives()-9; ++j) {</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">       3525 :       finalForces[fbase + j] = forcesToApply[tbase + j];</span></a>
+<a name="519"><span class="lineNum">     519 </span>            :     }</a>
+<a name="520"><span class="lineNum">     520 </span>            :     unsigned k=0;</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">        300 :     for(unsigned j=myvessels[i]-&gt;getNumberOfDerivatives()-9; j&lt;myvessels[i]-&gt;getNumberOfDerivatives(); ++j) {</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        270 :       finalForces[vbase + k] += forcesToApply[tbase + j]; k++;</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :     }</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         30 :     fbase += myvessels[i]-&gt;getNumberOfDerivatives() - 9;</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         30 :     tbase += myvessels[i]-&gt;getNumberOfDerivatives();</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :   }</a>
+<a name="527"><span class="lineNum">     527 </span>            :   // And set the final forces on the atoms</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         20 :   setForcesOnAtoms( finalForces );</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :   // Reset everything for next regular loop</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         20 :   in_apply=false;</span></a>
+<a name="531"><span class="lineNum">     531 </span>            : }</a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span>            : }</a>
+<a name="534"><span class="lineNum">     534 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkSelectionBase.cpp.func-sort-c.html b/coverage/analysis/LandmarkSelectionBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..45b38d9446
--- /dev/null
+++ b/coverage/analysis/LandmarkSelectionBase.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkSelectionBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkSelectionBase.cpp<span style="font-size: 80%;"> (<a href="LandmarkSelectionBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LandmarkSelectionBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#32">_ZN4PLMD8analysis21LandmarkSelectionBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#66">_ZNK4PLMD8analysis21LandmarkSelectionBase15voronoiAnalysisERKSt6vectorIjSaIjEERS2_IdSaIdEERS4_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#32">_ZN4PLMD8analysis21LandmarkSelectionBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#52">_ZN4PLMD8analysis21LandmarkSelectionBase15performAnalysisEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#25">_ZN4PLMD8analysis21LandmarkSelectionBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#48">_ZN4PLMD8analysis21LandmarkSelectionBase11selectFrameERKj</a></td>
+              <td class="coverFnHi">291</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkSelectionBase.cpp.func.html b/coverage/analysis/LandmarkSelectionBase.cpp.func.html
new file mode 100644
index 0000000000..888bb09f93
--- /dev/null
+++ b/coverage/analysis/LandmarkSelectionBase.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkSelectionBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkSelectionBase.cpp<span style="font-size: 80%;"> (<a href="LandmarkSelectionBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LandmarkSelectionBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#48">_ZN4PLMD8analysis21LandmarkSelectionBase11selectFrameERKj</a></td>
+              <td class="coverFnHi">291</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#52">_ZN4PLMD8analysis21LandmarkSelectionBase15performAnalysisEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#25">_ZN4PLMD8analysis21LandmarkSelectionBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#32">_ZN4PLMD8analysis21LandmarkSelectionBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#32">_ZN4PLMD8analysis21LandmarkSelectionBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.cpp.gcov.html#66">_ZNK4PLMD8analysis21LandmarkSelectionBase15voronoiAnalysisERKSt6vectorIjSaIjEERS2_IdSaIdEERS4_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkSelectionBase.cpp.gcov.html b/coverage/analysis/LandmarkSelectionBase.cpp.gcov.html
new file mode 100644
index 0000000000..e6e9d72211
--- /dev/null
+++ b/coverage/analysis/LandmarkSelectionBase.cpp.gcov.html
@@ -0,0 +1,162 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkSelectionBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkSelectionBase.cpp<span style="font-size: 80%;"> (source / <a href="LandmarkSelectionBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LandmarkSelectionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace analysis {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         20 : void LandmarkSelectionBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         20 :   AnalysisBase::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         40 :   keys.add(&quot;compulsory&quot;,&quot;NLANDMARKS&quot;,&quot;the number of landmarks that you would like to select&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         40 :   keys.addFlag(&quot;NOVORONOI&quot;,false,&quot;do not do a Voronoi analysis of the data to determine weights of final points&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         40 :   keys.addFlag(&quot;IGNORE_WEIGHTS&quot;,false,&quot;ignore the weights in the underlying analysis object&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         20 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         10 : LandmarkSelectionBase::LandmarkSelectionBase( const ActionOptions&amp; ao ):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   Action(ao),</a>
+<a name="36"><span class="lineNum">      36 </span>            :   AnalysisBase(ao),</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         10 :   nlandmarks(0)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         29 :   if( keywords.exists(&quot;NLANDMARKS&quot;) ) parse(&quot;NLANDMARKS&quot;,nlandmarks);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         10 :   log.printf(&quot;  selecting %u landmark points \n&quot;,nlandmarks);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         10 :   lweights.resize( nlandmarks );</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         10 :   parseFlag(&quot;NOVORONOI&quot;,novoronoi);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         18 :   if( !novoronoi &amp;&amp; !dissimilaritiesWereSet() ) error(&quot;cannot calculate voronoi weights without dissimilarity mesaure&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         10 :   if( !novoronoi ) log.printf(&quot;  ascribing weights to landmarks using voronoi analysis\n&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          2 :   else log.printf(&quot;  ascribing weights of original points to landmark\n&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         10 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        291 : void LandmarkSelectionBase::selectFrame( const unsigned&amp; iframe ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        291 :   landmark_indices.push_back( iframe );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        291 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         12 : void LandmarkSelectionBase::performAnalysis() {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         12 :   landmark_indices.resize(0); selectLandmarks();</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   plumed_dbg_assert( nlandmarks==getNumberOfDataPoints() );</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         12 :   if( lweights.size()!=nlandmarks ) lweights.resize( nlandmarks );</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         12 :   if( !novoronoi ) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          8 :     lweights.assign(lweights.size(),0.0);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          8 :     std::vector&lt;unsigned&gt; tmpass( my_input_data-&gt;getNumberOfDataPoints() );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          8 :     voronoiAnalysis( landmark_indices, lweights, tmpass );</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   } else {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         18 :     for(unsigned i=0; i&lt;nlandmarks; ++i) lweights[i]=my_input_data-&gt;getWeight( landmark_indices[i] );</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         12 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          8 : void LandmarkSelectionBase::voronoiAnalysis( const std::vector&lt;unsigned&gt;&amp; myindices, std::vector&lt;double&gt;&amp; lweights, std::vector&lt;unsigned&gt;&amp; assignments ) const {</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   plumed_dbg_assert( myindices.size()==lweights.size() &amp;&amp; assignments.size()==my_input_data-&gt;getNumberOfDataPoints() );</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          8 :   lweights.assign( lweights.size(), 0 );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          8 :   unsigned rank=comm.Get_rank(), size=comm.Get_size();</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        567 :   for(unsigned i=rank; i&lt;my_input_data-&gt;getNumberOfDataPoints(); i+=size) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        559 :     assignments[i]=0;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        559 :     double mindist=my_input_data-&gt;getDissimilarity( i, myindices[0] );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     125239 :     for(unsigned j=1; j&lt;nlandmarks; ++j) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     124680 :       double dist=my_input_data-&gt;getDissimilarity( i, myindices[j] );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     124680 :       if( dist&lt;mindist ) { mindist=dist; assignments[i]=j; }</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :     }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        559 :     lweights[ assignments[i] ] += my_input_data-&gt;getWeight(i);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   comm.Sum( &amp;lweights[0], lweights.size() );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :   comm.Sum( &amp;assignments[0], assignments.size() );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkSelectionBase.h.func-sort-c.html b/coverage/analysis/LandmarkSelectionBase.h.func-sort-c.html
new file mode 100644
index 0000000000..e93035cb8d
--- /dev/null
+++ b/coverage/analysis/LandmarkSelectionBase.h.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkSelectionBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkSelectionBase.h<span style="font-size: 80%;"> (<a href="LandmarkSelectionBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LandmarkSelectionBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#61">_ZNK4PLMD8analysis21LandmarkSelectionBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#80">_ZN4PLMD8analysis21LandmarkSelectionBase13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">531</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#85">_ZN4PLMD8analysis21LandmarkSelectionBase16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">62329</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#70">_ZNK4PLMD8analysis21LandmarkSelectionBase23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnHi">125002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#65">_ZNK4PLMD8analysis21LandmarkSelectionBase21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">126447</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#75">_ZN4PLMD8analysis21LandmarkSelectionBase9getWeightERKj</a></td>
+              <td class="coverFnHi">8361301</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkSelectionBase.h.func.html b/coverage/analysis/LandmarkSelectionBase.h.func.html
new file mode 100644
index 0000000000..84f4ca394e
--- /dev/null
+++ b/coverage/analysis/LandmarkSelectionBase.h.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkSelectionBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkSelectionBase.h<span style="font-size: 80%;"> (<a href="LandmarkSelectionBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LandmarkSelectionBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#80">_ZN4PLMD8analysis21LandmarkSelectionBase13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">531</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#85">_ZN4PLMD8analysis21LandmarkSelectionBase16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">62329</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#75">_ZN4PLMD8analysis21LandmarkSelectionBase9getWeightERKj</a></td>
+              <td class="coverFnHi">8361301</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#61">_ZNK4PLMD8analysis21LandmarkSelectionBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#65">_ZNK4PLMD8analysis21LandmarkSelectionBase21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">126447</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkSelectionBase.h.gcov.html#70">_ZNK4PLMD8analysis21LandmarkSelectionBase23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnHi">125002</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkSelectionBase.h.gcov.html b/coverage/analysis/LandmarkSelectionBase.h.gcov.html
new file mode 100644
index 0000000000..616a7e6459
--- /dev/null
+++ b/coverage/analysis/LandmarkSelectionBase.h.gcov.html
@@ -0,0 +1,169 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkSelectionBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkSelectionBase.h<span style="font-size: 80%;"> (source / <a href="LandmarkSelectionBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_analysis_LandmarkSelectionBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_analysis_LandmarkSelectionBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace analysis {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class LandmarkSelectionBase : public AnalysisBase {</a>
+<a name="31"><span class="lineNum">      31 </span>            :   friend class ReselectLandmarks;</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// The number of landmarks we are selecting</a>
+<a name="34"><span class="lineNum">      34 </span>            :   unsigned nlandmarks;</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// The weights of the landmark points</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::vector&lt;double&gt; lweights;</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// The indices of the landmarks in the original data set</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::vector&lt;unsigned&gt; landmark_indices;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// How do we treat weights</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool novoronoi, noweights;</a>
+<a name="41"><span class="lineNum">      41 </span>            : protected:</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Transfer frame i in the underlying action to the object we are going to analyze</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void selectFrame( const unsigned&amp; );</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Do a voronoi analysis</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void voronoiAnalysis( const std::vector&lt;unsigned&gt;&amp; myindices, std::vector&lt;double&gt;&amp; lweights, std::vector&lt;unsigned&gt;&amp; assignments ) const ;</a>
+<a name="46"><span class="lineNum">      46 </span>            : public:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="48"><span class="lineNum">      48 </span>            :   explicit LandmarkSelectionBase( const ActionOptions&amp; ao );</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Return the number of data points</a>
+<a name="50"><span class="lineNum">      50 </span>            :   unsigned getNumberOfDataPoints() const override;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Return the index of the data point in the base class</a>
+<a name="52"><span class="lineNum">      52 </span>            :   unsigned getDataPointIndexInBase( const unsigned&amp; idata ) const override;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Get the weight</a>
+<a name="54"><span class="lineNum">      54 </span>            :   double getWeight( const unsigned&amp; idata ) override;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Get a reference configuration</a>
+<a name="56"><span class="lineNum">      56 </span>            :   DataCollectionObject&amp; getStoredData( const unsigned&amp; idat, const bool&amp; calcdist ) override;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Select landmark configurations</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void performAnalysis() override;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   virtual void selectLandmarks()=0;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Get the squared dissimilarity between two reference configurations</a>
+<a name="61"><span class="lineNum">      61 </span>            :   double getDissimilarity( const unsigned&amp; i, const unsigned&amp; j ) override;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// This does nothing - it just ensures the final class is not abstract</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : };</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : inline</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     126447 : unsigned LandmarkSelectionBase::getNumberOfDataPoints() const {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     126447 :   return nlandmarks;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : inline</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">     125002 : unsigned LandmarkSelectionBase::getDataPointIndexInBase( const unsigned&amp; idata ) const {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">     125002 :   return AnalysisBase::getDataPointIndexInBase( landmark_indices[idata] );</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : inline</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">    8361301 : double LandmarkSelectionBase::getWeight( const unsigned&amp; idata ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    8361301 :   return lweights[idata];</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : inline</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        531 : DataCollectionObject&amp; LandmarkSelectionBase::getStoredData( const unsigned&amp; idat, const bool&amp; calcdist ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        531 :   return AnalysisBase::getStoredData( landmark_indices[idat], calcdist );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : inline</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      62329 : double LandmarkSelectionBase::getDissimilarity( const unsigned&amp; i, const unsigned&amp; j ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      62329 :   return AnalysisBase::getDissimilarity( landmark_indices[i], landmark_indices[j] );</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkStaged.cpp.func-sort-c.html b/coverage/analysis/LandmarkStaged.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0e1aa76046
--- /dev/null
+++ b/coverage/analysis/LandmarkStaged.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkStaged.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkStaged.cpp<span style="font-size: 80%;"> (<a href="LandmarkStaged.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryLo">12.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LandmarkStaged.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_126LandmarkStagedRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#64">_ZN4PLMD8analysis14LandmarkStaged15selectLandmarksEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#56">_ZN4PLMD8analysis14LandmarkStagedC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#56">_ZN4PLMD8analysis14LandmarkStagedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#50">_ZN4PLMD8analysis14LandmarkStaged16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_126LandmarkStagedRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_126LandmarkStagedRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkStaged.cpp.func.html b/coverage/analysis/LandmarkStaged.cpp.func.html
new file mode 100644
index 0000000000..0889c10217
--- /dev/null
+++ b/coverage/analysis/LandmarkStaged.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkStaged.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkStaged.cpp<span style="font-size: 80%;"> (<a href="LandmarkStaged.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryLo">12.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LandmarkStaged.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_126LandmarkStagedRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_126LandmarkStagedRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_126LandmarkStagedRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#64">_ZN4PLMD8analysis14LandmarkStaged15selectLandmarksEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#50">_ZN4PLMD8analysis14LandmarkStaged16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#56">_ZN4PLMD8analysis14LandmarkStagedC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LandmarkStaged.cpp.gcov.html#56">_ZN4PLMD8analysis14LandmarkStagedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/LandmarkStaged.cpp.gcov.html b/coverage/analysis/LandmarkStaged.cpp.gcov.html
new file mode 100644
index 0000000000..8aa99cbcb2
--- /dev/null
+++ b/coverage/analysis/LandmarkStaged.cpp.gcov.html
@@ -0,0 +1,211 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/LandmarkStaged.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - LandmarkStaged.cpp<span style="font-size: 80%;"> (source / <a href="LandmarkStaged.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryLo">12.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LandmarkSelectionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;iostream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC LANDMARKS LANDMARK_SELECT_STAGED</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Select a set of landmarks using the staged algorithm.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : \par Examples</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : */</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+ENDPLUMEDOC</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace analysis {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class LandmarkStaged : public LandmarkSelectionBase {</a>
+<a name="41"><span class="lineNum">      41 </span>            : private:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   unsigned seed;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double gamma;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   explicit LandmarkStaged( const ActionOptions&amp; ao );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void selectLandmarks() override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(LandmarkStaged,&quot;LANDMARK_SELECT_STAGED&quot;)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          2 : void LandmarkStaged::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          2 :   LandmarkSelectionBase::registerKeywords(keys);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;GAMMA&quot;,&quot;the gamma parameter to be used in weights&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;SEED&quot;,&quot;1234&quot;,&quot;a random number seed&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          2 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 : LandmarkStaged::LandmarkStaged( const ActionOptions&amp; ao ):</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   Action(ao),</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :   LandmarkSelectionBase(ao)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : {</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   parse(&quot;SEED&quot;,seed); parse(&quot;GAMMA&quot;,gamma);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   log.printf(&quot;  probability of selecting voronoi polyhedra equal to exp(-weight/%f) \n&quot;, gamma );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 : void LandmarkStaged::selectLandmarks() {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   unsigned int n = getNumberOfDataPoints(); // The number of landmarks to pick</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   unsigned int N = my_input_data-&gt;getNumberOfDataPoints();  // The total number of frames we can choose from</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   unsigned int m = static_cast&lt;int&gt;( std::sqrt(n*N) );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; fpslandmarks(m);</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   // Select first point at random</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   Random random; random.setSeed(-seed); double rand=random.RandU01();</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   fpslandmarks[0] = std::floor( N*rand );</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   // using FPS we want to find m landmarks where m = sqrt(nN)</a>
+<a name="76"><span class="lineNum">      76 </span>            :   // Now find distance to all other points</a>
+<a name="77"><span class="lineNum">      77 </span>            :   Matrix&lt;double&gt; distances( m, N );</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;N; ++i) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :     distances(0,i) = my_input_data-&gt;getDissimilarity( fpslandmarks[0], i );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   // Now find all other landmarks</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   for(unsigned i=1; i&lt;m; ++i) {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :     // Find point that has the largest minimum distance from the landmarks selected thus far</a>
+<a name="85"><span class="lineNum">      85 </span>            :     double maxd=0;</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;N; ++j) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :       double mind=distances(0,j);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :       for(unsigned k=1; k&lt;i; ++k) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :         if( distances(k,j)&lt;mind ) { mind=distances(k,j); }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :       }</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :       if( mind&gt;maxd ) { maxd=mind; fpslandmarks[i]=j; }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :     }</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     for(unsigned k=0; k&lt;N; ++k) distances(i,k) = my_input_data-&gt;getDissimilarity( fpslandmarks[i], k );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Initial FPS selection of m landmarks completed</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Now find voronoi weights of these m points</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; poly_assign( N );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; weights( m, 0 );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   voronoiAnalysis( fpslandmarks, weights, poly_assign );</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   //Calculate total weight of voronoi polyhedras</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   double vweight=0; for(unsigned i=0; i&lt;m; i++) vweight += std::exp( -weights[i] / gamma );</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   std::vector&lt;bool&gt; selected(N, false); unsigned ncount=0;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   while ( ncount&lt;n) {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : //  generate random number and check which point it belongs to. select only it was not selected before</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     double rand = vweight*random.RandU01();</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     double running_vweight=0;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     for(unsigned jpoly=0; jpoly&lt;m; ++jpoly) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :       running_vweight+=std::exp( -weights[jpoly] / gamma );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :       if( running_vweight&gt;=rand ) {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :         double tweight=0;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;poly_assign.size(); ++i) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :           if( poly_assign[i]==jpoly ) tweight += getWeight( i );</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :         }</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :         double rand_poly = tweight*random.RandU01();</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :         double running_tweight=0;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;N; ++i) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :           if( poly_assign[i]==jpoly ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :             running_tweight += getWeight( i );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :             if( running_tweight&gt;=rand_poly &amp;&amp; !selected[i] ) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :               selectFrame(i); selected[i]=true; ncount++; break;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :             } else if( running_tweight&gt;=rand_poly ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :               break;</a>
+<a name="126"><span class="lineNum">     126 </span>            :             }</a>
+<a name="127"><span class="lineNum">     127 </span>            :           }</a>
+<a name="128"><span class="lineNum">     128 </span>            :         }</a>
+<a name="129"><span class="lineNum">     129 </span>            :       }</a>
+<a name="130"><span class="lineNum">     130 </span>            :     }</a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/OutputColvarFile.cpp.func-sort-c.html b/coverage/analysis/OutputColvarFile.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7a14c31dd4
--- /dev/null
+++ b/coverage/analysis/OutputColvarFile.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/OutputColvarFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - OutputColvarFile.cpp<span style="font-size: 80%;"> (<a href="OutputColvarFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">97.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputColvarFile.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#68">_ZN4PLMD8analysis16OutputColvarFileC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#54">_ZNK4PLMD8analysis16OutputColvarFile11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_128OutputColvarFileRegisterMe606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#68">_ZN4PLMD8analysis16OutputColvarFileC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#60">_ZN4PLMD8analysis16OutputColvarFile16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#100">_ZN4PLMD8analysis16OutputColvarFile15performAnalysisEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_128OutputColvarFileRegisterMe60C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_128OutputColvarFileRegisterMe60D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/OutputColvarFile.cpp.func.html b/coverage/analysis/OutputColvarFile.cpp.func.html
new file mode 100644
index 0000000000..8e792fd914
--- /dev/null
+++ b/coverage/analysis/OutputColvarFile.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/OutputColvarFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - OutputColvarFile.cpp<span style="font-size: 80%;"> (<a href="OutputColvarFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">97.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputColvarFile.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_128OutputColvarFileRegisterMe606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_128OutputColvarFileRegisterMe60C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#58">_ZN4PLMD8analysis12_GLOBAL__N_128OutputColvarFileRegisterMe60D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#100">_ZN4PLMD8analysis16OutputColvarFile15performAnalysisEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#60">_ZN4PLMD8analysis16OutputColvarFile16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#68">_ZN4PLMD8analysis16OutputColvarFileC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#68">_ZN4PLMD8analysis16OutputColvarFileC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputColvarFile.cpp.gcov.html#54">_ZNK4PLMD8analysis16OutputColvarFile11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/OutputColvarFile.cpp.gcov.html b/coverage/analysis/OutputColvarFile.cpp.gcov.html
new file mode 100644
index 0000000000..b8103076f1
--- /dev/null
+++ b/coverage/analysis/OutputColvarFile.cpp.gcov.html
@@ -0,0 +1,202 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/OutputColvarFile.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - OutputColvarFile.cpp<span style="font-size: 80%;"> (source / <a href="OutputColvarFile.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">97.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;reference/ReferenceAtoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/ReferenceArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace analysis {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC ANALYSIS OUTPUT_ANALYSIS_DATA_TO_COLVAR</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : This can be used to output the data that has been stored in an Analysis object.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The most useful application of this method is to output all projections of all the</a>
+<a name="36"><span class="lineNum">      36 </span>            : points that were stored in an analysis object that performs some form of dimensionality</a>
+<a name="37"><span class="lineNum">      37 </span>            : reduction.  If you use the USE_DIMRED_DATA_FROM option below projections of all the</a>
+<a name="38"><span class="lineNum">      38 </span>            : stored points will be output to a file.  The positions of these projections will be calculated</a>
+<a name="39"><span class="lineNum">      39 </span>            : using that dimensionality reduction algorithms out-of-sample extension algorithm.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : */</a>
+<a name="44"><span class="lineNum">      44 </span>            : //+ENDPLUMEDOC</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : class OutputColvarFile : public AnalysisBase {</a>
+<a name="47"><span class="lineNum">      47 </span>            : private:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::string fmt;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::string filename;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   bool output_for_all_replicas;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;unsigned&gt; preps;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;std::string&gt; req_vals;</a>
+<a name="53"><span class="lineNum">      53 </span>            : public:</a>
+<a name="54"><span class="lineNum">      54 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="55"><span class="lineNum">      55 </span>            :   explicit OutputColvarFile( const ActionOptions&amp; );</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   void performAnalysis() override;</a>
+<a name="58"><span class="lineNum">      58 </span>            : };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      12544 : PLUMED_REGISTER_ACTION(OutputColvarFile,&quot;OUTPUT_ANALYSIS_DATA_TO_COLVAR&quot;)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         22 : void OutputColvarFile::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         22 :   AnalysisBase::registerKeywords( keys ); keys.use(&quot;ARG&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file to output to&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;REPLICA&quot;,&quot;0&quot;,&quot;the replicas for which you would like to output this information&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;0&quot;,&quot;the frequency with which to perform the required analysis and to output the data.  The default value of 0 tells plumed to use all the data&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format to output the data using&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         22 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         20 : OutputColvarFile::OutputColvarFile( const ActionOptions&amp; ao ):</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   Action(ao),</a>
+<a name="72"><span class="lineNum">      72 </span>            :   AnalysisBase(ao),</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         40 :   fmt(&quot;%f&quot;),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         20 :   output_for_all_replicas(false)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : {</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         60 :   parse(&quot;FILE&quot;,filename); parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         40 :   if( !getRestart() ) { OFile ofile; ofile.link(*this); ofile.setBackupString(&quot;analysis&quot;); ofile.backupAllFiles(filename); }</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         20 :   log.printf(&quot;  printing data to file named %s \n&quot;,filename.c_str() );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         20 :   if( getArguments().size()==0 ) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         12 :     std::vector&lt;std::string&gt; tmp_vals( my_input_data-&gt;getArgumentNames() );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         30 :     req_vals.resize( tmp_vals.size() ); for(unsigned i=0; i&lt;tmp_vals.size(); ++i) req_vals[i]=tmp_vals[i];</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         12 :   } else {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         32 :     req_vals.resize( getArguments().size() ); for(unsigned i=0; i&lt;req_vals.size(); ++i) req_vals[i]=getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         20 :   if( req_vals.size()==0 ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 :     log.printf(&quot;  outputting weights from input action \n&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   } else {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         14 :     log.printf(&quot;  outputting %s&quot;, req_vals[0].c_str() );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         22 :     for(unsigned i=1; i&lt;req_vals.size(); ++i) log.printf(&quot;,&quot;, req_vals[i].c_str() );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         14 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         40 :   std::string rep_data; parse(&quot;REPLICA&quot;,rep_data);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         20 :   if( rep_data==&quot;all&quot; ) output_for_all_replicas=true;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         20 :   else { preps.resize(1); Tools::convert( rep_data, preps[0] ); }</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         20 :   if( output_for_all_replicas ) log.printf(&quot;  outputting files for all replicas \n&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   else {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         20 :     log.printf(&quot;  outputting data for replicas &quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         40 :     for(unsigned i=0; i&lt;preps.size(); ++i) log.printf(&quot;%d &quot;, preps[i] );</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         20 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         24 : void OutputColvarFile::performAnalysis() {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         24 :   if( !output_for_all_replicas ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         24 :     bool found=false; unsigned myrep=plumed.multi_sim_comm.Get_rank();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         29 :     for(unsigned i=0; i&lt;preps.size(); ++i) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         24 :       if( myrep==preps[i] ) { found=true; break; }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     }</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         24 :     if( !found ) return;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Output the embedding as long lists of data</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         19 :   OFile gfile; gfile.link(*this);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         19 :   gfile.setBackupString(&quot;analysis&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         19 :   gfile.fmtField(fmt+&quot; &quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         19 :   gfile.open( filename );</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   // Print embedding coordinates</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       2599 :   for(unsigned i=0; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       2580 :     const DataCollectionObject&amp; mydata=getStoredData(i, false);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       6989 :     for(unsigned j=0; j&lt;req_vals.size(); ++j) gfile.printField( req_vals[j], mydata.getArgumentValue(req_vals[j]) );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       5160 :     gfile.printField( &quot;weight&quot;, getWeight(i) ); gfile.printField();</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         19 :   gfile.close();</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         19 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/OutputPDBFile.cpp.func-sort-c.html b/coverage/analysis/OutputPDBFile.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4e37746d53
--- /dev/null
+++ b/coverage/analysis/OutputPDBFile.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/OutputPDBFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - OutputPDBFile.cpp<span style="font-size: 80%;"> (<a href="OutputPDBFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputPDBFile.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#63">_ZN4PLMD8analysis13OutputPDBFileC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#50">_ZNK4PLMD8analysis13OutputPDBFile11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#54">_ZN4PLMD8analysis12_GLOBAL__N_125OutputPDBFileRegisterMe566createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#63">_ZN4PLMD8analysis13OutputPDBFileC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#81">_ZN4PLMD8analysis13OutputPDBFile15performAnalysisEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#56">_ZN4PLMD8analysis13OutputPDBFile16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#54">_ZN4PLMD8analysis12_GLOBAL__N_125OutputPDBFileRegisterMe56C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#54">_ZN4PLMD8analysis12_GLOBAL__N_125OutputPDBFileRegisterMe56D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/OutputPDBFile.cpp.func.html b/coverage/analysis/OutputPDBFile.cpp.func.html
new file mode 100644
index 0000000000..2eeccb5e7f
--- /dev/null
+++ b/coverage/analysis/OutputPDBFile.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/OutputPDBFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - OutputPDBFile.cpp<span style="font-size: 80%;"> (<a href="OutputPDBFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputPDBFile.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#54">_ZN4PLMD8analysis12_GLOBAL__N_125OutputPDBFileRegisterMe566createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#54">_ZN4PLMD8analysis12_GLOBAL__N_125OutputPDBFileRegisterMe56C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#54">_ZN4PLMD8analysis12_GLOBAL__N_125OutputPDBFileRegisterMe56D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#81">_ZN4PLMD8analysis13OutputPDBFile15performAnalysisEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#56">_ZN4PLMD8analysis13OutputPDBFile16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#63">_ZN4PLMD8analysis13OutputPDBFileC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#63">_ZN4PLMD8analysis13OutputPDBFileC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPDBFile.cpp.gcov.html#50">_ZNK4PLMD8analysis13OutputPDBFile11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/OutputPDBFile.cpp.gcov.html b/coverage/analysis/OutputPDBFile.cpp.gcov.html
new file mode 100644
index 0000000000..4d20c69b40
--- /dev/null
+++ b/coverage/analysis/OutputPDBFile.cpp.gcov.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/OutputPDBFile.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - OutputPDBFile.cpp<span style="font-size: 80%;"> (source / <a href="OutputPDBFile.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;reference/ReferenceAtoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/ReferenceArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace analysis {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC ANALYSIS OUTPUT_ANALYSIS_DATA_TO_PDB</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : This can be used to output the data that has been stored in an Analysis object.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : */</a>
+<a name="42"><span class="lineNum">      42 </span>            : //+ENDPLUMEDOC</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class OutputPDBFile : public AnalysisBase {</a>
+<a name="45"><span class="lineNum">      45 </span>            : private:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   PDB mypdb;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::string fmt;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::string filename;</a>
+<a name="49"><span class="lineNum">      49 </span>            : public:</a>
+<a name="50"><span class="lineNum">      50 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit OutputPDBFile( const ActionOptions&amp; );</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   void performAnalysis() override;</a>
+<a name="54"><span class="lineNum">      54 </span>            : };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(OutputPDBFile,&quot;OUTPUT_ANALYSIS_DATA_TO_PDB&quot;)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          8 : void OutputPDBFile::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          8 :   AnalysisBase::registerKeywords( keys );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file to output to&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format to use in the output file&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;0&quot;,&quot;the frequency with which to perform the required analysis and to output the data.  The default value of 0 tells plumed to use all the data&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          8 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          6 : OutputPDBFile::OutputPDBFile( const ActionOptions&amp; ao ):</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   Action(ao),</a>
+<a name="67"><span class="lineNum">      67 </span>            :   AnalysisBase(ao),</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          6 :   fmt(&quot;%f&quot;)</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : {</a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Get setup the pdb</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          6 :   mypdb.setAtomNumbers( my_input_data-&gt;getAtomIndexes() );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          6 :   mypdb.setArgumentNames( my_input_data-&gt;getArgumentNames() );</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   // Find a moldata object</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          6 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         12 :   if( ! moldat ) warning(&quot;PDB output files do not have atom types unless you use MOLDATA&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         18 :   parse(&quot;FILE&quot;,filename); parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         12 :   if( !getRestart() ) { OFile ofile; ofile.link(*this); ofile.setBackupString(&quot;analysis&quot;); ofile.backupAllFiles(filename); }</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          6 :   log.printf(&quot;  printing data to file named %s \n&quot;,filename.c_str() );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          6 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 : void OutputPDBFile::performAnalysis() {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   // Find a moldata object</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          8 :   auto* mymoldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   // Output the embedding in plumed pdb format</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         16 :   OFile afile; afile.link(*this); afile.setBackupString(&quot;analysis&quot;); std::size_t psign=fmt.find(&quot;%&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         16 :   afile.open( filename ); std::string descr=&quot;REMARK WEIGHT=%-&quot; + fmt.substr(psign+1) + &quot;\n&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        426 :   for(unsigned j=0; j&lt;getNumberOfDataPoints(); ++j) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        418 :     afile.printf(&quot;DESCRIPTION: analysis data from calculation done by %s at time %f \n&quot;,getLabel().c_str(),getTime() );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        836 :     if( dissimilaritiesWereSet() ) afile.printf(&quot;REMARK %s \n&quot;, getDissimilarityInstruction().c_str() );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        418 :     afile.printf(descr.c_str(),getWeight(j) ); getStoredData(j,false).transferDataToPDB( mypdb );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        418 :     if( plumed.getAtoms().usingNaturalUnits() ) mypdb.print( 1.0, mymoldat, afile, fmt );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         18 :     else mypdb.print( plumed.getAtoms().getUnits().getLength()/0.1, mymoldat, afile, fmt );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          8 :   afile.close();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          8 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/PrintDissimilarityMatrix.cpp.func-sort-c.html b/coverage/analysis/PrintDissimilarityMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..be5ba8854c
--- /dev/null
+++ b/coverage/analysis/PrintDissimilarityMatrix.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/PrintDissimilarityMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - PrintDissimilarityMatrix.cpp<span style="font-size: 80%;"> (<a href="PrintDissimilarityMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PrintDissimilarityMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#57">_ZN4PLMD8analysis24PrintDissimilarityMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#45">_ZNK4PLMD8analysis24PrintDissimilarityMatrix11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_136PrintDissimilarityMatrixRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#57">_ZN4PLMD8analysis24PrintDissimilarityMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#69">_ZN4PLMD8analysis24PrintDissimilarityMatrix15performAnalysisEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#50">_ZN4PLMD8analysis24PrintDissimilarityMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_136PrintDissimilarityMatrixRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_136PrintDissimilarityMatrixRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/PrintDissimilarityMatrix.cpp.func.html b/coverage/analysis/PrintDissimilarityMatrix.cpp.func.html
new file mode 100644
index 0000000000..b4a2e170fb
--- /dev/null
+++ b/coverage/analysis/PrintDissimilarityMatrix.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/PrintDissimilarityMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - PrintDissimilarityMatrix.cpp<span style="font-size: 80%;"> (<a href="PrintDissimilarityMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PrintDissimilarityMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_136PrintDissimilarityMatrixRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_136PrintDissimilarityMatrixRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#48">_ZN4PLMD8analysis12_GLOBAL__N_136PrintDissimilarityMatrixRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#69">_ZN4PLMD8analysis24PrintDissimilarityMatrix15performAnalysisEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#50">_ZN4PLMD8analysis24PrintDissimilarityMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#57">_ZN4PLMD8analysis24PrintDissimilarityMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#57">_ZN4PLMD8analysis24PrintDissimilarityMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PrintDissimilarityMatrix.cpp.gcov.html#45">_ZNK4PLMD8analysis24PrintDissimilarityMatrix11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/PrintDissimilarityMatrix.cpp.gcov.html b/coverage/analysis/PrintDissimilarityMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..a59e0f36e0
--- /dev/null
+++ b/coverage/analysis/PrintDissimilarityMatrix.cpp.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/PrintDissimilarityMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - PrintDissimilarityMatrix.cpp<span style="font-size: 80%;"> (source / <a href="PrintDissimilarityMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC ANALYSIS PRINT_DISSIMILARITY_MATRIX</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Print the matrix of dissimilarities between a trajectory of atomic configurations.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \par Examples</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : //+ENDPLUMEDOC</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace analysis {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class PrintDissimilarityMatrix : public AnalysisBase {</a>
+<a name="40"><span class="lineNum">      40 </span>            : private:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::string fmt;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   std::string fname;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit PrintDissimilarityMatrix( const ActionOptions&amp; ao );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void performAnalysis() override;</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(PrintDissimilarityMatrix,&quot;PRINT_DISSIMILARITY_MATRIX&quot;)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         10 : void PrintDissimilarityMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         10 :   AnalysisBase::registerKeywords( keys );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;name of file on which to output the data&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format to use for the output of numbers&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;0&quot;,&quot;the frequency with which to perform the required analysis and to output the data.  The default value of 0 tells plumed to use all the data&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         10 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          8 : PrintDissimilarityMatrix::PrintDissimilarityMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   Action(ao),</a>
+<a name="61"><span class="lineNum">      61 </span>            :   AnalysisBase(ao),</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          8 :   fmt(&quot;%f&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          8 :   if( !dissimilaritiesWereSet() ) error(&quot;dissimilarities have not been set in base classes&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         24 :   parse(&quot;FILE&quot;,fname); parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         16 :   if( !getRestart() ) { OFile ofile; ofile.link(*this); ofile.setBackupString(&quot;analysis&quot;); ofile.backupAllFiles(fname); }</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          8 :   log.printf(&quot;  printing to file named %s with formt %s \n&quot;,fname.c_str(), fmt.c_str() );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          8 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          9 : void PrintDissimilarityMatrix::performAnalysis() {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          9 :   std::string ofmt=&quot; &quot;+fmt;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         18 :   OFile ofile; ofile.setBackupString(&quot;analysis&quot;); ofile.open(fname);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         69 :   for(unsigned i=0; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        574 :     for(unsigned j=0; j&lt;getNumberOfDataPoints(); ++j) ofile.printf(ofmt.c_str(), sqrt( my_input_data-&gt;getDissimilarity( i,j ) ) );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         60 :     ofile.printf(&quot;\n&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   }</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          9 :   ofile.close();</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         18 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadAnalysisFrames.cpp.func-sort-c.html b/coverage/analysis/ReadAnalysisFrames.cpp.func-sort-c.html
new file mode 100644
index 0000000000..368ce1e4a0
--- /dev/null
+++ b/coverage/analysis/ReadAnalysisFrames.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadAnalysisFrames.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadAnalysisFrames.cpp<span style="font-size: 80%;"> (<a href="ReadAnalysisFrames.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReadAnalysisFrames.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#49">_ZN4PLMD8analysis18ReadAnalysisFramesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#99">_ZNK4PLMD8analysis18ReadAnalysisFrames27getDissimilarityInstructionB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#103">_ZNK4PLMD8analysis18ReadAnalysisFrames14getAtomIndexesEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#107">_ZN4PLMD8analysis18ReadAnalysisFrames16calculateWeightsEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#37">_ZN4PLMD8analysis12_GLOBAL__N_130ReadAnalysisFramesRegisterMe396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#49">_ZN4PLMD8analysis18ReadAnalysisFramesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#39">_ZN4PLMD8analysis18ReadAnalysisFrames16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#93">_ZN4PLMD8analysis18ReadAnalysisFrames15getArgumentListEv</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#37">_ZN4PLMD8analysis12_GLOBAL__N_130ReadAnalysisFramesRegisterMe39C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#37">_ZN4PLMD8analysis12_GLOBAL__N_130ReadAnalysisFramesRegisterMe39D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#128">_ZN4PLMD8analysis18ReadAnalysisFrames6updateEv</a></td>
+              <td class="coverFnHi">7500</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadAnalysisFrames.cpp.func.html b/coverage/analysis/ReadAnalysisFrames.cpp.func.html
new file mode 100644
index 0000000000..3faca5c91e
--- /dev/null
+++ b/coverage/analysis/ReadAnalysisFrames.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadAnalysisFrames.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadAnalysisFrames.cpp<span style="font-size: 80%;"> (<a href="ReadAnalysisFrames.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReadAnalysisFrames.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#37">_ZN4PLMD8analysis12_GLOBAL__N_130ReadAnalysisFramesRegisterMe396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#37">_ZN4PLMD8analysis12_GLOBAL__N_130ReadAnalysisFramesRegisterMe39C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#37">_ZN4PLMD8analysis12_GLOBAL__N_130ReadAnalysisFramesRegisterMe39D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#93">_ZN4PLMD8analysis18ReadAnalysisFrames15getArgumentListEv</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#107">_ZN4PLMD8analysis18ReadAnalysisFrames16calculateWeightsEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#39">_ZN4PLMD8analysis18ReadAnalysisFrames16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#128">_ZN4PLMD8analysis18ReadAnalysisFrames6updateEv</a></td>
+              <td class="coverFnHi">7500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#49">_ZN4PLMD8analysis18ReadAnalysisFramesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#49">_ZN4PLMD8analysis18ReadAnalysisFramesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#103">_ZNK4PLMD8analysis18ReadAnalysisFrames14getAtomIndexesEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.cpp.gcov.html#99">_ZNK4PLMD8analysis18ReadAnalysisFrames27getDissimilarityInstructionB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadAnalysisFrames.cpp.gcov.html b/coverage/analysis/ReadAnalysisFrames.cpp.gcov.html
new file mode 100644
index 0000000000..f964542386
--- /dev/null
+++ b/coverage/analysis/ReadAnalysisFrames.cpp.gcov.html
@@ -0,0 +1,232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadAnalysisFrames.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadAnalysisFrames.cpp<span style="font-size: 80%;"> (source / <a href="ReadAnalysisFrames.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReadAnalysisFrames.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC ANALYSIS COLLECT_FRAMES</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : This allows you to convert a trajectory and a dissimilarity matrix into a dissimilarity object</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : \par Examples</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : */</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+ENDPLUMEDOC</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace analysis {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">      12564 : PLUMED_REGISTER_ACTION(ReadAnalysisFrames,&quot;COLLECT_FRAMES&quot;)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         32 : void ReadAnalysisFrames::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         32 :   AnalysisBase::registerKeywords( keys );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         96 :   keys.remove(&quot;SERIAL&quot;); keys.remove(&quot;USE_OUTPUT_DATA_FROM&quot;); keys.use(&quot;ARG&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         64 :   keys.add(&quot;atoms-1&quot;,&quot;ATOMS&quot;,&quot;the atoms whose positions we are tracking for the purpose of analyzing the data&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         64 :   keys.add(&quot;atoms-1&quot;,&quot;STRIDE&quot;,&quot;the frequency with which data should be stored for analysis.  By default data is collected on every step&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;CLEAR&quot;,&quot;0&quot;,&quot;the frequency with which data should all be deleted and restarted&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         64 :   keys.add(&quot;optional&quot;,&quot;LOGWEIGHTS&quot;,&quot;list of actions that calculates log weights that should be used to weight configurations when calculating averages&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         32 :   ActionWithValue::useCustomisableComponents( keys );</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         32 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         30 : ReadAnalysisFrames::ReadAnalysisFrames( const ActionOptions&amp; ao ):</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   Action(ao),</a>
+<a name="53"><span class="lineNum">      53 </span>            :   AnalysisBase(ao),</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         30 :   clearonnextstep(false),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         30 :   wham_pointer(NULL),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         30 :   weights_calculated(false)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         30 :   parse(&quot;CLEAR&quot;,clearstride);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         30 :   if( clearstride!=0 ) log.printf(&quot;  clearing stored data every %u steps\n&quot;,clearstride);</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   // Get the names of the argumes</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         30 :   argument_names.resize( getNumberOfArguments() );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         64 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) argument_names[i]=getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   // Find the atom numbers to read in</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         60 :   parseAtomList(&quot;ATOMS&quot;,atom_numbers);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         30 :   if( atom_numbers.size()&gt;0 ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          5 :     log.printf(&quot;  monitoring positions of atoms &quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         79 :     for(unsigned i=0; i&lt;atom_numbers.size(); ++i) log.printf(&quot;%d &quot;,atom_numbers[i].serial() );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          5 :     log.printf(&quot;\n&quot;); requestAtoms(atom_numbers);</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   // Get stuff for any reweighting that should go on</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         60 :   std::vector&lt;std::string&gt; wwstr; parseVector(&quot;LOGWEIGHTS&quot;,wwstr);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         30 :   if( wwstr.size()&gt;0 ) log.printf(&quot;  reweighting using weights from &quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         30 :   std::vector&lt;Value*&gt; arg( ActionWithArguments::getArguments() );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;wwstr.size(); ++i) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         12 :     ActionWithValue* val = plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(wwstr[i]);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         12 :     if( !val ) error(&quot;could not find value named&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         12 :     weight_vals.push_back( val-&gt;copyOutput(val-&gt;getLabel()) );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         12 :     arg.push_back( val-&gt;copyOutput(val-&gt;getLabel()) );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         12 :     log.printf(&quot;%s &quot;,wwstr[i].c_str() );</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         30 :   if( wwstr.size()&gt;0 ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         12 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         12 :     wham_pointer = dynamic_cast&lt;bias::ReweightBase*&gt;( weight_vals[0]-&gt;getPntrToAction() );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         12 :     if( !wham_pointer ) wham_pointer = NULL;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         12 :     else if( !wham_pointer-&gt;buildsWeightStore() ) wham_pointer = NULL;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         12 :     if( wham_pointer &amp;&amp; weight_vals.size()!=1 ) error(&quot;can only extract weights from one wham object&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         18 :   } else log.printf(&quot;  weights are all equal to one\n&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         30 :   requestArguments( arg );</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   // Now add fake components to the underlying ActionWithValue for the arguments</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         64 :   for(unsigned i=0; i&lt;argument_names.size(); ++i) { addComponent( argument_names[i] ); componentIsNotPeriodic( argument_names[i] ); }</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         30 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         62 : std::vector&lt;Value*&gt; ReadAnalysisFrames::getArgumentList() {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         62 :   std::vector&lt;Value*&gt; arg_vals( ActionWithArguments::getArguments() );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         68 :   for(unsigned i=0; i&lt;weight_vals.size(); ++i) arg_vals.erase(arg_vals.end()-1);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         62 :   return arg_vals;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          5 : std::string ReadAnalysisFrames::getDissimilarityInstruction() const {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          5 :   return &quot;TYPE=UNKNOWN&quot;;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         12 : const std::vector&lt;AtomNumber&gt;&amp; ReadAnalysisFrames::getAtomIndexes() const {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :   return getAbsoluteIndexes();</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         26 : void ReadAnalysisFrames::calculateWeights() {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         26 :   weights_calculated=true;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         26 :   weights.resize( logweights.size() );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         26 :   if( weight_vals.empty() ) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       3261 :     for(unsigned i=0; i&lt;logweights.size(); ++i) weights[i]=1.0;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   } else {</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          7 :     if( wham_pointer ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          7 :       wham_pointer-&gt;calculateWeights( logweights.size() );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       2464 :       for(unsigned i=0; i&lt;logweights.size(); ++i) weights[i]=wham_pointer-&gt;getWeight(i);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :     } else {</a>
+<a name="119"><span class="lineNum">     119 </span>            :       // Find the maximum weight</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       double maxweight=logweights[0];</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       for(unsigned i=1; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :         if(logweights[i]&gt;maxweight) maxweight=logweights[i];</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :       }</a>
+<a name="124"><span class="lineNum">     124 </span>            :       // Calculate weights (no memory) -- business here with maxweight is to prevent overflows</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;logweights.size(); ++i) weights[i]=std::exp( logweights[i]-maxweight );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     }</a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         26 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       7500 : void ReadAnalysisFrames::update() {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       7500 :   if( getStep()==0 ) return;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // Delete everything we stored now that it has been analyzed</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       7472 :   if( clearonnextstep ) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          5 :     my_data_stash.clear(); my_data_stash.resize(0);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         10 :     logweights.clear(); logweights.resize(0);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          5 :     if( wham_pointer ) wham_pointer-&gt;clearData();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          5 :     clearonnextstep=false;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   // Get the weight and store it in the weights array</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      11684 :   double ww=0; for(unsigned i=0; i&lt;weight_vals.size(); ++i) ww+=weight_vals[i]-&gt;get();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       7472 :   weights_calculated=false; logweights.push_back(ww);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   // Now create the data collection object and push it back to be stored</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       7472 :   unsigned index = my_data_stash.size(); my_data_stash.push_back( DataCollectionObject() );</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       7472 :   my_data_stash[index].setAtomNumbersAndArgumentNames( getLabel(), atom_numbers, argument_names );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       7472 :   my_data_stash[index].setAtomPositions( getPositions() );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      16079 :   for(unsigned i=0; i&lt;argument_names.size(); ++i) my_data_stash[index].setArgument( argument_names[i], getArgument(i) );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       7472 :   if( clearstride&gt;0 ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        475 :     if( getStep()%clearstride==0 ) clearonnextstep=true;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadAnalysisFrames.h.func-sort-c.html b/coverage/analysis/ReadAnalysisFrames.h.func-sort-c.html
new file mode 100644
index 0000000000..4b2e8e9aca
--- /dev/null
+++ b/coverage/analysis/ReadAnalysisFrames.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadAnalysisFrames.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadAnalysisFrames.h<span style="font-size: 80%;"> (<a href="ReadAnalysisFrames.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReadAnalysisFrames.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#54">_ZN4PLMD8analysis18ReadAnalysisFrames15performAnalysisEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#56">_ZNK4PLMD8analysis18ReadAnalysisFrames11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#86">_ZNK4PLMD8analysis18ReadAnalysisFrames22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#76">_ZNK4PLMD8analysis18ReadAnalysisFrames21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">37013</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#81">_ZNK4PLMD8analysis18ReadAnalysisFrames23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnHi">125002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#97">_ZN4PLMD8analysis18ReadAnalysisFrames13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">522672</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#91">_ZN4PLMD8analysis18ReadAnalysisFrames9getWeightERKj</a></td>
+              <td class="coverFnHi">7777606</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadAnalysisFrames.h.func.html b/coverage/analysis/ReadAnalysisFrames.h.func.html
new file mode 100644
index 0000000000..efdec423fc
--- /dev/null
+++ b/coverage/analysis/ReadAnalysisFrames.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadAnalysisFrames.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadAnalysisFrames.h<span style="font-size: 80%;"> (<a href="ReadAnalysisFrames.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReadAnalysisFrames.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#97">_ZN4PLMD8analysis18ReadAnalysisFrames13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">522672</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#54">_ZN4PLMD8analysis18ReadAnalysisFrames15performAnalysisEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#91">_ZN4PLMD8analysis18ReadAnalysisFrames9getWeightERKj</a></td>
+              <td class="coverFnHi">7777606</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#56">_ZNK4PLMD8analysis18ReadAnalysisFrames11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#76">_ZNK4PLMD8analysis18ReadAnalysisFrames21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">37013</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#86">_ZNK4PLMD8analysis18ReadAnalysisFrames22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadAnalysisFrames.h.gcov.html#81">_ZNK4PLMD8analysis18ReadAnalysisFrames23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnHi">125002</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadAnalysisFrames.h.gcov.html b/coverage/analysis/ReadAnalysisFrames.h.gcov.html
new file mode 100644
index 0000000000..0846d340de
--- /dev/null
+++ b/coverage/analysis/ReadAnalysisFrames.h.gcov.html
@@ -0,0 +1,182 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadAnalysisFrames.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadAnalysisFrames.h<span style="font-size: 80%;"> (source / <a href="ReadAnalysisFrames.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_analysis_ReadAnalysisFrames_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_analysis_ReadAnalysisFrames_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;bias/ReweightBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace analysis {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class ReadAnalysisFrames : public AnalysisBase {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// The frequency with which to clear the data stash</a>
+<a name="34"><span class="lineNum">      34 </span>            :   unsigned clearstride;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   bool clearonnextstep;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// The list of argument names that we are storing</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;std::string&gt; argument_names;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// The list of atom numbers that we are storing</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;AtomNumber&gt; atom_numbers;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// The biases we are using in reweighting and the args we store them separately</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::vector&lt;Value*&gt; weight_vals;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// The object that calculates weights using WHAM</a>
+<a name="43"><span class="lineNum">      43 </span>            :   bias::ReweightBase* wham_pointer;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// The weights of all the data points</a>
+<a name="45"><span class="lineNum">      45 </span>            :   bool weights_calculated;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::vector&lt;double&gt; logweights, weights;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// The data that has been collected from the trajectory</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::vector&lt;DataCollectionObject&gt; my_data_stash;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Calculate the weights of the various points from the logweights</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void calculateWeights();</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit ReadAnalysisFrames( const ActionOptions&amp; ao );</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void update() override;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// This does nothing</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   void performAnalysis() override {}</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : /// This does nothing - it just ensures the final class is not abstract</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Get the number of data points</a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned getNumberOfDataPoints() const override;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Get the index of the data point</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned getDataPointIndexInBase( const unsigned&amp; idata ) const override;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Get the input arguments</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;Value*&gt; getArgumentList() override;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Have dissimilarities between thses objects been calculated</a>
+<a name="66"><span class="lineNum">      66 </span>            :   bool dissimilaritiesWereSet() const override;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// How are dissimilarities calcualted is not known</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::string getDissimilarityInstruction() const override;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Get the weight of one of the objects</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double getWeight( const unsigned&amp; idat ) override;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Get the reference configuration</a>
+<a name="72"><span class="lineNum">      72 </span>            :   DataCollectionObject &amp; getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Get the list of atoms that are being stored</a>
+<a name="74"><span class="lineNum">      74 </span>            :   const std::vector&lt;AtomNumber&gt;&amp; getAtomIndexes() const override;</a>
+<a name="75"><span class="lineNum">      75 </span>            : };</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : inline</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      37013 : unsigned ReadAnalysisFrames::getNumberOfDataPoints() const {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      37013 :   return my_data_stash.size();</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : inline</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     125002 : unsigned ReadAnalysisFrames::getDataPointIndexInBase( const unsigned&amp; idata ) const {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">     125002 :   return idata;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : inline</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 : bool ReadAnalysisFrames::dissimilaritiesWereSet() const {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : inline</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    7777606 : double ReadAnalysisFrames::getWeight( const unsigned&amp; idat ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    7777606 :   if( !weights_calculated ) calculateWeights();</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    7777606 :   return weights[idat];</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : inline</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     522672 : DataCollectionObject &amp; ReadAnalysisFrames::getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) {</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   plumed_dbg_assert( idata&lt;my_data_stash.size() );</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     522672 :   return my_data_stash[idata];</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadDissimilarityMatrix.cpp.func-sort-c.html b/coverage/analysis/ReadDissimilarityMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f8357319f6
--- /dev/null
+++ b/coverage/analysis/ReadDissimilarityMatrix.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadDissimilarityMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadDissimilarityMatrix.cpp<span style="font-size: 80%;"> (<a href="ReadDissimilarityMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryMed">82.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReadDissimilarityMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#69">_ZN4PLMD8analysis23ReadDissimilarityMatrix15performAnalysisEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#83">_ZN4PLMD8analysis23ReadDissimilarityMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#71">_ZNK4PLMD8analysis23ReadDissimilarityMatrix11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#144">_ZNK4PLMD8analysis23ReadDissimilarityMatrix23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#74">_ZN4PLMD8analysis12_GLOBAL__N_135ReadDissimilarityMatrixRegisterMe766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#103">_ZN4PLMD8analysis23ReadDissimilarityMatrix12runFinalJobsEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#83">_ZN4PLMD8analysis23ReadDissimilarityMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#76">_ZN4PLMD8analysis23ReadDissimilarityMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#152">_ZN4PLMD8analysis23ReadDissimilarityMatrix13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#101">_ZN4PLMD8analysis23ReadDissimilarityMatrix6updateEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#59">_ZNK4PLMD8analysis23ReadDissimilarityMatrix22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#158">_ZN4PLMD8analysis23ReadDissimilarityMatrix9getWeightERKj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#139">_ZNK4PLMD8analysis23ReadDissimilarityMatrix21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">257</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#148">_ZN4PLMD8analysis23ReadDissimilarityMatrix16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">334</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#74">_ZN4PLMD8analysis12_GLOBAL__N_135ReadDissimilarityMatrixRegisterMe76C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#74">_ZN4PLMD8analysis12_GLOBAL__N_135ReadDissimilarityMatrixRegisterMe76D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadDissimilarityMatrix.cpp.func.html b/coverage/analysis/ReadDissimilarityMatrix.cpp.func.html
new file mode 100644
index 0000000000..6f049b42e0
--- /dev/null
+++ b/coverage/analysis/ReadDissimilarityMatrix.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadDissimilarityMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadDissimilarityMatrix.cpp<span style="font-size: 80%;"> (<a href="ReadDissimilarityMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryMed">82.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReadDissimilarityMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#74">_ZN4PLMD8analysis12_GLOBAL__N_135ReadDissimilarityMatrixRegisterMe766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#74">_ZN4PLMD8analysis12_GLOBAL__N_135ReadDissimilarityMatrixRegisterMe76C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#74">_ZN4PLMD8analysis12_GLOBAL__N_135ReadDissimilarityMatrixRegisterMe76D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#103">_ZN4PLMD8analysis23ReadDissimilarityMatrix12runFinalJobsEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#152">_ZN4PLMD8analysis23ReadDissimilarityMatrix13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#69">_ZN4PLMD8analysis23ReadDissimilarityMatrix15performAnalysisEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#148">_ZN4PLMD8analysis23ReadDissimilarityMatrix16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">334</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#76">_ZN4PLMD8analysis23ReadDissimilarityMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#101">_ZN4PLMD8analysis23ReadDissimilarityMatrix6updateEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#158">_ZN4PLMD8analysis23ReadDissimilarityMatrix9getWeightERKj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#83">_ZN4PLMD8analysis23ReadDissimilarityMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#83">_ZN4PLMD8analysis23ReadDissimilarityMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#71">_ZNK4PLMD8analysis23ReadDissimilarityMatrix11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#139">_ZNK4PLMD8analysis23ReadDissimilarityMatrix21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">257</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#59">_ZNK4PLMD8analysis23ReadDissimilarityMatrix22dissimilaritiesWereSetEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReadDissimilarityMatrix.cpp.gcov.html#144">_ZNK4PLMD8analysis23ReadDissimilarityMatrix23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReadDissimilarityMatrix.cpp.gcov.html b/coverage/analysis/ReadDissimilarityMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..69a6dae486
--- /dev/null
+++ b/coverage/analysis/ReadDissimilarityMatrix.cpp.gcov.html
@@ -0,0 +1,241 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReadDissimilarityMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReadDissimilarityMatrix.cpp<span style="font-size: 80%;"> (source / <a href="ReadDissimilarityMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryMed">82.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ReadAnalysisFrames.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionSetup.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC ANALYSIS READ_DISSIMILARITY_MATRIX</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Read a matrix of dissimilarities between a trajectory of atomic configurations from a file.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : //+ENDPLUMEDOC</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace analysis {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class ReadDissimilarityMatrix : public AnalysisBase {</a>
+<a name="45"><span class="lineNum">      45 </span>            : private:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   unsigned nnodes;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;DataCollectionObject&gt; fake_data;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::string fname, wfile;</a>
+<a name="49"><span class="lineNum">      49 </span>            : //  Matrix&lt;double&gt; dissimilarities;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; dissimilarities;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;double&gt; weights;</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="54"><span class="lineNum">      54 </span>            :   explicit ReadDissimilarityMatrix( const ActionOptions&amp; ao );</a>
+<a name="55"><span class="lineNum">      55 </span>            :   unsigned getNumberOfDataPoints() const override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : // Return the index of the data point in the base class</a>
+<a name="57"><span class="lineNum">      57 </span>            :   unsigned getDataPointIndexInBase( const unsigned&amp; idata ) const override;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// This gives an error as if we read in the matrix we dont have the coordinates</a>
+<a name="59"><span class="lineNum">      59 </span>            :   DataCollectionObject&amp; getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) override;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Tell everyone we have dissimilarities</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         11 :   bool dissimilaritiesWereSet() const override { return true; }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Get the dissimilarity between two data points</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double getDissimilarity( const unsigned&amp;, const unsigned&amp; ) override;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Get the weight from the input file</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double getWeight( const unsigned&amp; idata ) override;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Just tell plumed to stop</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void update() override;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Read in the dissimilarity matrix</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void runFinalJobs() override;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// This does nothing</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   void performAnalysis() override {};</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Overwrite virtual function in base class</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ReadDissimilarityMatrix,&quot;READ_DISSIMILARITY_MATRIX&quot;)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 : void ReadDissimilarityMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          4 :   AnalysisBase::registerKeywords( keys );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;an input file containing the matrix of dissimilarities&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;WFILE&quot;,&quot;input file containing weights of points&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :   keys.reset_style(&quot;USE_OUTPUT_DATA_FROM&quot;,&quot;optional&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 : ReadDissimilarityMatrix::ReadDissimilarityMatrix( const ActionOptions&amp; ao ):</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   Action(ao),</a>
+<a name="87"><span class="lineNum">      87 </span>            :   AnalysisBase(ao),</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :   nnodes(1)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          2 :   setStride(1); // Set the stride equal to one to ensure we don't get stuck in an infinite loop</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   std::vector&lt;ActionSetup*&gt; setupActions=plumed.getActionSet().select&lt;ActionSetup*&gt;();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 :   if( my_input_data &amp;&amp; (plumed.getActionSet().size()-setupActions.size())!=1 ) error(&quot;should only be this action and the READ_ANALYSIS_FRAMES command in the input file&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   if( !my_input_data &amp;&amp; plumed.getActionSet().size()!=0 ) error(&quot;read dissimilarity matrix command must be at top of input file&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   parse(&quot;FILE&quot;,fname);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   log.printf(&quot;  reading dissimilarity matrix from file %s \n&quot;,fname.c_str() );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          4 :   parse(&quot;WFILE&quot;,wfile);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   if( wfile.length()&gt;0 ) log.printf(&quot;  reading weights of nodes from file named %s \n&quot;,wfile.c_str() );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   else log.printf(&quot;  setting weights of all nodes equal to one\n&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          2 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          7 : void ReadDissimilarityMatrix::update() { if(!my_input_data) plumed.stop(); }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 : void ReadDissimilarityMatrix::runFinalJobs() {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   IFile mfile; mfile.open(fname);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   // Read in first line</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 :   std::vector&lt;std::string&gt; words; nnodes=0;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   while( nnodes==0 ) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :     Tools::getParsedLine( mfile, words );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :     nnodes=words.size();</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :   std::vector&lt;double&gt; tmpdis( nnodes );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         20 :   for(unsigned j=0; j&lt;nnodes; ++j) Tools::convert( words[j], tmpdis[j] );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          2 :   dissimilarities.push_back( tmpdis );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         18 :   while( Tools::getParsedLine( mfile, words ) ) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         16 :     if( words.size()!=nnodes ) error(&quot;bad formatting in matrix file&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        192 :     for(unsigned j=0; j&lt;nnodes; ++j) Tools::convert( words[j], tmpdis[j] );</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         16 :     dissimilarities.push_back( tmpdis );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :   mfile.close();</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :   if( my_input_data &amp;&amp; dissimilarities.size()!=getNumberOfDataPoints() ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     error(&quot;mismatch between number of data points in trajectory and the dimensions of the dissimilarity matrix&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :   if( !my_input_data ) fake_data.resize( dissimilarities.size() );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :   weights.resize( dissimilarities.size() );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   if( wfile.length()&gt;0 ) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     IFile wfilef; wfilef.open(wfile);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;weights.size(); ++i) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :       Tools::getParsedLine( wfilef, words ); Tools::convert( words[0], weights[i] );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     }</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     wfilef.close();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :   } else {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :     weights.assign(weights.size(),1.0);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        257 : unsigned ReadDissimilarityMatrix::getNumberOfDataPoints() const {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        302 :   if( my_input_data ) return AnalysisBase::getNumberOfDataPoints();</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        212 :   return dissimilarities.size();</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 : unsigned ReadDissimilarityMatrix::getDataPointIndexInBase( const unsigned&amp; idata ) const {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   return idata;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        334 : double ReadDissimilarityMatrix::getDissimilarity( const unsigned&amp; iframe, const unsigned&amp; jframe ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        334 :   return dissimilarities[iframe][jframe]*dissimilarities[iframe][jframe];</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          5 : DataCollectionObject&amp; ReadDissimilarityMatrix::getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          5 :   plumed_massert( !calcdist, &quot;cannot calc dist as this data was read in from input&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         10 :   if( my_input_data ) return AnalysisBase::getStoredData( idata, calcdist );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   return fake_data[idata];</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         18 : double ReadDissimilarityMatrix::getWeight( const unsigned&amp; idata ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         18 :   plumed_assert( idata&lt;dissimilarities.size() ); return weights[idata];</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReselectLandmarks.cpp.func-sort-c.html b/coverage/analysis/ReselectLandmarks.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1ba937c312
--- /dev/null
+++ b/coverage/analysis/ReselectLandmarks.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReselectLandmarks.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReselectLandmarks.cpp<span style="font-size: 80%;"> (<a href="ReselectLandmarks.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReselectLandmarks.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#55">_ZN4PLMD8analysis17ReselectLandmarksC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#47">_ZN4PLMD8analysis12_GLOBAL__N_129ReselectLandmarksRegisterMe496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#67">_ZN4PLMD8analysis17ReselectLandmarks15selectLandmarksEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#55">_ZN4PLMD8analysis17ReselectLandmarksC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#49">_ZN4PLMD8analysis17ReselectLandmarks16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#47">_ZN4PLMD8analysis12_GLOBAL__N_129ReselectLandmarksRegisterMe49C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#47">_ZN4PLMD8analysis12_GLOBAL__N_129ReselectLandmarksRegisterMe49D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReselectLandmarks.cpp.func.html b/coverage/analysis/ReselectLandmarks.cpp.func.html
new file mode 100644
index 0000000000..5e0d28d306
--- /dev/null
+++ b/coverage/analysis/ReselectLandmarks.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReselectLandmarks.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReselectLandmarks.cpp<span style="font-size: 80%;"> (<a href="ReselectLandmarks.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReselectLandmarks.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#47">_ZN4PLMD8analysis12_GLOBAL__N_129ReselectLandmarksRegisterMe496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#47">_ZN4PLMD8analysis12_GLOBAL__N_129ReselectLandmarksRegisterMe49C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#47">_ZN4PLMD8analysis12_GLOBAL__N_129ReselectLandmarksRegisterMe49D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#67">_ZN4PLMD8analysis17ReselectLandmarks15selectLandmarksEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#49">_ZN4PLMD8analysis17ReselectLandmarks16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#55">_ZN4PLMD8analysis17ReselectLandmarksC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReselectLandmarks.cpp.gcov.html#55">_ZN4PLMD8analysis17ReselectLandmarksC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/ReselectLandmarks.cpp.gcov.html b/coverage/analysis/ReselectLandmarks.cpp.gcov.html
new file mode 100644
index 0000000000..4d9cf48b0c
--- /dev/null
+++ b/coverage/analysis/ReselectLandmarks.cpp.gcov.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/ReselectLandmarks.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - ReselectLandmarks.cpp<span style="font-size: 80%;"> (source / <a href="ReselectLandmarks.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LandmarkSelectionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC LANDMARKS RESELECT_LANDMARKS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This allows us to use one measure in landmark selection and a different measure in dimensionality reduction</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : */</a>
+<a name="35"><span class="lineNum">      35 </span>            : //+ENDPLUMEDOC</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace analysis {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class ReselectLandmarks : public LandmarkSelectionBase {</a>
+<a name="41"><span class="lineNum">      41 </span>            : private:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   LandmarkSelectionBase* mylandmarks;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit ReselectLandmarks( const ActionOptions&amp; ao );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void selectLandmarks() override;</a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(ReselectLandmarks,&quot;RESELECT_LANDMARKS&quot;)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          3 : void ReselectLandmarks::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          3 :   LandmarkSelectionBase::registerKeywords(keys);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          3 :   keys.remove(&quot;NLANDMARKS&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;LANDMARKS&quot;,&quot;the action that selects the landmarks that you want to reselect using this action&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          3 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          1 : ReselectLandmarks::ReselectLandmarks( const ActionOptions&amp; ao ):</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   Action(ao),</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          1 :   LandmarkSelectionBase(ao)</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          1 :   std::string datastr; parse(&quot;LANDMARKS&quot;,datastr);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :   mylandmarks = plumed.getActionSet().selectWithLabel&lt;LandmarkSelectionBase*&gt;( datastr );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          1 :   if( !mylandmarks ) error(&quot;input to LANDMARKS is not a landmark selection action&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          1 :   nlandmarks = mylandmarks-&gt;nlandmarks;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          1 :   if( (mylandmarks-&gt;my_input_data)-&gt;getNumberOfDataPoints()!=my_input_data-&gt;getNumberOfDataPoints() ) error(&quot;mismatch between amount of landmark class and base class&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          1 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          1 : void ReselectLandmarks::selectLandmarks() {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;mylandmarks-&gt;getNumberOfDataPoints(); ++i) selectFrame( mylandmarks-&gt;getDataPointIndexInBase(i) );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/SelectRandomFrames.cpp.func-sort-c.html b/coverage/analysis/SelectRandomFrames.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0821bde752
--- /dev/null
+++ b/coverage/analysis/SelectRandomFrames.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/SelectRandomFrames.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - SelectRandomFrames.cpp<span style="font-size: 80%;"> (<a href="SelectRandomFrames.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SelectRandomFrames.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_130SelectRandomFramesRegisterMe476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#59">_ZN4PLMD8analysis18SelectRandomFrames15selectLandmarksEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#52">_ZN4PLMD8analysis18SelectRandomFramesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#52">_ZN4PLMD8analysis18SelectRandomFramesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#47">_ZN4PLMD8analysis18SelectRandomFrames16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_130SelectRandomFramesRegisterMe47C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_130SelectRandomFramesRegisterMe47D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/SelectRandomFrames.cpp.func.html b/coverage/analysis/SelectRandomFrames.cpp.func.html
new file mode 100644
index 0000000000..3c3098bf8c
--- /dev/null
+++ b/coverage/analysis/SelectRandomFrames.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/SelectRandomFrames.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - SelectRandomFrames.cpp<span style="font-size: 80%;"> (<a href="SelectRandomFrames.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SelectRandomFrames.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_130SelectRandomFramesRegisterMe476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_130SelectRandomFramesRegisterMe47C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#45">_ZN4PLMD8analysis12_GLOBAL__N_130SelectRandomFramesRegisterMe47D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#59">_ZN4PLMD8analysis18SelectRandomFrames15selectLandmarksEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#47">_ZN4PLMD8analysis18SelectRandomFrames16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#52">_ZN4PLMD8analysis18SelectRandomFramesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectRandomFrames.cpp.gcov.html#52">_ZN4PLMD8analysis18SelectRandomFramesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/SelectRandomFrames.cpp.gcov.html b/coverage/analysis/SelectRandomFrames.cpp.gcov.html
new file mode 100644
index 0000000000..3e1da0bcda
--- /dev/null
+++ b/coverage/analysis/SelectRandomFrames.cpp.gcov.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/SelectRandomFrames.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - SelectRandomFrames.cpp<span style="font-size: 80%;"> (source / <a href="SelectRandomFrames.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LandmarkSelectionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC LANDMARKS LANDMARK_SELECT_RANDOM</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Select a random set of landmarks from a large set of configurations.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \par Examples</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : //+ENDPLUMEDOC</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace analysis {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class SelectRandomFrames : public LandmarkSelectionBase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   unsigned seed;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit SelectRandomFrames( const ActionOptions&amp; ao );</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void selectLandmarks() override;</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(SelectRandomFrames,&quot;LANDMARK_SELECT_RANDOM&quot;)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          2 : void SelectRandomFrames::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 :   LandmarkSelectionBase::registerKeywords(keys);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;SEED&quot;,&quot;1234&quot;,&quot;a random number seed&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          2 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 : SelectRandomFrames::SelectRandomFrames( const ActionOptions&amp; ao ):</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   Action(ao),</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   LandmarkSelectionBase(ao)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :   parse(&quot;SEED&quot;,seed);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 : void SelectRandomFrames::selectLandmarks() {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   Random r; r.setSeed(-seed);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   unsigned nframe=my_input_data-&gt;getNumberOfDataPoints();</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   unsigned nland=getNumberOfDataPoints();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   std::vector&lt;bool&gt; selected( nframe, false );</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   unsigned fcount=0;</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   while (fcount&lt;nland) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     unsigned iframe = std::floor( r.U01()*nframe );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :     if (!selected[iframe]) {</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :       selected[iframe]=true;</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :       selectFrame( iframe );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :       ++fcount;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     }</a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/SelectWithStride.cpp.func-sort-c.html b/coverage/analysis/SelectWithStride.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5a22f74d6a
--- /dev/null
+++ b/coverage/analysis/SelectWithStride.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/SelectWithStride.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - SelectWithStride.cpp<span style="font-size: 80%;"> (<a href="SelectWithStride.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SelectWithStride.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#48">_ZN4PLMD8analysis16SelectWithStrideC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#42">_ZN4PLMD8analysis12_GLOBAL__N_128SelectWithStrideRegisterMe446createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#48">_ZN4PLMD8analysis16SelectWithStrideC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#54">_ZN4PLMD8analysis16SelectWithStride15selectLandmarksEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#44">_ZN4PLMD8analysis16SelectWithStride16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#42">_ZN4PLMD8analysis12_GLOBAL__N_128SelectWithStrideRegisterMe44C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#42">_ZN4PLMD8analysis12_GLOBAL__N_128SelectWithStrideRegisterMe44D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/SelectWithStride.cpp.func.html b/coverage/analysis/SelectWithStride.cpp.func.html
new file mode 100644
index 0000000000..66d9db88b7
--- /dev/null
+++ b/coverage/analysis/SelectWithStride.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/SelectWithStride.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - SelectWithStride.cpp<span style="font-size: 80%;"> (<a href="SelectWithStride.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SelectWithStride.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#42">_ZN4PLMD8analysis12_GLOBAL__N_128SelectWithStrideRegisterMe446createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#42">_ZN4PLMD8analysis12_GLOBAL__N_128SelectWithStrideRegisterMe44C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#42">_ZN4PLMD8analysis12_GLOBAL__N_128SelectWithStrideRegisterMe44D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#54">_ZN4PLMD8analysis16SelectWithStride15selectLandmarksEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#44">_ZN4PLMD8analysis16SelectWithStride16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#48">_ZN4PLMD8analysis16SelectWithStrideC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SelectWithStride.cpp.gcov.html#48">_ZN4PLMD8analysis16SelectWithStrideC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/SelectWithStride.cpp.gcov.html b/coverage/analysis/SelectWithStride.cpp.gcov.html
new file mode 100644
index 0000000000..5bda920ae3
--- /dev/null
+++ b/coverage/analysis/SelectWithStride.cpp.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/SelectWithStride.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - SelectWithStride.cpp<span style="font-size: 80%;"> (source / <a href="SelectWithStride.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LandmarkSelectionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC LANDMARKS LANDMARK_SELECT_STRIDE</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Select every kth landmark from the trajectory.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : \par Examples</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : */</a>
+<a name="32"><span class="lineNum">      32 </span>            : //+ENDPLUMEDOC</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace analysis {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class SelectWithStride : public LandmarkSelectionBase {</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit SelectWithStride( const ActionOptions&amp; ao );</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void selectLandmarks() override;</a>
+<a name="42"><span class="lineNum">      42 </span>            : };</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(SelectWithStride,&quot;LANDMARK_SELECT_STRIDE&quot;)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         10 : void SelectWithStride::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         10 :   LandmarkSelectionBase::registerKeywords( keys );</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         10 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          8 : SelectWithStride::SelectWithStride( const ActionOptions&amp; ao ):</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   Action(ao),</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          8 :   LandmarkSelectionBase(ao)</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          8 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         10 : void SelectWithStride::selectLandmarks() {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         10 :   unsigned stride = std::floor( my_input_data-&gt;getNumberOfDataPoints() / getNumberOfDataPoints() ), max=stride*getNumberOfDataPoints();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        296 :   for(unsigned i=0; i&lt;max; i+=stride) selectFrame( i );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         10 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/WhamHistogram.cpp.func-sort-c.html b/coverage/analysis/WhamHistogram.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e0777acb16
--- /dev/null
+++ b/coverage/analysis/WhamHistogram.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/WhamHistogram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - WhamHistogram.cpp<span style="font-size: 80%;"> (<a href="WhamHistogram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WhamHistogram.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#94">_ZN4PLMD8analysis13WhamHistogramC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#79">_ZN4PLMD8analysis12_GLOBAL__N_125WhamHistogramRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#94">_ZN4PLMD8analysis13WhamHistogramC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#81">_ZN4PLMD8analysis13WhamHistogram16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#79">_ZN4PLMD8analysis12_GLOBAL__N_125WhamHistogramRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#79">_ZN4PLMD8analysis12_GLOBAL__N_125WhamHistogramRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/WhamHistogram.cpp.func.html b/coverage/analysis/WhamHistogram.cpp.func.html
new file mode 100644
index 0000000000..6914b5d1fc
--- /dev/null
+++ b/coverage/analysis/WhamHistogram.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/WhamHistogram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - WhamHistogram.cpp<span style="font-size: 80%;"> (<a href="WhamHistogram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WhamHistogram.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#79">_ZN4PLMD8analysis12_GLOBAL__N_125WhamHistogramRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#79">_ZN4PLMD8analysis12_GLOBAL__N_125WhamHistogramRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#79">_ZN4PLMD8analysis12_GLOBAL__N_125WhamHistogramRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#81">_ZN4PLMD8analysis13WhamHistogram16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#94">_ZN4PLMD8analysis13WhamHistogramC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamHistogram.cpp.gcov.html#94">_ZN4PLMD8analysis13WhamHistogramC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/WhamHistogram.cpp.gcov.html b/coverage/analysis/WhamHistogram.cpp.gcov.html
new file mode 100644
index 0000000000..bbc073b0f9
--- /dev/null
+++ b/coverage/analysis/WhamHistogram.cpp.gcov.html
@@ -0,0 +1,198 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/WhamHistogram.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - WhamHistogram.cpp<span style="font-size: 80%;"> (source / <a href="WhamHistogram.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionShortcut.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace analysis {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC REWEIGHTING WHAM_HISTOGRAM</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This can be used to output the a histogram using the weighted histogram technique</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This shortcut action allows you to calculate a histogram using the weighted histogram</a>
+<a name="33"><span class="lineNum">      33 </span>            : analysis technique.  For more detail on how this the weights for configurations are</a>
+<a name="34"><span class="lineNum">      34 </span>            : computed see \ref REWEIGHT_WHAM</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input can be used to analyze the output from a series of umbrella sampling calculations.</a>
+<a name="39"><span class="lineNum">      39 </span>            : The trajectory from each of the simulations run with the different biases should be concatenated into a</a>
+<a name="40"><span class="lineNum">      40 </span>            : single trajectory before running the following analysis script on the concatenated trajectory using PLUMED</a>
+<a name="41"><span class="lineNum">      41 </span>            : driver.  The umbrella sampling simulations that will be analyzed using the script below applied a harmonic</a>
+<a name="42"><span class="lineNum">      42 </span>            : restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values.  The script</a>
+<a name="43"><span class="lineNum">      43 </span>            : below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm</a>
+<a name="44"><span class="lineNum">      44 </span>            : to determine a weight for each configuration in the concatenated trajectory.  A histogram is then constructed from</a>
+<a name="45"><span class="lineNum">      45 </span>            : the configurations visited and their weights.  This histogram is then converted into a free energy surface and output</a>
+<a name="46"><span class="lineNum">      46 </span>            : to a file called fes.dat</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \plumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : #SETTINGS NREPLICAS=4</a>
+<a name="50"><span class="lineNum">      50 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="51"><span class="lineNum">      51 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="52"><span class="lineNum">      52 </span>            : rp: RESTRAINT ARG=phi KAPPA=50.0 ...</a>
+<a name="53"><span class="lineNum">      53 </span>            :   AT=@replicas:{</a>
+<a name="54"><span class="lineNum">      54 </span>            :         -3.00000000000000000000</a>
+<a name="55"><span class="lineNum">      55 </span>            :         -1.45161290322580645168</a>
+<a name="56"><span class="lineNum">      56 </span>            :         .09677419354838709664</a>
+<a name="57"><span class="lineNum">      57 </span>            :         1.64516129032258064496</a>
+<a name="58"><span class="lineNum">      58 </span>            :      }</a>
+<a name="59"><span class="lineNum">      59 </span>            : ...</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : hh: WHAM_HISTOGRAM ARG=phi BIAS=rp.bias TEMP=300 GRID_MIN=-pi GRID_MAX=pi GRID_BIN=50</a>
+<a name="62"><span class="lineNum">      62 </span>            : fes: CONVERT_TO_FES GRID=hh TEMP=300</a>
+<a name="63"><span class="lineNum">      63 </span>            : DUMPGRID GRID=fes FILE=fes.dat</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : The script above must be run with multiple replicas using the following command:</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \verbatim</a>
+<a name="69"><span class="lineNum">      69 </span>            : mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endverbatim</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : class WhamHistogram : public ActionShortcut {</a>
+<a name="76"><span class="lineNum">      76 </span>            : public:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="78"><span class="lineNum">      78 </span>            :   explicit WhamHistogram( const ActionOptions&amp; );</a>
+<a name="79"><span class="lineNum">      79 </span>            : };</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(WhamHistogram,&quot;WHAM_HISTOGRAM&quot;)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 : void WhamHistogram::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   ActionShortcut::registerKeywords( keys );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;the arguments that you would like to make the histogram for&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;BIAS&quot;,&quot;*.bias&quot;,&quot;the value of the biases to use when performing WHAM&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;TEMP&quot;,&quot;the temperature at which the simulation was run&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the data should be stored to perform WHAM&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;GRID_MIN&quot;,&quot;the minimum to use for the grid&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;GRID_MAX&quot;,&quot;the maximum to use for the grid&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;GRID_BIN&quot;,&quot;the number of bins to use for the grid&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;BANDWIDTH&quot;,&quot;the bandwidth for kernel density estimation&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          8 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 : WhamHistogram::WhamHistogram( const ActionOptions&amp; ao ) :</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   Action(ao),</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   ActionShortcut(ao)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : {</a>
+<a name="100"><span class="lineNum">     100 </span>            :   // Input for REWEIGHT_WHAM</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   std::string rew_line = getShortcutLabel() + &quot;_weights: REWEIGHT_WHAM&quot;;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         18 :   std::string bias; parse(&quot;BIAS&quot;,bias); rew_line += &quot; ARG=&quot; + bias;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         12 :   std::string temp; parse(&quot;TEMP&quot;,temp); rew_line += &quot; TEMP=&quot; + temp;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   readInputLine( rew_line );</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Input for COLLECT_FRAMES</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :   std::string col_line = getShortcutLabel() + &quot;_collect: COLLECT_FRAMES LOGWEIGHTS=&quot; + getShortcutLabel() + &quot;_weights&quot;;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         18 :   std::string stride; parse(&quot;STRIDE&quot;,stride); col_line += &quot; STRIDE=&quot; + stride;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   std::string arg; parse(&quot;ARG&quot;,arg); col_line += &quot; ARG=&quot; + arg;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          6 :   readInputLine( col_line );</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Input for HISTOGRAM</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         12 :   std::string histo_line = getShortcutLabel() + &quot;: HISTOGRAM ARG=&quot; + getShortcutLabel() + &quot;_collect.*&quot;;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         18 :   std::string min; parse(&quot;GRID_MIN&quot;,min); histo_line += &quot; GRID_MIN=&quot; + min;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         18 :   std::string max; parse(&quot;GRID_MAX&quot;,max); histo_line += &quot; GRID_MAX=&quot; + max;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         12 :   std::string bin; parse(&quot;GRID_BIN&quot;,bin); histo_line += &quot; GRID_BIN=&quot; + bin;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         12 :   std::string bw=&quot;&quot;; parse(&quot;BANDWIDTH&quot;,bw);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          6 :   if( bw!=&quot;&quot; ) histo_line += &quot; BANDWIDTH=&quot; + bw;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   else histo_line += &quot; KERNEL=DISCRETE&quot;;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 :   readInputLine( histo_line );</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/WhamWeights.cpp.func-sort-c.html b/coverage/analysis/WhamWeights.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f657041c3b
--- /dev/null
+++ b/coverage/analysis/WhamWeights.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/WhamWeights.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - WhamWeights.cpp<span style="font-size: 80%;"> (<a href="WhamWeights.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WhamWeights.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#84">_ZN4PLMD8analysis11WhamWeightsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#84">_ZN4PLMD8analysis11WhamWeightsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#73">_ZN4PLMD8analysis12_GLOBAL__N_123WhamWeightsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#75">_ZN4PLMD8analysis11WhamWeights16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#73">_ZN4PLMD8analysis12_GLOBAL__N_123WhamWeightsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#73">_ZN4PLMD8analysis12_GLOBAL__N_123WhamWeightsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/WhamWeights.cpp.func.html b/coverage/analysis/WhamWeights.cpp.func.html
new file mode 100644
index 0000000000..c9e9afa538
--- /dev/null
+++ b/coverage/analysis/WhamWeights.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/WhamWeights.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - WhamWeights.cpp<span style="font-size: 80%;"> (<a href="WhamWeights.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WhamWeights.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#75">_ZN4PLMD8analysis11WhamWeights16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#84">_ZN4PLMD8analysis11WhamWeightsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#84">_ZN4PLMD8analysis11WhamWeightsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#73">_ZN4PLMD8analysis12_GLOBAL__N_123WhamWeightsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#73">_ZN4PLMD8analysis12_GLOBAL__N_123WhamWeightsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WhamWeights.cpp.gcov.html#73">_ZN4PLMD8analysis12_GLOBAL__N_123WhamWeightsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
+</html>
diff --git a/coverage/analysis/WhamWeights.cpp.gcov.html b/coverage/analysis/WhamWeights.cpp.gcov.html
new file mode 100644
index 0000000000..608dce345a
--- /dev/null
+++ b/coverage/analysis/WhamWeights.cpp.gcov.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis/WhamWeights.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">analysis</a> - WhamWeights.cpp<span style="font-size: 80%;"> (source / <a href="WhamWeights.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionShortcut.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace analysis {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC REWEIGHTING WHAM_WEIGHTS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate and output weights for configurations using the weighted histogram analysis method.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This shortcut action allows you to calculate and output weights computed using the weighted histogram</a>
+<a name="33"><span class="lineNum">      33 </span>            : analysis technique.  For more detail on how this technique works see \ref REWEIGHT_WHAM</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \par Examples</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The following input can be used to analyze the output from a series of umbrella sampling calculations.</a>
+<a name="38"><span class="lineNum">      38 </span>            : The trajectory from each of the simulations run with the different biases should be concatenated into a</a>
+<a name="39"><span class="lineNum">      39 </span>            : single trajectory before running the following analysis script on the concatenated trajectory using PLUMED</a>
+<a name="40"><span class="lineNum">      40 </span>            : driver.  The umbrella sampling simulations that will be analyzed using the script below applied a harmonic</a>
+<a name="41"><span class="lineNum">      41 </span>            : restraint that restrained the torsional angle involving atoms 5, 7, 9 and 15 to particular values.  The script</a>
+<a name="42"><span class="lineNum">      42 </span>            : below calculates the reweighting weights for each of the trajectories and then applies the binless WHAM algorithm</a>
+<a name="43"><span class="lineNum">      43 </span>            : to determine a weight for each configuration in the concatenated trajectory.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : #SETTINGS NREPLICAS=4</a>
+<a name="47"><span class="lineNum">      47 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="48"><span class="lineNum">      48 </span>            : rp: RESTRAINT ARG=phi KAPPA=50.0 ...</a>
+<a name="49"><span class="lineNum">      49 </span>            :   AT=@replicas:{</a>
+<a name="50"><span class="lineNum">      50 </span>            :         -3.00000000000000000000</a>
+<a name="51"><span class="lineNum">      51 </span>            :         -1.45161290322580645168</a>
+<a name="52"><span class="lineNum">      52 </span>            :         .09677419354838709664</a>
+<a name="53"><span class="lineNum">      53 </span>            :         1.64516129032258064496</a>
+<a name="54"><span class="lineNum">      54 </span>            :      }</a>
+<a name="55"><span class="lineNum">      55 </span>            : ...</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : WHAM_WEIGHTS BIAS=rp.bias TEMP=300 FILE=wham-weights</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The script above must be run with multiple replicas using the following command:</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \verbatim</a>
+<a name="63"><span class="lineNum">      63 </span>            : mpirun -np 4 plumed driver --mf_xtc alltraj.xtc --multi 4</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endverbatim</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : //+ENDPLUMEDOC</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : class WhamWeights : public ActionShortcut {</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   explicit WhamWeights( const ActionOptions&amp; );</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(WhamWeights,&quot;WHAM_WEIGHTS&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          8 : void WhamWeights::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          8 :   ActionShortcut::registerKeywords( keys ); keys.remove(&quot;LABEL&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;BIAS&quot;,&quot;*.bias&quot;,&quot;the value of the biases to use when performing WHAM&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;TEMP&quot;,&quot;the temperature at which the simulation was run&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the bias should be stored to perform WHAM&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the file on which to output the WHAM weights&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format to use for the real numbers in the output file&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 : WhamWeights::WhamWeights( const ActionOptions&amp; ao ) :</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   Action(ao),</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          6 :   ActionShortcut(ao)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Input for REWEIGHT_WHAM</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 :   std::string rew_line = getShortcutLabel() + &quot;_weights: REWEIGHT_WHAM&quot;;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         18 :   std::string bias; parse(&quot;BIAS&quot;,bias); rew_line += &quot; ARG=&quot; + bias;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         12 :   std::string temp; parse(&quot;TEMP&quot;,temp); rew_line += &quot; TEMP=&quot; + temp;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   readInputLine( rew_line );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   // Input for COLLECT_FRAMES</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         12 :   std::string col_line = getShortcutLabel() + &quot;_collect: COLLECT_FRAMES LOGWEIGHTS=&quot; + getShortcutLabel() + &quot;_weights&quot;;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         12 :   std::string stride; parse(&quot;STRIDE&quot;,stride); col_line += &quot; STRIDE=&quot; + stride;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   readInputLine( col_line );</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   // Input for line to output data</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         12 :   std::string out_line=&quot;OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=&quot; + getShortcutLabel() + &quot;_collect&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         12 :   std::string file; parse(&quot;FILE&quot;,file); out_line += &quot; FILE=&quot; + file;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         12 :   std::string fmt=&quot;%f&quot;; parse(&quot;FMT&quot;,fmt); out_line += &quot; FMT=&quot; + fmt;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :   readInputLine( out_line );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/index-sort-f.html b/coverage/analysis/index-sort-f.html
new file mode 100644
index 0000000000..e8bdcd8c86
--- /dev/null
+++ b/coverage/analysis/index-sort-f.html
@@ -0,0 +1,333 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - analysis</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">859</td>
+            <td class="headerCovTableEntry">971</td>
+            <td class="headerCovTableEntryMed">88.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntry">202</td>
+            <td class="headerCovTableEntryMed">77.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SelectRandomFrames.cpp.gcov.html">SelectRandomFrames.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.0%"><img src="../snow.png" width=75 height=10 alt="25.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">5 / 20</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkStaged.cpp.gcov.html">LandmarkStaged.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=13 height=10 alt="12.8%"><img src="../snow.png" width=87 height=10 alt="12.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">12.8&nbsp;%</td>
+      <td class="coverNumLo">6 / 47</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadAnalysisFrames.h.gcov.html">ReadAnalysisFrames.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.2%"><img src="../snow.png" width=31 height=10 alt="69.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">4 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AnalysisBase.h.gcov.html">AnalysisBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="72.7%"><img src="../snow.png" width=27 height=10 alt="72.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">24 / 33</td>
+      <td class="coverPerLo">68.4&nbsp;%</td>
+      <td class="coverNumLo">13 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Average.cpp.gcov.html">Average.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputColvarFile.cpp.gcov.html">OutputColvarFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.9%"><img src="../snow.png" width=2 height=10 alt="97.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.9&nbsp;%</td>
+      <td class="coverNumHi">47 / 48</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputPDBFile.cpp.gcov.html">OutputPDBFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">29 / 30</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PrintDissimilarityMatrix.cpp.gcov.html">PrintDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 23</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadDissimilarityMatrix.cpp.gcov.html">ReadDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.3%"><img src="../snow.png" width=18 height=10 alt="82.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.3&nbsp;%</td>
+      <td class="coverNumMed">51 / 62</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html">EuclideanDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">50 / 60</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageVessel.cpp.gcov.html">AverageVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 24</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkSelectionBase.cpp.gcov.html">LandmarkSelectionBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WhamWeights.cpp.gcov.html">WhamWeights.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AnalysisBase.cpp.gcov.html">AnalysisBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.9%"><img src="../snow.png" width=3 height=10 alt="96.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.9&nbsp;%</td>
+      <td class="coverNumHi">31 / 32</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkSelectionBase.h.gcov.html">LandmarkSelectionBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WhamHistogram.cpp.gcov.html">WhamHistogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FarthestPointSampling.cpp.gcov.html">FarthestPointSampling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReselectLandmarks.cpp.gcov.html">ReselectLandmarks.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SelectWithStride.cpp.gcov.html">SelectWithStride.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Committor.cpp.gcov.html">Committor.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">74 / 74</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Histogram.cpp.gcov.html">Histogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.6%"><img src="../snow.png" width=2 height=10 alt="97.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">203 / 208</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadAnalysisFrames.cpp.gcov.html">ReadAnalysisFrames.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.9%"><img src="../snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">74 / 78</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataCollectionObject.h.gcov.html">DataCollectionObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageVessel.h.gcov.html">AverageVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataCollectionObject.cpp.gcov.html">DataCollectionObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/index-sort-l.html b/coverage/analysis/index-sort-l.html
new file mode 100644
index 0000000000..953aaa8766
--- /dev/null
+++ b/coverage/analysis/index-sort-l.html
@@ -0,0 +1,333 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - analysis</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">859</td>
+            <td class="headerCovTableEntry">971</td>
+            <td class="headerCovTableEntryMed">88.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntry">202</td>
+            <td class="headerCovTableEntryMed">77.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkStaged.cpp.gcov.html">LandmarkStaged.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=13 height=10 alt="12.8%"><img src="../snow.png" width=87 height=10 alt="12.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">12.8&nbsp;%</td>
+      <td class="coverNumLo">6 / 47</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SelectRandomFrames.cpp.gcov.html">SelectRandomFrames.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.0%"><img src="../snow.png" width=75 height=10 alt="25.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">5 / 20</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadAnalysisFrames.h.gcov.html">ReadAnalysisFrames.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.2%"><img src="../snow.png" width=31 height=10 alt="69.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">4 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AnalysisBase.h.gcov.html">AnalysisBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="72.7%"><img src="../snow.png" width=27 height=10 alt="72.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">24 / 33</td>
+      <td class="coverPerLo">68.4&nbsp;%</td>
+      <td class="coverNumLo">13 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataCollectionObject.h.gcov.html">DataCollectionObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadDissimilarityMatrix.cpp.gcov.html">ReadDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.3%"><img src="../snow.png" width=18 height=10 alt="82.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.3&nbsp;%</td>
+      <td class="coverNumMed">51 / 62</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html">EuclideanDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">50 / 60</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Average.cpp.gcov.html">Average.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkSelectionBase.h.gcov.html">LandmarkSelectionBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageVessel.cpp.gcov.html">AverageVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 24</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadAnalysisFrames.cpp.gcov.html">ReadAnalysisFrames.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.9%"><img src="../snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">74 / 78</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PrintDissimilarityMatrix.cpp.gcov.html">PrintDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 23</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputPDBFile.cpp.gcov.html">OutputPDBFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">29 / 30</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AnalysisBase.cpp.gcov.html">AnalysisBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.9%"><img src="../snow.png" width=3 height=10 alt="96.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.9&nbsp;%</td>
+      <td class="coverNumHi">31 / 32</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Histogram.cpp.gcov.html">Histogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.6%"><img src="../snow.png" width=2 height=10 alt="97.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">203 / 208</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputColvarFile.cpp.gcov.html">OutputColvarFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.9%"><img src="../snow.png" width=2 height=10 alt="97.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.9&nbsp;%</td>
+      <td class="coverNumHi">47 / 48</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageVessel.h.gcov.html">AverageVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SelectWithStride.cpp.gcov.html">SelectWithStride.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReselectLandmarks.cpp.gcov.html">ReselectLandmarks.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataCollectionObject.cpp.gcov.html">DataCollectionObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WhamWeights.cpp.gcov.html">WhamWeights.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FarthestPointSampling.cpp.gcov.html">FarthestPointSampling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WhamHistogram.cpp.gcov.html">WhamHistogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkSelectionBase.cpp.gcov.html">LandmarkSelectionBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Committor.cpp.gcov.html">Committor.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">74 / 74</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/analysis/index.html b/coverage/analysis/index.html
new file mode 100644
index 0000000000..79b06f2bf4
--- /dev/null
+++ b/coverage/analysis/index.html
@@ -0,0 +1,333 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - analysis</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - analysis</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">859</td>
+            <td class="headerCovTableEntry">971</td>
+            <td class="headerCovTableEntryMed">88.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">156</td>
+            <td class="headerCovTableEntry">202</td>
+            <td class="headerCovTableEntryMed">77.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AnalysisBase.cpp.gcov.html">AnalysisBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.9%"><img src="../snow.png" width=3 height=10 alt="96.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.9&nbsp;%</td>
+      <td class="coverNumHi">31 / 32</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AnalysisBase.h.gcov.html">AnalysisBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="72.7%"><img src="../snow.png" width=27 height=10 alt="72.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">24 / 33</td>
+      <td class="coverPerLo">68.4&nbsp;%</td>
+      <td class="coverNumLo">13 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Average.cpp.gcov.html">Average.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageVessel.cpp.gcov.html">AverageVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 24</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageVessel.h.gcov.html">AverageVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Committor.cpp.gcov.html">Committor.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">74 / 74</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataCollectionObject.cpp.gcov.html">DataCollectionObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataCollectionObject.h.gcov.html">DataCollectionObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EuclideanDissimilarityMatrix.cpp.gcov.html">EuclideanDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">50 / 60</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FarthestPointSampling.cpp.gcov.html">FarthestPointSampling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Histogram.cpp.gcov.html">Histogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.6%"><img src="../snow.png" width=2 height=10 alt="97.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">203 / 208</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkSelectionBase.cpp.gcov.html">LandmarkSelectionBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkSelectionBase.h.gcov.html">LandmarkSelectionBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LandmarkStaged.cpp.gcov.html">LandmarkStaged.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=13 height=10 alt="12.8%"><img src="../snow.png" width=87 height=10 alt="12.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">12.8&nbsp;%</td>
+      <td class="coverNumLo">6 / 47</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputColvarFile.cpp.gcov.html">OutputColvarFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.9%"><img src="../snow.png" width=2 height=10 alt="97.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.9&nbsp;%</td>
+      <td class="coverNumHi">47 / 48</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputPDBFile.cpp.gcov.html">OutputPDBFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">29 / 30</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PrintDissimilarityMatrix.cpp.gcov.html">PrintDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 23</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadAnalysisFrames.cpp.gcov.html">ReadAnalysisFrames.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.9%"><img src="../snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">74 / 78</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadAnalysisFrames.h.gcov.html">ReadAnalysisFrames.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.2%"><img src="../snow.png" width=31 height=10 alt="69.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">4 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReadDissimilarityMatrix.cpp.gcov.html">ReadDissimilarityMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.3%"><img src="../snow.png" width=18 height=10 alt="82.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.3&nbsp;%</td>
+      <td class="coverNumMed">51 / 62</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReselectLandmarks.cpp.gcov.html">ReselectLandmarks.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SelectRandomFrames.cpp.gcov.html">SelectRandomFrames.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=25 height=10 alt="25.0%"><img src="../snow.png" width=75 height=10 alt="25.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">5 / 20</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SelectWithStride.cpp.gcov.html">SelectWithStride.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WhamHistogram.cpp.gcov.html">WhamHistogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WhamWeights.cpp.gcov.html">WhamWeights.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/annfunc/ANN.cpp.func-sort-c.html b/coverage/annfunc/ANN.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e45c345bfd
--- /dev/null
+++ b/coverage/annfunc/ANN.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - annfunc/ANN.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">annfunc</a> - ANN.cpp<span style="font-size: 80%;"> (<a href="ANN.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ANN.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#125">_ZN4PLMD8function7annfunc3ANNC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#108">_ZN4PLMD8function7annfunc12_GLOBAL__N_116ANNRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#125">_ZN4PLMD8function7annfunc3ANNC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#110">_ZN4PLMD8function7annfunc3ANN16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#211">_ZN4PLMD8function7annfunc3ANN30calculate_output_of_each_layerERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1638</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#364">_ZN4PLMD8function7annfunc3ANN9calculateEv</a></td>
+              <td class="coverFnHi">1638</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#273">_ZN4PLMD8function7annfunc3ANN9back_propERSt6vectorIS3_IdSaIdEESaIS5_EEi</a></td>
+              <td class="coverFnHi">2184</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#108">_ZN4PLMD8function7annfunc12_GLOBAL__N_116ANNRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#108">_ZN4PLMD8function7annfunc12_GLOBAL__N_116ANNRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/annfunc/ANN.cpp.func.html b/coverage/annfunc/ANN.cpp.func.html
new file mode 100644
index 0000000000..0560089fbd
--- /dev/null
+++ b/coverage/annfunc/ANN.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - annfunc/ANN.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">annfunc</a> - ANN.cpp<span style="font-size: 80%;"> (<a href="ANN.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ANN.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#108">_ZN4PLMD8function7annfunc12_GLOBAL__N_116ANNRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#108">_ZN4PLMD8function7annfunc12_GLOBAL__N_116ANNRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#108">_ZN4PLMD8function7annfunc12_GLOBAL__N_116ANNRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#110">_ZN4PLMD8function7annfunc3ANN16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#211">_ZN4PLMD8function7annfunc3ANN30calculate_output_of_each_layerERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1638</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#273">_ZN4PLMD8function7annfunc3ANN9back_propERSt6vectorIS3_IdSaIdEESaIS5_EEi</a></td>
+              <td class="coverFnHi">2184</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#364">_ZN4PLMD8function7annfunc3ANN9calculateEv</a></td>
+              <td class="coverFnHi">1638</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#125">_ZN4PLMD8function7annfunc3ANNC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ANN.cpp.gcov.html#125">_ZN4PLMD8function7annfunc3ANNC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/annfunc/ANN.cpp.gcov.html b/coverage/annfunc/ANN.cpp.gcov.html
new file mode 100644
index 0000000000..f08d10b2e8
--- /dev/null
+++ b/coverage/annfunc/ANN.cpp.gcov.html
@@ -0,0 +1,473 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - annfunc/ANN.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">annfunc</a> - ANN.cpp<span style="font-size: 80%;"> (source / <a href="ANN.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : MIT License</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : Copyright (c) 2019 Wei Chen and Andrew Ferguson</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : Permission is hereby granted, free of charge, to any person obtaining a copy</a>
+<a name="7"><span class="lineNum">       7 </span>            : of this software and associated documentation files (the &quot;Software&quot;), to deal</a>
+<a name="8"><span class="lineNum">       8 </span>            : in the Software without restriction, including without limitation the rights</a>
+<a name="9"><span class="lineNum">       9 </span>            : to use, copy, modify, merge, publish, distribute, sublicense, and/or sell</a>
+<a name="10"><span class="lineNum">      10 </span>            : copies of the Software, and to permit persons to whom the Software is</a>
+<a name="11"><span class="lineNum">      11 </span>            : furnished to do so, subject to the following conditions:</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : The above copyright notice and this permission notice shall be included in all</a>
+<a name="14"><span class="lineNum">      14 </span>            : copies or substantial portions of the Software.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            : THE SOFTWARE IS PROVIDED &quot;AS IS&quot;, WITHOUT WARRANTY OF ANY KIND, EXPRESS OR</a>
+<a name="17"><span class="lineNum">      17 </span>            : IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,</a>
+<a name="18"><span class="lineNum">      18 </span>            : FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE</a>
+<a name="19"><span class="lineNum">      19 </span>            : AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER</a>
+<a name="20"><span class="lineNum">      20 </span>            : LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,</a>
+<a name="21"><span class="lineNum">      21 </span>            : OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE</a>
+<a name="22"><span class="lineNum">      22 </span>            : SOFTWARE.</a>
+<a name="23"><span class="lineNum">      23 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;function/Function.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;function/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;cassert&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;iostream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : // #include &lt;stdio.h&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : using namespace std;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // #define DEBUG</a>
+<a name="36"><span class="lineNum">      36 </span>            : // #define DEBUG_2</a>
+<a name="37"><span class="lineNum">      37 </span>            : // #define DEBUG_3</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace function {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace annfunc {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : //+PLUMEDOC ANNMOD_Function ANN</a>
+<a name="44"><span class="lineNum">      44 </span>            : /*</a>
+<a name="45"><span class="lineNum">      45 </span>            : Calculates the ANN-function.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : This module implements ANN class, which is a subclass of Function class.</a>
+<a name="48"><span class="lineNum">      48 </span>            : ANN class takes multi-dimensional arrays as inputs for a fully-connected feedforward neural network</a>
+<a name="49"><span class="lineNum">      49 </span>            : with specified neural network weights and generates corresponding outputs.</a>
+<a name="50"><span class="lineNum">      50 </span>            : The ANN outputs can be used as collective variables, inputs for other collective variables,</a>
+<a name="51"><span class="lineNum">      51 </span>            : or inputs for data analysis tools.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \par Examples</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : Assume we have an ANN with numbers of nodes being [2, 3, 1], and weights connecting layer 0 and 1 are</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : [[1,2], [3,4], [5,6]]</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : weights connecting layer 1 and 2 are</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : [[7,8,9]]</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : Bias for layer 1 and 2 are [10, 11, 12] and [13], respectively.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : All activation functions are Tanh.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : Then if input variables are l_0_out_0, l_0_out_1, the corresponding ANN function object can be defined using</a>
+<a name="68"><span class="lineNum">      68 </span>            : following plumed script:</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : ANN ...</a>
+<a name="72"><span class="lineNum">      72 </span>            : LABEL=ann</a>
+<a name="73"><span class="lineNum">      73 </span>            : ARG=l_0_out_0,l_0_out_1</a>
+<a name="74"><span class="lineNum">      74 </span>            : NUM_LAYERS=3</a>
+<a name="75"><span class="lineNum">      75 </span>            : NUM_NODES=2,3,1</a>
+<a name="76"><span class="lineNum">      76 </span>            : ACTIVATIONS=Tanh,Tanh</a>
+<a name="77"><span class="lineNum">      77 </span>            : WEIGHTS0=1,2,3,4,5,6</a>
+<a name="78"><span class="lineNum">      78 </span>            : WEIGHTS1=7,8,9</a>
+<a name="79"><span class="lineNum">      79 </span>            : BIASES0=10,11,12</a>
+<a name="80"><span class="lineNum">      80 </span>            : BIASES1=13</a>
+<a name="81"><span class="lineNum">      81 </span>            : ... ANN</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endplumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : To access its components, we use &quot;ann.node-0&quot;, &quot;ann.node-1&quot;, ..., which represents the components of neural network outputs.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : */</a>
+<a name="88"><span class="lineNum">      88 </span>            : //+ENDPLUMEDOC</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : class ANN : public Function</a>
+<a name="91"><span class="lineNum">      91 </span>            : {</a>
+<a name="92"><span class="lineNum">      92 </span>            : private:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   int num_layers;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   vector&lt;int&gt; num_nodes;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   vector&lt;string&gt; activations;   // activation functions</a>
+<a name="96"><span class="lineNum">      96 </span>            :   vector&lt;vector&lt;double&gt; &gt; weights;  // flattened weight arrays</a>
+<a name="97"><span class="lineNum">      97 </span>            :   vector&lt;vector&lt;double&gt; &gt; biases;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   vector&lt;vector&lt;double&gt; &gt; output_of_each_layer;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   vector&lt;vector&lt;double&gt; &gt; input_of_each_layer;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   vector&lt;double** &gt; coeff;  // weight matrix arrays, reshaped from &quot;weights&quot;</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : public:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="104"><span class="lineNum">     104 </span>            :   explicit ANN(const ActionOptions&amp;);</a>
+<a name="105"><span class="lineNum">     105 </span>            :   virtual void calculate();</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void calculate_output_of_each_layer(const vector&lt;double&gt;&amp; input);</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void back_prop(vector&lt;vector&lt;double&gt; &gt;&amp; derivatives_of_each_layer, int index_of_output_component);</a>
+<a name="108"><span class="lineNum">     108 </span>            : };</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(ANN,&quot;ANN&quot;)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          7 : void ANN::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          7 :   Function::registerKeywords(keys);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         14 :   keys.use(&quot;ARG&quot;); keys.use(&quot;PERIODIC&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;, &quot;NUM_LAYERS&quot;, &quot;number of layers of the neural network&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;, &quot;NUM_NODES&quot;, &quot;numbers of nodes in each layer of the neural network&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;, &quot;ACTIVATIONS&quot;, &quot;activation functions for the neural network&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         14 :   keys.add(&quot;numbered&quot;, &quot;WEIGHTS&quot;, &quot;flattened weight arrays connecting adjacent layers, &quot;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :            &quot;WEIGHTS0 represents flattened weight array connecting layer 0 and layer 1, &quot;</a>
+<a name="120"><span class="lineNum">     120 </span>            :            &quot;WEIGHTS1 represents flattened weight array connecting layer 1 and layer 2, ...&quot;);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         14 :   keys.add(&quot;numbered&quot;, &quot;BIASES&quot;, &quot;bias array for each layer of the neural network, &quot;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :            &quot;BIASES0 represents bias array for layer 1, BIASES1 represents bias array for layer 2, ...&quot;);</a>
+<a name="123"><span class="lineNum">     123 </span>            :   // since v2.2 plumed requires all components be registered</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         14 :   keys.addOutputComponent(&quot;node&quot;, &quot;default&quot;, &quot;components of ANN outputs&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          7 : }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          5 : ANN::ANN(const ActionOptions&amp;ao):</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   Action(ao),</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          5 :   Function(ao)</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : {</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          5 :   parse(&quot;NUM_LAYERS&quot;, num_layers);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          5 :   num_nodes = vector&lt;int&gt;(num_layers);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         10 :   activations = vector&lt;string&gt;(num_layers - 1);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         10 :   output_of_each_layer = vector&lt;vector&lt;double&gt; &gt;(num_layers);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         10 :   input_of_each_layer = vector&lt;vector&lt;double&gt; &gt;(num_layers);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          5 :   coeff = vector&lt;double** &gt;(num_layers - 1);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          5 :   parseVector(&quot;NUM_NODES&quot;, num_nodes);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          5 :   parseVector(&quot;ACTIVATIONS&quot;, activations);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          5 :   log.printf(&quot;\nactivations = &quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         15 :   for (auto ss: activations) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         10 :     log.printf(&quot;%s, &quot;, ss.c_str());</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          5 :   log.printf(&quot;\nnum_nodes = &quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         20 :   for (auto ss: num_nodes) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         15 :     log.printf(&quot;%d, &quot;, ss);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            :   vector&lt;double&gt; temp_single_coeff, temp_single_bias;</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         10 :   for (int ii = 0; ; ii ++) {</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     // parse coeff</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         30 :     if( !parseNumberedVector(&quot;WEIGHTS&quot;, ii, temp_single_coeff) ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          5 :       temp_single_coeff=weights[ii-1];</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :       break;</a>
+<a name="153"><span class="lineNum">     153 </span>            :     }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         10 :     weights.push_back(temp_single_coeff);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         10 :     log.printf(&quot;size of temp_single_coeff = %lu\n&quot;, temp_single_coeff.size());</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         10 :     log.printf(&quot;size of weights = %lu\n&quot;, weights.size());</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     // parse bias</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         20 :     if( !parseNumberedVector(&quot;BIASES&quot;, ii, temp_single_bias) ) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :       temp_single_bias=biases[ii-1];</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         10 :     biases.push_back(temp_single_bias);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         10 :     log.printf(&quot;size of temp_single_bias = %lu\n&quot;, temp_single_bias.size());</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         10 :     log.printf(&quot;size of biases = %lu\n&quot;, biases.size());</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          5 :   if(getNumberOfArguments() != num_nodes[0]) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     error(&quot;Number of arguments is wrong&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          5 :   auto temp_coeff = weights;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         15 :   for (int ii = 0; ii &lt; num_layers - 1; ii ++) {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     int num_of_rows, num_of_cols; // num of rows/cols for the coeff matrix of this connection</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         10 :     num_of_rows = num_nodes[ii + 1];</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         10 :     num_of_cols = num_nodes[ii];</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     assert (num_of_rows * num_of_cols == temp_coeff[ii].size()); // check whether the size matches</a>
+<a name="176"><span class="lineNum">     176 </span>            :     // create a 2d array to hold coefficients</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         10 :     coeff[ii] = new double*[num_of_rows];</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         32 :     for (int kk = 0; kk &lt; num_of_rows; kk ++) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         22 :       coeff[ii][kk] = new double[num_of_cols];</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         61 :     for (int jj = 0; jj &lt; temp_coeff[ii].size(); jj ++) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         51 :       coeff[ii][jj / num_of_cols][jj % num_of_cols] = temp_coeff[ii][jj];</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            :   // check coeff</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         15 :   for (int ii = 0; ii &lt; num_layers - 1; ii ++) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         10 :     log.printf(&quot;coeff %d = \n&quot;, ii);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         32 :     for (int jj = 0; jj &lt; num_nodes[ii + 1]; jj ++) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         73 :       for (int kk = 0; kk &lt; num_nodes[ii]; kk ++) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         51 :         log.printf(&quot;%f &quot;, coeff[ii][jj][kk]);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       }</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         22 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :     }</a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            :   // check bias</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         15 :   for (int ii = 0; ii &lt; num_layers - 1; ii ++) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         10 :     log.printf(&quot;bias %d = \n&quot;, ii);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         32 :     for (int jj = 0; jj &lt; num_nodes[ii + 1]; jj ++) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         22 :       log.printf(&quot;%f &quot;, biases[ii][jj]);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         10 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          5 :   log.printf(&quot;initialization ended\n&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   // create components</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         12 :   for (int ii = 0; ii &lt; num_nodes[num_layers - 1]; ii ++) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          7 :     string name_of_this_component = &quot;node-&quot; + to_string(ii);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          7 :     addComponentWithDerivatives(name_of_this_component);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          7 :     componentIsNotPeriodic(name_of_this_component);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          5 :   checkRead();</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         10 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1638 : void ANN::calculate_output_of_each_layer(const vector&lt;double&gt;&amp; input) {</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   // first layer</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1638 :   output_of_each_layer[0] = input;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   // following layers</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       4914 :   for(int ii = 1; ii &lt; num_nodes.size(); ii ++) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       3276 :     output_of_each_layer[ii].resize(num_nodes[ii]);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       3276 :     input_of_each_layer[ii].resize(num_nodes[ii]);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :     // first calculate input</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      10374 :     for (int jj = 0; jj &lt; num_nodes[ii]; jj ++) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       7098 :       input_of_each_layer[ii][jj] = biases[ii - 1][jj];  // add bias term</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      23478 :       for (int kk = 0; kk &lt; num_nodes[ii - 1]; kk ++) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      16380 :         input_of_each_layer[ii][jj] += coeff[ii - 1][jj][kk] * output_of_each_layer[ii - 1][kk];</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :       }</a>
+<a name="226"><span class="lineNum">     226 </span>            :     }</a>
+<a name="227"><span class="lineNum">     227 </span>            :     // then get output</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       3276 :     if (activations[ii - 1] == string(&quot;Linear&quot;)) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       1092 :       for(int jj = 0; jj &lt; num_nodes[ii]; jj ++) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        546 :         output_of_each_layer[ii][jj] = input_of_each_layer[ii][jj];</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :       }</a>
+<a name="232"><span class="lineNum">     232 </span>            :     }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       2730 :     else if (activations[ii - 1] == string(&quot;Tanh&quot;)) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       7644 :       for(int jj = 0; jj &lt; num_nodes[ii]; jj ++) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       5460 :         output_of_each_layer[ii][jj] = tanh(input_of_each_layer[ii][jj]);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :       }</a>
+<a name="237"><span class="lineNum">     237 </span>            :     }</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        546 :     else if (activations[ii - 1] == string(&quot;Circular&quot;)) {</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :       assert (num_nodes[ii] % 2 == 0);</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       1092 :       for(int jj = 0; jj &lt; num_nodes[ii] / 2; jj ++) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        546 :         double radius = sqrt(input_of_each_layer[ii][2 * jj] * input_of_each_layer[ii][2 * jj]</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        546 :                              +input_of_each_layer[ii][2 * jj + 1] * input_of_each_layer[ii][2 * jj + 1]);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        546 :         output_of_each_layer[ii][2 * jj] = input_of_each_layer[ii][2 * jj] / radius;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        546 :         output_of_each_layer[ii][2 * jj + 1] = input_of_each_layer[ii][2 * jj + 1] / radius;</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :       }</a>
+<a name="247"><span class="lineNum">     247 </span>            :     }</a>
+<a name="248"><span class="lineNum">     248 </span>            :     else {</a>
+<a name="249"><span class="lineNum">     249 </span>            :       printf(&quot;layer type not found!\n\n&quot;);</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     }</a>
+<a name="252"><span class="lineNum">     252 </span>            :   }</a>
+<a name="253"><span class="lineNum">     253 </span>            : #ifdef DEBUG_2</a>
+<a name="254"><span class="lineNum">     254 </span>            :   // print out the result for debugging</a>
+<a name="255"><span class="lineNum">     255 </span>            :   printf(&quot;output_of_each_layer = \n&quot;);</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // for (int ii = num_layers - 1; ii &lt; num_layers; ii ++) {</a>
+<a name="257"><span class="lineNum">     257 </span>            :   for (int ii = 0; ii &lt; num_layers; ii ++) {</a>
+<a name="258"><span class="lineNum">     258 </span>            :     printf(&quot;layer[%d]: &quot;, ii);</a>
+<a name="259"><span class="lineNum">     259 </span>            :     if (ii != 0) {</a>
+<a name="260"><span class="lineNum">     260 </span>            :       cout &lt;&lt; activations[ii - 1] &lt;&lt; &quot;\t&quot;;</a>
+<a name="261"><span class="lineNum">     261 </span>            :     }</a>
+<a name="262"><span class="lineNum">     262 </span>            :     else {</a>
+<a name="263"><span class="lineNum">     263 </span>            :       cout &lt;&lt; &quot;input \t&quot; ;</a>
+<a name="264"><span class="lineNum">     264 </span>            :     }</a>
+<a name="265"><span class="lineNum">     265 </span>            :     for (int jj = 0; jj &lt; num_nodes[ii]; jj ++) {</a>
+<a name="266"><span class="lineNum">     266 </span>            :       printf(&quot;%lf\t&quot;, output_of_each_layer[ii][jj]);</a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :     printf(&quot;\n&quot;);</a>
+<a name="269"><span class="lineNum">     269 </span>            :   }</a>
+<a name="270"><span class="lineNum">     270 </span>            :   printf(&quot;\n&quot;);</a>
+<a name="271"><span class="lineNum">     271 </span>            : #endif</a>
+<a name="272"><span class="lineNum">     272 </span>            :   return;</a>
+<a name="273"><span class="lineNum">     273 </span>            : }</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       2184 : void ANN::back_prop(vector&lt;vector&lt;double&gt; &gt;&amp; derivatives_of_each_layer, int index_of_output_component) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       2184 :   derivatives_of_each_layer = output_of_each_layer;  // the data structure and size should be the same, so I simply deep copy it</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   // first calculate derivatives for bottleneck layer</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       5460 :   for (int ii = 0; ii &lt; num_nodes[num_nodes.size() - 1]; ii ++ ) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       3276 :     if (ii == index_of_output_component) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       2184 :       derivatives_of_each_layer[num_nodes.size() - 1][ii] = 1;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     }</a>
+<a name="282"><span class="lineNum">     282 </span>            :     else {</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       1092 :       derivatives_of_each_layer[num_nodes.size() - 1][ii] = 0;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :     }</a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span>            :   // the use back propagation to calculate derivatives for previous layers</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       6552 :   for (int jj = num_nodes.size() - 2; jj &gt;= 0; jj --) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       4368 :     if (activations[jj] == string(&quot;Circular&quot;)) {</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :       vector&lt;double&gt; temp_derivative_of_input_for_this_layer;</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       1092 :       temp_derivative_of_input_for_this_layer.resize(num_nodes[jj + 1]);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : #ifdef DEBUG</a>
+<a name="292"><span class="lineNum">     292 </span>            :       assert (num_nodes[jj + 1] % 2 == 0);</a>
+<a name="293"><span class="lineNum">     293 </span>            : #endif</a>
+<a name="294"><span class="lineNum">     294 </span>            :       // first calculate the derivative of input from derivative of output of this circular layer</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       2184 :       for(int ii = 0; ii &lt; num_nodes[jj + 1] / 2; ii ++) {</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :         // printf(&quot;size of input_of_each_layer[%d] = %d\n&quot;,jj,  input_of_each_layer[jj].size());</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       1092 :         double x_p = input_of_each_layer[jj + 1][2 * ii];</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1092 :         double x_q = input_of_each_layer[jj + 1][2 * ii + 1];</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       1092 :         double radius = sqrt(x_p * x_p + x_q * x_q);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1092 :         temp_derivative_of_input_for_this_layer[2 * ii] = x_q / (radius * radius * radius)</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       1092 :             * (x_q * derivatives_of_each_layer[jj + 1][2 * ii]</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       1092 :                - x_p * derivatives_of_each_layer[jj + 1][2 * ii + 1]);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       1092 :         temp_derivative_of_input_for_this_layer[2 * ii + 1] = x_p / (radius * radius * radius)</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       1092 :             * (x_p * derivatives_of_each_layer[jj + 1][2 * ii + 1]</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1092 :                - x_q * derivatives_of_each_layer[jj + 1][2 * ii]);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :       }</a>
+<a name="307"><span class="lineNum">     307 </span>            : #ifdef DEBUG</a>
+<a name="308"><span class="lineNum">     308 </span>            :       for (int mm = 0; mm &lt; num_nodes[jj + 1]; mm ++) {</a>
+<a name="309"><span class="lineNum">     309 </span>            :         printf(&quot;temp_derivative_of_input_for_this_layer[%d] = %lf\n&quot;, mm, temp_derivative_of_input_for_this_layer[mm]);</a>
+<a name="310"><span class="lineNum">     310 </span>            :         printf(&quot;derivatives_of_each_layer[%d + 1][%d] = %lf\n&quot;, jj, mm, derivatives_of_each_layer[jj + 1][mm]);</a>
+<a name="311"><span class="lineNum">     311 </span>            :       }</a>
+<a name="312"><span class="lineNum">     312 </span>            : #endif</a>
+<a name="313"><span class="lineNum">     313 </span>            :       // the calculate the derivative of output of layer jj, from derivative of input of layer (jj + 1)</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       4368 :       for (int mm = 0; mm &lt; num_nodes[jj]; mm ++) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       3276 :         derivatives_of_each_layer[jj][mm] = 0;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       9828 :         for (int kk = 0; kk &lt; num_nodes[jj + 1]; kk ++) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       6552 :           derivatives_of_each_layer[jj][mm] += coeff[jj][kk][mm] \</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       6552 :                                                * temp_derivative_of_input_for_this_layer[kk];</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : #ifdef DEBUG</a>
+<a name="320"><span class="lineNum">     320 </span>            :           printf(&quot;derivatives_of_each_layer[%d][%d] = %lf\n&quot;, jj, mm, derivatives_of_each_layer[jj][mm]);</a>
+<a name="321"><span class="lineNum">     321 </span>            :           printf(&quot;coeff[%d][%d][%d] = %lf\n&quot;, jj, kk, mm, coeff[jj][kk][mm]);</a>
+<a name="322"><span class="lineNum">     322 </span>            : #endif</a>
+<a name="323"><span class="lineNum">     323 </span>            :         }</a>
+<a name="324"><span class="lineNum">     324 </span>            :       }</a>
+<a name="325"><span class="lineNum">     325 </span>            :       // TODO: should be fine, pass all tests, although there seems to be some problems here previously</a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span>            :     else {</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">      10920 :       for (int mm = 0; mm &lt; num_nodes[jj]; mm ++) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       7644 :         derivatives_of_each_layer[jj][mm] = 0;</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">      24024 :         for (int kk = 0; kk &lt; num_nodes[jj + 1]; kk ++) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">      16380 :           if (activations[jj] == string(&quot;Tanh&quot;)) {</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :             // printf(&quot;tanh\n&quot;);</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">      14742 :             derivatives_of_each_layer[jj][mm] += derivatives_of_each_layer[jj + 1][kk] \</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      14742 :                                                  * coeff[jj][kk][mm] \</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      14742 :                                                  * (1 - output_of_each_layer[jj + 1][kk] * output_of_each_layer[jj + 1][kk]);</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :           }</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">       1638 :           else if (activations[jj] == string(&quot;Linear&quot;)) {</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :             // printf(&quot;linear\n&quot;);</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       1638 :             derivatives_of_each_layer[jj][mm] += derivatives_of_each_layer[jj + 1][kk] \</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       1638 :                                                  * coeff[jj][kk][mm] \</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       1638 :                                                  * 1;</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :           }</a>
+<a name="343"><span class="lineNum">     343 </span>            :           else {</a>
+<a name="344"><span class="lineNum">     344 </span>            :             printf(&quot;layer type not found!\n\n&quot;);</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :             return;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :           }</a>
+<a name="347"><span class="lineNum">     347 </span>            :         }</a>
+<a name="348"><span class="lineNum">     348 </span>            :       }</a>
+<a name="349"><span class="lineNum">     349 </span>            :     }</a>
+<a name="350"><span class="lineNum">     350 </span>            :   }</a>
+<a name="351"><span class="lineNum">     351 </span>            : #ifdef DEBUG</a>
+<a name="352"><span class="lineNum">     352 </span>            :   // print out the result for debugging</a>
+<a name="353"><span class="lineNum">     353 </span>            :   printf(&quot;derivatives_of_each_layer = \n&quot;);</a>
+<a name="354"><span class="lineNum">     354 </span>            :   for (int ii = 0; ii &lt; num_layers; ii ++) {</a>
+<a name="355"><span class="lineNum">     355 </span>            :     printf(&quot;layer[%d]: &quot;, ii);</a>
+<a name="356"><span class="lineNum">     356 </span>            :     for (int jj = 0; jj &lt; num_nodes[ii]; jj ++) {</a>
+<a name="357"><span class="lineNum">     357 </span>            :       printf(&quot;%lf\t&quot;, derivatives_of_each_layer[ii][jj]);</a>
+<a name="358"><span class="lineNum">     358 </span>            :     }</a>
+<a name="359"><span class="lineNum">     359 </span>            :     printf(&quot;\n&quot;);</a>
+<a name="360"><span class="lineNum">     360 </span>            :   }</a>
+<a name="361"><span class="lineNum">     361 </span>            :   printf(&quot;\n&quot;);</a>
+<a name="362"><span class="lineNum">     362 </span>            : #endif</a>
+<a name="363"><span class="lineNum">     363 </span>            :   return;</a>
+<a name="364"><span class="lineNum">     364 </span>            : }</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       1638 : void ANN::calculate() {</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">       1638 :   vector&lt;double&gt; input_layer_data(num_nodes[0]);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">       4914 :   for (int ii = 0; ii &lt; num_nodes[0]; ii ++) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       3276 :     input_layer_data[ii] = getArgument(ii);</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :   }</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">       1638 :   calculate_output_of_each_layer(input_layer_data);</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :   vector&lt;vector&lt;double&gt; &gt; derivatives_of_each_layer;</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">       3822 :   for (int ii = 0; ii &lt; num_nodes[num_layers - 1]; ii ++) {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">       2184 :     back_prop(derivatives_of_each_layer, ii);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">       2184 :     string name_of_this_component = &quot;node-&quot; + to_string(ii);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">       2184 :     Value* value_new=getPntrToComponent(name_of_this_component);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">       2184 :     value_new -&gt; set(output_of_each_layer[num_layers - 1][ii]);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       6552 :     for (int jj = 0; jj &lt; num_nodes[0]; jj ++) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       4368 :       value_new -&gt; setDerivative(jj, derivatives_of_each_layer[0][jj]);  // TODO: setDerivative or addDerivative?</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     }</a>
+<a name="384"><span class="lineNum">     384 </span>            : #ifdef DEBUG_3</a>
+<a name="385"><span class="lineNum">     385 </span>            :     printf(&quot;derivatives = &quot;);</a>
+<a name="386"><span class="lineNum">     386 </span>            :     for (int jj = 0; jj &lt; num_nodes[0]; jj ++) {</a>
+<a name="387"><span class="lineNum">     387 </span>            :       printf(&quot;%f &quot;, value_new -&gt; getDerivative(jj));</a>
+<a name="388"><span class="lineNum">     388 </span>            :     }</a>
+<a name="389"><span class="lineNum">     389 </span>            :     printf(&quot;\n&quot;);</a>
+<a name="390"><span class="lineNum">     390 </span>            : #endif</a>
+<a name="391"><span class="lineNum">     391 </span>            :   }</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       3276 : }</span></a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            : }</a>
+<a name="396"><span class="lineNum">     396 </span>            : }</a>
+<a name="397"><span class="lineNum">     397 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/annfunc/index-sort-f.html b/coverage/annfunc/index-sort-f.html
new file mode 100644
index 0000000000..06982566ca
--- /dev/null
+++ b/coverage/annfunc/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - annfunc</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - annfunc</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ANN.cpp.gcov.html">ANN.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.1%"><img src="../snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/annfunc/index-sort-l.html b/coverage/annfunc/index-sort-l.html
new file mode 100644
index 0000000000..2422133ec4
--- /dev/null
+++ b/coverage/annfunc/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - annfunc</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - annfunc</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ANN.cpp.gcov.html">ANN.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.1%"><img src="../snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/annfunc/index.html b/coverage/annfunc/index.html
new file mode 100644
index 0000000000..bb68c79523
--- /dev/null
+++ b/coverage/annfunc/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - annfunc</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - annfunc</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ANN.cpp.gcov.html">ANN.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.1%"><img src="../snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ABMD.cpp.func-sort-c.html b/coverage/bias/ABMD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5c4e82357f
--- /dev/null
+++ b/coverage/bias/ABMD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ABMD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ABMD.cpp<span style="font-size: 80%;"> (<a href="ABMD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ABMD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#109">_ZN4PLMD4bias4ABMDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#93">_ZN4PLMD4bias12_GLOBAL__N_116ABMDRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#109">_ZN4PLMD4bias4ABMDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#95">_ZN4PLMD4bias4ABMD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#148">_ZN4PLMD4bias4ABMD9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#93">_ZN4PLMD4bias12_GLOBAL__N_116ABMDRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#93">_ZN4PLMD4bias12_GLOBAL__N_116ABMDRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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new file mode 100644
index 0000000000..c8d972c9c6
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ABMD.cpp<span style="font-size: 80%;"> (<a href="ABMD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
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+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#93">_ZN4PLMD4bias12_GLOBAL__N_116ABMDRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#93">_ZN4PLMD4bias12_GLOBAL__N_116ABMDRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#95">_ZN4PLMD4bias4ABMD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#148">_ZN4PLMD4bias4ABMD9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#109">_ZN4PLMD4bias4ABMDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ABMD.cpp.gcov.html#109">_ZN4PLMD4bias4ABMDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
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diff --git a/coverage/bias/ABMD.cpp.gcov.html b/coverage/bias/ABMD.cpp.gcov.html
new file mode 100644
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+  <title>LCOV - plumed test coverage - bias/ABMD.cpp</title>
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ABMD.cpp<span style="font-size: 80%;"> (source / <a href="ABMD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;ctime&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace bias {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC BIAS ABMD</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Adds a ratchet-and-pawl like restraint on one or more variables.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This action can be used to evolve a system towards a target value in</a>
+<a name="35"><span class="lineNum">      35 </span>            : CV space using an harmonic potential moving with the thermal fluctuations of the CV</a>
+<a name="36"><span class="lineNum">      36 </span>            : \cite ballone \cite provasi10abmd \cite camilloni11abmd. The biasing potential in this</a>
+<a name="37"><span class="lineNum">      37 </span>            : method is as follows:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$</a>
+<a name="40"><span class="lineNum">      40 </span>            : V(\rho(t)) = \left \{ \begin{array}{ll} \frac{K}{2}\left(\rho(t)-\rho_m(t)\right)^2, &amp;\rho(t)&gt;\rho_m(t)\\</a>
+<a name="41"><span class="lineNum">      41 </span>            :               0, &amp; \rho(t)\le\rho_m(t), \end{array} \right .</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f$</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : where</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \f$</a>
+<a name="49"><span class="lineNum">      49 </span>            : \rho(t)=\left(CV(t)-TO\right)^2</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f$</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : and</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \f$</a>
+<a name="57"><span class="lineNum">      57 </span>            : \rho_m(t)=\min_{0\le\tau\le t}\rho(\tau)+\eta(t)</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f$.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The method is based on the introduction of a biasing potential which is zero when</a>
+<a name="61"><span class="lineNum">      61 </span>            : the system is moving towards the desired arrival point and which damps the</a>
+<a name="62"><span class="lineNum">      62 </span>            : fluctuations when the system attempts to move in the opposite direction. As in the</a>
+<a name="63"><span class="lineNum">      63 </span>            : case of the ratchet and pawl system, propelled by thermal motion of the solvent</a>
+<a name="64"><span class="lineNum">      64 </span>            : molecules, the biasing potential does not exert work on the system. \f$\eta(t)\f$ is</a>
+<a name="65"><span class="lineNum">      65 </span>            : an additional white noise acting on the minimum position of the bias.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \par Examples</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : The following input sets up two biases, one on the distance between atoms 3 and 5</a>
+<a name="70"><span class="lineNum">      70 </span>            : and another on the distance between atoms 2 and 4. The two target values are defined</a>
+<a name="71"><span class="lineNum">      71 </span>            : using TO and the two strength using KAPPA. The total energy of the bias is printed.</a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="74"><span class="lineNum">      74 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="75"><span class="lineNum">      75 </span>            : ABMD ARG=d1,d2 TO=1.0,1.5 KAPPA=5.0,5.0 LABEL=abmd</a>
+<a name="76"><span class="lineNum">      76 </span>            : PRINT ARG=abmd.bias,abmd.d1_min,abmd.d2_min</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endplumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : class ABMD : public Bias {</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;double&gt; to;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;double&gt; min;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;double&gt; kappa;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;double&gt; temp;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   std::vector&lt;int&gt; seed;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;Random&gt; random;</a>
+<a name="89"><span class="lineNum">      89 </span>            : public:</a>
+<a name="90"><span class="lineNum">      90 </span>            :   explicit ABMD(const ActionOptions&amp;);</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void calculate() override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(ABMD,&quot;ABMD&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          3 : void ABMD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          3 :   Bias::registerKeywords(keys);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          3 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;TO&quot;,&quot;The array of target values&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;The array of force constants.&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;MIN&quot;,&quot;Array of starting values for the bias (set rho_m(t), otherwise it is set using the current value of ARG)&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;NOISE&quot;,&quot;Array of white noise intensities (add a temperature to the ABMD)&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;SEED&quot;,&quot;Array of seeds for the white noise (add a temperature to the ABMD)&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;_min&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :                           &quot; These quantities will be named with the arguments of the bias followed by &quot;</a>
+<a name="108"><span class="lineNum">     108 </span>            :                           &quot;the character string _min. These quantities tell the user the minimum value assumed by rho_m(t).&quot;);</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          3 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 : ABMD::ABMD(const ActionOptions&amp;ao):</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   to(getNumberOfArguments(),0.0),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   min(getNumberOfArguments(),-1.0),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          1 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :   temp(getNumberOfArguments(),0.0),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :   seed(getNumberOfArguments(),std::time(0)),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   random(getNumberOfArguments())</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : {</a>
+<a name="120"><span class="lineNum">     120 </span>            :   // Note : parseVector will check that number of arguments is correct</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          1 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   parseVector(&quot;MIN&quot;,min);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :   if(min.size()==0) min.assign(getNumberOfArguments(),-1.0);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 :   if(min.size()!=getNumberOfArguments()) error(&quot;MIN array should have the same size as ARG array&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :   parseVector(&quot;NOISE&quot;,temp);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   parseVector(&quot;SEED&quot;,seed);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          1 :   parseVector(&quot;TO&quot;,to);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   log.printf(&quot;  min&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;min.size(); i++) log.printf(&quot; %f&quot;,min[i]);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          1 :   log.printf(&quot;  to&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;to.size(); i++) log.printf(&quot; %f&quot;,to[i]);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   log.printf(&quot;  with force constant&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :     std::string str_min=getPntrToArgument(i)-&gt;getName()+&quot;_min&quot;;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :     addComponent(str_min); componentIsNotPeriodic(str_min);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :     if(min[i]!=-1.0) getPntrToComponent(str_min)-&gt;set(min[i]);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {random[i].setSeed(-seed[i]);}</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 :   addComponent(&quot;force2&quot;); componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          5 : void ABMD::calculate() {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   double ene=0.0;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   double totf2=0.0;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          5 :     const double cv=difference(i,to[i],getArgument(i));</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          5 :     const double cv2=cv*cv;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          5 :     const double k=kappa[i];</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     double noise=0.;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          5 :     double diff=temp[i];</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          5 :     if(diff&gt;0) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          5 :       noise = 2.*random[i].Gaussian()*diff;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          5 :       if(cv2&lt;=diff) { diff=0.; temp[i]=0.; }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            :     // min &lt; 0 means that the variable has not been used in the input file, so the current position of the CV is used</a>
+<a name="165"><span class="lineNum">     165 </span>            :     // cv2 &lt; min means that the collective variable is nearer to the target value than at any other previous time so</a>
+<a name="166"><span class="lineNum">     166 </span>            :     // min is set to the CV value</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          5 :     if(min[i]&lt;0.||cv2&lt;min[i]) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :       min[i] = cv2;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     } else {</a>
+<a name="170"><span class="lineNum">     170 </span>            :       // otherwise a noise is added to the minimum value</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 :       min[i] += noise;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 :       const double f = -2.*k*(cv2-min[i])*cv;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :       setOutputForce(i,f);</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          4 :       ene += 0.5*k*(cv2-min[i])*(cv2-min[i]);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          4 :       totf2+=f*f;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :     }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          5 :     getPntrToComponent(i+1)-&gt;set(min[i]);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            :   setBias(ene);</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          5 :   getPntrToComponent(&quot;force2&quot;)-&gt;set(totf2);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          5 : }</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Bias.cpp.func-sort-c.html b/coverage/bias/Bias.cpp.func-sort-c.html
new file mode 100644
index 0000000000..49aec3ac62
--- /dev/null
+++ b/coverage/bias/Bias.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Bias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Bias.cpp<span style="font-size: 80%;"> (<a href="Bias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Bias.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#26">_ZN4PLMD4bias4BiasC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#26">_ZN4PLMD4bias4BiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">682</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#48">_ZN4PLMD4bias4Bias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">733</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#58">_ZN4PLMD4bias4Bias5applyEv</a></td>
+              <td class="coverFnHi">78588</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Bias.cpp.func.html b/coverage/bias/Bias.cpp.func.html
new file mode 100644
index 0000000000..3f0164ae65
--- /dev/null
+++ b/coverage/bias/Bias.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Bias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Bias.cpp<span style="font-size: 80%;"> (<a href="Bias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Bias.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#48">_ZN4PLMD4bias4Bias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">733</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#58">_ZN4PLMD4bias4Bias5applyEv</a></td>
+              <td class="coverFnHi">78588</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#26">_ZN4PLMD4bias4BiasC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.cpp.gcov.html#26">_ZN4PLMD4bias4BiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">682</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Bias.cpp.gcov.html b/coverage/bias/Bias.cpp.gcov.html
new file mode 100644
index 0000000000..74a63deeb6
--- /dev/null
+++ b/coverage/bias/Bias.cpp.gcov.html
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Bias.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Bias.cpp<span style="font-size: 80%;"> (source / <a href="Bias.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace bias {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        682 : Bias::Bias(const ActionOptions&amp;ao):</span></a>
+<a name="29"><span class="lineNum">      29 </span>            :   Action(ao),</a>
+<a name="30"><span class="lineNum">      30 </span>            :   ActionPilot(ao),</a>
+<a name="31"><span class="lineNum">      31 </span>            :   ActionWithValue(ao),</a>
+<a name="32"><span class="lineNum">      32 </span>            :   ActionWithArguments(ao),</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        682 :   outputForces(getNumberOfArguments(),0.0)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        679 :   addComponentWithDerivatives(&quot;bias&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        679 :   componentIsNotPeriodic(&quot;bias&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        679 :   valueBias=getPntrToComponent(&quot;bias&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        679 :   if(getStride()&gt;1) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          3 :     log&lt;&lt;&quot;  multiple time step &quot;&lt;&lt;getStride()&lt;&lt;&quot; &quot;;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          6 :     log&lt;&lt;cite(&quot;Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   }</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       4496 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       3817 :     (getPntrToArgument(i)-&gt;getPntrToAction())-&gt;turnOnDerivatives();</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   }</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        679 :   ActionWithValue::turnOnDerivatives();</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        682 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        733 : void Bias::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        733 :   Action::registerKeywords(keys);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        733 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        733 :   ActionWithValue::registerKeywords(keys);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        733 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1466 :   keys.add(&quot;hidden&quot;,&quot;STRIDE&quot;,&quot;the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        733 :   componentsAreNotOptional(keys);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1466 :   keys.addOutputComponent(&quot;bias&quot;,&quot;default&quot;,&quot;the instantaneous value of the bias potential&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        733 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      78588 : void Bias::apply() {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      78588 :   const unsigned noa=getNumberOfArguments();</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      78588 :   const unsigned ncp=getNumberOfComponents();</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      78588 :   if(onStep()) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      78588 :     double gstr = static_cast&lt;double&gt;(getStride());</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     224527 :     for(unsigned i=0; i&lt;noa; ++i) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     145939 :       getPntrToArgument(i)-&gt;addForce(gstr*outputForces[i]);</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     }</a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   // additional forces on the bias component</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      78588 :   std::vector&lt;double&gt; f(noa,0.0);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      78588 :   std::vector&lt;double&gt; forces(noa);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool at_least_one_forced=false;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     398305 :   for(unsigned i=0; i&lt;ncp; ++i) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     319717 :     if(getPntrToComponent(i)-&gt;applyForce(forces)) {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :       at_least_one_forced=true;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        913 :       for(unsigned j=0; j&lt;noa; j++) f[j]+=forces[j];</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     }</a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      78588 :   if(at_least_one_forced &amp;&amp; !onStep()) error(&quot;you are biasing a bias with an inconsistent STRIDE&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      79429 :   if(at_least_one_forced) for(unsigned i=0; i&lt;noa; ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        559 :       getPntrToArgument(i)-&gt;addForce(f[i]);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :     }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      78588 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Bias.h.func-sort-c.html b/coverage/bias/Bias.h.func-sort-c.html
new file mode 100644
index 0000000000..95ab36956f
--- /dev/null
+++ b/coverage/bias/Bias.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Bias.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Bias.h<span style="font-size: 80%;"> (<a href="Bias.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Bias.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.h.gcov.html#71">_ZN4PLMD4bias4Bias22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">795</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Bias.h.func.html b/coverage/bias/Bias.h.func.html
new file mode 100644
index 0000000000..92cabd2e1e
--- /dev/null
+++ b/coverage/bias/Bias.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Bias.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Bias.h<span style="font-size: 80%;"> (<a href="Bias.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Bias.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Bias.h.gcov.html#71">_ZN4PLMD4bias4Bias22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">795</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Bias.h.gcov.html b/coverage/bias/Bias.h.gcov.html
new file mode 100644
index 0000000000..a2601202c6
--- /dev/null
+++ b/coverage/bias/Bias.h.gcov.html
@@ -0,0 +1,157 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Bias.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Bias.h<span style="font-size: 80%;"> (source / <a href="Bias.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_bias_Bias_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_bias_Bias_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #define PLUMED_BIAS_INIT(ao) Action(ao),Bias(ao)</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace bias {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /**</a>
+<a name="35"><span class="lineNum">      35 </span>            : \ingroup INHERIT</a>
+<a name="36"><span class="lineNum">      36 </span>            : This is the abstract base class to use for implementing new simulation biases, within it there is</a>
+<a name="37"><span class="lineNum">      37 </span>            : information as to how to go about implementing a new bias.</a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class Bias :</a>
+<a name="41"><span class="lineNum">      41 </span>            :   public ActionPilot,</a>
+<a name="42"><span class="lineNum">      42 </span>            :   public ActionWithValue,</a>
+<a name="43"><span class="lineNum">      43 </span>            :   public ActionWithArguments</a>
+<a name="44"><span class="lineNum">      44 </span>            : {</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// the vector of the forces</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::vector&lt;double&gt; outputForces;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// the pointer to the bias component</a>
+<a name="48"><span class="lineNum">      48 </span>            :   Value *valueBias;</a>
+<a name="49"><span class="lineNum">      49 </span>            : protected:</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// set the force from the bias on argument i, this automatically set the partial derivative of the bias with respect to i to -f</a>
+<a name="51"><span class="lineNum">      51 </span>            :   void setOutputForce(int i,double f);</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// set the value of the bias</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void setBias(double bias);</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit Bias(const ActionOptions&amp;ao);</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void apply() override;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="59"><span class="lineNum">      59 </span>            : };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : inline</a>
+<a name="62"><span class="lineNum">      62 </span>            : void Bias::setOutputForce(int i,double f) {</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">     141271 :   outputForces[i]=f;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">     142382 :   valueBias-&gt;addDerivative(i,-f);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : inline</a>
+<a name="68"><span class="lineNum">      68 </span>            : void Bias::setBias(double bias) {</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      78335 :   valueBias-&gt;set(bias);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      38433 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : inline</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        795 : unsigned Bias::getNumberOfDerivatives() {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        795 :   return getNumberOfArguments();</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : #endif</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/BiasValue.cpp.func-sort-c.html b/coverage/bias/BiasValue.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c835b6a54a
--- /dev/null
+++ b/coverage/bias/BiasValue.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/BiasValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - BiasValue.cpp<span style="font-size: 80%;"> (<a href="BiasValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BiasValue.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#92">_ZN4PLMD4bias9BiasValueC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#80">_ZN4PLMD4bias12_GLOBAL__N_121BiasValueRegisterMe826createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#92">_ZN4PLMD4bias9BiasValueC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#82">_ZN4PLMD4bias9BiasValue16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#103">_ZN4PLMD4bias9BiasValue9calculateEv</a></td>
+              <td class="coverFnHi">472</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#80">_ZN4PLMD4bias12_GLOBAL__N_121BiasValueRegisterMe82C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#80">_ZN4PLMD4bias12_GLOBAL__N_121BiasValueRegisterMe82D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/BiasValue.cpp.func.html b/coverage/bias/BiasValue.cpp.func.html
new file mode 100644
index 0000000000..203ba55fb0
--- /dev/null
+++ b/coverage/bias/BiasValue.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/BiasValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - BiasValue.cpp<span style="font-size: 80%;"> (<a href="BiasValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BiasValue.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#80">_ZN4PLMD4bias12_GLOBAL__N_121BiasValueRegisterMe826createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#80">_ZN4PLMD4bias12_GLOBAL__N_121BiasValueRegisterMe82C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#80">_ZN4PLMD4bias12_GLOBAL__N_121BiasValueRegisterMe82D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#82">_ZN4PLMD4bias9BiasValue16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#103">_ZN4PLMD4bias9BiasValue9calculateEv</a></td>
+              <td class="coverFnHi">472</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#92">_ZN4PLMD4bias9BiasValueC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasValue.cpp.gcov.html#92">_ZN4PLMD4bias9BiasValueC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/BiasValue.cpp.gcov.html b/coverage/bias/BiasValue.cpp.gcov.html
new file mode 100644
index 0000000000..fdf92664bb
--- /dev/null
+++ b/coverage/bias/BiasValue.cpp.gcov.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/BiasValue.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - BiasValue.cpp<span style="font-size: 80%;"> (source / <a href="BiasValue.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace bias {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC BIAS BIASVALUE</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Takes the value of one variable and use it as a bias</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This is the simplest possible bias: the bias potential is equal to a collective variable.</a>
+<a name="33"><span class="lineNum">      33 </span>            : It is useful to create custom biasing potential, e.g. applying a function (see \ref Function)</a>
+<a name="34"><span class="lineNum">      34 </span>            : to some collective variable then using the value of this function directly as a bias.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input tells plumed to use the value of the distance between atoms 3 and 5</a>
+<a name="39"><span class="lineNum">      39 </span>            : and the value of the distance between atoms 2 and 4 as biases.</a>
+<a name="40"><span class="lineNum">      40 </span>            : It then tells plumed to print the energy of the restraint</a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="43"><span class="lineNum">      43 </span>            : DISTANCE ATOMS=3,6 LABEL=d2</a>
+<a name="44"><span class="lineNum">      44 </span>            : BIASVALUE ARG=d1,d2 LABEL=b</a>
+<a name="45"><span class="lineNum">      45 </span>            : PRINT ARG=d1,d2,b.d1_bias,b.d2_bias</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : Another thing one can do is asking one system to follow</a>
+<a name="49"><span class="lineNum">      49 </span>            : a circle in sin/cos according a  time dependence</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : t: TIME</a>
+<a name="53"><span class="lineNum">      53 </span>            : # this just print cos and sin of time</a>
+<a name="54"><span class="lineNum">      54 </span>            : cos: MATHEVAL ARG=t VAR=t FUNC=cos(t) PERIODIC=NO</a>
+<a name="55"><span class="lineNum">      55 </span>            : sin: MATHEVAL ARG=t VAR=t FUNC=sin(t) PERIODIC=NO</a>
+<a name="56"><span class="lineNum">      56 </span>            : c1: COM ATOMS=1,2</a>
+<a name="57"><span class="lineNum">      57 </span>            : c2: COM ATOMS=3,4</a>
+<a name="58"><span class="lineNum">      58 </span>            : d: DISTANCE COMPONENTS ATOMS=c1,c2</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=t,cos,sin,d.x,d.y,d.z STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="60"><span class="lineNum">      60 </span>            : # this calculates sine and cosine of a projected component of distance</a>
+<a name="61"><span class="lineNum">      61 </span>            : mycos:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=x/sqrt(x*x+y*y) PERIODIC=NO</a>
+<a name="62"><span class="lineNum">      62 </span>            : mysin:  MATHEVAL ARG=d.x,d.y  VAR=x,y   FUNC=y/sqrt(x*x+y*y) PERIODIC=NO</a>
+<a name="63"><span class="lineNum">      63 </span>            : # this creates a moving spring so that the system follows a circle-like dynamics</a>
+<a name="64"><span class="lineNum">      64 </span>            : # but it is not a bias, it is a simple value now</a>
+<a name="65"><span class="lineNum">      65 </span>            : vv1:  MATHEVAL ARG=mycos,mysin,cos,sin VAR=mc,ms,c,s  FUNC=100*((mc-c)^2+(ms-s)^2) PERIODIC=NO</a>
+<a name="66"><span class="lineNum">      66 </span>            : # this takes the value calculated with matheval and uses as a bias</a>
+<a name="67"><span class="lineNum">      67 </span>            : cc: BIASVALUE ARG=vv1</a>
+<a name="68"><span class="lineNum">      68 </span>            : # some printout</a>
+<a name="69"><span class="lineNum">      69 </span>            : PRINT ARG=t,cos,sin,d.x,d.y,d.z,mycos,mysin,cc.vv1_bias STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : class BiasValue : public Bias {</a>
+<a name="76"><span class="lineNum">      76 </span>            : public:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   explicit BiasValue(const ActionOptions&amp;);</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void calculate() override;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="80"><span class="lineNum">      80 </span>            : };</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      12568 : PLUMED_REGISTER_ACTION(BiasValue,&quot;BIASVALUE&quot;)</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         34 : void BiasValue::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         34 :   Bias::registerKeywords(keys);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         34 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   // Should be _bias below</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         68 :   keys.addOutputComponent(&quot;_bias&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :                           &quot;these quantities will named with  the arguments of the bias followed by &quot;</a>
+<a name="90"><span class="lineNum">      90 </span>            :                           &quot;the character string _bias. These quantities tell the user how much the bias is &quot;</a>
+<a name="91"><span class="lineNum">      91 </span>            :                           &quot;due to each of the colvars.&quot;);</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         34 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         32 : BiasValue::BiasValue(const ActionOptions&amp;ao):</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         32 :   PLUMED_BIAS_INIT(ao)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         32 :   checkRead();</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   // add one bias for each argument</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         65 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         33 :     std::string ss=getPntrToArgument(i)-&gt;getName()+&quot;_bias&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         33 :     addComponent(ss); componentIsNotPeriodic(ss);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         32 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        472 : void BiasValue::calculate() {</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   double bias=0.0;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        950 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :     double val; val=getArgument(i);</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        478 :     getPntrToComponent(i+1)-&gt;set(val);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        478 :     setOutputForce(i,-1.);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        478 :     bias+=val;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span>            :   setBias(bias);</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        472 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ExtendedLagrangian.cpp.func-sort-c.html b/coverage/bias/ExtendedLagrangian.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9d88be011a
--- /dev/null
+++ b/coverage/bias/ExtendedLagrangian.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ExtendedLagrangian.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ExtendedLagrangian.cpp<span style="font-size: 80%;"> (<a href="ExtendedLagrangian.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExtendedLagrangian.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#145">_ZN4PLMD4bias18ExtendedLagrangianC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#127">_ZN4PLMD4bias12_GLOBAL__N_131ExtendedLagrangianRegisterMe1296createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#145">_ZN4PLMD4bias18ExtendedLagrangianC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#129">_ZN4PLMD4bias18ExtendedLagrangian16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#238">_ZN4PLMD4bias18ExtendedLagrangian6updateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#213">_ZN4PLMD4bias18ExtendedLagrangian9calculateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#127">_ZN4PLMD4bias12_GLOBAL__N_131ExtendedLagrangianRegisterMe129C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#127">_ZN4PLMD4bias12_GLOBAL__N_131ExtendedLagrangianRegisterMe129D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ExtendedLagrangian.cpp.func.html b/coverage/bias/ExtendedLagrangian.cpp.func.html
new file mode 100644
index 0000000000..00a0067540
--- /dev/null
+++ b/coverage/bias/ExtendedLagrangian.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ExtendedLagrangian.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ExtendedLagrangian.cpp<span style="font-size: 80%;"> (<a href="ExtendedLagrangian.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExtendedLagrangian.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#127">_ZN4PLMD4bias12_GLOBAL__N_131ExtendedLagrangianRegisterMe1296createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#127">_ZN4PLMD4bias12_GLOBAL__N_131ExtendedLagrangianRegisterMe129C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#127">_ZN4PLMD4bias12_GLOBAL__N_131ExtendedLagrangianRegisterMe129D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#129">_ZN4PLMD4bias18ExtendedLagrangian16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#238">_ZN4PLMD4bias18ExtendedLagrangian6updateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#213">_ZN4PLMD4bias18ExtendedLagrangian9calculateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#145">_ZN4PLMD4bias18ExtendedLagrangianC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtendedLagrangian.cpp.gcov.html#145">_ZN4PLMD4bias18ExtendedLagrangianC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ExtendedLagrangian.cpp.gcov.html b/coverage/bias/ExtendedLagrangian.cpp.gcov.html
new file mode 100644
index 0000000000..b269ddb8d3
--- /dev/null
+++ b/coverage/bias/ExtendedLagrangian.cpp.gcov.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ExtendedLagrangian.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ExtendedLagrangian.cpp<span style="font-size: 80%;"> (source / <a href="ExtendedLagrangian.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace bias {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC BIAS EXTENDED_LAGRANGIAN</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Add extended Lagrangian.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This action can be used to create fictitious collective variables coupled to the real ones.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Given \f$x_i\f$ the \f$i\f$th argument of this bias potential, potential</a>
+<a name="37"><span class="lineNum">      37 </span>            : and kinetic contributions are added to the energy of the system as</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            :   V=\sum_i \frac{k_i}{2} (x_i-s_i)^2 + \sum_i \frac{\dot{s}_i^2}{2m_i}</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f].</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : The resulting potential is thus similar to a \ref RESTRAINT,</a>
+<a name="43"><span class="lineNum">      43 </span>            : but the restraint center moved with time following Hamiltonian</a>
+<a name="44"><span class="lineNum">      44 </span>            : dynamics with mass \f$m_i\f$.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : This bias potential accepts thus vectorial keywords (one element per argument)</a>
+<a name="47"><span class="lineNum">      47 </span>            : to define the coupling constant (KAPPA) and a relaxation time \f$tau\f$ (TAU).</a>
+<a name="48"><span class="lineNum">      48 </span>            : The mass is them computed as \f$m=k(\frac{\tau}{2\pi})^2\f$.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : Notice that this action creates several components.</a>
+<a name="51"><span class="lineNum">      51 </span>            : The ones named XX_fict are the fictitious coordinates. It is possible</a>
+<a name="52"><span class="lineNum">      52 </span>            : to add further forces on them by means of other bias potential,</a>
+<a name="53"><span class="lineNum">      53 </span>            : e.g. to obtain an indirect \ref METAD as in \cite continua .</a>
+<a name="54"><span class="lineNum">      54 </span>            : Also notice that the velocities of the fictitious coordinates</a>
+<a name="55"><span class="lineNum">      55 </span>            : are reported (XX_vfict). However, printed velocities are the ones</a>
+<a name="56"><span class="lineNum">      56 </span>            : at the previous step.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : It is also possible to provide a non-zero friction (one value per component).</a>
+<a name="59"><span class="lineNum">      59 </span>            : This is then used to implement a Langevin thermostat, so as to implement</a>
+<a name="60"><span class="lineNum">      60 </span>            : TAMD/dAFED method \cite Maragliano2006 \cite AbramsJ2008 . Notice that</a>
+<a name="61"><span class="lineNum">      61 </span>            : here a massive Langevin thermostat is used, whereas usually</a>
+<a name="62"><span class="lineNum">      62 </span>            : TAMD employs an overamped Langevin dynamics and dAFED</a>
+<a name="63"><span class="lineNum">      63 </span>            : a Gaussian thermostat.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \warning</a>
+<a name="66"><span class="lineNum">      66 </span>            : The bias potential is reported in the component bias.</a>
+<a name="67"><span class="lineNum">      67 </span>            : Notice that this bias potential, although formally compatible with</a>
+<a name="68"><span class="lineNum">      68 </span>            : replica exchange framework, probably does not work as expected in that case.</a>
+<a name="69"><span class="lineNum">      69 </span>            : Indeed, since fictitious coordinates are not swapped upon exchange,</a>
+<a name="70"><span class="lineNum">      70 </span>            : acceptace can be expected to be extremely low unless (by chance) two neighboring</a>
+<a name="71"><span class="lineNum">      71 </span>            : replicas have the fictitious variables located properly in space.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \warning</a>
+<a name="74"><span class="lineNum">      74 </span>            : \ref RESTART is not properly supported by this action. Indeed,</a>
+<a name="75"><span class="lineNum">      75 </span>            : at every start the position of the fictitious variable is reset to the value</a>
+<a name="76"><span class="lineNum">      76 </span>            : of the real variable, and its velocity is set to zero.</a>
+<a name="77"><span class="lineNum">      77 </span>            : This is not expected to introduce big errors, but certainly is</a>
+<a name="78"><span class="lineNum">      78 </span>            : introducing a small inconsistency between a single long run</a>
+<a name="79"><span class="lineNum">      79 </span>            : and many shorter runs.</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \par Examples</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : The following input tells plumed to perform a metadynamics</a>
+<a name="84"><span class="lineNum">      84 </span>            : with an extended Lagrangian on two torsional angles.</a>
+<a name="85"><span class="lineNum">      85 </span>            : \plumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="87"><span class="lineNum">      87 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="88"><span class="lineNum">      88 </span>            : ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1</a>
+<a name="89"><span class="lineNum">      89 </span>            : METAD ARG=ex.phi_fict,ex.psi_fict PACE=100 SIGMA=0.35,0.35 HEIGHT=0.1</a>
+<a name="90"><span class="lineNum">      90 </span>            : # monitor the two variables</a>
+<a name="91"><span class="lineNum">      91 </span>            : PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR</a>
+<a name="92"><span class="lineNum">      92 </span>            : \endplumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : The following input tells plumed to perform a TAMD (or dAFED)</a>
+<a name="95"><span class="lineNum">      95 </span>            : calculation on two torsional angles, keeping the two variables</a>
+<a name="96"><span class="lineNum">      96 </span>            : at a fictitious temperature of 3000K with a Langevin thermostat</a>
+<a name="97"><span class="lineNum">      97 </span>            : with friction 10</a>
+<a name="98"><span class="lineNum">      98 </span>            : \plumedfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="100"><span class="lineNum">     100 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="101"><span class="lineNum">     101 </span>            : ex: EXTENDED_LAGRANGIAN ARG=phi,psi KAPPA=20,20.0 TAU=0.1,0.1 FRICTION=10,10 TEMP=3000</a>
+<a name="102"><span class="lineNum">     102 </span>            : # monitor the two variables</a>
+<a name="103"><span class="lineNum">     103 </span>            : PRINT STRIDE=10 ARG=phi,psi,ex.phi_fict,ex.psi_fict FILE=COLVAR</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endplumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : */</a>
+<a name="107"><span class="lineNum">     107 </span>            : //+ENDPLUMEDOC</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : class ExtendedLagrangian : public Bias {</a>
+<a name="110"><span class="lineNum">     110 </span>            :   bool firsttime;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;double&gt; fict;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;double&gt; vfict;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;double&gt; vfict_laststep;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;double&gt; ffict;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   std::vector&lt;double&gt; kappa;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::vector&lt;double&gt; tau;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;double&gt; friction;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   std::vector&lt;Value*&gt; fictValue;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::vector&lt;Value*&gt; vfictValue;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   double kbt;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   Random rand;</a>
+<a name="122"><span class="lineNum">     122 </span>            : public:</a>
+<a name="123"><span class="lineNum">     123 </span>            :   explicit ExtendedLagrangian(const ActionOptions&amp;);</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void calculate() override;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   void update() override;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="127"><span class="lineNum">     127 </span>            : };</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ExtendedLagrangian,&quot;EXTENDED_LAGRANGIAN&quot;)</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 : void ExtendedLagrangian::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          4 :   Bias::registerKeywords(keys);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;specifies that the restraint is harmonic and what the values of the force constants on each of the variables are&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;TAU&quot;,&quot;specifies that the restraint is harmonic and what the values of the force constants on each of the variables are&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;FRICTION&quot;,&quot;0.0&quot;,&quot;add a friction to the variable&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - needed when FRICTION is present. If not provided will be taken from MD code (if available)&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 :   componentsAreNotOptional(keys);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;_fict&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :                           &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="141"><span class="lineNum">     141 </span>            :                           &quot;the character string _tilde. It is possible to add forces on these variable.&quot;);</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;_vfict&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :                           &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="144"><span class="lineNum">     144 </span>            :                           &quot;the character string _tilde. It is NOT possible to add forces on these variable.&quot;);</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          4 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 : ExtendedLagrangian::ExtendedLagrangian(const ActionOptions&amp;ao):</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   firsttime(true),</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          4 :   fict(getNumberOfArguments(),0.0),</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          2 :   vfict(getNumberOfArguments(),0.0),</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          2 :   vfict_laststep(getNumberOfArguments(),0.0),</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :   ffict(getNumberOfArguments(),0.0),</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          2 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   tau(getNumberOfArguments(),0.0),</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :   friction(getNumberOfArguments(),0.0),</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :   fictValue(getNumberOfArguments(),NULL),</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          2 :   vfictValue(getNumberOfArguments(),NULL),</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          4 :   kbt(0.0)</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : {</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :   parseVector(&quot;TAU&quot;,tau);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          2 :   parseVector(&quot;FRICTION&quot;,friction);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 :   double temp=-1.0;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :   if(temp&gt;=0.0) kbt=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   else kbt=plumed.getAtoms().getKbT();</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :   log.printf(&quot;  with harmonic force constant&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :   log.printf(&quot;  with relaxation time&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;tau.size(); i++) log.printf(&quot; %f&quot;,tau[i]);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   bool hasFriction=false;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) if(friction[i]&gt;0.0) hasFriction=true;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :   if(hasFriction) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :     log.printf(&quot;  with friction&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;friction.size(); i++) log.printf(&quot; %f&quot;,friction[i]);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          2 :   log.printf(&quot;  and kbt&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :   log.printf(&quot; %f&quot;,kbt);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          4 :     std::string comp=getPntrToArgument(i)-&gt;getName()+&quot;_fict&quot;;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 :     addComponentWithDerivatives(comp);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          4 :     if(getPntrToArgument(i)-&gt;isPeriodic()) {</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :       std::string a,b;</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          4 :       getPntrToArgument(i)-&gt;getDomain(a,b);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          4 :       componentIsPeriodic(comp,a,b);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :     } else componentIsNotPeriodic(comp);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          4 :     fictValue[i]=getPntrToComponent(comp);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          4 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_vfict&quot;;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          4 :     addComponent(comp);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 :     componentIsNotPeriodic(comp);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          4 :     vfictValue[i]=getPntrToComponent(comp);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          4 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Iannuzzi, Laio, and Parrinello, Phys. Rev. Lett. 90, 238302 (2003)&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          2 :   if(hasFriction) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          4 :     log&lt;&lt;plumed.cite(&quot;Maragliano and Vanden-Eijnden, Chem. Phys. Lett. 426, 168 (2006)&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          4 :     log&lt;&lt;plumed.cite(&quot;Abrams and Tuckerman, J. Phys. Chem. B 112, 15742 (2008)&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          2 : }</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         24 : void ExtendedLagrangian::calculate() {</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         24 :   if(firsttime) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          4 :       fict[i]=getArgument(i);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :     }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          2 :     firsttime=false;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span>            :   double ene=0.0;</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         72 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         48 :     const double cv=difference(i,fict[i],getArgument(i));</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         48 :     const double k=kappa[i];</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         48 :     const double f=-k*cv;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         48 :     ene+=0.5*k*cv*cv;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :     setOutputForce(i,f);</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         48 :     ffict[i]=-f;</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   };</a>
+<a name="232"><span class="lineNum">     232 </span>            :   setBias(ene);</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         72 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         48 :     fict[i]=fictValue[i]-&gt;bringBackInPbc(fict[i]);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         48 :     fictValue[i]-&gt;set(fict[i]);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         48 :     vfictValue[i]-&gt;set(vfict_laststep[i]);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         24 : }</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         24 : void ExtendedLagrangian::update() {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         24 :   double dt=getTimeStep()*getStride();</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         72 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         48 :     double mass=kappa[i]*tau[i]*tau[i]/(4*pi*pi); // should be k/omega**2</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         48 :     double c1=std::exp(-0.5*friction[i]*dt);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         48 :     double c2=std::sqrt(kbt*(1.0-c1*c1)/mass);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : // consider additional forces on the fictitious particle</a>
+<a name="247"><span class="lineNum">     247 </span>            : // (e.g. MetaD stuff)</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         48 :     ffict[i]+=fictValue[i]-&gt;getForce();</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : // update velocity (half step)</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         48 :     vfict[i]+=ffict[i]*0.5*dt/mass;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : // thermostat (half step)</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         48 :     vfict[i]=c1*vfict[i]+c2*rand.Gaussian();</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : // save full step velocity to be dumped at next step</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         48 :     vfict_laststep[i]=vfict[i];</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : // thermostat (half step)</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         48 :     vfict[i]=c1*vfict[i]+c2*rand.Gaussian();</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : // update velocity (half step)</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         48 :     vfict[i]+=ffict[i]*0.5*dt/mass;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : // update position (full step)</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         48 :     fict[i]+=vfict[i]*dt;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         24 : }</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/External.cpp.func-sort-c.html b/coverage/bias/External.cpp.func-sort-c.html
new file mode 100644
index 0000000000..197224f3ba
--- /dev/null
+++ b/coverage/bias/External.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/External.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - External.cpp<span style="font-size: 80%;"> (<a href="External.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="External.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#130">_ZN4PLMD4bias8ExternalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#119">_ZN4PLMD4bias12_GLOBAL__N_121ExternalRegisterMe1216createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#130">_ZN4PLMD4bias8ExternalC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#121">_ZN4PLMD4bias8External16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#160">_ZN4PLMD4bias8External9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#119">_ZN4PLMD4bias12_GLOBAL__N_121ExternalRegisterMe121C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#119">_ZN4PLMD4bias12_GLOBAL__N_121ExternalRegisterMe121D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/External.cpp.func.html b/coverage/bias/External.cpp.func.html
new file mode 100644
index 0000000000..a91f64141c
--- /dev/null
+++ b/coverage/bias/External.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/External.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - External.cpp<span style="font-size: 80%;"> (<a href="External.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="External.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#119">_ZN4PLMD4bias12_GLOBAL__N_121ExternalRegisterMe1216createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#119">_ZN4PLMD4bias12_GLOBAL__N_121ExternalRegisterMe121C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#119">_ZN4PLMD4bias12_GLOBAL__N_121ExternalRegisterMe121D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#121">_ZN4PLMD4bias8External16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#160">_ZN4PLMD4bias8External9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#130">_ZN4PLMD4bias8ExternalC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="External.cpp.gcov.html#130">_ZN4PLMD4bias8ExternalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/External.cpp.gcov.html b/coverage/bias/External.cpp.gcov.html
new file mode 100644
index 0000000000..b8b183fb65
--- /dev/null
+++ b/coverage/bias/External.cpp.gcov.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/External.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - External.cpp<span style="font-size: 80%;"> (source / <a href="External.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace bias {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC BIAS EXTERNAL</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculate a restraint that is defined on a grid that is read during start up</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \par Examples</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The following is an input for a calculation with an external potential that is</a>
+<a name="38"><span class="lineNum">      38 </span>            : defined in the file bias.dat and that acts on the distance between atoms 3 and 5.</a>
+<a name="39"><span class="lineNum">      39 </span>            : \plumedfile</a>
+<a name="40"><span class="lineNum">      40 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="41"><span class="lineNum">      41 </span>            : EXTERNAL ARG=d1 FILE=bias.grid LABEL=external</a>
+<a name="42"><span class="lineNum">      42 </span>            : \endplumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : The bias.grid will then look something like this:</a>
+<a name="45"><span class="lineNum">      45 </span>            : \auxfile{bias.grid}</a>
+<a name="46"><span class="lineNum">      46 </span>            : #! FIELDS d1 external.bias der_d1</a>
+<a name="47"><span class="lineNum">      47 </span>            : #! SET min_d1 1.14</a>
+<a name="48"><span class="lineNum">      48 </span>            : #! SET max_d1 1.32</a>
+<a name="49"><span class="lineNum">      49 </span>            : #! SET nbins_d1 6</a>
+<a name="50"><span class="lineNum">      50 </span>            : #! SET periodic_d1 false</a>
+<a name="51"><span class="lineNum">      51 </span>            :    1.1400   0.0031   0.1101</a>
+<a name="52"><span class="lineNum">      52 </span>            :    1.1700   0.0086   0.2842</a>
+<a name="53"><span class="lineNum">      53 </span>            :    1.2000   0.0222   0.6648</a>
+<a name="54"><span class="lineNum">      54 </span>            :    1.2300   0.0521   1.4068</a>
+<a name="55"><span class="lineNum">      55 </span>            :    1.2600   0.1120   2.6873</a>
+<a name="56"><span class="lineNum">      56 </span>            :    1.2900   0.2199   4.6183</a>
+<a name="57"><span class="lineNum">      57 </span>            :    1.3200   0.3948   7.1055</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endauxfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : This should then be followed by the value of the potential and its derivative</a>
+<a name="61"><span class="lineNum">      61 </span>            : at 100 equally spaced points along the distance between 0 and 1.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : You can also include grids that are a function of more than one collective</a>
+<a name="64"><span class="lineNum">      64 </span>            : variable.  For instance the following would be the input for an external</a>
+<a name="65"><span class="lineNum">      65 </span>            : potential acting on two torsional angles:</a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : TORSION ATOMS=4,5,6,7 LABEL=t1</a>
+<a name="68"><span class="lineNum">      68 </span>            : TORSION ATOMS=6,7,8,9 LABEL=t2</a>
+<a name="69"><span class="lineNum">      69 </span>            : EXTERNAL ARG=t1,t2 FILE=bias2.grid LABEL=ext</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The file bias2.grid for this calculation would need to look something like this:</a>
+<a name="73"><span class="lineNum">      73 </span>            : \auxfile{bias2.grid}</a>
+<a name="74"><span class="lineNum">      74 </span>            : #! FIELDS t1 t2 ext.bias der_t1 der_t2</a>
+<a name="75"><span class="lineNum">      75 </span>            : #! SET min_t1 -pi</a>
+<a name="76"><span class="lineNum">      76 </span>            : #! SET max_t1 pi</a>
+<a name="77"><span class="lineNum">      77 </span>            : #! SET nbins_t1 3</a>
+<a name="78"><span class="lineNum">      78 </span>            : #! SET periodic_t1 true</a>
+<a name="79"><span class="lineNum">      79 </span>            : #! SET min_t2 -pi</a>
+<a name="80"><span class="lineNum">      80 </span>            : #! SET max_t2 pi</a>
+<a name="81"><span class="lineNum">      81 </span>            : #! SET nbins_t2 3</a>
+<a name="82"><span class="lineNum">      82 </span>            : #! SET periodic_t2 true</a>
+<a name="83"><span class="lineNum">      83 </span>            :  -3.141593 -3.141593 0.000000 -0.000000 -0.000000</a>
+<a name="84"><span class="lineNum">      84 </span>            :  -1.047198 -3.141593 0.000000 0.000000 -0.000000</a>
+<a name="85"><span class="lineNum">      85 </span>            :  1.047198 -3.141593 0.000000 -0.000000 -0.000000</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :  -3.141593 -1.047198 0.000000 -0.000000 0.000000</a>
+<a name="88"><span class="lineNum">      88 </span>            :  -1.047198 -1.047198 0.007922 0.033185 0.033185</a>
+<a name="89"><span class="lineNum">      89 </span>            :  1.047198 -1.047198 0.007922 -0.033185 0.033185</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :  -3.141593 1.047198 0.000000 -0.000000 -0.000000</a>
+<a name="92"><span class="lineNum">      92 </span>            :  -1.047198 1.047198 0.007922 0.033185 -0.033185</a>
+<a name="93"><span class="lineNum">      93 </span>            :  1.047198 1.047198 0.007922 -0.033185 -0.033185</a>
+<a name="94"><span class="lineNum">      94 </span>            : \endauxfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : This would be then followed by 100 blocks of data.  In the first block of data the</a>
+<a name="97"><span class="lineNum">      97 </span>            : value of t1 (the value in the first column) is kept fixed and the value of</a>
+<a name="98"><span class="lineNum">      98 </span>            : the function is given at 100 equally spaced values for t2 between \f$-pi\f$ and \f$+pi\f$.  In the</a>
+<a name="99"><span class="lineNum">      99 </span>            : second block of data t1 is fixed at \f$-pi + \frac{2pi}{100}\f$ and the value of the function is</a>
+<a name="100"><span class="lineNum">     100 </span>            : given at 100 equally spaced values for t2 between \f$-pi\f$ and \f$+pi\f$. In the third block of</a>
+<a name="101"><span class="lineNum">     101 </span>            : data the same is done but t1 is fixed at \f$-pi + \frac{4pi}{100}\f$ and so on until you get to</a>
+<a name="102"><span class="lineNum">     102 </span>            : the one hundredth block of data where t1 is fixed at \f$+pi\f$.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : Please note the order that the order of arguments in the plumed.dat file must be the same as</a>
+<a name="105"><span class="lineNum">     105 </span>            : the order of arguments in the header of the grid file.</a>
+<a name="106"><span class="lineNum">     106 </span>            : */</a>
+<a name="107"><span class="lineNum">     107 </span>            : //+ENDPLUMEDOC</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : class External : public Bias {</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : private:</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::unique_ptr&lt;GridBase&gt; BiasGrid_;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double scale_;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : public:</a>
+<a name="116"><span class="lineNum">     116 </span>            :   explicit External(const ActionOptions&amp;);</a>
+<a name="117"><span class="lineNum">     117 </span>            :   void calculate() override;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="119"><span class="lineNum">     119 </span>            : };</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      12507 : PLUMED_REGISTER_ACTION(External,&quot;EXTERNAL&quot;)</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 : void External::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          4 :   Bias::registerKeywords(keys);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          4 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file containing the external potential.&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          8 :   keys.addFlag(&quot;NOSPLINE&quot;,false,&quot;specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          8 :   keys.addFlag(&quot;SPARSE&quot;,false,&quot;specifies that the external potential uses a sparse grid&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;SCALE&quot;,&quot;1.0&quot;,&quot;a factor that multiplies the external potential, useful to invert free energies&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          4 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 : External::External(const ActionOptions&amp; ao):</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   PLUMED_BIAS_INIT(ao)</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : {</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::string filename;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 :   parse(&quot;FILE&quot;,filename);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :   if( filename.length()==0 ) error(&quot;No external potential file was specified&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :   bool sparsegrid=false;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :   parseFlag(&quot;SPARSE&quot;,sparsegrid);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   bool nospline=false;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :   parseFlag(&quot;NOSPLINE&quot;,nospline);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          2 :   bool spline=!nospline;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 :   parse(&quot;SCALE&quot;,scale_);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :   log.printf(&quot;  External potential from file %s\n&quot;,filename.c_str());</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :   log.printf(&quot;  Multiplied by %lf\n&quot;,scale_);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   if(spline) {log.printf(&quot;  External potential uses spline interpolation\n&quot;);}</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :   if(sparsegrid) {log.printf(&quot;  External potential uses sparse grid\n&quot;);}</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : // read grid</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :   IFile gridfile; gridfile.open(filename);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          1 :   std::string funcl=getLabel() + &quot;.bias&quot;;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   BiasGrid_=GridBase::create(funcl,getArguments(),gridfile,sparsegrid,spline,true);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   if(BiasGrid_-&gt;getDimension()!=getNumberOfArguments()) error(&quot;mismatch between dimensionality of input grid and number of arguments&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :     if( getPntrToArgument(i)-&gt;isPeriodic()!=BiasGrid_-&gt;getIsPeriodic()[i] ) error(&quot;periodicity mismatch between arguments and input bias&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          6 : }</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          5 : void External::calculate()</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : {</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          5 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          5 :   std::vector&lt;double&gt; cv(ncv), der(ncv);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;ncv; ++i) {cv[i]=getArgument(i);}</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          5 :   double ene=scale_*BiasGrid_-&gt;getValueAndDerivatives(cv,der);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   setBias(ene);</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         10 :     const double f=-scale_*der[i];</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         10 :     setOutputForce(i,f);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          5 : }</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/LWalls.cpp.func-sort-c.html b/coverage/bias/LWalls.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6209e28391
--- /dev/null
+++ b/coverage/bias/LWalls.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/LWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - LWalls.cpp<span style="font-size: 80%;"> (<a href="LWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LWalls.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#87">_ZN4PLMD4bias6LWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#74">_ZN4PLMD4bias12_GLOBAL__N_118LWallsRegisterMe766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#87">_ZN4PLMD4bias6LWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#76">_ZN4PLMD4bias6LWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#122">_ZN4PLMD4bias6LWalls9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#74">_ZN4PLMD4bias12_GLOBAL__N_118LWallsRegisterMe76C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#74">_ZN4PLMD4bias12_GLOBAL__N_118LWallsRegisterMe76D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/LWalls.cpp.func.html b/coverage/bias/LWalls.cpp.func.html
new file mode 100644
index 0000000000..1e1f11fb8f
--- /dev/null
+++ b/coverage/bias/LWalls.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/LWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - LWalls.cpp<span style="font-size: 80%;"> (<a href="LWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LWalls.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#74">_ZN4PLMD4bias12_GLOBAL__N_118LWallsRegisterMe766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#74">_ZN4PLMD4bias12_GLOBAL__N_118LWallsRegisterMe76C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#74">_ZN4PLMD4bias12_GLOBAL__N_118LWallsRegisterMe76D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#76">_ZN4PLMD4bias6LWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#122">_ZN4PLMD4bias6LWalls9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#87">_ZN4PLMD4bias6LWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#87">_ZN4PLMD4bias6LWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/LWalls.cpp.gcov.html b/coverage/bias/LWalls.cpp.gcov.html
new file mode 100644
index 0000000000..baaaeae0b9
--- /dev/null
+++ b/coverage/bias/LWalls.cpp.gcov.html
@@ -0,0 +1,224 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/LWalls.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - LWalls.cpp<span style="font-size: 80%;"> (source / <a href="LWalls.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace bias {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC BIAS LOWER_WALLS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Defines a wall for the value of one or more collective variables,</a>
+<a name="31"><span class="lineNum">      31 </span>            :  which limits the region of the phase space accessible during the simulation.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : The restraining potential starts acting on the system when the value of the CV is greater</a>
+<a name="34"><span class="lineNum">      34 </span>            : (in the case of UPPER_WALLS) or lower (in the case of LOWER_WALLS) than a certain limit \f$a_i\f$ (AT)</a>
+<a name="35"><span class="lineNum">      35 </span>            : minus an offset \f$o_i\f$ (OFFSET).</a>
+<a name="36"><span class="lineNum">      36 </span>            : The expression for the bias due to the wall is given by:</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \f$</a>
+<a name="39"><span class="lineNum">      39 </span>            :   \sum_i {k_i}((x_i-a_i+o_i)/s_i)^e_i</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f$</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f$k_i\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s_i\f$ (EPS) a rescaling factor and</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f$e_i\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFFSET = 0.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The following input tells plumed to add both a lower and an upper walls on the distance</a>
+<a name="49"><span class="lineNum">      49 </span>            : between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits</a>
+<a name="50"><span class="lineNum">      50 </span>            : are defined at different values. The strength of the walls is the same for the four cases.</a>
+<a name="51"><span class="lineNum">      51 </span>            : It also tells plumed to print the energy of the walls.</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="54"><span class="lineNum">      54 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="55"><span class="lineNum">      55 </span>            : UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall</a>
+<a name="56"><span class="lineNum">      56 </span>            : LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=uwall.bias,lwall.bias</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : (See also \ref DISTANCE and \ref PRINT).</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : */</a>
+<a name="62"><span class="lineNum">      62 </span>            : //+ENDPLUMEDOC</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : class LWalls : public Bias {</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;double&gt; at;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;double&gt; kappa;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;double&gt; exp;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;double&gt; eps;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;double&gt; offset;</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit LWalls(const ActionOptions&amp;);</a>
+<a name="72"><span class="lineNum">      72 </span>            :   void calculate() override;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(LWalls,&quot;LOWER_WALLS&quot;)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          3 : void LWalls::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          3 :   Bias::registerKeywords(keys);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;the positions of the wall. The a_i in the expression for a wall.&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;the force constant for the wall.  The k_i in the expression for a wall.&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET&quot;,&quot;0.0&quot;,&quot;the offset for the start of the wall.  The o_i in the expression for a wall.&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;EXP&quot;,&quot;2.0&quot;,&quot;the powers for the walls.  The e_i in the expression for a wall.&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;EPS&quot;,&quot;1.0&quot;,&quot;the values for s_i in the expression for a wall&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 : LWalls::LWalls(const ActionOptions&amp;ao):</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   at(getNumberOfArguments(),0),</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          1 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          1 :   exp(getNumberOfArguments(),2.0),</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 :   eps(getNumberOfArguments(),1.0),</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   offset(getNumberOfArguments(),0.0)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : {</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Note sizes of these vectors are automatically checked by parseVector :-)</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          1 :   parseVector(&quot;OFFSET&quot;,offset);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          1 :   parseVector(&quot;EPS&quot;,eps);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          1 :   parseVector(&quot;EXP&quot;,exp);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 :   parseVector(&quot;AT&quot;,at);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          1 :   log.printf(&quot;  at&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;at.size(); i++) log.printf(&quot; %f&quot;,at[i]);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          1 :   log.printf(&quot;  with an offset&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;offset.size(); i++) log.printf(&quot; %f&quot;,offset[i]);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 :   log.printf(&quot;  with force constant&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   log.printf(&quot;  and exponent&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;exp.size(); i++) log.printf(&quot; %f&quot;,exp[i]);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :   log.printf(&quot;  rescaled&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;eps.size(); i++) log.printf(&quot; %f&quot;,eps[i]);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   addComponent(&quot;force2&quot;); componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          5 : void LWalls::calculate() {</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   double ene = 0.0;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   double totf2 = 0.0;</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     double f = 0.0;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          5 :     const double cv=difference(i,at[i],getArgument(i));</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          5 :     const double off=offset[i];</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          5 :     const double epsilon=eps[i];</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          5 :     const double lscale = (cv-off)/epsilon;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          5 :     if( lscale &lt; 0.) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          5 :       const double k=kappa[i];</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          5 :       const double exponent=exp[i];</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          5 :       double power = std::pow( lscale, exponent );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          5 :       f = -( k / epsilon ) * exponent * power / lscale;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          5 :       ene += k * power;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          5 :       totf2 += f * f;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            :     setOutputForce(i,f);</a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            :   setBias(ene);</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          5 :   getPntrToComponent(&quot;force2&quot;)-&gt;set(totf2);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          5 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MaxEnt.cpp.func-sort-c.html b/coverage/bias/MaxEnt.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d84c8a0d25
--- /dev/null
+++ b/coverage/bias/MaxEnt.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MaxEnt.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MaxEnt.cpp<span style="font-size: 80%;"> (<a href="MaxEnt.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">227</td>
+            <td class="headerCovTableEntry">236</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MaxEnt.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#199">_ZN4PLMD4bias6MaxEntC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#325">_ZN4PLMD4bias6MaxEnt15ReadLagrangiansERNS_5IFileE</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#161">_ZN4PLMD4bias12_GLOBAL__N_119MaxEntRegisterMe1636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#199">_ZN4PLMD4bias6MaxEntC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#163">_ZN4PLMD4bias6MaxEnt16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#409">_ZN4PLMD4bias6MaxEnt13update_lambdaEv</a></td>
+              <td class="coverFnHi">550</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#343">_ZN4PLMD4bias6MaxEnt16WriteLagrangiansERSt6vectorIdSaIdEERNS_5OFileE</a></td>
+              <td class="coverFnHi">550</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#161">_ZN4PLMD4bias12_GLOBAL__N_119MaxEntRegisterMe163C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#161">_ZN4PLMD4bias12_GLOBAL__N_119MaxEntRegisterMe163D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#469">_ZN4PLMD4bias6MaxEnt6updateEv</a></td>
+              <td class="coverFnHi">5050</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#451">_ZN4PLMD4bias6MaxEnt9calculateEv</a></td>
+              <td class="coverFnHi">5050</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#360">_ZN4PLMD4bias6MaxEnt13compute_errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">5302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#395">_ZN4PLMD4bias6MaxEnt23check_lambda_boundariesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERd</a></td>
+              <td class="coverFnHi">5302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#373">_ZN4PLMD4bias6MaxEnt14convert_lambdaERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">119118</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MaxEnt.cpp.func.html b/coverage/bias/MaxEnt.cpp.func.html
new file mode 100644
index 0000000000..e16f8a7993
--- /dev/null
+++ b/coverage/bias/MaxEnt.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MaxEnt.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MaxEnt.cpp<span style="font-size: 80%;"> (<a href="MaxEnt.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">227</td>
+            <td class="headerCovTableEntry">236</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MaxEnt.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#161">_ZN4PLMD4bias12_GLOBAL__N_119MaxEntRegisterMe1636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#161">_ZN4PLMD4bias12_GLOBAL__N_119MaxEntRegisterMe163C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#161">_ZN4PLMD4bias12_GLOBAL__N_119MaxEntRegisterMe163D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#360">_ZN4PLMD4bias6MaxEnt13compute_errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">5302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#409">_ZN4PLMD4bias6MaxEnt13update_lambdaEv</a></td>
+              <td class="coverFnHi">550</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#373">_ZN4PLMD4bias6MaxEnt14convert_lambdaERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">119118</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#325">_ZN4PLMD4bias6MaxEnt15ReadLagrangiansERNS_5IFileE</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#343">_ZN4PLMD4bias6MaxEnt16WriteLagrangiansERSt6vectorIdSaIdEERNS_5OFileE</a></td>
+              <td class="coverFnHi">550</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#163">_ZN4PLMD4bias6MaxEnt16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#395">_ZN4PLMD4bias6MaxEnt23check_lambda_boundariesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERd</a></td>
+              <td class="coverFnHi">5302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#469">_ZN4PLMD4bias6MaxEnt6updateEv</a></td>
+              <td class="coverFnHi">5050</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#451">_ZN4PLMD4bias6MaxEnt9calculateEv</a></td>
+              <td class="coverFnHi">5050</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#199">_ZN4PLMD4bias6MaxEntC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MaxEnt.cpp.gcov.html#199">_ZN4PLMD4bias6MaxEntC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MaxEnt.cpp.gcov.html b/coverage/bias/MaxEnt.cpp.gcov.html
new file mode 100644
index 0000000000..428e755fe3
--- /dev/null
+++ b/coverage/bias/MaxEnt.cpp.gcov.html
@@ -0,0 +1,564 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MaxEnt.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MaxEnt.cpp<span style="font-size: 80%;"> (source / <a href="MaxEnt.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">227</td>
+            <td class="headerCovTableEntry">236</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : // The original implementation of this method was contributed</a>
+<a name="31"><span class="lineNum">      31 </span>            : // by Andrea Cesari (andreacesari90@gmail.com).</a>
+<a name="32"><span class="lineNum">      32 </span>            : // Copyright has been then transferred to PLUMED developers</a>
+<a name="33"><span class="lineNum">      33 </span>            : // (see https://github.com/plumed/plumed2/blob/master/.github/CONTRIBUTING.md)</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace bias {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC BIAS MAXENT</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Add a linear biasing potential on one or more variables that satisfies a maximum entropy principle.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Add a linear biasing potential on one or more variables \f$f_{i}\left(\boldsymbol{x}\right)\f$ satisfying the maximum entropy principle as proposed in Ref. \cite cesari2016maxent .</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \warning</a>
+<a name="45"><span class="lineNum">      45 </span>            :     Notice that syntax is still under revision and might change</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The resulting biasing potential is given by:</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            :   V_{BIAS}(\boldsymbol{x},t)=K_{B}T\sum_{i=1}^{\#arguments}f_{i}(\boldsymbol{x},t)\lambda_{i}(t)</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : Lagrangian multipliers \f$ \lambda_{i}\f$ are updated, every PACE steps, according to the following update rule:</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f[</a>
+<a name="53"><span class="lineNum">      53 </span>            : \lambda_{i}=\lambda_{i}+\frac{k_{i}}{1+\frac{t}{\tau_{i}}}\left(f_{exp,i}+\xi_{i}\lambda_{i}-f_{i}(\boldsymbol{x})\right)</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f]</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f$k\f$ set the initial value of the learning rate and its units are \f$[observable]^{-2}ps^{-1}\f$. This can be set with the keyword KAPPA.</a>
+<a name="56"><span class="lineNum">      56 </span>            : The number of components for any KAPPA vector must be equal to the number of arguments of the action.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : Variable \f$ \xi_{i}(\lambda) \f$ is related to the chosen prior to model experimental errors. If a GAUSSIAN prior is used then:</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f[</a>
+<a name="60"><span class="lineNum">      60 </span>            : \xi_{i}(\lambda)=-\lambda_{i}\sigma^{2}</a>
+<a name="61"><span class="lineNum">      61 </span>            : \f]</a>
+<a name="62"><span class="lineNum">      62 </span>            : where \f$ \sigma \f$ is the typical expected error on the observable \f$ f_i\f$.</a>
+<a name="63"><span class="lineNum">      63 </span>            : For a LAPLACE prior:</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f[</a>
+<a name="65"><span class="lineNum">      65 </span>            : \xi_{i}(\lambda)=-\frac{\lambda_{i}\sigma^{2}}{1-\frac{\lambda^{2}\sigma^{2}}{2}}</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \f]</a>
+<a name="68"><span class="lineNum">      68 </span>            : The value of \f$ \xi(\lambda,t)\f$ is written in output as a component named: argument name followed by the string _error.</a>
+<a name="69"><span class="lineNum">      69 </span>            : Setting \f$ \sigma =0\f$ is equivalent to enforce a pure Maximum Entropy restraint without any noise modelling.</a>
+<a name="70"><span class="lineNum">      70 </span>            : This method can be also used to enforce inequality restraint as shown in following examples.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : Notice that a similar method is available as \ref EDS, although with different features and using a different optimization algorithm.</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \par Examples</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : The following input tells plumed to restrain the distance between atoms 7 and 15</a>
+<a name="77"><span class="lineNum">      77 </span>            : and the distance between atoms 2 and 19, at different equilibrium</a>
+<a name="78"><span class="lineNum">      78 </span>            : values, and to print the energy of the restraint.</a>
+<a name="79"><span class="lineNum">      79 </span>            : Lagrangian multiplier will be printed on a file called restraint.LAGMULT with a stride set by the variable PACE to 200ps.</a>
+<a name="80"><span class="lineNum">      80 </span>            : Moreover plumed will compute the average of each Lagrangian multiplier in the window [TSTART,TEND] and use that to continue the simulations with fixed Lagrangian multipliers.</a>
+<a name="81"><span class="lineNum">      81 </span>            : \plumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : DISTANCE ATOMS=7,15 LABEL=d1</a>
+<a name="83"><span class="lineNum">      83 </span>            : DISTANCE ATOMS=2,19 LABEL=d2</a>
+<a name="84"><span class="lineNum">      84 </span>            : MAXENT ...</a>
+<a name="85"><span class="lineNum">      85 </span>            : ARG=d1,d2</a>
+<a name="86"><span class="lineNum">      86 </span>            : TYPE=EQUAL</a>
+<a name="87"><span class="lineNum">      87 </span>            : AT=0.2,0.5</a>
+<a name="88"><span class="lineNum">      88 </span>            : KAPPA=35000.0,35000.0</a>
+<a name="89"><span class="lineNum">      89 </span>            : TAU=0.02,0.02</a>
+<a name="90"><span class="lineNum">      90 </span>            : PACE=200</a>
+<a name="91"><span class="lineNum">      91 </span>            : TSTART=100</a>
+<a name="92"><span class="lineNum">      92 </span>            : TEND=500</a>
+<a name="93"><span class="lineNum">      93 </span>            : LABEL=restraint</a>
+<a name="94"><span class="lineNum">      94 </span>            : ... MAXENT</a>
+<a name="95"><span class="lineNum">      95 </span>            : PRINT ARG=restraint.bias</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endplumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : Lagrangian multipliers will be printed on a file called restraint.bias</a>
+<a name="98"><span class="lineNum">      98 </span>            : The following input tells plumed to restrain the distance between atoms 7 and 15</a>
+<a name="99"><span class="lineNum">      99 </span>            : to be greater than 0.2 and to print the energy of the restraint</a>
+<a name="100"><span class="lineNum">     100 </span>            : \plumedfile</a>
+<a name="101"><span class="lineNum">     101 </span>            : DISTANCE ATOMS=7,15 LABEL=d</a>
+<a name="102"><span class="lineNum">     102 </span>            : MAXENT ARG=d TYPE=INEQUAL&gt; AT=0.02 KAPPA=35000.0 TAU=3 LABEL=restraint</a>
+<a name="103"><span class="lineNum">     103 </span>            : PRINT ARG=restraint.bias</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endplumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : (See also \ref DISTANCE and \ref PRINT).</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : */</a>
+<a name="109"><span class="lineNum">     109 </span>            : //+ENDPLUMEDOC</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : class MaxEnt : public Bias {</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;double&gt; at;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;double&gt; kappa;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;double&gt; lambda;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   std::vector&lt;double&gt; avgx;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::vector&lt;double&gt; work;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;double&gt; oldlambda;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   std::vector&lt;double&gt; tau;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::vector&lt;double&gt; avglambda;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::vector&lt;double&gt; avglambda_restart;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::vector&lt;double&gt; expected_eps;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;double&gt; apply_weights;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   double sigma;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   double tstart;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double tend;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   double avgstep; //current number of samples over which to compute the average. Check if could be replaced bu getStep()</a>
+<a name="127"><span class="lineNum">     127 </span>            :   long long int pace_;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   long long int stride_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   double totalWork;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   double BetaReweightBias;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   double simtemp;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::vector&lt;ActionWithValue*&gt; biases;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::string type;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::string error_type;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   double alpha;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   double avg_counter;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   int learn_replica;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   Value* valueForce2;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   Value* valueWork;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   OFile lagmultOfile_;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   IFile ifile;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::string lagmultfname;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::string ifilesnames;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::string fmt;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   bool isFirstStep;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   bool reweight;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   bool no_broadcast;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   bool printFirstStep;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   std::vector&lt;bool&gt; done_average;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   int myrep,nrep;</a>
+<a name="151"><span class="lineNum">     151 </span>            : public:</a>
+<a name="152"><span class="lineNum">     152 </span>            :   explicit MaxEnt(const ActionOptions&amp;);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void calculate() override;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   void update() override;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void update_lambda();</a>
+<a name="156"><span class="lineNum">     156 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void ReadLagrangians(IFile &amp;ifile);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void WriteLagrangians(std::vector&lt;double&gt; &amp;lagmult,OFile &amp;file);</a>
+<a name="159"><span class="lineNum">     159 </span>            :   double compute_error(const std::string &amp;err_type,double l);</a>
+<a name="160"><span class="lineNum">     160 </span>            :   double convert_lambda(const std::string &amp;type,double lold);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void check_lambda_boundaries(const std::string &amp;err_type,double &amp;l);</a>
+<a name="162"><span class="lineNum">     162 </span>            : };</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      12604 : PLUMED_REGISTER_ACTION(MaxEnt,&quot;MAXENT&quot;)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         52 : void MaxEnt::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         52 :   Bias::registerKeywords(keys);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         52 :   componentsAreNotOptional(keys);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         52 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        104 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;0.0&quot;,&quot;specifies the initial value for the learning rate&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        104 :   keys.add(&quot;compulsory&quot;,&quot;TAU&quot;,&quot;Specify the dumping time for the learning rate.&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        104 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;specify the restraint type. &quot;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :            &quot;EQUAL to restrain the variable at a given equilibrium value &quot;</a>
+<a name="173"><span class="lineNum">     173 </span>            :            &quot;INEQUAL&lt; to restrain the variable to be smaller than a given value &quot;</a>
+<a name="174"><span class="lineNum">     174 </span>            :            &quot;INEQUAL&gt; to restrain the variable to be greater than a given value&quot;);</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;ERROR_TYPE&quot;,&quot;specify the prior on the error to use.&quot;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :            &quot;GAUSSIAN: use a Gaussian prior &quot;</a>
+<a name="177"><span class="lineNum">     177 </span>            :            &quot;LAPLACE: use a Laplace prior&quot;);</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;TSTART&quot;,&quot;time from where to start averaging the Lagrangian multiplier. By default no average is computed, hence lambda is updated every PACE steps&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;TEND&quot;,&quot;time in ps where to stop to compute the average of Lagrangian multiplier. From this time until the end of the simulation Lagrangian multipliers are kept fix to the average computed between TSTART and TEND;&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;ALPHA&quot;,&quot;default=1.0; To be used with LAPLACE KEYWORD, allows to choose a prior function proportional to a Gaussian times an exponential function. ALPHA=1 correspond to the LAPLACE prior.&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        104 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;the position of the restraint&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;SIGMA&quot;,&quot;The typical errors expected on observable&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;Lagrangian multipliers output file. The default name is: label name followed by the string .LAGMULT &quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;LEARN_REPLICA&quot;,&quot;In a multiple replica environment specify which is the reference replica. By default replica 0 will be used.&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;APPLY_WEIGHTS&quot;,&quot;Vector of weights containing 1 in correspondence of each replica that will receive the Lagrangian multiplier from the current one.&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;PACE&quot;,&quot;the frequency for Lagrangian multipliers update&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;PRINT_STRIDE&quot;,&quot;stride of Lagrangian multipliers output file. If no STRIDE is passed they are written every time they are updated (PACE).&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;specify format for Lagrangian multipliers files (useful to decrease the number of digits in regtests)&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        104 :   keys.addFlag(&quot;REWEIGHT&quot;,false,&quot;to be used with plumed driver in order to reweight a trajectory a posteriori&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        104 :   keys.addFlag(&quot;NO_BROADCAST&quot;,false,&quot;If active will avoid Lagrangian multipliers to be communicated to other replicas.&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        104 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature.  This is required if you are reweighting.&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        104 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential&quot;);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        104 :   keys.addOutputComponent(&quot;work&quot;,&quot;default&quot;,&quot;the instantaneous value of the work done by the biasing force&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        104 :   keys.addOutputComponent(&quot;_work&quot;,&quot;default&quot;,&quot;the instantaneous value of the work done by the biasing force for each argument. &quot;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :                           &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="196"><span class="lineNum">     196 </span>            :                           &quot;the character string _work.&quot;);</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        104 :   keys.addOutputComponent(&quot;_error&quot;,&quot;default&quot;,&quot;Instantaneous values of the discrepancy between the observable and the restraint center&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        104 :   keys.addOutputComponent(&quot;_coupling&quot;,&quot;default&quot;,&quot;Instantaneous values of Lagrangian multipliers. They are also written by default in a separate output file.&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         52 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         52 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         50 : MaxEnt::MaxEnt(const ActionOptions&amp;ao):</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        100 :   at(getNumberOfArguments()),</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         50 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         50 :   lambda(getNumberOfArguments(),0.0),</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         50 :   avgx(getNumberOfArguments(),0.0),</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         50 :   oldlambda(getNumberOfArguments(),0.0),</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         50 :   tau(getNumberOfArguments(),getTimeStep()),</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         50 :   avglambda(getNumberOfArguments(),0.0),</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         50 :   avglambda_restart(getNumberOfArguments(),0.0),</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         50 :   expected_eps(getNumberOfArguments(),0.0),</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         50 :   sigma(0.0),</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         50 :   pace_(100),</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         50 :   stride_(100),</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         50 :   alpha(1.0),</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         50 :   avg_counter(0.0),</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         50 :   isFirstStep(true),</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         50 :   reweight(false),</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         50 :   no_broadcast(false),</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         50 :   printFirstStep(true),</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        150 :   done_average(getNumberOfArguments(),false)</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : {</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         50 :   if(comm.Get_rank()==0) nrep=multi_sim_comm.Get_size();</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         50 :   if(comm.Get_rank()==0) myrep=multi_sim_comm.Get_rank();</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         50 :   comm.Bcast(nrep,0);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         50 :   comm.Bcast(myrep,0);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         50 :   parseFlag(&quot;NO_BROADCAST&quot;,no_broadcast);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   //if(no_broadcast){</a>
+<a name="229"><span class="lineNum">     229 </span>            :   //for(int irep=0;irep&lt;nrep;irep++){</a>
+<a name="230"><span class="lineNum">     230 </span>            :   //  if(irep!=myrep)</a>
+<a name="231"><span class="lineNum">     231 </span>            :   //    apply_weights[irep]=0.0;}</a>
+<a name="232"><span class="lineNum">     232 </span>            :   //}</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         50 :   avgstep=1.0;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         50 :   tstart=-1.0;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         50 :   tend=-1.0;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         50 :   totalWork=0.0;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         50 :   learn_replica=0;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         50 :   parse(&quot;LEARN_REPLICA&quot;,learn_replica);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        100 :   parseVector(&quot;APPLY_WEIGHTS&quot;,apply_weights);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         50 :   if(apply_weights.size()==0) apply_weights.resize(nrep,1.0);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         50 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         50 :   parseVector(&quot;AT&quot;,at);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         50 :   parseVector(&quot;TAU&quot;,tau);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        100 :   parse(&quot;TYPE&quot;,type);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   error_type=&quot;GAUSSIAN&quot;;</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         50 :   parse(&quot;ERROR_TYPE&quot;,error_type);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         50 :   parse(&quot;ALPHA&quot;,alpha);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         50 :   parse(&quot;SIGMA&quot;,sigma);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         50 :   parse(&quot;TSTART&quot;,tstart);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         50 :   if(tstart &lt;0 &amp;&amp; tstart != -1.0) error(&quot;TSTART should be a positive number&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         50 :   parse(&quot;TEND&quot;,tend);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         50 :   if(tend&lt;0 &amp;&amp; tend != -1.0) error(&quot;TSTART should be a positive number&quot;);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         50 :   if(tend&lt;tstart) error(&quot;TEND should be &gt;= TSTART&quot;);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         50 :   lagmultfname=getLabel()+&quot;.LAGMULT&quot;;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         50 :   parse(&quot;FILE&quot;,lagmultfname);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         50 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         50 :   parse(&quot;PACE&quot;,pace_);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         50 :   if(pace_&lt;=0 ) error(&quot;frequency for Lagrangian multipliers update (PACE) is nonsensical&quot;);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         50 :   stride_=pace_;  //if no STRIDE is passed, then Lagrangian multipliers willbe printed at each update</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         50 :   parse(&quot;PRINT_STRIDE&quot;,stride_);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         50 :   if(stride_&lt;=0 ) error(&quot;frequency for Lagrangian multipliers printing (STRIDE) is nonsensical&quot;);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         50 :   simtemp=0.;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         50 :   parse(&quot;TEMP&quot;,simtemp);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         50 :   if(simtemp&gt;0) simtemp*=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :   else simtemp=plumed.getAtoms().getKbT();</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         50 :   parseFlag(&quot;REWEIGHT&quot;,reweight);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         50 :   if(simtemp&lt;=0 &amp;&amp; reweight) error(&quot;Set the temperature (TEMP) if you want to do reweighting.&quot;);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         50 :   checkRead();</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         50 :   log.printf(&quot;  at&quot;);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        532 :   for(unsigned i=0; i&lt;at.size(); i++) log.printf(&quot; %f&quot;,at[i]);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         50 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         50 :   log.printf(&quot;  with initial learning rate for optimization of&quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        532 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         50 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         50 :   log.printf(&quot;Dumping times for the learning rates are (ps): &quot;);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        532 :   for(unsigned i=0; i&lt;tau.size(); i++) log.printf(&quot; %f&quot;,tau[i]);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         50 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         50 :   log.printf(&quot;Lagrangian multipliers are updated every %lld steps (PACE)\n&quot;,pace_);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         50 :   log.printf(&quot;Lagrangian multipliers output file %s\n&quot;,lagmultfname.c_str());</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         50 :   log.printf(&quot;Lagrangian multipliers are written every %lld steps (PRINT_STRIDE)\n&quot;,stride_);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         50 :   if(fmt.length()&gt;0)</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         50 :     log.printf(&quot;The format for real number in Lagrangian multipliers file is %s\n&quot;,fmt.c_str());</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         50 :   if(tstart &gt;-1.0 &amp;&amp; tend&gt;-1.0)</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         14 :     log.printf(&quot;Lagrangian multipliers are averaged from %lf ps to %lf ps\n&quot;,tstart,tend);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         50 :   if(no_broadcast)</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :     log.printf(&quot;Using NO_BROADCAST options. Lagrangian multipliers will not be comunicated to other replicas.\n&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   //for(int irep=0;irep&lt;nrep;irep++){</a>
+<a name="291"><span class="lineNum">     291 </span>            :   //  if(apply_weights[irep]!=0)</a>
+<a name="292"><span class="lineNum">     292 </span>            :   //    log.printf(&quot;%d&quot;,irep);</a>
+<a name="293"><span class="lineNum">     293 </span>            :   //  }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        100 :   addComponent(&quot;force2&quot;); componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        100 :   addComponent(&quot;work&quot;); componentIsNotPeriodic(&quot;work&quot;);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         50 :   valueForce2=getPntrToComponent(&quot;force2&quot;);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         50 :   valueWork=getPntrToComponent(&quot;work&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :   std::string comp;</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">        532 :   for(unsigned i=0; i&lt; getNumberOfArguments() ; i++) {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        482 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_coupling&quot;;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        482 :     addComponent(comp); componentIsNotPeriodic(comp);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        482 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_work&quot;;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        482 :     addComponent(comp); componentIsNotPeriodic(comp);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        482 :     work.push_back(0.); // initialize the work value</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        482 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_error&quot;;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">        482 :     addComponent(comp); componentIsNotPeriodic(comp);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :   }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   std::string fname;</a>
+<a name="310"><span class="lineNum">     310 </span>            :   fname=lagmultfname;</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         50 :   ifile.link(*this);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         50 :   if(ifile.FileExist(fname)) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         37 :     ifile.open(fname);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         37 :     if(getRestart()) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         37 :       log.printf(&quot;  Restarting from: %s\n&quot;,fname.c_str());</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         37 :       ReadLagrangians(ifile);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         37 :       printFirstStep=false;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         37 :     ifile.reset(false);</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   }</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         50 :   lagmultOfile_.link(*this);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         50 :   lagmultOfile_.open(fname);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        100 :   if(fmt.length()&gt;0) {fmt=&quot; &quot;+fmt; lagmultOfile_.fmtField(fmt);}</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         50 : }</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : ////MEMBER FUNCTIONS</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         37 : void MaxEnt::ReadLagrangians(IFile &amp;ifile)</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : {</a>
+<a name="329"><span class="lineNum">     329 </span>            :   double dummy;</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        888 :   while(ifile.scanField(&quot;time&quot;,dummy)) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       4708 :     for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       4301 :       ifile.scanField(getPntrToArgument(j)-&gt;getName()+&quot;_coupling&quot;,lambda[j]);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       4301 :       if(dummy&gt;=tstart &amp;&amp; dummy &lt;=tend)</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         42 :         avglambda[j]+=lambda[j];</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">       4301 :       if(dummy&gt;=tend) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       4231 :         avglambda[j]=lambda[j];</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :         done_average[j]=true;</a>
+<a name="338"><span class="lineNum">     338 </span>            :       }</a>
+<a name="339"><span class="lineNum">     339 </span>            :     }</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">        407 :     if(dummy&gt;=tstart &amp;&amp; dummy &lt;=tend)</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          6 :       avg_counter++;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">        407 :     ifile.scanField();</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         37 : }</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        550 : void MaxEnt::WriteLagrangians(std::vector&lt;double&gt; &amp;lagmult,OFile &amp;file) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">        550 :   if(printFirstStep) {</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">        143 :     unsigned ncv=getNumberOfArguments();</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        143 :     file.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">       1144 :     for(unsigned i=0; i&lt;ncv; ++i)</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">       2002 :       file.printField(getPntrToArgument(i)-&gt;getName()+&quot;_coupling&quot;,lagmult[i]);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        143 :     file.printField();</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   } else {</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        407 :     if(!isFirstStep) {</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        370 :       unsigned ncv=getNumberOfArguments();</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        370 :       file.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       4280 :       for(unsigned i=0; i&lt;ncv; ++i)</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       7820 :         file.printField(getPntrToArgument(i)-&gt;getName()+&quot;_coupling&quot;,lagmult[i]);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        370 :       file.printField();</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :     }</a>
+<a name="360"><span class="lineNum">     360 </span>            :   }</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        550 : }</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       5302 : double MaxEnt::compute_error(const std::string &amp;err_type,double l) {</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       5302 :   double sigma2=std::pow(sigma,2.0);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">       5302 :   double l2=convert_lambda(type,l);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :   double return_error=0;</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       5302 :   if(err_type==&quot;GAUSSIAN&quot; &amp;&amp; sigma!=0.0)</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :     return_error=-l2*sigma2;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   else {</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">       5302 :     if(err_type==&quot;LAPLACE&quot; &amp;&amp; sigma!=0) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       5302 :       return_error=-l2*sigma2/(1.0-l2*l2*sigma2/(alpha+1));</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :     }</a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">       5302 :   return return_error;</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : }</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">     119118 : double MaxEnt::convert_lambda(const std::string &amp;type,double lold) {</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   double return_lambda=0;</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">     119118 :   if(type==&quot;EQUAL&quot;)</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :     return_lambda=lold;</a>
+<a name="379"><span class="lineNum">     379 </span>            :   else {</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">       5302 :     if(type==&quot;INEQUAL&gt;&quot;) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :       if(lold&gt;0.0)</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :         return_lambda=0.0;</a>
+<a name="383"><span class="lineNum">     383 </span>            :       else</a>
+<a name="384"><span class="lineNum">     384 </span>            :         return_lambda=lold;</a>
+<a name="385"><span class="lineNum">     385 </span>            :     }</a>
+<a name="386"><span class="lineNum">     386 </span>            :     else {</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       5302 :       if(type==&quot;INEQUAL&lt;&quot;) {</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :         if(lold&lt;0.0)</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :           return_lambda=0.0;</a>
+<a name="390"><span class="lineNum">     390 </span>            :         else</a>
+<a name="391"><span class="lineNum">     391 </span>            :           return_lambda=lold;</a>
+<a name="392"><span class="lineNum">     392 </span>            :       }</a>
+<a name="393"><span class="lineNum">     393 </span>            :     }</a>
+<a name="394"><span class="lineNum">     394 </span>            :   }</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">     119118 :   return return_lambda;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : }</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">       5302 : void MaxEnt::check_lambda_boundaries(const std::string &amp;err_type,double &amp;l) {</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       5302 :   if(err_type==&quot;LAPLACE&quot; &amp;&amp; sigma !=0 ) {</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       5302 :     double l2=convert_lambda(err_type,l);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       5302 :     if(l2 &lt;-(std::sqrt(alpha+1)/sigma-0.01)) {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :       l=-(std::sqrt(alpha+1)/sigma-0.01);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :       log.printf(&quot;Lambda exceeded the allowed range\n&quot;);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :     }</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       5302 :     if(l2&gt;(std::sqrt(alpha+1)/sigma-0.01)) {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :       l=std::sqrt(alpha+1)/sigma-0.01;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineNoCov">          0 :       log.printf(&quot;Lambda exceeded the allowed range\n&quot;);</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :     }</a>
+<a name="408"><span class="lineNum">     408 </span>            :   }</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">       5302 : }</span></a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        550 : void MaxEnt::update_lambda() {</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span>            :   double totalWork_=0.0;</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">        550 :   const double time=getTime();</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        550 :   const double step=getStep();</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        550 :   double KbT=simtemp;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :   double learning_rate;</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">        550 :   if(reweight)</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        396 :     BetaReweightBias=plumed.getBias()/KbT;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   else</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        154 :     BetaReweightBias=0.0;</span></a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">       5852 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">       5302 :     const double k=kappa[i];</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">       5302 :     double cv=(getArgument(i)+compute_error(error_type,lambda[i])-at[i]);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">       5302 :     if(reweight)</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">       4224 :       learning_rate=1.0*k/(1+step/tau[i]);</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :     else</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       1078 :       learning_rate=1.0*k/(1+time/tau[i]);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">       5302 :     lambda[i]+=learning_rate*cv*std::exp(-BetaReweightBias); //update Lagrangian multipliers and reweight them if REWEIGHT is set</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">       5302 :     check_lambda_boundaries(error_type,lambda[i]);      //check that Lagrangians multipliers not exceed the allowed range</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">       5890 :     if(time&gt;=tstart &amp;&amp; time &lt;=tend &amp;&amp; !done_average[i]) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        546 :       avglambda[i]+=convert_lambda(type,lambda[i]); //compute the average of Lagrangian multipliers over the required time window</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :     }</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">       5302 :     if(time&gt;=tend &amp;&amp; tend &gt;=0) { //setting tend&lt;0 will disable this feature</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         98 :       if(!done_average[i]) {</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">         91 :         avglambda[i]=avglambda[i]/avg_counter;</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :         done_average[i]=true;</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         91 :         lambda[i]=avglambda[i];</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :       }</a>
+<a name="441"><span class="lineNum">     441 </span>            :       else</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          7 :         lambda[i]=avglambda[i]; //keep Lagrangian multipliers fixed to the previously computed average.</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     }</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">       5302 :     work[i]+=(convert_lambda(type,lambda[i])-oldlambda[i])*getArgument(i); //compute the work performed in updating lambda</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">       5302 :     totalWork_+=work[i];</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">       5302 :     totalWork=totalWork_;</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">       5302 :     oldlambda[i]=convert_lambda(type,lambda[i]);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :   };</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">        550 :   if(time&gt;=tstart &amp;&amp; time &lt;=tend)</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">         84 :     avg_counter++;</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        550 : }</span></a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">       5050 : void MaxEnt::calculate() {</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :   double totf2=0.0;</a>
+<a name="455"><span class="lineNum">     455 </span>            :   double ene=0.0;</a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">       5050 :   double KbT=simtemp;</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">      53732 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">      97364 :     getPntrToComponent(getPntrToArgument(i)-&gt;getName()+&quot;_error&quot;)-&gt;set(expected_eps[i]);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">      48682 :     getPntrToComponent(getPntrToArgument(i)-&gt;getName()+&quot;_work&quot;)-&gt;set(work[i]);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">      48682 :     valueWork-&gt;set(totalWork);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">      48682 :     getPntrToComponent(getPntrToArgument(i)-&gt;getName()+&quot;_coupling&quot;)-&gt;set(lambda[i]);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">      48682 :     const double f=-KbT*convert_lambda(type,lambda[i])*apply_weights[myrep];</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">      48682 :     totf2+=f*f;</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">      48682 :     ene+=KbT*convert_lambda(type,lambda[i])*getArgument(i)*apply_weights[myrep];</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">      48682 :     setOutputForce(i,f);</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :   }</a>
+<a name="467"><span class="lineNum">     467 </span>            :   setBias(ene);</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">       5050 :   valueForce2-&gt;set(totf2);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">       5050 : }</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">       5050 : void MaxEnt::update() {</span></a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">       5050 :   if(getStep()%stride_ == 0)</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        550 :     WriteLagrangians(lambda,lagmultOfile_);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">       5050 :   if(getStep()%pace_ == 0) {</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">        550 :     update_lambda();</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">        550 :     if(!no_broadcast) {</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        550 :       if(comm.Get_rank()==0) //Comunicate Lagrangian multipliers from reference replica to higher ones</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        462 :         multi_sim_comm.Bcast(lambda,learn_replica);</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :     }</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">        550 :     comm.Bcast(lambda,0);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   }</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">       5050 :   isFirstStep=false;</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">       5050 : }</span></a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span>            : }</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MetaD.cpp.func-sort-c.html b/coverage/bias/MetaD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4b0ca001c2
--- /dev/null
+++ b/coverage/bias/MetaD.cpp.func-sort-c.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MetaD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MetaD.cpp<span style="font-size: 80%;"> (<a href="MetaD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">955</td>
+            <td class="headerCovTableEntry">1083</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MetaD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1703">_ZN4PLMD4bias5MetaD24getGaussianNormalizationERKNS1_8GaussianE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#598">_ZN4PLMD4bias5MetaDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1433">_ZN4PLMD4bias5MetaD17logTemperingSpecsERKNS1_14TemperingSpecsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2263">_ZN4PLMD4bias5MetaD11updateNlistEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#485">_ZN4PLMD4bias5MetaD16noStretchWarningEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1888">_ZN4PLMD4bias5MetaD12temperHeightERdRKNS1_14TemperingSpecsEd</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2175">_ZN4PLMD4bias5MetaD24computeReweightingFactorEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1410">_ZN4PLMD4bias5MetaD18readTemperingSpecsERNS1_14TemperingSpecsE</a></td>
+              <td class="coverFnHi">151</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2240">_ZN4PLMD4bias5MetaD29updateFrequencyAdaptiveStrideEv</a></td>
+              <td class="coverFnHi">154</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#397">_ZN4PLMD4bias5MetaD14TemperingSpecsC2EbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ddd</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#520">_ZN4PLMD4bias12_GLOBAL__N_118MetaDRegisterMe5226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">157</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#598">_ZN4PLMD4bias5MetaDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">157</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#522">_ZN4PLMD4bias5MetaD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#592">_ZN4PLMD4bias5MetaD25registerTemperingKeywordsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RNS_8KeywordsE</a></td>
+              <td class="coverFnHi">159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1727">_ZN4PLMD4bias5MetaD16evaluateGaussianERKSt6vectorIdSaIdEERKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2206">_ZN4PLMD4bias5MetaD24getTransitionBarrierBiasEv</a></td>
+              <td class="coverFnHi">273</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1612">_ZN4PLMD4bias5MetaD7getBiasERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">285</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1558">_ZN4PLMD4bias5MetaD18getGaussianSupportERKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">640</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1860">_ZN4PLMD4bias5MetaD9getHeightERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2736</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1463">_ZN4PLMD4bias5MetaD13writeGaussianERKNS1_8GaussianERNS_5OFileE</a></td>
+              <td class="coverFnHi">2922</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#520">_ZN4PLMD4bias12_GLOBAL__N_118MetaDRegisterMe522C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#520">_ZN4PLMD4bias12_GLOBAL__N_118MetaDRegisterMe522D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1514">_ZN4PLMD4bias5MetaD11addGaussianERKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">5200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#381">_ZN4PLMD4bias5MetaD8GaussianC2EbdRKSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">5200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1441">_ZN4PLMD4bias5MetaD13readGaussiansEPNS_5IFileE</a></td>
+              <td class="coverFnHi">6036</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1942">_ZN4PLMD4bias5MetaD6updateEv</a></td>
+              <td class="coverFnHi">6239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2101">_ZN4PLMD4bias5MetaD11scanOneHillEPNS_5IFileERSt6vectorINS_5ValueESaIS5_EERS4_IdSaIdEESB_RdRb</a></td>
+              <td class="coverFnHi">8152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1640">_ZN4PLMD4bias5MetaD21getBiasAndDerivativesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">8395</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1897">_ZN4PLMD4bias5MetaD9calculateEv</a></td>
+              <td class="coverFnHi">8435</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2255">_ZNK4PLMD4bias5MetaD19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">8435</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1781">_ZN4PLMD4bias5MetaD30evaluateGaussianAndDerivativesERKSt6vectorIdSaIdEERKNS1_8GaussianERS4_SA_</a></td>
+              <td class="coverFnHi">2409166</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MetaD.cpp.func.html b/coverage/bias/MetaD.cpp.func.html
new file mode 100644
index 0000000000..d722ce3e4a
--- /dev/null
+++ b/coverage/bias/MetaD.cpp.func.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MetaD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MetaD.cpp<span style="font-size: 80%;"> (<a href="MetaD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">955</td>
+            <td class="headerCovTableEntry">1083</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MetaD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#520">_ZN4PLMD4bias12_GLOBAL__N_118MetaDRegisterMe5226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">157</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#520">_ZN4PLMD4bias12_GLOBAL__N_118MetaDRegisterMe522C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#520">_ZN4PLMD4bias12_GLOBAL__N_118MetaDRegisterMe522D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1514">_ZN4PLMD4bias5MetaD11addGaussianERKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">5200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2101">_ZN4PLMD4bias5MetaD11scanOneHillEPNS_5IFileERSt6vectorINS_5ValueESaIS5_EERS4_IdSaIdEESB_RdRb</a></td>
+              <td class="coverFnHi">8152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2263">_ZN4PLMD4bias5MetaD11updateNlistEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1888">_ZN4PLMD4bias5MetaD12temperHeightERdRKNS1_14TemperingSpecsEd</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1441">_ZN4PLMD4bias5MetaD13readGaussiansEPNS_5IFileE</a></td>
+              <td class="coverFnHi">6036</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1463">_ZN4PLMD4bias5MetaD13writeGaussianERKNS1_8GaussianERNS_5OFileE</a></td>
+              <td class="coverFnHi">2922</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#397">_ZN4PLMD4bias5MetaD14TemperingSpecsC2EbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESA_ddd</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1727">_ZN4PLMD4bias5MetaD16evaluateGaussianERKSt6vectorIdSaIdEERKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#485">_ZN4PLMD4bias5MetaD16noStretchWarningEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#522">_ZN4PLMD4bias5MetaD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1433">_ZN4PLMD4bias5MetaD17logTemperingSpecsERKNS1_14TemperingSpecsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1558">_ZN4PLMD4bias5MetaD18getGaussianSupportERKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">640</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1410">_ZN4PLMD4bias5MetaD18readTemperingSpecsERNS1_14TemperingSpecsE</a></td>
+              <td class="coverFnHi">151</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1640">_ZN4PLMD4bias5MetaD21getBiasAndDerivativesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">8395</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2175">_ZN4PLMD4bias5MetaD24computeReweightingFactorEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1703">_ZN4PLMD4bias5MetaD24getGaussianNormalizationERKNS1_8GaussianE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2206">_ZN4PLMD4bias5MetaD24getTransitionBarrierBiasEv</a></td>
+              <td class="coverFnHi">273</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#592">_ZN4PLMD4bias5MetaD25registerTemperingKeywordsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RNS_8KeywordsE</a></td>
+              <td class="coverFnHi">159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2240">_ZN4PLMD4bias5MetaD29updateFrequencyAdaptiveStrideEv</a></td>
+              <td class="coverFnHi">154</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1781">_ZN4PLMD4bias5MetaD30evaluateGaussianAndDerivativesERKSt6vectorIdSaIdEERKNS1_8GaussianERS4_SA_</a></td>
+              <td class="coverFnHi">2409166</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1942">_ZN4PLMD4bias5MetaD6updateEv</a></td>
+              <td class="coverFnHi">6239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1612">_ZN4PLMD4bias5MetaD7getBiasERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">285</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#381">_ZN4PLMD4bias5MetaD8GaussianC2EbdRKSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">5200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1897">_ZN4PLMD4bias5MetaD9calculateEv</a></td>
+              <td class="coverFnHi">8435</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#1860">_ZN4PLMD4bias5MetaD9getHeightERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2736</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#598">_ZN4PLMD4bias5MetaDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">157</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#598">_ZN4PLMD4bias5MetaDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetaD.cpp.gcov.html#2255">_ZNK4PLMD4bias5MetaD19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">8435</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MetaD.cpp.gcov.html b/coverage/bias/MetaD.cpp.gcov.html
new file mode 100644
index 0000000000..7ac40b1294
--- /dev/null
+++ b/coverage/bias/MetaD.cpp.gcov.html
@@ -0,0 +1,2395 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MetaD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MetaD.cpp<span style="font-size: 80%;"> (source / <a href="MetaD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">955</td>
+            <td class="headerCovTableEntry">1083</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/FlexibleBin.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;ctime&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;numeric&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if defined(__PLUMED_HAS_GETCWD)</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;unistd.h&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #endif</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace bias {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : //+PLUMEDOC BIAS METAD</a>
+<a name="44"><span class="lineNum">      44 </span>            : /*</a>
+<a name="45"><span class="lineNum">      45 </span>            : Used to performed metadynamics on one or more collective variables.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : In a metadynamics simulations a history dependent bias composed of</a>
+<a name="48"><span class="lineNum">      48 </span>            : intermittently added Gaussian functions is added to the potential \cite metad.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \f[</a>
+<a name="51"><span class="lineNum">      51 </span>            : V(\vec{s},t) = \sum_{ k \tau &lt; t} W(k \tau)</a>
+<a name="52"><span class="lineNum">      52 </span>            : \exp\left(</a>
+<a name="53"><span class="lineNum">      53 </span>            : -\sum_{i=1}^{d} \frac{(s_i-s_i^{(0)}(k \tau))^2}{2\sigma_i^2}</a>
+<a name="54"><span class="lineNum">      54 </span>            : \right).</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f]</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : This potential forces the system away from the kinetic traps in the potential energy surface</a>
+<a name="58"><span class="lineNum">      58 </span>            : and out into the unexplored parts of the energy landscape. Information on the Gaussian</a>
+<a name="59"><span class="lineNum">      59 </span>            : functions from which this potential is composed is output to a file called HILLS, which</a>
+<a name="60"><span class="lineNum">      60 </span>            : is used both the restart the calculation and to reconstruct the free energy as a function of the CVs.</a>
+<a name="61"><span class="lineNum">      61 </span>            : The free energy can be reconstructed from a metadynamics calculation because the final bias is given</a>
+<a name="62"><span class="lineNum">      62 </span>            : by:</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \f[</a>
+<a name="65"><span class="lineNum">      65 </span>            : V(\vec{s}) = -F(\vec{s})</a>
+<a name="66"><span class="lineNum">      66 </span>            : \f]</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : During post processing the free energy can be calculated in this way using the \ref sum_hills</a>
+<a name="69"><span class="lineNum">      69 </span>            : utility.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : In the simplest possible implementation of a metadynamics calculation the expense of a metadynamics</a>
+<a name="72"><span class="lineNum">      72 </span>            : calculation increases with the length of the simulation as one has to, at every step, evaluate</a>
+<a name="73"><span class="lineNum">      73 </span>            : the values of a larger and larger number of Gaussian kernels. To avoid this issue you can</a>
+<a name="74"><span class="lineNum">      74 </span>            : store the bias on a grid.  This approach is similar to that proposed in \cite babi08jcp but has the</a>
+<a name="75"><span class="lineNum">      75 </span>            : advantage that the grid spacing is independent on the Gaussian width.</a>
+<a name="76"><span class="lineNum">      76 </span>            : Notice that you should provide the grid boundaries (GRID_MIN and GRID_MAX) and either the number of bins</a>
+<a name="77"><span class="lineNum">      77 </span>            : for every collective variable (GRID_BIN) or the desired grid spacing (GRID_SPACING).</a>
+<a name="78"><span class="lineNum">      78 </span>            : In case you provide both PLUMED will use the most conservative choice (highest number of bins) for each dimension.</a>
+<a name="79"><span class="lineNum">      79 </span>            : In case you do not provide any information about bin size (neither GRID_BIN nor GRID_SPACING)</a>
+<a name="80"><span class="lineNum">      80 </span>            : PLUMED will use 1/5 of the Gaussian width (SIGMA) as grid spacing if the width is fixed or 1/5 of the minimum</a>
+<a name="81"><span class="lineNum">      81 </span>            : Gaussian width (SIGMA_MIN) if the width is variable. This default choice should be reasonable for most applications.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : Alternatively to the use of grids, it is possible to use a neighbor list to decrease the cost of evaluating the bias,</a>
+<a name="84"><span class="lineNum">      84 </span>            : this can be enabled using NLIST. NLIST can be beneficial with more than 2 collective variables, where GRID becomes</a>
+<a name="85"><span class="lineNum">      85 </span>            : expensive and memory consuming. The neighbor list will be updated everytime the CVs go farther than a cut-off value</a>
+<a name="86"><span class="lineNum">      86 </span>            : from the position they were at last neighbor list update. Gaussians are added to the neigbhor list if their center</a>
+<a name="87"><span class="lineNum">      87 </span>            : is within 6.*DP2CUTOFF*sigma*sigma. While the list is updated if the CVs are farther from the center than 0.5 of the</a>
+<a name="88"><span class="lineNum">      88 </span>            : standard deviation of the Gaussian center distribution of the list. These parameters (6 and 0.5) can be modified using</a>
+<a name="89"><span class="lineNum">      89 </span>            : NLIST_PARAMETERS. Note that the use of neighbor list does not provide the exact bias.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : Metadynamics can be restarted either from a HILLS file as well as from a GRID, in this second</a>
+<a name="92"><span class="lineNum">      92 </span>            : case one can first save a GRID using GRID_WFILE (and GRID_WSTRIDE) and at a later stage read</a>
+<a name="93"><span class="lineNum">      93 </span>            : it using GRID_RFILE.</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : The work performed by the METAD bias can be calculated using CALC_WORK, note that this is expensive when not using grids.</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : Another option that is available in plumed is well-tempered metadynamics \cite Barducci:2008. In this</a>
+<a name="98"><span class="lineNum">      98 </span>            : variant of metadynamics the heights of the Gaussian hills are scaled at each step so the bias is now</a>
+<a name="99"><span class="lineNum">      99 </span>            : given by:</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : \f[</a>
+<a name="102"><span class="lineNum">     102 </span>            : V({s},t)= \sum_{t'=0,\tau_G,2\tau_G,\dots}^{t'&lt;t} W e^{-V({s}({q}(t'),t')/\Delta T} \exp\left(</a>
+<a name="103"><span class="lineNum">     103 </span>            : -\sum_{i=1}^{d} \frac{(s_i({q})-s_i({q}(t'))^2}{2\sigma_i^2}</a>
+<a name="104"><span class="lineNum">     104 </span>            : \right),</a>
+<a name="105"><span class="lineNum">     105 </span>            : \f]</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : This method ensures that the bias converges more smoothly. It should be noted that, in the case of well-tempered metadynamics, in</a>
+<a name="108"><span class="lineNum">     108 </span>            : the output printed the Gaussian height is re-scaled using the bias factor.</a>
+<a name="109"><span class="lineNum">     109 </span>            : Also notice that with well-tempered metadynamics the HILLS file does not contain the bias,</a>
+<a name="110"><span class="lineNum">     110 </span>            : but the negative of the free-energy estimate. This choice has the advantage that</a>
+<a name="111"><span class="lineNum">     111 </span>            : one can restart a simulation using a different value for the \f$\Delta T\f$. The applied bias will be scaled accordingly.</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : Note that you can use here also the flexible Gaussian approach  \cite Branduardi:2012dl</a>
+<a name="114"><span class="lineNum">     114 </span>            : in which you can adapt the Gaussian to the extent of Cartesian space covered by a variable or</a>
+<a name="115"><span class="lineNum">     115 </span>            : to the space in collective variable covered in a given time. In this case the width of the deposited</a>
+<a name="116"><span class="lineNum">     116 </span>            : Gaussian potential is denoted by one value only that is a Cartesian space (ADAPTIVE=GEOM) or a time</a>
+<a name="117"><span class="lineNum">     117 </span>            : (ADAPTIVE=DIFF). Note that a specific integration technique for the deposited Gaussian kernels</a>
+<a name="118"><span class="lineNum">     118 </span>            : should be used in this case. Check the documentation for utility sum_hills.</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : With the keyword INTERVAL one changes the metadynamics algorithm setting the bias force equal to zero</a>
+<a name="121"><span class="lineNum">     121 </span>            : outside boundary \cite baftizadeh2012protein. If, for example, metadynamics is performed on a CV s and one is interested only</a>
+<a name="122"><span class="lineNum">     122 </span>            : to the free energy for s &gt; boundary, the history dependent potential is still updated according to the above</a>
+<a name="123"><span class="lineNum">     123 </span>            : equations but the metadynamics force is set to zero for s &lt; boundary. Notice that Gaussian kernels are added also</a>
+<a name="124"><span class="lineNum">     124 </span>            : if s &lt; boundary, as the tails of these Gaussian kernels influence VG in the relevant region s &gt; boundary. In this way, the</a>
+<a name="125"><span class="lineNum">     125 </span>            : force on the system in the region s &gt; boundary comes from both metadynamics and the force field, in the region</a>
+<a name="126"><span class="lineNum">     126 </span>            : s &lt; boundary only from the latter. This approach allows obtaining a history-dependent bias potential VG that</a>
+<a name="127"><span class="lineNum">     127 </span>            : fluctuates around a stable estimator, equal to the negative of the free energy far enough from the</a>
+<a name="128"><span class="lineNum">     128 </span>            : boundaries. Note that:</a>
+<a name="129"><span class="lineNum">     129 </span>            : - It works only for one-dimensional biases;</a>
+<a name="130"><span class="lineNum">     130 </span>            : - It works both with and without GRID;</a>
+<a name="131"><span class="lineNum">     131 </span>            : - The interval limit boundary in a region where the free energy derivative is not large;</a>
+<a name="132"><span class="lineNum">     132 </span>            : - If in the region outside the limit boundary the system has a free energy minimum, the INTERVAL keyword should</a>
+<a name="133"><span class="lineNum">     133 </span>            :   be used together with a \ref UPPER_WALLS or \ref LOWER_WALLS at boundary.</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : As a final note, since version 2.0.2 when the system is outside of the selected interval the force</a>
+<a name="136"><span class="lineNum">     136 </span>            : is set to zero and the bias value to the value at the corresponding boundary. This allows acceptances</a>
+<a name="137"><span class="lineNum">     137 </span>            : for replica exchange methods to be computed correctly.</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : Multiple walkers  \cite multiplewalkers can also be used. See below the examples.</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : The \f$c(t)\f$ reweighting factor can also be calculated on the fly using the equations</a>
+<a name="143"><span class="lineNum">     143 </span>            : presented in \cite Tiwary_jp504920s.</a>
+<a name="144"><span class="lineNum">     144 </span>            : The expression used to calculate \f$c(t)\f$ follows directly from Eq. 3 in \cite Tiwary_jp504920s,</a>
+<a name="145"><span class="lineNum">     145 </span>            : where \f$F(\vec{s})=-\gamma/(\gamma-1) V(\vec{s})\f$.</a>
+<a name="146"><span class="lineNum">     146 </span>            : This gives smoother results than equivalent Eqs. 13 and Eqs. 14 in that paper.</a>
+<a name="147"><span class="lineNum">     147 </span>            : The \f$c(t)\f$ is given by the rct component while the bias</a>
+<a name="148"><span class="lineNum">     148 </span>            : normalized by \f$c(t)\f$ is given by the rbias component (rbias=bias-rct) which can be used</a>
+<a name="149"><span class="lineNum">     149 </span>            : to obtain a reweighted histogram.</a>
+<a name="150"><span class="lineNum">     150 </span>            : The calculation of \f$c(t)\f$ is enabled by using the keyword CALC_RCT.</a>
+<a name="151"><span class="lineNum">     151 </span>            : By default \f$c(t)\f$ is updated every time the bias changes, but if this slows down the simulation</a>
+<a name="152"><span class="lineNum">     152 </span>            : the keyword RCT_USTRIDE can be set to a value higher than 1.</a>
+<a name="153"><span class="lineNum">     153 </span>            : This option requires that a grid is used.</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : Additional material and examples can be also found in the tutorials:</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : - \ref lugano-3</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : Concurrent metadynamics</a>
+<a name="160"><span class="lineNum">     160 </span>            : as done e.g. in Ref. \cite gil2015enhanced . This indeed can be obtained by using the METAD</a>
+<a name="161"><span class="lineNum">     161 </span>            : action multiple times in the same input file.</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : \par Examples</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : The following input is for a standard metadynamics calculation using as</a>
+<a name="166"><span class="lineNum">     166 </span>            : collective variables the distance between atoms 3 and 5</a>
+<a name="167"><span class="lineNum">     167 </span>            : and the distance between atoms 2 and 4. The value of the CVs and</a>
+<a name="168"><span class="lineNum">     168 </span>            : the metadynamics bias potential are written to the COLVAR file every 100 steps.</a>
+<a name="169"><span class="lineNum">     169 </span>            : \plumedfile</a>
+<a name="170"><span class="lineNum">     170 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="171"><span class="lineNum">     171 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="172"><span class="lineNum">     172 </span>            : METAD ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3 PACE=500 LABEL=restraint</a>
+<a name="173"><span class="lineNum">     173 </span>            : PRINT ARG=d1,d2,restraint.bias STRIDE=100  FILE=COLVAR</a>
+<a name="174"><span class="lineNum">     174 </span>            : \endplumedfile</a>
+<a name="175"><span class="lineNum">     175 </span>            : (See also \ref DISTANCE \ref PRINT).</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : \par</a>
+<a name="178"><span class="lineNum">     178 </span>            : If you use adaptive Gaussian kernels, with diffusion scheme where you use</a>
+<a name="179"><span class="lineNum">     179 </span>            : a Gaussian that should cover the space of 20 time steps in collective variables.</a>
+<a name="180"><span class="lineNum">     180 </span>            : Note that in this case the histogram correction is needed when summing up hills.</a>
+<a name="181"><span class="lineNum">     181 </span>            : \plumedfile</a>
+<a name="182"><span class="lineNum">     182 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="183"><span class="lineNum">     183 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="184"><span class="lineNum">     184 </span>            : METAD ARG=d1,d2 SIGMA=20 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=DIFF</a>
+<a name="185"><span class="lineNum">     185 </span>            : PRINT ARG=d1,d2,restraint.bias STRIDE=100  FILE=COLVAR</a>
+<a name="186"><span class="lineNum">     186 </span>            : \endplumedfile</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : \par</a>
+<a name="189"><span class="lineNum">     189 </span>            : If you use adaptive Gaussian kernels, with geometrical scheme where you use</a>
+<a name="190"><span class="lineNum">     190 </span>            : a Gaussian that should cover the space of 0.05 nm in Cartesian space.</a>
+<a name="191"><span class="lineNum">     191 </span>            : Note that in this case the histogram correction is needed when summing up hills.</a>
+<a name="192"><span class="lineNum">     192 </span>            : \plumedfile</a>
+<a name="193"><span class="lineNum">     193 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="194"><span class="lineNum">     194 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="195"><span class="lineNum">     195 </span>            : METAD ARG=d1,d2 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=GEOM</a>
+<a name="196"><span class="lineNum">     196 </span>            : PRINT ARG=d1,d2,restraint.bias STRIDE=100  FILE=COLVAR</a>
+<a name="197"><span class="lineNum">     197 </span>            : \endplumedfile</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : \par</a>
+<a name="200"><span class="lineNum">     200 </span>            : When using adaptive Gaussian kernels you might want to limit how the hills width can change.</a>
+<a name="201"><span class="lineNum">     201 </span>            : You can use SIGMA_MIN and SIGMA_MAX keywords.</a>
+<a name="202"><span class="lineNum">     202 </span>            : The sigmas should specified in terms of CV so you should use the CV units.</a>
+<a name="203"><span class="lineNum">     203 </span>            : Note that if you use a negative number, this means that the limit is not set.</a>
+<a name="204"><span class="lineNum">     204 </span>            : Note also that in this case the histogram correction is needed when summing up hills.</a>
+<a name="205"><span class="lineNum">     205 </span>            : \plumedfile</a>
+<a name="206"><span class="lineNum">     206 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="207"><span class="lineNum">     207 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="208"><span class="lineNum">     208 </span>            : METAD ...</a>
+<a name="209"><span class="lineNum">     209 </span>            :   ARG=d1,d2 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint ADAPTIVE=GEOM</a>
+<a name="210"><span class="lineNum">     210 </span>            :   SIGMA_MIN=0.2,0.1 SIGMA_MAX=0.5,1.0</a>
+<a name="211"><span class="lineNum">     211 </span>            : ... METAD</a>
+<a name="212"><span class="lineNum">     212 </span>            : PRINT ARG=d1,d2,restraint.bias STRIDE=100  FILE=COLVAR</a>
+<a name="213"><span class="lineNum">     213 </span>            : \endplumedfile</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : \par</a>
+<a name="216"><span class="lineNum">     216 </span>            : Multiple walkers can be also use as in  \cite multiplewalkers</a>
+<a name="217"><span class="lineNum">     217 </span>            : These are enabled by setting the number of walker used, the id of the</a>
+<a name="218"><span class="lineNum">     218 </span>            : current walker which interprets the input file, the directory where the</a>
+<a name="219"><span class="lineNum">     219 </span>            : hills containing files resides, and the frequency to read the other walkers.</a>
+<a name="220"><span class="lineNum">     220 </span>            : Here is an example</a>
+<a name="221"><span class="lineNum">     221 </span>            : \plumedfile</a>
+<a name="222"><span class="lineNum">     222 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="223"><span class="lineNum">     223 </span>            : METAD ...</a>
+<a name="224"><span class="lineNum">     224 </span>            :    ARG=d1 SIGMA=0.05 HEIGHT=0.3 PACE=500 LABEL=restraint</a>
+<a name="225"><span class="lineNum">     225 </span>            :    WALKERS_N=10</a>
+<a name="226"><span class="lineNum">     226 </span>            :    WALKERS_ID=3</a>
+<a name="227"><span class="lineNum">     227 </span>            :    WALKERS_DIR=../</a>
+<a name="228"><span class="lineNum">     228 </span>            :    WALKERS_RSTRIDE=100</a>
+<a name="229"><span class="lineNum">     229 </span>            : ... METAD</a>
+<a name="230"><span class="lineNum">     230 </span>            : \endplumedfile</a>
+<a name="231"><span class="lineNum">     231 </span>            : where  WALKERS_N is the total number of walkers, WALKERS_ID is the</a>
+<a name="232"><span class="lineNum">     232 </span>            : id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory</a>
+<a name="233"><span class="lineNum">     233 </span>            : where all the walkers are located. WALKERS_RSTRIDE is the number of step between</a>
+<a name="234"><span class="lineNum">     234 </span>            : one update and the other. Since version 2.2.5, hills files are automatically</a>
+<a name="235"><span class="lineNum">     235 </span>            : flushed every WALKERS_RSTRIDE steps.</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : \par</a>
+<a name="238"><span class="lineNum">     238 </span>            : The \f$c(t)\f$ reweighting factor can be calculated on the fly using the equations</a>
+<a name="239"><span class="lineNum">     239 </span>            : presented in \cite Tiwary_jp504920s as described above.</a>
+<a name="240"><span class="lineNum">     240 </span>            : This is enabled by using the keyword CALC_RCT,</a>
+<a name="241"><span class="lineNum">     241 </span>            : and can be done only if the bias is defined on a grid.</a>
+<a name="242"><span class="lineNum">     242 </span>            : \plumedfile</a>
+<a name="243"><span class="lineNum">     243 </span>            : phi: TORSION ATOMS=1,2,3,4</a>
+<a name="244"><span class="lineNum">     244 </span>            : psi: TORSION ATOMS=5,6,7,8</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : METAD ...</a>
+<a name="247"><span class="lineNum">     247 </span>            :  LABEL=metad</a>
+<a name="248"><span class="lineNum">     248 </span>            :  ARG=phi,psi SIGMA=0.20,0.20 HEIGHT=1.20 BIASFACTOR=5 TEMP=300.0 PACE=500</a>
+<a name="249"><span class="lineNum">     249 </span>            :  GRID_MIN=-pi,-pi GRID_MAX=pi,pi GRID_BIN=150,150</a>
+<a name="250"><span class="lineNum">     250 </span>            :  CALC_RCT</a>
+<a name="251"><span class="lineNum">     251 </span>            :  RCT_USTRIDE=10</a>
+<a name="252"><span class="lineNum">     252 </span>            : ... METAD</a>
+<a name="253"><span class="lineNum">     253 </span>            : \endplumedfile</a>
+<a name="254"><span class="lineNum">     254 </span>            : Here we have asked that the calculation is performed every 10 hills deposition by using</a>
+<a name="255"><span class="lineNum">     255 </span>            : RCT_USTRIDE keyword. If this keyword is not given, the calculation will</a>
+<a name="256"><span class="lineNum">     256 </span>            : by default be performed every time the bias changes. The \f$c(t)\f$ reweighting factor will be given</a>
+<a name="257"><span class="lineNum">     257 </span>            : in the rct component while the instantaneous value of the bias potential</a>
+<a name="258"><span class="lineNum">     258 </span>            : normalized using the \f$c(t)\f$ reweighting factor is given in the rbias component</a>
+<a name="259"><span class="lineNum">     259 </span>            : [rbias=bias-rct] which can be used to obtain a reweighted histogram or</a>
+<a name="260"><span class="lineNum">     260 </span>            : free energy surface using the \ref HISTOGRAM analysis.</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : \par</a>
+<a name="263"><span class="lineNum">     263 </span>            : The kinetics of the transitions between basins can also be analyzed on the fly as</a>
+<a name="264"><span class="lineNum">     264 </span>            : in \cite PRL230602. The flag ACCELERATION turn on accumulation of the acceleration</a>
+<a name="265"><span class="lineNum">     265 </span>            : factor that can then be used to determine the rate. This method can be used together</a>
+<a name="266"><span class="lineNum">     266 </span>            : with \ref COMMITTOR analysis to stop the simulation when the system get to the target basin.</a>
+<a name="267"><span class="lineNum">     267 </span>            : It must be used together with Well-Tempered Metadynamics. If restarting from a previous</a>
+<a name="268"><span class="lineNum">     268 </span>            : metadynamics you need to use the ACCELERATION_RFILE keyword to give the name of the</a>
+<a name="269"><span class="lineNum">     269 </span>            : data file from which the previous value of the acceleration factor should be read, otherwise the</a>
+<a name="270"><span class="lineNum">     270 </span>            : calculation of the acceleration factor will be wrong.</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            : \par</a>
+<a name="273"><span class="lineNum">     273 </span>            : By using the flag FREQUENCY_ADAPTIVE the frequency adaptive scheme introduced in \cite Wang-JCP-2018</a>
+<a name="274"><span class="lineNum">     274 </span>            : is turned on. The frequency for hill addition then changes dynamically based on the acceleration factor</a>
+<a name="275"><span class="lineNum">     275 </span>            : according to the following equation</a>
+<a name="276"><span class="lineNum">     276 </span>            : \f[</a>
+<a name="277"><span class="lineNum">     277 </span>            : \tau_{\mathrm{dep}}(t) =</a>
+<a name="278"><span class="lineNum">     278 </span>            : \min\left[</a>
+<a name="279"><span class="lineNum">     279 </span>            : \tau_0 \cdot</a>
+<a name="280"><span class="lineNum">     280 </span>            : \max\left[\frac{\alpha(t)}{\theta},1\right]</a>
+<a name="281"><span class="lineNum">     281 </span>            : ,\tau_{c}</a>
+<a name="282"><span class="lineNum">     282 </span>            : \right]</a>
+<a name="283"><span class="lineNum">     283 </span>            : \f]</a>
+<a name="284"><span class="lineNum">     284 </span>            : where \f$\tau_0\f$ is the initial hill addition frequency given by the PACE keyword,</a>
+<a name="285"><span class="lineNum">     285 </span>            : \f$\tau_{c}\f$ is the maximum allowed frequency given by the FA_MAX_PACE keyword,</a>
+<a name="286"><span class="lineNum">     286 </span>            : \f$\alpha(t)\f$ is the instantaneous acceleration factor at time \f$t\f$,</a>
+<a name="287"><span class="lineNum">     287 </span>            : and \f$\theta\f$ is a threshold value that acceleration factor has to reach before</a>
+<a name="288"><span class="lineNum">     288 </span>            : triggering a change in the hill addition frequency given by the FA_MIN_ACCELERATION keyword.</a>
+<a name="289"><span class="lineNum">     289 </span>            : The frequency for updating the hill addition frequency according to this equation is</a>
+<a name="290"><span class="lineNum">     290 </span>            : given by the FA_UPDATE_FREQUENCY keyword, by default it is the same as the value given</a>
+<a name="291"><span class="lineNum">     291 </span>            : in PACE. The hill hill addition frequency increase monotonously such that if the</a>
+<a name="292"><span class="lineNum">     292 </span>            : instantaneous acceleration factor is lower than in the previous updating step the</a>
+<a name="293"><span class="lineNum">     293 </span>            : previous \f$\tau_{\mathrm{dep}}\f$ is kept rather than updating it to a lower value.</a>
+<a name="294"><span class="lineNum">     294 </span>            : The instantaneous hill addition frequency \f$\tau_{\mathrm{dep}}(t)\f$ is outputted</a>
+<a name="295"><span class="lineNum">     295 </span>            : to pace component. Note that if restarting from a previous metadynamics run you need to</a>
+<a name="296"><span class="lineNum">     296 </span>            : use the ACCELERATION_RFILE keyword to read in the acceleration factors from the</a>
+<a name="297"><span class="lineNum">     297 </span>            : previous run, otherwise the hill addition frequency will start from the initial</a>
+<a name="298"><span class="lineNum">     298 </span>            : frequency.</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : \par</a>
+<a name="302"><span class="lineNum">     302 </span>            : You can also provide a target distribution using the keyword TARGET</a>
+<a name="303"><span class="lineNum">     303 </span>            : \cite white2015designing</a>
+<a name="304"><span class="lineNum">     304 </span>            : \cite marinelli2015ensemble</a>
+<a name="305"><span class="lineNum">     305 </span>            : \cite gil2016empirical</a>
+<a name="306"><span class="lineNum">     306 </span>            : The TARGET should be a grid containing a free-energy (i.e. the -\f$k_B\f$T*log of the desired target distribution).</a>
+<a name="307"><span class="lineNum">     307 </span>            : Gaussian kernels will then be scaled by a factor</a>
+<a name="308"><span class="lineNum">     308 </span>            : \f[</a>
+<a name="309"><span class="lineNum">     309 </span>            : e^{\beta(\tilde{F}(s)-\tilde{F}_{max})}</a>
+<a name="310"><span class="lineNum">     310 </span>            : \f]</a>
+<a name="311"><span class="lineNum">     311 </span>            : Here \f$\tilde{F}(s)\f$ is the free energy defined on the grid and \f$\tilde{F}_{max}\f$ its maximum value.</a>
+<a name="312"><span class="lineNum">     312 </span>            : Notice that we here used the maximum value as in ref \cite gil2016empirical</a>
+<a name="313"><span class="lineNum">     313 </span>            : This choice allows to avoid exceedingly large Gaussian kernels to be added. However,</a>
+<a name="314"><span class="lineNum">     314 </span>            : it could make the Gaussian too small. You should always choose carefully the HEIGHT parameter</a>
+<a name="315"><span class="lineNum">     315 </span>            : in this case.</a>
+<a name="316"><span class="lineNum">     316 </span>            : The grid file should be similar to other PLUMED grid files in that it should contain</a>
+<a name="317"><span class="lineNum">     317 </span>            : both the target free-energy and its derivatives.</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            : Notice that if you wish your simulation to converge to the target free energy you should use</a>
+<a name="320"><span class="lineNum">     320 </span>            : the DAMPFACTOR command to provide a global tempering \cite dama2014well</a>
+<a name="321"><span class="lineNum">     321 </span>            : Alternatively, if you use a BIASFACTOR your simulation will converge to a free</a>
+<a name="322"><span class="lineNum">     322 </span>            : energy that is a linear combination of the target free energy and of the intrinsic free energy</a>
+<a name="323"><span class="lineNum">     323 </span>            : determined by the original force field.</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            : \plumedfile</a>
+<a name="326"><span class="lineNum">     326 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="327"><span class="lineNum">     327 </span>            : METAD ...</a>
+<a name="328"><span class="lineNum">     328 </span>            :  LABEL=t1</a>
+<a name="329"><span class="lineNum">     329 </span>            :  ARG=d1 SIGMA=0.05 TAU=200 DAMPFACTOR=100 PACE=250</a>
+<a name="330"><span class="lineNum">     330 </span>            :  GRID_MIN=1.14 GRID_MAX=1.32 GRID_BIN=6</a>
+<a name="331"><span class="lineNum">     331 </span>            :  TARGET=dist.grid</a>
+<a name="332"><span class="lineNum">     332 </span>            : ... METAD</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            : PRINT ARG=d1,t1.bias STRIDE=100 FILE=COLVAR</a>
+<a name="335"><span class="lineNum">     335 </span>            : \endplumedfile</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            : The file dist.dat for this calculation would read:</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : \auxfile{dist.grid}</a>
+<a name="340"><span class="lineNum">     340 </span>            : #! FIELDS d1 t1.target der_d1</a>
+<a name="341"><span class="lineNum">     341 </span>            : #! SET min_d1 1.14</a>
+<a name="342"><span class="lineNum">     342 </span>            : #! SET max_d1 1.32</a>
+<a name="343"><span class="lineNum">     343 </span>            : #! SET nbins_d1  6</a>
+<a name="344"><span class="lineNum">     344 </span>            : #! SET periodic_d1 false</a>
+<a name="345"><span class="lineNum">     345 </span>            :    1.1400   0.0031   0.1101</a>
+<a name="346"><span class="lineNum">     346 </span>            :    1.1700   0.0086   0.2842</a>
+<a name="347"><span class="lineNum">     347 </span>            :    1.2000   0.0222   0.6648</a>
+<a name="348"><span class="lineNum">     348 </span>            :    1.2300   0.0521   1.4068</a>
+<a name="349"><span class="lineNum">     349 </span>            :    1.2600   0.1120   2.6873</a>
+<a name="350"><span class="lineNum">     350 </span>            :    1.2900   0.2199   4.6183</a>
+<a name="351"><span class="lineNum">     351 </span>            :    1.3200   0.3948   7.1055</a>
+<a name="352"><span class="lineNum">     352 </span>            : \endauxfile</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : Notice that BIASFACTOR can also be chosen as equal to 1. In this case one will perform</a>
+<a name="355"><span class="lineNum">     355 </span>            : unbiased sampling. Instead of using HEIGHT, one should provide the TAU parameter.</a>
+<a name="356"><span class="lineNum">     356 </span>            : \plumedfile</a>
+<a name="357"><span class="lineNum">     357 </span>            : d: DISTANCE ATOMS=3,5</a>
+<a name="358"><span class="lineNum">     358 </span>            : METAD ARG=d SIGMA=0.1 TAU=4.0 TEMP=300 PACE=100 BIASFACTOR=1.0</a>
+<a name="359"><span class="lineNum">     359 </span>            : \endplumedfile</a>
+<a name="360"><span class="lineNum">     360 </span>            : The HILLS file obtained will still work with `plumed sum_hills` so as to plot a free-energy.</a>
+<a name="361"><span class="lineNum">     361 </span>            : The case where this makes sense is probably that of RECT simulations.</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            : Regarding RECT simulations, you can also use the RECT keyword so as to avoid using multiple input files.</a>
+<a name="364"><span class="lineNum">     364 </span>            : For instance, a single input file will be</a>
+<a name="365"><span class="lineNum">     365 </span>            : \plumedfile</a>
+<a name="366"><span class="lineNum">     366 </span>            : d: DISTANCE ATOMS=3,5</a>
+<a name="367"><span class="lineNum">     367 </span>            : METAD ARG=d SIGMA=0.1 TAU=4.0 TEMP=300 PACE=100 RECT=1.0,1.5,2.0,3.0</a>
+<a name="368"><span class="lineNum">     368 </span>            : \endplumedfile</a>
+<a name="369"><span class="lineNum">     369 </span>            : The number of elements in the RECT array should be equal to the number of replicas.</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span>            : */</a>
+<a name="372"><span class="lineNum">     372 </span>            : //+ENDPLUMEDOC</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : class MetaD : public Bias {</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : private:</a>
+<a name="377"><span class="lineNum">     377 </span>            :   struct Gaussian {</a>
+<a name="378"><span class="lineNum">     378 </span>            :     bool   multivariate; // this is required to discriminate the one dimensional case</a>
+<a name="379"><span class="lineNum">     379 </span>            :     double height;</a>
+<a name="380"><span class="lineNum">     380 </span>            :     std::vector&lt;double&gt; center;</a>
+<a name="381"><span class="lineNum">     381 </span>            :     std::vector&lt;double&gt; sigma;</a>
+<a name="382"><span class="lineNum">     382 </span>            :     std::vector&lt;double&gt; invsigma;</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       5200 :     Gaussian(const bool m, const double h, const std::vector&lt;double&gt;&amp; c, const std::vector&lt;double&gt;&amp; s):</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       5200 :       multivariate(m),height(h),center(c),sigma(s),invsigma(s) {</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :       // to avoid troubles from zero element in flexible hills</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">      15137 :       for(unsigned i=0; i&lt;invsigma.size(); ++i) {</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       9937 :         if(std::abs(invsigma[i])&gt;1.e-20) invsigma[i]=1.0/invsigma[i] ;</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :         else invsigma[i]=0.0;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :       }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">       5200 :     }</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :   };</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          8 :   struct TemperingSpecs {</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :     bool is_active;</a>
+<a name="394"><span class="lineNum">     394 </span>            :     std::string name_stem;</a>
+<a name="395"><span class="lineNum">     395 </span>            :     std::string name;</a>
+<a name="396"><span class="lineNum">     396 </span>            :     double biasf;</a>
+<a name="397"><span class="lineNum">     397 </span>            :     double threshold;</a>
+<a name="398"><span class="lineNum">     398 </span>            :     double alpha;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">        156 :     inline TemperingSpecs(bool is_active, const std::string &amp;name_stem, const std::string &amp;name, double biasf, double threshold, double alpha) :</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        156 :       is_active(is_active), name_stem(name_stem), name(name), biasf(biasf), threshold(threshold), alpha(alpha)</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">        156 :     {}</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :   };</a>
+<a name="403"><span class="lineNum">     403 </span>            :   // general setup</a>
+<a name="404"><span class="lineNum">     404 </span>            :   double kbt_;</a>
+<a name="405"><span class="lineNum">     405 </span>            :   int stride_;</a>
+<a name="406"><span class="lineNum">     406 </span>            :   bool calc_work_;</a>
+<a name="407"><span class="lineNum">     407 </span>            :   // well-tempered MetaD</a>
+<a name="408"><span class="lineNum">     408 </span>            :   bool welltemp_;</a>
+<a name="409"><span class="lineNum">     409 </span>            :   double biasf_;</a>
+<a name="410"><span class="lineNum">     410 </span>            :   // output files format</a>
+<a name="411"><span class="lineNum">     411 </span>            :   std::string fmt_;</a>
+<a name="412"><span class="lineNum">     412 </span>            :   // first step?</a>
+<a name="413"><span class="lineNum">     413 </span>            :   bool isFirstStep_;</a>
+<a name="414"><span class="lineNum">     414 </span>            :   // Gaussian starting parameters</a>
+<a name="415"><span class="lineNum">     415 </span>            :   double height0_;</a>
+<a name="416"><span class="lineNum">     416 </span>            :   std::vector&lt;double&gt; sigma0_;</a>
+<a name="417"><span class="lineNum">     417 </span>            :   std::vector&lt;double&gt; sigma0min_;</a>
+<a name="418"><span class="lineNum">     418 </span>            :   std::vector&lt;double&gt; sigma0max_;</a>
+<a name="419"><span class="lineNum">     419 </span>            :   // Gaussians</a>
+<a name="420"><span class="lineNum">     420 </span>            :   std::vector&lt;Gaussian&gt; hills_;</a>
+<a name="421"><span class="lineNum">     421 </span>            :   std::unique_ptr&lt;FlexibleBin&gt; flexbin_;</a>
+<a name="422"><span class="lineNum">     422 </span>            :   int adaptive_;</a>
+<a name="423"><span class="lineNum">     423 </span>            :   OFile hillsOfile_;</a>
+<a name="424"><span class="lineNum">     424 </span>            :   std::vector&lt;std::unique_ptr&lt;IFile&gt;&gt; ifiles_;</a>
+<a name="425"><span class="lineNum">     425 </span>            :   std::vector&lt;std::string&gt; ifilesnames_;</a>
+<a name="426"><span class="lineNum">     426 </span>            :   // Grids</a>
+<a name="427"><span class="lineNum">     427 </span>            :   bool grid_;</a>
+<a name="428"><span class="lineNum">     428 </span>            :   std::unique_ptr&lt;GridBase&gt; BiasGrid_;</a>
+<a name="429"><span class="lineNum">     429 </span>            :   OFile gridfile_;</a>
+<a name="430"><span class="lineNum">     430 </span>            :   bool storeOldGrids_;</a>
+<a name="431"><span class="lineNum">     431 </span>            :   int wgridstride_;</a>
+<a name="432"><span class="lineNum">     432 </span>            :   // multiple walkers</a>
+<a name="433"><span class="lineNum">     433 </span>            :   int mw_n_;</a>
+<a name="434"><span class="lineNum">     434 </span>            :   std::string mw_dir_;</a>
+<a name="435"><span class="lineNum">     435 </span>            :   int mw_id_;</a>
+<a name="436"><span class="lineNum">     436 </span>            :   int mw_rstride_;</a>
+<a name="437"><span class="lineNum">     437 </span>            :   bool walkers_mpi_;</a>
+<a name="438"><span class="lineNum">     438 </span>            :   unsigned mpi_nw_;</a>
+<a name="439"><span class="lineNum">     439 </span>            :   // flying gaussians</a>
+<a name="440"><span class="lineNum">     440 </span>            :   bool flying_;</a>
+<a name="441"><span class="lineNum">     441 </span>            :   // kinetics from metadynamics</a>
+<a name="442"><span class="lineNum">     442 </span>            :   bool acceleration_;</a>
+<a name="443"><span class="lineNum">     443 </span>            :   double acc_;</a>
+<a name="444"><span class="lineNum">     444 </span>            :   double acc_restart_mean_;</a>
+<a name="445"><span class="lineNum">     445 </span>            :   // transition-tempering metadynamics</a>
+<a name="446"><span class="lineNum">     446 </span>            :   bool calc_max_bias_;</a>
+<a name="447"><span class="lineNum">     447 </span>            :   double max_bias_;</a>
+<a name="448"><span class="lineNum">     448 </span>            :   bool calc_transition_bias_;</a>
+<a name="449"><span class="lineNum">     449 </span>            :   double transition_bias_;</a>
+<a name="450"><span class="lineNum">     450 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; transitionwells_;</a>
+<a name="451"><span class="lineNum">     451 </span>            :   static const size_t n_tempering_options_ = 1;</a>
+<a name="452"><span class="lineNum">     452 </span>            :   static const std::string tempering_names_[1][2];</a>
+<a name="453"><span class="lineNum">     453 </span>            :   double dampfactor_;</a>
+<a name="454"><span class="lineNum">     454 </span>            :   struct TemperingSpecs tt_specs_;</a>
+<a name="455"><span class="lineNum">     455 </span>            :   std::string targetfilename_;</a>
+<a name="456"><span class="lineNum">     456 </span>            :   std::unique_ptr&lt;GridBase&gt; TargetGrid_;</a>
+<a name="457"><span class="lineNum">     457 </span>            :   // frequency adaptive metadynamics</a>
+<a name="458"><span class="lineNum">     458 </span>            :   int current_stride_;</a>
+<a name="459"><span class="lineNum">     459 </span>            :   bool freq_adaptive_;</a>
+<a name="460"><span class="lineNum">     460 </span>            :   int fa_update_frequency_;</a>
+<a name="461"><span class="lineNum">     461 </span>            :   int fa_max_stride_;</a>
+<a name="462"><span class="lineNum">     462 </span>            :   double fa_min_acceleration_;</a>
+<a name="463"><span class="lineNum">     463 </span>            :   // intervals</a>
+<a name="464"><span class="lineNum">     464 </span>            :   double uppI_;</a>
+<a name="465"><span class="lineNum">     465 </span>            :   double lowI_;</a>
+<a name="466"><span class="lineNum">     466 </span>            :   bool doInt_;</a>
+<a name="467"><span class="lineNum">     467 </span>            :   // reweighting</a>
+<a name="468"><span class="lineNum">     468 </span>            :   bool calc_rct_;</a>
+<a name="469"><span class="lineNum">     469 </span>            :   double reweight_factor_;</a>
+<a name="470"><span class="lineNum">     470 </span>            :   unsigned rct_ustride_;</a>
+<a name="471"><span class="lineNum">     471 </span>            :   // work</a>
+<a name="472"><span class="lineNum">     472 </span>            :   double work_;</a>
+<a name="473"><span class="lineNum">     473 </span>            :   // neighbour list stuff</a>
+<a name="474"><span class="lineNum">     474 </span>            :   bool nlist_;</a>
+<a name="475"><span class="lineNum">     475 </span>            :   bool nlist_update_;</a>
+<a name="476"><span class="lineNum">     476 </span>            :   unsigned nlist_steps_;</a>
+<a name="477"><span class="lineNum">     477 </span>            :   std::array&lt;double,2&gt; nlist_param_;</a>
+<a name="478"><span class="lineNum">     478 </span>            :   std::vector&lt;Gaussian&gt; nlist_hills_;</a>
+<a name="479"><span class="lineNum">     479 </span>            :   std::vector&lt;double&gt; nlist_center_;</a>
+<a name="480"><span class="lineNum">     480 </span>            :   std::vector&lt;double&gt; nlist_dev2_;</a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span>            :   double stretchA=1.0;</a>
+<a name="483"><span class="lineNum">     483 </span>            :   double stretchB=0.0;</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            :   bool noStretchWarningDone=false;</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">         12 :   void noStretchWarning() {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         12 :     if(!noStretchWarningDone) {</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          3 :       log&lt;&lt;&quot;\nWARNING: you are using a HILLS file with Gaussian kernels, PLUMED 2.8 uses stretched Gaussians by default\n&quot;;</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :     }</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">         12 :     noStretchWarningDone=true;</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         12 :   }</span></a>
+<a name="493"><span class="lineNum">     493 </span>            : </a>
+<a name="494"><span class="lineNum">     494 </span>            :   static void registerTemperingKeywords(const std::string &amp;name_stem, const std::string &amp;name, Keywords &amp;keys);</a>
+<a name="495"><span class="lineNum">     495 </span>            :   void   readTemperingSpecs(TemperingSpecs &amp;t_specs);</a>
+<a name="496"><span class="lineNum">     496 </span>            :   void   logTemperingSpecs(const TemperingSpecs &amp;t_specs);</a>
+<a name="497"><span class="lineNum">     497 </span>            :   void   readGaussians(IFile*);</a>
+<a name="498"><span class="lineNum">     498 </span>            :   void   writeGaussian(const Gaussian&amp;,OFile&amp;);</a>
+<a name="499"><span class="lineNum">     499 </span>            :   void   addGaussian(const Gaussian&amp;);</a>
+<a name="500"><span class="lineNum">     500 </span>            :   double getHeight(const std::vector&lt;double&gt;&amp;);</a>
+<a name="501"><span class="lineNum">     501 </span>            :   void   temperHeight(double &amp;height, const TemperingSpecs &amp;t_specs, const double tempering_bias);</a>
+<a name="502"><span class="lineNum">     502 </span>            :   double getBias(const std::vector&lt;double&gt;&amp;);</a>
+<a name="503"><span class="lineNum">     503 </span>            :   double getBiasAndDerivatives(const std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;);</a>
+<a name="504"><span class="lineNum">     504 </span>            :   double evaluateGaussian(const std::vector&lt;double&gt;&amp;, const Gaussian&amp;);</a>
+<a name="505"><span class="lineNum">     505 </span>            :   double evaluateGaussianAndDerivatives(const std::vector&lt;double&gt;&amp;, const Gaussian&amp;,std::vector&lt;double&gt;&amp;,std::vector&lt;double&gt;&amp;);</a>
+<a name="506"><span class="lineNum">     506 </span>            :   double getGaussianNormalization(const Gaussian&amp;);</a>
+<a name="507"><span class="lineNum">     507 </span>            :   std::vector&lt;unsigned&gt; getGaussianSupport(const Gaussian&amp;);</a>
+<a name="508"><span class="lineNum">     508 </span>            :   bool   scanOneHill(IFile* ifile, std::vector&lt;Value&gt;&amp; v, std::vector&lt;double&gt;&amp; center, std::vector&lt;double&gt;&amp; sigma, double&amp; height, bool&amp; multivariate);</a>
+<a name="509"><span class="lineNum">     509 </span>            :   void   computeReweightingFactor();</a>
+<a name="510"><span class="lineNum">     510 </span>            :   double getTransitionBarrierBias();</a>
+<a name="511"><span class="lineNum">     511 </span>            :   void   updateFrequencyAdaptiveStride();</a>
+<a name="512"><span class="lineNum">     512 </span>            :   void   updateNlist();</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            : public:</a>
+<a name="515"><span class="lineNum">     515 </span>            :   explicit MetaD(const ActionOptions&amp;);</a>
+<a name="516"><span class="lineNum">     516 </span>            :   void calculate() override;</a>
+<a name="517"><span class="lineNum">     517 </span>            :   void update() override;</a>
+<a name="518"><span class="lineNum">     518 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="519"><span class="lineNum">     519 </span>            :   bool checkNeedsGradients()const override;</a>
+<a name="520"><span class="lineNum">     520 </span>            : };</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">      12809 : PLUMED_REGISTER_ACTION(MetaD,&quot;METAD&quot;)</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">        159 : void MetaD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">        159 :   Bias::registerKeywords(keys);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;rbias&quot;,&quot;CALC_RCT&quot;,&quot;the instantaneous value of the bias normalized using the c(t) reweighting factor [rbias=bias-rct].&quot;</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :                           &quot;This component can be used to obtain a reweighted histogram.&quot;);</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;rct&quot;,&quot;CALC_RCT&quot;,&quot;the reweighting factor \\f$c(t)\\f$.&quot;);</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;work&quot;,&quot;CALC_WORK&quot;,&quot;accumulator for work&quot;);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;acc&quot;,&quot;ACCELERATION&quot;,&quot;the metadynamics acceleration factor&quot;);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;maxbias&quot;, &quot;CALC_MAX_BIAS&quot;, &quot;the maximum of the metadynamics V(s, t)&quot;);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;transbias&quot;, &quot;CALC_TRANSITION_BIAS&quot;, &quot;the metadynamics transition bias V*(t)&quot;);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;pace&quot;,&quot;FREQUENCY_ADAPTIVE&quot;,&quot;the hill addition frequency when employing frequency adaptive metadynamics&quot;);</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;nlker&quot;,&quot;NLIST&quot;,&quot;number of hills in the neighbor list&quot;);</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">        318 :   keys.addOutputComponent(&quot;nlsteps&quot;,&quot;NLIST&quot;,&quot;number of steps from last neighbor list update&quot;);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">        159 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">        318 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;the widths of the Gaussian hills&quot;);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">        318 :   keys.add(&quot;compulsory&quot;,&quot;PACE&quot;,&quot;the frequency for hill addition&quot;);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">        318 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;HILLS&quot;,&quot;a file in which the list of added hills is stored&quot;);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;HEIGHT&quot;,&quot;the heights of the Gaussian hills. Compulsory unless TAU and either BIASFACTOR or DAMPFACTOR are given&quot;);</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;specify format for HILLS files (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;BIASFACTOR&quot;,&quot;use well tempered metadynamics and use this bias factor.  Please note you must also specify temp&quot;);</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">        318 :   keys.addFlag(&quot;CALC_WORK&quot;,false,&quot;calculate the total accumulated work done by the bias since last restart&quot;);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;RECT&quot;,&quot;list of bias factors for all the replicas&quot;);</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;DAMPFACTOR&quot;,&quot;damp hills with exp(-max(V)/(kT*DAMPFACTOR)&quot;);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">        318 :   for (size_t i = 0; i &lt; n_tempering_options_; i++) {</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">        159 :     registerTemperingKeywords(tempering_names_[i][0], tempering_names_[i][1], keys);</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :   }</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;TARGET&quot;,&quot;target to a predefined distribution&quot;);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - this is only needed if you are doing well-tempered metadynamics&quot;);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;TAU&quot;,&quot;in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau&quot;);</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">        318 :   keys.addFlag(&quot;CALC_RCT&quot;,false,&quot;calculate the c(t) reweighting factor and use that to obtain the normalized bias [rbias=bias-rct].&quot;</span></a>
+<a name="553"><span class="lineNum">     553 </span>            :                &quot;This method is not compatible with metadynamics not on a grid.&quot;);</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;RCT_USTRIDE&quot;,&quot;the update stride for calculating the \\f$c(t)\\f$ reweighting factor.&quot;</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :            &quot;The default 1, so \\f$c(t)\\f$ is updated every time the bias is updated.&quot;);</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_MIN&quot;,&quot;the lower bounds for the grid&quot;);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_MAX&quot;,&quot;the upper bounds for the grid&quot;);</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_BIN&quot;,&quot;the number of bins for the grid&quot;);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_SPACING&quot;,&quot;the approximate grid spacing (to be used as an alternative or together with GRID_BIN)&quot;);</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">        318 :   keys.addFlag(&quot;GRID_SPARSE&quot;,false,&quot;use a sparse grid to store hills&quot;);</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">        318 :   keys.addFlag(&quot;GRID_NOSPLINE&quot;,false,&quot;don't use spline interpolation with grids&quot;);</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_WSTRIDE&quot;,&quot;write the grid to a file every N steps&quot;);</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_WFILE&quot;,&quot;the file on which to write the grid&quot;);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;GRID_RFILE&quot;,&quot;a grid file from which the bias should be read at the initial step of the simulation&quot;);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">        318 :   keys.addFlag(&quot;STORE_GRIDS&quot;,false,&quot;store all the grid files the calculation generates. They will be deleted if this keyword is not present&quot;);</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">        318 :   keys.addFlag(&quot;NLIST&quot;,false,&quot;Use neighbor list for kernels summation, faster but experimental&quot;);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;, &quot;NLIST_PARAMETERS&quot;,&quot;(default=6.,0.5) the two cutoff parameters for the Gaussians neighbor list&quot;);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;ADAPTIVE&quot;,&quot;use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme. Sigma is one number that has distance units or time step dimensions&quot;);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MAX&quot;,&quot;the upper bounds for the sigmas (in CV units) when using adaptive hills. Negative number means no bounds &quot;);</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MIN&quot;,&quot;the lower bounds for the sigmas (in CV units) when using adaptive hills. Negative number means no bounds &quot;);</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;WALKERS_ID&quot;, &quot;walker id&quot;);</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;WALKERS_N&quot;, &quot;number of walkers&quot;);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;WALKERS_DIR&quot;, &quot;shared directory with the hills files from all the walkers&quot;);</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;WALKERS_RSTRIDE&quot;,&quot;stride for reading hills files&quot;);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        318 :   keys.addFlag(&quot;WALKERS_MPI&quot;,false,&quot;Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR&quot;);</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;INTERVAL&quot;,&quot;one dimensional lower and upper limits, outside the limits the system will not feel the biasing force.&quot;);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        318 :   keys.addFlag(&quot;FLYING_GAUSSIAN&quot;,false,&quot;Switch on flying Gaussian method, must be used with WALKERS_MPI&quot;);</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">        318 :   keys.addFlag(&quot;ACCELERATION&quot;,false,&quot;Set to TRUE if you want to compute the metadynamics acceleration factor.&quot;);</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;ACCELERATION_RFILE&quot;,&quot;a data file from which the acceleration should be read at the initial step of the simulation&quot;);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">        318 :   keys.addFlag(&quot;CALC_MAX_BIAS&quot;, false, &quot;Set to TRUE if you want to compute the maximum of the metadynamics V(s, t)&quot;);</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">        318 :   keys.addFlag(&quot;CALC_TRANSITION_BIAS&quot;, false, &quot;Set to TRUE if you want to compute a metadynamics transition bias V*(t)&quot;);</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">        318 :   keys.add(&quot;numbered&quot;, &quot;TRANSITIONWELL&quot;, &quot;This keyword appears multiple times as TRANSITIONWELL followed by an integer. Each specifies the coordinates for one well as in transition-tempered metadynamics. At least one must be provided.&quot;);</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">        318 :   keys.addFlag(&quot;FREQUENCY_ADAPTIVE&quot;,false,&quot;Set to TRUE if you want to enable frequency adaptive metadynamics such that the frequency for hill addition to change dynamically based on the acceleration factor.&quot;);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;FA_UPDATE_FREQUENCY&quot;,&quot;the frequency for updating the hill addition pace in frequency adaptive metadynamics, by default this is equal to the value given in PACE&quot;);</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;FA_MAX_PACE&quot;,&quot;the maximum hill addition frequency allowed in frequency adaptive metadynamics. By default there is no maximum value.&quot;);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;,&quot;FA_MIN_ACCELERATION&quot;,&quot;only update the hill addition pace in frequency adaptive metadynamics after reaching the minimum acceleration factor given here. By default it is 1.0.&quot;);</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">        159 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">        159 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">        159 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">        159 : }</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            : const std::string MetaD::tempering_names_[1][2] = {{&quot;TT&quot;, &quot;transition tempered&quot;}};</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">        159 : void MetaD::registerTemperingKeywords(const std::string &amp;name_stem, const std::string &amp;name, Keywords &amp;keys) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;, name_stem + &quot;BIASFACTOR&quot;, &quot;use &quot; + name + &quot; metadynamics with this bias factor.  Please note you must also specify temp&quot;);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;, name_stem + &quot;BIASTHRESHOLD&quot;, &quot;use &quot; + name + &quot; metadynamics with this bias threshold.  Please note you must also specify &quot; + name_stem + &quot;BIASFACTOR&quot;);</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">        318 :   keys.add(&quot;optional&quot;, name_stem + &quot;ALPHA&quot;, &quot;use &quot; + name + &quot; metadynamics with this hill size decay exponent parameter.  Please note you must also specify &quot; + name_stem + &quot;BIASFACTOR&quot;);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">        159 : }</span></a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">        157 : MetaD::MetaD(const ActionOptions&amp; ao):</span></a>
+<a name="601"><span class="lineNum">     601 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">        156 :   kbt_(0.0),</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">        156 :   stride_(0),</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        156 :   calc_work_(false),</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        156 :   welltemp_(false),</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">        156 :   biasf_(-1.0),</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">        156 :   isFirstStep_(true),</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">        156 :   height0_(std::numeric_limits&lt;double&gt;::max()),</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">        156 :   adaptive_(FlexibleBin::none),</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">        156 :   grid_(false),</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">        156 :   wgridstride_(0),</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">        156 :   mw_n_(1), mw_dir_(&quot;&quot;), mw_id_(0), mw_rstride_(1),</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">        156 :   walkers_mpi_(false), mpi_nw_(0),</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">        156 :   flying_(false),</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">        156 :   acceleration_(false), acc_(0.0), acc_restart_mean_(0.0),</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">        156 :   calc_max_bias_(false), max_bias_(0.0),</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">        156 :   calc_transition_bias_(false), transition_bias_(0.0),</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">        156 :   dampfactor_(0.0),</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        312 :   tt_specs_(false, &quot;TT&quot;, &quot;Transition Tempered&quot;, -1.0, 0.0, 1.0),</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">        156 :   current_stride_(0),</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">        156 :   freq_adaptive_(false),</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        156 :   fa_update_frequency_(0),</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        156 :   fa_max_stride_(0),</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">        156 :   fa_min_acceleration_(1.0),</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">        156 :   uppI_(-1), lowI_(-1), doInt_(false),</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        156 :   calc_rct_(false),</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">        156 :   reweight_factor_(0.0),</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">        156 :   rct_ustride_(1),</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">        156 :   work_(0),</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">        156 :   nlist_(false),</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">        156 :   nlist_update_(false),</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">        469 :   nlist_steps_(0)</span></a>
+<a name="633"><span class="lineNum">     633 </span>            : {</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">        156 :   if(!dp2cutoffNoStretch()) {</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">        156 :     stretchA=dp2cutoffA;</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">        156 :     stretchB=dp2cutoffB;</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :   }</a>
+<a name="638"><span class="lineNum">     638 </span>            :   // parse the flexible hills</a>
+<a name="639"><span class="lineNum">     639 </span>            :   std::string adaptiveoption;</a>
+<a name="640"><span class="lineNum">     640 </span>            :   adaptiveoption=&quot;NONE&quot;;</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">        312 :   parse(&quot;ADAPTIVE&quot;,adaptiveoption);</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">        156 :   if(adaptiveoption==&quot;GEOM&quot;) {</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">         22 :     log.printf(&quot;  Uses Geometry-based hills width: sigma must be in distance units and only one sigma is needed\n&quot;);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">         22 :     adaptive_=FlexibleBin::geometry;</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">        134 :   } else if(adaptiveoption==&quot;DIFF&quot;) {</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">          3 :     log.printf(&quot;  Uses Diffusion-based hills width: sigma must be in time steps and only one sigma is needed\n&quot;);</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          3 :     adaptive_=FlexibleBin::diffusion;</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">        131 :   } else if(adaptiveoption==&quot;NONE&quot;) {</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">        130 :     adaptive_=FlexibleBin::none;</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :   } else {</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          1 :     error(&quot;I do not know this type of adaptive scheme&quot;);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :   }</a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">        155 :   parse(&quot;FMT&quot;,fmt_);</span></a>
+<a name="655"><span class="lineNum">     655 </span>            : </a>
+<a name="656"><span class="lineNum">     656 </span>            :   // parse the sigma</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">        155 :   parseVector(&quot;SIGMA&quot;,sigma0_);</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">        155 :   if(adaptive_==FlexibleBin::none) {</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :     // if you use normal sigma you need one sigma per argument</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">        130 :     if( sigma0_.size()!=getNumberOfArguments() ) error(&quot;number of arguments does not match number of SIGMA parameters&quot;);</span></a>
+<a name="661"><span class="lineNum">     661 </span>            :   } else {</a>
+<a name="662"><span class="lineNum">     662 </span>            :     // if you use flexible hills you need one sigma</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         25 :     if(sigma0_.size()!=1) {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">          1 :       error(&quot;If you choose ADAPTIVE you need only one sigma according to your choice of type (GEOM/DIFF)&quot;);</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :     }</a>
+<a name="666"><span class="lineNum">     666 </span>            :     // if adaptive then the number must be an integer</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         24 :     if(adaptive_==FlexibleBin::diffusion) {</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">          3 :       if(int(sigma0_[0])-sigma0_[0]&gt;1.e-9 || int(sigma0_[0])-sigma0_[0] &lt;-1.e-9 || int(sigma0_[0])&lt;1 ) {</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :         error(&quot;In case of adaptive hills with diffusion, the sigma must be an integer which is the number of time steps\n&quot;);</span></a>
+<a name="670"><span class="lineNum">     670 </span>            :       }</a>
+<a name="671"><span class="lineNum">     671 </span>            :     }</a>
+<a name="672"><span class="lineNum">     672 </span>            :     // here evtl parse the sigma min and max values</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">         48 :     parseVector(&quot;SIGMA_MIN&quot;,sigma0min_);</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">         24 :     if(sigma0min_.size()&gt;0 &amp;&amp; sigma0min_.size()!=getNumberOfArguments()) {</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">          1 :       error(&quot;the number of SIGMA_MIN values be the same of the number of the arguments&quot;);</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">         23 :     } else if(sigma0min_.size()==0) {</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         23 :       sigma0min_.resize(getNumberOfArguments());</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         67 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {sigma0min_[i]=-1.;}</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :     }</a>
+<a name="680"><span class="lineNum">     680 </span>            : </a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         46 :     parseVector(&quot;SIGMA_MAX&quot;,sigma0max_);</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         23 :     if(sigma0max_.size()&gt;0 &amp;&amp; sigma0max_.size()!=getNumberOfArguments()) {</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">          1 :       error(&quot;the number of SIGMA_MAX values be the same of the number of the arguments&quot;);</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         22 :     } else if(sigma0max_.size()==0) {</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">         22 :       sigma0max_.resize(getNumberOfArguments());</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         64 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {sigma0max_[i]=-1.;}</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :     }</a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">         44 :     flexbin_=Tools::make_unique&lt;FlexibleBin&gt;(adaptive_,this,sigma0_[0],sigma0min_,sigma0max_);</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :   }</a>
+<a name="691"><span class="lineNum">     691 </span>            : </a>
+<a name="692"><span class="lineNum">     692 </span>            :   // note: HEIGHT is not compulsory, since one could use the TAU keyword, see below</a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">        152 :   parse(&quot;HEIGHT&quot;,height0_);</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">        152 :   parse(&quot;PACE&quot;,stride_);</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">        151 :   if(stride_&lt;=0) error(&quot;frequency for hill addition is nonsensical&quot;);</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">        151 :   current_stride_ = stride_;</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">        159 :   std::string hillsfname=&quot;HILLS&quot;;</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">        151 :   parse(&quot;FILE&quot;,hillsfname);</span></a>
+<a name="699"><span class="lineNum">     699 </span>            : </a>
+<a name="700"><span class="lineNum">     700 </span>            :   // Manually set to calculate special bias quantities</a>
+<a name="701"><span class="lineNum">     701 </span>            :   // throughout the course of simulation. (These are chosen due to</a>
+<a name="702"><span class="lineNum">     702 </span>            :   // relevance for tempering and event-driven logic as well.)</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">        151 :   parseFlag(&quot;CALC_MAX_BIAS&quot;, calc_max_bias_);</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">        305 :   parseFlag(&quot;CALC_TRANSITION_BIAS&quot;, calc_transition_bias_);</span></a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            :   std::vector&lt;double&gt; rect_biasf_;</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">        302 :   parseVector(&quot;RECT&quot;,rect_biasf_);</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">        151 :   if(rect_biasf_.size()&gt;0) {</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         18 :     int r=0;</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">         18 :     if(comm.Get_rank()==0) r=multi_sim_comm.Get_rank();</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">         18 :     comm.Bcast(r,0);</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">         18 :     biasf_=rect_biasf_[r];</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">         18 :     log&lt;&lt;&quot;  You are using RECT\n&quot;;</span></a>
+<a name="714"><span class="lineNum">     714 </span>            :   } else {</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">        266 :     parse(&quot;BIASFACTOR&quot;,biasf_);</span></a>
+<a name="716"><span class="lineNum">     716 </span>            :   }</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">        151 :   if( biasf_&lt;1.0  &amp;&amp; biasf_!=-1.0) error(&quot;well tempered bias factor is nonsensical&quot;);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">        151 :   parse(&quot;DAMPFACTOR&quot;,dampfactor_);</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">        151 :   double temp=0.0;</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">        151 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">        151 :   if(temp&gt;0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">         95 :   else kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">        151 :   if(biasf_&gt;=1.0) {</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">         38 :     if(kbt_==0.0) error(&quot;Unless the MD engine passes the temperature to plumed, with well-tempered metad you must specify it using TEMP&quot;);</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">         38 :     welltemp_=true;</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :   }</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">        151 :   if(dampfactor_&gt;0.0) {</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">          2 :     if(kbt_==0.0) error(&quot;Unless the MD engine passes the temperature to plumed, with damped metad you must specify it using TEMP&quot;);</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :   }</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">        151 :   parseFlag(&quot;CALC_WORK&quot;,calc_work_);</span></a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span>            :   // Set transition tempering parameters.</a>
+<a name="734"><span class="lineNum">     734 </span>            :   // Transition wells are read later via calc_transition_bias_.</a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">        151 :   readTemperingSpecs(tt_specs_);</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">        151 :   if (tt_specs_.is_active) calc_transition_bias_ = true;</span></a>
+<a name="737"><span class="lineNum">     737 </span>            : </a>
+<a name="738"><span class="lineNum">     738 </span>            :   // If any previous option specified to calculate a transition bias,</a>
+<a name="739"><span class="lineNum">     739 </span>            :   // now read the transition wells for that quantity.</a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">        151 :   if (calc_transition_bias_) {</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">         13 :     std::vector&lt;double&gt; tempcoords(getNumberOfArguments());</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">         26 :     for (unsigned i = 0; ; i++) {</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">         78 :       if (!parseNumberedVector(&quot;TRANSITIONWELL&quot;, i, tempcoords) ) break;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">         26 :       if (tempcoords.size() != getNumberOfArguments()) {</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :         error(&quot;incorrect number of coordinates for transition tempering well&quot;);</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :       }</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">         26 :       transitionwells_.push_back(tempcoords);</span></a>
+<a name="748"><span class="lineNum">     748 </span>            :     }</a>
+<a name="749"><span class="lineNum">     749 </span>            :   }</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">        302 :   parse(&quot;TARGET&quot;,targetfilename_);</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">        151 :   if(targetfilename_.length()&gt;0 &amp;&amp; kbt_==0.0)  error(&quot;with TARGET temperature must be specified&quot;);</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">        151 :   double tau=0.0;</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">        151 :   parse(&quot;TAU&quot;,tau);</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">        151 :   if(tau==0.0) {</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">        129 :     if(height0_==std::numeric_limits&lt;double&gt;::max()) error(&quot;At least one between HEIGHT and TAU should be specified&quot;);</span></a>
+<a name="757"><span class="lineNum">     757 </span>            :     // if tau is not set, we compute it here from the other input parameters</a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">        129 :     if(welltemp_) tau=(kbt_*(biasf_-1.0))/height0_*getTimeStep()*stride_;</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">        110 :     else if(dampfactor_&gt;0.0) tau=(kbt_*dampfactor_)/height0_*getTimeStep()*stride_;</span></a>
+<a name="760"><span class="lineNum">     760 </span>            :   } else {</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">         22 :     if(height0_!=std::numeric_limits&lt;double&gt;::max()) error(&quot;At most one between HEIGHT and TAU should be specified&quot;);</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">         22 :     if(welltemp_) {</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">         19 :       if(biasf_!=1.0) height0_=(kbt_*(biasf_-1.0))/tau*getTimeStep()*stride_;</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">          4 :       else           height0_=kbt_/tau*getTimeStep()*stride_; // special case for gamma=1</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :     }</a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">          3 :     else if(dampfactor_&gt;0.0) height0_=(kbt_*dampfactor_)/tau*getTimeStep()*stride_;</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">          1 :     else error(&quot;TAU only makes sense in well-tempered or damped metadynamics&quot;);</span></a>
+<a name="768"><span class="lineNum">     768 </span>            :   }</a>
+<a name="769"><span class="lineNum">     769 </span>            : </a>
+<a name="770"><span class="lineNum">     770 </span>            :   // Grid Stuff</a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">        153 :   std::vector&lt;std::string&gt; gmin(getNumberOfArguments());</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">        300 :   parseVector(&quot;GRID_MIN&quot;,gmin);</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">        150 :   if(gmin.size()!=getNumberOfArguments() &amp;&amp; gmin.size()!=0) error(&quot;not enough values for GRID_MIN&quot;);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">        150 :   std::vector&lt;std::string&gt; gmax(getNumberOfArguments());</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">        300 :   parseVector(&quot;GRID_MAX&quot;,gmax);</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">        150 :   if(gmax.size()!=getNumberOfArguments() &amp;&amp; gmax.size()!=0) error(&quot;not enough values for GRID_MAX&quot;);</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">        150 :   std::vector&lt;unsigned&gt; gbin(getNumberOfArguments());</span></a>
+<a name="778"><span class="lineNum">     778 </span>            :   std::vector&lt;double&gt;   gspacing;</a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">        300 :   parseVector(&quot;GRID_BIN&quot;,gbin);</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">        150 :   if(gbin.size()!=getNumberOfArguments() &amp;&amp; gbin.size()!=0) error(&quot;not enough values for GRID_BIN&quot;);</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">        300 :   parseVector(&quot;GRID_SPACING&quot;,gspacing);</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">        150 :   if(gspacing.size()!=getNumberOfArguments() &amp;&amp; gspacing.size()!=0) error(&quot;not enough values for GRID_SPACING&quot;);</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">        150 :   if(gmin.size()!=gmax.size()) error(&quot;GRID_MAX and GRID_MIN should be either present or absent&quot;);</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">        150 :   if(gspacing.size()!=0 &amp;&amp; gmin.size()==0) error(&quot;If GRID_SPACING is present also GRID_MIN and GRID_MAX should be present&quot;);</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">        150 :   if(gbin.size()!=0     &amp;&amp; gmin.size()==0) error(&quot;If GRID_BIN is present also GRID_MIN and GRID_MAX should be present&quot;);</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">        150 :   if(gmin.size()!=0) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">         61 :     if(gbin.size()==0 &amp;&amp; gspacing.size()==0) {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">          6 :       if(adaptive_==FlexibleBin::none) {</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">          6 :         log&lt;&lt;&quot;  Binsize not specified, 1/5 of sigma will be be used\n&quot;;</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">          6 :         plumed_assert(sigma0_.size()==getNumberOfArguments());</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">          6 :         gspacing.resize(getNumberOfArguments());</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">         13 :         for(unsigned i=0; i&lt;gspacing.size(); i++) gspacing[i]=0.2*sigma0_[i];</span></a>
+<a name="793"><span class="lineNum">     793 </span>            :       } else {</a>
+<a name="794"><span class="lineNum">     794 </span>            :         // with adaptive hills and grid a sigma min must be specified</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;sigma0min_.size(); i++) if(sigma0min_[i]&lt;=0) error(&quot;When using ADAPTIVE Gaussians on a grid SIGMA_MIN must be specified&quot;);</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineNoCov">          0 :         log&lt;&lt;&quot;  Binsize not specified, 1/5 of sigma_min will be be used\n&quot;;</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineNoCov">          0 :         gspacing.resize(getNumberOfArguments());</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;gspacing.size(); i++) gspacing[i]=0.2*sigma0min_[i];</span></a>
+<a name="799"><span class="lineNum">     799 </span>            :       }</a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">         55 :     } else if(gspacing.size()!=0 &amp;&amp; gbin.size()==0) {</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">          2 :       log&lt;&lt;&quot;  The number of bins will be estimated from GRID_SPACING\n&quot;;</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">         53 :     } else if(gspacing.size()!=0 &amp;&amp; gbin.size()!=0) {</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">          1 :       log&lt;&lt;&quot;  You specified both GRID_BIN and GRID_SPACING\n&quot;;</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">          1 :       log&lt;&lt;&quot;  The more conservative (highest) number of bins will be used for each variable\n&quot;;</span></a>
+<a name="805"><span class="lineNum">     805 </span>            :     }</a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">         61 :     if(gbin.size()==0) gbin.assign(getNumberOfArguments(),1);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">         73 :     if(gspacing.size()!=0) for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="808"><span class="lineNum">     808 </span>            :         double a,b;</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">         13 :         Tools::convert(gmin[i],a);</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">         12 :         Tools::convert(gmax[i],b);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">         12 :         unsigned n=std::ceil(((b-a)/gspacing[i]));</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         12 :         if(gbin[i]&lt;n) gbin[i]=n;</span></a>
+<a name="813"><span class="lineNum">     813 </span>            :       }</a>
+<a name="814"><span class="lineNum">     814 </span>            :   }</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">        149 :   if(gbin.size()&gt;0) grid_=true;</span></a>
+<a name="816"><span class="lineNum">     816 </span>            : </a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">        149 :   bool sparsegrid=false;</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">        149 :   parseFlag(&quot;GRID_SPARSE&quot;,sparsegrid);</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">        149 :   bool nospline=false;</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">        149 :   parseFlag(&quot;GRID_NOSPLINE&quot;,nospline);</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">        149 :   bool spline=!nospline;</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">        300 :   parse(&quot;GRID_WSTRIDE&quot;,wgridstride_);</span></a>
+<a name="823"><span class="lineNum">     823 </span>            :   std::string gridfilename_;</a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        149 :   parse(&quot;GRID_WFILE&quot;,gridfilename_);</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">        149 :   parseFlag(&quot;STORE_GRIDS&quot;,storeOldGrids_);</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">        149 :   if(grid_ &amp;&amp; gridfilename_.length()&gt;0) {</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">         19 :     if(wgridstride_==0 ) error(&quot;frequency with which to output grid not specified use GRID_WSTRIDE&quot;);</span></a>
+<a name="828"><span class="lineNum">     828 </span>            :   }</a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">        149 :   if(grid_ &amp;&amp; wgridstride_&gt;0) {</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">         20 :     if(gridfilename_.length()==0) error(&quot;grid filename not specified use GRID_WFILE&quot;);</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :   }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            :   std::string gridreadfilename_;</a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">        149 :   parse(&quot;GRID_RFILE&quot;,gridreadfilename_);</span></a>
+<a name="835"><span class="lineNum">     835 </span>            : </a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">        149 :   if(!grid_&amp;&amp;gridfilename_.length()&gt; 0) error(&quot;To write a grid you need first to define it!&quot;);</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">        149 :   if(!grid_&amp;&amp;gridreadfilename_.length()&gt;0) error(&quot;To read a grid you need first to define it!&quot;);</span></a>
+<a name="838"><span class="lineNum">     838 </span>            : </a>
+<a name="839"><span class="lineNum">     839 </span>            :   /*setup neighbor list stuff*/</a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">        298 :   parseFlag(&quot;NLIST&quot;, nlist_);</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">        149 :   nlist_center_.resize(getNumberOfArguments());</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">        149 :   nlist_dev2_.resize(getNumberOfArguments());</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">        150 :   if(nlist_&amp;&amp;grid_) error(&quot;NLIST and GRID cannot be combined!&quot;);</span></a>
+<a name="844"><span class="lineNum">     844 </span>            :   std::vector&lt;double&gt; nlist_param;</a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">        298 :   parseVector(&quot;NLIST_PARAMETERS&quot;,nlist_param);</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">        149 :   if(nlist_param.size()==0)</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :   {</a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">        149 :     nlist_param_[0]=6.0;//*DP2CUTOFF -&gt; max distance of neighbors</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">        149 :     nlist_param_[1]=0.5;//*nlist_dev2_[i] -&gt; condition for rebuilding</span></a>
+<a name="850"><span class="lineNum">     850 </span>            :   }</a>
+<a name="851"><span class="lineNum">     851 </span>            :   else</a>
+<a name="852"><span class="lineNum">     852 </span>            :   {</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :     plumed_massert(nlist_param.size()==2,&quot;two cutoff parameters are needed for the neighbor list&quot;);</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :     plumed_massert(nlist_param[0]&gt;1.0,&quot;the first of NLIST_PARAMETERS must be greater than 1. The smaller the first, the smaller should be the second as well&quot;);</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineNoCov">          0 :     const double min_PARAM_1=(1.-1./std::sqrt(nlist_param[0]/2))+0.16;</span></a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :     plumed_massert(nlist_param[1]&gt;0,&quot;the second of NLIST_PARAMETERS must be greater than 0&quot;);</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineNoCov">          0 :     plumed_massert(nlist_param[1]&lt;=min_PARAM_1,&quot;the second of NLIST_PARAMETERS must be smaller to avoid systematic errors. Largest suggested value is: 1.16-1/sqrt(PARAM_0/2) = &quot;+std::to_string(min_PARAM_1));</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineNoCov">          0 :     nlist_param_[0]=nlist_param[0];</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineNoCov">          0 :     nlist_param_[1]=nlist_param[1];</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :   }</a>
+<a name="861"><span class="lineNum">     861 </span>            : </a>
+<a name="862"><span class="lineNum">     862 </span>            :   // Reweighting factor rct</a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">        149 :   parseFlag(&quot;CALC_RCT&quot;,calc_rct_);</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">        149 :   if (calc_rct_) plumed_massert(grid_,&quot;CALC_RCT is supported only if bias is on a grid&quot;);</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">        149 :   parse(&quot;RCT_USTRIDE&quot;,rct_ustride_);</span></a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">        149 :   if(dampfactor_&gt;0.0) {</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">          2 :     if(!grid_) error(&quot;With DAMPFACTOR you should use grids&quot;);</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :   }</a>
+<a name="870"><span class="lineNum">     870 </span>            : </a>
+<a name="871"><span class="lineNum">     871 </span>            :   // Multiple walkers</a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">        149 :   parse(&quot;WALKERS_N&quot;,mw_n_);</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">        149 :   parse(&quot;WALKERS_ID&quot;,mw_id_);</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">        149 :   if(mw_n_&lt;=mw_id_) error(&quot;walker ID should be a numerical value less than the total number of walkers&quot;);</span></a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">        149 :   parse(&quot;WALKERS_DIR&quot;,mw_dir_);</span></a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">        149 :   parse(&quot;WALKERS_RSTRIDE&quot;,mw_rstride_);</span></a>
+<a name="877"><span class="lineNum">     877 </span>            : </a>
+<a name="878"><span class="lineNum">     878 </span>            :   // MPI version</a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">        149 :   parseFlag(&quot;WALKERS_MPI&quot;,walkers_mpi_);</span></a>
+<a name="880"><span class="lineNum">     880 </span>            : </a>
+<a name="881"><span class="lineNum">     881 </span>            :   //If this Action is not compiled with MPI the user is informed and we exit gracefully</a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">        149 :   if(walkers_mpi_) {</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">         39 :     plumed_assert(Communicator::plumedHasMPI()) &lt;&lt; &quot;Invalid walkers configuration: WALKERS_MPI flag requires MPI compilation&quot;;</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         40 :     plumed_assert(Communicator::initialized()) &lt;&lt; &quot;Invalid walkers configuration: WALKERS_MPI needs the communicator correctly initialized.&quot;;</span></a>
+<a name="885"><span class="lineNum">     885 </span>            :   }</a>
+<a name="886"><span class="lineNum">     886 </span>            : </a>
+<a name="887"><span class="lineNum">     887 </span>            :   // Flying Gaussian</a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineCov">        148 :   parseFlag(&quot;FLYING_GAUSSIAN&quot;, flying_);</span></a>
+<a name="889"><span class="lineNum">     889 </span>            : </a>
+<a name="890"><span class="lineNum">     890 </span>            :   // Inteval keyword</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">        149 :   std::vector&lt;double&gt; tmpI(2);</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">        296 :   parseVector(&quot;INTERVAL&quot;,tmpI);</span></a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">        148 :   if(tmpI.size()!=2&amp;&amp;tmpI.size()!=0) error(&quot;both a lower and an upper limits must be provided with INTERVAL&quot;);</span></a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">        148 :   else if(tmpI.size()==2) {</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">          2 :     lowI_=tmpI.at(0);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">          2 :     uppI_=tmpI.at(1);</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">          2 :     if(getNumberOfArguments()!=1) error(&quot;INTERVAL limits correction works only for monodimensional metadynamics!&quot;);</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">          2 :     if(uppI_&lt;lowI_) error(&quot;The Upper limit must be greater than the Lower limit!&quot;);</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">          2 :     if(getPntrToArgument(0)-&gt;isPeriodic()) error(&quot;INTERVAL cannot be used with periodic variables!&quot;);</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">          2 :     doInt_=true;</span></a>
+<a name="901"><span class="lineNum">     901 </span>            :   }</a>
+<a name="902"><span class="lineNum">     902 </span>            : </a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">        296 :   parseFlag(&quot;ACCELERATION&quot;,acceleration_);</span></a>
+<a name="904"><span class="lineNum">     904 </span>            :   // Check for a restart acceleration if acceleration is active.</a>
+<a name="905"><span class="lineNum">     905 </span>            :   std::string acc_rfilename;</a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">        148 :   if(acceleration_) {</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">          8 :     parse(&quot;ACCELERATION_RFILE&quot;, acc_rfilename);</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :   }</a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">        148 :   freq_adaptive_=false;</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">        148 :   parseFlag(&quot;FREQUENCY_ADAPTIVE&quot;,freq_adaptive_);</span></a>
+<a name="912"><span class="lineNum">     912 </span>            :   //</a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">        148 :   fa_update_frequency_=0;</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">        148 :   parse(&quot;FA_UPDATE_FREQUENCY&quot;,fa_update_frequency_);</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">        148 :   if(fa_update_frequency_!=0 &amp;&amp; !freq_adaptive_) {</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;It doesn't make sense to use the FA_MAX_PACE keyword if frequency adaptive METAD hasn't been activated by using the FREQUENCY_ADAPTIVE flag&quot;);</span></a>
+<a name="917"><span class="lineNum">     917 </span>            :   }</a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">        148 :   if(fa_update_frequency_==0 &amp;&amp; freq_adaptive_) {</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :     fa_update_frequency_=stride_;</span></a>
+<a name="920"><span class="lineNum">     920 </span>            :   }</a>
+<a name="921"><span class="lineNum">     921 </span>            :   //</a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">        148 :   fa_max_stride_=0;</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">        148 :   parse(&quot;FA_MAX_PACE&quot;,fa_max_stride_);</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">        148 :   if(fa_max_stride_!=0 &amp;&amp; !freq_adaptive_) {</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;It doesn't make sense to use the FA_MAX_PACE keyword if frequency adaptive METAD hasn't been activated by using the FREQUENCY_ADAPTIVE flag&quot;);</span></a>
+<a name="926"><span class="lineNum">     926 </span>            :   }</a>
+<a name="927"><span class="lineNum">     927 </span>            :   //</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">        148 :   fa_min_acceleration_=1.0;</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">        148 :   parse(&quot;FA_MIN_ACCELERATION&quot;,fa_min_acceleration_);</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">        148 :   if(fa_min_acceleration_!=1.0 &amp;&amp; !freq_adaptive_) {</span></a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;It doesn't make sense to use the FA_MIN_ACCELERATION keyword if frequency adaptive METAD hasn't been activated by using the FREQUENCY_ADAPTIVE flag&quot;);</span></a>
+<a name="932"><span class="lineNum">     932 </span>            :   }</a>
+<a name="933"><span class="lineNum">     933 </span>            : </a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">        148 :   checkRead();</span></a>
+<a name="935"><span class="lineNum">     935 </span>            : </a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">        148 :   log.printf(&quot;  Gaussian width &quot;);</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">        148 :   if (adaptive_==FlexibleBin::diffusion)log.printf(&quot; (Note: The units of sigma are in timesteps) &quot;);</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">        148 :   if (adaptive_==FlexibleBin::geometry)log.printf(&quot; (Note: The units of sigma are in dist units) &quot;);</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">        396 :   for(unsigned i=0; i&lt;sigma0_.size(); ++i) log.printf(&quot; %f&quot;,sigma0_[i]);</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">        148 :   log.printf(&quot;  Gaussian height %f\n&quot;,height0_);</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">        148 :   log.printf(&quot;  Gaussian deposition pace %d\n&quot;,stride_);</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">        148 :   log.printf(&quot;  Gaussian file %s\n&quot;,hillsfname.c_str());</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">        148 :   if(welltemp_) {</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">         38 :     log.printf(&quot;  Well-Tempered Bias Factor %f\n&quot;,biasf_);</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">         38 :     log.printf(&quot;  Hills relaxation time (tau) %f\n&quot;,tau);</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">         38 :     log.printf(&quot;  KbT %f\n&quot;,kbt_);</span></a>
+<a name="947"><span class="lineNum">     947 </span>            :   }</a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span>            :   // Transition tempered metadynamics options</a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">        148 :   if (tt_specs_.is_active) {</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">          3 :     logTemperingSpecs(tt_specs_);</span></a>
+<a name="952"><span class="lineNum">     952 </span>            :     // Check that the appropriate transition bias quantity is calculated.</a>
+<a name="953"><span class="lineNum">     953 </span>            :     // (Should never trip, given that the flag is automatically set.)</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">          3 :     if (!calc_transition_bias_) {</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineNoCov">          0 :       error(&quot; transition tempering requires calculation of a transition bias&quot;);</span></a>
+<a name="956"><span class="lineNum">     956 </span>            :     }</a>
+<a name="957"><span class="lineNum">     957 </span>            :   }</a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span>            :   // Overall tempering sanity check (this gets tricky when multiple are active).</a>
+<a name="960"><span class="lineNum">     960 </span>            :   // When multiple temperings are active, it's fine to have one tempering attempt</a>
+<a name="961"><span class="lineNum">     961 </span>            :   // to increase hill size with increasing bias, so long as the others can shrink</a>
+<a name="962"><span class="lineNum">     962 </span>            :   // the hills faster than it increases their size in the long-time limit.</a>
+<a name="963"><span class="lineNum">     963 </span>            :   // This set of checks ensures that the hill sizes eventually decay to zero as c(t)</a>
+<a name="964"><span class="lineNum">     964 </span>            :   // diverges to infinity.</a>
+<a name="965"><span class="lineNum">     965 </span>            :   // The alpha parameter allows hills to decay as 1/t^alpha instead of 1/t,</a>
+<a name="966"><span class="lineNum">     966 </span>            :   // a slower decay, so as t -&gt; infinity, only the temperings with the largest</a>
+<a name="967"><span class="lineNum">     967 </span>            :   // alphas govern the final asymptotic decay. (Alpha helps prevent false convergence.)</a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">        148 :   if (welltemp_ || dampfactor_ &gt; 0.0 || tt_specs_.is_active) {</span></a>
+<a name="969"><span class="lineNum">     969 </span>            :     // Determine the number of active temperings.</a>
+<a name="970"><span class="lineNum">     970 </span>            :     int n_active = 0;</a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">         43 :     if (welltemp_) n_active++;</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">         43 :     if (dampfactor_ &gt; 0.0) n_active++;</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">         43 :     if (tt_specs_.is_active) n_active++;</span></a>
+<a name="974"><span class="lineNum">     974 </span>            :     // Find the greatest alpha.</a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">         43 :     double greatest_alpha = 0.0;</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">         43 :     if (welltemp_) greatest_alpha = std::max(greatest_alpha, 1.0);</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">         45 :     if (dampfactor_ &gt; 0.0) greatest_alpha = std::max(greatest_alpha, 1.0);</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">         46 :     if (tt_specs_.is_active) greatest_alpha = std::max(greatest_alpha, tt_specs_.alpha);</span></a>
+<a name="979"><span class="lineNum">     979 </span>            :     // Find the least alpha.</a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">         43 :     double least_alpha = 1.0;</span></a>
+<a name="981"><span class="lineNum">     981 </span>            :     if (welltemp_) least_alpha = std::min(least_alpha, 1.0);</a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">         43 :     if (dampfactor_ &gt; 0.0) least_alpha = std::min(least_alpha, 1.0);</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">         44 :     if (tt_specs_.is_active) least_alpha = std::min(least_alpha, tt_specs_.alpha);</span></a>
+<a name="984"><span class="lineNum">     984 </span>            :     // Find the inverse harmonic average of the delta T parameters for all</a>
+<a name="985"><span class="lineNum">     985 </span>            :     // of the temperings with the greatest alpha values.</a>
+<a name="986"><span class="lineNum">     986 </span>            :     double total_governing_deltaT_inv = 0.0;</a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">         43 :     if (welltemp_ &amp;&amp; 1.0 == greatest_alpha &amp;&amp; biasf_ != 1.0) total_governing_deltaT_inv += 1.0 / (biasf_ - 1.0);</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">         43 :     if (dampfactor_ &gt; 0.0 &amp;&amp; 1.0 == greatest_alpha) total_governing_deltaT_inv += 1.0 / (dampfactor_);</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">         43 :     if (tt_specs_.is_active &amp;&amp; tt_specs_.alpha == greatest_alpha) total_governing_deltaT_inv += 1.0 / (tt_specs_.biasf - 1.0);</span></a>
+<a name="990"><span class="lineNum">     990 </span>            :     // Give a newbie-friendly error message for people using one tempering if</a>
+<a name="991"><span class="lineNum">     991 </span>            :     // only one is active.</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">         43 :     if (n_active == 1 &amp;&amp; total_governing_deltaT_inv &lt; 0.0) {</span></a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineNoCov">          0 :       error(&quot;for stable tempering, the bias factor must be greater than one&quot;);</span></a>
+<a name="994"><span class="lineNum">     994 </span>            :       // Give a slightly more complex error message to users stacking multiple</a>
+<a name="995"><span class="lineNum">     995 </span>            :       // tempering options at a time, but all with uniform alpha values.</a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">         43 :     } else if (total_governing_deltaT_inv &lt; 0.0 &amp;&amp; greatest_alpha == least_alpha) {</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineNoCov">          0 :       error(&quot;for stable tempering, the sum of the inverse Delta T parameters must be greater than zero!&quot;);</span></a>
+<a name="998"><span class="lineNum">     998 </span>            :       // Give the most technical error message to users stacking multiple tempering</a>
+<a name="999"><span class="lineNum">     999 </span>            :       // options with different alpha parameters.</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">         43 :     } else if (total_governing_deltaT_inv &lt; 0.0 &amp;&amp; greatest_alpha != least_alpha) {</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineNoCov">          0 :       error(&quot;for stable tempering, the sum of the inverse Delta T parameters for the greatest asymptotic hill decay exponents must be greater than zero!&quot;);</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     }</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   }</a>
+<a name="1004"><span class="lineNum">    1004 </span>            : </a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">        148 :   if(doInt_) log.printf(&quot;  Upper and Lower limits boundaries for the bias are activated at %f - %f\n&quot;, lowI_, uppI_);</span></a>
+<a name="1006"><span class="lineNum">    1006 </span>            : </a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">        148 :   if(grid_) {</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineCov">         60 :     log.printf(&quot;  Grid min&quot;);</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">        161 :     for(unsigned i=0; i&lt;gmin.size(); ++i) log.printf(&quot; %s&quot;,gmin[i].c_str() );</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">         60 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">         60 :     log.printf(&quot;  Grid max&quot;);</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">        161 :     for(unsigned i=0; i&lt;gmax.size(); ++i) log.printf(&quot; %s&quot;,gmax[i].c_str() );</span></a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">         60 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">         60 :     log.printf(&quot;  Grid bin&quot;);</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">        161 :     for(unsigned i=0; i&lt;gbin.size(); ++i) log.printf(&quot; %u&quot;,gbin[i]);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">         60 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">         60 :     if(spline) {log.printf(&quot;  Grid uses spline interpolation\n&quot;);}</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">         60 :     if(sparsegrid) {log.printf(&quot;  Grid uses sparse grid\n&quot;);}</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">         60 :     if(wgridstride_&gt;0) {log.printf(&quot;  Grid is written on file %s with stride %d\n&quot;,gridfilename_.c_str(),wgridstride_);}</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            :   }</a>
+<a name="1021"><span class="lineNum">    1021 </span>            : </a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">        148 :   if(mw_n_&gt;1) {</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">          6 :     if(walkers_mpi_) error(&quot;MPI version of multiple walkers is not compatible with filesystem version of multiple walkers&quot;);</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">          6 :     log.printf(&quot;  %d multiple walkers active\n&quot;,mw_n_);</span></a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineCov">          6 :     log.printf(&quot;  walker id %d\n&quot;,mw_id_);</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">          6 :     log.printf(&quot;  reading stride %d\n&quot;,mw_rstride_);</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">          6 :     if(mw_dir_!=&quot;&quot;)log.printf(&quot;  directory with hills files %s\n&quot;,mw_dir_.c_str());</span></a>
+<a name="1028"><span class="lineNum">    1028 </span>            :   } else {</a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">        142 :     if(walkers_mpi_) {</span></a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">         38 :       log.printf(&quot;  Multiple walkers active using MPI communnication\n&quot;);</span></a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">         38 :       if(mw_dir_!=&quot;&quot;)log.printf(&quot;  directory with hills files %s\n&quot;,mw_dir_.c_str());</span></a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">         38 :       if(comm.Get_rank()==0) {</span></a>
+<a name="1033"><span class="lineNum">    1033 </span>            :         // Only root of group can communicate with other walkers</a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">         23 :         mpi_nw_=multi_sim_comm.Get_size();</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            :       }</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :       // Communicate to the other members of the same group</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :       // info abount number of walkers and walker index</a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">         38 :       comm.Bcast(mpi_nw_,0);</span></a>
+<a name="1039"><span class="lineNum">    1039 </span>            :     }</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   }</a>
+<a name="1041"><span class="lineNum">    1041 </span>            : </a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">        148 :   if(flying_) {</span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">          6 :     if(!walkers_mpi_) error(&quot;Flying Gaussian method must be used with MPI version of multiple walkers&quot;);</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">          6 :     log.printf(&quot;  Flying Gaussian method with %d walkers active\n&quot;,mpi_nw_);</span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            :   }</a>
+<a name="1046"><span class="lineNum">    1046 </span>            : </a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">        148 :   if(nlist_) {</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">          1 :     addComponent(&quot;nlker&quot;);</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">          1 :     componentIsNotPeriodic(&quot;nlker&quot;);</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">          1 :     addComponent(&quot;nlsteps&quot;);</span></a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">          2 :     componentIsNotPeriodic(&quot;nlsteps&quot;);</span></a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   }</a>
+<a name="1053"><span class="lineNum">    1053 </span>            : </a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">        148 :   if(calc_rct_) {</span></a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">         12 :     addComponent(&quot;rbias&quot;); componentIsNotPeriodic(&quot;rbias&quot;);</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">         12 :     addComponent(&quot;rct&quot;); componentIsNotPeriodic(&quot;rct&quot;);</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">          6 :     log.printf(&quot;  The c(t) reweighting factor will be calculated every %u hills\n&quot;,rct_ustride_);</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">         12 :     getPntrToComponent(&quot;rct&quot;)-&gt;set(reweight_factor_);</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   }</a>
+<a name="1060"><span class="lineNum">    1060 </span>            : </a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">        150 :   if(calc_work_) { addComponent(&quot;work&quot;); componentIsNotPeriodic(&quot;work&quot;); }</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            : </a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">        148 :   if(acceleration_) {</span></a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">          4 :     if (kbt_ == 0.0) {</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineNoCov">          0 :       error(&quot;The calculation of the acceleration works only if simulation temperature has been defined&quot;);</span></a>
+<a name="1066"><span class="lineNum">    1066 </span>            :     }</a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">          4 :     log.printf(&quot;  calculation on the fly of the acceleration factor\n&quot;);</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">         12 :     addComponent(&quot;acc&quot;); componentIsNotPeriodic(&quot;acc&quot;);</span></a>
+<a name="1069"><span class="lineNum">    1069 </span>            :     // Set the initial value of the the acceleration.</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :     // If this is not a restart, set to 1.0.</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">          4 :     if (acc_rfilename.length() == 0) {</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">          4 :       getPntrToComponent(&quot;acc&quot;)-&gt;set(1.0);</span></a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">          2 :       if(getRestart()) {</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">          1 :         log.printf(&quot;  WARNING: calculating the acceleration factor in a restarted run without reading in the previous value will most likely lead to incorrect results.\n&quot;);</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">          1 :         log.printf(&quot;           You should use the ACCELERATION_RFILE keyword.\n&quot;);</span></a>
+<a name="1076"><span class="lineNum">    1076 </span>            :       }</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :       // Otherwise, read and set the restart value.</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     } else {</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :       // Restart of acceleration does not make sense if the restart timestep is zero.</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :       //if (getStep() == 0) {</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :       //  error(&quot;Restarting calculation of acceleration factors works only if simulation timestep is restarted correctly&quot;);</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :       //}</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :       // Open the ACCELERATION_RFILE.</a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">          2 :       IFile acc_rfile;</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">          2 :       acc_rfile.link(*this);</span></a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">          2 :       if(acc_rfile.FileExist(acc_rfilename)) {</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">          2 :         acc_rfile.open(acc_rfilename);</span></a>
+<a name="1088"><span class="lineNum">    1088 </span>            :       } else {</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :         error(&quot;The ACCELERATION_RFILE file you want to read: &quot; + acc_rfilename + &quot;, cannot be found!&quot;);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :       }</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :       // Read the file to find the restart acceleration.</a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">          2 :       double acc_rmean=0.0;</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">          2 :       double acc_rtime=0.0;</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            :       bool found=false;</a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">          2 :       std::string acclabel = getLabel() + &quot;.acc&quot;;</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">          2 :       acc_rfile.allowIgnoredFields();</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">        248 :       while(acc_rfile.scanField(&quot;time&quot;, acc_rtime)) {</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">        122 :         acc_rfile.scanField(acclabel, acc_rmean);</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">        122 :         acc_rfile.scanField();</span></a>
+<a name="1100"><span class="lineNum">    1100 </span>            :         found=true;</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :       }</a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">          2 :       if(!found) error(&quot;The ACCELERATION_RFILE file you want to read: &quot; + acc_rfilename + &quot;, does not contain a time field!&quot;);</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">          2 :       acc_restart_mean_ = acc_rmean;</span></a>
+<a name="1104"><span class="lineNum">    1104 </span>            :       // Set component based on the read values.</a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">          2 :       getPntrToComponent(&quot;acc&quot;)-&gt;set(acc_rmean);</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">          2 :       log.printf(&quot;  initial acceleration factor read from file %s: value of %f at time %f\n&quot;,acc_rfilename.c_str(),acc_rmean,acc_rtime);</span></a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">          2 :     }</span></a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   }</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">        148 :   if (calc_max_bias_) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineNoCov">          0 :     if (!grid_) error(&quot;Calculating the maximum bias on the fly works only with a grid&quot;);</span></a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineNoCov">          0 :     log.printf(&quot;  calculation on the fly of the maximum bias max(V(s,t)) \n&quot;);</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineNoCov">          0 :     addComponent(&quot;maxbias&quot;);</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineNoCov">          0 :     componentIsNotPeriodic(&quot;maxbias&quot;);</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   }</a>
+<a name="1116"><span class="lineNum">    1116 </span>            : </a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineCov">        148 :   if (calc_transition_bias_) {</span></a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">         13 :     if (!grid_) error(&quot;Calculating the transition bias on the fly works only with a grid&quot;);</span></a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">         13 :     log.printf(&quot;  calculation on the fly of the transition bias V*(t)\n&quot;);</span></a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">         13 :     addComponent(&quot;transbias&quot;);</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">         13 :     componentIsNotPeriodic(&quot;transbias&quot;);</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">         13 :     log&lt;&lt;&quot;  Number of transition wells &quot;&lt;&lt;transitionwells_.size()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">         13 :     if (transitionwells_.size() == 0) error(&quot;Calculating the transition bias on the fly requires definition of at least one transition well&quot;);</span></a>
+<a name="1124"><span class="lineNum">    1124 </span>            :     // Check that a grid is in use.</a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">         13 :     if (!grid_) error(&quot; transition barrier finding requires a grid for the bias&quot;);</span></a>
+<a name="1126"><span class="lineNum">    1126 </span>            :     // Log the wells and check that they are in the grid.</a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">         39 :     for (unsigned i = 0; i &lt; transitionwells_.size(); i++) {</span></a>
+<a name="1128"><span class="lineNum">    1128 </span>            :       // Log the coordinate.</a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">         26 :       log.printf(&quot;  Transition well %d at coordinate &quot;, i);</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">         64 :       for (unsigned j = 0; j &lt; getNumberOfArguments(); j++) log.printf(&quot;%f &quot;, transitionwells_[i][j]);</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">         26 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="1132"><span class="lineNum">    1132 </span>            :       // Check that the coordinate is in the grid.</a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">         64 :       for (unsigned j = 0; j &lt; getNumberOfArguments(); j++) {</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            :         double max, min;</a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">         38 :         Tools::convert(gmin[j], min);</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">         38 :         Tools::convert(gmax[j], max);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">         38 :         if (transitionwells_[i][j] &lt; min || transitionwells_[i][j] &gt; max) error(&quot; transition well is not in grid&quot;);</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :       }</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :     }</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            : </a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">        148 :   if(freq_adaptive_) {</span></a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">          2 :     if(!acceleration_) {</span></a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Frequency adaptive metadynamics only works if the calculation of the acceleration factor is enabled with the ACCELERATION keyword\n&quot;);</span></a>
+<a name="1145"><span class="lineNum">    1145 </span>            :     }</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">          2 :     if(walkers_mpi_) {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Combining frequency adaptive metadynamics with MPI multiple walkers is not allowed&quot;);</span></a>
+<a name="1148"><span class="lineNum">    1148 </span>            :     }</a>
+<a name="1149"><span class="lineNum">    1149 </span>            : </a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">          2 :     log.printf(&quot;  Frequency adaptive metadynamics enabled\n&quot;);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">          2 :     if(getRestart() &amp;&amp; acc_rfilename.length() == 0) {</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineNoCov">          0 :       log.printf(&quot;  WARNING: using the frequency adaptive scheme in a restarted run without reading in the previous value of the acceleration factor will most likely lead to incorrect results.\n&quot;);</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineNoCov">          0 :       log.printf(&quot;           You should use the ACCELERATION_RFILE keyword.\n&quot;);</span></a>
+<a name="1154"><span class="lineNum">    1154 </span>            :     }</a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">          2 :     log.printf(&quot;  The frequency for hill addition will change dynamically based on the metadynamics acceleration factor\n&quot;);</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">          2 :     log.printf(&quot;  The hill addition frequency will be updated every %d steps\n&quot;,fa_update_frequency_);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">          2 :     if(fa_min_acceleration_&gt;1.0) {</span></a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">          2 :       log.printf(&quot;  The hill addition frequency will only be updated once the metadynamics acceleration factor becomes larger than %.1f \n&quot;,fa_min_acceleration_);</span></a>
+<a name="1159"><span class="lineNum">    1159 </span>            :     }</a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">          2 :     if(fa_max_stride_!=0) {</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">          2 :       log.printf(&quot;  The hill addition frequency will not become larger than %d steps\n&quot;,fa_max_stride_);</span></a>
+<a name="1162"><span class="lineNum">    1162 </span>            :     }</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">          4 :     addComponent(&quot;pace&quot;); componentIsNotPeriodic(&quot;pace&quot;);</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">          2 :     updateFrequencyAdaptiveStride();</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            :   }</a>
+<a name="1166"><span class="lineNum">    1166 </span>            : </a>
+<a name="1167"><span class="lineNum">    1167 </span>            :   // initializing and checking grid</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :   bool restartedFromGrid=false;  // restart from grid file</a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">        148 :   if(grid_) {</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">         60 :     if(!(gridreadfilename_.length()&gt;0)) {</span></a>
+<a name="1171"><span class="lineNum">    1171 </span>            :       // check for mesh and sigma size</a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineCov">        116 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="1173"><span class="lineNum">    1173 </span>            :         double a,b;</a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineCov">         74 :         Tools::convert(gmin[i],a);</span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineCov">         74 :         Tools::convert(gmax[i],b);</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">         74 :         double mesh=(b-a)/((double)gbin[i]);</span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">         74 :         if(adaptive_==FlexibleBin::none) {</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">         74 :           if(mesh&gt;0.5*sigma0_[i]) log&lt;&lt;&quot;  WARNING: Using a METAD with a Grid Spacing larger than half of the Gaussians width (SIGMA) can produce artifacts\n&quot;;</span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            :         } else {</a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :           if(sigma0min_[i]&lt;0.) error(&quot;When using ADAPTIVE Gaussians on a grid SIGMA_MIN must be specified&quot;);</span></a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineNoCov">          0 :           if(mesh&gt;0.5*sigma0min_[i]) log&lt;&lt;&quot;  WARNING: to use a METAD with a GRID and ADAPTIVE you need to set a Grid Spacing lower than half of the Gaussians (SIGMA_MIN) \n&quot;;</span></a>
+<a name="1182"><span class="lineNum">    1182 </span>            :         }</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :       }</a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineCov">         42 :       std::string funcl=getLabel() + &quot;.bias&quot;;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">         42 :       if(!sparsegrid) {BiasGrid_=Tools::make_unique&lt;Grid&gt;(funcl,getArguments(),gmin,gmax,gbin,spline,true);}</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineCov">          6 :       else {BiasGrid_=Tools::make_unique&lt;SparseGrid&gt;(funcl,getArguments(),gmin,gmax,gbin,spline,true);}</span></a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">         42 :       std::vector&lt;std::string&gt; actualmin=BiasGrid_-&gt;getMin();</span></a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">         42 :       std::vector&lt;std::string&gt; actualmax=BiasGrid_-&gt;getMax();</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">        116 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            :         std::string is;</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineCov">         74 :         Tools::convert(i,is);</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineCov">         74 :         if(gmin[i]!=actualmin[i]) error(&quot;GRID_MIN[&quot;+is+&quot;] must be adjusted to &quot;+actualmin[i]+&quot; to fit periodicity&quot;);</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineCov">         74 :         if(gmax[i]!=actualmax[i]) error(&quot;GRID_MAX[&quot;+is+&quot;] must be adjusted to &quot;+actualmax[i]+&quot; to fit periodicity&quot;);</span></a>
+<a name="1194"><span class="lineNum">    1194 </span>            :       }</a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineCov">         42 :     } else {</span></a>
+<a name="1196"><span class="lineNum">    1196 </span>            :       // read the grid in input, find the keys</a>
+<a name="1197"><span class="lineNum">    1197 </span>            : #ifdef __PLUMED_HAS_GETCWD</a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineCov">         18 :       if(walkers_mpi_&amp;&amp;gridreadfilename_.at(0)!='/') {</span></a>
+<a name="1199"><span class="lineNum">    1199 </span>            :         //if possible the root replica will share its current folder so that all walkers will read the same file</a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineNoCov">          0 :         char cwd[4096]= {0};</span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            :         const char* ret=getcwd(cwd,4096);</a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineNoCov">          0 :         plumed_assert(ret)&lt;&lt;&quot;Name of current directory too long, increase buffer size&quot;;</span></a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineNoCov">          0 :         gridreadfilename_ = &quot;/&quot; + gridreadfilename_;</span></a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineNoCov">          0 :         gridreadfilename_ = ret + gridreadfilename_;</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineNoCov">          0 :         if(comm.Get_rank()==0) multi_sim_comm.Bcast(gridreadfilename_,0);</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :         comm.Bcast(gridreadfilename_,0);</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            :       }</a>
+<a name="1208"><span class="lineNum">    1208 </span>            : #endif</a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">         18 :       IFile gridfile;</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">         18 :       gridfile.link(*this);</span></a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineCov">         18 :       if(gridfile.FileExist(gridreadfilename_)) {</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineCov">         18 :         gridfile.open(gridreadfilename_);</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            :       } else {</a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineNoCov">          0 :         error(&quot;The GRID file you want to read: &quot; + gridreadfilename_ + &quot;, cannot be found!&quot;);</span></a>
+<a name="1215"><span class="lineNum">    1215 </span>            :       }</a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineCov">         18 :       std::string funcl=getLabel() + &quot;.bias&quot;;</span></a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">         36 :       BiasGrid_=GridBase::create(funcl, getArguments(), gridfile, gmin, gmax, gbin, sparsegrid, spline, true);</span></a>
+<a name="1218"><span class="lineNum">    1218 </span><span class="lineCov">         18 :       if(BiasGrid_-&gt;getDimension()!=getNumberOfArguments()) error(&quot;mismatch between dimensionality of input grid and number of arguments&quot;);</span></a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">         45 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">         54 :         if( getPntrToArgument(i)-&gt;isPeriodic()!=BiasGrid_-&gt;getIsPeriodic()[i] ) error(&quot;periodicity mismatch between arguments and input bias&quot;);</span></a>
+<a name="1221"><span class="lineNum">    1221 </span>            :         double a, b;</a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">         27 :         Tools::convert(gmin[i],a);</span></a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">         27 :         Tools::convert(gmax[i],b);</span></a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">         27 :         double mesh=(b-a)/((double)gbin[i]);</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">         27 :         if(mesh&gt;0.5*sigma0_[i]) log&lt;&lt;&quot;  WARNING: Using a METAD with a Grid Spacing larger than half of the Gaussians width can produce artifacts\n&quot;;</span></a>
+<a name="1226"><span class="lineNum">    1226 </span>            :       }</a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">         18 :       log.printf(&quot;  Restarting from %s\n&quot;,gridreadfilename_.c_str());</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">         18 :       if(getRestart()) restartedFromGrid=true;</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">         18 :     }</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   }</a>
+<a name="1231"><span class="lineNum">    1231 </span>            : </a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   // if we are restarting from GRID and using WALKERS_MPI we can check that all walkers have actually read the grid</a>
+<a name="1233"><span class="lineNum">    1233 </span><span class="lineCov">        148 :   if(getRestart()&amp;&amp;walkers_mpi_) {</span></a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">          9 :     std::vector&lt;int&gt; restarted(mpi_nw_,0);</span></a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineCov">          9 :     if(comm.Get_rank()==0) multi_sim_comm.Allgather(int(restartedFromGrid), restarted);</span></a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineCov">          9 :     comm.Bcast(restarted,0);</span></a>
+<a name="1237"><span class="lineNum">    1237 </span>            :     int result = std::accumulate(restarted.begin(),restarted.end(),0);</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">          9 :     if(result!=0&amp;&amp;result!=mpi_nw_) error(&quot;in this WALKERS_MPI run some replica have restarted from GRID while other do not!&quot;);</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            :   }</a>
+<a name="1240"><span class="lineNum">    1240 </span>            : </a>
+<a name="1241"><span class="lineNum">    1241 </span>            : #ifdef __PLUMED_HAS_GETCWD</a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineCov">        186 :   if(walkers_mpi_&amp;&amp;mw_dir_==&quot;&quot;&amp;&amp;hillsfname.at(0)!='/') {</span></a>
+<a name="1243"><span class="lineNum">    1243 </span>            :     //if possible the root replica will share its current folder so that all walkers will read the same file</a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">         38 :     char cwd[4096]= {0};</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :     const char* ret=getcwd(cwd,4096);</a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">         38 :     plumed_assert(ret)&lt;&lt;&quot;Name of current directory too long, increase buffer size&quot;;</span></a>
+<a name="1247"><span class="lineNum">    1247 </span>            :     mw_dir_ = ret;</a>
+<a name="1248"><span class="lineNum">    1248 </span><span class="lineCov">         38 :     mw_dir_ = mw_dir_ + &quot;/&quot;;</span></a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">         38 :     if(comm.Get_rank()==0) multi_sim_comm.Bcast(mw_dir_,0);</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">         38 :     comm.Bcast(mw_dir_,0);</span></a>
+<a name="1251"><span class="lineNum">    1251 </span>            :   }</a>
+<a name="1252"><span class="lineNum">    1252 </span>            : #endif</a>
+<a name="1253"><span class="lineNum">    1253 </span>            : </a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   // creating std::vector of ifile* for hills reading</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :   // open all files at the beginning and read Gaussians if restarting</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :   bool restartedFromHills=false;  // restart from hills files</a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">        308 :   for(int i=0; i&lt;mw_n_; ++i) {</span></a>
+<a name="1258"><span class="lineNum">    1258 </span>            :     std::string fname;</a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineCov">        160 :     if(mw_dir_!=&quot;&quot;) {</span></a>
+<a name="1260"><span class="lineNum">    1260 </span><span class="lineCov">         47 :       if(mw_n_&gt;1) {</span></a>
+<a name="1261"><span class="lineNum">    1261 </span><span class="lineCov">          9 :         std::stringstream out; out &lt;&lt; i;</span></a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineCov">         18 :         fname = mw_dir_+&quot;/&quot;+hillsfname+&quot;.&quot;+out.str();</span></a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">         47 :       } else if(walkers_mpi_) {</span></a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineCov">         76 :         fname = mw_dir_+&quot;/&quot;+hillsfname;</span></a>
+<a name="1265"><span class="lineNum">    1265 </span>            :       } else {</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :         fname = hillsfname;</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :       }</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :     } else {</a>
+<a name="1269"><span class="lineNum">    1269 </span><span class="lineCov">        113 :       if(mw_n_&gt;1) {</span></a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineCov">          9 :         std::stringstream out; out &lt;&lt; i;</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">         18 :         fname = hillsfname+&quot;.&quot;+out.str();</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineCov">          9 :       } else {</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :         fname = hillsfname;</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :       }</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :     }</a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">        160 :     ifiles_.emplace_back(Tools::make_unique&lt;IFile&gt;());</span></a>
+<a name="1277"><span class="lineNum">    1277 </span>            :     // this is just a shortcut pointer to the last element:</a>
+<a name="1278"><span class="lineNum">    1278 </span>            :     IFile *ifile = ifiles_.back().get();</a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">        160 :     ifilesnames_.push_back(fname);</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">        160 :     ifile-&gt;link(*this);</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">        160 :     if(ifile-&gt;FileExist(fname)) {</span></a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineCov">         35 :       ifile-&gt;open(fname);</span></a>
+<a name="1283"><span class="lineNum">    1283 </span><span class="lineCov">         35 :       if(getRestart()&amp;&amp;!restartedFromGrid) {</span></a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">         19 :         log.printf(&quot;  Restarting from %s:&quot;,ifilesnames_[i].c_str());</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineCov">         19 :         readGaussians(ifiles_[i].get());</span></a>
+<a name="1286"><span class="lineNum">    1286 </span>            :         restartedFromHills=true;</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :       }</a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">         35 :       ifiles_[i]-&gt;reset(false);</span></a>
+<a name="1289"><span class="lineNum">    1289 </span>            :       // close only the walker own hills file for later writing</a>
+<a name="1290"><span class="lineNum">    1290 </span><span class="lineCov">         35 :       if(i==mw_id_) ifiles_[i]-&gt;close();</span></a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     } else {</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :       // in case a file does not exist and we are restarting, complain that the file was not found</a>
+<a name="1293"><span class="lineNum">    1293 </span><span class="lineCov">        125 :       if(getRestart()&amp;&amp;!restartedFromGrid) error(&quot;restart file &quot;+fname+&quot; not found&quot;);</span></a>
+<a name="1294"><span class="lineNum">    1294 </span>            :     }</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :   }</a>
+<a name="1296"><span class="lineNum">    1296 </span>            : </a>
+<a name="1297"><span class="lineNum">    1297 </span>            :   // if we are restarting from FILE and using WALKERS_MPI we can check that all walkers have actually read the FILE</a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineCov">        148 :   if(getRestart()&amp;&amp;walkers_mpi_) {</span></a>
+<a name="1299"><span class="lineNum">    1299 </span><span class="lineCov">          9 :     std::vector&lt;int&gt; restarted(mpi_nw_,0);</span></a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">          9 :     if(comm.Get_rank()==0) multi_sim_comm.Allgather(int(restartedFromHills), restarted);</span></a>
+<a name="1301"><span class="lineNum">    1301 </span><span class="lineCov">          9 :     comm.Bcast(restarted,0);</span></a>
+<a name="1302"><span class="lineNum">    1302 </span>            :     int result = std::accumulate(restarted.begin(),restarted.end(),0);</a>
+<a name="1303"><span class="lineNum">    1303 </span><span class="lineCov">          9 :     if(result!=0&amp;&amp;result!=mpi_nw_) error(&quot;in this WALKERS_MPI run some replica have restarted from FILE while other do not!&quot;);</span></a>
+<a name="1304"><span class="lineNum">    1304 </span>            :   }</a>
+<a name="1305"><span class="lineNum">    1305 </span>            : </a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">        148 :   comm.Barrier();</span></a>
+<a name="1307"><span class="lineNum">    1307 </span>            :   // this barrier is needed when using walkers_mpi</a>
+<a name="1308"><span class="lineNum">    1308 </span>            :   // to be sure that all files have been read before</a>
+<a name="1309"><span class="lineNum">    1309 </span>            :   // backing them up</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   // it should not be used when walkers_mpi is false otherwise</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :   // it would introduce troubles when using replicas without METAD</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :   // (e.g. in bias exchange with a neutral replica)</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :   // see issue #168 on github</a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineCov">        148 :   if(comm.Get_rank()==0 &amp;&amp; walkers_mpi_) multi_sim_comm.Barrier();</span></a>
+<a name="1315"><span class="lineNum">    1315 </span>            : </a>
+<a name="1316"><span class="lineNum">    1316 </span><span class="lineCov">        148 :   if(targetfilename_.length()&gt;0) {</span></a>
+<a name="1317"><span class="lineNum">    1317 </span><span class="lineCov">          2 :     IFile gridfile; gridfile.open(targetfilename_);</span></a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineCov">          2 :     std::string funcl=getLabel() + &quot;.target&quot;;</span></a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">          4 :     TargetGrid_=GridBase::create(funcl,getArguments(),gridfile,false,false,true);</span></a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">          2 :     if(TargetGrid_-&gt;getDimension()!=getNumberOfArguments()) error(&quot;mismatch between dimensionality of input grid and number of arguments&quot;);</span></a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1322"><span class="lineNum">    1322 </span><span class="lineCov">          4 :       if( getPntrToArgument(i)-&gt;isPeriodic()!=TargetGrid_-&gt;getIsPeriodic()[i] ) error(&quot;periodicity mismatch between arguments and input bias&quot;);</span></a>
+<a name="1323"><span class="lineNum">    1323 </span>            :     }</a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">          2 :   }</span></a>
+<a name="1325"><span class="lineNum">    1325 </span>            : </a>
+<a name="1326"><span class="lineNum">    1326 </span><span class="lineCov">        148 :   if(getRestart()) {</span></a>
+<a name="1327"><span class="lineNum">    1327 </span>            :     // if this is a restart the neighbor list should be immediately updated</a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineCov">         37 :     if(nlist_) nlist_update_=true;</span></a>
+<a name="1329"><span class="lineNum">    1329 </span>            :     // Calculate the Tiwary-Parrinello reweighting factor if we are restarting from previous hills</a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">         37 :     if(calc_rct_) computeReweightingFactor();</span></a>
+<a name="1331"><span class="lineNum">    1331 </span>            :     // Calculate all special bias quantities desired if restarting with nonzero bias.</a>
+<a name="1332"><span class="lineNum">    1332 </span><span class="lineCov">         37 :     if(calc_max_bias_) {</span></a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineNoCov">          0 :       max_bias_ = BiasGrid_-&gt;getMaxValue();</span></a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineNoCov">          0 :       getPntrToComponent(&quot;maxbias&quot;)-&gt;set(max_bias_);</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            :     }</a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineCov">         37 :     if(calc_transition_bias_) {</span></a>
+<a name="1337"><span class="lineNum">    1337 </span><span class="lineCov">         13 :       transition_bias_ = getTransitionBarrierBias();</span></a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineCov">         26 :       getPntrToComponent(&quot;transbias&quot;)-&gt;set(transition_bias_);</span></a>
+<a name="1339"><span class="lineNum">    1339 </span>            :     }</a>
+<a name="1340"><span class="lineNum">    1340 </span>            :   }</a>
+<a name="1341"><span class="lineNum">    1341 </span>            : </a>
+<a name="1342"><span class="lineNum">    1342 </span>            :   // open grid file for writing</a>
+<a name="1343"><span class="lineNum">    1343 </span><span class="lineCov">        148 :   if(wgridstride_&gt;0) {</span></a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineCov">         19 :     gridfile_.link(*this);</span></a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineCov">         19 :     if(walkers_mpi_) {</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineNoCov">          0 :       int r=0;</span></a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineNoCov">          0 :       if(comm.Get_rank()==0) r=multi_sim_comm.Get_rank();</span></a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineNoCov">          0 :       comm.Bcast(r,0);</span></a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineNoCov">          0 :       if(r&gt;0) gridfilename_=&quot;/dev/null&quot;;</span></a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineNoCov">          0 :       gridfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="1351"><span class="lineNum">    1351 </span>            :     }</a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">         19 :     if(mw_n_&gt;1) gridfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineCov">         19 :     gridfile_.open(gridfilename_);</span></a>
+<a name="1354"><span class="lineNum">    1354 </span>            :   }</a>
+<a name="1355"><span class="lineNum">    1355 </span>            : </a>
+<a name="1356"><span class="lineNum">    1356 </span>            :   // open hills file for writing</a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineCov">        148 :   hillsOfile_.link(*this);</span></a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineCov">        148 :   if(walkers_mpi_) {</span></a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineCov">         38 :     int r=0;</span></a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineCov">         38 :     if(comm.Get_rank()==0) r=multi_sim_comm.Get_rank();</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineCov">         38 :     comm.Bcast(r,0);</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineCov">         38 :     if(r&gt;0) ifilesnames_[mw_id_]=&quot;/dev/null&quot;;</span></a>
+<a name="1363"><span class="lineNum">    1363 </span><span class="lineCov">         76 :     hillsOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="1364"><span class="lineNum">    1364 </span>            :   }</a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineCov">        154 :   if(mw_n_&gt;1) hillsOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineCov">        148 :   hillsOfile_.open(ifilesnames_[mw_id_]);</span></a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineCov">        148 :   if(fmt_.length()&gt;0) hillsOfile_.fmtField(fmt_);</span></a>
+<a name="1368"><span class="lineNum">    1368 </span><span class="lineCov">        148 :   hillsOfile_.addConstantField(&quot;multivariate&quot;);</span></a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineCov">        148 :   hillsOfile_.addConstantField(&quot;kerneltype&quot;);</span></a>
+<a name="1370"><span class="lineNum">    1370 </span><span class="lineCov">        148 :   if(doInt_) {</span></a>
+<a name="1371"><span class="lineNum">    1371 </span><span class="lineCov">          4 :     hillsOfile_.addConstantField(&quot;lower_int&quot;).printField(&quot;lower_int&quot;,lowI_);</span></a>
+<a name="1372"><span class="lineNum">    1372 </span><span class="lineCov">          4 :     hillsOfile_.addConstantField(&quot;upper_int&quot;).printField(&quot;upper_int&quot;,uppI_);</span></a>
+<a name="1373"><span class="lineNum">    1373 </span>            :   }</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :   hillsOfile_.setHeavyFlush();</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   // output periodicities of variables</a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineCov">        415 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) hillsOfile_.setupPrintValue( getPntrToArgument(i) );</span></a>
+<a name="1377"><span class="lineNum">    1377 </span>            : </a>
+<a name="1378"><span class="lineNum">    1378 </span>            :   bool concurrent=false;</a>
+<a name="1379"><span class="lineNum">    1379 </span><span class="lineCov">        148 :   const ActionSet&amp;actionSet(plumed.getActionSet());</span></a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">        541 :   for(const auto &amp; p : actionSet) if(dynamic_cast&lt;MetaD*&gt;(p.get())) { concurrent=true; break; }</span></a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineCov">        148 :   if(concurrent) log&lt;&lt;&quot;  You are using concurrent metadynamics\n&quot;;</span></a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineCov">        148 :   if(rect_biasf_.size()&gt;0) {</span></a>
+<a name="1383"><span class="lineNum">    1383 </span><span class="lineCov">         18 :     if(walkers_mpi_) {</span></a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineCov">         12 :       log&lt;&lt;&quot;  You are using RECT in its 'altruistic' implementation\n&quot;;</span></a>
+<a name="1385"><span class="lineNum">    1385 </span>            :     }{</a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineCov">         18 :       log&lt;&lt;&quot;  You are using RECT\n&quot;;</span></a>
+<a name="1387"><span class="lineNum">    1387 </span>            :     }</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :   }</a>
+<a name="1389"><span class="lineNum">    1389 </span>            : </a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineCov">        296 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Laio and Parrinello, PNAS 99, 12562 (2002)&quot;);</span></a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineCov">        186 :   if(welltemp_) log&lt;&lt;plumed.cite(&quot;Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603 (2008)&quot;);</span></a>
+<a name="1392"><span class="lineNum">    1392 </span><span class="lineCov">        148 :   if(tt_specs_.is_active) {</span></a>
+<a name="1393"><span class="lineNum">    1393 </span><span class="lineCov">          6 :     log &lt;&lt; plumed.cite(&quot;Dama, Rotskoff, Parrinello, and Voth, J. Chem. Theory Comput. 10, 3626 (2014)&quot;);</span></a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineCov">          6 :     log &lt;&lt; plumed.cite(&quot;Dama, Parrinello, and Voth, Phys. Rev. Lett. 112, 240602 (2014)&quot;);</span></a>
+<a name="1395"><span class="lineNum">    1395 </span>            :   }</a>
+<a name="1396"><span class="lineNum">    1396 </span><span class="lineCov">        192 :   if(mw_n_&gt;1||walkers_mpi_) log&lt;&lt;plumed.cite(&quot;Raiteri, Laio, Gervasio, Micheletti, and Parrinello, J. Phys. Chem. B 110, 3533 (2006)&quot;);</span></a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">        169 :   if(adaptive_!=FlexibleBin::none) log&lt;&lt;plumed.cite(&quot;Branduardi, Bussi, and Parrinello, J. Chem. Theory Comput. 8, 2247 (2012)&quot;);</span></a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineCov">        150 :   if(doInt_) log&lt;&lt;plumed.cite(&quot;Baftizadeh, Cossio, Pietrucci, and Laio, Curr. Phys. Chem. 2, 79 (2012)&quot;);</span></a>
+<a name="1399"><span class="lineNum">    1399 </span><span class="lineCov">        152 :   if(acceleration_) log&lt;&lt;plumed.cite(&quot;Pratyush and Parrinello, Phys. Rev. Lett. 111, 230602 (2013)&quot;);</span></a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineCov">        154 :   if(calc_rct_) log&lt;&lt;plumed.cite(&quot;Pratyush and Parrinello, J. Phys. Chem. B, 119, 736 (2015)&quot;);</span></a>
+<a name="1401"><span class="lineNum">    1401 </span><span class="lineCov">        228 :   if(concurrent || rect_biasf_.size()&gt;0) log&lt;&lt;plumed.cite(&quot;Gil-Ley and Bussi, J. Chem. Theory Comput. 11, 1077 (2015)&quot;);</span></a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">        160 :   if(rect_biasf_.size()&gt;0 &amp;&amp; walkers_mpi_) log&lt;&lt;plumed.cite(&quot;Hosek, Toulcova, Bortolato, and Spiwok, J. Phys. Chem. B 120, 2209 (2016)&quot;);</span></a>
+<a name="1403"><span class="lineNum">    1403 </span><span class="lineCov">        148 :   if(targetfilename_.length()&gt;0) {</span></a>
+<a name="1404"><span class="lineNum">    1404 </span><span class="lineCov">          4 :     log&lt;&lt;plumed.cite(&quot;White, Dama, and Voth, J. Chem. Theory Comput. 11, 2451 (2015)&quot;);</span></a>
+<a name="1405"><span class="lineNum">    1405 </span><span class="lineCov">          4 :     log&lt;&lt;plumed.cite(&quot;Marinelli and Faraldo-Go�mez,  Biophys. J. 108, 2779 (2015)&quot;);</span></a>
+<a name="1406"><span class="lineNum">    1406 </span><span class="lineCov">          4 :     log&lt;&lt;plumed.cite(&quot;Gil-Ley, Bottaro, and Bussi, J. Chem. Theory Comput. 12, 2790 (2016)&quot;);</span></a>
+<a name="1407"><span class="lineNum">    1407 </span>            :   }</a>
+<a name="1408"><span class="lineNum">    1408 </span><span class="lineCov">        150 :   if(freq_adaptive_) log&lt;&lt;plumed.cite(&quot;Wang, Valsson, Tiwary, Parrinello, and Lindorff-Larsen, J. Chem. Phys. 149, 072309 (2018)&quot;);</span></a>
+<a name="1409"><span class="lineNum">    1409 </span><span class="lineCov">        148 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="1410"><span class="lineNum">    1410 </span><span class="lineCov">        396 : }</span></a>
+<a name="1411"><span class="lineNum">    1411 </span>            : </a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">        151 : void MetaD::readTemperingSpecs(TemperingSpecs &amp;t_specs)</span></a>
+<a name="1413"><span class="lineNum">    1413 </span>            : {</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :   // Set global tempering parameters.</a>
+<a name="1415"><span class="lineNum">    1415 </span><span class="lineCov">        151 :   parse(t_specs.name_stem + &quot;BIASFACTOR&quot;, t_specs.biasf);</span></a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineCov">        151 :   if (t_specs.biasf != -1.0) {</span></a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineCov">          3 :     if (kbt_ == 0.0) {</span></a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineNoCov">          0 :       error(&quot;Unless the MD engine passes the temperature to plumed, with tempered metad you must specify it using TEMP&quot;);</span></a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     }</a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineCov">          3 :     if (t_specs.biasf == 1.0) {</span></a>
+<a name="1421"><span class="lineNum">    1421 </span><span class="lineNoCov">          0 :       error(&quot;A bias factor of 1 corresponds to zero delta T and zero hill size, so it is not allowed.&quot;);</span></a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     }</a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineCov">          3 :     t_specs.is_active = true;</span></a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineCov">          3 :     parse(t_specs.name_stem + &quot;BIASTHRESHOLD&quot;, t_specs.threshold);</span></a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineCov">          3 :     if (t_specs.threshold &lt; 0.0) {</span></a>
+<a name="1426"><span class="lineNum">    1426 </span><span class="lineNoCov">          0 :       error(t_specs.name + &quot; bias threshold is nonsensical&quot;);</span></a>
+<a name="1427"><span class="lineNum">    1427 </span>            :     }</a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineCov">          3 :     parse(t_specs.name_stem + &quot;ALPHA&quot;, t_specs.alpha);</span></a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineCov">          3 :     if (t_specs.alpha &lt;= 0.0 || t_specs.alpha &gt; 1.0) {</span></a>
+<a name="1430"><span class="lineNum">    1430 </span><span class="lineNoCov">          0 :       error(t_specs.name + &quot; decay shape parameter alpha is nonsensical&quot;);</span></a>
+<a name="1431"><span class="lineNum">    1431 </span>            :     }</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :   }</a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineCov">        151 : }</span></a>
+<a name="1434"><span class="lineNum">    1434 </span>            : </a>
+<a name="1435"><span class="lineNum">    1435 </span><span class="lineCov">          3 : void MetaD::logTemperingSpecs(const TemperingSpecs &amp;t_specs)</span></a>
+<a name="1436"><span class="lineNum">    1436 </span>            : {</a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">          3 :   log.printf(&quot;  %s bias factor %f\n&quot;, t_specs.name.c_str(), t_specs.biasf);</span></a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineCov">          3 :   log.printf(&quot;  KbT %f\n&quot;, kbt_);</span></a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineCov">          3 :   if (t_specs.threshold != 0.0) log.printf(&quot;  %s bias threshold %f\n&quot;, t_specs.name.c_str(), t_specs.threshold);</span></a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineCov">          3 :   if (t_specs.alpha != 1.0) log.printf(&quot;  %s decay shape parameter alpha %f\n&quot;, t_specs.name.c_str(), t_specs.alpha);</span></a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineCov">          3 : }</span></a>
+<a name="1442"><span class="lineNum">    1442 </span>            : </a>
+<a name="1443"><span class="lineNum">    1443 </span><span class="lineCov">       6036 : void MetaD::readGaussians(IFile *ifile)</span></a>
+<a name="1444"><span class="lineNum">    1444 </span>            : {</a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineCov">       6036 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineCov">       6036 :   std::vector&lt;double&gt; center(ncv);</span></a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineCov">       6036 :   std::vector&lt;double&gt; sigma(ncv);</span></a>
+<a name="1448"><span class="lineNum">    1448 </span>            :   double height;</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :   int nhills=0;</a>
+<a name="1450"><span class="lineNum">    1450 </span><span class="lineCov">       6036 :   bool multivariate=false;</span></a>
+<a name="1451"><span class="lineNum">    1451 </span>            : </a>
+<a name="1452"><span class="lineNum">    1452 </span>            :   std::vector&lt;Value&gt; tmpvalues;</a>
+<a name="1453"><span class="lineNum">    1453 </span><span class="lineCov">      18121 :   for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) tmpvalues.push_back( Value( this, getPntrToArgument(j)-&gt;getName(), false ) );</span></a>
+<a name="1454"><span class="lineNum">    1454 </span>            : </a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineCov">       8152 :   while(scanOneHill(ifile,tmpvalues,center,sigma,height,multivariate))</span></a>
+<a name="1456"><span class="lineNum">    1456 </span>            :   {</a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineCov">       2116 :     nhills++;</span></a>
+<a name="1458"><span class="lineNum">    1458 </span>            :     // note that for gamma=1 we store directly -F</a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineCov">       2116 :     if(welltemp_ &amp;&amp; biasf_&gt;1.0) height*=(biasf_-1.0)/biasf_;</span></a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineCov">       2116 :     addGaussian(Gaussian(multivariate,height,center,sigma));</span></a>
+<a name="1461"><span class="lineNum">    1461 </span>            :   }</a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">       6036 :   log.printf(&quot;      %d Gaussians read\n&quot;,nhills);</span></a>
+<a name="1463"><span class="lineNum">    1463 </span><span class="lineCov">      12072 : }</span></a>
+<a name="1464"><span class="lineNum">    1464 </span>            : </a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineCov">       2922 : void MetaD::writeGaussian(const Gaussian&amp; hill, OFile&amp;file)</span></a>
+<a name="1466"><span class="lineNum">    1466 </span>            : {</a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">       2922 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineCov">       2922 :   file.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineCov">       8194 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineCov">       5272 :     file.printField(getPntrToArgument(i),hill.center[i]);</span></a>
+<a name="1471"><span class="lineNum">    1471 </span>            :   }</a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineCov">       5844 :   hillsOfile_.printField(&quot;kerneltype&quot;,&quot;stretched-gaussian&quot;);</span></a>
+<a name="1473"><span class="lineNum">    1473 </span><span class="lineCov">       2922 :   if(hill.multivariate) {</span></a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineCov">        892 :     hillsOfile_.printField(&quot;multivariate&quot;,&quot;true&quot;);</span></a>
+<a name="1475"><span class="lineNum">    1475 </span>            :     Matrix&lt;double&gt; mymatrix(ncv,ncv);</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :     unsigned k=0;</a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">       1047 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineCov">       1357 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1479"><span class="lineNum">    1479 </span>            :         // recompose the full inverse matrix</a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">        756 :         mymatrix(i,j)=mymatrix(j,i)=hill.sigma[k];</span></a>
+<a name="1481"><span class="lineNum">    1481 </span><span class="lineCov">        756 :         k++;</span></a>
+<a name="1482"><span class="lineNum">    1482 </span>            :       }</a>
+<a name="1483"><span class="lineNum">    1483 </span>            :     }</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :     // invert it</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :     Matrix&lt;double&gt; invmatrix(ncv,ncv);</a>
+<a name="1486"><span class="lineNum">    1486 </span><span class="lineCov">        446 :     Invert(mymatrix,invmatrix);</span></a>
+<a name="1487"><span class="lineNum">    1487 </span>            :     // enforce symmetry</a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineCov">       1047 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineCov">       1357 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineCov">        756 :         invmatrix(i,j)=invmatrix(j,i);</span></a>
+<a name="1491"><span class="lineNum">    1491 </span>            :       }</a>
+<a name="1492"><span class="lineNum">    1492 </span>            :     }</a>
+<a name="1493"><span class="lineNum">    1493 </span>            : </a>
+<a name="1494"><span class="lineNum">    1494 </span>            :     // do cholesky so to have a &quot;sigma like&quot; number</a>
+<a name="1495"><span class="lineNum">    1495 </span>            :     Matrix&lt;double&gt; lower(ncv,ncv);</a>
+<a name="1496"><span class="lineNum">    1496 </span><span class="lineCov">        446 :     cholesky(invmatrix,lower);</span></a>
+<a name="1497"><span class="lineNum">    1497 </span>            :     // loop in band form</a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineCov">       1047 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineCov">       1357 :       for(unsigned j=0; j&lt;ncv-i; j++) {</span></a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineCov">       1512 :         file.printField(&quot;sigma_&quot;+getPntrToArgument(j+i)-&gt;getName()+&quot;_&quot;+getPntrToArgument(j)-&gt;getName(),lower(j+i,j));</span></a>
+<a name="1501"><span class="lineNum">    1501 </span>            :       }</a>
+<a name="1502"><span class="lineNum">    1502 </span>            :     }</a>
+<a name="1503"><span class="lineNum">    1503 </span>            :   } else {</a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineCov">       4952 :     hillsOfile_.printField(&quot;multivariate&quot;,&quot;false&quot;);</span></a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineCov">       7147 :     for(unsigned i=0; i&lt;ncv; ++i)</span></a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineCov">       9342 :       file.printField(&quot;sigma_&quot;+getPntrToArgument(i)-&gt;getName(),hill.sigma[i]);</span></a>
+<a name="1507"><span class="lineNum">    1507 </span>            :   }</a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineCov">       2922 :   double height=hill.height;</span></a>
+<a name="1509"><span class="lineNum">    1509 </span>            :   // note that for gamma=1 we store directly -F</a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineCov">       2922 :   if(welltemp_ &amp;&amp; biasf_&gt;1.0) height*=biasf_/(biasf_-1.0);</span></a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineCov">       5844 :   file.printField(&quot;height&quot;,height).printField(&quot;biasf&quot;,biasf_);</span></a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineCov">       4431 :   if(mw_n_&gt;1) file.printField(&quot;clock&quot;,int(std::time(0)));</span></a>
+<a name="1513"><span class="lineNum">    1513 </span><span class="lineCov">       2922 :   file.printField();</span></a>
+<a name="1514"><span class="lineNum">    1514 </span><span class="lineCov">       2922 : }</span></a>
+<a name="1515"><span class="lineNum">    1515 </span>            : </a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">       5200 : void MetaD::addGaussian(const Gaussian&amp; hill)</span></a>
+<a name="1517"><span class="lineNum">    1517 </span>            : {</a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineCov">       5200 :   if(grid_) {</span></a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineCov">        640 :     size_t ncv=getNumberOfArguments();</span></a>
+<a name="1520"><span class="lineNum">    1520 </span><span class="lineCov">        640 :     std::vector&lt;unsigned&gt; nneighb=getGaussianSupport(hill);</span></a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineCov">        640 :     std::vector&lt;Grid::index_t&gt; neighbors=BiasGrid_-&gt;getNeighbors(hill.center,nneighb);</span></a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineCov">        640 :     std::vector&lt;double&gt; der(ncv);</span></a>
+<a name="1523"><span class="lineNum">    1523 </span><span class="lineCov">        640 :     std::vector&lt;double&gt; xx(ncv);</span></a>
+<a name="1524"><span class="lineNum">    1524 </span><span class="lineCov">        640 :     if(comm.Get_size()==1) {</span></a>
+<a name="1525"><span class="lineNum">    1525 </span>            :       // for performance reasons and thread safety</a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineCov">        544 :       std::vector&lt;double&gt; dp(ncv);</span></a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineCov">      55324 :       for(size_t i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="1528"><span class="lineNum">    1528 </span><span class="lineCov">      54780 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">     158922 :         for(unsigned j=0; j&lt;ncv; ++j) der[j]=0.0;</span></a>
+<a name="1530"><span class="lineNum">    1530 </span><span class="lineCov">      54780 :         BiasGrid_-&gt;getPoint(ineigh,xx);</span></a>
+<a name="1531"><span class="lineNum">    1531 </span><span class="lineCov">      54780 :         double bias=evaluateGaussianAndDerivatives(xx,hill,der,dp);</span></a>
+<a name="1532"><span class="lineNum">    1532 </span><span class="lineCov">      54780 :         BiasGrid_-&gt;addValueAndDerivatives(ineigh,bias,der);</span></a>
+<a name="1533"><span class="lineNum">    1533 </span>            :       }</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :     } else {</a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineCov">         96 :       unsigned stride=comm.Get_size();</span></a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineCov">         96 :       unsigned rank=comm.Get_rank();</span></a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineCov">         96 :       std::vector&lt;double&gt; allder(ncv*neighbors.size(),0.0);</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">         96 :       std::vector&lt;double&gt; n_der(ncv,0.0);</span></a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineCov">         96 :       std::vector&lt;double&gt; allbias(neighbors.size(),0.0);</span></a>
+<a name="1540"><span class="lineNum">    1540 </span>            :       // for performance reasons and thread safety</a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineCov">         96 :       std::vector&lt;double&gt; dp(ncv);</span></a>
+<a name="1542"><span class="lineNum">    1542 </span><span class="lineCov">      27148 :       for(unsigned i=rank; i&lt;neighbors.size(); i+=stride) {</span></a>
+<a name="1543"><span class="lineNum">    1543 </span><span class="lineCov">      27052 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineCov">      81156 :         for(unsigned j=0; j&lt;ncv; ++j) n_der[j]=0.0;</span></a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineCov">      27052 :         BiasGrid_-&gt;getPoint(ineigh,xx);</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineCov">      27052 :         allbias[i]=evaluateGaussianAndDerivatives(xx,hill,n_der,dp);</span></a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineCov">      81156 :         for(unsigned j=0; j&lt;ncv; j++) allder[ncv*i+j]=n_der[j];</span></a>
+<a name="1548"><span class="lineNum">    1548 </span>            :       }</a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineCov">         96 :       comm.Sum(allbias);</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">         96 :       comm.Sum(allder);</span></a>
+<a name="1551"><span class="lineNum">    1551 </span><span class="lineCov">     103200 :       for(unsigned i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineCov">     103104 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineCov">     309312 :         for(unsigned j=0; j&lt;ncv; ++j) der[j]=allder[ncv*i+j];</span></a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineCov">     103104 :         BiasGrid_-&gt;addValueAndDerivatives(ineigh,allbias[i],der);</span></a>
+<a name="1555"><span class="lineNum">    1555 </span>            :       }</a>
+<a name="1556"><span class="lineNum">    1556 </span>            :     }</a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineCov">       4560 :   } else hills_.push_back(hill);</span></a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineCov">       5200 : }</span></a>
+<a name="1559"><span class="lineNum">    1559 </span>            : </a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineCov">        640 : std::vector&lt;unsigned&gt; MetaD::getGaussianSupport(const Gaussian&amp; hill)</span></a>
+<a name="1561"><span class="lineNum">    1561 </span>            : {</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :   std::vector&lt;unsigned&gt; nneigh;</a>
+<a name="1563"><span class="lineNum">    1563 </span>            :   std::vector&lt;double&gt; cutoff;</a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineCov">        640 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="1565"><span class="lineNum">    1565 </span>            : </a>
+<a name="1566"><span class="lineNum">    1566 </span>            :   // traditional or flexible hill?</a>
+<a name="1567"><span class="lineNum">    1567 </span><span class="lineCov">        640 :   if(hill.multivariate) {</span></a>
+<a name="1568"><span class="lineNum">    1568 </span>            :     unsigned k=0;</a>
+<a name="1569"><span class="lineNum">    1569 </span>            :     Matrix&lt;double&gt; mymatrix(ncv,ncv);</a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1571"><span class="lineNum">    1571 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1572"><span class="lineNum">    1572 </span>            :         // recompose the full inverse matrix</a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineNoCov">          0 :         mymatrix(i,j)=mymatrix(j,i)=hill.sigma[k];</span></a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineNoCov">          0 :         k++;</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            :       }</a>
+<a name="1576"><span class="lineNum">    1576 </span>            :     }</a>
+<a name="1577"><span class="lineNum">    1577 </span>            :     // Reinvert so to have the ellipses</a>
+<a name="1578"><span class="lineNum">    1578 </span>            :     Matrix&lt;double&gt; myinv(ncv,ncv);</a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineNoCov">          0 :     Invert(mymatrix,myinv);</span></a>
+<a name="1580"><span class="lineNum">    1580 </span>            :     Matrix&lt;double&gt; myautovec(ncv,ncv);</a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineNoCov">          0 :     std::vector&lt;double&gt; myautoval(ncv); //should I take this or their square root?</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineNoCov">          0 :     diagMat(myinv,myautoval,myautovec);</span></a>
+<a name="1583"><span class="lineNum">    1583 </span>            :     double maxautoval=0.;</a>
+<a name="1584"><span class="lineNum">    1584 </span>            :     unsigned ind_maxautoval; ind_maxautoval=ncv;</a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineNoCov">          0 :       if(myautoval[i]&gt;maxautoval) {maxautoval=myautoval[i]; ind_maxautoval=i;}</span></a>
+<a name="1587"><span class="lineNum">    1587 </span>            :     }</a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1589"><span class="lineNum">    1589 </span><span class="lineNoCov">          0 :       cutoff.push_back(std::sqrt(2.0*dp2cutoff)*std::abs(std::sqrt(maxautoval)*myautovec(i,ind_maxautoval)));</span></a>
+<a name="1590"><span class="lineNum">    1590 </span>            :     }</a>
+<a name="1591"><span class="lineNum">    1591 </span>            :   } else {</a>
+<a name="1592"><span class="lineNum">    1592 </span><span class="lineCov">       1618 :     for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineCov">        978 :       cutoff.push_back(std::sqrt(2.0*dp2cutoff)*hill.sigma[i]);</span></a>
+<a name="1594"><span class="lineNum">    1594 </span>            :     }</a>
+<a name="1595"><span class="lineNum">    1595 </span>            :   }</a>
+<a name="1596"><span class="lineNum">    1596 </span>            : </a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineCov">        640 :   if(doInt_) {</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineCov">          2 :     if(hill.center[0]+cutoff[0] &gt; uppI_ || hill.center[0]-cutoff[0] &lt; lowI_) {</span></a>
+<a name="1599"><span class="lineNum">    1599 </span>            :       // in this case, we updated the entire grid to avoid problems</a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineCov">          2 :       return BiasGrid_-&gt;getNbin();</span></a>
+<a name="1601"><span class="lineNum">    1601 </span>            :     } else {</a>
+<a name="1602"><span class="lineNum">    1602 </span><span class="lineNoCov">          0 :       nneigh.push_back( static_cast&lt;unsigned&gt;(ceil(cutoff[0]/BiasGrid_-&gt;getDx()[0])) );</span></a>
+<a name="1603"><span class="lineNum">    1603 </span>            :       return nneigh;</a>
+<a name="1604"><span class="lineNum">    1604 </span>            :     }</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :   } else {</a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">       1614 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1607"><span class="lineNum">    1607 </span><span class="lineCov">        976 :       nneigh.push_back( static_cast&lt;unsigned&gt;(ceil(cutoff[i]/BiasGrid_-&gt;getDx()[i])) );</span></a>
+<a name="1608"><span class="lineNum">    1608 </span>            :     }</a>
+<a name="1609"><span class="lineNum">    1609 </span>            :   }</a>
+<a name="1610"><span class="lineNum">    1610 </span>            : </a>
+<a name="1611"><span class="lineNum">    1611 </span>            :   return nneigh;</a>
+<a name="1612"><span class="lineNum">    1612 </span>            : }</a>
+<a name="1613"><span class="lineNum">    1613 </span>            : </a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineCov">        285 : double MetaD::getBias(const std::vector&lt;double&gt;&amp; cv)</span></a>
+<a name="1615"><span class="lineNum">    1615 </span>            : {</a>
+<a name="1616"><span class="lineNum">    1616 </span><span class="lineCov">        285 :   double bias=0.0;</span></a>
+<a name="1617"><span class="lineNum">    1617 </span><span class="lineCov">        285 :   if(grid_) bias = BiasGrid_-&gt;getValue(cv);</span></a>
+<a name="1618"><span class="lineNum">    1618 </span>            :   else {</a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineCov">         82 :     unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineCov">         82 :     unsigned stride=comm.Get_size();</span></a>
+<a name="1621"><span class="lineNum">    1621 </span><span class="lineCov">         82 :     unsigned rank=comm.Get_rank();</span></a>
+<a name="1622"><span class="lineNum">    1622 </span>            : </a>
+<a name="1623"><span class="lineNum">    1623 </span><span class="lineCov">         82 :     if(!nlist_) {</span></a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineCov">         82 :       #pragma omp parallel num_threads(nt)</span></a>
+<a name="1625"><span class="lineNum">    1625 </span>            :       {</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :         #pragma omp for reduction(+:bias) nowait</a>
+<a name="1627"><span class="lineNum">    1627 </span>            :         for(unsigned i=rank; i&lt;hills_.size(); i+=stride) bias+=evaluateGaussian(cv,hills_[i]);</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :       }</a>
+<a name="1629"><span class="lineNum">    1629 </span>            :     } else {</a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineNoCov">          0 :       #pragma omp parallel num_threads(nt)</span></a>
+<a name="1631"><span class="lineNum">    1631 </span>            :       {</a>
+<a name="1632"><span class="lineNum">    1632 </span>            :         #pragma omp for reduction(+:bias) nowait</a>
+<a name="1633"><span class="lineNum">    1633 </span>            :         for(unsigned i=rank; i&lt;nlist_hills_.size(); i+=stride) bias+=evaluateGaussian(cv,nlist_hills_[i]);</a>
+<a name="1634"><span class="lineNum">    1634 </span>            :       }</a>
+<a name="1635"><span class="lineNum">    1635 </span>            :     }</a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineCov">         82 :     comm.Sum(bias);</span></a>
+<a name="1637"><span class="lineNum">    1637 </span>            :   }</a>
+<a name="1638"><span class="lineNum">    1638 </span>            : </a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineCov">        285 :   return bias;</span></a>
+<a name="1640"><span class="lineNum">    1640 </span>            : }</a>
+<a name="1641"><span class="lineNum">    1641 </span>            : </a>
+<a name="1642"><span class="lineNum">    1642 </span><span class="lineCov">       8395 : double MetaD::getBiasAndDerivatives(const std::vector&lt;double&gt;&amp; cv, std::vector&lt;double&gt;&amp; der)</span></a>
+<a name="1643"><span class="lineNum">    1643 </span>            : {</a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineCov">       8395 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineCov">       8395 :   double bias=0.0;</span></a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineCov">       8395 :   if(grid_) {</span></a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineCov">       1506 :     std::vector&lt;double&gt; vder(ncv);</span></a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">       1506 :     bias=BiasGrid_-&gt;getValueAndDerivatives(cv,vder);</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">       3498 :     for(unsigned i=0; i&lt;ncv; i++) der[i]=vder[i];</span></a>
+<a name="1650"><span class="lineNum">    1650 </span>            :   } else {</a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineCov">       6889 :     unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="1652"><span class="lineNum">    1652 </span><span class="lineCov">       6889 :     unsigned stride=comm.Get_size();</span></a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineCov">       6889 :     unsigned rank=comm.Get_rank();</span></a>
+<a name="1654"><span class="lineNum">    1654 </span>            : </a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineCov">       6889 :     if(!nlist_) {</span></a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineCov">       6884 :       if(hills_.size()&lt;2*nt*stride||nt==1) {</span></a>
+<a name="1657"><span class="lineNum">    1657 </span>            :         // for performance reasons and thread safety</a>
+<a name="1658"><span class="lineNum">    1658 </span><span class="lineCov">       2587 :         std::vector&lt;double&gt; dp(ncv);</span></a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineCov">       6704 :         for(unsigned i=rank; i&lt;hills_.size(); i+=stride) {</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">       4117 :           bias+=evaluateGaussianAndDerivatives(cv,hills_[i],der,dp);</span></a>
+<a name="1661"><span class="lineNum">    1661 </span>            :         }</a>
+<a name="1662"><span class="lineNum">    1662 </span>            :       } else {</a>
+<a name="1663"><span class="lineNum">    1663 </span><span class="lineCov">       4297 :         #pragma omp parallel num_threads(nt)</span></a>
+<a name="1664"><span class="lineNum">    1664 </span>            :         {</a>
+<a name="1665"><span class="lineNum">    1665 </span>            :           std::vector&lt;double&gt; omp_deriv(ncv,0.);</a>
+<a name="1666"><span class="lineNum">    1666 </span>            :           // for performance reasons and thread safety</a>
+<a name="1667"><span class="lineNum">    1667 </span>            :           std::vector&lt;double&gt; dp(ncv);</a>
+<a name="1668"><span class="lineNum">    1668 </span>            :           #pragma omp for reduction(+:bias) nowait</a>
+<a name="1669"><span class="lineNum">    1669 </span>            :           for(unsigned i=rank; i&lt;hills_.size(); i+=stride) {</a>
+<a name="1670"><span class="lineNum">    1670 </span>            :             bias+=evaluateGaussianAndDerivatives(cv,hills_[i],omp_deriv,dp);</a>
+<a name="1671"><span class="lineNum">    1671 </span>            :           }</a>
+<a name="1672"><span class="lineNum">    1672 </span>            :           #pragma omp critical</a>
+<a name="1673"><span class="lineNum">    1673 </span>            :           for(unsigned i=0; i&lt;ncv; i++) der[i]+=omp_deriv[i];</a>
+<a name="1674"><span class="lineNum">    1674 </span>            :         }</a>
+<a name="1675"><span class="lineNum">    1675 </span>            :       }</a>
+<a name="1676"><span class="lineNum">    1676 </span>            :     } else {</a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineCov">          5 :       if(hills_.size()&lt;2*nt*stride||nt==1) {</span></a>
+<a name="1678"><span class="lineNum">    1678 </span>            :         // for performance reasons and thread safety</a>
+<a name="1679"><span class="lineNum">    1679 </span><span class="lineNoCov">          0 :         std::vector&lt;double&gt; dp(ncv);</span></a>
+<a name="1680"><span class="lineNum">    1680 </span><span class="lineNoCov">          0 :         for(unsigned i=rank; i&lt;nlist_hills_.size(); i+=stride) {</span></a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineNoCov">          0 :           bias+=evaluateGaussianAndDerivatives(cv,nlist_hills_[i],der,dp);</span></a>
+<a name="1682"><span class="lineNum">    1682 </span>            :         }</a>
+<a name="1683"><span class="lineNum">    1683 </span>            :       } else {</a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineCov">          5 :         #pragma omp parallel num_threads(nt)</span></a>
+<a name="1685"><span class="lineNum">    1685 </span>            :         {</a>
+<a name="1686"><span class="lineNum">    1686 </span>            :           std::vector&lt;double&gt; omp_deriv(ncv,0.);</a>
+<a name="1687"><span class="lineNum">    1687 </span>            :           // for performance reasons and thread safety</a>
+<a name="1688"><span class="lineNum">    1688 </span>            :           std::vector&lt;double&gt; dp(ncv);</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :           #pragma omp for reduction(+:bias) nowait</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :           for(unsigned i=rank; i&lt;nlist_hills_.size(); i+=stride) {</a>
+<a name="1691"><span class="lineNum">    1691 </span>            :             bias+=evaluateGaussianAndDerivatives(cv,nlist_hills_[i],omp_deriv,dp);</a>
+<a name="1692"><span class="lineNum">    1692 </span>            :           }</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :           #pragma omp critical</a>
+<a name="1694"><span class="lineNum">    1694 </span>            :           for(unsigned i=0; i&lt;ncv; i++) der[i]+=omp_deriv[i];</a>
+<a name="1695"><span class="lineNum">    1695 </span>            :         }</a>
+<a name="1696"><span class="lineNum">    1696 </span>            :       }</a>
+<a name="1697"><span class="lineNum">    1697 </span>            :     }</a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineCov">       6889 :     comm.Sum(bias);</span></a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineCov">       6889 :     comm.Sum(der);</span></a>
+<a name="1700"><span class="lineNum">    1700 </span>            :   }</a>
+<a name="1701"><span class="lineNum">    1701 </span>            : </a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineCov">       8395 :   return bias;</span></a>
+<a name="1703"><span class="lineNum">    1703 </span>            : }</a>
+<a name="1704"><span class="lineNum">    1704 </span>            : </a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineNoCov">          0 : double MetaD::getGaussianNormalization(const Gaussian&amp; hill)</span></a>
+<a name="1706"><span class="lineNum">    1706 </span>            : {</a>
+<a name="1707"><span class="lineNum">    1707 </span>            :   double norm=1;</a>
+<a name="1708"><span class="lineNum">    1708 </span><span class="lineNoCov">          0 :   unsigned ncv=hill.center.size();</span></a>
+<a name="1709"><span class="lineNum">    1709 </span>            : </a>
+<a name="1710"><span class="lineNum">    1710 </span><span class="lineNoCov">          0 :   if(hill.multivariate) {</span></a>
+<a name="1711"><span class="lineNum">    1711 </span>            :     // recompose the full sigma from the upper diag cholesky</a>
+<a name="1712"><span class="lineNum">    1712 </span>            :     unsigned k=0;</a>
+<a name="1713"><span class="lineNum">    1713 </span>            :     Matrix&lt;double&gt; mymatrix(ncv,ncv);</a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineNoCov">          0 :         mymatrix(i,j)=mymatrix(j,i)=hill.sigma[k]; // recompose the full inverse matrix</span></a>
+<a name="1717"><span class="lineNum">    1717 </span><span class="lineNoCov">          0 :         k++;</span></a>
+<a name="1718"><span class="lineNum">    1718 </span>            :       }</a>
+<a name="1719"><span class="lineNum">    1719 </span><span class="lineNoCov">          0 :       double ldet; logdet( mymatrix, ldet );</span></a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineNoCov">          0 :       norm = std::exp( ldet );  // Not sure here if mymatrix is sigma or inverse</span></a>
+<a name="1721"><span class="lineNum">    1721 </span>            :     }</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :   } else {</a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;hill.sigma.size(); i++) norm*=hill.sigma[i];</span></a>
+<a name="1724"><span class="lineNum">    1724 </span>            :   }</a>
+<a name="1725"><span class="lineNum">    1725 </span>            : </a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineNoCov">          0 :   return norm*std::pow(2*pi,static_cast&lt;double&gt;(ncv)/2.0);</span></a>
+<a name="1727"><span class="lineNum">    1727 </span>            : }</a>
+<a name="1728"><span class="lineNum">    1728 </span>            : </a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineCov">        192 : double MetaD::evaluateGaussian(const std::vector&lt;double&gt;&amp; cv, const Gaussian&amp; hill)</span></a>
+<a name="1730"><span class="lineNum">    1730 </span>            : {</a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineCov">        192 :   unsigned ncv=cv.size();</span></a>
+<a name="1732"><span class="lineNum">    1732 </span>            : </a>
+<a name="1733"><span class="lineNum">    1733 </span>            :   // I use a pointer here because cv is const (and should be const)</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :   // but when using doInt it is easier to locally replace cv[0] with</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :   // the upper/lower limit in case it is out of range</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :   double tmpcv[1];</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :   const double *pcv=NULL; // pointer to cv</a>
+<a name="1738"><span class="lineNum">    1738 </span><span class="lineCov">        192 :   if(ncv&gt;0) pcv=&amp;cv[0];</span></a>
+<a name="1739"><span class="lineNum">    1739 </span><span class="lineCov">        192 :   if(doInt_) {</span></a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineNoCov">          0 :     plumed_assert(ncv==1);</span></a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineNoCov">          0 :     tmpcv[0]=cv[0];</span></a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineNoCov">          0 :     if(cv[0]&lt;lowI_) tmpcv[0]=lowI_;</span></a>
+<a name="1743"><span class="lineNum">    1743 </span><span class="lineNoCov">          0 :     if(cv[0]&gt;uppI_) tmpcv[0]=uppI_;</span></a>
+<a name="1744"><span class="lineNum">    1744 </span>            :     pcv=&amp;(tmpcv[0]);</a>
+<a name="1745"><span class="lineNum">    1745 </span>            :   }</a>
+<a name="1746"><span class="lineNum">    1746 </span>            : </a>
+<a name="1747"><span class="lineNum">    1747 </span>            :   double dp2=0.0;</a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineCov">        192 :   if(hill.multivariate) {</span></a>
+<a name="1749"><span class="lineNum">    1749 </span>            :     unsigned k=0;</a>
+<a name="1750"><span class="lineNum">    1750 </span>            :     // recompose the full sigma from the upper diag cholesky</a>
+<a name="1751"><span class="lineNum">    1751 </span>            :     Matrix&lt;double&gt; mymatrix(ncv,ncv);</a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineNoCov">          0 :         mymatrix(i,j)=mymatrix(j,i)=hill.sigma[k]; // recompose the full inverse matrix</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineNoCov">          0 :         k++;</span></a>
+<a name="1756"><span class="lineNum">    1756 </span>            :       }</a>
+<a name="1757"><span class="lineNum">    1757 </span>            :     }</a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineNoCov">          0 :       double dp_i=difference(i,hill.center[i],pcv[i]);</span></a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineNoCov">          0 :         if(i==j) {</span></a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineNoCov">          0 :           dp2+=dp_i*dp_i*mymatrix(i,j)*0.5;</span></a>
+<a name="1763"><span class="lineNum">    1763 </span>            :         } else {</a>
+<a name="1764"><span class="lineNum">    1764 </span><span class="lineNoCov">          0 :           double dp_j=difference(j,hill.center[j],pcv[j]);</span></a>
+<a name="1765"><span class="lineNum">    1765 </span><span class="lineNoCov">          0 :           dp2+=dp_i*dp_j*mymatrix(i,j);</span></a>
+<a name="1766"><span class="lineNum">    1766 </span>            :         }</a>
+<a name="1767"><span class="lineNum">    1767 </span>            :       }</a>
+<a name="1768"><span class="lineNum">    1768 </span>            :     }</a>
+<a name="1769"><span class="lineNum">    1769 </span>            :   } else {</a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineCov">        576 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1771"><span class="lineNum">    1771 </span><span class="lineCov">        384 :       double dp=difference(i,hill.center[i],pcv[i])*hill.invsigma[i];</span></a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineCov">        384 :       dp2+=dp*dp;</span></a>
+<a name="1773"><span class="lineNum">    1773 </span>            :     }</a>
+<a name="1774"><span class="lineNum">    1774 </span><span class="lineCov">        192 :     dp2*=0.5;</span></a>
+<a name="1775"><span class="lineNum">    1775 </span>            :   }</a>
+<a name="1776"><span class="lineNum">    1776 </span>            : </a>
+<a name="1777"><span class="lineNum">    1777 </span>            :   double bias=0.0;</a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineCov">        192 :   if(dp2&lt;dp2cutoff) bias=hill.height*(stretchA*std::exp(-dp2)+stretchB);</span></a>
+<a name="1779"><span class="lineNum">    1779 </span>            : </a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineCov">        192 :   return bias;</span></a>
+<a name="1781"><span class="lineNum">    1781 </span>            : }</a>
+<a name="1782"><span class="lineNum">    1782 </span>            : </a>
+<a name="1783"><span class="lineNum">    1783 </span><span class="lineCov">    2409166 : double MetaD::evaluateGaussianAndDerivatives(const std::vector&lt;double&gt;&amp; cv, const Gaussian&amp; hill, std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; dp_)</span></a>
+<a name="1784"><span class="lineNum">    1784 </span>            : {</a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineCov">    2409166 :   unsigned ncv=cv.size();</span></a>
+<a name="1786"><span class="lineNum">    1786 </span>            : </a>
+<a name="1787"><span class="lineNum">    1787 </span>            :   // I use a pointer here because cv is const (and should be const)</a>
+<a name="1788"><span class="lineNum">    1788 </span>            :   // but when using doInt it is easier to locally replace cv[0] with</a>
+<a name="1789"><span class="lineNum">    1789 </span>            :   // the upper/lower limit in case it is out of range</a>
+<a name="1790"><span class="lineNum">    1790 </span>            :   const double *pcv=NULL; // pointer to cv</a>
+<a name="1791"><span class="lineNum">    1791 </span>            :   double tmpcv[1]; // tmp array with cv (to be used with doInt_)</a>
+<a name="1792"><span class="lineNum">    1792 </span><span class="lineCov">    2409166 :   if(ncv&gt;0) pcv=&amp;cv[0];</span></a>
+<a name="1793"><span class="lineNum">    1793 </span><span class="lineCov">    2409166 :   if(doInt_) {</span></a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineCov">        602 :     plumed_assert(ncv==1);</span></a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineCov">        602 :     tmpcv[0]=cv[0];</span></a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineCov">        602 :     if(cv[0]&lt;lowI_) tmpcv[0]=lowI_;</span></a>
+<a name="1797"><span class="lineNum">    1797 </span><span class="lineCov">        602 :     if(cv[0]&gt;uppI_) tmpcv[0]=uppI_;</span></a>
+<a name="1798"><span class="lineNum">    1798 </span>            :     pcv=&amp;(tmpcv[0]);</a>
+<a name="1799"><span class="lineNum">    1799 </span>            :   }</a>
+<a name="1800"><span class="lineNum">    1800 </span>            : </a>
+<a name="1801"><span class="lineNum">    1801 </span>            :   bool int_der=false;</a>
+<a name="1802"><span class="lineNum">    1802 </span><span class="lineCov">    2409166 :   if(doInt_) {</span></a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineCov">        602 :     if(cv[0]&lt;lowI_ || cv[0]&gt;uppI_) int_der=true;</span></a>
+<a name="1804"><span class="lineNum">    1804 </span>            :   }</a>
+<a name="1805"><span class="lineNum">    1805 </span>            : </a>
+<a name="1806"><span class="lineNum">    1806 </span>            :   double dp2=0.0;</a>
+<a name="1807"><span class="lineNum">    1807 </span>            :   double bias=0.0;</a>
+<a name="1808"><span class="lineNum">    1808 </span><span class="lineCov">    2409166 :   if(hill.multivariate) {</span></a>
+<a name="1809"><span class="lineNum">    1809 </span>            :     unsigned k=0;</a>
+<a name="1810"><span class="lineNum">    1810 </span>            :     // recompose the full sigma from the upper diag cholesky</a>
+<a name="1811"><span class="lineNum">    1811 </span>            :     Matrix&lt;double&gt; mymatrix(ncv,ncv);</a>
+<a name="1812"><span class="lineNum">    1812 </span><span class="lineCov">     161635 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1813"><span class="lineNum">    1813 </span><span class="lineCov">     162513 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1814"><span class="lineNum">    1814 </span><span class="lineCov">      81476 :         mymatrix(i,j)=mymatrix(j,i)=hill.sigma[k]; // recompose the full inverse matrix</span></a>
+<a name="1815"><span class="lineNum">    1815 </span><span class="lineCov">      81476 :         k++;</span></a>
+<a name="1816"><span class="lineNum">    1816 </span>            :       }</a>
+<a name="1817"><span class="lineNum">    1817 </span>            :     }</a>
+<a name="1818"><span class="lineNum">    1818 </span><span class="lineCov">     161635 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1819"><span class="lineNum">    1819 </span><span class="lineCov">      81037 :       dp_[i]=difference(i,hill.center[i],pcv[i]);</span></a>
+<a name="1820"><span class="lineNum">    1820 </span><span class="lineCov">     162513 :       for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="1821"><span class="lineNum">    1821 </span><span class="lineCov">      81476 :         if(i==j) {</span></a>
+<a name="1822"><span class="lineNum">    1822 </span><span class="lineCov">      81037 :           dp2+=dp_[i]*dp_[i]*mymatrix(i,j)*0.5;</span></a>
+<a name="1823"><span class="lineNum">    1823 </span>            :         } else {</a>
+<a name="1824"><span class="lineNum">    1824 </span><span class="lineCov">        439 :           double dp_j=difference(j,hill.center[j],pcv[j]);</span></a>
+<a name="1825"><span class="lineNum">    1825 </span><span class="lineCov">        439 :           dp2+=dp_[i]*dp_j*mymatrix(i,j);</span></a>
+<a name="1826"><span class="lineNum">    1826 </span>            :         }</a>
+<a name="1827"><span class="lineNum">    1827 </span>            :       }</a>
+<a name="1828"><span class="lineNum">    1828 </span>            :     }</a>
+<a name="1829"><span class="lineNum">    1829 </span><span class="lineCov">      80598 :     if(dp2&lt;dp2cutoff) {</span></a>
+<a name="1830"><span class="lineNum">    1830 </span><span class="lineCov">      77683 :       bias=hill.height*std::exp(-dp2);</span></a>
+<a name="1831"><span class="lineNum">    1831 </span><span class="lineCov">      77683 :       if(!int_der) {</span></a>
+<a name="1832"><span class="lineNum">    1832 </span><span class="lineCov">     155673 :         for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1833"><span class="lineNum">    1833 </span>            :           double tmp=0.0;</a>
+<a name="1834"><span class="lineNum">    1834 </span><span class="lineCov">     156594 :           for(unsigned j=0; j&lt;ncv; j++) tmp += dp_[j]*mymatrix(i,j)*bias;</span></a>
+<a name="1835"><span class="lineNum">    1835 </span><span class="lineCov">      77990 :           der[i]-=tmp*stretchA;</span></a>
+<a name="1836"><span class="lineNum">    1836 </span>            :         }</a>
+<a name="1837"><span class="lineNum">    1837 </span>            :       } else {</a>
+<a name="1838"><span class="lineNum">    1838 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;ncv; i++) der[i]=0.;</span></a>
+<a name="1839"><span class="lineNum">    1839 </span>            :       }</a>
+<a name="1840"><span class="lineNum">    1840 </span><span class="lineCov">      77683 :       bias=stretchA*bias+hill.height*stretchB;</span></a>
+<a name="1841"><span class="lineNum">    1841 </span>            :     }</a>
+<a name="1842"><span class="lineNum">    1842 </span>            :   } else {</a>
+<a name="1843"><span class="lineNum">    1843 </span><span class="lineCov">    6976062 :     for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="1844"><span class="lineNum">    1844 </span><span class="lineCov">    4647494 :       dp_[i]=difference(i,hill.center[i],pcv[i])*hill.invsigma[i];</span></a>
+<a name="1845"><span class="lineNum">    1845 </span><span class="lineCov">    4647494 :       dp2+=dp_[i]*dp_[i];</span></a>
+<a name="1846"><span class="lineNum">    1846 </span>            :     }</a>
+<a name="1847"><span class="lineNum">    1847 </span><span class="lineCov">    2328568 :     dp2*=0.5;</span></a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineCov">    2328568 :     if(dp2&lt;dp2cutoff) {</span></a>
+<a name="1849"><span class="lineNum">    1849 </span><span class="lineCov">    1356599 :       bias=hill.height*std::exp(-dp2);</span></a>
+<a name="1850"><span class="lineNum">    1850 </span><span class="lineCov">    1356599 :       if(!int_der) {</span></a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineCov">    4061018 :         for(unsigned i=0; i&lt;ncv; i++) der[i]-=bias*dp_[i]*hill.invsigma[i]*stretchA;</span></a>
+<a name="1852"><span class="lineNum">    1852 </span>            :       } else {</a>
+<a name="1853"><span class="lineNum">    1853 </span><span class="lineCov">        478 :         for(unsigned i=0; i&lt;ncv; i++) der[i]=0.;</span></a>
+<a name="1854"><span class="lineNum">    1854 </span>            :       }</a>
+<a name="1855"><span class="lineNum">    1855 </span><span class="lineCov">    1356599 :       bias=stretchA*bias+hill.height*stretchB;</span></a>
+<a name="1856"><span class="lineNum">    1856 </span>            :     }</a>
+<a name="1857"><span class="lineNum">    1857 </span>            :   }</a>
+<a name="1858"><span class="lineNum">    1858 </span>            : </a>
+<a name="1859"><span class="lineNum">    1859 </span><span class="lineCov">    2409166 :   return bias;</span></a>
+<a name="1860"><span class="lineNum">    1860 </span>            : }</a>
+<a name="1861"><span class="lineNum">    1861 </span>            : </a>
+<a name="1862"><span class="lineNum">    1862 </span><span class="lineCov">       2736 : double MetaD::getHeight(const std::vector&lt;double&gt;&amp; cv)</span></a>
+<a name="1863"><span class="lineNum">    1863 </span>            : {</a>
+<a name="1864"><span class="lineNum">    1864 </span><span class="lineCov">       2736 :   double height=height0_;</span></a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineCov">       2736 :   if(welltemp_) {</span></a>
+<a name="1866"><span class="lineNum">    1866 </span><span class="lineCov">        275 :     double vbias = getBias(cv);</span></a>
+<a name="1867"><span class="lineNum">    1867 </span><span class="lineCov">        275 :     if(biasf_&gt;1.0) {</span></a>
+<a name="1868"><span class="lineNum">    1868 </span><span class="lineCov">        259 :       height = height0_*std::exp(-vbias/(kbt_*(biasf_-1.0)));</span></a>
+<a name="1869"><span class="lineNum">    1869 </span>            :     } else {</a>
+<a name="1870"><span class="lineNum">    1870 </span>            :       // notice that if gamma=1 we store directly -F</a>
+<a name="1871"><span class="lineNum">    1871 </span><span class="lineCov">         16 :       height = height0_*std::exp(-vbias/kbt_);</span></a>
+<a name="1872"><span class="lineNum">    1872 </span>            :     }</a>
+<a name="1873"><span class="lineNum">    1873 </span>            :   }</a>
+<a name="1874"><span class="lineNum">    1874 </span><span class="lineCov">       2736 :   if(dampfactor_&gt;0.0) {</span></a>
+<a name="1875"><span class="lineNum">    1875 </span><span class="lineCov">         18 :     plumed_assert(BiasGrid_);</span></a>
+<a name="1876"><span class="lineNum">    1876 </span><span class="lineCov">         18 :     double m=BiasGrid_-&gt;getMaxValue();</span></a>
+<a name="1877"><span class="lineNum">    1877 </span><span class="lineCov">         18 :     height*=std::exp(-m/(kbt_*(dampfactor_)));</span></a>
+<a name="1878"><span class="lineNum">    1878 </span>            :   }</a>
+<a name="1879"><span class="lineNum">    1879 </span><span class="lineCov">       2736 :   if (tt_specs_.is_active) {</span></a>
+<a name="1880"><span class="lineNum">    1880 </span><span class="lineCov">         60 :     double vbarrier = transition_bias_;</span></a>
+<a name="1881"><span class="lineNum">    1881 </span><span class="lineCov">         60 :     temperHeight(height, tt_specs_, vbarrier);</span></a>
+<a name="1882"><span class="lineNum">    1882 </span>            :   }</a>
+<a name="1883"><span class="lineNum">    1883 </span><span class="lineCov">       2736 :   if(TargetGrid_) {</span></a>
+<a name="1884"><span class="lineNum">    1884 </span><span class="lineCov">         18 :     double f=TargetGrid_-&gt;getValue(cv)-TargetGrid_-&gt;getMaxValue();</span></a>
+<a name="1885"><span class="lineNum">    1885 </span><span class="lineCov">         18 :     height*=std::exp(f/kbt_);</span></a>
+<a name="1886"><span class="lineNum">    1886 </span>            :   }</a>
+<a name="1887"><span class="lineNum">    1887 </span><span class="lineCov">       2736 :   return height;</span></a>
+<a name="1888"><span class="lineNum">    1888 </span>            : }</a>
+<a name="1889"><span class="lineNum">    1889 </span>            : </a>
+<a name="1890"><span class="lineNum">    1890 </span><span class="lineCov">         60 : void MetaD::temperHeight(double&amp; height, const TemperingSpecs&amp; t_specs, const double tempering_bias)</span></a>
+<a name="1891"><span class="lineNum">    1891 </span>            : {</a>
+<a name="1892"><span class="lineNum">    1892 </span><span class="lineCov">         60 :   if (t_specs.alpha == 1.0) {</span></a>
+<a name="1893"><span class="lineNum">    1893 </span><span class="lineCov">         80 :     height *= std::exp(-std::max(0.0, tempering_bias - t_specs.threshold) / (kbt_ * (t_specs.biasf - 1.0)));</span></a>
+<a name="1894"><span class="lineNum">    1894 </span>            :   } else {</a>
+<a name="1895"><span class="lineNum">    1895 </span><span class="lineCov">         40 :     height *= std::pow(1 + (1 - t_specs.alpha) / t_specs.alpha * std::max(0.0, tempering_bias - t_specs.threshold) / (kbt_ * (t_specs.biasf - 1.0)), - t_specs.alpha / (1 - t_specs.alpha));</span></a>
+<a name="1896"><span class="lineNum">    1896 </span>            :   }</a>
+<a name="1897"><span class="lineNum">    1897 </span><span class="lineCov">         60 : }</span></a>
+<a name="1898"><span class="lineNum">    1898 </span>            : </a>
+<a name="1899"><span class="lineNum">    1899 </span><span class="lineCov">       8435 : void MetaD::calculate()</span></a>
+<a name="1900"><span class="lineNum">    1900 </span>            : {</a>
+<a name="1901"><span class="lineNum">    1901 </span>            :   // this is because presently there is no way to properly pass information</a>
+<a name="1902"><span class="lineNum">    1902 </span>            :   // on adaptive hills (diff) after exchanges:</a>
+<a name="1903"><span class="lineNum">    1903 </span><span class="lineCov">       8435 :   if(adaptive_==FlexibleBin::diffusion &amp;&amp; getExchangeStep()) error(&quot;ADAPTIVE=DIFF is not compatible with replica exchange&quot;);</span></a>
+<a name="1904"><span class="lineNum">    1904 </span>            : </a>
+<a name="1905"><span class="lineNum">    1905 </span><span class="lineCov">       8435 :   const unsigned ncv=getNumberOfArguments();</span></a>
+<a name="1906"><span class="lineNum">    1906 </span><span class="lineCov">       8435 :   std::vector&lt;double&gt; cv(ncv);</span></a>
+<a name="1907"><span class="lineNum">    1907 </span><span class="lineCov">      21082 :   for(unsigned i=0; i&lt;ncv; ++i) cv[i]=getArgument(i);</span></a>
+<a name="1908"><span class="lineNum">    1908 </span>            : </a>
+<a name="1909"><span class="lineNum">    1909 </span><span class="lineCov">       8435 :   if(nlist_) {</span></a>
+<a name="1910"><span class="lineNum">    1910 </span><span class="lineCov">          5 :     nlist_steps_++;</span></a>
+<a name="1911"><span class="lineNum">    1911 </span><span class="lineCov">          5 :     if(getExchangeStep()) nlist_update_=true;</span></a>
+<a name="1912"><span class="lineNum">    1912 </span>            :     else {</a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineCov">         11 :       for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="1914"><span class="lineNum">    1914 </span><span class="lineCov">          8 :         double d = difference(i, cv[i], nlist_center_[i]);</span></a>
+<a name="1915"><span class="lineNum">    1915 </span><span class="lineCov">          8 :         double nk_dist2 = d*d/nlist_dev2_[i];</span></a>
+<a name="1916"><span class="lineNum">    1916 </span><span class="lineCov">          8 :         if(nk_dist2&gt;nlist_param_[1]) {nlist_update_=true; break;}</span></a>
+<a name="1917"><span class="lineNum">    1917 </span>            :       }</a>
+<a name="1918"><span class="lineNum">    1918 </span>            :     }</a>
+<a name="1919"><span class="lineNum">    1919 </span><span class="lineCov">          5 :     if(nlist_update_) updateNlist();</span></a>
+<a name="1920"><span class="lineNum">    1920 </span>            :   }</a>
+<a name="1921"><span class="lineNum">    1921 </span>            : </a>
+<a name="1922"><span class="lineNum">    1922 </span>            :   double ene = 0.;</a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineCov">       8435 :   std::vector&lt;double&gt; der(ncv,0.);</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineCov">       8435 :   if(biasf_!=1.0) ene = getBiasAndDerivatives(cv,der);</span></a>
+<a name="1925"><span class="lineNum">    1925 </span>            :   setBias(ene);</a>
+<a name="1926"><span class="lineNum">    1926 </span><span class="lineCov">      21082 :   for(unsigned i=0; i&lt;ncv; i++) setOutputForce(i,-der[i]);</span></a>
+<a name="1927"><span class="lineNum">    1927 </span>            : </a>
+<a name="1928"><span class="lineNum">    1928 </span><span class="lineCov">       8440 :   if(calc_work_) getPntrToComponent(&quot;work&quot;)-&gt;set(work_);</span></a>
+<a name="1929"><span class="lineNum">    1929 </span><span class="lineCov">       8545 :   if(calc_rct_) getPntrToComponent(&quot;rbias&quot;)-&gt;set(ene - reweight_factor_);</span></a>
+<a name="1930"><span class="lineNum">    1930 </span>            :   // calculate the acceleration factor</a>
+<a name="1931"><span class="lineNum">    1931 </span><span class="lineCov">       8435 :   if(acceleration_&amp;&amp;!isFirstStep_) {</span></a>
+<a name="1932"><span class="lineNum">    1932 </span><span class="lineCov">        329 :     acc_ += static_cast&lt;double&gt;(getStride()) * std::exp(ene/(kbt_));</span></a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineCov">        329 :     const double mean_acc = acc_/((double) getStep());</span></a>
+<a name="1934"><span class="lineNum">    1934 </span><span class="lineCov">        329 :     getPntrToComponent(&quot;acc&quot;)-&gt;set(mean_acc);</span></a>
+<a name="1935"><span class="lineNum">    1935 </span><span class="lineCov">       8435 :   } else if (acceleration_ &amp;&amp; isFirstStep_ &amp;&amp; acc_restart_mean_ &gt; 0.0) {</span></a>
+<a name="1936"><span class="lineNum">    1936 </span><span class="lineCov">          2 :     acc_ = acc_restart_mean_ * static_cast&lt;double&gt;(getStep());</span></a>
+<a name="1937"><span class="lineNum">    1937 </span><span class="lineCov">          2 :     if(freq_adaptive_) {</span></a>
+<a name="1938"><span class="lineNum">    1938 </span>            :       // has to be done here if restarting, as the acc is not defined before</a>
+<a name="1939"><span class="lineNum">    1939 </span><span class="lineCov">          1 :       updateFrequencyAdaptiveStride();</span></a>
+<a name="1940"><span class="lineNum">    1940 </span>            :     }</a>
+<a name="1941"><span class="lineNum">    1941 </span>            :   }</a>
+<a name="1942"><span class="lineNum">    1942 </span><span class="lineCov">       8435 : }</span></a>
+<a name="1943"><span class="lineNum">    1943 </span>            : </a>
+<a name="1944"><span class="lineNum">    1944 </span><span class="lineCov">       6239 : void MetaD::update()</span></a>
+<a name="1945"><span class="lineNum">    1945 </span>            : {</a>
+<a name="1946"><span class="lineNum">    1946 </span>            :   // adding hills criteria (could be more complex though)</a>
+<a name="1947"><span class="lineNum">    1947 </span>            :   bool nowAddAHill;</a>
+<a name="1948"><span class="lineNum">    1948 </span><span class="lineCov">       6239 :   if(getStep()%current_stride_==0 &amp;&amp; !isFirstStep_) nowAddAHill=true;</span></a>
+<a name="1949"><span class="lineNum">    1949 </span>            :   else {</a>
+<a name="1950"><span class="lineNum">    1950 </span>            :     nowAddAHill=false;</a>
+<a name="1951"><span class="lineNum">    1951 </span><span class="lineCov">       3503 :     isFirstStep_=false;</span></a>
+<a name="1952"><span class="lineNum">    1952 </span>            :   }</a>
+<a name="1953"><span class="lineNum">    1953 </span>            : </a>
+<a name="1954"><span class="lineNum">    1954 </span><span class="lineCov">       6239 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="1955"><span class="lineNum">    1955 </span><span class="lineCov">       6239 :   std::vector&lt;double&gt; cv(ncv);</span></a>
+<a name="1956"><span class="lineNum">    1956 </span><span class="lineCov">      16690 :   for(unsigned i=0; i&lt;ncv; ++i) cv[i] = getArgument(i);</span></a>
+<a name="1957"><span class="lineNum">    1957 </span>            : </a>
+<a name="1958"><span class="lineNum">    1958 </span>            :   double vbias=0.;</a>
+<a name="1959"><span class="lineNum">    1959 </span><span class="lineCov">       6239 :   if(calc_work_) vbias=getBias(cv);</span></a>
+<a name="1960"><span class="lineNum">    1960 </span>            : </a>
+<a name="1961"><span class="lineNum">    1961 </span>            :   // if you use adaptive, call the FlexibleBin</a>
+<a name="1962"><span class="lineNum">    1962 </span>            :   bool multivariate=false;</a>
+<a name="1963"><span class="lineNum">    1963 </span><span class="lineCov">       6239 :   if(adaptive_!=FlexibleBin::none) {</span></a>
+<a name="1964"><span class="lineNum">    1964 </span><span class="lineCov">        778 :     flexbin_-&gt;update(nowAddAHill);</span></a>
+<a name="1965"><span class="lineNum">    1965 </span>            :     multivariate=true;</a>
+<a name="1966"><span class="lineNum">    1966 </span>            :   }</a>
+<a name="1967"><span class="lineNum">    1967 </span>            : </a>
+<a name="1968"><span class="lineNum">    1968 </span>            :   std::vector&lt;double&gt; thissigma;</a>
+<a name="1969"><span class="lineNum">    1969 </span><span class="lineCov">       6239 :   if(nowAddAHill) {</span></a>
+<a name="1970"><span class="lineNum">    1970 </span>            :     // add a Gaussian</a>
+<a name="1971"><span class="lineNum">    1971 </span><span class="lineCov">       2736 :     double height=getHeight(cv);</span></a>
+<a name="1972"><span class="lineNum">    1972 </span>            :     // returns upper diagonal inverse</a>
+<a name="1973"><span class="lineNum">    1973 </span><span class="lineCov">       3110 :     if(adaptive_!=FlexibleBin::none) thissigma=flexbin_-&gt;getInverseMatrix();</span></a>
+<a name="1974"><span class="lineNum">    1974 </span>            :     // returns normal sigma</a>
+<a name="1975"><span class="lineNum">    1975 </span><span class="lineCov">       2362 :     else thissigma=sigma0_;</span></a>
+<a name="1976"><span class="lineNum">    1976 </span>            : </a>
+<a name="1977"><span class="lineNum">    1977 </span>            :     // In case we use walkers_mpi, it is now necessary to communicate with other replicas.</a>
+<a name="1978"><span class="lineNum">    1978 </span><span class="lineCov">       2736 :     if(walkers_mpi_) {</span></a>
+<a name="1979"><span class="lineNum">    1979 </span>            :       // Allocate arrays to store all walkers hills</a>
+<a name="1980"><span class="lineNum">    1980 </span><span class="lineCov">        174 :       std::vector&lt;double&gt; all_cv(mpi_nw_*ncv,0.0);</span></a>
+<a name="1981"><span class="lineNum">    1981 </span><span class="lineCov">        174 :       std::vector&lt;double&gt; all_sigma(mpi_nw_*thissigma.size(),0.0);</span></a>
+<a name="1982"><span class="lineNum">    1982 </span><span class="lineCov">        174 :       std::vector&lt;double&gt; all_height(mpi_nw_,0.0);</span></a>
+<a name="1983"><span class="lineNum">    1983 </span><span class="lineCov">        174 :       std::vector&lt;int&gt;    all_multivariate(mpi_nw_,0);</span></a>
+<a name="1984"><span class="lineNum">    1984 </span><span class="lineCov">        174 :       if(comm.Get_rank()==0) {</span></a>
+<a name="1985"><span class="lineNum">    1985 </span>            :         // Communicate (only root)</a>
+<a name="1986"><span class="lineNum">    1986 </span><span class="lineCov">         99 :         multi_sim_comm.Allgather(cv,all_cv);</span></a>
+<a name="1987"><span class="lineNum">    1987 </span><span class="lineCov">         99 :         multi_sim_comm.Allgather(thissigma,all_sigma);</span></a>
+<a name="1988"><span class="lineNum">    1988 </span>            :         // notice that if gamma=1 we store directly -F so this scaling is not necessary:</a>
+<a name="1989"><span class="lineNum">    1989 </span><span class="lineCov">         99 :         multi_sim_comm.Allgather(height*(biasf_&gt;1.0?biasf_/(biasf_-1.0):1.0),all_height);</span></a>
+<a name="1990"><span class="lineNum">    1990 </span><span class="lineCov">         99 :         multi_sim_comm.Allgather(int(multivariate),all_multivariate);</span></a>
+<a name="1991"><span class="lineNum">    1991 </span>            :       }</a>
+<a name="1992"><span class="lineNum">    1992 </span>            :       // Share info with group members</a>
+<a name="1993"><span class="lineNum">    1993 </span><span class="lineCov">        174 :       comm.Bcast(all_cv,0);</span></a>
+<a name="1994"><span class="lineNum">    1994 </span><span class="lineCov">        174 :       comm.Bcast(all_sigma,0);</span></a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineCov">        174 :       comm.Bcast(all_height,0);</span></a>
+<a name="1996"><span class="lineNum">    1996 </span><span class="lineCov">        174 :       comm.Bcast(all_multivariate,0);</span></a>
+<a name="1997"><span class="lineNum">    1997 </span>            : </a>
+<a name="1998"><span class="lineNum">    1998 </span>            :       // Flying Gaussian</a>
+<a name="1999"><span class="lineNum">    1999 </span><span class="lineCov">        174 :       if (flying_) {</span></a>
+<a name="2000"><span class="lineNum">    2000 </span><span class="lineCov">         54 :         hills_.clear();</span></a>
+<a name="2001"><span class="lineNum">    2001 </span><span class="lineCov">         54 :         comm.Barrier();</span></a>
+<a name="2002"><span class="lineNum">    2002 </span>            :       }</a>
+<a name="2003"><span class="lineNum">    2003 </span>            : </a>
+<a name="2004"><span class="lineNum">    2004 </span><span class="lineCov">        696 :       for(unsigned i=0; i&lt;mpi_nw_; i++) {</span></a>
+<a name="2005"><span class="lineNum">    2005 </span>            :         // actually add hills one by one</a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineCov">        522 :         std::vector&lt;double&gt; cv_now(ncv);</span></a>
+<a name="2007"><span class="lineNum">    2007 </span><span class="lineCov">        522 :         std::vector&lt;double&gt; sigma_now(thissigma.size());</span></a>
+<a name="2008"><span class="lineNum">    2008 </span><span class="lineCov">       1566 :         for(unsigned j=0; j&lt;ncv; j++) cv_now[j]=all_cv[i*ncv+j];</span></a>
+<a name="2009"><span class="lineNum">    2009 </span><span class="lineCov">       1674 :         for(unsigned j=0; j&lt;thissigma.size(); j++) sigma_now[j]=all_sigma[i*thissigma.size()+j];</span></a>
+<a name="2010"><span class="lineNum">    2010 </span>            :         // notice that if gamma=1 we store directly -F so this scaling is not necessary:</a>
+<a name="2011"><span class="lineNum">    2011 </span><span class="lineCov">        522 :         double fact=(biasf_&gt;1.0?(biasf_-1.0)/biasf_:1.0);</span></a>
+<a name="2012"><span class="lineNum">    2012 </span><span class="lineCov">        522 :         Gaussian newhill=Gaussian(all_multivariate[i],all_height[i]*fact,cv_now,sigma_now);</span></a>
+<a name="2013"><span class="lineNum">    2013 </span><span class="lineCov">        522 :         addGaussian(newhill);</span></a>
+<a name="2014"><span class="lineNum">    2014 </span><span class="lineCov">        522 :         if(!flying_) writeGaussian(newhill,hillsOfile_);</span></a>
+<a name="2015"><span class="lineNum">    2015 </span><span class="lineCov">        522 :       }</span></a>
+<a name="2016"><span class="lineNum">    2016 </span>            :     } else {</a>
+<a name="2017"><span class="lineNum">    2017 </span><span class="lineCov">       2562 :       Gaussian newhill=Gaussian(multivariate,height,cv,thissigma);</span></a>
+<a name="2018"><span class="lineNum">    2018 </span><span class="lineCov">       2562 :       addGaussian(newhill);</span></a>
+<a name="2019"><span class="lineNum">    2019 </span><span class="lineCov">       2562 :       writeGaussian(newhill,hillsOfile_);</span></a>
+<a name="2020"><span class="lineNum">    2020 </span><span class="lineCov">       2562 :     }</span></a>
+<a name="2021"><span class="lineNum">    2021 </span>            : </a>
+<a name="2022"><span class="lineNum">    2022 </span>            :     // this is to update the hills neighbor list</a>
+<a name="2023"><span class="lineNum">    2023 </span><span class="lineCov">       2736 :     if(nlist_) nlist_update_=true;</span></a>
+<a name="2024"><span class="lineNum">    2024 </span>            :   }</a>
+<a name="2025"><span class="lineNum">    2025 </span>            : </a>
+<a name="2026"><span class="lineNum">    2026 </span>            :   // this should be outside of the if block in case</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :   // mw_rstride_ is not a multiple of stride_</a>
+<a name="2028"><span class="lineNum">    2028 </span><span class="lineCov">       6239 :   if(mw_n_&gt;1 &amp;&amp; getStep()%mw_rstride_==0) hillsOfile_.flush();</span></a>
+<a name="2029"><span class="lineNum">    2029 </span>            : </a>
+<a name="2030"><span class="lineNum">    2030 </span><span class="lineCov">       6239 :   if(calc_work_) {</span></a>
+<a name="2031"><span class="lineNum">    2031 </span><span class="lineCov">          5 :     if(nlist_) updateNlist();</span></a>
+<a name="2032"><span class="lineNum">    2032 </span><span class="lineCov">          5 :     double vbias1=getBias(cv);</span></a>
+<a name="2033"><span class="lineNum">    2033 </span><span class="lineCov">          5 :     work_+=vbias1-vbias;</span></a>
+<a name="2034"><span class="lineNum">    2034 </span>            :   }</a>
+<a name="2035"><span class="lineNum">    2035 </span>            : </a>
+<a name="2036"><span class="lineNum">    2036 </span>            :   // dump grid on file</a>
+<a name="2037"><span class="lineNum">    2037 </span><span class="lineCov">       6239 :   if(wgridstride_&gt;0&amp;&amp;(getStep()%wgridstride_==0||getCPT())) {</span></a>
+<a name="2038"><span class="lineNum">    2038 </span>            :     // in case old grids are stored, a sequence of grids should appear</a>
+<a name="2039"><span class="lineNum">    2039 </span>            :     // this call results in a repetition of the header:</a>
+<a name="2040"><span class="lineNum">    2040 </span><span class="lineCov">         91 :     if(storeOldGrids_) gridfile_.clearFields();</span></a>
+<a name="2041"><span class="lineNum">    2041 </span>            :     // in case only latest grid is stored, file should be rewound</a>
+<a name="2042"><span class="lineNum">    2042 </span>            :     // this will overwrite previously written grids</a>
+<a name="2043"><span class="lineNum">    2043 </span>            :     else {</a>
+<a name="2044"><span class="lineNum">    2044 </span><span class="lineCov">         51 :       int r = 0;</span></a>
+<a name="2045"><span class="lineNum">    2045 </span><span class="lineCov">         51 :       if(walkers_mpi_) {</span></a>
+<a name="2046"><span class="lineNum">    2046 </span><span class="lineNoCov">          0 :         if(comm.Get_rank()==0) r=multi_sim_comm.Get_rank();</span></a>
+<a name="2047"><span class="lineNum">    2047 </span><span class="lineNoCov">          0 :         comm.Bcast(r,0);</span></a>
+<a name="2048"><span class="lineNum">    2048 </span>            :       }</a>
+<a name="2049"><span class="lineNum">    2049 </span><span class="lineCov">         51 :       if(r==0) gridfile_.rewind();</span></a>
+<a name="2050"><span class="lineNum">    2050 </span>            :     }</a>
+<a name="2051"><span class="lineNum">    2051 </span><span class="lineCov">         91 :     BiasGrid_-&gt;writeToFile(gridfile_);</span></a>
+<a name="2052"><span class="lineNum">    2052 </span>            :     // if a single grid is stored, it is necessary to flush it, otherwise</a>
+<a name="2053"><span class="lineNum">    2053 </span>            :     // the file might stay empty forever (when a single grid is not large enough to</a>
+<a name="2054"><span class="lineNum">    2054 </span>            :     // trigger flushing from the operating system).</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :     // on the other hand, if grids are stored one after the other this is</a>
+<a name="2056"><span class="lineNum">    2056 </span>            :     // no necessary, and we leave the flushing control to the user as usual</a>
+<a name="2057"><span class="lineNum">    2057 </span>            :     // (with FLUSH keyword)</a>
+<a name="2058"><span class="lineNum">    2058 </span><span class="lineCov">         91 :     if(!storeOldGrids_) gridfile_.flush();</span></a>
+<a name="2059"><span class="lineNum">    2059 </span>            :   }</a>
+<a name="2060"><span class="lineNum">    2060 </span>            : </a>
+<a name="2061"><span class="lineNum">    2061 </span>            :   // if multiple walkers and time to read Gaussians</a>
+<a name="2062"><span class="lineNum">    2062 </span><span class="lineCov">       6239 :   if(mw_n_&gt;1 &amp;&amp; getStep()%mw_rstride_==0) {</span></a>
+<a name="2063"><span class="lineNum">    2063 </span><span class="lineCov">      12048 :     for(int i=0; i&lt;mw_n_; ++i) {</span></a>
+<a name="2064"><span class="lineNum">    2064 </span>            :       // don't read your own Gaussians</a>
+<a name="2065"><span class="lineNum">    2065 </span><span class="lineCov">       9036 :       if(i==mw_id_) continue;</span></a>
+<a name="2066"><span class="lineNum">    2066 </span>            :       // if the file is not open yet</a>
+<a name="2067"><span class="lineNum">    2067 </span><span class="lineCov">       6024 :       if(!(ifiles_[i]-&gt;isOpen())) {</span></a>
+<a name="2068"><span class="lineNum">    2068 </span>            :         // check if it exists now and open it!</a>
+<a name="2069"><span class="lineNum">    2069 </span><span class="lineCov">          7 :         if(ifiles_[i]-&gt;FileExist(ifilesnames_[i])) {</span></a>
+<a name="2070"><span class="lineNum">    2070 </span><span class="lineCov">          7 :           ifiles_[i]-&gt;open(ifilesnames_[i]);</span></a>
+<a name="2071"><span class="lineNum">    2071 </span><span class="lineCov">          7 :           ifiles_[i]-&gt;reset(false);</span></a>
+<a name="2072"><span class="lineNum">    2072 </span>            :         }</a>
+<a name="2073"><span class="lineNum">    2073 </span>            :         // otherwise read the new Gaussians</a>
+<a name="2074"><span class="lineNum">    2074 </span>            :       } else {</a>
+<a name="2075"><span class="lineNum">    2075 </span><span class="lineCov">       6017 :         log.printf(&quot;  Reading hills from %s:&quot;,ifilesnames_[i].c_str());</span></a>
+<a name="2076"><span class="lineNum">    2076 </span><span class="lineCov">       6017 :         readGaussians(ifiles_[i].get());</span></a>
+<a name="2077"><span class="lineNum">    2077 </span><span class="lineCov">       6017 :         ifiles_[i]-&gt;reset(false);</span></a>
+<a name="2078"><span class="lineNum">    2078 </span>            :       }</a>
+<a name="2079"><span class="lineNum">    2079 </span>            :     }</a>
+<a name="2080"><span class="lineNum">    2080 </span>            :     // this is to update the hills neighbor list</a>
+<a name="2081"><span class="lineNum">    2081 </span><span class="lineCov">       3012 :     if(nlist_) nlist_update_=true;</span></a>
+<a name="2082"><span class="lineNum">    2082 </span>            :   }</a>
+<a name="2083"><span class="lineNum">    2083 </span>            : </a>
+<a name="2084"><span class="lineNum">    2084 </span>            :   // Recalculate special bias quantities whenever the bias has been changed by the update.</a>
+<a name="2085"><span class="lineNum">    2085 </span><span class="lineCov">       6239 :   bool bias_has_changed = (nowAddAHill || (mw_n_ &gt; 1 &amp;&amp; getStep() % mw_rstride_ == 0));</span></a>
+<a name="2086"><span class="lineNum">    2086 </span><span class="lineCov">       6239 :   if (calc_rct_ &amp;&amp; bias_has_changed &amp;&amp; getStep()%(stride_*rct_ustride_)==0) computeReweightingFactor();</span></a>
+<a name="2087"><span class="lineNum">    2087 </span><span class="lineCov">       6239 :   if (calc_max_bias_ &amp;&amp; bias_has_changed) {</span></a>
+<a name="2088"><span class="lineNum">    2088 </span><span class="lineNoCov">          0 :     max_bias_ = BiasGrid_-&gt;getMaxValue();</span></a>
+<a name="2089"><span class="lineNum">    2089 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;maxbias&quot;)-&gt;set(max_bias_);</span></a>
+<a name="2090"><span class="lineNum">    2090 </span>            :   }</a>
+<a name="2091"><span class="lineNum">    2091 </span><span class="lineCov">       6239 :   if (calc_transition_bias_ &amp;&amp; bias_has_changed) {</span></a>
+<a name="2092"><span class="lineNum">    2092 </span><span class="lineCov">        260 :     transition_bias_ = getTransitionBarrierBias();</span></a>
+<a name="2093"><span class="lineNum">    2093 </span><span class="lineCov">        520 :     getPntrToComponent(&quot;transbias&quot;)-&gt;set(transition_bias_);</span></a>
+<a name="2094"><span class="lineNum">    2094 </span>            :   }</a>
+<a name="2095"><span class="lineNum">    2095 </span>            : </a>
+<a name="2096"><span class="lineNum">    2096 </span>            :   // Frequency adaptive metadynamics - update hill addition frequency</a>
+<a name="2097"><span class="lineNum">    2097 </span><span class="lineCov">       6239 :   if(freq_adaptive_ &amp;&amp; getStep()%fa_update_frequency_==0) {</span></a>
+<a name="2098"><span class="lineNum">    2098 </span><span class="lineCov">        151 :     updateFrequencyAdaptiveStride();</span></a>
+<a name="2099"><span class="lineNum">    2099 </span>            :   }</a>
+<a name="2100"><span class="lineNum">    2100 </span><span class="lineCov">       6239 : }</span></a>
+<a name="2101"><span class="lineNum">    2101 </span>            : </a>
+<a name="2102"><span class="lineNum">    2102 </span>            : /// takes a pointer to the file and a template std::string with values v and gives back the next center, sigma and height</a>
+<a name="2103"><span class="lineNum">    2103 </span><span class="lineCov">       8152 : bool MetaD::scanOneHill(IFile* ifile, std::vector&lt;Value&gt;&amp; tmpvalues, std::vector&lt;double&gt;&amp; center, std::vector&lt;double&gt;&amp; sigma, double&amp; height, bool&amp; multivariate)</span></a>
+<a name="2104"><span class="lineNum">    2104 </span>            : {</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :   double dummy;</a>
+<a name="2106"><span class="lineNum">    2106 </span><span class="lineCov">       8152 :   multivariate=false;</span></a>
+<a name="2107"><span class="lineNum">    2107 </span><span class="lineCov">      16304 :   if(ifile-&gt;scanField(&quot;time&quot;,dummy)) {</span></a>
+<a name="2108"><span class="lineNum">    2108 </span><span class="lineCov">       2116 :     unsigned ncv=tmpvalues.size();</span></a>
+<a name="2109"><span class="lineNum">    2109 </span><span class="lineCov">       6302 :     for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="2110"><span class="lineNum">    2110 </span><span class="lineCov">       4186 :       ifile-&gt;scanField( &amp;tmpvalues[i] );</span></a>
+<a name="2111"><span class="lineNum">    2111 </span><span class="lineCov">       4186 :       if( tmpvalues[i].isPeriodic() &amp;&amp; ! getPntrToArgument(i)-&gt;isPeriodic() ) {</span></a>
+<a name="2112"><span class="lineNum">    2112 </span><span class="lineNoCov">          0 :         error(&quot;in hills file periodicity for variable &quot; + tmpvalues[i].getName() + &quot; does not match periodicity in input&quot;);</span></a>
+<a name="2113"><span class="lineNum">    2113 </span><span class="lineCov">       4186 :       } else if( tmpvalues[i].isPeriodic() ) {</span></a>
+<a name="2114"><span class="lineNum">    2114 </span><span class="lineNoCov">          0 :         std::string imin, imax; tmpvalues[i].getDomain( imin, imax );</span></a>
+<a name="2115"><span class="lineNum">    2115 </span><span class="lineNoCov">          0 :         std::string rmin, rmax; getPntrToArgument(i)-&gt;getDomain( rmin, rmax );</span></a>
+<a name="2116"><span class="lineNum">    2116 </span><span class="lineNoCov">          0 :         if( imin!=rmin || imax!=rmax ) {</span></a>
+<a name="2117"><span class="lineNum">    2117 </span><span class="lineNoCov">          0 :           error(&quot;in hills file periodicity for variable &quot; + tmpvalues[i].getName() + &quot; does not match periodicity in input&quot;);</span></a>
+<a name="2118"><span class="lineNum">    2118 </span>            :         }</a>
+<a name="2119"><span class="lineNum">    2119 </span>            :       }</a>
+<a name="2120"><span class="lineNum">    2120 </span><span class="lineCov">       4186 :       center[i]=tmpvalues[i].get();</span></a>
+<a name="2121"><span class="lineNum">    2121 </span>            :     }</a>
+<a name="2122"><span class="lineNum">    2122 </span>            :     // scan for kerneltype</a>
+<a name="2123"><span class="lineNum">    2123 </span><span class="lineCov">       2116 :     std::string ktype=&quot;stretched-gaussian&quot;;</span></a>
+<a name="2124"><span class="lineNum">    2124 </span><span class="lineCov">       6339 :     if( ifile-&gt;FieldExist(&quot;kerneltype&quot;) ) ifile-&gt;scanField(&quot;kerneltype&quot;,ktype);</span></a>
+<a name="2125"><span class="lineNum">    2125 </span><span class="lineCov">       2116 :     if( ktype==&quot;gaussian&quot; ) {</span></a>
+<a name="2126"><span class="lineNum">    2126 </span><span class="lineCov">         12 :       noStretchWarning();</span></a>
+<a name="2127"><span class="lineNum">    2127 </span><span class="lineCov">       2104 :     } else if( ktype!=&quot;stretched-gaussian&quot;) {</span></a>
+<a name="2128"><span class="lineNum">    2128 </span><span class="lineNoCov">          0 :       error(&quot;non Gaussian kernels are not supported in MetaD&quot;);</span></a>
+<a name="2129"><span class="lineNum">    2129 </span>            :     }</a>
+<a name="2130"><span class="lineNum">    2130 </span>            :     // scan for multivariate label: record the actual file position so to eventually rewind</a>
+<a name="2131"><span class="lineNum">    2131 </span>            :     std::string sss;</a>
+<a name="2132"><span class="lineNum">    2132 </span><span class="lineCov">       4232 :     ifile-&gt;scanField(&quot;multivariate&quot;,sss);</span></a>
+<a name="2133"><span class="lineNum">    2133 </span><span class="lineCov">       2116 :     if(sss==&quot;true&quot;) multivariate=true;</span></a>
+<a name="2134"><span class="lineNum">    2134 </span><span class="lineCov">       2116 :     else if(sss==&quot;false&quot;) multivariate=false;</span></a>
+<a name="2135"><span class="lineNum">    2135 </span><span class="lineNoCov">          0 :     else plumed_merror(&quot;cannot parse multivariate = &quot;+ sss);</span></a>
+<a name="2136"><span class="lineNum">    2136 </span><span class="lineCov">       2116 :     if(multivariate) {</span></a>
+<a name="2137"><span class="lineNum">    2137 </span><span class="lineNoCov">          0 :       sigma.resize(ncv*(ncv+1)/2);</span></a>
+<a name="2138"><span class="lineNum">    2138 </span>            :       Matrix&lt;double&gt; upper(ncv,ncv);</a>
+<a name="2139"><span class="lineNum">    2139 </span>            :       Matrix&lt;double&gt; lower(ncv,ncv);</a>
+<a name="2140"><span class="lineNum">    2140 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="2141"><span class="lineNum">    2141 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;ncv-i; j++) {</span></a>
+<a name="2142"><span class="lineNum">    2142 </span><span class="lineNoCov">          0 :           ifile-&gt;scanField(&quot;sigma_&quot;+getPntrToArgument(j+i)-&gt;getName()+&quot;_&quot;+getPntrToArgument(j)-&gt;getName(),lower(j+i,j));</span></a>
+<a name="2143"><span class="lineNum">    2143 </span><span class="lineNoCov">          0 :           upper(j,j+i)=lower(j+i,j);</span></a>
+<a name="2144"><span class="lineNum">    2144 </span>            :         }</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :       }</a>
+<a name="2146"><span class="lineNum">    2146 </span>            :       Matrix&lt;double&gt; mymult(ncv,ncv);</a>
+<a name="2147"><span class="lineNum">    2147 </span>            :       Matrix&lt;double&gt; invmatrix(ncv,ncv);</a>
+<a name="2148"><span class="lineNum">    2148 </span><span class="lineNoCov">          0 :       mult(lower,upper,mymult);</span></a>
+<a name="2149"><span class="lineNum">    2149 </span>            :       // now invert and get the sigmas</a>
+<a name="2150"><span class="lineNum">    2150 </span><span class="lineNoCov">          0 :       Invert(mymult,invmatrix);</span></a>
+<a name="2151"><span class="lineNum">    2151 </span>            :       // put the sigmas in the usual order: upper diagonal (this time in normal form and not in band form)</a>
+<a name="2152"><span class="lineNum">    2152 </span>            :       unsigned k=0;</a>
+<a name="2153"><span class="lineNum">    2153 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="2154"><span class="lineNum">    2154 </span><span class="lineNoCov">          0 :         for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="2155"><span class="lineNum">    2155 </span><span class="lineNoCov">          0 :           sigma[k]=invmatrix(i,j);</span></a>
+<a name="2156"><span class="lineNum">    2156 </span><span class="lineNoCov">          0 :           k++;</span></a>
+<a name="2157"><span class="lineNum">    2157 </span>            :         }</a>
+<a name="2158"><span class="lineNum">    2158 </span>            :       }</a>
+<a name="2159"><span class="lineNum">    2159 </span>            :     } else {</a>
+<a name="2160"><span class="lineNum">    2160 </span><span class="lineCov">       6302 :       for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="2161"><span class="lineNum">    2161 </span><span class="lineCov">       8372 :         ifile-&gt;scanField(&quot;sigma_&quot;+getPntrToArgument(i)-&gt;getName(),sigma[i]);</span></a>
+<a name="2162"><span class="lineNum">    2162 </span>            :       }</a>
+<a name="2163"><span class="lineNum">    2163 </span>            :     }</a>
+<a name="2164"><span class="lineNum">    2164 </span>            : </a>
+<a name="2165"><span class="lineNum">    2165 </span><span class="lineCov">       2116 :     ifile-&gt;scanField(&quot;height&quot;,height);</span></a>
+<a name="2166"><span class="lineNum">    2166 </span><span class="lineCov">       2116 :     ifile-&gt;scanField(&quot;biasf&quot;,dummy);</span></a>
+<a name="2167"><span class="lineNum">    2167 </span><span class="lineCov">       6165 :     if(ifile-&gt;FieldExist(&quot;clock&quot;)) ifile-&gt;scanField(&quot;clock&quot;,dummy);</span></a>
+<a name="2168"><span class="lineNum">    2168 </span><span class="lineCov">       4232 :     if(ifile-&gt;FieldExist(&quot;lower_int&quot;)) ifile-&gt;scanField(&quot;lower_int&quot;,dummy);</span></a>
+<a name="2169"><span class="lineNum">    2169 </span><span class="lineCov">       4232 :     if(ifile-&gt;FieldExist(&quot;upper_int&quot;)) ifile-&gt;scanField(&quot;upper_int&quot;,dummy);</span></a>
+<a name="2170"><span class="lineNum">    2170 </span><span class="lineCov">       2116 :     ifile-&gt;scanField();</span></a>
+<a name="2171"><span class="lineNum">    2171 </span>            :     return true;</a>
+<a name="2172"><span class="lineNum">    2172 </span>            :   } else {</a>
+<a name="2173"><span class="lineNum">    2173 </span>            :     return false;</a>
+<a name="2174"><span class="lineNum">    2174 </span>            :   }</a>
+<a name="2175"><span class="lineNum">    2175 </span>            : }</a>
+<a name="2176"><span class="lineNum">    2176 </span>            : </a>
+<a name="2177"><span class="lineNum">    2177 </span><span class="lineCov">        102 : void MetaD::computeReweightingFactor()</span></a>
+<a name="2178"><span class="lineNum">    2178 </span>            : {</a>
+<a name="2179"><span class="lineNum">    2179 </span><span class="lineCov">        102 :   if(biasf_==1.0) { // in this case we have no bias, so reweight factor is 0.0</span></a>
+<a name="2180"><span class="lineNum">    2180 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;rct&quot;)-&gt;set(0.0);</span></a>
+<a name="2181"><span class="lineNum">    2181 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="2182"><span class="lineNum">    2182 </span>            :   }</a>
+<a name="2183"><span class="lineNum">    2183 </span>            : </a>
+<a name="2184"><span class="lineNum">    2184 </span><span class="lineCov">        102 :   double Z_0=0; //proportional to the integral of exp(-beta*F)</span></a>
+<a name="2185"><span class="lineNum">    2185 </span><span class="lineCov">        102 :   double Z_V=0; //proportional to the integral of exp(-beta*(F+V))</span></a>
+<a name="2186"><span class="lineNum">    2186 </span><span class="lineCov">        102 :   double minusBetaF=biasf_/(biasf_-1.)/kbt_;</span></a>
+<a name="2187"><span class="lineNum">    2187 </span><span class="lineCov">        102 :   double minusBetaFplusV=1./(biasf_-1.)/kbt_;</span></a>
+<a name="2188"><span class="lineNum">    2188 </span><span class="lineCov">        102 :   if (biasf_==-1.0) { //non well-tempered case</span></a>
+<a name="2189"><span class="lineNum">    2189 </span><span class="lineNoCov">          0 :     minusBetaF=1./kbt_;</span></a>
+<a name="2190"><span class="lineNum">    2190 </span>            :     minusBetaFplusV=0;</a>
+<a name="2191"><span class="lineNum">    2191 </span>            :   }</a>
+<a name="2192"><span class="lineNum">    2192 </span><span class="lineCov">        102 :   max_bias_=BiasGrid_-&gt;getMaxValue(); //to avoid exp overflow</span></a>
+<a name="2193"><span class="lineNum">    2193 </span>            : </a>
+<a name="2194"><span class="lineNum">    2194 </span><span class="lineCov">        102 :   const unsigned rank=comm.Get_rank();</span></a>
+<a name="2195"><span class="lineNum">    2195 </span><span class="lineCov">        102 :   const unsigned stride=comm.Get_size();</span></a>
+<a name="2196"><span class="lineNum">    2196 </span><span class="lineCov">     920504 :   for (Grid::index_t t=rank; t&lt;BiasGrid_-&gt;getSize(); t+=stride) {</span></a>
+<a name="2197"><span class="lineNum">    2197 </span><span class="lineCov">     920402 :     const double val=BiasGrid_-&gt;getValue(t);</span></a>
+<a name="2198"><span class="lineNum">    2198 </span><span class="lineCov">     920402 :     Z_0+=std::exp(minusBetaF*(val-max_bias_));</span></a>
+<a name="2199"><span class="lineNum">    2199 </span><span class="lineCov">     920402 :     Z_V+=std::exp(minusBetaFplusV*(val-max_bias_));</span></a>
+<a name="2200"><span class="lineNum">    2200 </span>            :   }</a>
+<a name="2201"><span class="lineNum">    2201 </span><span class="lineCov">        102 :   comm.Sum(Z_0);</span></a>
+<a name="2202"><span class="lineNum">    2202 </span><span class="lineCov">        102 :   comm.Sum(Z_V);</span></a>
+<a name="2203"><span class="lineNum">    2203 </span>            : </a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineCov">        102 :   reweight_factor_=kbt_*std::log(Z_0/Z_V)+max_bias_;</span></a>
+<a name="2205"><span class="lineNum">    2205 </span><span class="lineCov">        204 :   getPntrToComponent(&quot;rct&quot;)-&gt;set(reweight_factor_);</span></a>
+<a name="2206"><span class="lineNum">    2206 </span>            : }</a>
+<a name="2207"><span class="lineNum">    2207 </span>            : </a>
+<a name="2208"><span class="lineNum">    2208 </span><span class="lineCov">        273 : double MetaD::getTransitionBarrierBias()</span></a>
+<a name="2209"><span class="lineNum">    2209 </span>            : {</a>
+<a name="2210"><span class="lineNum">    2210 </span>            :   // If there is only one well of interest, return the bias at that well point.</a>
+<a name="2211"><span class="lineNum">    2211 </span><span class="lineCov">        273 :   if (transitionwells_.size() == 1) {</span></a>
+<a name="2212"><span class="lineNum">    2212 </span><span class="lineNoCov">          0 :     double tb_bias = getBias(transitionwells_[0]);</span></a>
+<a name="2213"><span class="lineNum">    2213 </span><span class="lineNoCov">          0 :     return tb_bias;</span></a>
+<a name="2214"><span class="lineNum">    2214 </span>            : </a>
+<a name="2215"><span class="lineNum">    2215 </span>            :     // Otherwise, check for the least barrier bias between all pairs of wells.</a>
+<a name="2216"><span class="lineNum">    2216 </span>            :     // Note that because the paths can be considered edges between the wells' nodes</a>
+<a name="2217"><span class="lineNum">    2217 </span>            :     // to make a graph and the path barriers satisfy certain cycle inequalities, it</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :     // is sufficient to look at paths corresponding to a minimal spanning tree of the</a>
+<a name="2219"><span class="lineNum">    2219 </span>            :     // overall graph rather than examining every edge in the graph.</a>
+<a name="2220"><span class="lineNum">    2220 </span>            :     // For simplicity, I chose the star graph with center well 0 as the spanning tree.</a>
+<a name="2221"><span class="lineNum">    2221 </span>            :     // It is most efficient to start the path searches from the wells that are</a>
+<a name="2222"><span class="lineNum">    2222 </span>            :     // expected to be sampled last, so transitionwell_[0] should correspond to the</a>
+<a name="2223"><span class="lineNum">    2223 </span>            :     // starting well. With this choice the searches will terminate in one step until</a>
+<a name="2224"><span class="lineNum">    2224 </span>            :     // transitionwell_[1] is sampled.</a>
+<a name="2225"><span class="lineNum">    2225 </span>            :   } else {</a>
+<a name="2226"><span class="lineNum">    2226 </span>            :     double least_transition_bias;</a>
+<a name="2227"><span class="lineNum">    2227 </span><span class="lineCov">        273 :     std::vector&lt;double&gt; sink = transitionwells_[0];</span></a>
+<a name="2228"><span class="lineNum">    2228 </span><span class="lineCov">        273 :     std::vector&lt;double&gt; source = transitionwells_[1];</span></a>
+<a name="2229"><span class="lineNum">    2229 </span><span class="lineCov">        273 :     least_transition_bias = BiasGrid_-&gt;findMaximalPathMinimum(source, sink);</span></a>
+<a name="2230"><span class="lineNum">    2230 </span><span class="lineCov">        273 :     for (unsigned i = 2; i &lt; transitionwells_.size(); i++) {</span></a>
+<a name="2231"><span class="lineNum">    2231 </span><span class="lineNoCov">          0 :       if (least_transition_bias == 0.0) {</span></a>
+<a name="2232"><span class="lineNum">    2232 </span>            :         break;</a>
+<a name="2233"><span class="lineNum">    2233 </span>            :       }</a>
+<a name="2234"><span class="lineNum">    2234 </span><span class="lineNoCov">          0 :       source = transitionwells_[i];</span></a>
+<a name="2235"><span class="lineNum">    2235 </span><span class="lineNoCov">          0 :       double curr_transition_bias = BiasGrid_-&gt;findMaximalPathMinimum(source, sink);</span></a>
+<a name="2236"><span class="lineNum">    2236 </span><span class="lineNoCov">          0 :       least_transition_bias = fmin(curr_transition_bias, least_transition_bias);</span></a>
+<a name="2237"><span class="lineNum">    2237 </span>            :     }</a>
+<a name="2238"><span class="lineNum">    2238 </span>            :     return least_transition_bias;</a>
+<a name="2239"><span class="lineNum">    2239 </span>            :   }</a>
+<a name="2240"><span class="lineNum">    2240 </span>            : }</a>
+<a name="2241"><span class="lineNum">    2241 </span>            : </a>
+<a name="2242"><span class="lineNum">    2242 </span><span class="lineCov">        154 : void MetaD::updateFrequencyAdaptiveStride()</span></a>
+<a name="2243"><span class="lineNum">    2243 </span>            : {</a>
+<a name="2244"><span class="lineNum">    2244 </span><span class="lineCov">        154 :   plumed_massert(freq_adaptive_,&quot;should only be used if frequency adaptive metadynamics is enabled&quot;);</span></a>
+<a name="2245"><span class="lineNum">    2245 </span><span class="lineCov">        154 :   plumed_massert(acceleration_,&quot;frequency adaptive metadynamics can only be used if the acceleration factor is calculated&quot;);</span></a>
+<a name="2246"><span class="lineNum">    2246 </span><span class="lineCov">        154 :   const double mean_acc = acc_/((double) getStep());</span></a>
+<a name="2247"><span class="lineNum">    2247 </span><span class="lineCov">        154 :   int tmp_stride= stride_*floor((mean_acc/fa_min_acceleration_)+0.5);</span></a>
+<a name="2248"><span class="lineNum">    2248 </span><span class="lineCov">        154 :   if(mean_acc &gt;= fa_min_acceleration_) {</span></a>
+<a name="2249"><span class="lineNum">    2249 </span><span class="lineCov">        129 :     if(tmp_stride &gt; current_stride_) {current_stride_ = tmp_stride;}</span></a>
+<a name="2250"><span class="lineNum">    2250 </span>            :   }</a>
+<a name="2251"><span class="lineNum">    2251 </span><span class="lineCov">        154 :   if(fa_max_stride_!=0 &amp;&amp; current_stride_&gt;fa_max_stride_) {</span></a>
+<a name="2252"><span class="lineNum">    2252 </span><span class="lineNoCov">          0 :     current_stride_=fa_max_stride_;</span></a>
+<a name="2253"><span class="lineNum">    2253 </span>            :   }</a>
+<a name="2254"><span class="lineNum">    2254 </span><span class="lineCov">        154 :   getPntrToComponent(&quot;pace&quot;)-&gt;set(current_stride_);</span></a>
+<a name="2255"><span class="lineNum">    2255 </span><span class="lineCov">        154 : }</span></a>
+<a name="2256"><span class="lineNum">    2256 </span>            : </a>
+<a name="2257"><span class="lineNum">    2257 </span><span class="lineCov">       8435 : bool MetaD::checkNeedsGradients()const</span></a>
+<a name="2258"><span class="lineNum">    2258 </span>            : {</a>
+<a name="2259"><span class="lineNum">    2259 </span><span class="lineCov">       8435 :   if(adaptive_==FlexibleBin::geometry) {</span></a>
+<a name="2260"><span class="lineNum">    2260 </span><span class="lineCov">        192 :     if(getStep()%stride_==0 &amp;&amp; !isFirstStep_) return true;</span></a>
+<a name="2261"><span class="lineNum">    2261 </span><span class="lineCov">        109 :     else return false;</span></a>
+<a name="2262"><span class="lineNum">    2262 </span>            :   } else return false;</a>
+<a name="2263"><span class="lineNum">    2263 </span>            : }</a>
+<a name="2264"><span class="lineNum">    2264 </span>            : </a>
+<a name="2265"><span class="lineNum">    2265 </span><span class="lineCov">          4 : void MetaD::updateNlist()</span></a>
+<a name="2266"><span class="lineNum">    2266 </span>            : {</a>
+<a name="2267"><span class="lineNum">    2267 </span>            :   // no need to check for neighbors</a>
+<a name="2268"><span class="lineNum">    2268 </span><span class="lineCov">          4 :   if(hills_.size()==0) return;</span></a>
+<a name="2269"><span class="lineNum">    2269 </span>            : </a>
+<a name="2270"><span class="lineNum">    2270 </span>            :   // here we generate the neighbor list</a>
+<a name="2271"><span class="lineNum">    2271 </span><span class="lineCov">          4 :   nlist_hills_.clear();</span></a>
+<a name="2272"><span class="lineNum">    2272 </span>            :   std::vector&lt;Gaussian&gt; local_flat_nl;</a>
+<a name="2273"><span class="lineNum">    2273 </span><span class="lineCov">          4 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="2274"><span class="lineNum">    2274 </span><span class="lineCov">          4 :   if(hills_.size()&lt;2*nt) nt=1;</span></a>
+<a name="2275"><span class="lineNum">    2275 </span><span class="lineCov">          4 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="2276"><span class="lineNum">    2276 </span>            :   {</a>
+<a name="2277"><span class="lineNum">    2277 </span>            :     std::vector&lt;Gaussian&gt; private_flat_nl;</a>
+<a name="2278"><span class="lineNum">    2278 </span>            :     #pragma omp for nowait</a>
+<a name="2279"><span class="lineNum">    2279 </span>            :     for(unsigned k=0; k&lt;hills_.size(); k++)</a>
+<a name="2280"><span class="lineNum">    2280 </span>            :     {</a>
+<a name="2281"><span class="lineNum">    2281 </span>            :       double dist2=0;</a>
+<a name="2282"><span class="lineNum">    2282 </span>            :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++)</a>
+<a name="2283"><span class="lineNum">    2283 </span>            :       {</a>
+<a name="2284"><span class="lineNum">    2284 </span>            :         const double d=difference(i,getArgument(i),hills_[k].center[i])/hills_[k].sigma[i];</a>
+<a name="2285"><span class="lineNum">    2285 </span>            :         dist2+=d*d;</a>
+<a name="2286"><span class="lineNum">    2286 </span>            :       }</a>
+<a name="2287"><span class="lineNum">    2287 </span>            :       if(dist2&lt;=nlist_param_[0]*dp2cutoff) private_flat_nl.push_back(hills_[k]);</a>
+<a name="2288"><span class="lineNum">    2288 </span>            :     }</a>
+<a name="2289"><span class="lineNum">    2289 </span>            :     #pragma omp critical</a>
+<a name="2290"><span class="lineNum">    2290 </span>            :     local_flat_nl.insert(local_flat_nl.end(), private_flat_nl.begin(), private_flat_nl.end());</a>
+<a name="2291"><span class="lineNum">    2291 </span>            :   }</a>
+<a name="2292"><span class="lineNum">    2292 </span><span class="lineCov">          4 :   nlist_hills_ = local_flat_nl;</span></a>
+<a name="2293"><span class="lineNum">    2293 </span>            : </a>
+<a name="2294"><span class="lineNum">    2294 </span>            :   // here we set some properties that are used to decide when to update it again</a>
+<a name="2295"><span class="lineNum">    2295 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) nlist_center_[i]=getArgument(i);</span></a>
+<a name="2296"><span class="lineNum">    2296 </span>            :   std::vector&lt;double&gt; dev2;</a>
+<a name="2297"><span class="lineNum">    2297 </span><span class="lineCov">          4 :   dev2.resize(getNumberOfArguments(),0);</span></a>
+<a name="2298"><span class="lineNum">    2298 </span><span class="lineCov">         46 :   for(unsigned k=0; k&lt;nlist_hills_.size(); k++)</span></a>
+<a name="2299"><span class="lineNum">    2299 </span>            :   {</a>
+<a name="2300"><span class="lineNum">    2300 </span><span class="lineCov">        126 :     for(unsigned i=0; i&lt;getNumberOfArguments(); i++)</span></a>
+<a name="2301"><span class="lineNum">    2301 </span>            :     {</a>
+<a name="2302"><span class="lineNum">    2302 </span><span class="lineCov">         84 :       const double d=difference(i,getArgument(i),nlist_hills_[k].center[i]);</span></a>
+<a name="2303"><span class="lineNum">    2303 </span><span class="lineCov">         84 :       dev2[i]+=d*d;</span></a>
+<a name="2304"><span class="lineNum">    2304 </span>            :     }</a>
+<a name="2305"><span class="lineNum">    2305 </span>            :   }</a>
+<a name="2306"><span class="lineNum">    2306 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="2307"><span class="lineNum">    2307 </span><span class="lineCov">          8 :     if(dev2[i]&gt;0.) nlist_dev2_[i]=dev2[i]/static_cast&lt;double&gt;(nlist_hills_.size());</span></a>
+<a name="2308"><span class="lineNum">    2308 </span><span class="lineNoCov">          0 :     else nlist_dev2_[i]=hills_.back().sigma[i]*hills_.back().sigma[i];</span></a>
+<a name="2309"><span class="lineNum">    2309 </span>            :   }</a>
+<a name="2310"><span class="lineNum">    2310 </span>            : </a>
+<a name="2311"><span class="lineNum">    2311 </span>            :   // we are done</a>
+<a name="2312"><span class="lineNum">    2312 </span><span class="lineCov">          4 :   getPntrToComponent(&quot;nlker&quot;)-&gt;set(nlist_hills_.size());</span></a>
+<a name="2313"><span class="lineNum">    2313 </span><span class="lineCov">          4 :   getPntrToComponent(&quot;nlsteps&quot;)-&gt;set(nlist_steps_);</span></a>
+<a name="2314"><span class="lineNum">    2314 </span><span class="lineCov">          4 :   nlist_steps_=0;</span></a>
+<a name="2315"><span class="lineNum">    2315 </span><span class="lineCov">          4 :   nlist_update_=false;</span></a>
+<a name="2316"><span class="lineNum">    2316 </span><span class="lineCov">          4 : }</span></a>
+<a name="2317"><span class="lineNum">    2317 </span>            : </a>
+<a name="2318"><span class="lineNum">    2318 </span>            : }</a>
+<a name="2319"><span class="lineNum">    2319 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MovingRestraint.cpp.func-sort-c.html b/coverage/bias/MovingRestraint.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d1504b1ca8
--- /dev/null
+++ b/coverage/bias/MovingRestraint.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MovingRestraint.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MovingRestraint.cpp<span style="font-size: 80%;"> (<a href="MovingRestraint.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MovingRestraint.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#148">_ZN4PLMD4bias15MovingRestraintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#115">_ZN4PLMD4bias12_GLOBAL__N_128MovingRestraintRegisterMe1176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#148">_ZN4PLMD4bias15MovingRestraintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#117">_ZN4PLMD4bias15MovingRestraint16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#206">_ZN4PLMD4bias15MovingRestraint9calculateEv</a></td>
+              <td class="coverFnHi">566</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#115">_ZN4PLMD4bias12_GLOBAL__N_128MovingRestraintRegisterMe117C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#115">_ZN4PLMD4bias12_GLOBAL__N_128MovingRestraintRegisterMe117D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/MovingRestraint.cpp.func.html b/coverage/bias/MovingRestraint.cpp.func.html
new file mode 100644
index 0000000000..7eea19f53a
--- /dev/null
+++ b/coverage/bias/MovingRestraint.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MovingRestraint.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MovingRestraint.cpp<span style="font-size: 80%;"> (<a href="MovingRestraint.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MovingRestraint.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#115">_ZN4PLMD4bias12_GLOBAL__N_128MovingRestraintRegisterMe1176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#115">_ZN4PLMD4bias12_GLOBAL__N_128MovingRestraintRegisterMe117C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#115">_ZN4PLMD4bias12_GLOBAL__N_128MovingRestraintRegisterMe117D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#117">_ZN4PLMD4bias15MovingRestraint16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#206">_ZN4PLMD4bias15MovingRestraint9calculateEv</a></td>
+              <td class="coverFnHi">566</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#148">_ZN4PLMD4bias15MovingRestraintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MovingRestraint.cpp.gcov.html#148">_ZN4PLMD4bias15MovingRestraintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+</html>
diff --git a/coverage/bias/MovingRestraint.cpp.gcov.html b/coverage/bias/MovingRestraint.cpp.gcov.html
new file mode 100644
index 0000000000..0daa3b19a1
--- /dev/null
+++ b/coverage/bias/MovingRestraint.cpp.gcov.html
@@ -0,0 +1,342 @@
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/MovingRestraint.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - MovingRestraint.cpp<span style="font-size: 80%;"> (source / <a href="MovingRestraint.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace bias {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC BIAS MOVINGRESTRAINT</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Add a time-dependent, harmonic restraint on one or more variables.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This form of bias can be used to performed steered MD \cite Grubmuller3</a>
+<a name="33"><span class="lineNum">      33 </span>            : and Jarzynski sampling \cite jarzynski.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The harmonic restraint on your system is given by:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : V(\vec{s},t) = \frac{1}{2} \kappa(t) ( \vec{s} - \vec{s}_0(t) )^2</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The time dependence of \f$\kappa\f$ and \f$\vec{s}_0\f$ are specified by a list of</a>
+<a name="42"><span class="lineNum">      42 </span>            : STEP, KAPPA and AT keywords.  These keywords tell plumed what values \f$\kappa\f$ and \f$\vec{s}_0\f$</a>
+<a name="43"><span class="lineNum">      43 </span>            : should have at the time specified by the corresponding STEP keyword.  In between these times</a>
+<a name="44"><span class="lineNum">      44 </span>            : the values of \f$\kappa\f$ and \f$\vec{s}_0\f$ are linearly interpolated.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : Additional material and examples can be also found in the tutorial \ref belfast-5</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \par Examples</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The following input is dragging the distance between atoms 2 and 4</a>
+<a name="51"><span class="lineNum">      51 </span>            : from 1 to 2 in the first 1000 steps, then back in the next 1000 steps.</a>
+<a name="52"><span class="lineNum">      52 </span>            : In the following 500 steps the restraint is progressively switched off.</a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : DISTANCE ATOMS=2,4 LABEL=d</a>
+<a name="55"><span class="lineNum">      55 </span>            : MOVINGRESTRAINT ...</a>
+<a name="56"><span class="lineNum">      56 </span>            :   ARG=d</a>
+<a name="57"><span class="lineNum">      57 </span>            :   STEP0=0    AT0=1.0 KAPPA0=100.0</a>
+<a name="58"><span class="lineNum">      58 </span>            :   STEP1=1000 AT1=2.0</a>
+<a name="59"><span class="lineNum">      59 </span>            :   STEP2=2000 AT2=1.0</a>
+<a name="60"><span class="lineNum">      60 </span>            :   STEP3=2500         KAPPA3=0.0</a>
+<a name="61"><span class="lineNum">      61 </span>            : ... MOVINGRESTRAINT</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : The following input is progressively building restraints</a>
+<a name="64"><span class="lineNum">      64 </span>            : distances between atoms 1 and 5 and between atoms 2 and 4</a>
+<a name="65"><span class="lineNum">      65 </span>            : in the first 1000 steps. Afterwards, the restraint is kept</a>
+<a name="66"><span class="lineNum">      66 </span>            : static.</a>
+<a name="67"><span class="lineNum">      67 </span>            : \plumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : DISTANCE ATOMS=1,5 LABEL=d1</a>
+<a name="69"><span class="lineNum">      69 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="70"><span class="lineNum">      70 </span>            : MOVINGRESTRAINT ...</a>
+<a name="71"><span class="lineNum">      71 </span>            :   ARG=d1,d2</a>
+<a name="72"><span class="lineNum">      72 </span>            :   STEP0=0    AT0=1.0,1.5 KAPPA0=0.0,0.0</a>
+<a name="73"><span class="lineNum">      73 </span>            :   STEP1=1000 AT1=1.0,1.5 KAPPA1=1.0,1.0</a>
+<a name="74"><span class="lineNum">      74 </span>            : ... MOVINGRESTRAINT</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : The following input is progressively bringing atoms 1 and 2</a>
+<a name="77"><span class="lineNum">      77 </span>            : close to each other with an upper wall</a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : DISTANCE ATOMS=1,2 LABEL=d1</a>
+<a name="80"><span class="lineNum">      80 </span>            : MOVINGRESTRAINT ...</a>
+<a name="81"><span class="lineNum">      81 </span>            :   ARG=d1</a>
+<a name="82"><span class="lineNum">      82 </span>            :   VERSE=U</a>
+<a name="83"><span class="lineNum">      83 </span>            :   STEP0=0    AT0=1.0 KAPPA0=10.0</a>
+<a name="84"><span class="lineNum">      84 </span>            :   STEP1=1000 AT1=0.0</a>
+<a name="85"><span class="lineNum">      85 </span>            : ... MOVINGRESTRAINT</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endplumedfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : By default the Action is issuing some values which are</a>
+<a name="89"><span class="lineNum">      89 </span>            : the work on each degree of freedom, the center of the harmonic potential,</a>
+<a name="90"><span class="lineNum">      90 </span>            : the total bias deposited</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : (See also \ref DISTANCE).</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : \attention Work is not computed properly when KAPPA is time dependent.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : */</a>
+<a name="97"><span class="lineNum">      97 </span>            : //+ENDPLUMEDOC</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : class MovingRestraint : public Bias {</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; at;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; kappa;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;long long int&gt; step;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;double&gt; oldaa;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;double&gt; oldk;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;double&gt; olddpotdk;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;double&gt; oldf;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt;std::string&gt; verse;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;double&gt; work;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double tot_work;</a>
+<a name="111"><span class="lineNum">     111 </span>            : public:</a>
+<a name="112"><span class="lineNum">     112 </span>            :   explicit MovingRestraint(const ActionOptions&amp;);</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void calculate() override;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="115"><span class="lineNum">     115 </span>            : };</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(MovingRestraint,&quot;MOVINGRESTRAINT&quot;)</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 : void MovingRestraint::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          6 :   Bias::registerKeywords(keys);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;VERSE&quot;,&quot;B&quot;,&quot;Tells plumed whether the restraint is only acting for CV larger (U) or smaller (L) than &quot;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :            &quot;the restraint or whether it is acting on both sides (B)&quot;);</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;STEP&quot;,&quot;This keyword appears multiple times as STEP\\f$x\\f$ with x=0,1,2,...,n. Each value given represents &quot;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :            &quot;the MD step at which the restraint parameters take the values KAPPA\\f$x\\f$ and AT\\f$x\\f$.&quot;);</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         12 :   keys.reset_style(&quot;STEP&quot;,&quot;compulsory&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;AT&quot;,&quot;AT\\f$x\\f$ is equal to the position of the restraint at time STEP\\f$x\\f$. For intermediate times this parameter &quot;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :            &quot;is linearly interpolated. If no AT\\f$x\\f$ is specified for STEP\\f$x\\f$ then the values of AT are kept constant &quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;during the interval of time between STEP\\f$x-1\\f$ and STEP\\f$x\\f$.&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         12 :   keys.reset_style(&quot;AT&quot;,&quot;compulsory&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;KAPPA&quot;,&quot;KAPPA\\f$x\\f$ is equal to the value of the force constants at time STEP\\f$x\\f$. For intermediate times this &quot;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :            &quot;parameter is linearly interpolated.  If no KAPPA\\f$x\\f$ is specified for STEP\\f$x\\f$ then the values of KAPPA\\f$x\\f$ &quot;</a>
+<a name="133"><span class="lineNum">     133 </span>            :            &quot;are kept constant during the interval of time between STEP\\f$x-1\\f$ and STEP\\f$x\\f$.&quot;);</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         12 :   keys.reset_style(&quot;KAPPA&quot;,&quot;compulsory&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;work&quot;,&quot;default&quot;,&quot;the total work performed changing this restraint&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;_cntr&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :                           &quot;these quantities will named with  the arguments of the bias followed by &quot;</a>
+<a name="139"><span class="lineNum">     139 </span>            :                           &quot;the character string _cntr. These quantities give the instantaneous position &quot;</a>
+<a name="140"><span class="lineNum">     140 </span>            :                           &quot;of the center of the harmonic potential.&quot;);</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;_work&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :                           &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="143"><span class="lineNum">     143 </span>            :                           &quot;the character string _work. These quantities tell the user how much work has &quot;</a>
+<a name="144"><span class="lineNum">     144 </span>            :                           &quot;been done by the potential in dragging the system along the various colvar axis.&quot;);</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;_kappa&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere in the input file. &quot;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :                           &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="147"><span class="lineNum">     147 </span>            :                           &quot;the character string _kappa. These quantities tell the user the time dependent value of kappa.&quot;);</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          6 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          4 : MovingRestraint::MovingRestraint(const ActionOptions&amp;ao):</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   verse(getNumberOfArguments())</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : {</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :   parseVector(&quot;VERSE&quot;,verse);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          4 :   std::vector&lt;long long int&gt; ss(1); ss[0]=-1;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; kk( getNumberOfArguments() ), aa( getNumberOfArguments() );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         10 :   for(int i=0;; i++) {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :     // Read in step</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         28 :     if( !parseNumberedVector(&quot;STEP&quot;,i,ss) ) break;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         19 :     for(unsigned j=0; j&lt;step.size(); j++) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          9 :       if(ss[0]&lt;step[j]) error(&quot;in moving restraint step number must always increase&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     }</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         10 :     step.push_back(ss[0]);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            :     // Try to read kappa</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         20 :     if( !parseNumberedVector(&quot;KAPPA&quot;,i,kk) ) kk=kappa[i-1];</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         10 :     kappa.push_back(kk);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :     // Now read AT</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         20 :     if( !parseNumberedVector(&quot;AT&quot;,i,aa) ) aa=at[i-1];</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         10 :     at.push_back(aa);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         10 :   }</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         14 :   for(unsigned i=0; i&lt;step.size(); i++) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         10 :     log.printf(&quot;  step%u %lld\n&quot;,i,step[i]);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         10 :     log.printf(&quot;  at&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         22 :     for(unsigned j=0; j&lt;at[i].size(); j++) log.printf(&quot; %f&quot;,at[i][j]);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         10 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         10 :     log.printf(&quot;  with force constant&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         22 :     for(unsigned j=0; j&lt;kappa[i].size(); j++) log.printf(&quot; %f&quot;,kappa[i][j]);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         10 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   };</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         12 :   addComponent(&quot;force2&quot;); componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   // add the centers of the restraint as additional components that can be retrieved (useful for debug)</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::string comp;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          9 :   for(unsigned i=0; i&lt; getNumberOfArguments() ; i++) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          5 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_cntr&quot;; // each spring has its own center</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          5 :     addComponent(comp); componentIsNotPeriodic(comp);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          5 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_work&quot;; // each spring has its own work</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          5 :     addComponent(comp); componentIsNotPeriodic(comp);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          5 :     comp=getPntrToArgument(i)-&gt;getName()+&quot;_kappa&quot;; // each spring has its own kappa</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          5 :     addComponent(comp); componentIsNotPeriodic(comp);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          5 :     work.push_back(0.); // initialize the work value</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          8 :   addComponent(&quot;work&quot;); componentIsNotPeriodic(&quot;work&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          4 :   tot_work=0.0;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 :   log&lt;&lt;&quot;  Bibliography &quot;;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          8 :   log&lt;&lt;cite(&quot;Grubmuller, Heymann, and Tavan, Science 271, 997 (1996)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          4 : }</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        566 : void MovingRestraint::calculate() {</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   double ene=0.0;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   double totf2=0.0;</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        566 :   unsigned narg=getNumberOfArguments();</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        566 :   long long int now=getStep();</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        566 :   std::vector&lt;double&gt; kk(narg),aa(narg),f(narg),dpotdk(narg);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        566 :   if(now&lt;=step[0]) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          3 :     kk=kappa[0];</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          3 :     aa=at[0];</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          3 :     oldaa=at[0];</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          3 :     oldk=kappa[0];</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          3 :     olddpotdk.resize(narg);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          3 :     oldf.resize(narg);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        563 :   } else if(now&gt;=step[step.size()-1]) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         47 :     kk=kappa[step.size()-1];</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         47 :     aa=at[step.size()-1];</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   } else {</a>
+<a name="225"><span class="lineNum">     225 </span>            :     unsigned i=0;</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        521 :     for(i=1; i&lt;step.size()-1; i++) if(now&lt;step[i]) break;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        516 :     double c2=(now-step[i-1])/double(step[i]-step[i-1]);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        516 :     double c1=1.0-c2;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       1040 :     for(unsigned j=0; j&lt;narg; j++) kk[j]=(c1*kappa[i-1][j]+c2*kappa[i][j]);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       1040 :     for(unsigned j=0; j&lt;narg; j++) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        524 :       const double a1=at[i-1][j];</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        524 :       const double a2=at[i][j];</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        524 :       aa[j]=(c1*a1+c2*(a1+difference(j,a1,a2)));</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     }</a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        566 :   tot_work=0.0;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       1142 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        576 :     const double cv=difference(i,aa[i],getArgument(i)); // this gives: getArgument(i) - aa[i]</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       1152 :     getPntrToComponent(getPntrToArgument(i)-&gt;getName()+&quot;_cntr&quot;)-&gt;set(aa[i]);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        576 :     const double k=kk[i];</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        576 :     f[i]=-k*cv;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        576 :     if(verse[i]==&quot;U&quot; &amp;&amp; cv&lt;0) continue;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        576 :     if(verse[i]==&quot;L&quot; &amp;&amp; cv&gt;0) continue;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">       1728 :     plumed_assert(verse[i]==&quot;U&quot; || verse[i]==&quot;L&quot; || verse[i]==&quot;B&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        576 :     dpotdk[i]=0.5*cv*cv;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        576 :     if(oldaa.size()==aa.size() &amp;&amp; oldf.size()==f.size()) work[i]+=0.5*(oldf[i]+f[i])*(aa[i]-oldaa[i]) + 0.5*( dpotdk[i]+olddpotdk[i] )*(kk[i]-oldk[i]);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       1152 :     getPntrToComponent(getPntrToArgument(i)-&gt;getName()+&quot;_work&quot;)-&gt;set(work[i]);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       1152 :     getPntrToComponent(getPntrToArgument(i)-&gt;getName()+&quot;_kappa&quot;)-&gt;set(kk[i]);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        576 :     tot_work+=work[i];</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        576 :     ene+=0.5*k*cv*cv;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        576 :     setOutputForce(i,f[i]);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        576 :     totf2+=f[i]*f[i];</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   };</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        566 :   getPntrToComponent(&quot;work&quot;)-&gt;set(tot_work);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        566 :   oldf=f;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        566 :   oldaa=aa;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        566 :   oldk=kk;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        566 :   olddpotdk=dpotdk;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   setBias(ene);</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       1132 :   getPntrToComponent(&quot;force2&quot;)-&gt;set(totf2);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        566 : }</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/PBMetaD.cpp.func-sort-c.html b/coverage/bias/PBMetaD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c164f25dbf
--- /dev/null
+++ b/coverage/bias/PBMetaD.cpp.func-sort-c.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/PBMetaD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - PBMetaD.cpp<span style="font-size: 80%;"> (<a href="PBMetaD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">570</td>
+            <td class="headerCovTableEntry">646</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PBMetaD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#307">_ZN4PLMD4bias7PBMetaD16noStretchWarningEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#370">_ZN4PLMD4bias7PBMetaDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#894">_ZN4PLMD4bias7PBMetaD13readGaussiansEjPNS_5IFileE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1257">_ZN4PLMD4bias7PBMetaD11scanOneHillEjPNS_5IFileERSt6vectorINS_5ValueESaIS5_EERS4_IdSaIdEESB_RdRb</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#330">_ZN4PLMD4bias12_GLOBAL__N_120PBMetaDRegisterMe3326createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">41</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#370">_ZN4PLMD4bias7PBMetaDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">41</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#332">_ZN4PLMD4bias7PBMetaD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">43</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#976">_ZN4PLMD4bias7PBMetaD18getGaussianSupportEjRKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">196</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1112">_ZN4PLMD4bias7PBMetaD6updateEv</a></td>
+              <td class="coverFnHi">335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1068">_ZN4PLMD4bias7PBMetaD9calculateEv</a></td>
+              <td class="coverFnHi">335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1308">_ZNK4PLMD4bias7PBMetaD19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#915">_ZN4PLMD4bias7PBMetaD13writeGaussianEjRKNS1_8GaussianEPNS_5OFileE</a></td>
+              <td class="coverFnHi">1100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#939">_ZN4PLMD4bias7PBMetaD11addGaussianEjRKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">1108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#245">_ZN4PLMD4bias7PBMetaD8GaussianC2ERKSt6vectorIdSaIdEES7_db</a></td>
+              <td class="coverFnHi">1108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1002">_ZN4PLMD4bias7PBMetaD21getBiasAndDerivativesEjRKSt6vectorIdSaIdEEPd</a></td>
+              <td class="coverFnHi">1269</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#330">_ZN4PLMD4bias12_GLOBAL__N_120PBMetaDRegisterMe332C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#330">_ZN4PLMD4bias12_GLOBAL__N_120PBMetaDRegisterMe332D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1027">_ZN4PLMD4bias7PBMetaD16evaluateGaussianEjRKSt6vectorIdSaIdEERKNS1_8GaussianEPd</a></td>
+              <td class="coverFnHi">8664</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/PBMetaD.cpp.func.html b/coverage/bias/PBMetaD.cpp.func.html
new file mode 100644
index 0000000000..7377c11247
--- /dev/null
+++ b/coverage/bias/PBMetaD.cpp.func.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/PBMetaD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - PBMetaD.cpp<span style="font-size: 80%;"> (<a href="PBMetaD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">570</td>
+            <td class="headerCovTableEntry">646</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PBMetaD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#330">_ZN4PLMD4bias12_GLOBAL__N_120PBMetaDRegisterMe3326createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">41</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#330">_ZN4PLMD4bias12_GLOBAL__N_120PBMetaDRegisterMe332C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#330">_ZN4PLMD4bias12_GLOBAL__N_120PBMetaDRegisterMe332D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#939">_ZN4PLMD4bias7PBMetaD11addGaussianEjRKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">1108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1257">_ZN4PLMD4bias7PBMetaD11scanOneHillEjPNS_5IFileERSt6vectorINS_5ValueESaIS5_EERS4_IdSaIdEESB_RdRb</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#894">_ZN4PLMD4bias7PBMetaD13readGaussiansEjPNS_5IFileE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#915">_ZN4PLMD4bias7PBMetaD13writeGaussianEjRKNS1_8GaussianEPNS_5OFileE</a></td>
+              <td class="coverFnHi">1100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1027">_ZN4PLMD4bias7PBMetaD16evaluateGaussianEjRKSt6vectorIdSaIdEERKNS1_8GaussianEPd</a></td>
+              <td class="coverFnHi">8664</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#307">_ZN4PLMD4bias7PBMetaD16noStretchWarningEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#332">_ZN4PLMD4bias7PBMetaD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">43</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#976">_ZN4PLMD4bias7PBMetaD18getGaussianSupportEjRKNS1_8GaussianE</a></td>
+              <td class="coverFnHi">196</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1002">_ZN4PLMD4bias7PBMetaD21getBiasAndDerivativesEjRKSt6vectorIdSaIdEEPd</a></td>
+              <td class="coverFnHi">1269</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1112">_ZN4PLMD4bias7PBMetaD6updateEv</a></td>
+              <td class="coverFnHi">335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#245">_ZN4PLMD4bias7PBMetaD8GaussianC2ERKSt6vectorIdSaIdEES7_db</a></td>
+              <td class="coverFnHi">1108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1068">_ZN4PLMD4bias7PBMetaD9calculateEv</a></td>
+              <td class="coverFnHi">335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#370">_ZN4PLMD4bias7PBMetaDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">41</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#370">_ZN4PLMD4bias7PBMetaDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PBMetaD.cpp.gcov.html#1308">_ZNK4PLMD4bias7PBMetaD19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">335</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/PBMetaD.cpp.gcov.html b/coverage/bias/PBMetaD.cpp.gcov.html
new file mode 100644
index 0000000000..d58476cea7
--- /dev/null
+++ b/coverage/bias/PBMetaD.cpp.gcov.html
@@ -0,0 +1,1396 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/PBMetaD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - PBMetaD.cpp<span style="font-size: 80%;"> (source / <a href="PBMetaD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">570</td>
+            <td class="headerCovTableEntry">646</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/FlexibleBin.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;ctime&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;numeric&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #if defined(__PLUMED_HAS_GETCWD)</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;unistd.h&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #endif</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace bias {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : //+PLUMEDOC BIAS PBMETAD</a>
+<a name="44"><span class="lineNum">      44 </span>            : /*</a>
+<a name="45"><span class="lineNum">      45 </span>            : Used to performed Parallel Bias metadynamics.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : This action activate Parallel Bias Metadynamics (PBMetaD) \cite pbmetad, a version of metadynamics \cite metad in which</a>
+<a name="48"><span class="lineNum">      48 </span>            : multiple low-dimensional bias potentials are applied in parallel.</a>
+<a name="49"><span class="lineNum">      49 </span>            : In the current implementation, these have the form of mono-dimensional metadynamics bias</a>
+<a name="50"><span class="lineNum">      50 </span>            : potentials:</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \f[</a>
+<a name="53"><span class="lineNum">      53 </span>            : {V(s_1,t), ..., V(s_N,t)}</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f]</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : where:</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \f[</a>
+<a name="59"><span class="lineNum">      59 </span>            : V(s_i,t) = \sum_{ k \tau &lt; t} W_i(k \tau)</a>
+<a name="60"><span class="lineNum">      60 </span>            : \exp\left(</a>
+<a name="61"><span class="lineNum">      61 </span>            : - \frac{(s_i-s_i^{(0)}(k \tau))^2}{2\sigma_i^2}</a>
+<a name="62"><span class="lineNum">      62 </span>            : \right).</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f]</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : To ensure the convergence of each mono-dimensional bias potential to the corresponding free energy,</a>
+<a name="66"><span class="lineNum">      66 </span>            : at each deposition step the Gaussian heights are multiplied by the so-called conditional term:</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \f[</a>
+<a name="69"><span class="lineNum">      69 </span>            : W_i(k \tau)=W_0 \frac{\exp\left(</a>
+<a name="70"><span class="lineNum">      70 </span>            : - \frac{V(s_i,k \tau)}{k_B T}</a>
+<a name="71"><span class="lineNum">      71 </span>            : \right)}{\sum_{i=1}^N</a>
+<a name="72"><span class="lineNum">      72 </span>            : \exp\left(</a>
+<a name="73"><span class="lineNum">      73 </span>            : - \frac{V(s_i,k \tau)}{k_B T}</a>
+<a name="74"><span class="lineNum">      74 </span>            : \right)}</a>
+<a name="75"><span class="lineNum">      75 </span>            : \f]</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : where \f$W_0\f$ is the initial Gaussian height.</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : The PBMetaD bias potential is defined by:</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \f[</a>
+<a name="82"><span class="lineNum">      82 </span>            : V_{PB}(\vec{s},t) = -k_B T \log{\sum_{i=1}^N</a>
+<a name="83"><span class="lineNum">      83 </span>            : \exp\left(</a>
+<a name="84"><span class="lineNum">      84 </span>            : - \frac{V(s_i,t)}{k_B T}</a>
+<a name="85"><span class="lineNum">      85 </span>            : \right)}.</a>
+<a name="86"><span class="lineNum">      86 </span>            : \f]</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : Information on the Gaussian functions that build each bias potential are printed to</a>
+<a name="90"><span class="lineNum">      90 </span>            : multiple HILLS files, which</a>
+<a name="91"><span class="lineNum">      91 </span>            : are used both to restart the calculation and to reconstruct the mono-dimensional</a>
+<a name="92"><span class="lineNum">      92 </span>            : free energies as a function of the corresponding CVs.</a>
+<a name="93"><span class="lineNum">      93 </span>            : These can be reconstructed using the \ref sum_hills utility because the final bias is given</a>
+<a name="94"><span class="lineNum">      94 </span>            : by:</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \f[</a>
+<a name="97"><span class="lineNum">      97 </span>            : V(s_i) = -F(s_i)</a>
+<a name="98"><span class="lineNum">      98 </span>            : \f]</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : Currently, only a subset of the \ref METAD options are available in PBMetaD.</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : The bias potentials can be stored on a grid to increase performances of long PBMetaD simulations.</a>
+<a name="103"><span class="lineNum">     103 </span>            : You should</a>
+<a name="104"><span class="lineNum">     104 </span>            : provide either the number of bins for every collective variable (GRID_BIN) or</a>
+<a name="105"><span class="lineNum">     105 </span>            : the desired grid spacing (GRID_SPACING). In case you provide both PLUMED will use</a>
+<a name="106"><span class="lineNum">     106 </span>            : the most conservative choice (highest number of bins) for each dimension.</a>
+<a name="107"><span class="lineNum">     107 </span>            : In case you do not provide any information about bin size (neither GRID_BIN nor GRID_SPACING)</a>
+<a name="108"><span class="lineNum">     108 </span>            : and if Gaussian width is fixed PLUMED will use 1/5 of the Gaussian width as grid spacing.</a>
+<a name="109"><span class="lineNum">     109 </span>            : This default choice should be reasonable for most applications.</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : Another option that is available is well-tempered metadynamics \cite Barducci:2008. In this</a>
+<a name="112"><span class="lineNum">     112 </span>            : variant of PBMetaD the heights of the Gaussian hills are scaled at each step by the</a>
+<a name="113"><span class="lineNum">     113 </span>            : additional well-tempered metadynamics term.</a>
+<a name="114"><span class="lineNum">     114 </span>            : This  ensures that each bias converges more smoothly. It should be noted that, in the case of well-tempered metadynamics, in</a>
+<a name="115"><span class="lineNum">     115 </span>            : the output printed the Gaussian height is re-scaled using the bias factor.</a>
+<a name="116"><span class="lineNum">     116 </span>            : Also notice that with well-tempered metadynamics the HILLS files do not contain the bias,</a>
+<a name="117"><span class="lineNum">     117 </span>            : but the negative of the free-energy estimate. This choice has the advantage that</a>
+<a name="118"><span class="lineNum">     118 </span>            : one can restart a simulation using a different value for the \f$\Delta T\f$. The applied bias will be scaled accordingly.</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : Note that you can use here also the flexible Gaussian approach  \cite Branduardi:2012dl</a>
+<a name="121"><span class="lineNum">     121 </span>            : in which you can adapt the Gaussian to the extent of Cartesian space covered by a variable or</a>
+<a name="122"><span class="lineNum">     122 </span>            : to the space in collective variable covered in a given time. In this case the width of the deposited</a>
+<a name="123"><span class="lineNum">     123 </span>            : Gaussian potential is denoted by one value only that is a Cartesian space (ADAPTIVE=GEOM) or a time</a>
+<a name="124"><span class="lineNum">     124 </span>            : (ADAPTIVE=DIFF). Note that a specific integration technique for the deposited Gaussian kernels</a>
+<a name="125"><span class="lineNum">     125 </span>            : should be used in this case. Check the documentation for utility sum_hills.</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : With the keyword INTERVAL one changes the metadynamics algorithm setting the bias force equal to zero</a>
+<a name="128"><span class="lineNum">     128 </span>            : outside boundary \cite baftizadeh2012protein. If, for example, metadynamics is performed on a CV s and one is interested only</a>
+<a name="129"><span class="lineNum">     129 </span>            : to the free energy for s &gt; boundary, the history dependent potential is still updated according to the above</a>
+<a name="130"><span class="lineNum">     130 </span>            : equations but the metadynamics force is set to zero for s &lt; boundary. Notice that Gaussian kernels are added also</a>
+<a name="131"><span class="lineNum">     131 </span>            : if s &lt; boundary, as the tails of these Gaussian kernels influence VG in the relevant region s &gt; boundary. In this way, the</a>
+<a name="132"><span class="lineNum">     132 </span>            : force on the system in the region s &gt; boundary comes from both metadynamics and the force field, in the region</a>
+<a name="133"><span class="lineNum">     133 </span>            : s &lt; boundary only from the latter. This approach allows obtaining a history-dependent bias potential VG that</a>
+<a name="134"><span class="lineNum">     134 </span>            : fluctuates around a stable estimator, equal to the negative of the free energy far enough from the</a>
+<a name="135"><span class="lineNum">     135 </span>            : boundaries. Note that:</a>
+<a name="136"><span class="lineNum">     136 </span>            : - It works only for one-dimensional biases;</a>
+<a name="137"><span class="lineNum">     137 </span>            : - It works both with and without GRID;</a>
+<a name="138"><span class="lineNum">     138 </span>            : - The interval limit boundary in a region where the free energy derivative is not large;</a>
+<a name="139"><span class="lineNum">     139 </span>            : - If in the region outside the limit boundary the system has a free energy minimum, the INTERVAL keyword should</a>
+<a name="140"><span class="lineNum">     140 </span>            :   be used together with a \ref UPPER_WALLS or \ref LOWER_WALLS at boundary.</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : For systems with multiple CVs that share identical properties, PBMetaD with partitioned families can be used</a>
+<a name="143"><span class="lineNum">     143 </span>            : to group them under one bias potential that each contributes to \cite Prakash2018PF. This is done with a list</a>
+<a name="144"><span class="lineNum">     144 </span>            : of PF keywords, where each PF* argument contains the list of CVs from ARG to be placed in that family. Once</a>
+<a name="145"><span class="lineNum">     145 </span>            : invoked, each CV in ARG must be placed in exactly one PF, even if it results in families containing only one CV.</a>
+<a name="146"><span class="lineNum">     146 </span>            : Additionally, in cases where each of SIGMA or GRID entry would correspond to each ARG entry, they now correspond to</a>
+<a name="147"><span class="lineNum">     147 </span>            : each PF and must be adjusted accordingly.</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : Multiple walkers  \cite multiplewalkers can also be used. See below the examples.</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : \par Examples</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : The following input is for PBMetaD calculation using as</a>
+<a name="154"><span class="lineNum">     154 </span>            : collective variables the distance between atoms 3 and 5</a>
+<a name="155"><span class="lineNum">     155 </span>            : and the distance between atoms 2 and 4. The value of the CVs and</a>
+<a name="156"><span class="lineNum">     156 </span>            : the PBMetaD bias potential are written to the COLVAR file every 100 steps.</a>
+<a name="157"><span class="lineNum">     157 </span>            : \plumedfile</a>
+<a name="158"><span class="lineNum">     158 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="159"><span class="lineNum">     159 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="160"><span class="lineNum">     160 </span>            : PBMETAD ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3 PACE=500 LABEL=pb FILE=HILLS_d1,HILLS_d2</a>
+<a name="161"><span class="lineNum">     161 </span>            : PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR</a>
+<a name="162"><span class="lineNum">     162 </span>            : \endplumedfile</a>
+<a name="163"><span class="lineNum">     163 </span>            : (See also \ref DISTANCE and \ref PRINT).</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : \par</a>
+<a name="166"><span class="lineNum">     166 </span>            : If you use well-tempered metadynamics, you should specify a single bias factor and initial</a>
+<a name="167"><span class="lineNum">     167 </span>            : Gaussian height.</a>
+<a name="168"><span class="lineNum">     168 </span>            : \plumedfile</a>
+<a name="169"><span class="lineNum">     169 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="170"><span class="lineNum">     170 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="171"><span class="lineNum">     171 </span>            : PBMETAD ...</a>
+<a name="172"><span class="lineNum">     172 </span>            : ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3</a>
+<a name="173"><span class="lineNum">     173 </span>            : PACE=500 BIASFACTOR=8 LABEL=pb</a>
+<a name="174"><span class="lineNum">     174 </span>            : FILE=HILLS_d1,HILLS_d2</a>
+<a name="175"><span class="lineNum">     175 </span>            : ... PBMETAD</a>
+<a name="176"><span class="lineNum">     176 </span>            : PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR</a>
+<a name="177"><span class="lineNum">     177 </span>            : \endplumedfile</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : \par</a>
+<a name="180"><span class="lineNum">     180 </span>            : Using partitioned families, each CV in ARG must be in exactly one family. Here,</a>
+<a name="181"><span class="lineNum">     181 </span>            : the distance between atoms 1,2 is degenerate with 2,4, but not with the</a>
+<a name="182"><span class="lineNum">     182 </span>            : distance between 3,5. Note that two SIGMA are provided to match the two PF.</a>
+<a name="183"><span class="lineNum">     183 </span>            : \plumedfile</a>
+<a name="184"><span class="lineNum">     184 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="185"><span class="lineNum">     185 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="186"><span class="lineNum">     186 </span>            : DISTANCE ATOMS=1,2 LABEL=d3</a>
+<a name="187"><span class="lineNum">     187 </span>            : PBMETAD ...</a>
+<a name="188"><span class="lineNum">     188 </span>            : ARG=d1,d2,d3 SIGMA=0.2,0.2 HEIGHT=0.3</a>
+<a name="189"><span class="lineNum">     189 </span>            : PF0=d1 PF1=d2,d3</a>
+<a name="190"><span class="lineNum">     190 </span>            : PACE=500 BIASFACTOR=8 LABEL=pb</a>
+<a name="191"><span class="lineNum">     191 </span>            : FILE=HILLS_d1,HILLS_d2</a>
+<a name="192"><span class="lineNum">     192 </span>            : ... PBMETAD</a>
+<a name="193"><span class="lineNum">     193 </span>            : PRINT ARG=d1,d2,d3,pb.bias STRIDE=100 FILE=COLVAR</a>
+<a name="194"><span class="lineNum">     194 </span>            : \endplumedfile</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : \par</a>
+<a name="197"><span class="lineNum">     197 </span>            : The following input enables the MPI version of multiple-walkers.</a>
+<a name="198"><span class="lineNum">     198 </span>            : \plumedfile</a>
+<a name="199"><span class="lineNum">     199 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="200"><span class="lineNum">     200 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="201"><span class="lineNum">     201 </span>            : PBMETAD ...</a>
+<a name="202"><span class="lineNum">     202 </span>            : ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3</a>
+<a name="203"><span class="lineNum">     203 </span>            : PACE=500 BIASFACTOR=8 LABEL=pb</a>
+<a name="204"><span class="lineNum">     204 </span>            : FILE=HILLS_d1,HILLS_d2</a>
+<a name="205"><span class="lineNum">     205 </span>            : WALKERS_MPI</a>
+<a name="206"><span class="lineNum">     206 </span>            : ... PBMETAD</a>
+<a name="207"><span class="lineNum">     207 </span>            : PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR</a>
+<a name="208"><span class="lineNum">     208 </span>            : \endplumedfile</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : \par</a>
+<a name="211"><span class="lineNum">     211 </span>            : The disk version of multiple-walkers can be</a>
+<a name="212"><span class="lineNum">     212 </span>            : enabled by setting the number of walker used, the id of the</a>
+<a name="213"><span class="lineNum">     213 </span>            : current walker which interprets the input file, the directory where the</a>
+<a name="214"><span class="lineNum">     214 </span>            : hills containing files resides, and the frequency to read the other walkers.</a>
+<a name="215"><span class="lineNum">     215 </span>            : Here is an example</a>
+<a name="216"><span class="lineNum">     216 </span>            : \plumedfile</a>
+<a name="217"><span class="lineNum">     217 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="218"><span class="lineNum">     218 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="219"><span class="lineNum">     219 </span>            : PBMETAD ...</a>
+<a name="220"><span class="lineNum">     220 </span>            : ARG=d1,d2 SIGMA=0.2,0.2 HEIGHT=0.3</a>
+<a name="221"><span class="lineNum">     221 </span>            : PACE=500 BIASFACTOR=8 LABEL=pb</a>
+<a name="222"><span class="lineNum">     222 </span>            : FILE=HILLS_d1,HILLS_d2</a>
+<a name="223"><span class="lineNum">     223 </span>            : WALKERS_N=10</a>
+<a name="224"><span class="lineNum">     224 </span>            : WALKERS_ID=3</a>
+<a name="225"><span class="lineNum">     225 </span>            : WALKERS_DIR=../</a>
+<a name="226"><span class="lineNum">     226 </span>            : WALKERS_RSTRIDE=100</a>
+<a name="227"><span class="lineNum">     227 </span>            : ... PBMETAD</a>
+<a name="228"><span class="lineNum">     228 </span>            : PRINT ARG=d1,d2,pb.bias STRIDE=100 FILE=COLVAR</a>
+<a name="229"><span class="lineNum">     229 </span>            : \endplumedfile</a>
+<a name="230"><span class="lineNum">     230 </span>            : where  WALKERS_N is the total number of walkers, WALKERS_ID is the</a>
+<a name="231"><span class="lineNum">     231 </span>            : id of the present walker (starting from 0 ) and the WALKERS_DIR is the directory</a>
+<a name="232"><span class="lineNum">     232 </span>            : where all the walkers are located. WALKERS_RSTRIDE is the number of step between</a>
+<a name="233"><span class="lineNum">     233 </span>            : one update and the other.</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : */</a>
+<a name="236"><span class="lineNum">     236 </span>            : //+ENDPLUMEDOC</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : class PBMetaD : public Bias {</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : private:</a>
+<a name="241"><span class="lineNum">     241 </span>            :   struct Gaussian {</a>
+<a name="242"><span class="lineNum">     242 </span>            :     std::vector&lt;double&gt; center;</a>
+<a name="243"><span class="lineNum">     243 </span>            :     std::vector&lt;double&gt; sigma;</a>
+<a name="244"><span class="lineNum">     244 </span>            :     double height;</a>
+<a name="245"><span class="lineNum">     245 </span>            :     bool   multivariate; // this is required to discriminate the one dimensional case</a>
+<a name="246"><span class="lineNum">     246 </span>            :     std::vector&lt;double&gt; invsigma;</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       1108 :     Gaussian(const std::vector&lt;double&gt; &amp; center,const std::vector&lt;double&gt; &amp; sigma, double height, bool multivariate):</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       1108 :       center(center),sigma(sigma),height(height),multivariate(multivariate),invsigma(sigma) {</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :       // to avoid troubles from zero element in flexible hills</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       2216 :         for(unsigned i=0; i&lt;invsigma.size(); ++i) if(std::abs(invsigma[i])&gt;1.e-20) invsigma[i]=1.0/invsigma[i] ; else invsigma[i]=0.0;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       1108 :     }</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :   };</a>
+<a name="253"><span class="lineNum">     253 </span>            :   // general setup</a>
+<a name="254"><span class="lineNum">     254 </span>            :   double kbt_;</a>
+<a name="255"><span class="lineNum">     255 </span>            :   int stride_;</a>
+<a name="256"><span class="lineNum">     256 </span>            :   // well-tempered MetaD</a>
+<a name="257"><span class="lineNum">     257 </span>            :   bool welltemp_;</a>
+<a name="258"><span class="lineNum">     258 </span>            :   double biasf_;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   // output files format</a>
+<a name="260"><span class="lineNum">     260 </span>            :   std::string fmt_;</a>
+<a name="261"><span class="lineNum">     261 </span>            :   // first step?</a>
+<a name="262"><span class="lineNum">     262 </span>            :   bool isFirstStep_;</a>
+<a name="263"><span class="lineNum">     263 </span>            :   // Gaussian starting parameters</a>
+<a name="264"><span class="lineNum">     264 </span>            :   double height0_;</a>
+<a name="265"><span class="lineNum">     265 </span>            :   std::vector&lt;double&gt; sigma0_;</a>
+<a name="266"><span class="lineNum">     266 </span>            :   std::vector&lt;double&gt; sigma0min_;</a>
+<a name="267"><span class="lineNum">     267 </span>            :   std::vector&lt;double&gt; sigma0max_;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   // Gaussians</a>
+<a name="269"><span class="lineNum">     269 </span>            :   std::vector&lt;std::vector&lt;Gaussian&gt; &gt; hills_;</a>
+<a name="270"><span class="lineNum">     270 </span>            :   std::vector&lt;FlexibleBin&gt; flexbin_;</a>
+<a name="271"><span class="lineNum">     271 </span>            :   int adaptive_;</a>
+<a name="272"><span class="lineNum">     272 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; hillsOfiles_;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   std::vector&lt;std::unique_ptr&lt;IFile&gt;&gt; ifiles_;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   std::vector&lt;std::string&gt; ifilesnames_;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   // Grids</a>
+<a name="276"><span class="lineNum">     276 </span>            :   bool grid_;</a>
+<a name="277"><span class="lineNum">     277 </span>            :   std::vector&lt;std::unique_ptr&lt;GridBase&gt;&gt; BiasGrids_;</a>
+<a name="278"><span class="lineNum">     278 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; gridfiles_;</a>
+<a name="279"><span class="lineNum">     279 </span>            :   int wgridstride_;</a>
+<a name="280"><span class="lineNum">     280 </span>            :   // Partitioned Families</a>
+<a name="281"><span class="lineNum">     281 </span>            :   unsigned int pf_n_; // initialize number of partitioned families</a>
+<a name="282"><span class="lineNum">     282 </span>            :   std::vector&lt;int&gt; pfs_; //std::vector length of arguments that holds which pf# each cv belongs in</a>
+<a name="283"><span class="lineNum">     283 </span>            :   std::vector&lt;Value*&gt; pfhold_; // std::vector length of pf_n which stores a pointer to the first argument fed to each family</a>
+<a name="284"><span class="lineNum">     284 </span>            :   bool do_pf_; // if partitioned families are enabled</a>
+<a name="285"><span class="lineNum">     285 </span>            :   // multiple walkers</a>
+<a name="286"><span class="lineNum">     286 </span>            :   int mw_n_;</a>
+<a name="287"><span class="lineNum">     287 </span>            :   std::string mw_dir_;</a>
+<a name="288"><span class="lineNum">     288 </span>            :   int mw_id_;</a>
+<a name="289"><span class="lineNum">     289 </span>            :   int mw_rstride_;</a>
+<a name="290"><span class="lineNum">     290 </span>            :   bool walkers_mpi_;</a>
+<a name="291"><span class="lineNum">     291 </span>            :   size_t mpi_nw_;</a>
+<a name="292"><span class="lineNum">     292 </span>            :   unsigned mpi_id_;</a>
+<a name="293"><span class="lineNum">     293 </span>            :   std::vector&lt;std::string&gt; hillsfname_;</a>
+<a name="294"><span class="lineNum">     294 </span>            :   // intervals</a>
+<a name="295"><span class="lineNum">     295 </span>            :   std::vector&lt;double&gt; uppI_;</a>
+<a name="296"><span class="lineNum">     296 </span>            :   std::vector&lt;double&gt; lowI_;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   std::vector&lt;bool&gt;  doInt_;</a>
+<a name="298"><span class="lineNum">     298 </span>            :   // variable for selector</a>
+<a name="299"><span class="lineNum">     299 </span>            :   std::string selector_;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   bool  do_select_;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   unsigned select_value_;</a>
+<a name="302"><span class="lineNum">     302 </span>            :   unsigned current_value_;</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   double stretchA=1.0;</a>
+<a name="305"><span class="lineNum">     305 </span>            :   double stretchB=0.0;</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   bool noStretchWarningDone=false;</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :   void noStretchWarning() {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :     if(!noStretchWarningDone) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;\nWARNING: you are using a HILLS file with Gaussian kernels, PLUMED 2.8 uses stretched Gaussians by default\n&quot;;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :     }</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     noStretchWarningDone=true;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            :   void   readGaussians(unsigned iarg, IFile*);</a>
+<a name="317"><span class="lineNum">     317 </span>            :   void   writeGaussian(unsigned iarg, const Gaussian&amp;, OFile*);</a>
+<a name="318"><span class="lineNum">     318 </span>            :   void   addGaussian(unsigned iarg, const Gaussian&amp;);</a>
+<a name="319"><span class="lineNum">     319 </span>            :   double getBiasAndDerivatives(unsigned iarg, const std::vector&lt;double&gt;&amp;, double* der=NULL);</a>
+<a name="320"><span class="lineNum">     320 </span>            :   double evaluateGaussian(unsigned iarg, const std::vector&lt;double&gt;&amp;, const Gaussian&amp;,double* der=NULL);</a>
+<a name="321"><span class="lineNum">     321 </span>            :   std::vector&lt;unsigned&gt; getGaussianSupport(unsigned iarg, const Gaussian&amp;);</a>
+<a name="322"><span class="lineNum">     322 </span>            :   bool   scanOneHill(unsigned iarg, IFile *ifile,  std::vector&lt;Value&gt; &amp;v, std::vector&lt;double&gt; &amp;center, std::vector&lt;double&gt;  &amp;sigma, double &amp;height, bool &amp;multivariate);</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : public:</a>
+<a name="325"><span class="lineNum">     325 </span>            :   explicit PBMetaD(const ActionOptions&amp;);</a>
+<a name="326"><span class="lineNum">     326 </span>            :   void calculate() override;</a>
+<a name="327"><span class="lineNum">     327 </span>            :   void update() override;</a>
+<a name="328"><span class="lineNum">     328 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="329"><span class="lineNum">     329 </span>            :   bool checkNeedsGradients()const override;</a>
+<a name="330"><span class="lineNum">     330 </span>            : };</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      12586 : PLUMED_REGISTER_ACTION(PBMetaD,&quot;PBMETAD&quot;)</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         43 : void PBMetaD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         43 :   Bias::registerKeywords(keys);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         43 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         86 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;the widths of the Gaussian hills&quot;);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         86 :   keys.add(&quot;compulsory&quot;,&quot;PACE&quot;,&quot;the frequency for hill addition, one for all biases&quot;);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;files in which the lists of added hills are stored, default names are assigned using arguments if FILE is not found&quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;HEIGHT&quot;,&quot;the height of the Gaussian hills, one for all biases. Compulsory unless TAU, TEMP and BIASFACTOR are given&quot;);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;specify format for HILLS files (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;BIASFACTOR&quot;,&quot;use well tempered metadynamics with this bias factor, one for all biases.  Please note you must also specify temp&quot;);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - this is only needed if you are doing well-tempered metadynamics&quot;);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;TAU&quot;,&quot;in well tempered metadynamics, sets height to (k_B Delta T*pace*timestep)/tau&quot;);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_MIN&quot;,&quot;the lower bounds for the grid&quot;);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_MAX&quot;,&quot;the upper bounds for the grid&quot;);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_BIN&quot;,&quot;the number of bins for the grid&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_SPACING&quot;,&quot;the approximate grid spacing (to be used as an alternative or together with GRID_BIN)&quot;);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         86 :   keys.addFlag(&quot;GRID_SPARSE&quot;,false,&quot;use a sparse grid to store hills&quot;);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         86 :   keys.addFlag(&quot;GRID_NOSPLINE&quot;,false,&quot;don't use spline interpolation with grids&quot;);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_WSTRIDE&quot;, &quot;frequency for dumping the grid&quot;);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_WFILES&quot;, &quot;dump grid for the bias, default names are used if GRID_WSTRIDE is used without GRID_WFILES.&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;GRID_RFILES&quot;, &quot;read grid for the bias&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;ADAPTIVE&quot;,&quot;use a geometric (=GEOM) or diffusion (=DIFF) based hills width scheme. Sigma is one number that has distance units or timestep dimensions&quot;);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MAX&quot;,&quot;the upper bounds for the sigmas (in CV units) when using adaptive hills. Negative number means no bounds &quot;);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MIN&quot;,&quot;the lower bounds for the sigmas (in CV units) when using adaptive hills. Negative number means no bounds &quot;);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         86 :   keys.add(&quot;numbered&quot;,&quot;PF&quot;, &quot;specify which CVs belong in a partitioned family. Once a PF is specified, all CVs in ARG must be placed in a PF even if there is one CV per PF�&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;SELECTOR&quot;, &quot;add forces and do update based on the value of SELECTOR&quot;);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;SELECTOR_ID&quot;, &quot;value of SELECTOR&quot;);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;WALKERS_ID&quot;, &quot;walker id&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;WALKERS_N&quot;, &quot;number of walkers&quot;);</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;WALKERS_DIR&quot;, &quot;shared directory with the hills files from all the walkers&quot;);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;WALKERS_RSTRIDE&quot;,&quot;stride for reading hills files&quot;);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         86 :   keys.addFlag(&quot;WALKERS_MPI&quot;,false,&quot;Switch on MPI version of multiple walkers - not compatible with WALKERS_* options other than WALKERS_DIR&quot;);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;INTERVAL_MIN&quot;,&quot;one dimensional lower limits, outside the limits the system will not feel the biasing force.&quot;);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         86 :   keys.add(&quot;optional&quot;,&quot;INTERVAL_MAX&quot;,&quot;one dimensional upper limits, outside the limits the system will not feel the biasing force.&quot;);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         43 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         43 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         43 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         43 : }</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         41 : PBMetaD::PBMetaD(const ActionOptions&amp; ao):</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         41 :   kbt_(0.0),</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         41 :   stride_(0),</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         41 :   welltemp_(false),</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         41 :   biasf_(1.0),</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         41 :   isFirstStep_(true),</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         41 :   height0_(std::numeric_limits&lt;double&gt;::max()),</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         41 :   adaptive_(FlexibleBin::none),</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         41 :   grid_(false),</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         41 :   wgridstride_(0),</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         41 :   pf_n_(0), do_pf_(false),</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         41 :   mw_n_(1), mw_dir_(&quot;&quot;), mw_id_(0), mw_rstride_(1),</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         41 :   walkers_mpi_(false), mpi_nw_(0),</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         41 :   do_select_(false)</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : {</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            :   // parse the flexible hills</a>
+<a name="390"><span class="lineNum">     390 </span>            :   std::string adaptiveoption;</a>
+<a name="391"><span class="lineNum">     391 </span>            :   adaptiveoption=&quot;NONE&quot;;</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         82 :   parse(&quot;ADAPTIVE&quot;,adaptiveoption);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         41 :   if(adaptiveoption==&quot;GEOM&quot;) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :     log.printf(&quot;  Uses Geometry-based hills width: sigma must be in distance units and only one sigma is needed\n&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :     adaptive_=FlexibleBin::geometry;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         41 :   } else if(adaptiveoption==&quot;DIFF&quot;) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          4 :     log.printf(&quot;  Uses Diffusion-based hills width: sigma must be in time steps and only one sigma is needed\n&quot;);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          4 :     adaptive_=FlexibleBin::diffusion;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         37 :   } else if(adaptiveoption==&quot;NONE&quot;) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         37 :     adaptive_=FlexibleBin::none;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   } else {</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :     error(&quot;I do not know this type of adaptive scheme&quot;);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         41 :   parse(&quot;FMT&quot;,fmt_);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   // Partitioned Families - fill with -1 to mark as invalid</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         41 :   pfs_.assign(getNumberOfArguments(), -1);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         41 :   pfhold_.resize(getNumberOfArguments());</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   std::vector&lt;Value*&gt; familyargs;</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         41 :   for(int i = 0;; i++) {</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         94 :     parseArgumentList(&quot;PF&quot;, i, familyargs);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         47 :     if (familyargs.empty()) break;</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">          6 :     do_pf_ = true;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;  Identified Partitioned Family &quot; &lt;&lt; i &lt;&lt; &quot;:&quot;;</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         15 :     for (unsigned j = 0; j &lt; familyargs.size(); j++) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          9 :       log &lt;&lt; &quot; &quot; &lt;&lt; familyargs[j]-&gt;getName();</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :       // loop through the argument list to make sure it exists and assign it</a>
+<a name="420"><span class="lineNum">     420 </span>            :       bool foundArg = false;</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         36 :       for (unsigned argnum = 0; argnum &lt; getNumberOfArguments(); argnum++) {</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         27 :         if (familyargs[j]-&gt;getName() == getPntrToArgument(argnum)-&gt;getName()) {</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :           foundArg = true;</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          9 :           if (pfs_[argnum] != -1) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :             error(familyargs[j]-&gt;getName() + &quot; already present in PF&quot; + std::to_string(pfs_[argnum]));</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :           }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          9 :           pfs_[argnum] = i;  // store the pf# for each cv</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          9 :           if (pfhold_[i] == nullptr) {</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :             // if this is the first argument in the family, store a pointer for it (this is for HILLS &amp; GRID files)</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          6 :             pfhold_[i] = getPntrToArgument(argnum);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :           }</a>
+<a name="432"><span class="lineNum">     432 </span>            :         }</a>
+<a name="433"><span class="lineNum">     433 </span>            :       }</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          9 :       if (!foundArg) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :         error(familyargs[j]-&gt;getName() + &quot; in PF&quot; + std::to_string(i) + &quot; not found in ARG&quot;);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :       }</a>
+<a name="437"><span class="lineNum">     437 </span>            :     }</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          6 :     pf_n_++;</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          6 :   }</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :   // if PF were specified, every argument gets treated as its own PF</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         41 :   if (!do_pf_) {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         38 :     pf_n_ = getNumberOfArguments();</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        114 :     for(unsigned i=0; i &lt; pf_n_; i++) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         76 :       pfhold_[i] = getPntrToArgument(i);</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         76 :       pfs_[i] = i;</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :     }</a>
+<a name="449"><span class="lineNum">     449 </span>            :   } else {</a>
+<a name="450"><span class="lineNum">     450 </span>            :     // If we are doing PF, make sure each argument got assigned to a family.</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         12 :     for (unsigned i = 0; i &lt; getNumberOfArguments(); i++) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          9 :       if (pfs_[i] == -1) error(getPntrToArgument(i)-&gt;getName() + &quot; was not assigned a PF&quot;);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     }</a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            :   // parse the sigma</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         41 :   parseVector(&quot;SIGMA&quot;,sigma0_);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         41 :   if(adaptive_==FlexibleBin::none) {</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :     // if you use normal sigma you need one sigma per argument</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         37 :     if( sigma0_.size()!=pf_n_ ) {</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :       std::string fields = do_pf_ ? &quot;PFs&quot; : &quot;arguments&quot;;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :       error(&quot;number of &quot; + fields + &quot; does not match number of SIGMA parameters&quot;);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :     }</a>
+<a name="464"><span class="lineNum">     464 </span>            :   } else {</a>
+<a name="465"><span class="lineNum">     465 </span>            :     // if you use flexible hills you need one sigma</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          4 :     if(sigma0_.size()!=1) {</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :       error(&quot;If you choose ADAPTIVE you need only one sigma according to your choice of type (GEOM/DIFF)&quot;);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :     }</a>
+<a name="469"><span class="lineNum">     469 </span>            :     // if adaptive then the number must be an integer</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          4 :     if(adaptive_==FlexibleBin::diffusion) {</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          4 :       if(int(sigma0_[0])-sigma0_[0]&gt;1.e-9 || int(sigma0_[0])-sigma0_[0] &lt;-1.e-9 || int(sigma0_[0])&lt;1 ) {</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :         error(&quot;In case of adaptive hills with diffusion, the sigma must be an integer which is the number of time steps\n&quot;);</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :       }</a>
+<a name="474"><span class="lineNum">     474 </span>            :     }</a>
+<a name="475"><span class="lineNum">     475 </span>            :     // here evtl parse the sigma min and max values</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          8 :     parseVector(&quot;SIGMA_MIN&quot;,sigma0min_);</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          4 :     if(sigma0min_.size()&gt;0 &amp;&amp; sigma0min_.size()!=pf_n_) {</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :       error(&quot;the number of SIGMA_MIN values be the same of the number of the arguments/PF&quot;);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          4 :     } else if(sigma0min_.size()==0) {</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 :       sigma0min_.resize(pf_n_);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;pf_n_; i++) {sigma0min_[i]=-1.;}</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :     }</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          8 :     parseVector(&quot;SIGMA_MAX&quot;,sigma0max_);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          4 :     if(sigma0max_.size()&gt;0 &amp;&amp; sigma0max_.size()!=pf_n_) {</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :       error(&quot;the number of SIGMA_MAX values be the same of the number of the arguments/PF&quot;);</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          4 :     } else if(sigma0max_.size()==0) {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          4 :       sigma0max_.resize(pf_n_);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         12 :       for(unsigned i=0; i&lt;pf_n_; i++) {sigma0max_[i]=-1.;}</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :     }</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         12 :     for(unsigned i=0; i&lt;pf_n_; i++) {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :       std::vector&lt;double&gt; tmp_smin, tmp_smax;</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          8 :       tmp_smin.resize(1,sigma0min_[i]);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          8 :       tmp_smax.resize(1,sigma0max_[i]);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         16 :       flexbin_.push_back(FlexibleBin(adaptive_,this,i,sigma0_[0],tmp_smin,tmp_smax));</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :     }</a>
+<a name="498"><span class="lineNum">     498 </span>            :   }</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            :   // note: HEIGHT is not compulsory, since one could use the TAU keyword, see below</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         41 :   parse(&quot;HEIGHT&quot;,height0_);</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         41 :   parse(&quot;PACE&quot;,stride_);</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         41 :   if(stride_&lt;=0) error(&quot;frequency for hill addition is nonsensical&quot;);</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         82 :   parseVector(&quot;FILE&quot;,hillsfname_);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         41 :   if(hillsfname_.size()==0) {</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt; pf_n_; i++) {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         18 :       std::string name = do_pf_ ? &quot;HILLS.PF&quot;+std::to_string(i) : &quot;HILLS.&quot;+getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">         18 :       hillsfname_.push_back(name);</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :     }</a>
+<a name="512"><span class="lineNum">     512 </span>            :   }</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         41 :   if( hillsfname_.size()!=pf_n_ ) {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :     error(&quot;number of FILE arguments does not match number of HILLS files&quot;);</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :   }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         41 :   parse(&quot;BIASFACTOR&quot;,biasf_);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         41 :   if( biasf_&lt;1.0 ) error(&quot;well tempered bias factor is nonsensical&quot;);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         41 :   double temp=0.0;</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         41 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         41 :   if(temp&gt;0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 :   else kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         41 :   if(biasf_&gt;1.0) {</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         40 :     if(kbt_==0.0) error(&quot;Unless the MD engine passes the temperature to plumed, with well-tempered metad you must specify it using TEMP&quot;);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         40 :     welltemp_=true;</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :   }</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         41 :   double tau=0.0;</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         41 :   parse(&quot;TAU&quot;,tau);</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         41 :   if(tau==0.0) {</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         41 :     if(height0_==std::numeric_limits&lt;double&gt;::max()) error(&quot;At least one between HEIGHT and TAU should be specified&quot;);</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :     // if tau is not set, we compute it here from the other input parameters</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         41 :     if(welltemp_) tau=(kbt_*(biasf_-1.0))/height0_*getTimeStep()*stride_;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   } else {</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :     if(!welltemp_)error(&quot;TAU only makes sense in well-tempered metadynamics&quot;);</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :     if(height0_!=std::numeric_limits&lt;double&gt;::max()) error(&quot;At most one between HEIGHT and TAU should be specified&quot;);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :     height0_=(kbt_*(biasf_-1.0))/tau*getTimeStep()*stride_;</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :   }</a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span>            :   // Multiple walkers</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">         41 :   parse(&quot;WALKERS_N&quot;,mw_n_);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         41 :   parse(&quot;WALKERS_ID&quot;,mw_id_);</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         41 :   if(mw_n_&lt;=mw_id_) error(&quot;walker ID should be a numerical value less than the total number of walkers&quot;);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         41 :   parse(&quot;WALKERS_DIR&quot;,mw_dir_);</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         41 :   parse(&quot;WALKERS_RSTRIDE&quot;,mw_rstride_);</span></a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :   // MPI version</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         41 :   parseFlag(&quot;WALKERS_MPI&quot;,walkers_mpi_);</span></a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            :   // Grid file</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         82 :   parse(&quot;GRID_WSTRIDE&quot;,wgridstride_);</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   std::vector&lt;std::string&gt; gridfilenames_;</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         41 :   parseVector(&quot;GRID_WFILES&quot;,gridfilenames_);</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         41 :   if (wgridstride_ == 0 &amp;&amp; gridfilenames_.size() &gt; 0) {</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineNoCov">          0 :     error(&quot;frequency with which to output grid not specified use GRID_WSTRIDE&quot;);</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :   }</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         41 :   if(gridfilenames_.size()==0 &amp;&amp; wgridstride_ &gt; 0) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         12 :     for(unsigned i=0; i&lt;pf_n_; i++) {</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">          8 :       std::string name = do_pf_ ? &quot;GRID.PF&quot;+std::to_string(i) : &quot;GRID.&quot;+getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">          8 :       gridfilenames_.push_back(name);</span></a>
+<a name="561"><span class="lineNum">     561 </span>            :     }</a>
+<a name="562"><span class="lineNum">     562 </span>            :   }</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         41 :   if(gridfilenames_.size() &gt; 0 &amp;&amp; hillsfname_.size() &gt; 0 &amp;&amp; gridfilenames_.size() != hillsfname_.size())</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :     error(&quot;number of GRID_WFILES arguments does not match number of HILLS files&quot;);</span></a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span>            :   // Read grid</a>
+<a name="567"><span class="lineNum">     567 </span>            :   std::vector&lt;std::string&gt; gridreadfilenames_;</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         41 :   parseVector(&quot;GRID_RFILES&quot;,gridreadfilenames_);</span></a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span>            :   // Grid Stuff</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">         41 :   std::vector&lt;std::string&gt; gmin(pf_n_);</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         82 :   parseVector(&quot;GRID_MIN&quot;,gmin);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         41 :   if(gmin.size()!=pf_n_ &amp;&amp; gmin.size()!=0) error(&quot;not enough values for GRID_MIN&quot;);</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         41 :   std::vector&lt;std::string&gt; gmax(pf_n_);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         82 :   parseVector(&quot;GRID_MAX&quot;,gmax);</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         41 :   if(gmax.size()!=pf_n_ &amp;&amp; gmax.size()!=0) error(&quot;not enough values for GRID_MAX&quot;);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         41 :   std::vector&lt;unsigned&gt; gbin(pf_n_);</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :   std::vector&lt;double&gt;   gspacing;</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         82 :   parseVector(&quot;GRID_BIN&quot;,gbin);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         41 :   if(gbin.size()!=pf_n_ &amp;&amp; gbin.size()!=0) error(&quot;not enough values for GRID_BIN&quot;);</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         82 :   parseVector(&quot;GRID_SPACING&quot;,gspacing);</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         41 :   if(gspacing.size()!=pf_n_ &amp;&amp; gspacing.size()!=0) error(&quot;not enough values for GRID_SPACING&quot;);</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         41 :   if(gmin.size()!=gmax.size()) error(&quot;GRID_MAX and GRID_MIN should be either present or absent&quot;);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         41 :   if(gspacing.size()!=0 &amp;&amp; gmin.size()==0) error(&quot;If GRID_SPACING is present also GRID_MIN and GRID_MAX should be present&quot;);</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         41 :   if(gbin.size()!=0     &amp;&amp; gmin.size()==0) error(&quot;If GRID_BIN is present also GRID_MIN and GRID_MAX should be present&quot;);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         41 :   if(gmin.size()!=0) {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">          9 :     if(gbin.size()==0 &amp;&amp; gspacing.size()==0) {</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">          9 :       if(adaptive_==FlexibleBin::none) {</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">          5 :         log&lt;&lt;&quot;  Binsize not specified, 1/5 of sigma will be be used\n&quot;;</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">          5 :         plumed_assert(sigma0_.size()==pf_n_);</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">          5 :         gspacing.resize(pf_n_);</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">         15 :         for(unsigned i=0; i&lt;gspacing.size(); i++) gspacing[i]=0.2*sigma0_[i];</span></a>
+<a name="593"><span class="lineNum">     593 </span>            :       } else {</a>
+<a name="594"><span class="lineNum">     594 </span>            :         // with adaptive hills and grid a sigma min must be specified</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         12 :         for(unsigned i=0; i&lt;sigma0min_.size(); i++) if(sigma0min_[i]&lt;=0) error(&quot;When using ADAPTIVE Gaussians on a grid SIGMA_MIN must be specified&quot;);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">          4 :         log&lt;&lt;&quot;  Binsize not specified, 1/5 of sigma_min will be be used\n&quot;;</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          4 :         gspacing.resize(pf_n_);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         12 :         for(unsigned i=0; i&lt;gspacing.size(); i++) gspacing[i]=0.2*sigma0min_[i];</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :       }</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :     } else if(gspacing.size()!=0 &amp;&amp; gbin.size()==0) {</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;  The number of bins will be estimated from GRID_SPACING\n&quot;;</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :     } else if(gspacing.size()!=0 &amp;&amp; gbin.size()!=0) {</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;  You specified both GRID_BIN and GRID_SPACING\n&quot;;</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;  The more conservative (highest) number of bins will be used for each variable\n&quot;;</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :     }</a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">          9 :     if(gbin.size()==0) gbin.assign(pf_n_,1);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         27 :     if(gspacing.size()!=0) for(unsigned i=0; i&lt;pf_n_; i++) {</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :         double a,b;</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         18 :         Tools::convert(gmin[i],a);</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         18 :         Tools::convert(gmax[i],b);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         18 :         unsigned n=std::ceil(((b-a)/gspacing[i]));</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         18 :         if(gbin[i]&lt;n) gbin[i]=n;</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :       }</a>
+<a name="614"><span class="lineNum">     614 </span>            :   }</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         41 :   if(gbin.size()&gt;0) grid_=true;</span></a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         41 :   bool sparsegrid=false;</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         41 :   parseFlag(&quot;GRID_SPARSE&quot;,sparsegrid);</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         41 :   bool nospline=false;</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         41 :   parseFlag(&quot;GRID_NOSPLINE&quot;,nospline);</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">         41 :   bool spline=!nospline;</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         41 :   if(!grid_&amp;&amp;gridfilenames_.size() &gt; 0) error(&quot;To write a grid you need first to define it!&quot;);</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         41 :   if(!grid_&amp;&amp;gridreadfilenames_.size() &gt; 0) error(&quot;To read a grid you need first to define it!&quot;);</span></a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         41 :   doInt_.resize(pf_n_,false);</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :   // Interval keyword</a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         41 :   parseVector(&quot;INTERVAL_MIN&quot;,lowI_);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         82 :   parseVector(&quot;INTERVAL_MAX&quot;,uppI_);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :   // various checks</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         41 :   if(lowI_.size()!=uppI_.size()) error(&quot;both a lower and an upper limits must be provided with INTERVAL&quot;);</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         41 :   if(lowI_.size()!=0 &amp;&amp; lowI_.size()!=pf_n_) error(&quot;check number of argument of INTERVAL&quot;);</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">         49 :   for(unsigned i=0; i&lt;lowI_.size(); ++i) {</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">          8 :     if(uppI_[i]&lt;lowI_[i]) error(&quot;The Upper limit must be greater than the Lower limit!&quot;);</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">          8 :     if(pfhold_[i]-&gt;isPeriodic()) warning(&quot;INTERVAL is not used for periodic variables&quot;);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :     else doInt_[i]=true;</a>
+<a name="636"><span class="lineNum">     636 </span>            :   }</a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span>            :   // parse selector stuff</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">         82 :   parse(&quot;SELECTOR&quot;, selector_);</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">         41 :   if(selector_.length()&gt;0) {</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 :     do_select_ = true;</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :     parse(&quot;SELECTOR_ID&quot;, select_value_);</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :   }</a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">         41 :   checkRead();</span></a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         41 :   log.printf(&quot;  Gaussian width &quot;);</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">         41 :   if (adaptive_==FlexibleBin::diffusion)log.printf(&quot; (Note: The units of sigma are in timesteps) &quot;);</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">         41 :   if (adaptive_==FlexibleBin::geometry)log.printf(&quot; (Note: The units of sigma are in dist units) &quot;);</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">        119 :   for(unsigned i=0; i&lt;sigma0_.size(); ++i) log.printf(&quot; %f&quot;,sigma0_[i]);</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         41 :   log.printf(&quot;  Gaussian height %f\n&quot;,height0_);</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         41 :   log.printf(&quot;  Gaussian deposition pace %d\n&quot;,stride_);</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">         41 :   log.printf(&quot;  Gaussian files &quot;);</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">        123 :   for(unsigned i=0; i&lt;hillsfname_.size(); ++i) log.printf(&quot;%s &quot;,hillsfname_[i].c_str());</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         41 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">         41 :   if(welltemp_) {</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">         40 :     log.printf(&quot;  Well-Tempered Bias Factor %f\n&quot;,biasf_);</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">         40 :     log.printf(&quot;  Hills relaxation time (tau) %f\n&quot;,tau);</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">         40 :     log.printf(&quot;  KbT %f\n&quot;,kbt_);</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :   }</a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         41 :   if(do_select_) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :     log.printf(&quot;  Add forces and update bias based on the value of SELECTOR %s\n&quot;,selector_.c_str());</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :     log.printf(&quot;  Id of the SELECTOR for this action %u\n&quot;, select_value_);</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :   }</a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         41 :   if(mw_n_&gt;1) {</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :     if(walkers_mpi_) error(&quot;MPI version of multiple walkers is not compatible with filesystem version of multiple walkers&quot;);</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :     log.printf(&quot;  %d multiple walkers active\n&quot;,mw_n_);</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :     log.printf(&quot;  walker id %d\n&quot;,mw_id_);</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :     log.printf(&quot;  reading stride %d\n&quot;,mw_rstride_);</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :     if(mw_dir_!=&quot;&quot;)log.printf(&quot;  directory with hills files %s\n&quot;,mw_dir_.c_str());</span></a>
+<a name="673"><span class="lineNum">     673 </span>            :   } else {</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">         41 :     if(walkers_mpi_) {</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">         34 :       log.printf(&quot;  Multiple walkers active using MPI communnication\n&quot;);</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">         34 :       if(mw_dir_!=&quot;&quot;)log.printf(&quot;  directory with hills files %s\n&quot;,mw_dir_.c_str());</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         34 :       if(comm.Get_rank()==0) {</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :         // Only root of group can communicate with other walkers</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">         18 :         mpi_nw_ = multi_sim_comm.Get_size();</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         18 :         mpi_id_ = multi_sim_comm.Get_rank();</span></a>
+<a name="681"><span class="lineNum">     681 </span>            :       }</a>
+<a name="682"><span class="lineNum">     682 </span>            :       // Communicate to the other members of the same group</a>
+<a name="683"><span class="lineNum">     683 </span>            :       // info abount number of walkers and walker index</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         34 :       comm.Bcast(mpi_nw_,0);</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">         34 :       comm.Bcast(mpi_id_,0);</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :     }</a>
+<a name="687"><span class="lineNum">     687 </span>            :   }</a>
+<a name="688"><span class="lineNum">     688 </span>            : </a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">        123 :   for(unsigned i=0; i&lt;doInt_.size(); i++) {</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         82 :     if(doInt_[i]) log.printf(&quot;  Upper and Lower limits boundaries for the bias of CV %u are activated\n&quot;, i);</span></a>
+<a name="691"><span class="lineNum">     691 </span>            :   }</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         41 :   if(grid_) {</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">          9 :     log.printf(&quot;  Grid min&quot;);</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt;gmin.size(); ++i) log.printf(&quot; %s&quot;,gmin[i].c_str() );</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">          9 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">          9 :     log.printf(&quot;  Grid max&quot;);</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt;gmax.size(); ++i) log.printf(&quot; %s&quot;,gmax[i].c_str() );</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">          9 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">          9 :     log.printf(&quot;  Grid bin&quot;);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt;gbin.size(); ++i) log.printf(&quot; %u&quot;,gbin[i]);</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">          9 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">          9 :     if(spline) {log.printf(&quot;  Grid uses spline interpolation\n&quot;);}</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">          9 :     if(sparsegrid) {log.printf(&quot;  Grid uses sparse grid\n&quot;);}</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">          9 :     if(wgridstride_&gt;0) {</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         18 :       for(unsigned i=0; i&lt;gridfilenames_.size(); ++i) {</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">         12 :         log.printf(&quot;  Grid is written on file %s with stride %d\n&quot;,gridfilenames_[i].c_str(),wgridstride_);</span></a>
+<a name="707"><span class="lineNum">     707 </span>            :       }</a>
+<a name="708"><span class="lineNum">     708 </span>            :     }</a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">          9 :     if(gridreadfilenames_.size()&gt;0) {</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">          3 :       for(unsigned i=0; i&lt;gridreadfilenames_.size(); ++i) {</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">          2 :         log.printf(&quot;  Reading bias from grid in file %s \n&quot;,gridreadfilenames_[i].c_str());</span></a>
+<a name="712"><span class="lineNum">     712 </span>            :       }</a>
+<a name="713"><span class="lineNum">     713 </span>            :     }</a>
+<a name="714"><span class="lineNum">     714 </span>            :   }</a>
+<a name="715"><span class="lineNum">     715 </span>            : </a>
+<a name="716"><span class="lineNum">     716 </span>            :   // initializing vector of hills</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">         41 :   hills_.resize(pf_n_);</span></a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            :   // restart from external grid</a>
+<a name="720"><span class="lineNum">     720 </span>            :   bool restartedFromGrid=false;</a>
+<a name="721"><span class="lineNum">     721 </span>            : </a>
+<a name="722"><span class="lineNum">     722 </span>            :   // initializing and checking grid</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">         41 :   if(grid_) {</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :     // check for mesh and sigma size</a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt;pf_n_; i++) {</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :       double a,b;</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">         18 :       int family = pfs_[i]; // point to families instead of arguments</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">         18 :       Tools::convert(gmin[family],a);</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">         18 :       Tools::convert(gmax[family],b);</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">         18 :       double mesh=(b-a)/((double)gbin[family]);</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">         18 :       if(adaptive_==FlexibleBin::none) {</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">         10 :         if(mesh&gt;0.5*sigma0_[i]) log&lt;&lt;&quot;  WARNING: Using a PBMETAD with a Grid Spacing larger than half of the Gaussians width can produce artifacts\n&quot;;</span></a>
+<a name="733"><span class="lineNum">     733 </span>            :       } else {</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">          8 :         if(mesh&gt;0.5*sigma0min_[i]||sigma0min_[i]&lt;0.) log&lt;&lt;&quot;  WARNING: to use a PBMETAD with a GRID and ADAPTIVE you need to set a Grid Spacing larger than half of the Gaussians \n&quot;;</span></a>
+<a name="735"><span class="lineNum">     735 </span>            :       }</a>
+<a name="736"><span class="lineNum">     736 </span>            :     }</a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">          9 :     std::string funcl=getLabel() + &quot;.bias&quot;;</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt;pf_n_; ++i) {</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">         18 :       std::vector&lt;Value*&gt; args(1);</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">         18 :       args[0] = pfhold_[i];  //Use first argument in family for interactions.</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">         18 :       std::vector&lt;std::string&gt; gmin_t(1);</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">         18 :       std::vector&lt;std::string&gt; gmax_t(1);</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">         18 :       std::vector&lt;unsigned&gt;    gbin_t(1);</span></a>
+<a name="744"><span class="lineNum">     744 </span>            :       gmin_t[0] = gmin[i];</a>
+<a name="745"><span class="lineNum">     745 </span>            :       gmax_t[0] = gmax[i];</a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">         18 :       gbin_t[0] = gbin[i];</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">         18 :       std::unique_ptr&lt;GridBase&gt; BiasGrid_;</span></a>
+<a name="748"><span class="lineNum">     748 </span>            :       // Read grid from file</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">         18 :       if(gridreadfilenames_.size()&gt;0) {</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">          2 :         IFile gridfile;</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">          2 :         gridfile.link(*this);</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">          2 :         if(gridfile.FileExist(gridreadfilenames_[i])) {</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">          2 :           gridfile.open(gridreadfilenames_[i]);</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :         } else {</a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :           error(&quot;The GRID file you want to read: &quot; + gridreadfilenames_[i] + &quot;, cannot be found!&quot;);</span></a>
+<a name="756"><span class="lineNum">     756 </span>            :         }</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">          2 :         std::string funcl = getLabel() + &quot;.bias&quot;;</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">          4 :         BiasGrid_=GridBase::create(funcl, args, gridfile, gmin_t, gmax_t, gbin_t, sparsegrid, spline, true);</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">          2 :         if(BiasGrid_-&gt;getDimension() != args.size()) {</span></a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineNoCov">          0 :           error(&quot;mismatch between dimensionality of input grid and number of arguments&quot;);</span></a>
+<a name="761"><span class="lineNum">     761 </span>            :         }</a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">          4 :         if(pfhold_[i]-&gt;isPeriodic() != BiasGrid_-&gt;getIsPeriodic()[0]) {</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineNoCov">          0 :           error(&quot;periodicity mismatch between arguments and input bias&quot;);</span></a>
+<a name="764"><span class="lineNum">     764 </span>            :         }</a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">          2 :         log.printf(&quot;  Restarting from %s:\n&quot;,gridreadfilenames_[i].c_str());</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">          2 :         if(getRestart()) restartedFromGrid=true;</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">          2 :       } else {</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">         16 :         if(!sparsegrid) {BiasGrid_=Tools::make_unique&lt;Grid&gt;(funcl,args,gmin_t,gmax_t,gbin_t,spline,true);}</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :         else           {BiasGrid_=Tools::make_unique&lt;SparseGrid&gt;(funcl,args,gmin_t,gmax_t,gbin_t,spline,true);}</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">         16 :         std::vector&lt;std::string&gt; actualmin=BiasGrid_-&gt;getMin();</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">         16 :         std::vector&lt;std::string&gt; actualmax=BiasGrid_-&gt;getMax();</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :         std::string is;</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">         16 :         Tools::convert(i,is);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">         16 :         if(gmin_t[0]!=actualmin[0]) error(&quot;GRID_MIN[&quot;+is+&quot;] must be adjusted to &quot;+actualmin[0]+&quot; to fit periodicity&quot;);</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">         16 :         if(gmax_t[0]!=actualmax[0]) error(&quot;GRID_MAX[&quot;+is+&quot;] must be adjusted to &quot;+actualmax[0]+&quot; to fit periodicity&quot;);</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">         16 :       }</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">         18 :       BiasGrids_.emplace_back(std::move(BiasGrid_));</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">         36 :     }</span></a>
+<a name="779"><span class="lineNum">     779 </span>            :   }</a>
+<a name="780"><span class="lineNum">     780 </span>            : </a>
+<a name="781"><span class="lineNum">     781 </span>            : </a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            : // creating vector of ifile* for hills reading</a>
+<a name="784"><span class="lineNum">     784 </span>            : // open all files at the beginning and read Gaussians if restarting</a>
+<a name="785"><span class="lineNum">     785 </span>            : </a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">         82 :   for(int j=0; j&lt;mw_n_; ++j) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">        123 :     for(unsigned i=0; i&lt;hillsfname_.size(); ++i) {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">         82 :       unsigned k=j*hillsfname_.size()+i;</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :       std::string fname;</a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">         82 :       if(mw_dir_!=&quot;&quot;) {</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineNoCov">          0 :         if(mw_n_&gt;1) {</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineNoCov">          0 :           std::stringstream out; out &lt;&lt; j;</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineNoCov">          0 :           fname = mw_dir_+&quot;/&quot;+hillsfname_[i]+&quot;.&quot;+out.str();</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineNoCov">          0 :         } else if(walkers_mpi_) {</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineNoCov">          0 :           fname = mw_dir_+&quot;/&quot;+hillsfname_[i];</span></a>
+<a name="796"><span class="lineNum">     796 </span>            :         } else {</a>
+<a name="797"><span class="lineNum">     797 </span>            :           fname = hillsfname_[i];</a>
+<a name="798"><span class="lineNum">     798 </span>            :         }</a>
+<a name="799"><span class="lineNum">     799 </span>            :       } else {</a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">         82 :         if(mw_n_&gt;1) {</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineNoCov">          0 :           std::stringstream out; out &lt;&lt; j;</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineNoCov">          0 :           fname = hillsfname_[i]+&quot;.&quot;+out.str();</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineNoCov">          0 :         } else {</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :           fname = hillsfname_[i];</a>
+<a name="805"><span class="lineNum">     805 </span>            :         }</a>
+<a name="806"><span class="lineNum">     806 </span>            :       }</a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">         82 :       ifiles_.emplace_back(Tools::make_unique&lt;IFile&gt;());</span></a>
+<a name="808"><span class="lineNum">     808 </span>            :       // this is just a shortcut pointer to the last element:</a>
+<a name="809"><span class="lineNum">     809 </span>            :       IFile *ifile = ifiles_.back().get();</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">         82 :       ifile-&gt;link(*this);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">         82 :       ifilesnames_.push_back(fname);</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         82 :       if(ifile-&gt;FileExist(fname)) {</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         18 :         ifile-&gt;open(fname);</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         18 :         if(getRestart()&amp;&amp;!restartedFromGrid) {</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">          2 :           log.printf(&quot;  Restarting from %s:&quot;,ifilesnames_[k].c_str());</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">          2 :           readGaussians(i,ifiles_[k].get());</span></a>
+<a name="817"><span class="lineNum">     817 </span>            :         }</a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">         18 :         ifiles_[k]-&gt;reset(false);</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :         // close only the walker own hills file for later writing</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         18 :         if(j==mw_id_) ifiles_[k]-&gt;close();</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :       } else {</a>
+<a name="822"><span class="lineNum">     822 </span>            :         // in case a file does not exist and we are restarting, complain that the file was not found</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">         64 :         if(getRestart()) log&lt;&lt;&quot;  WARNING: restart file &quot;&lt;&lt;fname&lt;&lt;&quot; not found\n&quot;;</span></a>
+<a name="824"><span class="lineNum">     824 </span>            :       }</a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span>            :   }</a>
+<a name="827"><span class="lineNum">     827 </span>            : </a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         41 :   comm.Barrier();</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">         41 :   if(comm.Get_rank()==0 &amp;&amp; walkers_mpi_) multi_sim_comm.Barrier();</span></a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span>            :   // open hills files for writing</a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">        123 :   for(unsigned i=0; i&lt;hillsfname_.size(); ++i) {</span></a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">         82 :     auto ofile=Tools::make_unique&lt;OFile&gt;();</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">         82 :     ofile-&gt;link(*this);</span></a>
+<a name="835"><span class="lineNum">     835 </span>            :     // if MPI multiple walkers, only rank 0 will write to file</a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">         82 :     if(walkers_mpi_) {</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">         68 :       int r=0;</span></a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">         68 :       if(comm.Get_rank()==0) r=multi_sim_comm.Get_rank();</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">         68 :       comm.Bcast(r,0);</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">         68 :       if(r&gt;0) ifilesnames_[mw_id_*hillsfname_.size()+i]=&quot;/dev/null&quot;;</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">        136 :       ofile-&gt;enforceSuffix(&quot;&quot;);</span></a>
+<a name="842"><span class="lineNum">     842 </span>            :     }</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         82 :     if(mw_n_&gt;1) ofile-&gt;enforceSuffix(&quot;&quot;);</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">         82 :     ofile-&gt;open(ifilesnames_[mw_id_*hillsfname_.size()+i]);</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">         82 :     if(fmt_.length()&gt;0) ofile-&gt;fmtField(fmt_);</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">        164 :     ofile-&gt;addConstantField(&quot;multivariate&quot;);</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">        164 :     ofile-&gt;addConstantField(&quot;kerneltype&quot;);</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">         82 :     if(doInt_[i]) {</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">         16 :       ofile-&gt;addConstantField(&quot;lower_int&quot;).printField(&quot;lower_int&quot;,lowI_[i]);</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">         16 :       ofile-&gt;addConstantField(&quot;upper_int&quot;).printField(&quot;upper_int&quot;,uppI_[i]);</span></a>
+<a name="851"><span class="lineNum">     851 </span>            :     }</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">         82 :     ofile-&gt;setHeavyFlush();</span></a>
+<a name="853"><span class="lineNum">     853 </span>            :     // output periodicities of variables</a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">         82 :     ofile-&gt;setupPrintValue( pfhold_[i] );  //assuming cvs in the same family have the same periodicity and boundaries.</span></a>
+<a name="855"><span class="lineNum">     855 </span>            :     // push back</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">         82 :     hillsOfiles_.emplace_back(std::move(ofile));</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">         82 :   }</span></a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span>            :   // Dump grid to files</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">         41 :   if(wgridstride_ &gt; 0) {</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">         18 :     for(unsigned i = 0; i &lt; gridfilenames_.size(); ++i) {</span></a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">         12 :       auto ofile=Tools::make_unique&lt;OFile&gt;();</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">         12 :       ofile-&gt;link(*this);</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">         12 :       std::string gridfname_tmp = gridfilenames_[i];</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">         12 :       if(walkers_mpi_) {</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">          8 :         int r = 0;</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">          8 :         if(comm.Get_rank() == 0) {</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">          4 :           r = multi_sim_comm.Get_rank();</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :         }</a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">          8 :         comm.Bcast(r, 0);</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">          8 :         if(r&gt;0) {</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :           gridfname_tmp = &quot;/dev/null&quot;;</a>
+<a name="873"><span class="lineNum">     873 </span>            :         }</a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">         16 :         ofile-&gt;enforceSuffix(&quot;&quot;);</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :       }</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">         12 :       if(mw_n_&gt;1) ofile-&gt;enforceSuffix(&quot;&quot;);</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">         12 :       ofile-&gt;open(gridfname_tmp);</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">         12 :       ofile-&gt;setHeavyFlush();</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">         12 :       gridfiles_.emplace_back(std::move(ofile));</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">         12 :     }</span></a>
+<a name="881"><span class="lineNum">     881 </span>            :   }</a>
+<a name="882"><span class="lineNum">     882 </span>            : </a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">         82 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Pfaendtner and Bonomi. J. Chem. Theory Comput. 11, 5062 (2015)&quot;);</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         49 :   if(doInt_[0]) log&lt;&lt;plumed.cite(</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">          8 :                        &quot;Baftizadeh, Cossio, Pietrucci, and Laio, Curr. Phys. Chem. 2, 79 (2012)&quot;);</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">        109 :   if(mw_n_&gt;1||walkers_mpi_) log&lt;&lt;plumed.cite(</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">         68 :                                    &quot;Raiteri, Laio, Gervasio, Micheletti, and Parrinello, J. Phys. Chem. B 110, 3533 (2006)&quot;);</span></a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineCov">         49 :   if(adaptive_!=FlexibleBin::none) log&lt;&lt;plumed.cite(</span></a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">          8 :                                           &quot;Branduardi, Bussi, and Parrinello, J. Chem. Theory Comput. 8, 2247 (2012)&quot;);</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">         44 :   if (do_pf_) log&lt;&lt;plumed.cite(&quot;Prakash, Fu, Bonomi, and Pfaendtner, J. Chem. Theory Comput. 14, 4985 (2018)&quot;);</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">         41 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            : </a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">         82 : }</span></a>
+<a name="895"><span class="lineNum">     895 </span>            : </a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">          2 : void PBMetaD::readGaussians(unsigned iarg, IFile *ifile)</span></a>
+<a name="897"><span class="lineNum">     897 </span>            : {</a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">          2 :   std::vector&lt;double&gt; center(1);</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">          2 :   std::vector&lt;double&gt; sigma(1);</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :   double height;</a>
+<a name="901"><span class="lineNum">     901 </span>            :   int nhills=0;</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">          2 :   bool multivariate=false;</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">          2 :   int family=pfs_[iarg];</span></a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span>            :   std::vector&lt;Value&gt; tmpvalues;</a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">          4 :   tmpvalues.push_back( Value( this, pfhold_[family]-&gt;getName(), false ) );</span></a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">         10 :   while(scanOneHill(iarg,ifile,tmpvalues,center,sigma,height,multivariate)) {</span></a>
+<a name="909"><span class="lineNum">     909 </span>            :     ;</a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">          8 :     nhills++;</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">          8 :     if(welltemp_) {height*=(biasf_-1.0)/biasf_;}</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">          8 :     addGaussian(family, Gaussian(center,sigma,height,multivariate));</span></a>
+<a name="913"><span class="lineNum">     913 </span>            :   }</a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">          2 :   log.printf(&quot;      %d Gaussians read\n&quot;,nhills);</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">          4 : }</span></a>
+<a name="916"><span class="lineNum">     916 </span>            : </a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">       1100 : void PBMetaD::writeGaussian(unsigned iarg, const Gaussian&amp; hill, OFile *ofile)</span></a>
+<a name="918"><span class="lineNum">     918 </span>            : {</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">       1100 :   int family=pfs_[iarg];</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">       2200 :   ofile-&gt;printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">       1100 :   ofile-&gt;printField(pfhold_[family],hill.center[0]);</span></a>
+<a name="922"><span class="lineNum">     922 </span>            : </a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">       2200 :   ofile-&gt;printField(&quot;kerneltype&quot;,&quot;stretched-gaussian&quot;);</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">       1100 :   if(hill.multivariate) {</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">        288 :     ofile-&gt;printField(&quot;multivariate&quot;,&quot;true&quot;);</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">        144 :     double lower = std::sqrt(1./hill.sigma[0]);</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">        288 :     ofile-&gt;printField(&quot;sigma_&quot;+pfhold_[family]-&gt;getName()+&quot;_&quot;+</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">        144 :                       pfhold_[family]-&gt;getName(),lower);</span></a>
+<a name="929"><span class="lineNum">     929 </span>            :   } else {</a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">       1912 :     ofile-&gt;printField(&quot;multivariate&quot;,&quot;false&quot;);</span></a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">       1912 :     ofile-&gt;printField(&quot;sigma_&quot;+pfhold_[family]-&gt;getName(),hill.sigma[0]);</span></a>
+<a name="932"><span class="lineNum">     932 </span>            :   }</a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">       1100 :   double height=hill.height;</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">       1100 :   if(welltemp_) height *= biasf_/(biasf_-1.0);</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">       1100 :   ofile-&gt;printField(&quot;height&quot;,height);</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">       1100 :   ofile-&gt;printField(&quot;biasf&quot;,biasf_);</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">       1100 :   if(mw_n_&gt;1) ofile-&gt;printField(&quot;clock&quot;,int(std::time(0)));</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">       1100 :   ofile-&gt;printField();</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">       1100 : }</span></a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">       1108 : void PBMetaD::addGaussian(unsigned iarg, const Gaussian&amp; hill)</span></a>
+<a name="942"><span class="lineNum">     942 </span>            : {</a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">       1108 :   if(!grid_) {hills_[iarg].push_back(hill);}</span></a>
+<a name="944"><span class="lineNum">     944 </span>            :   else {</a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">        196 :     std::vector&lt;unsigned&gt; nneighb=getGaussianSupport(iarg, hill);</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">        196 :     std::vector&lt;Grid::index_t&gt; neighbors=BiasGrids_[iarg]-&gt;getNeighbors(hill.center,nneighb);</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">        196 :     std::vector&lt;double&gt; der(1);</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">        196 :     std::vector&lt;double&gt; xx(1);</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">        196 :     if(comm.Get_size()==1) {</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">       1064 :       for(unsigned i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">       1036 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">       1036 :         der[0]=0.0;</span></a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">       1036 :         BiasGrids_[iarg]-&gt;getPoint(ineigh,xx);</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">       1036 :         double bias=evaluateGaussian(iarg,xx,hill,&amp;der[0]);</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">       1036 :         BiasGrids_[iarg]-&gt;addValueAndDerivatives(ineigh,bias,der);</span></a>
+<a name="956"><span class="lineNum">     956 </span>            :       }</a>
+<a name="957"><span class="lineNum">     957 </span>            :     } else {</a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">        168 :       unsigned stride=comm.Get_size();</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">        168 :       unsigned rank=comm.Get_rank();</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">        168 :       std::vector&lt;double&gt; allder(neighbors.size(),0.0);</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">        168 :       std::vector&lt;double&gt; allbias(neighbors.size(),0.0);</span></a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">       3276 :       for(unsigned i=rank; i&lt;neighbors.size(); i+=stride) {</span></a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">       3108 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">       3108 :         BiasGrids_[iarg]-&gt;getPoint(ineigh,xx);</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">       3108 :         allbias[i]=evaluateGaussian(iarg,xx,hill,&amp;allder[i]);</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :       }</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">        168 :       comm.Sum(allbias);</span></a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">        168 :       comm.Sum(allder);</span></a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">       6384 :       for(unsigned i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">       6216 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">       6216 :         der[0]=allder[i];</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">       6216 :         BiasGrids_[iarg]-&gt;addValueAndDerivatives(ineigh,allbias[i],der);</span></a>
+<a name="973"><span class="lineNum">     973 </span>            :       }</a>
+<a name="974"><span class="lineNum">     974 </span>            :     }</a>
+<a name="975"><span class="lineNum">     975 </span>            :   }</a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">       1108 : }</span></a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">        196 : std::vector&lt;unsigned&gt; PBMetaD::getGaussianSupport(unsigned iarg, const Gaussian&amp; hill)</span></a>
+<a name="979"><span class="lineNum">     979 </span>            : {</a>
+<a name="980"><span class="lineNum">     980 </span>            :   std::vector&lt;unsigned&gt; nneigh;</a>
+<a name="981"><span class="lineNum">     981 </span>            :   double cutoff;</a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">        196 :   if(hill.multivariate) {</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">        144 :     double maxautoval=1./hill.sigma[0];</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">        144 :     cutoff=std::sqrt(2.0*dp2cutoff*maxautoval);</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :   } else {</a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">         52 :     cutoff=std::sqrt(2.0*dp2cutoff)*hill.sigma[0];</span></a>
+<a name="987"><span class="lineNum">     987 </span>            :   }</a>
+<a name="988"><span class="lineNum">     988 </span>            : </a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">        196 :   if(doInt_[iarg]) {</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">        144 :     if(hill.center[0]+cutoff &gt; uppI_[iarg] || hill.center[0]-cutoff &lt; lowI_[iarg]) {</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :       // in this case, we updated the entire grid to avoid problems</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineNoCov">          0 :       return BiasGrids_[iarg]-&gt;getNbin();</span></a>
+<a name="993"><span class="lineNum">     993 </span>            :     } else {</a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">        144 :       nneigh.push_back( static_cast&lt;unsigned&gt;(ceil(cutoff/BiasGrids_[iarg]-&gt;getDx()[0])));</span></a>
+<a name="995"><span class="lineNum">     995 </span>            :       return nneigh;</a>
+<a name="996"><span class="lineNum">     996 </span>            :     }</a>
+<a name="997"><span class="lineNum">     997 </span>            :   }</a>
+<a name="998"><span class="lineNum">     998 </span>            : </a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">         52 :   nneigh.push_back( static_cast&lt;unsigned&gt;(ceil(cutoff/BiasGrids_[iarg]-&gt;getDx()[0])) );</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            : </a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   return nneigh;</a>
+<a name="1002"><span class="lineNum">    1002 </span>            : }</a>
+<a name="1003"><span class="lineNum">    1003 </span>            : </a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">       1269 : double PBMetaD::getBiasAndDerivatives(unsigned iarg, const std::vector&lt;double&gt;&amp; cv, double* der)</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            : {</a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">       1269 :   double bias=0.0;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">       1269 :   int family = pfs_[iarg];</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineCov">       1269 :   if(!grid_) {</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">       1000 :     unsigned stride=comm.Get_size();</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">       1000 :     unsigned rank=comm.Get_rank();</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">       5520 :     for(unsigned i=rank; i&lt;hills_[family].size(); i+=stride) {</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">       4520 :       bias += evaluateGaussian(iarg,cv,hills_[family][i],der);</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :     }</a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">       1000 :     comm.Sum(bias);</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">       1000 :     if(der) comm.Sum(der,1);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            :   } else {</a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">        269 :     if(der) {</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">        145 :       std::vector&lt;double&gt; vder(1);</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">        145 :       bias = BiasGrids_[family]-&gt;getValueAndDerivatives(cv,vder);</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">        145 :       der[0] = vder[0];</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            :     } else {</a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">        124 :       bias = BiasGrids_[family]-&gt;getValue(cv);</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            :     }</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :   }</a>
+<a name="1025"><span class="lineNum">    1025 </span>            : </a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">       1269 :   return bias;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span>            : }</a>
+<a name="1028"><span class="lineNum">    1028 </span>            : </a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">       8664 : double PBMetaD::evaluateGaussian(unsigned iarg, const std::vector&lt;double&gt;&amp; cv, const Gaussian&amp; hill, double* der)</span></a>
+<a name="1030"><span class="lineNum">    1030 </span>            : {</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   double bias=0.0;</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : // I use a pointer here because cv is const (and should be const)</a>
+<a name="1033"><span class="lineNum">    1033 </span>            : // but when using doInt it is easier to locally replace cv[0] with</a>
+<a name="1034"><span class="lineNum">    1034 </span>            : // the upper/lower limit in case it is out of range</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :   const double *pcv=NULL;</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   double tmpcv[1]; // tmp array with cv (to be used with doInt_)</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">       8664 :   tmpcv[0]=cv[0];</span></a>
+<a name="1038"><span class="lineNum">    1038 </span>            :   bool isOutOfInt = false;</a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">       8664 :   if(doInt_[iarg]) {</span></a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">       2664 :     if(cv[0]&lt;lowI_[iarg]) { tmpcv[0]=lowI_[iarg]; isOutOfInt = true; }</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">       2664 :     else if(cv[0]&gt;uppI_[iarg]) { tmpcv[0]=uppI_[iarg]; isOutOfInt = true; }</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            :   }</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :   pcv=&amp;(tmpcv[0]);</a>
+<a name="1044"><span class="lineNum">    1044 </span>            : </a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">       8664 :   if(hill.multivariate) {</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">       2664 :     double dp  = difference(iarg, hill.center[0], pcv[0]);</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">       2664 :     double dp2 = 0.5 * dp * dp * hill.sigma[0];</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">       2664 :     if(dp2&lt;dp2cutoff) {</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">       2534 :       bias = hill.height*std::exp(-dp2);</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">       2534 :       if(der &amp;&amp; !isOutOfInt) {</span></a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">       2534 :         der[0] += -bias * dp * hill.sigma[0] * stretchA;</span></a>
+<a name="1052"><span class="lineNum">    1052 </span>            :       }</a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">       2534 :       bias=stretchA*bias+hill.height*stretchB;</span></a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     }</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   } else {</a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">       6000 :     double dp  = difference(iarg, hill.center[0], pcv[0]) * hill.invsigma[0];</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">       6000 :     double dp2 = 0.5 * dp * dp;</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">       6000 :     if(dp2&lt;dp2cutoff) {</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">       5938 :       bias = hill.height*std::exp(-dp2);</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">       5938 :       if(der &amp;&amp; !isOutOfInt) {</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">       3682 :         der[0] += -bias * dp * hill.invsigma[0] * stretchA;</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            :       }</a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">       5938 :       bias=stretchA*bias+hill.height*stretchB;</span></a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     }</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   }</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : </a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">       8664 :   return bias;</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            : }</a>
+<a name="1069"><span class="lineNum">    1069 </span>            : </a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">        335 : void PBMetaD::calculate()</span></a>
+<a name="1071"><span class="lineNum">    1071 </span>            : {</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :   // this is because presently there is no way to properly pass information</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   // on adaptive hills (diff) after exchanges:</a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">        335 :   if(adaptive_==FlexibleBin::diffusion &amp;&amp; getExchangeStep()) error(&quot;ADAPTIVE=DIFF is not compatible with replica exchange&quot;);</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            : </a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">        335 :   std::vector&lt;double&gt; cv(1);</span></a>
+<a name="1077"><span class="lineNum">    1077 </span>            :   double der[1];</a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">        335 :   std::vector&lt;double&gt; bias(getNumberOfArguments());</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">        335 :   std::vector&lt;double&gt; deriv(getNumberOfArguments());</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            : </a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">        335 :   double ncv = (double) getNumberOfArguments();</span></a>
+<a name="1082"><span class="lineNum">    1082 </span>            :   double bmin = 1.0e+19;</a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">       1020 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">        685 :     cv[0]    = getArgument(i);</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">        685 :     der[0]   = 0.0;</span></a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">        685 :     bias[i]  = getBiasAndDerivatives(i, cv, der);</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">        685 :     deriv[i] = der[0];</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">        685 :     if(bias[i] &lt; bmin) bmin = bias[i];</span></a>
+<a name="1089"><span class="lineNum">    1089 </span>            :   }</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   double ene = 0.;</a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">       1020 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">        685 :     ene += std::exp((-bias[i]+bmin)/kbt_);</span></a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   }</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   // set Forces - set them to zero if SELECTOR is active</a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">        335 :   if(do_select_) current_value_ = static_cast&lt;unsigned&gt;(plumed.passMap[selector_]);</span></a>
+<a name="1097"><span class="lineNum">    1097 </span>            : </a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">        335 :   if(!do_select_ || select_value_==current_value_) {</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">       1020 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">        685 :       const double f = - std::exp((-bias[i]+bmin)/kbt_) / (ene) * deriv[i];</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">        685 :       setOutputForce(i, f);</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     }</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   }</a>
+<a name="1104"><span class="lineNum">    1104 </span>            : </a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">        335 :   if(do_select_ &amp;&amp; select_value_!=current_value_) {</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) setOutputForce(i, 0.0);</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   }</a>
+<a name="1108"><span class="lineNum">    1108 </span>            : </a>
+<a name="1109"><span class="lineNum">    1109 </span>            :   // set bias</a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">        335 :   ene = -kbt_ * (std::log(ene) - std::log(ncv)) + bmin;</span></a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   setBias(ene);</a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineCov">        335 : }</span></a>
+<a name="1113"><span class="lineNum">    1113 </span>            : </a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">        335 : void PBMetaD::update()</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            : {</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :   bool multivariate;</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   // adding hills criteria</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   bool nowAddAHill;</a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">        335 :   if(getStep()%stride_==0 &amp;&amp; !isFirstStep_) nowAddAHill=true;</span></a>
+<a name="1120"><span class="lineNum">    1120 </span>            :   else {</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     nowAddAHill=false;</a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">         49 :     isFirstStep_=false;</span></a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   }</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : </a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   // if you use adaptive, call the FlexibleBin</a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">        335 :   if(adaptive_!=FlexibleBin::none) {</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">        120 :     for(unsigned i=0; i&lt;getNumberOfArguments(); i++) flexbin_[i].update(nowAddAHill,i);</span></a>
+<a name="1128"><span class="lineNum">    1128 </span>            :     multivariate=true;</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   } else {</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :     multivariate=false;</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   }</a>
+<a name="1132"><span class="lineNum">    1132 </span>            : </a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">        335 :   if(nowAddAHill &amp;&amp; (!do_select_ || select_value_==current_value_)) {</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     // get all biases and heights</a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">        286 :     std::vector&lt;double&gt; cv(getNumberOfArguments());</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">        286 :     std::vector&lt;double&gt; bias(getNumberOfArguments());</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">        286 :     std::vector&lt;double&gt; thissigma(getNumberOfArguments());</span></a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">        286 :     std::vector&lt;double&gt; height(getNumberOfArguments());</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">        286 :     std::vector&lt;double&gt; cv_tmp(1);</span></a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineCov">        286 :     std::vector&lt;double&gt; sigma_tmp(1);</span></a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     double norm = 0.0;</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :     double bmin = 1.0e+19;</a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">        870 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">        584 :       int family=pfs_[i];</span></a>
+<a name="1145"><span class="lineNum">    1145 </span>            :       // get flex/sigmas for each family and assign them to this args sigma</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">        584 :       if(adaptive_!=FlexibleBin::none) thissigma[i]=flexbin_[family].getInverseMatrix(i)[0];</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">        512 :       else thissigma[i]=sigma0_[family];</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">        584 :       cv[i]     = getArgument(i);</span></a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">        584 :       cv_tmp[0] = getArgument(i);</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">        584 :       bias[i] = getBiasAndDerivatives(i, cv_tmp);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">        584 :       if(bias[i] &lt; bmin) bmin = bias[i];</span></a>
+<a name="1152"><span class="lineNum">    1152 </span>            :     }</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :     // calculate heights and norm</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">        870 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">        584 :       double h = std::exp((-bias[i]+bmin)/kbt_);</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">        584 :       norm += h;</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">        584 :       height[i] = h;</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :     }</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :     // normalize and apply welltemp correction</a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">        870 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">        584 :       height[i] *=  height0_ / norm;</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">        584 :       if(welltemp_) height[i] *= std::exp(-bias[i]/(kbt_*(biasf_-1.0)));</span></a>
+<a name="1163"><span class="lineNum">    1163 </span>            :     }</a>
+<a name="1164"><span class="lineNum">    1164 </span>            : </a>
+<a name="1165"><span class="lineNum">    1165 </span>            :     // MPI Multiple walkers: share hills and add them all</a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">        286 :     if(walkers_mpi_) {</span></a>
+<a name="1167"><span class="lineNum">    1167 </span>            :       // Allocate arrays to store all walkers hills</a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineCov">        258 :       std::vector&lt;double&gt; all_cv(mpi_nw_*cv.size(), 0.0);</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">        258 :       std::vector&lt;double&gt; all_sigma(mpi_nw_*getNumberOfArguments(), 0.0);</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">        258 :       std::vector&lt;double&gt; all_height(mpi_nw_*height.size(), 0.0);</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineCov">        258 :       if(comm.Get_rank()==0) {</span></a>
+<a name="1172"><span class="lineNum">    1172 </span>            :         // fill in value</a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineCov">        390 :         for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineCov">        260 :           unsigned j = mpi_id_ * getNumberOfArguments() + i;</span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineCov">        260 :           all_cv[j] = cv[i];</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">        260 :           all_sigma[j]  = thissigma[i];</span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">        260 :           all_height[j] = height[i];</span></a>
+<a name="1178"><span class="lineNum">    1178 </span>            :         }</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :         // Communicate (only root)</a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineCov">        130 :         multi_sim_comm.Sum(&amp;all_cv[0], all_cv.size());</span></a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineCov">        130 :         multi_sim_comm.Sum(&amp;all_sigma[0], all_sigma.size());</span></a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">        130 :         multi_sim_comm.Sum(&amp;all_height[0], all_height.size());</span></a>
+<a name="1183"><span class="lineNum">    1183 </span>            :       }</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :       // Share info with group members</a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">        258 :       comm.Sum(&amp;all_cv[0], all_cv.size());</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineCov">        258 :       comm.Sum(&amp;all_sigma[0], all_sigma.size());</span></a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">        258 :       comm.Sum(&amp;all_height[0], all_height.size());</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :       // now add hills one by one</a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">        774 :       for(unsigned j=0; j&lt;mpi_nw_; ++j) {</span></a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineCov">       1548 :         for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1191"><span class="lineNum">    1191 </span>            :           // Add CVs of same family together and write to same file</a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineCov">       1032 :           int family = pfs_[i];</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineCov">       1032 :           cv_tmp[0]    = all_cv[j*cv.size()+i];</span></a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineCov">       1032 :           double height_tmp = all_height[j*cv.size()+i];</span></a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineCov">       1032 :           sigma_tmp[0] = all_sigma[j*cv.size()+i];</span></a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineCov">       1032 :           Gaussian newhill = Gaussian(cv_tmp, sigma_tmp, height_tmp, multivariate);</span></a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineCov">       1032 :           addGaussian(family, newhill);</span></a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineCov">       1032 :           writeGaussian(i, newhill, hillsOfiles_[family].get());</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineCov">       1032 :         }</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            :       }</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :       // just add your own hills</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :     } else {</a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineCov">         96 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1204"><span class="lineNum">    1204 </span>            :         // Add CVs of same family together and write to same file</a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">         68 :         int family = pfs_[i];</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">         68 :         cv_tmp[0] = cv[i];</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">         68 :         if(adaptive_!=FlexibleBin::none) sigma_tmp[0]=thissigma[i];</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">         68 :         else sigma_tmp[0] = sigma0_[family];</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">         68 :         Gaussian newhill = Gaussian(cv_tmp, sigma_tmp, height[i], multivariate);</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">         68 :         addGaussian(family, newhill);</span></a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineCov">         68 :         writeGaussian(i, newhill, hillsOfiles_[family].get());</span></a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineCov">         68 :       }</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            :     }</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :   }</a>
+<a name="1215"><span class="lineNum">    1215 </span>            : </a>
+<a name="1216"><span class="lineNum">    1216 </span>            :   // write grid files</a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">        335 :   if(wgridstride_&gt;0 &amp;&amp; (getStep()%wgridstride_==0 || getCPT())) {</span></a>
+<a name="1218"><span class="lineNum">    1218 </span><span class="lineCov">         14 :     int r = 0;</span></a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">         14 :     if(walkers_mpi_) {</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">          4 :       if(comm.Get_rank()==0) r=multi_sim_comm.Get_rank();</span></a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineCov">          4 :       comm.Bcast(r,0);</span></a>
+<a name="1222"><span class="lineNum">    1222 </span>            :     }</a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">         14 :     if(r==0) {</span></a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">         36 :       for(unsigned i=0; i&lt;gridfiles_.size(); ++i) {</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">         24 :         gridfiles_[i]-&gt;rewind();</span></a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">         24 :         BiasGrids_[i]-&gt;writeToFile(*gridfiles_[i]);</span></a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">         24 :         gridfiles_[i]-&gt;flush();</span></a>
+<a name="1228"><span class="lineNum">    1228 </span>            :       }</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :     }</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   }</a>
+<a name="1231"><span class="lineNum">    1231 </span>            : </a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   // if multiple walkers and time to read Gaussians</a>
+<a name="1233"><span class="lineNum">    1233 </span><span class="lineCov">        335 :   if(mw_n_&gt;1 &amp;&amp; getStep()%mw_rstride_==0) {</span></a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineNoCov">          0 :     for(int j=0; j&lt;mw_n_; ++j) {</span></a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;hillsfname_.size(); ++i) {</span></a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineNoCov">          0 :         unsigned k=j*hillsfname_.size()+i;</span></a>
+<a name="1237"><span class="lineNum">    1237 </span>            :         // don't read your own Gaussians</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineNoCov">          0 :         if(j==mw_id_) continue;</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            :         // if the file is not open yet</a>
+<a name="1240"><span class="lineNum">    1240 </span><span class="lineNoCov">          0 :         if(!(ifiles_[k]-&gt;isOpen())) {</span></a>
+<a name="1241"><span class="lineNum">    1241 </span>            :           // check if it exists now and open it!</a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineNoCov">          0 :           if(ifiles_[k]-&gt;FileExist(ifilesnames_[k])) {</span></a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineNoCov">          0 :             ifiles_[k]-&gt;open(ifilesnames_[k]);</span></a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineNoCov">          0 :             ifiles_[k]-&gt;reset(false);</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :           }</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :           // otherwise read the new Gaussians</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :         } else {</a>
+<a name="1248"><span class="lineNum">    1248 </span><span class="lineNoCov">          0 :           log.printf(&quot;  Reading hills from %s:&quot;,ifilesnames_[k].c_str());</span></a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineNoCov">          0 :           readGaussians(i,ifiles_[k].get());</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineNoCov">          0 :           ifiles_[k]-&gt;reset(false);</span></a>
+<a name="1251"><span class="lineNum">    1251 </span>            :         }</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :       }</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :     }</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   }</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : </a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineCov">        335 : }</span></a>
+<a name="1257"><span class="lineNum">    1257 </span>            : </a>
+<a name="1258"><span class="lineNum">    1258 </span>            : /// takes a pointer to the file and a template string with values v and gives back the next center, sigma and height</a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineCov">         10 : bool PBMetaD::scanOneHill(unsigned iarg, IFile *ifile, std::vector&lt;Value&gt; &amp;tmpvalues, std::vector&lt;double&gt; &amp;center, std::vector&lt;double&gt; &amp;sigma, double &amp;height, bool &amp;multivariate)</span></a>
+<a name="1260"><span class="lineNum">    1260 </span>            : {</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :   double dummy;</a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineCov">         10 :   multivariate=false;</span></a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">         10 :   Value* argPtr = pfhold_[pfs_[iarg]];</span></a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineCov">         20 :   if(ifile-&gt;scanField(&quot;time&quot;,dummy)) {</span></a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineCov">          8 :     ifile-&gt;scanField( &amp;tmpvalues[0] );</span></a>
+<a name="1266"><span class="lineNum">    1266 </span><span class="lineCov">          8 :     if( tmpvalues[0].isPeriodic() &amp;&amp; ! argPtr-&gt;isPeriodic() ) {</span></a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineNoCov">          0 :       error(&quot;in hills file periodicity for variable &quot; + tmpvalues[0].getName() + &quot; does not match periodicity in input&quot;);</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineCov">          8 :     } else if( tmpvalues[0].isPeriodic() ) {</span></a>
+<a name="1269"><span class="lineNum">    1269 </span><span class="lineNoCov">          0 :       std::string imin, imax; tmpvalues[0].getDomain( imin, imax );</span></a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineNoCov">          0 :       std::string rmin, rmax; argPtr-&gt;getDomain( rmin, rmax );</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineNoCov">          0 :       if( imin!=rmin || imax!=rmax ) {</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineNoCov">          0 :         error(&quot;in hills file periodicity for variable &quot; + tmpvalues[0].getName() + &quot; does not match periodicity in input&quot;);</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :       }</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :     }</a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">          8 :     center[0]=tmpvalues[0].get();</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">          8 :     std::string ktype=&quot;stretched-gaussian&quot;;</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineCov">         24 :     if( ifile-&gt;FieldExist(&quot;kerneltype&quot;) ) ifile-&gt;scanField(&quot;kerneltype&quot;,ktype);</span></a>
+<a name="1278"><span class="lineNum">    1278 </span>            : </a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">          8 :     if( ktype==&quot;gaussian&quot; ) {</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineNoCov">          0 :       noStretchWarning();</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">          8 :     } else if( ktype!=&quot;stretched-gaussian&quot;) {</span></a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineNoCov">          0 :       error(&quot;non Gaussian kernels are not supported in MetaD&quot;);</span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            :     }</a>
+<a name="1284"><span class="lineNum">    1284 </span>            : </a>
+<a name="1285"><span class="lineNum">    1285 </span>            :     std::string sss;</a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineCov">         16 :     ifile-&gt;scanField(&quot;multivariate&quot;,sss);</span></a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineCov">          8 :     if(sss==&quot;true&quot;) multivariate=true;</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">          8 :     else if(sss==&quot;false&quot;) multivariate=false;</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineNoCov">          0 :     else plumed_merror(&quot;cannot parse multivariate = &quot;+ sss);</span></a>
+<a name="1290"><span class="lineNum">    1290 </span><span class="lineCov">          8 :     if(multivariate) {</span></a>
+<a name="1291"><span class="lineNum">    1291 </span><span class="lineNoCov">          0 :       ifile-&gt;scanField(&quot;sigma_&quot;+argPtr-&gt;getName()+&quot;_&quot;+</span></a>
+<a name="1292"><span class="lineNum">    1292 </span>            :                        argPtr-&gt;getName(),sigma[0]);</a>
+<a name="1293"><span class="lineNum">    1293 </span><span class="lineNoCov">          0 :       sigma[0] = 1./(sigma[0]*sigma[0]);</span></a>
+<a name="1294"><span class="lineNum">    1294 </span>            :     } else {</a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineCov">         16 :       ifile-&gt;scanField(&quot;sigma_&quot;+argPtr-&gt;getName(),sigma[0]);</span></a>
+<a name="1296"><span class="lineNum">    1296 </span>            :     }</a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineCov">          8 :     ifile-&gt;scanField(&quot;height&quot;,height);</span></a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineCov">          8 :     ifile-&gt;scanField(&quot;biasf&quot;,dummy);</span></a>
+<a name="1299"><span class="lineNum">    1299 </span><span class="lineCov">         16 :     if(ifile-&gt;FieldExist(&quot;clock&quot;)) ifile-&gt;scanField(&quot;clock&quot;,dummy);</span></a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">         16 :     if(ifile-&gt;FieldExist(&quot;lower_int&quot;)) ifile-&gt;scanField(&quot;lower_int&quot;,dummy);</span></a>
+<a name="1301"><span class="lineNum">    1301 </span><span class="lineCov">         16 :     if(ifile-&gt;FieldExist(&quot;upper_int&quot;)) ifile-&gt;scanField(&quot;upper_int&quot;,dummy);</span></a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineCov">          8 :     ifile-&gt;scanField();</span></a>
+<a name="1303"><span class="lineNum">    1303 </span>            :     return true;</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :   } else {</a>
+<a name="1305"><span class="lineNum">    1305 </span>            :     return false;</a>
+<a name="1306"><span class="lineNum">    1306 </span>            :   }</a>
+<a name="1307"><span class="lineNum">    1307 </span>            : </a>
+<a name="1308"><span class="lineNum">    1308 </span>            : }</a>
+<a name="1309"><span class="lineNum">    1309 </span>            : </a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineCov">        335 : bool PBMetaD::checkNeedsGradients()const</span></a>
+<a name="1311"><span class="lineNum">    1311 </span>            : {</a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">        335 :   if(adaptive_==FlexibleBin::geometry) {</span></a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineNoCov">          0 :     if(getStep()%stride_==0 &amp;&amp; !isFirstStep_) return true;</span></a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineNoCov">          0 :     else return false;</span></a>
+<a name="1315"><span class="lineNum">    1315 </span>            :   } else return false;</a>
+<a name="1316"><span class="lineNum">    1316 </span>            : }</a>
+<a name="1317"><span class="lineNum">    1317 </span>            : </a>
+<a name="1318"><span class="lineNum">    1318 </span>            : }</a>
+<a name="1319"><span class="lineNum">    1319 </span>            : }</a>
+<a name="1320"><span class="lineNum">    1320 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Restraint.cpp.func-sort-c.html b/coverage/bias/Restraint.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e9c89d51b3
--- /dev/null
+++ b/coverage/bias/Restraint.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Restraint.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Restraint.cpp<span style="font-size: 80%;"> (<a href="Restraint.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Restraint.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#79">_ZN4PLMD4bias9RestraintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#68">_ZN4PLMD4bias12_GLOBAL__N_121RestraintRegisterMe706createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#79">_ZN4PLMD4bias9RestraintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#70">_ZN4PLMD4bias9Restraint16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">180</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#68">_ZN4PLMD4bias12_GLOBAL__N_121RestraintRegisterMe70C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#68">_ZN4PLMD4bias12_GLOBAL__N_121RestraintRegisterMe70D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#106">_ZN4PLMD4bias9Restraint9calculateEv</a></td>
+              <td class="coverFnHi">4670</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Restraint.cpp.func.html b/coverage/bias/Restraint.cpp.func.html
new file mode 100644
index 0000000000..9182ef5568
--- /dev/null
+++ b/coverage/bias/Restraint.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Restraint.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Restraint.cpp<span style="font-size: 80%;"> (<a href="Restraint.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Restraint.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#68">_ZN4PLMD4bias12_GLOBAL__N_121RestraintRegisterMe706createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#68">_ZN4PLMD4bias12_GLOBAL__N_121RestraintRegisterMe70C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#68">_ZN4PLMD4bias12_GLOBAL__N_121RestraintRegisterMe70D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#70">_ZN4PLMD4bias9Restraint16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">180</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#106">_ZN4PLMD4bias9Restraint9calculateEv</a></td>
+              <td class="coverFnHi">4670</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#79">_ZN4PLMD4bias9RestraintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restraint.cpp.gcov.html#79">_ZN4PLMD4bias9RestraintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/Restraint.cpp.gcov.html b/coverage/bias/Restraint.cpp.gcov.html
new file mode 100644
index 0000000000..759ab058cf
--- /dev/null
+++ b/coverage/bias/Restraint.cpp.gcov.html
@@ -0,0 +1,203 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/Restraint.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - Restraint.cpp<span style="font-size: 80%;"> (source / <a href="Restraint.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace bias {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC BIAS RESTRAINT</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Adds harmonic and/or linear restraints on one or more variables.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : Either or both</a>
+<a name="33"><span class="lineNum">      33 </span>            : of SLOPE and KAPPA must be present to specify the linear and harmonic force constants</a>
+<a name="34"><span class="lineNum">      34 </span>            : respectively.  The resulting potential is given by:</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f[</a>
+<a name="36"><span class="lineNum">      36 </span>            :   \sum_i \frac{k_i}{2} (x_i-a_i)^2 + m_i*(x_i-a_i)</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f].</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The number of components for any vector of force constants must be equal to the number</a>
+<a name="40"><span class="lineNum">      40 </span>            : of arguments to the action.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Additional material and examples can be also found in the tutorial \ref lugano-2</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \par Examples</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : The following input tells plumed to restrain the distance between atoms 3 and 5</a>
+<a name="47"><span class="lineNum">      47 </span>            : and the distance between atoms 2 and 4, at different equilibrium</a>
+<a name="48"><span class="lineNum">      48 </span>            : values, and to print the energy of the restraint</a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="51"><span class="lineNum">      51 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="52"><span class="lineNum">      52 </span>            : RESTRAINT ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 LABEL=restraint</a>
+<a name="53"><span class="lineNum">      53 </span>            : PRINT ARG=restraint.bias</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endplumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : */</a>
+<a name="57"><span class="lineNum">      57 </span>            : //+ENDPLUMEDOC</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : class Restraint : public Bias {</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;double&gt; at;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::vector&lt;double&gt; kappa;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;double&gt; slope;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   Value* valueForce2;</a>
+<a name="64"><span class="lineNum">      64 </span>            : public:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   explicit Restraint(const ActionOptions&amp;);</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void calculate() override;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="68"><span class="lineNum">      68 </span>            : };</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      12857 : PLUMED_REGISTER_ACTION(Restraint,&quot;RESTRAINT&quot;)</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        180 : void Restraint::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        180 :   Bias::registerKeywords(keys);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        180 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        360 :   keys.add(&quot;compulsory&quot;,&quot;SLOPE&quot;,&quot;0.0&quot;,&quot;specifies that the restraint is linear and what the values of the force constants on each of the variables are&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        360 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;0.0&quot;,&quot;specifies that the restraint is harmonic and what the values of the force constants on each of the variables are&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        360 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;the position of the restraint&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        360 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        180 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        178 : Restraint::Restraint(const ActionOptions&amp;ao):</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        350 :   at(getNumberOfArguments()),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        175 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        353 :   slope(getNumberOfArguments(),0.0)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : {</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        175 :   parseVector(&quot;SLOPE&quot;,slope);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        175 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        175 :   parseVector(&quot;AT&quot;,at);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        175 :   checkRead();</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        175 :   log.printf(&quot;  at&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        385 :   for(unsigned i=0; i&lt;at.size(); i++) log.printf(&quot; %f&quot;,at[i]);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        175 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        175 :   log.printf(&quot;  with harmonic force constant&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        385 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        175 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        175 :   log.printf(&quot;  and linear force constant&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        385 :   for(unsigned i=0; i&lt;slope.size(); i++) log.printf(&quot; %f&quot;,slope[i]);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        175 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        175 :   addComponent(&quot;force2&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        175 :   componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        175 :   valueForce2=getPntrToComponent(&quot;force2&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        178 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       4670 : void Restraint::calculate() {</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   double ene=0.0;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double totf2=0.0;</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       9607 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       4937 :     const double cv=difference(i,at[i],getArgument(i));</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       4937 :     const double k=kappa[i];</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       4937 :     const double m=slope[i];</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4937 :     const double f=-(k*cv+m);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       4937 :     ene+=0.5*k*cv*cv+m*cv;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     setOutputForce(i,f);</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       4937 :     totf2+=f*f;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   }</a>
+<a name="120"><span class="lineNum">     120 </span>            :   setBias(ene);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       4670 :   valueForce2-&gt;set(totf2);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       4670 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBase.cpp.func-sort-c.html b/coverage/bias/ReweightBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fa5f69e397
--- /dev/null
+++ b/coverage/bias/ReweightBase.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBase.cpp<span style="font-size: 80%;"> (<a href="ReweightBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReweightBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#36">_ZN4PLMD4bias12ReweightBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#36">_ZN4PLMD4bias12ReweightBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#27">_ZN4PLMD4bias12ReweightBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#49">_ZN4PLMD4bias12ReweightBase9calculateEv</a></td>
+              <td class="coverFnHi">6232</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBase.cpp.func.html b/coverage/bias/ReweightBase.cpp.func.html
new file mode 100644
index 0000000000..893e68c787
--- /dev/null
+++ b/coverage/bias/ReweightBase.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBase.cpp<span style="font-size: 80%;"> (<a href="ReweightBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReweightBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#27">_ZN4PLMD4bias12ReweightBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#49">_ZN4PLMD4bias12ReweightBase9calculateEv</a></td>
+              <td class="coverFnHi">6232</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#36">_ZN4PLMD4bias12ReweightBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.cpp.gcov.html#36">_ZN4PLMD4bias12ReweightBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBase.cpp.gcov.html b/coverage/bias/ReweightBase.cpp.gcov.html
new file mode 100644
index 0000000000..b51f7236fd
--- /dev/null
+++ b/coverage/bias/ReweightBase.cpp.gcov.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBase.cpp<span style="font-size: 80%;"> (source / <a href="ReweightBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReweightBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace bias {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         28 : void ReweightBase::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         28 :   Action::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         28 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         28 :   ActionWithArguments::registerKeywords( keys );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         28 :   keys.setComponentsIntroduction(&quot;This action calculates the logarithm of a weight for reweighting&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         56 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature.  This is not required if your MD code passes this quantity to PLUMED&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         28 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         28 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         20 : ReweightBase::ReweightBase(const ActionOptions&amp;ao):</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   Action(ao),</a>
+<a name="40"><span class="lineNum">      40 </span>            :   ActionWithValue(ao),</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         20 :   ActionWithArguments(ao)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         20 :   simtemp=0.; parse(&quot;TEMP&quot;,simtemp);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         20 :   if(simtemp&gt;0) simtemp*=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 :   else simtemp=plumed.getAtoms().getKbT();</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         20 :   if(simtemp==0) error(&quot;The MD engine does not pass the temperature to plumed so you have to specify it using TEMP&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   // Create something to hold the weight</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         20 :   addValue(); setNotPeriodic();</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         20 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       6232 : void ReweightBase::calculate() {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       6232 :   double weight = getLogWeight();</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       6232 :   setValue( weight );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       6232 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBase.h.func-sort-c.html b/coverage/bias/ReweightBase.h.func-sort-c.html
new file mode 100644
index 0000000000..0c91deea9b
--- /dev/null
+++ b/coverage/bias/ReweightBase.h.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBase.h<span style="font-size: 80%;"> (<a href="ReweightBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReweightBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#42">_ZN4PLMD4bias12ReweightBase16calculateWeightsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#39">_ZN4PLMD4bias12ReweightBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#45">_ZN4PLMD4bias12ReweightBase9clearDataEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#44">_ZNK4PLMD4bias12ReweightBase9getWeightERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#40">_ZNK4PLMD4bias12ReweightBase17buildsWeightStoreEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#46">_ZN4PLMD4bias12ReweightBase5applyEv</a></td>
+              <td class="coverFnHi">6232</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBase.h.func.html b/coverage/bias/ReweightBase.h.func.html
new file mode 100644
index 0000000000..63b26cd728
--- /dev/null
+++ b/coverage/bias/ReweightBase.h.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBase.h<span style="font-size: 80%;"> (<a href="ReweightBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReweightBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#42">_ZN4PLMD4bias12ReweightBase16calculateWeightsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#39">_ZN4PLMD4bias12ReweightBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#46">_ZN4PLMD4bias12ReweightBase5applyEv</a></td>
+              <td class="coverFnHi">6232</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#45">_ZN4PLMD4bias12ReweightBase9clearDataEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#40">_ZNK4PLMD4bias12ReweightBase17buildsWeightStoreEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBase.h.gcov.html#44">_ZNK4PLMD4bias12ReweightBase9getWeightERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBase.h.gcov.html b/coverage/bias/ReweightBase.h.gcov.html
new file mode 100644
index 0000000000..30d7d1551c
--- /dev/null
+++ b/coverage/bias/ReweightBase.h.gcov.html
@@ -0,0 +1,129 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBase.h<span style="font-size: 80%;"> (source / <a href="ReweightBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_bias_ReweightBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_bias_ReweightBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace bias {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class ReweightBase :</a>
+<a name="32"><span class="lineNum">      32 </span>            :   public ActionWithValue,</a>
+<a name="33"><span class="lineNum">      33 </span>            :   public ActionWithArguments</a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span>            : protected:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// The temperature at which you are running the simulation</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double simtemp;</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit ReweightBase(const ActionOptions&amp;ao);</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :   unsigned getNumberOfDerivatives() override { return 0; }</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          7 :   virtual bool buildsWeightStore() const { return false; }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   void calculate() override;</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :   virtual void calculateWeights( const unsigned&amp; nframes ) {}</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   virtual double getLogWeight() = 0;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 :   virtual double getWeight( const unsigned&amp; iweight ) const { plumed_error(); }</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   virtual void clearData() {}</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       6232 :   void apply() override {}</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : };</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : }</a>
+<a name="53"><span class="lineNum">      53 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBias.cpp.func-sort-c.html b/coverage/bias/ReweightBias.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f7e5f1ba35
--- /dev/null
+++ b/coverage/bias/ReweightBias.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBias.cpp<span style="font-size: 80%;"> (<a href="ReweightBias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReweightBias.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#83">_ZN4PLMD4bias12ReweightBiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#83">_ZN4PLMD4bias12ReweightBiasC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#76">_ZN4PLMD4bias12_GLOBAL__N_124ReweightBiasRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#78">_ZN4PLMD4bias12ReweightBias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#89">_ZN4PLMD4bias12ReweightBias12getLogWeightEv</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#76">_ZN4PLMD4bias12_GLOBAL__N_124ReweightBiasRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#76">_ZN4PLMD4bias12_GLOBAL__N_124ReweightBiasRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBias.cpp.func.html b/coverage/bias/ReweightBias.cpp.func.html
new file mode 100644
index 0000000000..5dd9964935
--- /dev/null
+++ b/coverage/bias/ReweightBias.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBias.cpp<span style="font-size: 80%;"> (<a href="ReweightBias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReweightBias.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#89">_ZN4PLMD4bias12ReweightBias12getLogWeightEv</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#78">_ZN4PLMD4bias12ReweightBias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#83">_ZN4PLMD4bias12ReweightBiasC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#83">_ZN4PLMD4bias12ReweightBiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#76">_ZN4PLMD4bias12_GLOBAL__N_124ReweightBiasRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#76">_ZN4PLMD4bias12_GLOBAL__N_124ReweightBiasRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightBias.cpp.gcov.html#76">_ZN4PLMD4bias12_GLOBAL__N_124ReweightBiasRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightBias.cpp.gcov.html b/coverage/bias/ReweightBias.cpp.gcov.html
new file mode 100644
index 0000000000..f7792e4ace
--- /dev/null
+++ b/coverage/bias/ReweightBias.cpp.gcov.html
@@ -0,0 +1,174 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightBias.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightBias.cpp<span style="font-size: 80%;"> (source / <a href="ReweightBias.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReweightBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC REWEIGHTING REWEIGHT_BIAS</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Calculate weights for ensemble averages that negate the effect the bias has on the region of phase space explored</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : If a static or pseudo-static bias \f$V(x,t')\f$ is acting on</a>
+<a name="30"><span class="lineNum">      30 </span>            : the system we can remove the bias and get the unbiased probability distribution using:</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            : \langle P(s',t) \rangle = \frac{ \sum_{t'}^t \delta( s(x) - s' ) \exp\left( +\frac{V(x,t')}{k_B T} \right) }{ \sum_t'^t \exp\left( +\frac{V(x,t')}{k_B T} \right) }</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : The weights calculated by this action are equal to \f$\exp\left( +\frac{V(x,t')}{k_B T} \right)\f$ these weights can then be used in any action</a>
+<a name="37"><span class="lineNum">      37 </span>            : that computes ensemble averages.  For example this action can be used in tandem with \ref HISTOGRAM or \ref AVERAGE.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : In the following example there is a fixed restraint on the distance between atoms 1 and 2.  Clearly, this</a>
+<a name="42"><span class="lineNum">      42 </span>            : restraint will have an effect on the region of phase space that will be sampled when an MD simulation is</a>
+<a name="43"><span class="lineNum">      43 </span>            : run using this variable.  Consequently, when the histogram as a function of the distance, \f$x\f$, is accumulated,</a>
+<a name="44"><span class="lineNum">      44 </span>            : we use reweighting into order to discount the effect of the bias from our final histogram.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : x: DISTANCE ATOMS=1,2</a>
+<a name="48"><span class="lineNum">      48 </span>            : RESTRAINT ARG=x SLOPE=1.0 AT=0.0</a>
+<a name="49"><span class="lineNum">      49 </span>            : bias: REWEIGHT_BIAS TEMP=300</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : HISTOGRAM ...</a>
+<a name="52"><span class="lineNum">      52 </span>            :   ARG=x</a>
+<a name="53"><span class="lineNum">      53 </span>            :   GRID_MIN=0.0</a>
+<a name="54"><span class="lineNum">      54 </span>            :   GRID_MAX=3.0</a>
+<a name="55"><span class="lineNum">      55 </span>            :   GRID_BIN=100</a>
+<a name="56"><span class="lineNum">      56 </span>            :   BANDWIDTH=0.1</a>
+<a name="57"><span class="lineNum">      57 </span>            :   LOGWEIGHTS=bias</a>
+<a name="58"><span class="lineNum">      58 </span>            :   LABEL=hB</a>
+<a name="59"><span class="lineNum">      59 </span>            : ... HISTOGRAM</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : */</a>
+<a name="66"><span class="lineNum">      66 </span>            : //+ENDPLUMEDOC</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : namespace PLMD {</a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace bias {</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : class ReweightBias : public ReweightBase {</a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit ReweightBias(const ActionOptions&amp;ao);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double getLogWeight() override;</a>
+<a name="76"><span class="lineNum">      76 </span>            : };</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(ReweightBias,&quot;REWEIGHT_BIAS&quot;)</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          5 : void ReweightBias::registerKeywords(Keywords&amp; keys ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          5 :   ReweightBase::registerKeywords( keys ); keys.remove(&quot;ARG&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;*.bias&quot;,&quot;the biases that must be taken into account when reweighting&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          5 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          3 : ReweightBias::ReweightBias(const ActionOptions&amp;ao):</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   Action(ao),</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 :   ReweightBase(ao)</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          3 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1007 : double ReweightBias::getLogWeight() {</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   // Retrieve the bias</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       2014 :   double bias=0.0; for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) bias+=getArgument(i);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1007 :   return bias / simtemp;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightMetad.cpp.func-sort-c.html b/coverage/bias/ReweightMetad.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c9e0f56dd2
--- /dev/null
+++ b/coverage/bias/ReweightMetad.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightMetad.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightMetad.cpp<span style="font-size: 80%;"> (<a href="ReweightMetad.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReweightMetad.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#80">_ZN4PLMD4bias13ReweightMetadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_125ReweightMetadRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#80">_ZN4PLMD4bias13ReweightMetadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#86">_ZN4PLMD4bias13ReweightMetad12getLogWeightEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#75">_ZN4PLMD4bias13ReweightMetad16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_125ReweightMetadRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_125ReweightMetadRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightMetad.cpp.func.html b/coverage/bias/ReweightMetad.cpp.func.html
new file mode 100644
index 0000000000..f58df3fef3
--- /dev/null
+++ b/coverage/bias/ReweightMetad.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightMetad.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightMetad.cpp<span style="font-size: 80%;"> (<a href="ReweightMetad.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReweightMetad.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_125ReweightMetadRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_125ReweightMetadRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_125ReweightMetadRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#86">_ZN4PLMD4bias13ReweightMetad12getLogWeightEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#75">_ZN4PLMD4bias13ReweightMetad16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#80">_ZN4PLMD4bias13ReweightMetadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightMetad.cpp.gcov.html#80">_ZN4PLMD4bias13ReweightMetadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightMetad.cpp.gcov.html b/coverage/bias/ReweightMetad.cpp.gcov.html
new file mode 100644
index 0000000000..3c22c0f2fe
--- /dev/null
+++ b/coverage/bias/ReweightMetad.cpp.gcov.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightMetad.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightMetad.cpp<span style="font-size: 80%;"> (source / <a href="ReweightMetad.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ReweightBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC REWEIGHTING REWEIGHT_METAD</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Calculate the weights configurations should contribute to the histogram in a simulation in which a metadynamics bias acts upon the system.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : This command allows you to use the reweighting algorithm discussed in \cite PratyushReweighting when constructing a histogram</a>
+<a name="30"><span class="lineNum">      30 </span>            : of the configurations visited during a metadynamics simulation.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : In the following example there is a metadynamics bias acting on the distance between atoms 1 and 2.  Clearly, this</a>
+<a name="35"><span class="lineNum">      35 </span>            : bias will have an effect on the region of phase space that will be sampled when an MD simulation is</a>
+<a name="36"><span class="lineNum">      36 </span>            : run using this variable.  Consequently, when the histogram as a function of the angle, \f$a\f$, is accumulated,</a>
+<a name="37"><span class="lineNum">      37 </span>            : we use reweighting into order to discount the effect of the bias from our final histogram.  We do not use</a>
+<a name="38"><span class="lineNum">      38 </span>            : \ref REWEIGHT_BIAS here, however, as the bias changes with time.  We thus use the reweighting algorithm for</a>
+<a name="39"><span class="lineNum">      39 </span>            : metadynamics instead.  Notice also that we have to specify how often we would like to calculate the c(t) reweighting</a>
+<a name="40"><span class="lineNum">      40 </span>            : factor and the grid over which we calculate c(t) in the input to the METAD command.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : a: ANGLE ATOMS=1,2,3</a>
+<a name="44"><span class="lineNum">      44 </span>            : x: DISTANCE ATOMS=1,2</a>
+<a name="45"><span class="lineNum">      45 </span>            : METAD ARG=x PACE=100 SIGMA=0.1 HEIGHT=1.5 BIASFACTOR=5 GRID_MIN=0 GRID_MAX=10 GRID_BIN=100 CALC_RCT RCT_USTRIDE=50</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : bias: REWEIGHT_METAD TEMP=300</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : HISTOGRAM ...</a>
+<a name="50"><span class="lineNum">      50 </span>            :   ARG=a</a>
+<a name="51"><span class="lineNum">      51 </span>            :   GRID_MIN=0.0</a>
+<a name="52"><span class="lineNum">      52 </span>            :   GRID_MAX=pi</a>
+<a name="53"><span class="lineNum">      53 </span>            :   GRID_BIN=100</a>
+<a name="54"><span class="lineNum">      54 </span>            :   BANDWIDTH=0.1</a>
+<a name="55"><span class="lineNum">      55 </span>            :   LOGWEIGHTS=bias</a>
+<a name="56"><span class="lineNum">      56 </span>            :   LABEL=hB</a>
+<a name="57"><span class="lineNum">      57 </span>            : ... HISTOGRAM</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : DUMPGRID GRID=hB FILE=histoB STRIDE=1 FMT=%8.4f</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : */</a>
+<a name="63"><span class="lineNum">      63 </span>            : //+ENDPLUMEDOC</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : namespace PLMD {</a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace bias {</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class ReweightMetad : public ReweightBase {</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit ReweightMetad(const ActionOptions&amp;ao);</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double getLogWeight() override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(ReweightMetad,&quot;REWEIGHT_METAD&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          3 : void ReweightMetad::registerKeywords(Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          3 :   ReweightBase::registerKeywords( keys ); keys.remove(&quot;ARG&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;*.rbias&quot;,&quot;the biases that must be taken into account when reweighting&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 : ReweightMetad::ReweightMetad(const ActionOptions&amp;ao):</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   Action(ao),</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          1 :   ReweightBase(ao)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : {</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 : double ReweightMetad::getLogWeight() {</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   // Retrieve the bias</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          4 :   double bias=0.0; for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) bias+=getArgument(i);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   return bias / simtemp;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightTemperaturePressure.cpp.func-sort-c.html b/coverage/bias/ReweightTemperaturePressure.cpp.func-sort-c.html
new file mode 100644
index 0000000000..32a423c111
--- /dev/null
+++ b/coverage/bias/ReweightTemperaturePressure.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightTemperaturePressure.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightTemperaturePressure.cpp<span style="font-size: 80%;"> (<a href="ReweightTemperaturePressure.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">97.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReweightTemperaturePressure.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#200">_ZN4PLMD4bias27ReweightTemperaturePressureC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#188">_ZN4PLMD4bias12_GLOBAL__N_140ReweightTemperaturePressureRegisterMe1906createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#200">_ZN4PLMD4bias27ReweightTemperaturePressureC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#190">_ZN4PLMD4bias27ReweightTemperaturePressure16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#248">_ZN4PLMD4bias27ReweightTemperaturePressure12getLogWeightEv</a></td>
+              <td class="coverFnHi">1001</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#188">_ZN4PLMD4bias12_GLOBAL__N_140ReweightTemperaturePressureRegisterMe190C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#188">_ZN4PLMD4bias12_GLOBAL__N_140ReweightTemperaturePressureRegisterMe190D2Ev</a></td>
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+            <td class="headerValue">2024-10-09 13:38:15</td>
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+            <td class="headerCovTableEntry">6</td>
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+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#248">_ZN4PLMD4bias27ReweightTemperaturePressure12getLogWeightEv</a></td>
+              <td class="coverFnHi">1001</td>
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+              <td class="coverFn"><a href="ReweightTemperaturePressure.cpp.gcov.html#190">_ZN4PLMD4bias27ReweightTemperaturePressure16registerKeywordsERNS_8KeywordsE</a></td>
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diff --git a/coverage/bias/ReweightTemperaturePressure.cpp.gcov.html b/coverage/bias/ReweightTemperaturePressure.cpp.gcov.html
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+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">97.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+
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+      <td><br></td>
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+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2019-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ReweightBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC REWEIGHTING REWEIGHT_TEMP_PRESS</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Calculate weights for ensemble averages at temperatures and/or pressures different than those used in your original simulation.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : We can use our knowledge of the probability distribution in the canonical (N\f$\mathcal{V}\f$T) or the isothermal-isobaric ensemble (NPT) to reweight the data</a>
+<a name="32"><span class="lineNum">      32 </span>            : contained in trajectories and obtain ensemble averages at different temperatures and/or pressures.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : Consider the ensemble average of an observable \f$O(\mathbf{R},\mathcal{V})\f$ that depends on the atomic coordinates \f$\mathbf{R}\f$ and the volume \f$\mathcal{V}\f$.</a>
+<a name="35"><span class="lineNum">      35 </span>            : This observable is in practice any collective variable (CV) calculated by Plumed.</a>
+<a name="36"><span class="lineNum">      36 </span>            : The ensemble average of the observable in an ensemble \f$ \xi' \f$  can be calculated from a simulation performed in an ensemble \f$ \xi \f$ using:</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : \langle O(\mathbf{R},\mathcal{V}) \rangle_{\xi'} = \frac{\langle O(\mathbf{R},\mathcal{V}) w(\mathbf{R},\mathcal{V}) \rangle_{\xi}}</a>
+<a name="39"><span class="lineNum">      39 </span>            :                                                      {\langle w(\mathbf{R},\mathcal{V}) \rangle_{\xi}}</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f]</a>
+<a name="41"><span class="lineNum">      41 </span>            : where \f$\langle \cdot \rangle_{\xi}\f$ and  \f$\langle \cdot \rangle_{\xi'}\f$ are mean values in the simulated and targeted ensemble, respectively, \f$ E(\mathbf{R}) \f$ is the potential energy of the system, and \f$ w (\mathbf{R},\mathcal{V}) \f$ are the appropriate weights to take from \f$ \xi \f$ to \f$ \xi' \f$.</a>
+<a name="42"><span class="lineNum">      42 </span>            : This action calculates the weights  \f$ w (\mathbf{R},\mathcal{V}) \f$ and handles 4 different cases:</a>
+<a name="43"><span class="lineNum">      43 </span>            :   1. Change of temperature from T to T' at constant volume. That is to say, from a simulation performed in the N\f$\mathcal{V}\f$T (canonical) ensemble, obtain an ensemble average in the N\f$\mathcal{V}\f$T' ensemble. The weights in this case are  \f$ w(\mathbf{R},\mathcal{V}) = e^{(\beta-\beta')E(\mathbf{R})} \f$ with \f$ \beta \f$ and \f$ \beta' \f$ the inverse temperatures.</a>
+<a name="44"><span class="lineNum">      44 </span>            :   2. Change of temperature from T to T' at constant pressure. That is to say, from a simulation performed in the NPT (isothermal-isobaric) ensemble, obtain an ensemble average in the NPT' ensemble. The weights in this case are \f$ w(\mathbf{R},\mathcal{V}) = e^{(\beta-\beta')(E(\mathbf{R}) + P\mathcal{V}) } \f$.</a>
+<a name="45"><span class="lineNum">      45 </span>            :   3. Change of pressure from P to P' at constant temperature. That is to say, from a simulation performed in the NPT (isothermal-isobaric) ensemble, obtain an ensemble average in the NP'T ensemble. The weights in this case are \f$ w(\mathbf{R},\mathcal{V}) = e^{\beta (P - P') \mathcal{V}} \f$.</a>
+<a name="46"><span class="lineNum">      46 </span>            :   4. Change of temperature and pressure from T,P to T',P'. That is to say, from a simulation performed in the NPT (isothermal-isobaric) ensemble, obtain an ensemble average in the NP'T' ensemble. The weights in this case are \f$ w(\mathbf{R},\mathcal{V}) = e^{(\beta-\beta')E(\mathbf{R}) + (\beta P - \beta' P') \mathcal{V}} \f$.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : These weights can be used in any action that computes ensemble averages.</a>
+<a name="49"><span class="lineNum">      49 </span>            : For example this action can be used in tandem with \ref HISTOGRAM or \ref AVERAGE.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The above equation is often impractical since the overlap between the distributions of energy and volume at different temperatures and pressures is only significant for neighboring temperatures and pressures.</a>
+<a name="53"><span class="lineNum">      53 </span>            : For this reason an unbiased simulation is of little use to reweight at different temperatures and/or pressures.</a>
+<a name="54"><span class="lineNum">      54 </span>            : A successful approach has been altering the probability of observing a configuration in order to increase this overlap \cite wanglandau.</a>
+<a name="55"><span class="lineNum">      55 </span>            : This is done through a bias potential \f$ V(\mathbf{s}) \f$ where \f$ \mathbf{s} \f$ is a set of CVs, that often is the energy (and possibly the volume).</a>
+<a name="56"><span class="lineNum">      56 </span>            : In order to calculate ensemble averages, also the effect of this bias must be taken into account.</a>
+<a name="57"><span class="lineNum">      57 </span>            : The ensemble average of the observable in the ensemble \f$ \xi' \f$ can be calculated from a biased simulation performed in the ensemble \f$\xi\f$ with bias \f$ V(\mathbf{s}) \f$ using:</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f[</a>
+<a name="59"><span class="lineNum">      59 </span>            : \langle O(\mathbf{R},\mathcal{V}) \rangle_{\xi'} = \frac{\langle O(\mathbf{R},\mathcal{V})  w (\mathbf{R},\mathcal{V}) e^{\beta V(\mathbf{s})}  \rangle_{\xi,V}}</a>
+<a name="60"><span class="lineNum">      60 </span>            :                                                      {\langle w (\mathbf{R},\mathcal{V})  e^{\beta V(\mathbf{s})}  \rangle_{\xi,V}}</a>
+<a name="61"><span class="lineNum">      61 </span>            : \f]</a>
+<a name="62"><span class="lineNum">      62 </span>            : where \f$\langle \cdot \rangle_{\xi,V}\f$ is a mean value in the biased ensemble with static bias \f$ V(\mathbf{s}) \f$.</a>
+<a name="63"><span class="lineNum">      63 </span>            : Therefore in order to reweight the trajectory at different temperatures and/or pressures one must use the weights calculated by this action \f$ w (\mathbf{R},\mathcal{V}) \f$ together with the weights of \ref REWEIGHT_BIAS (see the examples below).</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : The bias potential \f$ V(\mathbf{s}) \f$ can be constructed with \ref METAD using \ref ENERGY as a CV \cite mich+04prl.</a>
+<a name="66"><span class="lineNum">      66 </span>            : More specialized tools are available, for instance using bespoke target distributions such as \ref TD_MULTICANONICAL and \ref TD_MULTITHERMAL_MULTIBARIC \cite Piaggi-PRL-2019 \cite Piaggi-JCP-2019 within \ref VES.</a>
+<a name="67"><span class="lineNum">      67 </span>            : In the latter algorithms the interval of temperatures and pressures in which the trajectory can be reweighted is chosen explicitly.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \par Examples</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : We consider the 4 cases described above.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : The following input can be used to postprocess a molecular dynamics trajectory of a system of 1000 particles run at 500 K and constant volume using a static bias potential.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : \plumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : energy: READ FILE=COLVAR VALUES=energy  IGNORE_TIME</a>
+<a name="77"><span class="lineNum">      77 </span>            : distance: READ FILE=COLVAR VALUES=distance  IGNORE_TIME</a>
+<a name="78"><span class="lineNum">      78 </span>            : mybias: READ FILE=COLVAR VALUES=mybias.bias  IGNORE_TIME</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : # Shift energy (to avoid numerical issues)</a>
+<a name="81"><span class="lineNum">      81 </span>            : renergy: COMBINE ARG=energy PARAMETERS=-13250 PERIODIC=NO</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : # Weights</a>
+<a name="84"><span class="lineNum">      84 </span>            : bias_weights: REWEIGHT_BIAS TEMP=500 ARG=mybias.bias</a>
+<a name="85"><span class="lineNum">      85 </span>            : temp_press_weights: REWEIGHT_TEMP_PRESS TEMP=500 REWEIGHT_TEMP=300 ENERGY=renergy</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : # Ensemble average of the distance at 300 K</a>
+<a name="88"><span class="lineNum">      88 </span>            : avg_dist: AVERAGE ARG=distance LOGWEIGHTS=bias_weights,temp_press_weights</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : PRINT ARG=avg_dist FILE=COLVAR_REWEIGHT STRIDE=1</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endplumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : Clearly, in performing the analysis above we would read from the potential energy, a distance, and the value of the bias potential from a COLVAR file like the one shown below.  We would then be able</a>
+<a name="94"><span class="lineNum">      94 </span>            : to calculate the ensemble average of the distance at 300 K.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \auxfile{COLVAR}</a>
+<a name="97"><span class="lineNum">      97 </span>            : #! FIELDS time energy volume mybias.bias distance</a>
+<a name="98"><span class="lineNum">      98 </span>            :  10000.000000 -13133.769283 7.488921 63.740530 0.10293</a>
+<a name="99"><span class="lineNum">      99 </span>            :  10001.000000 -13200.239722 7.116548 36.691988 0.16253</a>
+<a name="100"><span class="lineNum">     100 </span>            :  10002.000000 -13165.108850 7.202273 44.408815 0.17625</a>
+<a name="101"><span class="lineNum">     101 </span>            : \endauxfile</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : The next three inputs can be used to postprocess a molecular dynamics trajectory of a system of 1000 particles run at 500 K and 1 bar using a static bias potential.</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : We read from a file COLVAR the potential energy, the volume, and the value of the bias potential and calculate the ensemble average of the (particle) density at 300 K and 1 bar (the simulation temperature was 500 K).</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : \plumedfile</a>
+<a name="108"><span class="lineNum">     108 </span>            : energy: READ FILE=COLVAR VALUES=energy  IGNORE_TIME</a>
+<a name="109"><span class="lineNum">     109 </span>            : volume: READ FILE=COLVAR VALUES=volume  IGNORE_TIME</a>
+<a name="110"><span class="lineNum">     110 </span>            : mybias: READ FILE=COLVAR VALUES=mybias.bias  IGNORE_TIME</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : # Shift energy and volume (to avoid numerical issues)</a>
+<a name="113"><span class="lineNum">     113 </span>            : rvol: COMBINE ARG=volume PARAMETERS=7.8 PERIODIC=NO</a>
+<a name="114"><span class="lineNum">     114 </span>            : renergy: COMBINE ARG=energy PARAMETERS=-13250 PERIODIC=NO</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : # Weights</a>
+<a name="117"><span class="lineNum">     117 </span>            : bias_weights: REWEIGHT_BIAS TEMP=500 ARG=mybias.bias</a>
+<a name="118"><span class="lineNum">     118 </span>            : temp_press_weights: REWEIGHT_TEMP_PRESS TEMP=500 REWEIGHT_TEMP=300 PRESSURE=0.06022140857 ENERGY=renergy VOLUME=rvol</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : # Ensemble average of the volume at 300 K</a>
+<a name="121"><span class="lineNum">     121 </span>            : avg_vol: AVERAGE ARG=volume LOGWEIGHTS=bias_weights,temp_press_weights</a>
+<a name="122"><span class="lineNum">     122 </span>            : # Ensemble average of the density at 300 K</a>
+<a name="123"><span class="lineNum">     123 </span>            : avg_density: CUSTOM ARG=avg_vol FUNC=1000/x PERIODIC=NO</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : PRINT ARG=avg_density FILE=COLVAR_REWEIGHT STRIDE=1</a>
+<a name="126"><span class="lineNum">     126 </span>            : \endplumedfile</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : In the next example we calculate the ensemble average of the (particle) density at 500 K and 300 MPa (the simulation pressure was 1 bar).</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : \plumedfile</a>
+<a name="131"><span class="lineNum">     131 </span>            : volume: READ FILE=COLVAR VALUES=volume  IGNORE_TIME</a>
+<a name="132"><span class="lineNum">     132 </span>            : mybias: READ FILE=COLVAR VALUES=mybias.bias  IGNORE_TIME</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : # Shift volume (to avoid numerical issues)</a>
+<a name="135"><span class="lineNum">     135 </span>            : rvol: COMBINE ARG=volume PARAMETERS=7.8 PERIODIC=NO</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : # Weights</a>
+<a name="138"><span class="lineNum">     138 </span>            : bias_weights: REWEIGHT_BIAS TEMP=500 ARG=mybias.bias</a>
+<a name="139"><span class="lineNum">     139 </span>            : temp_press_weights: REWEIGHT_TEMP_PRESS TEMP=500 PRESSURE=0.06022140857 REWEIGHT_PRESSURE=180.66422571 VOLUME=volume</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : # Ensemble average of the volume at 300 K and 300 MPa</a>
+<a name="142"><span class="lineNum">     142 </span>            : avg_vol: AVERAGE ARG=volume LOGWEIGHTS=bias_weights,temp_press_weights</a>
+<a name="143"><span class="lineNum">     143 </span>            : # Ensemble average of the density at 300 K and 300 MPa</a>
+<a name="144"><span class="lineNum">     144 </span>            : avg_density: CUSTOM ARG=avg_vol FUNC=1000/x PERIODIC=NO</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : PRINT ARG=avg_density FILE=COLVAR_REWEIGHT STRIDE=1</a>
+<a name="147"><span class="lineNum">     147 </span>            : \endplumedfile</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : In this final example we calculate the ensemble average of the (particle) density at 300 K and 300 MPa (the simulation temperature and pressure were 500 K and 1 bar).</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : \plumedfile</a>
+<a name="153"><span class="lineNum">     153 </span>            : energy: READ FILE=COLVAR VALUES=energy  IGNORE_TIME</a>
+<a name="154"><span class="lineNum">     154 </span>            : volume: READ FILE=COLVAR VALUES=volume  IGNORE_TIME</a>
+<a name="155"><span class="lineNum">     155 </span>            : mybias: READ FILE=COLVAR VALUES=mybias.bias  IGNORE_TIME</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : # Shift energy and volume (to avoid numerical issues)</a>
+<a name="158"><span class="lineNum">     158 </span>            : rvol: COMBINE ARG=volume PARAMETERS=7.8 PERIODIC=NO</a>
+<a name="159"><span class="lineNum">     159 </span>            : renergy: COMBINE ARG=energy PARAMETERS=-13250 PERIODIC=NO</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : # Weights</a>
+<a name="162"><span class="lineNum">     162 </span>            : bias_weights: REWEIGHT_BIAS TEMP=500 ARG=mybias.bias</a>
+<a name="163"><span class="lineNum">     163 </span>            : temp_press_weights: REWEIGHT_TEMP_PRESS TEMP=500 REWEIGHT_TEMP=300 PRESSURE=0.06022140857 REWEIGHT_PRESSURE=180.66422571 ENERGY=renergy VOLUME=rvol</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : # Ensemble average of the volume at 300 K and 300 MPa</a>
+<a name="166"><span class="lineNum">     166 </span>            : avg_vol: AVERAGE ARG=volume LOGWEIGHTS=bias_weights,temp_press_weights</a>
+<a name="167"><span class="lineNum">     167 </span>            : # Ensemble average of the density at 300 K and 300 MPa</a>
+<a name="168"><span class="lineNum">     168 </span>            : avg_density: CUSTOM ARG=avg_vol FUNC=1000/x PERIODIC=NO</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : PRINT ARG=avg_density FILE=COLVAR_REWEIGHT STRIDE=1</a>
+<a name="171"><span class="lineNum">     171 </span>            : \endplumedfile</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : */</a>
+<a name="174"><span class="lineNum">     174 </span>            : //+ENDPLUMEDOC</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : namespace PLMD {</a>
+<a name="177"><span class="lineNum">     177 </span>            : namespace bias {</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : class ReweightTemperaturePressure : public ReweightBase {</a>
+<a name="180"><span class="lineNum">     180 </span>            : private:</a>
+<a name="181"><span class="lineNum">     181 </span>            : ///</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double rpress_, press_, rtemp_;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   std::vector&lt;Value*&gt; myenergy, myvol;</a>
+<a name="184"><span class="lineNum">     184 </span>            : public:</a>
+<a name="185"><span class="lineNum">     185 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="186"><span class="lineNum">     186 </span>            :   explicit ReweightTemperaturePressure(const ActionOptions&amp;ao);</a>
+<a name="187"><span class="lineNum">     187 </span>            :   double getLogWeight() override;</a>
+<a name="188"><span class="lineNum">     188 </span>            : };</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(ReweightTemperaturePressure,&quot;REWEIGHT_TEMP_PRESS&quot;)</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          6 : void ReweightTemperaturePressure::registerKeywords(Keywords&amp; keys ) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          6 :   ReweightBase::registerKeywords( keys );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          6 :   keys.remove(&quot;ARG&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;ENERGY&quot;,&quot;Energy&quot;);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;VOLUME&quot;,&quot;Volume&quot;);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;REWEIGHT_PRESSURE&quot;,&quot;Reweighting pressure&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;PRESSURE&quot;,&quot;The system pressure&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;REWEIGHT_TEMP&quot;,&quot;Reweighting temperature&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          6 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 : ReweightTemperaturePressure::ReweightTemperaturePressure(const ActionOptions&amp;ao):</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   Action(ao),</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          4 :   ReweightBase(ao)</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : {</a>
+<a name="206"><span class="lineNum">     206 </span>            :   // Initialize to not defined (negative)</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          4 :   rpress_=-1;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          4 :   press_=-1;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          4 :   rtemp_=-1;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          4 :   parse(&quot;REWEIGHT_PRESSURE&quot;,rpress_);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          4 :   parse(&quot;PRESSURE&quot;,press_);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          4 :   parse(&quot;REWEIGHT_TEMP&quot;,rtemp_);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          4 :   rtemp_*=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          8 :   parseArgumentList(&quot;ENERGY&quot;,myenergy);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          4 :   if(!myenergy.empty()) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          3 :     log.printf(&quot;  with energies: &quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;myenergy.size(); i++) log.printf(&quot; %s&quot;,myenergy[i]-&gt;getName().c_str());</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          3 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span>            :   //requestArguments(myenergy);</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          8 :   parseArgumentList(&quot;VOLUME&quot;,myvol);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          4 :   if(!myvol.empty()) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          3 :     log.printf(&quot;  with volumes: &quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;myvol.size(); i++) log.printf(&quot; %s&quot;,myvol[i]-&gt;getName().c_str());</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          3 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   std::vector&lt;Value*&gt; conc;</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          4 :   conc.insert(conc.begin(), myenergy.begin(), myenergy.end());</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          4 :   conc.insert(conc.end(), myvol.begin(), myvol.end());</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          4 :   requestArguments(conc);</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   // 4 possible cases</a>
+<a name="236"><span class="lineNum">     236 </span>            :   // Case 1) Reweight from T to T' with V=const (canonical)</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          4 :   if (rtemp_&gt;=0 &amp;&amp; press_&lt;0 &amp;&amp; rpress_&lt;0 &amp;&amp; !myenergy.empty() &amp;&amp; myvol.empty() ) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          1 :     log.printf(&quot;  reweighting simulation from temperature %f to temperature %f at constant volume \n&quot;,simtemp/plumed.getAtoms().getKBoltzmann(),rtemp_/plumed.getAtoms().getKBoltzmann() );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          1 :     log.printf(&quot;  WARNING: If the simulation is performed at constant pressure add the keywords PRESSURE and VOLUME \n&quot; );</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   }</a>
+<a name="241"><span class="lineNum">     241 </span>            :   // Case 2) Reweight from T to T' with P=const (isothermal-isobaric)</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          3 :   else if (rtemp_&gt;=0 &amp;&amp; press_&gt;=0 &amp;&amp; rpress_&lt;0 &amp;&amp; !myenergy.empty() &amp;&amp; !myvol.empty() ) log.printf(&quot;  reweighting simulation from temperature %f to temperature %f at constant pressure %f \n&quot;,simtemp/plumed.getAtoms().getKBoltzmann(),rtemp_/plumed.getAtoms().getKBoltzmann(), press_ );</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   // Case 3) Reweight from P to P' with T=const (isothermal-isobaric)</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :   else if (rtemp_&lt;0 &amp;&amp; press_&gt;=0 &amp;&amp; rpress_&gt;=0 &amp;&amp; myenergy.empty() &amp;&amp; !myvol.empty() ) log.printf(&quot;  reweighting simulation from pressure %f to pressure %f at constant temperature %f\n&quot;,press_,rpress_,simtemp/plumed.getAtoms().getKBoltzmann() );</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   // Case 4) Reweight from T,P to T',P' (isothermal-isobaric)</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          1 :   else if (rtemp_&gt;0 &amp;&amp; press_&gt;=0 &amp;&amp; rpress_&gt;=0 &amp;&amp; !myenergy.empty() &amp;&amp; !myvol.empty() ) log.printf(&quot;  reweighting simulation from temperature %f and pressure %f to temperature %f and pressure %f \n&quot;,simtemp/plumed.getAtoms().getKBoltzmann(), press_, rtemp_/plumed.getAtoms().getKBoltzmann(), rpress_);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :   else error(&quot;Combination of ENERGY, VOLUME, REWEIGHT_PRESSURE, PRESSURE and REWEIGHT_TEMP not supported. Please refer to the manual for supported combinations.&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          4 : }</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       1001 : double ReweightTemperaturePressure::getLogWeight() {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       2002 :   double energy=0.0; for(unsigned i=0; i&lt;myenergy.size(); ++i) energy+=getArgument(i);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       2002 :   double volume=0.0; for(unsigned i=0; i&lt;myvol.size(); ++i) volume+=getArgument(myenergy.size()+i);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   // 4 possible cases</a>
+<a name="254"><span class="lineNum">     254 </span>            :   // Case 1) Reweight from T to T' with V=const (canonical)</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">       1001 :   if (rtemp_&gt;=0 &amp;&amp; press_&lt;0 &amp;&amp; rpress_&lt;0) return ((1.0/simtemp)- (1.0/rtemp_) )*energy;</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   // Case 2) Reweight from T to T' with P=const (isothermal-isobaric)</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       1001 :   else if (rtemp_&gt;=0 &amp;&amp; press_&gt;=0 &amp;&amp; rpress_&lt;0)  return ((1.0/simtemp)- (1.0/rtemp_) )*energy + ((1.0/simtemp) - (1.0/rtemp_))*press_*volume;</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   // Case 3) Reweight from P to P' with T=const (isothermal-isobaric)</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       1001 :   else if (rtemp_&lt;0 &amp;&amp; press_&gt;=0 &amp;&amp; rpress_&gt;=0)  return (1.0/simtemp)*(press_ - rpress_)*volume;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   // Case 4) Reweight from T,P to T',P' (isothermal-isobaric)</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       1001 :   else if (rtemp_&gt;0 &amp;&amp; press_&gt;=0 &amp;&amp; rpress_&gt;=0) return ((1.0/simtemp)- (1.0/rtemp_) )*energy + ((1.0/simtemp)*press_ - (1.0/rtemp_)*rpress_ )*volume;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   else return 0;</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/ReweightWham.cpp.func-sort-c.html b/coverage/bias/ReweightWham.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8e72dcfc23
--- /dev/null
+++ b/coverage/bias/ReweightWham.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightWham.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightWham.cpp<span style="font-size: 80%;"> (<a href="ReweightWham.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">91.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReweightWham.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#125">_ZN4PLMD4bias12ReweightWham9clearDataEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#103">_ZN4PLMD4bias12ReweightWhamC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#134">_ZN4PLMD4bias12ReweightWham16calculateWeightsERKj</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#103">_ZN4PLMD4bias12ReweightWhamC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#94">_ZN4PLMD4bias12_GLOBAL__N_124ReweightWhamRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#87">_ZNK4PLMD4bias12ReweightWham17buildsWeightStoreEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#96">_ZN4PLMD4bias12ReweightWham16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#129">_ZNK4PLMD4bias12ReweightWham9getWeightERKj</a></td>
+              <td class="coverFnHi">2457</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#94">_ZN4PLMD4bias12_GLOBAL__N_124ReweightWhamRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#94">_ZN4PLMD4bias12_GLOBAL__N_124ReweightWhamRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#113">_ZN4PLMD4bias12ReweightWham12getLogWeightEv</a></td>
+              <td class="coverFnHi">4224</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</html>
diff --git a/coverage/bias/ReweightWham.cpp.func.html b/coverage/bias/ReweightWham.cpp.func.html
new file mode 100644
index 0000000000..0457192b5f
--- /dev/null
+++ b/coverage/bias/ReweightWham.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightWham.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightWham.cpp<span style="font-size: 80%;"> (<a href="ReweightWham.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">91.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReweightWham.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#113">_ZN4PLMD4bias12ReweightWham12getLogWeightEv</a></td>
+              <td class="coverFnHi">4224</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#134">_ZN4PLMD4bias12ReweightWham16calculateWeightsERKj</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#96">_ZN4PLMD4bias12ReweightWham16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#125">_ZN4PLMD4bias12ReweightWham9clearDataEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#103">_ZN4PLMD4bias12ReweightWhamC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#103">_ZN4PLMD4bias12ReweightWhamC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#94">_ZN4PLMD4bias12_GLOBAL__N_124ReweightWhamRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#94">_ZN4PLMD4bias12_GLOBAL__N_124ReweightWhamRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#94">_ZN4PLMD4bias12_GLOBAL__N_124ReweightWhamRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#87">_ZNK4PLMD4bias12ReweightWham17buildsWeightStoreEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReweightWham.cpp.gcov.html#129">_ZNK4PLMD4bias12ReweightWham9getWeightERKj</a></td>
+              <td class="coverFnHi">2457</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/bias/ReweightWham.cpp.gcov.html b/coverage/bias/ReweightWham.cpp.gcov.html
new file mode 100644
index 0000000000..485fd1adea
--- /dev/null
+++ b/coverage/bias/ReweightWham.cpp.gcov.html
@@ -0,0 +1,253 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/ReweightWham.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - ReweightWham.cpp<span style="font-size: 80%;"> (source / <a href="ReweightWham.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">91.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReweightBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC REWEIGHTING REWEIGHT_WHAM</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate the weights for configurations using the weighted histogram analysis method.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : Suppose that you have run multiple \f$N\f$ trajectories each of which was computed by integrating a different biased Hamiltonian. We can calculate the probability of observing</a>
+<a name="31"><span class="lineNum">      31 </span>            : the set of configurations during the \f$N\f$ trajectories that we ran using the product of multinomial distributions shown below:</a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            : P( \vec{T} ) \propto \prod_{j=1}^M \prod_{k=1}^N (c_k w_{kj} p_j)^{t_{kj}}</a>
+<a name="34"><span class="lineNum">      34 </span>            : \label{eqn:wham1}</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f]</a>
+<a name="36"><span class="lineNum">      36 </span>            : In this expression the second product runs over the biases that were used when calculating the \f$N\f$ trajectories.  The first product then runs over the</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f$M\f$ bins in our histogram.  The \f$p_j\f$ variable that is inside this product is the quantity we wish to extract; namely, the unbiased probability of</a>
+<a name="38"><span class="lineNum">      38 </span>            : having a set of CV values that lie within the range for the \f$j\f$th bin.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The quantity that we can easily extract from our simulations, \f$t_{kj}\f$, however, measures the number of frames from trajectory \f$k\f$ that are inside the \f$j\f$th bin.</a>
+<a name="41"><span class="lineNum">      41 </span>            : To interpret this quantity we must consider the bias that acts on each of the replicas so the \f$w_{kj}\f$ term is introduced.  This quantity is calculated as:</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : w_{kj} =</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : and is essentially the factor that we have to multiply the unbiased probability of being in the bin by in order to get the probability that we would be inside this same bin in</a>
+<a name="46"><span class="lineNum">      46 </span>            : the \f$k\f$th of our biased simulations.  Obviously, these \f$w_{kj}\f$ values depend on the value that the CVs take and also on the particular trajectory that we are investigating</a>
+<a name="47"><span class="lineNum">      47 </span>            : all of which, remember, have different simulation biases.  Finally, \f$c_k\f$ is a free parameter that ensures that, for each \f$k\f$, the biased probability is normalized.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : We can use the equation for the probability that was given above to find a set of values for \f$p_j\f$ that maximizes the likelihood of observing the trajectory.</a>
+<a name="50"><span class="lineNum">      50 </span>            : This constrained optimization must be performed using a set of Lagrange multipliers, \f$\lambda_k\f$, that ensure that each of the biased probability distributions</a>
+<a name="51"><span class="lineNum">      51 </span>            : are normalized, that is \f$\sum_j c_kw_{kj}p_j=1\f$.  Furthermore, as the problem is made easier if the quantity in the equation above is replaced by its logarithm</a>
+<a name="52"><span class="lineNum">      52 </span>            : we actually chose to minimize</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f[</a>
+<a name="54"><span class="lineNum">      54 </span>            : \mathcal{L}= \sum_{j=1}^M \sum_{k=1}^N t_{kj} \ln c_k  w_{kj} p_j + \sum_k\lambda_k \left( \sum_{j=1}^N c_k w_{kj} p_j - 1 \right)</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f]</a>
+<a name="56"><span class="lineNum">      56 </span>            : After some manipulations the following (WHAM) equations emerge:</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f[</a>
+<a name="58"><span class="lineNum">      58 </span>            : \begin{aligned}</a>
+<a name="59"><span class="lineNum">      59 </span>            : p_j &amp; \propto \frac{\sum_{k=1}^N t_{kj}}{\sum_k c_k w_{kj}} \\</a>
+<a name="60"><span class="lineNum">      60 </span>            : c_k &amp; =\frac{1}{\sum_{j=1}^M w_{kj} p_j}</a>
+<a name="61"><span class="lineNum">      61 </span>            : \end{aligned}</a>
+<a name="62"><span class="lineNum">      62 </span>            : \f]</a>
+<a name="63"><span class="lineNum">      63 </span>            : which can be solved by computing the \f$p_j\f$ values using the first of the two equations above with an initial guess for the \f$c_k\f$ values and by then refining</a>
+<a name="64"><span class="lineNum">      64 </span>            : these \f$p_j\f$ values using the \f$c_k\f$ values that are obtained by inserting the \f$p_j\f$ values obtained into the second of the two equations above.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : Notice that only \f$\sum_k t_{kj}\f$, which is the total number of configurations from all the replicas that enter the \f$j\f$th bin, enters the WHAM equations above.</a>
+<a name="67"><span class="lineNum">      67 </span>            : There is thus no need to record which replica generated each of the frames.  One can thus simply gather the trajectories from all the replicas together at the outset.</a>
+<a name="68"><span class="lineNum">      68 </span>            : This observation is important as it is the basis of the binless formulation of WHAM that is implemented within PLUMED.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : namespace PLMD {</a>
+<a name="76"><span class="lineNum">      76 </span>            : namespace bias {</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : class ReweightWham : public ReweightBase {</a>
+<a name="79"><span class="lineNum">      79 </span>            : private:</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double thresh;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   unsigned nreplicas;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   unsigned maxiter;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool weightsCalculated;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;double&gt; stored_biases;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;double&gt; final_weights;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit ReweightWham(const ActionOptions&amp;ao);</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         12 :   bool buildsWeightStore() const override { return true; }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   void calculateWeights( const unsigned&amp; nframes ) override;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void clearData() override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   double getLogWeight() override;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   double getWeight( const unsigned&amp; iweight ) const override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(ReweightWham,&quot;REWEIGHT_WHAM&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         14 : void ReweightWham::registerKeywords(Keywords&amp; keys ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         14 :   ReweightBase::registerKeywords( keys ); keys.remove(&quot;ARG&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;*.bias&quot;,&quot;the biases that must be taken into account when reweighting&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;MAXITER&quot;,&quot;1000&quot;,&quot;maximum number of iterations for WHAM algorithm&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;WHAMTOL&quot;,&quot;1e-10&quot;,&quot;threshold for convergence of WHAM algorithm&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         14 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         12 : ReweightWham::ReweightWham(const ActionOptions&amp;ao):</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   Action(ao),</a>
+<a name="107"><span class="lineNum">     107 </span>            :   ReweightBase(ao),</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   weightsCalculated(false)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         24 :   parse(&quot;MAXITER&quot;,maxiter); parse(&quot;WHAMTOL&quot;,thresh);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         12 :   if(comm.Get_rank()==0) nreplicas=multi_sim_comm.Get_size();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         12 :   comm.Bcast(nreplicas,0);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         12 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4224 : double ReweightWham::getLogWeight() {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       4224 :   if( getStep()==0 ) return 1.0;  // This is here as first step is ignored in all analyses</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       4212 :   weightsCalculated=false;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       8424 :   double bias=0.0; for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) bias+=getArgument(i);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       4212 :   std::vector&lt;double&gt; biases(nreplicas,0.0);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       4212 :   if(comm.Get_rank()==0) multi_sim_comm.Allgather(bias,biases);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       4212 :   comm.Bcast(biases,0);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      29484 :   for(unsigned i=0; i&lt;biases.size(); i++) stored_biases.push_back( biases[i] );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   return 1.0;</a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 : void ReweightWham::clearData() {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   stored_biases.resize(0);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       2457 : double ReweightWham::getWeight( const unsigned&amp; iweight ) const {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   plumed_dbg_assert( weightsCalculated &amp;&amp; iweight&lt;final_weights.size() );</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       2457 :   return final_weights[iweight];</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          7 : void ReweightWham::calculateWeights( const unsigned&amp; nframes ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          7 :   if( stored_biases.size()!=nreplicas*nframes ) error(&quot;wrong number of weights stored&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Get the minimum value of the bias</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          7 :   double minv = *min_element(std::begin(stored_biases), std::end(stored_biases));</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   // Resize final weights array</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          7 :   plumed_assert( stored_biases.size()%nreplicas==0 );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          7 :   final_weights.resize( stored_biases.size() / nreplicas, 1.0 );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   // Offset and exponential of the bias</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          7 :   std::vector&lt;double&gt; expv( stored_biases.size() );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      14749 :   for(unsigned i=0; i&lt;expv.size(); ++i) expv[i] = std::exp( (-stored_biases[i]+minv) / simtemp );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Initialize Z</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          7 :   std::vector&lt;double&gt; Z( nreplicas, 1.0 ), oldZ( nreplicas );</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   // Now the iterative loop to calculate the WHAM weights</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       2674 :   for(unsigned iter=0; iter&lt;maxiter; ++iter) {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     // Store Z</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      18718 :     for(unsigned j=0; j&lt;Z.size(); ++j) oldZ[j]=Z[j];</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :     // Recompute weights</a>
+<a name="153"><span class="lineNum">     153 </span>            :     double norm=0;</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     941248 :     for(unsigned j=0; j&lt;final_weights.size(); ++j) {</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :       double ew=0;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">    6570018 :       for(unsigned k=0; k&lt;Z.size(); ++k) ew += expv[j*Z.size()+k]  / Z[k];</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">     938574 :       final_weights[j] = 1.0 / ew; norm += final_weights[j];</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :     }</a>
+<a name="159"><span class="lineNum">     159 </span>            :     // Normalize weights</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">     941248 :     for(unsigned j=0; j&lt;final_weights.size(); ++j) final_weights[j] /= norm;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :     // Recompute Z</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      18718 :     for(unsigned j=0; j&lt;Z.size(); ++j) Z[j] = 0.0;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     941248 :     for(unsigned j=0; j&lt;final_weights.size(); ++j) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">    6570018 :       for(unsigned k=0; k&lt;Z.size(); ++k) Z[k] += final_weights[j]*expv[j*Z.size()+k];</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     }</a>
+<a name="166"><span class="lineNum">     166 </span>            :     // Normalize Z and compute change in Z</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      18718 :     double change=0; norm=0; for(unsigned k=0; k&lt;Z.size(); ++k) norm+=Z[k];</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      18718 :     for(unsigned k=0; k&lt;Z.size(); ++k) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      16044 :       Z[k] /= norm; double d = std::log( Z[k] / oldZ[k] ); change += d*d;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       2681 :     if( change&lt;thresh ) { weightsCalculated=true; return; }</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   error(&quot;Too many iterations in WHAM&quot; );</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/UWalls.cpp.func-sort-c.html b/coverage/bias/UWalls.cpp.func-sort-c.html
new file mode 100644
index 0000000000..910e10ee5c
--- /dev/null
+++ b/coverage/bias/UWalls.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/UWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - UWalls.cpp<span style="font-size: 80%;"> (<a href="UWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="UWalls.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#86">_ZN4PLMD4bias6UWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_118UWallsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#86">_ZN4PLMD4bias6UWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#75">_ZN4PLMD4bias6UWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_118UWallsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_118UWallsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#121">_ZN4PLMD4bias6UWalls9calculateEv</a></td>
+              <td class="coverFnHi">28015</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/UWalls.cpp.func.html b/coverage/bias/UWalls.cpp.func.html
new file mode 100644
index 0000000000..a4f6b216f5
--- /dev/null
+++ b/coverage/bias/UWalls.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/UWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - UWalls.cpp<span style="font-size: 80%;"> (<a href="UWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="UWalls.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_118UWallsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_118UWallsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD4bias12_GLOBAL__N_118UWallsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#75">_ZN4PLMD4bias6UWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#121">_ZN4PLMD4bias6UWalls9calculateEv</a></td>
+              <td class="coverFnHi">28015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#86">_ZN4PLMD4bias6UWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#86">_ZN4PLMD4bias6UWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/UWalls.cpp.gcov.html b/coverage/bias/UWalls.cpp.gcov.html
new file mode 100644
index 0000000000..0133fc33f4
--- /dev/null
+++ b/coverage/bias/UWalls.cpp.gcov.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias/UWalls.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">bias</a> - UWalls.cpp<span style="font-size: 80%;"> (source / <a href="UWalls.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace bias {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC BIAS UPPER_WALLS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Defines a wall for the value of one or more collective variables,</a>
+<a name="31"><span class="lineNum">      31 </span>            :  which limits the region of the phase space accessible during the simulation.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : The restraining potential starts acting on the system when the value of the CV is greater</a>
+<a name="34"><span class="lineNum">      34 </span>            : (in the case of UPPER_WALLS) or lower (in the case of LOWER_WALLS) than a certain limit \f$a_i\f$ (AT)</a>
+<a name="35"><span class="lineNum">      35 </span>            : minus an offset \f$o_i\f$ (OFFSET).</a>
+<a name="36"><span class="lineNum">      36 </span>            : The expression for the bias due to the wall is given by:</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \f$</a>
+<a name="39"><span class="lineNum">      39 </span>            :   \sum_i {k_i}((x_i-a_i+o_i)/s_i)^e_i</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f$</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f$k_i\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s_i\f$ (EPS) a rescaling factor and</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f$e_i\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFFSET = 0.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The following input tells plumed to add both a lower and an upper walls on the distance</a>
+<a name="49"><span class="lineNum">      49 </span>            : between atoms 3 and 5 and the distance between atoms 2 and 4. The lower and upper limits</a>
+<a name="50"><span class="lineNum">      50 </span>            : are defined at different values. The strength of the walls is the same for the four cases.</a>
+<a name="51"><span class="lineNum">      51 </span>            : It also tells plumed to print the energy of the walls.</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : DISTANCE ATOMS=3,5 LABEL=d1</a>
+<a name="54"><span class="lineNum">      54 </span>            : DISTANCE ATOMS=2,4 LABEL=d2</a>
+<a name="55"><span class="lineNum">      55 </span>            : UPPER_WALLS ARG=d1,d2 AT=1.0,1.5 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=uwall</a>
+<a name="56"><span class="lineNum">      56 </span>            : LOWER_WALLS ARG=d1,d2 AT=0.0,1.0 KAPPA=150.0,150.0 EXP=2,2 EPS=1,1 OFFSET=0,0 LABEL=lwall</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=uwall.bias,lwall.bias</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : */</a>
+<a name="61"><span class="lineNum">      61 </span>            : //+ENDPLUMEDOC</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : class UWalls : public Bias {</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;double&gt; at;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;double&gt; kappa;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;double&gt; exp;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;double&gt; eps;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;double&gt; offset;</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   explicit UWalls(const ActionOptions&amp;);</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void calculate() override;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12538 : PLUMED_REGISTER_ACTION(UWalls,&quot;UPPER_WALLS&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         19 : void UWalls::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         19 :   Bias::registerKeywords(keys);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         19 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         38 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;the positions of the wall. The a_i in the expression for a wall.&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         38 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;the force constant for the wall.  The k_i in the expression for a wall.&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         38 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET&quot;,&quot;0.0&quot;,&quot;the offset for the start of the wall.  The o_i in the expression for a wall.&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         38 :   keys.add(&quot;compulsory&quot;,&quot;EXP&quot;,&quot;2.0&quot;,&quot;the powers for the walls.  The e_i in the expression for a wall.&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         38 :   keys.add(&quot;compulsory&quot;,&quot;EPS&quot;,&quot;1.0&quot;,&quot;the values for s_i in the expression for a wall&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         38 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         19 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         17 : UWalls::UWalls(const ActionOptions&amp;ao):</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         34 :   at(getNumberOfArguments(),0),</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         17 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         17 :   exp(getNumberOfArguments(),2.0),</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         17 :   eps(getNumberOfArguments(),1.0),</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         34 :   offset(getNumberOfArguments(),0.0)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : {</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Note : the sizes of these vectors are checked automatically by parseVector</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         17 :   parseVector(&quot;OFFSET&quot;,offset);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         17 :   parseVector(&quot;EPS&quot;,eps);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         17 :   parseVector(&quot;EXP&quot;,exp);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         17 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         17 :   parseVector(&quot;AT&quot;,at);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         17 :   checkRead();</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         17 :   log.printf(&quot;  at&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         34 :   for(unsigned i=0; i&lt;at.size(); i++) log.printf(&quot; %f&quot;,at[i]);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         17 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         17 :   log.printf(&quot;  with an offset&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         34 :   for(unsigned i=0; i&lt;offset.size(); i++) log.printf(&quot; %f&quot;,offset[i]);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         17 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         17 :   log.printf(&quot;  with force constant&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         34 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         17 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         17 :   log.printf(&quot;  and exponent&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         34 :   for(unsigned i=0; i&lt;exp.size(); i++) log.printf(&quot; %f&quot;,exp[i]);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         17 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         17 :   log.printf(&quot;  rescaled&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         34 :   for(unsigned i=0; i&lt;eps.size(); i++) log.printf(&quot; %f&quot;,eps[i]);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         17 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         34 :   addComponent(&quot;force2&quot;); componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         17 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      28015 : void UWalls::calculate() {</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   double ene=0.0;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double totf2=0.0;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      56030 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     double f = 0.0;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      28015 :     const double cv=difference(i,at[i],getArgument(i));</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      28015 :     const double off=offset[i];</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      28015 :     const double epsilon=eps[i];</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      28015 :     const double uscale = (cv+off)/epsilon;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      28015 :     if( uscale &gt; 0.) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          6 :       const double k=kappa[i];</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          6 :       const double exponent=exp[i];</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          6 :       double power = pow( uscale, exponent );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          6 :       f = -( k / epsilon ) * exponent * power / uscale;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :       ene += k * power;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          6 :       totf2 += f * f;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     }</a>
+<a name="140"><span class="lineNum">     140 </span>            :     setOutputForce(i,f);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            :   setBias(ene);</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      28015 :   getPntrToComponent(&quot;force2&quot;)-&gt;set(totf2);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      28015 : }</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/index-sort-f.html b/coverage/bias/index-sort-f.html
new file mode 100644
index 0000000000..4542fd2e9b
--- /dev/null
+++ b/coverage/bias/index-sort-f.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - bias</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2393</td>
+            <td class="headerCovTableEntry">2617</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">143</td>
+            <td class="headerCovTableEntry">167</td>
+            <td class="headerCovTableEntryMed">85.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBase.h.gcov.html">ReweightBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">2 / 6</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">2 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBase.cpp.gcov.html">ReweightBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 20</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bias.cpp.gcov.html">Bias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightWham.cpp.gcov.html">ReweightWham.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.8%"><img src="../snow.png" width=8 height=10 alt="91.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.8&nbsp;%</td>
+      <td class="coverNumHi">45 / 49</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBias.cpp.gcov.html">ReweightBias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UWalls.cpp.gcov.html">UWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">55 / 55</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="External.cpp.gcov.html">External.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">40 / 40</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ABMD.cpp.gcov.html">ABMD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightTemperaturePressure.cpp.gcov.html">ReweightTemperaturePressure.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.9%"><img src="../snow.png" width=2 height=10 alt="97.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.9&nbsp;%</td>
+      <td class="coverNumHi">46 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightMetad.cpp.gcov.html">ReweightMetad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LWalls.cpp.gcov.html">LWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">55 / 55</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MovingRestraint.cpp.gcov.html">MovingRestraint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">101 / 101</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Restraint.cpp.gcov.html">Restraint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">40 / 40</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BiasValue.cpp.gcov.html">BiasValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExtendedLagrangian.cpp.gcov.html">ExtendedLagrangian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">93 / 94</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PBMetaD.cpp.gcov.html">PBMetaD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">570 / 646</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MaxEnt.cpp.gcov.html">MaxEnt.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">227 / 236</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetaD.cpp.gcov.html">MetaD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">955 / 1083</td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bias.h.gcov.html">Bias.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/index-sort-l.html b/coverage/bias/index-sort-l.html
new file mode 100644
index 0000000000..22c0b857ac
--- /dev/null
+++ b/coverage/bias/index-sort-l.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - bias</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2393</td>
+            <td class="headerCovTableEntry">2617</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">143</td>
+            <td class="headerCovTableEntry">167</td>
+            <td class="headerCovTableEntryMed">85.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBase.h.gcov.html">ReweightBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">2 / 6</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">2 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetaD.cpp.gcov.html">MetaD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">955 / 1083</td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PBMetaD.cpp.gcov.html">PBMetaD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">570 / 646</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightWham.cpp.gcov.html">ReweightWham.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.8%"><img src="../snow.png" width=8 height=10 alt="91.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.8&nbsp;%</td>
+      <td class="coverNumHi">45 / 49</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBase.cpp.gcov.html">ReweightBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 20</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MaxEnt.cpp.gcov.html">MaxEnt.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">227 / 236</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightTemperaturePressure.cpp.gcov.html">ReweightTemperaturePressure.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.9%"><img src="../snow.png" width=2 height=10 alt="97.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.9&nbsp;%</td>
+      <td class="coverNumHi">46 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExtendedLagrangian.cpp.gcov.html">ExtendedLagrangian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">93 / 94</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bias.h.gcov.html">Bias.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBias.cpp.gcov.html">ReweightBias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightMetad.cpp.gcov.html">ReweightMetad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BiasValue.cpp.gcov.html">BiasValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bias.cpp.gcov.html">Bias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="External.cpp.gcov.html">External.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">40 / 40</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Restraint.cpp.gcov.html">Restraint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">40 / 40</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UWalls.cpp.gcov.html">UWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">55 / 55</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LWalls.cpp.gcov.html">LWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">55 / 55</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ABMD.cpp.gcov.html">ABMD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MovingRestraint.cpp.gcov.html">MovingRestraint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">101 / 101</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/bias/index.html b/coverage/bias/index.html
new file mode 100644
index 0000000000..6bebf73fa3
--- /dev/null
+++ b/coverage/bias/index.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - bias</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - bias</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2393</td>
+            <td class="headerCovTableEntry">2617</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">143</td>
+            <td class="headerCovTableEntry">167</td>
+            <td class="headerCovTableEntryMed">85.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ABMD.cpp.gcov.html">ABMD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bias.cpp.gcov.html">Bias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bias.h.gcov.html">Bias.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BiasValue.cpp.gcov.html">BiasValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExtendedLagrangian.cpp.gcov.html">ExtendedLagrangian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">93 / 94</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="External.cpp.gcov.html">External.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">40 / 40</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LWalls.cpp.gcov.html">LWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">55 / 55</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MaxEnt.cpp.gcov.html">MaxEnt.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">227 / 236</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetaD.cpp.gcov.html">MetaD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">955 / 1083</td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MovingRestraint.cpp.gcov.html">MovingRestraint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">101 / 101</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PBMetaD.cpp.gcov.html">PBMetaD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">570 / 646</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Restraint.cpp.gcov.html">Restraint.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">40 / 40</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBase.cpp.gcov.html">ReweightBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 20</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBase.h.gcov.html">ReweightBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">2 / 6</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">2 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightBias.cpp.gcov.html">ReweightBias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightMetad.cpp.gcov.html">ReweightMetad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightTemperaturePressure.cpp.gcov.html">ReweightTemperaturePressure.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.9%"><img src="../snow.png" width=2 height=10 alt="97.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.9&nbsp;%</td>
+      <td class="coverNumHi">46 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReweightWham.cpp.gcov.html">ReweightWham.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.8%"><img src="../snow.png" width=8 height=10 alt="91.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.8&nbsp;%</td>
+      <td class="coverNumHi">45 / 49</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UWalls.cpp.gcov.html">UWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">55 / 55</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Completion.cpp.func-sort-c.html b/coverage/cltools/Completion.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b6fd3d80f8
--- /dev/null
+++ b/coverage/cltools/Completion.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Completion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Completion.cpp<span style="font-size: 80%;"> (<a href="Completion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">27.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Completion.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#74">_ZN4PLMD7cltools10Completion4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#68">_ZN4PLMD7cltools10CompletionC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#62">_ZN4PLMD7cltools12_GLOBAL__N_120CompletionRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#57">_ZNK4PLMD7cltools10Completion11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#64">_ZN4PLMD7cltools10Completion16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#62">_ZN4PLMD7cltools12_GLOBAL__N_120CompletionRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#62">_ZN4PLMD7cltools12_GLOBAL__N_120CompletionRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Completion.cpp.func.html b/coverage/cltools/Completion.cpp.func.html
new file mode 100644
index 0000000000..8d7f70d4ab
--- /dev/null
+++ b/coverage/cltools/Completion.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Completion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Completion.cpp<span style="font-size: 80%;"> (<a href="Completion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">27.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Completion.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#64">_ZN4PLMD7cltools10Completion16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#74">_ZN4PLMD7cltools10Completion4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#68">_ZN4PLMD7cltools10CompletionC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#62">_ZN4PLMD7cltools12_GLOBAL__N_120CompletionRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#62">_ZN4PLMD7cltools12_GLOBAL__N_120CompletionRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#62">_ZN4PLMD7cltools12_GLOBAL__N_120CompletionRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Completion.cpp.gcov.html#57">_ZNK4PLMD7cltools10Completion11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Completion.cpp.gcov.html b/coverage/cltools/Completion.cpp.gcov.html
new file mode 100644
index 0000000000..7583cadc28
--- /dev/null
+++ b/coverage/cltools/Completion.cpp.gcov.html
@@ -0,0 +1,211 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Completion.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Completion.cpp<span style="font-size: 80%;"> (source / <a href="Completion.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">27.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;vector&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;iostream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace cltools {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC TOOLS completion</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Dumps the body of a bash function to be used for auto completion.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Users will typically not need this command.</a>
+<a name="40"><span class="lineNum">      40 </span>            : See more at \ref BashAutocompletion</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \verbatim</a>
+<a name="45"><span class="lineNum">      45 </span>            : plumed completion</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endverbatim</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : */</a>
+<a name="50"><span class="lineNum">      50 </span>            : //+ENDPLUMEDOC</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : class Completion:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   public CLTool</a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span>            : public:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="57"><span class="lineNum">      57 </span>            :   explicit Completion(const CLToolOptions&amp; co );</a>
+<a name="58"><span class="lineNum">      58 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          4 :     return &quot;dump a function usable for programmable completion&quot;;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   }</a>
+<a name="62"><span class="lineNum">      62 </span>            : };</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      12508 : PLUMED_REGISTER_CLTOOL(Completion,&quot;completion&quot;)</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       4168 : void Completion::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       4168 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          4 : Completion::Completion(const CLToolOptions&amp; co ):</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          4 :   CLTool(co)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          4 :   inputdata=commandline;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          4 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 : int Completion::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   static const char completion [] = {</a>
+<a name="78"><span class="lineNum">      78 </span>            : #include &quot;completion.xxd&quot;</a>
+<a name="79"><span class="lineNum">      79 </span>            : // cppcheck-suppress syntaxError</a>
+<a name="80"><span class="lineNum">      80 </span>            :     , 0x00</a>
+<a name="81"><span class="lineNum">      81 </span>            :   };</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::fprintf(out,&quot;local cmds=\&quot;help -h --help&quot;);</a>
+<a name="83"><span class="lineNum">      83 </span>            : // Build list of available C++ tools:</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   std::vector&lt;std::string&gt; availableCxx=cltoolRegister().list();</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : // Build list of available shell tools:</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   std::vector&lt;std::string&gt; tmp=Tools::ls(std::string(config::getPlumedRoot()+&quot;/scripts&quot;));</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;tmp.size(); ++j) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     size_t ff=tmp[j].find(&quot;.sh&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     if(ff==std::string::npos) tmp[j].erase();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :     else                 tmp[j].erase(ff);</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;availableCxx.size(); j++) std::fprintf(out,&quot; %s&quot;,availableCxx[j].c_str());</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;tmp.size(); ++j) if(tmp[j].length()&gt;0) std::fprintf(out,&quot; %s&quot;,tmp[j].c_str());</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   std::fprintf(out,&quot;\&quot;\n&quot;);</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;availableCxx.size(); j++) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     std::string s=availableCxx[j];</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : // handle - sign (convert to underscore)</a>
+<a name="99"><span class="lineNum">      99 </span>            :     for(;;) {</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :       size_t n=s.find(&quot;-&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :       if(n==std::string::npos) break;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :       s[n]='_';</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :     std::fprintf(out,&quot;local cmd_keys_%s=\&quot;&quot;,s.c_str());</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     std::vector&lt;std::string&gt; keys=cltoolRegister().getKeys(availableCxx[j]);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     for(unsigned k=0; k&lt;keys.size(); k++) {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : // handle --help/-h</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :       std::string s=keys[k];</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :       for(;;) {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :         size_t n=s.find(&quot;/&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :         if(n==std::string::npos) break;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :         s[n]=' ';</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :       std::fprintf(out,&quot; %s&quot;,s.c_str());</a>
+<a name="115"><span class="lineNum">     115 </span>            :     }</a>
+<a name="116"><span class="lineNum">     116 </span>            :     std::fprintf(out,&quot;\&quot;\n&quot;);</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::fprintf(out,&quot;%s\n&quot;,completion);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   std::string name=config::getPlumedProgramName();</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::fprintf(out,</a>
+<a name="123"><span class="lineNum">     123 </span>            :                &quot;############################################\n&quot;</a>
+<a name="124"><span class="lineNum">     124 </span>            :                &quot;## ADD THESE COMMANDS TO YOUR .bashrc FILE:\n&quot;</a>
+<a name="125"><span class="lineNum">     125 </span>            :                &quot;############################################\n&quot;</a>
+<a name="126"><span class="lineNum">     126 </span>            :                &quot;# _%s() { eval \&quot;$(%s --no-mpi completion 2&gt;/dev/null)\&quot;;}\n&quot;</a>
+<a name="127"><span class="lineNum">     127 </span>            :                &quot;# complete -F _%s -o default %s\n&quot;</a>
+<a name="128"><span class="lineNum">     128 </span>            :                &quot;############################################\n&quot;,</a>
+<a name="129"><span class="lineNum">     129 </span>            :                name.c_str(),name.c_str(),name.c_str(),name.c_str());</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   return 0;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : } // End of namespace</a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Driver.cpp.func-sort-c.html b/coverage/cltools/Driver.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f595d9dabd
--- /dev/null
+++ b/coverage/cltools/Driver.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Driver.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Driver.cpp<span style="font-size: 80%;"> (<a href="Driver.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">543</td>
+            <td class="headerCovTableEntry">607</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Driver.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#1112">_ZN4PLMD7cltools6DriverIfE28evaluateNumericalDerivativesERKxRNS_10PlumedMainERKSt6vectorIfSaIfEESB_SB_RS9_RKdSC_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#266">_ZN4PLMD7cltools6DriverIfE4mainEP8_IO_FILES4_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#488">_ZZN4PLMD7cltools6DriverIfE4mainEP8_IO_FILES4_RNS_12CommunicatorEENKUlPvE0_clES7_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#257">_ZN4PLMD7cltools6DriverIfEC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#263">_ZNK4PLMD7cltools6DriverIdE11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#1112">_ZN4PLMD7cltools6DriverIdE28evaluateNumericalDerivativesERKxRNS_10PlumedMainERKSt6vectorIdSaIdEESB_SB_RS9_RKdSC_</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#488">_ZZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorEENKUlPvE0_clES7_</a></td>
+              <td class="coverFnHi">247</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#266">_ZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#257">_ZN4PLMD7cltools6DriverIdEC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">808</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#208">_ZN4PLMD7cltools6DriverIdE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#208">_ZN4PLMD7cltools6DriverIfE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#182">_ZN4PLMD7cltoolsL11register_cbEPvPNS_7molfile11vmdplugin_tE</a></td>
+              <td class="coverFnHi">75024</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Driver.cpp.func.html b/coverage/cltools/Driver.cpp.func.html
new file mode 100644
index 0000000000..9803226ca8
--- /dev/null
+++ b/coverage/cltools/Driver.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Driver.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Driver.cpp<span style="font-size: 80%;"> (<a href="Driver.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">543</td>
+            <td class="headerCovTableEntry">607</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Driver.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#208">_ZN4PLMD7cltools6DriverIdE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#1112">_ZN4PLMD7cltools6DriverIdE28evaluateNumericalDerivativesERKxRNS_10PlumedMainERKSt6vectorIdSaIdEESB_SB_RS9_RKdSC_</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#266">_ZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#257">_ZN4PLMD7cltools6DriverIdEC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">808</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#208">_ZN4PLMD7cltools6DriverIfE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#1112">_ZN4PLMD7cltools6DriverIfE28evaluateNumericalDerivativesERKxRNS_10PlumedMainERKSt6vectorIfSaIfEESB_SB_RS9_RKdSC_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#266">_ZN4PLMD7cltools6DriverIfE4mainEP8_IO_FILES4_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#257">_ZN4PLMD7cltools6DriverIfEC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#182">_ZN4PLMD7cltoolsL11register_cbEPvPNS_7molfile11vmdplugin_tE</a></td>
+              <td class="coverFnHi">75024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#263">_ZNK4PLMD7cltools6DriverIdE11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#488">_ZZN4PLMD7cltools6DriverIdE4mainEP8_IO_FILES4_RNS_12CommunicatorEENKUlPvE0_clES7_</a></td>
+              <td class="coverFnHi">247</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Driver.cpp.gcov.html#488">_ZZN4PLMD7cltools6DriverIfE4mainEP8_IO_FILES4_RNS_12CommunicatorEENKUlPvE0_clES7_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Driver.cpp.gcov.html b/coverage/cltools/Driver.cpp.gcov.html
new file mode 100644
index 0000000000..3c3887e4e0
--- /dev/null
+++ b/coverage/cltools/Driver.cpp.gcov.html
@@ -0,0 +1,1248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Driver.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Driver.cpp<span style="font-size: 80%;"> (source / <a href="Driver.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">543</td>
+            <td class="headerCovTableEntry">607</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionShortcut.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cstdio&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;cstring&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;vector&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;map&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;memory&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;tools/FileBase.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;xdrfile/xdrfile_trr.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;xdrfile/xdrfile_xtc.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // when using molfile plugin</a>
+<a name="46"><span class="lineNum">      46 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="47"><span class="lineNum">      47 </span>            : #ifndef __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS</a>
+<a name="48"><span class="lineNum">      48 </span>            : /* Use the internal ones. Alternatively:</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *    ifeq (,$(findstring __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS,$(CPPFLAGS)))</a>
+<a name="50"><span class="lineNum">      50 </span>            :  *    CPPFLAGS+=-I../molfile</a>
+<a name="51"><span class="lineNum">      51 </span>            :  */</a>
+<a name="52"><span class="lineNum">      52 </span>            : #include &quot;molfile/libmolfile_plugin.h&quot;</a>
+<a name="53"><span class="lineNum">      53 </span>            : #include &quot;molfile/molfile_plugin.h&quot;</a>
+<a name="54"><span class="lineNum">      54 </span>            : using namespace PLMD::molfile;</a>
+<a name="55"><span class="lineNum">      55 </span>            : #else</a>
+<a name="56"><span class="lineNum">      56 </span>            : #include &lt;libmolfile_plugin.h&gt;</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &lt;molfile_plugin.h&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : #endif</a>
+<a name="59"><span class="lineNum">      59 </span>            : #endif</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace PLMD {</a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace cltools {</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : //+PLUMEDOC TOOLS driver-float</a>
+<a name="65"><span class="lineNum">      65 </span>            : /*</a>
+<a name="66"><span class="lineNum">      66 </span>            : Equivalent to driver, but using single precision reals.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : The purpose of this tool is just to test what PLUMED does when linked from</a>
+<a name="69"><span class="lineNum">      69 </span>            : a single precision code.  The documentation is identical to that for \ref driver</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \par Examples</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \verbatim</a>
+<a name="74"><span class="lineNum">      74 </span>            : plumed driver-float --plumed plumed.dat --ixyz trajectory.xyz</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endverbatim</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : See also examples in \ref driver</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : //</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : //+PLUMEDOC TOOLS driver</a>
+<a name="85"><span class="lineNum">      85 </span>            : /*</a>
+<a name="86"><span class="lineNum">      86 </span>            : driver is a tool that allows one to to use plumed to post-process an existing trajectory.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : The input to driver is specified using the command line arguments described below.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : In addition, you can use the special \subpage READ command inside your plumed input</a>
+<a name="91"><span class="lineNum">      91 </span>            : to read in colvar files that were generated during your MD simulation.  The values</a>
+<a name="92"><span class="lineNum">      92 </span>            : read in can then be treated like calculated colvars.</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : \warning</a>
+<a name="95"><span class="lineNum">      95 </span>            : Notice that by default the driver has no knowledge about the masses and charges</a>
+<a name="96"><span class="lineNum">      96 </span>            : of your atoms! Thus, if you want to compute quantities depending charges (e.g. \ref DHENERGY)</a>
+<a name="97"><span class="lineNum">      97 </span>            : or masses (e.g. \ref COM) you should pass the proper information to the driver.</a>
+<a name="98"><span class="lineNum">      98 </span>            : You can do it either with the --pdb option or with the --mc option. The latter</a>
+<a name="99"><span class="lineNum">      99 </span>            : will read a file produced by \ref DUMPMASSCHARGE .</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : \par Examples</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The following command tells plumed to post process the trajectory contained in `trajectory.xyz`</a>
+<a name="105"><span class="lineNum">     105 </span>            :  by performing the actions described in the input file `plumed.dat`.  If an action that takes the</a>
+<a name="106"><span class="lineNum">     106 </span>            : stride keyword is given a stride equal to \f$n\f$ then it will be performed only on every \f$n\f$th</a>
+<a name="107"><span class="lineNum">     107 </span>            : frames in the trajectory file.</a>
+<a name="108"><span class="lineNum">     108 </span>            : \verbatim</a>
+<a name="109"><span class="lineNum">     109 </span>            : plumed driver --plumed plumed.dat --ixyz trajectory.xyz</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endverbatim</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : Notice that `xyz` files are expected to be in internal PLUMED units, that is by default nm.</a>
+<a name="113"><span class="lineNum">     113 </span>            : You can change this behavior by using the `--length-units` option:</a>
+<a name="114"><span class="lineNum">     114 </span>            : \verbatim</a>
+<a name="115"><span class="lineNum">     115 </span>            : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --length-units A</a>
+<a name="116"><span class="lineNum">     116 </span>            : \endverbatim</a>
+<a name="117"><span class="lineNum">     117 </span>            : The strings accepted by the `--length-units` options are the same ones accepted by the \ref UNITS action.</a>
+<a name="118"><span class="lineNum">     118 </span>            : Other file formats typically have their default coordinates (e.g., `gro` files are always in nm)</a>
+<a name="119"><span class="lineNum">     119 </span>            : and it thus should not be necessary to use the `--length-units` option. Additionally,</a>
+<a name="120"><span class="lineNum">     120 </span>            : consider that the units used by the `driver` might be different by the units used in the PLUMED input</a>
+<a name="121"><span class="lineNum">     121 </span>            : file `plumed.dat`. For instance consider the command:</a>
+<a name="122"><span class="lineNum">     122 </span>            : \verbatim</a>
+<a name="123"><span class="lineNum">     123 </span>            : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --length-units A</a>
+<a name="124"><span class="lineNum">     124 </span>            : \endverbatim</a>
+<a name="125"><span class="lineNum">     125 </span>            : where `plumed.dat` is</a>
+<a name="126"><span class="lineNum">     126 </span>            : \plumedfile</a>
+<a name="127"><span class="lineNum">     127 </span>            : # no explicit UNITS action here</a>
+<a name="128"><span class="lineNum">     128 </span>            : d: DISTANCE ATOMS=1,2</a>
+<a name="129"><span class="lineNum">     129 </span>            : PRINT ARG=d FILE=colvar</a>
+<a name="130"><span class="lineNum">     130 </span>            : \endplumedfile</a>
+<a name="131"><span class="lineNum">     131 </span>            : In this case, the driver reads the `xyz` file assuming it to contain coordinates in Angstrom units.</a>
+<a name="132"><span class="lineNum">     132 </span>            : However, the resulting `colvar` file contains a distance expressed in nm.</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : The following command tells plumed to post process the trajectory contained in trajectory.xyz.</a>
+<a name="135"><span class="lineNum">     135 </span>            :  by performing the actions described in the input file plumed.dat.</a>
+<a name="136"><span class="lineNum">     136 </span>            : \verbatim</a>
+<a name="137"><span class="lineNum">     137 </span>            : plumed driver --plumed plumed.dat --ixyz trajectory.xyz --trajectory-stride 100 --timestep 0.001</a>
+<a name="138"><span class="lineNum">     138 </span>            : \endverbatim</a>
+<a name="139"><span class="lineNum">     139 </span>            : Here though</a>
+<a name="140"><span class="lineNum">     140 </span>            : `--trajectory-stride` is set equal to the frequency with which frames were output during the trajectory</a>
+<a name="141"><span class="lineNum">     141 </span>            : and the `--timestep` is equal to the simulation timestep.  As such the `STRIDE` parameters in the `plumed.dat`</a>
+<a name="142"><span class="lineNum">     142 </span>            : files are referred to the original timestep and any files output resemble those that would have been generated</a>
+<a name="143"><span class="lineNum">     143 </span>            : had we run the calculation we are running with driver when the MD simulation was running.</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : PLUMED can read xyz files (in PLUMED units) and gro files (in nm). In addition,</a>
+<a name="146"><span class="lineNum">     146 </span>            : PLUMED includes by default support for a</a>
+<a name="147"><span class="lineNum">     147 </span>            : subset of the trajectory file formats supported by VMD, e.g. xtc and dcd:</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : \verbatim</a>
+<a name="150"><span class="lineNum">     150 </span>            : plumed driver --plumed plumed.dat --pdb diala.pdb --mf_xtc traj.xtc --trajectory-stride 100 --timestep 0.001</a>
+<a name="151"><span class="lineNum">     151 </span>            : \endverbatim</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : where `--mf_` prefixes the extension of one of the accepted molfile plugin format.</a>
+<a name="154"><span class="lineNum">     154 </span>            : If PLUMED has been \ref Installation &quot;installed&quot; with full molfile support, other formats will be available.</a>
+<a name="155"><span class="lineNum">     155 </span>            : Just type `plumed driver --help` to see which plugins are available.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : Molfile plugin require periodic cell to be triangular (i.e. first vector oriented along x and</a>
+<a name="158"><span class="lineNum">     158 </span>            : second vector in xy plane). This is true for many MD codes. However, it could be false</a>
+<a name="159"><span class="lineNum">     159 </span>            : if you rotate the coordinates in your trajectory before reading them in the driver.</a>
+<a name="160"><span class="lineNum">     160 </span>            : Also notice that some formats (e.g. amber crd) do not specify atom number. In this case you can use</a>
+<a name="161"><span class="lineNum">     161 </span>            : the `--natoms` option:</a>
+<a name="162"><span class="lineNum">     162 </span>            : \verbatim</a>
+<a name="163"><span class="lineNum">     163 </span>            : plumed driver --plumed plumed.dat --imf_crd trajectory.crd --natoms 128</a>
+<a name="164"><span class="lineNum">     164 </span>            : \endverbatim</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : Check the available molfile plugins and limitations at [this link](http://www.ks.uiuc.edu/Research/vmd/plugins/molfile/).</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : Additionally, you can use the xdrfile implementation of xtc and trr. To this aim, just</a>
+<a name="169"><span class="lineNum">     169 </span>            : download and install properly the xdrfile library (see [this link](http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library)).</a>
+<a name="170"><span class="lineNum">     170 </span>            : If the xdrfile library is installed properly the PLUMED configure script should be able to</a>
+<a name="171"><span class="lineNum">     171 </span>            : detect it and enable it.</a>
+<a name="172"><span class="lineNum">     172 </span>            : Notice that the xdrfile implementation of xtc and trr</a>
+<a name="173"><span class="lineNum">     173 </span>            : is more robust than the molfile one, since it provides support for generic cell shapes.</a>
+<a name="174"><span class="lineNum">     174 </span>            : In addition, it allows \ref DUMPATOMS to write compressed xtc files.</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : */</a>
+<a name="178"><span class="lineNum">     178 </span>            : //+ENDPLUMEDOC</a>
+<a name="179"><span class="lineNum">     179 </span>            : //</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="182"><span class="lineNum">     182 </span>            : static std::vector&lt;molfile_plugin_t *&gt; plugins;</a>
+<a name="183"><span class="lineNum">     183 </span>            : static std::map &lt;std::string, unsigned&gt; pluginmap;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      75024 : static int register_cb(void *v, vmdplugin_t *p) {</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   //const char *key = p-&gt;name;</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     150048 :   const auto ret = pluginmap.insert ( std::pair&lt;std::string,unsigned&gt;(std::string(p-&gt;name),plugins.size()) );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      75024 :   if (ret.second==false) {</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     //cerr&lt;&lt;&quot;MOLFILE: found duplicate plugin for &quot;&lt;&lt;key&lt;&lt;&quot; : not inserted &quot;&lt;&lt;endl;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   } else {</a>
+<a name="190"><span class="lineNum">     190 </span>            :     //cerr&lt;&lt;&quot;MOLFILE: loading plugin &quot;&lt;&lt;key&lt;&lt;&quot; number &quot;&lt;&lt;plugins.size()-1&lt;&lt;endl;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      75024 :     plugins.push_back(reinterpret_cast&lt;molfile_plugin_t *&gt;(p));</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      75024 :   return VMDPLUGIN_SUCCESS;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+<a name="195"><span class="lineNum">     195 </span>            : #endif</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : template&lt;typename real&gt;</a>
+<a name="198"><span class="lineNum">     198 </span>            : class Driver : public CLTool {</a>
+<a name="199"><span class="lineNum">     199 </span>            : public:</a>
+<a name="200"><span class="lineNum">     200 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="201"><span class="lineNum">     201 </span>            :   explicit Driver(const CLToolOptions&amp; co );</a>
+<a name="202"><span class="lineNum">     202 </span>            :   int main(FILE* in,FILE*out,Communicator&amp; pc) override;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   void evaluateNumericalDerivatives( const long long int&amp; step, PlumedMain&amp; p, const std::vector&lt;real&gt;&amp; coordinates,</a>
+<a name="204"><span class="lineNum">     204 </span>            :                                      const std::vector&lt;real&gt;&amp; masses, const std::vector&lt;real&gt;&amp; charges,</a>
+<a name="205"><span class="lineNum">     205 </span>            :                                      std::vector&lt;real&gt;&amp; cell, const double&amp; base, std::vector&lt;real&gt;&amp; numder );</a>
+<a name="206"><span class="lineNum">     206 </span>            :   std::string description()const override;</a>
+<a name="207"><span class="lineNum">     207 </span>            : };</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : template&lt;typename real&gt;</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       8336 : void Driver&lt;real&gt;::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       8336 :   CLTool::registerKeywords( keys ); keys.isDriver();</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      16672 :   keys.addFlag(&quot;--help-debug&quot;,false,&quot;print special options that can be used to create regtests&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      16672 :   keys.add(&quot;compulsory&quot;,&quot;--plumed&quot;,&quot;plumed.dat&quot;,&quot;specify the name of the plumed input file&quot;);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      16672 :   keys.add(&quot;compulsory&quot;,&quot;--timestep&quot;,&quot;1.0&quot;,&quot;the timestep that was used in the calculation that produced this trajectory in picoseconds&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      16672 :   keys.add(&quot;compulsory&quot;,&quot;--trajectory-stride&quot;,&quot;1&quot;,&quot;the frequency with which frames were output to this trajectory during the simulation&quot;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :            &quot; (0 means that the number of the step is read from the trajectory file,&quot;</a>
+<a name="217"><span class="lineNum">     217 </span>            :            &quot; currently working only for xtc/trr files read with --ixtc/--trr)&quot;</a>
+<a name="218"><span class="lineNum">     218 </span>            :           );</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      16672 :   keys.add(&quot;compulsory&quot;,&quot;--multi&quot;,&quot;0&quot;,&quot;set number of replicas for multi environment (needs MPI)&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      16672 :   keys.addFlag(&quot;--noatoms&quot;,false,&quot;don't read in a trajectory.  Just use colvar files as specified in plumed.dat&quot;);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      16672 :   keys.addFlag(&quot;--parse-only&quot;,false,&quot;read the plumed input file and stop&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      16672 :   keys.addFlag(&quot;--restart&quot;,false,&quot;makes driver behave as if restarting&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      16672 :   keys.add(&quot;atoms&quot;,&quot;--ixyz&quot;,&quot;the trajectory in xyz format&quot;);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      16672 :   keys.add(&quot;atoms&quot;,&quot;--igro&quot;,&quot;the trajectory in gro format&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      16672 :   keys.add(&quot;atoms&quot;,&quot;--idlp4&quot;,&quot;the trajectory in DL_POLY_4 format&quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      16672 :   keys.add(&quot;atoms&quot;,&quot;--ixtc&quot;,&quot;the trajectory in xtc format (xdrfile implementation)&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      16672 :   keys.add(&quot;atoms&quot;,&quot;--itrr&quot;,&quot;the trajectory in trr format (xdrfile implementation)&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--shortcut-ofile&quot;,&quot;the name of the file to output info on the way shortcuts have been expanded.  If there are no shortcuts in your input file nothing is output&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--length-units&quot;,&quot;units for length, either as a string or a number&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--mass-units&quot;,&quot;units for mass in pdb and mc file, either as a string or a number&quot;);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--charge-units&quot;,&quot;units for charge in pdb and mc file, either as a string or a number&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--kt&quot;,&quot;set \\f$k_B T\\f$, it will not be necessary to specify temperature in input file&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--dump-forces&quot;,&quot;dump the forces on a file&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--dump-forces-fmt&quot;,&quot;( default=%%f ) the format to use to dump the forces&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      16672 :   keys.addFlag(&quot;--dump-full-virial&quot;,false,&quot;with --dump-forces, it dumps the 9 components of the virial&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--pdb&quot;,&quot;provides a pdb with masses and charges&quot;);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--mc&quot;,&quot;provides a file with masses and charges as produced with DUMPMASSCHARGE&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--box&quot;,&quot;comma-separated box dimensions (3 for orthorhombic, 9 for generic)&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--natoms&quot;,&quot;provides number of atoms - only used if file format does not contain number of atoms&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--initial-step&quot;,&quot;provides a number for the initial step, default is 0&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">      16672 :   keys.add(&quot;optional&quot;,&quot;--debug-forces&quot;,&quot;output a file containing the forces due to the bias evaluated using numerical derivatives &quot;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :            &quot;and using the analytical derivatives implemented in plumed&quot;);</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      16672 :   keys.add(&quot;hidden&quot;,&quot;--debug-float&quot;,&quot;[yes/no] turns on the single precision version (to check float interface)&quot;);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">      16672 :   keys.add(&quot;hidden&quot;,&quot;--debug-dd&quot;,&quot;[yes/no] use a fake domain decomposition&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      16672 :   keys.add(&quot;hidden&quot;,&quot;--debug-pd&quot;,&quot;[yes/no] use a fake particle decomposition&quot;);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">      16672 :   keys.add(&quot;hidden&quot;,&quot;--debug-grex&quot;,&quot;use a fake gromacs-like replica exchange, specify exchange stride&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      16672 :   keys.add(&quot;hidden&quot;,&quot;--debug-grex-log&quot;,&quot;log file for debug=grex&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       8336 :   MOLFILE_INIT_ALL</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       8336 :   MOLFILE_REGISTER_ALL(NULL, register_cb)</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">      83360 :   for(unsigned i=0; i&lt;plugins.size(); i++) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">     150048 :     std::string kk=&quot;--mf_&quot;+std::string(plugins[i]-&gt;name);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">     150048 :     std::string mm=&quot; molfile: the trajectory in &quot;+std::string(plugins[i]-&gt;name)+&quot; format &quot; ;</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">     150048 :     keys.add(&quot;atoms&quot;,kk,mm);</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :   }</a>
+<a name="256"><span class="lineNum">     256 </span>            : #endif</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       8336 : }</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : template&lt;typename real&gt;</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        812 : Driver&lt;real&gt;::Driver(const CLToolOptions&amp; co ):</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        812 :   CLTool(co)</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : {</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        812 :   inputdata=commandline;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        812 : }</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : template&lt;typename real&gt;</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          4 : std::string Driver&lt;real&gt;::description()const { return &quot;analyze trajectories with plumed&quot;; }</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : template&lt;typename real&gt;</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        804 : int Driver&lt;real&gt;::main(FILE* in,FILE*out,Communicator&amp; pc) {</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        804 :   Units units;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        804 :   PDB pdb;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : // Parse everything</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        804 :   bool printhelpdebug; parseFlag(&quot;--help-debug&quot;,printhelpdebug);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        804 :   if( printhelpdebug ) {</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     std::fprintf(out,&quot;%s&quot;,</a>
+<a name="277"><span class="lineNum">     277 </span>            :                  &quot;Additional options for debug (only to be used in regtest):\n&quot;</a>
+<a name="278"><span class="lineNum">     278 </span>            :                  &quot;  [--debug-float yes]     : turns on the single precision version (to check float interface)\n&quot;</a>
+<a name="279"><span class="lineNum">     279 </span>            :                  &quot;  [--debug-dd yes]        : use a fake domain decomposition\n&quot;</a>
+<a name="280"><span class="lineNum">     280 </span>            :                  &quot;  [--debug-pd yes]        : use a fake particle decomposition\n&quot;</a>
+<a name="281"><span class="lineNum">     281 </span>            :                 );</a>
+<a name="282"><span class="lineNum">     282 </span>            :     return 0;</a>
+<a name="283"><span class="lineNum">     283 </span>            :   }</a>
+<a name="284"><span class="lineNum">     284 </span>            :   // Are we reading trajectory data</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        804 :   bool noatoms; parseFlag(&quot;--noatoms&quot;,noatoms);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">       1608 :   bool parseOnly; parseFlag(&quot;--parse-only&quot;,parseOnly);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        804 :   std::string full_outputfile; parse(&quot;--shortcut-ofile&quot;,full_outputfile);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       1608 :   bool restart; parseFlag(&quot;--restart&quot;,restart);</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            :   std::string fakein;</a>
+<a name="291"><span class="lineNum">     291 </span>            :   bool debug_float=false;</a>
+<a name="292"><span class="lineNum">     292 </span>            :   fakein=&quot;&quot;;</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1608 :   if(parse(&quot;--debug-float&quot;,fakein)) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :     if(fakein==&quot;yes&quot;) debug_float=true;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     else if(fakein==&quot;no&quot;) debug_float=false;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     else error(&quot;--debug-float should have argument yes or no&quot;);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :   if(debug_float &amp;&amp; sizeof(real)!=sizeof(float)) {</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :     auto cl=cltoolRegister().create(CLToolOptions(&quot;driver-float&quot;));</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :     cl-&gt;setInputData(this-&gt;getInputData());</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :     int ret=cl-&gt;main(in,out,pc);</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     return ret;</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :   bool debug_pd=false;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   fakein=&quot;&quot;;</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       1608 :   if(parse(&quot;--debug-pd&quot;,fakein)) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         12 :     if(fakein==&quot;yes&quot;) debug_pd=true;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :     else if(fakein==&quot;no&quot;) debug_pd=false;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :     else error(&quot;--debug-pd should have argument yes or no&quot;);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   }</a>
+<a name="313"><span class="lineNum">     313 </span>            :   if(debug_pd) std::fprintf(out,&quot;DEBUGGING PARTICLE DECOMPOSITION\n&quot;);</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            :   bool debug_dd=false;</a>
+<a name="316"><span class="lineNum">     316 </span>            :   fakein=&quot;&quot;;</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       1608 :   if(parse(&quot;--debug-dd&quot;,fakein)) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         60 :     if(fakein==&quot;yes&quot;) debug_dd=true;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :     else if(fakein==&quot;no&quot;) debug_dd=false;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :     else error(&quot;--debug-dd should have argument yes or no&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :   }</a>
+<a name="322"><span class="lineNum">     322 </span>            :   if(debug_dd) std::fprintf(out,&quot;DEBUGGING DOMAIN DECOMPOSITION\n&quot;);</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        804 :   if( debug_pd || debug_dd ) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         72 :     if(noatoms) error(&quot;cannot debug without atoms&quot;);</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            : // set up for multi replica driver:</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        804 :   int multi=0;</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        804 :   parse(&quot;--multi&quot;,multi);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        804 :   Communicator intracomm;</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        804 :   Communicator intercomm;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        804 :   if(multi) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">        170 :     int ntot=pc.Get_size();</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        170 :     int nintra=ntot/multi;</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        170 :     if(multi*nintra!=ntot) error(&quot;invalid number of processes for multi environment&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        170 :     pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        170 :     pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   } else {</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">        634 :     intracomm.Set_comm(pc.Get_comm());</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :   }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            : // set up for debug replica exchange:</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        804 :   bool debug_grex=parse(&quot;--debug-grex&quot;,fakein);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        804 :   int  grex_stride=0;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :   FILE*grex_log=NULL;</a>
+<a name="347"><span class="lineNum">     347 </span>            : // call fclose when fp goes out of scope</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        967 :   auto deleter=[](FILE* f) { if(f) std::fclose(f); };</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; grex_log_deleter(grex_log,deleter);</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        804 :   if(debug_grex) {</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         30 :     if(noatoms) error(&quot;must have atoms to debug_grex&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         30 :     if(multi&lt;2)  error(&quot;--debug_grex needs --multi with at least two replicas&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         30 :     Tools::convert(fakein,grex_stride);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         30 :     std::string n; Tools::convert(intercomm.Get_rank(),n);</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :     std::string file;</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         60 :     parse(&quot;--debug-grex-log&quot;,file);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         30 :     if(file.length()&gt;0) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         60 :       file+=&quot;.&quot;+n;</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         30 :       grex_log=std::fopen(file.c_str(),&quot;w&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :       grex_log_deleter.reset(grex_log);</a>
+<a name="362"><span class="lineNum">     362 </span>            :     }</a>
+<a name="363"><span class="lineNum">     363 </span>            :   }</a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            : // Read the plumed input file name</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        804 :   std::string plumedFile; parse(&quot;--plumed&quot;,plumedFile);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : // the timestep</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        804 :   double t; parse(&quot;--timestep&quot;,t);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        804 :   real timestep=real(t);</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : // the stride</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        804 :   unsigned stride; parse(&quot;--trajectory-stride&quot;,stride);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : // are we writing forces</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        804 :   std::string dumpforces(&quot;&quot;), debugforces(&quot;&quot;), dumpforcesFmt(&quot;%f&quot;);;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        804 :   bool dumpfullvirial=false;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        804 :   if(!noatoms) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        750 :     parse(&quot;--dump-forces&quot;,dumpforces);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">       1500 :     parse(&quot;--debug-forces&quot;,debugforces);</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :   }</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">       1618 :   if(dumpforces!=&quot;&quot; || debugforces!=&quot;&quot; ) parse(&quot;--dump-forces-fmt&quot;,dumpforcesFmt);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">       1243 :   if(dumpforces!=&quot;&quot;) parseFlag(&quot;--dump-full-virial&quot;,dumpfullvirial);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        804 :   if( debugforces!=&quot;&quot; &amp;&amp; (debug_dd || debug_pd) ) error(&quot;cannot debug forces and domain/particle decomposition at same time&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :   if( debugforces!=&quot;&quot; &amp;&amp; sizeof(real)!=sizeof(double) ) error(&quot;cannot debug forces in single precision mode&quot;);</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        804 :   real kt=-1.0;</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       1608 :   parse(&quot;--kt&quot;,kt);</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :   std::string trajectory_fmt;</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            :   bool use_molfile=false;</a>
+<a name="389"><span class="lineNum">     389 </span>            :   molfile_plugin_t *api=NULL;</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            : // Read in an xyz file</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        804 :   std::string trajectoryFile(&quot;&quot;), pdbfile(&quot;&quot;), mcfile(&quot;&quot;);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        804 :   bool pbc_cli_given=false; std::vector&lt;double&gt; pbc_cli_box(9,0.0);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        804 :   int command_line_natoms=-1;</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        804 :   if(!noatoms) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">       1500 :     std::string traj_xyz; parse(&quot;--ixyz&quot;,traj_xyz);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       1500 :     std::string traj_gro; parse(&quot;--igro&quot;,traj_gro);</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       1500 :     std::string traj_dlp4; parse(&quot;--idlp4&quot;,traj_dlp4);</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :     std::string traj_xtc;</a>
+<a name="401"><span class="lineNum">     401 </span>            :     std::string traj_trr;</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">        750 :     parse(&quot;--ixtc&quot;,traj_xtc);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">        750 :     parse(&quot;--itrr&quot;,traj_trr);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       7500 :     for(unsigned i=0; i&lt;plugins.size(); i++) {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">      13500 :       std::string molfile_key=&quot;--mf_&quot;+std::string(plugins[i]-&gt;name);</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :       std::string traj_molfile;</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">       6750 :       parse(molfile_key,traj_molfile);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">       6750 :       if(traj_molfile.length()&gt;0) {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">        247 :         std::fprintf(out,&quot;\nDRIVER: Found molfile format trajectory %s with name %s\n&quot;,plugins[i]-&gt;name,traj_molfile.c_str());</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :         trajectoryFile=traj_molfile;</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">        494 :         trajectory_fmt=std::string(plugins[i]-&gt;name);</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :         use_molfile=true;</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">        247 :         api = plugins[i];</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :       }</a>
+<a name="416"><span class="lineNum">     416 </span>            :     }</a>
+<a name="417"><span class="lineNum">     417 </span>            : #endif</a>
+<a name="418"><span class="lineNum">     418 </span>            :     { // check that only one fmt is specified</a>
+<a name="419"><span class="lineNum">     419 </span>            :       int nn=0;</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">        750 :       if(traj_xyz.length()&gt;0) nn++;</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        750 :       if(traj_gro.length()&gt;0) nn++;</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        750 :       if(traj_dlp4.length()&gt;0) nn++;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        750 :       if(traj_xtc.length()&gt;0) nn++;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        750 :       if(traj_trr.length()&gt;0) nn++;</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">        750 :       if(nn&gt;1) {</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :         std::fprintf(stderr,&quot;ERROR: cannot provide more than one trajectory file\n&quot;);</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :         return 1;</a>
+<a name="428"><span class="lineNum">     428 </span>            :       }</a>
+<a name="429"><span class="lineNum">     429 </span>            :     }</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        750 :     if(traj_xyz.length()&gt;0 &amp;&amp; trajectoryFile.length()==0) {</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :       trajectoryFile=traj_xyz;</a>
+<a name="432"><span class="lineNum">     432 </span>            :       trajectory_fmt=&quot;xyz&quot;;</a>
+<a name="433"><span class="lineNum">     433 </span>            :     }</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        750 :     if(traj_gro.length()&gt;0 &amp;&amp; trajectoryFile.length()==0) {</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :       trajectoryFile=traj_gro;</a>
+<a name="436"><span class="lineNum">     436 </span>            :       trajectory_fmt=&quot;gro&quot;;</a>
+<a name="437"><span class="lineNum">     437 </span>            :     }</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">        750 :     if(traj_dlp4.length()&gt;0 &amp;&amp; trajectoryFile.length()==0) {</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :       trajectoryFile=traj_dlp4;</a>
+<a name="440"><span class="lineNum">     440 </span>            :       trajectory_fmt=&quot;dlp4&quot;;</a>
+<a name="441"><span class="lineNum">     441 </span>            :     }</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">        750 :     if(traj_xtc.length()&gt;0 &amp;&amp; trajectoryFile.length()==0) {</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :       trajectoryFile=traj_xtc;</a>
+<a name="444"><span class="lineNum">     444 </span>            :       trajectory_fmt=&quot;xdr-xtc&quot;;</a>
+<a name="445"><span class="lineNum">     445 </span>            :     }</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        750 :     if(traj_trr.length()&gt;0 &amp;&amp; trajectoryFile.length()==0) {</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :       trajectoryFile=traj_trr;</a>
+<a name="448"><span class="lineNum">     448 </span>            :       trajectory_fmt=&quot;xdr-trr&quot;;</a>
+<a name="449"><span class="lineNum">     449 </span>            :     }</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">        750 :     if(trajectoryFile.length()==0&amp;&amp;!parseOnly) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot;ERROR: missing trajectory data\n&quot;);</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :       return 1;</a>
+<a name="453"><span class="lineNum">     453 </span>            :     }</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">       1500 :     std::string lengthUnits(&quot;&quot;); parse(&quot;--length-units&quot;,lengthUnits);</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">        750 :     if(lengthUnits.length()&gt;0) units.setLength(lengthUnits);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">       1500 :     std::string chargeUnits(&quot;&quot;); parse(&quot;--charge-units&quot;,chargeUnits);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        750 :     if(chargeUnits.length()&gt;0) units.setCharge(chargeUnits);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">       1500 :     std::string massUnits(&quot;&quot;); parse(&quot;--mass-units&quot;,massUnits);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        750 :     if(massUnits.length()&gt;0) units.setMass(massUnits);</span></a>
+<a name="460"><span class="lineNum">     460 </span>            : </a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">       1500 :     parse(&quot;--pdb&quot;,pdbfile);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">        750 :     if(pdbfile.length()&gt;0) {</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         75 :       bool check=pdb.read(pdbfile,false,1.0);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         75 :       if(!check) error(&quot;error reading pdb file&quot;);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :     }</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">       1500 :     parse(&quot;--mc&quot;,mcfile);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">       1500 :     std::string pbc_cli_list; parse(&quot;--box&quot;,pbc_cli_list);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">        750 :     if(pbc_cli_list.length()&gt;0) {</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :       pbc_cli_given=true;</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         30 :       std::vector&lt;std::string&gt; words=Tools::getWords(pbc_cli_list,&quot;,&quot;);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         30 :       if(words.size()==3) {</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        120 :         for(int i=0; i&lt;3; i++) std::sscanf(words[i].c_str(),&quot;%100lf&quot;,&amp;(pbc_cli_box[4*i]));</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :       } else if(words.size()==9) {</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :         for(int i=0; i&lt;9; i++) std::sscanf(words[i].c_str(),&quot;%100lf&quot;,&amp;(pbc_cli_box[i]));</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :       } else {</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 :         std::string msg=&quot;ERROR: cannot parse command-line box &quot;+pbc_cli_list;</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :         std::fprintf(stderr,&quot;%s\n&quot;,msg.c_str());</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :         return 1;</a>
+<a name="481"><span class="lineNum">     481 </span>            :       }</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         30 :     }</span></a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">       1500 :     parse(&quot;--natoms&quot;,command_line_natoms);</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span>            :   }</a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        247 :   auto mf_deleter=[api](void* h_in) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        247 :     if(h_in) {</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        247 :       std::unique_ptr&lt;std::lock_guard&lt;std::mutex&gt;&gt; lck;</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        442 :       if(api-&gt;is_reentrant==VMDPLUGIN_THREADUNSAFE) lck=Tools::molfile_lock();</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        247 :       api-&gt;close_file_read(h_in);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">        247 :     }</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :   };</a>
+<a name="497"><span class="lineNum">     497 </span>            :   void *h_in=NULL;</a>
+<a name="498"><span class="lineNum">     498 </span>            :   std::unique_ptr&lt;void,decltype(mf_deleter)&gt; h_in_deleter(h_in,mf_deleter);</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            :   molfile_timestep_t ts_in; // this is the structure that has the timestep</a>
+<a name="501"><span class="lineNum">     501 </span>            : // a std::vector&lt;float&gt; with the same scope as ts_in</a>
+<a name="502"><span class="lineNum">     502 </span>            : // it is necessary in order to store the pointer to ts_in.coords</a>
+<a name="503"><span class="lineNum">     503 </span>            :   std::vector&lt;float&gt; ts_in_coords;</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        804 :   ts_in.coords=ts_in_coords.data();</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        804 :   ts_in.velocities=NULL;</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        804 :   ts_in.A=-1; // we use this to check whether cell is provided or not</span></a>
+<a name="507"><span class="lineNum">     507 </span>            : #endif</a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">        804 :   if(debug_dd &amp;&amp; debug_pd) error(&quot;cannot use debug-dd and debug-pd at the same time&quot;);</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">        804 :   if(debug_pd || debug_dd) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         72 :     if( !Communicator::initialized() ) error(&quot;needs mpi for debug-pd&quot;);</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :   }</a>
+<a name="515"><span class="lineNum">     515 </span>            : </a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        804 :   PlumedMain p; if( parseOnly ) p.activateParseOnlyMode();</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">       1608 :   p.cmd(&quot;setRealPrecision&quot;,(int)sizeof(real));</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :   int checknatoms=-1;</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">        804 :   long long int step=0;</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">        804 :   parse(&quot;--initial-step&quot;,step);</span></a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        806 :   if(restart) p.cmd(&quot;setRestart&quot;,1);</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">        804 :   if(Communicator::initialized()) {</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">        305 :     if(multi) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">        414 :       if(intracomm.Get_rank()==0) p.cmd(&quot;GREX setMPIIntercomm&quot;,&amp;intercomm.Get_comm());</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">        510 :       p.cmd(&quot;GREX setMPIIntracomm&quot;,&amp;intracomm.Get_comm());</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">        340 :       p.cmd(&quot;GREX init&quot;);</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :     }</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">        915 :     p.cmd(&quot;setMPIComm&quot;,&amp;intracomm.Get_comm());</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :   }</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">       1608 :   p.cmd(&quot;setMDLengthUnits&quot;,units.getLength());</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">       1608 :   p.cmd(&quot;setMDChargeUnits&quot;,units.getCharge());</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">       1608 :   p.cmd(&quot;setMDMassUnits&quot;,units.getMass());</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">       1608 :   p.cmd(&quot;setMDEngine&quot;,&quot;driver&quot;);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">       1608 :   p.cmd(&quot;setTimestep&quot;,timestep);</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">       2412 :   if( !parseOnly || full_outputfile.length()==0 ) p.cmd(&quot;setPlumedDat&quot;,plumedFile.c_str());</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">       1608 :   p.cmd(&quot;setLog&quot;,out);</span></a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span>            :   int natoms;</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">        804 :   int lvl=0;</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">        804 :   int pb=1;</span></a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">        804 :   if(parseOnly) {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :     if(command_line_natoms&lt;0) error(&quot;--parseOnly requires setting the number of atoms with --natoms&quot;);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :     natoms=command_line_natoms;</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :   }</a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        804 :   FILE* fp=NULL; FILE* fp_forces=NULL; OFile fp_dforces;</span></a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="553"><span class="lineNum">     553 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_forces_deleter(fp_forces,deleter);</a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">          5 :   auto xdr_deleter=[](xdrfile::XDRFILE* xd) { if(xd) xdrfile::xdrfile_close(xd); };</span></a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span>            :   xdrfile::XDRFILE* xd=NULL;</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span>            :   std::unique_ptr&lt;xdrfile::XDRFILE,decltype(xdr_deleter)&gt; xd_deleter(xd,xdr_deleter);</a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">        804 :   if(!noatoms&amp;&amp;!parseOnly) {</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">        750 :     if (trajectoryFile==&quot;-&quot;)</span></a>
+<a name="563"><span class="lineNum">     563 </span>            :       fp=in;</a>
+<a name="564"><span class="lineNum">     564 </span>            :     else {</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">        750 :       if(multi) {</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :         std::string n;</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">        170 :         Tools::convert(intercomm.Get_rank(),n);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">        340 :         std::string testfile=FileBase::appendSuffix(trajectoryFile,&quot;.&quot;+n);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">        170 :         FILE* tmp_fp=std::fopen(testfile.c_str(),&quot;r&quot;);</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :         // no exceptions here</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">        170 :         if(tmp_fp) { std::fclose(tmp_fp); trajectoryFile=testfile;}</span></a>
+<a name="572"><span class="lineNum">     572 </span>            :       }</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        750 :       if(use_molfile==true) {</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        247 :         std::unique_ptr&lt;std::lock_guard&lt;std::mutex&gt;&gt; lck;</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">        442 :         if(api-&gt;is_reentrant==VMDPLUGIN_THREADUNSAFE) lck=Tools::molfile_lock();</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        247 :         h_in = api-&gt;open_file_read(trajectoryFile.c_str(), trajectory_fmt.c_str(), &amp;natoms);</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :         h_in_deleter.reset(h_in);</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">        247 :         if(natoms==MOLFILE_NUMATOMS_UNKNOWN) {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">          2 :           if(command_line_natoms&gt;=0) natoms=command_line_natoms;</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :           else error(&quot;this file format does not provide number of atoms; use --natoms on the command line&quot;);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :         }</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">        247 :         ts_in_coords.resize(3*natoms);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">        247 :         ts_in.coords = ts_in_coords.data();</span></a>
+<a name="585"><span class="lineNum">     585 </span>            : #endif</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">       1251 :       } else if(trajectory_fmt==&quot;xdr-xtc&quot; || trajectory_fmt==&quot;xdr-trr&quot;) {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">          5 :         xd=xdrfile::xdrfile_open(trajectoryFile.c_str(),&quot;r&quot;);</span></a>
+<a name="588"><span class="lineNum">     588 </span>            :         xd_deleter.reset(xd);</a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">          5 :         if(!xd) {</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :           std::string msg=&quot;ERROR: Error opening trajectory file &quot;+trajectoryFile;</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :           std::fprintf(stderr,&quot;%s\n&quot;,msg.c_str());</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :           return 1;</a>
+<a name="593"><span class="lineNum">     593 </span>            :         }</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          5 :         if(trajectory_fmt==&quot;xdr-xtc&quot;) xdrfile::read_xtc_natoms(&amp;trajectoryFile[0],&amp;natoms);</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          5 :         if(trajectory_fmt==&quot;xdr-trr&quot;) xdrfile::read_trr_natoms(&amp;trajectoryFile[0],&amp;natoms);</span></a>
+<a name="596"><span class="lineNum">     596 </span>            :       } else {</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">        498 :         fp=std::fopen(trajectoryFile.c_str(),&quot;r&quot;);</span></a>
+<a name="598"><span class="lineNum">     598 </span>            :         fp_deleter.reset(fp);</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">        498 :         if(!fp) {</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :           std::string msg=&quot;ERROR: Error opening trajectory file &quot;+trajectoryFile;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :           std::fprintf(stderr,&quot;%s\n&quot;,msg.c_str());</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :           return 1;</a>
+<a name="603"><span class="lineNum">     603 </span>            :         }</a>
+<a name="604"><span class="lineNum">     604 </span>            :       }</a>
+<a name="605"><span class="lineNum">     605 </span>            :     }</a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">        750 :     if(dumpforces.length()&gt;0) {</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">        439 :       if(Communicator::initialized() &amp;&amp; pc.Get_size()&gt;1) {</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :         std::string n;</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">        228 :         Tools::convert(pc.Get_rank(),n);</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">        456 :         dumpforces+=&quot;.&quot;+n;</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :       }</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">        439 :       fp_forces=std::fopen(dumpforces.c_str(),&quot;w&quot;);</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :       fp_forces_deleter.reset(fp_forces);</a>
+<a name="614"><span class="lineNum">     614 </span>            :     }</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">        750 :     if(debugforces.length()&gt;0) {</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         11 :       if(Communicator::initialized() &amp;&amp; pc.Get_size()&gt;1) {</span></a>
+<a name="617"><span class="lineNum">     617 </span>            :         std::string n;</a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">          6 :         Tools::convert(pc.Get_rank(),n);</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         12 :         debugforces+=&quot;.&quot;+n;</span></a>
+<a name="620"><span class="lineNum">     620 </span>            :       }</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">         11 :       fp_dforces.open(debugforces);</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :     }</a>
+<a name="623"><span class="lineNum">     623 </span>            :   }</a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span>            :   std::string line;</a>
+<a name="626"><span class="lineNum">     626 </span>            :   std::vector&lt;real&gt; coordinates;</a>
+<a name="627"><span class="lineNum">     627 </span>            :   std::vector&lt;real&gt; forces;</a>
+<a name="628"><span class="lineNum">     628 </span>            :   std::vector&lt;real&gt; masses;</a>
+<a name="629"><span class="lineNum">     629 </span>            :   std::vector&lt;real&gt; charges;</a>
+<a name="630"><span class="lineNum">     630 </span>            :   std::vector&lt;real&gt; cell;</a>
+<a name="631"><span class="lineNum">     631 </span>            :   std::vector&lt;real&gt; virial;</a>
+<a name="632"><span class="lineNum">     632 </span>            :   std::vector&lt;real&gt; numder;</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            : // variables to test particle decomposition</a>
+<a name="635"><span class="lineNum">     635 </span>            :   int pd_nlocal=0;</a>
+<a name="636"><span class="lineNum">     636 </span>            :   int pd_start=0;</a>
+<a name="637"><span class="lineNum">     637 </span>            : // variables to test random decomposition (=domain decomposition)</a>
+<a name="638"><span class="lineNum">     638 </span>            :   std::vector&lt;int&gt;  dd_gatindex;</a>
+<a name="639"><span class="lineNum">     639 </span>            :   std::vector&lt;int&gt;  dd_g2l;</a>
+<a name="640"><span class="lineNum">     640 </span>            :   std::vector&lt;real&gt; dd_masses;</a>
+<a name="641"><span class="lineNum">     641 </span>            :   std::vector&lt;real&gt; dd_charges;</a>
+<a name="642"><span class="lineNum">     642 </span>            :   std::vector&lt;real&gt; dd_forces;</a>
+<a name="643"><span class="lineNum">     643 </span>            :   std::vector&lt;real&gt; dd_coordinates;</a>
+<a name="644"><span class="lineNum">     644 </span>            :   int dd_nlocal=0;</a>
+<a name="645"><span class="lineNum">     645 </span>            : // random stream to choose decompositions</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">        804 :   Random rnd;</span></a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">        804 :   if(trajectory_fmt==&quot;dlp4&quot;) {</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          2 :     if(!Tools::getline(fp,line)) error(&quot;error reading title&quot;);</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          2 :     if(!Tools::getline(fp,line)) error(&quot;error reading atoms&quot;);</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          2 :     std::sscanf(line.c_str(),&quot;%d %d %d&quot;,&amp;lvl,&amp;pb,&amp;natoms);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            :   }</a>
+<a name="654"><span class="lineNum">     654 </span>            :   bool lstep=true;</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">     244065 :   while(true) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">     244869 :     if(!noatoms&amp;&amp;!parseOnly) {</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">      44529 :       if(use_molfile==true) {</span></a>
+<a name="658"><span class="lineNum">     658 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">      18588 :         std::unique_ptr&lt;std::lock_guard&lt;std::mutex&gt;&gt; lck;</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">      37040 :         if(api-&gt;is_reentrant==VMDPLUGIN_THREADUNSAFE) lck=Tools::molfile_lock();</span></a>
+<a name="661"><span class="lineNum">     661 </span>            :         int rc;</a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">      18588 :         rc = api-&gt;read_next_timestep(h_in, natoms, &amp;ts_in);</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">      18588 :         if(rc==MOLFILE_EOF) {</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :           break;</a>
+<a name="665"><span class="lineNum">     665 </span>            :         }</a>
+<a name="666"><span class="lineNum">     666 </span>            : #endif</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">      47160 :       } else if(trajectory_fmt==&quot;xyz&quot; || trajectory_fmt==&quot;gro&quot; || trajectory_fmt==&quot;dlp4&quot;) {</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">      25872 :         if(!Tools::getline(fp,line)) break;</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :       }</a>
+<a name="670"><span class="lineNum">     670 </span>            :     }</a>
+<a name="671"><span class="lineNum">     671 </span>            :     bool first_step=false;</a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">     244128 :     if(!noatoms&amp;&amp;!parseOnly) {</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">      71664 :       if(use_molfile==false &amp;&amp; (trajectory_fmt==&quot;xyz&quot; || trajectory_fmt==&quot;gro&quot;)) {</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">      25358 :         if(trajectory_fmt==&quot;gro&quot;) if(!Tools::getline(fp,line)) error(&quot;premature end of trajectory file&quot;);</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">      25358 :         std::sscanf(line.c_str(),&quot;%100d&quot;,&amp;natoms);</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :       }</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">      69235 :       if(use_molfile==false &amp;&amp; trajectory_fmt==&quot;dlp4&quot;) {</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :         char xa[9];</a>
+<a name="679"><span class="lineNum">     679 </span>            :         int xb,xc,xd;</a>
+<a name="680"><span class="lineNum">     680 </span>            :         double t;</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         20 :         std::sscanf(line.c_str(),&quot;%8s %lld %d %d %d %lf&quot;,xa,&amp;step,&amp;xb,&amp;xc,&amp;xd,&amp;t);</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         20 :         if (lstep) {</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">          4 :           p.cmd(&quot;setTimestep&quot;,real(t));</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :           lstep = false;</a>
+<a name="685"><span class="lineNum">     685 </span>            :         }</a>
+<a name="686"><span class="lineNum">     686 </span>            :       }</a>
+<a name="687"><span class="lineNum">     687 </span>            :     }</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">     244128 :     if(checknatoms&lt;0 &amp;&amp; !noatoms) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">        750 :       pd_nlocal=natoms;</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :       pd_start=0;</a>
+<a name="691"><span class="lineNum">     691 </span>            :       first_step=true;</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">        750 :       masses.assign(natoms,std::numeric_limits&lt;real&gt;::quiet_NaN());</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">        750 :       charges.assign(natoms,std::numeric_limits&lt;real&gt;::quiet_NaN());</span></a>
+<a name="694"><span class="lineNum">     694 </span>            : //case pdb: structure</a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">        750 :       if(pdbfile.length()&gt;0) {</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">      28092 :         for(unsigned i=0; i&lt;pdb.size(); ++i) {</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">      28017 :           AtomNumber an=pdb.getAtomNumbers()[i];</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :           unsigned index=an.index();</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">      28017 :           if( index&gt;=unsigned(natoms) ) error(&quot;atom index in pdb exceeds the number of atoms in trajectory&quot;);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">      28017 :           masses[index]=pdb.getOccupancy()[i];</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">      28017 :           charges[index]=pdb.getBeta()[i];</span></a>
+<a name="702"><span class="lineNum">     702 </span>            :         }</a>
+<a name="703"><span class="lineNum">     703 </span>            :       }</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">        750 :       if(mcfile.length()&gt;0) {</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">          5 :         IFile ifile;</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">          5 :         ifile.open(mcfile);</span></a>
+<a name="707"><span class="lineNum">     707 </span>            :         int index; double mass; double charge;</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">       1138 :         while(ifile.scanField(&quot;index&quot;,index).scanField(&quot;mass&quot;,mass).scanField(&quot;charge&quot;,charge).scanField()) {</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">        564 :           masses[index]=mass;</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">        564 :           charges[index]=charge;</span></a>
+<a name="711"><span class="lineNum">     711 </span>            :         }</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">          5 :       }</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">     243378 :     } else if( checknatoms&lt;0 &amp;&amp; noatoms ) {</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">         54 :       natoms=0;</span></a>
+<a name="715"><span class="lineNum">     715 </span>            :     }</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">     244128 :     if( checknatoms&lt;0 ) {</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">        804 :       if(kt&gt;=0) {</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">          6 :         p.cmd(&quot;setKbT&quot;,kt);</span></a>
+<a name="719"><span class="lineNum">     719 </span>            :       }</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">        804 :       checknatoms=natoms;</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">       1608 :       p.cmd(&quot;setNatoms&quot;,natoms);</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">       1608 :       p.cmd(&quot;init&quot;);</span></a>
+<a name="723"><span class="lineNum">     723 </span>            :       // Check if we have been asked to output the long version of the input and if there are shortcuts</a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">        804 :       if( parseOnly &amp;&amp; full_outputfile.length()&gt;0 ) {</span></a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            :         // Read in the plumed input file and store what is in there</a>
+<a name="727"><span class="lineNum">     727 </span>            :         std::map&lt;std::string,std::vector&lt;std::string&gt; &gt; data;</a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :         IFile ifile; ifile.open(plumedFile); std::vector&lt;std::string&gt; words;</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineNoCov">          0 :         while( Tools::getParsedLine(ifile,words) &amp;&amp; !p.getEndPlumed() ) {</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineNoCov">          0 :           p.readInputWords(words); Action* aa=p.getActionSet()[p.getActionSet().size()-1].get();</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :           ActionWithValue* av=dynamic_cast&lt;ActionWithValue*&gt;(aa);</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineNoCov">          0 :           if( av &amp;&amp; aa-&gt;getDefaultString().length()&gt;0 ) {</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineNoCov">          0 :             std::vector&lt;std::string&gt; def; def.push_back( &quot;defaults &quot; + aa-&gt;getDefaultString() );</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineNoCov">          0 :             data[ aa-&gt;getLabel() ] = def;</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineNoCov">          0 :           }</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :           ActionShortcut* as=dynamic_cast&lt;ActionShortcut*&gt;( aa );</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineNoCov">          0 :           if( as ) {</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :             if( aa-&gt;getDefaultString().length()&gt;0 ) {</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :               std::vector&lt;std::string&gt; def; def.push_back( &quot;defaults &quot; + aa-&gt;getDefaultString() );</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :               data[ as-&gt;getShortcutLabel() ] = def;</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 :             }</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineNoCov">          0 :             if( data.find( as-&gt;getShortcutLabel() )!=data.end() ) {</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineNoCov">          0 :               std::vector&lt;std::string&gt; shortcut_commands = as-&gt;getSavedInputLines();</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :               for(unsigned i=0; i&lt;shortcut_commands.size(); ++i) data[ as-&gt;getShortcutLabel() ].push_back( shortcut_commands[i] );</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :             } else data[ as-&gt;getShortcutLabel() ] = as-&gt;getSavedInputLines();</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :           }</a>
+<a name="747"><span class="lineNum">     747 </span>            :         }</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineNoCov">          0 :         ifile.close();</span></a>
+<a name="749"><span class="lineNum">     749 </span>            :         // Only output the full version of the input file if there are shortcuts</a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :         if( data.size()&gt;0 ) {</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineNoCov">          0 :           OFile long_file; long_file.open( full_outputfile ); long_file.printf(&quot;{\n&quot;); bool firstpass=true;</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineNoCov">          0 :           for(auto&amp; x : data ) {</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :             if( !firstpass ) long_file.printf(&quot;   },\n&quot;);</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineNoCov">          0 :             long_file.printf(&quot;   \&quot;%s\&quot; : {\n&quot;, x.first.c_str() );</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :             plumed_assert( x.second.size()&gt;0 ); unsigned sstart=0;</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineNoCov">          0 :             if( x.second[0].find(&quot;defaults&quot;)!=std::string::npos ) {</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 :               sstart=1; long_file.printf(&quot;      \&quot;defaults\&quot; : \&quot;%s\&quot;&quot;, x.second[0].substr( 9 ).c_str() );</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :               if( x.second.size()&gt;1 ) long_file.printf(&quot;,\n&quot;); else long_file.printf(&quot;\n&quot;);</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :             }</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineNoCov">          0 :             if( x.second.size()&gt;sstart ) {</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineNoCov">          0 :               long_file.printf(&quot;      \&quot;expansion\&quot; : \&quot;%s&quot;, x.second[sstart].c_str() );</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :               for(unsigned j=sstart+1; j&lt;x.second.size(); ++j) long_file.printf(&quot;\\n%s&quot;, x.second[j].c_str() );</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineNoCov">          0 :               long_file.printf(&quot;\&quot;\n&quot;);</span></a>
+<a name="764"><span class="lineNum">     764 </span>            :             }</a>
+<a name="765"><span class="lineNum">     765 </span>            :             firstpass=false;</a>
+<a name="766"><span class="lineNum">     766 </span>            :           }</a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineNoCov">          0 :           long_file.printf(&quot;   }\n}\n&quot;); long_file.close();</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">        804 :       if(parseOnly) break;</span></a>
+<a name="771"><span class="lineNum">     771 </span>            :     }</a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">     244128 :     if(checknatoms!=natoms) {</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineNoCov">          0 :       std::string stepstr; Tools::convert(step,stepstr);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineNoCov">          0 :       error(&quot;number of atoms in frame &quot; + stepstr + &quot; does not match number of atoms in first frame&quot;);</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :     }</a>
+<a name="776"><span class="lineNum">     776 </span>            : </a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">     244128 :     coordinates.assign(3*natoms,real(0.0));</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">     244128 :     forces.assign(3*natoms,real(0.0));</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">     244128 :     cell.assign(9,real(0.0));</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">     244128 :     virial.assign(9,real(0.0));</span></a>
+<a name="781"><span class="lineNum">     781 </span>            : </a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">     244128 :     if( first_step || rnd.U01()&gt;0.5) {</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">     123694 :       if(debug_pd) {</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">        152 :         int npe=intracomm.Get_size();</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">        152 :         std::vector&lt;int&gt; loc(npe,0);</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">        152 :         std::vector&lt;int&gt; start(npe,0);</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">        608 :         for(int i=0; i&lt;npe-1; i++) {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">        456 :           int cc=(natoms*2*rnd.U01())/npe;</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">        456 :           if(start[i]+cc&gt;natoms) cc=natoms-start[i];</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">        456 :           loc[i]=cc;</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">        456 :           start[i+1]=start[i]+loc[i];</span></a>
+<a name="792"><span class="lineNum">     792 </span>            :         }</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">        152 :         loc[npe-1]=natoms-start[npe-1];</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">        152 :         intracomm.Bcast(loc,0);</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">        152 :         intracomm.Bcast(start,0);</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">        152 :         pd_nlocal=loc[intracomm.Get_rank()];</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">        152 :         pd_start=start[intracomm.Get_rank()];</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">        152 :         if(intracomm.Get_rank()==0) {</span></a>
+<a name="799"><span class="lineNum">     799 </span>            :           std::fprintf(out,&quot;\nDRIVER: Reassigning particle decomposition\n&quot;);</a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">        190 :           std::fprintf(out,&quot;DRIVER: &quot;); for(int i=0; i&lt;npe; i++) std::fprintf(out,&quot;%d &quot;,loc[i]); printf(&quot;\n&quot;);</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">        190 :           std::fprintf(out,&quot;DRIVER: &quot;); for(int i=0; i&lt;npe; i++) std::fprintf(out,&quot;%d &quot;,start[i]); printf(&quot;\n&quot;);</span></a>
+<a name="802"><span class="lineNum">     802 </span>            :         }</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">        304 :         p.cmd(&quot;setAtomsNlocal&quot;,pd_nlocal);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">        304 :         p.cmd(&quot;setAtomsContiguous&quot;,pd_start);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">     123542 :       } else if(debug_dd) {</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">        956 :         int npe=intracomm.Get_size();</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">        956 :         int rank=intracomm.Get_rank();</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">        956 :         dd_charges.assign(natoms,0.0);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">        956 :         dd_masses.assign(natoms,0.0);</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">        956 :         dd_gatindex.assign(natoms,-1);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">        956 :         dd_g2l.assign(natoms,-1);</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">        956 :         dd_coordinates.assign(3*natoms,0.0);</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">        956 :         dd_forces.assign(3*natoms,0.0);</span></a>
+<a name="814"><span class="lineNum">     814 </span>            :         dd_nlocal=0;</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">      53786 :         for(int i=0; i&lt;natoms; ++i) {</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">      52830 :           double r=rnd.U01()*npe;</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">     112376 :           int n; for(n=0; n&lt;npe; n++) if(n+1&gt;r)break;</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">      52830 :           plumed_assert(n&lt;npe);</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">      52830 :           if(n==rank) {</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">      19827 :             dd_gatindex[dd_nlocal]=i;</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">      19827 :             dd_g2l[i]=dd_nlocal;</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">      19827 :             dd_charges[dd_nlocal]=charges[i];</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">      19827 :             dd_masses[dd_nlocal]=masses[i];</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">      19827 :             dd_nlocal++;</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :           }</a>
+<a name="826"><span class="lineNum">     826 </span>            :         }</a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">        956 :         if(intracomm.Get_rank()==0) {</span></a>
+<a name="828"><span class="lineNum">     828 </span>            :           std::fprintf(out,&quot;\nDRIVER: Reassigning domain decomposition\n&quot;);</a>
+<a name="829"><span class="lineNum">     829 </span>            :         }</a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">       1912 :         p.cmd(&quot;setAtomsNlocal&quot;,dd_nlocal);</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">       1912 :         p.cmd(&quot;setAtomsGatindex&quot;,&amp;dd_gatindex[0],dd_nlocal);</span></a>
+<a name="832"><span class="lineNum">     832 </span>            :       }</a>
+<a name="833"><span class="lineNum">     833 </span>            :     }</a>
+<a name="834"><span class="lineNum">     834 </span>            : </a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">     244128 :     int plumedStopCondition=0;</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">     244128 :     if(!noatoms) {</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">      43788 :       if(use_molfile) {</span></a>
+<a name="838"><span class="lineNum">     838 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">      18341 :         if(pbc_cli_given==false) {</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">      18320 :           if(ts_in.A&gt;0.0) { // this is negative if molfile does not provide box</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :             // info on the cell: convert using pbcset.tcl from pbctools in vmd distribution</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">      18315 :             real cosBC=cos(real(ts_in.alpha)*pi/180.);</span></a>
+<a name="843"><span class="lineNum">     843 </span>            :             //double sinBC=std::sin(ts_in.alpha*pi/180.);</a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">      18315 :             real cosAC=std::cos(real(ts_in.beta)*pi/180.);</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">      18315 :             real cosAB=std::cos(real(ts_in.gamma)*pi/180.);</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">      18315 :             real sinAB=std::sin(real(ts_in.gamma)*pi/180.);</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">      18315 :             real Ax=real(ts_in.A);</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">      18315 :             real Bx=real(ts_in.B)*cosAB;</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">      18315 :             real By=real(ts_in.B)*sinAB;</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">      18315 :             real Cx=real(ts_in.C)*cosAC;</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">      18315 :             real Cy=(real(ts_in.C)*real(ts_in.B)*cosBC-Cx*Bx)/By;</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">      18315 :             real Cz=std::sqrt(real(ts_in.C)*real(ts_in.C)-Cx*Cx-Cy*Cy);</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">      18315 :             cell[0]=Ax/10.; cell[1]=0.; cell[2]=0.;</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">      18315 :             cell[3]=Bx/10.; cell[4]=By/10.; cell[5]=0.;</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">      18315 :             cell[6]=Cx/10.; cell[7]=Cy/10.; cell[8]=Cz/10.;</span></a>
+<a name="856"><span class="lineNum">     856 </span>            :           } else {</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">          5 :             cell[0]=0.0; cell[1]=0.0; cell[2]=0.0;</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">          5 :             cell[3]=0.0; cell[4]=0.0; cell[5]=0.0;</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">          5 :             cell[6]=0.0; cell[7]=0.0; cell[8]=0.0;</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :           }</a>
+<a name="861"><span class="lineNum">     861 </span>            :         } else {</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">        210 :           for(unsigned i=0; i&lt;9; i++)cell[i]=pbc_cli_box[i];</span></a>
+<a name="863"><span class="lineNum">     863 </span>            :         }</a>
+<a name="864"><span class="lineNum">     864 </span>            :         // info on coords</a>
+<a name="865"><span class="lineNum">     865 </span>            :         // the order is xyzxyz...</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">   62421815 :         for(int i=0; i&lt;3*natoms; i++) {</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">   62403474 :           coordinates[i]=real(ts_in.coords[i])/real(10.); //convert to nm</span></a>
+<a name="868"><span class="lineNum">     868 </span>            :           //cerr&lt;&lt;&quot;COOR &quot;&lt;&lt;coordinates[i]&lt;&lt;endl;</a>
+<a name="869"><span class="lineNum">     869 </span>            :         }</a>
+<a name="870"><span class="lineNum">     870 </span>            : #endif</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">      50864 :       } else if(trajectory_fmt==&quot;xdr-xtc&quot; || trajectory_fmt==&quot;xdr-trr&quot;) {</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :         int localstep;</a>
+<a name="873"><span class="lineNum">     873 </span>            :         float time;</a>
+<a name="874"><span class="lineNum">     874 </span>            :         xdrfile::matrix box;</a>
+<a name="875"><span class="lineNum">     875 </span>            : // here we cannot use a std::vector&lt;rvec&gt; since it does not compile.</a>
+<a name="876"><span class="lineNum">     876 </span>            : // we thus use a std::unique_ptr&lt;rvec[]&gt;</a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">         69 :         auto pos=Tools::make_unique&lt;xdrfile::rvec[]&gt;(natoms);</span></a>
+<a name="878"><span class="lineNum">     878 </span>            :         float prec,lambda;</a>
+<a name="879"><span class="lineNum">     879 </span>            :         int ret=xdrfile::exdrOK;</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">         69 :         if(trajectory_fmt==&quot;xdr-xtc&quot;) ret=xdrfile::read_xtc(xd,natoms,&amp;localstep,&amp;time,box,pos.get(),&amp;prec);</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">         69 :         if(trajectory_fmt==&quot;xdr-trr&quot;) ret=xdrfile::read_trr(xd,natoms,&amp;localstep,&amp;time,&amp;lambda,box,pos.get(),NULL,NULL);</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">         69 :         if(stride==0) step=localstep;</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">         69 :         if(ret==xdrfile::exdrENDOFFILE) break;</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         67 :         if(ret!=xdrfile::exdrOK) break;</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">        832 :         for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++) cell[3*i+j]=box[i][j];</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">      10976 :         for(int i=0; i&lt;natoms; i++) for(unsigned j=0; j&lt;3; j++)</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">       8184 :             coordinates[3*i+j]=real(pos[i][j]);</span></a>
+<a name="888"><span class="lineNum">     888 </span>            :       } else {</a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">      25378 :         if(trajectory_fmt==&quot;xyz&quot;) {</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">      23018 :           if(!Tools::getline(fp,line)) error(&quot;premature end of trajectory file&quot;);</span></a>
+<a name="891"><span class="lineNum">     891 </span>            : </a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">      23018 :           std::vector&lt;double&gt; celld(9,0.0);</span></a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">      23018 :           if(pbc_cli_given==false) {</span></a>
+<a name="894"><span class="lineNum">     894 </span>            :             std::vector&lt;std::string&gt; words;</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">      45624 :             words=Tools::getWords(line);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">      22812 :             if(words.size()==3) {</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">      22239 :               std::sscanf(line.c_str(),&quot;%100lf %100lf %100lf&quot;,&amp;celld[0],&amp;celld[4],&amp;celld[8]);</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">        573 :             } else if(words.size()==9) {</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">        573 :               std::sscanf(line.c_str(),&quot;%100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf %100lf&quot;,</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :                           &amp;celld[0], &amp;celld[1], &amp;celld[2],</a>
+<a name="901"><span class="lineNum">     901 </span>            :                           &amp;celld[3], &amp;celld[4], &amp;celld[5],</a>
+<a name="902"><span class="lineNum">     902 </span>            :                           &amp;celld[6], &amp;celld[7], &amp;celld[8]);</a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineNoCov">          0 :             } else error(&quot;needed box in second line of xyz file&quot;);</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">      22812 :           } else {                      // from command line</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">        206 :             celld=pbc_cli_box;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :           }</a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">     230180 :           for(unsigned i=0; i&lt;9; i++)cell[i]=real(celld[i]);</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :         }</a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">      25378 :         if(trajectory_fmt==&quot;dlp4&quot;) {</span></a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">         20 :           std::vector&lt;double&gt; celld(9,0.0);</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">         20 :           if(pbc_cli_given==false) {</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">         20 :             if(!Tools::getline(fp,line)) error(&quot;error reading vector a of cell&quot;);</span></a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">         20 :             std::sscanf(line.c_str(),&quot;%lf %lf %lf&quot;,&amp;celld[0],&amp;celld[1],&amp;celld[2]);</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         20 :             if(!Tools::getline(fp,line)) error(&quot;error reading vector b of cell&quot;);</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">         20 :             std::sscanf(line.c_str(),&quot;%lf %lf %lf&quot;,&amp;celld[3],&amp;celld[4],&amp;celld[5]);</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">         20 :             if(!Tools::getline(fp,line)) error(&quot;error reading vector c of cell&quot;);</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">         20 :             std::sscanf(line.c_str(),&quot;%lf %lf %lf&quot;,&amp;celld[6],&amp;celld[7],&amp;celld[8]);</span></a>
+<a name="918"><span class="lineNum">     918 </span>            :           } else {</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :             celld=pbc_cli_box;</span></a>
+<a name="920"><span class="lineNum">     920 </span>            :           }</a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">        200 :           for(auto i=0; i&lt;9; i++)cell[i]=real(celld[i])*0.1;</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :         }</a>
+<a name="923"><span class="lineNum">     923 </span>            :         int ddist=0;</a>
+<a name="924"><span class="lineNum">     924 </span>            :         // Read coordinates</a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">    2433968 :         for(int i=0; i&lt;natoms; i++) {</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">    2408590 :           bool ok=Tools::getline(fp,line);</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">    2408590 :           if(!ok) error(&quot;premature end of trajectory file&quot;);</span></a>
+<a name="928"><span class="lineNum">     928 </span>            :           double cc[3];</a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">    2408590 :           if(trajectory_fmt==&quot;xyz&quot;) {</span></a>
+<a name="930"><span class="lineNum">     930 </span>            :             char dummy[1000];</a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">    1695476 :             int ret=std::sscanf(line.c_str(),&quot;%999s %100lf %100lf %100lf&quot;,dummy,&amp;cc[0],&amp;cc[1],&amp;cc[2]);</span></a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">    1695476 :             if(ret!=4) error(&quot;cannot read line&quot;+line);</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">     713114 :           } else if(trajectory_fmt==&quot;gro&quot;) {</span></a>
+<a name="934"><span class="lineNum">     934 </span>            :             // do the gromacs way</a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">     712474 :             if(!i) {</span></a>
+<a name="936"><span class="lineNum">     936 </span>            :               //</a>
+<a name="937"><span class="lineNum">     937 </span>            :               // calculate the distance between dots (as in gromacs gmxlib/confio.c, routine get_w_conf )</a>
+<a name="938"><span class="lineNum">     938 </span>            :               //</a>
+<a name="939"><span class="lineNum">     939 </span>            :               const char      *p1, *p2, *p3;</a>
+<a name="940"><span class="lineNum">     940 </span>            :               p1 = std::strchr(line.c_str(), '.');</a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">       2340 :               if (p1 == NULL) error(&quot;seems there are no coordinates in the gro file&quot;);</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">       2340 :               p2 = std::strchr(&amp;p1[1], '.');</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">       2340 :               if (p2 == NULL) error(&quot;seems there is only one coordinates in the gro file&quot;);</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">       2340 :               ddist = p2 - p1;</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">       2340 :               p3 = std::strchr(&amp;p2[1], '.');</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">       2340 :               if (p3 == NULL)error(&quot;seems there are only two coordinates in the gro file&quot;);</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">       2340 :               if (p3 - p2 != ddist)error(&quot;not uniform spacing in fields in the gro file&quot;);</span></a>
+<a name="948"><span class="lineNum">     948 </span>            :             }</a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">     712474 :             Tools::convert(line.substr(20,ddist),cc[0]);</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">     712474 :             Tools::convert(line.substr(20+ddist,ddist),cc[1]);</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">    1424948 :             Tools::convert(line.substr(20+ddist+ddist,ddist),cc[2]);</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">        640 :           } else if(trajectory_fmt==&quot;dlp4&quot;) {</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :             char dummy[9];</a>
+<a name="954"><span class="lineNum">     954 </span>            :             int idummy;</a>
+<a name="955"><span class="lineNum">     955 </span>            :             double m,c;</a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">        640 :             std::sscanf(line.c_str(),&quot;%8s %d %lf %lf&quot;,dummy,&amp;idummy,&amp;m,&amp;c);</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">        640 :             masses[i]=real(m);</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">        640 :             charges[i]=real(c);</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">        640 :             if(!Tools::getline(fp,line)) error(&quot;error reading coordinates&quot;);</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">        640 :             std::sscanf(line.c_str(),&quot;%lf %lf %lf&quot;,&amp;cc[0],&amp;cc[1],&amp;cc[2]);</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">        640 :             cc[0]*=0.1;</span></a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">        640 :             cc[1]*=0.1;</span></a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">        640 :             cc[2]*=0.1;</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">        640 :             if(lvl&gt;0) {</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">        640 :               if(!Tools::getline(fp,line)) error(&quot;error skipping velocities&quot;);</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :             }</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">        640 :             if(lvl&gt;1) {</span></a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">        640 :               if(!Tools::getline(fp,line)) error(&quot;error skipping forces&quot;);</span></a>
+<a name="969"><span class="lineNum">     969 </span>            :             }</a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineNoCov">          0 :           } else plumed_error();</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">    2408590 :           if(!debug_pd || ( i&gt;=pd_start &amp;&amp; i&lt;pd_start+pd_nlocal) ) {</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">    2389150 :             coordinates[3*i]=real(cc[0]);</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">    2389150 :             coordinates[3*i+1]=real(cc[1]);</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">    2389150 :             coordinates[3*i+2]=real(cc[2]);</span></a>
+<a name="975"><span class="lineNum">     975 </span>            :           }</a>
+<a name="976"><span class="lineNum">     976 </span>            :         }</a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">      25378 :         if(trajectory_fmt==&quot;gro&quot;) {</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">       2340 :           if(!Tools::getline(fp,line)) error(&quot;premature end of trajectory file&quot;);</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">       2340 :           std::vector&lt;std::string&gt; words=Tools::getWords(line);</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">       2340 :           if(words.size()&lt;3) error(&quot;cannot understand box format&quot;);</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">       2340 :           Tools::convert(words[0],cell[0]);</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">       2340 :           Tools::convert(words[1],cell[4]);</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">       2340 :           Tools::convert(words[2],cell[8]);</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">       2340 :           if(words.size()&gt;3) Tools::convert(words[3],cell[1]);</span></a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">       2340 :           if(words.size()&gt;4) Tools::convert(words[4],cell[2]);</span></a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">       2340 :           if(words.size()&gt;5) Tools::convert(words[5],cell[3]);</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">       2340 :           if(words.size()&gt;6) Tools::convert(words[6],cell[5]);</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">       2340 :           if(words.size()&gt;7) Tools::convert(words[7],cell[6]);</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">       2340 :           if(words.size()&gt;8) Tools::convert(words[8],cell[7]);</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">       2340 :         }</span></a>
+<a name="991"><span class="lineNum">     991 </span>            : </a>
+<a name="992"><span class="lineNum">     992 </span>            :       }</a>
+<a name="993"><span class="lineNum">     993 </span>            : </a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">      87566 :       p.cmd(&quot;setStepLongLong&quot;,step);</span></a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">      87566 :       p.cmd(&quot;setStopFlag&quot;,&amp;plumedStopCondition);</span></a>
+<a name="996"><span class="lineNum">     996 </span>            : </a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">      43783 :       if(debug_dd) {</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">      38944 :         for(int i=0; i&lt;dd_nlocal; ++i) {</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">      37156 :           int kk=dd_gatindex[i];</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">      37156 :           dd_coordinates[3*i+0]=coordinates[3*kk+0];</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">      37156 :           dd_coordinates[3*i+1]=coordinates[3*kk+1];</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">      37156 :           dd_coordinates[3*i+2]=coordinates[3*kk+2];</span></a>
+<a name="1003"><span class="lineNum">    1003 </span>            :         }</a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">       3576 :         p.cmd(&quot;setForces&quot;,&amp;dd_forces[0],3*dd_nlocal);</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">       3576 :         p.cmd(&quot;setPositions&quot;,&amp;dd_coordinates[0],3*dd_nlocal);</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">       3576 :         p.cmd(&quot;setMasses&quot;,&amp;dd_masses[0],dd_nlocal);</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">       3576 :         p.cmd(&quot;setCharges&quot;,&amp;dd_charges[0],dd_nlocal);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            :       } else {</a>
+<a name="1009"><span class="lineNum">    1009 </span>            : // this is required to avoid troubles when the last domain</a>
+<a name="1010"><span class="lineNum">    1010 </span>            : // contains zero atoms</a>
+<a name="1011"><span class="lineNum">    1011 </span>            : // Basically, for empty domains we pass null pointers</a>
+<a name="1012"><span class="lineNum">    1012 </span>            : #define fix_pd(xx) (pd_nlocal!=0?&amp;xx:NULL)</a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">     125985 :         p.cmd(&quot;setForces&quot;,fix_pd(forces[3*pd_start]),3*pd_nlocal);</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">     125985 :         p.cmd(&quot;setPositions&quot;,fix_pd(coordinates[3*pd_start]),3*pd_nlocal);</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">     125985 :         p.cmd(&quot;setMasses&quot;,fix_pd(masses[pd_start]),pd_nlocal);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">     125985 :         p.cmd(&quot;setCharges&quot;,fix_pd(charges[pd_start]),pd_nlocal);</span></a>
+<a name="1017"><span class="lineNum">    1017 </span>            :       }</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">      87566 :       p.cmd(&quot;setBox&quot;,cell.data(),9);</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">      87566 :       p.cmd(&quot;setVirial&quot;,virial.data(),9);</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            :     } else {</a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">     400680 :       p.cmd(&quot;setStepLongLong&quot;,step);</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">     400680 :       p.cmd(&quot;setStopFlag&quot;,&amp;plumedStopCondition);</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            :     }</a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">     488246 :     p.cmd(&quot;calc&quot;);</span></a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineCov">     244123 :     if(debugforces.length()&gt;0) {</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">         25 :       virial.assign(9,real(0.0));</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">         25 :       forces.assign(3*natoms,real(0.0));</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">         50 :       p.cmd(&quot;prepareCalc&quot;);</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">         50 :       p.cmd(&quot;performCalcNoUpdate&quot;);</span></a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     }</a>
+<a name="1031"><span class="lineNum">    1031 </span>            : </a>
+<a name="1032"><span class="lineNum">    1032 </span>            : // this is necessary as only processor zero is adding to the virial:</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">     244123 :     intracomm.Bcast(virial,0);</span></a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">     244123 :     if(debug_pd) intracomm.Sum(forces);</span></a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">     244123 :     if(debug_dd) {</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">      38944 :       for(int i=0; i&lt;dd_nlocal; i++) {</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">      37156 :         forces[3*dd_gatindex[i]+0]=dd_forces[3*i+0];</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">      37156 :         forces[3*dd_gatindex[i]+1]=dd_forces[3*i+1];</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">      37156 :         forces[3*dd_gatindex[i]+2]=dd_forces[3*i+2];</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :       }</a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">       1788 :       dd_forces.assign(3*natoms,0.0);</span></a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">       1788 :       intracomm.Sum(forces);</span></a>
+<a name="1043"><span class="lineNum">    1043 </span>            :     }</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">     244123 :     if(debug_grex &amp;&amp;step%grex_stride==0) {</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">        228 :       p.cmd(&quot;GREX savePositions&quot;);</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">        114 :       if(intracomm.Get_rank()&gt;0) {</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">        114 :         p.cmd(&quot;GREX prepare&quot;);</span></a>
+<a name="1048"><span class="lineNum">    1048 </span>            :       } else {</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">         57 :         int r=intercomm.Get_rank();</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">         57 :         int n=intercomm.Get_size();</span></a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">         57 :         int partner=r+(2*((r+step/grex_stride)%2))-1;</span></a>
+<a name="1052"><span class="lineNum">    1052 </span>            :         if(partner&lt;0)partner=0;</a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">         57 :         if(partner&gt;=n) partner=n-1;</span></a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">        114 :         p.cmd(&quot;GREX setPartner&quot;,partner);</span></a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">        114 :         p.cmd(&quot;GREX calculate&quot;);</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">        114 :         p.cmd(&quot;GREX shareAllDeltaBias&quot;);</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">        228 :         for(int i=0; i&lt;n; i++) {</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">        171 :           std::string s; Tools::convert(i,s);</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">        342 :           real a=std::numeric_limits&lt;real&gt;::quiet_NaN(); s=&quot;GREX getDeltaBias &quot;+s; p.cmd(s,&amp;a);</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">        171 :           if(grex_log) std::fprintf(grex_log,&quot; %f&quot;,a);</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            :         }</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">         57 :         if(grex_log) std::fprintf(grex_log,&quot;\n&quot;);</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            :       }</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     }</a>
+<a name="1065"><span class="lineNum">    1065 </span>            : </a>
+<a name="1066"><span class="lineNum">    1066 </span>            : </a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">     244123 :     if(fp_forces) {</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">      22264 :       std::fprintf(fp_forces,&quot;%d\n&quot;,natoms);</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">      44528 :       std::string fmtv=dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot;\n&quot;;</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">      44528 :       std::string fmt=dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot; &quot;+dumpforcesFmt+&quot;\n&quot;;</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">      22264 :       if(dumpfullvirial) {</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">        350 :         std::fprintf(fp_forces,fmtv.c_str(),virial[0],virial[1],virial[2],virial[3],virial[4],virial[5],virial[6],virial[7],virial[8]);</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :       } else {</a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">      21914 :         std::fprintf(fp_forces,fmt.c_str(),virial[0],virial[4],virial[8]);</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            :       }</a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">      22264 :       fmt=&quot;X &quot;+fmt;</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">    2155085 :       for(int i=0; i&lt;natoms; i++)</span></a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">    2132821 :         std::fprintf(fp_forces,fmt.c_str(),forces[3*i],forces[3*i+1],forces[3*i+2]);</span></a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     }</a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">     244123 :     if(debugforces.length()&gt;0) {</span></a>
+<a name="1081"><span class="lineNum">    1081 </span>            :       // Now call the routine to work out the derivatives numerically</a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">         25 :       numder.assign(3*natoms+9,real(0.0)); real base=0;</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">         50 :       p.cmd(&quot;getBias&quot;,&amp;base);</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">         25 :       if( std::abs(base)&lt;epsilon ) printf(&quot;WARNING: bias for configuration appears to be zero so debugging forces is trivial&quot;);</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">         25 :       evaluateNumericalDerivatives( step, p, coordinates, masses, charges, cell, base, numder );</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            : </a>
+<a name="1087"><span class="lineNum">    1087 </span>            :       // And output everything to a file</a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">         25 :       fp_dforces.fmtField(&quot; &quot; + dumpforcesFmt);</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">       1795 :       for(int i=0; i&lt;3*natoms; ++i) {</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineCov">       1770 :         fp_dforces.printField(&quot;parameter&quot;,(int)i);</span></a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">       3540 :         fp_dforces.printField(&quot;analytical&quot;,forces[i]);</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">       1770 :         fp_dforces.printField(&quot;numerical&quot;,-numder[i]);</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">       1770 :         fp_dforces.printField();</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            :       }</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :       // And print the virial</a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">        250 :       for(int i=0; i&lt;9; ++i) {</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">        225 :         fp_dforces.printField(&quot;parameter&quot;,3*natoms+i );</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">        225 :         fp_dforces.printField(&quot;analytical&quot;,virial[i] );</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">        225 :         fp_dforces.printField(&quot;numerical&quot;,-numder[3*natoms+i]);</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">        225 :         fp_dforces.printField();</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            :       }</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     }</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : </a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">     244123 :     if(plumedStopCondition) break;</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">     244065 :     step+=stride;</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   }</a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">       1608 :   if(!parseOnly) p.cmd(&quot;runFinalJobs&quot;);</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   return 0;</a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">       3216 : }</span></a>
+<a name="1112"><span class="lineNum">    1112 </span>            : </a>
+<a name="1113"><span class="lineNum">    1113 </span>            : template&lt;typename real&gt;</a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">         25 : void Driver&lt;real&gt;::evaluateNumericalDerivatives( const long long int&amp; step, PlumedMain&amp; p, const std::vector&lt;real&gt;&amp; coordinates,</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            :     const std::vector&lt;real&gt;&amp; masses, const std::vector&lt;real&gt;&amp; charges,</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :     std::vector&lt;real&gt;&amp; cell, const double&amp; base, std::vector&lt;real&gt;&amp; numder ) {</a>
+<a name="1117"><span class="lineNum">    1117 </span>            : </a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">         25 :   int natoms = coordinates.size() / 3; real delta = std::sqrt(epsilon);</span></a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">         25 :   std::vector&lt;Vector&gt; pos(natoms); real bias=0;</span></a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">         25 :   std::vector&lt;real&gt; fake_forces( 3*natoms ), fake_virial(9);</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">        615 :   for(int i=0; i&lt;natoms; ++i) {</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">       2360 :     for(unsigned j=0; j&lt;3; ++j) pos[i][j]=coordinates[3*i+j];</span></a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   }</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : </a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">        615 :   for(int i=0; i&lt;natoms; ++i) {</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">       2360 :     for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">       1770 :       pos[i][j]=pos[i][j]+delta;</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">       3540 :       p.cmd(&quot;setStepLongLong&quot;,step);</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">       3540 :       p.cmd(&quot;setPositions&quot;,&amp;pos[0][0],3*natoms);</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">       3540 :       p.cmd(&quot;setForces&quot;,&amp;fake_forces[0],3*natoms);</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">       3540 :       p.cmd(&quot;setMasses&quot;,&amp;masses[0],natoms);</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">       3540 :       p.cmd(&quot;setCharges&quot;,&amp;charges[0],natoms);</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">       3540 :       p.cmd(&quot;setBox&quot;,&amp;cell[0],9);</span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">       3540 :       p.cmd(&quot;setVirial&quot;,&amp;fake_virial[0],9);</span></a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">       3540 :       p.cmd(&quot;prepareCalc&quot;);</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">       3540 :       p.cmd(&quot;performCalcNoUpdate&quot;);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">       3540 :       p.cmd(&quot;getBias&quot;,&amp;bias);</span></a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">       1770 :       pos[i][j]=coordinates[3*i+j];</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">       1770 :       numder[3*i+j] = (bias - base) / delta;</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            :     }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            : </a>
+<a name="1143"><span class="lineNum">    1143 </span>            :   // Create the cell</a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">         25 :   Tensor box( cell[0], cell[1], cell[2], cell[3], cell[4], cell[5], cell[6], cell[7], cell[8] );</span></a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   // And the virial</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">         25 :   Pbc pbc; pbc.setBox( box ); Tensor nvirial;</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">        325 :   for(unsigned i=0; i&lt;3; i++) for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">        225 :       double arg0=box(i,k);</span></a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">       5535 :       for(int j=0; j&lt;natoms; ++j) pos[j]=pbc.realToScaled( pos[j] );</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">        225 :       cell[3*i+k]=box(i,k)=box(i,k)+delta; pbc.setBox(box);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">       5535 :       for(int j=0; j&lt;natoms; j++) pos[j]=pbc.scaledToReal( pos[j] );</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">        450 :       p.cmd(&quot;setStepLongLong&quot;,step);</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineCov">        450 :       p.cmd(&quot;setPositions&quot;,&amp;pos[0][0],3*natoms);</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">        450 :       p.cmd(&quot;setForces&quot;,&amp;fake_forces[0],3*natoms);</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">        450 :       p.cmd(&quot;setMasses&quot;,&amp;masses[0],natoms);</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">        450 :       p.cmd(&quot;setCharges&quot;,&amp;charges[0],natoms);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">        450 :       p.cmd(&quot;setBox&quot;,&amp;cell[0],9);</span></a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">        450 :       p.cmd(&quot;setVirial&quot;,&amp;fake_virial[0],9);</span></a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineCov">        450 :       p.cmd(&quot;prepareCalc&quot;);</span></a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">        450 :       p.cmd(&quot;performCalcNoUpdate&quot;);</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">        450 :       p.cmd(&quot;getBias&quot;,&amp;bias);</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">        225 :       cell[3*i+k]=box(i,k)=arg0; pbc.setBox(box);</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">      21465 :       for(int j=0; j&lt;natoms; j++) for(unsigned n=0; n&lt;3; ++n) pos[j][n]=coordinates[3*j+n];</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">        225 :       nvirial(i,k) = ( bias - base ) / delta;</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            :     }</a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">         25 :   nvirial=-matmul(box.transpose(),nvirial);</span></a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">        325 :   for(unsigned i=0; i&lt;3; i++) for(unsigned k=0; k&lt;3; k++)  numder[3*natoms+3*i+k] = nvirial(i,k);</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            : </a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">         25 : }</span></a>
+<a name="1170"><span class="lineNum">    1170 </span>            : </a>
+<a name="1171"><span class="lineNum">    1171 </span>            : }</a>
+<a name="1172"><span class="lineNum">    1172 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/DriverDouble.cpp.func-sort-c.html b/coverage/cltools/DriverDouble.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4582d52ab4
--- /dev/null
+++ b/coverage/cltools/DriverDouble.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/DriverDouble.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - DriverDouble.cpp<span style="font-size: 80%;"> (<a href="DriverDouble.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DriverDouble.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverDouble.cpp.gcov.html#31">_ZN4PLMD7cltools12_GLOBAL__N_122DriverDoubleRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">808</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverDouble.cpp.gcov.html#31">_ZN4PLMD7cltools12_GLOBAL__N_122DriverDoubleRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverDouble.cpp.gcov.html#31">_ZN4PLMD7cltools12_GLOBAL__N_122DriverDoubleRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/DriverDouble.cpp.func.html b/coverage/cltools/DriverDouble.cpp.func.html
new file mode 100644
index 0000000000..cf8fb2e1b0
--- /dev/null
+++ b/coverage/cltools/DriverDouble.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/DriverDouble.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - DriverDouble.cpp<span style="font-size: 80%;"> (<a href="DriverDouble.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DriverDouble.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverDouble.cpp.gcov.html#31">_ZN4PLMD7cltools12_GLOBAL__N_122DriverDoubleRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">808</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverDouble.cpp.gcov.html#31">_ZN4PLMD7cltools12_GLOBAL__N_122DriverDoubleRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverDouble.cpp.gcov.html#31">_ZN4PLMD7cltools12_GLOBAL__N_122DriverDoubleRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/DriverDouble.cpp.gcov.html b/coverage/cltools/DriverDouble.cpp.gcov.html
new file mode 100644
index 0000000000..ab04e2d31b
--- /dev/null
+++ b/coverage/cltools/DriverDouble.cpp.gcov.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/DriverDouble.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - DriverDouble.cpp<span style="font-size: 80%;"> (source / <a href="DriverDouble.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Driver.cpp&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace cltools {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : // We instantiate here the template version of Driver so as</a>
+<a name="29"><span class="lineNum">      29 </span>            : // to accelerate parallel compilation.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : typedef Driver&lt;double&gt; DriverDouble;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">      13312 : PLUMED_REGISTER_CLTOOL(DriverDouble,&quot;driver&quot;)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : }</a>
+<a name="36"><span class="lineNum">      36 </span>            : }</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/DriverFloat.cpp.func-sort-c.html b/coverage/cltools/DriverFloat.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9e66929ae4
--- /dev/null
+++ b/coverage/cltools/DriverFloat.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/DriverFloat.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - DriverFloat.cpp<span style="font-size: 80%;"> (<a href="DriverFloat.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DriverFloat.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#36">_ZN4PLMD7cltools12_GLOBAL__N_121DriverFloatRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#33">_ZNK4PLMD7cltools6DriverIfE11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#36">_ZN4PLMD7cltools12_GLOBAL__N_121DriverFloatRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#36">_ZN4PLMD7cltools12_GLOBAL__N_121DriverFloatRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/DriverFloat.cpp.func.html b/coverage/cltools/DriverFloat.cpp.func.html
new file mode 100644
index 0000000000..825a18de78
--- /dev/null
+++ b/coverage/cltools/DriverFloat.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/DriverFloat.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - DriverFloat.cpp<span style="font-size: 80%;"> (<a href="DriverFloat.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DriverFloat.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#36">_ZN4PLMD7cltools12_GLOBAL__N_121DriverFloatRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#36">_ZN4PLMD7cltools12_GLOBAL__N_121DriverFloatRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#36">_ZN4PLMD7cltools12_GLOBAL__N_121DriverFloatRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DriverFloat.cpp.gcov.html#33">_ZNK4PLMD7cltools6DriverIfE11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/DriverFloat.cpp.gcov.html b/coverage/cltools/DriverFloat.cpp.gcov.html
new file mode 100644
index 0000000000..6f8775e4ba
--- /dev/null
+++ b/coverage/cltools/DriverFloat.cpp.gcov.html
@@ -0,0 +1,118 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/DriverFloat.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - DriverFloat.cpp<span style="font-size: 80%;"> (source / <a href="DriverFloat.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Driver.cpp&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace cltools {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : // We instantiate here the template version of Driver so as</a>
+<a name="29"><span class="lineNum">      29 </span>            : // to accelerate parallel compilation.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : typedef Driver&lt;float&gt; DriverFloat;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /// Specialized version</a>
+<a name="34"><span class="lineNum">      34 </span>            : template&lt;&gt;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          4 : std::string Driver&lt;float&gt;::description()const { return &quot;analyze trajectories with plumed (single precision version)&quot;; }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      12508 : PLUMED_REGISTER_CLTOOL(DriverFloat,&quot;driver-float&quot;)</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : }</a>
+<a name="41"><span class="lineNum">      41 </span>            : }</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenExample.cpp.func-sort-c.html b/coverage/cltools/GenExample.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ff780a8ed8
--- /dev/null
+++ b/coverage/cltools/GenExample.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenExample.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenExample.cpp<span style="font-size: 80%;"> (<a href="GenExample.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">220</td>
+            <td class="headerCovTableEntryLo">7.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GenExample.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#173">_ZN4PLMD7cltools10GenExample15createLongInputERKSt6vectorIS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESaISA_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#212">_ZN4PLMD7cltools10GenExample17printExampleInputERKSt6vectorIS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESaISA_EERKS8_SG_RSt14basic_ofstreamIcS6_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#98">_ZN4PLMD7cltools10GenExample4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#89">_ZN4PLMD7cltools10GenExampleC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#78">_ZN4PLMD7cltools12_GLOBAL__N_120GenExampleRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#71">_ZNK4PLMD7cltools10GenExample11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#80">_ZN4PLMD7cltools10GenExample16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#78">_ZN4PLMD7cltools12_GLOBAL__N_120GenExampleRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#78">_ZN4PLMD7cltools12_GLOBAL__N_120GenExampleRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenExample.cpp.func.html b/coverage/cltools/GenExample.cpp.func.html
new file mode 100644
index 0000000000..7f8a45bf74
--- /dev/null
+++ b/coverage/cltools/GenExample.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenExample.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenExample.cpp<span style="font-size: 80%;"> (<a href="GenExample.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">220</td>
+            <td class="headerCovTableEntryLo">7.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GenExample.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#173">_ZN4PLMD7cltools10GenExample15createLongInputERKSt6vectorIS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESaISA_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#80">_ZN4PLMD7cltools10GenExample16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#212">_ZN4PLMD7cltools10GenExample17printExampleInputERKSt6vectorIS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESaISA_EERKS8_SG_RSt14basic_ofstreamIcS6_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#98">_ZN4PLMD7cltools10GenExample4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#89">_ZN4PLMD7cltools10GenExampleC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#78">_ZN4PLMD7cltools12_GLOBAL__N_120GenExampleRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#78">_ZN4PLMD7cltools12_GLOBAL__N_120GenExampleRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#78">_ZN4PLMD7cltools12_GLOBAL__N_120GenExampleRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenExample.cpp.gcov.html#71">_ZNK4PLMD7cltools10GenExample11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenExample.cpp.gcov.html b/coverage/cltools/GenExample.cpp.gcov.html
new file mode 100644
index 0000000000..fda79f6eed
--- /dev/null
+++ b/coverage/cltools/GenExample.cpp.gcov.html
@@ -0,0 +1,426 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenExample.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenExample.cpp<span style="font-size: 80%;"> (source / <a href="GenExample.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">220</td>
+            <td class="headerCovTableEntryLo">7.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2019-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionWithVirtualAtom.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionShortcut.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;cstdio&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;string&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;vector&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;iostream&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;fstream&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace cltools {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : //+PLUMEDOC TOOLS gen_example</a>
+<a name="43"><span class="lineNum">      43 </span>            : /*</a>
+<a name="44"><span class="lineNum">      44 </span>            : gen_example is a tool that you can use to construct an example for the manual that users can interact with to understand</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : The example constructed by this action is in html. In all probability you will never need to use this</a>
+<a name="47"><span class="lineNum">      47 </span>            : tool. However, it is used within the scripts that generate the html manual for PLUMED.  If you need to use this</a>
+<a name="48"><span class="lineNum">      48 </span>            : tool outside those scripts the input is specified using the following command line arguments.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \par Examples</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following generates an example based on the contents of the plumed file plumed.dat</a>
+<a name="53"><span class="lineNum">      53 </span>            : \verbatim</a>
+<a name="54"><span class="lineNum">      54 </span>            : plumed gen_example --plumed plumed.dat --status working</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endverbatim</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : class GenExample:</a>
+<a name="62"><span class="lineNum">      62 </span>            :   public CLTool</a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span>            : private:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   int multi;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::string status, version;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   Communicator intracomm;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   Communicator intercomm;</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit GenExample(const CLToolOptions&amp; co );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          4 :     return &quot;construct an example for the manual that users can interact with&quot;;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void printExampleInput( const std::vector&lt;std::vector&lt;std::string&gt; &gt;&amp; input, const std::string&amp; egname, const std::string&amp; divname, std::ofstream&amp; ofile );</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;std::vector&lt;std::string&gt; &gt; createLongInput( const std::vector&lt;std::vector&lt;std::string&gt; &gt;&amp; input );</a>
+<a name="78"><span class="lineNum">      78 </span>            : };</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      12508 : PLUMED_REGISTER_CLTOOL(GenExample,&quot;gen_example&quot;)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       4168 : void GenExample::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--plumed&quot;,&quot;plumed.dat&quot;,&quot;convert the input in this file to the html manual&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--out&quot;,&quot;example.html&quot;,&quot;the file on which to output the example in html&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--name&quot;,&quot;ppp&quot;,&quot;the name to use for this particular input&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--status&quot;,&quot;nobadge&quot;,&quot;whether or not the input file works&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--multi&quot;,&quot;0&quot;,&quot;set number of replicas for multi environment (needs MPI)&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       4168 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 : GenExample::GenExample(const CLToolOptions&amp; co ):</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   CLTool(co),</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          4 :   multi(0),</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          8 :   status(&quot;nobadge&quot;),</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 :   version(&quot;master&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          4 :   inputdata=commandline;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          4 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 : int GenExample::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : // set up for multi replica driver:</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   parse(&quot;--multi&quot;,multi);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   if(multi) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     int ntot=pc.Get_size(); int nintra=ntot/multi;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     if(multi*nintra!=ntot) error(&quot;invalid number of processes for multi environment&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     pc.Split(pc.Get_rank()/nintra,pc.Get_rank(),intracomm);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     pc.Split(pc.Get_rank()%nintra,pc.Get_rank(),intercomm);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   } else {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     intracomm.Set_comm(pc.Get_comm());</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   if( config::getVersionLong().find(&quot;dev&quot;)==std::string::npos ) version=&quot;v&quot;+config::getVersion();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   std::string fname, egname, outfile; parse(&quot;--plumed&quot;,fname);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   parse(&quot;--name&quot;,egname); parse(&quot;--out&quot;,outfile); parse(&quot;--status&quot;,status);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :   int r=0;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   if(intracomm.Get_rank()==0) r=intercomm.Get_rank();</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   intracomm.Bcast(r,0);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   if(r&gt;0) outfile=&quot;/dev/null&quot;;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :   IFile ifile; ifile.open(fname); ifile.allowNoEOL(); std::ofstream ofile; ofile.open(outfile); std::vector&lt;bool&gt; shortcuts;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   bool hasshortcuts=false, endplumed=false; std::vector&lt;std::vector&lt;std::string&gt; &gt; input; std::vector&lt;std::string&gt; words;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :   while( Tools::getParsedLine(ifile, words, false) ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     input.push_back( words ); shortcuts.push_back( false );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     if( words.empty() || words[0].find(&quot;#&quot;)!=std::string::npos || endplumed ) continue;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     std::vector&lt;std::string&gt; interpreted( words ); Tools::interpretLabel(interpreted);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :     if( interpreted[0]==&quot;ENDPLUMED&quot; ) { endplumed=true; continue; }</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     Keywords keys; actionRegister().getKeywords( interpreted[0], keys );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     if( status==&quot;working&quot; &amp;&amp; keys.exists(&quot;IS_SHORTCUT&quot;) ) hasshortcuts=shortcuts[shortcuts.size()-1]=true;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   ifile.close();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :   if( hasshortcuts ) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;div style=\&quot;width: 80%; float:left\&quot; id=\&quot;value_details_&quot;&lt;&lt;egname&lt;&lt;&quot;\&quot;&gt; Click on the labels of the actions for more information on what each action computes &lt;/div&gt;\n&quot;;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;div style=\&quot;width: 10%; float:left\&quot;&gt;&lt;button type=\&quot;button\&quot; id=\&quot;&quot;&lt;&lt;egname&lt;&lt;&quot;_button\&quot; onclick=\'swapInput(\&quot;&quot;&lt;&lt;egname&lt;&lt;&quot;\&quot;)\'&gt;contract shortcuts&lt;/button&gt;&lt;/div&gt;&quot;;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   } else {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;div style=\&quot;width: 90%; float:left\&quot; id=\&quot;value_details_&quot;&lt;&lt;egname&lt;&lt;&quot;\&quot;&gt; Click on the labels of the actions for more information on what each action computes &lt;/div&gt;\n&quot;;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   ofile&lt;&lt;&quot;&lt;div style=\&quot;width: 10%; float:left\&quot;&gt;&quot;;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   ofile&lt;&lt;&quot;&lt;img src=\&quot;https://img.shields.io/badge/&quot;;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   if(status==&quot;working&quot;) ofile&lt;&lt;version&lt;&lt;&quot;-passing-green&quot;;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   else if(status==&quot;broken&quot;) ofile&lt;&lt;version&lt;&lt;&quot;-failed-red&quot;;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   else if(status==&quot;loads&quot;) ofile&lt;&lt;&quot;with-LOAD-yellow&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   else if(status==&quot;incomplete&quot;) ofile&lt;&lt;version&lt;&lt;&quot;-incomplete-yellow&quot;;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   else error(&quot;unknown status&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :   ofile&lt;&lt;&quot;.svg\&quot; alt=\&quot;tested on &quot;&lt;&lt;version&lt;&lt;&quot;\&quot; /&gt;&lt;/div&gt;&quot;;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   ofile.flush();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   if( hasshortcuts ) {</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     // Write out the short version of the input</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;div style=\&quot;width: 100%; float:left\&quot; id=\&quot;input_&quot;&lt;&lt;egname&lt;&lt;&quot;\&quot;&gt;&lt;/div&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     // Write an extra pre to make sure the html after the example is put in the right place on the page</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;pre style=\&quot;width: 97%;\&quot; class=\&quot;fragment\&quot;&gt;&lt;/pre&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;script type=\&quot;text/javascript\&quot;&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;if (window.addEventListener) { // Mozilla, Netscape, Firefox&quot;&lt;&lt;std::endl;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;    window.addEventListener('load', &quot;&lt;&lt;egname&lt;&lt;&quot;Load, false);&quot;&lt;&lt;std::endl;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;} else if (window.attachEvent) { // IE&quot;&lt;&lt;std::endl;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;    window.attachEvent('onload', &quot;&lt;&lt;egname&lt;&lt;&quot;Load);&quot;&lt;&lt;std::endl;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;}&quot;&lt;&lt;std::endl;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;function &quot;&lt;&lt;egname&lt;&lt;&quot;Load(event) {&quot;&lt;&lt;std::endl;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;       swapInput(\&quot;&quot;&lt;&lt;egname&lt;&lt;&quot;\&quot;);&quot;&lt;&lt;std::endl;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;}&quot;&lt;&lt;std::endl;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;/script&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;div style=\&quot;display:none;\&quot; id=\&quot;&quot;&lt;&lt;egname&lt;&lt;&quot;short\&quot;&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     printExampleInput( input, egname + &quot;short&quot;, egname, ofile );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;/div&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     // Write out long version of the input</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;div style=\&quot;display:none;\&quot; id=\&quot;&quot;&lt;&lt;egname&lt;&lt;&quot;long\&quot;&gt;&quot;;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     std::vector&lt;std::vector&lt;std::string&gt; &gt; long_input = createLongInput( input );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     printExampleInput( long_input, egname + &quot;long&quot;, egname, ofile );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     ofile&lt;&lt;&quot;&lt;/div&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   } else printExampleInput( input, egname, egname, ofile );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   ofile.close(); return 0;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 : std::vector&lt;std::vector&lt;std::string&gt; &gt; GenExample::createLongInput( const std::vector&lt;std::vector&lt;std::string&gt; &gt;&amp; input ) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;std::string&gt; &gt; long_input; PlumedMain myplumed; int rr=sizeof(double), natoms=10000000; double kt=2.49;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   myplumed.cmd(&quot;setRealPrecision&quot;,&amp;rr);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :   if(Communicator::initialized()) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     if(multi) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :       if(intracomm.Get_rank()==0) myplumed.cmd(&quot;GREX setMPIIntercomm&quot;,&amp;intercomm.Get_comm());</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :       myplumed.cmd(&quot;GREX setMPIIntracomm&quot;,&amp;intracomm.Get_comm()); myplumed.cmd(&quot;GREX init&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     myplumed.cmd(&quot;setMPIComm&quot;,&amp;intracomm.Get_comm());</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   bool endplumed=false; myplumed.cmd(&quot;setNatoms&quot;,&amp;natoms); myplumed.cmd(&quot;setKbT&quot;,&amp;kt); myplumed.cmd(&quot;init&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   for(unsigned ll=0; ll&lt;input.size(); ++ll) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     if( input[ll].empty() || endplumed ) { long_input.push_back( input[ll] ); continue; }</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     if( input[ll][0].find(&quot;#&quot;)!=std::string::npos ) { long_input.push_back( input[ll] ); continue; }</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     std::vector&lt;std::string&gt; interpreted( input[ll] ); Tools::interpretLabel(interpreted);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :     if( interpreted[0]==&quot;ENDPLUMED&quot; ) { endplumed=true; long_input.push_back( input[ll] ); continue; }</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     Keywords keys; plumed_assert( actionRegister().check( interpreted[0] ) );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     actionRegister().getKeywords( interpreted[0], keys ); std::string lab, myinputline;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     if( Tools::parse(interpreted, &quot;LABEL&quot;, lab ) ) myinputline = lab + &quot;: &quot;;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     myinputline += interpreted[0] + &quot; &quot;; bool trailingcomment=false;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     for(unsigned i=1; i&lt;interpreted.size(); ++i) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       if( trailingcomment &amp;&amp; interpreted[i]==&quot;@newline&quot;) { trailingcomment=false; continue; }</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :       if( interpreted[i].find(&quot;#&quot;)!=std::string::npos ) { trailingcomment=true; continue; }</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :       if( interpreted[i]==&quot;@newline&quot; || interpreted[i]==&quot;...&quot; ) continue;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :       std::size_t pos = 0;  while ((pos = interpreted[i].find(&quot;@newline&quot;,pos)) != std::string::npos) { interpreted[i].replace(pos, 8, &quot;\n&quot;); pos++; }</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :       myinputline += interpreted[i] + &quot; &quot;;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :     }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     if( status==&quot;working&quot; &amp;&amp; keys.exists(&quot;IS_SHORTCUT&quot;) ) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :       myplumed.readInputLine( myinputline );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :       ActionShortcut* as=dynamic_cast&lt;ActionShortcut*&gt;( myplumed.getActionSet()[myplumed.getActionSet().size()-1].get() );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :       plumed_assert( as ); std::vector&lt;std::string&gt; shortcut_commands = as-&gt;getSavedInputLines();</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;shortcut_commands.size(); ++i) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :         std::vector&lt;std::string&gt; words = Tools::getWords( shortcut_commands[i] ); long_input.push_back( words );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :     } else { long_input.push_back( input[ll] ); myplumed.readInputLine( myinputline ); }</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :   return long_input;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 : void GenExample::printExampleInput( const std::vector&lt;std::vector&lt;std::string&gt; &gt;&amp; input, const std::string&amp; egname, const std::string&amp; divname, std::ofstream&amp; ofile ) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   PlumedMain myplumed; int rr=sizeof(double), natoms=10000000; double kt=2.49;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   myplumed.cmd(&quot;setRealPrecision&quot;,&amp;rr);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   if(Communicator::initialized()) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :     if(multi) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :       if(intracomm.Get_rank()==0) myplumed.cmd(&quot;GREX setMPIIntercomm&quot;,&amp;intercomm.Get_comm());</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :       myplumed.cmd(&quot;GREX setMPIIntracomm&quot;,&amp;intracomm.Get_comm()); myplumed.cmd(&quot;GREX init&quot;);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :     myplumed.cmd(&quot;setMPIComm&quot;,&amp;intracomm.Get_comm());</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :   myplumed.cmd(&quot;setNatoms&quot;,&amp;natoms); myplumed.cmd(&quot;setKbT&quot;,&amp;kt); myplumed.cmd(&quot;init&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   std::vector&lt;std::string&gt; labellist; bool endplumed=false;</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :   ofile&lt;&lt;&quot;&lt;pre style=\&quot;width: 97%;\&quot; class=\&quot;fragment\&quot;&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   for(unsigned ll=0; ll&lt;input.size(); ++ll) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     if( input[ll].empty() ) { ofile&lt;&lt;std::endl; continue; }</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     if( input[ll][0].find(&quot;#&quot;)!=std::string::npos || endplumed ) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :       ofile&lt;&lt;&quot;&lt;span style=\&quot;color:blue\&quot;&gt;&quot;&lt;&lt;input[ll][0];</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :       for(unsigned i=1; i&lt;input[ll].size(); ++i) ofile&lt;&lt;&quot; &quot;&lt;&lt;input[ll][i];</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :       ofile&lt;&lt;&quot;&lt;/span&gt;&quot;&lt;&lt;std::endl;;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     } else {</a>
+<a name="234"><span class="lineNum">     234 </span>            :       // Interpret the label if this needs to be done</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :       std::vector&lt;std::string&gt; interpreted( input[ll] ); Tools::interpretLabel(interpreted); std::string lab, myinputline;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :       // Now read in the label</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :       if( Tools::parse(interpreted,&quot;LABEL&quot;,lab) ) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :         ofile&lt;&lt;&quot;&lt;b name=\&quot;&quot;&lt;&lt;egname&lt;&lt;lab&lt;&lt;&quot;\&quot; onclick=\'showPath(\&quot;&quot;&lt;&lt;divname&lt;&lt;&quot;\&quot;,\&quot;&quot;&lt;&lt;egname&lt;&lt;lab&lt;&lt;&quot;\&quot;)\'&gt;&quot;&lt;&lt;lab&lt;&lt;&quot;: &lt;/b&gt;&quot;;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :         labellist.push_back(lab); myinputline = lab + &quot;: &quot;;</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :       }</a>
+<a name="241"><span class="lineNum">     241 </span>            :       // Print the keyword in use in the action</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :       std::string action = interpreted[0]; myinputline += interpreted[0] + &quot; &quot;;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :       if( action==&quot;ENDPLUMED&quot; ) endplumed=true;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :       Keywords keys; actionRegister().getKeywords( interpreted[0], keys );</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :       // Handle conversion of action names to links</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :       std::transform(action.begin(), action.end(), action.begin(), [](unsigned char c) { return std::tolower(c); });</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :       ofile&lt;&lt;&quot;&lt;a href=\&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/&quot;;</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :       for(unsigned n=0;; ++n) {</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :         std::size_t und=action.find_first_of(&quot;_&quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :         if( und==std::string::npos ) break;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :         std::string first=action.substr(0,und);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :         for(auto c : first ) { if( isdigit(c) ) ofile&lt;&lt;c; else ofile&lt;&lt;&quot;_&quot;&lt;&lt;c; }</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :         ofile&lt;&lt;&quot;_&quot;; action=action.substr(und+1);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :       for(auto c : action ) { if( isdigit(c) ) ofile&lt;&lt;c; else ofile&lt;&lt;&quot;_&quot;&lt;&lt;c; }</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :       ofile&lt;&lt;&quot;.html\&quot; style=\&quot;color:green\&quot;&gt;&quot;&lt;&lt;interpreted[0]&lt;&lt;&quot;&lt;/a&gt; &quot;;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :       // And write out everything else in the input line</a>
+<a name="258"><span class="lineNum">     258 </span>            :       bool trailingcomment=false;</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :       for(unsigned i=1; i&lt;interpreted.size(); ++i) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :         if( interpreted[i]==&quot;@newline&quot; &amp;&amp; i==1 ) { ofile&lt;&lt;&quot;...&quot;&lt;&lt;std::endl&lt;&lt;&quot;   &quot;; continue; }</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :         else if( interpreted[i]==&quot;@newline&quot; ) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :           if( trailingcomment ) { ofile&lt;&lt;&quot;&lt;/span&gt;&quot;; trailingcomment=false; }</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :           if( interpreted[i+1]==&quot;...&quot; ) ofile&lt;&lt;std::endl;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :           else ofile&lt;&lt;std::endl&lt;&lt;&quot;   &quot;;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :         } else if( interpreted[i]==&quot;__FILL__&quot; ) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :           if( status!=&quot;incomplete&quot; ) error(&quot;found __FILL__ statement but status is &quot; + status);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :           ofile&lt;&lt;&quot;&lt;span style=\&quot;background-color:yellow\&quot;&gt;__FILL__&lt;/span&gt;&quot;;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :           continue;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :         } else if( interpreted[i]==action ) continue;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :         if( interpreted[i].find(&quot;#&quot;)!=std::string::npos ) { trailingcomment=true; ofile&lt;&lt;&quot;&lt;span style=\&quot;color:blue\&quot;&gt;&quot;; }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :         if( !trailingcomment ) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :           std::size_t eq=interpreted[i].find_first_of(&quot;=&quot;);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :           if( eq!=std::string::npos ) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :             std::string keyword=interpreted[i].substr(0,eq), rest=interpreted[i].substr(eq+1);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot;&lt;div class=\&quot;tooltip\&quot;&gt;&quot;&lt;&lt;keyword&lt;&lt;&quot;&lt;div class=\&quot;right\&quot;&gt;&quot;&lt;&lt;keys.getTooltip(keyword)&lt;&lt;&quot;&lt;i&gt;&lt;/i&gt;&lt;/div&gt;&lt;/div&gt;&quot;;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :             if( rest==&quot;__FILL__&quot; ) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :               if( status!=&quot;incomplete&quot; ) error(&quot;found __FILL__ statement but status is &quot; + status);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :               ofile&lt;&lt;&quot;=&lt;span style=\&quot;background-color:yellow\&quot;&gt;__FILL__&lt;/span&gt;&quot;;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :             } else if( rest.find_first_of(&quot;{&quot;)!=std::string::npos ) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :               std::size_t pos = 0;  while ((pos = rest.find(&quot;@newline&quot;,pos)) != std::string::npos) { rest.replace(pos, 8, &quot;\n&quot;); pos++; }</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :               ofile&lt;&lt;&quot;=&quot;&lt;&lt;rest&lt;&lt;&quot; &quot;; myinputline += keyword + &quot;=&quot; + rest + &quot; &quot;;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :             } else {</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :               std::vector&lt;std::string&gt; args=Tools::getWords(rest,&quot;\t\n ,&quot;); ofile&lt;&lt;&quot;=&quot;;</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :               for(unsigned i=0; i&lt;args.size(); ++i) {</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :                 bool islabel=false; std::string thislab;</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :                 for(unsigned j=0; j&lt;labellist.size(); ++j) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :                   std::size_t dot=args[i].find_first_of(&quot;.&quot;); std::string lll=args[i].substr(0,dot);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :                   if( lll==labellist[j] ) { islabel=true; thislab=labellist[j]; break; }</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :                 }</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :                 if( islabel ) ofile&lt;&lt;&quot;&lt;b name=\&quot;&quot;&lt;&lt;egname&lt;&lt;thislab&lt;&lt;&quot;\&quot;&gt;&quot;&lt;&lt;args[i]&lt;&lt;&quot;&lt;/b&gt;&quot;;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :                 else ofile&lt;&lt;args[i];</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :                 if( i!=args.size()-1 ) ofile&lt;&lt;&quot;,&quot;;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :               }</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :               myinputline += interpreted[i] + &quot; &quot;;</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :             }</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot; &quot;;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :           } else if( interpreted[i]!=&quot;@newline&quot; &amp;&amp; interpreted[i]!=&quot;...&quot; ) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :             myinputline += interpreted[i] + &quot; &quot;;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot;&lt;div class=\&quot;tooltip\&quot;&gt;&quot;&lt;&lt;interpreted[i]&lt;&lt;&quot;&lt;div class=\&quot;right\&quot;&gt;&quot;&lt;&lt;keys.getTooltip(interpreted[i])&lt;&lt;&quot;&lt;i&gt;&lt;/i&gt;&lt;/div&gt;&lt;/div&gt; &quot;;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :           } else if( interpreted[i]==&quot;...&quot; ) ofile&lt;&lt;&quot;...&quot;;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :         } else ofile&lt;&lt;interpreted[i]&lt;&lt;&quot; &quot;;</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :       }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :       if( trailingcomment ) ofile&lt;&lt;&quot;&lt;/span&gt;&quot;;</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :       // This builds the hidden content that tells the user about what is calculated</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :       if( status==&quot;working&quot; ) {</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :         ofile&lt;&lt;&quot;&lt;span style=\&quot;display:none;\&quot; id=\&quot;&quot;&lt;&lt;egname&lt;&lt;lab&lt;&lt;&quot;\&quot;&gt;&quot;;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :         ofile&lt;&lt;&quot;The &quot;&lt;&lt;interpreted[0]&lt;&lt;&quot; action with label &lt;b&gt;&quot;&lt;&lt;lab&lt;&lt;&quot;&lt;/b&gt;&quot;;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :         myplumed.readInputLine( myinputline );</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :         ActionWithValue* av=dynamic_cast&lt;ActionWithValue*&gt;( myplumed.getActionSet().selectWithLabel&lt;Action*&gt;(lab) );</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :         if( av ) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :           if( av-&gt;getNumberOfComponents()==1 ) { ofile&lt;&lt;&quot; calculates a single scalar value&quot;; }</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :           else if( av-&gt;getNumberOfComponents()&gt;0 ) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot; calculates the following quantities:&quot;&lt;&lt;std::endl;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot;&lt;table  align=\&quot;center\&quot; frame=\&quot;void\&quot; width=\&quot;95%%\&quot; cellpadding=\&quot;5%%\&quot;&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot;&lt;tr&gt;&lt;td width=\&quot;5%%\&quot;&gt;&lt;b&gt; Quantity &lt;/b&gt;  &lt;/td&gt;&lt;td&gt;&lt;b&gt; Description &lt;/b&gt; &lt;/td&gt;&lt;/tr&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :             unsigned ncomp = av-&gt;getNumberOfComponents();</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :             for(unsigned k=0; k&lt;ncomp; ++k ) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :               std::string myname = av-&gt;copyOutput(k)-&gt;getName(); std::size_t dot=myname.find_first_of(&quot;.&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :               std::string tname=myname.substr(dot+1); std::size_t und=tname.find_last_of(&quot;_&quot;); std::size_t hyph=tname.find_first_of(&quot;-&quot;);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :               if( und!=std::string::npos &amp;&amp; hyph!=std::string::npos ) plumed_merror(&quot;cannot use underscore and hyphen in name&quot;);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :               ofile&lt;&lt;&quot;&lt;tr&gt;&lt;td width=\&quot;5%%\&quot;&gt;&quot;&lt;&lt;myname&lt;&lt;&quot;&lt;/td&gt;&lt;td&gt;&quot;;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :               if( und!=std::string::npos ) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :                 ofile&lt;&lt;keys.getOutputComponentDescription(tname.substr(und))&lt;&lt;&quot; This particular component measures this quantity for the input CV named &quot;;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :                 ofile&lt;&lt;tname.substr(0,und);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :               } else if( hyph!=std::string::npos ) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :                 ofile&lt;&lt;keys.getOutputComponentDescription(tname.substr(0,hyph))&lt;&lt;&quot;  This is the &quot;&lt;&lt;tname.substr(hyph+1)&lt;&lt;&quot;th of these quantities&quot;;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :               } else ofile&lt;&lt;keys.getOutputComponentDescription(tname);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :               ofile&lt;&lt;&quot;&lt;/td&gt;&lt;/tr&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :             }</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :             ofile&lt;&lt;&quot;&lt;/table&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :           }</a>
+<a name="334"><span class="lineNum">     334 </span>            :         } else {</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :           ActionWithVirtualAtom* avv=dynamic_cast&lt;ActionWithVirtualAtom*&gt;( myplumed.getActionSet().selectWithLabel&lt;Action*&gt;(lab) );</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :           if( avv ) ofile&lt;&lt;&quot; calculates the position of a virtual atom&quot;;</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :           else if( interpreted[0]==&quot;GROUP&quot; ) ofile&lt;&lt;&quot; defines a group of atoms so that they can be referred to later in the input&quot;;</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :         }</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :         ofile&lt;&lt;&quot;&lt;/span&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :       } else {</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :         ofile&lt;&lt;&quot;&lt;span style=\&quot;display:none;\&quot; id=\&quot;&quot;&lt;&lt;egname&lt;&lt;lab&lt;&lt;&quot;\&quot;&gt; You cannot view the components that are calculated by each action for this input file. Sorry &lt;/span&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :       }</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :     ofile.flush();</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   ofile&lt;&lt;&quot;&lt;/pre&gt;&quot;&lt;&lt;std::endl;</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            : } // End of namespace</a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenJson.cpp.func-sort-c.html b/coverage/cltools/GenJson.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fd9fd92e62
--- /dev/null
+++ b/coverage/cltools/GenJson.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenJson.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenJson.cpp<span style="font-size: 80%;"> (<a href="GenJson.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GenJson.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#75">_ZN4PLMD7cltools7GenJson4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#55">_ZNK4PLMD7cltools7GenJson11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_117GenJsonRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#67">_ZN4PLMD7cltools7GenJsonC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_117GenJsonRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_117GenJsonRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#62">_ZN4PLMD7cltools7GenJson16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenJson.cpp.func.html b/coverage/cltools/GenJson.cpp.func.html
new file mode 100644
index 0000000000..b126cede12
--- /dev/null
+++ b/coverage/cltools/GenJson.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenJson.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenJson.cpp<span style="font-size: 80%;"> (<a href="GenJson.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GenJson.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_117GenJsonRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_117GenJsonRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_117GenJsonRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#62">_ZN4PLMD7cltools7GenJson16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#75">_ZN4PLMD7cltools7GenJson4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#67">_ZN4PLMD7cltools7GenJsonC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenJson.cpp.gcov.html#55">_ZNK4PLMD7cltools7GenJson11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenJson.cpp.gcov.html b/coverage/cltools/GenJson.cpp.gcov.html
new file mode 100644
index 0000000000..8c4e7e10c8
--- /dev/null
+++ b/coverage/cltools/GenJson.cpp.gcov.html
@@ -0,0 +1,257 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenJson.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenJson.cpp<span style="font-size: 80%;"> (source / <a href="GenJson.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2022,2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstdio&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;string&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;iostream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace cltools {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC TOOLS gen_json</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : gen_json constructs a json file that includes a dictionary of actions, the keywords for those actions and the components and outputs this to standard output</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The following command generates the json file</a>
+<a name="42"><span class="lineNum">      42 </span>            : \verbatim</a>
+<a name="43"><span class="lineNum">      43 </span>            : plumed gen_json</a>
+<a name="44"><span class="lineNum">      44 </span>            : \endverbatim</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : class GenJson : public CLTool {</a>
+<a name="51"><span class="lineNum">      51 </span>            : private:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::string version;</a>
+<a name="53"><span class="lineNum">      53 </span>            : public:</a>
+<a name="54"><span class="lineNum">      54 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="55"><span class="lineNum">      55 </span>            :   explicit GenJson(const CLToolOptions&amp; co );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :     return &quot;print out a json file that contains the pluemd syntax&quot;;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   }</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      12509 : PLUMED_REGISTER_CLTOOL(GenJson,&quot;gen_json&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4168 : void GenJson::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--actions&quot;,&quot;a file containing one line descriptions of the various actions&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       4168 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          5 : GenJson::GenJson(const CLToolOptions&amp; co ):</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   CLTool(co),</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          5 :   version(&quot;master&quot;)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          5 :   inputdata=commandline;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         15 :   if( config::getVersionLong().find(&quot;dev&quot;)==std::string::npos ) version=&quot;v&quot;+config::getVersion();</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          5 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          1 : int GenJson::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :   std::string line(&quot;&quot;), actionfile; parse(&quot;--actions&quot;,actionfile);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          1 :   IFile myfile; myfile.open(actionfile); bool stat;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::map&lt;std::string,std::string&gt; action_map;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        313 :   while((stat=myfile.getline(line))) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        312 :     std::size_t col = line.find_first_of(&quot;:&quot;); std::string docs = line.substr(col+1);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        312 :     if( docs.find(&quot;\\&quot;)!=std::string::npos ) error(&quot;found invalid backslash character in first line of documentation for action &quot; + line.substr(0,col) );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        624 :     action_map.insert(std::pair&lt;std::string,std::string&gt;( line.substr(0,col), docs ) );</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 :   myfile.close();</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :   // Cycle over all the action names</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;{&quot;&lt;&lt;std::endl;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Get the vimlink</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   std::cout&lt;&lt;&quot;  \&quot;vimlink\&quot; : \&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/_vim_syntax.html\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   // And the replicas link</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   std::cout&lt;&lt;&quot;  \&quot;replicalink\&quot; : \&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/special-replica-syntax.html\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   // Get the names of all the actions</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          1 :   std::vector&lt;std::string&gt; action_names( actionRegister().getActionNames() );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        293 :   for(unsigned i=0; i&lt;action_names.size(); ++i) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        876 :     std::cout&lt;&lt;&quot;  \&quot;&quot;&lt;&lt;action_names[i]&lt;&lt;'&quot;'&lt;&lt;&quot;: {&quot;&lt;&lt;std::endl; std::string action=action_names[i];</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :     // Handle conversion of action names to links</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        584 :     std::cout&lt;&lt;&quot;    \&quot;hyperlink\&quot; : \&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/&quot;;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       3626 :     std::transform(action.begin(), action.end(), action.begin(), [](unsigned char c) { return std::tolower(c); });</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     while(true) {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        479 :       std::size_t und=action.find_first_of(&quot;_&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        479 :       if( und==std::string::npos ) break;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        187 :       std::string first=action.substr(0,und);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       2237 :       for(auto c : first ) { if( isdigit(c) ) std::cout&lt;&lt;c; else std::cout&lt;&lt;&quot;_&quot;&lt;&lt;c; }</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        374 :       std::cout&lt;&lt;&quot;_&quot;; action=action.substr(und+1);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        187 :     }</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       4536 :     for(auto c : action ) { if( isdigit(c) ) std::cout&lt;&lt;c; else std::cout&lt;&lt;&quot;_&quot;&lt;&lt;c; }</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        292 :     std::cout&lt;&lt;&quot;.html\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        584 :     std::cout&lt;&lt;&quot;    \&quot;description\&quot; : \&quot;&quot;&lt;&lt;action_map[action_names[i]]&lt;&lt;&quot;\&quot;,\n&quot;;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     // Now output keyword information</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        292 :     Keywords keys; actionRegister().getKeywords( action_names[i], keys );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        292 :     std::cout&lt;&lt;&quot;    \&quot;syntax\&quot; : {&quot;&lt;&lt;std::endl;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       4778 :     for(unsigned j=0; j&lt;keys.size(); ++j) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4486 :       std::string desc = keys.getKeywordDescription( keys.getKeyword(j) );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       4486 :       if( desc.find(&quot;default=&quot;)!=std::string::npos ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       2984 :         std::size_t brac=desc.find_first_of(&quot;)&quot;); desc = desc.substr(brac+1);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :       }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       4486 :       std::size_t dot=desc.find_first_of(&quot;.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      22430 :       std::cout&lt;&lt;&quot;       \&quot;&quot;&lt;&lt;keys.getKeyword(j)&lt;&lt;&quot;\&quot; : { \&quot;type\&quot;: \&quot;&quot;&lt;&lt;keys.getStyle(keys.getKeyword(j))&lt;&lt;&quot;\&quot;, \&quot;description\&quot;: \&quot;&quot;&lt;&lt;desc.substr(0,dot)&lt;&lt;&quot;\&quot;, \&quot;multiple\&quot;: &quot;&lt;&lt;keys.numbered( keys.getKeyword(j) )&lt;&lt;&quot;}&quot;;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       5000 :       if( j==keys.size()-1 &amp;&amp; !keys.exists(&quot;HAS_VALUES&quot;) ) std::cout&lt;&lt;std::endl; else std::cout&lt;&lt;&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        584 :     if( keys.exists(&quot;HAS_VALUES&quot;) ) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        222 :       std::cout&lt;&lt;&quot;       \&quot;output\&quot; : {&quot;&lt;&lt;std::endl;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        222 :       std::vector&lt;std::string&gt; components( keys.getOutputComponents() );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :       // Check if we have a value</a>
+<a name="127"><span class="lineNum">     127 </span>            :       bool hasvalue=true;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       2279 :       for(unsigned k=0; k&lt;components.size(); ++k) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       4250 :         if( keys.getOutputComponentFlag( components[k] )==&quot;default&quot; ) { hasvalue=false; break; }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :       }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        222 :       if( hasvalue ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        154 :         std::cout&lt;&lt;&quot;         \&quot;value\&quot;: {&quot;&lt;&lt;std::endl;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        154 :         std::cout&lt;&lt;&quot;           \&quot;flag\&quot;: \&quot;value\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        154 :         std::cout&lt;&lt;&quot;           \&quot;description\&quot;: \&quot;a scalar quantity\&quot;&quot;&lt;&lt;std::endl;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        154 :         if( components.size()==0 ) std::cout&lt;&lt;&quot;         }&quot;&lt;&lt;std::endl; else std::cout&lt;&lt;&quot;         },&quot;&lt;&lt;std::endl;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :       }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       2620 :       for(unsigned k=0; k&lt;components.size(); ++k) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       4796 :         std::cout&lt;&lt;&quot;         \&quot;&quot;&lt;&lt;components[k]&lt;&lt;&quot;\&quot; : {&quot;&lt;&lt;std::endl;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       7194 :         std::cout&lt;&lt;&quot;           \&quot;flag\&quot;: \&quot;&quot;&lt;&lt;keys.getOutputComponentFlag( components[k] )&lt;&lt;&quot;\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       2398 :         std::string desc=keys.getOutputComponentDescription( components[k] ); std::size_t dot=desc.find_first_of(&quot;.&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       7194 :         std::cout&lt;&lt;&quot;           \&quot;description\&quot;: \&quot;&quot;&lt;&lt;desc.substr(0,dot)&lt;&lt;&quot;\&quot;&quot;&lt;&lt;std::endl;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       2398 :         if( k==components.size()-1 ) std::cout&lt;&lt;&quot;         }&quot;&lt;&lt;std::endl; else std::cout&lt;&lt;&quot;         },&quot;&lt;&lt;std::endl;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :       }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        222 :       std::cout&lt;&lt;&quot;       }&quot;&lt;&lt;std::endl;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        222 :     }</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        292 :     std::cout&lt;&lt;&quot;    },&quot;&lt;&lt;std::endl;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     // This ensures that \n is replaced by \\n</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        292 :     std::string unsafen=&quot;\n&quot;, safen=&quot;\\n&quot;, helpstr = keys.getHelpString();</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        292 :     for( std::size_t pos = helpstr.find(&quot;\n&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      11298 :          pos != std::string::npos;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      11006 :          pos = helpstr.find(&quot;\n&quot;, pos)</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      11006 :        ) { helpstr.replace(pos, unsafen.size(), safen); pos += safen.size(); }</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        584 :     std::cout&lt;&lt;&quot;    \&quot;help\&quot; : \&quot;&quot;&lt;&lt;helpstr&lt;&lt;&quot;\&quot;\n&quot;;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        292 :     std::cout&lt;&lt;&quot;  },&quot;&lt;&lt;std::endl;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        292 :   }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   // Get all the special groups</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;  \&quot;groups\&quot; : {&quot;&lt;&lt;std::endl;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;    \&quot;@allatoms\&quot; : { \n&quot;&lt;&lt;std::endl;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;        \&quot;description\&quot; : \&quot;refers to all the MD codes atoms and PLUMEDs vatoms\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :   std::cout&lt;&lt;&quot;        \&quot;link\&quot; : \&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/_group.html\&quot;&quot;&lt;&lt;std::endl;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;    },&quot;&lt;&lt;std::endl;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;    \&quot;@mdatoms\&quot; : { \n&quot;&lt;&lt;std::endl;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;        \&quot;description\&quot; : \&quot;refers to all the MD codes atoms but not PLUMEDs vatoms\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   std::cout&lt;&lt;&quot;        \&quot;link\&quot; : \&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/_group.html\&quot;&quot;&lt;&lt;std::endl;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   // Now print all the special keywords in molinfo</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 :   std::map&lt;std::string,std::string&gt; specials( GenericMolInfo::getSpecialKeywords() );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         36 :   for(auto const&amp; s : specials ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         35 :     std::cout&lt;&lt;&quot;    },&quot;&lt;&lt;std::endl;</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         70 :     std::cout&lt;&lt;&quot;    \&quot;&quot;&lt;&lt;s.first&lt;&lt;&quot;\&quot; : { \n&quot;&lt;&lt;std::endl;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         70 :     std::cout&lt;&lt;&quot;        \&quot;description\&quot; : \&quot;&quot;&lt;&lt;s.second&lt;&lt;&quot;\&quot;,&quot;&lt;&lt;std::endl;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         70 :     std::cout&lt;&lt;&quot;        \&quot;link\&quot; : \&quot;https://www.plumed.org/doc-&quot;&lt;&lt;version&lt;&lt;&quot;/user-doc/html/_m_o_l_i_n_f_o.html\&quot;&quot;&lt;&lt;std::endl;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;        }&quot;&lt;&lt;std::endl;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;  }&quot;&lt;&lt;std::endl;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 :   std::cout&lt;&lt;&quot;}&quot;&lt;&lt;std::endl;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          1 :   return 0;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          2 : }</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : } // End of namespace</a>
+<a name="181"><span class="lineNum">     181 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenTemplate.cpp.func-sort-c.html b/coverage/cltools/GenTemplate.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7533887e36
--- /dev/null
+++ b/coverage/cltools/GenTemplate.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenTemplate.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenTemplate.cpp<span style="font-size: 80%;"> (<a href="GenTemplate.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">56.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GenTemplate.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#76">_ZN4PLMD7cltools11GenTemplate4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#70">_ZN4PLMD7cltools11GenTemplateC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#61">_ZN4PLMD7cltools12_GLOBAL__N_121GenTemplateRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#56">_ZNK4PLMD7cltools11GenTemplate11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#63">_ZN4PLMD7cltools11GenTemplate16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#61">_ZN4PLMD7cltools12_GLOBAL__N_121GenTemplateRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#61">_ZN4PLMD7cltools12_GLOBAL__N_121GenTemplateRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenTemplate.cpp.func.html b/coverage/cltools/GenTemplate.cpp.func.html
new file mode 100644
index 0000000000..5b6cf07952
--- /dev/null
+++ b/coverage/cltools/GenTemplate.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenTemplate.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenTemplate.cpp<span style="font-size: 80%;"> (<a href="GenTemplate.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">56.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GenTemplate.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#63">_ZN4PLMD7cltools11GenTemplate16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#76">_ZN4PLMD7cltools11GenTemplate4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#70">_ZN4PLMD7cltools11GenTemplateC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#61">_ZN4PLMD7cltools12_GLOBAL__N_121GenTemplateRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#61">_ZN4PLMD7cltools12_GLOBAL__N_121GenTemplateRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#61">_ZN4PLMD7cltools12_GLOBAL__N_121GenTemplateRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenTemplate.cpp.gcov.html#56">_ZNK4PLMD7cltools11GenTemplate11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/GenTemplate.cpp.gcov.html b/coverage/cltools/GenTemplate.cpp.gcov.html
new file mode 100644
index 0000000000..e90a0ed086
--- /dev/null
+++ b/coverage/cltools/GenTemplate.cpp.gcov.html
@@ -0,0 +1,178 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/GenTemplate.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - GenTemplate.cpp<span style="font-size: 80%;"> (source / <a href="GenTemplate.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">56.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdio&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;iostream&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace cltools {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC TOOLS gentemplate</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : gentemplate is a tool that you can use to construct template inputs for the various actions</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The templates generated by this tool are primarily for use with Toni Giorgino's VMD GUI.  It may be</a>
+<a name="38"><span class="lineNum">      38 </span>            : useful however to use this tool as a quick aid memoir.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : The following generates template input for the action DISTANCE.</a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : plumed gentemplate --action DISTANCE</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endverbatim</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : */</a>
+<a name="49"><span class="lineNum">      49 </span>            : //+ENDPLUMEDOC</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : class GenTemplate:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   public CLTool</a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit GenTemplate(const CLToolOptions&amp; co );</a>
+<a name="57"><span class="lineNum">      57 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          4 :     return &quot;print out a template input for a particular action&quot;;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      12508 : PLUMED_REGISTER_CLTOOL(GenTemplate,&quot;gentemplate&quot;)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       4168 : void GenTemplate::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--action&quot;,&quot;print the template for this particular action&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--list&quot;,false,&quot;print a list of the available actions&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--include-optional&quot;,false,&quot;also print optional modifiers&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       4168 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          4 : GenTemplate::GenTemplate(const CLToolOptions&amp; co ):</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          4 :   CLTool(co)</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : {</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          4 :   inputdata=commandline;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          4 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 : int GenTemplate::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::string action;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   bool list_templates=false;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   parseFlag(&quot;--list&quot;,list_templates);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   if(list_templates) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;actionRegister()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     return 0;</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   } else if(parse(&quot;--action&quot;,action)) {</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     bool include_optional;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     parseFlag(&quot;--include-optional&quot;,include_optional);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :     if( !actionRegister().printTemplate(action,include_optional) ) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :       error(&quot;there is no registered action named &quot; + action);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :       return 1;</a>
+<a name="93"><span class="lineNum">      93 </span>            :     }</a>
+<a name="94"><span class="lineNum">      94 </span>            :   } else return 1;</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   return 0;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : } // End of namespace</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Info.cpp.func-sort-c.html b/coverage/cltools/Info.cpp.func-sort-c.html
new file mode 100644
index 0000000000..bb0be83226
--- /dev/null
+++ b/coverage/cltools/Info.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Info.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Info.cpp<span style="font-size: 80%;"> (<a href="Info.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryMed">83.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Info.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#54">_ZNK4PLMD7cltools4Info11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#80">_ZN4PLMD7cltools4Info4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">1853</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#59">_ZN4PLMD7cltools12_GLOBAL__N_114InfoRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">1857</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#74">_ZN4PLMD7cltools4InfoC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">1857</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#59">_ZN4PLMD7cltools12_GLOBAL__N_114InfoRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#59">_ZN4PLMD7cltools12_GLOBAL__N_114InfoRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#61">_ZN4PLMD7cltools4Info16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Info.cpp.func.html b/coverage/cltools/Info.cpp.func.html
new file mode 100644
index 0000000000..202ea25ffc
--- /dev/null
+++ b/coverage/cltools/Info.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Info.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Info.cpp<span style="font-size: 80%;"> (<a href="Info.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryMed">83.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Info.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#59">_ZN4PLMD7cltools12_GLOBAL__N_114InfoRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">1857</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#59">_ZN4PLMD7cltools12_GLOBAL__N_114InfoRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#59">_ZN4PLMD7cltools12_GLOBAL__N_114InfoRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#61">_ZN4PLMD7cltools4Info16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#80">_ZN4PLMD7cltools4Info4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">1853</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#74">_ZN4PLMD7cltools4InfoC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">1857</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Info.cpp.gcov.html#54">_ZNK4PLMD7cltools4Info11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Info.cpp.gcov.html b/coverage/cltools/Info.cpp.gcov.html
new file mode 100644
index 0000000000..7cadf2a17b
--- /dev/null
+++ b/coverage/cltools/Info.cpp.gcov.html
@@ -0,0 +1,199 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Info.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Info.cpp<span style="font-size: 80%;"> (source / <a href="Info.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryMed">83.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdio&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace cltools {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC TOOLS info</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : This tool allows you to obtain information about your plumed version</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : You can specify the information you require using the following command line</a>
+<a name="37"><span class="lineNum">      37 </span>            : arguments</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The following command returns the root directory for your plumed distribution.</a>
+<a name="42"><span class="lineNum">      42 </span>            : \verbatim</a>
+<a name="43"><span class="lineNum">      43 </span>            : plumed info --root</a>
+<a name="44"><span class="lineNum">      44 </span>            : \endverbatim</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : */</a>
+<a name="47"><span class="lineNum">      47 </span>            : //+ENDPLUMEDOC</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : class Info:</a>
+<a name="50"><span class="lineNum">      50 </span>            :   public CLTool</a>
+<a name="51"><span class="lineNum">      51 </span>            : {</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="54"><span class="lineNum">      54 </span>            :   explicit Info(const CLToolOptions&amp; co );</a>
+<a name="55"><span class="lineNum">      55 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          4 :     return &quot;provide informations about plumed&quot;;</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   }</a>
+<a name="59"><span class="lineNum">      59 </span>            : };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      14361 : PLUMED_REGISTER_CLTOOL(Info,&quot;info&quot;)</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       4168 : void Info::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--configuration&quot;,false,&quot;prints the configuration file&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--root&quot;,false,&quot;print the location of the root directory for the plumed source&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--user-doc&quot;,false,&quot;print the location of user manual (html)&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--developer-doc&quot;,false,&quot;print the location of user manual (html)&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--version&quot;,false,&quot;print the version number&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--long-version&quot;,false,&quot;print the version number (long version)&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--git-version&quot;,false,&quot;print the version number (git version, if available)&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--include-dir&quot;,false,&quot;print the location of the include dir&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--soext&quot;,false,&quot;print the extension of shared libraries (so or dylib)&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       4168 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       1857 : Info::Info(const CLToolOptions&amp; co ):</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1857 :   CLTool(co)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       1857 :   inputdata=commandline;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       1857 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       1853 : int Info::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1853 :   bool printconfiguration; parseFlag(&quot;--configuration&quot;,printconfiguration);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1853 :   bool printroot; parseFlag(&quot;--root&quot;,printroot);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1853 :   bool printuserdoc; parseFlag(&quot;--user-doc&quot;,printuserdoc);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1853 :   bool printdeveloperdoc; parseFlag(&quot;--developer-doc&quot;,printdeveloperdoc);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1853 :   bool printversion; parseFlag(&quot;--version&quot;,printversion);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1853 :   bool printlongversion; parseFlag(&quot;--long-version&quot;,printlongversion);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1853 :   bool printgitversion; parseFlag(&quot;--git-version&quot;,printgitversion);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1853 :   bool printincludedir; parseFlag(&quot;--include-dir&quot;,printincludedir);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1853 :   bool printsoext; parseFlag(&quot;--soext&quot;,printsoext);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       2461 :   if(printroot) std::fprintf(out,&quot;%s\n&quot;,config::getPlumedRoot().c_str());</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1884 :   if(printconfiguration) std::fprintf(out,&quot;%s&quot;,config::getMakefile().c_str());</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1853 :   if(printincludedir) std::fprintf(out,&quot;%s\n&quot;,config::getPlumedIncludedir().c_str());</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1853 :   if(printuserdoc) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     std::string userdoc=config::getPlumedHtmldir()+&quot;/user-doc/html/index.html&quot;;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     FILE *ff=std::fopen(userdoc.c_str(),&quot;r&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :     // no exception here</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     if(ff) std::fclose(ff);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :     else userdoc=&quot;http://www.plumed.org/doc-v&quot; + config::getVersion() + &quot;/user-doc/html/index.html&quot;;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     std::fprintf(out,&quot;%s\n&quot;,userdoc.c_str());</a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1853 :   if(printdeveloperdoc) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     std::string developerdoc=config::getPlumedHtmldir()+&quot;/developer-doc/html/index.html&quot;;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     FILE *ff=std::fopen(developerdoc.c_str(),&quot;r&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     // no exception here</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     if(ff) std::fclose(ff);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     else developerdoc=&quot;http://www.plumed.org/doc-v&quot; + config::getVersion() + &quot;/developer-doc/html/index.html&quot;;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     std::fprintf(out,&quot;%s\n&quot;,developerdoc.c_str());</a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1853 :   if(printversion) std::fprintf(out,&quot;%s\n&quot;,config::getVersion().c_str());</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1853 :   if(printlongversion) std::fprintf(out,&quot;%s\n&quot;,config::getVersionLong().c_str());</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1853 :   if(printgitversion) std::fprintf(out,&quot;%s\n&quot;,config::getVersionGit().c_str());</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       3067 :   if(printsoext) std::fprintf(out,&quot;%s\n&quot;,config::getSoExt().c_str());</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       1853 :   return 0;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Manual.cpp.func-sort-c.html b/coverage/cltools/Manual.cpp.func-sort-c.html
new file mode 100644
index 0000000000..14ec564a4b
--- /dev/null
+++ b/coverage/cltools/Manual.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Manual.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Manual.cpp<span style="font-size: 80%;"> (<a href="Manual.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Manual.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#59">_ZNK4PLMD7cltools6Manual11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#79">_ZN4PLMD7cltools6Manual4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#64">_ZN4PLMD7cltools12_GLOBAL__N_116ManualRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#73">_ZN4PLMD7cltools6ManualC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#64">_ZN4PLMD7cltools12_GLOBAL__N_116ManualRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#64">_ZN4PLMD7cltools12_GLOBAL__N_116ManualRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#66">_ZN4PLMD7cltools6Manual16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Manual.cpp.func.html b/coverage/cltools/Manual.cpp.func.html
new file mode 100644
index 0000000000..7581a85a13
--- /dev/null
+++ b/coverage/cltools/Manual.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Manual.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Manual.cpp<span style="font-size: 80%;"> (<a href="Manual.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Manual.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#64">_ZN4PLMD7cltools12_GLOBAL__N_116ManualRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#64">_ZN4PLMD7cltools12_GLOBAL__N_116ManualRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#64">_ZN4PLMD7cltools12_GLOBAL__N_116ManualRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#66">_ZN4PLMD7cltools6Manual16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#79">_ZN4PLMD7cltools6Manual4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#73">_ZN4PLMD7cltools6ManualC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Manual.cpp.gcov.html#59">_ZNK4PLMD7cltools6Manual11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/Manual.cpp.gcov.html b/coverage/cltools/Manual.cpp.gcov.html
new file mode 100644
index 0000000000..95ec132e7a
--- /dev/null
+++ b/coverage/cltools/Manual.cpp.gcov.html
@@ -0,0 +1,177 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/Manual.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - Manual.cpp<span style="font-size: 80%;"> (source / <a href="Manual.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace cltools {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC TOOLS manual</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : manual is a tool that you can use to construct the manual page for</a>
+<a name="37"><span class="lineNum">      37 </span>            : a particular action</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The manual constructed by this action is in html. In all probability you will never need to use this</a>
+<a name="40"><span class="lineNum">      40 </span>            : tool. However, it is used within the scripts that generate the html manual for PLUMED.  If you need to use this</a>
+<a name="41"><span class="lineNum">      41 </span>            : tool outside those scripts the input is specified using the following command line arguments.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The following generates the html manual for the action DISTANCE.</a>
+<a name="46"><span class="lineNum">      46 </span>            : \verbatim</a>
+<a name="47"><span class="lineNum">      47 </span>            : plumed manual --action DISTANCE</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endverbatim</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : */</a>
+<a name="52"><span class="lineNum">      52 </span>            : //+ENDPLUMEDOC</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : class Manual:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   public CLTool</a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="59"><span class="lineNum">      59 </span>            :   explicit Manual(const CLToolOptions&amp; co );</a>
+<a name="60"><span class="lineNum">      60 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          4 :     return &quot;print out a description of the keywords for an action in html&quot;;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   }</a>
+<a name="64"><span class="lineNum">      64 </span>            : };</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      12801 : PLUMED_REGISTER_CLTOOL(Manual,&quot;manual&quot;)</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       4168 : void Manual::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--action&quot;,&quot;print the manual for this particular action&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--vim&quot;,false,&quot;print the keywords in vim syntax&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--spelling&quot;,false,&quot;print a list of the keywords and component names for the spell checker&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       4168 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        297 : Manual::Manual(const CLToolOptions&amp; co ):</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        297 :   CLTool(co)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        297 :   inputdata=commandline;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        297 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        293 : int Manual::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::string action;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        586 :   if( !parse(&quot;--action&quot;,action) ) return 1;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        293 :   std::cerr&lt;&lt;&quot;LIST OF DOCUMENTED ACTIONS:\n&quot;;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        293 :   std::cerr&lt;&lt;actionRegister()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        293 :   std::cerr&lt;&lt;&quot;LIST OF DOCUMENTED COMMAND LINE TOOLS:\n&quot;;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        293 :   std::cerr&lt;&lt;cltoolRegister()&lt;&lt;&quot;\n\n&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        293 :   bool vimout; parseFlag(&quot;--vim&quot;,vimout);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        293 :   bool spellout; parseFlag(&quot;--spelling&quot;,spellout);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        293 :   if( vimout &amp;&amp; spellout ) error(&quot;can only use one of --vim and --spelling at a time&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        293 :   if( !actionRegister().printManual(action,vimout,spellout) &amp;&amp; !cltoolRegister().printManual(action,spellout) ) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          1 :     std::fprintf(stderr,&quot;specified action is not registered\n&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :     return 1;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   return 0;</a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : } // End of namespace</a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/PdbRenumber.cpp.func-sort-c.html b/coverage/cltools/PdbRenumber.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c4ba8da791
--- /dev/null
+++ b/coverage/cltools/PdbRenumber.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/PdbRenumber.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - PdbRenumber.cpp<span style="font-size: 80%;"> (<a href="PdbRenumber.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PdbRenumber.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#126">_ZN4PLMD7cltools11PdbRenumber4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#105">_ZNK4PLMD7cltools11PdbRenumber11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#120">_ZN4PLMD7cltools11PdbRenumberC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#110">_ZN4PLMD7cltools12_GLOBAL__N_121PdbRenumberRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#112">_ZN4PLMD7cltools11PdbRenumber16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#110">_ZN4PLMD7cltools12_GLOBAL__N_121PdbRenumberRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#110">_ZN4PLMD7cltools12_GLOBAL__N_121PdbRenumberRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/PdbRenumber.cpp.func.html b/coverage/cltools/PdbRenumber.cpp.func.html
new file mode 100644
index 0000000000..7f2b9dd37c
--- /dev/null
+++ b/coverage/cltools/PdbRenumber.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/PdbRenumber.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - PdbRenumber.cpp<span style="font-size: 80%;"> (<a href="PdbRenumber.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PdbRenumber.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#112">_ZN4PLMD7cltools11PdbRenumber16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#126">_ZN4PLMD7cltools11PdbRenumber4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#120">_ZN4PLMD7cltools11PdbRenumberC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#110">_ZN4PLMD7cltools12_GLOBAL__N_121PdbRenumberRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#110">_ZN4PLMD7cltools12_GLOBAL__N_121PdbRenumberRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#110">_ZN4PLMD7cltools12_GLOBAL__N_121PdbRenumberRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PdbRenumber.cpp.gcov.html#105">_ZNK4PLMD7cltools11PdbRenumber11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/PdbRenumber.cpp.gcov.html b/coverage/cltools/PdbRenumber.cpp.gcov.html
new file mode 100644
index 0000000000..aef86d16a1
--- /dev/null
+++ b/coverage/cltools/PdbRenumber.cpp.gcov.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/PdbRenumber.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - PdbRenumber.cpp<span style="font-size: 80%;"> (source / <a href="PdbRenumber.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/h36.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdio&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;string&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;vector&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;array&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;limits&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace cltools {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC TOOLS pdbrenumber</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Modify atom numbers in a PDB, possibly using hybrid-36 coding.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : When reading a PDB files, PLUMED honors the serial number of each atom.</a>
+<a name="43"><span class="lineNum">      43 </span>            : This command can be used to process a PDB file changing the atom serial numbers.</a>
+<a name="44"><span class="lineNum">      44 </span>            : Notice that the resulting list might have gaps. It is however fundamental</a>
+<a name="45"><span class="lineNum">      45 </span>            : that atom numbers correspond to those used within the MD code.</a>
+<a name="46"><span class="lineNum">      46 </span>            : Importantly, if the serial number of an atom is greater than 99999, it is</a>
+<a name="47"><span class="lineNum">      47 </span>            : written in hybrid-36 notation (see \ref pdbreader).</a>
+<a name="48"><span class="lineNum">      48 </span>            : The main use of \ref pdbrenumber is thus that of producing files where atoms</a>
+<a name="49"><span class="lineNum">      49 </span>            : are numbered using hybrid-36 convention.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The output PDB file is identical to the input PDB file, except for the atom number</a>
+<a name="52"><span class="lineNum">      52 </span>            : field.</a>
+<a name="53"><span class="lineNum">      53 </span>            : The rest of the line is written unchanged</a>
+<a name="54"><span class="lineNum">      54 </span>            : to the output file, even if it is incorrectly formatted. Residue numbers are not touched,</a>
+<a name="55"><span class="lineNum">      55 </span>            : and atom numbers in the input file are ignored.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : By default, \ref pdbreader  just sets the numbers as progressive starting from 1.</a>
+<a name="61"><span class="lineNum">      61 </span>            : For instance the following command:</a>
+<a name="62"><span class="lineNum">      62 </span>            : \verbatim</a>
+<a name="63"><span class="lineNum">      63 </span>            : &gt; plumed pdbrenumber --ipdb input.pdb --opdb output.pdb</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endverbatim</a>
+<a name="65"><span class="lineNum">      65 </span>            : will copy file `input.pdb` to `output.pdb` replacing all the serial atoms with</a>
+<a name="66"><span class="lineNum">      66 </span>            : increasing numbers starting from one. Atoms that have an index that is greater than 99999 will be written</a>
+<a name="67"><span class="lineNum">      67 </span>            : in the output PDB file in hybrid-36 code.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : It is possible to set a different serial number for the first atom, letting the</a>
+<a name="70"><span class="lineNum">      70 </span>            : following ones grow by one at each line. Here for instance the first atom</a>
+<a name="71"><span class="lineNum">      71 </span>            : will be assigned serial 1000, the second serial 1001, etc:</a>
+<a name="72"><span class="lineNum">      72 </span>            : \verbatim</a>
+<a name="73"><span class="lineNum">      73 </span>            : &gt; plumed pdbrenumber --ipdb input.pdb --opdb output.pdb --firstatomnumber 1000</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endverbatim</a>
+<a name="75"><span class="lineNum">      75 </span>            : If the first atom number is &gt;99999, it should be given as a decimal number (not in hybrid-36 code).</a>
+<a name="76"><span class="lineNum">      76 </span>            : However, numbers &gt;99999 in the output PDB file will be written in hybrid-36 code.</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : As an alternative, one can provide a list of atoms as one per line in an auxiliary file.</a>
+<a name="79"><span class="lineNum">      79 </span>            : \verbatim</a>
+<a name="80"><span class="lineNum">      80 </span>            : &gt; plumed pdbrenumber --ipdb input.pdb --opdb output.pdb --atomnumbers list.txt</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endverbatim</a>
+<a name="82"><span class="lineNum">      82 </span>            : The `list.txt` file might be something like this</a>
+<a name="83"><span class="lineNum">      83 </span>            : \verbatim</a>
+<a name="84"><span class="lineNum">      84 </span>            : 120000</a>
+<a name="85"><span class="lineNum">      85 </span>            : 120001</a>
+<a name="86"><span class="lineNum">      86 </span>            : 120002</a>
+<a name="87"><span class="lineNum">      87 </span>            : 1</a>
+<a name="88"><span class="lineNum">      88 </span>            : 2</a>
+<a name="89"><span class="lineNum">      89 </span>            : 3</a>
+<a name="90"><span class="lineNum">      90 </span>            : \endverbatim</a>
+<a name="91"><span class="lineNum">      91 </span>            : Numbers &gt;99999 in the list should be provided as decimal numbers (not in hybrid-36 code).</a>
+<a name="92"><span class="lineNum">      92 </span>            : However, numbers &gt;99999 in the output PDB file will be written in hybrid-36 code.</a>
+<a name="93"><span class="lineNum">      93 </span>            : Notice that there should be at least enough lines in `list.txt` as many atoms in the PDB file.</a>
+<a name="94"><span class="lineNum">      94 </span>            : Additional lines in `list.txt` will just be ignored.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : */</a>
+<a name="98"><span class="lineNum">      98 </span>            : //+ENDPLUMEDOC</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : class PdbRenumber:</a>
+<a name="101"><span class="lineNum">     101 </span>            :   public CLTool</a>
+<a name="102"><span class="lineNum">     102 </span>            : {</a>
+<a name="103"><span class="lineNum">     103 </span>            : public:</a>
+<a name="104"><span class="lineNum">     104 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="105"><span class="lineNum">     105 </span>            :   explicit PdbRenumber(const CLToolOptions&amp; co );</a>
+<a name="106"><span class="lineNum">     106 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          4 :     return &quot;Modify atom numbers in a PDB, possibly using hybrid-36 coding&quot;;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span>            : };</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      12511 : PLUMED_REGISTER_CLTOOL(PdbRenumber,&quot;pdbrenumber&quot;)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       4168 : void PdbRenumber::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--ipdb&quot;,&quot;specify the name of the input PDB file&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--opdb&quot;,&quot;specify the name of the output PDB file&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--firstatomnumber&quot;,&quot;specify the desired serial number of the first atom of the output file&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--atomnumbers&quot;,&quot;specify the desired serial numbers of the atoms of the output file using a separate list&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       4168 : }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          7 : PdbRenumber::PdbRenumber(const CLToolOptions&amp; co ):</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          7 :   CLTool(co)</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          7 :   inputdata=commandline;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          7 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          3 : int PdbRenumber::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :   std::string ipdb;</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          6 :   parse(&quot;--ipdb&quot;,ipdb);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::string opdb;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          3 :   parse(&quot;--opdb&quot;,opdb);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          3 :   unsigned iat=0;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :   parse(&quot;--firstatomnumber&quot;,iat);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   std::string atomnumbers;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          6 :   parse(&quot;--atomnumbers&quot;,atomnumbers);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          3 :   plumed_assert(ipdb.length()&gt;0) &lt;&lt; &quot;please specify the input PDB with --ipdb&quot;;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 :   plumed_assert(opdb.length()&gt;0) &lt;&lt; &quot;please specify the onput PDB with --opdb&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::fprintf(out,&quot;  with input PDB: %s\n&quot;,ipdb.c_str());</a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::fprintf(out,&quot;  with output PDB: %s\n&quot;,opdb.c_str());</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;unsigned&gt; serials;</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          3 :   if(atomnumbers.length()&gt;0) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :     plumed_assert(iat==0) &lt;&lt; &quot;it is not possible to use both --atomnumbers and --firstatomnumber&quot;;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     std::fprintf(out,&quot;  reading atom numbers from file %s\n&quot;,atomnumbers.c_str());</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :     IFile ifile;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :     ifile.open(atomnumbers);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     std::string line;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          7 :     while(ifile.getline(line)) {</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :       int i;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          6 :       Tools::convert(line,i);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          6 :       serials.push_back(i);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :   } else {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :     if(iat==0) iat=1;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          2 :     std::fprintf(out,&quot;  with atoms starting from %u\n&quot;,iat);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   IFile ifile;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          3 :   ifile.open(ipdb);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          3 :   OFile ofile;</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          3 :   ofile.open(opdb);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::string line;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     100112 :   while(ifile.getline(line)) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     100109 :     std::string record=line.substr(0,6);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     100109 :     Tools::trim(record);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     100109 :     if(record==&quot;ATOM&quot; || record==&quot;HETATM&quot;) {</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :       std::array&lt;char,6&gt; at;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     100109 :       unsigned ii=iat;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     100109 :       if(serials.size()&gt;0) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          6 :         plumed_assert(iat&lt;serials.size()) &lt;&lt; &quot;there are more atoms in the PDB than serials in the file&quot;;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          6 :         ii=serials[iat];</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :       }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">     100109 :       const char* msg = h36::hy36encode(5,ii,&amp;at[0]);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     100109 :       plumed_assert(msg==nullptr) &lt;&lt; msg;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">     100109 :       at[5]=0;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     200218 :       ofile &lt;&lt; line.substr(0,6) &lt;&lt; &amp;at[0] &lt;&lt; line.substr(11) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">     100109 :       iat++;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     } else {</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :       if(record==&quot;END&quot; || record==&quot;ENDMDL&quot;) iat=0;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :       ofile &lt;&lt; line &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     }</a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          3 :   return 0;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          3 : }</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : } // End of namespace</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/SimpleMD.cpp.func-sort-c.html b/coverage/cltools/SimpleMD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5e2ab80136
--- /dev/null
+++ b/coverage/cltools/SimpleMD.cpp.func-sort-c.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/SimpleMD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - SimpleMD.cpp<span style="font-size: 80%;"> (<a href="SimpleMD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SimpleMD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#82">_ZNK4PLMD7cltools8SimpleMD11descriptionB5cxx11Ev</a></td>
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+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#298">_ZN4PLMD7cltools8SimpleMD14compute_engkinEiRKSt6vectorIdSaIdEERKS2_INS_13VectorGenericILj3EEESaIS8_EERd</a></td>
+              <td class="coverFnHi">5700</td>
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+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#258">_ZN4PLMD7cltools8SimpleMD14compute_forcesEiddRKSt6vectorINS_13VectorGenericILj3EEESaIS4_EEPKddRKS2_IS2_IiSaIiEESaISC_EERS6_Rd</a></td>
+              <td class="coverFnHi">5709</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#308">_ZN4PLMD7cltools8SimpleMD10thermostatEiiRKSt6vectorIdSaIdEEdddRS2_INS_13VectorGenericILj3EEESaIS8_EERdRNS_6RandomE</a></td>
+              <td class="coverFnHi">11400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#221">_ZN4PLMD7cltools8SimpleMD3pbcEPKdRKNS_13VectorGenericILj3EEERS5_</a></td>
+              <td class="coverFnHi">9982883</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/SimpleMD.cpp.func.html b/coverage/cltools/SimpleMD.cpp.func.html
new file mode 100644
index 0000000000..4212de8a70
--- /dev/null
+++ b/coverage/cltools/SimpleMD.cpp.func.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/SimpleMD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - SimpleMD.cpp<span style="font-size: 80%;"> (<a href="SimpleMD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SimpleMD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#599">_ZN4PLMD7cltools12_GLOBAL__N_118SimpleMDRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#599">_ZN4PLMD7cltools12_GLOBAL__N_118SimpleMDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#599">_ZN4PLMD7cltools12_GLOBAL__N_118SimpleMDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
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+              <td class="coverFnHi">5700</td>
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+            </tr>
+    <tr>
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+              <td class="coverFnHi">11400</td>
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+              <td class="coverFnHi">458</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#298">_ZN4PLMD7cltools8SimpleMD14compute_engkinEiRKSt6vectorIdSaIdEERKS2_INS_13VectorGenericILj3EEESaIS8_EERd</a></td>
+              <td class="coverFnHi">5700</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#258">_ZN4PLMD7cltools8SimpleMD14compute_forcesEiddRKSt6vectorINS_13VectorGenericILj3EEESaIS4_EEPKddRKS2_IS2_IiSaIiEESaISC_EERS6_Rd</a></td>
+              <td class="coverFnHi">5709</td>
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+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#194">_ZN4PLMD7cltools8SimpleMD14read_positionsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorINS_13VectorGenericILj3EEESaISC_EEPd</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#324">_ZN4PLMD7cltools8SimpleMD15write_positionsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRKSt6vectorINS_13VectorGenericILj3EEESaISC_EEPKdb</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#94">_ZN4PLMD7cltools8SimpleMD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#371">_ZN4PLMD7cltools8SimpleMD16write_statisticsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEidiiddd</a></td>
+              <td class="coverFnHi">174</td>
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+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#215">_ZN4PLMD7cltools8SimpleMD20randomize_velocitiesEiidRKSt6vectorIdSaIdEERS2_INS_13VectorGenericILj3EEESaIS8_EERNS_6RandomE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#221">_ZN4PLMD7cltools8SimpleMD3pbcEPKdRKNS_13VectorGenericILj3EEERS5_</a></td>
+              <td class="coverFnHi">9982883</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#392">_ZN4PLMD7cltools8SimpleMD4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#112">_ZN4PLMD7cltools8SimpleMDC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleMD.cpp.gcov.html#82">_ZNK4PLMD7cltools8SimpleMD11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/SimpleMD.cpp.gcov.html b/coverage/cltools/SimpleMD.cpp.gcov.html
new file mode 100644
index 0000000000..959bfcfdd3
--- /dev/null
+++ b/coverage/cltools/SimpleMD.cpp.gcov.html
@@ -0,0 +1,684 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/SimpleMD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - SimpleMD.cpp<span style="font-size: 80%;"> (source / <a href="SimpleMD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdio&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cmath&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;vector&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;memory&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace cltools {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : //+PLUMEDOC TOOLS simplemd</a>
+<a name="38"><span class="lineNum">      38 </span>            : /*</a>
+<a name="39"><span class="lineNum">      39 </span>            : simplemd allows one to do molecular dynamics on systems of Lennard-Jones atoms.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The input to simplemd is specified in an input file. Configurations are input and</a>
+<a name="42"><span class="lineNum">      42 </span>            : output in xyz format. The input file should contain one directive per line.</a>
+<a name="43"><span class="lineNum">      43 </span>            : The directives available are as follows:</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : You run an MD simulation using simplemd with the following command:</a>
+<a name="48"><span class="lineNum">      48 </span>            : \verbatim</a>
+<a name="49"><span class="lineNum">      49 </span>            : plumed simplemd &lt; in</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endverbatim</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following is an example of an input file for a simplemd calculation. This file</a>
+<a name="53"><span class="lineNum">      53 </span>            : instructs simplemd to do 50 steps of MD at a temperature of 0.722</a>
+<a name="54"><span class="lineNum">      54 </span>            : \verbatim</a>
+<a name="55"><span class="lineNum">      55 </span>            : inputfile input.xyz</a>
+<a name="56"><span class="lineNum">      56 </span>            : outputfile output.xyz</a>
+<a name="57"><span class="lineNum">      57 </span>            : temperature 0.722</a>
+<a name="58"><span class="lineNum">      58 </span>            : tstep 0.005</a>
+<a name="59"><span class="lineNum">      59 </span>            : friction 1</a>
+<a name="60"><span class="lineNum">      60 </span>            : forcecutoff 2.5</a>
+<a name="61"><span class="lineNum">      61 </span>            : listcutoff  3.0</a>
+<a name="62"><span class="lineNum">      62 </span>            : nstep 50</a>
+<a name="63"><span class="lineNum">      63 </span>            : nconfig 10 trajectory.xyz</a>
+<a name="64"><span class="lineNum">      64 </span>            : nstat   10 energies.dat</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endverbatim</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : If you run the following a description of all the directives that can be used in the</a>
+<a name="68"><span class="lineNum">      68 </span>            : input file will be output.</a>
+<a name="69"><span class="lineNum">      69 </span>            : \verbatim</a>
+<a name="70"><span class="lineNum">      70 </span>            : plumed simplemd --help</a>
+<a name="71"><span class="lineNum">      71 </span>            : \endverbatim</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : */</a>
+<a name="74"><span class="lineNum">      74 </span>            : //+ENDPLUMEDOC</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : // simple static function to close a file</a>
+<a name="77"><span class="lineNum">      77 </span>            : // defined once here since it's used in many places in this file</a>
+<a name="78"><span class="lineNum">      78 </span>            : // in addition, this seems the only way to use it in the write_statistics_fp_deleter member</a>
+<a name="79"><span class="lineNum">      79 </span>            : static void (*deleter)(FILE* f) = [](FILE* f) { if(f) std::fclose(f); };</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class SimpleMD:</a>
+<a name="82"><span class="lineNum">      82 </span>            :   public PLMD::CLTool</a>
+<a name="83"><span class="lineNum">      83 </span>            : {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :     return &quot;run lj code&quot;;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :   bool write_positions_first;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   bool write_statistics_first;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   int write_statistics_last_time_reopened;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   FILE* write_statistics_fp;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; write_statistics_fp_deleter{nullptr,deleter};</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : public:</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       4168 :   static void registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;nstep&quot;,&quot;The number of steps of dynamics you want to run&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;temperature&quot;,&quot;NVE&quot;,&quot;the temperature at which you wish to run the simulation in LJ units&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;friction&quot;,&quot;off&quot;,&quot;The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;tstep&quot;,&quot;0.005&quot;,&quot;the integration timestep in LJ units&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;epsilon&quot;,&quot;1.0&quot;,&quot;LJ parameter&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;sigma&quot;,&quot;1.0&quot;,&quot;LJ parameter&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;inputfile&quot;,&quot;An xyz file containing the initial configuration of the system&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;forcecutoff&quot;,&quot;2.5&quot;,&quot;&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;listcutoff&quot;,&quot;3.0&quot;,&quot;&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;outputfile&quot;,&quot;An output xyz file containing the final configuration of the system&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;nconfig&quot;,&quot;10&quot;,&quot;The frequency with which to write configurations to the trajectory file followed by the name of the trajectory file&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;nstat&quot;,&quot;1&quot;,&quot;The frequency with which to write the statistics to the statistics file followed by the name of the statistics file&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;idum&quot;,&quot;0&quot;,&quot;The random number seed&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;ndim&quot;,&quot;3&quot;,&quot;The dimensionality of the system (some interesting LJ clusters are two dimensional)&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;wrapatoms&quot;,&quot;false&quot;,&quot;If true, atomic coordinates are written wrapped in minimal cell&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       4168 :   }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         13 :   explicit SimpleMD( const CLToolOptions&amp; co ) :</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     CLTool(co),</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         13 :     write_positions_first(true),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         13 :     write_statistics_first(true),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         13 :     write_statistics_last_time_reopened(0),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         13 :     write_statistics_fp(NULL)</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         13 :     inputdata=ifile;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         13 :   }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : private:</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   void</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          9 :   read_input(double&amp; temperature,</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :              double&amp; tstep,</a>
+<a name="129"><span class="lineNum">     129 </span>            :              double&amp; friction,</a>
+<a name="130"><span class="lineNum">     130 </span>            :              double&amp; forcecutoff,</a>
+<a name="131"><span class="lineNum">     131 </span>            :              double&amp; listcutoff,</a>
+<a name="132"><span class="lineNum">     132 </span>            :              int&amp;    nstep,</a>
+<a name="133"><span class="lineNum">     133 </span>            :              int&amp;    nconfig,</a>
+<a name="134"><span class="lineNum">     134 </span>            :              int&amp;    nstat,</a>
+<a name="135"><span class="lineNum">     135 </span>            :              bool&amp;   wrapatoms,</a>
+<a name="136"><span class="lineNum">     136 </span>            :              std::string&amp; inputfile,</a>
+<a name="137"><span class="lineNum">     137 </span>            :              std::string&amp; outputfile,</a>
+<a name="138"><span class="lineNum">     138 </span>            :              std::string&amp; trajfile,</a>
+<a name="139"><span class="lineNum">     139 </span>            :              std::string&amp; statfile,</a>
+<a name="140"><span class="lineNum">     140 </span>            :              int&amp;    ndim,</a>
+<a name="141"><span class="lineNum">     141 </span>            :              int&amp;    idum,</a>
+<a name="142"><span class="lineNum">     142 </span>            :              double&amp; epsilon,</a>
+<a name="143"><span class="lineNum">     143 </span>            :              double&amp; sigma)</a>
+<a name="144"><span class="lineNum">     144 </span>            :   {</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :     // Read everything from input file</a>
+<a name="147"><span class="lineNum">     147 </span>            :     char buffer1[256];</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         18 :     std::string tempstr; parse(&quot;temperature&quot;,tempstr);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          9 :     if( tempstr!=&quot;NVE&quot; ) Tools::convert(tempstr,temperature);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         18 :     parse(&quot;tstep&quot;,tstep);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         18 :     std::string frictionstr; parse(&quot;friction&quot;,frictionstr);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          9 :     if( tempstr!=&quot;NVE&quot; ) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          9 :       if(frictionstr==&quot;off&quot;) error(&quot;Specify friction for thermostat&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          9 :       Tools::convert(frictionstr,friction);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          9 :     parse(&quot;forcecutoff&quot;,forcecutoff);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          9 :     parse(&quot;listcutoff&quot;,listcutoff);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          9 :     parse(&quot;nstep&quot;,nstep);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          9 :     parse(&quot;idum&quot;,idum);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          9 :     parse(&quot;epsilon&quot;,epsilon);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          9 :     parse(&quot;sigma&quot;,sigma);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :     // Read in stuff with sanity checks</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         18 :     parse(&quot;inputfile&quot;,inputfile);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          9 :     if(inputfile.length()==0) error(&quot;Specify input file&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         18 :     parse(&quot;outputfile&quot;,outputfile);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          9 :     if(outputfile.length()==0) error(&quot;Specify output file&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         18 :     std::string nconfstr; parse(&quot;nconfig&quot;,nconfstr);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          9 :     std::sscanf(nconfstr.c_str(),&quot;%100d %255s&quot;,&amp;nconfig,buffer1);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     trajfile=buffer1;</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          9 :     if(trajfile.length()==0) error(&quot;Specify traj file&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         18 :     std::string nstatstr; parse(&quot;nstat&quot;,nstatstr);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 :     std::sscanf(nstatstr.c_str(),&quot;%100d %255s&quot;,&amp;nstat,buffer1);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     statfile=buffer1;</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          9 :     if(statfile.length()==0) error(&quot;Specify stat file&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          9 :     parse(&quot;ndim&quot;,ndim);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          9 :     if(ndim&lt;1 || ndim&gt;3) error(&quot;ndim should be 1,2 or 3&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     std::string w;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          9 :     parse(&quot;wrapatoms&quot;,w);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          9 :     wrapatoms=false;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          9 :     if(w.length()&gt;0 &amp;&amp; (w[0]=='T' || w[0]=='t')) wrapatoms=true;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          9 :   }</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          9 :   void read_natoms(const std::string &amp; inputfile,int &amp; natoms) {</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : // read the number of atoms in file &quot;input.xyz&quot;</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          9 :     FILE* fp=std::fopen(inputfile.c_str(),&quot;r&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          9 :     if(!fp) error(std::string(&quot;file &quot;) + inputfile + std::string(&quot; not found&quot;));</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : // call fclose when fp goes out of scope</a>
+<a name="190"><span class="lineNum">     190 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          9 :     int ret=std::fscanf(fp,&quot;%1000d&quot;,&amp;natoms);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          9 :     if(ret==0) plumed_error() &lt;&lt;&quot;Error reading number of atoms from file &quot;&lt;&lt;inputfile;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          9 :   }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          9 :   void read_positions(const std::string&amp; inputfile,int natoms,std::vector&lt;Vector&gt;&amp; positions,double cell[3]) {</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : // read positions and cell from a file called inputfile</a>
+<a name="198"><span class="lineNum">     198 </span>            : // natoms (input variable) and number of atoms in the file should be consistent</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          9 :     FILE* fp=std::fopen(inputfile.c_str(),&quot;r&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          9 :     if(!fp) error(std::string(&quot;file &quot;) + inputfile + std::string(&quot; not found&quot;));</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : // call fclose when fp goes out of scope</a>
+<a name="202"><span class="lineNum">     202 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :     char buffer[256];</a>
+<a name="205"><span class="lineNum">     205 </span>            :     char atomname[256];</a>
+<a name="206"><span class="lineNum">     206 </span>            :     char* cret=fgets(buffer,256,fp);</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          9 :     if(cret==nullptr) plumed_error() &lt;&lt;&quot;Error reading buffer from file &quot;&lt;&lt;inputfile;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          9 :     int ret=std::fscanf(fp,&quot;%1000lf %1000lf %1000lf&quot;,&amp;cell[0],&amp;cell[1],&amp;cell[2]);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          9 :     if(ret==0) plumed_error() &lt;&lt;&quot;Error reading cell line from file &quot;&lt;&lt;inputfile;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        779 :     for(int i=0; i&lt;natoms; i++) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        770 :       ret=std::fscanf(fp,&quot;%255s %1000lf %1000lf %1000lf&quot;,atomname,&amp;positions[i][0],&amp;positions[i][1],&amp;positions[i][2]);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : // note: atomname is read but not used</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        770 :       if(ret==0) plumed_error() &lt;&lt;&quot;Error reading atom line from file &quot;&lt;&lt;inputfile;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :     }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          9 :   }</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          9 :   void randomize_velocities(const int natoms,const int ndim,const double temperature,const std::vector&lt;double&gt;&amp;masses,std::vector&lt;Vector&gt;&amp; velocities,Random&amp;random) {</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : // randomize the velocities according to the temperature</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       3075 :     for(int iatom=0; iatom&lt;natoms; iatom++) for(int i=0; i&lt;ndim; i++)</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       2296 :         velocities[iatom][i]=std::sqrt(temperature/masses[iatom])*random.Gaussian();</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          9 :   }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">    9982883 :   void pbc(const double cell[3],const Vector &amp; vin,Vector &amp; vout) {</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : // apply periodic boundary condition to a vector</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">   39931532 :     for(int i=0; i&lt;3; i++) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">   29948649 :       vout[i]=vin[i]-std::floor(vin[i]/cell[i]+0.5)*cell[i];</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">    9982883 :   }</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       5700 :   void check_list(const int natoms,const std::vector&lt;Vector&gt;&amp; positions,const std::vector&lt;Vector&gt;&amp;positions0,const double listcutoff,</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :                   const double forcecutoff,bool &amp; recompute)</a>
+<a name="232"><span class="lineNum">     232 </span>            :   {</a>
+<a name="233"><span class="lineNum">     233 </span>            : // check if the neighbour list have to be recomputed</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       5700 :     recompute=false;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       5700 :     auto delta2=(0.5*(listcutoff-forcecutoff))*(0.5*(listcutoff-forcecutoff));</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : // if ANY atom moved more than half of the skin thickness, recompute is set to .true.</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">     217300 :     for(int iatom=0; iatom&lt;natoms; iatom++) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">     211600 :       if(modulo2(positions[iatom]-positions0[iatom])&gt;delta2) recompute=true;</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       5700 :   }</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        458 :   void compute_list(const int natoms,const std::vector&lt;Vector&gt;&amp; positions,const double cell[3],const double listcutoff,</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :                     std::vector&lt;std::vector&lt;int&gt; &gt;&amp; list) {</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        458 :     double listcutoff2=listcutoff*listcutoff; // squared list cutoff</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        458 :     list.assign(natoms,std::vector&lt;int&gt;());</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        458 :     #   pragma omp parallel for num_threads(OpenMP::getNumThreads()) schedule(static,1)</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :     for(int iatom=0; iatom&lt;natoms-1; iatom++) {</a>
+<a name="249"><span class="lineNum">     249 </span>            :       for(int jatom=iatom+1; jatom&lt;natoms; jatom++) {</a>
+<a name="250"><span class="lineNum">     250 </span>            :         auto distance=positions[iatom]-positions[jatom];</a>
+<a name="251"><span class="lineNum">     251 </span>            :         Vector distance_pbc; // minimum-image distance of the two atoms</a>
+<a name="252"><span class="lineNum">     252 </span>            :         pbc(cell,distance,distance_pbc);</a>
+<a name="253"><span class="lineNum">     253 </span>            : // if the interparticle distance is larger than the cutoff, skip</a>
+<a name="254"><span class="lineNum">     254 </span>            :         if(modulo2(distance_pbc)&gt;listcutoff2)continue;</a>
+<a name="255"><span class="lineNum">     255 </span>            :         list[iatom].push_back(jatom);</a>
+<a name="256"><span class="lineNum">     256 </span>            :       }</a>
+<a name="257"><span class="lineNum">     257 </span>            :     }</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        458 :   }</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       5709 :   void compute_forces(const int natoms,double epsilon, double sigma,const std::vector&lt;Vector&gt;&amp; positions,const double cell[3],</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :                       double forcecutoff,const std::vector&lt;std::vector&lt;int&gt; &gt;&amp; list,std::vector&lt;Vector&gt;&amp; forces,double &amp; engconf)</a>
+<a name="262"><span class="lineNum">     262 </span>            :   {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       5709 :     double forcecutoff2=forcecutoff*forcecutoff; // squared force cutoff</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       5709 :     engconf=0.0;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     double engconf_tmp=0.0; // separate variable for reduction (gcc 4.8 does not make reductions on references)</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">     855189 :     for(int i=0; i&lt;natoms; i++)for(int k=0; k&lt;3; k++) forces[i][k]=0.0;</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       5709 :     double engcorrection=4.0*epsilon*(1.0/std::pow(forcecutoff2/(sigma*sigma),6.0)-1.0/std::pow(forcecutoff2/(sigma*sigma),3)); // energy necessary shift the potential avoiding discontinuities</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       5709 :     #   pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     {</a>
+<a name="270"><span class="lineNum">     270 </span>            :       std::vector&lt;Vector&gt; omp_forces(forces.size());</a>
+<a name="271"><span class="lineNum">     271 </span>            :       #pragma omp for reduction(+:engconf_tmp) schedule(static,1) nowait</a>
+<a name="272"><span class="lineNum">     272 </span>            :       for(int iatom=0; iatom&lt;natoms-1; iatom++) {</a>
+<a name="273"><span class="lineNum">     273 </span>            :         for(int jlist=0; jlist&lt;list[iatom].size(); jlist++) {</a>
+<a name="274"><span class="lineNum">     274 </span>            :           const int jatom=list[iatom][jlist];</a>
+<a name="275"><span class="lineNum">     275 </span>            :           auto distance=positions[iatom]-positions[jatom];</a>
+<a name="276"><span class="lineNum">     276 </span>            :           Vector distance_pbc;    // minimum-image distance of the two atoms</a>
+<a name="277"><span class="lineNum">     277 </span>            :           pbc(cell,distance,distance_pbc);</a>
+<a name="278"><span class="lineNum">     278 </span>            :           auto distance_pbc2=modulo2(distance_pbc);   // squared minimum-image distance</a>
+<a name="279"><span class="lineNum">     279 </span>            : // if the interparticle distance is larger than the cutoff, skip</a>
+<a name="280"><span class="lineNum">     280 </span>            :           if(distance_pbc2&gt;forcecutoff2) continue;</a>
+<a name="281"><span class="lineNum">     281 </span>            :           auto distance_pbcm2=sigma*sigma/distance_pbc2;</a>
+<a name="282"><span class="lineNum">     282 </span>            :           auto distance_pbcm6=distance_pbcm2*distance_pbcm2*distance_pbcm2;</a>
+<a name="283"><span class="lineNum">     283 </span>            :           auto distance_pbcm8=distance_pbcm6*distance_pbcm2;</a>
+<a name="284"><span class="lineNum">     284 </span>            :           auto distance_pbcm12=distance_pbcm6*distance_pbcm6;</a>
+<a name="285"><span class="lineNum">     285 </span>            :           auto distance_pbcm14=distance_pbcm12*distance_pbcm2;</a>
+<a name="286"><span class="lineNum">     286 </span>            :           engconf_tmp+=4.0*epsilon*(distance_pbcm12 - distance_pbcm6) - engcorrection;</a>
+<a name="287"><span class="lineNum">     287 </span>            :           auto f=24.0*distance_pbc*(2.0*distance_pbcm14-distance_pbcm8)*epsilon/sigma;</a>
+<a name="288"><span class="lineNum">     288 </span>            :           omp_forces[iatom]+=f;</a>
+<a name="289"><span class="lineNum">     289 </span>            :           omp_forces[jatom]-=f;</a>
+<a name="290"><span class="lineNum">     290 </span>            :         }</a>
+<a name="291"><span class="lineNum">     291 </span>            :       }</a>
+<a name="292"><span class="lineNum">     292 </span>            :       #     pragma omp critical</a>
+<a name="293"><span class="lineNum">     293 </span>            :       for(unsigned i=0; i&lt;omp_forces.size(); i++) forces[i]+=omp_forces[i];</a>
+<a name="294"><span class="lineNum">     294 </span>            :     }</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       5709 :     engconf=engconf_tmp;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       5709 :   }</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       5700 :   void compute_engkin(const int natoms,const std::vector&lt;double&gt;&amp; masses,const std::vector&lt;Vector&gt;&amp; velocities,double &amp; engkin)</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :   {</a>
+<a name="302"><span class="lineNum">     302 </span>            : // calculate the kinetic energy from the velocities</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       5700 :     engkin=0.0;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     217300 :     for(int iatom=0; iatom&lt;natoms; iatom++) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     211600 :       engkin+=0.5*masses[iatom]*modulo2(velocities[iatom]);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     }</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       5700 :   }</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      11400 :   void thermostat(const int natoms,const int ndim,const std::vector&lt;double&gt;&amp; masses,const double dt,const double friction,</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :                   const double temperature,std::vector&lt;Vector&gt;&amp; velocities,double &amp; engint,Random &amp; random) {</a>
+<a name="312"><span class="lineNum">     312 </span>            : // Langevin thermostat, implemented as described in Bussi and Parrinello, Phys. Rev. E (2007)</a>
+<a name="313"><span class="lineNum">     313 </span>            : // it is a linear combination of old velocities and new, randomly chosen, velocity,</a>
+<a name="314"><span class="lineNum">     314 </span>            : // with proper coefficients</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      11400 :     double c1=std::exp(-friction*dt);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">     434600 :     for(int iatom=0; iatom&lt;natoms; iatom++) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     423200 :       double c2=std::sqrt((1.0-c1*c1)*temperature/masses[iatom]);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">    1636800 :       for(int i=0; i&lt;ndim; i++) {</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">    1213600 :         engint+=0.5*masses[iatom]*velocities[iatom][i]*velocities[iatom][i];</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">    1213600 :         velocities[iatom][i]=c1*velocities[iatom][i]+c2*random.Gaussian();</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">    1213600 :         engint-=0.5*masses[iatom]*velocities[iatom][i]*velocities[iatom][i];</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :       }</a>
+<a name="323"><span class="lineNum">     323 </span>            :     }</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      11400 :   }</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         39 :   void write_positions(const std::string&amp; trajfile,int natoms,const std::vector&lt;Vector&gt;&amp; positions,const double cell[3],const bool wrapatoms)</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :   {</a>
+<a name="328"><span class="lineNum">     328 </span>            : // write positions on file trajfile</a>
+<a name="329"><span class="lineNum">     329 </span>            : // positions are appended at the end of the file</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         39 :     Vector pos;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :     FILE*fp;</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         39 :     if(write_positions_first) {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          9 :       fp=std::fopen(trajfile.c_str(),&quot;w&quot;);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          9 :       write_positions_first=false;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :     } else {</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         30 :       fp=std::fopen(trajfile.c_str(),&quot;a&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     }</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         39 :     plumed_assert(fp);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : // call fclose when fp goes out of scope</a>
+<a name="340"><span class="lineNum">     340 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="341"><span class="lineNum">     341 </span>            :     std::fprintf(fp,&quot;%d\n&quot;,natoms);</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         39 :     std::fprintf(fp,&quot;%f %f %f\n&quot;,cell[0],cell[1],cell[2]);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">       3847 :     for(int iatom=0; iatom&lt;natoms; iatom++) {</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : // usually, it is better not to apply pbc here, so that diffusion</a>
+<a name="345"><span class="lineNum">     345 </span>            : // is more easily calculated from a trajectory file:</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">       3808 :       if(wrapatoms) pbc(cell,positions[iatom],pos);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       2728 :       else pos=positions[iatom];</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       3808 :       std::fprintf(fp,&quot;Ar %10.7f %10.7f %10.7f\n&quot;,pos[0],pos[1],pos[2]);</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :     }</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         39 :   }</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          9 :   void write_final_positions(const std::string&amp; outputfile,int natoms,const std::vector&lt;Vector&gt;&amp; positions,const double cell[3],const bool wrapatoms)</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :   {</a>
+<a name="354"><span class="lineNum">     354 </span>            : // write positions on file outputfile</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          9 :     Vector pos;</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :     FILE*fp;</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          9 :     fp=std::fopen(outputfile.c_str(),&quot;w&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          9 :     plumed_assert(fp);</span></a>
+<a name="359"><span class="lineNum">     359 </span>            : // call fclose when fp goes out of scope</a>
+<a name="360"><span class="lineNum">     360 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="361"><span class="lineNum">     361 </span>            :     std::fprintf(fp,&quot;%d\n&quot;,natoms);</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          9 :     std::fprintf(fp,&quot;%f %f %f\n&quot;,cell[0],cell[1],cell[2]);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">        779 :     for(int iatom=0; iatom&lt;natoms; iatom++) {</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : // usually, it is better not to apply pbc here, so that diffusion</a>
+<a name="365"><span class="lineNum">     365 </span>            : // is more easily calculated from a trajectory file:</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        770 :       if(wrapatoms) pbc(cell,positions[iatom],pos);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        554 :       else pos=positions[iatom];</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        770 :       std::fprintf(fp,&quot;Ar %10.7f %10.7f %10.7f\n&quot;,pos[0],pos[1],pos[2]);</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :     }</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          9 :   }</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        174 :   void write_statistics(const std::string &amp; statfile,const int istep,const double tstep,</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :                         const int natoms,const int ndim,const double engkin,const double engconf,const double engint) {</a>
+<a name="375"><span class="lineNum">     375 </span>            : // write statistics on file statfile</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        174 :     if(write_statistics_first) {</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : // first time this routine is called, open the file</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          9 :       write_statistics_fp=std::fopen(statfile.c_str(),&quot;w&quot;);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :       write_statistics_fp_deleter.reset(write_statistics_fp);</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">          9 :       write_statistics_first=false;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :     }</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        174 :     if(istep-write_statistics_last_time_reopened&gt;100) {</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : // every 100 steps, reopen the file to flush the buffer</a>
+<a name="384"><span class="lineNum">     384 </span>            :       write_statistics_fp_deleter.reset(nullptr); // close file</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         16 :       write_statistics_fp=std::fopen(statfile.c_str(),&quot;a&quot;);</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :       write_statistics_fp_deleter.reset(write_statistics_fp);</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         16 :       write_statistics_last_time_reopened=istep;</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :     }</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        174 :     std::fprintf(write_statistics_fp,&quot;%d %f %f %f %f %f\n&quot;,istep,istep*tstep,2.0*engkin/double(ndim*natoms),engconf,engkin+engconf,engkin+engconf+engint);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        174 :   }</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          9 :   int main(FILE* in,FILE*out,PLMD::Communicator&amp; pc) override {</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :     int            natoms;       // number of atoms</a>
+<a name="396"><span class="lineNum">     396 </span>            :     std::vector&lt;Vector&gt; positions;    // atomic positions</a>
+<a name="397"><span class="lineNum">     397 </span>            :     std::vector&lt;Vector&gt; velocities;   // velocities</a>
+<a name="398"><span class="lineNum">     398 </span>            :     std::vector&lt;double&gt; masses;       // masses</a>
+<a name="399"><span class="lineNum">     399 </span>            :     std::vector&lt;Vector&gt; forces;       // forces</a>
+<a name="400"><span class="lineNum">     400 </span>            :     double         cell[3];      // cell size</a>
+<a name="401"><span class="lineNum">     401 </span>            :     double         cell9[3][3];  // cell size</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            : // neighbour list variables</a>
+<a name="404"><span class="lineNum">     404 </span>            : // see Allen and Tildesey book for details</a>
+<a name="405"><span class="lineNum">     405 </span>            :     std::vector&lt; std::vector&lt;int&gt; &gt;  list; // neighbour list</a>
+<a name="406"><span class="lineNum">     406 </span>            :     std::vector&lt;Vector&gt; positions0;   // reference atomic positions, i.e. positions when the neighbour list</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : // input parameters</a>
+<a name="409"><span class="lineNum">     409 </span>            : // all of them have a reasonable default value, set in read_input()</a>
+<a name="410"><span class="lineNum">     410 </span>            :     double      tstep;             // simulation timestep</a>
+<a name="411"><span class="lineNum">     411 </span>            :     double      temperature;       // temperature</a>
+<a name="412"><span class="lineNum">     412 </span>            :     double      friction;          // friction for Langevin dynamics (for NVE, use 0)</a>
+<a name="413"><span class="lineNum">     413 </span>            :     double      listcutoff;        // cutoff for neighbour list</a>
+<a name="414"><span class="lineNum">     414 </span>            :     double      forcecutoff;       // cutoff for forces</a>
+<a name="415"><span class="lineNum">     415 </span>            :     int         nstep;             // number of steps</a>
+<a name="416"><span class="lineNum">     416 </span>            :     int         nconfig;           // stride for output of configurations</a>
+<a name="417"><span class="lineNum">     417 </span>            :     int         nstat;             // stride for output of statistics</a>
+<a name="418"><span class="lineNum">     418 </span>            :     int         ndim;              // dimensionality of the system (1, 2, or 3)</a>
+<a name="419"><span class="lineNum">     419 </span>            :     int         idum;              // seed</a>
+<a name="420"><span class="lineNum">     420 </span>            :     int         plumedWantsToStop; // stop flag</a>
+<a name="421"><span class="lineNum">     421 </span>            :     bool        wrapatoms;         // if true, atomic coordinates are written wrapped in minimal cell</a>
+<a name="422"><span class="lineNum">     422 </span>            :     std::string inputfile;         // name of file with starting configuration (xyz)</a>
+<a name="423"><span class="lineNum">     423 </span>            :     std::string outputfile;        // name of file with final configuration (xyz)</a>
+<a name="424"><span class="lineNum">     424 </span>            :     std::string trajfile;          // name of the trajectory file (xyz)</a>
+<a name="425"><span class="lineNum">     425 </span>            :     std::string statfile;          // name of the file with statistics</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :     double      epsilon, sigma;    // LJ parameters</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            :     double engkin;                 // kinetic energy</a>
+<a name="430"><span class="lineNum">     430 </span>            :     double engconf;                // configurational energy</a>
+<a name="431"><span class="lineNum">     431 </span>            :     double engint;                 // integral for conserved energy in Langevin dynamics</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :     bool recompute_list;           // control if the neighbour list have to be recomputed</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          9 :     Random random;                 // random numbers stream</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          9 :     std::unique_ptr&lt;PlumedMain&gt; plumed;</span></a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span>            : // Commenting the next line it is possible to switch-off plumed</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         18 :     plumed=Tools::make_unique&lt;PLMD::PlumedMain&gt;();</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         18 :     if(plumed) plumed-&gt;cmd(&quot;setRealPrecision&quot;,int(sizeof(double)));</span></a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          9 :     read_input(temperature,tstep,friction,forcecutoff,</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :                listcutoff,nstep,nconfig,nstat,</a>
+<a name="446"><span class="lineNum">     446 </span>            :                wrapatoms,inputfile,outputfile,trajfile,statfile,</a>
+<a name="447"><span class="lineNum">     447 </span>            :                ndim,idum,epsilon,sigma);</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            : // number of atoms is read from file inputfile</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          9 :     read_natoms(inputfile,natoms);</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            : // write the parameters in output so they can be checked</a>
+<a name="453"><span class="lineNum">     453 </span>            :     std::fprintf(out,&quot;%s %s\n&quot;,&quot;Starting configuration           :&quot;,inputfile.c_str());</a>
+<a name="454"><span class="lineNum">     454 </span>            :     std::fprintf(out,&quot;%s %s\n&quot;,&quot;Final configuration              :&quot;,outputfile.c_str());</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %d\n&quot;,&quot;Number of atoms                  :&quot;,natoms);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Temperature                      :&quot;,temperature);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Time step                        :&quot;,tstep);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Friction                         :&quot;,friction);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Cutoff for forces                :&quot;,forcecutoff);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Cutoff for neighbour list        :&quot;,listcutoff);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %d\n&quot;,&quot;Number of steps                  :&quot;,nstep);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %d\n&quot;,&quot;Stride for trajectory            :&quot;,nconfig);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :     std::fprintf(out,&quot;%s %s\n&quot;,&quot;Trajectory file                  :&quot;,trajfile.c_str());</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %d\n&quot;,&quot;Stride for statistics            :&quot;,nstat);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :     std::fprintf(out,&quot;%s %s\n&quot;,&quot;Statistics file                  :&quot;,statfile.c_str());</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %d\n&quot;,&quot;Dimensionality                   :&quot;,ndim);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %d\n&quot;,&quot;Seed                             :&quot;,idum);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %s\n&quot;,&quot;Are atoms wrapped on output?     :&quot;,(wrapatoms?&quot;T&quot;:&quot;F&quot;));</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Epsilon                          :&quot;,epsilon);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          9 :     std::fprintf(out,&quot;%s %f\n&quot;,&quot;Sigma                            :&quot;,sigma);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            : // Setting the seed</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          9 :     random.setSeed(idum);</span></a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            : // allocation of dynamical arrays</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          9 :     positions.resize(natoms);</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          9 :     positions0.resize(natoms);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          9 :     velocities.resize(natoms);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          9 :     forces.resize(natoms);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          9 :     masses.resize(natoms);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          9 :     list.resize(natoms);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            : // masses are hard-coded to 1</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        779 :     for(int i=0; i&lt;natoms; ++i) masses[i]=1.0;</span></a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span>            : // energy integral initialized to 0</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          9 :     engint=0.0;</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            : // positions are read from file inputfile</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          9 :     read_positions(inputfile,natoms,positions,cell);</span></a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            : // velocities are randomized according to temperature</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          9 :     randomize_velocities(natoms,ndim,temperature,masses,velocities,random);</span></a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          9 :     if(plumed) {</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;setNoVirial&quot;);</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;setNatoms&quot;,natoms);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;setMDEngine&quot;,&quot;simpleMD&quot;);</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;setTimestep&quot;,tstep);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;setPlumedDat&quot;,&quot;plumed.dat&quot;);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          9 :       int pversion=0;</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;getApiVersion&quot;,&amp;pversion);</span></a>
+<a name="503"><span class="lineNum">     503 </span>            : // setting kbT is only implemented with api&gt;1</a>
+<a name="504"><span class="lineNum">     504 </span>            : // even if not necessary in principle in SimpleMD (which is part of plumed)</a>
+<a name="505"><span class="lineNum">     505 </span>            : // we leave the check here as a reference</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         18 :       if(pversion&gt;1) plumed-&gt;cmd(&quot;setKbT&quot;,temperature);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         18 :       plumed-&gt;cmd(&quot;init&quot;);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :     }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : // neighbour list are computed, and reference positions are saved</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">          9 :     compute_list(natoms,positions,cell,listcutoff,list);</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span>            :     int list_size=0;</a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">        779 :     for(int i=0; i&lt;list.size(); i++) list_size+=list[i].size();</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :     std::fprintf(out,&quot;List size: %d\n&quot;,list_size);</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        779 :     for(int iatom=0; iatom&lt;natoms; ++iatom) positions0[iatom]=positions[iatom];</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : // forces are computed before starting md</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          9 :     compute_forces(natoms,epsilon,sigma,positions,cell,forcecutoff,list,forces,engconf);</span></a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            : // remove forces if ndim&lt;3</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">          9 :     if(ndim&lt;3)</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         30 :       for(int iatom=0; iatom&lt;natoms; ++iatom) for(int k=ndim; k&lt;3; ++k) forces[iatom][k]=0.0;</span></a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            : // here is the main md loop</a>
+<a name="526"><span class="lineNum">     526 </span>            : // Langevin thermostat is applied before and after a velocity-Verlet integrator</a>
+<a name="527"><span class="lineNum">     527 </span>            : // the overall structure is:</a>
+<a name="528"><span class="lineNum">     528 </span>            : //   thermostat</a>
+<a name="529"><span class="lineNum">     529 </span>            : //   update velocities</a>
+<a name="530"><span class="lineNum">     530 </span>            : //   update positions</a>
+<a name="531"><span class="lineNum">     531 </span>            : //   (eventually recompute neighbour list)</a>
+<a name="532"><span class="lineNum">     532 </span>            : //   compute forces</a>
+<a name="533"><span class="lineNum">     533 </span>            : //   update velocities</a>
+<a name="534"><span class="lineNum">     534 </span>            : //   thermostat</a>
+<a name="535"><span class="lineNum">     535 </span>            : //   (eventually dump output informations)</a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">       5709 :     for(int istep=0; istep&lt;nstep; istep++) {</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">       5700 :       thermostat(natoms,ndim,masses,0.5*tstep,friction,temperature,velocities,engint,random);</span></a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">     217300 :       for(int iatom=0; iatom&lt;natoms; iatom++)</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">     211600 :         velocities[iatom]+=forces[iatom]*0.5*tstep/masses[iatom];</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">     217300 :       for(int iatom=0; iatom&lt;natoms; iatom++)</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">     211600 :         positions[iatom]+=velocities[iatom]*tstep;</span></a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span>            : // a check is performed to decide whether to recalculate the neighbour list</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">       5700 :       check_list(natoms,positions,positions0,listcutoff,forcecutoff,recompute_list);</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">       5700 :       if(recompute_list) {</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        449 :         compute_list(natoms,positions,cell,listcutoff,list);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">      44295 :         for(int iatom=0; iatom&lt;natoms; ++iatom) positions0[iatom]=positions[iatom];</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :         int list_size=0;</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">      44295 :         for(int i=0; i&lt;list.size(); i++) list_size+=list[i].size();</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :         std::fprintf(out,&quot;List size: %d\n&quot;,list_size);</a>
+<a name="553"><span class="lineNum">     553 </span>            :       }</a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">       5700 :       compute_forces(natoms,epsilon,sigma,positions,cell,forcecutoff,list,forces,engconf);</span></a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">       5700 :       if(plumed) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">       5700 :         plumedWantsToStop=0;</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">      74100 :         for(int i=0; i&lt;3; i++)for(int k=0; k&lt;3; k++) cell9[i][k]=0.0;</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">      22800 :         for(int i=0; i&lt;3; i++) cell9[i][i]=cell[i];</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setStep&quot;,istep+1);</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setMasses&quot;,&amp;masses[0]);</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setForces&quot;,&amp;forces[0][0]);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setEnergy&quot;,engconf);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setPositions&quot;,&amp;positions[0][0]);</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setBox&quot;,&amp;cell9[0][0]);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;setStopFlag&quot;,&amp;plumedWantsToStop);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">      11400 :         plumed-&gt;cmd(&quot;calc&quot;);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">       5700 :         if(plumedWantsToStop) nstep=istep;</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :       }</a>
+<a name="571"><span class="lineNum">     571 </span>            : // remove forces if ndim&lt;3</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">       5700 :       if(ndim&lt;3)</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">      60000 :         for(int iatom=0; iatom&lt;natoms; ++iatom) for(int k=ndim; k&lt;3; ++k) forces[iatom][k]=0.0;</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">     217300 :       for(int iatom=0; iatom&lt;natoms; iatom++)</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">     211600 :         velocities[iatom]+=forces[iatom]*0.5*tstep/masses[iatom];</span></a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">       5700 :       thermostat(natoms,ndim,masses,0.5*tstep,friction,temperature,velocities,engint,random);</span></a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span>            : // kinetic energy is calculated</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">       5700 :       compute_engkin(natoms,masses,velocities,engkin);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span>            : // eventually, write positions and statistics</a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">       5700 :       if((istep+1)%nconfig==0) write_positions(trajfile,natoms,positions,cell,wrapatoms);</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">       5700 :       if((istep+1)%nstat==0)   write_statistics(statfile,istep+1,tstep,natoms,ndim,engkin,engconf,engint);</span></a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span>            :     }</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span>            : // call final plumed jobs</a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         18 :     plumed-&gt;cmd(&quot;runFinalJobs&quot;);</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            : // write final positions</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">          9 :     write_final_positions(outputfile,natoms,positions,cell,wrapatoms);</span></a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          9 :     return 0;</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         18 :   }</span></a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span>            : </a>
+<a name="599"><span class="lineNum">     599 </span>            : };</a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">      12517 : PLUMED_REGISTER_CLTOOL(SimpleMD,&quot;simplemd&quot;)</span></a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span>            : }</a>
+<a name="604"><span class="lineNum">     604 </span>            : }</a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/SumHills.cpp.func-sort-c.html b/coverage/cltools/SumHills.cpp.func-sort-c.html
new file mode 100644
index 0000000000..888c6a467d
--- /dev/null
+++ b/coverage/cltools/SumHills.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/SumHills.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - SumHills.cpp<span style="font-size: 80%;"> (<a href="SumHills.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">196</td>
+            <td class="headerCovTableEntry">216</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SumHills.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#223">_ZNK4PLMD7cltools14CLToolSumHills11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#533">_ZN4PLMD7cltools14CLToolSumHills18findCvsAndPeriodicERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorISA_IS7_SaIS7_EESaISC_EERSC_SG_RbRS7_SI_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#225">_ZN4PLMD7cltools14CLToolSumHills4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#618">_ZN4PLMD7cltools12_GLOBAL__N_124CLToolSumHillsRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#217">_ZN4PLMD7cltools14CLToolSumHillsC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#618">_ZN4PLMD7cltools12_GLOBAL__N_124CLToolSumHillsRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#618">_ZN4PLMD7cltools12_GLOBAL__N_124CLToolSumHillsRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#196">_ZN4PLMD7cltools14CLToolSumHills16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/SumHills.cpp.func.html b/coverage/cltools/SumHills.cpp.func.html
new file mode 100644
index 0000000000..c6f6d7666b
--- /dev/null
+++ b/coverage/cltools/SumHills.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/SumHills.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - SumHills.cpp<span style="font-size: 80%;"> (<a href="SumHills.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">196</td>
+            <td class="headerCovTableEntry">216</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SumHills.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#618">_ZN4PLMD7cltools12_GLOBAL__N_124CLToolSumHillsRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#618">_ZN4PLMD7cltools12_GLOBAL__N_124CLToolSumHillsRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#618">_ZN4PLMD7cltools12_GLOBAL__N_124CLToolSumHillsRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#196">_ZN4PLMD7cltools14CLToolSumHills16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#533">_ZN4PLMD7cltools14CLToolSumHills18findCvsAndPeriodicERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorISA_IS7_SaIS7_EESaISC_EERSC_SG_RbRS7_SI_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#225">_ZN4PLMD7cltools14CLToolSumHills4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#217">_ZN4PLMD7cltools14CLToolSumHillsC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SumHills.cpp.gcov.html#223">_ZNK4PLMD7cltools14CLToolSumHills11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/SumHills.cpp.gcov.html b/coverage/cltools/SumHills.cpp.gcov.html
new file mode 100644
index 0000000000..29ab899ebd
--- /dev/null
+++ b/coverage/cltools/SumHills.cpp.gcov.html
@@ -0,0 +1,701 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/SumHills.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - SumHills.cpp<span style="font-size: 80%;"> (source / <a href="SumHills.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">196</td>
+            <td class="headerCovTableEntry">216</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstdio&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;string&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;vector&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;iostream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace cltools {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC TOOLS sum_hills</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : sum_hills is a tool that allows one to to use plumed to post-process an existing hills/colvar file</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : a typical case is about the integration of a hills file:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \verbatim</a>
+<a name="50"><span class="lineNum">      50 </span>            : plumed sum_hills  --hills PATHTOMYHILLSFILE</a>
+<a name="51"><span class="lineNum">      51 </span>            : \endverbatim</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : The default name for the output file will be fes.dat</a>
+<a name="54"><span class="lineNum">      54 </span>            : Note that starting from this version plumed will automatically detect the</a>
+<a name="55"><span class="lineNum">      55 </span>            : number of the variables you have and their periodicity.</a>
+<a name="56"><span class="lineNum">      56 </span>            : Additionally, if you use flexible hills (multivariate Gaussian kernels), plumed will understand it from the HILLS file.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The sum_hills tool will also accept multiple files that will be integrated one after the other</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \verbatim</a>
+<a name="61"><span class="lineNum">      61 </span>            : plumed sum_hills  --hills PATHTOMYHILLSFILE1,PATHTOMYHILLSFILE2,PATHTOMYHILLSFILE3</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endverbatim</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : if you want to integrate out some variable you do</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \verbatim</a>
+<a name="67"><span class="lineNum">      67 </span>            : plumed sum_hills  --hills PATHTOMYHILLSFILE   --idw t1 --kt 0.6</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endverbatim</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : where with --idw you define the variables that you want</a>
+<a name="71"><span class="lineNum">      71 </span>            : all the others will be integrated out. --kt defines the temperature of the system in energy units.</a>
+<a name="72"><span class="lineNum">      72 </span>            : (be consistent with the units you have in your hills: plumed will not check this for you)</a>
+<a name="73"><span class="lineNum">      73 </span>            : If you need more variables then you may use a comma separated syntax</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : \verbatim</a>
+<a name="76"><span class="lineNum">      76 </span>            : plumed sum_hills  --hills PATHTOMYHILLSFILE   --idw t1,t2 --kt 0.6</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endverbatim</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : You can define the output grid only with the number of bins you want</a>
+<a name="80"><span class="lineNum">      80 </span>            : while min/max will be detected for you</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : \verbatim</a>
+<a name="83"><span class="lineNum">      83 </span>            : plumed sum_hills --bin 99,99 --hills PATHTOMYHILLSFILE</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endverbatim</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : or full grid specification</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \verbatim</a>
+<a name="89"><span class="lineNum">      89 </span>            : plumed sum_hills --bin 99,99 --min -pi,-pi --max pi,pi --hills PATHTOMYHILLSFILE</a>
+<a name="90"><span class="lineNum">      90 </span>            : \endverbatim</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : You can of course use numbers instead of -pi/pi.</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : You can use a --stride keyword to have a dump each bunch of hills you read</a>
+<a name="95"><span class="lineNum">      95 </span>            : \verbatim</a>
+<a name="96"><span class="lineNum">      96 </span>            : plumed sum_hills --stride 300 --hills PATHTOMYHILLSFILE</a>
+<a name="97"><span class="lineNum">      97 </span>            : \endverbatim</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : You can also have, in case of well tempered metadynamics, only the negative</a>
+<a name="100"><span class="lineNum">     100 </span>            : bias instead of the free energy through the keyword --negbias</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : \verbatim</a>
+<a name="103"><span class="lineNum">     103 </span>            : plumed sum_hills --negbias --hills PATHTOMYHILLSFILE</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endverbatim</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : Here the default name will be negativebias.dat</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : From time to time you might need to use HILLS or a COLVAR file</a>
+<a name="109"><span class="lineNum">     109 </span>            : as it was just a simple set  of points from which you want to build</a>
+<a name="110"><span class="lineNum">     110 </span>            : a free energy by using -(1/beta)log(P)</a>
+<a name="111"><span class="lineNum">     111 </span>            : then you use --histo</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : \verbatim</a>
+<a name="114"><span class="lineNum">     114 </span>            : plumed sum_hills --histo PATHTOMYCOLVARORHILLSFILE  --sigma 0.2,0.2 --kt 0.6</a>
+<a name="115"><span class="lineNum">     115 </span>            : \endverbatim</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : in this case you need a --kt to do the reweighting and then you</a>
+<a name="118"><span class="lineNum">     118 </span>            : need also some width (with the --sigma keyword) for the histogram calculation (actually will be done with</a>
+<a name="119"><span class="lineNum">     119 </span>            : Gaussian kernels, so it will be a continuous histogram)</a>
+<a name="120"><span class="lineNum">     120 </span>            : Here the default output will be histo.dat.</a>
+<a name="121"><span class="lineNum">     121 </span>            : Note that also here you can have multiple input files separated by a comma.</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : Additionally, if you want to do histogram and hills from the same file you can do as this</a>
+<a name="124"><span class="lineNum">     124 </span>            : \verbatim</a>
+<a name="125"><span class="lineNum">     125 </span>            : plumed sum_hills --hills --histo PATHTOMYCOLVARORHILLSFILE  --sigma 0.2,0.2 --kt 0.6</a>
+<a name="126"><span class="lineNum">     126 </span>            : \endverbatim</a>
+<a name="127"><span class="lineNum">     127 </span>            : The two files can be eventually the same</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : Another interesting thing one can do is monitor the difference in blocks as a metadynamics goes on.</a>
+<a name="130"><span class="lineNum">     130 </span>            : When the bias deposited is constant over the whole domain one can consider to be at convergence.</a>
+<a name="131"><span class="lineNum">     131 </span>            : This can be done with the --nohistory keyword</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : \verbatim</a>
+<a name="134"><span class="lineNum">     134 </span>            : plumed sum_hills --stride 300 --hills PATHTOMYHILLSFILE  --nohistory</a>
+<a name="135"><span class="lineNum">     135 </span>            : \endverbatim</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : and similarly one can do the same for an histogram file</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : \verbatim</a>
+<a name="140"><span class="lineNum">     140 </span>            : plumed sum_hills --histo PATHTOMYCOLVARORHILLSFILE  --sigma 0.2,0.2 --kt 0.6 --nohistory</a>
+<a name="141"><span class="lineNum">     141 </span>            : \endverbatim</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : just to check the hypothetical free energy calculated in single blocks of time during a simulation</a>
+<a name="144"><span class="lineNum">     144 </span>            : and not in a cumulative way</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : Output format can be controlled via the --fmt field</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : \verbatim</a>
+<a name="149"><span class="lineNum">     149 </span>            : plumed sum_hills --hills PATHTOMYHILLSFILE  --fmt %8.3f</a>
+<a name="150"><span class="lineNum">     150 </span>            : \endverbatim</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : where here we chose a float with length of 8 and 3 digits</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : The output can be named in a arbitrary way  :</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : \verbatim</a>
+<a name="157"><span class="lineNum">     157 </span>            : plumed sum_hills --hills PATHTOMYHILLSFILE  --outfile myfes.dat</a>
+<a name="158"><span class="lineNum">     158 </span>            : \endverbatim</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : will produce a file myfes.dat which contains the free energy.</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : If you use stride, this keyword is the suffix</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : \verbatim</a>
+<a name="165"><span class="lineNum">     165 </span>            : plumed sum_hills --hills PATHTOMYHILLSFILE  --outfile myfes_ --stride 100</a>
+<a name="166"><span class="lineNum">     166 </span>            : \endverbatim</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : will produce myfes_0.dat,  myfes_1.dat, myfes_2.dat etc.</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : The same is true for the output coming from histogram</a>
+<a name="171"><span class="lineNum">     171 </span>            : \verbatim</a>
+<a name="172"><span class="lineNum">     172 </span>            : plumed sum_hills --histo HILLS --kt 2.5 --sigma 0.01 --outhisto myhisto.dat</a>
+<a name="173"><span class="lineNum">     173 </span>            : \endverbatim</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : is producing a file myhisto.dat</a>
+<a name="176"><span class="lineNum">     176 </span>            : while, when using stride, this is the suffix</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : \verbatim</a>
+<a name="179"><span class="lineNum">     179 </span>            : plumed sum_hills --histo HILLS --kt 2.5 --sigma 0.01 --outhisto myhisto_ --stride 100</a>
+<a name="180"><span class="lineNum">     180 </span>            : \endverbatim</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : that gives  myhisto_0.dat,  myhisto_1.dat,  myhisto_3.dat etc..</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : */</a>
+<a name="185"><span class="lineNum">     185 </span>            : //+ENDPLUMEDOC</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : class CLToolSumHills : public CLTool {</a>
+<a name="188"><span class="lineNum">     188 </span>            : public:</a>
+<a name="189"><span class="lineNum">     189 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="190"><span class="lineNum">     190 </span>            :   explicit CLToolSumHills(const CLToolOptions&amp; co );</a>
+<a name="191"><span class="lineNum">     191 </span>            :   int main(FILE* in,FILE*out,Communicator&amp; pc) override;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   std::string description()const override;</a>
+<a name="193"><span class="lineNum">     193 </span>            : /// find a list of variables present, if they are periodic and which is the period</a>
+<a name="194"><span class="lineNum">     194 </span>            : /// return false if the file does not exist</a>
+<a name="195"><span class="lineNum">     195 </span>            :   static bool findCvsAndPeriodic(const std::string &amp; filename, std::vector&lt; std::vector &lt;std::string&gt; &gt; &amp;cvs,std::vector&lt;std::string&gt; &amp;pmin,std::vector&lt;std::string&gt; &amp;pmax, bool &amp;multivariate, std::string &amp;lowI_, std::string &amp;uppI_);</a>
+<a name="196"><span class="lineNum">     196 </span>            : };</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       4168 : void CLToolSumHills::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--help-debug&quot;,false,&quot;print special options that can be used to create regtests&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--hills&quot;,&quot;specify the name of the hills file&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--histo&quot;,&quot;specify the name of the file for histogram a colvar/hills file is good&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--stride&quot;,&quot;specify the stride for integrating hills file (default 0=never)&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--min&quot;,&quot;the lower bounds for the grid&quot;);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--max&quot;,&quot;the upper bounds for the grid&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--bin&quot;,&quot;the number of bins for the grid&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--spacing&quot;,&quot;grid spacing, alternative to the number of bins&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--idw&quot;,&quot;specify the variables to be used for the free-energy/histogram (default is all). With --hills the other variables will be integrated out, with --histo the other variables won't be considered&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--outfile&quot;,&quot;specify the output file for sumhills&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--outhisto&quot;,&quot;specify the output file for the histogram&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--kt&quot;,&quot;specify temperature in energy units for integrating out variables&quot;);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--sigma&quot;,&quot; a vector that specify the sigma for binning (only needed when doing histogram &quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--negbias&quot;,false,&quot; print the negative bias instead of the free energy (only needed with well tempered runs and flexible hills) &quot;);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--nohistory&quot;,false,&quot; to be used with --stride:  it splits the bias/histogram in pieces without previous history &quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;--mintozero&quot;,false,&quot; it translate all the minimum value in bias/histogram to zero (useful to compare results) &quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;--fmt&quot;,&quot;specify the output format&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       4168 : }</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         13 : CLToolSumHills::CLToolSumHills(const CLToolOptions&amp; co ):</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         13 :   CLTool(co)</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         13 :   inputdata=commandline;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         13 : }</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 : std::string CLToolSumHills::description()const { return &quot;sum the hills with  plumed&quot;; }</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          9 : int CLToolSumHills::main(FILE* in,FILE*out,Communicator&amp; pc) {</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : // Read the hills input file name</a>
+<a name="230"><span class="lineNum">     230 </span>            :   std::vector&lt;std::string&gt; hillsFiles;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   bool dohills;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         18 :   dohills=parseVector(&quot;--hills&quot;,hillsFiles);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : // Read the histogram file</a>
+<a name="234"><span class="lineNum">     234 </span>            :   std::vector&lt;std::string&gt; histoFiles;</a>
+<a name="235"><span class="lineNum">     235 </span>            :   bool dohisto;</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          9 :   dohisto=parseVector(&quot;--histo&quot;,histoFiles);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          9 :   plumed_massert(dohisto || dohills,&quot;you should use --histo or/and --hills command&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   std::vector&lt; std::vector&lt;std::string&gt; &gt; vcvs;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   std::vector&lt;std::string&gt; vpmin;</a>
+<a name="242"><span class="lineNum">     242 </span>            :   std::vector&lt;std::string&gt; vpmax;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   std::string lowI_, uppI_;</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          9 :   if(dohills) {</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :     // parse it as it was a restart</a>
+<a name="246"><span class="lineNum">     246 </span>            :     bool vmultivariate;</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          8 :     findCvsAndPeriodic(hillsFiles[0], vcvs, vpmin, vpmax, vmultivariate, lowI_, uppI_);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            :   std::vector&lt; std::vector&lt;std::string&gt; &gt; hcvs;</a>
+<a name="251"><span class="lineNum">     251 </span>            :   std::vector&lt;std::string&gt; hpmin;</a>
+<a name="252"><span class="lineNum">     252 </span>            :   std::vector&lt;std::string&gt; hpmax;</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   std::vector&lt;std::string&gt; sigma;</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          9 :   if(dohisto) {</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :     bool hmultivariate;</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          1 :     findCvsAndPeriodic(histoFiles[0], hcvs, hpmin, hpmax, hmultivariate, lowI_, uppI_);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :     // here need also the vector of sigmas</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          2 :     parseVector(&quot;--sigma&quot;,sigma);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 :     if(sigma.size()==0)plumed_merror(&quot;you should define --sigma vector when using histogram&quot;);</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     lowI_=uppI_=&quot;-1.&quot;;  // Interval is not use for histograms</a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          9 :   if(dohisto &amp;&amp; dohills) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :     plumed_massert(vcvs==hcvs,&quot;variables for histogram and bias should have the same labels&quot;);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :     plumed_massert(hpmin==vpmin,&quot;variables for histogram and bias should have the same min for periodicity&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :     plumed_massert(hpmax==vpmax,&quot;variables for histogram and bias should have the same max for periodicity&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   // now put into a neutral vector</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            :   std::vector&lt; std::vector&lt;std::string&gt; &gt; cvs;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   std::vector&lt;std::string&gt; pmin;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   std::vector&lt;std::string&gt; pmax;</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          9 :   if(dohills) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          8 :     cvs=vcvs;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          8 :     pmin=vpmin;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          8 :     pmax=vpmax;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   }</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          9 :   if(dohisto) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          1 :     cvs=hcvs;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          1 :     pmin=hpmin;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          1 :     pmax=hpmax;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   // setup grids</a>
+<a name="289"><span class="lineNum">     289 </span>            :   unsigned grid_check=0;</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          9 :   std::vector&lt;std::string&gt; gmin(cvs.size());</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         18 :   if(parseVector(&quot;--min&quot;,gmin)) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          4 :     if(gmin.size()!=cvs.size() &amp;&amp; gmin.size()!=0) plumed_merror(&quot;not enough values for --min&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :     grid_check++;</a>
+<a name="294"><span class="lineNum">     294 </span>            :   }</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          9 :   std::vector&lt;std::string&gt; gmax(cvs.size() );</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         18 :   if(parseVector(&quot;--max&quot;,gmax)) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          4 :     if(gmax.size()!=cvs.size() &amp;&amp; gmax.size()!=0) plumed_merror(&quot;not enough values for --max&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          4 :     grid_check++;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   }</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          9 :   std::vector&lt;std::string&gt; gbin(cvs.size());</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :   bool grid_has_bin; grid_has_bin=false;</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         18 :   if(parseVector(&quot;--bin&quot;,gbin)) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          5 :     if(gbin.size()!=cvs.size() &amp;&amp; gbin.size()!=0) plumed_merror(&quot;not enough values for --bin&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :     grid_has_bin=true;</a>
+<a name="305"><span class="lineNum">     305 </span>            :   }</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          9 :   std::vector&lt;std::string&gt; gspacing(cvs.size());</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   bool grid_has_spacing; grid_has_spacing=false;</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         18 :   if(parseVector(&quot;--spacing&quot;,gspacing)) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          1 :     if(gspacing.size()!=cvs.size() &amp;&amp; gspacing.size()!=0) plumed_merror(&quot;not enough values for --spacing&quot;);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     grid_has_spacing=true;</a>
+<a name="311"><span class="lineNum">     311 </span>            :   }</a>
+<a name="312"><span class="lineNum">     312 </span>            :   // allowed: no grids only bin</a>
+<a name="313"><span class="lineNum">     313 </span>            :   // not allowed: partial grid definition</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          9 :   plumed_massert( gmin.size()==gmax.size() &amp;&amp; (gmin.size()==0 ||  gmin.size()==cvs.size() ),&quot;you should specify --min and --max together with same number of components&quot;);</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          9 :   PlumedMain plumed;</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :   std::string ss;</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          9 :   unsigned nn=1;</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :   ss=&quot;setNatoms&quot;;</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          9 :   plumed.cmd(ss,&amp;nn);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          9 :   if(Communicator::initialized())  plumed.cmd(&quot;setMPIComm&quot;,&amp;pc.Get_comm());</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         18 :   plumed.cmd(&quot;init&quot;,&amp;nn);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          9 :   std::vector &lt;bool&gt; isdone(cvs.size(),false);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         26 :   for(unsigned i=0; i&lt;cvs.size(); i++) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         17 :     if(!isdone[i]) {</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :       isdone[i]=true;</a>
+<a name="329"><span class="lineNum">     329 </span>            :       std::vector&lt;std::string&gt; actioninput;</a>
+<a name="330"><span class="lineNum">     330 </span>            :       std::vector &lt;unsigned&gt; inds;</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         17 :       actioninput.push_back(&quot;FAKE&quot;);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         34 :       actioninput.push_back(&quot;ATOMS=1&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         34 :       actioninput.push_back(&quot;LABEL=&quot;+cvs[i][0]);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :       std::vector&lt;std::string&gt; comps, periods;</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         17 :       if(cvs[i].size()&gt;1) {comps.push_back(cvs[i][1]); inds.push_back(i);}</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         17 :       periods.push_back(pmin[i]); periods.push_back(pmax[i]);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         25 :       for(unsigned j=i+1; j&lt;cvs.size(); j++) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          8 :         if(cvs[i][0]==cvs[j][0] &amp;&amp; !isdone[j]) {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :           if(cvs[i].size()==1 || cvs[j].size()==1  )plumed_merror(&quot;you cannot have twice the same label and no components &quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :           if(cvs[j].size()&gt;1) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :             comps.push_back(cvs[j][1]);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :             periods.push_back(pmin[j]); periods.push_back(pmax[j]);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :             isdone[j]=true; inds.push_back(j);</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :           }</a>
+<a name="345"><span class="lineNum">     345 </span>            :         }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :       }</a>
+<a name="348"><span class="lineNum">     348 </span>            :       // drain all the components</a>
+<a name="349"><span class="lineNum">     349 </span>            :       std::string addme;</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         17 :       if(comps.size()&gt;0) {</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :         addme=&quot;COMPONENTS=&quot;;</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          1 :         for(unsigned i=0; i&lt;comps.size()-1; i++)addme+=comps[i]+&quot;,&quot;;</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :         addme+=comps.back();</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          1 :         actioninput.push_back(addme);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :       }</a>
+<a name="356"><span class="lineNum">     356 </span>            :       // periodicity (always explicit here)</a>
+<a name="357"><span class="lineNum">     357 </span>            :       addme=&quot;PERIODIC=&quot;;</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         34 :       for(unsigned j=0; j&lt;periods.size()-1; j++) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         34 :         addme+=periods[j]+&quot;,&quot;;</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :       }</a>
+<a name="361"><span class="lineNum">     361 </span>            :       addme+=periods.back();</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         17 :       actioninput.push_back(addme);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         18 :       for(unsigned j=0; j&lt;inds.size(); j++) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          1 :         unsigned jj; jj=inds[j];</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          1 :         if(grid_check==2) {</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :           double gm;</a>
+<a name="367"><span class="lineNum">     367 </span>            :           double pm;</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          1 :           if(pmin[jj]!=&quot;none&quot;) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          1 :             Tools::convert(gmin[jj],gm);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          1 :             Tools::convert(pmin[jj],pm);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">          1 :             if(  gm&lt;pm  ) {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :               plumed_merror(&quot;Periodicity issue : GRID_MIN value ( &quot;+gmin[jj]+&quot; ) is less than periodicity in HILLS file in &quot;+cvs[jj][0]+ &quot; ( &quot;+pmin[jj]+&quot; ) &quot;);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :             }</a>
+<a name="374"><span class="lineNum">     374 </span>            :           }</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          1 :           if(pmax[jj]!=&quot;none&quot;) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          1 :             Tools::convert(gmax[jj],gm);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          1 :             Tools::convert(pmax[jj],pm);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          1 :             if(  gm&gt;pm ) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :               plumed_merror(&quot;Periodicity issue : GRID_MAX value ( &quot;+gmax[jj]+&quot; ) is more than periodicity in HILLS file in &quot;+cvs[jj][0]+ &quot; ( &quot;+pmax[jj]+&quot; ) &quot;);</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :             }</a>
+<a name="381"><span class="lineNum">     381 </span>            :           }</a>
+<a name="382"><span class="lineNum">     382 </span>            :         }</a>
+<a name="383"><span class="lineNum">     383 </span>            :       }</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            : //  for(unsigned i=0;i&lt; actioninput.size();i++){</a>
+<a name="386"><span class="lineNum">     386 </span>            : //    cerr&lt;&lt;&quot;AA &quot;&lt;&lt;actioninput[i]&lt;&lt;endl;</a>
+<a name="387"><span class="lineNum">     387 </span>            : //  }</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         17 :       plumed.readInputWords(actioninput);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         34 :     }</span></a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            :   }</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          9 :   unsigned ncv=cvs.size();</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   std::vector&lt;std::string&gt; actioninput;</a>
+<a name="394"><span class="lineNum">     394 </span>            :   std::vector&lt;std::string&gt; idw;</a>
+<a name="395"><span class="lineNum">     395 </span>            :   // check if the variables to be used are correct</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         18 :   if(parseVector(&quot;--idw&quot;,idw)) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;idw.size(); i++) {</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :       bool found=false;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          6 :       for(unsigned j=0; j&lt;cvs.size(); j++) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          4 :         if(cvs[j].size()&gt;1) {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :           if(idw[i]==cvs[j][0]+&quot;.&quot;+cvs[j][1])found=true;</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :         } else {</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          4 :           if(idw[i]==cvs[j][0])found=true;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :         }</a>
+<a name="405"><span class="lineNum">     405 </span>            :       }</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          2 :       if(!found)plumed_merror(&quot;variable &quot;+idw[i]+&quot; is not found in the bunch of cvs: revise your --idw option&quot; );</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :     }</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          2 :     plumed_massert( idw.size()&lt;=cvs.size(),&quot;the number of variables to be integrated should be at most equal to the total number of cvs  &quot;);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     // in this case you need a beta factor!</a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">          9 :   std::string kt; kt=std::string(&quot;1.&quot;);// assign an arbitrary value just in case that idw.size()==cvs.size()</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          9 :   if ( dohisto || idw.size()!=0  ) {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          6 :     plumed_massert(parse(&quot;--kt&quot;,kt),&quot;if you make a dimensionality reduction (--idw) or a histogram (--histo) then you need to define --kt &quot;);</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   std::string addme;</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          9 :   actioninput.push_back(&quot;FUNCSUMHILLS&quot;);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         18 :   actioninput.push_back(&quot;ISCLTOOL&quot;);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            :   // set names</a>
+<a name="423"><span class="lineNum">     423 </span>            :   std::string outfile;</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         18 :   if(parse(&quot;--outfile&quot;,outfile)) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :     actioninput.push_back(&quot;OUTHILLS=&quot;+outfile);</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :   }</a>
+<a name="427"><span class="lineNum">     427 </span>            :   std::string outhisto;</a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         18 :   if(parse(&quot;--outhisto&quot;,outhisto)) {</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          2 :     actioninput.push_back(&quot;OUTHISTO=&quot;+outhisto);</span></a>
+<a name="430"><span class="lineNum">     430 </span>            :   }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :   addme=&quot;ARG=&quot;;</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         17 :   for(unsigned i=0; i&lt;(ncv-1); i++) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          8 :     if(cvs[i].size()==1) {</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         16 :       addme+=std::string(cvs[i][0])+&quot;,&quot;;</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :     } else {</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :       addme+=std::string(cvs[i][0])+&quot;.&quot;+std::string(cvs[i][1])+&quot;,&quot;;</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     }</a>
+<a name="440"><span class="lineNum">     440 </span>            :   }</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          9 :   if(cvs[ncv-1].size()==1) {</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         16 :     addme+=std::string(cvs[ncv-1][0]);</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :   } else {</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          2 :     addme+=std::string(cvs[ncv-1][0])+&quot;.&quot;+std::string(cvs[ncv-1][1]);</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   }</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          9 :   actioninput.push_back(addme);</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   //for(unsigned i=0;i&lt; actioninput.size();i++){</a>
+<a name="448"><span class="lineNum">     448 </span>            :   //  cerr&lt;&lt;&quot;AA &quot;&lt;&lt;actioninput[i]&lt;&lt;endl;</a>
+<a name="449"><span class="lineNum">     449 </span>            :   //}</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          9 :   if(dohills) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">          9 :     addme=&quot;HILLSFILES=&quot;; for(unsigned i=0; i&lt;hillsFiles.size()-1; i++)addme+=hillsFiles[i]+&quot;,&quot;; addme+=hillsFiles[hillsFiles.size()-1];</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          8 :     actioninput.push_back(addme);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     // set the grid</a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          9 :   if(grid_check==2) {</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          7 :     addme=&quot;GRID_MAX=&quot;; for(unsigned i=0; i&lt;(ncv-1); i++)addme+=gmax[i]+&quot;,&quot;; addme+=gmax[ncv-1];</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          4 :     actioninput.push_back(addme);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          7 :     addme=&quot;GRID_MIN=&quot;; for(unsigned i=0; i&lt;(ncv-1); i++)addme+=gmin[i]+&quot;,&quot;; addme+=gmin[ncv-1];</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          4 :     actioninput.push_back(addme);</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :   }</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          9 :   if(grid_has_bin) {</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         10 :     addme=&quot;GRID_BIN=&quot;; for(unsigned i=0; i&lt;(ncv-1); i++)addme+=gbin[i]+&quot;,&quot;; addme+=gbin[ncv-1];</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          5 :     actioninput.push_back(addme);</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :   }</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          9 :   if(grid_has_spacing) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          1 :     addme=&quot;GRID_SPACING=&quot;; for(unsigned i=0; i&lt;(ncv-1); i++)addme+=gspacing[i]+&quot;,&quot;; addme+=gspacing[ncv-1];</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          1 :     actioninput.push_back(addme);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :   }</a>
+<a name="469"><span class="lineNum">     469 </span>            :   std::string  stride; stride=&quot;&quot;;</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         18 :   if(parse(&quot;--stride&quot;,stride)) {</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          1 :     actioninput.push_back(&quot;INITSTRIDE=&quot;+stride);</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :     bool  nohistory;</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          1 :     parseFlag(&quot;--nohistory&quot;,nohistory);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          1 :     if(nohistory) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :       actioninput.push_back(&quot;NOHISTORY&quot;);</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :     }</a>
+<a name="477"><span class="lineNum">     477 </span>            :   }</a>
+<a name="478"><span class="lineNum">     478 </span>            :   bool  mintozero;</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          9 :   parseFlag(&quot;--mintozero&quot;,mintozero);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          9 :   if(mintozero) {</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :     actioninput.push_back(&quot;MINTOZERO&quot;);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   }</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          9 :   if(idw.size()!=0) {</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :     addme=&quot;PROJ=&quot;;</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          2 :     for(unsigned i=0; i&lt;idw.size()-1; i++) {addme+=idw[i]+&quot;,&quot;;}</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :     addme+=idw.back();</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          2 :     actioninput.push_back(addme);</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   }</a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          9 :   if(dohisto) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          1 :     if(idw.size()==0) {</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          1 :       if(sigma.size()!=hcvs.size()) plumed_merror(&quot;you should define as many --sigma vector as the number of collective variable used for the histogram &quot;);</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :     } else {</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :       if(idw.size()!=sigma.size()) plumed_merror(&quot;you should define as many --sigma vector as the number of collective variable used for the histogram &quot;);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     }</a>
+<a name="496"><span class="lineNum">     496 </span>            :   }</a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          9 :   if(idw.size()!=0 || dohisto) {</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          6 :     actioninput.push_back(&quot;KT=&quot;+kt);</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :   }</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          9 :   if(dohisto) {</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          1 :     addme=&quot;HISTOFILES=&quot;; for(unsigned i=0; i&lt;histoFiles.size()-1; i++) {addme+=histoFiles[i]+&quot;,&quot;;} addme+=histoFiles[histoFiles.size()-1];</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          1 :     actioninput.push_back(addme);</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            :     addme=&quot;HISTOSIGMA=&quot;;</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          2 :     for(unsigned i=0; i&lt;sigma.size()-1; i++) {addme+=sigma[i]+&quot;,&quot;;}</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :     addme+=sigma.back();</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">          1 :     actioninput.push_back(addme);</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :   }</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            :   bool negbias;</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">          9 :   parseFlag(&quot;--negbias&quot;,negbias);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          9 :   if(negbias) {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          2 :     actioninput.push_back(&quot;NEGBIAS&quot;);</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :   }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">          9 :   if(lowI_!=uppI_) {</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :     addme=&quot;INTERVAL=&quot;; addme+=lowI_+&quot;,&quot;; addme+=uppI_;</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :     actioninput.push_back(addme);</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :   }</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            :   std::string fmt; fmt=&quot;&quot;;</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         18 :   parse(&quot;--fmt&quot;,fmt);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         18 :   if(fmt!=&quot;&quot;)actioninput.push_back(&quot;FMT=&quot;+fmt);</span></a>
+<a name="525"><span class="lineNum">     525 </span>            : </a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            : //  for(unsigned i=0;i&lt; actioninput.size();i++){</a>
+<a name="528"><span class="lineNum">     528 </span>            : //   cerr&lt;&lt;&quot;AA &quot;&lt;&lt;actioninput[i]&lt;&lt;endl;</a>
+<a name="529"><span class="lineNum">     529 </span>            : //  }</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          9 :   plumed.readInputWords(actioninput);</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :   // if not a grid, then set it up automatically</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">          9 :   return 0;</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         27 : }</span></a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">          9 : bool CLToolSumHills::findCvsAndPeriodic(const std::string &amp; filename, std::vector&lt; std::vector&lt;std::string&gt;  &gt; &amp;cvs, std::vector&lt;std::string&gt; &amp;pmin,std::vector&lt;std::string&gt; &amp;pmax, bool &amp;multivariate, std::string &amp;lowI_, std::string &amp;uppI_) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          9 :   IFile ifile;</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          9 :   ifile.allowIgnoredFields();</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :   std::vector&lt;std::string&gt; fields;</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">          9 :   if(ifile.FileExist(filename)) {</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :     cvs.clear(); pmin.clear(); pmax.clear();</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">          9 :     ifile.open(filename);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">          9 :     ifile.scanFieldList(fields);</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :     bool before_sigma=true;</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">        121 :     for(unsigned i=0; i&lt;fields.size(); i++) {</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :       size_t pos = 0;</a>
+<a name="546"><span class="lineNum">     546 </span>            :       size_t founds,foundm,foundp;</a>
+<a name="547"><span class="lineNum">     547 </span>            :       //found=(fields[i].find(&quot;sigma_&quot;, pos) || fields[i].find(&quot;min_&quot;, pos) || fields[i].find(&quot;max_&quot;, pos) ) ;</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        112 :       founds=fields[i].find(&quot;sigma_&quot;, pos)  ;</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">        112 :       foundm=fields[i].find(&quot;min_&quot;, pos)  ;</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        112 :       foundp=fields[i].find(&quot;max_&quot;, pos)  ;</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">        112 :       if (founds!=std::string::npos || foundm!=std::string::npos ||  foundp!=std::string::npos )before_sigma=false;</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :       // cvs are after time and before sigmas</a>
+<a name="553"><span class="lineNum">     553 </span>            :       size_t  found;</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">        112 :       found=fields[i].find(&quot;time&quot;, pos);</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">        112 :       if( found==std::string::npos &amp;&amp; before_sigma) {</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :         // separate the components</a>
+<a name="557"><span class="lineNum">     557 </span>            :         size_t dot=fields[i].find_first_of('.');</a>
+<a name="558"><span class="lineNum">     558 </span>            :         std::vector&lt;std::string&gt; ss;</a>
+<a name="559"><span class="lineNum">     559 </span>            :         // this loop does not take into account repetitions</a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         17 :         if(dot!=std::string::npos) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">          1 :           std::string a=fields[i].substr(0,dot);</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">          1 :           std::string name=fields[i].substr(dot+1);</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">          1 :           ss.push_back(a);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">          1 :           ss.push_back(name);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          1 :           cvs.push_back(ss);</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :         } else {</a>
+<a name="567"><span class="lineNum">     567 </span>            :           std::vector&lt;std::string&gt; ss;</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         16 :           ss.push_back(fields[i]);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">         16 :           cvs.push_back(ss);</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">         16 :         }</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :         //std::cerr&lt;&lt;&quot;found variable number  &quot;&lt;&lt;cvs.size()&lt;&lt;&quot; :  &quot;&lt;&lt;cvs.back()[0]&lt;&lt;std::endl;</a>
+<a name="572"><span class="lineNum">     572 </span>            :         //if((cvs.back()).size()!=1){</a>
+<a name="573"><span class="lineNum">     573 </span>            :         //      std::cerr&lt;&lt;&quot;component    &quot;&lt;&lt;(cvs.back()).back()&lt;&lt;std::endl;</a>
+<a name="574"><span class="lineNum">     574 </span>            :         //}</a>
+<a name="575"><span class="lineNum">     575 </span>            :         // get periodicity</a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         17 :         pmin.push_back(&quot;none&quot;);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         34 :         pmax.push_back(&quot;none&quot;);</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         18 :         std::string mm; if((cvs.back()).size()&gt;1) {mm=cvs.back()[0]+&quot;.&quot;+cvs.back()[1];} else {mm=cvs.back()[0];}</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         34 :         if(ifile.FieldExist(&quot;min_&quot;+mm)) {</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :           std::string val;</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         28 :           ifile.scanField(&quot;min_&quot;+mm,val);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :           pmin[pmin.size()-1]=val;</a>
+<a name="583"><span class="lineNum">     583 </span>            :           // std::cerr&lt;&lt;&quot;found min   :  &quot;&lt;&lt;pmin.back()&lt;&lt;std::endl;</a>
+<a name="584"><span class="lineNum">     584 </span>            :         }</a>
+<a name="585"><span class="lineNum">     585 </span>            :         //std::cerr&lt;&lt;&quot;found min   :  &quot;&lt;&lt;pmin.back()&lt;&lt;std::endl;</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         34 :         if(ifile.FieldExist(&quot;max_&quot;+mm)) {</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :           std::string val;</a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         28 :           ifile.scanField(&quot;max_&quot;+mm,val);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :           pmax[pmax.size()-1]=val;</a>
+<a name="590"><span class="lineNum">     590 </span>            :           // std::cerr&lt;&lt;&quot;found max   :  &quot;&lt;&lt;pmax.back()&lt;&lt;std::endl;</a>
+<a name="591"><span class="lineNum">     591 </span>            :         }</a>
+<a name="592"><span class="lineNum">     592 </span>            :         //std::cerr&lt;&lt;&quot;found max   :  &quot;&lt;&lt;pmax.back()&lt;&lt;std::endl;</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         17 :       }</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :     }</a>
+<a name="595"><span class="lineNum">     595 </span>            :     // is multivariate ???</a>
+<a name="596"><span class="lineNum">     596 </span>            :     std::string sss;</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          9 :     multivariate=false;</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         18 :     if(ifile.FieldExist(&quot;multivariate&quot;)) {</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :       ;</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         18 :       ifile.scanField(&quot;multivariate&quot;,sss);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">          9 :       if(sss==&quot;true&quot;) { multivariate=true;}</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">          3 :       else if(sss==&quot;false&quot;) { multivariate=false;}</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :     }</a>
+<a name="604"><span class="lineNum">     604 </span>            :     // do interval?</a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">         18 :     if(ifile.FieldExist(&quot;lower_int&quot;)) {</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :       ifile.scanField(&quot;lower_int&quot;,lowI_);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :       ifile.scanField(&quot;upper_int&quot;,uppI_);</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :     } else {</a>
+<a name="609"><span class="lineNum">     609 </span>            :       lowI_=&quot;-1.&quot;;</a>
+<a name="610"><span class="lineNum">     610 </span>            :       uppI_=&quot;-1.&quot;;</a>
+<a name="611"><span class="lineNum">     611 </span>            :     }</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">          9 :     ifile.scanField();</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :     return true;</a>
+<a name="614"><span class="lineNum">     614 </span>            :   } else {</a>
+<a name="615"><span class="lineNum">     615 </span>            :     return false;</a>
+<a name="616"><span class="lineNum">     616 </span>            :   }</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">          9 : }</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span>            : </a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">      12517 : PLUMED_REGISTER_CLTOOL(CLToolSumHills,&quot;sum_hills&quot;)</span></a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            : }</a>
+<a name="625"><span class="lineNum">     625 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/index-sort-f.html b/coverage/cltools/index-sort-f.html
new file mode 100644
index 0000000000..76530f3605
--- /dev/null
+++ b/coverage/cltools/index-sort-f.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - cltools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1359</td>
+            <td class="headerCovTableEntry">1699</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">112</td>
+            <td class="headerCovTableEntryHi">92.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenExample.cpp.gcov.html">GenExample.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=8 height=10 alt="7.7%"><img src="../snow.png" width=92 height=10 alt="7.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">7.7&nbsp;%</td>
+      <td class="coverNumLo">17 / 220</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Driver.cpp.gcov.html">Driver.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.5%"><img src="../snow.png" width=11 height=10 alt="89.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">543 / 607</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Completion.cpp.gcov.html">Completion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=28 height=10 alt="27.8%"><img src="../snow.png" width=72 height=10 alt="27.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">27.8&nbsp;%</td>
+      <td class="coverNumLo">10 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="kT.cpp.gcov.html">kT.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.2%"><img src="../snow.png" width=37 height=10 alt="63.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenTemplate.cpp.gcov.html">GenTemplate.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=57 height=10 alt="56.5%"><img src="../snow.png" width=43 height=10 alt="56.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">56.5&nbsp;%</td>
+      <td class="coverNumLo">13 / 23</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DriverDouble.cpp.gcov.html">DriverDouble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DriverFloat.cpp.gcov.html">DriverFloat.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenJson.cpp.gcov.html">GenJson.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">92 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Manual.cpp.gcov.html">Manual.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PdbRenumber.cpp.gcov.html">PdbRenumber.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">51 / 53</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pesmd.cpp.gcov.html">pesmd.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">128 / 128</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Info.cpp.gcov.html">Info.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.0%"><img src="../snow.png" width=17 height=10 alt="83.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.0&nbsp;%</td>
+      <td class="coverNumMed">39 / 47</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SumHills.cpp.gcov.html">SumHills.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">196 / 216</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleMD.cpp.gcov.html">SimpleMD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">231 / 231</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/index-sort-l.html b/coverage/cltools/index-sort-l.html
new file mode 100644
index 0000000000..4c8ea60a64
--- /dev/null
+++ b/coverage/cltools/index-sort-l.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - cltools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1359</td>
+            <td class="headerCovTableEntry">1699</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">112</td>
+            <td class="headerCovTableEntryHi">92.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenExample.cpp.gcov.html">GenExample.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=8 height=10 alt="7.7%"><img src="../snow.png" width=92 height=10 alt="7.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">7.7&nbsp;%</td>
+      <td class="coverNumLo">17 / 220</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Completion.cpp.gcov.html">Completion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=28 height=10 alt="27.8%"><img src="../snow.png" width=72 height=10 alt="27.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">27.8&nbsp;%</td>
+      <td class="coverNumLo">10 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenTemplate.cpp.gcov.html">GenTemplate.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=57 height=10 alt="56.5%"><img src="../snow.png" width=43 height=10 alt="56.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">56.5&nbsp;%</td>
+      <td class="coverNumLo">13 / 23</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="kT.cpp.gcov.html">kT.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.2%"><img src="../snow.png" width=37 height=10 alt="63.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Info.cpp.gcov.html">Info.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.0%"><img src="../snow.png" width=17 height=10 alt="83.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.0&nbsp;%</td>
+      <td class="coverNumMed">39 / 47</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Driver.cpp.gcov.html">Driver.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.5%"><img src="../snow.png" width=11 height=10 alt="89.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">543 / 607</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SumHills.cpp.gcov.html">SumHills.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">196 / 216</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PdbRenumber.cpp.gcov.html">PdbRenumber.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">51 / 53</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DriverDouble.cpp.gcov.html">DriverDouble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DriverFloat.cpp.gcov.html">DriverFloat.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Manual.cpp.gcov.html">Manual.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenJson.cpp.gcov.html">GenJson.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">92 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pesmd.cpp.gcov.html">pesmd.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">128 / 128</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleMD.cpp.gcov.html">SimpleMD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">231 / 231</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/index.html b/coverage/cltools/index.html
new file mode 100644
index 0000000000..5495b758df
--- /dev/null
+++ b/coverage/cltools/index.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - cltools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1359</td>
+            <td class="headerCovTableEntry">1699</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">112</td>
+            <td class="headerCovTableEntryHi">92.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Completion.cpp.gcov.html">Completion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=28 height=10 alt="27.8%"><img src="../snow.png" width=72 height=10 alt="27.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">27.8&nbsp;%</td>
+      <td class="coverNumLo">10 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Driver.cpp.gcov.html">Driver.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.5%"><img src="../snow.png" width=11 height=10 alt="89.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">543 / 607</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DriverDouble.cpp.gcov.html">DriverDouble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DriverFloat.cpp.gcov.html">DriverFloat.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenExample.cpp.gcov.html">GenExample.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=8 height=10 alt="7.7%"><img src="../snow.png" width=92 height=10 alt="7.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">7.7&nbsp;%</td>
+      <td class="coverNumLo">17 / 220</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenJson.cpp.gcov.html">GenJson.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">92 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenTemplate.cpp.gcov.html">GenTemplate.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=57 height=10 alt="56.5%"><img src="../snow.png" width=43 height=10 alt="56.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">56.5&nbsp;%</td>
+      <td class="coverNumLo">13 / 23</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Info.cpp.gcov.html">Info.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.0%"><img src="../snow.png" width=17 height=10 alt="83.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.0&nbsp;%</td>
+      <td class="coverNumMed">39 / 47</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Manual.cpp.gcov.html">Manual.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PdbRenumber.cpp.gcov.html">PdbRenumber.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">51 / 53</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleMD.cpp.gcov.html">SimpleMD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">231 / 231</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SumHills.cpp.gcov.html">SumHills.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">196 / 216</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="kT.cpp.gcov.html">kT.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.2%"><img src="../snow.png" width=37 height=10 alt="63.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pesmd.cpp.gcov.html">pesmd.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">128 / 128</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/kT.cpp.func-sort-c.html b/coverage/cltools/kT.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1c2990dbf6
--- /dev/null
+++ b/coverage/cltools/kT.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/kT.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - kT.cpp<span style="font-size: 80%;"> (<a href="kT.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="kT.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#74">_ZN4PLMD7cltools2kt4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_112ktRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#68">_ZN4PLMD7cltools2ktC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#55">_ZNK4PLMD7cltools2kt11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_112ktRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_112ktRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#62">_ZN4PLMD7cltools2kt16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/kT.cpp.func.html b/coverage/cltools/kT.cpp.func.html
new file mode 100644
index 0000000000..315e93f557
--- /dev/null
+++ b/coverage/cltools/kT.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/kT.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - kT.cpp<span style="font-size: 80%;"> (<a href="kT.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="kT.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_112ktRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_112ktRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#60">_ZN4PLMD7cltools12_GLOBAL__N_112ktRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#62">_ZN4PLMD7cltools2kt16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#74">_ZN4PLMD7cltools2kt4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#68">_ZN4PLMD7cltools2ktC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="kT.cpp.gcov.html#55">_ZNK4PLMD7cltools2kt11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/kT.cpp.gcov.html b/coverage/cltools/kT.cpp.gcov.html
new file mode 100644
index 0000000000..9f6d99781e
--- /dev/null
+++ b/coverage/cltools/kT.cpp.gcov.html
@@ -0,0 +1,163 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/kT.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - kT.cpp<span style="font-size: 80%;"> (source / <a href="kT.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstdio&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;string&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace cltools {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC TOOLS kt</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Print out the value of k_B T at a particular temperature</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The following command will tell you the value of \f$k_BT\f$ when T is equal</a>
+<a name="41"><span class="lineNum">      41 </span>            : to 300 K in eV</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : plumed kt --temp 300 --units eV</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endverbatim</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : class kt:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   public CLTool</a>
+<a name="52"><span class="lineNum">      52 </span>            : {</a>
+<a name="53"><span class="lineNum">      53 </span>            : public:</a>
+<a name="54"><span class="lineNum">      54 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="55"><span class="lineNum">      55 </span>            :   explicit kt(const CLToolOptions&amp; co );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc) override;</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          4 :   std::string description()const override {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :     return &quot;print out the value of kT at a particular temperature&quot;;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   }</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      12508 : PLUMED_REGISTER_CLTOOL(kt,&quot;kt&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4168 : void kt::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--temp&quot;,&quot;print the manual for this particular action&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--units&quot;,&quot;kj/mol&quot;,&quot;the units of energy can be kj/mol, kcal/mol, j/mol, eV or the conversion factor from kj/mol&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       4168 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          4 : kt::kt(const CLToolOptions&amp; co ):</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          4 :   CLTool(co)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          4 :   inputdata=commandline;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          4 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 : int kt::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   std::string unitname; parse(&quot;--units&quot;,unitname);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   Units units; units.setEnergy( unitname );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   double temp; parse(&quot;--temp&quot;,temp);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   double kk=(kBoltzmann*temp)/units.getEnergy();</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::fprintf(out,&quot;When the temperature is %f kelvin kT is equal to %f %s\n&quot;,temp,kk,unitname.c_str());</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   return 0;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : } // End of namespace</a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/pesmd.cpp.func-sort-c.html b/coverage/cltools/pesmd.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ef65ac2539
--- /dev/null
+++ b/coverage/cltools/pesmd.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/pesmd.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - pesmd.cpp<span style="font-size: 80%;"> (<a href="pesmd.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">128</td>
+            <td class="headerCovTableEntry">128</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="pesmd.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#123">_ZN4PLMD7cltools5PesMD10read_inputERdS2_S2_RiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIdSaIdEES3_RbSE_S3_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#163">_ZN4PLMD7cltools5PesMD4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#97">_ZNK4PLMD7cltools5PesMD11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#308">_ZN4PLMD7cltools12_GLOBAL__N_115PesMDRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#308">_ZN4PLMD7cltools12_GLOBAL__N_115PesMDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#308">_ZN4PLMD7cltools12_GLOBAL__N_115PesMDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#101">_ZN4PLMD7cltools5PesMD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/pesmd.cpp.func.html b/coverage/cltools/pesmd.cpp.func.html
new file mode 100644
index 0000000000..d85bd59d42
--- /dev/null
+++ b/coverage/cltools/pesmd.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/pesmd.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - pesmd.cpp<span style="font-size: 80%;"> (<a href="pesmd.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">128</td>
+            <td class="headerCovTableEntry">128</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="pesmd.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#308">_ZN4PLMD7cltools12_GLOBAL__N_115PesMDRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#308">_ZN4PLMD7cltools12_GLOBAL__N_115PesMDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#308">_ZN4PLMD7cltools12_GLOBAL__N_115PesMDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#123">_ZN4PLMD7cltools5PesMD10read_inputERdS2_S2_RiRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIdSaIdEES3_RbSE_S3_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#101">_ZN4PLMD7cltools5PesMD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#163">_ZN4PLMD7cltools5PesMD4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="pesmd.cpp.gcov.html#97">_ZNK4PLMD7cltools5PesMD11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/cltools/pesmd.cpp.gcov.html b/coverage/cltools/pesmd.cpp.gcov.html
new file mode 100644
index 0000000000..130715ff37
--- /dev/null
+++ b/coverage/cltools/pesmd.cpp.gcov.html
@@ -0,0 +1,389 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - cltools/pesmd.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">cltools</a> - pesmd.cpp<span style="font-size: 80%;"> (source / <a href="pesmd.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">128</td>
+            <td class="headerCovTableEntry">128</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdio&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;memory&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC TOOLS pesmd</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Pesmd allows one to do (biased) Langevin dynamics on a two-dimensional potential energy surface.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The energy landscape that you are moving about on is specified using a plumed input file.</a>
+<a name="38"><span class="lineNum">      38 </span>            : The directives that are available for this command line tool are as follows:</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : You run a Langevin simulation using pesmd with the following command:</a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : plumed pesmd &lt; input</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endverbatim</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The following is an example of an input file for a pesmd simulation. This file</a>
+<a name="48"><span class="lineNum">      48 </span>            : instructs pesmd to do 50 steps of Langevin dynamics on a 2D potential energy surface</a>
+<a name="49"><span class="lineNum">      49 </span>            : at a temperature of 0.722</a>
+<a name="50"><span class="lineNum">      50 </span>            : \verbatim</a>
+<a name="51"><span class="lineNum">      51 </span>            : temperature 0.722</a>
+<a name="52"><span class="lineNum">      52 </span>            : tstep 0.005</a>
+<a name="53"><span class="lineNum">      53 </span>            : friction 1</a>
+<a name="54"><span class="lineNum">      54 </span>            : dimension 2</a>
+<a name="55"><span class="lineNum">      55 </span>            : nstep 50</a>
+<a name="56"><span class="lineNum">      56 </span>            : ipos 0.0 0.0</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endverbatim</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : If you run the following a description of all the directives that can be used in the</a>
+<a name="60"><span class="lineNum">      60 </span>            : input file will be output.</a>
+<a name="61"><span class="lineNum">      61 </span>            : \verbatim</a>
+<a name="62"><span class="lineNum">      62 </span>            : plumed pesmd --help</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endverbatim</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : The energy landscape to explore is given within the plumed input file.  For example the following</a>
+<a name="66"><span class="lineNum">      66 </span>            : example input uses \ref MATHEVAL to define a two dimensional potential.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \verbatim</a>
+<a name="69"><span class="lineNum">      69 </span>            : d1: DISTANCE ATOMS=1,2 COMPONENTS</a>
+<a name="70"><span class="lineNum">      70 </span>            : ff: MATHEVAL ARG=d1.x,d1,y PERIODIC=NO FUNC=()</a>
+<a name="71"><span class="lineNum">      71 </span>            : bb: BIASVALUE ARG=ff</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endverbatim</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : Atom 1 is placed at the origin.  The x and y components on our surface are the</a>
+<a name="75"><span class="lineNum">      75 </span>            : positions of the particle on our two dimensional energy landscape.  By calculating the</a>
+<a name="76"><span class="lineNum">      76 </span>            : vector connecting atom 1 (the origin) to atom 2 (the position of our particle) we are thus</a>
+<a name="77"><span class="lineNum">      77 </span>            : getting the position of the atom on the energy landscape.  This is then inserted into the function</a>
+<a name="78"><span class="lineNum">      78 </span>            : that is calculated on the second line.  The value of this function is then used as a bias.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : We can also specify a potential on a grid and look at the dynamics on this function using pesmd.</a>
+<a name="81"><span class="lineNum">      81 </span>            : A plumed input for an example such as this one might look something like this:</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \verbatim</a>
+<a name="84"><span class="lineNum">      84 </span>            : d1: DISTANCE ATOMS=1,2 COMPONENTS</a>
+<a name="85"><span class="lineNum">      85 </span>            : bb: EXTERNAL ARG=d1.x,d1,y FILE=fes.dat</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endverbatim</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : In this way we can use pesmd to do a dynamics on a free energy surface calculated using metadynamics</a>
+<a name="89"><span class="lineNum">      89 </span>            : and sum_hills.  On a final note once we have defined our potential we can use all the biasing functions</a>
+<a name="90"><span class="lineNum">      90 </span>            : within plumed in addition in order to do a biased dynamics on the potential energy landscape of interest.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : */</a>
+<a name="93"><span class="lineNum">      93 </span>            : //+ENDPLUMEDOC</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : namespace PLMD {</a>
+<a name="96"><span class="lineNum">      96 </span>            : namespace cltools {</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : class PesMD  : public PLMD::CLTool {</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          4 :   std::string description() const override {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          4 :     return &quot;Langevin dynamics on PLUMED energy landscape&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span>            : public:</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       4168 :   static void registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;nstep&quot;,&quot;The number of steps of dynamics you want to run&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;temperature&quot;,&quot;NVE&quot;,&quot;the temperature at which you wish to run the simulation in LJ units&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;friction&quot;,&quot;off&quot;,&quot;The friction (in LJ units) for the Langevin thermostat that is used to keep the temperature constant&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;tstep&quot;,&quot;0.005&quot;,&quot;the integration timestep in LJ units&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;dimension&quot;,&quot;the dimension of your energy landscape&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;plumed&quot;,&quot;plumed.dat&quot;,&quot;the name of the plumed input file containing the potential&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;ipos&quot;,&quot;0.0&quot;,&quot;the initial position of the system&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       8336 :     keys.add(&quot;compulsory&quot;,&quot;idum&quot;,&quot;0&quot;,&quot;The random number seed&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       8336 :     keys.addFlag(&quot;periodic&quot;,false,&quot;are your input coordinates periodic&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       8336 :     keys.add(&quot;optional&quot;,&quot;min&quot;,&quot;minimum value the coordinates can take for a periodic domain&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       8336 :     keys.add(&quot;optional&quot;,&quot;max&quot;,&quot;maximum value the coordinates can take for a periodic domain&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4168 :   }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          7 :   explicit PesMD( const CLToolOptions&amp; co ) :</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          7 :     CLTool(co)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   {</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          7 :     inputdata=ifile;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : private:</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   void read_input(double&amp; temperature,</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :                   double&amp; tstep,</a>
+<a name="127"><span class="lineNum">     127 </span>            :                   double&amp; friction,</a>
+<a name="128"><span class="lineNum">     128 </span>            :                   int&amp; dim,</a>
+<a name="129"><span class="lineNum">     129 </span>            :                   std::string&amp; plumedin,</a>
+<a name="130"><span class="lineNum">     130 </span>            :                   std::vector&lt;double&gt;&amp; ipos,</a>
+<a name="131"><span class="lineNum">     131 </span>            :                   int&amp;    nstep,</a>
+<a name="132"><span class="lineNum">     132 </span>            :                   bool&amp;   lperiod,</a>
+<a name="133"><span class="lineNum">     133 </span>            :                   std::vector&lt;double&gt;&amp; periods,</a>
+<a name="134"><span class="lineNum">     134 </span>            :                   int&amp;    idum)</a>
+<a name="135"><span class="lineNum">     135 </span>            :   {</a>
+<a name="136"><span class="lineNum">     136 </span>            :     // Read everything from input file</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :     std::string tempstr; parse(&quot;temperature&quot;,tempstr);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :     if( tempstr!=&quot;NVE&quot; ) Tools::convert(tempstr,temperature);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          6 :     parse(&quot;tstep&quot;,tstep);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          6 :     std::string frictionstr; parse(&quot;friction&quot;,frictionstr);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          3 :     if( tempstr!=&quot;NVE&quot; ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          3 :       if(frictionstr==&quot;off&quot;) error(&quot;pecify friction for thermostat&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 :       Tools::convert(frictionstr,friction);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          6 :     parse(&quot;plumed&quot;,plumedin); parse(&quot;dimension&quot;,dim);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          6 :     parse(&quot;nstep&quot;,nstep); parse(&quot;idum&quot;,idum);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          3 :     ipos.resize( dim ); parseVector(&quot;ipos&quot;,ipos);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          3 :     parseFlag(&quot;periodic&quot;,lperiod);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :     if( lperiod ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          2 :       if( dim&gt;3 ) error(&quot;can only do three dimensional periodic functions&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          2 :       std::vector&lt;double&gt; min( dim ); parseVector(&quot;min&quot;,min);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :       std::vector&lt;double&gt; max( dim ); parseVector(&quot;max&quot;,max);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          2 :       periods.resize( dim );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          7 :       for(int i=0; i&lt;dim; ++i) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          5 :         if( max[i]&lt;min[i] ) error(&quot;invalid periods specified max is less than min&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          5 :         periods[i]=max[i]-min[i];</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :       }</a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          3 :   }</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : public:</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   int main( FILE* in, FILE* out, PLMD::Communicator&amp; pc) override {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     std::string plumedin; std::vector&lt;double&gt; ipos;</a>
+<a name="167"><span class="lineNum">     167 </span>            :     double temp, tstep, friction; bool lperiod;</a>
+<a name="168"><span class="lineNum">     168 </span>            :     int dim, nsteps, seed; std::vector&lt;double&gt; periods;</a>
+<a name="169"><span class="lineNum">     169 </span>            :     int plumedWantsToStop;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          3 :     Random random;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          3 :     read_input( temp, tstep, friction, dim, plumedin, ipos, nsteps, lperiod, periods, seed );</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     // Setup random number generator</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          3 :     random.setSeed(seed);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :     // Setup box if we have periodic domain</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; box(9, 0.0);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          3 :     if( lperiod &amp;&amp; dim==1 ) { box[0]=box[4]=box[8]=periods[0]; }</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :     else if( lperiod &amp;&amp; dim==2 ) { box[0]=periods[0]; box[4]=box[8]=periods[1]; }</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :     else if( lperiod &amp;&amp; dim==3 ) { box[0]=periods[0]; box[4]=periods[1]; box[8]=periods[2]; }</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          1 :     else if( lperiod ) error(&quot;invalid dimension for periodic potential must be 1, 2 or 3&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :     // Create plumed object and initialize</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          3 :     auto plumed=Tools::make_unique&lt;PLMD::PlumedMain&gt;();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          3 :     int s=sizeof(double);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          9 :     plumed-&gt;cmd(&quot;setRealPrecision&quot;,&amp;s);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          3 :     if(Communicator::initialized()) plumed-&gt;cmd(&quot;setMPIComm&quot;,&amp;pc.Get_comm());</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setNoVirial&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          3 :     int natoms=( std::floor(dim/3) +  2 );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setNatoms&quot;,&amp;natoms);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setMDEngine&quot;,&quot;pesmd&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setTimestep&quot;,&amp;tstep);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setPlumedDat&quot;,plumedin.c_str());</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;init&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :     // Now create some fake atoms</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          3 :     int nat = std::floor( dim/3 ) + 1;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; masses( 1+nat, 1 );</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          3 :     std::vector&lt;Vector&gt; velocities( nat ), positions( nat+1 ), forces( nat+1 );</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     // Will set these properly eventually</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          3 :     int k=0; positions[0].zero(); // Atom zero is fixed at origin</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         19 :     for(int i=0; i&lt;nat; ++i) for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         12 :         if( k&lt;dim ) { positions[1+i][j]=ipos[k]; } else { positions[1+i][j]=0;}</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         12 :         k++;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :       }</a>
+<a name="206"><span class="lineNum">     206 </span>            :     // And initialize the velocities</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         19 :     for(int i=0; i&lt;nat; ++i) for(int j=0; j&lt;3; ++j) velocities[i][j]=random.Gaussian() * std::sqrt( temp );</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :     // And calculate the kinetic energy</a>
+<a name="209"><span class="lineNum">     209 </span>            :     double tke=0;</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          7 :     for(int i=0; i&lt;nat; ++i) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         10 :       for(int j=0; j&lt;3; ++j) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          9 :         if( 3*i+j&gt;dim-1 ) break;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :         tke += 0.5*velocities[i][j]*velocities[i][j];</a>
+<a name="214"><span class="lineNum">     214 </span>            :       }</a>
+<a name="215"><span class="lineNum">     215 </span>            :     }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :     // Now call plumed to get initial forces</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          3 :     int istep=0; double zero=0;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setStep&quot;,&amp;istep);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setMasses&quot;,&amp;masses[0]);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          3 :     Tools::set_to_zero(forces);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setForces&quot;,&amp;forces[0][0]);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setEnergy&quot;,&amp;zero);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          5 :     if( lperiod ) plumed-&gt;cmd(&quot;setBox&quot;,&amp;box[0]);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;setPositions&quot;,&amp;positions[0][0]);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          6 :     plumed-&gt;cmd(&quot;calc&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :     double therm_eng=0;</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          3 :     FILE* fp=fopen(&quot;stats.out&quot;,&quot;w+&quot;);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        153 :     for(int istep=0; istep&lt;nsteps; ++istep) {</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        150 :       if( istep%20==0 &amp;&amp; pc.Get_rank()==0 ) std::printf(&quot;Doing step %i\n&quot;,istep);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :       // Langevin thermostat</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        150 :       double lscale=std::exp(-0.5*tstep/friction);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        150 :       double lrand=std::sqrt((1.-lscale*lscale)*temp);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        350 :       for(int j=0; j&lt;nat; ++j) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        500 :         for(int k=0; k&lt;3; ++k) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        450 :           if( 3*j+k&gt;dim-1 ) break;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        300 :           therm_eng=therm_eng+0.5*velocities[j][k]*velocities[j][k];</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        300 :           velocities[j][k]=lscale*velocities[j][k]+lrand*random.Gaussian();</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        300 :           therm_eng=therm_eng-0.5*velocities[j][k]*velocities[0][k];</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :         }</a>
+<a name="246"><span class="lineNum">     246 </span>            :       }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :       // First step of velocity verlet</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        350 :       for(int j=0; j&lt;nat; ++j) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        500 :         for(int k=0; k&lt;3; ++k) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        450 :           if( 3*j+k&gt;dim-1 ) break;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        300 :           velocities[j][k] = velocities[j][k] + 0.5*tstep*forces[1+j][k];</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        300 :           positions[1+j][k] = positions[1+j][k] + tstep*velocities[j][k];</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :         }</a>
+<a name="255"><span class="lineNum">     255 </span>            :       }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        150 :       int istepplusone=istep+1;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        150 :       plumedWantsToStop=0;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;setStep&quot;,&amp;istepplusone);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;setMasses&quot;,&amp;masses[0]);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        150 :       Tools::set_to_zero(forces);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;setForces&quot;,&amp;forces[0][0]);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        150 :       double fenergy=0.0;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;setEnergy&quot;,&amp;fenergy);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;setPositions&quot;,&amp;positions[0][0]);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;setStopFlag&quot;,&amp;plumedWantsToStop);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        300 :       plumed-&gt;cmd(&quot;calc&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :       // if(istep%2000==0) plumed-&gt;cmd(&quot;writeCheckPointFile&quot;);</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        150 :       if(plumedWantsToStop) nsteps=istep;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :       // Second step of velocity verlet</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        350 :       for(int j=0; j&lt;nat; ++j) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        500 :         for(int k=0; k&lt;3; ++k) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        450 :           if( 3*j+k&gt;dim-1 ) break;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        300 :           velocities[j][k] = velocities[j][k] + 0.5*tstep*forces[1+j][k];</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :         }</a>
+<a name="277"><span class="lineNum">     277 </span>            :       }</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :       // Langevin thermostat</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        150 :       lscale=std::exp(-0.5*tstep/friction);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        150 :       lrand=std::sqrt((1.-lscale*lscale)*temp);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        350 :       for(int j=0; j&lt;nat; ++j) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        500 :         for(int k=0; k&lt;3; ++k) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        450 :           if( 3*j+k&gt;dim-1) break;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        300 :           therm_eng=therm_eng+0.5*velocities[j][k]*velocities[j][k];</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">        300 :           velocities[j][k]=lscale*velocities[j][k]+lrand*random.Gaussian();</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        300 :           therm_eng=therm_eng-0.5*velocities[j][k]*velocities[j][k];</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :         }</a>
+<a name="289"><span class="lineNum">     289 </span>            :       }</a>
+<a name="290"><span class="lineNum">     290 </span>            :       // Calculate total kinetic energy</a>
+<a name="291"><span class="lineNum">     291 </span>            :       tke=0;</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        350 :       for(int i=0; i&lt;nat; ++i) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        500 :         for(int j=0; j&lt;3; ++j) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        450 :           if( 3*i+j&gt;dim-1 ) break;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        300 :           tke += 0.5*velocities[i][j]*velocities[i][j];</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :         }</a>
+<a name="297"><span class="lineNum">     297 </span>            :       }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :       // Print everything</a>
+<a name="300"><span class="lineNum">     300 </span>            :       // conserved = potential+1.5*ttt+therm_eng;</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        150 :       if( pc.Get_rank()==0 ) std::fprintf(fp,&quot;%i %f %f %f \n&quot;, istep, istep*tstep, tke, therm_eng );</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :     }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          3 :     fclose(fp);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          3 :     return 0;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          3 :   }</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : };</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      12511 : PLUMED_REGISTER_CLTOOL(PesMD,&quot;pesmd&quot;)</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            : }</a>
+<a name="313"><span class="lineNum">     313 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Angle.cpp.func-sort-c.html b/coverage/colvar/Angle.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d61298f2ed
--- /dev/null
+++ b/coverage/colvar/Angle.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Angle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Angle.cpp<span style="font-size: 80%;"> (<a href="Angle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Angle.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#96">_ZN4PLMD6colvar5AngleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#89">_ZN4PLMD6colvar12_GLOBAL__N_117AngleRegisterMe916createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#96">_ZN4PLMD6colvar5AngleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#91">_ZN4PLMD6colvar5Angle16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#124">_ZN4PLMD6colvar5Angle9calculateEv</a></td>
+              <td class="coverFnHi">304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#89">_ZN4PLMD6colvar12_GLOBAL__N_117AngleRegisterMe91C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#89">_ZN4PLMD6colvar12_GLOBAL__N_117AngleRegisterMe91D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Angle.cpp.func.html b/coverage/colvar/Angle.cpp.func.html
new file mode 100644
index 0000000000..caa5ff760c
--- /dev/null
+++ b/coverage/colvar/Angle.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Angle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Angle.cpp<span style="font-size: 80%;"> (<a href="Angle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Angle.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#89">_ZN4PLMD6colvar12_GLOBAL__N_117AngleRegisterMe916createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#89">_ZN4PLMD6colvar12_GLOBAL__N_117AngleRegisterMe91C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#89">_ZN4PLMD6colvar12_GLOBAL__N_117AngleRegisterMe91D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#91">_ZN4PLMD6colvar5Angle16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#124">_ZN4PLMD6colvar5Angle9calculateEv</a></td>
+              <td class="coverFnHi">304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#96">_ZN4PLMD6colvar5AngleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#96">_ZN4PLMD6colvar5AngleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Angle.cpp.gcov.html b/coverage/colvar/Angle.cpp.gcov.html
new file mode 100644
index 0000000000..890bf2f10f
--- /dev/null
+++ b/coverage/colvar/Angle.cpp.gcov.html
@@ -0,0 +1,224 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Angle.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Angle.cpp<span style="font-size: 80%;"> (source / <a href="Angle.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Angle.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR ANGLE</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate an angle.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This command can be used to compute the angle between three atoms. Alternatively</a>
+<a name="34"><span class="lineNum">      34 </span>            : if four atoms appear in the atom</a>
+<a name="35"><span class="lineNum">      35 </span>            : specification it calculates the angle between</a>
+<a name="36"><span class="lineNum">      36 </span>            : two vectors identified by two pairs of atoms.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : If _three_ atoms are given, the angle is defined as:</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{23}}{</a>
+<a name="41"><span class="lineNum">      41 </span>            : |{\bf r}_{21}| |{\bf r}_{23}|}\right)</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f]</a>
+<a name="43"><span class="lineNum">      43 </span>            : Here \f$ {\bf r}_{ij}\f$ is the distance vector among the</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f$i\f$th and the \f$j\f$th listed atom.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : If _four_ atoms are given, the angle is defined as:</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{34}}{</a>
+<a name="49"><span class="lineNum">      49 </span>            : |{\bf r}_{21}| |{\bf r}_{34}|}\right)</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : Notice that angles defined in this way are non-periodic variables and</a>
+<a name="53"><span class="lineNum">      53 </span>            : their value is limited by definition between 0 and \f$\pi\f$.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The vectors \f$ {\bf r}_{ij}\f$ are by default evaluated taking</a>
+<a name="56"><span class="lineNum">      56 </span>            : periodic boundary conditions into account.</a>
+<a name="57"><span class="lineNum">      57 </span>            : This behavior can be changed with the NOPBC flag.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \par Examples</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : This command tells plumed to calculate the angle between the vector connecting atom 1 to atom 2 and</a>
+<a name="62"><span class="lineNum">      62 </span>            : the vector connecting atom 2 to atom 3 and to print it on file COLVAR1. At the same time,</a>
+<a name="63"><span class="lineNum">      63 </span>            : the angle between vector connecting atom 1 to atom 2 and the vector connecting atom 3 to atom 4 is printed</a>
+<a name="64"><span class="lineNum">      64 </span>            : on file COLVAR2.</a>
+<a name="65"><span class="lineNum">      65 </span>            : \plumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : a: ANGLE ATOMS=1,2,3</a>
+<a name="68"><span class="lineNum">      68 </span>            : # equivalently one could state:</a>
+<a name="69"><span class="lineNum">      69 </span>            : # a: ANGLE ATOMS=1,2,2,3</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : b: ANGLE ATOMS=1,2,3,4</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : PRINT ARG=a FILE=COLVAR1</a>
+<a name="74"><span class="lineNum">      74 </span>            : PRINT ARG=b FILE=COLVAR2</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : */</a>
+<a name="79"><span class="lineNum">      79 </span>            : //+ENDPLUMEDOC</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class Angle : public Colvar {</a>
+<a name="82"><span class="lineNum">      82 </span>            :   bool pbc;</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   explicit Angle(const ActionOptions&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span>            : // active methods:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void calculate() override;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="89"><span class="lineNum">      89 </span>            : };</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      12539 : PLUMED_REGISTER_ACTION(Angle,&quot;ANGLE&quot;)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         20 : void Angle::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         20 :   Colvar::registerKeywords(keys);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         40 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the list of atoms involved in this collective variable (either 3 or 4 atoms)&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         20 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         18 : Angle::Angle(const ActionOptions&amp;ao):</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         18 :   pbc(true)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         18 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         18 :   bool nopbc=!pbc;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         18 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         18 :   pbc=!nopbc;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         18 :   if(atoms.size()==3) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         12 :     log.printf(&quot;  between atoms %d %d %d\n&quot;,atoms[0].serial(),atoms[1].serial(),atoms[2].serial());</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         12 :     atoms.resize(4);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         12 :     atoms[3]=atoms[2];</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         12 :     atoms[2]=atoms[1];</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          6 :   } else if(atoms.size()==4) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          5 :     log.printf(&quot;  between lines %d-%d and %d-%d\n&quot;,atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial());</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   } else error(&quot;Number of specified atoms should be either 3 or 4&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         17 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         17 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         17 :   requestAtoms(atoms);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         17 :   checkRead();</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         19 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : // calculator</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        304 : void Angle::calculate() {</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        304 :   if(pbc) makeWhole();</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        304 :   Vector dij,dik;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        304 :   dij=delta(getPosition(2),getPosition(3));</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        304 :   dik=delta(getPosition(1),getPosition(0));</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        304 :   Vector ddij,ddik;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   PLMD::Angle a;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        304 :   double angle=a.compute(dij,dik,ddij,ddik);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        304 :   setAtomsDerivatives(0,ddik);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        304 :   setAtomsDerivatives(1,-ddik);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        304 :   setAtomsDerivatives(2,-ddij);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        304 :   setAtomsDerivatives(3,ddij);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        304 :   setValue           (angle);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        304 :   setBoxDerivativesNoPbc();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        304 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Cell.cpp.func-sort-c.html b/coverage/colvar/Cell.cpp.func-sort-c.html
new file mode 100644
index 0000000000..40f9a79d84
--- /dev/null
+++ b/coverage/colvar/Cell.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Cell.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Cell.cpp<span style="font-size: 80%;"> (<a href="Cell.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Cell.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#58">_ZN4PLMD6colvar4CellC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#56">_ZN4PLMD6colvar12_GLOBAL__N_116CellRegisterMe586createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#58">_ZN4PLMD6colvar4CellC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#76">_ZN4PLMD6colvar4Cell16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#94">_ZN4PLMD6colvar4Cell9calculateEv</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#56">_ZN4PLMD6colvar12_GLOBAL__N_116CellRegisterMe58C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#56">_ZN4PLMD6colvar12_GLOBAL__N_116CellRegisterMe58D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Cell.cpp.func.html b/coverage/colvar/Cell.cpp.func.html
new file mode 100644
index 0000000000..d14970ef3a
--- /dev/null
+++ b/coverage/colvar/Cell.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Cell.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Cell.cpp<span style="font-size: 80%;"> (<a href="Cell.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Cell.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#56">_ZN4PLMD6colvar12_GLOBAL__N_116CellRegisterMe586createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#56">_ZN4PLMD6colvar12_GLOBAL__N_116CellRegisterMe58C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#56">_ZN4PLMD6colvar12_GLOBAL__N_116CellRegisterMe58D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#76">_ZN4PLMD6colvar4Cell16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#94">_ZN4PLMD6colvar4Cell9calculateEv</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#58">_ZN4PLMD6colvar4CellC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Cell.cpp.gcov.html#58">_ZN4PLMD6colvar4CellC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Cell.cpp.gcov.html b/coverage/colvar/Cell.cpp.gcov.html
new file mode 100644
index 0000000000..9bc54169ce
--- /dev/null
+++ b/coverage/colvar/Cell.cpp.gcov.html
@@ -0,0 +1,185 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Cell.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Cell.cpp<span style="font-size: 80%;"> (source / <a href="Cell.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR CELL</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate the components of the simulation cell</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : The following input tells plumed to print the squared modulo of each of the three lattice vectors</a>
+<a name="35"><span class="lineNum">      35 </span>            : \plumedfile</a>
+<a name="36"><span class="lineNum">      36 </span>            : cell: CELL</a>
+<a name="37"><span class="lineNum">      37 </span>            : aaa:    COMBINE ARG=cell.ax,cell.ay,cell.az POWERS=2,2,2 PERIODIC=NO</a>
+<a name="38"><span class="lineNum">      38 </span>            : bbb:    COMBINE ARG=cell.bx,cell.by,cell.bz POWERS=2,2,2 PERIODIC=NO</a>
+<a name="39"><span class="lineNum">      39 </span>            : ccc:    COMBINE ARG=cell.cx,cell.cy,cell.cz POWERS=2,2,2 PERIODIC=NO</a>
+<a name="40"><span class="lineNum">      40 </span>            : PRINT ARG=aaa,bbb,ccc</a>
+<a name="41"><span class="lineNum">      41 </span>            : \endplumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : */</a>
+<a name="44"><span class="lineNum">      44 </span>            : //+ENDPLUMEDOC</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : class Cell : public Colvar {</a>
+<a name="48"><span class="lineNum">      48 </span>            :   Value* components[3][3];</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit Cell(const ActionOptions&amp;);</a>
+<a name="52"><span class="lineNum">      52 </span>            : // active methods:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void calculate() override;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Register all the keywords for this action</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="56"><span class="lineNum">      56 </span>            : };</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(Cell,&quot;CELL&quot;)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          9 : Cell::Cell(const ActionOptions&amp;ao):</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          9 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : {</a>
+<a name="63"><span class="lineNum">      63 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;ax&quot;); componentIsNotPeriodic(&quot;ax&quot;); components[0][0]=getPntrToComponent(&quot;ax&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;ay&quot;); componentIsNotPeriodic(&quot;ay&quot;); components[0][1]=getPntrToComponent(&quot;ay&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;az&quot;); componentIsNotPeriodic(&quot;az&quot;); components[0][2]=getPntrToComponent(&quot;az&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;bx&quot;); componentIsNotPeriodic(&quot;bx&quot;); components[1][0]=getPntrToComponent(&quot;bx&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;by&quot;); componentIsNotPeriodic(&quot;by&quot;); components[1][1]=getPntrToComponent(&quot;by&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;bz&quot;); componentIsNotPeriodic(&quot;bz&quot;); components[1][2]=getPntrToComponent(&quot;bz&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;cx&quot;); componentIsNotPeriodic(&quot;cx&quot;); components[2][0]=getPntrToComponent(&quot;cx&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;cy&quot;); componentIsNotPeriodic(&quot;cy&quot;); components[2][1]=getPntrToComponent(&quot;cy&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         27 :   addComponentWithDerivatives(&quot;cz&quot;); componentIsNotPeriodic(&quot;cz&quot;); components[2][2]=getPntrToComponent(&quot;cz&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          9 :   requestAtoms(atoms);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          9 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         11 : void Cell::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         11 :   Action::registerKeywords( keys );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         11 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         11 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         11 :   componentsAreNotOptional(keys);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;ax&quot;,&quot;default&quot;,&quot;the ax component of the cell matrix&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;ay&quot;,&quot;default&quot;,&quot;the ay component of the cell matrix&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;az&quot;,&quot;default&quot;,&quot;the az component of the cell matrix&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;bx&quot;,&quot;default&quot;,&quot;the bx component of the cell matrix&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;by&quot;,&quot;default&quot;,&quot;the by component of the cell matrix&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;bz&quot;,&quot;default&quot;,&quot;the bz component of the cell matrix&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;cx&quot;,&quot;default&quot;,&quot;the cx component of the cell matrix&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;cy&quot;,&quot;default&quot;,&quot;the cy component of the cell matrix&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         22 :   keys.addOutputComponent(&quot;cz&quot;,&quot;default&quot;,&quot;the cz component of the cell matrix&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         11 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : // calculator</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        150 : void Cell::calculate() {</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1950 :   for(int i=0; i&lt;3; i++) for(int j=0; j&lt;3; j++) components[i][j]-&gt;set(getBox()[i][j]);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1950 :   for(int l=0; l&lt;3; l++) for(int m=0; m&lt;3; m++) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       5400 :       Tensor der; for(int i=0; i&lt;3; i++) der[i][m]=getBox()[l][i];</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1350 :       setBoxDerivatives(components[l][m],-der);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        150 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Constant.cpp.func-sort-c.html b/coverage/colvar/Constant.cpp.func-sort-c.html
new file mode 100644
index 0000000000..48a1e731fd
--- /dev/null
+++ b/coverage/colvar/Constant.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Constant.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Constant.cpp<span style="font-size: 80%;"> (<a href="Constant.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Constant.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#69">_ZN4PLMD6colvar8ConstantC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#67">_ZN4PLMD6colvar12_GLOBAL__N_120ConstantRegisterMe696createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#69">_ZN4PLMD6colvar8ConstantC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#105">_ZN4PLMD6colvar8Constant16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">41</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#116">_ZN4PLMD6colvar8Constant9calculateEv</a></td>
+              <td class="coverFnHi">3401</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#67">_ZN4PLMD6colvar12_GLOBAL__N_120ConstantRegisterMe69C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#67">_ZN4PLMD6colvar12_GLOBAL__N_120ConstantRegisterMe69D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Constant.cpp.func.html b/coverage/colvar/Constant.cpp.func.html
new file mode 100644
index 0000000000..73d9d0f191
--- /dev/null
+++ b/coverage/colvar/Constant.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Constant.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Constant.cpp<span style="font-size: 80%;"> (<a href="Constant.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Constant.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#67">_ZN4PLMD6colvar12_GLOBAL__N_120ConstantRegisterMe696createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#67">_ZN4PLMD6colvar12_GLOBAL__N_120ConstantRegisterMe69C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#67">_ZN4PLMD6colvar12_GLOBAL__N_120ConstantRegisterMe69D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#105">_ZN4PLMD6colvar8Constant16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">41</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#116">_ZN4PLMD6colvar8Constant9calculateEv</a></td>
+              <td class="coverFnHi">3401</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#69">_ZN4PLMD6colvar8ConstantC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Constant.cpp.gcov.html#69">_ZN4PLMD6colvar8ConstantC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Constant.cpp.gcov.html b/coverage/colvar/Constant.cpp.gcov.html
new file mode 100644
index 0000000000..5e83a39ddc
--- /dev/null
+++ b/coverage/colvar/Constant.cpp.gcov.html
@@ -0,0 +1,209 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Constant.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Constant.cpp<span style="font-size: 80%;"> (source / <a href="Constant.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace colvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC COLVAR CONSTANT</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Return one or more constant quantities with or without derivatives.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : Useful in combination with functions that</a>
+<a name="35"><span class="lineNum">      35 </span>            : takes in input constants or parameters.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The following input instructs plumed to compute the distance</a>
+<a name="40"><span class="lineNum">      40 </span>            : between atoms 1 and 2. If this distance is between 1.0 and 2.0, it is</a>
+<a name="41"><span class="lineNum">      41 </span>            : printed. If it is lower than 1.0 (larger than 2.0), 1.0 (2.0) is printed</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \plumedfile</a>
+<a name="44"><span class="lineNum">      44 </span>            : cn: CONSTANT VALUES=1.0,2.0</a>
+<a name="45"><span class="lineNum">      45 </span>            : dis: DISTANCE ATOMS=1,2</a>
+<a name="46"><span class="lineNum">      46 </span>            : sss: SORT ARG=cn.v-0,dis,cn.v-1</a>
+<a name="47"><span class="lineNum">      47 </span>            : PRINT ARG=sss.2</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : In case you want to pass a single value you can use VALUE:</a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : cn: CONSTANT VALUE=1.0</a>
+<a name="53"><span class="lineNum">      53 </span>            : dis: DISTANCE ATOMS=1,2</a>
+<a name="54"><span class="lineNum">      54 </span>            : sss: SORT ARG=cn,dis</a>
+<a name="55"><span class="lineNum">      55 </span>            : PRINT ARG=sss.1</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : class Constant : public Colvar {</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;double&gt; values;</a>
+<a name="63"><span class="lineNum">      63 </span>            : public:</a>
+<a name="64"><span class="lineNum">      64 </span>            :   explicit Constant(const ActionOptions&amp;);</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void calculate() override;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="67"><span class="lineNum">      67 </span>            : };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      12582 : PLUMED_REGISTER_ACTION(Constant,&quot;CONSTANT&quot;)</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         39 : Constant::Constant(const ActionOptions&amp;ao):</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         39 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         39 :   bool noderiv=false;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         39 :   parseFlag(&quot;NODERIV&quot;,noderiv);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         78 :   parseVector(&quot;VALUES&quot;,values);</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;double&gt; value;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         78 :   parseVector(&quot;VALUE&quot;,value);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         39 :   if(values.size()==0&amp;&amp;value.size()==0) error(&quot;One should use either VALUE or VALUES&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         39 :   if(values.size()!=0&amp;&amp;value.size()!=0) error(&quot;One should use either VALUE or VALUES&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         39 :   if(value.size()&gt;1) error(&quot;VALUE cannot take more than one number&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         39 :   if(values.size()==0) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         11 :     values.resize(1);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         11 :     values[0]=value[0];</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         39 :   checkRead();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         39 :   if(values.size()==1) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         38 :     if(!noderiv) addValueWithDerivatives();</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     else addValue();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         38 :     setNotPeriodic();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         38 :     setValue(values[0]);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          1 :   } else if(values.size()&gt;1) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;values.size(); i++) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 :       if(!noderiv) addComponentWithDerivatives(&quot;v-&quot;+num);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :       else addComponent(&quot;v-&quot;+num);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :       componentIsNotPeriodic(&quot;v-&quot;+num);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :       Value* comp=getPntrToComponent(&quot;v-&quot;+num);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :       comp-&gt;set(values[i]);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :     }</a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span>            : // fake request to avoid errors:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         39 :   requestAtoms(atoms);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         39 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         41 : void Constant::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         41 :   Colvar::registerKeywords( keys );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         41 :   componentsAreNotOptional(keys);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         41 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         82 :   keys.add(&quot;optional&quot;,&quot;VALUES&quot;,&quot;The values of the constants&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         82 :   keys.add(&quot;optional&quot;,&quot;VALUE&quot;,&quot;The value of the constant&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         82 :   keys.addFlag(&quot;NODERIV&quot;,false,&quot;Set to TRUE if you want values without derivatives.&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         82 :   keys.addOutputComponent(&quot;v&quot;,&quot;default&quot;,&quot;the # value&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         41 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : // calculator</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       3401 : void Constant::calculate() {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       3401 :   if(values.size()==1) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       3396 :     setValue(values[0]);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       3396 :     return;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;values.size(); i++) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         10 :     Value* comp=getPntrToComponent(i);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         10 :     comp-&gt;set(values[i]);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ContactMap.cpp.func-sort-c.html b/coverage/colvar/ContactMap.cpp.func-sort-c.html
new file mode 100644
index 0000000000..61d5b88d55
--- /dev/null
+++ b/coverage/colvar/ContactMap.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ContactMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ContactMap.cpp<span style="font-size: 80%;"> (<a href="ContactMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntry">132</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ContactMap.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#113">_ZN4PLMD6colvar10ContactMap18checkFieldsAllowedEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#141">_ZN4PLMD6colvar10ContactMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#141">_ZN4PLMD6colvar10ContactMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_123ContactMapRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#118">_ZN4PLMD6colvar10ContactMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#255">_ZN4PLMD6colvar10ContactMap9calculateEv</a></td>
+              <td class="coverFnHi">2215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_123ContactMapRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_123ContactMapRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ContactMap.cpp.func.html b/coverage/colvar/ContactMap.cpp.func.html
new file mode 100644
index 0000000000..a244962e59
--- /dev/null
+++ b/coverage/colvar/ContactMap.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ContactMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ContactMap.cpp<span style="font-size: 80%;"> (<a href="ContactMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntry">132</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ContactMap.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#118">_ZN4PLMD6colvar10ContactMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#113">_ZN4PLMD6colvar10ContactMap18checkFieldsAllowedEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#255">_ZN4PLMD6colvar10ContactMap9calculateEv</a></td>
+              <td class="coverFnHi">2215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#141">_ZN4PLMD6colvar10ContactMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#141">_ZN4PLMD6colvar10ContactMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_123ContactMapRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_123ContactMapRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContactMap.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_123ContactMapRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ContactMap.cpp.gcov.html b/coverage/colvar/ContactMap.cpp.gcov.html
new file mode 100644
index 0000000000..0ae2841514
--- /dev/null
+++ b/coverage/colvar/ContactMap.cpp.gcov.html
@@ -0,0 +1,402 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ContactMap.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ContactMap.cpp<span style="font-size: 80%;"> (source / <a href="ContactMap.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntry">132</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace colvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC COLVAR CONTACTMAP</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculate the distances between a number of pairs of atoms and transform each distance by a switching function.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : The transformed distance can be compared with a reference value in order to calculate the squared distance</a>
+<a name="35"><span class="lineNum">      35 </span>            : between two contact maps. Each distance can also be weighted for a given value. CONTACTMAP can be used together</a>
+<a name="36"><span class="lineNum">      36 </span>            : with \ref FUNCPATHMSD to define a path in the contactmap space.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The individual contact map distances related to each contact can be accessed as components</a>
+<a name="39"><span class="lineNum">      39 </span>            : named `cm.contact-1`, `cm.contact-2`, etc, assuming that the label of the CONTACTMAP is `cm`.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The following example calculates switching functions based on the distances between atoms</a>
+<a name="44"><span class="lineNum">      44 </span>            : 1 and 2, 3 and 4 and 4 and 5. The values of these three switching functions are then output</a>
+<a name="45"><span class="lineNum">      45 </span>            : to a file named colvar.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \plumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : CONTACTMAP ATOMS1=1,2 ATOMS2=3,4 ATOMS3=4,5 ATOMS4=5,6 SWITCH={RATIONAL R_0=1.5} LABEL=f1</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=f1.* FILE=colvar</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following example calculates the difference of the current contact map with respect</a>
+<a name="53"><span class="lineNum">      53 </span>            : to a reference provided. In this case REFERENCE is the fraction of contact that is formed</a>
+<a name="54"><span class="lineNum">      54 </span>            : (i.e. the distance between two atoms transformed with the SWITCH), while R_0 is the contact</a>
+<a name="55"><span class="lineNum">      55 </span>            : distance. WEIGHT gives the relative weight of each contact to the final distance measure.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : CONTACTMAP ...</a>
+<a name="59"><span class="lineNum">      59 </span>            : ATOMS1=1,2 REFERENCE1=0.1 WEIGHT1=0.5</a>
+<a name="60"><span class="lineNum">      60 </span>            : ATOMS2=3,4 REFERENCE2=0.5 WEIGHT2=1.0</a>
+<a name="61"><span class="lineNum">      61 </span>            : ATOMS3=4,5 REFERENCE3=0.25 WEIGHT3=1.0</a>
+<a name="62"><span class="lineNum">      62 </span>            : ATOMS4=5,6 REFERENCE4=0.0 WEIGHT4=0.5</a>
+<a name="63"><span class="lineNum">      63 </span>            : SWITCH={RATIONAL R_0=1.5}</a>
+<a name="64"><span class="lineNum">      64 </span>            : LABEL=cmap</a>
+<a name="65"><span class="lineNum">      65 </span>            : CMDIST</a>
+<a name="66"><span class="lineNum">      66 </span>            : ... CONTACTMAP</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : PRINT ARG=cmap FILE=colvar</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : The next example calculates calculates fraction of native contacts (Q)</a>
+<a name="72"><span class="lineNum">      72 </span>            : for Trp-cage mini-protein. R_0 is the distance at which the switch function is guaranteed to</a>
+<a name="73"><span class="lineNum">      73 </span>            : be 1.0 – it doesn't really matter for Q and  should be something very small, like 1 A.</a>
+<a name="74"><span class="lineNum">      74 </span>            : REF is the reference distance for the contact, e.g. the distance from a crystal structure.</a>
+<a name="75"><span class="lineNum">      75 </span>            : LAMBDA is the tolerance for the distance – if set to 1.0, the contact would have to have exactly</a>
+<a name="76"><span class="lineNum">      76 </span>            : the reference value to be formed; instead for lambda values of 1.5–1.8 are usually used to allow some slack.</a>
+<a name="77"><span class="lineNum">      77 </span>            : BETA is the softness of the switch function, default is 50nm.</a>
+<a name="78"><span class="lineNum">      78 </span>            : WEIGHT is the 1/(number of contacts) giving equal weight to each contact.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : When using native contact Q switch function, please cite \cite best2013</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : \plumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : # The full (much-longer) example available in regtest/basic/rt72/</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : CONTACTMAP ...</a>
+<a name="86"><span class="lineNum">      86 </span>            : ATOMS1=1,67 SWITCH1={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.4059} WEIGHT1=0.003597</a>
+<a name="87"><span class="lineNum">      87 </span>            : ATOMS2=1,68 SWITCH2={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.4039} WEIGHT2=0.003597</a>
+<a name="88"><span class="lineNum">      88 </span>            : ATOMS3=1,69 SWITCH3={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3215} WEIGHT3=0.003597</a>
+<a name="89"><span class="lineNum">      89 </span>            : ATOMS4=5,61 SWITCH4={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.4277} WEIGHT4=0.003597</a>
+<a name="90"><span class="lineNum">      90 </span>            : ATOMS5=5,67 SWITCH5={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3851} WEIGHT5=0.003597</a>
+<a name="91"><span class="lineNum">      91 </span>            : ATOMS6=5,68 SWITCH6={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3811} WEIGHT6=0.003597</a>
+<a name="92"><span class="lineNum">      92 </span>            : ATOMS7=5,69 SWITCH7={Q R_0=0.01 BETA=50.0 LAMBDA=1.5 REF=0.3133} WEIGHT7=0.003597</a>
+<a name="93"><span class="lineNum">      93 </span>            : LABEL=cmap</a>
+<a name="94"><span class="lineNum">      94 </span>            : SUM</a>
+<a name="95"><span class="lineNum">      95 </span>            : ... CONTACTMAP</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : PRINT ARG=cmap FILE=colvar</a>
+<a name="98"><span class="lineNum">      98 </span>            : \endplumedfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : (See also \ref switchingfunction)</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : */</a>
+<a name="102"><span class="lineNum">     102 </span>            : //+ENDPLUMEDOC</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : class ContactMap : public Colvar {</a>
+<a name="105"><span class="lineNum">     105 </span>            : private:</a>
+<a name="106"><span class="lineNum">     106 </span>            :   bool pbc, serial, docomp, dosum, docmdist;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::unique_ptr&lt;NeighborList&gt; nl;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt;SwitchingFunction&gt; sfs;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;double&gt; reference, weight;</a>
+<a name="110"><span class="lineNum">     110 </span>            : public:</a>
+<a name="111"><span class="lineNum">     111 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="112"><span class="lineNum">     112 </span>            :   explicit ContactMap(const ActionOptions&amp;);</a>
+<a name="113"><span class="lineNum">     113 </span>            : // active methods:</a>
+<a name="114"><span class="lineNum">     114 </span>            :   void calculate() override;</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   void checkFieldsAllowed() override {}</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : };</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(ContactMap,&quot;CONTACTMAP&quot;)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         10 : void ContactMap::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         10 :   Colvar::registerKeywords( keys );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the contacts you wish to calculate. &quot;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one contact will be &quot;</a>
+<a name="124"><span class="lineNum">     124 </span>            :            &quot;calculated for each ATOM keyword you specify.&quot;);</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         20 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;SWITCH&quot;,&quot;The switching functions to use for each of the contacts in your map. &quot;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :            &quot;You can either specify a global switching function using SWITCH or one &quot;</a>
+<a name="128"><span class="lineNum">     128 </span>            :            &quot;switching function for each contact. Details of the various switching &quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;functions you can use are provided on \\ref switchingfunction.&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;REFERENCE&quot;,&quot;A reference value for a given contact, by default is 0.0 &quot;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :            &quot;You can either specify a global reference value using REFERENCE or one &quot;</a>
+<a name="132"><span class="lineNum">     132 </span>            :            &quot;reference value for each contact.&quot;);</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;WEIGHT&quot;,&quot;A weight value for a given contact, by default is 1.0 &quot;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :            &quot;You can either specify a global weight value using WEIGHT or one &quot;</a>
+<a name="135"><span class="lineNum">     135 </span>            :            &quot;weight value for each contact.&quot;);</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         20 :   keys.reset_style(&quot;SWITCH&quot;,&quot;compulsory&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         20 :   keys.addFlag(&quot;SUM&quot;,false,&quot;calculate the sum of all the contacts in the input&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         20 :   keys.addFlag(&quot;CMDIST&quot;,false,&quot;calculate the distance with respect to the provided reference contact map&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         20 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         20 :   keys.addOutputComponent(&quot;contact&quot;,&quot;default&quot;,&quot;By not using SUM or CMDIST each contact will be stored in a component&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         10 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          8 : ContactMap::ContactMap(const ActionOptions&amp;ao):</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          8 :   pbc(true),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          8 :   serial(false),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          8 :   docomp(true),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          8 :   dosum(false),</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          8 :   docmdist(false)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : {</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          8 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          8 :   parseFlag(&quot;SUM&quot;,dosum);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          8 :   parseFlag(&quot;CMDIST&quot;,docmdist);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          8 :   if(docmdist==true&amp;&amp;dosum==true) error(&quot;You cannot use SUM and CMDIST together&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          8 :   bool nopbc=!pbc;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          8 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          8 :   pbc=!nopbc;</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Read in the atoms</a>
+<a name="160"><span class="lineNum">     160 </span>            :   std::vector&lt;AtomNumber&gt; t, ga_lista, gb_lista;</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          8 :   for(int i=1;; ++i ) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       1186 :     parseAtomList(&quot;ATOMS&quot;, i, t );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        593 :     if( t.empty() ) break;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        585 :     if( t.size()!=2 ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :       std::string ss; Tools::convert(i,ss);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       error(&quot;ATOMS&quot; + ss + &quot; keyword has the wrong number of atoms&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        585 :     ga_lista.push_back(t[0]); gb_lista.push_back(t[1]);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        585 :     t.resize(0);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :     // Add a value for this contact</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        585 :     std::string num; Tools::convert(i,num);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        595 :     if(!dosum&amp;&amp;!docmdist) {addComponentWithDerivatives(&quot;contact-&quot;+num); componentIsNotPeriodic(&quot;contact-&quot;+num);}</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        585 :   }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   // Create neighbour lists</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         16 :   nl=Tools::make_unique&lt;NeighborList&gt;(ga_lista,gb_lista,serial,true,pbc,getPbc(),comm);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   // Read in switching functions</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          8 :   std::string errors; sfs.resize( ga_lista.size() ); unsigned nswitch=0;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        593 :   for(unsigned i=0; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        585 :     std::string num, sw1; Tools::convert(i+1, num);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       1170 :     if( !parseNumbered( &quot;SWITCH&quot;, i+1, sw1 ) ) break;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        585 :     nswitch++; sfs[i].set(sw1,errors);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        585 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH&quot; + num + &quot; keyword : &quot; + errors );</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          8 :   if( nswitch==0 ) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     std::string sw; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     if(sw.length()==0) error(&quot;no switching function specified use SWITCH keyword&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :       sfs[i].set(sw,errors);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :     }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          8 :   } else if( nswitch!=sfs.size()  ) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert(nswitch+1, num);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     error(&quot;missing SWITCH&quot; + num + &quot; keyword&quot;);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Read in reference values</a>
+<a name="200"><span class="lineNum">     200 </span>            :   nswitch=0;</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          8 :   reference.resize(ga_lista.size(), 0.);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         18 :   for(unsigned i=0; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         32 :     if( !parseNumbered( &quot;REFERENCE&quot;, i+1, reference[i] ) ) break;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         10 :     nswitch++;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          8 :   if( nswitch==0 ) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          6 :     parse(&quot;REFERENCE&quot;,reference[0]);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        575 :     for(unsigned i=1; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        569 :       reference[i]=reference[0];</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        569 :       nswitch++;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     }</a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          8 :   if(nswitch == 0 &amp;&amp; docmdist) error(&quot;with CMDIST one must use REFERENCE to setup the reference contact map&quot;);</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   // Read in weight values</a>
+<a name="216"><span class="lineNum">     216 </span>            :   nswitch=0;</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          8 :   weight.resize(ga_lista.size(), 1.0);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        588 :   for(unsigned i=0; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1162 :     if( !parseNumbered( &quot;WEIGHT&quot;, i+1, weight[i] ) ) break;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        580 :     nswitch++;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          8 :   if( nswitch==0 ) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          1 :     parse(&quot;WEIGHT&quot;,weight[0]);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          5 :     for(unsigned i=1; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :       weight[i]=weight[0];</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :     }</a>
+<a name="227"><span class="lineNum">     227 </span>            :     nswitch = ga_lista.size();</a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   // Output details of all contacts</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        593 :   for(unsigned i=0; i&lt;sfs.size(); ++i) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        585 :     log.printf(&quot;  The %uth contact is calculated from atoms : %d %d. Inflection point of switching function is at %s. Reference contact value is %f\n&quot;,</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       1170 :                i+1, ga_lista[i].serial(), gb_lista[i].serial(), ( sfs[i].description() ).c_str(), reference[i] );</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          8 :   if(dosum) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          5 :     addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          5 :     log.printf(&quot;  colvar is sum of all contacts in contact map\n&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   }</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          8 :   if(docmdist) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 :     addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          2 :     log.printf(&quot;  colvar is distance between the contact map matrix and the provided reference matrix\n&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          8 :   if(dosum || docmdist) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          7 :     docomp=false;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   } else {</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          1 :     serial=true;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          1 :     docomp=true;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   }</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :   // Set up if it is just a list of contacts</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          8 :   requestAtoms(nl-&gt;getFullAtomList());</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          8 : }</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       2215 : void ContactMap::calculate() {</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       2215 :   double ncoord=0.;</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       2215 :   Tensor virial;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       2215 :   std::vector&lt;Vector&gt; deriv(getNumberOfAtoms());</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   unsigned stride;</a>
+<a name="264"><span class="lineNum">     264 </span>            :   unsigned rank;</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       2215 :   if(serial) {</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :     // when using components the parallelisation do not work</a>
+<a name="267"><span class="lineNum">     267 </span>            :     stride=1;</a>
+<a name="268"><span class="lineNum">     268 </span>            :     rank=0;</a>
+<a name="269"><span class="lineNum">     269 </span>            :   } else {</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       2210 :     stride=comm.Get_size();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       2210 :     rank=comm.Get_rank();</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :   }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : // sum over close pairs</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">     149835 :   for(unsigned i=rank; i&lt;nl-&gt;size(); i+=stride) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">     147620 :     Vector distance;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">     147620 :     unsigned i0=nl-&gt;getClosePair(i).first;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">     147620 :     unsigned i1=nl-&gt;getClosePair(i).second;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">     147620 :     if(pbc) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">     147620 :       distance=pbcDistance(getPosition(i0),getPosition(i1));</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     } else {</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :       distance=delta(getPosition(i0),getPosition(i1));</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     147620 :     double dfunc=0.;</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">     147620 :     double coord = weight[i]*(sfs[i].calculate(distance.modulo(), dfunc) - reference[i]);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     147620 :     Vector tmpder = weight[i]*dfunc*distance;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     147620 :     Tensor tmpvir = weight[i]*dfunc*Tensor(distance,distance);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     147620 :     if(!docmdist) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     146595 :       deriv[i0] -= tmpder;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     146595 :       deriv[i1] += tmpder;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">     146595 :       virial    -= tmpvir;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     146595 :       ncoord    += coord;</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :     } else {</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       1025 :       tmpder *= 2.*coord;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       1025 :       tmpvir *= 2.*coord;</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       1025 :       deriv[i0] -= tmpder;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1025 :       deriv[i1] += tmpder;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       1025 :       virial    -= tmpvir;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1025 :       ncoord    += coord*coord;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :     }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">     147620 :     if(docomp) {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         25 :       Value* val=getPntrToComponent( i );</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         25 :       setAtomsDerivatives( val, i0, deriv[i0] );</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         25 :       setAtomsDerivatives( val, i1, deriv[i1] );</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         25 :       setBoxDerivatives( val, -tmpvir );</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :       val-&gt;set(coord);</a>
+<a name="309"><span class="lineNum">     309 </span>            :     }</a>
+<a name="310"><span class="lineNum">     310 </span>            :   }</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       2215 :   if(!serial) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       2210 :     comm.Sum(&amp;ncoord,1);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       2210 :     if(!deriv.empty()) comm.Sum(&amp;deriv[0][0],3*deriv.size());</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       2210 :     comm.Sum(&amp;virial[0][0],9);</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :   }</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       2215 :   if( !docomp ) {</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">     297400 :     for(unsigned i=0; i&lt;deriv.size(); ++i) setAtomsDerivatives(i,deriv[i]);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       2210 :     setValue           (ncoord);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       2210 :     setBoxDerivatives  (virial);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   }</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       2215 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            : }</a>
+<a name="326"><span class="lineNum">     326 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Coordination.cpp.func-sort-c.html b/coverage/colvar/Coordination.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d5b0dfe335
--- /dev/null
+++ b/coverage/colvar/Coordination.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Coordination.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Coordination.cpp<span style="font-size: 80%;"> (<a href="Coordination.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Coordination.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#116">_ZN4PLMD6colvar12CoordinationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#116">_ZN4PLMD6colvar12CoordinationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">185</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#103">_ZN4PLMD6colvar12_GLOBAL__N_125CoordinationRegisterMe1056createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">185</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#105">_ZN4PLMD6colvar12Coordination16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">187</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#103">_ZN4PLMD6colvar12_GLOBAL__N_125CoordinationRegisterMe105C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#103">_ZN4PLMD6colvar12_GLOBAL__N_125CoordinationRegisterMe105D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#144">_ZNK4PLMD6colvar12Coordination7pairingEdRdjj</a></td>
+              <td class="coverFnHi">15263796</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Coordination.cpp.func.html b/coverage/colvar/Coordination.cpp.func.html
new file mode 100644
index 0000000000..d49c5e20bc
--- /dev/null
+++ b/coverage/colvar/Coordination.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Coordination.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Coordination.cpp<span style="font-size: 80%;"> (<a href="Coordination.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Coordination.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#105">_ZN4PLMD6colvar12Coordination16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">187</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#116">_ZN4PLMD6colvar12CoordinationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">185</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#116">_ZN4PLMD6colvar12CoordinationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#103">_ZN4PLMD6colvar12_GLOBAL__N_125CoordinationRegisterMe1056createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">185</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#103">_ZN4PLMD6colvar12_GLOBAL__N_125CoordinationRegisterMe105C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#103">_ZN4PLMD6colvar12_GLOBAL__N_125CoordinationRegisterMe105D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Coordination.cpp.gcov.html#144">_ZNK4PLMD6colvar12Coordination7pairingEdRdjj</a></td>
+              <td class="coverFnHi">15263796</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Coordination.cpp.gcov.html b/coverage/colvar/Coordination.cpp.gcov.html
new file mode 100644
index 0000000000..09f34720f6
--- /dev/null
+++ b/coverage/colvar/Coordination.cpp.gcov.html
@@ -0,0 +1,230 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Coordination.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Coordination.cpp<span style="font-size: 80%;"> (source / <a href="Coordination.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CoordinationBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR COORDINATION</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate coordination numbers.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This keyword can be used to calculate the number of contacts between two groups of atoms</a>
+<a name="34"><span class="lineNum">      34 </span>            : and is defined as</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f[</a>
+<a name="36"><span class="lineNum">      36 </span>            : \sum_{i\in A} \sum_{i\in B} s_{ij}</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f]</a>
+<a name="38"><span class="lineNum">      38 </span>            : where \f$s_{ij}\f$ is 1 if the contact between atoms \f$i\f$ and \f$j\f$ is formed,</a>
+<a name="39"><span class="lineNum">      39 </span>            : zero otherwise.</a>
+<a name="40"><span class="lineNum">      40 </span>            : In actuality, \f$s_{ij}\f$ is replaced with a switching function so as to ensure that the calculated CV has continuous derivatives.</a>
+<a name="41"><span class="lineNum">      41 </span>            : The default switching function is:</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : s_{ij} = \frac{ 1 - \left(\frac{{\bf r}_{ij}-d_0}{r_0}\right)^n } { 1 - \left(\frac{{\bf r}_{ij}-d_0}{r_0}\right)^m }</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : but it can be changed using the optional SWITCH option.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : To make your calculation faster you can use a neighbor list, which makes it that only a</a>
+<a name="48"><span class="lineNum">      48 </span>            : relevant subset of the pairwise distance are calculated at every step.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : If GROUPB is empty, it will sum the \f$\frac{N(N-1)}{2}\f$ pairs in GROUPA. This avoids computing</a>
+<a name="51"><span class="lineNum">      51 </span>            : twice permuted indexes (e.g. pair (i,j) and (j,i)) thus running at twice the speed.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : Notice that if there are common atoms between GROUPA and GROUPB the switching function should be</a>
+<a name="54"><span class="lineNum">      54 </span>            : equal to one. These &quot;self contacts&quot; are discarded by plumed (since version 2.1),</a>
+<a name="55"><span class="lineNum">      55 </span>            : so that they actually count as &quot;zero&quot;.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following example instructs plumed to calculate the total coordination number of the atoms in group 1-10 with the atoms in group 20-100.  For atoms 1-10 coordination numbers are calculated that count the number of atoms from the second group that are within 0.3 nm of the central atom.  A neighbor list is used to make this calculation faster, this neighbor list is updated every 100 steps.</a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : COORDINATION GROUPA=1-10 GROUPB=20-100 R_0=0.3 NLIST NL_CUTOFF=0.5 NL_STRIDE=100</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endplumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : The following is a dummy example which should compute the value 0 because the self interaction</a>
+<a name="66"><span class="lineNum">      66 </span>            : of atom 1 is skipped. Notice that in plumed 2.0 &quot;self interactions&quot; were not skipped, and the</a>
+<a name="67"><span class="lineNum">      67 </span>            : same calculation should return 1.</a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : c: COORDINATION GROUPA=1 GROUPB=1 R_0=0.3</a>
+<a name="70"><span class="lineNum">      70 </span>            : PRINT ARG=c STRIDE=10</a>
+<a name="71"><span class="lineNum">      71 </span>            : \endplumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : Here's an example that shows what happens when providing COORDINATION with</a>
+<a name="74"><span class="lineNum">      74 </span>            : a single group:</a>
+<a name="75"><span class="lineNum">      75 </span>            : \plumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : # define some huge group:</a>
+<a name="77"><span class="lineNum">      77 </span>            : group: GROUP ATOMS=1-1000</a>
+<a name="78"><span class="lineNum">      78 </span>            : # Here's coordination of a group against itself:</a>
+<a name="79"><span class="lineNum">      79 </span>            : c1: COORDINATION GROUPA=group GROUPB=group R_0=0.3</a>
+<a name="80"><span class="lineNum">      80 </span>            : # Here's coordination within a single group:</a>
+<a name="81"><span class="lineNum">      81 </span>            : x: COORDINATION GROUPA=group R_0=0.3</a>
+<a name="82"><span class="lineNum">      82 </span>            : # This is just multiplying times 2 the variable x:</a>
+<a name="83"><span class="lineNum">      83 </span>            : c2: COMBINE ARG=x COEFFICIENTS=2 PERIODIC=NO</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : # the two variables c1 and c2 should be identical, but the calculation of c2 is twice faster</a>
+<a name="86"><span class="lineNum">      86 </span>            : # since it runs on half of the pairs.</a>
+<a name="87"><span class="lineNum">      87 </span>            : PRINT ARG=c1,c2 STRIDE=10</a>
+<a name="88"><span class="lineNum">      88 </span>            : \endplumedfile</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : */</a>
+<a name="93"><span class="lineNum">      93 </span>            : //+ENDPLUMEDOC</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : class Coordination : public CoordinationBase {</a>
+<a name="96"><span class="lineNum">      96 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : public:</a>
+<a name="99"><span class="lineNum">      99 </span>            :   explicit Coordination(const ActionOptions&amp;);</a>
+<a name="100"><span class="lineNum">     100 </span>            : // active methods:</a>
+<a name="101"><span class="lineNum">     101 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="102"><span class="lineNum">     102 </span>            :   double pairing(double distance,double&amp;dfunc,unsigned i,unsigned j)const override;</a>
+<a name="103"><span class="lineNum">     103 </span>            : };</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      12869 : PLUMED_REGISTER_ACTION(Coordination,&quot;COORDINATION&quot;)</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        187 : void Coordination::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        187 :   CoordinationBase::registerKeywords(keys);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        374 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        374 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        374 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        374 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        374 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="115"><span class="lineNum">     115 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        187 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        185 : Coordination::Coordination(const ActionOptions&amp;ao):</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   Action(ao),</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        185 :   CoordinationBase(ao)</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : {</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::string sw,errors;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        370 :   parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        185 :   if(sw.length()&gt;0) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        136 :     switchingFunction.set(sw,errors);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        134 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   } else {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         49 :     int nn=6;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         49 :     int mm=0;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         49 :     double d0=0.0;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         49 :     double r0=0.0;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         49 :     parse(&quot;R_0&quot;,r0);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         49 :     if(r0&lt;=0.0) error(&quot;R_0 should be explicitly specified and positive&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         49 :     parse(&quot;D_0&quot;,d0);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         49 :     parse(&quot;NN&quot;,nn);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         47 :     parse(&quot;MM&quot;,mm);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         47 :     switchingFunction.set(nn,mm,r0,d0);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        180 :   checkRead();</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        365 :   log&lt;&lt;&quot;  contacts are counted with cutoff &quot;&lt;&lt;switchingFunction.description()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        195 : }</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">   15263796 : double Coordination::pairing(double distance,double&amp;dfunc,unsigned i,unsigned j)const {</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   (void) i; // avoid warnings</a>
+<a name="148"><span class="lineNum">     148 </span>            :   (void) j; // avoid warnings</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">   15263796 :   return switchingFunction.calculateSqr(distance,dfunc);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/CoordinationBase.cpp.func-sort-c.html b/coverage/colvar/CoordinationBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..410604b395
--- /dev/null
+++ b/coverage/colvar/CoordinationBase.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/CoordinationBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - CoordinationBase.cpp<span style="font-size: 80%;"> (<a href="CoordinationBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoordinationBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#39">_ZN4PLMD6colvar16CoordinationBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#105">_ZN4PLMD6colvar16CoordinationBaseD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#105">_ZN4PLMD6colvar16CoordinationBaseD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#39">_ZN4PLMD6colvar16CoordinationBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#105">_ZN4PLMD6colvar16CoordinationBaseD2Ev</a></td>
+              <td class="coverFnHi">194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#28">_ZN4PLMD6colvar16CoordinationBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#125">_ZN4PLMD6colvar16CoordinationBase9calculateEv</a></td>
+              <td class="coverFnHi">3132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#109">_ZN4PLMD6colvar16CoordinationBase7prepareEv</a></td>
+              <td class="coverFnHi">3357</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/CoordinationBase.cpp.func.html b/coverage/colvar/CoordinationBase.cpp.func.html
new file mode 100644
index 0000000000..3b225be43f
--- /dev/null
+++ b/coverage/colvar/CoordinationBase.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/CoordinationBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - CoordinationBase.cpp<span style="font-size: 80%;"> (<a href="CoordinationBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CoordinationBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#28">_ZN4PLMD6colvar16CoordinationBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#109">_ZN4PLMD6colvar16CoordinationBase7prepareEv</a></td>
+              <td class="coverFnHi">3357</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#125">_ZN4PLMD6colvar16CoordinationBase9calculateEv</a></td>
+              <td class="coverFnHi">3132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#39">_ZN4PLMD6colvar16CoordinationBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#39">_ZN4PLMD6colvar16CoordinationBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#105">_ZN4PLMD6colvar16CoordinationBaseD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#105">_ZN4PLMD6colvar16CoordinationBaseD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationBase.cpp.gcov.html#105">_ZN4PLMD6colvar16CoordinationBaseD2Ev</a></td>
+              <td class="coverFnHi">194</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/CoordinationBase.cpp.gcov.html b/coverage/colvar/CoordinationBase.cpp.gcov.html
new file mode 100644
index 0000000000..c44a8f7a40
--- /dev/null
+++ b/coverage/colvar/CoordinationBase.cpp.gcov.html
@@ -0,0 +1,288 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/CoordinationBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - CoordinationBase.cpp<span style="font-size: 80%;"> (source / <a href="CoordinationBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CoordinationBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace colvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        200 : void CoordinationBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        200 :   Colvar::registerKeywords(keys);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        400 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        400 :   keys.addFlag(&quot;PAIR&quot;,false,&quot;Pair only 1st element of the 1st group with 1st element in the second, etc&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        400 :   keys.addFlag(&quot;NLIST&quot;,false,&quot;Use a neighbor list to speed up the calculation&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        400 :   keys.add(&quot;optional&quot;,&quot;NL_CUTOFF&quot;,&quot;The cutoff for the neighbor list&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        400 :   keys.add(&quot;optional&quot;,&quot;NL_STRIDE&quot;,&quot;The frequency with which we are updating the atoms in the neighbor list&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        400 :   keys.add(&quot;atoms&quot;,&quot;GROUPA&quot;,&quot;First list of atoms&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        400 :   keys.add(&quot;atoms&quot;,&quot;GROUPB&quot;,&quot;Second list of atoms (if empty, N*(N-1)/2 pairs in GROUPA are counted)&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        200 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        194 : CoordinationBase::CoordinationBase(const ActionOptions&amp;ao):</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        194 :   pbc(true),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        194 :   serial(false),</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        194 :   invalidateList(true),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        194 :   firsttime(true)</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : {</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        388 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;AtomNumber&gt; ga_lista,gb_lista;</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        194 :   parseAtomList(&quot;GROUPA&quot;,ga_lista);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        194 :   parseAtomList(&quot;GROUPB&quot;,gb_lista);</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        194 :   bool nopbc=!pbc;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        194 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        194 :   pbc=!nopbc;</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : // pair stuff</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        194 :   bool dopair=false;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        194 :   parseFlag(&quot;PAIR&quot;,dopair);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : // neighbor list stuff</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        194 :   bool doneigh=false;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        194 :   double nl_cut=0.0;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        194 :   int nl_st=0;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        194 :   parseFlag(&quot;NLIST&quot;,doneigh);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        194 :   if(doneigh) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         24 :     parse(&quot;NL_CUTOFF&quot;,nl_cut);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         24 :     if(nl_cut&lt;=0.0) error(&quot;NL_CUTOFF should be explicitly specified and positive&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         24 :     parse(&quot;NL_STRIDE&quot;,nl_st);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         24 :     if(nl_st&lt;=0) error(&quot;NL_STRIDE should be explicitly specified and positive&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        194 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        194 :   if(gb_lista.size()&gt;0) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        207 :     if(doneigh)  nl=Tools::make_unique&lt;NeighborList&gt;(ga_lista,gb_lista,serial,dopair,pbc,getPbc(),comm,nl_cut,nl_st);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        318 :     else         nl=Tools::make_unique&lt;NeighborList&gt;(ga_lista,gb_lista,serial,dopair,pbc,getPbc(),comm);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   } else {</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         11 :     if(doneigh)  nl=Tools::make_unique&lt;NeighborList&gt;(ga_lista,serial,pbc,getPbc(),comm,nl_cut,nl_st);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         22 :     else         nl=Tools::make_unique&lt;NeighborList&gt;(ga_lista,serial,pbc,getPbc(),comm);</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        194 :   requestAtoms(nl-&gt;getFullAtomList());</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        194 :   log.printf(&quot;  between two groups of %u and %u atoms\n&quot;,static_cast&lt;unsigned&gt;(ga_lista.size()),static_cast&lt;unsigned&gt;(gb_lista.size()));</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        194 :   log.printf(&quot;  first group:\n&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       5465 :   for(unsigned int i=0; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       5271 :     if ( (i+1) % 25 == 0 ) log.printf(&quot;  \n&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       5271 :     log.printf(&quot;  %d&quot;, ga_lista[i].serial());</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        194 :   log.printf(&quot;  \n  second group:\n&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      10817 :   for(unsigned int i=0; i&lt;gb_lista.size(); ++i) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      10623 :     if ( (i+1) % 25 == 0 ) log.printf(&quot;  \n&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      10623 :     log.printf(&quot;  %d&quot;, gb_lista[i].serial());</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        194 :   log.printf(&quot;  \n&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        194 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        194 :   if(dopair) log.printf(&quot;  with PAIR option\n&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        194 :   if(doneigh) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         24 :     log.printf(&quot;  using neighbor lists with\n&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         24 :     log.printf(&quot;  update every %d steps and cutoff %f\n&quot;,nl_st,nl_cut);</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        194 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        194 : CoordinationBase::~CoordinationBase() {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : // destructor required to delete forward declared class</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        194 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       3357 : void CoordinationBase::prepare() {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       3357 :   if(nl-&gt;getStride()&gt;0) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        216 :     if(firsttime || (getStep()%nl-&gt;getStride()==0)) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        179 :       requestAtoms(nl-&gt;getFullAtomList());</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        179 :       invalidateList=true;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        179 :       firsttime=false;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     } else {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         37 :       requestAtoms(nl-&gt;getReducedAtomList());</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         37 :       invalidateList=false;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         37 :       if(getExchangeStep()) error(&quot;Neighbor lists should be updated on exchange steps - choose a NL_STRIDE which divides the exchange stride!&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        216 :     if(getExchangeStep()) firsttime=true;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       3357 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : // calculator</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       3132 : void CoordinationBase::calculate()</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : {</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       3132 :   double ncoord=0.;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       3132 :   Tensor virial;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       3132 :   std::vector&lt;Vector&gt; deriv(getNumberOfAtoms());</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       3132 :   if(nl-&gt;getStride()&gt;0 &amp;&amp; invalidateList) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        143 :     nl-&gt;update(getPositions());</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   unsigned stride;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   unsigned rank;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       3132 :   if(serial) {</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     stride=1;</a>
+<a name="142"><span class="lineNum">     142 </span>            :     rank=0;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   } else {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       3132 :     stride=comm.Get_size();</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       3132 :     rank=comm.Get_rank();</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       3132 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       3132 :   const unsigned nn=nl-&gt;size();</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       3132 :   if(nt*stride*10&gt;nn) nt=1;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       3132 :   const unsigned elementsPerRank = std::ceil(double(nn)/stride);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       3132 :   const unsigned int start= rank*elementsPerRank;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       3132 :   const unsigned int end = ((start + elementsPerRank)&lt; nn)?(start + elementsPerRank): nn;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       3132 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   {</a>
+<a name="158"><span class="lineNum">     158 </span>            :     std::vector&lt;Vector&gt; omp_deriv(getPositions().size());</a>
+<a name="159"><span class="lineNum">     159 </span>            :     Tensor omp_virial;</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            :     #pragma omp for reduction(+:ncoord) nowait</a>
+<a name="162"><span class="lineNum">     162 </span>            :     for(unsigned int i=start; i&lt;end; ++i) {</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            :       Vector distance;</a>
+<a name="165"><span class="lineNum">     165 </span>            :       const unsigned i0=nl-&gt;getClosePair(i).first;</a>
+<a name="166"><span class="lineNum">     166 </span>            :       const unsigned i1=nl-&gt;getClosePair(i).second;</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :       if(getAbsoluteIndex(i0)==getAbsoluteIndex(i1)) continue;</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            :       if(pbc) {</a>
+<a name="171"><span class="lineNum">     171 </span>            :         distance=pbcDistance(getPosition(i0),getPosition(i1));</a>
+<a name="172"><span class="lineNum">     172 </span>            :       } else {</a>
+<a name="173"><span class="lineNum">     173 </span>            :         distance=delta(getPosition(i0),getPosition(i1));</a>
+<a name="174"><span class="lineNum">     174 </span>            :       }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :       double dfunc=0.;</a>
+<a name="177"><span class="lineNum">     177 </span>            :       ncoord += pairing(distance.modulo2(), dfunc,i0,i1);</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :       Vector dd(dfunc*distance);</a>
+<a name="180"><span class="lineNum">     180 </span>            :       Tensor vv(dd,distance);</a>
+<a name="181"><span class="lineNum">     181 </span>            :       if(nt&gt;1) {</a>
+<a name="182"><span class="lineNum">     182 </span>            :         omp_deriv[i0]-=dd;</a>
+<a name="183"><span class="lineNum">     183 </span>            :         omp_deriv[i1]+=dd;</a>
+<a name="184"><span class="lineNum">     184 </span>            :         omp_virial-=vv;</a>
+<a name="185"><span class="lineNum">     185 </span>            :       } else {</a>
+<a name="186"><span class="lineNum">     186 </span>            :         deriv[i0]-=dd;</a>
+<a name="187"><span class="lineNum">     187 </span>            :         deriv[i1]+=dd;</a>
+<a name="188"><span class="lineNum">     188 </span>            :         virial-=vv;</a>
+<a name="189"><span class="lineNum">     189 </span>            :       }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :     }</a>
+<a name="192"><span class="lineNum">     192 </span>            :     #pragma omp critical</a>
+<a name="193"><span class="lineNum">     193 </span>            :     if(nt&gt;1) {</a>
+<a name="194"><span class="lineNum">     194 </span>            :       for(unsigned i=0; i&lt;getPositions().size(); i++)</a>
+<a name="195"><span class="lineNum">     195 </span>            :         deriv[i]+=omp_deriv[i];</a>
+<a name="196"><span class="lineNum">     196 </span>            :       virial+=omp_virial;</a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       3132 :   if(!serial) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       3132 :     comm.Sum(ncoord);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       3132 :     if(!deriv.empty()) comm.Sum(&amp;deriv[0][0],3*deriv.size());</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       3132 :     comm.Sum(virial);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">     378180 :   for(unsigned i=0; i&lt;deriv.size(); ++i) setAtomsDerivatives(i,deriv[i]);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       3132 :   setValue           (ncoord);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       3132 :   setBoxDerivatives  (virial);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       3132 : }</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/DHEnergy.cpp.func-sort-c.html b/coverage/colvar/DHEnergy.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d40e9cdb14
--- /dev/null
+++ b/coverage/colvar/DHEnergy.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/DHEnergy.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - DHEnergy.cpp<span style="font-size: 80%;"> (<a href="DHEnergy.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">94.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DHEnergy.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#105">_ZN4PLMD6colvar8DHEnergyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_120DHEnergyRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#105">_ZN4PLMD6colvar8DHEnergyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#75">_ZN4PLMD6colvar8DHEnergy16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#127">_ZNK4PLMD6colvar8DHEnergy7pairingEdRdjj</a></td>
+              <td class="coverFnHi">840</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_120DHEnergyRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_120DHEnergyRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/DHEnergy.cpp.func.html b/coverage/colvar/DHEnergy.cpp.func.html
new file mode 100644
index 0000000000..2a8106f94b
--- /dev/null
+++ b/coverage/colvar/DHEnergy.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/DHEnergy.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - DHEnergy.cpp<span style="font-size: 80%;"> (<a href="DHEnergy.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">94.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DHEnergy.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_120DHEnergyRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_120DHEnergyRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_120DHEnergyRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#75">_ZN4PLMD6colvar8DHEnergy16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#105">_ZN4PLMD6colvar8DHEnergyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#105">_ZN4PLMD6colvar8DHEnergyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DHEnergy.cpp.gcov.html#127">_ZNK4PLMD6colvar8DHEnergy7pairingEdRdjj</a></td>
+              <td class="coverFnHi">840</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/DHEnergy.cpp.gcov.html b/coverage/colvar/DHEnergy.cpp.gcov.html
new file mode 100644
index 0000000000..aab248ae8e
--- /dev/null
+++ b/coverage/colvar/DHEnergy.cpp.gcov.html
@@ -0,0 +1,220 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/DHEnergy.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - DHEnergy.cpp<span style="font-size: 80%;"> (source / <a href="DHEnergy.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">94.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CoordinationBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace colvar {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC COLVAR DHENERGY</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculate Debye-Huckel interaction energy among GROUPA and GROUPB.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This variable calculates the electrostatic interaction among GROUPA and GROUPB</a>
+<a name="36"><span class="lineNum">      36 </span>            : using a Debye-Huckel approximation defined as</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : \frac{1}{4\pi\epsilon_r\epsilon_0}</a>
+<a name="39"><span class="lineNum">      39 </span>            : \sum_{i\in A} \sum_{j \in B} q_i q_j</a>
+<a name="40"><span class="lineNum">      40 </span>            : \frac{e^{-\kappa |{\bf r}_{ij}|}}{|{\bf r}_{ij}|}</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : This collective variable can be used to analyze or induce electrostatically driven reactions \cite do13jctc.</a>
+<a name="44"><span class="lineNum">      44 </span>            : Notice that the value of the DHENERGY is returned in plumed units (see \ref UNITS).</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : If GROUPB is empty, it will sum the N*(N-1)/2 pairs in GROUPA. This avoids computing</a>
+<a name="47"><span class="lineNum">      47 </span>            : twice permuted indexes (e.g. pair (i,j) and (j,i)) thus running at twice the speed.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Notice that if there are common atoms between GROUPA and GROUPB their interaction is discarded.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : # this is printing the electrostatic interaction between two groups of atoms</a>
+<a name="56"><span class="lineNum">      56 </span>            : dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=dh</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : */</a>
+<a name="61"><span class="lineNum">      61 </span>            : //+ENDPLUMEDOC</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : class DHEnergy : public CoordinationBase {</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double k; // Inverse Debye screening length</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double constant;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double epsilon;</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : public:</a>
+<a name="69"><span class="lineNum">      69 </span>            :   explicit DHEnergy(const ActionOptions&amp;);</a>
+<a name="70"><span class="lineNum">      70 </span>            : // active methods:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double pairing(double distance,double&amp;dfunc,unsigned i,unsigned j)const override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(DHEnergy,&quot;DHENERGY&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         10 : void DHEnergy::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         10 :   CoordinationBase::registerKeywords(keys);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;I&quot;,&quot;1.0&quot;,&quot;Ionic strength (M)&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;TEMP&quot;,&quot;300.0&quot;,&quot;Simulation temperature (K)&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;EPSILON&quot;,&quot;80.0&quot;,&quot;Dielectric constant of solvent&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         10 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : /*</a>
+<a name="85"><span class="lineNum">      85 </span>            : Global constants in SI unit used in this calculation:</a>
+<a name="86"><span class="lineNum">      86 </span>            :       N_A = 6.0221412927 * 10^(23) mol^(-1) : Avogadro number</a>
+<a name="87"><span class="lineNum">      87 </span>            :       q = 1.60217656535 * 10^(-19) C : proton charge</a>
+<a name="88"><span class="lineNum">      88 </span>            :       e_0 = 8.854187817620 * 10^(-12) C^2/(N*m^2) : vacuum's dielectric constant</a>
+<a name="89"><span class="lineNum">      89 </span>            :       k_B = 1.380648813 * 10^(-23) N*m/K : Boltzmann constant</a>
+<a name="90"><span class="lineNum">      90 </span>            : In SI unit, Debye Huckel CV is defined as:</a>
+<a name="91"><span class="lineNum">      91 </span>            :       DHen = \sum_i\sum_j (q_i*q_j*q^2*N_A)/(4*pi*eps*e_0) * exp(-k*|f_ij|)/(|f_ij|)</a>
+<a name="92"><span class="lineNum">      92 </span>            :              + \sum_i\sum_j (q_i*q_j*q^2*N_A)/(4*pi*epp*e_0) * (1/|r_ij| - 1/|f_ij|)</a>
+<a name="93"><span class="lineNum">      93 </span>            :            = (q^2*N_A)/(4*pi*e_0) * \sum_i\sum_j q_i*q_j * (exp(-k*|f_ij|)/(eps*|f_ij|) + 1/epp*(1/|r_ij| - 1/|f_ij|))</a>
+<a name="94"><span class="lineNum">      94 </span>            : (in which |f_ij| = \sqrt(|r_ij|^2+\sigma_i*\sigma_j*exp(-|r_ij|^2/4*\sigma_i*\sigma_j)),</a>
+<a name="95"><span class="lineNum">      95 </span>            :  \sigma_i and \sigma_j are the effective Born radius.)</a>
+<a name="96"><span class="lineNum">      96 </span>            : For an efficient calculation, we group constants and variables into groups:</a>
+<a name="97"><span class="lineNum">      97 </span>            :       constant = (q^2*N_A)/(4*pi*e_0)</a>
+<a name="98"><span class="lineNum">      98 </span>            :       tmp = 1/eps*exp(-k*|f_ij|)/(|f_ij|) + 1/epp*(1/|r_ij| - 1/|f_ij|)</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : To speed up the loop calculation, constant can be modified as followed:</a>
+<a name="101"><span class="lineNum">     101 </span>            :       constant= (q^2*N_A)/(4*pi*e_0*10^(-9))*10^(-3) (kJ/mol)</a>
+<a name="102"><span class="lineNum">     102 </span>            :               = ((1.60217656535*10^(-19))^2*6.0221412927*10^(23)*10^(-3))/(4*3.14159265*8.854187817620*10^(-12)*10^(-9))</a>
+<a name="103"><span class="lineNum">     103 </span>            :               = 138.935458111 (kJ/mol)</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : */</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          8 : DHEnergy::DHEnergy(const ActionOptions&amp;ao):</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   Action(ao),</a>
+<a name="109"><span class="lineNum">     109 </span>            :   CoordinationBase(ao),</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          8 :   k(0.0),</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          8 :   constant(0.0)</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : {</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double I,T;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          8 :   parse(&quot;I&quot;,I);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          8 :   parse(&quot;TEMP&quot;,T);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          8 :   parse(&quot;EPSILON&quot;,epsilon);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          8 :   if( plumed.getAtoms().usingNaturalUnits() ) error(&quot;DHENERGY cannot be used for calculations performed with natural units&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          8 :   constant=138.935458111/atoms.getUnits().getEnergy()/atoms.getUnits().getLength()*atoms.getUnits().getCharge()*atoms.getUnits().getCharge();</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          8 :   k=std::sqrt(I/(epsilon*T))*502.903741125*atoms.getUnits().getLength();</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          8 :   log&lt;&lt;&quot;  with solvent dielectric constant &quot;&lt;&lt;epsilon&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          8 :   log&lt;&lt;&quot;  at temperature &quot;&lt;&lt;T&lt;&lt;&quot; K\n&quot;;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 :   log&lt;&lt;&quot;  at ionic strength &quot;&lt;&lt;I&lt;&lt; &quot;M\n&quot;;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   log&lt;&lt;&quot;  these parameters correspond to a screening length of &quot;&lt;&lt;(1.0/k)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         16 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Do, Carloni, Varani and Bussi, J. Chem. Theory Comput. 9, 1720 (2013)&quot;)&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          8 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        840 : double DHEnergy::pairing(double distance2,double&amp;dfunc,unsigned i,unsigned j)const {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        840 :   double distance=std::sqrt(distance2);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        840 :   if(getAbsoluteIndex(i)==getAbsoluteIndex(j)) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     dfunc=0.0;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     return 0.0;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   }</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        840 :   double invdistance=1.0/distance;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        840 :   double tmp=std::exp(-k*distance)*invdistance*constant*getCharge(i)*getCharge(j)/epsilon;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        840 :   double dtmp=-(k+invdistance)*tmp;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        840 :   dfunc=dtmp*invdistance;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        840 :   return tmp;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/DRMSD.cpp.func-sort-c.html b/coverage/colvar/DRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2555f28086
--- /dev/null
+++ b/coverage/colvar/DRMSD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/DRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - DRMSD.cpp<span style="font-size: 80%;"> (<a href="DRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#133">_ZN4PLMD6colvar5DRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#120">_ZN4PLMD6colvar12_GLOBAL__N_118DRMSDRegisterMe1226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#133">_ZN4PLMD6colvar5DRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#122">_ZN4PLMD6colvar5DRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#180">_ZN4PLMD6colvar5DRMSD9calculateEv</a></td>
+              <td class="coverFnHi">595</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#120">_ZN4PLMD6colvar12_GLOBAL__N_118DRMSDRegisterMe122C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#120">_ZN4PLMD6colvar12_GLOBAL__N_118DRMSDRegisterMe122D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/DRMSD.cpp.func.html b/coverage/colvar/DRMSD.cpp.func.html
new file mode 100644
index 0000000000..16a3c8ba50
--- /dev/null
+++ b/coverage/colvar/DRMSD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/DRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - DRMSD.cpp<span style="font-size: 80%;"> (<a href="DRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#120">_ZN4PLMD6colvar12_GLOBAL__N_118DRMSDRegisterMe1226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#120">_ZN4PLMD6colvar12_GLOBAL__N_118DRMSDRegisterMe122C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#120">_ZN4PLMD6colvar12_GLOBAL__N_118DRMSDRegisterMe122D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#122">_ZN4PLMD6colvar5DRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#180">_ZN4PLMD6colvar5DRMSD9calculateEv</a></td>
+              <td class="coverFnHi">595</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#133">_ZN4PLMD6colvar5DRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#133">_ZN4PLMD6colvar5DRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/DRMSD.cpp.gcov.html b/coverage/colvar/DRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..b176151a1d
--- /dev/null
+++ b/coverage/colvar/DRMSD.cpp.gcov.html
@@ -0,0 +1,269 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/DRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - DRMSD.cpp<span style="font-size: 80%;"> (source / <a href="DRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;reference/DRMSD.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace colvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC DCOLVAR DRMSD</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Calculate the distance RMSD with respect to a reference structure.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : To calculate the root-mean-square deviation between the atoms in two configurations</a>
+<a name="38"><span class="lineNum">      38 </span>            : you must first superimpose the two structures in some ways.  Obviously, it is the internal vibrational</a>
+<a name="39"><span class="lineNum">      39 </span>            : motions of the structure - i.e. not the translations and rotations - that are interesting. However,</a>
+<a name="40"><span class="lineNum">      40 </span>            : aligning two structures by removing the translational and rotational motions is not easy.  Furthermore,</a>
+<a name="41"><span class="lineNum">      41 </span>            : in some cases there can be alignment issues caused by so-called frame-fitting problems. It is thus</a>
+<a name="42"><span class="lineNum">      42 </span>            : often cheaper and easier to calculate the distances between all the pairs of atoms.  The distance</a>
+<a name="43"><span class="lineNum">      43 </span>            : between the two structures, \f$\mathbf{X}^a\f$ and \f$\mathbf{X}^b\f$ can then be measured as:</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \f[</a>
+<a name="46"><span class="lineNum">      46 </span>            : d(\mathbf{X}^A, \mathbf{X}^B) = \sqrt{\frac{1}{N(N-1)} \sum_{i \ne j} [ d(\mathbf{x}_i^a,\mathbf{x}_j^a) - d(\mathbf{x}_i^b,\mathbf{x}_j^b) ]^2}</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f]</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : where \f$N\f$ is the number of atoms and \f$d(\mathbf{x}_i,\mathbf{x}_j)\f$ represents the distance between</a>
+<a name="50"><span class="lineNum">      50 </span>            : atoms \f$i\f$ and \f$j\f$.  Clearly, this representation of the configuration is invariant to translation and rotation.</a>
+<a name="51"><span class="lineNum">      51 </span>            : However, it can become expensive to calculate when the number of atoms is large.  This can be resolved</a>
+<a name="52"><span class="lineNum">      52 </span>            : within the DRMSD colvar by setting LOWER_CUTOFF and UPPER_CUTOFF.  These keywords ensure that only</a>
+<a name="53"><span class="lineNum">      53 </span>            : pairs of atoms that are within a certain range are incorporated into the above sum.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : In PDB files the atomic coordinates and box lengths should be in Angstroms unless</a>
+<a name="56"><span class="lineNum">      56 </span>            : you are working with natural units.  If you are working with natural units then the coordinates</a>
+<a name="57"><span class="lineNum">      57 </span>            : should be in your natural length unit.  For more details on the PDB file format visit http://www.wwpdb.org/docs.html</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \par Examples</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The following tells plumed to calculate the distance RMSD between</a>
+<a name="62"><span class="lineNum">      62 </span>            : the positions of the atoms in the reference file and their instantaneous</a>
+<a name="63"><span class="lineNum">      63 </span>            : position. Only pairs of atoms whose distance in the reference structure is within</a>
+<a name="64"><span class="lineNum">      64 </span>            : 0.1 and 0.8 nm are considered.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : DRMSD REFERENCE=file1.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : The reference file is a PDB file that looks like this</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \auxfile{file1.pdb}</a>
+<a name="73"><span class="lineNum">      73 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="74"><span class="lineNum">      74 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="75"><span class="lineNum">      75 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="76"><span class="lineNum">      76 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="77"><span class="lineNum">      77 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="78"><span class="lineNum">      78 </span>            : END</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endauxfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : The following tells plumed to calculate a DRMSD value for a pair of molecules.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \plumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : DRMSD REFERENCE=file2.pdb LOWER_CUTOFF=0.1 UPPER_CUTOFF=0.8 TYPE=INTER-DRMSD</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endplumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : In the input reference file (file.pdb) the atoms in each of the two molecules are separated by a TER</a>
+<a name="88"><span class="lineNum">      88 </span>            : command as shown below.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \auxfile{file2.pdb}</a>
+<a name="91"><span class="lineNum">      91 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="92"><span class="lineNum">      92 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="93"><span class="lineNum">      93 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="94"><span class="lineNum">      94 </span>            : TER</a>
+<a name="95"><span class="lineNum">      95 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="96"><span class="lineNum">      96 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="97"><span class="lineNum">      97 </span>            : END</a>
+<a name="98"><span class="lineNum">      98 </span>            : \endauxfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : In this example the INTER-DRMSD type ensures that the set of distances from which the final</a>
+<a name="101"><span class="lineNum">     101 </span>            : quantity is computed involve one atom from each of the two molecules.  If this is replaced</a>
+<a name="102"><span class="lineNum">     102 </span>            : by INTRA-DRMSD then only those distances involving pairs of atoms that are both in the same</a>
+<a name="103"><span class="lineNum">     103 </span>            : molecule are computed.</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : */</a>
+<a name="106"><span class="lineNum">     106 </span>            : //+ENDPLUMEDOC</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : class DRMSD : public Colvar {</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   bool pbc_;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   MultiValue myvals;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ReferenceValuePack mypack;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::unique_ptr&lt;PLMD::DRMSD&gt; drmsd_;</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : public:</a>
+<a name="117"><span class="lineNum">     117 </span>            :   explicit DRMSD(const ActionOptions&amp;);</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void calculate() override;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="120"><span class="lineNum">     120 </span>            : };</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      12527 : PLUMED_REGISTER_ACTION(DRMSD,&quot;DRMSD&quot;)</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         14 : void DRMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         14 :   Colvar::registerKeywords(keys);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;LOWER_CUTOFF&quot;,&quot;only pairs of atoms further than LOWER_CUTOFF are considered in the calculation.&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;UPPER_CUTOFF&quot;,&quot;only pairs of atoms closer than UPPER_CUTOFF are considered in the calculation.&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;DRMSD&quot;,&quot;what kind of DRMSD would you like to calculate.  You can use either the normal DRMSD involving all the distances between &quot;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :            &quot;the atoms in your molecule.  Alternatively, if you have multiple molecules you can use the type INTER-DRMSD &quot;</a>
+<a name="131"><span class="lineNum">     131 </span>            :            &quot;to compute DRMSD values involving only those distances between the atoms at least two molecules or the type INTRA-DRMSD &quot;</a>
+<a name="132"><span class="lineNum">     132 </span>            :            &quot;to compute DRMSD values involving only those distances between atoms in the same molecule&quot;);</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         14 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         12 : DRMSD::DRMSD(const ActionOptions&amp;ao):</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         12 :   PLUMED_COLVAR_INIT(ao), pbc_(true), myvals(1,0), mypack(0,0,myvals)</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : {</a>
+<a name="138"><span class="lineNum">     138 </span>            :   std::string reference;</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         12 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   double lcutoff;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         12 :   parse(&quot;LOWER_CUTOFF&quot;,lcutoff);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   double ucutoff;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         12 :   parse(&quot;UPPER_CUTOFF&quot;,ucutoff);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         12 :   bool nopbc(false);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         13 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         12 :   pbc_=!nopbc;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         12 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         12 :   PDB pdb;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         24 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :     error(&quot;missing input file &quot; + reference );</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   // store target_ distance</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         11 :   std::string type; parse(&quot;TYPE&quot;,type);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         22 :   drmsd_=metricRegister().create&lt;PLMD::DRMSD&gt;( type );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         11 :   drmsd_-&gt;setBoundsOnDistances( !nopbc, lcutoff, ucutoff );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         11 :   drmsd_-&gt;read( pdb );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         11 :   checkRead();</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         11 :   drmsd_-&gt;getAtomRequests( atoms );</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : //   drmsd_-&gt;setNumberOfAtoms( atoms.size() );</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         11 :   requestAtoms( atoms );</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   // Setup the derivative pack</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         11 :   myvals.resize( 1, 3*atoms.size()+9 ); mypack.resize( 0, atoms.size() );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        129 :   for(unsigned i=0; i&lt;atoms.size(); ++i) mypack.setAtomIndex( i, i );</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         11 :   log.printf(&quot;  reference from file %s\n&quot;,reference.c_str());</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         11 :   log.printf(&quot;  which contains %d atoms\n&quot;,getNumberOfAtoms());</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         11 :   log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        129 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        118 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        118 :     log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   }</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         11 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         28 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : // calculator</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        595 : void DRMSD::calculate() {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        595 :   double drmsd; Tensor virial; mypack.clear();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        595 :   drmsd=drmsd_-&gt;calculate(getPositions(), getPbc(), mypack, false);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        595 :   setValue(drmsd);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       9285 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) { if( myvals.isActive(3*i) ) setAtomsDerivatives( i, mypack.getAtomDerivative(i) ); }</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        595 :   setBoxDerivatives( mypack.getBoxDerivatives() );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        595 : }</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
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diff --git a/coverage/colvar/Dimer.cpp.func-sort-c.html b/coverage/colvar/Dimer.cpp.func-sort-c.html
new file mode 100644
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Dimer.cpp<span style="font-size: 80%;"> (<a href="Dimer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryHi">92.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Dimer.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
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+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#160">_ZN4PLMD6colvar5DimerC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_118DimerRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#291">_ZN4PLMD6colvar5Dimer16consistencyCheckEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#160">_ZN4PLMD6colvar5DimerC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#145">_ZN4PLMD6colvar5Dimer16registerKeywordsERNS_8KeywordsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#235">_ZN4PLMD6colvar5Dimer9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_118DimerRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_118DimerRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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diff --git a/coverage/colvar/Dimer.cpp.func.html b/coverage/colvar/Dimer.cpp.func.html
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Dimer.cpp<span style="font-size: 80%;"> (<a href="Dimer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryHi">92.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+              <td class="coverFnHi">2</td>
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+    <tr>
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+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_118DimerRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#291">_ZN4PLMD6colvar5Dimer16consistencyCheckEv</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#145">_ZN4PLMD6colvar5Dimer16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
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+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#235">_ZN4PLMD6colvar5Dimer9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#160">_ZN4PLMD6colvar5DimerC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
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+              <td class="coverFn"><a href="Dimer.cpp.gcov.html#160">_ZN4PLMD6colvar5DimerC2ERKNS_13ActionOptionsE</a></td>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Dimer.cpp</title>
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+</head>
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+<body>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Dimer.cpp<span style="font-size: 80%;"> (source / <a href="Dimer.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryHi">92.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR DIMER</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : This CV computes the dimer interaction energy for a collection of dimers.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Each dimer represents an atom, as described in the dimer paper \cite dimer-metad.</a>
+<a name="34"><span class="lineNum">      34 </span>            : A system of N atoms is thus represented with N dimers, each</a>
+<a name="35"><span class="lineNum">      35 </span>            : Dimer being composed of two beads and eventually a virtual site representing its center of mass.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : A typical configuration for a dimerized system has the following ordering of atoms:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : 1    TAG1 X Y Z          N atoms representing the first bead of each Dimer</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : 2    TAG2 X Y Z</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : ...</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : N    TAGN X Y Z          N atoms representing the second bead of each Dimer</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : N+1  TAG1 X Y Z</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : N+2  TAG2 X Y Z</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : ...</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : 2N   TAGN X Y Z          Optional: N atoms representing the center of mass of each Dimer</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : 2N+1 TAG1 X Y Z</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : 2N+2 TAG2 X Y Z</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : ...</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : 3N   TAGN X Y Z          The configuration might go on with un-dimerized atoms (like a solvent)</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : 3N+1</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : 3N+2</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : ...</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : The Dimer interaction energy is defined between atoms x and N+x, for x=1,...,N and is</a>
+<a name="71"><span class="lineNum">      71 </span>            : characterized by two parameters Q and DSIGMA. These are passed as mandatory arguments along with</a>
+<a name="72"><span class="lineNum">      72 </span>            : the temperature of the system.</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \par Examples</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : This line tells Plumed to compute the Dimer interaction energy for every dimer in the system.</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endplumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : If the simulation doesn't use virtual sites for the dimers centers of mass,</a>
+<a name="83"><span class="lineNum">      83 </span>            : Plumed has to know in order to determine correctly the total number of dimers from</a>
+<a name="84"><span class="lineNum">      84 </span>            : the total number of atoms:</a>
+<a name="85"><span class="lineNum">      85 </span>            : \plumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002 NOVSITES</a>
+<a name="87"><span class="lineNum">      87 </span>            : \endplumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : The NOVSITES flag is not required if one provides the atom serials of each Dimer. These are</a>
+<a name="90"><span class="lineNum">      90 </span>            : defined through two lists of atoms provided __instead__ of the ALLATOMS keyword.</a>
+<a name="91"><span class="lineNum">      91 </span>            : For example, the Dimer interaction energy of dimers specified by beads (1;23),(5;27),(7;29) is:</a>
+<a name="92"><span class="lineNum">      92 </span>            : \plumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002</a>
+<a name="94"><span class="lineNum">      94 </span>            : \endplumedfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : Note that the ATOMS1,ATOMS2 keywords can support atom groups and</a>
+<a name="97"><span class="lineNum">      97 </span>            : interval notation as defined in \ref GROUP.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : In a Replica Exchange simulation the keyword DSIGMA can be used in two ways:</a>
+<a name="101"><span class="lineNum">     101 </span>            : if a plumed.n.dat file is provided for each replica, then DSIGMA is passed as a single value,</a>
+<a name="102"><span class="lineNum">     102 </span>            : like in the previous examples, and each replica will read its own DSIGMA value. If</a>
+<a name="103"><span class="lineNum">     103 </span>            : a unique plumed.dat is given, DSIGMA has to be a list containing a value for each replica.</a>
+<a name="104"><span class="lineNum">     104 </span>            : For 4 replicas:</a>
+<a name="105"><span class="lineNum">     105 </span>            : \plumedfile</a>
+<a name="106"><span class="lineNum">     106 </span>            : #SETTINGS NREPLICAS=4</a>
+<a name="107"><span class="lineNum">     107 </span>            : dim: DIMER TEMP=300 Q=0.5 ATOMS1=1,5,7 ATOMS2=23,27,29 DSIGMA=0.002,0.002,0.004,0.01</a>
+<a name="108"><span class="lineNum">     108 </span>            : \endplumedfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : \par Usage of the CV</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : The dimer interaction is not coded in the driver program and has to be inserted</a>
+<a name="114"><span class="lineNum">     114 </span>            : in the Hamiltonian of the system as a linear RESTRAINT (see \ref RESTRAINT):</a>
+<a name="115"><span class="lineNum">     115 </span>            : \plumedfile</a>
+<a name="116"><span class="lineNum">     116 </span>            : dim: DIMER TEMP=300 Q=0.5 ALLATOMS DSIGMA=0.002</a>
+<a name="117"><span class="lineNum">     117 </span>            : RESTRAINT ARG=dim AT=0 KAPPA=0 SLOPE=1 LABEL=dimforces</a>
+<a name="118"><span class="lineNum">     118 </span>            : \endplumedfile</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : In a replica exchange, Metadynamics (see \ref METAD) can be used on the Dimer CV to reduce</a>
+<a name="121"><span class="lineNum">     121 </span>            : the number of replicas. Just keep in mind that METAD SIGMA values should be tuned</a>
+<a name="122"><span class="lineNum">     122 </span>            : in the standard way for each replica according to the value of DSIGMA.</a>
+<a name="123"><span class="lineNum">     123 </span>            : */</a>
+<a name="124"><span class="lineNum">     124 </span>            : //+ENDPLUMEDOC</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : class Dimer : public Colvar {</a>
+<a name="127"><span class="lineNum">     127 </span>            : public:</a>
+<a name="128"><span class="lineNum">     128 </span>            :   static void registerKeywords( Keywords&amp; keys);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   explicit Dimer(const ActionOptions&amp;);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   void calculate() override;</a>
+<a name="131"><span class="lineNum">     131 </span>            : protected:</a>
+<a name="132"><span class="lineNum">     132 </span>            :   bool trimer,useall;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   int myrank, nranks;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   double qexp,temperature,beta,dsigma;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::vector&lt;double&gt; dsigmas;</a>
+<a name="136"><span class="lineNum">     136 </span>            : private:</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void consistencyCheck();</a>
+<a name="138"><span class="lineNum">     138 </span>            :   std::vector&lt;AtomNumber&gt; usedatoms1;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   std::vector&lt;AtomNumber&gt; usedatoms2;</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : };</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Dimer, &quot;DIMER&quot;)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 : void Dimer::registerKeywords( Keywords&amp; keys) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          4 :   Colvar::registerKeywords(keys);</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;DSIGMA&quot;,&quot;The interaction strength of the dimer bond.&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;, &quot;Q&quot;, &quot;The exponent of the dimer potential.&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;, &quot;TEMP&quot;, &quot;The temperature (in Kelvin) of the simulation.&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;, &quot;ATOMS1&quot;, &quot;The list of atoms representing the first bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;, &quot;ATOMS2&quot;, &quot;The list of atoms representing the second bead of each Dimer being considered by this CV. Used if ALLATOMS flag is missing&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          8 :   keys.addFlag(&quot;ALLATOMS&quot;, false, &quot;Use EVERY atom of the system. Overrides ATOMS keyword.&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          8 :   keys.addFlag(&quot;NOVSITES&quot;, false, &quot;If present the configuration is without virtual sites at the centroid positions.&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 : }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          2 : Dimer::Dimer(const ActionOptions&amp; ao):</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : {</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          4 :   log&lt;&lt;&quot; Bibliography &quot;&lt;&lt;plumed.cite(&quot;M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   parseVector(&quot;DSIGMA&quot;,dsigmas);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          2 :   parse(&quot;Q&quot;,qexp);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          4 :   parse(&quot;TEMP&quot;,temperature);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :   parseFlag(&quot;ALLATOMS&quot;,useall);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :   trimer=true;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   bool notrim;</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   parseFlag(&quot;NOVSITES&quot;,notrim);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   trimer=!notrim;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :   nranks=multi_sim_comm.Get_size();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :   myrank=multi_sim_comm.Get_rank();</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :   if(dsigmas.size()==1)</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :     dsigma=dsigmas[0];</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   else</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :     dsigma=dsigmas[myrank];</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :   if(useall)</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   {</a>
+<a name="191"><span class="lineNum">     191 </span>            :     // go with every atom in the system but not the virtuals...</a>
+<a name="192"><span class="lineNum">     192 </span>            :     int natoms;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          1 :     if(trimer)</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          1 :       natoms= 2*getTotAtoms()/3;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     else</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       natoms=getTotAtoms()/2;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         45 :     for(unsigned int i=0; i&lt;((unsigned int)natoms); i++)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     {</a>
+<a name="200"><span class="lineNum">     200 </span>            :       AtomNumber ati;</a>
+<a name="201"><span class="lineNum">     201 </span>            :       ati.setIndex(i);</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         44 :       atoms.push_back(ati);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     }</a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span>            :   else  // serials for the first beads of each dimer are given</a>
+<a name="206"><span class="lineNum">     206 </span>            :   {</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          1 :     parseAtomList(&quot;ATOMS1&quot;,usedatoms1);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :     parseAtomList(&quot;ATOMS2&quot;,usedatoms2);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            :     int isz1 = usedatoms1.size();</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          5 :     for(unsigned int i=0; i&lt;isz1; i++)</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     {</a>
+<a name="214"><span class="lineNum">     214 </span>            :       AtomNumber ati;</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          4 :       ati.setIndex(usedatoms1[i].index());</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          4 :       atoms.push_back(ati);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :     int isz2 = usedatoms2.size();</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          5 :     for(unsigned int i=0; i&lt;isz2; i++)</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     {</a>
+<a name="222"><span class="lineNum">     222 </span>            :       AtomNumber atip2;</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          4 :       atip2.setIndex(usedatoms2[i].index());</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          4 :       atoms.push_back(atip2);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          2 :   consistencyCheck();</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          2 :   beta = 1./(kBoltzmann*temperature);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          2 :   addValueWithDerivatives();  // allocate</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 :   requestAtoms(atoms);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          2 :   setNotPeriodic();</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          2 : }</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          4 : void Dimer::calculate()</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          4 :   double cv_val=0;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          4 :   Tensor virial;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   std::vector&lt;Vector&gt; derivatives;</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          4 :   std::vector&lt;Vector&gt; my_pos=getPositions();</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          4 :   int atms = my_pos.size();</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   std::vector&lt;Vector&gt; der_b2;</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         38 :   for(int i=0; i&lt;atms/2; i++)</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   {</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         34 :     Vector dist;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         34 :     dist = pbcDistance(my_pos[i],my_pos[i+atms/2]);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :     double distquad=0;</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        136 :     for(int j=0; j&lt;3; j++)</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        102 :       distquad += dist[j]*dist[j];</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         34 :     double dsigquad = dsigma*dsigma;</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         34 :     double fac1 = 1.0 + distquad/(2*qexp*dsigquad);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         34 :     double fac1qm1 = std::pow(fac1,qexp-1);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         34 :     cv_val += (fac1*fac1qm1-1.0)/beta;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         34 :     Vector der_val;</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         34 :     Vector mder_val;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        136 :     for(int j=0; j&lt;3; j++)</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :     {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        102 :       der_val[j] = -fac1qm1*dist[j]/(dsigquad*beta);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        102 :       mder_val[j]=-der_val[j];</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     }</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         34 :     derivatives.push_back(der_val);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         34 :     der_b2.push_back(mder_val);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :     // virial part: each dimer contributes -x_{ij}*ds/dx_{ij}  (s is the CV)</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         34 :     double dfunc = fac1qm1/(beta*dsigquad);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         34 :     Vector dd(dfunc*dist);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         34 :     Tensor vv(dd,dist);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         34 :     virial -= vv;</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :   }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          4 :   derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         72 :   for(unsigned int i=0; i&lt;derivatives.size(); i++)</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         68 :     setAtomsDerivatives(i,derivatives[i]);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          4 :   setValue(cv_val);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          4 :   setBoxDerivatives(virial);</span></a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          4 : }</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : /*****************</a>
+<a name="290"><span class="lineNum">     290 </span>            : There are some conditions that a valid input should satisfy.</a>
+<a name="291"><span class="lineNum">     291 </span>            : These are checked here and PLUMED error handlers are (eventually) called.</a>
+<a name="292"><span class="lineNum">     292 </span>            : ******************/</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          2 : void Dimer::consistencyCheck()</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : {</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          2 :   if(!useall &amp;&amp; usedatoms1.size()!=usedatoms2.size())</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     error(&quot;The provided atom lists are of different sizes.&quot;);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          2 :   if(qexp&lt;0.5 || qexp&gt;1)</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :     warning(&quot;Dimer CV is meant to be used with q-exponents between 0.5 and 1. We are not responsible for any black hole. :-)&quot;);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          2 :   if(dsigma&lt;0)</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :     error(&quot;Please use positive sigma values for the Dimer strength constant&quot;);</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          2 :   if(temperature&lt;0)</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :     error(&quot;Please, use a positive value for the temperature...&quot;);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   // if dsigmas has only one element means that either</a>
+<a name="308"><span class="lineNum">     308 </span>            :   // you are using different plumed.x.dat files or a plumed.dat with a single replica</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          2 :   if(dsigmas.size()!=nranks &amp;&amp; dsigmas.size()!=1)</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :     error(&quot;Mismatch between provided sigmas and number of replicas&quot;);</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          2 : }</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : }</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Dipole.cpp.func-sort-c.html b/coverage/colvar/Dipole.cpp.func-sort-c.html
new file mode 100644
index 0000000000..591bac634d
--- /dev/null
+++ b/coverage/colvar/Dipole.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Dipole.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Dipole.cpp<span style="font-size: 80%;"> (<a href="Dipole.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Dipole.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#80">_ZN4PLMD6colvar6DipoleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#69">_ZN4PLMD6colvar12_GLOBAL__N_118DipoleRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#80">_ZN4PLMD6colvar6DipoleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#71">_ZN4PLMD6colvar6Dipole16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#108">_ZN4PLMD6colvar6Dipole9calculateEv</a></td>
+              <td class="coverFnHi">923</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#69">_ZN4PLMD6colvar12_GLOBAL__N_118DipoleRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#69">_ZN4PLMD6colvar12_GLOBAL__N_118DipoleRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Dipole.cpp.func.html b/coverage/colvar/Dipole.cpp.func.html
new file mode 100644
index 0000000000..97c8f3add4
--- /dev/null
+++ b/coverage/colvar/Dipole.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Dipole.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Dipole.cpp<span style="font-size: 80%;"> (<a href="Dipole.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Dipole.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#69">_ZN4PLMD6colvar12_GLOBAL__N_118DipoleRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#69">_ZN4PLMD6colvar12_GLOBAL__N_118DipoleRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#69">_ZN4PLMD6colvar12_GLOBAL__N_118DipoleRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#71">_ZN4PLMD6colvar6Dipole16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#108">_ZN4PLMD6colvar6Dipole9calculateEv</a></td>
+              <td class="coverFnHi">923</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#80">_ZN4PLMD6colvar6DipoleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Dipole.cpp.gcov.html#80">_ZN4PLMD6colvar6DipoleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Dipole.cpp.gcov.html b/coverage/colvar/Dipole.cpp.gcov.html
new file mode 100644
index 0000000000..47ea7c806d
--- /dev/null
+++ b/coverage/colvar/Dipole.cpp.gcov.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Dipole.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Dipole.cpp<span style="font-size: 80%;"> (source / <a href="Dipole.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR DIPOLE</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate the dipole moment for a group of atoms.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="33"><span class="lineNum">      33 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.5,</a>
+<a name="34"><span class="lineNum">      34 </span>            : by considering the ordered list of atoms and rebuilding the molecule with a procedure</a>
+<a name="35"><span class="lineNum">      35 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="36"><span class="lineNum">      36 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="37"><span class="lineNum">      37 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="40"><span class="lineNum">      40 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="41"><span class="lineNum">      41 </span>            : periodic image.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The following tells plumed to calculate the dipole of the group of atoms containing</a>
+<a name="46"><span class="lineNum">      46 </span>            : the atoms from 1-10 and print it every 5 steps</a>
+<a name="47"><span class="lineNum">      47 </span>            : \plumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : d: DIPOLE GROUP=1-10</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT FILE=output STRIDE=5 ARG=d</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \attention</a>
+<a name="53"><span class="lineNum">      53 </span>            : If the total charge Q of the group in non zero, then a charge Q/N will be subtracted to every atom,</a>
+<a name="54"><span class="lineNum">      54 </span>            : where N is the number of atoms. This implies that the dipole (which for a charged system depends</a>
+<a name="55"><span class="lineNum">      55 </span>            : on the position) is computed on the geometric center of the group.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : class Dipole : public Colvar {</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;AtomNumber&gt; ga_lista;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   bool components;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool nopbc;</a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   explicit Dipole(const ActionOptions&amp;);</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void calculate() override;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="69"><span class="lineNum">      69 </span>            : };</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      12612 : PLUMED_REGISTER_ACTION(Dipole,&quot;DIPOLE&quot;)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         56 : void Dipole::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         56 :   Colvar::registerKeywords(keys);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        112 :   keys.add(&quot;atoms&quot;,&quot;GROUP&quot;,&quot;the group of atoms we are calculating the dipole moment for&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        112 :   keys.addFlag(&quot;COMPONENTS&quot;,false,&quot;calculate the x, y and z components of the dipole separately and store them as label.x, label.y and label.z&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;x&quot;,&quot;COMPONENTS&quot;,&quot;the x-component of the dipole&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;y&quot;,&quot;COMPONENTS&quot;,&quot;the y-component of the dipole&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;z&quot;,&quot;COMPONENTS&quot;,&quot;the z-component of the dipole&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         56 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         54 : Dipole::Dipole(const ActionOptions&amp;ao):</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         54 :   components(false)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : {</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         54 :   parseAtomList(&quot;GROUP&quot;,ga_lista);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         54 :   parseFlag(&quot;COMPONENTS&quot;,components);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         54 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         54 :   checkRead();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         54 :   if(components) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 :     addComponentWithDerivatives(&quot;x&quot;); componentIsNotPeriodic(&quot;x&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          4 :     addComponentWithDerivatives(&quot;y&quot;); componentIsNotPeriodic(&quot;y&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          6 :     addComponentWithDerivatives(&quot;z&quot;); componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   } else {</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         52 :     addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         54 :   log.printf(&quot;  of %u atoms\n&quot;,static_cast&lt;unsigned&gt;(ga_lista.size()));</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        379 :   for(unsigned int i=0; i&lt;ga_lista.size(); ++i) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        325 :     log.printf(&quot;  %d&quot;, ga_lista[i].serial());</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         54 :   log.printf(&quot;  \n&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         54 :   if(nopbc) log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         16 :   else      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         54 :   requestAtoms(ga_lista);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         54 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : // calculator</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        923 : void Dipole::calculate()</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        923 :   if(!nopbc) makeWhole();</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   double ctot=0.;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   unsigned N=getNumberOfAtoms();</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        923 :   std::vector&lt;double&gt; charges(N);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        923 :   Vector dipje;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       7258 :   for(unsigned i=0; i&lt;N; ++i) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       6335 :     charges[i]=getCharge(i);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       6335 :     ctot+=charges[i];</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        923 :   ctot/=(double)N;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       7258 :   for(unsigned i=0; i&lt;N; ++i) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       6335 :     charges[i]-=ctot;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       6335 :     dipje += charges[i]*getPosition(i);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        923 :   if(!components) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        778 :     double dipole = dipje.modulo();</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        778 :     double idip = 1./dipole;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       6243 :     for(unsigned i=0; i&lt;N; i++) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       5465 :       double dfunc=charges[i]*idip;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       5465 :       setAtomsDerivatives(i,dfunc*dipje);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :     }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        778 :     setBoxDerivativesNoPbc();</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        778 :     setValue(dipole);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   } else {</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        145 :     Value* valuex=getPntrToComponent(&quot;x&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        145 :     Value* valuey=getPntrToComponent(&quot;y&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        145 :     Value* valuez=getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1015 :     for(unsigned i=0; i&lt;N; i++) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        870 :       setAtomsDerivatives(valuex,i,charges[i]*Vector(1.0,0.0,0.0));</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        870 :       setAtomsDerivatives(valuey,i,charges[i]*Vector(0.0,1.0,0.0));</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        870 :       setAtomsDerivatives(valuez,i,charges[i]*Vector(0.0,0.0,1.0));</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        145 :     setBoxDerivativesNoPbc(valuex);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        145 :     setBoxDerivativesNoPbc(valuey);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        145 :     setBoxDerivativesNoPbc(valuez);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        145 :     valuex-&gt;set(dipje[0]);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        145 :     valuey-&gt;set(dipje[1]);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        145 :     valuez-&gt;set(dipje[2]);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        923 : }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Distance.cpp.func-sort-c.html b/coverage/colvar/Distance.cpp.func-sort-c.html
new file mode 100644
index 0000000000..25336c2065
--- /dev/null
+++ b/coverage/colvar/Distance.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Distance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Distance.cpp<span style="font-size: 80%;"> (<a href="Distance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Distance.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#131">_ZN4PLMD6colvar8DistanceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_121DistanceRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">466</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#131">_ZN4PLMD6colvar8DistanceC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">466</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#118">_ZN4PLMD6colvar8Distance16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">468</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_121DistanceRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_121DistanceRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#173">_ZN4PLMD6colvar8Distance9calculateEv</a></td>
+              <td class="coverFnHi">42384</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Distance.cpp.func.html b/coverage/colvar/Distance.cpp.func.html
new file mode 100644
index 0000000000..d26ad14a70
--- /dev/null
+++ b/coverage/colvar/Distance.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Distance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Distance.cpp<span style="font-size: 80%;"> (<a href="Distance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Distance.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_121DistanceRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">466</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_121DistanceRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#116">_ZN4PLMD6colvar12_GLOBAL__N_121DistanceRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#118">_ZN4PLMD6colvar8Distance16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">468</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#173">_ZN4PLMD6colvar8Distance9calculateEv</a></td>
+              <td class="coverFnHi">42384</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#131">_ZN4PLMD6colvar8DistanceC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">466</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distance.cpp.gcov.html#131">_ZN4PLMD6colvar8DistanceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Distance.cpp.gcov.html b/coverage/colvar/Distance.cpp.gcov.html
new file mode 100644
index 0000000000..99f977deaa
--- /dev/null
+++ b/coverage/colvar/Distance.cpp.gcov.html
@@ -0,0 +1,305 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Distance.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Distance.cpp<span style="font-size: 80%;"> (source / <a href="Distance.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR DISTANCE</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate the distance between a pair of atoms.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : By default the distance is computed taking into account periodic</a>
+<a name="34"><span class="lineNum">      34 </span>            : boundary conditions. This behavior can be changed with the NOPBC flag.</a>
+<a name="35"><span class="lineNum">      35 </span>            : Moreover, single components in Cartesian space (x,y, and z, with COMPONENTS)</a>
+<a name="36"><span class="lineNum">      36 </span>            : or single components projected to the three lattice vectors (a,b, and c, with SCALED_COMPONENTS)</a>
+<a name="37"><span class="lineNum">      37 </span>            : can be also computed.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Notice that Cartesian components will not have the proper periodicity!</a>
+<a name="40"><span class="lineNum">      40 </span>            : If you have to study e.g. the permeation of a molecule across a membrane,</a>
+<a name="41"><span class="lineNum">      41 </span>            : better to use SCALED_COMPONENTS.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The following input tells plumed to print the distance between atoms 3 and 5,</a>
+<a name="46"><span class="lineNum">      46 </span>            : the distance between atoms 2 and 4 and the x component of the distance between atoms 2 and 4.</a>
+<a name="47"><span class="lineNum">      47 </span>            : \plumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : d1:  DISTANCE ATOMS=3,5</a>
+<a name="49"><span class="lineNum">      49 </span>            : d2:  DISTANCE ATOMS=2,4</a>
+<a name="50"><span class="lineNum">      50 </span>            : d2c: DISTANCE ATOMS=2,4 COMPONENTS</a>
+<a name="51"><span class="lineNum">      51 </span>            : PRINT ARG=d1,d2,d2c.x</a>
+<a name="52"><span class="lineNum">      52 </span>            : \endplumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The following input computes the end-to-end distance for a polymer</a>
+<a name="55"><span class="lineNum">      55 </span>            : of 100 atoms and keeps it at a value around 5.</a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : WHOLEMOLECULES ENTITY0=1-100</a>
+<a name="58"><span class="lineNum">      58 </span>            : e2e: DISTANCE ATOMS=1,100 NOPBC</a>
+<a name="59"><span class="lineNum">      59 </span>            : RESTRAINT ARG=e2e KAPPA=1 AT=5</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : Notice that NOPBC is used</a>
+<a name="63"><span class="lineNum">      63 </span>            : to be sure that if the end-to-end distance is larger than half the simulation</a>
+<a name="64"><span class="lineNum">      64 </span>            : box the distance is compute properly. Also notice that, since many MD</a>
+<a name="65"><span class="lineNum">      65 </span>            : codes break molecules across cell boundary, it might be necessary to</a>
+<a name="66"><span class="lineNum">      66 </span>            : use the \ref WHOLEMOLECULES keyword (also notice that it should be</a>
+<a name="67"><span class="lineNum">      67 </span>            : _before_ distance). The list of atoms provided to \ref WHOLEMOLECULES</a>
+<a name="68"><span class="lineNum">      68 </span>            : here contains all the atoms between 1 and 100. Strictly speaking, this</a>
+<a name="69"><span class="lineNum">      69 </span>            : is not necessary. If you know for sure that atoms with difference in</a>
+<a name="70"><span class="lineNum">      70 </span>            : the index say equal to 10 are _not_ going to be farther than half cell</a>
+<a name="71"><span class="lineNum">      71 </span>            : you can e.g. use</a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : WHOLEMOLECULES ENTITY0=1,10,20,30,40,50,60,70,80,90,100</a>
+<a name="74"><span class="lineNum">      74 </span>            : e2e: DISTANCE ATOMS=1,100 NOPBC</a>
+<a name="75"><span class="lineNum">      75 </span>            : RESTRAINT ARG=e2e KAPPA=1 AT=5</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : Just be sure that the ordered list provide to \ref WHOLEMOLECULES has the following</a>
+<a name="78"><span class="lineNum">      78 </span>            : properties:</a>
+<a name="79"><span class="lineNum">      79 </span>            : - Consecutive atoms should be closer than half-cell throughout the entire simulation.</a>
+<a name="80"><span class="lineNum">      80 </span>            : - Atoms required later for the distance (e.g. 1 and 100) should be included in the list</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : The following example shows how to take into account periodicity e.g.</a>
+<a name="83"><span class="lineNum">      83 </span>            : in z-component of a distance</a>
+<a name="84"><span class="lineNum">      84 </span>            : \plumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : # this is a center of mass of a large group</a>
+<a name="86"><span class="lineNum">      86 </span>            : c: COM ATOMS=1-100</a>
+<a name="87"><span class="lineNum">      87 </span>            : # this is the distance between atom 101 and the group</a>
+<a name="88"><span class="lineNum">      88 </span>            : d: DISTANCE ATOMS=c,101 COMPONENTS</a>
+<a name="89"><span class="lineNum">      89 </span>            : # this makes a new variable, dd, equal to d and periodic, with domain -10,10</a>
+<a name="90"><span class="lineNum">      90 </span>            : # this is the right choise if e.g. the cell is orthorombic and its size in</a>
+<a name="91"><span class="lineNum">      91 </span>            : # z direction is 20.</a>
+<a name="92"><span class="lineNum">      92 </span>            : dz: COMBINE ARG=d.z PERIODIC=-10,10</a>
+<a name="93"><span class="lineNum">      93 </span>            : # metadynamics on dd</a>
+<a name="94"><span class="lineNum">      94 </span>            : METAD ARG=dz SIGMA=0.1 HEIGHT=0.1 PACE=200</a>
+<a name="95"><span class="lineNum">      95 </span>            : \endplumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : Using SCALED_COMPONENTS this problem should not arise because they are always periodic</a>
+<a name="98"><span class="lineNum">      98 </span>            : with domain (-0.5,+0.5).</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : */</a>
+<a name="104"><span class="lineNum">     104 </span>            : //+ENDPLUMEDOC</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : class Distance : public Colvar {</a>
+<a name="107"><span class="lineNum">     107 </span>            :   bool components;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   bool scaled_components;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   bool pbc;</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : public:</a>
+<a name="112"><span class="lineNum">     112 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="113"><span class="lineNum">     113 </span>            :   explicit Distance(const ActionOptions&amp;);</a>
+<a name="114"><span class="lineNum">     114 </span>            : // active methods:</a>
+<a name="115"><span class="lineNum">     115 </span>            :   void calculate() override;</a>
+<a name="116"><span class="lineNum">     116 </span>            : };</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      13434 : PLUMED_REGISTER_ACTION(Distance,&quot;DISTANCE&quot;)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        468 : void Distance::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        468 :   Colvar::registerKeywords( keys );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        936 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the pair of atom that we are calculating the distance between&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        936 :   keys.addFlag(&quot;COMPONENTS&quot;,false,&quot;calculate the x, y and z components of the distance separately and store them as label.x, label.y and label.z&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        936 :   keys.addFlag(&quot;SCALED_COMPONENTS&quot;,false,&quot;calculate the a, b and c scaled components of the distance separately and store them as label.a, label.b and label.c&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        936 :   keys.addOutputComponent(&quot;x&quot;,&quot;COMPONENTS&quot;,&quot;the x-component of the vector connecting the two atoms&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        936 :   keys.addOutputComponent(&quot;y&quot;,&quot;COMPONENTS&quot;,&quot;the y-component of the vector connecting the two atoms&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        936 :   keys.addOutputComponent(&quot;z&quot;,&quot;COMPONENTS&quot;,&quot;the z-component of the vector connecting the two atoms&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        936 :   keys.addOutputComponent(&quot;a&quot;,&quot;SCALED_COMPONENTS&quot;,&quot;the normalized projection on the first lattice vector of the vector connecting the two atoms&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        936 :   keys.addOutputComponent(&quot;b&quot;,&quot;SCALED_COMPONENTS&quot;,&quot;the normalized projection on the second lattice vector of the vector connecting the two atoms&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        936 :   keys.addOutputComponent(&quot;c&quot;,&quot;SCALED_COMPONENTS&quot;,&quot;the normalized projection on the third lattice vector of the vector connecting the two atoms&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        468 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        466 : Distance::Distance(const ActionOptions&amp;ao):</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        466 :   components(false),</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        466 :   scaled_components(false),</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        466 :   pbc(true)</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        932 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        466 :   if(atoms.size()!=2)</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :     error(&quot;Number of specified atoms should be 2&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        465 :   parseFlag(&quot;COMPONENTS&quot;,components);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        465 :   parseFlag(&quot;SCALED_COMPONENTS&quot;,scaled_components);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        465 :   bool nopbc=!pbc;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        465 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        465 :   pbc=!nopbc;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        465 :   checkRead();</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        465 :   log.printf(&quot;  between atoms %d %d\n&quot;,atoms[0].serial(),atoms[1].serial());</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        465 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        465 :   if(components &amp;&amp; scaled_components) error(&quot;COMPONENTS and SCALED_COMPONENTS are not compatible&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        464 :   if(components) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         62 :     addComponentWithDerivatives(&quot;x&quot;); componentIsNotPeriodic(&quot;x&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         62 :     addComponentWithDerivatives(&quot;y&quot;); componentIsNotPeriodic(&quot;y&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         62 :     addComponentWithDerivatives(&quot;z&quot;); componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         31 :     log&lt;&lt;&quot;  WARNING: components will not have the proper periodicity - see manual\n&quot;;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        433 :   } else if(scaled_components) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          6 :     addComponentWithDerivatives(&quot;a&quot;); componentIsPeriodic(&quot;a&quot;,&quot;-0.5&quot;,&quot;+0.5&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          6 :     addComponentWithDerivatives(&quot;b&quot;); componentIsPeriodic(&quot;b&quot;,&quot;-0.5&quot;,&quot;+0.5&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          8 :     addComponentWithDerivatives(&quot;c&quot;); componentIsPeriodic(&quot;c&quot;,&quot;-0.5&quot;,&quot;+0.5&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   } else {</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        431 :     addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        464 :   requestAtoms(atoms);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        468 : }</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : // calculator</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      42384 : void Distance::calculate() {</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      42384 :   if(pbc) makeWhole();</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      42384 :   Vector distance=delta(getPosition(0),getPosition(1));</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      42384 :   const double value=distance.modulo();</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      42384 :   const double invvalue=1.0/value;</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      42384 :   if(components) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        394 :     Value* valuex=getPntrToComponent(&quot;x&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        394 :     Value* valuey=getPntrToComponent(&quot;y&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        394 :     Value* valuez=getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        394 :     setAtomsDerivatives (valuex,0,Vector(-1,0,0));</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        394 :     setAtomsDerivatives (valuex,1,Vector(+1,0,0));</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        394 :     setBoxDerivativesNoPbc(valuex);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        394 :     valuex-&gt;set(distance[0]);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        394 :     setAtomsDerivatives (valuey,0,Vector(0,-1,0));</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        394 :     setAtomsDerivatives (valuey,1,Vector(0,+1,0));</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        394 :     setBoxDerivativesNoPbc(valuey);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        394 :     valuey-&gt;set(distance[1]);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        394 :     setAtomsDerivatives (valuez,0,Vector(0,0,-1));</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        394 :     setAtomsDerivatives (valuez,1,Vector(0,0,+1));</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        394 :     setBoxDerivativesNoPbc(valuez);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        394 :     valuez-&gt;set(distance[2]);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      41990 :   } else if(scaled_components) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         11 :     Value* valuea=getPntrToComponent(&quot;a&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         11 :     Value* valueb=getPntrToComponent(&quot;b&quot;);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         22 :     Value* valuec=getPntrToComponent(&quot;c&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         11 :     Vector d=getPbc().realToScaled(distance);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         11 :     setAtomsDerivatives (valuea,0,matmul(getPbc().getInvBox(),Vector(-1,0,0)));</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         11 :     setAtomsDerivatives (valuea,1,matmul(getPbc().getInvBox(),Vector(+1,0,0)));</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         11 :     valuea-&gt;set(Tools::pbc(d[0]));</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         11 :     setAtomsDerivatives (valueb,0,matmul(getPbc().getInvBox(),Vector(0,-1,0)));</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         11 :     setAtomsDerivatives (valueb,1,matmul(getPbc().getInvBox(),Vector(0,+1,0)));</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         11 :     valueb-&gt;set(Tools::pbc(d[1]));</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         11 :     setAtomsDerivatives (valuec,0,matmul(getPbc().getInvBox(),Vector(0,0,-1)));</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         11 :     setAtomsDerivatives (valuec,1,matmul(getPbc().getInvBox(),Vector(0,0,+1)));</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         11 :     valuec-&gt;set(Tools::pbc(d[2]));</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   } else {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      41979 :     setAtomsDerivatives(0,-invvalue*distance);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      41979 :     setAtomsDerivatives(1,invvalue*distance);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      41979 :     setBoxDerivativesNoPbc();</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      41979 :     setValue           (value);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      42384 : }</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/EEFSolv.cpp.func-sort-c.html b/coverage/colvar/EEFSolv.cpp.func-sort-c.html
new file mode 100644
index 0000000000..26dc63083a
--- /dev/null
+++ b/coverage/colvar/EEFSolv.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/EEFSolv.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - EEFSolv.cpp<span style="font-size: 80%;"> (<a href="EEFSolv.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">230</td>
+            <td class="headerCovTableEntry">244</td>
+            <td class="headerCovTableEntryHi">94.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EEFSolv.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#111">_ZN4PLMD6colvar7EEFSolvC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#100">_ZN4PLMD6colvar12_GLOBAL__N_120EEFSolvRegisterMe1026createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#395">_ZN4PLMD6colvar7EEFSolv12setupTypeMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#871">_ZN4PLMD6colvar7EEFSolv13setupValueMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#303">_ZN4PLMD6colvar7EEFSolv14setupConstantsERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IdSaIdEESaIS9_EEb</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#111">_ZN4PLMD6colvar7EEFSolvC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#102">_ZN4PLMD6colvar7EEFSolv16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#148">_ZN4PLMD6colvar7EEFSolv13update_neighbEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#179">_ZN4PLMD6colvar7EEFSolv9calculateEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#100">_ZN4PLMD6colvar12_GLOBAL__N_120EEFSolvRegisterMe102C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#100">_ZN4PLMD6colvar12_GLOBAL__N_120EEFSolvRegisterMe102D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/EEFSolv.cpp.func.html b/coverage/colvar/EEFSolv.cpp.func.html
new file mode 100644
index 0000000000..0c44ed9dad
--- /dev/null
+++ b/coverage/colvar/EEFSolv.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/EEFSolv.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - EEFSolv.cpp<span style="font-size: 80%;"> (<a href="EEFSolv.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">230</td>
+            <td class="headerCovTableEntry">244</td>
+            <td class="headerCovTableEntryHi">94.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EEFSolv.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#100">_ZN4PLMD6colvar12_GLOBAL__N_120EEFSolvRegisterMe1026createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#100">_ZN4PLMD6colvar12_GLOBAL__N_120EEFSolvRegisterMe102C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#100">_ZN4PLMD6colvar12_GLOBAL__N_120EEFSolvRegisterMe102D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#395">_ZN4PLMD6colvar7EEFSolv12setupTypeMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#871">_ZN4PLMD6colvar7EEFSolv13setupValueMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#148">_ZN4PLMD6colvar7EEFSolv13update_neighbEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#303">_ZN4PLMD6colvar7EEFSolv14setupConstantsERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IdSaIdEESaIS9_EEb</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#102">_ZN4PLMD6colvar7EEFSolv16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#179">_ZN4PLMD6colvar7EEFSolv9calculateEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#111">_ZN4PLMD6colvar7EEFSolvC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EEFSolv.cpp.gcov.html#111">_ZN4PLMD6colvar7EEFSolvC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/EEFSolv.cpp.gcov.html b/coverage/colvar/EEFSolv.cpp.gcov.html
new file mode 100644
index 0000000000..d95d238ba1
--- /dev/null
+++ b/coverage/colvar/EEFSolv.cpp.gcov.html
@@ -0,0 +1,1252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/EEFSolv.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - EEFSolv.cpp<span style="font-size: 80%;"> (source / <a href="EEFSolv.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">230</td>
+            <td class="headerCovTableEntry">244</td>
+            <td class="headerCovTableEntryHi">94.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /* This class was originally written by Thomas Loehr */</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;initializer_list&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #define INV_PI_SQRT_PI 0.179587122</a>
+<a name="34"><span class="lineNum">      34 </span>            : #define KCAL_TO_KJ 4.184</a>
+<a name="35"><span class="lineNum">      35 </span>            : #define ANG_TO_NM 0.1</a>
+<a name="36"><span class="lineNum">      36 </span>            : #define ANG3_TO_NM3 0.001</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace colvar {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC COLVAR EEFSOLV</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Calculates EEF1 solvation free energy for a group of atoms.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : EEF1 is a solvent-accessible surface area based model, where the free energy of solvation is computed using a pairwise interaction term for non-hydrogen atoms:</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            :     \Delta G^\mathrm{solv}_i = \Delta G^\mathrm{ref}_i - \sum_{j \neq i} f_i(r_{ij}) V_j</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : where \f$\Delta G^\mathrm{solv}_i\f$ is the free energy of solvation, \f$\Delta G^\mathrm{ref}_i\f$ is the reference solvation free energy, \f$V_j\f$ is the volume of atom \f$j\f$ and</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f[</a>
+<a name="51"><span class="lineNum">      51 </span>            :     f_i(r) 4\pi r^2 = \frac{2}{\sqrt{\pi}} \frac{\Delta G^\mathrm{free}_i}{\lambda_i} \exp\left\{ - \frac{(r-R_i)^2}{\lambda^2_i}\right\}</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f]</a>
+<a name="53"><span class="lineNum">      53 </span>            : where \f$\Delta G^\mathrm{free}_i\f$ is the solvation free energy of the isolated group, \f$\lambda_i\f$ is the correlation length equal to the width of the first solvation shell and \f$R_i\f$ is the van der Waals radius of atom \f$i\f$.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The output from this collective variable, the free energy of solvation, can be used with the \ref BIASVALUE keyword to provide implicit solvation to a system. All parameters are designed to be used with a modified CHARMM36 force field. It takes only non-hydrogen atoms as input, these can be conveniently specified using the \ref GROUP action with the NDX_GROUP parameter. To speed up the calculation, EEFSOLV internally uses a neighbor list with a cutoff dependent on the type of atom (maximum of 1.95 nm). This cutoff can be extended further by using the NL_BUFFER keyword.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \par Examples</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \plumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : #SETTINGS MOLFILE=regtest/basic/rt77/peptide.pdb</a>
+<a name="61"><span class="lineNum">      61 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb</a>
+<a name="62"><span class="lineNum">      62 </span>            : WHOLEMOLECULES ENTITY0=1-111</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : # This allows us to select only non-hydrogen atoms</a>
+<a name="65"><span class="lineNum">      65 </span>            : #SETTINGS AUXFILE=regtest/basic/rt77/index.ndx</a>
+<a name="66"><span class="lineNum">      66 </span>            : protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : # We extend the cutoff by 0.1 nm and update the neighbor list every 40 steps</a>
+<a name="69"><span class="lineNum">      69 </span>            : solv: EEFSOLV ATOMS=protein-h</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : # Here we actually add our calculated energy back to the potential</a>
+<a name="72"><span class="lineNum">      72 </span>            : bias: BIASVALUE ARG=solv</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : PRINT ARG=solv FILE=SOLV</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : class EEFSolv : public Colvar {</a>
+<a name="81"><span class="lineNum">      81 </span>            : private:</a>
+<a name="82"><span class="lineNum">      82 </span>            :   bool pbc;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool serial;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   double delta_g_ref;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   double nl_buffer;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   unsigned nl_stride;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned nl_update;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;std::vector&lt;unsigned&gt; &gt; nl;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;std::vector&lt;bool&gt; &gt; nlexpo;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; parameter;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void setupConstants(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;double&gt; &gt; &amp;parameter, bool tcorr);</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::map&lt;std::string, std::map&lt;std::string, std::string&gt; &gt; setupTypeMap();</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::map&lt;std::string, std::vector&lt;double&gt; &gt; setupValueMap();</a>
+<a name="94"><span class="lineNum">      94 </span>            :   void update_neighb();</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : public:</a>
+<a name="97"><span class="lineNum">      97 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="98"><span class="lineNum">      98 </span>            :   explicit EEFSolv(const ActionOptions&amp;);</a>
+<a name="99"><span class="lineNum">      99 </span>            :   void calculate() override;</a>
+<a name="100"><span class="lineNum">     100 </span>            : };</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(EEFSolv,&quot;EEFSOLV&quot;)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          7 : void EEFSolv::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          7 :   Colvar::registerKeywords(keys);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         14 :   keys.add(&quot;atoms&quot;, &quot;ATOMS&quot;, &quot;The atoms to be included in the calculation, e.g. the whole protein.&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;, &quot;NL_BUFFER&quot;, &quot;0.1&quot;, &quot;The buffer to the intrinsic cutoff used when calculating pairwise interactions.&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;, &quot;NL_STRIDE&quot;, &quot;40&quot;, &quot;The frequency with which the neighbor list is updated.&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         14 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         14 :   keys.addFlag(&quot;TEMP_CORRECTION&quot;, false, &quot;Correct free energy of solvation constants for temperatures different from 298.15 K&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          7 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          5 : EEFSolv::EEFSolv(const ActionOptions&amp;ao):</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          5 :   pbc(true),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          5 :   serial(false),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          5 :   delta_g_ref(0.),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          5 :   nl_buffer(0.1),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          5 :   nl_stride(40),</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          5 :   nl_update(0)</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : {</a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         10 :   parseAtomList(&quot;ATOMS&quot;, atoms);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   const unsigned size = atoms.size();</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          5 :   bool tcorr = false;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          5 :   parseFlag(&quot;TEMP_CORRECTION&quot;, tcorr);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          5 :   parse(&quot;NL_BUFFER&quot;, nl_buffer);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          5 :   parse(&quot;NL_STRIDE&quot;, nl_stride);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          5 :   bool nopbc = !pbc;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          5 :   parseFlag(&quot;NOPBC&quot;, nopbc);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          5 :   pbc = !nopbc;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          5 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          5 :   checkRead();</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         10 :   log &lt;&lt; &quot;  Bibliography &quot; &lt;&lt; plumed.cite(&quot;Lazaridis T, Karplus M, Proteins Struct. Funct. Genet. 35, 133 (1999)&quot;); log &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          5 :   nl.resize(size);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          5 :   nlexpo.resize(size);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          5 :   parameter.resize(size, std::vector&lt;double&gt;(4, 0));</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          5 :   setupConstants(atoms, parameter, tcorr);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          5 :   addValueWithDerivatives();</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          5 :   setNotPeriodic();</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          5 :   requestAtoms(atoms);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          5 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         30 : void EEFSolv::update_neighb() {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   const double lower_c2 = 0.24 * 0.24; // this is the cut-off for bonded atoms</a>
+<a name="152"><span class="lineNum">     152 </span>            :   const unsigned size = getNumberOfAtoms();</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1830 :   for (unsigned i=0; i&lt;size; i++) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       1800 :     nl[i].clear();</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     nlexpo[i].clear();</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1800 :     const Vector posi = getPosition(i);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :     // Loop through neighboring atoms, add the ones below cutoff</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      54900 :     for (unsigned j=i+1; j&lt;size; j++) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      53100 :       if(parameter[i][1]==0&amp;&amp;parameter[j][1]==0) continue;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">      51750 :       const double d2 = delta(posi, getPosition(j)).modulo2();</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      51750 :       if (d2 &lt; lower_c2 &amp;&amp; j &lt; i+14) {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :         // crude approximation for i-i+1/2 interactions,</a>
+<a name="164"><span class="lineNum">     164 </span>            :         // we want to exclude atoms separated by less than three bonds</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       2695 :         continue;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :       }</a>
+<a name="167"><span class="lineNum">     167 </span>            :       // We choose the maximum lambda value and use a more conservative cutoff</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      49055 :       double mlambda = 1./parameter[i][2];</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      49055 :       if (1./parameter[j][2] &gt; mlambda) mlambda = 1./parameter[j][2];</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      49055 :       const double c2 = (2. * mlambda + nl_buffer) * (2. * mlambda + nl_buffer);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      49055 :       if (d2 &lt; c2 ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      26069 :         nl[i].push_back(j);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      26069 :         if(parameter[i][2] == parameter[j][2] &amp;&amp; parameter[i][3] == parameter[j][3]) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       5175 :           nlexpo[i].push_back(true);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      20894 :         } else nlexpo[i].push_back(false);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :       }</a>
+<a name="177"><span class="lineNum">     177 </span>            :     }</a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         30 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         30 : void EEFSolv::calculate() {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         30 :   if(pbc) makeWhole();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         30 :   if(getExchangeStep()) nl_update = 0;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         30 :   if(nl_update==0) update_neighb();</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   const unsigned size=getNumberOfAtoms();</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         30 :   double bias = 0.0;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         30 :   std::vector&lt;Vector&gt; deriv(size, Vector(0,0,0));</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   unsigned stride;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   unsigned rank;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         30 :   if(serial) {</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :     stride=1;</a>
+<a name="194"><span class="lineNum">     194 </span>            :     rank=0;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   } else {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         30 :     stride=comm.Get_size();</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         30 :     rank=comm.Get_rank();</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         30 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         30 :   if(nt*stride*10&gt;size) nt=1;</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         30 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   {</a>
+<a name="205"><span class="lineNum">     205 </span>            :     std::vector&lt;Vector&gt; deriv_omp(size, Vector(0,0,0));</a>
+<a name="206"><span class="lineNum">     206 </span>            :     #pragma omp for reduction(+:bias) nowait</a>
+<a name="207"><span class="lineNum">     207 </span>            :     for (unsigned i=rank; i&lt;size; i+=stride) {</a>
+<a name="208"><span class="lineNum">     208 </span>            :       const Vector posi = getPosition(i);</a>
+<a name="209"><span class="lineNum">     209 </span>            :       double fedensity = 0.0;</a>
+<a name="210"><span class="lineNum">     210 </span>            :       Vector deriv_i;</a>
+<a name="211"><span class="lineNum">     211 </span>            :       const double vdw_volume_i   = parameter[i][0];</a>
+<a name="212"><span class="lineNum">     212 </span>            :       const double delta_g_free_i = parameter[i][1];</a>
+<a name="213"><span class="lineNum">     213 </span>            :       const double inv_lambda_i   = parameter[i][2];</a>
+<a name="214"><span class="lineNum">     214 </span>            :       const double vdw_radius_i   = parameter[i][3];</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :       // The pairwise interactions are unsymmetric, but we can get away with calculating the distance only once</a>
+<a name="217"><span class="lineNum">     217 </span>            :       for (unsigned i_nl=0; i_nl&lt;nl[i].size(); i_nl++) {</a>
+<a name="218"><span class="lineNum">     218 </span>            :         const unsigned j = nl[i][i_nl];</a>
+<a name="219"><span class="lineNum">     219 </span>            :         const double vdw_volume_j   = parameter[j][0];</a>
+<a name="220"><span class="lineNum">     220 </span>            :         const double delta_g_free_j = parameter[j][1];</a>
+<a name="221"><span class="lineNum">     221 </span>            :         const double inv_lambda_j   = parameter[j][2];</a>
+<a name="222"><span class="lineNum">     222 </span>            :         const double vdw_radius_j   = parameter[j][3];</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :         const Vector dist     = delta(posi, getPosition(j));</a>
+<a name="225"><span class="lineNum">     225 </span>            :         const double rij      = dist.modulo();</a>
+<a name="226"><span class="lineNum">     226 </span>            :         const double inv_rij  = 1.0 / rij;</a>
+<a name="227"><span class="lineNum">     227 </span>            :         const double inv_rij2 = inv_rij * inv_rij;</a>
+<a name="228"><span class="lineNum">     228 </span>            :         const double fact_ij  = inv_rij2 * delta_g_free_i * vdw_volume_j * INV_PI_SQRT_PI * inv_lambda_i;</a>
+<a name="229"><span class="lineNum">     229 </span>            :         const double fact_ji  = inv_rij2 * delta_g_free_j * vdw_volume_i * INV_PI_SQRT_PI * inv_lambda_j;</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :         // in this case we can calculate a single exponential</a>
+<a name="232"><span class="lineNum">     232 </span>            :         if(!nlexpo[i][i_nl]) {</a>
+<a name="233"><span class="lineNum">     233 </span>            :           // i-j interaction</a>
+<a name="234"><span class="lineNum">     234 </span>            :           if(inv_rij &gt; 0.5*inv_lambda_i &amp;&amp; delta_g_free_i!=0.)</a>
+<a name="235"><span class="lineNum">     235 </span>            :           {</a>
+<a name="236"><span class="lineNum">     236 </span>            :             const double e_arg = (rij - vdw_radius_i)*inv_lambda_i;</a>
+<a name="237"><span class="lineNum">     237 </span>            :             const double expo  = std::exp(-e_arg*e_arg);</a>
+<a name="238"><span class="lineNum">     238 </span>            :             const double fact  = expo*fact_ij;</a>
+<a name="239"><span class="lineNum">     239 </span>            :             const double e_deriv = inv_rij*fact*(inv_rij + e_arg*inv_lambda_i);</a>
+<a name="240"><span class="lineNum">     240 </span>            :             const Vector dd    = e_deriv*dist;</a>
+<a name="241"><span class="lineNum">     241 </span>            :             fedensity    += fact;</a>
+<a name="242"><span class="lineNum">     242 </span>            :             deriv_i      += dd;</a>
+<a name="243"><span class="lineNum">     243 </span>            :             if(nt&gt;1) deriv_omp[j] -= dd;</a>
+<a name="244"><span class="lineNum">     244 </span>            :             else deriv[j] -= dd;</a>
+<a name="245"><span class="lineNum">     245 </span>            :           }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :           // j-i interaction</a>
+<a name="248"><span class="lineNum">     248 </span>            :           if(inv_rij &gt; 0.5*inv_lambda_j &amp;&amp; delta_g_free_j!=0.)</a>
+<a name="249"><span class="lineNum">     249 </span>            :           {</a>
+<a name="250"><span class="lineNum">     250 </span>            :             const double e_arg = (rij - vdw_radius_j)*inv_lambda_j;</a>
+<a name="251"><span class="lineNum">     251 </span>            :             const double expo  = std::exp(-e_arg*e_arg);</a>
+<a name="252"><span class="lineNum">     252 </span>            :             const double fact  = expo*fact_ji;</a>
+<a name="253"><span class="lineNum">     253 </span>            :             const double e_deriv = inv_rij*fact*(inv_rij + e_arg*inv_lambda_j);</a>
+<a name="254"><span class="lineNum">     254 </span>            :             const Vector dd    = e_deriv*dist;</a>
+<a name="255"><span class="lineNum">     255 </span>            :             fedensity    += fact;</a>
+<a name="256"><span class="lineNum">     256 </span>            :             deriv_i      += dd;</a>
+<a name="257"><span class="lineNum">     257 </span>            :             if(nt&gt;1) deriv_omp[j] -= dd;</a>
+<a name="258"><span class="lineNum">     258 </span>            :             else deriv[j] -= dd;</a>
+<a name="259"><span class="lineNum">     259 </span>            :           }</a>
+<a name="260"><span class="lineNum">     260 </span>            :         } else {</a>
+<a name="261"><span class="lineNum">     261 </span>            :           // i-j interaction</a>
+<a name="262"><span class="lineNum">     262 </span>            :           if(inv_rij &gt; 0.5*inv_lambda_i)</a>
+<a name="263"><span class="lineNum">     263 </span>            :           {</a>
+<a name="264"><span class="lineNum">     264 </span>            :             const double e_arg = (rij - vdw_radius_i)*inv_lambda_i;</a>
+<a name="265"><span class="lineNum">     265 </span>            :             const double expo  = std::exp(-e_arg*e_arg);</a>
+<a name="266"><span class="lineNum">     266 </span>            :             const double fact  = expo*(fact_ij + fact_ji);</a>
+<a name="267"><span class="lineNum">     267 </span>            :             const double e_deriv = inv_rij*fact*(inv_rij + e_arg*inv_lambda_i);</a>
+<a name="268"><span class="lineNum">     268 </span>            :             const Vector dd    = e_deriv*dist;</a>
+<a name="269"><span class="lineNum">     269 </span>            :             fedensity    += fact;</a>
+<a name="270"><span class="lineNum">     270 </span>            :             deriv_i      += dd;</a>
+<a name="271"><span class="lineNum">     271 </span>            :             if(nt&gt;1) deriv_omp[j] -= dd;</a>
+<a name="272"><span class="lineNum">     272 </span>            :             else deriv[j] -= dd;</a>
+<a name="273"><span class="lineNum">     273 </span>            :           }</a>
+<a name="274"><span class="lineNum">     274 </span>            :         }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :       }</a>
+<a name="277"><span class="lineNum">     277 </span>            :       if(nt&gt;1) deriv_omp[i] += deriv_i;</a>
+<a name="278"><span class="lineNum">     278 </span>            :       else deriv[i] += deriv_i;</a>
+<a name="279"><span class="lineNum">     279 </span>            :       bias += 0.5*fedensity;</a>
+<a name="280"><span class="lineNum">     280 </span>            :     }</a>
+<a name="281"><span class="lineNum">     281 </span>            :     #pragma omp critical</a>
+<a name="282"><span class="lineNum">     282 </span>            :     if(nt&gt;1) for(unsigned i=0; i&lt;size; i++) deriv[i]+=deriv_omp[i];</a>
+<a name="283"><span class="lineNum">     283 </span>            :   }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         30 :   if(!serial) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         30 :     comm.Sum(bias);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         30 :     if(!deriv.empty()) comm.Sum(&amp;deriv[0][0],3*deriv.size());</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   }</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         30 :   Tensor virial;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       1830 :   for(unsigned i=0; i&lt;size; i++) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       1800 :     setAtomsDerivatives(i, -deriv[i]);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1800 :     virial += Tensor(getPosition(i), -deriv[i]);</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   }</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         30 :   setBoxDerivatives(-virial);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         30 :   setValue(delta_g_ref - bias);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :   // Keep track of the neighbourlist updates</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         30 :   nl_update++;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         30 :   if (nl_update == nl_stride) {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         30 :     nl_update = 0;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         30 : }</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          5 : void EEFSolv::setupConstants(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;double&gt; &gt; &amp;parameter, bool tcorr) {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; parameter_temp;</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         10 :   parameter_temp.resize(atoms.size(), std::vector&lt;double&gt;(7,0));</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :   std::map&lt;std::string, std::vector&lt;double&gt; &gt; valuemap;</a>
+<a name="309"><span class="lineNum">     309 </span>            :   std::map&lt;std::string, std::map&lt;std::string, std::string&gt; &gt; typemap;</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          5 :   valuemap = setupValueMap();</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          5 :   typemap  = setupTypeMap();</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          5 :   auto * moldat = plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :   bool cter=false;</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          5 :   if (moldat) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          5 :     log&lt;&lt;&quot;  MOLINFO DATA found with label &quot; &lt;&lt;moldat-&gt;getLabel()&lt;&lt;&quot;, using proper atom names\n&quot;;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        305 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :       // Get atom and residue names</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        300 :       std::string Aname = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        300 :       std::string Rname = moldat-&gt;getResidueName(atoms[i]);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        300 :       std::string Atype = typemap[Rname][Aname];</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :       // Check for terminal COOH or COO- (different atomtypes &amp; parameters!)</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        598 :       if (Aname == &quot;OT1&quot; || Aname == &quot;OXT&quot;) {</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :         // We create a temporary AtomNumber object to access future atoms</a>
+<a name="326"><span class="lineNum">     326 </span>            :         unsigned ai = atoms[i].index();</a>
+<a name="327"><span class="lineNum">     327 </span>            :         AtomNumber tmp_an;</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          2 :         tmp_an.setIndex(ai + 2);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          2 :         if (moldat-&gt;checkForAtom(tmp_an) &amp;&amp; moldat-&gt;getAtomName(tmp_an) == &quot;HT2&quot;) {</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :           // COOH</a>
+<a name="331"><span class="lineNum">     331 </span>            :           Atype = &quot;OB&quot;;</a>
+<a name="332"><span class="lineNum">     332 </span>            :         } else {</a>
+<a name="333"><span class="lineNum">     333 </span>            :           // COO-</a>
+<a name="334"><span class="lineNum">     334 </span>            :           Atype = &quot;OC&quot;;</a>
+<a name="335"><span class="lineNum">     335 </span>            :         }</a>
+<a name="336"><span class="lineNum">     336 </span>            :         cter = true;</a>
+<a name="337"><span class="lineNum">     337 </span>            :       }</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        302 :       if (Aname == &quot;OT2&quot; || (cter == true &amp;&amp; Aname == &quot;O&quot;)) {</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :         unsigned ai = atoms[i].index();</a>
+<a name="340"><span class="lineNum">     340 </span>            :         AtomNumber tmp_an;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          2 :         tmp_an.setIndex(ai + 1);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          2 :         if (moldat-&gt;checkForAtom(tmp_an) &amp;&amp; moldat-&gt;getAtomName(tmp_an) == &quot;HT2&quot;) {</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :           // COOH</a>
+<a name="344"><span class="lineNum">     344 </span>            :           Atype = &quot;OH1&quot;;</a>
+<a name="345"><span class="lineNum">     345 </span>            :         } else {</a>
+<a name="346"><span class="lineNum">     346 </span>            :           // COO-</a>
+<a name="347"><span class="lineNum">     347 </span>            :           Atype = &quot;OC&quot;;</a>
+<a name="348"><span class="lineNum">     348 </span>            :         }</a>
+<a name="349"><span class="lineNum">     349 </span>            :       }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            :       // Check for H-atoms</a>
+<a name="352"><span class="lineNum">     352 </span>            :       char type;</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        300 :       char first = Aname.at(0);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :       // GOLDEN RULE: type is first letter, if not a number</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        300 :       if (!isdigit(first)) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :         type = first;</a>
+<a name="358"><span class="lineNum">     358 </span>            :         // otherwise is the second</a>
+<a name="359"><span class="lineNum">     359 </span>            :       } else {</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :         type = Aname.at(1);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :       }</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">        300 :       if (type == 'H') {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :         error(&quot;EEF1-SB does not allow the use of hydrogen atoms!\n&quot;);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :       }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :       // Lookup atomtype in table or throw exception if its not there</a>
+<a name="368"><span class="lineNum">     368 </span>            :       try {</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        300 :         parameter_temp[i] = valuemap.at(Atype);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :       } catch (const std::exception &amp;e) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :         log &lt;&lt; &quot;Type: &quot; &lt;&lt; Atype &lt;&lt; &quot;  Name: &quot; &lt;&lt; Aname &lt;&lt; &quot;  Residue: &quot; &lt;&lt; Rname &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :         error(&quot;Invalid atom type!\n&quot;);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            :       // Temperature correction</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        300 :       if (tcorr &amp;&amp; parameter[i][1] &gt; 0.0) {</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :         const double t0 = 298.15;</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :         const double delta_g_ref_t0 = parameter_temp[i][1];</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :         const double delta_h_ref_t0 = parameter_temp[i][3];</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :         const double delta_cp = parameter_temp[i][4];</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :         const double delta_s_ref_t0 = (delta_h_ref_t0 - delta_g_ref_t0) / t0;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :         const double t = plumed.getAtoms().getKbT() / plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :         parameter_temp[i][1] -= delta_s_ref_t0 * (t - t0) - delta_cp * t * std::log(t / t0) + delta_cp * (t - t0);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :         parameter_temp[i][2] *= parameter_temp[i][1] / delta_g_ref_t0;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :       }</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        300 :       parameter[i][0] = parameter_temp[i][0];</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        300 :       parameter[i][1] = parameter_temp[i][2];</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        300 :       parameter[i][2] = parameter_temp[i][5];</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        300 :       parameter[i][3] = parameter_temp[i][6];</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :     }</a>
+<a name="391"><span class="lineNum">     391 </span>            :   } else {</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :     error(&quot;MOLINFO DATA not found\n&quot;);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   }</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        305 :   for(unsigned i=0; i&lt;atoms.size(); ++i) delta_g_ref += parameter_temp[i][1];</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          5 : }</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          5 : std::map&lt;std::string, std::map&lt;std::string, std::string&gt; &gt; EEFSolv::setupTypeMap()  {</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   std::map&lt;std::string, std::map&lt;std::string, std::string&gt; &gt; typemap;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         40 :   typemap[&quot;ACE&quot;] = {</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :     {&quot;CH3&quot;, &quot;CT3&quot;},</a>
+<a name="401"><span class="lineNum">     401 </span>            :     {&quot;HH31&quot;,&quot;HA3&quot;},</a>
+<a name="402"><span class="lineNum">     402 </span>            :     {&quot;HH32&quot;,&quot;HA3&quot;},</a>
+<a name="403"><span class="lineNum">     403 </span>            :     {&quot;HH33&quot;,&quot;HA3&quot;},</a>
+<a name="404"><span class="lineNum">     404 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="405"><span class="lineNum">     405 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         30 :   };</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         60 :   typemap[&quot;ALA&quot;] = {</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="409"><span class="lineNum">     409 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="410"><span class="lineNum">     410 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="411"><span class="lineNum">     411 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="412"><span class="lineNum">     412 </span>            :     {&quot;CB&quot;,  &quot;CT3&quot;},</a>
+<a name="413"><span class="lineNum">     413 </span>            :     {&quot;HB1&quot;, &quot;HA3&quot;},</a>
+<a name="414"><span class="lineNum">     414 </span>            :     {&quot;HB2&quot;, &quot;HA3&quot;},</a>
+<a name="415"><span class="lineNum">     415 </span>            :     {&quot;HB3&quot;, &quot;HA3&quot;},</a>
+<a name="416"><span class="lineNum">     416 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="417"><span class="lineNum">     417 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         50 :   };</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        130 :   typemap[&quot;ARG&quot;] = {</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :     {&quot;N&quot;,    &quot;NH1&quot;},</a>
+<a name="421"><span class="lineNum">     421 </span>            :     {&quot;HN&quot;,   &quot;H&quot;  },</a>
+<a name="422"><span class="lineNum">     422 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot;},</a>
+<a name="423"><span class="lineNum">     423 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot;},</a>
+<a name="424"><span class="lineNum">     424 </span>            :     {&quot;CB&quot;,   &quot;CT2&quot;},</a>
+<a name="425"><span class="lineNum">     425 </span>            :     {&quot;HB1&quot;,  &quot;HA2&quot;},</a>
+<a name="426"><span class="lineNum">     426 </span>            :     {&quot;HB2&quot;,  &quot;HA2&quot;},</a>
+<a name="427"><span class="lineNum">     427 </span>            :     {&quot;CG&quot;,   &quot;CT2&quot;},</a>
+<a name="428"><span class="lineNum">     428 </span>            :     {&quot;HG1&quot;,  &quot;HA2&quot;},</a>
+<a name="429"><span class="lineNum">     429 </span>            :     {&quot;HG2&quot;,  &quot;HA2&quot;},</a>
+<a name="430"><span class="lineNum">     430 </span>            :     {&quot;CD&quot;,   &quot;CT2&quot;},</a>
+<a name="431"><span class="lineNum">     431 </span>            :     {&quot;HD1&quot;,  &quot;HA2&quot;},</a>
+<a name="432"><span class="lineNum">     432 </span>            :     {&quot;HD2&quot;,  &quot;HA2&quot;},</a>
+<a name="433"><span class="lineNum">     433 </span>            :     {&quot;NE&quot;,   &quot;NC2&quot;},</a>
+<a name="434"><span class="lineNum">     434 </span>            :     {&quot;HE&quot;,   &quot;HC&quot; },</a>
+<a name="435"><span class="lineNum">     435 </span>            :     {&quot;CZ&quot;,   &quot;C&quot;  },</a>
+<a name="436"><span class="lineNum">     436 </span>            :     {&quot;NH1&quot;,  &quot;NC2&quot;},</a>
+<a name="437"><span class="lineNum">     437 </span>            :     {&quot;HH11&quot;, &quot;HC&quot; },</a>
+<a name="438"><span class="lineNum">     438 </span>            :     {&quot;HH12&quot;, &quot;HC&quot; },</a>
+<a name="439"><span class="lineNum">     439 </span>            :     {&quot;NH2&quot;,  &quot;NC2&quot;},</a>
+<a name="440"><span class="lineNum">     440 </span>            :     {&quot;HH21&quot;, &quot;HC&quot; },</a>
+<a name="441"><span class="lineNum">     441 </span>            :     {&quot;HH22&quot;, &quot;HC&quot; },</a>
+<a name="442"><span class="lineNum">     442 </span>            :     {&quot;C&quot;,    &quot;C&quot;  },</a>
+<a name="443"><span class="lineNum">     443 </span>            :     {&quot;O&quot;,    &quot;O&quot;  }</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">        120 :   };</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         80 :   typemap[&quot;ASN&quot;] = {</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :     {&quot;N&quot;,    &quot;NH1&quot;},</a>
+<a name="447"><span class="lineNum">     447 </span>            :     {&quot;HN&quot;,   &quot;H&quot;  },</a>
+<a name="448"><span class="lineNum">     448 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot;},</a>
+<a name="449"><span class="lineNum">     449 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot;},</a>
+<a name="450"><span class="lineNum">     450 </span>            :     {&quot;CB&quot;,   &quot;CT2&quot;},</a>
+<a name="451"><span class="lineNum">     451 </span>            :     {&quot;HB1&quot;,  &quot;HA2&quot;},</a>
+<a name="452"><span class="lineNum">     452 </span>            :     {&quot;HB2&quot;,  &quot;HA2&quot;},</a>
+<a name="453"><span class="lineNum">     453 </span>            :     {&quot;CG&quot;,   &quot;CC&quot; },</a>
+<a name="454"><span class="lineNum">     454 </span>            :     {&quot;OD1&quot;,  &quot;O&quot;  },</a>
+<a name="455"><span class="lineNum">     455 </span>            :     {&quot;ND2&quot;,  &quot;NH2&quot;},</a>
+<a name="456"><span class="lineNum">     456 </span>            :     {&quot;HD21&quot;, &quot;H&quot;  },</a>
+<a name="457"><span class="lineNum">     457 </span>            :     {&quot;HD22&quot;, &quot;H&quot;  },</a>
+<a name="458"><span class="lineNum">     458 </span>            :     {&quot;C&quot;,    &quot;C&quot;  },</a>
+<a name="459"><span class="lineNum">     459 </span>            :     {&quot;O&quot;,    &quot;O&quot;  }</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         70 :   };</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         75 :   typemap[&quot;ASPP&quot;] = {</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="463"><span class="lineNum">     463 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="464"><span class="lineNum">     464 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="465"><span class="lineNum">     465 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="466"><span class="lineNum">     466 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="467"><span class="lineNum">     467 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="468"><span class="lineNum">     468 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="469"><span class="lineNum">     469 </span>            :     {&quot;CG&quot;,  &quot;CD&quot; },</a>
+<a name="470"><span class="lineNum">     470 </span>            :     {&quot;OD1&quot;, &quot;OB&quot; },</a>
+<a name="471"><span class="lineNum">     471 </span>            :     {&quot;OD2&quot;, &quot;OH1&quot;},</a>
+<a name="472"><span class="lineNum">     472 </span>            :     {&quot;HD2&quot;, &quot;H&quot;  },</a>
+<a name="473"><span class="lineNum">     473 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="474"><span class="lineNum">     474 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         65 :   };</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         70 :   typemap[&quot;ASP&quot;] = {</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="478"><span class="lineNum">     478 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="479"><span class="lineNum">     479 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="480"><span class="lineNum">     480 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="481"><span class="lineNum">     481 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="482"><span class="lineNum">     482 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="483"><span class="lineNum">     483 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="484"><span class="lineNum">     484 </span>            :     {&quot;CG&quot;,  &quot;CC&quot; },</a>
+<a name="485"><span class="lineNum">     485 </span>            :     {&quot;OD1&quot;, &quot;OC&quot; },</a>
+<a name="486"><span class="lineNum">     486 </span>            :     {&quot;OD2&quot;, &quot;OC&quot; },</a>
+<a name="487"><span class="lineNum">     487 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="488"><span class="lineNum">     488 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         60 :   };</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         65 :   typemap[&quot;CYS&quot;] = {</span></a>
+<a name="491"><span class="lineNum">     491 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="492"><span class="lineNum">     492 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="493"><span class="lineNum">     493 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="494"><span class="lineNum">     494 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="495"><span class="lineNum">     495 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="496"><span class="lineNum">     496 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="497"><span class="lineNum">     497 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="498"><span class="lineNum">     498 </span>            :     {&quot;SG&quot;,  &quot;S&quot;  },</a>
+<a name="499"><span class="lineNum">     499 </span>            :     {&quot;HG1&quot;, &quot;HS&quot; },</a>
+<a name="500"><span class="lineNum">     500 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="501"><span class="lineNum">     501 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         55 :   };</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         95 :   typemap[&quot;GLN&quot;] = {</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :     {&quot;N&quot;,    &quot;NH1&quot; },</a>
+<a name="505"><span class="lineNum">     505 </span>            :     {&quot;HN&quot;,   &quot;H&quot;   },</a>
+<a name="506"><span class="lineNum">     506 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot; },</a>
+<a name="507"><span class="lineNum">     507 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot; },</a>
+<a name="508"><span class="lineNum">     508 </span>            :     {&quot;CB&quot;,   &quot;CT2&quot; },</a>
+<a name="509"><span class="lineNum">     509 </span>            :     {&quot;HB1&quot;,  &quot;HA2&quot; },</a>
+<a name="510"><span class="lineNum">     510 </span>            :     {&quot;HB2&quot;,  &quot;HA2&quot; },</a>
+<a name="511"><span class="lineNum">     511 </span>            :     {&quot;CG&quot;,   &quot;CT2&quot; },</a>
+<a name="512"><span class="lineNum">     512 </span>            :     {&quot;HG1&quot;,  &quot;HA2&quot; },</a>
+<a name="513"><span class="lineNum">     513 </span>            :     {&quot;HG2&quot;,  &quot;HA2&quot; },</a>
+<a name="514"><span class="lineNum">     514 </span>            :     {&quot;CD&quot;,   &quot;CC&quot;  },</a>
+<a name="515"><span class="lineNum">     515 </span>            :     {&quot;OE1&quot;,  &quot;O&quot;   },</a>
+<a name="516"><span class="lineNum">     516 </span>            :     {&quot;NE2&quot;,  &quot;NH2&quot; },</a>
+<a name="517"><span class="lineNum">     517 </span>            :     {&quot;HE21&quot;, &quot;H&quot;   },</a>
+<a name="518"><span class="lineNum">     518 </span>            :     {&quot;HE22&quot;, &quot;H&quot;   },</a>
+<a name="519"><span class="lineNum">     519 </span>            :     {&quot;C&quot;,    &quot;C&quot;   },</a>
+<a name="520"><span class="lineNum">     520 </span>            :     {&quot;O&quot;,    &quot;O&quot;   }</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         85 :   };</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         90 :   typemap[&quot;GLUP&quot;] = {</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="524"><span class="lineNum">     524 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="525"><span class="lineNum">     525 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="526"><span class="lineNum">     526 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="527"><span class="lineNum">     527 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="528"><span class="lineNum">     528 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="529"><span class="lineNum">     529 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="530"><span class="lineNum">     530 </span>            :     {&quot;CG&quot;,  &quot;CT2&quot;},</a>
+<a name="531"><span class="lineNum">     531 </span>            :     {&quot;HG1&quot;, &quot;HA2&quot;},</a>
+<a name="532"><span class="lineNum">     532 </span>            :     {&quot;HG2&quot;, &quot;HA2&quot;},</a>
+<a name="533"><span class="lineNum">     533 </span>            :     {&quot;CD&quot;,  &quot;CD&quot; },</a>
+<a name="534"><span class="lineNum">     534 </span>            :     {&quot;OE1&quot;, &quot;OB&quot; },</a>
+<a name="535"><span class="lineNum">     535 </span>            :     {&quot;OE2&quot;, &quot;OH1&quot;},</a>
+<a name="536"><span class="lineNum">     536 </span>            :     {&quot;HE2&quot;, &quot;H&quot;  },</a>
+<a name="537"><span class="lineNum">     537 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="538"><span class="lineNum">     538 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         80 :   };</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         85 :   typemap[&quot;GLU&quot;] = {</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="542"><span class="lineNum">     542 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="543"><span class="lineNum">     543 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="544"><span class="lineNum">     544 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="545"><span class="lineNum">     545 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="546"><span class="lineNum">     546 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="547"><span class="lineNum">     547 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="548"><span class="lineNum">     548 </span>            :     {&quot;CG&quot;,  &quot;CT2&quot;},</a>
+<a name="549"><span class="lineNum">     549 </span>            :     {&quot;HG1&quot;, &quot;HA2&quot;},</a>
+<a name="550"><span class="lineNum">     550 </span>            :     {&quot;HG2&quot;, &quot;HA2&quot;},</a>
+<a name="551"><span class="lineNum">     551 </span>            :     {&quot;CD&quot;,  &quot;CC&quot; },</a>
+<a name="552"><span class="lineNum">     552 </span>            :     {&quot;OE1&quot;, &quot;OC&quot; },</a>
+<a name="553"><span class="lineNum">     553 </span>            :     {&quot;OE2&quot;, &quot;OC&quot; },</a>
+<a name="554"><span class="lineNum">     554 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="555"><span class="lineNum">     555 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">         75 :   };</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         45 :   typemap[&quot;GLY&quot;] = {</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="559"><span class="lineNum">     559 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="560"><span class="lineNum">     560 </span>            :     {&quot;CA&quot;,  &quot;CT2&quot;},</a>
+<a name="561"><span class="lineNum">     561 </span>            :     {&quot;HA1&quot;, &quot;HB2&quot;},</a>
+<a name="562"><span class="lineNum">     562 </span>            :     {&quot;HA2&quot;, &quot;HB2&quot;},</a>
+<a name="563"><span class="lineNum">     563 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="564"><span class="lineNum">     564 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         35 :   };</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         95 :   typemap[&quot;HSD&quot;] = {</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="568"><span class="lineNum">     568 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="569"><span class="lineNum">     569 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="570"><span class="lineNum">     570 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="571"><span class="lineNum">     571 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="572"><span class="lineNum">     572 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="573"><span class="lineNum">     573 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="574"><span class="lineNum">     574 </span>            :     {&quot;ND1&quot;, &quot;NR1&quot;},</a>
+<a name="575"><span class="lineNum">     575 </span>            :     {&quot;HD1&quot;, &quot;H&quot;  },</a>
+<a name="576"><span class="lineNum">     576 </span>            :     {&quot;CG&quot;,  &quot;CPH1&quot;},</a>
+<a name="577"><span class="lineNum">     577 </span>            :     {&quot;CE1&quot;, &quot;CPH2&quot;},</a>
+<a name="578"><span class="lineNum">     578 </span>            :     {&quot;HE1&quot;, &quot;HR1&quot;},</a>
+<a name="579"><span class="lineNum">     579 </span>            :     {&quot;NE2&quot;, &quot;NR2&quot;},</a>
+<a name="580"><span class="lineNum">     580 </span>            :     {&quot;CD2&quot;, &quot;CPH1&quot;},</a>
+<a name="581"><span class="lineNum">     581 </span>            :     {&quot;HD2&quot;, &quot;HR3&quot;},</a>
+<a name="582"><span class="lineNum">     582 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="583"><span class="lineNum">     583 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         85 :   };</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         95 :   typemap[&quot;HIS&quot;] = {</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="587"><span class="lineNum">     587 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="588"><span class="lineNum">     588 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="589"><span class="lineNum">     589 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="590"><span class="lineNum">     590 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="591"><span class="lineNum">     591 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="592"><span class="lineNum">     592 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="593"><span class="lineNum">     593 </span>            :     {&quot;ND1&quot;, &quot;NR2&quot;},</a>
+<a name="594"><span class="lineNum">     594 </span>            :     {&quot;CG&quot;,  &quot;CPH1&quot;},</a>
+<a name="595"><span class="lineNum">     595 </span>            :     {&quot;CE1&quot;, &quot;CPH2&quot;},</a>
+<a name="596"><span class="lineNum">     596 </span>            :     {&quot;HE1&quot;, &quot;HR1&quot;},</a>
+<a name="597"><span class="lineNum">     597 </span>            :     {&quot;NE2&quot;, &quot;NR1&quot;},</a>
+<a name="598"><span class="lineNum">     598 </span>            :     {&quot;HE2&quot;, &quot;H&quot;  },</a>
+<a name="599"><span class="lineNum">     599 </span>            :     {&quot;CD2&quot;, &quot;CPH1&quot;},</a>
+<a name="600"><span class="lineNum">     600 </span>            :     {&quot;HD2&quot;, &quot;HR3&quot;},</a>
+<a name="601"><span class="lineNum">     601 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="602"><span class="lineNum">     602 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         85 :   };</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         95 :   typemap[&quot;HSE&quot;] = {</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="606"><span class="lineNum">     606 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="607"><span class="lineNum">     607 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="608"><span class="lineNum">     608 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="609"><span class="lineNum">     609 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="610"><span class="lineNum">     610 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="611"><span class="lineNum">     611 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="612"><span class="lineNum">     612 </span>            :     {&quot;ND1&quot;, &quot;NR2&quot;},</a>
+<a name="613"><span class="lineNum">     613 </span>            :     {&quot;CG&quot;,  &quot;CPH1&quot;},</a>
+<a name="614"><span class="lineNum">     614 </span>            :     {&quot;CE1&quot;, &quot;CPH2&quot;},</a>
+<a name="615"><span class="lineNum">     615 </span>            :     {&quot;HE1&quot;, &quot;HR1&quot;},</a>
+<a name="616"><span class="lineNum">     616 </span>            :     {&quot;NE2&quot;, &quot;NR1&quot;},</a>
+<a name="617"><span class="lineNum">     617 </span>            :     {&quot;HE2&quot;, &quot;H&quot;  },</a>
+<a name="618"><span class="lineNum">     618 </span>            :     {&quot;CD2&quot;, &quot;CPH1&quot;},</a>
+<a name="619"><span class="lineNum">     619 </span>            :     {&quot;HD2&quot;, &quot;HR3&quot;},</a>
+<a name="620"><span class="lineNum">     620 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="621"><span class="lineNum">     621 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         85 :   };</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        100 :   typemap[&quot;HSP&quot;] = {</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="625"><span class="lineNum">     625 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="626"><span class="lineNum">     626 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="627"><span class="lineNum">     627 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="628"><span class="lineNum">     628 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="629"><span class="lineNum">     629 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="630"><span class="lineNum">     630 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="631"><span class="lineNum">     631 </span>            :     {&quot;CD2&quot;, &quot;CPH1&quot;},</a>
+<a name="632"><span class="lineNum">     632 </span>            :     {&quot;HD2&quot;, &quot;HR1&quot;},</a>
+<a name="633"><span class="lineNum">     633 </span>            :     {&quot;CG&quot;,  &quot;CPH1&quot;},</a>
+<a name="634"><span class="lineNum">     634 </span>            :     {&quot;NE2&quot;, &quot;NR3&quot;},</a>
+<a name="635"><span class="lineNum">     635 </span>            :     {&quot;HE2&quot;, &quot;H&quot;  },</a>
+<a name="636"><span class="lineNum">     636 </span>            :     {&quot;ND1&quot;, &quot;NR3&quot;},</a>
+<a name="637"><span class="lineNum">     637 </span>            :     {&quot;HD1&quot;, &quot;H&quot;  },</a>
+<a name="638"><span class="lineNum">     638 </span>            :     {&quot;CE1&quot;, &quot;CPH2&quot;},</a>
+<a name="639"><span class="lineNum">     639 </span>            :     {&quot;HE1&quot;, &quot;HR2&quot;},</a>
+<a name="640"><span class="lineNum">     640 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="641"><span class="lineNum">     641 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">         90 :   };</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">        105 :   typemap[&quot;ILE&quot;] = {</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :     {&quot;N&quot;,    &quot;NH1&quot;},</a>
+<a name="645"><span class="lineNum">     645 </span>            :     {&quot;HN&quot;,   &quot;H&quot;  },</a>
+<a name="646"><span class="lineNum">     646 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot;},</a>
+<a name="647"><span class="lineNum">     647 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot;},</a>
+<a name="648"><span class="lineNum">     648 </span>            :     {&quot;CB&quot;,   &quot;CT1&quot;},</a>
+<a name="649"><span class="lineNum">     649 </span>            :     {&quot;HB&quot;,   &quot;HA1&quot;},</a>
+<a name="650"><span class="lineNum">     650 </span>            :     {&quot;CG2&quot;,  &quot;CT3&quot;},</a>
+<a name="651"><span class="lineNum">     651 </span>            :     {&quot;HG21&quot;, &quot;HA3&quot;},</a>
+<a name="652"><span class="lineNum">     652 </span>            :     {&quot;HG22&quot;, &quot;HA3&quot;},</a>
+<a name="653"><span class="lineNum">     653 </span>            :     {&quot;HG23&quot;, &quot;HA3&quot;},</a>
+<a name="654"><span class="lineNum">     654 </span>            :     {&quot;CG1&quot;,  &quot;CT2&quot;},</a>
+<a name="655"><span class="lineNum">     655 </span>            :     {&quot;HG11&quot;, &quot;HA2&quot;},</a>
+<a name="656"><span class="lineNum">     656 </span>            :     {&quot;HG12&quot;, &quot;HA2&quot;},</a>
+<a name="657"><span class="lineNum">     657 </span>            :     {&quot;CD&quot;,   &quot;CT3&quot;},</a>
+<a name="658"><span class="lineNum">     658 </span>            :     {&quot;HD1&quot;,  &quot;HA3&quot;},</a>
+<a name="659"><span class="lineNum">     659 </span>            :     {&quot;HD2&quot;,  &quot;HA3&quot;},</a>
+<a name="660"><span class="lineNum">     660 </span>            :     {&quot;HD3&quot;,  &quot;HA3&quot;},</a>
+<a name="661"><span class="lineNum">     661 </span>            :     {&quot;C&quot;,    &quot;C&quot;  },</a>
+<a name="662"><span class="lineNum">     662 </span>            :     {&quot;O&quot;,    &quot;O&quot;  }</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         95 :   };</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">        105 :   typemap[&quot;LEU&quot;] = {</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :     {&quot;N&quot;,    &quot;NH1&quot;},</a>
+<a name="666"><span class="lineNum">     666 </span>            :     {&quot;HN&quot;,   &quot;H&quot;  },</a>
+<a name="667"><span class="lineNum">     667 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot;},</a>
+<a name="668"><span class="lineNum">     668 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot;},</a>
+<a name="669"><span class="lineNum">     669 </span>            :     {&quot;CB&quot;,   &quot;CT2&quot;},</a>
+<a name="670"><span class="lineNum">     670 </span>            :     {&quot;HB1&quot;,  &quot;HA2&quot;},</a>
+<a name="671"><span class="lineNum">     671 </span>            :     {&quot;HB2&quot;,  &quot;HA2&quot;},</a>
+<a name="672"><span class="lineNum">     672 </span>            :     {&quot;CG&quot;,   &quot;CT1&quot;},</a>
+<a name="673"><span class="lineNum">     673 </span>            :     {&quot;HG&quot;,   &quot;HA1&quot;},</a>
+<a name="674"><span class="lineNum">     674 </span>            :     {&quot;CD1&quot;,  &quot;CT3&quot;},</a>
+<a name="675"><span class="lineNum">     675 </span>            :     {&quot;HD11&quot;, &quot;HA3&quot;},</a>
+<a name="676"><span class="lineNum">     676 </span>            :     {&quot;HD12&quot;, &quot;HA3&quot;},</a>
+<a name="677"><span class="lineNum">     677 </span>            :     {&quot;HD13&quot;, &quot;HA3&quot;},</a>
+<a name="678"><span class="lineNum">     678 </span>            :     {&quot;CD2&quot;,  &quot;CT3&quot;},</a>
+<a name="679"><span class="lineNum">     679 </span>            :     {&quot;HD21&quot;, &quot;HA3&quot;},</a>
+<a name="680"><span class="lineNum">     680 </span>            :     {&quot;HD22&quot;, &quot;HA3&quot;},</a>
+<a name="681"><span class="lineNum">     681 </span>            :     {&quot;HD23&quot;, &quot;HA3&quot;},</a>
+<a name="682"><span class="lineNum">     682 </span>            :     {&quot;C&quot;,    &quot;C&quot;  },</a>
+<a name="683"><span class="lineNum">     683 </span>            :     {&quot;O&quot;,    &quot;O&quot;  }</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         95 :   };</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">        120 :   typemap[&quot;LYS&quot;] = {</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="687"><span class="lineNum">     687 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="688"><span class="lineNum">     688 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="689"><span class="lineNum">     689 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="690"><span class="lineNum">     690 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="691"><span class="lineNum">     691 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="692"><span class="lineNum">     692 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="693"><span class="lineNum">     693 </span>            :     {&quot;CG&quot;,  &quot;CT2&quot;},</a>
+<a name="694"><span class="lineNum">     694 </span>            :     {&quot;HG1&quot;, &quot;HA2&quot;},</a>
+<a name="695"><span class="lineNum">     695 </span>            :     {&quot;HG2&quot;, &quot;HA2&quot;},</a>
+<a name="696"><span class="lineNum">     696 </span>            :     {&quot;CD&quot;,  &quot;CT2&quot;},</a>
+<a name="697"><span class="lineNum">     697 </span>            :     {&quot;HD1&quot;, &quot;HA2&quot;},</a>
+<a name="698"><span class="lineNum">     698 </span>            :     {&quot;HD2&quot;, &quot;HA2&quot;},</a>
+<a name="699"><span class="lineNum">     699 </span>            :     {&quot;CE&quot;,  &quot;CT2&quot;},</a>
+<a name="700"><span class="lineNum">     700 </span>            :     {&quot;HE1&quot;, &quot;HA2&quot;},</a>
+<a name="701"><span class="lineNum">     701 </span>            :     {&quot;HE2&quot;, &quot;HA2&quot;},</a>
+<a name="702"><span class="lineNum">     702 </span>            :     {&quot;NZ&quot;,  &quot;NH3&quot;},</a>
+<a name="703"><span class="lineNum">     703 </span>            :     {&quot;HZ1&quot;, &quot;HC&quot; },</a>
+<a name="704"><span class="lineNum">     704 </span>            :     {&quot;HZ2&quot;, &quot;HC&quot; },</a>
+<a name="705"><span class="lineNum">     705 </span>            :     {&quot;HZ3&quot;, &quot;HC&quot; },</a>
+<a name="706"><span class="lineNum">     706 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="707"><span class="lineNum">     707 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">        110 :   };</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         95 :   typemap[&quot;MET&quot;] = {</span></a>
+<a name="710"><span class="lineNum">     710 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="711"><span class="lineNum">     711 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="712"><span class="lineNum">     712 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="713"><span class="lineNum">     713 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="714"><span class="lineNum">     714 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="715"><span class="lineNum">     715 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="716"><span class="lineNum">     716 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="717"><span class="lineNum">     717 </span>            :     {&quot;CG&quot;,  &quot;CT2&quot;},</a>
+<a name="718"><span class="lineNum">     718 </span>            :     {&quot;HG1&quot;, &quot;HA2&quot;},</a>
+<a name="719"><span class="lineNum">     719 </span>            :     {&quot;HG2&quot;, &quot;HA2&quot;},</a>
+<a name="720"><span class="lineNum">     720 </span>            :     {&quot;SD&quot;,  &quot;S&quot;  },</a>
+<a name="721"><span class="lineNum">     721 </span>            :     {&quot;CE&quot;,  &quot;CT3&quot;},</a>
+<a name="722"><span class="lineNum">     722 </span>            :     {&quot;HE1&quot;, &quot;HA3&quot;},</a>
+<a name="723"><span class="lineNum">     723 </span>            :     {&quot;HE2&quot;, &quot;HA3&quot;},</a>
+<a name="724"><span class="lineNum">     724 </span>            :     {&quot;HE3&quot;, &quot;HA3&quot;},</a>
+<a name="725"><span class="lineNum">     725 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="726"><span class="lineNum">     726 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">         85 :   };</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">         40 :   typemap[&quot;NMA&quot;] = {</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="730"><span class="lineNum">     730 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="731"><span class="lineNum">     731 </span>            :     {&quot;CH3&quot;, &quot;CT3&quot;},</a>
+<a name="732"><span class="lineNum">     732 </span>            :     {&quot;HH31&quot;,&quot;HA3&quot;},</a>
+<a name="733"><span class="lineNum">     733 </span>            :     {&quot;HH32&quot;,&quot;HA3&quot;},</a>
+<a name="734"><span class="lineNum">     734 </span>            :     {&quot;HH33&quot;,&quot;HA3&quot;},</a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         30 :   };</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">        110 :   typemap[&quot;PHE&quot;] = {</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="738"><span class="lineNum">     738 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="739"><span class="lineNum">     739 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="740"><span class="lineNum">     740 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="741"><span class="lineNum">     741 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="742"><span class="lineNum">     742 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="743"><span class="lineNum">     743 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="744"><span class="lineNum">     744 </span>            :     {&quot;CG&quot;,  &quot;CA&quot; },</a>
+<a name="745"><span class="lineNum">     745 </span>            :     {&quot;CD1&quot;, &quot;CA&quot; },</a>
+<a name="746"><span class="lineNum">     746 </span>            :     {&quot;HD1&quot;, &quot;HP&quot; },</a>
+<a name="747"><span class="lineNum">     747 </span>            :     {&quot;CE1&quot;, &quot;CA&quot; },</a>
+<a name="748"><span class="lineNum">     748 </span>            :     {&quot;HE1&quot;, &quot;HP&quot; },</a>
+<a name="749"><span class="lineNum">     749 </span>            :     {&quot;CZ&quot;,  &quot;CA&quot; },</a>
+<a name="750"><span class="lineNum">     750 </span>            :     {&quot;HZ&quot;,  &quot;HP&quot; },</a>
+<a name="751"><span class="lineNum">     751 </span>            :     {&quot;CD2&quot;, &quot;CA&quot; },</a>
+<a name="752"><span class="lineNum">     752 </span>            :     {&quot;HD2&quot;, &quot;HP&quot; },</a>
+<a name="753"><span class="lineNum">     753 </span>            :     {&quot;CE2&quot;, &quot;CA&quot; },</a>
+<a name="754"><span class="lineNum">     754 </span>            :     {&quot;HE2&quot;, &quot;HP&quot; },</a>
+<a name="755"><span class="lineNum">     755 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="756"><span class="lineNum">     756 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">        100 :   };</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">         80 :   typemap[&quot;PRO&quot;] = {</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :     {&quot;N&quot;,   &quot;N&quot;  },</a>
+<a name="760"><span class="lineNum">     760 </span>            :     {&quot;CD&quot;,  &quot;CP3&quot;},</a>
+<a name="761"><span class="lineNum">     761 </span>            :     {&quot;HD1&quot;, &quot;HA2&quot;},</a>
+<a name="762"><span class="lineNum">     762 </span>            :     {&quot;HD2&quot;, &quot;HA2&quot;},</a>
+<a name="763"><span class="lineNum">     763 </span>            :     {&quot;CA&quot;,  &quot;CP1&quot;},</a>
+<a name="764"><span class="lineNum">     764 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="765"><span class="lineNum">     765 </span>            :     {&quot;CB&quot;,  &quot;CP2&quot;},</a>
+<a name="766"><span class="lineNum">     766 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="767"><span class="lineNum">     767 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="768"><span class="lineNum">     768 </span>            :     {&quot;CG&quot;,  &quot;CP2&quot;},</a>
+<a name="769"><span class="lineNum">     769 </span>            :     {&quot;HG1&quot;, &quot;HA2&quot;},</a>
+<a name="770"><span class="lineNum">     770 </span>            :     {&quot;HG2&quot;, &quot;HA2&quot;},</a>
+<a name="771"><span class="lineNum">     771 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="772"><span class="lineNum">     772 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">         70 :   };</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">         65 :   typemap[&quot;SER&quot;] = {</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="776"><span class="lineNum">     776 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="777"><span class="lineNum">     777 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="778"><span class="lineNum">     778 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="779"><span class="lineNum">     779 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="780"><span class="lineNum">     780 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="781"><span class="lineNum">     781 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="782"><span class="lineNum">     782 </span>            :     {&quot;OG&quot;,  &quot;OH1&quot;},</a>
+<a name="783"><span class="lineNum">     783 </span>            :     {&quot;HG1&quot;, &quot;H&quot;  },</a>
+<a name="784"><span class="lineNum">     784 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="785"><span class="lineNum">     785 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">         55 :   };</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">         80 :   typemap[&quot;THR&quot;] = {</span></a>
+<a name="788"><span class="lineNum">     788 </span>            :     {&quot;N&quot;,    &quot;NH1&quot;},</a>
+<a name="789"><span class="lineNum">     789 </span>            :     {&quot;HN&quot;,   &quot;H&quot;  },</a>
+<a name="790"><span class="lineNum">     790 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot;},</a>
+<a name="791"><span class="lineNum">     791 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot;},</a>
+<a name="792"><span class="lineNum">     792 </span>            :     {&quot;CB&quot;,   &quot;CT1&quot;},</a>
+<a name="793"><span class="lineNum">     793 </span>            :     {&quot;HB&quot;,   &quot;HA1&quot;},</a>
+<a name="794"><span class="lineNum">     794 </span>            :     {&quot;OG1&quot;,  &quot;OH1&quot;},</a>
+<a name="795"><span class="lineNum">     795 </span>            :     {&quot;HG1&quot;,  &quot;H&quot;  },</a>
+<a name="796"><span class="lineNum">     796 </span>            :     {&quot;CG2&quot;,  &quot;CT3&quot;},</a>
+<a name="797"><span class="lineNum">     797 </span>            :     {&quot;HG21&quot;, &quot;HA3&quot;},</a>
+<a name="798"><span class="lineNum">     798 </span>            :     {&quot;HG22&quot;, &quot;HA3&quot;},</a>
+<a name="799"><span class="lineNum">     799 </span>            :     {&quot;HG23&quot;, &quot;HA3&quot;},</a>
+<a name="800"><span class="lineNum">     800 </span>            :     {&quot;C&quot;,    &quot;C&quot;  },</a>
+<a name="801"><span class="lineNum">     801 </span>            :     {&quot;O&quot;,    &quot;O&quot;  }</a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">         70 :   };</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">        130 :   typemap[&quot;TRP&quot;] = {</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="805"><span class="lineNum">     805 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="806"><span class="lineNum">     806 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="807"><span class="lineNum">     807 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="808"><span class="lineNum">     808 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="809"><span class="lineNum">     809 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="810"><span class="lineNum">     810 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="811"><span class="lineNum">     811 </span>            :     {&quot;CG&quot;,  &quot;CY&quot; },</a>
+<a name="812"><span class="lineNum">     812 </span>            :     {&quot;CD1&quot;, &quot;CA&quot; },</a>
+<a name="813"><span class="lineNum">     813 </span>            :     {&quot;HD1&quot;, &quot;HP&quot; },</a>
+<a name="814"><span class="lineNum">     814 </span>            :     {&quot;NE1&quot;, &quot;NY&quot; },</a>
+<a name="815"><span class="lineNum">     815 </span>            :     {&quot;HE1&quot;, &quot;H&quot;  },</a>
+<a name="816"><span class="lineNum">     816 </span>            :     {&quot;CE2&quot;, &quot;CPT&quot;},</a>
+<a name="817"><span class="lineNum">     817 </span>            :     {&quot;CD2&quot;, &quot;CPT&quot;},</a>
+<a name="818"><span class="lineNum">     818 </span>            :     {&quot;CE3&quot;, &quot;CAI&quot;},</a>
+<a name="819"><span class="lineNum">     819 </span>            :     {&quot;HE3&quot;, &quot;HP&quot; },</a>
+<a name="820"><span class="lineNum">     820 </span>            :     {&quot;CZ3&quot;, &quot;CA&quot; },</a>
+<a name="821"><span class="lineNum">     821 </span>            :     {&quot;HZ3&quot;, &quot;HP&quot; },</a>
+<a name="822"><span class="lineNum">     822 </span>            :     {&quot;CZ2&quot;, &quot;CAI&quot;},</a>
+<a name="823"><span class="lineNum">     823 </span>            :     {&quot;HZ2&quot;, &quot;HP&quot; },</a>
+<a name="824"><span class="lineNum">     824 </span>            :     {&quot;CH2&quot;, &quot;CA&quot; },</a>
+<a name="825"><span class="lineNum">     825 </span>            :     {&quot;HH2&quot;, &quot;HP&quot; },</a>
+<a name="826"><span class="lineNum">     826 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="827"><span class="lineNum">     827 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">        120 :   };</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">        115 :   typemap[&quot;TYR&quot;] = {</span></a>
+<a name="830"><span class="lineNum">     830 </span>            :     {&quot;N&quot;,   &quot;NH1&quot;},</a>
+<a name="831"><span class="lineNum">     831 </span>            :     {&quot;HN&quot;,  &quot;H&quot;  },</a>
+<a name="832"><span class="lineNum">     832 </span>            :     {&quot;CA&quot;,  &quot;CT1&quot;},</a>
+<a name="833"><span class="lineNum">     833 </span>            :     {&quot;HA&quot;,  &quot;HB1&quot;},</a>
+<a name="834"><span class="lineNum">     834 </span>            :     {&quot;CB&quot;,  &quot;CT2&quot;},</a>
+<a name="835"><span class="lineNum">     835 </span>            :     {&quot;HB1&quot;, &quot;HA2&quot;},</a>
+<a name="836"><span class="lineNum">     836 </span>            :     {&quot;HB2&quot;, &quot;HA2&quot;},</a>
+<a name="837"><span class="lineNum">     837 </span>            :     {&quot;CG&quot;,  &quot;CA&quot; },</a>
+<a name="838"><span class="lineNum">     838 </span>            :     {&quot;CD1&quot;, &quot;CA&quot; },</a>
+<a name="839"><span class="lineNum">     839 </span>            :     {&quot;HD1&quot;, &quot;HP&quot; },</a>
+<a name="840"><span class="lineNum">     840 </span>            :     {&quot;CE1&quot;, &quot;CA&quot; },</a>
+<a name="841"><span class="lineNum">     841 </span>            :     {&quot;HE1&quot;, &quot;HP&quot; },</a>
+<a name="842"><span class="lineNum">     842 </span>            :     {&quot;CZ&quot;,  &quot;CA&quot; },</a>
+<a name="843"><span class="lineNum">     843 </span>            :     {&quot;OH&quot;,  &quot;OH1&quot;},</a>
+<a name="844"><span class="lineNum">     844 </span>            :     {&quot;HH&quot;,  &quot;H&quot;  },</a>
+<a name="845"><span class="lineNum">     845 </span>            :     {&quot;CD2&quot;, &quot;CA&quot; },</a>
+<a name="846"><span class="lineNum">     846 </span>            :     {&quot;HD2&quot;, &quot;HP&quot; },</a>
+<a name="847"><span class="lineNum">     847 </span>            :     {&quot;CE2&quot;, &quot;CA&quot; },</a>
+<a name="848"><span class="lineNum">     848 </span>            :     {&quot;HE2&quot;, &quot;HP&quot; },</a>
+<a name="849"><span class="lineNum">     849 </span>            :     {&quot;C&quot;,   &quot;C&quot;  },</a>
+<a name="850"><span class="lineNum">     850 </span>            :     {&quot;O&quot;,   &quot;O&quot;  }</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">        105 :   };</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">         90 :   typemap[&quot;VAL&quot;] = {</span></a>
+<a name="853"><span class="lineNum">     853 </span>            :     {&quot;N&quot;,    &quot;NH1&quot;},</a>
+<a name="854"><span class="lineNum">     854 </span>            :     {&quot;HN&quot;,   &quot;H&quot;  },</a>
+<a name="855"><span class="lineNum">     855 </span>            :     {&quot;CA&quot;,   &quot;CT1&quot;},</a>
+<a name="856"><span class="lineNum">     856 </span>            :     {&quot;HA&quot;,   &quot;HB1&quot;},</a>
+<a name="857"><span class="lineNum">     857 </span>            :     {&quot;CB&quot;,   &quot;CT1&quot;},</a>
+<a name="858"><span class="lineNum">     858 </span>            :     {&quot;HB&quot;,   &quot;HA1&quot;},</a>
+<a name="859"><span class="lineNum">     859 </span>            :     {&quot;CG1&quot;,  &quot;CT3&quot;},</a>
+<a name="860"><span class="lineNum">     860 </span>            :     {&quot;HG11&quot;, &quot;HA3&quot;},</a>
+<a name="861"><span class="lineNum">     861 </span>            :     {&quot;HG12&quot;, &quot;HA3&quot;},</a>
+<a name="862"><span class="lineNum">     862 </span>            :     {&quot;HG13&quot;, &quot;HA3&quot;},</a>
+<a name="863"><span class="lineNum">     863 </span>            :     {&quot;CG2&quot;,  &quot;CT3&quot;},</a>
+<a name="864"><span class="lineNum">     864 </span>            :     {&quot;HG21&quot;, &quot;HA3&quot;},</a>
+<a name="865"><span class="lineNum">     865 </span>            :     {&quot;HG22&quot;, &quot;HA3&quot;},</a>
+<a name="866"><span class="lineNum">     866 </span>            :     {&quot;HG23&quot;, &quot;HA3&quot;},</a>
+<a name="867"><span class="lineNum">     867 </span>            :     {&quot;C&quot;,    &quot;C&quot;  },</a>
+<a name="868"><span class="lineNum">     868 </span>            :     {&quot;O&quot;,    &quot;O&quot;  }</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">         80 :   };</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">          5 :   return typemap;</span></a>
+<a name="871"><span class="lineNum">     871 </span>            : }</a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">          5 : std::map&lt;std::string, std::vector&lt;double&gt; &gt; EEFSolv::setupValueMap() {</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :   // Volume ∆Gref ∆Gfree ∆H ∆Cp λ vdw_radius</a>
+<a name="875"><span class="lineNum">     875 </span>            :   std::map&lt;std::string, std::vector&lt;double&gt; &gt; valuemap;</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">          5 :   valuemap[&quot;C&quot;] = {</span></a>
+<a name="877"><span class="lineNum">     877 </span>            :     ANG3_TO_NM3 * 14.720,</a>
+<a name="878"><span class="lineNum">     878 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="879"><span class="lineNum">     879 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="880"><span class="lineNum">     880 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="881"><span class="lineNum">     881 </span>            :     KCAL_TO_KJ * 0.0,</a>
+<a name="882"><span class="lineNum">     882 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="883"><span class="lineNum">     883 </span>            :     0.20,</a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">          5 :   };</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">          5 :   valuemap[&quot;CD&quot;] = {</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :     ANG3_TO_NM3 * 14.720,</a>
+<a name="887"><span class="lineNum">     887 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="888"><span class="lineNum">     888 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="889"><span class="lineNum">     889 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="890"><span class="lineNum">     890 </span>            :     KCAL_TO_KJ * 0.0,</a>
+<a name="891"><span class="lineNum">     891 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="892"><span class="lineNum">     892 </span>            :     0.20,</a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">          5 :   };</span></a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">          5 :   valuemap[&quot;CT1&quot;] = {</span></a>
+<a name="895"><span class="lineNum">     895 </span>            :     ANG3_TO_NM3 * 11.507,</a>
+<a name="896"><span class="lineNum">     896 </span>            :     KCAL_TO_KJ * -0.187,</a>
+<a name="897"><span class="lineNum">     897 </span>            :     KCAL_TO_KJ * -0.187,</a>
+<a name="898"><span class="lineNum">     898 </span>            :     KCAL_TO_KJ * 0.876,</a>
+<a name="899"><span class="lineNum">     899 </span>            :     KCAL_TO_KJ * 0.0,</a>
+<a name="900"><span class="lineNum">     900 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="901"><span class="lineNum">     901 </span>            :     0.20,</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">          5 :   };</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">          5 :   valuemap[&quot;CT2&quot;] = {</span></a>
+<a name="904"><span class="lineNum">     904 </span>            :     ANG3_TO_NM3 * 18.850,</a>
+<a name="905"><span class="lineNum">     905 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="906"><span class="lineNum">     906 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="907"><span class="lineNum">     907 </span>            :     KCAL_TO_KJ * -0.610,</a>
+<a name="908"><span class="lineNum">     908 </span>            :     KCAL_TO_KJ * 18.6,</a>
+<a name="909"><span class="lineNum">     909 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="910"><span class="lineNum">     910 </span>            :     0.20,</a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">          5 :   };</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">          5 :   valuemap[&quot;CT2A&quot;] = {</span></a>
+<a name="913"><span class="lineNum">     913 </span>            :     ANG3_TO_NM3 * 18.666,</a>
+<a name="914"><span class="lineNum">     914 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="915"><span class="lineNum">     915 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="916"><span class="lineNum">     916 </span>            :     KCAL_TO_KJ * -0.610,</a>
+<a name="917"><span class="lineNum">     917 </span>            :     KCAL_TO_KJ * 18.6,</a>
+<a name="918"><span class="lineNum">     918 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="919"><span class="lineNum">     919 </span>            :     0.20,</a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">          5 :   };</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">          5 :   valuemap[&quot;CT3&quot;] = {</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :     ANG3_TO_NM3 * 27.941,</a>
+<a name="923"><span class="lineNum">     923 </span>            :     KCAL_TO_KJ * 1.089,</a>
+<a name="924"><span class="lineNum">     924 </span>            :     KCAL_TO_KJ * 1.089,</a>
+<a name="925"><span class="lineNum">     925 </span>            :     KCAL_TO_KJ * -1.779,</a>
+<a name="926"><span class="lineNum">     926 </span>            :     KCAL_TO_KJ * 35.6,</a>
+<a name="927"><span class="lineNum">     927 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="928"><span class="lineNum">     928 </span>            :     0.204,</a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">          5 :   };</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">          5 :   valuemap[&quot;CPH1&quot;] = {</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :     ANG3_TO_NM3 * 5.275,</a>
+<a name="932"><span class="lineNum">     932 </span>            :     KCAL_TO_KJ * 0.057,</a>
+<a name="933"><span class="lineNum">     933 </span>            :     KCAL_TO_KJ * 0.080,</a>
+<a name="934"><span class="lineNum">     934 </span>            :     KCAL_TO_KJ * -0.973,</a>
+<a name="935"><span class="lineNum">     935 </span>            :     KCAL_TO_KJ * 6.9,</a>
+<a name="936"><span class="lineNum">     936 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="937"><span class="lineNum">     937 </span>            :     0.18,</a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">          5 :   };</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">          5 :   valuemap[&quot;CPH2&quot;] = {</span></a>
+<a name="940"><span class="lineNum">     940 </span>            :     ANG3_TO_NM3 * 11.796,</a>
+<a name="941"><span class="lineNum">     941 </span>            :     KCAL_TO_KJ * 0.057,</a>
+<a name="942"><span class="lineNum">     942 </span>            :     KCAL_TO_KJ * 0.080,</a>
+<a name="943"><span class="lineNum">     943 </span>            :     KCAL_TO_KJ * -0.973,</a>
+<a name="944"><span class="lineNum">     944 </span>            :     KCAL_TO_KJ * 6.9,</a>
+<a name="945"><span class="lineNum">     945 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="946"><span class="lineNum">     946 </span>            :     0.18,</a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">          5 :   };</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">          5 :   valuemap[&quot;CPT&quot;] = {</span></a>
+<a name="949"><span class="lineNum">     949 </span>            :     ANG3_TO_NM3 * 4.669,</a>
+<a name="950"><span class="lineNum">     950 </span>            :     KCAL_TO_KJ * -0.890,</a>
+<a name="951"><span class="lineNum">     951 </span>            :     KCAL_TO_KJ * -0.890,</a>
+<a name="952"><span class="lineNum">     952 </span>            :     KCAL_TO_KJ * 2.220,</a>
+<a name="953"><span class="lineNum">     953 </span>            :     KCAL_TO_KJ * 6.9,</a>
+<a name="954"><span class="lineNum">     954 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="955"><span class="lineNum">     955 </span>            :     0.186,</a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">          5 :   };</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">          5 :   valuemap[&quot;CY&quot;] = {</span></a>
+<a name="958"><span class="lineNum">     958 </span>            :     ANG3_TO_NM3 * 10.507,</a>
+<a name="959"><span class="lineNum">     959 </span>            :     KCAL_TO_KJ * -0.890,</a>
+<a name="960"><span class="lineNum">     960 </span>            :     KCAL_TO_KJ * -0.890,</a>
+<a name="961"><span class="lineNum">     961 </span>            :     KCAL_TO_KJ * 2.220,</a>
+<a name="962"><span class="lineNum">     962 </span>            :     KCAL_TO_KJ * 6.9,</a>
+<a name="963"><span class="lineNum">     963 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="964"><span class="lineNum">     964 </span>            :     0.199,</a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">          5 :   };</span></a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineCov">          5 :   valuemap[&quot;CP1&quot;] = {</span></a>
+<a name="967"><span class="lineNum">     967 </span>            :     ANG3_TO_NM3 * 25.458,</a>
+<a name="968"><span class="lineNum">     968 </span>            :     KCAL_TO_KJ * -0.187,</a>
+<a name="969"><span class="lineNum">     969 </span>            :     KCAL_TO_KJ * -0.187,</a>
+<a name="970"><span class="lineNum">     970 </span>            :     KCAL_TO_KJ * 0.876,</a>
+<a name="971"><span class="lineNum">     971 </span>            :     KCAL_TO_KJ * 0.0,</a>
+<a name="972"><span class="lineNum">     972 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="973"><span class="lineNum">     973 </span>            :     0.227,</a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">          5 :   };</span></a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">          5 :   valuemap[&quot;CP2&quot;] = {</span></a>
+<a name="976"><span class="lineNum">     976 </span>            :     ANG3_TO_NM3 * 19.880,</a>
+<a name="977"><span class="lineNum">     977 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="978"><span class="lineNum">     978 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="979"><span class="lineNum">     979 </span>            :     KCAL_TO_KJ * -0.610,</a>
+<a name="980"><span class="lineNum">     980 </span>            :     KCAL_TO_KJ * 18.6,</a>
+<a name="981"><span class="lineNum">     981 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="982"><span class="lineNum">     982 </span>            :     0.217,</a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">          5 :   };</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">          5 :   valuemap[&quot;CP3&quot;] = {</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :     ANG3_TO_NM3 * 26.731,</a>
+<a name="986"><span class="lineNum">     986 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="987"><span class="lineNum">     987 </span>            :     KCAL_TO_KJ * 0.372,</a>
+<a name="988"><span class="lineNum">     988 </span>            :     KCAL_TO_KJ * -0.610,</a>
+<a name="989"><span class="lineNum">     989 </span>            :     KCAL_TO_KJ * 18.6,</a>
+<a name="990"><span class="lineNum">     990 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="991"><span class="lineNum">     991 </span>            :     0.217,</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">          5 :   };</span></a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">          5 :   valuemap[&quot;CC&quot;] = {</span></a>
+<a name="994"><span class="lineNum">     994 </span>            :     ANG3_TO_NM3 * 16.539,</a>
+<a name="995"><span class="lineNum">     995 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="996"><span class="lineNum">     996 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="997"><span class="lineNum">     997 </span>            :     KCAL_TO_KJ * 0.000,</a>
+<a name="998"><span class="lineNum">     998 </span>            :     KCAL_TO_KJ * 0.0,</a>
+<a name="999"><span class="lineNum">     999 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :     0.20,</a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">          5 :   valuemap[&quot;CAI&quot;] = {</span></a>
+<a name="1003"><span class="lineNum">    1003 </span>            :     ANG3_TO_NM3 * 18.249,</a>
+<a name="1004"><span class="lineNum">    1004 </span>            :     KCAL_TO_KJ * 0.057,</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :     KCAL_TO_KJ * 0.057,</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :     KCAL_TO_KJ * -0.973,</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :     KCAL_TO_KJ * 6.9,</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :     0.199,</a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">          5 :   valuemap[&quot;CA&quot;] = {</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :     ANG3_TO_NM3 * 18.249,</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :     KCAL_TO_KJ * 0.057,</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :     KCAL_TO_KJ * 0.057,</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :     KCAL_TO_KJ * -0.973,</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :     KCAL_TO_KJ * 6.9,</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :     0.199,</a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">          5 :   valuemap[&quot;N&quot;] = {</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            :     ANG3_TO_NM3 * 0.000,</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :     KCAL_TO_KJ * -1.000,</a>
+<a name="1023"><span class="lineNum">    1023 </span>            :     KCAL_TO_KJ * -1.000,</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :     KCAL_TO_KJ * -1.250,</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :     KCAL_TO_KJ * 8.8,</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1027"><span class="lineNum">    1027 </span>            :     0.185,</a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">          5 :   valuemap[&quot;NR1&quot;] = {</span></a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     ANG3_TO_NM3 * 15.273,</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :     KCAL_TO_KJ * -9.059,</a>
+<a name="1034"><span class="lineNum">    1034 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :     0.185,</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">          5 :   valuemap[&quot;NR2&quot;] = {</span></a>
+<a name="1039"><span class="lineNum">    1039 </span>            :     ANG3_TO_NM3 * 15.111,</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :     KCAL_TO_KJ * -3.820,</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     KCAL_TO_KJ * -3.820,</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     KCAL_TO_KJ * -4.654,</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     0.185,</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">          5 :   valuemap[&quot;NR3&quot;] = {</span></a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     ANG3_TO_NM3 * 15.071,</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     KCAL_TO_KJ * -9.059,</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     0.185,</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">          5 :   valuemap[&quot;NH1&quot;] = {</span></a>
+<a name="1057"><span class="lineNum">    1057 </span>            :     ANG3_TO_NM3 * 10.197,</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     KCAL_TO_KJ * -9.059,</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :     0.185,</a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">          5 :   valuemap[&quot;NH2&quot;] = {</span></a>
+<a name="1066"><span class="lineNum">    1066 </span>            :     ANG3_TO_NM3 * 18.182,</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :     KCAL_TO_KJ * -9.059,</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     0.185,</a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">          5 :   valuemap[&quot;NH3&quot;] = {</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     ANG3_TO_NM3 * 18.817,</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :     KCAL_TO_KJ * -20.000,</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :     KCAL_TO_KJ * -20.000,</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     KCAL_TO_KJ * -25.000,</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     KCAL_TO_KJ * -18.0,</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     1. / (ANG_TO_NM * 6.0),</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     0.185,</a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">          5 :   valuemap[&quot;NC2&quot;] = {</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :     ANG3_TO_NM3 * 18.215,</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     KCAL_TO_KJ * -10.000,</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :     KCAL_TO_KJ * -10.000,</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :     KCAL_TO_KJ * -12.000,</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     KCAL_TO_KJ * -7.0,</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :     1. / (ANG_TO_NM * 6.0),</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :     0.185,</a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">          5 :   valuemap[&quot;NY&quot;] = {</span></a>
+<a name="1093"><span class="lineNum">    1093 </span>            :     ANG3_TO_NM3 * 12.001,</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :     KCAL_TO_KJ * -5.950,</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :     KCAL_TO_KJ * -9.059,</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :     0.185,</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">          5 :   valuemap[&quot;NP&quot;] = {</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            :     ANG3_TO_NM3 * 4.993,</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :     KCAL_TO_KJ * -20.000,</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :     KCAL_TO_KJ * -20.000,</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :     KCAL_TO_KJ * -25.000,</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :     KCAL_TO_KJ * -18.0,</a>
+<a name="1107"><span class="lineNum">    1107 </span>            :     1. / (ANG_TO_NM * 6.0),</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :     0.185,</a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">          5 :   valuemap[&quot;O&quot;] = {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span>            :     ANG3_TO_NM3 * 11.772,</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :     KCAL_TO_KJ * -5.330,</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :     KCAL_TO_KJ * -5.330,</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :     KCAL_TO_KJ * -5.787,</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     0.170,</a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">          5 :   valuemap[&quot;OB&quot;] = {</span></a>
+<a name="1120"><span class="lineNum">    1120 </span>            :     ANG3_TO_NM3 * 11.694,</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     KCAL_TO_KJ * -5.330,</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     KCAL_TO_KJ * -5.330,</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :     KCAL_TO_KJ * -5.787,</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :     KCAL_TO_KJ * -8.8,</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :     0.170,</a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">          5 :   valuemap[&quot;OC&quot;] = {</span></a>
+<a name="1129"><span class="lineNum">    1129 </span>            :     ANG3_TO_NM3 * 12.003,</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :     KCAL_TO_KJ * -10.000,</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :     KCAL_TO_KJ * -10.000,</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :     KCAL_TO_KJ * -12.000,</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     KCAL_TO_KJ * -9.4,</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     1. / (ANG_TO_NM * 6.0),</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :     0.170,</a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">          5 :   valuemap[&quot;OH1&quot;] = {</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     ANG3_TO_NM3 * 15.528,</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :     KCAL_TO_KJ * -5.920,</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :     KCAL_TO_KJ * -5.920,</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     KCAL_TO_KJ * -9.264,</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :     KCAL_TO_KJ * -11.2,</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :     0.177,</a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">          5 :   valuemap[&quot;OS&quot;] = {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span>            :     ANG3_TO_NM3 * 6.774,</a>
+<a name="1148"><span class="lineNum">    1148 </span>            :     KCAL_TO_KJ * -2.900,</a>
+<a name="1149"><span class="lineNum">    1149 </span>            :     KCAL_TO_KJ * -2.900,</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :     KCAL_TO_KJ * -3.150,</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :     KCAL_TO_KJ * -4.8,</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :     0.177,</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">          5 :   valuemap[&quot;S&quot;] = {</span></a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     ANG3_TO_NM3 * 20.703,</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :     KCAL_TO_KJ * -3.240,</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :     KCAL_TO_KJ * -3.240,</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :     KCAL_TO_KJ * -4.475,</a>
+<a name="1160"><span class="lineNum">    1160 </span>            :     KCAL_TO_KJ * -39.9,</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :     0.20,</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">          5 :   valuemap[&quot;SM&quot;] = {</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            :     ANG3_TO_NM3 * 21.306,</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :     KCAL_TO_KJ * -3.240,</a>
+<a name="1167"><span class="lineNum">    1167 </span>            :     KCAL_TO_KJ * -3.240,</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :     KCAL_TO_KJ * -4.475,</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :     KCAL_TO_KJ * -39.9,</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :     1. / (ANG_TO_NM * 3.5),</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :     0.197,</a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineCov">          5 :   };</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineCov">          5 :   return valuemap;</span></a>
+<a name="1174"><span class="lineNum">    1174 </span>            : }</a>
+<a name="1175"><span class="lineNum">    1175 </span>            : }</a>
+<a name="1176"><span class="lineNum">    1176 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ERMSD.cpp.func-sort-c.html b/coverage/colvar/ERMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..59b234af06
--- /dev/null
+++ b/coverage/colvar/ERMSD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ERMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ERMSD.cpp<span style="font-size: 80%;"> (<a href="ERMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ERMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#126">_ZN4PLMD6colvar5ERMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#114">_ZN4PLMD6colvar12_GLOBAL__N_118ERMSDRegisterMe1166createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#126">_ZN4PLMD6colvar5ERMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#116">_ZN4PLMD6colvar5ERMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#191">_ZN4PLMD6colvar5ERMSD9calculateEv</a></td>
+              <td class="coverFnHi">222</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#114">_ZN4PLMD6colvar12_GLOBAL__N_118ERMSDRegisterMe116C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#114">_ZN4PLMD6colvar12_GLOBAL__N_118ERMSDRegisterMe116D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ERMSD.cpp.func.html b/coverage/colvar/ERMSD.cpp.func.html
new file mode 100644
index 0000000000..ffdf064a8e
--- /dev/null
+++ b/coverage/colvar/ERMSD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ERMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ERMSD.cpp<span style="font-size: 80%;"> (<a href="ERMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ERMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#114">_ZN4PLMD6colvar12_GLOBAL__N_118ERMSDRegisterMe1166createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#114">_ZN4PLMD6colvar12_GLOBAL__N_118ERMSDRegisterMe116C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#114">_ZN4PLMD6colvar12_GLOBAL__N_118ERMSDRegisterMe116D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#116">_ZN4PLMD6colvar5ERMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#191">_ZN4PLMD6colvar5ERMSD9calculateEv</a></td>
+              <td class="coverFnHi">222</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#126">_ZN4PLMD6colvar5ERMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#126">_ZN4PLMD6colvar5ERMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <title>LCOV - plumed test coverage - colvar/ERMSD.cpp</title>
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+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ERMSD.cpp<span style="font-size: 80%;"> (source / <a href="ERMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
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+    </tr>
+
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+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /*</a>
+<a name="24"><span class="lineNum">      24 </span>            :  This vast majority of the source code in this file was writting by</a>
+<a name="25"><span class="lineNum">      25 </span>            :  Sandro Bottaro with some help from Giovanni Bussi</a>
+<a name="26"><span class="lineNum">      26 </span>            : */</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/ERMSD.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace colvar {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : //+PLUMEDOC COLVAR ERMSD</a>
+<a name="40"><span class="lineNum">      40 </span>            : /*</a>
+<a name="41"><span class="lineNum">      41 </span>            : Calculate eRMSD with respect to a reference structure.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : eRMSD is a metric developed for measuring distances between three-dimensional RNA structures.</a>
+<a name="44"><span class="lineNum">      44 </span>            : The standard RMSD measure is highly inaccurate when measuring distances among three-dimensional</a>
+<a name="45"><span class="lineNum">      45 </span>            : structures of nucleic acids.</a>
+<a name="46"><span class="lineNum">      46 </span>            : It is not unusual, for example, that two RNA structures with low RMSD (i.e. less than 0.4nm) display a completely different network of base-base interactions.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : eRMSD measures the distance between structures by considering only the relative positions and orientations of nucleobases. The eRMSD can be considered as a vectorial version of contact maps and it is calculated as follows:</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : 1. Set up a local reference system in the center of the six-membered ring of each nucleobase in a molecule.</a>
+<a name="51"><span class="lineNum">      51 </span>            :    The xy plane lies on the plane of the nucleobase, and it is oriented such that the Watson-Crick interaction is always at \f$\theta\approx 60^{\circ}\f$.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : 2. Calculate all pairwise distance vectors \f$\vec{r}_{i,j}\f$ among base centers.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : 3. Rescale distance vectors as \f$\tilde{\vec{r}}_{i,j}=(r_x/a,r_y/a,r_z/b)\f$, where  a=b=5 \f$\r{A}\f$, c=3 \f$\r{A}\f$. This rescaling has the effect of weighting more deviations on the z-axis with respect to the x/y directions.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : 4. Calculate the G vectors</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \f[</a>
+<a name="60"><span class="lineNum">      60 </span>            : \vec{G}(\tilde{\vec{r}}) = (\sin(\gamma \tilde{r}) \tilde{r}_x/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_y/\tilde{r},\sin(\gamma \tilde{r}) \tilde{r}_z/\tilde{r}, 1+\cos(\gamma \tilde{r})) \times</a>
+<a name="61"><span class="lineNum">      61 </span>            : \frac{\Theta(\tilde{r}_{cutoff}-\tilde{r})}{\gamma}</a>
+<a name="62"><span class="lineNum">      62 </span>            : \f]</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : Here, \f$ \gamma = \pi/\tilde{r}_{cutoff}\f$ and \f$ \Theta \f$ is the Heaviside step function. The default cutoff is set to 2.4.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : 5. The eRMSD between two structures \f$ \alpha \f$ and \f$ \beta \f$ reads</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \f[</a>
+<a name="69"><span class="lineNum">      69 </span>            : eRMSD = \sqrt{\frac{1}{N} \sum_{j,k} \vert \vec{G}(\tilde{\vec{r}}_{jk}^{\alpha}) - \vec{G}(\tilde{\vec{r}}_{jk}^{\beta}) \vert^2 }</a>
+<a name="70"><span class="lineNum">      70 </span>            : \f]</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : Using the default cutoff, two structures with eRMSD of 0.7 or lower can be considered as significantly similar. A full description of the eRMSD can be found in \cite bott14</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : ERMSD is computed using the position of three atoms on the 6-membered ring of each involved nucleobase. The atoms should be:</a>
+<a name="75"><span class="lineNum">      75 </span>            : - C2,C4,C6 for pyrimdines</a>
+<a name="76"><span class="lineNum">      76 </span>            : - C2,C6,C4 for purines</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : The different order for purines and pyrimidines is fundamental and allows you to compute ERMSD between structures with different</a>
+<a name="79"><span class="lineNum">      79 </span>            : sequences as well! Notice that the simplest way to avoid mistakes in choosing these atoms is to use the `@lcs-#` strings</a>
+<a name="80"><span class="lineNum">      80 </span>            : as shown in the examples (see also \ref MOLINFO).</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : \warning Notice that the ERMSD implemented here is not integrated with the other metrics in plumed. As a consequence, it is not (yet) possible</a>
+<a name="83"><span class="lineNum">      83 </span>            : to e.g. build path collective variables using ERMSD</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : \warning Notice that ERMSD expect a single molecule and makes coordinate whole before anything else. As such, results might be unexpected</a>
+<a name="86"><span class="lineNum">      86 </span>            : for a multi molecular system.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \par Examples</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : Calculate the eRMSD from reference structure reference.pdb using the default cutoff (2.4). The list of residues involved in the calculation has to be specified. In this example, the eRMSD is calculated</a>
+<a name="91"><span class="lineNum">      91 </span>            : considering residues 1,2,3,4,5,6.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : \plumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : #SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb</a>
+<a name="95"><span class="lineNum">      95 </span>            : MOLINFO STRUCTURE=reference.pdb</a>
+<a name="96"><span class="lineNum">      96 </span>            : eRMSD1: ERMSD REFERENCE=reference.pdb ATOMS=@lcs-1,@lcs-2,@lcs-3,@lcs-4,@lcs-5,@lcs-6</a>
+<a name="97"><span class="lineNum">      97 </span>            : \endplumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : */</a>
+<a name="100"><span class="lineNum">     100 </span>            : //+ENDPLUMEDOC</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : class ERMSD : public Colvar {</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;Vector&gt; derivs;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   PLMD::ERMSD ermsd;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   bool pbc;</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : public:</a>
+<a name="111"><span class="lineNum">     111 </span>            :   explicit ERMSD(const ActionOptions&amp;);</a>
+<a name="112"><span class="lineNum">     112 </span>            :   void calculate() override;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(ERMSD,&quot;ERMSD&quot;)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 : void ERMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 :   Colvar::registerKeywords(keys);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;CUTOFF&quot;,&quot;2.4&quot;,&quot;only pairs of atoms closer than CUTOFF are considered in the calculation.&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         12 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the list of atoms (use lcs)&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;PAIRS&quot;,&quot;List of pairs considered. All pairs are considered if this value is not specified.&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          6 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          4 : ERMSD::ERMSD(const ActionOptions&amp;ao):</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          4 :   PLUMED_COLVAR_INIT(ao), pbc(true)</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : {</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::string reference;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          4 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   double cutoff=2.4;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 :   parse(&quot;CUTOFF&quot;,cutoff);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   bool nopbc(false);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :   pbc=!nopbc;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   std::vector&lt;AtomNumber&gt; atoms_;</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          8 :   parseAtomList(&quot;ATOMS&quot;,atoms_);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::vector&lt;unsigned&gt; pairs_;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          4 :   parseVector(&quot;PAIRS&quot;,pairs_);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          4 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          4 :   if(atoms_.size()&lt;6) error(&quot;at least six atoms should be specified&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          4 :   if(atoms_.size()%3!=0) error(&quot;Atoms are not multiple of 3&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   if(pairs_.size()%2!=0) error(&quot;pairs are not multiple of 2&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   //checkRead();</a>
+<a name="156"><span class="lineNum">     156 </span>            :   //log.printf(&quot;  of atoms&quot;);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   //for(unsigned i=0;i&lt;atoms.size();++i) log.printf(&quot; %d&quot;,atoms[i].serial());</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //requestAtoms(atoms);</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          4 :   PDB pdb;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          8 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     error(&quot;missing input file &quot; + reference );</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   // store target_ distance</a>
+<a name="165"><span class="lineNum">     165 </span>            :   std::vector &lt;Vector&gt; reference_positions;</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          4 :   unsigned natoms = atoms_.size();</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          4 :   log.printf(&quot;Read %u atoms\n&quot;,natoms);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          4 :   reference_positions.resize(natoms);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        856 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        852 :     reference_positions[i] = pdb.getPosition(atoms_[i]);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     //log.printf(&quot;%f %f %f \n&quot;,reference_positions[i][0],reference_positions[i][1],reference_positions[i][2]);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : // shift to count from zero</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         28 :   for(unsigned i=0; i&lt;pairs_.size(); ++i) pairs_[i]--;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          4 :   ermsd.setReference(reference_positions,pairs_,cutoff/atoms.getUnits().getLength());</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          4 :   requestAtoms(atoms_);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :   derivs.resize(natoms);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          4 :   log.printf(&quot;  reference from file %s\n&quot;,reference.c_str());</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :   log.printf(&quot;  which contains %u atoms\n&quot;,natoms);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          4 :   log&lt;&lt;&quot;  Bibliography &quot;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          8 :      &lt;&lt;plumed.cite(&quot;Bottaro, Di Palma, and Bussi, Nucleic Acids Res. 42, 13306 (2014)&quot;)</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         12 :      &lt;&lt;plumed.cite(&quot;Bottaro, Banas, Sponer, and Bussi, J. Phys. Chem. Lett. 7, 4032 (2016)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          8 : }</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : // calculator</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        222 : void ERMSD::calculate() {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : // set derivatives to zero</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        222 :   Tools::set_to_zero(derivs);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   double ermsdist;</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        222 :   Tensor virial;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : // This is a trick to avoid explicit virial calculation</a>
+<a name="199"><span class="lineNum">     199 </span>            : // 1. we make the molecule whole</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        222 :   makeWhole();</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : // 2. we ignore pbcs</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        222 :   Pbc fake_pbc;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : // Notice that this might have problems when having 2 RNA molecules (hybridization).</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        222 :   ermsdist=ermsd.calculate(getPositions(),fake_pbc,derivs,virial);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        222 :   const double scale=atoms.getUnits().getLength();</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        222 :   setValue(ermsdist*scale);</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      47508 :   for(unsigned i=0; i&lt;derivs.size(); ++i) {setAtomsDerivatives(i,derivs[i]*scale);}</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        222 :   setBoxDerivativesNoPbc();</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        222 : }</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Energy.cpp.func-sort-c.html b/coverage/colvar/Energy.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5bbbfb7c7a
--- /dev/null
+++ b/coverage/colvar/Energy.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Energy.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Energy.cpp<span style="font-size: 80%;"> (<a href="Energy.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Energy.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#75">_ZN4PLMD6colvar6EnergyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#96">_ZN4PLMD6colvar6Energy22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_118EnergyRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#75">_ZN4PLMD6colvar6EnergyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#89">_ZN4PLMD6colvar6Energy16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#100">_ZN4PLMD6colvar6Energy7prepareEv</a></td>
+              <td class="coverFnHi">3989</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#105">_ZN4PLMD6colvar6Energy9calculateEv</a></td>
+              <td class="coverFnHi">3989</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_118EnergyRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_118EnergyRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Energy.cpp.func.html b/coverage/colvar/Energy.cpp.func.html
new file mode 100644
index 0000000000..a7f82b2bcd
--- /dev/null
+++ b/coverage/colvar/Energy.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Energy.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Energy.cpp<span style="font-size: 80%;"> (<a href="Energy.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Energy.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_118EnergyRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_118EnergyRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#73">_ZN4PLMD6colvar12_GLOBAL__N_118EnergyRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#89">_ZN4PLMD6colvar6Energy16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#96">_ZN4PLMD6colvar6Energy22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#100">_ZN4PLMD6colvar6Energy7prepareEv</a></td>
+              <td class="coverFnHi">3989</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#105">_ZN4PLMD6colvar6Energy9calculateEv</a></td>
+              <td class="coverFnHi">3989</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#75">_ZN4PLMD6colvar6EnergyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Energy.cpp.gcov.html#75">_ZN4PLMD6colvar6EnergyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Energy.cpp.gcov.html b/coverage/colvar/Energy.cpp.gcov.html
new file mode 100644
index 0000000000..834e7007f0
--- /dev/null
+++ b/coverage/colvar/Energy.cpp.gcov.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Energy.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Energy.cpp<span style="font-size: 80%;"> (source / <a href="Energy.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace colvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC COLVAR ENERGY</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculate the total potential energy of the simulation box.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : The potential energy can be biased e.g. with umbrella sampling \cite bart-karp98jpcb or with well-tempered metadynamics \cite Bonomi:2009p17935.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : Notice that this CV could be unavailable with some MD code. When</a>
+<a name="37"><span class="lineNum">      37 </span>            : it is available, and when also replica exchange is available,</a>
+<a name="38"><span class="lineNum">      38 </span>            : metadynamics applied to ENERGY can be used to decrease the</a>
+<a name="39"><span class="lineNum">      39 </span>            : number of required replicas.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \bug This \ref ENERGY does not include long tail corrections.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Thus when using e.g. LAMMPS `&quot;pair_modify tail yes&quot;` or GROMACS `&quot;DispCorr Ener&quot;` (or `&quot;DispCorr EnerPres&quot;`),</a>
+<a name="43"><span class="lineNum">      43 </span>            : the potential energy from \ref ENERGY will be slightly different form the one of the MD code.</a>
+<a name="44"><span class="lineNum">      44 </span>            : You should still be able to use \ref ENERGY and then reweight your simulation with the correct MD energy value.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \bug Acceptance for replica exchange when \ref ENERGY is biased</a>
+<a name="47"><span class="lineNum">      47 </span>            : is computed correctly only if all the replicas have the same</a>
+<a name="48"><span class="lineNum">      48 </span>            : potential energy function. This is for instance not true when</a>
+<a name="49"><span class="lineNum">      49 </span>            : using GROMACS with lambda replica exchange or with plumed-hrex branch.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \par Examples</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : The following input instructs plumed to print the energy of the system</a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : ene: ENERGY</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=ene</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : */</a>
+<a name="60"><span class="lineNum">      60 </span>            : //+ENDPLUMEDOC</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : class Energy : public Colvar {</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   explicit Energy(const ActionOptions&amp;);</a>
+<a name="67"><span class="lineNum">      67 </span>            : // active methods:</a>
+<a name="68"><span class="lineNum">      68 </span>            :   void prepare() override;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void calculate() override;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="72"><span class="lineNum">      72 </span>            : };</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12584 : PLUMED_REGISTER_ACTION(Energy,&quot;ENERGY&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         40 : Energy::Energy(const ActionOptions&amp;ao):</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         40 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : {</a>
+<a name="80"><span class="lineNum">      80 </span>            : //  if(checkNumericalDerivatives())</a>
+<a name="81"><span class="lineNum">      81 </span>            : //    error(&quot;Cannot use NUMERICAL_DERIVATIVES with ENERGY&quot;);</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         40 :   isEnergy=true;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         40 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         40 :   getPntrToValue()-&gt;resizeDerivatives(1);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         40 :   log&lt;&lt;&quot;  Bibliography &quot;;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         80 :   log&lt;&lt;plumed.cite(&quot;Bartels and Karplus, J. Phys. Chem. B 102, 865 (1998)&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         80 :   log&lt;&lt;plumed.cite(&quot;Bonomi and Parrinello, J. Comp. Chem. 30, 1615 (2009)&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         40 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         40 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         42 : void Energy::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         42 :   Action::registerKeywords( keys );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         42 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         42 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         42 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         42 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 : unsigned Energy::getNumberOfDerivatives() {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   return 1;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       3989 : void Energy::prepare() {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       3989 :   plumed.getAtoms().setCollectEnergy(true);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       3989 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : // calculator</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       3989 : void Energy::calculate() {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       3989 :   setValue( getEnergy() );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       3989 :   getPntrToComponent(0)-&gt;addDerivative(0,1.0);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       3989 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ExtraCV.cpp.func-sort-c.html b/coverage/colvar/ExtraCV.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fe939e6377
--- /dev/null
+++ b/coverage/colvar/ExtraCV.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ExtraCV.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ExtraCV.cpp<span style="font-size: 80%;"> (<a href="ExtraCV.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExtraCV.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#64">_ZN4PLMD6colvar7ExtraCVC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#62">_ZN4PLMD6colvar12_GLOBAL__N_119ExtraCVRegisterMe646createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#64">_ZN4PLMD6colvar7ExtraCVC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#83">_ZN4PLMD6colvar7ExtraCV22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#75">_ZN4PLMD6colvar7ExtraCV16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#87">_ZN4PLMD6colvar7ExtraCV7prepareEv</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#92">_ZN4PLMD6colvar7ExtraCV9calculateEv</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#62">_ZN4PLMD6colvar12_GLOBAL__N_119ExtraCVRegisterMe64C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#62">_ZN4PLMD6colvar12_GLOBAL__N_119ExtraCVRegisterMe64D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ExtraCV.cpp.func.html b/coverage/colvar/ExtraCV.cpp.func.html
new file mode 100644
index 0000000000..8b2f2c957d
--- /dev/null
+++ b/coverage/colvar/ExtraCV.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ExtraCV.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ExtraCV.cpp<span style="font-size: 80%;"> (<a href="ExtraCV.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExtraCV.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#62">_ZN4PLMD6colvar12_GLOBAL__N_119ExtraCVRegisterMe646createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#62">_ZN4PLMD6colvar12_GLOBAL__N_119ExtraCVRegisterMe64C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#62">_ZN4PLMD6colvar12_GLOBAL__N_119ExtraCVRegisterMe64D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#75">_ZN4PLMD6colvar7ExtraCV16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#83">_ZN4PLMD6colvar7ExtraCV22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#87">_ZN4PLMD6colvar7ExtraCV7prepareEv</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#92">_ZN4PLMD6colvar7ExtraCV9calculateEv</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#64">_ZN4PLMD6colvar7ExtraCVC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExtraCV.cpp.gcov.html#64">_ZN4PLMD6colvar7ExtraCVC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ExtraCV.cpp.gcov.html b/coverage/colvar/ExtraCV.cpp.gcov.html
new file mode 100644
index 0000000000..78168ebb2f
--- /dev/null
+++ b/coverage/colvar/ExtraCV.cpp.gcov.html
@@ -0,0 +1,180 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ExtraCV.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ExtraCV.cpp<span style="font-size: 80%;"> (source / <a href="ExtraCV.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace colvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC COLVAR EXTRACV</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Allow PLUMED to use collective variables computed in the MD engine.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This feature requires the MD engine to use special instructions to pass to PLUMED the value of</a>
+<a name="35"><span class="lineNum">      35 </span>            : some pre-computed collective variable. Check the documentation of the MD code to find out which</a>
+<a name="36"><span class="lineNum">      36 </span>            : collective variables can be computed and passed to PLUMED. These variables can then be accessed by</a>
+<a name="37"><span class="lineNum">      37 </span>            : name using the EXTRACV action.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : This example takes the lambda variable pre-computed in GROMACS and apply to it a restraint to keep</a>
+<a name="42"><span class="lineNum">      42 </span>            : it close to the value 3.</a>
+<a name="43"><span class="lineNum">      43 </span>            : \plumedfile</a>
+<a name="44"><span class="lineNum">      44 </span>            : l: EXTRACV NAME=lambda</a>
+<a name="45"><span class="lineNum">      45 </span>            : RESTRAINT ARG=l KAPPA=10 AT=3</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : */</a>
+<a name="50"><span class="lineNum">      50 </span>            : //+ENDPLUMEDOC</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : class ExtraCV : public Colvar {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::string name;</a>
+<a name="55"><span class="lineNum">      55 </span>            : public:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit ExtraCV(const ActionOptions&amp;);</a>
+<a name="57"><span class="lineNum">      57 </span>            : // active methods:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void prepare() override;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void calculate() override;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="62"><span class="lineNum">      62 </span>            : };</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(ExtraCV,&quot;EXTRACV&quot;)</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          3 : ExtraCV::ExtraCV(const ActionOptions&amp;ao):</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          3 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : {</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          3 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          3 :   getPntrToValue()-&gt;resizeDerivatives(1);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          3 :   parse(&quot;NAME&quot;,name);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          3 :   log&lt;&lt;&quot;  name: &quot;&lt;&lt;name&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          3 :   isExtraCV=true;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   setExtraCV(name);</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          3 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          5 : void ExtraCV::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          5 :   Action::registerKeywords( keys );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          5 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          5 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          5 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;NAME&quot;,&quot;name of the CV as computed by the MD engine&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          5 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 : unsigned ExtraCV::getNumberOfDerivatives() {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          4 :   return 1;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         72 : void ExtraCV::prepare() {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         72 :   atoms.setExtraCVNeeded(name,true);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         72 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : // calculator</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         72 : void ExtraCV::calculate() {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         72 :   double value=plumed.getAtoms().getExtraCV(name);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         72 :   setValue( value );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         72 :   getPntrToComponent(0)-&gt;addDerivative(0,1.0);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         72 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Fake.cpp.func-sort-c.html b/coverage/colvar/Fake.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5ea4479fe9
--- /dev/null
+++ b/coverage/colvar/Fake.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Fake.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Fake.cpp<span style="font-size: 80%;"> (<a href="Fake.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryMed">81.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Fake.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#113">_ZN4PLMD6colvar10ColvarFake9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#59">_ZN4PLMD6colvar10ColvarFakeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#59">_ZN4PLMD6colvar10ColvarFakeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#48">_ZN4PLMD6colvar12_GLOBAL__N_122ColvarFakeRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#50">_ZN4PLMD6colvar10ColvarFake16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#48">_ZN4PLMD6colvar12_GLOBAL__N_122ColvarFakeRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#48">_ZN4PLMD6colvar12_GLOBAL__N_122ColvarFakeRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Fake.cpp.func.html b/coverage/colvar/Fake.cpp.func.html
new file mode 100644
index 0000000000..d16400f4e8
--- /dev/null
+++ b/coverage/colvar/Fake.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Fake.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Fake.cpp<span style="font-size: 80%;"> (<a href="Fake.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryMed">81.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Fake.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#50">_ZN4PLMD6colvar10ColvarFake16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#113">_ZN4PLMD6colvar10ColvarFake9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#59">_ZN4PLMD6colvar10ColvarFakeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#59">_ZN4PLMD6colvar10ColvarFakeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#48">_ZN4PLMD6colvar12_GLOBAL__N_122ColvarFakeRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#48">_ZN4PLMD6colvar12_GLOBAL__N_122ColvarFakeRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fake.cpp.gcov.html#48">_ZN4PLMD6colvar12_GLOBAL__N_122ColvarFakeRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Fake.cpp.gcov.html b/coverage/colvar/Fake.cpp.gcov.html
new file mode 100644
index 0000000000..c97115c953
--- /dev/null
+++ b/coverage/colvar/Fake.cpp.gcov.html
@@ -0,0 +1,199 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Fake.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Fake.cpp<span style="font-size: 80%;"> (source / <a href="Fake.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryMed">81.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR FAKE</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This is a fake colvar container used by cltools or various other actions that supports input and period definitions</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \plumedfile</a>
+<a name="35"><span class="lineNum">      35 </span>            : FAKE ATOMS=1 PERIODIC=-3.14,3.14   LABEL=d2</a>
+<a name="36"><span class="lineNum">      36 </span>            : \endplumedfile</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : //+ENDPLUMEDOC</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class ColvarFake : public Colvar {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit ColvarFake(const ActionOptions&amp;);</a>
+<a name="46"><span class="lineNum">      46 </span>            : // active methods:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void calculate() override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      12538 : PLUMED_REGISTER_ACTION(ColvarFake,&quot;FAKE&quot;)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         19 : void ColvarFake::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         19 :   Colvar::registerKeywords( keys );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         38 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the fake atom index, a number is enough&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         38 :   keys.reserve(&quot;compulsory&quot;,&quot;PERIODIC&quot;,&quot;if the output of your function is periodic then you should specify the periodicity of the function.  If the output is not periodic you must state this using PERIODIC=NO,NO (one for the lower and the other for the upper boundary). For multicomponents then it is PERIODIC=mincomp1,maxcomp1,mincomp2,maxcomp2  etc &quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         19 :   keys.use(&quot;PERIODIC&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         38 :   keys.add(&quot;optional&quot;,&quot;COMPONENTS&quot;,&quot;additional components that this variable is supposed to have. Periodicity is ruled by PERIODIC keyword &quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         19 :   useCustomisableComponents(keys);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         19 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         17 : ColvarFake::ColvarFake(const ActionOptions&amp;ao):</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         17 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         34 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;std::string&gt; comps;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   // multiple components for this variable</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         34 :   parseVector(&quot;COMPONENTS&quot;,comps);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         17 :   if(comps.size()!=0) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 :     for(unsigned i=0; i&lt;comps.size(); i++) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          1 :       addComponentWithDerivatives(comps[i]);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     }</a>
+<a name="74"><span class="lineNum">      74 </span>            :     // periodicity</a>
+<a name="75"><span class="lineNum">      75 </span>            :   } else {</a>
+<a name="76"><span class="lineNum">      76 </span>            :     // only one component for this variable</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         16 :     addValueWithDerivatives();</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   }</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;std::string&gt; period;</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         34 :   parseVector(&quot;PERIODIC&quot;,period);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         17 :   if(period.size()!=0) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         17 :     plumed_massert(static_cast&lt;unsigned&gt;(getNumberOfComponents()*2)==period.size(),&quot;the periodicty should coincide with the number of components&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         17 :     if(comps.size()!=0) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :       for(int i=0; i&lt;getNumberOfComponents(); i++) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          1 :         std::string pp=comps[i];</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 :         if(period[i*2]!=&quot;none&quot; &amp;&amp; period[i*2+1]!=&quot;none&quot; ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          1 :           componentIsPeriodic(pp,period[i*2],period[i*2+1]);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :         } else {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :           componentIsNotPeriodic(pp);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :         }</a>
+<a name="91"><span class="lineNum">      91 </span>            :       }</a>
+<a name="92"><span class="lineNum">      92 </span>            :     } else {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         29 :       if(period[0]!=&quot;none&quot; &amp;&amp; period[1]!=&quot;none&quot; ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         13 :         setPeriodic(period[0],period[1]);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :       } else {</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          3 :         setNotPeriodic();</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :       }</a>
+<a name="98"><span class="lineNum">      98 </span>            :     }</a>
+<a name="99"><span class="lineNum">      99 </span>            :   } else {</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     if(comps.size()!=0) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :       for(int i=0; i&lt;getNumberOfComponents(); i++) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :         componentIsNotPeriodic(getPntrToComponent(i)-&gt;getName());</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :       }</a>
+<a name="104"><span class="lineNum">     104 </span>            :     } else {</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :       setNotPeriodic();</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :     }</a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         17 :   checkRead();</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         17 :   requestAtoms(atoms);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         34 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : // calculator</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 : void ColvarFake::calculate() {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;you should never have got here&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/GHBFIX.cpp.func-sort-c.html b/coverage/colvar/GHBFIX.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3fa19ae49f
--- /dev/null
+++ b/coverage/colvar/GHBFIX.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/GHBFIX.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - GHBFIX.cpp<span style="font-size: 80%;"> (<a href="GHBFIX.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GHBFIX.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#96">_ZN4PLMD6colvar6GHBFIXC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#83">_ZN4PLMD6colvar12_GLOBAL__N_118GHBFIXRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#96">_ZN4PLMD6colvar6GHBFIXC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#85">_ZN4PLMD6colvar6GHBFIX16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#169">_ZNK4PLMD6colvar6GHBFIX7pairingEdRdjj</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#83">_ZN4PLMD6colvar12_GLOBAL__N_118GHBFIXRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#83">_ZN4PLMD6colvar12_GLOBAL__N_118GHBFIXRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/GHBFIX.cpp.func.html b/coverage/colvar/GHBFIX.cpp.func.html
new file mode 100644
index 0000000000..8a58e18d3b
--- /dev/null
+++ b/coverage/colvar/GHBFIX.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/GHBFIX.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - GHBFIX.cpp<span style="font-size: 80%;"> (<a href="GHBFIX.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GHBFIX.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#83">_ZN4PLMD6colvar12_GLOBAL__N_118GHBFIXRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#83">_ZN4PLMD6colvar12_GLOBAL__N_118GHBFIXRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#83">_ZN4PLMD6colvar12_GLOBAL__N_118GHBFIXRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#85">_ZN4PLMD6colvar6GHBFIX16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#96">_ZN4PLMD6colvar6GHBFIXC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#96">_ZN4PLMD6colvar6GHBFIXC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GHBFIX.cpp.gcov.html#169">_ZNK4PLMD6colvar6GHBFIX7pairingEdRdjj</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/GHBFIX.cpp.gcov.html b/coverage/colvar/GHBFIX.cpp.gcov.html
new file mode 100644
index 0000000000..6c53663f7e
--- /dev/null
+++ b/coverage/colvar/GHBFIX.cpp.gcov.html
@@ -0,0 +1,294 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/GHBFIX.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - GHBFIX.cpp<span style="font-size: 80%;"> (source / <a href="GHBFIX.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2021-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CoordinationBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;string&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace colvar {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC COLVAR GHBFIX</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculate the GHBFIX interaction energy among GROUPA and GROUPB</a>
+<a name="39"><span class="lineNum">      39 </span>            : using a potential defined in Kührova� et al., Improving the performance of the AMBER RNA force field by</a>
+<a name="40"><span class="lineNum">      40 </span>            : tuning the hydrogen-bonding interactions, JCTC, 2019. Essentially it is a switching function being -1 for small distances and 0 for large distances with a smooth interpolation in the middle. This can be scaled as desired by specifying interaction scaling parameters and energy units.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : This collective variable can be used to analyze hydrogen bond interactions, or to generate bias potentials.</a>
+<a name="43"><span class="lineNum">      43 </span>            : Notice that the value of the GHBFIX is returned in plumed units (see \ref UNITS), if not specified differently via ENERGY_UNITS.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : This example prints the GHBFIX interaction in kcal/mol between two groups of atoms using D_0, D_MAX and C</a>
+<a name="47"><span class="lineNum">      47 </span>            : It is applied in the functional form introduced in the pioneering paper.</a>
+<a name="48"><span class="lineNum">      48 </span>            : The types of atoms 1-6 should be defined in typesTable_examples.dat while their interaction parameters should be defined in scalingParameters_examples.dat in kBT units.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \plumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : #SETTINGS AUXFOLDER=regtest/basic/rt-ghbfix</a>
+<a name="52"><span class="lineNum">      52 </span>            : gh: GHBFIX PAIR GROUPA=1,2,3 GROUP=4,5,6 D_0=0.2 D_MAX=0.3 C=0.8 TYPES=typesTable_examples.dat PARAMS=scalingParameters_examples.dat ENERGY_UNITS=kcal/mol</a>
+<a name="53"><span class="lineNum">      53 </span>            : PRINT FILE=output ARG=gh</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endplumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : */</a>
+<a name="57"><span class="lineNum">      57 </span>            : //+ENDPLUMEDOC</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : class GHBFIX : public CoordinationBase {</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   double dmax;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double dmax_squared;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double d0;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double c;</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;unsigned&gt; typesTable;</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;double&gt; etas;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   unsigned n;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :   double dmax2;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double A;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   double B;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double C;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   double D;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   explicit GHBFIX(const ActionOptions&amp;);</a>
+<a name="80"><span class="lineNum">      80 </span>            : // active methods:</a>
+<a name="81"><span class="lineNum">      81 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="82"><span class="lineNum">      82 </span>            :   double pairing(double distance,double&amp;dfunc,unsigned i,unsigned j)const override;</a>
+<a name="83"><span class="lineNum">      83 </span>            : };</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(GHBFIX,&quot;GHBFIX&quot;)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 : void GHBFIX::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          3 :   CoordinationBase::registerKeywords(keys);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;ENERGY_UNITS&quot;,&quot;the value of ENERGY_UNITS in the switching function&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;TYPES&quot;,&quot;the value of TYPES in the switching function&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;PARAMS&quot;,&quot;the value of PARAMS in the switching function&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;D_MAX&quot;,&quot;the value of D_MAX in the switching function&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;the value of D_0 in the switching function&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;C&quot;,&quot;the value of C in the switching function&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          3 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          1 : GHBFIX::GHBFIX(const ActionOptions&amp;ao):</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   Action(ao),</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          1 :   CoordinationBase(ao)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::string types;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::string params;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          1 :   std::string energy_units =&quot;plumed&quot; ;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :   parse(&quot;D_MAX&quot;,dmax);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   dmax_squared = dmax*dmax;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          1 :   parse(&quot;D_0&quot;,d0);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          1 :   parse(&quot;C&quot;,c);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :   parse(&quot;TYPES&quot;,types);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 :   parse(&quot;PARAMS&quot;,params);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          1 :   parse(&quot;ENERGY_UNITS&quot;,energy_units);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   dmax2 = dmax-d0;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :   A = (-c*dmax2*dmax2)/((1-c)*dmax2*dmax2);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :   B = (2*dmax2)/((1-c)*dmax2*dmax2);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   C = -1/((1-c)*dmax2*dmax2);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          1 :   D = 1/(c*dmax2*dmax2);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::map&lt;std::string,unsigned&gt; MapTypesTable;</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   //typesTable</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 :   IFile typesfile;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :   typesfile.link(*this);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   typesfile.open(types);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   std::string itype;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   while(typesfile.scanField(&quot;itype&quot;,itype).scanField()) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :     plumed_assert(itype.empty()==false)&lt;&lt;&quot;itype is empty&quot;;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :     if (MapTypesTable.empty()) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 :       MapTypesTable.insert({itype, 0});</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     }</a>
+<a name="134"><span class="lineNum">     134 </span>            :     else if (MapTypesTable.count(itype) == 0) {</a>
+<a name="135"><span class="lineNum">     135 </span>            :       unsigned currentMax = 0;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          2 :       for(auto it = MapTypesTable.cbegin(); it != MapTypesTable.cend(); ++it ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :         if (it -&gt;second &gt; currentMax) {</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :           currentMax = it-&gt;second;</a>
+<a name="139"><span class="lineNum">     139 </span>            :         }</a>
+<a name="140"><span class="lineNum">     140 </span>            :       }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :       MapTypesTable.insert({itype, currentMax+1});</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :     typesTable.push_back(MapTypesTable[itype]);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 :   n = (int)*std::max_element(std::begin(typesTable), std::end(typesTable));</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :   n+=1;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   //scalingParameters</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          1 :   etas.resize(n*n,0.0);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :   IFile etafile;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :   etafile.open(params);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::string it,jt;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   double eta;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         14 :   while(etafile.scanField(&quot;itype&quot;,it).scanField(&quot;jtype&quot;,jt).scanField(&quot;eta&quot;,eta).scanField()) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          6 :     plumed_assert(it.empty()==false)&lt;&lt;&quot;itype is empty&quot;;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          6 :     plumed_assert(jt.empty()==false)&lt;&lt;&quot;jtype is empty&quot;;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          6 :     etas[n*MapTypesTable[it]+MapTypesTable[jt]]=eta;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   if(energy_units!=&quot;plumed&quot;) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :     Units units;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :     units.setEnergy(energy_units);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          5 :     for(auto i=0; i&lt;etas.size(); i++) etas[i]*=units.getEnergy()/atoms.getUnits().getEnergy();</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :   }</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          3 : }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        150 : double GHBFIX::pairing(double distance2,double&amp;dfunc,unsigned i,unsigned j)const {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        150 :   const auto i1=getAbsoluteIndex(i).index();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        150 :   plumed_assert(i1&lt;typesTable.size())&lt;&lt;&quot;your types table only covers &quot;&lt;&lt;typesTable.size()&lt;&lt;&quot; atoms, but you are trying to access atom number &quot;&lt;&lt;(i1+1);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        150 :   const auto t1=typesTable[i1];</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        150 :   const auto i2=getAbsoluteIndex(j).index();</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        150 :   plumed_assert(i2&lt;typesTable.size())&lt;&lt;&quot;your types table only covers &quot;&lt;&lt;typesTable.size()&lt;&lt;&quot; atoms, but you are trying to access atom number &quot;&lt;&lt;(i2+1);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        150 :   const auto t2=typesTable[i2];</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        150 :   const double scale=etas[n*t1+t2];</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   double result;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        150 :   if(distance2&gt;dmax_squared) {</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     result=0.;</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          1 :     dfunc=0.0;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          1 :     return result;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        149 :   double distance=std::sqrt(distance2);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        149 :   const double rdist = (distance-d0);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        149 :   if(rdist&lt;=0.) {</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :     result=-1.;</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        100 :     dfunc=0.0;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   } else {</a>
+<a name="196"><span class="lineNum">     196 </span>            :     result=-1.;</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         49 :     dfunc=0.0;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         49 :     if (rdist &gt; c*dmax2) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          9 :       result+=(A + B*rdist + C*rdist*rdist);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          9 :       dfunc+=B+2*C*rdist;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         40 :     } else if (rdist &gt; 0.0) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         40 :       result+=D*(rdist*rdist);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         40 :       dfunc+=2*D*rdist;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         49 :     dfunc/=distance;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        149 :   result*=scale;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        149 :   dfunc*=scale;</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        149 :   return result;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Gyration.cpp.func-sort-c.html b/coverage/colvar/Gyration.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f90d9d9a50
--- /dev/null
+++ b/coverage/colvar/Gyration.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Gyration.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Gyration.cpp<span style="font-size: 80%;"> (<a href="Gyration.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">186</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Gyration.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#99">_ZN4PLMD6colvar8GyrationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#90">_ZN4PLMD6colvar12_GLOBAL__N_120GyrationRegisterMe926createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#99">_ZN4PLMD6colvar8GyrationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#92">_ZN4PLMD6colvar8Gyration16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#157">_ZN4PLMD6colvar8Gyration9calculateEv</a></td>
+              <td class="coverFnHi">1195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#90">_ZN4PLMD6colvar12_GLOBAL__N_120GyrationRegisterMe92C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#90">_ZN4PLMD6colvar12_GLOBAL__N_120GyrationRegisterMe92D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Gyration.cpp.func.html b/coverage/colvar/Gyration.cpp.func.html
new file mode 100644
index 0000000000..9076a97722
--- /dev/null
+++ b/coverage/colvar/Gyration.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Gyration.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Gyration.cpp<span style="font-size: 80%;"> (<a href="Gyration.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">186</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Gyration.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#90">_ZN4PLMD6colvar12_GLOBAL__N_120GyrationRegisterMe926createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#90">_ZN4PLMD6colvar12_GLOBAL__N_120GyrationRegisterMe92C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#90">_ZN4PLMD6colvar12_GLOBAL__N_120GyrationRegisterMe92D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#92">_ZN4PLMD6colvar8Gyration16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#157">_ZN4PLMD6colvar8Gyration9calculateEv</a></td>
+              <td class="coverFnHi">1195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#99">_ZN4PLMD6colvar8GyrationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gyration.cpp.gcov.html#99">_ZN4PLMD6colvar8GyrationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Gyration.cpp.gcov.html b/coverage/colvar/Gyration.cpp.gcov.html
new file mode 100644
index 0000000000..44e05f00be
--- /dev/null
+++ b/coverage/colvar/Gyration.cpp.gcov.html
@@ -0,0 +1,448 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Gyration.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Gyration.cpp<span style="font-size: 80%;"> (source / <a href="Gyration.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">186</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR GYRATION</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate the radius of gyration, or other properties related to it.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : The different properties can be calculated and selected by the TYPE keyword:</a>
+<a name="34"><span class="lineNum">      34 </span>            : the Radius of Gyration (RADIUS); the Trace of the Gyration Tensor (TRACE);</a>
+<a name="35"><span class="lineNum">      35 </span>            : the Largest Principal Moment of the Gyration Tensor (GTPC_1); the middle Principal Moment of the Gyration Tensor (GTPC_2);</a>
+<a name="36"><span class="lineNum">      36 </span>            : the Smallest Principal Moment of the Gyration Tensor (GTPC_3); the Asphericiry (ASPHERICITY); the Acylindricity (ACYLINDRICITY);</a>
+<a name="37"><span class="lineNum">      37 </span>            : the Relative Shape Anisotropy (KAPPA2); the Smallest Principal Radius Of Gyration (GYRATION_3);</a>
+<a name="38"><span class="lineNum">      38 </span>            : the Middle Principal Radius of Gyration (GYRATION_2); the Largest Principal Radius of Gyration (GYRATION_1).</a>
+<a name="39"><span class="lineNum">      39 </span>            : A derivation of all these different variants can be found in \cite Vymetal:2011gv</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The radius of gyration is calculated using:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : s_{\rm Gyr}=\Big ( \frac{\sum_i^{n}</a>
+<a name="45"><span class="lineNum">      45 </span>            :  m_i \vert {r}_i -{r}_{\rm COM} \vert ^2 }{\sum_i^{n} m_i} \Big)^{1/2}</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : with the position of the center of mass \f${r}_{\rm COM}\f$ given by:</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \f[</a>
+<a name="51"><span class="lineNum">      51 </span>            : {r}_{\rm COM}=\frac{\sum_i^{n} {r}_i\ m_i }{\sum_i^{n} m_i}</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f]</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The radius of gyration usually makes sense when atoms used for the calculation</a>
+<a name="55"><span class="lineNum">      55 </span>            : are all part of the same molecule.</a>
+<a name="56"><span class="lineNum">      56 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="57"><span class="lineNum">      57 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.2,</a>
+<a name="58"><span class="lineNum">      58 </span>            : by considering the ordered list of atoms and rebuilding the broken entities using a procedure</a>
+<a name="59"><span class="lineNum">      59 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="60"><span class="lineNum">      60 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="61"><span class="lineNum">      61 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="64"><span class="lineNum">      64 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="65"><span class="lineNum">      65 </span>            : periodic image.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \par Examples</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : The following input tells plumed to print the radius of gyration of the</a>
+<a name="71"><span class="lineNum">      71 </span>            : chain containing atoms 10 to 20.</a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : GYRATION TYPE=RADIUS ATOMS=10-20 LABEL=rg</a>
+<a name="74"><span class="lineNum">      74 </span>            : PRINT ARG=rg STRIDE=1 FILE=colvar</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : class Gyration : public Colvar {</a>
+<a name="81"><span class="lineNum">      81 </span>            : private:</a>
+<a name="82"><span class="lineNum">      82 </span>            :   enum CV_TYPE {RADIUS, TRACE, GTPC_1, GTPC_2, GTPC_3, ASPHERICITY, ACYLINDRICITY, KAPPA2, GYRATION_3, GYRATION_2, GYRATION_1, TOT};</a>
+<a name="83"><span class="lineNum">      83 </span>            :   int rg_type;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   bool use_masses;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   bool nopbc;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit Gyration(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void calculate() override;</a>
+<a name="90"><span class="lineNum">      90 </span>            : };</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      12568 : PLUMED_REGISTER_ACTION(Gyration,&quot;GYRATION&quot;)</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         35 : void Gyration::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         35 :   Colvar::registerKeywords(keys);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         70 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the group of atoms that you are calculating the Gyration Tensor for&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         70 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;RADIUS&quot;,&quot;The type of calculation relative to the Gyration Tensor you want to perform&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         70 :   keys.addFlag(&quot;MASS_WEIGHTED&quot;,false,&quot;set the masses of all the atoms equal to one&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         35 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         33 : Gyration::Gyration(const ActionOptions&amp;ao):</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         33 :   use_masses(false),</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         33 :   nopbc(false)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : {</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         65 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         32 :   if(atoms.size()==0) error(&quot;no atoms specified&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         66 :   parseFlag(&quot;MASS_WEIGHTED&quot;,use_masses);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   std::string Type;</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         32 :   parse(&quot;TYPE&quot;,Type);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         32 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         32 :   checkRead();</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         32 :   if(Type==&quot;RADIUS&quot;) rg_type=RADIUS;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         21 :   else if(Type==&quot;TRACE&quot;) rg_type=TRACE;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         19 :   else if(Type==&quot;GTPC_1&quot;) rg_type=GTPC_1;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         17 :   else if(Type==&quot;GTPC_2&quot;) rg_type=GTPC_2;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         15 :   else if(Type==&quot;GTPC_3&quot;) rg_type=GTPC_3;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         13 :   else if(Type==&quot;ASPHERICITY&quot;) rg_type=ASPHERICITY;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         11 :   else if(Type==&quot;ACYLINDRICITY&quot;) rg_type=ACYLINDRICITY;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          9 :   else if(Type==&quot;KAPPA2&quot;) rg_type=KAPPA2;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          7 :   else if(Type==&quot;RGYR_3&quot;) rg_type=GYRATION_3;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          5 :   else if(Type==&quot;RGYR_2&quot;) rg_type=GYRATION_2;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   else if(Type==&quot;RGYR_1&quot;) rg_type=GYRATION_1;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   else error(&quot;Unknown GYRATION type&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         31 :   switch(rg_type)</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   {</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         11 :   case RADIUS:   log.printf(&quot;  GYRATION RADIUS (Rg);&quot;); break;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :   case TRACE:  log.printf(&quot;  TRACE OF THE GYRATION TENSOR;&quot;); break;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :   case GTPC_1: log.printf(&quot;  THE LARGEST PRINCIPAL MOMENT OF THE GYRATION TENSOR (S'_1);&quot;); break;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   case GTPC_2: log.printf(&quot;  THE MIDDLE PRINCIPAL MOMENT OF THE GYRATION TENSOR (S'_2);&quot;);  break;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          2 :   case GTPC_3: log.printf(&quot;  THE SMALLEST PRINCIPAL MOMENT OF THE GYRATION TENSOR (S'_3);&quot;); break;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          2 :   case ASPHERICITY: log.printf(&quot;  THE ASPHERICITY (b');&quot;); break;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          2 :   case ACYLINDRICITY: log.printf(&quot;  THE ACYLINDRICITY (c');&quot;); break;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :   case KAPPA2: log.printf(&quot;  THE RELATIVE SHAPE ANISOTROPY (kappa^2);&quot;); break;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :   case GYRATION_3: log.printf(&quot;  THE SMALLEST PRINCIPAL RADIUS OF GYRATION (r_g3);&quot;); break;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :   case GYRATION_2: log.printf(&quot;  THE MIDDLE PRINCIPAL RADIUS OF GYRATION (r_g2);&quot;); break;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   case GYRATION_1: log.printf(&quot;  THE LARGEST PRINCIPAL RADIUS OF GYRATION (r_g1);&quot;); break;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         50 :   if(rg_type&gt;TRACE) log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Jiri� Vymetal and Jiri� Vondrasek, J. Phys. Chem. A 115, 11455 (2011)&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         31 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         31 :   log.printf(&quot;  atoms involved : &quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        233 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         31 :   if(nopbc) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          4 :     log&lt;&lt;&quot;  PBC will be ignored\n&quot;;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   } else {</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         27 :     log&lt;&lt;&quot;  broken molecules will be rebuilt assuming atoms are in the proper order\n&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         31 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         31 :   requestAtoms(atoms);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         35 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       1195 : void Gyration::calculate() {</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1195 :   if(!nopbc) makeWhole();</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       1195 :   Vector com;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   double totmass = 0.;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       1195 :   if( use_masses ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       totmass+=getMass(i);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :       com+=getMass(i)*getPosition(i);</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span>            :   } else {</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1195 :     totmass = static_cast&lt;double&gt;(getNumberOfAtoms());</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      10373 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       9178 :       com+=getPosition(i);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     }</a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1195 :   com /= totmass;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       1195 :   double rgyr=0.;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       1195 :   std::vector&lt;Vector&gt; derivatives( getNumberOfAtoms() );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       1195 :   Tensor virial;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       1195 :   if(rg_type==RADIUS||rg_type==TRACE) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        795 :     if( use_masses ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :         const Vector diff = delta( com, getPosition(i) );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :         rgyr          += getMass(i)*diff.modulo2();</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :         derivatives[i] = diff*getMass(i);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :         virial        -= Tensor(getPosition(i),derivatives[i]);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :       }</a>
+<a name="190"><span class="lineNum">     190 </span>            :     } else {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       7973 :       for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       7178 :         const Vector diff = delta( com, getPosition(i) );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       7178 :         rgyr          += diff.modulo2();</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       7178 :         derivatives[i] = diff;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       7178 :         virial        -= Tensor(getPosition(i),derivatives[i]);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       }</a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            :     double fact;</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        795 :     if(rg_type==RADIUS) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        665 :       rgyr = std::sqrt(rgyr/totmass);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        665 :       fact = 1./(rgyr*totmass);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :     } else {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        130 :       rgyr = 2.*rgyr;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       fact = 4;</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        795 :     setValue(rgyr);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       7973 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) setAtomsDerivatives(i,fact*derivatives[i]);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        795 :     setBoxDerivatives(fact*virial);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :     return;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        400 :   Tensor3d gyr_tens;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   //calculate gyration tensor</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        400 :   if( use_masses ) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :       const Vector diff=delta( com, getPosition(i) );</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :       gyr_tens[0][0]+=getMass(i)*diff[0]*diff[0];</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :       gyr_tens[1][1]+=getMass(i)*diff[1]*diff[1];</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :       gyr_tens[2][2]+=getMass(i)*diff[2]*diff[2];</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :       gyr_tens[0][1]+=getMass(i)*diff[0]*diff[1];</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :       gyr_tens[0][2]+=getMass(i)*diff[0]*diff[2];</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :       gyr_tens[1][2]+=getMass(i)*diff[1]*diff[2];</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :     }</a>
+<a name="225"><span class="lineNum">     225 </span>            :   } else {</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       2400 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       2000 :       const Vector diff=delta( com, getPosition(i) );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       2000 :       gyr_tens[0][0]+=diff[0]*diff[0];</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       2000 :       gyr_tens[1][1]+=diff[1]*diff[1];</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       2000 :       gyr_tens[2][2]+=diff[2]*diff[2];</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       2000 :       gyr_tens[0][1]+=diff[0]*diff[1];</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       2000 :       gyr_tens[0][2]+=diff[0]*diff[2];</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       2000 :       gyr_tens[1][2]+=diff[1]*diff[2];</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     }</a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   // first make the matrix symmetric</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        400 :   gyr_tens[1][0] = gyr_tens[0][1];</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        400 :   gyr_tens[2][0] = gyr_tens[0][2];</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        400 :   gyr_tens[2][1] = gyr_tens[1][2];</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        400 :   Tensor3d ttransf,transf;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        400 :   Vector princ_comp,prefactor;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   //diagonalize gyration tensor</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        400 :   diagMatSym(gyr_tens, princ_comp, ttransf);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        400 :   transf=transpose(ttransf);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   //sort eigenvalues and eigenvectors</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        400 :   if (princ_comp[0]&lt;princ_comp[1]) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        400 :     double tmp=princ_comp[0]; princ_comp[0]=princ_comp[1]; princ_comp[1]=tmp;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       1600 :     for (unsigned i=0; i&lt;3; i++) {tmp=transf[i][0]; transf[i][0]=transf[i][1]; transf[i][1]=tmp;}</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   }</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        400 :   if (princ_comp[1]&lt;princ_comp[2]) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        400 :     double tmp=princ_comp[1]; princ_comp[1]=princ_comp[2]; princ_comp[2]=tmp;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       1600 :     for (unsigned i=0; i&lt;3; i++) {tmp=transf[i][1]; transf[i][1]=transf[i][2]; transf[i][2]=tmp;}</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        400 :   if (princ_comp[0]&lt;princ_comp[1]) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        400 :     double tmp=princ_comp[0]; princ_comp[0]=princ_comp[1]; princ_comp[1]=tmp;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       1600 :     for (unsigned i=0; i&lt;3; i++) {tmp=transf[i][0]; transf[i][0]=transf[i][1]; transf[i][1]=tmp;}</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span>            :   //calculate determinant of transformation matrix</a>
+<a name="260"><span class="lineNum">     260 </span>            :   double det = determinant(transf);</a>
+<a name="261"><span class="lineNum">     261 </span>            :   // transformation matrix for rotation must have positive determinant, otherwise multiply one column by (-1)</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        400 :   if(det&lt;0) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       1600 :     for(unsigned j=0; j&lt;3; j++) transf[j][2]=-transf[j][2];</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        400 :     det = -det;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        400 :   if(std::abs(det-1.)&gt;0.0001) error(&quot;Plumed Error: Cannot diagonalize gyration tensor\n&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        400 :   switch(rg_type) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        135 :   case GTPC_1:</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   case GTPC_2:</a>
+<a name="270"><span class="lineNum">     270 </span>            :   case GTPC_3:</a>
+<a name="271"><span class="lineNum">     271 </span>            :   {</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        135 :     int pc_index = rg_type-2; //index of principal component</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        135 :     rgyr=std::sqrt(princ_comp[pc_index]/totmass);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        135 :     double rm = rgyr*totmass;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        135 :     if(rm&gt;1e-6) prefactor[pc_index]=1.0/rm; //some parts of derivate</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     break;</a>
+<a name="277"><span class="lineNum">     277 </span>            :   }</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   case GYRATION_3:        //the smallest principal radius of gyration</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   {</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :     rgyr=std::sqrt((princ_comp[1]+princ_comp[2])/totmass);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :     double rm = rgyr*totmass;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :     if (rm&gt;1e-6) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :       prefactor[1]=1.0/rm;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :       prefactor[2]=1.0/rm;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span>            :     break;</a>
+<a name="287"><span class="lineNum">     287 </span>            :   }</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        130 :   case GYRATION_2:       //the midle principal radius of gyration</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   {</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        130 :     rgyr=std::sqrt((princ_comp[0]+princ_comp[2])/totmass);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        130 :     double rm = rgyr*totmass;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        130 :     if (rm&gt;1e-6) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        130 :       prefactor[0]=1.0/rm;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        130 :       prefactor[2]=1.0/rm;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :     }</a>
+<a name="296"><span class="lineNum">     296 </span>            :     break;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :   case GYRATION_1:      //the largest principal radius of gyration</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   {</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :     rgyr=std::sqrt((princ_comp[0]+princ_comp[1])/totmass);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :     double rm = rgyr*totmass;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :     if (rm&gt;1e-6) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :       prefactor[0]=1.0/rm;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :       prefactor[1]=1.0/rm;</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :     }</a>
+<a name="306"><span class="lineNum">     306 </span>            :     break;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          5 :   case ASPHERICITY:</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   {</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          5 :     rgyr=std::sqrt((princ_comp[0]-0.5*(princ_comp[1]+princ_comp[2]))/totmass);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          5 :     double rm = rgyr*totmass;</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          5 :     if (rm&gt;1e-6) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          5 :       prefactor[0]= 1.0/rm;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          5 :       prefactor[1]=-0.5/rm;</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          5 :       prefactor[2]=-0.5/rm;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :     }</a>
+<a name="317"><span class="lineNum">     317 </span>            :     break;</a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :   case ACYLINDRICITY:</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   {</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :     rgyr=std::sqrt((princ_comp[1]-princ_comp[2])/totmass);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :     double rm = rgyr*totmass;</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     if (rm&gt;1e-6) {  //avoid division by zero</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :       prefactor[1]= 1.0/rm;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :       prefactor[2]=-1.0/rm;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span>            :     break;</a>
+<a name="328"><span class="lineNum">     328 </span>            :   }</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        130 :   case KAPPA2: // relative shape anisotropy</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :   {</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        130 :     double trace = princ_comp[0]+princ_comp[1]+princ_comp[2];</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        130 :     double tmp=princ_comp[0]*princ_comp[1]+ princ_comp[1]*princ_comp[2]+ princ_comp[0]*princ_comp[2];</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        130 :     rgyr=1.0-3*(tmp/(trace*trace));</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">        130 :     if (rgyr&gt;1e-6) {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        130 :       prefactor[0]= -3*((princ_comp[1]+princ_comp[2])-2*tmp/trace)/(trace*trace) *2;</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        130 :       prefactor[1]= -3*((princ_comp[0]+princ_comp[2])-2*tmp/trace)/(trace*trace) *2;</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        130 :       prefactor[2]= -3*((princ_comp[0]+princ_comp[1])-2*tmp/trace)/(trace*trace) *2;</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :     }</a>
+<a name="339"><span class="lineNum">     339 </span>            :     break;</a>
+<a name="340"><span class="lineNum">     340 </span>            :   }</a>
+<a name="341"><span class="lineNum">     341 </span>            :   }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">        400 :   if(use_masses) {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :       Vector tX;</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :       const Vector diff=delta( com,getPosition(i) );</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :       //project atomic postional vectors to diagonalized frame</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;3; j++) tX[j]=transf[0][j]*diff[0]+transf[1][j]*diff[1]+transf[2][j]*diff[2];</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;3; j++) derivatives[i][j]=getMass(i)*(prefactor[0]*transf[j][0]*tX[0]+</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :             prefactor[1]*transf[j][1]*tX[1]+</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :             prefactor[2]*transf[j][2]*tX[2]);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :       setAtomsDerivatives(i,derivatives[i]);</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :     }</a>
+<a name="354"><span class="lineNum">     354 </span>            :   } else {</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">       2400 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       2000 :       Vector tX;</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       2000 :       const Vector diff=delta( com,getPosition(i) );</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :       //project atomic postional vectors to diagonalized frame</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">       8000 :       for(unsigned j=0; j&lt;3; j++) tX[j]=transf[0][j]*diff[0]+transf[1][j]*diff[1]+transf[2][j]*diff[2];</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">       8000 :       for(unsigned j=0; j&lt;3; j++) derivatives[i][j]=prefactor[0]*transf[j][0]*tX[0]+</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">      12000 :             prefactor[1]*transf[j][1]*tX[1]+</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       6000 :             prefactor[2]*transf[j][2]*tX[2];</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       2000 :       setAtomsDerivatives(i,derivatives[i]);</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :     }</a>
+<a name="365"><span class="lineNum">     365 </span>            :   }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        400 :   setValue(rgyr);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        400 :   setBoxDerivativesNoPbc();</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : }</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span>            : }</a>
+<a name="372"><span class="lineNum">     372 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/MultiRMSD.cpp.func-sort-c.html b/coverage/colvar/MultiRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e432afad3c
--- /dev/null
+++ b/coverage/colvar/MultiRMSD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/MultiRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - MultiRMSD.cpp<span style="font-size: 80%;"> (<a href="MultiRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">97.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#150">_ZN4PLMD6colvar9MultiRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_122MultiRMSDRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#150">_ZN4PLMD6colvar9MultiRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#143">_ZN4PLMD6colvar9MultiRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#193">_ZN4PLMD6colvar9MultiRMSD9calculateEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_122MultiRMSDRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_122MultiRMSDRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/MultiRMSD.cpp.func.html b/coverage/colvar/MultiRMSD.cpp.func.html
new file mode 100644
index 0000000000..bc0b65b985
--- /dev/null
+++ b/coverage/colvar/MultiRMSD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/MultiRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - MultiRMSD.cpp<span style="font-size: 80%;"> (<a href="MultiRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">97.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_122MultiRMSDRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_122MultiRMSDRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#141">_ZN4PLMD6colvar12_GLOBAL__N_122MultiRMSDRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#143">_ZN4PLMD6colvar9MultiRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#193">_ZN4PLMD6colvar9MultiRMSD9calculateEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#150">_ZN4PLMD6colvar9MultiRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiRMSD.cpp.gcov.html#150">_ZN4PLMD6colvar9MultiRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/MultiRMSD.cpp.gcov.html b/coverage/colvar/MultiRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..ca89e0c9c8
--- /dev/null
+++ b/coverage/colvar/MultiRMSD.cpp.gcov.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/MultiRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - MultiRMSD.cpp<span style="font-size: 80%;"> (source / <a href="MultiRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">97.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;reference/MultiDomainRMSD.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace colvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class MultiRMSD : public Colvar {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            :   std::unique_ptr&lt;PLMD::MultiDomainRMSD&gt; rmsd;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   bool squared;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   MultiValue myvals;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   ReferenceValuePack mypack;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   bool nopbc;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   explicit MultiRMSD(const ActionOptions&amp;);</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void calculate() override;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : //+PLUMEDOC DCOLVAR MULTI_RMSD</a>
+<a name="48"><span class="lineNum">      48 </span>            : /*</a>
+<a name="49"><span class="lineNum">      49 </span>            : Calculate the RMSD distance moved by a number of separated domains from their positions in a reference structure.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : When you have large proteins the calculation of the root mean squared deviation between all the atoms in a reference</a>
+<a name="53"><span class="lineNum">      53 </span>            : structure and the instantaneous configuration becomes prohibitively expensive.  You may thus instead want to calculate</a>
+<a name="54"><span class="lineNum">      54 </span>            : the RMSD between the atoms in a set of domains of your protein and your reference structure.  That is to say:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \f[</a>
+<a name="57"><span class="lineNum">      57 </span>            : d(X,X_r) = \sqrt{ \sum_{i} w_i\vert X_i - X_i' \vert^2 }</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f]</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : where here the sum is over the domains of the protein, \f$X_i\f$ represents the positions of the atoms in domain \f$i\f$</a>
+<a name="61"><span class="lineNum">      61 </span>            : in the instantaneous configuration and \f$X_i'\f$ is the positions of the atoms in domain \f$i\f$ in the reference</a>
+<a name="62"><span class="lineNum">      62 </span>            : configuration.  \f$w_i\f$ is an optional weight.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The distances for each of the domains in the above sum can be calculated using the \ref DRMSD or \ref RMSD measures or</a>
+<a name="65"><span class="lineNum">      65 </span>            : using a combination of these distance.  The reference configuration is specified in a pdb file like the one below:</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \auxfile{file1.pdb}</a>
+<a name="68"><span class="lineNum">      68 </span>            : ATOM      2  O   ALA     2      -0.926  -2.447  -0.497  1.00  1.00      DIA  O</a>
+<a name="69"><span class="lineNum">      69 </span>            : ATOM      4  HNT ALA     2       0.533  -0.396   1.184  1.00  1.00      DIA  H</a>
+<a name="70"><span class="lineNum">      70 </span>            : ATOM      6  HT1 ALA     2      -0.216  -2.590   1.371  1.00  1.00      DIA  H</a>
+<a name="71"><span class="lineNum">      71 </span>            : ATOM      7  HT2 ALA     2      -0.309  -1.255   2.315  1.00  1.00      DIA  H</a>
+<a name="72"><span class="lineNum">      72 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="73"><span class="lineNum">      73 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="74"><span class="lineNum">      74 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="75"><span class="lineNum">      75 </span>            : TER</a>
+<a name="76"><span class="lineNum">      76 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="77"><span class="lineNum">      77 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="78"><span class="lineNum">      78 </span>            : ATOM     16  HN  ALA     2       1.713   1.021  -0.873  1.00  1.00      DIA  H</a>
+<a name="79"><span class="lineNum">      79 </span>            : ATOM     18  HA  ALA     2       0.099  -0.774  -2.218  1.00  1.00      DIA  H</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOM     19  CB  ALA     2       2.063  -1.223  -1.276  1.00  1.00      DIA  C</a>
+<a name="81"><span class="lineNum">      81 </span>            : ATOM     20  HB1 ALA     2       2.670  -0.716  -2.057  1.00  1.00      DIA  H</a>
+<a name="82"><span class="lineNum">      82 </span>            : ATOM     21  HB2 ALA     2       2.556  -1.051  -0.295  1.00  1.00      DIA  H</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM     22  HB3 ALA     2       2.070  -2.314  -1.490  1.00  1.00      DIA  H</a>
+<a name="84"><span class="lineNum">      84 </span>            : END</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endauxfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : with the TER keyword being used to separate the various domains in you protein.</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \par Examples</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : The following tells plumed to calculate the RMSD distance between</a>
+<a name="93"><span class="lineNum">      93 </span>            : the positions of the atoms in the reference file and their instantaneous</a>
+<a name="94"><span class="lineNum">      94 </span>            : position.  The Kearsley algorithm for each of the domains.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \plumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : MULTI_RMSD REFERENCE=file1.pdb TYPE=MULTI-OPTIMAL</a>
+<a name="98"><span class="lineNum">      98 </span>            : \endplumedfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : The following tells plumed to calculate the RMSD distance between the positions of</a>
+<a name="101"><span class="lineNum">     101 </span>            : the atoms in the domains of reference the reference structure and their instantaneous</a>
+<a name="102"><span class="lineNum">     102 </span>            : positions.  Here distances are calculated using the \ref DRMSD measure.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : \plumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : MULTI_RMSD REFERENCE=file1.pdb TYPE=MULTI-DRMSD</a>
+<a name="106"><span class="lineNum">     106 </span>            : \endplumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : in this case it is possible to use the following DRMSD options in the pdb file using the REMARK syntax:</a>
+<a name="109"><span class="lineNum">     109 </span>            : \verbatim</a>
+<a name="110"><span class="lineNum">     110 </span>            : NOPBC to calculate distances without PBC</a>
+<a name="111"><span class="lineNum">     111 </span>            : LOWER_CUTOFF=# only pairs of atoms further than LOWER_CUTOFF are considered in the calculation</a>
+<a name="112"><span class="lineNum">     112 </span>            : UPPER_CUTOFF=# only pairs of atoms further than UPPER_CUTOFF are considered in the calculation</a>
+<a name="113"><span class="lineNum">     113 </span>            : \endverbatim</a>
+<a name="114"><span class="lineNum">     114 </span>            : as shown in the following example</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : \auxfile{file2.pdb}</a>
+<a name="117"><span class="lineNum">     117 </span>            : REMARK NOPBC</a>
+<a name="118"><span class="lineNum">     118 </span>            : REMARK LOWER_CUTOFF=0.1</a>
+<a name="119"><span class="lineNum">     119 </span>            : REMARK UPPER_CUTOFF=0.8</a>
+<a name="120"><span class="lineNum">     120 </span>            : ATOM      2  O   ALA     2      -0.926  -2.447  -0.497  1.00  1.00      DIA  O</a>
+<a name="121"><span class="lineNum">     121 </span>            : ATOM      4  HNT ALA     2       0.533  -0.396   1.184  1.00  1.00      DIA  H</a>
+<a name="122"><span class="lineNum">     122 </span>            : ATOM      6  HT1 ALA     2      -0.216  -2.590   1.371  1.00  1.00      DIA  H</a>
+<a name="123"><span class="lineNum">     123 </span>            : ATOM      7  HT2 ALA     2      -0.309  -1.255   2.315  1.00  1.00      DIA  H</a>
+<a name="124"><span class="lineNum">     124 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="125"><span class="lineNum">     125 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="126"><span class="lineNum">     126 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="127"><span class="lineNum">     127 </span>            : TER</a>
+<a name="128"><span class="lineNum">     128 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="129"><span class="lineNum">     129 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="130"><span class="lineNum">     130 </span>            : ATOM     16  HN  ALA     2       1.713   1.021  -0.873  1.00  1.00      DIA  H</a>
+<a name="131"><span class="lineNum">     131 </span>            : ATOM     18  HA  ALA     2       0.099  -0.774  -2.218  1.00  1.00      DIA  H</a>
+<a name="132"><span class="lineNum">     132 </span>            : ATOM     19  CB  ALA     2       2.063  -1.223  -1.276  1.00  1.00      DIA  C</a>
+<a name="133"><span class="lineNum">     133 </span>            : ATOM     20  HB1 ALA     2       2.670  -0.716  -2.057  1.00  1.00      DIA  H</a>
+<a name="134"><span class="lineNum">     134 </span>            : ATOM     21  HB2 ALA     2       2.556  -1.051  -0.295  1.00  1.00      DIA  H</a>
+<a name="135"><span class="lineNum">     135 </span>            : ATOM     22  HB3 ALA     2       2.070  -2.314  -1.490  1.00  1.00      DIA  H</a>
+<a name="136"><span class="lineNum">     136 </span>            : END</a>
+<a name="137"><span class="lineNum">     137 </span>            : \endauxfile</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : */</a>
+<a name="141"><span class="lineNum">     141 </span>            : //+ENDPLUMEDOC</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(MultiRMSD,&quot;MULTI_RMSD&quot;)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          5 : void MultiRMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          5 :   Colvar::registerKeywords(keys);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;MULTI-SIMPLE&quot;,&quot;the manner in which RMSD alignment is performed.  Should be MULTI-OPTIMAL, MULTI-OPTIMAL-FAST,  MULTI-SIMPLE or MULTI-DRMSD.&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         10 :   keys.addFlag(&quot;SQUARED&quot;,false,&quot; This should be set if you want the mean squared displacement instead of the root mean squared displacement&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          5 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          3 : MultiRMSD::MultiRMSD(const ActionOptions&amp;ao):</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 :   PLUMED_COLVAR_INIT(ao),squared(false),myvals(1,0), mypack(0,0,myvals),nopbc(false)</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : {</a>
+<a name="155"><span class="lineNum">     155 </span>            :   std::string reference;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          6 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::string type;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 :   type.assign(&quot;SIMPLE&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          3 :   parse(&quot;TYPE&quot;,type);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          3 :   parseFlag(&quot;SQUARED&quot;,squared);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          3 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          3 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   PDB pdb;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          6 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     error(&quot;missing input file &quot; + reference );</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          6 :   rmsd=metricRegister().create&lt;MultiDomainRMSD&gt;(type,pdb);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   // Do not align molecule if we are doing DRMSD for domains and NOPBC has been specified in input</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          6 :   if( pdb.hasFlag(&quot;NOPBC&quot;) ) nopbc=true;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          3 :   rmsd-&gt;getAtomRequests( atoms );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :   requestAtoms( atoms );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :   myvals.resize( 1, 3*atoms.size()+9 ); mypack.resize( 0, atoms.size() );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         48 :   for(unsigned i=0; i&lt;atoms.size(); ++i) mypack.setAtomIndex( i, i );</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          3 :   log.printf(&quot;  reference from file %s\n&quot;,reference.c_str());</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :   log.printf(&quot;  which contains %d atoms\n&quot;,getNumberOfAtoms());</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          3 :   log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         48 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         45 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         45 :     log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          3 :   log.printf(&quot;  method for alignment : %s \n&quot;,type.c_str() );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          3 :   if(squared)log.printf(&quot;  chosen to use SQUARED option for MSD instead of RMSD\n&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          6 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : // calculator</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         15 : void MultiRMSD::calculate() {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         15 :   if(!nopbc) makeWhole();</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         15 :   double r=rmsd-&gt;calculate( getPositions(), getPbc(), mypack, squared );</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         15 :   setValue(r);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        240 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) setAtomsDerivatives( i, mypack.getAtomDerivative(i) );</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         15 :   if( !mypack.virialWasSet() ) setBoxDerivativesNoPbc();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          5 :   else setBoxDerivatives( mypack.getBoxDerivatives() );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         15 : }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PCARMSD.cpp.func-sort-c.html b/coverage/colvar/PCARMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a1d584fb70
--- /dev/null
+++ b/coverage/colvar/PCARMSD.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PCARMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PCARMSD.cpp<span style="font-size: 80%;"> (<a href="PCARMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PCARMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#112">_ZN4PLMD6colvar7PCARMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#101">_ZN4PLMD6colvar12_GLOBAL__N_120PCARMSDRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#112">_ZN4PLMD6colvar7PCARMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#168">_ZZN4PLMD6colvar7PCARMSDC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#103">_ZN4PLMD6colvar7PCARMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#206">_ZN4PLMD6colvar7PCARMSD9calculateEv</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#101">_ZN4PLMD6colvar12_GLOBAL__N_120PCARMSDRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#101">_ZN4PLMD6colvar12_GLOBAL__N_120PCARMSDRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PCARMSD.cpp.func.html b/coverage/colvar/PCARMSD.cpp.func.html
new file mode 100644
index 0000000000..f3763c6547
--- /dev/null
+++ b/coverage/colvar/PCARMSD.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PCARMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PCARMSD.cpp<span style="font-size: 80%;"> (<a href="PCARMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PCARMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#101">_ZN4PLMD6colvar12_GLOBAL__N_120PCARMSDRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#101">_ZN4PLMD6colvar12_GLOBAL__N_120PCARMSDRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#101">_ZN4PLMD6colvar12_GLOBAL__N_120PCARMSDRegisterMe103D2Ev</a></td>
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+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#103">_ZN4PLMD6colvar7PCARMSD16registerKeywordsERNS_8KeywordsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#206">_ZN4PLMD6colvar7PCARMSD9calculateEv</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#112">_ZN4PLMD6colvar7PCARMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#112">_ZN4PLMD6colvar7PCARMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCARMSD.cpp.gcov.html#168">_ZZN4PLMD6colvar7PCARMSDC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PCARMSD.cpp.gcov.html b/coverage/colvar/PCARMSD.cpp.gcov.html
new file mode 100644
index 0000000000..4805c7e2ad
--- /dev/null
+++ b/coverage/colvar/PCARMSD.cpp.gcov.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PCARMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PCARMSD.cpp<span style="font-size: 80%;"> (source / <a href="PCARMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryHi">98.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace colvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class PCARMSD : public Colvar {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            :   std::unique_ptr&lt;PLMD::RMSD&gt; rmsd;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   bool squared;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   bool nopbc;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::vector&lt; std::vector&lt;Vector&gt; &gt; eigenvectors;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;PDB&gt; pdbv;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   std::vector&lt;std::string&gt; pca_names;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   explicit PCARMSD(const ActionOptions&amp;);</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void calculate() override;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : //+PLUMEDOC DCOLVAR PCARMSD</a>
+<a name="48"><span class="lineNum">      48 </span>            : /*</a>
+<a name="49"><span class="lineNum">      49 </span>            : Calculate the PCA components for a number of provided eigenvectors and an average structure.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : For information on this method ( see \cite Sutto:2010 and \cite spiwok ). Performs optimal alignment at every step and reports the rmsd so you know if you are far or close from the average structure.</a>
+<a name="52"><span class="lineNum">      52 </span>            : It takes the average structure and eigenvectors in form of a pdb.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Note that beta and occupancy values in the pdb are neglected and all the weights are placed to 1 (differently from the RMSD colvar for example)</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \par Examples</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : PCARMSD AVERAGE=file.pdb EIGENVECTORS=eigenvectors.pdb</a>
+<a name="59"><span class="lineNum">      59 </span>            : \endplumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The input is taken so to be compatible with the output you get from g_covar utility of gromacs (suitably adapted to have a pdb input format).</a>
+<a name="62"><span class="lineNum">      62 </span>            : The reference configuration (file.pdb) will thus be in a file that looks something like this:</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \auxfile{file.pdb}</a>
+<a name="65"><span class="lineNum">      65 </span>            : TITLE     Average structure</a>
+<a name="66"><span class="lineNum">      66 </span>            : MODEL        1</a>
+<a name="67"><span class="lineNum">      67 </span>            : ATOM      1  CL  ALA     1       1.042  -3.070   0.946  1.00  0.00</a>
+<a name="68"><span class="lineNum">      68 </span>            : ATOM      5  CLP ALA     1       0.416  -2.033   0.132  1.00  0.00</a>
+<a name="69"><span class="lineNum">      69 </span>            : ATOM      6  OL  ALA     1       0.415  -2.082  -0.976  1.00  0.00</a>
+<a name="70"><span class="lineNum">      70 </span>            : ATOM      7  NL  ALA     1      -0.134  -1.045   0.677  1.00  0.00</a>
+<a name="71"><span class="lineNum">      71 </span>            : ATOM      9  CA  ALA     1      -0.774   0.053   0.003  1.00  0.00</a>
+<a name="72"><span class="lineNum">      72 </span>            : TER</a>
+<a name="73"><span class="lineNum">      73 </span>            : ENDMDL</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endauxfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : while the eigenvectors will be in a pdb file (eigenvectors.pdb) that looks something like this:</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \auxfile{eigenvectors.pdb}</a>
+<a name="79"><span class="lineNum">      79 </span>            : TITLE     frame t= -1.000</a>
+<a name="80"><span class="lineNum">      80 </span>            : MODEL        1</a>
+<a name="81"><span class="lineNum">      81 </span>            : ATOM      1  CL  ALA     1       1.194  -2.988   0.724  1.00  0.00</a>
+<a name="82"><span class="lineNum">      82 </span>            : ATOM      5  CLP ALA     1      -0.996   0.042   0.144  1.00  0.00</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM      6  OL  ALA     1      -1.246  -0.178  -0.886  1.00  0.00</a>
+<a name="84"><span class="lineNum">      84 </span>            : ATOM      7  NL  ALA     1      -2.296   0.272   0.934  1.00  0.00</a>
+<a name="85"><span class="lineNum">      85 </span>            : ATOM      9  CA  ALA     1      -0.436   2.292   0.814  1.00  0.00</a>
+<a name="86"><span class="lineNum">      86 </span>            : TER</a>
+<a name="87"><span class="lineNum">      87 </span>            : ENDMDL</a>
+<a name="88"><span class="lineNum">      88 </span>            : TITLE     frame t= 0.000</a>
+<a name="89"><span class="lineNum">      89 </span>            : MODEL        1</a>
+<a name="90"><span class="lineNum">      90 </span>            : ATOM      1  CL  ALA     1       1.042  -3.070   0.946  1.00  0.00</a>
+<a name="91"><span class="lineNum">      91 </span>            : ATOM      5  CLP ALA     1      -0.774   0.053   0.003  1.00  0.00</a>
+<a name="92"><span class="lineNum">      92 </span>            : ATOM      6  OL  ALA     1      -0.849  -0.166  -1.034  1.00  0.00</a>
+<a name="93"><span class="lineNum">      93 </span>            : ATOM      7  NL  ALA     1      -2.176   0.260   0.563  1.00  0.00</a>
+<a name="94"><span class="lineNum">      94 </span>            : ATOM      9  CA  ALA     1       0.314   1.825   0.962  1.00  0.00</a>
+<a name="95"><span class="lineNum">      95 </span>            : TER</a>
+<a name="96"><span class="lineNum">      96 </span>            : ENDMDL</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : \endauxfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : */</a>
+<a name="101"><span class="lineNum">     101 </span>            : //+ENDPLUMEDOC</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(PCARMSD,&quot;PCARMSD&quot;)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 : void PCARMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 :   Colvar::registerKeywords(keys);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;AVERAGE&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;EIGENVECTORS&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;eig&quot;,&quot;default&quot;,&quot;the projections on each eigenvalue are stored on values labeled eig-1, eig-2, ...&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;residual&quot;,&quot;default&quot;,&quot;the distance of the present configuration from the configuration supplied as AVERAGE in terms of mean squared displacement after optimal alignment &quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          8 :   keys.addFlag(&quot;SQUARED_ROOT&quot;,false,&quot; This should be set if you want RMSD instead of mean squared displacement &quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          4 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 : PCARMSD::PCARMSD(const ActionOptions&amp;ao):</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          2 :   squared(true),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   nopbc(false)</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : {</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::string f_average;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          4 :   parse(&quot;AVERAGE&quot;,f_average);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::string type;</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   type.assign(&quot;OPTIMAL&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::string f_eigenvectors;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :   parse(&quot;EIGENVECTORS&quot;,f_eigenvectors);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   bool sq;  parseFlag(&quot;SQUARED_ROOT&quot;,sq);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 :   if (sq) { squared=false; }</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   PDB pdb;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   if( !pdb.read(f_average,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     error(&quot;missing input file &quot; + f_average );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 :   rmsd=Tools::make_unique&lt;RMSD&gt;();</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   bool remove_com=true;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   bool normalize_weights=true;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   // here align and displace are a simple vector of ones</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         24 :   std::vector&lt;double&gt; align; align=pdb.getOccupancy(); for(unsigned i=0; i&lt;align.size(); i++) {align[i]=1.;} ;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         24 :   std::vector&lt;double&gt; displace;  displace=pdb.getBeta(); for(unsigned i=0; i&lt;displace.size(); i++) {displace[i]=1.;} ;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   // reset again to reimpose unifrom weights (safe to disable this)</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 :   rmsd-&gt;set(align,displace,pdb.getPositions(),type,remove_com,normalize_weights);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   requestAtoms( pdb.getAtomNumbers() );</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :   addComponentWithDerivatives(&quot;residual&quot;); componentIsNotPeriodic(&quot;residual&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :   log.printf(&quot;  average from file %s\n&quot;,f_average.c_str());</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   log.printf(&quot;  which contains %d atoms\n&quot;,getNumberOfAtoms());</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :   log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         24 :   for(unsigned i=0; i&lt;pdb.getAtomNumbers().size(); ++i) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         22 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         22 :     log.printf(&quot;%d &quot;,pdb.getAtomNumbers()[i].serial());</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :   log.printf(&quot;  method for alignment : %s \n&quot;,type.c_str() );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :   if(nopbc) log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :   else      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          4 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Spiwok, Lipovova and Kralova, JPCB, 111, 3073 (2007)  &quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          4 :   log&lt;&lt;&quot; &quot;&lt;&lt;plumed.cite( &quot;Sutto, D'Abramo, Gervasio, JCTC, 6, 3640 (2010)&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   unsigned neigenvects;</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 :   neigenvects=0;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   // now get the eigenvectors</a>
+<a name="166"><span class="lineNum">     166 </span>            :   // open the file</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   if (FILE* fp=this-&gt;fopen(f_eigenvectors.c_str(),&quot;r&quot;))</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   {</a>
+<a name="169"><span class="lineNum">     169 </span>            : // call fclose when exiting this block</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :     auto deleter=[this](FILE* f) { this-&gt;fclose(f); };</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :     std::vector&lt;AtomNumber&gt; aaa;</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  Opening the eigenvectors file &quot;&lt;&lt;f_eigenvectors.c_str()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     bool do_read=true;</a>
+<a name="176"><span class="lineNum">     176 </span>            :     unsigned nat=0;</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         72 :     while (do_read) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         72 :       PDB mypdb;</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :       // check the units for reading this file: how can they make sense?</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        144 :       do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         72 :       if(do_read) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         70 :         neigenvects++;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         70 :         if(mypdb.getAtomNumbers().size()==0) error(&quot;number of atoms in a frame should be more than zero&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         70 :         if(nat==0) nat=mypdb.getAtomNumbers().size();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         70 :         if(nat!=mypdb.getAtomNumbers().size()) error(&quot;frames should have the same number of atoms&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         70 :         if(aaa.empty()) aaa=mypdb.getAtomNumbers();</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        140 :         if(aaa!=mypdb.getAtomNumbers()) error(&quot;frames should contain same atoms in same order&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         70 :         log&lt;&lt;&quot;  Found eigenvector: &quot;&lt;&lt;neigenvects&lt;&lt;&quot; containing  &quot;&lt;&lt;mypdb.getAtomNumbers().size()&lt;&lt;&quot; atoms\n&quot;;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         70 :         pdbv.push_back(mypdb);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         70 :         eigenvectors.push_back(mypdb.getPositions());</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       } else {break ;}</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         72 :     }</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  Found total &quot;&lt;&lt;neigenvects&lt;&lt; &quot; eigenvectors in the file &quot;&lt;&lt;f_eigenvectors.c_str()&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          2 :     if(neigenvects==0) error(&quot;at least one eigenvector is expected&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 :   }</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   // the components</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         72 :   for(unsigned i=0; i&lt;neigenvects; i++) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         70 :     std::string num; Tools::convert( i, num );</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        140 :     std::string name; name=std::string(&quot;eig-&quot;)+num;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         70 :     pca_names.push_back(name);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         70 :     addComponentWithDerivatives(name); componentIsNotPeriodic(name);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          2 :   turnOnDerivatives();</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          4 : }</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : // calculator</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       1092 : void PCARMSD::calculate() {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1092 :   if(!nopbc) makeWhole();</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       1092 :   Tensor rotation,invrotation;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   Matrix&lt;std::vector&lt;Vector&gt; &gt; drotdpos(3,3);</a>
+<a name="212"><span class="lineNum">     212 </span>            :   std::vector&lt;Vector&gt; alignedpos;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   std::vector&lt;Vector&gt; centeredpos;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   std::vector&lt;Vector&gt; centeredref;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   std::vector&lt;Vector&gt; ddistdpos;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1092 :   double r=rmsd-&gt;calc_PCAelements( getPositions(), ddistdpos, rotation,  drotdpos, alignedpos,centeredpos, centeredref,squared);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       1092 :   invrotation=rotation.transpose();</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       2184 :   Value* verr=getPntrToComponent(&quot;residual&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   verr-&gt;set(r);</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      13104 :   for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      12012 :     setAtomsDerivatives (verr,iat,ddistdpos[iat]);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   std::vector&lt; Vector &gt; der;</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       1092 :   der.resize(getNumberOfAtoms());</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      39312 :   for(unsigned i=0; i&lt;eigenvectors.size(); i++) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      38220 :     Value* value=getPntrToComponent(pca_names[i].c_str());</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     double val; val=0.;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     458640 :     for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">     420420 :       val+=dotProduct(alignedpos[iat]-centeredref[iat],eigenvectors[i][iat]);   der[iat].zero();</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     }</a>
+<a name="235"><span class="lineNum">     235 </span>            :     value-&gt;set(val);</a>
+<a name="236"><span class="lineNum">     236 </span>            :     // here the loop is reversed to better suit the structure of the derivative of the rotation matrix</a>
+<a name="237"><span class="lineNum">     237 </span>            :     double tmp1;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">     152880 :     for(unsigned a=0; a&lt;3; a++) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">     458640 :       for(unsigned b=0; b&lt;3; b++) {</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :         tmp1=0.;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">    4127760 :         for(unsigned n=0; n&lt;getNumberOfAtoms(); n++) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">    3783780 :           tmp1+=centeredpos[n][b]*eigenvectors[i][n][a];</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :         }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">    4127760 :         for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    3783780 :           der[iat]+=drotdpos[a][b][iat]*tmp1;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :         }</a>
+<a name="247"><span class="lineNum">     247 </span>            :       }</a>
+<a name="248"><span class="lineNum">     248 </span>            :     }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      38220 :     Vector v1;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">     458640 :     for(unsigned n=0; n&lt;getNumberOfAtoms(); n++) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">     420420 :       v1+=(1./getNumberOfAtoms())*matmul(invrotation,eigenvectors[i][n]);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">     458640 :     for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">     420420 :       der[iat]+=matmul(invrotation,eigenvectors[i][iat])-v1;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">     420420 :       setAtomsDerivatives (value,iat,der[iat]);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :     }</a>
+<a name="257"><span class="lineNum">     257 </span>            :   }</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">      40404 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) setBoxDerivativesNoPbc( getPntrToComponent(i) );</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       1092 : }</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSD.cpp.func-sort-c.html b/coverage/colvar/PathMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7cb747c1f8
--- /dev/null
+++ b/coverage/colvar/PathMSD.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSD.cpp<span style="font-size: 80%;"> (<a href="PathMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PathMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#105">_ZN4PLMD6colvar7PathMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#96">_ZN4PLMD6colvar12_GLOBAL__N_119PathMSDRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#105">_ZN4PLMD6colvar7PathMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#98">_ZN4PLMD6colvar7PathMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#96">_ZN4PLMD6colvar12_GLOBAL__N_119PathMSDRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#96">_ZN4PLMD6colvar12_GLOBAL__N_119PathMSDRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSD.cpp.func.html b/coverage/colvar/PathMSD.cpp.func.html
new file mode 100644
index 0000000000..5325a90832
--- /dev/null
+++ b/coverage/colvar/PathMSD.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSD.cpp<span style="font-size: 80%;"> (<a href="PathMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PathMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#96">_ZN4PLMD6colvar12_GLOBAL__N_119PathMSDRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#96">_ZN4PLMD6colvar12_GLOBAL__N_119PathMSDRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#96">_ZN4PLMD6colvar12_GLOBAL__N_119PathMSDRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#98">_ZN4PLMD6colvar7PathMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#105">_ZN4PLMD6colvar7PathMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSD.cpp.gcov.html#105">_ZN4PLMD6colvar7PathMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSD.cpp.gcov.html b/coverage/colvar/PathMSD.cpp.gcov.html
new file mode 100644
index 0000000000..02277c5cd6
--- /dev/null
+++ b/coverage/colvar/PathMSD.cpp.gcov.html
@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSD.cpp<span style="font-size: 80%;"> (source / <a href="PathMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathMSDBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR PATHMSD</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This Colvar calculates path collective variables.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This is the Path Collective Variables implementation</a>
+<a name="33"><span class="lineNum">      33 </span>            : ( see \cite brand07 ).</a>
+<a name="34"><span class="lineNum">      34 </span>            : This variable computes the progress along a given set of frames that is provided</a>
+<a name="35"><span class="lineNum">      35 </span>            : in input (&quot;sss&quot; component) and the distance from them (&quot;zzz&quot; component).</a>
+<a name="36"><span class="lineNum">      36 </span>            : (see below).</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="39"><span class="lineNum">      39 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.5,</a>
+<a name="40"><span class="lineNum">      40 </span>            : by considering the ordered list of atoms and rebuilding molecules with a procedure</a>
+<a name="41"><span class="lineNum">      41 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="42"><span class="lineNum">      42 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="43"><span class="lineNum">      43 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="46"><span class="lineNum">      46 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="47"><span class="lineNum">      47 </span>            : periodic image.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : Here below is a case where you have defined three frames and you want to</a>
+<a name="52"><span class="lineNum">      52 </span>            : calculate the progress along the path and the distance from it in p1</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : p1: PATHMSD REFERENCE=file.pdb  LAMBDA=500.0 NEIGH_STRIDE=4 NEIGH_SIZE=8</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=p1.sss,p1.zzz STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optional but</a>
+<a name="60"><span class="lineNum">      60 </span>            : recommended for performance) and states that the neighbor list will be calculated every 4</a>
+<a name="61"><span class="lineNum">      61 </span>            : steps and consider only the closest 8 member to the actual md snapshots.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : This input must be accompanied by a REFERENCE PDB file in which the positions of each of the frames are specified</a>
+<a name="64"><span class="lineNum">      64 </span>            : separated using either END or ENDMDL as shown below:</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \auxfile{file.pdb}</a>
+<a name="67"><span class="lineNum">      67 </span>            : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00</a>
+<a name="68"><span class="lineNum">      68 </span>            : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00</a>
+<a name="69"><span class="lineNum">      69 </span>            : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00</a>
+<a name="70"><span class="lineNum">      70 </span>            : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00</a>
+<a name="71"><span class="lineNum">      71 </span>            : END</a>
+<a name="72"><span class="lineNum">      72 </span>            : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00</a>
+<a name="73"><span class="lineNum">      73 </span>            : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00</a>
+<a name="74"><span class="lineNum">      74 </span>            : ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00</a>
+<a name="75"><span class="lineNum">      75 </span>            : ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00</a>
+<a name="76"><span class="lineNum">      76 </span>            : END</a>
+<a name="77"><span class="lineNum">      77 </span>            : ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00</a>
+<a name="78"><span class="lineNum">      78 </span>            : ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00</a>
+<a name="79"><span class="lineNum">      79 </span>            : ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00</a>
+<a name="81"><span class="lineNum">      81 </span>            : END</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endauxfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : \note</a>
+<a name="85"><span class="lineNum">      85 </span>            : The implementation of this collective variable and of \ref PROPERTYMAP</a>
+<a name="86"><span class="lineNum">      86 </span>            : is shared, as well as most input options.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : */</a>
+<a name="90"><span class="lineNum">      90 </span>            : //+ENDPLUMEDOC</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : class PathMSD : public PathMSDBase {</a>
+<a name="93"><span class="lineNum">      93 </span>            : public:</a>
+<a name="94"><span class="lineNum">      94 </span>            :   explicit PathMSD(const ActionOptions&amp;);</a>
+<a name="95"><span class="lineNum">      95 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      12532 : PLUMED_REGISTER_ACTION(PathMSD,&quot;PATHMSD&quot;)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         16 : void PathMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         16 :   PathMSDBase::registerKeywords(keys);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         16 :   componentsAreNotOptional(keys);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         32 :   keys.addOutputComponent(&quot;sss&quot;,&quot;default&quot;,&quot;the position on the path&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         32 :   keys.addOutputComponent(&quot;zzz&quot;,&quot;default&quot;,&quot;the distance from the path&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         16 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         14 : PathMSD::PathMSD(const ActionOptions&amp;ao):</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         14 :   Action(ao),PathMSDBase(ao)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         14 :   checkRead();</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         14 :   log&lt;&lt;&quot;  Bibliography &quot;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         28 :      &lt;&lt;plumed.cite(&quot;Branduardi, Gervasio, Parrinello J. Chem. Phys. 126, 054103 (2007)&quot;)</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         28 :      &lt;&lt;&quot;\n&quot;;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   // no need to read anything</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         28 :   addComponentWithDerivatives(&quot;sss&quot;); componentIsNotPeriodic(&quot;sss&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         28 :   addComponentWithDerivatives(&quot;zzz&quot;); componentIsNotPeriodic(&quot;zzz&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         14 :   requestAtoms(pdbv[0].getAtomNumbers());</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         14 :   double i=1.;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        634 :   for(unsigned it=0 ; it&lt;nframes ; ++it) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        620 :     std::vector&lt;double&gt; v; v.push_back(i);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        620 :     indexvec.push_back(v); i+=1.;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         14 : }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSDBase.cpp.func-sort-c.html b/coverage/colvar/PathMSDBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6438621a2a
--- /dev/null
+++ b/coverage/colvar/PathMSDBase.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSDBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSDBase.cpp<span style="font-size: 80%;"> (<a href="PathMSDBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">178</td>
+            <td class="headerCovTableEntry">182</td>
+            <td class="headerCovTableEntryHi">97.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PathMSDBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#43">_ZN4PLMD6colvar11PathMSDBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#138">_ZN4PLMD6colvar11PathMSDBaseD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#138">_ZN4PLMD6colvar11PathMSDBaseD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#43">_ZN4PLMD6colvar11PathMSDBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#138">_ZN4PLMD6colvar11PathMSDBaseD2Ev</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#67">_ZZN4PLMD6colvar11PathMSDBaseC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#32">_ZN4PLMD6colvar11PathMSDBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#141">_ZN4PLMD6colvar11PathMSDBase9calculateEv</a></td>
+              <td class="coverFnHi">11179</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSDBase.cpp.func.html b/coverage/colvar/PathMSDBase.cpp.func.html
new file mode 100644
index 0000000000..80edf28ea2
--- /dev/null
+++ b/coverage/colvar/PathMSDBase.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSDBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSDBase.cpp<span style="font-size: 80%;"> (<a href="PathMSDBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">178</td>
+            <td class="headerCovTableEntry">182</td>
+            <td class="headerCovTableEntryHi">97.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PathMSDBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#32">_ZN4PLMD6colvar11PathMSDBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#141">_ZN4PLMD6colvar11PathMSDBase9calculateEv</a></td>
+              <td class="coverFnHi">11179</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#43">_ZN4PLMD6colvar11PathMSDBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#43">_ZN4PLMD6colvar11PathMSDBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#138">_ZN4PLMD6colvar11PathMSDBaseD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#138">_ZN4PLMD6colvar11PathMSDBaseD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#138">_ZN4PLMD6colvar11PathMSDBaseD2Ev</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathMSDBase.cpp.gcov.html#67">_ZZN4PLMD6colvar11PathMSDBaseC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSDBase.cpp.gcov.html b/coverage/colvar/PathMSDBase.cpp.gcov.html
new file mode 100644
index 0000000000..352af30b3a
--- /dev/null
+++ b/coverage/colvar/PathMSDBase.cpp.gcov.html
@@ -0,0 +1,409 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSDBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSDBase.cpp<span style="font-size: 80%;"> (source / <a href="PathMSDBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">178</td>
+            <td class="headerCovTableEntry">182</td>
+            <td class="headerCovTableEntryHi">97.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathMSDBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace colvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         29 : void PathMSDBase::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         29 :   Colvar::registerKeywords(keys);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         58 :   keys.add(&quot;compulsory&quot;,&quot;LAMBDA&quot;,&quot;the lambda parameter is needed for smoothing, is in the units of plumed&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         58 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;the pdb is needed to provide the various milestones&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;,&quot;NEIGH_SIZE&quot;,&quot;size of the neighbor list&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;,&quot;NEIGH_STRIDE&quot;,&quot;how often the neighbor list needs to be calculated in time units&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;, &quot;EPSILON&quot;, &quot;(default=-1) the maximum distance between the close and the current structure, the positive value turn on the close structure method&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;, &quot;LOG_CLOSE&quot;, &quot;(default=0) value 1 enables logging regarding the close structure&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;, &quot;DEBUG_CLOSE&quot;, &quot;(default=0) value 1 enables extensive debugging info regarding the close structure, the simulation will run much slower&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         29 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         25 : PathMSDBase::PathMSDBase(const ActionOptions&amp;ao):</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         25 :   nopbc(false),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         25 :   neigh_size(-1),</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         25 :   neigh_stride(-1),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         25 :   epsilonClose(-1),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         25 :   debugClose(0),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         25 :   logClose(0),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         25 :   computeRefClose(false),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         25 :   nframes(0)</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : {</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         25 :   parse(&quot;LAMBDA&quot;,lambda);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         25 :   parse(&quot;NEIGH_SIZE&quot;,neigh_size);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         25 :   parse(&quot;NEIGH_STRIDE&quot;,neigh_stride);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         25 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         25 :   parse(&quot;EPSILON&quot;, epsilonClose);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         25 :   parse(&quot;LOG_CLOSE&quot;, logClose);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         25 :   parse(&quot;DEBUG_CLOSE&quot;, debugClose);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         25 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   // open the file</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         25 :   if (FILE* fp=this-&gt;fopen(reference.c_str(),&quot;r&quot;))</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   {</a>
+<a name="68"><span class="lineNum">      68 </span>            : // call fclose when exiting this block</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         25 :     auto deleter=[this](FILE* f) { this-&gt;fclose(f); };</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :     std::vector&lt;AtomNumber&gt; aaa;</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         25 :     log&lt;&lt;&quot;Opening reference file &quot;&lt;&lt;reference.c_str()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :     bool do_read=true;</a>
+<a name="75"><span class="lineNum">      75 </span>            :     unsigned nat=0;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       1107 :     while (do_read) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1107 :       PDB mypdb;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       1107 :       RMSD mymsd;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       2214 :       do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       1107 :       if(do_read) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1082 :         nframes++;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       1082 :         if(mypdb.getAtomNumbers().size()==0) error(&quot;number of atoms in a frame should be more than zero&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1082 :         if(nat==0) nat=mypdb.getAtomNumbers().size();</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1082 :         if(nat!=mypdb.getAtomNumbers().size()) error(&quot;frames should have the same number of atoms&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1082 :         if(aaa.empty()) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         25 :           aaa=mypdb.getAtomNumbers();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         25 :           log.printf(&quot;  found %zu atoms in input \n&quot;,aaa.size());</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         25 :           log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        346 :           for(unsigned i=0; i&lt;aaa.size(); ++i) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        321 :             if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        321 :             log.printf(&quot;%d &quot;,aaa[i].serial());</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :           }</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         25 :           log.printf(&quot;\n&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :         }</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       2164 :         if(aaa!=mypdb.getAtomNumbers()) error(&quot;frames should contain same atoms in same order&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1082 :         log&lt;&lt;&quot;Found PDB: &quot;&lt;&lt;nframes&lt;&lt;&quot; containing  &quot;&lt;&lt;mypdb.getAtomNumbers().size()&lt;&lt;&quot; atoms\n&quot;;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1082 :         pdbv.push_back(mypdb);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1082 :         derivs_s.resize(mypdb.getAtomNumbers().size());</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1082 :         derivs_z.resize(mypdb.getAtomNumbers().size());</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1082 :         mymsd.set(mypdb,&quot;OPTIMAL&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1082 :         msdv.push_back(mymsd); // the vector that stores the frames</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :       } else {break ;}</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1107 :     }</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         25 :     log&lt;&lt;&quot;Found TOTAL &quot;&lt;&lt;nframes&lt;&lt; &quot; PDB in the file &quot;&lt;&lt;reference.c_str()&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         25 :     if(nframes==0) error(&quot;at least one frame expected&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :     //set up rmsdRefClose, initialize it to the first structure loaded from reference file</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         25 :     rmsdPosClose.set(pdbv[0], &quot;OPTIMAL&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         25 :     firstPosClose = true;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         25 :   }</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         25 :   if(neigh_stride&gt;0 || neigh_size&gt;0) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         14 :     if(neigh_size&gt;int(nframes)) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :       log.printf(&quot; List size required ( %d ) is too large: resizing to the maximum number of frames required: %u  \n&quot;,neigh_size,nframes);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       neigh_size=nframes;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     }</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         14 :     log.printf(&quot;  Neighbor list enabled: \n&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         14 :     log.printf(&quot;                size   :  %d elements\n&quot;,neigh_size);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         14 :     log.printf(&quot;                stride :  %d timesteps \n&quot;,neigh_stride);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   } else {</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         11 :     log.printf(&quot;  Neighbor list NOT enabled \n&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         25 :   if (epsilonClose &gt; 0) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :     log.printf(&quot; Computing with the close structure, epsilon = %lf\n&quot;, epsilonClose);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 :     log &lt;&lt; &quot;  Bibliography &quot; &lt;&lt; plumed.cite(&quot;Pazurikova J, Krenek A, Spiwok V, Simkova M J. Chem. Phys. 146, 115101 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            :   else {</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         23 :     debugClose = 0;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         23 :     logClose = 0;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         25 :   if (debugClose)</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :     log.printf(&quot; Extensive debug info regarding close structure turned on\n&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         25 :   rotationRefClose.resize(nframes);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         25 :   savedIndices = std::vector&lt;unsigned&gt;(nframes);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         25 :   if(nopbc) log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         24 :   else      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         25 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         25 : PathMSDBase::~PathMSDBase() {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         75 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      11179 : void PathMSDBase::calculate() {</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      11179 :   if(neigh_size&gt;0 &amp;&amp; getExchangeStep()) error(&quot;Neighbor lists for this collective variable are not compatible with replica exchange, sorry for that!&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   //log.printf(&quot;NOW CALCULATE! \n&quot;);</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      11179 :   if(!nopbc) makeWhole();</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   // resize the list to full</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      11179 :   if(imgVec.empty()) { // this is the signal that means: recalculate all</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       7164 :     imgVec.resize(nframes);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     #pragma omp simd</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       7164 :     for(unsigned i=0; i&lt;nframes; i++) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">     300920 :       imgVec[i].property=indexvec[i];</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">     300920 :       imgVec[i].index=i;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : // THIS IS THE HEAVY PART (RMSD STUFF)</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      11179 :   unsigned stride=comm.Get_size();</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      11179 :   unsigned rank=comm.Get_rank();</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      11179 :   size_t nat=pdbv[0].size();</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      11179 :   plumed_assert(nat&gt;0);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      11179 :   plumed_assert(nframes&gt;0);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      11179 :   plumed_assert(imgVec.size()&gt;0);</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      11179 :   std::vector&lt;Tensor&gt; tmp_rotationRefClose(nframes);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      11179 :   if (epsilonClose &gt; 0) {</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     //compute rmsd between positions and close structure, save rotation matrix, drotation_drr01</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       1092 :     double posclose = rmsdPosClose.calc_Rot_DRotDRr01(getPositions(), rotationPosClose, drotationPosCloseDrr01, true);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     //if we compute for the first time or the existing close structure is too far from current structure</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1092 :     if (firstPosClose || (posclose &gt; epsilonClose)) {</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :       //set the current structure as close one for a few next steps</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         16 :       if (logClose)</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         16 :         log &lt;&lt; &quot;PLUMED_CLOSE: new close structure, rmsd pos close &quot; &lt;&lt; posclose &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         16 :       rmsdPosClose.clear();</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         16 :       rmsdPosClose.setReference(getPositions());</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :       //as this is a new close structure, we need to save the rotation matrices fitted to the reference structures</a>
+<a name="183"><span class="lineNum">     183 </span>            :       // and we need to accurately recalculate for all reference structures</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         16 :       computeRefClose = true;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         16 :       imgVec.resize(nframes);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        688 :       for(unsigned i=0; i&lt;nframes; i++) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        672 :         imgVec[i].property=indexvec[i];</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        672 :         imgVec[i].index=i;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :       }</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         16 :       firstPosClose = false;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         16 :     }</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     else {</a>
+<a name="193"><span class="lineNum">     193 </span>            :       //the current structure is pretty close to the close structure, so we use saved rotation matrices to decrease the complexity of rmsd comuptation</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1076 :       if (debugClose)</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1076 :         log &lt;&lt; &quot;PLUMED-CLOSE: old close structure, rmsd pos close &quot; &lt;&lt; posclose &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       1076 :       computeRefClose = false;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      11179 :   std::vector&lt;double&gt; tmp_distances(imgVec.size(),0.0);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   std::vector&lt;Vector&gt; tmp_derivs;</a>
+<a name="202"><span class="lineNum">     202 </span>            : // this array is a merge of all tmp_derivs, so as to allow a single comm.Sum below</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      11179 :   std::vector&lt;Vector&gt; tmp_derivs2(imgVec.size()*nat);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : // if imgVec.size() is less than nframes, it means that only some msd will be calculated</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      11179 :   if (epsilonClose &gt; 0) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       1092 :     if (computeRefClose) {</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :       //recompute rotation matrices accurately</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        688 :       for(unsigned i=rank; i&lt;imgVec.size(); i+=stride) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        672 :         tmp_distances[i] = msdv[imgVec[i].index].calc_Rot(getPositions(), tmp_derivs, tmp_rotationRefClose[imgVec[i].index], true);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        672 :         plumed_assert(tmp_derivs.size()==nat);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :         #pragma omp simd</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       8736 :         for(unsigned j=0; j&lt;nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :       }</a>
+<a name="215"><span class="lineNum">     215 </span>            :     }</a>
+<a name="216"><span class="lineNum">     216 </span>            :     else {</a>
+<a name="217"><span class="lineNum">     217 </span>            :       //approximate distance with saved rotation matrices</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      46268 :       for(unsigned i=rank; i&lt;imgVec.size(); i+=stride) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      45192 :         tmp_distances[i] = msdv[imgVec[i].index].calculateWithCloseStructure(getPositions(), tmp_derivs, rotationPosClose, rotationRefClose[imgVec[i].index], drotationPosCloseDrr01, true);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      45192 :         plumed_assert(tmp_derivs.size()==nat);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :         #pragma omp simd</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">     587496 :         for(unsigned j=0; j&lt;nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      45192 :         if (debugClose) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      45192 :           double withclose = tmp_distances[i];</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      45192 :           RMSD opt;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      45192 :           opt.setType(&quot;OPTIMAL&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      90384 :           opt.setReference(msdv[imgVec[i].index].getReference());</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :           std::vector&lt;Vector&gt; ders;</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      45192 :           double withoutclose = opt.calculate(getPositions(), ders, true);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      45192 :           float difference = std::abs(withoutclose-withclose);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      45192 :           log&lt;&lt;&quot;PLUMED-CLOSE: difference original &quot;&lt;&lt;withoutclose;</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      45192 :           log&lt;&lt;&quot; - with close &quot;&lt;&lt;withclose&lt;&lt;&quot; = &quot;&lt;&lt;difference&lt;&lt;&quot;, step &quot;&lt;&lt;getStep()&lt;&lt;&quot;, i &quot;&lt;&lt;i&lt;&lt;&quot; imgVec[i].index &quot;&lt;&lt;imgVec[i].index&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      45192 :         }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :       }</a>
+<a name="235"><span class="lineNum">     235 </span>            :     }</a>
+<a name="236"><span class="lineNum">     236 </span>            :   }</a>
+<a name="237"><span class="lineNum">     237 </span>            :   else {</a>
+<a name="238"><span class="lineNum">     238 </span>            :     // store temporary local results</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">     297781 :     for(unsigned i=rank; i&lt;imgVec.size(); i+=stride) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">     287694 :       tmp_distances[i]=msdv[imgVec[i].index].calculate(getPositions(),tmp_derivs,true);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">     287694 :       plumed_assert(tmp_derivs.size()==nat);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :       #pragma omp simd</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">    3729822 :       for(unsigned j=0; j&lt;nat; j++) tmp_derivs2[i*nat+j]=tmp_derivs[j];</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :     }</a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : // reduce over all processors</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">      11179 :   comm.Sum(tmp_distances);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      11179 :   comm.Sum(tmp_derivs2);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      11179 :   if (epsilonClose &gt; 0 &amp;&amp; computeRefClose) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         16 :     comm.Sum(tmp_rotationRefClose);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        688 :     for (unsigned i=0; i&lt;nframes; i++) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        672 :       rotationRefClose[i] = tmp_rotationRefClose[i];</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :     }</a>
+<a name="255"><span class="lineNum">     255 </span>            :   }</a>
+<a name="256"><span class="lineNum">     256 </span>            : // assign imgVec[i].distance and imgVec[i].distder</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">     482329 :   for(size_t i=0; i&lt;imgVec.size(); i++) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">     471150 :     imgVec[i].distance=tmp_distances[i];</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">     471150 :     imgVec[i].distder.assign(&amp;tmp_derivs2[i*nat],nat+&amp;tmp_derivs2[i*nat]);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : // END OF THE HEAVY PART</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   std::vector&lt;Value*&gt; val_s_path;</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      11179 :   if(labels.size()&gt;0) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">      18018 :     for(unsigned i=0; i&lt;labels.size(); i++) { val_s_path.push_back(getPntrToComponent(labels[i].c_str()));}</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   } else {</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       5173 :     val_s_path.push_back(getPntrToComponent(&quot;sss&quot;));</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   }</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">      22358 :   Value* val_z_path=getPntrToComponent(&quot;zzz&quot;);</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">      28364 :   std::vector&lt;double&gt; s_path(val_s_path.size()); for(unsigned i=0; i&lt;s_path.size(); i++)s_path[i]=0.;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :   double partition=0.;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   double tmp;</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   // clean vector</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">      11179 :   Tools::set_to_zero(derivs_z);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">     482329 :   for(auto &amp; it : imgVec) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">     471150 :     it.similarity=std::exp(-lambda*(it.distance));</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">    1194552 :     for(unsigned i=0; i&lt;s_path.size(); i++) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">     723402 :       s_path[i]+=(it.property[i])*it.similarity;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     }</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">     471150 :     partition+=it.similarity;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">      28364 :   for(unsigned i=0; i&lt;s_path.size(); i++) { s_path[i]/=partition;  val_s_path[i]-&gt;set(s_path[i]) ;}</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">      11179 :   val_z_path-&gt;set(-(1./lambda)*std::log(partition));</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      28364 :   for(unsigned j=0; j&lt;s_path.size(); j++) {</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :     // clean up</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">      17185 :     Tools::set_to_zero(derivs_s);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :     // do the derivative</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">     740587 :     for(const auto &amp; it : imgVec) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     723402 :       double expval=it.similarity;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">     723402 :       tmp=lambda*expval*(s_path[j]-it.property[j])/partition;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :       #pragma omp simd</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">   10117428 :       for(unsigned i=0; i&lt; derivs_s.size(); i++) { derivs_s[i]+=tmp*it.distder[i] ;}</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     723402 :       if(j==0) {</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :         #pragma omp simd</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">    6585900 :         for(unsigned i=0; i&lt; derivs_z.size(); i++) { derivs_z[i]+=it.distder[i]*expval/partition;}</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :       }</a>
+<a name="301"><span class="lineNum">     301 </span>            :     }</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">     240386 :     for(unsigned i=0; i&lt; derivs_s.size(); i++) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">     223201 :       setAtomsDerivatives (val_s_path[j],i,derivs_s[i]);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     223201 :       if(j==0) {setAtomsDerivatives (val_z_path,i,derivs_z[i]);}</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :     }</a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">      28364 :   for(unsigned i=0; i&lt;val_s_path.size(); ++i) setBoxDerivativesNoPbc(val_s_path[i]);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">      11179 :   setBoxDerivativesNoPbc(val_z_path);</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   //</a>
+<a name="310"><span class="lineNum">     310 </span>            :   //  here set next round neighbors</a>
+<a name="311"><span class="lineNum">     311 </span>            :   //</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">      11179 :   if (neigh_size&gt;0) {</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :     //if( int(getStep())%int(neigh_stride/getTimeStep())==0 ){</a>
+<a name="314"><span class="lineNum">     314 </span>            :     // enforce consistency: the stride is in time steps</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       7153 :     if( int(getStep())%int(neigh_stride)==0 ) {</span></a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :       // next round do it all:empty the vector</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       7153 :       imgVec.clear();</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :     }</a>
+<a name="320"><span class="lineNum">     320 </span>            :     // time to analyze the results:</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       7153 :     if(imgVec.size()==nframes) {</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :       //sort by msd</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :       sort(imgVec.begin(), imgVec.end(), imgOrderByDist());</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :       //resize</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :       imgVec.resize(neigh_size);</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span>            :   }</a>
+<a name="328"><span class="lineNum">     328 </span>            :   //log.printf(&quot;CALCULATION DONE! \n&quot;);</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">      11179 : }</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            : }</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSDBase.h.func-sort-c.html b/coverage/colvar/PathMSDBase.h.func-sort-c.html
new file mode 100644
index 0000000000..01b619c4ac
--- /dev/null
+++ b/coverage/colvar/PathMSDBase.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSDBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSDBase.h<span style="font-size: 80%;"> (<a href="PathMSDBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PathMSDBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSDBase.h.func.html b/coverage/colvar/PathMSDBase.h.func.html
new file mode 100644
index 0000000000..f4c98a9964
--- /dev/null
+++ b/coverage/colvar/PathMSDBase.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSDBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSDBase.h<span style="font-size: 80%;"> (<a href="PathMSDBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PathMSDBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PathMSDBase.h.gcov.html b/coverage/colvar/PathMSDBase.h.gcov.html
new file mode 100644
index 0000000000..0c1044e3f8
--- /dev/null
+++ b/coverage/colvar/PathMSDBase.h.gcov.html
@@ -0,0 +1,177 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PathMSDBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PathMSDBase.h<span style="font-size: 80%;"> (source / <a href="PathMSDBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_colvar_PathMSDBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_colvar_PathMSDBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace colvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class PathMSDBase : public Colvar {</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// this class is a general container for path stuff</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     300920 :   class ImagePath {</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   public:</a>
+<a name="38"><span class="lineNum">      38 </span>            :     // cardinal indexing: needed to map over msd</a>
+<a name="39"><span class="lineNum">      39 </span>            :     unsigned index;</a>
+<a name="40"><span class="lineNum">      40 </span>            :     // spiwok indexing</a>
+<a name="41"><span class="lineNum">      41 </span>            :     std::vector&lt;double&gt; property;</a>
+<a name="42"><span class="lineNum">      42 </span>            :     // distance</a>
+<a name="43"><span class="lineNum">      43 </span>            :     double distance;</a>
+<a name="44"><span class="lineNum">      44 </span>            :     // similarity (exp - lambda distance) or other</a>
+<a name="45"><span class="lineNum">      45 </span>            :     double similarity;</a>
+<a name="46"><span class="lineNum">      46 </span>            :     // derivatives of the distance</a>
+<a name="47"><span class="lineNum">      47 </span>            :     std::vector&lt;Vector&gt; distder;</a>
+<a name="48"><span class="lineNum">      48 </span>            :     // here one can add a pointer to a value (hypothetically providing a distance from a point)</a>
+<a name="49"><span class="lineNum">      49 </span>            :   };</a>
+<a name="50"><span class="lineNum">      50 </span>            :   struct imgOrderByDist {</a>
+<a name="51"><span class="lineNum">      51 </span>            :     bool operator ()(ImagePath const&amp; a, ImagePath const&amp; b) {</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :       return (a).distance &lt; (b).distance;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :     }</a>
+<a name="54"><span class="lineNum">      54 </span>            :   };</a>
+<a name="55"><span class="lineNum">      55 </span>            :   struct imgOrderBySimilarity {</a>
+<a name="56"><span class="lineNum">      56 </span>            :     bool operator ()(ImagePath const&amp; a, ImagePath const&amp; b) {</a>
+<a name="57"><span class="lineNum">      57 </span>            :       return (a).similarity &gt; (b).similarity;</a>
+<a name="58"><span class="lineNum">      58 </span>            :     }</a>
+<a name="59"><span class="lineNum">      59 </span>            :   };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool nopbc;</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            :   double lambda;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   int neigh_size;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   int neigh_stride;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;RMSD&gt; msdv;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::string reference;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;Vector&gt; derivs_s;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;Vector&gt; derivs_z;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector &lt;ImagePath&gt; imgVec; // this can be used for doing neighlist</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :   //variables used for the close structure method, i is the number of reference structures</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double epsilonClose; //the maximal distance between the close and the current structure before reassignment</a>
+<a name="74"><span class="lineNum">      74 </span>            :   int debugClose; //turns on debug mode</a>
+<a name="75"><span class="lineNum">      75 </span>            :   int logClose; //turns on logging</a>
+<a name="76"><span class="lineNum">      76 </span>            :   RMSD rmsdPosClose; //rmsd between the current and the close structure</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool firstPosClose; //flag indicating the first time we need to calculate the distance between the close and the current structure</a>
+<a name="78"><span class="lineNum">      78 </span>            :   bool computeRefClose; //flag indicating necessity to recompute accurately all distances and rotation matrices between the close structure and reference str</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;Tensor&gt; rotationRefClose; //Tensor[i] saved rotation matrices between the close structure and reference structures</a>
+<a name="80"><span class="lineNum">      80 </span>            :   Tensor rotationPosClose; //rotation matrix between the close and the current structure</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; drotationPosCloseDrr01; //Tensor[3][3]; //derivation of the rotation matrix w.r.t rr01, necessary for calculation of derivations</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;unsigned&gt; savedIndices; //saved indices of imgVec from previous steps, used for recalculating after neighbourlist update</a>
+<a name="83"><span class="lineNum">      83 </span>            : protected:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;PDB&gt; pdbv;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;std::string&gt; labels;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; indexvec; // use double to allow isomaps</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned nframes;</a>
+<a name="88"><span class="lineNum">      88 </span>            : public:</a>
+<a name="89"><span class="lineNum">      89 </span>            :   explicit PathMSDBase(const ActionOptions&amp;);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   ~PathMSDBase();</a>
+<a name="91"><span class="lineNum">      91 </span>            : // active methods:</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void calculate() override;</a>
+<a name="93"><span class="lineNum">      93 </span>            : //  virtual void prepare();</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="95"><span class="lineNum">      95 </span>            : };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : #endif</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Position.cpp.func-sort-c.html b/coverage/colvar/Position.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3dd188a22a
--- /dev/null
+++ b/coverage/colvar/Position.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Position.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Position.cpp<span style="font-size: 80%;"> (<a href="Position.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Position.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#97">_ZN4PLMD6colvar8PositionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#82">_ZN4PLMD6colvar12_GLOBAL__N_120PositionRegisterMe846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#97">_ZN4PLMD6colvar8PositionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#84">_ZN4PLMD6colvar8Position16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">89</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#82">_ZN4PLMD6colvar12_GLOBAL__N_120PositionRegisterMe84C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#82">_ZN4PLMD6colvar12_GLOBAL__N_120PositionRegisterMe84D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#132">_ZN4PLMD6colvar8Position9calculateEv</a></td>
+              <td class="coverFnHi">8037</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Position.cpp.func.html b/coverage/colvar/Position.cpp.func.html
new file mode 100644
index 0000000000..795bc4b4c5
--- /dev/null
+++ b/coverage/colvar/Position.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Position.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Position.cpp<span style="font-size: 80%;"> (<a href="Position.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Position.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#82">_ZN4PLMD6colvar12_GLOBAL__N_120PositionRegisterMe846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#82">_ZN4PLMD6colvar12_GLOBAL__N_120PositionRegisterMe84C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#82">_ZN4PLMD6colvar12_GLOBAL__N_120PositionRegisterMe84D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#84">_ZN4PLMD6colvar8Position16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">89</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#132">_ZN4PLMD6colvar8Position9calculateEv</a></td>
+              <td class="coverFnHi">8037</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#97">_ZN4PLMD6colvar8PositionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Position.cpp.gcov.html#97">_ZN4PLMD6colvar8PositionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Position.cpp.gcov.html b/coverage/colvar/Position.cpp.gcov.html
new file mode 100644
index 0000000000..fb8f48879a
--- /dev/null
+++ b/coverage/colvar/Position.cpp.gcov.html
@@ -0,0 +1,253 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Position.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Position.cpp<span style="font-size: 80%;"> (source / <a href="Position.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR POSITION</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate the components of the position of an atom.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Notice that single components will not have the proper periodicity!</a>
+<a name="34"><span class="lineNum">      34 </span>            : If you need the values to be consistent through PBC you should use SCALED_COMPONENTS,</a>
+<a name="35"><span class="lineNum">      35 </span>            : which defines values that by construction are in the -0.5,0.5 domain. This is</a>
+<a name="36"><span class="lineNum">      36 </span>            : similar to the equivalent flag for \ref DISTANCE.</a>
+<a name="37"><span class="lineNum">      37 </span>            : Also notice that by default the minimal image distance from the</a>
+<a name="38"><span class="lineNum">      38 </span>            : origin is considered (can be changed with NOPBC).</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \attention</a>
+<a name="41"><span class="lineNum">      41 </span>            : This variable should be used with extreme care since it allows to easily go into troubles. See comments below.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : This variable can be safely used only if</a>
+<a name="44"><span class="lineNum">      44 </span>            : Hamiltonian is not invariant for translation (i.e. there are other absolute positions which are biased, e.g. by position restraints)</a>
+<a name="45"><span class="lineNum">      45 </span>            : and cell size and shapes are fixed through the simulation.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : If you are not in this situation and still want to use the absolute position of an atom you should first fix the reference frame.</a>
+<a name="48"><span class="lineNum">      48 </span>            : This can be done e.g. using \ref FIT_TO_TEMPLATE.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \par Examples</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : # align to a template</a>
+<a name="54"><span class="lineNum">      54 </span>            : FIT_TO_TEMPLATE REFERENCE=ref.pdb</a>
+<a name="55"><span class="lineNum">      55 </span>            : p: POSITION ATOM=3</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=p.x,p.y,p.z</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The reference position is specified in a pdb file like the one shown below</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \auxfile{ref.pdb}</a>
+<a name="62"><span class="lineNum">      62 </span>            : ATOM      3  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="63"><span class="lineNum">      63 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="64"><span class="lineNum">      64 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="65"><span class="lineNum">      65 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="66"><span class="lineNum">      66 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="67"><span class="lineNum">      67 </span>            : END</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endauxfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : */</a>
+<a name="71"><span class="lineNum">      71 </span>            : //+ENDPLUMEDOC</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : class Position : public Colvar {</a>
+<a name="74"><span class="lineNum">      74 </span>            :   bool scaled_components;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool pbc;</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="79"><span class="lineNum">      79 </span>            :   explicit Position(const ActionOptions&amp;);</a>
+<a name="80"><span class="lineNum">      80 </span>            : // active methods:</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void calculate() override;</a>
+<a name="82"><span class="lineNum">      82 </span>            : };</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      12677 : PLUMED_REGISTER_ACTION(Position,&quot;POSITION&quot;)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         89 : void Position::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         89 :   Colvar::registerKeywords( keys );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         89 :   componentsAreNotOptional(keys);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        178 :   keys.add(&quot;atoms&quot;,&quot;ATOM&quot;,&quot;the atom number&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        178 :   keys.addFlag(&quot;SCALED_COMPONENTS&quot;,false,&quot;calculate the a, b and c scaled components of the position separately and store them as label.a, label.b and label.c&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        178 :   keys.addOutputComponent(&quot;x&quot;,&quot;default&quot;,&quot;the x-component of the atom position&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        178 :   keys.addOutputComponent(&quot;y&quot;,&quot;default&quot;,&quot;the y-component of the atom position&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        178 :   keys.addOutputComponent(&quot;z&quot;,&quot;default&quot;,&quot;the z-component of the atom position&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        178 :   keys.addOutputComponent(&quot;a&quot;,&quot;SCALED_COMPONENTS&quot;,&quot;the normalized projection on the first lattice vector of the atom position&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        178 :   keys.addOutputComponent(&quot;b&quot;,&quot;SCALED_COMPONENTS&quot;,&quot;the normalized projection on the second lattice vector of the atom position&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        178 :   keys.addOutputComponent(&quot;c&quot;,&quot;SCALED_COMPONENTS&quot;,&quot;the normalized projection on the third lattice vector of the atom position&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         89 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         87 : Position::Position(const ActionOptions&amp;ao):</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         87 :   scaled_components(false),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         87 :   pbc(true)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        174 :   parseAtomList(&quot;ATOM&quot;,atoms);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         87 :   if(atoms.size()!=1)</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :     error(&quot;Number of specified atoms should be 1&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         86 :   parseFlag(&quot;SCALED_COMPONENTS&quot;,scaled_components);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         86 :   bool nopbc=!pbc;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         86 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         86 :   pbc=!nopbc;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         86 :   checkRead();</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         86 :   log.printf(&quot;  for atom %d\n&quot;,atoms[0].serial());</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         86 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          4 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         86 :   if(scaled_components) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         12 :     addComponentWithDerivatives(&quot;a&quot;); componentIsPeriodic(&quot;a&quot;,&quot;-0.5&quot;,&quot;+0.5&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         12 :     addComponentWithDerivatives(&quot;b&quot;); componentIsPeriodic(&quot;b&quot;,&quot;-0.5&quot;,&quot;+0.5&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         12 :     addComponentWithDerivatives(&quot;c&quot;); componentIsPeriodic(&quot;c&quot;,&quot;-0.5&quot;,&quot;+0.5&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   } else {</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        164 :     addComponentWithDerivatives(&quot;x&quot;); componentIsNotPeriodic(&quot;x&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        164 :     addComponentWithDerivatives(&quot;y&quot;); componentIsNotPeriodic(&quot;y&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        165 :     addComponentWithDerivatives(&quot;z&quot;); componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         82 :     log&lt;&lt;&quot;  WARNING: components will not have the proper periodicity - see manual\n&quot;;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         86 :   requestAtoms(atoms);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         88 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : // calculator</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       8037 : void Position::calculate() {</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       8037 :   Vector distance;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       8037 :   if(pbc) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       7992 :     distance=pbcDistance(Vector(0.0,0.0,0.0),getPosition(0));</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   } else {</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         45 :     distance=delta(Vector(0.0,0.0,0.0),getPosition(0));</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       8037 :   if(scaled_components) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         41 :     Value* valuea=getPntrToComponent(&quot;a&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         41 :     Value* valueb=getPntrToComponent(&quot;b&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         82 :     Value* valuec=getPntrToComponent(&quot;c&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         41 :     Vector d=getPbc().realToScaled(distance);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         41 :     setAtomsDerivatives (valuea,0,matmul(getPbc().getInvBox(),Vector(+1,0,0)));</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         41 :     valuea-&gt;set(Tools::pbc(d[0]));</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         41 :     setAtomsDerivatives (valueb,0,matmul(getPbc().getInvBox(),Vector(0,+1,0)));</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         41 :     valueb-&gt;set(Tools::pbc(d[1]));</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         41 :     setAtomsDerivatives (valuec,0,matmul(getPbc().getInvBox(),Vector(0,0,+1)));</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         41 :     valuec-&gt;set(Tools::pbc(d[2]));</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   } else {</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       7996 :     Value* valuex=getPntrToComponent(&quot;x&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       7996 :     Value* valuey=getPntrToComponent(&quot;y&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       7996 :     Value* valuez=getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       7996 :     setAtomsDerivatives (valuex,0,Vector(+1,0,0));</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       7996 :     setBoxDerivatives   (valuex,Tensor(distance,Vector(-1,0,0)));</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       7996 :     valuex-&gt;set(distance[0]);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       7996 :     setAtomsDerivatives (valuey,0,Vector(0,+1,0));</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       7996 :     setBoxDerivatives   (valuey,Tensor(distance,Vector(0,-1,0)));</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       7996 :     valuey-&gt;set(distance[1]);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       7996 :     setAtomsDerivatives (valuez,0,Vector(0,0,+1));</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       7996 :     setBoxDerivatives   (valuez,Tensor(distance,Vector(0,0,-1)));</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       7996 :     valuez-&gt;set(distance[2]);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       8037 : }</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ProjectionOnAxis.cpp.func-sort-c.html b/coverage/colvar/ProjectionOnAxis.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4d33d56940
--- /dev/null
+++ b/coverage/colvar/ProjectionOnAxis.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ProjectionOnAxis.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ProjectionOnAxis.cpp<span style="font-size: 80%;"> (<a href="ProjectionOnAxis.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ProjectionOnAxis.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#87">_ZN4PLMD6colvar16ProjectionOnAxisC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#77">_ZN4PLMD6colvar12_GLOBAL__N_128ProjectionOnAxisRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#87">_ZN4PLMD6colvar16ProjectionOnAxisC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#79">_ZN4PLMD6colvar16ProjectionOnAxis16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#116">_ZN4PLMD6colvar16ProjectionOnAxis9calculateEv</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#77">_ZN4PLMD6colvar12_GLOBAL__N_128ProjectionOnAxisRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#77">_ZN4PLMD6colvar12_GLOBAL__N_128ProjectionOnAxisRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ProjectionOnAxis.cpp.func.html b/coverage/colvar/ProjectionOnAxis.cpp.func.html
new file mode 100644
index 0000000000..43f041cc63
--- /dev/null
+++ b/coverage/colvar/ProjectionOnAxis.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ProjectionOnAxis.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ProjectionOnAxis.cpp<span style="font-size: 80%;"> (<a href="ProjectionOnAxis.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ProjectionOnAxis.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#77">_ZN4PLMD6colvar12_GLOBAL__N_128ProjectionOnAxisRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#77">_ZN4PLMD6colvar12_GLOBAL__N_128ProjectionOnAxisRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#77">_ZN4PLMD6colvar12_GLOBAL__N_128ProjectionOnAxisRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#79">_ZN4PLMD6colvar16ProjectionOnAxis16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#116">_ZN4PLMD6colvar16ProjectionOnAxis9calculateEv</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#87">_ZN4PLMD6colvar16ProjectionOnAxisC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectionOnAxis.cpp.gcov.html#87">_ZN4PLMD6colvar16ProjectionOnAxisC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/ProjectionOnAxis.cpp.gcov.html b/coverage/colvar/ProjectionOnAxis.cpp.gcov.html
new file mode 100644
index 0000000000..873f025956
--- /dev/null
+++ b/coverage/colvar/ProjectionOnAxis.cpp.gcov.html
@@ -0,0 +1,245 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/ProjectionOnAxis.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - ProjectionOnAxis.cpp<span style="font-size: 80%;"> (source / <a href="ProjectionOnAxis.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Angle.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR PROJECTION_ON_AXIS</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate a position based on the projection along and extension from a defined axis.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This variable takes 3 input atoms or pseudoatoms, using the two AXIS_ATOMS to define a linear vector.</a>
+<a name="34"><span class="lineNum">      34 </span>            : The position of the ATOM is then calculated relative to this vector, with two output components.</a>
+<a name="35"><span class="lineNum">      35 </span>            : The projection on the axis (proj) is the distance along the axis from the ATOM to the origin.</a>
+<a name="36"><span class="lineNum">      36 </span>            : The extension (ext) is the orthogonal distance between the ATOM and the axis.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : This command tells plumed to define an axis, by calculating a vector that passes through atom 1 and atom 2.</a>
+<a name="41"><span class="lineNum">      41 </span>            : The position of atom 3 as a projection along this vector is calculated and printed to COLVAR1.</a>
+<a name="42"><span class="lineNum">      42 </span>            : At the same time, the perpendicular distance of atom 3 from the axis, the extension, is printed to COLVAR2.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : poa: PROJECTION_ON_AXIS AXIS_ATOMS=1,2 ATOM=3</a>
+<a name="46"><span class="lineNum">      46 </span>            : PRINT ARG=poa.proj FILE=COLVAR1</a>
+<a name="47"><span class="lineNum">      47 </span>            : PRINT ARG=poa.ext FILE=COLVAR2</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : A particular application of this variable could be to study the motion of a ligand relative to its binding pocket on a protein.</a>
+<a name="51"><span class="lineNum">      51 </span>            : In this set of commands, the anchor points a1 and a2 are defined using example atom numbers within the protein.</a>
+<a name="52"><span class="lineNum">      52 </span>            : As a2 is attempting to be as close as possible to the center of the binding pocket, a COM is used when there are no suitable protein atoms.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Similarly, a COM is used to define the position of the ligand in lig1.</a>
+<a name="54"><span class="lineNum">      54 </span>            : The calculated projection of lig1 along the axis defined between a1 and a2 is printed to COLVAR1.</a>
+<a name="55"><span class="lineNum">      55 </span>            : The calculated perpendicular extension of lig1 from the axis defined between a1 and a2 is printed to COLVAR2.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : a1: GROUP ATOMS=3754            # Anchor point 1</a>
+<a name="59"><span class="lineNum">      59 </span>            : a2: COM ATOMS=3019,4329,4744    # Anchor point 2</a>
+<a name="60"><span class="lineNum">      60 </span>            : lig1: COM ATOMS=5147-5190       # Ligand</a>
+<a name="61"><span class="lineNum">      61 </span>            : pp: PROJECTION_ON_AXIS AXIS_ATOMS=a1,a2 ATOM=lig1</a>
+<a name="62"><span class="lineNum">      62 </span>            : PRINT ARG=pp.proj FILE=COLVAR1</a>
+<a name="63"><span class="lineNum">      63 </span>            : PRINT ARG=pp.ext FILE=COLVAR2</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : //+ENDPLUMEDOC</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : class ProjectionOnAxis : public Colvar {</a>
+<a name="70"><span class="lineNum">      70 </span>            :   bool pbc;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   explicit ProjectionOnAxis(const ActionOptions&amp;);</a>
+<a name="74"><span class="lineNum">      74 </span>            : // Active methods:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   virtual void calculate();</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="77"><span class="lineNum">      77 </span>            : };</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(ProjectionOnAxis,&quot;PROJECTION_ON_AXIS&quot;)</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          3 : void ProjectionOnAxis::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          3 :   Colvar::registerKeywords(keys);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;,&quot;AXIS_ATOMS&quot;,&quot;The atoms that define the direction of the axis of interest&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;,&quot;ATOM&quot;,&quot;The atom whose position we want to project on the axis of interest&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;proj&quot;,&quot;COMPONENTS&quot;,&quot;The value of the projection along the axis&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;ext&quot;,&quot;COMPONENTS&quot;,&quot;The value of the extension from the axis&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 : ProjectionOnAxis::ProjectionOnAxis(const ActionOptions&amp;ao):</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          1 :   pbc(true)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::vector&lt;AtomNumber&gt; axis_atoms;</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   parseAtomList(&quot;AXIS_ATOMS&quot;,axis_atoms);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          1 :   if( axis_atoms.size()!=2 ) error(&quot;There should only be two atoms specified to AXIS_ATOMS keyword&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   parseAtomList(&quot;ATOM&quot;,atom);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          1 :   if( atom.size()!=1 ) error(&quot;There should only be one atom specified to ATOM keyword&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          1 :   log.printf(&quot;  calculating projection of vector connecting atom %d and atom %d on vector connecting atom %d and atom %d \n&quot;,</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :              axis_atoms[0].serial(), atom[0].serial(), axis_atoms[0].serial(), axis_atoms[1].serial() );</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :   bool nopbc=!pbc;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          1 :   pbc=!nopbc;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          1 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   else    log.printf(&quot;  not using periodic boundary conditions\n&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Add values to store data</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   addComponentWithDerivatives(&quot;proj&quot;); componentIsNotPeriodic(&quot;proj&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :   addComponentWithDerivatives(&quot;ext&quot;); componentIsNotPeriodic(&quot;ext&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   // Get all the atom positions</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          1 :   axis_atoms.push_back( atom[0] );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 :   requestAtoms(axis_atoms);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          1 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : // Calculator</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         25 : void ProjectionOnAxis::calculate() {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         25 :   Vector rik, rjk;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         25 :   if( pbc ) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         25 :     rik = pbcDistance( getPosition(2), getPosition(0) );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         25 :     rjk = pbcDistance( getPosition(2), getPosition(1) );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   } else {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     rik = delta( getPosition(2), getPosition(0) );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     rjk = delta( getPosition(2), getPosition(1) );</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         25 :   Vector rij = delta( rik, rjk ); double dij = rij.modulo();</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         25 :   Vector nij = (1.0/dij)*rij; Tensor dij_a1;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   // Derivative of director connecting atom1 - atom2 wrt the position of atom 1</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         25 :   dij_a1(0,0) = ( -(nij[1]*nij[1]+nij[2]*nij[2])/dij );   // dx/dx</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         25 :   dij_a1(0,1) = (  nij[0]*nij[1]/dij );                   // dx/dy</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         25 :   dij_a1(0,2) = (  nij[0]*nij[2]/dij );                   // dx/dz</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         25 :   dij_a1(1,0) = (  nij[1]*nij[0]/dij );                   // dy/dx</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         25 :   dij_a1(1,1) = ( -(nij[0]*nij[0]+nij[2]*nij[2])/dij );   // dy/dy</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         25 :   dij_a1(1,2) = (  nij[1]*nij[2]/dij );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         25 :   dij_a1(2,0) = (  nij[2]*nij[0]/dij );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         25 :   dij_a1(2,1) = (  nij[2]*nij[1]/dij );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         25 :   dij_a1(2,2) = ( -(nij[1]*nij[1]+nij[0]*nij[0])/dij );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // Calculate dot product and derivatives</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         25 :   double d = dotProduct( -rik, nij );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         25 :   Vector dd1 = matmul(-rik, dij_a1) - nij;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         25 :   Vector dd2 = matmul(rik, dij_a1);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         25 :   Vector dd3 = nij;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         50 :   Value* pval=getPntrToComponent(&quot;proj&quot;); pval-&gt;set( d );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         25 :   setAtomsDerivatives( pval, 0, dd1 );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         25 :   setAtomsDerivatives( pval, 1, dd2 );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         25 :   setAtomsDerivatives( pval, 2, dd3 );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         25 :   setBoxDerivatives( pval, -Tensor( rik, dd1 ) - Tensor( rjk, dd2 ) );</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Calculate derivatives of perpendicular distance from axis</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         25 :   double c = std::sqrt( rik.modulo2() - d*d ); double invc = (1.0/c);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   // Calculate derivatives of the other thing</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         25 :   Vector der1 = invc*(rik - d*dd1);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         25 :   Vector der2 = invc*(-d*dd2);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         25 :   Vector der3 = invc*(-rik - d*dd3);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         50 :   Value* cval=getPntrToComponent(&quot;ext&quot;); cval-&gt;set( c );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         25 :   setAtomsDerivatives( cval, 0, der1 );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         25 :   setAtomsDerivatives( cval, 1, der2 );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         25 :   setAtomsDerivatives( cval, 2, der3 );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         25 :   setBoxDerivatives( cval, -Tensor( rik, der1 ) - Tensor( rjk, der2 ) );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         25 : }</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PropertyMap.cpp.func-sort-c.html b/coverage/colvar/PropertyMap.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5970a8ee71
--- /dev/null
+++ b/coverage/colvar/PropertyMap.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PropertyMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PropertyMap.cpp<span style="font-size: 80%;"> (<a href="PropertyMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PropertyMap.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#104">_ZN4PLMD6colvar11PropertyMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#104">_ZN4PLMD6colvar11PropertyMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#95">_ZN4PLMD6colvar12_GLOBAL__N_123PropertyMapRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#97">_ZN4PLMD6colvar11PropertyMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#95">_ZN4PLMD6colvar12_GLOBAL__N_123PropertyMapRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#95">_ZN4PLMD6colvar12_GLOBAL__N_123PropertyMapRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PropertyMap.cpp.func.html b/coverage/colvar/PropertyMap.cpp.func.html
new file mode 100644
index 0000000000..752562c239
--- /dev/null
+++ b/coverage/colvar/PropertyMap.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PropertyMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PropertyMap.cpp<span style="font-size: 80%;"> (<a href="PropertyMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PropertyMap.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#97">_ZN4PLMD6colvar11PropertyMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#104">_ZN4PLMD6colvar11PropertyMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#104">_ZN4PLMD6colvar11PropertyMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#95">_ZN4PLMD6colvar12_GLOBAL__N_123PropertyMapRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#95">_ZN4PLMD6colvar12_GLOBAL__N_123PropertyMapRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#95">_ZN4PLMD6colvar12_GLOBAL__N_123PropertyMapRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/PropertyMap.cpp.gcov.html b/coverage/colvar/PropertyMap.cpp.gcov.html
new file mode 100644
index 0000000000..1cef64027b
--- /dev/null
+++ b/coverage/colvar/PropertyMap.cpp.gcov.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/PropertyMap.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - PropertyMap.cpp<span style="font-size: 80%;"> (source / <a href="PropertyMap.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathMSDBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR PROPERTYMAP</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate generic property maps.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This Colvar calculates the property maps according to the work of Spiwok \cite Spiwok:2011ce.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Basically it calculates</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f{eqnarray*}{</a>
+<a name="37"><span class="lineNum">      37 </span>            : X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i  \exp(-\lambda D_i(x))} \\</a>
+<a name="38"><span class="lineNum">      38 </span>            : Y=\frac{\sum_i Y_i*\exp(-\lambda D_i(x))}{\sum_i  \exp(-\lambda D_i(x))} \\</a>
+<a name="39"><span class="lineNum">      39 </span>            : \cdots\\</a>
+<a name="40"><span class="lineNum">      40 </span>            : zzz=-\frac{1}{\lambda}\log(\sum_i  \exp(-\lambda D_i(x)))</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f}</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where the parameters \f$X_i\f$  and  \f$Y_i\f$ are provided in the input pdb (allv.pdb in this case) and</a>
+<a name="44"><span class="lineNum">      44 </span>            :  \f$D_i(x)\f$  is the mean squared displacement after optimal alignment calculated on the pdb frames you input (see Kearsley).</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="48"><span class="lineNum">      48 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.5,</a>
+<a name="49"><span class="lineNum">      49 </span>            : by considering the ordered list of atoms and rebuilding molecules using a procedure</a>
+<a name="50"><span class="lineNum">      50 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="51"><span class="lineNum">      51 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="52"><span class="lineNum">      52 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="55"><span class="lineNum">      55 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="56"><span class="lineNum">      56 </span>            : periodic image.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : p3: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4</a>
+<a name="62"><span class="lineNum">      62 </span>            : PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endplumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optional but</a>
+<a name="66"><span class="lineNum">      66 </span>            : recommended for performance) and states that the neighbor list will be calculated every 4</a>
+<a name="67"><span class="lineNum">      67 </span>            : steps and consider only the closest 8 member to the actual md snapshots.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : In this case the input line instructs plumed to look for two properties X and Y with attached values in the REMARK</a>
+<a name="70"><span class="lineNum">      70 </span>            : line of the reference pdb (Note: No spaces from X and = and 1 !!!!).</a>
+<a name="71"><span class="lineNum">      71 </span>            : e.g.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \auxfile{allv.pdb}</a>
+<a name="74"><span class="lineNum">      74 </span>            : REMARK X=1 Y=2</a>
+<a name="75"><span class="lineNum">      75 </span>            : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00</a>
+<a name="76"><span class="lineNum">      76 </span>            : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00</a>
+<a name="77"><span class="lineNum">      77 </span>            : END</a>
+<a name="78"><span class="lineNum">      78 </span>            : REMARK X=2 Y=3</a>
+<a name="79"><span class="lineNum">      79 </span>            : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00</a>
+<a name="81"><span class="lineNum">      81 </span>            : END</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endauxfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : \note</a>
+<a name="85"><span class="lineNum">      85 </span>            : The implementation of this collective variable and of \ref PATHMSD</a>
+<a name="86"><span class="lineNum">      86 </span>            : is shared, as well as most input options.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : */</a>
+<a name="89"><span class="lineNum">      89 </span>            : //+ENDPLUMEDOC</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : class PropertyMap : public PathMSDBase {</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit PropertyMap(const ActionOptions&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="95"><span class="lineNum">      95 </span>            : };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      12526 : PLUMED_REGISTER_ACTION(PropertyMap,&quot;PROPERTYMAP&quot;)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         13 : void PropertyMap::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         13 :   PathMSDBase::registerKeywords(keys);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         26 :   keys.add(&quot;compulsory&quot;,&quot;PROPERTY&quot;,&quot;the property to be used in the indexing: this goes in the REMARK field of the reference&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         13 :   ActionWithValue::useCustomisableComponents(keys);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         26 :   keys.addOutputComponent(&quot;zzz&quot;,&quot;default&quot;,&quot;the minimum distance from the reference points&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         13 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         11 : PropertyMap::PropertyMap(const ActionOptions&amp;ao):</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   Action(ao),</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         11 :   PathMSDBase(ao)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : {</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // this is the only additional keyword needed</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         11 :   parseVector(&quot;PROPERTY&quot;,labels);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         11 :   checkRead();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         11 :   log&lt;&lt;&quot;  Bibliography &quot;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         22 :      &lt;&lt;plumed.cite(&quot;Spiwok V, Kralova B  J. Chem. Phys. 135,  224504 (2011)&quot;)</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         22 :      &lt;&lt;&quot;\n&quot;;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         11 :   if(labels.size()==0) {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     const std::size_t buflen=500;</a>
+<a name="118"><span class="lineNum">     118 </span>            :     char buf[buflen];</a>
+<a name="119"><span class="lineNum">     119 </span>            :     std::snprintf(buf,buflen,&quot;Need to specify PROPERTY with this action\n&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     plumed_merror(buf);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   } else {</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         33 :     for(unsigned i=0; i&lt;labels.size(); i++) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         22 :       log&lt;&lt;&quot; found custom propety to be found in the REMARK line: &quot;&lt;&lt;labels[i].c_str()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         22 :       addComponentWithDerivatives(labels[i]); componentIsNotPeriodic(labels[i]);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     }</a>
+<a name="126"><span class="lineNum">     126 </span>            :     // add distance anyhow</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         22 :     addComponentWithDerivatives(&quot;zzz&quot;); componentIsNotPeriodic(&quot;zzz&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     //reparse the REMARK field and pick the index</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        473 :     for(unsigned i=0; i&lt;pdbv.size(); i++) {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :       // now look for X=1.34555 Y=5.6677</a>
+<a name="131"><span class="lineNum">     131 </span>            :       std::vector&lt;double&gt; labelvals;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       1386 :       for(unsigned j=0; j&lt;labels.size(); j++) {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :         double val;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        924 :         if( pdbv[i].getArgumentValue(labels[j],val) ) {labelvals.push_back(val);}</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :         else {</a>
+<a name="136"><span class="lineNum">     136 </span>            :           const std::size_t buflen=500;</a>
+<a name="137"><span class="lineNum">     137 </span>            :           char buf[buflen];</a>
+<a name="138"><span class="lineNum">     138 </span>            :           std::snprintf(buf,buflen,&quot;PROPERTY LABEL \&quot; %s \&quot; NOT FOUND IN REMARK FOR FRAME %u \n&quot;,labels[j].c_str(),i);</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :           plumed_merror(buf);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :         };</a>
+<a name="141"><span class="lineNum">     141 </span>            :       }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        462 :       indexvec.push_back(labelvals);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         11 :   requestAtoms(pdbv[0].getAtomNumbers());</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         11 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Puckering.cpp.func-sort-c.html b/coverage/colvar/Puckering.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b8b027a78f
--- /dev/null
+++ b/coverage/colvar/Puckering.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Puckering.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Puckering.cpp<span style="font-size: 80%;"> (<a href="Puckering.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">229</td>
+            <td class="headerCovTableEntry">230</td>
+            <td class="headerCovTableEntryHi">99.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Puckering.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#97">_ZN4PLMD6colvar9PuckeringC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#79">_ZN4PLMD6colvar12_GLOBAL__N_121PuckeringRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#97">_ZN4PLMD6colvar9PuckeringC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#81">_ZN4PLMD6colvar9Puckering16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#227">_ZN4PLMD6colvar9Puckering11calculate6mEv</a></td>
+              <td class="coverFnHi">103</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#140">_ZN4PLMD6colvar9Puckering11calculate5mEv</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#134">_ZN4PLMD6colvar9Puckering9calculateEv</a></td>
+              <td class="coverFnHi">397</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#79">_ZN4PLMD6colvar12_GLOBAL__N_121PuckeringRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#79">_ZN4PLMD6colvar12_GLOBAL__N_121PuckeringRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Puckering.cpp.func.html b/coverage/colvar/Puckering.cpp.func.html
new file mode 100644
index 0000000000..b97fcd426f
--- /dev/null
+++ b/coverage/colvar/Puckering.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Puckering.cpp<span style="font-size: 80%;"> (<a href="Puckering.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">229</td>
+            <td class="headerCovTableEntry">230</td>
+            <td class="headerCovTableEntryHi">99.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Puckering.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#79">_ZN4PLMD6colvar12_GLOBAL__N_121PuckeringRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#79">_ZN4PLMD6colvar12_GLOBAL__N_121PuckeringRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#79">_ZN4PLMD6colvar12_GLOBAL__N_121PuckeringRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#140">_ZN4PLMD6colvar9Puckering11calculate5mEv</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#227">_ZN4PLMD6colvar9Puckering11calculate6mEv</a></td>
+              <td class="coverFnHi">103</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#81">_ZN4PLMD6colvar9Puckering16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#134">_ZN4PLMD6colvar9Puckering9calculateEv</a></td>
+              <td class="coverFnHi">397</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#97">_ZN4PLMD6colvar9PuckeringC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Puckering.cpp.gcov.html#97">_ZN4PLMD6colvar9PuckeringC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Puckering.cpp.gcov.html b/coverage/colvar/Puckering.cpp.gcov.html
new file mode 100644
index 0000000000..6f3f3d0ab3
--- /dev/null
+++ b/coverage/colvar/Puckering.cpp.gcov.html
@@ -0,0 +1,496 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Puckering.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Puckering.cpp<span style="font-size: 80%;"> (source / <a href="Puckering.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">229</td>
+            <td class="headerCovTableEntry">230</td>
+            <td class="headerCovTableEntryHi">99.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace colvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC COLVAR PUCKERING</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            :  Calculate sugar pseudorotation coordinates.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            :  This command can be used to calculate ring's pseudorotations in sugars (puckers). It works for both</a>
+<a name="35"><span class="lineNum">      35 </span>            :  5-membered and 6-membered rings. Notice that there are two different implementations depending if</a>
+<a name="36"><span class="lineNum">      36 </span>            :  one passes 5 or 6 atoms in the ATOMS keyword.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            :  For 5-membered rings the implementation is the one discussed in \cite huang2014improvement .</a>
+<a name="39"><span class="lineNum">      39 </span>            :  This implementation is simple and can be used in RNA to distinguish C2'-endo and C3'-endo conformations.</a>
+<a name="40"><span class="lineNum">      40 </span>            :  Both the polar coordinates (phs and amp) and the Cartesian coordinates (Zx and Zy) are provided.</a>
+<a name="41"><span class="lineNum">      41 </span>            :  C2'-endo conformations have negative Zx, whereas C3'-endo conformations have positive Zy.</a>
+<a name="42"><span class="lineNum">      42 </span>            :  Notation is consistent with \cite huang2014improvement .</a>
+<a name="43"><span class="lineNum">      43 </span>            :  The five atoms should be provided as C4',O4',C1',C2',C3'.</a>
+<a name="44"><span class="lineNum">      44 </span>            :  Notice that this is the same order that can be obtained using the \ref MOLINFO syntax (see example below).</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            :  For 6-membered rings the implementation is the general Cremer-Pople one \cite cremer1975general</a>
+<a name="47"><span class="lineNum">      47 </span>            :  as also discussed in \cite biarnes2007conformational .</a>
+<a name="48"><span class="lineNum">      48 </span>            :  This implementation provides both a triplet with Cartesian components (qx, qy, and qz)</a>
+<a name="49"><span class="lineNum">      49 </span>            :  and a triplet of polar components (amplitude, phi, and theta).</a>
+<a name="50"><span class="lineNum">      50 </span>            :  Applications of this particular implementation are to be published (paper in preparation).</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :  \note The 6-membered ring implementation distributed with previous versions of PLUMED lead to</a>
+<a name="53"><span class="lineNum">      53 </span>            :  qx and qy values that had an opposite sign with respect to those originally defined in \cite cremer1975general.</a>
+<a name="54"><span class="lineNum">      54 </span>            :  The bug is fixed in version 2.5.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :  Components of this action are:</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :  \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            :  This input tells plumed to print the puckering phase angle of the second nucleotide of a RNA molecule on file COLVAR.</a>
+<a name="61"><span class="lineNum">      61 </span>            :  \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            :  #SETTINGS MOLFILE=regtest/basic/rt65/AA.pdb</a>
+<a name="63"><span class="lineNum">      63 </span>            :  MOLINFO STRUCTURE=rna.pdb MOLTYPE=rna</a>
+<a name="64"><span class="lineNum">      64 </span>            :  PUCKERING ATOMS=@sugar-2 LABEL=puck</a>
+<a name="65"><span class="lineNum">      65 </span>            :  PRINT ARG=puck.phs FILE=COLVAR</a>
+<a name="66"><span class="lineNum">      66 </span>            :  \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : */</a>
+<a name="69"><span class="lineNum">      69 </span>            : //+ENDPLUMEDOC</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : class Puckering : public Colvar {</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : public:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit Puckering(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void calculate() override;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void calculate5m();</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void calculate6m();</a>
+<a name="79"><span class="lineNum">      79 </span>            : };</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      12611 : PLUMED_REGISTER_ACTION(Puckering,&quot;PUCKERING&quot;)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         56 : void Puckering::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         56 :   Colvar::registerKeywords( keys );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         56 :   keys.remove(&quot;NOPBC&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        112 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the five or six atoms of the sugar ring in the proper order&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;phs&quot;,&quot;default&quot;,&quot;Pseudorotation phase (5 membered rings)&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;amp&quot;,&quot;default&quot;,&quot;Pseudorotation amplitude (5 membered rings)&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;Zx&quot;,&quot;default&quot;,&quot;Pseudorotation x Cartesian component (5 membered rings)&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;Zy&quot;,&quot;default&quot;,&quot;Pseudorotation y Cartesian component (5 membered rings)&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;phi&quot;,&quot;default&quot;,&quot;Pseudorotation phase (6 membered rings)&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;theta&quot;,&quot;default&quot;,&quot;Theta angle (6 membered rings)&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;amplitude&quot;,&quot;default&quot;,&quot;Pseudorotation amplitude (6 membered rings)&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;qx&quot;,&quot;default&quot;,&quot;Cartesian component x (6 membered rings)&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;qy&quot;,&quot;default&quot;,&quot;Cartesian component y (6 membered rings)&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        112 :   keys.addOutputComponent(&quot;qz&quot;,&quot;default&quot;,&quot;Cartesian component z (6 membered rings)&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         56 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         54 : Puckering::Puckering(const ActionOptions&amp;ao):</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         54 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        108 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         54 :   if(atoms.size()!=5 &amp;&amp; atoms.size()!=6) error(&quot;only for 5 or 6-membered rings&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         53 :   checkRead();</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         53 :   if(atoms.size()==5) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         52 :     log.printf(&quot;  between atoms %d %d %d %d %d\n&quot;,atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial(),atoms[4].serial());</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          1 :   } else if(atoms.size()==6) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :     log.printf(&quot;  between atoms %d %d %d %d %d %d\n&quot;,atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial(),atoms[4].serial(),atoms[5].serial());</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   } else error(&quot;ATOMS should specify 5 atoms&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         53 :   if(atoms.size()==5) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        156 :     addComponentWithDerivatives(&quot;phs&quot;); componentIsPeriodic(&quot;phs&quot;,&quot;-pi&quot;,&quot;pi&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        104 :     addComponentWithDerivatives(&quot;amp&quot;); componentIsNotPeriodic(&quot;amp&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        104 :     addComponentWithDerivatives(&quot;Zx&quot;); componentIsNotPeriodic(&quot;Zx&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        156 :     addComponentWithDerivatives(&quot;Zy&quot;); componentIsNotPeriodic(&quot;Zy&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   } else if(atoms.size()==6) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 :     addComponentWithDerivatives(&quot;qx&quot;); componentIsNotPeriodic(&quot;qx&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :     addComponentWithDerivatives(&quot;qy&quot;); componentIsNotPeriodic(&quot;qy&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :     addComponentWithDerivatives(&quot;qz&quot;); componentIsNotPeriodic(&quot;qz&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 :     addComponentWithDerivatives(&quot;phi&quot;); componentIsPeriodic(&quot;phi&quot;,&quot;0&quot;,&quot;2pi&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :     addComponentWithDerivatives(&quot;theta&quot;); componentIsNotPeriodic(&quot;theta&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 :     addComponentWithDerivatives(&quot;amplitude&quot;); componentIsNotPeriodic(&quot;amplitude&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         53 :   log&lt;&lt;&quot;  Bibliography &quot;;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        105 :   if(atoms.size()==5) log&lt;&lt;plumed.cite(&quot;Huang, Giese, Lee, York, J. Chem. Theory Comput. 10, 1538 (2014)&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         55 :   if(atoms.size()==6) log&lt;&lt;plumed.cite(&quot;Cremer and Pople, J. Am. Chem. Soc. 97, 1354 (1975)&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         53 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         53 :   requestAtoms(atoms);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         55 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : // calculator</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        397 : void Puckering::calculate() {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        397 :   makeWhole();</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        397 :   if(getNumberOfAtoms()==5) calculate5m();</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        103 :   else calculate6m();</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        397 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        294 : void Puckering::calculate5m() {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        294 :   Vector d0,d1,d2,d3,d4,d5;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        294 :   d0=delta(getPosition(2),getPosition(1));</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        294 :   d1=delta(getPosition(3),getPosition(2));</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        294 :   d2=delta(getPosition(4),getPosition(3));</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        294 :   d3=delta(getPosition(4),getPosition(3));</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        294 :   d4=delta(getPosition(0),getPosition(4));</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        294 :   d5=delta(getPosition(1),getPosition(0));</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        294 :   Vector dd0,dd1,dd2,dd3,dd4,dd5;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   PLMD::Torsion t;</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        294 :   double v1=t.compute(d0,d1,d2,dd0,dd1,dd2);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        294 :   double v3=t.compute(d3,d4,d5,dd3,dd4,dd5);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        294 :   double Zx=(v1+v3)/(2.0*std::cos(4.0*pi/5.0));</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        294 :   double Zy=(v1-v3)/(2.0*std::sin(4.0*pi/5.0));</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        294 :   double phase=std::atan2(Zy,Zx);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        294 :   double amplitude=std::sqrt(Zx*Zx+Zy*Zy);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       1764 :   Vector dZx_dR[5];</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       1764 :   Vector dZy_dR[5];</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        294 :   dZx_dR[0]=(dd5-dd4);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        294 :   dZx_dR[1]=(dd0-dd5);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        294 :   dZx_dR[2]=(dd1-dd0);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        294 :   dZx_dR[3]=(dd2+dd3-dd1);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        294 :   dZx_dR[4]=(dd4-dd3-dd2);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        294 :   dZy_dR[0]=(dd4-dd5);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        294 :   dZy_dR[1]=(dd0+dd5);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        294 :   dZy_dR[2]=(dd1-dd0);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        294 :   dZy_dR[3]=(dd2-dd3-dd1);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        294 :   dZy_dR[4]=(dd3-dd4-dd2);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       1764 :   for(unsigned j=0; j&lt;5; j++) dZx_dR[j]*=(1.0/(2.0*std::cos(4.0*pi/5.0)));</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       1764 :   for(unsigned j=0; j&lt;5; j++) dZy_dR[j]*=(1.0/(2.0*std::sin(4.0*pi/5.0)));</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       1764 :   Vector dphase_dR[5];</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       1764 :   for(unsigned j=0; j&lt;5; j++) dphase_dR[j]=(1.0/(Zx*Zx+Zy*Zy))*(-Zy*dZx_dR[j] + Zx*dZy_dR[j]);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       1764 :   Vector damplitude_dR[5];</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       1764 :   for(unsigned j=0; j&lt;5; j++) damplitude_dR[j]=(1.0/amplitude)*(Zx*dZx_dR[j] + Zy*dZy_dR[j]);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        588 :   Value* vzx=getPntrToComponent(&quot;Zx&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   vzx-&gt;set(Zx);</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzx,0, dZx_dR[0]);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzx,1, dZx_dR[1]);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzx,2, dZx_dR[2]);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzx,3, dZx_dR[3]);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzx,4, dZx_dR[4]);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        294 :   setBoxDerivativesNoPbc(vzx);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        588 :   Value* vzy=getPntrToComponent(&quot;Zy&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   vzy-&gt;set(Zy);</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzy,0, dZy_dR[0]);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzy,1, dZy_dR[1]);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzy,2, dZy_dR[2]);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzy,3, dZy_dR[3]);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        294 :   setAtomsDerivatives (vzy,4, dZy_dR[4]);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        294 :   setBoxDerivativesNoPbc(vzy);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        588 :   Value* vph=getPntrToComponent(&quot;phs&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   vph-&gt;set(phase);</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        294 :   setAtomsDerivatives (vph,0, dphase_dR[0]);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        294 :   setAtomsDerivatives (vph,1, dphase_dR[1]);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        294 :   setAtomsDerivatives (vph,2, dphase_dR[2]);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        294 :   setAtomsDerivatives (vph,3, dphase_dR[3]);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        294 :   setAtomsDerivatives (vph,4, dphase_dR[4]);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        294 :   setBoxDerivativesNoPbc(vph);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        588 :   Value* vam=getPntrToComponent(&quot;amp&quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   vam-&gt;set(amplitude);</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        294 :   setAtomsDerivatives (vam,0, damplitude_dR[0]);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        294 :   setAtomsDerivatives (vam,1, damplitude_dR[1]);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        294 :   setAtomsDerivatives (vam,2, damplitude_dR[2]);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        294 :   setAtomsDerivatives (vam,3, damplitude_dR[3]);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        294 :   setAtomsDerivatives (vam,4, damplitude_dR[4]);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        294 :   setBoxDerivativesNoPbc(vam);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        294 : }</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        103 : void Puckering::calculate6m() {</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; r(6);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        721 :   for(unsigned i=0; i&lt;6; i++) r[i]=getPosition(i);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; R(6);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        103 :   Vector center;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) center+=r[j]/6.0;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) R[j]=(r[j]-center);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        103 :   Vector Rp,Rpp;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) Rp +=R[j]*std::sin(2.0/6.0*pi*j);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) Rpp+=R[j]*std::cos(2.0/6.0*pi*j);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        103 :   Vector n=crossProduct(Rp,Rpp);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        103 :   Vector nhat=n/modulo(n);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        103 :   Tensor dn_dRp=dcrossDv1(Rp,Rpp);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        103 :   Tensor dn_dRpp=dcrossDv2(Rp,Rpp);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        103 :   Tensor dnhat_dn= 1.0/modulo(n)*( Tensor::identity() - extProduct(nhat,nhat));</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        103 :   Tensor dnhat_dRp=matmul(dnhat_dn,dn_dRp);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        103 :   Tensor dnhat_dRpp=matmul(dnhat_dn,dn_dRpp);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        103 :   std::vector&lt;double&gt; z(6);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) z[j]=dotProduct(R[j],nhat);</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        103 :   std::vector&lt;std::vector&lt;Vector&gt; &gt; dz_dR(6);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) dz_dR[j].resize(6);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       4429 :   for(unsigned i=0; i&lt;6; i++) for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       3708 :       if(i==j) dz_dR[i][j]+=nhat;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       3708 :       dz_dR[i][j]+=matmul(R[i],dnhat_dRp)*std::sin(2.0/6.0*pi*j);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       3708 :       dz_dR[i][j]+=matmul(R[i],dnhat_dRpp)*std::cos(2.0/6.0*pi*j);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :     }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   double B=0.0;</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) B+=z[j]*std::cos(4.0/6.0*pi*j);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dB_dR(6);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       4429 :   for(unsigned i=0; i&lt;6; i++) for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       3708 :       dB_dR[i]+=dz_dR[j][i]*std::cos(4.0/6.0*pi*j);</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :     }</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        103 :   Vector Bsum;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) Bsum+=dB_dR[j];</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) dB_dR[j]-=Bsum/6.0;;</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   double A=0.0;</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) A+=z[j]*std::sin(4.0/6.0*pi*j);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dA_dR(6);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       4429 :   for(unsigned i=0; i&lt;6; i++) for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       3708 :       dA_dR[i]+=dz_dR[j][i]*std::sin(4.0/6.0*pi*j);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :     }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        103 :   Vector Asum;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) Asum+=dA_dR[j];</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) dA_dR[j]-=Asum/6.0;;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :   double C=0.0;</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) C+=z[j]*Tools::fastpow(-1.0,(j));</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dC_dR(6);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       4429 :   for(unsigned i=0; i&lt;6; i++) for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       3708 :       dC_dR[i]+=dz_dR[j][i]*Tools::fastpow(-1.0,(j));</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :     }</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        103 :   Vector Csum;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) Csum+=dC_dR[j];</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) dC_dR[j]-=Csum/6.0;;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : // qx</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        103 :   double qx = -A/std::sqrt(3);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : // qx derivaties</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dqx_dR(6);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        618 :     dqx_dR[j]=-1/std::sqrt(3) * dA_dR[j];</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        206 :   Value* vqx=getPntrToComponent(&quot;qx&quot;);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   vqx-&gt;set(qx);</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqx,0, dqx_dR[0] );</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqx,1, dqx_dR[1] );</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqx,2, dqx_dR[2] );</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqx,3, dqx_dR[3] );</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqx,4, dqx_dR[4] );</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqx,5, dqx_dR[5] );</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        103 :   setBoxDerivativesNoPbc(vqx);</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            : // qy</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        103 :   double qy = B/std::sqrt(3);</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : // qy derivatives</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dqy_dR(6);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        618 :     dqy_dR[j]=1/std::sqrt(3) * dB_dR[j];</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        206 :   Value* vqy=getPntrToComponent(&quot;qy&quot;);</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   vqy-&gt;set(qy);</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqy,0, dqy_dR[0] );</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqy,1, dqy_dR[1] );</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqy,2, dqy_dR[2] );</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqy,3, dqy_dR[3] );</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqy,4, dqy_dR[4] );</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqy,5, dqy_dR[5] );</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        103 :   setBoxDerivativesNoPbc(vqy);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : // qz</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">        103 :   double qz = C/std::sqrt(6);</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : // qz derivatives</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dqz_dR(6);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        618 :     dqz_dR[j]=1/std::sqrt(6) * dC_dR[j];</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">        206 :   Value* vqz=getPntrToComponent(&quot;qz&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :   vqz-&gt;set(qz);</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqz,0, dqz_dR[0] );</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqz,1, dqz_dR[1] );</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqz,2, dqz_dR[2] );</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqz,3, dqz_dR[3] );</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqz,4, dqz_dR[4] );</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        103 :   setAtomsDerivatives (vqz,5, dqz_dR[5] );</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        103 :   setBoxDerivativesNoPbc(vqz);</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            : // PHASE</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">        103 :   double phi=std::atan2(-A,B);</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : // PHASE DERIVATIVES</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dphi_dR(6);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        618 :     dphi_dR[j]=1.0/(A*A+B*B) * (-B*dA_dR[j] + A*dB_dR[j]);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :   }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        206 :   Value* vphi=getPntrToComponent(&quot;phi&quot;);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   vphi-&gt;set(phi);</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        103 :   setAtomsDerivatives (vphi,0, dphi_dR[0] );</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        103 :   setAtomsDerivatives (vphi,1, dphi_dR[1] );</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        103 :   setAtomsDerivatives (vphi,2, dphi_dR[2] );</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        103 :   setAtomsDerivatives (vphi,3, dphi_dR[3] );</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        103 :   setAtomsDerivatives (vphi,4, dphi_dR[4] );</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        103 :   setAtomsDerivatives (vphi,5, dphi_dR[5] );</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        103 :   setBoxDerivativesNoPbc(vphi);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : //  AMPLITUDE</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">        103 :   double amplitude=std::sqrt((2*(A*A+B*B)+C*C)/6);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span>            : //  AMPLITUDE DERIVATIES</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; damplitude_dR(6);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        721 :   for (unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        618 :     damplitude_dR[j]=0.5*std::sqrt(2.0/6.0)/(std::sqrt(A*A+B*B+0.5*C*C)) * (2*A*dA_dR[j] + 2*B*dB_dR[j] + C*dC_dR[j]);</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        206 :   Value* vamplitude=getPntrToComponent(&quot;amplitude&quot;);</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :   vamplitude-&gt;set(amplitude);</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        103 :   setAtomsDerivatives (vamplitude,0, damplitude_dR[0] );</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        103 :   setAtomsDerivatives (vamplitude,1, damplitude_dR[1] );</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        103 :   setAtomsDerivatives (vamplitude,2, damplitude_dR[2] );</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        103 :   setAtomsDerivatives (vamplitude,3, damplitude_dR[3] );</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        103 :   setAtomsDerivatives (vamplitude,4, damplitude_dR[4] );</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        103 :   setAtomsDerivatives (vamplitude,5, damplitude_dR[5] );</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        103 :   setBoxDerivativesNoPbc(vamplitude);</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            : //  THETA</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        103 :   double theta=std::acos( C / std::sqrt(2.*(A*A+B*B) +C*C ) );</span></a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : //  THETA DERIVATIVES</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        103 :   std::vector&lt;Vector&gt; dtheta_dR(6);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">        721 :   for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">        618 :     dtheta_dR[j]=1.0/(3.0*std::sqrt(2)*amplitude*amplitude) * (C/(std::sqrt(A*A+B*B)) * (A*dA_dR[j] + B*dB_dR[j]) - std::sqrt(A*A+B*B)*dC_dR[j]);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">        206 :   Value* vtheta=getPntrToComponent(&quot;theta&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :   vtheta-&gt;set(theta);</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">        103 :   setAtomsDerivatives (vtheta,0, dtheta_dR[0] );</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">        103 :   setAtomsDerivatives (vtheta,1, dtheta_dR[1] );</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">        103 :   setAtomsDerivatives (vtheta,2, dtheta_dR[2] );</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">        103 :   setAtomsDerivatives (vtheta,3, dtheta_dR[3] );</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">        103 :   setAtomsDerivatives (vtheta,4, dtheta_dR[4] );</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        103 :   setAtomsDerivatives (vtheta,5, dtheta_dR[5] );</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">        103 :   setBoxDerivativesNoPbc(vtheta);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">        206 : }</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            : }</a>
+<a name="417"><span class="lineNum">     417 </span>            : }</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/RMSD.cpp.func-sort-c.html b/coverage/colvar/RMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..07b73558a3
--- /dev/null
+++ b/coverage/colvar/RMSD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/RMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - RMSD.cpp<span style="font-size: 80%;"> (<a href="RMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#169">_ZN4PLMD6colvar4RMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#160">_ZN4PLMD6colvar12_GLOBAL__N_117RMSDRegisterMe1626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#169">_ZN4PLMD6colvar4RMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#162">_ZN4PLMD6colvar4RMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#160">_ZN4PLMD6colvar12_GLOBAL__N_117RMSDRegisterMe162C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#160">_ZN4PLMD6colvar12_GLOBAL__N_117RMSDRegisterMe162D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#221">_ZN4PLMD6colvar4RMSD9calculateEv</a></td>
+              <td class="coverFnHi">40496</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/RMSD.cpp.func.html b/coverage/colvar/RMSD.cpp.func.html
new file mode 100644
index 0000000000..399baac6a3
--- /dev/null
+++ b/coverage/colvar/RMSD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/RMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - RMSD.cpp<span style="font-size: 80%;"> (<a href="RMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="RMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#160">_ZN4PLMD6colvar12_GLOBAL__N_117RMSDRegisterMe1626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#160">_ZN4PLMD6colvar12_GLOBAL__N_117RMSDRegisterMe162C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#169">_ZN4PLMD6colvar4RMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">78</td>
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+              <td class="coverFn"><a href="RMSD.cpp.gcov.html#169">_ZN4PLMD6colvar4RMSDC2ERKNS_13ActionOptionsE</a></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/colvar/RMSD.cpp.gcov.html b/coverage/colvar/RMSD.cpp.gcov.html
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - RMSD.cpp<span style="font-size: 80%;"> (source / <a href="RMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
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+          </tr>
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+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
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+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;reference/RMSDBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace colvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class RMSD : public Colvar {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            :   MultiValue myvals;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   ReferenceValuePack mypack;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::unique_ptr&lt;PLMD::RMSDBase&gt; rmsd;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   bool squared;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   bool nopbc;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   explicit RMSD(const ActionOptions&amp;);</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void calculate() override;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : //+PLUMEDOC DCOLVAR RMSD</a>
+<a name="48"><span class="lineNum">      48 </span>            : /*</a>
+<a name="49"><span class="lineNum">      49 </span>            : Calculate the RMSD with respect to a reference structure.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The aim with this colvar it to calculate something like:</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \f[</a>
+<a name="54"><span class="lineNum">      54 </span>            : d(X,X') = \vert X-X' \vert</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f]</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : where \f$ X \f$ is the instantaneous position of all the atoms in the system and</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f$ X' \f$ is the positions of the atoms in some reference structure provided as input.</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f$ d(X,X') \f$ thus measures the distance all the atoms have moved away from this reference configuration.</a>
+<a name="60"><span class="lineNum">      60 </span>            : Oftentimes, it is only the internal motions of the structure - i.e. not the translations of the center of</a>
+<a name="61"><span class="lineNum">      61 </span>            : mass or the rotations of the reference frame - that are interesting.  Hence, when calculating the</a>
+<a name="62"><span class="lineNum">      62 </span>            : the root-mean-square deviation between the atoms in two configurations</a>
+<a name="63"><span class="lineNum">      63 </span>            : you must first superimpose the two structures in some way. At present PLUMED provides two distinct ways</a>
+<a name="64"><span class="lineNum">      64 </span>            : of performing this superposition.  The first method is applied when you use TYPE=SIMPLE in the input</a>
+<a name="65"><span class="lineNum">      65 </span>            : line.  This instruction tells PLUMED that the root mean square deviation is to be calculated after the</a>
+<a name="66"><span class="lineNum">      66 </span>            : positions of the geometric centers in the reference and instantaneous configurations are aligned.  In</a>
+<a name="67"><span class="lineNum">      67 </span>            : other words \f$d(X,x')\f$ is to be calculated using:</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \f[</a>
+<a name="70"><span class="lineNum">      70 </span>            :  d(X,X') = \sqrt{ \sum_i \sum_\alpha^{x,y,z}  \frac{w_i}{\sum_j w_j}( X_{i,\alpha}-com_\alpha(X)-{X'}_{i,\alpha}+com_\alpha(X') )^2 }</a>
+<a name="71"><span class="lineNum">      71 </span>            : \f]</a>
+<a name="72"><span class="lineNum">      72 </span>            : with</a>
+<a name="73"><span class="lineNum">      73 </span>            : \f[</a>
+<a name="74"><span class="lineNum">      74 </span>            : com_\alpha(X)= \sum_i  \frac{w'_{i}}{\sum_j w'_j}X_{i,\alpha}</a>
+<a name="75"><span class="lineNum">      75 </span>            : \f]</a>
+<a name="76"><span class="lineNum">      76 </span>            : and</a>
+<a name="77"><span class="lineNum">      77 </span>            : \f[</a>
+<a name="78"><span class="lineNum">      78 </span>            : com_\alpha(X')= \sum_i  \frac{w'_{i}}{\sum_j w'_j}X'_{i,\alpha}</a>
+<a name="79"><span class="lineNum">      79 </span>            : \f]</a>
+<a name="80"><span class="lineNum">      80 </span>            : Obviously, \f$ com_\alpha(X) \f$ and  \f$ com_\alpha(X') \f$  represent the positions of the center of mass in the reference</a>
+<a name="81"><span class="lineNum">      81 </span>            : and instantaneous configurations if the weights $w'$ are set equal to the atomic masses.  If the weights are all set equal to</a>
+<a name="82"><span class="lineNum">      82 </span>            : one, however, \f$com_\alpha(X) \f$ and  \f$ com_\alpha(X') \f$ are the positions of the geometric centers.</a>
+<a name="83"><span class="lineNum">      83 </span>            : Notice that there are sets of weights:  \f$ w' \f$ and  \f$ w \f$. The first is used to calculate the position of the center of mass</a>
+<a name="84"><span class="lineNum">      84 </span>            : (so it determines how the atoms are \e aligned).  Meanwhile, the second is used when calculating how far the atoms have actually been</a>
+<a name="85"><span class="lineNum">      85 </span>            : \e displaced.  These weights are assigned in the reference configuration that you provide as input (i.e. the appear in the input file</a>
+<a name="86"><span class="lineNum">      86 </span>            : to this action that you set using REFERENCE=whatever.pdb).  This input reference configuration consists of a simple pdb file</a>
+<a name="87"><span class="lineNum">      87 </span>            : containing the set of atoms for which you want to calculate the RMSD displacement and their positions in the reference configuration.</a>
+<a name="88"><span class="lineNum">      88 </span>            : It is important to note that the indices in this pdb need to be set correctly.  The indices in this file determine the indices of the</a>
+<a name="89"><span class="lineNum">      89 </span>            : instantaneous atomic positions that are used by PLUMED when calculating this colvar.  As such if you want to calculate the RMSD distance</a>
+<a name="90"><span class="lineNum">      90 </span>            : moved by the first, fourth, sixth and twenty eighth atoms in the MD codes input file then the indices of the corresponding reference positions in this pdb</a>
+<a name="91"><span class="lineNum">      91 </span>            : file should be set equal to 1, 4, 6 and 28.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : The pdb input file should also contain the values of \f$w\f$ and \f$w'\f$. In particular, the OCCUPANCY column (the first column after the coordinates)</a>
+<a name="94"><span class="lineNum">      94 </span>            : is used provides the values of \f$ w'\f$ that are used to calculate the position of the center of mass.  The BETA column (the second column</a>
+<a name="95"><span class="lineNum">      95 </span>            : after the Cartesian coordinates) is used to provide the \f$ w \f$ values which are used in the the calculation of the displacement.</a>
+<a name="96"><span class="lineNum">      96 </span>            : Please note that it is possible to use fractional values for beta and for the occupancy. However, we recommend you only do this when</a>
+<a name="97"><span class="lineNum">      97 </span>            : you really know what you are doing however as the results can be rather strange.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : In PDB files the atomic coordinates and box lengths should be in Angstroms unless</a>
+<a name="100"><span class="lineNum">     100 </span>            : you are working with natural units.  If you are working with natural units then the coordinates</a>
+<a name="101"><span class="lineNum">     101 </span>            : should be in your natural length unit.  For more details on the PDB file format visit http://www.wwpdb.org/docs.html.</a>
+<a name="102"><span class="lineNum">     102 </span>            : Make sure your PDB file is correctly formatted as explained \ref pdbreader &quot;in this page&quot;.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : A different method is used to calculate the RMSD distance when you use TYPE=OPTIMAL on the input line.  In this case  the root mean square</a>
+<a name="105"><span class="lineNum">     105 </span>            : deviation is calculated after the positions of geometric centers in the reference and instantaneous configurations are aligned AND after</a>
+<a name="106"><span class="lineNum">     106 </span>            : an optimal alignment of the two frames is performed so that motion due to rotation of the reference frame between the two structures is</a>
+<a name="107"><span class="lineNum">     107 </span>            : removed.  The equation for \f$d(X,X')\f$ in this case reads:</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : \f[</a>
+<a name="110"><span class="lineNum">     110 </span>            : d(X,X') = \sqrt{ \sum_i \sum_\alpha^{x,y,z}  \frac{w_i}{\sum_j w_j}[ X_{i,\alpha}-com_\alpha(X)- \sum_\beta M(X,X',w')_{\alpha,\beta}({X'}_{i,\beta}-com_\beta(X')) ]^2 }</a>
+<a name="111"><span class="lineNum">     111 </span>            : \f]</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : where \f$ M(X,X',w') \f$ is the optimal alignment matrix which is calculated using the Kearsley \cite kearsley algorithm.  Again different sets of</a>
+<a name="114"><span class="lineNum">     114 </span>            : weights are used for the alignment (\f$w'\f$) and for the displacement calculations (\f$w\f$).</a>
+<a name="115"><span class="lineNum">     115 </span>            : This gives a great deal of flexibility as it allows you to use a different sets of atoms (which may or may not overlap) for the alignment and displacement</a>
+<a name="116"><span class="lineNum">     116 </span>            : parts of the calculation. This may be very useful when you want to calculate how a ligand moves about in a protein cavity as you can use the protein as a reference</a>
+<a name="117"><span class="lineNum">     117 </span>            : system and do no alignment of the ligand.</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : (Note: when this form of RMSD is used to calculate the secondary structure variables (\ref ALPHARMSD, \ref ANTIBETARMSD and \ref PARABETARMSD</a>
+<a name="120"><span class="lineNum">     120 </span>            : all the atoms in the segment are assumed to be part of both the alignment and displacement sets and all weights are set equal to one)</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : Please note that there are a number of other methods for calculating the distance between the instantaneous configuration and a reference configuration</a>
+<a name="123"><span class="lineNum">     123 </span>            : that are available in plumed.  More information on these various methods can be found in the section of the manual on \ref dists.</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="126"><span class="lineNum">     126 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.5,</a>
+<a name="127"><span class="lineNum">     127 </span>            : by considering the ordered list of atoms and rebuilding molecules using a procedure</a>
+<a name="128"><span class="lineNum">     128 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="129"><span class="lineNum">     129 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="130"><span class="lineNum">     130 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="133"><span class="lineNum">     133 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="134"><span class="lineNum">     134 </span>            : periodic image.</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \par Examples</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : The following tells plumed to calculate the RMSD distance between</a>
+<a name="139"><span class="lineNum">     139 </span>            : the positions of the atoms in the reference file and their instantaneous</a>
+<a name="140"><span class="lineNum">     140 </span>            : position.  The Kearsley algorithm is used so this is done optimally.</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : \plumedfile</a>
+<a name="143"><span class="lineNum">     143 </span>            : RMSD REFERENCE=file.pdb TYPE=OPTIMAL</a>
+<a name="144"><span class="lineNum">     144 </span>            : \endplumedfile</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : The reference configuration is specified in a pdb file that will have a format similar to the one shown below:</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : \auxfile{file.pdb}</a>
+<a name="149"><span class="lineNum">     149 </span>            : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00</a>
+<a name="150"><span class="lineNum">     150 </span>            : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00</a>
+<a name="151"><span class="lineNum">     151 </span>            : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00</a>
+<a name="152"><span class="lineNum">     152 </span>            : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00</a>
+<a name="153"><span class="lineNum">     153 </span>            : ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00</a>
+<a name="154"><span class="lineNum">     154 </span>            : END</a>
+<a name="155"><span class="lineNum">     155 </span>            : \endauxfile</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : ...</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : */</a>
+<a name="160"><span class="lineNum">     160 </span>            : //+ENDPLUMEDOC</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      12658 : PLUMED_REGISTER_ACTION(RMSD,&quot;RMSD&quot;)</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         80 : void RMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         80 :   Colvar::registerKeywords(keys);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        160 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        160 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;SIMPLE&quot;,&quot;the manner in which RMSD alignment is performed.  Should be OPTIMAL or SIMPLE.&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        160 :   keys.addFlag(&quot;SQUARED&quot;,false,&quot; This should be set if you want mean squared displacement instead of RMSD &quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         80 : }</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         78 : RMSD::RMSD(const ActionOptions&amp;ao):</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        158 :   myvals(1,0),</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         78 :   mypack(0,0,myvals),</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         78 :   squared(false),</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        156 :   nopbc(false)</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : {</a>
+<a name="178"><span class="lineNum">     178 </span>            :   std::string reference;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        158 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   std::string type;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         78 :   type.assign(&quot;SIMPLE&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         78 :   parse(&quot;TYPE&quot;,type);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         78 :   parseFlag(&quot;SQUARED&quot;,squared);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         80 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         78 :   checkRead();</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         78 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         78 :   PDB pdb;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        156 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          1 :     error(&quot;missing input file &quot; + reference );</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        154 :   rmsd=metricRegister().create&lt;RMSDBase&gt;(type,pdb);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         77 :   rmsd-&gt;getAtomRequests( atoms );</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : //  rmsd-&gt;setNumberOfAtoms( atoms.size() );</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         77 :   requestAtoms( atoms );</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   // Setup the derivative pack</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         77 :   myvals.resize( 1, 3*atoms.size()+9 ); mypack.resize( 0, atoms.size() );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       3833 :   for(unsigned i=0; i&lt;atoms.size(); ++i) mypack.setAtomIndex( i, i );</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         76 :   log.printf(&quot;  reference from file %s\n&quot;,reference.c_str());</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         76 :   log.printf(&quot;  which contains %d atoms\n&quot;,getNumberOfAtoms());</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         76 :   log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       3833 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       3757 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       3757 :     log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         76 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         76 :   log.printf(&quot;  method for alignment : %s \n&quot;,type.c_str() );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         76 :   if(squared)log.printf(&quot;  chosen to use SQUARED option for MSD instead of RMSD\n&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         76 :   if(nopbc) log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         19 :   else      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        164 : }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : // calculator</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      40496 : void RMSD::calculate() {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      40496 :   if(!nopbc) makeWhole();</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      40496 :   double r=rmsd-&gt;calculate( getPositions(), mypack, squared );</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      40496 :   setValue(r);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">   14617727 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) setAtomsDerivatives( i, mypack.getAtomDerivative(i) );</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      40496 :   Tensor virial; plumed_dbg_assert( !mypack.virialWasSet() );</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      40496 :   setBoxDerivativesNoPbc();</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      40496 : }</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : }</a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Template.cpp.func-sort-c.html b/coverage/colvar/Template.cpp.func-sort-c.html
new file mode 100644
index 0000000000..72b3386ea2
--- /dev/null
+++ b/coverage/colvar/Template.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Template.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Template.cpp<span style="font-size: 80%;"> (<a href="Template.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryLo">22.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Template.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#57">_ZN4PLMD6colvar12_GLOBAL__N_120TemplateRegisterMe596createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#91">_ZN4PLMD6colvar8Template9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#67">_ZN4PLMD6colvar8TemplateC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#67">_ZN4PLMD6colvar8TemplateC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#59">_ZN4PLMD6colvar8Template16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#57">_ZN4PLMD6colvar12_GLOBAL__N_120TemplateRegisterMe59C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#57">_ZN4PLMD6colvar12_GLOBAL__N_120TemplateRegisterMe59D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Template.cpp.func.html b/coverage/colvar/Template.cpp.func.html
new file mode 100644
index 0000000000..96276297bd
--- /dev/null
+++ b/coverage/colvar/Template.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Template.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Template.cpp<span style="font-size: 80%;"> (<a href="Template.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryLo">22.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Template.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#57">_ZN4PLMD6colvar12_GLOBAL__N_120TemplateRegisterMe596createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#57">_ZN4PLMD6colvar12_GLOBAL__N_120TemplateRegisterMe59C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#57">_ZN4PLMD6colvar12_GLOBAL__N_120TemplateRegisterMe59D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#59">_ZN4PLMD6colvar8Template16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#91">_ZN4PLMD6colvar8Template9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#67">_ZN4PLMD6colvar8TemplateC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Template.cpp.gcov.html#67">_ZN4PLMD6colvar8TemplateC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Template.cpp.gcov.html b/coverage/colvar/Template.cpp.gcov.html
new file mode 100644
index 0000000000..10d841c2bf
--- /dev/null
+++ b/coverage/colvar/Template.cpp.gcov.html
@@ -0,0 +1,190 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Template.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Template.cpp<span style="font-size: 80%;"> (source / <a href="Template.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryLo">22.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR TEMPLATE</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This file provides a template for if you want to introduce a new CV.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : &lt;!-----You should add a description of your CV here----&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \par Examples</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : &lt;!---You should put an example of how to use your CV here---&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \plumedfile</a>
+<a name="39"><span class="lineNum">      39 </span>            : # This should be a sample input.</a>
+<a name="40"><span class="lineNum">      40 </span>            : t: TEMPLATE ATOMS=1,2</a>
+<a name="41"><span class="lineNum">      41 </span>            : PRINT ARG=t STRIDE=100 FILE=COLVAR</a>
+<a name="42"><span class="lineNum">      42 </span>            : \endplumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : &lt;!---You should reference here the other actions used in this example---&gt;</a>
+<a name="44"><span class="lineNum">      44 </span>            : (see also \ref PRINT)</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : */</a>
+<a name="47"><span class="lineNum">      47 </span>            : //+ENDPLUMEDOC</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : class Template : public Colvar {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   bool pbc;</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit Template(const ActionOptions&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span>            : // active methods:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void calculate() override;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="57"><span class="lineNum">      57 </span>            : };</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(Template,&quot;TEMPLATE&quot;)</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 : void Template::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :   Colvar::registerKeywords(keys);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          4 :   keys.addFlag(&quot;TEMPLATE_DEFAULT_OFF_FLAG&quot;,false,&quot;flags that are by default not performed should be specified like this&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;TEMPLATE_COMPULSORY&quot;,&quot;all compulsory keywords should be added like this with a description here&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;TEMPLATE_OPTIONAL&quot;,&quot;all optional keywords that have input should be added like a description here&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          4 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the keyword with which you specify what atoms to use should be added like this&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 : Template::Template(const ActionOptions&amp;ao):</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   pbc(true)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   if(atoms.size()!=2)</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :     error(&quot;Number of specified atoms should be 2&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :   bool nopbc=!pbc;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   pbc=!nopbc;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   log.printf(&quot;  between atoms %d %d\n&quot;,atoms[0].serial(),atoms[1].serial());</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :   requestAtoms(atoms);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : // calculator</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : void Template::calculate() {</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   Vector distance;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   if(pbc) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     distance=pbcDistance(getPosition(0),getPosition(1));</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   } else {</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     distance=delta(getPosition(0),getPosition(1));</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   const double value=distance.modulo();</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   const double invvalue=1.0/value;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   setAtomsDerivatives(0,-invvalue*distance);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   setAtomsDerivatives(1,invvalue*distance);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   setBoxDerivatives  (-invvalue*Tensor(distance,distance));</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   setValue           (value);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Torsion.cpp.func-sort-c.html b/coverage/colvar/Torsion.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9ff7879c6b
--- /dev/null
+++ b/coverage/colvar/Torsion.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Torsion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Torsion.cpp<span style="font-size: 80%;"> (<a href="Torsion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Torsion.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#109">_ZN4PLMD6colvar7TorsionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#98">_ZN4PLMD6colvar12_GLOBAL__N_120TorsionRegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">657</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#109">_ZN4PLMD6colvar7TorsionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">657</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#100">_ZN4PLMD6colvar7Torsion16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">659</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#98">_ZN4PLMD6colvar12_GLOBAL__N_120TorsionRegisterMe100C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#98">_ZN4PLMD6colvar12_GLOBAL__N_120TorsionRegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#162">_ZN4PLMD6colvar7Torsion9calculateEv</a></td>
+              <td class="coverFnHi">34591</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Torsion.cpp.func.html b/coverage/colvar/Torsion.cpp.func.html
new file mode 100644
index 0000000000..bbf82f4db4
--- /dev/null
+++ b/coverage/colvar/Torsion.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Torsion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Torsion.cpp<span style="font-size: 80%;"> (<a href="Torsion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Torsion.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#98">_ZN4PLMD6colvar12_GLOBAL__N_120TorsionRegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">657</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#98">_ZN4PLMD6colvar12_GLOBAL__N_120TorsionRegisterMe100C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#98">_ZN4PLMD6colvar12_GLOBAL__N_120TorsionRegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#100">_ZN4PLMD6colvar7Torsion16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">659</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#162">_ZN4PLMD6colvar7Torsion9calculateEv</a></td>
+              <td class="coverFnHi">34591</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#109">_ZN4PLMD6colvar7TorsionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">657</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#109">_ZN4PLMD6colvar7TorsionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Torsion.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Torsion.cpp<span style="font-size: 80%;"> (source / <a href="Torsion.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace colvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR TORSION</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate a torsional angle.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This command can be used to compute the torsion between four atoms or alternatively</a>
+<a name="34"><span class="lineNum">      34 </span>            : to calculate the angle between two vectors projected on the plane</a>
+<a name="35"><span class="lineNum">      35 </span>            : orthogonal to an axis.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : This input tells plumed to print the torsional angle between atoms 1, 2, 3 and 4</a>
+<a name="40"><span class="lineNum">      40 </span>            : on file COLVAR.</a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : t: TORSION ATOMS=1,2,3,4</a>
+<a name="43"><span class="lineNum">      43 </span>            : # this is an alternative, equivalent, definition:</a>
+<a name="44"><span class="lineNum">      44 </span>            : # t: TORSION VECTOR1=2,1 AXIS=2,3 VECTOR2=3,4</a>
+<a name="45"><span class="lineNum">      45 </span>            : PRINT ARG=t FILE=COLVAR</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : If you are working with a protein you can specify the special named torsion angles \f$\phi\f$, \f$\psi\f$, \f$\omega\f$ and \f$\chi_1\f$</a>
+<a name="49"><span class="lineNum">      49 </span>            : by using TORSION in combination with the \ref MOLINFO command.  This can be done by using the following</a>
+<a name="50"><span class="lineNum">      50 </span>            : syntax.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="54"><span class="lineNum">      54 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb</a>
+<a name="55"><span class="lineNum">      55 </span>            : t1: TORSION ATOMS=@phi-3</a>
+<a name="56"><span class="lineNum">      56 </span>            : t2: TORSION ATOMS=@psi-4</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=t1,t2 FILE=colvar STRIDE=10</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.</a>
+<a name="61"><span class="lineNum">      61 </span>            : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the fourth residue of the protein.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : Both of the previous examples specify that the torsion angle should be calculated based on the position of four atoms.</a>
+<a name="64"><span class="lineNum">      64 </span>            : For the first example in particular the assumption when the torsion is specified in this way is that there are chemical</a>
+<a name="65"><span class="lineNum">      65 </span>            : bonds between atoms 1 and 2, atoms 2 and 3 and atoms 3 and 4. In general, however, a torsional angle measures the angle</a>
+<a name="66"><span class="lineNum">      66 </span>            : between two planes, which have at least one vector in common.  As shown below, there is thus an alternate, more general, way</a>
+<a name="67"><span class="lineNum">      67 </span>            : through which we can define a torsional angle:</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : t1: TORSION VECTOR1=1,2 AXIS=3,4 VECTOR2=5,6</a>
+<a name="71"><span class="lineNum">      71 </span>            : PRINT ARG=t1 FILE=colvar STRIDE=20</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : This input instructs PLUMED to calculate the angle between the plane containing the vector connecting atoms 1 and 2 and the vector</a>
+<a name="75"><span class="lineNum">      75 </span>            : connecting atoms 3 and 4 and the plane containing this second vector and the vector connecting atoms 5 and 6.  We can even use</a>
+<a name="76"><span class="lineNum">      76 </span>            : PLUMED to calculate the torsional angle between two bond vectors around the z-axis as shown below:</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : a0: FIXEDATOM AT=0,0,0</a>
+<a name="80"><span class="lineNum">      80 </span>            : az: FIXEDATOM AT=0,0,1</a>
+<a name="81"><span class="lineNum">      81 </span>            : t1: TORSION VECTOR1=1,2 AXIS=a0,az VECTOR2=5,6</a>
+<a name="82"><span class="lineNum">      82 </span>            : PRINT ARG=t1 FILE=colvar STRIDE=20</a>
+<a name="83"><span class="lineNum">      83 </span>            : \endplumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : */</a>
+<a name="87"><span class="lineNum">      87 </span>            : //+ENDPLUMEDOC</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : class Torsion : public Colvar {</a>
+<a name="90"><span class="lineNum">      90 </span>            :   bool pbc;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   bool do_cosine;</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : public:</a>
+<a name="94"><span class="lineNum">      94 </span>            :   explicit Torsion(const ActionOptions&amp;);</a>
+<a name="95"><span class="lineNum">      95 </span>            : // active methods:</a>
+<a name="96"><span class="lineNum">      96 </span>            :   void calculate() override;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="98"><span class="lineNum">      98 </span>            : };</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      13816 : PLUMED_REGISTER_ACTION(Torsion,&quot;TORSION&quot;)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        659 : void Torsion::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        659 :   Colvar::registerKeywords( keys );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1318 :   keys.add(&quot;atoms-1&quot;,&quot;ATOMS&quot;,&quot;the four atoms involved in the torsional angle&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1318 :   keys.add(&quot;atoms-2&quot;,&quot;AXIS&quot;,&quot;two atoms that define an axis.  You can use this to find the angle in the plane perpendicular to the axis between the vectors specified using the VECTOR1 and VECTOR2 keywords.&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1318 :   keys.add(&quot;atoms-2&quot;,&quot;VECTOR1&quot;,&quot;two atoms that define a vector.  You can use this in combination with VECTOR2 and AXIS&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1318 :   keys.add(&quot;atoms-2&quot;,&quot;VECTOR2&quot;,&quot;two atoms that define a vector.  You can use this in combination with VECTOR1 and AXIS&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1318 :   keys.addFlag(&quot;COSINE&quot;,false,&quot;calculate cosine instead of dihedral&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        659 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        657 : Torsion::Torsion(const ActionOptions&amp;ao):</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        657 :   pbc(true),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        657 :   do_cosine(false)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : {</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::vector&lt;AtomNumber&gt; atoms,v1,v2,axis;</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        657 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        657 :   parseAtomList(&quot;VECTOR1&quot;,v1);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        657 :   parseAtomList(&quot;VECTOR2&quot;,v2);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        657 :   parseAtomList(&quot;AXIS&quot;,axis);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        657 :   parseFlag(&quot;COSINE&quot;,do_cosine);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        657 :   bool nopbc=!pbc;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        657 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        657 :   pbc=!nopbc;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        657 :   checkRead();</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        657 :   if(atoms.size()==4) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        652 :     if(!(v1.empty() &amp;&amp; v2.empty() &amp;&amp; axis.empty()))</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 :       error(&quot;ATOMS keyword is not compatible with VECTOR1, VECTOR2 and AXIS keywords&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        651 :     log.printf(&quot;  between atoms %d %d %d %d\n&quot;,atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial());</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        651 :     atoms.resize(6);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        651 :     atoms[5]=atoms[3];</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        651 :     atoms[4]=atoms[2];</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        651 :     atoms[3]=atoms[2];</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        651 :     atoms[2]=atoms[1];</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          5 :   } else if(atoms.empty()) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :     if(!(v1.size()==2 &amp;&amp; v2.size()==2 &amp;&amp; axis.size()==2))</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       error(&quot;VECTOR1, VECTOR2 and AXIS should specify 2 atoms each&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :     log.printf(&quot;  between lines %d-%d and %d-%d, projected on the plane orthogonal to line %d-%d\n&quot;,</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :                v1[0].serial(),v1[1].serial(),v2[0].serial(),v2[1].serial(),axis[0].serial(),axis[1].serial());</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 :     atoms.resize(6);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          4 :     atoms[0]=v1[1];</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          4 :     atoms[1]=v1[0];</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :     atoms[2]=axis[0];</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 :     atoms[3]=axis[1];</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          4 :     atoms[4]=v2[0];</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          4 :     atoms[5]=v2[1];</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   } else error(&quot;ATOMS should specify 4 atoms&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        655 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        112 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        655 :   if(do_cosine) log.printf(&quot;  calculating cosine instead of torsion\n&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        655 :   addValueWithDerivatives();</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1312 :   if(!do_cosine) setPeriodic(&quot;-pi&quot;,&quot;pi&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :   else setNotPeriodic();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        655 :   requestAtoms(atoms);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        659 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : // calculator</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      34591 : void Torsion::calculate() {</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      34591 :   Vector d0,d1,d2;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      34591 :   if(pbc) makeWhole();</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      34591 :   d0=delta(getPosition(1),getPosition(0));</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      34591 :   d1=delta(getPosition(3),getPosition(2));</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      34591 :   d2=delta(getPosition(5),getPosition(4));</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      34591 :   Vector dd0,dd1,dd2;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   PLMD::Torsion t;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      34591 :   double torsion=t.compute(d0,d1,d2,dd0,dd1,dd2);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      34591 :   if(do_cosine) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     dd0 *= -std::sin(torsion);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     dd1 *= -std::sin(torsion);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     dd2 *= -std::sin(torsion);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     torsion = std::cos(torsion);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      34591 :   setAtomsDerivatives(0,dd0);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      34591 :   setAtomsDerivatives(1,-dd0);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      34591 :   setAtomsDerivatives(2,dd1);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      34591 :   setAtomsDerivatives(3,-dd1);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      34591 :   setAtomsDerivatives(4,dd2);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">      34591 :   setAtomsDerivatives(5,-dd2);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      34591 :   setValue           (torsion);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      34591 :   setBoxDerivativesNoPbc();</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      34591 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Volume.cpp.func-sort-c.html b/coverage/colvar/Volume.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0c769ffa5c
--- /dev/null
+++ b/coverage/colvar/Volume.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Volume.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Volume.cpp<span style="font-size: 80%;"> (<a href="Volume.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Volume.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#54">_ZN4PLMD6colvar6VolumeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#52">_ZN4PLMD6colvar12_GLOBAL__N_118VolumeRegisterMe546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#54">_ZN4PLMD6colvar6VolumeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#64">_ZN4PLMD6colvar6Volume16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#72">_ZN4PLMD6colvar6Volume9calculateEv</a></td>
+              <td class="coverFnHi">148</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#52">_ZN4PLMD6colvar12_GLOBAL__N_118VolumeRegisterMe54C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#52">_ZN4PLMD6colvar12_GLOBAL__N_118VolumeRegisterMe54D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Volume.cpp.func.html b/coverage/colvar/Volume.cpp.func.html
new file mode 100644
index 0000000000..4673e7c8f1
--- /dev/null
+++ b/coverage/colvar/Volume.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Volume.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Volume.cpp<span style="font-size: 80%;"> (<a href="Volume.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Volume.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#52">_ZN4PLMD6colvar12_GLOBAL__N_118VolumeRegisterMe546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#52">_ZN4PLMD6colvar12_GLOBAL__N_118VolumeRegisterMe54C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#52">_ZN4PLMD6colvar12_GLOBAL__N_118VolumeRegisterMe54D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#64">_ZN4PLMD6colvar6Volume16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#72">_ZN4PLMD6colvar6Volume9calculateEv</a></td>
+              <td class="coverFnHi">148</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#54">_ZN4PLMD6colvar6VolumeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Volume.cpp.gcov.html#54">_ZN4PLMD6colvar6VolumeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/Volume.cpp.gcov.html b/coverage/colvar/Volume.cpp.gcov.html
new file mode 100644
index 0000000000..88cc412d17
--- /dev/null
+++ b/coverage/colvar/Volume.cpp.gcov.html
@@ -0,0 +1,161 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar/Volume.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">colvar</a> - Volume.cpp<span style="font-size: 80%;"> (source / <a href="Volume.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace colvar {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC COLVAR VOLUME</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate the volume of the simulation box.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : The following input tells plumed to print the volume of the system</a>
+<a name="35"><span class="lineNum">      35 </span>            : \plumedfile</a>
+<a name="36"><span class="lineNum">      36 </span>            : vol: VOLUME</a>
+<a name="37"><span class="lineNum">      37 </span>            : PRINT ARG=vol</a>
+<a name="38"><span class="lineNum">      38 </span>            : \endplumedfile</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : */</a>
+<a name="41"><span class="lineNum">      41 </span>            : //+ENDPLUMEDOC</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class Volume : public Colvar {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : public:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit Volume(const ActionOptions&amp;);</a>
+<a name="48"><span class="lineNum">      48 </span>            : // active methods:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void calculate() override;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Register all the keywords for this action</a>
+<a name="51"><span class="lineNum">      51 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="52"><span class="lineNum">      52 </span>            : };</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(Volume,&quot;VOLUME&quot;)</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          9 : Volume::Volume(const ActionOptions&amp;ao):</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          9 :   PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : {</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          9 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          9 :   requestAtoms(atoms);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          9 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         11 : void Volume::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         11 :   Action::registerKeywords( keys );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         11 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         11 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         11 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : // calculator</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        148 : void Volume::calculate() {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        148 :   double v=getBox().determinant();</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        148 :   setBoxDerivatives(-v*Tensor::identity());</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        148 :   setValue         (v);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        148 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/index-sort-f.html b/coverage/colvar/index-sort-f.html
new file mode 100644
index 0000000000..19096e5f34
--- /dev/null
+++ b/coverage/colvar/index-sort-f.html
@@ -0,0 +1,393 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - colvar</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2101</td>
+            <td class="headerCovTableEntry">2235</td>
+            <td class="headerCovTableEntryHi">94.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">184</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryMed">82.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Template.cpp.gcov.html">Template.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="22.9%"><img src="../snow.png" width=77 height=10 alt="22.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.9&nbsp;%</td>
+      <td class="coverNumLo">8 / 35</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoordinationBase.cpp.gcov.html">CoordinationBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">92 / 93</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSDBase.cpp.gcov.html">PathMSDBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.8%"><img src="../snow.png" width=2 height=10 alt="97.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.8&nbsp;%</td>
+      <td class="coverNumHi">178 / 182</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Fake.cpp.gcov.html">Fake.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.6%"><img src="../snow.png" width=18 height=10 alt="81.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.6&nbsp;%</td>
+      <td class="coverNumMed">31 / 38</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactMap.cpp.gcov.html">ContactMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">121 / 132</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PropertyMap.cpp.gcov.html">PropertyMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">25 / 27</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSD.cpp.gcov.html">PathMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.cpp.gcov.html">ERMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">51 / 52</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angle.cpp.gcov.html">Angle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">38 / 39</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Coordination.cpp.gcov.html">Coordination.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsion.cpp.gcov.html">Torsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">66 / 72</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DHEnergy.cpp.gcov.html">DHEnergy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.1%"><img src="../snow.png" width=6 height=10 alt="94.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.1&nbsp;%</td>
+      <td class="coverNumHi">32 / 34</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Constant.cpp.gcov.html">Constant.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">43 / 45</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Cell.cpp.gcov.html">Cell.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GHBFIX.cpp.gcov.html">GHBFIX.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">77 / 77</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Volume.cpp.gcov.html">Volume.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiRMSD.cpp.gcov.html">MultiRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.7%"><img src="../snow.png" width=2 height=10 alt="97.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.7&nbsp;%</td>
+      <td class="coverNumHi">42 / 43</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Dipole.cpp.gcov.html">Dipole.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gyration.cpp.gcov.html">Gyration.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">144 / 186</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.cpp.gcov.html">RMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ProjectionOnAxis.cpp.gcov.html">ProjectionOnAxis.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">60 / 63</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Distance.cpp.gcov.html">Distance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">82 / 82</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRMSD.cpp.gcov.html">DRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">44 / 44</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Position.cpp.gcov.html">Position.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">66 / 66</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCARMSD.cpp.gcov.html">PCARMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">94 / 95</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Dimer.cpp.gcov.html">Dimer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.2%"><img src="../snow.png" width=8 height=10 alt="92.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.2&nbsp;%</td>
+      <td class="coverNumHi">83 / 90</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExtraCV.cpp.gcov.html">ExtraCV.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Energy.cpp.gcov.html">Energy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Puckering.cpp.gcov.html">Puckering.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.6%"><img src="../snow.png" width=1 height=10 alt="99.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.6&nbsp;%</td>
+      <td class="coverNumHi">229 / 230</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EEFSolv.cpp.gcov.html">EEFSolv.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.3%"><img src="../snow.png" width=6 height=10 alt="94.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.3&nbsp;%</td>
+      <td class="coverNumHi">230 / 244</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSDBase.h.gcov.html">PathMSDBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/index-sort-l.html b/coverage/colvar/index-sort-l.html
new file mode 100644
index 0000000000..2c8bc2b831
--- /dev/null
+++ b/coverage/colvar/index-sort-l.html
@@ -0,0 +1,393 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - colvar</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2101</td>
+            <td class="headerCovTableEntry">2235</td>
+            <td class="headerCovTableEntryHi">94.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">184</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryMed">82.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Template.cpp.gcov.html">Template.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="22.9%"><img src="../snow.png" width=77 height=10 alt="22.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.9&nbsp;%</td>
+      <td class="coverNumLo">8 / 35</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSDBase.h.gcov.html">PathMSDBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gyration.cpp.gcov.html">Gyration.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">144 / 186</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Fake.cpp.gcov.html">Fake.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.6%"><img src="../snow.png" width=18 height=10 alt="81.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.6&nbsp;%</td>
+      <td class="coverNumMed">31 / 38</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsion.cpp.gcov.html">Torsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">66 / 72</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactMap.cpp.gcov.html">ContactMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">121 / 132</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Dimer.cpp.gcov.html">Dimer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.2%"><img src="../snow.png" width=8 height=10 alt="92.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.2&nbsp;%</td>
+      <td class="coverNumHi">83 / 90</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PropertyMap.cpp.gcov.html">PropertyMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">25 / 27</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DHEnergy.cpp.gcov.html">DHEnergy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.1%"><img src="../snow.png" width=6 height=10 alt="94.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.1&nbsp;%</td>
+      <td class="coverNumHi">32 / 34</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EEFSolv.cpp.gcov.html">EEFSolv.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.3%"><img src="../snow.png" width=6 height=10 alt="94.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.3&nbsp;%</td>
+      <td class="coverNumHi">230 / 244</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ProjectionOnAxis.cpp.gcov.html">ProjectionOnAxis.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">60 / 63</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Constant.cpp.gcov.html">Constant.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">43 / 45</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angle.cpp.gcov.html">Angle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">38 / 39</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiRMSD.cpp.gcov.html">MultiRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.7%"><img src="../snow.png" width=2 height=10 alt="97.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.7&nbsp;%</td>
+      <td class="coverNumHi">42 / 43</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSDBase.cpp.gcov.html">PathMSDBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.8%"><img src="../snow.png" width=2 height=10 alt="97.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.8&nbsp;%</td>
+      <td class="coverNumHi">178 / 182</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.cpp.gcov.html">ERMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">51 / 52</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoordinationBase.cpp.gcov.html">CoordinationBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">92 / 93</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCARMSD.cpp.gcov.html">PCARMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">94 / 95</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Puckering.cpp.gcov.html">Puckering.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.6%"><img src="../snow.png" width=1 height=10 alt="99.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.6&nbsp;%</td>
+      <td class="coverNumHi">229 / 230</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Volume.cpp.gcov.html">Volume.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSD.cpp.gcov.html">PathMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExtraCV.cpp.gcov.html">ExtraCV.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Energy.cpp.gcov.html">Energy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Coordination.cpp.gcov.html">Coordination.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Cell.cpp.gcov.html">Cell.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRMSD.cpp.gcov.html">DRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">44 / 44</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.cpp.gcov.html">RMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Dipole.cpp.gcov.html">Dipole.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Position.cpp.gcov.html">Position.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">66 / 66</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GHBFIX.cpp.gcov.html">GHBFIX.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">77 / 77</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Distance.cpp.gcov.html">Distance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">82 / 82</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/colvar/index.html b/coverage/colvar/index.html
new file mode 100644
index 0000000000..b45fa8e4e1
--- /dev/null
+++ b/coverage/colvar/index.html
@@ -0,0 +1,393 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - colvar</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - colvar</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2101</td>
+            <td class="headerCovTableEntry">2235</td>
+            <td class="headerCovTableEntryHi">94.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">184</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryMed">82.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angle.cpp.gcov.html">Angle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">38 / 39</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Cell.cpp.gcov.html">Cell.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Constant.cpp.gcov.html">Constant.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">43 / 45</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContactMap.cpp.gcov.html">ContactMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">121 / 132</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Coordination.cpp.gcov.html">Coordination.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoordinationBase.cpp.gcov.html">CoordinationBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">92 / 93</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DHEnergy.cpp.gcov.html">DHEnergy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.1%"><img src="../snow.png" width=6 height=10 alt="94.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.1&nbsp;%</td>
+      <td class="coverNumHi">32 / 34</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRMSD.cpp.gcov.html">DRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">44 / 44</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Dimer.cpp.gcov.html">Dimer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.2%"><img src="../snow.png" width=8 height=10 alt="92.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.2&nbsp;%</td>
+      <td class="coverNumHi">83 / 90</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Dipole.cpp.gcov.html">Dipole.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Distance.cpp.gcov.html">Distance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">82 / 82</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EEFSolv.cpp.gcov.html">EEFSolv.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.3%"><img src="../snow.png" width=6 height=10 alt="94.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.3&nbsp;%</td>
+      <td class="coverNumHi">230 / 244</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.cpp.gcov.html">ERMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">51 / 52</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Energy.cpp.gcov.html">Energy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExtraCV.cpp.gcov.html">ExtraCV.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Fake.cpp.gcov.html">Fake.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.6%"><img src="../snow.png" width=18 height=10 alt="81.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.6&nbsp;%</td>
+      <td class="coverNumMed">31 / 38</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GHBFIX.cpp.gcov.html">GHBFIX.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">77 / 77</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gyration.cpp.gcov.html">Gyration.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">144 / 186</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiRMSD.cpp.gcov.html">MultiRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.7%"><img src="../snow.png" width=2 height=10 alt="97.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.7&nbsp;%</td>
+      <td class="coverNumHi">42 / 43</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCARMSD.cpp.gcov.html">PCARMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.9%"><img src="../snow.png" width=1 height=10 alt="98.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.9&nbsp;%</td>
+      <td class="coverNumHi">94 / 95</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSD.cpp.gcov.html">PathMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSDBase.cpp.gcov.html">PathMSDBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.8%"><img src="../snow.png" width=2 height=10 alt="97.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.8&nbsp;%</td>
+      <td class="coverNumHi">178 / 182</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathMSDBase.h.gcov.html">PathMSDBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Position.cpp.gcov.html">Position.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">66 / 66</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ProjectionOnAxis.cpp.gcov.html">ProjectionOnAxis.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">60 / 63</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PropertyMap.cpp.gcov.html">PropertyMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">25 / 27</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Puckering.cpp.gcov.html">Puckering.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.6%"><img src="../snow.png" width=1 height=10 alt="99.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.6&nbsp;%</td>
+      <td class="coverNumHi">229 / 230</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.cpp.gcov.html">RMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Template.cpp.gcov.html">Template.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=23 height=10 alt="22.9%"><img src="../snow.png" width=77 height=10 alt="22.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.9&nbsp;%</td>
+      <td class="coverNumLo">8 / 35</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsion.cpp.gcov.html">Torsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">66 / 72</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Volume.cpp.gcov.html">Volume.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/Config.inc.func-sort-c.html b/coverage/config/Config.inc.func-sort-c.html
new file mode 100644
index 0000000000..9c6312b5c1
--- /dev/null
+++ b/coverage/config/Config.inc.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config/Config.inc - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">config</a> - Config.inc<span style="font-size: 80%;"> (<a href="Config.inc.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryLo">14.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">16.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Config.inc.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#163">_ZN4PLMD6config10hasMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#130">_ZN4PLMD6config11getMakefileB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#139">_ZN4PLMD6config11hasMathevalEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#58">_ZN4PLMD6config11isInstalledEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#33">_ZN4PLMD6config12_GLOBAL__N_120escapeForSingleQuoteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#49">_ZN4PLMD6config12plumed_soextEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#109">_ZN4PLMD6config13getEnvCommandB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#126">_ZN4PLMD6config13getVersionGitB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#50">_ZN4PLMD6config14plumed_htmldirEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#73">_ZN4PLMD6config16getPlumedHtmldirB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#51">_ZN4PLMD6config17plumed_includedirEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#187">_ZN4PLMD6config18getCompilationDateB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#191">_ZN4PLMD6config18getCompilationTimeB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#171">_ZN4PLMD6config18hasExternalMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#85">_ZN4PLMD6config19getPlumedIncludedirB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#52">_ZN4PLMD6config19plumed_program_nameEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#97">_ZN4PLMD6config20getPlumedProgramNameB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#179">_ZN4PLMD6config7hasZlibEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#54">_ZN4PLMD6config8getSoExtB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#155">_ZN4PLMD6config9hasCregexEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#147">_ZN4PLMD6config9hasDlopenEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#118">_ZN4PLMD6config10getVersionB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#122">_ZN4PLMD6config14getVersionLongB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#48">_ZN4PLMD6config11plumed_rootEv</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#62">_ZN4PLMD6config13getPlumedRootB5cxx11Ev</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/Config.inc.func.html b/coverage/config/Config.inc.func.html
new file mode 100644
index 0000000000..15b9a69431
--- /dev/null
+++ b/coverage/config/Config.inc.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config/Config.inc - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">config</a> - Config.inc<span style="font-size: 80%;"> (<a href="Config.inc.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryLo">14.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">16.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Config.inc.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#118">_ZN4PLMD6config10getVersionB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#163">_ZN4PLMD6config10hasMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#130">_ZN4PLMD6config11getMakefileB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#139">_ZN4PLMD6config11hasMathevalEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#58">_ZN4PLMD6config11isInstalledEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#48">_ZN4PLMD6config11plumed_rootEv</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#33">_ZN4PLMD6config12_GLOBAL__N_120escapeForSingleQuoteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#49">_ZN4PLMD6config12plumed_soextEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#109">_ZN4PLMD6config13getEnvCommandB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#62">_ZN4PLMD6config13getPlumedRootB5cxx11Ev</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#126">_ZN4PLMD6config13getVersionGitB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#122">_ZN4PLMD6config14getVersionLongB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#50">_ZN4PLMD6config14plumed_htmldirEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#73">_ZN4PLMD6config16getPlumedHtmldirB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#51">_ZN4PLMD6config17plumed_includedirEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#187">_ZN4PLMD6config18getCompilationDateB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#191">_ZN4PLMD6config18getCompilationTimeB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#171">_ZN4PLMD6config18hasExternalMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#85">_ZN4PLMD6config19getPlumedIncludedirB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#52">_ZN4PLMD6config19plumed_program_nameEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#97">_ZN4PLMD6config20getPlumedProgramNameB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#179">_ZN4PLMD6config7hasZlibEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#54">_ZN4PLMD6config8getSoExtB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#155">_ZN4PLMD6config9hasCregexEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Config.inc.gcov.html#147">_ZN4PLMD6config9hasDlopenEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/Config.inc.gcov.html b/coverage/config/Config.inc.gcov.html
new file mode 100644
index 0000000000..ce7d1f860d
--- /dev/null
+++ b/coverage/config/Config.inc.gcov.html
@@ -0,0 +1,276 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config/Config.inc</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">config</a> - Config.inc<span style="font-size: 80%;"> (source / <a href="Config.inc.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryLo">14.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">16.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Config.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;version.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace config {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace {</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// local tool that, given a string, returns a new string which is:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// - enclosed in single quotes (')</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// - with all single quotes escaped</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 : std::string escapeForSingleQuote(const std::string&amp; input) {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::string escaped;</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineNoCov">          0 :   for (char c : input) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :     if (c == '\'') {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :       escaped += &quot;'\\''&quot;;</a>
+<a name="40"><span class="lineNum">      40 </span>            :     } else {</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :       escaped += c;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :     }</a>
+<a name="43"><span class="lineNum">      43 </span>            :   }</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :   return &quot;'&quot; + escaped + &quot;'&quot;;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : }</a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // This is a fix to allow conda to correctly replace paths in binary files.</a>
+<a name="49"><span class="lineNum">      49 </span>            : // These functions should not be static or they will be optimized away!</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        294 : const char* plumed_root() {return &quot;/home/runner/work/plumed2/plumed2/&quot;;}</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 : const char* plumed_soext() {return &quot;so&quot;;}</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 : const char* plumed_htmldir() {return &quot;xxxxNAxxxx&quot;;}</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 : const char* plumed_includedir() {return &quot;xxxxNAxxxx&quot;;}</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 : const char* plumed_program_name() {return &quot;xxxxNAxxxx&quot;;}</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 : std::string getSoExt() {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   return plumed_soext();</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 : bool isInstalled() {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        294 : std::string getPlumedRoot() {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        294 :   char *env = std::getenv(&quot;PLUMED_ROOT&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::string ss;</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        294 :   if( env == NULL) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        294 :     ss=plumed_root();</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   } else {</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   }</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        294 :   return ss;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 : std::string getPlumedHtmldir() {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   if(!isInstalled()) return getPlumedRoot();</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :   char *env = std::getenv(&quot;PLUMED_HTMLDIR&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::string ss;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   if( env == NULL) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :     ss=plumed_htmldir();</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   } else {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span>            :   return ss;</a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 : std::string getPlumedIncludedir() {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :   if(!isInstalled()) return getPlumedRoot()+&quot;/src/include&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   char *env = std::getenv(&quot;PLUMED_INCLUDEDIR&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::string ss;</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   if( env == NULL) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     ss=plumed_includedir();</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   } else {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            :   return ss;</a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 : std::string getPlumedProgramName() {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   if(!isInstalled()) return &quot;plumed&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   char *env = std::getenv(&quot;PLUMED_PROGRAM_NAME&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::string ss;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   if( env == NULL) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     ss=plumed_program_name();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   } else {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span>            :   return ss;</a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 : std::string getEnvCommand() {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   return &quot;env PLUMED_ROOT=&quot;+escapeForSingleQuote(getPlumedRoot())+</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :          &quot; PLUMED_VERSION=&quot;+escapeForSingleQuote(getVersionLong())+</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :          &quot; PLUMED_HTMLDIR=&quot;+escapeForSingleQuote(getPlumedHtmldir())+</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :          &quot; PLUMED_INCLUDEDIR=&quot;+escapeForSingleQuote(getPlumedIncludedir())+</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :          &quot; PLUMED_PROGRAM_NAME=&quot;+escapeForSingleQuote(getPlumedProgramName())+</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :          &quot; PLUMED_IS_INSTALLED='&quot;+(false?&quot;yes&quot;:&quot;no&quot;)+&quot;'&quot;;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          1 : std::string getVersion() {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          1 :   return PLUMED_VERSION_SHORT;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 : std::string getVersionLong() {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :   return PLUMED_VERSION_LONG;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 : std::string getVersionGit() {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :   return PLUMED_VERSION_GIT;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 : std::string getMakefile() {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   static const unsigned char confu [] = {</a>
+<a name="134"><span class="lineNum">     134 </span>            : #include &quot;Makefile.conf.xxd&quot;</a>
+<a name="135"><span class="lineNum">     135 </span>            :     , 0x00</a>
+<a name="136"><span class="lineNum">     136 </span>            :   };</a>
+<a name="137"><span class="lineNum">     137 </span>            :   auto conf=(char*)confu;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   return std::string(conf,conf+std::strlen(conf));</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : bool hasMatheval() {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : #ifdef __PLUMED_HAS_MATHEVAL</a>
+<a name="143"><span class="lineNum">     143 </span>            :   return true;</a>
+<a name="144"><span class="lineNum">     144 </span>            : #else</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : #endif</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 : bool hasDlopen() {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : #else</a>
+<a name="153"><span class="lineNum">     153 </span>            :   return false;</a>
+<a name="154"><span class="lineNum">     154 </span>            : #endif</a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 : bool hasCregex() {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : #ifdef __PLUMED_HAS_CREGEX</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : #else</a>
+<a name="161"><span class="lineNum">     161 </span>            :   return false;</a>
+<a name="162"><span class="lineNum">     162 </span>            : #endif</a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : bool hasMolfile() {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : #else</a>
+<a name="169"><span class="lineNum">     169 </span>            :   return false;</a>
+<a name="170"><span class="lineNum">     170 </span>            : #endif</a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 : bool hasExternalMolfile() {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : #ifdef __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS</a>
+<a name="175"><span class="lineNum">     175 </span>            :   return true;</a>
+<a name="176"><span class="lineNum">     176 </span>            : #else</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : #endif</a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 : bool hasZlib() {</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : #else</a>
+<a name="185"><span class="lineNum">     185 </span>            :   return false;</a>
+<a name="186"><span class="lineNum">     186 </span>            : #endif</a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 : std::string getCompilationDate() {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   return __DATE__;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 : std::string getCompilationTime() {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   return __TIME__;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/ConfigInstall.inc.func-sort-c.html b/coverage/config/ConfigInstall.inc.func-sort-c.html
new file mode 100644
index 0000000000..ac1ed8b224
--- /dev/null
+++ b/coverage/config/ConfigInstall.inc.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config/ConfigInstall.inc - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">config</a> - ConfigInstall.inc<span style="font-size: 80%;"> (<a href="ConfigInstall.inc.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryMed">78.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">76.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ConfigInstall.inc.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#163">_ZN4PLMD6config10hasMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#139">_ZN4PLMD6config11hasMathevalEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#171">_ZN4PLMD6config18hasExternalMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#179">_ZN4PLMD6config7hasZlibEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#155">_ZN4PLMD6config9hasCregexEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#147">_ZN4PLMD6config9hasDlopenEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#118">_ZN4PLMD6config10getVersionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#130">_ZN4PLMD6config11getMakefileB5cxx11Ev</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#51">_ZN4PLMD6config17plumed_includedirEv</a></td>
+              <td class="coverFnHi">667</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#109">_ZN4PLMD6config13getEnvCommandB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#50">_ZN4PLMD6config14plumed_htmldirEv</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#73">_ZN4PLMD6config16getPlumedHtmldirB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#85">_ZN4PLMD6config19getPlumedIncludedirB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#52">_ZN4PLMD6config19plumed_program_nameEv</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#97">_ZN4PLMD6config20getPlumedProgramNameB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#126">_ZN4PLMD6config13getVersionGitB5cxx11Ev</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#187">_ZN4PLMD6config18getCompilationDateB5cxx11Ev</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#191">_ZN4PLMD6config18getCompilationTimeB5cxx11Ev</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#49">_ZN4PLMD6config12plumed_soextEv</a></td>
+              <td class="coverFnHi">1215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#54">_ZN4PLMD6config8getSoExtB5cxx11Ev</a></td>
+              <td class="coverFnHi">1215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#122">_ZN4PLMD6config14getVersionLongB5cxx11Ev</a></td>
+              <td class="coverFnHi">1679</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#58">_ZN4PLMD6config11isInstalledEv</a></td>
+              <td class="coverFnHi">2642</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#33">_ZN4PLMD6config12_GLOBAL__N_120escapeForSingleQuoteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3340</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#48">_ZN4PLMD6config11plumed_rootEv</a></td>
+              <td class="coverFnHi">7217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#62">_ZN4PLMD6config13getPlumedRootB5cxx11Ev</a></td>
+              <td class="coverFnHi">7217</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/ConfigInstall.inc.func.html b/coverage/config/ConfigInstall.inc.func.html
new file mode 100644
index 0000000000..b140d6b560
--- /dev/null
+++ b/coverage/config/ConfigInstall.inc.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config/ConfigInstall.inc - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">config</a> - ConfigInstall.inc<span style="font-size: 80%;"> (<a href="ConfigInstall.inc.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryMed">78.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">76.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ConfigInstall.inc.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#118">_ZN4PLMD6config10getVersionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#163">_ZN4PLMD6config10hasMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#130">_ZN4PLMD6config11getMakefileB5cxx11Ev</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#139">_ZN4PLMD6config11hasMathevalEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#58">_ZN4PLMD6config11isInstalledEv</a></td>
+              <td class="coverFnHi">2642</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#48">_ZN4PLMD6config11plumed_rootEv</a></td>
+              <td class="coverFnHi">7217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#33">_ZN4PLMD6config12_GLOBAL__N_120escapeForSingleQuoteERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3340</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#49">_ZN4PLMD6config12plumed_soextEv</a></td>
+              <td class="coverFnHi">1215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#109">_ZN4PLMD6config13getEnvCommandB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#62">_ZN4PLMD6config13getPlumedRootB5cxx11Ev</a></td>
+              <td class="coverFnHi">7217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#126">_ZN4PLMD6config13getVersionGitB5cxx11Ev</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#122">_ZN4PLMD6config14getVersionLongB5cxx11Ev</a></td>
+              <td class="coverFnHi">1679</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#50">_ZN4PLMD6config14plumed_htmldirEv</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#73">_ZN4PLMD6config16getPlumedHtmldirB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#51">_ZN4PLMD6config17plumed_includedirEv</a></td>
+              <td class="coverFnHi">667</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#187">_ZN4PLMD6config18getCompilationDateB5cxx11Ev</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#191">_ZN4PLMD6config18getCompilationTimeB5cxx11Ev</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#171">_ZN4PLMD6config18hasExternalMolfileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#85">_ZN4PLMD6config19getPlumedIncludedirB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#52">_ZN4PLMD6config19plumed_program_nameEv</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#97">_ZN4PLMD6config20getPlumedProgramNameB5cxx11Ev</a></td>
+              <td class="coverFnHi">668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#179">_ZN4PLMD6config7hasZlibEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#54">_ZN4PLMD6config8getSoExtB5cxx11Ev</a></td>
+              <td class="coverFnHi">1215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#155">_ZN4PLMD6config9hasCregexEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConfigInstall.inc.gcov.html#147">_ZN4PLMD6config9hasDlopenEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/ConfigInstall.inc.gcov.html b/coverage/config/ConfigInstall.inc.gcov.html
new file mode 100644
index 0000000000..3adb63509d
--- /dev/null
+++ b/coverage/config/ConfigInstall.inc.gcov.html
@@ -0,0 +1,276 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config/ConfigInstall.inc</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">config</a> - ConfigInstall.inc<span style="font-size: 80%;"> (source / <a href="ConfigInstall.inc.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryMed">78.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">76.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Config.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;version.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace config {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace {</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// local tool that, given a string, returns a new string which is:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// - enclosed in single quotes (')</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// - with all single quotes escaped</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       3340 : std::string escapeForSingleQuote(const std::string&amp; input) {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::string escaped;</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      66805 :   for (char c : input) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      63465 :     if (c == '\'') {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :       escaped += &quot;'\\''&quot;;</a>
+<a name="40"><span class="lineNum">      40 </span>            :     } else {</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      63465 :       escaped += c;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :     }</a>
+<a name="43"><span class="lineNum">      43 </span>            :   }</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       6680 :   return &quot;'&quot; + escaped + &quot;'&quot;;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : }</a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // This is a fix to allow conda to correctly replace paths in binary files.</a>
+<a name="49"><span class="lineNum">      49 </span>            : // These functions should not be static or they will be optimized away!</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       7217 : const char* plumed_root() {return &quot;/home/runner/opt/lib/plumed&quot;;}</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1215 : const char* plumed_soext() {return &quot;so&quot;;}</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        668 : const char* plumed_htmldir() {return &quot;/home/runner/opt/share/doc/plumed&quot;;}</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        667 : const char* plumed_includedir() {return &quot;/home/runner/opt/include&quot;;}</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        668 : const char* plumed_program_name() {return &quot;plumed&quot;;}</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       1215 : std::string getSoExt() {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1215 :   return plumed_soext();</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       2642 : bool isInstalled() {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       2642 :   return true;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       7217 : std::string getPlumedRoot() {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       7217 :   char *env = std::getenv(&quot;PLUMED_ROOT&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::string ss;</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       7217 :   if( env == NULL) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       7217 :     ss=plumed_root();</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   } else {</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   }</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       7217 :   return ss;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        668 : std::string getPlumedHtmldir() {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        668 :   if(!isInstalled()) return getPlumedRoot();</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        668 :   char *env = std::getenv(&quot;PLUMED_HTMLDIR&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::string ss;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        668 :   if( env == NULL) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        668 :     ss=plumed_htmldir();</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   } else {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span>            :   return ss;</a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        668 : std::string getPlumedIncludedir() {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        668 :   if(!isInstalled()) return getPlumedRoot()+&quot;/src/include&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        668 :   char *env = std::getenv(&quot;PLUMED_INCLUDEDIR&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::string ss;</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        668 :   if( env == NULL) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        667 :     ss=plumed_includedir();</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   } else {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :     ss=std::string( env );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            :   return ss;</a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        668 : std::string getPlumedProgramName() {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        668 :   if(!isInstalled()) return &quot;plumed&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        668 :   char *env = std::getenv(&quot;PLUMED_PROGRAM_NAME&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::string ss;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        668 :   if( env == NULL) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        668 :     ss=plumed_program_name();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   } else {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     ss=std::string( env );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span>            :   return ss;</a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        668 : std::string getEnvCommand() {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1336 :   return &quot;env PLUMED_ROOT=&quot;+escapeForSingleQuote(getPlumedRoot())+</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       2672 :          &quot; PLUMED_VERSION=&quot;+escapeForSingleQuote(getVersionLong())+</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       2672 :          &quot; PLUMED_HTMLDIR=&quot;+escapeForSingleQuote(getPlumedHtmldir())+</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       2672 :          &quot; PLUMED_INCLUDEDIR=&quot;+escapeForSingleQuote(getPlumedIncludedir())+</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       2672 :          &quot; PLUMED_PROGRAM_NAME=&quot;+escapeForSingleQuote(getPlumedProgramName())+</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       2004 :          &quot; PLUMED_IS_INSTALLED='&quot;+(true?&quot;yes&quot;:&quot;no&quot;)+&quot;'&quot;;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          4 : std::string getVersion() {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          4 :   return PLUMED_VERSION_SHORT;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       1679 : std::string getVersionLong() {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       1679 :   return PLUMED_VERSION_LONG;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       1007 : std::string getVersionGit() {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       1007 :   return PLUMED_VERSION_GIT;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         31 : std::string getMakefile() {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   static const unsigned char confu [] = {</a>
+<a name="134"><span class="lineNum">     134 </span>            : #include &quot;Makefile.conf.xxd&quot;</a>
+<a name="135"><span class="lineNum">     135 </span>            :     , 0x00</a>
+<a name="136"><span class="lineNum">     136 </span>            :   };</a>
+<a name="137"><span class="lineNum">     137 </span>            :   auto conf=(char*)confu;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         31 :   return std::string(conf,conf+std::strlen(conf));</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : bool hasMatheval() {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : #ifdef __PLUMED_HAS_MATHEVAL</a>
+<a name="143"><span class="lineNum">     143 </span>            :   return true;</a>
+<a name="144"><span class="lineNum">     144 </span>            : #else</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : #endif</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 : bool hasDlopen() {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : #else</a>
+<a name="153"><span class="lineNum">     153 </span>            :   return false;</a>
+<a name="154"><span class="lineNum">     154 </span>            : #endif</a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 : bool hasCregex() {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : #ifdef __PLUMED_HAS_CREGEX</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : #else</a>
+<a name="161"><span class="lineNum">     161 </span>            :   return false;</a>
+<a name="162"><span class="lineNum">     162 </span>            : #endif</a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : bool hasMolfile() {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : #ifdef __PLUMED_HAS_MOLFILE_PLUGINS</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : #else</a>
+<a name="169"><span class="lineNum">     169 </span>            :   return false;</a>
+<a name="170"><span class="lineNum">     170 </span>            : #endif</a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 : bool hasExternalMolfile() {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : #ifdef __PLUMED_HAS_EXTERNAL_MOLFILE_PLUGINS</a>
+<a name="175"><span class="lineNum">     175 </span>            :   return true;</a>
+<a name="176"><span class="lineNum">     176 </span>            : #else</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : #endif</a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 : bool hasZlib() {</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   return true;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : #else</a>
+<a name="185"><span class="lineNum">     185 </span>            :   return false;</a>
+<a name="186"><span class="lineNum">     186 </span>            : #endif</a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       1007 : std::string getCompilationDate() {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       1007 :   return __DATE__;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       1007 : std::string getCompilationTime() {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1007 :   return __TIME__;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/index-sort-f.html b/coverage/config/index-sort-f.html
new file mode 100644
index 0000000000..26c3c378ad
--- /dev/null
+++ b/coverage/config/index-sort-f.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - config</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryLo">46.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryLo">46.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Config.inc.gcov.html">Config.inc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=14 height=10 alt="14.5%"><img src="../snow.png" width=86 height=10 alt="14.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">14.5&nbsp;%</td>
+      <td class="coverNumLo">10 / 69</td>
+      <td class="coverPerLo">16.0&nbsp;%</td>
+      <td class="coverNumLo">4 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConfigInstall.inc.gcov.html">ConfigInstall.inc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.3%"><img src="../snow.png" width=22 height=10 alt="78.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.3&nbsp;%</td>
+      <td class="coverNumMed">54 / 69</td>
+      <td class="coverPerMed">76.0&nbsp;%</td>
+      <td class="coverNumMed">19 / 25</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/index-sort-l.html b/coverage/config/index-sort-l.html
new file mode 100644
index 0000000000..d381d97342
--- /dev/null
+++ b/coverage/config/index-sort-l.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - config</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryLo">46.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryLo">46.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Config.inc.gcov.html">Config.inc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=14 height=10 alt="14.5%"><img src="../snow.png" width=86 height=10 alt="14.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">14.5&nbsp;%</td>
+      <td class="coverNumLo">10 / 69</td>
+      <td class="coverPerLo">16.0&nbsp;%</td>
+      <td class="coverNumLo">4 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConfigInstall.inc.gcov.html">ConfigInstall.inc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.3%"><img src="../snow.png" width=22 height=10 alt="78.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.3&nbsp;%</td>
+      <td class="coverNumMed">54 / 69</td>
+      <td class="coverPerMed">76.0&nbsp;%</td>
+      <td class="coverNumMed">19 / 25</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/config/index.html b/coverage/config/index.html
new file mode 100644
index 0000000000..7cbabee3a5
--- /dev/null
+++ b/coverage/config/index.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - config</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - config</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryLo">46.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryLo">46.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Config.inc.gcov.html">Config.inc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=14 height=10 alt="14.5%"><img src="../snow.png" width=86 height=10 alt="14.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">14.5&nbsp;%</td>
+      <td class="coverNumLo">10 / 69</td>
+      <td class="coverPerLo">16.0&nbsp;%</td>
+      <td class="coverNumLo">4 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConfigInstall.inc.gcov.html">ConfigInstall.inc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.3%"><img src="../snow.png" width=22 height=10 alt="78.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.3&nbsp;%</td>
+      <td class="coverNumMed">54 / 69</td>
+      <td class="coverPerMed">76.0&nbsp;%</td>
+      <td class="coverNumMed">19 / 25</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Action.cpp.func-sort-c.html b/coverage/core/Action.cpp.func-sort-c.html
new file mode 100644
index 0000000000..237fd14ddb
--- /dev/null
+++ b/coverage/core/Action.cpp.func-sort-c.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Action.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Action.cpp<span style="font-size: 80%;"> (<a href="Action.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntry">154</td>
+            <td class="headerCovTableEntryMed">79.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Action.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#189">_ZN4PLMD6Action12clearOptionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#245">_ZN4PLMD6Action16calculateFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#228">_ZN4PLMD6Action29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#224">_ZN4PLMD6Action4exitEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#101">_ZN4PLMD6ActionD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#236">_ZNK4PLMD6Action5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#128">_ZN4PLMD6Action10getKeywordERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#261">_ZN4PLMD6Action4citeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#107">_ZN4PLMD6Action5fopenEPKcS2_</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#117">_ZN4PLMD6Action6fcloseEP8_IO_FILE</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#241">_ZN4PLMD6Action7warningERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">129</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#183">_ZN4PLMD6Action9setOptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">267</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#272">_ZNK4PLMD6Action6getCPTEv</a></td>
+              <td class="coverFnHi">1095</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#101">_ZN4PLMD6ActionD2Ev</a></td>
+              <td class="coverFnHi">14301</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#40">_ZN4PLMD13ActionOptionsC2ERKS0_RKNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#55">_ZN4PLMD6ActionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#33">_ZN4PLMD13ActionOptionsC2ERNS_10PlumedMainERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EE</a></td>
+              <td class="coverFnHi">14304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#47">_ZN4PLMD6Action16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14881</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#218">_ZNK4PLMD6Action11getTimeStepEv</a></td>
+              <td class="coverFnHi">16292</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#122">_ZN4PLMD6Action6fflushEv</a></td>
+              <td class="coverFnHi">18057</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#199">_ZN4PLMD6Action9checkReadEv</a></td>
+              <td class="coverFnHi">27861</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#257">_ZNK4PLMD6Action15getExchangeStepEv</a></td>
+              <td class="coverFnHi">28109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#146">_ZN4PLMD6Action9parseFlagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERb</a></td>
+              <td class="coverFnHi">40900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#195">_ZN4PLMD6Action17clearDependenciesEv</a></td>
+              <td class="coverFnHi">189162</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#232">_ZN4PLMD6Action7prepareEv</a></td>
+              <td class="coverFnHi">325089</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#165">_ZN4PLMD6Action13addDependencyEPS0_</a></td>
+              <td class="coverFnHi">1084028</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#266">_ZNK4PLMD6Action11checkUpdateEv</a></td>
+              <td class="coverFnHi">1642986</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#214">_ZNK4PLMD6Action7getTimeEv</a></td>
+              <td class="coverFnHi">2991243</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#169">_ZN4PLMD6Action8activateEv</a></td>
+              <td class="coverFnHi">3214026</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#210">_ZNK4PLMD6Action7getStepEv</a></td>
+              <td class="coverFnHi">4557159</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Action.cpp.func.html b/coverage/core/Action.cpp.func.html
new file mode 100644
index 0000000000..72693f0c57
--- /dev/null
+++ b/coverage/core/Action.cpp.func.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Action.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Action.cpp<span style="font-size: 80%;"> (<a href="Action.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntry">154</td>
+            <td class="headerCovTableEntryMed">79.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Action.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#40">_ZN4PLMD13ActionOptionsC2ERKS0_RKNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#33">_ZN4PLMD13ActionOptionsC2ERNS_10PlumedMainERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EE</a></td>
+              <td class="coverFnHi">14304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#128">_ZN4PLMD6Action10getKeywordERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.cpp.gcov.html#189">_ZN4PLMD6Action12clearOptionsEv</a></td>
+              <td class="coverFnLo">0</td>
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+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Action.cpp.gcov.html b/coverage/core/Action.cpp.gcov.html
new file mode 100644
index 0000000000..710bba2d03
--- /dev/null
+++ b/coverage/core/Action.cpp.gcov.html
@@ -0,0 +1,355 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Action.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Action.cpp<span style="font-size: 80%;"> (source / <a href="Action.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntry">154</td>
+            <td class="headerCovTableEntryMed">79.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Action.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Log.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Keywords ActionOptions::emptyKeys;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">      14304 : ActionOptions::ActionOptions(PlumedMain&amp;p,const std::vector&lt;std::string&gt;&amp;l):</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">      14304 :   plumed(p),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      14304 :   line(l),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      14304 :   keys(emptyKeys)</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : {</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      14304 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      14302 : ActionOptions::ActionOptions(const ActionOptions&amp;ao,const Keywords&amp;keys):</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      14302 :   plumed(ao.plumed),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      14302 :   line(ao.line),</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      14302 :   keys(keys)</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : {</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      14302 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      14881 : void Action::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      14881 :   plumed_assert( keys.size()==0 );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      29762 :   keys.add( &quot;hidden&quot;, &quot;LABEL&quot;, &quot;a label for the action so that its output can be referenced in the input to other actions.  Actions with scalar output are referenced using their label only.  Actions with vector output must have a separate label for every component.  Individual components are then referred to using label.component&quot; );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      29762 :   keys.reserve(&quot;optional&quot;,&quot;UPDATE_FROM&quot;,&quot;Only update this action from this time&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      29762 :   keys.reserve(&quot;optional&quot;,&quot;UPDATE_UNTIL&quot;,&quot;Only update this action until this time&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      29762 :   keys.reserve(&quot;optional&quot;,&quot;RESTART&quot;,&quot;allows per-action setting of restart (YES/NO/AUTO)&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      14881 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      14302 : Action::Action(const ActionOptions&amp;ao):</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      14302 :   name(ao.line[0]),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      14302 :   line(ao.line),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      14302 :   update_from(std::numeric_limits&lt;double&gt;::max()),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      14302 :   update_until(std::numeric_limits&lt;double&gt;::max()),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      14302 :   active(false),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      14302 :   restart(ao.plumed.getRestart()),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      14302 :   doCheckPoint(ao.plumed.getCPT()),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      14302 :   plumed(ao.plumed),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      14302 :   log(plumed.getLog()),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      14302 :   comm(plumed.comm),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      14302 :   multi_sim_comm(plumed.multi_sim_comm),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      14302 :   keywords(ao.keys)</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : {</a>
+<a name="71"><span class="lineNum">      71 </span>            :   line.erase(line.begin());</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      14302 :   log.printf(&quot;Action %s\n&quot;,name.c_str());</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      14302 :   if(comm.Get_rank()==0) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       7867 :     replica_index=multi_sim_comm.Get_rank();</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      14302 :   comm.Bcast(replica_index,0);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      42715 :   if ( keywords.exists(&quot;LABEL&quot;) ) { parse(&quot;LABEL&quot;,label); }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      14302 :   if(label.length()==0) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       2421 :     std::string s; Tools::convert(plumed.getActionSet().size(),s);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       4842 :     label=&quot;@&quot;+s;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      14302 :   if( plumed.getActionSet().selectWithLabel&lt;Action*&gt;(label) ) error(&quot;label &quot; + label + &quot; has been already used&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      14302 :   log.printf(&quot;  with label %s\n&quot;,label.c_str());</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      30365 :   if ( keywords.exists(&quot;UPDATE_FROM&quot;) ) parse(&quot;UPDATE_FROM&quot;,update_from);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      14302 :   if(update_from!=std::numeric_limits&lt;double&gt;::max()) log.printf(&quot;  only update from time %f\n&quot;,update_from);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      30365 :   if ( keywords.exists(&quot;UPDATE_UNTIL&quot;) ) parse(&quot;UPDATE_UNTIL&quot;,update_until);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      14302 :   if(update_until!=std::numeric_limits&lt;double&gt;::max()) log.printf(&quot;  only update until time %f\n&quot;,update_until);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      28604 :   if ( keywords.exists(&quot;RESTART&quot;) ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1821 :     std::string srestart=&quot;AUTO&quot;;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       1820 :     parse(&quot;RESTART&quot;,srestart);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1820 :     if( plumed.parseOnlyMode() ) restart=false;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1820 :     else if(srestart==&quot;YES&quot;) restart=true;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1738 :     else if(srestart==&quot;NO&quot;)  restart=false;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1716 :     else if(srestart==&quot;AUTO&quot;) {</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :       // do nothing, this is the default</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :     } else error(&quot;RESTART should be either YES, NO, or AUTO&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      14302 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      28602 : Action::~Action() {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      14301 :   if(files.size()!=0) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;WARNING: some files open in action &quot;+getLabel()+&quot; where not properly closed. This could lead to data loss!!\n&quot;;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      28602 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         73 : FILE* Action::fopen(const char *path, const char *mode) {</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   bool write(false);</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        146 :   for(const char*p=mode; *p; p++) if(*p=='w' || *p=='a' || *p=='+') write=true;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   FILE* fp;</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         73 :   if(write &amp;&amp; comm.Get_rank()!=0) fp=plumed.fopen(&quot;/dev/null&quot;,mode);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         73 :   else      fp=plumed.fopen(path,mode);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         73 :   files.insert(fp);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         73 :   return fp;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         91 : int Action::fclose(FILE*fp) {</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   files.erase(fp);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         91 :   return plumed.fclose(fp);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      18057 : void Action::fflush() {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      18057 :   for(const auto &amp; p : files) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     std::fflush(p);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      18057 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         33 : std::string Action::getKeyword(const std::string&amp; key) {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Check keyword has been registered</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         33 :   plumed_massert(keywords.exists(key), &quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::string outkey;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         33 :   if( Tools::getKey(line,key,outkey ) ) return key + outkey;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :   if( keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     if( keywords.getDefaultValue(key,outkey) ) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :       if( outkey.length()==0 ) error(&quot;keyword &quot; + key + &quot; has weird default value&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       return key + &quot;=&quot; +  outkey;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     } else {</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :       error(&quot;keyword &quot; + key + &quot; is compulsory for this action&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   return &quot;&quot;;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      40900 : void Action::parseFlag(const std::string&amp;key,bool &amp; t) {</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   // Check keyword has been registered</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      40900 :   plumed_massert(keywords.exists(key), &quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Check keyword is a flag</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      81800 :   if(!keywords.style(key,&quot;nohtml&quot;)) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      79255 :     plumed_massert( keywords.style(key,&quot;vessel&quot;) || keywords.style(key,&quot;flag&quot;) || keywords.style(key,&quot;hidden&quot;), &quot;keyword &quot; + key + &quot; is not a flag&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Read in the flag otherwise get the default value from the keywords object</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      40900 :   if(!Tools::parseFlag(line,key,t)) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      81530 :     if( keywords.style(key,&quot;nohtml&quot;) || keywords.style(key,&quot;vessel&quot;) ) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       2644 :       t=false;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      36799 :     } else if ( !keywords.getLogicalDefault(key,t) ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :       log.printf(&quot;ERROR in action %s with label %s : flag %s has no default&quot;,name.c_str(),label.c_str(),key.c_str() );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :       plumed_error();</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :     }</a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      40900 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">    1084028 : void Action::addDependency(Action*action) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">    1084028 :   after.push_back(action);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">    1084028 : }</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">    3214026 : void Action::activate() {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : // preparation step is called only the first time an Action is activated.</a>
+<a name="173"><span class="lineNum">     173 </span>            : // since it could change its dependences (e.g. in an ActionAtomistic which is</a>
+<a name="174"><span class="lineNum">     174 </span>            : // accessing to a virtual atom), this is done just before dependencies are</a>
+<a name="175"><span class="lineNum">     175 </span>            : // activated</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">    3214026 :   if(!active) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">    1650947 :     this-&gt;unlockRequests();</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    1650947 :     prepare();</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">    1650947 :     this-&gt;lockRequests();</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   } else return;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">    3586596 :   for(const auto &amp; p : after) p-&gt;activate();</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    1650947 :   active=true;</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        267 : void Action::setOption(const std::string &amp;s) {</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : // This overloads the action and activate some options</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        267 :   options.insert(s);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        448 :   for(const auto &amp; p : after) p-&gt;setOption(s);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        267 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 : void Action::clearOptions() {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : // This overloads the action and activate some options</a>
+<a name="193"><span class="lineNum">     193 </span>            :   options.clear();</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">     189162 : void Action::clearDependencies() {</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   after.clear();</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     189162 : }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      27861 : void Action::checkRead() {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      27861 :   if(!line.empty()) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     std::string msg=&quot;cannot understand the following words from the input line : &quot;;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;line.size(); i++) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :       if(i&gt;0) msg = msg + &quot;, &quot;;</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       msg = msg + line[i];</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     error(msg);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      27861 : }</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">    4557159 : long long int Action::getStep()const {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">    4557159 :   return plumed.getStep();</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">    2991243 : double Action::getTime()const {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">    2991243 :   return plumed.getAtoms().getTimeStep()*getStep();</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      16292 : double Action::getTimeStep()const {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      16292 :   return plumed.getAtoms().getTimeStep();</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 : void Action::exit(int c) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   plumed.exit(c);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 : void Action::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;if you get here it means that you are trying to use numerical derivatives for a class that does not implement them&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">     325089 : void Action::prepare() {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     325089 :   return;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         30 : [[noreturn]] void Action::error( const std::string &amp; msg ) const {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         30 :   log.printf(&quot;ERROR in input to action %s with label %s : %s \n \n&quot;, name.c_str(), label.c_str(), msg.c_str() );</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         90 :   plumed_merror(&quot;ERROR in input to action &quot; + name + &quot; with label &quot; + label + &quot; : &quot; + msg );</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        129 : void Action::warning( const std::string &amp; msg ) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        129 :   log.printf(&quot;WARNING for action %s with label %s : %s \n&quot;, name.c_str(), label.c_str(), msg.c_str() );</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        129 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 : void Action::calculateFromPDB( const PDB&amp; pdb ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   activate();</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   for(const auto &amp; p : after) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :     ActionWithValue*av=dynamic_cast&lt;ActionWithValue*&gt;(p);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     if(av) { av-&gt;clearInputForces(); av-&gt;clearDerivatives(); }</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :     p-&gt;readAtomsFromPDB( pdb );</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :     p-&gt;calculate();</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :   readAtomsFromPDB( pdb );</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   calculate();</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">      28109 : bool Action::getExchangeStep()const {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">      28109 :   return plumed.getExchangeStep();</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         40 : std::string Action::cite(const std::string&amp;s) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         40 :   return plumed.cite(s);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : /// Check if action should be updated.</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">    1642986 : bool Action::checkUpdate()const {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">    1642986 :   double t=getTime();</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">    1642986 :   if(t&lt;update_until &amp;&amp; (update_from==std::numeric_limits&lt;double&gt;::max() || t&gt;=update_from)) return true;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        510 :   else return false;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       1095 : bool Action::getCPT()const {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1095 :   return plumed.getCPT();</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : }</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : }</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Action.h.func-sort-c.html b/coverage/core/Action.h.func-sort-c.html
new file mode 100644
index 0000000000..78cecac5be
--- /dev/null
+++ b/coverage/core/Action.h.func-sort-c.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Action.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Action.h<span style="font-size: 80%;"> (<a href="Action.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">94.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Action.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#282">_ZN4PLMD6Action16readAtomsFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorIxEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseImEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorIeEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIxEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">520</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#331">_ZN4PLMD6Action13parseNumberedIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRT_</a></td>
+              <td class="coverFnHi">1164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">1313</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_iRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">2144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#331">_ZN4PLMD6Action13parseNumberedINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_iRT_</a></td>
+              <td class="coverFnHi">3628</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">3647</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">5296</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">11179</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#226">_ZN4PLMD6Action12runFinalJobsEv</a></td>
+              <td class="coverFnHi">13508</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">18608</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">22509</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_</a></td>
+              <td class="coverFnHi">29674</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#258">_ZNK4PLMD6Action25checkNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">260031</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#221">_ZN4PLMD6Action6updateEv</a></td>
+              <td class="coverFnHi">412363</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#196">_ZN4PLMD6Action12lockRequestsEv</a></td>
+              <td class="coverFnHi">945438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#197">_ZN4PLMD6Action14unlockRequestsEv</a></td>
+              <td class="coverFnHi">945438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#412">_ZNK4PLMD6Action10isOptionOnERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1404474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#261">_ZNK4PLMD6Action19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">1642172</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#216">_ZN4PLMD6Action12beforeUpdateEv</a></td>
+              <td class="coverFnHi">1815324</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#401">_ZN4PLMD6Action10deactivateEv</a></td>
+              <td class="coverFnHi">1833169</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Action.h.func.html b/coverage/core/Action.h.func.html
new file mode 100644
index 0000000000..150337a195
--- /dev/null
+++ b/coverage/core/Action.h.func.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Action.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Action.h<span style="font-size: 80%;"> (<a href="Action.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">94.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Action.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#401">_ZN4PLMD6Action10deactivateEv</a></td>
+              <td class="coverFnHi">1833169</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">18608</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">11179</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#342">_ZN4PLMD6Action11parseVectorIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">520</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#216">_ZN4PLMD6Action12beforeUpdateEv</a></td>
+              <td class="coverFnHi">1815324</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#196">_ZN4PLMD6Action12lockRequestsEv</a></td>
+              <td class="coverFnHi">945438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#226">_ZN4PLMD6Action12runFinalJobsEv</a></td>
+              <td class="coverFnHi">13508</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#331">_ZN4PLMD6Action13parseNumberedINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_iRT_</a></td>
+              <td class="coverFnHi">3628</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#331">_ZN4PLMD6Action13parseNumberedIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRT_</a></td>
+              <td class="coverFnHi">1164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#197">_ZN4PLMD6Action14unlockRequestsEv</a></td>
+              <td class="coverFnHi">945438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#282">_ZN4PLMD6Action16readAtomsFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_iRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">2144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">1313</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorIeEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#381">_ZN4PLMD6Action19parseNumberedVectorIxEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS7_RT_</a></td>
+              <td class="coverFnHi">29674</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">22509</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIiEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">5296</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">3647</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseImEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#307">_ZN4PLMD6Action5parseIxEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#221">_ZN4PLMD6Action6updateEv</a></td>
+              <td class="coverFnHi">412363</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#412">_ZNK4PLMD6Action10isOptionOnERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1404474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#261">_ZNK4PLMD6Action19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">1642172</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Action.h.gcov.html#258">_ZNK4PLMD6Action25checkNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">260031</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Action.h.gcov.html b/coverage/core/Action.h.gcov.html
new file mode 100644
index 0000000000..a25d9b9bdc
--- /dev/null
+++ b/coverage/core/Action.h.gcov.html
@@ -0,0 +1,506 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Action.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Action.h<span style="font-size: 80%;"> (source / <a href="Action.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">94.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_Action_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_Action_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;vector&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;set&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Keywords.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Log.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class PDB;</a>
+<a name="34"><span class="lineNum">      34 </span>            : class PlumedMain;</a>
+<a name="35"><span class="lineNum">      35 </span>            : class Communicator;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class ActionWithValue;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : /// This class is used to bring the relevant information to the Action constructor.</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Only Action and ActionRegister class can access to its content, which is</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// kept private to other classes, and may change in the future.</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      28606 : class ActionOptions {</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   friend class Action;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   friend class ActionRegister;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Reference to main PlumedMain object</a>
+<a name="45"><span class="lineNum">      45 </span>            :   PlumedMain&amp; plumed;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Input line which sets up the action</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;std::string&gt; line;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// The documentation for this action</a>
+<a name="49"><span class="lineNum">      49 </span>            :   const Keywords&amp; keys;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   static Keywords emptyKeys;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Constructor</a>
+<a name="53"><span class="lineNum">      53 </span>            :   ActionOptions(PlumedMain&amp;p,const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span>            :   ActionOptions(const ActionOptions&amp;,const Keywords&amp; keys);</a>
+<a name="55"><span class="lineNum">      55 </span>            : };</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Base class for all the input Actions.</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The input Actions are more or less corresponding to the directives</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// in the plumed.dat file and are applied in order at each time-step.</a>
+<a name="60"><span class="lineNum">      60 </span>            : class Action {</a>
+<a name="61"><span class="lineNum">      61 </span>            :   friend class ActionShortcut;</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Name of the directive in the plumed.dat file.</a>
+<a name="64"><span class="lineNum">      64 </span>            :   const std::string name;</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Label of the Action, as set with LABEL= in the plumed.dat file.</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::string label;</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Directive line.</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// This line is progressively erased during Action construction</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// so as to check if all the present keywords are correct.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;std::string&gt; line;</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Update only after this time.</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double update_from;</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Update only until this time.</a>
+<a name="78"><span class="lineNum">      78 </span>            :   double update_until;</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : public:</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Check if action should be updated.</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool checkUpdate()const;</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : public:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   typedef std::vector&lt;Action*&gt; Dependencies;</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : private:</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Actions on which this Action depends.</a>
+<a name="90"><span class="lineNum">      90 </span>            :   Dependencies after;</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Switch to activate Action on this step.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   bool active;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Option that you might have enabled</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::set&lt;std::string&gt; options;</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   bool restart;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   bool doCheckPoint;</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : /// The set of default arguments that we are using</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::string defaults;</a>
+<a name="104"><span class="lineNum">     104 </span>            : public:</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Reference to main plumed object</a>
+<a name="107"><span class="lineNum">     107 </span>            :   PlumedMain&amp; plumed;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Reference to the log stream</a>
+<a name="110"><span class="lineNum">     110 </span>            :   Log&amp; log;</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : /// Specify that this Action depends on another one</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void addDependency(Action*);</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Clear the dependence list for this Action</a>
+<a name="116"><span class="lineNum">     116 </span>            :   void clearDependencies();</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : /// Return the present timestep</a>
+<a name="119"><span class="lineNum">     119 </span>            :   long long int getStep()const;</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Return the present time</a>
+<a name="122"><span class="lineNum">     122 </span>            :   double getTime()const;</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Return the timestep</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double getTimeStep()const;</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Return true if we are doing a restart</a>
+<a name="128"><span class="lineNum">     128 </span>            :   bool getRestart()const;</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : /// Return true if we are doing at a checkpoint step</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool getCPT()const;</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Just read one of the keywords and return the whole thing as a string</a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::string getKeyword(const std::string&amp; key);</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Parse one keyword as generic type</a>
+<a name="137"><span class="lineNum">     137 </span>            :   template&lt;class T&gt;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void parse(const std::string&amp;key,T&amp;t);</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Parse one numbered keyword as generic type</a>
+<a name="141"><span class="lineNum">     141 </span>            :   template&lt;class T&gt;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   bool parseNumbered(const std::string&amp;key, const int no, T&amp;t);</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : /// Parse one keyword as std::vector</a>
+<a name="145"><span class="lineNum">     145 </span>            :   template&lt;class T&gt;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void parseVector(const std::string&amp;key,std::vector&lt;T&gt;&amp;t);</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : /// Parse a vector with a number</a>
+<a name="149"><span class="lineNum">     149 </span>            :   template&lt;class T&gt;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   bool parseNumberedVector(const std::string&amp; key, const int no, std::vector&lt;T&gt;&amp;t);</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Parse one keyword as boolean flag</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void parseFlag(const std::string&amp;key,bool&amp;t);</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : /// Crash calculation and print documentation</a>
+<a name="156"><span class="lineNum">     156 </span>            :   [[noreturn]] void error( const std::string &amp; msg ) const;</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : /// Issue a warning</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void warning( const std::string &amp; msg );</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : /// Exit with error code c</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void exit(int c=0);</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : ///</a>
+<a name="165"><span class="lineNum">     165 </span>            :   std::set&lt;FILE*&gt; files;</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : public:</a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Standard constructor from ActionOptions</a>
+<a name="169"><span class="lineNum">     169 </span>            :   explicit Action(const ActionOptions&amp;);</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// Destructor</a>
+<a name="171"><span class="lineNum">     171 </span>            :   virtual ~Action();</a>
+<a name="172"><span class="lineNum">     172 </span>            : private:</a>
+<a name="173"><span class="lineNum">     173 </span>            : /// Copy constructor is deleted</a>
+<a name="174"><span class="lineNum">     174 </span>            :   Action(const Action&amp;a) = delete;</a>
+<a name="175"><span class="lineNum">     175 </span>            : /// Assignment operator is deleted</a>
+<a name="176"><span class="lineNum">     176 </span>            :   Action&amp; operator=(const Action&amp;a) = delete;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   int replica_index;</a>
+<a name="178"><span class="lineNum">     178 </span>            : public:</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// Check if Action was properly read.</a>
+<a name="180"><span class="lineNum">     180 </span>            : /// This checks if Action::line is empty. It must be called after</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// a final Action has been initialized</a>
+<a name="182"><span class="lineNum">     182 </span>            :   void checkRead();</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :   Communicator&amp; comm;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   Communicator&amp; multi_sim_comm;</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   const Keywords&amp; keywords;</a>
+<a name="188"><span class="lineNum">     188 </span>            : /// Prepare an Action for calculation</a>
+<a name="189"><span class="lineNum">     189 </span>            : /// This can be used by Action if they need some special preparation</a>
+<a name="190"><span class="lineNum">     190 </span>            : /// before calculation. Typical case is for collective variables</a>
+<a name="191"><span class="lineNum">     191 </span>            : /// which would like to change their list of requested atoms.</a>
+<a name="192"><span class="lineNum">     192 </span>            : /// By default (if not overridden) does nothing.</a>
+<a name="193"><span class="lineNum">     193 </span>            :   virtual void prepare();</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : /// Register all the relevant keywords for the action</a>
+<a name="196"><span class="lineNum">     196 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">     945438 :   virtual void lockRequests() {}</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     945438 :   virtual void unlockRequests() {}</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : /// Calculate an Action.</a>
+<a name="202"><span class="lineNum">     202 </span>            : /// This method is called one or more times per step.</a>
+<a name="203"><span class="lineNum">     203 </span>            : /// The set of all Actions is calculated in forward order.</a>
+<a name="204"><span class="lineNum">     204 </span>            :   virtual void calculate()=0;</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : /// Apply an Action.</a>
+<a name="207"><span class="lineNum">     207 </span>            : /// This method is called one time per step.</a>
+<a name="208"><span class="lineNum">     208 </span>            : /// The set of all Actions is applied in backward order.</a>
+<a name="209"><span class="lineNum">     209 </span>            :   virtual void apply()=0;</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : /// Before Update.</a>
+<a name="212"><span class="lineNum">     212 </span>            : /// This is a special method that is called just</a>
+<a name="213"><span class="lineNum">     213 </span>            : /// before the update() method. It can be used by</a>
+<a name="214"><span class="lineNum">     214 </span>            : /// actions that want to do something irrespectively</a>
+<a name="215"><span class="lineNum">     215 </span>            : /// of the fact that update() is active or not.</a>
+<a name="216"><span class="lineNum">     216 </span>            : /// In other words, this is *always* called, even when action</a>
+<a name="217"><span class="lineNum">     217 </span>            : /// is not active.</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">    1815324 :   virtual void beforeUpdate() {}</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : /// Update.</a>
+<a name="221"><span class="lineNum">     221 </span>            : /// This method is called one time per step.</a>
+<a name="222"><span class="lineNum">     222 </span>            : /// The set of all Actions is updated in forward order.</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     412363 :   virtual void update() {}</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : /// RunFinalJobs</a>
+<a name="226"><span class="lineNum">     226 </span>            : /// This method is called once at the very end of the calculation.</a>
+<a name="227"><span class="lineNum">     227 </span>            : /// The set of all Actions in run for the final time in forward order.</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      13508 :   virtual void runFinalJobs() {}</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : /// Tell to the Action to flush open files</a>
+<a name="231"><span class="lineNum">     231 </span>            :   void fflush();</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : /// Returns the label</a>
+<a name="234"><span class="lineNum">     234 </span>            :   const std::string &amp; getLabel()const;</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : /// Returns the name</a>
+<a name="237"><span class="lineNum">     237 </span>            :   const std::string &amp; getName()const;</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : /// Set action to active</a>
+<a name="240"><span class="lineNum">     240 </span>            :   virtual void activate();</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : ///</a>
+<a name="243"><span class="lineNum">     243 </span>            :   virtual void setOption(const std::string &amp;s);</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   virtual void clearOptions();</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : /// Set action to inactive</a>
+<a name="248"><span class="lineNum">     248 </span>            :   virtual void deactivate();</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : /// Check if action is active</a>
+<a name="251"><span class="lineNum">     251 </span>            :   bool isActive()const;</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : /// Check if an option is on</a>
+<a name="254"><span class="lineNum">     254 </span>            :   bool isOptionOn(const std::string &amp;s)const;</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            : /// Return dependencies</a>
+<a name="257"><span class="lineNum">     257 </span>            :   const Dependencies &amp; getDependencies()const {return after;}</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : /// Check if numerical derivatives should be performed</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">     260031 :   virtual bool checkNumericalDerivatives()const {return false;}</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : /// Check if the action needs gradient</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">    1642172 :   virtual bool checkNeedsGradients()const {return false;}</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : /// Perform calculation using numerical derivatives</a>
+<a name="266"><span class="lineNum">     266 </span>            : /// N.B. only pass an ActionWithValue to this routine if you know exactly what you</a>
+<a name="267"><span class="lineNum">     267 </span>            : /// are doing.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   virtual void calculateNumericalDerivatives( ActionWithValue* a=NULL );</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            : /// Opens a file.</a>
+<a name="271"><span class="lineNum">     271 </span>            : /// This is similar to plain fopen, but with some extra functionality.</a>
+<a name="272"><span class="lineNum">     272 </span>            : /// * When opened for writing, processors other than the one with rank 0 just open /dev/null</a>
+<a name="273"><span class="lineNum">     273 </span>            : /// * PlumedMain::fopen is used, so that other tricks may appear (see \ref PlumedMain::fopen)</a>
+<a name="274"><span class="lineNum">     274 </span>            :   FILE *fopen(const char *path, const char *mode);</a>
+<a name="275"><span class="lineNum">     275 </span>            : /// Closes a file opened with Action::fclose().</a>
+<a name="276"><span class="lineNum">     276 </span>            :   int   fclose(FILE*fp);</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : /// Calculate the action given a pdb file as input.  This is used to initialize</a>
+<a name="279"><span class="lineNum">     279 </span>            : /// things like distance from a point in CV map space given a pdb as an input file</a>
+<a name="280"><span class="lineNum">     280 </span>            :   void calculateFromPDB( const PDB&amp;  );</a>
+<a name="281"><span class="lineNum">     281 </span>            : /// This is overwritten in ActionAtomistic so that we can read</a>
+<a name="282"><span class="lineNum">     282 </span>            : /// the atoms from the pdb input file rather than taking them from the</a>
+<a name="283"><span class="lineNum">     283 </span>            : /// MD code</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :   virtual void readAtomsFromPDB( const PDB&amp;  ) {}</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : /// Check if we are on an exchange step</a>
+<a name="286"><span class="lineNum">     286 </span>            :   bool getExchangeStep()const;</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : /// Cite a paper see PlumedMain::cite</a>
+<a name="289"><span class="lineNum">     289 </span>            :   std::string cite(const std::string&amp;s);</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : /// Get the defaults</a>
+<a name="292"><span class="lineNum">     292 </span>            :   std::string getDefaultString() const ;</a>
+<a name="293"><span class="lineNum">     293 </span>            : };</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : /////////////////////</a>
+<a name="296"><span class="lineNum">     296 </span>            : // FAST INLINE METHODS</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : inline</a>
+<a name="299"><span class="lineNum">     299 </span>            : const std::string &amp; Action::getLabel()const {</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">   60597121 :   return label;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : inline</a>
+<a name="304"><span class="lineNum">     304 </span>            : const std::string &amp; Action::getName()const {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       7743 :   return name;</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : }</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : template&lt;class T&gt;</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">      61251 : void Action::parse(const std::string&amp;key,T&amp;t) {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   // Check keyword has been registered</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      61251 :   plumed_massert(keywords.exists(key),&quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   // Now try to read the keyword</a>
+<a name="314"><span class="lineNum">     314 </span>            :   std::string def;</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      61251 :   bool present=Tools::findKeyword(line,key);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      61251 :   bool found=Tools::parse(line,key,t,replica_index);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">      61254 :   if(present &amp;&amp; !found) error(&quot;keyword &quot; + key +&quot; could not be read correctly&quot;);</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :   // If it isn't read and it is compulsory see if a default value was specified</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">     140268 :   if ( !found &amp;&amp; (keywords.style(key,&quot;compulsory&quot;) || keywords.style(key,&quot;hidden&quot;)) ) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       8134 :     if( keywords.getDefaultValue(key,def) ) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       2851 :       if( def.length()==0 || !Tools::convertNoexcept(def,t) ) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :         plumed_error() &lt;&lt;&quot;ERROR in action &quot;&lt;&lt;name&lt;&lt;&quot; with label &quot;&lt;&lt;label&lt;&lt;&quot; : keyword &quot;&lt;&lt;key&lt;&lt;&quot; has weird default value&quot;;</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :       }</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       5702 :       defaults += &quot; &quot; + key + &quot;=&quot; + def;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">      10566 :     } else if( keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          3 :       error(&quot;keyword &quot; + key + &quot; is compulsory for this action&quot;);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :     }</a>
+<a name="329"><span class="lineNum">     329 </span>            :   }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">      61248 : }</span></a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            : template&lt;class T&gt;</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       4792 : bool Action::parseNumbered(const std::string&amp;key, const int no, T&amp;t) {</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :   // Check keyword has been registered</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">       4792 :   plumed_massert(keywords.exists(key),&quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       4792 :   if( !keywords.numbered(key) ) error(&quot;numbered keywords are not allowed for &quot; + key );</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            :   // Now try to read the keyword</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       4792 :   std::string num; Tools::convert(no,num);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       9584 :   return Tools::parse(line,key+num,t,replica_index);</span></a>
+<a name="341"><span class="lineNum">     341 </span>            : }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            : template&lt;class T&gt;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">      30338 : void Action::parseVector(const std::string&amp;key,std::vector&lt;T&gt;&amp;t) {</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   // Check keyword has been registered</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">      30338 :   plumed_massert(keywords.exists(key), &quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">      30338 :   unsigned size=t.size(); bool skipcheck=false;</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      30338 :   if(size==0) skipcheck=true;</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            :   // Now try to read the keyword</a>
+<a name="351"><span class="lineNum">     351 </span>            :   std::string def; T val;</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">      30338 :   bool present=Tools::findKeyword(line,key);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">      30338 :   bool found=Tools::parseVector(line,key,t,replica_index);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">      30339 :   if(present &amp;&amp; !found) error(&quot;keyword &quot; + key +&quot; could not be read correctly&quot;);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            :   // Check vectors size is correct (not if this is atoms or ARG)</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">      60674 :   if( !keywords.style(key,&quot;atoms&quot;) &amp;&amp; found ) {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : //     bool skipcheck=false;</a>
+<a name="359"><span class="lineNum">     359 </span>            : //     if( keywords.style(key,&quot;compulsory&quot;) ){ keywords.getDefaultValue(key,def); skipcheck=(def==&quot;nosize&quot;); }</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">      13567 :     if( !skipcheck &amp;&amp; t.size()!=size ) error(&quot;vector read in for keyword &quot; + key + &quot; has the wrong size&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            :   // If it isn't read and it is compulsory see if a default value was specified</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">      43628 :   if ( !found &amp;&amp; (keywords.style(key,&quot;compulsory&quot;) || keywords.style(key,&quot;hidden&quot;)) ) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">        980 :     if( keywords.getDefaultValue(key,def) ) {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        878 :       if( def.length()==0 || !Tools::convertNoexcept(def,val) ) {</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :         plumed_error() &lt;&lt;&quot;ERROR in action &quot;&lt;&lt;name&lt;&lt;&quot; with label &quot;&lt;&lt;label&lt;&lt;&quot; : keyword &quot;&lt;&lt;key&lt;&lt;&quot; has weird default value&quot;;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :       } else {</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        878 :         if(t.size()&gt;0) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       1586 :           for(unsigned i=0; i&lt;t.size(); ++i) t[i]=val;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">       1586 :           defaults += &quot; &quot; + key + &quot;=&quot; + def; for(unsigned i=1; i&lt;t.size(); ++i) defaults += &quot;,&quot; + def;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        556 :         } else { t.push_back(val); defaults += &quot; &quot; + key + &quot;=&quot; + def; }</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :       }</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        204 :     } else if( keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          4 :       error(&quot;keyword &quot; + key + &quot; is compulsory for this action&quot;);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     }</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">      29354 :   } else if ( !found ) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">       6055 :     t.resize(0);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">      30334 : }</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            : template&lt;class T&gt;</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       3503 : bool Action::parseNumberedVector(const std::string&amp;key, const int no, std::vector&lt;T&gt;&amp;t) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       3503 :   plumed_massert(keywords.exists(key),&quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       3503 :   if( !keywords.numbered(key) ) error(&quot;numbered keywords are not allowed for &quot; + key );</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       3503 :   unsigned size=t.size(); bool skipcheck=false;</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       3503 :   if(size==0) skipcheck=true;</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">       3503 :   std::string num; Tools::convert(no,num);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">       3503 :   bool present=Tools::findKeyword(line,key);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">       3503 :   bool found=Tools::parseVector(line,key+num,t,replica_index);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       3503 :   if(present &amp;&amp; !found) error(&quot;keyword &quot; + key +&quot; could not be read correctly&quot;);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       7006 :   if(  keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         90 :     if (!skipcheck &amp;&amp; found &amp;&amp; t.size()!=size ) error(&quot;vector read in for keyword &quot; + key + num + &quot; has the wrong size&quot;);</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       3413 :   } else if ( !found ) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">       1039 :     t.resize(0);</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   }</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       3503 :   return found;</span></a>
+<a name="400"><span class="lineNum">     400 </span>            : }</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            : inline</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">    1833169 : void Action::deactivate() {</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :   options.clear();</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">    1833169 :   active=false;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">    1833169 : }</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : inline</a>
+<a name="409"><span class="lineNum">     409 </span>            : bool Action::isActive()const {</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">    7867463 :   return active;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : }</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span>            : inline</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">    1404474 : bool Action::isOptionOn(const std::string &amp;s)const {</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">    1404474 :   return options.count(s);</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : }</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            : inline</a>
+<a name="419"><span class="lineNum">     419 </span>            : bool Action::getRestart()const {</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">       3651 :   return restart;</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : }</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span>            : inline</a>
+<a name="424"><span class="lineNum">     424 </span>            : std::string Action::getDefaultString() const {</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :   return defaults;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            : }</a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span>            : }</a>
+<a name="429"><span class="lineNum">     429 </span>            : #endif</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAnyorder.cpp.func-sort-c.html b/coverage/core/ActionAnyorder.cpp.func-sort-c.html
new file mode 100644
index 0000000000..32737d8057
--- /dev/null
+++ b/coverage/core/ActionAnyorder.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAnyorder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAnyorder.cpp<span style="font-size: 80%;"> (<a href="ActionAnyorder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionAnyorder.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.cpp.gcov.html#32">_ZN4PLMD14ActionAnyorder16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.cpp.gcov.html#27">_ZN4PLMD14ActionAnyorderC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.cpp.gcov.html#27">_ZN4PLMD14ActionAnyorderC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">105</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAnyorder.cpp.func.html b/coverage/core/ActionAnyorder.cpp.func.html
new file mode 100644
index 0000000000..fa9ac30558
--- /dev/null
+++ b/coverage/core/ActionAnyorder.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAnyorder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAnyorder.cpp<span style="font-size: 80%;"> (<a href="ActionAnyorder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionAnyorder.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.cpp.gcov.html#32">_ZN4PLMD14ActionAnyorder16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.cpp.gcov.html#27">_ZN4PLMD14ActionAnyorderC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.cpp.gcov.html#27">_ZN4PLMD14ActionAnyorderC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">105</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAnyorder.cpp.gcov.html b/coverage/core/ActionAnyorder.cpp.gcov.html
new file mode 100644
index 0000000000..1684838e94
--- /dev/null
+++ b/coverage/core/ActionAnyorder.cpp.gcov.html
@@ -0,0 +1,114 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAnyorder.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAnyorder.cpp<span style="font-size: 80%;"> (source / <a href="ActionAnyorder.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionAnyorder.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        105 : ActionAnyorder::ActionAnyorder(const ActionOptions&amp;ao):</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        105 :   Action(ao)</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        105 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 : void ActionAnyorder::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 :   Action::registerKeywords(keys);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAnyorder.h.func-sort-c.html b/coverage/core/ActionAnyorder.h.func-sort-c.html
new file mode 100644
index 0000000000..add5bf3926
--- /dev/null
+++ b/coverage/core/ActionAnyorder.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAnyorder.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAnyorder.h<span style="font-size: 80%;"> (<a href="ActionAnyorder.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionAnyorder.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.h.gcov.html#41">_ZN4PLMD14ActionAnyorder5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.h.gcov.html#39">_ZN4PLMD14ActionAnyorder9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAnyorder.h.func.html b/coverage/core/ActionAnyorder.h.func.html
new file mode 100644
index 0000000000..c298102c94
--- /dev/null
+++ b/coverage/core/ActionAnyorder.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAnyorder.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAnyorder.h<span style="font-size: 80%;"> (<a href="ActionAnyorder.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionAnyorder.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.h.gcov.html#41">_ZN4PLMD14ActionAnyorder5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAnyorder.h.gcov.html#39">_ZN4PLMD14ActionAnyorder9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAnyorder.h.gcov.html b/coverage/core/ActionAnyorder.h.gcov.html
new file mode 100644
index 0000000000..461e19ad97
--- /dev/null
+++ b/coverage/core/ActionAnyorder.h.gcov.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAnyorder.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAnyorder.h<span style="font-size: 80%;"> (source / <a href="ActionAnyorder.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionAnyorder_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionAnyorder_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : /**</a>
+<a name="30"><span class="lineNum">      30 </span>            : \ingroup MULTIINHERIT</a>
+<a name="31"><span class="lineNum">      31 </span>            : Action used to create a PLMD::Action that can go both before and after ActionSetup actions.</a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         87 : class ActionAnyorder :</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   public virtual Action {</a>
+<a name="35"><span class="lineNum">      35 </span>            : public:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Constructor</a>
+<a name="37"><span class="lineNum">      37 </span>            :   explicit ActionAnyorder(const ActionOptions&amp;ao);</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Creator of keywords</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Do nothing.</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Do nothing.</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : };</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAtomistic.cpp.func-sort-c.html b/coverage/core/ActionAtomistic.cpp.func-sort-c.html
new file mode 100644
index 0000000000..29b3d45f33
--- /dev/null
+++ b/coverage/core/ActionAtomistic.cpp.func-sort-c.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAtomistic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAtomistic.cpp<span style="font-size: 80%;"> (<a href="ActionAtomistic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">186</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">77.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionAtomistic.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#273">_ZN4PLMD15ActionAtomistic16readAtomsFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#91">_ZN4PLMD15ActionAtomistic9changeBoxERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#41">_ZN4PLMD15ActionAtomisticC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#36">_ZN4PLMD15ActionAtomisticD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#36">_ZN4PLMD15ActionAtomisticD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#87">_ZN4PLMD15ActionAtomistic29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#95">_ZN4PLMD15ActionAtomistic35calculateAtomicNumericalDerivativesEPNS_15ActionWithValueERKj</a></td>
+              <td class="coverFnHi">492</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#235">_ZN4PLMD15ActionAtomistic16setForcesOnAtomsERKSt6vectorIdSaIdEEj</a></td>
+              <td class="coverFnHi">624</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#41">_ZN4PLMD15ActionAtomisticC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10255</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#36">_ZN4PLMD15ActionAtomisticD2Ev</a></td>
+              <td class="coverFnHi">10255</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#57">_ZN4PLMD15ActionAtomistic12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">10274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#52">_ZN4PLMD15ActionAtomistic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10524</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#166">_ZN4PLMD15ActionAtomistic17interpretAtomListERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS1_INS_10AtomNumberESaISB_EE</a></td>
+              <td class="coverFnHi">11421</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#150">_ZN4PLMD15ActionAtomistic13parseAtomListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorINS_10AtomNumberESaISA_EE</a></td>
+              <td class="coverFnHi">11774</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#154">_ZN4PLMD15ActionAtomistic13parseAtomListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorINS_10AtomNumberESaISA_EE</a></td>
+              <td class="coverFnHi">13759</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#294">_ZN4PLMD15ActionAtomistic17updateUniqueLocalEv</a></td>
+              <td class="coverFnHi">19923</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#286">_ZN4PLMD15ActionAtomistic9makeWholeEv</a></td>
+              <td class="coverFnHi">106316</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#254">_ZN4PLMD15ActionAtomistic11applyForcesEv</a></td>
+              <td class="coverFnHi">166117</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#221">_ZN4PLMD15ActionAtomistic13retrieveAtomsEv</a></td>
+              <td class="coverFnHi">166580</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#264">_ZN4PLMD15ActionAtomistic17clearOutputForcesEv</a></td>
+              <td class="coverFnHi">166580</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#83">_ZNK4PLMD15ActionAtomistic8pbcApplyERSt6vectorINS_13VectorGenericILj3EEESaIS3_EEj</a></td>
+              <td class="coverFnHi">220663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#79">_ZNK4PLMD15ActionAtomistic11pbcDistanceERKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnHi">182588013</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAtomistic.cpp.func.html b/coverage/core/ActionAtomistic.cpp.func.html
new file mode 100644
index 0000000000..d76cddc499
--- /dev/null
+++ b/coverage/core/ActionAtomistic.cpp.func.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAtomistic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAtomistic.cpp<span style="font-size: 80%;"> (<a href="ActionAtomistic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">186</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">77.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionAtomistic.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#254">_ZN4PLMD15ActionAtomistic11applyForcesEv</a></td>
+              <td class="coverFnHi">166117</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#57">_ZN4PLMD15ActionAtomistic12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">10274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#150">_ZN4PLMD15ActionAtomistic13parseAtomListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorINS_10AtomNumberESaISA_EE</a></td>
+              <td class="coverFnHi">11774</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#154">_ZN4PLMD15ActionAtomistic13parseAtomListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorINS_10AtomNumberESaISA_EE</a></td>
+              <td class="coverFnHi">13759</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#221">_ZN4PLMD15ActionAtomistic13retrieveAtomsEv</a></td>
+              <td class="coverFnHi">166580</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#273">_ZN4PLMD15ActionAtomistic16readAtomsFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#52">_ZN4PLMD15ActionAtomistic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10524</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#235">_ZN4PLMD15ActionAtomistic16setForcesOnAtomsERKSt6vectorIdSaIdEEj</a></td>
+              <td class="coverFnHi">624</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#264">_ZN4PLMD15ActionAtomistic17clearOutputForcesEv</a></td>
+              <td class="coverFnHi">166580</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#166">_ZN4PLMD15ActionAtomistic17interpretAtomListERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS1_INS_10AtomNumberESaISB_EE</a></td>
+              <td class="coverFnHi">11421</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#294">_ZN4PLMD15ActionAtomistic17updateUniqueLocalEv</a></td>
+              <td class="coverFnHi">19923</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#87">_ZN4PLMD15ActionAtomistic29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#95">_ZN4PLMD15ActionAtomistic35calculateAtomicNumericalDerivativesEPNS_15ActionWithValueERKj</a></td>
+              <td class="coverFnHi">492</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#91">_ZN4PLMD15ActionAtomistic9changeBoxERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#286">_ZN4PLMD15ActionAtomistic9makeWholeEv</a></td>
+              <td class="coverFnHi">106316</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#41">_ZN4PLMD15ActionAtomisticC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#41">_ZN4PLMD15ActionAtomisticC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10255</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#36">_ZN4PLMD15ActionAtomisticD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#36">_ZN4PLMD15ActionAtomisticD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#36">_ZN4PLMD15ActionAtomisticD2Ev</a></td>
+              <td class="coverFnHi">10255</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#79">_ZNK4PLMD15ActionAtomistic11pbcDistanceERKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnHi">182588013</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.cpp.gcov.html#83">_ZNK4PLMD15ActionAtomistic8pbcApplyERSt6vectorINS_13VectorGenericILj3EEESaIS3_EEj</a></td>
+              <td class="coverFnHi">220663</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAtomistic.cpp<span style="font-size: 80%;"> (source / <a href="ActionAtomistic.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">186</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">77.3 %</td>
+          </tr>
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+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;GenericMolInfo.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      10255 : ActionAtomistic::~ActionAtomistic() {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : // forget the pending request</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      10255 :   atoms.remove(this);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      10255 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      10255 : ActionAtomistic::ActionAtomistic(const ActionOptions&amp;ao):</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   Action(ao),</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      10255 :   lockRequestAtoms(false),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      10255 :   donotretrieve(false),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      10255 :   donotforce(false),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      10255 :   atoms(plumed.getAtoms())</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : {</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      10255 :   atoms.add(this);</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : //  if(atoms.getNatoms()==0) error(&quot;Cannot perform calculations involving atoms without atoms&quot;);</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      10255 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      10524 : void ActionAtomistic::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   (void) keys; // avoid warning</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      10524 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      10274 : void ActionAtomistic::requestAtoms(const std::vector&lt;AtomNumber&gt; &amp; a, const bool clearDep) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      10274 :   plumed_massert(!lockRequestAtoms,&quot;requested atom list can only be changed in the prepare() method&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      10274 :   int nat=a.size();</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      10274 :   indexes=a;</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      10274 :   positions.resize(nat);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      10274 :   forces.resize(nat);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      10274 :   masses.resize(nat);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      10274 :   charges.resize(nat);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      10274 :   int n=atoms.positions.size();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      10274 :   if(clearDep) clearDependencies();</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      10274 :   unique.clear();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    1386343 :   for(unsigned i=0; i&lt;indexes.size(); i++) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    1376072 :     if(indexes[i].index()&gt;=n) { std::string num; Tools::convert( indexes[i].serial(),num ); error(&quot;atom &quot; + num + &quot; out of range&quot;); }</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    1376069 :     if(atoms.isVirtualAtom(indexes[i])) addDependency(atoms.getVirtualAtomsAction(indexes[i]));</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : // only real atoms are requested to lower level Atoms class</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    1368844 :     else unique.push_back(indexes[i]);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      10273 :   Tools::removeDuplicates(unique);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      10273 :   updateUniqueLocal();</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      10273 :   atoms.unique.clear();</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      10273 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">  182588013 : Vector ActionAtomistic::pbcDistance(const Vector &amp;v1,const Vector &amp;v2)const {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">  182588013 :   return pbc.distance(v1,v2);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     220663 : void ActionAtomistic::pbcApply(std::vector&lt;Vector&gt;&amp; dlist, unsigned max_index)const {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     220663 :   pbc.apply(dlist, max_index);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     220663 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        195 : void ActionAtomistic::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        195 :   calculateAtomicNumericalDerivatives( a, 0 );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        195 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : void ActionAtomistic::changeBox( const Tensor&amp; newbox ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   pbc.setBox( newbox );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        492 : void ActionAtomistic::calculateAtomicNumericalDerivatives( ActionWithValue* a, const unsigned&amp; startnum ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        492 :   if(!a) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        279 :     a=dynamic_cast&lt;ActionWithValue*&gt;(this);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        279 :     plumed_massert(a,&quot;only Actions with a value can be differentiated&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        492 :   const size_t nval=a-&gt;getNumberOfComponents();</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        492 :   const size_t natoms=getNumberOfAtoms();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        492 :   std::vector&lt;Vector&gt; value(nval*natoms);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        492 :   std::vector&lt;Tensor&gt; valuebox(nval);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        492 :   std::vector&lt;Vector&gt; savedPositions(natoms);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   const double delta=std::sqrt(epsilon);</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      91856 :   for(int i=0; i&lt;natoms; i++) for(int k=0; k&lt;3; k++) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      68523 :       savedPositions[i][k]=positions[i][k];</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      68523 :       positions[i][k]=positions[i][k]+delta;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      68523 :       a-&gt;calculate();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      68523 :       positions[i][k]=savedPositions[i][k];</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     202917 :       for(int j=0; j&lt;nval; j++) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     134394 :         value[j*natoms+i][k]=a-&gt;getOutputQuantity(j);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :       }</a>
+<a name="118"><span class="lineNum">     118 </span>            :     }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        492 :   Tensor box(pbc.getBox());</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       6396 :   for(int i=0; i&lt;3; i++) for(int k=0; k&lt;3; k++) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       4428 :       double arg0=box(i,k);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     209997 :       for(int j=0; j&lt;natoms; j++) positions[j]=pbc.realToScaled(positions[j]);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       4428 :       box(i,k)=box(i,k)+delta;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       4428 :       pbc.setBox(box);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">     209997 :       for(int j=0; j&lt;natoms; j++) positions[j]=pbc.scaledToReal(positions[j]);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       4428 :       a-&gt;calculate();</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       4428 :       box(i,k)=arg0;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       4428 :       pbc.setBox(box);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     209997 :       for(int j=0; j&lt;natoms; j++) positions[j]=savedPositions[j];</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      19512 :       for(int j=0; j&lt;nval; j++) valuebox[j](i,k)=a-&gt;getOutputQuantity(j);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        492 :   a-&gt;calculate();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        492 :   a-&gt;clearDerivatives();</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       2168 :   for(int j=0; j&lt;nval; j++) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1676 :     Value* v=a-&gt;copyOutput(j);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     double ref=v-&gt;get();</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       1676 :     if(v-&gt;hasDerivatives()) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">     100117 :       for(int i=0; i&lt;natoms; i++) for(int k=0; k&lt;3; k++) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      74532 :           double d=(value[j*natoms+i][k]-ref)/delta;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      74532 :           v-&gt;addDerivative(startnum+3*i+k,d);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :         }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        741 :       Tensor virial;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       9633 :       for(int i=0; i&lt;3; i++) for(int k=0; k&lt;3; k++)virial(i,k)= (valuebox[j](i,k)-ref)/delta;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : // BE CAREFUL WITH NON ORTHOROMBIC CELL</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        741 :       virial=-matmul(box.transpose(),virial);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       9633 :       for(int i=0; i&lt;3; i++) for(int k=0; k&lt;3; k++) v-&gt;addDerivative(startnum+3*natoms+3*k+i,virial(k,i));</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     }</a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        492 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      11774 : void ActionAtomistic::parseAtomList(const std::string&amp;key, std::vector&lt;AtomNumber&gt; &amp;t) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      11774 :   parseAtomList(key,-1,t);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      11773 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      13759 : void ActionAtomistic::parseAtomList(const std::string&amp;key,const int num, std::vector&lt;AtomNumber&gt; &amp;t) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      13759 :   plumed_massert( keywords.style(key,&quot;atoms&quot;) || keywords.style(key,&quot;hidden&quot;), &quot;keyword &quot; + key + &quot; should be registered as atoms&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   std::vector&lt;std::string&gt; strings;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      13759 :   if( num&lt;0 ) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      11774 :     parseVector(key,strings);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">      11773 :     if(strings.empty()) return;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   } else {</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       1985 :     if ( !parseNumberedVector(key,num,strings) ) return;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      11220 :   interpretAtomList( strings, t );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      13759 : }</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      11421 : void ActionAtomistic::interpretAtomList(std::vector&lt;std::string&gt;&amp; strings, std::vector&lt;AtomNumber&gt; &amp;t) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      11421 :   Tools::interpretRanges(strings); t.resize(0);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     456069 :   for(unsigned i=0; i&lt;strings.size(); ++i) {</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     AtomNumber atom;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     444648 :     bool ok=Tools::convertNoexcept(strings[i],atom); // this is converting strings to AtomNumbers</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     444648 :     if(ok) t.push_back(atom);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : // here we check if this is a special symbol for MOLINFO</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     444648 :     if( !ok &amp;&amp; strings[i].compare(0,1,&quot;@&quot;)==0 ) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        631 :       std::string symbol=strings[i].substr(1);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        631 :       if(symbol==&quot;allatoms&quot;) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         10 :         const auto n=plumed.getAtoms().getNatoms() + plumed.getAtoms().getNVirtualAtoms();</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         10 :         t.reserve(t.size()+n);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        365 :         for(unsigned i=0; i&lt;n; i++) t.push_back(AtomNumber::index(i));</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :         ok=true;</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        621 :       } else if(symbol==&quot;mdatoms&quot;) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          4 :         const auto n=plumed.getAtoms().getNatoms();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :         t.reserve(t.size()+n);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        228 :         for(unsigned i=0; i&lt;n; i++) t.push_back(AtomNumber::index(i));</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :         ok=true;</a>
+<a name="187"><span class="lineNum">     187 </span>            :       } else {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        617 :         auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        617 :         if( moldat ) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        617 :           std::vector&lt;AtomNumber&gt; atom_list; moldat-&gt;interpretSymbol( symbol, atom_list );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        617 :           if( atom_list.size()&gt;0 ) { ok=true; t.insert(t.end(),atom_list.begin(),atom_list.end()); }</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :           else { error(strings[i] + &quot; is not a label plumed knows&quot;); }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :         } else {</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :           error(&quot;atoms specified using @ symbol but no MOLINFO was available&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :         }</a>
+<a name="196"><span class="lineNum">     196 </span>            :       }</a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span>            : // here we check if the atom name is the name of a group</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     444017 :     if(!ok) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       7613 :       if(atoms.groups.count(strings[i])) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :         const auto m=atoms.groups.find(strings[i]);</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        394 :         t.insert(t.end(),m-&gt;second.begin(),m-&gt;second.end());</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :         ok=true;</a>
+<a name="204"><span class="lineNum">     204 </span>            :       }</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            : // here we check if the atom name is the name of an added virtual atom</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">     444254 :     if(!ok) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       7219 :       const ActionSet&amp;actionSet(plumed.getActionSet());</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    6088236 :       for(const auto &amp; a : actionSet) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">    6088236 :         ActionWithVirtualAtom* c=dynamic_cast&lt;ActionWithVirtualAtom*&gt;(a.get());</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">    6088236 :         if(c) if(c-&gt;getLabel()==strings[i]) {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :             ok=true;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       7219 :             t.push_back(c-&gt;getIndex());</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :             break;</a>
+<a name="215"><span class="lineNum">     215 </span>            :           }</a>
+<a name="216"><span class="lineNum">     216 </span>            :       }</a>
+<a name="217"><span class="lineNum">     217 </span>            :     }</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     437429 :     if(!ok) error(&quot;it was not possible to interpret atom name &quot; + strings[i]);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :     // plumed_massert(ok,&quot;it was not possible to interpret atom name &quot; + strings[i]);</a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      11421 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     166580 : void ActionAtomistic::retrieveAtoms() {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     166580 :   pbc=atoms.pbc;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     166580 :   Colvar*cc=dynamic_cast&lt;Colvar*&gt;(this);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">     166580 :   if(cc &amp;&amp; cc-&gt;checkIsEnergy()) energy=atoms.getEnergy();</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">     166580 :   if(donotretrieve) return;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">     162682 :   chargesWereSet=atoms.chargesWereSet();</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   const std::vector&lt;Vector&gt; &amp; p(atoms.positions);</a>
+<a name="230"><span class="lineNum">     230 </span>            :   const std::vector&lt;double&gt; &amp; c(atoms.charges);</a>
+<a name="231"><span class="lineNum">     231 </span>            :   const std::vector&lt;double&gt; &amp; m(atoms.masses);</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">    4345427 :   for(unsigned j=0; j&lt;indexes.size(); j++) positions[j]=p[indexes[j].index()];</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">    4345427 :   for(unsigned j=0; j&lt;indexes.size(); j++) charges[j]=c[indexes[j].index()];</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">    4345427 :   for(unsigned j=0; j&lt;indexes.size(); j++) masses[j]=m[indexes[j].index()];</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        624 : void ActionAtomistic::setForcesOnAtoms(const std::vector&lt;double&gt;&amp; forcesToApply, unsigned ind) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        624 :   if(donotforce) return;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">     213170 :   for(unsigned i=0; i&lt;indexes.size(); ++i) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">     212546 :     forces[i][0]=forcesToApply[ind]; ind++;</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">     212546 :     forces[i][1]=forcesToApply[ind]; ind++;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">     212546 :     forces[i][2]=forcesToApply[ind]; ind++;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        624 :   virial(0,0)=forcesToApply[ind]; ind++;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        624 :   virial(0,1)=forcesToApply[ind]; ind++;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        624 :   virial(0,2)=forcesToApply[ind]; ind++;</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        624 :   virial(1,0)=forcesToApply[ind]; ind++;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        624 :   virial(1,1)=forcesToApply[ind]; ind++;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        624 :   virial(1,2)=forcesToApply[ind]; ind++;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        624 :   virial(2,0)=forcesToApply[ind]; ind++;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        624 :   virial(2,1)=forcesToApply[ind]; ind++;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        624 :   virial(2,2)=forcesToApply[ind];</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   plumed_dbg_assert( ind+1==forcesToApply.size());</a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">     166117 : void ActionAtomistic::applyForces() {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">     166117 :   if(donotforce) return;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">     162219 :   std::vector&lt;Vector&gt;&amp; f(atoms.forces);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">     162219 :   Tensor&amp; v(atoms.virial);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">    4325477 :   for(unsigned j=0; j&lt;indexes.size(); j++) f[indexes[j].index()]+=forces[j];</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">     162219 :   v+=virial;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">     162219 :   atoms.forceOnEnergy+=forceOnEnergy;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">     162219 :   if(extraCV.length()&gt;0) atoms.updateExtraCVForce(extraCV,forceOnExtraCV);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">     166580 : void ActionAtomistic::clearOutputForces() {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">     166580 :   virial.zero();</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">     166580 :   if(donotforce) return;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">     162682 :   Tools::set_to_zero(forces);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">     162682 :   forceOnEnergy=0.0;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">     162682 :   forceOnExtraCV=0.0;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 : void ActionAtomistic::readAtomsFromPDB(const PDB&amp; pdb) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :   Colvar*cc=dynamic_cast&lt;Colvar*&gt;(this);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :   if(cc &amp;&amp; cc-&gt;checkIsEnergy()) error(&quot;can't read energies from pdb files&quot;);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;indexes.size(); j++) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :     if( indexes[j].index()&gt;pdb.size() ) error(&quot;there are not enough atoms in the input pdb file&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :     if( pdb.getAtomNumbers()[j].index()!=indexes[j].index() ) error(&quot;there are atoms missing in the pdb file&quot;);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :     positions[j]=pdb.getPositions()[indexes[j].index()];</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :   }</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;indexes.size(); j++) charges[j]=pdb.getBeta()[indexes[j].index()];</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;indexes.size(); j++) masses[j]=pdb.getOccupancy()[indexes[j].index()];</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     106316 : void ActionAtomistic::makeWhole() {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">    1152064 :   for(unsigned j=0; j&lt;positions.size()-1; ++j) {</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :     const Vector &amp; first (positions[j]);</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">    1045748 :     Vector &amp; second (positions[j+1]);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">    1045748 :     second=first+pbcDistance(first,second);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">     106316 : }</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">      19923 : void ActionAtomistic::updateUniqueLocal() {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">      19923 :   if(atoms.dd &amp;&amp; atoms.shuffledAtoms&gt;0) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       9706 :     unique_local.clear();</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      91318 :     for(auto pp=unique.begin(); pp!=unique.end(); ++pp) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">      81612 :       if(atoms.g2l[pp-&gt;index()]&gt;=0) unique_local.push_back(*pp); // already sorted</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :     }</a>
+<a name="302"><span class="lineNum">     302 </span>            :   } else {</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">      10217 :     unique_local=unique; // copy</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">      19923 : }</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAtomistic.h.func-sort-c.html b/coverage/core/ActionAtomistic.h.func-sort-c.html
new file mode 100644
index 0000000000..6f21cc2879
--- /dev/null
+++ b/coverage/core/ActionAtomistic.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAtomistic.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAtomistic.h<span style="font-size: 80%;"> (<a href="ActionAtomistic.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionAtomistic.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#231">_ZNK4PLMD15ActionAtomistic18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">160</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#225">_ZNK4PLMD15ActionAtomistic9getChargeEi</a></td>
+              <td class="coverFnHi">63884</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#281">_ZN4PLMD15ActionAtomistic12lockRequestsEv</a></td>
+              <td class="coverFnHi">152576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#286">_ZN4PLMD15ActionAtomistic14unlockRequestsEv</a></td>
+              <td class="coverFnHi">152576</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAtomistic.h.func.html b/coverage/core/ActionAtomistic.h.func.html
new file mode 100644
index 0000000000..41ec8fc588
--- /dev/null
+++ b/coverage/core/ActionAtomistic.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAtomistic.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAtomistic.h<span style="font-size: 80%;"> (<a href="ActionAtomistic.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionAtomistic.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#281">_ZN4PLMD15ActionAtomistic12lockRequestsEv</a></td>
+              <td class="coverFnHi">152576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#286">_ZN4PLMD15ActionAtomistic14unlockRequestsEv</a></td>
+              <td class="coverFnHi">152576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#231">_ZNK4PLMD15ActionAtomistic18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">160</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionAtomistic.h.gcov.html#225">_ZNK4PLMD15ActionAtomistic9getChargeEi</a></td>
+              <td class="coverFnHi">63884</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionAtomistic.h.gcov.html b/coverage/core/ActionAtomistic.h.gcov.html
new file mode 100644
index 0000000000..1c1f4d65fd
--- /dev/null
+++ b/coverage/core/ActionAtomistic.h.gcov.html
@@ -0,0 +1,397 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionAtomistic.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionAtomistic.h<span style="font-size: 80%;"> (source / <a href="ActionAtomistic.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionAtomistic_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionAtomistic_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Tensor.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/ForwardDecl.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;map&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class Pbc;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class PDB;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : /// \ingroup MULTIINHERIT</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Action used to create objects that access the positions of the atoms from the MD code</a>
+<a name="40"><span class="lineNum">      40 </span>            : class ActionAtomistic :</a>
+<a name="41"><span class="lineNum">      41 </span>            :   virtual public Action</a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::vector&lt;AtomNumber&gt; indexes;         // the set of needed atoms</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// unique should be an ordered set since we later create a vector containing the corresponding indexes</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::vector&lt;AtomNumber&gt;  unique;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// unique_local should be an ordered set since we later create a vector containing the corresponding indexes</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::vector&lt;AtomNumber&gt;  unique_local;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::vector&lt;Vector&gt;   positions;       // positions of the needed atoms</a>
+<a name="50"><span class="lineNum">      50 </span>            :   double                energy;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   ForwardDecl&lt;Pbc&gt;      pbc_fwd;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   Pbc&amp;                  pbc=*pbc_fwd;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   Tensor                virial;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;double&gt;   masses;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   bool                  chargesWereSet;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::vector&lt;double&gt;   charges;</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::vector&lt;Vector&gt;   forces;          // forces on the needed atoms</a>
+<a name="59"><span class="lineNum">      59 </span>            :   double                forceOnEnergy;</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   double                forceOnExtraCV;</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            :   std::string           extraCV;</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   bool                  lockRequestAtoms; // forbid changes to request atoms</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            :   bool                  donotretrieve;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool                  donotforce;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : protected:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   Atoms&amp;                atoms;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   void setExtraCV(const std::string &amp;name);</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : public:</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Request an array of atoms.</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// This method is used to ask for a list of atoms. Atoms</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// should be asked for by number. If this routine is called</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// during the simulation, atoms will be available at the next step</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// MAYBE WE HAVE TO FIND SOMETHING MORE CLEAR FOR DYNAMIC</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// LISTS OF ATOMS</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void requestAtoms(const std::vector&lt;AtomNumber&gt; &amp; a, const bool clearDep=true);</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Get position of i-th atom (access by relative index)</a>
+<a name="84"><span class="lineNum">      84 </span>            :   const Vector &amp; getPosition(int)const;</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Get position of i-th atom (access by absolute AtomNumber).</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// With direct access to the global atom array.</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// \warning Should be only used by actions that need to read the shared position array.</a>
+<a name="88"><span class="lineNum">      88 </span>            : ///          This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   const Vector &amp; getGlobalPosition(AtomNumber)const;</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// Get modifiable position of i-th atom (access by absolute AtomNumber).</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// \warning Should be only used by actions that need to modify the shared position array.</a>
+<a name="92"><span class="lineNum">      92 </span>            : ///          This array is insensitive to local changes such as makeWhole(), numerical derivatives, etc.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   Vector &amp; modifyGlobalPosition(AtomNumber);</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Get total number of atoms, including virtual ones.</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Can be used to make a loop on modifyGlobalPosition or getGlobalPosition.</a>
+<a name="96"><span class="lineNum">      96 </span>            :   unsigned getTotAtoms()const;</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Get modifiable force of i-th atom (access by absolute AtomNumber).</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// \warning  Should be used by action that need to modify the stored atomic forces.</a>
+<a name="99"><span class="lineNum">      99 </span>            : ///           This should be used with great care since the plumed core does</a>
+<a name="100"><span class="lineNum">     100 </span>            : ///           not usually keep all these forces up to date. In particular,</a>
+<a name="101"><span class="lineNum">     101 </span>            : ///           if an action require this, one should during constructor</a>
+<a name="102"><span class="lineNum">     102 </span>            : ///           call allowToAccessGlobalForces().</a>
+<a name="103"><span class="lineNum">     103 </span>            : ///           Notice that for efficiency reason plumed does not check if this is done!</a>
+<a name="104"><span class="lineNum">     104 </span>            :   Vector &amp; modifyGlobalForce(AtomNumber);</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Get modifiable virial</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Should be used by action that need to modify the stored virial</a>
+<a name="107"><span class="lineNum">     107 </span>            :   Tensor &amp; modifyGlobalVirial();</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Get modifiable PBC</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Should be used by action that need to modify the stored box</a>
+<a name="110"><span class="lineNum">     110 </span>            :   Pbc &amp; modifyGlobalPbc();</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// Get box shape</a>
+<a name="112"><span class="lineNum">     112 </span>            :   const Tensor &amp; getBox()const;</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Get the array of all positions</a>
+<a name="114"><span class="lineNum">     114 </span>            :   const std::vector&lt;Vector&gt; &amp; getPositions()const;</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Get energy</a>
+<a name="116"><span class="lineNum">     116 </span>            :   const double &amp; getEnergy()const;</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Get mass of i-th atom</a>
+<a name="118"><span class="lineNum">     118 </span>            :   double getMass(int i)const;</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Get charge of i-th atom</a>
+<a name="120"><span class="lineNum">     120 </span>            :   double getCharge(int i)const;</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Get a reference to forces array</a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;Vector&gt; &amp; modifyForces();</a>
+<a name="123"><span class="lineNum">     123 </span>            : /// Get a reference to virial array</a>
+<a name="124"><span class="lineNum">     124 </span>            :   Tensor &amp; modifyVirial();</a>
+<a name="125"><span class="lineNum">     125 </span>            : /// Get a reference to force on energy</a>
+<a name="126"><span class="lineNum">     126 </span>            :   double &amp; modifyForceOnEnergy();</a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Get a reference to force on extraCV</a>
+<a name="128"><span class="lineNum">     128 </span>            :   double &amp; modifyForceOnExtraCV();</a>
+<a name="129"><span class="lineNum">     129 </span>            : /// Get number of available atoms</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov"> 4193471173 :   unsigned getNumberOfAtoms()const {return indexes.size();}</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : /// Compute the pbc distance between two positions</a>
+<a name="132"><span class="lineNum">     132 </span>            :   Vector pbcDistance(const Vector&amp;,const Vector&amp;)const;</a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Applies  PBCs to a seriens of positions or distances</a>
+<a name="134"><span class="lineNum">     134 </span>            :   void pbcApply(std::vector&lt;Vector&gt;&amp; dlist, unsigned max_index=0) const;</a>
+<a name="135"><span class="lineNum">     135 </span>            : /// Get the vector of absolute indexes</a>
+<a name="136"><span class="lineNum">     136 </span>            :   virtual const std::vector&lt;AtomNumber&gt; &amp; getAbsoluteIndexes()const;</a>
+<a name="137"><span class="lineNum">     137 </span>            : /// Get the absolute index of an atom</a>
+<a name="138"><span class="lineNum">     138 </span>            :   AtomNumber getAbsoluteIndex(int i)const;</a>
+<a name="139"><span class="lineNum">     139 </span>            : /// Parse a list of atoms without a numbered keyword</a>
+<a name="140"><span class="lineNum">     140 </span>            :   void parseAtomList(const std::string&amp;key,std::vector&lt;AtomNumber&gt; &amp;t);</a>
+<a name="141"><span class="lineNum">     141 </span>            : /// Parse an list of atom with a numbred keyword</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void parseAtomList(const std::string&amp;key,const int num, std::vector&lt;AtomNumber&gt; &amp;t);</a>
+<a name="143"><span class="lineNum">     143 </span>            : /// Convert a set of read in strings into an atom list (this is used in parseAtomList)</a>
+<a name="144"><span class="lineNum">     144 </span>            :   void interpretAtomList( std::vector&lt;std::string&gt;&amp; strings, std::vector&lt;AtomNumber&gt; &amp;t);</a>
+<a name="145"><span class="lineNum">     145 </span>            : /// Change the box shape</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void changeBox( const Tensor&amp; newbox );</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// Get reference to Pbc</a>
+<a name="148"><span class="lineNum">     148 </span>            :   const Pbc &amp; getPbc() const;</a>
+<a name="149"><span class="lineNum">     149 </span>            : /// Add the forces to the atoms</a>
+<a name="150"><span class="lineNum">     150 </span>            :   void setForcesOnAtoms( const std::vector&lt;double&gt;&amp; forcesToApply, unsigned ind=0 );</a>
+<a name="151"><span class="lineNum">     151 </span>            : /// Skip atom retrieval - use with care.</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// If this function is called during initialization, then atoms are</a>
+<a name="153"><span class="lineNum">     153 </span>            : /// not going to be retrieved. Can be used for optimization. Notice that</a>
+<a name="154"><span class="lineNum">     154 </span>            : /// calling getPosition(int) in an Action where DoNotRetrieve() was called might</a>
+<a name="155"><span class="lineNum">     155 </span>            : /// lead to undefined behavior.</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         41 :   void doNotRetrieve() {donotretrieve=true;}</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : /// Skip atom forces - use with care.</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// If this function is called during initialization, then forces are</a>
+<a name="159"><span class="lineNum">     159 </span>            : /// not going to be propagated. Can be used for optimization.</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         41 :   void doNotForce() {donotforce=true;}</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : /// Make atoms whole, assuming they are in the proper order</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void makeWhole();</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// Allow calls to modifyGlobalForce()</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          9 :   void allowToAccessGlobalForces() {atoms.zeroallforces=true;}</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : /// updates local unique atoms</a>
+<a name="166"><span class="lineNum">     166 </span>            :   void updateUniqueLocal();</a>
+<a name="167"><span class="lineNum">     167 </span>            : public:</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : // virtual functions:</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   explicit ActionAtomistic(const ActionOptions&amp;ao);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   ~ActionAtomistic();</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   void clearOutputForces();</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : /// N.B. only pass an ActionWithValue to this routine if you know exactly what you</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// are doing.  The default will be correct for the vast majority of cases</a>
+<a name="180"><span class="lineNum">     180 </span>            :   void   calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// Numerical derivative routine to use when using Actions that inherit from BOTH</a>
+<a name="182"><span class="lineNum">     182 </span>            : /// ActionWithArguments and ActionAtomistic</a>
+<a name="183"><span class="lineNum">     183 </span>            :   void calculateAtomicNumericalDerivatives( ActionWithValue* a, const unsigned&amp; startnum );</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   virtual void retrieveAtoms();</a>
+<a name="186"><span class="lineNum">     186 </span>            :   void applyForces();</a>
+<a name="187"><span class="lineNum">     187 </span>            :   void lockRequests() override;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   void unlockRequests() override;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   const std::vector&lt;AtomNumber&gt; &amp; getUnique()const;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   const std::vector&lt;AtomNumber&gt; &amp; getUniqueLocal()const;</a>
+<a name="191"><span class="lineNum">     191 </span>            : /// Read in an input file containing atom positions and calculate the action for the atomic</a>
+<a name="192"><span class="lineNum">     192 </span>            : /// configuration therin</a>
+<a name="193"><span class="lineNum">     193 </span>            :   void readAtomsFromPDB( const PDB&amp; pdb ) override;</a>
+<a name="194"><span class="lineNum">     194 </span>            : };</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : inline</a>
+<a name="197"><span class="lineNum">     197 </span>            : const Vector &amp; ActionAtomistic::getPosition(int i)const {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">  544823535 :   return positions[i];</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : inline</a>
+<a name="202"><span class="lineNum">     202 </span>            : const Vector &amp; ActionAtomistic::getGlobalPosition(AtomNumber i)const {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     291526 :   return atoms.positions[i.index()];</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : inline</a>
+<a name="207"><span class="lineNum">     207 </span>            : Vector &amp; ActionAtomistic::modifyGlobalPosition(AtomNumber i) {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     351804 :   return atoms.positions[i.index()];</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : inline</a>
+<a name="212"><span class="lineNum">     212 </span>            : Vector &amp; ActionAtomistic::modifyGlobalForce(AtomNumber i) {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      16318 :   return atoms.forces[i.index()];</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : inline</a>
+<a name="217"><span class="lineNum">     217 </span>            : Tensor &amp; ActionAtomistic::modifyGlobalVirial() {</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        125 :   return atoms.virial;</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : inline</a>
+<a name="222"><span class="lineNum">     222 </span>            : double ActionAtomistic::getMass(int i)const {</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     499772 :   return masses[i];</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : inline</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      63884 : double ActionAtomistic::getCharge(int i) const {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      63884 :   if( !chargesWereSet ) error(&quot;charges were not passed to plumed&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      63884 :   return charges[i];</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : inline</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        160 : const std::vector&lt;AtomNumber&gt; &amp; ActionAtomistic::getAbsoluteIndexes()const {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        161 :   return indexes;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : inline</a>
+<a name="238"><span class="lineNum">     238 </span>            : AtomNumber ActionAtomistic::getAbsoluteIndex(int i)const {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">  126943401 :   return indexes[i];</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : inline</a>
+<a name="243"><span class="lineNum">     243 </span>            : const std::vector&lt;Vector&gt; &amp; ActionAtomistic::getPositions()const {</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">     562796 :   return positions;</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : inline</a>
+<a name="248"><span class="lineNum">     248 </span>            : const double &amp; ActionAtomistic::getEnergy()const {</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       3989 :   return energy;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : }</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : inline</a>
+<a name="253"><span class="lineNum">     253 </span>            : const Tensor &amp; ActionAtomistic::getBox()const {</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">      25194 :   return pbc.getBox();</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : inline</a>
+<a name="258"><span class="lineNum">     258 </span>            : std::vector&lt;Vector&gt; &amp; ActionAtomistic::modifyForces() {</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">     115636 :   return forces;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : inline</a>
+<a name="263"><span class="lineNum">     263 </span>            : Tensor &amp; ActionAtomistic::modifyVirial() {</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">     130101 :   return virial;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : inline</a>
+<a name="268"><span class="lineNum">     268 </span>            : double &amp; ActionAtomistic::modifyForceOnEnergy() {</a>
+<a name="269"><span class="lineNum">     269 </span>            :   return forceOnEnergy;</a>
+<a name="270"><span class="lineNum">     270 </span>            : }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            : inline</a>
+<a name="273"><span class="lineNum">     273 </span>            : double &amp; ActionAtomistic::modifyForceOnExtraCV() {</a>
+<a name="274"><span class="lineNum">     274 </span>            :   return forceOnExtraCV;</a>
+<a name="275"><span class="lineNum">     275 </span>            : }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            : inline</a>
+<a name="278"><span class="lineNum">     278 </span>            : const Pbc &amp; ActionAtomistic::getPbc() const {</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">     581015 :   return pbc;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : }</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            : inline</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">     152576 : void ActionAtomistic::lockRequests() {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">     167163 :   lockRequestAtoms=true;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     152576 : }</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : inline</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     152576 : void ActionAtomistic::unlockRequests() {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     167163 :   lockRequestAtoms=false;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     152576 : }</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            : inline</a>
+<a name="293"><span class="lineNum">     293 </span>            : const std::vector&lt;AtomNumber&gt; &amp; ActionAtomistic::getUnique()const {</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        546 :   return unique;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : inline</a>
+<a name="298"><span class="lineNum">     298 </span>            : const std::vector&lt;AtomNumber&gt; &amp; ActionAtomistic::getUniqueLocal()const {</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      55184 :   return unique_local;</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : }</a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : inline</a>
+<a name="303"><span class="lineNum">     303 </span>            : unsigned ActionAtomistic::getTotAtoms()const {</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">      32095 :   return atoms.positions.size();</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : inline</a>
+<a name="308"><span class="lineNum">     308 </span>            : Pbc &amp; ActionAtomistic::modifyGlobalPbc() {</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         77 :   return atoms.pbc;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : }</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            : inline</a>
+<a name="313"><span class="lineNum">     313 </span>            : void ActionAtomistic::setExtraCV(const std::string &amp;name) {</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          3 :   extraCV=name;</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          3 : }</span></a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionPilot.cpp.func-sort-c.html b/coverage/core/ActionPilot.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0dfd9a923d
--- /dev/null
+++ b/coverage/core/ActionPilot.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionPilot.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionPilot.cpp<span style="font-size: 80%;"> (<a href="ActionPilot.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionPilot.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#26">_ZN4PLMD11ActionPilotC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#47">_ZN4PLMD11ActionPilot9setStrideERKi</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#26">_ZN4PLMD11ActionPilotC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2637</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#24">_ZN4PLMD11ActionPilot16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2704</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#43">_ZNK4PLMD11ActionPilot9getStrideEv</a></td>
+              <td class="coverFnHi">81233</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#38">_ZNK4PLMD11ActionPilot6onStepEv</a></td>
+              <td class="coverFnHi">1448395</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionPilot.cpp.func.html b/coverage/core/ActionPilot.cpp.func.html
new file mode 100644
index 0000000000..bae1091c7f
--- /dev/null
+++ b/coverage/core/ActionPilot.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionPilot.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionPilot.cpp<span style="font-size: 80%;"> (<a href="ActionPilot.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionPilot.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#24">_ZN4PLMD11ActionPilot16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2704</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#47">_ZN4PLMD11ActionPilot9setStrideERKi</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#26">_ZN4PLMD11ActionPilotC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#26">_ZN4PLMD11ActionPilotC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2637</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#38">_ZNK4PLMD11ActionPilot6onStepEv</a></td>
+              <td class="coverFnHi">1448395</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionPilot.cpp.gcov.html#43">_ZNK4PLMD11ActionPilot9getStrideEv</a></td>
+              <td class="coverFnHi">81233</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionPilot.cpp.gcov.html b/coverage/core/ActionPilot.cpp.gcov.html
new file mode 100644
index 0000000000..49cc75ca06
--- /dev/null
+++ b/coverage/core/ActionPilot.cpp.gcov.html
@@ -0,0 +1,131 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionPilot.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionPilot.cpp<span style="font-size: 80%;"> (source / <a href="ActionPilot.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span><span class="lineCov">       2704 : void ActionPilot::registerKeywords(Keywords&amp; keys) {}</span></a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">       2637 : ActionPilot::ActionPilot(const ActionOptions&amp;ao):</span></a>
+<a name="29"><span class="lineNum">      29 </span>            :   Action(ao),</a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">       2637 :   stride(1)</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">       5274 :   if( keywords.exists(&quot;STRIDE&quot;) ) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       2579 :     parse(&quot;STRIDE&quot;,stride);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       5158 :     if( !keywords.style(&quot;STRIDE&quot;,&quot;hidden&quot;) ) log.printf(&quot;  with stride %d\n&quot;,stride);</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   } else {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         58 :     stride=0;</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   }</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       2637 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">    1448395 : bool ActionPilot::onStep()const {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">    1448395 :   if( stride&gt;0 ) return getStep()%stride==0;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   return false;</a>
+<a name="43"><span class="lineNum">      43 </span>            : }</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      81233 : int ActionPilot::getStride()const {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      81233 :   return stride;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         17 : void ActionPilot::setStride(const int&amp; n) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         17 :   stride=n;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         17 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionPilot.h.func-sort-c.html b/coverage/core/ActionPilot.h.func-sort-c.html
new file mode 100644
index 0000000000..a1084c21cb
--- /dev/null
+++ b/coverage/core/ActionPilot.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionPilot.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionPilot.h<span style="font-size: 80%;"> (<a href="ActionPilot.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionPilot.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionPilot.h.func.html b/coverage/core/ActionPilot.h.func.html
new file mode 100644
index 0000000000..5ed8e6df84
--- /dev/null
+++ b/coverage/core/ActionPilot.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionPilot.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionPilot.h<span style="font-size: 80%;"> (<a href="ActionPilot.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionPilot.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionPilot.h.gcov.html b/coverage/core/ActionPilot.h.gcov.html
new file mode 100644
index 0000000000..6df8fa076e
--- /dev/null
+++ b/coverage/core/ActionPilot.h.gcov.html
@@ -0,0 +1,134 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionPilot.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionPilot.h<span style="font-size: 80%;"> (source / <a href="ActionPilot.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionPilot_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionPilot_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : /**</a>
+<a name="30"><span class="lineNum">      30 </span>            : \ingroup MULTIINHERIT</a>
+<a name="31"><span class="lineNum">      31 </span>            : This is used to create PLMD::Action objects that are run with some set frequency.</a>
+<a name="32"><span class="lineNum">      32 </span>            : Any PLMD::Action</a>
+<a name="33"><span class="lineNum">      33 </span>            : that does not inherit from PLMD::Action is only run when some other Action requires the output from</a>
+<a name="34"><span class="lineNum">      34 </span>            : it in order to run.  This class is used in PLMD::Bias</a>
+<a name="35"><span class="lineNum">      35 </span>            :  Action which drives the execution of other Action's.</a>
+<a name="36"><span class="lineNum">      36 </span>            :  Action's of this kind are executed with a fixed stride</a>
+<a name="37"><span class="lineNum">      37 </span>            :  which is specified on the directive line with a STRIDE= keyword</a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       1523 : class ActionPilot:</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   public virtual Action</a>
+<a name="41"><span class="lineNum">      41 </span>            : {</a>
+<a name="42"><span class="lineNum">      42 </span>            :   int stride; // multiple time step</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   explicit ActionPilot(const ActionOptions&amp;);</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Create the keywords for actionPilot</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Check if the action is active on this step</a>
+<a name="48"><span class="lineNum">      48 </span>            :   virtual bool onStep()const;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Set the value of the stride</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void setStride( const int&amp; n );</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Get the stride</a>
+<a name="52"><span class="lineNum">      52 </span>            :   int getStride()const;</a>
+<a name="53"><span class="lineNum">      53 </span>            : };</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : #endif</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionRegister.cpp.func-sort-c.html b/coverage/core/ActionRegister.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4b5b9ffa73
--- /dev/null
+++ b/coverage/core/ActionRegister.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionRegister.cpp<span style="font-size: 80%;"> (<a href="ActionRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionRegister.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#107">_ZN4PLMD14ActionRegister13printTemplateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#91">_ZN4PLMD14ActionRegister11printManualERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKbSA_</a></td>
+              <td class="coverFnHi">293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#124">_ZN4PLMDlsERSoRKNS_14ActionRegisterE</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#117">_ZNK4PLMD14ActionRegister14getActionNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">296</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#86">_ZN4PLMD14ActionRegister11getKeywordsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">584</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#28">_ZN4PLMD14ActionRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#69">_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#64">_ZN4PLMD14ActionRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">15183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#49">_ZN4PLMD14ActionRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS_6ActionESt14default_deleteIS8_EERKNS_13ActionOptionsEEPFvRNS_8KeywordsEE</a></td>
+              <td class="coverFnHi">1217057</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#41">_ZN4PLMD14ActionRegister6removeEPFSt10unique_ptrINS_6ActionESt14default_deleteIS2_EERKNS_13ActionOptionsEE</a></td>
+              <td class="coverFnHi">1217057</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#36">_ZN4PLMD14actionRegisterEv</a></td>
+              <td class="coverFnHi">2449301</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionRegister.cpp.func.html b/coverage/core/ActionRegister.cpp.func.html
new file mode 100644
index 0000000000..0399413c8d
--- /dev/null
+++ b/coverage/core/ActionRegister.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionRegister.cpp<span style="font-size: 80%;"> (<a href="ActionRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionRegister.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#86">_ZN4PLMD14ActionRegister11getKeywordsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">584</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#91">_ZN4PLMD14ActionRegister11printManualERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKbSA_</a></td>
+              <td class="coverFnHi">293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#107">_ZN4PLMD14ActionRegister13printTemplateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#49">_ZN4PLMD14ActionRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS_6ActionESt14default_deleteIS8_EERKNS_13ActionOptionsEEPFvRNS_8KeywordsEE</a></td>
+              <td class="coverFnHi">1217057</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#64">_ZN4PLMD14ActionRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">15183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#69">_ZN4PLMD14ActionRegister6createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#41">_ZN4PLMD14ActionRegister6removeEPFSt10unique_ptrINS_6ActionESt14default_deleteIS2_EERKNS_13ActionOptionsEE</a></td>
+              <td class="coverFnHi">1217057</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#28">_ZN4PLMD14ActionRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#36">_ZN4PLMD14actionRegisterEv</a></td>
+              <td class="coverFnHi">2449301</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#124">_ZN4PLMDlsERSoRKNS_14ActionRegisterE</a></td>
+              <td class="coverFnHi">294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionRegister.cpp.gcov.html#117">_ZNK4PLMD14ActionRegister14getActionNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">296</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionRegister.cpp.gcov.html b/coverage/core/ActionRegister.cpp.gcov.html
new file mode 100644
index 0000000000..d9ee644cf9
--- /dev/null
+++ b/coverage/core/ActionRegister.cpp.gcov.html
@@ -0,0 +1,218 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionRegister.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionRegister.cpp<span style="font-size: 80%;"> (source / <a href="ActionRegister.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Action.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;algorithm&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iostream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">       4168 : ActionRegister::~ActionRegister() {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">       4168 :   if(m.size()&gt;0) {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineNoCov">          0 :     std::string names=&quot;&quot;;</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :     for(const auto &amp; p : m) names+=p.first+&quot; &quot;;</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;WARNING: Directive &quot;+ names +&quot; has not been properly unregistered. This might lead to memory leak!!\n&quot;;</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   }</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       4168 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">    2449301 : ActionRegister&amp; actionRegister() {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">    2449301 :   static ActionRegister ans;</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">    2449301 :   return ans;</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : }</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">    1217057 : void ActionRegister::remove(creator_pointer f) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">  103699898 :   for(auto p=m.begin(); p!=m.end(); ++p) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">  103699898 :     if((*p).second==f) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">    1217057 :       m.erase(p); break;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :     }</a>
+<a name="48"><span class="lineNum">      48 </span>            :   }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">    1217057 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">    1217057 : void ActionRegister::add(std::string key,creator_pointer f,keywords_pointer k) {</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   // this force each action to be registered as an uppercase string</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">    6160308 :   if ( std::any_of( std::begin( key ), std::end( key ), []( char c ) { return ( std::islower( c ) ); } ) ) plumed_error() &lt;&lt; &quot;Action: &quot; + key + &quot; cannot be registered, use only UPPERCASE characters&quot;;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   if(m.count(key)) {</a>
+<a name="55"><span class="lineNum">      55 </span>            :     m.erase(key);</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :     disabled.insert(key);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   } else {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">    1217057 :     m.insert(std::pair&lt;std::string,creator_pointer&gt;(key,f));</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :     // Store a pointer to the function that creates keywords</a>
+<a name="60"><span class="lineNum">      60 </span>            :     // A pointer is stored and not the keywords because all</a>
+<a name="61"><span class="lineNum">      61 </span>            :     // Vessels must be dynamically loaded before the actions.</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">    1217057 :     mk.insert(std::pair&lt;std::string,keywords_pointer&gt;(key,k));</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   };</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">    1217057 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      15183 : bool ActionRegister::check(const std::string &amp; key) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      15179 :   if(m.count(key)&gt;0 &amp;&amp; mk.count(key)&gt;0) return true;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   return false;</a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      14304 : std::unique_ptr&lt;Action&gt; ActionRegister::create(const ActionOptions&amp;ao) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      14304 :   if(ao.line.size()&lt;1)return NULL;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   // Create a copy of the manual locally. The manual is</a>
+<a name="74"><span class="lineNum">      74 </span>            :   // then added to the ActionOptions. This allows us to</a>
+<a name="75"><span class="lineNum">      75 </span>            :   // ensure during construction that all the keywords for</a>
+<a name="76"><span class="lineNum">      76 </span>            :   // the action have been documented. In addition, we can</a>
+<a name="77"><span class="lineNum">      77 </span>            :   // generate the documentation when the user makes an error</a>
+<a name="78"><span class="lineNum">      78 </span>            :   // in the input.</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      14304 :   std::unique_ptr&lt;Action&gt; action;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      14304 :   if( check(ao.line[0]) ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      14302 :     Keywords keys; mk[ao.line[0]](keys);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      14302 :     ActionOptions nao( ao,keys );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      28566 :     action=m[ao.line[0]](nao);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      14302 :   }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   return action;</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      14304 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        584 : bool ActionRegister::getKeywords(const std::string&amp; action, Keywords&amp; keys) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        584 :   if ( check(action) ) {  mk[action](keys); return true; }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   return false;</a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        293 : bool ActionRegister::printManual(const std::string&amp; action, const bool&amp; vimout, const bool&amp; spellout) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        293 :   if ( check(action) ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        292 :     Keywords keys; getKeywords( action, keys );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        292 :     if( vimout ) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        292 :       printf(&quot;%s&quot;,action.c_str()); keys.print_vim(); printf(&quot;\n&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     } else if( spellout ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :       keys.print_spelling();</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :     } else {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :       keys.print_html();</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     }</a>
+<a name="103"><span class="lineNum">     103 </span>            :     return true;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        292 :   } else {</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :     return false;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 : bool ActionRegister::printTemplate(const std::string&amp; action, bool include_optional) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   if( check(action) ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     Keywords keys; mk[action](keys);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     keys.print_template(action, include_optional);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     return true;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   } else {</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     return false;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        296 : std::vector&lt;std::string&gt; ActionRegister::getActionNames() const {</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::vector&lt;std::string&gt; s;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      86729 :   for(const auto &amp; it : m) s.push_back(it.first);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        296 :   std::sort(s.begin(),s.end());</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        296 :   return s;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        294 : std::ostream &amp; operator&lt;&lt;(std::ostream &amp;log,const ActionRegister&amp;ar) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        294 :   std::vector&lt;std::string&gt; s(ar.getActionNames());</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      86143 :   for(unsigned i=0; i&lt;s.size(); i++) log&lt;&lt;&quot;  &quot;&lt;&lt;s[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        294 :   if(!ar.disabled.empty()) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     s.assign(ar.disabled.size(),&quot;&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     std::copy(ar.disabled.begin(),ar.disabled.end(),s.begin());</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     std::sort(s.begin(),s.end());</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;+++++++ WARNING +++++++\n&quot;;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;The following keywords have been registered more than once and will be disabled:\n&quot;;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;s.size(); i++) log&lt;&lt;&quot;  - &quot;&lt;&lt;s[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;+++++++ END WARNING +++++++\n&quot;;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   };</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        294 :   return log;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        294 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSet.cpp.func-sort-c.html b/coverage/core/ActionSet.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3d2eb323e3
--- /dev/null
+++ b/coverage/core/ActionSet.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSet.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSet.cpp<span style="font-size: 80%;"> (<a href="ActionSet.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionSet.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.cpp.gcov.html#35">_ZN4PLMD9ActionSet11clearDeleteEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.cpp.gcov.html#24">_ZN4PLMD9ActionSetC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.cpp.gcov.html#29">_ZN4PLMD9ActionSetD2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSet.cpp.func.html b/coverage/core/ActionSet.cpp.func.html
new file mode 100644
index 0000000000..b685a7853c
--- /dev/null
+++ b/coverage/core/ActionSet.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSet.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSet.cpp<span style="font-size: 80%;"> (<a href="ActionSet.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionSet.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.cpp.gcov.html#35">_ZN4PLMD9ActionSet11clearDeleteEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.cpp.gcov.html#24">_ZN4PLMD9ActionSetC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.cpp.gcov.html#29">_ZN4PLMD9ActionSetD2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSet.cpp.gcov.html b/coverage/core/ActionSet.cpp.gcov.html
new file mode 100644
index 0000000000..cf23088687
--- /dev/null
+++ b/coverage/core/ActionSet.cpp.gcov.html
@@ -0,0 +1,118 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSet.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSet.cpp<span style="font-size: 80%;"> (source / <a href="ActionSet.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span><span class="lineCov">     805268 : ActionSet::ActionSet(PlumedMain&amp;p):</span></a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">     805268 :   plumed(p) {</span></a>
+<a name="28"><span class="lineNum">      28 </span>            :   (void) plumed; // to suppress warning about &quot;unused plumed&quot;</a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     805268 : }</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">     805268 : ActionSet::~ActionSet()</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : {</a>
+<a name="33"><span class="lineNum">      33 </span>            : // required in order to deallocate in reverse order:</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     819530 :   for(int i=size()-1; i&gt;=0; i--) (*this)[i].reset();</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     805268 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          1 : void ActionSet::clearDelete() {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">          3 :   for(int i=size()-1; i&gt;=0; i--) (*this)[i].reset();</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          1 :   clear();</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          1 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSet.h.func-sort-c.html b/coverage/core/ActionSet.h.func-sort-c.html
new file mode 100644
index 0000000000..08b5f81e72
--- /dev/null
+++ b/coverage/core/ActionSet.h.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSet.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSet.h<span style="font-size: 80%;"> (<a href="ActionSet.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionSet.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_3ves14BasisFunctionsEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_3ves18TargetDistributionEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_3ves7VesBiasEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#111">_ZNK4PLMD9ActionSet12getLabelListIPNS_15ActionWithValueEEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_4maze9OptimizerEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_8analysis21LandmarkSelectionBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6dimred27DimensionalityReductionBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_11ActionSetupEEESt6vectorIT_SaIS5_EEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6adjmat19AdjacencyMatrixBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_4maze4LossEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6adjmat14ClusteringBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#130">_ZNK4PLMD9ActionSet12selectLatestIPNS_3piv3PIVEEET_PKNS_6ActionE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_4opes12ExpansionCVsEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_8analysis12AnalysisBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_7generic4ReadEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_3ves7VesBiasEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_10vesselbase16ActionWithVesselEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">118</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_3ves14BasisFunctionsEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">241</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_15ActionWithValueEEESt6vectorIT_SaIS5_EEv</a></td>
+              <td class="coverFnHi">321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_11multicolvar15MultiColvarBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">386</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_3ves18TargetDistributionEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#130">_ZNK4PLMD9ActionSet12selectLatestIPNS_14GenericMolInfoEEET_PKNS_6ActionE</a></td>
+              <td class="coverFnHi">993</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6ActionEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">14302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_11ActionPilotEEESt6vectorIT_SaIS5_EEv</a></td>
+              <td class="coverFnHi">15151</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_15ActionWithValueEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1081659</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSet.h.func.html b/coverage/core/ActionSet.h.func.html
new file mode 100644
index 0000000000..1f0677de08
--- /dev/null
+++ b/coverage/core/ActionSet.h.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSet.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSet.h<span style="font-size: 80%;"> (<a href="ActionSet.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionSet.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#111">_ZNK4PLMD9ActionSet12getLabelListIPNS_15ActionWithValueEEENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#130">_ZNK4PLMD9ActionSet12selectLatestIPNS_14GenericMolInfoEEET_PKNS_6ActionE</a></td>
+              <td class="coverFnHi">993</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#130">_ZNK4PLMD9ActionSet12selectLatestIPNS_3piv3PIVEEET_PKNS_6ActionE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_10vesselbase16ActionWithVesselEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">118</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_11multicolvar15MultiColvarBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">386</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_15ActionWithValueEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1081659</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_3ves14BasisFunctionsEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">241</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_3ves18TargetDistributionEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_3ves7VesBiasEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_4maze4LossEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_4maze9OptimizerEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6ActionEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">14302</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6adjmat14ClusteringBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6adjmat19AdjacencyMatrixBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_6dimred27DimensionalityReductionBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_8analysis12AnalysisBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#92">_ZNK4PLMD9ActionSet15selectWithLabelIPNS_8analysis21LandmarkSelectionBaseEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_11ActionPilotEEESt6vectorIT_SaIS5_EEv</a></td>
+              <td class="coverFnHi">15151</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_11ActionSetupEEESt6vectorIT_SaIS5_EEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_15ActionWithValueEEESt6vectorIT_SaIS5_EEv</a></td>
+              <td class="coverFnHi">321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_3ves14BasisFunctionsEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_3ves18TargetDistributionEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_3ves7VesBiasEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_4opes12ExpansionCVsEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSet.h.gcov.html#82">_ZNK4PLMD9ActionSet6selectIPNS_7generic4ReadEEESt6vectorIT_SaIS6_EEv</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSet.h.gcov.html b/coverage/core/ActionSet.h.gcov.html
new file mode 100644
index 0000000000..c1c3cf30ed
--- /dev/null
+++ b/coverage/core/ActionSet.h.gcov.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSet.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSet.h<span style="font-size: 80%;"> (source / <a href="ActionSet.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionSet_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionSet_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;memory&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class PlumedMain;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /// std::vector containing the sequence of Action to be done.</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// It is a vector of Action*, and as such it has the entire</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// std::vector interface. Moreover, it implements methods to extract</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// Acion* of a given type (select&lt;T&gt;()), NOT of a given type (selectNot&lt;T&gt;())</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// or to find an Action with a given label (selectWithLabel())</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Finally, since it holds pointers, there is a clearDelete() function</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// which deletes the pointers before deleting the vector</a>
+<a name="39"><span class="lineNum">      39 </span>            : class ActionSet:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   public std::vector&lt;std::unique_ptr&lt;Action&gt;&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            : {</a>
+<a name="42"><span class="lineNum">      42 </span>            :   PlumedMain&amp; plumed;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   explicit ActionSet(PlumedMain&amp;p);</a>
+<a name="45"><span class="lineNum">      45 </span>            :   ~ActionSet();</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Clear and deletes all the included pointers.</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void clearDelete();</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Extract pointers to all Action's of type T</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// To extract all Colvar , use select&lt;Colvar*&gt;();</a>
+<a name="51"><span class="lineNum">      51 </span>            :   template &lt;class T&gt;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;T&gt; select()const;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Extract pointers to all Action's which are not of type T</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// E.g., to extract all noncolvars, use</a>
+<a name="55"><span class="lineNum">      55 </span>            : ///    selectNot&lt;Colvar*&gt;();</a>
+<a name="56"><span class="lineNum">      56 </span>            :   template &lt;class T&gt;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;Action*&gt; selectNot()const;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Extract pointer to an action labeled s, only if it is of</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// type T. E.g., to extract an action labeled &quot;pippo&quot;, use selectWithLabel&lt;Action*&gt;(&quot;pippo&quot;)</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// If you want it to be a Colvar, use selectWithLabel&lt;Colvar*&gt;(pippo). If it is</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// not found, it returns NULL</a>
+<a name="62"><span class="lineNum">      62 </span>            :   template &lt;class T&gt;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   T selectWithLabel(const std::string&amp;s)const;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// get the labels in the list of actions in form of a string (useful to debug)</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Only classes that can be dynamic casted to T are reported</a>
+<a name="66"><span class="lineNum">      66 </span>            :   template &lt;class T&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::string getLabelList() const;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// get the labels in the form of a vector of strings</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Only classes that can be dynamic casted to T are reported</a>
+<a name="70"><span class="lineNum">      70 </span>            :   template &lt;class T&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;std::string&gt; getLabelVector() const;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Extract pointer to last action of type T located before</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// action. If action is not in ActionSet or if there is no action of type T</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// returns NULL.</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Typically to be used as selectLatest&lt;Type&gt;(this);</a>
+<a name="76"><span class="lineNum">      76 </span>            :   template &lt;class T&gt;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   T selectLatest(const Action*action)const;</a>
+<a name="78"><span class="lineNum">      78 </span>            : };</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : /////</a>
+<a name="81"><span class="lineNum">      81 </span>            : // INLINE IMPLEMENTATIONS:</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : template &lt;class T&gt;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      15590 : std::vector&lt;T&gt; ActionSet::select()const {</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;T&gt; ret;</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    6253504 :   for(const auto &amp; p : (*this)) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    6237914 :     T t=dynamic_cast&lt;T&gt;(p.get());</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    6237914 :     if(t) ret.push_back(t);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   };</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      15590 :   return ret;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : template &lt;class T&gt;</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    1097301 : T ActionSet::selectWithLabel(const std::string&amp;s)const {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    9461825 :   for(const auto &amp; p : (*this)) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    3276047 :     T t=dynamic_cast&lt;T&gt;(p.get());</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    9447321 :     if(t &amp;&amp; dynamic_cast&lt;Action*&gt;(t)-&gt;getLabel()==s) return t;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   };</a>
+<a name="99"><span class="lineNum">      99 </span>            :   return NULL;</a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : template &lt;class T&gt;</a>
+<a name="103"><span class="lineNum">     103 </span>            : std::vector&lt;Action*&gt; ActionSet::selectNot()const {</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;Action*&gt; ret;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   for(const auto &amp; p : (*this)) {</a>
+<a name="106"><span class="lineNum">     106 </span>            :     T t=dynamic_cast&lt;T&gt;(p);</a>
+<a name="107"><span class="lineNum">     107 </span>            :     if(!t) ret.push_back(p.get());</a>
+<a name="108"><span class="lineNum">     108 </span>            :   };</a>
+<a name="109"><span class="lineNum">     109 </span>            :   return ret;</a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : template &lt;class T&gt;</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 : std::string ActionSet::getLabelList() const {</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::string outlist;</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          5 :   for(const auto &amp; p : (*this)) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          8 :     if(dynamic_cast&lt;T&gt;(p.get())) outlist+=p-&gt;getLabel()+&quot; &quot;;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   };</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   return  outlist;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : template &lt;class T&gt;</a>
+<a name="123"><span class="lineNum">     123 </span>            : std::vector&lt;std::string&gt; ActionSet::getLabelVector() const {</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::vector&lt;std::string&gt; outlist;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   for(const auto &amp; p : (*this)) {</a>
+<a name="126"><span class="lineNum">     126 </span>            :     if(dynamic_cast&lt;T&gt;(p.get())) outlist.push_back(p-&gt;getLabel());</a>
+<a name="127"><span class="lineNum">     127 </span>            :   };</a>
+<a name="128"><span class="lineNum">     128 </span>            :   return  outlist;</a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : template &lt;class T&gt;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       1005 : T ActionSet::selectLatest(const Action*action) const {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   T t=nullptr;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      13074 :   for(const auto &amp; p : (*this)) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      12109 :     if(p.get()==action) return t;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      12069 :     T r=dynamic_cast&lt;T&gt;(p.get());</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      12069 :     if(r) t=r;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   return t;</a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : #endif</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSetup.cpp.func-sort-c.html b/coverage/core/ActionSetup.cpp.func-sort-c.html
new file mode 100644
index 0000000000..35e53972c9
--- /dev/null
+++ b/coverage/core/ActionSetup.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSetup.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSetup.cpp<span style="font-size: 80%;"> (<a href="ActionSetup.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionSetup.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.cpp.gcov.html#28">_ZN4PLMD11ActionSetupC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.cpp.gcov.html#28">_ZN4PLMD11ActionSetupC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.cpp.gcov.html#38">_ZN4PLMD11ActionSetup16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSetup.cpp.func.html b/coverage/core/ActionSetup.cpp.func.html
new file mode 100644
index 0000000000..19718fb276
--- /dev/null
+++ b/coverage/core/ActionSetup.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSetup.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSetup.cpp<span style="font-size: 80%;"> (<a href="ActionSetup.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionSetup.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.cpp.gcov.html#38">_ZN4PLMD11ActionSetup16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.cpp.gcov.html#28">_ZN4PLMD11ActionSetupC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.cpp.gcov.html#28">_ZN4PLMD11ActionSetupC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSetup.cpp.gcov.html b/coverage/core/ActionSetup.cpp.gcov.html
new file mode 100644
index 0000000000..157dcc2d14
--- /dev/null
+++ b/coverage/core/ActionSetup.cpp.gcov.html
@@ -0,0 +1,121 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSetup.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSetup.cpp<span style="font-size: 80%;"> (source / <a href="ActionSetup.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionSetup.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionAnyorder.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         78 : ActionSetup::ActionSetup(const ActionOptions&amp;ao):</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         78 :   Action(ao)</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : {</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         78 :   const ActionSet&amp; actionset(plumed.getActionSet());</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         81 :   for(const auto &amp; p : actionset) {</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : // check that all the preceding actions are ActionSetup</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          3 :     if( !dynamic_cast&lt;ActionSetup*&gt;(p.get()) &amp;&amp; !dynamic_cast&lt;ActionAnyorder*&gt;(p.get()) ) error(&quot;Action &quot; + getLabel() + &quot; is a setup action, and should be only preceded by other setup actions or by actions that can be used in any order.&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   }</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         78 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        173 : void ActionSetup::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        173 :   Action::registerKeywords(keys);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        173 :   keys.remove(&quot;LABEL&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        173 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSetup.h.func-sort-c.html b/coverage/core/ActionSetup.h.func-sort-c.html
new file mode 100644
index 0000000000..a1f67e984c
--- /dev/null
+++ b/coverage/core/ActionSetup.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSetup.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSetup.h<span style="font-size: 80%;"> (<a href="ActionSetup.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionSetup.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.h.gcov.html#41">_ZN4PLMD11ActionSetup5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.h.gcov.html#39">_ZN4PLMD11ActionSetup9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSetup.h.func.html b/coverage/core/ActionSetup.h.func.html
new file mode 100644
index 0000000000..bbfa0717c1
--- /dev/null
+++ b/coverage/core/ActionSetup.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSetup.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSetup.h<span style="font-size: 80%;"> (<a href="ActionSetup.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionSetup.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.h.gcov.html#41">_ZN4PLMD11ActionSetup5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionSetup.h.gcov.html#39">_ZN4PLMD11ActionSetup9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionSetup.h.gcov.html b/coverage/core/ActionSetup.h.gcov.html
new file mode 100644
index 0000000000..cb52f8f647
--- /dev/null
+++ b/coverage/core/ActionSetup.h.gcov.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionSetup.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionSetup.h<span style="font-size: 80%;"> (source / <a href="ActionSetup.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionSetup_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionSetup_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : /**</a>
+<a name="30"><span class="lineNum">      30 </span>            : \ingroup MULTIINHERIT</a>
+<a name="31"><span class="lineNum">      31 </span>            : Action used to create a PLMD::Action that do something during setup only e.g. PLMD::SetupUnits</a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          1 : class ActionSetup :</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   public virtual Action {</a>
+<a name="35"><span class="lineNum">      35 </span>            : public:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Constructor</a>
+<a name="37"><span class="lineNum">      37 </span>            :   explicit ActionSetup(const ActionOptions&amp;ao);</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Creator of keywords</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Do nothing.</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Do nothing.</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : };</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionShortcut.cpp.func-sort-c.html b/coverage/core/ActionShortcut.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4dc309320f
--- /dev/null
+++ b/coverage/core/ActionShortcut.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionShortcut.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionShortcut.cpp<span style="font-size: 80%;"> (<a href="ActionShortcut.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionShortcut.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#31">_ZN4PLMD14ActionShortcutC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#61">_ZNK4PLMD14ActionShortcut18getSavedInputLinesB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#31">_ZN4PLMD14ActionShortcutC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#26">_ZN4PLMD14ActionShortcut16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#42">_ZN4PLMD14ActionShortcut13readInputLineERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#57">_ZNK4PLMD14ActionShortcut16getShortcutLabelB5cxx11Ev</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionShortcut.cpp.func.html b/coverage/core/ActionShortcut.cpp.func.html
new file mode 100644
index 0000000000..54e38eed1d
--- /dev/null
+++ b/coverage/core/ActionShortcut.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionShortcut.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionShortcut.cpp<span style="font-size: 80%;"> (<a href="ActionShortcut.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionShortcut.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#42">_ZN4PLMD14ActionShortcut13readInputLineERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#26">_ZN4PLMD14ActionShortcut16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#31">_ZN4PLMD14ActionShortcutC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#31">_ZN4PLMD14ActionShortcutC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#57">_ZNK4PLMD14ActionShortcut16getShortcutLabelB5cxx11Ev</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.cpp.gcov.html#61">_ZNK4PLMD14ActionShortcut18getSavedInputLinesB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionShortcut.cpp.gcov.html b/coverage/core/ActionShortcut.cpp.gcov.html
new file mode 100644
index 0000000000..f4b3bed4df
--- /dev/null
+++ b/coverage/core/ActionShortcut.cpp.gcov.html
@@ -0,0 +1,143 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionShortcut.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionShortcut.cpp<span style="font-size: 80%;"> (source / <a href="ActionShortcut.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionShortcut.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         18 : void ActionShortcut::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         18 :   Action::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         36 :   keys.add(&quot;hidden&quot;,&quot;IS_SHORTCUT&quot;,&quot;hidden keyword to tell if actions are shortcuts so that example generator can provide expansions of shortcuts&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         18 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         12 : ActionShortcut::ActionShortcut(const ActionOptions&amp;ao):</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   Action(ao),</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         12 :   shortcutlabel(label)</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : {</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         12 :   std::string s; Tools::convert(plumed.getActionSet().size(),s);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         12 :   if( shortcutlabel==(&quot;@&quot; + s) ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          6 :     std::string t; Tools::convert(plumed.getActionSet().size()+1,t);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         12 :     shortcutlabel=&quot;@&quot; + t;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         12 :   } else label = (&quot;@&quot; + s);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         12 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         36 : void ActionShortcut::readInputLine( const std::string&amp; input ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         36 :   std::string f_input = input; savedInputLines.push_back( input );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         36 :   if( update_from!=std::numeric_limits&lt;double&gt;::max() ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :     std::string ufrom; Tools::convert( update_from, ufrom ); f_input += &quot; UPDATE_FROM=&quot; + ufrom;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         36 :   if( update_until!=std::numeric_limits&lt;double&gt;::max() ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :     std::string util; Tools::convert( update_until, util ); f_input += &quot; UPDATE_UNTIL=&quot; + util;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   }</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         72 :   if( keywords.exists(&quot;RESTART&quot;) ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :     if( restart ) f_input += &quot; RESTART=YES&quot;;</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :     if( !restart ) f_input += &quot; RESTART=NO&quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         36 :   plumed.readInputLine( f_input );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         36 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         54 : const std::string &amp; ActionShortcut::getShortcutLabel() const {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         54 :   return shortcutlabel;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 : std::vector&lt;std::string&gt; ActionShortcut::getSavedInputLines() const {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   return savedInputLines;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionShortcut.h.func-sort-c.html b/coverage/core/ActionShortcut.h.func-sort-c.html
new file mode 100644
index 0000000000..9b24196279
--- /dev/null
+++ b/coverage/core/ActionShortcut.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionShortcut.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionShortcut.h<span style="font-size: 80%;"> (<a href="ActionShortcut.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionShortcut.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.h.gcov.html#46">_ZN4PLMD14ActionShortcut5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.h.gcov.html#44">_ZN4PLMD14ActionShortcut9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionShortcut.h.func.html b/coverage/core/ActionShortcut.h.func.html
new file mode 100644
index 0000000000..956a5f74a2
--- /dev/null
+++ b/coverage/core/ActionShortcut.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionShortcut.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionShortcut.h<span style="font-size: 80%;"> (<a href="ActionShortcut.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionShortcut.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.h.gcov.html#46">_ZN4PLMD14ActionShortcut5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionShortcut.h.gcov.html#44">_ZN4PLMD14ActionShortcut9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionShortcut.h.gcov.html b/coverage/core/ActionShortcut.h.gcov.html
new file mode 100644
index 0000000000..62a0948f6c
--- /dev/null
+++ b/coverage/core/ActionShortcut.h.gcov.html
@@ -0,0 +1,131 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionShortcut.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionShortcut.h<span style="font-size: 80%;"> (source / <a href="ActionShortcut.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionShortcut_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionShortcut_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : /**</a>
+<a name="30"><span class="lineNum">      30 </span>            : \ingroup MULTIINHERIT</a>
+<a name="31"><span class="lineNum">      31 </span>            : Action used to create a command that expands to multiple PLMD::Action commands when read in during input</a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : class ActionShortcut :</a>
+<a name="34"><span class="lineNum">      34 </span>            :   public virtual Action {</a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::string shortcutlabel;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;std::string&gt; savedInputLines;</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   const std::string &amp; getShortcutLabel() const ;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Constructor</a>
+<a name="42"><span class="lineNum">      42 </span>            :   explicit ActionShortcut(const ActionOptions&amp;ao);</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Read a line of input and create appropriate actions</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void readInputLine( const std::string&amp; input );</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Do nothing.</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Do nothing.</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Get the lines of the shortcut that were read in</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;std::string&gt; getSavedInputLines() const ;</a>
+<a name="51"><span class="lineNum">      51 </span>            : };</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithArguments.cpp.func-sort-c.html b/coverage/core/ActionWithArguments.cpp.func-sort-c.html
new file mode 100644
index 0000000000..29795355b0
--- /dev/null
+++ b/coverage/core/ActionWithArguments.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithArguments.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithArguments.cpp<span style="font-size: 80%;"> (<a href="ActionWithArguments.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">148</td>
+            <td class="headerCovTableEntry">162</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithArguments.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#253">_ZN4PLMD19ActionWithArgumentsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#235">_ZN4PLMD19ActionWithArguments24requestExtraDependenciesERKSt6vectorIPNS_5ValueESaIS3_EE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#55">_ZN4PLMD19ActionWithArguments17parseArgumentListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIPNS_5ValueESaISB_EE</a></td>
+              <td class="coverFnHi">53</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#270">_ZN4PLMD19ActionWithArguments29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#296">_ZNK4PLMD19ActionWithArguments13getProjectionEjj</a></td>
+              <td class="coverFnHi">261</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#304">_ZN4PLMD19ActionWithArguments20addForcesOnArgumentsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">350</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#207">_ZN4PLMD19ActionWithArguments21expandArgKeywordInPDBERKNS_3PDBE</a></td>
+              <td class="coverFnHi">416</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#253">_ZN4PLMD19ActionWithArgumentsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2868</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#46">_ZN4PLMD19ActionWithArguments17parseArgumentListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIPNS_5ValueESaISB_EE</a></td>
+              <td class="coverFnHi">2908</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#64">_ZN4PLMD19ActionWithArguments21interpretArgumentListERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS1_IPNS_5ValueESaISD_EE</a></td>
+              <td class="coverFnHi">3016</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#33">_ZN4PLMD19ActionWithArguments16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3067</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#215">_ZN4PLMD19ActionWithArguments16requestArgumentsERKSt6vectorIPNS_5ValueESaIS3_EE</a></td>
+              <td class="coverFnHi">178984</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithArguments.cpp.func.html b/coverage/core/ActionWithArguments.cpp.func.html
new file mode 100644
index 0000000000..1bfb933406
--- /dev/null
+++ b/coverage/core/ActionWithArguments.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithArguments.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithArguments.cpp<span style="font-size: 80%;"> (<a href="ActionWithArguments.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">148</td>
+            <td class="headerCovTableEntry">162</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithArguments.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#33">_ZN4PLMD19ActionWithArguments16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3067</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#215">_ZN4PLMD19ActionWithArguments16requestArgumentsERKSt6vectorIPNS_5ValueESaIS3_EE</a></td>
+              <td class="coverFnHi">178984</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#46">_ZN4PLMD19ActionWithArguments17parseArgumentListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIPNS_5ValueESaISB_EE</a></td>
+              <td class="coverFnHi">2908</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#55">_ZN4PLMD19ActionWithArguments17parseArgumentListERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEiRSt6vectorIPNS_5ValueESaISB_EE</a></td>
+              <td class="coverFnHi">53</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#304">_ZN4PLMD19ActionWithArguments20addForcesOnArgumentsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">350</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#207">_ZN4PLMD19ActionWithArguments21expandArgKeywordInPDBERKNS_3PDBE</a></td>
+              <td class="coverFnHi">416</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#64">_ZN4PLMD19ActionWithArguments21interpretArgumentListERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERS1_IPNS_5ValueESaISD_EE</a></td>
+              <td class="coverFnHi">3016</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#235">_ZN4PLMD19ActionWithArguments24requestExtraDependenciesERKSt6vectorIPNS_5ValueESaIS3_EE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#270">_ZN4PLMD19ActionWithArguments29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#253">_ZN4PLMD19ActionWithArgumentsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#253">_ZN4PLMD19ActionWithArgumentsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2868</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.cpp.gcov.html#296">_ZNK4PLMD19ActionWithArguments13getProjectionEjj</a></td>
+              <td class="coverFnHi">261</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithArguments.cpp.gcov.html b/coverage/core/ActionWithArguments.cpp.gcov.html
new file mode 100644
index 0000000000..b558922897
--- /dev/null
+++ b/coverage/core/ActionWithArguments.cpp.gcov.html
@@ -0,0 +1,386 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithArguments.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithArguments.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithArguments.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">148</td>
+            <td class="headerCovTableEntry">162</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithArguments.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #ifdef __PLUMED_HAS_CREGEX</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstring&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;regex.h&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #endif</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       3067 : void ActionWithArguments::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       6134 :   keys.reserve(&quot;numbered&quot;,&quot;ARG&quot;,&quot;the input for this action is the scalar output from one or more other actions. The particular scalars that you will use &quot;</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :                &quot;are referenced using the label of the action. If the label appears on its own then it is assumed that the Action calculates &quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            :                &quot;a single scalar value.  The value of this scalar is thus used as the input to this new action.  If * or *.* appears the &quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            :                &quot;scalars calculated by all the proceeding actions in the input file are taken.  Some actions have multi-component outputs and &quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :                &quot;each component of the output has a specific label.  For example a \\ref DISTANCE action labelled dist may have three components &quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            :                &quot;x, y and z.  To take just the x component you should use dist.x, if you wish to take all three components then use dist.*.&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            :                &quot;More information on the referencing of Actions can be found in the section of the manual on the PLUMED \\ref Syntax.  &quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            :                &quot;Scalar values can also be &quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            :                &quot;referenced using POSIX regular expressions as detailed in the section on \\ref Regex. To use this feature you you must compile &quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            :                &quot;PLUMED with the appropriate flag.&quot;);</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       3067 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       2908 : void ActionWithArguments::parseArgumentList(const std::string&amp;key,std::vector&lt;Value*&gt;&amp;arg) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       2908 :   std::string def; std::vector&lt;std::string&gt; c; arg.clear(); parseVector(key,c);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       3394 :   if( c.size()==0 &amp;&amp; (keywords.style(key,&quot;compulsory&quot;) || keywords.style(key,&quot;hidden&quot;)) ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :     if( keywords.getDefaultValue(key,def) ) c.push_back( def );</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :     else return;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   }</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       2908 :   interpretArgumentList(c,arg);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       2908 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         53 : bool ActionWithArguments::parseArgumentList(const std::string&amp;key,int i,std::vector&lt;Value*&gt;&amp;arg) {</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::vector&lt;std::string&gt; c;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   arg.clear();</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         53 :   if(parseNumberedVector(key,i,c)) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         12 :     interpretArgumentList(c,arg);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :     return true;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   } else return false;</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         53 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       3016 : void ActionWithArguments::interpretArgumentList(const std::vector&lt;std::string&gt;&amp; c, std::vector&lt;Value*&gt;&amp;arg) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       8499 :   for(unsigned i=0; i&lt;c.size(); i++) {</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     // is a regex? then just interpret it. The signal is ()</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       5486 :     if(!c[i].compare(0,1,&quot;(&quot;)) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        201 :       unsigned l=c[i].length();</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        201 :       if(!c[i].compare(l-1,1,&quot;)&quot;)) {</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :         // start regex parsing</a>
+<a name="73"><span class="lineNum">      73 </span>            : #ifdef __PLUMED_HAS_CREGEX</a>
+<a name="74"><span class="lineNum">      74 </span>            :         // take the string enclosed in quotes and put in round brackets</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        200 :         std::string myregex=c[i];</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :         //log&lt;&lt;&quot;  Evaluating regexp for this action: &quot;&lt;&lt;myregex&lt;&lt;&quot;\n&quot;;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :         regex_t reg; // regular expression</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        200 :         int errcode=regcomp(&amp;reg, myregex.c_str(),REG_EXTENDED|REG_NEWLINE); // compile the regular expression</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        200 :         if(errcode) {</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :           // one can check the errors asking to regerror</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          1 :           size_t errbuf_size = regerror(errcode, &amp;reg, NULL, 0);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :           std::vector&lt;char&gt; errbuf(errbuf_size);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          1 :           regerror(errcode, &amp;reg, errbuf.data(), errbuf_size);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          3 :           plumed_error()&lt;&lt;&quot;Error parsing regular expression: &quot;&lt;&lt;errbuf.data();</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :         }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :         // call regfree when reg goes out of scope</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        199 :         auto deleter=[](regex_t* r) { regfree(r); };</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :         std::unique_ptr&lt;regex_t,decltype(deleter)&gt; reg_deleter(&amp;reg,deleter);</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        199 :         plumed_massert(reg.re_nsub==1,&quot;I can parse with only one subexpression&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :         regmatch_t match;</a>
+<a name="95"><span class="lineNum">      95 </span>            :         // select all the actions that have a value</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        199 :         std::vector&lt;ActionWithValue*&gt; all=plumed.getActionSet().select&lt;ActionWithValue*&gt;();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        199 :         if( all.empty() ) error(&quot;your input file is not telling plumed to calculate anything&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :         bool found_something=false;</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1522 :         for(unsigned j=0; j&lt;all.size(); j++) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1323 :           std::vector&lt;std::string&gt; ss=all[j]-&gt;getComponentsVector();</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     220386 :           for(unsigned  k=0; k&lt;ss.size(); ++k) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     219063 :             unsigned ll=std::strlen(ss[k].c_str())+1;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">     219063 :             std::vector&lt;char&gt; str(ll);</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :             std::strcpy(&amp;str[0],ss[k].c_str());</a>
+<a name="105"><span class="lineNum">     105 </span>            :             const char *ppstr=&amp;str[0];</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">     219063 :             if(!regexec(&amp;reg, ppstr, reg.re_nsub, &amp;match, 0)) {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :               //log.printf(&quot;  Something matched with \&quot;%s\&quot; : &quot;,ss[k].c_str());</a>
+<a name="108"><span class="lineNum">     108 </span>            :               do {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      27856 :                 if (match.rm_so != -1) {        /* The regex is matching part of a string */</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      27856 :                   size_t matchlen = match.rm_eo - match.rm_so;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      27856 :                   std::vector&lt;char&gt; submatch(matchlen+1);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      27856 :                   std::strncpy(submatch.data(), ppstr+match.rm_so, matchlen+1);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      27856 :                   submatch[matchlen]='\0';</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :                   //log.printf(&quot;  subpattern %s\n&quot;, submatch.data());</a>
+<a name="115"><span class="lineNum">     115 </span>            :                   // this is the match: try to see if it is a valid action</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      27856 :                   std::string putativeVal(submatch.data());</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      27856 :                   if( all[j]-&gt;exists(putativeVal) ) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      21369 :                     arg.push_back(all[j]-&gt;copyOutput(putativeVal));</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :                     found_something=true;</a>
+<a name="120"><span class="lineNum">     120 </span>            :                     //log.printf(&quot;  Action %s added! \n&quot;,putativeVal.c_str());</a>
+<a name="121"><span class="lineNum">     121 </span>            :                   }</a>
+<a name="122"><span class="lineNum">     122 </span>            :                 }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      27856 :                 ppstr += match.rm_eo;   /* Restart from last match */</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      27856 :               } while(!regexec(&amp;reg,ppstr,reg.re_nsub,&amp;match,0));</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :             }</a>
+<a name="126"><span class="lineNum">     126 </span>            :           }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       1323 :         }</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        199 :         if(!found_something) plumed_error()&lt;&lt;&quot;There isn't any action matching your regex &quot; &lt;&lt; myregex;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : #else</a>
+<a name="130"><span class="lineNum">     130 </span>            :         plumed_merror(&quot;Regexp support not compiled!&quot;);</a>
+<a name="131"><span class="lineNum">     131 </span>            : #endif</a>
+<a name="132"><span class="lineNum">     132 </span>            :       } else {</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :         plumed_merror(&quot;did you want to use regexp to input arguments? enclose it between two round braces (...) with no spaces!&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :       }</a>
+<a name="135"><span class="lineNum">     135 </span>            :     } else {</a>
+<a name="136"><span class="lineNum">     136 </span>            :       std::size_t dot=c[i].find_first_of('.');</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       5285 :       std::string a=c[i].substr(0,dot);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       5285 :       std::string name=c[i].substr(dot+1);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       5285 :       if(c[i].find(&quot;.&quot;)!=std::string::npos) {   // if it contains a dot:</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1877 :         if(a==&quot;*&quot; &amp;&amp; name==&quot;*&quot;) {</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :           // Take all values from all actions</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :           std::vector&lt;ActionWithValue*&gt; all=plumed.getActionSet().select&lt;ActionWithValue*&gt;();</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :           if( all.empty() ) error(&quot;your input file is not telling plumed to calculate anything&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          9 :           for(unsigned j=0; j&lt;all.size(); j++) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         18 :             for(int k=0; k&lt;all[j]-&gt;getNumberOfComponents(); ++k) arg.push_back(all[j]-&gt;copyOutput(k));</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :           }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1867 :         } else if ( name==&quot;*&quot;) {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :           // Take all the values from an action with a specific name</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        532 :           ActionWithValue* action=plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(a);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        532 :           if(!action) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :             std::string str=&quot; (hint! the actions with value in this ActionSet are: &quot;;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :             str+=plumed.getActionSet().getLabelList&lt;ActionWithValue*&gt;()+&quot;)&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :             error(&quot;cannot find action named &quot; + a + str);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :           }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        532 :           if( action-&gt;getNumberOfComponents()==0 ) error(&quot;found &quot; + a +&quot;.* indicating use all components calculated by action with label &quot; + a + &quot; but this action has no components&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       5592 :           for(int k=0; k&lt;action-&gt;getNumberOfComponents(); ++k) arg.push_back(action-&gt;copyOutput(k));</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1335 :         } else if ( a==&quot;*&quot; ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :           // Take components from all actions with a specific name</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          8 :           std::vector&lt;ActionWithValue*&gt; all=plumed.getActionSet().select&lt;ActionWithValue*&gt;();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          8 :           if( all.empty() ) error(&quot;your input file is not telling plumed to calculate anything&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :           unsigned nval=0;</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         36 :           for(unsigned j=0; j&lt;all.size(); j++) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         56 :             std::string flab; flab=all[j]-&gt;getLabel() + &quot;.&quot; + name;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         28 :             if( all[j]-&gt;exists(flab) ) { arg.push_back(all[j]-&gt;copyOutput(flab)); nval++; }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :           }</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          8 :           if(nval==0) error(&quot;found no actions with a component called &quot; + name );</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :         } else {</a>
+<a name="168"><span class="lineNum">     168 </span>            :           // Take values with a specific name</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1327 :           ActionWithValue* action=plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(a);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       1327 :           if(!action) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :             std::string str=&quot; (hint! the actions with value in this ActionSet are: &quot;;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :             str+=plumed.getActionSet().getLabelList&lt;ActionWithValue*&gt;()+&quot;)&quot;;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :             error(&quot;cannot find action named &quot; + a +str);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :           }</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1327 :           if( !(action-&gt;exists(c[i])) ) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :             std::string str=&quot; (hint! the components in this actions are: &quot;;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :             str+=action-&gt;getComponentsList()+&quot;)&quot;;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :             error(&quot;action &quot; + a + &quot; has no component named &quot; + name + str);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :           } ;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       1327 :           arg.push_back(action-&gt;copyOutput(c[i]));</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :         }</a>
+<a name="182"><span class="lineNum">     182 </span>            :       } else {    // if it doesn't contain a dot</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       3417 :         if(c[i]==&quot;*&quot;) {</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :           // Take all values from all actions</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        104 :           std::vector&lt;ActionWithValue*&gt; all=plumed.getActionSet().select&lt;ActionWithValue*&gt;();</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        104 :           if( all.empty() ) error(&quot;your input file is not telling plumed to calculate anything&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        700 :           for(unsigned j=0; j&lt;all.size(); j++) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       1281 :             for(int k=0; k&lt;all[j]-&gt;getNumberOfComponents(); ++k) arg.push_back(all[j]-&gt;copyOutput(k));</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :           }</a>
+<a name="190"><span class="lineNum">     190 </span>            :         } else {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       3313 :           ActionWithValue* action=plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(c[i]);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       3313 :           if(!action) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          1 :             std::string str=&quot; (hint! the actions with value in this ActionSet are: &quot;;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          2 :             str+=plumed.getActionSet().getLabelList&lt;ActionWithValue*&gt;()+&quot;)&quot;;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          3 :             error(&quot;cannot find action named &quot; + c[i] + str );</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :           }</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       3312 :           if( !(action-&gt;exists(c[i])) ) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :             std::string str=&quot; (hint! the components in this actions are: &quot;;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :             str+=action-&gt;getComponentsList()+&quot;)&quot;;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :             error(&quot;action &quot; + c[i] + &quot; has no component named &quot; + c[i] +str);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :           };</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       3313 :           arg.push_back(action-&gt;copyOutput(c[i]));</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :         }</a>
+<a name="204"><span class="lineNum">     204 </span>            :       }</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       3013 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        416 : void ActionWithArguments::expandArgKeywordInPDB( const PDB&amp; pdb ) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        416 :   std::vector&lt;std::string&gt; arg_names = pdb.getArgumentNames();</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        416 :   if( arg_names.size()&gt;0 ) {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     std::vector&lt;Value*&gt; arg_vals;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         80 :     interpretArgumentList( arg_names, arg_vals );</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        416 : }</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     178984 : void ActionWithArguments::requestArguments(const std::vector&lt;Value*&gt; &amp;arg) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     178984 :   plumed_massert(!lockRequestArguments,&quot;requested argument list can only be changed in the prepare() method&quot;);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">     178984 :   arguments=arg;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     178984 :   clearDependencies();</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   std::string fullname;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   std::string name;</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">    1255318 :   for(unsigned i=0; i&lt;arguments.size(); i++) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">    1076334 :     fullname=arguments[i]-&gt;getName();</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">    1076334 :     if(fullname.find(&quot;.&quot;)!=std::string::npos) {</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :       std::size_t dot=fullname.find_first_of('.');</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">     738706 :       name=fullname.substr(0,dot);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     } else {</a>
+<a name="229"><span class="lineNum">     229 </span>            :       name=fullname;</a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">    1076334 :     ActionWithValue* action=plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(name);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">    1076334 :     plumed_massert(action,&quot;cannot find action named (in requestArguments - this is weird)&quot; + name);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">    1076334 :     addDependency(action);</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     178984 : }</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          4 : void ActionWithArguments::requestExtraDependencies(const std::vector&lt;Value*&gt; &amp;extra) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          4 :   plumed_massert(!lockRequestArguments,&quot;requested argument list can only be changed in the prepare() method&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   std::string fullname;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   std::string name;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          9 :   for(unsigned i=0; i&lt;extra.size(); i++) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          5 :     fullname=extra[i]-&gt;getName();</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          5 :     if(fullname.find(&quot;.&quot;)!=std::string::npos) {</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :       std::size_t dot=fullname.find_first_of('.');</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :       name=fullname.substr(0,dot);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :     } else {</a>
+<a name="247"><span class="lineNum">     247 </span>            :       name=fullname;</a>
+<a name="248"><span class="lineNum">     248 </span>            :     }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          5 :     ActionWithValue* action=plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(name);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          5 :     plumed_massert(action,&quot;cannot find action named (in requestArguments - this is weird)&quot; + name);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          5 :     addDependency(action);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :   }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          4 : }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">       2868 : ActionWithArguments::ActionWithArguments(const ActionOptions&amp;ao):</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   Action(ao),</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       2868 :   lockRequestArguments(false)</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : {</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       5739 :   if( keywords.exists(&quot;ARG&quot;) ) {</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :     std::vector&lt;Value*&gt; arg;</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       5550 :     parseArgumentList(&quot;ARG&quot;,arg);</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       2772 :     if(!arg.empty()) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       2629 :       log.printf(&quot;  with arguments&quot;);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      25943 :       for(unsigned i=0; i&lt;arg.size(); i++) log.printf(&quot; %s&quot;,arg[i]-&gt;getName().c_str());</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       2629 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       2772 :     requestArguments(arg);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   }</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       2865 : }</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         58 : void ActionWithArguments::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         58 :   if(!a) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         58 :     a=dynamic_cast&lt;ActionWithValue*&gt;(this);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         58 :     plumed_massert(a,&quot;cannot compute numerical derivatives for an action without values&quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :   }</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         58 :   const size_t nval=a-&gt;getNumberOfComponents();</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   const size_t npar=arguments.size();</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         58 :   std::vector&lt;double&gt; value (nval*npar);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        161 :   for(int i=0; i&lt;npar; i++) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        103 :     double arg0=arguments[i]-&gt;get();</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        103 :     arguments[i]-&gt;set(arg0+std::sqrt(epsilon));</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        103 :     a-&gt;calculate();</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        103 :     arguments[i]-&gt;set(arg0);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">       1367 :     for(int j=0; j&lt;nval; j++) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       1264 :       value[i*nval+j]=a-&gt;getOutputQuantity(j);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         58 :   a-&gt;calculate();</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         58 :   a-&gt;clearDerivatives();</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       1192 :   for(int j=0; j&lt;nval; j++) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1134 :     Value* v=a-&gt;copyOutput(j);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       1534 :     if( v-&gt;hasDerivatives() ) for(int i=0; i&lt;npar; i++) v-&gt;addDerivative(i,(value[i*nval+j]-a-&gt;getOutputQuantity(j))/std::sqrt(epsilon));</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   }</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         58 : }</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">        261 : double ActionWithArguments::getProjection(unsigned i,unsigned j)const {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        261 :   plumed_massert(i&lt;arguments.size(),&quot; making projections with an index which  is too large&quot;);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">        261 :   plumed_massert(j&lt;arguments.size(),&quot; making projections with an index which  is too large&quot;);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        261 :   const Value* v1=arguments[i];</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        261 :   const Value* v2=arguments[j];</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        261 :   return Value::projection(*v1,*v2);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : }</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        350 : void ActionWithArguments::addForcesOnArguments( const std::vector&lt;double&gt;&amp; forces ) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">        474 :   for(unsigned i=0; i&lt;arguments.size(); ++i) arguments[i]-&gt;addForce( forces[i] );</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">        350 : }</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithArguments.h.func-sort-c.html b/coverage/core/ActionWithArguments.h.func-sort-c.html
new file mode 100644
index 0000000000..b80b49b6b9
--- /dev/null
+++ b/coverage/core/ActionWithArguments.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithArguments.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithArguments.h<span style="font-size: 80%;"> (<a href="ActionWithArguments.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithArguments.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#74">_ZN4PLMD19ActionWithArgumentsD2Ev</a></td>
+              <td class="coverFnHi">2865</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#124">_ZNK4PLMD19ActionWithArguments12getArgumentsEv</a></td>
+              <td class="coverFnHi">458199</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#114">_ZN4PLMD19ActionWithArguments12lockRequestsEv</a></td>
+              <td class="coverFnHi">538344</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#119">_ZN4PLMD19ActionWithArguments14unlockRequestsEv</a></td>
+              <td class="coverFnHi">538344</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#99">_ZNK4PLMD19ActionWithArguments20getNumberOfArgumentsEv</a></td>
+              <td class="coverFnHi">4121297985</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithArguments.h.func.html b/coverage/core/ActionWithArguments.h.func.html
new file mode 100644
index 0000000000..1f6bd30bfd
--- /dev/null
+++ b/coverage/core/ActionWithArguments.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithArguments.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithArguments.h<span style="font-size: 80%;"> (<a href="ActionWithArguments.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithArguments.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#114">_ZN4PLMD19ActionWithArguments12lockRequestsEv</a></td>
+              <td class="coverFnHi">538344</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#119">_ZN4PLMD19ActionWithArguments14unlockRequestsEv</a></td>
+              <td class="coverFnHi">538344</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#74">_ZN4PLMD19ActionWithArgumentsD2Ev</a></td>
+              <td class="coverFnHi">2865</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#124">_ZNK4PLMD19ActionWithArguments12getArgumentsEv</a></td>
+              <td class="coverFnHi">458199</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithArguments.h.gcov.html#99">_ZNK4PLMD19ActionWithArguments20getNumberOfArgumentsEv</a></td>
+              <td class="coverFnHi">4121297985</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithArguments.h.gcov.html b/coverage/core/ActionWithArguments.h.gcov.html
new file mode 100644
index 0000000000..e6e79ddb01
--- /dev/null
+++ b/coverage/core/ActionWithArguments.h.gcov.html
@@ -0,0 +1,208 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithArguments.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithArguments.h<span style="font-size: 80%;"> (source / <a href="ActionWithArguments.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionWithArguments_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionWithArguments_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /**</a>
+<a name="32"><span class="lineNum">      32 </span>            : \ingroup MULTIINHERIT</a>
+<a name="33"><span class="lineNum">      33 </span>            : This is used to create PLMD::Action objects that take the output from some other Action as input.</a>
+<a name="34"><span class="lineNum">      34 </span>            : This is used in PLMD::Function and PLMD::Bias</a>
+<a name="35"><span class="lineNum">      35 </span>            :  PLMD::Action objects that inherit from PLMD::ActionWithArguments take</a>
+<a name="36"><span class="lineNum">      36 </span>            :  values and components calculated in other PLMD::Action objects and</a>
+<a name="37"><span class="lineNum">      37 </span>            :  use this information to calculate some new function.  If you have</a>
+<a name="38"><span class="lineNum">      38 </span>            :  only one list of arguments you should use the reserved keyword &lt;b&gt; ARG &lt;/b&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            :  when you use parseArgumentList.</a>
+<a name="40"><span class="lineNum">      40 </span>            : */</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class ActionWithArguments:</a>
+<a name="43"><span class="lineNum">      43 </span>            :   public virtual Action</a>
+<a name="44"><span class="lineNum">      44 </span>            : {</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;Value*&gt; arguments;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   bool lockRequestArguments;</a>
+<a name="47"><span class="lineNum">      47 </span>            : protected:</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// This changes the arg keyword in the pdb file</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void expandArgKeywordInPDB( const PDB&amp; pdb );</a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Get the scalar product between the gradients of two variables</a>
+<a name="52"><span class="lineNum">      52 </span>            :   double getProjection(unsigned i,unsigned j)const;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Registers the list of keywords</a>
+<a name="54"><span class="lineNum">      54 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Returns the value of an argument</a>
+<a name="56"><span class="lineNum">      56 </span>            :   double getArgument( const unsigned n ) const;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Return a pointer to specific argument</a>
+<a name="58"><span class="lineNum">      58 </span>            :   Value* getPntrToArgument( const unsigned n );</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Returns the number of arguments</a>
+<a name="60"><span class="lineNum">      60 </span>            :   virtual unsigned getNumberOfArguments() const ;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Takes the difference taking into account pbc for arg i</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double difference(int, double, double) const;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Takes one value and brings it back into the pbc of argument i</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double bringBackInPbc(int i,double d1)const;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Parse a list of arguments</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void parseArgumentList(const std::string&amp;key,std::vector&lt;Value*&gt;&amp;args);</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Parse a numbered list of arguments</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool parseArgumentList(const std::string&amp;key,int i,std::vector&lt;Value*&gt;&amp;args);</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Setup the dependencies</a>
+<a name="70"><span class="lineNum">      70 </span>            :   void requestArguments(const std::vector&lt;Value*&gt; &amp;arg);</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void requestExtraDependencies(const std::vector&lt;Value*&gt; &amp;extra);</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Add forces to arguments (used in apply)</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void addForcesOnArguments( const std::vector&lt;double&gt;&amp; forces );</a>
+<a name="74"><span class="lineNum">      74 </span>            : public:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   explicit ActionWithArguments(const ActionOptions&amp;);</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       2865 :   virtual ~ActionWithArguments() {}</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Calculate the numerical derivatives</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// N.B. only pass an ActionWithValue to this routine if you know exactly what you</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// are doing.  The default will be correct for the vast majority of cases</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void lockRequests() override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void unlockRequests() override;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Returns an array of pointers to the arguments</a>
+<a name="84"><span class="lineNum">      84 </span>            :   virtual const std::vector&lt;Value*&gt;    &amp; getArguments() const ;</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Convert a list of argument names into a list of pointers to the values</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void interpretArgumentList(const std::vector&lt;std::string&gt;&amp; c, std::vector&lt;Value*&gt;&amp;arg);</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : inline</a>
+<a name="91"><span class="lineNum">      91 </span>            : Value* ActionWithArguments::getPntrToArgument( const unsigned n ) {</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    4560155 :   return arguments[n];</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : inline</a>
+<a name="96"><span class="lineNum">      96 </span>            : double ActionWithArguments::getArgument(const unsigned n) const {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     824185 :   return arguments[n]-&gt;get();</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : inline</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov"> 4121297985 : unsigned ActionWithArguments::getNumberOfArguments()const {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov"> 4121315823 :   return arguments.size();</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : inline</a>
+<a name="106"><span class="lineNum">     106 </span>            : double ActionWithArguments::difference(int i,double d1,double d2)const {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    4860134 :   return arguments[i]-&gt;difference(d1,d2);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : inline</a>
+<a name="111"><span class="lineNum">     111 </span>            : double ActionWithArguments::bringBackInPbc(int i,double d1)const {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1427 :   return arguments[i]-&gt;bringBackInPbc(d1);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : inline</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     538344 : void ActionWithArguments::lockRequests() {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     552931 :   lockRequestArguments=true;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     538344 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : inline</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     538344 : void ActionWithArguments::unlockRequests() {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     552931 :   lockRequestArguments=false;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     538344 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : inline</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">     458199 : const std::vector&lt;Value*&gt; &amp; ActionWithArguments::getArguments() const {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     462013 :   return arguments;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithValue.cpp.func-sort-c.html b/coverage/core/ActionWithValue.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fc15d7b9d6
--- /dev/null
+++ b/coverage/core/ActionWithValue.cpp.func-sort-c.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithValue.cpp<span style="font-size: 80%;"> (<a href="ActionWithValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">112</td>
+            <td class="headerCovTableEntry">125</td>
+            <td class="headerCovTableEntryMed">89.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithValue.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#36">_ZN4PLMD15ActionWithValue23noAnalyticalDerivativesERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#53">_ZN4PLMD15ActionWithValueC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#62">_ZN4PLMD15ActionWithValueD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#62">_ZN4PLMD15ActionWithValueD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#88">_ZNK4PLMD15ActionWithValue10copyOutputERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#192">_ZN4PLMD15ActionWithValue22componentIsNotPeriodicERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">30290</td>
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+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#66">_ZN4PLMD15ActionWithValue16clearInputForcesEv</a></td>
+              <td class="coverFnHi">1390052</td>
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+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#203">_ZN4PLMD15ActionWithValue20setGradientsIfNeededEv</a></td>
+              <td class="coverFnHi">1390052</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#70">_ZN4PLMD15ActionWithValue16clearDerivativesEv</a></td>
+              <td class="coverFnHi">1392832</td>
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+    <tr>
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+              <td class="coverFnHi">2139583</td>
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+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#209">_ZN4PLMD15ActionWithValue17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">3493159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#221">_ZN4PLMD15ActionWithValue18getPntrToComponentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10598447</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#167">_ZNK4PLMD15ActionWithValue12getComponentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10628829</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#81">_ZNK4PLMD15ActionWithValue6existsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10661669</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#125">_ZN4PLMD15ActionWithValue14getPntrToValueEv</a></td>
+              <td class="coverFnHi">16586097</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithValue.cpp.func.html b/coverage/core/ActionWithValue.cpp.func.html
new file mode 100644
index 0000000000..7d05e07822
--- /dev/null
+++ b/coverage/core/ActionWithValue.cpp.func.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithValue.cpp<span style="font-size: 80%;"> (<a href="ActionWithValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">112</td>
+            <td class="headerCovTableEntry">125</td>
+            <td class="headerCovTableEntryMed">89.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithValue.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#119">_ZN4PLMD15ActionWithValue11setPeriodicERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">681</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#133">_ZN4PLMD15ActionWithValue12addComponentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">22633</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#125">_ZN4PLMD15ActionWithValue14getPntrToValueEv</a></td>
+              <td class="coverFnHi">16586097</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#112">_ZN4PLMD15ActionWithValue14setNotPeriodicEv</a></td>
+              <td class="coverFnHi">1720</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#70">_ZN4PLMD15ActionWithValue16clearDerivativesEv</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#66">_ZN4PLMD15ActionWithValue16clearInputForcesEv</a></td>
+              <td class="coverFnHi">1390052</td>
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+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#26">_ZN4PLMD15ActionWithValue16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4607</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">10598447</td>
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+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#226">_ZN4PLMD15ActionWithValue18getPntrToComponentEi</a></td>
+              <td class="coverFnHi">2139583</td>
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+    <tr>
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+              <td class="coverFnHi">92</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#203">_ZN4PLMD15ActionWithValue20setGradientsIfNeededEv</a></td>
+              <td class="coverFnHi">1390052</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#192">_ZN4PLMD15ActionWithValue22componentIsNotPeriodicERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">30290</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#107">_ZN4PLMD15ActionWithValue23addValueWithDerivativesEv</a></td>
+              <td class="coverFnHi">2345</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#36">_ZN4PLMD15ActionWithValue23noAnalyticalDerivativesERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#41">_ZN4PLMD15ActionWithValue24componentsAreNotOptionalERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">1293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#47">_ZN4PLMD15ActionWithValue25useCustomisableComponentsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">256</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#150">_ZN4PLMD15ActionWithValue27addComponentWithDerivativesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#102">_ZN4PLMD15ActionWithValue8addValueEv</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#53">_ZN4PLMD15ActionWithValueC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#53">_ZN4PLMD15ActionWithValueC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#62">_ZN4PLMD15ActionWithValueD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#62">_ZN4PLMD15ActionWithValueD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#62">_ZN4PLMD15ActionWithValueD2Ev</a></td>
+              <td class="coverFnHi">4183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#88">_ZNK4PLMD15ActionWithValue10copyOutputERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">26186</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#95">_ZNK4PLMD15ActionWithValue10copyOutputERKj</a></td>
+              <td class="coverFnHi">10913</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#167">_ZNK4PLMD15ActionWithValue12getComponentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10628829</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#176">_ZNK4PLMD15ActionWithValue17getComponentsListB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#184">_ZNK4PLMD15ActionWithValue19getComponentsVectorB5cxx11Ev</a></td>
+              <td class="coverFnHi">1376</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.cpp.gcov.html#81">_ZNK4PLMD15ActionWithValue6existsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10661669</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithValue.cpp.gcov.html b/coverage/core/ActionWithValue.cpp.gcov.html
new file mode 100644
index 0000000000..4fa73b4cde
--- /dev/null
+++ b/coverage/core/ActionWithValue.cpp.gcov.html
@@ -0,0 +1,309 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithValue.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithValue.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithValue.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">112</td>
+            <td class="headerCovTableEntry">125</td>
+            <td class="headerCovTableEntryMed">89.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">       4607 : void ActionWithValue::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       4607 :   keys.setComponentsIntroduction(&quot;By default the value of the calculated quantity can be referenced elsewhere in the &quot;</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :                                  &quot;input file by using the label of the action.  Alternatively this Action can be used &quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            :                                  &quot;to calculate the following quantities by employing the keywords listed &quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            :                                  &quot;below.  These quantities can be referenced elsewhere in the input by using this Action's &quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            :                                  &quot;label followed by a dot and the name of the quantity required from the list below.&quot;);</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       9214 :   keys.addFlag(&quot;NUMERICAL_DERIVATIVES&quot;, false, &quot;calculate the derivatives for these quantities numerically&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       9214 :   keys.add(&quot;hidden&quot;,&quot;HAS_VALUES&quot;,&quot;this is used in json output to determine those actions that have values&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       4607 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 : void ActionWithValue::noAnalyticalDerivatives(Keywords&amp; keys) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :   keys.addFlag(&quot;NUMERICAL_DERIVATIVES&quot;,false,&quot;analytical derivatives are not implemented for this keyword so numerical derivatives are always used&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       1293 : void ActionWithValue::componentsAreNotOptional(Keywords&amp; keys) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       1293 :   keys.setComponentsIntroduction(&quot;By default this Action calculates the following quantities. These quantities can &quot;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :                                  &quot;be referenced elsewhere in the input by using this Action's label followed by a &quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            :                                  &quot;dot and the name of the quantity required from the list below.&quot;);</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1293 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        256 : void ActionWithValue::useCustomisableComponents(Keywords&amp; keys) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        256 :   keys.setComponentsIntroduction(&quot;The names of the components in this action can be customized by the user in the &quot;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :                                  &quot;actions input file.  However, in addition to the components that can be customized the &quot;</a>
+<a name="52"><span class="lineNum">      52 </span>            :                                  &quot;following quantities will always be output&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        256 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       4183 : ActionWithValue::ActionWithValue(const ActionOptions&amp;ao):</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   Action(ao),</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       4183 :   noderiv(true),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       4183 :   numericalDerivatives(false)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      12079 :   if( keywords.exists(&quot;NUMERICAL_DERIVATIVES&quot;) ) parseFlag(&quot;NUMERICAL_DERIVATIVES&quot;,numericalDerivatives);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       4183 :   if(numericalDerivatives) log.printf(&quot;  using numerical derivatives\n&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       4183 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4183 : ActionWithValue::~ActionWithValue() {</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : // empty destructor to delete unique_ptr</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       4183 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    1390052 : void ActionWithValue::clearInputForces() {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">    3471459 :   for(unsigned i=0; i&lt;values.size(); i++) values[i]-&gt;clearInputForce();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    1390052 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    1392832 : void ActionWithValue::clearDerivatives() {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">    1392832 :   unsigned nt = OpenMP::getNumThreads();</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    1392832 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   {</a>
+<a name="76"><span class="lineNum">      76 </span>            :     #pragma omp for</a>
+<a name="77"><span class="lineNum">      77 </span>            :     for(unsigned i=0; i&lt;values.size(); i++) values[i]-&gt;clearDerivatives();</a>
+<a name="78"><span class="lineNum">      78 </span>            :   }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">    1392832 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : // -- These are the routine for copying the value pointers to other classes -- //</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">   10661669 : bool ActionWithValue::exists( const std::string&amp; name ) const {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">  116536953 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">  105901311 :     if (values[i]-&gt;name==name) return true;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span>            :   return false;</a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      26186 : Value* ActionWithValue::copyOutput( const std::string&amp; name ) const {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">   11307989 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">   11307989 :     if (values[i]-&gt;name==name) return values[i].get();</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;there is no pointer with name &quot; + name);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      10913 : Value* ActionWithValue::copyOutput( const unsigned&amp; n ) const {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      10913 :   plumed_massert(n&lt;values.size(),&quot;you have requested a pointer that is out of bounds&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      10913 :   return values[n].get();</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : // -- HERE WE HAVE THE STUFF FOR THE DEFAULT VALUE -- //</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         56 : void ActionWithValue::addValue() {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         56 :   plumed_massert(values.empty(),&quot;You have already added the default value for this action&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         56 :   values.emplace_back(Tools::make_unique&lt;Value&gt;(this,getLabel(), false ) );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         56 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       2345 : void ActionWithValue::addValueWithDerivatives() {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       2345 :   plumed_massert(values.empty(),&quot;You have already added the default value for this action&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       2345 :   values.emplace_back(Tools::make_unique&lt;Value&gt;(this,getLabel(), true ) );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       2345 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1720 : void ActionWithValue::setNotPeriodic() {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1720 :   plumed_massert(values.size()==1,&quot;The number of components is not equal to one&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       1720 :   plumed_massert(values[0]-&gt;name==getLabel(), &quot;The value you are trying to set is not the default&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       1720 :   values[0]-&gt;min=0; values[0]-&gt;max=0;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1720 :   values[0]-&gt;setupPeriodicity();</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1720 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        681 : void ActionWithValue::setPeriodic( const std::string&amp; min, const std::string&amp; max ) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        681 :   plumed_massert(values.size()==1,&quot;The number of components is not equal to one&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        681 :   plumed_massert(values[0]-&gt;name==getLabel(), &quot;The value you are trying to set is not the default&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        681 :   values[0]-&gt;setDomain( min, max );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        681 : }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">   16586097 : Value* ActionWithValue::getPntrToValue() {</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   plumed_dbg_massert(values.size()==1,&quot;The number of components is not equal to one&quot;);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   plumed_dbg_massert(values[0]-&gt;name==getLabel(), &quot;The value you are trying to retrieve is not the default&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">   16586097 :   return values[0].get();</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : // -- HERE WE HAVE THE STUFF FOR NAMED VALUES / COMPONENTS -- //</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      22633 : void ActionWithValue::addComponent( const std::string&amp; name ) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      22633 :   if( !keywords.outputComponentExists(name,true) ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;a description of component &quot; + name + &quot; has not been added to the manual. Components should be registered like keywords in &quot;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :                   &quot;registerKeywords as described in the developer docs.&quot;);</a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      45266 :   std::string thename; thename=getLabel() + &quot;.&quot; + name;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">   18683668 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">   18661035 :     plumed_massert(values[i]-&gt;name!=getLabel(),&quot;Cannot mix single values with components&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">   18661035 :     plumed_massert(values[i]-&gt;name!=thename,&quot;there is already a value with this name: &quot;+thename);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">   18661035 :     plumed_massert(values[i]-&gt;name!=thename&amp;&amp;name!=&quot;bias&quot;,&quot;Since PLUMED 2.3 the component 'bias' is automatically added to all biases by the general constructor!\n&quot;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :                    &quot;Remove the line addComponent(\&quot;bias\&quot;) from your bias.&quot;);</a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      22633 :   values.emplace_back(Tools::make_unique&lt;Value&gt;(this,thename, false ) );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      22633 :   std::string msg=&quot;  added component to this action:  &quot;+thename+&quot; \n&quot;;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      22633 :   log.printf(msg.c_str());</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      22633 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      10848 : void ActionWithValue::addComponentWithDerivatives( const std::string&amp; name ) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      10848 :   if( !keywords.outputComponentExists(name,true) ) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;a description of component &quot; + name + &quot; has not been added to the manual. Components should be registered like keywords in &quot;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :                   &quot;registerKeywords as described in the developer doc.&quot;);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      21696 :   std::string thename; thename=getLabel() + &quot;.&quot; + name;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">    2442051 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    2431203 :     plumed_massert(values[i]-&gt;name!=getLabel(),&quot;Cannot mix single values with components&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    2431203 :     plumed_massert(values[i]-&gt;name!=thename,&quot;there is already a value with this name: &quot;+thename);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    2431203 :     plumed_massert(values[i]-&gt;name!=thename&amp;&amp;name!=&quot;bias&quot;,&quot;Since PLUMED 2.3 the component 'bias' is automatically added to all biases by the general constructor!\n&quot;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :                    &quot;Remove the line addComponentWithDerivatives(\&quot;bias\&quot;) from your bias.&quot;);</a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      10848 :   values.emplace_back(Tools::make_unique&lt;Value&gt;(this,thename, true ) );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      10848 :   std::string msg=&quot;  added component to this action:  &quot;+thename+&quot; \n&quot;;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      10848 :   log.printf(msg.c_str());</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      10848 : }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">   10628829 : int ActionWithValue::getComponent( const std::string&amp; name ) const {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">   10628829 :   plumed_massert( !exists( getLabel() ), &quot;You should not be calling this routine if you are using a value&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">   21257658 :   std::string thename; thename=getLabel() + &quot;.&quot; + name;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">   64113392 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">   10628829 :     if (values[i]-&gt;name==thename) return i;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;there is no component with name &quot; + name);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 : std::string ActionWithValue::getComponentsList( ) const {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   std::string complist;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     complist+=values[i]-&gt;name+&quot; &quot;;</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   return complist;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       1376 : std::vector&lt;std::string&gt; ActionWithValue::getComponentsVector( ) const {</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   std::vector&lt;std::string&gt; complist;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">     220524 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">     219148 :     complist.push_back(values[i]-&gt;name);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1376 :   return complist;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      30290 : void ActionWithValue::componentIsNotPeriodic( const std::string&amp; name ) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      30290 :   int kk=getComponent(name);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      30290 :   values[kk]-&gt;min=0; values[kk]-&gt;max=0;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      30290 :   values[kk]-&gt;setupPeriodicity();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      30290 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         92 : void ActionWithValue::componentIsPeriodic( const std::string&amp; name, const std::string&amp; min, const std::string&amp; max ) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         92 :   int kk=getComponent(name);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         92 :   values[kk]-&gt;setDomain(min,max);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         92 : }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">    1390052 : void ActionWithValue::setGradientsIfNeeded() {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">    2780104 :   if(isOptionOn(&quot;GRADIENTS&quot;)) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        366 :     for(unsigned i=0; i&lt;values.size(); i++) values[i]-&gt;setGradients();</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    1390052 : }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">    3493159 : void ActionWithValue::turnOnDerivatives() {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   // Turn on the derivatives</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">    3493159 :   noderiv=false;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   // Resize the derivatives</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov"> 4106212557 :   for(unsigned i=0; i&lt;values.size(); ++i) values[i]-&gt;resizeDerivatives( getNumberOfDerivatives() );</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   // And turn on the derivatives in all actions on which we are dependent</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">    7085676 :   for(unsigned i=0; i&lt;getDependencies().size(); ++i) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">    3592517 :     ActionWithValue* vv=dynamic_cast&lt;ActionWithValue*&gt;( getDependencies()[i] );</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">    3592517 :     if(vv) vv-&gt;turnOnDerivatives();</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">    3493159 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">   10598447 : Value* ActionWithValue::getPntrToComponent( const std::string&amp; name ) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">   10598447 :   int kk=getComponent(name);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">   10598447 :   return values[kk].get();</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">    2139583 : Value* ActionWithValue::getPntrToComponent( int n ) {</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   plumed_dbg_massert(n&lt;values.size(),&quot;you have requested a pointer that is out of bounds&quot;);</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">    2139583 :   return values[n].get();</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithValue.h.func-sort-c.html b/coverage/core/ActionWithValue.h.func-sort-c.html
new file mode 100644
index 0000000000..83c74a84ab
--- /dev/null
+++ b/coverage/core/ActionWithValue.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithValue.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithValue.h<span style="font-size: 80%;"> (<a href="ActionWithValue.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithValue.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#165">_ZN4PLMD15ActionWithValue18checkFieldsAllowedEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#199">_ZN4PLMD15ActionWithValue23useNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#210">_ZNK4PLMD15ActionWithValue25doNotCalculateDerivativesEv</a></td>
+              <td class="coverFnHi">5924</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#172">_ZNK4PLMD15ActionWithValue17getOutputQuantityEj</a></td>
+              <td class="coverFnHi">153914</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#187">_ZN4PLMD15ActionWithValue8setValueERKd</a></td>
+              <td class="coverFnHi">194218</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#205">_ZNK4PLMD15ActionWithValue25checkNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">1634139</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#178">_ZNK4PLMD15ActionWithValue17getOutputQuantityERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2780554</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithValue.h.func.html b/coverage/core/ActionWithValue.h.func.html
new file mode 100644
index 0000000000..0419b521cb
--- /dev/null
+++ b/coverage/core/ActionWithValue.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithValue.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithValue.h<span style="font-size: 80%;"> (<a href="ActionWithValue.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithValue.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#165">_ZN4PLMD15ActionWithValue18checkFieldsAllowedEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#199">_ZN4PLMD15ActionWithValue23useNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#187">_ZN4PLMD15ActionWithValue8setValueERKd</a></td>
+              <td class="coverFnHi">194218</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#178">_ZNK4PLMD15ActionWithValue17getOutputQuantityERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2780554</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#172">_ZNK4PLMD15ActionWithValue17getOutputQuantityEj</a></td>
+              <td class="coverFnHi">153914</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#205">_ZNK4PLMD15ActionWithValue25checkNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">1634139</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithValue.h.gcov.html#210">_ZNK4PLMD15ActionWithValue25doNotCalculateDerivativesEv</a></td>
+              <td class="coverFnHi">5924</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithValue.h.gcov.html b/coverage/core/ActionWithValue.h.gcov.html
new file mode 100644
index 0000000000..5b9c94e9dc
--- /dev/null
+++ b/coverage/core/ActionWithValue.h.gcov.html
@@ -0,0 +1,296 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithValue.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithValue.h<span style="font-size: 80%;"> (source / <a href="ActionWithValue.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionWithValue_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionWithValue_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;memory&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /**</a>
+<a name="34"><span class="lineNum">      34 </span>            : \ingroup MULTIINHERIT</a>
+<a name="35"><span class="lineNum">      35 </span>            : Used to create a PLMD::Action that has some scalar or vectorial output that may or may not have some derivatives.</a>
+<a name="36"><span class="lineNum">      36 </span>            : This is used for PLMD::Bias, PLMD::Colvar and PLMD::Function</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The vast majority of the PLMD::Action objects that are implemented in</a>
+<a name="39"><span class="lineNum">      39 </span>            : plumed calculate some quantity or a set of quantities.  This could be</a>
+<a name="40"><span class="lineNum">      40 </span>            : the value of a CV, the value of a function or the potential due to a bias.</a>
+<a name="41"><span class="lineNum">      41 </span>            : PLMD::ActionWithValue provides the functionality for storing these quantities</a>
+<a name="42"><span class="lineNum">      42 </span>            : and (in tandem with PLMD::ActionWithArguments) the functionality for passing</a>
+<a name="43"><span class="lineNum">      43 </span>            : quantities between PLMD::Actions.  When you are deciding what quantities</a>
+<a name="44"><span class="lineNum">      44 </span>            : your new PLMD::Action will need to store using PLMD::ActionWithValue you must</a>
+<a name="45"><span class="lineNum">      45 </span>            : ask yourself the following two questions:</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : - Do I need to differentiate my output quantities</a>
+<a name="48"><span class="lineNum">      48 </span>            : - Is my PLMD::Action calculating a single thing or does the output have multiple components</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : If the answer to the first of these questions is yes then you must setup your values</a>
+<a name="51"><span class="lineNum">      51 </span>            : you using either PLMD::ActionWithValue::addValueWithDerivatives() or</a>
+<a name="52"><span class="lineNum">      52 </span>            : PLMD::ActionWithValue::addComponentWithDerivatives.  If the answer is no you</a>
+<a name="53"><span class="lineNum">      53 </span>            : can set up values using PLMD::ActionWithValue::addValue() or PLMD::ActionWithValue::addComponent().</a>
+<a name="54"><span class="lineNum">      54 </span>            : The precise routine you use to setup your values will depend on your answer to the</a>
+<a name="55"><span class="lineNum">      55 </span>            : second question.  As you are probably aware if the output of your PLMD::Action is a</a>
+<a name="56"><span class="lineNum">      56 </span>            : single quantity you can reference that quantity in the input file using the label of the</a>
+<a name="57"><span class="lineNum">      57 </span>            : PLMD::Action it was calculated in.  If your action &lt;b&gt; outputs only one quantity &lt;/b&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : we call that quantity the &lt;b&gt; value &lt;/b&gt; of the Action.  To set the &lt;b&gt; value &lt;/b&gt; and get pointers to it</a>
+<a name="59"><span class="lineNum">      59 </span>            : you should &lt;b&gt; use the set of routines that have the word value in the name &lt;/b&gt;.  If, by contrast,</a>
+<a name="60"><span class="lineNum">      60 </span>            : your PLMD::Action calculates multiple quantities then these quantities are referenced in input using the</a>
+<a name="61"><span class="lineNum">      61 </span>            : label.component syntax.  We refer to these &lt;b&gt; multiple quantities &lt;/b&gt; the &lt;b&gt; components &lt;/b&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : of the PLMD::Action.  Perhaps unsurprisingly, when you manipulate the &lt;b&gt; components &lt;/b&gt; of an</a>
+<a name="63"><span class="lineNum">      63 </span>            : PLMD::Action you should use &lt;b&gt; the routines with the word component in the name. &lt;/b&gt;</a>
+<a name="64"><span class="lineNum">      64 </span>            : */</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : class ActionWithValue :</a>
+<a name="67"><span class="lineNum">      67 </span>            :   public virtual Action</a>
+<a name="68"><span class="lineNum">      68 </span>            : {</a>
+<a name="69"><span class="lineNum">      69 </span>            : private:</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// An array containing the values for this action</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; values;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Are we skipping the calculation of the derivatives</a>
+<a name="73"><span class="lineNum">      73 </span>            :   bool noderiv;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Are we using numerical derivatives to differentiate</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool numericalDerivatives;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Return the index for the component named name</a>
+<a name="77"><span class="lineNum">      77 </span>            :   int getComponent( const std::string&amp; name ) const;</a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : // -------- The action has one value only  ---------------- //</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Add a value with the name label</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void addValue();</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// Add a value with the name label that has derivatives</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void addValueWithDerivatives();</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Set your default value to have no periodicity</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void setNotPeriodic();</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Set the value to be periodic with a particular domain</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void setPeriodic( const std::string&amp; min, const std::string&amp; max );</a>
+<a name="90"><span class="lineNum">      90 </span>            : protected:</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Get a pointer to the default value</a>
+<a name="92"><span class="lineNum">      92 </span>            :   Value* getPntrToValue();</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Set the default value (the one without name)</a>
+<a name="94"><span class="lineNum">      94 </span>            :   void setValue(const double&amp; d);</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : // -------- The action has multiple components ---------- //</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : public:</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Add a value with a name like label.name</a>
+<a name="100"><span class="lineNum">     100 </span>            :   void addComponent( const std::string&amp; name );</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Add a value with a name like label.name that has derivatives</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void addComponentWithDerivatives( const std::string&amp; name );</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Set your value component to have no periodicity</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void componentIsNotPeriodic( const std::string&amp; name );</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Set the value to be periodic with a particular domain</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void componentIsPeriodic( const std::string&amp; name, const std::string&amp; min, const std::string&amp; max );</a>
+<a name="107"><span class="lineNum">     107 </span>            : protected:</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Return a pointer to the component by index</a>
+<a name="109"><span class="lineNum">     109 </span>            :   Value* getPntrToComponent(int i);</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// Return a pointer to the value by name</a>
+<a name="111"><span class="lineNum">     111 </span>            :   Value* getPntrToComponent(const std::string&amp; name);</a>
+<a name="112"><span class="lineNum">     112 </span>            : public:</a>
+<a name="113"><span class="lineNum">     113 </span>            :   explicit ActionWithValue(const ActionOptions&amp;ao);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ~ActionWithValue();</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : /// Register all the relevant keywords for the action</a>
+<a name="117"><span class="lineNum">     117 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="118"><span class="lineNum">     118 </span>            : /// Insist that numerical derivatives should always be used for an action and make this fact appear in the manual</a>
+<a name="119"><span class="lineNum">     119 </span>            :   static void noAnalyticalDerivatives(Keywords&amp; keys);</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// Puts a message into the manual that the components always output</a>
+<a name="121"><span class="lineNum">     121 </span>            :   static void componentsAreNotOptional(Keywords&amp; keys);</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// The components in the action will depend on the user</a>
+<a name="123"><span class="lineNum">     123 </span>            :   static void useCustomisableComponents(Keywords&amp; keys);</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Are we not calculating derivatives</a>
+<a name="125"><span class="lineNum">     125 </span>            :   virtual bool doNotCalculateDerivatives() const ;</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// Get the value of one of the components of the PLMD::Action</a>
+<a name="127"><span class="lineNum">     127 </span>            :   double getOutputQuantity( const unsigned j ) const ;</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// Get the value with a specific name (N.B. if there is no such value this returns zero)</a>
+<a name="129"><span class="lineNum">     129 </span>            :   double getOutputQuantity( const std::string&amp; name ) const ;</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : //  --- Routines for passing stuff to ActionWithArguments -- //</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Check if a value with a particular name is present.  This is only used in PLMD::ActionWithArguments.</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// You should not use it when manipulating components.</a>
+<a name="135"><span class="lineNum">     135 </span>            :   bool exists( const std::string&amp; name ) const;</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Return a pointer to the value with name (this is used to retrieve values in other PLMD::Actions)</a>
+<a name="137"><span class="lineNum">     137 </span>            : /// You should NEVER use this routine to refer to the components of your PLMD::Action.  Use</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// getPntrToComponent instead.</a>
+<a name="139"><span class="lineNum">     139 </span>            :   Value* copyOutput( const std::string&amp;name ) const;</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Return a pointer to the value with this number (this is used to retrieve values in other PLMD::Actions)</a>
+<a name="141"><span class="lineNum">     141 </span>            : /// You should NEVER use this routine to refer to the components of your PLMD::Action.  Use</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// getPntrToComponent instead.</a>
+<a name="143"><span class="lineNum">     143 </span>            :   Value* copyOutput( const unsigned&amp; n ) const;</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// get a string that contains all the available components</a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::string getComponentsList( ) const ;</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// get a vector that contains the label for all the components</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;std::string&gt; getComponentsVector( ) const ;</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : // -- Routines for everything else -- //</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Returns the number of values defined</a>
+<a name="153"><span class="lineNum">     153 </span>            :   int getNumberOfComponents() const ;</a>
+<a name="154"><span class="lineNum">     154 </span>            : /// Clear the forces on the values</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void clearInputForces();</a>
+<a name="156"><span class="lineNum">     156 </span>            : /// Clear the derivatives of values wrt parameters</a>
+<a name="157"><span class="lineNum">     157 </span>            :   virtual void clearDerivatives();</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// Calculate the gradients and store them for all the values (need for projections)</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void setGradientsIfNeeded();</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Set the value</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void setValue(Value*,double);</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// Check if numerical derivatives should be used</a>
+<a name="163"><span class="lineNum">     163 </span>            :   bool checkNumericalDerivatives() const override;</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// This forces the class to use numerical derivatives</a>
+<a name="165"><span class="lineNum">     165 </span>            :   void useNumericalDerivatives();</a>
+<a name="166"><span class="lineNum">     166 </span>            : // These are things for using vectors of values as fields</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :   virtual void checkFieldsAllowed() { error(&quot;cannot use this action as a field&quot;); }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   virtual unsigned getNumberOfDerivatives()=0;</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// Activate the calculation of derivatives</a>
+<a name="170"><span class="lineNum">     170 </span>            :   virtual void turnOnDerivatives();</a>
+<a name="171"><span class="lineNum">     171 </span>            : };</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : inline</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     153914 : double ActionWithValue::getOutputQuantity(const unsigned j) const {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     153914 :   plumed_massert(j&lt;values.size(),&quot;index requested is out of bounds&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     153914 :   return values[j]-&gt;get();</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : inline</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">    2780554 : double ActionWithValue::getOutputQuantity( const std::string&amp; name ) const {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">    5561108 :   std::string thename; thename=getLabel() + &quot;.&quot; + name;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    6469144 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">    3775975 :     if( values[i]-&gt;name==thename ) return values[i]-&gt;value;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            :   return 0.0;</a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : inline</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">     194218 : void ActionWithValue::setValue(const double&amp; d) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">     194218 :   plumed_massert(values.size()==1, &quot;cannot use setValue in multi-component actions&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     194218 :   plumed_massert(values[0]-&gt;name==getLabel(), &quot;The value you are trying to set is not the default&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">     194218 :   values[0]-&gt;set(d);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">     194218 : }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : inline</a>
+<a name="196"><span class="lineNum">     196 </span>            : int ActionWithValue::getNumberOfComponents() const {</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">     142732 :   return values.size();</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : inline</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          2 : void ActionWithValue::useNumericalDerivatives() {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 :   plumed_massert( keywords.exists(&quot;NUMERICAL_DERIVATIVES&quot;), &quot;numerical derivatives are not permitted for this action&quot; );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          2 :   numericalDerivatives=true;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          2 : }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : inline</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">    1634139 : bool ActionWithValue::checkNumericalDerivatives() const {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">    1634183 :   return numericalDerivatives;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : inline</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       5924 : bool ActionWithValue::doNotCalculateDerivatives() const {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">   68373610 :   return noderiv;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithVirtualAtom.cpp.func-sort-c.html b/coverage/core/ActionWithVirtualAtom.cpp.func-sort-c.html
new file mode 100644
index 0000000000..77e7e41dab
--- /dev/null
+++ b/coverage/core/ActionWithVirtualAtom.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithVirtualAtom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithVirtualAtom.cpp<span style="font-size: 80%;"> (<a href="ActionWithVirtualAtom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithVirtualAtom.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#31">_ZN4PLMD21ActionWithVirtualAtomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#39">_ZN4PLMD21ActionWithVirtualAtomD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#39">_ZN4PLMD21ActionWithVirtualAtomD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#58">_ZN4PLMD21ActionWithVirtualAtom12setGradientsEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#75">_ZN4PLMD21ActionWithVirtualAtom17setBoxDerivativesERKSt5arrayINS_13TensorGenericILj3ELj3EEELm3EE</a></td>
+              <td class="coverFnHi">605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#84">_ZN4PLMD21ActionWithVirtualAtom22setBoxDerivativesNoPbcEv</a></td>
+              <td class="coverFnHi">605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#53">_ZN4PLMD21ActionWithVirtualAtom12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EE</a></td>
+              <td class="coverFnHi">7167</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#31">_ZN4PLMD21ActionWithVirtualAtomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#39">_ZN4PLMD21ActionWithVirtualAtomD2Ev</a></td>
+              <td class="coverFnHi">7178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#25">_ZN4PLMD21ActionWithVirtualAtom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7188</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#43">_ZN4PLMD21ActionWithVirtualAtom5applyEv</a></td>
+              <td class="coverFnHi">14338</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#100">_ZN4PLMD21ActionWithVirtualAtom20setGradientsIfNeededEv</a></td>
+              <td class="coverFnHi">14422</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithVirtualAtom.cpp.func.html b/coverage/core/ActionWithVirtualAtom.cpp.func.html
new file mode 100644
index 0000000000..2c4dcd7f9c
--- /dev/null
+++ b/coverage/core/ActionWithVirtualAtom.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithVirtualAtom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithVirtualAtom.cpp<span style="font-size: 80%;"> (<a href="ActionWithVirtualAtom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithVirtualAtom.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#53">_ZN4PLMD21ActionWithVirtualAtom12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EE</a></td>
+              <td class="coverFnHi">7167</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#58">_ZN4PLMD21ActionWithVirtualAtom12setGradientsEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#25">_ZN4PLMD21ActionWithVirtualAtom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7188</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#75">_ZN4PLMD21ActionWithVirtualAtom17setBoxDerivativesERKSt5arrayINS_13TensorGenericILj3ELj3EEELm3EE</a></td>
+              <td class="coverFnHi">605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#100">_ZN4PLMD21ActionWithVirtualAtom20setGradientsIfNeededEv</a></td>
+              <td class="coverFnHi">14422</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#84">_ZN4PLMD21ActionWithVirtualAtom22setBoxDerivativesNoPbcEv</a></td>
+              <td class="coverFnHi">605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#43">_ZN4PLMD21ActionWithVirtualAtom5applyEv</a></td>
+              <td class="coverFnHi">14338</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#31">_ZN4PLMD21ActionWithVirtualAtomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#31">_ZN4PLMD21ActionWithVirtualAtomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7178</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#39">_ZN4PLMD21ActionWithVirtualAtomD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#39">_ZN4PLMD21ActionWithVirtualAtomD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVirtualAtom.cpp.gcov.html#39">_ZN4PLMD21ActionWithVirtualAtomD2Ev</a></td>
+              <td class="coverFnHi">7178</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithVirtualAtom.cpp.gcov.html b/coverage/core/ActionWithVirtualAtom.cpp.gcov.html
new file mode 100644
index 0000000000..5fc84bd473
--- /dev/null
+++ b/coverage/core/ActionWithVirtualAtom.cpp.gcov.html
@@ -0,0 +1,184 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithVirtualAtom.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithVirtualAtom.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithVirtualAtom.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">       7188 : void ActionWithVirtualAtom::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">       7188 :   Action::registerKeywords(keys);</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       7188 :   ActionAtomistic::registerKeywords(keys);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">      14376 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the list of atoms which are involved the virtual atom's definition&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">       7188 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       7178 : ActionWithVirtualAtom::ActionWithVirtualAtom(const ActionOptions&amp;ao):</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   Action(ao),</a>
+<a name="35"><span class="lineNum">      35 </span>            :   ActionAtomistic(ao),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       7178 :   index(atoms.addVirtualAtom(this))</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       7178 :   log&lt;&lt;&quot;  serial associated to this virtual atom is &quot;&lt;&lt;index.serial()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       7178 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       7178 : ActionWithVirtualAtom::~ActionWithVirtualAtom() {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       7178 :   atoms.removeVirtualAtom(this);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       7178 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      14338 : void ActionWithVirtualAtom::apply() {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      14338 :   Vector &amp; f(atoms.forces[index.index()]);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      94976 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) modifyForces()[i]=matmul(derivatives[i],f);</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   Tensor &amp; v(modifyVirial());</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      57352 :   for(unsigned i=0; i&lt;3; i++) v+=boxDerivatives[i]*f[i];</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      14338 :   f.zero(); // after propagating the force to the atoms used to compute the vatom, we reset this to zero</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   // this is necessary to avoid double counting if then one tries to compute the total force on the c.o.m. of the system.</a>
+<a name="52"><span class="lineNum">      52 </span>            :   // notice that this is currently done in FIT_TO_TEMPLATE</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      14338 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       7167 : void ActionWithVirtualAtom::requestAtoms(const std::vector&lt;AtomNumber&gt; &amp; a) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       7167 :   ActionAtomistic::requestAtoms(a);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       7167 :   derivatives.resize(a.size());</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       7167 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          9 : void ActionWithVirtualAtom::setGradients() {</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   gradients.clear();</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         45 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         36 :     AtomNumber an=getAbsoluteIndex(i);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :     // this case if the atom is a virtual one</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         36 :     if(atoms.isVirtualAtom(an)) {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :       const ActionWithVirtualAtom* a=atoms.getVirtualAtomsAction(an);</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         36 :       for(const auto &amp; p : a-&gt;gradients) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         30 :         gradients[p.first]+=matmul(derivatives[i],p.second);</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :       }</a>
+<a name="70"><span class="lineNum">      70 </span>            :       // this case if the atom is a normal one</a>
+<a name="71"><span class="lineNum">      71 </span>            :     } else {</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         30 :       gradients[an]+=derivatives[i];</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     }</a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          9 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        605 : void ActionWithVirtualAtom::setBoxDerivatives(const std::array&lt;Tensor,3&gt; &amp;d) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        605 :   boxDerivatives=d;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : // Subtract the trivial part coming from a distorsion applied to the ghost atom first.</a>
+<a name="80"><span class="lineNum">      80 </span>            : // Notice that this part alone should exactly cancel the already accumulated virial</a>
+<a name="81"><span class="lineNum">      81 </span>            : // due to forces on this atom.</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        605 :   Vector pos=atoms.positions[index.index()];</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       7865 :   for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++) boxDerivatives[j][i][j]+=pos[i];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        605 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        605 : void ActionWithVirtualAtom::setBoxDerivativesNoPbc() {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        605 :   std::array&lt;Tensor,3&gt; bd;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      24200 :   for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++) for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : // Notice that this expression is very similar to the one used in Colvar::setBoxDerivativesNoPbc().</a>
+<a name="90"><span class="lineNum">      90 </span>            : // Indeed, we have the negative of a sum over dependent atoms (l) of the external product between positions</a>
+<a name="91"><span class="lineNum">      91 </span>            : // and derivatives. Notice that this only works only when Pbc have not been used to compute</a>
+<a name="92"><span class="lineNum">      92 </span>            : // derivatives.</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      16902 :         for(unsigned l=0; l&lt;getNumberOfAtoms(); l++) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        567 :           bd[k][i][j]-=getPosition(l)[i]*derivatives[l][j][k];</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :         }</a>
+<a name="96"><span class="lineNum">      96 </span>            :       }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        605 :   setBoxDerivatives(bd);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        605 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      14422 : void ActionWithVirtualAtom::setGradientsIfNeeded() {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      28844 :   if(isOptionOn(&quot;GRADIENTS&quot;)) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          9 :     setGradients() ;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      14422 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithVirtualAtom.h.func-sort-c.html b/coverage/core/ActionWithVirtualAtom.h.func-sort-c.html
new file mode 100644
index 0000000000..329c0c1fb4
--- /dev/null
+++ b/coverage/core/ActionWithVirtualAtom.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithVirtualAtom.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithVirtualAtom.h<span style="font-size: 80%;"> (<a href="ActionWithVirtualAtom.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithVirtualAtom.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithVirtualAtom.h.func.html b/coverage/core/ActionWithVirtualAtom.h.func.html
new file mode 100644
index 0000000000..5c2e22da53
--- /dev/null
+++ b/coverage/core/ActionWithVirtualAtom.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithVirtualAtom.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithVirtualAtom.h<span style="font-size: 80%;"> (<a href="ActionWithVirtualAtom.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithVirtualAtom.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ActionWithVirtualAtom.h.gcov.html b/coverage/core/ActionWithVirtualAtom.h.gcov.html
new file mode 100644
index 0000000000..df91f2d606
--- /dev/null
+++ b/coverage/core/ActionWithVirtualAtom.h.gcov.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ActionWithVirtualAtom.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ActionWithVirtualAtom.h<span style="font-size: 80%;"> (source / <a href="ActionWithVirtualAtom.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_ActionWithVirtualAtom_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_ActionWithVirtualAtom_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tensor.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;array&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /**</a>
+<a name="35"><span class="lineNum">      35 </span>            : \ingroup INHERIT</a>
+<a name="36"><span class="lineNum">      36 </span>            : Inherit from here if you are calculating the position of a virtual atom (eg a center of mass)</a>
+<a name="37"><span class="lineNum">      37 </span>            : */</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Class to add a single virtual atom to the system.</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// (it might be extended to add multiple virtual atoms).</a>
+<a name="41"><span class="lineNum">      41 </span>            : class ActionWithVirtualAtom:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   public ActionAtomistic</a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span>            :   const AtomNumber index;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;Tensor&gt; derivatives;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::array&lt;Tensor,3&gt; boxDerivatives;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::map&lt;AtomNumber,Tensor&gt; gradients;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   void apply() override;</a>
+<a name="49"><span class="lineNum">      49 </span>            : protected:</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Set position of the virtual atom</a>
+<a name="51"><span class="lineNum">      51 </span>            :   void setPosition(const Vector &amp;);</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Set its mass</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void setMass(double);</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Set its charge</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void setCharge(double);</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Request atoms on which the calculation depends</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void requestAtoms(const std::vector&lt;AtomNumber&gt; &amp; a);</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Set the derivatives of virtual atom coordinate wrt atoms on which it dependes</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void setAtomsDerivatives(const std::vector&lt;Tensor&gt; &amp;d);</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Set the box derivatives.</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// This should be an array of size 3. First index corresponds</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// to the components of the virtual atom.</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Notice that this routine subtract the trivial term coming from cell deformation</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// since this term is already implicitly included. Indeed, if the vatom</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// position is a linear function of atomic coordinates it is not necessary</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// to call this function (implicit term is fine) (e.g. vatom::COM and vatom::Center).</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// On the other hand if the vatom position is a non-linear function of atomic coordinates this</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// should be called (see vatom::Ghost).</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void setBoxDerivatives(const std::array&lt;Tensor,3&gt; &amp;d);</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Set box derivatives automatically.</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// It should be called after the settomsDerivatives has been used for all</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// single atoms.</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// \warning It only works for virtual atoms NOT using PBCs!</a>
+<a name="74"><span class="lineNum">      74 </span>            : ///          This implies that all atoms used + the new virtual atom should be</a>
+<a name="75"><span class="lineNum">      75 </span>            : ///          in the same periodic image.</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void setBoxDerivativesNoPbc();</a>
+<a name="77"><span class="lineNum">      77 </span>            : public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void setGradients();</a>
+<a name="79"><span class="lineNum">      79 </span>            :   const std::map&lt;AtomNumber,Tensor&gt; &amp; getGradients()const;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Return the atom id of the corresponding virtual atom</a>
+<a name="81"><span class="lineNum">      81 </span>            :   AtomNumber getIndex()const;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   explicit ActionWithVirtualAtom(const ActionOptions&amp;ao);</a>
+<a name="83"><span class="lineNum">      83 </span>            :   ~ActionWithVirtualAtom();</a>
+<a name="84"><span class="lineNum">      84 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void setGradientsIfNeeded();</a>
+<a name="86"><span class="lineNum">      86 </span>            : };</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : inline</a>
+<a name="89"><span class="lineNum">      89 </span>            : AtomNumber ActionWithVirtualAtom::getIndex()const {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       7219 :   return index;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : inline</a>
+<a name="94"><span class="lineNum">      94 </span>            : void ActionWithVirtualAtom::setPosition(const Vector &amp; pos) {</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      14422 :   atoms.positions[index.index()]=pos;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        598 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : inline</a>
+<a name="99"><span class="lineNum">      99 </span>            : void ActionWithVirtualAtom::setMass(double m) {</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      14422 :   atoms.masses[index.index()]=m;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      13808 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : inline</a>
+<a name="104"><span class="lineNum">     104 </span>            : void ActionWithVirtualAtom::setCharge(double c) {</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      14418 :   atoms.charges[index.index()]=c;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      13808 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : inline</a>
+<a name="109"><span class="lineNum">     109 </span>            : void ActionWithVirtualAtom::setAtomsDerivatives(const std::vector&lt;Tensor&gt; &amp;d) {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      14422 :   derivatives=d;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      14422 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : inline</a>
+<a name="114"><span class="lineNum">     114 </span>            : const std::map&lt;AtomNumber,Tensor&gt; &amp; ActionWithVirtualAtom::getGradients()const {</a>
+<a name="115"><span class="lineNum">     115 </span>            :   return gradients;</a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Atoms.cpp.func-sort-c.html b/coverage/core/Atoms.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ebfeed9b80
--- /dev/null
+++ b/coverage/core/Atoms.cpp.func-sort-c.html
@@ -0,0 +1,312 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Atoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Atoms.cpp<span style="font-size: 80%;"> (<a href="Atoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">404</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Atoms.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.cpp.gcov.html#619">_ZN4PLMD5Atoms14getLocalMassesERSt6vectorIdSaIdEE</a></td>
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+    <tr>
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+              <td class="coverFnHi">27123</td>
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+              <td class="coverFnHi">3210555</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Atoms.cpp.func.html b/coverage/core/Atoms.cpp.func.html
new file mode 100644
index 0000000000..cc57b86069
--- /dev/null
+++ b/coverage/core/Atoms.cpp.func.html
@@ -0,0 +1,312 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Atoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Atoms.cpp<span style="font-size: 80%;"> (<a href="Atoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">404</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Atoms.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.cpp.gcov.html#649">_ZN4PLMD5Atoms10getExtraCVERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.cpp.gcov.html#602">_ZN4PLMD5Atoms10readBinaryERSi</a></td>
+              <td class="coverFnHi">114</td>
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+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Atoms.cpp.gcov.html b/coverage/core/Atoms.cpp.gcov.html
new file mode 100644
index 0000000000..a80cfb966d
--- /dev/null
+++ b/coverage/core/Atoms.cpp.gcov.html
@@ -0,0 +1,748 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Atoms.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Atoms.cpp<span style="font-size: 80%;"> (source / <a href="Atoms.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">404</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;MDAtoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;algorithm&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;string&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cmath&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : /// We assume that charges and masses are constant along the simulation</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Set this to false if you want to revert to the original (expensive) behavior</a>
+<a name="37"><span class="lineNum">      37 </span>            : static const bool shareMassAndChargeOnlyAtFirstStep=true;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Use a priority_queue to merge unique vectors.</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// export PLUMED_MERGE_VECTORS_PRIORITY_QUEUE=yes to use a priority_queue.</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Might be faster with some settings, but appears to not be in practice.</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// This option is for testing and might be removed.</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      27123 : static bool getenvMergeVectorsPriorityQueue() noexcept {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      27123 :   static const auto* res=std::getenv(&quot;PLUMED_MERGE_VECTORS_PRIORITY_QUEUE&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      27123 :   return res;</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Use unique list of atoms to manipulate forces and positions.</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// A unique list of atoms is used to manipulate forces and positions in MPI parallel runs.</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// In serial runs, this is done if convenient. The code currently contain</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// some heuristic to decide if the unique list should be used or not.</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// An env var can be used to override this decision.</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// export PLUMED_FORCE_UNIQUE=yes  # enforce using the unique list in serial runs</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// export PLUMED_FORCE_UNIQUE=no   # enforce not using the unique list in serial runs</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// export PLUMED_FORCE_UNIQUE=auto # choose heuristically</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// default: auto</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      53319 : static const char* getenvForceUnique() noexcept {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      53319 :   static const auto* res=std::getenv(&quot;PLUMED_FORCE_UNIQUE&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      53319 :   return res;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : }</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : class PlumedMain;</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">     805268 : Atoms::Atoms(PlumedMain&amp;plumed):</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     805268 :   natoms(0),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     805268 :   md_energy(0.0),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     805268 :   energy(0.0),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     805268 :   dataCanBeSet(false),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     805268 :   collectEnergy(false),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     805268 :   energyHasBeenSet(false),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     805268 :   positionsHaveBeenSet(0),</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">     805268 :   massesHaveBeenSet(false),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">     805268 :   chargesHaveBeenSet(false),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     805268 :   boxHasBeenSet(false),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     805268 :   forcesHaveBeenSet(0),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     805268 :   virialHasBeenSet(false),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     805268 :   massAndChargeOK(false),</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     805268 :   shuffledAtoms(0),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     805268 :   mdatoms(MDAtomsBase::create(sizeof(double))),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     805268 :   plumed(plumed),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     805268 :   naturalUnits(false),</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     805268 :   MDnaturalUnits(false),</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     805268 :   timestep(0.0),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">     805268 :   forceOnEnergy(0.0),</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     805268 :   zeroallforces(false),</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     805268 :   kbT(0.0),</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     805268 :   asyncSent(false),</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     805268 :   atomsNeeded(false),</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">    1610536 :   ddStep(0)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : {</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     805268 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     805268 : Atoms::~Atoms() {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     805268 :   if(actions.size()&gt;0) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;WARNING: there is some inconsistency in action added to atoms, as some of them were not properly destroyed. This might indicate an internal bug!!\n&quot;;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    1610536 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     256144 : void Atoms::startStep() {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     256144 :   collectEnergy=false; energyHasBeenSet=false; positionsHaveBeenSet=0;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     256144 :   massesHaveBeenSet=false; chargesHaveBeenSet=false; boxHasBeenSet=false;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     256144 :   forcesHaveBeenSet=0; virialHasBeenSet=false; dataCanBeSet=true;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">     256144 :   resetExtraCVNeeded();</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">     256144 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      51647 : void Atoms::setBox(const TypesafePtr &amp; p) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      51647 :   mdatoms-&gt;setBox(p);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      51647 :   Tensor b; mdatoms-&gt;getBox(b); boxHasBeenSet=true;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      51647 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      55788 : void Atoms::setPositions(const TypesafePtr &amp; p) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      55788 :   plumed_massert( dataCanBeSet,&quot;setPositions must be called after setStep in MD code interface&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      55788 :   plumed_massert( p || gatindex.size()==0, &quot;NULL position pointer with non-zero local atoms&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      55788 :   mdatoms-&gt;setp(p); positionsHaveBeenSet=3;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      55788 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      55792 : void Atoms::setMasses(const TypesafePtr &amp; p) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      55795 :   plumed_massert( dataCanBeSet,&quot;setMasses must be called after setStep in MD code interface&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      55789 :   plumed_massert( p || gatindex.size()==0, &quot;NULL mass pointer with non-zero local atoms&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      55789 :   mdatoms-&gt;setm(p); massesHaveBeenSet=true;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      55789 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      45883 : void Atoms::setCharges(const TypesafePtr &amp; p) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      45883 :   plumed_massert( dataCanBeSet, &quot;setCharges must be called after setStep in MD code interface&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      45883 :   plumed_massert( p || gatindex.size()==0, &quot;NULL charges pointer with non-zero local atoms&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      45883 :   mdatoms-&gt;setc(p); chargesHaveBeenSet=true;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      45883 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      45989 : void Atoms::setVirial(const TypesafePtr &amp; p) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      45989 :   plumed_massert( dataCanBeSet,&quot;setVirial must be called after setStep in MD code interface&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      45989 :   mdatoms-&gt;setVirial(p); virialHasBeenSet=true;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      45987 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       9792 : void Atoms::setEnergy(const TypesafePtr &amp; p) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       9792 :   plumed_massert( dataCanBeSet,&quot;setEnergy must be called after setStep in MD code interface&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       9792 :   MD2double(p,md_energy);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       9792 :   md_energy*=MDUnits.getEnergy()/units.getEnergy();</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       9792 :   energyHasBeenSet=true;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       9792 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      55788 : void Atoms::setForces(const TypesafePtr &amp; p) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      55788 :   plumed_massert( dataCanBeSet,&quot;setForces must be called after setStep in MD code interface&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      55788 :   plumed_massert( p || gatindex.size()==0, &quot;NULL force pointer with non-zero local atoms&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      55788 :   forcesHaveBeenSet=3;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      55788 :   mdatoms-&gt;setf(p);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      55788 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          3 : void Atoms::setPositions(const TypesafePtr &amp; p,int i) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :   plumed_massert( dataCanBeSet,&quot;setPositions must be called after setStep in MD code interface&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :   plumed_massert( p || gatindex.size()==0, &quot;NULL positions pointer with non-zero local atoms&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          3 :   mdatoms-&gt;setp(p,i); positionsHaveBeenSet++;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 : }</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          3 : void Atoms::setForces(const TypesafePtr &amp; p,int i) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          3 :   plumed_massert( dataCanBeSet,&quot;setForces must be called after setStep in MD code interface&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 :   plumed_massert( p || gatindex.size()==0, &quot;NULL force pointer with non-zero local atoms&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 :   mdatoms-&gt;setf(p,i); forcesHaveBeenSet++;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          3 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">      54195 : void Atoms::share() {</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : // At first step I scatter all the atoms so as to store their mass and charge</a>
+<a name="163"><span class="lineNum">     163 </span>            : // Notice that this works with the assumption that charges and masses are</a>
+<a name="164"><span class="lineNum">     164 </span>            : // not changing during the simulation!</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      54195 :   if(!massAndChargeOK &amp;&amp; shareMassAndChargeOnlyAtFirstStep) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        876 :     shareAll();</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        876 :     return;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      53319 :   if(!getenvForceUnique() || !std::strcmp(getenvForceUnique(),&quot;auto&quot;)) {</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     unsigned largest=0;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     256701 :     for(unsigned i=0; i&lt;actions.size(); i++) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     203382 :       if(actions[i]-&gt;isActive()) {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :         auto l=actions[i]-&gt;getUnique().size();</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     154014 :         if(l&gt;largest) largest=l;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :       }</a>
+<a name="177"><span class="lineNum">     177 </span>            :     }</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">      53319 :     if(largest*2&lt;natoms) unique_serial=true;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      26693 :     else unique_serial=false;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   } else if(!std::strcmp(getenvForceUnique(),&quot;yes&quot;)) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     unique_serial=true;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   } else if(!std::strcmp(getenvForceUnique(),&quot;no&quot;)) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     unique_serial=false;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   } else {</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     plumed_error()&lt;&lt;&quot;PLUMED_FORCE_UNIQUE set to unknown value &quot;&lt;&lt;getenvForceUnique();</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      53319 :   if(unique_serial || !(int(gatindex.size())==natoms &amp;&amp; shuffledAtoms==0)) {</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     std::vector&lt;const std::vector&lt;AtomNumber&gt;*&gt; vectors;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      27014 :     vectors.reserve(actions.size());</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     117203 :     for(unsigned i=0; i&lt;actions.size(); i++) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      90189 :       if(actions[i]-&gt;isActive()) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      66031 :         if(!actions[i]-&gt;getUnique().empty()) {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :           // unique are the local atoms</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      55184 :           vectors.push_back(&amp;actions[i]-&gt;getUniqueLocal());</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :         }</a>
+<a name="197"><span class="lineNum">     197 </span>            :       }</a>
+<a name="198"><span class="lineNum">     198 </span>            :     }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      27014 :     if(!vectors.empty()) atomsNeeded=true;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      27014 :     unique.clear();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      27014 :     Tools::mergeSortedVectors(vectors,unique,getenvMergeVectorsPriorityQueue());</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   } else {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     139498 :     for(unsigned i=0; i&lt;actions.size(); i++) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     113193 :       if(actions[i]-&gt;isActive()) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      87983 :         if(!actions[i]-&gt;getUnique().empty()) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      78676 :           atomsNeeded=true;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :         }</a>
+<a name="208"><span class="lineNum">     208 </span>            :       }</a>
+<a name="209"><span class="lineNum">     209 </span>            :     }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      53319 :   share(unique);</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        990 : void Atoms::shareAll() {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        990 :   unique.clear();</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   // keep in unique only those atoms that are local</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        990 :   if(dd &amp;&amp; shuffledAtoms&gt;0) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      17616 :     for(int i=0; i&lt;natoms; i++) if(g2l[i]&gt;=0) unique.push_back(AtomNumber::index(i)); // already sorted</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   } else {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        804 :     unique.resize(natoms);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     831815 :     for(int i=0; i&lt;natoms; i++) unique[i]=AtomNumber::index(i);</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        990 :   atomsNeeded=true;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        990 :   share(unique);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        990 : }</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      54309 : void Atoms::share(const std::vector&lt;AtomNumber&gt;&amp; unique) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      54309 :   plumed_assert( positionsHaveBeenSet==3 &amp;&amp; massesHaveBeenSet );</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      54309 :   virial.zero();</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      54309 :   if(zeroallforces || (int(gatindex.size())==natoms &amp;&amp; !unique_serial)) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      27168 :     Tools::set_to_zero(forces);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   } else {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">     403148 :     for(const auto &amp; p : unique) forces[p.index()].zero();</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      28990 :     for(unsigned i=getNatoms(); i&lt;positions.size(); i++) forces[i].zero(); // virtual atoms</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      54309 :   forceOnEnergy=0.0;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      54309 :   mdatoms-&gt;getBox(box);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">      54309 :   if(!atomsNeeded) return;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      53067 :   atomsNeeded=false;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      53067 :   if(!(int(gatindex.size())==natoms &amp;&amp; shuffledAtoms==0)) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">       2212 :     uniq_index.resize(unique.size());</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      32705 :     for(unsigned i=0; i&lt;unique.size(); i++) uniq_index[i]=g2l[unique[i].index()];</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       2212 :     mdatoms-&gt;getPositions(unique,uniq_index,positions);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      50855 :   } else if(unique_serial) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      23746 :     uniq_index.resize(unique.size());</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">     371042 :     for(unsigned i=0; i&lt;unique.size(); i++) uniq_index[i]=unique[i].index();</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">      23746 :     mdatoms-&gt;getPositions(unique,uniq_index,positions);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   } else {</a>
+<a name="254"><span class="lineNum">     254 </span>            : // faster version, which retrieves all atoms</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">      27109 :     mdatoms-&gt;getPositions(0,natoms,positions);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : // how many double per atom should be scattered:</a>
+<a name="260"><span class="lineNum">     260 </span>            :   int ndata=3;</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">      53067 :   if(!massAndChargeOK) {</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :     ndata=5;</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        876 :     masses.assign(masses.size(),std::numeric_limits&lt;double&gt;::quiet_NaN());</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        876 :     charges.assign(charges.size(),std::numeric_limits&lt;double&gt;::quiet_NaN());</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        876 :     mdatoms-&gt;getCharges(gatindex,charges);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        876 :     mdatoms-&gt;getMasses(gatindex,masses);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   }</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">      53067 :   if(dd &amp;&amp; shuffledAtoms&gt;0) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       2142 :     if(dd.async) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       9510 :       for(unsigned i=0; i&lt;dd.mpi_request_positions.size(); i++) dd.mpi_request_positions[i].wait();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       9510 :       for(unsigned i=0; i&lt;dd.mpi_request_index.size(); i++)     dd.mpi_request_index[i].wait();</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       2142 :     int count=0;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      29223 :     for(const auto &amp; p : unique) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      27081 :       dd.indexToBeSent[count]=p.index();</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">      27081 :       dd.positionsToBeSent[ndata*count+0]=positions[p.index()][0];</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      27081 :       dd.positionsToBeSent[ndata*count+1]=positions[p.index()][1];</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">      27081 :       dd.positionsToBeSent[ndata*count+2]=positions[p.index()][2];</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      27081 :       if(!massAndChargeOK) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       2477 :         dd.positionsToBeSent[ndata*count+3]=masses[p.index()];</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       2477 :         dd.positionsToBeSent[ndata*count+4]=charges[p.index()];</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :       }</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">      27081 :       count++;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">       2142 :     if(dd.async) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       2122 :       asyncSent=true;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       2122 :       dd.mpi_request_positions.resize(dd.Get_size());</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       2122 :       dd.mpi_request_index.resize(dd.Get_size());</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       9710 :       for(int i=0; i&lt;dd.Get_size(); i++) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       7588 :         dd.mpi_request_index[i]=dd.Isend(&amp;dd.indexToBeSent[0],count,i,666);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       7588 :         dd.mpi_request_positions[i]=dd.Isend(&amp;dd.positionsToBeSent[0],ndata*count,i,667);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :       }</a>
+<a name="294"><span class="lineNum">     294 </span>            :     } else {</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         20 :       const int n=(dd.Get_size());</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         20 :       std::vector&lt;int&gt; counts(n);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         20 :       std::vector&lt;int&gt; displ(n);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         20 :       std::vector&lt;int&gt; counts5(n);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         20 :       std::vector&lt;int&gt; displ5(n);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         20 :       dd.Allgather(count,counts);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         20 :       displ[0]=0;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         80 :       for(int i=1; i&lt;n; ++i) displ[i]=displ[i-1]+counts[i-1];</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        100 :       for(int i=0; i&lt;n; ++i) counts5[i]=counts[i]*ndata;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        100 :       for(int i=0; i&lt;n; ++i) displ5[i]=displ[i]*ndata;</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         20 :       dd.Allgatherv(&amp;dd.indexToBeSent[0],count,&amp;dd.indexToBeReceived[0],&amp;counts[0],&amp;displ[0]);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         20 :       dd.Allgatherv(&amp;dd.positionsToBeSent[0],ndata*count,&amp;dd.positionsToBeReceived[0],&amp;counts5[0],&amp;displ5[0]);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         20 :       int tot=displ[n-1]+counts[n-1];</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       1620 :       for(int i=0; i&lt;tot; i++) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1600 :         positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">       1600 :         positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       1600 :         positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       1600 :         if(!massAndChargeOK) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        432 :           masses[dd.indexToBeReceived[i]]      =dd.positionsToBeReceived[ndata*i+3];</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">        432 :           charges[dd.indexToBeReceived[i]]     =dd.positionsToBeReceived[ndata*i+4];</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :         }</a>
+<a name="316"><span class="lineNum">     316 </span>            :       }</a>
+<a name="317"><span class="lineNum">     317 </span>            :     }</a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">      54309 : void Atoms::wait() {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      54309 :   dataCanBeSet=false; // Everything should be set by this stage</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : // How many double per atom should be scattered</a>
+<a name="324"><span class="lineNum">     324 </span>            :   std::size_t ndata=3;</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      54309 :   if(!massAndChargeOK)ndata=5;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      54309 :   if(dd) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">      21601 :     dd.Bcast(box,0);</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">      54309 :   pbc.setBox(box);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      54309 :   if(collectEnergy) energy=md_energy;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      54309 :   if(dd &amp;&amp; shuffledAtoms&gt;0) {</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : // receive toBeReceived</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       2142 :     if(asyncSent) {</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :       Communicator::Status status;</a>
+<a name="338"><span class="lineNum">     338 </span>            :       std::size_t count=0;</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       9710 :       for(int i=0; i&lt;dd.Get_size(); i++) {</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       7588 :         dd.Recv(&amp;dd.indexToBeReceived[count],dd.indexToBeReceived.size()-count,i,666,status);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       7588 :         int c=status.Get_count&lt;int&gt;();</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       7588 :         dd.Recv(&amp;dd.positionsToBeReceived[ndata*count],dd.positionsToBeReceived.size()-ndata*count,i,667);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">       7588 :         count+=c;</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :       }</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">      64820 :       for(int i=0; i&lt;count; i++) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">      62698 :         positions[dd.indexToBeReceived[i]][0]=dd.positionsToBeReceived[ndata*i+0];</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">      62698 :         positions[dd.indexToBeReceived[i]][1]=dd.positionsToBeReceived[ndata*i+1];</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      62698 :         positions[dd.indexToBeReceived[i]][2]=dd.positionsToBeReceived[ndata*i+2];</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">      62698 :         if(!massAndChargeOK) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">       5946 :           masses[dd.indexToBeReceived[i]]      =dd.positionsToBeReceived[ndata*i+3];</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">       5946 :           charges[dd.indexToBeReceived[i]]     =dd.positionsToBeReceived[ndata*i+4];</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :         }</a>
+<a name="353"><span class="lineNum">     353 </span>            :       }</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">       2122 :       asyncSent=false;</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :     }</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       2142 :     if(collectEnergy) dd.Sum(energy);</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   }</a>
+<a name="358"><span class="lineNum">     358 </span>            : // I take note that masses and charges have been set once for all</a>
+<a name="359"><span class="lineNum">     359 </span>            : // at the beginning of the simulation.</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">      54309 :   if(shareMassAndChargeOnlyAtFirstStep) massAndChargeOK=true;</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">      54309 : }</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">      54185 : void Atoms::updateForces() {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">      54185 :   plumed_assert( forcesHaveBeenSet==3 );</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">      54185 :   if(forceOnEnergy*forceOnEnergy&gt;epsilon) {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         50 :     double alpha=1.0-forceOnEnergy;</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         50 :     mdatoms-&gt;rescaleForces(gatindex,alpha);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         50 :     mdatoms-&gt;updateForces(gatindex,forces);</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :   } else {</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      54135 :     if(!unique_serial &amp;&amp; int(gatindex.size())==natoms &amp;&amp; shuffledAtoms==0) mdatoms-&gt;updateForces(gatindex,forces);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      27027 :     else mdatoms-&gt;updateForces(unique,uniq_index,forces);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">      54185 :   if( !plumed.novirial &amp;&amp; dd.Get_rank()==0 ) {</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      39613 :     plumed_assert( virialHasBeenSet );</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      39613 :     mdatoms-&gt;updateVirial(virial);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   }</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">      54185 : }</span></a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        986 : void Atoms::setNatoms(int n) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        986 :   natoms=n;</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        986 :   positions.resize(n);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        986 :   forces.resize(n);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        986 :   masses.resize(n);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        986 :   charges.resize(n);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        986 :   gatindex.resize(n);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">     839573 :   for(unsigned i=0; i&lt;gatindex.size(); i++) gatindex[i]=i;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        986 : }</span></a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      10255 : void Atoms::add(ActionAtomistic*a) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">      10255 :   actions.push_back(a);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">      10255 : }</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">      10255 : void Atoms::remove(ActionAtomistic*a) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">      10255 :   auto f=find(actions.begin(),actions.end(),a);</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">      10255 :   plumed_massert(f!=actions.end(),&quot;cannot remove an action registered to atoms&quot;);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">      10255 :   actions.erase(f);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">      10255 : }</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">        339 : void Atoms::DomainDecomposition::enable(Communicator&amp; c) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">        339 :   on=true;</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">        339 :   Set_comm(c.Get_comm());</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">        339 :   async=Get_size()&lt;10;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">        339 :   if(std::getenv(&quot;PLUMED_ASYNC_SHARE&quot;)) {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          4 :     std::string s(std::getenv(&quot;PLUMED_ASYNC_SHARE&quot;));</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          4 :     if(s==&quot;yes&quot;) async=true;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          4 :     else if(s==&quot;no&quot;) async=false;</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :     else plumed_merror(&quot;PLUMED_ASYNC_SHARE variable is set to &quot; + s + &quot;; should be yes or no&quot;);</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        339 : }</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">       1479 : void Atoms::setAtomsNlocal(int n) {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">       1479 :   gatindex.resize(n);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">       1479 :   g2l.resize(natoms,-1);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       1479 :   if(dd) {</span></a>
+<a name="417"><span class="lineNum">     417 </span>            : // Since these vectors are sent with MPI by using e.g.</a>
+<a name="418"><span class="lineNum">     418 </span>            : // &amp;dd.positionsToBeSent[0]</a>
+<a name="419"><span class="lineNum">     419 </span>            : // we make sure they are non-zero-sized so as to</a>
+<a name="420"><span class="lineNum">     420 </span>            : // avoid errors when doing boundary check</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">       1447 :     if(n==0) n++;</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">       1447 :     dd.positionsToBeSent.resize(n*5,0.0);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">       1447 :     dd.positionsToBeReceived.resize(natoms*5,0.0);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">       1447 :     dd.indexToBeSent.resize(n,0);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">       1447 :     dd.indexToBeReceived.resize(natoms,0);</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :   }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">       1479 : }</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">        988 : void Atoms::setAtomsGatindex(const TypesafePtr &amp; g,bool fortran) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        988 :   plumed_massert( g || gatindex.size()==0, &quot;NULL gatindex pointer with non-zero local atoms&quot;);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :   auto gg=g.get&lt;const int*&gt;(gatindex.size());</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        988 :   ddStep=plumed.getStep();</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        988 :   if(fortran) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;gatindex.size(); i++) gatindex[i]=gg[i]-1;</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :   } else {</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">      22140 :     for(unsigned i=0; i&lt;gatindex.size(); i++) gatindex[i]=gg[i];</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :   }</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">      57530 :   for(unsigned i=0; i&lt;g2l.size(); i++) g2l[i]=-1;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">        988 :   if( gatindex.size()==natoms ) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          9 :     shuffledAtoms=0;</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">       1005 :     for(unsigned i=0; i&lt;gatindex.size(); i++) {</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">        996 :       if( gatindex[i]!=i ) { shuffledAtoms=1; break; }</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     }</a>
+<a name="444"><span class="lineNum">     444 </span>            :   } else {</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        979 :     shuffledAtoms=1;</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :   }</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        988 :   if(dd) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        956 :     dd.Sum(shuffledAtoms);</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   }</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">      22140 :   for(unsigned i=0; i&lt;gatindex.size(); i++) g2l[gatindex[i]]=i;</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">      10390 :   for(unsigned i=0; i&lt;actions.size(); i++) {</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     // keep in unique only those atoms that are local</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">       9402 :     actions[i]-&gt;updateUniqueLocal();</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :   }</a>
+<a name="456"><span class="lineNum">     456 </span>            :   unique.clear();</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        988 : }</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        491 : void Atoms::setAtomsContiguous(int start) {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">        491 :   ddStep=plumed.getStep();</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">     185344 :   for(unsigned i=0; i&lt;gatindex.size(); i++) gatindex[i]=start+i;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">     197656 :   for(unsigned i=0; i&lt;g2l.size(); i++) g2l[i]=-1;</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">     185344 :   for(unsigned i=0; i&lt;gatindex.size(); i++) g2l[gatindex[i]]=i;</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        491 :   if(gatindex.size()&lt;natoms) shuffledAtoms=1;</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">        739 :   for(unsigned i=0; i&lt;actions.size(); i++) {</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :     // keep in unique only those atoms that are local</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">        248 :     actions[i]-&gt;updateUniqueLocal();</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :   }</a>
+<a name="469"><span class="lineNum">     469 </span>            :   unique.clear();</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">        491 : }</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">        877 : void Atoms::setRealPrecision(int p) {</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">       1754 :   mdatoms=MDAtomsBase::create(p);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        877 : }</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">       1873 : int Atoms::getRealPrecision()const {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">       1873 :   return mdatoms-&gt;getRealPrecision();</span></a>
+<a name="478"><span class="lineNum">     478 </span>            : }</a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">      13198 : void Atoms::MD2double(const TypesafePtr &amp; m,double&amp;d)const {</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">      13198 :   plumed_assert(mdatoms); mdatoms-&gt;MD2double(m,d);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">      13198 : }</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">       2390 : void Atoms::double2MD(const double&amp;d,const TypesafePtr &amp; m)const {</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">       2390 :   plumed_assert(mdatoms); mdatoms-&gt;double2MD(d,m);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">       2390 : }</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">       1027 : void Atoms::updateUnits() {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">       1027 :   mdatoms-&gt;setUnits(units,MDUnits);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">       1027 : }</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        866 : void Atoms::setTimeStep(const TypesafePtr &amp; p) {</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        866 :   MD2double(p,timestep);</span></a>
+<a name="493"><span class="lineNum">     493 </span>            : // The following is to avoid extra digits in case the MD code uses floats</a>
+<a name="494"><span class="lineNum">     494 </span>            : // e.g.: float f=0.002 when converted to double becomes 0.002000000094995</a>
+<a name="495"><span class="lineNum">     495 </span>            : // To avoid this, we keep only up to 6 significant digits after first one</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">        866 :   if(getRealPrecision()&lt;=4) {</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :     double magnitude=std::pow(10,std::floor(std::log10(timestep)));</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :     timestep=std::round(timestep/magnitude*1e6)/1e6*magnitude;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :   }</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        866 : }</span></a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">    3210555 : double Atoms::getTimeStep()const {</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">    3210555 :   return timestep/units.getTime()*MDUnits.getTime();</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : }</a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         59 : void Atoms::setKbT(const TypesafePtr &amp; p) {</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         59 :   MD2double(p,kbT);</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         59 : }</span></a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">       1294 : double Atoms::getKbT()const {</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">       1294 :   return kbT/units.getEnergy()*MDUnits.getEnergy();</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : }</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        116 : void Atoms::createFullList(const TypesafePtr &amp; n) {</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        116 :   if(!massAndChargeOK &amp;&amp; shareMassAndChargeOnlyAtFirstStep) {</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">          7 :     n.set(int(natoms));</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">          7 :     fullList.resize(natoms);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">        803 :     for(unsigned i=0; i&lt;natoms; i++) fullList[i]=i;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :   } else {</a>
+<a name="521"><span class="lineNum">     521 </span>            : // We update here the unique list defined at Atoms::unique.</a>
+<a name="522"><span class="lineNum">     522 </span>            : // This is not very clear, and probably should be coded differently.</a>
+<a name="523"><span class="lineNum">     523 </span>            : // Hopefully this fix the longstanding issue with NAMD.</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">        109 :     unique.clear();</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :     std::vector&lt;const std::vector&lt;AtomNumber&gt;*&gt; vectors;</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">        892 :     for(unsigned i=0; i&lt;actions.size(); i++) {</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">        783 :       if(actions[i]-&gt;isActive()) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">        625 :         if(!actions[i]-&gt;getUnique().empty()) {</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">        546 :           atomsNeeded=true;</span></a>
+<a name="530"><span class="lineNum">     530 </span>            :           // unique are the local atoms</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">        546 :           vectors.push_back(&amp;actions[i]-&gt;getUnique());</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :         }</a>
+<a name="533"><span class="lineNum">     533 </span>            :       }</a>
+<a name="534"><span class="lineNum">     534 </span>            :     }</a>
+<a name="535"><span class="lineNum">     535 </span>            :     unique.clear();</a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">        109 :     Tools::mergeSortedVectors(vectors,unique,getenvMergeVectorsPriorityQueue());</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">        109 :     fullList.clear();</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">        109 :     fullList.reserve(unique.size());</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">       5012 :     for(const auto &amp; p : unique) fullList.push_back(p.index());</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">        109 :     n.set(int(fullList.size()));</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :   }</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">        116 : }</span></a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">        116 : void Atoms::getFullList(const TypesafePtr &amp; x) {</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :   auto xx=x.template get&lt;const int**&gt;();</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">        116 :   if(!fullList.empty()) *xx=&amp;fullList[0];</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">          6 :   else *xx=NULL;</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        116 : }</span></a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        116 : void Atoms::clearFullList() {</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">        116 :   fullList.resize(0);</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">        116 : }</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">       1007 : void Atoms::init() {</span></a>
+<a name="555"><span class="lineNum">     555 </span>            : // Default: set domain decomposition to NO-decomposition, waiting for</a>
+<a name="556"><span class="lineNum">     556 </span>            : // further instruction</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">       1007 :   if(dd) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">        339 :     setAtomsNlocal(natoms);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">        339 :     setAtomsContiguous(0);</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :   }</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">       1007 : }</span></a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">        339 : void Atoms::setDomainDecomposition(Communicator&amp; comm) {</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">        339 :   dd.enable(comm);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">        339 : }</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">      14356 : void Atoms::resizeVectors(unsigned n) {</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">      14356 :   positions.resize(n);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">      14356 :   forces.resize(n);</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">      14356 :   masses.resize(n);</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">      14356 :   charges.resize(n);</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">      14356 : }</span></a>
+<a name="573"><span class="lineNum">     573 </span>            : </a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">       7178 : AtomNumber Atoms::addVirtualAtom(ActionWithVirtualAtom*a) {</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">       7178 :   unsigned n=positions.size();</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">       7178 :   resizeVectors(n+1);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">       7178 :   virtualAtomsActions.push_back(a);</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">       7178 :   return AtomNumber::index(n);</span></a>
+<a name="579"><span class="lineNum">     579 </span>            : }</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">       7178 : void Atoms::removeVirtualAtom(ActionWithVirtualAtom*a) {</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">       7178 :   unsigned n=positions.size();</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">       7178 :   plumed_massert(a==virtualAtomsActions[virtualAtomsActions.size()-1],&quot;virtual atoms should be destroyed in reverse creation order&quot;);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">       7178 :   resizeVectors(n-1);</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :   virtualAtomsActions.pop_back();</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">       7178 : }</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">        132 : void Atoms::insertGroup(const std::string&amp;name,const std::vector&lt;AtomNumber&gt;&amp;a) {</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :   plumed_massert(groups.count(name)==0,&quot;group named &quot;+name+&quot; already exists&quot;);</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">        132 :   groups[name]=a;</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">        132 : }</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">        132 : void Atoms::removeGroup(const std::string&amp;name) {</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 :   plumed_massert(groups.count(name)==1,&quot;cannot remove group named &quot;+name);</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :   groups.erase(name);</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">        132 : }</span></a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">        114 : void Atoms::writeBinary(std::ostream&amp;o)const {</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">        114 :   o.write(reinterpret_cast&lt;const char*&gt;(&amp;positions[0][0]),natoms*3*sizeof(double));</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">        114 :   o.write(reinterpret_cast&lt;const char*&gt;(&amp;box(0,0)),9*sizeof(double));</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">        114 :   o.write(reinterpret_cast&lt;const char*&gt;(&amp;energy),sizeof(double));</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">        114 : }</span></a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        114 : void Atoms::readBinary(std::istream&amp;i) {</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        114 :   i.read(reinterpret_cast&lt;char*&gt;(&amp;positions[0][0]),natoms*3*sizeof(double));</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">        114 :   i.read(reinterpret_cast&lt;char*&gt;(&amp;box(0,0)),9*sizeof(double));</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">        114 :   i.read(reinterpret_cast&lt;char*&gt;(&amp;energy),sizeof(double));</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">        114 :   pbc.setBox(box);</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">        114 : }</span></a>
+<a name="610"><span class="lineNum">     610 </span>            : </a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">        596 : double Atoms::getKBoltzmann()const {</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">        596 :   if(naturalUnits || MDnaturalUnits) return 1.0;</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">        590 :   else return kBoltzmann/units.getEnergy();</span></a>
+<a name="614"><span class="lineNum">     614 </span>            : }</a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 : double Atoms::getMDKBoltzmann()const {</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :   if(naturalUnits || MDnaturalUnits) return 1.0;</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :   else return kBoltzmann/MDUnits.getEnergy();</span></a>
+<a name="619"><span class="lineNum">     619 </span>            : }</a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 : void Atoms::getLocalMasses(std::vector&lt;double&gt;&amp; localMasses) {</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :   localMasses.resize(gatindex.size());</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;gatindex.size(); i++) localMasses[i] = masses[gatindex[i]];</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        450 : void Atoms::getLocalPositions(std::vector&lt;Vector&gt;&amp; localPositions) {</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">        450 :   localPositions.resize(gatindex.size());</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">        450 :   mdatoms-&gt;getLocalPositions(localPositions);</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">        450 : }</span></a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">        450 : void Atoms::getLocalForces(std::vector&lt;Vector&gt;&amp; localForces) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">        450 :   localForces.resize(gatindex.size());</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">      16650 :   for(unsigned i=0; i&lt;gatindex.size(); i++) localForces[i] = forces[gatindex[i]];</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">        450 : }</span></a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 : void Atoms::getLocalMDForces(std::vector&lt;Vector&gt;&amp; localForces) {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :   localForces.resize(gatindex.size());</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;gatindex.size(); i++) {</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :     localForces[i] = mdatoms-&gt;getMDforces(i);</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :   }</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">         30 : void Atoms::setExtraCV(const std::string &amp;name,const TypesafePtr &amp; p) {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">         30 :   mdatoms-&gt;setExtraCV(name,p);</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">         30 : }</span></a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         30 : void Atoms::setExtraCVForce(const std::string &amp;name,const TypesafePtr &amp; p) {</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">         30 :   mdatoms-&gt;setExtraCVForce(name,p);</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">         30 : }</span></a>
+<a name="650"><span class="lineNum">     650 </span>            : </a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         72 : double Atoms::getExtraCV(const std::string &amp;name) {</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         72 :   return mdatoms-&gt;getExtraCV(name);</span></a>
+<a name="653"><span class="lineNum">     653 </span>            : }</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         48 : void Atoms::updateExtraCVForce(const std::string &amp;name,double f) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">         48 :   mdatoms-&gt;updateExtraCVForce(name,f);</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">         48 : }</span></a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">         72 : void Atoms::setExtraCVNeeded(const std::string &amp;name,bool needed) {</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">         72 :   mdatoms-&gt;setExtraCVNeeded(name,needed);</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         72 : }</span></a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         10 : bool Atoms::isExtraCVNeeded(const std::string &amp;name) const {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         10 :   return mdatoms-&gt;isExtraCVNeeded(name);</span></a>
+<a name="665"><span class="lineNum">     665 </span>            : }</a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">     256144 : void Atoms::resetExtraCVNeeded() {</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">     256144 :   mdatoms-&gt;resetExtraCVNeeded();</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">     256144 : }</span></a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span>            : </a>
+<a name="672"><span class="lineNum">     672 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Atoms.h.func-sort-c.html b/coverage/core/Atoms.h.func-sort-c.html
new file mode 100644
index 0000000000..ae12008320
--- /dev/null
+++ b/coverage/core/Atoms.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Atoms.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Atoms.h<span style="font-size: 80%;"> (<a href="Atoms.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Atoms.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.h.gcov.html#207">_ZNK4PLMD5Atoms9getEnergyEv</a></td>
+              <td class="coverFnHi">3989</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.h.gcov.html#132">_ZN4PLMD5Atoms19DomainDecompositionC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Atoms.h.func.html b/coverage/core/Atoms.h.func.html
new file mode 100644
index 0000000000..e1828bfcdd
--- /dev/null
+++ b/coverage/core/Atoms.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Atoms.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Atoms.h<span style="font-size: 80%;"> (<a href="Atoms.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Atoms.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.h.gcov.html#132">_ZN4PLMD5Atoms19DomainDecompositionC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Atoms.h.gcov.html#207">_ZNK4PLMD5Atoms9getEnergyEv</a></td>
+              <td class="coverFnHi">3989</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Atoms.h.gcov.html b/coverage/core/Atoms.h.gcov.html
new file mode 100644
index 0000000000..d012a7da8c
--- /dev/null
+++ b/coverage/core/Atoms.h.gcov.html
@@ -0,0 +1,379 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Atoms.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Atoms.h<span style="font-size: 80%;"> (source / <a href="Atoms.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_Atoms_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_Atoms_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/TypesafePtr.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tensor.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/ForwardDecl.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;vector&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;map&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;string&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;memory&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class MDAtomsBase;</a>
+<a name="40"><span class="lineNum">      40 </span>            : class PlumedMain;</a>
+<a name="41"><span class="lineNum">      41 </span>            : class ActionAtomistic;</a>
+<a name="42"><span class="lineNum">      42 </span>            : class ActionWithVirtualAtom;</a>
+<a name="43"><span class="lineNum">      43 </span>            : class Pbc;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Class containing atom related quantities from the MD code.</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// IT IS STILL UNDOCUMENTED. IT PROBABLY NEEDS A STRONG CLEANUP</a>
+<a name="47"><span class="lineNum">      47 </span>            : class Atoms</a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span>            :   friend class ActionAtomistic;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   friend class ActionWithVirtualAtom;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   int natoms;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   bool unique_serial=false; // use unique in serial mode</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;AtomNumber&gt; unique;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;unsigned&gt; uniq_index;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Map global indexes to local indexes</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// E.g. g2l[i] is the position of atom i in the array passed from the MD engine.</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Called &quot;global to local&quot; since originally it was used to map global indexes to local</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// ones used in domain decomposition. However, it is now also used for the NAMD-like</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// interface, where only a small number of atoms is passed to plumed.</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;int&gt; g2l;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::vector&lt;Vector&gt; positions;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;Vector&gt; forces;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   std::vector&lt;double&gt; masses;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;double&gt; charges;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;ActionWithVirtualAtom*&gt; virtualAtomsActions;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   Tensor box;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   ForwardDecl&lt;Pbc&gt; pbc_fwd;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   Pbc&amp;   pbc=*pbc_fwd;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   Tensor virial;</a>
+<a name="70"><span class="lineNum">      70 </span>            : // this is the energy set by each processor:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   double md_energy;</a>
+<a name="72"><span class="lineNum">      72 </span>            : // this is the summed energy:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double energy;</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool   dataCanBeSet;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   bool   collectEnergy;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool   energyHasBeenSet;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   unsigned positionsHaveBeenSet;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   bool massesHaveBeenSet;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool chargesHaveBeenSet;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   bool boxHasBeenSet;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   unsigned forcesHaveBeenSet;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool virialHasBeenSet;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   bool massAndChargeOK;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   unsigned shuffledAtoms;</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   std::map&lt;std::string,std::vector&lt;AtomNumber&gt; &gt; groups;</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   void resizeVectors(unsigned);</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;int&gt; fullList;</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::unique_ptr&lt;MDAtomsBase&gt; mdatoms;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   PlumedMain &amp; plumed;</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   Units MDUnits;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   Units units;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   bool naturalUnits;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   bool MDnaturalUnits;</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   double timestep;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   double forceOnEnergy;</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : /// if set to true, all the forces in the global array are zeroes</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// at every step. It should not be necessary in general, but it is</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// for actions accessing to modifyGlobalForce() (e.g. FIT_TO_TEMPLATE).</a>
+<a name="109"><span class="lineNum">     109 </span>            :   bool zeroallforces;</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   double kbT;</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;ActionAtomistic*&gt; actions;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;int&gt;    gatindex;</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   bool asyncSent;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   bool atomsNeeded;</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   class DomainDecomposition:</a>
+<a name="120"><span class="lineNum">     120 </span>            :     public Communicator</a>
+<a name="121"><span class="lineNum">     121 </span>            :   {</a>
+<a name="122"><span class="lineNum">     122 </span>            :   public:</a>
+<a name="123"><span class="lineNum">     123 </span>            :     bool on;</a>
+<a name="124"><span class="lineNum">     124 </span>            :     bool async;</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :     std::vector&lt;Communicator::Request&gt; mpi_request_positions;</a>
+<a name="127"><span class="lineNum">     127 </span>            :     std::vector&lt;Communicator::Request&gt; mpi_request_index;</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :     std::vector&lt;double&gt; positionsToBeSent;</a>
+<a name="130"><span class="lineNum">     130 </span>            :     std::vector&lt;double&gt; positionsToBeReceived;</a>
+<a name="131"><span class="lineNum">     131 </span>            :     std::vector&lt;int&gt;    indexToBeSent;</a>
+<a name="132"><span class="lineNum">     132 </span>            :     std::vector&lt;int&gt;    indexToBeReceived;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">     186072 :     operator bool() const {return on;}</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     805268 :     DomainDecomposition():</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">     805268 :       on(false), async(false)</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     805268 :     {}</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     void enable(Communicator&amp; c);</a>
+<a name="138"><span class="lineNum">     138 </span>            :   };</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   DomainDecomposition dd;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   long long int ddStep;  //last step in which dd happened</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   void share(const std::vector&lt;AtomNumber&gt;&amp;);</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : public:</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   explicit Atoms(PlumedMain&amp;plumed);</a>
+<a name="148"><span class="lineNum">     148 </span>            :   ~Atoms();</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   void init();</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   void share();</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void shareAll();</a>
+<a name="154"><span class="lineNum">     154 </span>            :   void wait();</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void updateForces();</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   void setRealPrecision(int);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   int  getRealPrecision()const;</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   void setTimeStep(const TypesafePtr &amp;);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   double getTimeStep()const;</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   void setKbT(const TypesafePtr &amp;);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   double getKbT()const;</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   void setNatoms(int);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   int getNatoms()const;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   int getNVirtualAtoms()const;</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            :   const long long int&amp; getDdStep()const;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   const std::vector&lt;int&gt;&amp; getGatindex()const;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   const Pbc&amp; getPbc()const;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   void getLocalMasses(std::vector&lt;double&gt;&amp;);</a>
+<a name="174"><span class="lineNum">     174 </span>            :   void getLocalPositions(std::vector&lt;Vector&gt;&amp;);</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void getLocalForces(std::vector&lt;Vector&gt;&amp;);</a>
+<a name="176"><span class="lineNum">     176 </span>            :   void getLocalMDForces(std::vector&lt;Vector&gt;&amp;);</a>
+<a name="177"><span class="lineNum">     177 </span>            :   const Tensor&amp; getVirial()const;</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       3989 :   void setCollectEnergy(bool b) { collectEnergy=b; }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   void setDomainDecomposition(Communicator&amp;);</a>
+<a name="182"><span class="lineNum">     182 </span>            :   void setAtomsGatindex(const TypesafePtr &amp;,bool);</a>
+<a name="183"><span class="lineNum">     183 </span>            :   void setAtomsContiguous(int);</a>
+<a name="184"><span class="lineNum">     184 </span>            :   void setAtomsNlocal(int);</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   void startStep();</a>
+<a name="187"><span class="lineNum">     187 </span>            :   void setEnergy(const TypesafePtr &amp;);</a>
+<a name="188"><span class="lineNum">     188 </span>            :   void setBox(const TypesafePtr &amp;);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   void setVirial(const TypesafePtr &amp;);</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void setPositions(const TypesafePtr &amp;);</a>
+<a name="191"><span class="lineNum">     191 </span>            :   void setPositions(const TypesafePtr &amp;,int);</a>
+<a name="192"><span class="lineNum">     192 </span>            :   void setForces(const TypesafePtr &amp;);</a>
+<a name="193"><span class="lineNum">     193 </span>            :   void setForces(const TypesafePtr &amp;,int);</a>
+<a name="194"><span class="lineNum">     194 </span>            :   void setMasses(const TypesafePtr &amp;);</a>
+<a name="195"><span class="lineNum">     195 </span>            :   void setCharges(const TypesafePtr &amp;);</a>
+<a name="196"><span class="lineNum">     196 </span>            :   bool chargesWereSet() const ;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   bool boxWasSet() const ;</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   void MD2double(const TypesafePtr &amp; m,double&amp;d)const;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   void double2MD(const double&amp;d,const TypesafePtr &amp; m)const;</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   void createFullList(const TypesafePtr &amp;);</a>
+<a name="203"><span class="lineNum">     203 </span>            :   void getFullList(const TypesafePtr &amp;);</a>
+<a name="204"><span class="lineNum">     204 </span>            :   void clearFullList();</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   void add(ActionAtomistic*);</a>
+<a name="207"><span class="lineNum">     207 </span>            :   void remove(ActionAtomistic*);</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       3989 :   double getEnergy()const {plumed_assert(collectEnergy &amp;&amp; energyHasBeenSet); return energy;}</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         96 :   bool isEnergyNeeded()const {return collectEnergy;}</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         45 :   void setMDEnergyUnits(double d) {MDUnits.setEnergy(d);}</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        810 :   void setMDLengthUnits(double d) {MDUnits.setLength(d);}</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          6 :   void setMDTimeUnits(double d) {MDUnits.setTime(d);}</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        810 :   void setMDChargeUnits(double d) {MDUnits.setCharge(d);}</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        810 :   void setMDMassUnits(double d) {MDUnits.setMass(d);}</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   const Units&amp; getMDUnits() {return MDUnits;}</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         20 :   void setUnits(const Units&amp;u) {units=u;}</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   const Units&amp; getUnits() {return units;}</a>
+<a name="221"><span class="lineNum">     221 </span>            :   void updateUnits();</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   AtomNumber addVirtualAtom(ActionWithVirtualAtom*);</a>
+<a name="224"><span class="lineNum">     224 </span>            :   void removeVirtualAtom(ActionWithVirtualAtom*);</a>
+<a name="225"><span class="lineNum">     225 </span>            :   ActionWithVirtualAtom* getVirtualAtomsAction(AtomNumber)const;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   bool isVirtualAtom(AtomNumber)const;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   void insertGroup(const std::string&amp;name,const std::vector&lt;AtomNumber&gt;&amp;a);</a>
+<a name="228"><span class="lineNum">     228 </span>            :   void removeGroup(const std::string&amp;name);</a>
+<a name="229"><span class="lineNum">     229 </span>            :   void writeBinary(std::ostream&amp;)const;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   void readBinary(std::istream&amp;);</a>
+<a name="231"><span class="lineNum">     231 </span>            :   double getKBoltzmann()const;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   double getMDKBoltzmann()const;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   bool usingNaturalUnits()const;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         20 :   void setNaturalUnits(bool n) {naturalUnits=n;}</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   void setMDNaturalUnits(bool n) {MDnaturalUnits=n;}</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   void setExtraCV(const std::string &amp;name,const TypesafePtr &amp; p);</a>
+<a name="238"><span class="lineNum">     238 </span>            :   void setExtraCVForce(const std::string &amp;name,const TypesafePtr &amp; p);</a>
+<a name="239"><span class="lineNum">     239 </span>            :   double getExtraCV(const std::string &amp;name);</a>
+<a name="240"><span class="lineNum">     240 </span>            :   void updateExtraCVForce(const std::string &amp;name,double f);</a>
+<a name="241"><span class="lineNum">     241 </span>            :   void setExtraCVNeeded(const std::string &amp;name,bool needed=true);</a>
+<a name="242"><span class="lineNum">     242 </span>            :   bool isExtraCVNeeded(const std::string &amp;name) const;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   void resetExtraCVNeeded();</a>
+<a name="244"><span class="lineNum">     244 </span>            : };</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : inline</a>
+<a name="247"><span class="lineNum">     247 </span>            : int Atoms::getNatoms()const {</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">     800903 :   return natoms;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : inline</a>
+<a name="252"><span class="lineNum">     252 </span>            : int Atoms::getNVirtualAtoms()const {</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         10 :   return virtualAtomsActions.size();</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            : inline</a>
+<a name="257"><span class="lineNum">     257 </span>            : const long long int&amp; Atoms::getDdStep()const {</a>
+<a name="258"><span class="lineNum">     258 </span>            :   return ddStep;</a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : inline</a>
+<a name="262"><span class="lineNum">     262 </span>            : const std::vector&lt;int&gt;&amp; Atoms::getGatindex()const {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          9 :   return gatindex;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            : inline</a>
+<a name="267"><span class="lineNum">     267 </span>            : const Pbc&amp; Atoms::getPbc()const {</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        900 :   return pbc;</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : inline</a>
+<a name="272"><span class="lineNum">     272 </span>            : bool Atoms::isVirtualAtom(AtomNumber i)const {</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">    1384097 :   return i.index()&gt;=(unsigned) getNatoms();</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : inline</a>
+<a name="277"><span class="lineNum">     277 </span>            : ActionWithVirtualAtom* Atoms::getVirtualAtomsAction(AtomNumber i)const {</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       7234 :   return virtualAtomsActions[i.index()-getNatoms()];</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : inline</a>
+<a name="282"><span class="lineNum">     282 </span>            : bool Atoms::usingNaturalUnits() const {</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       2464 :   return naturalUnits || MDnaturalUnits;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            : }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : inline</a>
+<a name="287"><span class="lineNum">     287 </span>            : bool Atoms::chargesWereSet() const {</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     176490 :   return chargesHaveBeenSet;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : }</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : inline</a>
+<a name="292"><span class="lineNum">     292 </span>            : bool Atoms::boxWasSet() const {</a>
+<a name="293"><span class="lineNum">     293 </span>            :   return boxHasBeenSet;</a>
+<a name="294"><span class="lineNum">     294 </span>            : }</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            : inline</a>
+<a name="297"><span class="lineNum">     297 </span>            : const Tensor&amp; Atoms::getVirial()const {</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">        450 :   return virial;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : }</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : }</a>
+<a name="303"><span class="lineNum">     303 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLTool.cpp.func-sort-c.html b/coverage/core/CLTool.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ee8f25be2c
--- /dev/null
+++ b/coverage/core/CLTool.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLTool.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLTool.cpp<span style="font-size: 80%;"> (<a href="CLTool.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CLTool.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#209">_ZN4PLMD6CLTool5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#144">_ZN4PLMD6CLTool13readInputFileEiPPcP8_IO_FILES4_</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#68">_ZN4PLMD6CLTool19readCommandLineArgsEiPPcP8_IO_FILE</a></td>
+              <td class="coverFnHi">2972</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#126">_ZN4PLMD6CLTool21setRemainingToDefaultEP8_IO_FILE</a></td>
+              <td class="coverFnHi">3024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#58">_ZN4PLMD6CLTool9readInputEiPPcP8_IO_FILES4_</a></td>
+              <td class="coverFnHi">3024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#26">_ZN4PLMD13CLToolOptionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#32">_ZN4PLMD13CLToolOptionsC2ERKS0_RKNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#42">_ZN4PLMD6CLToolC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#49">_ZN4PLMD6CLTool9parseFlagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERb</a></td>
+              <td class="coverFnHi">20945</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#38">_ZN4PLMD6CLTool16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">58352</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLTool.cpp.func.html b/coverage/core/CLTool.cpp.func.html
new file mode 100644
index 0000000000..f4e8804d36
--- /dev/null
+++ b/coverage/core/CLTool.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLTool.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLTool.cpp<span style="font-size: 80%;"> (<a href="CLTool.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CLTool.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#26">_ZN4PLMD13CLToolOptionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#32">_ZN4PLMD13CLToolOptionsC2ERKS0_RKNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#144">_ZN4PLMD6CLTool13readInputFileEiPPcP8_IO_FILES4_</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#38">_ZN4PLMD6CLTool16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">58352</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#68">_ZN4PLMD6CLTool19readCommandLineArgsEiPPcP8_IO_FILE</a></td>
+              <td class="coverFnHi">2972</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#126">_ZN4PLMD6CLTool21setRemainingToDefaultEP8_IO_FILE</a></td>
+              <td class="coverFnHi">3024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#209">_ZN4PLMD6CLTool5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#49">_ZN4PLMD6CLTool9parseFlagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERb</a></td>
+              <td class="coverFnHi">20945</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#58">_ZN4PLMD6CLTool9readInputEiPPcP8_IO_FILES4_</a></td>
+              <td class="coverFnHi">3024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.cpp.gcov.html#42">_ZN4PLMD6CLToolC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLTool.cpp.gcov.html b/coverage/core/CLTool.cpp.gcov.html
new file mode 100644
index 0000000000..0dd688a694
--- /dev/null
+++ b/coverage/core/CLTool.cpp.gcov.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLTool.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLTool.cpp<span style="font-size: 80%;"> (source / <a href="CLTool.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : Keywords CLToolOptions::emptyKeys;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">       3088 : CLToolOptions::CLToolOptions(const std::string &amp;name):</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       3088 :   line(1,name),</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">       3088 :   keys(emptyKeys)</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">       3088 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       3088 : CLToolOptions::CLToolOptions(const CLToolOptions&amp; co, const Keywords&amp; k):</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       3088 :   line(co.line),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       3088 :   keys(k)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       3088 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      58352 : void CLTool::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     116704 :   keys.addFlag(&quot;--help/-h&quot;,false,&quot;print this help&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      58352 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       3088 : CLTool::CLTool(const CLToolOptions&amp; co ):</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       3088 :   name(co.line[0]),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       3088 :   keywords(co.keys),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       3088 :   inputdata(unset)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       3088 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      20945 : void CLTool::parseFlag( const std::string&amp;key, bool&amp;t ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      20945 :   plumed_massert(keywords.exists(key),&quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      41890 :   plumed_massert(keywords.style(key,&quot;flag&quot;),&quot;keyword &quot; + key + &quot; has not been registered as a flag&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   plumed_assert(inputData.count(key)&gt;0);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      41890 :   if( inputData[key]==&quot;true&quot;) t=true;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      37446 :   else if( inputData[key]==&quot;false&quot;) t=false;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   else plumed_error();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      20945 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       3024 : bool CLTool::readInput( int argc, char**argv, FILE* in, FILE*out ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       3024 :   plumed_massert( inputdata!=unset,&quot;You have not specified where your tool reads its input. &quot;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :                   &quot;If it is from the command line (like driver) add inputdata=commandline to the &quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            :                   &quot;tools constructor. If it reads everything from an input file (like simplemd) &quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            :                   &quot;add inputdata=ifile to the tools constructor&quot;);</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       3024 :   if(inputdata==commandline) return readCommandLineArgs( argc, argv, out );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         52 :   if(inputdata==ifile) return readInputFile( argc, argv, in, out );</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   return true;</a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       2972 : bool CLTool::readCommandLineArgs( int argc, char**argv, FILE*out ) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       2972 :   plumed_assert(inputdata==commandline);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       2972 :   std::string prefix(&quot;&quot;), a(&quot;&quot;), thiskey;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   // Set all flags to default false</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      56704 :   for(unsigned k=0; k&lt;keywords.size(); ++k) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      53732 :     thiskey=keywords.get(k);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     131760 :     if( keywords.style(thiskey,&quot;flag&quot;) ) inputData.insert(std::pair&lt;std::string,std::string&gt;(thiskey,&quot;false&quot;));</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   // Read command line arguments</a>
+<a name="81"><span class="lineNum">      81 </span>            :   bool printhelp=false;</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      12309 :   for(int i=1; i&lt;argc; i++) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      18674 :     a=prefix+argv[i];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       9337 :     if(a.length()==0) continue;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      18674 :     if(a==&quot;-h&quot; || a==&quot;--help&quot;) {</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :       printhelp=true;</a>
+<a name="87"><span class="lineNum">      87 </span>            :     } else {</a>
+<a name="88"><span class="lineNum">      88 </span>            :       bool found=false;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     304598 :       for(unsigned k=0; k&lt;keywords.size(); ++k) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">     295261 :         thiskey=keywords.get(k);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     590522 :         if( keywords.style(thiskey,&quot;flag&quot;) ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      60380 :           if( a==thiskey ) { found=true; inputData[thiskey]=&quot;true&quot;; }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :         } else {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     234881 :           if( a==thiskey ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       3299 :             prefix=thiskey+&quot;=&quot;; found=true;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       6598 :             inputData.insert(std::pair&lt;std::string,std::string&gt;(thiskey,&quot;&quot;));</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     463164 :           } else if(Tools::startWith(a,thiskey+&quot;=&quot;)) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       3818 :             a.erase(0,a.find(&quot;=&quot;)+1); prefix=&quot;&quot;; found=true;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :             if(inputData.count(thiskey)==0) {</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1040 :               inputData.insert(std::pair&lt;std::string,std::string&gt;(thiskey,a));</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :             } else {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       3298 :               inputData[thiskey]=a;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :             }</a>
+<a name="104"><span class="lineNum">     104 </span>            :           }</a>
+<a name="105"><span class="lineNum">     105 </span>            :         }</a>
+<a name="106"><span class="lineNum">     106 </span>            :       }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       9337 :       if(!found) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :         std::fprintf(stderr,&quot;ERROR in input for command line tool %s : %s option is unknown \n\n&quot;, name.c_str(), a.c_str() );</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :         std::fprintf(out,&quot;Usage: %s &lt; inputFile \n&quot;, name.c_str() );</a>
+<a name="110"><span class="lineNum">     110 </span>            :         std::fprintf(out,&quot;inputFile should contain one directive per line.  The directives should come from amongst the following\n\n&quot;);</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :         keywords.print( out );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :         printhelp=true;</a>
+<a name="113"><span class="lineNum">     113 </span>            :       }</a>
+<a name="114"><span class="lineNum">     114 </span>            :     }</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       9337 :     if(printhelp) break;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       2972 :   if(!printhelp) setRemainingToDefault(out);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       2972 :   if(printhelp) {</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     std::fprintf(out,&quot;Usage: %s [options] \n\n&quot;, name.c_str() );</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     keywords.print( out );</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       2972 :   return !printhelp;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       3024 : void CLTool::setRemainingToDefault(FILE* out) {</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::string def, thiskey;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      57764 :   for(unsigned k=0; k&lt;keywords.size(); ++k) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      54740 :     thiskey=keywords.get(k);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     109480 :     if( keywords.style(thiskey,&quot;compulsory&quot;) ) {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :       if( inputData.count(thiskey)==0 ) {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1644 :         if( keywords.getDefaultValue(thiskey,def) ) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1644 :           plumed_assert( def.length()&gt;0 );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       3288 :           inputData.insert(std::pair&lt;std::string,std::string&gt;(thiskey,def));</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :         } else {</a>
+<a name="138"><span class="lineNum">     138 </span>            :           std::fprintf(out,&quot;ERROR : argument %s is compulsory. Use --help option for help\n&quot;,thiskey.c_str() );</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :           plumed_error();</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :         }</a>
+<a name="141"><span class="lineNum">     141 </span>            :       }</a>
+<a name="142"><span class="lineNum">     142 </span>            :     }</a>
+<a name="143"><span class="lineNum">     143 </span>            :   }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       3024 : }</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         52 : bool CLTool::readInputFile( int argc, char**argv, FILE* in, FILE*out ) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         52 :   plumed_assert(inputdata==ifile);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   // Check if use is just asking for help</a>
+<a name="150"><span class="lineNum">     150 </span>            :   std::string a;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         95 :   for(int i=1; i&lt;argc; i++) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         43 :     a=argv[i];</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         43 :     if(a.length()==0) continue;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         86 :     if(a==&quot;-h&quot; || a==&quot;--help&quot;) {</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :       std::fprintf(out,&quot;Usage: %s &lt; inputFile \n&quot;, name.c_str() );</a>
+<a name="156"><span class="lineNum">     156 </span>            :       std::fprintf(out,&quot;inputFile should contain one directive per line.  The directives should come from amongst the following\n\n&quot;);</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :       keywords.print( out );</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :       return false;</a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   FILE* mystdin=in;</a>
+<a name="163"><span class="lineNum">     163 </span>            : // call fclose when fp_deleter goes out of scope</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         43 :   auto deleter=[](FILE* f) { std::fclose(f); };</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(nullptr,deleter);</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         52 :   if(argc==2) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         43 :     mystdin=std::fopen(argv[1],&quot;r&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         43 :     if(!mystdin) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot;ERROR: cannot open file %s\n\n&quot;,argv[1]);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :       std::fprintf(out,&quot;Usage: %s &lt; inputFile \n&quot;, name.c_str() );</a>
+<a name="172"><span class="lineNum">     172 </span>            :       std::fprintf(out,&quot;inputFile should contain one directive per line.  The directives should come from amongst the following\n\n&quot;);</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :       keywords.print( out );</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :       return false;</a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            :     fp_deleter.reset(mystdin);</a>
+<a name="177"><span class="lineNum">     177 </span>            :   }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         52 :   plumed_assert(mystdin);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   char buffer[256]; std::string line; line.resize(256);</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        864 :   while(fgets(buffer,256,mystdin)) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     line=buffer;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      24516 :     for(unsigned i=0; i&lt;line.length(); ++i) if(line[i]=='#' || line[i]=='\n') line.erase(i);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        812 :     Tools::stripLeadingAndTrailingBlanks( line );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        812 :     if(line.length()==0) continue;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        775 :     std::sscanf(line.c_str(),&quot;%255s&quot;,buffer);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        775 :     std::string keyword=buffer; bool found=false;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      16236 :     for(unsigned i=0; i&lt;keywords.size(); ++i) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      15461 :       std::string thiskey=keywords.get(i);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      15461 :       if(thiskey==keyword) {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :         found=true;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        775 :         std::size_t keypos=line.find_first_of(keyword)+keyword.length();</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1550 :         inputData.insert(std::pair&lt;std::string,std::string&gt;(thiskey,line.substr(keypos)));</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        775 :         Tools::stripLeadingAndTrailingBlanks( inputData[thiskey] );</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       }</a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        775 :     if(!found) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot;ERROR in input for command line tool %s : unknown keyword %s found in input file\n\n&quot;,name.c_str(),keyword.c_str());</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :       std::fprintf(out,&quot;Usage: %s &lt; inputFile \n&quot;, name.c_str() );</a>
+<a name="201"><span class="lineNum">     201 </span>            :       std::fprintf(out,&quot;inputFile should contain one directive per line.  The directives should come from amongst the following\n\n&quot;);</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :       keywords.print( out );</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       return false;</a>
+<a name="204"><span class="lineNum">     204 </span>            :     }</a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         52 :   setRemainingToDefault(out);</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   return true;</a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 : [[noreturn]] void CLTool::error( const std::string&amp; msg ) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   std::fprintf(stderr,&quot;ERROR : in input for command line tool %s : %s\n&quot;,name.c_str(),msg.c_str());</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLTool.h.func-sort-c.html b/coverage/core/CLTool.h.func-sort-c.html
new file mode 100644
index 0000000000..e54a08ccd4
--- /dev/null
+++ b/coverage/core/CLTool.h.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLTool.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLTool.h<span style="font-size: 80%;"> (<a href="CLTool.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryLo">70.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CLTool.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIfEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#97">_ZN4PLMD6CLToolD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#95">_ZNK4PLMD6CLTool11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorIiEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIyEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseImEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_RSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">166</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIxEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">852</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIiEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">1590</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">1698</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#97">_ZN4PLMD6CLToolD2Ev</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_RT_</a></td>
+              <td class="coverFnHi">22488</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLTool.h.func.html b/coverage/core/CLTool.h.func.html
new file mode 100644
index 0000000000..7dddcebe68
--- /dev/null
+++ b/coverage/core/CLTool.h.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLTool.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLTool.h<span style="font-size: 80%;"> (<a href="CLTool.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryLo">70.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CLTool.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_RSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">166</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorIiEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#115">_ZN4PLMD6CLTool11parseVectorIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISB_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS7_RT_</a></td>
+              <td class="coverFnHi">22488</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">1698</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIfEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIiEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">1590</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">852</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseImEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIxEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#101">_ZN4PLMD6CLTool5parseIyEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#97">_ZN4PLMD6CLToolD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#97">_ZN4PLMD6CLToolD2Ev</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLTool.h.gcov.html#95">_ZNK4PLMD6CLTool11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLTool.h.gcov.html b/coverage/core/CLTool.h.gcov.html
new file mode 100644
index 0000000000..183e1efef6
--- /dev/null
+++ b/coverage/core/CLTool.h.gcov.html
@@ -0,0 +1,241 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLTool.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLTool.h<span style="font-size: 80%;"> (source / <a href="CLTool.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryLo">70.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_CLTool_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_CLTool_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cstdio&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Keywords.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class Communicator;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       6176 : class CLToolOptions {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   friend class CLTool;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   friend class CLToolRegister;</a>
+<a name="38"><span class="lineNum">      38 </span>            : private:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;std::string&gt; line;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// The documentation for this command line tool</a>
+<a name="41"><span class="lineNum">      41 </span>            :   const Keywords&amp; keys;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static Keywords emptyKeys;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   explicit CLToolOptions(const std::string &amp;name);</a>
+<a name="45"><span class="lineNum">      45 </span>            :   CLToolOptions(const CLToolOptions&amp; co, const Keywords&amp; k);</a>
+<a name="46"><span class="lineNum">      46 </span>            : };</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : /**</a>
+<a name="49"><span class="lineNum">      49 </span>            : \ingroup INHERIT</a>
+<a name="50"><span class="lineNum">      50 </span>            : This is the abstract base class to use for implementing new command line tool, within it there</a>
+<a name="51"><span class="lineNum">      51 </span>            : is \ref AddingACLTool &quot;information&quot; as to how to go about implemneting a new tool.</a>
+<a name="52"><span class="lineNum">      52 </span>            : */</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : class CLTool {</a>
+<a name="55"><span class="lineNum">      55 </span>            : private:</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The name of this command line tool</a>
+<a name="57"><span class="lineNum">      57 </span>            :   const std::string name;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The list of keywords for this CLTool</a>
+<a name="59"><span class="lineNum">      59 </span>            :   const Keywords&amp; keywords;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// The data read in from the command line stored in a map with the keywords</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::map&lt;std::string,std::string&gt; inputData;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Read the arguments from the command line</a>
+<a name="63"><span class="lineNum">      63 </span>            :   bool readCommandLineArgs( int argc, char**argv, FILE*out );</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Read the arguments from an input file specified on the command line</a>
+<a name="65"><span class="lineNum">      65 </span>            :   bool readInputFile( int argc, char**argv, FILE* in, FILE*out );</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Set arguments from the default options provided to Keywords</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void setRemainingToDefault(FILE* out);</a>
+<a name="68"><span class="lineNum">      68 </span>            : public:</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Set the input data:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   void setInputData(const std::map&lt;std::string,std::string&gt;&amp;inputData) {</a>
+<a name="71"><span class="lineNum">      71 </span>            :     this-&gt;inputData=inputData;</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   const std::map&lt;std::string,std::string&gt;&amp;getInputData() {</a>
+<a name="74"><span class="lineNum">      74 </span>            :     return this-&gt;inputData;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span>            : protected:</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Get the value of one of the command line arguments</a>
+<a name="78"><span class="lineNum">      78 </span>            :   template&lt;class T&gt;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   bool parse(const std::string&amp;key,T&amp;t);</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Find out whether one of the command line flags is present or not</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void parseFlag(const std::string&amp;key,bool&amp;t);</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Crash the command line tool with an error</a>
+<a name="83"><span class="lineNum">      83 </span>            :   [[noreturn]] void error(const std::string&amp; msg);</a>
+<a name="84"><span class="lineNum">      84 </span>            :   template&lt;class T&gt;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   bool parseVector(const std::string&amp;key,std::vector&lt;T&gt;&amp;t);</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// How is the input specified on the command line or in an input file</a>
+<a name="88"><span class="lineNum">      88 </span>            :   enum {unset,commandline,ifile} inputdata;</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Create the help keywords</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit CLTool(const CLToolOptions&amp; co );</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Read the arguments from the command line</a>
+<a name="93"><span class="lineNum">      93 </span>            :   bool readInput( int argc, char**argv, FILE* in, FILE*out );</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// virtual function mapping to the specific main for each tool</a>
+<a name="95"><span class="lineNum">      95 </span>            :   virtual int main( FILE* in, FILE*out, Communicator&amp;pc )=0;</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// virtual function returning a one-line descriptor for the tool</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   virtual std::string description()const {return &quot;(no description available)&quot;;}</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : /// virtual destructor to allow inheritance</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       3088 :   virtual ~CLTool() {}</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : };</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : template&lt;class T&gt;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      27552 : bool CLTool::parse(const std::string&amp;key,T&amp;t) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      27552 :   plumed_massert(keywords.exists(key),&quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      55104 :   if(keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     if(inputData.count(key)==0) error(&quot;missing data for keyword &quot; + key);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       4092 :     bool check=Tools::convertNoexcept(inputData[key],t);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       4092 :     if(!check) error(&quot;data input for keyword &quot; + key + &quot; has wrong type&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     return true;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      21619 :   if( inputData.count(key)==0 ) return false;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1841 :   Tools::convert(inputData[key],t);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1841 :   return true;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : // very limited support and check: take more from core/Action.h parseVector</a>
+<a name="116"><span class="lineNum">     116 </span>            : template&lt;class T&gt;</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        366 : bool CLTool::parseVector(const std::string&amp;key,std::vector&lt;T&gt;&amp;t) {</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   // Check keyword has been registered</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        366 :   plumed_massert(keywords.exists(key), &quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   // initial size</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        366 :   unsigned size=t.size();</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   bool skipcheck=false;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        366 :   if(size==0) skipcheck=true; // if the vector in input has size zero, skip the check if size of input vector is the same of argument read</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   // check if there is some value</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        732 :   plumed_massert(inputData[key]!=&quot;false&quot;,&quot;compulsory keyword &quot;+std::string(key)+&quot;has no data&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        366 :   std::vector&lt;std::string&gt; words=Tools::getWords(inputData[key],&quot;\t\n ,&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        366 :   t.resize(0);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        366 :   if(words.size()==0)return false;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        773 :   for(unsigned i=0; i&lt;words.size(); ++i) {</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     T v;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        487 :     Tools::convert(words[i],v);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        487 :     t.push_back(v);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span>            :   // check the size</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        286 :   if( !skipcheck &amp;&amp; t.size()!=size ) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;vector read in for keyword  &quot;+key+&quot; has wrong size&quot; );</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::string def;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   T val;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        572 :   if ( keywords.style(key,&quot;compulsory&quot;) &amp;&amp; t.size()==0 ) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     if( keywords.getDefaultValue(key,def) ) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :       if( def.length()==0 || !Tools::convertNoexcept(def,val) ) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;ERROR in keyword &quot;+key+ &quot; has weird default value&quot; );</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :       } else {</a>
+<a name="149"><span class="lineNum">     149 </span>            :         // GB: before it was like this, but clearly if t.size()==0 this was not doing anything</a>
+<a name="150"><span class="lineNum">     150 </span>            :         // for(unsigned i=0; i&lt;t.size(); ++i) t[i]=val;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :         t.resize(1);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :         t[0]=val;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       }</a>
+<a name="154"><span class="lineNum">     154 </span>            :     } else {</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;keyword &quot; + key + &quot; is compulsory for this action&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     }</a>
+<a name="157"><span class="lineNum">     157 </span>            :   }</a>
+<a name="158"><span class="lineNum">     158 </span>            :   return true;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        366 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLToolMain.cpp.func-sort-c.html b/coverage/core/CLToolMain.cpp.func-sort-c.html
new file mode 100644
index 0000000000..83245da879
--- /dev/null
+++ b/coverage/core/CLToolMain.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLToolMain.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLToolMain.cpp<span style="font-size: 80%;"> (<a href="CLToolMain.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryMed">80.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CLToolMain.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#132">_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#38">_ZN4PLMD10CLToolMainC2Ev</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#45">_ZN4PLMD10CLToolMainD0Ev</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#45">_ZN4PLMD10CLToolMainD2Ev</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#51">_ZN4PLMD10CLToolMain3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">12906</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLToolMain.cpp.func.html b/coverage/core/CLToolMain.cpp.func.html
new file mode 100644
index 0000000000..e06a24bf0b
--- /dev/null
+++ b/coverage/core/CLToolMain.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLToolMain.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLToolMain.cpp<span style="font-size: 80%;"> (<a href="CLToolMain.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryMed">80.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CLToolMain.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#51">_ZN4PLMD10CLToolMain3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">12906</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#132">_ZN4PLMD10CLToolMain3runEiPPcP8_IO_FILES4_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#38">_ZN4PLMD10CLToolMainC2Ev</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#45">_ZN4PLMD10CLToolMainD0Ev</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolMain.cpp.gcov.html#45">_ZN4PLMD10CLToolMainD2Ev</a></td>
+              <td class="coverFnHi">4217</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLToolMain.cpp.gcov.html b/coverage/core/CLToolMain.cpp.gcov.html
new file mode 100644
index 0000000000..d6e5ac1228
--- /dev/null
+++ b/coverage/core/CLToolMain.cpp.gcov.html
@@ -0,0 +1,367 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLToolMain.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLToolMain.cpp<span style="font-size: 80%;"> (source / <a href="CLToolMain.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryMed">80.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLToolMain.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/DLLoader.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;string&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cstdio&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;iostream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;algorithm&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;memory&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;unordered_map&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       4217 : CLToolMain::CLToolMain():</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       4217 :   argc(0),</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       4217 :   in(stdin),</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       4217 :   out(stdout)</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : {</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       4217 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       8434 : CLToolMain::~CLToolMain() {</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : // empty destructor to delete unique_ptr</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       8434 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : #define CHECK_NULL(val,word) plumed_massert(val,&quot;NULL pointer received in cmd(\&quot;CLTool &quot; + word + &quot;\&quot;)&quot;);</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      12906 : void CLToolMain::cmd(const std::string&amp; word,const TypesafePtr &amp; val) {</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : // Enumerate all possible commands:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   enum {</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &quot;CLToolMainEnum.inc&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : // Static object (initialized once) containing the map of commands:</a>
+<a name="61"><span class="lineNum">      61 </span>            :   const static std::unordered_map&lt;std::string, int&gt; word_map = {</a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &quot;CLToolMainMap.inc&quot;</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      50130 :   };</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      12906 :   std::vector&lt;std::string&gt; words=Tools::getWords(word);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      12906 :   unsigned nw=words.size();</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      12906 :   if(nw==0) {</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     // do nothing</a>
+<a name="69"><span class="lineNum">      69 </span>            :   } else {</a>
+<a name="70"><span class="lineNum">      70 </span>            :     int iword=-1;</a>
+<a name="71"><span class="lineNum">      71 </span>            :     const char*const*v;</a>
+<a name="72"><span class="lineNum">      72 </span>            :     const char*vv;</a>
+<a name="73"><span class="lineNum">      73 </span>            :     const auto it=word_map.find(words[0]);</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      12906 :     if(it!=word_map.end()) iword=it-&gt;second;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12906 :     switch(iword) {</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :     case cmd_setArgc:</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       4133 :       CHECK_NULL(val,word);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       4133 :       argc=val.get&lt;int&gt;();</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       4133 :       break;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     case cmd_setArgv:</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       4133 :       CHECK_NULL(val,word);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       4133 :       v=val.get&lt;const char*const*&gt;(argc);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      26792 :       for(int i=0; i&lt;argc; ++i) argv.push_back(std::string(v[i]));</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :       break;</a>
+<a name="85"><span class="lineNum">      85 </span>            :     case cmd_setArgvLine:</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         84 :       CHECK_NULL(val,word);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :       vv=val.get&lt;const char*&gt;();</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         84 :       argv=Tools::getWords(vv);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         84 :       break;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :     case cmd_setIn:</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :       CHECK_NULL(val,word);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :       in=val.get&lt;FILE*&gt;();</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :     case cmd_setOut:</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          1 :       CHECK_NULL(val,word);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          1 :       out=val.get&lt;FILE*&gt;();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        338 :     case cmd_setMPIComm:</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        338 :       comm.Set_comm(val);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :       break;</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :     case cmd_setMPIFComm:</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :       comm.Set_fcomm(val);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :       break;</a>
+<a name="104"><span class="lineNum">     104 </span>            :     case cmd_run:</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       4217 :       CHECK_NULL(val,word);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       4217 :       argc=argv.size();</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :       {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      27364 :         int n=0; for(int i=0; i&lt;argc; ++i) n+=argv[i].length()+1;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       4217 :         std::vector&lt;char&gt; args(n);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       4217 :         std::vector&lt;char*&gt; vvv(argc);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :         char* ptr=&amp;args[0];</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      27364 :         for(int i=0; i&lt;argc; ++i) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      23147 :           vvv[i]=ptr;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     199570 :           for(unsigned c=0; c&lt;argv[i].length(); ++c) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     176423 :             *ptr=argv[i][c]; ptr++;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :           }</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      23147 :           *ptr=0; ptr++;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :         }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       4217 :         val.set(int(run(argc,&amp;vvv[0],in,out,comm)));</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :       }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       4217 :       break;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     default:</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;cannot interpret cmd(\&quot;CLTool &quot; + word + &quot;\&quot;). check plumed developers manual to see the available commands.&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :       break;</a>
+<a name="125"><span class="lineNum">     125 </span>            :     }</a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      12906 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : /**</a>
+<a name="130"><span class="lineNum">     130 </span>            : This is the entry point to the command line tools</a>
+<a name="131"><span class="lineNum">     131 </span>            : included in the plumed library.</a>
+<a name="132"><span class="lineNum">     132 </span>            : */</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       4217 : int CLToolMain::run(int argc, char **argv,FILE*in,FILE*out,Communicator&amp; pc) {</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   int i;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   bool printhelp=false;</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       4217 :   DLLoader dlloader;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       4217 :   std::string root=config::getPlumedRoot();</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   bool standalone_executable=false;</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : // Start parsing options</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       4217 :   std::string prefix(&quot;&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       4217 :   std::string a(&quot;&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       8012 :   for(i=1; i&lt;argc; i++) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      16024 :     a=prefix+argv[i];</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       8012 :     if(a.length()==0) continue;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      24036 :     if(a==&quot;help&quot; || a==&quot;-h&quot; || a==&quot;--help&quot;) {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :       printhelp=true;</a>
+<a name="152"><span class="lineNum">     152 </span>            :       break;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-mpi&quot;) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :       if(Communicator::initialized()) return 0;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :       else return 1;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-cregex&quot;) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :       return (config::hasCregex()?0:1);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-dlopen&quot;) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :       return (config::hasDlopen()?0:1);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-molfile&quot;) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :       return (config::hasMolfile()?0:1);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-external-molfile&quot;) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :       return (config::hasExternalMolfile()?0:1);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-zlib&quot;) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :       return (config::hasZlib()?0:1);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       8008 :     } else if(a==&quot;--has-xdrfile&quot;) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :       return 0; // always ok</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       8008 :     } else if(a==&quot;--is-installed&quot;) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        638 :       return (config::isInstalled()?0:1);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       7370 :     } else if(a==&quot;--no-mpi&quot;) {</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : // this is ignored, as it is parsed in main</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       3795 :       continue;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       3575 :     } else if(a==&quot;--mpi&quot;) {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : // this is ignored, as it is parsed in main</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       3575 :     } else if(a==&quot;--standalone-executable&quot;) {</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :       standalone_executable=true;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       7150 :     } else if(Tools::startWith(a,&quot;--load=&quot;)) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :       a.erase(0,a.find(&quot;=&quot;)+1);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :       prefix=&quot;&quot;;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :       void *p=dlloader.load(a);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :       if(!p) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :         std::fprintf(stderr,&quot;ERROR: cannot load library %s\n&quot;,a.c_str());</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :         std::fprintf(stderr,&quot;ERROR: %s\n&quot;,dlloader.error().c_str());</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :         return 1;</a>
+<a name="186"><span class="lineNum">     186 </span>            :       }</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       3575 :     } else if(a==&quot;--load&quot;) {</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :       prefix=&quot;--load=&quot;;</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       3575 :     } else if(a[0]=='-') {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :       std::string msg=&quot;ERROR: Unknown option &quot; +a;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot;%s\n&quot;,msg.c_str());</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :       return 1;</a>
+<a name="193"><span class="lineNum">     193 </span>            :     } else break;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : // Check if plumedRoot/patches/ directory exists (as a further check)</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       3579 :   if(!standalone_executable) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       3579 :     std::vector&lt;std::string&gt; files=Tools::ls(root);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       3579 :     if(find(files.begin(),files.end(),&quot;patches&quot;)==files.end()) {</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :       std::string msg=</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :         &quot;WARNING: I cannot find &quot;+root+&quot;/patches/ directory. Set PLUMED_ROOT or reinstall PLUMED\n\n&quot;;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot;%s&quot;,msg.c_str());</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       3579 :   }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : // Build list of available C++ tools:</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       3579 :   std::vector&lt;std::string&gt; availableCxx=cltoolRegister().list();</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : // Build list of available shell tools:</a>
+<a name="209"><span class="lineNum">     209 </span>            :   std::vector&lt;std::string&gt; availableShell;</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       3579 :   if(!standalone_executable) {</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     std::vector&lt;std::string&gt; tmp;</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       7158 :     tmp=Tools::ls(std::string(root+&quot;/scripts&quot;));</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      28632 :     for(unsigned j=0; j&lt;tmp.size(); ++j) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      25053 :       size_t ff=tmp[j].find(&quot;.sh&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      25053 :       if(ff==std::string::npos) tmp[j].erase();</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      25053 :       else                 tmp[j].erase(ff);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     }</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      28632 :     for(unsigned j=0; j&lt;tmp.size(); ++j) if(tmp[j].length()&gt;0) availableShell.push_back(tmp[j]);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       3579 :   }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       3579 :   if(printhelp) {</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     std::string msg=</a>
+<a name="223"><span class="lineNum">     223 </span>            :       &quot;Usage: plumed [options] [command] [command options]\n&quot;</a>
+<a name="224"><span class="lineNum">     224 </span>            :       &quot;  plumed [command] -h|--help: to print help for a specific command\n&quot;</a>
+<a name="225"><span class="lineNum">     225 </span>            :       &quot;Options:\n&quot;</a>
+<a name="226"><span class="lineNum">     226 </span>            :       &quot;  [help|-h|--help]          : to print this help\n&quot;</a>
+<a name="227"><span class="lineNum">     227 </span>            :       &quot;  [--is-installed]          : fails if plumed is not installed\n&quot;</a>
+<a name="228"><span class="lineNum">     228 </span>            :       &quot;  [--has-mpi]               : fails if plumed is running without MPI\n&quot;</a>
+<a name="229"><span class="lineNum">     229 </span>            :       &quot;  [--has-dlopen]            : fails if plumed is compiled without dlopen\n&quot;</a>
+<a name="230"><span class="lineNum">     230 </span>            :       &quot;  [--load LIB]              : loads a shared object (typically a plugin library)\n&quot;</a>
+<a name="231"><span class="lineNum">     231 </span>            :       &quot;  [--standalone-executable] : tells plumed not to look for commands implemented as scripts\n&quot;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          4 :       &quot;Commands:\n&quot;;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     std::fprintf(out,&quot;%s&quot;,msg.c_str());</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         68 :     for(unsigned j=0; j&lt;availableCxx.size(); ++j) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        128 :       auto cl=cltoolRegister().create(CLToolOptions(availableCxx[j]));</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         64 :       plumed_assert(cl);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        128 :       std::string manual=availableCxx[j]+&quot; : &quot;+cl-&gt;description();</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :       std::fprintf(out,&quot;  plumed %s\n&quot;, manual.c_str());</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         64 :     }</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         32 :     for(unsigned j=0; j&lt;availableShell.size(); ++j) {</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :       std::string manual;</a>
+<a name="242"><span class="lineNum">     242 </span>            : #ifdef __PLUMED_HAS_POPEN</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         56 :       std::string cmd=config::getEnvCommand()+&quot; \&quot;&quot;+root+&quot;/scripts/&quot;+availableShell[j]+&quot;.sh\&quot; --description&quot;;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         28 :       FILE *fp=popen(cmd.c_str(),&quot;r&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :       std::string line;</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         56 :       while(Tools::getline(fp,line))manual+=line;</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         28 :       pclose(fp);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : #else</a>
+<a name="249"><span class="lineNum">     249 </span>            :       manual=&quot;(doc not avail)&quot;;</a>
+<a name="250"><span class="lineNum">     250 </span>            : #endif</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         56 :       manual= availableShell[j]+&quot; : &quot;+manual;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :       std::fprintf(out,&quot;  plumed %s\n&quot;, manual.c_str());</a>
+<a name="253"><span class="lineNum">     253 </span>            :     }</a>
+<a name="254"><span class="lineNum">     254 </span>            :     return 0;</a>
+<a name="255"><span class="lineNum">     255 </span>            :   }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       3575 :   if(i==argc) {</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :     std::fprintf(out,&quot;%s&quot;,&quot;Nothing to do. Use 'plumed help' for help\n&quot;);</a>
+<a name="258"><span class="lineNum">     258 </span>            :     return 0;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : // this is the command to be executed:</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       3575 :   std::string command(argv[i]);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       3575 :   if(find(availableCxx.begin(),availableCxx.end(),command)!=availableCxx.end()) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       6048 :     auto cl=cltoolRegister().create(CLToolOptions(command));</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       3024 :     plumed_assert(cl);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :     // Read the command line options (returns false if we are just printing help)</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       3024 :     if( !cl-&gt;readInput( argc-i,&amp;argv[i],in,out ) ) { return 0; }</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       3024 :     int ret=cl-&gt;main(in,out,pc);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     return ret;</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       3024 :   }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        551 :   if(find(availableShell.begin(),availableShell.end(),command)!=availableShell.end()) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        551 :     plumed_massert(in==stdin,&quot;shell tools can only work on stdin&quot;);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        551 :     plumed_massert(out==stdout,&quot;shell tools can only work on stdin&quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       1102 :     std::string cmd=config::getEnvCommand()+&quot; \&quot;&quot;+root+&quot;/scripts/&quot;+command+&quot;.sh\&quot;&quot;;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       2089 :     for(int j=i+1; j&lt;argc; j++) cmd+=std::string(&quot; &quot;)+argv[j];</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        551 :     int r=std::system(cmd.c_str());</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : // this is necessary since system seems to return numbers which are multiple</a>
+<a name="280"><span class="lineNum">     280 </span>            : // of 256. this would make the interpretation by the shell wrong</a>
+<a name="281"><span class="lineNum">     281 </span>            : // I just return 1 in case of failure and 0 in case of success</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        551 :     if(r!=0) return 1;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        439 :     else return 0;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   std::string msg=&quot;ERROR: unknown command &quot; + command + &quot;. Use 'plumed help' for help&quot;;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :   std::fprintf(stderr,&quot;%s\n&quot;,msg.c_str());</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   return 1;</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       7796 : }</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLToolRegister.cpp.func-sort-c.html b/coverage/core/CLToolRegister.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5905952aca
--- /dev/null
+++ b/coverage/core/CLToolRegister.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLToolRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLToolRegister.cpp<span style="font-size: 80%;"> (<a href="CLToolRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryLo">67.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CLToolRegister.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#104">_ZNK4PLMD14CLToolRegister7getKeysERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#92">_ZN4PLMD14CLToolRegister11printManualERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKb</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#77">_ZN4PLMDlsERSoRKNS_14CLToolRegisterE</a></td>
+              <td class="coverFnHi">293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#66">_ZN4PLMD14CLToolRegister6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#61">_ZNK4PLMD14CLToolRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3089</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#114">_ZNK4PLMD14CLToolRegister4listB5cxx11Ev</a></td>
+              <td class="coverFnHi">3872</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#29">_ZN4PLMD14CLToolRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#50">_ZN4PLMD14CLToolRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS_6CLToolESt14default_deleteIS8_EERKNS_13CLToolOptionsEEPFvRNS_8KeywordsEE</a></td>
+              <td class="coverFnHi">66688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#42">_ZN4PLMD14CLToolRegister6removeEPFSt10unique_ptrINS_6CLToolESt14default_deleteIS2_EERKNS_13CLToolOptionsEE</a></td>
+              <td class="coverFnHi">66688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#37">_ZN4PLMD14cltoolRegisterEv</a></td>
+              <td class="coverFnHi">140337</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLToolRegister.cpp.func.html b/coverage/core/CLToolRegister.cpp.func.html
new file mode 100644
index 0000000000..ab306812f4
--- /dev/null
+++ b/coverage/core/CLToolRegister.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLToolRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLToolRegister.cpp<span style="font-size: 80%;"> (<a href="CLToolRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryLo">67.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CLToolRegister.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#92">_ZN4PLMD14CLToolRegister11printManualERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKb</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#50">_ZN4PLMD14CLToolRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS_6CLToolESt14default_deleteIS8_EERKNS_13CLToolOptionsEEPFvRNS_8KeywordsEE</a></td>
+              <td class="coverFnHi">66688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#66">_ZN4PLMD14CLToolRegister6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">3088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#42">_ZN4PLMD14CLToolRegister6removeEPFSt10unique_ptrINS_6CLToolESt14default_deleteIS2_EERKNS_13CLToolOptionsEE</a></td>
+              <td class="coverFnHi">66688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#29">_ZN4PLMD14CLToolRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#37">_ZN4PLMD14cltoolRegisterEv</a></td>
+              <td class="coverFnHi">140337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#77">_ZN4PLMDlsERSoRKNS_14CLToolRegisterE</a></td>
+              <td class="coverFnHi">293</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#114">_ZNK4PLMD14CLToolRegister4listB5cxx11Ev</a></td>
+              <td class="coverFnHi">3872</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#61">_ZNK4PLMD14CLToolRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3089</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CLToolRegister.cpp.gcov.html#104">_ZNK4PLMD14CLToolRegister7getKeysERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/CLToolRegister.cpp.gcov.html b/coverage/core/CLToolRegister.cpp.gcov.html
new file mode 100644
index 0000000000..204d6613d8
--- /dev/null
+++ b/coverage/core/CLToolRegister.cpp.gcov.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/CLToolRegister.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - CLToolRegister.cpp<span style="font-size: 80%;"> (source / <a href="CLToolRegister.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryLo">67.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CLToolRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CLTool.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;algorithm&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iostream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">       4168 : CLToolRegister::~CLToolRegister() {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">       4168 :   if(m.size()&gt;0) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :     std::string names=&quot;&quot;;</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 :     for(const auto &amp; p : m) names+=p.first+&quot; &quot;;</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;WARNING: CLTools &quot;+ names +&quot; has not been properly unregistered. This might lead to memory leak!!\n&quot;;</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   }</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       4168 : }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     140337 : CLToolRegister&amp; cltoolRegister() {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     140337 :   static CLToolRegister ans;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     140337 :   return ans;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : }</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      66688 : void CLToolRegister::remove(creator_pointer f) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">     483488 :   for(auto p=m.begin(); p!=m.end(); ++p) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">     483488 :     if((*p).second==f) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      66688 :       m.erase(p); break;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :     }</a>
+<a name="49"><span class="lineNum">      49 </span>            :   }</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      66688 : }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      66688 : void CLToolRegister::add(std::string key,creator_pointer f,keywords_pointer kf) {</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   if(m.count(key)) {</a>
+<a name="54"><span class="lineNum">      54 </span>            :     m.erase(key);</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :     disabled.insert(key);</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   } else {</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      66688 :     m.insert(std::pair&lt;std::string,creator_pointer&gt;(key,f));</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      66688 :     Keywords keys; kf(keys);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      66688 :     mk.insert(std::pair&lt;std::string,Keywords&gt;(key,keys));</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      66688 :   };</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      66688 : }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       3089 : bool CLToolRegister::check(const std::string &amp; key)const {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       3088 :   if(m.count(key)&gt;0) return true;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   return false;</a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       3088 : std::unique_ptr&lt;CLTool&gt; CLToolRegister::create(const CLToolOptions&amp;ao) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       3088 :   if(ao.line.size()&lt;1)return NULL;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       3088 :   std::unique_ptr&lt;CLTool&gt; cltool;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       3088 :   if(check(ao.line[0])) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       3088 :     CLToolOptions nao( ao,mk[ao.line[0]] );</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       6176 :     cltool=m[ao.line[0]](nao);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span>            :   return cltool;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       3088 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        293 : std::ostream &amp; operator&lt;&lt;(std::ostream &amp;log,const CLToolRegister&amp;ar) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        293 :   std::vector&lt;std::string&gt; s(ar.list());</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       4981 :   for(unsigned i=0; i&lt;s.size(); i++) log&lt;&lt;&quot;  &quot;&lt;&lt;s[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        293 :   if(!ar.disabled.empty()) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     s.assign(ar.disabled.size(),&quot;&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :     std::copy(ar.disabled.begin(),ar.disabled.end(),s.begin());</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :     std::sort(s.begin(),s.end());</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;+++++++ WARNING +++++++\n&quot;;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;The following keywords have been registered more than once and will be disabled:\n&quot;;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;s.size(); i++) log&lt;&lt;&quot;  - &quot;&lt;&lt;s[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;+++++++ END WARNING +++++++\n&quot;;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   };</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        293 :   return log;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        293 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 : bool CLToolRegister::printManual( const std::string&amp; cltool, const bool&amp; spelling ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          1 :   if( spelling &amp;&amp; check(cltool) ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     mk[cltool].print_spelling();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     return true;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          1 :   } else if ( check(cltool) ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     mk[cltool].print_html();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     return true;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   } else {</a>
+<a name="102"><span class="lineNum">     102 </span>            :     return false;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 : std::vector&lt;std::string&gt; CLToolRegister::getKeys(const std::string&amp; cltool)const {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   if ( check(cltool) ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :     return mk.find(cltool)-&gt;second.getKeys();</a>
+<a name="109"><span class="lineNum">     109 </span>            :   } else {</a>
+<a name="110"><span class="lineNum">     110 </span>            :     std::vector&lt;std::string&gt; empty;</a>
+<a name="111"><span class="lineNum">     111 </span>            :     return empty;</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       3872 : std::vector&lt;std::string&gt; CLToolRegister::list()const {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;std::string&gt; s;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      65824 :   for(const auto &amp; it : m) s.push_back(it.first);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       3872 :   std::sort(s.begin(),s.end());</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       3872 :   return s;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Colvar.cpp.func-sort-c.html b/coverage/core/Colvar.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6572a32f7d
--- /dev/null
+++ b/coverage/core/Colvar.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Colvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Colvar.cpp<span style="font-size: 80%;"> (<a href="Colvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Colvar.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#27">_ZN4PLMD6ColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#27">_ZN4PLMD6ColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1898</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#36">_ZN4PLMD6Colvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">1915</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#43">_ZN4PLMD6Colvar12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EE</a></td>
+              <td class="coverFnHi">2286</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#51">_ZN4PLMD6Colvar5applyEv</a></td>
+              <td class="coverFnHi">115636</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#114">_ZN4PLMD6Colvar22setBoxDerivativesNoPbcEPNS_5ValueE</a></td>
+              <td class="coverFnHi">190405</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Colvar.cpp.func.html b/coverage/core/Colvar.cpp.func.html
new file mode 100644
index 0000000000..256af415ed
--- /dev/null
+++ b/coverage/core/Colvar.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Colvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Colvar.cpp<span style="font-size: 80%;"> (<a href="Colvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Colvar.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#43">_ZN4PLMD6Colvar12requestAtomsERKSt6vectorINS_10AtomNumberESaIS2_EE</a></td>
+              <td class="coverFnHi">2286</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#36">_ZN4PLMD6Colvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">1915</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#114">_ZN4PLMD6Colvar22setBoxDerivativesNoPbcEPNS_5ValueE</a></td>
+              <td class="coverFnHi">190405</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#51">_ZN4PLMD6Colvar5applyEv</a></td>
+              <td class="coverFnHi">115636</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#27">_ZN4PLMD6ColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.cpp.gcov.html#27">_ZN4PLMD6ColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1898</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Colvar.cpp.gcov.html b/coverage/core/Colvar.cpp.gcov.html
new file mode 100644
index 0000000000..2250985ae1
--- /dev/null
+++ b/coverage/core/Colvar.cpp.gcov.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Colvar.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Colvar.cpp<span style="font-size: 80%;"> (source / <a href="Colvar.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;vector&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       1898 : Colvar::Colvar(const ActionOptions&amp;ao):</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :   Action(ao),</a>
+<a name="31"><span class="lineNum">      31 </span>            :   ActionAtomistic(ao),</a>
+<a name="32"><span class="lineNum">      32 </span>            :   ActionWithValue(ao),</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       1898 :   isEnergy(false),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       1898 :   isExtraCV(false)</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       1898 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       1915 : void Colvar::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       1915 :   Action::registerKeywords( keys );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       1915 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       1915 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       3830 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       1915 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       2286 : void Colvar::requestAtoms(const std::vector&lt;AtomNumber&gt; &amp; a) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       2286 :   plumed_massert(!isEnergy,&quot;request atoms should not be called if this is energy&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : // Tell actionAtomistic what atoms we are getting</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       2286 :   ActionAtomistic::requestAtoms(a);</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : // Resize the derivatives of all atoms</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       6013 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) getPntrToComponent(i)-&gt;resizeDerivatives(3*a.size()+9);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       2285 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     115636 : void Colvar::apply() {</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;Vector&gt;&amp;   f(modifyForces());</a>
+<a name="55"><span class="lineNum">      55 </span>            :   Tensor&amp;           v(modifyVirial());</a>
+<a name="56"><span class="lineNum">      56 </span>            :   const unsigned    nat=getNumberOfAtoms();</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">     115636 :   const unsigned    ncp=getNumberOfComponents();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">     115636 :   const unsigned    fsz=f.size();</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned stride=1;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   unsigned rank=0;</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     115636 :   if(ncp&gt;4*comm.Get_size()) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       1560 :     stride=comm.Get_size();</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       1560 :     rank=comm.Get_rank();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     115636 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     115636 :   if(nt&gt;ncp/(4*stride)) nt=1;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     115636 :   if(!isEnergy &amp;&amp; !isExtraCV) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     111599 :     #pragma omp parallel num_threads(nt)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :     {</a>
+<a name="73"><span class="lineNum">      73 </span>            :       std::vector&lt;Vector&gt; omp_f(fsz);</a>
+<a name="74"><span class="lineNum">      74 </span>            :       Tensor              omp_v;</a>
+<a name="75"><span class="lineNum">      75 </span>            :       std::vector&lt;double&gt; forces(3*nat+9);</a>
+<a name="76"><span class="lineNum">      76 </span>            :       #pragma omp for</a>
+<a name="77"><span class="lineNum">      77 </span>            :       for(unsigned i=rank; i&lt;ncp; i+=stride) {</a>
+<a name="78"><span class="lineNum">      78 </span>            :         if(getPntrToComponent(i)-&gt;applyForce(forces)) {</a>
+<a name="79"><span class="lineNum">      79 </span>            :           for(unsigned j=0; j&lt;nat; ++j) {</a>
+<a name="80"><span class="lineNum">      80 </span>            :             omp_f[j][0]+=forces[3*j+0];</a>
+<a name="81"><span class="lineNum">      81 </span>            :             omp_f[j][1]+=forces[3*j+1];</a>
+<a name="82"><span class="lineNum">      82 </span>            :             omp_f[j][2]+=forces[3*j+2];</a>
+<a name="83"><span class="lineNum">      83 </span>            :           }</a>
+<a name="84"><span class="lineNum">      84 </span>            :           omp_v(0,0)+=forces[3*nat+0];</a>
+<a name="85"><span class="lineNum">      85 </span>            :           omp_v(0,1)+=forces[3*nat+1];</a>
+<a name="86"><span class="lineNum">      86 </span>            :           omp_v(0,2)+=forces[3*nat+2];</a>
+<a name="87"><span class="lineNum">      87 </span>            :           omp_v(1,0)+=forces[3*nat+3];</a>
+<a name="88"><span class="lineNum">      88 </span>            :           omp_v(1,1)+=forces[3*nat+4];</a>
+<a name="89"><span class="lineNum">      89 </span>            :           omp_v(1,2)+=forces[3*nat+5];</a>
+<a name="90"><span class="lineNum">      90 </span>            :           omp_v(2,0)+=forces[3*nat+6];</a>
+<a name="91"><span class="lineNum">      91 </span>            :           omp_v(2,1)+=forces[3*nat+7];</a>
+<a name="92"><span class="lineNum">      92 </span>            :           omp_v(2,2)+=forces[3*nat+8];</a>
+<a name="93"><span class="lineNum">      93 </span>            :         }</a>
+<a name="94"><span class="lineNum">      94 </span>            :       }</a>
+<a name="95"><span class="lineNum">      95 </span>            :       #pragma omp critical</a>
+<a name="96"><span class="lineNum">      96 </span>            :       {</a>
+<a name="97"><span class="lineNum">      97 </span>            :         for(unsigned j=0; j&lt;nat; ++j) f[j]+=omp_f[j];</a>
+<a name="98"><span class="lineNum">      98 </span>            :         v+=omp_v;</a>
+<a name="99"><span class="lineNum">      99 </span>            :       }</a>
+<a name="100"><span class="lineNum">     100 </span>            :     }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     111599 :     if(ncp&gt;4*comm.Get_size()) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1560 :       if(fsz&gt;0) comm.Sum(&amp;f[0][0],3*fsz);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1560 :       comm.Sum(&amp;v[0][0],9);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :     }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       4037 :   } else if( isEnergy ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       3989 :     std::vector&lt;double&gt; forces(1);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       3989 :     if(getPntrToComponent(0)-&gt;applyForce(forces)) modifyForceOnEnergy()+=forces[0];</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         48 :   } else if( isExtraCV ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         48 :     std::vector&lt;double&gt; forces(1);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         48 :     if(getPntrToComponent(0)-&gt;applyForce(forces)) modifyForceOnExtraCV()+=forces[0];</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     115636 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     190405 : void Colvar::setBoxDerivativesNoPbc(Value* v) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     190405 :   Tensor virial;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   unsigned nat=getNumberOfAtoms();</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">   33615697 :   for(unsigned i=0; i&lt;nat; i++) virial-=Tensor(getPosition(i),</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">   16712646 :                                           Vector(v-&gt;getDerivative(3*i+0),</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :                                               v-&gt;getDerivative(3*i+1),</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">   33425292 :                                               v-&gt;getDerivative(3*i+2)));</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     190405 :   setBoxDerivatives(v,virial);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     190405 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Colvar.h.func-sort-c.html b/coverage/core/Colvar.h.func-sort-c.html
new file mode 100644
index 0000000000..5f8eced252
--- /dev/null
+++ b/coverage/core/Colvar.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Colvar.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Colvar.h<span style="font-size: 80%;"> (<a href="Colvar.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Colvar.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#67">_ZN4PLMD6ColvarD2Ev</a></td>
+              <td class="coverFnHi">1897</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#110">_ZN4PLMD6Colvar22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4913</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#100">_ZN4PLMD6Colvar17setBoxDerivativesERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">13257</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#105">_ZN4PLMD6Colvar22setBoxDerivativesNoPbcEv</a></td>
+              <td class="coverFnHi">119018</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#81">_ZN4PLMD6Colvar17setBoxDerivativesEPNS_5ValueERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">229075</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#95">_ZN4PLMD6Colvar19setAtomsDerivativesEiRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">16401018</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#73">_ZN4PLMD6Colvar19setAtomsDerivativesEPNS_5ValueEiRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">18212413</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Colvar.h.func.html b/coverage/core/Colvar.h.func.html
new file mode 100644
index 0000000000..36979603c0
--- /dev/null
+++ b/coverage/core/Colvar.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Colvar.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Colvar.h<span style="font-size: 80%;"> (<a href="Colvar.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Colvar.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#81">_ZN4PLMD6Colvar17setBoxDerivativesEPNS_5ValueERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">229075</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#100">_ZN4PLMD6Colvar17setBoxDerivativesERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">13257</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#73">_ZN4PLMD6Colvar19setAtomsDerivativesEPNS_5ValueEiRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">18212413</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#95">_ZN4PLMD6Colvar19setAtomsDerivativesEiRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">16401018</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#110">_ZN4PLMD6Colvar22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4913</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#105">_ZN4PLMD6Colvar22setBoxDerivativesNoPbcEv</a></td>
+              <td class="coverFnHi">119018</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Colvar.h.gcov.html#67">_ZN4PLMD6ColvarD2Ev</a></td>
+              <td class="coverFnHi">1897</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Colvar.h.gcov.html b/coverage/core/Colvar.h.gcov.html
new file mode 100644
index 0000000000..d57b423b7d
--- /dev/null
+++ b/coverage/core/Colvar.h.gcov.html
@@ -0,0 +1,195 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Colvar.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Colvar.h<span style="font-size: 80%;"> (source / <a href="Colvar.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_Colvar_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_Colvar_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #define PLUMED_COLVAR_INIT(ao) Action(ao),Colvar(ao)</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /**</a>
+<a name="34"><span class="lineNum">      34 </span>            : \ingroup INHERIT</a>
+<a name="35"><span class="lineNum">      35 </span>            : This is the abstract base class to use for implementing new collective variables, within it there is</a>
+<a name="36"><span class="lineNum">      36 </span>            : \ref AddingAColvar &quot;information&quot; as to how to go about implementing a new CV.</a>
+<a name="37"><span class="lineNum">      37 </span>            : */</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class Colvar :</a>
+<a name="40"><span class="lineNum">      40 </span>            :   public ActionAtomistic,</a>
+<a name="41"><span class="lineNum">      41 </span>            :   public ActionWithValue</a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span>            : private:</a>
+<a name="44"><span class="lineNum">      44 </span>            : protected:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   bool isEnergy;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   bool isExtraCV;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void requestAtoms(const std::vector&lt;AtomNumber&gt; &amp; a);</a>
+<a name="48"><span class="lineNum">      48 </span>            : // Set the derivatives for a particular atom equal to the input Vector</a>
+<a name="49"><span class="lineNum">      49 </span>            : // This routine is called setAtomsDerivatives because not because you</a>
+<a name="50"><span class="lineNum">      50 </span>            : // are setting the derivative of many atoms but because you are setting</a>
+<a name="51"><span class="lineNum">      51 </span>            : // the derivatives of a particular atom.  The s is an apostrophe s</a>
+<a name="52"><span class="lineNum">      52 </span>            : // but you can't put apostrophes in function names</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void           setAtomsDerivatives(int,const Vector&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void           setAtomsDerivatives(Value*,int,const Vector&amp;);</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void           setBoxDerivatives(const Tensor&amp;);</a>
+<a name="56"><span class="lineNum">      56 </span>            :   void           setBoxDerivatives(Value*,const Tensor&amp;);</a>
+<a name="57"><span class="lineNum">      57 </span>            :   const Tensor &amp; getBoxDerivatives()const;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   const double &amp; getForce()const;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void apply() override;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Set box derivatives automatically.</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// It should be called after the setAtomsDerivatives has been used for all</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// single atoms.</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// \warning It only works for collective variable NOT using PBCs!</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void           setBoxDerivativesNoPbc();</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void           setBoxDerivativesNoPbc(Value*);</a>
+<a name="66"><span class="lineNum">      66 </span>            : public:</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     116006 :   bool checkIsEnergy() {return isEnergy;}</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   explicit Colvar(const ActionOptions&amp;);</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1897 :   ~Colvar() {}</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="71"><span class="lineNum">      71 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="72"><span class="lineNum">      72 </span>            : };</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : inline</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">   18212413 : void Colvar::setAtomsDerivatives(Value*v,int i,const Vector&amp;d) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">   18212413 :   v-&gt;addDerivative(3*i+0,d[0]);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">   18212413 :   v-&gt;addDerivative(3*i+1,d[1]);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">   18212413 :   v-&gt;addDerivative(3*i+2,d[2]);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">   18212413 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : inline</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     229075 : void Colvar::setBoxDerivatives(Value* v,const Tensor&amp;d) {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   unsigned nat=getNumberOfAtoms();</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+0,d(0,0));</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+1,d(0,1));</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+2,d(0,2));</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+3,d(1,0));</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+4,d(1,1));</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+5,d(1,2));</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+6,d(2,0));</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+7,d(2,1));</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     229075 :   v-&gt;addDerivative(3*nat+8,d(2,2));</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     229075 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : inline</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">   16401018 : void Colvar::setAtomsDerivatives(int i,const Vector&amp;d) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">   16401018 :   setAtomsDerivatives(getPntrToValue(),i,d);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">   16401018 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : inline</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      13257 : void Colvar::setBoxDerivatives(const Tensor&amp;d) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      13257 :   setBoxDerivatives(getPntrToValue(),d);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      13257 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : inline</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">     119018 : void Colvar::setBoxDerivativesNoPbc() {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     119018 :   setBoxDerivativesNoPbc(getPntrToValue());</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     119018 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : inline</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       4913 : unsigned Colvar::getNumberOfDerivatives() {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       4913 :   return 3*getNumberOfAtoms() + 9;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/DataFetchingObject.cpp.func-sort-c.html b/coverage/core/DataFetchingObject.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4b5d9980d9
--- /dev/null
+++ b/coverage/core/DataFetchingObject.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/DataFetchingObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - DataFetchingObject.cpp<span style="font-size: 80%;"> (<a href="DataFetchingObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryLo">68.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DataFetchingObject.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#91">_ZN4PLMD18DataFetchingObject9get_shapeERKNS_9ActionSetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESB_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#140">_ZN4PLMD23DataFetchingObjectTypedIfE14finishDataGrabEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#119">_ZN4PLMD23DataFetchingObjectTypedIfE7setDataERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#113">_ZN4PLMD23DataFetchingObjectTypedIfEC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIfED0Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIfED2Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#70">_ZN4PLMD18DataFetchingObject8get_rankERKNS_9ActionSetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESB_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">64</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#119">_ZN4PLMD23DataFetchingObjectTypedIdE7setDataERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">64</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#64">_ZN4PLMD18DataFetchingObject10findActionERKNS_9ActionSetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#140">_ZN4PLMD23DataFetchingObjectTypedIdE14finishDataGrabEv</a></td>
+              <td class="coverFnHi">254039</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#58">_ZNK4PLMD18DataFetchingObject8activateEv</a></td>
+              <td class="coverFnHi">256426</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#113">_ZN4PLMD23DataFetchingObjectTypedIdEC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">806144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIdED0Ev</a></td>
+              <td class="coverFnHi">806144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIdED2Ev</a></td>
+              <td class="coverFnHi">806144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#43">_ZN4PLMD18DataFetchingObject6createEjRNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">806145</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#53">_ZN4PLMD18DataFetchingObjectC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">806145</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/DataFetchingObject.cpp.func.html b/coverage/core/DataFetchingObject.cpp.func.html
new file mode 100644
index 0000000000..5c8ebcac2c
--- /dev/null
+++ b/coverage/core/DataFetchingObject.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/DataFetchingObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - DataFetchingObject.cpp<span style="font-size: 80%;"> (<a href="DataFetchingObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryLo">68.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DataFetchingObject.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#64">_ZN4PLMD18DataFetchingObject10findActionERKNS_9ActionSetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#43">_ZN4PLMD18DataFetchingObject6createEjRNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">806145</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#70">_ZN4PLMD18DataFetchingObject8get_rankERKNS_9ActionSetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESB_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">64</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#91">_ZN4PLMD18DataFetchingObject9get_shapeERKNS_9ActionSetERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESB_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#53">_ZN4PLMD18DataFetchingObjectC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">806145</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#140">_ZN4PLMD23DataFetchingObjectTypedIdE14finishDataGrabEv</a></td>
+              <td class="coverFnHi">254039</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#119">_ZN4PLMD23DataFetchingObjectTypedIdE7setDataERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">64</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#113">_ZN4PLMD23DataFetchingObjectTypedIdEC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">806144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIdED0Ev</a></td>
+              <td class="coverFnHi">806144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIdED2Ev</a></td>
+              <td class="coverFnHi">806144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#140">_ZN4PLMD23DataFetchingObjectTypedIfE14finishDataGrabEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#119">_ZN4PLMD23DataFetchingObjectTypedIfE7setDataERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#113">_ZN4PLMD23DataFetchingObjectTypedIfEC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIfED0Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#38">_ZN4PLMD23DataFetchingObjectTypedIfED2Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.cpp.gcov.html#58">_ZNK4PLMD18DataFetchingObject8activateEv</a></td>
+              <td class="coverFnHi">256426</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/DataFetchingObject.cpp.gcov.html b/coverage/core/DataFetchingObject.cpp.gcov.html
new file mode 100644
index 0000000000..c47ee36124
--- /dev/null
+++ b/coverage/core/DataFetchingObject.cpp.gcov.html
@@ -0,0 +1,235 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/DataFetchingObject.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - DataFetchingObject.cpp<span style="font-size: 80%;"> (source / <a href="DataFetchingObject.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryLo">68.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DataFetchingObject.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Value.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/TypesafePtr.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : template &lt;class T&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : class DataFetchingObjectTyped : public DataFetchingObject {</a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// A map containing the data we are grabbing</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::map&lt;std::string,TypesafePtr&gt; data;</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   explicit DataFetchingObjectTyped(PlumedMain&amp;plumed);</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">    1612290 :   ~DataFetchingObjectTyped() {}</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   void setData( const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; outval ) override;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   void finishDataGrab() override;</a>
+<a name="43"><span class="lineNum">      43 </span>            : };</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">     806145 : std::unique_ptr&lt;DataFetchingObject&gt; DataFetchingObject::create(unsigned n, PlumedMain&amp; p) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">     806145 :   if(n==sizeof(double)) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">     806144 :     return Tools::make_unique&lt;DataFetchingObjectTyped&lt;double&gt;&gt;(p);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :   } else  if(n==sizeof(float)) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :     return Tools::make_unique&lt;DataFetchingObjectTyped&lt;float&gt;&gt;(p);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   }</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   std::string pp; Tools::convert(n,pp);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;cannot create an MD interface with sizeof(real)==&quot;+ pp);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">     806145 : DataFetchingObject::DataFetchingObject(PlumedMain&amp;p):</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     806145 :   plumed(p)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">     806145 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">     256426 : bool DataFetchingObject::activate() const {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">     257066 :   for(unsigned j=0; j&lt;myactions.size(); ++j) myactions[j]-&gt;activate();</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     256426 :   if( myactions.size()&gt;0 ) return true;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   return false;</a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        128 : ActionWithValue* DataFetchingObject::findAction( const ActionSet&amp; a, const std::string&amp; key ) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        128 :   std::string aname = key; std::size_t dot = key.find(&quot;.&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        128 :   if( dot!=std::string::npos ) aname = key.substr(0,dot);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        256 :   return a.selectWithLabel&lt;ActionWithValue*&gt;( aname );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         64 : void DataFetchingObject::get_rank( const ActionSet&amp; a, const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; dims ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         64 :   plumed_assert( Tools::getWords(key,&quot;\t\n ,&quot;).size()==1 );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         64 :   plumed_massert( key.find(&quot;*&quot;)==std::string::npos, &quot;cannot use wildcards in python interface&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            :   // Find the appropriate action and store value containing quantity of interest</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         64 :   ActionWithValue* myv = findAction( a, key );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         64 :   Value* val = myv-&gt;copyOutput( key );</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   // Now work out what we are returning for this action</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         64 :   if( type==&quot;&quot; ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :     // Return a single value in this case</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         64 :     dims.set(long(1));</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   } else if( type==&quot;derivatives&quot; ) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;not yet implemented&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   } else if( type==&quot;forces&quot; ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;not yet implemented&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   } else {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;invalid type specifier&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         64 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : void DataFetchingObject::get_shape( const ActionSet&amp; a, const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; dims ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   plumed_assert( Tools::getWords(key,&quot;\t\n ,&quot;).size()==1 );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   plumed_massert( key.find(&quot;*&quot;)==std::string::npos, &quot;cannot use wildcards in python interface&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Find the appropriate action and store value containing quantity of interest</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   ActionWithValue* myv = findAction( a, key );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   Value* val = myv-&gt;copyOutput( key );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   // Now work out what we are returning for this action</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   if( type==&quot;&quot; ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :     // Return a single value in this case</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     dims.set(long(1));</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   } else if( type==&quot;derivatives&quot; ) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;not yet implemented&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   } else if( type==&quot;forces&quot; ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;not yet implemented&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   } else {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;invalid type specifier&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : template &lt;class T&gt;</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     806145 : DataFetchingObjectTyped&lt;T&gt;::DataFetchingObjectTyped(PlumedMain&amp;p):</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     806145 :   DataFetchingObject(p)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     806145 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : template &lt;class T&gt;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         64 : void DataFetchingObjectTyped&lt;T&gt;::setData( const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; outval ) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         64 :   plumed_assert( Tools::getWords(key,&quot;\t\n ,&quot;).size()==1 );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         64 :   plumed_massert( key.find(&quot;*&quot;)==std::string::npos, &quot;cannot use wildcards in python interface&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        128 :   plumed_massert( !data.count(key + &quot; &quot; + type), &quot;already collecting this data elsewhere&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   // Add the space to store the data to the data map</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         64 :   T* f=outval.get&lt;T*&gt;();</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        128 :   data.insert(std::pair&lt;std::string,TypesafePtr&gt;(key + &quot; &quot; + type,f));</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :   // Find the appropriate action and store value containing quantity of interest</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         64 :   ActionWithValue* myv = DataFetchingObject::findAction( plumed.getActionSet(), key );</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Store the action if not already stored</a>
+<a name="132"><span class="lineNum">     132 </span>            :   bool found=false;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       1056 :   for(const auto &amp; p : myactions) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        992 :     if( p-&gt;getLabel()==myv-&gt;getLabel() ) { found=true; break; }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         64 :   if( !found ) myactions.push_back( myv );</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   // Store the value</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         64 :   myvalues.push_back( myv-&gt;copyOutput( key ) );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         64 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : template &lt;class T&gt;</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">     254039 : void DataFetchingObjectTyped&lt;T&gt;::finishDataGrab() {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   // Run over all values and collect data</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">     254679 :   for(const auto &amp; p : myvalues ) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1280 :     auto val=data.find(p-&gt;getName() + &quot; &quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1280 :     if( data.find(p-&gt;getName() + &quot; &quot;)!=data.end() ) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        640 :       val-&gt;second.set(static_cast&lt;T&gt;( p-&gt;get() ));</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1280 :     if( data.find(p-&gt;getName() + &quot; derivatives&quot;)!=data.end() ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;not implemented yet&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     }</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1280 :     if( data.find(p-&gt;getName() + &quot; forces&quot;)!=data.end() ) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;not implemented yet&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     }</a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     254039 : }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/DataFetchingObject.h.func-sort-c.html b/coverage/core/DataFetchingObject.h.func-sort-c.html
new file mode 100644
index 0000000000..63870bf6cc
--- /dev/null
+++ b/coverage/core/DataFetchingObject.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/DataFetchingObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - DataFetchingObject.h<span style="font-size: 80%;"> (<a href="DataFetchingObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DataFetchingObject.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.h.gcov.html#50">_ZN4PLMD18DataFetchingObjectD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.h.gcov.html#50">_ZN4PLMD18DataFetchingObjectD2Ev</a></td>
+              <td class="coverFnHi">806145</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/DataFetchingObject.h.func.html b/coverage/core/DataFetchingObject.h.func.html
new file mode 100644
index 0000000000..995f7cf11a
--- /dev/null
+++ b/coverage/core/DataFetchingObject.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/DataFetchingObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - DataFetchingObject.h<span style="font-size: 80%;"> (<a href="DataFetchingObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DataFetchingObject.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.h.gcov.html#50">_ZN4PLMD18DataFetchingObjectD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DataFetchingObject.h.gcov.html#50">_ZN4PLMD18DataFetchingObjectD2Ev</a></td>
+              <td class="coverFnHi">806145</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/DataFetchingObject.h.gcov.html b/coverage/core/DataFetchingObject.h.gcov.html
new file mode 100644
index 0000000000..3fc9693a70
--- /dev/null
+++ b/coverage/core/DataFetchingObject.h.gcov.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/DataFetchingObject.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - DataFetchingObject.h<span style="font-size: 80%;"> (source / <a href="DataFetchingObject.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_DataFetchingObject_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_DataFetchingObject_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;set&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;map&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;memory&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/TypesafePtr.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class ActionSet;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class PlumedMain;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class ActionWithValue;</a>
+<a name="38"><span class="lineNum">      38 </span>            : class Value;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class DataFetchingObject {</a>
+<a name="41"><span class="lineNum">      41 </span>            : protected:</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Pointers to the various actions required by the grabber</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;ActionWithValue*&gt; myactions;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// The values required by the user</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;Value*&gt; myvalues;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// A copy of the plumed main object</a>
+<a name="47"><span class="lineNum">      47 </span>            :   PlumedMain &amp; plumed;</a>
+<a name="48"><span class="lineNum">      48 </span>            : public:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static std::unique_ptr&lt;DataFetchingObject&gt; create(unsigned n, PlumedMain&amp; p);</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// A constructor so that we can create the plumed main object</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit DataFetchingObject(PlumedMain&amp;p);</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     806145 :   virtual ~DataFetchingObject() {}</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : ///</a>
+<a name="54"><span class="lineNum">      54 </span>            :   bool activate() const ;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Return the rank required for a particular key</a>
+<a name="56"><span class="lineNum">      56 </span>            :   static void get_rank( const ActionSet&amp; a, const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; rank );</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Return the shape required for a particular key</a>
+<a name="58"><span class="lineNum">      58 </span>            :   static void get_shape( const ActionSet&amp; a, const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; dims );</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Find the action that calculates a particular value</a>
+<a name="60"><span class="lineNum">      60 </span>            :   static ActionWithValue* findAction( const ActionSet&amp; a, const std::string&amp; key );</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Set the pointer to the data</a>
+<a name="62"><span class="lineNum">      62 </span>            :   virtual void setData( const std::string&amp; key, const std::string&amp; type, const TypesafePtr &amp; outval )=0;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// After calc has been performed grab all the data and put it in the relevant arrays</a>
+<a name="64"><span class="lineNum">      64 </span>            :   virtual void finishDataGrab()=0;</a>
+<a name="65"><span class="lineNum">      65 </span>            : };</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ExchangePatterns.cpp.func-sort-c.html b/coverage/core/ExchangePatterns.cpp.func-sort-c.html
new file mode 100644
index 0000000000..11c9ed53c2
--- /dev/null
+++ b/coverage/core/ExchangePatterns.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ExchangePatterns.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ExchangePatterns.cpp<span style="font-size: 80%;"> (<a href="ExchangePatterns.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryLo">19.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">28.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExchangePatterns.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#40">_ZN4PLMD16ExchangePatterns7getFlagERi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#49">_ZN4PLMD16ExchangePatterns7getListERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#36">_ZN4PLMD16ExchangePatterns7setFlagEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#32">_ZN4PLMD16ExchangePatterns7setNofREi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#44">_ZN4PLMD16ExchangePatterns7setSeedEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#25">_ZN4PLMD16ExchangePatternsC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#30">_ZN4PLMD16ExchangePatternsD2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ExchangePatterns.cpp.func.html b/coverage/core/ExchangePatterns.cpp.func.html
new file mode 100644
index 0000000000..dea8ea5cbf
--- /dev/null
+++ b/coverage/core/ExchangePatterns.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ExchangePatterns.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ExchangePatterns.cpp<span style="font-size: 80%;"> (<a href="ExchangePatterns.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryLo">19.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">28.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExchangePatterns.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#40">_ZN4PLMD16ExchangePatterns7getFlagERi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#49">_ZN4PLMD16ExchangePatterns7getListERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#36">_ZN4PLMD16ExchangePatterns7setFlagEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#32">_ZN4PLMD16ExchangePatterns7setNofREi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#44">_ZN4PLMD16ExchangePatterns7setSeedEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#25">_ZN4PLMD16ExchangePatternsC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExchangePatterns.cpp.gcov.html#30">_ZN4PLMD16ExchangePatternsD2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ExchangePatterns.cpp.gcov.html b/coverage/core/ExchangePatterns.cpp.gcov.html
new file mode 100644
index 0000000000..1227f1c9f5
--- /dev/null
+++ b/coverage/core/ExchangePatterns.cpp.gcov.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ExchangePatterns.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ExchangePatterns.cpp<span style="font-size: 80%;"> (source / <a href="ExchangePatterns.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryLo">19.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">28.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ExchangePatterns.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">     805268 : ExchangePatterns::ExchangePatterns():</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">     805268 :   PatternFlag(NONE),</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     805268 :   NumberOfReplicas(1)</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">     805268 : {}</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     805268 : ExchangePatterns::~ExchangePatterns() {}</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 : void ExchangePatterns::setNofR(const int nrepl) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 :   NumberOfReplicas=nrepl;</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 : void ExchangePatterns::setFlag(const int flag) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :   PatternFlag=flag;</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineNoCov">          0 : void ExchangePatterns::getFlag(int &amp;flag) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :   flag=PatternFlag;</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 : void ExchangePatterns::setSeed(const int seed)</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : {</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :   random.setSeed(seed);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 : void ExchangePatterns::getList(const TypesafePtr &amp; ind)</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : {</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   auto iind=ind.get&lt;int*&gt;(NumberOfReplicas);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   switch(PatternFlag)</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   {</a>
+<a name="56"><span class="lineNum">      56 </span>            :   case RANDOM:</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :     for(int i=0; i&lt;NumberOfReplicas; i++) {</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :       int stat=1;</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :       while(stat) {</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :         stat=0;</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :         iind[i] = (int) (random.U01()*NumberOfReplicas);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :         for(int j=0; j&lt;i; j++) if(iind[i]==iind[j]) stat=1;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :       }</a>
+<a name="64"><span class="lineNum">      64 </span>            :     }</a>
+<a name="65"><span class="lineNum">      65 </span>            :     break;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   case NEIGHBOR:</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :     for(int i=0; i&lt;NumberOfReplicas; i++) iind[i]=i;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     break;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/FlexibleBin.cpp.func-sort-c.html b/coverage/core/FlexibleBin.cpp.func-sort-c.html
new file mode 100644
index 0000000000..acb491e997
--- /dev/null
+++ b/coverage/core/FlexibleBin.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/FlexibleBin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - FlexibleBin.cpp<span style="font-size: 80%;"> (<a href="FlexibleBin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FlexibleBin.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#164">_ZNK4PLMD11FlexibleBin9getMatrixEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#68">_ZN4PLMD11FlexibleBinC2EiPNS_19ActionWithArgumentsEjRKdRSt6vectorIdSaIdEERKS7_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#30">_ZN4PLMD11FlexibleBinC2EiPNS_19ActionWithArgumentsERKdRSt6vectorIdSaIdEERKS7_</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#310">_ZNK4PLMD11FlexibleBin16getInverseMatrixEj</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#171">_ZN4PLMD11FlexibleBin6updateEbj</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#221">_ZNK4PLMD11FlexibleBin16getInverseMatrixEv</a></td>
+              <td class="coverFnHi">374</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#101">_ZN4PLMD11FlexibleBin6updateEb</a></td>
+              <td class="coverFnHi">778</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/FlexibleBin.cpp.func.html b/coverage/core/FlexibleBin.cpp.func.html
new file mode 100644
index 0000000000..8aed7f4d97
--- /dev/null
+++ b/coverage/core/FlexibleBin.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/FlexibleBin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - FlexibleBin.cpp<span style="font-size: 80%;"> (<a href="FlexibleBin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FlexibleBin.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#101">_ZN4PLMD11FlexibleBin6updateEb</a></td>
+              <td class="coverFnHi">778</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#171">_ZN4PLMD11FlexibleBin6updateEbj</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#30">_ZN4PLMD11FlexibleBinC2EiPNS_19ActionWithArgumentsERKdRSt6vectorIdSaIdEERKS7_</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#68">_ZN4PLMD11FlexibleBinC2EiPNS_19ActionWithArgumentsEjRKdRSt6vectorIdSaIdEERKS7_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#310">_ZNK4PLMD11FlexibleBin16getInverseMatrixEj</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#221">_ZNK4PLMD11FlexibleBin16getInverseMatrixEv</a></td>
+              <td class="coverFnHi">374</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FlexibleBin.cpp.gcov.html#164">_ZNK4PLMD11FlexibleBin9getMatrixEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/FlexibleBin.cpp.gcov.html b/coverage/core/FlexibleBin.cpp.gcov.html
new file mode 100644
index 0000000000..f264d6532d
--- /dev/null
+++ b/coverage/core/FlexibleBin.cpp.gcov.html
@@ -0,0 +1,412 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/FlexibleBin.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - FlexibleBin.cpp<span style="font-size: 80%;"> (source / <a href="FlexibleBin.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;FlexibleBin.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithArguments.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cmath&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;iostream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         22 : FlexibleBin::FlexibleBin(int type, ActionWithArguments *paction, double const &amp;d, std::vector&lt;double&gt; &amp;smin, const std::vector&lt;double&gt; &amp;smax):</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         22 :   type(type),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         22 :   paction(paction),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         22 :   sigma(d),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         22 :   sigmamin(smin),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         22 :   sigmamax(smax)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span>            :   // initialize the averages and the variance matrices</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         22 :   if(type==diffusion) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          3 :     unsigned ncv=paction-&gt;getNumberOfArguments();</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; average(ncv*(ncv+1)/2);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; variance(ncv*(ncv+1)/2);</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   }</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         22 :   paction-&gt;log&lt;&lt;&quot;  Limits for sigmas using adaptive hills:  \n&quot;;</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         64 :   for(unsigned i=0; i&lt;paction-&gt;getNumberOfArguments(); ++i) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         42 :     paction-&gt;log&lt;&lt;&quot;   CV  &quot;&lt;&lt;paction-&gt;getPntrToArgument(i)-&gt;getName()&lt;&lt;&quot;:\n&quot;;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         42 :     if(sigmamin[i]&gt;0.) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 :       limitmin.push_back(true);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :       paction-&gt;log&lt;&lt;&quot;       Min &quot;&lt;&lt;sigmamin[i];</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :       sigmamin[i]*=sigmamin[i]; // this is because the matrix which is calculated is the sigmasquared</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :     } else {</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         42 :       limitmin.push_back(false);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         42 :       paction-&gt;log&lt;&lt;&quot;       Min No &quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         42 :     if(sigmamax[i]&gt;0.) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :       limitmax.push_back(true);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :       paction-&gt;log&lt;&lt;&quot;       Max &quot;&lt;&lt;sigmamax[i];</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :       sigmamax[i]*=sigmamax[i];</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :     } else {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         42 :       limitmax.push_back(false);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         42 :       paction-&gt;log&lt;&lt;&quot;       Max No &quot;;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         42 :     paction-&gt;log&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         22 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Constructure for 1D FB for PBMETAD</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          8 : FlexibleBin::FlexibleBin(int type, ActionWithArguments *paction, unsigned iarg,</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          8 :                          double const &amp;d, std::vector&lt;double&gt; &amp;smin, const std::vector&lt;double&gt; &amp;smax):</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          8 :   type(type),paction(paction),sigma(d),sigmamin(smin),sigmamax(smax)</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : {</a>
+<a name="74"><span class="lineNum">      74 </span>            :   // initialize the averages and the variance matrices</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          8 :   if(type==diffusion) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          8 :     std::vector&lt;double&gt; average(1);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          8 :     std::vector&lt;double&gt; variance(1);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          8 :   paction-&gt;log&lt;&lt;&quot;  Limits for sigmas using adaptive hills:  \n&quot;;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 :   paction-&gt;log&lt;&lt;&quot;   CV  &quot;&lt;&lt;paction-&gt;getPntrToArgument(iarg)-&gt;getName()&lt;&lt;&quot;:\n&quot;;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   if(sigmamin[0]&gt;0.) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :     limitmin.push_back(true);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 :     paction-&gt;log&lt;&lt;&quot;       Min &quot;&lt;&lt;sigmamin[0];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :     sigmamin[0]*=sigmamin[0];</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   } else {</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     limitmin.push_back(false);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     paction-&gt;log&lt;&lt;&quot;       Min No &quot;;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   }</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          8 :   if(sigmamax[0]&gt;0.) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :     limitmax.push_back(true);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :     paction-&gt;log&lt;&lt;&quot;       Max &quot;&lt;&lt;sigmamax[0];</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     sigmamax[0]*=sigmamax[0];</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   } else {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          8 :     limitmax.push_back(false);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          8 :     paction-&gt;log&lt;&lt;&quot;       Max No &quot;;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          8 :   paction-&gt;log&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          8 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Update the flexible bin</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// in case of diffusion based: update at every step</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// in case of gradient based: update only when you add the hill</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        778 : void FlexibleBin::update(bool nowAddAHill) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        778 :   unsigned ncv=paction-&gt;getNumberOfArguments();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        778 :   unsigned dimension=ncv*(ncv+1)/2;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;double&gt; delta;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;double&gt; cv;</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        778 :   double decay=1./sigma;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   // this is done all the times from scratch. It is not an accumulator</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // here update the flexible bin according to the needs</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        778 :   switch (type) {</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   // This should be called every time</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        586 :   case diffusion:</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     // if you use this below then the decay is in time units</a>
+<a name="115"><span class="lineNum">     115 </span>            :     //double decay=paction-&gt;getTimeStep()/sigma;</a>
+<a name="116"><span class="lineNum">     116 </span>            :     // to be consistent with the rest of the program: everything is better to be in timesteps</a>
+<a name="117"><span class="lineNum">     117 </span>            :     // THE AVERAGE VALUE</a>
+<a name="118"><span class="lineNum">     118 </span>            :     // beware: the pbc</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        586 :     delta.resize(ncv);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1172 :     for(unsigned i=0; i&lt;ncv; i++) cv.push_back(paction-&gt;getArgument(i));</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        586 :     if(average.size()==0) { // initial time: just set the initial vector</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :       average.resize(ncv);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 :       for(unsigned i=0; i&lt;ncv; i++) average[i]=cv[i];</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :     } else { // accumulate</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       1168 :       for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        584 :         delta[i]=paction-&gt;difference(i,average[i],cv[i]);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        584 :         average[i]+=decay*delta[i];</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        584 :         average[i]=paction-&gt;bringBackInPbc(i,average[i]); // equation 8 of &quot;Metadynamics with adaptive Gaussians&quot;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :       }</a>
+<a name="130"><span class="lineNum">     130 </span>            :     }</a>
+<a name="131"><span class="lineNum">     131 </span>            :     // THE VARIANCE</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        586 :     if(variance.size()==0) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :       variance.resize(dimension,0.); // nonredundant members dimension=ncv*(ncv+1)/2;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     } else {</a>
+<a name="135"><span class="lineNum">     135 </span>            :       unsigned k=0;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1168 :       for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1168 :         for(unsigned j=i; j&lt;ncv; j++) { // upper diagonal loop</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        584 :           variance[k]+=decay*(delta[i]*delta[j]-variance[k]);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        584 :           k++;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :         }</a>
+<a name="141"><span class="lineNum">     141 </span>            :       }</a>
+<a name="142"><span class="lineNum">     142 </span>            :     }</a>
+<a name="143"><span class="lineNum">     143 </span>            :     break;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        192 :   case geometry:</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :     //this calculates in variance the \nabla CV_i \dot \nabla CV_j</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        192 :     variance.resize(dimension);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     // now the signal for retrieving the gradients should be already given by checkNeedsGradients.</a>
+<a name="148"><span class="lineNum">     148 </span>            :     // here just do the projections</a>
+<a name="149"><span class="lineNum">     149 </span>            :     // note that the call  checkNeedsGradients() in BiasMetaD takes care of switching on the call to gradients</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        192 :     if (nowAddAHill) { // geometry is sync with hill deposition</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :       unsigned k=0;</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        249 :       for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        415 :         for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :           // eq 12 of &quot;Metadynamics with adaptive Gaussians&quot;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        249 :           variance[k]=sigma*sigma*(paction-&gt;getProjection(i,j));</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        249 :           k++;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :         }</a>
+<a name="158"><span class="lineNum">     158 </span>            :       }</a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :     break;</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   default:</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;This flexible bin method is not recognized&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        778 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 : std::vector&lt;double&gt; FlexibleBin::getMatrix() const {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :   return variance;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : /// Update the flexible bin for PBMetaD like FlexBin</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// in case of diffusion based: update at every step</a>
+<a name="172"><span class="lineNum">     172 </span>            : /// in case of gradient based: update only when you add the hill</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         80 : void FlexibleBin::update(bool nowAddAHill, unsigned iarg) {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   // this is done all the times from scratch. It is not an accumulator</a>
+<a name="175"><span class="lineNum">     175 </span>            :   // here update the flexible bin according to the needs</a>
+<a name="176"><span class="lineNum">     176 </span>            :   std::vector&lt;double&gt; cv;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::vector&lt;double&gt; delta;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   // if you use this below then the decay is in time units</a>
+<a name="179"><span class="lineNum">     179 </span>            :   // to be consistent with the rest of the program: everything is better to be in timesteps</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         80 :   double decay=1./sigma;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         80 :   switch (type) {</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   // This should be called every time</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         80 :   case diffusion:</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     // THE AVERAGE VALUE</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         80 :     delta.resize(1);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         80 :     cv.push_back(paction-&gt;getArgument(iarg));</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         80 :     if(average.size()==0) { // initial time: just set the initial vector</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          8 :       average.resize(1);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          8 :       average[0]=cv[0];</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :     } else { // accumulate</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         72 :       delta[0]=paction-&gt;difference(iarg,average[0],cv[0]);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         72 :       average[0]+=decay*delta[0];</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         72 :       average[0]=paction-&gt;bringBackInPbc(iarg,average[0]); // equation 8 of &quot;Metadynamics with adaptive Gaussians&quot;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     }</a>
+<a name="195"><span class="lineNum">     195 </span>            :     // THE VARIANCE</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         80 :     if(variance.size()==0) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          8 :       variance.resize(1,0.); // nonredundant members dimension=ncv*(ncv+1)/2;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     } else {</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         72 :       variance[0]+=decay*(delta[0]*delta[0]-variance[0]);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span>            :     break;</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   case geometry:</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     //this calculates in variance the \nabla CV_i \dot \nabla CV_j</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     variance.resize(1);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     // now the signal for retrieving the gradients should be already given by checkNeedsGradients.</a>
+<a name="206"><span class="lineNum">     206 </span>            :     // here just do the projections</a>
+<a name="207"><span class="lineNum">     207 </span>            :     // note that the call  checkNeedsGradients() in BiasMetaD takes care of switching on the call to gradients</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     if (nowAddAHill) { // geometry is sync with hill deposition</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :       // eq 12 of &quot;Metadynamics with adaptive Gaussians&quot;</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :       variance[0]=sigma*sigma*(paction-&gt;getProjection(iarg,iarg));</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     }</a>
+<a name="212"><span class="lineNum">     212 </span>            :     break;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   default:</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;This flexible bin is not recognized&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         80 : }</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : ///</a>
+<a name="219"><span class="lineNum">     219 </span>            : /// Calculate the matrix of  (dcv_i/dx)*(dcv_j/dx)^-1</a>
+<a name="220"><span class="lineNum">     220 </span>            : /// that is needed for the metrics in metadynamics</a>
+<a name="221"><span class="lineNum">     221 </span>            : ///</a>
+<a name="222"><span class="lineNum">     222 </span>            : ///</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        374 : std::vector&lt;double&gt; FlexibleBin::getInverseMatrix() const {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        374 :   unsigned ncv=paction-&gt;getNumberOfArguments();</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   Matrix&lt;double&gt; matrix(ncv,ncv);</a>
+<a name="226"><span class="lineNum">     226 </span>            :   unsigned i,j,k;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   k=0;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   // place the matrix in a complete matrix for compatibility</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        831 :   for (i=0; i&lt;ncv; i++) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        997 :     for (j=i; j&lt;ncv; j++) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        540 :       matrix(j,i)=matrix(i,j)=variance[k];</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        540 :       k++;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     }</a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span>            : #define NEWFLEX</a>
+<a name="236"><span class="lineNum">     236 </span>            : #ifdef NEWFLEX</a>
+<a name="237"><span class="lineNum">     237 </span>            :   // diagonalize to impose boundaries (only if boundaries are set)</a>
+<a name="238"><span class="lineNum">     238 </span>            :   Matrix&lt;double&gt;      eigenvecs(ncv,ncv);</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        374 :   std::vector&lt;double&gt; eigenvals(ncv);</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   //eigenvecs: first is eigenvec number, second is eigenvec component</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        374 :   if(diagMat( matrix, eigenvals, eigenvecs )!=0) {plumed_merror(&quot;diagonalization in FlexibleBin failed! This matrix is weird\n&quot;);};</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        831 :   for (i=0; i&lt;ncv; i++) { //loop on the dimension</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        457 :     if( limitmax[i] ) {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :       //limit every  component that is larger</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :       for (j=0; j&lt;ncv; j++) { //loop on components</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :         if(std::pow(eigenvals[j]*eigenvecs[j][i],2)&gt;std::pow(sigmamax[i],2) ) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :           eigenvals[j]=std::sqrt(std::pow(sigmamax[i]/(eigenvecs[j][i]),2))*copysign(1.,eigenvals[j]);</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :         }</a>
+<a name="251"><span class="lineNum">     251 </span>            :       }</a>
+<a name="252"><span class="lineNum">     252 </span>            :     }</a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        831 :   for (i=0; i&lt;ncv; i++) { //loop on the dimension</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     // find the largest one:  if it is smaller than min  then rescale</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        457 :     if( limitmin[i] ) {</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :       unsigned imax=0;</a>
+<a name="258"><span class="lineNum">     258 </span>            :       double fmax=-1.e10;</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :       for (j=0; j&lt;ncv; j++) { //loop on components</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :         double fact=std::pow(eigenvals[j]*eigenvecs[j][i],2);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :         if(fact&gt;fmax) {</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :           fmax=fact; imax=j;</a>
+<a name="263"><span class="lineNum">     263 </span>            :         }</a>
+<a name="264"><span class="lineNum">     264 </span>            :       }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :       if(fmax&lt;std::pow(sigmamin[i],2) ) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :         eigenvals[imax]=std::sqrt(std::pow(sigmamin[i]/(eigenvecs[imax][i]),2))*copysign(1.,eigenvals[imax]);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :       }</a>
+<a name="268"><span class="lineNum">     268 </span>            :     }</a>
+<a name="269"><span class="lineNum">     269 </span>            :   }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   // normalize eigenvecs</a>
+<a name="272"><span class="lineNum">     272 </span>            :   Matrix&lt;double&gt; newinvmatrix(ncv,ncv);</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        831 :   for (i=0; i&lt;ncv; i++) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       1080 :     for (j=0; j&lt;ncv; j++) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        623 :       newinvmatrix[j][i]=eigenvecs[j][i]/eigenvals[j];</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     }</a>
+<a name="277"><span class="lineNum">     277 </span>            :   }</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        374 :   std::vector&lt;double&gt; uppervec(ncv*(ncv+1)/2);</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   k=0;</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        831 :   for (i=0; i&lt;ncv; i++) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        997 :     for (j=i; j&lt;ncv; j++) {</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :       double scal=0;</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       1329 :       for(unsigned l=0; l&lt;ncv; ++l) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        789 :         scal+=eigenvecs[l][i]*newinvmatrix[l][j];</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :       }</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        540 :       uppervec[k]=scal; k++;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span>            : #else</a>
+<a name="291"><span class="lineNum">     291 </span>            :   // get the inverted matrix</a>
+<a name="292"><span class="lineNum">     292 </span>            :   Matrix&lt;double&gt; invmatrix(ncv,ncv);</a>
+<a name="293"><span class="lineNum">     293 </span>            :   Invert(matrix,invmatrix);</a>
+<a name="294"><span class="lineNum">     294 </span>            :   std::vector&lt;double&gt; uppervec(ncv*(ncv+1)/2);</a>
+<a name="295"><span class="lineNum">     295 </span>            :   // upper diagonal of the inverted matrix (that is symmetric)</a>
+<a name="296"><span class="lineNum">     296 </span>            :   k=0;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   for (i=0; i&lt;ncv; i++) {</a>
+<a name="298"><span class="lineNum">     298 </span>            :     for (j=i; j&lt;ncv; j++) {</a>
+<a name="299"><span class="lineNum">     299 </span>            :       uppervec[k]=invmatrix(i,j);</a>
+<a name="300"><span class="lineNum">     300 </span>            :       k++;</a>
+<a name="301"><span class="lineNum">     301 </span>            :     }</a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span>            : #endif</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        374 :   return uppervec;</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : ///</a>
+<a name="308"><span class="lineNum">     308 </span>            : /// Calculate the matrix of  (dcv_i/dx)*(dcv_j/dx)^-1</a>
+<a name="309"><span class="lineNum">     309 </span>            : /// that is needed for the metrics in metadynamics</a>
+<a name="310"><span class="lineNum">     310 </span>            : /// for PBMetaD like FlexBin</a>
+<a name="311"><span class="lineNum">     311 </span>            : ///</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         72 : std::vector&lt;double&gt; FlexibleBin::getInverseMatrix(unsigned iarg) const {</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :   // diagonalize to impose boundaries (only if boundaries are set)</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         72 :   std::vector&lt;double&gt; eigenvals(1, variance[0]);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         72 :   if( limitmax[0] ) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :     if(eigenvals[0]&gt;sigmamax[0]) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :       eigenvals[0]=sigmamax[0];</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            :   // find the largest one:  if it is smaller than min  then rescale</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         72 :   if( limitmin[0] ) {</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :     double fmax=-1.e10;</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         72 :     double fact=eigenvals[0];</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         72 :     if(fact&gt;fmax) {</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :       fmax=fact;</a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         72 :     if(fmax&lt;sigmamin[0]) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         72 :       eigenvals[0]=sigmamin[0];</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :     }</a>
+<a name="330"><span class="lineNum">     330 </span>            :   }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         72 :   std::vector&lt;double&gt; uppervec(1,1./eigenvals[0]);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         72 :   return uppervec;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GREX.cpp.func-sort-c.html b/coverage/core/GREX.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8d3efdbc80
--- /dev/null
+++ b/coverage/core/GREX.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GREX.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GREX.cpp<span style="font-size: 80%;"> (<a href="GREX.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntryLo">73.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GREX.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#184">_ZN4PLMD4GREX13savePositionsEv</a></td>
+              <td class="coverFnHi">114</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#194">_ZN4PLMD4GREX9calculateEv</a></td>
+              <td class="coverFnHi">114</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#30">_ZN4PLMD4GREXC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">204</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#44">_ZN4PLMD4GREXD0Ev</a></td>
+              <td class="coverFnHi">204</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#44">_ZN4PLMD4GREXD2Ev</a></td>
+              <td class="coverFnHi">204</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#52">_ZN4PLMD4GREX3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">1077</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GREX.cpp.func.html b/coverage/core/GREX.cpp.func.html
new file mode 100644
index 0000000000..124266a8cc
--- /dev/null
+++ b/coverage/core/GREX.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GREX.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GREX.cpp<span style="font-size: 80%;"> (<a href="GREX.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntryLo">73.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GREX.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#184">_ZN4PLMD4GREX13savePositionsEv</a></td>
+              <td class="coverFnHi">114</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#52">_ZN4PLMD4GREX3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">1077</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#194">_ZN4PLMD4GREX9calculateEv</a></td>
+              <td class="coverFnHi">114</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#30">_ZN4PLMD4GREXC2ERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">204</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#44">_ZN4PLMD4GREXD0Ev</a></td>
+              <td class="coverFnHi">204</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GREX.cpp.gcov.html#44">_ZN4PLMD4GREXD2Ev</a></td>
+              <td class="coverFnHi">204</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GREX.cpp.gcov.html b/coverage/core/GREX.cpp.gcov.html
new file mode 100644
index 0000000000..e06fe0da18
--- /dev/null
+++ b/coverage/core/GREX.cpp.gcov.html
@@ -0,0 +1,298 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GREX.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GREX.cpp<span style="font-size: 80%;"> (source / <a href="GREX.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntryLo">73.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;GREX.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;sstream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;unordered_map&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        204 : GREX::GREX(PlumedMain&amp;p):</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        204 :   initialized(false),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        204 :   plumedMain(p),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        204 :   atoms(p.getAtoms()),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        204 :   partner(-1), // = unset</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        204 :   localDeltaBias(0),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        204 :   foreignDeltaBias(0),</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        204 :   localUNow(0),</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        204 :   localUSwap(0),</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        204 :   myreplica(-1) // = unset</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        204 :   p.setSuffix(&quot;.NA&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        204 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        408 : GREX::~GREX() {</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : // empty destructor to delete unique_ptr</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        408 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : #define CHECK_INIT(ini,word) plumed_massert(ini,&quot;cmd(\&quot;&quot; + word +&quot;\&quot;) should be only used after GREX initialization&quot;)</a>
+<a name="51"><span class="lineNum">      51 </span>            : #define CHECK_NOTINIT(ini,word) plumed_massert(!(ini),&quot;cmd(\&quot;&quot; + word +&quot;\&quot;) should be only used before GREX initialization&quot;)</a>
+<a name="52"><span class="lineNum">      52 </span>            : #define CHECK_NOTNULL(val,word) plumed_massert(val,&quot;NULL pointer received in cmd(\&quot;GREX &quot; + word + &quot;\&quot;)&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1077 : void GREX::cmd(const std::string&amp;key,const TypesafePtr &amp; val) {</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : // Enumerate all possible commands:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   enum {</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &quot;GREXEnum.inc&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : // Static object (initialized once) containing the map of commands:</a>
+<a name="61"><span class="lineNum">      61 </span>            :   const static std::unordered_map&lt;std::string, int&gt; word_map = {</a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &quot;GREXMap.inc&quot;</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       4494 :   };</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1077 :   std::vector&lt;std::string&gt; words=Tools::getWords(key);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1077 :   unsigned nw=words.size();</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       1077 :   if(nw==0) {</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     // do nothing</a>
+<a name="69"><span class="lineNum">      69 </span>            :   } else {</a>
+<a name="70"><span class="lineNum">      70 </span>            :     int iword=-1;</a>
+<a name="71"><span class="lineNum">      71 </span>            :     const auto it=word_map.find(words[0]);</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       1077 :     if(it!=word_map.end()) iword=it-&gt;second;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       1077 :     switch(iword) {</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :     case cmd_initialized:</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :       CHECK_NOTNULL(val,key);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :       val.set(int(initialized));</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :       break;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        204 :     case cmd_setMPIIntracomm:</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        204 :       CHECK_NOTINIT(initialized,key);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        408 :       intracomm.Set_comm(val.get&lt;const void*&gt;());</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        204 :       break;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        156 :     case cmd_setMPIIntercomm:</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        156 :       CHECK_NOTINIT(initialized,key);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        312 :       intercomm.Set_comm(val.get&lt;const void*&gt;());</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        312 :       plumedMain.multi_sim_comm.Set_comm(val.get&lt;const void*&gt;());</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        156 :       break;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     case cmd_setMPIFIntracomm:</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :       CHECK_NOTINIT(initialized,key);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :       intracomm.Set_fcomm(val.get&lt;const void*&gt;());</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :     case cmd_setMPIFIntercomm:</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :       CHECK_NOTINIT(initialized,key);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :       intercomm.Set_fcomm(val.get&lt;const void*&gt;());</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :       plumedMain.multi_sim_comm.Set_fcomm(val.get&lt;const void*&gt;());</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        204 :     case cmd_init:</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        204 :       CHECK_NOTINIT(initialized,key);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        204 :       initialized=true;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : // note that for PEs!=root this is automatically 0 (comm defaults to MPI_COMM_SELF)</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        204 :       myreplica=intercomm.Get_rank();</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        204 :       intracomm.Sum(myreplica);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :       {</a>
+<a name="103"><span class="lineNum">     103 </span>            :         std::string s;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        204 :         Tools::convert(myreplica,s);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        408 :         plumedMain.setSuffix(&quot;.&quot;+s);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :       }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        204 :       break;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         57 :     case cmd_prepare:</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         57 :       CHECK_INIT(initialized,key);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         57 :       if(intracomm.Get_rank()==0) return;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         57 :       intracomm.Bcast(partner,0);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         57 :       calculate();</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :       break;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         57 :     case cmd_setPartner:</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         57 :       CHECK_INIT(initialized,key);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         57 :       partner=val.get&lt;int&gt;();</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         57 :       break;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        114 :     case cmd_savePositions:</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        114 :       CHECK_INIT(initialized,key);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        114 :       savePositions();</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :       break;</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         57 :     case cmd_calculate:</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         57 :       CHECK_INIT(initialized,key);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         57 :       if(intracomm.Get_rank()!=0) return;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         57 :       intracomm.Bcast(partner,0);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         57 :       calculate();</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :       break;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :     case cmd_getLocalDeltaBias:</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :       CHECK_INIT(initialized,key);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :       CHECK_NOTNULL(val,key);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :       atoms.double2MD(localDeltaBias/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     case cmd_cacheLocalUNow:</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :       CHECK_INIT(initialized,key);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :       CHECK_NOTNULL(val,key);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :       {</a>
+<a name="137"><span class="lineNum">     137 </span>            :         double x;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :         atoms.MD2double(val,x);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :         localUNow=x*(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :         intracomm.Sum(localUNow);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :       }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     case cmd_cacheLocalUSwap:</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :       CHECK_INIT(initialized,key);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :       CHECK_NOTNULL(val,key);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :       {</a>
+<a name="147"><span class="lineNum">     147 </span>            :         double x;</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :         atoms.MD2double(val,x);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :         localUSwap=x*(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :         intracomm.Sum(localUSwap);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :       }</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :     case cmd_getForeignDeltaBias:</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :       CHECK_INIT(initialized,key);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :       CHECK_NOTNULL(val,key);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :       atoms.double2MD(foreignDeltaBias/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         57 :     case cmd_shareAllDeltaBias:</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         57 :       CHECK_INIT(initialized,key);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         57 :       if(intracomm.Get_rank()!=0) return;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         57 :       allDeltaBias.assign(intercomm.Get_size(),0.0);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         57 :       allDeltaBias[intercomm.Get_rank()]=localDeltaBias;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         57 :       intercomm.Sum(allDeltaBias);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :       break;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        171 :     case cmd_getDeltaBias:</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        171 :       CHECK_INIT(initialized,key);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        171 :       CHECK_NOTNULL(val,key);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        171 :       plumed_assert(nw==2);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        171 :       plumed_massert(allDeltaBias.size()==static_cast&lt;unsigned&gt;(intercomm.Get_size()),</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :                      &quot;to retrieve bias with cmd(\&quot;GREX getDeltaBias\&quot;), first share it with cmd(\&quot;GREX shareAllDeltaBias\&quot;)&quot;);</a>
+<a name="171"><span class="lineNum">     171 </span>            :       {</a>
+<a name="172"><span class="lineNum">     172 </span>            :         unsigned rep;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        171 :         Tools::convert(words[1],rep);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        171 :         plumed_massert(rep&lt;allDeltaBias.size(),&quot;replica index passed to cmd(\&quot;GREX getDeltaBias\&quot;) is out of range&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        171 :         double d=allDeltaBias[rep]/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy());</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        171 :         atoms.double2MD(d,val);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :       }</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        171 :       break;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     default:</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;cannot interpret cmd(\&quot; GREX&quot; + key + &quot;\&quot;). check plumed developers manual to see the available commands.&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :       break;</a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span>            :   }</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       1077 : }</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        114 : void GREX::savePositions() {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        114 :   plumedMain.prepareDependencies();</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        114 :   plumedMain.resetActive(true);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        114 :   atoms.shareAll();</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        114 :   plumedMain.waitData();</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        114 :   std::ostringstream o;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        114 :   atoms.writeBinary(o);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        114 :   buffer=o.str();</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        114 : }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        114 : void GREX::calculate() {</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   unsigned nn=buffer.size();</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        114 :   std::vector&lt;char&gt; rbuf(nn);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        114 :   localDeltaBias=-plumedMain.getBias();</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        114 :   if(intracomm.Get_rank()==0) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         57 :     Communicator::Request req=intercomm.Isend(buffer,partner,1066);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         57 :     intercomm.Recv(rbuf,partner,1066);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         57 :     req.wait();</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        114 :   intracomm.Bcast(rbuf,0);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        114 :   std::istringstream i(std::string(&amp;rbuf[0],rbuf.size()));</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        114 :   atoms.readBinary(i);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        114 :   plumedMain.setExchangeStep(true);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        114 :   plumedMain.prepareDependencies();</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        114 :   plumedMain.justCalculate();</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        114 :   plumedMain.setExchangeStep(false);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        114 :   localDeltaBias+=plumedMain.getBias();</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        114 :   localDeltaBias+=localUSwap-localUNow;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        114 :   if(intracomm.Get_rank()==0) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         57 :     Communicator::Request req=intercomm.Isend(localDeltaBias,partner,1067);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         57 :     intercomm.Recv(foreignDeltaBias,partner,1067);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         57 :     req.wait();</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        114 :   intracomm.Bcast(foreignDeltaBias,0);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        228 : }</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GenericMolInfo.cpp.func-sort-c.html b/coverage/core/GenericMolInfo.cpp.func-sort-c.html
new file mode 100644
index 0000000000..43b3a32d7c
--- /dev/null
+++ b/coverage/core/GenericMolInfo.cpp.func-sort-c.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GenericMolInfo.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GenericMolInfo.cpp<span style="font-size: 80%;"> (<a href="GenericMolInfo.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntryMed">85.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GenericMolInfo.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#55">_ZN4PLMD14GenericMolInfoC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#51">_ZN4PLMD14GenericMolInfoD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#350">_ZNK4PLMD14GenericMolInfo10getChainIDB5cxx11ENS_10AtomNumberE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#127">_ZN4PLMD14GenericMolInfo18getSpecialKeywordsB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#358">_ZNK4PLMD14GenericMolInfo7isWholeEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#167">_ZN4PLMD14GenericMolInfo11getBackboneERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERKS7_RS1_IS1_INS_10AtomNumberESaISD_EESaISF_EE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#55">_ZN4PLMD14GenericMolInfoC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#51">_ZN4PLMD14GenericMolInfoD0Ev</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#51">_ZN4PLMD14GenericMolInfoD1Ev</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#39">_ZN4PLMD14GenericMolInfo16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">89</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#334">_ZNK4PLMD14GenericMolInfo12checkForAtomENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">249</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#245">_ZN4PLMD14GenericMolInfo15interpretSymbolERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorINS_10AtomNumberESaISA_EE</a></td>
+              <td class="coverFnHi">617</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#362">_ZN4PLMD14GenericMolInfo7prepareEv</a></td>
+              <td class="coverFnHi">5127</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#346">_ZNK4PLMD14GenericMolInfo14getResidueNameB5cxx11ENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">15015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#342">_ZNK4PLMD14GenericMolInfo10getPDBsizeEv</a></td>
+              <td class="coverFnHi">17337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#354">_ZNK4PLMD14GenericMolInfo11getPositionENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">37702</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#330">_ZNK4PLMD14GenericMolInfo11getAtomNameB5cxx11ENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">47043</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#338">_ZNK4PLMD14GenericMolInfo16getResidueNumberENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">61067</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GenericMolInfo.cpp.func.html b/coverage/core/GenericMolInfo.cpp.func.html
new file mode 100644
index 0000000000..9d5f904e30
--- /dev/null
+++ b/coverage/core/GenericMolInfo.cpp.func.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GenericMolInfo.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GenericMolInfo.cpp<span style="font-size: 80%;"> (<a href="GenericMolInfo.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntryMed">85.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GenericMolInfo.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#167">_ZN4PLMD14GenericMolInfo11getBackboneERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EERKS7_RS1_IS1_INS_10AtomNumberESaISD_EESaISF_EE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#245">_ZN4PLMD14GenericMolInfo15interpretSymbolERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorINS_10AtomNumberESaISA_EE</a></td>
+              <td class="coverFnHi">617</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#39">_ZN4PLMD14GenericMolInfo16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">89</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#127">_ZN4PLMD14GenericMolInfo18getSpecialKeywordsB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#362">_ZN4PLMD14GenericMolInfo7prepareEv</a></td>
+              <td class="coverFnHi">5127</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#55">_ZN4PLMD14GenericMolInfoC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#55">_ZN4PLMD14GenericMolInfoC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#51">_ZN4PLMD14GenericMolInfoD0Ev</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#51">_ZN4PLMD14GenericMolInfoD1Ev</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#51">_ZN4PLMD14GenericMolInfoD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#350">_ZNK4PLMD14GenericMolInfo10getChainIDB5cxx11ENS_10AtomNumberE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#342">_ZNK4PLMD14GenericMolInfo10getPDBsizeEv</a></td>
+              <td class="coverFnHi">17337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#330">_ZNK4PLMD14GenericMolInfo11getAtomNameB5cxx11ENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">47043</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#354">_ZNK4PLMD14GenericMolInfo11getPositionENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">37702</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#334">_ZNK4PLMD14GenericMolInfo12checkForAtomENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">249</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#346">_ZNK4PLMD14GenericMolInfo14getResidueNameB5cxx11ENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">15015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#338">_ZNK4PLMD14GenericMolInfo16getResidueNumberENS_10AtomNumberE</a></td>
+              <td class="coverFnHi">61067</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.cpp.gcov.html#358">_ZNK4PLMD14GenericMolInfo7isWholeEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GenericMolInfo.cpp.gcov.html b/coverage/core/GenericMolInfo.cpp.gcov.html
new file mode 100644
index 0000000000..a5a3354ebb
--- /dev/null
+++ b/coverage/core/GenericMolInfo.cpp.gcov.html
@@ -0,0 +1,448 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GenericMolInfo.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GenericMolInfo.cpp<span style="font-size: 80%;"> (source / <a href="GenericMolInfo.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntryMed">85.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;GenericMolInfo.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/MolDataClass.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : This action is defined in core/ as it is used by other actions.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Anyway, it is registered in setup/, so that excluding that module from</a>
+<a name="37"><span class="lineNum">      37 </span>            : compilation will exclude it from plumed.</a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         89 : void GenericMolInfo::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         89 :   ActionSetup::registerKeywords(keys);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        178 :   keys.add(&quot;compulsory&quot;,&quot;STRUCTURE&quot;,&quot;a file in pdb format containing a reference structure. &quot;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :            &quot;This is used to defines the atoms in the various residues, chains, etc . &quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            :            &quot;For more details on the PDB file format visit http://www.wwpdb.org/docs.html&quot;);</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        178 :   keys.add(&quot;compulsory&quot;,&quot;MOLTYPE&quot;,&quot;protein&quot;,&quot;what kind of molecule is contained in the pdb file - usually not needed since protein/RNA/DNA are compatible&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        178 :   keys.add(&quot;compulsory&quot;,&quot;PYTHON_BIN&quot;,&quot;default&quot;,&quot;python interpreter&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        178 :   keys.add(&quot;atoms&quot;,&quot;CHAIN&quot;,&quot;(for masochists ( mostly Davide Branduardi ) ) The atoms involved in each of the chains of interest in the structure.&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        178 :   keys.add(&quot;hidden&quot;,&quot;STRIDE&quot;,&quot;frequency for resetting the python interpreter. Should be 1.&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        178 :   keys.addFlag(&quot;WHOLE&quot;, false, &quot;The reference structure is whole, i.e. not broken by PBC&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         89 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        174 : GenericMolInfo::~GenericMolInfo() {</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : // empty destructor to delete unique_ptr</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        261 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         87 : GenericMolInfo::GenericMolInfo( const ActionOptions&amp;ao ):</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   Action(ao),</a>
+<a name="59"><span class="lineNum">      59 </span>            :   ActionAnyorder(ao),</a>
+<a name="60"><span class="lineNum">      60 </span>            :   ActionPilot(ao),</a>
+<a name="61"><span class="lineNum">      61 </span>            :   ActionAtomistic(ao),</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         87 :   iswhole_(false)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         87 :   plumed_assert(getStride()==1);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   // Read what is contained in the pdb file</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         87 :   parse(&quot;MOLTYPE&quot;,mytype);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   // check if whole</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         87 :   parseFlag(&quot;WHOLE&quot;, iswhole_);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         87 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         87 :   if( moldat ) log&lt;&lt;&quot;  overriding last MOLINFO with label &quot; &lt;&lt; moldat-&gt;getLabel()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   std::vector&lt;AtomNumber&gt; backbone;</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        174 :   parseAtomList(&quot;CHAIN&quot;,backbone);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         87 :   if( read_backbone.size()==0 ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :     for(unsigned i=1;; ++i) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        174 :       parseAtomList(&quot;CHAIN&quot;,i,backbone);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         87 :       if( backbone.size()==0 ) break;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :       read_backbone.push_back(backbone);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :       backbone.resize(0);</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :     }</a>
+<a name="83"><span class="lineNum">      83 </span>            :   } else {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :     read_backbone.push_back(backbone);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         87 :   if( read_backbone.size()==0 ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         87 :     parse(&quot;STRUCTURE&quot;,reference);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        174 :     if( ! pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()))plumed_merror(&quot;missing input file &quot; + reference );</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         87 :     std::vector&lt;std::string&gt; chains; pdb.getChainNames( chains );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         87 :     log.printf(&quot;  pdb file named %s contains %u chains \n&quot;,reference.c_str(), static_cast&lt;unsigned&gt;(chains.size()));</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        248 :     for(unsigned i=0; i&lt;chains.size(); ++i) {</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :       unsigned start,end; std::string errmsg;</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        161 :       pdb.getResidueRange( chains[i], start, end, errmsg );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        161 :       if( errmsg.length()!=0 ) error( errmsg );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :       AtomNumber astart,aend;</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        161 :       pdb.getAtomRange( chains[i], astart, aend, errmsg );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        161 :       if( errmsg.length()!=0 ) error( errmsg );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        161 :       log.printf(&quot;  chain named %s contains residues %u to %u and atoms %u to %u \n&quot;,chains[i].c_str(),start,end,astart.serial(),aend.serial());</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :     std::string python_bin;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        174 :     parse(&quot;PYTHON_BIN&quot;,python_bin);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         87 :     if(python_bin==&quot;no&quot;) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;  python interpreter disabled\n&quot;;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     } else {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        174 :       pythonCmd=config::getEnvCommand();</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         87 :       if(python_bin!=&quot;default&quot;) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :         log&lt;&lt;&quot;  forcing python interpreter: &quot;&lt;&lt;python_bin&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :         pythonCmd+=&quot; env PLUMED_PYTHON_BIN=&quot;+python_bin;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :       }</a>
+<a name="113"><span class="lineNum">     113 </span>            :       bool sorted=true;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         87 :       const auto &amp; at=pdb.getAtomNumbers();</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      90730 :       for(unsigned i=0; i&lt;at.size(); i++) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      90643 :         if(at[i].index()!=i) sorted=false;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :       }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         87 :       if(!sorted) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 :         log&lt;&lt;&quot;  PDB is not sorted, python interpreter will be disabled\n&quot;;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         85 :       } else if(!Subprocess::available()) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :         log&lt;&lt;&quot;  subprocess is not available, python interpreter will be disabled\n&quot;;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :       } else {</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         85 :         enablePythonInterpreter=true;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :       }</a>
+<a name="125"><span class="lineNum">     125 </span>            :     }</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         87 :   }</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         87 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          1 : std::map&lt;std::string,std::string&gt; GenericMolInfo::getSpecialKeywords() {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   std::map&lt;std::string,std::string&gt; mapkeys;</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@mda:&quot;,&quot;atom selection built using syntax for &lt;a href=\\\&quot;https://docs.mdanalysis.org/stable/documentation_pages/selections.html\\\&quot;&gt;MDAnalysis&lt;/a&gt;&quot;) );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@mdt:&quot;,&quot;atom selection built using syntax for &lt;a href=\\\&quot;https://www.mdtraj.org/1.9.8.dev0/index.html\\\&quot;&gt;mdtraj&lt;/a&gt;&quot;) );</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@vmdexec:&quot;,&quot;atom selection built using syntax for &lt;a href=\\\&quot;https://www.ks.uiuc.edu/Research/vmd/\\\&quot;&gt;VMD&lt;/a&gt;&quot;) );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@vmd:&quot;,&quot;atom selection built using syntax for &lt;a href=\\\&quot;https://www.ks.uiuc.edu/Research/vmd/\\\&quot;&gt;VMD&lt;/a&gt; python module&quot;) );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@nucleic&quot;,&quot;all atoms that are part of a DNA or RNA molecule&quot;) );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@protein&quot;,&quot;all atoms that are part of a protein&quot;) );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@water&quot;,&quot;all water molecules&quot;) );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@ions&quot;,&quot;all the ions&quot;) );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@hydrogens&quot;,&quot;all hydrogen atoms&quot;) );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@nonhydrogens&quot;,&quot;all non hydrogen atoms&quot;) );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@phi-&quot;,&quot;the four atoms that are required to calculate the phi dihedral for&quot;) );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@psi-&quot;,&quot;the four atoms that are required to calculate the psi dihedral for&quot;) );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@omega-&quot;,&quot;the four atoms that are required to calculate the omega dihedral for&quot;) );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@chi1-&quot;,&quot;the four atoms that are required to calculate the chi1 dihedral for&quot;) );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@chi2-&quot;,&quot;the four atoms that are required to calculate the chi2 dihedral for&quot;) );</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@chi3-&quot;,&quot;the four atoms that are required to calculate the chi3 dihedral for&quot;) );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@chi4-&quot;,&quot;the four atoms that are required to calculate the chi4 dihedral for&quot;) );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@chi5-&quot;,&quot;the four atoms that are required to calculate the chi5 dihedral for&quot;) );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@sidechain-&quot;,&quot;the protein sidechain atoms in&quot;) );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@back-&quot;,&quot;the protein/dna/rna backbone atoms in&quot;) );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@alpha-&quot;,&quot;the four atoms that are required to calculate the alpha backbone dihedral for&quot;) );</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@beta-&quot;,&quot;the four atoms that are required to calculate the beta backbone dihedral for&quot;) );</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@gamma-&quot;,&quot;the four atoms that are required to calculate the gamma backbone dihedral for&quot;) );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@delta-&quot;,&quot;the four atoms that are required to calculate the delta backbone dihedral for&quot;) );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@epsilon-&quot;,&quot;the four atoms that are required to calculate the backbone epsilon dihedral for&quot;) );</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@zeta-&quot;,&quot;the four atoms that are required to calculate the zeta backbone dihedral for&quot;) );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@v0-&quot;,&quot;the four atoms that are required to calculate the v0 sugar dihedral for&quot;) );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@v1-&quot;,&quot;the four atoms that are required to calculate the v1 sugar dihedral for&quot;) );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@v2-&quot;,&quot;the four atoms that are required to calculate the v2 sugar dihedral for&quot;) );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@v3-&quot;,&quot;the four atoms that are required to calculate the v3 sugar dihedral for&quot;) );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@v4-&quot;,&quot;the four atoms that are required to calculate the v4 sugar dihedral for&quot;) );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@chi-&quot;,&quot;the four atoms that are required to alcullate the chi dihedral for&quot;) );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@sugar-&quot;,&quot;the heavy atoms of the sugar in&quot;) );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@base-&quot;,&quot;the heavy atoms of the base in&quot;) );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          1 :   mapkeys.insert( std::pair&lt;std::string,std::string&gt;(&quot;@lcs-&quot;,&quot;an ordered triplet of atoms on the 6-membered ring of the nucleobase in&quot;) );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :   return mapkeys;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         25 : void GenericMolInfo::getBackbone( std::vector&lt;std::string&gt;&amp; restrings, const std::string&amp; fortype, std::vector&lt; std::vector&lt;AtomNumber&gt; &gt;&amp; backbone ) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         25 :   if( fortype!=mytype ) error(&quot;cannot calculate a variable designed for &quot; + fortype + &quot; molecules for molecule type &quot; + mytype );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         25 :   if( MolDataClass::numberOfAtomsPerResidueInBackbone( mytype )==0 ) error(&quot;backbone is not defined for molecule type &quot; + mytype );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         25 :   if( read_backbone.size()!=0 ) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :     if( restrings.size()!=1 ) error(&quot;cannot interpret anything other than all for residues when using CHAIN keywords&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     if( restrings[0]!=&quot;all&quot; ) error(&quot;cannot interpret anything other than all for residues when using CHAIN keywords&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     backbone.resize( read_backbone.size() );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;read_backbone.size(); ++i) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :       backbone[i].resize( read_backbone[i].size() );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;read_backbone[i].size(); ++j) backbone[i][j]=read_backbone[i][j];</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span>            :   } else {</a>
+<a name="182"><span class="lineNum">     182 </span>            :     bool useter=false; // This is used to deal with terminal groups in WHOLEMOLECULES</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         25 :     if( restrings.size()==1 ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         23 :       useter=( restrings[0].find(&quot;ter&quot;)!=std::string::npos );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         23 :       if( restrings[0].find(&quot;all&quot;)!=std::string::npos ) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         21 :         std::vector&lt;std::string&gt; chains; pdb.getChainNames( chains );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        348 :         for(unsigned i=0; i&lt;chains.size(); ++i) {</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :           unsigned r_start, r_end; std::string errmsg, mm, nn;</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        327 :           pdb.getResidueRange( chains[i], r_start, r_end, errmsg );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        327 :           if( !useter ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        327 :             std::string resname = pdb.getResidueName( r_start );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        327 :             if( MolDataClass::isTerminalGroup( mytype, resname ) ) r_start++;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        327 :             resname = pdb.getResidueName( r_end );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        327 :             if( MolDataClass::isTerminalGroup( mytype, resname ) ) r_end--;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :           }</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        327 :           Tools::convert(r_start,mm); Tools::convert(r_end,nn);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        348 :           if(i==0) restrings[0] = mm + &quot;-&quot; + nn;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        612 :           else restrings.push_back(  mm + &quot;-&quot; + nn );</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :         }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         21 :       }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :     }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         25 :     Tools::interpretRanges(restrings);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :     // Convert the list of involved residues into a list of segments of chains</a>
+<a name="205"><span class="lineNum">     205 </span>            :     int nk, nj; std::vector&lt; std::vector&lt;unsigned&gt; &gt; segments;</a>
+<a name="206"><span class="lineNum">     206 </span>            :     std::vector&lt;unsigned&gt; thissegment;</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         25 :     Tools::convert(restrings[0],nk); thissegment.push_back(nk);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       2652 :     for(unsigned i=1; i&lt;restrings.size(); ++i) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       2627 :       Tools::convert(restrings[i-1],nk);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       2627 :       Tools::convert(restrings[i],nj);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       7265 :       if( (nk+1)!=nj || pdb.getChainID(nk)!=pdb.getChainID(nj) ) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        308 :         segments.push_back(thissegment);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        308 :         thissegment.resize(0);</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :       }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       2627 :       thissegment.push_back(nj);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :     }</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         25 :     segments.push_back( thissegment );</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :     // And now get the backbone atoms from each segment</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         25 :     backbone.resize( segments.size() );</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     std::vector&lt;AtomNumber&gt; atomnumbers;</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        358 :     for(unsigned i=0; i&lt;segments.size(); ++i) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       2985 :       for(unsigned j=0; j&lt;segments[i].size(); ++j) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       2652 :         std::string resname=pdb.getResidueName( segments[i][j] );</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       2652 :         if( !MolDataClass::allowedResidue(mytype, resname) ) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :           std::string num; Tools::convert( segments[i][j], num );</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :           error(&quot;residue &quot; + num + &quot; is not recognized for moltype &quot; + mytype );</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :         }</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       2652 :         if( !useter &amp;&amp; MolDataClass::isTerminalGroup( mytype, resname ) ) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :           std::string num; Tools::convert( segments[i][j], num );</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :           error(&quot;residue &quot; + num + &quot; appears to be a terminal group&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :         }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       2652 :         if( resname==&quot;GLY&quot; ) warning(&quot;GLY residues are achiral - assuming HA1 atom is in CB position&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       2652 :         MolDataClass::getBackboneForResidue( mytype, segments[i][j], pdb, atomnumbers );</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       2652 :         if( atomnumbers.size()==0 ) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :           std::string num; Tools::convert( segments[i][j], num );</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :           error(&quot;Could not find required backbone atom in residue number &quot; + num );</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :         } else {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      15912 :           for(unsigned k=0; k&lt;atomnumbers.size(); ++k) backbone[i].push_back( atomnumbers[k] );</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :         }</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       2652 :         atomnumbers.resize(0);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :       }</a>
+<a name="243"><span class="lineNum">     243 </span>            :     }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         25 :   }</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         25 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        617 : void GenericMolInfo::interpretSymbol( const std::string&amp; symbol, std::vector&lt;AtomNumber&gt;&amp; atoms ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       2414 :   if(Tools::startWith(symbol,&quot;mdt:&quot;) || Tools::startWith(symbol,&quot;mda:&quot;) || Tools::startWith(symbol,&quot;vmd:&quot;) || Tools::startWith(symbol,&quot;vmdexec:&quot;)) {</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         24 :     plumed_assert(enablePythonInterpreter);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         48 :     log&lt;&lt;&quot;  symbol &quot; + symbol + &quot; will be sent to python interpreter\n&quot;;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         24 :     if(!selector_running) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          3 :       log&lt;&lt;&quot;  MOLINFO &quot;&lt;&lt;getLabel()&lt;&lt;&quot;: starting python interpreter\n&quot;;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          3 :       if(comm.Get_rank()==0) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          4 :         selector=Tools::make_unique&lt;Subprocess&gt;(pythonCmd+&quot; \&quot;&quot;+config::getPlumedRoot()+&quot;\&quot;/scripts/selector.sh --pdb &quot; + reference);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          2 :         selector-&gt;stop();</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :       }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          3 :       selector_running=true;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :     }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         24 :     atoms.resize(0);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         24 :     if(comm.Get_rank()==0) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         16 :       int ok=0;</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :       std::string error_msg;</a>
+<a name="267"><span class="lineNum">     267 </span>            :       // this is a complicated way to have the exception propagated with MPI.</a>
+<a name="268"><span class="lineNum">     268 </span>            :       // It is necessary since only one process calls the selector.</a>
+<a name="269"><span class="lineNum">     269 </span>            :       // Probably I should recycle the exception propagation at library boundaries</a>
+<a name="270"><span class="lineNum">     270 </span>            :       // to allow transferring the exception to other processes.</a>
+<a name="271"><span class="lineNum">     271 </span>            :       try {</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         16 :         plumed_assert(selector) &lt;&lt; &quot;Python interpreter is disabled, selection &quot; + symbol + &quot; cannot be interpreted&quot;;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :         auto h=selector-&gt;contStop(); // stops again when it goes out of scope</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         16 :         (*selector) &lt;&lt; symbol &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         16 :         selector-&gt;flush();</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :         std::string res;</a>
+<a name="277"><span class="lineNum">     277 </span>            :         std::vector&lt;std::string&gt; words;</a>
+<a name="278"><span class="lineNum">     278 </span>            :         while(true) {</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         16 :           selector-&gt;getline(res);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         32 :           words=Tools::getWords(res);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         32 :           if(!words.empty() &amp;&amp; words[0]==&quot;Error&quot;) plumed_error()&lt;&lt;res;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         32 :           if(!words.empty() &amp;&amp; words[0]==&quot;Selection:&quot;) break;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :         }</a>
+<a name="284"><span class="lineNum">     284 </span>            :         words.erase(words.begin());</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        712 :         for(const auto &amp; w : words) {</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :           int n;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        696 :           if(w.empty()) continue;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        696 :           Tools::convert(w,n);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       1392 :           atoms.push_back(AtomNumber::serial(n));</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :         }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         16 :         ok=1;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         32 :       } catch (const Exception &amp; e) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :         error_msg=e.what();</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         16 :       comm.Bcast(ok,0);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         16 :       if(!ok) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :         size_t s=error_msg.length();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :         comm.Bcast(s,0);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :         comm.Bcast(error_msg,0);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :         throw Exception()&lt;&lt;error_msg;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :       }</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         16 :       size_t nat=atoms.size();</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         16 :       comm.Bcast(nat,0);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         16 :       comm.Bcast(atoms,0);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :     } else {</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          8 :       int ok=0;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :       std::string error_msg;</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          8 :       comm.Bcast(ok,0);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          8 :       if(!ok) {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :         size_t s;</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :         comm.Bcast(s,0);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :         error_msg.resize(s);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :         comm.Bcast(error_msg,0);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :         throw Exception()&lt;&lt;error_msg;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :       }</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          8 :       size_t nat=0;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          8 :       comm.Bcast(nat,0);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          8 :       atoms.resize(nat);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          8 :       comm.Bcast(atoms,0);</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :     }</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         24 :     log&lt;&lt;&quot;  selection interpreted using &quot;;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         54 :     if(Tools::startWith(symbol,&quot;mdt:&quot;)) log&lt;&lt;&quot;mdtraj &quot;&lt;&lt;cite(&quot;McGibbon et al, Biophys. J., 109, 1528 (2015)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         66 :     if(Tools::startWith(symbol,&quot;mda:&quot;)) log&lt;&lt;&quot;MDAnalysis &quot;&lt;&lt;cite(&quot;Gowers et al, Proceedings of the 15th Python in Science Conference, doi:10.25080/majora-629e541a-00e (2016)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         48 :     if(Tools::startWith(symbol,&quot;vmdexec:&quot;)) log&lt;&lt;&quot;VMD &quot;&lt;&lt;cite(&quot;Humphrey, Dalke, and Schulten, K., J. Molec. Graphics, 14, 33 (1996)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         48 :     if(Tools::startWith(symbol,&quot;vmd:&quot;)) log&lt;&lt;&quot;VMD (github.com/Eigenstate/vmd-python) &quot;&lt;&lt;cite(&quot;Humphrey, Dalke, and Schulten, K., J. Molec. Graphics, 14, 33 (1996)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         24 :     return;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :   }</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        593 :   MolDataClass::specialSymbol( mytype, symbol, pdb, atoms );</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        593 :   if(atoms.empty()) error(symbol + &quot; not found in your MOLINFO structure&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      47043 : std::string GenericMolInfo::getAtomName(AtomNumber a)const {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">      47043 :   return pdb.getAtomName(a);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        249 : bool GenericMolInfo::checkForAtom(AtomNumber a)const {</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        249 :   return pdb.checkForAtom(a);</span></a>
+<a name="338"><span class="lineNum">     338 </span>            : }</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      61067 : unsigned GenericMolInfo::getResidueNumber(AtomNumber a)const {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      61067 :   return pdb.getResidueNumber(a);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : }</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">      17337 : unsigned GenericMolInfo::getPDBsize()const {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">      17337 :   return pdb.size();</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : }</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      15015 : std::string GenericMolInfo::getResidueName(AtomNumber a)const {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">      15015 :   return pdb.getResidueName(a);</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 : std::string GenericMolInfo::getChainID(AtomNumber a)const {</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :   return pdb.getChainID(a);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">      37702 : Vector GenericMolInfo::getPosition(AtomNumber a)const {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">      37702 :   return pdb.getPosition(a);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : }</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          2 : bool GenericMolInfo::isWhole() const {</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          2 :   return iswhole_;</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : }</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">       5127 : void GenericMolInfo::prepare() {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">       5127 :   if(selector_running) {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          3 :     log&lt;&lt;&quot;  MOLINFO &quot;&lt;&lt;getLabel()&lt;&lt;&quot;: killing python interpreter\n&quot;;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :     selector.reset();</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          3 :     selector_running=false;</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :   }</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       5127 : }</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GenericMolInfo.h.func-sort-c.html b/coverage/core/GenericMolInfo.h.func-sort-c.html
new file mode 100644
index 0000000000..51aecb3444
--- /dev/null
+++ b/coverage/core/GenericMolInfo.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GenericMolInfo.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GenericMolInfo.h<span style="font-size: 80%;"> (<a href="GenericMolInfo.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GenericMolInfo.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.h.gcov.html#65">_ZN4PLMD14GenericMolInfo5applyEv</a></td>
+              <td class="coverFnHi">5127</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.h.gcov.html#64">_ZN4PLMD14GenericMolInfo9calculateEv</a></td>
+              <td class="coverFnHi">5127</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GenericMolInfo.h.func.html b/coverage/core/GenericMolInfo.h.func.html
new file mode 100644
index 0000000000..bdf367d555
--- /dev/null
+++ b/coverage/core/GenericMolInfo.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GenericMolInfo.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GenericMolInfo.h<span style="font-size: 80%;"> (<a href="GenericMolInfo.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GenericMolInfo.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.h.gcov.html#65">_ZN4PLMD14GenericMolInfo5applyEv</a></td>
+              <td class="coverFnHi">5127</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GenericMolInfo.h.gcov.html#64">_ZN4PLMD14GenericMolInfo9calculateEv</a></td>
+              <td class="coverFnHi">5127</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/GenericMolInfo.h.gcov.html b/coverage/core/GenericMolInfo.h.gcov.html
new file mode 100644
index 0000000000..1f576e2a06
--- /dev/null
+++ b/coverage/core/GenericMolInfo.h.gcov.html
@@ -0,0 +1,165 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/GenericMolInfo.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - GenericMolInfo.h<span style="font-size: 80%;"> (source / <a href="GenericMolInfo.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_GenericMolInfo_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_GenericMolInfo_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionSetup.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionPilot.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ActionAnyorder.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/ForwardDecl.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Subprocess.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;memory&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;map&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class PDB;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class GenericMolInfo :</a>
+<a name="40"><span class="lineNum">      40 </span>            :   public ActionAnyorder,</a>
+<a name="41"><span class="lineNum">      41 </span>            :   public ActionPilot,</a>
+<a name="42"><span class="lineNum">      42 </span>            :   public ActionAtomistic {</a>
+<a name="43"><span class="lineNum">      43 </span>            : private:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   ForwardDecl&lt;PDB&gt; pdb_fwd;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// A pdb file containing the topology</a>
+<a name="46"><span class="lineNum">      46 </span>            :   PDB&amp; pdb=*pdb_fwd;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// The type of molecule in the pdb</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::string mytype;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// The name of the reference pdb file</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string reference;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// The backbone that was read in from the pdb file</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt; std::vector&lt;AtomNumber&gt; &gt; read_backbone;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Python interpreter is enabled</a>
+<a name="54"><span class="lineNum">      54 </span>            :   bool enablePythonInterpreter=false;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Python command</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::string pythonCmd;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Selector subprocess</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::unique_ptr&lt;Subprocess&gt; selector;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Track is selector is running</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Needed on Get_rank()&gt;0</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool selector_running=false;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Structure in pdb file is whole</a>
+<a name="63"><span class="lineNum">      63 </span>            :   bool iswhole_;</a>
+<a name="64"><span class="lineNum">      64 </span>            : public:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   ~GenericMolInfo();</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       5127 :   void calculate() override {}</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       5127 :   void apply() override {}</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="69"><span class="lineNum">      69 </span>            :   static std::map&lt;std::string,std::string&gt; getSpecialKeywords();</a>
+<a name="70"><span class="lineNum">      70 </span>            :   explicit GenericMolInfo(const ActionOptions&amp;ao);</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void getBackbone( std::vector&lt;std::string&gt;&amp; resstrings, const std::string&amp; fortype, std::vector&lt; std::vector&lt;AtomNumber&gt; &gt;&amp; backbone );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::string getAtomName(AtomNumber a)const;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   bool checkForAtom(AtomNumber a)const;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   unsigned getResidueNumber(AtomNumber a)const;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::string getChainID(AtomNumber a)const;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   Vector getPosition(AtomNumber a)const;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool isWhole() const;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   unsigned getPDBsize()const ;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::string getResidueName(AtomNumber a)const;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void interpretSymbol( const std::string&amp; symbol, std::vector&lt;AtomNumber&gt;&amp; atoms );</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Calculate is used to kill the python interpreter.</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// We do this in order to avoid possible interference or slowing down of the simulation</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// due to the extra subprocess.</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void prepare() override;</a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/MDAtoms.cpp.func-sort-c.html b/coverage/core/MDAtoms.cpp.func-sort-c.html
new file mode 100644
index 0000000000..39d8e29ce0
--- /dev/null
+++ b/coverage/core/MDAtoms.cpp.func-sort-c.html
@@ -0,0 +1,340 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/MDAtoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - MDAtoms.cpp<span style="font-size: 80%;"> (<a href="MDAtoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntry">181</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntryLo">49.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MDAtoms.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#94">_ZN4PLMD12MDAtomsTypedIfE10getExtraCVERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#86">_ZN4PLMD12MDAtomsTypedIfE10setExtraCVERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#269">_ZN4PLMD12MDAtomsTypedIfE12updateForcesERKSt6vectorINS_10AtomNumberESaIS3_EERKS2_IjSaIjEERKS2_INS_13VectorGenericILj3EEESaISD_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#292">_ZN4PLMD12MDAtomsTypedIfE12updateForcesERKSt6vectorIiSaIiEERKS2_INS_13VectorGenericILj3EEESaIS8_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#308">_ZN4PLMD12MDAtomsTypedIfE13rescaleForcesERKSt6vectorIiSaIiEEd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#90">_ZN4PLMD12MDAtomsTypedIfE15setExtraCVForceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#107">_ZN4PLMD12MDAtomsTypedIfE16setExtraCVNeededERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#117">_ZN4PLMD12MDAtomsTypedIfE18resetExtraCVNeededEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#103">_ZN4PLMD12MDAtomsTypedIfE18updateExtraCVForceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#387">_ZN4PLMD12MDAtomsTypedIfE4setcERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#347">_ZN4PLMD12MDAtomsTypedIfE4setfERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#372">_ZN4PLMD12MDAtomsTypedIfE4setfERKNS_11TypesafePtrEi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#381">_ZN4PLMD12MDAtomsTypedIfE4setmERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MDAtoms.cpp.gcov.html#331">_ZN4PLMD12MDAtomsTypedIfE4setpERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnLo">0</td>
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diff --git a/coverage/core/MDAtoms.cpp.func.html b/coverage/core/MDAtoms.cpp.func.html
new file mode 100644
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/MDAtoms.cpp.gcov.html b/coverage/core/MDAtoms.cpp.gcov.html
new file mode 100644
index 0000000000..90aea471e4
--- /dev/null
+++ b/coverage/core/MDAtoms.cpp.gcov.html
@@ -0,0 +1,480 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/MDAtoms.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - MDAtoms.cpp<span style="font-size: 80%;"> (source / <a href="MDAtoms.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntry">181</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntryLo">49.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MDAtoms.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;algorithm&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;map&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : template&lt;typename T&gt;</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     107752 : static void getPointers(const TypesafePtr &amp; p,const TypesafePtr &amp; px,const TypesafePtr &amp; py,const TypesafePtr &amp; pz,unsigned maxel,T*&amp;ppx,T*&amp;ppy,T*&amp;ppz,unsigned &amp; stride) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     107752 :   if(p) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     107714 :     auto p_=p.get&lt;T*&gt;({maxel,3});</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     107714 :     ppx=p_;</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     107714 :     ppy=p_+1;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     107714 :     ppz=p_+2;</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     107714 :     stride=3;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         38 :   } else if(px &amp;&amp; py &amp;&amp; pz) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          2 :     ppx=px.get&lt;T*&gt;(maxel);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          2 :     ppy=py.get&lt;T*&gt;(maxel);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          2 :     ppz=pz.get&lt;T*&gt;(maxel);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          2 :     stride=1;</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   } else {</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         36 :     ppx=nullptr;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         36 :     ppy=nullptr;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         36 :     ppz=nullptr;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         36 :     stride=0;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   }</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     107752 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Class containing the pointers to the MD data</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// It is templated so that single and double precision versions coexist</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// IT IS STILL UNDOCUMENTED. IT PROBABLY NEEDS A STRONG CLEANUP</a>
+<a name="57"><span class="lineNum">      57 </span>            : template &lt;class T&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : class MDAtomsTyped:</a>
+<a name="59"><span class="lineNum">      59 </span>            :   public MDAtomsBase</a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span>            :   T scalep=1.0; // factor to scale positions</a>
+<a name="62"><span class="lineNum">      62 </span>            :   T scalef=1.0; // factor to scale forces</a>
+<a name="63"><span class="lineNum">      63 </span>            :   T scaleb=1.0; // factor to scale box</a>
+<a name="64"><span class="lineNum">      64 </span>            :   T scalev=1.0; // factor to scale virial</a>
+<a name="65"><span class="lineNum">      65 </span>            :   T scalec=1.0; // factor to scale charges</a>
+<a name="66"><span class="lineNum">      66 </span>            :   T scalem=1.0; // factor to scale masses</a>
+<a name="67"><span class="lineNum">      67 </span>            :   TypesafePtr m;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   TypesafePtr c;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   TypesafePtr p;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   TypesafePtr px,py,pz;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   TypesafePtr f;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   TypesafePtr fx,fy,fz;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   TypesafePtr box;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   TypesafePtr virial;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::map&lt;std::string,TypesafePtr&gt; extraCV;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::map&lt;std::string,TypesafePtr&gt; extraCVForce;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::map&lt;std::string,bool&gt; extraCVNeeded;</a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void setm(const TypesafePtr &amp; m) override;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void setc(const TypesafePtr &amp; m) override;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void setBox(const TypesafePtr &amp; ) override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void setp(const TypesafePtr &amp; p) override;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void setVirial(const TypesafePtr &amp; ) override;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void setf(const TypesafePtr &amp; f) override;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void setp(const TypesafePtr &amp; p,int i) override;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void setf(const TypesafePtr &amp; f,int i) override;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void setUnits(const Units&amp;,const Units&amp;) override;</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         30 :   void setExtraCV(const std::string &amp;name,const TypesafePtr &amp; p) override {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         30 :     p.get&lt;T&gt;(); // just check type and discard pointer</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         30 :     extraCV[name]=p.copy();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         30 :   }</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         30 :   void setExtraCVForce(const std::string &amp;name,const TypesafePtr &amp; p) override {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         30 :     p.get&lt;T*&gt;(); // just check type and discard pointer</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         30 :     extraCVForce[name]=p.copy();</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         30 :   }</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         72 :   double getExtraCV(const std::string &amp;name) override {</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :     auto search=extraCV.find(name);</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         72 :     if(search != extraCV.end()) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         72 :       return static_cast&lt;double&gt;(search-&gt;second.template get&lt;T&gt;());</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :     } else {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :       plumed_error() &lt;&lt; &quot;Unable to access extra cv named '&quot; &lt;&lt; name &lt;&lt; &quot;'.\nNotice that extra cvs need to be calculated in the MD code.&quot;;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     }</a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         48 :   void updateExtraCVForce(const std::string &amp;name,double f) override {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         48 :     *extraCVForce[name].template get&lt;T*&gt;()+=static_cast&lt;T&gt;(f);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         48 :   }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         72 :   void setExtraCVNeeded(const std::string &amp;name,bool needed=true) override {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         72 :     extraCVNeeded[name]=needed;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         72 :   }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         10 :   bool isExtraCVNeeded(const std::string &amp;name) const override {</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     auto search=extraCVNeeded.find(name);</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         10 :     if(search != extraCVNeeded.end()) return search-&gt;second;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     return false;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     256144 :   void resetExtraCVNeeded() override {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     256171 :     for(auto &amp; i : extraCVNeeded) i.second=false;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     256144 :   }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      13198 :   void MD2double(const TypesafePtr &amp; m,double&amp;d)const override {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      13198 :     d=double(m.template get&lt;T&gt;());</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      13198 :   }</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       2390 :   void double2MD(const double&amp;d,const TypesafePtr &amp; m)const override {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       2390 :     m.set(T(d));</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       2390 :   }</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :   Vector getMDforces(const unsigned index)const override {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :     unsigned stride;</a>
+<a name="131"><span class="lineNum">     131 </span>            :     const T* ffx;</a>
+<a name="132"><span class="lineNum">     132 </span>            :     const T* ffy;</a>
+<a name="133"><span class="lineNum">     133 </span>            :     const T* ffz;</a>
+<a name="134"><span class="lineNum">     134 </span>            :     // node: index+1 because we are supposed to pass here the size of the array, which should be at least the element we are asking for + 1</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     getPointers(f,fx,fy,fz,index+1,ffx,ffy,ffz,stride);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     Vector force(ffx[stride*index],ffy[stride*index],ffz[stride*index]);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     return force/scalef;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void getBox(Tensor &amp;) const override;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   void getPositions(const std::vector&lt;int&gt;&amp;index,std::vector&lt;Vector&gt;&amp;positions) const override;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void getPositions(const std::vector&lt;AtomNumber&gt;&amp;index,const std::vector&lt;unsigned&gt;&amp;i,std::vector&lt;Vector&gt;&amp;positions) const override;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void getPositions(unsigned j,unsigned k,std::vector&lt;Vector&gt;&amp;positions) const override;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   void getLocalPositions(std::vector&lt;Vector&gt;&amp;p) const override;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   void getMasses(const std::vector&lt;int&gt;&amp;index,std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   void getCharges(const std::vector&lt;int&gt;&amp;index,std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void updateVirial(const Tensor&amp;) const override;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void updateForces(const std::vector&lt;int&gt;&amp;index,const std::vector&lt;Vector&gt;&amp;) override;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   void updateForces(const std::vector&lt;AtomNumber&gt;&amp;index,const std::vector&lt;unsigned&gt;&amp;i,const std::vector&lt;Vector&gt;&amp;forces) override;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void rescaleForces(const std::vector&lt;int&gt;&amp;index,double factor) override;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   unsigned  getRealPrecision()const override;</a>
+<a name="151"><span class="lineNum">     151 </span>            : };</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : template &lt;class T&gt;</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1027 : void MDAtomsTyped&lt;T&gt;::setUnits(const Units&amp; units,const Units&amp; MDUnits) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       1027 :   double lscale=units.getLength()/MDUnits.getLength();</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       1027 :   double escale=units.getEnergy()/MDUnits.getEnergy();</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1027 :   double cscale=units.getCharge()/MDUnits.getCharge();</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1027 :   double mscale=units.getMass()/MDUnits.getMass();</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : // scalep and scaleb are used to convert MD to plumed</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1027 :   scalep=1.0/lscale;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1027 :   scaleb=1.0/lscale;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : // scalef and scalev are used to convert plumed to MD</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       1027 :   scalef=escale/lscale;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       1027 :   scalev=escale;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       1027 :   scalec=1.0/cscale;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       1027 :   scalem=1.0/mscale;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1027 : }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : template &lt;class T&gt;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     105956 : void MDAtomsTyped&lt;T&gt;::getBox(Tensor&amp;box)const {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     105956 :   auto b=this-&gt;box.template get&lt;const T*&gt;({3,3});</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">    1328924 :   if(b) for(int i=0; i&lt;3; i++)for(int j=0; j&lt;3; j++) box(i,j)=b[3*i+j]*scaleb;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       4042 :   else box.zero();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     105956 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : template &lt;class T&gt;</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 : void MDAtomsTyped&lt;T&gt;::getPositions(const std::vector&lt;int&gt;&amp;index,std::vector&lt;Vector&gt;&amp;positions)const {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   unsigned stride;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   const T* ppx;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   const T* ppy;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   const T* ppz;</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   getPointers(p,px,py,pz,index.size(),ppx,ppy,ppz,stride);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   plumed_assert(index.size()==0 || (ppx &amp;&amp; ppy &amp;&amp; ppz));</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : // cannot be parallelized with omp because access to positions is not ordered</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;index.size(); ++i) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     positions[index[i]][0]=ppx[stride*i]*scalep;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     positions[index[i]][1]=ppy[stride*i]*scalep;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     positions[index[i]][2]=ppz[stride*i]*scalep;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : template &lt;class T&gt;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      25958 : void MDAtomsTyped&lt;T&gt;::getPositions(const std::vector&lt;AtomNumber&gt;&amp;index,const std::vector&lt;unsigned&gt;&amp;i, std::vector&lt;Vector&gt;&amp;positions)const {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   unsigned stride;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   const T* ppx;</a>
+<a name="196"><span class="lineNum">     196 </span>            :   const T* ppy;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   const T* ppz;</a>
+<a name="198"><span class="lineNum">     198 </span>            : #ifndef NDEBUG</a>
+<a name="199"><span class="lineNum">     199 </span>            : // bounds are only checked in debug mode since they require this extra step that is potentially expensive</a>
+<a name="200"><span class="lineNum">     200 </span>            :   const unsigned maxel=(i.size()&gt;0?*std::max_element(i.begin(),i.end())+1:0);</a>
+<a name="201"><span class="lineNum">     201 </span>            : #else</a>
+<a name="202"><span class="lineNum">     202 </span>            :   const unsigned maxel=0;</a>
+<a name="203"><span class="lineNum">     203 </span>            : #endif</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      25958 :   getPointers(p,px,py,pz,maxel,ppx,ppy,ppz,stride);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      25958 :   plumed_assert(index.size()==0 || (ppx &amp;&amp; ppy &amp;&amp; ppz));</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : // cannot be parallelized with omp because access to positions is not ordered</a>
+<a name="207"><span class="lineNum">     207 </span>            :   unsigned k=0;</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     403747 :   for(const auto &amp; p : index) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     377789 :     positions[p.index()][0]=ppx[stride*i[k]]*scalep;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     377789 :     positions[p.index()][1]=ppy[stride*i[k]]*scalep;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">     377789 :     positions[p.index()][2]=ppz[stride*i[k]]*scalep;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     377789 :     k++;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      25958 : }</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : template &lt;class T&gt;</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      27109 : void MDAtomsTyped&lt;T&gt;::getPositions(unsigned j,unsigned k,std::vector&lt;Vector&gt;&amp;positions)const {</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   unsigned stride;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   const T* ppx;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   const T* ppy;</a>
+<a name="221"><span class="lineNum">     221 </span>            :   const T* ppz;</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      27109 :   getPointers(p,px,py,pz,k,ppx,ppy,ppz,stride);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      27109 :   plumed_assert(k==j || (ppx &amp;&amp; ppy &amp;&amp; ppz));</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      27109 :   #pragma omp parallel for num_threads(OpenMP::getGoodNumThreads(&amp;positions[j],(k-j)))</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   for(unsigned i=j; i&lt;k; ++i) {</a>
+<a name="226"><span class="lineNum">     226 </span>            :     positions[i][0]=ppx[stride*i]*scalep;</a>
+<a name="227"><span class="lineNum">     227 </span>            :     positions[i][1]=ppy[stride*i]*scalep;</a>
+<a name="228"><span class="lineNum">     228 </span>            :     positions[i][2]=ppz[stride*i]*scalep;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      27109 : }</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : template &lt;class T&gt;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        450 : void MDAtomsTyped&lt;T&gt;::getLocalPositions(std::vector&lt;Vector&gt;&amp;positions)const {</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   unsigned stride;</a>
+<a name="236"><span class="lineNum">     236 </span>            :   const T* ppx;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   const T* ppy;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   const T* ppz;</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        450 :   getPointers(p,px,py,pz,positions.size(),ppx,ppy,ppz,stride);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        450 :   plumed_assert(positions.size()==0 || (ppx &amp;&amp; ppy &amp;&amp; ppz));</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        450 :   #pragma omp parallel for num_threads(OpenMP::getGoodNumThreads(positions))</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   for(unsigned i=0; i&lt;positions.size(); ++i) {</a>
+<a name="243"><span class="lineNum">     243 </span>            :     positions[i][0]=ppx[stride*i]*scalep;</a>
+<a name="244"><span class="lineNum">     244 </span>            :     positions[i][1]=ppy[stride*i]*scalep;</a>
+<a name="245"><span class="lineNum">     245 </span>            :     positions[i][2]=ppz[stride*i]*scalep;</a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        450 : }</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : template &lt;class T&gt;</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        876 : void MDAtomsTyped&lt;T&gt;::getMasses(const std::vector&lt;int&gt;&amp;index,std::vector&lt;double&gt;&amp;masses)const {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        876 :   auto mm=m.get&lt;const T*&gt;(index.size());</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">     835240 :   if(mm) for(unsigned i=0; i&lt;index.size(); ++i) masses[index[i]]=scalem*mm[i];</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   else  for(unsigned i=0; i&lt;index.size(); ++i) masses[index[i]]=0.0;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        876 : }</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : template &lt;class T&gt;</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        876 : void MDAtomsTyped&lt;T&gt;::getCharges(const std::vector&lt;int&gt;&amp;index,std::vector&lt;double&gt;&amp;charges)const {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        876 :   auto cc=c.get&lt;const T*&gt;(index.size());</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">     833653 :   if(cc) for(unsigned i=0; i&lt;index.size(); ++i) charges[index[i]]=scalec*cc[i];</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       1587 :   else  for(unsigned i=0; i&lt;index.size(); ++i) charges[index[i]]=0.0;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        876 : }</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : template &lt;class T&gt;</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      39613 : void MDAtomsTyped&lt;T&gt;::updateVirial(const Tensor&amp;virial)const {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">      39613 :   auto v=this-&gt;virial.template get&lt;T*&gt;({3,3});</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">     514969 :   if(v) for(int i=0; i&lt;3; i++)for(int j=0; j&lt;3; j++) v[3*i+j]+=T(virial(i,j)*scalev);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      39613 : }</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            : template &lt;class T&gt;</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      27027 : void MDAtomsTyped&lt;T&gt;::updateForces(const std::vector&lt;AtomNumber&gt;&amp;index,const std::vector&lt;unsigned&gt;&amp;i,const std::vector&lt;Vector&gt;&amp;forces) {</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :   unsigned stride;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   T* ffx;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   T* ffy;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   T* ffz;</a>
+<a name="276"><span class="lineNum">     276 </span>            : #ifndef NDEBUG</a>
+<a name="277"><span class="lineNum">     277 </span>            : // bounds are only checked in debug mode since they require this extra step that is potentially expensive</a>
+<a name="278"><span class="lineNum">     278 </span>            :   const unsigned maxel=(i.size()&gt;0?*std::max_element(i.begin(),i.end())+1:0);</a>
+<a name="279"><span class="lineNum">     279 </span>            : #else</a>
+<a name="280"><span class="lineNum">     280 </span>            :   const unsigned maxel=0;</a>
+<a name="281"><span class="lineNum">     281 </span>            : #endif</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">      27027 :   getPointers(f,fx,fy,fz,maxel,ffx,ffy,ffz,stride);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">      27027 :   plumed_assert(index.size()==0 || (ffx &amp;&amp; ffy &amp;&amp; ffz));</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   unsigned k=0;</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     399162 :   for(const auto &amp; p : index) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">     372135 :     ffx[stride*i[k]]+=scalef*T(forces[p.index()][0]);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     372135 :     ffy[stride*i[k]]+=scalef*T(forces[p.index()][1]);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     372135 :     ffz[stride*i[k]]+=scalef*T(forces[p.index()][2]);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     372135 :     k++;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">      27027 : }</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            : template &lt;class T&gt;</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      27158 : void MDAtomsTyped&lt;T&gt;::updateForces(const std::vector&lt;int&gt;&amp;index,const std::vector&lt;Vector&gt;&amp;forces) {</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   unsigned stride;</a>
+<a name="296"><span class="lineNum">     296 </span>            :   T* ffx;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   T* ffy;</a>
+<a name="298"><span class="lineNum">     298 </span>            :   T* ffz;</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      27158 :   getPointers(f,fx,fy,fz,index.size(),ffx,ffy,ffz,stride);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">      27158 :   plumed_assert(index.size()==0 || (ffx &amp;&amp; ffy &amp;&amp; ffz));</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">      27158 :   #pragma omp parallel for num_threads(OpenMP::getGoodNumThreads(ffx,stride*index.size()))</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   for(unsigned i=0; i&lt;index.size(); ++i) {</a>
+<a name="303"><span class="lineNum">     303 </span>            :     ffx[stride*i]+=scalef*T(forces[index[i]][0]);</a>
+<a name="304"><span class="lineNum">     304 </span>            :     ffy[stride*i]+=scalef*T(forces[index[i]][1]);</a>
+<a name="305"><span class="lineNum">     305 </span>            :     ffz[stride*i]+=scalef*T(forces[index[i]][2]);</a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">      27158 : }</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : template &lt;class T&gt;</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         50 : void MDAtomsTyped&lt;T&gt;::rescaleForces(const std::vector&lt;int&gt;&amp;index,double factor) {</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   unsigned stride;</a>
+<a name="312"><span class="lineNum">     312 </span>            :   T* ffx;</a>
+<a name="313"><span class="lineNum">     313 </span>            :   T* ffy;</a>
+<a name="314"><span class="lineNum">     314 </span>            :   T* ffz;</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         50 :   getPointers(f,fx,fy,fz,index.size(),ffx,ffy,ffz,stride);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         50 :   plumed_assert(index.size()==0 || (ffx &amp;&amp; ffy &amp;&amp; ffz));</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         50 :   auto v=virial.get&lt;T*&gt;({3,3});</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         50 :   if(v) for(unsigned i=0; i&lt;3; i++)for(unsigned j=0; j&lt;3; j++) v[3*i+j]*=T(factor);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         50 :   #pragma omp parallel for num_threads(OpenMP::getGoodNumThreads(ffx,stride*index.size()))</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   for(unsigned i=0; i&lt;index.size(); ++i) {</a>
+<a name="321"><span class="lineNum">     321 </span>            :     ffx[stride*i]*=T(factor);</a>
+<a name="322"><span class="lineNum">     322 </span>            :     ffy[stride*i]*=T(factor);</a>
+<a name="323"><span class="lineNum">     323 </span>            :     ffz[stride*i]*=T(factor);</a>
+<a name="324"><span class="lineNum">     324 </span>            :   }</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         50 : }</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            : template &lt;class T&gt;</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       1873 : unsigned MDAtomsTyped&lt;T&gt;::getRealPrecision()const {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       1873 :   return sizeof(T);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            : template &lt;class T&gt;</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">      55788 : void MDAtomsTyped&lt;T&gt;::setp(const TypesafePtr &amp; pp) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      55788 :   pp.get&lt;const T*&gt;(); // just check type and discard pointer</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      55788 :   p=pp.copy();</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">      55788 :   px=TypesafePtr();</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      55788 :   py=TypesafePtr();</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      55788 :   pz=TypesafePtr();</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      55788 : }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : template &lt;class T&gt;</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">      51647 : void MDAtomsTyped&lt;T&gt;::setBox(const TypesafePtr &amp; pp) {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">      51647 :   pp.get&lt;const T*&gt;({3,3}); // just check type and size and discard pointer</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">      51647 :   box=pp.copy();</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">      51647 : }</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            : template &lt;class T&gt;</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">      55788 : void MDAtomsTyped&lt;T&gt;::setf(const TypesafePtr &amp; ff) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">      55788 :   ff.get&lt;T*&gt;(); // just check type and discard pointer</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">      55788 :   f=ff.copy();</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">      55788 :   fx=TypesafePtr();</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">      55788 :   fy=TypesafePtr();</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">      55788 :   fz=TypesafePtr();</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      55788 : }</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : template &lt;class T&gt;</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          3 : void MDAtomsTyped&lt;T&gt;::setp(const TypesafePtr &amp; pp,int i) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          3 :   p=TypesafePtr();</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          3 :   pp.get&lt;const T*&gt;(); // just check type and discard pointer</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          3 :   if(i==0)px=pp.copy();</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          3 :   if(i==1)py=pp.copy();</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          3 :   if(i==2)pz=pp.copy();</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          3 : }</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            : template &lt;class T&gt;</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">      45989 : void MDAtomsTyped&lt;T&gt;::setVirial(const TypesafePtr &amp; pp) {</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">      45989 :   pp.get&lt;T*&gt;({3,3}); // just check type and size and discard pointer</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">      45987 :   virial=pp.copy();</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      45987 : }</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            : template &lt;class T&gt;</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          3 : void MDAtomsTyped&lt;T&gt;::setf(const TypesafePtr &amp; ff,int i) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          3 :   f=TypesafePtr();;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          3 :   ff.get&lt;T*&gt;(); // just check type and discard pointer</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          3 :   if(i==0)fx=ff.copy();</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          3 :   if(i==1)fy=ff.copy();</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">          3 :   if(i==2)fz=ff.copy();</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">          3 : }</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            : template &lt;class T&gt;</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">      55789 : void MDAtomsTyped&lt;T&gt;::setm(const TypesafePtr &amp; m) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">      55789 :   m.get&lt;const T*&gt;(); // just check type and discard pointer</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      55789 :   this-&gt;m=m.copy();</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">      55789 : }</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            : template &lt;class T&gt;</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      45883 : void MDAtomsTyped&lt;T&gt;::setc(const TypesafePtr &amp; c) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      45883 :   c.get&lt;const T*&gt;(); // just check type and discard pointer</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">      45883 :   this-&gt;c=c.copy();</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">      45883 : }</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">     806145 : std::unique_ptr&lt;MDAtomsBase&gt; MDAtomsBase::create(unsigned p) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">     806145 :   if(p==sizeof(double)) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">     806144 :     return Tools::make_unique&lt;MDAtomsTyped&lt;double&gt;&gt;();</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          1 :   } else if (p==sizeof(float)) {</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          1 :     return Tools::make_unique&lt;MDAtomsTyped&lt;float&gt;&gt;();</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :   }</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :   plumed_error() &lt;&lt; &quot;Cannot create an MD interface with sizeof(real)==&quot; &lt;&lt; p;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : }</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            : }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ModuleMap.cpp.func-sort-c.html b/coverage/core/ModuleMap.cpp.func-sort-c.html
new file mode 100644
index 0000000000..38ea1328c4
--- /dev/null
+++ b/coverage/core/ModuleMap.cpp.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ModuleMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ModuleMap.cpp<span style="font-size: 80%;"> (<a href="ModuleMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ModuleMap.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ModuleMap.cpp.gcov.html#23">_ZN4PLMD12getModuleMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">292</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ModuleMap.cpp.func.html b/coverage/core/ModuleMap.cpp.func.html
new file mode 100644
index 0000000000..82726faff7
--- /dev/null
+++ b/coverage/core/ModuleMap.cpp.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ModuleMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ModuleMap.cpp<span style="font-size: 80%;"> (<a href="ModuleMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ModuleMap.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ModuleMap.cpp.gcov.html#23">_ZN4PLMD12getModuleMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">292</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/ModuleMap.cpp.gcov.html b/coverage/core/ModuleMap.cpp.gcov.html
new file mode 100644
index 0000000000..c17be873b0
--- /dev/null
+++ b/coverage/core/ModuleMap.cpp.gcov.html
@@ -0,0 +1,107 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/ModuleMap.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - ModuleMap.cpp<span style="font-size: 80%;"> (source / <a href="ModuleMap.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2024-2024 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ModuleMap.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span><span class="lineCov">        292 : const std::map&lt;std::string,std::string&gt; &amp; getModuleMap() {</span></a>
+<a name="26"><span class="lineNum">      26 </span>            :   static const std::map&lt;std::string,std::string&gt; actionToModule= {</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ModuleMap.inc&quot;</a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        584 :   };</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        292 :   return actionToModule;</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : }</a>
+<a name="31"><span class="lineNum">      31 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMain.cpp.func-sort-c.html b/coverage/core/PlumedMain.cpp.func-sort-c.html
new file mode 100644
index 0000000000..bb281d3985
--- /dev/null
+++ b/coverage/core/PlumedMain.cpp.func-sort-c.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMain.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMain.cpp<span style="font-size: 80%;"> (<a href="PlumedMain.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">644</td>
+            <td class="headerCovTableEntry">721</td>
+            <td class="headerCovTableEntryMed">89.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PlumedMain.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1148">_ZN4PLMD10PlumedMain21activateParseOnlyModeEv</a></td>
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+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#916">_ZN4PLMD10PlumedMain8waitDataEv</a></td>
+              <td class="coverFnHi">256297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#855">_ZN4PLMD10PlumedMain19prepareDependenciesEv</a></td>
+              <td class="coverFnHi">256426</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#222">_ZN4PLMD10PlumedMainD0Ev</a></td>
+              <td class="coverFnHi">804455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#193">_ZN4PLMD10PlumedMainC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#222">_ZN4PLMD10PlumedMainD2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#234">_ZN4PLMD10PlumedMain3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">1118951</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1140">_ZN4PLMD10PlumedMain24decreaseReferenceCounterEv</a></td>
+              <td class="coverFnHi">8804428</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1136">_ZN4PLMD10PlumedMain24increaseReferenceCounterEv</a></td>
+              <td class="coverFnHi">8805343</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMain.cpp.func.html b/coverage/core/PlumedMain.cpp.func.html
new file mode 100644
index 0000000000..746a5265d4
--- /dev/null
+++ b/coverage/core/PlumedMain.cpp.func.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMain.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMain.cpp<span style="font-size: 80%;"> (<a href="PlumedMain.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">644</td>
+            <td class="headerCovTableEntry">721</td>
+            <td class="headerCovTableEntryMed">89.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PlumedMain.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1118">_ZN4PLMD10PlumedMain10insertFileERNS_8FileBaseE</a></td>
+              <td class="coverFnHi">4536</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#908">_ZN4PLMD10PlumedMain11performCalcEv</a></td>
+              <td class="coverFnHi">254039</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#846">_ZN4PLMD10PlumedMain11prepareCalcEv</a></td>
+              <td class="coverFnHi">256099</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#923">_ZN4PLMD10PlumedMain13justCalculateEv</a></td>
+              <td class="coverFnHi">256297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#744">_ZN4PLMD10PlumedMain13readInputFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">883</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#757">_ZN4PLMD10PlumedMain13readInputFileERNS_5IFileE</a></td>
+              <td class="coverFnHi">884</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#764">_ZN4PLMD10PlumedMain13readInputLineERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">358</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#777">_ZN4PLMD10PlumedMain14readInputLinesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#805">_ZN4PLMD10PlumedMain14readInputWordsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE</a></td>
+              <td class="coverFnHi">14463</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#981">_ZN4PLMD10PlumedMain17backwardPropagateEv</a></td>
+              <td class="coverFnHi">256173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#903">_ZN4PLMD10PlumedMain19performCalcNoForcesEv</a></td>
+              <td class="coverFnHi">10</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#897">_ZN4PLMD10PlumedMain19performCalcNoUpdateEv</a></td>
+              <td class="coverFnHi">2134</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#855">_ZN4PLMD10PlumedMain19prepareDependenciesEv</a></td>
+              <td class="coverFnHi">256426</td>
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+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1148">_ZN4PLMD10PlumedMain21activateParseOnlyModeEv</a></td>
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+              <td class="coverFnHi">8804428</td>
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+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1136">_ZN4PLMD10PlumedMain24increaseReferenceCounterEv</a></td>
+              <td class="coverFnHi">8805343</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1130">_ZN4PLMD10PlumedMain25runJobsAtEndOfCalculationEv</a></td>
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+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#703">_ZN4PLMD10PlumedMain4initEv</a></td>
+              <td class="coverFnHi">1007</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1051">_ZN4PLMD10PlumedMain4loadERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1126">_ZN4PLMD10PlumedMain4stopEv</a></td>
+              <td class="coverFnHi">65</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1093">_ZN4PLMD10PlumedMain5fopenEPKcS2_</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1104">_ZN4PLMD10PlumedMain6fcloseEP8_IO_FILE</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1112">_ZN4PLMD10PlumedMain6fflushEv</a></td>
+              <td class="coverFnHi">1539</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#837">_ZN4PLMD10PlumedMain6getLogEv</a></td>
+              <td class="coverFnHi">14302</td>
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+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1021">_ZN4PLMD10PlumedMain6updateEv</a></td>
+              <td class="coverFnHi">254118</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#916">_ZN4PLMD10PlumedMain8waitDataEv</a></td>
+              <td class="coverFnHi">256297</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1122">_ZN4PLMD10PlumedMain9eraseFileERNS_8FileBaseE</a></td>
+              <td class="coverFnHi">4833</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#976">_ZN4PLMD10PlumedMain9justApplyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#889">_ZN4PLMD10PlumedMain9shareDataEv</a></td>
+              <td class="coverFnHi">256183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#193">_ZN4PLMD10PlumedMainC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#222">_ZN4PLMD10PlumedMainD0Ev</a></td>
+              <td class="coverFnHi">804455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#222">_ZN4PLMD10PlumedMainD2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#180">_ZN4PLMD12_GLOBAL__N_114CountInstancesD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#67">_ZN4PLMDL9testThrowEPKc</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1152">_ZNK4PLMD10PlumedMain13parseOnlyModeEv</a></td>
+              <td class="coverFnHi">1820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1144">_ZNK4PLMD10PlumedMain24useCountReferenceCounterEv</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1085">_ZNK4PLMD10PlumedMain7getBiasEv</a></td>
+              <td class="coverFnHi">2805</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMain.cpp.gcov.html#1089">_ZNK4PLMD10PlumedMain7getWorkEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMain.cpp.gcov.html b/coverage/core/PlumedMain.cpp.gcov.html
new file mode 100644
index 0000000000..0e53e946bf
--- /dev/null
+++ b/coverage/core/PlumedMain.cpp.gcov.html
@@ -0,0 +1,1240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMain.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMain.cpp<span style="font-size: 80%;"> (source / <a href="PlumedMain.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">644</td>
+            <td class="headerCovTableEntry">721</td>
+            <td class="headerCovTableEntryMed">89.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionPilot.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;CLToolMain.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;ExchangePatterns.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;GREX.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/Citations.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;tools/DLLoader.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;tools/Log.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;tools/Stopwatch.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;tools/TypesafePtr.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;lepton/Exception.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;DataFetchingObject.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="47"><span class="lineNum">      47 </span>            : #include &lt;cstdio&gt;</a>
+<a name="48"><span class="lineNum">      48 </span>            : #include &lt;cstring&gt;</a>
+<a name="49"><span class="lineNum">      49 </span>            : #include &lt;set&gt;</a>
+<a name="50"><span class="lineNum">      50 </span>            : #include &lt;unordered_map&gt;</a>
+<a name="51"><span class="lineNum">      51 </span>            : #include &lt;exception&gt;</a>
+<a name="52"><span class="lineNum">      52 </span>            : #include &lt;stdexcept&gt;</a>
+<a name="53"><span class="lineNum">      53 </span>            : #include &lt;ios&gt;</a>
+<a name="54"><span class="lineNum">      54 </span>            : #include &lt;new&gt;</a>
+<a name="55"><span class="lineNum">      55 </span>            : #include &lt;typeinfo&gt;</a>
+<a name="56"><span class="lineNum">      56 </span>            : #include &lt;iostream&gt;</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &lt;algorithm&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="59"><span class="lineNum">      59 </span>            : #include &lt;system_error&gt;</a>
+<a name="60"><span class="lineNum">      60 </span>            : #include &lt;future&gt;</a>
+<a name="61"><span class="lineNum">      61 </span>            : #include &lt;memory&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : #include &lt;functional&gt;</a>
+<a name="63"><span class="lineNum">      63 </span>            : #endif</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace PLMD {</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Small utility just used in this file to throw arbitrary exceptions</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         38 : [[noreturn]] static void testThrow(const char* what) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         76 :   auto words=Tools::getWords(what);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         38 :   plumed_assert(words.size()&gt;0);</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : #define __PLUMED_THROW_NOMSG(type) if(words[0]==#type) throw type()</a>
+<a name="73"><span class="lineNum">      73 </span>            : #define __PLUMED_THROW_MSG(type) if(words[0]==#type) throw type(what)</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         39 :   __PLUMED_THROW_MSG(PLMD::ExceptionError);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         38 :   __PLUMED_THROW_MSG(PLMD::ExceptionDebug);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         37 :   __PLUMED_THROW_MSG(PLMD::Exception);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         36 :   __PLUMED_THROW_MSG(PLMD::lepton::Exception);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         34 :   __PLUMED_THROW_NOMSG(std::bad_exception);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         33 :   __PLUMED_THROW_NOMSG(std::bad_array_new_length);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : #endif</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         32 :   __PLUMED_THROW_NOMSG(std::bad_alloc);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         31 :   __PLUMED_THROW_NOMSG(std::bad_function_call);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         30 :   __PLUMED_THROW_NOMSG(std::bad_weak_ptr);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : #endif</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         29 :   __PLUMED_THROW_NOMSG(std::bad_cast);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         28 :   __PLUMED_THROW_NOMSG(std::bad_typeid);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         27 :   __PLUMED_THROW_MSG(std::underflow_error);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         26 :   __PLUMED_THROW_MSG(std::overflow_error);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         25 :   __PLUMED_THROW_MSG(std::range_error);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         24 :   __PLUMED_THROW_MSG(std::runtime_error);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         23 :   __PLUMED_THROW_MSG(std::out_of_range);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         22 :   __PLUMED_THROW_MSG(std::length_error);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         21 :   __PLUMED_THROW_MSG(std::domain_error);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         20 :   __PLUMED_THROW_MSG(std::invalid_argument);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         19 :   __PLUMED_THROW_MSG(std::logic_error);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         18 :   if(words[0]==&quot;std::system_error&quot;) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :     plumed_assert(words.size()&gt;2);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     int error_code;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 :     Tools::convert(words[2],error_code);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          4 :     if(words[1]==&quot;std::generic_category&quot;) throw std::system_error(error_code,std::generic_category(),what);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          3 :     if(words[1]==&quot;std::system_category&quot;) throw std::system_error(error_code,std::system_category(),what);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :     if(words[1]==&quot;std::iostream_category&quot;) throw std::system_error(error_code,std::iostream_category(),what);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :     if(words[1]==&quot;std::future_category&quot;) throw std::system_error(error_code,std::future_category(),what);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : #endif</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         14 :   if(words[0]==&quot;std::ios_base::failure&quot;) {</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 :     int error_code=0;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :     if(words.size()&gt;2) Tools::convert(words[2],error_code);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          1 :     if(words.size()&gt;1 &amp;&amp; words[1]==&quot;std::generic_category&quot;) throw std::ios_base::failure(what,std::error_code(error_code,std::generic_category()));</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :     if(words.size()&gt;1 &amp;&amp; words[1]==&quot;std::system_category&quot;) throw std::ios_base::failure(what,std::error_code(error_code,std::system_category()));</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :     if(words.size()&gt;1 &amp;&amp; words[1]==&quot;std::iostream_category&quot;) throw std::ios_base::failure(what,std::error_code(error_code,std::iostream_category()));</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :     if(words.size()&gt;1 &amp;&amp; words[1]==&quot;std::future_category&quot;) throw std::ios_base::failure(what,std::error_code(error_code,std::future_category()));</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : #endif</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :     throw std::ios_base::failure(what);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         13 :   if(words[0]==&quot;int&quot;) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 :     int value=0;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :     if(words.size()&gt;1) Tools::convert(words[1],value);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :     throw value;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         12 :   if(words[0]==&quot;test_nested1&quot;) {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :     try {</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         12 :       throw Exception(std::string(&quot;inner &quot;)+what);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          6 :     } catch(...) {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :       try {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         18 :         std::throw_with_nested(Exception(std::string(&quot;middle &quot;)+what));</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          6 :       } catch(...) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         18 :         std::throw_with_nested(Exception(std::string(&quot;outer &quot;)+what));</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :       }</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          6 :     }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          6 :   if(words[0]==&quot;test_nested2&quot;) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     try {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 :       throw std::bad_alloc();</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          3 :     } catch(...) {</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :       try {</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          9 :         std::throw_with_nested(Exception(std::string(&quot;middle &quot;)+what));</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          3 :       } catch(...) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          9 :         std::throw_with_nested(Exception(std::string(&quot;outer &quot;)+what));</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          3 :       }</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :     }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 :   if(words[0]==&quot;test_nested3&quot;) {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :     try {</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :       throw &quot;inner&quot;;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :     } catch(...) {</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       try {</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          6 :         std::throw_with_nested(Exception(std::string(&quot;middle &quot;)+what));</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :       } catch(...) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          6 :         std::throw_with_nested(Exception(std::string(&quot;outer &quot;)+what));</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :       }</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          2 :     }</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   plumed_error() &lt;&lt; &quot;unknown exception &quot; &lt;&lt; what;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         38 : }</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : namespace {</a>
+<a name="169"><span class="lineNum">     169 </span>            : // This is an internal tool used to count how many PlumedMain objects have been created</a>
+<a name="170"><span class="lineNum">     170 </span>            : // and if they were correctly destroyed.</a>
+<a name="171"><span class="lineNum">     171 </span>            : // When using debug options, it leads to a crash</a>
+<a name="172"><span class="lineNum">     172 </span>            : // Otherwise, it just prints a message</a>
+<a name="173"><span class="lineNum">     173 </span>            : class CountInstances {</a>
+<a name="174"><span class="lineNum">     174 </span>            :   std::atomic&lt;int&gt; counter{};</a>
+<a name="175"><span class="lineNum">     175 </span>            : public:</a>
+<a name="176"><span class="lineNum">     176 </span>            :   void increase() noexcept {</a>
+<a name="177"><span class="lineNum">     177 </span>            :     ++counter;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            :   void decrease() noexcept {</a>
+<a name="180"><span class="lineNum">     180 </span>            :     --counter;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       4168 :   ~CountInstances() {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       4168 :     if(counter!=0) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :       std::cerr&lt;&lt;&quot;WARNING: internal inconsistency in allocated PlumedMain instances (&quot; &lt;&lt;counter&lt;&lt; &quot;)\n&quot;;</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : #ifndef NDEBUG</a>
+<a name="186"><span class="lineNum">     186 </span>            :       std::abort();</a>
+<a name="187"><span class="lineNum">     187 </span>            : #endif</a>
+<a name="188"><span class="lineNum">     188 </span>            :     }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       4168 :   }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : };</a>
+<a name="191"><span class="lineNum">     191 </span>            : static CountInstances countInstances;</a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     805268 : PlumedMain::PlumedMain():</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     805268 :   initialized(false),</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : // automatically write on log in destructor</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">     805268 :   stopwatch_fwd(log),</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     805268 :   step(0),</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">     805268 :   active(false),</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     805268 :   mydatafetcher(DataFetchingObject::create(sizeof(double),*this)),</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     805268 :   endPlumed(false),</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     805268 :   atoms_fwd(*this),</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     805268 :   actionSet_fwd(*this),</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     805268 :   bias(0.0),</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">     805268 :   work(0.0),</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">     805268 :   exchangeStep(false),</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     805268 :   restart(false),</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     805268 :   doCheckPoint(false),</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     805268 :   doParseOnly(false),</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">     805268 :   stopNow(false),</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     805268 :   novirial(false),</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">     805268 :   detailedTimers(false),</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">    1610536 :   gpuDeviceId(-1)</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : {</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     805268 :   increaseReferenceCounter();</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     805268 :   log.link(comm);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">    1610536 :   log.setLinePrefix(&quot;PLUMED: &quot;);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   // this is at last so as to avoid inconsistencies if an exception is thrown</a>
+<a name="220"><span class="lineNum">     220 </span>            :   countInstances.increase(); // noexcept</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">     805268 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : // destructor needed to delete forward declarated objects</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">    1609723 : PlumedMain::~PlumedMain() {</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   countInstances.decrease();</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">    3220259 : }</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : /////////////////////////////////////////////////////////////</a>
+<a name="229"><span class="lineNum">     229 </span>            : //  MAIN INTERPRETER</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : #define CHECK_INIT(ini,word) plumed_massert(ini,&quot;cmd(\&quot;&quot; + word +&quot;\&quot;) should be only used after plumed initialization&quot;)</a>
+<a name="232"><span class="lineNum">     232 </span>            : #define CHECK_NOTINIT(ini,word) plumed_massert(!(ini),&quot;cmd(\&quot;&quot; + word +&quot;\&quot;) should be only used before plumed initialization&quot;)</a>
+<a name="233"><span class="lineNum">     233 </span>            : #define CHECK_NOTNULL(val,word) plumed_massert(val,&quot;NULL pointer received in cmd(\&quot;&quot; + word + &quot;\&quot;)&quot;);</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">    1118951 : void PlumedMain::cmd(const std::string &amp; word,const TypesafePtr &amp; val) {</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : // Enumerate all possible commands:</a>
+<a name="239"><span class="lineNum">     239 </span>            :   enum {</a>
+<a name="240"><span class="lineNum">     240 </span>            : #include &quot;PlumedMainEnum.inc&quot;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   };</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : // Static object (initialized once) containing the map of commands:</a>
+<a name="244"><span class="lineNum">     244 </span>            :   const static std::unordered_map&lt;std::string, int&gt; word_map = {</a>
+<a name="245"><span class="lineNum">     245 </span>            : #include &quot;PlumedMainMap.inc&quot;</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">    1454939 :   };</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   try {</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">    1118951 :     auto ss=stopwatch.startPause();</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">    1118951 :     std::vector&lt;std::string&gt; words=Tools::getWords(word);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">    1118951 :     unsigned nw=words.size();</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">    1118951 :     if(nw==0) {</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :       // do nothing</a>
+<a name="256"><span class="lineNum">     256 </span>            :     } else {</a>
+<a name="257"><span class="lineNum">     257 </span>            :       int iword=-1;</a>
+<a name="258"><span class="lineNum">     258 </span>            :       double d;</a>
+<a name="259"><span class="lineNum">     259 </span>            :       const auto it=word_map.find(words[0]);</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">    1118951 :       if(it!=word_map.end()) iword=it-&gt;second;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">    1118944 :       switch(iword) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      51647 :       case cmd_setBox:</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">      51647 :         CHECK_INIT(initialized,word);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">      51647 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      51647 :         atoms.setBox(val);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :         break;</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">      55788 :       case cmd_setPositions:</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      55788 :         CHECK_INIT(initialized,word);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">      55788 :         atoms.setPositions(val);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :         break;</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      55792 :       case cmd_setMasses:</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">      55792 :         CHECK_INIT(initialized,word);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">      55792 :         atoms.setMasses(val);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :         break;</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      45883 :       case cmd_setCharges:</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      45883 :         CHECK_INIT(initialized,word);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">      45883 :         atoms.setCharges(val);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :         break;</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          1 :       case cmd_setPositionsX:</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          1 :         atoms.setPositions(val,0);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :         break;</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          1 :       case cmd_setPositionsY:</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          1 :         atoms.setPositions(val,1);</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :         break;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          1 :       case cmd_setPositionsZ:</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          1 :         atoms.setPositions(val,2);</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :         break;</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">      45989 :       case cmd_setVirial:</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">      45989 :         CHECK_INIT(initialized,word);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">      45989 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      45989 :         atoms.setVirial(val);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :         break;</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       9792 :       case cmd_setEnergy:</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       9792 :         CHECK_INIT(initialized,word);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       9792 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       9792 :         atoms.setEnergy(val);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :         break;</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">      55788 :       case cmd_setForces:</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">      55788 :         CHECK_INIT(initialized,word);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">      55788 :         atoms.setForces(val);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :         break;</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          1 :       case cmd_setForcesX:</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          1 :         atoms.setForces(val,0);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :         break;</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          1 :       case cmd_setForcesY:</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          1 :         atoms.setForces(val,1);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :         break;</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          1 :       case cmd_setForcesZ:</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          1 :         atoms.setForces(val,2);</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :         break;</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     254029 :       case cmd_calc:</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">     254029 :         CHECK_INIT(initialized,word);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">     254029 :         calc();</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :         break;</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         99 :       case cmd_prepareDependencies:</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         99 :         CHECK_INIT(initialized,word);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         99 :         prepareDependencies();</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :         break;</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         84 :       case cmd_shareData:</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         84 :         CHECK_INIT(initialized,word);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         84 :         shareData();</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :         break;</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       2070 :       case cmd_prepareCalc:</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       2070 :         CHECK_INIT(initialized,word);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       2070 :         prepareCalc();</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :         break;</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         10 :       case cmd_performCalc:</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         10 :         CHECK_INIT(initialized,word);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         10 :         performCalc();</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :         break;</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">       2134 :       case cmd_performCalcNoUpdate:</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">       2134 :         CHECK_INIT(initialized,word);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       2134 :         performCalcNoUpdate();</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :         break;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         10 :       case cmd_performCalcNoForces:</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         10 :         CHECK_INIT(initialized,word);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         10 :         performCalcNoForces();</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :         break;</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         79 :       case cmd_update:</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         79 :         CHECK_INIT(initialized,word);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         79 :         update();</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :         break;</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">       6090 :       case cmd_setStep:</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">       6090 :         CHECK_INIT(initialized,word);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">       6096 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       6087 :         step=val.get&lt;int&gt;();</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">       6087 :         atoms.startStep();</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :         break;</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 :       case cmd_setStepLong:</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :         step=val.get&lt;long int&gt;();</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :         atoms.startStep();</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :         break;</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">     250057 :       case cmd_setStepLongLong:</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">     250057 :         CHECK_INIT(initialized,word);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">     250057 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">     250057 :         step=val.get&lt;long long int&gt;();</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">     250057 :         atoms.startStep();</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :         break;</a>
+<a name="367"><span class="lineNum">     367 </span>            :       // words used less frequently:</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">       1140 :       case cmd_setAtomsNlocal:</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">       1140 :         CHECK_INIT(initialized,word);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       1140 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">       1140 :         atoms.setAtomsNlocal(val.get&lt;int&gt;());</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :         break;</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        988 :       case cmd_setAtomsGatindex:</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        988 :         CHECK_INIT(initialized,word);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        988 :         atoms.setAtomsGatindex(val,false);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :         break;</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :       case cmd_setAtomsFGatindex:</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :         atoms.setAtomsGatindex(val,true);</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :         break;</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        152 :       case cmd_setAtomsContiguous:</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        152 :         CHECK_INIT(initialized,word);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        152 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        152 :         atoms.setAtomsContiguous(val.get&lt;int&gt;());</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :         break;</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        116 :       case cmd_createFullList:</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        116 :         CHECK_INIT(initialized,word);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        116 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        116 :         atoms.createFullList(val);</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :         break;</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        116 :       case cmd_getFullList:</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        116 :         CHECK_INIT(initialized,word);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        116 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        116 :         atoms.getFullList(val);</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :         break;</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        116 :       case cmd_clearFullList:</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        116 :         CHECK_INIT(initialized,word);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        116 :         atoms.clearFullList();</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :         break;</a>
+<a name="400"><span class="lineNum">     400 </span>            :       /* ADDED WITH API==6 */</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         64 :       case cmd_getDataRank:</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         64 :         CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">        128 :         if( nw==2 ) DataFetchingObject::get_rank( actionSet, words[1], &quot;&quot;, val);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 :         else DataFetchingObject::get_rank( actionSet, words[1], words[2], val);</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :         break;</a>
+<a name="406"><span class="lineNum">     406 </span>            :       /* ADDED WITH API==6 */</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :       case cmd_getDataShape:</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :         if( nw==2 ) DataFetchingObject::get_shape( actionSet, words[1], &quot;&quot;, val );</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :         else DataFetchingObject::get_shape( actionSet, words[1], words[2], val );</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :         break;</a>
+<a name="412"><span class="lineNum">     412 </span>            :       /* ADDED WITH API==6 */</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         64 :       case cmd_setMemoryForData:</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         64 :         CHECK_INIT(initialized,words[0]); plumed_assert(nw==2 || nw==3);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        128 :         if( nw==2 ) mydatafetcher-&gt;setData( words[1], &quot;&quot;, val );</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :         else mydatafetcher-&gt;setData( words[1], words[2], val );</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :         break;</a>
+<a name="418"><span class="lineNum">     418 </span>            :       /* ADDED WITH API==6 */</a>
+<a name="419"><span class="lineNum">     419 </span>            :       case cmd_setErrorHandler:</a>
+<a name="420"><span class="lineNum">     420 </span>            :       {</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :         if(val) error_handler=*static_cast&lt;const plumed_error_handler*&gt;(val.get&lt;const void*&gt;());</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :         else error_handler.handler=NULL;</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :       }</a>
+<a name="424"><span class="lineNum">     424 </span>            :       break;</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :       case cmd_read:</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :         if(val)readInputFile(val.get&lt;const char*&gt;());</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :         else   readInputFile(&quot;plumed.dat&quot;);</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :         break;</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        274 :       case cmd_readInputLine:</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        274 :         CHECK_INIT(initialized,word);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        274 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        274 :         readInputLine(val.get&lt;const char*&gt;());</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        234 :         break;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          1 :       case cmd_readInputLines:</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          1 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          1 :         readInputLines(val.get&lt;const char*&gt;());</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          1 :         break;</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          1 :       case cmd_clear:</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          1 :         CHECK_INIT(initialized,word);</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          1 :         actionSet.clearDelete();</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :         break;</a>
+<a name="444"><span class="lineNum">     444 </span>            :       case cmd_getApiVersion:</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         42 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         42 :         val.set(int(10));</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :         break;</a>
+<a name="448"><span class="lineNum">     448 </span>            :       // commands which can be used only before initialization:</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">       1007 :       case cmd_init:</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">       1007 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">       1007 :         init();</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :         break;</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">        878 :       case cmd_setRealPrecision:</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">        878 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">        878 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        878 :         atoms.setRealPrecision(val.get&lt;int&gt;());</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">       1754 :         mydatafetcher=DataFetchingObject::create(val.get&lt;int&gt;(),*this);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">        877 :         break;</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        810 :       case cmd_setMDLengthUnits:</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">        810 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">        810 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">        810 :         atoms.MD2double(val,d);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">        810 :         atoms.setMDLengthUnits(d);</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :         break;</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">        810 :       case cmd_setMDChargeUnits:</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">        810 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">        810 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">        810 :         atoms.MD2double(val,d);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        810 :         atoms.setMDChargeUnits(d);</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :         break;</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">        810 :       case cmd_setMDMassUnits:</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">        810 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">        810 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        810 :         atoms.MD2double(val,d);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">        810 :         atoms.setMDMassUnits(d);</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :         break;</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">         45 :       case cmd_setMDEnergyUnits:</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         45 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         45 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         45 :         atoms.MD2double(val,d);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         45 :         atoms.setMDEnergyUnits(d);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :         break;</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          6 :       case cmd_setMDTimeUnits:</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          6 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          6 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          6 :         atoms.MD2double(val,d);</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          6 :         atoms.setMDTimeUnits(d);</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :         break;</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :       case cmd_setNaturalUnits:</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :         // set the boltzman constant for MD in natural units (kb=1)</a>
+<a name="491"><span class="lineNum">     491 </span>            :         // only needed in LJ codes if the MD is passing temperatures to plumed (so, not yet...)</a>
+<a name="492"><span class="lineNum">     492 </span>            :         // use as cmd(&quot;setNaturalUnits&quot;)</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :         atoms.setMDNaturalUnits(true);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :         break;</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         52 :       case cmd_setNoVirial:</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         52 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">         52 :         novirial=true;</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         52 :         break;</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        865 :       case cmd_setPlumedDat:</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        865 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        865 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">        865 :         plumedDat=val.get&lt;const char*&gt;();</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :         break;</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        339 :       case cmd_setMPIComm:</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        339 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        339 :         comm.Set_comm(val);</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">        339 :         atoms.setDomainDecomposition(comm);</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :         break;</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :       case cmd_setMPIFComm:</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :         comm.Set_fcomm(val);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :         atoms.setDomainDecomposition(comm);</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :         break;</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :       case cmd_setMPImultiSimComm:</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :         multi_sim_comm.Set_comm(val);</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :         break;</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">        990 :       case cmd_setNatoms:</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">        990 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">        990 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        990 :         atoms.setNatoms(val.get&lt;int&gt;());</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :         break;</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">        866 :       case cmd_setTimestep:</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">        866 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">        866 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">        866 :         atoms.setTimeStep(val);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :         break;</a>
+<a name="529"><span class="lineNum">     529 </span>            :       /* ADDED WITH API==2 */</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         59 :       case cmd_setKbT:</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">         59 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         59 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         59 :         atoms.setKbT(val);</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :         break;</a>
+<a name="535"><span class="lineNum">     535 </span>            :       /* ADDED WITH API==3 */</a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          8 :       case cmd_setRestart:</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          8 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          8 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">          8 :         if(val.get&lt;int&gt;()!=0) restart=true;</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :         break;</a>
+<a name="541"><span class="lineNum">     541 </span>            :       /* ADDED WITH API==4 */</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :       case cmd_doCheckPoint:</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :         doCheckPoint = false;</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :         if(val.get&lt;int&gt;()!=0) doCheckPoint = true;</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :         break;</a>
+<a name="548"><span class="lineNum">     548 </span>            :       /* ADDED WITH API==6 */</a>
+<a name="549"><span class="lineNum">     549 </span>            :       case cmd_setNumOMPthreads:</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :         {</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :           auto nt=val.get&lt;unsigned&gt;();</span></a>
+<a name="553"><span class="lineNum">     553 </span>            :           if(nt==0) nt=1;</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :           OpenMP::setNumThreads(nt);</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :         }</a>
+<a name="556"><span class="lineNum">     556 </span>            :         break;</a>
+<a name="557"><span class="lineNum">     557 </span>            :       /* ADDED WITH API==10 */</a>
+<a name="558"><span class="lineNum">     558 </span>            :       case cmd_setGpuDeviceId:</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :         {</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :           auto id=val.get&lt;int&gt;();</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :           if(id&gt;=0) gpuDeviceId=id;</span></a>
+<a name="563"><span class="lineNum">     563 </span>            :         }</a>
+<a name="564"><span class="lineNum">     564 </span>            :         break;</a>
+<a name="565"><span class="lineNum">     565 </span>            :       /* ADDED WITH API==6 */</a>
+<a name="566"><span class="lineNum">     566 </span>            :       /* only used for testing */</a>
+<a name="567"><span class="lineNum">     567 </span>            :       case cmd_throw:</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         38 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">         38 :         testThrow(val.get&lt;const char*&gt;());</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :       /* ADDED WITH API==10 */</a>
+<a name="571"><span class="lineNum">     571 </span>            :       case cmd_setNestedExceptions:</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         25 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         25 :         if(val.get&lt;int&gt;()!=0) nestedExceptions=true;</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">          1 :         else nestedExceptions=false;</span></a>
+<a name="575"><span class="lineNum">     575 </span>            :         break;</a>
+<a name="576"><span class="lineNum">     576 </span>            :       /* STOP API */</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        863 :       case cmd_setMDEngine:</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">        863 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">        863 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">        863 :         MDEngine=val.get&lt;const char*&gt;();</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :         break;</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">        850 :       case cmd_setLog:</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">        850 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">        850 :         log.link(val.get&lt;FILE*&gt;());</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :         break;</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         53 :       case cmd_setLogFile:</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         53 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         53 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">        152 :         log.open(val.get&lt;const char*&gt;());</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         53 :         break;</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :       // other commands that should be used after initialization:</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">     253956 :       case cmd_setStopFlag:</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">     253956 :         CHECK_INIT(initialized,word);</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">     253956 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">     253956 :         val.get&lt;int*&gt;(); // just check type and discard pointer</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">     253955 :         stopFlag=val.copy();</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">     253955 :         break;</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :       case cmd_getExchangesFlag:</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :         exchangePatterns.getFlag(*val.get&lt;int*&gt;()); // note: getFlag changes the value of the reference!</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :         break;</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :       case cmd_setExchangesSeed:</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :         exchangePatterns.setSeed(val.get&lt;int&gt;());</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :         break;</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :       case cmd_setNumberOfReplicas:</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :         exchangePatterns.setNofR(val.get&lt;int&gt;());</span></a>
+<a name="612"><span class="lineNum">     612 </span>            :         break;</a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineNoCov">          0 :       case cmd_getExchangesList:</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineNoCov">          0 :         CHECK_INIT(initialized,word);</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineNoCov">          0 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 :         exchangePatterns.getList(val.get&lt;int*&gt;());</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">        813 :       case cmd_runFinalJobs:</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        813 :         CHECK_INIT(initialized,word);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">        813 :         runJobsAtEndOfCalculation();</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :         break;</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         96 :       case cmd_isEnergyNeeded:</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         96 :         CHECK_INIT(initialized,word);</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">         96 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         96 :         if(atoms.isEnergyNeeded()) val.set(int(1));</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         96 :         else                       val.set(int(0));</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :         break;</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">       2172 :       case cmd_getBias:</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">       2172 :         CHECK_INIT(initialized,word);</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">       2172 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">       2172 :         atoms.double2MD(getBias()/(atoms.getMDUnits().getEnergy()/atoms.getUnits().getEnergy()),val);</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">       2172 :         break;</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :       case cmd_checkAction:</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">          2 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">          2 :         plumed_assert(nw==2);</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">          3 :         val.set(int(actionRegister().check(words[1]) ? 1:0));</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :         break;</a>
+<a name="638"><span class="lineNum">     638 </span>            :       case cmd_setExtraCV:</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">         30 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">         30 :         plumed_assert(nw==2);</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">         30 :         atoms.setExtraCV(words[1],val);</span></a>
+<a name="642"><span class="lineNum">     642 </span>            :         break;</a>
+<a name="643"><span class="lineNum">     643 </span>            :       case cmd_setExtraCVForce:</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">         30 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">         30 :         plumed_assert(nw==2);</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">         30 :         atoms.setExtraCVForce(words[1],val);</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :         break;</a>
+<a name="648"><span class="lineNum">     648 </span>            :       /* ADDED WITH API==10 */</a>
+<a name="649"><span class="lineNum">     649 </span>            :       case cmd_isExtraCVNeeded:</a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         10 :         CHECK_NOTNULL(val,word);</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         10 :         plumed_assert(nw==2);</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         10 :         if(atoms.isExtraCVNeeded(words[1])) val.set(int(1));</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">          6 :         else                                val.set(int(0));</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :         break;</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">       1077 :       case cmd_GREX:</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">       1077 :         if(!grex) grex=Tools::make_unique&lt;GREX&gt;(*this);</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">       1077 :         plumed_massert(grex,&quot;error allocating grex&quot;);</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :         {</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       1077 :           std::string kk=words[1];</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">       1248 :           for(unsigned i=2; i&lt;words.size(); i++) kk+=&quot; &quot;+words[i];</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">       2154 :           grex-&gt;cmd(kk.c_str(),val);</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :         }</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">       1077 :         break;</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">      12906 :       case cmd_CLTool:</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">      12906 :         CHECK_NOTINIT(initialized,word);</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">      12906 :         if(!cltool) cltool=Tools::make_unique&lt;CLToolMain&gt;();</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :         {</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">      12906 :           std::string kk=words[1];</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">      12906 :           for(unsigned i=2; i&lt;words.size(); i++) kk+=&quot; &quot;+words[i];</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">      25812 :           cltool-&gt;cmd(kk.c_str(),val);</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :         }</a>
+<a name="672"><span class="lineNum">     672 </span>            :         break;</a>
+<a name="673"><span class="lineNum">     673 </span>            :       /* ADDED WITH API==7 */</a>
+<a name="674"><span class="lineNum">     674 </span>            :       case cmd_convert:</a>
+<a name="675"><span class="lineNum">     675 </span>            :       {</a>
+<a name="676"><span class="lineNum">     676 </span>            :         double v;</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         57 :         plumed_assert(words.size()==2);</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         57 :         if(Tools::convertNoexcept(words[1],v)) atoms.double2MD(v,val);</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :       }</a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         57 :       break;</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">          7 :       default:</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         21 :         plumed_merror(&quot;cannot interpret cmd(\&quot;&quot; + word + &quot;\&quot;). check plumed developers manual to see the available commands.&quot;);</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :         break;</a>
+<a name="684"><span class="lineNum">     684 </span>            :       }</a>
+<a name="685"><span class="lineNum">     685 </span>            :     }</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">    1119149 :   } catch (...) {</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         99 :     if(log.isOpen()) {</span></a>
+<a name="689"><span class="lineNum">     689 </span>            :       try {</a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         54 :         log&lt;&lt;&quot;\n################################################################################\n&quot;;</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         54 :         log&lt;&lt;Tools::concatenateExceptionMessages();</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         54 :         log&lt;&lt;&quot;\n################################################################################\n&quot;;</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">         54 :         log.flush();</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :       } catch(...) {</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :         // ignore errors here.</a>
+<a name="696"><span class="lineNum">     696 </span>            :         // in any case, we are rethrowing this below</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :     }</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         99 :     throw;</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         99 :   }</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">    1118852 : }</span></a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span>            : ////////////////////////////////////////////////////////////////////////</a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">       1007 : void PlumedMain::init() {</span></a>
+<a name="706"><span class="lineNum">     706 </span>            : // check that initialization just happens once</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">       1007 :   initialized=true;</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">       1007 :   atoms.init();</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">       1007 :   if(!log.isOpen()) log.link(stdout);</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;PLUMED is starting\n&quot;;</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">       3021 :   log&lt;&lt;&quot;Version: &quot;&lt;&lt;config::getVersionLong()&lt;&lt;&quot; (git: &quot;&lt;&lt;config::getVersionGit()&lt;&lt;&quot;) &quot;</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">       4028 :      &lt;&lt;&quot;compiled on &quot; &lt;&lt;config::getCompilationDate() &lt;&lt; &quot; at &quot; &lt;&lt; config::getCompilationTime() &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Please cite these papers when using PLUMED &quot;;</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">       2014 :   log&lt;&lt;cite(&quot;The PLUMED consortium, Nat. Methods 16, 670 (2019)&quot;);</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">       2014 :   log&lt;&lt;cite(&quot;Tribello, Bonomi, Branduardi, Camilloni, and Bussi, Comput. Phys. Commun. 185, 604 (2014)&quot;);</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;For further information see the PLUMED web page at http://www.plumed.org\n&quot;;</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Root: &quot;&lt;&lt;config::getPlumedRoot()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">       2014 :   log&lt;&lt;&quot;For installed feature, see &quot;&lt;&lt;config::getPlumedRoot() + &quot;/src/config/config.txt\n&quot;;</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">       1007 :   log.printf(&quot;Molecular dynamics engine: %s\n&quot;,MDEngine.c_str());</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">       1007 :   log.printf(&quot;Precision of reals: %d\n&quot;,atoms.getRealPrecision());</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">       1788 :   log.printf(&quot;Running over %d %s\n&quot;,comm.Get_size(),(comm.Get_size()&gt;1?&quot;nodes&quot;:&quot;node&quot;));</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Number of threads: &quot;&lt;&lt;OpenMP::getNumThreads()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Cache line size: &quot;&lt;&lt;OpenMP::getCachelineSize()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">       1007 :   log.printf(&quot;Number of atoms: %d\n&quot;,atoms.getNatoms());</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">       1007 :   if(grex) log.printf(&quot;GROMACS-like replica exchange is on\n&quot;);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">       1007 :   log.printf(&quot;File suffix: %s\n&quot;,getSuffix().c_str());</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">       1007 :   if(plumedDat.length()&gt;0) {</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">        865 :     readInputFile(plumedDat);</span></a>
+<a name="730"><span class="lineNum">     730 </span>            :     plumedDat=&quot;&quot;;</a>
+<a name="731"><span class="lineNum">     731 </span>            :   }</a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">       1007 :   atoms.updateUnits();</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">       1007 :   log.printf(&quot;Timestep: %f\n&quot;,atoms.getTimeStep());</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">       1007 :   if(atoms.getKbT()&gt;0.0)</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         53 :     log.printf(&quot;KbT: %f\n&quot;,atoms.getKbT());</span></a>
+<a name="736"><span class="lineNum">     736 </span>            :   else {</a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">        954 :     log.printf(&quot;KbT has not been set by the MD engine\n&quot;);</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">        954 :     log.printf(&quot;It should be set by hand where needed\n&quot;);</span></a>
+<a name="739"><span class="lineNum">     739 </span>            :   }</a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Relevant bibliography:\n&quot;;</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">       1007 :   log&lt;&lt;citations;</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Please read and cite where appropriate!\n&quot;;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">       1007 :   log&lt;&lt;&quot;Finished setup\n&quot;;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">       1007 : }</span></a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">        883 : void PlumedMain::readInputFile(const std::string &amp; str) {</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">        883 :   plumed_assert(initialized);</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">        883 :   log&lt;&lt;&quot;FILE: &quot;&lt;&lt;str&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">        883 :   IFile ifile;</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">        883 :   ifile.link(*this);</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">        883 :   ifile.open(str);</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">        883 :   ifile.allowNoEOL();</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">        883 :   readInputFile(ifile);</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">        883 :   log&lt;&lt;&quot;END FILE: &quot;&lt;&lt;str&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">        883 :   log.flush();</span></a>
+<a name="756"><span class="lineNum">     756 </span>            : </a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">        883 : }</span></a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">        884 : void PlumedMain::readInputFile(IFile &amp; ifile) {</span></a>
+<a name="760"><span class="lineNum">     760 </span>            :   std::vector&lt;std::string&gt; words;</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">      14963 :   while(Tools::getParsedLine(ifile,words) &amp;&amp; !endPlumed) readInputWords(words);</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">        884 :   endPlumed=false;</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">        884 :   pilots=actionSet.select&lt;ActionPilot*&gt;();</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">        884 : }</span></a>
+<a name="765"><span class="lineNum">     765 </span>            : </a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">        358 : void PlumedMain::readInputLine(const std::string &amp; str) {</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">        358 :   plumed_assert(initialized);</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">        358 :   if(str.empty()) return;</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">        358 :   std::vector&lt;std::string&gt; words=Tools::getWords(str);</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">        358 :   citations.clear();</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">        358 :   readInputWords(words);</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">        318 :   if(!citations.empty()) {</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;Relevant bibliography:\n&quot;;</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">          2 :     log&lt;&lt;citations;</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;Please read and cite where appropriate!\n&quot;;</span></a>
+<a name="776"><span class="lineNum">     776 </span>            :   }</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">        358 : }</span></a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">          1 : void PlumedMain::readInputLines(const std::string &amp; str) {</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">          1 :   plumed_assert(initialized);</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">          1 :   if(str.empty()) return;</span></a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">          1 :   log&lt;&lt;&quot;FILE: (temporary)\n&quot;;</span></a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            :   // Open a temporary file</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">          1 :   auto fp=std::tmpfile();</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">          1 :   plumed_assert(fp);</span></a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span>            :   // make sure file is closed (and thus deleted) also if an exception occurs</a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">          1 :   auto deleter=[](FILE* fp) { std::fclose(fp); };</span></a>
+<a name="791"><span class="lineNum">     791 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">          1 :   auto ret=std::fputs(str.c_str(),fp);</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">          1 :   plumed_assert(ret!=EOF);</span></a>
+<a name="795"><span class="lineNum">     795 </span>            : </a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">          1 :   std::rewind(fp);</span></a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">          1 :   IFile ifile;</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">          1 :   ifile.link(*this);</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">          1 :   ifile.link(fp);</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">          1 :   ifile.allowNoEOL();</span></a>
+<a name="802"><span class="lineNum">     802 </span>            : </a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">          1 :   readInputFile(ifile);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">          1 :   log&lt;&lt;&quot;END FILE: (temporary)\n&quot;;</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">          1 : }</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">      14463 : void PlumedMain::readInputWords(const std::vector&lt;std::string&gt; &amp; words) {</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">      14463 :   plumed_assert(initialized);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">      14463 :   if(words.empty())return;</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">      14307 :   else if(words[0]==&quot;_SET_SUFFIX&quot;) {</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">          3 :     plumed_assert(words.size()==2);</span></a>
+<a name="812"><span class="lineNum">     812 </span>            :     setSuffix(words[1]);</a>
+<a name="813"><span class="lineNum">     813 </span>            :   } else {</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">      14304 :     std::vector&lt;std::string&gt; interpreted(words);</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">      14304 :     Tools::interpretLabel(interpreted);</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">      28570 :     auto action=actionRegister().create(ActionOptions(*this,interpreted));</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">      14266 :     if(!action) {</span></a>
+<a name="818"><span class="lineNum">     818 </span>            :       std::string msg;</a>
+<a name="819"><span class="lineNum">     819 </span>            :       msg =&quot;ERROR\nI cannot understand line:&quot;;</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         10 :       for(unsigned i=0; i&lt;interpreted.size(); ++i) msg+=&quot; &quot;+interpreted[i];</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :       msg+=&quot;\nMaybe a missing space or a typo?&quot;;</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">          2 :       log &lt;&lt; msg;</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">          2 :       log.flush();</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">          4 :       plumed_merror(msg);</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">      14264 :     action-&gt;checkRead();</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">      14264 :     actionSet.emplace_back(std::move(action));</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">      14306 :   };</span></a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">      28534 :   pilots=actionSet.select&lt;ActionPilot*&gt;();</span></a>
+<a name="831"><span class="lineNum">     831 </span>            : }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            : ////////////////////////////////////////////////////////////////////////</a>
+<a name="834"><span class="lineNum">     834 </span>            : </a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineNoCov">          0 : void PlumedMain::exit(int c) {</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineNoCov">          0 :   comm.Abort(c);</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="838"><span class="lineNum">     838 </span>            : </a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">      14302 : Log&amp; PlumedMain::getLog() {</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">      14302 :   return log;</span></a>
+<a name="841"><span class="lineNum">     841 </span>            : }</a>
+<a name="842"><span class="lineNum">     842 </span>            : </a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">     254029 : void PlumedMain::calc() {</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">     254029 :   prepareCalc();</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">     254029 :   performCalc();</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">     254029 : }</span></a>
+<a name="847"><span class="lineNum">     847 </span>            : </a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">     256099 : void PlumedMain::prepareCalc() {</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">     256099 :   prepareDependencies();</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">     256099 :   shareData();</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">     256099 : }</span></a>
+<a name="852"><span class="lineNum">     852 </span>            : </a>
+<a name="853"><span class="lineNum">     853 </span>            : //////////////////////////////////////////////////////////////////////////////////////////////////////////////////</a>
+<a name="854"><span class="lineNum">     854 </span>            : // here we have the main steps in &quot;calc()&quot;</a>
+<a name="855"><span class="lineNum">     855 </span>            : // they can be called individually, but the standard thing is to</a>
+<a name="856"><span class="lineNum">     856 </span>            : // traverse them in this order:</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">     256426 : void PlumedMain::prepareDependencies() {</span></a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span>            : // Stopwatch is stopped when sw goes out of scope</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">     256426 :   auto sw=stopwatch.startStop(&quot;1 Prepare dependencies&quot;);</span></a>
+<a name="861"><span class="lineNum">     861 </span>            : </a>
+<a name="862"><span class="lineNum">     862 </span>            : // activate all the actions which are on step</a>
+<a name="863"><span class="lineNum">     863 </span>            : // activation is recursive and enables also the dependencies</a>
+<a name="864"><span class="lineNum">     864 </span>            : // before doing that, the prepare() method is called to see if there is some</a>
+<a name="865"><span class="lineNum">     865 </span>            : // new/changed dependency (up to now, only useful for dependences on virtual atoms,</a>
+<a name="866"><span class="lineNum">     866 </span>            : // which can be dynamically changed).</a>
+<a name="867"><span class="lineNum">     867 </span>            : </a>
+<a name="868"><span class="lineNum">     868 </span>            : // First switch off all actions</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">    2089597 :   for(const auto &amp; p : actionSet) {</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">    1833171 :     p-&gt;deactivate();</span></a>
+<a name="871"><span class="lineNum">     871 </span>            :   }</a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            : // for optimization, an &quot;active&quot; flag remains false if no action at all is active</a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">     256426 :   active=mydatafetcher-&gt;activate();</span></a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">    1604078 :   for(unsigned i=0; i&lt;pilots.size(); ++i) {</span></a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">    1347652 :     if(pilots[i]-&gt;onStep()) {</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">    1277737 :       pilots[i]-&gt;activate();</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">    1277737 :       active=true;</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :     }</a>
+<a name="880"><span class="lineNum">     880 </span>            :   };</a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span>            : // also, if one of them is the total energy, tell to atoms that energy should be collected</a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">    2089597 :   for(const auto &amp; p : actionSet) {</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">    1833171 :     if(p-&gt;isActive()) {</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">    1651033 :       if(p-&gt;checkNeedsGradients()) p-&gt;setOption(&quot;GRADIENTS&quot;);</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :     }</a>
+<a name="887"><span class="lineNum">     887 </span>            :   }</a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">     256426 : }</span></a>
+<a name="890"><span class="lineNum">     890 </span>            : </a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">     256183 : void PlumedMain::shareData() {</span></a>
+<a name="892"><span class="lineNum">     892 </span>            : // atom positions are shared (but only if there is something to do)</a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">     256183 :   if(!active)return;</span></a>
+<a name="894"><span class="lineNum">     894 </span>            : // Stopwatch is stopped when sw goes out of scope</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">     254535 :   auto sw=stopwatch.startStop(&quot;2 Sharing data&quot;);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">     254535 :   if(atoms.getNatoms()&gt;0) atoms.share();</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">     254535 : }</span></a>
+<a name="898"><span class="lineNum">     898 </span>            : </a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">       2134 : void PlumedMain::performCalcNoUpdate() {</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">       2134 :   waitData();</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">       2134 :   justCalculate();</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">       2134 :   backwardPropagate();</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">       2134 : }</span></a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">         10 : void PlumedMain::performCalcNoForces() {</span></a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">         10 :   waitData();</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">         10 :   justCalculate();</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">         10 : }</span></a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">     254039 : void PlumedMain::performCalc() {</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">     254039 :   waitData();</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">     254039 :   justCalculate();</span></a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">     254039 :   backwardPropagate();</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">     254039 :   update();</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">     254039 :   mydatafetcher-&gt;finishDataGrab();</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">     254039 : }</span></a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">     256297 : void PlumedMain::waitData() {</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">     256297 :   if(!active)return;</span></a>
+<a name="920"><span class="lineNum">     920 </span>            : // Stopwatch is stopped when sw goes out of scope</a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">     254649 :   auto sw=stopwatch.startStop(&quot;3 Waiting for data&quot;);</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">     254649 :   if(atoms.getNatoms()&gt;0) atoms.wait();</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">     254649 : }</span></a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">     256297 : void PlumedMain::justCalculate() {</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">     256297 :   if(!active)return;</span></a>
+<a name="927"><span class="lineNum">     927 </span>            : // Stopwatch is stopped when sw goes out of scope</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">     254649 :   auto sw=stopwatch.startStop(&quot;4 Calculating (forward loop)&quot;);</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">     254649 :   bias=0.0;</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">     254649 :   work=0.0;</span></a>
+<a name="931"><span class="lineNum">     931 </span>            : </a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">     254649 :   int iaction=0;</span></a>
+<a name="933"><span class="lineNum">     933 </span>            : // calculate the active actions in order (assuming *backward* dependence)</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">    2077444 :   for(const auto &amp; pp : actionSet) {</span></a>
+<a name="935"><span class="lineNum">     935 </span>            :     Action* p(pp.get());</a>
+<a name="936"><span class="lineNum">     936 </span>            :     try {</a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">    1822795 :       if(p-&gt;isActive()) {</span></a>
+<a name="938"><span class="lineNum">     938 </span>            : // Stopwatch is stopped when sw goes out of scope.</a>
+<a name="939"><span class="lineNum">     939 </span>            : // We explicitly declare a Stopwatch::Handler here to allow for conditional initialization.</a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">    1650083 :         Stopwatch::Handler sw;</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">    1650083 :         if(detailedTimers) {</span></a>
+<a name="942"><span class="lineNum">     942 </span>            :           std::string actionNumberLabel;</a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">       1690 :           Tools::convert(iaction,actionNumberLabel);</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">       1690 :           const unsigned m=actionSet.size();</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">       5070 :           unsigned k=0; unsigned n=1; while(n&lt;m) { n*=10; k++; }</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">       1690 :           const int pad=k-actionNumberLabel.length();</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">       2815 :           for(int i=0; i&lt;pad; i++) actionNumberLabel=&quot; &quot;+actionNumberLabel;</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">       1690 :           sw=stopwatch.startStop(&quot;4A &quot;+actionNumberLabel+&quot; &quot;+p-&gt;getLabel());</span></a>
+<a name="949"><span class="lineNum">     949 </span>            :         }</a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">    1650083 :         ActionWithValue*av=dynamic_cast&lt;ActionWithValue*&gt;(p);</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">    1650083 :         ActionAtomistic*aa=dynamic_cast&lt;ActionAtomistic*&gt;(p);</span></a>
+<a name="952"><span class="lineNum">     952 </span>            :         {</a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">    1650083 :           if(av) av-&gt;clearInputForces();</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">    1650083 :           if(av) av-&gt;clearDerivatives();</span></a>
+<a name="955"><span class="lineNum">     955 </span>            :         }</a>
+<a name="956"><span class="lineNum">     956 </span>            :         {</a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">    1650083 :           if(aa) aa-&gt;clearOutputForces();</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">    1650083 :           if(aa) if(aa-&gt;isActive()) aa-&gt;retrieveAtoms();</span></a>
+<a name="959"><span class="lineNum">     959 </span>            :         }</a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">    1650083 :         if(p-&gt;checkNumericalDerivatives()) p-&gt;calculateNumericalDerivatives();</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">    1649516 :         else p-&gt;calculate();</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :         // This retrieves components called bias</a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">    1650083 :         if(av) {</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">    1390052 :           bias+=av-&gt;getOutputQuantity(&quot;bias&quot;);</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">    1390052 :           work+=av-&gt;getOutputQuantity(&quot;work&quot;);</span></a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineCov">    1390052 :           av-&gt;setGradientsIfNeeded();</span></a>
+<a name="967"><span class="lineNum">     967 </span>            :         }</a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">    1650083 :         ActionWithVirtualAtom*avv=dynamic_cast&lt;ActionWithVirtualAtom*&gt;(p);</span></a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">    1650083 :         if(avv)avv-&gt;setGradientsIfNeeded();</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">    1650083 :       }</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineNoCov">          0 :     } catch(...) {</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineNoCov">          0 :       plumed_error_nested() &lt;&lt; &quot;An error happened while calculating &quot; &lt;&lt; p-&gt;getLabel();</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">    1822795 :     iaction++;</span></a>
+<a name="975"><span class="lineNum">     975 </span>            :   }</a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">     254649 : }</span></a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineNoCov">          0 : void PlumedMain::justApply() {</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineNoCov">          0 :   backwardPropagate();</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :   update();</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="982"><span class="lineNum">     982 </span>            : </a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">     256173 : void PlumedMain::backwardPropagate() {</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">     256173 :   if(!active)return;</span></a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">     254525 :   int iaction=0;</span></a>
+<a name="986"><span class="lineNum">     986 </span>            : // Stopwatch is stopped when sw goes out of scope</a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">     254525 :   auto sw=stopwatch.startStop(&quot;5 Applying (backward loop)&quot;);</span></a>
+<a name="988"><span class="lineNum">     988 </span>            : // apply them in reverse order</a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">    2076366 :   for(auto pp=actionSet.rbegin(); pp!=actionSet.rend(); ++pp) {</span></a>
+<a name="990"><span class="lineNum">     990 </span>            :     const auto &amp; p(pp-&gt;get());</a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">    1821841 :     if(p-&gt;isActive()) {</span></a>
+<a name="992"><span class="lineNum">     992 </span>            : </a>
+<a name="993"><span class="lineNum">     993 </span>            : // Stopwatch is stopped when sw goes out of scope.</a>
+<a name="994"><span class="lineNum">     994 </span>            : // We explicitly declare a Stopwatch::Handler here to allow for conditional initialization.</a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">    1649321 :       Stopwatch::Handler sw;</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">    1649321 :       if(detailedTimers) {</span></a>
+<a name="997"><span class="lineNum">     997 </span>            :         std::string actionNumberLabel;</a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">       1690 :         Tools::convert(iaction,actionNumberLabel);</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">       1690 :         const unsigned m=actionSet.size();</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">       5070 :         unsigned k=0; unsigned n=1; while(n&lt;m) { n*=10; k++; }</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">       1690 :         const int pad=k-actionNumberLabel.length();</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">       2815 :         for(int i=0; i&lt;pad; i++) actionNumberLabel=&quot; &quot;+actionNumberLabel;</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">       1690 :         sw=stopwatch.startStop(&quot;5A &quot;+actionNumberLabel+&quot; &quot;+p-&gt;getLabel());</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :       }</a>
+<a name="1005"><span class="lineNum">    1005 </span>            : </a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">    1649321 :       p-&gt;apply();</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">    1649321 :       ActionAtomistic*a=dynamic_cast&lt;ActionAtomistic*&gt;(p);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            : // still ActionAtomistic has a special treatment, since they may need to add forces on atoms</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">    1649321 :       if(a) a-&gt;applyForces();</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            : </a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">    1649321 :     }</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">    1821841 :     iaction++;</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :   }</a>
+<a name="1014"><span class="lineNum">    1014 </span>            : </a>
+<a name="1015"><span class="lineNum">    1015 </span>            : // Stopwatch is stopped when sw goes out of scope.</a>
+<a name="1016"><span class="lineNum">    1016 </span>            : // We explicitly declare a Stopwatch::Handler here to allow for conditional initialization.</a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">     254525 :   Stopwatch::Handler sw1;</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">     254525 :   if(detailedTimers) sw1=stopwatch.startStop(&quot;5B Update forces&quot;);</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            : // this is updating the MD copy of the forces</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">     254525 :   if(atoms.getNatoms()&gt;0) atoms.updateForces();</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">     254525 : }</span></a>
+<a name="1022"><span class="lineNum">    1022 </span>            : </a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">     254118 : void PlumedMain::update() {</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">     254118 :   if(!active)return;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            : </a>
+<a name="1026"><span class="lineNum">    1026 </span>            : // Stopwatch is stopped when sw goes out of scope</a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">     252470 :   auto sw=stopwatch.startStop(&quot;6 Update&quot;);</span></a>
+<a name="1028"><span class="lineNum">    1028 </span>            : </a>
+<a name="1029"><span class="lineNum">    1029 </span>            : // update step (for statistics, etc)</a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">     252470 :   updateFlags.push(true);</span></a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">    2067824 :   for(const auto &amp; p : actionSet) {</span></a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">    1815354 :     p-&gt;beforeUpdate();</span></a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">    3457830 :     if(p-&gt;isActive() &amp;&amp; p-&gt;checkUpdate() &amp;&amp; updateFlagsTop()) p-&gt;update();</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :   }</a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">     504944 :   while(!updateFlags.empty()) updateFlags.pop();</span></a>
+<a name="1036"><span class="lineNum">    1036 </span>            :   if(!updateFlags.empty()) plumed_merror(&quot;non matching changes in the update flags&quot;);</a>
+<a name="1037"><span class="lineNum">    1037 </span>            : // Check that no action has told the calculation to stop</a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">     252470 :   if(stopNow) {</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">         65 :     if(stopFlag) stopFlag.set(int(1));</span></a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineNoCov">          0 :     else plumed_merror(&quot;your md code cannot handle plumed stop events - add a call to plumed.comm(stopFlag,stopCondition)&quot;);</span></a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   }</a>
+<a name="1042"><span class="lineNum">    1042 </span>            : </a>
+<a name="1043"><span class="lineNum">    1043 </span>            : // flush by default every 10000 steps</a>
+<a name="1044"><span class="lineNum">    1044 </span>            : // hopefully will not affect performance</a>
+<a name="1045"><span class="lineNum">    1045 </span>            : // also if receive checkpointing signal</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">     252470 :   if(step%10000==0||doCheckPoint) {</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">        978 :     fflush();</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">        978 :     log.flush();</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">      15654 :     for(const auto &amp; p : actionSet) p-&gt;fflush();</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   }</a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">     252470 : }</span></a>
+<a name="1052"><span class="lineNum">    1052 </span>            : </a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">          2 : void PlumedMain::load(const std::string&amp; ss) {</span></a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">          2 :   if(DLLoader::installed()) {</span></a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">          2 :     std::string s=ss;</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">          2 :     size_t n=s.find_last_of(&quot;.&quot;);</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">          3 :     std::string extension=&quot;&quot;;</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">          2 :     std::string base=s;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">          4 :     if(n!=std::string::npos &amp;&amp; n&lt;s.length()-1) extension=s.substr(n+1);</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">          4 :     if(n!=std::string::npos &amp;&amp; n&lt;s.length())   base=s.substr(0,n);</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">          2 :     if(extension==&quot;cpp&quot;) {</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            : // full path command, including environment setup</a>
+<a name="1063"><span class="lineNum">    1063 </span>            : // this will work even if plumed is not in the execution path or if it has been</a>
+<a name="1064"><span class="lineNum">    1064 </span>            : // installed with a name different from &quot;plumed&quot;</a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">          4 :       std::string cmd=config::getEnvCommand()+&quot; \&quot;&quot;+config::getPlumedRoot()+&quot;\&quot;/scripts/mklib.sh &quot;+s;</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">          2 :       log&lt;&lt;&quot;Executing: &quot;&lt;&lt;cmd;</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">          2 :       if(comm.Get_size()&gt;0) log&lt;&lt;&quot; (only on master node)&quot;;</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">          2 :       log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">          2 :       if(comm.Get_rank()==0) {</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">          2 :         int ret=std::system(cmd.c_str());</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">          3 :         if(ret!=0) plumed_error() &lt;&lt;&quot;An error happened while executing command &quot;&lt;&lt;cmd&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="1072"><span class="lineNum">    1072 </span>            :       }</a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">          1 :       comm.Barrier();</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">          2 :       base=&quot;./&quot;+base;</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     }</a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">          2 :     s=base+&quot;.&quot;+config::getSoExt();</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">          1 :     void *p=dlloader.load(s);</span></a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">          1 :     if(!p) {</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineNoCov">          0 :       plumed_error()&lt;&lt;&quot;I cannot load library &quot; &lt;&lt; ss &lt;&lt; &quot; &quot; &lt;&lt; dlloader.error();</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     }</a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;Loading shared library &quot;&lt;&lt;s.c_str()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;Here is the new list of available actions\n&quot;;</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">          1 :     log&lt;&lt;actionRegister();</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineNoCov">          0 :   } else plumed_error()&lt;&lt;&quot;While loading library &quot;&lt;&lt; ss &lt;&lt; &quot; loading was not enabled, please check if dlopen was found at configure time&quot;;</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">          1 : }</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            : </a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">       2805 : double PlumedMain::getBias() const {</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">       2805 :   return bias;</span></a>
+<a name="1089"><span class="lineNum">    1089 </span>            : }</a>
+<a name="1090"><span class="lineNum">    1090 </span>            : </a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">        450 : double PlumedMain::getWork() const {</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">        450 :   return work;</span></a>
+<a name="1093"><span class="lineNum">    1093 </span>            : }</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">         73 : FILE* PlumedMain::fopen(const char *path, const char *mode) {</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">         73 :   std::string mmode(mode);</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">         73 :   std::string ppath(path);</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">         73 :   std::string suffix(getSuffix());</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">         73 :   std::string ppathsuf=ppath+suffix;</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">         73 :   FILE*fp=std::fopen(const_cast&lt;char*&gt;(ppathsuf.c_str()),const_cast&lt;char*&gt;(mmode.c_str()));</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">         73 :   if(!fp) fp=std::fopen(const_cast&lt;char*&gt;(ppath.c_str()),const_cast&lt;char*&gt;(mmode.c_str()));</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">         73 :   plumed_massert(fp,&quot;file &quot; + ppath + &quot; cannot be found&quot;);</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">         73 :   return fp;</span></a>
+<a name="1104"><span class="lineNum">    1104 </span>            : }</a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">         91 : int PlumedMain::fclose(FILE*fp) {</span></a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">         91 :   return std::fclose(fp);</span></a>
+<a name="1108"><span class="lineNum">    1108 </span>            : }</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">       3798 : std::string PlumedMain::cite(const std::string&amp;item) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">       3798 :   return citations.cite(item);</span></a>
+<a name="1112"><span class="lineNum">    1112 </span>            : }</a>
+<a name="1113"><span class="lineNum">    1113 </span>            : </a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">       1539 : void PlumedMain::fflush() {</span></a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">       4799 :   for(const auto  &amp; p : files) {</span></a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">       3260 :     p-&gt;flush();</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   }</a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">       1539 : }</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            : </a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">       4536 : void PlumedMain::insertFile(FileBase&amp;f) {</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">       4536 :   files.insert(&amp;f);</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">       4536 : }</span></a>
+<a name="1123"><span class="lineNum">    1123 </span>            : </a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">       4833 : void PlumedMain::eraseFile(FileBase&amp;f) {</span></a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">       4833 :   files.erase(&amp;f);</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">       4833 : }</span></a>
+<a name="1127"><span class="lineNum">    1127 </span>            : </a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">         65 : void PlumedMain::stop() {</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">         65 :   stopNow=true;</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">         65 : }</span></a>
+<a name="1131"><span class="lineNum">    1131 </span>            : </a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">        813 : void PlumedMain::runJobsAtEndOfCalculation() {</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">      14561 :   for(const auto &amp; p : actionSet) {</span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">      13748 :     p-&gt;runFinalJobs();</span></a>
+<a name="1135"><span class="lineNum">    1135 </span>            :   }</a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">        813 : }</span></a>
+<a name="1137"><span class="lineNum">    1137 </span>            : </a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">    8805343 : unsigned PlumedMain::increaseReferenceCounter() noexcept {</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">    8805343 :   return ++referenceCounter;</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            : }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            : </a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">    8804428 : unsigned PlumedMain::decreaseReferenceCounter() noexcept {</span></a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">    8804428 :   return --referenceCounter;</span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            : }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : </a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">         42 : unsigned PlumedMain::useCountReferenceCounter() const noexcept {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">         42 :   return referenceCounter;</span></a>
+<a name="1148"><span class="lineNum">    1148 </span>            : }</a>
+<a name="1149"><span class="lineNum">    1149 </span>            : </a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineNoCov">          0 : void PlumedMain::activateParseOnlyMode() {</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineNoCov">          0 :   doParseOnly=true;</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1153"><span class="lineNum">    1153 </span>            : </a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">       1820 : bool PlumedMain::parseOnlyMode() const {</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">       1820 :   return doParseOnly;</span></a>
+<a name="1156"><span class="lineNum">    1156 </span>            : }</a>
+<a name="1157"><span class="lineNum">    1157 </span>            : </a>
+<a name="1158"><span class="lineNum">    1158 </span>            : #ifdef __PLUMED_HAS_PYTHON</a>
+<a name="1159"><span class="lineNum">    1159 </span>            : // This is here to stop cppcheck throwing an error</a>
+<a name="1160"><span class="lineNum">    1160 </span>            : #endif</a>
+<a name="1161"><span class="lineNum">    1161 </span>            : </a>
+<a name="1162"><span class="lineNum">    1162 </span>            : }</a>
+<a name="1163"><span class="lineNum">    1163 </span>            : </a>
+<a name="1164"><span class="lineNum">    1164 </span>            : //////////////////////////////////////////////////////////////////////////////////////////////////////////////////</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMain.h.func-sort-c.html b/coverage/core/PlumedMain.h.func-sort-c.html
new file mode 100644
index 0000000000..631563866a
--- /dev/null
+++ b/coverage/core/PlumedMain.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMain.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMain.h<span style="font-size: 80%;"> (<a href="PlumedMain.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PlumedMain.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMain.h.func.html b/coverage/core/PlumedMain.h.func.html
new file mode 100644
index 0000000000..031956bb16
--- /dev/null
+++ b/coverage/core/PlumedMain.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMain.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMain.h<span style="font-size: 80%;"> (<a href="PlumedMain.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PlumedMain.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMain.h.gcov.html b/coverage/core/PlumedMain.h.gcov.html
new file mode 100644
index 0000000000..90621075ed
--- /dev/null
+++ b/coverage/core/PlumedMain.h.gcov.html
@@ -0,0 +1,623 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMain.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMain.h<span style="font-size: 80%;"> (source / <a href="PlumedMain.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_PlumedMain_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_PlumedMain_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;WithCmd.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/ForwardDecl.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;vector&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;set&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;stack&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;memory&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;map&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;atomic&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // !!!!!!!!!!!!!!!!!!!!!!    DANGER   !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!11</a>
+<a name="37"><span class="lineNum">      37 </span>            : // THE FOLLOWING ARE DEFINITIONS WHICH ARE NECESSARY FOR DYNAMIC LOADING OF THE PLUMED KERNEL:</a>
+<a name="38"><span class="lineNum">      38 </span>            : // This section should be consistent with the Plumed.h file.</a>
+<a name="39"><span class="lineNum">      39 </span>            : // Since the Plumed.h file may be included in host MD codes, **NEVER** MODIFY THE CODE DOWN HERE</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : /* Generic function pointer */</a>
+<a name="42"><span class="lineNum">      42 </span>            : typedef void (*plumed_function_pointer)(void);</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : /* Holder for function pointer */</a>
+<a name="45"><span class="lineNum">      45 </span>            : typedef struct {</a>
+<a name="46"><span class="lineNum">      46 </span>            :   plumed_function_pointer p;</a>
+<a name="47"><span class="lineNum">      47 </span>            : } plumed_function_holder;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : // END OF DANGER</a>
+<a name="50"><span class="lineNum">      50 </span>            : ////////////////////////////////////////////////////////////</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : namespace PLMD {</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : class ActionAtomistic;</a>
+<a name="57"><span class="lineNum">      57 </span>            : class ActionPilot;</a>
+<a name="58"><span class="lineNum">      58 </span>            : class Log;</a>
+<a name="59"><span class="lineNum">      59 </span>            : class Atoms;</a>
+<a name="60"><span class="lineNum">      60 </span>            : class ActionSet;</a>
+<a name="61"><span class="lineNum">      61 </span>            : class DLLoader;</a>
+<a name="62"><span class="lineNum">      62 </span>            : class Communicator;</a>
+<a name="63"><span class="lineNum">      63 </span>            : class Stopwatch;</a>
+<a name="64"><span class="lineNum">      64 </span>            : class Citations;</a>
+<a name="65"><span class="lineNum">      65 </span>            : class ExchangePatterns;</a>
+<a name="66"><span class="lineNum">      66 </span>            : class FileBase;</a>
+<a name="67"><span class="lineNum">      67 </span>            : class DataFetchingObject;</a>
+<a name="68"><span class="lineNum">      68 </span>            : class TypesafePtr;</a>
+<a name="69"><span class="lineNum">      69 </span>            : class IFile;</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : /**</a>
+<a name="72"><span class="lineNum">      72 </span>            : Main plumed object.</a>
+<a name="73"><span class="lineNum">      73 </span>            : In MD engines this object is not manipulated directly but it is wrapped in</a>
+<a name="74"><span class="lineNum">      74 </span>            : plumed or PLMD::Plumed objects. Its main method is cmd(),</a>
+<a name="75"><span class="lineNum">      75 </span>            : which defines completely the external plumed interface.</a>
+<a name="76"><span class="lineNum">      76 </span>            : It does not contain any static data.</a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : class PlumedMain:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   public WithCmd</a>
+<a name="80"><span class="lineNum">      80 </span>            : {</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Pointers to files opened in actions associated to this object.</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Notice that with the current implementation this should be at the top of this</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// structure. Indeed, this should be destroyed *after* all the actions allocated</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// in this PlumedMain object have been destroyed.</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::set&lt;FileBase*&gt; files;</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Forward declaration.</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ForwardDecl&lt;Communicator&gt; comm_fwd;</a>
+<a name="88"><span class="lineNum">      88 </span>            : public:</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Communicator for plumed.</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// Includes all the processors used by plumed.</a>
+<a name="91"><span class="lineNum">      91 </span>            :   Communicator&amp;comm=*comm_fwd;</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : private:</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Forward declaration.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   ForwardDecl&lt;Communicator&gt; multi_sim_comm_fwd;</a>
+<a name="96"><span class="lineNum">      96 </span>            : public:</a>
+<a name="97"><span class="lineNum">      97 </span>            :   Communicator&amp;multi_sim_comm=*multi_sim_comm_fwd;</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : private:</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Error handler.</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Pointer to a function that is called an exception thrown within</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// the library is about to leave the library.</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Can be used to remap exceptions in case the plumed wrapper was compiled</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// with a different version of the C++ standard library.</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Should only be called from \ref plumed_plumedmain_cmd().</a>
+<a name="106"><span class="lineNum">     106 </span>            :   typedef struct {</a>
+<a name="107"><span class="lineNum">     107 </span>            :     void* ptr;</a>
+<a name="108"><span class="lineNum">     108 </span>            :     void(*handler)(void* ptr,int code,const char*);</a>
+<a name="109"><span class="lineNum">     109 </span>            :   } plumed_error_handler;</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   plumed_error_handler error_handler= {NULL,NULL};</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   bool nestedExceptions=false;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Forward declaration.</a>
+<a name="116"><span class="lineNum">     116 </span>            :   ForwardDecl&lt;DLLoader&gt; dlloader_fwd;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   DLLoader&amp; dlloader=*dlloader_fwd;</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::unique_ptr&lt;WithCmd&gt; cltool;</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::unique_ptr&lt;WithCmd&gt; grex;</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// Flag to avoid double initialization</a>
+<a name="123"><span class="lineNum">     123 </span>            :   bool  initialized;</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Name of MD engine</a>
+<a name="125"><span class="lineNum">     125 </span>            :   std::string MDEngine;</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Forward declaration.</a>
+<a name="128"><span class="lineNum">     128 </span>            :   ForwardDecl&lt;Log&gt; log_fwd;</a>
+<a name="129"><span class="lineNum">     129 </span>            : /// Log stream</a>
+<a name="130"><span class="lineNum">     130 </span>            :   Log&amp; log=*log_fwd;</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Forward declaration.</a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Should be placed after log since its constructor takes a log reference as an argument.</a>
+<a name="134"><span class="lineNum">     134 </span>            :   ForwardDecl&lt;Stopwatch&gt; stopwatch_fwd;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   Stopwatch&amp; stopwatch=*stopwatch_fwd;</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : /// Forward declaration.</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ForwardDecl&lt;Citations&gt; citations_fwd;</a>
+<a name="139"><span class="lineNum">     139 </span>            : /// tools/Citations.holder</a>
+<a name="140"><span class="lineNum">     140 </span>            :   Citations&amp; citations=*citations_fwd;</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : /// Present step number.</a>
+<a name="143"><span class="lineNum">     143 </span>            :   long long int step;</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : /// Condition for plumed to be active.</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// At every step, PlumedMain is checking if there are Action's requiring some work.</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// If at least one Action requires some work, this variable is set to true.</a>
+<a name="148"><span class="lineNum">     148 </span>            :   bool active;</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : /// Name of the input file</a>
+<a name="151"><span class="lineNum">     151 </span>            :   std::string plumedDat;</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : /// Object containing data we would like to grab and pass back</a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::unique_ptr&lt;DataFetchingObject&gt; mydatafetcher;</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : /// End of input file.</a>
+<a name="157"><span class="lineNum">     157 </span>            : /// Set to true to terminate reading</a>
+<a name="158"><span class="lineNum">     158 </span>            :   bool endPlumed;</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Forward declaration.</a>
+<a name="161"><span class="lineNum">     161 </span>            :   ForwardDecl&lt;Atoms&gt; atoms_fwd;</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// Object containing information about atoms (such as positions,...).</a>
+<a name="163"><span class="lineNum">     163 </span>            :   Atoms&amp;    atoms=*atoms_fwd;           // atomic coordinates</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : /// Forward declaration.</a>
+<a name="166"><span class="lineNum">     166 </span>            :   ForwardDecl&lt;ActionSet&gt; actionSet_fwd;</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// Set of actions found in plumed.dat file</a>
+<a name="168"><span class="lineNum">     168 </span>            :   ActionSet&amp; actionSet=*actionSet_fwd;</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : /// Set of Pilot actions.</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// These are the action the, if they are Pilot::onStep(), can trigger execution</a>
+<a name="172"><span class="lineNum">     172 </span>            :   std::vector&lt;ActionPilot*&gt; pilots;</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : /// Suffix string for file opening, useful for multiple simulations in the same directory</a>
+<a name="175"><span class="lineNum">     175 </span>            :   std::string suffix;</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : /// The total bias (=total energy of the restraints)</a>
+<a name="178"><span class="lineNum">     178 </span>            :   double bias;</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : /// The total work.</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// This computed by accumulating the change in external potentials.</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double work;</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : /// Forward declaration.</a>
+<a name="185"><span class="lineNum">     185 </span>            :   ForwardDecl&lt;ExchangePatterns&gt; exchangePatterns_fwd;</a>
+<a name="186"><span class="lineNum">     186 </span>            : /// Class of possible exchange patterns, used for BIASEXCHANGE but also for future parallel tempering</a>
+<a name="187"><span class="lineNum">     187 </span>            :   ExchangePatterns&amp; exchangePatterns=*exchangePatterns_fwd;</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : /// Set to true if on an exchange step</a>
+<a name="190"><span class="lineNum">     190 </span>            :   bool exchangeStep;</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : /// Flag for restart</a>
+<a name="193"><span class="lineNum">     193 </span>            :   bool restart;</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : /// Flag for checkpointig</a>
+<a name="196"><span class="lineNum">     196 </span>            :   bool doCheckPoint;</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : /// Flag for parse only mode -- basically just forces restart to turn off</a>
+<a name="199"><span class="lineNum">     199 </span>            :   bool doParseOnly;</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : private:</a>
+<a name="202"><span class="lineNum">     202 </span>            : /// Forward declaration.</a>
+<a name="203"><span class="lineNum">     203 </span>            :   ForwardDecl&lt;TypesafePtr&gt; stopFlag_fwd;</a>
+<a name="204"><span class="lineNum">     204 </span>            : public:</a>
+<a name="205"><span class="lineNum">     205 </span>            : /// Stuff to make plumed stop the MD code cleanly</a>
+<a name="206"><span class="lineNum">     206 </span>            :   TypesafePtr&amp; stopFlag=*stopFlag_fwd;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   bool stopNow;</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : /// Stack for update flags.</a>
+<a name="210"><span class="lineNum">     210 </span>            : /// Store information used in class \ref generic::UpdateIf</a>
+<a name="211"><span class="lineNum">     211 </span>            :   std::stack&lt;bool&gt; updateFlags;</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : public:</a>
+<a name="214"><span class="lineNum">     214 </span>            : /// Flag to switch off virial calculation (for debug and MD codes with no barostat)</a>
+<a name="215"><span class="lineNum">     215 </span>            :   bool novirial;</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : /// Flag to switch on detailed timers</a>
+<a name="218"><span class="lineNum">     218 </span>            :   bool detailedTimers;</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : /// GpuDevice Identifier</a>
+<a name="221"><span class="lineNum">     221 </span>            :   int gpuDeviceId;</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : /// Generic map string -&gt; double</a>
+<a name="224"><span class="lineNum">     224 </span>            : /// intended to pass information across Actions</a>
+<a name="225"><span class="lineNum">     225 </span>            :   std::map&lt;std::string,double&gt; passMap;</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            : /// Add a citation, returning a string containing the reference number, something like &quot;[10]&quot;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   std::string cite(const std::string&amp;);</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : /// Get number of threads that can be used by openmp</a>
+<a name="231"><span class="lineNum">     231 </span>            :   unsigned getNumThreads()const;</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : /// Get a reasonable number of threads so as to access to an array of size s located at x</a>
+<a name="234"><span class="lineNum">     234 </span>            :   template&lt;typename T&gt;</a>
+<a name="235"><span class="lineNum">     235 </span>            :   unsigned getGoodNumThreads(const T*x,unsigned s)const;</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : /// Get a reasonable number of threads so as to access to vector v;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   template&lt;typename T&gt;</a>
+<a name="239"><span class="lineNum">     239 </span>            :   unsigned getGoodNumThreads(const std::vector&lt;T&gt; &amp; v)const;</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : public:</a>
+<a name="242"><span class="lineNum">     242 </span>            :   PlumedMain();</a>
+<a name="243"><span class="lineNum">     243 </span>            : // this is to access to WithCmd versions of cmd (allowing overloading of a virtual method)</a>
+<a name="244"><span class="lineNum">     244 </span>            :   using WithCmd::cmd;</a>
+<a name="245"><span class="lineNum">     245 </span>            :   /**</a>
+<a name="246"><span class="lineNum">     246 </span>            :    cmd method, accessible with standard Plumed.h interface.</a>
+<a name="247"><span class="lineNum">     247 </span>            :    \param key The name of the command to be executed.</a>
+<a name="248"><span class="lineNum">     248 </span>            :    \param val The argument of the command to be executed.</a>
+<a name="249"><span class="lineNum">     249 </span>            :    It is called as plumed_cmd() or as PLMD::Plumed::cmd()</a>
+<a name="250"><span class="lineNum">     250 </span>            :    It is the interpreter for plumed commands. It basically contains the definition of the plumed interface.</a>
+<a name="251"><span class="lineNum">     251 </span>            :    If you want to add a new functionality to the interface between plumed</a>
+<a name="252"><span class="lineNum">     252 </span>            :    and an MD engine, this is the right place</a>
+<a name="253"><span class="lineNum">     253 </span>            :    Notice that this interface should always keep retro-compatibility</a>
+<a name="254"><span class="lineNum">     254 </span>            :   */</a>
+<a name="255"><span class="lineNum">     255 </span>            :   void cmd(const std::string&amp;key,const TypesafePtr &amp; val=nullptr) override;</a>
+<a name="256"><span class="lineNum">     256 </span>            :   ~PlumedMain();</a>
+<a name="257"><span class="lineNum">     257 </span>            :   /**</a>
+<a name="258"><span class="lineNum">     258 </span>            :     Turn on parse only mode to deactivate restart in all actions.</a>
+<a name="259"><span class="lineNum">     259 </span>            :     This is only used by plumed driver --parse-only</a>
+<a name="260"><span class="lineNum">     260 </span>            :   */</a>
+<a name="261"><span class="lineNum">     261 </span>            :   void activateParseOnlyMode();</a>
+<a name="262"><span class="lineNum">     262 </span>            :   /**</a>
+<a name="263"><span class="lineNum">     263 </span>            :     This checks if parse only mode is active and turns off any restart.</a>
+<a name="264"><span class="lineNum">     264 </span>            :   */</a>
+<a name="265"><span class="lineNum">     265 </span>            :   bool parseOnlyMode() const ;</a>
+<a name="266"><span class="lineNum">     266 </span>            :   /**</a>
+<a name="267"><span class="lineNum">     267 </span>            :     Read an input file.</a>
+<a name="268"><span class="lineNum">     268 </span>            :     \param str name of the file</a>
+<a name="269"><span class="lineNum">     269 </span>            :   */</a>
+<a name="270"><span class="lineNum">     270 </span>            :   void readInputFile(const std::string &amp; str);</a>
+<a name="271"><span class="lineNum">     271 </span>            :   /**</a>
+<a name="272"><span class="lineNum">     272 </span>            :     Read an input file.</a>
+<a name="273"><span class="lineNum">     273 </span>            :     \param ifile</a>
+<a name="274"><span class="lineNum">     274 </span>            :   */</a>
+<a name="275"><span class="lineNum">     275 </span>            :   void readInputFile(IFile &amp; ifile);</a>
+<a name="276"><span class="lineNum">     276 </span>            :   /**</a>
+<a name="277"><span class="lineNum">     277 </span>            :     Read an input string.</a>
+<a name="278"><span class="lineNum">     278 </span>            :     \param str name of the string</a>
+<a name="279"><span class="lineNum">     279 </span>            :   */</a>
+<a name="280"><span class="lineNum">     280 </span>            :   void readInputWords(const std::vector&lt;std::string&gt; &amp;  str);</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   /**</a>
+<a name="283"><span class="lineNum">     283 </span>            :     Read an input string.</a>
+<a name="284"><span class="lineNum">     284 </span>            :     \param str name of the string</a>
+<a name="285"><span class="lineNum">     285 </span>            :     At variance with readInputWords(), this is splitting the string into words</a>
+<a name="286"><span class="lineNum">     286 </span>            :   */</a>
+<a name="287"><span class="lineNum">     287 </span>            :   void readInputLine(const std::string &amp; str);</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   /**</a>
+<a name="290"><span class="lineNum">     290 </span>            :     Read an input buffer.</a>
+<a name="291"><span class="lineNum">     291 </span>            :     \param str name of the string</a>
+<a name="292"><span class="lineNum">     292 </span>            :     Same as readInputFile, but first write str on a temporary file and then read</a>
+<a name="293"><span class="lineNum">     293 </span>            :     that files. At variance with readInputLine, it can take care of comments and</a>
+<a name="294"><span class="lineNum">     294 </span>            :     continuation lines.</a>
+<a name="295"><span class="lineNum">     295 </span>            :   */</a>
+<a name="296"><span class="lineNum">     296 </span>            :   void readInputLines(const std::string &amp; str);</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :   /**</a>
+<a name="299"><span class="lineNum">     299 </span>            :     Initialize the object.</a>
+<a name="300"><span class="lineNum">     300 </span>            :     Should be called once.</a>
+<a name="301"><span class="lineNum">     301 </span>            :   */</a>
+<a name="302"><span class="lineNum">     302 </span>            :   void init();</a>
+<a name="303"><span class="lineNum">     303 </span>            :   /**</a>
+<a name="304"><span class="lineNum">     304 </span>            :     Prepare the calculation.</a>
+<a name="305"><span class="lineNum">     305 </span>            :     Here it is checked which are the active Actions and communication of the relevant atoms is initiated.</a>
+<a name="306"><span class="lineNum">     306 </span>            :     Shortcut for prepareDependencies() + shareData()</a>
+<a name="307"><span class="lineNum">     307 </span>            :   */</a>
+<a name="308"><span class="lineNum">     308 </span>            :   void prepareCalc();</a>
+<a name="309"><span class="lineNum">     309 </span>            :   /**</a>
+<a name="310"><span class="lineNum">     310 </span>            :     Prepare the list of active Actions and needed atoms.</a>
+<a name="311"><span class="lineNum">     311 </span>            :     Scan the Actions to see which are active and which are not, so as to prepare a list of</a>
+<a name="312"><span class="lineNum">     312 </span>            :     the atoms needed at this step.</a>
+<a name="313"><span class="lineNum">     313 </span>            :   */</a>
+<a name="314"><span class="lineNum">     314 </span>            :   void prepareDependencies();</a>
+<a name="315"><span class="lineNum">     315 </span>            :   /**</a>
+<a name="316"><span class="lineNum">     316 </span>            :     Share the needed atoms.</a>
+<a name="317"><span class="lineNum">     317 </span>            :     In asynchronous implementations, this method sends the required atoms to all the plumed processes,</a>
+<a name="318"><span class="lineNum">     318 </span>            :     without waiting for the communication to complete.</a>
+<a name="319"><span class="lineNum">     319 </span>            :   */</a>
+<a name="320"><span class="lineNum">     320 </span>            :   void shareData();</a>
+<a name="321"><span class="lineNum">     321 </span>            :   /**</a>
+<a name="322"><span class="lineNum">     322 </span>            :     Perform the calculation.</a>
+<a name="323"><span class="lineNum">     323 </span>            :     Shortcut for waitData() + justCalculate() + justApply().</a>
+<a name="324"><span class="lineNum">     324 </span>            :     Equivalently: waitData() + justCalculate() + backwardPropagate() + update().</a>
+<a name="325"><span class="lineNum">     325 </span>            :   */</a>
+<a name="326"><span class="lineNum">     326 </span>            :   void performCalc();</a>
+<a name="327"><span class="lineNum">     327 </span>            :   /**</a>
+<a name="328"><span class="lineNum">     328 </span>            :     Perform the calculation without update()</a>
+<a name="329"><span class="lineNum">     329 </span>            :     Shortcut for: waitData() + justCalculate() + backwardPropagate()</a>
+<a name="330"><span class="lineNum">     330 </span>            :   */</a>
+<a name="331"><span class="lineNum">     331 </span>            :   void performCalcNoUpdate();</a>
+<a name="332"><span class="lineNum">     332 </span>            :   /**</a>
+<a name="333"><span class="lineNum">     333 </span>            :     Perform the calculation without backpropagation nor update()</a>
+<a name="334"><span class="lineNum">     334 </span>            :     Shortcut for: waitData() + justCalculate()</a>
+<a name="335"><span class="lineNum">     335 </span>            :   */</a>
+<a name="336"><span class="lineNum">     336 </span>            :   void performCalcNoForces();</a>
+<a name="337"><span class="lineNum">     337 </span>            :   /**</a>
+<a name="338"><span class="lineNum">     338 </span>            :     Complete PLUMED calculation.</a>
+<a name="339"><span class="lineNum">     339 </span>            :     Shortcut for prepareCalc() + performCalc()</a>
+<a name="340"><span class="lineNum">     340 </span>            :   */</a>
+<a name="341"><span class="lineNum">     341 </span>            :   void calc();</a>
+<a name="342"><span class="lineNum">     342 </span>            :   /**</a>
+<a name="343"><span class="lineNum">     343 </span>            :     Scatters the needed atoms.</a>
+<a name="344"><span class="lineNum">     344 </span>            :     In asynchronous implementations, this method waits for the communications started in shareData()</a>
+<a name="345"><span class="lineNum">     345 </span>            :     to be completed. Otherwise, just send around needed atoms.</a>
+<a name="346"><span class="lineNum">     346 </span>            :   */</a>
+<a name="347"><span class="lineNum">     347 </span>            :   void waitData();</a>
+<a name="348"><span class="lineNum">     348 </span>            :   /**</a>
+<a name="349"><span class="lineNum">     349 </span>            :     Perform the forward loop on active actions.</a>
+<a name="350"><span class="lineNum">     350 </span>            :   */</a>
+<a name="351"><span class="lineNum">     351 </span>            :   void justCalculate();</a>
+<a name="352"><span class="lineNum">     352 </span>            :   /**</a>
+<a name="353"><span class="lineNum">     353 </span>            :     Backward propagate and update.</a>
+<a name="354"><span class="lineNum">     354 </span>            :     Shortcut for backwardPropagate() + update()</a>
+<a name="355"><span class="lineNum">     355 </span>            :     I leave it here for backward compatibility</a>
+<a name="356"><span class="lineNum">     356 </span>            :   */</a>
+<a name="357"><span class="lineNum">     357 </span>            :   void justApply();</a>
+<a name="358"><span class="lineNum">     358 </span>            :   /**</a>
+<a name="359"><span class="lineNum">     359 </span>            :     Perform the backward loop on active actions.</a>
+<a name="360"><span class="lineNum">     360 </span>            :     Needed to apply the forces back.</a>
+<a name="361"><span class="lineNum">     361 </span>            :   */</a>
+<a name="362"><span class="lineNum">     362 </span>            :   void backwardPropagate();</a>
+<a name="363"><span class="lineNum">     363 </span>            :   /**</a>
+<a name="364"><span class="lineNum">     364 </span>            :     Call the update() method.</a>
+<a name="365"><span class="lineNum">     365 </span>            :   */</a>
+<a name="366"><span class="lineNum">     366 </span>            :   void update();</a>
+<a name="367"><span class="lineNum">     367 </span>            :   /**</a>
+<a name="368"><span class="lineNum">     368 </span>            :     If there are calculations that need to be done at the very end of the calculations this</a>
+<a name="369"><span class="lineNum">     369 </span>            :     makes sures they are done</a>
+<a name="370"><span class="lineNum">     370 </span>            :   */</a>
+<a name="371"><span class="lineNum">     371 </span>            :   void runJobsAtEndOfCalculation();</a>
+<a name="372"><span class="lineNum">     372 </span>            : /// Reference to atoms object</a>
+<a name="373"><span class="lineNum">     373 </span>            :   Atoms&amp; getAtoms();</a>
+<a name="374"><span class="lineNum">     374 </span>            : /// Reference to the list of Action's</a>
+<a name="375"><span class="lineNum">     375 </span>            :   const ActionSet &amp; getActionSet()const;</a>
+<a name="376"><span class="lineNum">     376 </span>            : /// Referenge to the log stream</a>
+<a name="377"><span class="lineNum">     377 </span>            :   Log &amp; getLog();</a>
+<a name="378"><span class="lineNum">     378 </span>            : /// Return the number of the step</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">    4559088 :   long long int getStep()const {return step;}</span></a>
+<a name="380"><span class="lineNum">     380 </span>            : /// Stop the run</a>
+<a name="381"><span class="lineNum">     381 </span>            :   void exit(int c=0);</a>
+<a name="382"><span class="lineNum">     382 </span>            : /// Load a shared library</a>
+<a name="383"><span class="lineNum">     383 </span>            :   void load(const std::string&amp;);</a>
+<a name="384"><span class="lineNum">     384 </span>            : /// Get the suffix string</a>
+<a name="385"><span class="lineNum">     385 </span>            :   const std::string &amp; getSuffix()const;</a>
+<a name="386"><span class="lineNum">     386 </span>            : /// Set the suffix string</a>
+<a name="387"><span class="lineNum">     387 </span>            :   void setSuffix(const std::string&amp;);</a>
+<a name="388"><span class="lineNum">     388 </span>            : /// get the value of the bias</a>
+<a name="389"><span class="lineNum">     389 </span>            :   double getBias()const;</a>
+<a name="390"><span class="lineNum">     390 </span>            : /// get the value of the work</a>
+<a name="391"><span class="lineNum">     391 </span>            :   double getWork()const;</a>
+<a name="392"><span class="lineNum">     392 </span>            : /// Opens a file.</a>
+<a name="393"><span class="lineNum">     393 </span>            : /// Similar to plain fopen, but, if it finds an error in opening the file, it also tries with</a>
+<a name="394"><span class="lineNum">     394 </span>            : /// path+suffix.  This trick is useful for multiple replica simulations.</a>
+<a name="395"><span class="lineNum">     395 </span>            :   FILE* fopen(const char *path, const char *mode);</a>
+<a name="396"><span class="lineNum">     396 </span>            : /// Closes a file opened with PlumedMain::fopen()</a>
+<a name="397"><span class="lineNum">     397 </span>            :   int fclose(FILE*fp);</a>
+<a name="398"><span class="lineNum">     398 </span>            : /// Insert a file</a>
+<a name="399"><span class="lineNum">     399 </span>            :   void insertFile(FileBase&amp;);</a>
+<a name="400"><span class="lineNum">     400 </span>            : /// Erase a file</a>
+<a name="401"><span class="lineNum">     401 </span>            :   void eraseFile(FileBase&amp;);</a>
+<a name="402"><span class="lineNum">     402 </span>            : /// Flush all files</a>
+<a name="403"><span class="lineNum">     403 </span>            :   void fflush();</a>
+<a name="404"><span class="lineNum">     404 </span>            : /// Check if restarting</a>
+<a name="405"><span class="lineNum">     405 </span>            :   bool getRestart()const;</a>
+<a name="406"><span class="lineNum">     406 </span>            : /// Set restart flag</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         56 :   void setRestart(bool f) {if(!doParseOnly) restart=f;}</span></a>
+<a name="408"><span class="lineNum">     408 </span>            : /// Check if checkpointing</a>
+<a name="409"><span class="lineNum">     409 </span>            :   bool getCPT()const;</a>
+<a name="410"><span class="lineNum">     410 </span>            : /// Set exchangeStep flag</a>
+<a name="411"><span class="lineNum">     411 </span>            :   void setExchangeStep(bool f);</a>
+<a name="412"><span class="lineNum">     412 </span>            : /// Get exchangeStep flag</a>
+<a name="413"><span class="lineNum">     413 </span>            :   bool getExchangeStep()const;</a>
+<a name="414"><span class="lineNum">     414 </span>            : /// Stop the calculation cleanly (both the MD code and plumed)</a>
+<a name="415"><span class="lineNum">     415 </span>            :   void stop();</a>
+<a name="416"><span class="lineNum">     416 </span>            : /// Enforce active flag.</a>
+<a name="417"><span class="lineNum">     417 </span>            : /// This is a (bit dirty) hack to solve a bug. When there is no active ActionPilot,</a>
+<a name="418"><span class="lineNum">     418 </span>            : /// several shortcuts are used. However, these shortcuts can block GREX module.</a>
+<a name="419"><span class="lineNum">     419 </span>            : /// This function allows to enforce active plumed when doing exchanges,</a>
+<a name="420"><span class="lineNum">     420 </span>            : /// thus fixing the bug.</a>
+<a name="421"><span class="lineNum">     421 </span>            :   void resetActive(bool active);</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span>            : /// Access to exchange patterns</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :   ExchangePatterns&amp; getExchangePatterns() {return exchangePatterns;}</span></a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            : /// Push a state to update flags</a>
+<a name="427"><span class="lineNum">     427 </span>            :   void updateFlagsPush(bool);</a>
+<a name="428"><span class="lineNum">     428 </span>            : /// Pop a state from update flags</a>
+<a name="429"><span class="lineNum">     429 </span>            :   void updateFlagsPop();</a>
+<a name="430"><span class="lineNum">     430 </span>            : /// Get top of update flags</a>
+<a name="431"><span class="lineNum">     431 </span>            :   bool updateFlagsTop();</a>
+<a name="432"><span class="lineNum">     432 </span>            : /// Set end of input file</a>
+<a name="433"><span class="lineNum">     433 </span>            :   void setEndPlumed();</a>
+<a name="434"><span class="lineNum">     434 </span>            : /// Get the value of the end plumed flag</a>
+<a name="435"><span class="lineNum">     435 </span>            :   bool getEndPlumed() const ;</a>
+<a name="436"><span class="lineNum">     436 </span>            : /// Get the value of the gpuDeviceId</a>
+<a name="437"><span class="lineNum">     437 </span>            :   int getGpuDeviceId() const ;</a>
+<a name="438"><span class="lineNum">     438 </span>            : /// Call error handler.</a>
+<a name="439"><span class="lineNum">     439 </span>            : /// Should only be called from \ref plumed_plumedmain_cmd().</a>
+<a name="440"><span class="lineNum">     440 </span>            : /// If the error handler was not set, returns false.</a>
+<a name="441"><span class="lineNum">     441 </span>            :   bool callErrorHandler(int code,const char* msg)const;</a>
+<a name="442"><span class="lineNum">     442 </span>            : private:</a>
+<a name="443"><span class="lineNum">     443 </span>            :   std::atomic&lt;unsigned&gt; referenceCounter{};</a>
+<a name="444"><span class="lineNum">     444 </span>            : public:</a>
+<a name="445"><span class="lineNum">     445 </span>            : /// Atomically increase reference counter and return the new value</a>
+<a name="446"><span class="lineNum">     446 </span>            :   unsigned increaseReferenceCounter() noexcept;</a>
+<a name="447"><span class="lineNum">     447 </span>            : /// Atomically decrease reference counter and return the new value</a>
+<a name="448"><span class="lineNum">     448 </span>            :   unsigned decreaseReferenceCounter() noexcept;</a>
+<a name="449"><span class="lineNum">     449 </span>            : /// Report the reference counter</a>
+<a name="450"><span class="lineNum">     450 </span>            :   unsigned useCountReferenceCounter() const noexcept;</a>
+<a name="451"><span class="lineNum">     451 </span>            :   void enableNestedExceptions();</a>
+<a name="452"><span class="lineNum">     452 </span>            :   bool getNestedExceptions()const {</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         99 :     return nestedExceptions;</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span>            : };</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            : /////</a>
+<a name="458"><span class="lineNum">     458 </span>            : // FAST INLINE METHODS:</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            : inline</a>
+<a name="461"><span class="lineNum">     461 </span>            : const ActionSet &amp; PlumedMain::getActionSet()const {</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">    1109143 :   return actionSet;</span></a>
+<a name="463"><span class="lineNum">     463 </span>            : }</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span>            : inline</a>
+<a name="466"><span class="lineNum">     466 </span>            : Atoms&amp; PlumedMain::getAtoms() {</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">    3242728 :   return atoms;</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : }</a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            : inline</a>
+<a name="471"><span class="lineNum">     471 </span>            : const std::string &amp; PlumedMain::getSuffix()const {</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">       4858 :   return suffix;</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : }</a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            : inline</a>
+<a name="476"><span class="lineNum">     476 </span>            : void PlumedMain::setSuffix(const std::string&amp;s) {</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">        411 :   suffix=s;</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        411 : }</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span>            : inline</a>
+<a name="481"><span class="lineNum">     481 </span>            : bool PlumedMain::getRestart()const {</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">      14358 :   return restart;</span></a>
+<a name="483"><span class="lineNum">     483 </span>            : }</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            : inline</a>
+<a name="486"><span class="lineNum">     486 </span>            : bool PlumedMain::getCPT()const {</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">      14302 :   return doCheckPoint;</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : }</a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span>            : inline</a>
+<a name="491"><span class="lineNum">     491 </span>            : void PlumedMain::setExchangeStep(bool s) {</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        228 :   exchangeStep=s;</span></a>
+<a name="493"><span class="lineNum">     493 </span>            : }</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            : inline</a>
+<a name="496"><span class="lineNum">     496 </span>            : bool PlumedMain::getExchangeStep()const {</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">      28109 :   return exchangeStep;</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : }</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            : inline</a>
+<a name="501"><span class="lineNum">     501 </span>            : void PlumedMain::resetActive(bool active) {</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        114 :   this-&gt;active=active;</span></a>
+<a name="503"><span class="lineNum">     503 </span>            : }</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            : inline</a>
+<a name="506"><span class="lineNum">     506 </span>            : void PlumedMain::updateFlagsPush(bool on) {</a>
+<a name="507"><span class="lineNum">     507 </span>            :   updateFlags.push(on);</a>
+<a name="508"><span class="lineNum">     508 </span>            : }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : inline</a>
+<a name="511"><span class="lineNum">     511 </span>            : void PlumedMain::updateFlagsPop() {</a>
+<a name="512"><span class="lineNum">     512 </span>            :   updateFlags.pop();</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         12 : }</span></a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : inline</a>
+<a name="516"><span class="lineNum">     516 </span>            : bool PlumedMain::updateFlagsTop() {</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">    1642483 :   return updateFlags.top();</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : }</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            : inline</a>
+<a name="521"><span class="lineNum">     521 </span>            : void PlumedMain::setEndPlumed() {</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        263 :   endPlumed=true;</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : }</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            : inline</a>
+<a name="526"><span class="lineNum">     526 </span>            : bool PlumedMain::getEndPlumed() const {</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :   return endPlumed;</span></a>
+<a name="528"><span class="lineNum">     528 </span>            : }</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : inline</a>
+<a name="531"><span class="lineNum">     531 </span>            : int PlumedMain::getGpuDeviceId() const {</a>
+<a name="532"><span class="lineNum">     532 </span>            :   return gpuDeviceId;</a>
+<a name="533"><span class="lineNum">     533 </span>            : }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            : inline</a>
+<a name="536"><span class="lineNum">     536 </span>            : bool PlumedMain::callErrorHandler(int code,const char* msg)const {</a>
+<a name="537"><span class="lineNum">     537 </span>            :   if(error_handler.handler) {</a>
+<a name="538"><span class="lineNum">     538 </span>            :     error_handler.handler(error_handler.ptr,code,msg);</a>
+<a name="539"><span class="lineNum">     539 </span>            :     return true;</a>
+<a name="540"><span class="lineNum">     540 </span>            :   } else return false;</a>
+<a name="541"><span class="lineNum">     541 </span>            : }</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span>            : }</a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span>            : #endif</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMainInitializer.cpp.func-sort-c.html b/coverage/core/PlumedMainInitializer.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ff6ca450e2
--- /dev/null
+++ b/coverage/core/PlumedMainInitializer.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMainInitializer.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMainInitializer.cpp<span style="font-size: 80%;"> (<a href="PlumedMainInitializer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">211</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PlumedMainInitializer.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#51">_ZL13typesafeDebugPKc16plumed_safeptr_x</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#303">plumed_plumedmain_cmd_nothrow</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#94">plumed_plumedmain_use_count</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#244">_ZL16translate_nested24plumed_nothrow_handler_x</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#107">plumed_plumedmain_cmd_safe</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#120">_ZL17translate_current24plumed_nothrow_handler_xPPvPKc</a></td>
+              <td class="coverFnHi">111</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#100">plumed_plumedmain_cmd</a></td>
+              <td class="coverFnHi">357</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#364">_ZN4PLMD12_GLOBAL__N_121PlumedMainInitializerC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#408">_ZN4PLMD12_GLOBAL__N_121PlumedMainInitializerD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#270">plumed_plumedmain_cmd_safe_nothrow</a></td>
+              <td class="coverFnHi">14786</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#46">_ZL19getenvTypesafeDebugv</a></td>
+              <td class="coverFnHi">14881</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#69">plumed_plumedmain_create</a></td>
+              <td class="coverFnHi">804353</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#315">plumed_plumedmain_finalize</a></td>
+              <td class="coverFnHi">804353</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#335">plumed_symbol_table_init</a></td>
+              <td class="coverFnHi">808492</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#82">plumed_plumedmain_create_reference</a></td>
+              <td class="coverFnHi">8000075</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#88">plumed_plumedmain_delete_reference</a></td>
+              <td class="coverFnHi">8804428</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMainInitializer.cpp.func.html b/coverage/core/PlumedMainInitializer.cpp.func.html
new file mode 100644
index 0000000000..0e1af19996
--- /dev/null
+++ b/coverage/core/PlumedMainInitializer.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMainInitializer.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMainInitializer.cpp<span style="font-size: 80%;"> (<a href="PlumedMainInitializer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">211</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PlumedMainInitializer.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#51">_ZL13typesafeDebugPKc16plumed_safeptr_x</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#244">_ZL16translate_nested24plumed_nothrow_handler_x</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#120">_ZL17translate_current24plumed_nothrow_handler_xPPvPKc</a></td>
+              <td class="coverFnHi">111</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#46">_ZL19getenvTypesafeDebugv</a></td>
+              <td class="coverFnHi">14881</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#364">_ZN4PLMD12_GLOBAL__N_121PlumedMainInitializerC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#408">_ZN4PLMD12_GLOBAL__N_121PlumedMainInitializerD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#100">plumed_plumedmain_cmd</a></td>
+              <td class="coverFnHi">357</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#303">plumed_plumedmain_cmd_nothrow</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#107">plumed_plumedmain_cmd_safe</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#270">plumed_plumedmain_cmd_safe_nothrow</a></td>
+              <td class="coverFnHi">14786</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#69">plumed_plumedmain_create</a></td>
+              <td class="coverFnHi">804353</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#82">plumed_plumedmain_create_reference</a></td>
+              <td class="coverFnHi">8000075</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#88">plumed_plumedmain_delete_reference</a></td>
+              <td class="coverFnHi">8804428</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#315">plumed_plumedmain_finalize</a></td>
+              <td class="coverFnHi">804353</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#94">plumed_plumedmain_use_count</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedMainInitializer.cpp.gcov.html#335">plumed_symbol_table_init</a></td>
+              <td class="coverFnHi">808492</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/PlumedMainInitializer.cpp.gcov.html b/coverage/core/PlumedMainInitializer.cpp.gcov.html
new file mode 100644
index 0000000000..17135f8cb0
--- /dev/null
+++ b/coverage/core/PlumedMainInitializer.cpp.gcov.html
@@ -0,0 +1,494 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/PlumedMainInitializer.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - PlumedMainInitializer.cpp<span style="font-size: 80%;"> (source / <a href="PlumedMainInitializer.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">211</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PlumedMainInitializer.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;lepton/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstring&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;iostream&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #if defined __PLUMED_HAS_DLOPEN</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;dlfcn.h&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #endif</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;exception&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;stdexcept&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;ios&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;new&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;typeinfo&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;system_error&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;future&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &lt;memory&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &lt;functional&gt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #endif</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;tools/TypesafePtr.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;tools/Log.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      14881 : static bool getenvTypesafeDebug() noexcept {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      14881 :   static const auto* res=std::getenv(&quot;PLUMED_TYPESAFE_DEBUG&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      14881 :   return res;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 : static void typesafeDebug(const char*key,plumed_safeptr_x safe) noexcept {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   std::fprintf(stderr,&quot;+++ PLUMED_TYPESAFE_DEBUG %s %p %zu&quot;,key,safe.ptr,safe.nelem);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :   const size_t* shape=safe.shape;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   if(shape) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :     std::fprintf(stderr,&quot; (&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :     while(*shape!=0) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot; %zu&quot;,*shape);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :       shape++;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :     }</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :     std::fprintf(stderr,&quot; )&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   std::fprintf(stderr,&quot; %zx %p\n&quot;,safe.flags,safe.opt);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : // create should never throw</a>
+<a name="68"><span class="lineNum">      68 </span>            : // in case of a problem, it logs the error and return a null pointer</a>
+<a name="69"><span class="lineNum">      69 </span>            : // when loaded by an interface &gt;=2.5, this will result in a non valid plumed object.</a>
+<a name="70"><span class="lineNum">      70 </span>            : // earlier interfaces will just give a segfault or a failed assertion.</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     804353 : extern &quot;C&quot; void*plumed_plumedmain_create() {</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   try {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">     804353 :     return new PLMD::PlumedMain;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :   } catch(const std::exception &amp; e) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;+++ an error happened while creating a plumed object\n&quot;;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;e.what()&lt;&lt;std::endl;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     return nullptr;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   } catch(...) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;+++ an unknown error happened while creating a plumed object&quot;&lt;&lt;std::endl;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     return nullptr;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    8000075 : extern &quot;C&quot; unsigned plumed_plumedmain_create_reference(void*plumed) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    8000075 :   plumed_massert(plumed,&quot;trying to create a reference to a plumed object which is not initialized&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   auto p=static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    8000075 :   return p-&gt;increaseReferenceCounter();</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">    8804428 : extern &quot;C&quot; unsigned plumed_plumedmain_delete_reference(void*plumed) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    8804428 :   plumed_massert(plumed,&quot;trying to delete a reference to a plumed object which is not initialized&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   auto p=static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    8804428 :   return p-&gt;decreaseReferenceCounter();</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         42 : extern &quot;C&quot; unsigned plumed_plumedmain_use_count(void*plumed) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         42 :   plumed_massert(plumed,&quot;trying to delete a reference to a plumed object which is not initialized&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   auto p=static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         42 :   return p-&gt;useCountReferenceCounter();</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        357 : extern &quot;C&quot; void plumed_plumedmain_cmd(void*plumed,const char*key,const void*val) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        357 :   plumed_massert(plumed,&quot;trying to use a plumed object which is not initialized&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   auto p=static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        714 :   p-&gt;cmd(key,PLMD::TypesafePtr::unchecked(val));</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        357 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : extern &quot;C&quot; {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         95 :   static void plumed_plumedmain_cmd_safe(void*plumed,const char*key,plumed_safeptr_x safe) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         95 :     plumed_massert(plumed,&quot;trying to use a plumed object which is not initialized&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     auto p=static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         95 :     if(getenvTypesafeDebug()) typesafeDebug(key,safe);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        190 :     p-&gt;cmd(key,PLMD::TypesafePtr::fromSafePtr(&amp;safe));</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         95 :   }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Internal tool</a>
+<a name="118"><span class="lineNum">     118 </span>            : /// Throws the currently managed exception and call the nothrow handler.</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// If nested is not null, it is passed and then gets populated with a pointer that should</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// be called on the nested exception</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// If msg is not null, it overrides the message. Can be used to build a concatenated message.</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        111 : static void translate_current(plumed_nothrow_handler_x nothrow,void**nested=nullptr,const char*msg=nullptr) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        111 :   const void* opt[5]= {&quot;n&quot;,nested,nullptr,nullptr,nullptr};</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   try {</a>
+<a name="125"><span class="lineNum">     125 </span>            :     // this function needs to be called while catching an exception</a>
+<a name="126"><span class="lineNum">     126 </span>            :     // cppcheck-suppress rethrowNoCurrentException</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        111 :     throw;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        111 :   } catch(const PLMD::ExceptionTypeError &amp; e) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          8 :     if(!msg) msg=e.what();</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :     nothrow.handler(nothrow.ptr,20300,msg,opt);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         63 :   } catch(const PLMD::ExceptionError &amp; e) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         55 :     if(!msg) msg=e.what();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         55 :     nothrow.handler(nothrow.ptr,20200,msg,opt);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         56 :   } catch(const PLMD::ExceptionDebug &amp; e) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,20100,msg,opt);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         22 :   } catch(const PLMD::Exception &amp; e) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         21 :     if(!msg) msg=e.what();</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         21 :     nothrow.handler(nothrow.ptr,20000,msg,opt);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         22 :   } catch(const PLMD::lepton::Exception &amp; e) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,19900,msg,opt);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     // 11000 to 12000 are &quot;bad exceptions&quot;. message will be copied without new allocations</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   } catch(const std::bad_exception &amp; e) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11500,msg,opt);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :   } catch(const std::bad_array_new_length &amp; e) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11410,msg,opt);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : #endif</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   } catch(const std::bad_alloc &amp; e) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 :     if(!msg) msg=e.what();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          3 :     nothrow.handler(nothrow.ptr,11400,msg,opt);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :   } catch(const std::bad_function_call &amp; e) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11300,msg,opt);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :   } catch(const std::bad_weak_ptr &amp; e) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11200,msg,opt);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : #endif</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   } catch(const std::bad_cast &amp; e) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11100,msg,opt);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :   } catch(const std::bad_typeid &amp; e) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11000,msg,opt);</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     // not implemented yet: std::regex_error</a>
+<a name="170"><span class="lineNum">     170 </span>            :     // we do not allow regex yet due to portability problems with gcc 4.8</a>
+<a name="171"><span class="lineNum">     171 </span>            :     // as soon as we transition to using &lt;regex&gt; it should be straightforward to add</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 :   } catch(const std::ios_base::failure &amp; e) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 :     int value=e.code().value();</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 :     opt[2]=&quot;c&quot;; // &quot;c&quot; passes the error code.</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          1 :     opt[3]=&amp;value;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :     if(e.code().category()==std::generic_category()) nothrow.handler(nothrow.ptr,10230,msg,opt);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          1 :     else if(e.code().category()==std::system_category()) nothrow.handler(nothrow.ptr,10231,msg,opt);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :     else if(e.code().category()==std::iostream_category()) nothrow.handler(nothrow.ptr,10232,msg,opt);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     else if(e.code().category()==std::future_category()) nothrow.handler(nothrow.ptr,10233,msg,opt);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     else</a>
+<a name="183"><span class="lineNum">     183 </span>            : #endif</a>
+<a name="184"><span class="lineNum">     184 </span>            :       // 10239 represents std::ios_base::failure with default constructur</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :       nothrow.handler(nothrow.ptr,10239,msg,opt);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : #ifdef __PLUMED_LIBCXX11</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          5 :   } catch(const std::system_error &amp; e) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          4 :     if(!msg) msg=e.what();</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          4 :     int value=e.code().value();</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          4 :     opt[2]=&quot;c&quot;; // &quot;c&quot; passes the error code.</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          4 :     opt[3]=&amp;value;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          4 :     if(e.code().category()==std::generic_category()) nothrow.handler(nothrow.ptr,10220,msg,opt);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          3 :     else if(e.code().category()==std::system_category()) nothrow.handler(nothrow.ptr,10221,msg,opt);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          2 :     else if(e.code().category()==std::iostream_category()) nothrow.handler(nothrow.ptr,10222,msg,opt);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          1 :     else if(e.code().category()==std::future_category()) nothrow.handler(nothrow.ptr,10223,msg,opt);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :     // fallback to generic runtime_error</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     else nothrow.handler(nothrow.ptr,10200,msg,opt);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : #endif</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          5 :   } catch(const std::underflow_error &amp;e) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10215,msg,opt);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :   } catch(const std::overflow_error &amp;e) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10210,msg,opt);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          2 :   } catch(const std::range_error &amp;e) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10205,msg,opt);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :   } catch(const std::runtime_error &amp; e) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10200,msg,opt);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     // not implemented yet: std::future_error</a>
+<a name="212"><span class="lineNum">     212 </span>            :     // not clear how useful it would be.</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          2 :   } catch(const std::out_of_range &amp; e) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10120,msg,opt);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          2 :   } catch(const std::length_error &amp; e) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10115,msg,opt);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          2 :   } catch(const std::domain_error &amp; e) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10110,msg,opt);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 :   } catch(const std::invalid_argument &amp; e) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10105,msg,opt);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          2 :   } catch(const std::logic_error &amp; e) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          1 :     if(!msg) msg=e.what();</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10100,msg,opt);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     // generic exception. message will be copied without new allocations</a>
+<a name="229"><span class="lineNum">     229 </span>            :     // reports all non caught exceptions that are derived from std::exception</a>
+<a name="230"><span class="lineNum">     230 </span>            :     // for instance, boost exceptions would end up here</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          1 :   } catch(const std::exception &amp; e) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     if(!msg) msg=e.what();</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :     nothrow.handler(nothrow.ptr,10000,msg,opt);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          1 :   } catch(const char* m) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          1 :     if(!msg) msg=m;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,10000,msg,opt);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          1 :   } catch(const std::string &amp; s) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :     if(!msg) msg=s.c_str();</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :     nothrow.handler(nothrow.ptr,10000,msg,opt);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          1 :   } catch (...) {</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :     // if exception cannot be translated, we add a bad_exception to the stack</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          1 :     nothrow.handler(nothrow.ptr,11500,&quot;plumed could not translate exception&quot;,opt);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          1 :   }</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        111 : }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         45 : static void translate_nested(plumed_nothrow_handler_x nothrow) {</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   try {</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         45 :     throw;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         45 :   } catch (const std::nested_exception &amp; e) {</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : // If this exception has a nested one:</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         12 :     auto nothrow_nested=nothrow;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         12 :     nothrow_nested.ptr=nullptr;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : // translate the current exception asking the wrapper to allocate a new exception</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         12 :     translate_current(nothrow,&amp;nothrow_nested.ptr);</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : // if the wrapper cannot allocate the exception, this will be a nullptr</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         12 :     if(nothrow_nested.ptr) {</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :       try {</a>
+<a name="258"><span class="lineNum">     258 </span>            : // transfer control to the nested exception</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         12 :         e.rethrow_nested();</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         12 :       } catch (...) {</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : // recursively translate it</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         12 :         translate_nested(nothrow_nested);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         12 :       }</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :     }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         45 :   } catch (...) {</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : // otherwise, just translate the current exception</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         33 :     translate_current(nothrow);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         33 :   }</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         45 : }</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : extern &quot;C&quot; {</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">      14786 :   static void plumed_plumedmain_cmd_safe_nothrow(void*plumed,const char*key,plumed_safeptr_x safe,plumed_nothrow_handler_x nothrow) {</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : // This is a workaround for a suboptimal choice in PLUMED &lt;2.8</a>
+<a name="274"><span class="lineNum">     274 </span>            : // In particular, the only way to bypass the exception handling process was to call the plumed_plumedmain_cmd_safe</a>
+<a name="275"><span class="lineNum">     275 </span>            : // function directly.</a>
+<a name="276"><span class="lineNum">     276 </span>            : // With this modification, it is possible to just call the plumed_plumedmain_cmd_safe_nothrow function</a>
+<a name="277"><span class="lineNum">     277 </span>            : // passing a null error handler.</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      14786 :     if(!nothrow.handler) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :       plumed_plumedmain_cmd_safe(plumed,key,safe);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     }</a>
+<a name="282"><span class="lineNum">     282 </span>            :     auto p=static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</a>
+<a name="283"><span class="lineNum">     283 </span>            : // At library boundaries we translate exceptions to error codes.</a>
+<a name="284"><span class="lineNum">     284 </span>            : // This allows an exception to be catched also if the MD code</a>
+<a name="285"><span class="lineNum">     285 </span>            : // was linked against a different C++ library</a>
+<a name="286"><span class="lineNum">     286 </span>            :     try {</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">      14786 :       plumed_massert(plumed,&quot;trying to use a plumed object which is not initialized&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      14786 :       if(getenvTypesafeDebug()) typesafeDebug(key,safe);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">      29572 :       p-&gt;cmd(key,PLMD::TypesafePtr::fromSafePtr(&amp;safe));</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         99 :     } catch(...) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         99 :       if(p-&gt;getNestedExceptions()) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         33 :         translate_nested(nothrow);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :       } else {</a>
+<a name="294"><span class="lineNum">     294 </span>            : // In this case, we just consider the latest thrown exception and</a>
+<a name="295"><span class="lineNum">     295 </span>            : // supplement it with a concatenated message so as not to</a>
+<a name="296"><span class="lineNum">     296 </span>            : // loose information.</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         66 :         auto msg=PLMD::Tools::concatenateExceptionMessages();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         66 :         translate_current(nothrow,nullptr,msg.c_str());</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :       }</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         99 :     }</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span>            : }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : extern &quot;C&quot; {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   static void plumed_plumedmain_cmd_nothrow(void*plumed,const char*key,const void*val,plumed_nothrow_handler_x nothrow) {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     plumed_safeptr_x safe;</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :     plumed_assert(nothrow.handler) &lt;&lt; &quot;Accepting a null pointer here would make the calling code non compatible with plumed 2.5 to 2.7&quot;;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :     safe.ptr=val;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :     safe.nelem=0;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :     safe.shape=NULL;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :     safe.flags=0;</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :     safe.opt=NULL;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     plumed_plumedmain_cmd_safe_nothrow(plumed,key,safe,nothrow);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     804353 : extern &quot;C&quot; void plumed_plumedmain_finalize(void*plumed) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">     804353 :   plumed_massert(plumed,&quot;trying to deallocate a plumed object which is not initialized&quot;);</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : // I think it is not possible to replace this delete with a smart pointer</a>
+<a name="320"><span class="lineNum">     320 </span>            : // since the ownership of this pointer is in a C structure. GB</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">     804353 :   delete static_cast&lt;PLMD::PlumedMain*&gt;(plumed);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">     804353 : }</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : // values here should be consistent with those in plumed_symbol_table_init !!!!</a>
+<a name="325"><span class="lineNum">     325 </span>            : plumed_symbol_table_type_x plumed_symbol_table= {</a>
+<a name="326"><span class="lineNum">     326 </span>            :   4,</a>
+<a name="327"><span class="lineNum">     327 </span>            :   {plumed_plumedmain_create,plumed_plumedmain_cmd,plumed_plumedmain_finalize},</a>
+<a name="328"><span class="lineNum">     328 </span>            :   plumed_plumedmain_cmd_nothrow,</a>
+<a name="329"><span class="lineNum">     329 </span>            :   plumed_plumedmain_cmd_safe,</a>
+<a name="330"><span class="lineNum">     330 </span>            :   plumed_plumedmain_cmd_safe_nothrow,</a>
+<a name="331"><span class="lineNum">     331 </span>            :   plumed_plumedmain_create_reference,</a>
+<a name="332"><span class="lineNum">     332 </span>            :   plumed_plumedmain_delete_reference,</a>
+<a name="333"><span class="lineNum">     333 </span>            :   plumed_plumedmain_use_count</a>
+<a name="334"><span class="lineNum">     334 </span>            : };</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            : // values here should be consistent with those above !!!!</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">     808492 : extern &quot;C&quot; void plumed_symbol_table_init() {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">     808492 :   plumed_symbol_table.version=4;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">     808492 :   plumed_symbol_table.functions.create=plumed_plumedmain_create;</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">     808492 :   plumed_symbol_table.functions.cmd=plumed_plumedmain_cmd;</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">     808492 :   plumed_symbol_table.functions.finalize=plumed_plumedmain_finalize;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">     808492 :   plumed_symbol_table.cmd_nothrow=plumed_plumedmain_cmd_nothrow;</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">     808492 :   plumed_symbol_table.cmd_safe=plumed_plumedmain_cmd_safe;</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">     808492 :   plumed_symbol_table.cmd_safe_nothrow=plumed_plumedmain_cmd_safe_nothrow;</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">     808492 :   plumed_symbol_table.create_reference=plumed_plumedmain_create_reference;</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">     808492 :   plumed_symbol_table.delete_reference=plumed_plumedmain_delete_reference;</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">     808492 :   plumed_symbol_table.use_count=plumed_plumedmain_use_count;</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">     808492 : }</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : namespace PLMD {</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            : #define plumed_convert_fptr(ptr,fptr) { ptr=NULL; std::memcpy(&amp;ptr,&amp;fptr,(sizeof(fptr)&gt;sizeof(ptr)?sizeof(ptr):sizeof(fptr))); }</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : /// Static object which registers Plumed.</a>
+<a name="355"><span class="lineNum">     355 </span>            : /// This is a static object which, during its construction at startup,</a>
+<a name="356"><span class="lineNum">     356 </span>            : /// registers the pointers to plumed_plumedmain_create, plumed_plumedmain_cmd and plumed_plumedmain_finalize</a>
+<a name="357"><span class="lineNum">     357 </span>            : /// to the plumed_kernel_register function.</a>
+<a name="358"><span class="lineNum">     358 </span>            : /// Registration is only required with plumed loader &lt;=2.4, but we do it anyway in order to maintain</a>
+<a name="359"><span class="lineNum">     359 </span>            : /// backward compatibility. Notice that as of plumed 2.5 the plumed_kernel_register is found</a>
+<a name="360"><span class="lineNum">     360 </span>            : /// using dlsym, in order to allow the libplumedKernel library to be loadable also when</a>
+<a name="361"><span class="lineNum">     361 </span>            : /// the plumed_kernel_register symbol is not available.</a>
+<a name="362"><span class="lineNum">     362 </span>            : namespace {</a>
+<a name="363"><span class="lineNum">     363 </span>            : class PlumedMainInitializer {</a>
+<a name="364"><span class="lineNum">     364 </span>            :   const bool debug;</a>
+<a name="365"><span class="lineNum">     365 </span>            : public:</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       4168 :   PlumedMainInitializer():</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">       4168 :     debug(std::getenv(&quot;PLUMED_LOAD_DEBUG&quot;))</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   {</a>
+<a name="369"><span class="lineNum">     369 </span>            : // make sure static plumed_function_pointers is initialized here</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       4168 :     plumed_symbol_table_init();</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">       4168 :     if(debug) std::fprintf(stderr,&quot;+++ Initializing PLUMED with plumed_symbol_table version %i at %p\n&quot;,plumed_symbol_table.version,(void*)&amp;plumed_symbol_table);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : #if defined(__PLUMED_HAS_DLOPEN)</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">       4168 :     if(std::getenv(&quot;PLUMED_LOAD_SKIP_REGISTRATION&quot;)) {</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :       if(debug) std::fprintf(stderr,&quot;+++ Skipping registration +++\n&quot;);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :       return;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     }</a>
+<a name="377"><span class="lineNum">     377 </span>            :     typedef plumed_plumedmain_function_holder_x* (*plumed_kernel_register_type_x)(const plumed_plumedmain_function_holder_x*);</a>
+<a name="378"><span class="lineNum">     378 </span>            :     plumed_kernel_register_type_x plumed_kernel_register=nullptr;</a>
+<a name="379"><span class="lineNum">     379 </span>            :     void* handle=nullptr;</a>
+<a name="380"><span class="lineNum">     380 </span>            : #if defined(__PLUMED_HAS_RTLD_DEFAULT)</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       4168 :     if(debug) std::fprintf(stderr,&quot;+++ Registering functions. Looking in RTLD_DEFAULT +++\n&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       4168 :     void* dls=dlsym(RTLD_DEFAULT,&quot;plumed_kernel_register&quot;);</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : #else</a>
+<a name="384"><span class="lineNum">     384 </span>            :     handle=dlopen(NULL,RTLD_LOCAL);</a>
+<a name="385"><span class="lineNum">     385 </span>            :     if(debug) std::fprintf(stderr,&quot;+++ Registering functions. dlopen handle at %p +++\n&quot;,handle);</a>
+<a name="386"><span class="lineNum">     386 </span>            :     void* dls=dlsym(handle,&quot;plumed_kernel_register&quot;);</a>
+<a name="387"><span class="lineNum">     387 </span>            : #endif</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       4168 :     *(void **)(&amp;plumed_kernel_register)=dls;</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">       4168 :     if(debug) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :       if(plumed_kernel_register) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :         std::fprintf(stderr,&quot;+++ plumed_kernel_register found at %p +++\n&quot;,dls);</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :       }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :       else std::fprintf(stderr,&quot;+++ plumed_kernel_register not found +++\n&quot;);</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :     }</a>
+<a name="395"><span class="lineNum">     395 </span>            :     void*createp;</a>
+<a name="396"><span class="lineNum">     396 </span>            :     void*cmdp;</a>
+<a name="397"><span class="lineNum">     397 </span>            :     void*finalizep;</a>
+<a name="398"><span class="lineNum">     398 </span>            :     plumed_convert_fptr(createp,plumed_symbol_table.functions.create);</a>
+<a name="399"><span class="lineNum">     399 </span>            :     plumed_convert_fptr(cmdp,plumed_symbol_table.functions.cmd);</a>
+<a name="400"><span class="lineNum">     400 </span>            :     plumed_convert_fptr(finalizep,plumed_symbol_table.functions.finalize);</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       4168 :     if(plumed_kernel_register &amp;&amp; debug) std::fprintf(stderr,&quot;+++ Registering functions at %p (%p,%p,%p) +++\n&quot;,</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :           (void*)&amp;plumed_symbol_table.functions,createp,cmdp,finalizep);</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       4168 :     if(plumed_kernel_register) (*plumed_kernel_register)(&amp;plumed_symbol_table.functions);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : // Notice that handle could be null in the following cases:</a>
+<a name="405"><span class="lineNum">     405 </span>            : // - if we use RTLD_DEFAULT</a>
+<a name="406"><span class="lineNum">     406 </span>            : // - on Linux if we don't use RTLD_DEFAULT, since dlopen(NULL,RTLD_LOCAL) returns a null pointer.</a>
+<a name="407"><span class="lineNum">     407 </span>            :     if(handle) dlclose(handle);</a>
+<a name="408"><span class="lineNum">     408 </span>            : #endif</a>
+<a name="409"><span class="lineNum">     409 </span>            :   }</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">       4168 :   ~PlumedMainInitializer() {</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       4168 :     if(debug) std::fprintf(stderr,&quot;+++ Finalizing PLUMED with plumed_symbol_table at %p\n&quot;,(void*)&amp;plumed_symbol_table);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">       4168 :   }</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : } PlumedMainInitializerRegisterMe;</a>
+<a name="414"><span class="lineNum">     414 </span>            : }</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            : }</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/TargetDist.cpp.func-sort-c.html b/coverage/core/TargetDist.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3822053753
--- /dev/null
+++ b/coverage/core/TargetDist.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/TargetDist.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - TargetDist.cpp<span style="font-size: 80%;"> (<a href="TargetDist.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TargetDist.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDist.cpp.gcov.html#28">_ZN4PLMD10TargetDist4readERKNS_3PDBESt6vectorIPNS_5ValueESaIS6_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDist.cpp.gcov.html#48">_ZN4PLMD10TargetDist4readERKSt6vectorIdSaIdEES1_IPNS_5ValueESaIS7_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDist.cpp.gcov.html#57">_ZN4PLMD10TargetDist9calculateERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/TargetDist.cpp.func.html b/coverage/core/TargetDist.cpp.func.html
new file mode 100644
index 0000000000..cb35307968
--- /dev/null
+++ b/coverage/core/TargetDist.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/TargetDist.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - TargetDist.cpp<span style="font-size: 80%;"> (<a href="TargetDist.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TargetDist.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDist.cpp.gcov.html#28">_ZN4PLMD10TargetDist4readERKNS_3PDBESt6vectorIPNS_5ValueESaIS6_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDist.cpp.gcov.html#48">_ZN4PLMD10TargetDist4readERKSt6vectorIdSaIdEES1_IPNS_5ValueESaIS7_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDist.cpp.gcov.html#57">_ZN4PLMD10TargetDist9calculateERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/TargetDist.cpp.gcov.html b/coverage/core/TargetDist.cpp.gcov.html
new file mode 100644
index 0000000000..80935bdfab
--- /dev/null
+++ b/coverage/core/TargetDist.cpp.gcov.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/TargetDist.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - TargetDist.cpp<span style="font-size: 80%;"> (source / <a href="TargetDist.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;TargetDist.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Value.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineNoCov">          0 : void TargetDist::read( const PDB&amp; pdb, std::vector&lt;Value*&gt; ar ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span>            :   // Clear values in target actions</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ar.size(); ++i) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :     (ar[i]-&gt;getPntrToAction())-&gt;clearInputForces();</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 :     (ar[i]-&gt;getPntrToAction())-&gt;clearDerivatives();</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   }</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            :   // Calculate target actions from input in PDB file</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; targ( ar.size() );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ar.size(); ++i) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :     if( ar[i]-&gt;valueHasBeenSet() ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :       targ[i]=ar[i]-&gt;get();</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :     } else {</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :       (ar[i]-&gt;getPntrToAction())-&gt;calculateFromPDB( pdb );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :       targ[i]=ar[i]-&gt;get();</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :     }</a>
+<a name="46"><span class="lineNum">      46 </span>            :   }</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   read( targ, ar );</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 : void TargetDist::read( const std::vector&lt;double&gt;&amp; targ, std::vector&lt;Value*&gt; ar ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   plumed_assert( targ.size()==ar.size() );</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   target.resize( ar.size() ); args.resize( ar.size() );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   log.printf(&quot;  distance from this point in cv space : &quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;target.size(); ++i) { log.printf(&quot;%f &quot;, targ[i]); target[i]=targ[i]; args[i]=ar[i]; }</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 : double TargetDist::calculate( std::vector&lt;double&gt;&amp; derivs ) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :   plumed_assert( derivs.size()==args.size() );</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   double dist=0;</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;args.size(); ++i) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :     double tmp=args[i]-&gt;difference( target[i], args[i]-&gt;get() );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :     derivs[i]=tmp; dist+=tmp*tmp;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   dist=std::sqrt(dist);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;args.size(); ++i) derivs[i]/=dist;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   return dist;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Value.cpp.func-sort-c.html b/coverage/core/Value.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5b51bbde80
--- /dev/null
+++ b/coverage/core/Value.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Value.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Value.cpp<span style="font-size: 80%;"> (<a href="Value.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntryMed">86.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Value.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#192">_ZN4PLMD3addERKNS_5ValueEPS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#184">_ZN4PLMD4copyERKNS_5ValueEPS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#176">_ZN4PLMD4copyERKNS_5ValueERS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#46">_ZN4PLMD5ValueC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#120">_ZNK4PLMD5Value9getDomainERdS1_</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#126">_ZN4PLMD5Value12setGradientsEv</a></td>
+              <td class="coverFnHi">183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#157">_ZN4PLMD5Value10projectionERKS0_S2_</a></td>
+              <td class="coverFnHi">261</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#171">_ZN4PLMD5Value15getPntrToActionEv</a></td>
+              <td class="coverFnHi">4773</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#114">_ZNK4PLMD5Value9getDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_</a></td>
+              <td class="coverFnHi">27988</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#62">_ZN4PLMD5ValueC2EPNS_15ActionWithValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnHi">48514</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#94">_ZNK4PLMD5Value10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">965124</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#106">_ZN4PLMD5Value9setDomainERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">1151484</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#78">_ZN4PLMD5Value16setupPeriodicityEv</a></td>
+              <td class="coverFnHi">1183494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#89">_ZNK4PLMD5Value10isPeriodicEv</a></td>
+              <td class="coverFnHi">1665158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#102">_ZN4PLMD5Value14setNotPeriodicEv</a></td>
+              <td class="coverFnHi">3528238</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#31">_ZN4PLMD5ValueC2Ev</a></td>
+              <td class="coverFnHi">3561022</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Value.cpp.func.html b/coverage/core/Value.cpp.func.html
new file mode 100644
index 0000000000..44fcd84e0c
--- /dev/null
+++ b/coverage/core/Value.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Value.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Value.cpp<span style="font-size: 80%;"> (<a href="Value.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntryMed">86.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Value.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#192">_ZN4PLMD3addERKNS_5ValueEPS0_</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#184">_ZN4PLMD4copyERKNS_5ValueEPS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#176">_ZN4PLMD4copyERKNS_5ValueERS0_</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#157">_ZN4PLMD5Value10projectionERKS0_S2_</a></td>
+              <td class="coverFnHi">261</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#126">_ZN4PLMD5Value12setGradientsEv</a></td>
+              <td class="coverFnHi">183</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#102">_ZN4PLMD5Value14setNotPeriodicEv</a></td>
+              <td class="coverFnHi">3528238</td>
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+              <td class="coverFnHi">4773</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#78">_ZN4PLMD5Value16setupPeriodicityEv</a></td>
+              <td class="coverFnHi">1183494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#106">_ZN4PLMD5Value9setDomainERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">1151484</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#62">_ZN4PLMD5ValueC2EPNS_15ActionWithValueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnHi">48514</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#46">_ZN4PLMD5ValueC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#31">_ZN4PLMD5ValueC2Ev</a></td>
+              <td class="coverFnHi">3561022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#94">_ZNK4PLMD5Value10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">965124</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#89">_ZNK4PLMD5Value10isPeriodicEv</a></td>
+              <td class="coverFnHi">1665158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#114">_ZNK4PLMD5Value9getDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES7_</a></td>
+              <td class="coverFnHi">27988</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.cpp.gcov.html#120">_ZNK4PLMD5Value9getDomainERdS1_</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Value.cpp.gcov.html b/coverage/core/Value.cpp.gcov.html
new file mode 100644
index 0000000000..d3c92f93a9
--- /dev/null
+++ b/coverage/core/Value.cpp.gcov.html
@@ -0,0 +1,276 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Value.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Value.cpp<span style="font-size: 80%;"> (source / <a href="Value.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntryMed">86.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Value.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionAtomistic.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionWithArguments.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;PlumedMain.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">    3561022 : Value::Value():</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">    3561022 :   action(NULL),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">    3561022 :   value_set(false),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">    3561022 :   value(0.0),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">    3561022 :   inputForce(0.0),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">    3561022 :   hasForce(false),</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">    3561022 :   hasDeriv(true),</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">    3561022 :   periodicity(unset),</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">    3561022 :   min(0.0),</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">    3561022 :   max(0.0),</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">    3561022 :   max_minus_min(0.0),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">    3561022 :   inv_max_minus_min(0.0)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">    3561022 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         18 : Value::Value(const std::string&amp; name):</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         18 :   action(NULL),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         18 :   value_set(false),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         18 :   value(0.0),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         18 :   inputForce(0.0),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         18 :   hasForce(false),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         18 :   name(name),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         18 :   hasDeriv(true),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         18 :   periodicity(unset),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         18 :   min(0.0),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         18 :   max(0.0),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         18 :   max_minus_min(0.0),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         18 :   inv_max_minus_min(0.0)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : {</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         18 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      48514 : Value::Value(ActionWithValue* av, const std::string&amp; name, const bool withderiv):</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      48514 :   action(av),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      48514 :   value_set(false),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      48514 :   value(0.0),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      48514 :   inputForce(0.0),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      48514 :   hasForce(false),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      48514 :   name(name),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      48514 :   hasDeriv(withderiv),</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      48514 :   periodicity(unset),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      48514 :   min(0.0),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      48514 :   max(0.0),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      48514 :   max_minus_min(0.0),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      48514 :   inv_max_minus_min(0.0)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      48514 : }</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">    1183494 : void Value::setupPeriodicity() {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">    1183494 :   if( min==0 &amp;&amp; max==0 ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      32010 :     periodicity=notperiodic;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   } else {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    1151484 :     periodicity=periodic;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    1151484 :     max_minus_min=max-min;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    1151484 :     plumed_massert(max_minus_min&gt;0, &quot;your function has a very strange domain?&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    1151484 :     inv_max_minus_min=1.0/max_minus_min;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   }</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">    1183494 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    1665158 : bool Value::isPeriodic()const {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    1665158 :   plumed_massert(periodicity!=unset,&quot;periodicity should be set&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    1665158 :   return periodicity==periodic;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     965124 : bool Value::applyForce(std::vector&lt;double&gt;&amp; forces ) const {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     965124 :   if( !hasForce ) return false;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   plumed_dbg_massert( derivatives.size()==forces.size(),&quot; forces array has wrong size&quot; );</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     115265 :   const unsigned N=derivatives.size();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">   48883113 :   for(unsigned i=0; i&lt;N; ++i) forces[i]=inputForce*derivatives[i];</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   return true;</a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">    3528238 : void Value::setNotPeriodic() {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">    3528238 :   min=0; max=0; periodicity=notperiodic;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">    3528238 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">    1151484 : void Value::setDomain(const std::string&amp; pmin,const std::string&amp; pmax) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">    1151484 :   str_min=pmin;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">    1151484 :   if( !Tools::convertNoexcept(str_min,min) ) action-&gt;error(&quot;could not convert period string &quot; + str_min + &quot; to real&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">    1151484 :   str_max=pmax;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">    1151484 :   if( !Tools::convertNoexcept(str_max,max) ) action-&gt;error(&quot;could not convert period string &quot; + str_max + &quot; to read&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">    1151484 :   setupPeriodicity();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">    1151484 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      27988 : void Value::getDomain(std::string&amp;minout,std::string&amp;maxout) const {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      27988 :   plumed_massert(periodicity==periodic,&quot;function should be periodic&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      27988 :   minout=str_min;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      27988 :   maxout=str_max;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      27988 : }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         34 : void Value::getDomain(double&amp;minout,double&amp;maxout) const {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         34 :   plumed_massert(periodicity==periodic,&quot;function should be periodic&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         34 :   minout=min;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         34 :   maxout=max;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         34 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        183 : void Value::setGradients() {</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   // Can't do gradients if we don't have derivatives</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        183 :   if( !hasDeriv ) return;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   gradients.clear();</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        183 :   ActionAtomistic*aa=dynamic_cast&lt;ActionAtomistic*&gt;(action);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        183 :   ActionWithArguments*aw=dynamic_cast&lt;ActionWithArguments*&gt;(action);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        183 :   if(aa) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        100 :     const Atoms&amp;atoms((aa-&gt;plumed).getAtoms());</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       8092 :     for(unsigned j=0; j&lt;aa-&gt;getNumberOfAtoms(); ++j) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       7992 :       AtomNumber an=aa-&gt;getAbsoluteIndex(j);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       7992 :       if(atoms.isVirtualAtom(an)) {</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :         const ActionWithVirtualAtom* a=atoms.getVirtualAtomsAction(an);</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         33 :         for(const auto &amp; p : a-&gt;getGradients()) {</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : // controllare l'ordine del matmul:</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         30 :           gradients[p.first]+=matmul(Vector(derivatives[3*j],derivatives[3*j+1],derivatives[3*j+2]),p.second);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :         }</a>
+<a name="144"><span class="lineNum">     144 </span>            :       } else {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      31956 :         for(unsigned i=0; i&lt;3; i++) gradients[an][i]+=derivatives[3*j+i];</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :       }</a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         83 :   } else if(aw) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         83 :     std::vector&lt;Value*&gt; values=aw-&gt;getArguments();</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        249 :     for(unsigned j=0; j&lt;derivatives.size(); j++) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       8174 :       for(const auto &amp; p : values[j]-&gt;gradients) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       8008 :         AtomNumber iatom=p.first;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       8008 :         gradients[iatom]+=p.second*derivatives[j];</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :       }</a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   } else plumed_error();</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        261 : double Value::projection(const Value&amp; v1,const Value&amp;v2) {</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   double proj=0.0;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   const std::map&lt;AtomNumber,Vector&gt; &amp; grad1(v1.gradients);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   const std::map&lt;AtomNumber,Vector&gt; &amp; grad2(v2.gradients);</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      16167 :   for(const auto &amp; p1 : grad1) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      15906 :     AtomNumber a=p1.first;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     const auto p2=grad2.find(a);</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      15906 :     if(p2!=grad2.end()) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       8224 :       proj+=dotProduct(p1.second,(*p2).second);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        261 :   return proj;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       4773 : ActionWithValue* Value::getPntrToAction() {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       4773 :   plumed_assert( action!=NULL );</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       4773 :   return action;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 : void copy( const Value&amp; val1, Value&amp; val2 ) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   unsigned nder=val1.getNumberOfDerivatives();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   if( nder!=val2.getNumberOfDerivatives() ) { val2.resizeDerivatives( nder ); }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   val2.clearDerivatives();</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;val1.getNumberOfDerivatives(); ++i) val2.addDerivative( i, val1.getDerivative(i) );</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   val2.set( val1.get() );</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 : void copy( const Value&amp; val1, Value* val2 ) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   unsigned nder=val1.getNumberOfDerivatives();</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   if( nder!=val2-&gt;getNumberOfDerivatives() ) { val2-&gt;resizeDerivatives( nder ); }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   val2-&gt;clearDerivatives();</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;val1.getNumberOfDerivatives(); ++i) val2-&gt;addDerivative( i, val1.getDerivative(i) );</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   val2-&gt;set( val1.get() );</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 : void add( const Value&amp; val1, Value* val2 ) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   plumed_assert( val1.getNumberOfDerivatives()==val2-&gt;getNumberOfDerivatives() );</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;val1.getNumberOfDerivatives(); ++i) val2-&gt;addDerivative( i, val1.getDerivative(i) );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   val2-&gt;set( val1.get() + val2-&gt;get() );</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Value.h.func-sort-c.html b/coverage/core/Value.h.func-sort-c.html
new file mode 100644
index 0000000000..100ba6db25
--- /dev/null
+++ b/coverage/core/Value.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Value.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Value.h<span style="font-size: 80%;"> (<a href="Value.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Value.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#255">_ZN4PLMD5Value9chainRuleEd</a></td>
+              <td class="coverFnHi">434</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#296">_ZNK4PLMD5Value14bringBackInPbcEd</a></td>
+              <td class="coverFnHi">3173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#221">_ZNK4PLMD5Value22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">329870</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#156">_ZN4PLMD5Value16applyPeriodicityEv</a></td>
+              <td class="coverFnHi">44362816</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#284">_ZNK4PLMD5Value10differenceEdd</a></td>
+              <td class="coverFnHi">155958906</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Value.h.func.html b/coverage/core/Value.h.func.html
new file mode 100644
index 0000000000..14a8c91475
--- /dev/null
+++ b/coverage/core/Value.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Value.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Value.h<span style="font-size: 80%;"> (<a href="Value.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Value.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#156">_ZN4PLMD5Value16applyPeriodicityEv</a></td>
+              <td class="coverFnHi">44362816</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#255">_ZN4PLMD5Value9chainRuleEd</a></td>
+              <td class="coverFnHi">434</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#284">_ZNK4PLMD5Value10differenceEdd</a></td>
+              <td class="coverFnHi">155958906</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#296">_ZNK4PLMD5Value14bringBackInPbcEd</a></td>
+              <td class="coverFnHi">3173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Value.h.gcov.html#221">_ZNK4PLMD5Value22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">329870</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/Value.h.gcov.html b/coverage/core/Value.h.gcov.html
new file mode 100644
index 0000000000..34e1ac5ba4
--- /dev/null
+++ b/coverage/core/Value.h.gcov.html
@@ -0,0 +1,392 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/Value.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - Value.h<span style="font-size: 80%;"> (source / <a href="Value.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_Value_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_Value_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;map&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class ActionWithValue;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : /// \ingroup TOOLBOX</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// A class for holding the value of a function together with its derivatives.</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Typically, an  object of type PLMD::ActionWithValue will contain one</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// object of type PLUMD::Value that will be named after the label.  If the</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// PLMD::ActionWithValue is part of a class that calculates multiple components</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// then the class will contain multiple that will be called label.component-name</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// This class is used to pass information between different PLMD::Action</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// objects.  However, if you find a use for a tempory PLMD::Value in some method</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// you are implementing please feel free to use it.</a>
+<a name="46"><span class="lineNum">      46 </span>            : class Value {</a>
+<a name="47"><span class="lineNum">      47 </span>            :   friend class ActionWithValue;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// This copies the contents of a value into a second value (just the derivatives and value)</a>
+<a name="49"><span class="lineNum">      49 </span>            :   friend void copy( const Value&amp; val1, Value&amp; val2 );</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// This copies the contents of a value into a second value (but second value is a pointer)</a>
+<a name="51"><span class="lineNum">      51 </span>            :   friend void copy( const Value&amp; val, Value* val2 );</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// This adds some derivatives onto the value</a>
+<a name="53"><span class="lineNum">      53 </span>            :   friend void add( const Value&amp; val1, Value* valout );</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// This calculates val1*val2 and sorts out the derivatives</a>
+<a name="55"><span class="lineNum">      55 </span>            :   friend void product( const Value&amp; val1, const Value&amp; val2, Value&amp; valout );</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// This calculates va1/val2 and sorts out the derivatives</a>
+<a name="57"><span class="lineNum">      57 </span>            :   friend void quotient( const Value&amp; val1, const Value&amp; val2, Value* valout );</a>
+<a name="58"><span class="lineNum">      58 </span>            : private:</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// The action in which this quantity is calculated</a>
+<a name="60"><span class="lineNum">      60 </span>            :   ActionWithValue* action;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Had the value been set</a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool value_set;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// The value of the quantity</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double value;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// The force acting on this quantity</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double inputForce;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// A flag telling us we have a force acting on this quantity</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool hasForce;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// The derivatives of the quantity stored in value</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt;double&gt; derivatives;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::map&lt;AtomNumber,Vector&gt; gradients;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// The name of this quantiy</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::string name;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Does this quanity have derivatives</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool hasDeriv;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Is this quantity periodic</a>
+<a name="77"><span class="lineNum">      77 </span>            :   enum {unset,periodic,notperiodic} periodicity;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Various quantities that describe the domain of this value</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::string str_min, str_max;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double min,max;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double max_minus_min;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   double inv_max_minus_min;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Complete the setup of the periodicity</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void setupPeriodicity();</a>
+<a name="85"><span class="lineNum">      85 </span>            : // bring value within PBCs</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void applyPeriodicity();</a>
+<a name="87"><span class="lineNum">      87 </span>            : public:</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// A constructor that can be used to make Vectors of values</a>
+<a name="89"><span class="lineNum">      89 </span>            :   Value();</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// A constructor that can be used to make Vectors of named values</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit Value(const std::string&amp; name);</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// A constructor that is used throughout the code to setup the value poiters</a>
+<a name="93"><span class="lineNum">      93 </span>            :   Value(ActionWithValue* av, const std::string&amp; name, const bool withderiv);</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Set the value of the function</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void set(double);</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// Add something to the value of the function</a>
+<a name="97"><span class="lineNum">      97 </span>            :   void add(double);</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Get the value of the function</a>
+<a name="99"><span class="lineNum">      99 </span>            :   double get() const;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Find out if the value has been set</a>
+<a name="101"><span class="lineNum">     101 </span>            :   bool valueHasBeenSet() const;</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// Check if the value is periodic</a>
+<a name="103"><span class="lineNum">     103 </span>            :   bool isPeriodic() const;</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// Set the function not periodic</a>
+<a name="105"><span class="lineNum">     105 </span>            :   void setNotPeriodic();</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Set the domain of the function</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void setDomain(const std::string&amp;, const std::string&amp;);</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Get the domain of the quantity</a>
+<a name="109"><span class="lineNum">     109 </span>            :   void getDomain(std::string&amp;,std::string&amp;) const;</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// Get the domain of the quantity</a>
+<a name="111"><span class="lineNum">     111 </span>            :   void getDomain(double&amp;,double&amp;) const;</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// Get the name of the quantity</a>
+<a name="113"><span class="lineNum">     113 </span>            :   const std::string&amp; getName() const;</a>
+<a name="114"><span class="lineNum">     114 </span>            : /// Check whether or not this particular quantity has derivatives</a>
+<a name="115"><span class="lineNum">     115 </span>            :   bool hasDerivatives()const;</a>
+<a name="116"><span class="lineNum">     116 </span>            : /// Get the number of derivatives that this particular value has</a>
+<a name="117"><span class="lineNum">     117 </span>            :   unsigned getNumberOfDerivatives() const;</a>
+<a name="118"><span class="lineNum">     118 </span>            : /// Set the number of derivatives</a>
+<a name="119"><span class="lineNum">     119 </span>            :   void resizeDerivatives(int n);</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// Set all the derivatives to zero</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void clearDerivatives();</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// Add some derivative to the ith component of the derivatives array</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void addDerivative(unsigned i,double d);</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Set the value of the ith component of the derivatives array</a>
+<a name="125"><span class="lineNum">     125 </span>            :   void setDerivative(unsigned i, double d);</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// Apply the chain rule to the derivatives</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void chainRule(double df);</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// Get the derivative with respect to component n</a>
+<a name="129"><span class="lineNum">     129 </span>            :   double getDerivative(const unsigned n) const;</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// Clear the input force on the variable</a>
+<a name="131"><span class="lineNum">     131 </span>            :   void clearInputForce();</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Add some force on this value</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void  addForce(double f);</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Get the value of the force on this colvar</a>
+<a name="135"><span class="lineNum">     135 </span>            :   double getForce() const ;</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Apply the forces to the derivatives using the chain rule (if there are no forces this routine returns false)</a>
+<a name="137"><span class="lineNum">     137 </span>            :   bool applyForce( std::vector&lt;double&gt;&amp; forces ) const ;</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Calculate the difference between the instantaneous value of the function and some other point: other_point-inst_val</a>
+<a name="139"><span class="lineNum">     139 </span>            :   double difference(double)const;</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Calculate the difference between two values of this function: d2 -d1</a>
+<a name="141"><span class="lineNum">     141 </span>            :   double difference(double d1,double d2)const;</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// This returns the pointer to the action where this value is calculated</a>
+<a name="143"><span class="lineNum">     143 </span>            :   ActionWithValue* getPntrToAction();</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// Bring back one value into the correct pbc if needed, else give back the value</a>
+<a name="145"><span class="lineNum">     145 </span>            :   double bringBackInPbc(double d1)const;</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Get the difference between max and minimum of domain</a>
+<a name="147"><span class="lineNum">     147 </span>            :   double getMaxMinusMin()const;</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// This sets up the gradients</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void setGradients();</a>
+<a name="150"><span class="lineNum">     150 </span>            :   static double projection(const Value&amp;,const Value&amp;);</a>
+<a name="151"><span class="lineNum">     151 </span>            : };</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : void copy( const Value&amp; val1, Value&amp; val2 );</a>
+<a name="154"><span class="lineNum">     154 </span>            : void copy( const Value&amp; val1, Value* val2 );</a>
+<a name="155"><span class="lineNum">     155 </span>            : void add( const Value&amp; val1, Value* valout );</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : inline</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">   44362816 : void Value::applyPeriodicity() {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">   44362816 :   if(periodicity==periodic) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   30706194 :     value=min+difference(min,value);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">   30706194 :     if(value&lt;min)value+=max_minus_min;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">   44362816 : }</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : inline</a>
+<a name="166"><span class="lineNum">     166 </span>            : void product( const Value&amp; val1, const Value&amp; val2, Value&amp; valout ) {</a>
+<a name="167"><span class="lineNum">     167 </span>            :   plumed_assert( val1.derivatives.size()==val2.derivatives.size() );</a>
+<a name="168"><span class="lineNum">     168 </span>            :   if( valout.derivatives.size()!=val1.derivatives.size() ) valout.resizeDerivatives( val1.derivatives.size() );</a>
+<a name="169"><span class="lineNum">     169 </span>            :   valout.value_set=false;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   valout.clearDerivatives();</a>
+<a name="171"><span class="lineNum">     171 </span>            :   double u=val1.value;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   double v=val2.value;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   for(unsigned i=0; i&lt;val1.derivatives.size(); ++i) {</a>
+<a name="174"><span class="lineNum">     174 </span>            :     valout.addDerivative(i, u*val2.derivatives[i] + v*val1.derivatives[i] );</a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span>            :   valout.set( u*v );</a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : inline</a>
+<a name="180"><span class="lineNum">     180 </span>            : void quotient( const Value&amp; val1, const Value&amp; val2, Value* valout ) {</a>
+<a name="181"><span class="lineNum">     181 </span>            :   plumed_assert( val1.derivatives.size()==val2.derivatives.size() );</a>
+<a name="182"><span class="lineNum">     182 </span>            :   if( valout-&gt;derivatives.size()!=val1.derivatives.size() ) valout-&gt;resizeDerivatives( val1.derivatives.size() );</a>
+<a name="183"><span class="lineNum">     183 </span>            :   valout-&gt;value_set=false;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   valout-&gt;clearDerivatives();</a>
+<a name="185"><span class="lineNum">     185 </span>            :   double u=val1.get();</a>
+<a name="186"><span class="lineNum">     186 </span>            :   double v=val2.get();</a>
+<a name="187"><span class="lineNum">     187 </span>            :   for(unsigned i=0; i&lt;val1.getNumberOfDerivatives(); ++i) {</a>
+<a name="188"><span class="lineNum">     188 </span>            :     valout-&gt;addDerivative(i, v*val1.getDerivative(i) - u*val2.getDerivative(i) );</a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span>            :   valout-&gt;chainRule( 1/(v*v) ); valout-&gt;set( u / v );</a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : inline</a>
+<a name="194"><span class="lineNum">     194 </span>            : void Value::set(double v) {</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">   44352106 :   value_set=true;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">   44352106 :   value=v;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">   44163343 :   applyPeriodicity();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">   42537229 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : inline</a>
+<a name="201"><span class="lineNum">     201 </span>            : void Value::add(double v) {</a>
+<a name="202"><span class="lineNum">     202 </span>            :   value_set=true;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   value+=v;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   applyPeriodicity();</a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : inline</a>
+<a name="208"><span class="lineNum">     208 </span>            : double Value::get()const {</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    3224958 :   return value;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            : inline</a>
+<a name="213"><span class="lineNum">     213 </span>            : bool Value::valueHasBeenSet() const {</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :   return value_set;</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : inline</a>
+<a name="218"><span class="lineNum">     218 </span>            : const std::string&amp; Value::getName()const {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">    8650845 :   return name;</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : inline</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     329870 : unsigned Value::getNumberOfDerivatives() const {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     329870 :   plumed_massert(hasDeriv,&quot;the derivatives array for this value has zero size&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     329870 :   return derivatives.size();</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : inline</a>
+<a name="229"><span class="lineNum">     229 </span>            : double Value::getDerivative(const unsigned n) const {</a>
+<a name="230"><span class="lineNum">     230 </span>            :   plumed_dbg_massert(n&lt;derivatives.size(),&quot;you are asking for a derivative that is out of bounds&quot;);</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">   20355568 :   return derivatives[n];</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : inline</a>
+<a name="235"><span class="lineNum">     235 </span>            : bool Value::hasDerivatives() const {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      13272 :   return hasDeriv;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : inline</a>
+<a name="240"><span class="lineNum">     240 </span>            : void Value::resizeDerivatives(int n) {</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov"> 4102751000 :   if(hasDeriv) derivatives.resize(n);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : inline</a>
+<a name="245"><span class="lineNum">     245 </span>            : void Value::addDerivative(unsigned i,double d) {</a>
+<a name="246"><span class="lineNum">     246 </span>            :   plumed_dbg_massert(i&lt;derivatives.size(),&quot;derivative is out of bounds&quot;);</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">   22653065 :   derivatives[i]+=d;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         10 : }</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : inline</a>
+<a name="251"><span class="lineNum">     251 </span>            : void Value::setDerivative(unsigned i, double d) {</a>
+<a name="252"><span class="lineNum">     252 </span>            :   plumed_dbg_massert(i&lt;derivatives.size(),&quot;derivative is out of bounds&quot;);</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      63116 :   derivatives[i]=d;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            : inline</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        434 : void Value::chainRule(double df) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">      18368 :   for(unsigned i=0; i&lt;derivatives.size(); ++i) derivatives[i]*=df;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        434 : }</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : inline</a>
+<a name="262"><span class="lineNum">     262 </span>            : void Value::clearInputForce() {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">    2081407 :   hasForce=false;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">    2081407 :   inputForce=0.0;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : inline</a>
+<a name="268"><span class="lineNum">     268 </span>            : void Value::clearDerivatives() {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       2523 :   value_set=false;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   std::fill(derivatives.begin(), derivatives.end(), 0);</a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : inline</a>
+<a name="274"><span class="lineNum">     274 </span>            : void Value::addForce(double f) {</a>
+<a name="275"><span class="lineNum">     275 </span>            :   plumed_dbg_massert(hasDerivatives(),&quot;forces can only be added to values with derivatives&quot;);</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">     188505 :   hasForce=true;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">     188505 :   inputForce+=f;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       2623 : }</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            : inline</a>
+<a name="281"><span class="lineNum">     281 </span>            : double Value::getForce() const {</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       4823 :   return inputForce;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : }</a>
+<a name="284"><span class="lineNum">     284 </span>            : /// d2-d1</a>
+<a name="285"><span class="lineNum">     285 </span>            : inline</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">  155958906 : double Value::difference(double d1,double d2)const {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">  155958906 :   if(periodicity==notperiodic) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">   90590084 :     return d2-d1;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">   65368822 :   } else if(periodicity==periodic) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">   65368822 :     double s=(d2-d1)*inv_max_minus_min;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :     // remember: pbc brings the difference in a range of -0.5:0.5</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">   65368822 :     s=Tools::pbc(s);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">   65368822 :     return s*max_minus_min;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :   } else plumed_merror(&quot;periodicity should be set to compute differences&quot;);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : inline</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       3173 : double Value::bringBackInPbc(double d1)const {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       3173 :   return min+max_minus_min/2.+difference(min+max_minus_min/2., d1);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : }</a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : inline</a>
+<a name="303"><span class="lineNum">     303 </span>            : double Value::difference(double d)const {</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">  119526971 :   return difference(get(),d);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : inline</a>
+<a name="308"><span class="lineNum">     308 </span>            : double Value::getMaxMinusMin()const {</a>
+<a name="309"><span class="lineNum">     309 </span>            :   plumed_dbg_assert( periodicity==periodic );</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        518 :   return max_minus_min;</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : }</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : }</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            : #endif</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/WithCmd.h.func-sort-c.html b/coverage/core/WithCmd.h.func-sort-c.html
new file mode 100644
index 0000000000..95a3faeac3
--- /dev/null
+++ b/coverage/core/WithCmd.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/WithCmd.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - WithCmd.h<span style="font-size: 80%;"> (<a href="WithCmd.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WithCmd.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WithCmd.h.gcov.html#37">_ZN4PLMD7WithCmd3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrEmPKm</a></td>
+              <td class="coverFnHi">276090</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/WithCmd.h.func.html b/coverage/core/WithCmd.h.func.html
new file mode 100644
index 0000000000..7867416bd8
--- /dev/null
+++ b/coverage/core/WithCmd.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/WithCmd.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - WithCmd.h<span style="font-size: 80%;"> (<a href="WithCmd.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WithCmd.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WithCmd.h.gcov.html#37">_ZN4PLMD7WithCmd3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrEmPKm</a></td>
+              <td class="coverFnHi">276090</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/WithCmd.h.gcov.html b/coverage/core/WithCmd.h.gcov.html
new file mode 100644
index 0000000000..376df4ca14
--- /dev/null
+++ b/coverage/core/WithCmd.h.gcov.html
@@ -0,0 +1,129 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core/WithCmd.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">core</a> - WithCmd.h<span style="font-size: 80%;"> (source / <a href="WithCmd.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_core_WithCmd_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_core_WithCmd_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/TypesafePtr.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : /// Base for classes with cmd() method.</a>
+<a name="31"><span class="lineNum">      31 </span>            : /// This is an abstract base class for classes with</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// cmd() method.</a>
+<a name="33"><span class="lineNum">      33 </span>            : class WithCmd {</a>
+<a name="34"><span class="lineNum">      34 </span>            : public:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   virtual void cmd(const std::string&amp; key,const TypesafePtr &amp; val=nullptr)=0;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   void cmd(const std::string&amp; key,const TypesafePtr &amp; val,const std::size_t* shape) {</a>
+<a name="37"><span class="lineNum">      37 </span>            :     cmd(key,TypesafePtr::setNelemAndShape(val,0,shape));</a>
+<a name="38"><span class="lineNum">      38 </span>            :   }</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     276090 :   void cmd(const std::string&amp; key,const TypesafePtr &amp; val,std::size_t nelem, const std::size_t* shape=nullptr) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     276090 :     cmd(key,TypesafePtr::setNelemAndShape(val,nelem,shape));</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     276090 :   }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   virtual ~WithCmd();</a>
+<a name="43"><span class="lineNum">      43 </span>            : };</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : inline</a>
+<a name="46"><span class="lineNum">      46 </span>            : WithCmd::~WithCmd() {</a>
+<a name="47"><span class="lineNum">      47 </span>            : // do nothing</a>
+<a name="48"><span class="lineNum">      48 </span>            : // here just to allow inheriting from this class properly</a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/index-sort-f.html b/coverage/core/index-sort-f.html
new file mode 100644
index 0000000000..e9355fff4d
--- /dev/null
+++ b/coverage/core/index-sort-f.html
@@ -0,0 +1,533 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - core</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3237</td>
+            <td class="headerCovTableEntry">3767</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">431</td>
+            <td class="headerCovTableEntry">535</td>
+            <td class="headerCovTableEntryMed">80.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionShortcut.h.gcov.html">ActionShortcut.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSetup.h.gcov.html">ActionSetup.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAnyorder.h.gcov.html">ActionAnyorder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDist.cpp.gcov.html">TargetDist.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 27</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExchangePatterns.cpp.gcov.html">ExchangePatterns.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=19 height=10 alt="19.2%"><img src="../snow.png" width=81 height=10 alt="19.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">19.2&nbsp;%</td>
+      <td class="coverNumLo">5 / 26</td>
+      <td class="coverPerLo">28.6&nbsp;%</td>
+      <td class="coverNumLo">2 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAnyorder.cpp.gcov.html">ActionAnyorder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MDAtoms.cpp.gcov.html">MDAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">166 / 181</td>
+      <td class="coverPerLo">49.3&nbsp;%</td>
+      <td class="coverNumLo">33 / 67</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataFetchingObject.h.gcov.html">DataFetchingObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSetup.cpp.gcov.html">ActionSetup.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionShortcut.cpp.gcov.html">ActionShortcut.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="77.8%"><img src="../snow.png" width=22 height=10 alt="77.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">21 / 27</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVirtualAtom.cpp.gcov.html">ActionWithVirtualAtom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">46 / 46</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAtomistic.cpp.gcov.html">ActionAtomistic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">171 / 186</td>
+      <td class="coverPerMed">77.3&nbsp;%</td>
+      <td class="coverNumMed">17 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLTool.h.gcov.html">CLTool.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.6%"><img src="../snow.png" width=29 height=10 alt="70.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.6&nbsp;%</td>
+      <td class="coverNumLo">24 / 34</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Value.cpp.gcov.html">Value.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="86.6%"><img src="../snow.png" width=13 height=10 alt="86.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.6&nbsp;%</td>
+      <td class="coverNumMed">103 / 119</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataFetchingObject.cpp.gcov.html">DataFetchingObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=68 height=10 alt="68.1%"><img src="../snow.png" width=32 height=10 alt="68.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">68.1&nbsp;%</td>
+      <td class="coverNumLo">47 / 69</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Colvar.cpp.gcov.html">Colvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">42 / 42</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionPilot.cpp.gcov.html">ActionPilot.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenericMolInfo.cpp.gcov.html">GenericMolInfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.6%"><img src="../snow.png" width=14 height=10 alt="85.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.6&nbsp;%</td>
+      <td class="coverNumMed">190 / 222</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">15 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Action.cpp.gcov.html">Action.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.2%"><img src="../snow.png" width=21 height=10 alt="79.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.2&nbsp;%</td>
+      <td class="coverNumMed">122 / 154</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithValue.cpp.gcov.html">ActionWithValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.6%"><img src="../snow.png" width=10 height=10 alt="89.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.6&nbsp;%</td>
+      <td class="coverNumMed">112 / 125</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithValue.h.gcov.html">ActionWithValue.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.5%"><img src="../snow.png" width=5 height=10 alt="95.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FlexibleBin.cpp.gcov.html">FlexibleBin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 146</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMainInitializer.cpp.gcov.html">PlumedMainInitializer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.0%"><img src="../snow.png" width=19 height=10 alt="81.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">171 / 211</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSet.h.gcov.html">ActionSet.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">22 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLToolRegister.cpp.gcov.html">CLToolRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="67.2%"><img src="../snow.png" width=33 height=10 alt="67.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">67.2&nbsp;%</td>
+      <td class="coverNumLo">39 / 58</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLTool.cpp.gcov.html">CLTool.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.9%"><img src="../snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">85 / 99</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionRegister.cpp.gcov.html">ActionRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.2%"><img src="../snow.png" width=31 height=10 alt="69.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">45 / 65</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithArguments.cpp.gcov.html">ActionWithArguments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.4%"><img src="../snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">148 / 162</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMain.cpp.gcov.html">PlumedMain.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.3%"><img src="../snow.png" width=11 height=10 alt="89.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.3&nbsp;%</td>
+      <td class="coverNumMed">644 / 721</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">39 / 42</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Atoms.cpp.gcov.html">Atoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">404 / 428</td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">57 / 60</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Action.h.gcov.html">Action.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.5%"><img src="../snow.png" width=5 height=10 alt="94.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.5&nbsp;%</td>
+      <td class="coverNumHi">69 / 73</td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVirtualAtom.h.gcov.html">ActionWithVirtualAtom.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionPilot.h.gcov.html">ActionPilot.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMain.h.gcov.html">PlumedMain.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WithCmd.h.gcov.html">WithCmd.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ModuleMap.cpp.gcov.html">ModuleMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Atoms.h.gcov.html">Atoms.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">23 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenericMolInfo.h.gcov.html">GenericMolInfo.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSet.cpp.gcov.html">ActionSet.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAtomistic.h.gcov.html">ActionAtomistic.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithArguments.h.gcov.html">ActionWithArguments.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLToolMain.cpp.gcov.html">CLToolMain.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.7%"><img src="../snow.png" width=19 height=10 alt="80.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.7&nbsp;%</td>
+      <td class="coverNumMed">109 / 135</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Value.h.gcov.html">Value.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.3%"><img src="../snow.png" width=5 height=10 alt="95.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.3&nbsp;%</td>
+      <td class="coverNumHi">41 / 43</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GREX.cpp.gcov.html">GREX.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.6%"><img src="../snow.png" width=26 height=10 alt="73.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.6&nbsp;%</td>
+      <td class="coverNumLo">103 / 140</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Colvar.h.gcov.html">Colvar.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/index-sort-l.html b/coverage/core/index-sort-l.html
new file mode 100644
index 0000000000..ecc0ae82e3
--- /dev/null
+++ b/coverage/core/index-sort-l.html
@@ -0,0 +1,533 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - core</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3237</td>
+            <td class="headerCovTableEntry">3767</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">431</td>
+            <td class="headerCovTableEntry">535</td>
+            <td class="headerCovTableEntryMed">80.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionShortcut.h.gcov.html">ActionShortcut.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDist.cpp.gcov.html">TargetDist.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 27</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExchangePatterns.cpp.gcov.html">ExchangePatterns.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=19 height=10 alt="19.2%"><img src="../snow.png" width=81 height=10 alt="19.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">19.2&nbsp;%</td>
+      <td class="coverNumLo">5 / 26</td>
+      <td class="coverPerLo">28.6&nbsp;%</td>
+      <td class="coverNumLo">2 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSetup.h.gcov.html">ActionSetup.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAnyorder.h.gcov.html">ActionAnyorder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAnyorder.cpp.gcov.html">ActionAnyorder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLToolRegister.cpp.gcov.html">CLToolRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="67.2%"><img src="../snow.png" width=33 height=10 alt="67.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">67.2&nbsp;%</td>
+      <td class="coverNumLo">39 / 58</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataFetchingObject.cpp.gcov.html">DataFetchingObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=68 height=10 alt="68.1%"><img src="../snow.png" width=32 height=10 alt="68.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">68.1&nbsp;%</td>
+      <td class="coverNumLo">47 / 69</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionRegister.cpp.gcov.html">ActionRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.2%"><img src="../snow.png" width=31 height=10 alt="69.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">45 / 65</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLTool.h.gcov.html">CLTool.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.6%"><img src="../snow.png" width=29 height=10 alt="70.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.6&nbsp;%</td>
+      <td class="coverNumLo">24 / 34</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GREX.cpp.gcov.html">GREX.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.6%"><img src="../snow.png" width=26 height=10 alt="73.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.6&nbsp;%</td>
+      <td class="coverNumLo">103 / 140</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionShortcut.cpp.gcov.html">ActionShortcut.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="77.8%"><img src="../snow.png" width=22 height=10 alt="77.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">21 / 27</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FlexibleBin.cpp.gcov.html">FlexibleBin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 146</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Action.cpp.gcov.html">Action.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.2%"><img src="../snow.png" width=21 height=10 alt="79.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.2&nbsp;%</td>
+      <td class="coverNumMed">122 / 154</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLToolMain.cpp.gcov.html">CLToolMain.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.7%"><img src="../snow.png" width=19 height=10 alt="80.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.7&nbsp;%</td>
+      <td class="coverNumMed">109 / 135</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMainInitializer.cpp.gcov.html">PlumedMainInitializer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.0%"><img src="../snow.png" width=19 height=10 alt="81.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">171 / 211</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenericMolInfo.cpp.gcov.html">GenericMolInfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.6%"><img src="../snow.png" width=14 height=10 alt="85.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.6&nbsp;%</td>
+      <td class="coverNumMed">190 / 222</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">15 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLTool.cpp.gcov.html">CLTool.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.9%"><img src="../snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">85 / 99</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Value.cpp.gcov.html">Value.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="86.6%"><img src="../snow.png" width=13 height=10 alt="86.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.6&nbsp;%</td>
+      <td class="coverNumMed">103 / 119</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMain.h.gcov.html">PlumedMain.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMain.cpp.gcov.html">PlumedMain.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.3%"><img src="../snow.png" width=11 height=10 alt="89.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.3&nbsp;%</td>
+      <td class="coverNumMed">644 / 721</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">39 / 42</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithValue.cpp.gcov.html">ActionWithValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.6%"><img src="../snow.png" width=10 height=10 alt="89.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.6&nbsp;%</td>
+      <td class="coverNumMed">112 / 125</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithArguments.cpp.gcov.html">ActionWithArguments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.4%"><img src="../snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">148 / 162</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MDAtoms.cpp.gcov.html">MDAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">166 / 181</td>
+      <td class="coverPerLo">49.3&nbsp;%</td>
+      <td class="coverNumLo">33 / 67</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAtomistic.cpp.gcov.html">ActionAtomistic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">171 / 186</td>
+      <td class="coverPerMed">77.3&nbsp;%</td>
+      <td class="coverNumMed">17 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Atoms.cpp.gcov.html">Atoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">404 / 428</td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">57 / 60</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Action.h.gcov.html">Action.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.5%"><img src="../snow.png" width=5 height=10 alt="94.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.5&nbsp;%</td>
+      <td class="coverNumHi">69 / 73</td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Value.h.gcov.html">Value.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.3%"><img src="../snow.png" width=5 height=10 alt="95.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.3&nbsp;%</td>
+      <td class="coverNumHi">41 / 43</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithValue.h.gcov.html">ActionWithValue.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.5%"><img src="../snow.png" width=5 height=10 alt="95.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Atoms.h.gcov.html">Atoms.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">23 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataFetchingObject.h.gcov.html">DataFetchingObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionPilot.h.gcov.html">ActionPilot.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenericMolInfo.h.gcov.html">GenericMolInfo.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WithCmd.h.gcov.html">WithCmd.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ModuleMap.cpp.gcov.html">ModuleMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVirtualAtom.h.gcov.html">ActionWithVirtualAtom.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSet.cpp.gcov.html">ActionSet.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSetup.cpp.gcov.html">ActionSetup.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithArguments.h.gcov.html">ActionWithArguments.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionPilot.cpp.gcov.html">ActionPilot.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSet.h.gcov.html">ActionSet.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">22 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Colvar.h.gcov.html">Colvar.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAtomistic.h.gcov.html">ActionAtomistic.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Colvar.cpp.gcov.html">Colvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">42 / 42</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVirtualAtom.cpp.gcov.html">ActionWithVirtualAtom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">46 / 46</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/core/index.html b/coverage/core/index.html
new file mode 100644
index 0000000000..7784dbd0ee
--- /dev/null
+++ b/coverage/core/index.html
@@ -0,0 +1,533 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - core</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - core</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3237</td>
+            <td class="headerCovTableEntry">3767</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">431</td>
+            <td class="headerCovTableEntry">535</td>
+            <td class="headerCovTableEntryMed">80.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Action.cpp.gcov.html">Action.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.2%"><img src="../snow.png" width=21 height=10 alt="79.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.2&nbsp;%</td>
+      <td class="coverNumMed">122 / 154</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Action.h.gcov.html">Action.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.5%"><img src="../snow.png" width=5 height=10 alt="94.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.5&nbsp;%</td>
+      <td class="coverNumHi">69 / 73</td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAnyorder.cpp.gcov.html">ActionAnyorder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAnyorder.h.gcov.html">ActionAnyorder.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAtomistic.cpp.gcov.html">ActionAtomistic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">171 / 186</td>
+      <td class="coverPerMed">77.3&nbsp;%</td>
+      <td class="coverNumMed">17 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionAtomistic.h.gcov.html">ActionAtomistic.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionPilot.cpp.gcov.html">ActionPilot.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionPilot.h.gcov.html">ActionPilot.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionRegister.cpp.gcov.html">ActionRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=69 height=10 alt="69.2%"><img src="../snow.png" width=31 height=10 alt="69.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">45 / 65</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSet.cpp.gcov.html">ActionSet.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSet.h.gcov.html">ActionSet.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">22 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSetup.cpp.gcov.html">ActionSetup.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionSetup.h.gcov.html">ActionSetup.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionShortcut.cpp.gcov.html">ActionShortcut.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="77.8%"><img src="../snow.png" width=22 height=10 alt="77.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">21 / 27</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionShortcut.h.gcov.html">ActionShortcut.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithArguments.cpp.gcov.html">ActionWithArguments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.4%"><img src="../snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">148 / 162</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithArguments.h.gcov.html">ActionWithArguments.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithValue.cpp.gcov.html">ActionWithValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.6%"><img src="../snow.png" width=10 height=10 alt="89.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.6&nbsp;%</td>
+      <td class="coverNumMed">112 / 125</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithValue.h.gcov.html">ActionWithValue.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.5%"><img src="../snow.png" width=5 height=10 alt="95.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVirtualAtom.cpp.gcov.html">ActionWithVirtualAtom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">46 / 46</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVirtualAtom.h.gcov.html">ActionWithVirtualAtom.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Atoms.cpp.gcov.html">Atoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">404 / 428</td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">57 / 60</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Atoms.h.gcov.html">Atoms.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">23 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLTool.cpp.gcov.html">CLTool.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.9%"><img src="../snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">85 / 99</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLTool.h.gcov.html">CLTool.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.6%"><img src="../snow.png" width=29 height=10 alt="70.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.6&nbsp;%</td>
+      <td class="coverNumLo">24 / 34</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLToolMain.cpp.gcov.html">CLToolMain.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.7%"><img src="../snow.png" width=19 height=10 alt="80.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.7&nbsp;%</td>
+      <td class="coverNumMed">109 / 135</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CLToolRegister.cpp.gcov.html">CLToolRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="67.2%"><img src="../snow.png" width=33 height=10 alt="67.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">67.2&nbsp;%</td>
+      <td class="coverNumLo">39 / 58</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Colvar.cpp.gcov.html">Colvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">42 / 42</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Colvar.h.gcov.html">Colvar.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataFetchingObject.cpp.gcov.html">DataFetchingObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=68 height=10 alt="68.1%"><img src="../snow.png" width=32 height=10 alt="68.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">68.1&nbsp;%</td>
+      <td class="coverNumLo">47 / 69</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DataFetchingObject.h.gcov.html">DataFetchingObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExchangePatterns.cpp.gcov.html">ExchangePatterns.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=19 height=10 alt="19.2%"><img src="../snow.png" width=81 height=10 alt="19.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">19.2&nbsp;%</td>
+      <td class="coverNumLo">5 / 26</td>
+      <td class="coverPerLo">28.6&nbsp;%</td>
+      <td class="coverNumLo">2 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FlexibleBin.cpp.gcov.html">FlexibleBin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 146</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GREX.cpp.gcov.html">GREX.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.6%"><img src="../snow.png" width=26 height=10 alt="73.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.6&nbsp;%</td>
+      <td class="coverNumLo">103 / 140</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenericMolInfo.cpp.gcov.html">GenericMolInfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.6%"><img src="../snow.png" width=14 height=10 alt="85.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.6&nbsp;%</td>
+      <td class="coverNumMed">190 / 222</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">15 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GenericMolInfo.h.gcov.html">GenericMolInfo.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MDAtoms.cpp.gcov.html">MDAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">166 / 181</td>
+      <td class="coverPerLo">49.3&nbsp;%</td>
+      <td class="coverNumLo">33 / 67</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ModuleMap.cpp.gcov.html">ModuleMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMain.cpp.gcov.html">PlumedMain.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.3%"><img src="../snow.png" width=11 height=10 alt="89.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.3&nbsp;%</td>
+      <td class="coverNumMed">644 / 721</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">39 / 42</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMain.h.gcov.html">PlumedMain.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedMainInitializer.cpp.gcov.html">PlumedMainInitializer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.0%"><img src="../snow.png" width=19 height=10 alt="81.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">171 / 211</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDist.cpp.gcov.html">TargetDist.cpp</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 27</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Value.cpp.gcov.html">Value.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="86.6%"><img src="../snow.png" width=13 height=10 alt="86.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.6&nbsp;%</td>
+      <td class="coverNumMed">103 / 119</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Value.h.gcov.html">Value.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.3%"><img src="../snow.png" width=5 height=10 alt="95.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.3&nbsp;%</td>
+      <td class="coverNumHi">41 / 43</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WithCmd.h.gcov.html">WithCmd.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/BondOrientation.cpp.func-sort-c.html b/coverage/crystallization/BondOrientation.cpp.func-sort-c.html
new file mode 100644
index 0000000000..436f4c40df
--- /dev/null
+++ b/coverage/crystallization/BondOrientation.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/BondOrientation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - BondOrientation.cpp<span style="font-size: 80%;"> (<a href="BondOrientation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">91.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BondOrientation.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization15BondOrientationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#48">_ZN4PLMD15crystallization12_GLOBAL__N_127BondOrientationRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization15BondOrientationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#50">_ZN4PLMD15crystallization15BondOrientation16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#113">_ZNK4PLMD15crystallization15BondOrientation15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#102">_ZNK4PLMD15crystallization15BondOrientation15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#48">_ZN4PLMD15crystallization12_GLOBAL__N_127BondOrientationRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#48">_ZN4PLMD15crystallization12_GLOBAL__N_127BondOrientationRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/BondOrientation.cpp.func.html b/coverage/crystallization/BondOrientation.cpp.func.html
new file mode 100644
index 0000000000..e2610b7eb0
--- /dev/null
+++ b/coverage/crystallization/BondOrientation.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/BondOrientation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - BondOrientation.cpp<span style="font-size: 80%;"> (<a href="BondOrientation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">91.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BondOrientation.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#48">_ZN4PLMD15crystallization12_GLOBAL__N_127BondOrientationRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#48">_ZN4PLMD15crystallization12_GLOBAL__N_127BondOrientationRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#48">_ZN4PLMD15crystallization12_GLOBAL__N_127BondOrientationRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#50">_ZN4PLMD15crystallization15BondOrientation16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization15BondOrientationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization15BondOrientationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#113">_ZNK4PLMD15crystallization15BondOrientation15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BondOrientation.cpp.gcov.html#102">_ZNK4PLMD15crystallization15BondOrientation15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/BondOrientation.cpp.gcov.html b/coverage/crystallization/BondOrientation.cpp.gcov.html
new file mode 100644
index 0000000000..e034dcc3b3
--- /dev/null
+++ b/coverage/crystallization/BondOrientation.cpp.gcov.html
@@ -0,0 +1,211 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/BondOrientation.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - BondOrientation.cpp<span style="font-size: 80%;"> (source / <a href="BondOrientation.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">91.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC MCOLVAR BOND_DIRECTIONS</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Calculate the vectors connecting atoms that are within cutoff defined using a switching function.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : \par Examples</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : */</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+ENDPLUMEDOC</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace crystallization {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class BondOrientation : public VectorMultiColvar {</a>
+<a name="40"><span class="lineNum">      40 </span>            : private:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double rcut2;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit BondOrientation( const ActionOptions&amp; ao );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double calculateWeight( const unsigned&amp; current, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(BondOrientation,&quot;BOND_DIRECTIONS&quot;)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          4 : void BondOrientation::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          4 :   VectorMultiColvar::registerKeywords( keys );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the vectors you wish to calculate. &quot;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one vector will be &quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            :            &quot;specify the indices of two atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          8 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate the distance between each distinct pair of atoms in the group&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all &quot;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :            &quot;the atoms in GROUPB. This must be used in conjunction with GROUPB.&quot;);</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all the atoms &quot;</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :            &quot;in GROUPB. This must be used in conjunction with GROUPA.&quot;);</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;12&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="71"><span class="lineNum">      71 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          8 :   keys.use(&quot;VMEAN&quot;); keys.use(&quot;VSUM&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          4 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          2 : BondOrientation::BondOrientation( const ActionOptions&amp; ao ):</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   Action(ao),</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          2 :   VectorMultiColvar(ao)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span>            :   // Read atoms</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          2 :   weightHasDerivatives=true;</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          2 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 2, all_atoms );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   // Read in the switching function</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          4 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 :   if(sw.length()&gt;0) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :     switchingFunction.set(sw,errors);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   } else {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   log.printf(&quot;  orientation of those bonds with lengths are less than %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Set the link cell cutoff</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :   setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   double rcut = switchingFunction.get_dmax(); rcut2 = rcut*rcut;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   // Set the dimensionality of the vectors</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          2 :   setVectorDimensionality(3);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          2 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        150 : double BondOrientation::calculateWeight( const unsigned&amp; current, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        150 :   Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double distm=distance.modulo2();</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        150 :   if( distm&gt;rcut2 ) return 0.0;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         60 :   double df, ww=switchingFunction.calculateSqr( distm, df );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Derivatives of weights</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         60 :   addAtomDerivatives( 0, 0, -df*weight*distance, myatoms );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         60 :   addAtomDerivatives( 0, 1, df*weight*distance, myatoms );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         60 :   myatoms.addBoxDerivatives( 0, (-df)*weight*Tensor(distance,distance) );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         60 :   return ww;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         60 : void BondOrientation::calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         60 :   Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         60 :   addAtomDerivatives( 2, 0, Vector(-1.0,0,0), myatoms );</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         60 :   addAtomDerivatives( 2, 1, Vector(+1.0,0,0), myatoms );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         60 :   myatoms.addBoxDerivatives( 2, Tensor(distance,Vector(-1.0,0,0)) );</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         60 :   myatoms.addValue( 2, distance[0] );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         60 :   addAtomDerivatives( 3, 0, Vector(0,-1.0,0), myatoms );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         60 :   addAtomDerivatives( 3, 1, Vector(0,+1.0,0), myatoms );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         60 :   myatoms.addBoxDerivatives( 3, Tensor(distance,Vector(0,-1.0,0)) );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         60 :   myatoms.addValue( 3, distance[1] );</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         60 :   addAtomDerivatives( 4, 0, Vector(0,0,-1.0), myatoms );</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         60 :   addAtomDerivatives( 4, 1, Vector(0,0,+1.0), myatoms );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         60 :   myatoms.addBoxDerivatives( 4, Tensor(distance,Vector(0,0,-1.0)) );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         60 :   myatoms.addValue( 4, distance[2] );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         60 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/CubicHarmonicBase.cpp.func-sort-c.html b/coverage/crystallization/CubicHarmonicBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7414ff9b54
--- /dev/null
+++ b/coverage/crystallization/CubicHarmonicBase.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/CubicHarmonicBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - CubicHarmonicBase.cpp<span style="font-size: 80%;"> (<a href="CubicHarmonicBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryHi">93.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CubicHarmonicBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#51">_ZN4PLMD15crystallization17CubicHarmonicBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#51">_ZN4PLMD15crystallization17CubicHarmonicBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#31">_ZN4PLMD15crystallization17CubicHarmonicBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#95">_ZNK4PLMD15crystallization17CubicHarmonicBase7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">26142</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
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diff --git a/coverage/crystallization/CubicHarmonicBase.cpp.func.html b/coverage/crystallization/CubicHarmonicBase.cpp.func.html
new file mode 100644
index 0000000000..a41de3d26e
--- /dev/null
+++ b/coverage/crystallization/CubicHarmonicBase.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - CubicHarmonicBase.cpp<span style="font-size: 80%;"> (<a href="CubicHarmonicBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryHi">93.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CubicHarmonicBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#31">_ZN4PLMD15crystallization17CubicHarmonicBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#51">_ZN4PLMD15crystallization17CubicHarmonicBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#51">_ZN4PLMD15crystallization17CubicHarmonicBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.cpp.gcov.html#95">_ZNK4PLMD15crystallization17CubicHarmonicBase7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">26142</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/crystallization/CubicHarmonicBase.cpp.gcov.html b/coverage/crystallization/CubicHarmonicBase.cpp.gcov.html
new file mode 100644
index 0000000000..5a33e8c72e
--- /dev/null
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@@ -0,0 +1,226 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/CubicHarmonicBase.cpp</title>
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+</head>
+
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - CubicHarmonicBase.cpp<span style="font-size: 80%;"> (source / <a href="CubicHarmonicBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryHi">93.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CubicHarmonicBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : using namespace std;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace crystallization {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         12 : void CubicHarmonicBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         12 :   multicolvar::MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         36 :   keys.use(&quot;SPECIES&quot;); keys.use(&quot;SPECIESA&quot;); keys.use(&quot;SPECIESB&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         24 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;PHI&quot;,&quot;0.0&quot;,&quot;The Euler rotational angle phi&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;THETA&quot;,&quot;0.0&quot;,&quot;The Euler rotational angle theta&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;PSI&quot;,&quot;0.0&quot;,&quot;The Euler rotational angle psi&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         24 :   keys.addFlag(&quot;UNORMALIZED&quot;,false,&quot;calculate the sum of the components of the vector rather than the mean&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         48 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MAX&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         48 :   keys.use(&quot;MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         36 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         12 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          6 : CubicHarmonicBase::CubicHarmonicBase(const ActionOptions&amp;ao):</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   Action(ao),</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          6 :   MultiColvarBase(ao)</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span>            :   // Read in the switching function</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         12 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          6 :   if(sw.length()&gt;0) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          6 :     switchingFunction.set(sw,errors);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          6 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   } else {</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         18 :   double phi, theta, psi; parse(&quot;PHI&quot;,phi); parse(&quot;THETA&quot;,theta); parse(&quot;PSI&quot;,psi);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          6 :   log.printf(&quot;  creating rotation matrix with Euler angles phi=%f, theta=%f and psi=%f\n&quot;,phi,theta,psi);</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   // Calculate the rotation matrix http://mathworld.wolfram.com/EulerAngles.html</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          6 :   rotationmatrix[0][0]=std::cos(psi)*std::cos(phi)-std::cos(theta)*std::sin(phi)*std::sin(psi);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 :   rotationmatrix[0][1]=std::cos(psi)*std::sin(phi)+std::cos(theta)*std::cos(phi)*std::sin(psi);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          6 :   rotationmatrix[0][2]=std::sin(psi)*std::sin(theta);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          6 :   rotationmatrix[1][0]=-std::sin(psi)*std::cos(phi)-std::cos(theta)*std::sin(phi)*std::cos(psi);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          6 :   rotationmatrix[1][1]=-std::sin(psi)*std::sin(phi)+std::cos(theta)*std::cos(phi)*std::cos(psi);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          6 :   rotationmatrix[1][2]=std::cos(psi)*std::sin(theta);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          6 :   rotationmatrix[2][0]=std::sin(theta)*std::sin(phi);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          6 :   rotationmatrix[2][1]=-std::sin(theta)*std::cos(phi);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          6 :   rotationmatrix[2][2]=std::cos(theta);</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 :   log.printf(&quot;  measure crystallinity around central atom.  Includes those atoms within %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          6 :   parseFlag(&quot;UNORMALIZED&quot;,unormalized);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          6 :   if( unormalized ) log.printf(&quot;  output sum of vector functions \n&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          6 :   else log.printf(&quot;  output mean of vector functions \n&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Set the link cell cutoff</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 :   rcut2 = switchingFunction.get_dmax()*switchingFunction.get_dmax();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          6 :   setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   // And setup the ActionWithVessel</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   std::vector&lt;AtomNumber&gt; all_atoms; setupMultiColvarBase( all_atoms );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          6 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      26142 : double CubicHarmonicBase::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      26142 :   double dfunc; Vector rotatedis;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   // Calculate the coordination number</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      26142 :   Vector myder, rotateder, fder; unsigned nat=myatoms.getNumberOfAtoms();</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">    2517483 :   for(unsigned i=1; i&lt;nat; ++i) {</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :     Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :     double d2;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    3953726 :     if ( (d2=distance[0]*distance[0])&lt;rcut2 &amp;&amp;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">    1462385 :          (d2+=distance[1]*distance[1])&lt;rcut2 &amp;&amp;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">    3193615 :          (d2+=distance[2]*distance[2])&lt;rcut2 &amp;&amp;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :          d2&gt;epsilon ) {</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     328678 :       double sw = switchingFunction.calculateSqr( d2, dfunc );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     328678 :       rotatedis[0]=rotationmatrix[0][0]*distance[0]</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     328678 :                    +rotationmatrix[0][1]*distance[1]</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     328678 :                    +rotationmatrix[0][2]*distance[2];</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     328678 :       rotatedis[1]=rotationmatrix[1][0]*distance[0]</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     328678 :                    +rotationmatrix[1][1]*distance[1]</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     328678 :                    +rotationmatrix[1][2]*distance[2];</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     328678 :       rotatedis[2]=rotationmatrix[2][0]*distance[0]</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     328678 :                    +rotationmatrix[2][1]*distance[1]</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     328678 :                    +rotationmatrix[2][2]*distance[2];</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     328678 :       double tmp = calculateCubicHarmonic( rotatedis, d2, rotateder );</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">     328678 :       myder[0]=rotationmatrix[0][0]*rotateder[0]</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     328678 :                +rotationmatrix[1][0]*rotateder[1]</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">     328678 :                +rotationmatrix[2][0]*rotateder[2];</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     328678 :       myder[1]=rotationmatrix[0][1]*rotateder[0]</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     328678 :                +rotationmatrix[1][1]*rotateder[1]</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     328678 :                +rotationmatrix[2][1]*rotateder[2];</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     328678 :       myder[2]=rotationmatrix[0][2]*rotateder[0]</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">     328678 :                +rotationmatrix[1][2]*rotateder[1]</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     328678 :                +rotationmatrix[2][2]*rotateder[2];</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     328678 :       fder = (+dfunc)*tmp*distance + sw*myder;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">     328678 :       accumulateSymmetryFunction( 1, i, sw*tmp, fder, Tensor(distance,-fder), myatoms );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">     328678 :       accumulateSymmetryFunction( -1, i, sw, (+dfunc)*distance, (-dfunc)*Tensor(distance,distance), myatoms );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            :   // values -&gt; der of... value [0], weight[1], x coord [2], y, z... [more magic]</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      26142 :   updateActiveAtoms( myatoms );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      26142 :   if( !unormalized ) myatoms.getUnderlyingMultiValue().quotientRule( 1, 1 );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      26142 :   return myatoms.getValue(1); // this is equivalent to getting an &quot;atomic&quot; CV</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/CubicHarmonicBase.h.func-sort-c.html b/coverage/crystallization/CubicHarmonicBase.h.func-sort-c.html
new file mode 100644
index 0000000000..156a8d3d06
--- /dev/null
+++ b/coverage/crystallization/CubicHarmonicBase.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
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+  <title>LCOV - plumed test coverage - crystallization/CubicHarmonicBase.h - functions</title>
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+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - CubicHarmonicBase.h<span style="font-size: 80%;"> (<a href="CubicHarmonicBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CubicHarmonicBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.h.gcov.html#44">_ZN4PLMD15crystallization17CubicHarmonicBase10isPeriodicEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/CubicHarmonicBase.h.func.html b/coverage/crystallization/CubicHarmonicBase.h.func.html
new file mode 100644
index 0000000000..99fea4572c
--- /dev/null
+++ b/coverage/crystallization/CubicHarmonicBase.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/CubicHarmonicBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - CubicHarmonicBase.h<span style="font-size: 80%;"> (<a href="CubicHarmonicBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CubicHarmonicBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CubicHarmonicBase.h.gcov.html#44">_ZN4PLMD15crystallization17CubicHarmonicBase10isPeriodicEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/CubicHarmonicBase.h.gcov.html b/coverage/crystallization/CubicHarmonicBase.h.gcov.html
new file mode 100644
index 0000000000..e4d0195d3d
--- /dev/null
+++ b/coverage/crystallization/CubicHarmonicBase.h.gcov.html
@@ -0,0 +1,127 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/CubicHarmonicBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - CubicHarmonicBase.h<span style="font-size: 80%;"> (source / <a href="CubicHarmonicBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_crystallization_CubicHarmonicBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_crystallization_CubicHarmonicBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace crystallization {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class CubicHarmonicBase : public multicolvar::MultiColvarBase {</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            : //  double nl_cut;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   double rcut2;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   double rotationmatrix[3][3];</a>
+<a name="37"><span class="lineNum">      37 </span>            :   bool unormalized;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="39"><span class="lineNum">      39 </span>            : public:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="41"><span class="lineNum">      41 </span>            :   explicit CubicHarmonicBase(const ActionOptions&amp;);</a>
+<a name="42"><span class="lineNum">      42 </span>            : // active methods:</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   virtual double calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const = 0;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          7 :   bool isPeriodic() { return false; }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/EnvironmentSimilarity.cpp.func-sort-c.html b/coverage/crystallization/EnvironmentSimilarity.cpp.func-sort-c.html
new file mode 100644
index 0000000000..252e85d4f0
--- /dev/null
+++ b/coverage/crystallization/EnvironmentSimilarity.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/EnvironmentSimilarity.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - EnvironmentSimilarity.cpp<span style="font-size: 80%;"> (<a href="EnvironmentSimilarity.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">226</td>
+            <td class="headerCovTableEntry">240</td>
+            <td class="headerCovTableEntryHi">94.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EnvironmentSimilarity.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#245">_ZN4PLMD15crystallization21EnvironmentSimilarityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#215">_ZN4PLMD15crystallization12_GLOBAL__N_134EnvironmentSimilarityRegisterMe2176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#404">_ZN4PLMD15crystallization21EnvironmentSimilarity26parseReferenceEnvironmentsERSt6vectorIS2_INS_13VectorGenericILj3EEESaIS4_EESaIS6_EERS2_IS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISF_EESaISH_EERd</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#245">_ZN4PLMD15crystallization21EnvironmentSimilarityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#217">_ZN4PLMD15crystallization21EnvironmentSimilarity16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#204">_ZN4PLMD15crystallization21EnvironmentSimilarity10isPeriodicEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#395">_ZN4PLMD15crystallization21EnvironmentSimilarity11maxDistanceESt6vectorINS_13VectorGenericILj3EEESaIS4_EE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#215">_ZN4PLMD15crystallization12_GLOBAL__N_134EnvironmentSimilarityRegisterMe217C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#215">_ZN4PLMD15crystallization12_GLOBAL__N_134EnvironmentSimilarityRegisterMe217D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EnvironmentSimilarity.cpp.gcov.html#277">_ZNK4PLMD15crystallization21EnvironmentSimilarity7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">30144</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/EnvironmentSimilarity.cpp.func.html b/coverage/crystallization/EnvironmentSimilarity.cpp.func.html
new file mode 100644
index 0000000000..43b5237ac7
--- /dev/null
+++ b/coverage/crystallization/EnvironmentSimilarity.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/EnvironmentSimilarity.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - EnvironmentSimilarity.cpp<span style="font-size: 80%;"> (<a href="EnvironmentSimilarity.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">226</td>
+            <td class="headerCovTableEntry">240</td>
+            <td class="headerCovTableEntryHi">94.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EnvironmentSimilarity.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">30144</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/EnvironmentSimilarity.cpp.gcov.html b/coverage/crystallization/EnvironmentSimilarity.cpp.gcov.html
new file mode 100644
index 0000000000..7a09f7a34d
--- /dev/null
+++ b/coverage/crystallization/EnvironmentSimilarity.cpp.gcov.html
@@ -0,0 +1,644 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/EnvironmentSimilarity.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - EnvironmentSimilarity.cpp<span style="font-size: 80%;"> (source / <a href="EnvironmentSimilarity.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">226</td>
+            <td class="headerCovTableEntry">240</td>
+            <td class="headerCovTableEntryHi">94.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /* ----------------------------------------------------------------------</a>
+<a name="24"><span class="lineNum">      24 </span>            :    Contributing author: Pablo Piaggi (Princeton University)</a>
+<a name="25"><span class="lineNum">      25 </span>            : ------------------------------------------------------------------------- */</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;limits&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : using namespace std;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace crystallization {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : //+PLUMEDOC MCOLVAR ENVIRONMENTSIMILARITY</a>
+<a name="41"><span class="lineNum">      41 </span>            : /*</a>
+<a name="42"><span class="lineNum">      42 </span>            : Measure how similar the environment around atoms is to that found in some reference crystal structure.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This CV was introduced in this article \cite Piaggi-JCP-2019.</a>
+<a name="45"><span class="lineNum">      45 </span>            : The starting point for the definition of the CV is the local atomic density around an atom.</a>
+<a name="46"><span class="lineNum">      46 </span>            : We consider an environment \f$\chi\f$ around this atom and we define the density by</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            :  \rho_{\chi}(\mathbf{r})=\sum\limits_{i\in\chi} \exp\left(- \frac{|\mathbf{r}_i-\mathbf{r}|^2} {2\sigma^2} \right),</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f]</a>
+<a name="50"><span class="lineNum">      50 </span>            : where \f$i\f$ runs over the neighbors in the environment \f$\chi\f$, \f$\sigma\f$ is a broadening parameter, and \f$\mathbf{r}_i\f$ are the</a>
+<a name="51"><span class="lineNum">      51 </span>            : coordinates of the neighbors relative to the central atom.</a>
+<a name="52"><span class="lineNum">      52 </span>            : We now define a reference environment or template \f$\chi_0\f$ that contains \f$n\f$ reference positions \f$\{\mathbf{r}^0_1,...,\mathbf{r}^0_n\}\f$</a>
+<a name="53"><span class="lineNum">      53 </span>            : that describe, for instance, the nearest neighbors in a given lattice.</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f$\sigma\f$ is set using the SIGMA keyword and \f$\chi_0\f$ is chosen with the CRYSTAL_STRUCTURE keyword.</a>
+<a name="55"><span class="lineNum">      55 </span>            : If only the SPECIES keyword is given then the atoms defined there will be the central and neighboring atoms.</a>
+<a name="56"><span class="lineNum">      56 </span>            : If instead the SPECIESA and SPECIESB keywords are given then SPECIESA determines the central atoms and SPECIESB the neighbors.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The environments \f$\chi\f$ and \f$\chi_0\f$ are compared using the kernel,</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f[</a>
+<a name="60"><span class="lineNum">      60 </span>            :  k_{\chi_0}(\chi)= \int d\mathbf{r} \rho_{\chi}(\mathbf{r}) \rho_{\chi_0}(\mathbf{r}) .</a>
+<a name="61"><span class="lineNum">      61 </span>            : \f]</a>
+<a name="62"><span class="lineNum">      62 </span>            : Combining the two equations above and performing the integration analytically we obtain,</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f[</a>
+<a name="64"><span class="lineNum">      64 </span>            :  k_{\chi_0}(\chi)= \sum\limits_{i\in\chi} \sum\limits_{j\in\chi_0} \pi^{3/2} \sigma^3  \exp\left(- \frac{|\mathbf{r}_i-\mathbf{r}^0_j|^2} {4\sigma^2} \right).</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f]</a>
+<a name="66"><span class="lineNum">      66 </span>            : The kernel is finally normalized,</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f[</a>
+<a name="68"><span class="lineNum">      68 </span>            :  \tilde{k}_{\chi_0}(\chi)  = \frac{1}{n} \sum\limits_{i\in\chi} \sum\limits_{j\in\chi_0} \exp\left( - \frac{|\mathbf{r}_i-\mathbf{r}^0_j|^2} {4\sigma^2} \right),</a>
+<a name="69"><span class="lineNum">      69 </span>            : \f]</a>
+<a name="70"><span class="lineNum">      70 </span>            : such that \f$\tilde{k}_{\chi_0}(\chi_0) = 1\f$.</a>
+<a name="71"><span class="lineNum">      71 </span>            : The above kernel is computed for each atom in the SPECIES or SPECIESA keywords.</a>
+<a name="72"><span class="lineNum">      72 </span>            : This quantity is a multicolvar so you can compute it for multiple atoms using a single PLUMED action and then compute</a>
+<a name="73"><span class="lineNum">      73 </span>            : the average value for the atoms in your system, the number of atoms that have an \f$\tilde{k}_{\chi_0}\f$ value that is more that some target and</a>
+<a name="74"><span class="lineNum">      74 </span>            : so on.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : The kernel can be generalized to crystal structures described as a lattice with a basis of more than one atom.</a>
+<a name="77"><span class="lineNum">      77 </span>            : In this case there is more than one type of environment.</a>
+<a name="78"><span class="lineNum">      78 </span>            : We consider the case of \f$M\f$ environments \f$X = \chi_1,\chi_2,...,\chi_M\f$ and we define the kernel through a best match strategy:</a>
+<a name="79"><span class="lineNum">      79 </span>            : \f[</a>
+<a name="80"><span class="lineNum">      80 </span>            :  \tilde{k}_X(\chi)= \frac{1}{\lambda} \log \left ( \sum\limits_{l=1}^{M}\exp \left (\lambda \: \tilde{k}_{\chi_l}(\chi) \right ) \right ).</a>
+<a name="81"><span class="lineNum">      81 </span>            : \f]</a>
+<a name="82"><span class="lineNum">      82 </span>            : For a large enough \f$\lambda\f$ this expression will select the largest \f$\tilde{k}_{\chi_l}(\chi)\f$ with \f$\chi_l \in X\f$.</a>
+<a name="83"><span class="lineNum">      83 </span>            : This approach can be used, for instance, to target the hexagonal closed packed (HCP keyword) or the diamond structure (DIAMOND keyword).</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The CRYSTAL_STRUCTURE keyword can take the values SC (simple cubic), BCC (body centered cubic), FCC (face centered cubic),</a>
+<a name="86"><span class="lineNum">      86 </span>            : HCP (hexagonal closed pack), DIAMOND (cubic diamond), and CUSTOM (user defined).</a>
+<a name="87"><span class="lineNum">      87 </span>            : All options follow the same conventions as in the [lattice command](https://lammps.sandia.gov/doc/lattice.html) of [LAMMPS](https://lammps.sandia.gov/).</a>
+<a name="88"><span class="lineNum">      88 </span>            : If a CRYSTAL_STRUCTURE other than CUSTOM is used, then the lattice constants have to be specified using the keyword LATTICE_CONSTANTS.</a>
+<a name="89"><span class="lineNum">      89 </span>            : One value has to be specified for SC, BCC, FCC, and DIAMOND and two values have to be set for HCP (a and c lattice constants in that order).</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : If the CUSTOM option is used then the reference environments have to be specified by the user.</a>
+<a name="92"><span class="lineNum">      92 </span>            : The reference environments are specified in pdb files containing the distance vectors from the central atom to the neighbors.</a>
+<a name="93"><span class="lineNum">      93 </span>            : Make sure your PDB file is correctly formatted as explained \ref pdbreader &quot;in this page&quot;</a>
+<a name="94"><span class="lineNum">      94 </span>            : If only one reference environment is specified then the filename should be given as argument of the keyword REFERENCE.</a>
+<a name="95"><span class="lineNum">      95 </span>            : If instead several reference environments are given, then they have to be provided in separate pdb files and given as arguments of the</a>
+<a name="96"><span class="lineNum">      96 </span>            : keywords REFERENCE_1, REFERENCE_2, etc.</a>
+<a name="97"><span class="lineNum">      97 </span>            : If you have a reference crystal structure configuration you can use the [Environment Finder](https://github.com/PabloPiaggi/EnvironmentFinder) app to determine the reference environments that you should use.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : If multiple chemical species are involved in the calculation, it is possible to provide the atom types (names) both for atoms in the reference environments and in the simulation box.</a>
+<a name="100"><span class="lineNum">     100 </span>            : This information is provided in pdb files using the atom name field.</a>
+<a name="101"><span class="lineNum">     101 </span>            : The comparison between environments is performed taking into account whether the atom names match.</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : \par Examples</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : The following input calculates the ENVIRONMENTSIMILARITY kernel for 250 atoms in the system</a>
+<a name="106"><span class="lineNum">     106 </span>            : using the BCC atomic environment as target, and then calculates and prints the average value</a>
+<a name="107"><span class="lineNum">     107 </span>            :  for this quantity.</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : \plumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : ENVIRONMENTSIMILARITY SPECIES=1-250 SIGMA=0.05 LATTICE_CONSTANTS=0.423 CRYSTAL_STRUCTURE=BCC MEAN LABEL=es</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : PRINT ARG=es.mean FILE=COLVAR</a>
+<a name="113"><span class="lineNum">     113 </span>            : \endplumedfile</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : The next example compares the environments of the 96 selected atoms with a user specified reference</a>
+<a name="116"><span class="lineNum">     116 </span>            : environment. The reference environment is contained in the env1.pdb file. Once the kernel is computed</a>
+<a name="117"><span class="lineNum">     117 </span>            :  the average and the number of atoms with a kernel larger than 0.5 are computed.</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : \plumedfile</a>
+<a name="120"><span class="lineNum">     120 </span>            : ENVIRONMENTSIMILARITY ...</a>
+<a name="121"><span class="lineNum">     121 </span>            :  SPECIES=1-288:3</a>
+<a name="122"><span class="lineNum">     122 </span>            :  SIGMA=0.05</a>
+<a name="123"><span class="lineNum">     123 </span>            :  CRYSTAL_STRUCTURE=CUSTOM</a>
+<a name="124"><span class="lineNum">     124 </span>            :  REFERENCE=env1.pdb</a>
+<a name="125"><span class="lineNum">     125 </span>            :  LABEL=es</a>
+<a name="126"><span class="lineNum">     126 </span>            :  MEAN</a>
+<a name="127"><span class="lineNum">     127 </span>            :  MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}</a>
+<a name="128"><span class="lineNum">     128 </span>            : ... ENVIRONMENTSIMILARITY</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : PRINT ARG=es.mean,es.morethan FILE=COLVAR</a>
+<a name="131"><span class="lineNum">     131 </span>            : \endplumedfile</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : The next example is similar to the one above but in this case 4 reference environments are specified.</a>
+<a name="134"><span class="lineNum">     134 </span>            :  Each reference environment is given in a separate pdb file.</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \plumedfile</a>
+<a name="137"><span class="lineNum">     137 </span>            : ENVIRONMENTSIMILARITY ...</a>
+<a name="138"><span class="lineNum">     138 </span>            :  SPECIES=1-288:3</a>
+<a name="139"><span class="lineNum">     139 </span>            :  SIGMA=0.05</a>
+<a name="140"><span class="lineNum">     140 </span>            :  CRYSTAL_STRUCTURE=CUSTOM</a>
+<a name="141"><span class="lineNum">     141 </span>            :  REFERENCE_1=env1.pdb</a>
+<a name="142"><span class="lineNum">     142 </span>            :  REFERENCE_2=env2.pdb</a>
+<a name="143"><span class="lineNum">     143 </span>            :  REFERENCE_3=env3.pdb</a>
+<a name="144"><span class="lineNum">     144 </span>            :  REFERENCE_4=env4.pdb</a>
+<a name="145"><span class="lineNum">     145 </span>            :  LABEL=es</a>
+<a name="146"><span class="lineNum">     146 </span>            :  MEAN</a>
+<a name="147"><span class="lineNum">     147 </span>            :  MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}</a>
+<a name="148"><span class="lineNum">     148 </span>            : ... ENVIRONMENTSIMILARITY</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : PRINT ARG=es.mean,es.morethan FILE=COLVAR</a>
+<a name="151"><span class="lineNum">     151 </span>            : \endplumedfile</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : The following examples illustrates the use of pdb files to provide information about different chemical species:</a>
+<a name="154"><span class="lineNum">     154 </span>            : \plumedfile</a>
+<a name="155"><span class="lineNum">     155 </span>            : ENVIRONMENTSIMILARITY ...</a>
+<a name="156"><span class="lineNum">     156 </span>            :  SPECIES=1-6</a>
+<a name="157"><span class="lineNum">     157 </span>            :  SIGMA=0.05</a>
+<a name="158"><span class="lineNum">     158 </span>            :  CRYSTAL_STRUCTURE=CUSTOM</a>
+<a name="159"><span class="lineNum">     159 </span>            :  REFERENCE=env.pdb</a>
+<a name="160"><span class="lineNum">     160 </span>            :  LABEL=es</a>
+<a name="161"><span class="lineNum">     161 </span>            :  MEAN</a>
+<a name="162"><span class="lineNum">     162 </span>            :  MORE_THAN={RATIONAL R_0=0.5 NN=12 MM=24}</a>
+<a name="163"><span class="lineNum">     163 </span>            :  ATOM_NAMES_FILE=atom-names.pdb</a>
+<a name="164"><span class="lineNum">     164 </span>            : ... ENVIRONMENTSIMILARITY</a>
+<a name="165"><span class="lineNum">     165 </span>            : \endplumedfile</a>
+<a name="166"><span class="lineNum">     166 </span>            : Here the file env.pdb is:</a>
+<a name="167"><span class="lineNum">     167 </span>            : \verbatim</a>
+<a name="168"><span class="lineNum">     168 </span>            : ATOM      1    O MOL     1      -2.239  -1.296  -0.917  1.00  0.00           O</a>
+<a name="169"><span class="lineNum">     169 </span>            : ATOM      2    O MOL     1       0.000   0.000   2.751  1.00  0.00           O</a>
+<a name="170"><span class="lineNum">     170 </span>            : \endverbatim</a>
+<a name="171"><span class="lineNum">     171 </span>            : where atoms are of type O, and the atom-names.pdb file is:</a>
+<a name="172"><span class="lineNum">     172 </span>            : \verbatim</a>
+<a name="173"><span class="lineNum">     173 </span>            : ATOM      1  O       X   1       0.000   2.593   4.126  0.00  0.00           O</a>
+<a name="174"><span class="lineNum">     174 </span>            : ATOM      2  H       X   1       0.000   3.509   3.847  0.00  0.00           H</a>
+<a name="175"><span class="lineNum">     175 </span>            : ATOM      3  H       X   1       0.000   2.635   5.083  0.00  0.00           H</a>
+<a name="176"><span class="lineNum">     176 </span>            : ATOM      4  O       X   1       0.000   2.593  11.462  0.00  0.00           O</a>
+<a name="177"><span class="lineNum">     177 </span>            : ATOM      5  H       X   1       0.000   3.509  11.183  0.00  0.00           H</a>
+<a name="178"><span class="lineNum">     178 </span>            : ATOM      6  H       X   1       0.000   2.635  12.419  0.00  0.00           H</a>
+<a name="179"><span class="lineNum">     179 </span>            : \endverbatim</a>
+<a name="180"><span class="lineNum">     180 </span>            : where atoms are of type O and H.</a>
+<a name="181"><span class="lineNum">     181 </span>            : In this case, all atoms are used as centers, but only neighbors of type O are taken into account.</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : */</a>
+<a name="184"><span class="lineNum">     184 </span>            : //+ENDPLUMEDOC</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : class EnvironmentSimilarity : public multicolvar::MultiColvarBase {</a>
+<a name="188"><span class="lineNum">     188 </span>            : private:</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // All global variables end with underscore</a>
+<a name="190"><span class="lineNum">     190 </span>            :   // square of cutoff, square of broadening parameter</a>
+<a name="191"><span class="lineNum">     191 </span>            :   double rcut2_, sigmaSqr_;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   // lambda parameter for softmax function</a>
+<a name="193"><span class="lineNum">     193 </span>            :   double lambda_;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   // Array of Vectors to store the reference environments, i.e. the templates</a>
+<a name="195"><span class="lineNum">     195 </span>            :   std::vector&lt;std::vector&lt;Vector&gt;&gt; environments_;</a>
+<a name="196"><span class="lineNum">     196 </span>            :   // Array of strings to store the atom names of reference environments</a>
+<a name="197"><span class="lineNum">     197 </span>            :   std::vector&lt;std::vector&lt;std::string&gt;&gt; environmentsAtomNames_;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   // Use of atom names reference file</a>
+<a name="199"><span class="lineNum">     199 </span>            :   std::vector&lt;std::string&gt; atomNames_;</a>
+<a name="200"><span class="lineNum">     200 </span>            : public:</a>
+<a name="201"><span class="lineNum">     201 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="202"><span class="lineNum">     202 </span>            :   explicit EnvironmentSimilarity(const ActionOptions&amp;);</a>
+<a name="203"><span class="lineNum">     203 </span>            : // active methods:</a>
+<a name="204"><span class="lineNum">     204 </span>            :   virtual double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="205"><span class="lineNum">     205 </span>            : // Returns the number of coordinates of the field</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         17 :   bool isPeriodic() { return false; }</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : // Calculates maximum distance in an environment</a>
+<a name="208"><span class="lineNum">     208 </span>            :   double maxDistance(std::vector&lt;Vector&gt; environment);</a>
+<a name="209"><span class="lineNum">     209 </span>            :   // Parse everything connected to the definition of the reference environments</a>
+<a name="210"><span class="lineNum">     210 </span>            :   // First argument is the array of Vectors that stores the reference environments</a>
+<a name="211"><span class="lineNum">     211 </span>            :   // Second argument is the array of strings that stores the atom names of reference environments</a>
+<a name="212"><span class="lineNum">     212 </span>            :   // Third argument is the maximum distance in the ref environments and sets the</a>
+<a name="213"><span class="lineNum">     213 </span>            :   // cutoff for the cell lists</a>
+<a name="214"><span class="lineNum">     214 </span>            :   void parseReferenceEnvironments( std::vector&lt;std::vector&lt;Vector&gt;&gt;&amp; environments,  std::vector&lt;std::vector&lt;std::string&gt;&gt;&amp; environmentsAtomNames, double&amp; max_dist);</a>
+<a name="215"><span class="lineNum">     215 </span>            : };</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      12524 : PLUMED_REGISTER_ACTION(EnvironmentSimilarity,&quot;ENVIRONMENTSIMILARITY&quot;)</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         12 : void EnvironmentSimilarity::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         12 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         36 :   keys.use(&quot;SPECIES&quot;); keys.use(&quot;SPECIESA&quot;); keys.use(&quot;SPECIESB&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;0.1&quot;,&quot;Broadening parameter&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;CRYSTAL_STRUCTURE&quot;,&quot;FCC&quot;,&quot;Targeted crystal structure. Options are: &quot;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :            &quot;SC: simple cubic, &quot;</a>
+<a name="225"><span class="lineNum">     225 </span>            :            &quot;BCC: body center cubic, &quot;</a>
+<a name="226"><span class="lineNum">     226 </span>            :            &quot;FCC: face centered cubic, &quot;</a>
+<a name="227"><span class="lineNum">     227 </span>            :            &quot;HCP: hexagonal closed pack, &quot;</a>
+<a name="228"><span class="lineNum">     228 </span>            :            &quot;DIAMOND: cubic diamond, &quot;</a>
+<a name="229"><span class="lineNum">     229 </span>            :            &quot;CUSTOM: user defined &quot;</a>
+<a name="230"><span class="lineNum">     230 </span>            :            &quot; &quot;);</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         24 :   keys.add(&quot;optional&quot;,&quot;LATTICE_CONSTANTS&quot;,&quot;Lattice constants. Two comma separated values for HCP, &quot;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :            &quot;one value for all other CRYSTAL_STRUCTURES.&quot;);</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;LAMBDA&quot;,&quot;100&quot;,&quot;Lambda parameter&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         24 :   keys.add(&quot;optional&quot;,&quot;REFERENCE&quot;,&quot;PDB file with relative distances from central atom.&quot;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :            &quot; Use this keyword if you are targeting a single reference environment.&quot;);</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         24 :   keys.add(&quot;numbered&quot;,&quot;REFERENCE_&quot;,&quot;PDB files with relative distances from central atom.&quot;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :            &quot; Each file corresponds to one template.&quot;</a>
+<a name="238"><span class="lineNum">     238 </span>            :            &quot; Use these keywords if you are targeting more than one reference environment.&quot;);</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         24 :   keys.add(&quot;optional&quot;,&quot;ATOM_NAMES_FILE&quot;,&quot;PDB file with atom names for all atoms in SPECIES.&quot;</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :            &quot; Atoms in reference environments will be compared only if atom names match.&quot;);</a>
+<a name="241"><span class="lineNum">     241 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         48 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MAX&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         48 :   keys.use(&quot;MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         36 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         12 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         10 : EnvironmentSimilarity::EnvironmentSimilarity(const ActionOptions&amp;ao):</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   Action(ao),</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         10 :   MultiColvarBase(ao)</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : {</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         10 :   log.printf(&quot;  Please read and cite &quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         20 :   log &lt;&lt; plumed.cite(&quot;Piaggi and Parrinello, J. Chem. Phys. 150 (24), 244119 (2019)&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         10 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   // Parse everything connected to the definition of the reference environments</a>
+<a name="256"><span class="lineNum">     256 </span>            :   double max_dist_ref_vector;</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         10 :   parseReferenceEnvironments(environments_, environmentsAtomNames_, max_dist_ref_vector);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            :   double sigma;</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         10 :   parse(&quot;SIGMA&quot;, sigma);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         10 :   log.printf(&quot;  representing local density as a sum of Gaussians with standard deviation %f\n&quot;,sigma);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         10 :   sigmaSqr_=sigma*sigma;</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         10 :   lambda_=100;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         20 :   parse(&quot;LAMBDA&quot;, lambda_);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         10 :   if (environments_.size()&gt;1) log.printf(&quot;  using a soft max function with lambda %f\n&quot;,lambda_);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   // Set the link cell cutoff</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         10 :   double rcut = max_dist_ref_vector + 3*sigma;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         10 :   setLinkCellCutoff( rcut );</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         10 :   rcut2_ = rcut * rcut;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   // And setup the ActionWithVessel</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         10 :   std::vector&lt;AtomNumber&gt; all_atoms; setupMultiColvarBase( all_atoms ); checkRead();</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         10 :   plumed_massert(atomNames_.empty() || atomNames_.size()==getNumberOfAtoms(),&quot;mismatch between atoms in SPECIES and ATOM_NAMES_FILE&quot;);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         10 : }</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">      30144 : double EnvironmentSimilarity::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      30144 :   if (environments_.size()==1 &amp;&amp; atomNames_.empty() ) {</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     // One reference environment case - no atom names</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">     155464 :     for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :       const Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="284"><span class="lineNum">     284 </span>            :       double d2;</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     232452 :       if ( (d2=distance[0]*distance[0])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">      77840 :            (d2+=distance[1]*distance[1])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     194068 :            (d2+=distance[2]*distance[2])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :            d2&gt;epsilon ) {</a>
+<a name="289"><span class="lineNum">     289 </span>            :         // Iterate over atoms in the reference environment</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     236856 :         for(unsigned k=0; k&lt;environments_[0].size(); ++k) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     220400 :           Vector distanceFromRef=distance-environments_[0][k];</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">     220400 :           double value = std::exp(-distanceFromRef.modulo2()/(4*sigmaSqr_) )/environments_[0].size() ;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     220400 :           accumulateSymmetryFunction( 1, i, value, -(value/(2*sigmaSqr_))*distanceFromRef, (value/(2*sigmaSqr_))*Tensor(distance,distanceFromRef), myatoms );</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :         }</a>
+<a name="295"><span class="lineNum">     295 </span>            :       }</a>
+<a name="296"><span class="lineNum">     296 </span>            :     }</a>
+<a name="297"><span class="lineNum">     297 </span>            :     return myatoms.getValue(1);</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">      29292 :   } else if (atomNames_.empty()) {</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :     // More than one reference environment case - no atom names</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">      29196 :     std::vector&lt;double&gt; values(environments_.size()); //value for each template</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :     // First time calculate sums</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">    2808756 :     for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :       const Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="304"><span class="lineNum">     304 </span>            :       double d2;</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">    4534472 :       if ( (d2=distance[0]*distance[0])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">    1754912 :            (d2+=distance[1]*distance[1])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">    3469608 :            (d2+=distance[2]*distance[2])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :            d2&gt;epsilon ) {</a>
+<a name="309"><span class="lineNum">     309 </span>            :         // Iterate over templates</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">    1216388 :         for(unsigned j=0; j&lt;environments_.size(); ++j) {</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :           // Iterate over atoms in the template</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">    4893780 :           for(unsigned k=0; k&lt;environments_[j].size(); ++k) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">    3921936 :             Vector distanceFromRef=distance-environments_[j][k];</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">    3921936 :             values[j] += std::exp(-distanceFromRef.modulo2()/(4*sigmaSqr_) )/environments_[j].size() ;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :           }</a>
+<a name="316"><span class="lineNum">     316 </span>            :         }</a>
+<a name="317"><span class="lineNum">     317 </span>            :       }</a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            :     double sum=0;</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">     145188 :     for(unsigned j=0; j&lt;environments_.size(); ++j) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">     115992 :       values[j] = std::exp(lambda_*values[j]);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">     115992 :       sum += values[j];</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :     }</a>
+<a name="324"><span class="lineNum">     324 </span>            :     // Second time find derivatives</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">    2808756 :     for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :       const Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="327"><span class="lineNum">     327 </span>            :       double d2;</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">    4534472 :       if ( (d2=distance[0]*distance[0])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">    1754912 :            (d2+=distance[1]*distance[1])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">    3469608 :            (d2+=distance[2]*distance[2])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :            d2&gt;epsilon ) {</a>
+<a name="332"><span class="lineNum">     332 </span>            :         // Iterate over reference environment</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">    1216388 :         for(unsigned j=0; j&lt;environments_.size(); ++j) {</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :           // Iterate over atoms in the reference environment</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">    4893780 :           for(unsigned k=0; k&lt;environments_[j].size(); ++k) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">    3921936 :             Vector distanceFromRef=distance-environments_[j][k];</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">    3921936 :             double value = std::exp(-distanceFromRef.modulo2()/(4*sigmaSqr_) )/environments_[j].size() ;</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">    3921936 :             accumulateSymmetryFunction( 1, i, value, -(values[j]/sum)*(value/(2*sigmaSqr_))*distanceFromRef, (values[j]/sum)*(value/(2*sigmaSqr_))*Tensor(distance,distanceFromRef), myatoms );</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :           }</a>
+<a name="340"><span class="lineNum">     340 </span>            :         }</a>
+<a name="341"><span class="lineNum">     341 </span>            :       }</a>
+<a name="342"><span class="lineNum">     342 </span>            :     }</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">      29196 :     return std::log(sum)/lambda_;</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :   } else {</a>
+<a name="345"><span class="lineNum">     345 </span>            :     // Reference environments with atom names</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         96 :     std::vector&lt;double&gt; values(environments_.size()); //value for each template</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :     // First time calculate sums</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      27648 :     for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :       const Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="350"><span class="lineNum">     350 </span>            :       double d2;</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">      42816 :       if ( (d2=distance[0]*distance[0])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">      15264 :            (d2+=distance[1]*distance[1])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">      33216 :            (d2+=distance[2]*distance[2])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :            d2&gt;epsilon ) {</a>
+<a name="355"><span class="lineNum">     355 </span>            :         // Iterate over templates</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       9600 :         for(unsigned j=0; j&lt;environments_.size(); ++j) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :           // Iterate over atoms in the template</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">      38400 :           for(unsigned k=0; k&lt;environments_[j].size(); ++k) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">      30720 :             if (atomNames_[myatoms.getIndex(i)]==environmentsAtomNames_[j][k]) {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">       6144 :               Vector distanceFromRef=distance-environments_[j][k];</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">       6144 :               values[j] += std::exp(-distanceFromRef.modulo2()/(4*sigmaSqr_) )/environments_[j].size() ;</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :             }</a>
+<a name="363"><span class="lineNum">     363 </span>            :           }</a>
+<a name="364"><span class="lineNum">     364 </span>            :         }</a>
+<a name="365"><span class="lineNum">     365 </span>            :       }</a>
+<a name="366"><span class="lineNum">     366 </span>            :     }</a>
+<a name="367"><span class="lineNum">     367 </span>            :     double sum=0;</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        480 :     for(unsigned j=0; j&lt;environments_.size(); ++j) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        384 :       values[j] = std::exp(lambda_*values[j]);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        384 :       sum += values[j];</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :     }</a>
+<a name="372"><span class="lineNum">     372 </span>            :     // Second time find derivatives</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">      27648 :     for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :       const Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="375"><span class="lineNum">     375 </span>            :       double d2;</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      42816 :       if ( (d2=distance[0]*distance[0])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">      15264 :            (d2+=distance[1]*distance[1])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">      33216 :            (d2+=distance[2]*distance[2])&lt;rcut2_ &amp;&amp;</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :            d2&gt;epsilon ) {</a>
+<a name="380"><span class="lineNum">     380 </span>            :         // Iterate over reference environment</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       9600 :         for(unsigned j=0; j&lt;environments_.size(); ++j) {</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :           // Iterate over atoms in the reference environment</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">      38400 :           for(unsigned k=0; k&lt;environments_[j].size(); ++k) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">      30720 :             if (atomNames_[myatoms.getIndex(i)]==environmentsAtomNames_[j][k]) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       6144 :               Vector distanceFromRef=distance-environments_[j][k];</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       6144 :               double value = std::exp(-distanceFromRef.modulo2()/(4*sigmaSqr_) )/environments_[j].size() ;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       6144 :               accumulateSymmetryFunction( 1, i, value, -(values[j]/sum)*(value/(2*sigmaSqr_))*distanceFromRef, (values[j]/sum)*(value/(2*sigmaSqr_))*Tensor(distance,distanceFromRef), myatoms );</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :             }</a>
+<a name="389"><span class="lineNum">     389 </span>            :           }</a>
+<a name="390"><span class="lineNum">     390 </span>            :         }</a>
+<a name="391"><span class="lineNum">     391 </span>            :       }</a>
+<a name="392"><span class="lineNum">     392 </span>            :     }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         96 :     return std::log(sum)/lambda_;</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :   }</a>
+<a name="395"><span class="lineNum">     395 </span>            : }</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         17 : double EnvironmentSimilarity::maxDistance( std::vector&lt;Vector&gt; environment ) {</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   double max_dist = 0.0;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         85 :   for(unsigned i=0; i&lt;environment.size(); ++i) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         68 :     double norm=environment[i].modulo();</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         68 :     if (norm&gt;max_dist) max_dist=norm;</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :   }</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         17 :   return max_dist;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : }</a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         10 : void EnvironmentSimilarity::parseReferenceEnvironments( std::vector&lt;std::vector&lt;Vector&gt;&gt;&amp; environments, std::vector&lt;std::vector&lt;std::string&gt;&gt;&amp; environmentsAtomNames, double&amp; max_dist) {</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :   std::vector&lt;double&gt; lattice_constants;</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         20 :   parseVector(&quot;LATTICE_CONSTANTS&quot;, lattice_constants);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :   std::string crystal_structure;</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         20 :   parse(&quot;CRYSTAL_STRUCTURE&quot;, crystal_structure);</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :   // find crystal structure</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         10 :   if (crystal_structure == &quot;FCC&quot;) {</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          1 :     if (lattice_constants.size() != 1) error(&quot;Number of LATTICE_CONSTANTS arguments must be one for FCC&quot;);</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          1 :     environments.resize(1);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">          1 :     environments[0].resize(12);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          1 :     environments[0][0]  = Vector(+0.5,+0.5,+0.0)*lattice_constants[0];</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">          1 :     environments[0][1]  = Vector(-0.5,-0.5,+0.0)*lattice_constants[0];</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          1 :     environments[0][2]  = Vector(+0.5,-0.5,+0.0)*lattice_constants[0];</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          1 :     environments[0][3]  = Vector(-0.5,+0.5,+0.0)*lattice_constants[0];</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          1 :     environments[0][4]  = Vector(+0.5,+0.0,+0.5)*lattice_constants[0];</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">          1 :     environments[0][5]  = Vector(-0.5,+0.0,-0.5)*lattice_constants[0];</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          1 :     environments[0][6]  = Vector(-0.5,+0.0,+0.5)*lattice_constants[0];</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">          1 :     environments[0][7]  = Vector(+0.5,+0.0,-0.5)*lattice_constants[0];</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          1 :     environments[0][8]  = Vector(+0.0,+0.5,+0.5)*lattice_constants[0];</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          1 :     environments[0][9]  = Vector(+0.0,-0.5,-0.5)*lattice_constants[0];</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          1 :     environments[0][10] = Vector(+0.0,-0.5,+0.5)*lattice_constants[0];</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          1 :     environments[0][11] = Vector(+0.0,+0.5,-0.5)*lattice_constants[0];</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          1 :     max_dist = std::sqrt(2)*lattice_constants[0]/2.;</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          9 :   } else if (crystal_structure == &quot;SC&quot;) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :     if (lattice_constants.size() != 1) error(&quot;Number of LATTICE_CONSTANTS arguments must be one for SC&quot;);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :     environments.resize(1);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :     environments[0].resize(6);</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :     environments[0][0]  = Vector(+1.0,+0.0,+0.0)*lattice_constants[0];</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     environments[0][1]  = Vector(-1.0,+0.0,+0.0)*lattice_constants[0];</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :     environments[0][2]  = Vector(+0.0,+1.0,+0.0)*lattice_constants[0];</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :     environments[0][3]  = Vector(+0.0,-1.0,+0.0)*lattice_constants[0];</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :     environments[0][4]  = Vector(+0.0,+0.0,+1.0)*lattice_constants[0];</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :     environments[0][5]  = Vector(+0.0,+0.0,-1.0)*lattice_constants[0];</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :     max_dist = lattice_constants[0];</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          9 :   } else if (crystal_structure == &quot;BCC&quot;) {</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          2 :     if (lattice_constants.size() != 1) error(&quot;Number of LATTICE_CONSTANTS arguments must be one for BCC&quot;);</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          2 :     environments.resize(1);</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          2 :     environments[0].resize(14);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          2 :     environments[0][0]  = Vector(+0.5,+0.5,+0.5)*lattice_constants[0];</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          2 :     environments[0][1]  = Vector(-0.5,-0.5,-0.5)*lattice_constants[0];</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          2 :     environments[0][2]  = Vector(-0.5,+0.5,+0.5)*lattice_constants[0];</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          2 :     environments[0][3]  = Vector(+0.5,-0.5,+0.5)*lattice_constants[0];</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          2 :     environments[0][4]  = Vector(+0.5,+0.5,-0.5)*lattice_constants[0];</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          2 :     environments[0][5]  = Vector(-0.5,-0.5,+0.5)*lattice_constants[0];</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          2 :     environments[0][6]  = Vector(+0.5,-0.5,-0.5)*lattice_constants[0];</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">          2 :     environments[0][7]  = Vector(-0.5,+0.5,-0.5)*lattice_constants[0];</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          2 :     environments[0][8]  = Vector(+1.0,+0.0,+0.0)*lattice_constants[0];</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">          2 :     environments[0][9]  = Vector(+0.0,+1.0,+0.0)*lattice_constants[0];</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          2 :     environments[0][10] = Vector(+0.0,+0.0,+1.0)*lattice_constants[0];</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          2 :     environments[0][11] = Vector(-1.0,+0.0,+0.0)*lattice_constants[0];</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          2 :     environments[0][12] = Vector(+0.0,-1.0,+0.0)*lattice_constants[0];</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          2 :     environments[0][13] = Vector(+0.0,+0.0,-1.0)*lattice_constants[0];</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          2 :     max_dist = lattice_constants[0];</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          7 :   } else if (crystal_structure == &quot;HCP&quot;) {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          1 :     if (lattice_constants.size() != 2) error(&quot;Number of LATTICE_CONSTANTS arguments must be two for HCP&quot;);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          1 :     environments.resize(2);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          1 :     environments[0].resize(12);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          1 :     environments[1].resize(12);</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :     double sqrt3=std::sqrt(3);</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          1 :     environments[0][0]  = Vector(+0.5,+sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          1 :     environments[0][1]  = Vector(-0.5,+sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          1 :     environments[0][2]  = Vector(+0.5,-sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          1 :     environments[0][3]  = Vector(-0.5,-sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          1 :     environments[0][4]  = Vector(+1.0,+0.0,+0.0)      *lattice_constants[0];</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          1 :     environments[0][5]  = Vector(-1.0,+0.0,+0.0)      *lattice_constants[0];</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          1 :     environments[0][6]  = Vector(+0.5,+sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,+0.5)*lattice_constants[1];</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          1 :     environments[0][7]  = Vector(-0.5,+sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,+0.5)*lattice_constants[1];</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          1 :     environments[0][8]  = Vector(+0.0,-sqrt3/3.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,+0.5)*lattice_constants[1];</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          1 :     environments[0][9]  = Vector(+0.5,+sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,-0.5)*lattice_constants[1];</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">          1 :     environments[0][10] = Vector(-0.5,+sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,-0.5)*lattice_constants[1];</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          1 :     environments[0][11] = Vector(+0.0,-sqrt3/3.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,-0.5)*lattice_constants[1];</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          1 :     environments[1][0]  = Vector(+0.5,+sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          1 :     environments[1][1]  = Vector(-0.5,+sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          1 :     environments[1][2]  = Vector(+0.5,-sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          1 :     environments[1][3]  = Vector(-0.5,-sqrt3/2.0,+0.0)*lattice_constants[0];</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          1 :     environments[1][4]  = Vector(+1.0,+0.0,+0.0)      *lattice_constants[0];</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          1 :     environments[1][5]  = Vector(-1.0,+0.0,+0.0)      *lattice_constants[0];</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          1 :     environments[1][6]  = Vector(+0.5,-sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,+0.5)*lattice_constants[1];</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          1 :     environments[1][7]  = Vector(-0.5,-sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,+0.5)*lattice_constants[1];</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          1 :     environments[1][8]  = Vector(+0.0,+sqrt3/3.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,+0.5)*lattice_constants[1];</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          1 :     environments[1][9]  = Vector(+0.5,-sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,-0.5)*lattice_constants[1];</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          1 :     environments[1][10] = Vector(-0.5,-sqrt3/6.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,-0.5)*lattice_constants[1];</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          1 :     environments[1][11] = Vector(+0.0,+sqrt3/3.0,+0.0)*lattice_constants[0] + Vector(+0.0,+0.0,-0.5)*lattice_constants[1];</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          1 :     max_dist = lattice_constants[0];</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          6 :   } else if (crystal_structure == &quot;DIAMOND&quot;) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          1 :     if (lattice_constants.size() != 1) error(&quot;Number of LATTICE_CONSTANTS arguments must be one for DIAMOND&quot;);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          1 :     environments.resize(2);</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          1 :     environments[0].resize(4); environments[1].resize(4);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          1 :     environments[0][0]  = Vector(+1.0,+1.0,+1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          1 :     environments[0][1]  = Vector(-1.0,-1.0,+1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          1 :     environments[0][2]  = Vector(+1.0,-1.0,-1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          1 :     environments[0][3]  = Vector(-1.0,+1.0,-1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          1 :     environments[1][0]  = Vector(+1.0,-1.0,+1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          1 :     environments[1][1]  = Vector(-1.0,+1.0,+1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          1 :     environments[1][2]  = Vector(+1.0,+1.0,-1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          1 :     environments[1][3]  = Vector(-1.0,-1.0,-1.0)*lattice_constants[0]/4.0;</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          1 :     max_dist = std::sqrt(3)*lattice_constants[0]/4.0;</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          5 :   } else if (crystal_structure == &quot;CUSTOM&quot;) {</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :     std::string reffile;</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         10 :     parse(&quot;REFERENCE&quot;,reffile);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          5 :     if (!reffile.empty()) {</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :       // Case with one reference environment</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">          1 :       environments.resize(1); environmentsAtomNames.resize(1);</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          1 :       PDB pdb;</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">          2 :       if( !pdb.read(reffile,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()) )</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :         error(&quot;missing input file &quot; + reffile );</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">          1 :       unsigned natoms=pdb.getPositions().size();</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          1 :       environments[0].resize( natoms ); environmentsAtomNames[0].resize( natoms );</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          5 :       for(unsigned i=0; i&lt;natoms; ++i) environments[0][i]=pdb.getPositions()[i];</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">          5 :       for(unsigned i=0; i&lt;natoms; ++i) environmentsAtomNames[0][i]=pdb.getAtomName(pdb.getAtomNumbers()[i]);</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">          1 :       max_dist=maxDistance(environments[0]);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">          1 :       log.printf(&quot;  reading %d reference vectors from %s \n&quot;, natoms, reffile.c_str() );</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">          1 :     } else {</span></a>
+<a name="519"><span class="lineNum">     519 </span>            :       // Case with several reference environments</a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">          4 :       max_dist=0;</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         16 :       for(unsigned int i=1;; i++) {</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         40 :         if(!parseNumbered(&quot;REFERENCE_&quot;,i,reffile) ) {break;}</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         16 :         PDB pdb;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         32 :         if( !pdb.read(reffile,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()) )</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :           error(&quot;missing input file &quot; + reffile );</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         16 :         unsigned natoms=pdb.getPositions().size();</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :         std::vector&lt;Vector&gt; environment; std::vector&lt;std::string&gt; environmentAtomNames;</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         16 :         environment.resize( natoms ); environmentAtomNames.resize( natoms);</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         80 :         for(unsigned i=0; i&lt;natoms; ++i) environment[i]=pdb.getPositions()[i];</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         80 :         for(unsigned i=0; i&lt;natoms; ++i) environmentAtomNames[i]=pdb.getAtomName(pdb.getAtomNumbers()[i]);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">         16 :         environments.push_back(environment);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         16 :         environmentsAtomNames.push_back(environmentAtomNames);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         16 :         double norm = maxDistance(environment);</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">         16 :         if (norm&gt;max_dist) max_dist=norm;</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         16 :         log.printf(&quot;  Reference environment %d : reading %d reference vectors from %s \n&quot;, i, natoms, reffile.c_str() );</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         32 :       }</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :     }</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          5 :     if (environments.size()==0) error(&quot;No environments have been found! Please specify a PDB file in the REFERENCE &quot;</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :                                         &quot;or in the REFERENCE_1, REFERENCE_2, etc keywords&quot;);</a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">          5 :     log.printf(&quot;  Number of reference environments is %lu\n&quot;,environments.size() );</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">          5 :     log.printf(&quot;  Number of vectors per reference environment is %lu\n&quot;,environments[0].size() );</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :     std::string atomNamesFile;</a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         10 :     parse(&quot;ATOM_NAMES_FILE&quot;,atomNamesFile);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">          5 :     if (!atomNamesFile.empty()) {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">          1 :       PDB pdb;</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">          2 :       if( !pdb.read(atomNamesFile,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()) )</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :         error(&quot;missing input file &quot; + atomNamesFile);</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">          1 :       unsigned natoms=pdb.getPositions().size();</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">          1 :       atomNames_.resize( natoms );</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        385 :       for(unsigned i=0; i&lt;natoms; ++i) atomNames_[i]=pdb.getAtomName(pdb.getAtomNumbers()[i]);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          1 :       log.printf(&quot;  Read %d atoms from atom names file %s \n&quot;, natoms, atomNamesFile.c_str() );</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          1 :       log.printf(&quot;  Atoms in environments will be considered only if atom names match.\n&quot;);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          1 :     } else {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">          4 :       log.printf(&quot;  No atom names file has been given. Atoms in reference environments will be matched disregarding atom type.\n&quot;);</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :     }</a>
+<a name="556"><span class="lineNum">     556 </span>            :   } else {</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :     error(&quot;CRYSTAL_STRUCTURE=&quot; + crystal_structure + &quot; does not match any structures in the database&quot;);</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         10 :   log.printf(&quot;  targeting the %s crystal structure&quot;,crystal_structure.c_str());</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">         10 :   if (lattice_constants.size()&gt;0) log.printf(&quot; with lattice constants %f\n&quot;,lattice_constants[0]);</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">          5 :   else log.printf(&quot;\n&quot;);</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         10 :   log.printf(&quot;  maximum distance in the reference environment is %f\n&quot;,max_dist);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         10 : }</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            : }</a>
+<a name="568"><span class="lineNum">     568 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Fccubic.cpp.func-sort-c.html b/coverage/crystallization/Fccubic.cpp.func-sort-c.html
new file mode 100644
index 0000000000..39b445df95
--- /dev/null
+++ b/coverage/crystallization/Fccubic.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Fccubic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Fccubic.cpp<span style="font-size: 80%;"> (<a href="Fccubic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Fccubic.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#89">_ZN4PLMD15crystallization7FccubicC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#82">_ZN4PLMD15crystallization12_GLOBAL__N_119FccubicRegisterMe846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#89">_ZN4PLMD15crystallization7FccubicC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#84">_ZN4PLMD15crystallization7Fccubic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#82">_ZN4PLMD15crystallization12_GLOBAL__N_119FccubicRegisterMe84C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#82">_ZN4PLMD15crystallization12_GLOBAL__N_119FccubicRegisterMe84D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#102">_ZNK4PLMD15crystallization7Fccubic22calculateCubicHarmonicERKNS_13VectorGenericILj3EEERKdRS3_</a></td>
+              <td class="coverFnHi">320614</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Fccubic.cpp.func.html b/coverage/crystallization/Fccubic.cpp.func.html
new file mode 100644
index 0000000000..c6b0269925
--- /dev/null
+++ b/coverage/crystallization/Fccubic.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Fccubic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Fccubic.cpp<span style="font-size: 80%;"> (<a href="Fccubic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Fccubic.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#82">_ZN4PLMD15crystallization12_GLOBAL__N_119FccubicRegisterMe846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#82">_ZN4PLMD15crystallization12_GLOBAL__N_119FccubicRegisterMe84C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#82">_ZN4PLMD15crystallization12_GLOBAL__N_119FccubicRegisterMe84D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#84">_ZN4PLMD15crystallization7Fccubic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#89">_ZN4PLMD15crystallization7FccubicC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#89">_ZN4PLMD15crystallization7FccubicC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Fccubic.cpp.gcov.html#102">_ZNK4PLMD15crystallization7Fccubic22calculateCubicHarmonicERKNS_13VectorGenericILj3EEERKdRS3_</a></td>
+              <td class="coverFnHi">320614</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Fccubic.cpp.gcov.html b/coverage/crystallization/Fccubic.cpp.gcov.html
new file mode 100644
index 0000000000..979d51fbc3
--- /dev/null
+++ b/coverage/crystallization/Fccubic.cpp.gcov.html
@@ -0,0 +1,209 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Fccubic.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Fccubic.cpp<span style="font-size: 80%;"> (source / <a href="Fccubic.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CubicHarmonicBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : using namespace std;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace crystallization {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MCOLVAR FCCUBIC</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Measure how similar the environment around atoms is to that found in a FCC structure.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : This CV was introduced in this article \cite fcc-michele-1 and again in this article \cite fcc-michele-2</a>
+<a name="39"><span class="lineNum">      39 </span>            : This CV essentially determines whether the environment around any given atom is similar to that found in</a>
+<a name="40"><span class="lineNum">      40 </span>            : the FCC structure or not.  The function that is used to make this determination is as follows:</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : s_i = \frac{ \sum_{i \ne j} \sigma(r_{ij}) \left\{ a\left[ \frac{(x_{ij}y_{ij})^4 + (x_{ij}z_{ij})^4 + (y_{ij}z_{ij})^4}{r_{ij}^8} - \frac{\alpha (x_{ij}y_{ij}z_{ij})^4}{r_{ij}^{12}} \right] + b \right\} }{ \sum_{i \ne j} \sigma(r_{ij}) }</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : In this expression \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$ are the \f$x\f$, \f$y\f$ and \f$z\f$ components of the vector connecting atom \f$i\f$ to</a>
+<a name="47"><span class="lineNum">      47 </span>            : atom \f$j\f$ and \f$r_{ij}\f$ is the magnitude of this vector.  \f$\sigma(r_{ij})\f$ is a \ref switchingfunction that acts on the distance between</a>
+<a name="48"><span class="lineNum">      48 </span>            : atom \f$i\f$ and atom \f$j\f$ and its inclusion in the numerator and the denominator of the above expression as well as the fact that we are summing</a>
+<a name="49"><span class="lineNum">      49 </span>            : over all of the other atoms in the system ensures that we are calculating an average</a>
+<a name="50"><span class="lineNum">      50 </span>            : of the function of \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$ for the atoms in the first coordination sphere around atom \f$i\f$.  Lastly, \f$\alpha\f$</a>
+<a name="51"><span class="lineNum">      51 </span>            : is a parameter that can be set by the user, which by default is equal to three.  The values of \f$a\f$ and \f$b\f$ are calculated from \f$\alpha\f$ using:</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \f[</a>
+<a name="54"><span class="lineNum">      54 </span>            : a = \frac{ 80080}{ 2717 + 16 \alpha} \qquad \textrm{and} \qquad b = \frac{ 16(\alpha - 143) }{2717 + 16\alpha}</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f]</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : This quantity is once again a multicolvar so you can compute it for multiple atoms using a single PLUMED action and then compute</a>
+<a name="58"><span class="lineNum">      58 </span>            : the average value for the atoms in your system, the number of atoms that have an \f$s_i\f$ value that is more that some target and</a>
+<a name="59"><span class="lineNum">      59 </span>            : so on.  Notice also that you can rotate the reference frame if you are using a non-standard unit cell.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \par Examples</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : The following input calculates the FCCUBIC parameter for the 64 atoms in the system</a>
+<a name="64"><span class="lineNum">      64 </span>            : and then calculates and prints the average value for this quantity.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : FCCUBIC SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} MEAN LABEL=d</a>
+<a name="68"><span class="lineNum">      68 </span>            : PRINT ARG=d.* FILE=colv</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : */</a>
+<a name="72"><span class="lineNum">      72 </span>            : //+ENDPLUMEDOC</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : class Fccubic : public CubicHarmonicBase {</a>
+<a name="76"><span class="lineNum">      76 </span>            : private:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   double alpha, a1, b1;</a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="80"><span class="lineNum">      80 </span>            :   explicit Fccubic(const ActionOptions&amp;);</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const override;</a>
+<a name="82"><span class="lineNum">      82 </span>            : };</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(Fccubic,&quot;FCCUBIC&quot;)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 : void Fccubic::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          6 :   CubicHarmonicBase::registerKeywords( keys );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;ALPHA&quot;,&quot;3.0&quot;,&quot;The alpha parameter of the angular function&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          6 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 : Fccubic::Fccubic(const ActionOptions&amp;ao):</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   Action(ao),</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          4 :   CubicHarmonicBase(ao)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : {</a>
+<a name="95"><span class="lineNum">      95 </span>            :   // Scaling factors such that '1' corresponds to fcc lattice</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // and '0' corresponds to isotropic (liquid)</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          4 :   parse(&quot;ALPHA&quot;,alpha);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          4 :   a1 = 80080. / (2717. + 16*alpha); b1 = 16.*(alpha-143)/(2717+16*alpha);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          4 :   log.printf(&quot;  setting alpha parameter equal to %f \n&quot;,alpha);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   // And setup the ActionWithVessel</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">     320614 : double Fccubic::calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">     320614 :   double x2 = distance[0]*distance[0];</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">     320614 :   double x4 = x2*x2;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     320614 :   double y2 = distance[1]*distance[1];</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     320614 :   double y4 = y2*y2;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">     320614 :   double z2 = distance[2]*distance[2];</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     320614 :   double z4 = z2*z2;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     320614 :   double r8 = pow( d2, 4 );</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   double r12 = pow( d2, 6 );</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     320614 :   double tmp = ((x4*y4)+(x4*z4)+(y4*z4))/r8-alpha*x4*y4*z4/r12;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     320614 :   double t0 = (x2*y4+x2*z4)/r8-alpha*x2*y4*z4/r12;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     320614 :   double t1 = (y2*x4+y2*z4)/r8-alpha*y2*x4*z4/r12;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     320614 :   double t2 = (z2*x4+z2*y4)/r8-alpha*z2*x4*y4/r12;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     320614 :   double t3 = (2*tmp-alpha*x4*y4*z4/r12)/d2;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     320614 :   myder[0]=4*a1*distance[0]*(t0-t3);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">     320614 :   myder[1]=4*a1*distance[1]*(t1-t3);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">     320614 :   myder[2]=4*a1*distance[2]*(t2-t3);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">     320614 :   return a1*tmp+b1;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Gradient.cpp.func-sort-c.html b/coverage/crystallization/Gradient.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4d2804e83a
--- /dev/null
+++ b/coverage/crystallization/Gradient.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Gradient.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Gradient.cpp<span style="font-size: 80%;"> (<a href="Gradient.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Gradient.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#71">_ZN4PLMD15crystallization8GradientC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#60">_ZN4PLMD15crystallization12_GLOBAL__N_120GradientRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#71">_ZN4PLMD15crystallization8GradientC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#62">_ZN4PLMD15crystallization8Gradient16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#133">_ZN4PLMD15crystallization8Gradient12setupRegionsEv</a></td>
+              <td class="coverFnHi">232</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#60">_ZN4PLMD15crystallization12_GLOBAL__N_120GradientRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#60">_ZN4PLMD15crystallization12_GLOBAL__N_120GradientRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#137">_ZNK4PLMD15crystallization8Gradient19calculateAllVolumesERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">11600</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Gradient.cpp.func.html b/coverage/crystallization/Gradient.cpp.func.html
new file mode 100644
index 0000000000..265f095321
--- /dev/null
+++ b/coverage/crystallization/Gradient.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Gradient.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Gradient.cpp<span style="font-size: 80%;"> (<a href="Gradient.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Gradient.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#60">_ZN4PLMD15crystallization12_GLOBAL__N_120GradientRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#60">_ZN4PLMD15crystallization12_GLOBAL__N_120GradientRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#60">_ZN4PLMD15crystallization12_GLOBAL__N_120GradientRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#133">_ZN4PLMD15crystallization8Gradient12setupRegionsEv</a></td>
+              <td class="coverFnHi">232</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#62">_ZN4PLMD15crystallization8Gradient16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#71">_ZN4PLMD15crystallization8GradientC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#71">_ZN4PLMD15crystallization8GradientC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.cpp.gcov.html#137">_ZNK4PLMD15crystallization8Gradient19calculateAllVolumesERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">11600</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Gradient.cpp.gcov.html b/coverage/crystallization/Gradient.cpp.gcov.html
new file mode 100644
index 0000000000..2dc6853b72
--- /dev/null
+++ b/coverage/crystallization/Gradient.cpp.gcov.html
@@ -0,0 +1,243 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Gradient.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Gradient.cpp<span style="font-size: 80%;"> (source / <a href="Gradient.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Gradient.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace crystallization {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC MCOLVARF GRADIENT</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculate the gradient of the average value of a multicolvar value</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This command allows you to calculate the collective variable discussed in \cite fede-grad.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The input below calculates the gradient of the density of atoms in the manner</a>
+<a name="39"><span class="lineNum">      39 </span>            : described in \cite fede-grad in order to detect whether or not atoms are distributed</a>
+<a name="40"><span class="lineNum">      40 </span>            : uniformly along the x-axis of the simulation cell.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : d1: DENSITY SPECIES=1-50</a>
+<a name="44"><span class="lineNum">      44 </span>            : s1: GRADIENT ORIGIN=1 DATA=d1 DIR=x NBINS=4 SIGMA=1.0</a>
+<a name="45"><span class="lineNum">      45 </span>            : PRINT ARG=s1 FILE=colvar</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The input below calculates the coordination numbers of the 50 atoms in the simulation cell.</a>
+<a name="49"><span class="lineNum">      49 </span>            : The gradient of this quantity is then evaluated in the manner described using the equation above</a>
+<a name="50"><span class="lineNum">      50 </span>            : to detect whether the average values of the coordination number are uniformly distributed along the</a>
+<a name="51"><span class="lineNum">      51 </span>            : x-axis of the simulation cell.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : d2: COORDINATIONNUMBER SPECIES=1-50 SWITCH={RATIONAL R_0=2.0} MORE_THAN={EXP R_0=4.0}</a>
+<a name="55"><span class="lineNum">      55 </span>            : s2: GRADIENT ORIGIN=1 DATA=d2 DIR=x NBINS=4 SIGMA=1.0</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=s2 FILE=colvar</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : */</a>
+<a name="60"><span class="lineNum">      60 </span>            : //+ENDPLUMEDOC</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Gradient,&quot;GRADIENT&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 : void Gradient::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          4 :   VolumeGradientBase::registerKeywords( keys );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;ORIGIN&quot;,&quot;we will use the position of this atom as the origin in our calculation&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;DIR&quot;,&quot;xyz&quot;,&quot;the directions in which we are calculating the gradient.  Should be x, y, z, xy, xz, yz or xyz&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;NBINS&quot;,&quot;number of bins to use in each direction for the calculation of the gradient&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;1.0&quot;,&quot;the width of the function to be used for kernel density estimation&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;KERNEL&quot;,&quot;gaussian&quot;,&quot;the type of kernel function to be used&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          4 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 : Gradient::Gradient(const ActionOptions&amp;ao):</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   Action(ao),</a>
+<a name="75"><span class="lineNum">      75 </span>            :   VolumeGradientBase(ao),</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          2 :   nbins(3)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : {</a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          4 :   parseAtomList(&quot;ORIGIN&quot;,atom);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          2 :   if( atom.size()!=1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          2 :   log.printf(&quot;  origin is at position of atom : %d\n&quot;,atom[0].serial() );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   std::string direction; parse(&quot;DIR&quot;,direction);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :   std::vector&lt;unsigned&gt; tbins; parseVector(&quot;NBINS&quot;,tbins);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;tbins.size(); ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :     if( tbins[i]&lt;2 ) error(&quot;Number of grid points should be greater than 1&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 :   if( direction==&quot;x&quot; ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          2 :     if( tbins.size()!=1 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :     nbins[0]=tbins[0]; nbins[1]=0; nbins[2]=0;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :   } else if( direction==&quot;y&quot; ) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     if( tbins.size()!=1 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     nbins[0]=0; nbins[1]=tbins[0]; nbins[2]=0;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   } else if( direction==&quot;z&quot; ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     if( tbins.size()!=1 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     nbins[0]=0; nbins[1]=0; nbins[2]=tbins[0];</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   } else if( direction==&quot;xy&quot; ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     if( tbins.size()!=2 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     nbins[0]=tbins[0]; nbins[1]=tbins[1]; nbins[2]=0;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   } else if( direction==&quot;xz&quot; ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :     if( tbins.size()!=2 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     nbins[0]=tbins[0]; nbins[1]=0; nbins[2]=tbins[1];</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   } else if( direction==&quot;yz&quot; ) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :     if( tbins.size()!=2 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     nbins[0]=0; nbins[1]=tbins[0]; nbins[2]=tbins[1];</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   } else if( direction==&quot;xyz&quot; ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     if( tbins.size()!=3 ) error(&quot;mismatch between number of bins and direction&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     nbins[0]=tbins[0]; nbins[1]=tbins[1]; nbins[2]=tbins[2];</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   } else {</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     error( direction + &quot; is not valid gradient direction&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   // Find number of quantities</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   if( getPntrToMultiColvar()-&gt;isDensity() ) vend=2;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :   else if( getPntrToMultiColvar()-&gt;getNumberOfQuantities()==2 ) vend=2;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :   else vend = getPntrToMultiColvar()-&gt;getNumberOfQuantities();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   nquantities = vend + nbins[0] + nbins[1] + nbins[2];</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   // Output some nice information</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   std::string functype=getPntrToMultiColvar()-&gt;getName();</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         27 :   std::transform( functype.begin(), functype.end(), functype.begin(), [](unsigned char c) { return std::tolower(c); } );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :   log.printf(&quot;  calculating gradient of %s in %s direction \n&quot;,functype.c_str(), direction.c_str() );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          4 :   log&lt;&lt;&quot;  Bibliography:&quot;&lt;&lt;plumed.cite(&quot;Giberti, Tribello and Parrinello, J. Chem. Theory Comput., 9, 2526 (2013)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          4 :   parse(&quot;SIGMA&quot;,sigma); parse(&quot;KERNEL&quot;,kerneltype);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :   checkRead(); requestAtoms(atom);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :   // And setup the vessel</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   std::string input; addVessel( &quot;GRADIENT&quot;, input, -1 );</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   // And resize everything</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :   readVesselKeywords();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        232 : void Gradient::setupRegions() {</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : //  if( !getPbc().isOrthorombic() ) error(&quot;cell must be orthorhombic when using gradient&quot;);</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        232 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      11600 : void Gradient::calculateAllVolumes( const unsigned&amp; curr, MultiValue&amp; outvals ) const {</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   // Setup the bead</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      11600 :   HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( kerneltype );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      11600 :   Vector cpos = pbcDistance( getPosition(0), getPntrToMultiColvar()-&gt;getCentralAtomPos( curr ) );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   // Note we use the pbc from base multicolvar so that we get numerical derivatives correct</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      11600 :   Vector oderiv, fpos = (getPntrToMultiColvar()-&gt;getPbc()).realToScaled( cpos );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      11600 :   Vector deriv; unsigned nbase=vend; std::vector&lt;Vector&gt; refder(1); Tensor vir; vir.zero();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      46400 :   for(unsigned idir=0; idir&lt;3; ++idir) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      34800 :     deriv[0]=deriv[1]=deriv[2]=0.0;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      34800 :     double delx = 1.0 / static_cast&lt;double&gt;( nbins[idir] );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      81200 :     for(unsigned jbead=0; jbead&lt;nbins[idir]; ++jbead) {</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :       // Calculate what box we are in</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      46400 :       bead.set( -0.5+jbead*delx, -0.5+(jbead+1)*delx, sigma );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      46400 :       double weight=bead.calculate( fpos[0], deriv[idir] );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      46400 :       oderiv = (getPntrToMultiColvar()-&gt;getPbc()).realToScaled( deriv );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :       // Set and derivatives</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      46400 :       refder[0]=-oderiv; // vir = -Tensor(cpos,oderiv);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      46400 :       setNumberInVolume( nbase+jbead, curr, weight, oderiv, vir, refder, outvals );</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : //          addReferenceAtomDerivatives( nbase+jbead, 0, -oderiv );</a>
+<a name="160"><span class="lineNum">     160 </span>            : //          addBoxDerivatives( nbase+jbead, -Tensor(cpos,oderiv) );</a>
+<a name="161"><span class="lineNum">     161 </span>            :     }</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      34800 :     nbase += nbins[idir];</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      11600 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Gradient.h.func-sort-c.html b/coverage/crystallization/Gradient.h.func-sort-c.html
new file mode 100644
index 0000000000..40f2d928ba
--- /dev/null
+++ b/coverage/crystallization/Gradient.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Gradient.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Gradient.h<span style="font-size: 80%;"> (<a href="Gradient.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Gradient.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.h.gcov.html#51">_ZNK4PLMD15crystallization8Gradient21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">12064</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Gradient.h.func.html b/coverage/crystallization/Gradient.h.func.html
new file mode 100644
index 0000000000..e3f02e4d63
--- /dev/null
+++ b/coverage/crystallization/Gradient.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Gradient.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Gradient.h<span style="font-size: 80%;"> (<a href="Gradient.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Gradient.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Gradient.h.gcov.html#51">_ZNK4PLMD15crystallization8Gradient21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">12064</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Gradient.h.gcov.html b/coverage/crystallization/Gradient.h.gcov.html
new file mode 100644
index 0000000000..7c1e91e64d
--- /dev/null
+++ b/coverage/crystallization/Gradient.h.gcov.html
@@ -0,0 +1,135 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Gradient.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Gradient.h<span style="font-size: 80%;"> (source / <a href="Gradient.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_crystallization_Gradient_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_crystallization_Gradient_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/VolumeGradientBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace crystallization {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class Gradient : public multicolvar::VolumeGradientBase {</a>
+<a name="31"><span class="lineNum">      31 </span>            :   friend class GradientVessel;</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// The value of sigma</a>
+<a name="34"><span class="lineNum">      34 </span>            :   double sigma;</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// Number of quantities in use in this colvar</a>
+<a name="36"><span class="lineNum">      36 </span>            :   unsigned vend, nquantities;</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Number of bins in each direction</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::vector&lt;unsigned&gt; nbins;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// The type of kernel for the histogram</a>
+<a name="40"><span class="lineNum">      40 </span>            :   std::string kerneltype;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit Gradient(const ActionOptions&amp;);</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Get the number of quantities that are calculated each time</a>
+<a name="45"><span class="lineNum">      45 </span>            :   virtual unsigned getNumberOfQuantities() const ;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Check on pbc - is it orthorhombic</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void setupRegions();</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Calculate whats in the volume</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void calculateAllVolumes( const unsigned&amp; curr, MultiValue&amp; outvals ) const ;</a>
+<a name="50"><span class="lineNum">      50 </span>            : };</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : inline</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      12064 : unsigned Gradient::getNumberOfQuantities() const {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      12064 :   return nquantities;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+<a name="59"><span class="lineNum">      59 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/GradientVessel.cpp.func-sort-c.html b/coverage/crystallization/GradientVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3f91e20923
--- /dev/null
+++ b/coverage/crystallization/GradientVessel.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/GradientVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - GradientVessel.cpp<span style="font-size: 80%;"> (<a href="GradientVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryMed">84.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GradientVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#45">_ZN4PLMD15crystallization12_GLOBAL__N_124GradientVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#47">_ZN4PLMD15crystallization14GradientVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#85">_ZN4PLMD15crystallization14GradientVessel16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#56">_ZN4PLMD15crystallization14GradientVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#89">_ZN4PLMD15crystallization14GradientVessel6resizeEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#119">_ZN4PLMD15crystallization14GradientVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">232</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#45">_ZN4PLMD15crystallization12_GLOBAL__N_124GradientVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#45">_ZN4PLMD15crystallization12_GLOBAL__N_124GradientVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#51">_ZN4PLMD15crystallization14GradientVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#99">_ZNK4PLMD15crystallization14GradientVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">11600</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/GradientVessel.cpp.func.html b/coverage/crystallization/GradientVessel.cpp.func.html
new file mode 100644
index 0000000000..1465485737
--- /dev/null
+++ b/coverage/crystallization/GradientVessel.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/GradientVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - GradientVessel.cpp<span style="font-size: 80%;"> (<a href="GradientVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryMed">84.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GradientVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#45">_ZN4PLMD15crystallization12_GLOBAL__N_124GradientVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#45">_ZN4PLMD15crystallization12_GLOBAL__N_124GradientVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#45">_ZN4PLMD15crystallization12_GLOBAL__N_124GradientVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#51">_ZN4PLMD15crystallization14GradientVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#47">_ZN4PLMD15crystallization14GradientVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#85">_ZN4PLMD15crystallization14GradientVessel16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#119">_ZN4PLMD15crystallization14GradientVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">232</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#89">_ZN4PLMD15crystallization14GradientVessel6resizeEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#56">_ZN4PLMD15crystallization14GradientVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GradientVessel.cpp.gcov.html#99">_ZNK4PLMD15crystallization14GradientVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">11600</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/GradientVessel.cpp.gcov.html b/coverage/crystallization/GradientVessel.cpp.gcov.html
new file mode 100644
index 0000000000..a4d025d911
--- /dev/null
+++ b/coverage/crystallization/GradientVessel.cpp.gcov.html
@@ -0,0 +1,268 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/GradientVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - GradientVessel.cpp<span style="font-size: 80%;"> (source / <a href="GradientVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntryMed">84.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;vesselbase/VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/ActionVolume.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Gradient.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace crystallization {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class GradientVessel : public vesselbase::FunctionVessel {</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   bool isdens;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   size_t nweights, ncomponents;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::vector&lt;unsigned&gt; starts;</a>
+<a name="37"><span class="lineNum">      37 </span>            : public:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit GradientVessel( const vesselbase::VesselOptions&amp; da );</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::string value_descriptor();</a>
+<a name="42"><span class="lineNum">      42 </span>            :   void resize();</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const ;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer );</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      12506 : PLUMED_REGISTER_VESSEL(GradientVessel,&quot;GRADIENT&quot;)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          2 : void GradientVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 :   vesselbase::FunctionVessel::registerKeywords(keys);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          2 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       4168 : void GradientVessel::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;GRADIENT&quot;,&quot;calculate the gradient&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;gradient&quot;,&quot;GRADIENT&quot;,&quot;the gradient&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       4168 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          2 : GradientVessel::GradientVessel( const vesselbase::VesselOptions&amp; da ) :</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          2 :   FunctionVessel(da)</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 :   Gradient* vg=dynamic_cast&lt;Gradient*&gt;( getAction() );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :   plumed_assert( vg ); isdens=(vg-&gt;getPntrToMultiColvar())-&gt;isDensity();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :   nweights = vg-&gt;nbins[0] + vg-&gt;nbins[1] + vg-&gt;nbins[2];</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          2 :   if( (vg-&gt;getPntrToMultiColvar())-&gt;getNumberOfQuantities()&gt;2 ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :     ncomponents = (vg-&gt;getPntrToMultiColvar())-&gt;getNumberOfQuantities() - 2;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   } else {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 :     ncomponents = 1;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          2 :   starts.push_back(0);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 :   if( vg-&gt;nbins[0]&gt;0 ) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          2 :     starts.push_back( vg-&gt;nbins[0] );</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 :     if( vg-&gt;nbins[1]&gt;0 ) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :       starts.push_back( vg-&gt;nbins[0] + vg-&gt;nbins[1] );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :       if( vg-&gt;nbins[2]&gt;0 ) starts.push_back( nweights );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          2 :     } else if( vg-&gt;nbins[2]&gt;0 ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :       starts.push_back( nweights );</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :     }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   } else if( vg-&gt;nbins[1]&gt;0 ) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :     starts.push_back( vg-&gt;nbins[1] );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :     if( vg-&gt;nbins[2]&gt;0 ) starts.push_back( nweights );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   } else if( vg-&gt;nbins[2]&gt;0 ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     starts.push_back( nweights );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 : std::string GradientVessel::value_descriptor() {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :   return &quot;the gradient&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 : void GradientVessel::resize() {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          4 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :     unsigned nder=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :     resizeBuffer( (1+nder)*(ncomponents+1)*nweights );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :     getFinalValue()-&gt;resizeDerivatives( nder );</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   } else {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :     resizeBuffer( (ncomponents+1)*nweights );</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          4 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      11600 : void GradientVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   unsigned nder;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      11600 :   if( getAction()-&gt;derivativesAreRequired() ) nder=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   else nder=0;</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      11600 :   unsigned wstart, cstart; if( ncomponents==1 ) { cstart=1; wstart=2; } else { cstart=2; wstart=2+ncomponents; }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      58000 :   for(unsigned iw=0; iw&lt;nweights; ++iw) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      46400 :     unsigned xx = (ncomponents+1)*iw;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      46400 :     double weight=myvals.get(wstart+iw);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      46400 :     buffer[bufstart+xx*(nder+1)] += weight;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      46400 :     myvals.chainRule( wstart + iw, xx, 1, 0, 1.0, bufstart, buffer );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      92800 :     for(unsigned jc=0; jc&lt;ncomponents; ++jc) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      46400 :       double colvar=myvals.get( cstart + jc );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      46400 :       buffer[bufstart+(xx+1+jc)*(nder+1) ] += weight*colvar;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      46400 :       myvals.chainRule( cstart + jc, xx + 1 + jc, 1, 0, weight, bufstart, buffer );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      46400 :       myvals.chainRule( wstart + iw, xx + 1 + jc, 1, 0, colvar, bufstart, buffer );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      11600 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        232 : void GradientVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        232 :   std::vector&lt;double&gt; val_interm( ncomponents*nweights );</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   unsigned nder;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        232 :   if( getAction()-&gt;derivativesAreRequired() ) nder=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   else nder=0;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        232 :   Matrix&lt;double&gt; der_interm( ncomponents*nweights, nder ); der_interm=0;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        232 :   if( isdens ) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        580 :     for(unsigned iw=0; iw&lt;nweights; ++iw) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        464 :       val_interm[iw] = buffer[bufstart + 2*iw*(1+nder)];</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        464 :       if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        464 :         unsigned wstart = bufstart + 2*iw*(nder+1) + 1;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      75632 :         for(unsigned jder=0; jder&lt;nder; ++jder) der_interm( iw, jder ) += buffer[ wstart + jder ];</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :       }</a>
+<a name="135"><span class="lineNum">     135 </span>            :     }</a>
+<a name="136"><span class="lineNum">     136 </span>            :   } else {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        580 :     for(unsigned iw=0; iw&lt;nweights; ++iw) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        464 :       unsigned xx = (ncomponents+1)*iw;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        464 :       double ww=buffer[bufstart + xx*(1+nder)];</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        928 :       for(unsigned jc=0; jc&lt;ncomponents; ++jc) val_interm[ iw*ncomponents + jc ] = buffer[bufstart + (xx+1+jc)*(1+nder)] / ww;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        464 :       if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        464 :         unsigned wstart = bufstart + xx*(nder+1) + 1;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        928 :         for(unsigned jc=0; jc&lt;ncomponents; ++jc) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        464 :           unsigned bstart = bufstart + ( xx + 1 + jc )*(nder+1) + 1;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        464 :           double val = buffer[bufstart + (nder+1)*(xx+1+jc)];</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      75632 :           for(unsigned jder=0; jder&lt;nder; ++jder)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      75168 :             der_interm( iw*ncomponents + jc, jder ) = (1.0/ww)*buffer[bstart + jder] - (val/(ww*ww))*buffer[wstart + jder];</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :         }</a>
+<a name="149"><span class="lineNum">     149 </span>            :       }</a>
+<a name="150"><span class="lineNum">     150 </span>            :     }</a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   double tmp, diff2=0.0;</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        232 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     Value* fval=getFinalValue();</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        464 :     for(unsigned j=0; j&lt;starts.size()-1; ++j) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1160 :       for(unsigned bin=starts[j]; bin&lt;starts[j+1]; ++bin) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       1856 :         for(unsigned jc=0; jc&lt;ncomponents; ++jc) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        928 :           if( bin==starts[j] ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        232 :             tmp=val_interm[(starts[j+1]-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      37816 :             for(unsigned jder=0; jder&lt;nder; ++jder) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      37584 :               fval-&gt;addDerivative( jder, +2.0*tmp*der_interm( (starts[j+1]-1)*ncomponents + jc, jder) );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      37584 :               fval-&gt;addDerivative( jder, -2.0*tmp*der_interm( bin*ncomponents + jc, jder ) );</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :             }</a>
+<a name="166"><span class="lineNum">     166 </span>            :           } else {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        696 :             tmp=val_interm[(bin-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">     113448 :             for(unsigned jder=0; jder&lt;nder; ++jder) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     112752 :               fval-&gt;addDerivative( jder, +2.0*tmp*der_interm( (bin-1)*ncomponents + jc, jder) );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     112752 :               fval-&gt;addDerivative( jder, -2.0*tmp*der_interm( bin*ncomponents + jc, jder ) );</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :             }</a>
+<a name="172"><span class="lineNum">     172 </span>            :           }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        928 :           diff2+=tmp*tmp;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :         }</a>
+<a name="175"><span class="lineNum">     175 </span>            :       }</a>
+<a name="176"><span class="lineNum">     176 </span>            :     }</a>
+<a name="177"><span class="lineNum">     177 </span>            :   } else {</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;starts.size()-1; ++j) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :       for(unsigned bin=starts[j]; bin&lt;starts[j+1]; ++bin) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :         for(unsigned jc=0; jc&lt;ncomponents; ++jc) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :           if( bin==starts[j] ) tmp=val_interm[(starts[j+1]-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :           else tmp=val_interm[(bin-1)*ncomponents + jc] - val_interm[bin*ncomponents + jc];</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :           diff2+=tmp*tmp;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :         }</a>
+<a name="185"><span class="lineNum">     185 </span>            :       }</a>
+<a name="186"><span class="lineNum">     186 </span>            :     }</a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span>            :   setOutputValue( diff2 );</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        232 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/InterMolecularTorsions.cpp.func-sort-c.html b/coverage/crystallization/InterMolecularTorsions.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5d32eca20d
--- /dev/null
+++ b/coverage/crystallization/InterMolecularTorsions.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/InterMolecularTorsions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - InterMolecularTorsions.cpp<span style="font-size: 80%;"> (<a href="InterMolecularTorsions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">30.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="InterMolecularTorsions.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#94">_ZN4PLMD15crystallization12_GLOBAL__N_134InterMolecularTorsionsRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#90">_ZN4PLMD15crystallization22InterMolecularTorsions10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#91">_ZN4PLMD15crystallization22InterMolecularTorsions14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#115">_ZN4PLMD15crystallization22InterMolecularTorsionsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#115">_ZN4PLMD15crystallization22InterMolecularTorsionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#151">_ZNK4PLMD15crystallization22InterMolecularTorsions15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#163">_ZNK4PLMD15crystallization22InterMolecularTorsions7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#96">_ZN4PLMD15crystallization22InterMolecularTorsions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#94">_ZN4PLMD15crystallization12_GLOBAL__N_134InterMolecularTorsionsRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#94">_ZN4PLMD15crystallization12_GLOBAL__N_134InterMolecularTorsionsRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/InterMolecularTorsions.cpp.func.html b/coverage/crystallization/InterMolecularTorsions.cpp.func.html
new file mode 100644
index 0000000000..ae901ad648
--- /dev/null
+++ b/coverage/crystallization/InterMolecularTorsions.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
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+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/InterMolecularTorsions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - InterMolecularTorsions.cpp<span style="font-size: 80%;"> (<a href="InterMolecularTorsions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">30.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="InterMolecularTorsions.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#94">_ZN4PLMD15crystallization12_GLOBAL__N_134InterMolecularTorsionsRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#94">_ZN4PLMD15crystallization12_GLOBAL__N_134InterMolecularTorsionsRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#94">_ZN4PLMD15crystallization12_GLOBAL__N_134InterMolecularTorsionsRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#90">_ZN4PLMD15crystallization22InterMolecularTorsions10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#91">_ZN4PLMD15crystallization22InterMolecularTorsions14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#96">_ZN4PLMD15crystallization22InterMolecularTorsions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#115">_ZN4PLMD15crystallization22InterMolecularTorsionsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#115">_ZN4PLMD15crystallization22InterMolecularTorsionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#151">_ZNK4PLMD15crystallization22InterMolecularTorsions15calculateWeightERKjRKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterMolecularTorsions.cpp.gcov.html#163">_ZNK4PLMD15crystallization22InterMolecularTorsions7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/InterMolecularTorsions.cpp.gcov.html b/coverage/crystallization/InterMolecularTorsions.cpp.gcov.html
new file mode 100644
index 0000000000..b19d3947b9
--- /dev/null
+++ b/coverage/crystallization/InterMolecularTorsions.cpp.gcov.html
@@ -0,0 +1,269 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/InterMolecularTorsions.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - InterMolecularTorsions.cpp<span style="font-size: 80%;"> (source / <a href="InterMolecularTorsions.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">30.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC MCOLVARF INTERMOLECULARTORSIONS</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculate torsion angles between vectors on adjacent molecules</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This variable can be used to calculate the average torsional angles between vectors.  In other words,</a>
+<a name="36"><span class="lineNum">      36 </span>            : it can be used to compute quantities like this:</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : s = \frac{ \sum_{i \ne j} \sigma(r_{ij}) \theta_{ij} }{ \sum_{i \ne j} \sigma(r_{ij}) }</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f]</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Here the sums run over all pairs of molecules. \f$\sigma(r_{ij})\f$ is a \ref switchingfunction that</a>
+<a name="43"><span class="lineNum">      43 </span>            : action on the distance between the centers of molecules \f$i\f$ and \f$j\f$.  \f$\theta_{ij}\f$ is then</a>
+<a name="44"><span class="lineNum">      44 </span>            : the torsional angle between an orientation vector for molecule \f$i\f$ and molecule \f$j\f$.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : This command can be used to calculate the intermolecular torsional angles between the orientations of nearby molecules.  The orientation of a</a>
+<a name="47"><span class="lineNum">      47 </span>            : molecule can be calculated by using either the \ref MOLECULES or the \ref PLANES commands.  These two commands calculate the orientation of a</a>
+<a name="48"><span class="lineNum">      48 </span>            : bond in the molecule or the orientation of a plane containing three of the molecule's atoms.  Furthermore, when we use these commands we think of</a>
+<a name="49"><span class="lineNum">      49 </span>            : molecules as objects that lie at a point in space and that have an orientation.   This command calculates the torsional angles between the orientations</a>
+<a name="50"><span class="lineNum">      50 </span>            : of these objects.  We can then calculates functions of a large number of these torsional angles that measures things such as the number of torsional</a>
+<a name="51"><span class="lineNum">      51 </span>            : angles that are within a particular range.  Because it is often useful to only consider the torsional angles between objects that are within a certain</a>
+<a name="52"><span class="lineNum">      52 </span>            : distance of each other we can, when calculating these sums, perform a weighted sum and use a \ref switchingfunction to ensure that we focus on molecules</a>
+<a name="53"><span class="lineNum">      53 </span>            : that are close together.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \par Examples</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : The example input below is necessarily but gives you an idea of what can be achieved using this action.</a>
+<a name="58"><span class="lineNum">      58 </span>            : The orientations and positions of four molecules are defined using the \ref MOLECULES action as the position of the</a>
+<a name="59"><span class="lineNum">      59 </span>            : centers of mass of the two atoms specified and the direction of the vector connecting the two atoms that were specified.</a>
+<a name="60"><span class="lineNum">      60 </span>            : The torsional angles between the molecules are then calculated by the \ref INTERMOLECULARTORSIONS command labelled torsion_p.</a>
+<a name="61"><span class="lineNum">      61 </span>            : We then compute a \ref HISTOGRAM that shows the distribution that these torsional angles take in the structure.  The weight</a>
+<a name="62"><span class="lineNum">      62 </span>            : a given torsional angle contributes to this \ref HISTOGRAM is determined using a \ref switchingfunction that acts on the distance</a>
+<a name="63"><span class="lineNum">      63 </span>            : between the two molecules.  As such the torsional angles between molecules that are close together contribute a high weight to the</a>
+<a name="64"><span class="lineNum">      64 </span>            : histogram while the torsional angles between molecules that are far apart does not contribute to the histogram.  The histogram is</a>
+<a name="65"><span class="lineNum">      65 </span>            : averaged over the whole trajectory and output once all the trajectory frames have been read.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \plumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : m1: MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8</a>
+<a name="69"><span class="lineNum">      69 </span>            : torsion_p: INTERMOLECULARTORSIONS MOLS=m1 SWITCH={RATIONAL R_0=0.25 D_0=2.0 D_MAX=3.0}</a>
+<a name="70"><span class="lineNum">      70 </span>            : htt_p: HISTOGRAM DATA=torsion_p GRID_MIN=-pi GRID_MAX=pi BANDWIDTH=0.1 GRID_BIN=200 STRIDE=1</a>
+<a name="71"><span class="lineNum">      71 </span>            : DUMPGRID GRID=htt_p FILE=myhist.out</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : */</a>
+<a name="75"><span class="lineNum">      75 </span>            : //+ENDPLUMEDOC</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : namespace PLMD {</a>
+<a name="78"><span class="lineNum">      78 </span>            : namespace crystallization {</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : class InterMolecularTorsions : public multicolvar::MultiColvarBase {</a>
+<a name="81"><span class="lineNum">      81 </span>            : private:</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// The switching function that tells us if atoms are close enough together</a>
+<a name="83"><span class="lineNum">      83 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="86"><span class="lineNum">      86 </span>            :   explicit InterMolecularTorsions(const ActionOptions&amp;);</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Do the stuff with the switching functions</a>
+<a name="88"><span class="lineNum">      88 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Actually do the calculation</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Is the variable periodic</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :   bool isPeriodic() { return true; }</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   void retrieveDomain( std::string&amp; min, std::string&amp; max ) { min=&quot;-pi&quot;; max=&quot;+pi&quot;; }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(InterMolecularTorsions,&quot;INTERMOLECULARTORSIONS&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 : void InterMolecularTorsions::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          4 :   keys.add(&quot;atoms&quot;,&quot;MOLS&quot;,&quot;The molecules you would like to calculate the torsional angles between. This should be the label/s of \\ref MOLECULES or \\ref PLANES actions&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :   keys.add(&quot;atoms-1&quot;,&quot;MOLSA&quot;,&quot;In this version of the input the torsional angles between all pairs of atoms including one atom from MOLSA one atom from MOLSB will be computed. &quot;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :            &quot;This should be the label/s of \\ref MOLECULES or \\ref PLANES actions&quot;);</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 :   keys.add(&quot;atoms-1&quot;,&quot;MOLSB&quot;,&quot;In this version of the input the torsional angles between all pairs of atoms including one atom from MOLSA one atom from MOLSB will be computed. &quot;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :            &quot;This should be the label/s of \\ref MOLECULES or \\ref PLANES actions&quot;);</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="111"><span class="lineNum">     111 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="112"><span class="lineNum">     112 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   keys.remove(&quot;LOWMEM&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          4 :   keys.addFlag(&quot;LOWMEM&quot;,false,&quot;lower the memory requirements&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 : InterMolecularTorsions::InterMolecularTorsions(const ActionOptions&amp; ao):</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   Action(ao),</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   MultiColvarBase(ao)</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     if( getBaseMultiColvar(i)-&gt;getNumberOfQuantities()!=5 ) error(&quot;input multicolvar does not calculate molecular orientations&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span>            :   // The weight of this does have derivatives</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   weightHasDerivatives=true;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // Read in the switching function</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :   if(sw.length()&gt;0) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     switchingFunction.set(sw,errors);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   } else {</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   log.printf(&quot;  calculating number of links with atoms separation of %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   std::vector&lt;AtomNumber&gt; all_atoms; readTwoGroups( &quot;MOLS&quot;, &quot;MOLSA&quot;, &quot;MOLSB&quot;, all_atoms );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   setupMultiColvarBase( all_atoms ); setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     if( !getBaseMultiColvar(i)-&gt;hasDifferentiableOrientation() ) error(&quot;cannot use multicolvar of type &quot; + getBaseMultiColvar(i)-&gt;getName() );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Create holders for the collective variable</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   readVesselKeywords();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   plumed_assert( getNumberOfVessels()==0 );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   std::string input; addVessel( &quot;SUM&quot;, input, -1 );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   readVesselKeywords();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 : double InterMolecularTorsions::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :   double dfunc, sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 0, 0, (-dfunc)*weight*distance, myatoms );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 0, 1, (dfunc)*weight*distance, myatoms );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     myatoms.addBoxDerivatives( 0, (-dfunc)*weight*Tensor(distance,distance) );</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :   return sw;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : double InterMolecularTorsions::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   Vector v1, v2, dv1, dv2, dconn, conn = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   // Retrieve vectors</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; orient0( 5 ), orient1( 5 );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :   getInputData( 0, true, myatoms, orient0 );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   getInputData( 1, true, myatoms, orient1 );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;3; ++i) { v1[i]=orient0[2+i]; v2[i]=orient1[2+i]; }</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   if( getBaseMultiColvar(0)-&gt;getNumberOfQuantities()&lt;3 ) return 1.0;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   // Evaluate angle</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :   Torsion t; double angle = t.compute( v1, conn, v2, dv1, dconn, dv2 );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;3; ++i) { orient0[i+2]=dv1[i]; orient1[i+2]=dv2[i]; }</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   // And accumulate derivatives</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     MultiValue&amp; myder0=getInputDerivatives( 0, true, myatoms );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     mergeInputDerivatives( 1, 2, orient1.size(), 0, orient0, myder0, myatoms );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     MultiValue&amp; myder1=getInputDerivatives( 1, true, myatoms );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :     mergeInputDerivatives( 1, 2, orient0.size(), 1, orient1, myder1, myatoms );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 1, 0, -dconn, myatoms ); addAtomDerivatives( 1, 1, dconn, myatoms );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     myatoms.addBoxDerivatives( 1, -extProduct( conn, dconn ) );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   return angle;</a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/LocalSteinhardt.h.func-sort-c.html b/coverage/crystallization/LocalSteinhardt.h.func-sort-c.html
new file mode 100644
index 0000000000..47bc84b7f2
--- /dev/null
+++ b/coverage/crystallization/LocalSteinhardt.h.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/LocalSteinhardt.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - LocalSteinhardt.h<span style="font-size: 80%;"> (<a href="LocalSteinhardt.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryLo">72.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LocalSteinhardt.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#33">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q3EEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#33">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q4EEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#48">_ZNK4PLMD15crystallization15LocalSteinhardtINS0_2Q3EE21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#48">_ZNK4PLMD15crystallization15LocalSteinhardtINS0_2Q4EE21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#30">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q3EE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#30">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q4EE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#33">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q6EEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#30">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q6EE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#48">_ZNK4PLMD15crystallization15LocalSteinhardtINS0_2Q6EE21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnHi">43186</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/LocalSteinhardt.h.func.html b/coverage/crystallization/LocalSteinhardt.h.func.html
new file mode 100644
index 0000000000..4b432953ef
--- /dev/null
+++ b/coverage/crystallization/LocalSteinhardt.h.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/LocalSteinhardt.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - LocalSteinhardt.h<span style="font-size: 80%;"> (<a href="LocalSteinhardt.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryLo">72.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LocalSteinhardt.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#30">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q3EE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#33">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q3EEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#30">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q4EE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#33">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q4EEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#30">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q6EE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#33">_ZN4PLMD15crystallization15LocalSteinhardtINS0_2Q6EEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#48">_ZNK4PLMD15crystallization15LocalSteinhardtINS0_2Q3EE21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#48">_ZNK4PLMD15crystallization15LocalSteinhardtINS0_2Q4EE21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalSteinhardt.h.gcov.html#48">_ZNK4PLMD15crystallization15LocalSteinhardtINS0_2Q6EE21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESC_RS5_RSA_SE_</a></td>
+              <td class="coverFnHi">43186</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/LocalSteinhardt.h.gcov.html b/coverage/crystallization/LocalSteinhardt.h.gcov.html
new file mode 100644
index 0000000000..ef6e1909a1
--- /dev/null
+++ b/coverage/crystallization/LocalSteinhardt.h.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/LocalSteinhardt.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - LocalSteinhardt.h<span style="font-size: 80%;"> (source / <a href="LocalSteinhardt.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryLo">72.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_crystallization_LocalSteinhardt_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_crystallization_LocalSteinhardt_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;OrientationSphere.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace crystallization {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : template&lt;class T&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : class LocalSteinhardt : public OrientationSphere {</a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         11 :   static void registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         11 :     OrientationSphere::registerKeywords(keys);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         11 :   }</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          5 :   explicit LocalSteinhardt(const ActionOptions&amp; ao): Action(ao), OrientationSphere(ao)</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   {</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         12 :     for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">          7 :       T* mc=dynamic_cast&lt;T*&gt;( getBaseMultiColvar(i) );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          7 :       if(!mc) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :         if( getBaseMultiColvar(i)-&gt;getNumberOfBaseMultiColvars()==0 ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :           error(&quot;input action is not calculating the correct vectors&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :         }</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;getBaseMultiColvar(i)-&gt;getNumberOfBaseMultiColvars(); ++j) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :           T* mmc=dynamic_cast&lt;T*&gt;( getBaseMultiColvar(i)-&gt;getBaseMultiColvar(j) );</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 :           if( !mmc ) error(&quot;input action is not calculating the correct vectors&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :         }</a>
+<a name="47"><span class="lineNum">      47 </span>            :       }</a>
+<a name="48"><span class="lineNum">      48 </span>            :     }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          5 :   }</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      43186 :   double computeVectorFunction( const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :                                 Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const override {</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      43186 :     double dot=0; dconn.zero();</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">    1166022 :     for(unsigned k=2; k&lt;vec1.size(); ++k) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">    1122836 :       dot+=vec1[k]*vec2[k]; dvec1[k]=vec2[k]; dvec2[k]=vec1[k];</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      43186 :     return dot;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span>            : };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : }</a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/MoleculeOrientation.cpp.func-sort-c.html b/coverage/crystallization/MoleculeOrientation.cpp.func-sort-c.html
new file mode 100644
index 0000000000..15eb93f749
--- /dev/null
+++ b/coverage/crystallization/MoleculeOrientation.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/MoleculeOrientation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - MoleculeOrientation.cpp<span style="font-size: 80%;"> (<a href="MoleculeOrientation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MoleculeOrientation.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization19MoleculeOrientationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#91">_ZNK4PLMD15crystallization19MoleculeOrientation29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#62">_ZN4PLMD15crystallization12_GLOBAL__N_131MoleculeOrientationRegisterMe646createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization19MoleculeOrientationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#64">_ZN4PLMD15crystallization19MoleculeOrientation16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#62">_ZN4PLMD15crystallization12_GLOBAL__N_131MoleculeOrientationRegisterMe64C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#62">_ZN4PLMD15crystallization12_GLOBAL__N_131MoleculeOrientationRegisterMe64D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#129">_ZNK4PLMD15crystallization19MoleculeOrientation26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">4992</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#97">_ZNK4PLMD15crystallization19MoleculeOrientation15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">16584</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#118">_ZNK4PLMD15crystallization19MoleculeOrientation15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1041228</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/MoleculeOrientation.cpp.func.html b/coverage/crystallization/MoleculeOrientation.cpp.func.html
new file mode 100644
index 0000000000..9ed8adabb2
--- /dev/null
+++ b/coverage/crystallization/MoleculeOrientation.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/MoleculeOrientation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - MoleculeOrientation.cpp<span style="font-size: 80%;"> (<a href="MoleculeOrientation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MoleculeOrientation.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#62">_ZN4PLMD15crystallization12_GLOBAL__N_131MoleculeOrientationRegisterMe646createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#62">_ZN4PLMD15crystallization12_GLOBAL__N_131MoleculeOrientationRegisterMe64C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#62">_ZN4PLMD15crystallization12_GLOBAL__N_131MoleculeOrientationRegisterMe64D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#64">_ZN4PLMD15crystallization19MoleculeOrientation16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization19MoleculeOrientationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#73">_ZN4PLMD15crystallization19MoleculeOrientationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#97">_ZNK4PLMD15crystallization19MoleculeOrientation15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">16584</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#118">_ZNK4PLMD15crystallization19MoleculeOrientation15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1041228</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#129">_ZNK4PLMD15crystallization19MoleculeOrientation26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">4992</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculeOrientation.cpp.gcov.html#91">_ZNK4PLMD15crystallization19MoleculeOrientation29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/MoleculeOrientation.cpp.gcov.html b/coverage/crystallization/MoleculeOrientation.cpp.gcov.html
new file mode 100644
index 0000000000..532bf51a75
--- /dev/null
+++ b/coverage/crystallization/MoleculeOrientation.cpp.gcov.html
@@ -0,0 +1,227 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/MoleculeOrientation.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - MoleculeOrientation.cpp<span style="font-size: 80%;"> (source / <a href="MoleculeOrientation.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace crystallization {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC MCOLVAR MOLECULES</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate the vectors connecting a pair of atoms in order to represent the orientation of a molecule.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : At its simplest this command can be used to calculate the average length of an internal vector in a</a>
+<a name="33"><span class="lineNum">      33 </span>            : collection of different molecules.  When used in conjunction with MutiColvarFunctions in can be used</a>
+<a name="34"><span class="lineNum">      34 </span>            : to do a variety of more complex tasks.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input tells plumed to calculate the distances between two of the atoms in a molecule.</a>
+<a name="39"><span class="lineNum">      39 </span>            : This is done for the same set of atoms four different molecules and the average separation is then</a>
+<a name="40"><span class="lineNum">      40 </span>            : calculated.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : MOLECULES MOL1=1,2 MOL2=3,4 MOL3=5,6 MOL4=7,8 MEAN LABEL=mm</a>
+<a name="44"><span class="lineNum">      44 </span>            : PRINT ARG=mm.mean FILE=colvar</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : */</a>
+<a name="49"><span class="lineNum">      49 </span>            : //+ENDPLUMEDOC</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : class MoleculeOrientation : public VectorMultiColvar {</a>
+<a name="53"><span class="lineNum">      53 </span>            : private:</a>
+<a name="54"><span class="lineNum">      54 </span>            :   unsigned nvectors;</a>
+<a name="55"><span class="lineNum">      55 </span>            : public:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="57"><span class="lineNum">      57 </span>            :   explicit MoleculeOrientation( const ActionOptions&amp; ao );</a>
+<a name="58"><span class="lineNum">      58 </span>            :   AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned&amp; iatom ) const override;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   void normalizeVector( std::vector&lt;double&gt;&amp; vals ) const override;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   void normalizeVectorDerivatives( MultiValue&amp; myvals ) const override;</a>
+<a name="62"><span class="lineNum">      62 </span>            : };</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(MoleculeOrientation,&quot;MOLECULES&quot;)</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          6 : void MoleculeOrientation::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         12 :   VectorMultiColvar::registerKeywords( keys ); keys.use(&quot;MEAN&quot;); keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;MOL&quot;,&quot;The numerical indices of the atoms in the molecule. The orientation of the molecule is equal to &quot;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :            &quot;the vector connecting the first two atoms specified.  If a third atom is specified its position &quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :            &quot;is used to specify where the molecule is.  If a third atom is not present the molecule is assumed &quot;</a>
+<a name="71"><span class="lineNum">      71 </span>            :            &quot;to be at the center of the vector connecting the first two atoms.&quot;);</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         12 :   keys.reset_style(&quot;MOL&quot;,&quot;atoms&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          6 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          4 : MoleculeOrientation::MoleculeOrientation( const ActionOptions&amp; ao ):</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   Action(ao),</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          4 :   VectorMultiColvar(ao)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 :   readAtomsLikeKeyword(&quot;MOL&quot;,-1,all_atoms);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 :   nvectors = std::floor( ablocks.size() / 2 );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   if( ablocks.size()%2!=0 &amp;&amp; 2*nvectors+1!=ablocks.size() ) error(&quot;number of atoms in molecule specification is wrong.  Should be two or three.&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 :   if( all_atoms.size()==0 ) error(&quot;No atoms were specified&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :   setVectorDimensionality( 3*nvectors ); setupMultiColvarBase( all_atoms );</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          4 :   if( ablocks.size()==2*nvectors+1  ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          4 :     std::vector&lt;bool&gt; catom_ind(ablocks.size(), false); catom_ind[ablocks.size()-1]=true;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          4 :     setAtomsForCentralAtom( catom_ind );</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : AtomNumber MoleculeOrientation::getAbsoluteIndexOfCentralAtom( const unsigned&amp; iatom ) const {</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   plumed_dbg_assert( iatom&lt;atom_lab.size() );</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   plumed_assert( atom_lab[iatom].first==0 );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   return ActionAtomistic::getAbsoluteIndex( ablocks[0][atom_lab[iatom].second] );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      16584 : void MoleculeOrientation::calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      33168 :   for(unsigned i=0; i&lt;nvectors; ++i) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      16584 :     Vector distance; distance=getSeparation( myatoms.getPosition(2*i+0), myatoms.getPosition(2*i+1) );</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      16584 :     addAtomDerivatives( 2+3*i+0, 2*i+0, Vector(-1.0,0,0), myatoms );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      16584 :     addAtomDerivatives( 2+3*i+0, 2*i+1, Vector(+1.0,0,0), myatoms );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      16584 :     myatoms.addBoxDerivatives( 2+3*i+0, Tensor(distance,Vector(-1.0,0,0)) );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      16584 :     myatoms.addValue( 2+3*i+0, distance[0] );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      16584 :     addAtomDerivatives( 2+3*i+1, 2*i+0, Vector(0,-1.0,0), myatoms );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      16584 :     addAtomDerivatives( 2+3*i+1, 2*i+1, Vector(0,+1.0,0), myatoms );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      16584 :     myatoms.addBoxDerivatives( 2+3*i+1, Tensor(distance,Vector(0,-1.0,0)) );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      16584 :     myatoms.addValue( 2+3*i+1, distance[1] );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      16584 :     addAtomDerivatives( 2+3*i+2, 2*i+0, Vector(0,0,-1.0), myatoms );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      16584 :     addAtomDerivatives( 2+3*i+2, 2*i+1, Vector(0,0,+1.0), myatoms );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      16584 :     myatoms.addBoxDerivatives( 2+3*i+2, Tensor(distance,Vector(0,0,-1.0)) );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      16584 :     myatoms.addValue( 2+3*i+2, distance[2] );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      16584 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">    1041228 : void MoleculeOrientation::normalizeVector( std::vector&lt;double&gt;&amp; vals ) const {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    2082456 :   for(unsigned i=0; i&lt;nvectors; ++i) {</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     double norm=0;</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">    4164912 :     for(unsigned j=0; j&lt;3; ++j) norm += vals[2+3*i+j]*vals[2+3*i+j];</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">    1041228 :     norm = sqrt(norm);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">    1041228 :     double inorm = 1.0; if( norm&gt;epsilon ) inorm = 1.0 / norm;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">    4164912 :     for(unsigned j=0; j&lt;3; ++j) vals[2+3*i+j] = inorm*vals[2+3*i+j];</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">    1041228 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       4992 : void MoleculeOrientation::normalizeVectorDerivatives( MultiValue&amp; myvals ) const {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       4992 :   std::vector&lt;double&gt; weight( nvectors ), wdf( nvectors );</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       9984 :   for(unsigned ivec=0; ivec&lt;nvectors; ++ivec) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      19968 :     double v=0; for(unsigned jcomp=0; jcomp&lt;3; ++jcomp) v += myvals.get( 2+3*ivec+jcomp )*myvals.get( 2+3*ivec+jcomp );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       4992 :     v=sqrt(v); weight[ivec]=1.0; wdf[ivec]=1.0;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       4992 :     if( v&gt;epsilon ) { weight[ivec] = 1.0 / v; wdf[ivec] = 1.0 / ( v*v*v ); }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      54672 :   for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      49680 :     unsigned jder=myvals.getActiveIndex(j);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      99360 :     for(unsigned ivec=0; ivec&lt;nvectors; ++ivec) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">     198720 :       double comp2=0.0; for(unsigned jcomp=0; jcomp&lt;3; ++jcomp) comp2 += myvals.get(2+3*ivec+jcomp)*myvals.getDerivative( 2+3*ivec+jcomp, jder );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">     198720 :       for(unsigned jcomp=0; jcomp&lt;3; ++jcomp) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">     149040 :         myvals.setDerivative( 2+3*ivec+jcomp, jder, weight[ivec]*myvals.getDerivative( 2+3*ivec+jcomp, jder ) - wdf[ivec]*comp2*myvals.get(2+3*ivec+jcomp) );</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :       }</a>
+<a name="146"><span class="lineNum">     146 </span>            :     }</a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       4992 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/MoleculePlane.cpp.func-sort-c.html b/coverage/crystallization/MoleculePlane.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1023d0cab5
--- /dev/null
+++ b/coverage/crystallization/MoleculePlane.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/MoleculePlane.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - MoleculePlane.cpp<span style="font-size: 80%;"> (<a href="MoleculePlane.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryLo">73.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MoleculePlane.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#59">_ZN4PLMD15crystallization13MoleculePlaneC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#71">_ZNK4PLMD15crystallization13MoleculePlane29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#46">_ZN4PLMD15crystallization12_GLOBAL__N_125MoleculePlaneRegisterMe486createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#59">_ZN4PLMD15crystallization13MoleculePlaneC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#48">_ZN4PLMD15crystallization13MoleculePlane16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#46">_ZN4PLMD15crystallization12_GLOBAL__N_125MoleculePlaneRegisterMe48C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#46">_ZN4PLMD15crystallization12_GLOBAL__N_125MoleculePlaneRegisterMe48D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#77">_ZNK4PLMD15crystallization13MoleculePlane15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">8888</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/MoleculePlane.cpp.func.html b/coverage/crystallization/MoleculePlane.cpp.func.html
new file mode 100644
index 0000000000..10b8fc8533
--- /dev/null
+++ b/coverage/crystallization/MoleculePlane.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/MoleculePlane.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - MoleculePlane.cpp<span style="font-size: 80%;"> (<a href="MoleculePlane.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryLo">73.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MoleculePlane.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#46">_ZN4PLMD15crystallization12_GLOBAL__N_125MoleculePlaneRegisterMe486createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#46">_ZN4PLMD15crystallization12_GLOBAL__N_125MoleculePlaneRegisterMe48C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#46">_ZN4PLMD15crystallization12_GLOBAL__N_125MoleculePlaneRegisterMe48D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#48">_ZN4PLMD15crystallization13MoleculePlane16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#59">_ZN4PLMD15crystallization13MoleculePlaneC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#59">_ZN4PLMD15crystallization13MoleculePlaneC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#77">_ZNK4PLMD15crystallization13MoleculePlane15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">8888</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoleculePlane.cpp.gcov.html#71">_ZNK4PLMD15crystallization13MoleculePlane29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/MoleculePlane.cpp.gcov.html b/coverage/crystallization/MoleculePlane.cpp.gcov.html
new file mode 100644
index 0000000000..50438e9dc4
--- /dev/null
+++ b/coverage/crystallization/MoleculePlane.cpp.gcov.html
@@ -0,0 +1,226 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/MoleculePlane.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - MoleculePlane.cpp<span style="font-size: 80%;"> (source / <a href="MoleculePlane.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryLo">73.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace crystallization {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC MCOLVAR PLANES</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate the plane perpendicular to two vectors in order to represent the orientation of a planar molecule.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span>            : //+ENDPLUMEDOC</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class MoleculePlane : public VectorMultiColvar {</a>
+<a name="40"><span class="lineNum">      40 </span>            : private:</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit MoleculePlane( const ActionOptions&amp; ao );</a>
+<a name="44"><span class="lineNum">      44 </span>            :   AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned&amp; iatom ) const override;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="46"><span class="lineNum">      46 </span>            : };</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(MoleculePlane,&quot;PLANES&quot;)</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 : void MoleculePlane::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          4 :   VectorMultiColvar::registerKeywords( keys ); keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;MOL&quot;,&quot;The numerical indices of the atoms in the molecule. If three atoms are specified the orientation &quot;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :            &quot;of the molecule is taken as the normal to the plane containing the vector connecting the first and &quot;</a>
+<a name="54"><span class="lineNum">      54 </span>            :            &quot;second atoms and the vector connecting the second and third atoms.  If four atoms are specified the &quot;</a>
+<a name="55"><span class="lineNum">      55 </span>            :            &quot;orientation of the molecule is taken as the normal to the plane containing the vector connecting the &quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            :            &quot;first and second atoms and the vector connecting the third and fourth atoms. The molecule is always &quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            :            &quot;assumed to lie at the geometric center for the three/four atoms.&quot;);</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          8 :   keys.reset_style(&quot;MOL&quot;,&quot;atoms&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          4 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 : MoleculePlane::MoleculePlane( const ActionOptions&amp; ao ):</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   Action(ao),</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :   VectorMultiColvar(ao)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : {</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          4 :   readAtomsLikeKeyword(&quot;MOL&quot;,-1,all_atoms);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 :   if( ablocks.size()!=3 &amp;&amp; ablocks.size()!=4 ) error(&quot;number of atoms in molecule specification is wrong.  Should be three or four.&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          2 :   if( all_atoms.size()==0 ) error(&quot;No atoms were specified&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          2 :   setVectorDimensionality( 3 ); setupMultiColvarBase( all_atoms );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 : AtomNumber MoleculePlane::getAbsoluteIndexOfCentralAtom( const unsigned&amp; iatom ) const {</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   plumed_dbg_assert( iatom&lt;atom_lab.size() );</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   plumed_assert( atom_lab[iatom].first==0 );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   return ActionAtomistic::getAbsoluteIndex( ablocks[0][atom_lab[iatom].second] );</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       8888 : void MoleculePlane::calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       8888 :   Vector d1, d2, cp;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       8888 :   if( myatoms.getNumberOfAtoms()==3 ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       8888 :     d1=getSeparation( myatoms.getPosition(1), myatoms.getPosition(0) );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       8888 :     d2=getSeparation( myatoms.getPosition(1), myatoms.getPosition(2) );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   } else {</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :     d1=getSeparation( myatoms.getPosition(1), myatoms.getPosition(0) );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     d2=getSeparation( myatoms.getPosition(2), myatoms.getPosition(3) );</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       8888 :   cp = crossProduct( d1, d2 );</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       8888 :   addAtomDerivatives( 2, 0, crossProduct( Vector(-1.0,0,0), d2 ), myatoms );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       8888 :   if( myatoms.getNumberOfAtoms()==3 ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       8888 :     addAtomDerivatives( 2, 1, crossProduct( Vector(+1.0,0,0), d2 ) + crossProduct( Vector(-1.0,0,0), d1 ), myatoms );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       8888 :     addAtomDerivatives( 2, 2, crossProduct( Vector(+1.0,0,0), d1 ), myatoms );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   } else {</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 2, 1, crossProduct( Vector(+1.0,0,0), d2 ), myatoms );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 2, 2, crossProduct( Vector(-1.0,0,0), d1 ), myatoms );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 2, 3, crossProduct( Vector(+1.0,0,0), d1 ), myatoms );</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       8888 :   myatoms.addBoxDerivatives( 2, Tensor(d1,crossProduct(Vector(+1.0,0,0), d2)) + Tensor( d2, crossProduct(Vector(-1.0,0,0), d1)) );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       8888 :   myatoms.addValue( 2, cp[0] );</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       8888 :   addAtomDerivatives( 3, 0, crossProduct( Vector(0,-1.0,0), d2 ), myatoms );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       8888 :   if( myatoms.getNumberOfAtoms()==3 ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       8888 :     addAtomDerivatives( 3, 1, crossProduct( Vector(0,+1.0,0), d2 ) + crossProduct( Vector(0,-1.0,0), d1 ), myatoms );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       8888 :     addAtomDerivatives( 3, 2, crossProduct( Vector(0,+1.0,0), d1 ), myatoms );</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   } else {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 3, 1, crossProduct( Vector(0,+1.0,0), d2 ), myatoms );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 3, 2, crossProduct( Vector(0,-1.0,0), d1 ), myatoms );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 3, 3, crossProduct( Vector(0,+1.0,0), d1 ), myatoms );</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       8888 :   myatoms.addBoxDerivatives( 3, Tensor(d1,crossProduct(Vector(0,+1.0,0), d2)) + Tensor( d2, crossProduct(Vector(0,-1.0,0), d1)) );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       8888 :   myatoms.addValue( 3, cp[1] );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       8888 :   addAtomDerivatives( 4, 0, crossProduct( Vector(0,0,-1.0), d2 ), myatoms );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       8888 :   if( myatoms.getNumberOfAtoms()==3 ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       8888 :     addAtomDerivatives( 4, 1, crossProduct( Vector(0,0,+1.0), d2 ) + crossProduct( Vector(0,0,-1.0), d1 ), myatoms );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       8888 :     addAtomDerivatives( 4, 2, crossProduct( Vector(0,0,+1.0), d1 ), myatoms);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   } else {</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 4, 1, crossProduct( Vector(0,0,-1.0), d2 ), myatoms);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 4, 2, crossProduct( Vector(0,0,-1.0), d1 ), myatoms);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     addAtomDerivatives( 4, 3, crossProduct( Vector(0,0,+1.0), d1 ), myatoms);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       8888 :   myatoms.addBoxDerivatives( 4, Tensor(d1,crossProduct(Vector(0,0,+1.0), d2)) + Tensor( d2, crossProduct(Vector(0,0,-1.0), d1)) );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       8888 :   myatoms.addValue( 4, cp[2] );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       8888 : }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : // Vector MoleculePlane::getCentralAtom(){</a>
+<a name="128"><span class="lineNum">     128 </span>            : //   Vector com; com.zero();</a>
+<a name="129"><span class="lineNum">     129 </span>            : //   if( getNAtoms()==3 ){</a>
+<a name="130"><span class="lineNum">     130 </span>            : //       com+=(1.0/3.0)*getPosition(0);</a>
+<a name="131"><span class="lineNum">     131 </span>            : //       com+=(1.0/3.0)*getPosition(1);</a>
+<a name="132"><span class="lineNum">     132 </span>            : //       com+=(1.0/3.0)*getPosition(2);</a>
+<a name="133"><span class="lineNum">     133 </span>            : //       addCentralAtomDerivatives( 0, (1.0/3.0)*Tensor::identity() );</a>
+<a name="134"><span class="lineNum">     134 </span>            : //       addCentralAtomDerivatives( 1, (1.0/3.0)*Tensor::identity() );</a>
+<a name="135"><span class="lineNum">     135 </span>            : //       addCentralAtomDerivatives( 2, (1.0/3.0)*Tensor::identity() );</a>
+<a name="136"><span class="lineNum">     136 </span>            : //       return com;</a>
+<a name="137"><span class="lineNum">     137 </span>            : //   }</a>
+<a name="138"><span class="lineNum">     138 </span>            : //   com+=0.25*getPosition(0);</a>
+<a name="139"><span class="lineNum">     139 </span>            : //   com+=0.25*getPosition(1);</a>
+<a name="140"><span class="lineNum">     140 </span>            : //   com+=0.25*getPosition(2);</a>
+<a name="141"><span class="lineNum">     141 </span>            : //   com+=0.25*getPosition(3);</a>
+<a name="142"><span class="lineNum">     142 </span>            : //   addCentralAtomDerivatives( 0, 0.25*Tensor::identity() );</a>
+<a name="143"><span class="lineNum">     143 </span>            : //   addCentralAtomDerivatives( 1, 0.25*Tensor::identity() );</a>
+<a name="144"><span class="lineNum">     144 </span>            : //   addCentralAtomDerivatives( 2, 0.25*Tensor::identity() );</a>
+<a name="145"><span class="lineNum">     145 </span>            : //   addCentralAtomDerivatives( 3, 0.25*Tensor::identity() );</a>
+<a name="146"><span class="lineNum">     146 </span>            : //   return com;</a>
+<a name="147"><span class="lineNum">     147 </span>            : // }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/OrientationSphere.cpp.func-sort-c.html b/coverage/crystallization/OrientationSphere.cpp.func-sort-c.html
new file mode 100644
index 0000000000..742edf0cf7
--- /dev/null
+++ b/coverage/crystallization/OrientationSphere.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/OrientationSphere.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - OrientationSphere.cpp<span style="font-size: 80%;"> (<a href="OrientationSphere.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OrientationSphere.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#45">_ZN4PLMD15crystallization17OrientationSphereC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#45">_ZN4PLMD15crystallization17OrientationSphereC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#29">_ZN4PLMD15crystallization17OrientationSphere16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#69">_ZNK4PLMD15crystallization17OrientationSphere7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">7782</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/OrientationSphere.cpp.func.html b/coverage/crystallization/OrientationSphere.cpp.func.html
new file mode 100644
index 0000000000..a8f894245c
--- /dev/null
+++ b/coverage/crystallization/OrientationSphere.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/OrientationSphere.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - OrientationSphere.cpp<span style="font-size: 80%;"> (<a href="OrientationSphere.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OrientationSphere.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#29">_ZN4PLMD15crystallization17OrientationSphere16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#45">_ZN4PLMD15crystallization17OrientationSphereC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#45">_ZN4PLMD15crystallization17OrientationSphereC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.cpp.gcov.html#69">_ZNK4PLMD15crystallization17OrientationSphere7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">7782</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/OrientationSphere.cpp.gcov.html b/coverage/crystallization/OrientationSphere.cpp.gcov.html
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--- /dev/null
+++ b/coverage/crystallization/OrientationSphere.cpp.gcov.html
@@ -0,0 +1,207 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/OrientationSphere.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - OrientationSphere.cpp<span style="font-size: 80%;"> (source / <a href="OrientationSphere.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OrientationSphere.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : using namespace std;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace crystallization {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         21 : void OrientationSphere::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         21 :   multicolvar::MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="40"><span class="lineNum">      40 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         63 :   keys.use(&quot;SPECIES&quot;); keys.use(&quot;SPECIESA&quot;); keys.use(&quot;SPECIESB&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         63 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         84 :   keys.use(&quot;MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         42 :   keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         21 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         11 : OrientationSphere::OrientationSphere(const ActionOptions&amp;ao):</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   Action(ao),</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         11 :   MultiColvarBase(ao)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         11 :   if( getNumberOfBaseMultiColvars()&gt;1 ) warning(&quot;not sure if orientation sphere works with more than one base multicolvar - check numerical derivatives&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   // Read in the switching function</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         22 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         11 :   if(sw.length()&gt;0) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         11 :     switchingFunction.set(sw,errors);</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   } else {</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   }</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         11 :   log.printf(&quot;  degree of overlap in orientation between central molecule and those within %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         22 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Tribello, Giberti, Sosso, Salvalaglio and Parrinello, J. Chem. Theory Comput. 13, 1317 (2017)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   // Set the link cell cutoff</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         11 :   rcut2 = switchingFunction.get_dmax()*switchingFunction.get_dmax();</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         11 :   setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         11 :   std::vector&lt;AtomNumber&gt; all_atoms; setupMultiColvarBase( all_atoms );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         11 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       7782 : double OrientationSphere::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       7782 :   double sw, value=0, denom=0, dfunc; Vector ddistance;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       7782 :   unsigned ncomponents=getBaseMultiColvar(0)-&gt;getNumberOfQuantities();</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       7782 :   std::vector&lt;double&gt; catom_orient( ncomponents ), this_orient( ncomponents );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       7782 :   std::vector&lt;double&gt; this_der( ncomponents ), catom_der( ncomponents );</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       7782 :   getInputData( 0, true, myatoms, catom_orient );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       7782 :   MultiValue&amp; myder0=getInputDerivatives( 0, true, myatoms );</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">    1379893 :   for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :     Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="82"><span class="lineNum">      82 </span>            :     double d2;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    2611747 :     if ( (d2=distance[0]*distance[0])&lt;rcut2 &amp;&amp;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    1239636 :          (d2+=distance[1]*distance[1])&lt;rcut2 &amp;&amp;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    2501268 :          (d2+=distance[2]*distance[2])&lt;rcut2 &amp;&amp;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :          d2&gt;epsilon ) {</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    1069658 :       sw = switchingFunction.calculateSqr( d2, dfunc );</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">    1069658 :       getInputData( i, true, myatoms, this_orient );</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :       // Calculate the dot product wrt to this position</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    1069658 :       double f_dot = computeVectorFunction( distance, catom_orient, this_orient, ddistance, catom_der, this_der );</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    1069658 :       if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     233625 :         for(unsigned k=2; k&lt;catom_orient.size(); ++k) { this_der[k]*=sw; catom_der[k]*=sw; }</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      10227 :         MultiValue&amp; myder1=getInputDerivatives( i, true, myatoms );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      10227 :         mergeInputDerivatives( 1, 2, this_orient.size(), 0, catom_der, myder0, myatoms );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      10227 :         mergeInputDerivatives( 1, 2, catom_der.size(), i, this_der, myder1, myatoms );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      10227 :         addAtomDerivatives( 1, 0, f_dot*(-dfunc)*distance - sw*ddistance, myatoms );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      10227 :         addAtomDerivatives( 1, i, f_dot*(dfunc)*distance + sw*ddistance, myatoms );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      10227 :         myatoms.addBoxDerivatives( 1, (-dfunc)*f_dot*Tensor(distance,distance) - sw*extProduct(distance,ddistance) );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      10227 :         myder1.clearAll();</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      10227 :         addAtomDerivatives( -1, 0, (-dfunc)*distance, myatoms );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      10227 :         addAtomDerivatives( -1, i, (dfunc)*distance, myatoms );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      10227 :         myatoms.addTemporyBoxDerivatives( (-dfunc)*Tensor(distance,distance) );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :       }</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">    1069658 :       value += sw*f_dot;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">    1069658 :       denom += sw;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     }</a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       7782 :   double rdenom, df2, pref=calculateCoordinationPrefactor( denom, df2 );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       7782 :   if( std::fabs(denom)&gt;epsilon ) { rdenom = 1.0 / denom; }</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   else { plumed_assert(std::fabs(value)&lt;epsilon); rdenom=1.0; }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   // Now divide everything</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       7782 :   double rdenom2=rdenom*rdenom;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       7782 :   updateActiveAtoms( myatoms ); MultiValue&amp; myvals=myatoms.getUnderlyingMultiValue();</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      57486 :   for(unsigned i=0; i&lt;myvals.getNumberActive(); ++i) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      49704 :     unsigned ider=myvals.getActiveIndex(i);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     double  dgd=myvals.getTemporyDerivative(ider);</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      49704 :     myvals.setDerivative( 1, ider, rdenom*(pref*myvals.getDerivative(1,ider)+value*df2*dgd) - (value*pref*dgd)*rdenom2 );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      15564 :   return pref*rdenom*value;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/OrientationSphere.h.func-sort-c.html b/coverage/crystallization/OrientationSphere.h.func-sort-c.html
new file mode 100644
index 0000000000..7e905c7e64
--- /dev/null
+++ b/coverage/crystallization/OrientationSphere.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/OrientationSphere.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - OrientationSphere.h<span style="font-size: 80%;"> (<a href="OrientationSphere.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OrientationSphere.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.h.gcov.html#41">_ZN4PLMD15crystallization17OrientationSphere10isPeriodicEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.h.gcov.html#45">_ZNK4PLMD15crystallization17OrientationSphere30calculateCoordinationPrefactorERKdRd</a></td>
+              <td class="coverFnHi">3318</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/OrientationSphere.h.func.html b/coverage/crystallization/OrientationSphere.h.func.html
new file mode 100644
index 0000000000..10b29792c7
--- /dev/null
+++ b/coverage/crystallization/OrientationSphere.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/OrientationSphere.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - OrientationSphere.h<span style="font-size: 80%;"> (<a href="OrientationSphere.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OrientationSphere.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.h.gcov.html#41">_ZN4PLMD15crystallization17OrientationSphere10isPeriodicEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrientationSphere.h.gcov.html#45">_ZNK4PLMD15crystallization17OrientationSphere30calculateCoordinationPrefactorERKdRd</a></td>
+              <td class="coverFnHi">3318</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/OrientationSphere.h.gcov.html b/coverage/crystallization/OrientationSphere.h.gcov.html
new file mode 100644
index 0000000000..df32da42e6
--- /dev/null
+++ b/coverage/crystallization/OrientationSphere.h.gcov.html
@@ -0,0 +1,129 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/OrientationSphere.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - OrientationSphere.h<span style="font-size: 80%;"> (source / <a href="OrientationSphere.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_crystallization_OrientationSphere_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_crystallization_OrientationSphere_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace crystallization {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class OrientationSphere : public multicolvar::MultiColvarBase {</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   double rcut2;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="36"><span class="lineNum">      36 </span>            : public:</a>
+<a name="37"><span class="lineNum">      37 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="38"><span class="lineNum">      38 </span>            :   explicit OrientationSphere(const ActionOptions&amp;);</a>
+<a name="39"><span class="lineNum">      39 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   virtual double computeVectorFunction( const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="41"><span class="lineNum">      41 </span>            :                                         Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const = 0;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   virtual double calculateCoordinationPrefactor( const double&amp; coord, double&amp; df ) const ;</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         12 :   bool isPeriodic() { return false; }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : };</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : inline</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       3318 : double OrientationSphere::calculateCoordinationPrefactor( const double&amp; coord, double&amp; df ) const {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       3318 :   df=0.0; return 1.0;</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : }</a>
+<a name="53"><span class="lineNum">      53 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/PolymerAngles.cpp.func-sort-c.html b/coverage/crystallization/PolymerAngles.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2d6c220497
--- /dev/null
+++ b/coverage/crystallization/PolymerAngles.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/PolymerAngles.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - PolymerAngles.cpp<span style="font-size: 80%;"> (<a href="PolymerAngles.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PolymerAngles.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#80">_ZN4PLMD15crystallization13PolymerAnglesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#74">_ZN4PLMD15crystallization12_GLOBAL__N_125PolymerAnglesRegisterMe766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#80">_ZN4PLMD15crystallization13PolymerAnglesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#76">_ZN4PLMD15crystallization13PolymerAngles16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#90">_ZNK4PLMD15crystallization13PolymerAngles21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESA_RS3_RS8_SC_</a></td>
+              <td class="coverFnHi">616</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#74">_ZN4PLMD15crystallization12_GLOBAL__N_125PolymerAnglesRegisterMe76C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#74">_ZN4PLMD15crystallization12_GLOBAL__N_125PolymerAnglesRegisterMe76D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/PolymerAngles.cpp.func.html b/coverage/crystallization/PolymerAngles.cpp.func.html
new file mode 100644
index 0000000000..45164c721c
--- /dev/null
+++ b/coverage/crystallization/PolymerAngles.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/PolymerAngles.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - PolymerAngles.cpp<span style="font-size: 80%;"> (<a href="PolymerAngles.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PolymerAngles.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#74">_ZN4PLMD15crystallization12_GLOBAL__N_125PolymerAnglesRegisterMe766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#74">_ZN4PLMD15crystallization12_GLOBAL__N_125PolymerAnglesRegisterMe76C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#74">_ZN4PLMD15crystallization12_GLOBAL__N_125PolymerAnglesRegisterMe76D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#76">_ZN4PLMD15crystallization13PolymerAngles16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#80">_ZN4PLMD15crystallization13PolymerAnglesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#80">_ZN4PLMD15crystallization13PolymerAnglesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PolymerAngles.cpp.gcov.html#90">_ZNK4PLMD15crystallization13PolymerAngles21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESA_RS3_RS8_SC_</a></td>
+              <td class="coverFnHi">616</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/PolymerAngles.cpp.gcov.html b/coverage/crystallization/PolymerAngles.cpp.gcov.html
new file mode 100644
index 0000000000..e151959a85
--- /dev/null
+++ b/coverage/crystallization/PolymerAngles.cpp.gcov.html
@@ -0,0 +1,178 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/PolymerAngles.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - PolymerAngles.cpp<span style="font-size: 80%;"> (source / <a href="PolymerAngles.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OrientationSphere.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC MCOLVARF POLYMER_ANGLES</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Calculate a function to investigate the relative orientations of polymer angles</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : This CV takes the vectors calculated by a \ref PLANES action as input and computes the following function</a>
+<a name="30"><span class="lineNum">      30 </span>            : of the relative angles, \f$\theta\f$, between the vectors that are normal to the pairs of input vectors:</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            : s = \frac{ 3 \cos^2 \theta - 1 }{ 2 }</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This average of this quantity over all the vectors in the first coordination sphere around each of the PLANES specified</a>
+<a name="37"><span class="lineNum">      37 </span>            : is then calculated.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The example below calculates a set of vectors using the \ref PLANES action.  The average number for the function \f$s\f$</a>
+<a name="42"><span class="lineNum">      42 </span>            : defined above is then computed over the first coordination sphere of each of the centers of mass of the molecules that were</a>
+<a name="43"><span class="lineNum">      43 </span>            : used to define the planes.  Finally the average of these quantities is computed an printed to a file.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : PLANES ...</a>
+<a name="47"><span class="lineNum">      47 </span>            : MOL1=9,10,11</a>
+<a name="48"><span class="lineNum">      48 </span>            : MOL2=89,90,91</a>
+<a name="49"><span class="lineNum">      49 </span>            : MOL3=473,474,475</a>
+<a name="50"><span class="lineNum">      50 </span>            : MOL4=1161,1162,1163</a>
+<a name="51"><span class="lineNum">      51 </span>            : MOL5=1521,1522,1523</a>
+<a name="52"><span class="lineNum">      52 </span>            : MOL6=1593,1594,1595</a>
+<a name="53"><span class="lineNum">      53 </span>            : MOL7=1601,1602,1603</a>
+<a name="54"><span class="lineNum">      54 </span>            : MOL8=2201,2202,2203</a>
+<a name="55"><span class="lineNum">      55 </span>            : LABEL=m3</a>
+<a name="56"><span class="lineNum">      56 </span>            : ... PLANES</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : s3: POLYMER_ANGLES SPECIES=m3 LOWMEM SWITCH={RATIONAL R_0=0.6} MEAN</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=s3.mean FILE=colvar</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : */</a>
+<a name="63"><span class="lineNum">      63 </span>            : //+ENDPLUMEDOC</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : namespace PLMD {</a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace crystallization {</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class PolymerAngles : public OrientationSphere {</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit PolymerAngles(const ActionOptions&amp; ao);</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double computeVectorFunction( const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="73"><span class="lineNum">      73 </span>            :                                 Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const override;</a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(PolymerAngles,&quot;POLYMER_ANGLES&quot;)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          3 : void PolymerAngles::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          3 :   OrientationSphere::registerKeywords(keys);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 : PolymerAngles::PolymerAngles(const ActionOptions&amp; ao):</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   Action(ao),</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          1 :   OrientationSphere(ao)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : {</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 :   if( mybasemulticolvars.size()==0 ) error(&quot;SMAC must take multicolvar as input&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          1 :     if( (mybasemulticolvars[i]-&gt;getNumberOfQuantities()-2)%3!=0 ) error(&quot;POLYMER_ANGLES is only possible with three dimensional vectors&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          1 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        616 : double PolymerAngles::computeVectorFunction( const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :     Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const {</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        616 :   plumed_assert( (vec1.size()-2)==3 );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       2464 :   double dot = 0; for(unsigned k=0; k&lt;3; ++k) dot += vec1[2+k]*vec2[2+k];</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       2464 :   double ans = 1.5*dot*dot - 0.5; for(unsigned k=0; k&lt;3; ++k) { dvec1[2+k]=3*dot*vec2[2+k]; dvec2[2+k]=3*dot*vec1[2+k]; }</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        616 :   return ans;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Q3.cpp.func-sort-c.html b/coverage/crystallization/Q3.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1deaa6441b
--- /dev/null
+++ b/coverage/crystallization/Q3.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Q3.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q3.cpp<span style="font-size: 80%;"> (<a href="Q3.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">26.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Q3.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#185">_ZN4PLMD15crystallization12_GLOBAL__N_115Q3RegisterMe1876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#187">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q3RegisterMe1896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#193">_ZN4PLMD15crystallization2Q3C1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#193">_ZN4PLMD15crystallization2Q3C2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#189">_ZN4PLMD15crystallization2Q316registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#185">_ZN4PLMD15crystallization12_GLOBAL__N_115Q3RegisterMe187C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#185">_ZN4PLMD15crystallization12_GLOBAL__N_115Q3RegisterMe187D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#187">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q3RegisterMe189C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q3.cpp.gcov.html#187">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q3RegisterMe189D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Q3.cpp.func.html b/coverage/crystallization/Q3.cpp.func.html
new file mode 100644
index 0000000000..75504ab031
--- /dev/null
+++ b/coverage/crystallization/Q3.cpp.func.html
@@ -0,0 +1,108 @@
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+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">19</td>
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+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
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+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
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+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Steinhardt.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;LocalSteinhardt.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MCOLVAR Q3</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate 3rd order Steinhardt parameters.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : The 3rd order Steinhardt parameters allow us to measure the degree to which the first coordination shell</a>
+<a name="31"><span class="lineNum">      31 </span>            : around an atom is ordered.  The Steinhardt parameter for atom, \f$i\f$ is complex vector whose components are</a>
+<a name="32"><span class="lineNum">      32 </span>            : calculated using the following formula:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : q_{3m}(i) = \frac{\sum_j \sigma( r_{ij} ) Y_{3m}(\mathbf{r}_{ij}) }{\sum_j \sigma( r_{ij} ) }</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : where \f$Y_{3m}\f$ is one of the 3rd order spherical harmonics so \f$m\f$ is a number that runs from \f$-3\f$ to</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$+3\f$.  The function \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between</a>
+<a name="40"><span class="lineNum">      40 </span>            : atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set so that it the function is equal to one</a>
+<a name="41"><span class="lineNum">      41 </span>            : when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The Steinhardt parameters can be used to measure the degree of order in the system in a variety of different ways.  The</a>
+<a name="44"><span class="lineNum">      44 </span>            : simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            : Q_3(i) = \sqrt{ \sum_{m=-3}^3 q_{3m}(i)^{*} q_{3m}(i) }</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, when</a>
+<a name="51"><span class="lineNum">      51 </span>            : the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with this colvar it is the distribution of these normed quantities</a>
+<a name="52"><span class="lineNum">      52 </span>            : that is investigated.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : Other measures of order can be taken by averaging the components of the individual \f$q_3\f$ vectors individually or by taking dot products of</a>
+<a name="55"><span class="lineNum">      55 </span>            : the \f$q_{3}\f$ vectors on adjacent atoms.  More information on these variables can be found in the documentation for \ref LOCAL_Q3,</a>
+<a name="56"><span class="lineNum">      56 </span>            : \ref LOCAL_AVERAGE and \ref NLINKS.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following command calculates the average Q3 parameter for the 64 atoms in a box of Lennard Jones and prints this</a>
+<a name="61"><span class="lineNum">      61 </span>            : quantity to a file called colvar:</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \plumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q3</a>
+<a name="65"><span class="lineNum">      65 </span>            : PRINT ARG=q3.mean FILE=colvar</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : The following command calculates the histogram of Q3 parameters for the 64 atoms in a box of Lennard Jones and prints these</a>
+<a name="69"><span class="lineNum">      69 </span>            : quantities to a file called colvar:</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \plumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q3</a>
+<a name="73"><span class="lineNum">      73 </span>            : PRINT ARG=q3.* FILE=colvar</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : The following command could be used to measure the Q3 parameters that describe the arrangement of chlorine ions around the</a>
+<a name="77"><span class="lineNum">      77 </span>            : sodium atoms in sodium chloride.  The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input</a>
+<a name="78"><span class="lineNum">      78 </span>            : with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions.  Once again the average Q3 parameter is calculated and output to a</a>
+<a name="79"><span class="lineNum">      79 </span>            : file called colvar</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \plumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q3</a>
+<a name="83"><span class="lineNum">      83 </span>            : PRINT ARG=q3.mean FILE=colvar</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endplumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : If you simply want to examine the values of the Q3 parameters for each of the atoms in your system you can do so by exploiting the</a>
+<a name="87"><span class="lineNum">      87 </span>            : command \ref DUMPMULTICOLVAR as shown in the example below.  The following output file will output a file in an extended xyz format</a>
+<a name="88"><span class="lineNum">      88 </span>            : called q3.xyz for each frame of the analyzed MD trajectory.  The first column in this file will contain a dummy name for each of the</a>
+<a name="89"><span class="lineNum">      89 </span>            : atoms, columns 2-4 will then contain the x, y and z positions of the atoms, column 5 will contain the value of the Q3 parameter, columns</a>
+<a name="90"><span class="lineNum">      90 </span>            : 6-12 will contain the real parts of the director of the \f$q_{3m}\f$ vector while columns 12-19 will contain the imaginary parts of this director.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : \plumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : q3: Q3 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN</a>
+<a name="94"><span class="lineNum">      94 </span>            : DUMPMULTICOLVAR DATA=q3 FILE=q3.xyz</a>
+<a name="95"><span class="lineNum">      95 </span>            : \endplumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : */</a>
+<a name="98"><span class="lineNum">      98 </span>            : //+ENDPLUMEDOC</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : //+PLUMEDOC MCOLVARF LOCAL_Q3</a>
+<a name="101"><span class="lineNum">     101 </span>            : /*</a>
+<a name="102"><span class="lineNum">     102 </span>            : Calculate the local degree of order around an atoms by taking the average dot product between the q_3 vector on the central atom and the q_3 vector on the atoms in the first coordination sphere.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The \ref Q3 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere</a>
+<a name="105"><span class="lineNum">     105 </span>            : around a particular atom. The difficulty with these vectors comes when combining the order parameters from all of the individual atoms/molecules so as to get a</a>
+<a name="106"><span class="lineNum">     106 </span>            : measure of the global degree of order for the system. The simplest way of doing this - calculating the average Steinhardt parameter - can be problematic. If one is</a>
+<a name="107"><span class="lineNum">     107 </span>            : examining nucleation say only the order parameters for those atoms in the nucleus will change significantly when the nucleus forms. The order parameters for the</a>
+<a name="108"><span class="lineNum">     108 </span>            : atoms in the surrounding liquid will remain pretty much the same. As such if one models a small nucleus embedded in a very large amount of solution/melt any</a>
+<a name="109"><span class="lineNum">     109 </span>            : change in the average order parameter will be negligible. Substantial changes in the value of this average can be observed in simulations of nucleation but only</a>
+<a name="110"><span class="lineNum">     110 </span>            : because the number of atoms is relatively small.</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : When the average \ref Q3 parameter is used to bias the dynamics a problems</a>
+<a name="113"><span class="lineNum">     113 </span>            : can occur. These averaged coordinates cannot distinguish between the correct,</a>
+<a name="114"><span class="lineNum">     114 </span>            : single-nucleus pathway and a concerted pathway in which all the atoms rearrange</a>
+<a name="115"><span class="lineNum">     115 </span>            : themselves into their solid-like configuration simultaneously. This second type</a>
+<a name="116"><span class="lineNum">     116 </span>            : of pathway would be impossible in reality because there is a large entropic</a>
+<a name="117"><span class="lineNum">     117 </span>            : barrier that prevents concerted processes like this from happening.  However,</a>
+<a name="118"><span class="lineNum">     118 </span>            : in the finite sized systems that are commonly simulated this barrier is reduced</a>
+<a name="119"><span class="lineNum">     119 </span>            : substantially. As a result in simulations where average Steinhardt parameters</a>
+<a name="120"><span class="lineNum">     120 </span>            : are biased there are often quite dramatic system size effects</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : If one wants to simulate nucleation using some form on</a>
+<a name="123"><span class="lineNum">     123 </span>            : biased dynamics what is really required is an order parameter that measures:</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : - Whether or not the coordination spheres around atoms are ordered</a>
+<a name="126"><span class="lineNum">     126 </span>            : - Whether or not the atoms that are ordered are clustered together in a crystalline nucleus</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : \ref LOCAL_AVERAGE and \ref NLINKS are variables that can be combined with the Steinhardt parameters allow to calculate variables that satisfy these requirements.</a>
+<a name="129"><span class="lineNum">     129 </span>            : LOCAL_Q3 is another variable that can be used in these sorts of calculations. The LOCAL_Q3 parameter for a particular atom is a number that measures the extent to</a>
+<a name="130"><span class="lineNum">     130 </span>            : which the orientation of the atoms in the first coordination sphere of an atom match the orientation of the central atom.  It does this by calculating the following</a>
+<a name="131"><span class="lineNum">     131 </span>            : quantity for each of the atoms in the system:</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : \f[</a>
+<a name="134"><span class="lineNum">     134 </span>            :  s_i = \frac{ \sum_j \sigma( r_{ij} ) \sum_{m=-3}^3 q_{3m}^{*}(i)q_{3m}(j) }{ \sum_j \sigma( r_{ij} ) }</a>
+<a name="135"><span class="lineNum">     135 </span>            : \f]</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : where \f$q_{3m}(i)\f$ and \f$q_{3m}(j)\f$ are the 3rd order Steinhardt vectors calculated for atom \f$i\f$ and atom \f$j\f$ respectively and the asterisk denotes complex</a>
+<a name="138"><span class="lineNum">     138 </span>            : conjugation.  The function</a>
+<a name="139"><span class="lineNum">     139 </span>            : \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set</a>
+<a name="140"><span class="lineNum">     140 </span>            : so that it the function is equal to one when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.  The sum in the numerator</a>
+<a name="141"><span class="lineNum">     141 </span>            : of this expression is the dot product of the Steinhardt parameters for atoms \f$i\f$ and \f$j\f$ and thus measures the degree to which the orientations of these</a>
+<a name="142"><span class="lineNum">     142 </span>            : adjacent atoms is correlated.</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : \par Examples</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : The following command calculates the average value of the LOCAL_Q3 parameter for the 64 Lennard Jones atoms in the system under study and prints this</a>
+<a name="147"><span class="lineNum">     147 </span>            : quantity to a file called colvar.</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : \plumedfile</a>
+<a name="150"><span class="lineNum">     150 </span>            : Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q3</a>
+<a name="151"><span class="lineNum">     151 </span>            : LOCAL_Q3 SPECIES=q3 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq3</a>
+<a name="152"><span class="lineNum">     152 </span>            : PRINT ARG=lq3.mean FILE=colvar</a>
+<a name="153"><span class="lineNum">     153 </span>            : \endplumedfile</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : The following input calculates the distribution of LOCAL_Q3 parameters at any given time and outputs this information to a file.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : \plumedfile</a>
+<a name="158"><span class="lineNum">     158 </span>            : Q3 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q3</a>
+<a name="159"><span class="lineNum">     159 </span>            : LOCAL_Q3 SPECIES=q3 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq3</a>
+<a name="160"><span class="lineNum">     160 </span>            : PRINT ARG=lq3.* FILE=colvar</a>
+<a name="161"><span class="lineNum">     161 </span>            : \endplumedfile</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : The following calculates the LOCAL_Q3 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere</a>
+<a name="164"><span class="lineNum">     164 </span>            : are done with those of all the other atoms in the system.  The final quantity is the average and is outputted to a file</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : \plumedfile</a>
+<a name="167"><span class="lineNum">     167 </span>            : Q3 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q3a</a>
+<a name="168"><span class="lineNum">     168 </span>            : Q3 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q3b</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : LOCAL_Q3 SPECIES=q3a,q3b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w3</a>
+<a name="171"><span class="lineNum">     171 </span>            : PRINT ARG=w3.* FILE=colvar</a>
+<a name="172"><span class="lineNum">     172 </span>            : \endplumedfile</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : */</a>
+<a name="175"><span class="lineNum">     175 </span>            : //+ENDPLUMEDOC</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : namespace PLMD {</a>
+<a name="179"><span class="lineNum">     179 </span>            : namespace crystallization {</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : class Q3 : public Steinhardt {</a>
+<a name="182"><span class="lineNum">     182 </span>            : public:</a>
+<a name="183"><span class="lineNum">     183 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="184"><span class="lineNum">     184 </span>            :   explicit Q3( const ActionOptions&amp; ao );</a>
+<a name="185"><span class="lineNum">     185 </span>            : };</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(Q3,&quot;Q3&quot;)</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : typedef LocalSteinhardt&lt;Q3&gt; LOCAL_Q3;</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(LOCAL_Q3,&quot;LOCAL_Q3&quot;)</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          2 : void Q3::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          2 :   Steinhardt::registerKeywords( keys );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 : }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 : Q3::Q3(const ActionOptions&amp; ao ):</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   Action(ao),</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   Steinhardt(ao)</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : {</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   setAngularMomentum(3);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : // Spherical harmonics normalization:</a>
+<a name="202"><span class="lineNum">     202 </span>            : // even =  sqrt ( ((2l+1)*(l-m)!) / (4*pi*(l+m)!) )</a>
+<a name="203"><span class="lineNum">     203 </span>            : // odd  = -sqrt ( ((2l+1)*(l-m)!) / (4*pi*(l+m)!) )</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :   normaliz.resize( 4 );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :   normaliz[0] = sqrt( ( 7.0*6.0 ) / (4.0*pi*6.0) );</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :   normaliz[1] = -sqrt( ( 7.0*2.0 ) / (4.0*pi*24.0) );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :   normaliz[2] = sqrt( ( 7.0*1.0) / (4.0*pi*120.0) );</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :   normaliz[3] = -sqrt( ( 7.0*1.0) / (4.0*pi*720.0) );</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : // Legendre polynomial coefficients of order three</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   coeff_poly.resize( 4 );</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :   coeff_poly[0]=0.0;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   coeff_poly[1]=-1.5;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   coeff_poly[2]=0.0;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   coeff_poly[3]=2.5;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : }</a>
+<a name="222"><span class="lineNum">     222 </span>            : }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+</body>
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diff --git a/coverage/crystallization/Q4.cpp.func-sort-c.html b/coverage/crystallization/Q4.cpp.func-sort-c.html
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q4.cpp<span style="font-size: 80%;"> (<a href="Q4.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
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+
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+    <tr><td><br></td></tr>
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+              <td class="coverFn"><a href="Q4.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q4RegisterMe1886createERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFn"><a href="Q4.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q4RegisterMe186D2Ev</a></td>
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+              <td class="coverFn"><a href="Q4.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q4RegisterMe188C2Ev</a></td>
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+            </tr>
+  </table>
+  <br>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q4.cpp<span style="font-size: 80%;"> (<a href="Q4.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/crystallization/Q4.cpp.gcov.html b/coverage/crystallization/Q4.cpp.gcov.html
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q4.cpp<span style="font-size: 80%;"> (source / <a href="Q4.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
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+        </table>
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+    </tr>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Steinhardt.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;LocalSteinhardt.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MCOLVAR Q4</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate fourth order Steinhardt parameters.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : The fourth order Steinhardt parameters allow us to measure the degree to which the first coordination shell</a>
+<a name="31"><span class="lineNum">      31 </span>            : around an atom is ordered.  The Steinhardt parameter for atom, \f$i\f$ is complex vector whose components are</a>
+<a name="32"><span class="lineNum">      32 </span>            : calculated using the following formula:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : q_{4m}(i) = \frac{\sum_j \sigma( r_{ij} ) Y_{4m}(\mathbf{r}_{ij}) }{\sum_j \sigma( r_{ij} ) }</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : where \f$Y_{4m}\f$ is one of the fourth order spherical harmonics so \f$m\f$ is a number that runs from \f$-4\f$ to</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$+4\f$.  The function \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between</a>
+<a name="40"><span class="lineNum">      40 </span>            : atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set so that it the function is equal to one</a>
+<a name="41"><span class="lineNum">      41 </span>            : when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The Steinhardt parameters can be used to measure the degree of order in the system in a variety of different ways.  The</a>
+<a name="44"><span class="lineNum">      44 </span>            : simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            : Q_4(i) = \sqrt{ \sum_{m=-4}^4 q_{4m}(i)^{*} q_{4m}(i) }</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, when</a>
+<a name="51"><span class="lineNum">      51 </span>            : the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with this colvar it is the distribution of these normed quantities</a>
+<a name="52"><span class="lineNum">      52 </span>            : that is investigated.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : Other measures of order can be taken by averaging the components of the individual \f$q_4\f$ vectors individually or by taking dot products of</a>
+<a name="55"><span class="lineNum">      55 </span>            : the \f$q_{4}\f$ vectors on adjacent atoms.  More information on these variables can be found in the documentation for \ref LOCAL_Q4,</a>
+<a name="56"><span class="lineNum">      56 </span>            : \ref LOCAL_AVERAGE and \ref NLINKS.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following command calculates the average Q4 parameter for the 64 atoms in a box of Lennard Jones and prints this</a>
+<a name="61"><span class="lineNum">      61 </span>            : quantity to a file called colvar:</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \plumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q4</a>
+<a name="65"><span class="lineNum">      65 </span>            : PRINT ARG=q4.mean FILE=colvar</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : The following command calculates the histogram of Q4 parameters for the 64 atoms in a box of Lennard Jones and prints these</a>
+<a name="69"><span class="lineNum">      69 </span>            : quantities to a file called colvar:</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \plumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q4</a>
+<a name="73"><span class="lineNum">      73 </span>            : PRINT ARG=q4.* FILE=colvar</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : The following command could be used to measure the Q4 parameters that describe the arrangement of chlorine ions around the</a>
+<a name="77"><span class="lineNum">      77 </span>            : sodium atoms in sodium chloride.  The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input</a>
+<a name="78"><span class="lineNum">      78 </span>            : with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions.  Once again the average Q4 parameter is calculated and output to a</a>
+<a name="79"><span class="lineNum">      79 </span>            : file called colvar</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \plumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : Q4 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q4</a>
+<a name="83"><span class="lineNum">      83 </span>            : PRINT ARG=q4.mean FILE=colvar</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endplumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : If you simply want to examine the values of the Q4 parameters for each of the atoms in your system you can do so by exploiting the</a>
+<a name="87"><span class="lineNum">      87 </span>            : command \ref DUMPMULTICOLVAR as shown in the example below.  The following output file will output a file in an extended xyz format</a>
+<a name="88"><span class="lineNum">      88 </span>            : called q$.xyz for each frame of the analyzed MD trajectory.  The first column in this file will contain a dummy name for each of the</a>
+<a name="89"><span class="lineNum">      89 </span>            : atoms, columns 2-4 will then contain the x, y and z positions of the atoms, column 5 will contain the value of the Q4 parameter, columns</a>
+<a name="90"><span class="lineNum">      90 </span>            : 6-15 will contain the real parts of the director of the \f$q_{6m}\f$ vector while columns 15-24 will contain the imaginary parts of this director.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : \plumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : q4: Q4 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN</a>
+<a name="94"><span class="lineNum">      94 </span>            : DUMPMULTICOLVAR DATA=q4 FILE=q4.xyz</a>
+<a name="95"><span class="lineNum">      95 </span>            : \endplumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : */</a>
+<a name="98"><span class="lineNum">      98 </span>            : //+ENDPLUMEDOC</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : //+PLUMEDOC MCOLVARF LOCAL_Q4</a>
+<a name="101"><span class="lineNum">     101 </span>            : /*</a>
+<a name="102"><span class="lineNum">     102 </span>            : Calculate the local degree of order around an atoms by taking the average dot product between the q_4 vector on the central atom and the q_4 vector on the atoms in the first coordination sphere.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The \ref Q4 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere</a>
+<a name="105"><span class="lineNum">     105 </span>            : around a particular atom. The difficulty with these vectors comes when combining the order parameters from all of the individual atoms/molecules so as to get a</a>
+<a name="106"><span class="lineNum">     106 </span>            : measure of the global degree of order for the system. The simplest way of doing this - calculating the average Steinhardt parameter - can be problematic. If one is</a>
+<a name="107"><span class="lineNum">     107 </span>            : examining nucleation say only the order parameters for those atoms in the nucleus will change significantly when the nucleus forms. The order parameters for the</a>
+<a name="108"><span class="lineNum">     108 </span>            : atoms in the surrounding liquid will remain pretty much the same. As such if one models a small nucleus embedded in a very large amount of solution/melt any</a>
+<a name="109"><span class="lineNum">     109 </span>            : change in the average order parameter will be negligible. Substantial changes in the value of this average can be observed in simulations of nucleation but only</a>
+<a name="110"><span class="lineNum">     110 </span>            : because the number of atoms is relatively small.</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : When the average \ref Q4 parameter is used to bias the dynamics a problems</a>
+<a name="113"><span class="lineNum">     113 </span>            : can occur. These averaged coordinates cannot distinguish between the correct,</a>
+<a name="114"><span class="lineNum">     114 </span>            : single-nucleus pathway and a concerted pathway in which all the atoms rearrange</a>
+<a name="115"><span class="lineNum">     115 </span>            : themselves into their solid-like configuration simultaneously. This second type</a>
+<a name="116"><span class="lineNum">     116 </span>            : of pathway would be impossible in reality because there is a large entropic</a>
+<a name="117"><span class="lineNum">     117 </span>            : barrier that prevents concerted processes like this from happening.  However,</a>
+<a name="118"><span class="lineNum">     118 </span>            : in the finite sized systems that are commonly simulated this barrier is reduced</a>
+<a name="119"><span class="lineNum">     119 </span>            : substantially. As a result in simulations where average Steinhardt parameters</a>
+<a name="120"><span class="lineNum">     120 </span>            : are biased there are often quite dramatic system size effects</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : If one wants to simulate nucleation using some form on</a>
+<a name="123"><span class="lineNum">     123 </span>            : biased dynamics what is really required is an order parameter that measures:</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : - Whether or not the coordination spheres around atoms are ordered</a>
+<a name="126"><span class="lineNum">     126 </span>            : - Whether or not the atoms that are ordered are clustered together in a crystalline nucleus</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : \ref LOCAL_AVERAGE and \ref NLINKS are variables that can be combined with the Steinhardt parameters allow to calculate variables that satisfy these requirements.</a>
+<a name="129"><span class="lineNum">     129 </span>            : LOCAL_Q4 is another variable that can be used in these sorts of calculations. The LOCAL_Q4 parameter for a particular atom is a number that measures the extent to</a>
+<a name="130"><span class="lineNum">     130 </span>            : which the orientation of the atoms in the first coordination sphere of an atom match the orientation of the central atom.  It does this by calculating the following</a>
+<a name="131"><span class="lineNum">     131 </span>            : quantity for each of the atoms in the system:</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : \f[</a>
+<a name="134"><span class="lineNum">     134 </span>            :  s_i = \frac{ \sum_j \sigma( r_{ij} ) \sum_{m=-4}^4 q_{4m}^{*}(i)q_{4m}(j) }{ \sum_j \sigma( r_{ij} ) }</a>
+<a name="135"><span class="lineNum">     135 </span>            : \f]</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : where \f$q_{4m}(i)\f$ and \f$q_{4m}(j)\f$ are the fourth order Steinhardt vectors calculated for atom \f$i\f$ and atom \f$j\f$ respectively and the asterisk denotes</a>
+<a name="138"><span class="lineNum">     138 </span>            : complex conjugation.  The function</a>
+<a name="139"><span class="lineNum">     139 </span>            : \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set</a>
+<a name="140"><span class="lineNum">     140 </span>            : so that it the function is equal to one when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.  The sum in the numerator</a>
+<a name="141"><span class="lineNum">     141 </span>            : of this expression is the dot product of the Steinhardt parameters for atoms \f$i\f$ and \f$j\f$ and thus measures the degree to which the orientations of these</a>
+<a name="142"><span class="lineNum">     142 </span>            : adjacent atoms is correlated.</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : \par Examples</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : The following command calculates the average value of the LOCAL_Q4 parameter for the 64 Lennard Jones atoms in the system under study and prints this</a>
+<a name="147"><span class="lineNum">     147 </span>            : quantity to a file called colvar.</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : \plumedfile</a>
+<a name="150"><span class="lineNum">     150 </span>            : Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q4</a>
+<a name="151"><span class="lineNum">     151 </span>            : LOCAL_Q4 SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq4</a>
+<a name="152"><span class="lineNum">     152 </span>            : PRINT ARG=lq4.mean FILE=colvar</a>
+<a name="153"><span class="lineNum">     153 </span>            : \endplumedfile</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : The following input calculates the distribution of LOCAL_Q4 parameters at any given time and outputs this information to a file.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : \plumedfile</a>
+<a name="158"><span class="lineNum">     158 </span>            : Q4 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q4</a>
+<a name="159"><span class="lineNum">     159 </span>            : LOCAL_Q4 SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq4</a>
+<a name="160"><span class="lineNum">     160 </span>            : PRINT ARG=lq4.* FILE=colvar</a>
+<a name="161"><span class="lineNum">     161 </span>            : \endplumedfile</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : The following calculates the LOCAL_Q4 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere</a>
+<a name="164"><span class="lineNum">     164 </span>            : are done with those of all the other atoms in the system.  The final quantity is the average and is outputted to a file</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : \plumedfile</a>
+<a name="167"><span class="lineNum">     167 </span>            : Q4 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q4a</a>
+<a name="168"><span class="lineNum">     168 </span>            : Q4 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q4b</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : LOCAL_Q4 SPECIES=q4a,q4b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w4</a>
+<a name="171"><span class="lineNum">     171 </span>            : PRINT ARG=w4.* FILE=colvar</a>
+<a name="172"><span class="lineNum">     172 </span>            : \endplumedfile</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : */</a>
+<a name="175"><span class="lineNum">     175 </span>            : //+ENDPLUMEDOC</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : namespace PLMD {</a>
+<a name="178"><span class="lineNum">     178 </span>            : namespace crystallization {</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : class Q4 : public Steinhardt {</a>
+<a name="181"><span class="lineNum">     181 </span>            : public:</a>
+<a name="182"><span class="lineNum">     182 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="183"><span class="lineNum">     183 </span>            :   explicit Q4( const ActionOptions&amp; ao );</a>
+<a name="184"><span class="lineNum">     184 </span>            : };</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(Q4,&quot;Q4&quot;)</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : typedef LocalSteinhardt&lt;Q4&gt; LOCAL_Q4;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(LOCAL_Q4,&quot;LOCAL_Q4&quot;)</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          5 : void Q4::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          5 :   Steinhardt::registerKeywords( keys );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          5 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          3 : Q4::Q4(const ActionOptions&amp; ao ):</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   Action(ao),</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          3 :   Steinhardt(ao)</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          3 :   setAngularMomentum(4);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          3 :   normaliz.resize( 5 );</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          3 :   normaliz[0] = sqrt( ( 9.0*24.0 ) / (4.0*pi*24.0) );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          3 :   normaliz[1] = -sqrt( ( 9.0*6.0 ) / (4.0*pi*120.0) );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          3 :   normaliz[2] = sqrt( ( 9.0*2.0) / (4.0*pi*720.0) );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          3 :   normaliz[3] = -sqrt( ( 9.0*1) / (4.0*pi*5040.0) );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          3 :   normaliz[4] = sqrt( (9.0*1) / (4.0*pi*40320.0) );</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          3 :   coeff_poly.resize( 5 );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          3 :   coeff_poly[0]=0.375; coeff_poly[1]=0.0;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          3 :   coeff_poly[2]=-3.75; coeff_poly[3]=0.0;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          3 :   coeff_poly[4]=4.375;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          3 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Q6.cpp.func-sort-c.html b/coverage/crystallization/Q6.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b1401d5748
--- /dev/null
+++ b/coverage/crystallization/Q6.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Q6.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q6.cpp<span style="font-size: 80%;"> (<a href="Q6.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Q6.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#192">_ZN4PLMD15crystallization2Q6C2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q6RegisterMe1886createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q6RegisterMe1866createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#192">_ZN4PLMD15crystallization2Q6C1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#188">_ZN4PLMD15crystallization2Q616registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q6RegisterMe186C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q6RegisterMe186D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q6RegisterMe188C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q6RegisterMe188D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Q6.cpp.func.html b/coverage/crystallization/Q6.cpp.func.html
new file mode 100644
index 0000000000..198bd7c23e
--- /dev/null
+++ b/coverage/crystallization/Q6.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Q6.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q6.cpp<span style="font-size: 80%;"> (<a href="Q6.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Q6.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q6RegisterMe1866createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q6RegisterMe186C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#184">_ZN4PLMD15crystallization12_GLOBAL__N_115Q6RegisterMe186D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q6RegisterMe1886createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q6RegisterMe188C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#186">_ZN4PLMD15crystallization12_GLOBAL__N_121LOCAL_Q6RegisterMe188D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#188">_ZN4PLMD15crystallization2Q616registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#192">_ZN4PLMD15crystallization2Q6C1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Q6.cpp.gcov.html#192">_ZN4PLMD15crystallization2Q6C2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Q6.cpp.gcov.html b/coverage/crystallization/Q6.cpp.gcov.html
new file mode 100644
index 0000000000..44128ae594
--- /dev/null
+++ b/coverage/crystallization/Q6.cpp.gcov.html
@@ -0,0 +1,294 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Q6.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Q6.cpp<span style="font-size: 80%;"> (source / <a href="Q6.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Steinhardt.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;LocalSteinhardt.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MCOLVAR Q6</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Calculate sixth order Steinhardt parameters.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : The sixth order Steinhardt parameters allow us to measure the degree to which the first coordination shell</a>
+<a name="31"><span class="lineNum">      31 </span>            : around an atom is ordered.  The Steinhardt parameter for atom, \f$i\f$ is complex vector whose components are</a>
+<a name="32"><span class="lineNum">      32 </span>            : calculated using the following formula:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : q_{6m}(i) = \frac{\sum_j \sigma( r_{ij} ) Y_{6m}(\mathbf{r}_{ij}) }{\sum_j \sigma( r_{ij} ) }</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : where \f$Y_{6m}\f$ is one of the sixth order spherical harmonics so \f$m\f$ is a number that runs from \f$-6\f$ to</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$+6\f$.  The function \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between</a>
+<a name="40"><span class="lineNum">      40 </span>            : atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set so that it the function is equal to one</a>
+<a name="41"><span class="lineNum">      41 </span>            : when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The Steinhardt parameters can be used to measure the degree of order in the system in a variety of different ways.  The</a>
+<a name="44"><span class="lineNum">      44 </span>            : simplest way of measuring whether or not the coordination sphere is ordered is to simply take the norm of the above vector i.e.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            : Q_6(i) = \sqrt{ \sum_{m=-6}^6 q_{6m}(i)^{*} q_{6m}(i) }</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : This norm is small when the coordination shell is disordered and larger when the coordination shell is ordered. Furthermore, when</a>
+<a name="51"><span class="lineNum">      51 </span>            : the keywords LESS_THAN, MIN, MAX, HISTOGRAM, MEAN and so on are used with this colvar it is the distribution of these normed quantities</a>
+<a name="52"><span class="lineNum">      52 </span>            : that is investigated.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : Other measures of order can be taken by averaging the components of the individual \f$q_6\f$ vectors individually or by taking dot products of</a>
+<a name="55"><span class="lineNum">      55 </span>            : the \f$q_{6}\f$ vectors on adjacent atoms.  More information on these variables can be found in the documentation for \ref LOCAL_Q6,</a>
+<a name="56"><span class="lineNum">      56 </span>            : \ref LOCAL_AVERAGE and \ref NLINKS.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following command calculates the average Q6 parameter for the 64 atoms in a box of Lennard Jones and prints this</a>
+<a name="61"><span class="lineNum">      61 </span>            : quantity to a file called colvar:</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \plumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 MEAN LABEL=q6</a>
+<a name="65"><span class="lineNum">      65 </span>            : PRINT ARG=q6.mean FILE=colvar</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : The following command calculates the histogram of Q6 parameters for the 64 atoms in a box of Lennard Jones and prints these</a>
+<a name="69"><span class="lineNum">      69 </span>            : quantities to a file called colvar:</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \plumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=q6</a>
+<a name="73"><span class="lineNum">      73 </span>            : PRINT ARG=q6.* FILE=colvar</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : The following command could be used to measure the Q6 parameters that describe the arrangement of chlorine ions around the</a>
+<a name="77"><span class="lineNum">      77 </span>            : sodium atoms in sodium chloride.  The imagined system here is composed of 64 NaCl formula units and the atoms are arranged in the input</a>
+<a name="78"><span class="lineNum">      78 </span>            : with the 64 Na\f$^+\f$ ions followed by the 64 Cl\f$-\f$ ions.  Once again the average Q6 parameter is calculated and output to a</a>
+<a name="79"><span class="lineNum">      79 </span>            : file called colvar</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \plumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : Q6 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN LABEL=q6</a>
+<a name="83"><span class="lineNum">      83 </span>            : PRINT ARG=q6.mean FILE=colvar</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endplumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : If you simply want to examine the values of the Q6 parameters for each of the atoms in your system you can do so by exploiting the</a>
+<a name="87"><span class="lineNum">      87 </span>            : command \ref DUMPMULTICOLVAR as shown in the example below.  The following output file will output a file in an extended xyz format</a>
+<a name="88"><span class="lineNum">      88 </span>            : called q6.xyz for each frame of the analyzed MD trajectory.  The first column in this file will contain a dummy name for each of the</a>
+<a name="89"><span class="lineNum">      89 </span>            : atoms, columns 2-4 will then contain the x, y and z positions of the atoms, column 5 will contain the value of the Q6 parameter, columns</a>
+<a name="90"><span class="lineNum">      90 </span>            : 6-19 will contain the real parts of the director of the \f$q_{6m}\f$ vector while columns 20-33 will contain the imaginary parts of this director.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : \plumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : q6: Q6 SPECIESA=1-64 SPECIESB=65-128 D_0=1.3 R_0=0.2 MEAN</a>
+<a name="94"><span class="lineNum">      94 </span>            : DUMPMULTICOLVAR DATA=q6 FILE=q6.xyz</a>
+<a name="95"><span class="lineNum">      95 </span>            : \endplumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : */</a>
+<a name="98"><span class="lineNum">      98 </span>            : //+ENDPLUMEDOC</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : //+PLUMEDOC MCOLVARF LOCAL_Q6</a>
+<a name="101"><span class="lineNum">     101 </span>            : /*</a>
+<a name="102"><span class="lineNum">     102 </span>            : Calculate the local degree of order around an atoms by taking the average dot product between the q_6 vector on the central atom and the q_6 vector on the atoms in the first coordination sphere.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The \ref Q6 command allows one to calculate one complex vectors for each of the atoms in your system that describe the degree of order in the coordination sphere</a>
+<a name="105"><span class="lineNum">     105 </span>            : around a particular atom. The difficulty with these vectors comes when combining the order parameters from all of the individual atoms/molecules so as to get a</a>
+<a name="106"><span class="lineNum">     106 </span>            : measure of the global degree of order for the system. The simplest way of doing this - calculating the average Steinhardt parameter - can be problematic. If one is</a>
+<a name="107"><span class="lineNum">     107 </span>            : examining nucleation say only the order parameters for those atoms in the nucleus will change significantly when the nucleus forms. The order parameters for the</a>
+<a name="108"><span class="lineNum">     108 </span>            : atoms in the surrounding liquid will remain pretty much the same. As such if one models a small nucleus embedded in a very large amount of solution/melt any</a>
+<a name="109"><span class="lineNum">     109 </span>            : change in the average order parameter will be negligible. Substantial changes in the value of this average can be observed in simulations of nucleation but only</a>
+<a name="110"><span class="lineNum">     110 </span>            : because the number of atoms is relatively small.</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : When the average \ref Q6 parameter is used to bias the dynamics a problems</a>
+<a name="113"><span class="lineNum">     113 </span>            : can occur. These averaged coordinates cannot distinguish between the correct,</a>
+<a name="114"><span class="lineNum">     114 </span>            : single-nucleus pathway and a concerted pathway in which all the atoms rearrange</a>
+<a name="115"><span class="lineNum">     115 </span>            : themselves into their solid-like configuration simultaneously. This second type</a>
+<a name="116"><span class="lineNum">     116 </span>            : of pathway would be impossible in reality because there is a large entropic</a>
+<a name="117"><span class="lineNum">     117 </span>            : barrier that prevents concerted processes like this from happening.  However,</a>
+<a name="118"><span class="lineNum">     118 </span>            : in the finite sized systems that are commonly simulated this barrier is reduced</a>
+<a name="119"><span class="lineNum">     119 </span>            : substantially. As a result in simulations where average Steinhardt parameters</a>
+<a name="120"><span class="lineNum">     120 </span>            : are biased there are often quite dramatic system size effects</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : If one wants to simulate nucleation using some form on</a>
+<a name="123"><span class="lineNum">     123 </span>            : biased dynamics what is really required is an order parameter that measures:</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : - Whether or not the coordination spheres around atoms are ordered</a>
+<a name="126"><span class="lineNum">     126 </span>            : - Whether or not the atoms that are ordered are clustered together in a crystalline nucleus</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : \ref LOCAL_AVERAGE and \ref NLINKS are variables that can be combined with the Steinhardt parameters allow to calculate variables that satisfy these requirements.</a>
+<a name="129"><span class="lineNum">     129 </span>            : LOCAL_Q6 is another variable that can be used in these sorts of calculations. The LOCAL_Q6 parameter for a particular atom is a number that measures the extent to</a>
+<a name="130"><span class="lineNum">     130 </span>            : which the orientation of the atoms in the first coordination sphere of an atom match the orientation of the central atom.  It does this by calculating the following</a>
+<a name="131"><span class="lineNum">     131 </span>            : quantity for each of the atoms in the system:</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : \f[</a>
+<a name="134"><span class="lineNum">     134 </span>            :  s_i = \frac{ \sum_j \sigma( r_{ij} ) \sum_{m=-6}^6 q_{6m}^{*}(i)q_{6m}(j) }{ \sum_j \sigma( r_{ij} ) }</a>
+<a name="135"><span class="lineNum">     135 </span>            : \f]</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : where \f$q_{6m}(i)\f$ and \f$q_{6m}(j)\f$ are the sixth order Steinhardt vectors calculated for atom \f$i\f$ and atom \f$j\f$ respectively and the asterisk denotes</a>
+<a name="138"><span class="lineNum">     138 </span>            : complex conjugation.  The function</a>
+<a name="139"><span class="lineNum">     139 </span>            : \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set</a>
+<a name="140"><span class="lineNum">     140 </span>            : so that it the function is equal to one when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.  The sum in the numerator</a>
+<a name="141"><span class="lineNum">     141 </span>            : of this expression is the dot product of the Steinhardt parameters for atoms \f$i\f$ and \f$j\f$ and thus measures the degree to which the orientations of these</a>
+<a name="142"><span class="lineNum">     142 </span>            : adjacent atoms is correlated.</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : \par Examples</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : The following command calculates the average value of the LOCAL_Q6 parameter for the 64 Lennard Jones atoms in the system under study and prints this</a>
+<a name="147"><span class="lineNum">     147 </span>            : quantity to a file called colvar.</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : \plumedfile</a>
+<a name="150"><span class="lineNum">     150 </span>            : Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q6</a>
+<a name="151"><span class="lineNum">     151 </span>            : LOCAL_Q6 SPECIES=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=lq6</a>
+<a name="152"><span class="lineNum">     152 </span>            : PRINT ARG=lq6.mean FILE=colvar</a>
+<a name="153"><span class="lineNum">     153 </span>            : \endplumedfile</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : The following input calculates the distribution of LOCAL_Q6 parameters at any given time and outputs this information to a file.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : \plumedfile</a>
+<a name="158"><span class="lineNum">     158 </span>            : Q6 SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=q6</a>
+<a name="159"><span class="lineNum">     159 </span>            : LOCAL_Q6 SPECIES=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=1.0 NBINS=20 SMEAR=0.1} LABEL=lq6</a>
+<a name="160"><span class="lineNum">     160 </span>            : PRINT ARG=lq6.* FILE=colvar</a>
+<a name="161"><span class="lineNum">     161 </span>            : \endplumedfile</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : The following calculates the LOCAL_Q6 parameters for atoms 1-5 only. For each of these atoms comparisons of the geometry of the coordination sphere</a>
+<a name="164"><span class="lineNum">     164 </span>            : are done with those of all the other atoms in the system.  The final quantity is the average and is outputted to a file</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : \plumedfile</a>
+<a name="167"><span class="lineNum">     167 </span>            : Q6 SPECIESA=1-5 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q6a</a>
+<a name="168"><span class="lineNum">     168 </span>            : Q6 SPECIESA=6-64 SPECIESB=1-64 D_0=1.3 R_0=0.2 LABEL=q6b</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : LOCAL_Q6 SPECIES=q6a,q6b SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LOWMEM LABEL=w6</a>
+<a name="171"><span class="lineNum">     171 </span>            : PRINT ARG=w6.* FILE=colvar</a>
+<a name="172"><span class="lineNum">     172 </span>            : \endplumedfile</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : */</a>
+<a name="175"><span class="lineNum">     175 </span>            : //+ENDPLUMEDOC</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : namespace PLMD {</a>
+<a name="178"><span class="lineNum">     178 </span>            : namespace crystallization {</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : class Q6 : public Steinhardt {</a>
+<a name="181"><span class="lineNum">     181 </span>            : public:</a>
+<a name="182"><span class="lineNum">     182 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="183"><span class="lineNum">     183 </span>            :   explicit Q6( const ActionOptions&amp; ao );</a>
+<a name="184"><span class="lineNum">     184 </span>            : };</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">      12534 : PLUMED_REGISTER_ACTION(Q6,&quot;Q6&quot;)</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : typedef LocalSteinhardt&lt;Q6&gt; LOCAL_Q6;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(LOCAL_Q6,&quot;LOCAL_Q6&quot;)</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         17 : void Q6::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         17 :   Steinhardt::registerKeywords( keys );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         17 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         15 : Q6::Q6(const ActionOptions&amp; ao ):</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   Action(ao),</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         15 :   Steinhardt(ao)</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         15 :   setAngularMomentum(6);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         15 :   normaliz.resize( 7 );</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         15 :   normaliz[0] = sqrt( ( 13.0*720.0 ) / (4.0*pi*720.0) );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         15 :   normaliz[1] = -sqrt( ( 13.0*120.0 ) / (4.0*pi*5040) );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         15 :   normaliz[2] = sqrt( ( 13.0*24) / (4.0*pi*40320) );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         15 :   normaliz[3] = -sqrt( ( 13.0*6) / (4.0*pi*362880) );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         15 :   normaliz[4] = sqrt( (13.0*2) / (4.0*pi*3628800) );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         15 :   normaliz[5] = -sqrt( (13.0*1) / (4.0*pi*39916800) );</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         15 :   normaliz[6] = sqrt( (13.0*1) / (4.0*pi*479001600) );</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         15 :   coeff_poly.resize( 7 );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         15 :   coeff_poly[0]=-0.3125; coeff_poly[1]=0.0;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         15 :   coeff_poly[2]=6.5625; coeff_poly[3]=0.0;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         15 :   coeff_poly[4]=-19.6875; coeff_poly[5]=0.0;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         15 :   coeff_poly[6]=14.4375;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         15 : }</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/SMAC.cpp.func-sort-c.html b/coverage/crystallization/SMAC.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3d89b5a758
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+++ b/coverage/crystallization/SMAC.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/SMAC.cpp - functions</title>
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+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - SMAC.cpp<span style="font-size: 80%;"> (<a href="SMAC.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SMAC.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#146">_ZN4PLMD15crystallization4SMACC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#137">_ZN4PLMD15crystallization12_GLOBAL__N_117SMACRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#146">_ZN4PLMD15crystallization4SMACC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#139">_ZN4PLMD15crystallization4SMAC16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#137">_ZN4PLMD15crystallization12_GLOBAL__N_117SMACRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#137">_ZN4PLMD15crystallization12_GLOBAL__N_117SMACRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#200">_ZNK4PLMD15crystallization4SMAC30calculateCoordinationPrefactorERKdRd</a></td>
+              <td class="coverFnHi">4464</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#170">_ZNK4PLMD15crystallization4SMAC21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESA_RS3_RS8_SC_</a></td>
+              <td class="coverFnHi">1025856</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/SMAC.cpp.func.html b/coverage/crystallization/SMAC.cpp.func.html
new file mode 100644
index 0000000000..0f091a7335
--- /dev/null
+++ b/coverage/crystallization/SMAC.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/SMAC.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - SMAC.cpp<span style="font-size: 80%;"> (<a href="SMAC.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SMAC.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#137">_ZN4PLMD15crystallization12_GLOBAL__N_117SMACRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#137">_ZN4PLMD15crystallization12_GLOBAL__N_117SMACRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#137">_ZN4PLMD15crystallization12_GLOBAL__N_117SMACRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#139">_ZN4PLMD15crystallization4SMAC16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#146">_ZN4PLMD15crystallization4SMACC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#146">_ZN4PLMD15crystallization4SMACC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#170">_ZNK4PLMD15crystallization4SMAC21computeVectorFunctionERKNS_13VectorGenericILj3EEERKSt6vectorIdSaIdEESA_RS3_RS8_SC_</a></td>
+              <td class="coverFnHi">1025856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMAC.cpp.gcov.html#200">_ZNK4PLMD15crystallization4SMAC30calculateCoordinationPrefactorERKdRd</a></td>
+              <td class="coverFnHi">4464</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/SMAC.cpp.gcov.html b/coverage/crystallization/SMAC.cpp.gcov.html
new file mode 100644
index 0000000000..62c0932d51
--- /dev/null
+++ b/coverage/crystallization/SMAC.cpp.gcov.html
@@ -0,0 +1,283 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/SMAC.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - SMAC.cpp<span style="font-size: 80%;"> (source / <a href="SMAC.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OrientationSphere.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC MCOLVARF SMAC</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Calculate a variant on the SMAC collective variable</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : This variable is discussed in \cite smac-paper</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : The SMAC collective variable can be used to study the formation of molecular solids</a>
+<a name="34"><span class="lineNum">      34 </span>            : from either the melt or from solution.  The idea behind this variable is that what</a>
+<a name="35"><span class="lineNum">      35 </span>            : differentiates a molecular solid from a molecular liquid is an alignment of</a>
+<a name="36"><span class="lineNum">      36 </span>            : internal vectors in neighboring molecules.  In other words, the relative orientation</a>
+<a name="37"><span class="lineNum">      37 </span>            : of neighboring molecules is no longer random as it is in a liquid.  In a solid particular</a>
+<a name="38"><span class="lineNum">      38 </span>            : torsional angles between molecules are preferred.  As such this CV calculates the following</a>
+<a name="39"><span class="lineNum">      39 </span>            : average:</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : s_i = \frac{ \left\{ 1 - \psi\left[ \sum_{j \ne i} \sigma(r_{ij}) \right] \right\} \sum_{j \ne i} \sigma(r_{ij}) \sum_n K_n(\theta_{ij}) }{ \sum_{j \ne i} \sigma(r_{ij}) }</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : In this expression \f$r_{ij}\f$ is the distance between molecule \f$i\f$ and molecule \f$j\f$ and \f$\sigma(r_{ij})\f$ is a</a>
+<a name="46"><span class="lineNum">      46 </span>            : \ref switchingfunction that acts on this distance.  By including this switching function in the second summation in the</a>
+<a name="47"><span class="lineNum">      47 </span>            : numerator and in the denominator we are thus ensuring that we calculate an average over the molecules in the first coordination</a>
+<a name="48"><span class="lineNum">      48 </span>            : sphere of molecule \f$i\f$.  All molecules in higher coordination sphere will essentially contribute zero to the sums in the</a>
+<a name="49"><span class="lineNum">      49 </span>            : above expression because their \f$\sigma(r_{ij})\f$ will be very small.  \f$\psi\f$ is also a switching function.  The term</a>
+<a name="50"><span class="lineNum">      50 </span>            : including \f$\psi\f$ in the numerator is there to ensure that only those molecules that are attached to a reasonably large</a>
+<a name="51"><span class="lineNum">      51 </span>            : number of molecules.  It is important to include this &quot;more than&quot; switching function when you are simulating nucleation</a>
+<a name="52"><span class="lineNum">      52 </span>            : from solution with this CV.  Lastly, the $K_n functions are \ref kernelfunctions that take the torsion angle, \f$\theta_{ij}\f$, between the</a>
+<a name="53"><span class="lineNum">      53 </span>            : internal orientation vectors for molecules \f$i\f$ and \f$j\f$ as input.  These kernel functions should be set so that they are</a>
+<a name="54"><span class="lineNum">      54 </span>            : equal to one when the relative orientation of the molecules are as they are in the solid and equal to zero otherwise.</a>
+<a name="55"><span class="lineNum">      55 </span>            : The final \f$s_i\f$ quantity thus measures whether (on average) the molecules in the first coordination sphere around molecule \f$i\f$</a>
+<a name="56"><span class="lineNum">      56 </span>            : are oriented as they would be in the solid.  Furthermore, this Action is a multicolvar so you can calculate the \f$s_i\f$ values</a>
+<a name="57"><span class="lineNum">      57 </span>            : for all the molecules in your system simultaneously and then determine the average, the number less than and so on.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \par Examples</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : In the example below the orientation of the molecules in the system is determined by calculating the</a>
+<a name="62"><span class="lineNum">      62 </span>            : vector that connects a pair of atoms.  SMAC is then used to determine whether the molecules are sitting</a>
+<a name="63"><span class="lineNum">      63 </span>            : in a solid or liquid like environment.  We can determine whether the environment is solid or liquid like because in the solid the torsional angle between</a>
+<a name="64"><span class="lineNum">      64 </span>            : the bond vectors on adjacent molecules is close to 0 or \f$\pi\f$.  The final quantity that is output to the colvar</a>
+<a name="65"><span class="lineNum">      65 </span>            : file measures the number of molecules that have a SMAC parameter that is greater than 0.7.  N.B. By using</a>
+<a name="66"><span class="lineNum">      66 </span>            : the indices of three atoms for each of the MOL keywords below we are telling PLUMED to use the first two</a>
+<a name="67"><span class="lineNum">      67 </span>            : numbers to determine the orientation of the molecule that will ultimately be used when calculating the \f$\theta_{ij}\f$</a>
+<a name="68"><span class="lineNum">      68 </span>            : terms in the formula above.  The atom with the third index meanwhile is used when we calculate \f$r_{ij}\f$.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : MOLECULES ...</a>
+<a name="72"><span class="lineNum">      72 </span>            : MOL1=9,10,9</a>
+<a name="73"><span class="lineNum">      73 </span>            : MOL2=89,90,89</a>
+<a name="74"><span class="lineNum">      74 </span>            : MOL3=473,474,473</a>
+<a name="75"><span class="lineNum">      75 </span>            : MOL4=1161,1162,1161</a>
+<a name="76"><span class="lineNum">      76 </span>            : MOL5=1521,1522,1521</a>
+<a name="77"><span class="lineNum">      77 </span>            : MOL6=1593,1594,1593</a>
+<a name="78"><span class="lineNum">      78 </span>            : MOL7=1601,1602,1601</a>
+<a name="79"><span class="lineNum">      79 </span>            : MOL8=2201,2202,2201</a>
+<a name="80"><span class="lineNum">      80 </span>            : LABEL=m3</a>
+<a name="81"><span class="lineNum">      81 </span>            : ... MOLECULES</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : SMAC ...</a>
+<a name="84"><span class="lineNum">      84 </span>            :    SPECIES=m3 LOWMEM</a>
+<a name="85"><span class="lineNum">      85 </span>            :    KERNEL1={GAUSSIAN CENTER=0 SIGMA=0.480} KERNEL2={GAUSSIAN CENTER=pi SIGMA=0.480}</a>
+<a name="86"><span class="lineNum">      86 </span>            :    SWITCH={RATIONAL R_0=0.6} MORE_THAN={RATIONAL R_0=0.7} SWITCH_COORD={EXP R_0=4}</a>
+<a name="87"><span class="lineNum">      87 </span>            :    LABEL=s2</a>
+<a name="88"><span class="lineNum">      88 </span>            : ... SMAC</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : PRINT ARG=s2.* FILE=colvar</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endplumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : This second example works in a way that is very similar to the previous command.  Now, however,</a>
+<a name="94"><span class="lineNum">      94 </span>            : the orientation of the molecules is determined by finding the plane that contains the positions</a>
+<a name="95"><span class="lineNum">      95 </span>            : of three atoms.</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : \plumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : PLANES ...</a>
+<a name="99"><span class="lineNum">      99 </span>            : MOL1=9,10,11</a>
+<a name="100"><span class="lineNum">     100 </span>            : MOL2=89,90,91</a>
+<a name="101"><span class="lineNum">     101 </span>            : MOL3=473,474,475</a>
+<a name="102"><span class="lineNum">     102 </span>            : MOL4=1161,1162,1163</a>
+<a name="103"><span class="lineNum">     103 </span>            : MOL5=1521,1522,1523</a>
+<a name="104"><span class="lineNum">     104 </span>            : MOL6=1593,1594,1595</a>
+<a name="105"><span class="lineNum">     105 </span>            : MOL7=1601,1602,1603</a>
+<a name="106"><span class="lineNum">     106 </span>            : MOL8=2201,2202,2203</a>
+<a name="107"><span class="lineNum">     107 </span>            : VMEAN</a>
+<a name="108"><span class="lineNum">     108 </span>            : LABEL=m3</a>
+<a name="109"><span class="lineNum">     109 </span>            : ... PLANES</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : SMAC ...</a>
+<a name="112"><span class="lineNum">     112 </span>            :    SPECIES=m3 LOWMEM</a>
+<a name="113"><span class="lineNum">     113 </span>            :    KERNEL1={GAUSSIAN CENTER=0 SIGMA=0.480} KERNEL2={GAUSSIAN CENTER=pi SIGMA=0.480}</a>
+<a name="114"><span class="lineNum">     114 </span>            :    SWITCH={RATIONAL R_0=0.6} MORE_THAN={RATIONAL R_0=0.7} SWITCH_COORD={EXP R_0=3.0}</a>
+<a name="115"><span class="lineNum">     115 </span>            :    LABEL=s2</a>
+<a name="116"><span class="lineNum">     116 </span>            : ... SMAC</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : PRINT ARG=s2.* FILE=colvar</a>
+<a name="119"><span class="lineNum">     119 </span>            : \endplumedfile</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : */</a>
+<a name="122"><span class="lineNum">     122 </span>            : //+ENDPLUMEDOC</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : namespace PLMD {</a>
+<a name="125"><span class="lineNum">     125 </span>            : namespace crystallization {</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : class SMAC : public OrientationSphere {</a>
+<a name="128"><span class="lineNum">     128 </span>            : private:</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector&lt;KernelFunctions&gt; kernels;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   SwitchingFunction coord_switch;</a>
+<a name="131"><span class="lineNum">     131 </span>            : public:</a>
+<a name="132"><span class="lineNum">     132 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="133"><span class="lineNum">     133 </span>            :   explicit SMAC(const ActionOptions&amp; ao);</a>
+<a name="134"><span class="lineNum">     134 </span>            :   double computeVectorFunction( const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</a>
+<a name="135"><span class="lineNum">     135 </span>            :                                 Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const override;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   double calculateCoordinationPrefactor( const double&amp; coord, double&amp; df ) const override;</a>
+<a name="137"><span class="lineNum">     137 </span>            : };</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(SMAC,&quot;SMAC&quot;)</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          7 : void SMAC::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          7 :   OrientationSphere::registerKeywords(keys);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         14 :   keys.add(&quot;numbered&quot;,&quot;KERNEL&quot;,&quot;The kernels used in the function of the angle&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;SWITCH_COORD&quot;,&quot;This keyword is used to define the coordination switching function.&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         14 :   keys.reset_style(&quot;KERNEL&quot;,&quot;compulsory&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          7 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          5 : SMAC::SMAC(const ActionOptions&amp; ao):</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   Action(ao),</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          5 :   OrientationSphere(ao)</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : {</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          5 :   if( mybasemulticolvars.size()==0 ) error(&quot;SMAC must take multicolvar as input&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         11 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          6 :     if( (mybasemulticolvars[i]-&gt;getNumberOfQuantities()-2)%3!=0 ) error(&quot;SMAC is only possible with three dimensional vectors&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::string kernelinpt;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         10 :   for(int i=1;; i++) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         30 :     if( !parseNumbered(&quot;KERNEL&quot;,i,kernelinpt) ) break;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         10 :     KernelFunctions mykernel( kernelinpt );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         10 :     kernels.push_back( mykernel );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         10 :   }</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          5 :   if( kernels.size()==0 ) error(&quot;no kernels defined&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         10 :   std::string sw, errors; parse(&quot;SWITCH_COORD&quot;,sw);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          5 :   if(sw.length()==0) error(&quot;SWITCH_COORD keyword is missing&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          5 :   coord_switch.set(sw,errors);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          5 :   if(errors.length()&gt;0) error(&quot;the following errors were found in input to SWITCH_COORD : &quot; + errors );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          5 : }</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">    1025856 : double SMAC::computeVectorFunction( const Vector&amp; conn, const std::vector&lt;double&gt;&amp; vec1, const std::vector&lt;double&gt;&amp; vec2,</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :                                     Vector&amp; dconn, std::vector&lt;double&gt;&amp; dvec1, std::vector&lt;double&gt;&amp; dvec2 ) const {</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">    1025856 :   unsigned nvectors = ( vec1.size() - 2 ) / 3; plumed_assert( (vec1.size()-2)%3==0 );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">    1025856 :   std::vector&lt;Vector&gt; dv1(nvectors), dv2(nvectors), tdconn(nvectors); Torsion t; std::vector&lt;Vector&gt; v1(nvectors), v2(nvectors);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; pos;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    2051712 :   for(unsigned i=0; i&lt;nvectors; ++i) { pos.emplace_back( Tools::make_unique&lt;Value&gt;() ); pos[i]-&gt;setDomain( &quot;-pi&quot;, &quot;pi&quot; ); }</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">    2051712 :   for(unsigned j=0; j&lt;nvectors; ++j) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">    4103424 :     for(unsigned k=0; k&lt;3; ++k) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    3077568 :       v1[j][k]=vec1[2+3*j+k]; v2[j][k]=vec2[2+3*j+k];</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     }</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">    1025856 :     double angle = t.compute( v1[j], conn, v2[j], dv1[j], tdconn[j], dv2[j] );</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     pos[j]-&gt;set( angle );</a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">    1025856 :   auto pos_ptr=Tools::unique2raw(pos);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">    1025856 :   double ans=0; std::vector&lt;double&gt; deriv( nvectors ), df( nvectors, 0 );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">    3077568 :   for(unsigned i=0; i&lt;kernels.size(); ++i) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">    2051712 :     ans += kernels[i].evaluate( pos_ptr, deriv );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">    4103424 :     for(unsigned j=0; j&lt;nvectors; ++j) df[j] += deriv[j];</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">    2051712 :   dconn.zero(); for(unsigned j=0; j&lt;nvectors; ++j) dconn += df[j]*tdconn[j];</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">    2051712 :   for(unsigned j=0; j&lt;nvectors; ++j) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">    4103424 :     for(unsigned k=0; k&lt;3; ++k) { dvec1[2+3*j+k]=df[j]*dv1[j][k]; dvec2[2+3*j+k]=df[j]*dv2[j][k]; }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">    1025856 :   return ans;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">    1025856 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       4464 : double SMAC::calculateCoordinationPrefactor( const double&amp; coord, double&amp; df ) const {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       4464 :   double f=1-coord_switch.calculate( coord, df ); df*=-coord; return f;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/SimpleCubic.cpp.func-sort-c.html b/coverage/crystallization/SimpleCubic.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d0c42bc736
--- /dev/null
+++ b/coverage/crystallization/SimpleCubic.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/SimpleCubic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - SimpleCubic.cpp<span style="font-size: 80%;"> (<a href="SimpleCubic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SimpleCubic.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#82">_ZN4PLMD15crystallization11SimpleCubicC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#82">_ZN4PLMD15crystallization11SimpleCubicC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#76">_ZN4PLMD15crystallization12_GLOBAL__N_123SimpleCubicRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#78">_ZN4PLMD15crystallization11SimpleCubic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#89">_ZNK4PLMD15crystallization11SimpleCubic22calculateCubicHarmonicERKNS_13VectorGenericILj3EEERKdRS3_</a></td>
+              <td class="coverFnHi">4032</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#76">_ZN4PLMD15crystallization12_GLOBAL__N_123SimpleCubicRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#76">_ZN4PLMD15crystallization12_GLOBAL__N_123SimpleCubicRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/SimpleCubic.cpp.func.html b/coverage/crystallization/SimpleCubic.cpp.func.html
new file mode 100644
index 0000000000..0e9b638a1a
--- /dev/null
+++ b/coverage/crystallization/SimpleCubic.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/SimpleCubic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - SimpleCubic.cpp<span style="font-size: 80%;"> (<a href="SimpleCubic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SimpleCubic.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#78">_ZN4PLMD15crystallization11SimpleCubic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#82">_ZN4PLMD15crystallization11SimpleCubicC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#82">_ZN4PLMD15crystallization11SimpleCubicC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#76">_ZN4PLMD15crystallization12_GLOBAL__N_123SimpleCubicRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#76">_ZN4PLMD15crystallization12_GLOBAL__N_123SimpleCubicRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#76">_ZN4PLMD15crystallization12_GLOBAL__N_123SimpleCubicRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleCubic.cpp.gcov.html#89">_ZNK4PLMD15crystallization11SimpleCubic22calculateCubicHarmonicERKNS_13VectorGenericILj3EEERKdRS3_</a></td>
+              <td class="coverFnHi">4032</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/SimpleCubic.cpp.gcov.html b/coverage/crystallization/SimpleCubic.cpp.gcov.html
new file mode 100644
index 0000000000..828dafcb1f
--- /dev/null
+++ b/coverage/crystallization/SimpleCubic.cpp.gcov.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/SimpleCubic.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - SimpleCubic.cpp<span style="font-size: 80%;"> (source / <a href="SimpleCubic.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CubicHarmonicBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : using namespace std;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace crystallization {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC MCOLVAR SIMPLECUBIC</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Calculate whether or not the coordination spheres of atoms are arranged as they would be in a simple cubic structure.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : We can measure how similar the environment around atom \f$i\f$ is to a simple cubic structure is by evaluating</a>
+<a name="38"><span class="lineNum">      38 </span>            : the following quantity:</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            : s_i = \frac{ \sum_{i \ne j} \sigma(r_{ij}) \left[ \frac{ x_{ij}^4 + y_{ij}^4 + z_{ij}^4 }{r_{ij}^4} \right] }{ \sum_{i \ne j} \sigma(r_{ij}) }</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f]</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : In this expression \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$ are the \f$x\f$, \f$y\f$ and \f$z\f$ components of the vector connecting atom \f$i\f$ to</a>
+<a name="45"><span class="lineNum">      45 </span>            : atom \f$j\f$ and \f$r_{ij}\f$ is the magnitude of this vector.  \f$\sigma(r_{ij})\f$ is a \ref switchingfunction that acts on the distance between atom \f$i\f$ and atom \f$j\f$ and its inclusion in the numerator and the denominator of the above expression as well as the fact that we are summing</a>
+<a name="46"><span class="lineNum">      46 </span>            : over all of the other atoms in the system ensures that we are calculating an average</a>
+<a name="47"><span class="lineNum">      47 </span>            : of the function of \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$ for the atoms in the first coordination sphere around atom \f$i\f$.</a>
+<a name="48"><span class="lineNum">      48 </span>            : This quantity is once again a multicolvar so you can compute it for multiple atoms using a single PLUMED action and then compute</a>
+<a name="49"><span class="lineNum">      49 </span>            : the average value for the atoms in your system, the number of atoms that have an \f$s_i\f$ value that is more that some target and</a>
+<a name="50"><span class="lineNum">      50 </span>            : so on.  Notice also that you can rotate the reference frame if you are using a non-standard unit cell.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \par Examples</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The following input tells plumed to calculate the simple cubic parameter for the atoms 1-100 with themselves.</a>
+<a name="56"><span class="lineNum">      56 </span>            : The mean value is then calculated.</a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : SIMPLECUBIC SPECIES=1-100 R_0=1.0 MEAN</a>
+<a name="59"><span class="lineNum">      59 </span>            : \endplumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The following input tells plumed to look at the ways atoms 1-100 are within 3.0 are arranged about atoms</a>
+<a name="62"><span class="lineNum">      62 </span>            : from 101-110.  The number of simple cubic parameters that are greater than 0.8 is then output</a>
+<a name="63"><span class="lineNum">      63 </span>            : \plumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : SIMPLECUBIC SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=0.8 NN=6 MM=12 D_0=0}</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endplumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : //+ENDPLUMEDOC</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : class SimpleCubic : public CubicHarmonicBase {</a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit SimpleCubic(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const override;</a>
+<a name="76"><span class="lineNum">      76 </span>            : };</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(SimpleCubic,&quot;SIMPLECUBIC&quot;)</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 : void SimpleCubic::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          3 :   CubicHarmonicBase::registerKeywords( keys );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          3 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          1 : SimpleCubic::SimpleCubic(const ActionOptions&amp;ao):</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Action(ao),</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 :   CubicHarmonicBase(ao)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       4032 : double SimpleCubic::calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       4032 :   double x2 = distance[0]*distance[0];</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       4032 :   double x3 = distance[0]*x2;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       4032 :   double x4 = distance[0]*x3;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       4032 :   double y2 = distance[1]*distance[1];</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       4032 :   double y3 = distance[1]*y2;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       4032 :   double y4 = distance[1]*y3;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       4032 :   double z2 = distance[2]*distance[2];</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       4032 :   double z3 = distance[2]*z2;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       4032 :   double z4 = distance[2]*z3;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       4032 :   double r4 = pow( d2, 2 );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       4032 :   double tmp = ( x4 + y4 + z4 ) / r4;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       4032 :   double t1=(x2+y2+z2), t2=t1*t1, t3=(x4+y4+z4)/(t1*t2);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       4032 :   myder[0] = 4*x3/t2-4*distance[0]*t3;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       4032 :   myder[1] = 4*y3/t2-4*distance[1]*t3;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       4032 :   myder[2] = 4*z3/t2-4*distance[2]*t3;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       4032 :   return tmp;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Steinhardt.cpp.func-sort-c.html b/coverage/crystallization/Steinhardt.cpp.func-sort-c.html
new file mode 100644
index 0000000000..61f02edfda
--- /dev/null
+++ b/coverage/crystallization/Steinhardt.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Steinhardt.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Steinhardt.cpp<span style="font-size: 80%;"> (<a href="Steinhardt.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Steinhardt.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#42">_ZN4PLMD15crystallization10SteinhardtC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#66">_ZN4PLMD15crystallization10Steinhardt18setAngularMomentumERKj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#42">_ZN4PLMD15crystallization10SteinhardtC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#27">_ZN4PLMD15crystallization10Steinhardt16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#70">_ZNK4PLMD15crystallization10Steinhardt15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">74931</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#155">_ZNK4PLMD15crystallization10Steinhardt10deriv_polyERKjRKdRd</a></td>
+              <td class="coverFnHi">15435674</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Steinhardt.cpp.func.html b/coverage/crystallization/Steinhardt.cpp.func.html
new file mode 100644
index 0000000000..053a362331
--- /dev/null
+++ b/coverage/crystallization/Steinhardt.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <title>LCOV - plumed test coverage - crystallization/Steinhardt.cpp - functions</title>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Steinhardt.cpp<span style="font-size: 80%;"> (<a href="Steinhardt.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    </tr>
+
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#27">_ZN4PLMD15crystallization10Steinhardt16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#66">_ZN4PLMD15crystallization10Steinhardt18setAngularMomentumERKj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#42">_ZN4PLMD15crystallization10SteinhardtC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#42">_ZN4PLMD15crystallization10SteinhardtC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#155">_ZNK4PLMD15crystallization10Steinhardt10deriv_polyERKjRKdRd</a></td>
+              <td class="coverFnHi">15435674</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steinhardt.cpp.gcov.html#70">_ZNK4PLMD15crystallization10Steinhardt15calculateVectorERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">74931</td>
+            </tr>
+  </table>
+  <br>
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diff --git a/coverage/crystallization/Steinhardt.cpp.gcov.html b/coverage/crystallization/Steinhardt.cpp.gcov.html
new file mode 100644
index 0000000000..734b6ac221
--- /dev/null
+++ b/coverage/crystallization/Steinhardt.cpp.gcov.html
@@ -0,0 +1,251 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Steinhardt.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Steinhardt.cpp<span style="font-size: 80%;"> (source / <a href="Steinhardt.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Steinhardt.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;complex&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace crystallization {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         24 : void Steinhardt::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         24 :   VectorMultiColvar::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;12&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         48 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         72 :   keys.use(&quot;SPECIES&quot;); keys.use(&quot;SPECIESA&quot;); keys.use(&quot;SPECIESB&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         96 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        120 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;ALT_MIN&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         48 :   keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         24 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         18 : Steinhardt::Steinhardt( const ActionOptions&amp; ao ):</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   Action(ao),</a>
+<a name="46"><span class="lineNum">      46 </span>            :   VectorMultiColvar(ao),</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         18 :   tmom(0)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span>            :   // Read in the switching function</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         36 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         18 :   if(sw.length()&gt;0) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          6 :     switchingFunction.set(sw,errors);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   } else {</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         12 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         24 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         24 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         12 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         12 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   }</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         18 :   log.printf(&quot;  Steinhardt parameter of central atom and those within %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         36 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Tribello, Giberti, Sosso, Salvalaglio and Parrinello, J. Chem. Theory Comput. 13, 1317 (2017)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   // Set the link cell cutoff</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         18 :   setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         18 :   rcut = switchingFunction.get_dmax(); rcut2 = rcut*rcut;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         18 :   std::vector&lt;AtomNumber&gt; all_atoms; setupMultiColvarBase( all_atoms );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         18 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         18 : void Steinhardt::setAngularMomentum( const unsigned&amp; ang ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         18 :   tmom=ang; setVectorDimensionality( 2*(2*ang + 1) );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         18 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      74931 : void Steinhardt::calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   double dfunc, dpoly_ass, md, tq6, itq6, real_z, imag_z;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      74931 :   Vector dz, myrealvec, myimagvec, real_dz, imag_dz;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   // The square root of -1</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::complex&lt;double&gt; ii( 0.0, 1.0 ), dp_x, dp_y, dp_z;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      74931 :   unsigned ncomp=2*tmom+1;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   double sw, poly_ass, dlen; std::complex&lt;double&gt; powered;</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">    7465705 :   for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :     Vector&amp; distance=myatoms.getPosition(i);  // getSeparation( myatoms.getPosition(0), myatoms.getPosition(i) );</a>
+<a name="82"><span class="lineNum">      82 </span>            :     double d2;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">   12224372 :     if ( (d2=distance[0]*distance[0])&lt;rcut2 &amp;&amp;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    4833598 :          (d2+=distance[1]*distance[1])&lt;rcut2 &amp;&amp;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">   10872046 :          (d2+=distance[2]*distance[2])&lt;rcut2 &amp;&amp;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :          d2&gt;epsilon ) {</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    2408222 :       dlen = sqrt(d2);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">    2408222 :       sw = switchingFunction.calculate( dlen, dfunc );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">    2408222 :       accumulateSymmetryFunction( -1, i, sw, (+dfunc)*distance, (-dfunc)*Tensor( distance,distance ), myatoms );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    2408222 :       double dlen3 = d2*dlen;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :       // Do stuff for m=0</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    2408222 :       poly_ass=deriv_poly( 0, distance[2]/dlen, dpoly_ass );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :       // Derivatives of z/r wrt x, y, z</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    2408222 :       dz = -( distance[2] / dlen3 )*distance; dz[2] += (1.0 / dlen);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :       // Derivative wrt to the vector connecting the two atoms</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    2408222 :       myrealvec = (+sw)*dpoly_ass*dz + poly_ass*(+dfunc)*distance;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :       // Accumulate the derivatives</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">    2408222 :       accumulateSymmetryFunction( 2 + tmom, i, sw*poly_ass, myrealvec, Tensor( -myrealvec,distance ), myatoms );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :       // The complex number of which we have to take powers</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">    2408222 :       std::complex&lt;double&gt; com1( distance[0]/dlen,distance[1]/dlen );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :       powered = std::complex&lt;double&gt;(1.0,0.0);</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :       // Do stuff for all other m values</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">   15435674 :       for(unsigned m=1; m&lt;=tmom; ++m) {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :         // Calculate Legendre Polynomial</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">   13027452 :         poly_ass=deriv_poly( m, distance[2]/dlen, dpoly_ass );</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :         // Calculate power of complex number</a>
+<a name="110"><span class="lineNum">     110 </span>            :         // if(std::abs(com1)&gt;epsilon) powered=pow(com1,m-1);</a>
+<a name="111"><span class="lineNum">     111 </span>            :         // else if(m==1) powered=std::complex&lt;double&gt;(1.,0);</a>
+<a name="112"><span class="lineNum">     112 </span>            :         // else powered = std::complex&lt;double&gt;(0.,0.);</a>
+<a name="113"><span class="lineNum">     113 </span>            :         // Real and imaginary parts of z</a>
+<a name="114"><span class="lineNum">     114 </span>            :         real_z = real(com1*powered); imag_z = imag(com1*powered );</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :         // Calculate steinhardt parameter</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">   13027452 :         tq6=poly_ass*real_z;   // Real part of steinhardt parameter</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">   13027452 :         itq6=poly_ass*imag_z;  // Imaginary part of steinhardt parameter</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :         // Derivatives wrt ( x/r + iy )^m</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">   13027452 :         md=static_cast&lt;double&gt;(m);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">   13027452 :         dp_x = md*powered*( (1.0/dlen)-(distance[0]*distance[0])/dlen3-ii*(distance[0]*distance[1])/dlen3 );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">   13027452 :         dp_y = md*powered*( ii*(1.0/dlen)-(distance[0]*distance[1])/dlen3-ii*(distance[1]*distance[1])/dlen3 );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">   13027452 :         dp_z = md*powered*( -(distance[0]*distance[2])/dlen3-ii*(distance[1]*distance[2])/dlen3 );</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :         // Derivatives of real and imaginary parts of above</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">   13027452 :         real_dz[0] = real( dp_x ); real_dz[1] = real( dp_y ); real_dz[2] = real( dp_z );</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">   13027452 :         imag_dz[0] = imag( dp_x ); imag_dz[1] = imag( dp_y ); imag_dz[2] = imag( dp_z );</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :         // Complete derivative of steinhardt parameter</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">   13027452 :         myrealvec = (+sw)*dpoly_ass*real_z*dz + (+dfunc)*distance*tq6 + (+sw)*poly_ass*real_dz;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">   13027452 :         myimagvec = (+sw)*dpoly_ass*imag_z*dz + (+dfunc)*distance*itq6 + (+sw)*poly_ass*imag_dz;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :         // Real part</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">   13027452 :         accumulateSymmetryFunction( 2 + tmom + m, i, sw*tq6, myrealvec, Tensor( -myrealvec,distance ), myatoms );</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :         // Imaginary part</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">   13027452 :         accumulateSymmetryFunction( 2+ncomp+tmom+m, i, sw*itq6, myimagvec, Tensor( -myimagvec,distance ), myatoms );</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :         // Store -m part of vector</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">   13027452 :         double pref=pow(-1.0,m);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :         // -m part of vector is just +m part multiplied by (-1.0)**m and multiplied by complex</a>
+<a name="141"><span class="lineNum">     141 </span>            :         // conjugate of Legendre polynomial</a>
+<a name="142"><span class="lineNum">     142 </span>            :         // Real part</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">   13027452 :         accumulateSymmetryFunction( 2+tmom-m, i, pref*sw*tq6, pref*myrealvec, pref*Tensor( -myrealvec,distance ), myatoms );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :         // Imaginary part</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">   13027452 :         accumulateSymmetryFunction( 2+ncomp+tmom-m, i, -pref*sw*itq6, -pref*myimagvec, pref*Tensor( myimagvec,distance ), myatoms );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :         // Calculate next power of complex number</a>
+<a name="147"><span class="lineNum">     147 </span>            :         powered *= com1;</a>
+<a name="148"><span class="lineNum">     148 </span>            :       }</a>
+<a name="149"><span class="lineNum">     149 </span>            :     }</a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   // Normalize</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      74931 :   updateActiveAtoms( myatoms );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    1892577 :   for(unsigned i=0; i&lt;getNumberOfComponentsInVector(); ++i) myatoms.getUnderlyingMultiValue().quotientRule( 2+i, 2+i );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      74931 : }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">   15435674 : double Steinhardt::deriv_poly( const unsigned&amp; m, const double&amp; val, double&amp; df ) const {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   double fact=1.0;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">   58187996 :   for(unsigned j=1; j&lt;=m; ++j) fact=fact*j;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   15435674 :   double res=coeff_poly[m]*fact;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">   15435674 :   double pow=1.0, xi=val, dxi=1.0; df=0.0;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">   58187996 :   for(int i=m+1; i&lt;=tmom; ++i) {</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     double fact=1.0;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">  109266592 :     for(unsigned j=i-m+1; j&lt;=i; ++j) fact=fact*j;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">   42752322 :     res=res+coeff_poly[i]*fact*xi;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">   42752322 :     df = df + pow*coeff_poly[i]*fact*dxi;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">   42752322 :     xi=xi*val; dxi=dxi*val; pow+=1.0;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">   15435674 :   df = df*normaliz[m];</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">   15435674 :   return normaliz[m]*res;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Tetrahedral.cpp.func-sort-c.html b/coverage/crystallization/Tetrahedral.cpp.func-sort-c.html
new file mode 100644
index 0000000000..18d10329b4
--- /dev/null
+++ b/coverage/crystallization/Tetrahedral.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Tetrahedral.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Tetrahedral.cpp<span style="font-size: 80%;"> (<a href="Tetrahedral.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Tetrahedral.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#87">_ZN4PLMD15crystallization11TetrahedralC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#87">_ZN4PLMD15crystallization11TetrahedralC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#81">_ZN4PLMD15crystallization12_GLOBAL__N_123TetrahedralRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#83">_ZN4PLMD15crystallization11Tetrahedral16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#94">_ZNK4PLMD15crystallization11Tetrahedral22calculateCubicHarmonicERKNS_13VectorGenericILj3EEERKdRS3_</a></td>
+              <td class="coverFnHi">4032</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#81">_ZN4PLMD15crystallization12_GLOBAL__N_123TetrahedralRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#81">_ZN4PLMD15crystallization12_GLOBAL__N_123TetrahedralRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Tetrahedral.cpp.func.html b/coverage/crystallization/Tetrahedral.cpp.func.html
new file mode 100644
index 0000000000..b5bc88dcfb
--- /dev/null
+++ b/coverage/crystallization/Tetrahedral.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Tetrahedral.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Tetrahedral.cpp<span style="font-size: 80%;"> (<a href="Tetrahedral.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Tetrahedral.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#83">_ZN4PLMD15crystallization11Tetrahedral16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#87">_ZN4PLMD15crystallization11TetrahedralC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#87">_ZN4PLMD15crystallization11TetrahedralC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#81">_ZN4PLMD15crystallization12_GLOBAL__N_123TetrahedralRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#81">_ZN4PLMD15crystallization12_GLOBAL__N_123TetrahedralRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#81">_ZN4PLMD15crystallization12_GLOBAL__N_123TetrahedralRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tetrahedral.cpp.gcov.html#94">_ZNK4PLMD15crystallization11Tetrahedral22calculateCubicHarmonicERKNS_13VectorGenericILj3EEERKdRS3_</a></td>
+              <td class="coverFnHi">4032</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/Tetrahedral.cpp.gcov.html b/coverage/crystallization/Tetrahedral.cpp.gcov.html
new file mode 100644
index 0000000000..525ff4d2c2
--- /dev/null
+++ b/coverage/crystallization/Tetrahedral.cpp.gcov.html
@@ -0,0 +1,203 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/Tetrahedral.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - Tetrahedral.cpp<span style="font-size: 80%;"> (source / <a href="Tetrahedral.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CubicHarmonicBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : using namespace std;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace crystallization {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC MCOLVAR TETRAHEDRAL</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Calculate the degree to which the environment about ions has a tetrahedral order.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : We can measure the degree to which the atoms in the first coordination shell around any atom, \f$i\f$ is</a>
+<a name="38"><span class="lineNum">      38 </span>            : is arranged like a tetrahedron using the following function.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            :  s(i) = \frac{1}{\sum_j \sigma( r_{ij} )} \sum_j \sigma( r_{ij} )\left[ \frac{(x_{ij} + y_{ij} + z_{ij})^3}{r_{ij}^3} +</a>
+<a name="42"><span class="lineNum">      42 </span>            :                                                                         \frac{(x_{ij} - y_{ij} - z_{ij})^3}{r_{ij}^3} +</a>
+<a name="43"><span class="lineNum">      43 </span>            :                                                                         \frac{(-x_{ij} + y_{ij} - z_{ij})^3}{r_{ij}^3} +</a>
+<a name="44"><span class="lineNum">      44 </span>            :                                                                         \frac{(-x_{ij} - y_{ij} + z_{ij})^3}{r_{ij}^3} \right]</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Here \f$r_{ij}\f$ is the magnitude of the vector connecting atom \f$i\f$ to atom \f$j\f$ and \f$x_{ij}\f$, \f$y_{ij}\f$ and \f$z_{ij}\f$</a>
+<a name="48"><span class="lineNum">      48 </span>            : are its three components.  The function  \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between</a>
+<a name="49"><span class="lineNum">      49 </span>            : atoms \f$i\f$ and \f$j\f$.  The parameters of this function should be set so that the function is equal to one</a>
+<a name="50"><span class="lineNum">      50 </span>            : when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The following command calculates the average value of the TETRAHEDRAL parameter for a set of 64 atoms all of the same type</a>
+<a name="55"><span class="lineNum">      55 </span>            : and outputs this quantity to a file called colvar.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : tt: TETRAHEDRAL SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=tt.mean FILE=colvar</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The following command calculates the number of TETRAHEDRAL parameters that are greater than 0.8 in a set of 10 atoms.</a>
+<a name="63"><span class="lineNum">      63 </span>            : In this calculation it is assumed that there are two atom types A and B and that the first coordination sphere of the</a>
+<a name="64"><span class="lineNum">      64 </span>            : 10 atoms of type A contains atoms of type B.  The formula above is thus calculated for ten different A atoms and within</a>
+<a name="65"><span class="lineNum">      65 </span>            : it the sum over \f$j\f$ runs over 40 atoms of type B that could be in the first coordination sphere.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \plumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : tt: TETRAHEDRAL SPECIESA=1-10 SPECIESB=11-40 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=0.8}</a>
+<a name="69"><span class="lineNum">      69 </span>            : PRINT ARG=tt.* FILE=colvar</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : class Tetrahedral : public CubicHarmonicBase {</a>
+<a name="77"><span class="lineNum">      77 </span>            : public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="79"><span class="lineNum">      79 </span>            :   explicit Tetrahedral(const ActionOptions&amp;);</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Tetrahedral,&quot;TETRAHEDRAL&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          3 : void Tetrahedral::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          3 :   CubicHarmonicBase::registerKeywords( keys );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 : Tetrahedral::Tetrahedral(const ActionOptions&amp;ao):</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   Action(ao),</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          1 :   CubicHarmonicBase(ao)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       4032 : double Tetrahedral::calculateCubicHarmonic( const Vector&amp; distance, const double&amp; d2, Vector&amp; myder ) const {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       4032 :   double sp1 = +distance[0]+distance[1]+distance[2];</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       4032 :   double sp2 = +distance[0]-distance[1]-distance[2];</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       4032 :   double sp3 = -distance[0]+distance[1]-distance[2];</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       4032 :   double sp4 = -distance[0]-distance[1]+distance[2];</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   double sp1c = pow( sp1, 3 );</a>
+<a name="103"><span class="lineNum">     103 </span>            :   double sp2c = pow( sp2, 3 );</a>
+<a name="104"><span class="lineNum">     104 </span>            :   double sp3c = pow( sp3, 3 );</a>
+<a name="105"><span class="lineNum">     105 </span>            :   double sp4c = pow( sp4, 3 );</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       4032 :   double d1 = distance.modulo();</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   double r3 = pow( d1, 3 );</a>
+<a name="109"><span class="lineNum">     109 </span>            :   double r5 = pow( d1, 5 );</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       4032 :   double tmp = sp1c/r3 + sp2c/r3 + sp3c/r3 + sp4c/r3;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       4032 :   double t1=(3*sp1c)/r5; double tt1=((3*sp1*sp1)/r3);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       4032 :   double t2=(3*sp2c)/r5; double tt2=((3*sp2*sp2)/r3);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       4032 :   double t3=(3*sp3c)/r5; double tt3=((3*sp3*sp3)/r3);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       4032 :   double t4=(3*sp4c)/r5; double tt4=((3*sp4*sp4)/r3);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       4032 :   myder[0] = (tt1-(distance[0]*t1))  + (tt2-(distance[0]*t2))  + (-tt3-(distance[0]*t3))  + (-tt4-(distance[0]*t4));</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       4032 :   myder[1] = (tt1-(distance[1]*t1))  + (-tt2-(distance[1]*t2))  + (tt3-(distance[1]*t3))  + (-tt4-(distance[1]*t4));</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       4032 :   myder[2] = (tt1-(distance[2]*t1))  + (-tt2-(distance[2]*t2))  + (-tt3-(distance[2]*t3))  + (tt4-(distance[2]*t4));</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       4032 :   return tmp;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMean.cpp.func-sort-c.html b/coverage/crystallization/VectorMean.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7987ab35b2
--- /dev/null
+++ b/coverage/crystallization/VectorMean.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMean.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMean.cpp<span style="font-size: 80%;"> (<a href="VectorMean.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VectorMean.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#44">_ZN4PLMD15crystallization10VectorMean16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#60">_ZN4PLMD15crystallization10VectorMean16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#54">_ZN4PLMD15crystallization10VectorMeanC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_120VectorMeanRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#64">_ZN4PLMD15crystallization10VectorMean6resizeEv</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#92">_ZN4PLMD15crystallization10VectorMean6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1828</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#48">_ZN4PLMD15crystallization10VectorMean14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_120VectorMeanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_120VectorMeanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#75">_ZNK4PLMD15crystallization10VectorMean9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">14712</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
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diff --git a/coverage/crystallization/VectorMean.cpp.func.html b/coverage/crystallization/VectorMean.cpp.func.html
new file mode 100644
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+++ b/coverage/crystallization/VectorMean.cpp.func.html
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+
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+  <title>LCOV - plumed test coverage - crystallization/VectorMean.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMean.cpp<span style="font-size: 80%;"> (<a href="VectorMean.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VectorMean.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#48">_ZN4PLMD15crystallization10VectorMean14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#44">_ZN4PLMD15crystallization10VectorMean16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#60">_ZN4PLMD15crystallization10VectorMean16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#92">_ZN4PLMD15crystallization10VectorMean6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1828</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#64">_ZN4PLMD15crystallization10VectorMean6resizeEv</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#54">_ZN4PLMD15crystallization10VectorMeanC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_120VectorMeanRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_120VectorMeanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_120VectorMeanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMean.cpp.gcov.html#75">_ZNK4PLMD15crystallization10VectorMean9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">14712</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMean.cpp.gcov.html b/coverage/crystallization/VectorMean.cpp.gcov.html
new file mode 100644
index 0000000000..61ac7f7232
--- /dev/null
+++ b/coverage/crystallization/VectorMean.cpp.gcov.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMean.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMean.cpp<span style="font-size: 80%;"> (source / <a href="VectorMean.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;vesselbase/VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/ActionVolume.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace crystallization {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class VectorMean : public vesselbase::FunctionVessel {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   unsigned nder;</a>
+<a name="34"><span class="lineNum">      34 </span>            : public:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="37"><span class="lineNum">      37 </span>            :   explicit VectorMean( const vesselbase::VesselOptions&amp; da );</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::string value_descriptor();</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void resize();</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const ;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer );</a>
+<a name="42"><span class="lineNum">      42 </span>            : };</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      12510 : PLUMED_REGISTER_VESSEL(VectorMean,&quot;VMEAN&quot;)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          6 : void VectorMean::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          6 :   vesselbase::FunctionVessel::registerKeywords(keys);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          6 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       4168 : void VectorMean::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;VMEAN&quot;,&quot;calculate the norm of the mean vector.&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;vmean&quot;,&quot;VMEAN&quot;,&quot;the norm of the mean vector. The output component can be referred to elsewhere in the input &quot;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :                           &quot;file by using the label.vmean&quot;);</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       4168 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          6 : VectorMean::VectorMean( const vesselbase::VesselOptions&amp; da ) :</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   FunctionVessel(da),</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          6 :   nder(0)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          6 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          6 : std::string VectorMean::value_descriptor() {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          6 :   return &quot;the norm of the mean vector&quot;;</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         23 : void VectorMean::resize() {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         23 :   unsigned ncomp=getAction()-&gt;getNumberOfQuantities() - 2;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         23 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         16 :     nder=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         16 :     resizeBuffer( (1+nder)*(ncomp+1) ); getFinalValue()-&gt;resizeDerivatives( nder );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   } else {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          7 :     nder=0; resizeBuffer(ncomp+1);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         23 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      14712 : void VectorMean::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      14712 :   unsigned ncomp=getAction()-&gt;getNumberOfQuantities()-2;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      14712 :   double weight=myvals.get(0); plumed_dbg_assert( weight&gt;=getTolerance() );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      14712 :   buffer[bufstart] += weight;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      61240 :   for(unsigned i=0; i&lt;ncomp; ++i) buffer[bufstart + (1+i)*(1+nder)] += weight*myvals.get(2+i);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      14712 :   if( !getAction()-&gt;derivativesAreRequired() ) return;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      14712 :   if( diffweight ) myvals.chainRule( 0, 0, 1, 0, 1.0, bufstart, buffer );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      61240 :   for(unsigned i=0; i&lt;ncomp; ++i) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      46528 :     double colvar=myvals.get(2+i);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      46528 :     myvals.chainRule( 2+i, 1+i, 1, 0, weight, bufstart, buffer );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      46528 :     if( diffweight ) myvals.chainRule( 0, 1+i, 1, 0, colvar, bufstart, buffer );</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            :   return;</a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1828 : void VectorMean::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1828 :   unsigned ncomp=getAction()-&gt;getNumberOfQuantities()-2;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1828 :   double sum=0, ww=buffer[bufstart];</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       7358 :   for(unsigned i=0; i&lt;ncomp; ++i) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       5530 :     double tmp = buffer[bufstart+(nder+1)*(i+1)] / ww;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       5530 :     sum+=tmp*tmp;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1828 :   setOutputValue( sqrt(sum) );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       1828 :   if( !getAction()-&gt;derivativesAreRequired() ) return;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1828 :   Value* fval=getFinalValue(); double tw = 1.0 / sqrt(sum);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       7358 :   for(unsigned icomp=0; icomp&lt;ncomp; ++icomp) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       5530 :     double tmp = buffer[bufstart + (icomp+1)*(1+nder)] / ww;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       5530 :     unsigned bstart = bufstart + (1+icomp)*(nder+1) + 1;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     460636 :     for(unsigned jder=0; jder&lt;nder; ++jder) fval-&gt;addDerivative( jder, (tw*tmp/ww)*( buffer[bstart + jder] - tmp*buffer[bufstart + 1 + jder] ) );</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMultiColvar.cpp.func-sort-c.html b/coverage/crystallization/VectorMultiColvar.cpp.func-sort-c.html
new file mode 100644
index 0000000000..09a42b335a
--- /dev/null
+++ b/coverage/crystallization/VectorMultiColvar.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMultiColvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMultiColvar.cpp<span style="font-size: 80%;"> (<a href="VectorMultiColvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryMed">79.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VectorMultiColvar.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#47">_ZN4PLMD15crystallization17VectorMultiColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#55">_ZN4PLMD15crystallization17VectorMultiColvar23setVectorDimensionalityERKj</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#47">_ZN4PLMD15crystallization17VectorMultiColvarC2ERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#26">_ZN4PLMD15crystallization17VectorMultiColvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#94">_ZNK4PLMD15crystallization17VectorMultiColvar26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">29195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#88">_ZNK4PLMD15crystallization17VectorMultiColvar15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">64156</td>
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+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#63">_ZNK4PLMD15crystallization17VectorMultiColvar7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">100463</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMultiColvar.cpp.func.html b/coverage/crystallization/VectorMultiColvar.cpp.func.html
new file mode 100644
index 0000000000..e0b2a44217
--- /dev/null
+++ b/coverage/crystallization/VectorMultiColvar.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMultiColvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMultiColvar.cpp<span style="font-size: 80%;"> (<a href="VectorMultiColvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryMed">79.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VectorMultiColvar.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#105">_ZN4PLMD15crystallization17VectorMultiColvar16addForcesOnAtomsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#26">_ZN4PLMD15crystallization17VectorMultiColvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#59">_ZN4PLMD15crystallization17VectorMultiColvar22doNotCalculateDirectorEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#55">_ZN4PLMD15crystallization17VectorMultiColvar23setVectorDimensionalityERKj</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#47">_ZN4PLMD15crystallization17VectorMultiColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#47">_ZN4PLMD15crystallization17VectorMultiColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#88">_ZNK4PLMD15crystallization17VectorMultiColvar15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">64156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#94">_ZNK4PLMD15crystallization17VectorMultiColvar26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">29195</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.cpp.gcov.html#63">_ZNK4PLMD15crystallization17VectorMultiColvar7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">100463</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMultiColvar.cpp.gcov.html b/coverage/crystallization/VectorMultiColvar.cpp.gcov.html
new file mode 100644
index 0000000000..3a56311011
--- /dev/null
+++ b/coverage/crystallization/VectorMultiColvar.cpp.gcov.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMultiColvar.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMultiColvar.cpp<span style="font-size: 80%;"> (source / <a href="VectorMultiColvar.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryMed">79.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/BridgedMultiColvarFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace crystallization {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         38 : void VectorMultiColvar::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         38 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         38 :   keys.setComponentsIntroduction(&quot;When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in &quot;</span></a>
+<a name="31"><span class="lineNum">      31 </span>            :                                  &quot;regular collective variables.  The label is used to reference the full set of vectors calculated by &quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            :                                  &quot;the action.  This is usual when using \\ref multicolvarfunction. Generally when doing this the previously calculated &quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            :                                  &quot;multicolvar will be referenced using the DATA keyword rather than ARG.\n\n&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            :                                  &quot;This Action can be used to calculate the following scalar quantities directly.  These quantities are calculated by &quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            :                                  &quot;employing the keywords listed below. &quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            :                                  &quot;These quantities can then be referenced elsewhere in the input file by using this Action's label &quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            :                                  &quot;followed by a dot and the name of the quantity. All of them can be calculated multiple times &quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            :                                  &quot;with different parameters.  In this case the quantities calculated can be referenced elsewhere in the &quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            :                                  &quot;input by using the name of the quantity followed by a numerical identifier &quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :                                  &quot;e.g. &lt;em&gt;label&lt;/em&gt;.lessthan-1, &lt;em&gt;label&lt;/em&gt;.lessthan-2 etc.  When doing this and, for clarity we have &quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            :                                  &quot;made it so that the user can set the label for the components. As such by using the LABEL keyword in the description of the keyword &quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            :                                  &quot;input you can customize the component name.  In addition, you can calculate all of these scalar functions for &quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            :                                  &quot;one particular component of the calculated vector by making use of the COMPONENT keyword.  The first component is used to &quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            :                                  &quot;refer to the norm of the vector.  The individual components can then be referenced using the numbers 2, 3, and so on.  So &quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            :                                  &quot;as an example MEAN1={COMPONENT=1} calculates the average vector norm.  MEAN2={COMPONENT=2} by contrast calculates the mean &quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            :                                  &quot;for all of the first components of the vectors.&quot;);</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         38 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         26 : VectorMultiColvar::VectorMultiColvar(const ActionOptions&amp; ao):</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   Action(ao),</a>
+<a name="51"><span class="lineNum">      51 </span>            :   MultiColvarBase(ao),</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         26 :   store_director(true)</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   setLowMemOption(true);</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         26 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         26 : void VectorMultiColvar::setVectorDimensionality( const unsigned&amp; ncomp ) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         26 :   ncomponents = ncomp; resizeFunctions(); // This resize needs to be here to ensure buffers are set to correct size in base</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         26 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 : void VectorMultiColvar::doNotCalculateDirector() {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   store_director=false;    // Need a sanity check in here so that you don't use the same instance of Q4 to calculate vectors and directors</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     100463 : double VectorMultiColvar::compute( const unsigned&amp; taskIndex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   // Now calculate the vector</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     100463 :   calculateVector( myatoms );</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   // Sort out the active derivatives</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     100463 :   updateActiveAtoms( myatoms );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   // Now calculate the norm of the vector (this is what we return here)</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double norm=0;</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">    1994705 :   for(unsigned i=0; i&lt;ncomponents; ++i) norm += myatoms.getValue(2+i)*myatoms.getValue(2+i);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     100463 :   norm=sqrt(norm);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     100463 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      74901 :     double inorm = 1.0 / norm; std::vector&lt;double&gt; dervec( ncomponents );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    1498191 :     for(unsigned i=0; i&lt;ncomponents; ++i) dervec[i] = inorm*myatoms.getValue(2+i);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :     MultiValue&amp; myvals=myatoms.getUnderlyingMultiValue();</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">    7788750 :     for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">    7713849 :       unsigned jder=myvals.getActiveIndex(j);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">  183127731 :       for(unsigned i=0; i&lt;ncomponents; ++i) myvals.addDerivative( 1, jder, dervec[i]*myvals.getDerivative( 2+i, jder ) );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :     }</a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     100463 :   return norm;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      64156 : void VectorMultiColvar::normalizeVector( std::vector&lt;double&gt;&amp; vals ) const {</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   double inorm = 1.0;</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      64156 :   if( vals[1]&gt;epsilon ) inorm = 1.0 / vals[1];</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    1632096 :   for(unsigned i=2; i&lt;vals.size(); ++i) vals[i] = inorm*vals[i];</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      64156 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      29195 : void VectorMultiColvar::normalizeVectorDerivatives( MultiValue&amp; myvals ) const {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      29195 :   double v = myvals.get(1), weight = 1.0 / v,  wdf = 1.0 / ( v*v*v );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">    3570659 :   for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">    3541464 :     double comp2=0.0; unsigned jder=myvals.getActiveIndex(j);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">   85824660 :     for(unsigned jcomp=2; jcomp&lt;myvals.getNumberOfValues(); ++jcomp) comp2 += myvals.get(jcomp)*myvals.getDerivative( jcomp, jder );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">   85824660 :     for(unsigned jcomp=2; jcomp&lt;myvals.getNumberOfValues(); ++jcomp) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">   82283196 :       myvals.setDerivative( jcomp, jder, weight*myvals.getDerivative( jcomp, jder ) - wdf*comp2*myvals.get(jcomp) );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :     }</a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      29195 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 : void VectorMultiColvar::addForcesOnAtoms( const std::vector&lt;double&gt;&amp; inforces ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   plumed_dbg_assert( inforces.size()==getNumberOfDerivatives() );</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; oldforces( getNumberOfDerivatives() );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   getForcesFromVessels( oldforces );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;getNumberOfDerivatives(); ++i) oldforces[i]+=inforces[i];</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   setForcesOnAtoms( oldforces );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMultiColvar.h.func-sort-c.html b/coverage/crystallization/VectorMultiColvar.h.func-sort-c.html
new file mode 100644
index 0000000000..aa8f53cb11
--- /dev/null
+++ b/coverage/crystallization/VectorMultiColvar.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMultiColvar.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMultiColvar.h<span style="font-size: 80%;"> (<a href="VectorMultiColvar.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VectorMultiColvar.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#62">_ZNK4PLMD15crystallization17VectorMultiColvar28hasDifferentiableOrientationEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#48">_ZN4PLMD15crystallization17VectorMultiColvarD2Ev</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#50">_ZN4PLMD15crystallization17VectorMultiColvar10isPeriodicEv</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#76">_ZNK4PLMD15crystallization17VectorMultiColvar21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">1252604</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMultiColvar.h.func.html b/coverage/crystallization/VectorMultiColvar.h.func.html
new file mode 100644
index 0000000000..22cda6db04
--- /dev/null
+++ b/coverage/crystallization/VectorMultiColvar.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMultiColvar.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMultiColvar.h<span style="font-size: 80%;"> (<a href="VectorMultiColvar.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VectorMultiColvar.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#50">_ZN4PLMD15crystallization17VectorMultiColvar10isPeriodicEv</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#48">_ZN4PLMD15crystallization17VectorMultiColvarD2Ev</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#76">_ZNK4PLMD15crystallization17VectorMultiColvar21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">1252604</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorMultiColvar.h.gcov.html#62">_ZNK4PLMD15crystallization17VectorMultiColvar28hasDifferentiableOrientationEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorMultiColvar.h.gcov.html b/coverage/crystallization/VectorMultiColvar.h.gcov.html
new file mode 100644
index 0000000000..0b0c765b76
--- /dev/null
+++ b/coverage/crystallization/VectorMultiColvar.h.gcov.html
@@ -0,0 +1,161 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorMultiColvar.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorMultiColvar.h<span style="font-size: 80%;"> (source / <a href="VectorMultiColvar.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_crystallization_VectorMultiColvar_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_crystallization_VectorMultiColvar_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace crystallization {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class VectorMultiColvar : public multicolvar::MultiColvarBase {</a>
+<a name="33"><span class="lineNum">      33 </span>            :   friend class OrientationSphere;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   friend class VolumeGradientBase;</a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Are we storing the director of the vector of the vector</a>
+<a name="37"><span class="lineNum">      37 </span>            :   bool store_director;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// How many components does the vector have</a>
+<a name="39"><span class="lineNum">      39 </span>            :   unsigned ncomponents;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// These are tempory vectors that are used to store values and directors</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::vector&lt;double&gt; vv1, vv2;</a>
+<a name="42"><span class="lineNum">      42 </span>            : protected:</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Set the dimensionality of the vector</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void setVectorDimensionality( const unsigned&amp; );</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Used in vector average to add forces from vector the the forces from here</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void addForcesOnAtoms( const std::vector&lt;double&gt;&amp; inforces );</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="49"><span class="lineNum">      49 </span>            :   explicit VectorMultiColvar(const ActionOptions&amp;);</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         52 :   ~VectorMultiColvar() {}</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : /// The norm of a vector is not periodic</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         35 :   virtual bool isPeriodic() { return false; }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Calculate the multicolvar</a>
+<a name="54"><span class="lineNum">      54 </span>            : //  double doCalculation( const unsigned&amp; taskIndex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// This shouldn't do anything</a>
+<a name="56"><span class="lineNum">      56 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Calculate the vector</a>
+<a name="58"><span class="lineNum">      58 </span>            :   virtual void calculateVector( multicolvar::AtomValuePack&amp; myatoms ) const=0;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Get the number of components in the vector</a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned getNumberOfComponentsInVector() const ;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Get the number of quantities we are calculating per step</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned getNumberOfQuantities() const ;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Can we differentiate the orientation - yes we can the multicolvar is a vector</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :   bool hasDifferentiableOrientation() const { return true; }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : ///  This makes sure we are not calculating the director when we do LocalAverage</a>
+<a name="66"><span class="lineNum">      66 </span>            :   virtual void doNotCalculateDirector();</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// This does normalizeing of vectors for storeDataVessel</a>
+<a name="68"><span class="lineNum">      68 </span>            :   virtual void normalizeVector( std::vector&lt;double&gt;&amp; vals ) const ;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   virtual void normalizeVectorDerivatives( MultiValue&amp; myvals ) const ;</a>
+<a name="70"><span class="lineNum">      70 </span>            : };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : inline</a>
+<a name="73"><span class="lineNum">      73 </span>            : unsigned VectorMultiColvar::getNumberOfComponentsInVector() const {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    1892577 :   return ncomponents;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : inline</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    1252604 : unsigned VectorMultiColvar::getNumberOfQuantities() const {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">    1252604 :   return 2 + ncomponents;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : #endif</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorSum.cpp.func-sort-c.html b/coverage/crystallization/VectorSum.cpp.func-sort-c.html
new file mode 100644
index 0000000000..199381356a
--- /dev/null
+++ b/coverage/crystallization/VectorSum.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorSum.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorSum.cpp<span style="font-size: 80%;"> (<a href="VectorSum.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryLo">11.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">30.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VectorSum.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_119VectorSumRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#44">_ZN4PLMD15crystallization9VectorSum16registerKeywordsERNS_8KeywordsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#60">_ZN4PLMD15crystallization9VectorSum16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#91">_ZN4PLMD15crystallization9VectorSum6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#64">_ZN4PLMD15crystallization9VectorSum6resizeEv</a></td>
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+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#54">_ZN4PLMD15crystallization9VectorSumC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#75">_ZNK4PLMD15crystallization9VectorSum9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_119VectorSumRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_119VectorSumRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#48">_ZN4PLMD15crystallization9VectorSum14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorSum.cpp.func.html b/coverage/crystallization/VectorSum.cpp.func.html
new file mode 100644
index 0000000000..69234140e9
--- /dev/null
+++ b/coverage/crystallization/VectorSum.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorSum.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorSum.cpp<span style="font-size: 80%;"> (<a href="VectorSum.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryLo">11.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">30.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VectorSum.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_119VectorSumRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_119VectorSumRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#42">_ZN4PLMD15crystallization12_GLOBAL__N_119VectorSumRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#48">_ZN4PLMD15crystallization9VectorSum14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#44">_ZN4PLMD15crystallization9VectorSum16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#60">_ZN4PLMD15crystallization9VectorSum16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#91">_ZN4PLMD15crystallization9VectorSum6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#64">_ZN4PLMD15crystallization9VectorSum6resizeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#54">_ZN4PLMD15crystallization9VectorSumC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VectorSum.cpp.gcov.html#75">_ZNK4PLMD15crystallization9VectorSum9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/VectorSum.cpp.gcov.html b/coverage/crystallization/VectorSum.cpp.gcov.html
new file mode 100644
index 0000000000..26df154118
--- /dev/null
+++ b/coverage/crystallization/VectorSum.cpp.gcov.html
@@ -0,0 +1,190 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization/VectorSum.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">crystallization</a> - VectorSum.cpp<span style="font-size: 80%;"> (source / <a href="VectorSum.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryLo">11.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">30.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;vesselbase/VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/ActionVolume.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VectorMultiColvar.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace crystallization {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class VectorSum : public vesselbase::FunctionVessel {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   unsigned nder;</a>
+<a name="34"><span class="lineNum">      34 </span>            : public:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="37"><span class="lineNum">      37 </span>            :   explicit VectorSum( const vesselbase::VesselOptions&amp; da );</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::string value_descriptor();</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void resize();</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const ;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer );</a>
+<a name="42"><span class="lineNum">      42 </span>            : };</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      12504 : PLUMED_REGISTER_VESSEL(VectorSum,&quot;VSUM&quot;)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 : void VectorSum::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   vesselbase::FunctionVessel::registerKeywords(keys);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       4168 : void VectorSum::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;VSUM&quot;,&quot;calculate the norm of the sum of vectors.&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;vsum&quot;,&quot;VSUM&quot;,&quot;the norm of sum of vectors. The output component can be referred to elsewhere in the input &quot;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :                           &quot;file by using the label.vsum&quot;);</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       4168 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 : VectorSum::VectorSum( const vesselbase::VesselOptions&amp; da ) :</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   FunctionVessel(da),</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :   nder(0)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 : std::string VectorSum::value_descriptor() {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   return &quot;the norm of the mean vector&quot;;</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 : void VectorSum::resize() {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   unsigned ncomp=getAction()-&gt;getNumberOfQuantities() - 2;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     nder=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :     resizeBuffer( (1+nder)*ncomp ); getFinalValue()-&gt;resizeDerivatives( nder );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   } else {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :     nder=0; resizeBuffer(ncomp);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 : void VectorSum::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   unsigned ncomp=getAction()-&gt;getNumberOfQuantities()-2;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   double weight=myvals.get(0);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   plumed_dbg_assert( weight&gt;=getTolerance() );</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ncomp; ++i) buffer[bufstart + i*(1+nder)] += weight*myvals.get(2+i);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   if( !getAction()-&gt;derivativesAreRequired() ) return;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ncomp; ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     double colvar=myvals.get(2+i);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     myvals.chainRule( 2+i, i, 1, 0, weight, bufstart, buffer );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     if( diffweight ) myvals.chainRule( 0, i, 1, 0, colvar, bufstart, buffer );</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : void VectorSum::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   unsigned ncomp=getAction()-&gt;getNumberOfQuantities()-2;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   double sum=0;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ncomp; ++i) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     double tmp = buffer[bufstart+(nder+1)*i];</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     sum+=tmp*tmp;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   double tw = 1.0 / sqrt(sum);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   setOutputValue( sqrt(sum) );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   if( !getAction()-&gt;derivativesAreRequired() ) return;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   Value* fval=getFinalValue();</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   for(unsigned icomp=0; icomp&lt;ncomp; ++icomp) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     double tmp = buffer[bufstart + icomp*(1+nder)];</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     unsigned bstart = bufstart + icomp*(nder+1) + 1;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     for(unsigned jder=0; jder&lt;nder; ++jder) fval-&gt;addDerivative( jder, tw*tmp*buffer[bstart + jder] );</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/index-sort-f.html b/coverage/crystallization/index-sort-f.html
new file mode 100644
index 0000000000..6391877092
--- /dev/null
+++ b/coverage/crystallization/index-sort-f.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - crystallization</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1015</td>
+            <td class="headerCovTableEntry">1211</td>
+            <td class="headerCovTableEntryMed">83.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">187</td>
+            <td class="headerCovTableEntryMed">77.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InterMolecularTorsions.cpp.gcov.html">InterMolecularTorsions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">14 / 63</td>
+      <td class="coverPerLo">30.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorSum.cpp.gcov.html">VectorSum.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="11.9%"><img src="../snow.png" width=88 height=10 alt="11.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">11.9&nbsp;%</td>
+      <td class="coverNumLo">5 / 42</td>
+      <td class="coverPerLo">30.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q3.cpp.gcov.html">Q3.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=26 height=10 alt="26.3%"><img src="../snow.png" width=74 height=10 alt="26.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">26.3&nbsp;%</td>
+      <td class="coverNumLo">5 / 19</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalSteinhardt.h.gcov.html">LocalSteinhardt.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="72.2%"><img src="../snow.png" width=28 height=10 alt="72.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">72.2&nbsp;%</td>
+      <td class="coverNumLo">13 / 18</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMultiColvar.cpp.gcov.html">VectorMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.1%"><img src="../snow.png" width=21 height=10 alt="79.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.1&nbsp;%</td>
+      <td class="coverNumMed">34 / 43</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrientationSphere.cpp.gcov.html">OrientationSphere.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">60 / 66</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CubicHarmonicBase.cpp.gcov.html">CubicHarmonicBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.7%"><img src="../snow.png" width=6 height=10 alt="93.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.7&nbsp;%</td>
+      <td class="coverNumHi">74 / 79</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoleculePlane.cpp.gcov.html">MoleculePlane.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.1%"><img src="../snow.png" width=27 height=10 alt="73.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.1&nbsp;%</td>
+      <td class="coverNumLo">38 / 52</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q4.cpp.gcov.html">Q4.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoleculeOrientation.cpp.gcov.html">MoleculeOrientation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">53 / 56</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Steinhardt.cpp.gcov.html">Steinhardt.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">78 / 78</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Fccubic.cpp.gcov.html">Fccubic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PolymerAngles.cpp.gcov.html">PolymerAngles.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tetrahedral.cpp.gcov.html">Tetrahedral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleCubic.cpp.gcov.html">SimpleCubic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">25 / 25</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gradient.cpp.gcov.html">Gradient.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="71.8%"><img src="../snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">51 / 71</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BondOrientation.cpp.gcov.html">BondOrientation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.2%"><img src="../snow.png" width=9 height=10 alt="91.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.2&nbsp;%</td>
+      <td class="coverNumHi">52 / 57</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMAC.cpp.gcov.html">SMAC.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q6.cpp.gcov.html">Q6.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EnvironmentSimilarity.cpp.gcov.html">EnvironmentSimilarity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.2%"><img src="../snow.png" width=6 height=10 alt="94.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.2&nbsp;%</td>
+      <td class="coverNumHi">226 / 240</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CubicHarmonicBase.h.gcov.html">CubicHarmonicBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gradient.h.gcov.html">Gradient.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrientationSphere.h.gcov.html">OrientationSphere.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMultiColvar.h.gcov.html">VectorMultiColvar.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMean.cpp.gcov.html">VectorMean.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">44 / 44</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GradientVessel.cpp.gcov.html">GradientVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.2%"><img src="../snow.png" width=16 height=10 alt="84.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.2&nbsp;%</td>
+      <td class="coverNumMed">80 / 95</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/index-sort-l.html b/coverage/crystallization/index-sort-l.html
new file mode 100644
index 0000000000..c4c82cd8c7
--- /dev/null
+++ b/coverage/crystallization/index-sort-l.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - crystallization</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1015</td>
+            <td class="headerCovTableEntry">1211</td>
+            <td class="headerCovTableEntryMed">83.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">187</td>
+            <td class="headerCovTableEntryMed">77.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorSum.cpp.gcov.html">VectorSum.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="11.9%"><img src="../snow.png" width=88 height=10 alt="11.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">11.9&nbsp;%</td>
+      <td class="coverNumLo">5 / 42</td>
+      <td class="coverPerLo">30.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InterMolecularTorsions.cpp.gcov.html">InterMolecularTorsions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">14 / 63</td>
+      <td class="coverPerLo">30.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q3.cpp.gcov.html">Q3.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=26 height=10 alt="26.3%"><img src="../snow.png" width=74 height=10 alt="26.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">26.3&nbsp;%</td>
+      <td class="coverNumLo">5 / 19</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gradient.cpp.gcov.html">Gradient.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="71.8%"><img src="../snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">51 / 71</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalSteinhardt.h.gcov.html">LocalSteinhardt.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="72.2%"><img src="../snow.png" width=28 height=10 alt="72.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">72.2&nbsp;%</td>
+      <td class="coverNumLo">13 / 18</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoleculePlane.cpp.gcov.html">MoleculePlane.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.1%"><img src="../snow.png" width=27 height=10 alt="73.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.1&nbsp;%</td>
+      <td class="coverNumLo">38 / 52</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMultiColvar.cpp.gcov.html">VectorMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.1%"><img src="../snow.png" width=21 height=10 alt="79.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.1&nbsp;%</td>
+      <td class="coverNumMed">34 / 43</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GradientVessel.cpp.gcov.html">GradientVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.2%"><img src="../snow.png" width=16 height=10 alt="84.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.2&nbsp;%</td>
+      <td class="coverNumMed">80 / 95</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrientationSphere.cpp.gcov.html">OrientationSphere.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">60 / 66</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BondOrientation.cpp.gcov.html">BondOrientation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.2%"><img src="../snow.png" width=9 height=10 alt="91.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.2&nbsp;%</td>
+      <td class="coverNumHi">52 / 57</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CubicHarmonicBase.cpp.gcov.html">CubicHarmonicBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.7%"><img src="../snow.png" width=6 height=10 alt="93.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.7&nbsp;%</td>
+      <td class="coverNumHi">74 / 79</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EnvironmentSimilarity.cpp.gcov.html">EnvironmentSimilarity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.2%"><img src="../snow.png" width=6 height=10 alt="94.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.2&nbsp;%</td>
+      <td class="coverNumHi">226 / 240</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoleculeOrientation.cpp.gcov.html">MoleculeOrientation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">53 / 56</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CubicHarmonicBase.h.gcov.html">CubicHarmonicBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gradient.h.gcov.html">Gradient.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrientationSphere.h.gcov.html">OrientationSphere.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMultiColvar.h.gcov.html">VectorMultiColvar.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PolymerAngles.cpp.gcov.html">PolymerAngles.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q4.cpp.gcov.html">Q4.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q6.cpp.gcov.html">Q6.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tetrahedral.cpp.gcov.html">Tetrahedral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleCubic.cpp.gcov.html">SimpleCubic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">25 / 25</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Fccubic.cpp.gcov.html">Fccubic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMAC.cpp.gcov.html">SMAC.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMean.cpp.gcov.html">VectorMean.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">44 / 44</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Steinhardt.cpp.gcov.html">Steinhardt.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">78 / 78</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/crystallization/index.html b/coverage/crystallization/index.html
new file mode 100644
index 0000000000..c6fcda5d14
--- /dev/null
+++ b/coverage/crystallization/index.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - crystallization</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - crystallization</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1015</td>
+            <td class="headerCovTableEntry">1211</td>
+            <td class="headerCovTableEntryMed">83.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">187</td>
+            <td class="headerCovTableEntryMed">77.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BondOrientation.cpp.gcov.html">BondOrientation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.2%"><img src="../snow.png" width=9 height=10 alt="91.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.2&nbsp;%</td>
+      <td class="coverNumHi">52 / 57</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CubicHarmonicBase.cpp.gcov.html">CubicHarmonicBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.7%"><img src="../snow.png" width=6 height=10 alt="93.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.7&nbsp;%</td>
+      <td class="coverNumHi">74 / 79</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CubicHarmonicBase.h.gcov.html">CubicHarmonicBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EnvironmentSimilarity.cpp.gcov.html">EnvironmentSimilarity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.2%"><img src="../snow.png" width=6 height=10 alt="94.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.2&nbsp;%</td>
+      <td class="coverNumHi">226 / 240</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Fccubic.cpp.gcov.html">Fccubic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gradient.cpp.gcov.html">Gradient.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="71.8%"><img src="../snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">51 / 71</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Gradient.h.gcov.html">Gradient.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GradientVessel.cpp.gcov.html">GradientVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.2%"><img src="../snow.png" width=16 height=10 alt="84.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.2&nbsp;%</td>
+      <td class="coverNumMed">80 / 95</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InterMolecularTorsions.cpp.gcov.html">InterMolecularTorsions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">14 / 63</td>
+      <td class="coverPerLo">30.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalSteinhardt.h.gcov.html">LocalSteinhardt.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="72.2%"><img src="../snow.png" width=28 height=10 alt="72.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">72.2&nbsp;%</td>
+      <td class="coverNumLo">13 / 18</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoleculeOrientation.cpp.gcov.html">MoleculeOrientation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">53 / 56</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoleculePlane.cpp.gcov.html">MoleculePlane.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.1%"><img src="../snow.png" width=27 height=10 alt="73.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.1&nbsp;%</td>
+      <td class="coverNumLo">38 / 52</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrientationSphere.cpp.gcov.html">OrientationSphere.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">60 / 66</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrientationSphere.h.gcov.html">OrientationSphere.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PolymerAngles.cpp.gcov.html">PolymerAngles.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q3.cpp.gcov.html">Q3.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=26 height=10 alt="26.3%"><img src="../snow.png" width=74 height=10 alt="26.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">26.3&nbsp;%</td>
+      <td class="coverNumLo">5 / 19</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q4.cpp.gcov.html">Q4.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Q6.cpp.gcov.html">Q6.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMAC.cpp.gcov.html">SMAC.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleCubic.cpp.gcov.html">SimpleCubic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">25 / 25</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Steinhardt.cpp.gcov.html">Steinhardt.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">78 / 78</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tetrahedral.cpp.gcov.html">Tetrahedral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMean.cpp.gcov.html">VectorMean.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">44 / 44</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMultiColvar.cpp.gcov.html">VectorMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.1%"><img src="../snow.png" width=21 height=10 alt="79.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.1&nbsp;%</td>
+      <td class="coverNumMed">34 / 43</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorMultiColvar.h.gcov.html">VectorMultiColvar.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VectorSum.cpp.gcov.html">VectorSum.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="11.9%"><img src="../snow.png" width=88 height=10 alt="11.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">11.9&nbsp;%</td>
+      <td class="coverNumLo">5 / 42</td>
+      <td class="coverPerLo">30.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 10</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/ClassicalMultiDimensionalScaling.cpp.func-sort-c.html b/coverage/dimred/ClassicalMultiDimensionalScaling.cpp.func-sort-c.html
new file mode 100644
index 0000000000..10a135730d
--- /dev/null
+++ b/coverage/dimred/ClassicalMultiDimensionalScaling.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/ClassicalMultiDimensionalScaling.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - ClassicalMultiDimensionalScaling.cpp<span style="font-size: 80%;"> (<a href="ClassicalMultiDimensionalScaling.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+            <td class="headerValue">plumed test coverage</td>
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+            <td class="headerCovTableEntry">21</td>
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+            <td class="headerCovTableEntryHi">100.0 %</td>
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+            <td class="headerValue">2024-10-09 13:38:15</td>
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+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
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+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DimensionalityReductionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC DIMRED CLASSICAL_MDS</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Create a low-dimensional projection of a trajectory using the classical multidimensional</a>
+<a name="28"><span class="lineNum">      28 </span>            :  scaling algorithm.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : Multidimensional scaling (MDS) is similar to what is done when you make a map. You start with distances</a>
+<a name="31"><span class="lineNum">      31 </span>            : between London, Belfast, Paris and Dublin and then you try to arrange points on a piece of paper so that the (suitably scaled)</a>
+<a name="32"><span class="lineNum">      32 </span>            : distances between the points in your map representing each of those cities are related to the true distances between the cities.</a>
+<a name="33"><span class="lineNum">      33 </span>            : Stating this more mathematically MDS endeavors to find an &lt;a href=&quot;http://en.wikipedia.org/wiki/Isometry&quot;&gt;isometry&lt;/a&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : between points distributed in a high-dimensional space and a set of points distributed in a low-dimensional plane.</a>
+<a name="35"><span class="lineNum">      35 </span>            : In other words, if we have \f$M\f$ \f$D\f$-dimensional points, \f$\mathbf{X}\f$,</a>
+<a name="36"><span class="lineNum">      36 </span>            : and we can calculate dissimilarities between pairs them, \f$D_{ij}\f$, we can, with an MDS calculation, try to create \f$M\f$ projections,</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f$\mathbf{x}\f$, of the high dimensionality points in a \f$d\f$-dimensional linear space by trying to arrange the projections so that the</a>
+<a name="38"><span class="lineNum">      38 </span>            : Euclidean distances between pairs of them, \f$d_{ij}\f$, resemble the dissimilarities between the high dimensional points.  In short we minimize:</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            : \chi^2 = \sum_{i \ne j} \left( D_{ij} - d_{ij} \right)^2</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f]</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : where \f$D_{ij}\f$ is the distance between point \f$X^{i}\f$ and point \f$X^{j}\f$ and \f$d_{ij}\f$ is the distance between the projection</a>
+<a name="45"><span class="lineNum">      45 </span>            : of \f$X^{i}\f$, \f$x^i\f$, and the projection of \f$X^{j}\f$, \f$x^j\f$.  A tutorial on this approach can be used to analyze simulations</a>
+<a name="46"><span class="lineNum">      46 </span>            : can be found in the tutorial \ref lugano-5 and in the following &lt;a href=&quot;https://www.youtube.com/watch?v=ofC2qz0_9_A&amp;feature=youtu.be&quot; &gt; short video.&lt;/a&gt;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \par Examples</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The following command instructs plumed to construct a classical multidimensional scaling projection of a trajectory.</a>
+<a name="51"><span class="lineNum">      51 </span>            : The RMSD distance between atoms 1-256 have moved is used to measure the distances in the high-dimensional space.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : data: COLLECT_FRAMES ATOMS=1-256</a>
+<a name="55"><span class="lineNum">      55 </span>            : mat: EUCLIDEAN_DISSIMILARITIES USE_OUTPUT_DATA_FROM=data</a>
+<a name="56"><span class="lineNum">      56 </span>            : mds: CLASSICAL_MDS USE_OUTPUT_DATA_FROM=mat NLOW_DIM=2</a>
+<a name="57"><span class="lineNum">      57 </span>            : OUTPUT_ANALYSIS_DATA_TO_COLVAR USE_OUTPUT_DATA_FROM=mds FILE=rmsd-embed</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following section is for people who are interested in how this method works in detail. A solid understanding of this material is</a>
+<a name="61"><span class="lineNum">      61 </span>            : not necessary to use MDS.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \section dim-sec Method of optimization</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : The stress function can be minimized using a standard optimization algorithm such as conjugate gradients or steepest descent.</a>
+<a name="66"><span class="lineNum">      66 </span>            : However, it is more common to do this minimization using a technique known as classical scaling.  Classical scaling works by</a>
+<a name="67"><span class="lineNum">      67 </span>            : recognizing that each of the distances $D_{ij}$ in the above sum can be written as:</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \f[</a>
+<a name="70"><span class="lineNum">      70 </span>            : D_{ij}^2 = \sum_{\alpha} (X^i_\alpha - X^j_\alpha)^2 = \sum_\alpha (X^i_\alpha)^2 + (X^j_\alpha)^2 - 2X^i_\alpha X^j_\alpha</a>
+<a name="71"><span class="lineNum">      71 </span>            : \f]</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : We can use this expression and matrix algebra to calculate multiple distances at once.  For instance if we have three points,</a>
+<a name="74"><span class="lineNum">      74 </span>            : \f$\mathbf{X}\f$, we can write distances between them as:</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \f{eqnarray*}{</a>
+<a name="77"><span class="lineNum">      77 </span>            : D^2(\mathbf{X}) &amp;=&amp; \left[ \begin{array}{ccc}</a>
+<a name="78"><span class="lineNum">      78 </span>            : 0 &amp; d_{12}^2 &amp; d_{13}^2 \\</a>
+<a name="79"><span class="lineNum">      79 </span>            : d_{12}^2 &amp; 0 &amp; d_{23}^2 \\</a>
+<a name="80"><span class="lineNum">      80 </span>            : d_{13}^2 &amp; d_{23}^2 &amp; 0</a>
+<a name="81"><span class="lineNum">      81 </span>            : \end{array}\right] \\</a>
+<a name="82"><span class="lineNum">      82 </span>            : &amp;=&amp;</a>
+<a name="83"><span class="lineNum">      83 </span>            : \sum_\alpha \left[ \begin{array}{ccc}</a>
+<a name="84"><span class="lineNum">      84 </span>            : (X^1_\alpha)^2 &amp; (X^1_\alpha)^2 &amp; (X^1_\alpha)^2 \\</a>
+<a name="85"><span class="lineNum">      85 </span>            : (X^2_\alpha)^2 &amp; (X^2_\alpha)^2 &amp; (X^2_\alpha)^2 \\</a>
+<a name="86"><span class="lineNum">      86 </span>            : (X^3_\alpha)^2 &amp; (X^3_\alpha)^2 &amp; (X^3_\alpha)^2 \\</a>
+<a name="87"><span class="lineNum">      87 </span>            : \end{array}\right]</a>
+<a name="88"><span class="lineNum">      88 </span>            :  + \sum_\alpha \left[ \begin{array}{ccc}</a>
+<a name="89"><span class="lineNum">      89 </span>            : (X^1_\alpha)^2 &amp; (X^2_\alpha)^2 &amp; (X^3_\alpha)^2 \\</a>
+<a name="90"><span class="lineNum">      90 </span>            : (X^1_\alpha)^2 &amp; (X^2_\alpha)^2 &amp; (X^3_\alpha)^2 \\</a>
+<a name="91"><span class="lineNum">      91 </span>            : (X^1_\alpha)^2 &amp; (X^2_\alpha)^2 &amp; (X^3_\alpha)^2 \\</a>
+<a name="92"><span class="lineNum">      92 </span>            : \end{array}\right]</a>
+<a name="93"><span class="lineNum">      93 </span>            : - 2 \sum_\alpha \left[ \begin{array}{ccc}</a>
+<a name="94"><span class="lineNum">      94 </span>            : X^1_\alpha X^1_\alpha &amp; X^1_\alpha X^2_\alpha &amp; X^1_\alpha X^3_\alpha \\</a>
+<a name="95"><span class="lineNum">      95 </span>            : X^2_\alpha X^1_\alpha &amp; X^2_\alpha X^2_\alpha &amp; X^2_\alpha X^3_\alpha \\</a>
+<a name="96"><span class="lineNum">      96 </span>            : X^1_\alpha X^3_\alpha &amp; X^3_\alpha X^2_\alpha &amp; X^3_\alpha X^3_\alpha</a>
+<a name="97"><span class="lineNum">      97 </span>            : \end{array}\right] \nonumber \\</a>
+<a name="98"><span class="lineNum">      98 </span>            : &amp;=&amp; \mathbf{c 1^T} + \mathbf{1 c^T} - 2 \sum_\alpha \mathbf{x}_a \mathbf{x}^T_a =  \mathbf{c 1^T} + \mathbf{1 c^T} - 2\mathbf{X X^T}</a>
+<a name="99"><span class="lineNum">      99 </span>            : \f}</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : This last equation can be extended to situations when we have more than three points.  In it \f$\mathbf{X}\f$ is a matrix that has</a>
+<a name="102"><span class="lineNum">     102 </span>            : one high-dimensional point on each of its rows and \f$\mathbf{X^T}\f$ is its transpose.  \f$\mathbf{1}\f$ is an \f$M \times 1\f$ vector</a>
+<a name="103"><span class="lineNum">     103 </span>            : of ones and \f$\mathbf{c}\f$ is a vector with components given by:</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : \f[</a>
+<a name="106"><span class="lineNum">     106 </span>            : c_i = \sum_\alpha (x_\alpha^i)^2</a>
+<a name="107"><span class="lineNum">     107 </span>            : \f]</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : These quantities are the diagonal elements of \f$\mathbf{X X^T}\f$, which is a dot product or Gram Matrix that contains the</a>
+<a name="110"><span class="lineNum">     110 </span>            : dot product of the vector \f$X_i\f$ with the vector \f$X_j\f$ in element \f$i,j\f$.</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : In classical scaling we introduce a centering matrix \f$\mathbf{J}\f$ that is given by:</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : \f[</a>
+<a name="115"><span class="lineNum">     115 </span>            : \mathbf{J} = \mathbf{I} - \frac{1}{M} \mathbf{11^T}</a>
+<a name="116"><span class="lineNum">     116 </span>            : \f]</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : where \f$\mathbf{I}\f$ is the identity.  Multiplying the equations above from the front and back by this matrix and a factor of a \f$-\frac{1}{2}\f$ gives:</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : \f{eqnarray*}{</a>
+<a name="121"><span class="lineNum">     121 </span>            :  -\frac{1}{2} \mathbf{J} \mathbf{D}^2(\mathbf{X}) \mathbf{J} &amp;=&amp; -\frac{1}{2}\mathbf{J}( \mathbf{c 1^T} + \mathbf{1 c^T} - 2\mathbf{X X^T})\mathbf{J} \\</a>
+<a name="122"><span class="lineNum">     122 </span>            :  &amp;=&amp; -\frac{1}{2}\mathbf{J c 1^T J} - \frac{1}{2} \mathbf{J 1 c^T J} + \frac{1}{2} \mathbf{J}(2\mathbf{X X^T})\mathbf{J} \\</a>
+<a name="123"><span class="lineNum">     123 </span>            :  &amp;=&amp; \mathbf{ J X X^T J } = \mathbf{X X^T } \label{eqn:scaling}</a>
+<a name="124"><span class="lineNum">     124 </span>            : \f}</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : The fist two terms in this expression disappear because \f$\mathbf{1^T J}=\mathbf{J 1} =\mathbf{0}\f$, where \f$\mathbf{0}\f$</a>
+<a name="127"><span class="lineNum">     127 </span>            : is a matrix containing all zeros.  In the final step meanwhile we use the fact that the matrix of squared distances will not</a>
+<a name="128"><span class="lineNum">     128 </span>            : change when we translate all the points.  We can thus assume that the mean value, \f$\mu\f$, for each of the components, \f$\alpha\f$:</a>
+<a name="129"><span class="lineNum">     129 </span>            : \f[</a>
+<a name="130"><span class="lineNum">     130 </span>            : \mu_\alpha = \frac{1}{M} \sum_{i=1}^N \mathbf{X}^i_\alpha</a>
+<a name="131"><span class="lineNum">     131 </span>            : \f]</a>
+<a name="132"><span class="lineNum">     132 </span>            : is equal to 0 so the columns of \f$\mathbf{X}\f$ add up to 0.  This in turn means that each of the columns of</a>
+<a name="133"><span class="lineNum">     133 </span>            : \f$\mathbf{X X^T}\f$ adds up to zero, which is what allows us to write \f$\mathbf{ J X X^T J } = \mathbf{X X^T }\f$.</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : The matrix of squared distances is symmetric and positive-definite we can thus use the spectral decomposition to decompose it as:</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : \f[</a>
+<a name="138"><span class="lineNum">     138 </span>            : \Phi= \mathbf{V} \Lambda \mathbf{V}^T</a>
+<a name="139"><span class="lineNum">     139 </span>            : \f]</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : Furthermore, because the matrix we are diagonalizing, \f$\mathbf{X X^T}\f$, is the product of a matrix and its transpose</a>
+<a name="142"><span class="lineNum">     142 </span>            : we can use this decomposition to write:</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : \f[</a>
+<a name="145"><span class="lineNum">     145 </span>            : \mathbf{X} =\mathbf{V} \Lambda^\frac{1}{2}</a>
+<a name="146"><span class="lineNum">     146 </span>            : \f]</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : Much as in PCA there are generally a small number of large eigenvalues in \f$\Lambda\f$ and many small eigenvalues.</a>
+<a name="149"><span class="lineNum">     149 </span>            : We can safely use only the large eigenvalues and their corresponding eigenvectors to express the relationship between</a>
+<a name="150"><span class="lineNum">     150 </span>            : the coordinates \f$\mathbf{X}\f$.  This gives us our set of low-dimensional projections.</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : This derivation makes a number of assumptions about the how the low dimensional points should best be arranged to minimize</a>
+<a name="153"><span class="lineNum">     153 </span>            : the stress. If you use an interactive optimization algorithm such as SMACOF you may thus be able to find a better</a>
+<a name="154"><span class="lineNum">     154 </span>            : (lower-stress) projection of the points.  For more details on the assumptions made</a>
+<a name="155"><span class="lineNum">     155 </span>            : see &lt;a href=&quot;http://quest4rigor.com/tag/multidimensional-scaling/&quot;&gt; this website.&lt;/a&gt;</a>
+<a name="156"><span class="lineNum">     156 </span>            : */</a>
+<a name="157"><span class="lineNum">     157 </span>            : //+ENDPLUMEDOC</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : namespace PLMD {</a>
+<a name="160"><span class="lineNum">     160 </span>            : namespace dimred {</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : class ClassicalMultiDimensionalScaling : public DimensionalityReductionBase {</a>
+<a name="163"><span class="lineNum">     163 </span>            : public:</a>
+<a name="164"><span class="lineNum">     164 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="165"><span class="lineNum">     165 </span>            :   explicit ClassicalMultiDimensionalScaling( const ActionOptions&amp; ao );</a>
+<a name="166"><span class="lineNum">     166 </span>            :   void calculateProjections( const Matrix&lt;double&gt;&amp;, Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="167"><span class="lineNum">     167 </span>            : };</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      12518 : PLUMED_REGISTER_ACTION(ClassicalMultiDimensionalScaling,&quot;CLASSICAL_MDS&quot;)</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          9 : void ClassicalMultiDimensionalScaling::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          9 :   DimensionalityReductionBase::registerKeywords( keys );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 : }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          7 : ClassicalMultiDimensionalScaling::ClassicalMultiDimensionalScaling( const ActionOptions&amp; ao):</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   Action(ao),</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          7 :   DimensionalityReductionBase(ao)</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : {</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          7 :   if( dimredbase ) error(&quot;input to CLASSICAL_MDS should not be output from dimensionality reduction object&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          7 : }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         12 : void ClassicalMultiDimensionalScaling::calculateProjections( const Matrix&lt;double&gt;&amp; targets, Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   // Retrieve the distances from the dimensionality reduction object</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         12 :   double half=(-0.5); Matrix&lt;double&gt; distances( half*targets );</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // Apply centering transtion</a>
+<a name="187"><span class="lineNum">     187 </span>            :   unsigned n=distances.nrows(); double sum;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   // First HM</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       1564 :   for(unsigned i=0; i&lt;n; ++i) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">     389056 :     sum=0; for(unsigned j=0; j&lt;n; ++j) sum+=distances(i,j);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     389056 :     for(unsigned j=0; j&lt;n; ++j) distances(i,j) -= sum/n;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // Now (HM)H</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1564 :   for(unsigned i=0; i&lt;n; ++i) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     389056 :     sum=0; for(unsigned j=0; j&lt;n; ++j) sum+=distances(j,i);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     389056 :     for(unsigned j=0; j&lt;n; ++j) distances(j,i) -= sum/n;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Diagonalize matrix</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; eigval(n); Matrix&lt;double&gt; eigvec(n,n);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         12 :   diagMat( distances, eigval, eigvec );</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   // Pass final projections to map object</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       1564 :   for(unsigned i=0; i&lt;n; ++i) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       4654 :     for(unsigned j=0; j&lt;projections.ncols(); ++j) projections(i,j)=std::sqrt(eigval[n-1-j])*eigvec(n-1-j,i);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         12 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/DimensionalityReductionBase.cpp.func-sort-c.html b/coverage/dimred/DimensionalityReductionBase.cpp.func-sort-c.html
new file mode 100644
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+  <title>LCOV - plumed test coverage - dimred/DimensionalityReductionBase.cpp - functions</title>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - DimensionalityReductionBase.cpp<span style="font-size: 80%;"> (<a href="DimensionalityReductionBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  </table>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DimensionalityReductionBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#105">_ZN4PLMD6dimred27DimensionalityReductionBase15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#34">_ZN4PLMD6dimred27DimensionalityReductionBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#63">_ZN4PLMD6dimred27DimensionalityReductionBase15getArgumentListEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#34">_ZN4PLMD6dimred27DimensionalityReductionBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#74">_ZN4PLMD6dimred27DimensionalityReductionBase15performAnalysisEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#28">_ZN4PLMD6dimred27DimensionalityReductionBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#69">_ZN4PLMD6dimred27DimensionalityReductionBase13getProjectionERKjRSt6vectorIdSaIdEERd</a></td>
+              <td class="coverFnHi">1050</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/dimred/DimensionalityReductionBase.cpp.func.html b/coverage/dimred/DimensionalityReductionBase.cpp.func.html
new file mode 100644
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+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - DimensionalityReductionBase.cpp<span style="font-size: 80%;"> (<a href="DimensionalityReductionBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+              <td class="coverFnHi">1050</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#105">_ZN4PLMD6dimred27DimensionalityReductionBase15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#63">_ZN4PLMD6dimred27DimensionalityReductionBase15getArgumentListEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#74">_ZN4PLMD6dimred27DimensionalityReductionBase15performAnalysisEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#28">_ZN4PLMD6dimred27DimensionalityReductionBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#34">_ZN4PLMD6dimred27DimensionalityReductionBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.cpp.gcov.html#34">_ZN4PLMD6dimred27DimensionalityReductionBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/DimensionalityReductionBase.cpp.gcov.html b/coverage/dimred/DimensionalityReductionBase.cpp.gcov.html
new file mode 100644
index 0000000000..3324873655
--- /dev/null
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/DimensionalityReductionBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - DimensionalityReductionBase.cpp<span style="font-size: 80%;"> (source / <a href="DimensionalityReductionBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DimensionalityReductionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace dimred {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         30 : void DimensionalityReductionBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         30 :   analysis::AnalysisBase::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         60 :   keys.add(&quot;compulsory&quot;,&quot;NLOW_DIM&quot;,&quot;number of low-dimensional coordinates required&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         60 :   keys.addOutputComponent(&quot;coord&quot;,&quot;default&quot;,&quot;the low-dimensional projections of the various input configurations&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         30 : }</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         16 : DimensionalityReductionBase::DimensionalityReductionBase( const ActionOptions&amp; ao ):</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   Action(ao),</a>
+<a name="38"><span class="lineNum">      38 </span>            :   analysis::AnalysisBase(ao),</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         16 :   dimredbase(NULL)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span>            :   // Check that some dissimilarity information is available</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         16 :   if( my_input_data ) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         27 :     if( getName()!=&quot;PCA&quot; &amp;&amp; !dissimilaritiesWereSet() ) error(&quot;dissimilarities have not been calcualted in input actions&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :     // Now we check if the input was a dimensionality reduction object</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         15 :     dimredbase = dynamic_cast&lt;DimensionalityReductionBase*&gt;( my_input_data );</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            :   // Retrieve the dimension in the low dimensionality space</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         16 :   nlow=0;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         16 :   if( dimredbase ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          5 :     nlow=dimredbase-&gt;nlow;</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          5 :     log.printf(&quot;  projecting in %u dimensional space \n&quot;,nlow);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         22 :   } else if( keywords.exists(&quot;NLOW_DIM&quot;) ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         10 :     parse(&quot;NLOW_DIM&quot;,nlow);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         10 :     if( nlow&lt;1 ) error(&quot;dimensionality of low dimensional space must be at least one&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         10 :     log.printf(&quot;  projecting in %u dimensional space \n&quot;,nlow);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span>            :   // Now add fake components to the underlying ActionWithValue for the arguments</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::string num;</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         45 :   for(unsigned i=0; i&lt;nlow; ++i) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         87 :     Tools::convert(i+1,num); addComponent( &quot;coord-&quot; + num ); componentIsNotPeriodic( &quot;coord-&quot; + num );</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   }</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         16 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          2 : std::vector&lt;Value*&gt; DimensionalityReductionBase::getArgumentList() {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;Value*&gt; arglist( analysis::AnalysisBase::getArgumentList() );</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;nlow; ++i) arglist.push_back( getPntrToComponent(i) );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          2 :   return arglist;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1050 : void DimensionalityReductionBase::getProjection( const unsigned&amp; idata, std::vector&lt;double&gt;&amp; point, double&amp; weight ) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       1050 :   if( point.size()!=nlow ) point.resize( nlow );</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       3150 :   weight = getWeight(idata); for(unsigned i=0; i&lt;nlow; ++i) point[i]=projections(idata,i);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       1050 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         19 : void DimensionalityReductionBase::performAnalysis() {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         19 :   log.printf(&quot;Generating projections required by action %s \n&quot;,getLabel().c_str() );</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   // Resize the tempory array (this is used for out of sample)</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         19 :   dtargets.resize( getNumberOfDataPoints() );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   // Resize the projections array</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         19 :   projections.resize( getNumberOfDataPoints(), nlow );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   // Retrieve the projections from the previous calculation</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         19 :   if( dimredbase ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :     std::vector&lt;double&gt; newp( nlow ); double w;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1056 :     for(unsigned i=0; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1050 :       dimredbase-&gt;getProjection( i, newp, w ); plumed_dbg_assert( newp.size()==nlow );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       3150 :       for(unsigned j=0; j&lt;nlow; ++j) projections(i,j)=newp[j];</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     }</a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Calculate matrix of dissimilarities</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         19 :   Matrix&lt;double&gt; targets( getNumberOfDataPoints(), getNumberOfDataPoints() ); targets=0;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       2686 :   for(unsigned i=1; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     367354 :     for(unsigned j=0; j&lt;i; ++j) targets(i,j)=targets(j,i)=getDissimilarity( i, j );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span>            :   // This calculates the projections of the points</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         19 :   calculateProjections( targets, projections );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Now set the projection values in the underlying object</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         19 :   if( my_input_data ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       2620 :     for(unsigned idat=0; idat&lt;getNumberOfDataPoints(); ++idat) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       2602 :       analysis::DataCollectionObject&amp; myref=AnalysisBase::getStoredData(idat,false); std::string num;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       7804 :       for(unsigned i=0; i&lt;nlow; ++i) { Tools::convert(i+1,num); myref.setArgument( getLabel() + &quot;.coord-&quot; + num, projections(idat,i) ); }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     }</a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         19 :   log.printf(&quot;Generated projections required by action %s \n&quot;,getLabel().c_str() );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         19 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 : double DimensionalityReductionBase::calculateStress( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; d ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Zero derivative and stress accumulators</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;p.size(); ++i) d[i]=0.0;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   double stress=0; std::vector&lt;double&gt; dtmp( p.size() );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   // Now accumulate total stress on system</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;dtargets.size(); ++i) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     if( dtargets[i]&lt;epsilon ) continue ;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :     // Calculate distance in low dimensional space</a>
+<a name="118"><span class="lineNum">     118 </span>            :     double dd=0;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;p.size(); ++j) { dtmp[j]=p[j]-projections(i,j); dd+=dtmp[j]*dtmp[j]; }</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     dd = std::sqrt(dd);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :     // Now do transformations and calculate differences</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     double ddiff = dd - dtargets[i];</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :     // Calculate derivatives</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     double pref = 2.*getWeight(i) / dd;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;p.size(); ++j) d[j] += pref*ddiff*dtmp[j];</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :     // Accumulate the total stress</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     stress += getWeight(i)*ddiff*ddiff;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   return stress;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/DimensionalityReductionBase.h.func-sort-c.html b/coverage/dimred/DimensionalityReductionBase.h.func-sort-c.html
new file mode 100644
index 0000000000..6c0fd67d98
--- /dev/null
+++ b/coverage/dimred/DimensionalityReductionBase.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/DimensionalityReductionBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - DimensionalityReductionBase.h<span style="font-size: 80%;"> (<a href="DimensionalityReductionBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DimensionalityReductionBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.h.gcov.html#66">_ZN4PLMD6dimred27DimensionalityReductionBase17setTargetDistanceERKjRKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.h.gcov.html#62">_ZNK4PLMD6dimred27DimensionalityReductionBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/DimensionalityReductionBase.h.func.html b/coverage/dimred/DimensionalityReductionBase.h.func.html
new file mode 100644
index 0000000000..d3916e7adf
--- /dev/null
+++ b/coverage/dimred/DimensionalityReductionBase.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/DimensionalityReductionBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - DimensionalityReductionBase.h<span style="font-size: 80%;"> (<a href="DimensionalityReductionBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DimensionalityReductionBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.h.gcov.html#66">_ZN4PLMD6dimred27DimensionalityReductionBase17setTargetDistanceERKjRKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DimensionalityReductionBase.h.gcov.html#62">_ZNK4PLMD6dimred27DimensionalityReductionBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/DimensionalityReductionBase.h.gcov.html b/coverage/dimred/DimensionalityReductionBase.h.gcov.html
new file mode 100644
index 0000000000..9733258a6d
--- /dev/null
+++ b/coverage/dimred/DimensionalityReductionBase.h.gcov.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/DimensionalityReductionBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - DimensionalityReductionBase.h<span style="font-size: 80%;"> (source / <a href="DimensionalityReductionBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_dimred_DimensionalityReductionBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_dimred_DimensionalityReductionBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;analysis/AnalysisBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace dimred {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class DimensionalityReductionBase : public analysis::AnalysisBase {</a>
+<a name="31"><span class="lineNum">      31 </span>            :   friend class ProjectNonLandmarkPoints;</a>
+<a name="32"><span class="lineNum">      32 </span>            :   friend class SketchMapBase;</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// This are the target distances for a single point.</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// This is used when we do out of sample or pointwise global optimization</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::vector&lt;double&gt; dtargets;</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// The projections that were generated by the dimensionality reduction algorithm</a>
+<a name="38"><span class="lineNum">      38 </span>            :   Matrix&lt;double&gt; projections;</a>
+<a name="39"><span class="lineNum">      39 </span>            : protected:</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Dimensionality of low dimensional space</a>
+<a name="41"><span class="lineNum">      41 </span>            :   unsigned nlow;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// A pointer to any dimensionality reduction base that we have got projections from</a>
+<a name="43"><span class="lineNum">      43 </span>            :   DimensionalityReductionBase* dimredbase;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   explicit DimensionalityReductionBase( const ActionOptions&amp; );</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Get the ith data point (this returns the projection)</a>
+<a name="48"><span class="lineNum">      48 </span>            :   virtual void getProjection( const unsigned&amp; idata, std::vector&lt;double&gt;&amp; point, double&amp; weight );</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Actually perform the analysis</a>
+<a name="50"><span class="lineNum">      50 </span>            :   virtual void performAnalysis();</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Overwrite getArguments so we get arguments from underlying class</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;Value*&gt; getArgumentList();</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Calculate the projections of points</a>
+<a name="54"><span class="lineNum">      54 </span>            :   virtual void calculateProjections( const Matrix&lt;double&gt;&amp;, Matrix&lt;double&gt;&amp; )=0;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Set one of the elements in the target vector.  This target vector is used</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// when we use calculateStress when finding the projections of individual points.</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// For example this function is used in PLMD::dimred::ProjectOutOfSample</a>
+<a name="58"><span class="lineNum">      58 </span>            :   virtual void setTargetDistance( const unsigned&amp;, const double&amp; );</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Calculate the pointwise stress on one point when it is located at pp.</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// This function makes use of the distance data in dtargets</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// It is used in PLMD::dimred::ProjectOutOfSample and in pointwise optimisation</a>
+<a name="62"><span class="lineNum">      62 </span>            :   virtual double calculateStress( const std::vector&lt;double&gt;&amp; pp, std::vector&lt;double&gt;&amp; der );</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Overwrite virtual function in ActionWithVessel</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const { plumed_error(); }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : };</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : inline</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 : void DimensionalityReductionBase::setTargetDistance( const unsigned&amp; idata, const double&amp; dist ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   dtargets[idata]=dist;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/OutputPCAProjections.cpp.func-sort-c.html b/coverage/dimred/OutputPCAProjections.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9356c62c44
--- /dev/null
+++ b/coverage/dimred/OutputPCAProjections.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/OutputPCAProjections.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - OutputPCAProjections.cpp<span style="font-size: 80%;"> (<a href="OutputPCAProjections.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputPCAProjections.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#65">_ZN4PLMD6dimred19OutputPCAProjectionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#52">_ZNK4PLMD6dimred19OutputPCAProjection11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#56">_ZN4PLMD6dimred12_GLOBAL__N_131OutputPCAProjectionRegisterMe586createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#87">_ZN4PLMD6dimred19OutputPCAProjection15performAnalysisEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#65">_ZN4PLMD6dimred19OutputPCAProjectionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#58">_ZN4PLMD6dimred19OutputPCAProjection16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#56">_ZN4PLMD6dimred12_GLOBAL__N_131OutputPCAProjectionRegisterMe58C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#56">_ZN4PLMD6dimred12_GLOBAL__N_131OutputPCAProjectionRegisterMe58D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/OutputPCAProjections.cpp.func.html b/coverage/dimred/OutputPCAProjections.cpp.func.html
new file mode 100644
index 0000000000..e8f3d1a7d3
--- /dev/null
+++ b/coverage/dimred/OutputPCAProjections.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/OutputPCAProjections.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - OutputPCAProjections.cpp<span style="font-size: 80%;"> (<a href="OutputPCAProjections.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputPCAProjections.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#56">_ZN4PLMD6dimred12_GLOBAL__N_131OutputPCAProjectionRegisterMe586createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#56">_ZN4PLMD6dimred12_GLOBAL__N_131OutputPCAProjectionRegisterMe58C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#56">_ZN4PLMD6dimred12_GLOBAL__N_131OutputPCAProjectionRegisterMe58D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#87">_ZN4PLMD6dimred19OutputPCAProjection15performAnalysisEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#58">_ZN4PLMD6dimred19OutputPCAProjection16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#65">_ZN4PLMD6dimred19OutputPCAProjectionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#65">_ZN4PLMD6dimred19OutputPCAProjectionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputPCAProjections.cpp.gcov.html#52">_ZNK4PLMD6dimred19OutputPCAProjection11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/OutputPCAProjections.cpp.gcov.html b/coverage/dimred/OutputPCAProjections.cpp.gcov.html
new file mode 100644
index 0000000000..c6f78a5029
--- /dev/null
+++ b/coverage/dimred/OutputPCAProjections.cpp.gcov.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/OutputPCAProjections.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - OutputPCAProjections.cpp<span style="font-size: 80%;"> (source / <a href="OutputPCAProjections.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;analysis/AnalysisBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;reference/ReferenceAtoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/ReferenceArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;PCA.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace dimred {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC DIMRED OUTPUT_PCA_PROJECTION</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : This is used to output the projection calculated by principle component analysis</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : */</a>
+<a name="43"><span class="lineNum">      43 </span>            : //+ENDPLUMEDOC</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : class OutputPCAProjection : public analysis::AnalysisBase {</a>
+<a name="46"><span class="lineNum">      46 </span>            : private:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   PDB mypdb;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   PCA* mypca;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::string fmt;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string filename;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit OutputPCAProjection( const ActionOptions&amp; );</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const { plumed_error(); }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   void performAnalysis();</a>
+<a name="56"><span class="lineNum">      56 </span>            : };</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(OutputPCAProjection,&quot;OUTPUT_PCA_PROJECTION&quot;)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          4 : void OutputPCAProjection::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          4 :   analysis::AnalysisBase::registerKeywords( keys );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file to output to&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format to use in the output file&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;0&quot;,&quot;the frequency with which to perform the required analysis and to output the data.  The default value of 0 tells plumed to use all the data&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          4 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 : OutputPCAProjection::OutputPCAProjection( const ActionOptions&amp; ao ):</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   Action(ao),</a>
+<a name="69"><span class="lineNum">      69 </span>            :   analysis::AnalysisBase(ao),</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          2 :   fmt(&quot;%f&quot;)</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : {</a>
+<a name="72"><span class="lineNum">      72 </span>            :   // Setup the PCA object</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 :   mypca = dynamic_cast&lt;PCA*&gt;( my_input_data );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          2 :   if( !mypca ) error(&quot;input must be a PCA object&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            :   // Get setup the pdb</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          2 :   mypdb.setAtomNumbers( my_input_data-&gt;getAtomIndexes() );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          2 :   mypdb.setArgumentNames( (mypca-&gt;my_input_data)-&gt;getArgumentNames() );</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   // Find a moldata object</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          2 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          3 :   if( moldat ) warning(&quot;PDB output files do not have atom types unless you use MOLDATA&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :   parse(&quot;FILE&quot;,filename); parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :   if( !getRestart() ) { OFile ofile; ofile.link(*this); ofile.setBackupString(&quot;analysis&quot;); ofile.backupAllFiles(filename); }</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :   log.printf(&quot;  printing data to file named %s \n&quot;,filename.c_str() );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 : void OutputPCAProjection::performAnalysis() {</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Find a moldata object</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   auto* mymoldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   // Output the embedding in plumed pdb format</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   OFile afile; afile.link(*this); afile.setBackupString(&quot;analysis&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   mypdb.setAtomPositions( (mypca-&gt;myref)-&gt;getReferencePositions() );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 :   for(unsigned j=0; j&lt;mypca-&gt;getArguments().size(); ++j) mypdb.setArgumentValue( (mypca-&gt;getArguments()[j])-&gt;getName(), (mypca-&gt;myref)-&gt;getReferenceArgument(j) );</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   // And output the first frame</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   afile.open( filename ); afile.printf(&quot;REMARK TYPE=%s \n&quot;, mypca-&gt;mtype.c_str() );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :   if( plumed.getAtoms().usingNaturalUnits() ) mypdb.print( 1.0, mymoldat, afile, fmt );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   else mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, afile, fmt );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   // And now output the eigenvectors</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   for(unsigned dim=0; dim&lt;mypca-&gt;nlow; ++dim) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :     afile.printf(&quot;REMARK TYPE=DIRECTION \n&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 :     mypdb.setAtomPositions( mypca-&gt;directions[dim].getReferencePositions() );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          8 :     for(unsigned j=0; j&lt;mypca-&gt;getArguments().size(); ++j) mypdb.setArgumentValue( (mypca-&gt;getArguments()[j])-&gt;getName(), mypca-&gt;directions[dim].getReferenceArgument(j) );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 :     if( plumed.getAtoms().usingNaturalUnits() ) mypdb.print( 1.0, mymoldat, afile, fmt );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 :     else mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, afile, fmt );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 :   afile.close();</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/dimred/PCA.cpp.func-sort-c.html b/coverage/dimred/PCA.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ab611d0082
--- /dev/null
+++ b/coverage/dimred/PCA.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/PCA.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - PCA.cpp<span style="font-size: 80%;"> (<a href="PCA.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryMed">80.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.cpp.gcov.html#254">_ZN4PLMD6dimred3PCA13getProjectionERKjRSt6vectorIdSaIdEERd</a></td>
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+              <td class="coverFn"><a href="PCA.cpp.gcov.html#262">_ZN4PLMD6dimred3PCA13getProjectionERNS_8analysis20DataCollectionObjectERSt6vectorIdSaIdEE</a></td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/dimred/PCA.cpp.func.html b/coverage/dimred/PCA.cpp.func.html
new file mode 100644
index 0000000000..5998695036
--- /dev/null
+++ b/coverage/dimred/PCA.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/PCA.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
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+
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - PCA.cpp<span style="font-size: 80%;"> (<a href="PCA.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryMed">80.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PCA.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.cpp.gcov.html#98">_ZN4PLMD6dimred12_GLOBAL__N_116PCARegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
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+              <td class="coverFn"><a href="PCA.cpp.gcov.html#98">_ZN4PLMD6dimred12_GLOBAL__N_116PCARegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="PCA.cpp.gcov.html#254">_ZN4PLMD6dimred3PCA13getProjectionERKjRSt6vectorIdSaIdEERd</a></td>
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+    <tr>
+              <td class="coverFn"><a href="PCA.cpp.gcov.html#262">_ZN4PLMD6dimred3PCA13getProjectionERNS_8analysis20DataCollectionObjectERSt6vectorIdSaIdEE</a></td>
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+              <td class="coverFn"><a href="PCA.cpp.gcov.html#159">_ZN4PLMD6dimred3PCA15performAnalysisEv</a></td>
+              <td class="coverFnHi">3</td>
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+    <tr>
+              <td class="coverFn"><a href="PCA.cpp.gcov.html#100">_ZN4PLMD6dimred3PCA16registerKeywordsERNS_8KeywordsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="PCA.cpp.gcov.html#106">_ZN4PLMD6dimred3PCAC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
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+    <tr>
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+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/dimred/PCA.cpp.gcov.html b/coverage/dimred/PCA.cpp.gcov.html
new file mode 100644
index 0000000000..cf44d210cc
--- /dev/null
+++ b/coverage/dimred/PCA.cpp.gcov.html
@@ -0,0 +1,354 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/PCA.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - PCA.cpp<span style="font-size: 80%;"> (source / <a href="PCA.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryMed">80.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PCA.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/ReferenceValuePack.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;analysis/ReadAnalysisFrames.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC DIMRED PCA</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Perform principal component analysis (PCA) using either the positions of the atoms a large number of collective variables as input.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Principal component analysis is a statistical technique that uses an orthogonal transformation to convert a set of observations of</a>
+<a name="34"><span class="lineNum">      34 </span>            : poorly correlated variables into a set of linearly uncorrelated variables.  You can read more about the specifics of this technique</a>
+<a name="35"><span class="lineNum">      35 </span>            : here: https://en.wikipedia.org/wiki/Principal_component_analysis</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : When used with molecular dynamics simulations a set of frames taken from the trajectory, \f$\{X_i\}\f$, or the values of</a>
+<a name="38"><span class="lineNum">      38 </span>            : a number of collective variables which are calculated from the trajectory frames are used as input.  In this second instance your</a>
+<a name="39"><span class="lineNum">      39 </span>            : input to the PCA analysis algorithm is thus a set of high-dimensional vectors of collective variables.  However, if</a>
+<a name="40"><span class="lineNum">      40 </span>            : collective variables are calculated from the positions of the atoms or if the positions are used directly the assumption is that</a>
+<a name="41"><span class="lineNum">      41 </span>            : this input trajectory is a set of poorly correlated (high-dimensional) vectors.  After principal component analysis has been</a>
+<a name="42"><span class="lineNum">      42 </span>            : performed the output is a set of orthogonal vectors that describe the directions in which the largest motions have been seen.</a>
+<a name="43"><span class="lineNum">      43 </span>            : In other words, principal component analysis provides a method for lowering the dimensionality of the data contained in a trajectory.</a>
+<a name="44"><span class="lineNum">      44 </span>            : These output directions are some linear combination of the \f$x\f$, \f$y\f$ and \f$z\f$ positions if the positions were used as input</a>
+<a name="45"><span class="lineNum">      45 </span>            : or some linear combination of the input collective variables if a high-dimensional vector of collective variables was used as input.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : As explained on the Wikipedia page you must calculate the average and covariance for each of the input coordinates.  In other words, you must</a>
+<a name="48"><span class="lineNum">      48 </span>            : calculate the average structure and the amount the system fluctuates around this average structure.  The problem in doing so when the</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f$x\f$, \f$y\f$ and \f$z\f$ coordinates of a molecule are used as input is that the majority of the changes in the positions of the</a>
+<a name="50"><span class="lineNum">      50 </span>            : atoms comes from the translational and rotational degrees of freedom of the molecule.  The first six principal components will thus, most likely,</a>
+<a name="51"><span class="lineNum">      51 </span>            : be uninteresting.  Consequently, to remedy this problem PLUMED provides the functionality to perform an RMSD alignment of the all the structures</a>
+<a name="52"><span class="lineNum">      52 </span>            : to be analyzed to the first frame in the trajectory.  This can be used to effectively remove translational and/or rotational motions from</a>
+<a name="53"><span class="lineNum">      53 </span>            : consideration.  The resulting principal components thus describe vibrational motions of the molecule.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : If you wish to calculate the projection of a trajectory on a set of principal components calculated from this PCA action then the output can be</a>
+<a name="56"><span class="lineNum">      56 </span>            : used as input for the \ref PCAVARS action.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from changes in the positions</a>
+<a name="61"><span class="lineNum">      61 </span>            : of the first 22 atoms.  The TYPE=OPTIMAL instruction ensures that translational and rotational degrees of freedom are removed from consideration.</a>
+<a name="62"><span class="lineNum">      62 </span>            : The first two principal components will be output to a file called PCA-comp.pdb.  Trajectory frames will be collected on every step and the PCA calculation</a>
+<a name="63"><span class="lineNum">      63 </span>            : will be performed at the end of the simulation.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \plumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : ff: COLLECT_FRAMES ATOMS=1-22 STRIDE=1</a>
+<a name="67"><span class="lineNum">      67 </span>            : pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=OPTIMAL NLOW_DIM=2</a>
+<a name="68"><span class="lineNum">      68 </span>            : OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca FILE=PCA-comp.pdb</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : The following input instructs PLUMED to perform a principal component analysis in which the covariance matrix is calculated from changes in the six distances</a>
+<a name="72"><span class="lineNum">      72 </span>            : seen in the previous lines.  Notice that here the TYPE=EUCLIDEAN keyword is used to indicate that no alignment has to be done when calculating the various</a>
+<a name="73"><span class="lineNum">      73 </span>            : elements of the covariance matrix from the input vectors.  In this calculation the first two principal components will be output to a file called PCA-comp.pdb.</a>
+<a name="74"><span class="lineNum">      74 </span>            : Trajectory frames will be collected every five steps and the PCA calculation is performed every 1000 steps.  Consequently, if you run a 2000 step simulation the</a>
+<a name="75"><span class="lineNum">      75 </span>            : PCA analysis will be performed twice.  The REWEIGHT_BIAS action in this input tells PLUMED that rather that ascribing a weight of one to each of the frames</a>
+<a name="76"><span class="lineNum">      76 </span>            : when calculating averages and covariance matrices a reweighting should be performed based and each frames' weight in these calculations should be determined based on</a>
+<a name="77"><span class="lineNum">      77 </span>            : the current value of the instantaneous bias (see \ref REWEIGHT_BIAS).</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : \plumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="81"><span class="lineNum">      81 </span>            : d2: DISTANCE ATOMS=1,3</a>
+<a name="82"><span class="lineNum">      82 </span>            : d3: DISTANCE ATOMS=1,4</a>
+<a name="83"><span class="lineNum">      83 </span>            : d4: DISTANCE ATOMS=2,3</a>
+<a name="84"><span class="lineNum">      84 </span>            : d5: DISTANCE ATOMS=2,4</a>
+<a name="85"><span class="lineNum">      85 </span>            : d6: DISTANCE ATOMS=3,4</a>
+<a name="86"><span class="lineNum">      86 </span>            : rr: RESTRAINT ARG=d1 AT=0.1 KAPPA=10</a>
+<a name="87"><span class="lineNum">      87 </span>            : rbias: REWEIGHT_BIAS TEMP=300</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : ff: COLLECT_FRAMES ARG=d1,d2,d3,d4,d5,d6 LOGWEIGHTS=rbias STRIDE=5</a>
+<a name="90"><span class="lineNum">      90 </span>            : pca: PCA USE_OUTPUT_DATA_FROM=ff METRIC=EUCLIDEAN NLOW_DIM=2</a>
+<a name="91"><span class="lineNum">      91 </span>            : OUTPUT_PCA_PROJECTION USE_OUTPUT_DATA_FROM=pca STRIDE=100 FILE=PCA-comp.pdb</a>
+<a name="92"><span class="lineNum">      92 </span>            : \endplumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : */</a>
+<a name="95"><span class="lineNum">      95 </span>            : //+ENDPLUMEDOC</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : namespace PLMD {</a>
+<a name="98"><span class="lineNum">      98 </span>            : namespace dimred {</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(PCA,&quot;PCA&quot;)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          5 : void PCA::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         15 :   DimensionalityReductionBase::registerKeywords( keys ); keys.use(&quot;ARG&quot;); keys.reset_style(&quot;ARG&quot;,&quot;optional&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;METRIC&quot;,&quot;EUCLIDEAN&quot;,&quot;the method that you are going to use to measure the distances between points&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         10 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the list of atoms that you are going to use in the measure of distance that you are using&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          5 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 : PCA::PCA(const ActionOptions&amp;ao):</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   Action(ao),</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :   DimensionalityReductionBase(ao)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : {</a>
+<a name="112"><span class="lineNum">     112 </span>            :   // Get the input PDB file from the underlying ReadAnalysisFrames object</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          3 :   analysis::ReadAnalysisFrames* myframes = dynamic_cast&lt;analysis::ReadAnalysisFrames*&gt;( my_input_data );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 :   if( !myframes ) error(&quot;input to PCA should be ReadAnalysisFrames object&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          6 :   parse(&quot;METRIC&quot;,mtype); std::vector&lt;AtomNumber&gt; atoms;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          3 :   log.printf(&quot;  performing PCA analysis using %s metric \n&quot;, mtype.c_str() );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          3 :   if( my_input_data-&gt;getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :     parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          1 :     if( atoms.size()!=0 ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       mypdb.setAtomNumbers( atoms );</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :         bool found=false;</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;my_input_data-&gt;getAtomIndexes().size(); ++j) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :           if( my_input_data-&gt;getAtomIndexes()[j]==atoms[i] ) { found=true; break; }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :         }</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :         if( !found ) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :           std::string num; Tools::convert( atoms[i].serial(), num );</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :           error(&quot;atom number &quot; + num + &quot; is not stored in any action that has been input&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :         }</a>
+<a name="130"><span class="lineNum">     130 </span>            :       }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :       mypdb.addBlockEnd( atoms.size() );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 :     } else if( getNumberOfArguments()==0 ) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          1 :       mypdb.setAtomNumbers( my_input_data-&gt;getAtomIndexes() );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :       mypdb.addBlockEnd( my_input_data-&gt;getAtomIndexes().size() );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :       if( mtype==&quot;EUCLIDEAN&quot; ) mtype=&quot;OPTIMAL&quot;;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :     }</a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :   if( my_input_data-&gt;getArgumentNames().size()&gt;0 ) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :     if( getNumberOfArguments()==0 &amp;&amp; atoms.size()==0 ) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :       std::vector&lt;std::string&gt; argnames( my_input_data-&gt;getArgumentNames() );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :       mypdb.setArgumentNames( argnames ); requestArguments( my_input_data-&gt;getArgumentList() );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          2 :     } else {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :       std::vector&lt;Value*&gt; myargs( getArguments() );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :       std::vector&lt;std::string&gt; inargnames( my_input_data-&gt;getArgumentNames() );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :       std::vector&lt;std::string&gt; argnames( myargs.size() );</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;myargs.size(); ++i) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :         argnames[i]=myargs[i]-&gt;getName();</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :         bool found=false;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;inargnames.size(); ++j) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :           if( argnames[i]==inargnames[j] ) { found=true; break; }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :         }</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :         if( !found ) error(&quot;input named &quot; + my_input_data-&gt;getLabel() + &quot; does not store/calculate quantity named &quot; + argnames[i] );</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :       mypdb.setArgumentNames( argnames ); requestArguments( myargs );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 :   if( nlow==0 ) error(&quot;dimensionality of output not set&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          3 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          3 : void PCA::performAnalysis() {</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Align everything to the first frame</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          3 :   my_input_data-&gt;getStoredData( 0, false ).transferDataToPDB( mypdb );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          3 :   auto myconf0=metricRegister().create&lt;ReferenceConfiguration&gt;(mtype, mypdb);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   MultiValue myval( 1, myconf0-&gt;getNumberOfReferenceArguments() + 3*myconf0-&gt;getNumberOfReferencePositions() + 9 );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          3 :   ReferenceValuePack mypack( myconf0-&gt;getNumberOfReferenceArguments(), myconf0-&gt;getNumberOfReferencePositions(), myval );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;myconf0-&gt;getNumberOfReferencePositions(); ++i) mypack.setAtomIndex( i, i );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   // Setup some PCA storage</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          3 :   myconf0-&gt;setupPCAStorage ( mypack );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; displace( myconf0-&gt;getNumberOfReferencePositions() );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          3 :   if( myconf0-&gt;getNumberOfReferencePositions()&gt;0 ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :     ReferenceAtoms* at = dynamic_cast&lt;ReferenceAtoms*&gt;( myconf0.get() );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          1 :     displace = at-&gt;getDisplace();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   // Create some arrays to store the average position</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; sarg( myconf0-&gt;getNumberOfReferenceArguments(), 0 );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          3 :   std::vector&lt;Vector&gt; spos( myconf0-&gt;getNumberOfReferencePositions() );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;myconf0-&gt;getNumberOfReferencePositions(); ++i) spos[i].zero();</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   // Calculate the average displacement from the first frame</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          3 :   double norm=getWeight(0); std::vector&lt;double&gt; args( getNumberOfArguments() );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       1638 :   for(unsigned i=1; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       1635 :     my_input_data-&gt;getStoredData( i, false ).transferDataToPDB( mypdb );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       3815 :     for(unsigned j=0; j&lt;getArguments().size(); ++j) mypdb.getArgumentValue( getArguments()[j]-&gt;getName(), args[j] );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       1635 :     myconf0-&gt;calc( mypdb.getPositions(), getPbc(), getArguments(), args, mypack, true );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     // Accumulate average displacement of arguments (Here PBC could do fucked up things - really needs Berry Phase ) GAT</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       3815 :     for(unsigned j=0; j&lt;myconf0-&gt;getNumberOfReferenceArguments(); ++j) sarg[j] += 0.5*getWeight(i)*mypack.getArgumentDerivative(j);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     // Accumulate average displacement of position</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      13625 :     for(unsigned j=0; j&lt;myconf0-&gt;getNumberOfReferencePositions(); ++j) spos[j] += getWeight(i)*mypack.getAtomsDisplacementVector()[j] / displace[j];</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1635 :     norm += getWeight(i);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // Now normalise the displacements to get the average and add these to the first frame</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          3 :   double inorm = 1.0 / norm ;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          7 :   for(unsigned j=0; j&lt;myconf0-&gt;getNumberOfReferenceArguments(); ++j) sarg[j] = inorm*sarg[j] + myconf0-&gt;getReferenceArguments()[j];</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         25 :   for(unsigned j=0; j&lt;myconf0-&gt;getNumberOfReferencePositions(); ++j) spos[j] = inorm*spos[j] + myconf0-&gt;getReferencePositions()[j];</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   // Now accumulate the covariance</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          3 :   unsigned narg=myconf0-&gt;getNumberOfReferenceArguments(), natoms=myconf0-&gt;getNumberOfReferencePositions();</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          3 :   Matrix&lt;double&gt; covar( narg+3*natoms, narg+3*natoms ); covar=0;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1641 :   for(unsigned i=0; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1638 :     my_input_data-&gt;getStoredData( i, false ).transferDataToPDB( mypdb );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       3822 :     for(unsigned j=0; j&lt;getArguments().size(); ++j) mypdb.getArgumentValue( getArguments()[j]-&gt;getName(), args[j] );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       1638 :     myconf0-&gt;calc( mypdb.getPositions(), getPbc(), getArguments(), args, mypack, true );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       3822 :     for(unsigned jarg=0; jarg&lt;narg; ++jarg) {</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :       // Need sorting for PBC with GAT</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       2184 :       double jarg_d = 0.5*mypack.getArgumentDerivative(jarg) + myconf0-&gt;getReferenceArguments()[jarg] - sarg[jarg];</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       6552 :       for(unsigned karg=0; karg&lt;narg; ++karg) {</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :         // Need sorting for PBC with GAT</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       4368 :         double karg_d = 0.5*mypack.getArgumentDerivative(karg) + myconf0-&gt;getReferenceArguments()[karg] - sarg[karg];</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       4368 :         covar( jarg, karg ) += 0.25*getWeight(i)*jarg_d*karg_d; // mypack.getArgumentDerivative(jarg)*mypack.getArgumentDerivative(karg);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :       }</a>
+<a name="212"><span class="lineNum">     212 </span>            :     }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      13650 :     for(unsigned jat=0; jat&lt;natoms; ++jat) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      48048 :       for(unsigned jc=0; jc&lt;3; ++jc) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      36036 :         double jdisplace = mypack.getAtomsDisplacementVector()[jat][jc] / displace[jat] + myconf0-&gt;getReferencePositions()[jat][jc] - spos[jat][jc];</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     828828 :         for(unsigned kat=0; kat&lt;natoms; ++kat) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">    3171168 :           for(unsigned kc=0; kc&lt;3; ++kc) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">    2378376 :             double kdisplace = mypack.getAtomsDisplacementVector()[kat][kc] /displace[kat] + myconf0-&gt;getReferencePositions()[kat][kc] - spos[kat][kc];</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">    2378376 :             covar( narg+3*jat + jc, narg+3*kat + kc ) += getWeight(i)*jdisplace*kdisplace;</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :           }</a>
+<a name="221"><span class="lineNum">     221 </span>            :         }</a>
+<a name="222"><span class="lineNum">     222 </span>            :       }</a>
+<a name="223"><span class="lineNum">     223 </span>            :     }</a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span>            :   // Normalise</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         73 :   for(unsigned i=0; i&lt;covar.nrows(); ++i) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       4434 :     for(unsigned j=0; j&lt;covar.ncols(); ++j) covar(i,j) *= inorm;</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   // Diagonalise the covariance</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; eigval( narg+3*natoms );</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   Matrix&lt;double&gt; eigvec( narg+3*natoms, narg+3*natoms );</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          3 :   diagMat( covar, eigval, eigvec );</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   // Output the reference configuration</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          3 :   mypdb.setAtomPositions( spos );</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          7 :   for(unsigned j=0; j&lt;sarg.size(); ++j) mypdb.setArgumentValue( getArguments()[j]-&gt;getName(), sarg[j] );</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   // Reset the reference configuration</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          6 :   myref = metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, mypdb );</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   // Store and print the eigenvectors</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          3 :   std::vector&lt;Vector&gt; tmp_atoms( natoms );</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          9 :   for(unsigned dim=0; dim&lt;nlow; ++dim) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          6 :     unsigned idim = covar.ncols() - 1 - dim;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         14 :     for(unsigned i=0; i&lt;narg; ++i) mypdb.setArgumentValue( getArguments()[i]-&gt;getName(), eigvec(idim,i) );</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         50 :     for(unsigned i=0; i&lt;natoms; ++i) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        176 :       for(unsigned k=0; k&lt;3; ++k) tmp_atoms[i][k]=eigvec(idim,narg+3*i+k);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :     }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          6 :     mypdb.setAtomPositions( tmp_atoms );</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :     // Create a direction object so that we can calculate other PCA components</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         12 :     directions.push_back( Direction(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)));</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          6 :     directions[dim].read( mypdb );</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          3 : }</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 : void PCA::getProjection( const unsigned&amp; idata, std::vector&lt;double&gt;&amp; point, double&amp; weight ) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   if( point.size()!=nlow ) point.resize( nlow );</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   // Retrieve the weight</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :   weight = getWeight(idata);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   // Retrieve the data point</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   getProjection( my_input_data-&gt;getStoredData( idata, false ), point );</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        546 : void PCA::getProjection( analysis::DataCollectionObject&amp; myidata, std::vector&lt;double&gt;&amp; point ) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        546 :   myidata.transferDataToPDB( mypdb ); std::vector&lt;double&gt; args( getArguments().size() );</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       1638 :   for(unsigned j=0; j&lt;getArguments().size(); ++j) mypdb.getArgumentValue( getArguments()[j]-&gt;getName(), args[j] );</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   // Create some storage space</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        546 :   MultiValue myval( 1, 3*mypdb.getPositions().size() + args.size() + 9);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        546 :   ReferenceValuePack mypack( args.size(), mypdb.getPositions().size(), myval );</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        546 :   for(unsigned i=0; i&lt;mypdb.getPositions().size(); ++i) mypack.setAtomIndex( i, i );</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        546 :   myref-&gt;setupPCAStorage( mypack );</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :   // And calculate</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        546 :   myref-&gt;calculate( mypdb.getPositions(), getPbc(), getArguments(), mypack, true );</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       1638 :   for(unsigned i=0; i&lt;nlow; ++i) point[i]=myref-&gt;projectDisplacementOnVector( directions[i], getArguments(), args, mypack );</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1092 : }</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            : }</a>
+<a name="278"><span class="lineNum">     278 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/PCA.h.func-sort-c.html b/coverage/dimred/PCA.h.func-sort-c.html
new file mode 100644
index 0000000000..2505beb0bc
--- /dev/null
+++ b/coverage/dimred/PCA.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/PCA.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - PCA.h<span style="font-size: 80%;"> (<a href="PCA.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PCA.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.h.gcov.html#51">_ZN4PLMD6dimred3PCA15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.h.gcov.html#50">_ZN4PLMD6dimred3PCA17setTargetDistanceERKjRKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.h.gcov.html#49">_ZN4PLMD6dimred3PCA20calculateProjectionsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/PCA.h.func.html b/coverage/dimred/PCA.h.func.html
new file mode 100644
index 0000000000..0259b2fd00
--- /dev/null
+++ b/coverage/dimred/PCA.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/PCA.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - PCA.h<span style="font-size: 80%;"> (<a href="PCA.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PCA.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.h.gcov.html#51">_ZN4PLMD6dimred3PCA15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.h.gcov.html#50">_ZN4PLMD6dimred3PCA17setTargetDistanceERKjRKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCA.h.gcov.html#49">_ZN4PLMD6dimred3PCA20calculateProjectionsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/PCA.h.gcov.html b/coverage/dimred/PCA.h.gcov.html
new file mode 100644
index 0000000000..cba848e2ec
--- /dev/null
+++ b/coverage/dimred/PCA.h.gcov.html
@@ -0,0 +1,134 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/PCA.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - PCA.h<span style="font-size: 80%;"> (source / <a href="PCA.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_dimred_PCA_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_dimred_PCA_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;DimensionalityReductionBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;reference/Direction.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace dimred {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class PCA : public DimensionalityReductionBase {</a>
+<a name="34"><span class="lineNum">      34 </span>            :   friend class OutputPCAProjection;</a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// The way we are measuring distances</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::string mtype;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// The position of the reference configuration (the one we align to)</a>
+<a name="39"><span class="lineNum">      39 </span>            :   PDB mypdb;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// The eigenvectors for the displacements in argument space</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::string ofilename, fmt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// The eigenvectors that we are using</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::unique_ptr&lt;ReferenceConfiguration&gt; myref;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::vector&lt;Direction&gt; directions;</a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit PCA(const ActionOptions&amp;ao);</a>
+<a name="48"><span class="lineNum">      48 </span>            :   void performAnalysis() override;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void getProjection( const unsigned&amp; idata, std::vector&lt;double&gt;&amp; point, double&amp; weight ) override;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void getProjection( analysis::DataCollectionObject&amp; myidata, std::vector&lt;double&gt;&amp; point );</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   void calculateProjections( const Matrix&lt;double&gt;&amp;, Matrix&lt;double&gt;&amp; ) override { plumed_error(); }</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :   void setTargetDistance( const unsigned&amp;, const double&amp; ) override { plumed_error(); }</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   double calculateStress( const std::vector&lt;double&gt;&amp; pp, std::vector&lt;double&gt;&amp; der ) override { plumed_error(); }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/ProjectNonLandmarkPoints.cpp.func-sort-c.html b/coverage/dimred/ProjectNonLandmarkPoints.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e777fc2209
--- /dev/null
+++ b/coverage/dimred/ProjectNonLandmarkPoints.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/ProjectNonLandmarkPoints.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - ProjectNonLandmarkPoints.cpp<span style="font-size: 80%;"> (<a href="ProjectNonLandmarkPoints.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ProjectNonLandmarkPoints.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#96">_ZN4PLMD6dimred24ProjectNonLandmarkPoints15getArgumentListEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#76">_ZN4PLMD6dimred24ProjectNonLandmarkPointsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#64">_ZNK4PLMD6dimred24ProjectNonLandmarkPoints11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#67">_ZN4PLMD6dimred12_GLOBAL__N_136ProjectNonLandmarkPointsRegisterMe696createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#60">_ZN4PLMD6dimred24ProjectNonLandmarkPoints15performAnalysisEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#76">_ZN4PLMD6dimred24ProjectNonLandmarkPointsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#69">_ZN4PLMD6dimred24ProjectNonLandmarkPoints16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#122">_ZN4PLMD6dimred24ProjectNonLandmarkPoints13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">1046</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#102">_ZN4PLMD6dimred24ProjectNonLandmarkPoints18generateProjectionERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1046</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#67">_ZN4PLMD6dimred12_GLOBAL__N_136ProjectNonLandmarkPointsRegisterMe69C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#67">_ZN4PLMD6dimred12_GLOBAL__N_136ProjectNonLandmarkPointsRegisterMe69D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#129">_ZN4PLMD6dimred24ProjectNonLandmarkPoints15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">16744</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/ProjectNonLandmarkPoints.cpp.func.html b/coverage/dimred/ProjectNonLandmarkPoints.cpp.func.html
new file mode 100644
index 0000000000..8313c04e24
--- /dev/null
+++ b/coverage/dimred/ProjectNonLandmarkPoints.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/ProjectNonLandmarkPoints.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - ProjectNonLandmarkPoints.cpp<span style="font-size: 80%;"> (<a href="ProjectNonLandmarkPoints.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ProjectNonLandmarkPoints.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#67">_ZN4PLMD6dimred12_GLOBAL__N_136ProjectNonLandmarkPointsRegisterMe696createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#67">_ZN4PLMD6dimred12_GLOBAL__N_136ProjectNonLandmarkPointsRegisterMe69C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#67">_ZN4PLMD6dimred12_GLOBAL__N_136ProjectNonLandmarkPointsRegisterMe69D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#122">_ZN4PLMD6dimred24ProjectNonLandmarkPoints13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">1046</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#129">_ZN4PLMD6dimred24ProjectNonLandmarkPoints15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">16744</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#96">_ZN4PLMD6dimred24ProjectNonLandmarkPoints15getArgumentListEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#60">_ZN4PLMD6dimred24ProjectNonLandmarkPoints15performAnalysisEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#69">_ZN4PLMD6dimred24ProjectNonLandmarkPoints16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#102">_ZN4PLMD6dimred24ProjectNonLandmarkPoints18generateProjectionERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1046</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#76">_ZN4PLMD6dimred24ProjectNonLandmarkPointsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#76">_ZN4PLMD6dimred24ProjectNonLandmarkPointsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ProjectNonLandmarkPoints.cpp.gcov.html#64">_ZNK4PLMD6dimred24ProjectNonLandmarkPoints11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/ProjectNonLandmarkPoints.cpp.gcov.html b/coverage/dimred/ProjectNonLandmarkPoints.cpp.gcov.html
new file mode 100644
index 0000000000..00fc3c30c1
--- /dev/null
+++ b/coverage/dimred/ProjectNonLandmarkPoints.cpp.gcov.html
@@ -0,0 +1,213 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/ProjectNonLandmarkPoints.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - ProjectNonLandmarkPoints.cpp<span style="font-size: 80%;"> (source / <a href="ProjectNonLandmarkPoints.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/ConjugateGradient.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;analysis/AnalysisBase.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;DimensionalityReductionBase.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;PCA.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC DIMRED PROJECT_ALL_ANALYSIS_DATA</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Find projections of all non-landmark points using the embedding calculated by a dimensionality reduction optimization calculation.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : //+ENDPLUMEDOC</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace dimred {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class ProjectNonLandmarkPoints : public analysis::AnalysisBase {</a>
+<a name="45"><span class="lineNum">      45 </span>            : private:</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Tolerance for conjugate gradient algorithm</a>
+<a name="47"><span class="lineNum">      47 </span>            :   double cgtol;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Number of diemsions in low dimensional space</a>
+<a name="49"><span class="lineNum">      49 </span>            :   unsigned nlow;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// The class that calculates the projection of the data that is required</a>
+<a name="51"><span class="lineNum">      51 </span>            :   DimensionalityReductionBase* mybase;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Generate a projection of the ith data point - this is called in two routine</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void generateProjection( const unsigned&amp; idat, std::vector&lt;double&gt;&amp; point );</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit ProjectNonLandmarkPoints( const ActionOptions&amp; ao );</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Get a reference configuration (this returns the projection)</a>
+<a name="58"><span class="lineNum">      58 </span>            :   analysis::DataCollectionObject&amp; getStoredData( const unsigned&amp; idat, const bool&amp; calcdist );</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Overwrite getArguments so we get arguments from underlying class</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;Value*&gt; getArgumentList();</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// This does nothing -- projections are calculated when getDataPoint and getReferenceConfiguration are called</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :   void performAnalysis() {}</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : /// This just calls calculate stress in the underlying projection object</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double calculateStress( const std::vector&lt;double&gt;&amp; pp, std::vector&lt;double&gt;&amp; der );</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Overwrite virtual function in ActionWithVessel</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const { plumed_error(); }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ProjectNonLandmarkPoints,&quot;PROJECT_ALL_ANALYSIS_DATA&quot;)</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          4 : void ProjectNonLandmarkPoints::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          4 :   analysis::AnalysisBase::registerKeywords( keys );</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;PROJECTION&quot;,&quot;the projection that you wish to generate out-of-sample projections with&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;CGTOL&quot;,&quot;1E-6&quot;,&quot;the tolerance for the conjugate gradient optimization&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;coord&quot;,&quot;default&quot;,&quot;the low-dimensional projections of the various input configurations&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          4 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          2 : ProjectNonLandmarkPoints::ProjectNonLandmarkPoints( const ActionOptions&amp; ao ):</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   Action(ao),</a>
+<a name="80"><span class="lineNum">      80 </span>            :   analysis::AnalysisBase(ao),</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          2 :   mybase(NULL)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : {</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          2 :   std::string myproj; parse(&quot;PROJECTION&quot;,myproj);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :   mybase = plumed.getActionSet().selectWithLabel&lt;DimensionalityReductionBase*&gt;( myproj );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 :   if( !mybase ) error(&quot;could not find projection of data named &quot; + myproj );</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   // Add the dependency and set the dimensionality</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 :   addDependency( mybase ); nlow = mybase-&gt;nlow;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   // Add fake components to the underlying ActionWithValue for the arguments</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::string num;</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;nlow; ++i) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         12 :     Tools::convert(i+1,num); addComponent( &quot;coord-&quot; + num ); componentIsNotPeriodic( &quot;coord-&quot; + num );</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   log.printf(&quot;  generating out-of-sample projections using projection with label %s \n&quot;,myproj.c_str() );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 :   parse(&quot;CGTOL&quot;,cgtol);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 : std::vector&lt;Value*&gt; ProjectNonLandmarkPoints::getArgumentList() {</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::vector&lt;Value*&gt; arglist( analysis::AnalysisBase::getArgumentList() );</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;nlow; ++i) arglist.push_back( getPntrToComponent(i) );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   return arglist;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1046 : void ProjectNonLandmarkPoints::generateProjection( const unsigned&amp; idat, std::vector&lt;double&gt;&amp; point ) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1046 :   PCA* ispca = dynamic_cast&lt;PCA*&gt;( mybase );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1046 :   if( ispca ) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        546 :     ispca-&gt;getProjection( my_input_data-&gt;getStoredData(idat,false), point );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   } else {</a>
+<a name="109"><span class="lineNum">     109 </span>            :     ConjugateGradient&lt;ProjectNonLandmarkPoints&gt; myminimiser( this );</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        500 :     unsigned closest=0; double mindist = std::sqrt( getDissimilarity( mybase-&gt;getDataPointIndexInBase(0), idat ) );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        500 :     mybase-&gt;setTargetDistance( 0, mindist );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     125000 :     for(unsigned i=1; i&lt;mybase-&gt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">     124500 :       double dist = std::sqrt( getDissimilarity( mybase-&gt;getDataPointIndexInBase(i), idat ) );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     124500 :       mybase-&gt;setTargetDistance( i, dist );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     124500 :       if( dist&lt;mindist ) { mindist=dist; closest=i; }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span>            :     // Put the initial guess near to the closest landmark  -- may wish to use grid here again Sandip??</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        500 :     Random random; random.setSeed(-1234);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1500 :     for(unsigned j=0; j&lt;nlow; ++j) point[j]=mybase-&gt;projections(closest,j) + (random.RandU01() - 0.5)*0.01;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        500 :     myminimiser.minimise( cgtol, point, &amp;ProjectNonLandmarkPoints::calculateStress );</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       1046 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       1046 : analysis::DataCollectionObject&amp; ProjectNonLandmarkPoints::getStoredData( const unsigned&amp; idat, const bool&amp; calcdist ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       1046 :   std::vector&lt;double&gt; pp(nlow); generateProjection( idat, pp ); std::string num;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   analysis::DataCollectionObject&amp; myref=AnalysisBase::getStoredData(idat,calcdist);</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       3138 :   for(unsigned i=0; i&lt;nlow; ++i) { Tools::convert(i+1,num); myref.setArgument( getLabel() + &quot;.coord-&quot; + num, pp[i] ); }</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       1046 :   return myref;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      16744 : double ProjectNonLandmarkPoints::calculateStress( const std::vector&lt;double&gt;&amp; pp, std::vector&lt;double&gt;&amp; der ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      16744 :   return mybase-&gt;calculateStress( pp, der );</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/dimred/SMACOF.cpp.func-sort-c.html b/coverage/dimred/SMACOF.cpp.func-sort-c.html
new file mode 100644
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SMACOF.cpp<span style="font-size: 80%;"> (<a href="SMACOF.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SMACOF.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACOF.cpp.gcov.html#25">_ZN4PLMD6dimred6SMACOF3runERKNS_6MatrixIdEES5_RKdRKjRS3_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACOF.cpp.gcov.html#78">_ZN4PLMD6dimred6SMACOF14calculateSigmaERKNS_6MatrixIdEES5_S5_RS3_</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/dimred/SMACOF.cpp.func.html b/coverage/dimred/SMACOF.cpp.func.html
new file mode 100644
index 0000000000..48fbd754e0
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+++ b/coverage/dimred/SMACOF.cpp.func.html
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+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SMACOF.cpp<span style="font-size: 80%;"> (<a href="SMACOF.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
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+
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+  </table>
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+              <td class="coverFn"><a href="SMACOF.cpp.gcov.html#78">_ZN4PLMD6dimred6SMACOF14calculateSigmaERKNS_6MatrixIdEES5_S5_RS3_</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SMACOF.cpp.gcov.html#25">_ZN4PLMD6dimred6SMACOF3runERKNS_6MatrixIdEES5_RKdRKjRS3_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+  </table>
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diff --git a/coverage/dimred/SMACOF.cpp.gcov.html b/coverage/dimred/SMACOF.cpp.gcov.html
new file mode 100644
index 0000000000..452870f8a6
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+++ b/coverage/dimred/SMACOF.cpp.gcov.html
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SMACOF.cpp<span style="font-size: 80%;"> (source / <a href="SMACOF.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SMACOF.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace dimred {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">          1 : void SMACOF::run( const Matrix&lt;double&gt;&amp; Weights, const Matrix&lt;double&gt;&amp; Distances, const double&amp; tol, const unsigned&amp; maxloops, Matrix&lt;double&gt;&amp; InitialZ ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span>            :   unsigned M = Distances.nrows();</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            :   // Calculate V</a>
+<a name="31"><span class="lineNum">      31 </span>            :   Matrix&lt;double&gt; V(M,M); double totalWeight=0.;</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        501 :   for(unsigned i=0; i&lt;M; ++i) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     250500 :     for(unsigned j=0; j&lt;M; ++j) {</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     250000 :       if(i==j) continue;</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     249500 :       V(i,j)=-Weights(i,j);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     249500 :       if( j&lt;i ) totalWeight+=Weights(i,j);</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :     }</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     250500 :     for(unsigned j=0; j&lt;M; ++j) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     250000 :       if(i==j)continue;</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     249500 :       V(i,i)-=V(i,j);</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :     }</a>
+<a name="42"><span class="lineNum">      42 </span>            :   }</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            :   // And pseudo invert V</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          1 :   Matrix&lt;double&gt; mypseudo(M, M); pseudoInvert(V, mypseudo);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          1 :   Matrix&lt;double&gt; dists( M, M ); double myfirstsig = calculateSigma( Weights, Distances, InitialZ, dists ) / totalWeight;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            :   // initial sigma is made up of the original distances minus the distances between the projections all squared.</a>
+<a name="49"><span class="lineNum">      49 </span>            :   Matrix&lt;double&gt; temp( M, M ), BZ( M, M ), newZ( M, InitialZ.ncols() );</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         14 :   for(unsigned n=0; n&lt;maxloops; ++n) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         14 :     if(n==maxloops-1) plumed_merror(&quot;ran out of steps in SMACOF algorithm&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            :     // Recompute BZ matrix</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       7014 :     for(unsigned i=0; i&lt;M; ++i) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">    3507000 :       for(unsigned j=0; j&lt;M; ++j) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">    3500000 :         if(i==j) continue;  //skips over the diagonal elements</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">    3493000 :         if( dists(i,j)&gt;0 ) BZ(i,j) = -Weights(i,j)*Distances(i,j) / dists(i,j);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :         else BZ(i,j)=0.;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :       }</a>
+<a name="61"><span class="lineNum">      61 </span>            :       //the diagonal elements are -off diagonal elements BZ(i,i)-=BZ(i,j)   (Equation 8.25)</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       7000 :       BZ(i,i)=0; //create the space memory for the diagonal elements which are scalars</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">    3507000 :       for(unsigned j=0; j&lt;M; ++j) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">    3500000 :         if(i==j) continue;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">    3493000 :         BZ(i,i)-=BZ(i,j);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :       }</a>
+<a name="67"><span class="lineNum">      67 </span>            :     }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         14 :     mult( mypseudo, BZ, temp); mult(temp, InitialZ, newZ);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     //Compute new sigma</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         14 :     double newsig = calculateSigma( Weights, Distances, newZ, dists ) / totalWeight;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :     //Computing whether the algorithm has converged (has the mass of the potato changed</a>
+<a name="73"><span class="lineNum">      73 </span>            :     //when we put it back in the oven!)</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         14 :     if( std::fabs( newsig - myfirstsig )&lt;tol ) break;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     myfirstsig=newsig;</a>
+<a name="76"><span class="lineNum">      76 </span>            :     InitialZ = newZ;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   }</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 : }</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         15 : double SMACOF::calculateSigma( const Matrix&lt;double&gt;&amp; Weights, const Matrix&lt;double&gt;&amp; Distances, const Matrix&lt;double&gt;&amp; InitialZ, Matrix&lt;double&gt;&amp; dists ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   unsigned M = Distances.nrows(); double sigma=0;</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       7500 :   for(unsigned i=1; i&lt;M; ++i) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    1878735 :     for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    5613750 :       double dlow=0; for(unsigned k=0; k&lt;InitialZ.ncols(); ++k) { double tmp=InitialZ(i,k) - InitialZ(j,k); dlow+=tmp*tmp; }</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    1871250 :       dists(i,j)=dists(j,i)=std::sqrt(dlow); double tmp3 = Distances(i,j) - dists(i,j);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    1871250 :       sigma += Weights(i,j)*tmp3*tmp3;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :     }</a>
+<a name="88"><span class="lineNum">      88 </span>            :   }</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         15 :   return sigma;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMap.cpp.func-sort-c.html b/coverage/dimred/SketchMap.cpp.func-sort-c.html
new file mode 100644
index 0000000000..44d90b6d91
--- /dev/null
+++ b/coverage/dimred/SketchMap.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMap.cpp<span style="font-size: 80%;"> (<a href="SketchMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryLo">31.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMap.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#41">_ZN4PLMD6dimred12_GLOBAL__N_121SketchMapRegisterMe436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#59">_ZN4PLMD6dimred9SketchMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#59">_ZN4PLMD6dimred9SketchMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#43">_ZN4PLMD6dimred9SketchMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#41">_ZN4PLMD6dimred12_GLOBAL__N_121SketchMapRegisterMe43C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#41">_ZN4PLMD6dimred12_GLOBAL__N_121SketchMapRegisterMe43D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMap.cpp.func.html b/coverage/dimred/SketchMap.cpp.func.html
new file mode 100644
index 0000000000..38d2a57f00
--- /dev/null
+++ b/coverage/dimred/SketchMap.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMap.cpp<span style="font-size: 80%;"> (<a href="SketchMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryLo">31.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMap.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#41">_ZN4PLMD6dimred12_GLOBAL__N_121SketchMapRegisterMe436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#41">_ZN4PLMD6dimred12_GLOBAL__N_121SketchMapRegisterMe43C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#41">_ZN4PLMD6dimred12_GLOBAL__N_121SketchMapRegisterMe43D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#43">_ZN4PLMD6dimred9SketchMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#59">_ZN4PLMD6dimred9SketchMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMap.cpp.gcov.html#59">_ZN4PLMD6dimred9SketchMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMap.cpp.gcov.html b/coverage/dimred/SketchMap.cpp.gcov.html
new file mode 100644
index 0000000000..be12280501
--- /dev/null
+++ b/coverage/dimred/SketchMap.cpp.gcov.html
@@ -0,0 +1,181 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMap.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMap.cpp<span style="font-size: 80%;"> (source / <a href="SketchMap.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryLo">31.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionShortcut.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace dimred {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC DIMRED SKETCH_MAP</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This can be used to output the data that has been stored in an Analysis object.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Examples</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : */</a>
+<a name="35"><span class="lineNum">      35 </span>            : //+ENDPLUMEDOC</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class SketchMap : public ActionShortcut {</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit SketchMap( const ActionOptions&amp; );</a>
+<a name="41"><span class="lineNum">      41 </span>            : };</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(SketchMap,&quot;SKETCH_MAP&quot;)</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          2 : void SketchMap::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          2 :   ActionShortcut::registerKeywords( keys );</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;NLOW_DIM&quot;,&quot;the dimension of the low dimensional space in which the projections will be constructed&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;MATRIX&quot;,&quot;the matrix of distances between points that you want to reproduce in your sketch-map projection&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;HIGH_DIM_FUNCTION&quot;,&quot;the parameters of the switching function in the high dimensional space&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;LOW_DIM_FUNCTION&quot;,&quot;the parameters of the switching function in the low dimensional space&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;ANNEAL_RATE&quot;,&quot;0.5&quot;,&quot;the rate at which to do the annealing&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;ANNEAL_STEPS&quot;,&quot;10&quot;,&quot;the number of steps of annealing to do&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;CGTOL&quot;,&quot;1E-6&quot;,&quot;the tolerance for the conjugate gradient minimization&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : // Smap pointwise input</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;NCYCLES&quot;,&quot;5&quot;,&quot;the number of cycles of global optimization to attempt&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BUFFER&quot;,&quot;1.1&quot;,&quot;grid extent for search is (max projection - minimum projection) multiplied by this value&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;CGRID_SIZE&quot;,&quot;10&quot;,&quot;number of points to use in each grid direction&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;FGRID_SIZE&quot;,&quot;0&quot;,&quot;interpolate the grid onto this number of points -- only works in 2D&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          2 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 : SketchMap::SketchMap( const ActionOptions&amp; ao ) :</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   Action(ao),</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   ActionShortcut(ao)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : {</a>
+<a name="65"><span class="lineNum">      65 </span>            :   // Input for MDS</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   std::string mds_line = getShortcutLabel() + &quot;_mds: CLASSICAL_MDS&quot;;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   std::string nlow; parse(&quot;NLOW_DIM&quot;,nlow); mds_line += &quot; NLOW_DIM=&quot; + nlow;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   std::string mat; parse(&quot;MATRIX&quot;,mat); mds_line += &quot; USE_OUTPUT_DATA_FROM=&quot; + mat;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   readInputLine( mds_line );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Create generic input for all conjgrad cycles</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   std::string cgtol; parse(&quot;CGTOL&quot;,cgtol); std::string ncyc; parse(&quot;NCYCLES&quot;,ncyc); std::string buf; parse(&quot;BUFFER&quot;,buf);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   std::string cg_grid; parse(&quot;CGRID_SIZE&quot;,cg_grid); std::string fg_grid; parse(&quot;FGRID_SIZE&quot;,fg_grid);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   std::string cg_step_input = &quot; CGTOL=&quot; + cgtol; unsigned nlow_dim; Tools::convert( nlow, nlow_dim );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :   std::string pw_step_input = cg_step_input + &quot; NCYCLES=&quot; + ncyc + &quot; BUFFER=&quot; + buf;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   pw_step_input += &quot; CGRID_SIZE=&quot; + cg_grid; for(unsigned i=1; i&lt;nlow_dim; ++i) pw_step_input += &quot;,&quot; + cg_grid;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   pw_step_input += &quot; FGRID_SIZE=&quot; + fg_grid; for(unsigned i=1; i&lt;nlow_dim; ++i) pw_step_input += &quot;,&quot; + fg_grid;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   // Input for iterative distance matching</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   std::string imds_line_cg = getShortcutLabel() + &quot;_smap1_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=&quot; + getShortcutLabel() + &quot;_mds&quot;;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   std::string hd_func; parse(&quot;HIGH_DIM_FUNCTION&quot;,hd_func); imds_line_cg += &quot; HIGH_DIM_FUNCTION={&quot; + hd_func + &quot;}&quot;;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   std::string ld_func; parse(&quot;LOW_DIM_FUNCTION&quot;,ld_func); imds_line_cg += &quot; LOW_DIM_FUNCTION={&quot; + ld_func + &quot;}&quot;;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   imds_line_cg += cg_step_input + &quot; MIXPARAM=1.0&quot;; readInputLine( imds_line_cg );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :   std::string imds_line_pw = getShortcutLabel() + &quot;_smap1_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=&quot; + getShortcutLabel() + &quot;_smap1_cg&quot;;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   imds_line_pw += pw_step_input + &quot; MIXPARAM=1.0&quot;; readInputLine( imds_line_pw );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   // Now sketch-map</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   unsigned asteps; parse(&quot;ANNEAL_STEPS&quot;,asteps); std::string psmap = getShortcutLabel() + &quot;_smap1_pw&quot;;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   if( asteps&gt;1 ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     double smear; parse(&quot;ANNEAL_RATE&quot;, smear); double old_mix = 1.0; double new_mix = old_mix*smear;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;asteps; ++i) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :       std::string omix; Tools::convert( old_mix, omix ); std::string nmix; Tools::convert( new_mix, nmix );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :       imds_line_cg = getShortcutLabel() + &quot;_smap&quot; + nmix + &quot;_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=&quot; + getShortcutLabel() + &quot;_smap&quot; + omix + &quot;_pw&quot;;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :       imds_line_cg += cg_step_input + &quot; MIXPARAM=&quot; + nmix; readInputLine( imds_line_cg );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :       imds_line_pw = getShortcutLabel() + &quot;_smap&quot; + nmix + &quot;_pw: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=&quot; + getShortcutLabel() + &quot;_smap&quot; + omix + &quot;_cg&quot;;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :       imds_line_pw += pw_step_input + &quot; MIXPARAM=&quot; + nmix; readInputLine( imds_line_pw );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :       old_mix = new_mix; new_mix = old_mix*smear; psmap = getShortcutLabel() + &quot;_smap&quot; + nmix + &quot;_pw&quot;;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Final sketch-map with no mixing of distance matching</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   imds_line_cg = getShortcutLabel() + &quot;_smap_cg: SKETCHMAP_CONJGRAD USE_OUTPUT_DATA_FROM=&quot; + psmap + cg_step_input;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   readInputLine( imds_line_cg );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   imds_line_pw = getShortcutLabel() + &quot;: SKETCHMAP_POINTWISE USE_OUTPUT_DATA_FROM=&quot; + getShortcutLabel() + &quot;_smap_cg&quot; + pw_step_input;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   readInputLine( imds_line_pw );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapBase.cpp.func-sort-c.html b/coverage/dimred/SketchMapBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fcb76d4426
--- /dev/null
+++ b/coverage/dimred/SketchMapBase.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapBase.cpp<span style="font-size: 80%;"> (<a href="SketchMapBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMapBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#33">_ZN4PLMD6dimred13SketchMapBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#33">_ZN4PLMD6dimred13SketchMapBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#74">_ZN4PLMD6dimred13SketchMapBase20calculateProjectionsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#25">_ZN4PLMD6dimred13SketchMapBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#128">_ZN4PLMD6dimred13SketchMapBase19calculateFullStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">1913</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#100">_ZN4PLMD6dimred13SketchMapBase15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">41344</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapBase.cpp.func.html b/coverage/dimred/SketchMapBase.cpp.func.html
new file mode 100644
index 0000000000..d86b5beadd
--- /dev/null
+++ b/coverage/dimred/SketchMapBase.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapBase.cpp<span style="font-size: 80%;"> (<a href="SketchMapBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMapBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#100">_ZN4PLMD6dimred13SketchMapBase15calculateStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">41344</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#25">_ZN4PLMD6dimred13SketchMapBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#128">_ZN4PLMD6dimred13SketchMapBase19calculateFullStressERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">1913</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#74">_ZN4PLMD6dimred13SketchMapBase20calculateProjectionsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#33">_ZN4PLMD6dimred13SketchMapBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.cpp.gcov.html#33">_ZN4PLMD6dimred13SketchMapBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapBase.cpp.gcov.html b/coverage/dimred/SketchMapBase.cpp.gcov.html
new file mode 100644
index 0000000000..a091c65cb0
--- /dev/null
+++ b/coverage/dimred/SketchMapBase.cpp.gcov.html
@@ -0,0 +1,242 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapBase.cpp<span style="font-size: 80%;"> (source / <a href="SketchMapBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SketchMapBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace dimred {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         14 : void SketchMapBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         14 :   DimensionalityReductionBase::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         14 :   keys.remove(&quot;NLOW_DIM&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;HIGH_DIM_FUNCTION&quot;,&quot;as in input action&quot;,&quot;the parameters of the switching function in the high dimensional space&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;LOW_DIM_FUNCTION&quot;,&quot;as in input action&quot;,&quot;the parameters of the switching function in the low dimensional space&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;MIXPARAM&quot;,&quot;0.0&quot;,&quot;the amount of the pure distances to mix into the stress function&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         14 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          6 : SketchMapBase::SketchMapBase( const ActionOptions&amp; ao ):</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   Action(ao),</a>
+<a name="37"><span class="lineNum">      37 </span>            :   DimensionalityReductionBase(ao),</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">          6 :   smapbase(NULL),</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          6 :   normw(0.0)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span>            :   // Check if we have data from a input sketch-map object - we can reuse switching functions wahoo!!</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          6 :   if( dimredbase ) smapbase = dynamic_cast&lt;SketchMapBase*&gt;( dimredbase );</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            :   // Read in the switching functions</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::string linput,hinput, errors;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         12 :   parse(&quot;HIGH_DIM_FUNCTION&quot;,hinput);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          6 :   if( hinput==&quot;as in input action&quot; ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :     if( !smapbase ) error(&quot;high dimensional switching function has not been set - use HIGH_DIM_FUNCTION&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :     reuse_hd=true;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :     log.printf(&quot;  reusing high dimensional filter function defined in previous sketch-map action\n&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   } else {</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          5 :     reuse_hd=false;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          5 :     highdf.set(hinput,errors);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          5 :     if(errors.length()&gt;0) error(errors);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         10 :     log.printf(&quot;  filter function for dissimilarities in high dimensional space has cutoff %s \n&quot;,highdf.description().c_str() );</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         12 :   parse(&quot;LOW_DIM_FUNCTION&quot;,linput);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          6 :   if( linput==&quot;as in input action&quot; ) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          1 :     if( !smapbase ) error(&quot;low dimensional switching function has not been set - use LOW_DIM_FUNCTION&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          1 :     reuse_ld=true;</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :     log.printf(&quot;  reusing low dimensional filter function defined in previous sketch-map action\n&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   } else {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          5 :     reuse_ld=false;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          5 :     lowdf.set(linput,errors);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          5 :     if(errors.length()&gt;0) error(errors);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         10 :     log.printf(&quot;  filter function for distances in low dimensionality space has cutoff %s \n&quot;,lowdf.description().c_str() );</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Read the mixing parameter</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          6 :   parse(&quot;MIXPARAM&quot;,mixparam);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          6 :   if( mixparam&lt;0 || mixparam&gt;1 ) error(&quot;mixing parameter must be between 0 and 1&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          6 :   log.printf(&quot;  mixing %f of pure distances with %f of filtered distances \n&quot;,mixparam,1.-mixparam);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          7 : void SketchMapBase::calculateProjections( const Matrix&lt;double&gt;&amp; targets, Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          7 :   if( dtargets.size()!=targets.nrows() ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :     // These hold data so that we can do stress calculations</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          6 :     dtargets.resize( targets.nrows() ); ftargets.resize( targets.nrows() ); pweights.resize( targets.nrows() );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     // Matrices for storing input data</a>
+<a name="81"><span class="lineNum">      81 </span>            :     transformed.resize( targets.nrows(), targets.ncols() );</a>
+<a name="82"><span class="lineNum">      82 </span>            :     distances.resize( targets.nrows(), targets.ncols() );</a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   // Stores the weights in an array for faster access, as well as the normalization</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          7 :   normw=0;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1141 :   for(unsigned i=0; i&lt;targets.nrows() ; ++i) { pweights[i] = getWeight(i); normw+=pweights[i]; }</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          7 :   normw*=normw;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Transform the high dimensional distances</a>
+<a name="91"><span class="lineNum">      91 </span>            :   double df; distances=0.; transformed=0.;</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1134 :   for(unsigned i=1; i&lt;distances.ncols(); ++i) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     172838 :     for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     171711 :       distances(i,j)=distances(j,i)=std::sqrt( targets(i,j) );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     171711 :       transformed(i,j)=transformed(j,i)=transformHighDimensionalDistance( distances(i,j), df );</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :     }</a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span>            :   // And minimse</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          7 :   minimise( projections );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          7 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      41344 : double SketchMapBase::calculateStress( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; d ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   // Zero derivative and stress accumulators</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">     124032 :   for(unsigned i=0; i&lt;p.size(); ++i) d[i]=0.0;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      41344 :   double stress=0; std::vector&lt;double&gt; dtmp( p.size() );</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   // Now accumulate total stress on system</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    6687344 :   for(unsigned i=0; i&lt;ftargets.size(); ++i) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">    6646000 :     if( dtargets[i]&lt;epsilon ) continue ;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :     // Calculate distance in low dimensional space</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">    6615785 :     double dd=0;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">   19847355 :     for(unsigned j=0; j&lt;p.size(); ++j) { dtmp[j]=p[j]-projections(i,j); dd+=dtmp[j]*dtmp[j]; }</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">    6615785 :     dd = std::sqrt(dd);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :     // Now do transformations and calculate differences</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">    6615785 :     double df, fd = transformLowDimensionalDistance( dd, df );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">    6615785 :     double ddiff = dd - dtargets[i];</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">    6615785 :     double fdiff = fd - ftargets[i];</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :     // Calculate derivatives</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    6615785 :     double pref = 2.*getWeight(i) / dd ;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">   19847355 :     for(unsigned j=0; j&lt;p.size(); ++j) d[j] += pref*( (1-mixparam)*fdiff*df + mixparam*ddiff )*dtmp[j];</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :     // Accumulate the total stress</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">    6615785 :     stress += getWeight(i)*( (1-mixparam)*fdiff*fdiff + mixparam*ddiff*ddiff );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      41344 :   return stress;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       1913 : double SketchMapBase::calculateFullStress( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; d ) {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Zero derivative and stress accumulators</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     393213 :   for(unsigned i=0; i&lt;p.size(); ++i) d[i]=0.0;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       1913 :   double stress=0; std::vector&lt;double&gt; dtmp( nlow );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">     195650 :   for(unsigned i=1; i&lt;distances.nrows(); ++i) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     193737 :     double iweight = pweights[i];</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">   14802162 :     for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">   14608425 :       double jweight =  pweights[j];</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :       // Calculate distance in low dimensional space</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">   14608425 :       double dd=0;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">   43825275 :       for(unsigned k=0; k&lt;nlow; ++k) { dtmp[k]=p[nlow*i+k] - p[nlow*j+k]; dd+=dtmp[k]*dtmp[k]; }</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">   14608425 :       dd = std::sqrt(dd);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :       // Now do transformations and calculate differences</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">   14608425 :       double df, fd = transformLowDimensionalDistance( dd, df );</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">   14608425 :       double ddiff = dd - distances(i,j);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">   14608425 :       double fdiff = fd - transformed(i,j);;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :       // Calculate derivatives</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">   14608425 :       double pref = 2.*iweight*jweight*( (1-mixparam)*fdiff*df + mixparam*ddiff ) / dd;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">   43825275 :       for(unsigned k=0; k&lt;nlow; ++k) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">   29216850 :         double dterm=pref*dtmp[k]; d[nlow*i+k]+=dterm; d[nlow*j+k]-=dterm;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :       // Accumulate the total stress</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">   14608425 :       stress += iweight*jweight*( (1-mixparam)*fdiff*fdiff + mixparam*ddiff*ddiff );</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     }</a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">     393213 :   stress /= normw; for (unsigned k=0; k &lt; d.size(); ++k) d[k] /= normw;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1913 :   return stress;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapBase.h.func-sort-c.html b/coverage/dimred/SketchMapBase.h.func-sort-c.html
new file mode 100644
index 0000000000..b639d94241
--- /dev/null
+++ b/coverage/dimred/SketchMapBase.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapBase.h<span style="font-size: 80%;"> (<a href="SketchMapBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMapBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.h.gcov.html#85">_ZN4PLMD6dimred13SketchMapBase17setTargetDistanceERKjRKd</a></td>
+              <td class="coverFnHi">145000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.h.gcov.html#79">_ZNK4PLMD6dimred13SketchMapBase32transformHighDimensionalDistanceERKdRd</a></td>
+              <td class="coverFnHi">341661</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.h.gcov.html#73">_ZNK4PLMD6dimred13SketchMapBase31transformLowDimensionalDistanceERKdRd</a></td>
+              <td class="coverFnHi">26384110</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapBase.h.func.html b/coverage/dimred/SketchMapBase.h.func.html
new file mode 100644
index 0000000000..2581eb9e66
--- /dev/null
+++ b/coverage/dimred/SketchMapBase.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapBase.h<span style="font-size: 80%;"> (<a href="SketchMapBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMapBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.h.gcov.html#85">_ZN4PLMD6dimred13SketchMapBase17setTargetDistanceERKjRKd</a></td>
+              <td class="coverFnHi">145000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.h.gcov.html#73">_ZNK4PLMD6dimred13SketchMapBase31transformLowDimensionalDistanceERKdRd</a></td>
+              <td class="coverFnHi">26384110</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapBase.h.gcov.html#79">_ZNK4PLMD6dimred13SketchMapBase32transformHighDimensionalDistanceERKdRd</a></td>
+              <td class="coverFnHi">341661</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapBase.h.gcov.html b/coverage/dimred/SketchMapBase.h.gcov.html
new file mode 100644
index 0000000000..df84489710
--- /dev/null
+++ b/coverage/dimred/SketchMapBase.h.gcov.html
@@ -0,0 +1,169 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapBase.h<span style="font-size: 80%;"> (source / <a href="SketchMapBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_dimred_SketchMapBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_dimred_SketchMapBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;DimensionalityReductionBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace dimred {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class SketchMapBase : public DimensionalityReductionBase {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// To save us retyping switching functions many times the code will reuse the</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// ones from previous sketch-map objects</a>
+<a name="35"><span class="lineNum">      35 </span>            :   bool reuse_hd, reuse_ld;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Was previous action in chain a sketch-map action</a>
+<a name="37"><span class="lineNum">      37 </span>            :   SketchMapBase* smapbase;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Switching functions for low and high dimensional space</a>
+<a name="39"><span class="lineNum">      39 </span>            :   SwitchingFunction lowdf, highdf;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// This is used within calculate stress to hold the target distances and the</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// target values for the high dimensional switching function</a>
+<a name="42"><span class="lineNum">      42 </span>            :   std::vector&lt;double&gt; dtargets, ftargets, pweights;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Stress normalization (sum_ij w_i w_j)</a>
+<a name="44"><span class="lineNum">      44 </span>            :   double normw;</a>
+<a name="45"><span class="lineNum">      45 </span>            : protected:</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// This holds the target distances and target transformed distances</a>
+<a name="47"><span class="lineNum">      47 </span>            :   Matrix&lt;double&gt; distances, transformed;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// The fraction of pure distances to mix in when optimising</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double mixparam;</a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="52"><span class="lineNum">      52 </span>            :   explicit SketchMapBase( const ActionOptions&amp; );</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// This starts the process of calculating the projections</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void calculateProjections( const Matrix&lt;double&gt;&amp;, Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// This finishes the process of calculating the prjections</a>
+<a name="56"><span class="lineNum">      56 </span>            :   virtual void minimise( Matrix&lt;double&gt;&amp; )=0;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Apply the low dimensional switching function to the value val</a>
+<a name="58"><span class="lineNum">      58 </span>            :   double transformLowDimensionalDistance( const double&amp; val, double&amp; df ) const ;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Apply the high dimensional switching function to the value val</a>
+<a name="60"><span class="lineNum">      60 </span>            :   double transformHighDimensionalDistance( const double&amp; val, double&amp; df ) const ;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Set the target distance and from it calculate the target value for the switching function</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// This target vector is used when we use calculateStress when finding the projections of individual points.</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// For example this function is used in PLMD::dimred::ProjectOutOfSample</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void setTargetDistance( const unsigned&amp; idata, const double&amp; dist ) override;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Calculate the pointwise stress on one point when it is located at p.</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// This function makes use of the distance data in dtargets and ftargets</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// It is used in PLMD::dimred::ProjectOutOfSample and in pointwise optimisation</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double calculateStress( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; d ) override;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Calculate the total stress when the projections are placed at point p.  Notice</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// this is a vectorized version of the matrix of projections</a>
+<a name="71"><span class="lineNum">      71 </span>            :   double calculateFullStress( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; d );</a>
+<a name="72"><span class="lineNum">      72 </span>            : };</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : inline</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">   26384110 : double SketchMapBase::transformLowDimensionalDistance( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">   26384110 :   if( reuse_ld ) return smapbase-&gt;transformLowDimensionalDistance( val, df );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">   21473710 :   double ans=1.0 - lowdf.calculate( val, df ); df*=-val; return ans;</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : inline</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     341661 : double SketchMapBase::transformHighDimensionalDistance( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     341661 :   if( reuse_hd ) return smapbase-&gt;transformHighDimensionalDistance( val, df );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     316711 :   double ans=1.0 - highdf.calculate( val, df ); df*=-val; return ans;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : inline</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     145000 : void SketchMapBase::setTargetDistance( const unsigned&amp; idata, const double&amp; dist ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     145000 :   double df; dtargets[idata]=dist; ftargets[idata]=transformHighDimensionalDistance( dist, df );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     145000 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapConjGrad.cpp.func-sort-c.html b/coverage/dimred/SketchMapConjGrad.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b4623b8527
--- /dev/null
+++ b/coverage/dimred/SketchMapConjGrad.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapConjGrad.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapConjGrad.cpp<span style="font-size: 80%;"> (<a href="SketchMapConjGrad.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMapConjGrad.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#52">_ZN4PLMD6dimred17SketchMapConjGradC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#45">_ZN4PLMD6dimred12_GLOBAL__N_129SketchMapConjGradRegisterMe476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#52">_ZN4PLMD6dimred17SketchMapConjGradC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#60">_ZN4PLMD6dimred17SketchMapConjGrad8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#47">_ZN4PLMD6dimred17SketchMapConjGrad16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#45">_ZN4PLMD6dimred12_GLOBAL__N_129SketchMapConjGradRegisterMe47C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#45">_ZN4PLMD6dimred12_GLOBAL__N_129SketchMapConjGradRegisterMe47D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapConjGrad.cpp.func.html b/coverage/dimred/SketchMapConjGrad.cpp.func.html
new file mode 100644
index 0000000000..a1c0d403eb
--- /dev/null
+++ b/coverage/dimred/SketchMapConjGrad.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapConjGrad.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapConjGrad.cpp<span style="font-size: 80%;"> (<a href="SketchMapConjGrad.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMapConjGrad.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#45">_ZN4PLMD6dimred12_GLOBAL__N_129SketchMapConjGradRegisterMe476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#45">_ZN4PLMD6dimred12_GLOBAL__N_129SketchMapConjGradRegisterMe47C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#45">_ZN4PLMD6dimred12_GLOBAL__N_129SketchMapConjGradRegisterMe47D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#47">_ZN4PLMD6dimred17SketchMapConjGrad16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#60">_ZN4PLMD6dimred17SketchMapConjGrad8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#52">_ZN4PLMD6dimred17SketchMapConjGradC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapConjGrad.cpp.gcov.html#52">_ZN4PLMD6dimred17SketchMapConjGradC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapConjGrad.cpp.gcov.html b/coverage/dimred/SketchMapConjGrad.cpp.gcov.html
new file mode 100644
index 0000000000..72bf306097
--- /dev/null
+++ b/coverage/dimred/SketchMapConjGrad.cpp.gcov.html
@@ -0,0 +1,146 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapConjGrad.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapConjGrad.cpp<span style="font-size: 80%;"> (source / <a href="SketchMapConjGrad.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;SketchMapBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/ConjugateGradient.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC DIMRED SKETCHMAP_CONJGRAD</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Optimize the sketch-map stress function using conjugate gradients.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \par Examples</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : //+ENDPLUMEDOC</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace dimred {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class SketchMapConjGrad : public SketchMapBase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   double cgtol;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit SketchMapConjGrad( const ActionOptions&amp; ao );</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void minimise( Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(SketchMapConjGrad,&quot;SKETCHMAP_CONJGRAD&quot;)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          5 : void SketchMapConjGrad::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          5 :   SketchMapBase::registerKeywords( keys );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;CGTOL&quot;,&quot;1E-6&quot;,&quot;the tolerance for the conjugate gradient minimization&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          5 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 : SketchMapConjGrad::SketchMapConjGrad( const ActionOptions&amp; ao ):</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   Action(ao),</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          3 :   SketchMapBase(ao)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 :   parse(&quot;CGTOL&quot;,cgtol);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          3 :   log.printf(&quot;  tolerance for conjugate gradient algorithm equals %f \n&quot;,cgtol);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          3 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          4 : void SketchMapConjGrad::minimise( Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   ConjugateGradient&lt;SketchMapConjGrad&gt; mycgminimise( this );</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; myproj( projections.getVector() );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          4 :   mycgminimise.minimise( cgtol, myproj, &amp;SketchMapConjGrad::calculateFullStress );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          4 :   projections.setFromVector( myproj );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          4 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapPointwise.cpp.func-sort-c.html b/coverage/dimred/SketchMapPointwise.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0cdfd33feb
--- /dev/null
+++ b/coverage/dimred/SketchMapPointwise.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapPointwise.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapPointwise.cpp<span style="font-size: 80%;"> (<a href="SketchMapPointwise.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMapPointwise.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#59">_ZN4PLMD6dimred18SketchMapPointwiseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#48">_ZN4PLMD6dimred12_GLOBAL__N_130SketchMapPointwiseRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#84">_ZN4PLMD6dimred18SketchMapPointwise8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#59">_ZN4PLMD6dimred18SketchMapPointwiseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#50">_ZN4PLMD6dimred18SketchMapPointwise16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#48">_ZN4PLMD6dimred12_GLOBAL__N_130SketchMapPointwiseRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#48">_ZN4PLMD6dimred12_GLOBAL__N_130SketchMapPointwiseRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapPointwise.cpp.func.html b/coverage/dimred/SketchMapPointwise.cpp.func.html
new file mode 100644
index 0000000000..682397f67a
--- /dev/null
+++ b/coverage/dimred/SketchMapPointwise.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapPointwise.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapPointwise.cpp<span style="font-size: 80%;"> (<a href="SketchMapPointwise.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMapPointwise.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#48">_ZN4PLMD6dimred12_GLOBAL__N_130SketchMapPointwiseRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#48">_ZN4PLMD6dimred12_GLOBAL__N_130SketchMapPointwiseRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#48">_ZN4PLMD6dimred12_GLOBAL__N_130SketchMapPointwiseRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#50">_ZN4PLMD6dimred18SketchMapPointwise16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#84">_ZN4PLMD6dimred18SketchMapPointwise8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#59">_ZN4PLMD6dimred18SketchMapPointwiseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapPointwise.cpp.gcov.html#59">_ZN4PLMD6dimred18SketchMapPointwiseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapPointwise.cpp.gcov.html b/coverage/dimred/SketchMapPointwise.cpp.gcov.html
new file mode 100644
index 0000000000..22ef9e74c0
--- /dev/null
+++ b/coverage/dimred/SketchMapPointwise.cpp.gcov.html
@@ -0,0 +1,202 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapPointwise.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapPointwise.cpp<span style="font-size: 80%;"> (source / <a href="SketchMapPointwise.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;SketchMapBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/ConjugateGradient.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;gridtools/GridSearch.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC DIMRED SKETCHMAP_POINTWISE</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Optimize the sketch-map stress function using a pointwise global optimization algorithm.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : \par Examples</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : */</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+ENDPLUMEDOC</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace dimred {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class SketchMapPointwise : public SketchMapBase {</a>
+<a name="40"><span class="lineNum">      40 </span>            : private:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   unsigned ncycles;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double cgtol, gbuf;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;unsigned&gt; npoints, nfgrid;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   explicit SketchMapPointwise( const ActionOptions&amp; ao );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void minimise( Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(SketchMapPointwise,&quot;SKETCHMAP_POINTWISE&quot;)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          3 : void SketchMapPointwise::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          3 :   SketchMapBase::registerKeywords( keys );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;NCYCLES&quot;,&quot;5&quot;,&quot;the number of cycles of global optimization to attempt&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;CGTOL&quot;,&quot;1E-6&quot;,&quot;the tolerance for the conjugate gradient minimization&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;BUFFER&quot;,&quot;1.1&quot;,&quot;grid extent for search is (max projection - minimum projection) multiplied by this value&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;CGRID_SIZE&quot;,&quot;10&quot;,&quot;number of points to use in each grid direction&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FGRID_SIZE&quot;,&quot;0&quot;,&quot;interpolate the grid onto this number of points -- only works in 2D&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          3 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          1 : SketchMapPointwise::SketchMapPointwise( const ActionOptions&amp; ao ):</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   Action(ao),</a>
+<a name="63"><span class="lineNum">      63 </span>            :   SketchMapBase(ao),</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          2 :   npoints(nlow),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          1 :   nfgrid(nlow)</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          3 :   parseVector(&quot;CGRID_SIZE&quot;,npoints); parse(&quot;BUFFER&quot;,gbuf);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          1 :   if( npoints.size()!=nlow ) error(&quot;vector giving number of grid point in each direction has wrong size&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          2 :   parse(&quot;NCYCLES&quot;,ncycles); parse(&quot;CGTOL&quot;,cgtol);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 :   parseVector(&quot;FGRID_SIZE&quot;,nfgrid);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          1 :   if( nfgrid[0]!=0 &amp;&amp; nlow!=2 ) error(&quot;interpolation only works in two dimensions&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          1 :   log.printf(&quot;  doing %u cycles of global optimization sweeps\n&quot;,ncycles);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          1 :   log.printf(&quot;  using coarse grid of points that is %u&quot;,npoints[0]);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          1 :   log.printf(&quot; and that is %f larger than the difference between the position of the minimum and maximum projection \n&quot;,gbuf);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          2 :   for(unsigned j=1; j&lt;npoints.size(); ++j) log.printf(&quot; by %u&quot;,npoints[j]);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :   if( nfgrid[0]&gt;0 ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          1 :     log.printf(&quot;  interpolating stress onto grid of points that is %u&quot;,nfgrid[0]);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          2 :     for(unsigned j=1; j&lt;nfgrid.size(); ++j) log.printf(&quot; by %u&quot;,nfgrid[j]);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          1 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          1 :   log.printf(&quot;  tolerance for conjugate gradient algorithm equals %f \n&quot;,cgtol);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          1 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 : void SketchMapPointwise::minimise( Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; gmin( nlow ), gmax( nlow ), mypoint( nlow );</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   // Find the extent of the grid</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          3 :   for(unsigned j=0; j&lt;nlow; ++j) gmin[j]=gmax[j]=projections(0,j);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        100 :   for(unsigned i=1; i&lt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        297 :     for(unsigned j=0; j&lt;nlow; ++j) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        198 :       if( projections(i,j) &lt; gmin[j] ) gmin[j] = projections(i,j);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        198 :       if( projections(i,j) &gt; gmax[j] ) gmax[j] = projections(i,j);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          3 :   for(unsigned j=0; j&lt;nlow; ++j) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :     double gbuffer = 0.5*gbuf*( gmax[j]-gmin[j] ) - 0.5*( gmax[j]- gmin[j] );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :     gmin[j]-=gbuffer; gmax[j]+=gbuffer;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   // And do the search</a>
+<a name="103"><span class="lineNum">     103 </span>            :   ConjugateGradient&lt;SketchMapPointwise&gt; mycgminimise( this );</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          1 :   gridtools::GridSearch&lt;SketchMapPointwise&gt; mygridsearch( gmin, gmax, npoints, nfgrid, this );</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Run multiple loops over all projections</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;ncycles; ++i) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        202 :     for(unsigned j=0; j&lt;getNumberOfDataPoints(); ++j) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :       // Setup target distances and target functions for calculate stress</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      20200 :       for(unsigned k=0; k&lt;getNumberOfDataPoints(); ++k) setTargetDistance( k, distances(j,k)  );</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :       // Find current projection of jth point</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        600 :       for(unsigned k=0; k&lt;mypoint.size(); ++k) mypoint[k]=projections(j,k);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :       // Minimise using grid search</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        200 :       bool moved=mygridsearch.minimise( mypoint, &amp;SketchMapPointwise::calculateStress );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        200 :       if( moved ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :         // Reassign the new projection</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         66 :         for(unsigned k=0; k&lt;mypoint.size(); ++k) projections(j,k)=mypoint[k];</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :         // Minimise output using conjugate gradient</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         22 :         mycgminimise.minimise( cgtol, projections.getVector(), &amp;SketchMapPointwise::calculateFullStress );</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :       }</a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapRead.cpp.func-sort-c.html b/coverage/dimred/SketchMapRead.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a11fe63dc3
--- /dev/null
+++ b/coverage/dimred/SketchMapRead.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapRead.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapRead.cpp<span style="font-size: 80%;"> (<a href="SketchMapRead.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMapRead.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#168">_ZN4PLMD6dimred13SketchMapRead15getArgumentListEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#77">_ZN4PLMD6dimred13SketchMapReadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#163">_ZNK4PLMD6dimred13SketchMapRead23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#64">_ZN4PLMD6dimred12_GLOBAL__N_125SketchMapReadRegisterMe666createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#147">_ZN4PLMD6dimred13SketchMapRead8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#77">_ZN4PLMD6dimred13SketchMapReadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#99">_ZZN4PLMD6dimred13SketchMapReadC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#66">_ZN4PLMD6dimred13SketchMapRead16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#189">_ZN4PLMD6dimred13SketchMapRead9getWeightERKj</a></td>
+              <td class="coverFnHi">168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#159">_ZNK4PLMD6dimred13SketchMapRead21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#175">_ZN4PLMD6dimred13SketchMapRead16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">3486</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#64">_ZN4PLMD6dimred12_GLOBAL__N_125SketchMapReadRegisterMe66C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#64">_ZN4PLMD6dimred12_GLOBAL__N_125SketchMapReadRegisterMe66D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#155">_ZN4PLMD6dimred13SketchMapRead13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">7056</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapRead.cpp.func.html b/coverage/dimred/SketchMapRead.cpp.func.html
new file mode 100644
index 0000000000..13a295e3a5
--- /dev/null
+++ b/coverage/dimred/SketchMapRead.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapRead.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapRead.cpp<span style="font-size: 80%;"> (<a href="SketchMapRead.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMapRead.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#64">_ZN4PLMD6dimred12_GLOBAL__N_125SketchMapReadRegisterMe666createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#64">_ZN4PLMD6dimred12_GLOBAL__N_125SketchMapReadRegisterMe66C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#64">_ZN4PLMD6dimred12_GLOBAL__N_125SketchMapReadRegisterMe66D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#155">_ZN4PLMD6dimred13SketchMapRead13getStoredDataERKjRKb</a></td>
+              <td class="coverFnHi">7056</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#168">_ZN4PLMD6dimred13SketchMapRead15getArgumentListEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#175">_ZN4PLMD6dimred13SketchMapRead16getDissimilarityERKjS3_</a></td>
+              <td class="coverFnHi">3486</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#66">_ZN4PLMD6dimred13SketchMapRead16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#159">_ZNK4PLMD6dimred13SketchMapRead21getNumberOfDataPointsEv</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#163">_ZNK4PLMD6dimred13SketchMapRead23getDataPointIndexInBaseERKj</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="SketchMapRead.cpp.gcov.html#99">_ZZN4PLMD6dimred13SketchMapReadC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">1</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapRead.cpp.gcov.html b/coverage/dimred/SketchMapRead.cpp.gcov.html
new file mode 100644
index 0000000000..7a945f4d7f
--- /dev/null
+++ b/coverage/dimred/SketchMapRead.cpp.gcov.html
@@ -0,0 +1,273 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapRead.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapRead.cpp<span style="font-size: 80%;"> (source / <a href="SketchMapRead.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;SketchMapBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC DIMRED SKETCHMAP_READ</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Read in a sketch-map projection from an input file</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \par Examples</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : */</a>
+<a name="37"><span class="lineNum">      37 </span>            : //+ENDPLUMEDOC</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace dimred {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class SketchMapRead : public SketchMapBase {</a>
+<a name="43"><span class="lineNum">      43 </span>            : private:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::string mtype;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   PDB mypdb;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::vector&lt;Value*&gt; all_values;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;double&gt; weights;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// The list of properties in the property map</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::map&lt;std::string,std::vector&lt;double&gt; &gt; property;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// The data collection objects we have</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;analysis::DataCollectionObject&gt; data;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// The frames that we are using to calculate distances</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt; &gt; myframes;</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit SketchMapRead( const ActionOptions&amp; ao );</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void minimise( Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   analysis::DataCollectionObject&amp; getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) override;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   unsigned getNumberOfDataPoints() const override;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;Value*&gt; getArgumentList() override;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   unsigned getDataPointIndexInBase( const unsigned&amp; idata ) const override;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double getDissimilarity( const unsigned&amp; i, const unsigned&amp; j ) override;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double getWeight( const unsigned&amp; idata ) override;</a>
+<a name="64"><span class="lineNum">      64 </span>            : };</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(SketchMapRead,&quot;SKETCHMAP_READ&quot;)</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          3 : void SketchMapRead::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          3 :   SketchMapBase::registerKeywords( keys ); keys.remove(&quot;USE_OUTPUT_DATA_FROM&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;OPTIMAL-FAST&quot;,&quot;the manner in which distances are calculated. More information on the different &quot;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :            &quot;metrics that are available in PLUMED can be found in the section of the manual on &quot;</a>
+<a name="72"><span class="lineNum">      72 </span>            :            &quot;\\ref dists&quot;);</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;the file containing the sketch-map projection&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;PROPERTY&quot;,&quot;the property to be used in the index. This should be in the REMARK of the reference&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          6 :   keys.addFlag(&quot;DISABLE_CHECKS&quot;,false,&quot;disable checks on reference input structures.&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          3 :   useCustomisableComponents(keys);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          3 : }</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          1 : SketchMapRead::SketchMapRead( const ActionOptions&amp; ao ):</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   Action(ao),</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          1 :   SketchMapBase(ao)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : {</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          2 :   std::vector&lt;std::string&gt; propnames; parseVector(&quot;PROPERTY&quot;,propnames);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          1 :   if(propnames.size()==0) error(&quot;no properties were specified&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          1 :   nlow=propnames.size();</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;nlow; ++i) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          4 :     std::size_t dot=propnames[i].find_first_of( getLabel() + &quot;.&quot; ); std::string substr=propnames[i].c_str();</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :     if( dot!=std::string::npos ) { substr.erase(dot,getLabel().length()+1); }</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 :     log.printf(&quot;,%s&quot;, propnames[i].c_str() ); addComponent( substr ); componentIsNotPeriodic( substr );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          4 :     property.insert( std::pair&lt;std::string,std::vector&lt;double&gt; &gt;( propnames[i], std::vector&lt;double&gt;() ) );</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          1 :   log.printf(&quot;  mapped properties are %s &quot;,propnames[0].c_str() );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   for(unsigned i=1; i&lt;nlow; ++i) log.printf(&quot;,%s&quot;, propnames[i].c_str() );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          3 :   parse(&quot;TYPE&quot;,mtype); bool skipchecks; parseFlag(&quot;DISABLE_CHECKS&quot;,skipchecks);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   std::string ifilename; parse(&quot;REFERENCE&quot;,ifilename);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          1 :   FILE* fp=this-&gt;fopen(ifilename.c_str(),&quot;r&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          1 :   if(!fp) error(&quot;could not open reference file &quot; + ifilename );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : // call fclose when fp goes out of scope</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :   auto deleter=[this](FILE* f) { this-&gt;fclose(f); };</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Read in the embedding</a>
+<a name="106"><span class="lineNum">     106 </span>            :   bool do_read=true; double val, ww, wnorm=0, prop; unsigned nfram=0;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         85 :   while (do_read) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         85 :     PDB inpdb;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     // Read the pdb file</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        170 :     do_read=inpdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     // Break if we are done</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         85 :     if( !do_read ) break ;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     // Check for required properties</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        252 :     for(std::map&lt;std::string,std::vector&lt;double&gt; &gt;::iterator it=property.begin(); it!=property.end(); ++it) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        168 :       if( !inpdb.getArgumentValue( it-&gt;first, prop ) ) error(&quot;pdb input does not have contain property named &quot; + it-&gt;first );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        168 :       it-&gt;second.push_back(prop);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            :     // And read the frame ( create a measure )</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         84 :     myframes.emplace_back( metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, inpdb ) );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        168 :     if( !inpdb.getArgumentValue( &quot;WEIGHT&quot;, ww ) ) error(&quot;could not find weights in input pdb&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         84 :     weights.push_back( ww ); wnorm += ww; nfram++;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     // And create a data collection object</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         84 :     analysis::DataCollectionObject new_data; new_data.setAtomNumbersAndArgumentNames( getLabel(), inpdb.getAtomNumbers(), inpdb.getArgumentNames() );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         84 :     new_data.setAtomPositions( inpdb.getPositions() );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        504 :     for(unsigned i=0; i&lt;inpdb.getArgumentNames().size(); ++i) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        420 :       std::string aname = inpdb.getArgumentNames()[i];</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        420 :       if( !inpdb.getArgumentValue( aname, val ) ) error(&quot;failed to find argument named &quot; + aname);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        420 :       new_data.setArgument( aname, val );</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :     }</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         84 :     data.push_back( new_data );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         85 :   }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // Finish the setup of the object by getting the arguments and atoms that are required</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::vector&lt;AtomNumber&gt; atoms; std::vector&lt;std::string&gt; args;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         85 :   for(unsigned i=0; i&lt;myframes.size(); ++i) { weights[i] /= wnorm; myframes[i]-&gt;getAtomRequests( atoms, skipchecks ); myframes[i]-&gt;getArgumentRequests( args, skipchecks ); }</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   requestAtoms( atoms ); std::vector&lt;Value*&gt; req_args; std::vector&lt;std::string&gt; fargs;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;args.size(); ++i) {</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     bool found=false;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         12 :     for(std::map&lt;std::string,std::vector&lt;double&gt; &gt;::iterator it=property.begin(); it!=property.end(); ++it) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          9 :       if( args[i]==it-&gt;first ) { found=true; break; }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          5 :     if( !found ) { fargs.push_back( args[i] ); }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :   interpretArgumentList( fargs, req_args ); mypdb.setArgumentNames( fargs ); requestArguments( req_args );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :   if(nfram==0 ) error(&quot;no reference configurations were specified&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   log.printf(&quot; found %u configurations in file %s\n&quot;,nfram,ifilename.c_str() );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 : void SketchMapRead::minimise( Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   unsigned j=0;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :   for(std::map&lt;std::string,std::vector&lt;double&gt; &gt;::iterator it=property.begin(); it!=property.end(); ++it) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        170 :     for(unsigned i=0; i&lt;myframes.size(); ++i) projections(i,j) = it-&gt;second[i];</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :     j++;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          1 : }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       7056 : analysis::DataCollectionObject &amp; SketchMapRead::getStoredData( const unsigned&amp; idata, const bool&amp; calcdist ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       7056 :   return data[idata];</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        173 : unsigned SketchMapRead::getNumberOfDataPoints() const {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        173 :   return myframes.size();</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : unsigned SketchMapRead::getDataPointIndexInBase( const unsigned&amp; idata ) const {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   error(&quot;cannot use read in sketch-map to out of sample project data&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   return idata;</a>
+<a name="168"><span class="lineNum">     168 </span>            : }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 : std::vector&lt;Value*&gt; SketchMapRead::getArgumentList() {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   std::vector&lt;Value*&gt; arglist( ActionWithArguments::getArguments() );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;nlow; ++i) arglist.push_back( getPntrToComponent(i) );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   return arglist;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : // Highly unsatisfactory solution to problem GAT</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       3486 : double SketchMapRead::getDissimilarity( const unsigned&amp; i, const unsigned&amp; j ) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       3486 :   plumed_assert( i&lt;myframes.size() &amp;&amp; j&lt;myframes.size() );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       3486 :   if( i!=j ) {</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     double dd;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       3486 :     getStoredData( i, true ).transferDataToPDB( mypdb );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       3486 :     auto myref1=metricRegister().create&lt;ReferenceConfiguration&gt;(mtype, mypdb);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       3486 :     getStoredData( j, true ).transferDataToPDB( mypdb );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       3486 :     auto myref2=metricRegister().create&lt;ReferenceConfiguration&gt;(mtype, mypdb);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       3486 :     dd=distance( getPbc(), ActionWithArguments::getArguments(), myref1.get(), myref2.get(), true );</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     return dd;</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       3486 :   }</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   return 0.0;</a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        168 : double SketchMapRead::getWeight( const unsigned&amp; idata ) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        168 :   plumed_assert( idata&lt;weights.size() );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        168 :   return weights[idata];</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapSmacof.cpp.func-sort-c.html b/coverage/dimred/SketchMapSmacof.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2e51cc8e53
--- /dev/null
+++ b/coverage/dimred/SketchMapSmacof.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapSmacof.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapSmacof.cpp<span style="font-size: 80%;"> (<a href="SketchMapSmacof.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SketchMapSmacof.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#58">_ZN4PLMD6dimred15SketchMapSmacofC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#47">_ZN4PLMD6dimred12_GLOBAL__N_127SketchMapSmacofRegisterMe496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#67">_ZN4PLMD6dimred15SketchMapSmacof8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#58">_ZN4PLMD6dimred15SketchMapSmacofC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#82">_ZN4PLMD6dimred15SketchMapSmacof18recalculateWeightsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#49">_ZN4PLMD6dimred15SketchMapSmacof16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#47">_ZN4PLMD6dimred12_GLOBAL__N_127SketchMapSmacofRegisterMe49C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#47">_ZN4PLMD6dimred12_GLOBAL__N_127SketchMapSmacofRegisterMe49D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapSmacof.cpp.func.html b/coverage/dimred/SketchMapSmacof.cpp.func.html
new file mode 100644
index 0000000000..f450a4ffec
--- /dev/null
+++ b/coverage/dimred/SketchMapSmacof.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapSmacof.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapSmacof.cpp<span style="font-size: 80%;"> (<a href="SketchMapSmacof.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SketchMapSmacof.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#47">_ZN4PLMD6dimred12_GLOBAL__N_127SketchMapSmacofRegisterMe496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#47">_ZN4PLMD6dimred12_GLOBAL__N_127SketchMapSmacofRegisterMe49C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#47">_ZN4PLMD6dimred12_GLOBAL__N_127SketchMapSmacofRegisterMe49D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#49">_ZN4PLMD6dimred15SketchMapSmacof16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#82">_ZN4PLMD6dimred15SketchMapSmacof18recalculateWeightsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#67">_ZN4PLMD6dimred15SketchMapSmacof8minimiseERNS_6MatrixIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#58">_ZN4PLMD6dimred15SketchMapSmacofC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SketchMapSmacof.cpp.gcov.html#58">_ZN4PLMD6dimred15SketchMapSmacofC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SketchMapSmacof.cpp.gcov.html b/coverage/dimred/SketchMapSmacof.cpp.gcov.html
new file mode 100644
index 0000000000..429b16c08b
--- /dev/null
+++ b/coverage/dimred/SketchMapSmacof.cpp.gcov.html
@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SketchMapSmacof.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SketchMapSmacof.cpp<span style="font-size: 80%;"> (source / <a href="SketchMapSmacof.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;SketchMapBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;SMACOF.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC DIMRED SKETCHMAP_SMACOF</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Optimize the sketch-map stress function using the SMACOF algorithm.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \par Examples</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : //+ENDPLUMEDOC</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace dimred {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class SketchMapSmacof : public SketchMapBase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   unsigned max_smap, maxiter;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double smap_tol, iter_tol, regulariser;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double recalculateWeights( const Matrix&lt;double&gt;&amp; projections, Matrix&lt;double&gt;&amp; weights );</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit SketchMapSmacof( const ActionOptions&amp; ao );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void minimise( Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(SketchMapSmacof,&quot;SKETCHMAP_SMACOF&quot;)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          3 : void SketchMapSmacof::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          3 :   SketchMapBase::registerKeywords( keys );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;SMACOF_TOL&quot;,&quot;1E-4&quot;,&quot;the tolerance for each SMACOF cycle&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;SMACOF_MAXCYC&quot;,&quot;1000&quot;,&quot;maximum number of optimization cycles for SMACOF algorithm&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;SMAP_TOL&quot;,&quot;1E-4&quot;,&quot;the tolerance for sketch-map&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;SMAP_MAXCYC&quot;,&quot;100&quot;,&quot;maximum number of optimization cycles for iterative sketch-map algorithm&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;REGULARISE_PARAM&quot;,&quot;0.001&quot;,&quot;this is used to ensure that we don't divide by zero when updating weights&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          1 : SketchMapSmacof::SketchMapSmacof( const ActionOptions&amp; ao ):</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   Action(ao),</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :   SketchMapBase(ao)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          1 :   parse(&quot;REGULARISE_PARAM&quot;,regulariser);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          2 :   parse(&quot;SMACOF_MAXCYC&quot;,max_smap); parse(&quot;SMAP_MAXCYC&quot;,maxiter);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          2 :   parse(&quot;SMACOF_TOL&quot;,smap_tol); parse(&quot;SMAP_TOL&quot;,iter_tol);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          1 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          1 : void SketchMapSmacof::minimise( Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   Matrix&lt;double&gt; weights( distances.nrows(), distances.ncols() ); weights=0.;</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 :   double filt = recalculateWeights( projections, weights );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          1 :   for(unsigned i=0; i&lt;maxiter; ++i) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          1 :     SMACOF::run( weights, distances, smap_tol, max_smap, projections );</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     // Recalculate weights matrix and sigma</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          1 :     double newsig = recalculateWeights( projections, weights );</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     // Test whether or not the algorithm has converged</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :     if( std::fabs( newsig - filt )&lt;iter_tol ) break;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :     // Make initial sigma into new sigma so that the value of new sigma is used every time so that the error can be reduced</a>
+<a name="80"><span class="lineNum">      80 </span>            :     filt=newsig;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 : double SketchMapSmacof::recalculateWeights( const Matrix&lt;double&gt;&amp; projections, Matrix&lt;double&gt;&amp; weights ) {</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   double filt=0, totalWeight=0.;; double dr;</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1000 :   for(unsigned i=1; i&lt;weights.nrows(); ++i) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     250498 :     for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     249500 :       double ninj=getWeight(i)*getWeight(j); totalWeight += ninj;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :       double tempd=0;</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     748500 :       for(unsigned k=0; k&lt;projections.ncols(); ++k) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">     499000 :         double tmp = projections(i,k) - projections(j,k);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     499000 :         tempd += tmp*tmp;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :       }</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     249500 :       double dij=std::sqrt(tempd);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     249500 :       double fij = transformLowDimensionalDistance( dij, dr );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     249500 :       double filter=transformed(i,j)-fij;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     249500 :       double diff=distances(i,j) - dij;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     249500 :       if( std::fabs(diff)&lt;regulariser ) weights(i,j)=weights(j,i)=0.0;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     249403 :       else weights(i,j)=weights(j,i) = ninj*( (1-mixparam)*( filter*dr )/diff + mixparam );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">     249500 :       filt += ninj*( (1-mixparam)*filter*filter + mixparam*diff*diff );</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :     }</a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   return filt / totalWeight;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SmacoffMDS.cpp.func-sort-c.html b/coverage/dimred/SmacoffMDS.cpp.func-sort-c.html
new file mode 100644
index 0000000000..aac692e16c
--- /dev/null
+++ b/coverage/dimred/SmacoffMDS.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SmacoffMDS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SmacoffMDS.cpp<span style="font-size: 80%;"> (<a href="SmacoffMDS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">35.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SmacoffMDS.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#46">_ZN4PLMD6dimred12_GLOBAL__N_121SmacofMDSRegisterMe486createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#65">_ZN4PLMD6dimred9SmacofMDS20calculateProjectionsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#55">_ZN4PLMD6dimred9SmacofMDSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#55">_ZN4PLMD6dimred9SmacofMDSC2ERKNS_13ActionOptionsE</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#48">_ZN4PLMD6dimred9SmacofMDS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#46">_ZN4PLMD6dimred12_GLOBAL__N_121SmacofMDSRegisterMe48C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#46">_ZN4PLMD6dimred12_GLOBAL__N_121SmacofMDSRegisterMe48D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SmacoffMDS.cpp.func.html b/coverage/dimred/SmacoffMDS.cpp.func.html
new file mode 100644
index 0000000000..3f9a49779c
--- /dev/null
+++ b/coverage/dimred/SmacoffMDS.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SmacoffMDS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SmacoffMDS.cpp<span style="font-size: 80%;"> (<a href="SmacoffMDS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">35.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SmacoffMDS.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#46">_ZN4PLMD6dimred12_GLOBAL__N_121SmacofMDSRegisterMe486createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#46">_ZN4PLMD6dimred12_GLOBAL__N_121SmacofMDSRegisterMe48C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#46">_ZN4PLMD6dimred12_GLOBAL__N_121SmacofMDSRegisterMe48D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#48">_ZN4PLMD6dimred9SmacofMDS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#65">_ZN4PLMD6dimred9SmacofMDS20calculateProjectionsERKNS_6MatrixIdEERS3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#55">_ZN4PLMD6dimred9SmacofMDSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SmacoffMDS.cpp.gcov.html#55">_ZN4PLMD6dimred9SmacofMDSC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/SmacoffMDS.cpp.gcov.html b/coverage/dimred/SmacoffMDS.cpp.gcov.html
new file mode 100644
index 0000000000..98556de437
--- /dev/null
+++ b/coverage/dimred/SmacoffMDS.cpp.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred/SmacoffMDS.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">dimred</a> - SmacoffMDS.cpp<span style="font-size: 80%;"> (source / <a href="SmacoffMDS.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">35.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DimensionalityReductionBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;SMACOF.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC DIMRED SMACOF_MDS</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Optimize the multidimensional scaling stress function using the SMACOF algorithm.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \par Examples</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : */</a>
+<a name="33"><span class="lineNum">      33 </span>            : //+ENDPLUMEDOC</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace dimred {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class SmacofMDS : public DimensionalityReductionBase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   unsigned maxloops;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double tol;</a>
+<a name="42"><span class="lineNum">      42 </span>            : public:</a>
+<a name="43"><span class="lineNum">      43 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="44"><span class="lineNum">      44 </span>            :   explicit SmacofMDS( const ActionOptions&amp; );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void calculateProjections( const Matrix&lt;double&gt;&amp;, Matrix&lt;double&gt;&amp; ) override;</a>
+<a name="46"><span class="lineNum">      46 </span>            : };</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(SmacofMDS,&quot;SMACOF_MDS&quot;)</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 : void SmacofMDS::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          2 :   DimensionalityReductionBase::registerKeywords( keys );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          2 :   keys.remove(&quot;NLOW_DIM&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;SMACOF_TOL&quot;,&quot;1E-4&quot;,&quot;tolerance for the SMACOF optimization algorithm&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;SMACOF_MAXCYC&quot;,&quot;1000&quot;,&quot;maximum number of optimization cycles for SMACOF algorithm&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          2 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 : SmacofMDS::SmacofMDS( const ActionOptions&amp; ao):</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   Action(ao),</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   DimensionalityReductionBase(ao)</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   if( !dimredbase ) error(&quot;SMACOF must be initialized using output from dimensionality reduction object&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   parse(&quot;SMACOF_TOL&quot;,tol); parse(&quot;SMACOF_MAXCYC&quot;,maxloops);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   log.printf(&quot;  running smacof to convergence at %f or for a maximum of %u steps \n&quot;,tol,maxloops);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 : void SmacofMDS::calculateProjections( const Matrix&lt;double&gt;&amp; targets, Matrix&lt;double&gt;&amp; projections ) {</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   // Take the square root of all the distances and the weights</a>
+<a name="69"><span class="lineNum">      69 </span>            :   Matrix&lt;double&gt; weights( targets.nrows(), targets.ncols() );</a>
+<a name="70"><span class="lineNum">      70 </span>            :   Matrix&lt;double&gt; distances( targets.nrows(), targets.ncols() );</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   for(unsigned i=1; i&lt;distances.ncols(); ++i) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :       distances(i,j)=distances(j,i)=std::sqrt( targets(i,j) );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :       weights(i,j)=weights(j,i)=getWeight(i)*getWeight(j);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     }</a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span>            :   // And run SMACOF</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   SMACOF::run( weights, targets, tol, maxloops, projections );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/index-sort-f.html b/coverage/dimred/index-sort-f.html
new file mode 100644
index 0000000000..739430b465
--- /dev/null
+++ b/coverage/dimred/index-sort-f.html
@@ -0,0 +1,243 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - dimred</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">556</td>
+            <td class="headerCovTableEntry">656</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntry">108</td>
+            <td class="headerCovTableEntryLo">73.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DimensionalityReductionBase.h.gcov.html">DimensionalityReductionBase.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 4</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCA.h.gcov.html">PCA.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SmacoffMDS.cpp.gcov.html">SmacoffMDS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=35 height=10 alt="35.0%"><img src="../snow.png" width=65 height=10 alt="35.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 20</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMap.cpp.gcov.html">SketchMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=31 height=10 alt="31.2%"><img src="../snow.png" width=69 height=10 alt="31.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.2&nbsp;%</td>
+      <td class="coverNumLo">15 / 48</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DimensionalityReductionBase.cpp.gcov.html">DimensionalityReductionBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="79.7%"><img src="../snow.png" width=20 height=10 alt="79.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.7&nbsp;%</td>
+      <td class="coverNumMed">47 / 59</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputPCAProjections.cpp.gcov.html">OutputPCAProjections.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">35 / 36</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ProjectNonLandmarkPoints.cpp.gcov.html">ProjectNonLandmarkPoints.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">39 / 43</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCA.cpp.gcov.html">PCA.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.8%"><img src="../snow.png" width=19 height=10 alt="80.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.8&nbsp;%</td>
+      <td class="coverNumMed">97 / 120</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapRead.cpp.gcov.html">SketchMapRead.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.7%"><img src="../snow.png" width=7 height=10 alt="92.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.7&nbsp;%</td>
+      <td class="coverNumHi">76 / 82</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapBase.cpp.gcov.html">SketchMapBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">79 / 79</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapPointwise.cpp.gcov.html">SketchMapPointwise.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapConjGrad.cpp.gcov.html">SketchMapConjGrad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClassicalMultiDimensionalScaling.cpp.gcov.html">ClassicalMultiDimensionalScaling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapSmacof.cpp.gcov.html">SketchMapSmacof.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMACOF.cpp.gcov.html">SMACOF.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapBase.h.gcov.html">SketchMapBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/index-sort-l.html b/coverage/dimred/index-sort-l.html
new file mode 100644
index 0000000000..4d153795ff
--- /dev/null
+++ b/coverage/dimred/index-sort-l.html
@@ -0,0 +1,243 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - dimred</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">556</td>
+            <td class="headerCovTableEntry">656</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntry">108</td>
+            <td class="headerCovTableEntryLo">73.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCA.h.gcov.html">PCA.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DimensionalityReductionBase.h.gcov.html">DimensionalityReductionBase.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 4</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMap.cpp.gcov.html">SketchMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=31 height=10 alt="31.2%"><img src="../snow.png" width=69 height=10 alt="31.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.2&nbsp;%</td>
+      <td class="coverNumLo">15 / 48</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SmacoffMDS.cpp.gcov.html">SmacoffMDS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=35 height=10 alt="35.0%"><img src="../snow.png" width=65 height=10 alt="35.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 20</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DimensionalityReductionBase.cpp.gcov.html">DimensionalityReductionBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="79.7%"><img src="../snow.png" width=20 height=10 alt="79.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.7&nbsp;%</td>
+      <td class="coverNumMed">47 / 59</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCA.cpp.gcov.html">PCA.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.8%"><img src="../snow.png" width=19 height=10 alt="80.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.8&nbsp;%</td>
+      <td class="coverNumMed">97 / 120</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ProjectNonLandmarkPoints.cpp.gcov.html">ProjectNonLandmarkPoints.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">39 / 43</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapRead.cpp.gcov.html">SketchMapRead.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.7%"><img src="../snow.png" width=7 height=10 alt="92.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.7&nbsp;%</td>
+      <td class="coverNumHi">76 / 82</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMACOF.cpp.gcov.html">SMACOF.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputPCAProjections.cpp.gcov.html">OutputPCAProjections.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">35 / 36</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapBase.h.gcov.html">SketchMapBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapConjGrad.cpp.gcov.html">SketchMapConjGrad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClassicalMultiDimensionalScaling.cpp.gcov.html">ClassicalMultiDimensionalScaling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapSmacof.cpp.gcov.html">SketchMapSmacof.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapPointwise.cpp.gcov.html">SketchMapPointwise.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapBase.cpp.gcov.html">SketchMapBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">79 / 79</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/dimred/index.html b/coverage/dimred/index.html
new file mode 100644
index 0000000000..afcff6c33f
--- /dev/null
+++ b/coverage/dimred/index.html
@@ -0,0 +1,243 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - dimred</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - dimred</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">556</td>
+            <td class="headerCovTableEntry">656</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntry">108</td>
+            <td class="headerCovTableEntryLo">73.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ClassicalMultiDimensionalScaling.cpp.gcov.html">ClassicalMultiDimensionalScaling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DimensionalityReductionBase.cpp.gcov.html">DimensionalityReductionBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="79.7%"><img src="../snow.png" width=20 height=10 alt="79.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.7&nbsp;%</td>
+      <td class="coverNumMed">47 / 59</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DimensionalityReductionBase.h.gcov.html">DimensionalityReductionBase.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 4</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputPCAProjections.cpp.gcov.html">OutputPCAProjections.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">35 / 36</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCA.cpp.gcov.html">PCA.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.8%"><img src="../snow.png" width=19 height=10 alt="80.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.8&nbsp;%</td>
+      <td class="coverNumMed">97 / 120</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCA.h.gcov.html">PCA.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ProjectNonLandmarkPoints.cpp.gcov.html">ProjectNonLandmarkPoints.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">39 / 43</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SMACOF.cpp.gcov.html">SMACOF.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMap.cpp.gcov.html">SketchMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=31 height=10 alt="31.2%"><img src="../snow.png" width=69 height=10 alt="31.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">31.2&nbsp;%</td>
+      <td class="coverNumLo">15 / 48</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapBase.cpp.gcov.html">SketchMapBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">79 / 79</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapBase.h.gcov.html">SketchMapBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapConjGrad.cpp.gcov.html">SketchMapConjGrad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapPointwise.cpp.gcov.html">SketchMapPointwise.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapRead.cpp.gcov.html">SketchMapRead.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.7%"><img src="../snow.png" width=7 height=10 alt="92.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.7&nbsp;%</td>
+      <td class="coverNumHi">76 / 82</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SketchMapSmacof.cpp.gcov.html">SketchMapSmacof.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SmacoffMDS.cpp.gcov.html">SmacoffMDS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=35 height=10 alt="35.0%"><img src="../snow.png" width=65 height=10 alt="35.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 20</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DRR.cpp.func-sort-c.html b/coverage/drr/DRR.cpp.func-sort-c.html
new file mode 100644
index 0000000000..356057c7fd
--- /dev/null
+++ b/coverage/drr/DRR.cpp.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DRR.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DRR.cpp<span style="font-size: 80%;"> (<a href="DRR.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">328</td>
+            <td class="headerCovTableEntry">352</td>
+            <td class="headerCovTableEntryHi">93.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DRR.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#27">_ZNK4PLMD3drr7DRRAxis12isInBoundaryEd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#441">_ZN4PLMD3drr3ABF11mergewindowERKS1_S3_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#488">_ZN4PLMD3drr4CZAR11mergewindowERKS1_S3_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#394">_ZNK4PLMD3drr12DRRForceGrid15writeDivergenceERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#171">_ZN4PLMD3drr12DRRForceGrid5mergeERKSt6vectorINS0_7DRRAxisESaIS3_EES7_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#47">_ZN4PLMD3drr7DRRAxis5mergeERKS1_S3_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#510">_ZNK4PLMD3drr4CZAR16writeZCountZGradERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#98">_ZN4PLMD3drr12DRRForceGridC2ERKSt6vectorINS0_7DRRAxisESaIS3_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnHi">26</td>
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+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#335">_ZNK4PLMD3drr12DRRForceGrid10write1DPMFENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#76">_ZN4PLMD3drr12DRRForceGrid9fillTableERKSt6vectorIS2_IdSaIdEESaIS4_EE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#352">_ZNK4PLMD3drr12DRRForceGrid8writeAllERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#93">_ZN4PLMD3drr12DRRForceGridC2Ev</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#59">_ZN4PLMD3drr7DRRAxis15getMiddlePointsEv</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#412">_ZN4PLMD3drr3ABF13store_getbiasERKSt6vectorIdSaIdEES6_RS4_</a></td>
+              <td class="coverFnHi">123</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#179">_ZNK4PLMD3drr12DRRForceGrid20getAccumulatedForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#156">_ZN4PLMD3drr12DRRForceGrid5storeERKSt6vectorIdSaIdEES6_m</a></td>
+              <td class="coverFnHi">1723</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#34">_ZNK4PLMD3drr7DRRAxis14isRealPeriodicEv</a></td>
+              <td class="coverFnHi">5860</td>
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+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#217">_ZNK4PLMD3drr12DRRForceGrid13getDivergenceERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">64800</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#189">_ZNK4PLMD3drr12DRRForceGrid8getCountERKSt6vectorIdSaIdEEb</a></td>
+              <td class="coverFnHi">67612</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#199">_ZNK4PLMD3drr12DRRForceGrid11getGradientERKSt6vectorIdSaIdEEb</a></td>
+              <td class="coverFnHi">195576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#284">_ZNK4PLMD3drr12DRRForceGrid22getCountsLogDerivativeERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">195576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#462">_ZNK4PLMD3drr4CZAR11getGradientERKSt6vectorIdSaIdEEb</a></td>
+              <td class="coverFnHi">195576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#139">_ZNK4PLMD3drr12DRRForceGrid12isInBoundaryERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">393846</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#148">_ZNK4PLMD3drr12DRRForceGrid13sampleAddressERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1012383</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#70">_ZN4PLMD3drr12DRRForceGrid7index1DERKNS0_7DRRAxisEd</a></td>
+              <td class="coverFnHi">2407170</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DRR.cpp.func.html b/coverage/drr/DRR.cpp.func.html
new file mode 100644
index 0000000000..7797a969c3
--- /dev/null
+++ b/coverage/drr/DRR.cpp.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DRR.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DRR.cpp<span style="font-size: 80%;"> (<a href="DRR.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">328</td>
+            <td class="headerCovTableEntry">352</td>
+            <td class="headerCovTableEntryHi">93.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DRR.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#171">_ZN4PLMD3drr12DRRForceGrid5mergeERKSt6vectorINS0_7DRRAxisESaIS3_EES7_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#156">_ZN4PLMD3drr12DRRForceGrid5storeERKSt6vectorIdSaIdEES6_m</a></td>
+              <td class="coverFnHi">1723</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#70">_ZN4PLMD3drr12DRRForceGrid7index1DERKNS0_7DRRAxisEd</a></td>
+              <td class="coverFnHi">2407170</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#76">_ZN4PLMD3drr12DRRForceGrid9fillTableERKSt6vectorIS2_IdSaIdEESaIS4_EE</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#98">_ZN4PLMD3drr12DRRForceGridC2ERKSt6vectorINS0_7DRRAxisESaIS3_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#93">_ZN4PLMD3drr12DRRForceGridC2Ev</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.cpp.gcov.html#441">_ZN4PLMD3drr3ABF11mergewindowERKS1_S3_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DRR.cpp.gcov.html b/coverage/drr/DRR.cpp.gcov.html
new file mode 100644
index 0000000000..76cd3abd96
--- /dev/null
+++ b/coverage/drr/DRR.cpp.gcov.html
@@ -0,0 +1,631 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DRR.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DRR.cpp<span style="font-size: 80%;"> (source / <a href="DRR.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">328</td>
+            <td class="headerCovTableEntry">352</td>
+            <td class="headerCovTableEntryHi">93.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :     Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)</a>
+<a name="3"><span class="lineNum">       3 </span>            :     Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :     This program is free software: you can redistribute it and/or modify</a>
+<a name="6"><span class="lineNum">       6 </span>            :     it under the terms of the GNU Lesser General Public License as published</a>
+<a name="7"><span class="lineNum">       7 </span>            :     by the Free Software Foundation, either version 3 of the License, or</a>
+<a name="8"><span class="lineNum">       8 </span>            :     (at your option) any later version.</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            :     This program is distributed in the hope that it will be useful,</a>
+<a name="11"><span class="lineNum">      11 </span>            :     but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="12"><span class="lineNum">      12 </span>            :     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="13"><span class="lineNum">      13 </span>            :     GNU Lesser General Public License for more details.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            :     You should have received a copy of the GNU Lesser General Public License</a>
+<a name="16"><span class="lineNum">      16 </span>            :     along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="17"><span class="lineNum">      17 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="18"><span class="lineNum">      18 </span>            : #ifdef __PLUMED_HAS_BOOST_SERIALIZATION</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;DRR.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : </a>
+<a name="21"><span class="lineNum">      21 </span>            : namespace PLMD {</a>
+<a name="22"><span class="lineNum">      22 </span>            : namespace drr {</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : using std::vector;</a>
+<a name="25"><span class="lineNum">      25 </span>            : using std::string;</a>
+<a name="26"><span class="lineNum">      26 </span>            : using std::begin;</a>
+<a name="27"><span class="lineNum">      27 </span>            : using std::end;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineNoCov">          0 : bool DRRAxis::isInBoundary(double x) const {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineNoCov">          0 :   if (x &lt; min || x &gt; max)</span></a>
+<a name="31"><span class="lineNum">      31 </span>            :     return false;</a>
+<a name="32"><span class="lineNum">      32 </span>            :   else</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :     return true;</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : }</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       5860 : bool DRRAxis::isRealPeriodic() const {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       5860 :   if (periodic == true) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       5808 :     if (std::abs(domainMax - max) &lt; binWidth &amp;&amp;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       5796 :         std::abs(domainMin - min) &lt; binWidth) {</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :       return true;</a>
+<a name="41"><span class="lineNum">      41 </span>            :     } else {</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         12 :       return false;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :     }</a>
+<a name="44"><span class="lineNum">      44 </span>            :   } else {</a>
+<a name="45"><span class="lineNum">      45 </span>            :     return false;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   }</a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          4 : DRRAxis DRRAxis::merge(const DRRAxis &amp;d1, const DRRAxis &amp;d2) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 :   const double newmin = std::min(d1.min, d2.min);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          4 :   const double newmax = std::max(d1.max, d2.max);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          4 :   const double newWidth = d1.binWidth;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          4 :   const size_t newbins = size_t(std::nearbyint((newmax - newmin) / newWidth));</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          4 :   const bool newpbc = d1.periodic;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          4 :   const double newdmin = std::min(d1.domainMin, d2.domainMin);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          4 :   const double newdmax = std::max(d1.domainMax, d2.domainMax);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   DRRAxis result(newmin, newmax, newbins, newpbc, newdmin, newdmax);</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :   return result;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         60 : vector&lt;double&gt; DRRAxis::getMiddlePoints() {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         60 :   vector&lt;double&gt; result(nbins, 0);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         60 :   const double width = binWidth;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         60 :   double temp = min - width / 2;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         60 :   std::generate(begin(result), end(result), [&amp;temp, &amp;width]() {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       3382 :     temp += width;</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     return temp;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   });</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         60 :   return result;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    2407170 : size_t DRRForceGrid::index1D(const DRRAxis &amp;c, double x) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">    2407170 :   size_t idx = size_t(std::floor((x - c.min) / c.binWidth));</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    2407170 :   idx = (idx == c.nbins) ? (c.nbins - 1) : idx;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">    2407170 :   return idx;</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         34 : void DRRForceGrid::fillTable(const vector&lt;vector&lt;double&gt;&gt; &amp;in) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         34 :   table.resize(ndims, vector&lt;double&gt;(sampleSize, 0));</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         82 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :     size_t repeatAll = 1, repeatOne = 1;</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         62 :     for (size_t j = i + 1; j &lt; ndims; ++j)</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         14 :       repeatOne *= in[j].size();</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         62 :     for (size_t j = 0; j &lt; i; ++j)</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         14 :       repeatAll *= in[j].size();</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     size_t in_i_sz = in[i].size();</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       3390 :     for (size_t l = 0; l &lt; in_i_sz; ++l)</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       3342 :       std::fill_n(begin(table[i]) + l * repeatOne, repeatOne, in[i][l]);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        784 :     for (size_t k = 0; k &lt; repeatAll - 1; ++k)</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        736 :       std::copy_n(begin(table[i]), repeatOne * in_i_sz,</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        736 :                   begin(table[i]) + repeatOne * in_i_sz * (k + 1));</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         34 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         38 : DRRForceGrid::DRRForceGrid()</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         38 :   : suffix(&quot;&quot;), ndims(0), dimensions(0), sampleSize(0),</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         38 :     headers(&quot;&quot;), table(0), forces(0), samples(0), endpoints(0), shifts(0),</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         76 :     outputunit(1.0) {}</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         26 : DRRForceGrid::DRRForceGrid(const vector&lt;DRRAxis&gt; &amp;p_dimensions,</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         26 :                            const string &amp;p_suffix, bool initializeTable)</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         26 :   : suffix(p_suffix), ndims(p_dimensions.size()), dimensions(p_dimensions) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         26 :   sampleSize = 1;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         26 :   vector&lt;vector&lt;double&gt;&gt; mp(ndims);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         26 :   std::stringstream ss;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         26 :   ss &lt;&lt; &quot;# &quot; &lt;&lt; ndims &lt;&lt; '\n';</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         26 :   shifts.resize(ndims, 0);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         26 :   shifts[0] = 1;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         64 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         38 :     sampleSize = dimensions[i].nbins * sampleSize;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         38 :     mp[i] = dimensions[i].getMiddlePoints();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         38 :     if (i &gt; 0) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         12 :       shifts[i] = shifts[i - 1] * dimensions[i - 1].nbins;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     }</a>
+<a name="115"><span class="lineNum">     115 </span>            :     ss.precision(std::numeric_limits&lt;double&gt;::max_digits10);</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         76 :     ss &lt;&lt; std::fixed &lt;&lt; &quot;# &quot; &lt;&lt; dimensions[i].min &lt;&lt; ' '</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         76 :        &lt;&lt; dimensions[i].binWidth &lt;&lt; ' ' &lt;&lt; dimensions[i].nbins;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         38 :     if (dimensions[i].isPeriodic())</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         56 :       ss &lt;&lt; &quot; 1&quot; &lt;&lt; '\n';</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     else</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         20 :       ss &lt;&lt; &quot; 0&quot; &lt;&lt; '\n';</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         26 :   headers = ss.str();</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         26 :   if (initializeTable)</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         18 :     fillTable(mp);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         26 :   forces.resize(sampleSize * ndims, 0.0);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         26 :   samples.resize(sampleSize, 0);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         26 :   outputunit = 1.0;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   // For 1D pmf</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         26 :   if (ndims == 1) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         14 :     endpoints.resize(dimensions[0].nbins + 1, 0);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         14 :     double ep = dimensions[0].min;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         14 :     double stride = dimensions[0].binWidth;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        882 :     for (auto &amp;i : endpoints) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        868 :       i = ep;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        868 :       ep += stride;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     }</a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         26 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">     393846 : bool DRRForceGrid::isInBoundary(const vector&lt;double&gt; &amp;pos) const {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   bool result = true;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">    1175042 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">     782805 :     if (pos[i] &lt; dimensions[i].min || pos[i] &gt; dimensions[i].max)</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :       return false;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            :   return result;</a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">    1012383 : size_t DRRForceGrid::sampleAddress(const vector&lt;double&gt; &amp;pos) const {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   size_t saddr = 0;</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">    3029541 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">    2017158 :     saddr += shifts[i] * index1D(dimensions[i], pos[i]);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">    1012383 :   return saddr;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1723 : bool DRRForceGrid::store(const vector&lt;double&gt; &amp;pos, const vector&lt;double&gt; &amp;f,</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :                          unsigned long int nsamples) {</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1723 :   if (isInBoundary(pos)) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1714 :     if (nsamples == 0)</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :       return true;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        914 :     const size_t baseaddr = sampleAddress(pos);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        914 :     samples[baseaddr] += nsamples;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        914 :     auto it_fa = begin(forces) + baseaddr * ndims;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        914 :     std::transform(begin(f), end(f), it_fa, it_fa, std::plus&lt;double&gt;());</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        914 :     return true;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   } else {</a>
+<a name="169"><span class="lineNum">     169 </span>            :     return false;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 : vector&lt;DRRAxis&gt; DRRForceGrid::merge(const vector&lt;DRRAxis&gt; &amp;dA,</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :                                     const vector&lt;DRRAxis&gt; &amp;dB) {</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          4 :   vector&lt;DRRAxis&gt; dR(dA.size());</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          4 :   std::transform(begin(dA), end(dA), begin(dB), begin(dR), DRRAxis::merge);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 :   return dR;</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : vector&lt;double&gt;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       1600 : DRRForceGrid::getAccumulatedForces(const vector&lt;double&gt; &amp;pos) const {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       1600 :   vector&lt;double&gt; result(ndims, 0);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       1600 :   if (!isInBoundary(pos))</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     return result;</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        800 :   const size_t force_addr = sampleAddress(pos) * ndims;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        800 :   std::copy(begin(forces) + force_addr, begin(forces) + force_addr + ndims,</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :             begin(result));</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        800 :   return result;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      67612 : unsigned long int DRRForceGrid::getCount(const vector&lt;double&gt; &amp;pos,</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     bool SkipCheck) const {</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      67612 :   if (!SkipCheck) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1600 :     if (!isInBoundary(pos)) {</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :       return 0;</a>
+<a name="196"><span class="lineNum">     196 </span>            :     }</a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      66812 :   return samples[sampleAddress(pos)];</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     195576 : vector&lt;double&gt; DRRForceGrid::getGradient(const vector&lt;double&gt; &amp;pos,</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :     bool SkipCheck) const {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     195576 :   vector&lt;double&gt; result(ndims, 0);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     195576 :   if (!SkipCheck) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     162000 :     if (!isInBoundary(pos)) {</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :       return result;</a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     195576 :   const size_t baseaddr = sampleAddress(pos);</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   const unsigned long int &amp;count = samples[baseaddr];</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">     195576 :   if (count == 0)</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     return result;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">     195411 :   auto it_fa = begin(forces) + baseaddr * ndims;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">     195411 :   std::transform(it_fa, it_fa + ndims, begin(result),</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">     389802 :   [&amp;count](double fa) { return (-1.0) * fa / count; });</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     195411 :   return result;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      64800 : double DRRForceGrid::getDivergence(const vector&lt;double&gt; &amp;pos) const {</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   double div = 0.0;</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      64800 :   vector&lt;double&gt; grad_deriv(ndims, 0.0);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      64800 :   if (!isInBoundary(pos)) {</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :     return div;</a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      64800 :   const size_t force_addr = sampleAddress(pos) * ndims;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      64800 :   vector&lt;double&gt; grad = getGradient(pos);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">     194400 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">     129600 :     const double binWidth = dimensions[i].binWidth;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">     129600 :     vector&lt;double&gt; first = pos;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">     129600 :     first[i] = dimensions[i].min + binWidth * 0.5;</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">     129600 :     vector&lt;double&gt; last = pos;</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     129600 :     last[i] = dimensions[i].max - binWidth * 0.5;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">     129600 :     const size_t force_addr_first = sampleAddress(first) * ndims;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">     129600 :     const size_t force_addr_last = sampleAddress(last) * ndims;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     129600 :     if (force_addr == force_addr_first) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        720 :       if (dimensions[i].isRealPeriodic() == true) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        720 :         vector&lt;double&gt; next = pos;</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        720 :         next[i] += binWidth;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        720 :         const vector&lt;double&gt; grad_next = getGradient(next);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        720 :         const vector&lt;double&gt; grad_prev = getGradient(last);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        720 :         grad_deriv[i] = (grad_next[i] - grad_prev[i]) / (2.0 * binWidth);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :       } else {</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :         vector&lt;double&gt; next = pos;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :         next[i] += binWidth;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :         vector&lt;double&gt; next_2 = next;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :         next_2[i] += binWidth;</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :         const vector&lt;double&gt; grad_next = getGradient(next);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :         const vector&lt;double&gt; grad_next_2 = getGradient(next_2);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :         grad_deriv[i] =</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :           (grad_next_2[i] * -1.0 + grad_next[i] * 4.0 - grad[i] * 3.0) /</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :           (2.0 * binWidth);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :       }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">     128880 :     } else if (force_addr == force_addr_last) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        720 :       if (dimensions[i].isRealPeriodic() == true) {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        720 :         vector&lt;double&gt; prev = pos;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        720 :         prev[i] -= binWidth;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        720 :         const vector&lt;double&gt; grad_next = getGradient(first);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        720 :         const vector&lt;double&gt; grad_prev = getGradient(prev);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        720 :         grad_deriv[i] = (grad_next[i] - grad_prev[i]) / (2.0 * binWidth);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :       } else {</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :         vector&lt;double&gt; prev = pos;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :         prev[i] -= binWidth;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :         vector&lt;double&gt; prev_2 = prev;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :         prev_2[i] -= binWidth;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :         const vector&lt;double&gt; grad_prev = getGradient(prev);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :         const vector&lt;double&gt; grad_prev_2 = getGradient(prev_2);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :         grad_deriv[i] =</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :           (grad[i] * 3.0 - grad_prev[i] * 4.0 + grad_prev_2[i] * 1.0) /</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :           (2.0 * binWidth);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :       }</a>
+<a name="271"><span class="lineNum">     271 </span>            :     } else {</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">     128160 :       vector&lt;double&gt; prev = pos;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">     128160 :       prev[i] -= binWidth;</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">     128160 :       vector&lt;double&gt; next = pos;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">     128160 :       next[i] += binWidth;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">     128160 :       const vector&lt;double&gt; grad_next = getGradient(next);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">     128160 :       const vector&lt;double&gt; grad_prev = getGradient(prev);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">     128160 :       grad_deriv[i] = (grad_next[i] - grad_prev[i]) / (2.0 * binWidth);</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :     }</a>
+<a name="280"><span class="lineNum">     280 </span>            :   }</a>
+<a name="281"><span class="lineNum">     281 </span>            :   div = std::accumulate(begin(grad_deriv), end(grad_deriv), 0.0);</a>
+<a name="282"><span class="lineNum">     282 </span>            :   return div;</a>
+<a name="283"><span class="lineNum">     283 </span>            : }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            : vector&lt;double&gt;</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">     195576 : DRRForceGrid::getCountsLogDerivative(const vector&lt;double&gt; &amp;pos) const {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     195576 :   const size_t addr = sampleAddress(pos);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     195576 :   const unsigned long int count_this = samples[addr];</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     195576 :   vector&lt;double&gt; result(ndims, 0);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     585588 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     390012 :     const double binWidth = dimensions[i].binWidth;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :     const size_t addr_first =</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     390012 :       addr - shifts[i] * index1D(dimensions[i], pos[i]) + 0;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">     390012 :     const size_t addr_last = addr_first + shifts[i] * (dimensions[i].nbins - 1);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">     390012 :     if (addr == addr_first) {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       2210 :       if (dimensions[i].isRealPeriodic() == true) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       2178 :         const unsigned long int &amp;count_next = samples[addr + shifts[i]];</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :         const unsigned long int &amp;count_prev = samples[addr_last];</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       2178 :         if (count_next != 0 &amp;&amp; count_prev != 0)</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       2160 :           result[i] =</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       2160 :             (std::log(count_next) - std::log(count_prev)) / (2 * binWidth);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :       } else {</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         32 :         const unsigned long int &amp;count_next = samples[addr + shifts[i]];</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         32 :         const unsigned long int &amp;count_next2 = samples[addr + shifts[i] * 2];</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         32 :         if (count_next != 0 &amp;&amp; count_this != 0 &amp;&amp; count_next2 != 0)</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          6 :           result[i] =</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          6 :             (std::log(count_next2) * (-1.0) + std::log(count_next) * 4.0 -</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          6 :              std::log(count_this) * 3.0) /</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          6 :             (2.0 * binWidth);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :       }</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">     387802 :     } else if (addr == addr_last) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       2210 :       if (dimensions[i].isRealPeriodic() == true) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       2178 :         const unsigned long int &amp;count_prev = samples[addr - shifts[i]];</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :         const unsigned long int &amp;count_next = samples[addr_first];</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       2178 :         if (count_next != 0 &amp;&amp; count_prev != 0)</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       2160 :           result[i] =</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       2160 :             (std::log(count_next) - std::log(count_prev)) / (2 * binWidth);</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :       } else {</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         32 :         const unsigned long int &amp;count_prev = samples[addr - shifts[i]];</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         32 :         const unsigned long int &amp;count_prev2 = samples[addr - shifts[i] * 2];</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         32 :         if (count_prev != 0 &amp;&amp; count_this != 0 &amp;&amp; count_prev2 != 0)</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          6 :           result[i] = (std::log(count_this) * 3.0 - std::log(count_prev) * 4.0 +</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          6 :                        std::log(count_prev2)) /</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          6 :                       (2.0 * binWidth);</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :       }</a>
+<a name="326"><span class="lineNum">     326 </span>            :     } else {</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">     385592 :       const unsigned long int &amp;count_prev = samples[addr - shifts[i]];</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">     385592 :       const unsigned long int &amp;count_next = samples[addr + shifts[i]];</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">     385592 :       if (count_next != 0 &amp;&amp; count_prev != 0)</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">     385432 :         result[i] =</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">     385432 :           (std::log(count_next) - std::log(count_prev)) / (2 * binWidth);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :     }</a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">     195576 :   return result;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         26 : void DRRForceGrid::write1DPMF(string filename) const {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         52 :   filename += suffix + &quot;.pmf&quot;;</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   FILE *ppmf;</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         26 :   ppmf = fopen(filename.c_str(), &quot;w&quot;);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         26 :   const double w = dimensions[0].binWidth;</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :   double pmf = 0;</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         26 :   fprintf(ppmf, &quot;%.9f %.9f\n&quot;, endpoints[0], pmf);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">       1166 :   for (size_t i = 0; i &lt; dimensions[0].nbins; ++i) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">       1140 :     vector&lt;double&gt; pos(1, 0);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">       1140 :     pos[0] = table[0][i];</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       1140 :     const vector&lt;double&gt; f = getGradient(pos, true);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       1140 :     pmf += f[0] * w / outputunit;</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">       1140 :     fprintf(ppmf, &quot;%.9f %.9f\n&quot;, endpoints[i + 1], pmf);</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :   }</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         26 :   fclose(ppmf);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         26 : }</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         36 : void DRRForceGrid::writeAll(const string &amp;filename, bool addition) const {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         36 :   const string countname = filename + suffix + &quot;.count&quot;;</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         36 :   const string gradname = filename + suffix + &quot;.grad&quot;;</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         36 :   vector&lt;double&gt; pos(ndims, 0);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   FILE *pGrad, *pCount;</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         36 :   if (addition) {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          8 :     pGrad = fopen(gradname.c_str(), &quot;a&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          8 :     pCount = fopen(countname.c_str(), &quot;a&quot;);</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :   } else {</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         28 :     pGrad = fopen(gradname.c_str(), &quot;w&quot;);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         28 :     pCount = fopen(countname.c_str(), &quot;w&quot;);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :   }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :   char *buffer1, *buffer2;</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         36 :   buffer1 = (char *)malloc((sizeof(double)) * sampleSize * ndims);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         36 :   buffer2 = (char *)malloc((sizeof(double)) * sampleSize * ndims);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         36 :   setvbuf(pGrad, buffer1, _IOFBF, (sizeof(double)) * sampleSize * ndims);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         36 :   setvbuf(pCount, buffer2, _IOFBF, (sizeof(double)) * sampleSize * ndims);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         36 :   fwrite(headers.c_str(), sizeof(char), strlen(headers.c_str()), pGrad);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         36 :   fwrite(headers.c_str(), sizeof(char), strlen(headers.c_str()), pCount);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      66048 :   for (size_t i = 0; i &lt; sampleSize; ++i) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">     196896 :     for (size_t j = 0; j &lt; ndims; ++j) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">     130884 :       pos[j] = table[j][i];</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">     130884 :       fprintf(pGrad, &quot; %.9f&quot;, table[j][i]);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">     130884 :       fprintf(pCount, &quot; %.9f&quot;, table[j][i]);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :     }</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">      66012 :     fprintf(pCount, &quot; %lu\n&quot;, getCount(pos, true));</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">      66012 :     vector&lt;double&gt; f = getGradient(pos, true);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">     196896 :     for (size_t j = 0; j &lt; ndims; ++j) {</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">     130884 :       fprintf(pGrad, &quot; %.9f&quot;, (f[j] / outputunit));</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :     }</a>
+<a name="385"><span class="lineNum">     385 </span>            :     fprintf(pGrad, &quot;\n&quot;);</a>
+<a name="386"><span class="lineNum">     386 </span>            :   }</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         36 :   fclose(pGrad);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         36 :   fclose(pCount);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         36 :   free(buffer1);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         36 :   free(buffer2);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         36 :   if (ndims == 1) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         52 :     write1DPMF(filename);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   }</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         36 : }</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          2 : void DRRForceGrid::writeDivergence(const string &amp;filename) const {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          2 :   const string divname = filename + suffix + &quot;.div&quot;;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          2 :   vector&lt;double&gt; pos(ndims, 0);</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :   FILE *pDiv;</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          2 :   pDiv = fopen(divname.c_str(), &quot;w&quot;);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          2 :   fwrite(headers.c_str(), sizeof(char), strlen(headers.c_str()), pDiv);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">      64802 :   for (size_t i = 0; i &lt; sampleSize; ++i) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">     194400 :     for (size_t j = 0; j &lt; ndims; ++j) {</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">     129600 :       pos[j] = table[j][i];</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">     129600 :       fprintf(pDiv, &quot; %.9f&quot;, table[j][i]);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :     }</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">      64800 :     const double divergence = getDivergence(pos);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">      64800 :     fprintf(pDiv, &quot; %.9f&quot;, (divergence / outputunit));</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     fprintf(pDiv, &quot;\n&quot;);</a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">          2 :   fclose(pDiv);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">          2 : }</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">        123 : bool ABF::store_getbias(const vector&lt;double&gt; &amp;pos, const vector&lt;double&gt; &amp;f,</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :                         vector&lt;double&gt; &amp;fbias) {</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        123 :   if (!isInBoundary(pos)) {</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :     std::fill(begin(fbias), end(fbias), 0.0);</a>
+<a name="418"><span class="lineNum">     418 </span>            :     return false;</a>
+<a name="419"><span class="lineNum">     419 </span>            :   }</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">        123 :   const size_t baseaddr = sampleAddress(pos);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :   unsigned long int &amp;count = samples[baseaddr];</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        123 :   ++count;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        123 :   double factor = 2 * (static_cast&lt;double&gt;(count)) / mFullSamples - 1;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        123 :   auto it_fa = begin(forces) + baseaddr * ndims;</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :   auto it_fb = begin(fbias);</a>
+<a name="426"><span class="lineNum">     426 </span>            :   auto it_f = begin(f);</a>
+<a name="427"><span class="lineNum">     427 </span>            :   auto it_maxFactor = begin(mMaxFactors);</a>
+<a name="428"><span class="lineNum">     428 </span>            :   do {</a>
+<a name="429"><span class="lineNum">     429 </span>            :     // Clamp to [0,maxFactors]</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        207 :     factor = factor &lt; 0 ? 0 : factor &gt; (*it_maxFactor) ? (*it_maxFactor) : factor;</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        207 :     (*it_fa) += (*it_f); // Accumulate instantaneous force</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        207 :     (*it_fb) = factor * (*it_fa) * (-1.0) /</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        207 :                static_cast&lt;double&gt;(count); // Calculate bias force</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :     ++it_fa;</a>
+<a name="435"><span class="lineNum">     435 </span>            :     ++it_fb;</a>
+<a name="436"><span class="lineNum">     436 </span>            :     ++it_f;</a>
+<a name="437"><span class="lineNum">     437 </span>            :     ++it_maxFactor;</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">        207 :   } while (it_f != end(f));</span></a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span>            :   return true;</a>
+<a name="441"><span class="lineNum">     441 </span>            : }</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          2 : ABF ABF::mergewindow(const ABF &amp;aWA, const ABF &amp;aWB) {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          2 :   const vector&lt;DRRAxis&gt; dR = merge(aWA.dimensions, aWB.dimensions);</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          2 :   const string suffix = &quot;.abf&quot;;</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          2 :   ABF result(dR, suffix);</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          2 :   const size_t nrows = result.sampleSize;</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          2 :   const size_t ncols = result.ndims;</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          2 :   vector&lt;double&gt; pos(ncols, 0);</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">        402 :   for (size_t i = 0; i &lt; nrows; ++i) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        800 :     for (size_t j = 0; j &lt; ncols; ++j) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">        400 :       pos[j] = result.table[j][i];</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     }</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">        400 :     const unsigned long int countA = aWA.getCount(pos);</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">        400 :     const unsigned long int countB = aWB.getCount(pos);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        400 :     const vector&lt;double&gt; aForceA = aWA.getAccumulatedForces(pos);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        400 :     const vector&lt;double&gt; aForceB = aWB.getAccumulatedForces(pos);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">        400 :     result.store(pos, aForceA, countA);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        400 :     result.store(pos, aForceB, countB);</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :   }</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          2 :   return result;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">     195576 : vector&lt;double&gt; CZAR::getGradient(const vector&lt;double&gt; &amp;pos,</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :                                  bool SkipCheck) const {</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">     195576 :   vector&lt;double&gt; result(ndims, 0);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">     195576 :   if (!SkipCheck) {</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">     162000 :     if (!isInBoundary(pos)) {</span></a>
+<a name="469"><span class="lineNum">     469 </span>            :       return result;</a>
+<a name="470"><span class="lineNum">     470 </span>            :     }</a>
+<a name="471"><span class="lineNum">     471 </span>            :   }</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">     195576 :   if (kbt &lt;= std::numeric_limits&lt;double&gt;::epsilon()) {</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :     std::cerr &lt;&lt; &quot;ERROR! The kbt shouldn't be zero when use CZAR estimator. &quot;</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :               &lt;&lt; '\n';</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :     std::abort();</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :   }</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">     195576 :   const size_t baseaddr = sampleAddress(pos);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">     195576 :   const vector&lt;double&gt; log_deriv(getCountsLogDerivative(pos));</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :   const unsigned long int &amp;count = samples[baseaddr];</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">     195576 :   if (count == 0)</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :     return result;</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">     195421 :   auto it_fa = begin(forces) + baseaddr * ndims;</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">     195421 :   std::transform(it_fa, it_fa + ndims, begin(log_deriv), begin(result),</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">     389822 :   [&amp;count, this](double fa, double ld) {</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">     389822 :     return fa * (-1.0) / count - kbt * ld;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :   });</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">     195421 :   return result;</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : }</a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          2 : CZAR CZAR::mergewindow(const CZAR &amp;cWA, const CZAR &amp;cWB) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          2 :   const vector&lt;DRRAxis&gt; dR = merge(cWA.dimensions, cWB.dimensions);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          2 :   const double newkbt = cWA.kbt;</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          2 :   const string suffix = &quot;.czar&quot;;</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :   CZAR result(dR, suffix, newkbt);</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          2 :   const size_t nrows = result.sampleSize;</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          2 :   const size_t ncols = result.ndims;</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          2 :   vector&lt;double&gt; pos(ncols, 0);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">        402 :   for (size_t i = 0; i &lt; nrows; ++i) {</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        800 :     for (size_t j = 0; j &lt; ncols; ++j) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        400 :       pos[j] = result.table[j][i];</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :     }</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        400 :     const unsigned long int countA = cWA.getCount(pos);</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">        400 :     const unsigned long int countB = cWB.getCount(pos);</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        400 :     const vector&lt;double&gt; aForceA = cWA.getAccumulatedForces(pos);</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        400 :     const vector&lt;double&gt; aForceB = cWB.getAccumulatedForces(pos);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        400 :     result.store(pos, aForceA, countA);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        400 :     result.store(pos, aForceB, countB);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   }</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          2 :   return result;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         18 : void CZAR:: writeZCountZGrad(const string &amp;filename, bool addition) const {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         18 :   const string countname = filename + &quot;.zcount&quot;;</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         18 :   const string gradname = filename + &quot;.zgrad&quot;;</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         18 :   vector&lt;double&gt; pos(ndims, 0);</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :   FILE *pCount;</a>
+<a name="517"><span class="lineNum">     517 </span>            :   FILE *pGrad;</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         18 :   if (addition) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          4 :     pCount = fopen(countname.c_str(), &quot;a&quot;);</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">          4 :     pGrad = fopen(gradname.c_str(), &quot;a&quot;);</span></a>
+<a name="521"><span class="lineNum">     521 </span>            :   } else {</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         14 :     pCount = fopen(countname.c_str(), &quot;w&quot;);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         14 :     pGrad = fopen(gradname.c_str(), &quot;w&quot;);</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :   }</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         18 :   fwrite(headers.c_str(), sizeof(char), strlen(headers.c_str()), pCount);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         18 :   fwrite(headers.c_str(), sizeof(char), strlen(headers.c_str()), pGrad);</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">      33024 :   for (size_t i = 0; i &lt; sampleSize; ++i) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">      98448 :     for (size_t j = 0; j &lt; ndims; ++j) {</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">      65442 :       pos[j] = table[j][i];</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">      65442 :       fprintf(pCount, &quot; %.9f&quot;, table[j][i]);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">      65442 :       fprintf(pGrad, &quot; %.9f&quot;, table[j][i]);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :     }</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">      33006 :     const size_t baseaddr = sampleAddress(pos);</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :     const auto&amp; current_sample = samples[baseaddr];</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">      33006 :     fprintf(pCount, &quot; %lu\n&quot;, current_sample);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">      33006 :     if (current_sample == 0) {</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">        195 :       for (size_t j = 0; j &lt; ndims; ++j) {</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :         fprintf(pGrad, &quot; %.9f&quot;, 0.0);</a>
+<a name="539"><span class="lineNum">     539 </span>            :       }</a>
+<a name="540"><span class="lineNum">     540 </span>            :     } else {</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">      98253 :       for (size_t j = 0; j &lt; ndims; ++j) {</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">      65332 :         const double grad = -1.0 * forces[baseaddr * ndims + j] / current_sample;</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">      65332 :         fprintf(pGrad, &quot; %.9f&quot;, grad / outputunit);</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :       }</a>
+<a name="545"><span class="lineNum">     545 </span>            :     }</a>
+<a name="546"><span class="lineNum">     546 </span>            :     fprintf(pGrad, &quot;\n&quot;);</a>
+<a name="547"><span class="lineNum">     547 </span>            :   }</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         18 :   fclose(pCount);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         18 :   fclose(pGrad);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         18 : }</span></a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span>            : }</a>
+<a name="553"><span class="lineNum">     553 </span>            : }</a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DRR.h.func-sort-c.html b/coverage/drr/DRR.h.func-sort-c.html
new file mode 100644
index 0000000000..47ef056882
--- /dev/null
+++ b/coverage/drr/DRR.h.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DRR.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DRR.h<span style="font-size: 80%;"> (<a href="DRR.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DRR.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#203">_ZN4PLMD3drr12DRRForceGridD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#315">_ZN4PLMD3drr3ABFD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#341">_ZN4PLMD3drr4CZARD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#295">_ZN4PLMD3drr3ABFC2ERKSt6vectorINS0_7DRRAxisESaIS3_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEddb</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#341">_ZN4PLMD3drr4CZARD2Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#347">_ZN4PLMD3drr4CZAR9serializeIN5boost7archive15binary_iarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#300">_ZN4PLMD3drr3ABFC2ERKSt6vectorINS0_7DRRAxisESaIS3_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdRKS2_IdSaIdEEb</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#246">_ZN4PLMD3drr12DRRForceGrid4loadIN5boost7archive15binary_iarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#347">_ZN4PLMD3drr4CZAR9serializeIN5boost7archive15binary_oarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#127">_ZN4PLMD3drr7DRRAxis4loadIN5boost7archive15binary_iarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#315">_ZN4PLMD3drr3ABFD2Ev</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#239">_ZNK4PLMD3drr12DRRForceGrid4saveIN5boost7archive15binary_oarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#117">_ZNK4PLMD3drr7DRRAxis4saveIN5boost7archive15binary_oarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#203">_ZN4PLMD3drr12DRRForceGridD2Ev</a></td>
+              <td class="coverFnHi">76</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DRR.h.func.html b/coverage/drr/DRR.h.func.html
new file mode 100644
index 0000000000..5f12fabc0b
--- /dev/null
+++ b/coverage/drr/DRR.h.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DRR.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DRR.h<span style="font-size: 80%;"> (<a href="DRR.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DRR.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#246">_ZN4PLMD3drr12DRRForceGrid4loadIN5boost7archive15binary_iarchiveEEEvRT_j</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#203">_ZN4PLMD3drr12DRRForceGridD0Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#203">_ZN4PLMD3drr12DRRForceGridD2Ev</a></td>
+              <td class="coverFnHi">76</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRR.h.gcov.html#300">_ZN4PLMD3drr3ABFC2ERKSt6vectorINS0_7DRRAxisESaIS3_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEdRKS2_IdSaIdEEb</a></td>
+              <td class="coverFnHi">11</td>
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+    <tr>
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+    <tr>
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+    <tr>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DRR.h.gcov.html b/coverage/drr/DRR.h.gcov.html
new file mode 100644
index 0000000000..121f772d7b
--- /dev/null
+++ b/coverage/drr/DRR.h.gcov.html
@@ -0,0 +1,434 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DRR.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DRR.h<span style="font-size: 80%;"> (source / <a href="DRR.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :     Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)</a>
+<a name="3"><span class="lineNum">       3 </span>            :     Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :     This program is free software: you can redistribute it and/or modify</a>
+<a name="6"><span class="lineNum">       6 </span>            :     it under the terms of the GNU Lesser General Public License as published</a>
+<a name="7"><span class="lineNum">       7 </span>            :     by the Free Software Foundation, either version 3 of the License, or</a>
+<a name="8"><span class="lineNum">       8 </span>            :     (at your option) any later version.</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            :     This program is distributed in the hope that it will be useful,</a>
+<a name="11"><span class="lineNum">      11 </span>            :     but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="12"><span class="lineNum">      12 </span>            :     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="13"><span class="lineNum">      13 </span>            :     GNU Lesser General Public License for more details.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            :     You should have received a copy of the GNU Lesser General Public License</a>
+<a name="16"><span class="lineNum">      16 </span>            :     along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="17"><span class="lineNum">      17 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="18"><span class="lineNum">      18 </span>            : #ifndef __PLUMED_drr_DRR_h</a>
+<a name="19"><span class="lineNum">      19 </span>            : #define __PLUMED_drr_DRR_h</a>
+<a name="20"><span class="lineNum">      20 </span>            : // Build requirement: boost, c++11 compatible compiler.</a>
+<a name="21"><span class="lineNum">      21 </span>            : #ifdef __PLUMED_HAS_BOOST_SERIALIZATION</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;algorithm&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cmath&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cstddef&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;fstream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;iomanip&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;iterator&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;limits&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;numeric&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;sstream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // boost headers for serialization</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;boost/archive/binary_iarchive.hpp&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;boost/archive/binary_oarchive.hpp&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;boost/serialization/string.hpp&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;boost/serialization/vector.hpp&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace drr {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : using std::vector;</a>
+<a name="45"><span class="lineNum">      45 </span>            : using std::string;</a>
+<a name="46"><span class="lineNum">      46 </span>            : using std::begin;</a>
+<a name="47"><span class="lineNum">      47 </span>            : using std::end;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /// This class can store the minimum, maximum and bins of a dimension(axis).</a>
+<a name="50"><span class="lineNum">      50 </span>            : class DRRAxis {</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   /// Default empty constructor</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         64 :   DRRAxis() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         64 :     min = max = 0.0;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         64 :     nbins = 0;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         64 :     periodic = false;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         64 :     domainMax = domainMin = 0.0;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         64 :     binWidth = 0.0;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   }</a>
+<a name="60"><span class="lineNum">      60 </span>            :   /// Constructor using maximum value, minimum value and the number of bins(No</a>
+<a name="61"><span class="lineNum">      61 </span>            :   /// pbc)</a>
+<a name="62"><span class="lineNum">      62 </span>            :   DRRAxis(double l, double h, size_t n)</a>
+<a name="63"><span class="lineNum">      63 </span>            :     : min(l), max(h), nbins(n), periodic(false), domainMax(0), domainMin(0),</a>
+<a name="64"><span class="lineNum">      64 </span>            :       binWidth((max - min) / double(nbins)) {}</a>
+<a name="65"><span class="lineNum">      65 </span>            :   /// PBC-aware constructor</a>
+<a name="66"><span class="lineNum">      66 </span>            :   DRRAxis(double l, double h, size_t n, bool pbc, double dMax, double dMin)</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          4 :     : min(l), max(h), nbins(n), periodic(pbc), domainMax(dMax),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          4 :       domainMin(dMin), binWidth((max - min) / double(nbins)) {}</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   /// Set values</a>
+<a name="70"><span class="lineNum">      70 </span>            :   void set(double l, double h, size_t n, bool pbc = false, double dmin = 0,</a>
+<a name="71"><span class="lineNum">      71 </span>            :            double dmax = 0) {</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         38 :     min = l;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         38 :     max = h;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         38 :     nbins = n;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         38 :     periodic = pbc;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         38 :     domainMax = dmax;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         38 :     domainMin = dmin;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         38 :     binWidth = (max - min) / nbins;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   }</a>
+<a name="80"><span class="lineNum">      80 </span>            :   /// Set PBC data</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void setPeriodicity(double dmin, double dmax) {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         16 :     domainMax = dmax;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         16 :     domainMin = dmin;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         16 :     periodic = true;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span>            :   /// Getters</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         41 :   double getMin() const { return this-&gt;min; }</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         40 :   double getMax() const { return this-&gt;max; }</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         31 :   double getWidth() const { return binWidth; }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   double getDomainMax() const { return this-&gt;domainMax; }</a>
+<a name="91"><span class="lineNum">      91 </span>            :   double getDomainMin() const { return this-&gt;domainMin; }</a>
+<a name="92"><span class="lineNum">      92 </span>            :   size_t getBins() const { return this-&gt;nbins; }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   /// Check periodicity</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         60 :   bool isPeriodic() const { return this-&gt;periodic; }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   /// Check real periodicity, i.e. the maximum == the domain maximum</a>
+<a name="97"><span class="lineNum">      97 </span>            :   bool isRealPeriodic() const;</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   /// Check whether x is in this axis</a>
+<a name="100"><span class="lineNum">     100 </span>            :   bool isInBoundary(double x) const;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   /// Get an array of middle points of each bins</a>
+<a name="102"><span class="lineNum">     102 </span>            :   vector&lt;double&gt; getMiddlePoints();</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   /// Combine two axes if they share the same bin width.</a>
+<a name="105"><span class="lineNum">     105 </span>            :   static DRRAxis merge(const DRRAxis &amp;d1, const DRRAxis &amp;d2);</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   friend class DRRForceGrid;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : protected:</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double min;       // Minimum value of the axis</a>
+<a name="111"><span class="lineNum">     111 </span>            :   double max;       // Maximum value of the axis</a>
+<a name="112"><span class="lineNum">     112 </span>            :   size_t nbins;     // Number of bins</a>
+<a name="113"><span class="lineNum">     113 </span>            :   bool periodic;    // Periodicity</a>
+<a name="114"><span class="lineNum">     114 </span>            :   double domainMax; // Maximum value of the CV domain</a>
+<a name="115"><span class="lineNum">     115 </span>            :   double domainMin; // Minimum value of the CV domain</a>
+<a name="116"><span class="lineNum">     116 </span>            :   friend class boost::serialization::access;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   /// Use boost serialization</a>
+<a name="118"><span class="lineNum">     118 </span>            :   template &lt;typename Archive&gt;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         52 :   void save(Archive &amp;ar, const unsigned int version) const {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         52 :     ar &amp;min;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         52 :     ar &amp;max;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         52 :     ar &amp;nbins;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         52 :     ar &amp;periodic;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         52 :     ar &amp;domainMax;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         52 :     ar &amp;domainMin;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         52 :   }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   /// Split save and load. The bin width is calculated after initialization.</a>
+<a name="128"><span class="lineNum">     128 </span>            :   template &lt;typename Archive&gt;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         22 :   void load(Archive &amp;ar, const unsigned int version) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         22 :     ar &amp;min;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         22 :     ar &amp;max;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         22 :     ar &amp;nbins;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         22 :     ar &amp;periodic;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         22 :     ar &amp;domainMax;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         22 :     ar &amp;domainMin;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         22 :     binWidth = (max - min) / double(nbins);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         22 :   }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   template &lt;typename Archive&gt;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void serialize(Archive &amp;ar, const unsigned int version) {</a>
+<a name="140"><span class="lineNum">     140 </span>            :     boost::serialization::split_member(ar, *this, version);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : private:</a>
+<a name="144"><span class="lineNum">     144 </span>            :   double binWidth; // bin width</a>
+<a name="145"><span class="lineNum">     145 </span>            : };</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : /// A class for collecting instantaneous forces, calculating average forces and</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// build CV histogram.</a>
+<a name="149"><span class="lineNum">     149 </span>            : class DRRForceGrid {</a>
+<a name="150"><span class="lineNum">     150 </span>            : public:</a>
+<a name="151"><span class="lineNum">     151 </span>            :   /// Empty constructor</a>
+<a name="152"><span class="lineNum">     152 </span>            :   DRRForceGrid();</a>
+<a name="153"><span class="lineNum">     153 </span>            :   /// &quot;Real&quot; constructor</a>
+<a name="154"><span class="lineNum">     154 </span>            :   /// The 2D table vector is mainly used for print grid points in grad and count</a>
+<a name="155"><span class="lineNum">     155 </span>            :   /// file.</a>
+<a name="156"><span class="lineNum">     156 </span>            :   /// So when use binary output we can set initializeTable to false to save</a>
+<a name="157"><span class="lineNum">     157 </span>            :   /// memory.</a>
+<a name="158"><span class="lineNum">     158 </span>            :   explicit DRRForceGrid(const vector&lt;DRRAxis&gt; &amp;p_dimensions,</a>
+<a name="159"><span class="lineNum">     159 </span>            :                         const string &amp;p_suffix,</a>
+<a name="160"><span class="lineNum">     160 </span>            :                         bool initializeTable = true);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   /// Check whether a point is in this grid</a>
+<a name="162"><span class="lineNum">     162 </span>            :   bool isInBoundary(const vector&lt;double&gt; &amp;pos) const;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //  /// Get internal indices of a point</a>
+<a name="164"><span class="lineNum">     164 </span>            :   //  vector&lt;size_t&gt; index(const vector&lt;double&gt; &amp;pos) const;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   /// Get internal counts address of a point</a>
+<a name="166"><span class="lineNum">     166 </span>            :   size_t sampleAddress(const vector&lt;double&gt; &amp;pos) const;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   /// Store instantaneous forces of a point</a>
+<a name="168"><span class="lineNum">     168 </span>            :   /// nsamples &gt; 1 is useful for merging windows</a>
+<a name="169"><span class="lineNum">     169 </span>            :   bool store(const vector&lt;double&gt; &amp;pos, const vector&lt;double&gt; &amp;f,</a>
+<a name="170"><span class="lineNum">     170 </span>            :              unsigned long int nsamples = 1);</a>
+<a name="171"><span class="lineNum">     171 </span>            :   /// Get accumulated forces of a point</a>
+<a name="172"><span class="lineNum">     172 </span>            :   vector&lt;double&gt;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   getAccumulatedForces(const vector&lt;double&gt; &amp;pos) const;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   /// Get counts of a point</a>
+<a name="175"><span class="lineNum">     175 </span>            :   unsigned long int getCount(const vector&lt;double&gt; &amp;pos,</a>
+<a name="176"><span class="lineNum">     176 </span>            :                              bool SkipCheck = false) const;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   /// Virtual function! get gradients of a point</a>
+<a name="178"><span class="lineNum">     178 </span>            :   /// CZAR and naive(ABF) have different gradient formulae</a>
+<a name="179"><span class="lineNum">     179 </span>            :   virtual vector&lt;double&gt; getGradient(const vector&lt;double&gt; &amp;pos,</a>
+<a name="180"><span class="lineNum">     180 </span>            :                                      bool SkipCheck = false) const;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   /// Calculate divergence of the mean force field (experimental)</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double getDivergence(const vector&lt;double&gt; &amp;pos) const;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   /// Calculate dln(�)/dz, useful for CZAR</a>
+<a name="184"><span class="lineNum">     184 </span>            :   /// This function may be moved to CZAR class in the future</a>
+<a name="185"><span class="lineNum">     185 </span>            :   vector&lt;double&gt;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   getCountsLogDerivative(const vector&lt;double&gt; &amp;pos) const;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   /// Write grad file</a>
+<a name="188"><span class="lineNum">     188 </span>            : //   void writeGrad(string filename) const;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   /// Write 1D pmf file on one dimensional occasion</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void write1DPMF(string filename) const;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   /// Write count file</a>
+<a name="192"><span class="lineNum">     192 </span>            : //   void writeCount(string filename) const;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   /// Write necessary output file in one function (.grad and .count)</a>
+<a name="194"><span class="lineNum">     194 </span>            :   void writeAll(const string &amp;filename, bool addition = false) const;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   /// Output divergence (.div) (experimental)</a>
+<a name="196"><span class="lineNum">     196 </span>            :   void writeDivergence(const string &amp;filename) const;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   /// merge windows</a>
+<a name="198"><span class="lineNum">     198 </span>            :   static vector&lt;DRRAxis&gt; merge(const vector&lt;DRRAxis&gt; &amp;dA,</a>
+<a name="199"><span class="lineNum">     199 </span>            :                                const vector&lt;DRRAxis&gt; &amp;dB);</a>
+<a name="200"><span class="lineNum">     200 </span>            :   /// Get suffix</a>
+<a name="201"><span class="lineNum">     201 </span>            :   string getSuffix() const { return suffix; }</a>
+<a name="202"><span class="lineNum">     202 </span>            :   /// Set unit for .grad output</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          4 :   void setOutputUnit(double unit) { outputunit = unit; }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   /// Destructor</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        228 :   virtual ~DRRForceGrid() {}</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : protected:</a>
+<a name="208"><span class="lineNum">     208 </span>            :   /// The output suffix appended before .grad(.czar.grad) and</a>
+<a name="209"><span class="lineNum">     209 </span>            :   /// .count(.czar.count)</a>
+<a name="210"><span class="lineNum">     210 </span>            :   string suffix;</a>
+<a name="211"><span class="lineNum">     211 </span>            :   /// Number of dimensions</a>
+<a name="212"><span class="lineNum">     212 </span>            :   size_t ndims;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   /// Store each axes</a>
+<a name="214"><span class="lineNum">     214 </span>            :   vector&lt;DRRAxis&gt; dimensions;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   /// Size of samples</a>
+<a name="216"><span class="lineNum">     216 </span>            :   size_t sampleSize;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   /// The header lines of .grad and .count files</a>
+<a name="218"><span class="lineNum">     218 </span>            :   string headers;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   /// A table stores the middle points of all dimensions.</a>
+<a name="220"><span class="lineNum">     220 </span>            :   /// For output in .grad and .count files</a>
+<a name="221"><span class="lineNum">     221 </span>            :   vector&lt;vector&lt;double&gt;&gt; table;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   /// Store the average force of each bins</a>
+<a name="223"><span class="lineNum">     223 </span>            :   vector&lt;double&gt; forces;</a>
+<a name="224"><span class="lineNum">     224 </span>            :   /// Store counts of each bins</a>
+<a name="225"><span class="lineNum">     225 </span>            :   vector&lt;unsigned long int&gt; samples;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   /// Only for 1D pmf output</a>
+<a name="227"><span class="lineNum">     227 </span>            :   vector&lt;double&gt; endpoints;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   /// For faster indexing</a>
+<a name="229"><span class="lineNum">     229 </span>            :   /// shifts[0] = 1, shifts[n+1] = shifts[n] * dimensions[n].nbins</a>
+<a name="230"><span class="lineNum">     230 </span>            :   vector&lt;size_t&gt; shifts;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   /// For set different output units</a>
+<a name="232"><span class="lineNum">     232 </span>            :   double outputunit;</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            :   /// Miscellaneous helper functions</a>
+<a name="235"><span class="lineNum">     235 </span>            :   static size_t index1D(const DRRAxis &amp;c, double x);</a>
+<a name="236"><span class="lineNum">     236 </span>            :   void fillTable(const vector&lt;vector&lt;double&gt;&gt; &amp;in);</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            :   /// Boost serialization functions</a>
+<a name="239"><span class="lineNum">     239 </span>            :   friend class boost::serialization::access;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   template &lt;class Archive&gt;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         38 :   void save(Archive &amp;ar, const unsigned int version) const {</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     // Don't save all members.</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         38 :     ar &lt;&lt; suffix;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         38 :     ar &lt;&lt; dimensions;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         38 :     ar &lt;&lt; forces;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         38 :     ar &lt;&lt; samples;</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         38 :   }</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         16 :   template &lt;class Archive&gt; void load(Archive &amp;ar, const unsigned int version) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         16 :     ar &gt;&gt; suffix;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         16 :     ar &gt;&gt; dimensions;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         16 :     ar &gt;&gt; forces;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         16 :     ar &gt;&gt; samples;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     // Restore other members.</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         16 :     ndims = dimensions.size();</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         16 :     sampleSize = samples.size();</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         16 :     std::stringstream ss;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         16 :     ss &lt;&lt; &quot;# &quot; &lt;&lt; ndims &lt;&lt; '\n';</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         16 :     vector&lt;vector&lt;double&gt;&gt; mp(ndims);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         16 :     shifts.resize(ndims, 0);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         16 :     shifts[0] = 1;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         38 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         22 :       mp[i] = dimensions[i].getMiddlePoints();</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         22 :       if (i &gt; 0) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          6 :         shifts[i] = shifts[i - 1] * dimensions[i - 1].nbins;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :       }</a>
+<a name="266"><span class="lineNum">     266 </span>            :       ss.precision(std::numeric_limits&lt;double&gt;::max_digits10);</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         44 :       ss &lt;&lt; std::fixed &lt;&lt; &quot;# &quot; &lt;&lt; dimensions[i].min &lt;&lt; ' '</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         44 :          &lt;&lt; dimensions[i].binWidth &lt;&lt; ' ' &lt;&lt; dimensions[i].nbins;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         22 :       if (dimensions[i].isPeriodic())</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         24 :         ss &lt;&lt; &quot; 1&quot; &lt;&lt; '\n';</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :       else</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         20 :         ss &lt;&lt; &quot; 0&quot; &lt;&lt; '\n';</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         16 :     fillTable(mp);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         16 :     headers = ss.str();</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         16 :     outputunit = 1.0;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :     // For 1D pmf</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         16 :     if (ndims == 1) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         10 :       endpoints.resize(dimensions[0].nbins + 1, 0);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         10 :       double ep = dimensions[0].min;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         10 :       double stride = dimensions[0].binWidth;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       1020 :       for (auto it = begin(endpoints); it != end(endpoints); ++it) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       1010 :         (*it) = ep;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       1010 :         ep += stride;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :       }</a>
+<a name="286"><span class="lineNum">     286 </span>            :     }</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         16 :   }</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   template &lt;typename Archive&gt;</a>
+<a name="289"><span class="lineNum">     289 </span>            :   void serialize(Archive &amp;ar, const unsigned int version) {</a>
+<a name="290"><span class="lineNum">     290 </span>            :     boost::serialization::split_member(ar, *this, version);</a>
+<a name="291"><span class="lineNum">     291 </span>            :   }</a>
+<a name="292"><span class="lineNum">     292 </span>            : };</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : class ABF : public DRRForceGrid {</a>
+<a name="295"><span class="lineNum">     295 </span>            : public:</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         16 :   ABF() {}</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          2 :   ABF(const vector&lt;DRRAxis&gt; &amp;p_dimensions, const string &amp;p_suffix,</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :       double fullSamples = 500.0, double maxFactor = 1.0,</a>
+<a name="299"><span class="lineNum">     299 </span>            :       bool initializeTable = true)</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          2 :     : DRRForceGrid(p_dimensions, p_suffix, initializeTable),</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          2 :       mFullSamples(fullSamples), mMaxFactors(p_dimensions.size(), maxFactor) {}</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         11 :   ABF(const vector&lt;DRRAxis&gt; &amp;p_dimensions, const string &amp;p_suffix,</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :       double fullSamples, const vector&lt;double&gt;&amp; maxFactors,</a>
+<a name="304"><span class="lineNum">     304 </span>            :       bool initializeTable = true)</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         11 :     : DRRForceGrid(p_dimensions, p_suffix, initializeTable),</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         11 :       mFullSamples(fullSamples), mMaxFactors(maxFactors) {}</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   // Provide a setter for ABF parametres (fullsamples, maxfactor)</a>
+<a name="308"><span class="lineNum">     308 </span>            :   void setParameters(double fullSamples, const vector&lt;double&gt;&amp; maxFactors) {</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          1 :     mFullSamples = fullSamples;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          1 :     mMaxFactors = maxFactors;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          1 :   }</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   // Store the &quot;instantaneous&quot; spring force of a point and get ABF bias forces.</a>
+<a name="313"><span class="lineNum">     313 </span>            :   bool store_getbias(const vector&lt;double&gt; &amp;pos,</a>
+<a name="314"><span class="lineNum">     314 </span>            :                      const vector&lt;double&gt; &amp;f,</a>
+<a name="315"><span class="lineNum">     315 </span>            :                      vector&lt;double&gt; &amp;fbias);</a>
+<a name="316"><span class="lineNum">     316 </span>            :   static ABF mergewindow(const ABF &amp;aWA, const ABF &amp;aWB);</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         38 :   ~ABF() {}</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            : private:</a>
+<a name="320"><span class="lineNum">     320 </span>            :   // Parametres for calculate bias force</a>
+<a name="321"><span class="lineNum">     321 </span>            :   double mFullSamples;</a>
+<a name="322"><span class="lineNum">     322 </span>            :   vector&lt;double&gt; mMaxFactors;</a>
+<a name="323"><span class="lineNum">     323 </span>            :   // Boost serialization</a>
+<a name="324"><span class="lineNum">     324 </span>            :   friend class boost::serialization::access;</a>
+<a name="325"><span class="lineNum">     325 </span>            :   template &lt;typename Archive&gt;</a>
+<a name="326"><span class="lineNum">     326 </span>            :   void serialize(Archive &amp;ar, const unsigned int version) {</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         27 :     ar &amp;boost::serialization::base_object&lt;DRRForceGrid&gt;(*this);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :   }</a>
+<a name="329"><span class="lineNum">     329 </span>            : };</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         28 : class CZAR : public DRRForceGrid {</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : public:</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         16 :   CZAR() : kbt(0) {}</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :   CZAR(const vector&lt;DRRAxis&gt; &amp;p_dimensions, const string &amp;p_suffix,</a>
+<a name="335"><span class="lineNum">     335 </span>            :        double p_kbt, bool initializeTable = true)</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         13 :     : DRRForceGrid(p_dimensions, p_suffix, initializeTable), kbt(p_kbt) {}</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   vector&lt;double&gt; getGradient(const vector&lt;double&gt; &amp;pos,</a>
+<a name="338"><span class="lineNum">     338 </span>            :                              bool SkipCheck = false) const;</a>
+<a name="339"><span class="lineNum">     339 </span>            :   double getkbt() const { return kbt; }</a>
+<a name="340"><span class="lineNum">     340 </span>            :   void setkbt(double p_kbt) { kbt = p_kbt; }</a>
+<a name="341"><span class="lineNum">     341 </span>            :   static CZAR mergewindow(const CZAR &amp;cWA, const CZAR &amp;cWB);</a>
+<a name="342"><span class="lineNum">     342 </span>            :   void writeZCountZGrad(const string &amp;filename, bool addition = false) const;</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         23 :   ~CZAR() {}</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            : private:</a>
+<a name="346"><span class="lineNum">     346 </span>            :   double kbt;</a>
+<a name="347"><span class="lineNum">     347 </span>            :   friend class boost::serialization::access;</a>
+<a name="348"><span class="lineNum">     348 </span>            :   template &lt;typename Archive&gt;</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         27 :   void serialize(Archive &amp;ar, const unsigned int version) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         27 :     ar &amp;boost::serialization::base_object&lt;DRRForceGrid&gt;(*this);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         27 :     ar &amp;kbt;</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         27 :   }</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : };</a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : #endif</a>
+<a name="358"><span class="lineNum">     358 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/DynamicReferenceRestraining.cpp.func-sort-c.html b/coverage/drr/DynamicReferenceRestraining.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5032386335
--- /dev/null
+++ b/coverage/drr/DynamicReferenceRestraining.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DynamicReferenceRestraining.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DynamicReferenceRestraining.cpp<span style="font-size: 80%;"> (<a href="DynamicReferenceRestraining.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">403</td>
+            <td class="headerCovTableEntry">444</td>
+            <td class="headerCovTableEntryHi">90.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DynamicReferenceRestraining.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#332">_ZN4PLMD3drr27DynamicReferenceRestrainingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#707">_ZN4PLMD3drr27DynamicReferenceRestraining9calculateEv</a></td>
+              <td class="coverFnHi">123</td>
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+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
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+</html>
diff --git a/coverage/drr/DynamicReferenceRestraining.cpp.func.html b/coverage/drr/DynamicReferenceRestraining.cpp.func.html
new file mode 100644
index 0000000000..68c5ef5544
--- /dev/null
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+</head>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DynamicReferenceRestraining.cpp<span style="font-size: 80%;"> (<a href="DynamicReferenceRestraining.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">403</td>
+            <td class="headerCovTableEntry">444</td>
+            <td class="headerCovTableEntryHi">90.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#243">_ZN4PLMD3drr12_GLOBAL__N_140DynamicReferenceRestrainingRegisterMe2456createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#243">_ZN4PLMD3drr12_GLOBAL__N_140DynamicReferenceRestrainingRegisterMe245C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#243">_ZN4PLMD3drr12_GLOBAL__N_140DynamicReferenceRestrainingRegisterMe245D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#865">_ZN4PLMD3drr27DynamicReferenceRestraining10backupFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#887">_ZN4PLMD3drr27DynamicReferenceRestraining13is_file_existEPKc</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#245">_ZN4PLMD3drr27DynamicReferenceRestraining16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#845">_ZN4PLMD3drr27DynamicReferenceRestraining4loadERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#835">_ZN4PLMD3drr27DynamicReferenceRestraining4saveERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEx</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#799">_ZN4PLMD3drr27DynamicReferenceRestraining6updateEv</a></td>
+              <td class="coverFnHi">123</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#707">_ZN4PLMD3drr27DynamicReferenceRestraining9calculateEv</a></td>
+              <td class="coverFnHi">123</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#332">_ZN4PLMD3drr27DynamicReferenceRestrainingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicReferenceRestraining.cpp.gcov.html#332">_ZN4PLMD3drr27DynamicReferenceRestrainingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/drr/DynamicReferenceRestraining.cpp.gcov.html b/coverage/drr/DynamicReferenceRestraining.cpp.gcov.html
new file mode 100644
index 0000000000..61e0b2dc25
--- /dev/null
+++ b/coverage/drr/DynamicReferenceRestraining.cpp.gcov.html
@@ -0,0 +1,972 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/DynamicReferenceRestraining.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - DynamicReferenceRestraining.cpp<span style="font-size: 80%;"> (source / <a href="DynamicReferenceRestraining.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">403</td>
+            <td class="headerCovTableEntry">444</td>
+            <td class="headerCovTableEntryHi">90.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :     Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)</a>
+<a name="3"><span class="lineNum">       3 </span>            :     Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :     This program is free software: you can redistribute it and/or modify</a>
+<a name="6"><span class="lineNum">       6 </span>            :     it under the terms of the GNU Lesser General Public License as published</a>
+<a name="7"><span class="lineNum">       7 </span>            :     by the Free Software Foundation, either version 3 of the License, or</a>
+<a name="8"><span class="lineNum">       8 </span>            :     (at your option) any later version.</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            :     This program is distributed in the hope that it will be useful,</a>
+<a name="11"><span class="lineNum">      11 </span>            :     but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="12"><span class="lineNum">      12 </span>            :     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="13"><span class="lineNum">      13 </span>            :     GNU Lesser General Public License for more details.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            :     You should have received a copy of the GNU Lesser General Public License</a>
+<a name="16"><span class="lineNum">      16 </span>            :     along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="17"><span class="lineNum">      17 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="18"><span class="lineNum">      18 </span>            : #ifdef __PLUMED_HAS_BOOST_SERIALIZATION</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;DRR.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;colvar_UIestimator.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;boost/archive/binary_iarchive.hpp&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;boost/archive/binary_oarchive.hpp&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;boost/serialization/vector.hpp&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cmath&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;fstream&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;iomanip&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;iostream&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;limits&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;random&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;string&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : using namespace PLMD;</a>
+<a name="40"><span class="lineNum">      40 </span>            : using namespace bias;</a>
+<a name="41"><span class="lineNum">      41 </span>            : using namespace std;</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace PLMD {</a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace drr {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : //+PLUMEDOC EABFMOD_BIAS DRR</a>
+<a name="47"><span class="lineNum">      47 </span>            : /*</a>
+<a name="48"><span class="lineNum">      48 </span>            : Used to performed extended-system adaptive biasing force(eABF)</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : This method was introduced in \cite Lelievre2007.  It is used</a>
+<a name="51"><span class="lineNum">      51 </span>            :  on one or more collective variables. This method is also</a>
+<a name="52"><span class="lineNum">      52 </span>            :  called dynamic reference restraining(DRR) \cite Zheng2012 . A detailed description</a>
+<a name="53"><span class="lineNum">      53 </span>            :  of this module can be found at \cite Chen2018 .</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : For each collective variable \f$\xi_i\f$, a fictitious variable \f$\lambda_i\f$</a>
+<a name="56"><span class="lineNum">      56 </span>            : is attached through a spring. The fictitious variable \f$\lambda_i\f$ undergoes</a>
+<a name="57"><span class="lineNum">      57 </span>            : overdamped Langevin dynamics just like \ref EXTENDED_LAGRANGIAN. The ABF</a>
+<a name="58"><span class="lineNum">      58 </span>            : algorithm applies bias force on \f$\lambda_i\f$. The bias force acts on</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f$\lambda_i\f$ is the negative average spring force on \f$\lambda_i\f$, which</a>
+<a name="60"><span class="lineNum">      60 </span>            : enhances the sampling of \f$\lambda_i\f$.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \f[</a>
+<a name="63"><span class="lineNum">      63 </span>            : F_{bias}(\lambda_i)=k(\lambda_i-\langle\xi_i\rangle_{\lambda_i})</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f]</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : If spring force constant k is large enough, then \f$\xi_i\f$ synchronizes with</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f$\lambda_i\f$. The naive(ABF) estimator is just the negative</a>
+<a name="68"><span class="lineNum">      68 </span>            : average spring force of \f$\lambda_i\f$.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : The naive(ABF) estimator is biased. There are unbiased estimators such as</a>
+<a name="71"><span class="lineNum">      71 </span>            : CZAR(Corrected z-averaged restraint) \cite Lesage2016 and UI(Umbrella</a>
+<a name="72"><span class="lineNum">      72 </span>            : Integration).</a>
+<a name="73"><span class="lineNum">      73 </span>            : The CZAR estimates the gradients as:</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : \f[</a>
+<a name="76"><span class="lineNum">      76 </span>            : \frac{\partial{A}}{\partial{\xi_i}}\left({\xi}\right)=-\frac{1}{\beta}\frac{\partial\ln\tilde{\rho}\left(\xi\right)}{\partial{\xi_i}}+k\left(\langle\lambda_i\rangle_\xi-\xi_i\right)</a>
+<a name="77"><span class="lineNum">      77 </span>            : \f]</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : The UI estimates the gradients as:</a>
+<a name="80"><span class="lineNum">      80 </span>            : \f[</a>
+<a name="81"><span class="lineNum">      81 </span>            : A'(\xi^*)=\frac{{\sum_\lambda}N\left(\xi^*,\lambda\right)\left[\frac{\xi^*-\langle\xi\rangle_\lambda}{\beta\sigma_\lambda^2}-k(\xi^*-\lambda)\right]}{{\sum_\lambda}N\left(\xi^*,\lambda\right)}</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f]</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : The code performing UI(colvar_UIestimator.h) is contributed by Haohao Fu \cite Fu2016 .</a>
+<a name="85"><span class="lineNum">      85 </span>            : It may be slow. I only change the Boltzmann constant and output</a>
+<a name="86"><span class="lineNum">      86 </span>            : precision in it. For new version and issues, please see:</a>
+<a name="87"><span class="lineNum">      87 </span>            : https://github.com/fhh2626/colvars</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : After running eABF/DRR, the \ref drr_tool utility can be used to extract the gradients and counts files from .drrstate. Naive(ABF) estimator's result is in .abf.grad and .abf.count files and CZAR estimator's result is in .czar.grad and .czar.count files. The additional .zcount and .zgrad files contain the number of samples of \f$\boldsymbol{\xi}\f$, and the negative of \f$\boldsymbol{\xi}\f$-averaged spring forces, respectively, which are mainly for inspecting and debugging purpose. To get PMF, the abf_integrate(https://github.com/Colvars/colvars/tree/master/colvartools) is useful for numerically integrating the .czar.grad file.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \par Examples</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : The following input tells plumed to perform a eABF/DRR simulation on two</a>
+<a name="94"><span class="lineNum">      94 </span>            : torsional angles.</a>
+<a name="95"><span class="lineNum">      95 </span>            : \plumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="97"><span class="lineNum">      97 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : DRR ...</a>
+<a name="100"><span class="lineNum">     100 </span>            : LABEL=eabf</a>
+<a name="101"><span class="lineNum">     101 </span>            : ARG=phi,psi</a>
+<a name="102"><span class="lineNum">     102 </span>            : FULLSAMPLES=500</a>
+<a name="103"><span class="lineNum">     103 </span>            : GRID_MIN=-pi,-pi</a>
+<a name="104"><span class="lineNum">     104 </span>            : GRID_MAX=pi,pi</a>
+<a name="105"><span class="lineNum">     105 </span>            : GRID_BIN=180,180</a>
+<a name="106"><span class="lineNum">     106 </span>            : FRICTION=8.0,8.0</a>
+<a name="107"><span class="lineNum">     107 </span>            : TAU=0.5,0.5</a>
+<a name="108"><span class="lineNum">     108 </span>            : OUTPUTFREQ=50000</a>
+<a name="109"><span class="lineNum">     109 </span>            : HISTORYFREQ=500000</a>
+<a name="110"><span class="lineNum">     110 </span>            : ... DRR</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : # monitor the two variables, their fictitious variables and applied forces.</a>
+<a name="113"><span class="lineNum">     113 </span>            : PRINT STRIDE=10 ARG=phi,psi,eabf.phi_fict,eabf.psi_fict,eabf.phi_biasforce,eabf.psi_biasforce FILE=COLVAR</a>
+<a name="114"><span class="lineNum">     114 </span>            : \endplumedfile</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : The following input tells plumed to perform a eABF/DRR simulation on the</a>
+<a name="117"><span class="lineNum">     117 </span>            : distance of atom 10 and 92. The distance is restraint by \ref LOWER_WALLS and</a>
+<a name="118"><span class="lineNum">     118 </span>            : \ref UPPER_WALLS.</a>
+<a name="119"><span class="lineNum">     119 </span>            : \plumedfile</a>
+<a name="120"><span class="lineNum">     120 </span>            : dist1: DISTANCE ATOMS=10,92</a>
+<a name="121"><span class="lineNum">     121 </span>            : eabf_winall: DRR ARG=dist1 FULLSAMPLES=2000 GRID_MIN=1.20 GRID_MAX=3.20 GRID_BIN=200 FRICTION=8.0 TAU=0.5 OUTPUTFREQ=5000 HISTORYFREQ=500000</a>
+<a name="122"><span class="lineNum">     122 </span>            : uwall: UPPER_WALLS ARG=eabf_winall.dist1_fict AT=3.2 KAPPA=418.4</a>
+<a name="123"><span class="lineNum">     123 </span>            : lwall: LOWER_WALLS ARG=eabf_winall.dist1_fict AT=1.2 KAPPA=418.4</a>
+<a name="124"><span class="lineNum">     124 </span>            : PRINT STRIDE=10 ARG=dist1,eabf_winall.dist1_fict,eabf_winall.dist1_biasforce FILE=COLVAR</a>
+<a name="125"><span class="lineNum">     125 </span>            : \endplumedfile</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : It's also possible to run extended generalized adaptive biasing force (egABF) described in \cite Zhao2017 .</a>
+<a name="128"><span class="lineNum">     128 </span>            : An egABF example:</a>
+<a name="129"><span class="lineNum">     129 </span>            : \plumedfile</a>
+<a name="130"><span class="lineNum">     130 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="131"><span class="lineNum">     131 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : DRR ...</a>
+<a name="134"><span class="lineNum">     134 </span>            : LABEL=gabf_phi</a>
+<a name="135"><span class="lineNum">     135 </span>            : ARG=phi</a>
+<a name="136"><span class="lineNum">     136 </span>            : FULLSAMPLES=500</a>
+<a name="137"><span class="lineNum">     137 </span>            : GRID_MIN=-pi</a>
+<a name="138"><span class="lineNum">     138 </span>            : GRID_MAX=pi</a>
+<a name="139"><span class="lineNum">     139 </span>            : GRID_BIN=180</a>
+<a name="140"><span class="lineNum">     140 </span>            : FRICTION=8.0</a>
+<a name="141"><span class="lineNum">     141 </span>            : TAU=0.5</a>
+<a name="142"><span class="lineNum">     142 </span>            : OUTPUTFREQ=50000</a>
+<a name="143"><span class="lineNum">     143 </span>            : HISTORYFREQ=500000</a>
+<a name="144"><span class="lineNum">     144 </span>            : ... DRR</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : DRR ...</a>
+<a name="147"><span class="lineNum">     147 </span>            : LABEL=gabf_psi</a>
+<a name="148"><span class="lineNum">     148 </span>            : ARG=psi</a>
+<a name="149"><span class="lineNum">     149 </span>            : FULLSAMPLES=500</a>
+<a name="150"><span class="lineNum">     150 </span>            : GRID_MIN=-pi</a>
+<a name="151"><span class="lineNum">     151 </span>            : GRID_MAX=pi</a>
+<a name="152"><span class="lineNum">     152 </span>            : GRID_BIN=180</a>
+<a name="153"><span class="lineNum">     153 </span>            : FRICTION=8.0</a>
+<a name="154"><span class="lineNum">     154 </span>            : TAU=0.5</a>
+<a name="155"><span class="lineNum">     155 </span>            : OUTPUTFREQ=50000</a>
+<a name="156"><span class="lineNum">     156 </span>            : HISTORYFREQ=500000</a>
+<a name="157"><span class="lineNum">     157 </span>            : ... DRR</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : DRR ...</a>
+<a name="160"><span class="lineNum">     160 </span>            : LABEL=gabf_2d</a>
+<a name="161"><span class="lineNum">     161 </span>            : ARG=phi,psi</a>
+<a name="162"><span class="lineNum">     162 </span>            : EXTERNAL_FORCE=gabf_phi.phi_springforce,gabf_psi.psi_springforce</a>
+<a name="163"><span class="lineNum">     163 </span>            : EXTERNAL_FICT=gabf_phi.phi_fictNoPBC,gabf_psi.psi_fictNoPBC</a>
+<a name="164"><span class="lineNum">     164 </span>            : GRID_MIN=-pi,-pi</a>
+<a name="165"><span class="lineNum">     165 </span>            : GRID_MAX=pi,pi</a>
+<a name="166"><span class="lineNum">     166 </span>            : GRID_BIN=180,180</a>
+<a name="167"><span class="lineNum">     167 </span>            : NOBIAS</a>
+<a name="168"><span class="lineNum">     168 </span>            : OUTPUTFREQ=50000</a>
+<a name="169"><span class="lineNum">     169 </span>            : HISTORYFREQ=500000</a>
+<a name="170"><span class="lineNum">     170 </span>            : ... DRR</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : PRINT STRIDE=10 ARG=phi,psi FILE=COLVAR</a>
+<a name="173"><span class="lineNum">     173 </span>            : \endplumedfile</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :  */</a>
+<a name="176"><span class="lineNum">     176 </span>            : //+ENDPLUMEDOC</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : using std::vector;</a>
+<a name="179"><span class="lineNum">     179 </span>            : using std::string;</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : class DynamicReferenceRestraining : public Bias {</a>
+<a name="182"><span class="lineNum">     182 </span>            : private:</a>
+<a name="183"><span class="lineNum">     183 </span>            :   bool firsttime;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   bool nobias;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   vector&lt;double&gt; fictNoPBC;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   vector&lt;double&gt; real;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   vector&lt;double&gt; springlength; // spring lengths</a>
+<a name="188"><span class="lineNum">     188 </span>            :   vector&lt;double&gt; fict;         // coordinates of extended variables</a>
+<a name="189"><span class="lineNum">     189 </span>            :   vector&lt;double&gt; vfict;        // velocities of extended variables</a>
+<a name="190"><span class="lineNum">     190 </span>            :   vector&lt;double&gt; vfict_laststep;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   vector&lt;double&gt; ffict; // forces exerted on extended variables</a>
+<a name="192"><span class="lineNum">     192 </span>            :   vector&lt;double&gt; fbias; // bias forces from eABF</a>
+<a name="193"><span class="lineNum">     193 </span>            :   vector&lt;double&gt; kappa;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   vector&lt;double&gt; tau;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   vector&lt;double&gt; friction;</a>
+<a name="196"><span class="lineNum">     196 </span>            :   vector&lt;double&gt; etemp;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   vector&lt;double&gt; ffict_measured;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   vector&lt;double&gt; force_external;</a>
+<a name="199"><span class="lineNum">     199 </span>            :   vector&lt;double&gt; fict_external;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   vector&lt;Value *&gt; biasforceValue;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   vector&lt;Value *&gt; springforceValue;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   vector&lt;Value *&gt; fictValue;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   vector&lt;Value *&gt; vfictValue;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   vector&lt;Value *&gt; fictNoPBCValue;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   vector&lt;Value *&gt; externalForceValue;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   vector&lt;Value *&gt; externalFictValue;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   vector&lt;double&gt; c1;</a>
+<a name="208"><span class="lineNum">     208 </span>            :   vector&lt;double&gt; c2;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   vector&lt;double&gt; mass;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   vector&lt;DRRAxis&gt; delim;</a>
+<a name="211"><span class="lineNum">     211 </span>            :   string outputname;</a>
+<a name="212"><span class="lineNum">     212 </span>            :   string cptname;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   string outputprefix;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   const size_t ndims;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   double dt;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   double kbt;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   double outputfreq;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   double historyfreq;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   bool isRestart;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   bool useCZARestimator;</a>
+<a name="221"><span class="lineNum">     221 </span>            :   bool useUIestimator;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   bool mergeHistoryFiles;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   bool textoutput;</a>
+<a name="224"><span class="lineNum">     224 </span>            :   bool withExternalForce;</a>
+<a name="225"><span class="lineNum">     225 </span>            :   bool withExternalFict;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   vector&lt;unsigned&gt; reflectingWall;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   ABF ABFGrid;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   CZAR CZARestimator;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   double fullsamples;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   vector&lt;double&gt; maxFactors;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   UIestimator::UIestimator eabf_UI;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   Random rand;</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : public:</a>
+<a name="235"><span class="lineNum">     235 </span>            :   explicit DynamicReferenceRestraining(const ActionOptions &amp;);</a>
+<a name="236"><span class="lineNum">     236 </span>            :   void calculate();</a>
+<a name="237"><span class="lineNum">     237 </span>            :   void update();</a>
+<a name="238"><span class="lineNum">     238 </span>            :   void save(const string &amp;filename, long long int step);</a>
+<a name="239"><span class="lineNum">     239 </span>            :   void load(const string &amp;filename);</a>
+<a name="240"><span class="lineNum">     240 </span>            :   void backupFile(const string &amp;filename);</a>
+<a name="241"><span class="lineNum">     241 </span>            :   static void registerKeywords(Keywords &amp;keys);</a>
+<a name="242"><span class="lineNum">     242 </span>            :   bool is_file_exist(const char *fileName);</a>
+<a name="243"><span class="lineNum">     243 </span>            : };</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(DynamicReferenceRestraining, &quot;DRR&quot;)</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         14 : void DynamicReferenceRestraining::registerKeywords(Keywords &amp;keys) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         14 :   Bias::registerKeywords(keys);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         14 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;KAPPA&quot;, &quot;specifies that the restraint is harmonic and &quot;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :            &quot;what the values of the force constants on &quot;</a>
+<a name="252"><span class="lineNum">     252 </span>            :            &quot;each of the variables are (default to &quot;</a>
+<a name="253"><span class="lineNum">     253 </span>            :            &quot;\\f$k_BT\\f$/(GRID_SPACING)^2)&quot;);</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;TAU&quot;, &quot;0.5&quot;, &quot;specifies relaxation time on each of &quot;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :            &quot;variables are, similar to &quot;</a>
+<a name="256"><span class="lineNum">     256 </span>            :            &quot;extended Time Constant in Colvars&quot;);</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;FRICTION&quot;, &quot;8.0&quot;,</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :            &quot;add a friction to the variable, similar to extended Langevin Damping &quot;</a>
+<a name="259"><span class="lineNum">     259 </span>            :            &quot;in Colvars&quot;);</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;GRID_MIN&quot;, &quot;the lower bounds for the grid (GRID_BIN &quot;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :            &quot;or GRID_SPACING should be specified)&quot;);</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;GRID_MAX&quot;, &quot;the upper bounds for the grid (GRID_BIN &quot;</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :            &quot;or GRID_SPACING should be specified)&quot;);</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;REFLECTINGWALL&quot;, &quot;0&quot;, &quot;whether add reflecting walls &quot;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :            &quot;for each CV at GRID_MIN and GRID_MAX. Setting non-zero values will &quot;</a>
+<a name="266"><span class="lineNum">     266 </span>            :            &quot;enable this feature&quot;);</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;GRID_BIN&quot;, &quot;the number of bins for the grid&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;GRID_SPACING&quot;, &quot;the approximate grid spacing (to be &quot;</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :            &quot;used as an alternative or together &quot;</a>
+<a name="270"><span class="lineNum">     270 </span>            :            &quot;with GRID_BIN)&quot;);</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;ZGRID_MIN&quot;, &quot;the lower bounds for the grid (ZGRID_BIN&quot;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :            &quot; or ZGRID_SPACING should be specified)&quot;);</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;ZGRID_MAX&quot;, &quot;the upper bounds for the grid (ZGRID_BIN&quot;</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :            &quot; or ZGRID_SPACING should be specified)&quot;);</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;ZGRID_BIN&quot;, &quot;the number of bins for the grid&quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;ZGRID_SPACING&quot;, &quot;the approximate grid spacing (to be &quot;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :            &quot;used as an alternative or together &quot;</a>
+<a name="278"><span class="lineNum">     278 </span>            :            &quot;with ZGRID_BIN)&quot;);</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;EXTERNAL_FORCE&quot;, &quot;use forces from other action instead&quot;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :            &quot; of internal spring force, this disable the extended system!&quot;);</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;EXTERNAL_FICT&quot;, &quot;position of external fictitious &quot;</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :            &quot;particles, useful for UIESTIMATOR&quot;);</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;FULLSAMPLES&quot;, &quot;500&quot;,</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :            &quot;number of samples in a bin prior to application of the ABF&quot;);</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;MAXFACTOR&quot;, &quot;1.0&quot;,</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :            &quot;maximum scaling factor of biasing force&quot;);</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;OUTPUTFREQ&quot;, &quot;write results to a file every N steps&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;HISTORYFREQ&quot;, &quot;save history to a file every N steps&quot;);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         28 :   keys.addFlag(&quot;NOCZAR&quot;, false, &quot;disable the CZAR estimator&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         28 :   keys.addFlag(&quot;UI&quot;, false,</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :                &quot;enable the umbrella integration estimator&quot;);</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;UIRESTARTPREFIX&quot;,</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :            &quot;specify the restart files for umbrella integration&quot;);</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;OUTPUTPREFIX&quot;,</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :            &quot;specify the output prefix (default to the label name)&quot;);</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;TEMP&quot;, &quot;the system temperature - needed when FRICTION &quot;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :            &quot;is present. If not provided will be taken from &quot;</a>
+<a name="298"><span class="lineNum">     298 </span>            :            &quot;MD code (if available)&quot;);</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         28 :   keys.add(</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     &quot;optional&quot;, &quot;EXTTEMP&quot;,</a>
+<a name="301"><span class="lineNum">     301 </span>            :     &quot;the temperature of extended variables (default to system temperature)&quot;);</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;, &quot;DRR_RFILE&quot;,</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :            &quot;specifies the restart file (.drrstate file)&quot;);</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         28 :   keys.addFlag(&quot;NOBIAS&quot;, false, &quot;DO NOT apply bias forces.&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         28 :   keys.addFlag(&quot;TEXTOUTPUT&quot;, false, &quot;use text output for grad and count files &quot;</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :                &quot;instead of boost::serialization binary &quot;</a>
+<a name="307"><span class="lineNum">     307 </span>            :                &quot;output&quot;);</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         28 :   keys.addFlag(&quot;MERGEHISTORYFILES&quot;, false, &quot;output all historic results &quot;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :                &quot;to a single file rather than multiple .drrstate files. &quot;</a>
+<a name="310"><span class="lineNum">     310 </span>            :                &quot;This option is effective only when textOutput is on.&quot;);</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         14 :   componentsAreNotOptional(keys);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         28 :   keys.addOutputComponent(</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :     &quot;_fict&quot;, &quot;default&quot;,</a>
+<a name="314"><span class="lineNum">     314 </span>            :     &quot;one or multiple instances of this quantity can be referenced &quot;</a>
+<a name="315"><span class="lineNum">     315 </span>            :     &quot;elsewhere in the input file. &quot;</a>
+<a name="316"><span class="lineNum">     316 </span>            :     &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="317"><span class="lineNum">     317 </span>            :     &quot;the character string _tilde. It is possible to add forces on these &quot;</a>
+<a name="318"><span class="lineNum">     318 </span>            :     &quot;variable.&quot;);</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         28 :   keys.addOutputComponent(</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :     &quot;_vfict&quot;, &quot;default&quot;,</a>
+<a name="321"><span class="lineNum">     321 </span>            :     &quot;one or multiple instances of this quantity can be referenced &quot;</a>
+<a name="322"><span class="lineNum">     322 </span>            :     &quot;elsewhere in the input file. &quot;</a>
+<a name="323"><span class="lineNum">     323 </span>            :     &quot;These quantities will named with the arguments of the bias followed by &quot;</a>
+<a name="324"><span class="lineNum">     324 </span>            :     &quot;the character string _tilde. It is NOT possible to add forces on these &quot;</a>
+<a name="325"><span class="lineNum">     325 </span>            :     &quot;variable.&quot;);</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         28 :   keys.addOutputComponent(</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     &quot;_biasforce&quot;, &quot;default&quot;,</a>
+<a name="328"><span class="lineNum">     328 </span>            :     &quot;The bias force from eABF/DRR of the fictitious particle.&quot;);</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         28 :   keys.addOutputComponent(&quot;_springforce&quot;, &quot;default&quot;, &quot;Spring force between real CVs and extended CVs&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         28 :   keys.addOutputComponent(&quot;_fictNoPBC&quot;, &quot;default&quot;,</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :                           &quot;the positions of fictitious particles (without PBC).&quot;);</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         14 : }</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         12 : DynamicReferenceRestraining::DynamicReferenceRestraining(</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         12 :   const ActionOptions &amp;ao)</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         12 :   : PLUMED_BIAS_INIT(ao), firsttime(true), nobias(false),</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         12 :     fictNoPBC(getNumberOfArguments(), 0.0), real(getNumberOfArguments(), 0.0),</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         12 :     springlength(getNumberOfArguments(), 0.0),</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         12 :     fict(getNumberOfArguments(), 0.0), vfict(getNumberOfArguments(), 0.0),</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         12 :     vfict_laststep(getNumberOfArguments(), 0.0),</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         12 :     ffict(getNumberOfArguments(), 0.0), fbias(getNumberOfArguments(), 0.0),</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         12 :     kappa(getNumberOfArguments(), 0.0), tau(getNumberOfArguments(), 0.0),</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         12 :     friction(getNumberOfArguments(), 0.0), etemp(getNumberOfArguments(), 0.0),</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         12 :     ffict_measured(getNumberOfArguments(), 0.0),</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         12 :     biasforceValue(getNumberOfArguments(), NULL),</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         12 :     springforceValue(getNumberOfArguments(), NULL),</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         12 :     fictValue(getNumberOfArguments(), NULL),</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         12 :     vfictValue(getNumberOfArguments(), NULL),</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         12 :     fictNoPBCValue(getNumberOfArguments(), NULL),</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         12 :     externalForceValue(getNumberOfArguments(), NULL),</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         12 :     externalFictValue(getNumberOfArguments(), NULL),</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         12 :     c1(getNumberOfArguments(), 0.0),</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         12 :     c2(getNumberOfArguments(), 0.0), mass(getNumberOfArguments(), 0.0),</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         12 :     delim(getNumberOfArguments()), outputname(&quot;&quot;), cptname(&quot;&quot;),</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         12 :     outputprefix(&quot;&quot;), ndims(getNumberOfArguments()), dt(0.0), kbt(0.0),</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         12 :     outputfreq(0.0), historyfreq(-1.0), isRestart(false),</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         12 :     useCZARestimator(true), useUIestimator(false), mergeHistoryFiles(false),</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         12 :     textoutput(false), withExternalForce(false), withExternalFict(false),</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         12 :     reflectingWall(getNumberOfArguments(), 0),</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         36 :     maxFactors(getNumberOfArguments(), 1.0)</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : {</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: You now are using the extended adaptive biasing &quot;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :       &quot;force(eABF) method.&quot;</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: Some people also refer to it as dynamic reference &quot;</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :       &quot;restraining(DRR) method.&quot;</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: Currently the CZAR and naive(ABF on extended variables) &quot;</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :       &quot;estimator is enabled by default.&quot;</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: For reasons of performance, the umbrella integration &quot;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :       &quot;estimator is not enabled by default.&quot;</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: This method is originally implemented in &quot;</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :       &quot;colvars(https://github.com/colvars/colvars).&quot;</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: The code in plumed is heavily modified from &quot;</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :       &quot;ExtendedLagrangian.cpp and doesn't implemented all variants of &quot;</a>
+<a name="379"><span class="lineNum">     379 </span>            :       &quot;eABF/DRR.&quot;</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: The thermostat used here may be different from Colvars.&quot;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: To integrate the gradients file, you can use abf_integrate &quot;</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :       &quot;from https://github.com/colvars/colvars/tree/master/colvartools.&quot;</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: Please read relevant articles and use this biasing &quot;</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :       &quot;method carefully!&quot;</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         12 :       &lt;&lt; '\n';</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         12 :   parseFlag(&quot;NOBIAS&quot;, nobias);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         12 :   parseFlag(&quot;UI&quot;, useUIestimator);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         12 :   bool noCZAR = false;</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         12 :   parseFlag(&quot;NOCZAR&quot;, noCZAR);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : //   noCZAR == false ? useCZARestimator = true : useCZARestimator = false;</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         12 :   parseFlag(&quot;TEXTOUTPUT&quot;, textoutput);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         12 :   parseFlag(&quot;MERGEHISTORYFILES&quot;, mergeHistoryFiles);</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         12 :   parseVector(&quot;TAU&quot;, tau);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         12 :   parseVector(&quot;FRICTION&quot;, friction);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         12 :   parseVector(&quot;EXTTEMP&quot;, etemp);</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         12 :   parseVector(&quot;KAPPA&quot;, kappa);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         12 :   parseVector(&quot;REFLECTINGWALL&quot;, reflectingWall);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         12 :   double temp = -1.0;</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         12 :   parse(&quot;TEMP&quot;, temp);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         12 :   parse(&quot;FULLSAMPLES&quot;, fullsamples);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         12 :   parseVector(&quot;MAXFACTOR&quot;, maxFactors);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         12 :   parse(&quot;OUTPUTFREQ&quot;, outputfreq);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         12 :   parse(&quot;HISTORYFREQ&quot;, historyfreq);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         24 :   parse(&quot;OUTPUTPREFIX&quot;, outputprefix);</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :   string restart_prefix;</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         24 :   parse(&quot;DRR_RFILE&quot;, restart_prefix);</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   string uirprefix;</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         12 :   parse(&quot;UIRESTARTPREFIX&quot;, uirprefix);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         12 :   parseArgumentList(&quot;EXTERNAL_FORCE&quot;, externalForceValue);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         24 :   parseArgumentList(&quot;EXTERNAL_FICT&quot;, externalFictValue);</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         12 :   if (externalForceValue.empty()) {</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">         11 :     withExternalForce = false;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          1 :   } else if (externalForceValue.size() != ndims) {</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :     error(&quot;eABF/DRR: Number of forces doesn't match ARGS!&quot;);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :   } else {</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          1 :     withExternalForce = true;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         12 :   if (withExternalForce &amp;&amp; useUIestimator) {</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          1 :     if (externalFictValue.empty()) {</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :       error(&quot;eABF/DRR: No external fictitious particles specified. UI estimator needs it.&quot;);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          1 :     } else if(externalFictValue.size() != ndims) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :       error(&quot;eABF/DRR: Number of fictitious particles doesn't match ARGS!&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     } else {</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          1 :       withExternalFict = true;</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :     }</a>
+<a name="429"><span class="lineNum">     429 </span>            :   }</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         12 :   if (temp &gt;= 0.0)</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         12 :     kbt = plumed.getAtoms().getKBoltzmann() * temp;</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :   else {</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :     kbt = plumed.getAtoms().getKbT();</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     if (kbt &lt;= std::numeric_limits&lt;double&gt;::epsilon()) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :       error(&quot;eABF/DRR: It seems the MD engine does not setup the temperature correctly for PLUMED.&quot;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :             &quot;Please set it by the TEMP keyword manually.&quot;);</a>
+<a name="437"><span class="lineNum">     437 </span>            :     }</a>
+<a name="438"><span class="lineNum">     438 </span>            :   }</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         12 :   if (fullsamples &lt; 0.5) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :     fullsamples = 500.0;</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;eABF/DRR: The fullsamples parametre is not set. Set it to &quot;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :         &quot;500(default).&quot;</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :         &lt;&lt; '\n';</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         12 :   if (getRestart()) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          1 :     if (restart_prefix.length() != 0) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          1 :       isRestart = true;</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          1 :       firsttime = false;</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          1 :       load(restart_prefix);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :     } else {</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :       log &lt;&lt; &quot;eABF/DRR: You don't specify the file for restarting.&quot; &lt;&lt; '\n';</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :       log &lt;&lt; &quot;eABF/DRR: So I assume you are splitting windows.&quot; &lt;&lt; '\n';</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :       isRestart = false;</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :       firsttime = true;</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :     }</a>
+<a name="456"><span class="lineNum">     456 </span>            :   }</a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         12 :   vector&lt;string&gt; gmin(ndims);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         12 :   vector&lt;string&gt; zgmin(ndims);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         12 :   parseVector(&quot;GRID_MIN&quot;, gmin);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         24 :   parseVector(&quot;ZGRID_MIN&quot;, zgmin);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         12 :   if (gmin.size() != ndims)</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :     error(&quot;eABF/DRR: not enough values for GRID_MIN&quot;);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         12 :   if (zgmin.size() != ndims) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         33 :     log &lt;&lt; &quot;eABF/DRR: You didn't specify ZGRID_MIN. &quot; &lt;&lt; '\n'</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         11 :         &lt;&lt; &quot;eABF/DRR: The GRID_MIN will be used instead.&quot;;</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         11 :     zgmin = gmin;</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :   }</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         12 :   vector&lt;string&gt; gmax(ndims);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         12 :   vector&lt;string&gt; zgmax(ndims);</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         12 :   parseVector(&quot;GRID_MAX&quot;, gmax);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         24 :   parseVector(&quot;ZGRID_MAX&quot;, zgmax);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         12 :   if (gmax.size() != ndims)</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :     error(&quot;eABF/DRR: not enough values for GRID_MAX&quot;);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         12 :   if (zgmax.size() != ndims) {</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         33 :     log &lt;&lt; &quot;eABF/DRR: You didn't specify ZGRID_MAX. &quot; &lt;&lt; '\n'</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">         11 :         &lt;&lt; &quot;eABF/DRR: The GRID_MAX will be used instead.&quot;;</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         11 :     zgmax = gmax;</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :   }</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         12 :   vector&lt;unsigned&gt; gbin(ndims);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         12 :   vector&lt;unsigned&gt; zgbin(ndims);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         12 :   vector&lt;double&gt; gspacing(ndims);</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         12 :   vector&lt;double&gt; zgspacing(ndims);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         12 :   parseVector(&quot;GRID_BIN&quot;, gbin);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         12 :   parseVector(&quot;ZGRID_BIN&quot;, zgbin);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         12 :   parseVector(&quot;GRID_SPACING&quot;, gspacing);</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">         24 :   parseVector(&quot;ZGRID_SPACING&quot;, zgspacing);</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         12 :   if (gbin.size() != ndims) {</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          3 :     log &lt;&lt; &quot;eABF/DRR: You didn't specify GRID_BIN. Trying to use GRID_SPACING &quot;</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :         &quot;instead.&quot;</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          3 :         &lt;&lt; '\n';</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          3 :     if (gspacing.size() != ndims) {</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :       error(&quot;eABF/DRR: not enough values for GRID_BIN&quot;);</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :     } else {</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          3 :       gbin.resize(ndims);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          6 :       for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :         double l, h;</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          3 :         PLMD::Tools::convert(gmin[i], l);</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          3 :         PLMD::Tools::convert(gmax[i], h);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          3 :         gbin[i] = std::nearbyint((h - l) / gspacing[i]);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          3 :         gspacing[i] = (h - l) / gbin[i];</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          3 :         log &lt;&lt; &quot;GRID_BIN[&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot; &lt;&lt; gbin[i] &lt;&lt; '\n';</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :       }</a>
+<a name="504"><span class="lineNum">     504 </span>            :     }</a>
+<a name="505"><span class="lineNum">     505 </span>            :   }</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         12 :   if (zgbin.size() != ndims) {</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         11 :     log &lt;&lt; &quot;eABF/DRR: You didn't specify ZGRID_BIN. Trying to use ZGRID_SPACING instead.&quot; &lt;&lt; '\n';</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         11 :     if (zgspacing.size() != ndims) {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         11 :       log &lt;&lt; &quot;eABF/DRR: You didn't specify ZGRID_SPACING. Trying to use GRID_SPACING or GRID_BIN instead.&quot; &lt;&lt; '\n';</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">         11 :       zgbin = gbin;</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         11 :       zgspacing = gspacing;</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :     } else {</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :       zgbin.resize(ndims);</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :       for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :         double l, h;</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :         PLMD::Tools::convert(zgmin[i], l);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :         PLMD::Tools::convert(zgmax[i], h);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :         zgbin[i] = std::nearbyint((h - l) / zgspacing[i]);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :         zgspacing[i] = (h - l) / zgbin[i];</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :         log &lt;&lt; &quot;ZGRID_BIN[&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot; &lt;&lt; zgbin[i] &lt;&lt; '\n';</span></a>
+<a name="521"><span class="lineNum">     521 </span>            :       }</a>
+<a name="522"><span class="lineNum">     522 </span>            :     }</a>
+<a name="523"><span class="lineNum">     523 </span>            :   }</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         12 :   checkRead();</span></a>
+<a name="525"><span class="lineNum">     525 </span>            : </a>
+<a name="526"><span class="lineNum">     526 </span>            :   // Set up kbt for extended system</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: The fullsamples is &quot; &lt;&lt; fullsamples &lt;&lt; '\n';</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: The kbt(real system) is &quot; &lt;&lt; kbt &lt;&lt; '\n';</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         12 :   dt = getTimeStep() * getStride();</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;eABF/DRR: timestep = &quot; &lt;&lt; getTimeStep() &lt;&lt; &quot; ps with stride = &quot; &lt;&lt; getStride() &lt;&lt; &quot; steps\n&quot;;</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">         12 :   vector&lt;double&gt; ekbt(ndims, 0.0);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         12 :   if (etemp.size() != ndims) {</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         12 :     etemp.assign(ndims, kbt / plumed.getAtoms().getKBoltzmann());</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :   }</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         12 :   if (tau.size() != ndims) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineNoCov">          0 :     tau.assign(ndims, 0.5);</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :   }</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         12 :   if (friction.size() != ndims) {</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :     friction.assign(ndims, 8.0);</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :   }</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">         12 :   if (maxFactors.size() != ndims) {</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :     maxFactors.assign(ndims, 1.0);</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :   }</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         31 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The maximum scaling factor [&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot; &lt;&lt; maxFactors[i] &lt;&lt; '\n';</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         19 :     if (maxFactors[i] &gt; 1.0) {</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :       log &lt;&lt; &quot;eABF/DRR: Warning! The maximum scaling factor larger than 1.0 is not recommended!&quot; &lt;&lt; '\n';</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :     }</a>
+<a name="549"><span class="lineNum">     549 </span>            :   }</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         31 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         19 :     ekbt[i] = etemp[i] * plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The kbt(extended system) of [&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot; &lt;&lt; ekbt[i]</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         19 :         &lt;&lt; '\n';</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: relaxation time tau [&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot; &lt;&lt; tau[i] &lt;&lt; '\n';</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: Extended variable [&quot; &lt;&lt; i &lt;&lt; &quot;] has friction: &quot; &lt;&lt; friction[i] &lt;&lt; '\n';</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :   }</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            :   // Set up the force grid</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         12 :   vector&lt;DRRAxis&gt; zdelim(ndims);</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         31 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The &quot; &lt;&lt; i &lt;&lt; &quot; dimensional grid minimum is &quot; &lt;&lt; gmin[i]</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         19 :         &lt;&lt; '\n';</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The &quot; &lt;&lt; i &lt;&lt; &quot; dimensional grid maximum is &quot; &lt;&lt; gmax[i]</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         19 :         &lt;&lt; '\n';</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The &quot; &lt;&lt; i &lt;&lt; &quot; dimensional grid has &quot; &lt;&lt; gbin[i]</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         19 :         &lt;&lt; &quot; bins&quot; &lt;&lt; '\n';</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The &quot; &lt;&lt; i &lt;&lt; &quot; dimensional zgrid minimum is &quot; &lt;&lt; zgmin[i]</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         19 :         &lt;&lt; '\n';</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The &quot; &lt;&lt; i &lt;&lt; &quot; dimensional zgrid maximum is &quot; &lt;&lt; zgmax[i]</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">         19 :         &lt;&lt; '\n';</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: The &quot; &lt;&lt; i &lt;&lt; &quot; dimensional zgrid has &quot; &lt;&lt; zgbin[i]</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         19 :         &lt;&lt; &quot; bins&quot; &lt;&lt; '\n';</span></a>
+<a name="573"><span class="lineNum">     573 </span>            :     double l, h;</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         19 :     PLMD::Tools::convert(gmin[i], l);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         19 :     PLMD::Tools::convert(gmax[i], h);</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         19 :     delim[i].set(l, h, gbin[i]);</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :     double zl,zh;</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         19 :     PLMD::Tools::convert(zgmin[i], zl);</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         19 :     PLMD::Tools::convert(zgmax[i], zh);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         19 :     zdelim[i].set(zl, zh, zgbin[i]);</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :   }</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         12 :   if (kappa.size() != ndims) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">          9 :     kappa.resize(ndims, 0.0);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         25 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         16 :       if (kappa[i] &lt;= 0) {</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         16 :         log &lt;&lt; &quot;eABF/DRR: The spring force constant kappa[&quot; &lt;&lt; i</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         16 :             &lt;&lt; &quot;] is not set.&quot; &lt;&lt; '\n';</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         16 :         kappa[i] = ekbt[i] / (delim[i].getWidth() * delim[i].getWidth());</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         16 :         log &lt;&lt; &quot;eABF/DRR: set kappa[&quot; &lt;&lt; i</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         16 :             &lt;&lt; &quot;] according to bin width(ekbt/(binWidth^2)).&quot; &lt;&lt; '\n';</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :       }</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">         16 :       log &lt;&lt; &quot;eABF/DRR: The spring force constant kappa[&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot;</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         16 :           &lt;&lt; std::fixed &lt;&lt; std::setprecision(10) &lt;&lt; kappa[i] &lt;&lt; '\n';</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :     }</a>
+<a name="595"><span class="lineNum">     595 </span>            :   } else {</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">          3 :     log &lt;&lt; &quot;eABF/DRR: The kappa have been set manually.&quot; &lt;&lt; '\n';</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          6 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">          3 :       log &lt;&lt; &quot;eABF/DRR: The spring force constant kappa[&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot;</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">          3 :           &lt;&lt; std::fixed &lt;&lt; std::setprecision(10) &lt;&lt; kappa[i] &lt;&lt; '\n';</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :     }</a>
+<a name="601"><span class="lineNum">     601 </span>            :   }</a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         31 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         19 :     mass[i] = kappa[i] * tau[i] * tau[i] / (4 * pi * pi);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">         19 :     log &lt;&lt; &quot;eABF/DRR: Fictitious mass[&quot; &lt;&lt; i &lt;&lt; &quot;] is &quot; &lt;&lt; mass[i] &lt;&lt; '\n';</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">         19 :     c1[i] = exp(-0.5 * friction[i] * dt);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         19 :     c2[i] = sqrt(ekbt[i] * (1.0 - c1[i] * c1[i]) / mass[i]);</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :   }</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         31 :   for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :     // Position output</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         19 :     string comp = getPntrToArgument(i)-&gt;getName() + &quot;_fict&quot;;</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">         19 :     addComponentWithDerivatives(comp);</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         19 :     if (getPntrToArgument(i)-&gt;isPeriodic()) {</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :       string a, b;</a>
+<a name="616"><span class="lineNum">     616 </span>            :       double c, d;</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         16 :       getPntrToArgument(i)-&gt;getDomain(a, b);</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         16 :       getPntrToArgument(i)-&gt;getDomain(c, d);</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         16 :       componentIsPeriodic(comp, a, b);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         16 :       delim[i].setPeriodicity(c, d);</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :       zdelim[i].setPeriodicity(c, d);</a>
+<a name="622"><span class="lineNum">     622 </span>            :     } else</a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">          3 :       componentIsNotPeriodic(comp);</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">         19 :     fictValue[i] = getPntrToComponent(comp);</span></a>
+<a name="625"><span class="lineNum">     625 </span>            :     // Velocity output</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         19 :     comp = getPntrToArgument(i)-&gt;getName() + &quot;_vfict&quot;;</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         19 :     addComponent(comp);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         19 :     componentIsNotPeriodic(comp);</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">         19 :     vfictValue[i] = getPntrToComponent(comp);</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :     // Bias force from eABF/DRR output</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         19 :     comp = getPntrToArgument(i)-&gt;getName() + &quot;_biasforce&quot;;</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">         19 :     addComponent(comp);</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">         19 :     componentIsNotPeriodic(comp);</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">         19 :     biasforceValue[i] = getPntrToComponent(comp);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :     // Spring force output, useful for perform egABF and other analysis</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         19 :     comp = getPntrToArgument(i)-&gt;getName() + &quot;_springforce&quot;;</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">         19 :     addComponent(comp);</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">         19 :     componentIsNotPeriodic(comp);</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">         19 :     springforceValue[i] = getPntrToComponent(comp);</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :     // Position output, no pbc-aware</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">         19 :     comp = getPntrToArgument(i)-&gt;getName() + &quot;_fictNoPBC&quot;;</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">         19 :     addComponent(comp);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">         19 :     componentIsNotPeriodic(comp);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">         19 :     fictNoPBCValue[i] = getPntrToComponent(comp);</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :   }</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         12 :   if (outputprefix.length() == 0) {</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineNoCov">          0 :     outputprefix = getLabel();</span></a>
+<a name="649"><span class="lineNum">     649 </span>            :   }</a>
+<a name="650"><span class="lineNum">     650 </span>            :   // Support multiple replica</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         12 :   string replica_suffix = plumed.getSuffix();</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         12 :   if (replica_suffix.empty() == false) {</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">          4 :     outputprefix = outputprefix + replica_suffix;</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :   }</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         12 :   outputname = outputprefix + &quot;.drrstate&quot;;</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">         12 :   cptname = outputprefix + &quot;.cpt.drrstate&quot;;</span></a>
+<a name="657"><span class="lineNum">     657 </span>            : </a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">         12 :   if (!isRestart) {</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :     // If you want to use on-the-fly text output for CZAR and naive estimator,</a>
+<a name="660"><span class="lineNum">     660 </span>            :     // you should turn it to true first!</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         11 :     ABFGrid = ABF(delim, &quot;.abf&quot;, fullsamples, maxFactors, textoutput);</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :     // Just initialize it even useCZARestimator is off.</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         22 :     CZARestimator = CZAR(zdelim, &quot;.czar&quot;, kbt, textoutput);</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         11 :     log &lt;&lt; &quot;eABF/DRR: The init function of the grid is finished.&quot; &lt;&lt; '\n';</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :   } else {</a>
+<a name="666"><span class="lineNum">     666 </span>            :     // ABF Parametres are not saved in binary files</a>
+<a name="667"><span class="lineNum">     667 </span>            :     // So manully set them up</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">          1 :     ABFGrid.setParameters(fullsamples, maxFactors);</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :   }</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">         12 :   if (useCZARestimator) {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">         12 :     log &lt;&lt; &quot;eABF/DRR: Using corrected z-average restraint estimator of gradients&quot; &lt;&lt; '\n';</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">         12 :     log &lt;&lt; &quot;  Bibliography &quot; &lt;&lt; plumed.cite(&quot;Lesage, Lelièvre, Stoltz and Hénin, &quot;</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">         24 :                                             &quot;J. Phys. Chem. B 3676, 121 (2017)&quot;);</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">         12 :     log &lt;&lt; plumed.cite(&quot;Darve and Pohorille, J. Chem. Phys. 9169, 115 (2001)&quot;) &lt;&lt; '\n';</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :   }</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">         12 :   if (useUIestimator) {</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">          9 :     log &lt;&lt; &quot;eABF/DRR: Using umbrella integration(Zheng and Yang's) estimator &quot;</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :         &quot;of gradients.&quot;</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">          9 :         &lt;&lt; '\n';</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">          9 :     log &lt;&lt; &quot;eABF/DRR: The UI estimator code is contributed by Haohao Fu.&quot;</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">          9 :         &lt;&lt; '\n';</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         18 :     log &lt;&lt; &quot;  Bibliography &quot; &lt;&lt; plumed.cite(</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">         18 :           &quot;Fu, Shao, Chipot and Cai, J. Chem. Theory Comput. 3506, 12 (2016)&quot;);</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         18 :     log &lt;&lt; plumed.cite(&quot;Zheng and Yang, J. Chem. Theory Comput. 810, 8 (2012)&quot;);</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">          9 :     log &lt;&lt; plumed.cite(&quot;Darve and Pohorille, J. Chem. Phys. 9169, 115 (2001)&quot;) &lt;&lt; '\n';</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">          9 :     vector&lt;double&gt; lowerboundary(zdelim.size(), 0);</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">          9 :     vector&lt;double&gt; upperboundary(zdelim.size(), 0);</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">          9 :     vector&lt;double&gt; width(zdelim.size(), 0);</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">         24 :     for (size_t i = 0; i &lt; zdelim.size(); ++i) {</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         15 :       lowerboundary[i] = zdelim[i].getMin();</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         15 :       upperboundary[i] = zdelim[i].getMax();</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         15 :       width[i] = zdelim[i].getWidth();</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :     }</a>
+<a name="694"><span class="lineNum">     694 </span>            :     vector&lt;string&gt; input_filename;</a>
+<a name="695"><span class="lineNum">     695 </span>            :     bool uirestart = false;</a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">          9 :     if (isRestart &amp;&amp; (uirprefix.length() != 0)) {</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">          1 :       input_filename.push_back(uirprefix);</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :       uirestart = true;</a>
+<a name="699"><span class="lineNum">     699 </span>            :     }</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">          9 :     if (isRestart &amp;&amp; (uirprefix.length() == 0)) {</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :       input_filename.push_back(outputprefix);</span></a>
+<a name="702"><span class="lineNum">     702 </span>            :     }</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">          9 :     eabf_UI = UIestimator::UIestimator(</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">          9 :                 lowerboundary, upperboundary, width, kappa, outputprefix, int(outputfreq),</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         18 :                 uirestart, input_filename, kbt / plumed.getAtoms().getKBoltzmann());</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">          9 :   }</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         24 : }</span></a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">        123 : void DynamicReferenceRestraining::calculate() {</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">        123 :   long long int step_now = getStep();</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">        123 :   if (firsttime) {</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">         28 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">         17 :       fict[i] = getArgument(i);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">         17 :       if(reflectingWall[i] &amp;&amp; (fict[i]&gt;=delim[i].getMax() || fict[i]&lt;=delim[i].getMin())) {</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :         error(&quot;eABF/DRR: initial position not in the range of [gmin, gmax]!&quot;);</span></a>
+<a name="716"><span class="lineNum">     716 </span>            :       }</a>
+<a name="717"><span class="lineNum">     717 </span>            :     }</a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">         11 :     firsttime = false;</span></a>
+<a name="719"><span class="lineNum">     719 </span>            :   }</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">        123 :   if (step_now != 0) {</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">        111 :     if ((step_now % int(outputfreq)) == 0) {</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">         15 :       save(outputname, step_now);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">         15 :       if (textoutput) {</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">         10 :         ABFGrid.writeAll(outputprefix);</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">         10 :         if (useCZARestimator) {</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">         10 :           CZARestimator.writeAll(outputprefix);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">         10 :           CZARestimator.writeZCountZGrad(outputprefix);</span></a>
+<a name="728"><span class="lineNum">     728 </span>            :         }</a>
+<a name="729"><span class="lineNum">     729 </span>            :       }</a>
+<a name="730"><span class="lineNum">     730 </span>            :     }</a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">        111 :     if (historyfreq &gt; 0 &amp;&amp; (step_now % int(historyfreq)) == 0) {</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">          4 :       if (textoutput) {</span></a>
+<a name="733"><span class="lineNum">     733 </span>            :         const string filename =</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">          4 :           outputprefix + &quot;.another.drrstate&quot;;</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">          4 :         save(filename, step_now);</span></a>
+<a name="736"><span class="lineNum">     736 </span>            :         const string textfilename =</a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">          4 :           mergeHistoryFiles ? (outputprefix + &quot;.hist&quot;) : (outputprefix + &quot;.&quot; + std::to_string(step_now));</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">          4 :         ABFGrid.writeAll(textfilename, mergeHistoryFiles);</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">          4 :         if (useCZARestimator) {</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">          4 :           CZARestimator.writeAll(textfilename, mergeHistoryFiles);</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">          4 :           CZARestimator.writeZCountZGrad(textfilename, mergeHistoryFiles);</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :         }</a>
+<a name="743"><span class="lineNum">     743 </span>            :       } else {</a>
+<a name="744"><span class="lineNum">     744 </span>            :         const string filename =</a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :           outputprefix + &quot;.&quot; + std::to_string(step_now) + &quot;.drrstate&quot;;</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 :         save(filename, step_now);</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :       }</a>
+<a name="748"><span class="lineNum">     748 </span>            :     }</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">        111 :     if (getCPT()) {</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :       log &lt;&lt; &quot;eABF/DRR: The MD engine is writing checkpoint so we also write a &quot;</span></a>
+<a name="751"><span class="lineNum">     751 </span>            :           &quot;DRR state file at step: &quot;</a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineNoCov">          0 :           &lt;&lt; step_now &lt;&lt; &quot;.\n&quot;;</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :       save(cptname, step_now);</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :     }</a>
+<a name="755"><span class="lineNum">     755 </span>            :   }</a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">        123 :   if (withExternalForce == false) {</span></a>
+<a name="757"><span class="lineNum">     757 </span>            :     double ene = 0.0;</a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">        294 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">        183 :       real[i] = getArgument(i);</span></a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">        183 :       springlength[i] = difference(i, fict[i], real[i]);</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">        183 :       fictNoPBC[i] = real[i] - springlength[i];</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">        183 :       double f = -kappa[i] * springlength[i];</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">        183 :       ffict_measured[i] = -f;</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">        183 :       ene += 0.5 * kappa[i] * springlength[i] * springlength[i];</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :       setOutputForce(i, f);</a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">        183 :       ffict[i] = -f;</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">        183 :       fict[i] = fictValue[i]-&gt;bringBackInPbc(fict[i]);</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">        183 :       fictValue[i]-&gt;set(fict[i]);</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">        183 :       vfictValue[i]-&gt;set(vfict_laststep[i]);</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">        183 :       springforceValue[i]-&gt;set(ffict_measured[i]);</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">        183 :       fictNoPBCValue[i]-&gt;set(fictNoPBC[i]);</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :     }</a>
+<a name="773"><span class="lineNum">     773 </span>            :     setBias(ene);</a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">        111 :     ABFGrid.store_getbias(fict, ffict_measured, fbias);</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :   } else {</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">         36 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">         24 :       real[i] = getArgument(i);</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">         24 :       ffict_measured[i] = externalForceValue[i]-&gt;get();</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">         24 :       if (withExternalFict) {</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">         24 :         fictNoPBC[i] = externalFictValue[i]-&gt;get();</span></a>
+<a name="781"><span class="lineNum">     781 </span>            :       }</a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">         24 :       springforceValue[i]-&gt;set(ffict_measured[i]);</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">         24 :       fictNoPBCValue[i]-&gt;set(fictNoPBC[i]);</span></a>
+<a name="784"><span class="lineNum">     784 </span>            :     }</a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">         12 :     ABFGrid.store_getbias(real, ffict_measured, fbias);</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">         12 :     if (!nobias) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineNoCov">          0 :       for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineNoCov">          0 :         setOutputForce(i, fbias[i]);</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :       }</a>
+<a name="790"><span class="lineNum">     790 </span>            :     }</a>
+<a name="791"><span class="lineNum">     791 </span>            :   }</a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">        123 :   if (useCZARestimator) {</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">        123 :     CZARestimator.store(real, ffict_measured);</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :   }</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">        123 :   if (useUIestimator) {</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">         87 :     eabf_UI.update_output_filename(outputprefix);</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">        174 :     eabf_UI.update(int(step_now), real, fictNoPBC);</span></a>
+<a name="798"><span class="lineNum">     798 </span>            :   }</a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">        123 : }</span></a>
+<a name="800"><span class="lineNum">     800 </span>            : </a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">        123 : void DynamicReferenceRestraining::update() {</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">        123 :   if (withExternalForce == false) {</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">        294 :     for (size_t i = 0; i &lt; ndims; ++i) {</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :       // consider additional forces on the fictitious particle</a>
+<a name="805"><span class="lineNum">     805 </span>            :       // (e.g. MetaD stuff)</a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">        183 :       ffict[i] += fictValue[i]-&gt;getForce();</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">        183 :       if (!nobias) {</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">        183 :         ffict[i] += fbias[i];</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :       }</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">        183 :       biasforceValue[i]-&gt;set(fbias[i]);</span></a>
+<a name="811"><span class="lineNum">     811 </span>            :       // update velocity (half step)</a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">        183 :       vfict[i] += ffict[i] * 0.5 * dt / mass[i];</span></a>
+<a name="813"><span class="lineNum">     813 </span>            :       // thermostat (half step)</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">        183 :       vfict[i] = c1[i] * vfict[i] + c2[i] * rand.Gaussian();</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :       // save full step velocity to be dumped at next step</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">        183 :       vfict_laststep[i] = vfict[i];</span></a>
+<a name="817"><span class="lineNum">     817 </span>            :       // thermostat (half step)</a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">        183 :       vfict[i] = c1[i] * vfict[i] + c2[i] * rand.Gaussian();</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :       // update velocity (half step)</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">        183 :       vfict[i] += ffict[i] * 0.5 * dt / mass[i];</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :       // update position (full step)</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">        183 :       fict[i] += vfict[i] * dt;</span></a>
+<a name="823"><span class="lineNum">     823 </span>            :       // reflecting boundary</a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        183 :       if (reflectingWall[i]) {</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">         24 :         if (fict[i]&lt;delim[i].getMin()) {</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">          1 :           fict[i]=delim[i].getMin()+(delim[i].getMin()-fict[i]);</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">          1 :           vfict[i]*=-1.0;</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         23 :         } else if (fict[i]&gt;delim[i].getMax()) {</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineNoCov">          0 :           fict[i]=delim[i].getMax()-(fict[i]-delim[i].getMax());</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineNoCov">          0 :           vfict[i]*=-1.0;</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :         }</a>
+<a name="832"><span class="lineNum">     832 </span>            :       }</a>
+<a name="833"><span class="lineNum">     833 </span>            :     }</a>
+<a name="834"><span class="lineNum">     834 </span>            :   }</a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">        123 : }</span></a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">         19 : void DynamicReferenceRestraining::save(const string &amp;filename,</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :                                        long long int step) {</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">         19 :   std::ofstream out;</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">         19 :   out.open(filename.c_str(), std::ios::binary);</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">         19 :   boost::archive::binary_oarchive oa(out);</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">         19 :   oa &lt;&lt; step &lt;&lt; fict &lt;&lt; vfict &lt;&lt; vfict_laststep &lt;&lt; ffict &lt;&lt; ABFGrid</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         19 :      &lt;&lt; CZARestimator;</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">         19 :   out.close();</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">         19 : }</span></a>
+<a name="846"><span class="lineNum">     846 </span>            : </a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">          1 : void DynamicReferenceRestraining::load(const string &amp;rfile_prefix) {</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">          1 :   string replica_suffix = plumed.getSuffix();</span></a>
+<a name="849"><span class="lineNum">     849 </span>            :   string filename;</a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">          1 :   if (replica_suffix.empty() == true) {</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">          2 :     filename = rfile_prefix + &quot;.drrstate&quot;;</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :   } else {</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :     filename = rfile_prefix + &quot;.&quot; + replica_suffix + &quot;.drrstate&quot;;</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :   }</a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">          1 :   std::ifstream in;</span></a>
+<a name="856"><span class="lineNum">     856 </span>            :   long long int step;</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">          1 :   in.open(filename.c_str(), std::ios::binary);</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">          1 :   log &lt;&lt; &quot;eABF/DRR: Read restart file: &quot; &lt;&lt; filename &lt;&lt; '\n';</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">          1 :   boost::archive::binary_iarchive ia(in);</span></a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">          1 :   ia &gt;&gt; step &gt;&gt; fict &gt;&gt; vfict &gt;&gt; vfict_laststep &gt;&gt; ffict &gt;&gt; ABFGrid &gt;&gt;</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">          1 :      CZARestimator;</span></a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">          1 :   in.close();</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">          1 :   log &lt;&lt; &quot;eABF/DRR: Restart at step: &quot; &lt;&lt; step &lt;&lt; '\n';</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">          1 :   backupFile(filename);</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">          2 : }</span></a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">          1 : void DynamicReferenceRestraining::backupFile(const string &amp;filename) {</span></a>
+<a name="868"><span class="lineNum">     868 </span>            :   bool isSuccess = false;</a>
+<a name="869"><span class="lineNum">     869 </span>            :   long int i = 0;</a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">          2 :   while (!isSuccess) {</span></a>
+<a name="871"><span class="lineNum">     871 </span>            :     // If libstdc++ support C++17 we can simplify following code.</a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">          2 :     const string bckname = &quot;bck.&quot; + filename + &quot;.&quot; + std::to_string(i);</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">          1 :     if (is_file_exist(bckname.c_str())) {</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineNoCov">          0 :       ++i;</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :     } else {</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">          1 :       log &lt;&lt; &quot;eABF/DRR: Backup original restart file to &quot; &lt;&lt; bckname &lt;&lt; '\n';</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">          1 :       std::ifstream src(filename.c_str(), std::ios::binary);</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">          1 :       std::ofstream dst(bckname.c_str(), std::ios::binary);</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">          1 :       dst &lt;&lt; src.rdbuf();</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">          1 :       src.close();</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">          1 :       dst.close();</span></a>
+<a name="882"><span class="lineNum">     882 </span>            :       isSuccess = true;</a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">          1 :     }</span></a>
+<a name="884"><span class="lineNum">     884 </span>            :   }</a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">          1 : }</span></a>
+<a name="886"><span class="lineNum">     886 </span>            : </a>
+<a name="887"><span class="lineNum">     887 </span>            : // Copy from</a>
+<a name="888"><span class="lineNum">     888 </span>            : // stackoverflow(https://stackoverflow.com/questions/12774207/fastest-way-to-check-if-a-file-exist-using-standard-c-c11-c)</a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">          1 : bool DynamicReferenceRestraining::is_file_exist(const char *fileName) {</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">          1 :   std::ifstream infile(fileName);</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">          1 :   return infile.good();</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">          1 : }</span></a>
+<a name="893"><span class="lineNum">     893 </span>            : }</a>
+<a name="894"><span class="lineNum">     894 </span>            : }</a>
+<a name="895"><span class="lineNum">     895 </span>            : </a>
+<a name="896"><span class="lineNum">     896 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/colvar_UIestimator.h.func-sort-c.html b/coverage/drr/colvar_UIestimator.h.func-sort-c.html
new file mode 100644
index 0000000000..a883164ad8
--- /dev/null
+++ b/coverage/drr/colvar_UIestimator.h.func-sort-c.html
@@ -0,0 +1,208 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/colvar_UIestimator.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - colvar_UIestimator.h<span style="font-size: 80%;"> (<a href="colvar_UIestimator.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">299</td>
+            <td class="headerCovTableEntry">302</td>
+            <td class="headerCovTableEntryHi">99.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="colvar_UIestimator.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">7499</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">26790</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">171000</td>
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+            </tr>
+    <tr>
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+              <td class="coverFnHi">280499</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#218">_ZN4PLMD3drr11UIestimator8n_vectorIdE9convert_xERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">307607</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#155">_ZN4PLMD3drr11UIestimator8n_matrix5roundEd</a></td>
+              <td class="coverFnHi">1018791</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/colvar_UIestimator.h.func.html b/coverage/drr/colvar_UIestimator.h.func.html
new file mode 100644
index 0000000000..4522669bb4
--- /dev/null
+++ b/coverage/drr/colvar_UIestimator.h.func.html
@@ -0,0 +1,208 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/colvar_UIestimator.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - colvar_UIestimator.h<span style="font-size: 80%;"> (<a href="colvar_UIestimator.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">299</td>
+            <td class="headerCovTableEntry">302</td>
+            <td class="headerCovTableEntryHi">99.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="colvar_UIestimator.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#561">_ZN4PLMD3drr11UIestimator11UIestimator11calc_1D_pmfEv</a></td>
+              <td class="coverFnHi">9</td>
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+    <tr>
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+            </tr>
+    <tr>
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+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#202">_ZN4PLMD3drr11UIestimator8n_vectorIdE14increase_valueERKSt6vectorIdSaIdEERKd</a></td>
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+    <tr>
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+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#197">_ZN4PLMD3drr11UIestimator8n_vectorIdE9set_valueERKSt6vectorIdSaIdEERKd</a></td>
+              <td class="coverFnHi">26790</td>
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+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#167">_ZN4PLMD3drr11UIestimator8n_vectorIdEC2ERKSt6vectorIdSaIdEES8_S8_iRKd</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#166">_ZN4PLMD3drr11UIestimator8n_vectorIdEC2Ev</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#202">_ZN4PLMD3drr11UIestimator8n_vectorIiE14increase_valueERKSt6vectorIdSaIdEERKi</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#218">_ZN4PLMD3drr11UIestimator8n_vectorIiE9convert_xERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">7499</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#192">_ZN4PLMD3drr11UIestimator8n_vectorIiE9get_valueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">7196</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#197">_ZN4PLMD3drr11UIestimator8n_vectorIiE9set_valueERKSt6vectorIdSaIdEERKi</a></td>
+              <td class="coverFnHi">212</td>
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+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#167">_ZN4PLMD3drr11UIestimator8n_vectorIiEC2ERKSt6vectorIdSaIdEES8_S8_iRKi</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#166">_ZN4PLMD3drr11UIestimator8n_vectorIiEC2Ev</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="colvar_UIestimator.h.gcov.html#618">_ZNK4PLMD3drr11UIestimator11UIestimator9writeheadERSt14basic_ofstreamIcSt11char_traitsIcEE</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/colvar_UIestimator.h.gcov.html b/coverage/drr/colvar_UIestimator.h.gcov.html
new file mode 100644
index 0000000000..4e0a8aeb5e
--- /dev/null
+++ b/coverage/drr/colvar_UIestimator.h.gcov.html
@@ -0,0 +1,931 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/colvar_UIestimator.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - colvar_UIestimator.h<span style="font-size: 80%;"> (source / <a href="colvar_UIestimator.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">299</td>
+            <td class="headerCovTableEntry">302</td>
+            <td class="headerCovTableEntryHi">99.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :     Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)</a>
+<a name="3"><span class="lineNum">       3 </span>            :     Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :     This program is free software: you can redistribute it and/or modify</a>
+<a name="6"><span class="lineNum">       6 </span>            :     it under the terms of the GNU Lesser General Public License as published</a>
+<a name="7"><span class="lineNum">       7 </span>            :     by the Free Software Foundation, either version 3 of the License, or</a>
+<a name="8"><span class="lineNum">       8 </span>            :     (at your option) any later version.</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            :     This program is distributed in the hope that it will be useful,</a>
+<a name="11"><span class="lineNum">      11 </span>            :     but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="12"><span class="lineNum">      12 </span>            :     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="13"><span class="lineNum">      13 </span>            :     GNU Lesser General Public License for more details.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            :     You should have received a copy of the GNU Lesser General Public License</a>
+<a name="16"><span class="lineNum">      16 </span>            :     along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="17"><span class="lineNum">      17 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="18"><span class="lineNum">      18 </span>            : #ifndef __PLUMED_drr_colvar_UIestimator_h</a>
+<a name="19"><span class="lineNum">      19 </span>            : #define __PLUMED_drr_colvar_UIestimator_h</a>
+<a name="20"><span class="lineNum">      20 </span>            : // The original code(https://github.com/fhh2626/colvars/blob/master/src/colvar_UIestimator.h) has been modified by Haochuan Chen.</a>
+<a name="21"><span class="lineNum">      21 </span>            : // Modifications:</a>
+<a name="22"><span class="lineNum">      22 </span>            : // 1. Disable colvars related code.</a>
+<a name="23"><span class="lineNum">      23 </span>            : // 2. Change boltzmann constant.</a>
+<a name="24"><span class="lineNum">      24 </span>            : // 3. Change output precision.</a>
+<a name="25"><span class="lineNum">      25 </span>            : // I(Haochuan Chen) don't know how to maintain this code and how it runs. If you are interested in it, please contact Haohao Fu.</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;fstream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;string&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;iomanip&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;limits&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;typeinfo&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // only for colvar module!</a>
+<a name="37"><span class="lineNum">      37 </span>            : // when integrated into other code, just remove this line and &quot;...cvm::backup_file(...)&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : // #include &quot;colvarmodule.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace drr {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace UIestimator</a>
+<a name="44"><span class="lineNum">      44 </span>            : {</a>
+<a name="45"><span class="lineNum">      45 </span>            : const int Y_SIZE = 21;</a>
+<a name="46"><span class="lineNum">      46 </span>            : const int HALF_Y_SIZE = 10;</a>
+<a name="47"><span class="lineNum">      47 </span>            : const double BOLTZMANN = 0.0083144621;</a>
+<a name="48"><span class="lineNum">      48 </span>            : const int EXTENDED_X_SIZE = HALF_Y_SIZE;</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : class n_matrix    // spare matrix, stores the distribution matrix of n(x,y)</a>
+<a name="51"><span class="lineNum">      51 </span>            : {</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         21 :   n_matrix() {}</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          9 :   n_matrix(const std::vector&lt;double&gt; &amp; lowerboundary_p,   // lowerboundary of x</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :            const std::vector&lt;double&gt; &amp; upperboundary_p,   // upperboundary of</a>
+<a name="56"><span class="lineNum">      56 </span>            :            const std::vector&lt;double&gt; &amp; width_p,           // width of x</a>
+<a name="57"><span class="lineNum">      57 </span>            :            const int y_size)           // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          9 :     : lowerboundary(lowerboundary_p), upperboundary(upperboundary_p), width(width_p)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          9 :     this-&gt;dimension = lowerboundary.size();</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          9 :     this-&gt;y_size = y_size;     // keep in mind the internal (spare) matrix is stored in diagonal form</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          9 :     this-&gt;y_total_size = int(pow(y_size, dimension) + 0.000001);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :     // the range of the matrix is [lowerboundary, upperboundary]</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          9 :     x_total_size = 1;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         24 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     {</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         15 :       x_size.push_back(int((upperboundary[i] - lowerboundary[i]) / width[i] + 0.000001));</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         15 :       x_total_size *= x_size[i];</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :     // initialize the internal matrix</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          9 :     matrix.reserve(x_total_size);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        100 :     for (int i = 0; i &lt; x_total_size; i++)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     {</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        182 :       matrix.push_back(std::vector&lt;int&gt;(y_total_size, 0));</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          9 :     temp.resize(dimension);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          9 :   }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     171000 :   int inline get_value(const std::vector&lt;double&gt; &amp; x, const std::vector&lt;double&gt; &amp; y)</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   {</a>
+<a name="84"><span class="lineNum">      84 </span>            :     //if (matrix[convert_x(x)][convert_y(x, y)]!=0)</a>
+<a name="85"><span class="lineNum">      85 </span>            :     //{</a>
+<a name="86"><span class="lineNum">      86 </span>            :     //std::cout&lt;&lt;convert_x(x)&lt;&lt;&quot; &quot;&lt;&lt;convert_y(x, y)&lt;&lt;&quot; &quot;&lt;&lt;x[0]&lt;&lt;&quot; &quot;&lt;&lt;x[1]&lt;&lt;&quot; &quot;&lt;&lt;y[0]&lt;&lt;&quot; &quot;&lt;&lt;y[1]&lt;&lt;&quot; &quot;;</a>
+<a name="87"><span class="lineNum">      87 </span>            :     //std::cout&lt;&lt;matrix[convert_x(x)][convert_y(x, y)]&lt;&lt;&quot;sadasfdasaaaaaaaa&quot;&lt;&lt;std::endl;</a>
+<a name="88"><span class="lineNum">      88 </span>            :     //}</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     171000 :     return matrix[convert_x(x)][convert_y(x, y)];</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   void inline set_value(const std::vector&lt;double&gt; &amp; x, const std::vector&lt;double&gt; &amp; y, const int value)</a>
+<a name="93"><span class="lineNum">      93 </span>            :   {</a>
+<a name="94"><span class="lineNum">      94 </span>            :     matrix[convert_x(x)][convert_y(x,y)] = value;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         87 :   void inline increase_value(const std::vector&lt;double&gt; &amp; x, const std::vector&lt;double&gt; &amp; y, const int value)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   {</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         87 :     matrix[convert_x(x)][convert_y(x,y)] += value;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         87 :   }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : private:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;double&gt; lowerboundary;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;double&gt; upperboundary;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;double&gt; width;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   int dimension;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;int&gt; x_size;       // the size of x in each dimension</a>
+<a name="108"><span class="lineNum">     108 </span>            :   int x_total_size;              // the size of x of the internal matrix</a>
+<a name="109"><span class="lineNum">     109 </span>            :   int y_size;                    // the size of y in each dimension</a>
+<a name="110"><span class="lineNum">     110 </span>            :   int y_total_size;              // the size of y of the internal matrix</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;std::vector&lt;int&gt; &gt; matrix;  // the internal matrix</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;int&gt; temp;         // this vector is used in convert_x and convert_y to save computational resource</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     171087 :   int convert_x(const std::vector&lt;double&gt; &amp; x)        // convert real x value to its interal index</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     510684 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     {</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     339597 :       temp[i] = int((x[i] - lowerboundary[i]) / width[i] + 0.000001);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :     int index = 0;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     510684 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     {</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">     339597 :       if (i + 1 &lt; dimension)</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :       {</a>
+<a name="128"><span class="lineNum">     128 </span>            :         int x_temp = 1;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     337020 :         for (int j = i + 1; j &lt; dimension; j++)</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     168510 :           x_temp *= x_size[j];</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     168510 :         index += temp[i] * x_temp;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :       }</a>
+<a name="133"><span class="lineNum">     133 </span>            :       else</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     171087 :         index += temp[i];</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :     }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     171087 :     return index;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">     171087 :   int convert_y(const std::vector&lt;double&gt; &amp; x, const std::vector&lt;double&gt; &amp; y)        // convert real y value to its interal index</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   {</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">     510684 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">     339597 :       temp[i] = round((round(y[i] / width[i] + 0.000001) - round(x[i] / width[i] + 0.000001)) + (y_size - 1) / 2 + 0.000001);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :     int index = 0;</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">     510684 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     {</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">     339597 :       if (i + 1 &lt; dimension)</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">     168510 :         index += temp[i] * int(pow(y_size, dimension - i - 1) + 0.000001);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :       else</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     171087 :         index += temp[i];</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     171087 :     return index;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">    1018791 :   double round(double r)</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   {</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    1018791 :     return (r &gt; 0.0) ? floor(r + 0.5) : ceil(r - 0.5);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : };</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : // vector, store the sum_x, sum_x_square, count_y</a>
+<a name="164"><span class="lineNum">     164 </span>            : template &lt;typename T&gt;</a>
+<a name="165"><span class="lineNum">     165 </span>            : class n_vector</a>
+<a name="166"><span class="lineNum">     166 </span>            : {</a>
+<a name="167"><span class="lineNum">     167 </span>            : public:</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        126 :   n_vector() {}</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         92 :   n_vector(const std::vector&lt;double&gt; &amp; lowerboundary,   // lowerboundary of x</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :            const std::vector&lt;double&gt; &amp; upperboundary,   // upperboundary of</a>
+<a name="171"><span class="lineNum">     171 </span>            :            const std::vector&lt;double&gt; &amp; width_p,                // width of x</a>
+<a name="172"><span class="lineNum">     172 </span>            :            const int y_size,           // size of y, for example, ysize=7, then when x=1, the distribution of y in [-2,4] is considered</a>
+<a name="173"><span class="lineNum">     173 </span>            :            const T &amp; default_value)          //   the default value of T</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         92 :     :width(width_p)</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         92 :     this-&gt;dimension = lowerboundary.size();</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         92 :     x_total_size = 1;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        252 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        160 :       this-&gt;lowerboundary.push_back(lowerboundary[i] - (y_size - 1) / 2 * width[i] - 0.000001);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        160 :       this-&gt;upperboundary.push_back(upperboundary[i] + (y_size - 1) / 2 * width[i] + 0.000001);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        160 :       x_size.push_back(int((this-&gt;upperboundary[i] - this-&gt;lowerboundary[i]) / this-&gt;width[i] + 0.000001));</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        160 :       x_total_size *= x_size[i];</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :     // initialize the internal vector</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         92 :     vector.resize(x_total_size, default_value);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         92 :     temp.resize(dimension);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         92 :   }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     288432 :   T inline get_value(const std::vector&lt;double&gt; &amp; x)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     288432 :     return vector[convert_x(x)];</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      27227 :   void inline set_value(const std::vector&lt;double&gt; &amp; x, const T &amp; value)</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   {</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      27227 :     vector[convert_x(x)] = value;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      27227 :   }</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        409 :   void inline increase_value(const std::vector&lt;double&gt; &amp; x, const T &amp; value)</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   {</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        409 :     vector[convert_x(x)] += value;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        409 :   }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : private:</a>
+<a name="209"><span class="lineNum">     209 </span>            :   std::vector&lt;double&gt; lowerboundary;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   std::vector&lt;double&gt; upperboundary;</a>
+<a name="211"><span class="lineNum">     211 </span>            :   std::vector&lt;double&gt; width;</a>
+<a name="212"><span class="lineNum">     212 </span>            :   int dimension;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   std::vector&lt;int&gt; x_size;       // the size of x in each dimension</a>
+<a name="214"><span class="lineNum">     214 </span>            :   int x_total_size;              // the size of x of the internal matrix</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            :   std::vector&lt;T&gt; vector;  // the internal vector</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   std::vector&lt;int&gt; temp;         // this vector is used in convert_x and convert_y to save computational resource</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     316068 :   int convert_x(const std::vector&lt;double&gt; &amp; x)        // convert real x value to its interal index</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">     943161 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :     {</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     627093 :       temp[i] = int((x[i] - lowerboundary[i]) / width[i] + 0.000001);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :     int index = 0;</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">     943161 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :     {</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">     627093 :       if (i + 1 &lt; dimension)</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :       {</a>
+<a name="232"><span class="lineNum">     232 </span>            :         int x_temp = 1;</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">     622050 :         for (int j = i + 1; j &lt; dimension; j++)</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">     311025 :           x_temp *= x_size[j];</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     311025 :         index += temp[i] * x_temp;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :       }</a>
+<a name="237"><span class="lineNum">     237 </span>            :       else</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">     316068 :         index += temp[i];</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">     316068 :     return index;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span>            : };</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : class UIestimator      // the implemension of UI estimator</a>
+<a name="245"><span class="lineNum">     245 </span>            : {</a>
+<a name="246"><span class="lineNum">     246 </span>            : public:</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         12 :   UIestimator() {}</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   //called when (re)start an eabf simulation</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          9 :   UIestimator(const std::vector&lt;double&gt;&amp; lowerboundary_p,</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :               const std::vector&lt;double&gt;&amp; upperboundary_p,</a>
+<a name="252"><span class="lineNum">     252 </span>            :               const std::vector&lt;double&gt;&amp; width_p,</a>
+<a name="253"><span class="lineNum">     253 </span>            :               const std::vector&lt;double&gt;&amp; krestr_p,                // force constant in eABF</a>
+<a name="254"><span class="lineNum">     254 </span>            :               const std::string&amp; output_filename_p,              // the prefix of output files</a>
+<a name="255"><span class="lineNum">     255 </span>            :               const int output_freq_p,</a>
+<a name="256"><span class="lineNum">     256 </span>            :               const bool restart_p,                              // whether restart from a .count and a .grad file</a>
+<a name="257"><span class="lineNum">     257 </span>            :               const std::vector&lt;std::string&gt;&amp; input_filename_p,   // the prefixes of input files</a>
+<a name="258"><span class="lineNum">     258 </span>            :               const double temperature_p)</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          9 :     : lowerboundary(lowerboundary_p), upperboundary(upperboundary_p),</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          9 :       width(width_p), krestr(krestr_p),</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          9 :       output_filename(output_filename_p), output_freq(output_freq_p),</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          9 :       restart(restart_p), input_filename(input_filename_p),</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         18 :       temperature(temperature_p)</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :   {</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          9 :     dimension = lowerboundary.size();</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         24 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     {</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         30 :       sum_x.push_back(n_vector&lt;double&gt;(lowerboundary, upperboundary, width, Y_SIZE, 0.0));</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         30 :       sum_x_square.push_back(n_vector&lt;double&gt;(lowerboundary, upperboundary, width, Y_SIZE, 0.0));</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         30 :       x_av.push_back(n_vector&lt;double&gt;(lowerboundary, upperboundary, width, Y_SIZE, 0.0));</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         30 :       sigma_square.push_back(n_vector&lt;double&gt;(lowerboundary, upperboundary, width, Y_SIZE, 0.0));</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :     }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          9 :     count_y = n_vector&lt;int&gt;(lowerboundary, upperboundary, width, Y_SIZE, 0);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          9 :     distribution_x_y = n_matrix(lowerboundary, upperboundary, width, Y_SIZE);</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          9 :     grad = n_vector&lt;std::vector&lt;double&gt; &gt;(lowerboundary, upperboundary, width, 1, std::vector&lt;double&gt;(dimension, 0.0));</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          9 :     count = n_vector&lt;int&gt;(lowerboundary, upperboundary, width, 1, 0);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          9 :     written = false;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          9 :     written_1D = false;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          9 :     if (dimension == 1)</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :     {</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          3 :       std::vector&lt;double&gt; upperboundary_temp = upperboundary;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          3 :       upperboundary_temp[0] = upperboundary[0] + width[0];</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          3 :       oneD_pmf = n_vector&lt;double&gt;(lowerboundary, upperboundary_temp, width, 1, 0.0);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :     }</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          9 :     if (restart == true)</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :     {</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          1 :       input_grad = n_vector&lt;std::vector&lt;double&gt; &gt;(lowerboundary, upperboundary, width, 1, std::vector&lt;double&gt;(dimension, 0.0));</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          1 :       input_count = n_vector&lt;int&gt;(lowerboundary, upperboundary, width, 1, 0);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :       // initialize input_Grad and input_count</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          1 :       std::vector&lt;double&gt; loop_flag(dimension, 0);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          3 :       for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :       {</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          2 :         loop_flag[i] = lowerboundary[i];</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :       }</a>
+<a name="304"><span class="lineNum">     304 </span>            :       while (true)</a>
+<a name="305"><span class="lineNum">     305 </span>            :       {</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         27 :         for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :         {</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         36 :           input_grad.set_value(loop_flag, std::vector&lt;double&gt;(dimension,0));</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :         }</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          9 :         input_count.set_value(loop_flag, 0);</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            :         // iterate over any dimensions</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          9 :         int i = dimension - 1;</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :         while (true)</a>
+<a name="315"><span class="lineNum">     315 </span>            :         {</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         12 :           loop_flag[i] += width[i];</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         12 :           if (loop_flag[i] &gt; upperboundary[i] - width[i] + 0.00001)</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :           {</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          4 :             loop_flag[i] = lowerboundary[i];</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :             i--;</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          4 :             if (i &lt; 0)</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          1 :               goto INITIAL_LOOPEND;</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :           }</a>
+<a name="324"><span class="lineNum">     324 </span>            :           else</a>
+<a name="325"><span class="lineNum">     325 </span>            :             break;</a>
+<a name="326"><span class="lineNum">     326 </span>            :         }</a>
+<a name="327"><span class="lineNum">     327 </span>            :       }</a>
+<a name="328"><span class="lineNum">     328 </span>            : INITIAL_LOOPEND:</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          1 :       read_inputfiles(input_filename);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          9 :   }</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         42 :   ~UIestimator() {}</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :   // called from MD engine every step</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         87 :   bool update(const int step, std::vector&lt;double&gt; x, std::vector&lt;double&gt; y)</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   {</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            :     //std::cout&lt;&lt;&quot;weeeee: :&quot;&lt;&lt;std::endl;</a>
+<a name="340"><span class="lineNum">     340 </span>            :     //for (int i = 0; i &lt; dimension; i++)</a>
+<a name="341"><span class="lineNum">     341 </span>            :     //{</a>
+<a name="342"><span class="lineNum">     342 </span>            :     //  std::cout&lt;&lt;x[i]&lt;&lt;&quot; &quot;&lt;&lt;y[i]&lt;&lt;&quot; &quot;;</a>
+<a name="343"><span class="lineNum">     343 </span>            :     //}</a>
+<a name="344"><span class="lineNum">     344 </span>            :     //std::cout&lt;&lt;std::endl;</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         87 :     if (step % output_freq == 0)</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :     {</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         21 :       calc_pmf();</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         21 :       write_files();</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :       //write_interal_data();</a>
+<a name="351"><span class="lineNum">     351 </span>            :     }</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        246 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :     {</a>
+<a name="355"><span class="lineNum">     355 </span>            :       // for dihedral RC, it is possible that x = 179 and y = -179, should correct it</a>
+<a name="356"><span class="lineNum">     356 </span>            :       // may have problem, need to fix</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        159 :       if (x[i] &gt; 150 &amp;&amp; y[i] &lt; -150)</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :       {</a>
+<a name="359"><span class="lineNum">     359 </span>            :         //std::vector&lt;double&gt; x_temp(x);</a>
+<a name="360"><span class="lineNum">     360 </span>            :         //x_temp[i] -= 360;</a>
+<a name="361"><span class="lineNum">     361 </span>            :         //update(7, x_temp, y);</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :         y[i] += 360;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :       }</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        159 :       if (x[i] &lt; -150 &amp;&amp; y[i] &gt; 150)</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :       {</a>
+<a name="366"><span class="lineNum">     366 </span>            :         //std::vector&lt;double&gt; x_temp(x);</a>
+<a name="367"><span class="lineNum">     367 </span>            :         //x_temp[i] += 360;</a>
+<a name="368"><span class="lineNum">     368 </span>            :         //update(7, x_temp, y);</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :         y[i] -= 360;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :       }</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        159 :       if (x[i] &lt; lowerboundary[i] - EXTENDED_X_SIZE * width[i] + 0.00001 || x[i] &gt; upperboundary[i] + EXTENDED_X_SIZE * width[i] - 0.00001 \</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        159 :           || y[i] - x[i] &lt; -HALF_Y_SIZE * width[i] + 0.00001 || y[i] - x[i] &gt; HALF_Y_SIZE * width[i] - 0.00001 \</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        318 :           || y[i] - lowerboundary[i] &lt; -HALF_Y_SIZE * width[i] + 0.00001 || y[i] - upperboundary[i] &gt; HALF_Y_SIZE * width[i] - 0.00001)</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :         return false;</a>
+<a name="376"><span class="lineNum">     376 </span>            :     }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :     //for (int i = 0; i &lt; dimension; i++)</a>
+<a name="379"><span class="lineNum">     379 </span>            :     //{</a>
+<a name="380"><span class="lineNum">     380 </span>            :     //  std::cout&lt;&lt;x[i]&lt;&lt;&quot; &quot;&lt;&lt;y[i]&lt;&lt;&quot; &quot;;</a>
+<a name="381"><span class="lineNum">     381 </span>            :     //}</a>
+<a name="382"><span class="lineNum">     382 </span>            :     //std::cout&lt;&lt;std::endl;</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        246 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :     {</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        159 :       sum_x[i].increase_value(y, x[i]);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        159 :       sum_x_square[i].increase_value(y, x[i] * x[i]);</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :     }</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         87 :     count_y.increase_value(y, 1);</span></a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        246 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :     {</a>
+<a name="393"><span class="lineNum">     393 </span>            :       //if (x[i] &lt; lowerboundary[i] + 0.000001 || x[i] &gt; upperboundary[i] - 0.000001)</a>
+<a name="394"><span class="lineNum">     394 </span>            :       // adapt colvars precision</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">        159 :       if (x[i] &lt; lowerboundary[i] + 0.00001 || x[i] &gt; upperboundary[i] - 0.00001)</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :         return false;</a>
+<a name="397"><span class="lineNum">     397 </span>            :     }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         87 :     distribution_x_y.increase_value(x, y, 1);</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         87 :     return true;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   }</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            :   // update the output_filename</a>
+<a name="404"><span class="lineNum">     404 </span>            :   void update_output_filename(const std::string&amp; filename)</a>
+<a name="405"><span class="lineNum">     405 </span>            :   {</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         87 :     output_filename = filename;</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :   }</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            : private:</a>
+<a name="410"><span class="lineNum">     410 </span>            :   std::vector&lt;n_vector&lt;double&gt; &gt; sum_x;                        // the sum of x in each y bin</a>
+<a name="411"><span class="lineNum">     411 </span>            :   std::vector&lt;n_vector&lt;double&gt; &gt; sum_x_square;                 // the sum of x in each y bin</a>
+<a name="412"><span class="lineNum">     412 </span>            :   n_vector&lt;int&gt; count_y;                              // the distribution of y</a>
+<a name="413"><span class="lineNum">     413 </span>            :   n_matrix distribution_x_y;   // the distribution of &lt;x, y&gt; pair</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            :   int dimension;</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   std::vector&lt;double&gt; lowerboundary;</a>
+<a name="418"><span class="lineNum">     418 </span>            :   std::vector&lt;double&gt; upperboundary;</a>
+<a name="419"><span class="lineNum">     419 </span>            :   std::vector&lt;double&gt; width;</a>
+<a name="420"><span class="lineNum">     420 </span>            :   std::vector&lt;double&gt; krestr;</a>
+<a name="421"><span class="lineNum">     421 </span>            :   std::string output_filename;</a>
+<a name="422"><span class="lineNum">     422 </span>            :   int output_freq;</a>
+<a name="423"><span class="lineNum">     423 </span>            :   bool restart;</a>
+<a name="424"><span class="lineNum">     424 </span>            :   std::vector&lt;std::string&gt; input_filename;</a>
+<a name="425"><span class="lineNum">     425 </span>            :   double temperature;</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :   n_vector&lt;std::vector&lt;double&gt; &gt; grad;</a>
+<a name="428"><span class="lineNum">     428 </span>            :   n_vector&lt;int&gt; count;</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span>            :   n_vector&lt;double&gt; oneD_pmf;</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :   n_vector&lt;std::vector&lt;double&gt; &gt; input_grad;</a>
+<a name="433"><span class="lineNum">     433 </span>            :   n_vector&lt;int&gt; input_count;</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :   // used in double integration</a>
+<a name="436"><span class="lineNum">     436 </span>            :   std::vector&lt;n_vector&lt;double&gt; &gt; x_av;</a>
+<a name="437"><span class="lineNum">     437 </span>            :   std::vector&lt;n_vector&lt;double&gt; &gt; sigma_square;</a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span>            :   bool written;</a>
+<a name="440"><span class="lineNum">     440 </span>            :   bool written_1D;</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :   // calculate gradients from the internal variables</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         21 :   void calc_pmf()</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :   {</a>
+<a name="445"><span class="lineNum">     445 </span>            :     int norm;</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         21 :     std::vector&lt;double&gt; loop_flag(dimension, 0);</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         54 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :     {</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">         33 :       loop_flag[i] = lowerboundary[i] - HALF_Y_SIZE * width[i];</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :     }</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            :     while (true)</a>
+<a name="454"><span class="lineNum">     454 </span>            :     {</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">       6783 :       norm = count_y.get_value(loop_flag) &gt; 0 ? count_y.get_value(loop_flag) : 1;</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">      20106 :       for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :       {</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">      13323 :         x_av[i].set_value(loop_flag, sum_x[i].get_value(loop_flag) / norm);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">      13323 :         sigma_square[i].set_value(loop_flag, sum_x_square[i].get_value(loop_flag) / norm - x_av[i].get_value(loop_flag) * x_av[i].get_value(loop_flag));</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :       }</a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            :       // iterate over any dimensions</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">       6783 :       int i = dimension - 1;</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :       while (true)</a>
+<a name="465"><span class="lineNum">     465 </span>            :       {</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">       7063 :         loop_flag[i] += width[i];</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">       7063 :         if (loop_flag[i] &gt; upperboundary[i] + HALF_Y_SIZE * width[i] - width[i] + 0.00001)</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :         {</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        301 :           loop_flag[i] = lowerboundary[i] - HALF_Y_SIZE * width[i];</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">        301 :           i--;</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">        301 :           if (i &lt; 0)</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         21 :             goto LOOPEND;</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :         }</a>
+<a name="474"><span class="lineNum">     474 </span>            :         else</a>
+<a name="475"><span class="lineNum">     475 </span>            :           break;</a>
+<a name="476"><span class="lineNum">     476 </span>            :       }</a>
+<a name="477"><span class="lineNum">     477 </span>            :     }</a>
+<a name="478"><span class="lineNum">     478 </span>            : LOOPEND:</a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span>            :     // double integration</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         21 :     std::vector&lt;double&gt; av(dimension, 0);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         21 :     std::vector&lt;double&gt; diff_av(dimension, 0);</span></a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         21 :     std::vector&lt;double&gt; loop_flag_x(dimension, 0);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         21 :     std::vector&lt;double&gt; loop_flag_y(dimension, 0);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         54 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     {</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         33 :       loop_flag_x[i] = lowerboundary[i];</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         33 :       loop_flag_y[i] = loop_flag_x[i] - HALF_Y_SIZE * width[i];</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :     }</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            :     while (true)</a>
+<a name="493"><span class="lineNum">     493 </span>            :     {</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        203 :       norm = 0;</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">        546 :       for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :       {</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">        343 :         av[i] = 0;</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">        343 :         diff_av[i] = 0;</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        343 :         loop_flag_y[i] = loop_flag_x[i] - HALF_Y_SIZE * width[i];</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :       }</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            :       while (true)</a>
+<a name="503"><span class="lineNum">     503 </span>            :       {</a>
+<a name="504"><span class="lineNum">     504 </span>            :         //std::cout&lt;&lt;&quot;pppppppppppppppppppppp &quot;&lt;&lt;loop_flag_x[0]&lt;&lt;&quot; &quot;&lt;&lt;loop_flag_x[1]&lt;&lt;&quot; &quot;&lt;&lt;loop_flag_y[0]&lt;&lt;&quot; &quot;&lt;&lt;loop_flag_y[1]&lt;&lt;std::endl;</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">      57260 :         norm += distribution_x_y.get_value(loop_flag_x, loop_flag_y);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">     170520 :         for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :         {</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">     113260 :           if (sigma_square[i].get_value(loop_flag_y) &gt; 0.00001 || sigma_square[i].get_value(loop_flag_y) &lt; -0.00001)</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">        480 :             av[i] += distribution_x_y.get_value(loop_flag_x, loop_flag_y) * ( (loop_flag_x[i] + 0.5 * width[i]) - x_av[i].get_value(loop_flag_y)) / sigma_square[i].get_value(loop_flag_y);</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">     113260 :           diff_av[i] += distribution_x_y.get_value(loop_flag_x, loop_flag_y) * (loop_flag_x[i] - loop_flag_y[i]);</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :         }</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            :         // iterate over any dimensions</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">      57260 :         int i = dimension - 1;</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :         while (true)</a>
+<a name="517"><span class="lineNum">     517 </span>            :         {</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">      60060 :           loop_flag_y[i] += width[i];</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">      60060 :           if (loop_flag_y[i] &gt; loop_flag_x[i] + HALF_Y_SIZE * width[i] - width[i] + 0.00001)</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :           {</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">       3003 :             loop_flag_y[i] = loop_flag_x[i] - HALF_Y_SIZE * width[i];</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">       3003 :             i--;</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">       3003 :             if (i &lt; 0)</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">        203 :               goto LOOPEND2;</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :           }</a>
+<a name="526"><span class="lineNum">     526 </span>            :           else</a>
+<a name="527"><span class="lineNum">     527 </span>            :             break;</a>
+<a name="528"><span class="lineNum">     528 </span>            :         }</a>
+<a name="529"><span class="lineNum">     529 </span>            :       }</a>
+<a name="530"><span class="lineNum">     530 </span>            : LOOPEND2:</a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        203 :       std::vector&lt;double&gt; grad_temp(dimension, 0);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        546 :       for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :       {</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">        343 :         diff_av[i] /= (norm &gt; 0 ? norm : 1);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">        343 :         av[i] = BOLTZMANN * temperature * av[i] / (norm &gt; 0 ? norm : 1);</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">        343 :         grad_temp[i] = av[i] - krestr[i] * diff_av[i];</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :       }</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">        203 :       grad.set_value(loop_flag_x, grad_temp);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">        203 :       count.set_value(loop_flag_x, norm);</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span>            :       // iterate over any dimensions</a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">        203 :       int i = dimension - 1;</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :       while (true)</a>
+<a name="545"><span class="lineNum">     545 </span>            :       {</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">        243 :         loop_flag_x[i] += width[i];</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">        243 :         if (loop_flag_x[i] &gt; upperboundary[i] - width[i] + 0.00001)</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :         {</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         61 :           loop_flag_x[i] = lowerboundary[i];</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         61 :           i--;</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         61 :           if (i &lt; 0)</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         21 :             goto LOOPEND3;</span></a>
+<a name="553"><span class="lineNum">     553 </span>            :         }</a>
+<a name="554"><span class="lineNum">     554 </span>            :         else</a>
+<a name="555"><span class="lineNum">     555 </span>            :           break;</a>
+<a name="556"><span class="lineNum">     556 </span>            :       }</a>
+<a name="557"><span class="lineNum">     557 </span>            :     }</a>
+<a name="558"><span class="lineNum">     558 </span>            : LOOPEND3:;</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         21 :   }</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span>            :   // calculate 1D pmf</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">          9 :   void calc_1D_pmf()</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :   {</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          9 :     std::vector&lt;double&gt; last_position(1, 0);</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">          9 :     std::vector&lt;double&gt; position(1, 0);</span></a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span>            :     double min = 0;</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          9 :     double dG = 0;</span></a>
+<a name="570"><span class="lineNum">     570 </span>            : </a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">          9 :     oneD_pmf.set_value(lowerboundary, 0);</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">          9 :     last_position = lowerboundary;</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         72 :     for (double i = lowerboundary[0] + width[0]; i &lt; upperboundary[0] + 0.000001; i += width[0])</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :     {</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         63 :       position[0] = i + 0.000001;</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         63 :       if (restart == false || input_count.get_value(last_position) == 0)</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :       {</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         63 :         dG = oneD_pmf.get_value(last_position) + grad.get_value(last_position)[0] * width[0];</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :       }</a>
+<a name="580"><span class="lineNum">     580 </span>            :       else</a>
+<a name="581"><span class="lineNum">     581 </span>            :       {</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 :         dG = oneD_pmf.get_value(last_position) + ((grad.get_value(last_position)[0] * count.get_value(last_position) + input_grad.get_value(last_position)[0] * input_count.get_value(last_position)) / (count.get_value(last_position) + input_count.get_value(last_position))) * width[0];</span></a>
+<a name="583"><span class="lineNum">     583 </span>            :       }</a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         63 :       if (dG &lt; min)</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :         min = dG;</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         63 :       oneD_pmf.set_value(position, dG);</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         63 :       last_position[0] = i + 0.000001;</span></a>
+<a name="588"><span class="lineNum">     588 </span>            :     }</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         81 :     for (double i = lowerboundary[0]; i &lt; upperboundary[0] + 0.000001; i += width[0])</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :     {</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">         72 :       position[0] = i + 0.000001;</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         72 :       oneD_pmf.set_value(position, oneD_pmf.get_value(position) - min);</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :     }</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          9 :   }</span></a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            :   // write 1D pmf</a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">          9 :   void write_1D_pmf()</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :   {</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">          9 :     std::string pmf_filename = output_filename + &quot;.UI.pmf&quot;;</span></a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span>            :     // only for colvars module!</a>
+<a name="603"><span class="lineNum">     603 </span>            : //                      if (written_1D) cvm::backup_file(pmf_filename.c_str());</a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">          9 :     std::ofstream ofile_pmf(pmf_filename.c_str());</span></a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">          9 :     std::vector&lt;double&gt; position(1, 0);</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">         81 :     for (double i = lowerboundary[0]; i &lt; upperboundary[0] + 0.000001; i += width[0])</span></a>
+<a name="609"><span class="lineNum">     609 </span>            :     {</a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         72 :       ofile_pmf &lt;&lt; i &lt;&lt; &quot; &quot;;</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         72 :       position[0] = i + 0.000001;</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         72 :       ofile_pmf &lt;&lt; oneD_pmf.get_value(position) &lt;&lt; std::endl;</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :     }</a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">          9 :     ofile_pmf.close();</span></a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">          9 :     written_1D = true;</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         18 :   }</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span>            :   // write heads of the output files</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         63 :   void writehead(std::ofstream&amp; os) const</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :   {</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         63 :     os &lt;&lt; &quot;# &quot; &lt;&lt; dimension &lt;&lt; std::endl;</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        162 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :     {</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         99 :       os.precision(std::numeric_limits&lt;double&gt;::max_digits10);</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        198 :       os &lt;&lt; &quot;# &quot; &lt;&lt; std::fixed &lt;&lt; lowerboundary[i] &lt;&lt; &quot; &quot; &lt;&lt; width[i] &lt;&lt; &quot; &quot; &lt;&lt; int((upperboundary[i] - lowerboundary[i]) / width[i] + 0.000001) &lt;&lt; &quot; &quot; &lt;&lt; 0 &lt;&lt; std::endl;</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :     }</a>
+<a name="628"><span class="lineNum">     628 </span>            :     os &lt;&lt; std::endl;</a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">         63 :   }</span></a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            :   // write interal data, used for testing</a>
+<a name="632"><span class="lineNum">     632 </span>            : //   void write_interal_data()</a>
+<a name="633"><span class="lineNum">     633 </span>            : //   {</a>
+<a name="634"><span class="lineNum">     634 </span>            : //     std::string internal_filaname = output_filename + &quot;.UI.internal&quot;;</a>
+<a name="635"><span class="lineNum">     635 </span>            : //</a>
+<a name="636"><span class="lineNum">     636 </span>            : //     std::ofstream ofile_internal(internal_filaname.c_str());</a>
+<a name="637"><span class="lineNum">     637 </span>            : //</a>
+<a name="638"><span class="lineNum">     638 </span>            : //     std::vector&lt;double&gt; loop_flag(dimension, 0);</a>
+<a name="639"><span class="lineNum">     639 </span>            : //     for (int i = 0; i &lt; dimension; i++)</a>
+<a name="640"><span class="lineNum">     640 </span>            : //     {</a>
+<a name="641"><span class="lineNum">     641 </span>            : //       loop_flag[i] = lowerboundary[i];</a>
+<a name="642"><span class="lineNum">     642 </span>            : //     }</a>
+<a name="643"><span class="lineNum">     643 </span>            : //     while (true)</a>
+<a name="644"><span class="lineNum">     644 </span>            : //     {</a>
+<a name="645"><span class="lineNum">     645 </span>            : //       for (int i = 0; i &lt; dimension; i++)</a>
+<a name="646"><span class="lineNum">     646 </span>            : //       {</a>
+<a name="647"><span class="lineNum">     647 </span>            : //         ofile_internal &lt;&lt; loop_flag[i] + 0.5 * width[i] &lt;&lt; &quot; &quot;;</a>
+<a name="648"><span class="lineNum">     648 </span>            : //       }</a>
+<a name="649"><span class="lineNum">     649 </span>            : //</a>
+<a name="650"><span class="lineNum">     650 </span>            : //       for (int i = 0; i &lt; dimension; i++)</a>
+<a name="651"><span class="lineNum">     651 </span>            : //       {</a>
+<a name="652"><span class="lineNum">     652 </span>            : //         ofile_internal &lt;&lt; grad.get_value(loop_flag)[i] &lt;&lt; &quot; &quot;;</a>
+<a name="653"><span class="lineNum">     653 </span>            : //       }</a>
+<a name="654"><span class="lineNum">     654 </span>            : //</a>
+<a name="655"><span class="lineNum">     655 </span>            : //       std::vector&lt;double&gt; ii(dimension,0);</a>
+<a name="656"><span class="lineNum">     656 </span>            : //       for (double i = loop_flag[0] - 10; i &lt; loop_flag[0] + 10 + 0.00001; i+= width[0])</a>
+<a name="657"><span class="lineNum">     657 </span>            : //       {</a>
+<a name="658"><span class="lineNum">     658 </span>            : //         for (double j = loop_flag[1] - 10; j&lt; loop_flag[1] + 10 +0.00001; j+=width[1])</a>
+<a name="659"><span class="lineNum">     659 </span>            : //         {</a>
+<a name="660"><span class="lineNum">     660 </span>            : //           ii[0] = i;</a>
+<a name="661"><span class="lineNum">     661 </span>            : //           ii[1] = j;</a>
+<a name="662"><span class="lineNum">     662 </span>            : //           ofile_internal &lt;&lt; i &lt;&lt;&quot; &quot;&lt;&lt;j&lt;&lt;&quot; &quot;&lt;&lt; distribution_x_y.get_value(loop_flag,ii)&lt;&lt; &quot; &quot;;</a>
+<a name="663"><span class="lineNum">     663 </span>            : //         }</a>
+<a name="664"><span class="lineNum">     664 </span>            : //       }</a>
+<a name="665"><span class="lineNum">     665 </span>            : //       ofile_internal &lt;&lt; std::endl;</a>
+<a name="666"><span class="lineNum">     666 </span>            : //</a>
+<a name="667"><span class="lineNum">     667 </span>            : //       // iterate over any dimensions</a>
+<a name="668"><span class="lineNum">     668 </span>            : //       int i = dimension - 1;</a>
+<a name="669"><span class="lineNum">     669 </span>            : //       while (true)</a>
+<a name="670"><span class="lineNum">     670 </span>            : //       {</a>
+<a name="671"><span class="lineNum">     671 </span>            : //         loop_flag[i] += width[i];</a>
+<a name="672"><span class="lineNum">     672 </span>            : //         if (loop_flag[i] &gt; upperboundary[i] - width[i] + 0.00001)</a>
+<a name="673"><span class="lineNum">     673 </span>            : //         {</a>
+<a name="674"><span class="lineNum">     674 </span>            : //           loop_flag[i] = lowerboundary[i];</a>
+<a name="675"><span class="lineNum">     675 </span>            : //           i--;</a>
+<a name="676"><span class="lineNum">     676 </span>            : //           if (i &lt; 0)</a>
+<a name="677"><span class="lineNum">     677 </span>            : //             goto LOOPEND5;</a>
+<a name="678"><span class="lineNum">     678 </span>            : //         }</a>
+<a name="679"><span class="lineNum">     679 </span>            : //         else</a>
+<a name="680"><span class="lineNum">     680 </span>            : //           break;</a>
+<a name="681"><span class="lineNum">     681 </span>            : //       }</a>
+<a name="682"><span class="lineNum">     682 </span>            : //     }</a>
+<a name="683"><span class="lineNum">     683 </span>            : // LOOPEND5:</a>
+<a name="684"><span class="lineNum">     684 </span>            : //     ofile_internal.close();</a>
+<a name="685"><span class="lineNum">     685 </span>            : //   }</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span>            :   // write output files</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         21 :   void write_files()</span></a>
+<a name="689"><span class="lineNum">     689 </span>            :   {</a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         21 :     std::string grad_filename = output_filename + &quot;.UI.grad&quot;;</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         21 :     std::string hist_filename = output_filename + &quot;.UI.hist.grad&quot;;</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         21 :     std::string count_filename = output_filename + &quot;.UI.count&quot;;</span></a>
+<a name="693"><span class="lineNum">     693 </span>            : </a>
+<a name="694"><span class="lineNum">     694 </span>            :     // only for colvars module!</a>
+<a name="695"><span class="lineNum">     695 </span>            : //                      if (written) cvm::backup_file(grad_filename.c_str());</a>
+<a name="696"><span class="lineNum">     696 </span>            :     //if (written) cvm::backup_file(hist_filename.c_str());</a>
+<a name="697"><span class="lineNum">     697 </span>            : //                      if (written) cvm::backup_file(count_filename.c_str());</a>
+<a name="698"><span class="lineNum">     698 </span>            : </a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         21 :     std::ofstream ofile(grad_filename.c_str());</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         21 :     std::ofstream ofile_hist(hist_filename.c_str(), std::ios::app);</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">         21 :     std::ofstream ofile_count(count_filename.c_str());</span></a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         21 :     writehead(ofile);</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">         21 :     writehead(ofile_hist);</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         21 :     writehead(ofile_count);</span></a>
+<a name="706"><span class="lineNum">     706 </span>            : </a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         21 :     if (dimension == 1)</span></a>
+<a name="708"><span class="lineNum">     708 </span>            :     {</a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">          9 :       calc_1D_pmf();</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">          9 :       write_1D_pmf();</span></a>
+<a name="711"><span class="lineNum">     711 </span>            :     }</a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">         21 :     std::vector&lt;double&gt; loop_flag(dimension, 0);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">         54 :     for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="715"><span class="lineNum">     715 </span>            :     {</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">         33 :       loop_flag[i] = lowerboundary[i];</span></a>
+<a name="717"><span class="lineNum">     717 </span>            :     }</a>
+<a name="718"><span class="lineNum">     718 </span>            :     while (true)</a>
+<a name="719"><span class="lineNum">     719 </span>            :     {</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">        546 :       for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="721"><span class="lineNum">     721 </span>            :       {</a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">        343 :         ofile &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; loop_flag[i] + 0.5 * width[i] &lt;&lt; &quot; &quot;;</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">        343 :         ofile_hist &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; loop_flag[i] + 0.5 * width[i] &lt;&lt; &quot; &quot;;</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">        343 :         ofile_count &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; loop_flag[i] + 0.5 * width[i] &lt;&lt; &quot; &quot;;</span></a>
+<a name="725"><span class="lineNum">     725 </span>            :       }</a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">        203 :       if (restart == false)</span></a>
+<a name="728"><span class="lineNum">     728 </span>            :       {</a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">        492 :         for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="730"><span class="lineNum">     730 </span>            :         {</a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">        614 :           ofile &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; grad.get_value(loop_flag)[i] &lt;&lt; &quot; &quot;;</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">        614 :           ofile_hist &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; grad.get_value(loop_flag)[i] &lt;&lt; &quot; &quot;;</span></a>
+<a name="733"><span class="lineNum">     733 </span>            :         }</a>
+<a name="734"><span class="lineNum">     734 </span>            :         ofile &lt;&lt; std::endl;</a>
+<a name="735"><span class="lineNum">     735 </span>            :         ofile_hist &lt;&lt; std::endl;</a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">        185 :         ofile_count &lt;&lt; count.get_value(loop_flag) &lt;&lt; &quot; &quot; &lt;&lt;std::endl;</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :       }</a>
+<a name="738"><span class="lineNum">     738 </span>            :       else</a>
+<a name="739"><span class="lineNum">     739 </span>            :       {</a>
+<a name="740"><span class="lineNum">     740 </span>            :         double final_grad = 0;</a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">         54 :         for (int i = 0; i &lt; dimension; i++)</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :         {</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">         36 :           int total_count_temp = (count.get_value(loop_flag) + input_count.get_value(loop_flag));</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">         36 :           if (input_count.get_value(loop_flag) == 0)</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">         20 :             final_grad = grad.get_value(loop_flag)[i];</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :           else</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">         16 :             final_grad = ((grad.get_value(loop_flag)[i] * count.get_value(loop_flag) + input_grad.get_value(loop_flag)[i] * input_count.get_value(loop_flag)) / total_count_temp);</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">         36 :           ofile &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; final_grad &lt;&lt; &quot; &quot;;</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">         36 :           ofile_hist &lt;&lt; std::fixed &lt;&lt; std::setprecision(9) &lt;&lt; final_grad &lt;&lt; &quot; &quot;;</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :         }</a>
+<a name="751"><span class="lineNum">     751 </span>            :         ofile &lt;&lt; std::endl;</a>
+<a name="752"><span class="lineNum">     752 </span>            :         ofile_hist &lt;&lt; std::endl;</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         18 :         ofile_count &lt;&lt; (count.get_value(loop_flag) + input_count.get_value(loop_flag)) &lt;&lt; &quot; &quot; &lt;&lt;std::endl;</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :       }</a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span>            :       // iterate over any dimensions</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">        203 :       int i = dimension - 1;</span></a>
+<a name="758"><span class="lineNum">     758 </span>            :       while (true)</a>
+<a name="759"><span class="lineNum">     759 </span>            :       {</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">        243 :         loop_flag[i] += width[i];</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">        243 :         if (loop_flag[i] &gt; upperboundary[i] - width[i] + 0.00001)</span></a>
+<a name="762"><span class="lineNum">     762 </span>            :         {</a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">         61 :           loop_flag[i] = lowerboundary[i];</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">         61 :           i--;</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :           ofile &lt;&lt; std::endl;</a>
+<a name="766"><span class="lineNum">     766 </span>            :           ofile_hist &lt;&lt; std::endl;</a>
+<a name="767"><span class="lineNum">     767 </span>            :           ofile_count &lt;&lt; std::endl;</a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">         61 :           if (i &lt; 0)</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">         21 :             goto LOOPEND4;</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :         }</a>
+<a name="771"><span class="lineNum">     771 </span>            :         else</a>
+<a name="772"><span class="lineNum">     772 </span>            :           break;</a>
+<a name="773"><span class="lineNum">     773 </span>            :       }</a>
+<a name="774"><span class="lineNum">     774 </span>            :     }</a>
+<a name="775"><span class="lineNum">     775 </span>            : LOOPEND4:</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">         21 :     ofile.close();</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">         21 :     ofile_count.close();</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">         21 :     ofile_hist.close();</span></a>
+<a name="779"><span class="lineNum">     779 </span>            : </a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">         21 :     written = true;</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">         42 :   }</span></a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            :   // read input files</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">          1 :   void read_inputfiles(const std::vector&lt;std::string&gt;&amp; input_filename)</span></a>
+<a name="785"><span class="lineNum">     785 </span>            :   {</a>
+<a name="786"><span class="lineNum">     786 </span>            :     char sharp;</a>
+<a name="787"><span class="lineNum">     787 </span>            :     double nothing;</a>
+<a name="788"><span class="lineNum">     788 </span>            :     int dimension_temp;</a>
+<a name="789"><span class="lineNum">     789 </span>            : </a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">          1 :     std::vector&lt;double&gt; loop_bin_size(dimension, 0);</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">          1 :     std::vector&lt;double&gt; position_temp(dimension, 0);</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">          1 :     std::vector&lt;double&gt; grad_temp(dimension, 0);</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">          1 :     int count_temp = 0;</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">          2 :     for (unsigned int i = 0; i &lt; input_filename.size(); i++)</span></a>
+<a name="795"><span class="lineNum">     795 </span>            :     {</a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">          1 :       int size = 1, size_temp = 0;</span></a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">          1 :       std::string count_filename = input_filename[i] + &quot;.UI.count&quot;;</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">          1 :       std::string grad_filename = input_filename[i] + &quot;.UI.grad&quot;;</span></a>
+<a name="800"><span class="lineNum">     800 </span>            : </a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">          1 :       std::ifstream count_file(count_filename.c_str(), std::ios::in);</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">          1 :       std::ifstream grad_file(grad_filename.c_str(), std::ios::in);</span></a>
+<a name="803"><span class="lineNum">     803 </span>            : </a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">          1 :       count_file &gt;&gt; sharp &gt;&gt; dimension_temp;</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">          1 :       grad_file &gt;&gt; sharp &gt;&gt; dimension_temp;</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">          3 :       for (int j = 0; j &lt; dimension; j++)</span></a>
+<a name="808"><span class="lineNum">     808 </span>            :       {</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">          4 :         count_file &gt;&gt; sharp &gt;&gt; nothing &gt;&gt; nothing &gt;&gt; size_temp &gt;&gt; nothing;</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">          2 :         grad_file &gt;&gt; sharp &gt;&gt; nothing &gt;&gt; nothing &gt;&gt; nothing &gt;&gt; nothing;</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">          2 :         size *= size_temp;</span></a>
+<a name="812"><span class="lineNum">     812 </span>            :       }</a>
+<a name="813"><span class="lineNum">     813 </span>            : </a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         10 :       for (int j = 0; j &lt; size; j++)</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :       {</a>
+<a name="816"><span class="lineNum">     816 </span>            :         do</a>
+<a name="817"><span class="lineNum">     817 </span>            :         {</a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">         27 :           for (int k = 0; k &lt; dimension; k++)</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :           {</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         18 :             count_file &gt;&gt; position_temp[k];</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :             grad_file &gt;&gt; nothing;</a>
+<a name="822"><span class="lineNum">     822 </span>            :           }</a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">         27 :           for (int l = 0; l &lt; dimension; l++)</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :           {</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         18 :             grad_file &gt;&gt; grad_temp[l];</span></a>
+<a name="827"><span class="lineNum">     827 </span>            :           }</a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">          9 :           count_file &gt;&gt; count_temp;</span></a>
+<a name="829"><span class="lineNum">     829 </span>            :         }</a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">          9 :         while (position_temp[i] &lt; lowerboundary[i] - 0.000001 || position_temp[i] &gt; upperboundary[i] + 0.000001);</span></a>
+<a name="831"><span class="lineNum">     831 </span>            : </a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">          9 :         if (count_temp == 0)</span></a>
+<a name="833"><span class="lineNum">     833 </span>            :         {</a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">          5 :           continue;</span></a>
+<a name="835"><span class="lineNum">     835 </span>            :         }</a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">         12 :         for (int m = 0; m &lt; dimension; m++)</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :         {</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">          8 :           grad_temp[m] = (grad_temp[m] * count_temp + input_grad.get_value(position_temp)[m] * input_count.get_value(position_temp)) / (count_temp + input_count.get_value(position_temp));</span></a>
+<a name="840"><span class="lineNum">     840 </span>            :         }</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">          4 :         input_grad.set_value(position_temp, grad_temp);</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">          4 :         input_count.increase_value(position_temp, count_temp);</span></a>
+<a name="843"><span class="lineNum">     843 </span>            :       }</a>
+<a name="844"><span class="lineNum">     844 </span>            : </a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">          1 :       count_file.close();</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">          1 :       grad_file.close();</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">          1 :     }</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">          1 :   }</span></a>
+<a name="849"><span class="lineNum">     849 </span>            : };</a>
+<a name="850"><span class="lineNum">     850 </span>            : }</a>
+<a name="851"><span class="lineNum">     851 </span>            : </a>
+<a name="852"><span class="lineNum">     852 </span>            : }</a>
+<a name="853"><span class="lineNum">     853 </span>            : }</a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/drrtool.cpp.func-sort-c.html b/coverage/drr/drrtool.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e627a6ec7f
--- /dev/null
+++ b/coverage/drr/drrtool.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/drrtool.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - drrtool.cpp<span style="font-size: 80%;"> (<a href="drrtool.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryHi">94.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="drrtool.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#222">_ZN4PLMD3drr7drrtool14calcDivergenceERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#129">_ZN4PLMD3drr7drrtool10extractdrrERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#172">_ZN4PLMD3drr7drrtool12mergewindowsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EES8_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#211">_ZZN4PLMD3drr7drrtool12mergewindowsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EES8_ENKUlRKS8_SE_E0_clESE_SE_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#209">_ZZN4PLMD3drr7drrtool12mergewindowsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EES8_ENKUlS8_E_clES8_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#79">_ZNK4PLMD3drr7drrtool11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#104">_ZN4PLMD3drr7drrtool4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#87">_ZN4PLMD3drr12_GLOBAL__N_117drrtoolRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#99">_ZN4PLMD3drr7drrtoolC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#87">_ZN4PLMD3drr12_GLOBAL__N_117drrtoolRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#87">_ZN4PLMD3drr12_GLOBAL__N_117drrtoolRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#89">_ZN4PLMD3drr7drrtool16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/drrtool.cpp.func.html b/coverage/drr/drrtool.cpp.func.html
new file mode 100644
index 0000000000..eb955937a2
--- /dev/null
+++ b/coverage/drr/drrtool.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/drrtool.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - drrtool.cpp<span style="font-size: 80%;"> (<a href="drrtool.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryHi">94.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="drrtool.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#87">_ZN4PLMD3drr12_GLOBAL__N_117drrtoolRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#87">_ZN4PLMD3drr12_GLOBAL__N_117drrtoolRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#87">_ZN4PLMD3drr12_GLOBAL__N_117drrtoolRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#129">_ZN4PLMD3drr7drrtool10extractdrrERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#172">_ZN4PLMD3drr7drrtool12mergewindowsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EES8_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#222">_ZN4PLMD3drr7drrtool14calcDivergenceERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#89">_ZN4PLMD3drr7drrtool16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#104">_ZN4PLMD3drr7drrtool4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#99">_ZN4PLMD3drr7drrtoolC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#79">_ZNK4PLMD3drr7drrtool11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#211">_ZZN4PLMD3drr7drrtool12mergewindowsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EES8_ENKUlRKS8_SE_E0_clESE_SE_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="drrtool.cpp.gcov.html#209">_ZZN4PLMD3drr7drrtool12mergewindowsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EES8_ENKUlS8_E_clES8_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/drrtool.cpp.gcov.html b/coverage/drr/drrtool.cpp.gcov.html
new file mode 100644
index 0000000000..f71ad29b97
--- /dev/null
+++ b/coverage/drr/drrtool.cpp.gcov.html
@@ -0,0 +1,341 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr/drrtool.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">drr</a> - drrtool.cpp<span style="font-size: 80%;"> (source / <a href="drrtool.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryHi">94.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :     Copyright (c) 2017 of Haochuan Chen (excluding colvar_UIestimator.h)</a>
+<a name="3"><span class="lineNum">       3 </span>            :     Copyright (c) 2017 of Haohao Fu (colvar_UIestimator.h)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :     This program is free software: you can redistribute it and/or modify</a>
+<a name="6"><span class="lineNum">       6 </span>            :     it under the terms of the GNU Lesser General Public License as published</a>
+<a name="7"><span class="lineNum">       7 </span>            :     by the Free Software Foundation, either version 3 of the License, or</a>
+<a name="8"><span class="lineNum">       8 </span>            :     (at your option) any later version.</a>
+<a name="9"><span class="lineNum">       9 </span>            : </a>
+<a name="10"><span class="lineNum">      10 </span>            :     This program is distributed in the hope that it will be useful,</a>
+<a name="11"><span class="lineNum">      11 </span>            :     but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="12"><span class="lineNum">      12 </span>            :     MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="13"><span class="lineNum">      13 </span>            :     GNU Lesser General Public License for more details.</a>
+<a name="14"><span class="lineNum">      14 </span>            : </a>
+<a name="15"><span class="lineNum">      15 </span>            :     You should have received a copy of the GNU Lesser General Public License</a>
+<a name="16"><span class="lineNum">      16 </span>            :     along with this program.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="17"><span class="lineNum">      17 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="18"><span class="lineNum">      18 </span>            : #ifdef __PLUMED_HAS_BOOST_SERIALIZATION</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;cltools/CLTool.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;cltools/CLToolRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;config/Config.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;DRR.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;boost/archive/binary_iarchive.hpp&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;boost/archive/binary_oarchive.hpp&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;boost/serialization/vector.hpp&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;fstream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;iostream&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;string&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : using namespace PLMD;</a>
+<a name="35"><span class="lineNum">      35 </span>            : using namespace cltools;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace drr {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : //+PLUMEDOC EABFMOD_TOOLS drr_tool</a>
+<a name="41"><span class="lineNum">      41 </span>            : /*</a>
+<a name="42"><span class="lineNum">      42 </span>            :  - Extract .grad and .count files from the binary output .drrstate</a>
+<a name="43"><span class="lineNum">      43 </span>            :  - Merge windows</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The following command will extract .grad and .count files.</a>
+<a name="48"><span class="lineNum">      48 </span>            : \verbatim</a>
+<a name="49"><span class="lineNum">      49 </span>            : plumed drr_tool --extract eabf.drrstate</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endverbatim</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following command will merge windows of two .drrstate file, and output the</a>
+<a name="53"><span class="lineNum">      53 </span>            : .grad and .count files.</a>
+<a name="54"><span class="lineNum">      54 </span>            : \verbatim</a>
+<a name="55"><span class="lineNum">      55 </span>            : plumed drr_tool --merge win1.drrstate,win2.drrstate</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endverbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : After getting the .grad and .count file, you can do numerical integration by</a>
+<a name="59"><span class="lineNum">      59 </span>            : using abf_integrate tool from</a>
+<a name="60"><span class="lineNum">      60 </span>            : https://github.com/Colvars/colvars/tree/master/colvartools</a>
+<a name="61"><span class="lineNum">      61 </span>            : \verbatim</a>
+<a name="62"><span class="lineNum">      62 </span>            : abf_integrate eabf.czar.grad</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endverbatim</a>
+<a name="64"><span class="lineNum">      64 </span>            : \note</a>
+<a name="65"><span class="lineNum">      65 </span>            : The abf_integrate in colvartools is in kcal/mol, so it may be better to use --units kcal/mol when running drr_tool</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : //+ENDPLUMEDOC</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : using std::vector;</a>
+<a name="71"><span class="lineNum">      71 </span>            : using std::string;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : class drrtool : public CLTool {</a>
+<a name="74"><span class="lineNum">      74 </span>            : public:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static void registerKeywords(Keywords &amp;keys);</a>
+<a name="76"><span class="lineNum">      76 </span>            :   explicit drrtool(const CLToolOptions &amp;co);</a>
+<a name="77"><span class="lineNum">      77 </span>            :   int main(FILE *in, FILE *out, Communicator &amp;pc);</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void extractdrr(const vector&lt;string&gt; &amp;filename);</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void mergewindows(const vector&lt;string&gt; &amp;filename, string outputname);</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void calcDivergence(const vector&lt;string&gt; &amp;filename);</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 :   string description() const { return &quot;Extract or merge the drrstate files.&quot;; }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : private:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   bool verbosity;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   Units units;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   const string suffix{&quot;.drrstate&quot;};</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      12513 : PLUMED_REGISTER_CLTOOL(drrtool, &quot;drr_tool&quot;)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       4168 : void drrtool::registerKeywords(Keywords &amp;keys) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       4168 :   CLTool::registerKeywords(keys);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;, &quot;--extract&quot;, &quot;Extract drrstate file(s)&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;, &quot;--merge&quot;, &quot;Merge eABF windows&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;, &quot;--merge_output&quot;, &quot;The output filename of the merged result&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;, &quot;--divergence&quot;, &quot;Calculate divergence of gradient field (experimental)&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--units&quot;,&quot;kj/mol&quot;,&quot;the units of energy can be kj/mol, kcal/mol, j/mol, eV or the conversion factor from kj/mol&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       8336 :   keys.addFlag(&quot;-v&quot;, false, &quot;Verbose output&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       4168 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          9 : drrtool::drrtool(const CLToolOptions &amp;co) : CLTool(co) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          9 :   inputdata = commandline;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          9 :   verbosity = false;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          9 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          5 : int drrtool::main(FILE *in, FILE *out, Communicator &amp;pc) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         10 :   parseFlag(&quot;-v&quot;, verbosity);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   vector&lt;string&gt; stateFilesToExtract;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   string unitname;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          5 :   parse(&quot;--units&quot;,unitname);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          5 :   units.setEnergy( unitname );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          5 :   bool doextract = parseVector(&quot;--extract&quot;, stateFilesToExtract);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          5 :   if (doextract) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :     extractdrr(stateFilesToExtract);</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   }</a>
+<a name="116"><span class="lineNum">     116 </span>            :   vector&lt;string&gt; stateFilesToMerge;</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          5 :   bool domerge = parseVector(&quot;--merge&quot;, stateFilesToMerge);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          5 :   if (domerge) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     string merge_outputname;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :     parse(&quot;--merge_output&quot;, merge_outputname);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          4 :     mergewindows(stateFilesToMerge, merge_outputname);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span>            :   vector&lt;string&gt; stateFilesToDivergence;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          5 :   bool dodivergence = parseVector(&quot;--divergence&quot;, stateFilesToDivergence);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          5 :   if (dodivergence) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :     calcDivergence(stateFilesToDivergence);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          5 :   return 0;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         10 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 : void drrtool::extractdrr(const vector&lt;string&gt; &amp;filename) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :   #pragma omp parallel for</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   for (size_t j = 0; j &lt; filename.size(); ++j) {</a>
+<a name="134"><span class="lineNum">     134 </span>            :     std::ifstream in;</a>
+<a name="135"><span class="lineNum">     135 </span>            :     in.open(filename[j]);</a>
+<a name="136"><span class="lineNum">     136 </span>            :     boost::archive::binary_iarchive ia(in);</a>
+<a name="137"><span class="lineNum">     137 </span>            :     long long int step;</a>
+<a name="138"><span class="lineNum">     138 </span>            :     vector&lt;double&gt; fict;</a>
+<a name="139"><span class="lineNum">     139 </span>            :     vector&lt;double&gt; vfict;</a>
+<a name="140"><span class="lineNum">     140 </span>            :     vector&lt;double&gt; vfict_laststep;</a>
+<a name="141"><span class="lineNum">     141 </span>            :     vector&lt;double&gt; ffict;</a>
+<a name="142"><span class="lineNum">     142 </span>            :     ABF abfgrid;</a>
+<a name="143"><span class="lineNum">     143 </span>            :     CZAR czarestimator;</a>
+<a name="144"><span class="lineNum">     144 </span>            :     ia &gt;&gt; step &gt;&gt; fict &gt;&gt; vfict &gt;&gt; vfict_laststep &gt;&gt; ffict &gt;&gt; abfgrid &gt;&gt;</a>
+<a name="145"><span class="lineNum">     145 </span>            :        czarestimator;</a>
+<a name="146"><span class="lineNum">     146 </span>            :     in.close();</a>
+<a name="147"><span class="lineNum">     147 </span>            :     abfgrid.setOutputUnit(units.getEnergy());</a>
+<a name="148"><span class="lineNum">     148 </span>            :     czarestimator.setOutputUnit(units.getEnergy());</a>
+<a name="149"><span class="lineNum">     149 </span>            :     if (verbosity) {</a>
+<a name="150"><span class="lineNum">     150 </span>            :       std::cout &lt;&lt; &quot;Output units factor: &quot; &lt;&lt; units.getEnergy() &lt;&lt; '\n';</a>
+<a name="151"><span class="lineNum">     151 </span>            :       std::cout &lt;&lt; &quot;Dumping information of extended variables...&quot; &lt;&lt; '\n';</a>
+<a name="152"><span class="lineNum">     152 </span>            :       std::cout &lt;&lt; &quot;Step: &quot; &lt;&lt; step &lt;&lt; '\n';</a>
+<a name="153"><span class="lineNum">     153 </span>            :       for (size_t i = 0; i &lt; fict.size(); ++i) {</a>
+<a name="154"><span class="lineNum">     154 </span>            :         std::cout &lt;&lt; &quot;Dimension[&quot; &lt;&lt; i + 1 &lt;&lt; &quot;]:\n&quot;</a>
+<a name="155"><span class="lineNum">     155 </span>            :                   &lt;&lt; &quot;  Coordinate: &quot; &lt;&lt; fict[i] &lt;&lt; '\n'</a>
+<a name="156"><span class="lineNum">     156 </span>            :                   &lt;&lt; &quot;  Velocity: &quot; &lt;&lt; vfict[i] &lt;&lt; '\n'</a>
+<a name="157"><span class="lineNum">     157 </span>            :                   &lt;&lt; &quot;  Velocity(laststep): &quot; &lt;&lt; vfict_laststep[i] &lt;&lt; '\n'</a>
+<a name="158"><span class="lineNum">     158 </span>            :                   &lt;&lt; &quot;  Force: &quot; &lt;&lt; ffict[i] &lt;&lt; '\n';</a>
+<a name="159"><span class="lineNum">     159 </span>            :       }</a>
+<a name="160"><span class="lineNum">     160 </span>            :       std::cout &lt;&lt; &quot;Dumping counts and gradients from grids...&quot; &lt;&lt; '\n';</a>
+<a name="161"><span class="lineNum">     161 </span>            :     }</a>
+<a name="162"><span class="lineNum">     162 </span>            :     string outputname(filename[j]);</a>
+<a name="163"><span class="lineNum">     163 </span>            :     outputname.resize(outputname.length() - suffix.length());</a>
+<a name="164"><span class="lineNum">     164 </span>            :     if (verbosity)</a>
+<a name="165"><span class="lineNum">     165 </span>            :       std::cout &lt;&lt; &quot;Writing ABF(naive) estimator files...&quot; &lt;&lt; '\n';</a>
+<a name="166"><span class="lineNum">     166 </span>            :     abfgrid.writeAll(outputname);</a>
+<a name="167"><span class="lineNum">     167 </span>            :     if (verbosity)</a>
+<a name="168"><span class="lineNum">     168 </span>            :       std::cout &lt;&lt; &quot;Writing CZAR estimator files...&quot; &lt;&lt; '\n';</a>
+<a name="169"><span class="lineNum">     169 </span>            :     czarestimator.writeAll(outputname);</a>
+<a name="170"><span class="lineNum">     170 </span>            :     czarestimator.writeZCountZGrad(outputname);</a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 : void drrtool::mergewindows(const vector&lt;string&gt; &amp;filename, string outputname) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          2 :   if (filename.size() &lt; 2) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     std::cerr &lt;&lt; &quot;ERROR! You need at least two .drrstate file to merge windows!&quot; &lt;&lt; std::endl;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     std::abort();</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            :   // Read grid into abfs and czars;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   vector&lt;ABF&gt; abfs;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   vector&lt;CZAR&gt; czars;</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          6 :   for (auto it_fn = filename.begin(); it_fn != filename.end(); ++it_fn) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          4 :     std::ifstream in;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :     in.open((*it_fn));</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 :     boost::archive::binary_iarchive ia(in);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     long long int step;</a>
+<a name="187"><span class="lineNum">     187 </span>            :     vector&lt;double&gt; fict;</a>
+<a name="188"><span class="lineNum">     188 </span>            :     vector&lt;double&gt; vfict;</a>
+<a name="189"><span class="lineNum">     189 </span>            :     vector&lt;double&gt; vfict_laststep;</a>
+<a name="190"><span class="lineNum">     190 </span>            :     vector&lt;double&gt; ffict;</a>
+<a name="191"><span class="lineNum">     191 </span>            :     ABF abfgrid;</a>
+<a name="192"><span class="lineNum">     192 </span>            :     CZAR czarestimator;</a>
+<a name="193"><span class="lineNum">     193 </span>            :     ia &gt;&gt; step &gt;&gt; fict &gt;&gt; vfict &gt;&gt; vfict_laststep &gt;&gt; ffict &gt;&gt; abfgrid &gt;&gt;</a>
+<a name="194"><span class="lineNum">     194 </span>            :        czarestimator;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          4 :     abfgrid.setOutputUnit(units.getEnergy());</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :     czarestimator.setOutputUnit(units.getEnergy());</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          4 :     abfs.push_back(abfgrid);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          4 :     czars.push_back(czarestimator);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          4 :     in.close();</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          8 :   }</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          2 :   CZAR cmerged = CZAR::mergewindow(czars[0], czars[1]);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :   ABF amerged = ABF::mergewindow(abfs[0], abfs[1]);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          2 :   for (size_t i = 2; i &lt; czars.size(); ++i) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     cmerged = CZAR::mergewindow(cmerged, czars[i]);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :     amerged = ABF::mergewindow(amerged, abfs[i]);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          2 :   if (outputname.empty()) {</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :     // Generate new file name for merged grad and count</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          1 :     vector&lt;string&gt; tmp_name = filename;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          1 :     std::transform(std::begin(tmp_name), std::end(tmp_name), std::begin(tmp_name),</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 :     [&amp;](string s) {return s.substr(0, s.find(suffix));});</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          2 :     outputname = std::accumulate(std::begin(tmp_name), std::end(tmp_name), string(&quot;&quot;),</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          5 :     [](const string &amp; a, const string &amp; b) {return a + b + &quot;+&quot;;});</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          1 :     outputname.resize(outputname.size() - 1);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :     std::cerr &lt;&lt; &quot;You have not specified an output filename for the merged&quot;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          1 :               &lt;&lt; &quot; result, so the default name \&quot;&quot; + outputname</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          2 :               &lt;&lt; &quot;\&quot; is used here, which may yield unexpected behavior.\n&quot;;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 :   }</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          2 :   cmerged.writeAll(outputname);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          2 :   cmerged.writeZCountZGrad(outputname);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          2 :   amerged.writeAll(outputname);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          4 : }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          1 : void drrtool::calcDivergence(const vector&lt;string&gt; &amp;filename) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          1 :   #pragma omp parallel for</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   for (size_t j = 0; j &lt; filename.size(); ++j) {</a>
+<a name="227"><span class="lineNum">     227 </span>            :     std::ifstream in;</a>
+<a name="228"><span class="lineNum">     228 </span>            :     in.open(filename[j]);</a>
+<a name="229"><span class="lineNum">     229 </span>            :     boost::archive::binary_iarchive ia(in);</a>
+<a name="230"><span class="lineNum">     230 </span>            :     long long int step;</a>
+<a name="231"><span class="lineNum">     231 </span>            :     vector&lt;double&gt; fict;</a>
+<a name="232"><span class="lineNum">     232 </span>            :     vector&lt;double&gt; vfict;</a>
+<a name="233"><span class="lineNum">     233 </span>            :     vector&lt;double&gt; vfict_laststep;</a>
+<a name="234"><span class="lineNum">     234 </span>            :     vector&lt;double&gt; ffict;</a>
+<a name="235"><span class="lineNum">     235 </span>            :     ABF abfgrid;</a>
+<a name="236"><span class="lineNum">     236 </span>            :     CZAR czarestimator;</a>
+<a name="237"><span class="lineNum">     237 </span>            :     ia &gt;&gt; step &gt;&gt; fict &gt;&gt; vfict &gt;&gt; vfict_laststep &gt;&gt; ffict &gt;&gt; abfgrid &gt;&gt;</a>
+<a name="238"><span class="lineNum">     238 </span>            :        czarestimator;</a>
+<a name="239"><span class="lineNum">     239 </span>            :     in.close();</a>
+<a name="240"><span class="lineNum">     240 </span>            :     abfgrid.setOutputUnit(units.getEnergy());</a>
+<a name="241"><span class="lineNum">     241 </span>            :     czarestimator.setOutputUnit(units.getEnergy());</a>
+<a name="242"><span class="lineNum">     242 </span>            :     if (verbosity) {</a>
+<a name="243"><span class="lineNum">     243 </span>            :       std::cout &lt;&lt; &quot;Output units factor: &quot; &lt;&lt; units.getEnergy() &lt;&lt; '\n';</a>
+<a name="244"><span class="lineNum">     244 </span>            :       std::cout &lt;&lt; &quot;Dumping information of extended variables...&quot; &lt;&lt; '\n';</a>
+<a name="245"><span class="lineNum">     245 </span>            :       std::cout &lt;&lt; &quot;Step: &quot; &lt;&lt; step &lt;&lt; '\n';</a>
+<a name="246"><span class="lineNum">     246 </span>            :       for (size_t i = 0; i &lt; fict.size(); ++i) {</a>
+<a name="247"><span class="lineNum">     247 </span>            :         std::cout &lt;&lt; &quot;Dimension[&quot; &lt;&lt; i + 1 &lt;&lt; &quot;]:\n&quot;</a>
+<a name="248"><span class="lineNum">     248 </span>            :                   &lt;&lt; &quot;  Coordinate: &quot; &lt;&lt; fict[i] &lt;&lt; '\n'</a>
+<a name="249"><span class="lineNum">     249 </span>            :                   &lt;&lt; &quot;  Velocity: &quot; &lt;&lt; vfict[i] &lt;&lt; '\n'</a>
+<a name="250"><span class="lineNum">     250 </span>            :                   &lt;&lt; &quot;  Velocity(laststep): &quot; &lt;&lt; vfict_laststep[i] &lt;&lt; '\n'</a>
+<a name="251"><span class="lineNum">     251 </span>            :                   &lt;&lt; &quot;  Force: &quot; &lt;&lt; ffict[i] &lt;&lt; '\n';</a>
+<a name="252"><span class="lineNum">     252 </span>            :       }</a>
+<a name="253"><span class="lineNum">     253 </span>            :       std::cout &lt;&lt; &quot;Dumping counts and gradients from grids...&quot; &lt;&lt; '\n';</a>
+<a name="254"><span class="lineNum">     254 </span>            :     }</a>
+<a name="255"><span class="lineNum">     255 </span>            :     string outputname(filename[j]);</a>
+<a name="256"><span class="lineNum">     256 </span>            :     outputname.resize(outputname.length() - suffix.length());</a>
+<a name="257"><span class="lineNum">     257 </span>            :     abfgrid.writeDivergence(outputname);</a>
+<a name="258"><span class="lineNum">     258 </span>            :     czarestimator.writeDivergence(outputname);</a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 : }</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : } // End of namespace</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/index-sort-f.html b/coverage/drr/index-sort-f.html
new file mode 100644
index 0000000000..48d9881b11
--- /dev/null
+++ b/coverage/drr/index-sort-f.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - drr</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1194</td>
+            <td class="headerCovTableEntry">1266</td>
+            <td class="headerCovTableEntryHi">94.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryHi">94.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRR.h.gcov.html">DRR.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">99 / 99</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DynamicReferenceRestraining.cpp.gcov.html">DynamicReferenceRestraining.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.8%"><img src="../snow.png" width=9 height=10 alt="90.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.8&nbsp;%</td>
+      <td class="coverNumHi">403 / 444</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRR.cpp.gcov.html">DRR.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.2%"><img src="../snow.png" width=7 height=10 alt="93.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.2&nbsp;%</td>
+      <td class="coverNumHi">328 / 352</td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="drrtool.cpp.gcov.html">drrtool.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.2%"><img src="../snow.png" width=6 height=10 alt="94.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.2&nbsp;%</td>
+      <td class="coverNumHi">65 / 69</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="colvar_UIestimator.h.gcov.html">colvar_UIestimator.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.0%"><img src="../snow.png" width=1 height=10 alt="99.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.0&nbsp;%</td>
+      <td class="coverNumHi">299 / 302</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/index-sort-l.html b/coverage/drr/index-sort-l.html
new file mode 100644
index 0000000000..3799833c0d
--- /dev/null
+++ b/coverage/drr/index-sort-l.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - drr</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1194</td>
+            <td class="headerCovTableEntry">1266</td>
+            <td class="headerCovTableEntryHi">94.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryHi">94.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DynamicReferenceRestraining.cpp.gcov.html">DynamicReferenceRestraining.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.8%"><img src="../snow.png" width=9 height=10 alt="90.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.8&nbsp;%</td>
+      <td class="coverNumHi">403 / 444</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRR.cpp.gcov.html">DRR.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.2%"><img src="../snow.png" width=7 height=10 alt="93.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.2&nbsp;%</td>
+      <td class="coverNumHi">328 / 352</td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="drrtool.cpp.gcov.html">drrtool.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.2%"><img src="../snow.png" width=6 height=10 alt="94.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.2&nbsp;%</td>
+      <td class="coverNumHi">65 / 69</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="colvar_UIestimator.h.gcov.html">colvar_UIestimator.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.0%"><img src="../snow.png" width=1 height=10 alt="99.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.0&nbsp;%</td>
+      <td class="coverNumHi">299 / 302</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRR.h.gcov.html">DRR.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">99 / 99</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/drr/index.html b/coverage/drr/index.html
new file mode 100644
index 0000000000..e55f2e62f7
--- /dev/null
+++ b/coverage/drr/index.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - drr</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - drr</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1194</td>
+            <td class="headerCovTableEntry">1266</td>
+            <td class="headerCovTableEntryHi">94.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryHi">94.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRR.cpp.gcov.html">DRR.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.2%"><img src="../snow.png" width=7 height=10 alt="93.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.2&nbsp;%</td>
+      <td class="coverNumHi">328 / 352</td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRR.h.gcov.html">DRR.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">99 / 99</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DynamicReferenceRestraining.cpp.gcov.html">DynamicReferenceRestraining.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.8%"><img src="../snow.png" width=9 height=10 alt="90.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.8&nbsp;%</td>
+      <td class="coverNumHi">403 / 444</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="colvar_UIestimator.h.gcov.html">colvar_UIestimator.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.0%"><img src="../snow.png" width=1 height=10 alt="99.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.0&nbsp;%</td>
+      <td class="coverNumHi">299 / 302</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="drrtool.cpp.gcov.html">drrtool.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.2%"><img src="../snow.png" width=6 height=10 alt="94.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.2&nbsp;%</td>
+      <td class="coverNumHi">65 / 69</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/eds/EDS.cpp.func-sort-c.html b/coverage/eds/EDS.cpp.func-sort-c.html
new file mode 100644
index 0000000000..18d8715158
--- /dev/null
+++ b/coverage/eds/EDS.cpp.func-sort-c.html
@@ -0,0 +1,164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - eds/EDS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">eds</a> - EDS.cpp<span style="font-size: 80%;"> (<a href="EDS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">452</td>
+            <td class="headerCovTableEntry">488</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryMed">87.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EDS.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1170">_ZN4PLMD3eds3EDS17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#323">_ZN4PLMD3eds3EDSC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1165">_ZN4PLMD3eds3EDSD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#942">_ZN4PLMD3eds3EDS17calc_lm_step_sizeEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#965">_ZN4PLMD3eds3EDS20calc_covar_step_sizeEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#663">_ZN4PLMD3eds3EDS13readInRestartEb</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#989">_ZN4PLMD3eds3EDS20update_pseudo_virialEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#979">_ZN4PLMD3eds3EDS18calc_ssd_step_sizeEv</a></td>
+              <td class="coverFnHi">6</td>
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+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#278">_ZN4PLMD3eds12_GLOBAL__N_116EDSRegisterMe2806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1033">_ZN4PLMD3eds3EDS11update_biasEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#797">_ZN4PLMD3eds3EDS15setupOutRestartEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#917">_ZN4PLMD3eds3EDS16reset_statisticsEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#323">_ZN4PLMD3eds3EDSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1165">_ZN4PLMD3eds3EDSD0Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1165">_ZN4PLMD3eds3EDSD1Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#280">_ZN4PLMD3eds3EDS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#866">_ZN4PLMD3eds3EDS17update_statisticsEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#810">_ZN4PLMD3eds3EDS15writeOutRestartEv</a></td>
+              <td class="coverFnHi">27</td>
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+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#847">_ZN4PLMD3eds3EDS10apply_biasEv</a></td>
+              <td class="coverFnHi">40</td>
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+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1083">_ZN4PLMD3eds3EDS6updateEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#836">_ZN4PLMD3eds3EDS9calculateEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#278">_ZN4PLMD3eds12_GLOBAL__N_116EDSRegisterMe280C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#278">_ZN4PLMD3eds12_GLOBAL__N_116EDSRegisterMe280D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/eds/EDS.cpp.func.html b/coverage/eds/EDS.cpp.func.html
new file mode 100644
index 0000000000..0fb3d5dc78
--- /dev/null
+++ b/coverage/eds/EDS.cpp.func.html
@@ -0,0 +1,164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - eds/EDS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">eds</a> - EDS.cpp<span style="font-size: 80%;"> (<a href="EDS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">452</td>
+            <td class="headerCovTableEntry">488</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryMed">87.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EDS.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#278">_ZN4PLMD3eds12_GLOBAL__N_116EDSRegisterMe2806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#278">_ZN4PLMD3eds12_GLOBAL__N_116EDSRegisterMe280C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#278">_ZN4PLMD3eds12_GLOBAL__N_116EDSRegisterMe280D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#847">_ZN4PLMD3eds3EDS10apply_biasEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1033">_ZN4PLMD3eds3EDS11update_biasEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#663">_ZN4PLMD3eds3EDS13readInRestartEb</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#797">_ZN4PLMD3eds3EDS15setupOutRestartEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#810">_ZN4PLMD3eds3EDS15writeOutRestartEv</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#280">_ZN4PLMD3eds3EDS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#917">_ZN4PLMD3eds3EDS16reset_statisticsEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#942">_ZN4PLMD3eds3EDS17calc_lm_step_sizeEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1170">_ZN4PLMD3eds3EDS17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#866">_ZN4PLMD3eds3EDS17update_statisticsEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#979">_ZN4PLMD3eds3EDS18calc_ssd_step_sizeEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#965">_ZN4PLMD3eds3EDS20calc_covar_step_sizeEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#989">_ZN4PLMD3eds3EDS20update_pseudo_virialEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1083">_ZN4PLMD3eds3EDS6updateEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#836">_ZN4PLMD3eds3EDS9calculateEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#323">_ZN4PLMD3eds3EDSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#323">_ZN4PLMD3eds3EDSC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1165">_ZN4PLMD3eds3EDSD0Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1165">_ZN4PLMD3eds3EDSD1Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EDS.cpp.gcov.html#1165">_ZN4PLMD3eds3EDSD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/eds/EDS.cpp.gcov.html b/coverage/eds/EDS.cpp.gcov.html
new file mode 100644
index 0000000000..c8c25db39f
--- /dev/null
+++ b/coverage/eds/EDS.cpp.gcov.html
@@ -0,0 +1,1256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - eds/EDS.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">eds</a> - EDS.cpp<span style="font-size: 80%;"> (source / <a href="EDS.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">452</td>
+            <td class="headerCovTableEntry">488</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryMed">87.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2017 of Glen Hocky and Andrew White</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : The eds module is free software: you can redistribute it and/or modify</a>
+<a name="5"><span class="lineNum">       5 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="6"><span class="lineNum">       6 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="7"><span class="lineNum">       7 </span>            : (at your option) any later version.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : The eds module is distributed in the hope that it will be useful,</a>
+<a name="10"><span class="lineNum">      10 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="11"><span class="lineNum">      11 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="12"><span class="lineNum">      12 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="15"><span class="lineNum">      15 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="16"><span class="lineNum">      16 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="17"><span class="lineNum">      17 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="18"><span class="lineNum">      18 </span>            : #include &quot;bias/ReweightBase.h&quot;</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : using namespace PLMD;</a>
+<a name="30"><span class="lineNum">      30 </span>            : using namespace bias;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // namespace is lowercase to match</a>
+<a name="33"><span class="lineNum">      33 </span>            : // module names being all lowercase</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD</a>
+<a name="36"><span class="lineNum">      36 </span>            : {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace eds</a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : //+PLUMEDOC EDSMOD_BIAS EDS</a>
+<a name="41"><span class="lineNum">      41 </span>            : /*</a>
+<a name="42"><span class="lineNum">      42 </span>            : Add a linear bias on a set of observables.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This force is the same as the linear part of the bias in \ref</a>
+<a name="45"><span class="lineNum">      45 </span>            : RESTRAINT, but this bias has the ability to compute the prefactors</a>
+<a name="46"><span class="lineNum">      46 </span>            : adaptively using the scheme of White and Voth \cite white2014efficient</a>
+<a name="47"><span class="lineNum">      47 </span>            : in order to match target observable values for a set of CVs.</a>
+<a name="48"><span class="lineNum">      48 </span>            : Further updates to the algorithm are described in \cite hocky2017cgds</a>
+<a name="49"><span class="lineNum">      49 </span>            : and you can read a review on the method and its applications here: \cite Amirkulova2019Recent.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : You can</a>
+<a name="52"><span class="lineNum">      52 </span>            : see a tutorial on EDS specifically for biasing coordination number at</a>
+<a name="53"><span class="lineNum">      53 </span>            : &lt;a</a>
+<a name="54"><span class="lineNum">      54 </span>            : href=&quot;http://thewhitelab.org/blog/tutorial/2017/05/10/lammps-coordination-number-tutorial/&quot;&gt;</a>
+<a name="55"><span class="lineNum">      55 </span>            : Andrew White's webpage&lt;/a&gt;.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : The addition to the potential is of the form</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f[</a>
+<a name="59"><span class="lineNum">      59 </span>            :   \sum_i \frac{\alpha_i}{s_i} x_i</a>
+<a name="60"><span class="lineNum">      60 </span>            : \f]</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : where for CV \f$x_i\f$, a coupling constant \f${\alpha}_i\f$ is determined</a>
+<a name="63"><span class="lineNum">      63 </span>            : adaptively or set by the user to match a target value for</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f$x_i\f$. \f$s_i\f$ is a scale parameter, which by default is set to</a>
+<a name="65"><span class="lineNum">      65 </span>            : the target value. It may also be set separately.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \warning</a>
+<a name="68"><span class="lineNum">      68 </span>            : It is not possible to set the target value of the observable</a>
+<a name="69"><span class="lineNum">      69 </span>            : to zero with the default value of \f$s_i\f$ as this will cause a</a>
+<a name="70"><span class="lineNum">      70 </span>            : divide-by-zero error. Instead, set \f$s_i=1\f$ or modify the CV so the</a>
+<a name="71"><span class="lineNum">      71 </span>            : desired target value is no longer zero.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : Notice that a similar method is available as \ref MAXENT, although with different features and using a different optimization algorithm.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : \par Virial</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : The bias forces modify the virial and this can change your simulation density if the bias is used in an NPT simulation.</a>
+<a name="78"><span class="lineNum">      78 </span>            : One way to avoid changing the virial contribution from the bias is to add the keyword VIRIAL=1.0, which changes how the bias</a>
+<a name="79"><span class="lineNum">      79 </span>            : is computed to minimize its contribution to the virial. This can also lead to smaller magnitude biases that are more robust if</a>
+<a name="80"><span class="lineNum">      80 </span>            : transferred to other systems.  VIRIAL=1.0 can be a reasonable starting point and increasing the value changes the balance between matching</a>
+<a name="81"><span class="lineNum">      81 </span>            : the set-points and minimizing the virial. See \cite Amirkulova2019Recent for details on the equations. Since the coupling constants</a>
+<a name="82"><span class="lineNum">      82 </span>            : are unique with a single CV, VIRIAL is not applicable with a single CV. When used with multiple CVs, the CVs should be correlated</a>
+<a name="83"><span class="lineNum">      83 </span>            : which is almost always the case.</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : \par Weighting</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : EDS computes means and variances as part of its algorithm. If you are</a>
+<a name="88"><span class="lineNum">      88 </span>            : also using a biasing method like metadynamics, you may wish to remove</a>
+<a name="89"><span class="lineNum">      89 </span>            : the effect of this bias in your EDS computations so that EDS works on</a>
+<a name="90"><span class="lineNum">      90 </span>            : the canonical values (reweighted to be unbiased).  For example, you may be using</a>
+<a name="91"><span class="lineNum">      91 </span>            : metadynamics to bias a dihedral angle to enhance sampling and be using</a>
+<a name="92"><span class="lineNum">      92 </span>            : EDS to set the average distance between two particular atoms. Specifically:</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : \plumedfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : # set-up metadynamics</a>
+<a name="96"><span class="lineNum">      96 </span>            : t: TORSION ATOMS=1,2,3,4</a>
+<a name="97"><span class="lineNum">      97 </span>            : md: METAD ARG=d SIGMA=0.2 HEIGHT=0.3 PACE=500 TEMP=300</a>
+<a name="98"><span class="lineNum">      98 </span>            : # compute bias weights</a>
+<a name="99"><span class="lineNum">      99 </span>            : bias: REWEIGHT_METAD TEMP=300</a>
+<a name="100"><span class="lineNum">     100 </span>            : # now do EDS on distance while removing effect of metadynamics</a>
+<a name="101"><span class="lineNum">     101 </span>            : d: DISTANCE ATOMS=4,7</a>
+<a name="102"><span class="lineNum">     102 </span>            : eds: EDS ARG=d CENTER=3.0 PERIOD=100 TEMP=300 LOGWEIGHTS=bias</a>
+<a name="103"><span class="lineNum">     103 </span>            : \endplumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : This is an approximation though because EDS uses a finite samples while running to get means/variances.</a>
+<a name="106"><span class="lineNum">     106 </span>            : At the end of a run,</a>
+<a name="107"><span class="lineNum">     107 </span>            : you should ensure this approach worked and indeed your reweighted CV matches the target value.</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : \par Examples</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : The following input for a harmonic oscillator of two beads will</a>
+<a name="112"><span class="lineNum">     112 </span>            : adaptively find a linear bias to change the mean and variance to the</a>
+<a name="113"><span class="lineNum">     113 </span>            : target values. The PRINT line shows how to access the value of the</a>
+<a name="114"><span class="lineNum">     114 </span>            : coupling constants.</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : \plumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : dist: DISTANCE ATOMS=1,2</a>
+<a name="118"><span class="lineNum">     118 </span>            : # this is the squared of the distance</a>
+<a name="119"><span class="lineNum">     119 </span>            : dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : # bias mean and variance</a>
+<a name="122"><span class="lineNum">     122 </span>            : eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=100 TEMP=1.0</a>
+<a name="123"><span class="lineNum">     123 </span>            : PRINT ARG=dist,dist2,eds.dist_coupling,eds.dist2_coupling,eds.bias,eds.force2 FILE=colvars.dat STRIDE=100</a>
+<a name="124"><span class="lineNum">     124 </span>            : \endplumedfile</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : &lt;hr&gt;</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : Rather than trying to find the coupling constants adaptively, one can ramp up to a constant value.</a>
+<a name="129"><span class="lineNum">     129 </span>            : \plumedfile</a>
+<a name="130"><span class="lineNum">     130 </span>            : dist: DISTANCE ATOMS=1,2</a>
+<a name="131"><span class="lineNum">     131 </span>            : dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : # ramp couplings from 0,0 to -1,1 over 50000 steps</a>
+<a name="134"><span class="lineNum">     134 </span>            : eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 FIXED=-1,1 RAMP PERIOD=50000 TEMP=1.0</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : # same as above, except starting at -0.5,0.5 rather than default of 0,0</a>
+<a name="137"><span class="lineNum">     137 </span>            : eds2: EDS ARG=dist,dist2 CENTER=2.0,1.0 FIXED=-1,1 INIT=-0.5,0.5 RAMP PERIOD=50000 TEMP=1.0</a>
+<a name="138"><span class="lineNum">     138 </span>            : \endplumedfile</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : &lt;hr&gt;</a>
+<a name="141"><span class="lineNum">     141 </span>            : A restart file can be added to dump information needed to restart/continue simulation using these parameters every PERIOD.</a>
+<a name="142"><span class="lineNum">     142 </span>            : \plumedfile</a>
+<a name="143"><span class="lineNum">     143 </span>            : dist: DISTANCE ATOMS=1,2</a>
+<a name="144"><span class="lineNum">     144 </span>            : dist2: COMBINE ARG=dist POWERS=2 PERIODIC=NO</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : # add the option to write to a restart file</a>
+<a name="147"><span class="lineNum">     147 </span>            : eds: EDS ARG=dist,dist2 CENTER=2.0,1.0 PERIOD=100 TEMP=1.0 OUT_RESTART=checkpoint.eds</a>
+<a name="148"><span class="lineNum">     148 </span>            : \endplumedfile</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : The first few lines of the restart file that is output if we run a calculation with one CV will look something like this:</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : \auxfile{restart.eds}</a>
+<a name="153"><span class="lineNum">     153 </span>            : #! FIELDS time d1_center d1_set d1_target d1_coupling d1_maxrange d1_maxgrad d1_accum d1_mean d1_std</a>
+<a name="154"><span class="lineNum">     154 </span>            : #! SET adaptive  1</a>
+<a name="155"><span class="lineNum">     155 </span>            : #! SET update_period  1</a>
+<a name="156"><span class="lineNum">     156 </span>            : #! SET seed  0</a>
+<a name="157"><span class="lineNum">     157 </span>            : #! SET kbt    2.4943</a>
+<a name="158"><span class="lineNum">     158 </span>            :    0.0000   1.0000   0.0000   0.0000   0.0000   7.4830   0.1497   0.0000   0.0000   0.0000</a>
+<a name="159"><span class="lineNum">     159 </span>            :    1.0000   1.0000   0.0000   0.0000   0.0000   7.4830   0.1497   0.0000   0.0000   0.0000</a>
+<a name="160"><span class="lineNum">     160 </span>            :    2.0000   1.0000  -7.4830   0.0000   0.0000   7.4830   0.1497   0.0224   0.0000   0.0000</a>
+<a name="161"><span class="lineNum">     161 </span>            :    3.0000   1.0000  -7.4830   0.0000  -7.4830   7.4830   0.1497   0.0224   0.0000   0.0000</a>
+<a name="162"><span class="lineNum">     162 </span>            :    4.0000   1.0000  -7.4830   0.0000  -7.4830   7.4830   0.1497   0.0224   0.0000   0.0000</a>
+<a name="163"><span class="lineNum">     163 </span>            : \endauxfile</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : &lt;hr&gt;</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : Read in a previous restart file. Adding RESTART flag makes output append</a>
+<a name="168"><span class="lineNum">     168 </span>            : \plumedfile</a>
+<a name="169"><span class="lineNum">     169 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : eds: EDS ARG=d1 CENTER=2.0 PERIOD=100 TEMP=1.0 IN_RESTART=restart.eds RESTART=YES</a>
+<a name="172"><span class="lineNum">     172 </span>            : \endplumedfile</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : &lt;hr&gt;</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : Read in a previous restart file and freeze the bias at the final level from the previous simulation</a>
+<a name="177"><span class="lineNum">     177 </span>            : \plumedfile</a>
+<a name="178"><span class="lineNum">     178 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : eds: EDS ARG=d1 CENTER=2.0 TEMP=1.0 IN_RESTART=restart.eds FREEZE</a>
+<a name="181"><span class="lineNum">     181 </span>            : \endplumedfile</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : &lt;hr&gt;</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : Read in a previous restart file and freeze the bias at the mean from the previous simulation</a>
+<a name="186"><span class="lineNum">     186 </span>            : \plumedfile</a>
+<a name="187"><span class="lineNum">     187 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : eds: EDS ARG=d1 CENTER=2.0 TEMP=1.0 IN_RESTART=restart.eds FREEZE MEAN</a>
+<a name="190"><span class="lineNum">     190 </span>            : \endplumedfile</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : */</a>
+<a name="194"><span class="lineNum">     194 </span>            : //+ENDPLUMEDOC</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : class EDS : public Bias</a>
+<a name="197"><span class="lineNum">     197 </span>            : {</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : private:</a>
+<a name="200"><span class="lineNum">     200 </span>            :   /*We will get this and store it once, since on-the-fly changing number of CVs will be fatal*/</a>
+<a name="201"><span class="lineNum">     201 </span>            :   const unsigned int ncvs_;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   std::vector&lt;double&gt; center_;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   std::vector&lt;Value *&gt; center_values_;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   ReweightBase *logweights_; // weights to use if reweighting averages</a>
+<a name="205"><span class="lineNum">     205 </span>            :   std::vector&lt;double&gt; scale_;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   std::vector&lt;double&gt; current_coupling_;   // actually current coupling</a>
+<a name="207"><span class="lineNum">     207 </span>            :   std::vector&lt;double&gt; set_coupling_;       // what our coupling is ramping up to. Equal to current_coupling when gathering stats</a>
+<a name="208"><span class="lineNum">     208 </span>            :   std::vector&lt;double&gt; target_coupling_;    // used when loaded to reach a value</a>
+<a name="209"><span class="lineNum">     209 </span>            :   std::vector&lt;double&gt; max_coupling_range_; // used for adaptive range</a>
+<a name="210"><span class="lineNum">     210 </span>            :   std::vector&lt;double&gt; max_coupling_grad_;  // maximum allowed gradient</a>
+<a name="211"><span class="lineNum">     211 </span>            :   std::vector&lt;double&gt; coupling_rate_;</a>
+<a name="212"><span class="lineNum">     212 </span>            :   std::vector&lt;double&gt; coupling_accum_;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   std::vector&lt;double&gt; means_;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   std::vector&lt;double&gt; differences_;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   std::vector&lt;double&gt; alpha_vector_;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   std::vector&lt;double&gt; alpha_vector_2_;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   std::vector&lt;double&gt; ssds_;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   std::vector&lt;double&gt; step_size_;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   std::vector&lt;double&gt; pseudo_virial_;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   std::vector&lt;Value *&gt; out_coupling_;</a>
+<a name="221"><span class="lineNum">     221 </span>            :   Matrix&lt;double&gt; covar_;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   Matrix&lt;double&gt; covar2_;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   Matrix&lt;double&gt; lm_inv_;</a>
+<a name="224"><span class="lineNum">     224 </span>            :   std::string in_restart_name_;</a>
+<a name="225"><span class="lineNum">     225 </span>            :   std::string out_restart_name_;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   std::string fmt_;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   OFile out_restart_;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   IFile in_restart_;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   bool b_c_values_;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   bool b_adaptive_;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   bool b_freeze_;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   bool b_equil_;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   bool b_ramp_;</a>
+<a name="234"><span class="lineNum">     234 </span>            :   bool b_covar_;</a>
+<a name="235"><span class="lineNum">     235 </span>            :   bool b_restart_;</a>
+<a name="236"><span class="lineNum">     236 </span>            :   bool b_write_restart_;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   bool b_lm_;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   bool b_virial_;</a>
+<a name="239"><span class="lineNum">     239 </span>            :   bool b_update_virial_;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   bool b_weights_;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   int seed_;</a>
+<a name="242"><span class="lineNum">     242 </span>            :   int update_period_;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   int avg_coupling_count_;</a>
+<a name="244"><span class="lineNum">     244 </span>            :   int update_calls_;</a>
+<a name="245"><span class="lineNum">     245 </span>            :   double kbt_;</a>
+<a name="246"><span class="lineNum">     246 </span>            :   double multi_prop_;</a>
+<a name="247"><span class="lineNum">     247 </span>            :   double lm_mixing_par_;</a>
+<a name="248"><span class="lineNum">     248 </span>            :   double virial_scaling_;</a>
+<a name="249"><span class="lineNum">     249 </span>            :   double pseudo_virial_sum_; // net virial for all cvs in current period</a>
+<a name="250"><span class="lineNum">     250 </span>            :   double max_logweight_;     // maximum observed max logweight for period</a>
+<a name="251"><span class="lineNum">     251 </span>            :   double wsum_;              // sum of weights thus far</a>
+<a name="252"><span class="lineNum">     252 </span>            :   Random rand_;</a>
+<a name="253"><span class="lineNum">     253 </span>            :   Value *value_force2_;</a>
+<a name="254"><span class="lineNum">     254 </span>            :   Value *value_pressure_;</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            :   /*read input restart. b_mean sets if we use mean or final value for freeze*/</a>
+<a name="257"><span class="lineNum">     257 </span>            :   void readInRestart(const bool b_mean);</a>
+<a name="258"><span class="lineNum">     258 </span>            :   /*setup output restart*/</a>
+<a name="259"><span class="lineNum">     259 </span>            :   void setupOutRestart();</a>
+<a name="260"><span class="lineNum">     260 </span>            :   /*write output restart*/</a>
+<a name="261"><span class="lineNum">     261 </span>            :   void writeOutRestart();</a>
+<a name="262"><span class="lineNum">     262 </span>            :   void update_statistics();</a>
+<a name="263"><span class="lineNum">     263 </span>            :   void update_pseudo_virial();</a>
+<a name="264"><span class="lineNum">     264 </span>            :   void calc_lm_step_size();</a>
+<a name="265"><span class="lineNum">     265 </span>            :   void calc_covar_step_size();</a>
+<a name="266"><span class="lineNum">     266 </span>            :   void calc_ssd_step_size();</a>
+<a name="267"><span class="lineNum">     267 </span>            :   void reset_statistics();</a>
+<a name="268"><span class="lineNum">     268 </span>            :   void update_bias();</a>
+<a name="269"><span class="lineNum">     269 </span>            :   void apply_bias();</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : public:</a>
+<a name="272"><span class="lineNum">     272 </span>            :   explicit EDS(const ActionOptions &amp;);</a>
+<a name="273"><span class="lineNum">     273 </span>            :   void calculate();</a>
+<a name="274"><span class="lineNum">     274 </span>            :   void update();</a>
+<a name="275"><span class="lineNum">     275 </span>            :   void turnOnDerivatives();</a>
+<a name="276"><span class="lineNum">     276 </span>            :   static void registerKeywords(Keywords &amp;keys);</a>
+<a name="277"><span class="lineNum">     277 </span>            :   ~EDS();</a>
+<a name="278"><span class="lineNum">     278 </span>            : };</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(EDS, &quot;EDS&quot;)</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         10 : void EDS::registerKeywords(Keywords &amp;keys)</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : {</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         10 :   Bias::registerKeywords(keys);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         10 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;CENTER&quot;, &quot;The desired centers (equilibrium values) which will be sought during the adaptive linear biasing. This is for fixed centers&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;CENTER_ARG&quot;, &quot;The desired centers (equilibrium values) which will be sought during the adaptive linear biasing. &quot;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :            &quot;CENTER_ARG is for calculated centers, e.g. from a CV or analysis. &quot;);</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;PERIOD&quot;, &quot;Steps over which to adjust bias for adaptive or ramping&quot;);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;, &quot;RANGE&quot;, &quot;25.0&quot;, &quot;The (starting) maximum increase in coupling constant per PERIOD (in \\f$k_B T\\f$/[BIAS_SCALE unit]) for each CV biased&quot;);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;, &quot;SEED&quot;, &quot;0&quot;, &quot;Seed for random order of changing bias&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;, &quot;INIT&quot;, &quot;0&quot;, &quot;Starting value for coupling constant&quot;);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;, &quot;FIXED&quot;, &quot;0&quot;, &quot;Fixed target values for coupling constant. Non-adaptive.&quot;);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;BIAS_SCALE&quot;, &quot;A divisor to set the units of the bias. &quot;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :            &quot;If not set, this will be the CENTER value by default (as is done in White and Voth 2014).&quot;);</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;TEMP&quot;, &quot;The system temperature. If not provided will be taken from MD code (if available)&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;MULTI_PROP&quot;, &quot;What proportion of dimensions to update at each step. &quot;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :            &quot;Must be in interval [1,0), where 1 indicates all and any other indicates a stochastic update. &quot;</a>
+<a name="300"><span class="lineNum">     300 </span>            :            &quot;If not set, default is 1 / N, where N is the number of CVs. &quot;);</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;VIRIAL&quot;, &quot;Add an update penalty for having non-zero virial contributions. Only makes sense with multiple correlated CVs.&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;LOGWEIGHTS&quot;, &quot;Add weights to use for computing statistics. For example, if biasing with metadynamics.&quot;);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         20 :   keys.addFlag(&quot;LM&quot;, false, &quot;Use Levenberg-Marquadt algorithm along with simultaneous keyword. Otherwise use gradient descent.&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;, &quot;LM_MIXING&quot;, &quot;1&quot;, &quot;Initial mixing parameter when using Levenberg-Marquadt minimization.&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;RESTART_FMT&quot;, &quot;the format that should be used to output real numbers in EDS restarts&quot;);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;OUT_RESTART&quot;, &quot;Output file for all information needed to continue EDS simulation. &quot;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :            &quot;If you have the RESTART directive set (global or for EDS), this file will be appended to. &quot;</a>
+<a name="308"><span class="lineNum">     308 </span>            :            &quot;Note that the header will be printed again if appending.&quot;);</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;, &quot;IN_RESTART&quot;, &quot;Read this file to continue an EDS simulation. &quot;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :            &quot;If same as OUT_RESTART and you have not set the RESTART directive, the file will be backed-up and overwritten with new output. &quot;</a>
+<a name="311"><span class="lineNum">     311 </span>            :            &quot;If you do have the RESTART flag set and it is the same name as OUT_RESTART, this file will be appended.&quot;);</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         20 :   keys.addFlag(&quot;RAMP&quot;, false, &quot;Slowly increase bias constant to a fixed value&quot;);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         20 :   keys.addFlag(&quot;COVAR&quot;, false, &quot;Utilize the covariance matrix when updating the bias. Default Off, but may be enabled due to other options&quot;);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         20 :   keys.addFlag(&quot;FREEZE&quot;, false, &quot;Fix bias at current level (only used for restarting).&quot;);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         20 :   keys.addFlag(&quot;MEAN&quot;, false, &quot;Instead of using final bias level from restart, use average. Can only be used in conjunction with FREEZE&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         10 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         20 :   keys.addOutputComponent(&quot;force2&quot;, &quot;default&quot;, &quot;squared value of force from the bias&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         20 :   keys.addOutputComponent(&quot;pressure&quot;, &quot;default&quot;, &quot;If using virial keyword, this is the current sum of virial terms. It is in units of pressure (energy / vol^3)&quot;);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         20 :   keys.addOutputComponent(&quot;_coupling&quot;, &quot;default&quot;, &quot;For each named CV biased, there will be a corresponding output CV_coupling storing the current linear bias prefactor.&quot;);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         10 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          8 : EDS::EDS(const ActionOptions &amp;ao) : PLUMED_BIAS_INIT(ao),</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          8 :   ncvs_(getNumberOfArguments()),</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          8 :   scale_(ncvs_, 0.0),</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          8 :   current_coupling_(ncvs_, 0.0),</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          8 :   set_coupling_(ncvs_, 0.0),</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          8 :   target_coupling_(ncvs_, 0.0),</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          8 :   max_coupling_range_(ncvs_, 25.0),</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          8 :   max_coupling_grad_(ncvs_, 0.0),</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          8 :   coupling_rate_(ncvs_, 1.0),</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          8 :   coupling_accum_(ncvs_, 0.0),</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          8 :   means_(ncvs_, 0.0),</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          8 :   step_size_(ncvs_, 0.0),</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          8 :   pseudo_virial_(ncvs_),</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          8 :   out_coupling_(ncvs_, NULL),</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          8 :   in_restart_name_(&quot;&quot;),</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          8 :   out_restart_name_(&quot;&quot;),</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          8 :   fmt_(&quot;%f&quot;),</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          8 :   b_adaptive_(true),</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          8 :   b_freeze_(false),</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          8 :   b_equil_(true),</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          8 :   b_ramp_(false),</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          8 :   b_covar_(false),</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          8 :   b_restart_(false),</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          8 :   b_write_restart_(false),</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          8 :   b_lm_(false),</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          8 :   b_virial_(false),</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          8 :   b_weights_(false),</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          8 :   seed_(0),</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          8 :   update_period_(0),</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          8 :   avg_coupling_count_(1),</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          8 :   update_calls_(0),</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          8 :   kbt_(0.0),</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          8 :   multi_prop_(-1.0),</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          8 :   lm_mixing_par_(0.1),</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          8 :   virial_scaling_(0.),</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          8 :   pseudo_virial_sum_(0.0),</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          8 :   max_logweight_(0.0),</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          8 :   wsum_(0.0),</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         32 :   value_force2_(NULL)</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : {</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          8 :   double temp = -1.0;</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          8 :   bool b_mean = false;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :   std::vector&lt;Value *&gt; wvalues;</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          8 :   addComponent(&quot;force2&quot;);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          8 :   componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">          8 :   value_force2_ = getPntrToComponent(&quot;force2&quot;);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         20 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :   {</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         12 :     std::string comp = getPntrToArgument(i)-&gt;getName() + &quot;_coupling&quot;;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         12 :     addComponent(comp);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         12 :     componentIsNotPeriodic(comp);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         12 :     out_coupling_[i] = getPntrToComponent(comp);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          8 :   parseVector(&quot;CENTER&quot;, center_);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          8 :   parseArgumentList(&quot;CENTER_ARG&quot;, center_values_);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          8 :   parseArgumentList(&quot;LOGWEIGHTS&quot;, wvalues);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          8 :   parseVector(&quot;BIAS_SCALE&quot;, scale_);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">          8 :   parseVector(&quot;RANGE&quot;, max_coupling_range_);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">          8 :   parseVector(&quot;FIXED&quot;, target_coupling_);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">          8 :   parseVector(&quot;INIT&quot;, set_coupling_);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">          8 :   parse(&quot;PERIOD&quot;, update_period_);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">          8 :   parse(&quot;TEMP&quot;, temp);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">          8 :   parse(&quot;SEED&quot;, seed_);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          8 :   parse(&quot;MULTI_PROP&quot;, multi_prop_);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          8 :   parse(&quot;LM_MIXING&quot;, lm_mixing_par_);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          8 :   parse(&quot;RESTART_FMT&quot;, fmt_);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          8 :   parse(&quot;VIRIAL&quot;, virial_scaling_);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          8 :   fmt_ = &quot; &quot; + fmt_; // add space since parse strips them</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          8 :   parse(&quot;OUT_RESTART&quot;, out_restart_name_);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          8 :   parseFlag(&quot;LM&quot;, b_lm_);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          8 :   parseFlag(&quot;RAMP&quot;, b_ramp_);</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          8 :   parseFlag(&quot;FREEZE&quot;, b_freeze_);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          8 :   parseFlag(&quot;MEAN&quot;, b_mean);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          8 :   parseFlag(&quot;COVAR&quot;, b_covar_);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          8 :   parse(&quot;IN_RESTART&quot;, in_restart_name_);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            :   /*</a>
+<a name="406"><span class="lineNum">     406 </span>            :    * Things that are different when using changing centers:</a>
+<a name="407"><span class="lineNum">     407 </span>            :    * 1. Scale</a>
+<a name="408"><span class="lineNum">     408 </span>            :    * 2. The log file</a>
+<a name="409"><span class="lineNum">     409 </span>            :    * 3. Reading Restarts</a>
+<a name="410"><span class="lineNum">     410 </span>            :    */</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">          8 :   if (center_.size() == 0)</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :   {</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          1 :     if (center_values_.size() == 0)</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :       error(&quot;Must set either CENTER or CENTER_ARG&quot;);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          1 :     else if (center_values_.size() != ncvs_)</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :       error(&quot;CENTER_ARG must contain the same number of variables as ARG&quot;);</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          1 :     b_c_values_ = true;</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          1 :     center_.resize(ncvs_);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          1 :     log.printf(&quot;  EDS will use possibly varying centers\n&quot;);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :   }</a>
+<a name="422"><span class="lineNum">     422 </span>            :   else</a>
+<a name="423"><span class="lineNum">     423 </span>            :   {</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          7 :     if (center_.size() != ncvs_)</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :       error(&quot;Must have same number of CENTER arguments as ARG arguments&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          7 :     else if (center_values_.size() != 0)</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :       error(&quot;You can only set CENTER or CENTER_ARG. Not both&quot;);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          7 :     b_c_values_ = false;</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          7 :     log.printf(&quot;  EDS will use fixed centers\n&quot;);</span></a>
+<a name="430"><span class="lineNum">     430 </span>            :   }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :   // check for weights</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">          8 :   if (wvalues.size() &gt; 1)</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :   {</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :     error(&quot;LOGWEIGHTS can only support one weight set. Please only pass one action&quot;);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :   }</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          8 :   else if (wvalues.size() == 1)</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :   {</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          1 :     logweights_ = dynamic_cast&lt;ReweightBase *&gt;(wvalues[0]-&gt;getPntrToAction());</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          1 :     b_weights_ = true;</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   }</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          8 :   log.printf(&quot;  setting scaling:&quot;);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          8 :   if (scale_.size() &gt; 0 &amp;&amp; scale_.size() &lt; ncvs_)</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   {</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     error(&quot;the number of BIAS_SCALE values be the same as number of CVs&quot;);</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   }</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          8 :   else if (scale_.size() == 0 &amp;&amp; b_c_values_)</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   {</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :     log.printf(&quot; Setting SCALE to be 1 for all CVs\n&quot;);</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :     scale_.resize(ncvs_);</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :       scale_[i] = 1;</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          8 :   else if (scale_.size() == 0 &amp;&amp; !b_c_values_)</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :   {</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          2 :     log.printf(&quot; (default) &quot;);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          2 :     scale_.resize(ncvs_);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          6 :     for (unsigned int i = 0; i &lt; scale_.size(); ++i)</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :     {</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          4 :       if (center_[i] == 0)</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :         error(&quot;BIAS_SCALE parameter has been set to CENTER value of 0 (as is default). This will divide by 0, so giving up. See doc for EDS bias&quot;);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">          4 :       scale_[i] = center_[i];</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :     }</a>
+<a name="466"><span class="lineNum">     466 </span>            :   }</a>
+<a name="467"><span class="lineNum">     467 </span>            :   else</a>
+<a name="468"><span class="lineNum">     468 </span>            :   {</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         14 :     for (unsigned int i = 0; i &lt; scale_.size(); ++i)</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          8 :       log.printf(&quot; %f&quot;, scale_[i]);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :   }</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          8 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          8 :   if (b_lm_)</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :   {</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          1 :     log.printf(&quot;  EDS will perform Levenberg-Marquardt minimization with mixing parameter = %f\n&quot;, lm_mixing_par_);</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          1 :     differences_.resize(ncvs_);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          1 :     alpha_vector_.resize(ncvs_);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          1 :     alpha_vector_2_.resize(ncvs_);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          1 :     covar_.resize(ncvs_, ncvs_);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          1 :     covar2_.resize(ncvs_, ncvs_);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          1 :     lm_inv_.resize(ncvs_, ncvs_);</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          1 :     covar2_ *= 0;</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          1 :     lm_inv_ *= 0;</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          1 :     if (multi_prop_ != 1)</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :       log.printf(&quot;     WARNING - doing LM minimization but MULTI_PROP!=1\n&quot;);</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :   }</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          7 :   else if (b_covar_)</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :   {</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          1 :     log.printf(&quot;  EDS will utilize covariance matrix for update steps\n&quot;);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          1 :     covar_.resize(ncvs_, ncvs_);</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :   }</a>
+<a name="493"><span class="lineNum">     493 </span>            :   else</a>
+<a name="494"><span class="lineNum">     494 </span>            :   {</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          6 :     log.printf(&quot;  EDS will utilize variance for update steps\n&quot;);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          6 :     ssds_.resize(ncvs_);</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :   }</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          8 :   b_virial_ = virial_scaling_;</span></a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          8 :   if (b_virial_)</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :   {</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          1 :     if (ncvs_ == 1)</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :       error(&quot;Minimizing the virial is only valid with multiply correlated collective variables.&quot;);</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     // check that the CVs can be used to compute pseudo-virial</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          1 :     log.printf(&quot;  EDS will compute virials of CVs and penalize with scale of %f. Checking CVs are valid...&quot;, virial_scaling_);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          4 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :     {</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          3 :       auto a = dynamic_cast&lt;ActionAtomistic *&gt;(getPntrToArgument(i)-&gt;getPntrToAction());</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">          3 :       if (!a)</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 :         error(&quot;If using VIRIAL keyword, you must have normal CVs as arguments to EDS. Offending action: &quot; + getPntrToArgument(i)-&gt;getPntrToAction()-&gt;getName());</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :       // cppcheck-suppress nullPointerRedundantCheck</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          3 :       if (!(a-&gt;getPbc().isOrthorombic()))</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          3 :         log.printf(&quot;  WARNING: EDS Virial should have a orthorombic cell\n&quot;);</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :     }</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">          1 :     log.printf(&quot;done.\n&quot;);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">          1 :     addComponent(&quot;pressure&quot;);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">          1 :     componentIsNotPeriodic(&quot;pressure&quot;);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          1 :     value_pressure_ = getPntrToComponent(&quot;pressure&quot;);</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :   }</a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">          8 :   if (b_mean &amp;&amp; !b_freeze_)</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :   {</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :     error(&quot;EDS keyword MEAN can only be used along with keyword FREEZE&quot;);</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :   }</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">          8 :   if (in_restart_name_ != &quot;&quot;)</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :   {</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">          2 :     b_restart_ = true;</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          2 :     log.printf(&quot;  reading simulation information from file: %s\n&quot;, in_restart_name_.c_str());</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">          2 :     readInRestart(b_mean);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :   }</a>
+<a name="533"><span class="lineNum">     533 </span>            :   else</a>
+<a name="534"><span class="lineNum">     534 </span>            :   {</a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          6 :     if (temp &gt;= 0.0)</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          6 :       kbt_ = plumed.getAtoms().getKBoltzmann() * temp;</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :     else</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :       kbt_ = plumed.getAtoms().getKbT();</span></a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span>            :     // in driver, this results in kbt of 0</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">          6 :     if (kbt_ == 0)</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :     {</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :       error(&quot;  Unable to determine valid kBT. &quot;</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :             &quot;Could be because you are runnning from driver or MD didn't give temperature.\n&quot;</a>
+<a name="546"><span class="lineNum">     546 </span>            :             &quot;Consider setting temperature manually with the TEMP keyword.&quot;);</a>
+<a name="547"><span class="lineNum">     547 </span>            :       kbt_ = 1;</a>
+<a name="548"><span class="lineNum">     548 </span>            :     }</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">          6 :     log.printf(&quot;  kBT = %f\n&quot;, kbt_);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          6 :     log.printf(&quot;  Updating every %i steps\n&quot;, update_period_);</span></a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          6 :     if (!b_c_values_)</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :     {</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">          5 :       log.printf(&quot;  with centers:&quot;);</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">         14 :       for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="557"><span class="lineNum">     557 </span>            :       {</a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">          9 :         log.printf(&quot; %f &quot;, center_[i]);</span></a>
+<a name="559"><span class="lineNum">     559 </span>            :       }</a>
+<a name="560"><span class="lineNum">     560 </span>            :     }</a>
+<a name="561"><span class="lineNum">     561 </span>            :     else</a>
+<a name="562"><span class="lineNum">     562 </span>            :     {</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">          1 :       log.printf(&quot;  with actions centers:&quot;);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">          2 :       for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :       {</a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">          1 :         log.printf(&quot; %s &quot;, center_values_[i]-&gt;getName().c_str());</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :         // add dependency on these actions</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">          1 :         addDependency(center_values_[i]-&gt;getPntrToAction());</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :       }</a>
+<a name="570"><span class="lineNum">     570 </span>            :     }</a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">          6 :     log.printf(&quot;\n  with initial ranges / rates:\n&quot;);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         16 :     for (unsigned int i = 0; i &lt; max_coupling_range_.size(); ++i)</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :     {</a>
+<a name="575"><span class="lineNum">     575 </span>            :       // this is just an empirical guess. Bigger range, bigger grads. Less frequent updates, bigger changes</a>
+<a name="576"><span class="lineNum">     576 </span>            :       //</a>
+<a name="577"><span class="lineNum">     577 </span>            :       // using the current maxing out scheme, max_coupling_range is the biggest step that can be taken in any given interval</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         10 :       max_coupling_range_[i] *= kbt_;</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         10 :       max_coupling_grad_[i] = max_coupling_range_[i];</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         10 :       log.printf(&quot;    %f / %f\n&quot;, max_coupling_range_[i], max_coupling_grad_[i]);</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :     }</a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">          6 :     if (seed_ &gt; 0)</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :     {</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">          2 :       log.printf(&quot;  setting random seed = %i&quot;, seed_);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">          2 :       rand_.setSeed(seed_);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :     }</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         16 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         10 :       if (target_coupling_[i] != 0.0)</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">          1 :         b_adaptive_ = false;</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">          6 :     if (!b_adaptive_)</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :     {</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          1 :       if (b_ramp_)</span></a>
+<a name="596"><span class="lineNum">     596 </span>            :       {</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          1 :         log.printf(&quot;  ramping up coupling constants over %i steps\n&quot;, update_period_);</span></a>
+<a name="598"><span class="lineNum">     598 </span>            :       }</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">          1 :       log.printf(&quot;  with starting coupling constants&quot;);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">          2 :       for (unsigned int i = 0; i &lt; set_coupling_.size(); ++i)</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">          1 :         log.printf(&quot; %f&quot;, set_coupling_[i]);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">          1 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">          1 :       log.printf(&quot;  and final coupling constants&quot;);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">          2 :       for (unsigned int i = 0; i &lt; target_coupling_.size(); ++i)</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">          1 :         log.printf(&quot; %f&quot;, target_coupling_[i]);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">          1 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :     }</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            :     // now do setup</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">          6 :     if (b_ramp_)</span></a>
+<a name="612"><span class="lineNum">     612 </span>            :     {</a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">          1 :       update_period_ *= -1;</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :     }</a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         16 :     for (unsigned int i = 0; i &lt; set_coupling_.size(); ++i)</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         10 :       current_coupling_[i] = set_coupling_[i];</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span>            :     // if b_adaptive_, then first half will be used for equilibrating and second half for statistics</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">          6 :     if (update_period_ &gt; 0)</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :     {</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">          5 :       update_period_ /= 2;</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :     }</a>
+<a name="624"><span class="lineNum">     624 </span>            :   }</a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">          8 :   if (b_freeze_)</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :   {</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">          1 :     b_adaptive_ = false;</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">          1 :     update_period_ = 0;</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">          1 :     if (b_mean)</span></a>
+<a name="631"><span class="lineNum">     631 </span>            :     {</a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">          1 :       log.printf(&quot;  freezing bias at the average level from the restart file\n&quot;);</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :     }</a>
+<a name="634"><span class="lineNum">     634 </span>            :     else</a>
+<a name="635"><span class="lineNum">     635 </span>            :     {</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :       log.printf(&quot;  freezing bias at current level\n&quot;);</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :     }</a>
+<a name="638"><span class="lineNum">     638 </span>            :   }</a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">          8 :   if (multi_prop_ == -1.0)</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :   {</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">          5 :     log.printf(&quot;  Will update each dimension stochastically with probability 1 / number of CVs\n&quot;);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">          5 :     multi_prop_ = 1.0 / ncvs_;</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :   }</a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">          3 :   else if (multi_prop_ &gt; 0 &amp;&amp; multi_prop_ &lt;= 1.0)</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :   {</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          3 :     log.printf(&quot;  Will update each dimension stochastically with probability %f\n&quot;, multi_prop_);</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :   }</a>
+<a name="649"><span class="lineNum">     649 </span>            :   else</a>
+<a name="650"><span class="lineNum">     650 </span>            :   {</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 :     error(&quot;  MULTI_PROP must be between 0 and 1\n&quot;);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :   }</a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">          8 :   if (out_restart_name_.length() &gt; 0)</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :   {</a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">          8 :     log.printf(&quot;  writing restart information every %i steps to file %s with format %s\n&quot;, abs(update_period_), out_restart_name_.c_str(), fmt_.c_str());</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">          8 :     b_write_restart_ = true;</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">          8 :     setupOutRestart();</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :   }</a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         16 :   log &lt;&lt; &quot;  Bibliography &quot; &lt;&lt; plumed.cite(&quot;White and Voth, J. Chem. Theory Comput. 10 (8), 3023-3030 (2014)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         16 :   log &lt;&lt; &quot;  Bibliography &quot; &lt;&lt; plumed.cite(&quot;G. M. Hocky, T. Dannenhoffer-Lafage, G. A. Voth, J. Chem. Theory Comput. 13 (9), 4593-4603 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">          8 : }</span></a>
+<a name="664"><span class="lineNum">     664 </span>            : </a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">          2 : void EDS::readInRestart(const bool b_mean)</span></a>
+<a name="666"><span class="lineNum">     666 </span>            : {</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">          2 :   int adaptive_i = 0;</span></a>
+<a name="668"><span class="lineNum">     668 </span>            : </a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">          2 :   in_restart_.open(in_restart_name_);</span></a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">          4 :   if (in_restart_.FieldExist(&quot;kbt&quot;))</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :   {</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">          2 :     in_restart_.scanField(&quot;kbt&quot;, kbt_);</span></a>
+<a name="674"><span class="lineNum">     674 </span>            :   }</a>
+<a name="675"><span class="lineNum">     675 </span>            :   else</a>
+<a name="676"><span class="lineNum">     676 </span>            :   {</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :     error(&quot;No field 'kbt' in restart file&quot;);</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :   }</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">          2 :   log.printf(&quot;  with kBT = %f\n&quot;, kbt_);</span></a>
+<a name="680"><span class="lineNum">     680 </span>            : </a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">          4 :   if (in_restart_.FieldExist(&quot;update_period&quot;))</span></a>
+<a name="682"><span class="lineNum">     682 </span>            :   {</a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">          2 :     in_restart_.scanField(&quot;update_period&quot;, update_period_);</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :   }</a>
+<a name="685"><span class="lineNum">     685 </span>            :   else</a>
+<a name="686"><span class="lineNum">     686 </span>            :   {</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :     error(&quot;No field 'update_period' in restart file&quot;);</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :   }</a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">          2 :   log.printf(&quot;  Updating every %i steps\n&quot;, update_period_);</span></a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">          4 :   if (in_restart_.FieldExist(&quot;adaptive&quot;))</span></a>
+<a name="692"><span class="lineNum">     692 </span>            :   {</a>
+<a name="693"><span class="lineNum">     693 </span>            :     // note, no version of scanField for boolean</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">          2 :     in_restart_.scanField(&quot;adaptive&quot;, adaptive_i);</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :   }</a>
+<a name="696"><span class="lineNum">     696 </span>            :   else</a>
+<a name="697"><span class="lineNum">     697 </span>            :   {</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :     error(&quot;No field 'adaptive' in restart file&quot;);</span></a>
+<a name="699"><span class="lineNum">     699 </span>            :   }</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">          2 :   b_adaptive_ = bool(adaptive_i);</span></a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">          4 :   if (in_restart_.FieldExist(&quot;seed&quot;))</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :   {</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">          2 :     in_restart_.scanField(&quot;seed&quot;, seed_);</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :   }</a>
+<a name="706"><span class="lineNum">     706 </span>            :   else</a>
+<a name="707"><span class="lineNum">     707 </span>            :   {</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :     error(&quot;No field 'seed' in restart file&quot;);</span></a>
+<a name="709"><span class="lineNum">     709 </span>            :   }</a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">          2 :   if (seed_ &gt; 0)</span></a>
+<a name="711"><span class="lineNum">     711 </span>            :   {</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :     log.printf(&quot;  setting random seed = %i&quot;, seed_);</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :     rand_.setSeed(seed_);</span></a>
+<a name="714"><span class="lineNum">     714 </span>            :   }</a>
+<a name="715"><span class="lineNum">     715 </span>            : </a>
+<a name="716"><span class="lineNum">     716 </span>            :   double time, tmp;</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">          2 :   std::vector&lt;double&gt; avg_bias = std::vector&lt;double&gt;(center_.size());</span></a>
+<a name="718"><span class="lineNum">     718 </span>            :   unsigned int N = 0;</a>
+<a name="719"><span class="lineNum">     719 </span>            :   std::string cv_name;</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">         24 :   while (in_restart_.scanField(&quot;time&quot;, time))</span></a>
+<a name="722"><span class="lineNum">     722 </span>            :   {</a>
+<a name="723"><span class="lineNum">     723 </span>            : </a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">         20 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="725"><span class="lineNum">     725 </span>            :     {</a>
+<a name="726"><span class="lineNum">     726 </span>            :       cv_name = getPntrToArgument(i)-&gt;getName();</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_center&quot;, set_coupling_[i]);</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_set&quot;, set_coupling_[i]);</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_target&quot;, target_coupling_[i]);</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_coupling&quot;, current_coupling_[i]);</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_maxrange&quot;, max_coupling_range_[i]);</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_maxgrad&quot;, max_coupling_grad_[i]);</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_accum&quot;, coupling_accum_[i]);</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">         10 :       in_restart_.scanField(cv_name + &quot;_mean&quot;, means_[i]);</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         20 :       if (in_restart_.FieldExist(cv_name + &quot;_pseudovirial&quot;))</span></a>
+<a name="736"><span class="lineNum">     736 </span>            :       {</a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineNoCov">          0 :         if (b_virial_)</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :           in_restart_.scanField(cv_name + &quot;_pseudovirial&quot;, pseudo_virial_[i]);</span></a>
+<a name="739"><span class="lineNum">     739 </span>            :         else // discard the field</a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :           in_restart_.scanField(cv_name + &quot;_pseudovirial&quot;, tmp);</span></a>
+<a name="741"><span class="lineNum">     741 </span>            :       }</a>
+<a name="742"><span class="lineNum">     742 </span>            :       // unused due to difference between covar/nocovar</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">         20 :       in_restart_.scanField(cv_name + &quot;_std&quot;, tmp);</span></a>
+<a name="744"><span class="lineNum">     744 </span>            : </a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">         10 :       avg_bias[i] += current_coupling_[i];</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :     }</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">         10 :     N++;</span></a>
+<a name="748"><span class="lineNum">     748 </span>            : </a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">         10 :     in_restart_.scanField();</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :   }</a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">          2 :   log.printf(&quot;  with centers:&quot;);</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; center_.size(); ++i)</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :   {</a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">          2 :     log.printf(&quot; %f&quot;, center_[i]);</span></a>
+<a name="756"><span class="lineNum">     756 </span>            :   }</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">          2 :   log.printf(&quot;\n  and scaling:&quot;);</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; scale_.size(); ++i)</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :   {</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">          2 :     log.printf(&quot; %f&quot;, scale_[i]);</span></a>
+<a name="761"><span class="lineNum">     761 </span>            :   }</a>
+<a name="762"><span class="lineNum">     762 </span>            : </a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">          2 :   log.printf(&quot;\n  with initial ranges / rates:\n&quot;);</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; max_coupling_range_.size(); ++i)</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :   {</a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">          2 :     log.printf(&quot;    %f / %f\n&quot;, max_coupling_range_[i], max_coupling_grad_[i]);</span></a>
+<a name="767"><span class="lineNum">     767 </span>            :   }</a>
+<a name="768"><span class="lineNum">     768 </span>            : </a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">          2 :   if (!b_adaptive_ &amp;&amp; update_period_ &lt; 0)</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :   {</a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineNoCov">          0 :     log.printf(&quot;  ramping up coupling constants over %i steps\n&quot;, -update_period_);</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :   }</a>
+<a name="773"><span class="lineNum">     773 </span>            : </a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">          2 :   if (b_mean)</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :   {</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">          1 :     log.printf(&quot;Loaded in averages for coupling constants...\n&quot;);</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">          2 :     for (unsigned int i = 0; i &lt; current_coupling_.size(); ++i)</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">          1 :       current_coupling_[i] = avg_bias[i] / N;</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">          2 :     for (unsigned int i = 0; i &lt; current_coupling_.size(); ++i)</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">          1 :       set_coupling_[i] = avg_bias[i] / N;</span></a>
+<a name="781"><span class="lineNum">     781 </span>            :   }</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">          2 :   log.printf(&quot;  with current coupling constants:\n    &quot;);</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; current_coupling_.size(); ++i)</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">          2 :     log.printf(&quot; %f&quot;, current_coupling_[i]);</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">          2 :   log.printf(&quot;  with initial coupling constants:\n    &quot;);</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; set_coupling_.size(); ++i)</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">          2 :     log.printf(&quot; %f&quot;, set_coupling_[i]);</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">          2 :   log.printf(&quot;  and final coupling constants:\n    &quot;);</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; target_coupling_.size(); ++i)</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">          2 :     log.printf(&quot; %f&quot;, target_coupling_[i]);</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="795"><span class="lineNum">     795 </span>            : </a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">          2 :   in_restart_.close();</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">          2 : }</span></a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">          8 : void EDS::setupOutRestart()</span></a>
+<a name="800"><span class="lineNum">     800 </span>            : {</a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">          8 :   out_restart_.link(*this);</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">          8 :   out_restart_.fmtField(fmt_);</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">          8 :   out_restart_.open(out_restart_name_);</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :   out_restart_.setHeavyFlush();</a>
+<a name="805"><span class="lineNum">     805 </span>            : </a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">         16 :   out_restart_.addConstantField(&quot;adaptive&quot;).printField(&quot;adaptive&quot;, b_adaptive_);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">         16 :   out_restart_.addConstantField(&quot;update_period&quot;).printField(&quot;update_period&quot;, update_period_);</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">         16 :   out_restart_.addConstantField(&quot;seed&quot;).printField(&quot;seed&quot;, seed_);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">         16 :   out_restart_.addConstantField(&quot;kbt&quot;).printField(&quot;kbt&quot;, kbt_);</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">          8 : }</span></a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         27 : void EDS::writeOutRestart()</span></a>
+<a name="813"><span class="lineNum">     813 </span>            : {</a>
+<a name="814"><span class="lineNum">     814 </span>            :   std::string cv_name;</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">         27 :   out_restart_.printField(&quot;time&quot;, getTimeStep() * getStep());</span></a>
+<a name="816"><span class="lineNum">     816 </span>            : </a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">         66 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="818"><span class="lineNum">     818 </span>            :   {</a>
+<a name="819"><span class="lineNum">     819 </span>            :     cv_name = getPntrToArgument(i)-&gt;getName();</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_center&quot;, center_[i]);</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_set&quot;, set_coupling_[i]);</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_target&quot;, target_coupling_[i]);</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_coupling&quot;, current_coupling_[i]);</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_maxrange&quot;, max_coupling_range_[i]);</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_maxgrad&quot;, max_coupling_grad_[i]);</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         78 :     out_restart_.printField(cv_name + &quot;_accum&quot;, coupling_accum_[i]);</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">         39 :     out_restart_.printField(cv_name + &quot;_mean&quot;, means_[i]);</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         39 :     if (b_virial_)</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">         18 :       out_restart_.printField(cv_name + &quot;_pseudovirial&quot;, pseudo_virial_[i]);</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">         39 :     if (!b_covar_ &amp;&amp; !b_lm_)</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">         42 :       out_restart_.printField(cv_name + &quot;_std&quot;, ssds_[i] / (fmax(1, update_calls_ - 1)));</span></a>
+<a name="832"><span class="lineNum">     832 </span>            :     else</a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">         36 :       out_restart_.printField(cv_name + &quot;_std&quot;, covar_(i, i) / (fmax(1, update_calls_ - 1)));</span></a>
+<a name="834"><span class="lineNum">     834 </span>            :   }</a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">         27 :   out_restart_.printField();</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">         27 : }</span></a>
+<a name="837"><span class="lineNum">     837 </span>            : </a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">         40 : void EDS::calculate()</span></a>
+<a name="839"><span class="lineNum">     839 </span>            : {</a>
+<a name="840"><span class="lineNum">     840 </span>            : </a>
+<a name="841"><span class="lineNum">     841 </span>            :   // get center values from action if necessary</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">         40 :   if (b_c_values_)</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         10 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">          5 :       center_[i] = center_values_[i]-&gt;get();</span></a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">         40 :   apply_bias();</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">         40 : }</span></a>
+<a name="848"><span class="lineNum">     848 </span>            : </a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">         40 : void EDS::apply_bias()</span></a>
+<a name="850"><span class="lineNum">     850 </span>            : {</a>
+<a name="851"><span class="lineNum">     851 </span>            :   // Compute linear force as in &quot;restraint&quot;</a>
+<a name="852"><span class="lineNum">     852 </span>            :   double ene = 0, totf2 = 0, cv, m, f;</a>
+<a name="853"><span class="lineNum">     853 </span>            : </a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">        100 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="855"><span class="lineNum">     855 </span>            :   {</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">         60 :     cv = difference(i, center_[i], getArgument(i));</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">         60 :     m = current_coupling_[i];</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">         60 :     f = -m;</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">         60 :     ene += m * cv;</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :     setOutputForce(i, f);</a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">         60 :     totf2 += f * f;</span></a>
+<a name="862"><span class="lineNum">     862 </span>            :   }</a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span>            :   setBias(ene);</a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">         40 :   value_force2_-&gt;set(totf2);</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">         40 : }</span></a>
+<a name="867"><span class="lineNum">     867 </span>            : </a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">         12 : void EDS::update_statistics()</span></a>
+<a name="869"><span class="lineNum">     869 </span>            : {</a>
+<a name="870"><span class="lineNum">     870 </span>            :   double s, N, w = 1.0;</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; deltas(ncvs_);</span></a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            :   // update weight max, if necessary</a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">         12 :   if (b_weights_)</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :   {</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">          2 :     w = logweights_-&gt;getLogWeight();</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">          2 :     if (max_logweight_ &lt; w)</span></a>
+<a name="878"><span class="lineNum">     878 </span>            :     {</a>
+<a name="879"><span class="lineNum">     879 </span>            :       // we have new max. Need to shift existing values</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :       wsum_ *= exp(max_logweight_ - w);</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineNoCov">          0 :       max_logweight_ = w;</span></a>
+<a name="882"><span class="lineNum">     882 </span>            :     }</a>
+<a name="883"><span class="lineNum">     883 </span>            :     // convert to weight</a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">          2 :     w = exp(w - max_logweight_);</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">          2 :     wsum_ += w;</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :     N = wsum_;</a>
+<a name="887"><span class="lineNum">     887 </span>            :   }</a>
+<a name="888"><span class="lineNum">     888 </span>            :   else</a>
+<a name="889"><span class="lineNum">     889 </span>            :   {</a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">         10 :     N = fmax(1, update_calls_);</span></a>
+<a name="891"><span class="lineNum">     891 </span>            :   }</a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            :   // Welford, West, and Hanso online variance method</a>
+<a name="894"><span class="lineNum">     894 </span>            :   // with weights (default =  1.0)</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">         32 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="896"><span class="lineNum">     896 </span>            :   {</a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">         20 :     deltas[i] = difference(i, means_[i], getArgument(i)) * w;</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">         20 :     means_[i] += deltas[i] / N;</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">         20 :     if (!b_covar_ &amp;&amp; !b_lm_)</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">          8 :       ssds_[i] += deltas[i] * difference(i, means_[i], getArgument(i));</span></a>
+<a name="901"><span class="lineNum">     901 </span>            :   }</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">         12 :   if (b_covar_ || b_lm_)</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :   {</a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">         16 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="905"><span class="lineNum">     905 </span>            :     {</a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">         36 :       for (unsigned int j = i; j &lt; ncvs_; ++j)</span></a>
+<a name="907"><span class="lineNum">     907 </span>            :       {</a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">         24 :         s = (N - 1) * deltas[i] * deltas[j] / N / N - covar_(i, j) / N;</span></a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">         24 :         covar_(i, j) += s;</span></a>
+<a name="910"><span class="lineNum">     910 </span>            :         // do this so we don't double count</a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">         24 :         covar_(j, i) = covar_(i, j);</span></a>
+<a name="912"><span class="lineNum">     912 </span>            :       }</a>
+<a name="913"><span class="lineNum">     913 </span>            :     }</a>
+<a name="914"><span class="lineNum">     914 </span>            :   }</a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">         12 :   if (b_virial_)</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">          2 :     update_pseudo_virial();</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">         12 : }</span></a>
+<a name="918"><span class="lineNum">     918 </span>            : </a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">          8 : void EDS::reset_statistics()</span></a>
+<a name="920"><span class="lineNum">     920 </span>            : {</a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">         20 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :   {</a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">         12 :     means_[i] = 0;</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">         12 :     if (!b_covar_ &amp;&amp; !b_lm_)</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">          6 :       ssds_[i] = 0;</span></a>
+<a name="926"><span class="lineNum">     926 </span>            :   }</a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">          8 :   if (b_covar_ || b_lm_)</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">          8 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">         24 :       for (unsigned int j = 0; j &lt; ncvs_; ++j)</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">         18 :         covar_(i, j) = 0;</span></a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">          8 :   if (b_virial_)</span></a>
+<a name="932"><span class="lineNum">     932 </span>            :   {</a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">          4 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">          3 :       pseudo_virial_[i] = 0;</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">          1 :     pseudo_virial_sum_ = 0;</span></a>
+<a name="936"><span class="lineNum">     936 </span>            :   }</a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">          8 :   if (b_weights_)</span></a>
+<a name="938"><span class="lineNum">     938 </span>            :   {</a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">          2 :     wsum_ = 0;</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">          2 :     max_logweight_ = 0;</span></a>
+<a name="941"><span class="lineNum">     941 </span>            :   }</a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">          8 : }</span></a>
+<a name="943"><span class="lineNum">     943 </span>            : </a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">          1 : void EDS::calc_lm_step_size()</span></a>
+<a name="945"><span class="lineNum">     945 </span>            : {</a>
+<a name="946"><span class="lineNum">     946 </span>            :   // calulcate step size</a>
+<a name="947"><span class="lineNum">     947 </span>            :   // uses scale here, which by default is center</a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">          1 :   mult(covar_, covar_, covar2_);</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :   {</a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">          3 :     differences_[i] = difference(i, center_[i], means_[i]);</span></a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">          3 :     covar2_[i][i] += lm_mixing_par_ * covar2_[i][i];</span></a>
+<a name="954"><span class="lineNum">     954 </span>            :   }</a>
+<a name="955"><span class="lineNum">     955 </span>            : </a>
+<a name="956"><span class="lineNum">     956 </span>            :   // &quot;step_size_vec&quot; = 2*inv(covar*covar+ lambda diag(covar*covar))*covar*(mean-center)</a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">          1 :   mult(covar_, differences_, alpha_vector_);</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">          1 :   Invert(covar2_, lm_inv_);</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">          1 :   mult(lm_inv_, alpha_vector_, alpha_vector_2_);</span></a>
+<a name="960"><span class="lineNum">     960 </span>            : </a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :   {</a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">          3 :     step_size_[i] = 2 * alpha_vector_2_[i] / kbt_ / scale_[i];</span></a>
+<a name="964"><span class="lineNum">     964 </span>            :   }</a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">          1 : }</span></a>
+<a name="966"><span class="lineNum">     966 </span>            : </a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">          1 : void EDS::calc_covar_step_size()</span></a>
+<a name="968"><span class="lineNum">     968 </span>            : {</a>
+<a name="969"><span class="lineNum">     969 </span>            :   // calulcate step size</a>
+<a name="970"><span class="lineNum">     970 </span>            :   // uses scale here, which by default is center</a>
+<a name="971"><span class="lineNum">     971 </span>            :   double tmp;</a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">          4 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="973"><span class="lineNum">     973 </span>            :   {</a>
+<a name="974"><span class="lineNum">     974 </span>            :     tmp = 0;</a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">         12 :     for (unsigned int j = 0; j &lt; ncvs_; ++j)</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">          9 :       tmp += difference(i, center_[i], means_[i]) * covar_(i, j);</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">          3 :     step_size_[i] = 2 * tmp / kbt_ / scale_[i] * update_calls_ / fmax(1, update_calls_ - 1);</span></a>
+<a name="978"><span class="lineNum">     978 </span>            :   }</a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">          1 : }</span></a>
+<a name="980"><span class="lineNum">     980 </span>            : </a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">          6 : void EDS::calc_ssd_step_size()</span></a>
+<a name="982"><span class="lineNum">     982 </span>            : {</a>
+<a name="983"><span class="lineNum">     983 </span>            :   double tmp;</a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">         12 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :   {</a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">          6 :     tmp = 2. * difference(i, center_[i], means_[i]) * ssds_[i] / fmax(1, update_calls_ - 1);</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">          6 :     step_size_[i] = tmp / kbt_ / scale_[i];</span></a>
+<a name="988"><span class="lineNum">     988 </span>            :   }</a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">          6 : }</span></a>
+<a name="990"><span class="lineNum">     990 </span>            : </a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">          2 : void EDS::update_pseudo_virial()</span></a>
+<a name="992"><span class="lineNum">     992 </span>            : {</a>
+<a name="993"><span class="lineNum">     993 </span>            :   // We want to compute the bias force on each atom times the position</a>
+<a name="994"><span class="lineNum">     994 </span>            :   //  of the atoms.</a>
+<a name="995"><span class="lineNum">     995 </span>            :   double p, netp = 0, netpv = 0;</a>
+<a name="996"><span class="lineNum">     996 </span>            :   double volume = 0;</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">          8 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="998"><span class="lineNum">     998 </span>            :   {</a>
+<a name="999"><span class="lineNum">     999 </span>            :     // checked in setup to ensure this cast is valid.</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">          6 :     ActionAtomistic *cv = dynamic_cast&lt;ActionAtomistic *&gt;(getPntrToArgument(i)-&gt;getPntrToAction());</span></a>
+<a name="1001"><span class="lineNum">    1001 </span>            :     Tensor &amp;v(cv-&gt;modifyVirial());</a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">          6 :     Tensor box(cv-&gt;getBox());</span></a>
+<a name="1003"><span class="lineNum">    1003 </span>            :     const unsigned int natoms = cv-&gt;getNumberOfAtoms();</a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">          6 :     if (!volume)</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">          2 :       volume = box.determinant();</span></a>
+<a name="1006"><span class="lineNum">    1006 </span>            : </a>
+<a name="1007"><span class="lineNum">    1007 </span>            :     // pressure contribution is -dBias / dV</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :     // dBias / dV = alpha / w * dCV / dV</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :     // to get partial of CV wrt to volume</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :     // dCV/dV = sum dCV/dvij * vij / V</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :     // where vij is box element</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :     // add diagonal of virial tensor to get net pressure</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :     // TODO: replace this with adjugate (Jacobi's Formula)   for non-orthorombic case(?)</a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">          6 :     p = v(0, 0) * box(0, 0) + v(1, 1) * box(1, 1) + v(2, 2) * box(2, 2);</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">          6 :     p /= volume;</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">          6 :     netp += p;</span></a>
+<a name="1018"><span class="lineNum">    1018 </span>            : </a>
+<a name="1019"><span class="lineNum">    1019 </span>            :     // now scale for correct units in EDS algorithm</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">          6 :     p *= (volume) / (kbt_ * natoms);</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            : </a>
+<a name="1022"><span class="lineNum">    1022 </span>            :     // compute running mean of scaled</a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">          6 :     if (set_coupling_[i] != 0)</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineNoCov">          0 :       pseudo_virial_[i] = (p - pseudo_virial_[i]) / (fmax(1, update_calls_));</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :     else</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">          6 :       pseudo_virial_[i] = 0;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span>            :     // update net pressure</a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">          6 :     netpv += pseudo_virial_[i];</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            :   }</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :   // update pressure</a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">          2 :   value_pressure_-&gt;set(netp);</span></a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">          2 :   pseudo_virial_sum_ = netpv;</span></a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">          2 : }</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            : </a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">          8 : void EDS::update_bias()</span></a>
+<a name="1036"><span class="lineNum">    1036 </span>            : {</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">          8 :   log.flush();</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">          8 :   if (b_lm_)</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">          1 :     calc_lm_step_size();</span></a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">          7 :   else if (b_covar_)</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">          1 :     calc_covar_step_size();</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            :   else</a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">          6 :     calc_ssd_step_size();</span></a>
+<a name="1044"><span class="lineNum">    1044 </span>            : </a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">         20 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="1046"><span class="lineNum">    1046 </span>            :   {</a>
+<a name="1047"><span class="lineNum">    1047 </span>            : </a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     // multidimesional stochastic step</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">         12 :     if (ncvs_ == 1 || (rand_.RandU01() &lt; (multi_prop_)))</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :     {</a>
+<a name="1051"><span class="lineNum">    1051 </span>            : </a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">         12 :       if (b_virial_)</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            :       {</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :         // apply virial regularization</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :         //  P * dP/dcoupling</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :         //  coupling is already included in virial term due to plumed propogating from bias to forces</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :         //  thus we need to divide by it to get the derivative (since force is linear in coupling)</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">          3 :         if (fabs(set_coupling_[i]) &gt; 0.000000001) // my heuristic for if EDS has started to prevent / 0</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :           // scale^2 here is to align units</a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineNoCov">          0 :           step_size_[i] -= 2 * scale_[i] * scale_[i] * virial_scaling_ * pseudo_virial_sum_ * pseudo_virial_sum_ / set_coupling_[i];</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            :       }</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">         12 :       if (step_size_[i] == 0)</span></a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">          4 :         continue;</span></a>
+<a name="1064"><span class="lineNum">    1064 </span>            : </a>
+<a name="1065"><span class="lineNum">    1065 </span>            :       // clip gradient</a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">          8 :       step_size_[i] = copysign(fmin(fabs(step_size_[i]), max_coupling_grad_[i]), step_size_[i]);</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">          8 :       coupling_accum_[i] += step_size_[i] * step_size_[i];</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            : </a>
+<a name="1069"><span class="lineNum">    1069 </span>            :       // equation 5 in White and Voth, JCTC 2014</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :       // no negative sign because it's in step_size</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">          8 :       set_coupling_[i] += step_size_[i] * max_coupling_range_[i] / sqrt(coupling_accum_[i]);</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">          8 :       coupling_rate_[i] = (set_coupling_[i] - current_coupling_[i]) / update_period_;</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :     }</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :     else</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     {</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :       // do not change the bias</a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineNoCov">          0 :       coupling_rate_[i] = 0;</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     }</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   }</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : </a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   // reset means/vars</a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">          8 :   reset_statistics();</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">          8 : }</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            : </a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">         40 : void EDS::update()</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            : {</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :   // adjust parameters according to EDS recipe</a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">         40 :   update_calls_++;</span></a>
+<a name="1089"><span class="lineNum">    1089 </span>            : </a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   // if we aren't wating for the bias to equilibrate, set flag to collect data</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   // want statistics before writing restart</a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">         40 :   if (!b_equil_ &amp;&amp; update_period_ &gt; 0)</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">         12 :     update_statistics();</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   // write restart with correct statistics before bias update</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   // check if we're ramping or doing normal updates and then restart if needed. The ramping check</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   // is complicated because we could be frozen, finished ramping or not ramping.</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   // The + 2 is so we have an extra line showing that the bias isn't changing (for my sanity and yours)</a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">         40 :   if (b_write_restart_)</span></a>
+<a name="1100"><span class="lineNum">    1100 </span>            :   {</a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">         40 :     if (getStep() == 0 ||</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">         32 :         ((update_period_ &lt; 0 &amp;&amp; !b_freeze_ &amp;&amp; update_calls_ &lt;= fabs(update_period_) + 2) ||</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">         24 :          (update_period_ &gt; 0 &amp;&amp; update_calls_ % update_period_ == 0)))</span></a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">         27 :       writeOutRestart();</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            :   }</a>
+<a name="1106"><span class="lineNum">    1106 </span>            : </a>
+<a name="1107"><span class="lineNum">    1107 </span>            :   int b_finished_equil_flag = 1;</a>
+<a name="1108"><span class="lineNum">    1108 </span>            : </a>
+<a name="1109"><span class="lineNum">    1109 </span>            :   // assume forces already applied and saved</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   // are we ramping to a constant value and not done equilibrating?</a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">         40 :   if (update_period_ &lt; 0)</span></a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   {</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">          5 :     if (update_calls_ &lt;= fabs(update_period_) &amp;&amp; !b_freeze_)</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            :     {</a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">          4 :       for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">          2 :         current_coupling_[i] += (target_coupling_[i] - set_coupling_[i]) / fabs(update_period_);</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     }</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :     // make sure we don't reset update calls</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :     b_finished_equil_flag = 0;</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :   }</a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">         35 :   else if (update_period_ == 0)</span></a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   { // do we have a no-update case?</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :     // not updating</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :     // pass</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   }</a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">         30 :   else if (b_equil_)</span></a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   {</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :     // equilibrating</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :     // check if we've reached the setpoint</a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">         48 :     for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="1131"><span class="lineNum">    1131 </span>            :     {</a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">         30 :       if (coupling_rate_[i] == 0 || pow(current_coupling_[i] - set_coupling_[i], 2) &lt; pow(coupling_rate_[i], 2))</span></a>
+<a name="1133"><span class="lineNum">    1133 </span>            :       {</a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">         14 :         b_finished_equil_flag &amp;= 1;</span></a>
+<a name="1135"><span class="lineNum">    1135 </span>            :       }</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :       else</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :       {</a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">         16 :         current_coupling_[i] += coupling_rate_[i];</span></a>
+<a name="1139"><span class="lineNum">    1139 </span>            :         b_finished_equil_flag = 0;</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :       }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :   }</a>
+<a name="1143"><span class="lineNum">    1143 </span>            : </a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   // reduce all the flags</a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineCov">         40 :   if (b_equil_ &amp;&amp; b_finished_equil_flag)</span></a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   {</a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">         11 :     b_equil_ = false;</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">         11 :     update_calls_ = 0;</span></a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   }</a>
+<a name="1150"><span class="lineNum">    1150 </span>            : </a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   // Now we update coupling constant, if necessary</a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">         40 :   if (!b_equil_ &amp;&amp; update_period_ &gt; 0 &amp;&amp; update_calls_ == update_period_ &amp;&amp; !b_freeze_)</span></a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   {</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">          8 :     update_bias();</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">          8 :     update_calls_ = 0;</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">          8 :     avg_coupling_count_++;</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">          8 :     b_equil_ = true; // back to equilibration now</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   }                  // close update if</a>
+<a name="1159"><span class="lineNum">    1159 </span>            : </a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   // pass couplings out so they are accessible</a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">        100 :   for (unsigned int i = 0; i &lt; ncvs_; ++i)</span></a>
+<a name="1162"><span class="lineNum">    1162 </span>            :   {</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">         60 :     out_coupling_[i]-&gt;set(current_coupling_[i]);</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :   }</a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">         40 : }</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            : </a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">         16 : EDS::~EDS()</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            : {</a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">          8 :   out_restart_.close();</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">         24 : }</span></a>
+<a name="1171"><span class="lineNum">    1171 </span>            : </a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 : void EDS::turnOnDerivatives()</span></a>
+<a name="1173"><span class="lineNum">    1173 </span>            : {</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :   // do nothing</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :   // this is to avoid errors triggered when a bias is used as a CV</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :   // (This is done in ExtendedLagrangian.cpp)</a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1178"><span class="lineNum">    1178 </span>            : </a>
+<a name="1179"><span class="lineNum">    1179 </span>            : }</a>
+<a name="1180"><span class="lineNum">    1180 </span>            : } // close the 2 namespaces</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/eds/index-sort-f.html b/coverage/eds/index-sort-f.html
new file mode 100644
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+++ b/coverage/eds/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - eds</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - eds</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">452</td>
+            <td class="headerCovTableEntry">488</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryMed">87.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EDS.cpp.gcov.html">EDS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">452 / 488</td>
+      <td class="coverPerMed">87.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 23</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/eds/index-sort-l.html b/coverage/eds/index-sort-l.html
new file mode 100644
index 0000000000..fc0a40008f
--- /dev/null
+++ b/coverage/eds/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - eds</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - eds</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">452</td>
+            <td class="headerCovTableEntry">488</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryMed">87.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EDS.cpp.gcov.html">EDS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">452 / 488</td>
+      <td class="coverPerMed">87.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 23</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/eds/index.html b/coverage/eds/index.html
new file mode 100644
index 0000000000..a9ac50bc5a
--- /dev/null
+++ b/coverage/eds/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - eds</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - eds</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">452</td>
+            <td class="headerCovTableEntry">488</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryMed">87.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EDS.cpp.gcov.html">EDS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">452 / 488</td>
+      <td class="coverPerMed">87.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 23</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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new file mode 100644
index 0000000000..5a28029473
--- /dev/null
+++ b/coverage/fisst/FISST.cpp.func-sort-c.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst/FISST.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">fisst</a> - FISST.cpp<span style="font-size: 80%;"> (<a href="FISST.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">308</td>
+            <td class="headerCovTableEntryMed">80.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FISST.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#359">_ZN4PLMD5fisst5FISST13readInRestartEv</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#652">_ZN4PLMD5fisst5FISST17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#198">_ZN4PLMD5fisst5FISSTC2ERKNS_13ActionOptionsE</a></td>
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+    <tr>
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+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#165">_ZN4PLMD5fisst12_GLOBAL__N_118FISSTRegisterMe1676createERKNS_13ActionOptionsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#445">_ZN4PLMD5fisst5FISST15setupOutRestartEv</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#432">_ZN4PLMD5fisst5FISST18setupOutObservableEv</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#198">_ZN4PLMD5fisst5FISSTC1ERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#647">_ZN4PLMD5fisst5FISSTD0Ev</a></td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#647">_ZN4PLMD5fisst5FISSTD1Ev</a></td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#618">_ZN4PLMD5fisst5FISST25compute_observable_weightEv</a></td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#530">_ZN4PLMD5fisst5FISST10apply_biasEv</a></td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#598">_ZN4PLMD5fisst5FISST11update_biasEv</a></td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#459">_ZN4PLMD5fisst5FISST15writeOutRestartEv</a></td>
+              <td class="coverFnHi">10</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#551">_ZN4PLMD5fisst5FISST17update_statisticsEv</a></td>
+              <td class="coverFnHi">10</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#479">_ZN4PLMD5fisst5FISST18writeOutObservableEv</a></td>
+              <td class="coverFnHi">10</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#643">_ZN4PLMD5fisst5FISST6updateEv</a></td>
+              <td class="coverFnHi">10</td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#499">_ZN4PLMD5fisst5FISST9calculateEv</a></td>
+              <td class="coverFnHi">10</td>
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+              <td class="coverFn"><a href="FISST.cpp.gcov.html#349">_ZN4PLMD5fisst5FISST21NormalizeForceWeightsEv</a></td>
+              <td class="coverFnHi">12</td>
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+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#165">_ZN4PLMD5fisst12_GLOBAL__N_118FISSTRegisterMe167C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#165">_ZN4PLMD5fisst12_GLOBAL__N_118FISSTRegisterMe167D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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index 0000000000..a24de29267
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst/FISST.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">fisst</a> - FISST.cpp<span style="font-size: 80%;"> (<a href="FISST.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">308</td>
+            <td class="headerCovTableEntryMed">80.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FISST.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#165">_ZN4PLMD5fisst12_GLOBAL__N_118FISSTRegisterMe1676createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#165">_ZN4PLMD5fisst12_GLOBAL__N_118FISSTRegisterMe167C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#165">_ZN4PLMD5fisst12_GLOBAL__N_118FISSTRegisterMe167D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#530">_ZN4PLMD5fisst5FISST10apply_biasEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#598">_ZN4PLMD5fisst5FISST11update_biasEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#359">_ZN4PLMD5fisst5FISST13readInRestartEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#445">_ZN4PLMD5fisst5FISST15setupOutRestartEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#459">_ZN4PLMD5fisst5FISST15writeOutRestartEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#167">_ZN4PLMD5fisst5FISST16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#652">_ZN4PLMD5fisst5FISST17turnOnDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#551">_ZN4PLMD5fisst5FISST17update_statisticsEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#432">_ZN4PLMD5fisst5FISST18setupOutObservableEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#479">_ZN4PLMD5fisst5FISST18writeOutObservableEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#349">_ZN4PLMD5fisst5FISST21NormalizeForceWeightsEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#618">_ZN4PLMD5fisst5FISST25compute_observable_weightEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#643">_ZN4PLMD5fisst5FISST6updateEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#499">_ZN4PLMD5fisst5FISST9calculateEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#198">_ZN4PLMD5fisst5FISSTC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#198">_ZN4PLMD5fisst5FISSTC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#647">_ZN4PLMD5fisst5FISSTD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#647">_ZN4PLMD5fisst5FISSTD1Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FISST.cpp.gcov.html#647">_ZN4PLMD5fisst5FISSTD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/FISST.cpp.gcov.html b/coverage/fisst/FISST.cpp.gcov.html
new file mode 100644
index 0000000000..ae0182c529
--- /dev/null
+++ b/coverage/fisst/FISST.cpp.gcov.html
@@ -0,0 +1,738 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst/FISST.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">fisst</a> - FISST.cpp<span style="font-size: 80%;"> (source / <a href="FISST.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">308</td>
+            <td class="headerCovTableEntryMed">80.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2020 of Glen Hocky</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : The FISST module is free software: you can redistribute it and/or modify</a>
+<a name="5"><span class="lineNum">       5 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="6"><span class="lineNum">       6 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="7"><span class="lineNum">       7 </span>            : (at your option) any later version.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : The FISST module is distributed in the hope that it will be useful,</a>
+<a name="10"><span class="lineNum">      10 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="11"><span class="lineNum">      11 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="12"><span class="lineNum">      12 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="15"><span class="lineNum">      15 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="16"><span class="lineNum">      16 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="17"><span class="lineNum">      17 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="18"><span class="lineNum">      18 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;legendre_rule_fast.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iostream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : using namespace PLMD;</a>
+<a name="30"><span class="lineNum">      30 </span>            : using namespace bias;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //namespace is lowercase to match</a>
+<a name="33"><span class="lineNum">      33 </span>            : //module names being all lowercase</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace fisst {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC FISSTMOD_BIAS FISST</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Compute and apply the optimal linear force on an observable to enhance sampling of conformational distributions over a range of applied forces.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : This method is described in \cite Hartmann-FISST-2019</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : If the system's Hamiltonian is given by:</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f[</a>
+<a name="46"><span class="lineNum">      46 </span>            :     H(\vec{p},\vec{q}) = \sum_{j} \frac{p_j^2}{2m_j} + U(\vec{q}),</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f]</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : This bias modifies the Hamiltonian to be:</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f[</a>
+<a name="51"><span class="lineNum">      51 </span>            :   H'(\vec{p},\vec{q}) = H(\vec{p},\vec{q}) - \bar{F} Q</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f]</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : where for CV \f$Q\f$, a coupling constant \f${\bar{F}}\f$ is determined</a>
+<a name="55"><span class="lineNum">      55 </span>            : adaptively according to the FISST algorithm.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : Specifically,</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f[</a>
+<a name="59"><span class="lineNum">      59 </span>            : \bar{F}(Q)=\frac{ \int_{F_{min}}^{F_{max}} e^{\beta F Q(\vec{q})} \omega(F) F dF}{\int_{F_{min}}^{F_{max}} e^{\beta F Q(\vec{q})} \omega(F) dF},</a>
+<a name="60"><span class="lineNum">      60 </span>            : \f]</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : where \f$\vec{q}\f$ are the molecular coordinates of the system, and \f$w(F)\f$ is a weighting function that is learned on the fly for each force by the FISST algorithm (starting from an initial weight distribution, uniform by default).</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The target for \f$w(F)=1/Z_q(F)\f$, where</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f[</a>
+<a name="66"><span class="lineNum">      66 </span>            :     Z_q(F) \equiv \int d\vec{q} e^{-\beta U(\vec{q}) + \beta F Q(\vec{q})}.</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f]</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : FISST also computes and writes Observable Weights \f$W_F(\vec{q}_t)\f$ for a molecular configuration at time \f$t\f$, so that averages of other quantities \f$A(\vec{q})\f$ can be reconstructed later at different force values (over a trajectory with \f$T\f$ samples):</a>
+<a name="70"><span class="lineNum">      70 </span>            : \f[</a>
+<a name="71"><span class="lineNum">      71 </span>            :     \langle A \rangle_F = \frac{1}{T} \sum_t W_F(\vec{q}_t) A(\vec{q}_t).</a>
+<a name="72"><span class="lineNum">      72 </span>            : \f]</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : \par Examples</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : In the following example, an adaptive restraint is learned to bias the distance between two atoms in a system, for a force range of 0-100 pN.</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : \plumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : UNITS LENGTH=A TIME=fs ENERGY=kcal/mol</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : b1: GROUP ATOMS=1</a>
+<a name="83"><span class="lineNum">      83 </span>            : b2: GROUP ATOMS=12</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : dend: DISTANCE ATOMS=b1,b2</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : #The conversion factor is 69.4786 pN = 1 kcal/mol/Angstrom</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : #0 pN to 100 pN</a>
+<a name="90"><span class="lineNum">      90 </span>            : f: FISST MIN_FORCE=0 MAX_FORCE=1.44 PERIOD=100 NINTERPOLATE=31 ARG=dend OUT_RESTART=pull.restart.txt OUT_OBSERVABLE=pull.observable.txt OBSERVABLE_FREQ=1000</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : PRINT ARG=dend,f.dend_fbar,f.bias,f.force2 FILE=pull.colvar.txt STRIDE=1000</a>
+<a name="93"><span class="lineNum">      93 </span>            : \endplumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : */</a>
+<a name="97"><span class="lineNum">      97 </span>            : //+ENDPLUMEDOC</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : class FISST : public Bias {</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : private:</a>
+<a name="104"><span class="lineNum">     104 </span>            :   /*We will get this and store it once, since on-the-fly changing number of CVs will be fatal*/</a>
+<a name="105"><span class="lineNum">     105 </span>            :   const unsigned int ncvs_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;double&gt; center_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;double&gt; current_avg_force_;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;double&gt; forces_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   std::vector&lt;double&gt; force_weight_;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;double&gt; gauss_weight_;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;double&gt; partition_estimate_;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;double&gt; observable_weight_;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   std::string in_restart_name_;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::string out_restart_name_;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::string out_observable_name_;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   std::string fmt_;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::string initial_weight_dist_;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   OFile out_restart_;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   OFile out_observable_;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   IFile in_restart_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   bool b_freeze_;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   bool b_adaptive_;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   bool b_restart_;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   bool b_write_restart_;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   bool b_write_observable_;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   bool b_first_restart_sample_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   int period_;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   int reset_period_;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   int observable_freq_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   int n_interpolation_;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   int n_samples_;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   double kbt_;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   double beta_;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   //change min_force and max_force to vectors if going to do more than one cv</a>
+<a name="137"><span class="lineNum">     137 </span>            :   double max_force_;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   double min_force_;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   double initial_weight_rate_;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   double threshold_;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   Random rand_;</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   Value* value_force2_;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   void readInRestart();</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void NormalizeForceWeights();</a>
+<a name="147"><span class="lineNum">     147 </span>            :   /*setup output restart*/</a>
+<a name="148"><span class="lineNum">     148 </span>            :   void setupOutRestart();</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void setupOutObservable();</a>
+<a name="150"><span class="lineNum">     150 </span>            :   /*write output restart*/</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void writeOutRestart();</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void writeOutObservable();</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void update_statistics();</a>
+<a name="154"><span class="lineNum">     154 </span>            :   void update_bias();</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void apply_bias();</a>
+<a name="156"><span class="lineNum">     156 </span>            :   void compute_observable_weight();</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : public:</a>
+<a name="159"><span class="lineNum">     159 </span>            :   explicit FISST(const ActionOptions&amp;);</a>
+<a name="160"><span class="lineNum">     160 </span>            :   void calculate();</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void update();</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void turnOnDerivatives();</a>
+<a name="163"><span class="lineNum">     163 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   ~FISST();</a>
+<a name="165"><span class="lineNum">     165 </span>            : };</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(FISST,&quot;FISST&quot;)</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          4 : void FISST::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          4 :   Bias::registerKeywords(keys);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;PERIOD&quot;,&quot;Steps corresponding to the learning rate&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;RESET_PERIOD&quot;,&quot;Reset the learning statistics every time this number of steps comes around.&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;NINTERPOLATE&quot;,&quot;Number of grid points on which to do interpolation.&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MIN_FORCE&quot;,&quot;Minimum force (per CV) to use for sampling. Units: [Energy]/[CV]  (can be negative).&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MAX_FORCE&quot;,&quot;Maximum force (per CV) to use for sampling.&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;CENTER&quot;,&quot;0&quot;,&quot;The CV value at which the applied bias energy will be zero&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;KBT&quot;,&quot;The system temperature in units of KB*T. If not provided will be taken from MD code (if available)&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;INITIAL_WEIGHT_DIST&quot;,&quot;Starting distribution for the force weights (options: UNIFORM, EXP, GAUSS).&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;INITIAL_WEIGHT_RATE&quot;,&quot;Rate of decay for exponential and gaussian distributions. W(F)~exp(-r |F|^d).&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;RESTART_FMT&quot;,&quot;the format that should be used to output real numbers in FISST restarts.&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;OUT_RESTART&quot;,&quot;Output file for all information needed to continue FISST simulation.&quot;</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :            &quot;If you have the RESTART directive set (global or for FISST), this file will be appended to.&quot;</a>
+<a name="186"><span class="lineNum">     186 </span>            :            &quot;Note that the header will be printed again if appending.&quot;);</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;IN_RESTART&quot;,&quot;Read this file to continue an FISST simulation. &quot;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :            &quot;If same as OUT_RESTART and you have not set the RESTART directive, the file will be backed-up and overwritten with new output.&quot;</a>
+<a name="189"><span class="lineNum">     189 </span>            :            &quot;If you do have the RESTART flag set and it is the same name as OUT_RESTART, this file will be appended.&quot;);</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;OUT_OBSERVABLE&quot;,&quot;Output file putting weights needed to compute observables at different force values.&quot;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :            &quot;If you have the RESTART directive set (global or for FISST), this file will be appended to. &quot;</a>
+<a name="192"><span class="lineNum">     192 </span>            :            &quot;Note that the header will be printed again if appending.&quot;);</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;OBSERVABLE_FREQ&quot;,&quot;How often to write out observable weights (default=period).&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          8 :   keys.addFlag(&quot;FREEZE&quot;,false,&quot;Fix bias weights at current level (only used for restarting).&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          4 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;squared value of force from the bias.&quot;);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;_fbar&quot;,&quot;default&quot;, &quot;For each named CV biased, there will be a corresponding output CV_fbar storing the current linear bias prefactor.&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          4 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          2 : FISST::FISST(const ActionOptions&amp;ao):</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :   ncvs_(getNumberOfArguments()),</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :   current_avg_force_(ncvs_,0.0),</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          2 :   center_(ncvs_,0.0),</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   //change min_force and max_force to vectors if going to do more than one cv</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          2 :   min_force_(0.0),</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          2 :   max_force_(0.0),</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :   in_restart_name_(&quot;&quot;),</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          2 :   out_restart_name_(&quot;&quot;),</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          2 :   out_observable_name_(&quot;&quot;),</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 :   fmt_(&quot;%e&quot;),</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          2 :   b_freeze_(false),</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          2 :   b_restart_(false),</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          2 :   b_write_restart_(false),</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          2 :   b_write_observable_(false),</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          2 :   b_first_restart_sample_(true),</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          2 :   n_interpolation_(0),</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          2 :   n_samples_(0),</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          2 :   initial_weight_rate_(0),</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          2 :   initial_weight_dist_(&quot;UNIFORM&quot;),</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          2 :   period_(0),</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 :   reset_period_(0),</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          2 :   observable_freq_(0),</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          2 :   kbt_(0.0),</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          6 :   value_force2_(NULL)</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : {</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          2 :   if(ncvs_==0)</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     error(&quot;Must specify at least one CV with ARG&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   //temporary</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          2 :   if(ncvs_&gt;1)</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     error(&quot;FISST only supports using one CV right now&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          2 :   addComponent(&quot;force2&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          2 :   componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          2 :   value_force2_ = getPntrToComponent(&quot;force2&quot;);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          4 :   for(unsigned int i = 0; i&lt;ncvs_; i++) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :     std::string comp = getPntrToArgument(i)-&gt;getName() + &quot;_fbar&quot;;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          2 :     addComponent(comp);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 :     componentIsNotPeriodic(comp);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :   parseVector(&quot;CENTER&quot;,center_);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   //change min_force and max_force to vectors if going to do more than one cv</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          2 :   parse(&quot;MIN_FORCE&quot;,min_force_);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          2 :   parse(&quot;MAX_FORCE&quot;,max_force_);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          2 :   parse(&quot;PERIOD&quot;,period_);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          2 :   parse(&quot;RESET_PERIOD&quot;,reset_period_);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :   parse(&quot;INITIAL_WEIGHT_DIST&quot;,initial_weight_dist_);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          2 :   parse(&quot;INITIAL_WEIGHT_RATE&quot;,initial_weight_rate_);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 :   parse(&quot;OBSERVABLE_FREQ&quot;,observable_freq_);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          2 :   parse(&quot;NINTERPOLATE&quot;,n_interpolation_);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          2 :   parseFlag(&quot;FREEZE&quot;,b_freeze_);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          2 :   parse(&quot;KBT&quot;,kbt_);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          2 :   parse(&quot;RESTART_FMT&quot;, fmt_);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          2 :   fmt_ = &quot; &quot; + fmt_;//add space since parse strips them</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          2 :   parse(&quot;OUT_RESTART&quot;,out_restart_name_);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          2 :   parse(&quot;OUT_OBSERVABLE&quot;,out_observable_name_);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          2 :   parse(&quot;IN_RESTART&quot;,in_restart_name_);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          2 :   if(center_.size() != ncvs_)</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :     error(&quot;Must have same number of CENTER arguments as ARG arguments&quot;);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          2 :   if(in_restart_name_ != &quot;&quot;) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :     b_restart_ = true;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :     log.printf(&quot;  reading simulation information from file: %s\n&quot;,in_restart_name_.c_str());</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :     readInRestart();</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   } else {</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :     if(! kbt_ &gt; 0.0)</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          2 :       kbt_ = plumed.getAtoms().getKbT();</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :     //in driver, this results in kbt of 0</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          2 :     if(kbt_ == 0) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :       error(&quot;  Unable to determine valid kBT. &quot;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :             &quot;Could be because you are runnning from driver or MD didn't give temperature.\n&quot;</a>
+<a name="279"><span class="lineNum">     279 </span>            :             &quot;Consider setting temperature manually with the KBT keyword.&quot;);</a>
+<a name="280"><span class="lineNum">     280 </span>            :     }</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          2 :     log.printf(&quot;  kBT = %f\n&quot;,kbt_);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          2 :     log.printf(&quot;  Updating with a time scale of %i steps\n&quot;,period_);</span></a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          2 :     log.printf(&quot;  Using centers for CVs of:&quot;);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          4 :     for(unsigned int i = 0; i&lt; ncvs_; i++) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          2 :       log.printf(&quot; %f &quot;,center_[i]);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          2 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          2 :     observable_weight_.resize(n_interpolation_);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         64 :     for(unsigned int i = 0; i&lt;n_interpolation_; i++) observable_weight_[i] = 1.0;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          2 :     forces_.resize(n_interpolation_);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          2 :     force_weight_.resize(n_interpolation_);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :     //using code from the MIST project</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          2 :     gauss_weight_.resize(n_interpolation_);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          2 :     legendre_compute_glr(n_interpolation_, &amp;forces_[0], &amp;gauss_weight_[0]);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          2 :     rescale(min_force_, max_force_, n_interpolation_, &amp;forces_[0], &amp;gauss_weight_[0]);</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          2 :     log.printf(&quot;Using weight distribution %s with rate %f\n&quot;,initial_weight_dist_.c_str(),initial_weight_rate_);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          2 :     if(initial_weight_dist_ == &quot;UNIFORM&quot; ) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         32 :       for(unsigned int i = 0; i&lt;n_interpolation_; i++) force_weight_[i] = 1.0;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          1 :     else if (initial_weight_dist_ == &quot;EXP&quot; ) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         32 :       for(unsigned int i = 0; i&lt;n_interpolation_; i++) force_weight_[i] = exp(-fabs(forces_[i])*initial_weight_rate_);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     }</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :     else if (initial_weight_dist_ == &quot;GAUSS&quot; ) {</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :       for(unsigned int i = 0; i&lt;n_interpolation_; i++) force_weight_[i] = exp(-pow(forces_[i],2)*initial_weight_rate_);</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :     }</a>
+<a name="310"><span class="lineNum">     310 </span>            :     else {</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :       error(&quot;  Specified weight distribution is not from the allowed list.&quot;);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :     }</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          2 :     partition_estimate_.resize(n_interpolation_);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          2 :     NormalizeForceWeights();</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     double sum = 0.0;</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         64 :     for(unsigned int i = 0; i&lt;n_interpolation_; i++) {</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :       //setting partition estimate as 1/w_i</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         62 :       partition_estimate_[i] = 1/force_weight_[i];</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         62 :       log.printf(&quot;force/gauss weight/force_weight: %i %f %f %f\n&quot;,i,forces_[i],gauss_weight_[i],force_weight_[i]);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         62 :       sum+=gauss_weight_[i]*force_weight_[i];</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :     }</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          2 :     log.printf(&quot;--Sum_i w_i g_i: %f\n&quot;,sum);</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            :   //set inverse temperature</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          2 :   beta_ = 1/kbt_;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          2 :   if(b_freeze_ &amp;&amp; b_restart_) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :     log.printf(&quot;  freezing weights read in from the restart file\n&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          2 :   if(out_restart_name_.length()&gt;0) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          2 :     log.printf(&quot;  writing restart information every %i steps to file %s with format %s\n&quot;,abs(period_),out_restart_name_.c_str(), fmt_.c_str());</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          2 :     b_write_restart_ = true;</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          2 :     setupOutRestart();</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          2 :   if(out_observable_name_.length()&gt;0) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          2 :     if(observable_freq_==0) observable_freq_ = period_;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          2 :     log.printf(&quot;  writing observable information every %i steps to file %s with format %s\n&quot;,observable_freq_,out_observable_name_.c_str(), fmt_.c_str());</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          2 :     b_write_observable_ = true;</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          2 :     setupOutObservable();</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :   //add citation later:</a>
+<a name="348"><span class="lineNum">     348 </span>            :   //log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;&quot;)&lt;&lt;&quot;\n&quot;;</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          2 : }</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         12 : void FISST::NormalizeForceWeights() {</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   double denom = 0.0;</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        384 :   for(unsigned i=0; i&lt;n_interpolation_; i++)</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        372 :     denom += gauss_weight_[i] * force_weight_[i];</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        384 :   for(unsigned i=0; i&lt;n_interpolation_; i++)</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        372 :     force_weight_[i] /= denom;</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         12 : }</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 : void FISST::readInRestart() {</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :   in_restart_.open(in_restart_name_);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :   if(in_restart_.FieldExist(&quot;kbt&quot;)) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;kbt&quot;,kbt_);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :   } else { error(&quot;No field 'kbt' in restart file&quot;); }</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :   log.printf(&quot;  with kBT = %f\n&quot;,kbt_);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :   if(in_restart_.FieldExist(&quot;period&quot;)) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;period&quot;,period_);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :   } else { error(&quot;No field 'period' in restart file&quot;); }</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :   log.printf(&quot;  Updating every %i steps\n&quot;,period_);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : //this one can be optional</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :   if(in_restart_.FieldExist(&quot;reset_period&quot;)) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;reset_period&quot;,reset_period_);</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :   }</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :   log.printf(&quot;  Resetting statistics every %i steps\n&quot;,reset_period_);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :   if(in_restart_.FieldExist(&quot;n_interpolation&quot;)) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;n_interpolation&quot;,n_interpolation_);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :   } else { error(&quot;No field 'n_interpolation' in restart file&quot;); }</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :   if(in_restart_.FieldExist(&quot;min_force&quot;)) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;min_force&quot;,min_force_);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :   } else { error(&quot;No field 'min_force' in restart file&quot;); }</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :   if(in_restart_.FieldExist(&quot;max_force&quot;)) {</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;max_force&quot;,max_force_);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :   } else { error(&quot;No field 'max_force' in restart file&quot;); }</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :   log.printf(&quot;  with forces from min_force=%e to max_force=%e over %i bins\n&quot;,min_force_,max_force_,n_interpolation_);</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            :   unsigned int N = 0;</a>
+<a name="393"><span class="lineNum">     393 </span>            :   std::string cv_name;</a>
+<a name="394"><span class="lineNum">     394 </span>            :   double tmp, time;</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :   while(in_restart_.scanField(&quot;time&quot;,time)) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :     in_restart_.scanField(&quot;nsamples&quot;,n_samples_);</span></a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :     observable_weight_.resize(n_interpolation_);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :     partition_estimate_.resize(n_interpolation_);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :     force_weight_.resize(n_interpolation_);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :     gauss_weight_.resize(n_interpolation_);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :     forces_.resize(n_interpolation_);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :     for(unsigned int i = 0; i&lt;ncvs_; ++i) {</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :       cv_name = getPntrToArgument(i)-&gt;getName();</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :       in_restart_.scanField(cv_name,tmp);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :       for(unsigned int j =0; j&lt;n_interpolation_; ++j) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :         in_restart_.scanField(cv_name + &quot;_f&quot;+std::to_string(j),forces_[j]);</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :         in_restart_.scanField(cv_name + &quot;_g&quot;+std::to_string(j),gauss_weight_[j]);</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :         in_restart_.scanField(cv_name + &quot;_w&quot;+std::to_string(j),force_weight_[j]);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :         in_restart_.scanField(cv_name + &quot;_z&quot;+std::to_string(j),partition_estimate_[j]);</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :       }</a>
+<a name="414"><span class="lineNum">     414 </span>            :     }</a>
+<a name="415"><span class="lineNum">     415 </span>            :     N++;</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :     in_restart_.scanField();</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :   }</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   double sum = 0.0;</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :   for(unsigned int j =0; j&lt;n_interpolation_; ++j) {</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :     //clear observable weight, which will be set later</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :     observable_weight_[j] = 1.0;</span></a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            :     //setting partition estimate as 1/w_i</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :     log.printf(&quot;force/gauss weight/force_weight: %i %e %e %e\n&quot;,j,forces_[j],gauss_weight_[j],force_weight_[j]);</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :     sum+=gauss_weight_[j]*force_weight_[j];</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :   }</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :   log.printf(&quot;--Sum_i w_i g_i: %f\n&quot;,sum);</span></a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :   in_restart_.close();</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          2 : void FISST::setupOutObservable() {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          2 :   out_observable_.link(*this);</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          2 :   out_observable_.fmtField(fmt_);</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          2 :   out_observable_.open(out_observable_name_);</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :   out_observable_.setHeavyFlush();</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          4 :   out_observable_.addConstantField(&quot;kbt&quot;).printField(&quot;kbt&quot;,kbt_);</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          4 :   out_observable_.addConstantField(&quot;n_interpolation&quot;).printField(&quot;n_interpolation&quot;,n_interpolation_);</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          4 :   out_observable_.addConstantField(&quot;period&quot;).printField(&quot;period&quot;,period_);</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          4 :   out_observable_.addConstantField(&quot;min_force&quot;).printField(&quot;min_force&quot;,min_force_);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          4 :   out_observable_.addConstantField(&quot;max_force&quot;).printField(&quot;max_force&quot;,max_force_);</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          2 : }</span></a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          2 : void FISST::setupOutRestart() {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          2 :   out_restart_.link(*this);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          2 :   out_restart_.fmtField(fmt_);</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          2 :   out_restart_.open(out_restart_name_);</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :   out_restart_.setHeavyFlush();</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">          4 :   out_restart_.addConstantField(&quot;kbt&quot;).printField(&quot;kbt&quot;,kbt_);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          4 :   out_restart_.addConstantField(&quot;n_interpolation&quot;).printField(&quot;n_interpolation&quot;,n_interpolation_);</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          4 :   out_restart_.addConstantField(&quot;period&quot;).printField(&quot;period&quot;,period_);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          2 :   if(reset_period_&gt;0) out_restart_.addConstantField(&quot;reset_period&quot;).printField(&quot;reset_period&quot;,reset_period_);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          4 :   out_restart_.addConstantField(&quot;min_force&quot;).printField(&quot;min_force&quot;,min_force_);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          4 :   out_restart_.addConstantField(&quot;max_force&quot;).printField(&quot;max_force&quot;,max_force_);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          2 : }</span></a>
+<a name="460"><span class="lineNum">     460 </span>            : </a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         10 : void FISST::writeOutRestart() {</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :   std::string cv_name;</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         10 :   out_restart_.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         10 :   out_restart_.printField(&quot;nsamples&quot;,n_samples_);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         20 :   for(unsigned int i = 0; i&lt;ncvs_; ++i) {</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :     cv_name = getPntrToArgument(i)-&gt;getName();</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         10 :     double Q_i = difference(i, center_[i], getArgument(i));</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         10 :     out_restart_.printField(cv_name,Q_i);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">        320 :     for(int j = 0; j &lt; n_interpolation_; j++ ) {</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : //have to update this for multiple cvs</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">        620 :       out_restart_.printField(cv_name + &quot;_f&quot;+std::to_string(j),forces_[j]);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">        620 :       out_restart_.printField(cv_name + &quot;_g&quot;+std::to_string(j),gauss_weight_[j]);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        620 :       out_restart_.printField(cv_name + &quot;_w&quot;+std::to_string(j),force_weight_[j]);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">        620 :       out_restart_.printField(cv_name + &quot;_z&quot;+std::to_string(j),partition_estimate_[j]);</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :     }</a>
+<a name="477"><span class="lineNum">     477 </span>            :   }</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         10 :   out_restart_.printField();</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         10 : }</span></a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         10 : void FISST::writeOutObservable() {</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   std::string cv_name;</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         10 :   out_observable_.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         10 :   out_observable_.printField(&quot;nsamples&quot;,n_samples_);</span></a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         20 :   for(unsigned int i = 0; i&lt;ncvs_; ++i) {</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     cv_name = getPntrToArgument(i)-&gt;getName();</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         10 :     double Q_i = difference(i, center_[i], getArgument(i));</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         10 :     out_observable_.printField(cv_name,Q_i);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         10 :     out_observable_.printField(cv_name + &quot;_fbar&quot;,current_avg_force_[i]);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        320 :     for(int j = 0; j &lt; n_interpolation_; j++ ) {</span></a>
+<a name="492"><span class="lineNum">     492 </span>            : //have to update this for multiple cvs</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        620 :       out_observable_.printField(cv_name + &quot;_f&quot;+std::to_string(j),forces_[j]);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        620 :       out_observable_.printField(cv_name + &quot;_ow&quot;+std::to_string(j),observable_weight_[j]);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     }</a>
+<a name="496"><span class="lineNum">     496 </span>            :   }</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         10 :   out_observable_.printField();</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">         10 : }</span></a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         10 : void FISST::calculate() {</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         10 :   if(getStep() == 0 ) {</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          2 :     if(b_write_restart_) writeOutRestart();</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          2 :     if(b_write_observable_) writeOutObservable();</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :   }</a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         10 :   if(! b_freeze_) {</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         10 :     if(b_restart_ &amp;&amp; b_first_restart_sample_) {</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :       //dont' update statistics if restarting and first sample</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :       b_first_restart_sample_ = false;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :     }</a>
+<a name="512"><span class="lineNum">     512 </span>            :     else {</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         10 :       update_statistics();</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :     }</a>
+<a name="515"><span class="lineNum">     515 </span>            :   }</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         10 :   update_bias();</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         10 :   apply_bias();</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span>            :   //check about writing restart file</a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         10 :   if(getStep()&gt;0 &amp;&amp; getStep()%period_==0) {</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">          8 :     if(b_write_restart_) writeOutRestart();</span></a>
+<a name="522"><span class="lineNum">     522 </span>            :   }</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         10 :   if(getStep()&gt;0 &amp;&amp; getStep()%observable_freq_==0) {</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          8 :     if(b_write_observable_) {</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          8 :       compute_observable_weight();</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">          8 :       writeOutObservable();</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :     }</a>
+<a name="528"><span class="lineNum">     528 </span>            :   }</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         10 : }</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         10 : void FISST::apply_bias() {</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   //Compute linear force as in &quot;restraint&quot;</a>
+<a name="534"><span class="lineNum">     534 </span>            :   double ene = 0, totf2 = 0, cv, m, f;</a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         20 :   for(unsigned int i = 0; i &lt; ncvs_; ++i) {</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">         10 :     cv = difference(i, center_[i], getArgument(i));</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         10 :     double fbar = current_avg_force_[i];</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         10 :     ene -= fbar*cv;</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :     setOutputForce(i,fbar);</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">         10 :     totf2 += fbar*fbar;</span></a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         10 :     std::string fbar_name_ = getPntrToArgument(i)-&gt;getName() + &quot;_fbar&quot;;</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         10 :     Value* fbar_ = getPntrToComponent(fbar_name_);</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :     fbar_-&gt;set(fbar);</a>
+<a name="546"><span class="lineNum">     546 </span>            :   };</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            :   setBias(ene);</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         10 :   value_force2_-&gt;set(totf2);</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :   //log.flush();</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         10 : }</span></a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         10 : void FISST::update_statistics()  {</span></a>
+<a name="554"><span class="lineNum">     554 </span>            : //get stride is for multiple time stepping</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         10 :   double dt=getTimeStep()*getStride();</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">         10 :   double h = dt/(period_*getTimeStep());</span></a>
+<a name="557"><span class="lineNum">     557 </span>            :   double fbar_denum_integral = 0.0;</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         10 :   int step = getStep();</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         10 :   if(reset_period_&gt;0 &amp;&amp; step&gt;0 &amp;&amp; step%reset_period_==0) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :     n_samples_=1;</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :   }</a>
+<a name="563"><span class="lineNum">     563 </span>            :   else {</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         10 :     n_samples_++;</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :   }</a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         10 :   double d_n_samples = (double)n_samples_;</span></a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         20 :   for(unsigned int i = 0; i &lt; ncvs_; ++i) {</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">         10 :     double Q_i = difference(i, center_[i], getArgument(i));</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">        320 :     for(unsigned int j=0; j&lt;n_interpolation_; j++)</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :     {</a>
+<a name="572"><span class="lineNum">     572 </span>            :       //if multiple cvs, these need to be updated to have 2 columns</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        310 :       double f_j = forces_[j];</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        310 :       double w_j = force_weight_[j];</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        310 :       double g_j = gauss_weight_[j];</span></a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        310 :       fbar_denum_integral += g_j * w_j * exp(beta_*f_j * Q_i);</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :     }</a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">        320 :     for(unsigned int j=0; j&lt;n_interpolation_; j++)</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :     {</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">        310 :       double f_j = forces_[j];</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">        310 :       double sample_weight = exp(beta_*f_j * Q_i) / fbar_denum_integral;</span></a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">        310 :       partition_estimate_[j] = sample_weight/d_n_samples + partition_estimate_[j]*(d_n_samples-1)/(d_n_samples);</span></a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">        310 :       double w_jn = force_weight_[j];</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">        310 :       double z_jn = partition_estimate_[j];</span></a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">        310 :       double w_jp1 = (1.0 - h) * w_jn + h / z_jn;</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">        310 :       force_weight_[j] = w_jp1;</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :     }</a>
+<a name="593"><span class="lineNum">     593 </span>            :   }</a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span>            :   // make sure that the weights are normalised</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         10 :   NormalizeForceWeights();</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">         10 : }</span></a>
+<a name="598"><span class="lineNum">     598 </span>            : </a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         10 : void FISST::update_bias()</span></a>
+<a name="601"><span class="lineNum">     601 </span>            : {</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         20 :   for(unsigned int i = 0; i &lt; ncvs_; ++i) {</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         10 :     double Q_i = difference(i, center_[i], getArgument(i));</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :     double fbar_num_integral = 0.0;</a>
+<a name="605"><span class="lineNum">     605 </span>            :     double fbar_denum_integral = 0.0;</a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">        320 :     for(unsigned int j=0; j&lt;n_interpolation_; j++ ) {</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">        310 :       double f_j = forces_[j];</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">        310 :       double w_j = force_weight_[j];</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">        310 :       double g_j = gauss_weight_[j];</span></a>
+<a name="611"><span class="lineNum">     611 </span>            : </a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">        310 :       fbar_num_integral += g_j * f_j * w_j * exp(beta_*f_j*Q_i);</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">        310 :       fbar_denum_integral += g_j * w_j * exp(beta_*f_j*Q_i);</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :     }</a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         10 :     current_avg_force_[i] = fbar_num_integral/fbar_denum_integral;</span></a>
+<a name="617"><span class="lineNum">     617 </span>            :   }</a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         10 : }</span></a>
+<a name="619"><span class="lineNum">     619 </span>            : </a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">          8 : void FISST::compute_observable_weight() {</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">          8 :   double obs_num = (max_force_ - min_force_);</span></a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         16 :   for(unsigned int i = 0; i &lt; ncvs_; ++i) {</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">          8 :     double Q_i = difference(i, center_[i], getArgument(i));</span></a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        256 :     for(unsigned int j=0; j&lt;n_interpolation_; j++ ) {</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">        248 :       double z_j = partition_estimate_[j];</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">        248 :       double f_j = forces_[j];</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :       double denum_integral = 0.0;</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">       7936 :       for( unsigned int k=0; k&lt;n_interpolation_; k++ ) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">       7688 :         double f_k = forces_[k];</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">       7688 :         double w_k = force_weight_[k];</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">       7688 :         double g_k = gauss_weight_[k];</span></a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       7688 :         denum_integral += g_k * w_k * exp(beta_*(f_k-f_j)*Q_i);</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :       }</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">        248 :       observable_weight_[j] = obs_num/(denum_integral*z_j);</span></a>
+<a name="639"><span class="lineNum">     639 </span>            :     }</a>
+<a name="640"><span class="lineNum">     640 </span>            :   }</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">          8 : }</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span>            : </a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">         10 : void FISST::update() {</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :   //pass</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         10 : }</span></a>
+<a name="648"><span class="lineNum">     648 </span>            : </a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          4 : FISST::~FISST() {</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          2 :   out_restart_.close();</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          2 :   out_observable_.close();</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">          6 : }</span></a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineNoCov">          0 : void FISST::turnOnDerivatives() {</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :   // do nothing</a>
+<a name="656"><span class="lineNum">     656 </span>            :   // this is to avoid errors triggered when a bias is used as a CV</a>
+<a name="657"><span class="lineNum">     657 </span>            :   // (This is done in ExtendedLagrangian.cpp)</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="659"><span class="lineNum">     659 </span>            : </a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span>            : }</a>
+<a name="662"><span class="lineNum">     662 </span>            : }//close the 2 namespaces</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/index-sort-f.html b/coverage/fisst/index-sort-f.html
new file mode 100644
index 0000000000..6da95aedb1
--- /dev/null
+++ b/coverage/fisst/index-sort-f.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - fisst</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">319</td>
+            <td class="headerCovTableEntry">401</td>
+            <td class="headerCovTableEntryMed">79.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryMed">82.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FISST.cpp.gcov.html">FISST.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.2%"><img src="../snow.png" width=20 height=10 alt="80.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.2&nbsp;%</td>
+      <td class="coverNumMed">247 / 308</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="legendre_rule_fast.cpp.gcov.html">legendre_rule_fast.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">72 / 93</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/index-sort-l.html b/coverage/fisst/index-sort-l.html
new file mode 100644
index 0000000000..f0d1a8e806
--- /dev/null
+++ b/coverage/fisst/index-sort-l.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - fisst</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">319</td>
+            <td class="headerCovTableEntry">401</td>
+            <td class="headerCovTableEntryMed">79.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryMed">82.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="legendre_rule_fast.cpp.gcov.html">legendre_rule_fast.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">72 / 93</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FISST.cpp.gcov.html">FISST.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.2%"><img src="../snow.png" width=20 height=10 alt="80.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.2&nbsp;%</td>
+      <td class="coverNumMed">247 / 308</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/index.html b/coverage/fisst/index.html
new file mode 100644
index 0000000000..5416025914
--- /dev/null
+++ b/coverage/fisst/index.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - fisst</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">319</td>
+            <td class="headerCovTableEntry">401</td>
+            <td class="headerCovTableEntryMed">79.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryMed">82.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FISST.cpp.gcov.html">FISST.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.2%"><img src="../snow.png" width=20 height=10 alt="80.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.2&nbsp;%</td>
+      <td class="coverNumMed">247 / 308</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="legendre_rule_fast.cpp.gcov.html">legendre_rule_fast.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="77.4%"><img src="../snow.png" width=23 height=10 alt="77.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.4&nbsp;%</td>
+      <td class="coverNumMed">72 / 93</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/legendre_rule_fast.cpp.func-sort-c.html b/coverage/fisst/legendre_rule_fast.cpp.func-sort-c.html
new file mode 100644
index 0000000000..01d79b5ae6
--- /dev/null
+++ b/coverage/fisst/legendre_rule_fast.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst/legendre_rule_fast.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">fisst</a> - legendre_rule_fast.cpp<span style="font-size: 80%;"> (<a href="legendre_rule_fast.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="legendre_rule_fast.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#297">_ZN4PLMD5fisst21legendre_compute_glr2EdiPdS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#26">_ZN4PLMD5fisst20legendre_compute_glrEiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#110">_ZN4PLMD5fisst21legendre_compute_glr0EiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#172">_ZN4PLMD5fisst21legendre_compute_glr1EiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#395">_ZN4PLMD5fisst7rescaleEddiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#450">_ZN4PLMD5fisst7rk2_legEdddi</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#511">_ZN4PLMD5fisst7ts_multEPddi</a></td>
+              <td class="coverFnHi">330</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/legendre_rule_fast.cpp.func.html b/coverage/fisst/legendre_rule_fast.cpp.func.html
new file mode 100644
index 0000000000..4443785c1e
--- /dev/null
+++ b/coverage/fisst/legendre_rule_fast.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst/legendre_rule_fast.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">fisst</a> - legendre_rule_fast.cpp<span style="font-size: 80%;"> (<a href="legendre_rule_fast.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="legendre_rule_fast.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#26">_ZN4PLMD5fisst20legendre_compute_glrEiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#110">_ZN4PLMD5fisst21legendre_compute_glr0EiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#172">_ZN4PLMD5fisst21legendre_compute_glr1EiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#297">_ZN4PLMD5fisst21legendre_compute_glr2EdiPdS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#395">_ZN4PLMD5fisst7rescaleEddiPdS1_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#450">_ZN4PLMD5fisst7rk2_legEdddi</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="legendre_rule_fast.cpp.gcov.html#511">_ZN4PLMD5fisst7ts_multEPddi</a></td>
+              <td class="coverFnHi">330</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/fisst/legendre_rule_fast.cpp.gcov.html b/coverage/fisst/legendre_rule_fast.cpp.gcov.html
new file mode 100644
index 0000000000..94cdbdf3c4
--- /dev/null
+++ b/coverage/fisst/legendre_rule_fast.cpp.gcov.html
@@ -0,0 +1,641 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - fisst/legendre_rule_fast.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">fisst</a> - legendre_rule_fast.cpp<span style="font-size: 80%;"> (source / <a href="legendre_rule_fast.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntryMed">77.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2020 of Glen Hocky</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : The FISST module is free software: you can redistribute it and/or modify</a>
+<a name="5"><span class="lineNum">       5 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="6"><span class="lineNum">       6 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="7"><span class="lineNum">       7 </span>            : (at your option) any later version.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : The FISST module is distributed in the hope that it will be useful,</a>
+<a name="10"><span class="lineNum">      10 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="11"><span class="lineNum">      11 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="12"><span class="lineNum">      12 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="15"><span class="lineNum">      15 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="16"><span class="lineNum">      16 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="17"><span class="lineNum">      17 </span>            : //#ifndef __PLUMED_fisst_legendre_rule_fast_h</a>
+<a name="18"><span class="lineNum">      18 </span>            : //#define __PLUMED_fisst_legendre_rule_fast_h</a>
+<a name="19"><span class="lineNum">      19 </span>            : // adapted from:</a>
+<a name="20"><span class="lineNum">      20 </span>            : // https://people.sc.fsu.edu/~jburkardt/cpp_src/legendre_rule_fast/legendre_rule_fast.html</a>
+<a name="21"><span class="lineNum">      21 </span>            : //</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;legendre_rule_fast.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace fisst {</a>
+<a name="26"><span class="lineNum">      26 </span>            : //****************************************************************************80</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          2 : void legendre_compute_glr ( int n, double x[], double w[] )</span></a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //****************************************************************************80</a>
+<a name="31"><span class="lineNum">      31 </span>            : //</a>
+<a name="32"><span class="lineNum">      32 </span>            : //  Purpose:</a>
+<a name="33"><span class="lineNum">      33 </span>            : //</a>
+<a name="34"><span class="lineNum">      34 </span>            : //    LEGENDRE_COMPUTE_GLR: Legendre quadrature by the Glaser-Liu-Rokhlin method.</a>
+<a name="35"><span class="lineNum">      35 </span>            : //</a>
+<a name="36"><span class="lineNum">      36 </span>            : //  Licensing:</a>
+<a name="37"><span class="lineNum">      37 </span>            : //</a>
+<a name="38"><span class="lineNum">      38 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="39"><span class="lineNum">      39 </span>            : //</a>
+<a name="40"><span class="lineNum">      40 </span>            : //  Modified:</a>
+<a name="41"><span class="lineNum">      41 </span>            : //</a>
+<a name="42"><span class="lineNum">      42 </span>            : //    20 October 2009</a>
+<a name="43"><span class="lineNum">      43 </span>            : //</a>
+<a name="44"><span class="lineNum">      44 </span>            : //  Author:</a>
+<a name="45"><span class="lineNum">      45 </span>            : //</a>
+<a name="46"><span class="lineNum">      46 </span>            : //    Original C++ version by Nick Hale.</a>
+<a name="47"><span class="lineNum">      47 </span>            : //    This C++ version by John Burkardt.</a>
+<a name="48"><span class="lineNum">      48 </span>            : //</a>
+<a name="49"><span class="lineNum">      49 </span>            : //  Reference:</a>
+<a name="50"><span class="lineNum">      50 </span>            : //</a>
+<a name="51"><span class="lineNum">      51 </span>            : //    Andreas Glaser, Xiangtao Liu, Vladimir Rokhlin,</a>
+<a name="52"><span class="lineNum">      52 </span>            : //    A fast algorithm for the calculation of the roots of special functions,</a>
+<a name="53"><span class="lineNum">      53 </span>            : //    SIAM Journal on Scientific Computing,</a>
+<a name="54"><span class="lineNum">      54 </span>            : //    Volume 29, Number 4, pages 1420-1438, 2007.</a>
+<a name="55"><span class="lineNum">      55 </span>            : //</a>
+<a name="56"><span class="lineNum">      56 </span>            : //  Parameters:</a>
+<a name="57"><span class="lineNum">      57 </span>            : //</a>
+<a name="58"><span class="lineNum">      58 </span>            : //    Input, int N, the order.</a>
+<a name="59"><span class="lineNum">      59 </span>            : //</a>
+<a name="60"><span class="lineNum">      60 </span>            : //    Output, double X[N], the abscissas.</a>
+<a name="61"><span class="lineNum">      61 </span>            : //</a>
+<a name="62"><span class="lineNum">      62 </span>            : //    Output, double W[N], the weights.</a>
+<a name="63"><span class="lineNum">      63 </span>            : //</a>
+<a name="64"><span class="lineNum">      64 </span>            : {</a>
+<a name="65"><span class="lineNum">      65 </span>            :   int i;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double p;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double pp;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double w_sum;</a>
+<a name="69"><span class="lineNum">      69 </span>            : //</a>
+<a name="70"><span class="lineNum">      70 </span>            : //  Get the value and derivative of the N-th Legendre polynomial at 0.</a>
+<a name="71"><span class="lineNum">      71 </span>            : //</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          2 :   legendre_compute_glr0 ( n, &amp;p, &amp;pp );</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : //</a>
+<a name="74"><span class="lineNum">      74 </span>            : //  If N is odd, then zero is a root.</a>
+<a name="75"><span class="lineNum">      75 </span>            : //</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          2 :   if ( n % 2 == 1 )</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          2 :     x[(n-1)/2] = p;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          2 :     w[(n-1)/2] = pp;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span>            : //</a>
+<a name="82"><span class="lineNum">      82 </span>            : //  If N is even, we have to call a function to find the first root.</a>
+<a name="83"><span class="lineNum">      83 </span>            : //</a>
+<a name="84"><span class="lineNum">      84 </span>            :   else</a>
+<a name="85"><span class="lineNum">      85 </span>            :   {</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     legendre_compute_glr2 ( p, n, &amp;x[n/2], &amp;w[n/2] );</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span>            : //</a>
+<a name="89"><span class="lineNum">      89 </span>            : //  Get the complete set of roots and derivatives.</a>
+<a name="90"><span class="lineNum">      90 </span>            : //</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   legendre_compute_glr1 ( n, x, w );</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : //</a>
+<a name="93"><span class="lineNum">      93 </span>            : //  Compute the W.</a>
+<a name="94"><span class="lineNum">      94 </span>            : //</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         64 :   for ( i = 0; i &lt; n; i++ )</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         62 :     w[i] = 2.0 / ( 1.0 - x[i] ) / ( 1.0 + x[i] ) / w[i] / w[i];</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span>            :   w_sum = 0.0;</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         64 :   for ( i = 0; i &lt; n; i++ )</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         62 :     w_sum = w_sum + w[i];</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         64 :   for ( i = 0; i &lt; n; i++ )</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         62 :     w[i] = 2.0 * w[i] / w_sum;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 :   return;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : //****************************************************************************80</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 : void legendre_compute_glr0 ( int n, double *p, double *pp )</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : //****************************************************************************80</a>
+<a name="115"><span class="lineNum">     115 </span>            : //</a>
+<a name="116"><span class="lineNum">     116 </span>            : //  Purpose:</a>
+<a name="117"><span class="lineNum">     117 </span>            : //</a>
+<a name="118"><span class="lineNum">     118 </span>            : //    LEGENDRE_COMPUTE_GLR0 gets a starting value for the fast algorithm.</a>
+<a name="119"><span class="lineNum">     119 </span>            : //</a>
+<a name="120"><span class="lineNum">     120 </span>            : //  Licensing:</a>
+<a name="121"><span class="lineNum">     121 </span>            : //</a>
+<a name="122"><span class="lineNum">     122 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="123"><span class="lineNum">     123 </span>            : //</a>
+<a name="124"><span class="lineNum">     124 </span>            : //  Modified:</a>
+<a name="125"><span class="lineNum">     125 </span>            : //</a>
+<a name="126"><span class="lineNum">     126 </span>            : //    19 October 2009</a>
+<a name="127"><span class="lineNum">     127 </span>            : //</a>
+<a name="128"><span class="lineNum">     128 </span>            : //  Author:</a>
+<a name="129"><span class="lineNum">     129 </span>            : //</a>
+<a name="130"><span class="lineNum">     130 </span>            : //    Original C++ version by Nick Hale.</a>
+<a name="131"><span class="lineNum">     131 </span>            : //    This C++ version by John Burkardt.</a>
+<a name="132"><span class="lineNum">     132 </span>            : //</a>
+<a name="133"><span class="lineNum">     133 </span>            : //  Reference:</a>
+<a name="134"><span class="lineNum">     134 </span>            : //</a>
+<a name="135"><span class="lineNum">     135 </span>            : //    Andreas Glaser, Xiangtao Liu, Vladimir Rokhlin,</a>
+<a name="136"><span class="lineNum">     136 </span>            : //    A fast algorithm for the calculation of the roots of special functions,</a>
+<a name="137"><span class="lineNum">     137 </span>            : //    SIAM Journal on Scientific Computing,</a>
+<a name="138"><span class="lineNum">     138 </span>            : //    Volume 29, Number 4, pages 1420-1438, 2007.</a>
+<a name="139"><span class="lineNum">     139 </span>            : //</a>
+<a name="140"><span class="lineNum">     140 </span>            : //  Parameters:</a>
+<a name="141"><span class="lineNum">     141 </span>            : //</a>
+<a name="142"><span class="lineNum">     142 </span>            : //    Input, int N, the order of the Legendre polynomial.</a>
+<a name="143"><span class="lineNum">     143 </span>            : //</a>
+<a name="144"><span class="lineNum">     144 </span>            : //    Output, double *P, *PP, the value of the N-th Legendre polynomial</a>
+<a name="145"><span class="lineNum">     145 </span>            : //    and its derivative at 0.</a>
+<a name="146"><span class="lineNum">     146 </span>            : //</a>
+<a name="147"><span class="lineNum">     147 </span>            : {</a>
+<a name="148"><span class="lineNum">     148 </span>            :   double dk;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   int k;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   double pm1;</a>
+<a name="151"><span class="lineNum">     151 </span>            :   double pm2;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   double ppm1;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   double ppm2;</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   pm2 = 0.0;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   pm1 = 1.0;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   ppm2 = 0.0;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   ppm1 = 0.0;</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         64 :   for ( k = 0; k &lt; n; k++)</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   {</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         62 :     dk = ( double ) k;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         62 :     *p = - dk * pm2 / ( dk + 1.0 );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         62 :     *pp = ( ( 2.0 * dk + 1.0 ) * pm1 - dk * ppm2 ) / ( dk + 1.0 );</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     pm2 = pm1;</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         62 :     pm1 = *p;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :     ppm2 = ppm1;</a>
+<a name="168"><span class="lineNum">     168 </span>            :     ppm1 = *pp;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :   return;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : //****************************************************************************80</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 : void legendre_compute_glr1 ( int n, double *x, double *w )</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : //****************************************************************************80</a>
+<a name="177"><span class="lineNum">     177 </span>            : //</a>
+<a name="178"><span class="lineNum">     178 </span>            : //  Purpose:</a>
+<a name="179"><span class="lineNum">     179 </span>            : //</a>
+<a name="180"><span class="lineNum">     180 </span>            : //    LEGENDRE_COMPUTE_GLR1 gets the complete set of Legendre points and weights.</a>
+<a name="181"><span class="lineNum">     181 </span>            : //</a>
+<a name="182"><span class="lineNum">     182 </span>            : //  Discussion:</a>
+<a name="183"><span class="lineNum">     183 </span>            : //</a>
+<a name="184"><span class="lineNum">     184 </span>            : //    This routine requires that a starting estimate be provided for one</a>
+<a name="185"><span class="lineNum">     185 </span>            : //    root and its derivative.  This information will be stored in entry</a>
+<a name="186"><span class="lineNum">     186 </span>            : //    (N+1)/2 if N is odd, or N/2 if N is even, of X and W.</a>
+<a name="187"><span class="lineNum">     187 </span>            : //</a>
+<a name="188"><span class="lineNum">     188 </span>            : //  Licensing:</a>
+<a name="189"><span class="lineNum">     189 </span>            : //</a>
+<a name="190"><span class="lineNum">     190 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="191"><span class="lineNum">     191 </span>            : //</a>
+<a name="192"><span class="lineNum">     192 </span>            : //  Modified:</a>
+<a name="193"><span class="lineNum">     193 </span>            : //</a>
+<a name="194"><span class="lineNum">     194 </span>            : //    19 October 2009</a>
+<a name="195"><span class="lineNum">     195 </span>            : //</a>
+<a name="196"><span class="lineNum">     196 </span>            : //  Author:</a>
+<a name="197"><span class="lineNum">     197 </span>            : //</a>
+<a name="198"><span class="lineNum">     198 </span>            : //    Original C++ version by Nick Hale.</a>
+<a name="199"><span class="lineNum">     199 </span>            : //    This C++ version by John Burkardt.</a>
+<a name="200"><span class="lineNum">     200 </span>            : //</a>
+<a name="201"><span class="lineNum">     201 </span>            : //  Reference:</a>
+<a name="202"><span class="lineNum">     202 </span>            : //</a>
+<a name="203"><span class="lineNum">     203 </span>            : //    Andreas Glaser, Xiangtao Liu, Vladimir Rokhlin,</a>
+<a name="204"><span class="lineNum">     204 </span>            : //    A fast algorithm for the calculation of the roots of special functions,</a>
+<a name="205"><span class="lineNum">     205 </span>            : //    SIAM Journal on Scientific Computing,</a>
+<a name="206"><span class="lineNum">     206 </span>            : //    Volume 29, Number 4, pages 1420-1438, 2007.</a>
+<a name="207"><span class="lineNum">     207 </span>            : //</a>
+<a name="208"><span class="lineNum">     208 </span>            : //  Parameters:</a>
+<a name="209"><span class="lineNum">     209 </span>            : //</a>
+<a name="210"><span class="lineNum">     210 </span>            : //    Input, int N, the order of the Legendre polynomial.</a>
+<a name="211"><span class="lineNum">     211 </span>            : //</a>
+<a name="212"><span class="lineNum">     212 </span>            : //    Input/output, double X[N].  On input, a starting value</a>
+<a name="213"><span class="lineNum">     213 </span>            : //    has been set in one entry.  On output, the roots of the Legendre</a>
+<a name="214"><span class="lineNum">     214 </span>            : //    polynomial.</a>
+<a name="215"><span class="lineNum">     215 </span>            : //</a>
+<a name="216"><span class="lineNum">     216 </span>            : //    Input/output, double W[N].  On input, a starting value</a>
+<a name="217"><span class="lineNum">     217 </span>            : //    has been set in one entry.  On output, the derivatives of the Legendre</a>
+<a name="218"><span class="lineNum">     218 </span>            : //    polynomial at the zeros.</a>
+<a name="219"><span class="lineNum">     219 </span>            : //</a>
+<a name="220"><span class="lineNum">     220 </span>            : //  Local Parameters:</a>
+<a name="221"><span class="lineNum">     221 </span>            : //</a>
+<a name="222"><span class="lineNum">     222 </span>            : //    Local, int M, the number of terms in the Taylor expansion.</a>
+<a name="223"><span class="lineNum">     223 </span>            : //</a>
+<a name="224"><span class="lineNum">     224 </span>            : {</a>
+<a name="225"><span class="lineNum">     225 </span>            :   double dk;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   double dn;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   double h;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   int j;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   int k;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   int l;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   int m = 30;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   int n2;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   static double pi = 3.141592653589793;</a>
+<a name="234"><span class="lineNum">     234 </span>            :   int s;</a>
+<a name="235"><span class="lineNum">     235 </span>            :   double *u;</a>
+<a name="236"><span class="lineNum">     236 </span>            :   double *up;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   double xp;</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :   if ( n % 2 == 1 )</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   {</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 :     n2 = ( n - 1 ) / 2 - 1;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     s = 1;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span>            :   else</a>
+<a name="245"><span class="lineNum">     245 </span>            :   {</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :     n2 = n / 2 - 1;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :     s = 0;</a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :   u = new double[m+2];</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          2 :   up = new double[m+1];</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          2 :   dn = ( double ) n;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         32 :   for ( j = n2 + 1; j &lt; n - 1; j++ )</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   {</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         30 :     xp = x[j];</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         30 :     h = rk2_leg ( pi/2.0, -pi/2.0, xp, n ) - xp;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         30 :     u[0] = 0.0;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         30 :     u[1] = 0.0;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         30 :     u[2] = w[j];</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         30 :     up[0] = 0.0;</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         30 :     up[1] = u[2];</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        900 :     for ( k = 0; k &lt;= m - 2; k++ )</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :     {</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        870 :       dk = ( double ) k;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        870 :       u[k+3] =</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :         (</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        870 :           2.0 * xp * ( dk + 1.0 ) * u[k+2]</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        870 :           + ( dk * ( dk + 1.0 ) - dn * ( dn + 1.0 ) ) * u[k+1] / ( dk + 1.0 )</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        870 :         ) / ( 1.0 - xp ) / ( 1.0 + xp ) / ( dk + 2.0 );</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        870 :       up[k+2] = ( dk + 2.0 ) * u[k+3];</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :     }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        180 :     for ( l = 0; l &lt; 5; l++ )</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :     {</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        150 :       h = h - ts_mult ( u, h, m ) / ts_mult ( up, h, m-1 );</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :     }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         30 :     x[j+1] = xp + h;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         30 :     w[j+1] = ts_mult ( up, h, m - 1 );</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   }</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         34 :   for ( k = 0; k &lt;= n2 + s; k++ )</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :   {</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         32 :     x[k] = - x[n-1-k];</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         32 :     w[k] = w[n-1-k];</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   }</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          2 :   return;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : }</a>
+<a name="297"><span class="lineNum">     297 </span>            : //****************************************************************************80</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 : void legendre_compute_glr2 ( double pn0, int n, double *x1, double *d1 )</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : //****************************************************************************80</a>
+<a name="302"><span class="lineNum">     302 </span>            : //</a>
+<a name="303"><span class="lineNum">     303 </span>            : //  Purpose:</a>
+<a name="304"><span class="lineNum">     304 </span>            : //</a>
+<a name="305"><span class="lineNum">     305 </span>            : //    LEGENDRE_COMPUTE_GLR2 finds the first real root.</a>
+<a name="306"><span class="lineNum">     306 </span>            : //</a>
+<a name="307"><span class="lineNum">     307 </span>            : //  Discussion:</a>
+<a name="308"><span class="lineNum">     308 </span>            : //</a>
+<a name="309"><span class="lineNum">     309 </span>            : //    This function is only called if N is even.</a>
+<a name="310"><span class="lineNum">     310 </span>            : //</a>
+<a name="311"><span class="lineNum">     311 </span>            : //  Licensing:</a>
+<a name="312"><span class="lineNum">     312 </span>            : //</a>
+<a name="313"><span class="lineNum">     313 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="314"><span class="lineNum">     314 </span>            : //</a>
+<a name="315"><span class="lineNum">     315 </span>            : //  Modified:</a>
+<a name="316"><span class="lineNum">     316 </span>            : //</a>
+<a name="317"><span class="lineNum">     317 </span>            : //    19 October 2009</a>
+<a name="318"><span class="lineNum">     318 </span>            : //</a>
+<a name="319"><span class="lineNum">     319 </span>            : //  Author:</a>
+<a name="320"><span class="lineNum">     320 </span>            : //</a>
+<a name="321"><span class="lineNum">     321 </span>            : //    Original C++ version by Nick Hale.</a>
+<a name="322"><span class="lineNum">     322 </span>            : //    This C++ version by John Burkardt.</a>
+<a name="323"><span class="lineNum">     323 </span>            : //</a>
+<a name="324"><span class="lineNum">     324 </span>            : //  Reference:</a>
+<a name="325"><span class="lineNum">     325 </span>            : //</a>
+<a name="326"><span class="lineNum">     326 </span>            : //    Andreas Glaser, Xiangtao Liu, Vladimir Rokhlin,</a>
+<a name="327"><span class="lineNum">     327 </span>            : //    A fast algorithm for the calculation of the roots of special functions,</a>
+<a name="328"><span class="lineNum">     328 </span>            : //    SIAM Journal on Scientific Computing,</a>
+<a name="329"><span class="lineNum">     329 </span>            : //    Volume 29, Number 4, pages 1420-1438, 2007.</a>
+<a name="330"><span class="lineNum">     330 </span>            : //</a>
+<a name="331"><span class="lineNum">     331 </span>            : //  Parameters:</a>
+<a name="332"><span class="lineNum">     332 </span>            : //</a>
+<a name="333"><span class="lineNum">     333 </span>            : //    Input, double PN0, the value of the N-th Legendre polynomial</a>
+<a name="334"><span class="lineNum">     334 </span>            : //    at 0.</a>
+<a name="335"><span class="lineNum">     335 </span>            : //</a>
+<a name="336"><span class="lineNum">     336 </span>            : //    Input, int N, the order of the Legendre polynomial.</a>
+<a name="337"><span class="lineNum">     337 </span>            : //</a>
+<a name="338"><span class="lineNum">     338 </span>            : //    Output, double *X1, the first real root.</a>
+<a name="339"><span class="lineNum">     339 </span>            : //</a>
+<a name="340"><span class="lineNum">     340 </span>            : //    Output, double *D1, the derivative at X1.</a>
+<a name="341"><span class="lineNum">     341 </span>            : //</a>
+<a name="342"><span class="lineNum">     342 </span>            : //  Local Parameters:</a>
+<a name="343"><span class="lineNum">     343 </span>            : //</a>
+<a name="344"><span class="lineNum">     344 </span>            : //    Local, int M, the number of terms in the Taylor expansion.</a>
+<a name="345"><span class="lineNum">     345 </span>            : //</a>
+<a name="346"><span class="lineNum">     346 </span>            : {</a>
+<a name="347"><span class="lineNum">     347 </span>            :   double dk;</a>
+<a name="348"><span class="lineNum">     348 </span>            :   double dn;</a>
+<a name="349"><span class="lineNum">     349 </span>            :   int k;</a>
+<a name="350"><span class="lineNum">     350 </span>            :   int l;</a>
+<a name="351"><span class="lineNum">     351 </span>            :   int m = 30;</a>
+<a name="352"><span class="lineNum">     352 </span>            :   static double pi = 3.141592653589793;</a>
+<a name="353"><span class="lineNum">     353 </span>            :   double t;</a>
+<a name="354"><span class="lineNum">     354 </span>            :   double *u;</a>
+<a name="355"><span class="lineNum">     355 </span>            :   double *up;</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   t = 0.0;</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   *x1 = rk2_leg ( t, -pi/2.0, 0.0, n );</span></a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :   u = new double[m+2];</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :   up = new double[m+1];</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   dn = ( double ) n;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : //</a>
+<a name="365"><span class="lineNum">     365 </span>            : //  U[0] and UP[0] are never used.</a>
+<a name="366"><span class="lineNum">     366 </span>            : //  U[M+1] is set, but not used, and UP[M] is set and not used.</a>
+<a name="367"><span class="lineNum">     367 </span>            : //  What gives?</a>
+<a name="368"><span class="lineNum">     368 </span>            : //</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :   u[0] = 0.0;</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :   u[1] = pn0;</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :   up[0] = 0.0;</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :   for ( k = 0; k &lt;= m - 2; k = k + 2 )</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :   {</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :     dk = ( double ) k;</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :     u[k+2] = 0.0;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :     u[k+3] = ( dk * ( dk + 1.0 ) - dn * ( dn + 1.0 ) ) * u[k+1]</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :              / (dk + 1.0) / (dk + 2.0 );</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :     up[k+1] = 0.0;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :     up[k+2] = ( dk + 2.0 ) * u[k+3];</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :   for ( l = 0; l &lt; 5; l++ )</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :   {</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :     *x1 = *x1 - ts_mult ( u, *x1, m ) / ts_mult ( up, *x1, m-1 );</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :   *d1 = ts_mult ( up, *x1, m-1 );</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :   return;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : }</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            : //****************************************************************************80</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          2 : void rescale ( double a, double b, int n, double x[], double w[] )</span></a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : //****************************************************************************80</a>
+<a name="400"><span class="lineNum">     400 </span>            : //</a>
+<a name="401"><span class="lineNum">     401 </span>            : //  Purpose:</a>
+<a name="402"><span class="lineNum">     402 </span>            : //</a>
+<a name="403"><span class="lineNum">     403 </span>            : //    RESCALE rescales a Legendre quadrature rule from [-1,+1] to [A,B].</a>
+<a name="404"><span class="lineNum">     404 </span>            : //</a>
+<a name="405"><span class="lineNum">     405 </span>            : //  Licensing:</a>
+<a name="406"><span class="lineNum">     406 </span>            : //</a>
+<a name="407"><span class="lineNum">     407 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="408"><span class="lineNum">     408 </span>            : //</a>
+<a name="409"><span class="lineNum">     409 </span>            : //  Modified:</a>
+<a name="410"><span class="lineNum">     410 </span>            : //</a>
+<a name="411"><span class="lineNum">     411 </span>            : //    18 October 2009</a>
+<a name="412"><span class="lineNum">     412 </span>            : //</a>
+<a name="413"><span class="lineNum">     413 </span>            : //  Author:</a>
+<a name="414"><span class="lineNum">     414 </span>            : //</a>
+<a name="415"><span class="lineNum">     415 </span>            : //    Original MATLAB version by Nick Hale.</a>
+<a name="416"><span class="lineNum">     416 </span>            : //    C++ version by John Burkardt.</a>
+<a name="417"><span class="lineNum">     417 </span>            : //</a>
+<a name="418"><span class="lineNum">     418 </span>            : //  Reference:</a>
+<a name="419"><span class="lineNum">     419 </span>            : //</a>
+<a name="420"><span class="lineNum">     420 </span>            : //    Andreas Glaser, Xiangtao Liu, Vladimir Rokhlin,</a>
+<a name="421"><span class="lineNum">     421 </span>            : //    A fast algorithm for the calculation of the roots of special functions,</a>
+<a name="422"><span class="lineNum">     422 </span>            : //    SIAM Journal on Scientific Computing,</a>
+<a name="423"><span class="lineNum">     423 </span>            : //    Volume 29, Number 4, pages 1420-1438, 2007.</a>
+<a name="424"><span class="lineNum">     424 </span>            : //</a>
+<a name="425"><span class="lineNum">     425 </span>            : //  Parameters:</a>
+<a name="426"><span class="lineNum">     426 </span>            : //</a>
+<a name="427"><span class="lineNum">     427 </span>            : //    Input, double A, B, the endpoints of the new interval.</a>
+<a name="428"><span class="lineNum">     428 </span>            : //</a>
+<a name="429"><span class="lineNum">     429 </span>            : //    Input, int N, the order.</a>
+<a name="430"><span class="lineNum">     430 </span>            : //</a>
+<a name="431"><span class="lineNum">     431 </span>            : //    Input/output, double X[N], on input, the abscissas for [-1,+1].</a>
+<a name="432"><span class="lineNum">     432 </span>            : //    On output, the abscissas for [A,B].</a>
+<a name="433"><span class="lineNum">     433 </span>            : //</a>
+<a name="434"><span class="lineNum">     434 </span>            : //    Input/output, double W[N], on input, the weights for [-1,+1].</a>
+<a name="435"><span class="lineNum">     435 </span>            : //    On output, the weights for [A,B].</a>
+<a name="436"><span class="lineNum">     436 </span>            : //</a>
+<a name="437"><span class="lineNum">     437 </span>            : {</a>
+<a name="438"><span class="lineNum">     438 </span>            :   int i;</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         64 :   for ( i = 0; i &lt; n; i++ )</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   {</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         62 :     x[i] = ( ( a + b ) + ( b - a ) * x[i] ) / 2.0;</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :   }</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         64 :   for ( i = 0; i &lt; n; i++ )</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   {</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         62 :     w[i] = ( b - a ) * w[i] / 2.0;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   }</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          2 :   return;</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : }</a>
+<a name="450"><span class="lineNum">     450 </span>            : //****************************************************************************80</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         30 : double rk2_leg ( double t1, double t2, double x, int n )</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span>            : //****************************************************************************80</a>
+<a name="455"><span class="lineNum">     455 </span>            : //</a>
+<a name="456"><span class="lineNum">     456 </span>            : //  Purpose:</a>
+<a name="457"><span class="lineNum">     457 </span>            : //</a>
+<a name="458"><span class="lineNum">     458 </span>            : //    RK2_LEG advances the value of X(T) using a Runge-Kutta method.</a>
+<a name="459"><span class="lineNum">     459 </span>            : //</a>
+<a name="460"><span class="lineNum">     460 </span>            : //  Licensing:</a>
+<a name="461"><span class="lineNum">     461 </span>            : //</a>
+<a name="462"><span class="lineNum">     462 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="463"><span class="lineNum">     463 </span>            : //</a>
+<a name="464"><span class="lineNum">     464 </span>            : //  Modified:</a>
+<a name="465"><span class="lineNum">     465 </span>            : //</a>
+<a name="466"><span class="lineNum">     466 </span>            : //    22 October 2009</a>
+<a name="467"><span class="lineNum">     467 </span>            : //</a>
+<a name="468"><span class="lineNum">     468 </span>            : //  Author:</a>
+<a name="469"><span class="lineNum">     469 </span>            : //</a>
+<a name="470"><span class="lineNum">     470 </span>            : //    Original C++ version by Nick Hale.</a>
+<a name="471"><span class="lineNum">     471 </span>            : //    This C++ version by John Burkardt.</a>
+<a name="472"><span class="lineNum">     472 </span>            : //</a>
+<a name="473"><span class="lineNum">     473 </span>            : //  Parameters:</a>
+<a name="474"><span class="lineNum">     474 </span>            : //</a>
+<a name="475"><span class="lineNum">     475 </span>            : //    Input, double T1, T2, the range of the integration interval.</a>
+<a name="476"><span class="lineNum">     476 </span>            : //</a>
+<a name="477"><span class="lineNum">     477 </span>            : //    Input, double X, the value of X at T1.</a>
+<a name="478"><span class="lineNum">     478 </span>            : //</a>
+<a name="479"><span class="lineNum">     479 </span>            : //    Input, int N, the number of steps to take.</a>
+<a name="480"><span class="lineNum">     480 </span>            : //</a>
+<a name="481"><span class="lineNum">     481 </span>            : //    Output, double RK2_LEG, the value of X at T2.</a>
+<a name="482"><span class="lineNum">     482 </span>            : //</a>
+<a name="483"><span class="lineNum">     483 </span>            : {</a>
+<a name="484"><span class="lineNum">     484 </span>            :   double f;</a>
+<a name="485"><span class="lineNum">     485 </span>            :   double h;</a>
+<a name="486"><span class="lineNum">     486 </span>            :   int j;</a>
+<a name="487"><span class="lineNum">     487 </span>            :   double k1;</a>
+<a name="488"><span class="lineNum">     488 </span>            :   double k2;</a>
+<a name="489"><span class="lineNum">     489 </span>            :   int m = 10;</a>
+<a name="490"><span class="lineNum">     490 </span>            :   double snn1;</a>
+<a name="491"><span class="lineNum">     491 </span>            :   double t;</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         30 :   h = ( t2 - t1 ) / ( double ) m;</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         30 :   snn1 = sqrt ( ( double ) ( n * ( n + 1 ) ) );</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :   t = t1;</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">        330 :   for ( j = 0; j &lt; m; j++ )</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :   {</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        300 :     f = ( 1.0 - x ) * ( 1.0 + x );</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        300 :     k1 = - h * f / ( snn1 * sqrt ( f ) - 0.5 * x * sin ( 2.0 * t ) );</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        300 :     x = x + k1;</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">        300 :     t = t + h;</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        300 :     f = ( 1.0 - x ) * ( 1.0 + x );</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        300 :     k2 = - h * f / ( snn1 * sqrt ( f ) - 0.5 * x * sin ( 2.0 * t ) );</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        300 :     x = x + 0.5 * ( k2 - k1 );</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   }</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         30 :   return x;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : }</a>
+<a name="511"><span class="lineNum">     511 </span>            : //****************************************************************************80</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">        330 : double ts_mult ( double *u, double h, int n )</span></a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : //****************************************************************************80</a>
+<a name="516"><span class="lineNum">     516 </span>            : //</a>
+<a name="517"><span class="lineNum">     517 </span>            : //  Purpose:</a>
+<a name="518"><span class="lineNum">     518 </span>            : //</a>
+<a name="519"><span class="lineNum">     519 </span>            : //    TS_MULT evaluates a polynomial.</a>
+<a name="520"><span class="lineNum">     520 </span>            : //</a>
+<a name="521"><span class="lineNum">     521 </span>            : //  Licensing:</a>
+<a name="522"><span class="lineNum">     522 </span>            : //</a>
+<a name="523"><span class="lineNum">     523 </span>            : //    This code is distributed under the GNU LGPL license.</a>
+<a name="524"><span class="lineNum">     524 </span>            : //</a>
+<a name="525"><span class="lineNum">     525 </span>            : //  Modified:</a>
+<a name="526"><span class="lineNum">     526 </span>            : //</a>
+<a name="527"><span class="lineNum">     527 </span>            : //    17 May 2013</a>
+<a name="528"><span class="lineNum">     528 </span>            : //</a>
+<a name="529"><span class="lineNum">     529 </span>            : //  Author:</a>
+<a name="530"><span class="lineNum">     530 </span>            : //</a>
+<a name="531"><span class="lineNum">     531 </span>            : //    Original C++ version by Nick Hale.</a>
+<a name="532"><span class="lineNum">     532 </span>            : //    This C++ version by John Burkardt.</a>
+<a name="533"><span class="lineNum">     533 </span>            : //</a>
+<a name="534"><span class="lineNum">     534 </span>            : //  Parameters:</a>
+<a name="535"><span class="lineNum">     535 </span>            : //</a>
+<a name="536"><span class="lineNum">     536 </span>            : //    Input, double U[N+1], the polynomial coefficients.</a>
+<a name="537"><span class="lineNum">     537 </span>            : //    U[0] is ignored.</a>
+<a name="538"><span class="lineNum">     538 </span>            : //</a>
+<a name="539"><span class="lineNum">     539 </span>            : //    Input, double H, the polynomial argument.</a>
+<a name="540"><span class="lineNum">     540 </span>            : //</a>
+<a name="541"><span class="lineNum">     541 </span>            : //    Input, int N, the number of terms to compute.</a>
+<a name="542"><span class="lineNum">     542 </span>            : //</a>
+<a name="543"><span class="lineNum">     543 </span>            : //    Output, double TS_MULT, the value of the polynomial.</a>
+<a name="544"><span class="lineNum">     544 </span>            : //</a>
+<a name="545"><span class="lineNum">     545 </span>            : {</a>
+<a name="546"><span class="lineNum">     546 </span>            :   double hk;</a>
+<a name="547"><span class="lineNum">     547 </span>            :   int k;</a>
+<a name="548"><span class="lineNum">     548 </span>            :   double ts;</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            :   ts = 0.0;</a>
+<a name="551"><span class="lineNum">     551 </span>            :   hk = 1.0;</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">      10050 :   for ( k = 1; k&lt;= n; k++ )</span></a>
+<a name="553"><span class="lineNum">     553 </span>            :   {</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">       9720 :     ts = ts + u[k] * hk;</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">       9720 :     hk = hk * h;</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :   }</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        330 :   return ts;</span></a>
+<a name="558"><span class="lineNum">     558 </span>            : }</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span>            : //close the namespaces</a>
+<a name="561"><span class="lineNum">     561 </span>            : }</a>
+<a name="562"><span class="lineNum">     562 </span>            : }</a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            : //#endif</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Combine.cpp.func-sort-c.html b/coverage/function/Combine.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e963c476c2
--- /dev/null
+++ b/coverage/function/Combine.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Combine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Combine.cpp<span style="font-size: 80%;"> (<a href="Combine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">93.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Combine.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#99">_ZN4PLMD8function7CombineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#88">_ZN4PLMD8function12_GLOBAL__N_119CombineRegisterMe906createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#99">_ZN4PLMD8function7CombineC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#90">_ZN4PLMD8function7Combine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">139</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#88">_ZN4PLMD8function12_GLOBAL__N_119CombineRegisterMe90C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#88">_ZN4PLMD8function12_GLOBAL__N_119CombineRegisterMe90D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#141">_ZN4PLMD8function7Combine9calculateEv</a></td>
+              <td class="coverFnHi">7887</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Combine.cpp.func.html b/coverage/function/Combine.cpp.func.html
new file mode 100644
index 0000000000..8e6ca628b7
--- /dev/null
+++ b/coverage/function/Combine.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Combine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Combine.cpp<span style="font-size: 80%;"> (<a href="Combine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">93.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Combine.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#88">_ZN4PLMD8function12_GLOBAL__N_119CombineRegisterMe906createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#88">_ZN4PLMD8function12_GLOBAL__N_119CombineRegisterMe90C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#88">_ZN4PLMD8function12_GLOBAL__N_119CombineRegisterMe90D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#90">_ZN4PLMD8function7Combine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">139</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#141">_ZN4PLMD8function7Combine9calculateEv</a></td>
+              <td class="coverFnHi">7887</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#99">_ZN4PLMD8function7CombineC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Combine.cpp.gcov.html#99">_ZN4PLMD8function7CombineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Combine.cpp.gcov.html b/coverage/function/Combine.cpp.gcov.html
new file mode 100644
index 0000000000..c27754f18b
--- /dev/null
+++ b/coverage/function/Combine.cpp.gcov.html
@@ -0,0 +1,232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <title>LCOV - plumed test coverage - function/Combine.cpp</title>
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+</head>
+
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Combine.cpp<span style="font-size: 80%;"> (source / <a href="Combine.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">93.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Function.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace function {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC FUNCTION COMBINE</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate a polynomial combination of a set of other variables.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : The functional form of this function is</a>
+<a name="33"><span class="lineNum">      33 </span>            : \f[</a>
+<a name="34"><span class="lineNum">      34 </span>            : C=\sum_{i=1}^{N_{arg}} c_i (x_i-a_i)^{p_i}</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f]</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The coefficients c, the parameters a and the powers p are provided as vectors.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Notice that COMBINE is not able to predict which will be periodic domain</a>
+<a name="40"><span class="lineNum">      40 </span>            : of the computed value automatically. The user is thus forced to specify it</a>
+<a name="41"><span class="lineNum">      41 </span>            : explicitly. Use PERIODIC=NO if the resulting variable is not periodic,</a>
+<a name="42"><span class="lineNum">      42 </span>            : and PERIODIC=A,B where A and B are the two boundaries if the resulting variable</a>
+<a name="43"><span class="lineNum">      43 </span>            : is periodic.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \par Examples</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The following input tells plumed to print the distance between atoms 3 and 5</a>
+<a name="50"><span class="lineNum">      50 </span>            : its square (as computed from the x,y,z components) and the distance</a>
+<a name="51"><span class="lineNum">      51 </span>            : again as computed from the square root of the square.</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : DISTANCE LABEL=dist      ATOMS=3,5 COMPONENTS</a>
+<a name="54"><span class="lineNum">      54 </span>            : COMBINE  LABEL=distance2 ARG=dist.x,dist.y,dist.z POWERS=2,2,2 PERIODIC=NO</a>
+<a name="55"><span class="lineNum">      55 </span>            : COMBINE  LABEL=distance  ARG=distance2 POWERS=0.5 PERIODIC=NO</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=distance,distance2</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : (See also \ref PRINT and \ref DISTANCE).</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The following input tells plumed to add a restraint on the</a>
+<a name="61"><span class="lineNum">      61 </span>            : cube of a dihedral angle. Notice that since the angle has a</a>
+<a name="62"><span class="lineNum">      62 </span>            : periodic domain</a>
+<a name="63"><span class="lineNum">      63 </span>            : -pi,pi its cube has a domain -pi**3,pi**3.</a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : t: TORSION ATOMS=1,3,5,7</a>
+<a name="66"><span class="lineNum">      66 </span>            : c: COMBINE ARG=t POWERS=3 PERIODIC=-31.0062766802998,31.0062766802998</a>
+<a name="67"><span class="lineNum">      67 </span>            : RESTRAINT ARG=c KAPPA=10 AT=0</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : class Combine :</a>
+<a name="77"><span class="lineNum">      77 </span>            :   public Function</a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span>            :   bool normalize;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;double&gt; coefficients;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;double&gt; parameters;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;double&gt; powers;</a>
+<a name="83"><span class="lineNum">      83 </span>            : public:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   explicit Combine(const ActionOptions&amp;);</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void calculate() override;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      12775 : PLUMED_REGISTER_ACTION(Combine,&quot;COMBINE&quot;)</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        139 : void Combine::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        139 :   Function::registerKeywords(keys);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        278 :   keys.use(&quot;ARG&quot;); keys.use(&quot;PERIODIC&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        278 :   keys.add(&quot;compulsory&quot;,&quot;COEFFICIENTS&quot;,&quot;1.0&quot;,&quot;the coefficients of the arguments in your function&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        278 :   keys.add(&quot;compulsory&quot;,&quot;PARAMETERS&quot;,&quot;0.0&quot;,&quot;the parameters of the arguments in your function&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        278 :   keys.add(&quot;compulsory&quot;,&quot;POWERS&quot;,&quot;1.0&quot;,&quot;the powers to which you are raising each of the arguments in your function&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        278 :   keys.addFlag(&quot;NORMALIZE&quot;,false,&quot;normalize all the coefficients so that in total they are equal to one&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        139 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        137 : Combine::Combine(const ActionOptions&amp;ao):</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   Action(ao),</a>
+<a name="103"><span class="lineNum">     103 </span>            :   Function(ao),</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        137 :   normalize(false),</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        277 :   coefficients(getNumberOfArguments(),1.0),</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        140 :   parameters(getNumberOfArguments(),0.0),</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        277 :   powers(getNumberOfArguments(),1.0)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        273 :   parseVector(&quot;COEFFICIENTS&quot;,coefficients);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        136 :   if(coefficients.size()!=static_cast&lt;unsigned&gt;(getNumberOfArguments()))</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     error(&quot;Size of COEFFICIENTS array should be the same as number for arguments&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        271 :   parseVector(&quot;PARAMETERS&quot;,parameters);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        135 :   if(parameters.size()!=static_cast&lt;unsigned&gt;(getNumberOfArguments()))</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     error(&quot;Size of PARAMETERS array should be the same as number for arguments&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        269 :   parseVector(&quot;POWERS&quot;,powers);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        134 :   if(powers.size()!=static_cast&lt;unsigned&gt;(getNumberOfArguments()))</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     error(&quot;Size of POWERS array should be the same as number for arguments&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        137 :   parseFlag(&quot;NORMALIZE&quot;,normalize);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        134 :   if(normalize) {</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :     double n=0.0;</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         16 :     for(unsigned i=0; i&lt;coefficients.size(); i++) n+=coefficients[i];</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         16 :     for(unsigned i=0; i&lt;coefficients.size(); i++) coefficients[i]*=(1.0/n);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        134 :   addValueWithDerivatives();</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        134 :   checkRead();</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        134 :   log.printf(&quot;  with coefficients:&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        404 :   for(unsigned i=0; i&lt;coefficients.size(); i++) log.printf(&quot; %f&quot;,coefficients[i]);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        134 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        134 :   log.printf(&quot;  with parameters:&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        404 :   for(unsigned i=0; i&lt;parameters.size(); i++) log.printf(&quot; %f&quot;,parameters[i]);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        134 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        134 :   log.printf(&quot;  and powers:&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        404 :   for(unsigned i=0; i&lt;powers.size(); i++) log.printf(&quot; %f&quot;,powers[i]);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        134 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        140 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       7887 : void Combine::calculate() {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       7887 :   double combine=0.0;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      20242 :   for(unsigned i=0; i&lt;coefficients.size(); ++i) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      12355 :     double cv = (getArgument(i)-parameters[i]);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      12355 :     combine+=coefficients[i]*std::pow(cv,powers[i]);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      12355 :     setDerivative(i,coefficients[i]*powers[i]*std::pow(cv,powers[i]-1.0));</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   };</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       7887 :   setValue(combine);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       7887 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Custom.cpp.func-sort-c.html b/coverage/function/Custom.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9a2e13a64c
--- /dev/null
+++ b/coverage/function/Custom.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Custom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Custom.cpp<span style="font-size: 80%;"> (<a href="Custom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Custom.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#218">_ZN4PLMD8function6CustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#177">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe1796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#209">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe2116createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">387</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#218">_ZN4PLMD8function6CustomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">434</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#211">_ZN4PLMD8function6Custom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#177">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe179C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#177">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe179D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#209">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe211C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#209">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe211D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#282">_ZN4PLMD8function6Custom9calculateEv</a></td>
+              <td class="coverFnHi">39154</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Custom.cpp.func.html b/coverage/function/Custom.cpp.func.html
new file mode 100644
index 0000000000..0d96df48c6
--- /dev/null
+++ b/coverage/function/Custom.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Custom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Custom.cpp<span style="font-size: 80%;"> (<a href="Custom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Custom.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#177">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe1796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#177">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe179C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#177">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe179D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#209">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe2116createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">387</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#209">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe211C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#209">_ZN4PLMD8function12_GLOBAL__N_119CustomRegisterMe211D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#211">_ZN4PLMD8function6Custom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">438</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#282">_ZN4PLMD8function6Custom9calculateEv</a></td>
+              <td class="coverFnHi">39154</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#218">_ZN4PLMD8function6CustomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">434</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Custom.cpp.gcov.html#218">_ZN4PLMD8function6CustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Custom.cpp.gcov.html b/coverage/function/Custom.cpp.gcov.html
new file mode 100644
index 0000000000..b2e310ca83
--- /dev/null
+++ b/coverage/function/Custom.cpp.gcov.html
@@ -0,0 +1,376 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Custom.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Custom.cpp<span style="font-size: 80%;"> (source / <a href="Custom.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Function.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;lepton/Lepton.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace function {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC FUNCTION CUSTOM</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate a combination of variables using a custom expression.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This action computes an  arbitrary function of one or more</a>
+<a name="34"><span class="lineNum">      34 </span>            : collective variables. Arguments are chosen with the ARG keyword,</a>
+<a name="35"><span class="lineNum">      35 </span>            : and the function is provided with the FUNC string. Notice that this</a>
+<a name="36"><span class="lineNum">      36 </span>            : string should contain no space. Within FUNC, one can refer to the</a>
+<a name="37"><span class="lineNum">      37 </span>            : arguments as x,y,z, and t (up to four variables provided as ARG).</a>
+<a name="38"><span class="lineNum">      38 </span>            : This names can be customized using the VAR keyword (see examples below).</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : This function is implemented using the Lepton library, that allows to evaluate</a>
+<a name="41"><span class="lineNum">      41 </span>            : algebraic expressions and to automatically differentiate them.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : If you want a function that depends not only on collective variables</a>
+<a name="44"><span class="lineNum">      44 </span>            : but also on time you can use the \subpage TIME action.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The following input tells plumed to perform a metadynamics</a>
+<a name="49"><span class="lineNum">      49 </span>            : using as a CV the difference between two distances.</a>
+<a name="50"><span class="lineNum">      50 </span>            : \plumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : dAB: DISTANCE ATOMS=10,12</a>
+<a name="52"><span class="lineNum">      52 </span>            : dAC: DISTANCE ATOMS=10,15</a>
+<a name="53"><span class="lineNum">      53 </span>            : diff: CUSTOM ARG=dAB,dAC FUNC=y-x PERIODIC=NO</a>
+<a name="54"><span class="lineNum">      54 </span>            : # notice: the previous line could be replaced with the following</a>
+<a name="55"><span class="lineNum">      55 </span>            : # diff: COMBINE ARG=dAB,dAC COEFFICIENTS=-1,1</a>
+<a name="56"><span class="lineNum">      56 </span>            : METAD ARG=diff SIGMA=0.1 HEIGHT=0.5 BIASFACTOR=10 PACE=100</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : (see also \ref DISTANCE, \ref COMBINE, and \ref METAD).</a>
+<a name="59"><span class="lineNum">      59 </span>            : Notice that forces applied to diff will be correctly propagated</a>
+<a name="60"><span class="lineNum">      60 </span>            : to atoms 10, 12, and 15.</a>
+<a name="61"><span class="lineNum">      61 </span>            : Also notice that since CUSTOM is used without the VAR option</a>
+<a name="62"><span class="lineNum">      62 </span>            : the two arguments should be referred to as x and y in the expression FUNC.</a>
+<a name="63"><span class="lineNum">      63 </span>            : For simple functions</a>
+<a name="64"><span class="lineNum">      64 </span>            : such as this one it is possible to use \ref COMBINE.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : The following input tells plumed to print the angle between vectors</a>
+<a name="67"><span class="lineNum">      67 </span>            : identified by atoms 1,2 and atoms 2,3</a>
+<a name="68"><span class="lineNum">      68 </span>            : its square (as computed from the x,y,z components) and the distance</a>
+<a name="69"><span class="lineNum">      69 </span>            : again as computed from the square root of the square.</a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : DISTANCE LABEL=d1 ATOMS=1,2 COMPONENTS</a>
+<a name="72"><span class="lineNum">      72 </span>            : DISTANCE LABEL=d2 ATOMS=2,3 COMPONENTS</a>
+<a name="73"><span class="lineNum">      73 </span>            : CUSTOM ...</a>
+<a name="74"><span class="lineNum">      74 </span>            :   LABEL=theta</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ARG=d1.x,d1.y,d1.z,d2.x,d2.y,d2.z</a>
+<a name="76"><span class="lineNum">      76 </span>            :   VAR=ax,ay,az,bx,by,bz</a>
+<a name="77"><span class="lineNum">      77 </span>            :   FUNC=acos((ax*bx+ay*by+az*bz)/sqrt((ax*ax+ay*ay+az*az)*(bx*bx+by*by+bz*bz)))</a>
+<a name="78"><span class="lineNum">      78 </span>            :   PERIODIC=NO</a>
+<a name="79"><span class="lineNum">      79 </span>            : ... CUSTOM</a>
+<a name="80"><span class="lineNum">      80 </span>            : PRINT ARG=theta</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endplumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : (See also \ref PRINT and \ref DISTANCE).</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : Notice that this action implements a large number of functions (trigonometric, exp, log, etc).</a>
+<a name="85"><span class="lineNum">      85 </span>            : Among the useful functions, have a look at the step function (that is the Heaviside function).</a>
+<a name="86"><span class="lineNum">      86 </span>            : `step(x)` is defined as 1 when `x` is positive and `0` when x is negative. This allows for</a>
+<a name="87"><span class="lineNum">      87 </span>            : a straightforward implementation of if clauses.</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : For example, imagine that you want to implement a restraint that only acts when a</a>
+<a name="90"><span class="lineNum">      90 </span>            : distance is larger than 0.5. You can do it with</a>
+<a name="91"><span class="lineNum">      91 </span>            : \plumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : d: DISTANCE ATOMS=10,15</a>
+<a name="93"><span class="lineNum">      93 </span>            : m: CUSTOM ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO</a>
+<a name="94"><span class="lineNum">      94 </span>            : # check the function you are applying:</a>
+<a name="95"><span class="lineNum">      95 </span>            : PRINT ARG=d,m FILE=checkme</a>
+<a name="96"><span class="lineNum">      96 </span>            : RESTRAINT ARG=d AT=0.5 KAPPA=10.0</a>
+<a name="97"><span class="lineNum">      97 </span>            : \endplumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : (see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : The meaning of the function `0.5*step(0.5-x)+x*step(x-0.5)` is:</a>
+<a name="101"><span class="lineNum">     101 </span>            : - If x&lt;0.5 (step(0.5-x)!=0) use 0.5</a>
+<a name="102"><span class="lineNum">     102 </span>            : - If x&gt;0.5 (step(x-0.5)!=0) use x</a>
+<a name="103"><span class="lineNum">     103 </span>            : Notice that the same could have been obtained using an \ref UPPER_WALLS</a>
+<a name="104"><span class="lineNum">     104 </span>            : However, with CUSTOM you can create way more complex definitions.</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : \warning If you apply forces on the variable (as in the previous example) you should</a>
+<a name="107"><span class="lineNum">     107 </span>            : make sure that the variable is continuous!</a>
+<a name="108"><span class="lineNum">     108 </span>            : Conversely, if you are just analyzing a trajectory you can safely use</a>
+<a name="109"><span class="lineNum">     109 </span>            : discontinuous variables.</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : A possible continuity check with gnuplot is</a>
+<a name="112"><span class="lineNum">     112 </span>            : \verbatim</a>
+<a name="113"><span class="lineNum">     113 </span>            : # this allow to step function to be used in gnuplot:</a>
+<a name="114"><span class="lineNum">     114 </span>            : gnuplot&gt; step(x)=0.5*(erf(x*10000000)+1)</a>
+<a name="115"><span class="lineNum">     115 </span>            : # here you can test your function</a>
+<a name="116"><span class="lineNum">     116 </span>            : gnuplot&gt; p 0.5*step(0.5-x)+x*step(x-0.5)</a>
+<a name="117"><span class="lineNum">     117 </span>            : \endverbatim</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : Also notice that you can easily make logical operations on the conditions that you</a>
+<a name="120"><span class="lineNum">     120 </span>            : create. The equivalent of the AND operator is the product: `step(1.0-x)*step(x-0.5)` is</a>
+<a name="121"><span class="lineNum">     121 </span>            : only equal to 1 when x is between 0.5 and 1.0. By combining negation and AND you can obtain an OR. That is,</a>
+<a name="122"><span class="lineNum">     122 </span>            : `1-step(1.0-x)*step(x-0.5)` is only equal to 1 when x is outside the 0.5-1.0 interval.</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : CUSTOM can be used in combination with \ref DISTANCE to implement variants of the</a>
+<a name="125"><span class="lineNum">     125 </span>            : DISTANCE keyword that were present in PLUMED 1.3 and that allowed to compute</a>
+<a name="126"><span class="lineNum">     126 </span>            : the distance of a point from a line defined by two other points, or the progression</a>
+<a name="127"><span class="lineNum">     127 </span>            : along that line.</a>
+<a name="128"><span class="lineNum">     128 </span>            : \plumedfile</a>
+<a name="129"><span class="lineNum">     129 </span>            : # take center of atoms 1 to 10 as reference point 1</a>
+<a name="130"><span class="lineNum">     130 </span>            : p1: CENTER ATOMS=1-10</a>
+<a name="131"><span class="lineNum">     131 </span>            : # take center of atoms 11 to 20 as reference point 2</a>
+<a name="132"><span class="lineNum">     132 </span>            : p2: CENTER ATOMS=11-20</a>
+<a name="133"><span class="lineNum">     133 </span>            : # take center of atoms 21 to 30 as reference point 3</a>
+<a name="134"><span class="lineNum">     134 </span>            : p3: CENTER ATOMS=21-30</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : # compute distances</a>
+<a name="137"><span class="lineNum">     137 </span>            : d12: DISTANCE ATOMS=p1,p2</a>
+<a name="138"><span class="lineNum">     138 </span>            : d13: DISTANCE ATOMS=p1,p3</a>
+<a name="139"><span class="lineNum">     139 </span>            : d23: DISTANCE ATOMS=p2,p3</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : # compute progress variable of the projection of point p3</a>
+<a name="142"><span class="lineNum">     142 </span>            : # along the vector joining p1 and p2</a>
+<a name="143"><span class="lineNum">     143 </span>            : # notice that progress is measured from the middle point</a>
+<a name="144"><span class="lineNum">     144 </span>            : onaxis: CUSTOM ARG=d13,d23,d12 FUNC=(0.5*(y^2-x^2)/z) PERIODIC=NO</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : # compute between point p3 and the vector joining p1 and p2</a>
+<a name="147"><span class="lineNum">     147 </span>            : fromaxis: CUSTOM ARG=d13,d23,d12,onaxis VAR=x,y,z,o FUNC=(0.5*(y^2+x^2)-o^2-0.25*z^2) PERIODIC=NO</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : PRINT ARG=onaxis,fromaxis</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : \endplumedfile</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : Notice that these equations have been used to combine \ref RMSD</a>
+<a name="154"><span class="lineNum">     154 </span>            : from different snapshots of a protein so as to define</a>
+<a name="155"><span class="lineNum">     155 </span>            : progression (S) and distance (Z) variables \cite perez2015atp.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : */</a>
+<a name="159"><span class="lineNum">     159 </span>            : //+ENDPLUMEDOC</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : class Custom :</a>
+<a name="163"><span class="lineNum">     163 </span>            :   public Function</a>
+<a name="164"><span class="lineNum">     164 </span>            : {</a>
+<a name="165"><span class="lineNum">     165 </span>            :   lepton::CompiledExpression expression;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::vector&lt;lepton::CompiledExpression&gt; expression_deriv;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::vector&lt;std::string&gt; var;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   std::string func;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   std::vector&lt;double&gt; values;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   std::vector&lt;char*&gt; names;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::vector&lt;double*&gt; lepton_ref;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   std::vector&lt;double*&gt; lepton_ref_deriv;</a>
+<a name="173"><span class="lineNum">     173 </span>            : public:</a>
+<a name="174"><span class="lineNum">     174 </span>            :   explicit Custom(const ActionOptions&amp;);</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void calculate() override;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="177"><span class="lineNum">     177 </span>            : };</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      12598 : PLUMED_REGISTER_ACTION(Custom,&quot;CUSTOM&quot;)</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : //+PLUMEDOC FUNCTION MATHEVAL</a>
+<a name="182"><span class="lineNum">     182 </span>            : /*</a>
+<a name="183"><span class="lineNum">     183 </span>            : An alias to the CUSTOM function that can also be used to calaculate combinations of variables using a custom expression.</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : Documentation for this action is identical to that for \ref CUSTOM</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : This alias is kept in order to maintain compatibility with previous PLUMED versions.</a>
+<a name="188"><span class="lineNum">     188 </span>            : However, notice that as of PLUMED 2.5 the libmatheval library is not linked anymore,</a>
+<a name="189"><span class="lineNum">     189 </span>            : and the \ref MATHEVAL function is implemented using the Lepton library.</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : \par Examples</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : Just replace \ref CUSTOM with \ref MATHEVAL.</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : \plumedfile</a>
+<a name="196"><span class="lineNum">     196 </span>            : d: DISTANCE ATOMS=10,15</a>
+<a name="197"><span class="lineNum">     197 </span>            : m: MATHEVAL ARG=d FUNC=0.5*step(0.5-x)+x*step(x-0.5) PERIODIC=NO</a>
+<a name="198"><span class="lineNum">     198 </span>            : # check the function you are applying:</a>
+<a name="199"><span class="lineNum">     199 </span>            : PRINT ARG=d,m FILE=checkme</a>
+<a name="200"><span class="lineNum">     200 </span>            : RESTRAINT ARG=d AT=0.5 KAPPA=10.0</a>
+<a name="201"><span class="lineNum">     201 </span>            : \endplumedfile</a>
+<a name="202"><span class="lineNum">     202 </span>            : (see also \ref DISTANCE, \ref PRINT, and \ref RESTRAINT)</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : */</a>
+<a name="205"><span class="lineNum">     205 </span>            : //+ENDPLUMEDOC</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : class Matheval :</a>
+<a name="208"><span class="lineNum">     208 </span>            :   public Custom {</a>
+<a name="209"><span class="lineNum">     209 </span>            : };</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">      13278 : PLUMED_REGISTER_ACTION(Custom,&quot;MATHEVAL&quot;)</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        438 : void Custom::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        438 :   Function::registerKeywords(keys);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        876 :   keys.use(&quot;ARG&quot;); keys.use(&quot;PERIODIC&quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        876 :   keys.add(&quot;compulsory&quot;,&quot;FUNC&quot;,&quot;the function you wish to evaluate&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        876 :   keys.add(&quot;optional&quot;,&quot;VAR&quot;,&quot;the names to give each of the arguments in the function.  If you have up to three arguments in your function you can use x, y and z to refer to them.  Otherwise you must use this flag to give your variables names.&quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        438 : }</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        434 : Custom::Custom(const ActionOptions&amp;ao):</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   Action(ao),</a>
+<a name="222"><span class="lineNum">     222 </span>            :   Function(ao),</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        434 :   expression_deriv(getNumberOfArguments()),</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        434 :   values(getNumberOfArguments()),</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        434 :   names(getNumberOfArguments()),</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        434 :   lepton_ref(getNumberOfArguments(),nullptr),</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       1302 :   lepton_ref_deriv(getNumberOfArguments()*getNumberOfArguments(),nullptr)</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : {</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        868 :   parseVector(&quot;VAR&quot;,var);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        434 :   if(var.size()==0) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        421 :     var.resize(getNumberOfArguments());</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        421 :     if(getNumberOfArguments()&gt;3)</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :       error(&quot;Using more than 3 arguments you should explicitly write their names with VAR&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        421 :     if(var.size()&gt;0) var[0]=&quot;x&quot;;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        421 :     if(var.size()&gt;1) var[1]=&quot;y&quot;;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        421 :     if(var.size()&gt;2) var[2]=&quot;z&quot;;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        434 :   if(var.size()!=getNumberOfArguments())</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :     error(&quot;Size of VAR array should be the same as number of arguments&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        434 :   parse(&quot;FUNC&quot;,func);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        434 :   addValueWithDerivatives();</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        434 :   checkRead();</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        434 :   log.printf(&quot;  with function : %s\n&quot;,func.c_str());</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        434 :   log.printf(&quot;  with variables :&quot;);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        968 :   for(unsigned i=0; i&lt;var.size(); i++) log.printf(&quot; %s&quot;,var[i].c_str());</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        434 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        434 :   lepton::ParsedExpression pe=lepton::Parser::parse(func).optimize(lepton::Constants());</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        434 :   log&lt;&lt;&quot;  function as parsed by lepton: &quot;&lt;&lt;pe&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        434 :   expression=pe.createCompiledExpression();</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        942 :   for(auto &amp;p: expression.getVariables()) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        508 :     if(std::find(var.begin(),var.end(),p)==var.end()) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       error(&quot;variable &quot; + p + &quot; is not defined&quot;);</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        434 :   log&lt;&lt;&quot;  derivatives as computed by lepton:\n&quot;;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        968 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       1068 :     lepton::ParsedExpression pe=lepton::Parser::parse(func).differentiate(var[i]).optimize(lepton::Constants());</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        534 :     log&lt;&lt;&quot;    &quot;&lt;&lt;pe&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        534 :     expression_deriv[i]=pe.createCompiledExpression();</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        968 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     try {</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        534 :       lepton_ref[i]=&amp;expression.getVariableReference(var[i]);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         26 :     } catch(const PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : // this is necessary since in some cases lepton things a variable is not present even though it is present</a>
+<a name="269"><span class="lineNum">     269 </span>            : // e.g. func=0*x</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         26 :     }</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        968 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       1526 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++) {</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :       try {</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        992 :         lepton_ref_deriv[i*getNumberOfArguments()+j]=&amp;expression_deriv[i].getVariableReference(var[j]);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        513 :       } catch(const PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : // this is necessary since in some cases lepton things a variable is not present even though it is present</a>
+<a name="278"><span class="lineNum">     278 </span>            : // e.g. func=0*x</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        513 :       }</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :     }</a>
+<a name="281"><span class="lineNum">     281 </span>            :   }</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        434 : }</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">      39154 : void Custom::calculate() {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">      78949 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">      39795 :     if(lepton_ref[i]) *lepton_ref[i]=getArgument(i);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :   }</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      39154 :   setValue(expression.evaluate());</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">      78949 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">      82348 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">      42553 :       if(lepton_ref_deriv[i*getNumberOfArguments()+j]) *lepton_ref_deriv[i*getNumberOfArguments()+j]=getArgument(j);</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :     }</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">      39795 :     setDerivative(i,expression_deriv[i].evaluate());</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   }</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">      39154 : }</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : }</a>
+<a name="298"><span class="lineNum">     298 </span>            : }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Ensemble.cpp.func-sort-c.html b/coverage/function/Ensemble.cpp.func-sort-c.html
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+++ b/coverage/function/Ensemble.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Ensemble.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Ensemble.cpp<span style="font-size: 80%;"> (<a href="Ensemble.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntryLo">63.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Ensemble.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#82">_ZN4PLMD8function8EnsembleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#69">_ZN4PLMD8function12_GLOBAL__N_120EnsembleRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#82">_ZN4PLMD8function8EnsembleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#71">_ZN4PLMD8function8Ensemble16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#151">_ZN4PLMD8function8Ensemble9calculateEv</a></td>
+              <td class="coverFnHi">125</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#69">_ZN4PLMD8function12_GLOBAL__N_120EnsembleRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#69">_ZN4PLMD8function12_GLOBAL__N_120EnsembleRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Ensemble.cpp.func.html b/coverage/function/Ensemble.cpp.func.html
new file mode 100644
index 0000000000..b022059b64
--- /dev/null
+++ b/coverage/function/Ensemble.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Ensemble.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Ensemble.cpp<span style="font-size: 80%;"> (<a href="Ensemble.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntryLo">63.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Ensemble.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#69">_ZN4PLMD8function12_GLOBAL__N_120EnsembleRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#69">_ZN4PLMD8function12_GLOBAL__N_120EnsembleRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#69">_ZN4PLMD8function12_GLOBAL__N_120EnsembleRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#71">_ZN4PLMD8function8Ensemble16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#151">_ZN4PLMD8function8Ensemble9calculateEv</a></td>
+              <td class="coverFnHi">125</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#82">_ZN4PLMD8function8EnsembleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ensemble.cpp.gcov.html#82">_ZN4PLMD8function8EnsembleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Ensemble.cpp.gcov.html b/coverage/function/Ensemble.cpp.gcov.html
new file mode 100644
index 0000000000..570c00e7ca
--- /dev/null
+++ b/coverage/function/Ensemble.cpp.gcov.html
@@ -0,0 +1,342 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Ensemble.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Ensemble.cpp<span style="font-size: 80%;"> (source / <a href="Ensemble.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntryLo">63.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Function.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace function {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC FUNCTION ENSEMBLE</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculates the replica averaging of a collective variable over multiple replicas.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : Each collective variable is averaged separately and stored in a component labelled &lt;em&gt;label&lt;/em&gt;.cvlabel.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input tells plumed to calculate the distance between atoms 3 and 5</a>
+<a name="39"><span class="lineNum">      39 </span>            : and the average it over the available replicas.</a>
+<a name="40"><span class="lineNum">      40 </span>            : \plumedfile</a>
+<a name="41"><span class="lineNum">      41 </span>            : dist: DISTANCE ATOMS=3,5</a>
+<a name="42"><span class="lineNum">      42 </span>            : ens: ENSEMBLE ARG=dist</a>
+<a name="43"><span class="lineNum">      43 </span>            : PRINT ARG=dist,ens.dist</a>
+<a name="44"><span class="lineNum">      44 </span>            : \endplumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : */</a>
+<a name="47"><span class="lineNum">      47 </span>            : //+ENDPLUMEDOC</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : class Ensemble :</a>
+<a name="51"><span class="lineNum">      51 </span>            :   public Function</a>
+<a name="52"><span class="lineNum">      52 </span>            : {</a>
+<a name="53"><span class="lineNum">      53 </span>            :   unsigned ens_dim;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   unsigned my_repl;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   unsigned narg;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool     master;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   bool     do_reweight;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool     do_moments;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   bool     do_central;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   bool     do_powers;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   double   kbt;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double   moment;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double   power;</a>
+<a name="64"><span class="lineNum">      64 </span>            : public:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   explicit Ensemble(const ActionOptions&amp;);</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void     calculate() override;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="68"><span class="lineNum">      68 </span>            : };</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      12558 : PLUMED_REGISTER_ACTION(Ensemble,&quot;ENSEMBLE&quot;)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         29 : void Ensemble::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         29 :   Function::registerKeywords(keys);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         29 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         58 :   keys.addFlag(&quot;REWEIGHT&quot;,false,&quot;simple REWEIGHT using the latest ARG as energy&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         58 :   keys.addFlag(&quot;CENTRAL&quot;,false,&quot;calculate a central moment instead of a standard moment&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - this is only needed if you are reweighting&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;,&quot;MOMENT&quot;,&quot;the moment you want to calculate in alternative to the mean or the variance&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         58 :   keys.add(&quot;optional&quot;,&quot;POWER&quot;,&quot;the power of the mean (and moment)&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         29 :   ActionWithValue::useCustomisableComponents(keys);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         29 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         27 : Ensemble::Ensemble(const ActionOptions&amp;ao):</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Action(ao),</a>
+<a name="86"><span class="lineNum">      86 </span>            :   Function(ao),</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         27 :   do_reweight(false),</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         27 :   do_moments(false),</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         27 :   do_central(false),</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         27 :   do_powers(false),</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         27 :   kbt(-1.0),</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         27 :   moment(0),</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         27 :   power(0)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : {</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         27 :   parseFlag(&quot;REWEIGHT&quot;, do_reweight);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         27 :   double temp=0.0;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         27 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         27 :   if(do_reweight) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         12 :     if(temp&gt;0.0) kbt=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     else kbt=plumed.getAtoms().getKbT();</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         12 :     if(kbt==0.0) error(&quot;Unless the MD engine passes the temperature to plumed, with REWEIGHT you must specify TEMP&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         27 :   parse(&quot;MOMENT&quot;,moment);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         27 :   if(moment==1) error(&quot;MOMENT can be any number but for 0 and 1&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         27 :   if(moment!=0) do_moments=true;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         27 :   parseFlag(&quot;CENTRAL&quot;, do_central);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         27 :   if(!do_moments&amp;&amp;do_central) error(&quot;To calculate a CENTRAL moment you need to define for which MOMENT&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         27 :   parse(&quot;POWER&quot;,power);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         27 :   if(power==1) error(&quot;POWER can be any number but for 0 and 1&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         27 :   if(power!=0) do_powers=true;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         27 :   checkRead();</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         27 :   master = (comm.Get_rank()==0);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         27 :   ens_dim=0;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         27 :   my_repl=0;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         27 :   if(master) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         17 :     ens_dim=multi_sim_comm.Get_size();</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         17 :     my_repl=multi_sim_comm.Get_rank();</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         27 :   comm.Bcast(ens_dim,0);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         27 :   comm.Bcast(my_repl,0);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         27 :   if(ens_dim&lt;2) log.printf(&quot;WARNING: ENSEMBLE with one replica is not doing any averaging!\n&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // prepare output components, the number depending on reweighing or not</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         27 :   narg = getNumberOfArguments();</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         27 :   if(do_reweight) narg--;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   // these are the averages</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       3044 :   for(unsigned i=0; i&lt;narg; i++) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       3017 :     std::string s=getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       3017 :     addComponentWithDerivatives(s);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       3017 :     getPntrToComponent(i)-&gt;setNotPeriodic();</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span>            :   // these are the moments</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         27 :   if(do_moments) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;narg; i++) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       std::string s=getPntrToArgument(i)-&gt;getName()+&quot;_m&quot;;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :       addComponentWithDerivatives(s);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :       getPntrToComponent(i+narg)-&gt;setNotPeriodic();</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         27 :   log.printf(&quot;  averaging over %u replicas.\n&quot;, ens_dim);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         27 :   if(do_reweight) log.printf(&quot;  doing simple REWEIGHT using the latest ARGUMENT as energy.\n&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         27 :   if(do_moments&amp;&amp;!do_central)  log.printf(&quot;  calculating also the %lf standard moment\n&quot;, moment);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         27 :   if(do_moments&amp;&amp;do_central)   log.printf(&quot;  calculating also the %lf central moment\n&quot;, moment);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         27 :   if(do_powers)                log.printf(&quot;  calculating the %lf power of the mean (and moment)\n&quot;, power);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         27 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        125 : void Ensemble::calculate() {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   double norm = 0.0;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        125 :   double fact = 0.0;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   // calculate the weights either from BIAS</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        125 :   if(do_reweight) {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     std::vector&lt;double&gt; bias;</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     bias.resize(ens_dim);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     if(master) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :       bias[my_repl] = getArgument(narg);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :       if(ens_dim&gt;1) multi_sim_comm.Sum(&amp;bias[0], ens_dim);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;bias[0], ens_dim);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     const double maxbias = *(std::max_element(bias.begin(), bias.end()));</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ens_dim; ++i) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :       bias[i] = exp((bias[i]-maxbias)/kbt);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       norm += bias[i];</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :     fact = bias[my_repl]/norm;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     // or arithmetic ones</a>
+<a name="173"><span class="lineNum">     173 </span>            :   } else {</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        125 :     norm = static_cast&lt;double&gt;(ens_dim);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        125 :     fact = 1.0/norm;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        125 :   const double fact_kbt = fact/kbt;</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        125 :   std::vector&lt;double&gt; mean(narg);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        125 :   std::vector&lt;double&gt; dmean(narg,fact);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   // calculate the mean</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        125 :   if(master) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       2106 :     for(unsigned i=0; i&lt;narg; ++i) mean[i] = fact*getArgument(i);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         99 :     if(ens_dim&gt;1) multi_sim_comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        125 :   comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::vector&lt;double&gt; v_moment, dv_moment;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   // calculate other moments</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        125 :   if(do_moments) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     v_moment.resize(narg);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     dv_moment.resize(narg);</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     // standard moment</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     if(!do_central) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       if(master) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :           const double tmp = fact*std::pow(getArgument(i),moment-1);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :           v_moment[i]      = tmp*getArgument(i);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :           dv_moment[i]     = moment*tmp;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :         }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :         if(ens_dim&gt;1) multi_sim_comm.Sum(&amp;v_moment[0], narg);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       } else {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :           const double tmp = fact*std::pow(getArgument(i),moment-1);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :           dv_moment[i]     = moment*tmp;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :         }</a>
+<a name="208"><span class="lineNum">     208 </span>            :       }</a>
+<a name="209"><span class="lineNum">     209 </span>            :       // central moment</a>
+<a name="210"><span class="lineNum">     210 </span>            :     } else {</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       if(master) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :           const double tmp = std::pow(getArgument(i)-mean[i],moment-1);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :           v_moment[i]      = fact*tmp*(getArgument(i)-mean[i]);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :           dv_moment[i]     = moment*tmp*(fact-fact/norm);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :         }</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :         if(ens_dim&gt;1) multi_sim_comm.Sum(&amp;v_moment[0], narg);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :       } else {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :           const double tmp = std::pow(getArgument(i)-mean[i],moment-1);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :           dv_moment[i]     = moment*tmp*(fact-fact/norm);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :         }</a>
+<a name="223"><span class="lineNum">     223 </span>            :       }</a>
+<a name="224"><span class="lineNum">     224 </span>            :     }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;v_moment[0], narg);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   // calculate powers of moments</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        125 :   if(do_powers) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         72 :     for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         48 :       const double tmp1 = std::pow(mean[i],power-1);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         48 :       mean[i]          *= tmp1;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         48 :       dmean[i]         *= power*tmp1;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         48 :       if(do_moments) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :         const double tmp2 = std::pow(v_moment[i],power-1);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :         v_moment[i]      *= tmp2;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :         dv_moment[i]     *= power*tmp2;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :       }</a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span>            :   }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :   // set components</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       3358 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :     // set mean</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       3233 :     Value* v=getPntrToComponent(i);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">       3233 :     v-&gt;set(mean[i]);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       6466 :     setDerivative(v, i, dmean[i]);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       3233 :     if(do_reweight) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :       const double w_tmp = fact_kbt*(getArgument(i) - mean[i]);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :       setDerivative(v, narg, w_tmp);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       3233 :     if(do_moments) {</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :       // set moments</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       Value* u=getPntrToComponent(i+narg);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :       u-&gt;set(v_moment[i]);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :       setDerivative(u, i, dv_moment[i]);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :       if(do_reweight) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :         const double w_tmp = fact_kbt*(pow(getArgument(i),moment) - v_moment[i]);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :         setDerivative(u, narg, w_tmp);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :       }</a>
+<a name="261"><span class="lineNum">     261 </span>            :     }</a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        125 : }</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncPathGeneral.cpp.func-sort-c.html b/coverage/function/FuncPathGeneral.cpp.func-sort-c.html
new file mode 100644
index 0000000000..af8d1b8e6a
--- /dev/null
+++ b/coverage/function/FuncPathGeneral.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncPathGeneral.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncPathGeneral.cpp<span style="font-size: 80%;"> (<a href="FuncPathGeneral.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntryMed">77.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FuncPathGeneral.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#168">_ZN4PLMD8function15FuncPathGeneralC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#124">_ZN4PLMD8function12_GLOBAL__N_128FuncPathGeneralRegisterMe1266createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#126">_ZN4PLMD8function15FuncPathGeneral13loadReferenceEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#168">_ZN4PLMD8function15FuncPathGeneralC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#154">_ZN4PLMD8function15FuncPathGeneral16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#124">_ZN4PLMD8function12_GLOBAL__N_128FuncPathGeneralRegisterMe126C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#124">_ZN4PLMD8function12_GLOBAL__N_128FuncPathGeneralRegisterMe126D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#306">_ZN4PLMD8function15FuncPathGeneral7prepareEv</a></td>
+              <td class="coverFnHi">175001</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#235">_ZN4PLMD8function15FuncPathGeneral9calculateEv</a></td>
+              <td class="coverFnHi">175001</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncPathGeneral.cpp.func.html b/coverage/function/FuncPathGeneral.cpp.func.html
new file mode 100644
index 0000000000..7123338f02
--- /dev/null
+++ b/coverage/function/FuncPathGeneral.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncPathGeneral.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncPathGeneral.cpp<span style="font-size: 80%;"> (<a href="FuncPathGeneral.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntryMed">77.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FuncPathGeneral.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#124">_ZN4PLMD8function12_GLOBAL__N_128FuncPathGeneralRegisterMe1266createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#124">_ZN4PLMD8function12_GLOBAL__N_128FuncPathGeneralRegisterMe126C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#124">_ZN4PLMD8function12_GLOBAL__N_128FuncPathGeneralRegisterMe126D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#126">_ZN4PLMD8function15FuncPathGeneral13loadReferenceEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#154">_ZN4PLMD8function15FuncPathGeneral16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#306">_ZN4PLMD8function15FuncPathGeneral7prepareEv</a></td>
+              <td class="coverFnHi">175001</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#235">_ZN4PLMD8function15FuncPathGeneral9calculateEv</a></td>
+              <td class="coverFnHi">175001</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#168">_ZN4PLMD8function15FuncPathGeneralC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathGeneral.cpp.gcov.html#168">_ZN4PLMD8function15FuncPathGeneralC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncPathGeneral.cpp.gcov.html b/coverage/function/FuncPathGeneral.cpp.gcov.html
new file mode 100644
index 0000000000..7ec7ad3edf
--- /dev/null
+++ b/coverage/function/FuncPathGeneral.cpp.gcov.html
@@ -0,0 +1,417 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncPathGeneral.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncPathGeneral.cpp<span style="font-size: 80%;"> (source / <a href="FuncPathGeneral.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntryMed">77.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Function.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;limits&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace function {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC FUNCTION FUNCPATHGENERAL</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : This function calculates path collective variables (PCVs) using an arbitrary combination of collective variables.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The method used to calculate the PCVs that is used in this method is described in \cite Hovan2019.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This variable computes the progress along a given set of frames that is provided in an input file (&quot;s&quot; component) and the distance from them (&quot;z&quot; component).</a>
+<a name="38"><span class="lineNum">      38 </span>            : The input file could be a colvar file generated with plumed driver on a trajectory containing the frames.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The metric for the path collective variables takes the following form:</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : R[X - X_i] = \sum_{j=1}^M c_j^2 (x_j - x_{i,j})^2\,.</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : Here, the coefficients \f$c_j\f$ determine the relative weights of the collective variables \f$c_j\f$ in the metric.</a>
+<a name="47"><span class="lineNum">      47 </span>            : A value for the lambda coefficient also needs to be provided, typically chosen in such a way that it ensures a smooth variation of the &quot;s&quot; component.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : This command calculates the PCVs using the values from the file COLVAR_TRAJ and the provided values for the lambda and the coefficients.</a>
+<a name="52"><span class="lineNum">      52 </span>            : Since the columns in the file were not specified, the first one will be ignored (assumed to correspond to the time) and the rest used.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : FUNCPATHGENERAL ...</a>
+<a name="56"><span class="lineNum">      56 </span>            : LABEL=path</a>
+<a name="57"><span class="lineNum">      57 </span>            : LAMBDA=12.2</a>
+<a name="58"><span class="lineNum">      58 </span>            : REFERENCE=COLVAR_TRAJ</a>
+<a name="59"><span class="lineNum">      59 </span>            : COEFFICIENTS=0.3536,0.3536,0.3536,0.3536,0.7071</a>
+<a name="60"><span class="lineNum">      60 </span>            : ARG=d1,d2,d,t,drmsd</a>
+<a name="61"><span class="lineNum">      61 </span>            : ... FUNCPATHGENERAL</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The command below is a variation of the previous one, specifying a subset of the collective variables and using a neighbor list.</a>
+<a name="65"><span class="lineNum">      65 </span>            : The columns are zero-indexed.</a>
+<a name="66"><span class="lineNum">      66 </span>            : The neighbor list will include the 10 closest frames and will be recalculated every 20 steps.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : FUNCPATHGENERAL ...</a>
+<a name="70"><span class="lineNum">      70 </span>            : LABEL=path</a>
+<a name="71"><span class="lineNum">      71 </span>            : LAMBDA=5.0</a>
+<a name="72"><span class="lineNum">      72 </span>            : REFERENCE=COLVAR_TRAJ</a>
+<a name="73"><span class="lineNum">      73 </span>            : COLUMNS=2,3,4</a>
+<a name="74"><span class="lineNum">      74 </span>            : COEFFICIENTS=0.3536,0.3536,0.3536</a>
+<a name="75"><span class="lineNum">      75 </span>            : ARG=d2,d,t</a>
+<a name="76"><span class="lineNum">      76 </span>            : NEIGH_SIZE=10</a>
+<a name="77"><span class="lineNum">      77 </span>            : NEIGH_STRIDE=20</a>
+<a name="78"><span class="lineNum">      78 </span>            : ... FUNCPATHGENERAL</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : */</a>
+<a name="82"><span class="lineNum">      82 </span>            : //+ENDPLUMEDOC</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : class FuncPathGeneral : public Function {</a>
+<a name="85"><span class="lineNum">      85 </span>            :   double lambda;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   int neigh_size;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   double neigh_stride;</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;double&gt; coefficients;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; path_cv_values;</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   // For faster calculation</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::vector&lt;double&gt; expdists;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   // For calculating derivatives</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; numerators;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt;double&gt; s_path_ders;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;double&gt; z_path_ders;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   // For handling periodicity</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;double&gt; domains;</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::string reference;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;int&gt; columns;</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt; std::pair&lt;int,double&gt; &gt; neighpair;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector &lt;Value*&gt; allArguments;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Methods</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void loadReference();</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   struct pairordering {</a>
+<a name="113"><span class="lineNum">     113 </span>            :     bool operator ()(std::pair&lt;int, double&gt; const&amp; a, std::pair&lt;int, double&gt; const&amp; b) {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :       return (a).second &lt; (b).second;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     }</a>
+<a name="116"><span class="lineNum">     116 </span>            :   };</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : public:</a>
+<a name="119"><span class="lineNum">     119 </span>            :   explicit FuncPathGeneral(const ActionOptions&amp;);</a>
+<a name="120"><span class="lineNum">     120 </span>            : // Active methods:</a>
+<a name="121"><span class="lineNum">     121 </span>            :   virtual void calculate();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   virtual void prepare();</a>
+<a name="123"><span class="lineNum">     123 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="124"><span class="lineNum">     124 </span>            : };</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FuncPathGeneral, &quot;FUNCPATHGENERAL&quot;)</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          1 : void FuncPathGeneral::loadReference() {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          1 :   IFile input;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   input.open(reference);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 :   if (!input)</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Could not open the reference file!&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         18 :   while (input)</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   {</a>
+<a name="135"><span class="lineNum">     135 </span>            :     std::vector&lt;std::string&gt; strings;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         17 :     Tools::getParsedLine(input, strings);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         17 :     if (strings.empty())</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :       continue;</a>
+<a name="139"><span class="lineNum">     139 </span>            :     std::vector&lt;double&gt; colvarLine;</a>
+<a name="140"><span class="lineNum">     140 </span>            :     double value;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         16 :     int max = columns.empty() ? strings.size() : columns.size();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        128 :     for (int i = 0; i &lt; max; ++i)</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        112 :       int col = columns.empty() ? i : columns[i];</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :       // If no columns have been entered, ignore the first (time) and take the rest</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        112 :       if (columns.empty() &amp;&amp; i == 0)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         16 :         continue;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         96 :       Tools::convert(strings[col], value);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         96 :       colvarLine.push_back(value);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     }</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         16 :     path_cv_values.push_back(colvarLine);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         17 :   }</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          1 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          3 : void FuncPathGeneral::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 :   Function::registerKeywords(keys);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;LAMBDA&quot;, &quot;Lambda parameter required for smoothing&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;COEFFICIENTS&quot;, &quot;Coefficients to be assigned to the CVs&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;REFERENCE&quot;, &quot;Colvar file needed to provide the CV milestones&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;COLUMNS&quot;, &quot;List of columns in the reference colvar file specifying the CVs&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;NEIGH_SIZE&quot;, &quot;Size of the neighbor list&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;NEIGH_STRIDE&quot;, &quot;How often the neighbor list needs to be calculated in time units&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   componentsAreNotOptional(keys);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;s&quot;, &quot;default&quot;, &quot;Position on the path&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;z&quot;, &quot;default&quot;, &quot;Distance from the path&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          3 : }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 : FuncPathGeneral::FuncPathGeneral(const ActionOptions&amp;ao):</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   Action(ao),</a>
+<a name="172"><span class="lineNum">     172 </span>            :   Function(ao),</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          1 :   neigh_size(-1),</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :   neigh_stride(-1.)</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 :   parse(&quot;LAMBDA&quot;, lambda);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          1 :   parse(&quot;NEIGH_SIZE&quot;, neigh_size);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :   parse(&quot;NEIGH_STRIDE&quot;, neigh_stride);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          1 :   parse(&quot;REFERENCE&quot;, reference);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :   parseVector(&quot;COEFFICIENTS&quot;, coefficients);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          1 :   parseVector(&quot;COLUMNS&quot;, columns);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          1 :   log.printf(&quot;  lambda is %f\n&quot;, lambda);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :   if (getNumberOfArguments() != coefficients.size())</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;The numbers of coefficients and CVs are different!&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          1 :   if (!columns.empty()) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     if (columns.size() != coefficients.size())</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;The numbers of coefficients and columns are different!&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          1 :   log.printf(&quot;  Consistency check completed! Your path cvs look good!\n&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   // Load the reference colvar file</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          1 :   loadReference();</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            :   // Do some neighbour printout</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          1 :   if (neigh_stride &gt; 0. || neigh_size &gt; 0) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     if (static_cast&lt;unsigned&gt;(neigh_size) &gt; path_cv_values.size()) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :       log.printf(&quot; List size required ( %d ) is too large: resizing to the maximum number of arg required: %d  \n&quot;, neigh_size, getNumberOfArguments());</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :       neigh_size = path_cv_values.size();</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     log.printf(&quot;  Neighbour list enabled: \n&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     log.printf(&quot;                 size   :  %d elements\n&quot;, neigh_size);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     log.printf(&quot;                 stride :  %f time \n&quot;, neigh_stride);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   } else {</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          1 :     log.printf(&quot;  Neighbour list NOT enabled \n&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :   addComponentWithDerivatives(&quot;s&quot;); componentIsNotPeriodic(&quot;s&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          3 :   addComponentWithDerivatives(&quot;z&quot;); componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   // Initialise vectors</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; temp (coefficients.size());</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         17 :   for (unsigned i = 0; i &lt; path_cv_values.size(); ++i) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         16 :     numerators.push_back(temp);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         16 :     expdists.push_back(0.);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         16 :     s_path_ders.push_back(0.);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         16 :     z_path_ders.push_back(0.);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :   // Store the arguments</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          7 :   for (unsigned i=0; i&lt;getNumberOfArguments(); i++)</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          6 :     allArguments.push_back(getPntrToArgument(i));</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   // Get periodic domains, negative for not periodic, stores half the domain length (maximum difference)</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          7 :   for (unsigned i = 0; i &lt; allArguments.size(); ++i) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          6 :     if (allArguments[i]-&gt;isPeriodic()) {</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :       double min_lim, max_lim;</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :       allArguments[i]-&gt;getDomain(min_lim, max_lim);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       domains.push_back((max_lim - min_lim) / 2);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span>            :     else</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          6 :       domains.push_back(-1.);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          1 : }</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : // Calculator</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">     175001 : void FuncPathGeneral::calculate() {</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   double s_path = 0.;</a>
+<a name="239"><span class="lineNum">     239 </span>            :   double partition = 0.;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   double tmp, value, diff, expdist, s_der, z_der;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   int ii;</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   typedef std::vector&lt; std::pair&lt; int,double&gt; &gt;::iterator pairiter;</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    2975001 :   for (pairiter it = neighpair.begin(); it != neighpair.end(); ++it) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">    2800000 :     (*it).second = 0.;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">     175001 :   if (neighpair.empty()) {</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :     // Resize at the first step</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          1 :     neighpair.resize(path_cv_values.size());</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         17 :     for (unsigned i = 0; i &lt; path_cv_values.size(); ++i)</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         16 :       neighpair[i].first = i;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">     175001 :   Value* val_s_path=getPntrToComponent(&quot;s&quot;);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">     175001 :   Value* val_z_path=getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">    1225007 :   for(unsigned j = 0; j &lt; allArguments.size(); ++j) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">    1050006 :     value = allArguments[j]-&gt;get();</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">   17850102 :     for (pairiter it = neighpair.begin(); it != neighpair.end(); ++it) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">   16800096 :       diff = (value - path_cv_values[(*it).first][j]);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">   16800096 :       if (domains[j] &gt; 0) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :         if (diff &gt; domains[j])</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :           diff -= 2 * domains[j];</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :         if (diff &lt; -domains[j])</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :           diff += 2 * domains[j];</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :       }</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">   33600192 :       (*it).second += Tools::fastpow(coefficients[j] * diff, 2);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">   33600192 :       numerators[(*it).first][j] = 2 * Tools::fastpow(coefficients[j], 2) * diff;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :     }</a>
+<a name="272"><span class="lineNum">     272 </span>            :   }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">    2975017 :   for (pairiter it = neighpair.begin(); it != neighpair.end(); ++it) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">    2800016 :     expdist = std::exp(-lambda * (*it).second);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">    2800016 :     expdists[(*it).first] = expdist;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    2800016 :     s_path += ((*it).first + 1) * expdist;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">    2800016 :     partition += expdist;</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">     175001 :   if(partition==0.0) partition=std::numeric_limits&lt;double&gt;::min();</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">     175001 :   s_path /= partition;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   val_s_path-&gt;set(s_path);</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     175001 :   val_z_path-&gt;set(-(1. / lambda) * std::log(partition));</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :   // Derivatives</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">    2975017 :   for (pairiter it = neighpair.begin(); it != neighpair.end(); ++it) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">    2800016 :     ii = (*it).first;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">    2800016 :     tmp = lambda * expdists[ii] * (s_path - (ii + 1)) / partition;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">    2800016 :     s_path_ders[ii] = tmp;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">    2800016 :     z_path_ders[ii] = expdists[ii] / partition;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">    1225007 :   for (unsigned i = 0; i &lt; coefficients.size(); ++i) {</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :     s_der = 0.;</a>
+<a name="296"><span class="lineNum">     296 </span>            :     z_der = 0.;</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">   17850102 :     for (pairiter it = neighpair.begin(); it != neighpair.end(); ++it) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">   16800096 :       ii = (*it).first;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">   16800096 :       s_der += s_path_ders[ii] * numerators[ii][i];</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">   16800096 :       z_der += z_path_ders[ii] * numerators[ii][i];</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :     }</a>
+<a name="302"><span class="lineNum">     302 </span>            :     setDerivative(val_s_path, i, s_der);</a>
+<a name="303"><span class="lineNum">     303 </span>            :     setDerivative(val_z_path, i, z_der);</a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     175001 : }</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : // Prepare the required arguments</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">     175001 : void FuncPathGeneral::prepare() {</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   // Neighbour list: rank and activate the chain for the next step</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :   // Neighbour list: if neigh_size &lt; 0 never sort and keep the full vector</a>
+<a name="312"><span class="lineNum">     312 </span>            :   // Neighbour list: if neigh_size &gt; 0</a>
+<a name="313"><span class="lineNum">     313 </span>            :   //                 if the size is full -&gt; sort the vector and decide the dependencies for next step</a>
+<a name="314"><span class="lineNum">     314 </span>            :   //                 if the size is not full -&gt; check if next step will need the full dependency otherwise keep these dependencies</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">     175001 :   if (neigh_size &gt; 0) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :     if (neighpair.size() == path_cv_values.size()) {</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :       // The complete round has been done: need to sort, shorten and give it a go</a>
+<a name="319"><span class="lineNum">     319 </span>            :       // Sort the values</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :       std::sort(neighpair.begin(), neighpair.end(), pairordering());</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :       // Resize the effective list</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :       neighpair.resize(neigh_size);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :       log.printf(&quot;  NEIGHBOUR LIST NOW INCLUDES INDICES: &quot;);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :       for (int i = 0; i &lt; neigh_size; ++i)</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :         log.printf(&quot; %i &quot;,neighpair[i].first);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :       log.printf(&quot; \n&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     } else {</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :       if (int(getStep()) % int(neigh_stride / getTimeStep()) == 0) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :         log.printf(&quot; Time %f : recalculating full neighbour list \n&quot;, getStep() * getTimeStep());</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :         neighpair.resize(path_cv_values.size());</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :         for (unsigned i = 0; i &lt; path_cv_values.size(); ++i)</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :           neighpair[i].first = i;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :       }</a>
+<a name="334"><span class="lineNum">     334 </span>            :     }</a>
+<a name="335"><span class="lineNum">     335 </span>            :   }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">     175001 :   requestArguments(allArguments);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">     175001 : }</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            : }</a>
+<a name="341"><span class="lineNum">     341 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncPathMSD.cpp.func-sort-c.html b/coverage/function/FuncPathMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..bbd77ee133
--- /dev/null
+++ b/coverage/function/FuncPathMSD.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncPathMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncPathMSD.cpp<span style="font-size: 80%;"> (<a href="FuncPathMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FuncPathMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#228">_ZN4PLMD8function11FuncPathMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#228">_ZN4PLMD8function11FuncPathMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#216">_ZN4PLMD8function12_GLOBAL__N_124FuncPathMSDRegisterMe2186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#218">_ZN4PLMD8function11FuncPathMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#307">_ZN4PLMD8function11FuncPathMSD7prepareEv</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#273">_ZN4PLMD8function11FuncPathMSD9calculateEv</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#216">_ZN4PLMD8function12_GLOBAL__N_124FuncPathMSDRegisterMe218C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#216">_ZN4PLMD8function12_GLOBAL__N_124FuncPathMSDRegisterMe218D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncPathMSD.cpp.func.html b/coverage/function/FuncPathMSD.cpp.func.html
new file mode 100644
index 0000000000..6ee83cb8ba
--- /dev/null
+++ b/coverage/function/FuncPathMSD.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncPathMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncPathMSD.cpp<span style="font-size: 80%;"> (<a href="FuncPathMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FuncPathMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#218">_ZN4PLMD8function11FuncPathMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#307">_ZN4PLMD8function11FuncPathMSD7prepareEv</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#273">_ZN4PLMD8function11FuncPathMSD9calculateEv</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#228">_ZN4PLMD8function11FuncPathMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#228">_ZN4PLMD8function11FuncPathMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#216">_ZN4PLMD8function12_GLOBAL__N_124FuncPathMSDRegisterMe2186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#216">_ZN4PLMD8function12_GLOBAL__N_124FuncPathMSDRegisterMe218C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncPathMSD.cpp.gcov.html#216">_ZN4PLMD8function12_GLOBAL__N_124FuncPathMSDRegisterMe218D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncPathMSD.cpp.gcov.html b/coverage/function/FuncPathMSD.cpp.gcov.html
new file mode 100644
index 0000000000..714424d454
--- /dev/null
+++ b/coverage/function/FuncPathMSD.cpp.gcov.html
@@ -0,0 +1,444 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncPathMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncPathMSD.cpp<span style="font-size: 80%;"> (source / <a href="FuncPathMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntryHi">92.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Function.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace function {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC FUNCTION FUNCPATHMSD</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : This function calculates path collective variables.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This is the Path Collective Variables implementation</a>
+<a name="34"><span class="lineNum">      34 </span>            : ( see \cite brand07 ).</a>
+<a name="35"><span class="lineNum">      35 </span>            : This variable computes the progress along a given set of frames that is provided</a>
+<a name="36"><span class="lineNum">      36 </span>            : in input (&quot;s&quot; component) and the distance from them (&quot;z&quot; component).</a>
+<a name="37"><span class="lineNum">      37 </span>            : It is a function of mean squared displacement that are obtained by the joint use of mean squared displacement variables with the SQUARED flag</a>
+<a name="38"><span class="lineNum">      38 </span>            : (see below).</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Here below is a case where you have defined three frames and you want to</a>
+<a name="43"><span class="lineNum">      43 </span>            : calculate the progress along the path and the distance from it in p1</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : t1: RMSD REFERENCE=frame_1.pdb TYPE=OPTIMAL SQUARED</a>
+<a name="47"><span class="lineNum">      47 </span>            : t2: RMSD REFERENCE=frame_21.pdb TYPE=OPTIMAL SQUARED</a>
+<a name="48"><span class="lineNum">      48 </span>            : t3: RMSD REFERENCE=frame_42.pdb TYPE=OPTIMAL SQUARED</a>
+<a name="49"><span class="lineNum">      49 </span>            : p1: FUNCPATHMSD ARG=t1,t2,t3 LAMBDA=500.0</a>
+<a name="50"><span class="lineNum">      50 </span>            : PRINT ARG=t1,t2,t3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="51"><span class="lineNum">      51 </span>            : \endplumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : For this input you would then define the position of the reference coordinates in three separate pdb files.  The contents of the</a>
+<a name="54"><span class="lineNum">      54 </span>            : file frame_1.pdb are shown below:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \auxfile{frame_1.pdb}</a>
+<a name="57"><span class="lineNum">      57 </span>            : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00</a>
+<a name="58"><span class="lineNum">      58 </span>            : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00</a>
+<a name="59"><span class="lineNum">      59 </span>            : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00</a>
+<a name="60"><span class="lineNum">      60 </span>            : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00</a>
+<a name="61"><span class="lineNum">      61 </span>            : ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00</a>
+<a name="62"><span class="lineNum">      62 </span>            : END</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endauxfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : This is then frame.21.pdb:</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \auxfile{frame_21.pdb}</a>
+<a name="68"><span class="lineNum">      68 </span>            : ATOM      1  CL  ALA     1      -3.089   1.850   1.546  1.00  1.00</a>
+<a name="69"><span class="lineNum">      69 </span>            : ATOM      5  CLP ALA     1      -1.667   1.457   1.629  1.00  1.00</a>
+<a name="70"><span class="lineNum">      70 </span>            : ATOM      6  OL  ALA     1      -0.974   1.868   2.533  1.00  1.00</a>
+<a name="71"><span class="lineNum">      71 </span>            : ATOM      7  NL  ALA     1      -1.204   0.683   0.642  1.00  1.00</a>
+<a name="72"><span class="lineNum">      72 </span>            : ATOM      8  HL  ALA     1      -1.844   0.360  -0.021  1.00  1.00</a>
+<a name="73"><span class="lineNum">      73 </span>            : END</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endauxfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : and finally this is frame_42.pdb:</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \auxfile{frame_42.pdb}</a>
+<a name="79"><span class="lineNum">      79 </span>            : ATOM      1  CL  ALA     1      -3.257   1.605   1.105  1.00  1.00</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOM      5  CLP ALA     1      -1.941   1.459   0.447  1.00  1.00</a>
+<a name="81"><span class="lineNum">      81 </span>            : ATOM      6  OL  ALA     1      -1.481   2.369  -0.223  1.00  1.00</a>
+<a name="82"><span class="lineNum">      82 </span>            : ATOM      7  NL  ALA     1      -1.303   0.291   0.647  1.00  1.00</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM      8  HL  ALA     1      -1.743  -0.379   1.229  1.00  1.00</a>
+<a name="84"><span class="lineNum">      84 </span>            : END</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endauxfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : This second example shows how to define a PATH in \ref CONTACTMAP space:</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : \plumedfile</a>
+<a name="90"><span class="lineNum">      90 </span>            : CONTACTMAP ...</a>
+<a name="91"><span class="lineNum">      91 </span>            : ATOMS1=1,2 REFERENCE1=0.1</a>
+<a name="92"><span class="lineNum">      92 </span>            : ATOMS2=3,4 REFERENCE2=0.5</a>
+<a name="93"><span class="lineNum">      93 </span>            : ATOMS3=4,5 REFERENCE3=0.25</a>
+<a name="94"><span class="lineNum">      94 </span>            : ATOMS4=5,6 REFERENCE4=0.0</a>
+<a name="95"><span class="lineNum">      95 </span>            : SWITCH={RATIONAL R_0=1.5}</a>
+<a name="96"><span class="lineNum">      96 </span>            : LABEL=c1</a>
+<a name="97"><span class="lineNum">      97 </span>            : CMDIST</a>
+<a name="98"><span class="lineNum">      98 </span>            : ... CONTACTMAP</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : CONTACTMAP ...</a>
+<a name="101"><span class="lineNum">     101 </span>            : ATOMS1=1,2 REFERENCE1=0.3</a>
+<a name="102"><span class="lineNum">     102 </span>            : ATOMS2=3,4 REFERENCE2=0.9</a>
+<a name="103"><span class="lineNum">     103 </span>            : ATOMS3=4,5 REFERENCE3=0.45</a>
+<a name="104"><span class="lineNum">     104 </span>            : ATOMS4=5,6 REFERENCE4=0.1</a>
+<a name="105"><span class="lineNum">     105 </span>            : SWITCH={RATIONAL R_0=1.5}</a>
+<a name="106"><span class="lineNum">     106 </span>            : LABEL=c2</a>
+<a name="107"><span class="lineNum">     107 </span>            : CMDIST</a>
+<a name="108"><span class="lineNum">     108 </span>            : ... CONTACTMAP</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : CONTACTMAP ...</a>
+<a name="111"><span class="lineNum">     111 </span>            : ATOMS1=1,2 REFERENCE1=1.0</a>
+<a name="112"><span class="lineNum">     112 </span>            : ATOMS2=3,4 REFERENCE2=1.0</a>
+<a name="113"><span class="lineNum">     113 </span>            : ATOMS3=4,5 REFERENCE3=1.0</a>
+<a name="114"><span class="lineNum">     114 </span>            : ATOMS4=5,6 REFERENCE4=1.0</a>
+<a name="115"><span class="lineNum">     115 </span>            : SWITCH={RATIONAL R_0=1.5}</a>
+<a name="116"><span class="lineNum">     116 </span>            : LABEL=c3</a>
+<a name="117"><span class="lineNum">     117 </span>            : CMDIST</a>
+<a name="118"><span class="lineNum">     118 </span>            : ... CONTACTMAP</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : p1: FUNCPATHMSD ARG=c1,c2,c3 LAMBDA=500.0</a>
+<a name="121"><span class="lineNum">     121 </span>            : PRINT ARG=c1,c2,c3,p1.s,p1.z STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="122"><span class="lineNum">     122 </span>            : \endplumedfile</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : This third example shows how to define a PATH in \ref PIV space:</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : \plumedfile</a>
+<a name="127"><span class="lineNum">     127 </span>            : PIV ...</a>
+<a name="128"><span class="lineNum">     128 </span>            : LABEL=c1</a>
+<a name="129"><span class="lineNum">     129 </span>            : PRECISION=1000</a>
+<a name="130"><span class="lineNum">     130 </span>            : NLIST</a>
+<a name="131"><span class="lineNum">     131 </span>            : REF_FILE=Ref1.pdb</a>
+<a name="132"><span class="lineNum">     132 </span>            : PIVATOMS=2</a>
+<a name="133"><span class="lineNum">     133 </span>            : ATOMTYPES=A,B</a>
+<a name="134"><span class="lineNum">     134 </span>            : ONLYDIRECT</a>
+<a name="135"><span class="lineNum">     135 </span>            : SFACTOR=1.0,0.2</a>
+<a name="136"><span class="lineNum">     136 </span>            : SORT=1,1</a>
+<a name="137"><span class="lineNum">     137 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="138"><span class="lineNum">     138 </span>            : SWITCH2={RATIONAL R_0=0.5 MM=10 NN=5}</a>
+<a name="139"><span class="lineNum">     139 </span>            : NL_CUTOFF=1.2,1.2</a>
+<a name="140"><span class="lineNum">     140 </span>            : NL_STRIDE=10,10</a>
+<a name="141"><span class="lineNum">     141 </span>            : NL_SKIN=0.1,0.1</a>
+<a name="142"><span class="lineNum">     142 </span>            : ... PIV</a>
+<a name="143"><span class="lineNum">     143 </span>            : PIV ...</a>
+<a name="144"><span class="lineNum">     144 </span>            : LABEL=c2</a>
+<a name="145"><span class="lineNum">     145 </span>            : PRECISION=1000</a>
+<a name="146"><span class="lineNum">     146 </span>            : NLIST</a>
+<a name="147"><span class="lineNum">     147 </span>            : REF_FILE=Ref2.pdb</a>
+<a name="148"><span class="lineNum">     148 </span>            : PIVATOMS=2</a>
+<a name="149"><span class="lineNum">     149 </span>            : ATOMTYPES=A,B</a>
+<a name="150"><span class="lineNum">     150 </span>            : ONLYDIRECT</a>
+<a name="151"><span class="lineNum">     151 </span>            : SFACTOR=1.0,0.2</a>
+<a name="152"><span class="lineNum">     152 </span>            : SORT=1,1</a>
+<a name="153"><span class="lineNum">     153 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="154"><span class="lineNum">     154 </span>            : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="155"><span class="lineNum">     155 </span>            : NL_CUTOFF=1.2,1.2</a>
+<a name="156"><span class="lineNum">     156 </span>            : NL_STRIDE=10,10</a>
+<a name="157"><span class="lineNum">     157 </span>            : NL_SKIN=0.1,0.1</a>
+<a name="158"><span class="lineNum">     158 </span>            : ... PIV</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : p1: FUNCPATHMSD ARG=c1,c2 LAMBDA=0.180338</a>
+<a name="161"><span class="lineNum">     161 </span>            : METAD ARG=p1.s,p1.z SIGMA=0.01,0.2 HEIGHT=0.8 PACE=500   LABEL=res</a>
+<a name="162"><span class="lineNum">     162 </span>            : PRINT ARG=c1,c2,p1.s,p1.z,res.bias STRIDE=500  FILE=colvar FMT=%15.6f</a>
+<a name="163"><span class="lineNum">     163 </span>            : \endplumedfile</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : */</a>
+<a name="166"><span class="lineNum">     166 </span>            : //+ENDPLUMEDOC</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : class FuncPathMSD : public Function {</a>
+<a name="169"><span class="lineNum">     169 </span>            :   double lambda;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   int neigh_size;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   double neigh_stride;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   std::vector&lt; std::pair&lt;Value *,double&gt; &gt; neighpair;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   std::map&lt;Value *,double &gt; indexmap; // use double to allow isomaps</a>
+<a name="174"><span class="lineNum">     174 </span>            :   std::vector &lt;Value*&gt; allArguments;</a>
+<a name="175"><span class="lineNum">     175 </span>            : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</a>
+<a name="176"><span class="lineNum">     176 </span>            : // this below is useful when one wants to sort a vector of double and have back the order</a>
+<a name="177"><span class="lineNum">     177 </span>            : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</a>
+<a name="178"><span class="lineNum">     178 </span>            : // create a custom sorter</a>
+<a name="179"><span class="lineNum">     179 </span>            :   typedef std::vector&lt;double&gt;::const_iterator myiter;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   struct ordering {</a>
+<a name="181"><span class="lineNum">     181 </span>            :     bool operator ()(std::pair&lt;unsigned, myiter&gt; const&amp; a, std::pair&lt;unsigned, myiter&gt; const&amp; b) {</a>
+<a name="182"><span class="lineNum">     182 </span>            :       return *(a.second) &lt; *(b.second);</a>
+<a name="183"><span class="lineNum">     183 </span>            :     }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   };</a>
+<a name="185"><span class="lineNum">     185 </span>            : // sorting utility</a>
+<a name="186"><span class="lineNum">     186 </span>            :   std::vector&lt;int&gt; increasingOrder( std::vector&lt;double&gt; &amp;v) {</a>
+<a name="187"><span class="lineNum">     187 </span>            :     // make a pair</a>
+<a name="188"><span class="lineNum">     188 </span>            :     std::vector&lt; std::pair&lt;unsigned, myiter&gt; &gt; order(v.size());</a>
+<a name="189"><span class="lineNum">     189 </span>            :     unsigned n = 0;</a>
+<a name="190"><span class="lineNum">     190 </span>            :     for (myiter it = v.begin(); it != v.end(); ++it, ++n) {</a>
+<a name="191"><span class="lineNum">     191 </span>            :       order[n] = make_pair(n, it); // note: heere i do not put the values but the addresses that point to the value</a>
+<a name="192"><span class="lineNum">     192 </span>            :     }</a>
+<a name="193"><span class="lineNum">     193 </span>            :     // now sort according the second value</a>
+<a name="194"><span class="lineNum">     194 </span>            :     std::sort(order.begin(), order.end(), ordering());</a>
+<a name="195"><span class="lineNum">     195 </span>            :     std::vector&lt;int&gt; vv(v.size()); n=0;</a>
+<a name="196"><span class="lineNum">     196 </span>            :     for (const auto &amp; it : order) {</a>
+<a name="197"><span class="lineNum">     197 </span>            :       vv[n]=it.first; n++;</a>
+<a name="198"><span class="lineNum">     198 </span>            :     }</a>
+<a name="199"><span class="lineNum">     199 </span>            :     return vv;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   }</a>
+<a name="201"><span class="lineNum">     201 </span>            : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</a>
+<a name="202"><span class="lineNum">     202 </span>            : // XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            :   struct pairordering {</a>
+<a name="205"><span class="lineNum">     205 </span>            :     bool operator ()(std::pair&lt;Value *, double&gt; const&amp; a, std::pair&lt;Value*, double&gt; const&amp; b) {</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        437 :       return (a).second &gt; (b).second;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            :   };</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : public:</a>
+<a name="211"><span class="lineNum">     211 </span>            :   explicit FuncPathMSD(const ActionOptions&amp;);</a>
+<a name="212"><span class="lineNum">     212 </span>            : // active methods:</a>
+<a name="213"><span class="lineNum">     213 </span>            :   void calculate() override;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   void prepare() override;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="216"><span class="lineNum">     216 </span>            : };</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(FuncPathMSD,&quot;FUNCPATHMSD&quot;)</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          4 : void FuncPathMSD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          4 :   Function::registerKeywords(keys);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          4 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;LAMBDA&quot;,&quot;the lambda parameter is needed for smoothing, is in the units of plumed&quot;);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;NEIGH_SIZE&quot;,&quot;size of the neighbor list&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;NEIGH_STRIDE&quot;,&quot;how often the neighbor list needs to be calculated in time units&quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          4 :   componentsAreNotOptional(keys);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;s&quot;,&quot;default&quot;,&quot;the position on the path&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          8 :   keys.addOutputComponent(&quot;z&quot;,&quot;default&quot;,&quot;the distance from the path&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          4 : }</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          2 : FuncPathMSD::FuncPathMSD(const ActionOptions&amp;ao):</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   Action(ao),</a>
+<a name="232"><span class="lineNum">     232 </span>            :   Function(ao),</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 :   neigh_size(-1),</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          2 :   neigh_stride(-1.)</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : {</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          2 :   parse(&quot;LAMBDA&quot;,lambda);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          2 :   parse(&quot;NEIGH_SIZE&quot;,neigh_size);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :   parse(&quot;NEIGH_STRIDE&quot;,neigh_stride);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 :   log.printf(&quot;  lambda is %f\n&quot;,lambda);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   // list the action involved and check the type</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          2 :   std::string myname=getPntrToArgument(0)-&gt;getPntrToAction()-&gt;getName();</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :   if(myname!=&quot;RMSD&quot;&amp;&amp;myname!=&quot;CONTACTMAP&quot;&amp;&amp;myname!=&quot;DISTANCE&quot;&amp;&amp;myname!=&quot;PIV&quot;) error(&quot;One or more of your arguments is not of RMSD/CONTACTMAP/DISTANCE/PIV type!!!&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          6 :   for(unsigned i=1; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :     // for each value get the name and the label of the corresponding action</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          4 :     if( getPntrToArgument(i)-&gt;getPntrToAction()-&gt;getName()!=myname ) error(&quot;mismatch between the types of arguments&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          2 :   log.printf(&quot;  Consistency check completed! Your path cvs look good!\n&quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   // do some neighbor printout</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          2 :   if(neigh_stride&gt;0. || neigh_size&gt;0) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          1 :     if(neigh_size&gt;static_cast&lt;int&gt;(getNumberOfArguments())) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :       log.printf(&quot; List size required ( %d ) is too large: resizing to the maximum number of arg required: %d  \n&quot;,neigh_size,getNumberOfArguments());</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       neigh_size=getNumberOfArguments();</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          1 :     log.printf(&quot;  Neighbor list enabled: \n&quot;);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          1 :     log.printf(&quot;                size   :  %d elements\n&quot;,neigh_size);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          1 :     log.printf(&quot;                stride :  %f time \n&quot;,neigh_stride);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   } else {</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 :     log.printf(&quot;  Neighbor list NOT enabled \n&quot;);</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          4 :   addComponentWithDerivatives(&quot;s&quot;); componentIsNotPeriodic(&quot;s&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          4 :   addComponentWithDerivatives(&quot;z&quot;); componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :   // now backup the arguments</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++)allArguments.push_back(getPntrToArgument(i));</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   double i=1.;</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          8 :   for(const auto &amp; it : allArguments) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          6 :     indexmap[it]=i; i+=1.;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          2 : }</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : // calculator</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1092 : void FuncPathMSD::calculate() {</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : // log.printf(&quot;NOW CALCULATE! \n&quot;);</a>
+<a name="277"><span class="lineNum">     277 </span>            :   double s_path=0.;</a>
+<a name="278"><span class="lineNum">     278 </span>            :   double partition=0.;</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       1092 :   if(neighpair.empty()) { // at first step, resize it</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :     neighpair.resize(allArguments.size());</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;allArguments.size(); i++)neighpair[i].first=allArguments[i];</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :   }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       1092 :   Value* val_s_path=getPntrToComponent(&quot;s&quot;);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       2184 :   Value* val_z_path=getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       3959 :   for(auto &amp; it : neighpair) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       2867 :     it.second=std::exp(-lambda*(it.first-&gt;get()));</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       2867 :     s_path+=(indexmap[it.first])*it.second;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       2867 :     partition+=it.second;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :   }</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       1092 :   s_path/=partition;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   val_s_path-&gt;set(s_path);</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       1092 :   val_z_path-&gt;set(-(1./lambda)*std::log(partition));</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   int n=0;</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       3959 :   for(const auto &amp; it : neighpair) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       2867 :     double expval=it.second;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       2867 :     double tmp=lambda*expval*(s_path-(indexmap[it.first]))/partition;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :     setDerivative(val_s_path,n,tmp);</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       2867 :     setDerivative(val_z_path,n,expval/partition);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       2867 :     n++;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : //  log.printf(&quot;CALCULATION DONE! \n&quot;);</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1092 : }</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : ///</a>
+<a name="307"><span class="lineNum">     307 </span>            : /// this function updates the needed argument list</a>
+<a name="308"><span class="lineNum">     308 </span>            : ///</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1092 : void FuncPathMSD::prepare() {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :   // neighbor list: rank and activate the chain for the next step</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   // neighbor list: if neigh_size&lt;0 never sort and keep the full vector</a>
+<a name="314"><span class="lineNum">     314 </span>            :   // neighbor list: if neigh_size&gt;0</a>
+<a name="315"><span class="lineNum">     315 </span>            :   //                if the size is full -&gt; sort the vector and decide the dependencies for next step</a>
+<a name="316"><span class="lineNum">     316 </span>            :   //                if the size is not full -&gt; check if next step will need the full dependency otherwise keep this dependencies</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            :   // here just resize the neighpair. The real resizing of reinit will be done by the prepare stage that will modify the  list of arguments</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       1092 :   if (neigh_size&gt;0) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        546 :     if(neighpair.size()==allArguments.size()) { // I just did the complete round: need to sort, shorten and give it a go</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :       // sort the values</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        137 :       std::sort(neighpair.begin(),neighpair.end(),pairordering());</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :       // resize the effective list</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        137 :       neighpair.resize(neigh_size);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        137 :       log.printf(&quot;  NEIGH LIST NOW INCLUDE INDEXES: &quot;);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">        411 :       for(int i=0; i&lt;neigh_size; ++i) {log.printf(&quot; %f &quot;,indexmap[neighpair[i].first]);} log.printf(&quot; \n&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     } else {</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        409 :       if( int(getStep())%int(neigh_stride/getTimeStep())==0 ) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        137 :         log.printf(&quot; Time %f : recalculating full neighlist \n&quot;,getStep()*getTimeStep());</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        137 :         neighpair.resize(allArguments.size());</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        548 :         for(unsigned i=0; i&lt;allArguments.size(); i++)neighpair[i].first=allArguments[i];</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :       }</a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span>            :   } else {</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        546 :     if( int(getStep())==0) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          1 :       neighpair.resize(allArguments.size());</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          4 :       for(unsigned i=0; i&lt;allArguments.size(); i++)neighpair[i].first=allArguments[i];</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :     }</a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span>            :   std::vector&lt;Value*&gt; argstocall;</a>
+<a name="341"><span class="lineNum">     341 </span>            : //log.printf(&quot;PREPARING \n&quot;);</a>
+<a name="342"><span class="lineNum">     342 </span>            :   argstocall.clear();</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">       1092 :   if(!neighpair.empty()) {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">       3959 :     for(const auto &amp; it : neighpair) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">       2867 :       argstocall.push_back( it.first );</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :       //     log.printf(&quot;CALLING %p %f &quot;,(*it).first ,indexmap[(*it).first] );</a>
+<a name="347"><span class="lineNum">     347 </span>            :     }</a>
+<a name="348"><span class="lineNum">     348 </span>            :   } else {</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;allArguments.size(); i++) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :       argstocall.push_back(allArguments[i]);</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :     }</a>
+<a name="352"><span class="lineNum">     352 </span>            :   }</a>
+<a name="353"><span class="lineNum">     353 </span>            : // now the list of argument changes</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">       1092 :   requestArguments(argstocall);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : //now resize the derivatives as well</a>
+<a name="356"><span class="lineNum">     356 </span>            : //for each value in this action</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       3276 :   for(int i=0; i&lt; getNumberOfComponents(); i++) {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :     //resize the derivative to the number   the</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">       2184 :     getPntrToComponent(i)-&gt;clearDerivatives();</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">       2184 :     getPntrToComponent(i)-&gt;resizeDerivatives(getNumberOfArguments());</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span>            : //log.printf(&quot;PREPARING DONE! \n&quot;);</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       1092 : }</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            : }</a>
+<a name="366"><span class="lineNum">     366 </span>            : }</a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncSumHills.cpp.func-sort-c.html b/coverage/function/FuncSumHills.cpp.func-sort-c.html
new file mode 100644
index 0000000000..bb15b56911
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+++ b/coverage/function/FuncSumHills.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncSumHills.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncSumHills.cpp<span style="font-size: 80%;"> (<a href="FuncSumHills.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">295</td>
+            <td class="headerCovTableEntry">328</td>
+            <td class="headerCovTableEntryMed">89.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FuncSumHills.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#615">_ZN4PLMD8function12FuncSumHills9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#224">_ZN4PLMD8function12FuncSumHillsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#137">_ZN4PLMD8function12FilesHandler12getMinMaxBinESt6vectorIPNS_5ValueESaIS4_EERNS_12CommunicatorERS2_IdSaIdEESB_RS2_IjSaIjEERKSA_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#129">_ZN4PLMD8function12FilesHandler12getMinMaxBinESt6vectorIPNS_5ValueESaIS4_EERNS_12CommunicatorERS2_IdSaIdEESB_RS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#621">_ZN4PLMD8function12FuncSumHills21checkFilesAreExistingERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#224">_ZN4PLMD8function12FuncSumHillsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#197">_ZN4PLMD8function12_GLOBAL__N_125FuncSumHillsRegisterMe1996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#199">_ZN4PLMD8function12FuncSumHills16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#64">_ZN4PLMD8function12FilesHandlerC2ERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKbRNS_6ActionERNS_3LogE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#77">_ZN4PLMD8function12FilesHandler9readBunchEPNS_18BiasRepresentationEi</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#163">_ZN4PLMD8function5mylogEd</a></td>
+              <td class="coverFnHi">900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#167">_ZN4PLMD8function8mylogderEd</a></td>
+              <td class="coverFnHi">1800</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#197">_ZN4PLMD8function12_GLOBAL__N_125FuncSumHillsRegisterMe199C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#197">_ZN4PLMD8function12_GLOBAL__N_125FuncSumHillsRegisterMe199D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#145">_ZN4PLMD8function12FilesHandler11scanOneHillEPNS_18BiasRepresentationEPNS_5IFileE</a></td>
+              <td class="coverFnHi">5578</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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new file mode 100644
index 0000000000..8f63aba64c
--- /dev/null
+++ b/coverage/function/FuncSumHills.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncSumHills.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncSumHills.cpp<span style="font-size: 80%;"> (<a href="FuncSumHills.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">295</td>
+            <td class="headerCovTableEntry">328</td>
+            <td class="headerCovTableEntryMed">89.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FuncSumHills.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#145">_ZN4PLMD8function12FilesHandler11scanOneHillEPNS_18BiasRepresentationEPNS_5IFileE</a></td>
+              <td class="coverFnHi">5578</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#129">_ZN4PLMD8function12FilesHandler12getMinMaxBinESt6vectorIPNS_5ValueESaIS4_EERNS_12CommunicatorERS2_IdSaIdEESB_RS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#137">_ZN4PLMD8function12FilesHandler12getMinMaxBinESt6vectorIPNS_5ValueESaIS4_EERNS_12CommunicatorERS2_IdSaIdEESB_RS2_IjSaIjEERKSA_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#77">_ZN4PLMD8function12FilesHandler9readBunchEPNS_18BiasRepresentationEi</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#64">_ZN4PLMD8function12FilesHandlerC2ERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERKbRNS_6ActionERNS_3LogE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#199">_ZN4PLMD8function12FuncSumHills16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#621">_ZN4PLMD8function12FuncSumHills21checkFilesAreExistingERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#615">_ZN4PLMD8function12FuncSumHills9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#224">_ZN4PLMD8function12FuncSumHillsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#224">_ZN4PLMD8function12FuncSumHillsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#197">_ZN4PLMD8function12_GLOBAL__N_125FuncSumHillsRegisterMe1996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#197">_ZN4PLMD8function12_GLOBAL__N_125FuncSumHillsRegisterMe199C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#197">_ZN4PLMD8function12_GLOBAL__N_125FuncSumHillsRegisterMe199D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#163">_ZN4PLMD8function5mylogEd</a></td>
+              <td class="coverFnHi">900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FuncSumHills.cpp.gcov.html#167">_ZN4PLMD8function8mylogderEd</a></td>
+              <td class="coverFnHi">1800</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/FuncSumHills.cpp.gcov.html b/coverage/function/FuncSumHills.cpp.gcov.html
new file mode 100644
index 0000000000..d38efc7248
--- /dev/null
+++ b/coverage/function/FuncSumHills.cpp.gcov.html
@@ -0,0 +1,714 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/FuncSumHills.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - FuncSumHills.cpp<span style="font-size: 80%;"> (source / <a href="FuncSumHills.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">295</td>
+            <td class="headerCovTableEntry">328</td>
+            <td class="headerCovTableEntryMed">89.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Function.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/BiasRepresentation.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Stopwatch.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace function {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : //+PLUMEDOC FUNCTION FUNCSUMHILLS</a>
+<a name="38"><span class="lineNum">      38 </span>            : /*</a>
+<a name="39"><span class="lineNum">      39 </span>            : This function is intended to be called by the command line tool sum_hills.  It is meant to integrate a HILLS file or an HILLS file interpreted as a histogram in a variety of ways. It is, therefore, not expected that you use this during your dynamics (it will crash!)</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : In the future one could implement periodic integration during the metadynamics</a>
+<a name="42"><span class="lineNum">      42 </span>            : or straightforward MD as a tool to check convergence</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \par Examples</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : There are currently no examples for this keyword.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : */</a>
+<a name="49"><span class="lineNum">      49 </span>            : //+ENDPLUMEDOC</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         14 : class FilesHandler {</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector &lt;std::string&gt; filenames;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector &lt;std::unique_ptr&lt;IFile&gt;&gt;  ifiles;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   Action *action;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   Log *log;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool parallelread;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   unsigned beingread;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool isopen;</a>
+<a name="59"><span class="lineNum">      59 </span>            : public:</a>
+<a name="60"><span class="lineNum">      60 </span>            :   FilesHandler(const std::vector&lt;std::string&gt; &amp;filenames, const bool &amp;parallelread,  Action &amp;myaction, Log &amp;mylog);</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool readBunch(BiasRepresentation *br, int stride);</a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool scanOneHill(BiasRepresentation *br, IFile *ifile );</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void getMinMaxBin(std::vector&lt;Value*&gt; vals, Communicator &amp;cc, std::vector&lt;double&gt; &amp;vmin, std::vector&lt;double&gt; &amp;vmax, std::vector&lt;unsigned&gt; &amp;vbin);</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void getMinMaxBin(std::vector&lt;Value*&gt; vals, Communicator &amp;cc, std::vector&lt;double&gt; &amp;vmin, std::vector&lt;double&gt; &amp;vmax, std::vector&lt;unsigned&gt; &amp;vbin, const std::vector&lt;double&gt; &amp;histosigma);</a>
+<a name="65"><span class="lineNum">      65 </span>            : };</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         14 : FilesHandler::FilesHandler(const std::vector&lt;std::string&gt; &amp;filenames, const bool &amp;parallelread, Action &amp;action, Log &amp;mylog ):filenames(filenames),log(&amp;mylog),parallelread(parallelread),beingread(0),isopen(false) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         14 :   this-&gt;action=&amp;action;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         29 :   for(unsigned i=0; i&lt;filenames.size(); i++) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         15 :     auto ifile=Tools::make_unique&lt;IFile&gt;();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         15 :     ifile-&gt;link(action);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         15 :     plumed_massert((ifile-&gt;FileExist(filenames[i])), &quot;the file &quot;+filenames[i]+&quot; does not exist &quot; );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         15 :     ifiles.emplace_back(std::move(ifile));</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         15 :   }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         14 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : // note that the FileHandler is completely transparent respect to the biasrepresentation</a>
+<a name="78"><span class="lineNum">      78 </span>            : // no check are made at this level</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         15 : bool FilesHandler::readBunch(BiasRepresentation *br, int stride = -1) {</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool morefiles; morefiles=true;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         15 :   if(parallelread) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :     (*log)&lt;&lt;&quot;  doing parallelread \n&quot;;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;parallelread is not yet implemented !!!&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   } else {</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         15 :     (*log)&lt;&lt;&quot;  doing serialread \n&quot;;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     // read one by one hills</a>
+<a name="87"><span class="lineNum">      87 </span>            :     // is the type defined? if not, assume it is a gaussian</a>
+<a name="88"><span class="lineNum">      88 </span>            :     IFile *ff;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         15 :     ff=ifiles[beingread].get();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         15 :     if(!isopen) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         14 :       (*log)&lt;&lt;&quot;  opening file &quot;&lt;&lt;filenames[beingread]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         14 :       ff-&gt;open(filenames[beingread]); isopen=true;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :     }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         15 :     int n=0;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     while(true) {</a>
+<a name="96"><span class="lineNum">      96 </span>            :       bool fileisover=true;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       5578 :       while(scanOneHill(br,ff)) {</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :         // here do the dump if needed</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       5563 :         n=br-&gt;getNumberOfKernels();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       5563 :         if(stride&gt;0 &amp;&amp; n%stride==0 &amp;&amp; n!=0  ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :           (*log)&lt;&lt;&quot;  done with this chunk: now with &quot;&lt;&lt;n&lt;&lt;&quot; kernels  \n&quot;;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :           fileisover=false;</a>
+<a name="103"><span class="lineNum">     103 </span>            :           break;</a>
+<a name="104"><span class="lineNum">     104 </span>            :         }</a>
+<a name="105"><span class="lineNum">     105 </span>            :       }</a>
+<a name="106"><span class="lineNum">     106 </span>            :       if(fileisover) {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         15 :         (*log)&lt;&lt;&quot;  closing file &quot;&lt;&lt;filenames[beingread]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         15 :         ff-&gt;close();</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         15 :         isopen=false;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         15 :         (*log)&lt;&lt;&quot;  now total &quot;&lt;&lt;br-&gt;getNumberOfKernels()&lt;&lt;&quot; kernels \n&quot;;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         15 :         beingread++;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         15 :         if(beingread&lt;ifiles.size()) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 :           ff=ifiles[beingread].get(); ff-&gt;open(filenames[beingread]);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :           (*log)&lt;&lt;&quot;  opening file &quot;&lt;&lt;filenames[beingread]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          1 :           isopen=true;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :         } else {</a>
+<a name="117"><span class="lineNum">     117 </span>            :           morefiles=false;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         14 :           (*log)&lt;&lt;&quot;  final chunk: now with &quot;&lt;&lt;n&lt;&lt;&quot; kernels  \n&quot;;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :           break;</a>
+<a name="120"><span class="lineNum">     120 </span>            :         }</a>
+<a name="121"><span class="lineNum">     121 </span>            :       }</a>
+<a name="122"><span class="lineNum">     122 </span>            :       // if there are no more files to read and this file is over then quit</a>
+<a name="123"><span class="lineNum">     123 </span>            :       if(fileisover &amp;&amp; !morefiles) {break;}</a>
+<a name="124"><span class="lineNum">     124 </span>            :       // if you are in the middle of a file and you are here</a>
+<a name="125"><span class="lineNum">     125 </span>            :       // then means that you read what you need to read</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 :       if(!fileisover ) {break;}</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     }</a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         15 :   return morefiles;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 : void FilesHandler::getMinMaxBin(std::vector&lt;Value*&gt; vals, Communicator &amp;cc, std::vector&lt;double&gt; &amp;vmin, std::vector&lt;double&gt; &amp;vmax, std::vector&lt;unsigned&gt; &amp;vbin) {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // create the representation (no grid)</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   BiasRepresentation br(vals,cc);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   // read all the kernels</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   readBunch(&amp;br);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   // loop over the kernels and get the support</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   br.getMinMaxBin(vmin,vmax,vbin);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 : void FilesHandler::getMinMaxBin(std::vector&lt;Value*&gt; vals, Communicator &amp;cc, std::vector&lt;double&gt; &amp;vmin, std::vector&lt;double&gt; &amp;vmax, std::vector&lt;unsigned&gt; &amp;vbin, const std::vector&lt;double&gt; &amp;histosigma) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :   BiasRepresentation br(vals,cc,histosigma);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   // read all the kernels</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   readBunch(&amp;br);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   // loop over the kernels and get the support</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :   br.getMinMaxBin(vmin,vmax,vbin);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   //for(unsigned i=0;i&lt;vals.size();i++){cerr&lt;&lt;&quot;XXX &quot;&lt;&lt;vmin[i]&lt;&lt;&quot; &quot;&lt;&lt;vmax[i]&lt;&lt;&quot; &quot;&lt;&lt;vbin[i]&lt;&lt;&quot;\n&quot;;}</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       5578 : bool FilesHandler::scanOneHill(BiasRepresentation *br, IFile *ifile ) {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   double dummy;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      11156 :   if(ifile-&gt;scanField(&quot;time&quot;,dummy)) {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     //(*log)&lt;&lt;&quot;   scanning one hill: &quot;&lt;&lt;dummy&lt;&lt;&quot; \n&quot;;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      16689 :     if(ifile-&gt;FieldExist(&quot;biasf&quot;)) ifile-&gt;scanField(&quot;biasf&quot;,dummy);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      11126 :     if(ifile-&gt;FieldExist(&quot;clock&quot;)) ifile-&gt;scanField(&quot;clock&quot;,dummy);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     // keep this intermediate function in case you need to parse more data in the future</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       5563 :     br-&gt;pushKernel(ifile);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     //(*log)&lt;&lt;&quot;  read hill\n&quot;;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       5563 :     if(br-&gt;hasSigmaInInput())ifile-&gt;allowIgnoredFields();</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       5563 :     ifile-&gt;scanField();</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       5563 :     return true;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   } else {</a>
+<a name="160"><span class="lineNum">     160 </span>            :     return false;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            : }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        900 : double  mylog( double v1 ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        900 :   return std::log(v1);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1800 : double  mylogder( double v1 ) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       1800 :   return 1./v1;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : class FuncSumHills :</a>
+<a name="176"><span class="lineNum">     176 </span>            :   public Function</a>
+<a name="177"><span class="lineNum">     177 </span>            : {</a>
+<a name="178"><span class="lineNum">     178 </span>            :   std::vector&lt;std::string&gt; hillsFiles,histoFiles;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   std::vector&lt;std::string&gt; proj;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   int initstride;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   bool iscltool,integratehills,integratehisto,parallelread;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   bool negativebias;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   bool nohistory;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   bool minTOzero;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   bool doInt;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   double lowI_;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   double uppI_;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   double beta;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::string outhills,outhisto,fmt;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   std::unique_ptr&lt;BiasRepresentation&gt; biasrep;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   std::unique_ptr&lt;BiasRepresentation&gt; historep;</a>
+<a name="192"><span class="lineNum">     192 </span>            : public:</a>
+<a name="193"><span class="lineNum">     193 </span>            :   explicit FuncSumHills(const ActionOptions&amp;);</a>
+<a name="194"><span class="lineNum">     194 </span>            :   void calculate() override; // this probably is not needed</a>
+<a name="195"><span class="lineNum">     195 </span>            :   bool checkFilesAreExisting(const std::vector&lt;std::string&gt; &amp; hills );</a>
+<a name="196"><span class="lineNum">     196 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="197"><span class="lineNum">     197 </span>            : };</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(FuncSumHills,&quot;FUNCSUMHILLS&quot;)</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         11 : void FuncSumHills::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         11 :   Function::registerKeywords(keys);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         11 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;HILLSFILES&quot;,&quot; source file for hills creation(may be the same as HILLS)&quot;); // this can be a vector!</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;HISTOFILES&quot;,&quot; source file for histogram creation(may be the same as HILLS)&quot;); // also this can be a vector!</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;HISTOSIGMA&quot;,&quot; sigmas for binning when the histogram correction is needed    &quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;PROJ&quot;,&quot; only with sumhills: the projection on the CVs&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;KT&quot;,&quot; only with sumhills: the kt factor when projection on CVs&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;GRID_MIN&quot;,&quot;the lower bounds for the grid&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;GRID_MAX&quot;,&quot;the upper bounds for the grid&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;GRID_BIN&quot;,&quot;the number of bins for the grid&quot;);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;GRID_SPACING&quot;,&quot;the approximate grid spacing (to be used as an alternative or together with GRID_BIN)&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;INTERVAL&quot;,&quot;set one dimensional INTERVAL&quot;);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;OUTHILLS&quot;,&quot; output file for hills &quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;OUTHISTO&quot;,&quot; output file for histogram &quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;INITSTRIDE&quot;,&quot; stride if you want an initial dump &quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;STRIDE&quot;,&quot; stride when you do it on the fly &quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         22 :   keys.addFlag(&quot;ISCLTOOL&quot;,false,&quot;use via plumed command line: calculate at read phase and then go&quot;);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         22 :   keys.addFlag(&quot;PARALLELREAD&quot;,false,&quot;read parallel HILLS file&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         22 :   keys.addFlag(&quot;NEGBIAS&quot;,false,&quot;dump  negative bias ( -bias )   instead of the free energy: needed in well tempered with flexible hills &quot;);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         22 :   keys.addFlag(&quot;NOHISTORY&quot;,false,&quot;to be used with INITSTRIDE:  it splits the bias/histogram in pieces without previous history  &quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         22 :   keys.addFlag(&quot;MINTOZERO&quot;,false,&quot;translate the resulting bias/histogram to have the minimum to zero  &quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format that should be used to output real numbers&quot;);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         11 : }</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          9 : FuncSumHills::FuncSumHills(const ActionOptions&amp;ao):</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   Action(ao),</a>
+<a name="228"><span class="lineNum">     228 </span>            :   Function(ao),</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          9 :   initstride(-1),</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          9 :   iscltool(false),</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          9 :   integratehills(false),</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          9 :   integratehisto(false),</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          9 :   parallelread(false),</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          9 :   negativebias(false),</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          9 :   nohistory(false),</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          9 :   minTOzero(false),</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          9 :   doInt(false),</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          9 :   lowI_(-1.),</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          9 :   uppI_(-1.),</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          9 :   beta(-1.),</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          9 :   fmt(&quot;%14.9f&quot;)</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : {</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            :   // format</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          9 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          9 :   log&lt;&lt;&quot;  Output format is &quot;&lt;&lt;fmt&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   // here read</a>
+<a name="248"><span class="lineNum">     248 </span>            :   // Grid Stuff</a>
+<a name="249"><span class="lineNum">     249 </span>            :   std::vector&lt;std::string&gt; gmin;</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         18 :   parseVector(&quot;GRID_MIN&quot;,gmin);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          9 :   if(gmin.size()!=getNumberOfArguments() &amp;&amp; gmin.size()!=0) error(&quot;not enough values for GRID_MIN&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          9 :   plumed_massert(gmin.size()==getNumberOfArguments() || gmin.size()==0,&quot;need GRID_MIN argument for this&quot;) ;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   std::vector&lt;std::string&gt; gmax;</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         18 :   parseVector(&quot;GRID_MAX&quot;,gmax);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          9 :   if(gmax.size()!=getNumberOfArguments() &amp;&amp; gmax.size()!=0) error(&quot;not enough values for GRID_MAX&quot;);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          9 :   plumed_massert(gmax.size()==getNumberOfArguments() || gmax.size()==0,&quot;need GRID_MAX argument for this&quot;) ;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   std::vector&lt;unsigned&gt; gbin;</a>
+<a name="258"><span class="lineNum">     258 </span>            :   std::vector&lt;double&gt;   gspacing;</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         18 :   parseVector(&quot;GRID_BIN&quot;,gbin);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          9 :   plumed_massert(gbin.size()==getNumberOfArguments() || gbin.size()==0,&quot;need GRID_BIN argument for this&quot;) ;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          9 :   if(gbin.size()!=getNumberOfArguments() &amp;&amp; gbin.size()!=0) error(&quot;not enough values for GRID_BIN&quot;);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         18 :   parseVector(&quot;GRID_SPACING&quot;,gspacing);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          9 :   plumed_massert(gspacing.size()==getNumberOfArguments() || gspacing.size()==0,&quot;need GRID_SPACING argument for this&quot;) ;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          9 :   if(gspacing.size()!=getNumberOfArguments() &amp;&amp; gspacing.size()!=0) error(&quot;not enough values for GRID_SPACING&quot;);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          9 :   if(gspacing.size()!=0 &amp;&amp; gbin.size()==0) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  The number of bins will be estimated from GRID_SPACING\n&quot;;</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          8 :   } else if(gspacing.size()!=0 &amp;&amp; gbin.size()!=0) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  You specified both GRID_BIN and GRID_SPACING\n&quot;;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  The more conservative (highest) number of bins will be used for each variable\n&quot;;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         10 :   if(gspacing.size()!=0) for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          1 :       if(gbin.size()==0) gbin.assign(getNumberOfArguments(),1);</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :       double a,b;</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          1 :       Tools::convert(gmin[i],a);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          1 :       Tools::convert(gmax[i],b);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          1 :       unsigned n=std::ceil((b-a)/gspacing[i]);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          1 :       if(gbin[i]&lt;n) gbin[i]=n;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     }</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :   // Inteval keyword</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          9 :   std::vector&lt;double&gt; tmpI(2);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         18 :   parseVector(&quot;INTERVAL&quot;,tmpI);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          9 :   if(tmpI.size()!=2&amp;&amp;tmpI.size()!=0) error(&quot;both a lower and an upper limits must be provided with INTERVAL&quot;);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          9 :   else if(tmpI.size()==2) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :     lowI_=tmpI.at(0);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :     uppI_=tmpI.at(1);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     if(getNumberOfArguments()!=1) error(&quot;INTERVAL limits correction works only for monodimensional metadynamics!&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :     if(uppI_&lt;lowI_) error(&quot;The Upper limit must be greater than the Lower limit!&quot;);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :     doInt=true;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          9 :   if(doInt) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;  Upper and Lower limits boundaries for the bias are activated at &quot; &lt;&lt; lowI_ &lt;&lt; &quot; - &quot; &lt;&lt; uppI_&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;  Using the same values as boundaries for the grid if not other value was defined (default: 200 bins)\n&quot;;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :     std::ostringstream strsmin, strsmax;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     strsmin &lt;&lt; lowI_;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     strsmax &lt;&lt; uppI_;</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :     if(gmin.size()==0) gmin.push_back(strsmin.str());</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :     if(gmax.size()==0) gmax.push_back(strsmax.str());</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :     if(gbin.size()==0) gbin.push_back(200);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            :   // hills file:</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         18 :   parseVector(&quot;HILLSFILES&quot;,hillsFiles);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          9 :   if(hillsFiles.size()==0) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          1 :     integratehills=false; // default behaviour</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   } else {</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          8 :     integratehills=true;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         17 :     for(unsigned i=0; i&lt;hillsFiles.size(); i++) log&lt;&lt;&quot;  hillsfile  : &quot;&lt;&lt;hillsFiles[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   }</a>
+<a name="311"><span class="lineNum">     311 </span>            :   // histo file:</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         18 :   parseVector(&quot;HISTOFILES&quot;,histoFiles);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          9 :   if(histoFiles.size()==0) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          8 :     integratehisto=false;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :   } else {</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          1 :     integratehisto=true;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          2 :     for(unsigned i=0; i&lt;histoFiles.size(); i++) log&lt;&lt;&quot;  histofile  : &quot;&lt;&lt;histoFiles[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   std::vector&lt;double&gt; histoSigma;</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          9 :   if(integratehisto) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          1 :     parseVector(&quot;HISTOSIGMA&quot;,histoSigma);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;histoSigma.size(); i++) log&lt;&lt;&quot;  histosigma  : &quot;&lt;&lt;histoSigma[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   }</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :   // needs a projection?</a>
+<a name="326"><span class="lineNum">     326 </span>            :   proj.clear();</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          9 :   parseVector(&quot;PROJ&quot;,proj);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          9 :   if(integratehills) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          8 :     plumed_massert(proj.size()&lt;getNumberOfArguments(),&quot; The number of projection must be less than the full list of arguments &quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :   }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          9 :   if(integratehisto) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          1 :     plumed_massert(proj.size()&lt;=getNumberOfArguments(),&quot; The number of projection must be less or equal to the full list of arguments &quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          9 :   if(integratehisto&amp;&amp;proj.size()==0) {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;getNumberOfArguments(); i++) proj.push_back(getPntrToArgument(i)-&gt;getName());</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            :   // add some automatic hills width: not in case stride is defined</a>
+<a name="339"><span class="lineNum">     339 </span>            :   // since when you start from zero the automatic size will be zero!</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          9 :   if(gmin.size()==0 || gmax.size()==0) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          5 :     log&lt;&lt;&quot;   \n&quot;;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          5 :     log&lt;&lt;&quot;  No boundaries defined: need to do a prescreening of hills \n&quot;;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :     std::vector&lt;Value*&gt; tmphillsvalues, tmphistovalues;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          5 :     if(integratehills) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         12 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++)tmphillsvalues.push_back( getPntrToArgument(i) );</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :     }</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          5 :     if(integratehisto) {</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          3 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          2 :         std::string ss = getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          6 :         for(unsigned j=0; j&lt;proj.size(); j++) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          4 :           if(proj[j]==ss) tmphistovalues.push_back( getPntrToArgument(i) );</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :         }</a>
+<a name="353"><span class="lineNum">     353 </span>            :       }</a>
+<a name="354"><span class="lineNum">     354 </span>            :     }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          5 :     if(integratehills) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          4 :       FilesHandler hillsHandler(hillsFiles,parallelread,*this, log);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :       std::vector&lt;double&gt; vmin,vmax;</a>
+<a name="359"><span class="lineNum">     359 </span>            :       std::vector&lt;unsigned&gt; vbin;</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          4 :       hillsHandler.getMinMaxBin(tmphillsvalues,comm,vmin,vmax,vbin);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          4 :       log&lt;&lt;&quot;  found boundaries from hillsfile: \n&quot;;</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          4 :       gmin.resize(vmin.size());</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          4 :       gmax.resize(vmax.size());</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          4 :       if(gbin.size()==0) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          3 :         gbin=vbin;</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :       } else {</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          1 :         log&lt;&lt;&quot;  found nbins in input, this overrides the automatic choice \n&quot;;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :       }</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         12 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          8 :         Tools::convert(vmin[i],gmin[i]);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">          8 :         Tools::convert(vmax[i],gmax[i]);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          8 :         log&lt;&lt;&quot;  variable &quot;&lt;&lt; getPntrToArgument(i)-&gt;getName()&lt;&lt;&quot; min: &quot;&lt;&lt;gmin[i]&lt;&lt;&quot; max: &quot;&lt;&lt;gmax[i]&lt;&lt;&quot; nbin: &quot;&lt;&lt;gbin[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :       }</a>
+<a name="374"><span class="lineNum">     374 </span>            :     }</a>
+<a name="375"><span class="lineNum">     375 </span>            :     // if at this stage bins are not there then do it with histo</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          5 :     if(gmin.size()==0) {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          1 :       FilesHandler histoHandler(histoFiles,parallelread,*this, log);</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :       std::vector&lt;double&gt; vmin,vmax;</a>
+<a name="379"><span class="lineNum">     379 </span>            :       std::vector&lt;unsigned&gt; vbin;</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">          1 :       histoHandler.getMinMaxBin(tmphistovalues,comm,vmin,vmax,vbin,histoSigma);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          1 :       log&lt;&lt;&quot;  found boundaries from histofile: \n&quot;;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          1 :       gmin.resize(vmin.size());</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          1 :       gmax.resize(vmax.size());</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          1 :       if(gbin.size()==0) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :         gbin=vbin;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :       } else {</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">          1 :         log&lt;&lt;&quot;  found nbins in input, this overrides the automatic choice \n&quot;;</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :       }</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">          3 :       for(unsigned i=0; i&lt;proj.size(); i++) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">          2 :         Tools::convert(vmin[i],gmin[i]);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          2 :         Tools::convert(vmax[i],gmax[i]);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          2 :         log&lt;&lt;&quot;  variable &quot;&lt;&lt; proj[i] &lt;&lt;&quot; min: &quot;&lt;&lt;gmin[i]&lt;&lt;&quot; max: &quot;&lt;&lt;gmax[i]&lt;&lt;&quot; nbin: &quot;&lt;&lt;gbin[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :       }</a>
+<a name="394"><span class="lineNum">     394 </span>            :     }</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          5 :     log&lt;&lt;&quot;  done!\n&quot;;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          5 :     log&lt;&lt;&quot;   \n&quot;;</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          9 :   if( proj.size() != 0 || integratehisto==true  ) {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          3 :     parse(&quot;KT&quot;,beta);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          7 :     for(unsigned i=0; i&lt;proj.size(); i++) log&lt;&lt;&quot;  projection &quot;&lt;&lt;i&lt;&lt;&quot; : &quot;&lt;&lt;proj[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :     // this should be only for projection or free energy from histograms</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          3 :     plumed_massert(beta&gt;0.,&quot;if you make a projection or a histogram correction then you need KT flag!&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          3 :     beta=1./beta;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          3 :     log&lt;&lt;&quot;  beta is &quot;&lt;&lt;beta&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :   }</a>
+<a name="408"><span class="lineNum">     408 </span>            :   // is a cltool: then you start and then die</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">          9 :   parseFlag(&quot;ISCLTOOL&quot;,iscltool);</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   //</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">          9 :   parseFlag(&quot;NEGBIAS&quot;,negativebias);</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :   //</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          9 :   parseFlag(&quot;PARALLELREAD&quot;,parallelread);</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :   // stride</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">          9 :   parse(&quot;INITSTRIDE&quot;,initstride);</span></a>
+<a name="416"><span class="lineNum">     416 </span>            :   // output suffix or names</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">          9 :   if(initstride&lt;0) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          8 :     log&lt;&lt;&quot;  Doing only one integration: no stride \n&quot;;</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :     outhills=&quot;fes.dat&quot;; outhisto=&quot;histo.dat&quot;;</a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span>            :   else {</a>
+<a name="422"><span class="lineNum">     422 </span>            :     outhills=&quot;fes_&quot;; outhisto=&quot;histo_&quot;;</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  Doing integration slices every &quot;&lt;&lt;initstride&lt;&lt;&quot; kernels\n&quot;;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          1 :     parseFlag(&quot;NOHISTORY&quot;,nohistory);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          1 :     if(nohistory)log&lt;&lt;&quot;  nohistory: each stride block has no memory of the previous block\n&quot;;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :   }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          9 :   parseFlag(&quot;MINTOZERO&quot;,minTOzero);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          9 :   if(minTOzero)log&lt;&lt;&quot;  mintozero: bias/histogram will be translated to have the minimum value equal to zero\n&quot;;</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :   //what might it be this?</a>
+<a name="430"><span class="lineNum">     430 </span>            :   // here start</a>
+<a name="431"><span class="lineNum">     431 </span>            :   // want something right now?? do it and return</a>
+<a name="432"><span class="lineNum">     432 </span>            :   // your argument is a set of cvs</a>
+<a name="433"><span class="lineNum">     433 </span>            :   // then you need: a hills / a colvar-like file (to do a histogram)</a>
+<a name="434"><span class="lineNum">     434 </span>            :   // create a bias representation for this</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          9 :   if(iscltool) {</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            :     std::vector&lt;Value*&gt; tmphillsvalues, tmphistovalues;</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          9 :     if(integratehills) {</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         23 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :         // allocate a new value from the old one: no deriv here</a>
+<a name="441"><span class="lineNum">     441 </span>            :         // if we are summing hills then all the arguments are needed</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         15 :         tmphillsvalues.push_back( getPntrToArgument(i) );</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :       }</a>
+<a name="444"><span class="lineNum">     444 </span>            :     }</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          9 :     if(integratehisto) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          3 :       for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          2 :         std::string ss = getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          6 :         for(unsigned j=0; j&lt;proj.size(); j++) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          4 :           if(proj[j]==ss) tmphistovalues.push_back( getPntrToArgument(i) );</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :         }</a>
+<a name="451"><span class="lineNum">     451 </span>            :       }</a>
+<a name="452"><span class="lineNum">     452 </span>            :     }</a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span>            :     // check if the files exists</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          9 :     if(integratehills) {</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          8 :       checkFilesAreExisting(hillsFiles);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         16 :       biasrep=Tools::make_unique&lt;BiasRepresentation&gt;(tmphillsvalues,comm, gmin, gmax, gbin, doInt, lowI_, uppI_);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          8 :       if(negativebias) {</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          1 :         biasrep-&gt;setRescaledToBias(true);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          1 :         log&lt;&lt;&quot;  required the -bias instead of the free energy \n&quot;;</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          1 :         if(initstride&lt;0) {outhills=&quot;negativebias.dat&quot;;}</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :         else {outhills=&quot;negativebias_&quot;;}</a>
+<a name="463"><span class="lineNum">     463 </span>            :       }</a>
+<a name="464"><span class="lineNum">     464 </span>            :     }</a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          9 :     parse(&quot;OUTHILLS&quot;,outhills);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          9 :     parse(&quot;OUTHISTO&quot;,outhisto);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          9 :     if(integratehills)log&lt;&lt;&quot;  output file for fes/bias  is :  &quot;&lt;&lt;outhills&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          9 :     if(integratehisto)log&lt;&lt;&quot;  output file for histogram is :  &quot;&lt;&lt;outhisto&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          9 :     checkRead();</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          9 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          9 :     log&lt;&lt;&quot;  Now calculating...\n&quot;;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          9 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            :     // here it defines the column to be histogrammed, tmpvalues should be only</a>
+<a name="477"><span class="lineNum">     477 </span>            :     // the list of the collective variable one want to consider</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          9 :     if(integratehisto) {</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          1 :       checkFilesAreExisting(histoFiles);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          2 :       historep=Tools::make_unique&lt;BiasRepresentation&gt;(tmphistovalues,comm,gmin,gmax,gbin,histoSigma);</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :     }</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            :     // decide how to source hills ( serial/parallel )</a>
+<a name="484"><span class="lineNum">     484 </span>            :     // here below the input control</a>
+<a name="485"><span class="lineNum">     485 </span>            :     // say how many hills and it will read them from the</a>
+<a name="486"><span class="lineNum">     486 </span>            :     // bunch of files provided, will update the representation</a>
+<a name="487"><span class="lineNum">     487 </span>            :     // of hills (i.e. a list of hills and the associated grid)</a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span>            :     // decide how to source colvars ( serial parallel )</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          9 :     std::unique_ptr&lt;FilesHandler&gt; hillsHandler;</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          9 :     std::unique_ptr&lt;FilesHandler&gt; histoHandler;</span></a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         17 :     if(integratehills)  hillsHandler=Tools::make_unique&lt;FilesHandler&gt;(hillsFiles,parallelread,*this, log);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         10 :     if(integratehisto)  histoHandler=Tools::make_unique&lt;FilesHandler&gt;(histoFiles,parallelread,*this, log);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            : // Stopwatch is logged when it goes out of scope</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          9 :     Stopwatch sw(log);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            : // Stopwatch is stopped when swh goes out of scope</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          9 :     auto swh=sw.startStop(&quot;0 Summing hills&quot;);</span></a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            :     // read a number of hills and put in the bias representation</a>
+<a name="503"><span class="lineNum">     503 </span>            :     int nfiles=0;</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          9 :     bool ibias=integratehills; bool ihisto=integratehisto;</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     while(true) {</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         10 :       if(  integratehills  &amp;&amp; ibias  ) {</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          9 :         if(nohistory) {biasrep-&gt;clear(); log&lt;&lt;&quot;  clearing history before reading a new block\n&quot;;};</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">          9 :         log&lt;&lt;&quot;  reading hills: \n&quot;;</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          9 :         ibias=hillsHandler-&gt;readBunch(biasrep.get(),initstride) ; log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :       }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         10 :       if(  integratehisto  &amp;&amp; ihisto ) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          1 :         if(nohistory) {historep-&gt;clear(); log&lt;&lt;&quot;  clearing history before reading a new block\n&quot;;};</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          1 :         log&lt;&lt;&quot;  reading histogram: \n&quot;;</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">          1 :         ihisto=histoHandler-&gt;readBunch(historep.get(),initstride) ;  log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :       }</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            :       // dump: need to project?</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         10 :       if(proj.size()!=0) {</span></a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">          4 :         if(integratehills) {</span></a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">          3 :           log&lt;&lt;&quot;  Bias: Projecting on subgrid... \n&quot;;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          3 :           BiasWeight Bw(beta);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          3 :           Grid biasGrid=*(biasrep-&gt;getGridPtr());</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">          3 :           Grid smallGrid=biasGrid.project(proj,&amp;Bw);</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">          3 :           OFile gridfile; gridfile.link(*this);</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">          3 :           std::ostringstream ostr; ostr&lt;&lt;nfiles;</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :           std::string myout;</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          7 :           if(initstride&gt;0) { myout=outhills+ostr.str()+&quot;.dat&quot; ;} else {myout=outhills;}</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">          3 :           log&lt;&lt;&quot;  Bias: Writing subgrid on file &quot;&lt;&lt;myout&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">          3 :           gridfile.open(myout);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">          3 :           if(minTOzero) smallGrid.setMinToZero();</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :           smallGrid.setOutputFmt(fmt);</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">          3 :           smallGrid.writeToFile(gridfile);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          3 :           gridfile.close();</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          3 :           if(!ibias)integratehills=false;// once you get to the final bunch just give up</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          3 :         }</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :         // this should be removed</a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">          4 :         if(integratehisto) {</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">          1 :           log&lt;&lt;&quot;  Histo: Projecting on subgrid... \n&quot;;</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">          1 :           Grid histoGrid=*(historep-&gt;getGridPtr());</span></a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">          1 :           OFile gridfile; gridfile.link(*this);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">          1 :           std::ostringstream ostr; ostr&lt;&lt;nfiles;</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :           std::string myout;</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">          1 :           if(initstride&gt;0) { myout=outhisto+ostr.str()+&quot;.dat&quot; ;} else {myout=outhisto;}</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">          1 :           log&lt;&lt;&quot;  Histo: Writing subgrid on file &quot;&lt;&lt;myout&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">          1 :           gridfile.open(myout);</span></a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          1 :           histoGrid.applyFunctionAllValuesAndDerivatives(&amp;mylog,&amp;mylogder);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          1 :           histoGrid.scaleAllValuesAndDerivatives(-1./beta);</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">          1 :           if(minTOzero) histoGrid.setMinToZero();</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :           histoGrid.setOutputFmt(fmt);</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">          1 :           histoGrid.writeToFile(gridfile);</span></a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">          1 :           if(!ihisto)integratehisto=false;// once you get to the final bunch just give up</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">          1 :         }</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            :       } else {</a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">          6 :         if(integratehills) {</span></a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          6 :           Grid biasGrid=*(biasrep-&gt;getGridPtr());</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">          6 :           biasGrid.scaleAllValuesAndDerivatives(-1.);</span></a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">          6 :           OFile gridfile; gridfile.link(*this);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          6 :           std::ostringstream ostr; ostr&lt;&lt;nfiles;</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :           std::string myout;</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">          6 :           if(initstride&gt;0) { myout=outhills+ostr.str()+&quot;.dat&quot; ;} else {myout=outhills;}</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">          6 :           log&lt;&lt;&quot;  Writing full grid on file &quot;&lt;&lt;myout&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">          6 :           gridfile.open(myout);</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">          6 :           if(minTOzero) biasGrid.setMinToZero();</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :           biasGrid.setOutputFmt(fmt);</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">          6 :           biasGrid.writeToFile(gridfile);</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :           // rescale back prior to accumulate</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          6 :           if(!ibias)integratehills=false;// once you get to the final bunch just give up</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">          6 :         }</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">          6 :         if(integratehisto) {</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :           Grid histoGrid=*(historep-&gt;getGridPtr());</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :           // do this if you want a free energy from a grid, otherwise do not</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineNoCov">          0 :           histoGrid.applyFunctionAllValuesAndDerivatives(&amp;mylog,&amp;mylogder);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 :           histoGrid.scaleAllValuesAndDerivatives(-1./beta);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :           OFile gridfile; gridfile.link(*this);</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :           std::ostringstream ostr; ostr&lt;&lt;nfiles;</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :           std::string myout;</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :           if(initstride&gt;0) { myout=outhisto+ostr.str()+&quot;.dat&quot; ;} else {myout=outhisto;}</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineNoCov">          0 :           log&lt;&lt;&quot;  Writing full grid on file &quot;&lt;&lt;myout&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 :           gridfile.open(myout);</span></a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span>            :           // also this is useful only for free energy</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :           if(minTOzero) histoGrid.setMinToZero();</span></a>
+<a name="597"><span class="lineNum">     597 </span>            :           histoGrid.setOutputFmt(fmt);</a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :           histoGrid.writeToFile(gridfile);</span></a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :           if(!ihisto)integratehisto=false; // once you get to the final bunch just give up</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :         }</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :       }</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         10 :       if ( !ibias &amp;&amp; !ihisto) break; //when both are over then just quit</span></a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">          1 :       nfiles++;</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">          1 :     }</span></a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span>            :     return;</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">          9 :   }</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :   // just an initialization but you need to do something on the fly?: need to connect with a metad run and its grid representation</a>
+<a name="611"><span class="lineNum">     611 </span>            :   // your argument is a metad run</a>
+<a name="612"><span class="lineNum">     612 </span>            :   // if the grid does not exist crash and say that you need some data</a>
+<a name="613"><span class="lineNum">     613 </span>            :   // otherwise just link with it</a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">          9 : }</span></a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 : void FuncSumHills::calculate() {</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :   // this should be connected only with a grid representation to metadynamics</a>
+<a name="619"><span class="lineNum">     619 </span>            :   // at regular time just dump it</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;You should have never got here: this stuff is not yet implemented!&quot;);</span></a>
+<a name="621"><span class="lineNum">     621 </span>            : }</a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">          9 : bool FuncSumHills::checkFilesAreExisting(const std::vector&lt;std::string&gt; &amp; hills ) {</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">          9 :   plumed_massert(hills.size()!=0,&quot;the number of  files provided should be at least one&quot; );</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">          9 :   auto ifile=Tools::make_unique&lt;IFile&gt;();</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">          9 :   ifile-&gt;link(*this);</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         19 :   for(unsigned i=0; i&lt; hills.size(); i++) {</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         10 :     plumed_massert(ifile-&gt;FileExist(hills[i]),&quot;missing file &quot;+hills[i]);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :   }</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">          9 :   return true;</span></a>
+<a name="631"><span class="lineNum">     631 </span>            : </a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">          9 : }</span></a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            : }</a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span>            : }</a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Function.cpp.func-sort-c.html b/coverage/function/Function.cpp.func-sort-c.html
new file mode 100644
index 0000000000..63756dc207
--- /dev/null
+++ b/coverage/function/Function.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Function.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Function.cpp<span style="font-size: 80%;"> (<a href="Function.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">97.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Function.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#34">_ZN4PLMD8function8FunctionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#41">_ZN4PLMD8function8Function23addValueWithDerivativesEv</a></td>
+              <td class="coverFnHi">571</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#34">_ZN4PLMD8function8FunctionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">669</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#27">_ZN4PLMD8function8Function16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">699</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#57">_ZN4PLMD8function8Function27addComponentWithDerivativesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#63">_ZN4PLMD8function8Function5applyEv</a></td>
+              <td class="coverFnHi">225077</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Function.cpp.func.html b/coverage/function/Function.cpp.func.html
new file mode 100644
index 0000000000..10cfaf063b
--- /dev/null
+++ b/coverage/function/Function.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Function.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Function.cpp<span style="font-size: 80%;"> (<a href="Function.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">97.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Function.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#27">_ZN4PLMD8function8Function16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">699</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#41">_ZN4PLMD8function8Function23addValueWithDerivativesEv</a></td>
+              <td class="coverFnHi">571</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#57">_ZN4PLMD8function8Function27addComponentWithDerivativesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#63">_ZN4PLMD8function8Function5applyEv</a></td>
+              <td class="coverFnHi">225077</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#34">_ZN4PLMD8function8FunctionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.cpp.gcov.html#34">_ZN4PLMD8function8FunctionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">669</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Function.cpp.gcov.html b/coverage/function/Function.cpp.gcov.html
new file mode 100644
index 0000000000..5140256f2e
--- /dev/null
+++ b/coverage/function/Function.cpp.gcov.html
@@ -0,0 +1,178 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Function.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Function.cpp<span style="font-size: 80%;"> (source / <a href="Function.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">97.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Function.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace function {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        699 : void Function::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        699 :   Action::registerKeywords(keys);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        699 :   ActionWithValue::registerKeywords(keys);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        699 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       1398 :   keys.reserve(&quot;compulsory&quot;,&quot;PERIODIC&quot;,&quot;if the output of your function is periodic then you should specify the periodicity of the function.  If the output is not periodic you must state this using PERIODIC=NO&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        699 : }</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        669 : Function::Function(const ActionOptions&amp;ao):</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   Action(ao),</a>
+<a name="38"><span class="lineNum">      38 </span>            :   ActionWithValue(ao),</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        669 :   ActionWithArguments(ao)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        669 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        571 : void Function::addValueWithDerivatives() {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        571 :   plumed_massert( getNumberOfArguments()!=0, &quot;for functions you must requestArguments before adding values&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        571 :   ActionWithValue::addValueWithDerivatives();</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        571 :   getPntrToValue()-&gt;resizeDerivatives(getNumberOfArguments());</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1142 :   if( keywords.exists(&quot;PERIODIC&quot;) ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :     std::vector&lt;std::string&gt; period;</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1136 :     parseVector(&quot;PERIODIC&quot;,period);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1133 :     if(period.size()==1 &amp;&amp; period[0]==&quot;NO&quot;) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        565 :       setNotPeriodic();</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          3 :     } else if(period.size()==2) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 :       setPeriodic(period[0],period[1]);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :     } else error(&quot;missing PERIODIC keyword&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        568 :   }</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        571 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       3173 : void Function::addComponentWithDerivatives( const std::string&amp; name ) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       3173 :   plumed_massert( getNumberOfArguments()!=0, &quot;for functions you must requestArguments before adding values&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       3173 :   ActionWithValue::addComponentWithDerivatives(name);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       3173 :   getPntrToComponent(name)-&gt;resizeDerivatives(getNumberOfArguments());</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       3173 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     225077 : void Function::apply()</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     225077 :   const unsigned noa=getNumberOfArguments();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     225077 :   const unsigned ncp=getNumberOfComponents();</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     225077 :   const unsigned cgs=comm.Get_size();</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     225077 :   std::vector&lt;double&gt; f(noa,0.0);</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   unsigned stride=1;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   unsigned rank=0;</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     225077 :   if(ncp&gt;4*cgs) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 :     stride=comm.Get_size();</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          6 :     rank=comm.Get_rank();</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     225077 :   unsigned at_least_one_forced=0;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     225077 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(f)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   {</a>
+<a name="83"><span class="lineNum">      83 </span>            :     std::vector&lt;double&gt; omp_f(noa,0.0);</a>
+<a name="84"><span class="lineNum">      84 </span>            :     std::vector&lt;double&gt; forces(noa);</a>
+<a name="85"><span class="lineNum">      85 </span>            :     #pragma omp for reduction( + : at_least_one_forced)</a>
+<a name="86"><span class="lineNum">      86 </span>            :     for(unsigned i=rank; i&lt;ncp; i+=stride) {</a>
+<a name="87"><span class="lineNum">      87 </span>            :       if(getPntrToComponent(i)-&gt;applyForce(forces)) {</a>
+<a name="88"><span class="lineNum">      88 </span>            :         at_least_one_forced+=1;</a>
+<a name="89"><span class="lineNum">      89 </span>            :         for(unsigned j=0; j&lt;noa; j++) omp_f[j]+=forces[j];</a>
+<a name="90"><span class="lineNum">      90 </span>            :       }</a>
+<a name="91"><span class="lineNum">      91 </span>            :     }</a>
+<a name="92"><span class="lineNum">      92 </span>            :     #pragma omp critical</a>
+<a name="93"><span class="lineNum">      93 </span>            :     for(unsigned j=0; j&lt;noa; j++) f[j]+=omp_f[j];</a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     225077 :   if(noa&gt;0&amp;&amp;ncp&gt;4*cgs) { comm.Sum(&amp;f[0],noa); comm.Sum(at_least_one_forced); }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     290939 :   if(at_least_one_forced&gt;0) for(unsigned i=0; i&lt;noa; ++i) getPntrToArgument(i)-&gt;addForce(f[i]);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     225077 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Function.h.func-sort-c.html b/coverage/function/Function.h.func-sort-c.html
new file mode 100644
index 0000000000..f0cf362bbb
--- /dev/null
+++ b/coverage/function/Function.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Function.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Function.h<span style="font-size: 80%;"> (<a href="Function.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Function.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.h.gcov.html#46">_ZN4PLMD8function8FunctionD2Ev</a></td>
+              <td class="coverFnHi">669</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.h.gcov.html#58">_ZN4PLMD8function8Function13setDerivativeEid</a></td>
+              <td class="coverFnHi">52179</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.h.gcov.html#63">_ZN4PLMD8function8Function22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">3471295</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Function.h.func.html b/coverage/function/Function.h.func.html
new file mode 100644
index 0000000000..d8830cc09c
--- /dev/null
+++ b/coverage/function/Function.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Function.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Function.h<span style="font-size: 80%;"> (<a href="Function.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Function.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.h.gcov.html#58">_ZN4PLMD8function8Function13setDerivativeEid</a></td>
+              <td class="coverFnHi">52179</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.h.gcov.html#63">_ZN4PLMD8function8Function22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">3471295</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Function.h.gcov.html#46">_ZN4PLMD8function8FunctionD2Ev</a></td>
+              <td class="coverFnHi">669</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Function.h.gcov.html b/coverage/function/Function.h.gcov.html
new file mode 100644
index 0000000000..edc460729f
--- /dev/null
+++ b/coverage/function/Function.h.gcov.html
@@ -0,0 +1,149 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Function.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Function.h<span style="font-size: 80%;"> (source / <a href="Function.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_function_Function_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_function_Function_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace function {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /**</a>
+<a name="32"><span class="lineNum">      32 </span>            : \ingroup INHERIT</a>
+<a name="33"><span class="lineNum">      33 </span>            : This is the abstract base class to use for implementing new CV function, within it there is</a>
+<a name="34"><span class="lineNum">      34 </span>            : \ref AddingAFunction &quot;information&quot; as to how to go about implementing a new function.</a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class Function:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   public ActionWithValue,</a>
+<a name="39"><span class="lineNum">      39 </span>            :   public ActionWithArguments</a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span>            : protected:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   void setDerivative(int,double);</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void setDerivative(Value*,int,double);</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void addValueWithDerivatives();</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void addComponentWithDerivatives( const std::string&amp; name );</a>
+<a name="46"><span class="lineNum">      46 </span>            : public:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit Function(const ActionOptions&amp;);</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        669 :   virtual ~Function() {}</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   void apply() override;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="51"><span class="lineNum">      51 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="52"><span class="lineNum">      52 </span>            : };</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : inline</a>
+<a name="55"><span class="lineNum">      55 </span>            : void Function::setDerivative(Value*v,int i,double d) {</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      55089 :   v-&gt;addDerivative(i,d);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : inline</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      52179 : void Function::setDerivative(int i,double d) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      52179 :   setDerivative(getPntrToValue(),i,d);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      52179 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : inline</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">    3471295 : unsigned Function::getNumberOfDerivatives() {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">    3471295 :   return getNumberOfArguments();</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : #endif</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/LocalEnsemble.cpp.func-sort-c.html b/coverage/function/LocalEnsemble.cpp.func-sort-c.html
new file mode 100644
index 0000000000..29055ab7e7
--- /dev/null
+++ b/coverage/function/LocalEnsemble.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/LocalEnsemble.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - LocalEnsemble.cpp<span style="font-size: 80%;"> (<a href="LocalEnsemble.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LocalEnsemble.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#95">_ZN4PLMD8function13LocalEnsembleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#86">_ZN4PLMD8function12_GLOBAL__N_125LocalEnsembleRegisterMe886createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#95">_ZN4PLMD8function13LocalEnsembleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#88">_ZN4PLMD8function13LocalEnsemble16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#130">_ZN4PLMD8function13LocalEnsemble9calculateEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#86">_ZN4PLMD8function12_GLOBAL__N_125LocalEnsembleRegisterMe88C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#86">_ZN4PLMD8function12_GLOBAL__N_125LocalEnsembleRegisterMe88D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/LocalEnsemble.cpp.func.html b/coverage/function/LocalEnsemble.cpp.func.html
new file mode 100644
index 0000000000..968c45886a
--- /dev/null
+++ b/coverage/function/LocalEnsemble.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/LocalEnsemble.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - LocalEnsemble.cpp<span style="font-size: 80%;"> (<a href="LocalEnsemble.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LocalEnsemble.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#86">_ZN4PLMD8function12_GLOBAL__N_125LocalEnsembleRegisterMe886createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#86">_ZN4PLMD8function12_GLOBAL__N_125LocalEnsembleRegisterMe88C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#86">_ZN4PLMD8function12_GLOBAL__N_125LocalEnsembleRegisterMe88D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#88">_ZN4PLMD8function13LocalEnsemble16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#130">_ZN4PLMD8function13LocalEnsemble9calculateEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#95">_ZN4PLMD8function13LocalEnsembleC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalEnsemble.cpp.gcov.html#95">_ZN4PLMD8function13LocalEnsembleC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/LocalEnsemble.cpp.gcov.html b/coverage/function/LocalEnsemble.cpp.gcov.html
new file mode 100644
index 0000000000..0af5569159
--- /dev/null
+++ b/coverage/function/LocalEnsemble.cpp.gcov.html
@@ -0,0 +1,227 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/LocalEnsemble.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - LocalEnsemble.cpp<span style="font-size: 80%;"> (source / <a href="LocalEnsemble.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Function.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace function {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC FUNCTION LOCALENSEMBLE</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculates the average over multiple arguments.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : If more than one collective variable is given for each argument then they</a>
+<a name="34"><span class="lineNum">      34 </span>            : are averaged separately. The average is stored in a component labelled &lt;em&gt;label&lt;/em&gt;.cvlabel.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The following input tells plumed to calculate the chemical shifts for four</a>
+<a name="39"><span class="lineNum">      39 </span>            : different proteins in the same simulation box then average them, calculated</a>
+<a name="40"><span class="lineNum">      40 </span>            : the sum of the squared deviation with respect to the experimental values and</a>
+<a name="41"><span class="lineNum">      41 </span>            : applies a linear restraint.</a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : MOLINFO STRUCTURE=data/template.pdb</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : chaina: GROUP ATOMS=1-1640</a>
+<a name="46"><span class="lineNum">      46 </span>            : chainb: GROUP ATOMS=1641-3280</a>
+<a name="47"><span class="lineNum">      47 </span>            : chainc: GROUP ATOMS=3281-4920</a>
+<a name="48"><span class="lineNum">      48 </span>            : chaind: GROUP ATOMS=4921-6560</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : WHOLEMOLECULES ENTITY0=chaina ENTITY1=chainb ENTITY2=chainc ENTITY3=chaind</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : csa: CS2BACKBONE ATOMS=chaina NRES=100 DATA=data/ TEMPLATE=chaina.pdb NOPBC</a>
+<a name="53"><span class="lineNum">      53 </span>            : csb: CS2BACKBONE ATOMS=chainb NRES=100 DATA=data/ TEMPLATE=chainb.pdb NOPBC</a>
+<a name="54"><span class="lineNum">      54 </span>            : csc: CS2BACKBONE ATOMS=chainc NRES=100 DATA=data/ TEMPLATE=chainc.pdb NOPBC</a>
+<a name="55"><span class="lineNum">      55 </span>            : csd: CS2BACKBONE ATOMS=chaind NRES=100 DATA=data/ TEMPLATE=chaind.pdb NOPBC</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : ensca: LOCALENSEMBLE NUM=4 ARG1=(csa\.ca_.*) ARG2=(csb\.ca_.*) ARG3=(csc\.ca_.*) ARG4=(csd\.ca_.*)</a>
+<a name="58"><span class="lineNum">      58 </span>            : enscb: LOCALENSEMBLE NUM=4 ARG1=(csa\.cb_.*) ARG2=(csb\.cb_.*) ARG3=(csc\.cb_.*) ARG4=(csd\.cb_.*)</a>
+<a name="59"><span class="lineNum">      59 </span>            : ensco: LOCALENSEMBLE NUM=4 ARG1=(csa\.co_.*) ARG2=(csb\.co_.*) ARG3=(csc\.co_.*) ARG4=(csd\.co_.*)</a>
+<a name="60"><span class="lineNum">      60 </span>            : enshn: LOCALENSEMBLE NUM=4 ARG1=(csa\.hn_.*) ARG2=(csb\.hn_.*) ARG3=(csc\.hn_.*) ARG4=(csd\.hn_.*)</a>
+<a name="61"><span class="lineNum">      61 </span>            : ensnh: LOCALENSEMBLE NUM=4 ARG1=(csa\.nh_.*) ARG2=(csb\.nh_.*) ARG3=(csc\.nh_.*) ARG4=(csd\.nh_.*)</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : stca: STATS ARG=(ensca\.csa\.ca_.*) PARARG=(csa\.expca_.*) SQDEVSUM</a>
+<a name="64"><span class="lineNum">      64 </span>            : stcb: STATS ARG=(enscb\.csa\.cb_.*) PARARG=(csa\.expcb_.*) SQDEVSUM</a>
+<a name="65"><span class="lineNum">      65 </span>            : stco: STATS ARG=(ensco\.csa\.co_.*) PARARG=(csa\.expco_.*) SQDEVSUM</a>
+<a name="66"><span class="lineNum">      66 </span>            : sthn: STATS ARG=(enshn\.csa\.hn_.*) PARARG=(csa\.exphn_.*) SQDEVSUM</a>
+<a name="67"><span class="lineNum">      67 </span>            : stnh: STATS ARG=(ensnh\.csa\.nh_.*) PARARG=(csa\.expnh_.*) SQDEVSUM</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : res: RESTRAINT ARG=stca.*,stcb.*,stco.*,sthn.*,stnh.* AT=0.,0.,0.,0.,0. KAPPA=0.,0.,0.,0.,0 SLOPE=16.,16.,12.,24.,0.5</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : class LocalEnsemble :</a>
+<a name="77"><span class="lineNum">      77 </span>            :   public Function</a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span>            :   unsigned ens_dim;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   unsigned narg;</a>
+<a name="81"><span class="lineNum">      81 </span>            : public:</a>
+<a name="82"><span class="lineNum">      82 </span>            :   explicit LocalEnsemble(const ActionOptions&amp;);</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void     calculate() override;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(LocalEnsemble,&quot;LOCALENSEMBLE&quot;)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          4 : void LocalEnsemble::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          4 :   Function::registerKeywords(keys);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          4 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;NUM&quot;,&quot;the number of local replicas&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          4 :   useCustomisableComponents(keys);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 : LocalEnsemble::LocalEnsemble(const ActionOptions&amp;ao):</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   Action(ao),</a>
+<a name="99"><span class="lineNum">      99 </span>            :   Function(ao),</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   ens_dim(0)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          2 :   parse(&quot;NUM&quot;,ens_dim);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          2 :   if(ens_dim==0) error(&quot;NUM should be greater or equal to 1&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;Value*&gt; arg;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   int oldsize=-1;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          8 :   for(unsigned i=1; i&lt;=ens_dim; ++i ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :     std::vector&lt;Value*&gt; larg;</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         12 :     if(!parseArgumentList(&quot;ARG&quot;,i,larg)) break;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         18 :     for(unsigned j=0; j&lt;larg.size(); j++) arg.push_back(larg[j]);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          6 :     if(oldsize!=-1&amp;&amp;oldsize!=static_cast&lt;int&gt;(larg.size())) error(&quot;In LOCALENSEMBLE you should have the same number of arguments for each ARG keyword&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          6 :     oldsize = larg.size();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          6 :     if(!larg.empty()) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          6 :       log.printf(&quot;  with arguments %u: &quot;, i);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         18 :       for(unsigned j=0; j&lt;larg.size(); j++) log.printf(&quot; %s&quot;,larg[j]-&gt;getName().c_str());</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          6 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 :   requestArguments(arg);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   narg = arg.size()/ens_dim;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   // these are the averages</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;narg; i++) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          4 :     std::string s=getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          4 :     addComponentWithDerivatives(s);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          4 :     getPntrToComponent(i)-&gt;setNotPeriodic();</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :   log.printf(&quot;  averaging over %u replicas.\n&quot;, ens_dim);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         40 : void LocalEnsemble::calculate()</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         40 :   const double fact = 1.0/static_cast&lt;double&gt;(ens_dim);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         40 :   #pragma omp parallel for num_threads(OpenMP::getNumThreads())</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="137"><span class="lineNum">     137 </span>            :     double mean = 0.;</a>
+<a name="138"><span class="lineNum">     138 </span>            :     Value* v=getPntrToComponent(i);</a>
+<a name="139"><span class="lineNum">     139 </span>            :     for(unsigned j=0; j&lt;ens_dim; ++j) {</a>
+<a name="140"><span class="lineNum">     140 </span>            :       const unsigned index = j*narg+i;</a>
+<a name="141"><span class="lineNum">     141 </span>            :       setDerivative(v, index, fact);</a>
+<a name="142"><span class="lineNum">     142 </span>            :       mean += fact*getArgument(index);</a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            :     v-&gt;set(mean);</a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         40 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Piecewise.cpp.func-sort-c.html b/coverage/function/Piecewise.cpp.func-sort-c.html
new file mode 100644
index 0000000000..27addb88fe
--- /dev/null
+++ b/coverage/function/Piecewise.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Piecewise.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Piecewise.cpp<span style="font-size: 80%;"> (<a href="Piecewise.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Piecewise.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#91">_ZN4PLMD8function9PiecewiseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#77">_ZN4PLMD8function12_GLOBAL__N_121PiecewiseRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#91">_ZN4PLMD8function9PiecewiseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#79">_ZN4PLMD8function9Piecewise16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#123">_ZN4PLMD8function9Piecewise9calculateEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#77">_ZN4PLMD8function12_GLOBAL__N_121PiecewiseRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#77">_ZN4PLMD8function12_GLOBAL__N_121PiecewiseRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Piecewise.cpp.func.html b/coverage/function/Piecewise.cpp.func.html
new file mode 100644
index 0000000000..32da8e6530
--- /dev/null
+++ b/coverage/function/Piecewise.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Piecewise.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Piecewise.cpp<span style="font-size: 80%;"> (<a href="Piecewise.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Piecewise.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#77">_ZN4PLMD8function12_GLOBAL__N_121PiecewiseRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#77">_ZN4PLMD8function12_GLOBAL__N_121PiecewiseRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#77">_ZN4PLMD8function12_GLOBAL__N_121PiecewiseRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#79">_ZN4PLMD8function9Piecewise16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#123">_ZN4PLMD8function9Piecewise9calculateEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#91">_ZN4PLMD8function9PiecewiseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Piecewise.cpp.gcov.html#91">_ZN4PLMD8function9PiecewiseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Piecewise.cpp.gcov.html b/coverage/function/Piecewise.cpp.gcov.html
new file mode 100644
index 0000000000..7783bb8d28
--- /dev/null
+++ b/coverage/function/Piecewise.cpp.gcov.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Piecewise.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Piecewise.cpp<span style="font-size: 80%;"> (source / <a href="Piecewise.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Function.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace function {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC FUNCTION PIECEWISE</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Compute a piece wise straight line through its arguments that passes through a set of ordered control points.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : For variables less than the first</a>
+<a name="33"><span class="lineNum">      33 </span>            : (greater than the last) point, the value of the first (last) point is used.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \f[</a>
+<a name="36"><span class="lineNum">      36 </span>            : \frac{y_{i+1}-y_i}{x_{i+1}-x_i}(s-x_i)+y_i ;  if x_i&lt;s&lt;x_{i+1}</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f]</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : y_N ; if x&gt;x_{N-1}</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f]</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : y_1 ; if x&lt;x_0</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Control points are passed using the POINT0=... POINT1=... syntax as in the example below</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : If one argument is supplied, it results in a scalar quantity.</a>
+<a name="48"><span class="lineNum">      48 </span>            : If multiple arguments are supplied, it results</a>
+<a name="49"><span class="lineNum">      49 </span>            : in a vector of values. Each value will be named as the name of the original</a>
+<a name="50"><span class="lineNum">      50 </span>            : argument with suffix _pfunc.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : dist1: DISTANCE ATOMS=1,10</a>
+<a name="56"><span class="lineNum">      56 </span>            : dist2: DISTANCE ATOMS=2,11</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : pw: PIECEWISE POINT0=1,10 POINT1=2,PI POINT2=3,10 ARG=dist1</a>
+<a name="59"><span class="lineNum">      59 </span>            : ppww: PIECEWISE POINT0=1,10 POINT1=2,PI POINT2=3,10 ARG=dist1,dist2</a>
+<a name="60"><span class="lineNum">      60 </span>            : PRINT ARG=pw,ppww.dist1_pfunc,ppww.dist2_pfunc</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : */</a>
+<a name="65"><span class="lineNum">      65 </span>            : //+ENDPLUMEDOC</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class Piecewise :</a>
+<a name="69"><span class="lineNum">      69 </span>            :   public Function</a>
+<a name="70"><span class="lineNum">      70 </span>            : {</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;std::pair&lt;double,double&gt; &gt; points;</a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   explicit Piecewise(const ActionOptions&amp;);</a>
+<a name="74"><span class="lineNum">      74 </span>            :   void calculate() override;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="76"><span class="lineNum">      76 </span>            : };</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      12509 : PLUMED_REGISTER_ACTION(Piecewise,&quot;PIECEWISE&quot;)</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          5 : void Piecewise::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          5 :   Function::registerKeywords(keys);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          5 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         10 :   keys.add(&quot;numbered&quot;,&quot;POINT&quot;,&quot;This keyword is used to specify the various points in the function above.&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         10 :   keys.reset_style(&quot;POINT&quot;,&quot;compulsory&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          5 :   componentsAreNotOptional(keys);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         10 :   keys.addOutputComponent(&quot;_pfunc&quot;,&quot;default&quot;,&quot;one or multiple instances of this quantity can be referenced elsewhere &quot;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :                           &quot;in the input file.  These quantities will be named with the arguments of the &quot;</a>
+<a name="89"><span class="lineNum">      89 </span>            :                           &quot;function followed by the character string _pfunc.  These quantities tell the &quot;</a>
+<a name="90"><span class="lineNum">      90 </span>            :                           &quot;user the values of the piece wise functions of each of the arguments.&quot;);</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          5 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          3 : Piecewise::Piecewise(const ActionOptions&amp;ao):</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   Action(ao),</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          3 :   Function(ao)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          9 :   for(int i=0;; i++) {</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :     std::vector&lt;double&gt; pp;</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         24 :     if(!parseNumberedVector(&quot;POINT&quot;,i,pp) ) break;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          9 :     if(pp.size()!=2) error(&quot;points should be in x,y format&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          9 :     points.push_back(std::pair&lt;double,double&gt;(pp[0],pp[1]));</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          9 :     if(i&gt;0 &amp;&amp; points[i].first&lt;=points[i-1].first) error(&quot;points abscissas should be monotonously increasing&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          9 :   }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++)</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 :     if(getPntrToArgument(i)-&gt;isPeriodic())</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :       error(&quot;Cannot use PIECEWISE on periodic arguments&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   if(getNumberOfArguments()==1) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :     addValueWithDerivatives();</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 :     setNotPeriodic();</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   } else {</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 :       addComponentWithDerivatives( getPntrToArgument(i)-&gt;getName()+&quot;_pfunc&quot; );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :       getPntrToComponent(i)-&gt;setNotPeriodic();</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   log.printf(&quot;  on points:&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;points.size(); i++) log.printf(&quot;   (%f,%f)&quot;,points[i].first,points[i].second);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         10 : void Piecewise::calculate() {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     double val=getArgument(i);</a>
+<a name="128"><span class="lineNum">     128 </span>            :     unsigned p=0;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         37 :     for(; p&lt;points.size(); p++) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         33 :       if(val&lt;points[p].first) break;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     }</a>
+<a name="132"><span class="lineNum">     132 </span>            :     double f,d;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         15 :     if(p==0) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          5 :       f=points[0].second;</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :       d=0.0;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         10 :     } else if(p==points.size()) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :       f=points[points.size()-1].second;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :       d=0.0;</a>
+<a name="139"><span class="lineNum">     139 </span>            :     } else {</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          6 :       double m=(points[p].second-points[p-1].second) / (points[p].first-points[p-1].first);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          6 :       f=m*(val-points[p-1].first)+points[p-1].second;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :       d=m;</a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         15 :     if(getNumberOfArguments()==1) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          5 :       setValue(f);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          5 :       setDerivative(i,d);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     } else {</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         10 :       Value* v=getPntrToComponent(i);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         10 :       v-&gt;set(f);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :       v-&gt;addDerivative(i,d);</a>
+<a name="151"><span class="lineNum">     151 </span>            :     }</a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         10 : }</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Sort.cpp.func-sort-c.html b/coverage/function/Sort.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0d4c663f37
--- /dev/null
+++ b/coverage/function/Sort.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Sort.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Sort.cpp<span style="font-size: 80%;"> (<a href="Sort.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Sort.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#70">_ZN4PLMD8function4SortC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#86">_ZN4PLMD8function4Sort9calculateEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#62">_ZN4PLMD8function12_GLOBAL__N_116SortRegisterMe646createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#70">_ZN4PLMD8function4SortC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#64">_ZN4PLMD8function4Sort16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#62">_ZN4PLMD8function12_GLOBAL__N_116SortRegisterMe64C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#62">_ZN4PLMD8function12_GLOBAL__N_116SortRegisterMe64D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Sort.cpp.func.html b/coverage/function/Sort.cpp.func.html
new file mode 100644
index 0000000000..1b88339931
--- /dev/null
+++ b/coverage/function/Sort.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Sort.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Sort.cpp<span style="font-size: 80%;"> (<a href="Sort.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Sort.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#62">_ZN4PLMD8function12_GLOBAL__N_116SortRegisterMe646createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#62">_ZN4PLMD8function12_GLOBAL__N_116SortRegisterMe64C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#62">_ZN4PLMD8function12_GLOBAL__N_116SortRegisterMe64D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#64">_ZN4PLMD8function4Sort16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#86">_ZN4PLMD8function4Sort9calculateEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#70">_ZN4PLMD8function4SortC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sort.cpp.gcov.html#70">_ZN4PLMD8function4SortC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Sort.cpp.gcov.html b/coverage/function/Sort.cpp.gcov.html
new file mode 100644
index 0000000000..3f57203f72
--- /dev/null
+++ b/coverage/function/Sort.cpp.gcov.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Sort.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Sort.cpp<span style="font-size: 80%;"> (source / <a href="Sort.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Function.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace function {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC FUNCTION SORT</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This function can be used to sort colvars according to their magnitudes.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : \par Description of components</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This function sorts its arguments according to their magnitudes. The lowest argument will be</a>
+<a name="35"><span class="lineNum">      35 </span>            : labelled &lt;em&gt;label&lt;/em&gt;.1, the second lowest will be labelled &lt;em&gt;label&lt;/em&gt;.2 and so on.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The following input tells plumed to print the distance of the closest and of</a>
+<a name="40"><span class="lineNum">      40 </span>            : the farthest atoms to atom 1, chosen among atoms from 2 to 5</a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : d12:  DISTANCE ATOMS=1,2</a>
+<a name="43"><span class="lineNum">      43 </span>            : d13:  DISTANCE ATOMS=1,3</a>
+<a name="44"><span class="lineNum">      44 </span>            : d14:  DISTANCE ATOMS=1,4</a>
+<a name="45"><span class="lineNum">      45 </span>            : d15:  DISTANCE ATOMS=1,5</a>
+<a name="46"><span class="lineNum">      46 </span>            : sort: SORT ARG=d12,d13,d14,d15</a>
+<a name="47"><span class="lineNum">      47 </span>            : PRINT ARG=sort.1,sort.4</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : */</a>
+<a name="51"><span class="lineNum">      51 </span>            : //+ENDPLUMEDOC</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : class Sort :</a>
+<a name="55"><span class="lineNum">      55 </span>            :   public Function</a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   explicit Sort(const ActionOptions&amp;);</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void calculate() override;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      12527 : PLUMED_REGISTER_ACTION(Sort,&quot;SORT&quot;)</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         14 : void Sort::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         14 :   Function::registerKeywords(keys);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         14 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         14 :   useCustomisableComponents(keys);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         14 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         12 : Sort::Sort(const ActionOptions&amp;ao):</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   Action(ao),</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         12 :   Function(ao)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : {</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         35 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     std::string s;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         24 :     Tools::convert(i+1,s);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         24 :     if(getPntrToArgument(i)-&gt;isPeriodic())</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 :       error(&quot;Cannot sort periodic values (check argument &quot;+s+&quot;)&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         23 :     addComponentWithDerivatives(s);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         23 :     getPntrToComponent(i)-&gt;setNotPeriodic();</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         11 :   checkRead();</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         13 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         11 : void Sort::calculate() {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         11 :   std::vector&lt;std::pair&lt;double,int&gt; &gt; vals(getNumberOfArguments());</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         54 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         43 :     vals[i].first=getArgument(i);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : // In this manner I remember from which argument the component depends:</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         43 :     vals[i].second=i;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span>            : // STL sort sorts based on first element (value) then second (index)</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         11 :   std::sort(vals.begin(),vals.end());</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         54 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         43 :     Value* v=getPntrToComponent(i);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         43 :     v-&gt;set(vals[i].first);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         43 :     setDerivative(v,vals[i].second,1.0);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         11 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Stats.cpp.func-sort-c.html b/coverage/function/Stats.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2e9a6c37a5
--- /dev/null
+++ b/coverage/function/Stats.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Stats.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Stats.cpp<span style="font-size: 80%;"> (<a href="Stats.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Stats.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#85">_ZN4PLMD8function5StatsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#68">_ZN4PLMD8function12_GLOBAL__N_117StatsRegisterMe706createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#85">_ZN4PLMD8function5StatsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#70">_ZN4PLMD8function5Stats16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#151">_ZN4PLMD8function5Stats9calculateEv</a></td>
+              <td class="coverFnHi">122</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#68">_ZN4PLMD8function12_GLOBAL__N_117StatsRegisterMe70C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#68">_ZN4PLMD8function12_GLOBAL__N_117StatsRegisterMe70D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Stats.cpp.func.html b/coverage/function/Stats.cpp.func.html
new file mode 100644
index 0000000000..ed5ee7f424
--- /dev/null
+++ b/coverage/function/Stats.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Stats.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Stats.cpp<span style="font-size: 80%;"> (<a href="Stats.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Stats.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#68">_ZN4PLMD8function12_GLOBAL__N_117StatsRegisterMe706createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#68">_ZN4PLMD8function12_GLOBAL__N_117StatsRegisterMe70C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#68">_ZN4PLMD8function12_GLOBAL__N_117StatsRegisterMe70D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#70">_ZN4PLMD8function5Stats16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">33</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#151">_ZN4PLMD8function5Stats9calculateEv</a></td>
+              <td class="coverFnHi">122</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#85">_ZN4PLMD8function5StatsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stats.cpp.gcov.html#85">_ZN4PLMD8function5StatsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
+</html>
diff --git a/coverage/function/Stats.cpp.gcov.html b/coverage/function/Stats.cpp.gcov.html
new file mode 100644
index 0000000000..adf46c5158
--- /dev/null
+++ b/coverage/function/Stats.cpp.gcov.html
@@ -0,0 +1,315 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Stats.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Stats.cpp<span style="font-size: 80%;"> (source / <a href="Stats.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Function.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace function {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC FUNCTION STATS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculates statistical properties of a set of collective variables with respect to a set of reference values.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : In particular it calculates and stores as components the sum of the squared deviations, the correlation, the</a>
+<a name="33"><span class="lineNum">      33 </span>            : slope and the intercept of a linear fit.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The reference values can be either provided as values using PARAMETERS or using value without derivatives</a>
+<a name="36"><span class="lineNum">      36 </span>            : from other actions using PARARG (for example using experimental values from collective variables such as</a>
+<a name="37"><span class="lineNum">      37 </span>            : \ref CS2BACKBONE, \ref RDC, \ref NOE, \ref PRE).</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The following input tells plumed to print the distance between three couple of atoms</a>
+<a name="42"><span class="lineNum">      42 </span>            : and compare them with three reference distances.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : d1: DISTANCE ATOMS=10,50</a>
+<a name="46"><span class="lineNum">      46 </span>            : d2: DISTANCE ATOMS=1,100</a>
+<a name="47"><span class="lineNum">      47 </span>            : d3: DISTANCE ATOMS=45,75</a>
+<a name="48"><span class="lineNum">      48 </span>            : st: STATS ARG=d1,d2,d3 PARAMETERS=1.5,4.0,2.0</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=d1,d2,d3,st.*</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : */</a>
+<a name="53"><span class="lineNum">      53 </span>            : //+ENDPLUMEDOC</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : class Stats :</a>
+<a name="57"><span class="lineNum">      57 </span>            :   public Function</a>
+<a name="58"><span class="lineNum">      58 </span>            : {</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::vector&lt;double&gt; parameters;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   bool sqdonly;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool components;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool upperd;</a>
+<a name="63"><span class="lineNum">      63 </span>            : public:</a>
+<a name="64"><span class="lineNum">      64 </span>            :   explicit Stats(const ActionOptions&amp;);</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void calculate() override;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="67"><span class="lineNum">      67 </span>            : };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      12566 : PLUMED_REGISTER_ACTION(Stats,&quot;STATS&quot;)</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         33 : void Stats::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         33 :   Function::registerKeywords(keys);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         33 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         66 :   keys.add(&quot;optional&quot;,&quot;PARARG&quot;,&quot;the input for this action is the scalar output from one or more other actions without derivatives.&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         66 :   keys.add(&quot;optional&quot;,&quot;PARAMETERS&quot;,&quot;the parameters of the arguments in your function&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         66 :   keys.addFlag(&quot;SQDEVSUM&quot;,false,&quot;calculates only SQDEVSUM&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         66 :   keys.addFlag(&quot;SQDEV&quot;,false,&quot;calculates and store the SQDEV as components&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         66 :   keys.addFlag(&quot;UPPERDISTS&quot;,false,&quot;calculates and store the SQDEV as components&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;sqdevsum&quot;,&quot;default&quot;,&quot;the sum of the squared deviations between arguments and parameters&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;corr&quot;,&quot;default&quot;,&quot;the correlation between arguments and parameters&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;slope&quot;,&quot;default&quot;,&quot;the slope of a linear fit between arguments and parameters&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;intercept&quot;,&quot;default&quot;,&quot;the intercept of a linear fit between arguments and parameters&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;sqd&quot;,&quot;SQDEV&quot;,&quot;the squared deviations between arguments and parameters&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         33 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         31 : Stats::Stats(const ActionOptions&amp;ao):</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   Action(ao),</a>
+<a name="89"><span class="lineNum">      89 </span>            :   Function(ao),</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         31 :   sqdonly(false),</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         31 :   components(false),</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         31 :   upperd(false)</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         62 :   parseVector(&quot;PARAMETERS&quot;,parameters);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         31 :   if(parameters.size()!=static_cast&lt;unsigned&gt;(getNumberOfArguments())&amp;&amp;!parameters.empty())</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     error(&quot;Size of PARAMETERS array should be either 0 or the same as of the number of arguments in ARG1&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;Value*&gt; arg2;</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         62 :   parseArgumentList(&quot;PARARG&quot;,arg2);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         31 :   if(!arg2.empty()) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         14 :     if(parameters.size()&gt;0) error(&quot;It is not possible to use PARARG and PARAMETERS together&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         14 :     if(arg2.size()!=getNumberOfArguments()) error(&quot;Size of PARARG array should be the same as number for arguments in ARG&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       5912 :     for(unsigned i=0; i&lt;arg2.size(); i++) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       5898 :       parameters.push_back(arg2[i]-&gt;get());</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       5898 :       if(arg2[i]-&gt;hasDerivatives()==true) error(&quot;PARARG can only accept arguments without derivatives&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     }</a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         31 :   if(parameters.size()!=getNumberOfArguments())</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     error(&quot;PARARG or PARAMETERS arrays should include the same number of elements as the arguments in ARG&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         31 :   if(getNumberOfArguments()&lt;2) error(&quot;STATS need at least two arguments to be used&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         31 :   parseFlag(&quot;SQDEVSUM&quot;,sqdonly);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         31 :   parseFlag(&quot;SQDEV&quot;,components);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         31 :   parseFlag(&quot;UPPERDISTS&quot;,upperd);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         31 :   if(sqdonly&amp;&amp;components) error(&quot;You cannot used SQDEVSUM and SQDEV at the sametime&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         31 :   if(components) sqdonly = true;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         31 :   if(!arg2.empty()) log.printf(&quot;  using %zu parameters from inactive actions:&quot;, arg2.size());</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         17 :   else              log.printf(&quot;  using %zu parameters:&quot;, arg2.size());</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       6000 :   for(unsigned i=0; i&lt;parameters.size(); i++) log.printf(&quot; %f&quot;,parameters[i]);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         31 :   if(sqdonly) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         17 :     if(components) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         60 :       for(unsigned i=0; i&lt;parameters.size(); i++) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         48 :         std::string num; Tools::convert(i,num);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         48 :         addComponentWithDerivatives(&quot;sqd-&quot;+num);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         96 :         componentIsNotPeriodic(&quot;sqd-&quot;+num);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :       }</a>
+<a name="135"><span class="lineNum">     135 </span>            :     } else {</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          5 :       addComponentWithDerivatives(&quot;sqdevsum&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         10 :       componentIsNotPeriodic(&quot;sqdevsum&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :     }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   } else {</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         14 :     addComponentWithDerivatives(&quot;sqdevsum&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;sqdevsum&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         14 :     addComponentWithDerivatives(&quot;corr&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;corr&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         14 :     addComponentWithDerivatives(&quot;slope&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;slope&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         14 :     addComponentWithDerivatives(&quot;intercept&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         28 :     componentIsNotPeriodic(&quot;intercept&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         31 :   checkRead();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         31 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        122 : void Stats::calculate()</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : {</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        122 :   if(sqdonly) {</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :     double nsqd = 0.;</a>
+<a name="158"><span class="lineNum">     158 </span>            :     Value* val;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        106 :     if(!components) val=getPntrToComponent(&quot;sqdevsum&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        174 :     for(unsigned i=0; i&lt;parameters.size(); ++i) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        121 :       double dev = getArgument(i)-parameters[i];</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        121 :       if(upperd&amp;&amp;dev&lt;0) dev=0.;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        121 :       if(components) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :         val=getPntrToComponent(i);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :         val-&gt;set(dev*dev);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :       } else {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        121 :         nsqd += dev*dev;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :       }</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        121 :       setDerivative(val,i,2.*dev);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         53 :     if(!components) val-&gt;set(nsqd);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :   } else {</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :     double scx=0., scx2=0., scy=0., scy2=0., scxy=0.;</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       6230 :     for(unsigned i=0; i&lt;parameters.size(); ++i) {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :       const double tmpx=getArgument(i);</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       6161 :       const double tmpy=parameters[i];</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       6161 :       scx  += tmpx;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       6161 :       scx2 += tmpx*tmpx;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       6161 :       scy  += tmpy;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       6161 :       scy2 += tmpy*tmpy;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       6161 :       scxy += tmpx*tmpy;</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         69 :     const double ns = parameters.size();</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         69 :     const double num = ns*scxy - scx*scy;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         69 :     const double idev2x = 1./(ns*scx2-scx*scx);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         69 :     const double idevx = std::sqrt(idev2x);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         69 :     const double idevy = 1./std::sqrt(ns*scy2-scy*scy);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            :     /* sd */</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         69 :     const double nsqd = scx2 + scy2 - 2.*scxy;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :     /* correlation */</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         69 :     const double correlation = num * idevx * idevy;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     /* slope and intercept */</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         69 :     const double slope = num * idev2x;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         69 :     const double inter = (scy - slope * scx)/ns;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         69 :     Value* valuea=getPntrToComponent(&quot;sqdevsum&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         69 :     Value* valueb=getPntrToComponent(&quot;corr&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         69 :     Value* valuec=getPntrToComponent(&quot;slope&quot;);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        138 :     Value* valued=getPntrToComponent(&quot;intercept&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :     valuea-&gt;set(nsqd);</a>
+<a name="208"><span class="lineNum">     208 </span>            :     valueb-&gt;set(correlation);</a>
+<a name="209"><span class="lineNum">     209 </span>            :     valuec-&gt;set(slope);</a>
+<a name="210"><span class="lineNum">     210 </span>            :     valued-&gt;set(inter);</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :     /* derivatives */</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       6230 :     for(unsigned i=0; i&lt;parameters.size(); ++i) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       6161 :       const double common_d1 = (ns*parameters[i]-scy)*idevx;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       6161 :       const double common_d2 = num*(ns*getArgument(i)-scx)*idev2x*idevx;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       6161 :       const double common_d3 = common_d1 - common_d2;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :       /* sqdevsum */</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       6161 :       const double sq_der = 2.*(getArgument(i)-parameters[i]);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :       /* correlation */</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       6161 :       const double co_der = common_d3*idevy;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :       /* slope */</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       6161 :       const double sl_der = (common_d1-2.*common_d2)*idevx;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :       /* intercept */</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       6161 :       const double int_der = -(slope+ scx*sl_der)/ns;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :       setDerivative(valuea,i,sq_der);</a>
+<a name="228"><span class="lineNum">     228 </span>            :       setDerivative(valueb,i,co_der);</a>
+<a name="229"><span class="lineNum">     229 </span>            :       setDerivative(valuec,i,sl_der);</a>
+<a name="230"><span class="lineNum">     230 </span>            :       setDerivative(valued,i,int_der);</a>
+<a name="231"><span class="lineNum">     231 </span>            :     }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        122 : }</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Target.cpp.func-sort-c.html b/coverage/function/Target.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d4c3b4abe0
--- /dev/null
+++ b/coverage/function/Target.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Target.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Target.cpp<span style="font-size: 80%;"> (<a href="Target.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Target.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#106">_ZN4PLMD8function12_GLOBAL__N_119TargetRegisterMe1086createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#153">_ZN4PLMD8function6Target9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#118">_ZN4PLMD8function6TargetC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#118">_ZN4PLMD8function6TargetC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#108">_ZN4PLMD8function6Target16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#106">_ZN4PLMD8function12_GLOBAL__N_119TargetRegisterMe108C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#106">_ZN4PLMD8function12_GLOBAL__N_119TargetRegisterMe108D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Target.cpp.func.html b/coverage/function/Target.cpp.func.html
new file mode 100644
index 0000000000..1245c6bfb2
--- /dev/null
+++ b/coverage/function/Target.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Target.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Target.cpp<span style="font-size: 80%;"> (<a href="Target.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Target.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#106">_ZN4PLMD8function12_GLOBAL__N_119TargetRegisterMe1086createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#106">_ZN4PLMD8function12_GLOBAL__N_119TargetRegisterMe108C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#106">_ZN4PLMD8function12_GLOBAL__N_119TargetRegisterMe108D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#108">_ZN4PLMD8function6Target16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#153">_ZN4PLMD8function6Target9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#118">_ZN4PLMD8function6TargetC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Target.cpp.gcov.html#118">_ZN4PLMD8function6TargetC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/Target.cpp.gcov.html b/coverage/function/Target.cpp.gcov.html
new file mode 100644
index 0000000000..8e433c7887
--- /dev/null
+++ b/coverage/function/Target.cpp.gcov.html
@@ -0,0 +1,237 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function/Target.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">function</a> - Target.cpp<span style="font-size: 80%;"> (source / <a href="Target.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Function.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;reference/ArgumentOnlyDistance.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace function {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC DCOLVAR TARGET</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : This function measures the Pythagorean distance from a particular structure measured in the space defined by some set of collective variables.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This collective variable can be used to calculate something akin to:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : d(X,X') = \vert X - X' \vert</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where \f$ X \f$ is the instantaneous values for a set of collective variables for the system and</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f$ X' \f$ is the values that these self-same set of collective variables take in some reference structure provided as input.</a>
+<a name="45"><span class="lineNum">      45 </span>            : If we call our set of collective variables \f$\{s_i\}\f$ then this CV computes:</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            : d = \sqrt{ \sum_{i=1}^N (s_i - s_i^{(ref)})^2 }</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f]</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : where \f$s_i^{(ref)}\f$ are the values of the CVs in the reference structure and \f$N\f$ is the number of input CVs.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : We can also calculate normalized euclidean differences using this action and the METRIC=NORM-EUCLIDEAN flag.  In other words,</a>
+<a name="54"><span class="lineNum">      54 </span>            : we can compute:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \f[</a>
+<a name="57"><span class="lineNum">      57 </span>            : d = \sqrt{ \sum_{i=1}^N \sigma_i (s_i - s_i^{(ref)})^2 }</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f]</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : where \f$\sigma_i\f$ is a vector of weights.  Lastly, by using the METRIC=MAHALONOBIS we can compute Mahalonobis distances using:</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \f[</a>
+<a name="63"><span class="lineNum">      63 </span>            : d = \left( \mathbf{s} - \mathbf{s}^{(ref)} \right)^T \mathbf{\Sigma} \left( \mathbf{s} - \mathbf{s}^{(ref)} \right)</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f]</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : where \f$\mathbf{s}\f$ is a column vector containing the values of all the CVs and \f$\mathbf{s}^{(ref)}\f$ is a column vector</a>
+<a name="67"><span class="lineNum">      67 </span>            : containing the values of the CVs in the reference configuration.  \f$\mathbf{\Sigma}\f$ is then an \f$N \times N\f$ matrix that is</a>
+<a name="68"><span class="lineNum">      68 </span>            : specified in the input.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The following input calculates the distance between a reference configuration and the instantaneous position of the system in the trajectory.</a>
+<a name="73"><span class="lineNum">      73 </span>            : The position of the reference configuration is specified by providing the values of the distance between atoms 1 and 2 and atoms 3 and 4.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : \plumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="77"><span class="lineNum">      77 </span>            : d2: DISTANCE ATOMS=3,4</a>
+<a name="78"><span class="lineNum">      78 </span>            : t1: TARGET REFERENCE=reference.pdb TYPE=EUCLIDEAN</a>
+<a name="79"><span class="lineNum">      79 </span>            : PRINT ARG=t1 FILE=colvar</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endplumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : The contents of the file containing the reference structure (reference.pdb) is shown below.  As you can see you must provide information on the</a>
+<a name="83"><span class="lineNum">      83 </span>            : labels of the CVs that are being used to define the position of the reference configuration in this file together with the values that these</a>
+<a name="84"><span class="lineNum">      84 </span>            : quantities take in the reference configuration.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : \auxfile{reference.pdb}</a>
+<a name="87"><span class="lineNum">      87 </span>            : DESCRIPTION: a reference point.</a>
+<a name="88"><span class="lineNum">      88 </span>            : REMARK WEIGHT=1.0</a>
+<a name="89"><span class="lineNum">      89 </span>            : REMARK ARG=d1,d2</a>
+<a name="90"><span class="lineNum">      90 </span>            : REMARK d1=1.0 d2=1.0</a>
+<a name="91"><span class="lineNum">      91 </span>            : END</a>
+<a name="92"><span class="lineNum">      92 </span>            : \endauxfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : */</a>
+<a name="95"><span class="lineNum">      95 </span>            : //+ENDPLUMEDOC</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : class Target : public Function {</a>
+<a name="98"><span class="lineNum">      98 </span>            : private:</a>
+<a name="99"><span class="lineNum">      99 </span>            :   MultiValue myvals;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   ReferenceValuePack mypack;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::unique_ptr&lt;PLMD::ArgumentOnlyDistance&gt; target;</a>
+<a name="102"><span class="lineNum">     102 </span>            : public:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   explicit Target(const ActionOptions&amp;);</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void calculate() override;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   static void registerKeywords(Keywords&amp; keys );</a>
+<a name="106"><span class="lineNum">     106 </span>            : };</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(Target,&quot;TARGET&quot;)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 : void Target::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :   Function::registerKeywords(keys);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;EUCLIDEAN&quot;,&quot;the manner in which the distance should be calculated&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the reference structure. In the PDB file the atomic &quot;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :            &quot;coordinates and box lengths should be in Angstroms unless you are working with natural units. &quot;</a>
+<a name="115"><span class="lineNum">     115 </span>            :            &quot;If you are working with natural units then the coordinates should be in your natural length unit. &quot;</a>
+<a name="116"><span class="lineNum">     116 </span>            :            &quot;The charges and masses of the atoms (if required) should be inserted in the beta and occupancy &quot;</a>
+<a name="117"><span class="lineNum">     117 </span>            :            &quot;columns respectively. For more details on the PDB file format visit http://www.wwpdb.org/docs.html&quot;);</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 : Target::Target(const ActionOptions&amp;ao):</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   Action(ao),</a>
+<a name="122"><span class="lineNum">     122 </span>            :   Function(ao),</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :   myvals(1,0),</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :   mypack(0,0,myvals)</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : {</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :   std::string type; parse(&quot;TYPE&quot;,type);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :   std::string reference; parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   checkRead(); PDB pdb;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/plumed.getAtoms().getUnits().getLength()) )</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     error(&quot;missing input file &quot; + reference);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   // Use the base ActionWithArguments to expand things like a1.*</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :   expandArgKeywordInPDB( pdb );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   // Generate the reference structure</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :   target=metricRegister().create&lt;ArgumentOnlyDistance&gt;( type, pdb );</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Get the argument names</a>
+<a name="139"><span class="lineNum">     139 </span>            :   std::vector&lt;std::string&gt; args_to_retrieve;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   target-&gt;getArgumentRequests( args_to_retrieve, false );</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   // Get the arguments</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::vector&lt;Value*&gt; myargs;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   interpretArgumentList( args_to_retrieve, myargs );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   requestArguments( myargs );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   // Now create packs</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   myvals.resize( 1, myargs.size() );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   mypack.resize( myargs.size(), 0 );</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Create the value</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 : void Target::calculate() {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   mypack.clear(); double r=target-&gt;calculate( getArguments(), mypack, false ); setValue(r);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) setDerivative( i, mypack.getArgumentDerivative(i) );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : }</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/index-sort-f.html b/coverage/function/index-sort-f.html
new file mode 100644
index 0000000000..69d2af7239
--- /dev/null
+++ b/coverage/function/index-sort-f.html
@@ -0,0 +1,213 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - function</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">909</td>
+            <td class="headerCovTableEntry">1058</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryMed">84.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Target.cpp.gcov.html">Target.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">6 / 27</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Function.cpp.gcov.html">Function.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.5%"><img src="../snow.png" width=2 height=10 alt="97.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.5&nbsp;%</td>
+      <td class="coverNumHi">39 / 40</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sort.cpp.gcov.html">Sort.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 27</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Stats.cpp.gcov.html">Stats.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Ensemble.cpp.gcov.html">Ensemble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.1%"><img src="../snow.png" width=37 height=10 alt="63.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.1&nbsp;%</td>
+      <td class="coverNumLo">82 / 130</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalEnsemble.cpp.gcov.html">LocalEnsemble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Combine.cpp.gcov.html">Combine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.6%"><img src="../snow.png" width=6 height=10 alt="93.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.6&nbsp;%</td>
+      <td class="coverNumHi">44 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Piecewise.cpp.gcov.html">Piecewise.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncSumHills.cpp.gcov.html">FuncSumHills.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.9%"><img src="../snow.png" width=10 height=10 alt="89.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.9&nbsp;%</td>
+      <td class="coverNumMed">295 / 328</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncPathMSD.cpp.gcov.html">FuncPathMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">75 / 81</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncPathGeneral.cpp.gcov.html">FuncPathGeneral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="77.7%"><img src="../snow.png" width=22 height=10 alt="77.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.7&nbsp;%</td>
+      <td class="coverNumMed">101 / 130</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Custom.cpp.gcov.html">Custom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">58 / 61</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Function.h.gcov.html">Function.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.5%"><img src="../snow.png" width=12 height=10 alt="87.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/index-sort-l.html b/coverage/function/index-sort-l.html
new file mode 100644
index 0000000000..7754df3d97
--- /dev/null
+++ b/coverage/function/index-sort-l.html
@@ -0,0 +1,213 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - function</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">909</td>
+            <td class="headerCovTableEntry">1058</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryMed">84.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Target.cpp.gcov.html">Target.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">6 / 27</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Ensemble.cpp.gcov.html">Ensemble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.1%"><img src="../snow.png" width=37 height=10 alt="63.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.1&nbsp;%</td>
+      <td class="coverNumLo">82 / 130</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncPathGeneral.cpp.gcov.html">FuncPathGeneral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="77.7%"><img src="../snow.png" width=22 height=10 alt="77.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.7&nbsp;%</td>
+      <td class="coverNumMed">101 / 130</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Function.h.gcov.html">Function.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.5%"><img src="../snow.png" width=12 height=10 alt="87.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncSumHills.cpp.gcov.html">FuncSumHills.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.9%"><img src="../snow.png" width=10 height=10 alt="89.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.9&nbsp;%</td>
+      <td class="coverNumMed">295 / 328</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncPathMSD.cpp.gcov.html">FuncPathMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">75 / 81</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Combine.cpp.gcov.html">Combine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.6%"><img src="../snow.png" width=6 height=10 alt="93.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.6&nbsp;%</td>
+      <td class="coverNumHi">44 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Custom.cpp.gcov.html">Custom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">58 / 61</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Stats.cpp.gcov.html">Stats.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Function.cpp.gcov.html">Function.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.5%"><img src="../snow.png" width=2 height=10 alt="97.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.5&nbsp;%</td>
+      <td class="coverNumHi">39 / 40</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sort.cpp.gcov.html">Sort.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 27</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalEnsemble.cpp.gcov.html">LocalEnsemble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Piecewise.cpp.gcov.html">Piecewise.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/function/index.html b/coverage/function/index.html
new file mode 100644
index 0000000000..68e22dac10
--- /dev/null
+++ b/coverage/function/index.html
@@ -0,0 +1,213 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - function</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - function</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">909</td>
+            <td class="headerCovTableEntry">1058</td>
+            <td class="headerCovTableEntryMed">85.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryMed">84.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Combine.cpp.gcov.html">Combine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.6%"><img src="../snow.png" width=6 height=10 alt="93.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.6&nbsp;%</td>
+      <td class="coverNumHi">44 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Custom.cpp.gcov.html">Custom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">58 / 61</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Ensemble.cpp.gcov.html">Ensemble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.1%"><img src="../snow.png" width=37 height=10 alt="63.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.1&nbsp;%</td>
+      <td class="coverNumLo">82 / 130</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncPathGeneral.cpp.gcov.html">FuncPathGeneral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="77.7%"><img src="../snow.png" width=22 height=10 alt="77.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">77.7&nbsp;%</td>
+      <td class="coverNumMed">101 / 130</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncPathMSD.cpp.gcov.html">FuncPathMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.6%"><img src="../snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">75 / 81</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FuncSumHills.cpp.gcov.html">FuncSumHills.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.9%"><img src="../snow.png" width=10 height=10 alt="89.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.9&nbsp;%</td>
+      <td class="coverNumMed">295 / 328</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Function.cpp.gcov.html">Function.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.5%"><img src="../snow.png" width=2 height=10 alt="97.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.5&nbsp;%</td>
+      <td class="coverNumHi">39 / 40</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Function.h.gcov.html">Function.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.5%"><img src="../snow.png" width=12 height=10 alt="87.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalEnsemble.cpp.gcov.html">LocalEnsemble.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Piecewise.cpp.gcov.html">Piecewise.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sort.cpp.gcov.html">Sort.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 27</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Stats.cpp.gcov.html">Stats.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Target.cpp.gcov.html">Target.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">6 / 27</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/FPS.cpp.func-sort-c.html b/coverage/funnel/FPS.cpp.func-sort-c.html
new file mode 100644
index 0000000000..86664bb669
--- /dev/null
+++ b/coverage/funnel/FPS.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel/FPS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">funnel</a> - FPS.cpp<span style="font-size: 80%;"> (<a href="FPS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FPS.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#129">_ZN4PLMD6funnel9FUNNEL_PSC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#116">_ZN4PLMD6funnel12_GLOBAL__N_122FUNNEL_PSRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#129">_ZN4PLMD6funnel9FUNNEL_PSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#118">_ZN4PLMD6funnel9FUNNEL_PS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#193">_ZN4PLMD6funnel9FUNNEL_PS9calculateEv</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#116">_ZN4PLMD6funnel12_GLOBAL__N_122FUNNEL_PSRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#116">_ZN4PLMD6funnel12_GLOBAL__N_122FUNNEL_PSRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/FPS.cpp.func.html b/coverage/funnel/FPS.cpp.func.html
new file mode 100644
index 0000000000..7bd9c9720f
--- /dev/null
+++ b/coverage/funnel/FPS.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel/FPS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">funnel</a> - FPS.cpp<span style="font-size: 80%;"> (<a href="FPS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FPS.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#116">_ZN4PLMD6funnel12_GLOBAL__N_122FUNNEL_PSRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#116">_ZN4PLMD6funnel12_GLOBAL__N_122FUNNEL_PSRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#116">_ZN4PLMD6funnel12_GLOBAL__N_122FUNNEL_PSRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#118">_ZN4PLMD6funnel9FUNNEL_PS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#193">_ZN4PLMD6funnel9FUNNEL_PS9calculateEv</a></td>
+              <td class="coverFnHi">150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#129">_ZN4PLMD6funnel9FUNNEL_PSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FPS.cpp.gcov.html#129">_ZN4PLMD6funnel9FUNNEL_PSC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/FPS.cpp.gcov.html b/coverage/funnel/FPS.cpp.gcov.html
new file mode 100644
index 0000000000..5b62f74a50
--- /dev/null
+++ b/coverage/funnel/FPS.cpp.gcov.html
@@ -0,0 +1,397 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel/FPS.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">funnel</a> - FPS.cpp<span style="font-size: 80%;"> (source / <a href="FPS.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2019-2020</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of funnel code module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The FM code respects the CC BY-NC license.</a>
+<a name="7"><span class="lineNum">       7 </span>            :    Users are free to download, adapt and use the code as long as it is not for commercial purposes.</a>
+<a name="8"><span class="lineNum">       8 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="9"><span class="lineNum">       9 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="10"><span class="lineNum">      10 </span>            : #include &quot;colvar/ActionRegister.h&quot;</a>
+<a name="11"><span class="lineNum">      11 </span>            : #include &lt;string&gt;</a>
+<a name="12"><span class="lineNum">      12 </span>            : #include &lt;cmath&gt;</a>
+<a name="13"><span class="lineNum">      13 </span>            : #include &lt;cassert&gt;</a>
+<a name="14"><span class="lineNum">      14 </span>            : #include &lt;vector&gt;</a>
+<a name="15"><span class="lineNum">      15 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="16"><span class="lineNum">      16 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="17"><span class="lineNum">      17 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="18"><span class="lineNum">      18 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &lt;iostream&gt;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : </a>
+<a name="22"><span class="lineNum">      22 </span>            : using namespace std;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace funnel {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC FUNNELMOD_COLVAR FUNNEL_PS</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : FUNNEL_PS implements the Funnel-Metadynamics (FM) technique in PLUMED 2.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : Please read the FM \cite limongelli2013funnel \cite raniolo2020ligand papers to better understand the notions hereby reported.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This colvar evaluates the position of a ligand of interest with respect to a given line, built from the two points</a>
+<a name="34"><span class="lineNum">      34 </span>            : A and B, and should be used together with the \ref FUNNEL bias.</a>
+<a name="35"><span class="lineNum">      35 </span>            : The constructed line represents the axis of the funnel-shape restraint potential, which should be placed so</a>
+<a name="36"><span class="lineNum">      36 </span>            : as to include the portion of a macromolecule (i.e., protein, DNA, etc.) that should be explored.</a>
+<a name="37"><span class="lineNum">      37 </span>            : Since it is important that the position of the line is updated based on the motion of the macromolecule during</a>
+<a name="38"><span class="lineNum">      38 </span>            : the simulation, this colvar incorporates an alignment method. The latter uses the TYPE=OPTIMAL option to remove</a>
+<a name="39"><span class="lineNum">      39 </span>            : motions due to rotation and translation of the macromolecule with respect to a reference structure, which is</a>
+<a name="40"><span class="lineNum">      40 </span>            : provided by the user. In order to accomplish the task, an optimal alignment matrix is calculated using the</a>
+<a name="41"><span class="lineNum">      41 </span>            : Kearsley \cite kearsley algorithm.</a>
+<a name="42"><span class="lineNum">      42 </span>            : The reference structure should be given as a pdb file, containing only the atoms of the macromolecule or a</a>
+<a name="43"><span class="lineNum">      43 </span>            : selection of them (e.g., the protein CA atoms of secondary structures). In contrast to the methods reported in</a>
+<a name="44"><span class="lineNum">      44 </span>            : the \ref dists, the values reported in the occupancy and beta-factor columns of the pdb file are not important</a>
+<a name="45"><span class="lineNum">      45 </span>            : since they will be overwritten and replaced by the value 1.00 during the procedure. It is important to understand</a>
+<a name="46"><span class="lineNum">      46 </span>            : that all atoms in the file will be used for the alignment, even if they display 0.00 in the occupancy column.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The ligand can be represented by one single atom or the center of mass (COM) of a group of atoms that should be</a>
+<a name="49"><span class="lineNum">      49 </span>            : provided by the user.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : By default FUNNEL_PS is computed taking into account periodic boundary conditions. Since PLUMED 2.5, molecules are</a>
+<a name="52"><span class="lineNum">      52 </span>            : rebuilt using a procedure that is equivalent to that done in \ref WHOLEMOLECULES. We note that this action is local</a>
+<a name="53"><span class="lineNum">      53 </span>            : to this colvar, thus it does not modify the coordinates stored in PLUMED. Moreover, FUNNEL_PS requires an ANCHOR atom</a>
+<a name="54"><span class="lineNum">      54 </span>            : to be specified in order to facilitate the reconstruction of periodic boundary conditions. This atom should be the</a>
+<a name="55"><span class="lineNum">      55 </span>            : closest macromolecule's atom to the ligand and it should reduce the risk of ligand &quot;warping&quot; in the simulation box.</a>
+<a name="56"><span class="lineNum">      56 </span>            : Nevertheless, we highly recommend to add to the PLUMED input file a custom line of \ref WHOLEMOLECULES, in order to</a>
+<a name="57"><span class="lineNum">      57 </span>            : be sure of reconstructing the ligand together with the macromolecule (please look the examples). In this case, the user</a>
+<a name="58"><span class="lineNum">      58 </span>            : can use the NOPBC flag to turn off the internal periodic boundary condition reconstruction.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : FUNNEL_PS is divided in two components (fps.lp and fps.ld) which evaluate the projection of the ligand along the funnel line</a>
+<a name="61"><span class="lineNum">      61 </span>            : and the distance from it, respectively. The values attributed to these two components are then used together with the</a>
+<a name="62"><span class="lineNum">      62 </span>            : potential file created by the \ref FUNNEL bias to define if the ligand is within or not in the funnel-shape restraint</a>
+<a name="63"><span class="lineNum">      63 </span>            : potential. In the latter case, the potential will force the ligand to enter within the funnel boundaries.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \par Examples</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : The following input tells plumed to print the FUNNEL_PS components for the COM of a ligand. The inputs are a reference structure,</a>
+<a name="68"><span class="lineNum">      68 </span>            : which is the structure used for the alignment, the COM of the molecule we want to track, and 2 points in the Cartesian space</a>
+<a name="69"><span class="lineNum">      69 </span>            : (i.e., x, y, and z) to draw the line representing the funnel axis.</a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : lig: COM ATOMS=2446,2447,2448,2449,2451</a>
+<a name="72"><span class="lineNum">      72 </span>            : fps: FUNNEL_PS REFERENCE=protein.pdb LIGAND=lig POINTS=5.3478,-0.7278,2.4746,7.3785,6.7364,-9.3624</a>
+<a name="73"><span class="lineNum">      73 </span>            : PRINT ARG=fps.lp,fps.ld</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : It is recommended to add a line to force the reconstruction of the periodic boundary conditions. In the following example,</a>
+<a name="77"><span class="lineNum">      77 </span>            : \ref WHOLEMOLECULES was added to make sure that the ligand was reconstructed together with the protein. The list contains</a>
+<a name="78"><span class="lineNum">      78 </span>            : all the atoms reported in the start.pdb file followed by the ANCHOR atom and the ligand. All atoms should be contained in the</a>
+<a name="79"><span class="lineNum">      79 </span>            : same entity and the correct order.</a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : WHOLEMOLECULES ENTITY0=54,75,212,228,239,258,311,328,348,372,383,402,421,463,487,503,519,657,674,690,714,897,914,934,953,964,</a>
+<a name="82"><span class="lineNum">      82 </span>            : 974,985,1007,1018,1037,1247,1264,1283,1302,1324,1689,1708,1727,1738,1962,1984,1994,2312,2329,2349,2467,2490,2500,2517,2524,2536,</a>
+<a name="83"><span class="lineNum">      83 </span>            : 2547,2554,2569,2575,2591,2607,2635,2657,2676,2693,2700,2719,2735,2746,2770,2777,2788,2795,2805,2815,2832,2854,2868,2898,2904,</a>
+<a name="84"><span class="lineNum">      84 </span>            : 2911,2927,2948,2962,2472,3221,3224,3225,3228,3229,3231,3233,3235,3237</a>
+<a name="85"><span class="lineNum">      85 </span>            : lig: COM ATOMS=3221,3224,3225,3228,3229,3231,3233,3235,3237</a>
+<a name="86"><span class="lineNum">      86 </span>            : fps: FUNNEL_PS LIGAND=lig REFERENCE=start.pdb ANCHOR=2472 POINTS=4.724,5.369,4.069,4.597,5.721,4.343</a>
+<a name="87"><span class="lineNum">      87 </span>            : PRINT ARG=fps.lp,fps.ld</a>
+<a name="88"><span class="lineNum">      88 </span>            : \endplumedfile</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : */</a>
+<a name="91"><span class="lineNum">      91 </span>            : //+ENDPLUMEDOC</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : class FUNNEL_PS : public Colvar {</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Those are arrays that I created for the colvar</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt;AtomNumber&gt; ligand_com;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;AtomNumber&gt; anchor;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::vector&lt;AtomNumber&gt; numbers;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   bool pbc;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   PLMD::RMSD alignment;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   PLMD::PDB pdb;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   bool squared;</a>
+<a name="104"><span class="lineNum">     104 </span>            : private:</a>
+<a name="105"><span class="lineNum">     105 </span>            :   vector&lt;double&gt; points;</a>
+<a name="106"><span class="lineNum">     106 </span>            : public:</a>
+<a name="107"><span class="lineNum">     107 </span>            :   explicit FUNNEL_PS(const ActionOptions&amp;);</a>
+<a name="108"><span class="lineNum">     108 </span>            : // active methods:</a>
+<a name="109"><span class="lineNum">     109 </span>            :   virtual void calculate();</a>
+<a name="110"><span class="lineNum">     110 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="111"><span class="lineNum">     111 </span>            : // I need a method in RMSDCoreCalc and these were requested</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;double&gt; align;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;double&gt; displace;</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : using namespace std;</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(FUNNEL_PS,&quot;FUNNEL_PS&quot;)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          7 : void FUNNEL_PS::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          7 :   Colvar::registerKeywords( keys );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the structure you would like to align.&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         14 :   keys.add(&quot;atoms&quot;,&quot;LIGAND&quot;,&quot;This MUST be a single atom, normally the COM of the ligand&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         14 :   keys.add(&quot;atoms&quot;,&quot;ANCHOR&quot;,&quot;Closest protein atom to the ligand, picked to avoid pbc problems during the simulation&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;POINTS&quot;,&quot;6 values defining x, y, and z of the 2 points used to construct the line. The order should be A_x,A_y,A_z,B_x,B_y,B_z.&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         14 :   keys.addFlag(&quot;SQUARED-ROOT&quot;,false,&quot;Used to initialize the creation of the alignment variable&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         14 :   keys.addOutputComponent(&quot;lp&quot;,&quot;default&quot;,&quot;the position along the funnel line&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         14 :   keys.addOutputComponent(&quot;ld&quot;,&quot;default&quot;,&quot;the distance from the funnel line&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          7 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          5 : FUNNEL_PS::FUNNEL_PS(const ActionOptions&amp;ao):</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          5 :   pbc(true),squared(true)</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : {</a>
+<a name="135"><span class="lineNum">     135 </span>            :   string reference;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         10 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   string type;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          5 :   type.assign(&quot;OPTIMAL&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         10 :   parseAtomList(&quot;LIGAND&quot;,ligand_com);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          5 :   if(ligand_com.size()!=1)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     error(&quot;Number of specified atoms should be one, normally the COM of the ligand&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          5 :   parseVector(&quot;POINTS&quot;,points);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          5 :   bool nopbc=!pbc;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          5 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          5 :   pbc=!nopbc;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   bool sq;</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          5 :   parseFlag(&quot;SQUARED-ROOT&quot;,sq);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          5 :   if (sq) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     squared=false;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          5 :   parseAtomList(&quot;ANCHOR&quot;,anchor);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          5 :   checkRead();</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         10 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/ActionAtomistic::atoms.getUnits().getLength()) )</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :     error(&quot;missing input file &quot; + reference );</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            :   bool remove_com=true;</a>
+<a name="159"><span class="lineNum">     159 </span>            :   bool normalize_weights=true;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   // here displace is a simple vector of ones</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          5 :   align=pdb.getOccupancy();</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      16195 :   for(unsigned i=0; i&lt;align.size(); i++) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      16190 :     align[i]=1.;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   } ;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          5 :   displace=pdb.getBeta();</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      16195 :   for(unsigned i=0; i&lt;displace.size(); i++) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      16190 :     displace[i]=1.;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   } ;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   // reset again to reimpose uniform weights (safe to disable this)</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          5 :   alignment.set(align,displace,pdb.getPositions(),type,remove_com,normalize_weights);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // Array with inside both the structure to align and the atom to be aligned</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          5 :   numbers=pdb.getAtomNumbers();</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          5 :   numbers.push_back(anchor[0]);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          5 :   numbers.push_back(ligand_com[0]);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          5 :   log.printf(&quot;  average from file %s\n&quot;,reference.c_str());</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          5 :   log.printf(&quot;  method for alignment : %s \n&quot;,type.c_str() );</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          5 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          5 :   addComponentWithDerivatives(&quot;lp&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          5 :   componentIsNotPeriodic(&quot;lp&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          5 :   addComponentWithDerivatives(&quot;ld&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          5 :   componentIsNotPeriodic(&quot;ld&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          5 :   requestAtoms( numbers );</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          5 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : // calculator</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        150 : void FUNNEL_PS::calculate() {</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        150 :   if(pbc) makeWhole();</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        150 :   Tensor Rotation;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   Matrix&lt;std::vector&lt;Vector&gt; &gt; drotdpos(3,3);</a>
+<a name="201"><span class="lineNum">     201 </span>            :   std::vector&lt;Vector&gt; alignedpos;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   std::vector&lt;Vector&gt; centeredpos;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   std::vector&lt;Vector&gt; centeredref;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   std::vector&lt;Vector&gt; ddistdpos;</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   std::vector&lt;Vector&gt; buffer;</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        150 :   Vector centerreference;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        150 :   Vector centerpositions;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   // Created only to give the correct object to calc_FitElements</a>
+<a name="212"><span class="lineNum">     212 </span>            :   std::vector&lt;Vector&gt; sourceAllPositions;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   std::vector&lt;Vector&gt; sourcePositions;</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   // SourcePositions contains only the coordinates of the COM of the ligand, we need only this point</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        150 :   sourceAllPositions=getPositions();</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        150 :   sourcePositions=sourceAllPositions;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        150 :   sourcePositions.resize(sourcePositions.size()-2);// just the protein</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :   // The two points that define the axis : this can be moved in the initialization</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        150 :   Vector p1 = VectorGeneric&lt;3&gt;(points[0],points[1],points[2]);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        150 :   Vector p2 = VectorGeneric&lt;3&gt;(points[3],points[4],points[5]);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        150 :   Vector s = p2 - p1;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   // I call the method calc_FitElements that initializes all feature that I need</a>
+<a name="226"><span class="lineNum">     226 </span>            :   // except for centerreference that I need to calculate from scratch</a>
+<a name="227"><span class="lineNum">     227 </span>            :   // Buffer has no meaning but I had to fulfill the requirements of calc_FitElements</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        150 :   double rmsd = alignment.calc_FitElements( sourcePositions, Rotation, drotdpos, buffer, centerpositions, squared);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   // To Plumed developers: it would be interesting to make the functions to calculate centers of mass public or protected</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        150 :   centerreference.zero();</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     485850 :   for(unsigned i=0; i&lt;pdb.size(); i++) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">     485700 :     centerreference+=pdb.getPositions()[i]*align[i]/align.size();</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :   /*</a>
+<a name="237"><span class="lineNum">     237 </span>            :   // I cancelled the additional lines in the library of RMSD.h, thus I am missing the center of the reference</a>
+<a name="238"><span class="lineNum">     238 </span>            :   // Creating variable kito to extract only the center of the reference, since no method is calling</a>
+<a name="239"><span class="lineNum">     239 </span>            :   // function getReferenceCenter()</a>
+<a name="240"><span class="lineNum">     240 </span>            :   PLMD::RMSDCoreData* kito; kito = new RMSDCoreData(align,displace,sourcePositions,pdb-&gt;getPositions());</a>
+<a name="241"><span class="lineNum">     241 </span>            :   centerreference = kito-&gt;getReferenceCenter();</a>
+<a name="242"><span class="lineNum">     242 </span>            :   delete kito;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   */</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   // DEBUG</a>
+<a name="246"><span class="lineNum">     246 </span>            :   /*    log.printf(&quot; RMSD: %13.6lf\n&quot;,rmsd );</a>
+<a name="247"><span class="lineNum">     247 </span>            :       log.printf(&quot; cpos: %13.6lf %13.6lf %13.6lf\n&quot;,centerpositions[0],centerpositions[1],centerpositions[2] );</a>
+<a name="248"><span class="lineNum">     248 </span>            :       log.printf(&quot; Rotation: %13.6lf %13.6lf %13.6lf\n&quot;,Rotation[0][0],Rotation[0][1],Rotation[0][2] );</a>
+<a name="249"><span class="lineNum">     249 </span>            :       log.printf(&quot;           %13.6lf %13.6lf %13.6lf\n&quot;,Rotation[1][0],Rotation[1][1],Rotation[1][2] );</a>
+<a name="250"><span class="lineNum">     250 </span>            :       log.printf(&quot;           %13.6lf %13.6lf %13.6lf\n&quot;,Rotation[2][0],Rotation[2][1],Rotation[2][2] );</a>
+<a name="251"><span class="lineNum">     251 </span>            :   */</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            :   // the position is   Rot(ligand-com_prot_md)+ com_prot_ref</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        150 :   Vector ligand_centered =getPositions().back()-centerpositions;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        150 :   Vector ligand_aligned =matmul(Rotation,ligand_centered);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        150 :   Vector v = ligand_aligned +centerreference -p1;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // DEBUG</a>
+<a name="259"><span class="lineNum">     259 </span>            : //    log.printf(&quot; ligando: %13.6lf %13.6lf %13.6lf\n&quot;,getPositions().back()[0],getPositions().back()[1],getPositions().back()[2] );</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   //Projection vector v onto s</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        150 :   Vector prj = (dotProduct(s,v)/dotProduct(s,s))*s;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        150 :   const double prj_length = prj.modulo() ;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   const double inv_prj_length = 1.0/prj_length;</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        150 :   Vector height = v - prj;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        150 :   const double prj_height = height.modulo() ;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        150 :   const double inv_prj_height = 1.0/prj_height;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   // derivative of the prj: only on the com of the ligand</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        150 :   Vector der_prj;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        150 :   der_prj=s/s.modulo();</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :   // derivative of the height: only on the com of the ligand</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        150 :   Vector der_height(inv_prj_height*(height[0]-(s[0]/s.modulo2())*dotProduct(height,s)),</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        150 :                     inv_prj_height*(height[1]-(s[1]/s.modulo2())*dotProduct(height,s)),</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        150 :                     inv_prj_height*(height[2]-(s[2]/s.modulo2())*dotProduct(height,s)));</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        150 :   Value* valuelp=getPntrToComponent(&quot;lp&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        150 :   Value* valueld=getPntrToComponent(&quot;ld&quot;);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        150 :   valuelp-&gt;set(dotProduct(s,v)/s.modulo()); // this includes the sign</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :   valueld-&gt;set(prj_height);</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            :   // DEBUG</a>
+<a name="286"><span class="lineNum">     286 </span>            : //    log.printf(&quot; Dopo: %13.6lf  %13.6lf\n&quot;,dotProduct(s,v)/s.modulo(),prj_height );</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        150 :   setAtomsDerivatives(valuelp,getNumberOfAtoms()-1,matmul(transpose(Rotation),der_prj));</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        150 :   setAtomsDerivatives(valueld,getNumberOfAtoms()-1,matmul(transpose(Rotation),der_height));</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        150 :   Vector der_h;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        150 :   Vector der_l;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        150 :   double weight=1./float(getNumberOfAtoms()-2.);</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">     485850 :   for(unsigned iat=0; iat&lt;getNumberOfAtoms()-2; iat++) {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">     485700 :     der_h.zero();</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     485700 :     der_l.zero();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">    1942800 :     for(unsigned a=0; a&lt;3; a++) {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">    5828400 :       for(unsigned b=0; b&lt;3; b++) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">   17485200 :         for(unsigned g=0; g&lt;3; g++) {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">   13113900 :           der_h[a]+=der_height[b]*drotdpos[b][g][iat][a]*ligand_centered[g];</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">   13113900 :           der_l[a]+=der_prj[b]*drotdpos[b][g][iat][a]*ligand_centered[g];</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :         }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">    4371300 :         der_h[a]-=der_height[b]*Rotation[b][a]*weight;</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">    4371300 :         der_l[a]-=der_prj[b]*Rotation[b][a]*weight;</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :       }</a>
+<a name="307"><span class="lineNum">     307 </span>            :     }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">     485700 :     setAtomsDerivatives(valuelp,iat,der_l);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">     485700 :     setAtomsDerivatives(valueld,iat,der_h);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   }</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        150 :   setBoxDerivativesNoPbc(valuelp);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        150 :   setBoxDerivativesNoPbc(valueld);</span></a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        150 : }</span></a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : }</a>
+<a name="318"><span class="lineNum">     318 </span>            : }</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/Funnel.cpp.func-sort-c.html b/coverage/funnel/Funnel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e406e911e9
--- /dev/null
+++ b/coverage/funnel/Funnel.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel/Funnel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">funnel</a> - Funnel.cpp<span style="font-size: 80%;"> (<a href="Funnel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntryHi">99.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Funnel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#175">_ZN4PLMD6funnel6FunnelC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#286">_ZN4PLMD6funnel6Funnel10createBIASERKdS3_S3_S3_S3_S3_S3_S3_S3_RKbS3_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESD_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#141">_ZN4PLMD6funnel12_GLOBAL__N_119FunnelRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#175">_ZN4PLMD6funnel6FunnelC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#143">_ZN4PLMD6funnel6Funnel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#427">_ZN4PLMD6funnel6Funnel9calculateEv</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#141">_ZN4PLMD6funnel12_GLOBAL__N_119FunnelRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#141">_ZN4PLMD6funnel12_GLOBAL__N_119FunnelRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/Funnel.cpp.func.html b/coverage/funnel/Funnel.cpp.func.html
new file mode 100644
index 0000000000..85f230fea4
--- /dev/null
+++ b/coverage/funnel/Funnel.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel/Funnel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">funnel</a> - Funnel.cpp<span style="font-size: 80%;"> (<a href="Funnel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntryHi">99.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Funnel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#141">_ZN4PLMD6funnel12_GLOBAL__N_119FunnelRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#141">_ZN4PLMD6funnel12_GLOBAL__N_119FunnelRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#286">_ZN4PLMD6funnel6Funnel10createBIASERKdS3_S3_S3_S3_S3_S3_S3_S3_RKbS3_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESD_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#143">_ZN4PLMD6funnel6Funnel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#427">_ZN4PLMD6funnel6Funnel9calculateEv</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#175">_ZN4PLMD6funnel6FunnelC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Funnel.cpp.gcov.html#175">_ZN4PLMD6funnel6FunnelC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/Funnel.cpp.gcov.html b/coverage/funnel/Funnel.cpp.gcov.html
new file mode 100644
index 0000000000..130fa18911
--- /dev/null
+++ b/coverage/funnel/Funnel.cpp.gcov.html
@@ -0,0 +1,528 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel/Funnel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">funnel</a> - Funnel.cpp<span style="font-size: 80%;"> (source / <a href="Funnel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntryHi">99.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2019-2020</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of funnel code module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The FM code respects the CC BY-NC license.</a>
+<a name="7"><span class="lineNum">       7 </span>            :    Users are free to download, adapt and use the code as long as it is not for commercial purposes.</a>
+<a name="8"><span class="lineNum">       8 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="9"><span class="lineNum">       9 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="10"><span class="lineNum">      10 </span>            : #include &quot;bias/ActionRegister.h&quot;</a>
+<a name="11"><span class="lineNum">      11 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="12"><span class="lineNum">      12 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="13"><span class="lineNum">      13 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="14"><span class="lineNum">      14 </span>            : #include &lt;cstring&gt;</a>
+<a name="15"><span class="lineNum">      15 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="16"><span class="lineNum">      16 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="17"><span class="lineNum">      17 </span>            : #include &quot;tools/FileBase.h&quot;</a>
+<a name="18"><span class="lineNum">      18 </span>            : #include &lt;memory&gt;</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : </a>
+<a name="21"><span class="lineNum">      21 </span>            : using namespace std;</a>
+<a name="22"><span class="lineNum">      22 </span>            : using namespace PLMD::bias;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace funnel {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC FUNNELMOD_BIAS FUNNEL</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Calculate a funnel-shape restraint potential that is defined on a grid that is read during the setup.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : If the input file is not already present, it will create one with the name specified in the FILE flag.</a>
+<a name="33"><span class="lineNum">      33 </span>            : The potential has a two-dimensional resolution since it has been devised to be used with the two</a>
+<a name="34"><span class="lineNum">      34 </span>            : components of \ref FUNNEL_PS (i.e., fps.lp and fps.ld) and it is divided in two sections, a cone shape</a>
+<a name="35"><span class="lineNum">      35 </span>            : attached to a cylindrical one. The user can customize the shape of both the sections by modifying a</a>
+<a name="36"><span class="lineNum">      36 </span>            : number of flags. In particular the cone section of the funnel is calculated with the following formula:</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : MAX_Z=R_{cyl} + tg_{alpha} * (z_{cc} - MIN_S)</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f]</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : where  \f$ MAX_Z \f$ is the radius of the cone base,  \f$ R_{cyl} \f$ is the radius of the cylinder part,</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f$ tg_{alpha} \f$ is the angle regulating how steep the cone is, \f$ z_{cc} \f$ is the switching point</a>
+<a name="44"><span class="lineNum">      44 </span>            : between cone and cylinder, and \f$ MIN_S \f$ is the lowest possible value assumed by fps.lp of \ref FUNNEL_PS.</a>
+<a name="45"><span class="lineNum">      45 </span>            : As for the cylinder, it starts from the value of \f$ z_{cc} \f$ and stops at the value of \f$ MAX_S \f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : with a section of \f$ pi*r_{cyl}^2 \f$.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : There is the option of transforming the cone region into a sphere with the use of the SPHERE flag. In this</a>
+<a name="49"><span class="lineNum">      49 </span>            : case, the new shape will have a radius of \f$ z_{cc} \f$. It might be necessary tuning the SAFETY option</a>
+<a name="50"><span class="lineNum">      50 </span>            : to select how much the potential extends from the sphere.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The following is an input for a calculation with a funnel potential that is defined in the file BIAS</a>
+<a name="55"><span class="lineNum">      55 </span>            : and that acts on the collective variables defined by FUNNEL_PS.</a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : lig: COM ATOMS=3221,3224,3225,3228,3229,3231,3233,3235,3237</a>
+<a name="58"><span class="lineNum">      58 </span>            : fps: FUNNEL_PS LIGAND=lig REFERENCE=start.pdb ANCHOR=2472 POINTS=4.724,5.369,4.069,4.597,5.721,4.343</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : FUNNEL ARG=fps.lp,fps.ld ZCC=1.8 ALPHA=0.55 RCYL=0.1 MINS=-0.5 MAXS=3.7 KAPPA=35100 NBINS=500 NBINZ=500 FILE=BIAS LABEL=funnel</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : The BIAS will then look something like this:</a>
+<a name="64"><span class="lineNum">      64 </span>            : \auxfile{BIAS}</a>
+<a name="65"><span class="lineNum">      65 </span>            : #! FIELDS fps.lp fps.ld funnel.bias der_fps.lp der_fps.ld</a>
+<a name="66"><span class="lineNum">      66 </span>            : #! SET min_fps.lp -0.500000</a>
+<a name="67"><span class="lineNum">      67 </span>            : #! SET max_fps.lp 3.700000</a>
+<a name="68"><span class="lineNum">      68 </span>            : #! SET nbins_fps.lp 500.000000</a>
+<a name="69"><span class="lineNum">      69 </span>            : #! SET periodic_fps.lp false</a>
+<a name="70"><span class="lineNum">      70 </span>            : #! SET min_fps.ld 0.000000</a>
+<a name="71"><span class="lineNum">      71 </span>            : #! SET max_fps.ld 1.510142</a>
+<a name="72"><span class="lineNum">      72 </span>            : #! SET nbins_fps.ld 500.000000</a>
+<a name="73"><span class="lineNum">      73 </span>            : #! SET periodic_fps.ld false</a>
+<a name="74"><span class="lineNum">      74 </span>            :     -0.500000      0.000000      0.000000      0.000000      0.000000</a>
+<a name="75"><span class="lineNum">      75 </span>            :     -0.500000      0.003020      0.000000      0.000000      0.000000</a>
+<a name="76"><span class="lineNum">      76 </span>            :     -0.500000      0.006041      0.000000      0.000000      0.000000</a>
+<a name="77"><span class="lineNum">      77 </span>            :     -0.500000      0.009061      0.000000      0.000000      0.000000</a>
+<a name="78"><span class="lineNum">      78 </span>            :     -0.500000      0.012081      0.000000      0.000000      0.000000</a>
+<a name="79"><span class="lineNum">      79 </span>            :     -0.500000      0.015101      0.000000      0.000000      0.000000</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endauxfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : The Funnel potential should always be used in combination with the collective variable  \ref FUNNEL_PS, since it</a>
+<a name="83"><span class="lineNum">      83 </span>            : is constructed to take as inputs fps.lp and fps.ld (the former linepos and linedist of Funnel-Metadynamics</a>
+<a name="84"><span class="lineNum">      84 </span>            : \cite FM).  In the first block of data the value of fps.lp (the value in the first column) is kept fixed</a>
+<a name="85"><span class="lineNum">      85 </span>            : and the value of the function is given at 500 equally spaced values for fps.ld between 0 and 1.51. In</a>
+<a name="86"><span class="lineNum">      86 </span>            : the second block of data fps.lp is fixed at \f$-0.5 + \frac{4.2}{500}\f$ and the value of the function</a>
+<a name="87"><span class="lineNum">      87 </span>            : is given at 500 equally spaced values for fps.ld between 0 and 1.51. In the third block of data the same</a>
+<a name="88"><span class="lineNum">      88 </span>            : is done but fps.lp is fixed at \f$-0.5 + \frac{8.4}{100}\f$ and so on until you get to the five hundredth</a>
+<a name="89"><span class="lineNum">      89 </span>            : block of data where fps.lp is fixed at \f$3.7\f$.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : It is possible to switch the shape of the cone region, transforming it in a sphere, with the flag SPHERE.</a>
+<a name="92"><span class="lineNum">      92 </span>            : \plumedfile</a>
+<a name="93"><span class="lineNum">      93 </span>            : lig: COM ATOMS=545,546,547,548,549,550,551,552,553</a>
+<a name="94"><span class="lineNum">      94 </span>            : fps: FUNNEL_PS LIGAND=lig REFERENCE=ref.pdb ANCHOR=52 POINTS=2.793,3.696,3.942,3.607,4.298,3.452</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : FUNNEL ARG=fps.lp,fps.ld ZCC=4.0 RCYL=0.1 MINS=0.2 MAXS=4.9 KAPPA=100000 NBINS=500 NBINZ=500 SPHERE SAFETY=1.0 FILE=BIAS LABEL=funnel</a>
+<a name="97"><span class="lineNum">      97 </span>            : \endplumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : */</a>
+<a name="100"><span class="lineNum">     100 </span>            : //+ENDPLUMEDOC</a>
+<a name="101"><span class="lineNum">     101 </span>            : class Funnel : public Bias {</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : private:</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::unique_ptr&lt;GridBase&gt; BiasGrid_;</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :   /////////////////////</a>
+<a name="107"><span class="lineNum">     107 </span>            :   // old 2.3</a>
+<a name="108"><span class="lineNum">     108 </span>            :   //Grid* BiasGrid_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   /////////////////////</a>
+<a name="110"><span class="lineNum">     110 </span>            :   //Optional parameters</a>
+<a name="111"><span class="lineNum">     111 </span>            :   double NBINS;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   double NBINZ;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double MINS;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   double KAPPA;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   double RCYL;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   double safety;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   double slope;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   double ALPHA;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   //Compulsory parameters</a>
+<a name="120"><span class="lineNum">     120 </span>            :   double MAXS;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   double ZCC;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   double scale_;</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : public:</a>
+<a name="126"><span class="lineNum">     126 </span>            :   explicit Funnel(const ActionOptions&amp;);</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   // old Funnel-2.3</a>
+<a name="129"><span class="lineNum">     129 </span>            :   // ~Funnel();</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   void calculate();</a>
+<a name="132"><span class="lineNum">     132 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void createBIAS(const double&amp; R_cyl, const double&amp; z_cc, const double&amp; alpha, const double&amp; KAPPA,</a>
+<a name="134"><span class="lineNum">     134 </span>            :                   const double&amp; MIN_S, const double&amp; MAX_S, const double&amp; NBIN_S, const double&amp; NBIN_Z,</a>
+<a name="135"><span class="lineNum">     135 </span>            :                   const double&amp; safety, const bool&amp; sphere, const double&amp; slope, const string&amp; funcl,</a>
+<a name="136"><span class="lineNum">     136 </span>            :                   const string&amp; file);</a>
+<a name="137"><span class="lineNum">     137 </span>            : //  void createBIAS3D(const double&amp; R_cyl, const double&amp; z_cc, const double&amp; alpha,</a>
+<a name="138"><span class="lineNum">     138 </span>            : //                      const double&amp; KAPPA, const double&amp; MIN_S, const double&amp; MAX_S, const double&amp; NBIN_S,</a>
+<a name="139"><span class="lineNum">     139 </span>            : //                      const double&amp; NBIN_Z, const double&amp; safety, const bool&amp; sphere, const double&amp; slope,</a>
+<a name="140"><span class="lineNum">     140 </span>            : //                      const string&amp; funcl);</a>
+<a name="141"><span class="lineNum">     141 </span>            : };</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(Funnel,&quot;FUNNEL&quot;)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          6 : void Funnel::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          6 :   Bias::registerKeywords(keys);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          6 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         12 :   keys.addFlag(&quot;NOSPLINE&quot;,false,&quot;specifies that no spline interpolation is to be used when calculating the energy and forces due to the external potential&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         12 :   keys.addFlag(&quot;SPARSE&quot;,false,&quot;specifies that the external potential uses a sparse grid&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         12 :   keys.addFlag(&quot;SPHERE&quot;,false, &quot;The Funnel potential including the binding site can be spherical instead of a cone&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;SCALE&quot;,&quot;1.0&quot;,&quot;a factor that multiplies the external potential, useful to invert free energies&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : // old stuff?</a>
+<a name="153"><span class="lineNum">     153 </span>            :   //  componentsAreNotOptional(keys);</a>
+<a name="154"><span class="lineNum">     154 </span>            :   //  keys.addOutputComponent(&quot;bias&quot;,&quot;default&quot;,&quot;the instantaneous value of the bias potential&quot;);</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :   //Defining optional arguments</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;NBINS&quot;,&quot;number of bins along fps.lp&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;NBINZ&quot;,&quot;number of bins along fps.ld&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;MINS&quot;,&quot;minimum value assumed by fps.lp, if the ligand is able to go beyond this value the simulation will crash&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;KAPPA&quot;,&quot;constant to be used for the funnel-shape restraint potential&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;RCYL&quot;,&quot;radius of the cylindrical section&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;SAFETY&quot;,&quot;To be used in case the SPHERE flag is chosen, it regulates how much the potential extends (in nm)&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;SLOPE&quot;,&quot;Adjust the behavior of the potential outside the funnel, greater values than 1.0 will tend to push the ligand more towards the cylinder and vice versa&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;ALPHA&quot;,&quot;angle to change the width of the cone section&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   //Defining compulsory arguments</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;MAXS&quot;,&quot;MAXS&quot;,&quot;maximum value assumed by fps.lp&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;ZCC&quot;,&quot;ZCC&quot;,&quot;switching point between cylinder and cone&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;name of the Funnel potential file&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         12 :   keys.addFlag(&quot;WALKERS_MPI&quot;,false,&quot;To be used when gromacs + multiple walkers are used&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          6 : }</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : // Old version 2.3</a>
+<a name="173"><span class="lineNum">     173 </span>            : //Funnel::~Funnel(){</a>
+<a name="174"><span class="lineNum">     174 </span>            : //  delete BiasGrid_;</a>
+<a name="175"><span class="lineNum">     175 </span>            : //}</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 : Funnel::Funnel(const ActionOptions&amp; ao):</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="179"><span class="lineNum">     179 </span>            : // Old version 2.3</a>
+<a name="180"><span class="lineNum">     180 </span>            : // BiasGrid_(NULL),</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :   NBINS(500.0),</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :   NBINZ(500.0),</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          4 :   MINS(0.0),</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :   KAPPA(84.0),</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 :   RCYL(0.1),</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          4 :   safety(1.0),</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :   slope(1.0),</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          4 :   ALPHA(1.413)</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          4 :   bool sparsegrid=false;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          4 :   parseFlag(&quot;SPARSE&quot;,sparsegrid);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 :   bool nospline=false;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          4 :   parseFlag(&quot;NOSPLINE&quot;,nospline);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          4 :   bool spline=!nospline;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          4 :   bool walkers_mpi=false;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          4 :   parseFlag(&quot;WALKERS_MPI&quot;,walkers_mpi);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : //  bool components=false;</a>
+<a name="199"><span class="lineNum">     199 </span>            : //  parseFlag(&quot;POINTS&quot;,components);</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          4 :   bool sphere=false;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          4 :   parseFlag(&quot;SPHERE&quot;,sphere);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          8 :   parse(&quot;SAFETY&quot;,safety);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   string file;</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          8 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          4 :   if( file.length()==0 ) error(&quot;No funnel file name was specified&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          4 :   parse(&quot;SCALE&quot;,scale_);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   //Reading optional arguments</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          4 :   parse(&quot;KAPPA&quot;,KAPPA);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          4 :   parse(&quot;NBINS&quot;,NBINS);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          4 :   parse(&quot;NBINZ&quot;,NBINZ);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          4 :   parse(&quot;MINS&quot;,MINS);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          4 :   parse(&quot;RCYL&quot;,RCYL);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          4 :   parse(&quot;SLOPE&quot;,slope);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          4 :   parse(&quot;ALPHA&quot;,ALPHA);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   //Reading compulsory arguments</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          4 :   parse(&quot;MAXS&quot;,MAXS);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          4 :   parse(&quot;ZCC&quot;,ZCC);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          4 :   log.printf(&quot;  External potential from file %s\n&quot;,file.c_str());</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          4 :   log.printf(&quot;  Multiplied by %lf\n&quot;,scale_);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :   if(spline) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          4 :     log.printf(&quot;  External potential uses spline interpolation\n&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          4 :   if(sparsegrid) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     log.printf(&quot;  External potential uses sparse grid\n&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :   // Non più necessario dalla 2.3</a>
+<a name="233"><span class="lineNum">     233 </span>            : //  addComponent(&quot;bias&quot;); componentIsNotPeriodic(&quot;bias&quot;);</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          4 :   std::string funcl=getLabel() + &quot;.bias&quot;;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : //  int size = plumed.comm.Get_size();</a>
+<a name="238"><span class="lineNum">     238 </span>            : //  int rank = plumed.comm.Get_rank();</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          4 :   IFile I_hate_this;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          4 :   bool do_exist=I_hate_this.FileExist(file);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          4 :   if(walkers_mpi) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          2 :     if(comm.Get_rank()==0 &amp;&amp; multi_sim_comm.Get_rank()==0) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          1 :       if(!do_exist) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          1 :         createBIAS(RCYL, ZCC, ALPHA, KAPPA, MINS, MAXS, NBINS, NBINZ, safety, sphere, slope, funcl, file);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :       }</a>
+<a name="247"><span class="lineNum">     247 </span>            :     }</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          2 :     multi_sim_comm.Barrier();</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :   } else {</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :     if(comm.Get_rank()==0) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          2 :       if(!do_exist) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 :         createBIAS(RCYL, ZCC, ALPHA, KAPPA, MINS, MAXS, NBINS, NBINZ, safety, sphere, slope, funcl, file);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :       }</a>
+<a name="254"><span class="lineNum">     254 </span>            :     }</a>
+<a name="255"><span class="lineNum">     255 </span>            :   }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :   /*</a>
+<a name="258"><span class="lineNum">     258 </span>            :   if(comm.Get_rank()==0){</a>
+<a name="259"><span class="lineNum">     259 </span>            :     if(multi_sim_comm.Get_rank()==0 &amp;&amp; walkers_mpi){</a>
+<a name="260"><span class="lineNum">     260 </span>            :           if(!do_exist){</a>
+<a name="261"><span class="lineNum">     261 </span>            :                   createBIAS(RCYL, ZCC, ALPHA, KAPPA, MINS, MAXS, NBINS, NBINZ, safety, sphere, slope, funcl, file);</a>
+<a name="262"><span class="lineNum">     262 </span>            :           }</a>
+<a name="263"><span class="lineNum">     263 </span>            :     } else {</a>
+<a name="264"><span class="lineNum">     264 </span>            :           if(!do_exist){</a>
+<a name="265"><span class="lineNum">     265 </span>            :                   createBIAS(RCYL, ZCC, ALPHA, KAPPA, MINS, MAXS, NBINS, NBINZ, safety, sphere, slope, funcl, file);</a>
+<a name="266"><span class="lineNum">     266 </span>            :           }</a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :     if(walkers_mpi) multi_sim_comm.Barrier();</a>
+<a name="269"><span class="lineNum">     269 </span>            :   }</a>
+<a name="270"><span class="lineNum">     270 </span>            :   */</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          4 :   comm.Barrier();</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : // read grid</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          4 :   IFile gridfile;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          4 :   gridfile.open(file);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          8 :   BiasGrid_=Grid::create(funcl,getArguments(),gridfile,sparsegrid,spline,true);</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : //not necessary anymore?  gridfile.close();</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          4 :   if(BiasGrid_-&gt;getDimension()!=getNumberOfArguments()) error(&quot;mismatch between dimensionality of input grid and number of arguments&quot;);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         16 :     if( getPntrToArgument(i)-&gt;isPeriodic()!=BiasGrid_-&gt;getIsPeriodic()[i] ) error(&quot;periodicity mismatch between arguments and input bias&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   }</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          4 :   comm.Barrier();</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          4 :   if(comm.Get_rank()==0 &amp;&amp; walkers_mpi) multi_sim_comm.Barrier();</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          8 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Limongelli, Bonomi, and Parrinello, PNAS 110, 6358 (2013)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          8 : }</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          3 : void Funnel::createBIAS(const double&amp; R_cyl, const double&amp; z_cc, const double&amp; alpha,</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :                         const double&amp; KAPPA, const double&amp; MIN_S, const double&amp; MAX_S, const double&amp; NBIN_S,</a>
+<a name="290"><span class="lineNum">     290 </span>            :                         const double&amp; NBIN_Z, const double&amp; safety, const bool&amp; sphere, const double&amp; slope,</a>
+<a name="291"><span class="lineNum">     291 </span>            :                         const string&amp; funcl, const string&amp; file) {</a>
+<a name="292"><span class="lineNum">     292 </span>            :   //R_cyl and z_cc forms the parameters of the cylinder.</a>
+<a name="293"><span class="lineNum">     293 </span>            :   //alpha defines the angle in degrees.</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            :   //PARAMETERS OF THE CONE</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          3 :   double tg_alpha= tan(alpha);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :   //parameters for PROGRESSION</a>
+<a name="299"><span class="lineNum">     299 </span>            :   //parameters for DISTANCE</a>
+<a name="300"><span class="lineNum">     300 </span>            :   double MIN_Z=0;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   double MAX_Z;</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          3 :   if (sphere==false) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          2 :     MAX_Z=R_cyl + tg_alpha * (z_cc - MIN_S);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span>            :   else {</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          1 :     MAX_Z=z_cc+safety;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :   //bin size</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          3 :   double DX_Z = (MAX_Z - MIN_Z) / NBIN_Z;</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   double DX_S;</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          3 :   if (sphere==false) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          2 :     DX_S=(MAX_S - MIN_S) / NBIN_S;</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :   }</a>
+<a name="315"><span class="lineNum">     315 </span>            :   else {</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          1 :     DX_S=(MAX_S + z_cc + safety)/NBIN_S;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :   }</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :   double SS, Zmax, ZZ, D, d;</a>
+<a name="320"><span class="lineNum">     320 </span>            :   double POT, FZ, FS;</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          3 :   PLMD::OFile pof;</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          3 :   pof.open(file);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :   //Write the header</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          3 :   pof.printf(&quot;#! FIELDS %s %s %s der_%s der_%s \n&quot;, getPntrToArgument(0)-&gt;getName().c_str(), getPntrToArgument(1)-&gt;getName().c_str(), funcl.c_str(), getPntrToArgument(0)-&gt;getName().c_str(), getPntrToArgument(1)-&gt;getName().c_str());</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          3 :   if (sphere==false) pof.printf(&quot;#! SET min_%s %f\n&quot;, getPntrToArgument(0)-&gt;getName().c_str(), MIN_S);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          1 :   else pof.printf(&quot;#! SET min_%s %f\n&quot;, getPntrToArgument(0)-&gt;getName().c_str(), -z_cc-safety);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET max_%s %f\n&quot;, getPntrToArgument(0)-&gt;getName().c_str(), MAX_S);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET nbins_%s %f\n&quot;, getPntrToArgument(0)-&gt;getName().c_str(), NBIN_S);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET periodic_%s false\n&quot;, getPntrToArgument(0)-&gt;getName().c_str());</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET min_%s %f\n&quot;, getPntrToArgument(1)-&gt;getName().c_str(), MIN_Z);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET max_%s %f\n&quot;, getPntrToArgument(1)-&gt;getName().c_str(), MAX_Z);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET nbins_%s %f\n&quot;, getPntrToArgument(1)-&gt;getName().c_str(), NBIN_Z);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          3 :   pof.printf(&quot;#! SET periodic_%s false\n&quot;, getPntrToArgument(1)-&gt;getName().c_str());</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            :   //Calculate and write the GRID</a>
+<a name="338"><span class="lineNum">     338 </span>            :   //Cone or cylinder?</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       1506 :   for(int is=0; is &lt;= NBIN_S; is++) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       1503 :     if (sphere==false) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       1002 :       SS = MIN_S + is * DX_S;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :     }</a>
+<a name="344"><span class="lineNum">     344 </span>            :     else {</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        501 :       SS = - z_cc - safety + is * DX_S;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :     }</a>
+<a name="347"><span class="lineNum">     347 </span>            :     bool cone = false;</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       1503 :     if (sphere==false) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">       1002 :       if(SS &lt;= z_cc) cone = true;</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :     }</a>
+<a name="351"><span class="lineNum">     351 </span>            :     else {</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        501 :       if (SS &lt;= sqrt(pow(z_cc,2)-pow(R_cyl,2))) cone = true;</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :     }</a>
+<a name="354"><span class="lineNum">     354 </span>            :     //Set wall boundaries properly</a>
+<a name="355"><span class="lineNum">     355 </span>            :     if(cone == true) {</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        902 :       if(sphere==false) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        548 :         Zmax = R_cyl + (z_cc - SS) * tg_alpha;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :       }</a>
+<a name="359"><span class="lineNum">     359 </span>            :       else {</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">        354 :         if (SS &gt; -z_cc) {</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        277 :           Zmax = sqrt(pow(z_cc,2) - pow(SS,2));</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :         }</a>
+<a name="363"><span class="lineNum">     363 </span>            :         else {</a>
+<a name="364"><span class="lineNum">     364 </span>            :           Zmax = 0;</a>
+<a name="365"><span class="lineNum">     365 </span>            :         }</a>
+<a name="366"><span class="lineNum">     366 </span>            :       }</a>
+<a name="367"><span class="lineNum">     367 </span>            :     }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        601 :     else Zmax = R_cyl;</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">     754506 :     for(int iz=0; iz &lt;= NBIN_Z; iz++) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">     753003 :       ZZ = MIN_Z + iz * DX_Z;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            :       //Inside or outside?</a>
+<a name="374"><span class="lineNum">     374 </span>            :       bool inside;</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">     753003 :       if(ZZ &lt; Zmax) inside = true;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :       else inside = false;</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            :       if(inside == true) {</a>
+<a name="379"><span class="lineNum">     379 </span>            :         POT = 0;</a>
+<a name="380"><span class="lineNum">     380 </span>            :         FS = 0;</a>
+<a name="381"><span class="lineNum">     381 </span>            :         FZ = 0;</a>
+<a name="382"><span class="lineNum">     382 </span>            :       }</a>
+<a name="383"><span class="lineNum">     383 </span>            :       else {</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">     518149 :         if(cone == true) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">     235130 :           if(sphere==false) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">     127824 :             POT = 0.5 * KAPPA * (ZZ - Zmax) * (ZZ - Zmax);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">     127824 :             FZ = - KAPPA * (ZZ - Zmax);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">     127824 :             FS = - KAPPA * (ZZ - Zmax) * tg_alpha;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :           }</a>
+<a name="390"><span class="lineNum">     390 </span>            :           else {</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">     107306 :             D = sqrt(pow(ZZ,2)+pow(SS,2));</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">     107306 :             d = D - z_cc;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">     107306 :             POT = 0.5 * KAPPA * pow(d,2);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">     107306 :             FZ = - KAPPA * d * ZZ / D;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">     107306 :             FS = - KAPPA * d * SS / D;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :           }</a>
+<a name="397"><span class="lineNum">     397 </span>            :         }</a>
+<a name="398"><span class="lineNum">     398 </span>            :         else {</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">     283019 :           if(sphere==false) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">     212018 :             POT = 0.5 * KAPPA * (ZZ - Zmax) * (ZZ - Zmax);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">     212018 :             FZ = - KAPPA * (ZZ - Zmax);</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :             FS = 0;</a>
+<a name="403"><span class="lineNum">     403 </span>            :           }</a>
+<a name="404"><span class="lineNum">     404 </span>            :           else {</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">      71001 :             D = sqrt(pow(ZZ,2)+pow(SS,2));</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">      71001 :             d = D - z_cc;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">      71001 :             if(ZZ&gt;=R_cyl+slope*(SS-z_cc)) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">      45984 :               POT = 0.5 * KAPPA * pow(d,2);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">      45984 :               FZ = - KAPPA * d * ZZ / D;</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">      45984 :               FS = - KAPPA * d * SS / D;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :             }</a>
+<a name="412"><span class="lineNum">     412 </span>            :             else {</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">      25017 :               POT = 0.5 * KAPPA * pow(sqrt(pow((ZZ+slope*z_cc-R_cyl)/slope,2)+pow(ZZ,2))-</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :                                       z_cc,2);</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">      25017 :               FZ = - KAPPA*(sqrt(pow((ZZ+slope*z_cc-R_cyl)/slope,2)+pow(ZZ,2))-z_cc)*</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">      25017 :                    ZZ/sqrt(pow((ZZ+slope*z_cc-R_cyl)/slope,2)+pow(ZZ,2));</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :               FS = 0;</a>
+<a name="418"><span class="lineNum">     418 </span>            :             }</a>
+<a name="419"><span class="lineNum">     419 </span>            :           }</a>
+<a name="420"><span class="lineNum">     420 </span>            :         }</a>
+<a name="421"><span class="lineNum">     421 </span>            :       }</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">     753003 :       pof.printf(&quot;%13.6lf %13.6lf %13.6lf %13.6lf %13.6lf\n&quot;, SS, ZZ, POT, FS, FZ);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :     }</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">       1503 :     pof.printf(&quot;\n&quot;);</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :   }</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          3 :   pof.close();</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          3 : }</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">        120 : void Funnel::calculate()</span></a>
+<a name="430"><span class="lineNum">     430 </span>            : {</a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        120 :   unsigned ncv=getNumberOfArguments();</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        120 :   vector&lt;double&gt; cv(ncv), der(ncv);</span></a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        360 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">        240 :     cv[i]=getArgument(i);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :   }</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            : //  log.printf(&quot;  In Funnel: %13.6lf  %13.6lf\n&quot;, cv[0], cv[1]);</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        120 :   double ene=scale_*BiasGrid_-&gt;getValueAndDerivatives(cv,der);</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :   setBias(ene);</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            : // set Forces</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        360 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        240 :     const double f=-scale_*der[i];</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        240 :     setOutputForce(i,f);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :   }</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">        120 : }</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            : }</a>
+<a name="452"><span class="lineNum">     452 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/index-sort-f.html b/coverage/funnel/index-sort-f.html
new file mode 100644
index 0000000000..d137e76027
--- /dev/null
+++ b/coverage/funnel/index-sort-f.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - funnel</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">248</td>
+            <td class="headerCovTableEntry">253</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FPS.cpp.gcov.html">FPS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Funnel.cpp.gcov.html">Funnel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.3%"><img src="../snow.png" width=1 height=10 alt="99.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.3&nbsp;%</td>
+      <td class="coverNumHi">152 / 153</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/index-sort-l.html b/coverage/funnel/index-sort-l.html
new file mode 100644
index 0000000000..0e49c0b124
--- /dev/null
+++ b/coverage/funnel/index-sort-l.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - funnel</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">248</td>
+            <td class="headerCovTableEntry">253</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FPS.cpp.gcov.html">FPS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Funnel.cpp.gcov.html">Funnel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.3%"><img src="../snow.png" width=1 height=10 alt="99.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.3&nbsp;%</td>
+      <td class="coverNumHi">152 / 153</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/funnel/index.html b/coverage/funnel/index.html
new file mode 100644
index 0000000000..dd50faa4f3
--- /dev/null
+++ b/coverage/funnel/index.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - funnel</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - funnel</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">248</td>
+            <td class="headerCovTableEntry">253</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FPS.cpp.gcov.html">FPS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Funnel.cpp.gcov.html">Funnel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.3%"><img src="../snow.png" width=1 height=10 alt="99.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.3&nbsp;%</td>
+      <td class="coverNumHi">152 / 153</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gcov.css b/coverage/gcov.css
new file mode 100644
index 0000000000..0fcdff13ce
--- /dev/null
+++ b/coverage/gcov.css
@@ -0,0 +1,519 @@
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+body
+{
+  color: #000000;
+  background-color: #ffffff;
+}
+
+/* All views: standard link format*/
+a:link
+{
+  color: #284fa8;
+  text-decoration: underline;
+}
+
+/* All views: standard link - visited format */
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+{
+  color: #00cb40;
+  text-decoration: underline;
+}
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+}
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+  font-weight: bold;
+}
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+  color: #284fa8;
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+}
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+/* All views: header item coverage table heading */
+td.headerCovTableHead
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+  text-align: center;
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+  font-family: sans-serif;
+  font-size: 80%;
+  white-space: nowrap;
+}
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+/* All views: header item coverage table entry */
+td.headerCovTableEntry
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+  background-color: #a7fc9d;
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+{
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+  padding-top: 2px;
+  font-family: sans-serif;
+  font-style: italic;
+}
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+/* Directory view/File view (all)/Test case descriptions:
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+td.tableHead
+{
+  text-align: center;
+  color: #ffffff;
+  background-color: #6688d4;
+  font-family: sans-serif;
+  font-size: 120%;
+  font-weight: bold;
+  white-space: nowrap;
+  padding-left: 4px;
+  padding-right: 4px;
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+span.tableHeadSort
+{
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+/* Directory view/File view (all): filename entry format */
+td.coverFile
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+}
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+/* Directory view/File view (all): bar-graph outline color */
+td.coverBarOutline
+{
+  background-color: #000000;
+}
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+/* Directory view/File view (all): percentage entry for files with
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+td.coverPerHi
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+/* Directory view/File view (all): percentage entry for files with
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+{
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+  background-color: #ffea20;
+  font-weight: bold;
+  font-family: sans-serif;
+}
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+/* Directory view/File view (all): line count entry for files with
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+td.coverNumMed
+{
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+  padding-right: 10px;
+  background-color: #ffea20;
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+  font-family: sans-serif;
+}
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+/* Directory view/File view (all): percentage entry for files with
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+td.coverPerLo
+{
+  text-align: right;
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+  padding-right: 10px;
+  background-color: #ff0000;
+  font-weight: bold;
+  font-family: sans-serif;
+}
+
+/* Directory view/File view (all): line count entry for files with
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+{
+  text-align: right;
+  padding-left: 10px;
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+  white-space: nowrap;
+  font-family: sans-serif;
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+{
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+{
+  color: #B8D0FF;
+  font-size:80%;
+}
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+a.detail:active
+{
+  color: #ffffff;
+  font-size:80%;
+}
+
+/* File view (detail): test name entry */
+td.testName
+{
+  text-align: right;
+  padding-right: 10px;
+  background-color: #dae7fe;
+  font-family: sans-serif;
+}
+
+/* File view (detail): test percentage entry */
+td.testPer
+{
+  text-align: right;
+  padding-left: 10px;
+  padding-right: 10px; 
+  background-color: #dae7fe;
+  font-family: sans-serif;
+}
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+/* File view (detail): test lines count entry */
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+  padding-right: 10px; 
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+  font-family: sans-serif;
+}
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+/* Test case descriptions: test name format*/
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+{
+  font-family: sans-serif;
+  font-weight: bold;
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+/* Test case descriptions: description table body */
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+  padding-left: 30px;
+  padding-bottom: 10px;
+  padding-right: 30px;
+  background-color: #dae7fe;
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+  padding-right: 10px;
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+{
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+}  
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+}
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+  padding-left: 4px;
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+  font-size: 80%;
+}
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+{
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+  text-align: center;
+  white-space: nowrap;
+  padding-left: 2px;
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+  font-size: 80%;
+}
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+td.headerValueLegH
+{
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+  text-align: center;
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+  padding-left: 2px;
+  padding-right: 4px;
+  background-color: #a7fc9d;
+  font-size: 80%;
+}
+
+/* All views except source code view: legend format for low coverage */
+span.coverLegendCovLo
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-top: 2px;
+  background-color: #ff0000;
+}
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+/* All views except source code view: legend format for med coverage */
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+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-top: 2px;
+  background-color: #ffea20;
+}
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+/* All views except source code view: legend format for hi coverage */
+span.coverLegendCovHi
+{
+  padding-left: 10px;
+  padding-right: 10px;
+  padding-top: 2px;
+  background-color: #a7fc9d;
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diff --git a/coverage/generic/Debug.cpp.func-sort-c.html b/coverage/generic/Debug.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d17a21de38
--- /dev/null
+++ b/coverage/generic/Debug.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Debug.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Debug.cpp<span style="font-size: 80%;"> (<a href="Debug.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Debug.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#74">_ZN4PLMD7generic5DebugC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#61">_ZN4PLMD7generic12_GLOBAL__N_117DebugRegisterMe636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#74">_ZN4PLMD7generic5DebugC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#63">_ZN4PLMD7generic5Debug16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#105">_ZN4PLMD7generic5Debug5applyEv</a></td>
+              <td class="coverFnHi">140</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#57">_ZN4PLMD7generic5Debug9calculateEv</a></td>
+              <td class="coverFnHi">140</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#61">_ZN4PLMD7generic12_GLOBAL__N_117DebugRegisterMe63C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#61">_ZN4PLMD7generic12_GLOBAL__N_117DebugRegisterMe63D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Debug.cpp.func.html b/coverage/generic/Debug.cpp.func.html
new file mode 100644
index 0000000000..92d1c22ced
--- /dev/null
+++ b/coverage/generic/Debug.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Debug.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Debug.cpp<span style="font-size: 80%;"> (<a href="Debug.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Debug.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#61">_ZN4PLMD7generic12_GLOBAL__N_117DebugRegisterMe636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#61">_ZN4PLMD7generic12_GLOBAL__N_117DebugRegisterMe63C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#61">_ZN4PLMD7generic12_GLOBAL__N_117DebugRegisterMe63D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#63">_ZN4PLMD7generic5Debug16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#105">_ZN4PLMD7generic5Debug5applyEv</a></td>
+              <td class="coverFnHi">140</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#57">_ZN4PLMD7generic5Debug9calculateEv</a></td>
+              <td class="coverFnHi">140</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#74">_ZN4PLMD7generic5DebugC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Debug.cpp.gcov.html#74">_ZN4PLMD7generic5DebugC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Debug.cpp.gcov.html b/coverage/generic/Debug.cpp.gcov.html
new file mode 100644
index 0000000000..3955d18263
--- /dev/null
+++ b/coverage/generic/Debug.cpp.gcov.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Debug.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Debug.cpp<span style="font-size: 80%;"> (source / <a href="Debug.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace generic {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC GENERIC DEBUG</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Set some debug options.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : Can be used while debugging or optimizing plumed.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \plumedfile</a>
+<a name="39"><span class="lineNum">      39 </span>            : # print detailed (action-by-action) timers at the end of simulation</a>
+<a name="40"><span class="lineNum">      40 </span>            : DEBUG DETAILED_TIMERS</a>
+<a name="41"><span class="lineNum">      41 </span>            : # dump every two steps which are the atoms required from the MD code</a>
+<a name="42"><span class="lineNum">      42 </span>            : DEBUG logRequestedAtoms STRIDE=2</a>
+<a name="43"><span class="lineNum">      43 </span>            : \endplumedfile</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : */</a>
+<a name="46"><span class="lineNum">      46 </span>            : //+ENDPLUMEDOC</a>
+<a name="47"><span class="lineNum">      47 </span>            : class Debug:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   public ActionPilot</a>
+<a name="49"><span class="lineNum">      49 </span>            : {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   OFile ofile;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   bool logActivity;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   bool logRequestedAtoms;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   bool novirial;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   bool detailedTimers;</a>
+<a name="55"><span class="lineNum">      55 </span>            : public:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit Debug(const ActionOptions&amp;ao);</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Register all the relevant keywords for the action</a>
+<a name="58"><span class="lineNum">      58 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        140 :   void calculate() override {}</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   void apply() override;</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(Debug,&quot;DEBUG&quot;)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          8 : void Debug::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          8 :   Action::registerKeywords( keys );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          8 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which this action is to be performed&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         16 :   keys.addFlag(&quot;logActivity&quot;,false,&quot;write in the log which actions are inactive and which are inactive&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         16 :   keys.addFlag(&quot;logRequestedAtoms&quot;,false,&quot;write in the log which atoms have been requested at a given time&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         16 :   keys.addFlag(&quot;NOVIRIAL&quot;,false,&quot;switch off the virial contribution for the entirety of the simulation&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         16 :   keys.addFlag(&quot;DETAILED_TIMERS&quot;,false,&quot;switch on detailed timers&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output these quantities&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          8 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 : Debug::Debug(const ActionOptions&amp;ao):</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   Action(ao),</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ActionPilot(ao),</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          6 :   logActivity(false),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          6 :   logRequestedAtoms(false),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          6 :   novirial(false) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          6 :   parseFlag(&quot;logActivity&quot;,logActivity);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          6 :   if(logActivity) log.printf(&quot;  logging activity\n&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :   parseFlag(&quot;logRequestedAtoms&quot;,logRequestedAtoms);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          6 :   if(logRequestedAtoms) log.printf(&quot;  logging requested atoms\n&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 :   parseFlag(&quot;NOVIRIAL&quot;,novirial);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          6 :   if(novirial) log.printf(&quot;  Switching off virial contribution\n&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          6 :   if(novirial) plumed.novirial=true;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          6 :   parseFlag(&quot;DETAILED_TIMERS&quot;,detailedTimers);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          6 :   if(detailedTimers) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :     log.printf(&quot;  Detailed timing on\n&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 :     plumed.detailedTimers=true;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   ofile.link(*this);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::string file;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         12 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   if(file.length()&gt;0) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :     ofile.open(file);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :     log.printf(&quot;  on file %s\n&quot;,file.c_str());</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   } else {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :     log.printf(&quot;  on plumed log file\n&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :     ofile.link(log);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   checkRead();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        140 : void Debug::apply() {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        140 :   if(logActivity) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         10 :     const ActionSet&amp;actionSet(plumed.getActionSet());</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     int a=0;</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        115 :     for(const auto &amp; p : actionSet) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        105 :       if(dynamic_cast&lt;Debug*&gt;(p.get()))continue;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         90 :       if(p-&gt;isActive()) a++;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     };</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         10 :     if(a&gt;0) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          9 :       ofile&lt;&lt;&quot;activity at step &quot;&lt;&lt;getStep()&lt;&lt;&quot;: &quot;;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        107 :       for(const auto &amp; p : actionSet) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         98 :         if(dynamic_cast&lt;Debug*&gt;(p.get()))continue;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         85 :         if(p-&gt;isActive()) ofile.printf(&quot;+&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         27 :         else                 ofile.printf(&quot;-&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :       };</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          9 :       ofile.printf(&quot;\n&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     };</a>
+<a name="124"><span class="lineNum">     124 </span>            :   };</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        140 :   if(logRequestedAtoms) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         17 :     ofile&lt;&lt;&quot;requested atoms at step &quot;&lt;&lt;getStep()&lt;&lt;&quot;: &quot;;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     const int* l;</a>
+<a name="128"><span class="lineNum">     128 </span>            :     int n;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         34 :     plumed.cmd(&quot;createFullList&quot;,&amp;n);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         34 :     plumed.cmd(&quot;getFullList&quot;,&amp;l);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        213 :     for(int i=0; i&lt;n; i++) ofile.printf(&quot; %d&quot;,l[i]);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         17 :     ofile.printf(&quot;\n&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         34 :     plumed.cmd(&quot;clearFullList&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        140 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpAtoms.cpp.func-sort-c.html b/coverage/generic/DumpAtoms.cpp.func-sort-c.html
new file mode 100644
index 0000000000..487bb0f612
--- /dev/null
+++ b/coverage/generic/DumpAtoms.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpAtoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpAtoms.cpp<span style="font-size: 80%;"> (<a href="DumpAtoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpAtoms.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#158">_ZN4PLMD7generic9DumpAtomsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#302">_ZN4PLMD7generic9DumpAtomsD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_122DumpAtomsRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#158">_ZN4PLMD7generic9DumpAtomsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#302">_ZN4PLMD7generic9DumpAtomsD0Ev</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#302">_ZN4PLMD7generic9DumpAtomsD1Ev</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#143">_ZN4PLMD7generic9DumpAtoms16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">175</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_122DumpAtomsRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_122DumpAtomsRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#243">_ZN4PLMD7generic9DumpAtoms6updateEv</a></td>
+              <td class="coverFnHi">8876</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#137">_ZN4PLMD7generic9DumpAtoms5applyEv</a></td>
+              <td class="coverFnHi">8971</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#136">_ZN4PLMD7generic9DumpAtoms9calculateEv</a></td>
+              <td class="coverFnHi">8971</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpAtoms.cpp.func.html b/coverage/generic/DumpAtoms.cpp.func.html
new file mode 100644
index 0000000000..12416d2907
--- /dev/null
+++ b/coverage/generic/DumpAtoms.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpAtoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpAtoms.cpp<span style="font-size: 80%;"> (<a href="DumpAtoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpAtoms.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_122DumpAtomsRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_122DumpAtomsRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_122DumpAtomsRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#143">_ZN4PLMD7generic9DumpAtoms16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">175</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#137">_ZN4PLMD7generic9DumpAtoms5applyEv</a></td>
+              <td class="coverFnHi">8971</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#243">_ZN4PLMD7generic9DumpAtoms6updateEv</a></td>
+              <td class="coverFnHi">8876</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#136">_ZN4PLMD7generic9DumpAtoms9calculateEv</a></td>
+              <td class="coverFnHi">8971</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#158">_ZN4PLMD7generic9DumpAtomsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#158">_ZN4PLMD7generic9DumpAtomsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#302">_ZN4PLMD7generic9DumpAtomsD0Ev</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#302">_ZN4PLMD7generic9DumpAtomsD1Ev</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpAtoms.cpp.gcov.html#302">_ZN4PLMD7generic9DumpAtomsD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpAtoms.cpp.gcov.html b/coverage/generic/DumpAtoms.cpp.gcov.html
new file mode 100644
index 0000000000..3802c0c404
--- /dev/null
+++ b/coverage/generic/DumpAtoms.cpp.gcov.html
@@ -0,0 +1,390 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpAtoms.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpAtoms.cpp<span style="font-size: 80%;"> (source / <a href="DumpAtoms.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstdio&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;memory&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;xdrfile/xdrfile_xtc.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;xdrfile/xdrfile_trr.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD</a>
+<a name="39"><span class="lineNum">      39 </span>            : {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace generic {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : //+PLUMEDOC PRINTANALYSIS DUMPATOMS</a>
+<a name="43"><span class="lineNum">      43 </span>            : /*</a>
+<a name="44"><span class="lineNum">      44 </span>            : Dump selected atoms on a file.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : This command can be used to output the positions of a particular set of atoms.</a>
+<a name="47"><span class="lineNum">      47 </span>            : The atoms required are output in a xyz or gro formatted file.</a>
+<a name="48"><span class="lineNum">      48 </span>            : If PLUMED has been compiled with xdrfile support, then also xtc and trr files can be written.</a>
+<a name="49"><span class="lineNum">      49 </span>            : To this aim one should install xdrfile library (http://www.gromacs.org/Developer_Zone/Programming_Guide/XTC_Library).</a>
+<a name="50"><span class="lineNum">      50 </span>            : If the xdrfile library is installed properly the PLUMED configure script should be able to</a>
+<a name="51"><span class="lineNum">      51 </span>            : detect it and enable it.</a>
+<a name="52"><span class="lineNum">      52 </span>            : The type of file is automatically detected from the file extension, but can be also</a>
+<a name="53"><span class="lineNum">      53 </span>            : enforced with TYPE.</a>
+<a name="54"><span class="lineNum">      54 </span>            : Importantly, if your</a>
+<a name="55"><span class="lineNum">      55 </span>            : input file contains actions that edit the atoms position (e.g. \ref WHOLEMOLECULES)</a>
+<a name="56"><span class="lineNum">      56 </span>            : and the DUMPATOMS command appears after this instruction, then the edited</a>
+<a name="57"><span class="lineNum">      57 </span>            : atom positions are output.</a>
+<a name="58"><span class="lineNum">      58 </span>            : You can control the buffering of output using the \ref FLUSH keyword on a separate line.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : Units of the printed file can be controlled with the UNITS keyword. By default PLUMED units as</a>
+<a name="61"><span class="lineNum">      61 </span>            : controlled in the \ref UNITS command are used, but one can override it e.g. with UNITS=A.</a>
+<a name="62"><span class="lineNum">      62 </span>            : Notice that gro/xtc/trr files can only contain coordinates in nm.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \par Examples</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : The following input instructs plumed to print out the positions of atoms</a>
+<a name="67"><span class="lineNum">      67 </span>            : 1-10 together with the position of the center of mass of atoms 11-20 every</a>
+<a name="68"><span class="lineNum">      68 </span>            : 10 steps to a file called file.xyz.</a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : COM ATOMS=11-20 LABEL=c1</a>
+<a name="71"><span class="lineNum">      71 </span>            : DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : Notice that the coordinates in the xyz file will be expressed in nm, since these</a>
+<a name="74"><span class="lineNum">      74 </span>            : are the defaults units in PLUMED. If you want the xyz file to be expressed in A, you should use the</a>
+<a name="75"><span class="lineNum">      75 </span>            : following input</a>
+<a name="76"><span class="lineNum">      76 </span>            : \plumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : COM ATOMS=11-20 LABEL=c1</a>
+<a name="78"><span class="lineNum">      78 </span>            : DUMPATOMS STRIDE=10 FILE=file.xyz ATOMS=1-10,c1 UNITS=A</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : As an alternative, you might want to set all the length used by PLUMED to Angstrom using the \ref UNITS</a>
+<a name="81"><span class="lineNum">      81 </span>            : action. However, this latter choice will affect all your input and output.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : The following input is very similar but dumps a .gro (gromacs) file,</a>
+<a name="84"><span class="lineNum">      84 </span>            : which also contains atom and residue names.</a>
+<a name="85"><span class="lineNum">      85 </span>            : \plumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="87"><span class="lineNum">      87 </span>            : # this is required to have proper atom names:</a>
+<a name="88"><span class="lineNum">      88 </span>            : MOLINFO STRUCTURE=reference.pdb</a>
+<a name="89"><span class="lineNum">      89 </span>            : # if omitted, atoms will have &quot;X&quot; name...</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : COM ATOMS=11-20 LABEL=c1</a>
+<a name="92"><span class="lineNum">      92 </span>            : DUMPATOMS STRIDE=10 FILE=file.gro ATOMS=1-10,c1</a>
+<a name="93"><span class="lineNum">      93 </span>            : # notice that last atom is a virtual one and will not have</a>
+<a name="94"><span class="lineNum">      94 </span>            : # a correct name in the resulting gro file</a>
+<a name="95"><span class="lineNum">      95 </span>            : \endplumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : The `file.gro` will contain coordinates expressed in nm, since this is the convention for gro files.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : In case you have compiled PLUMED with `xdrfile` library, you might even write xtc or trr files as follows</a>
+<a name="100"><span class="lineNum">     100 </span>            : \plumedfile</a>
+<a name="101"><span class="lineNum">     101 </span>            : COM ATOMS=11-20 LABEL=c1</a>
+<a name="102"><span class="lineNum">     102 </span>            : DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1</a>
+<a name="103"><span class="lineNum">     103 </span>            : \endplumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : Notice that xtc files are significantly smaller than gro and xyz files.</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : Finally, consider that gro and xtc file store coordinates with limited precision set by the</a>
+<a name="107"><span class="lineNum">     107 </span>            : `PRECISION` keyword. Default value is 3, which means &quot;3 digits after dot&quot; in nm (1/1000 of a nm).</a>
+<a name="108"><span class="lineNum">     108 </span>            : The following will write a larger xtc file with high resolution coordinates:</a>
+<a name="109"><span class="lineNum">     109 </span>            : \plumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : COM ATOMS=11-20 LABEL=c1</a>
+<a name="111"><span class="lineNum">     111 </span>            : DUMPATOMS STRIDE=10 FILE=file.xtc ATOMS=1-10,c1 PRECISION=7</a>
+<a name="112"><span class="lineNum">     112 </span>            : \endplumedfile</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : */</a>
+<a name="117"><span class="lineNum">     117 </span>            : //+ENDPLUMEDOC</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : class DumpAtoms:</a>
+<a name="120"><span class="lineNum">     120 </span>            :   public ActionAtomistic,</a>
+<a name="121"><span class="lineNum">     121 </span>            :   public ActionPilot</a>
+<a name="122"><span class="lineNum">     122 </span>            : {</a>
+<a name="123"><span class="lineNum">     123 </span>            :   OFile of;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   double lenunit;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   int iprecision;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   std::vector&lt;std::string&gt; names;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   std::vector&lt;unsigned&gt;    residueNumbers;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   std::vector&lt;std::string&gt; residueNames;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::string type;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   std::string fmt_gro_pos;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::string fmt_gro_box;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::string fmt_xyz;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   xdrfile::XDRFILE* xd;</a>
+<a name="134"><span class="lineNum">     134 </span>            : public:</a>
+<a name="135"><span class="lineNum">     135 </span>            :   explicit DumpAtoms(const ActionOptions&amp;);</a>
+<a name="136"><span class="lineNum">     136 </span>            :   ~DumpAtoms();</a>
+<a name="137"><span class="lineNum">     137 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       8971 :   void calculate() override {}</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       8971 :   void apply() override {}</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   void update() override ;</a>
+<a name="141"><span class="lineNum">     141 </span>            : };</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      12850 : PLUMED_REGISTER_ACTION(DumpAtoms,&quot;DUMPATOMS&quot;)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        175 : void DumpAtoms::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        175 :   Action::registerKeywords( keys );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        175 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        175 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        350 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the atoms should be output&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        350 :   keys.add(&quot;atoms&quot;, &quot;ATOMS&quot;, &quot;the atom indices whose positions you would like to print out&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        350 :   keys.add(&quot;compulsory&quot;, &quot;FILE&quot;, &quot;file on which to output coordinates; extension is automatically detected&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        350 :   keys.add(&quot;compulsory&quot;, &quot;UNITS&quot;,&quot;PLUMED&quot;,&quot;the units in which to print out the coordinates. PLUMED means internal PLUMED units&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        350 :   keys.add(&quot;optional&quot;, &quot;PRECISION&quot;,&quot;The number of digits in trajectory file&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        350 :   keys.add(&quot;optional&quot;, &quot;TYPE&quot;,&quot;file type, either xyz, gro, xtc, or trr, can override an automatically detected file extension&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        175 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        175 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        175 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        175 : }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        173 : DumpAtoms::DumpAtoms(const ActionOptions&amp;ao):</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   Action(ao),</a>
+<a name="162"><span class="lineNum">     162 </span>            :   ActionAtomistic(ao),</a>
+<a name="163"><span class="lineNum">     163 </span>            :   ActionPilot(ao),</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        173 :   iprecision(3)</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : {</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::string file;</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        346 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        173 :   if(file.length()==0) error(&quot;name out output file was not specified&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        173 :   type=Tools::extension(file);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        173 :   log&lt;&lt;&quot;  file name &quot;&lt;&lt;file&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        345 :   if(type==&quot;gro&quot; || type==&quot;xyz&quot; || type==&quot;xtc&quot; || type==&quot;trr&quot;) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        157 :     log&lt;&lt;&quot;  file extension indicates a &quot;&lt;&lt;type&lt;&lt;&quot; file\n&quot;;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   } else {</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         16 :     log&lt;&lt;&quot;  file extension not detected, assuming xyz\n&quot;;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :     type=&quot;xyz&quot;;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   }</a>
+<a name="178"><span class="lineNum">     178 </span>            :   std::string ntype;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        346 :   parse(&quot;TYPE&quot;,ntype);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        173 :   if(ntype.length()&gt;0) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          5 :     if(ntype!=&quot;xyz&quot; &amp;&amp; ntype!=&quot;gro&quot; &amp;&amp; ntype!=&quot;xtc&quot; &amp;&amp; ntype!=&quot;trr&quot;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :       ) error(&quot;TYPE cannot be understood&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  file type enforced to be &quot;&lt;&lt;ntype&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     type=ntype;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   fmt_gro_pos=&quot;%8.3f&quot;;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   fmt_gro_box=&quot;%12.7f&quot;;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   fmt_xyz=&quot;%f&quot;;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   std::string precision;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        346 :   parse(&quot;PRECISION&quot;,precision);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        173 :   if(precision.length()&gt;0) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         92 :     Tools::convert(precision,iprecision);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         92 :     log&lt;&lt;&quot;  with precision &quot;&lt;&lt;iprecision&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :     std::string a,b;</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         92 :     Tools::convert(iprecision+5,a);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         92 :     Tools::convert(iprecision,b);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        184 :     fmt_gro_pos=&quot;%&quot;+a+&quot;.&quot;+b+&quot;f&quot;;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     fmt_gro_box=fmt_gro_pos;</a>
+<a name="201"><span class="lineNum">     201 </span>            :     fmt_xyz=fmt_gro_box;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        346 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        346 :   std::string unitname; parse(&quot;UNITS&quot;,unitname);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        173 :   if(unitname!=&quot;PLUMED&quot;) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          4 :     Units myunit; myunit.setLength(unitname);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          6 :     if(myunit.getLength()!=1.0 &amp;&amp; type==&quot;gro&quot;) error(&quot;gro files should be in nm&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          6 :     if(myunit.getLength()!=1.0 &amp;&amp; type==&quot;xtc&quot;) error(&quot;xtc files should be in nm&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          6 :     if(myunit.getLength()!=1.0 &amp;&amp; type==&quot;trr&quot;) error(&quot;trr files should be in nm&quot;);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          4 :     lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        413 :   } else if(type==&quot;gro&quot; || type==&quot;xtc&quot; || type==&quot;trr&quot;) lenunit=plumed.getAtoms().getUnits().getLength();</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        113 :   else lenunit=1.0;</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        173 :   checkRead();</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        173 :   of.link(*this);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        173 :   of.open(file);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   std::string path=of.getPath();</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        173 :   log&lt;&lt;&quot;  Writing on file &quot;&lt;&lt;path&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   std::string mode=of.getMode();</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        173 :   if(type==&quot;xtc&quot;) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          6 :     of.close();</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          6 :     xd=xdrfile::xdrfile_open(path.c_str(),mode.c_str());</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        167 :   } else if(type==&quot;trr&quot;) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          4 :     of.close();</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          4 :     xd=xdrfile::xdrfile_open(path.c_str(),mode.c_str());</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        173 :   log.printf(&quot;  printing the following atoms in %s :&quot;, unitname.c_str() );</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      18814 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot; %d&quot;,atoms[i].serial() );</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        173 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        173 :   requestAtoms(atoms);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        173 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        173 :   if( moldat ) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         56 :     log&lt;&lt;&quot;  MOLINFO DATA found with label &quot; &lt;&lt;moldat-&gt;getLabel()&lt;&lt;&quot;, using proper atom names\n&quot;;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         56 :     names.resize(atoms.size());</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       5835 :     for(unsigned i=0; i&lt;atoms.size(); i++) if(atoms[i].index()&lt;moldat-&gt;getPDBsize()) names[i]=moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         56 :     residueNumbers.resize(atoms.size());</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       5835 :     for(unsigned i=0; i&lt;residueNumbers.size(); ++i) if(atoms[i].index()&lt;moldat-&gt;getPDBsize()) residueNumbers[i]=moldat-&gt;getResidueNumber(atoms[i]);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         56 :     residueNames.resize(atoms.size());</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       5835 :     for(unsigned i=0; i&lt;residueNames.size(); ++i) if(atoms[i].index()&lt;moldat-&gt;getPDBsize()) residueNames[i]=moldat-&gt;getResidueName(atoms[i]);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   }</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        173 : }</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       8876 : void DumpAtoms::update() {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">       8876 :   if(type==&quot;xyz&quot;) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       8290 :     of.printf(&quot;%d\n&quot;,getNumberOfAtoms());</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       8290 :     const Tensor &amp; t(getPbc().getBox());</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       8290 :     if(getPbc().isOrthorombic()) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        348 :       of.printf((&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot;\n&quot;).c_str(),lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     } else {</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">      16232 :       of.printf((&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot;\n&quot;).c_str(),</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       8116 :                 lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       8116 :                 lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">       8116 :                 lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :                );</a>
+<a name="257"><span class="lineNum">     257 </span>            :     }</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">      52064 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :       const char* defname=&quot;X&quot;;</a>
+<a name="260"><span class="lineNum">     260 </span>            :       const char* name=defname;</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">      43774 :       if(names.size()&gt;0) if(names[i].length()&gt;0) name=names[i].c_str();</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      87548 :       of.printf((&quot;%s &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot;\n&quot;).c_str(),name,lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :     }</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        586 :   } else if(type==&quot;gro&quot;) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        466 :     const Tensor &amp; t(getPbc().getBox());</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        466 :     of.printf(&quot;Made with PLUMED t=%f\n&quot;,getTime()/plumed.getAtoms().getUnits().getTime());</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        466 :     of.printf(&quot;%d\n&quot;,getNumberOfAtoms());</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      38404 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :       const char* defname=&quot;X&quot;;</a>
+<a name="270"><span class="lineNum">     270 </span>            :       const char* name=defname;</a>
+<a name="271"><span class="lineNum">     271 </span>            :       unsigned residueNumber=0;</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">      37938 :       if(names.size()&gt;0) if(names[i].length()&gt;0) name=names[i].c_str();</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">      37938 :       if(residueNumbers.size()&gt;0) residueNumber=residueNumbers[i];</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      37938 :       std::string resname=&quot;&quot;;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      37938 :       if(residueNames.size()&gt;0) resname=residueNames[i];</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      75876 :       of.printf((&quot;%5u%-5s%5s%5d&quot;+fmt_gro_pos+fmt_gro_pos+fmt_gro_pos+&quot;\n&quot;).c_str(),</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :                 residueNumber%100000,resname.c_str(),name,getAbsoluteIndex(i).serial()%100000,</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      37938 :                 lenunit*getPosition(i)(0),lenunit*getPosition(i)(1),lenunit*getPosition(i)(2));</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :     }</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        932 :     of.printf((fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot; &quot;+fmt_gro_box+&quot;\n&quot;).c_str(),</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        466 :               lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2),</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        466 :               lenunit*t(0,1),lenunit*t(0,2),lenunit*t(1,0),</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        466 :               lenunit*t(1,2),lenunit*t(2,0),lenunit*t(2,1));</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        168 :   } else if(type==&quot;xtc&quot; || type==&quot;trr&quot;) {</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     xdrfile::matrix box;</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">        120 :     const Tensor &amp; t(getPbc().getBox());</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        120 :     int natoms=getNumberOfAtoms();</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        120 :     int step=getStep();</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        120 :     float time=getTime()/plumed.getAtoms().getUnits().getTime();</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        120 :     float precision=Tools::fastpow(10.0,iprecision);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       1560 :     for(int i=0; i&lt;3; i++) for(int j=0; j&lt;3; j++) box[i][j]=lenunit*t(i,j);</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : // here we cannot use a std::vector&lt;rvec&gt; since it does not compile.</a>
+<a name="293"><span class="lineNum">     293 </span>            : // we thus use a std::unique_ptr&lt;rvec[]&gt;</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        120 :     auto pos = Tools::make_unique&lt;xdrfile::rvec[]&gt;(natoms);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">      25464 :     for(int i=0; i&lt;natoms; i++) for(int j=0; j&lt;3; j++) pos[i][j]=lenunit*getPosition(i)(j);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        120 :     if(type==&quot;xtc&quot;) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         72 :       write_xtc(xd,natoms,step,time,box,&amp;pos[0],precision);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         48 :     } else if(type==&quot;trr&quot;) {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         48 :       write_trr(xd,natoms,step,time,0.0,box,&amp;pos[0],NULL,NULL);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     }</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :   } else plumed_merror(&quot;unknown file type &quot;+type);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       8876 : }</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        346 : DumpAtoms::~DumpAtoms() {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        173 :   if(type==&quot;xtc&quot;) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          6 :     xdrfile_close(xd);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">        167 :   } else if(type==&quot;trr&quot;) {</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          4 :     xdrfile_close(xd);</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   }</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        692 : }</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : }</a>
+<a name="314"><span class="lineNum">     314 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpDerivatives.cpp.func-sort-c.html b/coverage/generic/DumpDerivatives.cpp.func-sort-c.html
new file mode 100644
index 0000000000..95663b9837
--- /dev/null
+++ b/coverage/generic/DumpDerivatives.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpDerivatives.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpDerivatives.cpp<span style="font-size: 80%;"> (<a href="DumpDerivatives.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpDerivatives.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#84">_ZN4PLMD7generic15DumpDerivativesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#125">_ZN4PLMD7generic15DumpDerivativesD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#69">_ZN4PLMD7generic12_GLOBAL__N_127DumpDerivativesRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#84">_ZN4PLMD7generic15DumpDerivativesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#125">_ZN4PLMD7generic15DumpDerivativesD0Ev</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#125">_ZN4PLMD7generic15DumpDerivativesD1Ev</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#71">_ZN4PLMD7generic15DumpDerivatives16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#69">_ZN4PLMD7generic12_GLOBAL__N_127DumpDerivativesRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#69">_ZN4PLMD7generic12_GLOBAL__N_127DumpDerivativesRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#111">_ZN4PLMD7generic15DumpDerivatives6updateEv</a></td>
+              <td class="coverFnHi">13446</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#64">_ZN4PLMD7generic15DumpDerivatives5applyEv</a></td>
+              <td class="coverFnHi">13461</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#61">_ZN4PLMD7generic15DumpDerivatives9calculateEv</a></td>
+              <td class="coverFnHi">13503</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpDerivatives.cpp.func.html b/coverage/generic/DumpDerivatives.cpp.func.html
new file mode 100644
index 0000000000..af78e3a462
--- /dev/null
+++ b/coverage/generic/DumpDerivatives.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpDerivatives.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpDerivatives.cpp<span style="font-size: 80%;"> (<a href="DumpDerivatives.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpDerivatives.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#69">_ZN4PLMD7generic12_GLOBAL__N_127DumpDerivativesRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#69">_ZN4PLMD7generic12_GLOBAL__N_127DumpDerivativesRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#69">_ZN4PLMD7generic12_GLOBAL__N_127DumpDerivativesRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#71">_ZN4PLMD7generic15DumpDerivatives16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#64">_ZN4PLMD7generic15DumpDerivatives5applyEv</a></td>
+              <td class="coverFnHi">13461</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#111">_ZN4PLMD7generic15DumpDerivatives6updateEv</a></td>
+              <td class="coverFnHi">13446</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#61">_ZN4PLMD7generic15DumpDerivatives9calculateEv</a></td>
+              <td class="coverFnHi">13503</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#84">_ZN4PLMD7generic15DumpDerivativesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#84">_ZN4PLMD7generic15DumpDerivativesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#125">_ZN4PLMD7generic15DumpDerivativesD0Ev</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#125">_ZN4PLMD7generic15DumpDerivativesD1Ev</a></td>
+              <td class="coverFnHi">282</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpDerivatives.cpp.gcov.html#125">_ZN4PLMD7generic15DumpDerivativesD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpDerivatives.cpp.gcov.html b/coverage/generic/DumpDerivatives.cpp.gcov.html
new file mode 100644
index 0000000000..592ae35626
--- /dev/null
+++ b/coverage/generic/DumpDerivatives.cpp.gcov.html
@@ -0,0 +1,209 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpDerivatives.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpDerivatives.cpp<span style="font-size: 80%;"> (source / <a href="DumpDerivatives.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace generic {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC PRINTANALYSIS DUMPDERIVATIVES</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : For a CV this line in input instructs plumed to print the derivative of the CV with respect to the atom positions</a>
+<a name="36"><span class="lineNum">      36 </span>            : and the cell vectors (virial-like form).  In contrast, for a function or bias the derivative with respect to the input &quot;CVs&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : will be output.  This command is most often used to test whether or not analytic derivatives have been implemented correctly.  This</a>
+<a name="38"><span class="lineNum">      38 </span>            : can be done by outputting the derivatives calculated analytically and numerically.  You can control the buffering of output using the \ref FLUSH keyword.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : The following input instructs plumed to write a file called deriv that contains both the</a>
+<a name="43"><span class="lineNum">      43 </span>            : analytical and numerical derivatives of the distance between atoms 1 and 2.</a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : DISTANCE ATOMS=1,2 LABEL=distance</a>
+<a name="46"><span class="lineNum">      46 </span>            : DISTANCE ATOMS=1,2 LABEL=distanceN NUMERICAL_DERIVATIVES</a>
+<a name="47"><span class="lineNum">      47 </span>            : DUMPDERIVATIVES ARG=distance,distanceN STRIDE=1 FILE=deriv</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : (See also \ref DISTANCE)</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : */</a>
+<a name="53"><span class="lineNum">      53 </span>            : //+ENDPLUMEDOC</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : class DumpDerivatives :</a>
+<a name="56"><span class="lineNum">      56 </span>            :   public ActionPilot,</a>
+<a name="57"><span class="lineNum">      57 </span>            :   public ActionWithArguments</a>
+<a name="58"><span class="lineNum">      58 </span>            : {</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::string file;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::string fmt;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   OFile of;</a>
+<a name="62"><span class="lineNum">      62 </span>            : public:</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      13503 :   void calculate() override {}</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   explicit DumpDerivatives(const ActionOptions&amp;);</a>
+<a name="65"><span class="lineNum">      65 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      13461 :   void apply() override {}</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   void update() override;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   ~DumpDerivatives();</a>
+<a name="69"><span class="lineNum">      69 </span>            : };</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      13068 : PLUMED_REGISTER_ACTION(DumpDerivatives,&quot;DUMPDERIVATIVES&quot;)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        284 : void DumpDerivatives::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        284 :   Action::registerKeywords(keys);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        284 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        284 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        284 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        568 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the derivatives should be output&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        568 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output the derivatives&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        568 :   keys.add(&quot;compulsory&quot;,&quot;FMT&quot;,&quot;%15.10f&quot;,&quot;the format with which the derivatives should be output&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        284 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        284 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        284 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        284 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        282 : DumpDerivatives::DumpDerivatives(const ActionOptions&amp;ao):</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   Action(ao),</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ActionPilot(ao),</a>
+<a name="89"><span class="lineNum">      89 </span>            :   ActionWithArguments(ao),</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        282 :   fmt(&quot;%15.10f&quot;)</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : {</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        564 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        282 :   if( file.length()==0 ) error(&quot;name of output file was not specified&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        282 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        282 :   fmt=&quot; &quot;+fmt;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        282 :   of.link(*this);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        282 :   of.open(file);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        282 :   log.printf(&quot;  on file %s\n&quot;,file.c_str());</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        282 :   log.printf(&quot;  with format %s\n&quot;,fmt.c_str());</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   unsigned nargs=getNumberOfArguments();</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        282 :   if( nargs==0 ) error(&quot;no arguments specified&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        282 :   (getPntrToArgument(0)-&gt;getPntrToAction())-&gt;turnOnDerivatives();</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        282 :   unsigned npar=getPntrToArgument(0)-&gt;getNumberOfDerivatives();</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        282 :   if( npar==0 ) error(&quot;one or more arguments has no derivatives&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        896 :   for(unsigned i=1; i&lt;nargs; i++) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        614 :     (getPntrToArgument(i)-&gt;getPntrToAction())-&gt;turnOnDerivatives();</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        614 :     if( npar!=getPntrToArgument(i)-&gt;getNumberOfDerivatives() ) error(&quot;the number of derivatives must be the same in all values being dumped&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        282 :   checkRead();</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        282 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      13446 : void DumpDerivatives::update() {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      13446 :   unsigned npar=getPntrToArgument(0)-&gt;getNumberOfDerivatives();</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     915367 :   for(unsigned ipar=0; ipar&lt;npar; ipar++) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     901921 :     of.fmtField(&quot; %f&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     901921 :     of.printField(&quot;time&quot;,getTime());</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     901921 :     of.printField(&quot;parameter&quot;,(int)ipar);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">    4516889 :     for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">    3614968 :       of.fmtField(fmt);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    3614968 :       of.printField(getPntrToArgument(i)-&gt;getName(),getPntrToArgument(i)-&gt;getDerivative(ipar) );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     901921 :     of.printField();</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      13446 : }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        564 : DumpDerivatives::~DumpDerivatives() {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        564 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpForces.cpp.func-sort-c.html b/coverage/generic/DumpForces.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b867cd9471
--- /dev/null
+++ b/coverage/generic/DumpForces.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpForces.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpForces.cpp<span style="font-size: 80%;"> (<a href="DumpForces.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpForces.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#82">_ZN4PLMD7generic10DumpForcesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#111">_ZN4PLMD7generic10DumpForcesD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#82">_ZN4PLMD7generic10DumpForcesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#111">_ZN4PLMD7generic10DumpForcesD0Ev</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#111">_ZN4PLMD7generic10DumpForcesD1Ev</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#67">_ZN4PLMD7generic12_GLOBAL__N_122DumpForcesRegisterMe696createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#69">_ZN4PLMD7generic10DumpForces16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#62">_ZN4PLMD7generic10DumpForces5applyEv</a></td>
+              <td class="coverFnHi">400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#101">_ZN4PLMD7generic10DumpForces6updateEv</a></td>
+              <td class="coverFnHi">400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#59">_ZN4PLMD7generic10DumpForces9calculateEv</a></td>
+              <td class="coverFnHi">400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#67">_ZN4PLMD7generic12_GLOBAL__N_122DumpForcesRegisterMe69C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#67">_ZN4PLMD7generic12_GLOBAL__N_122DumpForcesRegisterMe69D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpForces.cpp.func.html b/coverage/generic/DumpForces.cpp.func.html
new file mode 100644
index 0000000000..41a394bee6
--- /dev/null
+++ b/coverage/generic/DumpForces.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpForces.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpForces.cpp<span style="font-size: 80%;"> (<a href="DumpForces.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpForces.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#69">_ZN4PLMD7generic10DumpForces16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#62">_ZN4PLMD7generic10DumpForces5applyEv</a></td>
+              <td class="coverFnHi">400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#101">_ZN4PLMD7generic10DumpForces6updateEv</a></td>
+              <td class="coverFnHi">400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#59">_ZN4PLMD7generic10DumpForces9calculateEv</a></td>
+              <td class="coverFnHi">400</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#82">_ZN4PLMD7generic10DumpForcesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#82">_ZN4PLMD7generic10DumpForcesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#111">_ZN4PLMD7generic10DumpForcesD0Ev</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#111">_ZN4PLMD7generic10DumpForcesD1Ev</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#111">_ZN4PLMD7generic10DumpForcesD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#67">_ZN4PLMD7generic12_GLOBAL__N_122DumpForcesRegisterMe696createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#67">_ZN4PLMD7generic12_GLOBAL__N_122DumpForcesRegisterMe69C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpForces.cpp.gcov.html#67">_ZN4PLMD7generic12_GLOBAL__N_122DumpForcesRegisterMe69D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpForces.cpp.gcov.html b/coverage/generic/DumpForces.cpp.gcov.html
new file mode 100644
index 0000000000..6bf1ab7117
--- /dev/null
+++ b/coverage/generic/DumpForces.cpp.gcov.html
@@ -0,0 +1,195 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpForces.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpForces.cpp<span style="font-size: 80%;"> (source / <a href="DumpForces.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace generic {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC PRINTANALYSIS DUMPFORCES</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Dump the force acting on one of a values in a file.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : For a CV this command will dump</a>
+<a name="35"><span class="lineNum">      35 </span>            : the force on the CV itself. Be aware that in order to have the forces on the atoms</a>
+<a name="36"><span class="lineNum">      36 </span>            : you should multiply the output from this argument by the output from DUMPDERIVATIVES.</a>
+<a name="37"><span class="lineNum">      37 </span>            : Furthermore, also note that you can output the forces on multiple quantities simultaneously</a>
+<a name="38"><span class="lineNum">      38 </span>            : by specifying more than one argument. You can control the buffering of output using the \ref FLUSH keyword.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The following input instructs plumed to write a file called forces that contains</a>
+<a name="44"><span class="lineNum">      44 </span>            : the force acting on the distance between atoms 1 and 2.</a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : DISTANCE ATOMS=1,2 LABEL=distance</a>
+<a name="47"><span class="lineNum">      47 </span>            : DUMPFORCES ARG=distance STRIDE=1 FILE=forces</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : */</a>
+<a name="51"><span class="lineNum">      51 </span>            : //+ENDPLUMEDOC</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : class DumpForces :</a>
+<a name="54"><span class="lineNum">      54 </span>            :   public ActionPilot,</a>
+<a name="55"><span class="lineNum">      55 </span>            :   public ActionWithArguments</a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::string file;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::string fmt;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   OFile of;</a>
+<a name="60"><span class="lineNum">      60 </span>            : public:</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        400 :   void calculate() override {}</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   explicit DumpForces(const ActionOptions&amp;);</a>
+<a name="63"><span class="lineNum">      63 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        400 :   void apply() override {}</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   void update() override;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   ~DumpForces();</a>
+<a name="67"><span class="lineNum">      67 </span>            : };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      12560 : PLUMED_REGISTER_ACTION(DumpForces,&quot;DUMPFORCES&quot;)</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         30 : void DumpForces::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         30 :   Action::registerKeywords(keys);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         30 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         30 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         30 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         60 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the forces should be output&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         60 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output the forces&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         60 :   keys.add(&quot;compulsory&quot;,&quot;FMT&quot;,&quot;%15.10f&quot;,&quot;the format with which the derivatives should be output&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         30 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         30 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         30 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         30 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         28 : DumpForces::DumpForces(const ActionOptions&amp;ao):</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Action(ao),</a>
+<a name="86"><span class="lineNum">      86 </span>            :   ActionPilot(ao),</a>
+<a name="87"><span class="lineNum">      87 </span>            :   ActionWithArguments(ao),</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         28 :   fmt(&quot;%15.10f&quot;)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         56 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         28 :   if( file.length()==0 ) error(&quot;name of file was not specified&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         28 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         28 :   fmt=&quot; &quot;+fmt;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         28 :   of.link(*this);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         28 :   of.open(file);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         28 :   log.printf(&quot;  on file %s\n&quot;,file.c_str());</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         28 :   log.printf(&quot;  with format %s\n&quot;,fmt.c_str());</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         28 :   if( getNumberOfArguments()==0 ) error(&quot;no arguments have been specified&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         28 :   checkRead();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         28 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        400 : void DumpForces::update() {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        400 :   of.fmtField(&quot; %f&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        400 :   of.printField(&quot;time&quot;,getTime());</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       4992 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       4592 :     of.fmtField(fmt);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       4592 :     of.printField(getPntrToArgument(i)-&gt;getName(),getPntrToArgument(i)-&gt;getForce());</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        400 :   of.printField();</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        400 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         56 : DumpForces::~DumpForces() {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         56 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpMassCharge.cpp.func-sort-c.html b/coverage/generic/DumpMassCharge.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c3222ddc4a
--- /dev/null
+++ b/coverage/generic/DumpMassCharge.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpMassCharge.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpMassCharge.cpp<span style="font-size: 80%;"> (<a href="DumpMassCharge.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpMassCharge.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#107">_ZN4PLMD7generic14DumpMassChargeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#181">_ZN4PLMD7generic14DumpMassChargeD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#94">_ZN4PLMD7generic12_GLOBAL__N_126DumpMassChargeRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#107">_ZN4PLMD7generic14DumpMassChargeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#181">_ZN4PLMD7generic14DumpMassChargeD0Ev</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#181">_ZN4PLMD7generic14DumpMassChargeD1Ev</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#96">_ZN4PLMD7generic14DumpMassCharge16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#90">_ZN4PLMD7generic14DumpMassCharge5applyEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#164">_ZN4PLMD7generic14DumpMassCharge6updateEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#157">_ZN4PLMD7generic14DumpMassCharge7prepareEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#89">_ZN4PLMD7generic14DumpMassCharge9calculateEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#94">_ZN4PLMD7generic12_GLOBAL__N_126DumpMassChargeRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#94">_ZN4PLMD7generic12_GLOBAL__N_126DumpMassChargeRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpMassCharge.cpp.func.html b/coverage/generic/DumpMassCharge.cpp.func.html
new file mode 100644
index 0000000000..1989dcdaa4
--- /dev/null
+++ b/coverage/generic/DumpMassCharge.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpMassCharge.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpMassCharge.cpp<span style="font-size: 80%;"> (<a href="DumpMassCharge.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpMassCharge.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#94">_ZN4PLMD7generic12_GLOBAL__N_126DumpMassChargeRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#94">_ZN4PLMD7generic12_GLOBAL__N_126DumpMassChargeRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#94">_ZN4PLMD7generic12_GLOBAL__N_126DumpMassChargeRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#96">_ZN4PLMD7generic14DumpMassCharge16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#90">_ZN4PLMD7generic14DumpMassCharge5applyEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#164">_ZN4PLMD7generic14DumpMassCharge6updateEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#157">_ZN4PLMD7generic14DumpMassCharge7prepareEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#89">_ZN4PLMD7generic14DumpMassCharge9calculateEv</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#107">_ZN4PLMD7generic14DumpMassChargeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#107">_ZN4PLMD7generic14DumpMassChargeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#181">_ZN4PLMD7generic14DumpMassChargeD0Ev</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#181">_ZN4PLMD7generic14DumpMassChargeD1Ev</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMassCharge.cpp.gcov.html#181">_ZN4PLMD7generic14DumpMassChargeD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpMassCharge.cpp.gcov.html b/coverage/generic/DumpMassCharge.cpp.gcov.html
new file mode 100644
index 0000000000..f4a6daa114
--- /dev/null
+++ b/coverage/generic/DumpMassCharge.cpp.gcov.html
@@ -0,0 +1,264 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpMassCharge.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpMassCharge.cpp<span style="font-size: 80%;"> (source / <a href="DumpMassCharge.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD</a>
+<a name="30"><span class="lineNum">      30 </span>            : {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace generic {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC PRINTANALYSIS DUMPMASSCHARGE</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Dump masses and charges on a selected file.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This command dumps a file containing charges and masses.</a>
+<a name="38"><span class="lineNum">      38 </span>            : It does so only once in the simulation (at first step).</a>
+<a name="39"><span class="lineNum">      39 </span>            : File can be recycled in the \ref driver tool.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : Notice that masses and charges are only written once at the beginning</a>
+<a name="42"><span class="lineNum">      42 </span>            : of the simulation. In case no atom list is provided, charges and</a>
+<a name="43"><span class="lineNum">      43 </span>            : masses for all atoms are written.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : You can add the DUMPMASSCHARGE action at the end of the plumed.dat</a>
+<a name="48"><span class="lineNum">      48 </span>            : file that you use during an MD simulations:</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \plumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : c1: COM ATOMS=1-10</a>
+<a name="52"><span class="lineNum">      52 </span>            : c2: COM ATOMS=11-20</a>
+<a name="53"><span class="lineNum">      53 </span>            : DUMPATOMS ATOMS=c1,c2 FILE=coms.xyz STRIDE=100</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : DUMPMASSCHARGE FILE=mcfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : In this way, you will be able to use the same masses while processing</a>
+<a name="59"><span class="lineNum">      59 </span>            : a trajectory from the \ref driver . To do so, you need to</a>
+<a name="60"><span class="lineNum">      60 </span>            : add the --mc flag on the driver command line, e.g.</a>
+<a name="61"><span class="lineNum">      61 </span>            : \verbatim</a>
+<a name="62"><span class="lineNum">      62 </span>            : plumed driver --mc mcfile --plumed plumed.dat --ixyz traj.xyz</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endverbatim</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : With the following input you can dump only the charges for a specific</a>
+<a name="66"><span class="lineNum">      66 </span>            : group:</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : solute_ions: GROUP ATOMS=1-121,200-2012</a>
+<a name="70"><span class="lineNum">      70 </span>            : DUMPATOMS FILE=traj.gro ATOMS=solute_ions STRIDE=100</a>
+<a name="71"><span class="lineNum">      71 </span>            : DUMPMASSCHARGE FILE=mcfile ATOMS=solute_ions</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : */</a>
+<a name="75"><span class="lineNum">      75 </span>            : //+ENDPLUMEDOC</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : class DumpMassCharge:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   public ActionAtomistic,</a>
+<a name="79"><span class="lineNum">      79 </span>            :   public ActionPilot</a>
+<a name="80"><span class="lineNum">      80 </span>            : {</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::string file;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   bool first;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool second;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   bool print_masses;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   bool print_charges;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   explicit DumpMassCharge(const ActionOptions&amp;);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ~DumpMassCharge();</a>
+<a name="89"><span class="lineNum">      89 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void prepare() override;</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         84 :   void calculate() override {}</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         84 :   void apply() override {}</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   void update() override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(DumpMassCharge,&quot;DUMPMASSCHARGE&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         14 : void DumpMassCharge::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         14 :   Action::registerKeywords( keys );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         14 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         14 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the atoms should be output&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         28 :   keys.add(&quot;atoms&quot;, &quot;ATOMS&quot;, &quot;the atom indices whose charges and masses you would like to print out&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;, &quot;FILE&quot;, &quot;file on which to output charges and masses.&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         28 :   keys.addFlag(&quot;ONLY_MASSES&quot;,false,&quot;Only output masses to file&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         28 :   keys.addFlag(&quot;ONLY_CHARGES&quot;,false,&quot;Only output charges to file&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         14 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         12 : DumpMassCharge::DumpMassCharge(const ActionOptions&amp;ao):</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   Action(ao),</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ActionAtomistic(ao),</a>
+<a name="112"><span class="lineNum">     112 </span>            :   ActionPilot(ao),</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         12 :   first(true),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         12 :   second(true),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         12 :   print_masses(true),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         12 :   print_charges(true)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : {</a>
+<a name="118"><span class="lineNum">     118 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         24 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         12 :   if(file.length()==0) error(&quot;name of output file was not specified&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         12 :   log.printf(&quot;  output written to file %s\n&quot;,file.c_str());</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         24 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         12 :   if(atoms.size()==0) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        720 :     for(int i=0; i&lt;plumed.getAtoms().getNatoms(); i++) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        712 :       atoms.push_back(AtomNumber::index(i));</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     }</a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         12 :   bool only_masses = false;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         12 :   parseFlag(&quot;ONLY_MASSES&quot;,only_masses);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         12 :   if(only_masses) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :     print_charges = false;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :     log.printf(&quot;  only masses will be written to file\n&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         12 :   bool only_charges = false;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         12 :   parseFlag(&quot;ONLY_CHARGES&quot;,only_charges);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         12 :   if(only_charges) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :     print_masses = false;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :     log.printf(&quot;  only charges will be written to file\n&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         12 :   checkRead();</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         12 :   log.printf(&quot;  printing the following atoms:&quot; );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1006 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot; %d&quot;,atoms[i].serial() );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         12 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         12 :   requestAtoms(atoms);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         12 :   if(only_masses &amp;&amp; only_charges) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;using both ONLY_MASSES and ONLY_CHARGES doesn't make sense&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         12 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         84 : void DumpMassCharge::prepare() {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         84 :   if(!first &amp;&amp; second) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         12 :     requestAtoms(std::vector&lt;AtomNumber&gt;());</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         12 :     second=false;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         84 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         84 : void DumpMassCharge::update() {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         84 :   if(!first) return;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         12 :   first=false;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         12 :   OFile of;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         12 :   of.link(*this);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         12 :   of.open(file);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       1006 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        994 :     int ii=getAbsoluteIndex(i).index();</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        994 :     of.printField(&quot;index&quot;,ii);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       1880 :     if(print_masses) {of.printField(&quot;mass&quot;,getMass(i));}</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       1880 :     if(print_charges) {of.printField(&quot;charge&quot;,getCharge(i));}</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        994 :     of.printField();</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   }</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         12 : }</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         24 : DumpMassCharge::~DumpMassCharge() {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         24 : }</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpProjections.cpp.func-sort-c.html b/coverage/generic/DumpProjections.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b1e5832169
--- /dev/null
+++ b/coverage/generic/DumpProjections.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpProjections.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpProjections.cpp<span style="font-size: 80%;"> (<a href="DumpProjections.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpProjections.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#80">_ZN4PLMD7generic15DumpProjectionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#112">_ZN4PLMD7generic15DumpProjectionsD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#80">_ZN4PLMD7generic15DumpProjectionsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
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+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#112">_ZN4PLMD7generic15DumpProjectionsD0Ev</a></td>
+              <td class="coverFnHi">1</td>
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+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#112">_ZN4PLMD7generic15DumpProjectionsD1Ev</a></td>
+              <td class="coverFnHi">1</td>
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+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#67">_ZN4PLMD7generic15DumpProjections16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#59">_ZN4PLMD7generic15DumpProjections5applyEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#101">_ZN4PLMD7generic15DumpProjections6updateEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#56">_ZN4PLMD7generic15DumpProjections9calculateEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#61">_ZNK4PLMD7generic15DumpProjections19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#65">_ZN4PLMD7generic12_GLOBAL__N_127DumpProjectionsRegisterMe67C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#65">_ZN4PLMD7generic12_GLOBAL__N_127DumpProjectionsRegisterMe67D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpProjections.cpp.func.html b/coverage/generic/DumpProjections.cpp.func.html
new file mode 100644
index 0000000000..af9c7888f7
--- /dev/null
+++ b/coverage/generic/DumpProjections.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpProjections.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpProjections.cpp<span style="font-size: 80%;"> (<a href="DumpProjections.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpProjections.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#65">_ZN4PLMD7generic12_GLOBAL__N_127DumpProjectionsRegisterMe676createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#65">_ZN4PLMD7generic12_GLOBAL__N_127DumpProjectionsRegisterMe67C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#65">_ZN4PLMD7generic12_GLOBAL__N_127DumpProjectionsRegisterMe67D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#67">_ZN4PLMD7generic15DumpProjections16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#59">_ZN4PLMD7generic15DumpProjections5applyEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#101">_ZN4PLMD7generic15DumpProjections6updateEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#56">_ZN4PLMD7generic15DumpProjections9calculateEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#80">_ZN4PLMD7generic15DumpProjectionsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#80">_ZN4PLMD7generic15DumpProjectionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#112">_ZN4PLMD7generic15DumpProjectionsD0Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#112">_ZN4PLMD7generic15DumpProjectionsD1Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#112">_ZN4PLMD7generic15DumpProjectionsD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpProjections.cpp.gcov.html#61">_ZNK4PLMD7generic15DumpProjections19checkNeedsGradientsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/DumpProjections.cpp.gcov.html b/coverage/generic/DumpProjections.cpp.gcov.html
new file mode 100644
index 0000000000..de63d514db
--- /dev/null
+++ b/coverage/generic/DumpProjections.cpp.gcov.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/DumpProjections.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - DumpProjections.cpp<span style="font-size: 80%;"> (source / <a href="DumpProjections.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace generic {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC PRINTANALYSIS DUMPPROJECTIONS</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Dump the derivatives with respect to the input parameters for one or more objects (generally CVs, functions or biases).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \par Examples</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : Compute the distance between two groups and write on a file the</a>
+<a name="38"><span class="lineNum">      38 </span>            : derivatives of this distance with respect to all the atoms of the two groups</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \plumedfile</a>
+<a name="41"><span class="lineNum">      41 </span>            : x1: CENTER ATOMS=1-10</a>
+<a name="42"><span class="lineNum">      42 </span>            : x2: CENTER ATOMS=11-20</a>
+<a name="43"><span class="lineNum">      43 </span>            : d: DISTANCE ATOMS=x1,x2</a>
+<a name="44"><span class="lineNum">      44 </span>            : DUMPPROJECTIONS ARG=d FILE=proj STRIDE=20</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : class DumpProjections :</a>
+<a name="51"><span class="lineNum">      51 </span>            :   public ActionPilot,</a>
+<a name="52"><span class="lineNum">      52 </span>            :   public ActionWithArguments</a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::string file;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::string fmt;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   OFile of;</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 :   void calculate() override {}</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   explicit DumpProjections(const ActionOptions&amp;);</a>
+<a name="60"><span class="lineNum">      60 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          3 :   void apply() override {}</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   void update() override;</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          3 :   bool checkNeedsGradients()const override {return true;}</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   ~DumpProjections();</a>
+<a name="65"><span class="lineNum">      65 </span>            : };</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(DumpProjections,&quot;DUMPPROJECTIONS&quot;)</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          3 : void DumpProjections::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          3 :   Action::registerKeywords(keys);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          3 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          3 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          3 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the derivatives should be output&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output the derivatives&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FMT&quot;,&quot;%15.10f&quot;,&quot;the format with which the derivatives should be output&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          3 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          3 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          3 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 : DumpProjections::DumpProjections(const ActionOptions&amp;ao):</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   Action(ao),</a>
+<a name="84"><span class="lineNum">      84 </span>            :   ActionPilot(ao),</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ActionWithArguments(ao),</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 :   fmt(&quot;%15.10f&quot;)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 :   if( file.length()==0 ) error(&quot;filename not specified&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          1 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          1 :   fmt=&quot; &quot;+fmt;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          1 :   of.open(file);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          1 :   log.printf(&quot;  on file %s\n&quot;,file.c_str());</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 :   log.printf(&quot;  with format %s\n&quot;,fmt.c_str());</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :     (getPntrToArgument(i)-&gt;getPntrToAction())-&gt;turnOnDerivatives();</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          1 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          3 : void DumpProjections::update() {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   of.fmtField(&quot; %f&quot;).printField(&quot;time&quot;,getTime());</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          9 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         18 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         12 :       of.fmtField(fmt);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         24 :       of.printField(getPntrToArgument(i)-&gt;getName()+&quot;-&quot;+getPntrToArgument(j)-&gt;getName(),getProjection(i,j));</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     }</a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          3 :   of.printField();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 : DumpProjections::~DumpProjections() {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/EffectiveEnergyDrift.cpp.func-sort-c.html b/coverage/generic/EffectiveEnergyDrift.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d81a56a153
--- /dev/null
+++ b/coverage/generic/EffectiveEnergyDrift.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/EffectiveEnergyDrift.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - EffectiveEnergyDrift.cpp<span style="font-size: 80%;"> (<a href="EffectiveEnergyDrift.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EffectiveEnergyDrift.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#137">_ZN4PLMD7generic20EffectiveEnergyDriftC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#191">_ZN4PLMD7generic20EffectiveEnergyDriftD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#121">_ZN4PLMD7generic12_GLOBAL__N_133EffectiveEnergyDriftRegisterMe1236createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#137">_ZN4PLMD7generic20EffectiveEnergyDriftC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#191">_ZN4PLMD7generic20EffectiveEnergyDriftD0Ev</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#191">_ZN4PLMD7generic20EffectiveEnergyDriftD1Ev</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#123">_ZN4PLMD7generic20EffectiveEnergyDrift16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#117">_ZN4PLMD7generic20EffectiveEnergyDrift5applyEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#195">_ZN4PLMD7generic20EffectiveEnergyDrift6updateEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#116">_ZN4PLMD7generic20EffectiveEnergyDrift9calculateEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#121">_ZN4PLMD7generic12_GLOBAL__N_133EffectiveEnergyDriftRegisterMe123C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#121">_ZN4PLMD7generic12_GLOBAL__N_133EffectiveEnergyDriftRegisterMe123D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/EffectiveEnergyDrift.cpp.func.html b/coverage/generic/EffectiveEnergyDrift.cpp.func.html
new file mode 100644
index 0000000000..5f002f3919
--- /dev/null
+++ b/coverage/generic/EffectiveEnergyDrift.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/EffectiveEnergyDrift.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - EffectiveEnergyDrift.cpp<span style="font-size: 80%;"> (<a href="EffectiveEnergyDrift.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EffectiveEnergyDrift.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#121">_ZN4PLMD7generic12_GLOBAL__N_133EffectiveEnergyDriftRegisterMe1236createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#121">_ZN4PLMD7generic12_GLOBAL__N_133EffectiveEnergyDriftRegisterMe123C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#121">_ZN4PLMD7generic12_GLOBAL__N_133EffectiveEnergyDriftRegisterMe123D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#123">_ZN4PLMD7generic20EffectiveEnergyDrift16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#117">_ZN4PLMD7generic20EffectiveEnergyDrift5applyEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#195">_ZN4PLMD7generic20EffectiveEnergyDrift6updateEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#116">_ZN4PLMD7generic20EffectiveEnergyDrift9calculateEv</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#137">_ZN4PLMD7generic20EffectiveEnergyDriftC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#137">_ZN4PLMD7generic20EffectiveEnergyDriftC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#191">_ZN4PLMD7generic20EffectiveEnergyDriftD0Ev</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#191">_ZN4PLMD7generic20EffectiveEnergyDriftD1Ev</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EffectiveEnergyDrift.cpp.gcov.html#191">_ZN4PLMD7generic20EffectiveEnergyDriftD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/EffectiveEnergyDrift.cpp.gcov.html b/coverage/generic/EffectiveEnergyDrift.cpp.gcov.html
new file mode 100644
index 0000000000..2240e8d20a
--- /dev/null
+++ b/coverage/generic/EffectiveEnergyDrift.cpp.gcov.html
@@ -0,0 +1,411 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/EffectiveEnergyDrift.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - EffectiveEnergyDrift.cpp<span style="font-size: 80%;"> (source / <a href="EffectiveEnergyDrift.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /*</a>
+<a name="24"><span class="lineNum">      24 </span>            :  This class was originally written by Marco Jacopo Ferrarotti</a>
+<a name="25"><span class="lineNum">      25 </span>            :  (marco.ferrarotti@gmail.com) and Giovanni Bussi</a>
+<a name="26"><span class="lineNum">      26 </span>            : */</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;algorithm&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace generic {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //+PLUMEDOC GENERIC EFFECTIVE_ENERGY_DRIFT</a>
+<a name="45"><span class="lineNum">      45 </span>            : /*</a>
+<a name="46"><span class="lineNum">      46 </span>            : Print the effective energy drift</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The method used to calculate the effective energy drift is described in Ref \cite Ferrarotti2015</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \par Examples</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : This is to monitor the effective energy drift for a metadynamics</a>
+<a name="55"><span class="lineNum">      55 </span>            : simulation on the Debye-Huckel energy. Since this variable is very expensive,</a>
+<a name="56"><span class="lineNum">      56 </span>            : it could be conveniently computed every second step.</a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : dh: DHENERGY GROUPA=1-10 GROUPB=11-20 EPSILON=80.0 I=0.1 TEMP=300.0</a>
+<a name="59"><span class="lineNum">      59 </span>            : METAD ARG=dh HEIGHT=0.5 SIGMA=0.1 PACE=500 STRIDE=2</a>
+<a name="60"><span class="lineNum">      60 </span>            : EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : This is to monitor if a restraint is too stiff</a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : d: DISTANCE ATOMS=10,20</a>
+<a name="66"><span class="lineNum">      66 </span>            : RESTRAINT ARG=d KAPPA=100000 AT=0.6</a>
+<a name="67"><span class="lineNum">      67 </span>            : EFFECTIVE_ENERGY_DRIFT PRINT_STRIDE=100 FILE=eff</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : */</a>
+<a name="71"><span class="lineNum">      71 </span>            : //+ENDPLUMEDOC</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : class EffectiveEnergyDrift:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   public ActionPilot {</a>
+<a name="76"><span class="lineNum">      76 </span>            :   OFile output;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   long long int printStride;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::string fmt;</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   double eed;</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   Atoms&amp; atoms;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;ActionWithValue*&gt; biases;</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   long long int pDdStep;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   int nLocalAtoms;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   int pNLocalAtoms;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;int&gt; pGatindex;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;Vector&gt; positions;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;Vector&gt; pPositions;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;Vector&gt; forces;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;Vector&gt; pForces;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   Tensor box,pbox;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   Tensor fbox,pfbox;</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            :   const int nProc;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt;int&gt; indexCnt;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;int&gt; indexDsp;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::vector&lt;int&gt; dataCnt;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;int&gt; dataDsp;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;int&gt; indexS;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;int&gt; indexR;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;double&gt; dataS;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;double&gt; dataR;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;int&gt; backmap;</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   double initialBias;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   bool isFirstStep;</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   bool ensemble;</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : public:</a>
+<a name="113"><span class="lineNum">     113 </span>            :   explicit EffectiveEnergyDrift(const ActionOptions&amp;);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ~EffectiveEnergyDrift();</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        450 :   void calculate() override {};</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        450 :   void apply() override {};</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   void update() override;</a>
+<a name="121"><span class="lineNum">     121 </span>            : };</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(EffectiveEnergyDrift,&quot;EFFECTIVE_ENERGY_DRIFT&quot;)</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         11 : void EffectiveEnergyDrift::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         11 :   Action::registerKeywords( keys );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         11 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;should be set to 1. Effective energy drift computation has to be active at each step.&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;, &quot;FILE&quot;, &quot;file on which to output the effective energy drift.&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;, &quot;PRINT_STRIDE&quot;, &quot;frequency to which output the effective energy drift on FILE&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         22 :   keys.addFlag(&quot;ENSEMBLE&quot;,false,&quot;Set to TRUE if you want to average over multiple replicas.&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format that should be used to output real numbers&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         11 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         11 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         11 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         11 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          9 : EffectiveEnergyDrift::EffectiveEnergyDrift(const ActionOptions&amp;ao):</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   Action(ao),</a>
+<a name="141"><span class="lineNum">     141 </span>            :   ActionPilot(ao),</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          9 :   fmt(&quot;%f&quot;),</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          9 :   eed(0.0),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          9 :   atoms(plumed.getAtoms()),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          9 :   nProc(plumed.comm.Get_size()),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          9 :   initialBias(0.0),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :   isFirstStep(true),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         27 :   ensemble(false)</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : {</a>
+<a name="150"><span class="lineNum">     150 </span>            :   //stride must be == 1</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          9 :   if(getStride()!=1) error(&quot;EFFECTIVE_ENERGY_DRIFT must have STRIDE=1 to work properly&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   //parse and open FILE</a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::string fileName;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         18 :   parse(&quot;FILE&quot;,fileName);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          9 :   if(fileName.length()==0) error(&quot;name out output file was not specified\n&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          9 :   output.link(*this);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          9 :   output.open(fileName);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   //parse PRINT_STRIDE</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          9 :   parse(&quot;PRINT_STRIDE&quot;,printStride);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            :   //parse FMT</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          9 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          9 :   fmt=&quot; &quot;+fmt;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          9 :   log.printf(&quot;  with format %s\n&quot;,fmt.c_str());</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   //parse ENSEMBLE</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          9 :   ensemble=false;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          9 :   parseFlag(&quot;ENSEMBLE&quot;,ensemble);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          9 :   if(ensemble&amp;&amp;comm.Get_rank()==0) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     if(multi_sim_comm.Get_size()&lt;2) error(&quot;You CANNOT run Replica-Averaged simulations without running multiple replicas!\n&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         18 :   log&lt;&lt;&quot;Bibliography &quot;&lt;&lt;cite(&quot;Ferrarotti, Bottaro, Perez-Villa, and Bussi, J. Chem. Theory Comput. 11, 139 (2015)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   //construct biases from ActionWithValue with a component named bias</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          9 :   std::vector&lt;ActionWithValue*&gt; tmpActions=plumed.getActionSet().select&lt;ActionWithValue*&gt;();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         27 :   for(unsigned i=0; i&lt;tmpActions.size(); i++) if(tmpActions[i]-&gt;exists(tmpActions[i]-&gt;getLabel()+&quot;.bias&quot;)) biases.push_back(tmpActions[i]);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :   //resize counters and displacements useful to communicate with MPI_Allgatherv</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          9 :   indexCnt.resize(nProc);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          9 :   indexDsp.resize(nProc);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          9 :   dataCnt.resize(nProc);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          9 :   dataDsp.resize(nProc);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   //resize the received buffers</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          9 :   indexR.resize(atoms.getNatoms());</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          9 :   dataR.resize(atoms.getNatoms()*6);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          9 :   backmap.resize(atoms.getNatoms());</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          9 : }</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         18 : EffectiveEnergyDrift::~EffectiveEnergyDrift() {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         18 : }</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        450 : void EffectiveEnergyDrift::update() {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        450 :   bool pbc=atoms.getPbc().isSet();</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   //retrieve data of local atoms</a>
+<a name="201"><span class="lineNum">     201 </span>            :   const std::vector&lt;int&gt;&amp; gatindex = atoms.getGatindex();</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        450 :   nLocalAtoms = gatindex.size();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        450 :   atoms.getLocalPositions(positions);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        450 :   atoms.getLocalForces(forces);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        450 :   if(pbc) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        450 :     Tensor B=atoms.getPbc().getBox();</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        450 :     Tensor IB=atoms.getPbc().getInvBox();</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        450 :     #pragma omp parallel for</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :     for(unsigned i=0; i&lt;positions.size(); ++i) {</a>
+<a name="210"><span class="lineNum">     210 </span>            :       positions[i]=matmul(positions[i],IB);</a>
+<a name="211"><span class="lineNum">     211 </span>            :       forces[i]=matmul(B,forces[i]);</a>
+<a name="212"><span class="lineNum">     212 </span>            :     }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        450 :     box=B;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        450 :     fbox=matmul(transpose(inverse(box)),atoms.getVirial());</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   //init stored data at the first step</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        450 :   if(isFirstStep) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          9 :     pDdStep=0;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          9 :     pGatindex = atoms.getGatindex();</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          9 :     pNLocalAtoms = pGatindex.size();</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          9 :     pPositions=positions;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          9 :     pForces=forces;</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          9 :     pbox=box;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          9 :     pfbox=fbox;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          9 :     initialBias=plumed.getBias();</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          9 :     isFirstStep=false;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :   //if the dd has changed we have to reshare the stored data</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        450 :   if(pDdStep&lt;atoms.getDdStep() &amp;&amp; nLocalAtoms&lt;atoms.getNatoms()) {</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     //prepare the data to be sent</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        204 :     indexS.resize(pNLocalAtoms);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        204 :     dataS.resize(pNLocalAtoms*6);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       5712 :     for(int i=0; i&lt;pNLocalAtoms; i++) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       5508 :       indexS[i] = pGatindex[i];</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       5508 :       dataS[i*6] = pPositions[i][0];</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       5508 :       dataS[i*6+1] = pPositions[i][1];</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       5508 :       dataS[i*6+2] = pPositions[i][2];</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">       5508 :       dataS[i*6+3] = pForces[i][0];</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       5508 :       dataS[i*6+4] = pForces[i][1];</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">       5508 :       dataS[i*6+5] = pForces[i][2];</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :     }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :     //setup the counters and displacements for the communication</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        204 :     plumed.comm.Allgather(&amp;pNLocalAtoms,1,&amp;indexCnt[0],1);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        204 :     indexDsp[0] = 0;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       1020 :     for(int i=0; i&lt;nProc; i++) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        816 :       dataCnt[i] = indexCnt[i]*6;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        816 :       if(i+1&lt;nProc) indexDsp[i+1] = indexDsp[i]+indexCnt[i];</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        816 :       dataDsp[i] = indexDsp[i]*6;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :     //share stored data</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        402 :     plumed.comm.Allgatherv((!indexS.empty()?&amp;indexS[0]:NULL), pNLocalAtoms, &amp;indexR[0], &amp;indexCnt[0], &amp;indexDsp[0]);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        402 :     plumed.comm.Allgatherv((!dataS.empty()?&amp;dataS[0]:NULL), pNLocalAtoms*6, &amp;dataR[0], &amp;dataCnt[0], &amp;dataDsp[0]);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :     //resize vectors to store the proper amount of data</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        204 :     pGatindex.resize(nLocalAtoms);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        204 :     pPositions.resize(nLocalAtoms);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        204 :     pForces.resize(nLocalAtoms);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :     //compute backmap</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">      22236 :     for(unsigned j=0; j&lt;indexR.size(); j++) backmap[indexR[j]]=j;</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :     //fill the vectors pGatindex, pPositions and pForces</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       5712 :     for(int i=0; i&lt;nLocalAtoms; i++) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       5508 :       int glb=backmap[gatindex[i]];</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       5508 :       pGatindex[i] = indexR[glb];</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       5508 :       pPositions[i][0] = dataR[glb*6];</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       5508 :       pPositions[i][1] = dataR[glb*6+1];</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       5508 :       pPositions[i][2] = dataR[glb*6+2];</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       5508 :       pForces[i][0] = dataR[glb*6+3];</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       5508 :       pForces[i][1] = dataR[glb*6+4];</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       5508 :       pForces[i][2] = dataR[glb*6+5];</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :     }</a>
+<a name="280"><span class="lineNum">     280 </span>            :   }</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   //compute the effective energy drift on local atoms</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        450 :   double eed_tmp=eed;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        450 :   #pragma omp parallel for reduction(+:eed_tmp)</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   for(int i=0; i&lt;nLocalAtoms; i++) {</a>
+<a name="287"><span class="lineNum">     287 </span>            :     Vector dst=delta(pPositions[i],positions[i]);</a>
+<a name="288"><span class="lineNum">     288 </span>            :     if(pbc) for(unsigned k=0; k&lt;3; k++) dst[k]=Tools::pbc(dst[k]);</a>
+<a name="289"><span class="lineNum">     289 </span>            :     eed_tmp += dotProduct(dst, forces[i]+pForces[i])*0.5;</a>
+<a name="290"><span class="lineNum">     290 </span>            :   }</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        450 :   eed=eed_tmp;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        450 :   if(plumed.comm.Get_rank()==0) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       1950 :     for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++)</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       1350 :         eed-=0.5*(pfbox(i,j)+fbox(i,j))*(box(i,j)-pbox(i,j));</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :   //print the effective energy drift on FILE with frequency PRINT_STRIDE</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        450 :   if(plumed.getStep()%printStride==0) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        450 :     double eedSum = eed;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     double bias = 0.0;</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            :     //we cannot just use plumed.getBias() because it will be ==0.0 if PRINT_STRIDE</a>
+<a name="306"><span class="lineNum">     306 </span>            :     //is not a multiple of the bias actions stride</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">        900 :     for(unsigned i=0; i&lt;biases.size(); i++) bias+=biases[i]-&gt;getOutputQuantity(&quot;bias&quot;);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        450 :     plumed.comm.Sum(&amp;eedSum,1);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        450 :     double effective = eedSum+bias-initialBias-plumed.getWork();</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :     // this is to take into account ensemble averaging</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        450 :     if(ensemble) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :       if(plumed.comm.Get_rank()==0) plumed.multi_sim_comm.Sum(&amp;effective,1);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :       else effective=0.;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :       plumed.comm.Sum(&amp;effective,1);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     }</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        450 :     output.fmtField(&quot; %f&quot;);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        450 :     output.printField(&quot;time&quot;,getTime());</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        450 :     output.fmtField(fmt);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        450 :     output.printField(&quot;effective-energy&quot;,effective);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        450 :     output.printField();</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   }</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :   //store the data of the current step</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">        450 :   pDdStep = atoms.getDdStep();</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">        450 :   pNLocalAtoms = nLocalAtoms;</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :   pPositions.swap(positions);</a>
+<a name="329"><span class="lineNum">     329 </span>            :   pForces.swap(forces);</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        450 :   pbox=box;</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        450 :   pfbox=fbox;</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        450 : }</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            : }</a>
+<a name="335"><span class="lineNum">     335 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/EndPlumed.cpp.func-sort-c.html b/coverage/generic/EndPlumed.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2652d5105f
--- /dev/null
+++ b/coverage/generic/EndPlumed.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/EndPlumed.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - EndPlumed.cpp<span style="font-size: 80%;"> (<a href="EndPlumed.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EndPlumed.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#60">_ZN4PLMD7generic9EndPlumed5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#59">_ZN4PLMD7generic9EndPlumed9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#63">_ZN4PLMD7generic12_GLOBAL__N_121EndPlumedRegisterMe656createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">263</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#69">_ZN4PLMD7generic9EndPlumedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">263</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#65">_ZN4PLMD7generic9EndPlumed16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">265</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#63">_ZN4PLMD7generic12_GLOBAL__N_121EndPlumedRegisterMe65C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#63">_ZN4PLMD7generic12_GLOBAL__N_121EndPlumedRegisterMe65D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/EndPlumed.cpp.func.html b/coverage/generic/EndPlumed.cpp.func.html
new file mode 100644
index 0000000000..c9f82d240d
--- /dev/null
+++ b/coverage/generic/EndPlumed.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/EndPlumed.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - EndPlumed.cpp<span style="font-size: 80%;"> (<a href="EndPlumed.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EndPlumed.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#63">_ZN4PLMD7generic12_GLOBAL__N_121EndPlumedRegisterMe656createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">263</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#63">_ZN4PLMD7generic12_GLOBAL__N_121EndPlumedRegisterMe65C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#63">_ZN4PLMD7generic12_GLOBAL__N_121EndPlumedRegisterMe65D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#65">_ZN4PLMD7generic9EndPlumed16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">265</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#60">_ZN4PLMD7generic9EndPlumed5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#59">_ZN4PLMD7generic9EndPlumed9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EndPlumed.cpp.gcov.html#69">_ZN4PLMD7generic9EndPlumedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">263</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/EndPlumed.cpp.gcov.html b/coverage/generic/EndPlumed.cpp.gcov.html
new file mode 100644
index 0000000000..7e7c2c0a32
--- /dev/null
+++ b/coverage/generic/EndPlumed.cpp.gcov.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/EndPlumed.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - EndPlumed.cpp<span style="font-size: 80%;"> (source / <a href="EndPlumed.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace generic {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC GENERIC ENDPLUMED</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Terminate plumed input.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Can be used to effectively comment out the rest of the input file.</a>
+<a name="34"><span class="lineNum">      34 </span>            : It can be useful to quickly ignore part of a long input file. However,</a>
+<a name="35"><span class="lineNum">      35 </span>            : one should keep in mind that when opening the file it might be difficult to</a>
+<a name="36"><span class="lineNum">      36 </span>            : find where the commented out part begins. Regular comments (with `#`) are</a>
+<a name="37"><span class="lineNum">      37 </span>            : usually easier to read. Notice that \ref VimSyntax &quot;VIM syntax&quot; should be able</a>
+<a name="38"><span class="lineNum">      38 </span>            : to detect this command and properly mark the rest of the file as a comment,</a>
+<a name="39"><span class="lineNum">      39 </span>            : although since vim doesn't parse the whole file it might fail in doing so for long</a>
+<a name="40"><span class="lineNum">      40 </span>            : input files.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : d: DISTANCE ATOMS=1,10</a>
+<a name="46"><span class="lineNum">      46 </span>            : PRINT ARG=d FILE=COLVAR STRIDE=10</a>
+<a name="47"><span class="lineNum">      47 </span>            : ENDPLUMED</a>
+<a name="48"><span class="lineNum">      48 </span>            : commands here are ignored</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=d FILE=COLVAR STRIDE=1</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : */</a>
+<a name="53"><span class="lineNum">      53 </span>            : //+ENDPLUMEDOC</a>
+<a name="54"><span class="lineNum">      54 </span>            : class EndPlumed:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   public Action</a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   explicit EndPlumed(const ActionOptions&amp;ao);</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Register all the relevant keywords for the action</a>
+<a name="60"><span class="lineNum">      60 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : };</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      12767 : PLUMED_REGISTER_ACTION(EndPlumed,&quot;ENDPLUMED&quot;)</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        265 : void EndPlumed::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        265 :   Action::registerKeywords( keys );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        265 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        263 : EndPlumed::EndPlumed(const ActionOptions&amp;ao):</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        263 :   Action(ao)</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        263 :   checkRead();</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        263 :   plumed.setEndPlumed();</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        263 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/FitToTemplate.cpp.func-sort-c.html b/coverage/generic/FitToTemplate.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ab64fb8442
--- /dev/null
+++ b/coverage/generic/FitToTemplate.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/FitToTemplate.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - FitToTemplate.cpp<span style="font-size: 80%;"> (<a href="FitToTemplate.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FitToTemplate.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#196">_ZN4PLMD7generic13FitToTemplate22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#210">_ZN4PLMD7generic13FitToTemplateC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#199">_ZN4PLMD7generic12_GLOBAL__N_126FitToTemplateRegisterMe2016createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#210">_ZN4PLMD7generic13FitToTemplateC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#201">_ZN4PLMD7generic13FitToTemplate16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#323">_ZN4PLMD7generic13FitToTemplate5applyEv</a></td>
+              <td class="coverFnHi">108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#290">_ZN4PLMD7generic13FitToTemplate9calculateEv</a></td>
+              <td class="coverFnHi">108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#199">_ZN4PLMD7generic12_GLOBAL__N_126FitToTemplateRegisterMe201C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#199">_ZN4PLMD7generic12_GLOBAL__N_126FitToTemplateRegisterMe201D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/FitToTemplate.cpp.func.html b/coverage/generic/FitToTemplate.cpp.func.html
new file mode 100644
index 0000000000..47b2023aab
--- /dev/null
+++ b/coverage/generic/FitToTemplate.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/FitToTemplate.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - FitToTemplate.cpp<span style="font-size: 80%;"> (<a href="FitToTemplate.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FitToTemplate.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#199">_ZN4PLMD7generic12_GLOBAL__N_126FitToTemplateRegisterMe2016createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#199">_ZN4PLMD7generic12_GLOBAL__N_126FitToTemplateRegisterMe201C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#199">_ZN4PLMD7generic12_GLOBAL__N_126FitToTemplateRegisterMe201D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#201">_ZN4PLMD7generic13FitToTemplate16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#196">_ZN4PLMD7generic13FitToTemplate22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#323">_ZN4PLMD7generic13FitToTemplate5applyEv</a></td>
+              <td class="coverFnHi">108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#290">_ZN4PLMD7generic13FitToTemplate9calculateEv</a></td>
+              <td class="coverFnHi">108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#210">_ZN4PLMD7generic13FitToTemplateC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FitToTemplate.cpp.gcov.html#210">_ZN4PLMD7generic13FitToTemplateC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/FitToTemplate.cpp.gcov.html b/coverage/generic/FitToTemplate.cpp.gcov.html
new file mode 100644
index 0000000000..80eee850ca
--- /dev/null
+++ b/coverage/generic/FitToTemplate.cpp.gcov.html
@@ -0,0 +1,450 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/FitToTemplate.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - FitToTemplate.cpp<span style="font-size: 80%;"> (source / <a href="FitToTemplate.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;vector&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;string&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &lt;memory&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace generic {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : //+PLUMEDOC GENERIC FIT_TO_TEMPLATE</a>
+<a name="46"><span class="lineNum">      46 </span>            : /*</a>
+<a name="47"><span class="lineNum">      47 </span>            : This action is used to align a molecule to a template.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : This can be used to move the coordinates stored in plumed</a>
+<a name="50"><span class="lineNum">      50 </span>            : so as to be aligned with a provided template in PDB format. Pdb should contain</a>
+<a name="51"><span class="lineNum">      51 </span>            : also weights for alignment (see the format of PDB files used e.g. for \ref RMSD).</a>
+<a name="52"><span class="lineNum">      52 </span>            : Make sure your PDB file is correctly formatted as explained \ref pdbreader &quot;in this page&quot;.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Weights for displacement are ignored, since no displacement is computed here.</a>
+<a name="54"><span class="lineNum">      54 </span>            : Notice that all atoms (not only those in the template) are aligned.</a>
+<a name="55"><span class="lineNum">      55 </span>            : To see what effect try</a>
+<a name="56"><span class="lineNum">      56 </span>            : the \ref DUMPATOMS directive to output the atomic positions.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : Also notice that PLUMED propagate forces correctly so that you can add a bias on a CV computed</a>
+<a name="59"><span class="lineNum">      59 </span>            : after alignment. For many CVs this has no effect, but in some case the alignment can</a>
+<a name="60"><span class="lineNum">      60 </span>            : change the result. Examples are:</a>
+<a name="61"><span class="lineNum">      61 </span>            : - \ref POSITION CV since it is affected by a rigid shift of the system.</a>
+<a name="62"><span class="lineNum">      62 </span>            : - \ref DISTANCE CV with COMPONENTS. Since the alignment could involve a rotation (with TYPE=OPTIMAL) the actual components could be different</a>
+<a name="63"><span class="lineNum">      63 </span>            :   from the original ones.</a>
+<a name="64"><span class="lineNum">      64 </span>            : - \ref CELL components for a similar reason.</a>
+<a name="65"><span class="lineNum">      65 </span>            : - \ref DISTANCE from a \ref FIXEDATOM, provided the fixed atom is introduced _after_ the \ref FIT_TO_TEMPLATE action.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \attention</a>
+<a name="68"><span class="lineNum">      68 </span>            : The implementation of TYPE=OPTIMAL is available but should be considered in testing phase. Please report any</a>
+<a name="69"><span class="lineNum">      69 </span>            : strange behavior.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \attention</a>
+<a name="72"><span class="lineNum">      72 </span>            : This directive modifies the stored position at the precise moment</a>
+<a name="73"><span class="lineNum">      73 </span>            : it is executed. This means that only collective variables</a>
+<a name="74"><span class="lineNum">      74 </span>            : which are below it in the input script will see the corrected positions.</a>
+<a name="75"><span class="lineNum">      75 </span>            : As a general rule, put it at the top of the input file. Also, unless you</a>
+<a name="76"><span class="lineNum">      76 </span>            : know exactly what you are doing, leave the default stride (1), so that</a>
+<a name="77"><span class="lineNum">      77 </span>            : this action is performed at every MD step.</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="80"><span class="lineNum">      80 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.5,</a>
+<a name="81"><span class="lineNum">      81 </span>            : by considering the ordered list of atoms and rebuilding the molecules using a procedure</a>
+<a name="82"><span class="lineNum">      82 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="83"><span class="lineNum">      83 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="84"><span class="lineNum">      84 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="87"><span class="lineNum">      87 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="88"><span class="lineNum">      88 </span>            : periodic image.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \par Examples</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : Align the atomic position to a template then print them.</a>
+<a name="93"><span class="lineNum">      93 </span>            : The following example is only translating the system so as</a>
+<a name="94"><span class="lineNum">      94 </span>            : to align the center of mass of a molecule to the one in the reference</a>
+<a name="95"><span class="lineNum">      95 </span>            : structure `ref.pdb`:</a>
+<a name="96"><span class="lineNum">      96 </span>            : \plumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : # dump coordinates before fitting, to see the difference:</a>
+<a name="98"><span class="lineNum">      98 </span>            : DUMPATOMS FILE=dump-before.xyz ATOMS=1-20</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : # fit coordinates to ref.pdb template</a>
+<a name="101"><span class="lineNum">     101 </span>            : # this is a &quot;TYPE=SIMPLE&quot; fit, so that only translations are used.</a>
+<a name="102"><span class="lineNum">     102 </span>            : FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : # dump coordinates after fitting, to see the difference:</a>
+<a name="105"><span class="lineNum">     105 </span>            : DUMPATOMS FILE=dump-after.xyz ATOMS=1-20</a>
+<a name="106"><span class="lineNum">     106 </span>            : \endplumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : The following example instead performs a rototranslational fit.</a>
+<a name="109"><span class="lineNum">     109 </span>            : \plumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : # dump coordinates before fitting, to see the difference:</a>
+<a name="111"><span class="lineNum">     111 </span>            : DUMPATOMS FILE=dump-before.xyz ATOMS=1-20</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : # fit coordinates to ref.pdb template</a>
+<a name="114"><span class="lineNum">     114 </span>            : # this is a &quot;TYPE=OPTIMAL&quot; fit, so that rototranslations are used.</a>
+<a name="115"><span class="lineNum">     115 </span>            : FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : # dump coordinates after fitting, to see the difference:</a>
+<a name="118"><span class="lineNum">     118 </span>            : DUMPATOMS FILE=dump-after.xyz ATOMS=1-20</a>
+<a name="119"><span class="lineNum">     119 </span>            : \endplumedfile</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : In both these cases the reference structure should be provided in a reference pdb file such as the one below:</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : \auxfile{ref.pdb}</a>
+<a name="124"><span class="lineNum">     124 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="125"><span class="lineNum">     125 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="126"><span class="lineNum">     126 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="127"><span class="lineNum">     127 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="128"><span class="lineNum">     128 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="129"><span class="lineNum">     129 </span>            : END</a>
+<a name="130"><span class="lineNum">     130 </span>            : \endauxfile</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : In the following example you see two completely equivalent way</a>
+<a name="133"><span class="lineNum">     133 </span>            : to restrain an atom close to a position that is defined in the reference</a>
+<a name="134"><span class="lineNum">     134 </span>            : frame of an aligned molecule. You could for instance use this command to calculate the</a>
+<a name="135"><span class="lineNum">     135 </span>            : position of the center of mass of a ligand after having aligned the atoms to the reference</a>
+<a name="136"><span class="lineNum">     136 </span>            : frame of the protein that is determined by aligning the atoms in the protein to the coordinates</a>
+<a name="137"><span class="lineNum">     137 </span>            : provided in the file ref.pdb</a>
+<a name="138"><span class="lineNum">     138 </span>            : \plumedfile</a>
+<a name="139"><span class="lineNum">     139 </span>            : # center of the ligand:</a>
+<a name="140"><span class="lineNum">     140 </span>            : center: CENTER ATOMS=100-110</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : FIT_TO_TEMPLATE REFERENCE=ref.pdb TYPE=OPTIMAL</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : # place a fixed atom in the protein reference coordinates:</a>
+<a name="145"><span class="lineNum">     145 </span>            : fix: FIXEDATOM AT=1.0,1.1,1.0</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : # take the distance between the fixed atom and the center of the ligand</a>
+<a name="148"><span class="lineNum">     148 </span>            : d: DISTANCE ATOMS=center,fix</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : # apply a restraint</a>
+<a name="151"><span class="lineNum">     151 </span>            : RESTRAINT ARG=d AT=0.0 KAPPA=100.0</a>
+<a name="152"><span class="lineNum">     152 </span>            : \endplumedfile</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : Notice that you could have obtained an (almost) identical result by adding a fictitious</a>
+<a name="155"><span class="lineNum">     155 </span>            : atom to `ref.pdb` with the serial number corresponding to the atom labelled `center` (there is no automatic way</a>
+<a name="156"><span class="lineNum">     156 </span>            : to get it, but in this example it should be the number of atoms of the system plus one),</a>
+<a name="157"><span class="lineNum">     157 </span>            : and properly setting the weights for alignment and displacement in \ref RMSD.</a>
+<a name="158"><span class="lineNum">     158 </span>            : There are two differences to be expected:</a>
+<a name="159"><span class="lineNum">     159 </span>            : (ab) \ref FIT_TO_TEMPLATE might be slower since it has to rototranslate all the available atoms and</a>
+<a name="160"><span class="lineNum">     160 </span>            : (b) variables employing periodic boundary conditions (such as \ref DISTANCE without `NOPBC`, as in the example above)</a>
+<a name="161"><span class="lineNum">     161 </span>            :   are allowed after \ref FIT_TO_TEMPLATE, whereas \ref RMSD expects the issues related to the periodic boundary conditions to be already solved.</a>
+<a name="162"><span class="lineNum">     162 </span>            : The latter means that before the \ref RMSD statement one should use \ref WRAPAROUND or \ref WHOLEMOLECULES to properly place</a>
+<a name="163"><span class="lineNum">     163 </span>            : the ligand.</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : */</a>
+<a name="167"><span class="lineNum">     167 </span>            : //+ENDPLUMEDOC</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : class FitToTemplate:</a>
+<a name="171"><span class="lineNum">     171 </span>            :   public ActionPilot,</a>
+<a name="172"><span class="lineNum">     172 </span>            :   public ActionAtomistic,</a>
+<a name="173"><span class="lineNum">     173 </span>            :   public ActionWithValue</a>
+<a name="174"><span class="lineNum">     174 </span>            : {</a>
+<a name="175"><span class="lineNum">     175 </span>            :   std::string type;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   bool nopbc;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::vector&lt;double&gt; weights;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   std::vector&lt;AtomNumber&gt; aligned;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   Vector center;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   Vector shift;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   // optimal alignment related stuff</a>
+<a name="182"><span class="lineNum">     182 </span>            :   std::unique_ptr&lt;PLMD::RMSD&gt; rmsd;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   Tensor rotation;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   Matrix&lt; std::vector&lt;Vector&gt; &gt; drotdpos;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   // not used anymore (see notes below at doNotRetrieve())</a>
+<a name="186"><span class="lineNum">     186 </span>            :   // std::vector&lt;Vector&gt; positions;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   std::vector&lt;Vector&gt; DDistDRef;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   std::vector&lt;Vector&gt; ddistdpos;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::vector&lt;Vector&gt; centeredpositions;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   Vector center_positions;</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : public:</a>
+<a name="194"><span class="lineNum">     194 </span>            :   explicit FitToTemplate(const ActionOptions&amp;ao);</a>
+<a name="195"><span class="lineNum">     195 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="196"><span class="lineNum">     196 </span>            :   void calculate() override;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   void apply() override;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :   unsigned getNumberOfDerivatives() override {plumed_merror(&quot;You should not call this function&quot;);};</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : };</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(FitToTemplate,&quot;FIT_TO_TEMPLATE&quot;)</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         11 : void FitToTemplate::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         11 :   Action::registerKeywords( keys );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         11 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which molecules are reassembled.  Unless you are completely certain about what you are doing leave this set equal to 1!&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a file in pdb format containing the reference structure and the atoms involved in the CV.&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;SIMPLE&quot;,&quot;the manner in which RMSD alignment is performed.  Should be OPTIMAL or SIMPLE.&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         22 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         11 : }</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          9 : FitToTemplate::FitToTemplate(const ActionOptions&amp;ao):</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   Action(ao),</a>
+<a name="214"><span class="lineNum">     214 </span>            :   ActionPilot(ao),</a>
+<a name="215"><span class="lineNum">     215 </span>            :   ActionAtomistic(ao),</a>
+<a name="216"><span class="lineNum">     216 </span>            :   ActionWithValue(ao),</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         18 :   nopbc(false)</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : {</a>
+<a name="219"><span class="lineNum">     219 </span>            :   std::string reference;</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          9 :   parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          9 :   type.assign(&quot;SIMPLE&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          9 :   parse(&quot;TYPE&quot;,type);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          9 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : // if(type!=&quot;SIMPLE&quot;) error(&quot;Only TYPE=SIMPLE is implemented in FIT_TO_TEMPLATE&quot;);</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          9 :   PDB pdb;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :   // read everything in ang and transform to nm if we are not in natural units</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         18 :   if( !pdb.read(reference,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength()) )</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :     error(&quot;missing input file &quot; + reference );</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          9 :   requestAtoms(pdb.getAtomNumbers());</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          9 :   log.printf(&quot;  found %zu atoms in input \n&quot;,pdb.getAtomNumbers().size());</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          9 :   log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;pdb.getAtomNumbers().size(); ++i) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         33 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         33 :     log.printf(&quot;%d &quot;,pdb.getAtomNumbers()[i].serial());</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          9 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          9 :   std::vector&lt;Vector&gt; positions=pdb.getPositions();</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          9 :   weights=pdb.getOccupancy();</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          9 :   aligned=pdb.getAtomNumbers();</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   // normalize weights</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         42 :   double n=0.0; for(unsigned i=0; i&lt;weights.size(); ++i) n+=weights[i];</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          9 :   if(n==0.0) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :     error(&quot;PDB file &quot; + reference + &quot; has zero weights. Please check the occupancy column.&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          9 :   n=1.0/n;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;weights.size(); ++i) weights[i]*=n;</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :   // normalize weights for rmsd calculation</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          9 :   std::vector&lt;double&gt; weights_measure=pdb.getBeta();</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         42 :   n=0.0; for(unsigned i=0; i&lt;weights_measure.size(); ++i) n+=weights_measure[i]; n=1.0/n;</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;weights_measure.size(); ++i) weights_measure[i]*=n;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :   // subtract the center</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;weights.size(); ++i) center+=positions[i]*weights[i];</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;weights.size(); ++i) positions[i]-=center;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         13 :   if(type==&quot;OPTIMAL&quot; or type==&quot;OPTIMAL-FAST&quot; ) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         10 :     rmsd=Tools::make_unique&lt;RMSD&gt;();</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          5 :     rmsd-&gt;set(weights,weights_measure,positions,type,false,false);// note: the reference is shifted now with center in the origin</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         10 :     log&lt;&lt;&quot;  Method chosen for fitting: &quot;&lt;&lt;rmsd-&gt;getMethod()&lt;&lt;&quot; \n&quot;;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          9 :   if(nopbc) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  Ignoring PBCs when doing alignment, make sure your molecule is whole!&lt;n&quot;;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :   }</a>
+<a name="274"><span class="lineNum">     274 </span>            :   // register the value of rmsd (might be useful sometimes)</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          9 :   addValue(); setNotPeriodic();</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :   // I remove this optimization now in order to use makeWhole()</a>
+<a name="278"><span class="lineNum">     278 </span>            :   // Notice that for FIT_TO_TEMPLATE TYPE=OPTIMAL a copy was made anyway</a>
+<a name="279"><span class="lineNum">     279 </span>            :   // (due to the need to store position to propagate forces on rotational matrix later)</a>
+<a name="280"><span class="lineNum">     280 </span>            :   // For FIT_TO_TEMPLATE TYPE=SIMPLE in principle we could use it and write an ad hoc</a>
+<a name="281"><span class="lineNum">     281 </span>            :   // version of makeWhole that only computes the center. Too lazy to do it now.</a>
+<a name="282"><span class="lineNum">     282 </span>            :   // In case we do it later, remember that uncommenting this line means that</a>
+<a name="283"><span class="lineNum">     283 </span>            :   // getPositions will not work anymore! GB</a>
+<a name="284"><span class="lineNum">     284 </span>            :   // doNotRetrieve();</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :   // this is required so as to allow modifyGlobalForce() to return correct</a>
+<a name="287"><span class="lineNum">     287 </span>            :   // also for forces that are not owned (and thus not zeored) by all processors.</a>
+<a name="288"><span class="lineNum">     288 </span>            :   allowToAccessGlobalForces();</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         18 : }</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        108 : void FitToTemplate::calculate() {</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        108 :   if(!nopbc) makeWhole();</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        108 :   if (type==&quot;SIMPLE&quot;) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         48 :     Vector cc;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        144 :     for(unsigned i=0; i&lt;aligned.size(); ++i) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         96 :       cc+=weights[i]*getPosition(i);</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :     }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         48 :     shift=center-cc;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         48 :     setValue(shift.modulo());</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       6420 :     for(unsigned i=0; i&lt;getTotAtoms(); i++) {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :       Vector &amp; ato (modifyGlobalPosition(AtomNumber::index(i)));</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       6372 :       ato+=shift;</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :     }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   }</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         60 :   else if( type==&quot;OPTIMAL&quot; or type==&quot;OPTIMAL-FAST&quot;) {</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :     // specific stuff that provides all that is needed</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         60 :     double r=rmsd-&gt;calc_FitElements( getPositions(), rotation,  drotdpos, centeredpositions, center_positions);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         60 :     setValue(r);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       8004 :     for(unsigned i=0; i&lt;getTotAtoms(); i++) {</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :       Vector &amp; ato (modifyGlobalPosition(AtomNumber::index(i)));</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       7944 :       ato=matmul(rotation,ato-center_positions)+center;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     }</a>
+<a name="318"><span class="lineNum">     318 </span>            : // rotate box</a>
+<a name="319"><span class="lineNum">     319 </span>            :     Pbc &amp; pbc(modifyGlobalPbc());</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         60 :     pbc.setBox(matmul(pbc.getBox(),transpose(rotation)));</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :   }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        108 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        108 : void FitToTemplate::apply() {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">        108 :   if (type==&quot;SIMPLE&quot;) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         48 :     Vector totForce;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       6420 :     for(unsigned i=0; i&lt;getTotAtoms(); i++) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       6372 :       totForce+=modifyGlobalForce(AtomNumber::index(i));</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span>            :     Tensor &amp; vv(modifyGlobalVirial());</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         48 :     vv+=Tensor(center,totForce);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        144 :     for(unsigned i=0; i&lt;aligned.size(); ++i) {</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :       Vector &amp; ff(modifyGlobalForce(aligned[i]));</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         96 :       ff-=totForce*weights[i];</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :     }</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         60 :   } else if ( type==&quot;OPTIMAL&quot; or type==&quot;OPTIMAL-FAST&quot;) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         60 :     Vector totForce;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       8004 :     for(unsigned i=0; i&lt;getTotAtoms(); i++) {</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :       Vector &amp; f(modifyGlobalForce(AtomNumber::index(i)));</a>
+<a name="341"><span class="lineNum">     341 </span>            : // rotate back forces</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       7944 :       f=matmul(transpose(rotation),f);</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : // accumulate rotated c.o.m. forces - this is already in the non rotated reference frame</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">       7944 :       totForce+=f;</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :     }</a>
+<a name="346"><span class="lineNum">     346 </span>            :     Tensor&amp; virial(modifyGlobalVirial());</a>
+<a name="347"><span class="lineNum">     347 </span>            : // notice that an extra Tensor(center,matmul(rotation,totForce)) is required to</a>
+<a name="348"><span class="lineNum">     348 </span>            : // compute the derivatives of the rotation with respect to center</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         60 :     Tensor ww=matmul(transpose(rotation),virial+Tensor(center,matmul(rotation,totForce)));</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : // rotate back virial</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         60 :     virial=matmul(transpose(rotation),matmul(virial,rotation));</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            : // now we compute the force due to alignment</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        360 :     for(unsigned i=0; i&lt;aligned.size(); i++) {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        300 :       Vector g;</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       1200 :       for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            : // this could be made faster computing only the diagonal of d</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        900 :         Tensor d=matmul(ww,RMSD::getMatrixFromDRot(drotdpos,i,k));</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">        900 :         g[k]=(d(0,0)+d(1,1)+d(2,2));</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :       }</a>
+<a name="361"><span class="lineNum">     361 </span>            : // here is the extra contribution</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        300 :       modifyGlobalForce(aligned[i])+=-g-weights[i]*totForce;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : // here it the contribution to the virial</a>
+<a name="364"><span class="lineNum">     364 </span>            : // notice that here we can use absolute positions since, for the alignment to be defined,</a>
+<a name="365"><span class="lineNum">     365 </span>            : // positions should be in one well defined periodic image</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        300 :       virial+=extProduct(getPosition(i),g);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :     }</a>
+<a name="368"><span class="lineNum">     368 </span>            : // finally, correction to the virial</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         60 :     virial+=extProduct(matmul(transpose(rotation),center),totForce);</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        108 : }</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            : }</a>
+<a name="374"><span class="lineNum">     374 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Flush.cpp.func-sort-c.html b/coverage/generic/Flush.cpp.func-sort-c.html
new file mode 100644
index 0000000000..323874e75f
--- /dev/null
+++ b/coverage/generic/Flush.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Flush.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Flush.cpp<span style="font-size: 80%;"> (<a href="Flush.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Flush.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#77">_ZN4PLMD7generic12_GLOBAL__N_117FlushRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#59">_ZN4PLMD7generic5FlushC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#79">_ZN4PLMD7generic5Flush16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#67">_ZN4PLMD7generic5Flush5applyEv</a></td>
+              <td class="coverFnHi">561</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#68">_ZN4PLMD7generic5Flush6updateEv</a></td>
+              <td class="coverFnHi">561</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#66">_ZN4PLMD7generic5Flush9calculateEv</a></td>
+              <td class="coverFnHi">561</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#77">_ZN4PLMD7generic12_GLOBAL__N_117FlushRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#77">_ZN4PLMD7generic12_GLOBAL__N_117FlushRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Flush.cpp.func.html b/coverage/generic/Flush.cpp.func.html
new file mode 100644
index 0000000000..514c568a43
--- /dev/null
+++ b/coverage/generic/Flush.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Flush.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Flush.cpp<span style="font-size: 80%;"> (<a href="Flush.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Flush.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#77">_ZN4PLMD7generic12_GLOBAL__N_117FlushRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#77">_ZN4PLMD7generic12_GLOBAL__N_117FlushRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#77">_ZN4PLMD7generic12_GLOBAL__N_117FlushRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#79">_ZN4PLMD7generic5Flush16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#67">_ZN4PLMD7generic5Flush5applyEv</a></td>
+              <td class="coverFnHi">561</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#68">_ZN4PLMD7generic5Flush6updateEv</a></td>
+              <td class="coverFnHi">561</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#66">_ZN4PLMD7generic5Flush9calculateEv</a></td>
+              <td class="coverFnHi">561</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Flush.cpp.gcov.html#59">_ZN4PLMD7generic5FlushC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Flush.cpp.gcov.html b/coverage/generic/Flush.cpp.gcov.html
new file mode 100644
index 0000000000..a2c5660715
--- /dev/null
+++ b/coverage/generic/Flush.cpp.gcov.html
@@ -0,0 +1,167 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Flush.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Flush.cpp<span style="font-size: 80%;"> (source / <a href="Flush.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace generic {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC GENERIC FLUSH</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : This command instructs plumed to flush all the open files with a user specified frequency.</a>
+<a name="33"><span class="lineNum">      33 </span>            : Notice that all files are flushed anyway every 10000 steps.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This</a>
+<a name="36"><span class="lineNum">      36 </span>            : is useful for preventing data loss that would otherwise arise as a consequence of the code</a>
+<a name="37"><span class="lineNum">      37 </span>            : storing data for printing in the buffers. Notice that wherever it is written in the</a>
+<a name="38"><span class="lineNum">      38 </span>            : plumed input file, it will flush all the open files.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : A command like this in the input will instruct plumed to flush all the output files every 100 steps</a>
+<a name="43"><span class="lineNum">      43 </span>            : \plumedfile</a>
+<a name="44"><span class="lineNum">      44 </span>            : d1: DISTANCE ATOMS=1,10</a>
+<a name="45"><span class="lineNum">      45 </span>            : PRINT ARG=d1 STRIDE=5 FILE=colvar1</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : FLUSH STRIDE=100</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : d2: DISTANCE ATOMS=2,11</a>
+<a name="50"><span class="lineNum">      50 </span>            : # also this print is flushed every 100 steps:</a>
+<a name="51"><span class="lineNum">      51 </span>            : PRINT ARG=d2 STRIDE=10 FILE=colvar2</a>
+<a name="52"><span class="lineNum">      52 </span>            : \endplumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : (see also \ref DISTANCE and \ref PRINT).</a>
+<a name="54"><span class="lineNum">      54 </span>            : */</a>
+<a name="55"><span class="lineNum">      55 </span>            : //+ENDPLUMEDOC</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : class Flush:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   public ActionPilot</a>
+<a name="59"><span class="lineNum">      59 </span>            : {</a>
+<a name="60"><span class="lineNum">      60 </span>            : public:</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         17 :   explicit Flush(const ActionOptions&amp;ao):</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :     Action(ao),</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         17 :     ActionPilot(ao)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   {</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         17 :     checkRead();</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         17 :   }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        561 :   void calculate() override {}</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        561 :   void apply() override {}</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        561 :   void update() override {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        561 :     plumed.fflush();</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        561 :     log.flush();</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        561 :     const ActionSet &amp; actionSet(plumed.getActionSet());</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       3942 :     for(const auto &amp; p : actionSet)</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       3381 :       p-&gt;fflush();</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        561 :   }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : };</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      12538 : PLUMED_REGISTER_ACTION(Flush,&quot;FLUSH&quot;)</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         19 : void Flush::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         19 :   Action::registerKeywords( keys );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         19 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         38 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;the frequency with which all the open files should be flushed&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         19 :   keys.remove(&quot;LABEL&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         19 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Group.cpp.func-sort-c.html b/coverage/generic/Group.cpp.func-sort-c.html
new file mode 100644
index 0000000000..51d08d6f67
--- /dev/null
+++ b/coverage/generic/Group.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Group.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Group.cpp<span style="font-size: 80%;"> (<a href="Group.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">63.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Group.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#138">_ZN4PLMD7generic5Group5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#137">_ZN4PLMD7generic5Group9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#143">_ZN4PLMD7generic5GroupC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#238">_ZN4PLMD7generic5GroupD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_118GroupRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#143">_ZN4PLMD7generic5GroupC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#238">_ZN4PLMD7generic5GroupD0Ev</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#238">_ZN4PLMD7generic5GroupD1Ev</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#227">_ZN4PLMD7generic5Group16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">134</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_118GroupRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_118GroupRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Group.cpp.func.html b/coverage/generic/Group.cpp.func.html
new file mode 100644
index 0000000000..e81839f849
--- /dev/null
+++ b/coverage/generic/Group.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Group.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Group.cpp<span style="font-size: 80%;"> (<a href="Group.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">63.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Group.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_118GroupRegisterMe1436createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_118GroupRegisterMe143C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#141">_ZN4PLMD7generic12_GLOBAL__N_118GroupRegisterMe143D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#227">_ZN4PLMD7generic5Group16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">134</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#138">_ZN4PLMD7generic5Group5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#137">_ZN4PLMD7generic5Group9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#143">_ZN4PLMD7generic5GroupC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#143">_ZN4PLMD7generic5GroupC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#238">_ZN4PLMD7generic5GroupD0Ev</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#238">_ZN4PLMD7generic5GroupD1Ev</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Group.cpp.gcov.html#238">_ZN4PLMD7generic5GroupD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Group.cpp.gcov.html b/coverage/generic/Group.cpp.gcov.html
new file mode 100644
index 0000000000..5e75770a52
--- /dev/null
+++ b/coverage/generic/Group.cpp.gcov.html
@@ -0,0 +1,322 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Group.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Group.cpp<span style="font-size: 80%;"> (source / <a href="Group.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">71</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">63.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;vector&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;algorithm&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace generic {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC GENERIC GROUP</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Define a group of atoms so that a particular list of atoms can be referenced with a single label in definitions of CVs or virtual atoms.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Atoms can be listed as comma separated numbers (i.e. `1,2,3,10,45,7,9`) , simple positive ranges</a>
+<a name="40"><span class="lineNum">      40 </span>            : (i.e. `20-40`), ranges with a stride either positive or negative (i.e. `20-40:2` or `80-50:-2`) or as</a>
+<a name="41"><span class="lineNum">      41 </span>            : comma separated combinations of all the former methods (`1,2,4,5,10-20,21-40:2,80-50:-2`).</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : Moreover, lists can be imported from ndx files (GROMACS format). Use `NDX_FILE` to set the name of</a>
+<a name="44"><span class="lineNum">      44 </span>            : the index file and `NDX_GROUP` to set the name of the group to be imported (default is first one).</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : It is also possible to remove atoms from a list and or sort them using keywords `REMOVE`, `SORT`, and `UNIQUE`.</a>
+<a name="47"><span class="lineNum">      47 </span>            : The flow is the following:</a>
+<a name="48"><span class="lineNum">      48 </span>            : - If `ATOMS` is present, then take the ordered list of atoms from the `ATOMS` keyword as a starting list.</a>
+<a name="49"><span class="lineNum">      49 </span>            : - Alternatively, if `NDX_FILE` is present, use the list obtained from the gromacs group.</a>
+<a name="50"><span class="lineNum">      50 </span>            : - If `REMOVE` is present, then remove the first occurrence of each of these atoms from the list.</a>
+<a name="51"><span class="lineNum">      51 </span>            :   If one tries to remove an atom that was not listed plumed adds a notice in the output.</a>
+<a name="52"><span class="lineNum">      52 </span>            :   An atom that is present twice in the original list might be removed twice.</a>
+<a name="53"><span class="lineNum">      53 </span>            : - If `SORT` is present, then the resulting list is sorted by increasing serial number.</a>
+<a name="54"><span class="lineNum">      54 </span>            : - If `UNIQUE` is present, then the resulting list is sorted by increasing serial number _and_ duplicate elements are removed.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : Notice that this command just creates a shortcut, and does not imply any real calculation.</a>
+<a name="57"><span class="lineNum">      57 </span>            : So, having a huge group defined does not slow down your calculation in any way.</a>
+<a name="58"><span class="lineNum">      58 </span>            : It is just convenient to better organize input files. Might be used in combination with</a>
+<a name="59"><span class="lineNum">      59 </span>            : the \ref INCLUDE command so as to store long group definitions in a separate file.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \par Examples</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : This command create a group of atoms containing atoms 1, 4, 7, 11 and 14 (labeled 'o'), and another containing</a>
+<a name="65"><span class="lineNum">      65 </span>            : atoms 2, 3, 5, 6, 8, 9, 12, and 13 (labeled 'h'):</a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : o: GROUP ATOMS=1,4,7,11,14</a>
+<a name="68"><span class="lineNum">      68 </span>            : h: GROUP ATOMS=2,3,5,6,8,9,12,13</a>
+<a name="69"><span class="lineNum">      69 </span>            : # compute the coordination among the two groups</a>
+<a name="70"><span class="lineNum">      70 </span>            : c: COORDINATION GROUPA=o GROUPB=h R_0=0.3</a>
+<a name="71"><span class="lineNum">      71 </span>            : # same could have been obtained without GROUP, just writing:</a>
+<a name="72"><span class="lineNum">      72 </span>            : # c: COORDINATION GROUPA=1,4,7,11,14 GROUPB=2,3,5,6,8,9,12,13</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : # print the coordination on file 'colvar'</a>
+<a name="75"><span class="lineNum">      75 </span>            : PRINT ARG=c FILE=colvar</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : Groups can be conveniently stored in a separate file.</a>
+<a name="79"><span class="lineNum">      79 </span>            : E.g. one could create a file named `groups.dat` which reads</a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : #SETTINGS FILENAME=groups.dat</a>
+<a name="82"><span class="lineNum">      82 </span>            : # this is groups.dat</a>
+<a name="83"><span class="lineNum">      83 </span>            : o: GROUP ATOMS=1,4,7,11,14</a>
+<a name="84"><span class="lineNum">      84 </span>            : h: GROUP ATOMS=2,3,5,6,8,9,12,13</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endplumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : and then include it in the main 'plumed.dat' file</a>
+<a name="87"><span class="lineNum">      87 </span>            : \plumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : INCLUDE FILE=groups.dat</a>
+<a name="89"><span class="lineNum">      89 </span>            : # compute the coordination among the two groups</a>
+<a name="90"><span class="lineNum">      90 </span>            : c: COORDINATION GROUPA=o GROUPB=h R_0=0.3</a>
+<a name="91"><span class="lineNum">      91 </span>            : # print the coordination on file 'colvar'</a>
+<a name="92"><span class="lineNum">      92 </span>            : PRINT ARG=c FILE=colvar</a>
+<a name="93"><span class="lineNum">      93 </span>            : \endplumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : The `groups.dat` file could be very long and include lists of thousand atoms without cluttering the main plumed.dat file.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : A GROMACS index file such as the one shown below:</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : \auxfile{index.ndx}</a>
+<a name="99"><span class="lineNum">      99 </span>            : [ Protein ]</a>
+<a name="100"><span class="lineNum">     100 </span>            : 1 3 5 7 9</a>
+<a name="101"><span class="lineNum">     101 </span>            : 2 4 6 8 10</a>
+<a name="102"><span class="lineNum">     102 </span>            : [ Group2 ]</a>
+<a name="103"><span class="lineNum">     103 </span>            : 30 31 32 33 34 35 36 37 38 39 40</a>
+<a name="104"><span class="lineNum">     104 </span>            : 5</a>
+<a name="105"><span class="lineNum">     105 </span>            : \endauxfile</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : can also be imported by using the GROUP keyword as shown below</a>
+<a name="108"><span class="lineNum">     108 </span>            : \plumedfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : # import group named 'Protein' from file index.ndx</a>
+<a name="110"><span class="lineNum">     110 </span>            : pro: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein</a>
+<a name="111"><span class="lineNum">     111 </span>            : # dump all the atoms of the protein on a trajectory file</a>
+<a name="112"><span class="lineNum">     112 </span>            : DUMPATOMS ATOMS=pro FILE=traj.gro</a>
+<a name="113"><span class="lineNum">     113 </span>            : \endplumedfile</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : A list can be edited with `REMOVE`. For instance, if you</a>
+<a name="116"><span class="lineNum">     116 </span>            : are using a water model with three atoms per molecule, you can</a>
+<a name="117"><span class="lineNum">     117 </span>            : easily construct the list of hydrogen atoms in this manner</a>
+<a name="118"><span class="lineNum">     118 </span>            : \plumedfile</a>
+<a name="119"><span class="lineNum">     119 </span>            : # take one atom every three, that is oxygens</a>
+<a name="120"><span class="lineNum">     120 </span>            : ox: GROUP ATOMS=1-90:3</a>
+<a name="121"><span class="lineNum">     121 </span>            : # take the remaining atoms, that is hydrogens</a>
+<a name="122"><span class="lineNum">     122 </span>            : hy: GROUP ATOMS=1-90 REMOVE=ox</a>
+<a name="123"><span class="lineNum">     123 </span>            : DUMPATOMS ATOMS=ox FILE=ox.gro</a>
+<a name="124"><span class="lineNum">     124 </span>            : DUMPATOMS ATOMS=hy FILE=hy.gro</a>
+<a name="125"><span class="lineNum">     125 </span>            : \endplumedfile</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : */</a>
+<a name="129"><span class="lineNum">     129 </span>            : //+ENDPLUMEDOC</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : class Group:</a>
+<a name="132"><span class="lineNum">     132 </span>            :   public ActionAtomistic</a>
+<a name="133"><span class="lineNum">     133 </span>            : {</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : public:</a>
+<a name="136"><span class="lineNum">     136 </span>            :   explicit Group(const ActionOptions&amp;ao);</a>
+<a name="137"><span class="lineNum">     137 </span>            :   ~Group();</a>
+<a name="138"><span class="lineNum">     138 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : };</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      12768 : PLUMED_REGISTER_ACTION(Group,&quot;GROUP&quot;)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        132 : Group::Group(const ActionOptions&amp;ao):</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   Action(ao),</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        132 :   ActionAtomistic(ao)</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : {</a>
+<a name="149"><span class="lineNum">     149 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        264 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   std::string ndxfile,ndxgroup;</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        132 :   parse(&quot;NDX_FILE&quot;,ndxfile);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        264 :   parse(&quot;NDX_GROUP&quot;,ndxgroup);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        132 :   if(ndxfile.length()&gt;0 &amp;&amp; atoms.size()&gt;0) error(&quot;either use explicit atom list or import from index file&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        132 :   if(ndxfile.length()==0 &amp;&amp; ndxgroup.size()&gt;0) error(&quot;NDX_GROUP can be only used is NDX_FILE is also used&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        132 :   if(ndxfile.length()&gt;0) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         35 :     if(ndxgroup.size()&gt;0) log&lt;&lt;&quot;  importing group '&quot;+ndxgroup+&quot;'&quot;;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          1 :     else                  log&lt;&lt;&quot;  importing first group&quot;;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         18 :     log&lt;&lt;&quot; from index file &quot;&lt;&lt;ndxfile&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         18 :     IFile ifile;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         18 :     ifile.open(ndxfile);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     std::string line;</a>
+<a name="165"><span class="lineNum">     165 </span>            :     std::string groupname;</a>
+<a name="166"><span class="lineNum">     166 </span>            :     bool firstgroup=true;</a>
+<a name="167"><span class="lineNum">     167 </span>            :     bool groupfound=false;</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       3835 :     while(ifile.getline(line)) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       3817 :       std::vector&lt;std::string&gt; words=Tools::getWords(line);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       7739 :       if(words.size()&gt;=3 &amp;&amp; words[0]==&quot;[&quot; &amp;&amp; words[2]==&quot;]&quot;) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        164 :         if(groupname.length()&gt;0) firstgroup=false;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :         groupname=words[1];</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        164 :         if(groupname==ndxgroup || ndxgroup.length()==0) groupfound=true;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       3653 :       } else if(groupname==ndxgroup || (firstgroup &amp;&amp; ndxgroup.length()==0)) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       6160 :         for(unsigned i=0; i&lt;words.size(); i++) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       5760 :           AtomNumber at; Tools::convert(words[i],at);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       5760 :           atoms.push_back(at);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :         }</a>
+<a name="179"><span class="lineNum">     179 </span>            :       }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       3817 :     }</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         18 :     if(!groupfound) error(&quot;group has not been found in index file&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         18 :   }</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :   std::vector&lt;AtomNumber&gt; remove;</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        264 :   parseAtomList(&quot;REMOVE&quot;,remove);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        132 :   if(remove.size()&gt;0) {</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     std::vector&lt;AtomNumber&gt; notfound;</a>
+<a name="188"><span class="lineNum">     188 </span>            :     unsigned k=0;</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  removing these atoms from the list:&quot;;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        114 :     for(unsigned i=0; i&lt;remove.size(); i++) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        112 :       const auto it = find(atoms.begin(),atoms.end(),remove[i]);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        112 :       if(it!=atoms.end()) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        111 :         if(k%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        111 :         log&lt;&lt;&quot; &quot;&lt;&lt;(*it).serial();</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        111 :         k++;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :         atoms.erase(it);</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          1 :       } else notfound.push_back(remove[i]);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          2 :     if(notfound.size()&gt;0) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          1 :       log&lt;&lt;&quot;  the following atoms were not found:&quot;;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :       for(unsigned i=0; i&lt;notfound.size(); i++) log&lt;&lt;&quot; &quot;&lt;&lt;notfound[i].serial();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          1 :       log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :     }</a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        132 :   bool sortme=false;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        132 :   parseFlag(&quot;SORT&quot;,sortme);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        132 :   if(sortme) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  atoms are sorted\n&quot;;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          1 :     sort(atoms.begin(),atoms.end());</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        132 :   bool unique=false;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        132 :   parseFlag(&quot;UNIQUE&quot;,unique);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        132 :   if(unique) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  sorting atoms and removing duplicates\n&quot;;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          1 :     Tools::removeDuplicates(atoms);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        132 :   this-&gt;atoms.insertGroup(getLabel(),atoms);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        132 :   log.printf(&quot;  list of atoms:&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">     183007 :   for(unsigned i=0; i&lt;atoms.size(); i++) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     182875 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     182875 :     log&lt;&lt;&quot; &quot;&lt;&lt;atoms[i].serial();</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   }</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        132 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        132 : }</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        134 : void Group::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        134 :   Action::registerKeywords( keys );</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        134 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        268 :   keys.add(&quot;atoms&quot;, &quot;ATOMS&quot;, &quot;the numerical indexes for the set of atoms in the group&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        268 :   keys.add(&quot;atoms&quot;, &quot;REMOVE&quot;,&quot;remove these atoms from the list&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        268 :   keys.addFlag(&quot;SORT&quot;,false,&quot;sort the resulting list&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        268 :   keys.addFlag(&quot;UNIQUE&quot;,false,&quot;sort atoms and remove duplicated ones&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        268 :   keys.add(&quot;optional&quot;, &quot;NDX_FILE&quot;, &quot;the name of index file (gromacs syntax)&quot;);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        268 :   keys.add(&quot;optional&quot;, &quot;NDX_GROUP&quot;, &quot;the name of the group to be imported (gromacs syntax) - first group found is used by default&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        134 : }</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        264 : Group::~Group() {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        132 :   atoms.removeGroup(getLabel());</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        264 : }</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+<a name="245"><span class="lineNum">     245 </span>            : }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Include.cpp.func-sort-c.html b/coverage/generic/Include.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ea1c2c7964
--- /dev/null
+++ b/coverage/generic/Include.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Include.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Include.cpp<span style="font-size: 80%;"> (<a href="Include.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Include.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#155">_ZN4PLMD7generic7Include5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#154">_ZN4PLMD7generic7Include9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#165">_ZN4PLMD7generic7IncludeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#158">_ZN4PLMD7generic12_GLOBAL__N_120IncludeRegisterMe1606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#165">_ZN4PLMD7generic7IncludeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#160">_ZN4PLMD7generic7Include16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#158">_ZN4PLMD7generic12_GLOBAL__N_120IncludeRegisterMe160C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#158">_ZN4PLMD7generic12_GLOBAL__N_120IncludeRegisterMe160D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Include.cpp.func.html b/coverage/generic/Include.cpp.func.html
new file mode 100644
index 0000000000..8bdee985d3
--- /dev/null
+++ b/coverage/generic/Include.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Include.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Include.cpp<span style="font-size: 80%;"> (<a href="Include.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Include.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#158">_ZN4PLMD7generic12_GLOBAL__N_120IncludeRegisterMe1606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#158">_ZN4PLMD7generic12_GLOBAL__N_120IncludeRegisterMe160C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#158">_ZN4PLMD7generic12_GLOBAL__N_120IncludeRegisterMe160D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#160">_ZN4PLMD7generic7Include16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#155">_ZN4PLMD7generic7Include5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#154">_ZN4PLMD7generic7Include9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#165">_ZN4PLMD7generic7IncludeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Include.cpp.gcov.html#165">_ZN4PLMD7generic7IncludeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Include.cpp.gcov.html b/coverage/generic/Include.cpp.gcov.html
new file mode 100644
index 0000000000..dbf2cd0cf1
--- /dev/null
+++ b/coverage/generic/Include.cpp.gcov.html
@@ -0,0 +1,255 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Include.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Include.cpp<span style="font-size: 80%;"> (source / <a href="Include.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionAnyorder.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace generic {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC GENERIC INCLUDE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Includes an external input file, similar to #include in C preprocessor.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Useful to split very large plumed.dat files. Notice that in PLUMED 2.4 this action</a>
+<a name="36"><span class="lineNum">      36 </span>            : cannot be used before the initial setup part of the file (e.g. in the part with \ref UNITS, \ref MOLINFO, etc).</a>
+<a name="37"><span class="lineNum">      37 </span>            : As of PLUMED 2.5, \ref INCLUDE can be used in any position of the file.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : This input:</a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : c1: COM ATOMS=1-100</a>
+<a name="44"><span class="lineNum">      44 </span>            : c2: COM ATOMS=101-202</a>
+<a name="45"><span class="lineNum">      45 </span>            : d: DISTANCE ATOMS=c1,c2</a>
+<a name="46"><span class="lineNum">      46 </span>            : PRINT ARG=d</a>
+<a name="47"><span class="lineNum">      47 </span>            : \endplumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : can be replaced with this input:</a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : INCLUDE FILE=pippo.dat</a>
+<a name="51"><span class="lineNum">      51 </span>            : d: DISTANCE ATOMS=c1,c2</a>
+<a name="52"><span class="lineNum">      52 </span>            : PRINT ARG=d</a>
+<a name="53"><span class="lineNum">      53 </span>            : \endplumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : where the content of file pippo.dat is</a>
+<a name="55"><span class="lineNum">      55 </span>            : \plumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : #SETTINGS FILENAME=pippo.dat</a>
+<a name="57"><span class="lineNum">      57 </span>            : # this is pippo.dat</a>
+<a name="58"><span class="lineNum">      58 </span>            : c1: COM ATOMS=1-100</a>
+<a name="59"><span class="lineNum">      59 </span>            : c2: COM ATOMS=101-202</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The files in this example are rather short, but imagine a case like this one:</a>
+<a name="63"><span class="lineNum">      63 </span>            : \plumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : INCLUDE FILE=groups.dat</a>
+<a name="65"><span class="lineNum">      65 </span>            : c: COORDINATION GROUPA=groupa GROUPB=groupb R_0=0.5</a>
+<a name="66"><span class="lineNum">      66 </span>            : METAD ARG=c HEIGHT=0.2 PACE=100 SIGMA=0.2 BIASFACTOR=5</a>
+<a name="67"><span class="lineNum">      67 </span>            : \endplumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : Here `groups.dat` could be a huge file containing group definitions.  This groups.dat file might look something</a>
+<a name="69"><span class="lineNum">      69 </span>            : like the following example but with more atom indices in the groups.</a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : #SETTINGS FILENAME=groups.dat</a>
+<a name="72"><span class="lineNum">      72 </span>            : # this is groups.dat</a>
+<a name="73"><span class="lineNum">      73 </span>            : groupa: GROUP ...</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ATOMS={</a>
+<a name="75"><span class="lineNum">      75 </span>            :     10</a>
+<a name="76"><span class="lineNum">      76 </span>            :     50</a>
+<a name="77"><span class="lineNum">      77 </span>            :     60</a>
+<a name="78"><span class="lineNum">      78 </span>            :     70</a>
+<a name="79"><span class="lineNum">      79 </span>            :     80</a>
+<a name="80"><span class="lineNum">      80 </span>            :     120</a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span>            : ...</a>
+<a name="83"><span class="lineNum">      83 </span>            : groupb: GROUP ...</a>
+<a name="84"><span class="lineNum">      84 </span>            :   ATOMS={</a>
+<a name="85"><span class="lineNum">      85 </span>            :     11</a>
+<a name="86"><span class="lineNum">      86 </span>            :     51</a>
+<a name="87"><span class="lineNum">      87 </span>            :     61</a>
+<a name="88"><span class="lineNum">      88 </span>            :     71</a>
+<a name="89"><span class="lineNum">      89 </span>            :     81</a>
+<a name="90"><span class="lineNum">      90 </span>            :     121</a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span>            : ...</a>
+<a name="93"><span class="lineNum">      93 </span>            : \endplumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : So, included files are the best place where one can store long definitions.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : Another case where INCLUDE is very useful is when running multi-replica simulations.</a>
+<a name="97"><span class="lineNum">      97 </span>            : Here different replicas might have different input files, but perhaps a large part of the</a>
+<a name="98"><span class="lineNum">      98 </span>            : input is shared. This part can be put in a common included file. For instance you could have</a>
+<a name="99"><span class="lineNum">      99 </span>            : `common.dat`:</a>
+<a name="100"><span class="lineNum">     100 </span>            : \plumedfile</a>
+<a name="101"><span class="lineNum">     101 </span>            : #SETTINGS FILENAME=common.dat</a>
+<a name="102"><span class="lineNum">     102 </span>            : # this is common.dat</a>
+<a name="103"><span class="lineNum">     103 </span>            : t: TORSION ATOMS=1,2,3,4</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endplumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : Then `plumed.0.dat`:</a>
+<a name="106"><span class="lineNum">     106 </span>            : \plumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : # this is plumed.0.dat</a>
+<a name="108"><span class="lineNum">     108 </span>            : INCLUDE FILE=common.dat</a>
+<a name="109"><span class="lineNum">     109 </span>            : RESTRAINT ARG=t AT=1.0 KAPPA=10</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endplumedfile</a>
+<a name="111"><span class="lineNum">     111 </span>            : And `plumed.1.dat`:</a>
+<a name="112"><span class="lineNum">     112 </span>            : \plumedfile</a>
+<a name="113"><span class="lineNum">     113 </span>            : # this is plumed.1.dat</a>
+<a name="114"><span class="lineNum">     114 </span>            : INCLUDE FILE=common.dat</a>
+<a name="115"><span class="lineNum">     115 </span>            : RESTRAINT ARG=t AT=1.2 KAPPA=10</a>
+<a name="116"><span class="lineNum">     116 </span>            : \endplumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : \warning</a>
+<a name="119"><span class="lineNum">     119 </span>            : Remember that when using multi replica simulations whenever plumed tried to open</a>
+<a name="120"><span class="lineNum">     120 </span>            : a file for reading it looks for a file with the replica suffix first.</a>
+<a name="121"><span class="lineNum">     121 </span>            : This is true also for files opened by INCLUDE!</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : As an example, the same result of the inputs above could have been obtained using</a>
+<a name="124"><span class="lineNum">     124 </span>            : the following `plumed.dat` file:</a>
+<a name="125"><span class="lineNum">     125 </span>            : \plumedfile</a>
+<a name="126"><span class="lineNum">     126 </span>            : #SETTINGS NREPLICAS=2</a>
+<a name="127"><span class="lineNum">     127 </span>            : t: TORSION ATOMS=1,2,3,4</a>
+<a name="128"><span class="lineNum">     128 </span>            : INCLUDE FILE=other.inc</a>
+<a name="129"><span class="lineNum">     129 </span>            : \endplumedfile</a>
+<a name="130"><span class="lineNum">     130 </span>            : Then `other.0.inc`:</a>
+<a name="131"><span class="lineNum">     131 </span>            : \plumedfile</a>
+<a name="132"><span class="lineNum">     132 </span>            : #SETTINGS FILENAME=other.0.inc</a>
+<a name="133"><span class="lineNum">     133 </span>            : # this is other.0.inc</a>
+<a name="134"><span class="lineNum">     134 </span>            : RESTRAINT ARG=t AT=1.0 KAPPA=10</a>
+<a name="135"><span class="lineNum">     135 </span>            : \endplumedfile</a>
+<a name="136"><span class="lineNum">     136 </span>            : And `other.1.inc`:</a>
+<a name="137"><span class="lineNum">     137 </span>            : \plumedfile</a>
+<a name="138"><span class="lineNum">     138 </span>            : #SETTINGS FILENAME=other.1.inc</a>
+<a name="139"><span class="lineNum">     139 </span>            : # this is other.1.inc</a>
+<a name="140"><span class="lineNum">     140 </span>            : RESTRAINT ARG=t AT=1.2 KAPPA=10</a>
+<a name="141"><span class="lineNum">     141 </span>            : \endplumedfile</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : */</a>
+<a name="148"><span class="lineNum">     148 </span>            : //+ENDPLUMEDOC</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : class Include :</a>
+<a name="151"><span class="lineNum">     151 </span>            :   public ActionAnyorder</a>
+<a name="152"><span class="lineNum">     152 </span>            : {</a>
+<a name="153"><span class="lineNum">     153 </span>            : public:</a>
+<a name="154"><span class="lineNum">     154 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="155"><span class="lineNum">     155 </span>            :   explicit Include(const ActionOptions&amp;ao);</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : };</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      12540 : PLUMED_REGISTER_ACTION(Include,&quot;INCLUDE&quot;)</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         20 : void Include::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         20 :   Action::registerKeywords(keys);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         40 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;file to be included&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         20 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         18 : Include::Include(const ActionOptions&amp;ao):</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   Action(ao),</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         18 :   ActionAnyorder(ao)</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : {</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::string f;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         18 :   parse(&quot;FILE&quot;,f);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         18 :   checkRead();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         18 :   plumed.readInputFile(f);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         18 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/MolInfo.cpp.func-sort-c.html b/coverage/generic/MolInfo.cpp.func-sort-c.html
new file mode 100644
index 0000000000..dad11d41d9
--- /dev/null
+++ b/coverage/generic/MolInfo.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/MolInfo.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - MolInfo.cpp<span style="font-size: 80%;"> (<a href="MolInfo.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MolInfo.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MolInfo.cpp.gcov.html#264">_ZN4PLMD7generic12_GLOBAL__N_120MolInfoRegisterMe2666createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolInfo.cpp.gcov.html#264">_ZN4PLMD7generic12_GLOBAL__N_120MolInfoRegisterMe266C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolInfo.cpp.gcov.html#264">_ZN4PLMD7generic12_GLOBAL__N_120MolInfoRegisterMe266D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/MolInfo.cpp.func.html b/coverage/generic/MolInfo.cpp.func.html
new file mode 100644
index 0000000000..f00eb74537
--- /dev/null
+++ b/coverage/generic/MolInfo.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/MolInfo.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - MolInfo.cpp<span style="font-size: 80%;"> (<a href="MolInfo.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MolInfo.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MolInfo.cpp.gcov.html#264">_ZN4PLMD7generic12_GLOBAL__N_120MolInfoRegisterMe2666createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolInfo.cpp.gcov.html#264">_ZN4PLMD7generic12_GLOBAL__N_120MolInfoRegisterMe266C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolInfo.cpp.gcov.html#264">_ZN4PLMD7generic12_GLOBAL__N_120MolInfoRegisterMe266D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/MolInfo.cpp.gcov.html b/coverage/generic/MolInfo.cpp.gcov.html
new file mode 100644
index 0000000000..670c2caec2
--- /dev/null
+++ b/coverage/generic/MolInfo.cpp.gcov.html
@@ -0,0 +1,345 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/MolInfo.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - MolInfo.cpp<span style="font-size: 80%;"> (source / <a href="MolInfo.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace generic {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC TOPOLOGY MOLINFO</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : This command is used to provide information on the molecules that are present in your system.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : The information on the molecules in your system can either be provided in the form of a pdb file</a>
+<a name="33"><span class="lineNum">      33 </span>            : or as a set of lists of atoms that describe the various chains in your system. If a pdb file</a>
+<a name="34"><span class="lineNum">      34 </span>            : is used plumed the MOLINFO command will endeavor to recognize the various chains and residues that</a>
+<a name="35"><span class="lineNum">      35 </span>            : make up the molecules in your system using the chainIDs and resnumbers from the pdb file. You can</a>
+<a name="36"><span class="lineNum">      36 </span>            : then use this information in later commands to specify atom lists in terms residues.  For example</a>
+<a name="37"><span class="lineNum">      37 </span>            : using this command you can find the backbone atoms in your structure automatically.</a>
+<a name="38"><span class="lineNum">      38 </span>            : Starting with PLUMED 2.7 you can use multiple MOLINFO actions. Every time you perform an atom</a>
+<a name="39"><span class="lineNum">      39 </span>            : selection, the last available MOLINFO action will be used. This allows you to provide multiple PDB</a>
+<a name="40"><span class="lineNum">      40 </span>            : files, for instance using different naming conventions (see \issue{134}).</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \warning</a>
+<a name="43"><span class="lineNum">      43 </span>            : Please be aware that the PDB parser in plumed is far from perfect. You should thus check the log file</a>
+<a name="44"><span class="lineNum">      44 </span>            : and examine what plumed is actually doing whenever you use the MOLINFO action.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Also make sure that the atoms are listed in the pdb with the correct order.</a>
+<a name="46"><span class="lineNum">      46 </span>            : If you are using gromacs, the safest way is to use reference pdb file</a>
+<a name="47"><span class="lineNum">      47 </span>            : generated with `gmx editconf -f topol.tpr -o reference.pdb`.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : More information of the PDB parser implemented in PLUMED can be found \ref pdbreader &quot;at this page&quot;.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : Providing `MOLTYPE=protein`, `MOLTYPE=rna`, or `MOLTYPE=dna` will instruct plumed to look</a>
+<a name="52"><span class="lineNum">      52 </span>            : for known residues from these three types of molecule. In other words, this is available for</a>
+<a name="53"><span class="lineNum">      53 </span>            : historical reasons and to allow future extensions where alternative lists will be provided.</a>
+<a name="54"><span class="lineNum">      54 </span>            : As of now, you can just ignore this keyword.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : Using \ref MOLINFO extends the possibility of atoms selection using the @ special</a>
+<a name="57"><span class="lineNum">      57 </span>            : symbol. The following shortcuts are available that do not refer to one specific residue:</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \verbatim</a>
+<a name="60"><span class="lineNum">      60 </span>            : @nucleic : all atoms that are part of a DNA or RNA molecule</a>
+<a name="61"><span class="lineNum">      61 </span>            : @protein : all atoms that are part of a protein</a>
+<a name="62"><span class="lineNum">      62 </span>            : @water : all water molecules</a>
+<a name="63"><span class="lineNum">      63 </span>            : @ions : all the ions</a>
+<a name="64"><span class="lineNum">      64 </span>            : @hydrogens : all hydrogen atoms (those for which the first non-number in the name is a H)</a>
+<a name="65"><span class="lineNum">      65 </span>            : @nonhydrogens : all non hydrogen atoms (those for which the first non-number in the name is not a H)</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endverbatim</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \warning</a>
+<a name="69"><span class="lineNum">      69 </span>            : Be careful since these choices are based on common names used in PDB files. Always check if</a>
+<a name="70"><span class="lineNum">      70 </span>            : the selected atoms are correct.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : In addition, atoms from a specific residue can be selected with a symbol in this form:</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \verbatim</a>
+<a name="75"><span class="lineNum">      75 </span>            : @&quot;definition&quot;-chain_residuenum</a>
+<a name="76"><span class="lineNum">      76 </span>            : @&quot;definition&quot;-chainresiduenum</a>
+<a name="77"><span class="lineNum">      77 </span>            : @&quot;definition&quot;-residuenum</a>
+<a name="78"><span class="lineNum">      78 </span>            : \endverbatim</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : So for example</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : \verbatim</a>
+<a name="83"><span class="lineNum">      83 </span>            : @psi-1 will select the atoms defining the psi torsion of residue 1</a>
+<a name="84"><span class="lineNum">      84 </span>            : @psi-C1  or @psi-C_1 will define the same torsion for residue 1 of chain C.</a>
+<a name="85"><span class="lineNum">      85 </span>            : @psi-3_1 will define the same torsion for residue 1 of chain 3.</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endverbatim</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : Using the underscore to separate chain and residue is available as of PLUMED 2.5 and allows selecting chains</a>
+<a name="89"><span class="lineNum">      89 </span>            : with a numeric id.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : In the following are listed the current available definitions:</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : For protein residues, the following groups are available:</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : \verbatim</a>
+<a name="96"><span class="lineNum">      96 </span>            : # quadruplets for dihedral angles</a>
+<a name="97"><span class="lineNum">      97 </span>            : @phi-#</a>
+<a name="98"><span class="lineNum">      98 </span>            : @psi-#</a>
+<a name="99"><span class="lineNum">      99 </span>            : @omega-#</a>
+<a name="100"><span class="lineNum">     100 </span>            : @chi1-#</a>
+<a name="101"><span class="lineNum">     101 </span>            : @chi2-#</a>
+<a name="102"><span class="lineNum">     102 </span>            : @chi3-#</a>
+<a name="103"><span class="lineNum">     103 </span>            : @chi4-#</a>
+<a name="104"><span class="lineNum">     104 </span>            : @chi5-#</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : # all sidechain atoms (excluding glycine, including all hydrogens)</a>
+<a name="107"><span class="lineNum">     107 </span>            : @sidechain-#</a>
+<a name="108"><span class="lineNum">     108 </span>            : # all backbone atoms (including hydrogens)</a>
+<a name="109"><span class="lineNum">     109 </span>            : @back-#</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endverbatim</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : that select the appropriate atoms that define each dihedral angle for residue #.</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : For DNA or RNA residues, the following groups are available:</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : \verbatim</a>
+<a name="117"><span class="lineNum">     117 </span>            : # quadruplets for backbone dihedral angles</a>
+<a name="118"><span class="lineNum">     118 </span>            : @alpha-#</a>
+<a name="119"><span class="lineNum">     119 </span>            : @beta-#</a>
+<a name="120"><span class="lineNum">     120 </span>            : @gamma-#</a>
+<a name="121"><span class="lineNum">     121 </span>            : @delta-#</a>
+<a name="122"><span class="lineNum">     122 </span>            : @epsilon-#</a>
+<a name="123"><span class="lineNum">     123 </span>            : @zeta-#</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : # quadruplets for sugar dihedral angles</a>
+<a name="126"><span class="lineNum">     126 </span>            : @v0-#</a>
+<a name="127"><span class="lineNum">     127 </span>            : @v1-#</a>
+<a name="128"><span class="lineNum">     128 </span>            : @v2-#</a>
+<a name="129"><span class="lineNum">     129 </span>            : @v3-#</a>
+<a name="130"><span class="lineNum">     130 </span>            : @v4-#</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : # quadruplet corresponding to the chi torsional angle</a>
+<a name="133"><span class="lineNum">     133 </span>            : @chi-#</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : # backbone, sugar, and base heavy atoms</a>
+<a name="136"><span class="lineNum">     136 </span>            : @back-#</a>
+<a name="137"><span class="lineNum">     137 </span>            : @sugar-#</a>
+<a name="138"><span class="lineNum">     138 </span>            : @base-#</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : # ordered triplets of atoms on the 6-membered ring of nucleobases</a>
+<a name="141"><span class="lineNum">     141 </span>            : # namely:</a>
+<a name="142"><span class="lineNum">     142 </span>            : #  C2/C4/C6 for pyrimidines</a>
+<a name="143"><span class="lineNum">     143 </span>            : #  C2/C6/C4 for purines</a>
+<a name="144"><span class="lineNum">     144 </span>            : @lcs-#</a>
+<a name="145"><span class="lineNum">     145 </span>            : \endverbatim</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : Notice that `zeta` and `epsilon` groups should not be used on 3' end residue and `alpha` and `beta`</a>
+<a name="148"><span class="lineNum">     148 </span>            : should not be used on 5' end residue.</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : Furthermore it is also possible to pick single atoms using the syntax</a>
+<a name="151"><span class="lineNum">     151 </span>            : `atom-chain_residuenum`, `@atom-chainresiduenum` or `@atom-residuenum`.</a>
+<a name="152"><span class="lineNum">     152 </span>            : As of PLUMED 2.5, this also works when the residue is not a protein/rna/dna residue.</a>
+<a name="153"><span class="lineNum">     153 </span>            : For instance, `@OW-100` will select oxygen of water molecule with residue number 100.</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : Finally, notice that other shortcuts are available even when not using the \ref MOLINFO command (see \ref atomSpecs).</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : \warning If a residue-chain is repeated twice in the reference pdb only the first entry will be selected.</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : \bug At the moment the HA1 atoms in a GLY residues are treated as if they are the CB atoms. This may or</a>
+<a name="160"><span class="lineNum">     160 </span>            : may not be true - GLY is problematic for secondary structure residues as it is achiral.</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : \bug If you use WHOLEMOLECULES RESIDUES=1-10 for a 18 amino acid protein</a>
+<a name="163"><span class="lineNum">     163 </span>            : ( 18 amino acids + 2 terminal groups = 20 residues ) the code will fail as it will not be able to</a>
+<a name="164"><span class="lineNum">     164 </span>            : interpret terminal residue 1.</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : \par Advanced atom selection with mdtraj or MDAnalysis</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : Since PLUMED 2.6 it is possible to use the expressive selection syntax of [mdtraj](http://mdtraj.org/latest/atom_selection.html) and/or [MDAnalysis](https://www.mdanalysis.org/docs/documentation_pages/selections.html):</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : \plumedfile</a>
+<a name="171"><span class="lineNum">     171 </span>            : MOLINFO STRUCTURE=helix.pdb PYTHON_BIN=python</a>
+<a name="172"><span class="lineNum">     172 </span>            : g1: GROUP ATOMS=@mda:backbone</a>
+<a name="173"><span class="lineNum">     173 </span>            : g2: GROUP ATOMS={@mda:{resnum 1 or resid 3:5}}</a>
+<a name="174"><span class="lineNum">     174 </span>            : g3: GROUP ATOMS={@mda:{resid 3:5} @mda:{resnum 1}}</a>
+<a name="175"><span class="lineNum">     175 </span>            : g4: GROUP ATOMS={@mdt:{protein and (backbone or resname ALA)}}</a>
+<a name="176"><span class="lineNum">     176 </span>            : g5: GROUP ATOMS={@mdt:{mass 5.5 to 20}} # masses guessed by mdtraj based on atom type!</a>
+<a name="177"><span class="lineNum">     177 </span>            : g6: GROUP ATOMS={@mda:{resid 3:5} @mda:{resnum 1} 1-10}</a>
+<a name="178"><span class="lineNum">     178 </span>            : \endplumedfile</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : Here `@mda:` indicates that `MDAnalysis` language is used, whereas `@mdt:` indicates that `mdtraj` language is used. Notice that these languages typically select atoms in order. If you want to specify a different order, you can chain definitions as in `g3` above (compare with `g2`). Selections can be also chained with standard PLUMED selections (see `g6`).</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : The double braces are required due to the way PLUMED parses atom lists. In particular:</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : - The outer braces are needed to show PLUMED where the `ATOMS=...` option ends.</a>
+<a name="185"><span class="lineNum">     185 </span>            : - The inner braces are needed to show PLUMED where each selector ends.</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : MDAnalysis also supports geometric selectors based on atomic coordinates. These selectors **are static** and return lists computed using the coordinates stored in the `MOLINFO` pdb file.</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : In order to use this syntax you should check the following points at runtime:</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : 1. `plumed --no-mpi config has subprocess` prints `subprocess on` (should be ok on most UNIX systems).</a>
+<a name="192"><span class="lineNum">     192 </span>            : 2. You have a python interpreter with mdtraj and/or MDAnalysis installed. You can check using:</a>
+<a name="193"><span class="lineNum">     193 </span>            :    - `python -c &quot;import mdtraj&quot;`</a>
+<a name="194"><span class="lineNum">     194 </span>            :    - `python -c &quot;import MDAnalysis&quot;`</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :    In order to install these packages refer to their documentation. Pip or conda install should be ok, provided you make sure the correct python interpreter is in the execution PATH at runtime. Notice that you will only need the package(s) related to the syntax that you want to use.</a>
+<a name="197"><span class="lineNum">     197 </span>            : 3. In case you installed these modules on a python with a different name (e.g. `python3.6`), the correct check is:</a>
+<a name="198"><span class="lineNum">     198 </span>            :    - `python3.6 -c &quot;import mdtraj&quot;`</a>
+<a name="199"><span class="lineNum">     199 </span>            :    - `python3.6 -c &quot;import MDAnalysis&quot;`</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :    If this is the case, you should set the environment variable `export PYTHON_BIN=python3.6` or `export PLUMED_PYTHON_BIN=python3.6` (higher priority). Alternatively, directly provide the interpreter in the PLUMED input file</a>
+<a name="202"><span class="lineNum">     202 </span>            :    using `MOLINFO PYTHON_BIN=python3.6` (even higher priority).</a>
+<a name="203"><span class="lineNum">     203 </span>            : 4. The PDB file that you provide to `MOLINFO` should have consecutive atom numbers starting from 1. This is currently enforced since reading atom numbers out of order (as PLUMED does) is not supported by other packages.</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : \par Advanced atom selection with VMD (experimental)</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : Similarly to the `@mda:` and `@mdt:` selectors above, you can use the two following selectors in order to</a>
+<a name="208"><span class="lineNum">     208 </span>            : access to [VMD](https://www.ks.uiuc.edu/Research/vmd/) syntax for atoms selection:</a>
+<a name="209"><span class="lineNum">     209 </span>            : - `@vmdexec:`: This selector launches an instance of VMD, so `vmd` executable should be in your execution path.</a>
+<a name="210"><span class="lineNum">     210 </span>            :   Might be very slow or even crash your simulation. Notice that even if `vmd` executable is used,</a>
+<a name="211"><span class="lineNum">     211 </span>            :   the implementation is still python based and so a working python interpreter should be provided.</a>
+<a name="212"><span class="lineNum">     212 </span>            : - `@vmd:`: This selector tries to import the `vmd` python module. Notice that the best way to obtain this module</a>
+<a name="213"><span class="lineNum">     213 </span>            :   is not within the standard VMD installer but rather by installing the python</a>
+<a name="214"><span class="lineNum">     214 </span>            :   module that can be found at [this link](http://github.com/Eigenstate/vmd-python).</a>
+<a name="215"><span class="lineNum">     215 </span>            :   The module is also available on [conda](https://anaconda.org/conda-forge/vmd-python).</a>
+<a name="216"><span class="lineNum">     216 </span>            :   You should make sure the module is available in the python interpreter used by MOLINFO</a>
+<a name="217"><span class="lineNum">     217 </span>            :   (check using the command `python -c &quot;import vmd&quot;`).</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            : These two selectors are experimental and might be removed at some point.</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : \par Examples</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : In the following example the MOLINFO command is used to provide the information on which atoms</a>
+<a name="224"><span class="lineNum">     224 </span>            : are in the backbone of a protein to the ALPHARMSD CV.</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : \plumedfile</a>
+<a name="227"><span class="lineNum">     227 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="228"><span class="lineNum">     228 </span>            : MOLINFO STRUCTURE=reference.pdb</a>
+<a name="229"><span class="lineNum">     229 </span>            : ALPHARMSD RESIDUES=all TYPE=DRMSD LESS_THAN={RATIONAL R_0=0.08 NN=8 MM=12} LABEL=a</a>
+<a name="230"><span class="lineNum">     230 </span>            : \endplumedfile</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : The following example prints the distance corresponding to the hydrogen bonds</a>
+<a name="233"><span class="lineNum">     233 </span>            : in a GC Watson-Crick pair.</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : \plumedfile</a>
+<a name="236"><span class="lineNum">     236 </span>            : #SETTINGS MOLFILE=regtest/basic/rt-ermsd/ref.pdb</a>
+<a name="237"><span class="lineNum">     237 </span>            : MOLINFO STRUCTURE=reference.pdb MOLTYPE=dna</a>
+<a name="238"><span class="lineNum">     238 </span>            : hb1: DISTANCE ATOMS=@N2-2,@O2-15</a>
+<a name="239"><span class="lineNum">     239 </span>            : hb2: DISTANCE ATOMS=@N1-2,@N3-15</a>
+<a name="240"><span class="lineNum">     240 </span>            : hb3: DISTANCE ATOMS=@O6-2,@N4-15</a>
+<a name="241"><span class="lineNum">     241 </span>            : PRINT ARG=hb1,hb2,hb3</a>
+<a name="242"><span class="lineNum">     242 </span>            : \endplumedfile</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : This example use MOLINFO to calculate torsion angles</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : \plumedfile</a>
+<a name="247"><span class="lineNum">     247 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="248"><span class="lineNum">     248 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb</a>
+<a name="249"><span class="lineNum">     249 </span>            : t1: TORSION ATOMS=@phi-3</a>
+<a name="250"><span class="lineNum">     250 </span>            : t2: TORSION ATOMS=@psi-4</a>
+<a name="251"><span class="lineNum">     251 </span>            : PRINT ARG=t1,t2 FILE=colvar STRIDE=10</a>
+<a name="252"><span class="lineNum">     252 </span>            : \endplumedfile</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : */</a>
+<a name="255"><span class="lineNum">     255 </span>            : //+ENDPLUMEDOC</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : /*</a>
+<a name="259"><span class="lineNum">     259 </span>            : This action is defined in core/ as it is used by other actions.</a>
+<a name="260"><span class="lineNum">     260 </span>            : Anyway, it is registered here, so that excluding this module from</a>
+<a name="261"><span class="lineNum">     261 </span>            : compilation will exclude it from plumed.</a>
+<a name="262"><span class="lineNum">     262 </span>            : */</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : typedef PLMD::GenericMolInfo MolInfo;</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">      12678 : PLUMED_REGISTER_ACTION(MolInfo,&quot;MOLINFO&quot;)</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : }</a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Plumed.cpp.func-sort-c.html b/coverage/generic/Plumed.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fe242c0e17
--- /dev/null
+++ b/coverage/generic/Plumed.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Plumed.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Plumed.cpp<span style="font-size: 80%;"> (<a href="Plumed.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">167</td>
+            <td class="headerCovTableEntry">179</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Plumed.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#165">_ZN4PLMD7generic6Plumed22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#185">_ZN4PLMD7generic6PlumedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#170">_ZN4PLMD7generic12_GLOBAL__N_119PlumedRegisterMe1726createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#185">_ZN4PLMD7generic6PlumedC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#199">_ZZN4PLMD7generic6PlumedC4ERKNS_13ActionOptionsEENKUlvE0_clEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#210">_ZZN4PLMD7generic6PlumedC4ERKNS_13ActionOptionsEENKUlvE1_clEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#191">_ZZN4PLMD7generic6PlumedC4ERKNS_13ActionOptionsEENKUlvE_clEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
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+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#394">_ZN4PLMD7generic6Plumed5applyEv</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#406">_ZN4PLMD7generic6Plumed6updateEv</a></td>
+              <td class="coverFnHi">104</td>
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+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#355">_ZN4PLMD7generic6Plumed9calculateEv</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#309">_ZN4PLMD7generic6Plumed7prepareEv</a></td>
+              <td class="coverFnHi">164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#170">_ZN4PLMD7generic12_GLOBAL__N_119PlumedRegisterMe172C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#170">_ZN4PLMD7generic12_GLOBAL__N_119PlumedRegisterMe172D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Plumed.cpp.func.html b/coverage/generic/Plumed.cpp.func.html
new file mode 100644
index 0000000000..a5ca9845b2
--- /dev/null
+++ b/coverage/generic/Plumed.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Plumed.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Plumed.cpp<span style="font-size: 80%;"> (<a href="Plumed.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">167</td>
+            <td class="headerCovTableEntry">179</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Plumed.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#170">_ZN4PLMD7generic12_GLOBAL__N_119PlumedRegisterMe1726createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#170">_ZN4PLMD7generic12_GLOBAL__N_119PlumedRegisterMe172C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#170">_ZN4PLMD7generic12_GLOBAL__N_119PlumedRegisterMe172D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#172">_ZN4PLMD7generic6Plumed16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#165">_ZN4PLMD7generic6Plumed22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#394">_ZN4PLMD7generic6Plumed5applyEv</a></td>
+              <td class="coverFnHi">104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#406">_ZN4PLMD7generic6Plumed6updateEv</a></td>
+              <td class="coverFnHi">104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#309">_ZN4PLMD7generic6Plumed7prepareEv</a></td>
+              <td class="coverFnHi">164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#355">_ZN4PLMD7generic6Plumed9calculateEv</a></td>
+              <td class="coverFnHi">134</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#185">_ZN4PLMD7generic6PlumedC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#185">_ZN4PLMD7generic6PlumedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#199">_ZZN4PLMD7generic6PlumedC4ERKNS_13ActionOptionsEENKUlvE0_clEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#210">_ZZN4PLMD7generic6PlumedC4ERKNS_13ActionOptionsEENKUlvE1_clEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.cpp.gcov.html#191">_ZZN4PLMD7generic6PlumedC4ERKNS_13ActionOptionsEENKUlvE_clEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Plumed.cpp.gcov.html b/coverage/generic/Plumed.cpp.gcov.html
new file mode 100644
index 0000000000..1eefe39571
--- /dev/null
+++ b/coverage/generic/Plumed.cpp.gcov.html
@@ -0,0 +1,495 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Plumed.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Plumed.cpp<span style="font-size: 80%;"> (source / <a href="Plumed.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">167</td>
+            <td class="headerCovTableEntry">179</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/PlumedHandle.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstring&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;dlfcn.h&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #endif</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;iostream&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace generic {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : //+PLUMEDOC GENERIC PLUMED</a>
+<a name="40"><span class="lineNum">      40 </span>            : /*</a>
+<a name="41"><span class="lineNum">      41 </span>            : Embed a separate PLUMED instance.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : This command can be used to embed a separate PLUMED instance.</a>
+<a name="44"><span class="lineNum">      44 </span>            : Only required atoms will be passed to that instance, using an interface</a>
+<a name="45"><span class="lineNum">      45 </span>            : that is similar to the one used when calling PLUMED from the NAMD engine.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Notice that the two instances are running in the same UNIX process, so that they cannot be perfectly isolated.</a>
+<a name="48"><span class="lineNum">      48 </span>            : However, most of the features are expected to work correctly.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : Notes:</a>
+<a name="51"><span class="lineNum">      51 </span>            : - The \ref LOAD action will not work correctly since registers will be shared among the two instances.</a>
+<a name="52"><span class="lineNum">      52 </span>            :   In particular, the loaded actions will be visible to both guest and host irrespective of where they are loaded from.</a>
+<a name="53"><span class="lineNum">      53 </span>            :   This can be fixed and will probably be fixed in a later version.</a>
+<a name="54"><span class="lineNum">      54 </span>            : - `CHDIR` is not thread safe.</a>
+<a name="55"><span class="lineNum">      55 </span>            :    However, in most implementations there will be a single process running PLUMED, with perhaps multiple OpenMP threads</a>
+<a name="56"><span class="lineNum">      56 </span>            :    spawn in order to parallelize the calculation of individual variables. So, this is likely not a problem.</a>
+<a name="57"><span class="lineNum">      57 </span>            : - MPI is working correctly. However, notice that the guest PLUMED will always run with a single process.</a>
+<a name="58"><span class="lineNum">      58 </span>            :   Multiple replicas should be handled correctly.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : As an advanced feature, one can use the option `KERNEL` to select the version of the guest PLUMED instance.</a>
+<a name="61"><span class="lineNum">      61 </span>            : In particular, an empty `KERNEL` (default) implies that the guest PLUMED instance is the same as the host one</a>
+<a name="62"><span class="lineNum">      62 </span>            : (no library is loaded).</a>
+<a name="63"><span class="lineNum">      63 </span>            : On the other hand, `KERNEL=/path/to/libplumedKernel.so` will allow specifying a library to be loaded for the</a>
+<a name="64"><span class="lineNum">      64 </span>            : guest instance.</a>
+<a name="65"><span class="lineNum">      65 </span>            : In addition to those mentioned above, this feature has limitations mostly related to</a>
+<a name="66"><span class="lineNum">      66 </span>            : clashes in the symbols defined in the different instances of the PLUMED library:</a>
+<a name="67"><span class="lineNum">      67 </span>            : - On OSX, if you load a KERNEL with version &gt;=2.5 there should be no problem thanks to the use</a>
+<a name="68"><span class="lineNum">      68 </span>            :   of two-level namespaces.</a>
+<a name="69"><span class="lineNum">      69 </span>            : - On OSX, if you load a KERNEL with version &lt;=2.4 there should be clashes in symbol resolution.</a>
+<a name="70"><span class="lineNum">      70 </span>            :   The only possible workarounds are:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   - If you are are using PLUMED with an MD code, it should be patched with `--runtime` and you should</a>
+<a name="72"><span class="lineNum">      72 </span>            :     `export PLUMED_LOAD_NAMESPACE=LOCAL` before starting the MD engine.</a>
+<a name="73"><span class="lineNum">      73 </span>            :   - If you are using PLUMED driver, you should launch the `plumed-runtime` executable (contained in the</a>
+<a name="74"><span class="lineNum">      74 </span>            :     `prefix/lib/plumed/` directory), export `PLUMED_KERNEL` equal to the path of the host kernel library</a>
+<a name="75"><span class="lineNum">      75 </span>            :    (as usual in runtime loading) and `export PLUMED_LOAD_NAMESPACE=LOCAL` before launching `plumed-runtime driver`.</a>
+<a name="76"><span class="lineNum">      76 </span>            : - On Linux, any `KERNEL` should in principle work correctly. To achieve namespace separation we are loading</a>
+<a name="77"><span class="lineNum">      77 </span>            :   the guest kernel with `RTLD_DEEPBIND`. However, this might create difficult to track problems in other linked libraries.</a>
+<a name="78"><span class="lineNum">      78 </span>            : - On Unix systems where `RTLD_DEEPBIND` is not available kernels will not load correctly.</a>
+<a name="79"><span class="lineNum">      79 </span>            : - In general, there might be unexpected crashes. Particularly difficult are situations where different</a>
+<a name="80"><span class="lineNum">      80 </span>            :   kernels were compiled with different libraries.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : A possible solution for the symbol clashes (not tested) could be to recompile the alternative PLUMED</a>
+<a name="83"><span class="lineNum">      83 </span>            : versions using separate C++ namespaces (e.g. `./configure CPPFLAGS=-DPLMD=PLMD_2_3`).</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : \todo</a>
+<a name="86"><span class="lineNum">      86 </span>            : - Add support for multiple time stepping (`STRIDE` different from 1).</a>
+<a name="87"><span class="lineNum">      87 </span>            : - Add the possibility to import CVs calculated in the host PLUMED instance into the guest PLUMED instance.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   Will be possible after \issue{83} will be closed.</a>
+<a name="89"><span class="lineNum">      89 </span>            : - Add the possibility to export CVs calculated in the guest PLUMED instance into the host PLUMED instance.</a>
+<a name="90"><span class="lineNum">      90 </span>            :   Could be implemented using the `DataFetchingObject` class.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : \par Examples</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : Here an example plumed file:</a>
+<a name="95"><span class="lineNum">      95 </span>            : \plumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : # plumed.dat</a>
+<a name="97"><span class="lineNum">      97 </span>            : p: PLUMED FILE=plumed2.dat</a>
+<a name="98"><span class="lineNum">      98 </span>            : PRINT ARG=p.bias FILE=COLVAR</a>
+<a name="99"><span class="lineNum">      99 </span>            : \endplumedfile</a>
+<a name="100"><span class="lineNum">     100 </span>            : `plumed2.dat` can be an arbitrary plumed input file, for instance</a>
+<a name="101"><span class="lineNum">     101 </span>            : \plumedfile</a>
+<a name="102"><span class="lineNum">     102 </span>            : #SETTINGS FILENAME=plumed2.dat</a>
+<a name="103"><span class="lineNum">     103 </span>            : # plumed2.dat</a>
+<a name="104"><span class="lineNum">     104 </span>            : d: DISTANCE ATOMS=1,10</a>
+<a name="105"><span class="lineNum">     105 </span>            : RESTRAINT ARG=d KAPPA=10 AT=2</a>
+<a name="106"><span class="lineNum">     106 </span>            : \endplumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : Now a more useful example.</a>
+<a name="109"><span class="lineNum">     109 </span>            : Imagine that you ran simulations using two different PLUMED input files.</a>
+<a name="110"><span class="lineNum">     110 </span>            : The files are long and complex and there are some clashes in the name of the variables (that is: same names</a>
+<a name="111"><span class="lineNum">     111 </span>            : are used in both files, same files are written, etc). In addition, files might have been written using different units (see \ref UNITS`).</a>
+<a name="112"><span class="lineNum">     112 </span>            : If you want to run a single simulation with a bias potential</a>
+<a name="113"><span class="lineNum">     113 </span>            : that is the sum of the two bias potentials, you can:</a>
+<a name="114"><span class="lineNum">     114 </span>            : - Place the two input files, as well as all the files required by plumed, in separate directories `directory1` and `directory2`.</a>
+<a name="115"><span class="lineNum">     115 </span>            : - Run with the following input file in the parent directory:</a>
+<a name="116"><span class="lineNum">     116 </span>            : \plumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : # plumed.dat</a>
+<a name="118"><span class="lineNum">     118 </span>            : PLUMED FILE=plumed.dat CHDIR=directory1</a>
+<a name="119"><span class="lineNum">     119 </span>            : PLUMED FILE=plumed.dat CHDIR=directory2</a>
+<a name="120"><span class="lineNum">     120 </span>            : \endplumedfile</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : */</a>
+<a name="123"><span class="lineNum">     123 </span>            : //+ENDPLUMEDOC</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : class Plumed:</a>
+<a name="126"><span class="lineNum">     126 </span>            :   public ActionAtomistic,</a>
+<a name="127"><span class="lineNum">     127 </span>            :   public ActionWithValue,</a>
+<a name="128"><span class="lineNum">     128 </span>            :   public ActionPilot</a>
+<a name="129"><span class="lineNum">     129 </span>            : {</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// True on root processor</a>
+<a name="131"><span class="lineNum">     131 </span>            :   const bool root;</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Separate directory.</a>
+<a name="133"><span class="lineNum">     133 </span>            :   const std::string directory;</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Interface to underlying plumed object.</a>
+<a name="135"><span class="lineNum">     135 </span>            :   PlumedHandle p;</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// API number.</a>
+<a name="137"><span class="lineNum">     137 </span>            :   const int API;</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Self communicator</a>
+<a name="139"><span class="lineNum">     139 </span>            :   Communicator comm_self;</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Intercommunicator</a>
+<a name="141"><span class="lineNum">     141 </span>            :   Communicator intercomm;</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// Detect first usage.</a>
+<a name="143"><span class="lineNum">     143 </span>            :   bool first=true;</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// Stop flag, used to stop e.g. in committor analysis</a>
+<a name="145"><span class="lineNum">     145 </span>            :   int stop=0;</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Index of requested atoms.</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;int&gt; index;</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// Masses of requested atoms.</a>
+<a name="149"><span class="lineNum">     149 </span>            :   std::vector&lt;double&gt; masses;</a>
+<a name="150"><span class="lineNum">     150 </span>            : /// Charges of requested atoms.</a>
+<a name="151"><span class="lineNum">     151 </span>            :   std::vector&lt;double&gt; charges;</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Forces on requested atoms.</a>
+<a name="153"><span class="lineNum">     153 </span>            :   std::vector&lt;double&gt; forces;</a>
+<a name="154"><span class="lineNum">     154 </span>            : /// Requested positions.</a>
+<a name="155"><span class="lineNum">     155 </span>            :   std::vector&lt;double&gt; positions;</a>
+<a name="156"><span class="lineNum">     156 </span>            : /// Applied virial.</a>
+<a name="157"><span class="lineNum">     157 </span>            :   Tensor virial;</a>
+<a name="158"><span class="lineNum">     158 </span>            : public:</a>
+<a name="159"><span class="lineNum">     159 </span>            : /// Constructor.</a>
+<a name="160"><span class="lineNum">     160 </span>            :   explicit Plumed(const ActionOptions&amp;);</a>
+<a name="161"><span class="lineNum">     161 </span>            : /// Documentation.</a>
+<a name="162"><span class="lineNum">     162 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="163"><span class="lineNum">     163 </span>            :   void prepare() override;</a>
+<a name="164"><span class="lineNum">     164 </span>            :   void calculate() override;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   void apply() override;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   void update() override;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :   unsigned getNumberOfDerivatives() override {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     return 0;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span>            : };</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(Plumed,&quot;PLUMED&quot;)</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         14 : void Plumed::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         14 :   Action::registerKeywords( keys );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         14 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         14 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;stride different from 1 are not supported yet&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;input file for the guest PLUMED instance&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;KERNEL&quot;,&quot;kernel to be used for the guest PLUMED instance (USE WITH CAUTION!)&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;LOG&quot;,&quot;log file for the guest PLUMED instance. By default the host log is used&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;CHDIR&quot;,&quot;run guest in a separate directory&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         28 :   keys.addFlag(&quot;NOREPLICAS&quot;,false,&quot;run multiple replicas as isolated ones, without letting them know that the host has multiple replicas&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         28 :   keys.addOutputComponent(&quot;bias&quot;,&quot;default&quot;,&quot;the instantaneous value of the bias potential&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         14 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         12 : Plumed::Plumed(const ActionOptions&amp;ao):</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   Action(ao),</a>
+<a name="189"><span class="lineNum">     189 </span>            :   ActionAtomistic(ao),</a>
+<a name="190"><span class="lineNum">     190 </span>            :   ActionWithValue(ao),</a>
+<a name="191"><span class="lineNum">     191 </span>            :   ActionPilot(ao),</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         24 :   root(comm.Get_rank()==0),</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         24 :   directory([&amp;]() {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   std::string directory;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         24 :   parse(&quot;CHDIR&quot;,directory);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         12 :   if(directory.length()&gt;0) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  running on separate directory &quot;&lt;&lt;directory&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         12 :   return directory;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : }()),</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         24 : p([&amp;]() {</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   std::string kernel;</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         24 :   parse(&quot;KERNEL&quot;,kernel);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         12 :   if(kernel.length()==0) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         11 :     log&lt;&lt;&quot;  using the current kernel\n&quot;;</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         11 :     return PlumedHandle();</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   } else {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  using the kernel &quot;&lt;&lt;kernel&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          1 :     return PlumedHandle::dlopen(kernel.c_str());</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span>            : }()),</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         24 : API([&amp;]() {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         12 :   int api=0;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         24 :   p.cmd(&quot;getApiVersion&quot;,&amp;api);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         12 :   log&lt;&lt;&quot;  reported API version is &quot;&lt;&lt;api&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   // note: this is required in order to have cmd performCalcNoUpdate and cmd update</a>
+<a name="217"><span class="lineNum">     217 </span>            :   // as a matter of fact, any version &lt;2.5 will not even load due to namespace pollution</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         12 :   plumed_assert(api&gt;3) &lt;&lt; &quot;API&gt;3 is required for the PLUMED action to work correctly\n&quot;;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         12 :   return api;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         24 : }())</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         12 :   Tools::DirectoryChanger directoryChanger(directory.c_str());</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   bool noreplicas;</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         12 :   parseFlag(&quot;NOREPLICAS&quot;,noreplicas);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   int nreps;</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         12 :   if(root) nreps=multi_sim_comm.Get_size();</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         12 :   comm.Bcast(nreps,0);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         12 :   if(nreps&gt;1) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          6 :     if(noreplicas) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;  running replicas as independent (no suffix used)\n&quot;;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     } else {</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          6 :       log&lt;&lt;&quot;  running replicas as standard multi replic (with suffix)\n&quot;;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          6 :       if(root) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          6 :         intercomm.Set_comm(&amp;multi_sim_comm.Get_comm());</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          9 :         p.cmd(&quot;GREX setMPIIntercomm&quot;,&amp;intercomm.Get_comm());</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          9 :         p.cmd(&quot;GREX setMPIIntracomm&quot;,&amp;comm_self.Get_comm());</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          6 :         p.cmd(&quot;GREX init&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :       }</a>
+<a name="240"><span class="lineNum">     240 </span>            :     }</a>
+<a name="241"><span class="lineNum">     241 </span>            :   } else {</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          6 :     if(noreplicas) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :       log&lt;&lt;&quot;  WARNING: flag NOREPLICAS ignored since we are running without replicas\n&quot;;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :     }</a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         12 :   int natoms=plumed.getAtoms().getNatoms();</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         12 :   plumed_assert(getStride()==1) &lt;&lt; &quot;currently only supports STRIDE=1&quot;;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         12 :   double dt=getTimeStep();</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            :   std::string file;</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         24 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         12 :   if(file.length()&gt;0) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         12 :     log&lt;&lt;&quot;  with input file &quot;&lt;&lt;file&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   } else plumed_error() &lt;&lt; &quot;you must provide an input file\n&quot;;</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            :   bool inherited_logfile=false;</a>
+<a name="260"><span class="lineNum">     260 </span>            :   std::string logfile;</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         24 :   parse(&quot;LOG&quot;,logfile);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         12 :   if(logfile.length()&gt;0) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  with log file &quot;&lt;&lt;logfile&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :     if(root) p.cmd(&quot;setLogFile&quot;,logfile.c_str());</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         12 :   } else if(log.getFILE()) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         12 :     log&lt;&lt;&quot;  with inherited log file\n&quot;;</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         18 :     if(root) p.cmd(&quot;setLog&quot;,log.getFILE());</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :     inherited_logfile=true;</a>
+<a name="269"><span class="lineNum">     269 </span>            :   } else {</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  with log on stdout\n&quot;;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :     if(root) p.cmd(&quot;setLog&quot;,stdout);</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :   }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         12 :   checkRead();</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setMDEngine&quot;,&quot;plumed&quot;);</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         12 :   double engunits=plumed.getAtoms().getUnits().getEnergy();</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setMDEnergyUnits&quot;,&amp;engunits);</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         12 :   double lenunits=plumed.getAtoms().getUnits().getLength();</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setMDLengthUnits&quot;,&amp;lenunits);</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         12 :   double timunits=plumed.getAtoms().getUnits().getTime();</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setMDTimeUnits&quot;,&amp;timunits);</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         12 :   double chaunits=plumed.getAtoms().getUnits().getCharge();</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setMDChargeUnits&quot;,&amp;chaunits);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         12 :   double masunits=plumed.getAtoms().getUnits().getMass();</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setMDMassUnits&quot;,&amp;masunits);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         12 :   double kbt=plumed.getAtoms().getKbT();</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setKbT&quot;,&amp;kbt);</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         12 :   int res=0;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         12 :   if(getRestart()) res=1;</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setRestart&quot;,&amp;res);</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setNatoms&quot;,&amp;natoms);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setTimestep&quot;,&amp;dt);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;setPlumedDat&quot;,file.c_str());</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         12 :   addComponentWithDerivatives(&quot;bias&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         12 :   componentIsNotPeriodic(&quot;bias&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         12 :   if(inherited_logfile) log&lt;&lt;&quot;++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n&quot;;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         18 :   if(root) p.cmd(&quot;init&quot;);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         12 :   if(inherited_logfile) log&lt;&lt;&quot;++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++\n&quot;;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         12 : }</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        164 : void Plumed::prepare() {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        164 :   Tools::DirectoryChanger directoryChanger(directory.c_str());</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        164 :   int step=getStep();</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">        253 :   if(root) p.cmd(&quot;setStep&quot;,&amp;step);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        253 :   if(root) p.cmd(&quot;prepareDependencies&quot;);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        164 :   int ene=0;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        253 :   if(root) p.cmd(&quot;isEnergyNeeded&quot;,&amp;ene);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        164 :   if(ene) plumed_error()&lt;&lt;&quot;It is not currently possible to use ENERGY in a guest PLUMED&quot;;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        164 :   int n=0;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        253 :   if(root) p.cmd(&quot;createFullList&quot;,&amp;n);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        164 :   const int *pointer=nullptr;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        253 :   if(root) p.cmd(&quot;getFullList&quot;,&amp;pointer);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        164 :   bool redo=(index.size()!=n);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        164 :   if(first) redo=true;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        164 :   first=false;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       4409 :   if(root &amp;&amp; !redo) for(int i=0; i&lt;n; i++) if(index[i]!=pointer[i]) { redo=true; break;};</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">        164 :   if(root &amp;&amp; redo) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         22 :     index.resize(n);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         22 :     masses.resize(n);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         22 :     forces.resize(3*n);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         22 :     positions.resize(3*n);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         22 :     charges.resize(n);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       1043 :     for(int i=0; i&lt;n; i++) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       1021 :       index[i]=pointer[i];</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :     };</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         44 :     p.cmd(&quot;setAtomsNlocal&quot;,&amp;n);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         44 :     p.cmd(&quot;setAtomsGatindex&quot;,index.data(),index.size());</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   }</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">        253 :   if(root) p.cmd(&quot;clearFullList&quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">        164 :   int tmp=0;</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        164 :   if(root &amp;&amp; redo) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         22 :     tmp=1;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        164 :   comm.Bcast(tmp,0);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        164 :   if(tmp) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         34 :     int s=index.size();</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         34 :     comm.Bcast(s,0);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         34 :     if(!root) index.resize(s);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         34 :     comm.Bcast(index,0);</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :     std::vector&lt;AtomNumber&gt; numbers;</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         34 :     numbers.reserve(index.size());</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       2138 :     for(auto i : index) numbers.emplace_back(AtomNumber::index(i));</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         34 :     requestAtoms(numbers);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :   }</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        164 : }</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        134 : void Plumed::calculate() {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        134 :   Tools::DirectoryChanger directoryChanger(directory.c_str());</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setStopFlag&quot;,&amp;stop);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">        134 :   Tensor box=getPbc().getBox();</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setBox&quot;,&amp;box[0][0],9);</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">        134 :   virial.zero();</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">      24875 :   for(int i=0; i&lt;forces.size(); i++) forces[i]=0.0;</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">       4238 :   for(int i=0; i&lt;masses.size(); i++) masses[i]=getMass(i);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       4238 :   for(int i=0; i&lt;charges.size(); i++) charges[i]=getCharge(i);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setMasses&quot;,masses.data(),masses.size());</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setCharges&quot;,charges.data(),charges.size());</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setPositions&quot;,positions.data(),positions.size());</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setForces&quot;,forces.data(),forces.size());</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;setVirial&quot;,&amp;virial[0][0],9);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">       4238 :   if(root) for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">       4104 :       positions[3*i+0]=getPosition(i)[0];</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">       4104 :       positions[3*i+1]=getPosition(i)[1];</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">       4104 :       positions[3*i+2]=getPosition(i)[2];</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :     }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;shareData&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;performCalcNoUpdate&quot;);</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        134 :   int s=forces.size();</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        134 :   comm.Bcast(s,0);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        134 :   if(!root) forces.resize(s);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        134 :   comm.Bcast(forces,0);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        134 :   comm.Bcast(virial,0);</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        134 :   double bias=0.0;</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        208 :   if(root) p.cmd(&quot;getBias&quot;,&amp;bias);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        134 :   comm.Bcast(bias,0);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        134 :   getPntrToComponent(&quot;bias&quot;)-&gt;set(bias);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        134 : }</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        104 : void Plumed::apply() {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        104 :   Tools::DirectoryChanger directoryChanger(directory.c_str());</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   auto &amp; f(modifyForces());</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       6596 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       6492 :     f[i][0]+=forces[3*i+0];</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       6492 :     f[i][1]+=forces[3*i+1];</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">       6492 :     f[i][2]+=forces[3*i+2];</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span>            :   auto &amp; v(modifyVirial());</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">        104 :   v+=virial;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">        104 : }</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">        104 : void Plumed::update() {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">        104 :   Tools::DirectoryChanger directoryChanger(directory.c_str());</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">        163 :   if(root) p.cmd(&quot;update&quot;);</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        104 :   comm.Bcast(stop,0);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">        104 :   if(stop) {</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  Action &quot; &lt;&lt; getLabel()&lt;&lt;&quot; asked to stop\n&quot;;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :     plumed.stop();</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        104 : }</span></a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            : }</a>
+<a name="419"><span class="lineNum">     419 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Print.cpp.func-sort-c.html b/coverage/generic/Print.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4d6c020896
--- /dev/null
+++ b/coverage/generic/Print.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Print.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Print.cpp<span style="font-size: 80%;"> (<a href="Print.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Print.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#109">_ZN4PLMD7generic5PrintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#172">_ZN4PLMD7generic5PrintD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#93">_ZN4PLMD7generic12_GLOBAL__N_117PrintRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#109">_ZN4PLMD7generic5PrintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#172">_ZN4PLMD7generic5PrintD0Ev</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#172">_ZN4PLMD7generic5PrintD1Ev</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#95">_ZN4PLMD7generic5Print16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#93">_ZN4PLMD7generic12_GLOBAL__N_117PrintRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#93">_ZN4PLMD7generic12_GLOBAL__N_117PrintRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#162">_ZN4PLMD7generic5Print6updateEv</a></td>
+              <td class="coverFnHi">211498</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#88">_ZN4PLMD7generic5Print5applyEv</a></td>
+              <td class="coverFnHi">212121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#84">_ZN4PLMD7generic5Print9calculateEv</a></td>
+              <td class="coverFnHi">212243</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#145">_ZN4PLMD7generic5Print7prepareEv</a></td>
+              <td class="coverFnHi">212366</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Print.cpp.func.html b/coverage/generic/Print.cpp.func.html
new file mode 100644
index 0000000000..765bf15f06
--- /dev/null
+++ b/coverage/generic/Print.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Print.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Print.cpp<span style="font-size: 80%;"> (<a href="Print.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Print.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#93">_ZN4PLMD7generic12_GLOBAL__N_117PrintRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#93">_ZN4PLMD7generic12_GLOBAL__N_117PrintRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#93">_ZN4PLMD7generic12_GLOBAL__N_117PrintRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#95">_ZN4PLMD7generic5Print16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#88">_ZN4PLMD7generic5Print5applyEv</a></td>
+              <td class="coverFnHi">212121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#162">_ZN4PLMD7generic5Print6updateEv</a></td>
+              <td class="coverFnHi">211498</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#145">_ZN4PLMD7generic5Print7prepareEv</a></td>
+              <td class="coverFnHi">212366</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#84">_ZN4PLMD7generic5Print9calculateEv</a></td>
+              <td class="coverFnHi">212243</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#109">_ZN4PLMD7generic5PrintC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#109">_ZN4PLMD7generic5PrintC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#172">_ZN4PLMD7generic5PrintD0Ev</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#172">_ZN4PLMD7generic5PrintD1Ev</a></td>
+              <td class="coverFnHi">820</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Print.cpp.gcov.html#172">_ZN4PLMD7generic5PrintD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Print.cpp.gcov.html b/coverage/generic/Print.cpp.gcov.html
new file mode 100644
index 0000000000..ece750165f
--- /dev/null
+++ b/coverage/generic/Print.cpp.gcov.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Print.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Print.cpp<span style="font-size: 80%;"> (source / <a href="Print.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace generic {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC PRINTANALYSIS PRINT</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Print quantities to a file.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This directive can be used multiple times</a>
+<a name="34"><span class="lineNum">      34 </span>            : in the input so you can print files with different strides or print different quantities</a>
+<a name="35"><span class="lineNum">      35 </span>            : to different files.  You can control the buffering of output using the \subpage FLUSH keyword.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Output file is either appended or backed up depending on the presence of the \ref RESTART action.</a>
+<a name="37"><span class="lineNum">      37 </span>            : A per-action `RESTART` keyword can be used as well.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Notice that printing happens in the so-called &quot;update&quot; phase. This implies that printing</a>
+<a name="40"><span class="lineNum">      40 </span>            : is affected by the presence of \ref UPDATE_IF actions. In addition, one might decide to start</a>
+<a name="41"><span class="lineNum">      41 </span>            : and stop printing at preassigned values of time using the `UPDATE_FROM` and `UPDATE_UNTIL` keywords.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Keep into account that even on steps when the action is not updated (and thus the file is not printed)</a>
+<a name="43"><span class="lineNum">      43 </span>            : the argument will be activated. In other words, if you use `UPDATE_FROM` to start printing at a given time,</a>
+<a name="44"><span class="lineNum">      44 </span>            : the collective variables this PRINT statement depends on will be computed also before that time.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The following input instructs plumed to print the distance between atoms 3 and 5 on a file</a>
+<a name="49"><span class="lineNum">      49 </span>            : called COLVAR every 10 steps, and the distance and total energy on a file called COLVAR_ALL</a>
+<a name="50"><span class="lineNum">      50 </span>            : every 1000 steps.</a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : # compute distance:</a>
+<a name="53"><span class="lineNum">      53 </span>            : distance: DISTANCE ATOMS=2,5</a>
+<a name="54"><span class="lineNum">      54 </span>            : # compute total energy (potential)</a>
+<a name="55"><span class="lineNum">      55 </span>            : energy: ENERGY</a>
+<a name="56"><span class="lineNum">      56 </span>            : # print distance on a file</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=distance          STRIDE=10   FILE=COLVAR</a>
+<a name="58"><span class="lineNum">      58 </span>            : # print both variables on another file</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=distance,energy   STRIDE=1000 FILE=COLVAR_ALL</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : Notice that \ref DISTANCE and \ref ENERGY are computed respectively every 10 and 1000 steps, that is</a>
+<a name="63"><span class="lineNum">      63 </span>            : only when required.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : */</a>
+<a name="66"><span class="lineNum">      66 </span>            : //+ENDPLUMEDOC</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class Print :</a>
+<a name="69"><span class="lineNum">      69 </span>            :   public ActionPilot,</a>
+<a name="70"><span class="lineNum">      70 </span>            :   public ActionWithArguments</a>
+<a name="71"><span class="lineNum">      71 </span>            : {</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::string file;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   OFile ofile;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   std::string fmt;</a>
+<a name="75"><span class="lineNum">      75 </span>            : // small internal utility</a>
+<a name="76"><span class="lineNum">      76 </span>            : /////////////////////////////////////////</a>
+<a name="77"><span class="lineNum">      77 </span>            : // these are crazy things just for debug:</a>
+<a name="78"><span class="lineNum">      78 </span>            : // they allow to change regularly the</a>
+<a name="79"><span class="lineNum">      79 </span>            : // printed argument</a>
+<a name="80"><span class="lineNum">      80 </span>            :   int rotate;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   int rotateCountdown;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   int rotateLast;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;Value*&gt; rotateArguments;</a>
+<a name="84"><span class="lineNum">      84 </span>            : /////////////////////////////////////////</a>
+<a name="85"><span class="lineNum">      85 </span>            : public:</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     212243 :   void calculate() override {}</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   void prepare() override;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit Print(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">     212121 :   void apply() override {}</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   void update() override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ~Print();</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      14144 : PLUMED_REGISTER_ACTION(Print,&quot;PRINT&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        822 : void Print::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        822 :   Action::registerKeywords(keys);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        822 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        822 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        822 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       1644 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the quantities of interest should be output&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1644 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;the name of the file on which to output these quantities&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1644 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format that should be used to output real numbers&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1644 :   keys.add(&quot;hidden&quot;,&quot;_ROTATE&quot;,&quot;some funky thing implemented by GBussi&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        822 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        822 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        822 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        822 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        820 : Print::Print(const ActionOptions&amp;ao):</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   Action(ao),</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ActionPilot(ao),</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ActionWithArguments(ao),</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        820 :   fmt(&quot;%f&quot;),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       1640 :   rotate(0)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        820 :   ofile.link(*this);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1640 :   parse(&quot;FILE&quot;,file);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        820 :   if(file.length()&gt;0) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        820 :     ofile.open(file);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        820 :     log.printf(&quot;  on file %s\n&quot;,file.c_str());</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   } else {</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     log.printf(&quot;  on plumed log file\n&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :     ofile.link(log);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        820 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        820 :   fmt=&quot; &quot;+fmt;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        820 :   log.printf(&quot;  with format %s\n&quot;,fmt.c_str());</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       6289 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) ofile.setupPrintValue( getPntrToArgument(i) );</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : /////////////////////////////////////////</a>
+<a name="132"><span class="lineNum">     132 </span>            : // these are crazy things just for debug:</a>
+<a name="133"><span class="lineNum">     133 </span>            : // they allow to change regularly the</a>
+<a name="134"><span class="lineNum">     134 </span>            : // printed argument</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        820 :   parse(&quot;_ROTATE&quot;,rotate);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        820 :   if(rotate&gt;0) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :     rotateCountdown=rotate;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) rotateArguments.push_back( getPntrToArgument(i) );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 :     std::vector&lt;Value*&gt; a(1,rotateArguments[0]);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :     requestArguments(std::vector&lt;Value*&gt;(1,rotateArguments[0]));</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :     rotateLast=0;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : /////////////////////////////////////////</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        820 :   checkRead();</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        820 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">     212366 : void Print::prepare() {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : /////////////////////////////////////////</a>
+<a name="149"><span class="lineNum">     149 </span>            : // these are crazy things just for debug:</a>
+<a name="150"><span class="lineNum">     150 </span>            : // they allow to change regularly the</a>
+<a name="151"><span class="lineNum">     151 </span>            : // printed argument</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     212366 :   if(rotate&gt;0) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          5 :     rotateCountdown--;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          5 :     if(rotateCountdown==0) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :       rotateCountdown=rotate;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :       rotateLast++;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :       rotateLast%=rotateArguments.size();</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :       requestArguments(std::vector&lt;Value*&gt;(1,rotateArguments[rotateLast]));</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : /////////////////////////////////////////</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     212366 : }</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     211498 : void Print::update() {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">     211498 :   ofile.fmtField(&quot; %f&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     211498 :   ofile.printField(&quot;time&quot;,getTime());</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">     742572 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">     531074 :     ofile.fmtField(fmt);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     531074 :     ofile.printField( getPntrToArgument(i), getArgument(i) );</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     211498 :   ofile.printField();</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     211498 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       1640 : Print::~Print() {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1640 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/RandomExchanges.cpp.func-sort-c.html b/coverage/generic/RandomExchanges.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1c4d9375c3
--- /dev/null
+++ b/coverage/generic/RandomExchanges.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/RandomExchanges.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - RandomExchanges.cpp<span style="font-size: 80%;"> (<a href="RandomExchanges.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">35.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RandomExchanges.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#81">_ZN4PLMD7generic12_GLOBAL__N_127RandomExchangesRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#78">_ZN4PLMD7generic15RandomExchanges5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#77">_ZN4PLMD7generic15RandomExchanges9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#88">_ZN4PLMD7generic15RandomExchangesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#83">_ZN4PLMD7generic15RandomExchanges16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#81">_ZN4PLMD7generic12_GLOBAL__N_127RandomExchangesRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#81">_ZN4PLMD7generic12_GLOBAL__N_127RandomExchangesRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/RandomExchanges.cpp.func.html b/coverage/generic/RandomExchanges.cpp.func.html
new file mode 100644
index 0000000000..a66cb1804d
--- /dev/null
+++ b/coverage/generic/RandomExchanges.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/RandomExchanges.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - RandomExchanges.cpp<span style="font-size: 80%;"> (<a href="RandomExchanges.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">35.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="RandomExchanges.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#81">_ZN4PLMD7generic12_GLOBAL__N_127RandomExchangesRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#81">_ZN4PLMD7generic12_GLOBAL__N_127RandomExchangesRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#81">_ZN4PLMD7generic12_GLOBAL__N_127RandomExchangesRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#83">_ZN4PLMD7generic15RandomExchanges16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#78">_ZN4PLMD7generic15RandomExchanges5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#77">_ZN4PLMD7generic15RandomExchanges9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RandomExchanges.cpp.gcov.html#88">_ZN4PLMD7generic15RandomExchangesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/RandomExchanges.cpp.gcov.html b/coverage/generic/RandomExchanges.cpp.gcov.html
new file mode 100644
index 0000000000..32704c15fe
--- /dev/null
+++ b/coverage/generic/RandomExchanges.cpp.gcov.html
@@ -0,0 +1,178 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/RandomExchanges.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - RandomExchanges.cpp<span style="font-size: 80%;"> (source / <a href="RandomExchanges.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">35.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ExchangePatterns.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace generic {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC GENERIC RANDOM_EXCHANGES</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Set random pattern for exchanges.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : In this way, exchanges will not be done between replicas with consecutive index, but</a>
+<a name="36"><span class="lineNum">      36 </span>            : will be done using a random pattern.  Typically used in bias exchange \cite piana.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : Using the following three input files one can run a bias exchange</a>
+<a name="41"><span class="lineNum">      41 </span>            : metadynamics simulation using a different angle in each replica.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Exchanges will be randomly tried between replicas 0-1, 0-2 and 1-2</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : Here is plumed.0.dat</a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : RANDOM_EXCHANGES</a>
+<a name="47"><span class="lineNum">      47 </span>            : t: TORSION ATOMS=1,2,3,4</a>
+<a name="48"><span class="lineNum">      48 </span>            : METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3</a>
+<a name="49"><span class="lineNum">      49 </span>            : \endplumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : Here is plumed.1.dat</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : RANDOM_EXCHANGES</a>
+<a name="54"><span class="lineNum">      54 </span>            : t: TORSION ATOMS=2,3,4,5</a>
+<a name="55"><span class="lineNum">      55 </span>            : METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : Here is plumed.2.dat</a>
+<a name="59"><span class="lineNum">      59 </span>            : \plumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : RANDOM_EXCHANGES</a>
+<a name="61"><span class="lineNum">      61 </span>            : t: TORSION ATOMS=3,4,5,6</a>
+<a name="62"><span class="lineNum">      62 </span>            : METAD ARG=t HEIGHT=0.1 PACE=100 SIGMA=0.3</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endplumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \warning Multi replica simulations are presently only working with gromacs.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \warning The directive should appear in input files for every replicas. In case SEED is specified, it</a>
+<a name="68"><span class="lineNum">      68 </span>            : should be the same in all input files.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : */</a>
+<a name="71"><span class="lineNum">      71 </span>            : //+ENDPLUMEDOC</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : class RandomExchanges:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   public Action</a>
+<a name="75"><span class="lineNum">      75 </span>            : {</a>
+<a name="76"><span class="lineNum">      76 </span>            : public:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="78"><span class="lineNum">      78 </span>            :   explicit RandomExchanges(const ActionOptions&amp;ao);</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(RandomExchanges,&quot;RANDOM_EXCHANGES&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 : void RandomExchanges::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :   Action::registerKeywords(keys);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;SEED&quot;,&quot;seed for random exchanges&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 : RandomExchanges::RandomExchanges(const ActionOptions&amp;ao):</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   Action(ao)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   plumed.getExchangePatterns().setFlag(ExchangePatterns::RANDOM);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : // I convert the seed to -seed because I think it is more general to use a positive seed in input</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   int seed=-1;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   parse(&quot;SEED&quot;,seed);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   if(seed&gt;=0) plumed.getExchangePatterns().setSeed(-seed);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Read.cpp.func-sort-c.html b/coverage/generic/Read.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0455804fc5
--- /dev/null
+++ b/coverage/generic/Read.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Read.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Read.cpp<span style="font-size: 80%;"> (<a href="Read.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Read.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#209">_ZN4PLMD7generic4Read22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#126">_ZN4PLMD7generic4ReadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#213">_ZN4PLMD7generic4Read17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#205">_ZN4PLMD7generic4Read7getFileEv</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#201">_ZNK4PLMD7generic4Read11getFilenameB5cxx11Ev</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#106">_ZN4PLMD7generic12_GLOBAL__N_117ReadRegisterMe1086createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#126">_ZN4PLMD7generic4ReadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#108">_ZN4PLMD7generic4Read16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#106">_ZN4PLMD7generic12_GLOBAL__N_117ReadRegisterMe108C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#106">_ZN4PLMD7generic12_GLOBAL__N_117ReadRegisterMe108D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#97">_ZN4PLMD7generic4Read5applyEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#244">_ZN4PLMD7generic4Read6updateEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#218">_ZN4PLMD7generic4Read7prepareEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#230">_ZN4PLMD7generic4Read9calculateEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Read.cpp.func.html b/coverage/generic/Read.cpp.func.html
new file mode 100644
index 0000000000..684c1ca96b
--- /dev/null
+++ b/coverage/generic/Read.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Read.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Read.cpp<span style="font-size: 80%;"> (<a href="Read.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Read.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#106">_ZN4PLMD7generic12_GLOBAL__N_117ReadRegisterMe1086createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#106">_ZN4PLMD7generic12_GLOBAL__N_117ReadRegisterMe108C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#106">_ZN4PLMD7generic12_GLOBAL__N_117ReadRegisterMe108D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#108">_ZN4PLMD7generic4Read16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#213">_ZN4PLMD7generic4Read17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#209">_ZN4PLMD7generic4Read22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#97">_ZN4PLMD7generic4Read5applyEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#244">_ZN4PLMD7generic4Read6updateEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#205">_ZN4PLMD7generic4Read7getFileEv</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#218">_ZN4PLMD7generic4Read7prepareEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#230">_ZN4PLMD7generic4Read9calculateEv</a></td>
+              <td class="coverFnHi">921318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#126">_ZN4PLMD7generic4ReadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#126">_ZN4PLMD7generic4ReadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Read.cpp.gcov.html#201">_ZNK4PLMD7generic4Read11getFilenameB5cxx11Ev</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Read.cpp.gcov.html b/coverage/generic/Read.cpp.gcov.html
new file mode 100644
index 0000000000..7c7ff49c59
--- /dev/null
+++ b/coverage/generic/Read.cpp.gcov.html
@@ -0,0 +1,332 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Read.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Read.cpp<span style="font-size: 80%;"> (source / <a href="Read.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">95</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;memory&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace generic {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC GENERIC READ</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Read quantities from a colvar file.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : This Action can be used with driver to read in a colvar file that was generated during</a>
+<a name="39"><span class="lineNum">      39 </span>            : an MD simulation</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Description of components</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The READ command will read those fields that are labelled with the text string given to the</a>
+<a name="44"><span class="lineNum">      44 </span>            : VALUE keyword.  It will also read in any fields that are labeled with the text string</a>
+<a name="45"><span class="lineNum">      45 </span>            : given to the VALUE keyword followed by a dot and a further string. If a single Value is read in</a>
+<a name="46"><span class="lineNum">      46 </span>            : this value can be referenced using the label of the Action.  Alternatively, if multiple quantities</a>
+<a name="47"><span class="lineNum">      47 </span>            : are read in, they can be referenced elsewhere in the input by using the label for the Action</a>
+<a name="48"><span class="lineNum">      48 </span>            : followed by a dot and the character string that appeared after the dot in the title of the field.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \par Examples</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : This input reads in data from a file called input_colvar.data that was generated</a>
+<a name="53"><span class="lineNum">      53 </span>            : in a calculation that involved PLUMED.  The first command reads in the data from the</a>
+<a name="54"><span class="lineNum">      54 </span>            : column headed phi1 while the second reads in the data from the column headed phi2.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : rphi1:       READ FILE=input_colvar.data  VALUES=phi1</a>
+<a name="58"><span class="lineNum">      58 </span>            : rphi2:       READ FILE=input_colvar.data  VALUES=phi2</a>
+<a name="59"><span class="lineNum">      59 </span>            : PRINT ARG=rphi1,rphi2 STRIDE=500  FILE=output_colvar.data</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The file input_colvar.data is just a normal colvar file as shown below</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \auxfile{input_colvar.data}</a>
+<a name="65"><span class="lineNum">      65 </span>            : #! FIELDS time phi psi metad.bias metad.rbias metad.rct</a>
+<a name="66"><span class="lineNum">      66 </span>            : #! SET min_phi -pi</a>
+<a name="67"><span class="lineNum">      67 </span>            : #! SET max_phi pi</a>
+<a name="68"><span class="lineNum">      68 </span>            : #! SET min_psi -pi</a>
+<a name="69"><span class="lineNum">      69 </span>            : #! SET max_psi pi</a>
+<a name="70"><span class="lineNum">      70 </span>            :  0.000000  -1.2379   0.8942   0.0000   0.0000   0.0000</a>
+<a name="71"><span class="lineNum">      71 </span>            :  1.000000  -1.4839   1.0482   0.0000   0.0000   0.0089</a>
+<a name="72"><span class="lineNum">      72 </span>            :  2.000000  -1.3243   0.6055   0.0753   0.0664   0.0184</a>
+<a name="73"><span class="lineNum">      73 </span>            : \endauxfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : class Read :</a>
+<a name="79"><span class="lineNum">      79 </span>            :   public ActionPilot,</a>
+<a name="80"><span class="lineNum">      80 </span>            :   public ActionWithValue</a>
+<a name="81"><span class="lineNum">      81 </span>            : {</a>
+<a name="82"><span class="lineNum">      82 </span>            : private:</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool ignore_time;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   bool ignore_forces;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   bool cloned_file;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   unsigned nlinesPerStep;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   std::string filename;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Unique pointer with the same scope as ifile.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::unique_ptr&lt;IFile&gt; ifile_ptr;</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// Pointer to input file.</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// It is either pointing to the content of ifile_ptr</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// or to the file it is cloned from.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   IFile* ifile;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; readvals;</a>
+<a name="95"><span class="lineNum">      95 </span>            : public:</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="97"><span class="lineNum">      97 </span>            :   explicit Read(const ActionOptions&amp;);</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void prepare() override;</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     921318 :   void apply() override {}</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   void calculate() override;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void update() override;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::string getFilename() const;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   IFile* getFile();</a>
+<a name="104"><span class="lineNum">     104 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   void turnOnDerivatives() override;</a>
+<a name="106"><span class="lineNum">     106 </span>            : };</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      12676 : PLUMED_REGISTER_ACTION(Read,&quot;READ&quot;)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         88 : void Read::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         88 :   Action::registerKeywords(keys);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         88 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         88 :   ActionWithValue::registerKeywords(keys);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        176 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the file should be read.&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        176 :   keys.add(&quot;compulsory&quot;,&quot;EVERY&quot;,&quot;1&quot;,&quot;only read every \\f$n\\f$th line of the colvar file. This should be used if the colvar was written more frequently than the trajectory.&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        176 :   keys.add(&quot;compulsory&quot;,&quot;VALUES&quot;,&quot;the values to read from the file&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        176 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file from which to read these quantities&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        176 :   keys.addFlag(&quot;IGNORE_TIME&quot;,false,&quot;ignore the time in the colvar file. When this flag is not present read will be quite strict &quot;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :                &quot;about the start time of the simulation and the stride between frames&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        176 :   keys.addFlag(&quot;IGNORE_FORCES&quot;,false,&quot;use this flag if the forces added by any bias can be safely ignored.  As an example forces can be &quot;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :                &quot;safely ignored if you are doing post processing that does not involve outputting forces&quot;);</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         88 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         88 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         88 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         88 :   ActionWithValue::useCustomisableComponents(keys);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         88 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         86 : Read::Read(const ActionOptions&amp;ao):</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   Action(ao),</a>
+<a name="130"><span class="lineNum">     130 </span>            :   ActionPilot(ao),</a>
+<a name="131"><span class="lineNum">     131 </span>            :   ActionWithValue(ao),</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         86 :   ignore_time(false),</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         86 :   ignore_forces(false),</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         86 :   nlinesPerStep(1)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : {</a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Read the file name from the input line</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         86 :   parse(&quot;FILE&quot;,filename);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Check if time is to be ignored</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         86 :   parseFlag(&quot;IGNORE_TIME&quot;,ignore_time);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   // Check if forces are to be ignored</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         86 :   parseFlag(&quot;IGNORE_FORCES&quot;,ignore_forces);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   // Open the file if it is not already opened</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         86 :   cloned_file=false;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         86 :   std::vector&lt;Read*&gt; other_reads=plumed.getActionSet().select&lt;Read*&gt;();</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        126 :   for(unsigned i=0; i&lt;other_reads.size(); ++i) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         40 :     if( other_reads[i]-&gt;getFilename()==filename ) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         37 :       ifile=other_reads[i]-&gt;getFile();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         37 :       cloned_file=true;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     }</a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         86 :   if( !cloned_file ) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        124 :     ifile_ptr=Tools::make_unique&lt;IFile&gt;();</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         62 :     ifile=ifile_ptr.get();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         62 :     if( !ifile-&gt;FileExist(filename) ) error(&quot;could not find file named &quot; + filename);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         62 :     ifile-&gt;link(*this);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         62 :     ifile-&gt;open(filename);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         62 :     ifile-&gt;allowIgnoredFields();</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         86 :   parse(&quot;EVERY&quot;,nlinesPerStep);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         86 :   if(nlinesPerStep&gt;1) log.printf(&quot;  only reading every %uth line of file %s\n&quot;,nlinesPerStep,filename.c_str() );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         84 :   else log.printf(&quot;  reading data from file %s\n&quot;,filename.c_str() );</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Find out what we are reading</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         86 :   std::vector&lt;std::string&gt; valread; parseVector(&quot;VALUES&quot;,valread);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         86 :   if(nlinesPerStep&gt;1 &amp;&amp; cloned_file) error(&quot;Opening a file multiple times and using EVERY is not allowed&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::size_t dot=valread[0].find_first_of('.');</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         86 :   if( valread[0].find(&quot;.&quot;)!=std::string::npos ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :     std::string label=valread[0].substr(0,dot);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          8 :     std::string name=valread[0].substr(dot+1);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          8 :     if( name==&quot;*&quot; ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :       if( valread.size()&gt;1 ) error(&quot;all values must be from the same Action when using READ&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :       std::vector&lt;std::string&gt; fieldnames;</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :       ifile-&gt;scanFieldList( fieldnames );</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          8 :       for(unsigned i=0; i&lt;fieldnames.size(); ++i) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          7 :         if( fieldnames[i].substr(0,dot)==label ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :           readvals.emplace_back(Tools::make_unique&lt;Value&gt;(this, fieldnames[i], false) ); addComponentWithDerivatives( fieldnames[i].substr(dot+1) );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          6 :           if( ifile-&gt;FieldExist(&quot;min_&quot; + fieldnames[i]) ) componentIsPeriodic( fieldnames[i].substr(dot+1), &quot;-pi&quot;,&quot;pi&quot; );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          6 :           else componentIsNotPeriodic( fieldnames[i].substr(dot+1) );</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :         }</a>
+<a name="181"><span class="lineNum">     181 </span>            :       }</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          1 :     } else {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          7 :       readvals.emplace_back(Tools::make_unique&lt;Value&gt;(this, valread[0], false) ); addComponentWithDerivatives( name );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         14 :       if( ifile-&gt;FieldExist(&quot;min_&quot; + valread[0]) ) componentIsPeriodic( valread[0].substr(dot+1), &quot;-pi&quot;, &quot;pi&quot; );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         14 :       else componentIsNotPeriodic( valread[0].substr(dot+1) );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          9 :       for(unsigned i=1; i&lt;valread.size(); ++i) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :         if( valread[i].substr(0,dot)!=label ) error(&quot;all values must be from the same Action when using READ&quot;);;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :         readvals.emplace_back(Tools::make_unique&lt;Value&gt;(this, valread[i], false) ); addComponentWithDerivatives( valread[i].substr(dot+1) );</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          4 :         if( ifile-&gt;FieldExist(&quot;min_&quot; + valread[i]) ) componentIsPeriodic( valread[i].substr(dot+1), &quot;-pi&quot;, &quot;pi&quot; );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          4 :         else componentIsNotPeriodic( valread[i].substr(dot+1) );</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       }</a>
+<a name="192"><span class="lineNum">     192 </span>            :     }</a>
+<a name="193"><span class="lineNum">     193 </span>            :   } else {</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         78 :     if( valread.size()!=1 ) error(&quot;all values must be from the same Action when using READ&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         78 :     readvals.emplace_back(Tools::make_unique&lt;Value&gt;(this, valread[0], false) ); addValueWithDerivatives();</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        165 :     if( ifile-&gt;FieldExist(&quot;min_&quot; + valread[0]) ) setPeriodic( &quot;-pi&quot;, &quot;pi&quot; );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         69 :     else setNotPeriodic();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         78 :     log.printf(&quot;  reading value %s and storing as %s\n&quot;,valread[0].c_str(),getLabel().c_str() );</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         86 :   checkRead();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        172 : }</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         40 : std::string Read::getFilename() const {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         40 :   return filename;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         37 : IFile* Read::getFile() {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         37 :   return ifile;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 : unsigned Read::getNumberOfDerivatives() {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   return 0;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         28 : void Read::turnOnDerivatives() {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         28 :   if( !ignore_forces ) error(&quot;cannot calculate derivatives for colvars that are read in from a file.  If you are postprocessing and &quot;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :                                &quot;these forces do not matter add the flag IGNORE_FORCES to all READ actions&quot;);</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         28 : }</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     921318 : void Read::prepare() {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">     921318 :   if( !cloned_file ) {</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     double du_time;</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     404026 :     if( !ifile-&gt;scanField(&quot;time&quot;,du_time) ) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :       error(&quot;Reached end of file &quot; + filename + &quot; before end of trajectory&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     202013 :     } else if( std::abs( du_time-getTime() )&gt;plumed.getAtoms().getTimeStep() &amp;&amp; !ignore_time ) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :       std::string str_dutime,str_ptime; Tools::convert(du_time,str_dutime); Tools::convert(getTime(),str_ptime);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       error(&quot;mismatched times in colvar files : colvar time=&quot; + str_dutime + &quot; plumed time=&quot; + str_ptime + &quot;. Add IGNORE_TIME to ignore error.&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">     921318 : }</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     921318 : void Read::calculate() {</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   std::string smin, smax;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">    2018830 :   for(unsigned i=0; i&lt;readvals.size(); ++i) {</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : // .get  returns the raw pointer</a>
+<a name="236"><span class="lineNum">     236 </span>            : // -&gt;get calls the Value::get() method</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">    1097512 :     ifile-&gt;scanField( readvals[i].get() );</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">    1097512 :     getPntrToComponent(i)-&gt;set( readvals[i]-&gt;get() );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">    1097512 :     if( readvals[i]-&gt;isPeriodic() ) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       3309 :       readvals[i]-&gt;getDomain( smin, smax );</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       3309 :       getPntrToComponent(i)-&gt;setDomain( smin, smax );</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     }</a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">     921318 : }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">     921318 : void Read::update() {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">     921318 :   if( !cloned_file ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">     404577 :     for(unsigned i=0; i&lt;nlinesPerStep; ++i) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">     202564 :       ifile-&gt;scanField(); double du_time;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">     405128 :       if( !ifile-&gt;scanField(&quot;time&quot;,du_time) &amp;&amp; plumed.getAtoms().getNatoms()==0 ) plumed.stop();</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     }</a>
+<a name="252"><span class="lineNum">     252 </span>            :   }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">     921318 : }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            : }</a>
+<a name="256"><span class="lineNum">     256 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/ResetCell.cpp.func-sort-c.html b/coverage/generic/ResetCell.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c6f66a1f64
--- /dev/null
+++ b/coverage/generic/ResetCell.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/ResetCell.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - ResetCell.cpp<span style="font-size: 80%;"> (<a href="ResetCell.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ResetCell.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#113">_ZN4PLMD7generic9ResetCellC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#104">_ZN4PLMD7generic12_GLOBAL__N_122ResetCellRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#113">_ZN4PLMD7generic9ResetCellC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#106">_ZN4PLMD7generic9ResetCell16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#165">_ZN4PLMD7generic9ResetCell5applyEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#128">_ZN4PLMD7generic9ResetCell9calculateEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#104">_ZN4PLMD7generic12_GLOBAL__N_122ResetCellRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#104">_ZN4PLMD7generic12_GLOBAL__N_122ResetCellRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/ResetCell.cpp.func.html b/coverage/generic/ResetCell.cpp.func.html
new file mode 100644
index 0000000000..d151a962d7
--- /dev/null
+++ b/coverage/generic/ResetCell.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/ResetCell.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - ResetCell.cpp<span style="font-size: 80%;"> (<a href="ResetCell.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ResetCell.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#104">_ZN4PLMD7generic12_GLOBAL__N_122ResetCellRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#104">_ZN4PLMD7generic12_GLOBAL__N_122ResetCellRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#104">_ZN4PLMD7generic12_GLOBAL__N_122ResetCellRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#106">_ZN4PLMD7generic9ResetCell16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#165">_ZN4PLMD7generic9ResetCell5applyEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#128">_ZN4PLMD7generic9ResetCell9calculateEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#113">_ZN4PLMD7generic9ResetCellC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ResetCell.cpp.gcov.html#113">_ZN4PLMD7generic9ResetCellC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/ResetCell.cpp.gcov.html b/coverage/generic/ResetCell.cpp.gcov.html
new file mode 100644
index 0000000000..281b90b1b3
--- /dev/null
+++ b/coverage/generic/ResetCell.cpp.gcov.html
@@ -0,0 +1,274 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/ResetCell.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - ResetCell.cpp<span style="font-size: 80%;"> (source / <a href="ResetCell.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace generic {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC GENERIC RESET_CELL</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : This action is used to rotate the full cell</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : This can be used to modify the periodic box. Notice that</a>
+<a name="40"><span class="lineNum">      40 </span>            : this is done at fixed scaled coordinates,</a>
+<a name="41"><span class="lineNum">      41 </span>            : so that also atomic coordinates for the entire system are affected.</a>
+<a name="42"><span class="lineNum">      42 </span>            : To see what effect try</a>
+<a name="43"><span class="lineNum">      43 </span>            : the \ref DUMPATOMS directive to output the atomic positions.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Also notice that PLUMED propagate forces correctly so that you can add a bias on a CV computed</a>
+<a name="46"><span class="lineNum">      46 </span>            : after rotation. See also \ref FIT_TO_TEMPLATE</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : Currently, only TYPE=TRIANGULAR is implemented, which allows one to reset</a>
+<a name="49"><span class="lineNum">      49 </span>            : the cell to a lower triangular one. Namely, a proper rotation is found that allows</a>
+<a name="50"><span class="lineNum">      50 </span>            : rotating the box so that the first lattice vector is in the form (ax,0,0),</a>
+<a name="51"><span class="lineNum">      51 </span>            : the second lattice vector is in the form (bx,by,0), and the third lattice vector is</a>
+<a name="52"><span class="lineNum">      52 </span>            : arbitrary.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \attention</a>
+<a name="55"><span class="lineNum">      55 </span>            : The implementation of this action is available but should be considered in testing phase. Please report any</a>
+<a name="56"><span class="lineNum">      56 </span>            : strange behavior.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \attention</a>
+<a name="59"><span class="lineNum">      59 </span>            : This directive modifies the stored position at the precise moment</a>
+<a name="60"><span class="lineNum">      60 </span>            : it is executed. This means that only collective variables</a>
+<a name="61"><span class="lineNum">      61 </span>            : which are below it in the input script will see the corrected positions.</a>
+<a name="62"><span class="lineNum">      62 </span>            : Unless you</a>
+<a name="63"><span class="lineNum">      63 </span>            : know exactly what you are doing, leave the default stride (1), so that</a>
+<a name="64"><span class="lineNum">      64 </span>            : this action is performed at every MD step.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \par Examples</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : Reset cell to be triangular after a rototranslational fit</a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : DUMPATOMS FILE=dump-original.xyz ATOMS=1-20</a>
+<a name="71"><span class="lineNum">      71 </span>            : FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=OPTIMAL</a>
+<a name="72"><span class="lineNum">      72 </span>            : DUMPATOMS FILE=dump-fit.xyz ATOMS=1-20</a>
+<a name="73"><span class="lineNum">      73 </span>            : RESET_CELL TYPE=TRIANGULAR</a>
+<a name="74"><span class="lineNum">      74 </span>            : DUMPATOMS FILE=dump-reset.xyz ATOMS=1-20</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : The reference file for the FIT_TO_TEMPLATE is just a normal pdb file with the format shown below:</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : \auxfile{ref.pdb}</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="81"><span class="lineNum">      81 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="82"><span class="lineNum">      82 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="84"><span class="lineNum">      84 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="85"><span class="lineNum">      85 </span>            : END</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endauxfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : */</a>
+<a name="89"><span class="lineNum">      89 </span>            : //+ENDPLUMEDOC</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : class ResetCell:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   public ActionPilot,</a>
+<a name="94"><span class="lineNum">      94 </span>            :   public ActionAtomistic</a>
+<a name="95"><span class="lineNum">      95 </span>            : {</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::string type;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   Tensor rotation,newbox;</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : public:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   explicit ResetCell(const ActionOptions&amp;ao);</a>
+<a name="101"><span class="lineNum">     101 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void calculate() override;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void apply() override;</a>
+<a name="104"><span class="lineNum">     104 </span>            : };</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ResetCell,&quot;RESET_CELL&quot;)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          4 : void ResetCell::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   Action::registerKeywords( keys );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          4 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which molecules are reassembled.  Unless you are completely certain about what you are doing leave this set equal to 1!&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;TRIANGULAR&quot;,&quot;the manner in which the cell is reset&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 : ResetCell::ResetCell(const ActionOptions&amp;ao):</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   Action(ao),</a>
+<a name="117"><span class="lineNum">     117 </span>            :   ActionPilot(ao),</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   ActionAtomistic(ao)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : {</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   type.assign(&quot;TRIANGULAR&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   parse(&quot;TYPE&quot;,type);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :   log&lt;&lt;&quot;  type: &quot;&lt;&lt;type&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :   if(type!=&quot;TRIANGULAR&quot;) error(&quot;undefined type &quot;+type);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         17 : void ResetCell::calculate() {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   Pbc &amp; pbc(modifyGlobalPbc());</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         17 :   Tensor box=pbc.getBox();</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : // moduli of lattice vectors</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         17 :   double a=modulo(box.getRow(0));</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         17 :   double b=modulo(box.getRow(1));</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         17 :   double c=modulo(box.getRow(2));</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : // cos-angle between lattice vectors</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         17 :   double ab=dotProduct(box.getRow(0),box.getRow(1))/(a*b);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         17 :   double ac=dotProduct(box.getRow(0),box.getRow(2))/(a*c);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         17 :   double bc=dotProduct(box.getRow(1),box.getRow(2))/(b*c);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : // generate a new set of lattice vectors as a lower triangular matrix</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         17 :   newbox[0][0]=a;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         17 :   newbox[1][0]=b*ab;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         17 :   newbox[1][1]=std::sqrt(b*b-newbox[1][0]*newbox[1][0]);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         17 :   newbox[2][0]=c*ac;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         17 :   newbox[2][1]=c*(bc-ac*ab)/std::sqrt(1-ab*ab);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         17 :   newbox[2][2]=std::sqrt(c*c-newbox[2][0]*newbox[2][0]-newbox[2][1]*newbox[2][1]);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         17 :   if(determinant(newbox)*determinant(box)&lt;0) newbox[2][2]=-newbox[2][2];</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : // rotation matrix from old to new coordinates</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         17 :   rotation=transpose(matmul(inverse(box),newbox));</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : // rotate all coordinates</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       1623 :   for(unsigned i=0; i&lt;getTotAtoms(); i++) {</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     Vector &amp; ato (modifyGlobalPosition(AtomNumber::index(i)));</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1606 :     ato=matmul(rotation,ato);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span>            : // rotate box</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         17 :   pbc.setBox(newbox);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         17 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         17 : void ResetCell::apply() {</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : // rotate back forces</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1623 :   for(unsigned i=0; i&lt;getTotAtoms(); i++) {</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     Vector &amp; f(modifyGlobalForce(AtomNumber::index(i)));</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1606 :     f=matmul(transpose(rotation),f);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   Tensor&amp; virial(modifyGlobalVirial());</a>
+<a name="175"><span class="lineNum">     175 </span>            : // I have no mathematical derivation for this.</a>
+<a name="176"><span class="lineNum">     176 </span>            : // The reasoning is the following.</a>
+<a name="177"><span class="lineNum">     177 </span>            : // virial= h^T * dU/dh, where h is the box matrix and dU/dh its derivatives.</a>
+<a name="178"><span class="lineNum">     178 </span>            : // The final virial should be rotationally invariant, that is symmetric.</a>
+<a name="179"><span class="lineNum">     179 </span>            : // in the rotated frame, dU/dh elements [0][1], [0][2], and [1][2] should</a>
+<a name="180"><span class="lineNum">     180 </span>            : // be changed so as to enforce rotational invariance. Thus we here have to</a>
+<a name="181"><span class="lineNum">     181 </span>            : // make the virial matrix symmetric.</a>
+<a name="182"><span class="lineNum">     182 </span>            : // Since h^T is upper triangular, it can be shown that any change in these elements</a>
+<a name="183"><span class="lineNum">     183 </span>            : // will only affect the corresponding elements of the virial matrix.</a>
+<a name="184"><span class="lineNum">     184 </span>            : // Thus, the only possibility is to set the corresponding elements</a>
+<a name="185"><span class="lineNum">     185 </span>            : // of the virial matrix equal to their symmetric ones.</a>
+<a name="186"><span class="lineNum">     186 </span>            : // GB</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         17 :   virial[0][1]=virial[1][0];</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         17 :   virial[0][2]=virial[2][0];</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         17 :   virial[1][2]=virial[2][1];</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : // rotate back virial</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         17 :   virial=matmul(transpose(rotation),matmul(virial,rotation));</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         17 : }</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Time.cpp.func-sort-c.html b/coverage/generic/Time.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4d37555888
--- /dev/null
+++ b/coverage/generic/Time.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Time.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Time.cpp<span style="font-size: 80%;"> (<a href="Time.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Time.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#52">_ZN4PLMD7generic12_GLOBAL__N_116TimeRegisterMe546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#49">_ZN4PLMD7generic4Time22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#48">_ZN4PLMD7generic4Time5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#67">_ZN4PLMD7generic4Time9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#59">_ZN4PLMD7generic4TimeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#59">_ZN4PLMD7generic4TimeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#54">_ZN4PLMD7generic4Time16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#52">_ZN4PLMD7generic12_GLOBAL__N_116TimeRegisterMe54C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#52">_ZN4PLMD7generic12_GLOBAL__N_116TimeRegisterMe54D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Time.cpp.func.html b/coverage/generic/Time.cpp.func.html
new file mode 100644
index 0000000000..867c72a05b
--- /dev/null
+++ b/coverage/generic/Time.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Time.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Time.cpp<span style="font-size: 80%;"> (<a href="Time.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Time.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#52">_ZN4PLMD7generic12_GLOBAL__N_116TimeRegisterMe546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#52">_ZN4PLMD7generic12_GLOBAL__N_116TimeRegisterMe54C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#52">_ZN4PLMD7generic12_GLOBAL__N_116TimeRegisterMe54D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#54">_ZN4PLMD7generic4Time16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#49">_ZN4PLMD7generic4Time22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#48">_ZN4PLMD7generic4Time5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#67">_ZN4PLMD7generic4Time9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#59">_ZN4PLMD7generic4TimeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Time.cpp.gcov.html#59">_ZN4PLMD7generic4TimeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/Time.cpp.gcov.html b/coverage/generic/Time.cpp.gcov.html
new file mode 100644
index 0000000000..1326243abc
--- /dev/null
+++ b/coverage/generic/Time.cpp.gcov.html
@@ -0,0 +1,155 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/Time.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - Time.cpp<span style="font-size: 80%;"> (source / <a href="Time.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;string&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cmath&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace generic {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC GENERIC TIME</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : retrieve the time of the simulation to be used elsewhere</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \par Examples</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \plumedfile</a>
+<a name="37"><span class="lineNum">      37 </span>            : TIME            LABEL=t1</a>
+<a name="38"><span class="lineNum">      38 </span>            : PRINT ARG=t1</a>
+<a name="39"><span class="lineNum">      39 </span>            : \endplumedfile</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : */</a>
+<a name="42"><span class="lineNum">      42 </span>            : //+ENDPLUMEDOC</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class Time : public ActionWithValue {</a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit Time(const ActionOptions&amp;);</a>
+<a name="48"><span class="lineNum">      48 </span>            : // active methods:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void calculate() override;</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   unsigned getNumberOfDerivatives() override { return 0; }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : };</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(Time,&quot;TIME&quot;)</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          2 : void Time::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          2 :   Action::registerKeywords( keys );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          2 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          2 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 : Time::Time(const ActionOptions&amp;ao):</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   Action(ao),ActionWithValue(ao)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   // resize derivative by hand to a nonzero value</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   getPntrToValue()-&gt;resizeDerivatives(1);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 : void Time::calculate() {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :   setValue           (getTime());</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/UpdateIf.cpp.func-sort-c.html b/coverage/generic/UpdateIf.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1941c5b283
--- /dev/null
+++ b/coverage/generic/UpdateIf.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/UpdateIf.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - UpdateIf.cpp<span style="font-size: 80%;"> (<a href="UpdateIf.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="UpdateIf.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#108">_ZN4PLMD7generic8UpdateIfC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#150">_ZN4PLMD7generic8UpdateIfD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#95">_ZN4PLMD7generic12_GLOBAL__N_120UpdateIfRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#108">_ZN4PLMD7generic8UpdateIfC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#150">_ZN4PLMD7generic8UpdateIfD0Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#150">_ZN4PLMD7generic8UpdateIfD1Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#97">_ZN4PLMD7generic8UpdateIf16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#141">_ZN4PLMD7generic8UpdateIf12beforeUpdateEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#91">_ZN4PLMD7generic8UpdateIf5applyEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#130">_ZN4PLMD7generic8UpdateIf7prepareEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#134">_ZN4PLMD7generic8UpdateIf9calculateEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#95">_ZN4PLMD7generic12_GLOBAL__N_120UpdateIfRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#95">_ZN4PLMD7generic12_GLOBAL__N_120UpdateIfRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/UpdateIf.cpp.func.html b/coverage/generic/UpdateIf.cpp.func.html
new file mode 100644
index 0000000000..c61e607d2e
--- /dev/null
+++ b/coverage/generic/UpdateIf.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/UpdateIf.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - UpdateIf.cpp<span style="font-size: 80%;"> (<a href="UpdateIf.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="UpdateIf.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#95">_ZN4PLMD7generic12_GLOBAL__N_120UpdateIfRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#95">_ZN4PLMD7generic12_GLOBAL__N_120UpdateIfRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#95">_ZN4PLMD7generic12_GLOBAL__N_120UpdateIfRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#141">_ZN4PLMD7generic8UpdateIf12beforeUpdateEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#97">_ZN4PLMD7generic8UpdateIf16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#91">_ZN4PLMD7generic8UpdateIf5applyEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#130">_ZN4PLMD7generic8UpdateIf7prepareEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#134">_ZN4PLMD7generic8UpdateIf9calculateEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#108">_ZN4PLMD7generic8UpdateIfC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#108">_ZN4PLMD7generic8UpdateIfC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#150">_ZN4PLMD7generic8UpdateIfD0Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#150">_ZN4PLMD7generic8UpdateIfD1Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UpdateIf.cpp.gcov.html#150">_ZN4PLMD7generic8UpdateIfD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/UpdateIf.cpp.gcov.html b/coverage/generic/UpdateIf.cpp.gcov.html
new file mode 100644
index 0000000000..137e3631b1
--- /dev/null
+++ b/coverage/generic/UpdateIf.cpp.gcov.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/UpdateIf.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - UpdateIf.cpp<span style="font-size: 80%;"> (source / <a href="UpdateIf.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace generic {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC PRINTANALYSIS UPDATE_IF</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Conditional update of other actions.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This action can be used to enable and disable the update step for the following actions</a>
+<a name="36"><span class="lineNum">      36 </span>            : depending on the value of its arguments. This allows for example to extract snapshots</a>
+<a name="37"><span class="lineNum">      37 </span>            : with value of some CVs in a given range.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : When called with MORE_THAN and/or LESS_THAN keywords, this action starts an if block.</a>
+<a name="40"><span class="lineNum">      40 </span>            : The block is executed if all the arguments are less than all the respective values</a>
+<a name="41"><span class="lineNum">      41 </span>            : in the LESS_THAN keyword (if present) and all the arguments are more than all the</a>
+<a name="42"><span class="lineNum">      42 </span>            : respective values</a>
+<a name="43"><span class="lineNum">      43 </span>            : in the MORE_THAN keyword (if present).</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : When called with the END flag, this action ends the corresponding IF block.</a>
+<a name="46"><span class="lineNum">      46 </span>            : Notice that in this case one should also provide the ARG keyword. It is recommended to</a>
+<a name="47"><span class="lineNum">      47 </span>            : use the same ARG keyword that was used to begin the block, so as to make the input more readable.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Of course, blocks can be nested at will.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : There are many potential usages for this keyword. One might e.g. decide to analyze some variable</a>
+<a name="52"><span class="lineNum">      52 </span>            : only when another variable is within a given range.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \warning</a>
+<a name="55"><span class="lineNum">      55 </span>            : Notice that not all the possible usage make</a>
+<a name="56"><span class="lineNum">      56 </span>            : particular sense. For example, conditionally updating a \ref METAD keyword</a>
+<a name="57"><span class="lineNum">      57 </span>            : (that is: adding hills only if a variable is within a given range)</a>
+<a name="58"><span class="lineNum">      58 </span>            : can lead to unexpected results.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \par Examples</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The following input instructs plumed dump all the snapshots where an atom is in touch with</a>
+<a name="63"><span class="lineNum">      63 </span>            : the solute.</a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : solute: GROUP ATOMS=1-124</a>
+<a name="66"><span class="lineNum">      66 </span>            : coord: COORDINATION GROUPA=solute GROUPB=500 R_0=0.5</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : # A coordination number higher than 0.5 indicate that there is at least one</a>
+<a name="69"><span class="lineNum">      69 </span>            : # atom of group `solute` at less than 5 A from atom number 500</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : UPDATE_IF ARG=coord MORE_THAN=0.5</a>
+<a name="72"><span class="lineNum">      72 </span>            : DUMPATOMS ATOMS=solute,500 FILE=output.xyz</a>
+<a name="73"><span class="lineNum">      73 </span>            : UPDATE_IF ARG=coord END</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : */</a>
+<a name="77"><span class="lineNum">      77 </span>            : //+ENDPLUMEDOC</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : class UpdateIf:</a>
+<a name="80"><span class="lineNum">      80 </span>            :   public ActionPilot,</a>
+<a name="81"><span class="lineNum">      81 </span>            :   public ActionWithArguments</a>
+<a name="82"><span class="lineNum">      82 </span>            : {</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;double&gt; lower;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;double&gt; upper;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   bool on;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   bool end;</a>
+<a name="87"><span class="lineNum">      87 </span>            : public:</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void prepare() override;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void calculate() override;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void beforeUpdate() override;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit UpdateIf(const ActionOptions&amp;);</a>
+<a name="92"><span class="lineNum">      92 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         28 :   void apply() override {}</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   ~UpdateIf();</a>
+<a name="95"><span class="lineNum">      95 </span>            : };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      12518 : PLUMED_REGISTER_ACTION(UpdateIf,&quot;UPDATE_IF&quot;)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          9 : void UpdateIf::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          9 :   Action::registerKeywords(keys);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          9 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          9 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          9 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         18 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the quantities of interest should be output&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         18 :   keys.addFlag(&quot;END&quot;,false,&quot;end&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         18 :   keys.add(&quot;optional&quot;,&quot;LESS_THAN&quot;,&quot;upper bound&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         18 :   keys.add(&quot;optional&quot;,&quot;MORE_THAN&quot;,&quot;lower bound&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          9 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          7 : UpdateIf::UpdateIf(const ActionOptions&amp;ao):</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   Action(ao),</a>
+<a name="112"><span class="lineNum">     112 </span>            :   ActionPilot(ao),</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ActionWithArguments(ao),</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          7 :   on(false),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          7 :   end(false)</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          7 :   parseFlag(&quot;END&quot;,end);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          7 :   parseVector(&quot;LESS_THAN&quot;,upper);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          7 :   parseVector(&quot;MORE_THAN&quot;,lower);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          7 :   if(end &amp;&amp; upper.size()!=0) error(&quot;END and LESS_THAN are not compatible&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          7 :   if(end &amp;&amp; lower.size()!=0) error(&quot;END and MORE_THAN are not compatible&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          7 :   if(upper.size()==0) upper.assign(getNumberOfArguments(),+std::numeric_limits&lt;double&gt;::max());</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          7 :   if(lower.size()==0) lower.assign(getNumberOfArguments(),-std::numeric_limits&lt;double&gt;::max());</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          7 :   if(upper.size()!=getNumberOfArguments()) error(&quot;LESS_THAN should have the same size as ARG&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          7 :   if(lower.size()!=getNumberOfArguments()) error(&quot;MORE_THAN should have the same size as ARG&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          8 :     log&lt;&lt;&quot;  boundaries for argument &quot;&lt;&lt;i&lt;&lt;&quot;    &quot;&lt;&lt;lower[i]&lt;&lt;&quot; &quot;&lt;&lt;upper[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          7 :   checkRead();</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          7 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         28 : void UpdateIf::prepare() {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         28 :   on=false;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         28 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         28 : void UpdateIf::calculate() {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         28 :   on=true;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         60 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         32 :     if(getArgument(i)&gt;=upper[i] || getArgument(i)&lt;=lower[i]) on=false;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         28 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         28 : void UpdateIf::beforeUpdate() {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         28 :   if(end) plumed.updateFlagsPop();</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   else {</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         23 :     if(on) plumed.updateFlagsPush(plumed.updateFlagsTop());</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :     else   plumed.updateFlagsPush(false);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         28 : }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         14 : UpdateIf::~UpdateIf() {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         14 : }</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/WholeMolecules.cpp.func-sort-c.html b/coverage/generic/WholeMolecules.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9fab796cbe
--- /dev/null
+++ b/coverage/generic/WholeMolecules.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/WholeMolecules.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - WholeMolecules.cpp<span style="font-size: 80%;"> (<a href="WholeMolecules.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WholeMolecules.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#134">_ZN4PLMD7generic14WholeMoleculesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#116">_ZN4PLMD7generic12_GLOBAL__N_127WholeMoleculesRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#134">_ZN4PLMD7generic14WholeMoleculesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#118">_ZN4PLMD7generic14WholeMolecules16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#113">_ZN4PLMD7generic14WholeMolecules5applyEv</a></td>
+              <td class="coverFnHi">3319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#225">_ZN4PLMD7generic14WholeMolecules9calculateEv</a></td>
+              <td class="coverFnHi">3319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#116">_ZN4PLMD7generic12_GLOBAL__N_127WholeMoleculesRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#116">_ZN4PLMD7generic12_GLOBAL__N_127WholeMoleculesRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/WholeMolecules.cpp.func.html b/coverage/generic/WholeMolecules.cpp.func.html
new file mode 100644
index 0000000000..ed2def41fa
--- /dev/null
+++ b/coverage/generic/WholeMolecules.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/WholeMolecules.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - WholeMolecules.cpp<span style="font-size: 80%;"> (<a href="WholeMolecules.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WholeMolecules.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#116">_ZN4PLMD7generic12_GLOBAL__N_127WholeMoleculesRegisterMe1186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#116">_ZN4PLMD7generic12_GLOBAL__N_127WholeMoleculesRegisterMe118C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#116">_ZN4PLMD7generic12_GLOBAL__N_127WholeMoleculesRegisterMe118D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#118">_ZN4PLMD7generic14WholeMolecules16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">38</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#113">_ZN4PLMD7generic14WholeMolecules5applyEv</a></td>
+              <td class="coverFnHi">3319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#225">_ZN4PLMD7generic14WholeMolecules9calculateEv</a></td>
+              <td class="coverFnHi">3319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#134">_ZN4PLMD7generic14WholeMoleculesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WholeMolecules.cpp.gcov.html#134">_ZN4PLMD7generic14WholeMoleculesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/WholeMolecules.cpp.gcov.html b/coverage/generic/WholeMolecules.cpp.gcov.html
new file mode 100644
index 0000000000..844f0b3b72
--- /dev/null
+++ b/coverage/generic/WholeMolecules.cpp.gcov.html
@@ -0,0 +1,319 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/WholeMolecules.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - WholeMolecules.cpp<span style="font-size: 80%;"> (source / <a href="WholeMolecules.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/Tree.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;vector&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;string&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace generic {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC GENERIC WHOLEMOLECULES</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : This action is used to rebuild molecules that can become split by the periodic boundary conditions.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : It is similar to the ALIGN_ATOMS keyword of plumed1, and is needed since some</a>
+<a name="46"><span class="lineNum">      46 </span>            : MD dynamics code (e.g. GROMACS) can break molecules during the calculation.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : Running some CVs without this command can cause there to be discontinuities changes</a>
+<a name="49"><span class="lineNum">      49 </span>            : in the CV value and artifacts in the calculations.  This command can be applied</a>
+<a name="50"><span class="lineNum">      50 </span>            : more than once.  To see what effect is has use a variable without pbc or use</a>
+<a name="51"><span class="lineNum">      51 </span>            : the \ref DUMPATOMS directive to output the atomic positions.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \attention</a>
+<a name="54"><span class="lineNum">      54 </span>            : This directive modifies the stored position at the precise moment</a>
+<a name="55"><span class="lineNum">      55 </span>            : it is executed. This means that only collective variables</a>
+<a name="56"><span class="lineNum">      56 </span>            : which are below it in the input script will see the corrected positions.</a>
+<a name="57"><span class="lineNum">      57 </span>            : As a general rule, put it at the top of the input file. Also, unless you</a>
+<a name="58"><span class="lineNum">      58 </span>            : know exactly what you are doing, leave the default stride (1), so that</a>
+<a name="59"><span class="lineNum">      59 </span>            : this action is performed at every MD step.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The way WHOLEMOLECULES modifies each of the listed entities is this:</a>
+<a name="62"><span class="lineNum">      62 </span>            : - First atom of the list is left in place</a>
+<a name="63"><span class="lineNum">      63 </span>            : - Each atom of the list is shifted by a lattice vectors so that it becomes as close as possible</a>
+<a name="64"><span class="lineNum">      64 </span>            :   to the previous one, iteratively.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : In this way, if an entity consists of a list of atoms such that consecutive atoms in the</a>
+<a name="67"><span class="lineNum">      67 </span>            : list are always closer than half a box side the entity will become whole.</a>
+<a name="68"><span class="lineNum">      68 </span>            : This can be usually achieved selecting consecutive atoms (1-100), but it is also possible</a>
+<a name="69"><span class="lineNum">      69 </span>            : to skip some atoms, provided consecutive chosen atoms are close enough.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \par Examples</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : This command instructs plumed to reconstruct the molecule containing atoms 1-20</a>
+<a name="74"><span class="lineNum">      74 </span>            : at every step of the calculation and dump them on a file.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \plumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : # to see the effect, one could dump the atoms as they were before molecule reconstruction:</a>
+<a name="78"><span class="lineNum">      78 </span>            : # DUMPATOMS FILE=dump-broken.xyz ATOMS=1-20</a>
+<a name="79"><span class="lineNum">      79 </span>            : WHOLEMOLECULES ENTITY0=1-20</a>
+<a name="80"><span class="lineNum">      80 </span>            : DUMPATOMS FILE=dump.xyz ATOMS=1-20</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endplumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : This command instructs plumed to reconstruct two molecules containing atoms 1-20 and 30-40</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : \plumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : WHOLEMOLECULES ENTITY0=1-20 ENTITY1=30-40</a>
+<a name="87"><span class="lineNum">      87 </span>            : DUMPATOMS FILE=dump.xyz ATOMS=1-20,30-40</a>
+<a name="88"><span class="lineNum">      88 </span>            : \endplumedfile</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : This command instructs plumed to reconstruct the chain of backbone atoms in a</a>
+<a name="91"><span class="lineNum">      91 </span>            : protein</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : \plumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="95"><span class="lineNum">      95 </span>            : MOLINFO STRUCTURE=helix.pdb</a>
+<a name="96"><span class="lineNum">      96 </span>            : WHOLEMOLECULES RESIDUES=all MOLTYPE=protein</a>
+<a name="97"><span class="lineNum">      97 </span>            : \endplumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : */</a>
+<a name="100"><span class="lineNum">     100 </span>            : //+ENDPLUMEDOC</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : class WholeMolecules:</a>
+<a name="104"><span class="lineNum">     104 </span>            :   public ActionPilot,</a>
+<a name="105"><span class="lineNum">     105 </span>            :   public ActionAtomistic</a>
+<a name="106"><span class="lineNum">     106 </span>            : {</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;std::vector&lt;AtomNumber&gt; &gt; groups;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt;std::vector&lt;AtomNumber&gt; &gt; roots;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;Vector&gt; refs;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   bool doemst, addref;</a>
+<a name="111"><span class="lineNum">     111 </span>            : public:</a>
+<a name="112"><span class="lineNum">     112 </span>            :   explicit WholeMolecules(const ActionOptions&amp;ao);</a>
+<a name="113"><span class="lineNum">     113 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="114"><span class="lineNum">     114 </span>            :   void calculate() override;</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       3319 :   void apply() override {}</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : };</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      12576 : PLUMED_REGISTER_ACTION(WholeMolecules,&quot;WHOLEMOLECULES&quot;)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         38 : void WholeMolecules::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         38 :   Action::registerKeywords( keys );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         38 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         38 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         76 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which molecules are reassembled.  Unless you are completely certain about what you are doing leave this set equal to 1!&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         76 :   keys.add(&quot;numbered&quot;,&quot;ENTITY&quot;,&quot;the atoms that make up a molecule that you wish to align. To specify multiple molecules use a list of ENTITY keywords: ENTITY0, ENTITY1,...&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         76 :   keys.reset_style(&quot;ENTITY&quot;,&quot;atoms&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         76 :   keys.add(&quot;residues&quot;,&quot;RESIDUES&quot;,&quot;this command specifies that the backbone atoms in a set of residues all must be aligned. It must be used in tandem with the \\ref MOLINFO &quot;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :            &quot;action and the MOLTYPE keyword. If you wish to use all the residues from all the chains in your system you can do so by &quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues &quot;</a>
+<a name="130"><span class="lineNum">     130 </span>            :            &quot;you are interested in as a list of numbers&quot;);</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         76 :   keys.add(&quot;optional&quot;,&quot;MOLTYPE&quot;,&quot;the type of molecule that is under study.  This is used to define the backbone atoms&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         76 :   keys.addFlag(&quot;EMST&quot;, false, &quot;Define atoms sequence in entities using an Euclidean minimum spanning tree&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         76 :   keys.addFlag(&quot;ADDREFERENCE&quot;, false, &quot;Define the reference position of the first atom of each entity using a PDB file&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         38 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         36 : WholeMolecules::WholeMolecules(const ActionOptions&amp;ao):</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   Action(ao),</a>
+<a name="138"><span class="lineNum">     138 </span>            :   ActionPilot(ao),</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ActionAtomistic(ao),</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         36 :   doemst(false), addref(false)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : {</a>
+<a name="142"><span class="lineNum">     142 </span>            :   // parse optional flags</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         36 :   parseFlag(&quot;EMST&quot;, doemst);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         72 :   parseFlag(&quot;ADDREFERENCE&quot;, addref);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // create groups from ENTITY</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         37 :   for(int i=0;; i++) {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     std::vector&lt;AtomNumber&gt; group;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        146 :     parseAtomList(&quot;ENTITY&quot;,i,group);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         73 :     if( group.empty() ) break;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         37 :     groups.push_back(group);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         37 :   }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   // Read residues to align from MOLINFO</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         72 :   std::vector&lt;std::string&gt; resstrings; parseVector(&quot;RESIDUES&quot;,resstrings);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         36 :   if( resstrings.size()&gt;0 ) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     if( resstrings.size()==1 ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :       if( resstrings[0]==&quot;all&quot; ) resstrings[0]=&quot;all-ter&quot;;   // Include terminal groups in alignment</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     std::string moltype; parse(&quot;MOLTYPE&quot;,moltype);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     if(moltype.length()==0) error(&quot;Found RESIDUES keyword without specification of the molecule - use MOLTYPE&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     if( !moldat ) error(&quot;MOLINFO is required to use RESIDUES&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     std::vector&lt; std::vector&lt;AtomNumber&gt; &gt; backatoms;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     moldat-&gt;getBackbone( resstrings, moltype, backatoms );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;backatoms.size(); ++i) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       groups.push_back( backatoms[i] );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   // check number of groups</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         36 :   if(groups.size()==0) error(&quot;no atoms found for WHOLEMOLECULES!&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // if using PDBs reorder atoms in groups based on proximity in PDB file</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         36 :   if(doemst) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :     auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :     if( !moldat ) error(&quot;MOLINFO is required to use EMST&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     // initialize tree</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :     Tree tree = Tree(moldat);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     // cycle on groups and reorder atoms</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;groups.size(); ++i) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :       groups[i] = tree.getTree(groups[i]);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :       // store root atoms</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :       roots.push_back(tree.getRoot());</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     }</a>
+<a name="186"><span class="lineNum">     186 </span>            :   } else {</a>
+<a name="187"><span class="lineNum">     187 </span>            :     // fill root vector with previous atom in groups</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         69 :     for(unsigned i=0; i&lt;groups.size(); ++i) {</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :       std::vector&lt;AtomNumber&gt; root;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       2661 :       for(unsigned j=0; j&lt;groups[i].size()-1; ++j) root.push_back(groups[i][j]);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       // store root atoms</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         35 :       roots.push_back(root);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :     }</a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   // adding reference if needed</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         36 :   if(addref) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          2 :     auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :     if( !moldat ) error(&quot;MOLINFO is required to use ADDREFERENCE&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;groups.size(); ++i) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :       // add reference position of first atom in entity</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 :       refs.push_back(moldat-&gt;getPosition(groups[i][0]));</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     }</a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   // print out info</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         73 :   for(unsigned i=0; i&lt;groups.size(); ++i) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         37 :     log.printf(&quot;  atoms in entity %d : &quot;,i);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       2943 :     for(unsigned j=0; j&lt;groups[i].size(); ++j) log.printf(&quot;%d &quot;,groups[i][j].serial() );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         37 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         37 :     if(addref) log.printf(&quot;     with reference position : %lf %lf %lf\n&quot;,refs[i][0],refs[i][1],refs[i][2]);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   // collect all atoms</a>
+<a name="215"><span class="lineNum">     215 </span>            :   std::vector&lt;AtomNumber&gt; merge;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         73 :   for(unsigned i=0; i&lt;groups.size(); ++i) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         37 :     merge.insert(merge.end(),groups[i].begin(),groups[i].end());</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         36 :   checkRead();</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         36 :   Tools::removeDuplicates(merge);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         36 :   requestAtoms(merge);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   doNotRetrieve();</a>
+<a name="224"><span class="lineNum">     224 </span>            :   doNotForce();</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         36 : }</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       3319 : void WholeMolecules::calculate() {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       6643 :   for(unsigned i=0; i&lt;groups.size(); ++i) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       3324 :     if(addref) {</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       Vector &amp; first (modifyGlobalPosition(groups[i][0]));</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         12 :       first = refs[i]+pbcDistance(refs[i],first);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">     294850 :     for(unsigned j=0; j&lt;groups[i].size()-1; ++j) {</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :       const Vector &amp; first (getGlobalPosition(roots[i][j]));</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     291526 :       Vector &amp; second (modifyGlobalPosition(groups[i][j+1]));</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">     291526 :       second=first+pbcDistance(first,second);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     }</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       3319 : }</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/WrapAround.cpp.func-sort-c.html b/coverage/generic/WrapAround.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5eb0e47d6b
--- /dev/null
+++ b/coverage/generic/WrapAround.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/WrapAround.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - WrapAround.cpp<span style="font-size: 80%;"> (<a href="WrapAround.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WrapAround.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#174">_ZN4PLMD7generic10WrapAroundC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#174">_ZN4PLMD7generic10WrapAroundC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#161">_ZN4PLMD7generic12_GLOBAL__N_123WrapAroundRegisterMe1636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#163">_ZN4PLMD7generic10WrapAround16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#158">_ZN4PLMD7generic10WrapAround5applyEv</a></td>
+              <td class="coverFnHi">579</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#215">_ZN4PLMD7generic10WrapAround9calculateEv</a></td>
+              <td class="coverFnHi">579</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#161">_ZN4PLMD7generic12_GLOBAL__N_123WrapAroundRegisterMe163C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#161">_ZN4PLMD7generic12_GLOBAL__N_123WrapAroundRegisterMe163D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/WrapAround.cpp.func.html b/coverage/generic/WrapAround.cpp.func.html
new file mode 100644
index 0000000000..fe29edb40b
--- /dev/null
+++ b/coverage/generic/WrapAround.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/WrapAround.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - WrapAround.cpp<span style="font-size: 80%;"> (<a href="WrapAround.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WrapAround.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#163">_ZN4PLMD7generic10WrapAround16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#158">_ZN4PLMD7generic10WrapAround5applyEv</a></td>
+              <td class="coverFnHi">579</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#215">_ZN4PLMD7generic10WrapAround9calculateEv</a></td>
+              <td class="coverFnHi">579</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#174">_ZN4PLMD7generic10WrapAroundC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#174">_ZN4PLMD7generic10WrapAroundC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#161">_ZN4PLMD7generic12_GLOBAL__N_123WrapAroundRegisterMe1636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#161">_ZN4PLMD7generic12_GLOBAL__N_123WrapAroundRegisterMe163C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WrapAround.cpp.gcov.html#161">_ZN4PLMD7generic12_GLOBAL__N_123WrapAroundRegisterMe163D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/WrapAround.cpp.gcov.html b/coverage/generic/WrapAround.cpp.gcov.html
new file mode 100644
index 0000000000..1feeb9bab1
--- /dev/null
+++ b/coverage/generic/WrapAround.cpp.gcov.html
@@ -0,0 +1,327 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic/WrapAround.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">generic</a> - WrapAround.cpp<span style="font-size: 80%;"> (source / <a href="WrapAround.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/AtomNumber.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;vector&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace generic {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC GENERIC WRAPAROUND</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Rebuild periodic boundary conditions around chosen atoms.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : Modify position of atoms indicated by ATOMS by shifting them by lattice vectors so that they are</a>
+<a name="44"><span class="lineNum">      44 </span>            : as close as possible to the atoms indicated by AROUND. More precisely, for every atom i</a>
+<a name="45"><span class="lineNum">      45 </span>            : in the ATOMS list the following procedure is performed:</a>
+<a name="46"><span class="lineNum">      46 </span>            : - The atom j among those in the AROUND list is searched that is closest to atom i.</a>
+<a name="47"><span class="lineNum">      47 </span>            : - The atom i is replaced with its periodic image that is closest to atom j.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : This action works similarly to \ref WHOLEMOLECULES in that it replaces atoms coordinate. Notice that only</a>
+<a name="50"><span class="lineNum">      50 </span>            : atoms specified with ATOMS are replaced, and that, at variance with \ref WHOLEMOLECULES,</a>
+<a name="51"><span class="lineNum">      51 </span>            : the order in which atoms are specified is irrelevant.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : This is often convenient at a post processing stage (using the \ref driver), but sometime</a>
+<a name="54"><span class="lineNum">      54 </span>            : it is required during the simulation if collective variables need atoms to be in a specific periodic image.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \attention This directive modifies the stored position at the precise moment it is executed. This means that only collective variables which are below it in the input script will see the corrected positions. As a general rule, put it at the top of the input file. Also, unless you know exactly what you are doing, leave the default stride (1), so that this action is performed at every MD step.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : Consider that the computational cost grows with the product</a>
+<a name="59"><span class="lineNum">      59 </span>            : of the size of the two lists (ATOMS and AROUND), so that this action can become very expensive.</a>
+<a name="60"><span class="lineNum">      60 </span>            : If you are using it to analyze a trajectory this is usually not a big problem. If you use it to</a>
+<a name="61"><span class="lineNum">      61 </span>            : analyze a simulation on the fly, e.g. with \ref DUMPATOMS to store a properly wrapped trajectory,</a>
+<a name="62"><span class="lineNum">      62 </span>            : consider the possibility of using the STRIDE keyword here (with great care).</a>
+<a name="63"><span class="lineNum">      63 </span>            : \par Examples</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : This command instructs plumed to move all the ions to their periodic image that is as close as possible to</a>
+<a name="66"><span class="lineNum">      66 </span>            : the rna group.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : rna: GROUP ATOMS=1-100</a>
+<a name="70"><span class="lineNum">      70 </span>            : ions: GROUP ATOMS=101-110</a>
+<a name="71"><span class="lineNum">      71 </span>            : # first make the rna molecule whole</a>
+<a name="72"><span class="lineNum">      72 </span>            : WHOLEMOLECULES ENTITY0=rna</a>
+<a name="73"><span class="lineNum">      73 </span>            : WRAPAROUND ATOMS=ions AROUND=rna</a>
+<a name="74"><span class="lineNum">      74 </span>            : DUMPATOMS FILE=dump.xyz ATOMS=rna,ions</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : In case you want to do it during a simulation and you only care about wrapping the ions in</a>
+<a name="78"><span class="lineNum">      78 </span>            : the `dump.xyz` file, you can use the following:</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : # add some restraint that do not require molecules to be whole:</a>
+<a name="82"><span class="lineNum">      82 </span>            : a: TORSION ATOMS=1,2,10,11</a>
+<a name="83"><span class="lineNum">      83 </span>            : RESTRAINT ARG=a AT=0.0 KAPPA=5</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : # then do the things that are required for dumping the trajectory</a>
+<a name="87"><span class="lineNum">      87 </span>            : # notice that they are all done every 100 steps, so as not to</a>
+<a name="88"><span class="lineNum">      88 </span>            : # unnecessarily overload the calculation</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : rna: GROUP ATOMS=1-100</a>
+<a name="91"><span class="lineNum">      91 </span>            : ions: GROUP ATOMS=101-110</a>
+<a name="92"><span class="lineNum">      92 </span>            : # first make the rna molecule whole</a>
+<a name="93"><span class="lineNum">      93 </span>            : WHOLEMOLECULES ENTITY0=rna STRIDE=100</a>
+<a name="94"><span class="lineNum">      94 </span>            : WRAPAROUND ATOMS=ions AROUND=rna STRIDE=100</a>
+<a name="95"><span class="lineNum">      95 </span>            : DUMPATOMS FILE=dump.xyz ATOMS=rna,ions STRIDE=100</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endplumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : Notice that if the biased variable requires a molecule to be whole, you might have to put</a>
+<a name="99"><span class="lineNum">      99 </span>            : just the \ref WHOLEMOLECULES command before computing that variable and leave the default STRIDE=1.</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : This command instructs plumed to center all atoms around the center of mass of a solute molecule.</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : \plumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : solute: GROUP ATOMS=1-100</a>
+<a name="105"><span class="lineNum">     105 </span>            : all: GROUP ATOMS=1-1000</a>
+<a name="106"><span class="lineNum">     106 </span>            : # center of the solute:</a>
+<a name="107"><span class="lineNum">     107 </span>            : # notice that since plumed 2.2 this also works if the</a>
+<a name="108"><span class="lineNum">     108 </span>            : # solute molecule is broken</a>
+<a name="109"><span class="lineNum">     109 </span>            : com: COM ATOMS=solute</a>
+<a name="110"><span class="lineNum">     110 </span>            : # notice that we wrap around a single atom. this should be fast</a>
+<a name="111"><span class="lineNum">     111 </span>            : WRAPAROUND ATOMS=all AROUND=com</a>
+<a name="112"><span class="lineNum">     112 </span>            : DUMPATOMS FILE=dump.xyz ATOMS=all</a>
+<a name="113"><span class="lineNum">     113 </span>            : \endplumedfile</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : Notice that whereas \ref WHOLEMOLECULES is designed to make molecules whole,</a>
+<a name="116"><span class="lineNum">     116 </span>            : \ref WRAPAROUND can easily break molecules. In the last example,</a>
+<a name="117"><span class="lineNum">     117 </span>            : if solvent (atoms 101-1000) is made e.g. of water, then water</a>
+<a name="118"><span class="lineNum">     118 </span>            : molecules could be broken by \ref WRAPAROUND (hydrogen could end up</a>
+<a name="119"><span class="lineNum">     119 </span>            : in an image and oxygen in another one).</a>
+<a name="120"><span class="lineNum">     120 </span>            : One solution is to use \ref WHOLEMOLECULES on _all_ the water molecules</a>
+<a name="121"><span class="lineNum">     121 </span>            : after \ref WRAPAROUND. This is tedious. A better solution is to use the</a>
+<a name="122"><span class="lineNum">     122 </span>            : GROUPBY option which is going</a>
+<a name="123"><span class="lineNum">     123 </span>            : to consider the atoms listed in ATOMS as a list of groups</a>
+<a name="124"><span class="lineNum">     124 </span>            : each of size GROUPBY. The first atom of the group will be brought</a>
+<a name="125"><span class="lineNum">     125 </span>            : close to the AROUND atoms. The following atoms of the group</a>
+<a name="126"><span class="lineNum">     126 </span>            : will be just brought close to the first atom of the group.</a>
+<a name="127"><span class="lineNum">     127 </span>            : Assuming that oxygen is the first atom of each water molecules,</a>
+<a name="128"><span class="lineNum">     128 </span>            : in the following examples all the water oxygen atoms will be brought</a>
+<a name="129"><span class="lineNum">     129 </span>            : close to the solute, and all the hydrogen atoms will be kept close</a>
+<a name="130"><span class="lineNum">     130 </span>            : to their related oxygen.</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : \plumedfile</a>
+<a name="133"><span class="lineNum">     133 </span>            : solute: GROUP ATOMS=1-100</a>
+<a name="134"><span class="lineNum">     134 </span>            : water: GROUP ATOMS=101-1000</a>
+<a name="135"><span class="lineNum">     135 </span>            : com: COM ATOMS=solute</a>
+<a name="136"><span class="lineNum">     136 </span>            : # notice that we wrap around a single atom. this should be fast</a>
+<a name="137"><span class="lineNum">     137 </span>            : WRAPAROUND ATOMS=solute AROUND=com</a>
+<a name="138"><span class="lineNum">     138 </span>            : # notice that we wrap around a single atom. this should be fast</a>
+<a name="139"><span class="lineNum">     139 </span>            : WRAPAROUND ATOMS=water AROUND=com GROUPBY=3</a>
+<a name="140"><span class="lineNum">     140 </span>            : DUMPATOMS FILE=dump.xyz ATOMS=solute,water</a>
+<a name="141"><span class="lineNum">     141 </span>            : \endplumedfile</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : */</a>
+<a name="144"><span class="lineNum">     144 </span>            : //+ENDPLUMEDOC</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : class WrapAround:</a>
+<a name="148"><span class="lineNum">     148 </span>            :   public ActionPilot,</a>
+<a name="149"><span class="lineNum">     149 </span>            :   public ActionAtomistic</a>
+<a name="150"><span class="lineNum">     150 </span>            : {</a>
+<a name="151"><span class="lineNum">     151 </span>            :   // cppcheck-suppress duplInheritedMember</a>
+<a name="152"><span class="lineNum">     152 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   std::vector&lt;AtomNumber&gt; reference;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   unsigned groupby;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   bool pair_;</a>
+<a name="156"><span class="lineNum">     156 </span>            : public:</a>
+<a name="157"><span class="lineNum">     157 </span>            :   explicit WrapAround(const ActionOptions&amp;ao);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void calculate() override;</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        579 :   void apply() override {}</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : };</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(WrapAround,&quot;WRAPAROUND&quot;)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          7 : void WrapAround::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          7 :   Action::registerKeywords( keys );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          7 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          7 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which molecules are reassembled.  Unless you are completely certain about what you are doing leave this set equal to 1!&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         14 :   keys.add(&quot;atoms&quot;,&quot;AROUND&quot;,&quot;reference atoms&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         14 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;wrapped atoms&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;GROUPBY&quot;,&quot;1&quot;,&quot;group atoms so as not to break molecules&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         14 :   keys.addFlag(&quot;PAIR&quot;, false, &quot;Pair atoms in AROUND and ATOMS groups&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          7 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          5 : WrapAround::WrapAround(const ActionOptions&amp;ao):</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   Action(ao),</a>
+<a name="178"><span class="lineNum">     178 </span>            :   ActionPilot(ao),</a>
+<a name="179"><span class="lineNum">     179 </span>            :   ActionAtomistic(ao),</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          5 :   groupby(1),</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          5 :   pair_(false)</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : {</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          5 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          5 :   parseAtomList(&quot;AROUND&quot;,reference);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          5 :   parse(&quot;GROUPBY&quot;,groupby);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          5 :   parseFlag(&quot;PAIR&quot;, pair_);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          5 :   log.printf(&quot;  atoms in reference :&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         11 :   for(unsigned j=0; j&lt;reference.size(); ++j) log.printf(&quot; %d&quot;,reference[j].serial() );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          5 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          5 :   log.printf(&quot;  atoms to be wrapped :&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        399 :   for(unsigned j=0; j&lt;atoms.size(); ++j) log.printf(&quot; %d&quot;,atoms[j].serial() );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          5 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          5 :   if(groupby&gt;1) log&lt;&lt;&quot;  atoms will be grouped by &quot;&lt;&lt;groupby&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          5 :   if(pair_) log.printf(&quot;  pairing atoms and references\n&quot;);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          5 :   if(atoms.size()%groupby!=0) error(&quot;number of atoms should be a multiple of groupby option&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   // additional checks with PAIR</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          5 :   if(pair_ &amp;&amp; atoms.size()!=reference.size()*groupby) error(&quot;with PAIR you must have: #ATOMS = #AROUND * #GROUPBY&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          5 :   checkRead();</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   // do not remove duplicates with pair</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          5 :   if(!pair_) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          5 :     if(groupby&lt;=1) Tools::removeDuplicates(atoms);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          5 :     Tools::removeDuplicates(reference);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          5 :   std::vector&lt;AtomNumber&gt; merged(atoms.size()+reference.size());</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          5 :   merge(atoms.begin(),atoms.end(),reference.begin(),reference.end(),merged.begin());</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          5 :   Tools::removeDuplicates(merged);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          5 :   requestAtoms(merged);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   doNotRetrieve();</a>
+<a name="214"><span class="lineNum">     214 </span>            :   doNotForce();</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          5 : }</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        579 : void WrapAround::calculate() {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      15012 :   for(unsigned i=0; i&lt;atoms.size(); i+=groupby) {</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :     Vector &amp; first (modifyGlobalPosition(atoms[i]));</a>
+<a name="220"><span class="lineNum">     220 </span>            :     double mindist2=std::numeric_limits&lt;double&gt;::max();</a>
+<a name="221"><span class="lineNum">     221 </span>            :     int closest=-1;</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      14433 :     if(pair_) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :       closest = i/groupby;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :     } else {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      29416 :       for(unsigned j=0; j&lt;reference.size(); ++j) {</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :         const Vector &amp; second (modifyGlobalPosition(reference[j]));</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      14983 :         const Vector distance=pbcDistance(first,second);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      14983 :         const double distance2=modulo2(distance);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      14983 :         if(distance2&lt;mindist2) {</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :           mindist2=distance2;</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      14713 :           closest=j;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :         }</a>
+<a name="233"><span class="lineNum">     233 </span>            :       }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      14433 :       plumed_massert(closest&gt;=0,&quot;closest not found&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      14433 :     Vector &amp; second (modifyGlobalPosition(reference[closest]));</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : // place first atom of the group</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      14433 :     first=second+pbcDistance(second,first);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : // then place other atoms close to the first of the group</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      14928 :     for(unsigned j=1; j&lt;groupby; j++) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        495 :       Vector &amp; second (modifyGlobalPosition(atoms[i+j]));</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        495 :       second=first+pbcDistance(first,second);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     }</a>
+<a name="244"><span class="lineNum">     244 </span>            :   }</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        579 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/index-sort-f.html b/coverage/generic/index-sort-f.html
new file mode 100644
index 0000000000..d915b1d5d2
--- /dev/null
+++ b/coverage/generic/index-sort-f.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - generic</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1210</td>
+            <td class="headerCovTableEntry">1275</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">177</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Time.cpp.gcov.html">Time.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">5 / 15</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">3 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RandomExchanges.cpp.gcov.html">RandomExchanges.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=36 height=10 alt="35.7%"><img src="../snow.png" width=64 height=10 alt="35.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 14</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Include.cpp.gcov.html">Include.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.6%"><img src="../snow.png" width=15 height=10 alt="84.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Group.cpp.gcov.html">Group.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.3%"><img src="../snow.png" width=3 height=10 alt="97.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.3&nbsp;%</td>
+      <td class="coverNumHi">71 / 73</td>
+      <td class="coverPerLo">63.6&nbsp;%</td>
+      <td class="coverNumLo">7 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EndPlumed.cpp.gcov.html">EndPlumed.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FitToTemplate.cpp.gcov.html">FitToTemplate.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">86 / 89</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpForces.cpp.gcov.html">DumpForces.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 38</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpDerivatives.cpp.gcov.html">DumpDerivatives.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EffectiveEnergyDrift.cpp.gcov.html">EffectiveEnergyDrift.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.9%"><img src="../snow.png" width=3 height=10 alt="96.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.9&nbsp;%</td>
+      <td class="coverNumHi">123 / 127</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpAtoms.cpp.gcov.html">DumpAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">119 / 121</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpProjections.cpp.gcov.html">DumpProjections.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpMassCharge.cpp.gcov.html">DumpMassCharge.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">62 / 63</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Print.cpp.gcov.html">Print.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">56 / 58</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UpdateIf.cpp.gcov.html">UpdateIf.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Read.cpp.gcov.html">Read.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">95 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Plumed.cpp.gcov.html">Plumed.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">167 / 179</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WholeMolecules.cpp.gcov.html">WholeMolecules.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">60 / 70</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WrapAround.cpp.gcov.html">WrapAround.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">53 / 54</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ResetCell.cpp.gcov.html">ResetCell.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Debug.cpp.gcov.html">Debug.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">57 / 57</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MolInfo.cpp.gcov.html">MolInfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Flush.cpp.gcov.html">Flush.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/index-sort-l.html b/coverage/generic/index-sort-l.html
new file mode 100644
index 0000000000..fdd9a727e1
--- /dev/null
+++ b/coverage/generic/index-sort-l.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - generic</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1210</td>
+            <td class="headerCovTableEntry">1275</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">177</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Time.cpp.gcov.html">Time.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">5 / 15</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">3 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RandomExchanges.cpp.gcov.html">RandomExchanges.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=36 height=10 alt="35.7%"><img src="../snow.png" width=64 height=10 alt="35.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 14</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EndPlumed.cpp.gcov.html">EndPlumed.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Include.cpp.gcov.html">Include.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.6%"><img src="../snow.png" width=15 height=10 alt="84.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WholeMolecules.cpp.gcov.html">WholeMolecules.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">60 / 70</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Plumed.cpp.gcov.html">Plumed.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">167 / 179</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Read.cpp.gcov.html">Read.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">95 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Print.cpp.gcov.html">Print.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">56 / 58</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FitToTemplate.cpp.gcov.html">FitToTemplate.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">86 / 89</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EffectiveEnergyDrift.cpp.gcov.html">EffectiveEnergyDrift.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.9%"><img src="../snow.png" width=3 height=10 alt="96.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.9&nbsp;%</td>
+      <td class="coverNumHi">123 / 127</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Group.cpp.gcov.html">Group.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.3%"><img src="../snow.png" width=3 height=10 alt="97.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.3&nbsp;%</td>
+      <td class="coverNumHi">71 / 73</td>
+      <td class="coverPerLo">63.6&nbsp;%</td>
+      <td class="coverNumLo">7 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WrapAround.cpp.gcov.html">WrapAround.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">53 / 54</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpAtoms.cpp.gcov.html">DumpAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">119 / 121</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpMassCharge.cpp.gcov.html">DumpMassCharge.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">62 / 63</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MolInfo.cpp.gcov.html">MolInfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Flush.cpp.gcov.html">Flush.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpForces.cpp.gcov.html">DumpForces.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 38</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpProjections.cpp.gcov.html">DumpProjections.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ResetCell.cpp.gcov.html">ResetCell.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UpdateIf.cpp.gcov.html">UpdateIf.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpDerivatives.cpp.gcov.html">DumpDerivatives.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Debug.cpp.gcov.html">Debug.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">57 / 57</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/generic/index.html b/coverage/generic/index.html
new file mode 100644
index 0000000000..a98eaf7036
--- /dev/null
+++ b/coverage/generic/index.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - generic</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - generic</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1210</td>
+            <td class="headerCovTableEntry">1275</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">177</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Debug.cpp.gcov.html">Debug.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">57 / 57</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpAtoms.cpp.gcov.html">DumpAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">119 / 121</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpDerivatives.cpp.gcov.html">DumpDerivatives.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpForces.cpp.gcov.html">DumpForces.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 38</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpMassCharge.cpp.gcov.html">DumpMassCharge.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">62 / 63</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpProjections.cpp.gcov.html">DumpProjections.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EffectiveEnergyDrift.cpp.gcov.html">EffectiveEnergyDrift.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.9%"><img src="../snow.png" width=3 height=10 alt="96.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.9&nbsp;%</td>
+      <td class="coverNumHi">123 / 127</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EndPlumed.cpp.gcov.html">EndPlumed.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FitToTemplate.cpp.gcov.html">FitToTemplate.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">86 / 89</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Flush.cpp.gcov.html">Flush.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Group.cpp.gcov.html">Group.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.3%"><img src="../snow.png" width=3 height=10 alt="97.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.3&nbsp;%</td>
+      <td class="coverNumHi">71 / 73</td>
+      <td class="coverPerLo">63.6&nbsp;%</td>
+      <td class="coverNumLo">7 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Include.cpp.gcov.html">Include.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.6%"><img src="../snow.png" width=15 height=10 alt="84.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MolInfo.cpp.gcov.html">MolInfo.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Plumed.cpp.gcov.html">Plumed.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">167 / 179</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Print.cpp.gcov.html">Print.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">56 / 58</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RandomExchanges.cpp.gcov.html">RandomExchanges.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=36 height=10 alt="35.7%"><img src="../snow.png" width=64 height=10 alt="35.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.7&nbsp;%</td>
+      <td class="coverNumLo">5 / 14</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Read.cpp.gcov.html">Read.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">95 / 100</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ResetCell.cpp.gcov.html">ResetCell.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Time.cpp.gcov.html">Time.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=33 height=10 alt="33.3%"><img src="../snow.png" width=67 height=10 alt="33.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">5 / 15</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">3 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UpdateIf.cpp.gcov.html">UpdateIf.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WholeMolecules.cpp.gcov.html">WholeMolecules.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">60 / 70</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WrapAround.cpp.gcov.html">WrapAround.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">53 / 54</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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diff --git a/coverage/gridtools/ActionWithGrid.cpp.func-sort-c.html b/coverage/gridtools/ActionWithGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a7c21c1f79
--- /dev/null
+++ b/coverage/gridtools/ActionWithGrid.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithGrid.cpp<span style="font-size: 80%;"> (<a href="ActionWithGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#35">_ZN4PLMD9gridtools14ActionWithGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#73">_ZN4PLMD9gridtools14ActionWithGrid17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools14ActionWithGrid10createGridERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#35">_ZN4PLMD9gridtools14ActionWithGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#27">_ZN4PLMD9gridtools14ActionWithGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#81">_ZN4PLMD9gridtools14ActionWithGrid9calculateEv</a></td>
+              <td class="coverFnHi">215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#102">_ZNK4PLMD9gridtools14ActionWithGrid7runTaskERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">57902</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithGrid.cpp.func.html b/coverage/gridtools/ActionWithGrid.cpp.func.html
new file mode 100644
index 0000000000..6e177bfede
--- /dev/null
+++ b/coverage/gridtools/ActionWithGrid.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithGrid.cpp<span style="font-size: 80%;"> (<a href="ActionWithGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools14ActionWithGrid10createGridERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#27">_ZN4PLMD9gridtools14ActionWithGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#73">_ZN4PLMD9gridtools14ActionWithGrid17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#81">_ZN4PLMD9gridtools14ActionWithGrid9calculateEv</a></td>
+              <td class="coverFnHi">215</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#35">_ZN4PLMD9gridtools14ActionWithGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#35">_ZN4PLMD9gridtools14ActionWithGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithGrid.cpp.gcov.html#102">_ZNK4PLMD9gridtools14ActionWithGrid7runTaskERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">57902</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithGrid.cpp.gcov.html b/coverage/gridtools/ActionWithGrid.cpp.gcov.html
new file mode 100644
index 0000000000..78cc0c9d6a
--- /dev/null
+++ b/coverage/gridtools/ActionWithGrid.cpp.gcov.html
@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithGrid.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithGrid.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace gridtools {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         88 : void ActionWithGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         88 :   vesselbase::ActionWithAveraging::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        176 :   keys.add(&quot;compulsory&quot;,&quot;BANDWIDTH&quot;,&quot;the bandwidths for kernel density estimation&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        176 :   keys.add(&quot;compulsory&quot;,&quot;KERNEL&quot;,&quot;gaussian&quot;,&quot;the kernel function you are using.  More details on  the kernels available &quot;</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :            &quot;in plumed plumed can be found in \\ref kernelfunctions.&quot;);</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        176 :   keys.add(&quot;optional&quot;,&quot;CONCENTRATION&quot;,&quot;the concentration parameter for Von Mises-Fisher distributions&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         88 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         70 : ActionWithGrid::ActionWithGrid( const ActionOptions&amp; ao):</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   Action(ao),</a>
+<a name="39"><span class="lineNum">      39 </span>            :   ActionWithAveraging(ao),</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         70 :   mygrid(NULL)</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : {</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         70 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         65 : std::unique_ptr&lt;GridVessel&gt; ActionWithGrid::createGrid( const std::string&amp; type, const std::string&amp; inputstr ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   // Start creating the input for the grid</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         65 :   std::string vstring = inputstr;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        130 :   if( keywords.exists(&quot;KERNEL&quot;) ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         90 :     std::string vconc; parse(&quot;CONCENTRATION&quot;,vconc);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         45 :     if( vconc.length()&gt;0 ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 :       vstring += &quot; TYPE=fibonacci CONCENTRATION=&quot; + vconc;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :     } else {</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         86 :       std::string kstring; parse(&quot;KERNEL&quot;,kstring);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         53 :       if( kstring==&quot;DISCRETE&quot; ) vstring += &quot; KERNEL=&quot; + kstring;</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         66 :       else vstring += &quot; KERNEL=&quot; + kstring + &quot; &quot; + getKeyword(&quot;BANDWIDTH&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     }</a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        130 :   vesselbase::VesselOptions da(&quot;mygrid&quot;,&quot;&quot;,-1,vstring,this);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         65 :   Keywords keys; gridtools::AverageOnGrid::registerKeywords( keys );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         65 :   vesselbase::VesselOptions dar( da, keys );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         65 :   std::unique_ptr&lt;GridVessel&gt; grid;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         65 :   if( type==&quot;histogram&quot; ) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         37 :     grid=Tools::make_unique&lt;HistogramOnGrid&gt;(dar);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         28 :   } else if( type==&quot;average&quot; ) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          8 :     grid=Tools::make_unique&lt;AverageOnGrid&gt;(dar);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         20 :   } else if( type==&quot;grid&quot; ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         40 :     grid=Tools::make_unique&lt;GridVessel&gt;(dar);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   } else {</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;no way to create grid of type &quot; + type );</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span>            :   // cppcheck-suppress danglingLifetime</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         65 :   mygrid=grid.get();</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         65 :   return grid;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         65 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         16 : void ActionWithGrid::turnOnDerivatives() {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         16 :   needsDerivatives(); ActionWithValue::turnOnDerivatives();</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         16 :   if( getStride()==1 ) setStride(0);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          8 :   else if( getStride()!=0 ) error(&quot;conflicting instructions for grid - stride was set but must be evaluated on every step for derivatives - remove STRIDE keyword&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         16 :   if( clearstride&gt;1 ) error(&quot;conflicting instructions for grid - CLEAR was set but grid must be reset on every step for derivatives - remove CLEAR keyword&quot; );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         16 :   if( weights.size()&gt;0 ) error(&quot;conflicting instructions for grid - LOGWEIGHTS was set but weights are not considered when derivatives of grid are evaluated - remove LOGWEIGHTS keyword&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         16 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        215 : void ActionWithGrid::calculate() {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   // Do nothing if derivatives are not required</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        215 :   if( doNotCalculateDerivatives() ) return;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   // Clear on every step</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         40 :   if( mygrid ) clearAverage();</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   // Should not be any reweighting so just set these accordingly</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         40 :   lweight=0; cweight=1.0;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Prepare to do the averaging</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         40 :   prepareForAveraging();</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   // Run all the tasks (if required</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         40 :   if( useRunAllTasks ) runAllTasks();</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   // This the averaging if it is not done using task list</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         20 :   else performOperations( true );</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Update the norm</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         40 :   if( mygrid ) mygrid-&gt;setNorm( cweight );</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   // Finish the averaging</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         40 :   finishAveraging();</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   // And reset for next step</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         40 :   if( mygrid ) mygrid-&gt;reset();</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      57902 : void ActionWithGrid::runTask( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Set the weight of this point</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      57902 :   myvals.setValue( 0, cweight ); compute( current, myvals );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      57902 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithInputGrid.cpp.func-sort-c.html b/coverage/gridtools/ActionWithInputGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..72121691da
--- /dev/null
+++ b/coverage/gridtools/ActionWithInputGrid.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithInputGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithInputGrid.cpp<span style="font-size: 80%;"> (<a href="ActionWithInputGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">91.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithInputGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#33">_ZN4PLMD9gridtools19ActionWithInputGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#72">_ZN4PLMD9gridtools19ActionWithInputGrid17performOperationsERKb</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#33">_ZN4PLMD9gridtools19ActionWithInputGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#59">_ZN4PLMD9gridtools19ActionWithInputGrid12clearAverageEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#27">_ZN4PLMD9gridtools19ActionWithInputGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#64">_ZN4PLMD9gridtools19ActionWithInputGrid19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithInputGrid.cpp.func.html b/coverage/gridtools/ActionWithInputGrid.cpp.func.html
new file mode 100644
index 0000000000..ecda5112b6
--- /dev/null
+++ b/coverage/gridtools/ActionWithInputGrid.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithInputGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithInputGrid.cpp<span style="font-size: 80%;"> (<a href="ActionWithInputGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">91.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithInputGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#59">_ZN4PLMD9gridtools19ActionWithInputGrid12clearAverageEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#27">_ZN4PLMD9gridtools19ActionWithInputGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#72">_ZN4PLMD9gridtools19ActionWithInputGrid17performOperationsERKb</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#64">_ZN4PLMD9gridtools19ActionWithInputGrid19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#33">_ZN4PLMD9gridtools19ActionWithInputGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.cpp.gcov.html#33">_ZN4PLMD9gridtools19ActionWithInputGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithInputGrid.cpp.gcov.html b/coverage/gridtools/ActionWithInputGrid.cpp.gcov.html
new file mode 100644
index 0000000000..8913f41a25
--- /dev/null
+++ b/coverage/gridtools/ActionWithInputGrid.cpp.gcov.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithInputGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithInputGrid.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithInputGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">91.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithInputGrid.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace gridtools {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         39 : void ActionWithInputGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         39 :   ActionWithGrid::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         78 :   keys.add(&quot;compulsory&quot;,&quot;GRID&quot;,&quot;the action that creates the input grid you would like to use&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         78 :   keys.add(&quot;optional&quot;,&quot;COMPONENT&quot;,&quot;if your input is a vector field use this to specify the component of the input vector field for which you wish to use&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         39 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         25 : ActionWithInputGrid::ActionWithInputGrid(const ActionOptions&amp;ao):</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   Action(ao),</a>
+<a name="37"><span class="lineNum">      37 </span>            :   ActionWithGrid(ao),</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         25 :   ingrid(NULL)</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : {</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         25 :   std::string mlab; parse(&quot;GRID&quot;,mlab);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         25 :   vesselbase::ActionWithVessel* mves= plumed.getActionSet().selectWithLabel&lt;vesselbase::ActionWithVessel*&gt;(mlab);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         25 :   if(!mves) error(&quot;action labelled &quot; +  mlab + &quot; does not exist or does not have vessels&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         25 :   addDependency(mves);</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;mves-&gt;getNumberOfVessels(); ++i) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         25 :     ingrid=dynamic_cast&lt;GridVessel*&gt;( mves-&gt;getPntrToVessel(i) );</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         25 :     if( ingrid ) break;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         25 :   if( !ingrid ) error(&quot;input action does not calculate a grid&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         25 :   if( ingrid-&gt;getNumberOfComponents()==1 ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         25 :     mycomp=0;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   } else {</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :     int tcomp=-1; parse(&quot;COMPONENT&quot;,tcomp);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :     if( tcomp&lt;0 ) error(&quot;component of vector field was not specified - use COMPONENT keyword&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :     mycomp=tcomp;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         25 :   log.printf(&quot;  using %uth component of grid calculated by action %s \n&quot;,mycomp,mves-&gt;getLabel().c_str() );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         25 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         26 : void ActionWithInputGrid::clearAverage() {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         52 :   if( mygrid-&gt;getType()==&quot;flat&quot; ) mygrid-&gt;setBounds( ingrid-&gt;getMin(), ingrid-&gt;getMax(), mygrid-&gt;getNbin(), mygrid-&gt;getGridSpacing() );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         26 :   ActionWithAveraging::clearAverage();</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         26 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         70 : void ActionWithInputGrid::prepareForAveraging() {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         70 :   if( checkAllActive() ) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      93583 :     for(unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      93513 :       if( ingrid-&gt;inactive(i) ) error(&quot;if FIND_CONTOUR is used with BUFFER option then other actions cannot be performed with grid&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     }</a>
+<a name="71"><span class="lineNum">      71 </span>            :   }</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         70 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         21 : void ActionWithInputGrid::performOperations( const bool&amp; from_update ) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         21 :   prepareForAveraging(); runAllTasks();</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         21 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithInputGrid.h.func-sort-c.html b/coverage/gridtools/ActionWithInputGrid.h.func-sort-c.html
new file mode 100644
index 0000000000..8d88b41db2
--- /dev/null
+++ b/coverage/gridtools/ActionWithInputGrid.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithInputGrid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithInputGrid.h<span style="font-size: 80%;"> (<a href="ActionWithInputGrid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithInputGrid.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#45">_ZN4PLMD9gridtools19ActionWithInputGrid5applyEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#43">_ZNK4PLMD9gridtools19ActionWithInputGrid14checkAllActiveEv</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#55">_ZNK4PLMD9gridtools19ActionWithInputGrid16getFunctionValueERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">32928</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#49">_ZNK4PLMD9gridtools19ActionWithInputGrid16getFunctionValueERKj</a></td>
+              <td class="coverFnHi">117146</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithInputGrid.h.func.html b/coverage/gridtools/ActionWithInputGrid.h.func.html
new file mode 100644
index 0000000000..684283238d
--- /dev/null
+++ b/coverage/gridtools/ActionWithInputGrid.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithInputGrid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithInputGrid.h<span style="font-size: 80%;"> (<a href="ActionWithInputGrid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithInputGrid.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#45">_ZN4PLMD9gridtools19ActionWithInputGrid5applyEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#43">_ZNK4PLMD9gridtools19ActionWithInputGrid14checkAllActiveEv</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#55">_ZNK4PLMD9gridtools19ActionWithInputGrid16getFunctionValueERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">32928</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputGrid.h.gcov.html#49">_ZNK4PLMD9gridtools19ActionWithInputGrid16getFunctionValueERKj</a></td>
+              <td class="coverFnHi">117146</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithInputGrid.h.gcov.html b/coverage/gridtools/ActionWithInputGrid.h.gcov.html
new file mode 100644
index 0000000000..ad868a4b31
--- /dev/null
+++ b/coverage/gridtools/ActionWithInputGrid.h.gcov.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithInputGrid.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithInputGrid.h<span style="font-size: 80%;"> (source / <a href="ActionWithInputGrid.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_ActionWithInputGrid_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_ActionWithInputGrid_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionWithGrid.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace gridtools {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class ActionWithInputGrid : public ActionWithGrid {</a>
+<a name="32"><span class="lineNum">      32 </span>            :   friend class DumpGrid;</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   unsigned mycomp;</a>
+<a name="35"><span class="lineNum">      35 </span>            : protected:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   GridVessel* ingrid;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double getFunctionValue( const unsigned&amp; ipoint ) const ;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   double getFunctionValue( const std::vector&lt;unsigned&gt;&amp; ip ) const ;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   double getFunctionValueAndDerivatives( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der ) const ;</a>
+<a name="40"><span class="lineNum">      40 </span>            : public:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="42"><span class="lineNum">      42 </span>            :   explicit ActionWithInputGrid(const ActionOptions&amp;ao);</a>
+<a name="43"><span class="lineNum">      43 </span>            :   void clearAverage() override;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void prepareForAveraging() override;</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         70 :   virtual bool checkAllActive() const { return true; }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   void performOperations( const bool&amp; from_update ) override;</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         28 :   void apply() override {};</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : inline</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     117146 : double ActionWithInputGrid::getFunctionValue( const unsigned&amp; ipoint ) const {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     117146 :   unsigned dim=ingrid-&gt;getDimension(); if( ingrid-&gt;noderiv ) dim=0;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     117146 :   return ingrid-&gt;getGridElement( ipoint, mycomp*(1+dim) );</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : }</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : inline</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      32928 : double ActionWithInputGrid::getFunctionValue( const std::vector&lt;unsigned&gt;&amp; ip ) const {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      32928 :   return getFunctionValue( ingrid-&gt;getIndex(ip) );</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : inline</a>
+<a name="62"><span class="lineNum">      62 </span>            : double ActionWithInputGrid::getFunctionValueAndDerivatives( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der ) const {</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       8545 :   return ingrid-&gt;getValueAndDerivatives( x, mycomp, der );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : #endif</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithIntegral.cpp.func-sort-c.html b/coverage/gridtools/ActionWithIntegral.cpp.func-sort-c.html
new file mode 100644
index 0000000000..dc7f0f3349
--- /dev/null
+++ b/coverage/gridtools/ActionWithIntegral.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithIntegral.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithIntegral.cpp<span style="font-size: 80%;"> (<a href="ActionWithIntegral.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithIntegral.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#31">_ZN4PLMD9gridtools18ActionWithIntegralC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#31">_ZN4PLMD9gridtools18ActionWithIntegralC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#25">_ZN4PLMD9gridtools18ActionWithIntegral16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#50">_ZN4PLMD9gridtools18ActionWithIntegral17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#55">_ZN4PLMD9gridtools18ActionWithIntegral5applyEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithIntegral.cpp.func.html b/coverage/gridtools/ActionWithIntegral.cpp.func.html
new file mode 100644
index 0000000000..2f2e68a697
--- /dev/null
+++ b/coverage/gridtools/ActionWithIntegral.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithIntegral.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithIntegral.cpp<span style="font-size: 80%;"> (<a href="ActionWithIntegral.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithIntegral.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#25">_ZN4PLMD9gridtools18ActionWithIntegral16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#50">_ZN4PLMD9gridtools18ActionWithIntegral17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#55">_ZN4PLMD9gridtools18ActionWithIntegral5applyEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#31">_ZN4PLMD9gridtools18ActionWithIntegralC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.cpp.gcov.html#31">_ZN4PLMD9gridtools18ActionWithIntegralC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithIntegral.cpp.gcov.html b/coverage/gridtools/ActionWithIntegral.cpp.gcov.html
new file mode 100644
index 0000000000..fe3539c7f5
--- /dev/null
+++ b/coverage/gridtools/ActionWithIntegral.cpp.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithIntegral.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithIntegral.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithIntegral.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithIntegral.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace gridtools {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">          6 : void ActionWithIntegral::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          6 :   ActionWithInputGrid::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         12 :   keys.remove(&quot;KERNEL&quot;); keys.remove(&quot;BANDWIDTH&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         18 :   keys.remove(&quot;CLEAR&quot;); keys.add(&quot;compulsory&quot;,&quot;CLEAR&quot;,&quot;1&quot;,&quot;the frequency with which to clear all the accumulated data.&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          6 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          4 : ActionWithIntegral::ActionWithIntegral(const ActionOptions&amp;ao):</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   Action(ao),</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          4 :   ActionWithInputGrid(ao)</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : {</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          4 :   plumed_assert( ingrid-&gt;getNumberOfComponents()==1 );</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   // Retrieve the volume of the grid (for integration)</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          4 :   volume = ingrid-&gt;getCellVolume();</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   // Create something that is going to calculate the sum of all the values</a>
+<a name="41"><span class="lineNum">      41 </span>            :   // at the various grid points - this is going to be the integral</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          8 :   std::string fake_input; addVessel( &quot;SUM&quot;, fake_input, -1 ); readVesselKeywords();</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   // Now create task list - number of tasks is equal to the number of grid points</a>
+<a name="44"><span class="lineNum">      44 </span>            :   // as we have to evaluate the function at each grid points</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1145 :   for(unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) addTaskToList(i);</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   // And activate all tasks</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          4 :   deactivateAllTasks();</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1145 :   for(unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) taskFlags[i]=1;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          4 :   lockContributors();</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 : }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          8 : void ActionWithIntegral::turnOnDerivatives() {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          8 :   ActionWithGrid::turnOnDerivatives();</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          8 :   forcesToApply.resize( ingrid-&gt;getNumberOfPoints() );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          8 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         20 : void ActionWithIntegral::apply() {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         20 :   if( getForcesFromVessels( forcesToApply ) ) ingrid-&gt;setForce( forcesToApply );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         20 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithIntegral.h.func-sort-c.html b/coverage/gridtools/ActionWithIntegral.h.func-sort-c.html
new file mode 100644
index 0000000000..8fb8c2cbe0
--- /dev/null
+++ b/coverage/gridtools/ActionWithIntegral.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithIntegral.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithIntegral.h<span style="font-size: 80%;"> (<a href="ActionWithIntegral.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithIntegral.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.h.gcov.html#41">_ZN4PLMD9gridtools18ActionWithIntegral10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.h.gcov.html#51">_ZN4PLMD9gridtools18ActionWithIntegral22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithIntegral.h.func.html b/coverage/gridtools/ActionWithIntegral.h.func.html
new file mode 100644
index 0000000000..f32d43e43e
--- /dev/null
+++ b/coverage/gridtools/ActionWithIntegral.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithIntegral.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithIntegral.h<span style="font-size: 80%;"> (<a href="ActionWithIntegral.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithIntegral.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.h.gcov.html#41">_ZN4PLMD9gridtools18ActionWithIntegral10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithIntegral.h.gcov.html#51">_ZN4PLMD9gridtools18ActionWithIntegral22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ActionWithIntegral.h.gcov.html b/coverage/gridtools/ActionWithIntegral.h.gcov.html
new file mode 100644
index 0000000000..497999972a
--- /dev/null
+++ b/coverage/gridtools/ActionWithIntegral.h.gcov.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ActionWithIntegral.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ActionWithIntegral.h<span style="font-size: 80%;"> (source / <a href="ActionWithIntegral.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_ActionWithIntegral_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_ActionWithIntegral_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionWithInputGrid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace gridtools {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class ActionWithIntegral : public ActionWithInputGrid {</a>
+<a name="31"><span class="lineNum">      31 </span>            : private:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   double volume;</a>
+<a name="33"><span class="lineNum">      33 </span>            :   std::vector&lt;double&gt; forcesToApply;</a>
+<a name="34"><span class="lineNum">      34 </span>            : protected:</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// Get the volume of a grid box</a>
+<a name="36"><span class="lineNum">      36 </span>            :   double getVolume() const ;</a>
+<a name="37"><span class="lineNum">      37 </span>            : public:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="39"><span class="lineNum">      39 </span>            :   explicit ActionWithIntegral(const ActionOptions&amp;ao);</a>
+<a name="40"><span class="lineNum">      40 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void turnOnDerivatives() override;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Unless I am mistaken an integral should never be a periodic function</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   void apply() override;</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : inline</a>
+<a name="48"><span class="lineNum">      48 </span>            : double ActionWithIntegral::getVolume() const {</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      11410 :   return volume;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : inline</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        102 : unsigned ActionWithIntegral::getNumberOfDerivatives() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        102 :   return ingrid-&gt;getNumberOfPoints();</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+<a name="59"><span class="lineNum">      59 </span>            : #endif</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/AverageOnGrid.cpp.func-sort-c.html b/coverage/gridtools/AverageOnGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..13b3521fbb
--- /dev/null
+++ b/coverage/gridtools/AverageOnGrid.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/AverageOnGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - AverageOnGrid.cpp<span style="font-size: 80%;"> (<a href="AverageOnGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AverageOnGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#29">_ZN4PLMD9gridtools13AverageOnGridC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#25">_ZN4PLMD9gridtools13AverageOnGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#49">_ZNK4PLMD9gridtools13AverageOnGrid14getGridElementERKjS3_</a></td>
+              <td class="coverFnHi">361766</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#41">_ZNK4PLMD9gridtools13AverageOnGrid10accumulateERKjRKdS5_RKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnHi">11825111</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/AverageOnGrid.cpp.func.html b/coverage/gridtools/AverageOnGrid.cpp.func.html
new file mode 100644
index 0000000000..68037e4aee
--- /dev/null
+++ b/coverage/gridtools/AverageOnGrid.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/AverageOnGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - AverageOnGrid.cpp<span style="font-size: 80%;"> (<a href="AverageOnGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AverageOnGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#25">_ZN4PLMD9gridtools13AverageOnGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#29">_ZN4PLMD9gridtools13AverageOnGridC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#41">_ZNK4PLMD9gridtools13AverageOnGrid10accumulateERKjRKdS5_RKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnHi">11825111</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.cpp.gcov.html#49">_ZNK4PLMD9gridtools13AverageOnGrid14getGridElementERKjS3_</a></td>
+              <td class="coverFnHi">361766</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/AverageOnGrid.cpp.gcov.html b/coverage/gridtools/AverageOnGrid.cpp.gcov.html
new file mode 100644
index 0000000000..23f1b3cb0b
--- /dev/null
+++ b/coverage/gridtools/AverageOnGrid.cpp.gcov.html
@@ -0,0 +1,145 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/AverageOnGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - AverageOnGrid.cpp<span style="font-size: 80%;"> (source / <a href="AverageOnGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AverageOnGrid.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace gridtools {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         65 : void AverageOnGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         65 :   HistogramOnGrid::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         65 : }</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          8 : AverageOnGrid::AverageOnGrid( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          8 :   HistogramOnGrid(da)</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          8 :   arg_names.push_back( &quot;density&quot; );</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          8 :   if( !discrete ) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         22 :     for(unsigned i=0; i&lt;dimension; ++i) arg_names.push_back( &quot;ddensity_&quot; + arg_names[i] );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          8 :     nper += (dimension+1);</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   } else {</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :     nper += 1;</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   }</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          8 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">   11825111 : void AverageOnGrid::accumulate( const unsigned&amp; ipoint, const double&amp; weight, const double&amp; dens, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; buffer ) const {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">   11825111 :   buffer[bufstart+nper*ipoint] += weight*dens; buffer[ bufstart+nper*(ipoint+1) - (dimension+1) ] += dens;</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">   11825111 :   if( der.size()&gt;0 ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">   47300036 :     for(unsigned j=0; j&lt;dimension; ++j) buffer[ bufstart+nper*ipoint + 1 + j ] += weight*der[j];</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">   47300036 :     for(unsigned j=0; j&lt;dimension; ++j) buffer[ bufstart+nper*(ipoint+1) - dimension + j ] += der[j];</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">   11825111 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     361766 : double AverageOnGrid::getGridElement( const unsigned&amp; ipoint, const unsigned&amp; jelement ) const {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     361766 :   if( noAverage() ) return getDataElement( nper*ipoint + jelement);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">     360566 :   if( jelement&gt;=(nper-(dimension+1)) ) return getDataElement( nper*ipoint + jelement );</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     360066 :   if( noderiv ) return getDataElement( nper*ipoint+jelement ) / getDataElement( nper*(1+ipoint) - 1);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   double rdenom = 1.0;</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">     360066 :   if( std::fabs(getDataElement( nper*(ipoint+1) -(dimension+1) ))&gt;epsilon ) rdenom = 1. / getDataElement( nper*(ipoint+1) - (dimension+1) );</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">     360066 :   unsigned jderiv = jelement%(1+dimension);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     360066 :   if( jderiv==0 ) return rdenom*getDataElement( nper*ipoint+jelement );</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">     203130 :   unsigned jfloor = std::floor( jelement / (1+dimension) );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     203130 :   return rdenom*getDataElement( nper*ipoint+jelement ) - rdenom*rdenom*getDataElement(nper*ipoint+jfloor)*getDataElement(nper*(ipoint+1) - (dimension+1) + jderiv);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/AverageOnGrid.h.func-sort-c.html b/coverage/gridtools/AverageOnGrid.h.func-sort-c.html
new file mode 100644
index 0000000000..14d329336a
--- /dev/null
+++ b/coverage/gridtools/AverageOnGrid.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/AverageOnGrid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - AverageOnGrid.h<span style="font-size: 80%;"> (<a href="AverageOnGrid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AverageOnGrid.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.h.gcov.html#36">_ZN4PLMD9gridtools13AverageOnGrid14getFinalForcesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.h.gcov.html#33">_ZNK4PLMD9gridtools13AverageOnGrid15accumulateForceERKjRKdRKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.h.gcov.html#40">_ZNK4PLMD9gridtools13AverageOnGrid21getNumberOfComponentsEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/AverageOnGrid.h.func.html b/coverage/gridtools/AverageOnGrid.h.func.html
new file mode 100644
index 0000000000..0261552f79
--- /dev/null
+++ b/coverage/gridtools/AverageOnGrid.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/AverageOnGrid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - AverageOnGrid.h<span style="font-size: 80%;"> (<a href="AverageOnGrid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AverageOnGrid.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.h.gcov.html#36">_ZN4PLMD9gridtools13AverageOnGrid14getFinalForcesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.h.gcov.html#33">_ZNK4PLMD9gridtools13AverageOnGrid15accumulateForceERKjRKdRKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AverageOnGrid.h.gcov.html#40">_ZNK4PLMD9gridtools13AverageOnGrid21getNumberOfComponentsEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/AverageOnGrid.h.gcov.html b/coverage/gridtools/AverageOnGrid.h.gcov.html
new file mode 100644
index 0000000000..aa9a0ab527
--- /dev/null
+++ b/coverage/gridtools/AverageOnGrid.h.gcov.html
@@ -0,0 +1,125 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/AverageOnGrid.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - AverageOnGrid.h<span style="font-size: 80%;"> (source / <a href="AverageOnGrid.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">33.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_AverageOnGrid_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_AverageOnGrid_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;HistogramOnGrid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace gridtools {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class AverageOnGrid : public HistogramOnGrid {</a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   explicit AverageOnGrid( const vesselbase::VesselOptions&amp; da );</a>
+<a name="34"><span class="lineNum">      34 </span>            :   void accumulate( const unsigned&amp; ipoint, const double&amp; weight, const double&amp; dens, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; buffer ) const override;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 :   void accumulateForce( const unsigned&amp; ipoint, const double&amp; weight, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; intforce ) const override { plumed_error(); }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   double getGridElement( const unsigned&amp; ipoint, const unsigned&amp; jelement ) const override;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   unsigned getNumberOfComponents() const override;</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   void getFinalForces( const std::vector&lt;double&gt;&amp; buffer, std::vector&lt;double&gt;&amp; finalForces ) override { plumed_error(); }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : };</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : inline</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          7 : unsigned AverageOnGrid::getNumberOfComponents() const {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          7 :   if( noderiv ) return nper - 1;</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          7 :   return nper / ( dimension + 1 ) - 1;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : }</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ContourFindingBase.cpp.func-sort-c.html b/coverage/gridtools/ContourFindingBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f98d4cb4c0
--- /dev/null
+++ b/coverage/gridtools/ContourFindingBase.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ContourFindingBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ContourFindingBase.cpp<span style="font-size: 80%;"> (<a href="ContourFindingBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ContourFindingBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.cpp.gcov.html#31">_ZN4PLMD9gridtools18ContourFindingBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.cpp.gcov.html#31">_ZN4PLMD9gridtools18ContourFindingBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.cpp.gcov.html#25">_ZN4PLMD9gridtools18ContourFindingBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ContourFindingBase.cpp.func.html b/coverage/gridtools/ContourFindingBase.cpp.func.html
new file mode 100644
index 0000000000..2c13394d7b
--- /dev/null
+++ b/coverage/gridtools/ContourFindingBase.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ContourFindingBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ContourFindingBase.cpp<span style="font-size: 80%;"> (<a href="ContourFindingBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ContourFindingBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.cpp.gcov.html#25">_ZN4PLMD9gridtools18ContourFindingBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.cpp.gcov.html#31">_ZN4PLMD9gridtools18ContourFindingBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.cpp.gcov.html#31">_ZN4PLMD9gridtools18ContourFindingBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ContourFindingBase.cpp.gcov.html b/coverage/gridtools/ContourFindingBase.cpp.gcov.html
new file mode 100644
index 0000000000..858d98fcff
--- /dev/null
+++ b/coverage/gridtools/ContourFindingBase.cpp.gcov.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ContourFindingBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ContourFindingBase.cpp<span style="font-size: 80%;"> (source / <a href="ContourFindingBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ContourFindingBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace gridtools {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">          9 : void ContourFindingBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          9 :   ActionWithInputGrid::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         18 :   keys.add(&quot;compulsory&quot;,&quot;CONTOUR&quot;,&quot;the value we would like to draw the contour at in the space&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         18 :   keys.remove(&quot;KERNEL&quot;); keys.remove(&quot;BANDWIDTH&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          9 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          3 : ContourFindingBase::ContourFindingBase(const ActionOptions&amp;ao):</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   Action(ao),</a>
+<a name="35"><span class="lineNum">      35 </span>            :   ActionWithInputGrid(ao),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          3 :   mymin(this)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">          3 :   if( ingrid-&gt;noDerivatives() ) error(&quot;cannot find contours if input grid has no derivatives&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          3 :   parse(&quot;CONTOUR&quot;,contour);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          3 :   log.printf(&quot;  calculating dividing surface along which function equals %f \n&quot;, contour);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          3 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : }</a>
+<a name="44"><span class="lineNum">      44 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ContourFindingBase.h.func-sort-c.html b/coverage/gridtools/ContourFindingBase.h.func-sort-c.html
new file mode 100644
index 0000000000..3723559369
--- /dev/null
+++ b/coverage/gridtools/ContourFindingBase.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ContourFindingBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ContourFindingBase.h<span style="font-size: 80%;"> (<a href="ContourFindingBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ContourFindingBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.h.gcov.html#46">_ZN4PLMD9gridtools18ContourFindingBase10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.h.gcov.html#44">_ZN4PLMD9gridtools18ContourFindingBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.h.gcov.html#55">_ZNK4PLMD9gridtools18ContourFindingBase24getDifferenceFromContourERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">8245</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ContourFindingBase.h.func.html b/coverage/gridtools/ContourFindingBase.h.func.html
new file mode 100644
index 0000000000..ca69993310
--- /dev/null
+++ b/coverage/gridtools/ContourFindingBase.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ContourFindingBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ContourFindingBase.h<span style="font-size: 80%;"> (<a href="ContourFindingBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ContourFindingBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.h.gcov.html#46">_ZN4PLMD9gridtools18ContourFindingBase10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.h.gcov.html#44">_ZN4PLMD9gridtools18ContourFindingBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ContourFindingBase.h.gcov.html#55">_ZNK4PLMD9gridtools18ContourFindingBase24getDifferenceFromContourERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">8245</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ContourFindingBase.h.gcov.html b/coverage/gridtools/ContourFindingBase.h.gcov.html
new file mode 100644
index 0000000000..26583eda59
--- /dev/null
+++ b/coverage/gridtools/ContourFindingBase.h.gcov.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ContourFindingBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ContourFindingBase.h<span style="font-size: 80%;"> (source / <a href="ContourFindingBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_ContourFindingBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_ContourFindingBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionWithInputGrid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/RootFindingBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace gridtools {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class ContourFindingBase : public ActionWithInputGrid {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// This is the object that does the root finding</a>
+<a name="34"><span class="lineNum">      34 </span>            :   RootFindingBase&lt;ContourFindingBase&gt; mymin;</a>
+<a name="35"><span class="lineNum">      35 </span>            : protected:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Where you would like to find the contour</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double contour;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Find a contour along line specified by direction</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void findContour( const std::vector&lt;double&gt;&amp; direction, std::vector&lt;double&gt;&amp; point ) const ;</a>
+<a name="40"><span class="lineNum">      40 </span>            : public:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="42"><span class="lineNum">      42 </span>            :   explicit ContourFindingBase(const ActionOptions&amp;ao);</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Get the contour value</a>
+<a name="44"><span class="lineNum">      44 </span>            :   double getDifferenceFromContour( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der ) const ;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Overwrite not needed stuff</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         32 :   unsigned getNumberOfDerivatives() override { return 0; }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : /// This is not periodic</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : };</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : inline</a>
+<a name="52"><span class="lineNum">      52 </span>            : void ContourFindingBase::findContour( const std::vector&lt;double&gt;&amp; direction, std::vector&lt;double&gt;&amp; point ) const {</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       1242 :   mymin.linesearch( direction, point, &amp;ContourFindingBase::getDifferenceFromContour );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1242 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : inline</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       8245 : double ContourFindingBase::getDifferenceFromContour( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der ) const {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       8345 :   return getFunctionValueAndDerivatives( x, der ) - contour;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ConvertToFES.cpp.func-sort-c.html b/coverage/gridtools/ConvertToFES.cpp.func-sort-c.html
new file mode 100644
index 0000000000..30632d9b55
--- /dev/null
+++ b/coverage/gridtools/ConvertToFES.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ConvertToFES.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ConvertToFES.cpp<span style="font-size: 80%;"> (<a href="ConvertToFES.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ConvertToFES.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#74">_ZN4PLMD9gridtools12ConvertToFES10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#89">_ZN4PLMD9gridtools12ConvertToFESC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#70">_ZN4PLMD9gridtools12ConvertToFES7prepareEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#140">_ZN4PLMD9gridtools12ConvertToFES12runFinalJobsEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#89">_ZN4PLMD9gridtools12ConvertToFESC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#79">_ZN4PLMD9gridtools12_GLOBAL__N_124ConvertToFESRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#69">_ZNK4PLMD9gridtools12ConvertToFES19ignoreNormalizationEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#81">_ZN4PLMD9gridtools12ConvertToFES16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#128">_ZN4PLMD9gridtools12ConvertToFES18finishComputationsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#71">_ZN4PLMD9gridtools12ConvertToFES19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#116">_ZNK4PLMD9gridtools12ConvertToFES21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">92</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#75">_ZNK4PLMD9gridtools12ConvertToFES6onStepEv</a></td>
+              <td class="coverFnHi">2234</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#79">_ZN4PLMD9gridtools12_GLOBAL__N_124ConvertToFESRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#79">_ZN4PLMD9gridtools12_GLOBAL__N_124ConvertToFESRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#121">_ZNK4PLMD9gridtools12ConvertToFES7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">14199</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ConvertToFES.cpp.func.html b/coverage/gridtools/ConvertToFES.cpp.func.html
new file mode 100644
index 0000000000..1e96cc345c
--- /dev/null
+++ b/coverage/gridtools/ConvertToFES.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ConvertToFES.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ConvertToFES.cpp<span style="font-size: 80%;"> (<a href="ConvertToFES.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ConvertToFES.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#74">_ZN4PLMD9gridtools12ConvertToFES10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#140">_ZN4PLMD9gridtools12ConvertToFES12runFinalJobsEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#81">_ZN4PLMD9gridtools12ConvertToFES16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#128">_ZN4PLMD9gridtools12ConvertToFES18finishComputationsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#71">_ZN4PLMD9gridtools12ConvertToFES19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#70">_ZN4PLMD9gridtools12ConvertToFES7prepareEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#89">_ZN4PLMD9gridtools12ConvertToFESC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#89">_ZN4PLMD9gridtools12ConvertToFESC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#79">_ZN4PLMD9gridtools12_GLOBAL__N_124ConvertToFESRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#79">_ZN4PLMD9gridtools12_GLOBAL__N_124ConvertToFESRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#79">_ZN4PLMD9gridtools12_GLOBAL__N_124ConvertToFESRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#69">_ZNK4PLMD9gridtools12ConvertToFES19ignoreNormalizationEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#116">_ZNK4PLMD9gridtools12ConvertToFES21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">92</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#75">_ZNK4PLMD9gridtools12ConvertToFES6onStepEv</a></td>
+              <td class="coverFnHi">2234</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConvertToFES.cpp.gcov.html#121">_ZNK4PLMD9gridtools12ConvertToFES7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">14199</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/ConvertToFES.cpp.gcov.html b/coverage/gridtools/ConvertToFES.cpp.gcov.html
new file mode 100644
index 0000000000..4b57f82ab8
--- /dev/null
+++ b/coverage/gridtools/ConvertToFES.cpp.gcov.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/ConvertToFES.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - ConvertToFES.cpp<span style="font-size: 80%;"> (source / <a href="ConvertToFES.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionWithInputGrid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC GRIDANALYSIS CONVERT_TO_FES</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Convert a histogram, H(x), to a free energy surface using F(x) = -k_B T ln H(x).</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : This action allows you to take a free energy surface that was calculated using the \ref HISTOGRAM</a>
+<a name="32"><span class="lineNum">      32 </span>            : action and to convert it to a free energy surface.  This transformation performed by doing:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : F(x) = -k_B T \ln H(x)</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The free energy calculated on a grid is output by this action and can be printed using \ref DUMPGRID</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : This is a typical example showing how CONVERT_TO_FES might be used when post processing a trajectory.</a>
+<a name="43"><span class="lineNum">      43 </span>            : The input below calculates the free energy as a function of the distance between atom 1 and atom 2.</a>
+<a name="44"><span class="lineNum">      44 </span>            : This is done by accumulating a histogram as a function of this distance using kernel density estimation</a>
+<a name="45"><span class="lineNum">      45 </span>            : and the HISTOGRAM action.  All the data within this trajectory is used in the construction of this</a>
+<a name="46"><span class="lineNum">      46 </span>            : HISTOGRAM.  Finally, once all the data has been read in, the histogram is converted to a free energy</a>
+<a name="47"><span class="lineNum">      47 </span>            : using the formula above and the free energy is output to a file called fes.dat</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : x: DISTANCE ATOMS=1,2</a>
+<a name="51"><span class="lineNum">      51 </span>            : hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1</a>
+<a name="52"><span class="lineNum">      52 </span>            : ff: CONVERT_TO_FES GRID=hA1 TEMP=300</a>
+<a name="53"><span class="lineNum">      53 </span>            : DUMPGRID GRID=ff FILE=fes.dat</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endplumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : */</a>
+<a name="57"><span class="lineNum">      57 </span>            : //+ENDPLUMEDOC</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : namespace PLMD {</a>
+<a name="60"><span class="lineNum">      60 </span>            : namespace gridtools {</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : class ConvertToFES : public ActionWithInputGrid {</a>
+<a name="63"><span class="lineNum">      63 </span>            : private:</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double simtemp;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   bool activated;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   bool mintozero;</a>
+<a name="67"><span class="lineNum">      67 </span>            : public:</a>
+<a name="68"><span class="lineNum">      68 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="69"><span class="lineNum">      69 </span>            :   explicit ConvertToFES(const ActionOptions&amp;ao);</a>
+<a name="70"><span class="lineNum">      70 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         15 :   bool ignoreNormalization() const override { return true; }</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         12 :   void prepare() override { activated=true; }</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         23 :   void prepareForAveraging() override { ActionWithInputGrid::prepareForAveraging(); activated=false; }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   void compute( const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void finishComputations( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       2234 :   bool onStep() const override { return activated; }</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   void runFinalJobs() override;</a>
+<a name="79"><span class="lineNum">      79 </span>            : };</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      12534 : PLUMED_REGISTER_ACTION(ConvertToFES,&quot;CONVERT_TO_FES&quot;)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         17 : void ConvertToFES::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         17 :   ActionWithInputGrid::registerKeywords( keys );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         34 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the temperature at which you are operating&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         34 :   keys.addFlag(&quot;MINTOZERO&quot;,false,&quot;set the minimum in the free energy to be equal to zero&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         51 :   keys.remove(&quot;STRIDE&quot;); keys.remove(&quot;KERNEL&quot;); keys.remove(&quot;BANDWIDTH&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         51 :   keys.remove(&quot;LOGWEIGHTS&quot;); keys.remove(&quot;CLEAR&quot;); keys.remove(&quot;NORMALIZATION&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         17 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         15 : ConvertToFES::ConvertToFES(const ActionOptions&amp;ao):</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   Action(ao),</a>
+<a name="93"><span class="lineNum">      93 </span>            :   ActionWithInputGrid(ao),</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         15 :   activated(false)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : {</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         15 :   plumed_assert( ingrid-&gt;getNumberOfComponents()==1 );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   // Create a grid</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         30 :   auto grid=createGrid( &quot;grid&quot;, &quot;COMPONENTS=&quot; + getLabel() + &quot; &quot; + ingrid-&gt;getInputString() );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         15 :   if( ingrid-&gt;noDerivatives() ) grid-&gt;setNoDerivatives();</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;double&gt; fspacing;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         15 :   grid-&gt;setBounds( ingrid-&gt;getMin(), ingrid-&gt;getMax(), ingrid-&gt;getNbin(), fspacing);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         15 :   setAveragingAction( std::move(grid), true );</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         30 :   simtemp=0.; parse(&quot;TEMP&quot;,simtemp); parseFlag(&quot;MINTOZERO&quot;,mintozero);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         15 :   if(simtemp&gt;0) simtemp*=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   else simtemp=plumed.getAtoms().getKbT();</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         15 :   if( simtemp==0 ) error(&quot;TEMP not set - use keyword TEMP&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Now create task list</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       8486 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) addTaskToList(i);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   // And activate all tasks</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         15 :   deactivateAllTasks();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       8486 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) taskFlags[i]=1;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         15 :   lockContributors();</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         15 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         92 : unsigned ConvertToFES::getNumberOfQuantities() const {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         92 :   if( mygrid-&gt;noDerivatives() ) return 2;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         64 :   return 2 + mygrid-&gt;getDimension();</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      14199 : void ConvertToFES::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      14199 :   double val=getFunctionValue( current ); myvals.setValue(1, -simtemp*std::log(val) );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      14199 :   if( !mygrid-&gt;noDerivatives() &amp;&amp; val&gt;0 ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      36998 :     for(unsigned i=0; i&lt;mygrid-&gt;getDimension(); ++i) myvals.setValue( 2+i, -(simtemp/val)*ingrid-&gt;getGridElement(current,i+1) );</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      14199 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         23 : void ConvertToFES::finishComputations( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         23 :   ActionWithVessel::finishComputations( buffer );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         23 :   if(!mintozero) return;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          2 :   double optval = mygrid-&gt;getGridElement( 0, 0 );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       2602 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       2600 :     double tval = mygrid-&gt;getGridElement( i, 0 );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       2600 :     if( tval&lt;optval || std::isnan(optval) ) { optval=tval; }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       2602 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) mygrid-&gt;addToGridElement( i, 0, -optval );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         15 : void ConvertToFES::runFinalJobs() {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         15 :   activated=true; update();</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         15 : }</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/DumpCube.cpp.func-sort-c.html b/coverage/gridtools/DumpCube.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5dec2cffe4
--- /dev/null
+++ b/coverage/gridtools/DumpCube.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/DumpCube.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - DumpCube.cpp<span style="font-size: 80%;"> (<a href="DumpCube.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpCube.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#78">_ZN4PLMD9gridtools8DumpCubeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#71">_ZN4PLMD9gridtools12_GLOBAL__N_120DumpCubeRegisterMe736createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#78">_ZN4PLMD9gridtools8DumpCubeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#73">_ZN4PLMD9gridtools8DumpCube16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#98">_ZNK4PLMD9gridtools8DumpCube9printGridERNS_5OFileE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#71">_ZN4PLMD9gridtools12_GLOBAL__N_120DumpCubeRegisterMe73C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#71">_ZN4PLMD9gridtools12_GLOBAL__N_120DumpCubeRegisterMe73D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/DumpCube.cpp.func.html b/coverage/gridtools/DumpCube.cpp.func.html
new file mode 100644
index 0000000000..4e447d3d6f
--- /dev/null
+++ b/coverage/gridtools/DumpCube.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/DumpCube.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - DumpCube.cpp<span style="font-size: 80%;"> (<a href="DumpCube.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpCube.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#71">_ZN4PLMD9gridtools12_GLOBAL__N_120DumpCubeRegisterMe736createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#71">_ZN4PLMD9gridtools12_GLOBAL__N_120DumpCubeRegisterMe73C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#71">_ZN4PLMD9gridtools12_GLOBAL__N_120DumpCubeRegisterMe73D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#73">_ZN4PLMD9gridtools8DumpCube16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#78">_ZN4PLMD9gridtools8DumpCubeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#78">_ZN4PLMD9gridtools8DumpCubeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpCube.cpp.gcov.html#98">_ZNK4PLMD9gridtools8DumpCube9printGridERNS_5OFileE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/DumpCube.cpp.gcov.html b/coverage/gridtools/DumpCube.cpp.gcov.html
new file mode 100644
index 0000000000..8b81d47248
--- /dev/null
+++ b/coverage/gridtools/DumpCube.cpp.gcov.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/DumpCube.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - DumpCube.cpp<span style="font-size: 80%;"> (source / <a href="DumpCube.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;GridPrintingBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC GRIDANALYSIS DUMPCUBE</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Output a three dimensional grid using the Gaussian cube file format.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : Suppose you have calculated the value of a function on a three dimensional grid.</a>
+<a name="31"><span class="lineNum">      31 </span>            : This function might be a \ref HISTOGRAM or it might be a free energy energy surface</a>
+<a name="32"><span class="lineNum">      32 </span>            : that was calculated from this histogram by using \ref CONVERT_TO_FES.  Alternatively,</a>
+<a name="33"><span class="lineNum">      33 </span>            : your function might be a phase-field that was calculated using \ref MULTICOLVARDENS.</a>
+<a name="34"><span class="lineNum">      34 </span>            : Whatever the function is, however, you obviously cannot show it using a typical contour</a>
+<a name="35"><span class="lineNum">      35 </span>            : plotting program such as gnuplot as you have three input variables.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : Tools like VMD have nice features for plotting these types of three dimensional functions</a>
+<a name="38"><span class="lineNum">      38 </span>            : but typically you are required to use a Gaussian cube file format to input the data.  This</a>
+<a name="39"><span class="lineNum">      39 </span>            : action thus allows you to output a function evaluated on a grid to a Gaussian cube file format.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The input below can be used to post process a trajectory.  A histogram as a function of the distance</a>
+<a name="44"><span class="lineNum">      44 </span>            : between atoms 1 and 2, the distance between atom 1 and 3 and the angle between the vector connecting atoms 1 and</a>
+<a name="45"><span class="lineNum">      45 </span>            : 2 and 1 and 3 is computed using kernel density estimation.  Once all the data contained in the trajectory has been read in and</a>
+<a name="46"><span class="lineNum">      46 </span>            : all the kernels have been added the resulting histogram is output to a file called histoA1.cube.  This file has the</a>
+<a name="47"><span class="lineNum">      47 </span>            : Gaussian cube file format.  The histogram can thus be visualized using tools such as VMD.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : x1: DISTANCE ATOMS=1,2</a>
+<a name="51"><span class="lineNum">      51 </span>            : x2: DISTANCE ATOMS=1,3</a>
+<a name="52"><span class="lineNum">      52 </span>            : x3: ANGLE ATOMS=1,2,3</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : hA1: HISTOGRAM ARG=x1,x2,x3 GRID_MIN=0.0,0.0,0.0 GRID_MAX=3.0,3.0,3.0 GRID_BIN=10,10,10 BANDWIDTH=1.0,1.0,1.0</a>
+<a name="55"><span class="lineNum">      55 </span>            : DUMPCUBE GRID=hA1 FILE=histoA1.cube</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace PLMD {</a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace gridtools {</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : class DumpCube : public GridPrintingBase {</a>
+<a name="65"><span class="lineNum">      65 </span>            : private:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   unsigned mycomp;</a>
+<a name="67"><span class="lineNum">      67 </span>            : public:</a>
+<a name="68"><span class="lineNum">      68 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="69"><span class="lineNum">      69 </span>            :   explicit DumpCube(const ActionOptions&amp;ao);</a>
+<a name="70"><span class="lineNum">      70 </span>            :   void printGrid( OFile&amp; ofile ) const override;</a>
+<a name="71"><span class="lineNum">      71 </span>            : };</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(DumpCube,&quot;DUMPCUBE&quot;)</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          8 : void DumpCube::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          8 :   GridPrintingBase::registerKeywords( keys );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;COMPONENT&quot;,&quot;if your input is a vector field use this to specify the component of the input vector field for which you wish to output&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          8 : }</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          6 : DumpCube::DumpCube(const ActionOptions&amp;ao):</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   Action(ao),</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          6 :   GridPrintingBase(ao)</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :   fmt = fmt + &quot; &quot;;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         12 :   if( ingrid-&gt;getType()!=&quot;flat&quot; ) error(&quot;cannot dump grid of type &quot; + ingrid-&gt;getType() + &quot; using DUMPCUBE&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          6 :   if( ingrid-&gt;getDimension()!=3 ) error(&quot;cannot print cube file if grid does not contain three dimensional data&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          6 :   if( ingrid-&gt;getNumberOfComponents()==1 ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          6 :     mycomp=0;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   } else {</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :     int tcomp=-1; parse(&quot;COMPONENT&quot;,tcomp);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     if( tcomp&lt;0 ) error(&quot;component of vector field was not specified - use COMPONENT keyword&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     mycomp=tcomp*(1+ingrid-&gt;getDimension()); if( ingrid-&gt;noDerivatives() ) mycomp=tcomp;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     log.printf(&quot;  using %dth component of grid \n&quot;,tcomp );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   checkRead();</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          8 : void DumpCube::printGrid( OFile&amp; ofile ) const {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          8 :   double lunit = ingrid-&gt;getCubeUnits();</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          8 :   ofile.printf(&quot;PLUMED CUBE FILE\n&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          8 :   ofile.printf(&quot;OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   // Number of atoms followed by position of origin (origin set so that center of grid is in center of cell)</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         16 :   std::string ostr = &quot;%d &quot; + fmt + fmt + fmt + &quot;\n&quot;;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          8 :   ofile.printf(ostr.c_str(),1,-0.5*lunit*ingrid-&gt;getGridExtent(0),-0.5*lunit*ingrid-&gt;getGridExtent(1),-0.5*lunit*ingrid-&gt;getGridExtent(2));</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          8 :   ofile.printf(ostr.c_str(),ingrid-&gt;getNbin()[0],lunit*ingrid-&gt;getGridSpacing()[0],0.0,0.0);  // Number of bins in each direction followed by</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          8 :   ofile.printf(ostr.c_str(),ingrid-&gt;getNbin()[1],0.0,lunit*ingrid-&gt;getGridSpacing()[1],0.0);  // shape of voxel</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         16 :   ofile.printf(ostr.c_str(),ingrid-&gt;getNbin()[2],0.0,0.0,lunit*ingrid-&gt;getGridSpacing()[2]);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          8 :   ofile.printf(ostr.c_str(),1,0.0,0.0,0.0); // Fake atom otherwise VMD doesn't work</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 :   std::vector&lt;unsigned&gt; pp(3); std::vector&lt;unsigned&gt; nbin( ingrid-&gt;getNbin() );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        112 :   for(pp[0]=0; pp[0]&lt;nbin[0]; ++pp[0]) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1800 :     for(pp[1]=0; pp[1]&lt;nbin[1]; ++pp[1]) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      40184 :       for(pp[2]=0; pp[2]&lt;nbin[2]; ++pp[2]) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      38488 :         ofile.printf(fmt.c_str(), ingrid-&gt;getGridElement( ingrid-&gt;getIndex(pp), mycomp ) );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      38488 :         if(pp[2]%6==5) ofile.printf(&quot;\n&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :       }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1696 :       ofile.printf(&quot;\n&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     }</a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          8 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/DumpGrid.cpp.func-sort-c.html b/coverage/gridtools/DumpGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..482d79c177
--- /dev/null
+++ b/coverage/gridtools/DumpGrid.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/DumpGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - DumpGrid.cpp<span style="font-size: 80%;"> (<a href="DumpGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#153">_ZN4PLMD9gridtools8DumpGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#147">_ZN4PLMD9gridtools12_GLOBAL__N_121DumpGridRegisterMe1496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#153">_ZN4PLMD9gridtools8DumpGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#149">_ZN4PLMD9gridtools8DumpGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">51</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#161">_ZNK4PLMD9gridtools8DumpGrid9printGridERNS_5OFileE</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#147">_ZN4PLMD9gridtools12_GLOBAL__N_121DumpGridRegisterMe149C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#147">_ZN4PLMD9gridtools12_GLOBAL__N_121DumpGridRegisterMe149D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/DumpGrid.cpp.func.html b/coverage/gridtools/DumpGrid.cpp.func.html
new file mode 100644
index 0000000000..faae84308d
--- /dev/null
+++ b/coverage/gridtools/DumpGrid.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/DumpGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - DumpGrid.cpp<span style="font-size: 80%;"> (<a href="DumpGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#147">_ZN4PLMD9gridtools12_GLOBAL__N_121DumpGridRegisterMe1496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#147">_ZN4PLMD9gridtools12_GLOBAL__N_121DumpGridRegisterMe149C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#147">_ZN4PLMD9gridtools12_GLOBAL__N_121DumpGridRegisterMe149D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#149">_ZN4PLMD9gridtools8DumpGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">51</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#153">_ZN4PLMD9gridtools8DumpGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#153">_ZN4PLMD9gridtools8DumpGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpGrid.cpp.gcov.html#161">_ZNK4PLMD9gridtools8DumpGrid9printGridERNS_5OFileE</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/DumpGrid.cpp.gcov.html b/coverage/gridtools/DumpGrid.cpp.gcov.html
new file mode 100644
index 0000000000..2ca95cb35d
--- /dev/null
+++ b/coverage/gridtools/DumpGrid.cpp.gcov.html
@@ -0,0 +1,272 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/DumpGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - DumpGrid.cpp<span style="font-size: 80%;"> (source / <a href="DumpGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;GridPrintingBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace gridtools {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC GRIDANALYSIS DUMPGRID</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Output the function on the grid to a file with the PLUMED grid format.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : PLUMED provides a number of actions that calculate the values of functions on grids.</a>
+<a name="34"><span class="lineNum">      34 </span>            : For instance, whenever you calculate a free energy as a function of a collective variable using</a>
+<a name="35"><span class="lineNum">      35 </span>            : \ref HISTOGRAM and \ref CONVERT_TO_FES you will generally want to output the value of the free energy at a number of points on a</a>
+<a name="36"><span class="lineNum">      36 </span>            : discrete grid that covers the CV space uniformly.  Alternatively you may want to calculate</a>
+<a name="37"><span class="lineNum">      37 </span>            : what value some symmetry function takes at different points inside your simulation cell using \ref MULTICOLVARDENS.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : This action allows you to output these functions calculated on a grid using a format that can be read in using gnuplot</a>
+<a name="40"><span class="lineNum">      40 </span>            : and other such plotting programs.  The file output using this action will have a header that contains some essential</a>
+<a name="41"><span class="lineNum">      41 </span>            : information about the function plotted and that looks something like this:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : #! FIELDS x y hA1 dhA1_x dhA1_x</a>
+<a name="45"><span class="lineNum">      45 </span>            : #! SET normalisation    2.0000</a>
+<a name="46"><span class="lineNum">      46 </span>            : #! SET min_x 0.0</a>
+<a name="47"><span class="lineNum">      47 </span>            : #! SET max_x 3.0</a>
+<a name="48"><span class="lineNum">      48 </span>            : #! SET nbins_x  100</a>
+<a name="49"><span class="lineNum">      49 </span>            : #! SET periodic_x false</a>
+<a name="50"><span class="lineNum">      50 </span>            : #! SET min_y 0.0</a>
+<a name="51"><span class="lineNum">      51 </span>            : #! SET max_y 3.0</a>
+<a name="52"><span class="lineNum">      52 </span>            : #! SET nbins_y  100</a>
+<a name="53"><span class="lineNum">      53 </span>            : #! SET periodic_y false</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endverbatim</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The header shown here tells us that we have grid showing the values that a function with two arguments x and y</a>
+<a name="57"><span class="lineNum">      57 </span>            : takes at various points in our cell.  The lines beneath the first line then tell us a little bit about these two</a>
+<a name="58"><span class="lineNum">      58 </span>            : input arguments.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The remaining lines of the file give us information on the positions of our grid points and the value the function and</a>
+<a name="61"><span class="lineNum">      61 </span>            : its partial derivatives with respect to x and y.  If the header is as above a list of values of the function that have</a>
+<a name="62"><span class="lineNum">      62 </span>            : x=0 and 100 values of y between 0.0 and 3.0 will be provided.  This block of data will be followed with a blank line.</a>
+<a name="63"><span class="lineNum">      63 </span>            : There will then be a second block of values which will all have been evaluated the same value of x and all possible values</a>
+<a name="64"><span class="lineNum">      64 </span>            : for y.  This block is then followed by a blank line again and this pattern continues until all points of the grid have been covered.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \par Examples</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="69"><span class="lineNum">      69 </span>            : and outputs a continuous histogram as a function of them at the end of the simulation.</a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="72"><span class="lineNum">      72 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="73"><span class="lineNum">      73 </span>            : HISTOGRAM ...</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ARG=r1,r2</a>
+<a name="75"><span class="lineNum">      75 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="76"><span class="lineNum">      76 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="77"><span class="lineNum">      77 </span>            :   GRID_BIN=200,200</a>
+<a name="78"><span class="lineNum">      78 </span>            :   BANDWIDTH=0.05,0.05</a>
+<a name="79"><span class="lineNum">      79 </span>            :   LABEL=hh</a>
+<a name="80"><span class="lineNum">      80 </span>            : ... HISTOGRAM</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : DUMPGRID GRID=hh FILE=histo</a>
+<a name="83"><span class="lineNum">      83 </span>            : \endplumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="86"><span class="lineNum">      86 </span>            : and outputs a discrete histogram as a function of them at the end of the simulation.</a>
+<a name="87"><span class="lineNum">      87 </span>            : \plumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="89"><span class="lineNum">      89 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="90"><span class="lineNum">      90 </span>            : HISTOGRAM ...</a>
+<a name="91"><span class="lineNum">      91 </span>            :   ARG=r1,r2</a>
+<a name="92"><span class="lineNum">      92 </span>            :   KERNEL=DISCRETE</a>
+<a name="93"><span class="lineNum">      93 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="94"><span class="lineNum">      94 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="95"><span class="lineNum">      95 </span>            :   GRID_BIN=200,200</a>
+<a name="96"><span class="lineNum">      96 </span>            :   LABEL=hh</a>
+<a name="97"><span class="lineNum">      97 </span>            : ... HISTOGRAM</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : DUMPGRID GRID=hh FILE=histo</a>
+<a name="100"><span class="lineNum">     100 </span>            : \endplumedfile</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="103"><span class="lineNum">     103 </span>            : and outputs the histogram accumulated thus far every 100000 steps.</a>
+<a name="104"><span class="lineNum">     104 </span>            : \plumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="106"><span class="lineNum">     106 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="107"><span class="lineNum">     107 </span>            : HISTOGRAM ...</a>
+<a name="108"><span class="lineNum">     108 </span>            :   ARG=r1,r2</a>
+<a name="109"><span class="lineNum">     109 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="110"><span class="lineNum">     110 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="111"><span class="lineNum">     111 </span>            :   GRID_BIN=200,200</a>
+<a name="112"><span class="lineNum">     112 </span>            :   BANDWIDTH=0.05,0.05</a>
+<a name="113"><span class="lineNum">     113 </span>            :   LABEL=hh</a>
+<a name="114"><span class="lineNum">     114 </span>            : ... HISTOGRAM</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : DUMPGRID GRID=hh FILE=histo STRIDE=100000</a>
+<a name="117"><span class="lineNum">     117 </span>            : \endplumedfile</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : The following input monitors two torsional angles during a simulation</a>
+<a name="120"><span class="lineNum">     120 </span>            : and outputs a separate histogram for each 100000 steps worth of trajectory.</a>
+<a name="121"><span class="lineNum">     121 </span>            : Notice how the CLEAR keyword is used here and how it is not used in the</a>
+<a name="122"><span class="lineNum">     122 </span>            : previous example.</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : \plumedfile</a>
+<a name="125"><span class="lineNum">     125 </span>            : TORSION ATOMS=1,2,3,4 LABEL=r1</a>
+<a name="126"><span class="lineNum">     126 </span>            : TORSION ATOMS=2,3,4,5 LABEL=r2</a>
+<a name="127"><span class="lineNum">     127 </span>            : HISTOGRAM ...</a>
+<a name="128"><span class="lineNum">     128 </span>            :   ARG=r1,r2 CLEAR=100000</a>
+<a name="129"><span class="lineNum">     129 </span>            :   GRID_MIN=-3.14,-3.14</a>
+<a name="130"><span class="lineNum">     130 </span>            :   GRID_MAX=3.14,3.14</a>
+<a name="131"><span class="lineNum">     131 </span>            :   GRID_BIN=200,200</a>
+<a name="132"><span class="lineNum">     132 </span>            :   BANDWIDTH=0.05,0.05</a>
+<a name="133"><span class="lineNum">     133 </span>            :   LABEL=hh</a>
+<a name="134"><span class="lineNum">     134 </span>            : ... HISTOGRAM</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : DUMPGRID GRID=hh FILE=histo STRIDE=100000</a>
+<a name="137"><span class="lineNum">     137 </span>            : \endplumedfile</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : */</a>
+<a name="140"><span class="lineNum">     140 </span>            : //+ENDPLUMEDOC</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : class DumpGrid : public GridPrintingBase {</a>
+<a name="143"><span class="lineNum">     143 </span>            : public:</a>
+<a name="144"><span class="lineNum">     144 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="145"><span class="lineNum">     145 </span>            :   explicit DumpGrid(const ActionOptions&amp;ao);</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void printGrid( OFile&amp; ofile ) const override;</a>
+<a name="147"><span class="lineNum">     147 </span>            : };</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      12602 : PLUMED_REGISTER_ACTION(DumpGrid,&quot;DUMPGRID&quot;)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         51 : void DumpGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         51 :   GridPrintingBase::registerKeywords( keys );</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         51 : }</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         49 : DumpGrid::DumpGrid(const ActionOptions&amp;ao):</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   Action(ao),</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         49 :   GridPrintingBase(ao)</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : {</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         98 :   if( ingrid-&gt;getType()!=&quot;flat&quot; ) error(&quot;cannot dump grid of type &quot; + ingrid-&gt;getType() + &quot; using DUMPGRID&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         98 :   fmt = &quot; &quot; + fmt; checkRead();</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         49 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         60 : void DumpGrid::printGrid( OFile&amp; ofile ) const {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         60 :   ofile.addConstantField(&quot;normalisation&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        128 :   for(unsigned i=0; i&lt;ingrid-&gt;getDimension(); ++i) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        136 :     ofile.addConstantField(&quot;min_&quot; + ingrid-&gt;getComponentName(i) );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        136 :     ofile.addConstantField(&quot;max_&quot; + ingrid-&gt;getComponentName(i) );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        136 :     ofile.addConstantField(&quot;nbins_&quot; + ingrid-&gt;getComponentName(i) );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        136 :     ofile.addConstantField(&quot;periodic_&quot; + ingrid-&gt;getComponentName(i) );</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         60 :   std::vector&lt;double&gt; xx( ingrid-&gt;getDimension() );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         60 :   std::vector&lt;unsigned&gt; ind( ingrid-&gt;getDimension() );</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     103636 :   for(unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     103576 :     ingrid-&gt;getIndices( i, ind );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     103576 :     if(i&gt;0 &amp;&amp; ingrid-&gt;getDimension()==2 &amp;&amp; ind[ingrid-&gt;getDimension()-2]==0) ofile.printf(&quot;\n&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     103576 :     ofile.fmtField(fmt); ofile.printField(&quot;normalisation&quot;, ingrid-&gt;getNorm() );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     306047 :     for(unsigned j=0; j&lt;ingrid-&gt;getDimension(); ++j) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     404942 :       ofile.printField(&quot;min_&quot; + ingrid-&gt;getComponentName(j), ingrid-&gt;getMin()[j] );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     404942 :       ofile.printField(&quot;max_&quot; + ingrid-&gt;getComponentName(j), ingrid-&gt;getMax()[j] );</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     404942 :       ofile.printField(&quot;nbins_&quot; + ingrid-&gt;getComponentName(j), static_cast&lt;int&gt;(ingrid-&gt;getNbin()[j]) );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">     219655 :       if( ingrid-&gt;isPeriodic(j) ) ofile.printField(&quot;periodic_&quot; + ingrid-&gt;getComponentName(j), &quot;true&quot; );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">     370574 :       else          ofile.printField(&quot;periodic_&quot; + ingrid-&gt;getComponentName(j), &quot;false&quot; );</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     }</a>
+<a name="185"><span class="lineNum">     185 </span>            :     // Retrieve and print the grid coordinates</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     103576 :     ingrid-&gt;getGridPointCoordinates(i, xx );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">     306047 :     for(unsigned j=0; j&lt;ingrid-&gt;getDimension(); ++j) { ofile.fmtField(fmt); ofile.printField(ingrid-&gt;getComponentName(j),xx[j]); }</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">     440087 :     for(unsigned j=0; j&lt;ingrid-&gt;getNumberOfQuantities(); ++j) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">     336511 :       ofile.fmtField(fmt); ofile.printField(ingrid-&gt;arg_names[ingrid-&gt;dimension+j], ingrid-&gt;getGridElement( i, j ) );</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :     }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     103576 :     ofile.printField();</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         60 : }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindContour.cpp.func-sort-c.html b/coverage/gridtools/FindContour.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1675061bc2
--- /dev/null
+++ b/coverage/gridtools/FindContour.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindContour.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindContour.cpp<span style="font-size: 80%;"> (<a href="FindContour.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryMed">84.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FindContour.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#105">_ZN4PLMD9gridtools11FindContour10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#122">_ZN4PLMD9gridtools11FindContourC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#103">_ZNK4PLMD9gridtools11FindContour14checkAllActiveEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#216">_ZN4PLMD9gridtools11FindContour15finishAveragingEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#122">_ZN4PLMD9gridtools11FindContourC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#111">_ZN4PLMD9gridtools12_GLOBAL__N_124FindContourRegisterMe1136createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#157">_ZN4PLMD9gridtools11FindContour19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#113">_ZN4PLMD9gridtools11FindContour16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#106">_ZNK4PLMD9gridtools11FindContour21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#199">_ZNK4PLMD9gridtools11FindContour7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">554</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#111">_ZN4PLMD9gridtools12_GLOBAL__N_124FindContourRegisterMe113C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#111">_ZN4PLMD9gridtools12_GLOBAL__N_124FindContourRegisterMe113D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindContour.cpp.func.html b/coverage/gridtools/FindContour.cpp.func.html
new file mode 100644
index 0000000000..6265d358e9
--- /dev/null
+++ b/coverage/gridtools/FindContour.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindContour.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindContour.cpp<span style="font-size: 80%;"> (<a href="FindContour.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryMed">84.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FindContour.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#105">_ZN4PLMD9gridtools11FindContour10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#216">_ZN4PLMD9gridtools11FindContour15finishAveragingEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#113">_ZN4PLMD9gridtools11FindContour16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#157">_ZN4PLMD9gridtools11FindContour19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#122">_ZN4PLMD9gridtools11FindContourC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#122">_ZN4PLMD9gridtools11FindContourC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#111">_ZN4PLMD9gridtools12_GLOBAL__N_124FindContourRegisterMe1136createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#111">_ZN4PLMD9gridtools12_GLOBAL__N_124FindContourRegisterMe113C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#111">_ZN4PLMD9gridtools12_GLOBAL__N_124FindContourRegisterMe113D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#103">_ZNK4PLMD9gridtools11FindContour14checkAllActiveEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#106">_ZNK4PLMD9gridtools11FindContour21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContour.cpp.gcov.html#199">_ZNK4PLMD9gridtools11FindContour7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">554</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindContour.cpp.gcov.html b/coverage/gridtools/FindContour.cpp.gcov.html
new file mode 100644
index 0000000000..3843e617b0
--- /dev/null
+++ b/coverage/gridtools/FindContour.cpp.gcov.html
@@ -0,0 +1,323 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindContour.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindContour.cpp<span style="font-size: 80%;"> (source / <a href="FindContour.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryMed">84.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/StoreDataVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ContourFindingBase.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC GRIDANALYSIS FIND_CONTOUR</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Find an isocontour in a smooth function.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : As discussed in the part of the manual on \ref Analysis PLUMED contains a number of tools that allow you to calculate</a>
+<a name="33"><span class="lineNum">      33 </span>            : a function on a grid.  The function on this grid might be a \ref HISTOGRAM as a function of a few collective variables</a>
+<a name="34"><span class="lineNum">      34 </span>            : or it might be a phase field that has been calculated using \ref MULTICOLVARDENS.  If this function has one or two input</a>
+<a name="35"><span class="lineNum">      35 </span>            : arguments it is relatively straightforward to plot the function.  If by contrast the data has a three or more dimensions</a>
+<a name="36"><span class="lineNum">      36 </span>            : it can be difficult to visualize.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : This action provides one tool for visualizing these functions.  It can be used to search for a set of points on a contour</a>
+<a name="39"><span class="lineNum">      39 </span>            : where the function takes a particular values.  In other words, for the function \f$f(x,y)\f$ this action would find a set</a>
+<a name="40"><span class="lineNum">      40 </span>            : of points \f$\{x_c,y_c\}\f$ that have:</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : f(x_c,y_c) - c = 0</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : where \f$c\f$ is some constant value that is specified by the user.  The points on this contour are detected using a variant</a>
+<a name="47"><span class="lineNum">      47 </span>            : on the marching squares or marching cubes algorithm, which you can find information on here:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : https://en.wikipedia.org/wiki/Marching_squares</a>
+<a name="50"><span class="lineNum">      50 </span>            : https://en.wikipedia.org/wiki/Marching_cubes</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : As such, and unlike \ref FIND_CONTOUR_SURFACE or \ref FIND_SPHERICAL_CONTOUR, the function input to this action can have any dimension.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Furthermore, the topology of the contour will be determined by the algorithm and does not need to be specified by the user.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \par Examples</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : The input below allows you to calculate something akin to a Willard-Chandler dividing surface \cite wcsurface.</a>
+<a name="58"><span class="lineNum">      58 </span>            : The simulation cell in this case contains a solid phase and a liquid phase.  The Willard-Chandler surface is the</a>
+<a name="59"><span class="lineNum">      59 </span>            : surface that separates the parts of the box containing the solid from the parts containing the liquid.  To compute the position</a>
+<a name="60"><span class="lineNum">      60 </span>            : of this surface  the \ref FCCUBIC symmetry function is calculated for each of the atoms in the system from on the geometry of the</a>
+<a name="61"><span class="lineNum">      61 </span>            : atoms in the first coordination sphere of each of the atoms.  These quantities are then transformed using a switching function.</a>
+<a name="62"><span class="lineNum">      62 </span>            : This procedure generates a single number for each atom in the system and this quantity has a value of one for atoms that are in</a>
+<a name="63"><span class="lineNum">      63 </span>            : parts of the box that resemble the solid structure and zero for atoms that are in parts of the box that resemble the liquid.</a>
+<a name="64"><span class="lineNum">      64 </span>            : The position of a virtual atom is then computed using \ref CENTER_OF_MULTICOLVAR and a phase field model is constructed using</a>
+<a name="65"><span class="lineNum">      65 </span>            : \ref MULTICOLVARDENS.  These procedure ensures that we have a continuous function that gives a measure of the average degree of</a>
+<a name="66"><span class="lineNum">      66 </span>            : solidness at each point in the simulation cell.  The Willard-Chandler dividing surface is calculated by finding a a set of points</a>
+<a name="67"><span class="lineNum">      67 </span>            : at which the value of this phase field is equal to 0.5.  This set of points is output to file called mycontour.dat.  A new contour</a>
+<a name="68"><span class="lineNum">      68 </span>            : is found on every single step for each frame that is read in.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : UNITS NATURAL</a>
+<a name="72"><span class="lineNum">      72 </span>            : FCCUBIC ...</a>
+<a name="73"><span class="lineNum">      73 </span>            :   SPECIES=1-96000 SWITCH={CUBIC D_0=1.2 D_MAX=1.5}</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ALPHA=27 PHI=0.0 THETA=-1.5708 PSI=-2.35619 LABEL=fcc</a>
+<a name="75"><span class="lineNum">      75 </span>            : ... FCCUBIC</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : tfcc: MTRANSFORM_MORE DATA=fcc LOWMEM SWITCH={SMAP R_0=0.5 A=8 B=8}</a>
+<a name="78"><span class="lineNum">      78 </span>            : center: CENTER_OF_MULTICOLVAR DATA=tfcc</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : dens: MULTICOLVARDENS ...</a>
+<a name="81"><span class="lineNum">      81 </span>            :   DATA=tfcc ORIGIN=center DIR=xyz</a>
+<a name="82"><span class="lineNum">      82 </span>            :   NBINS=80,80,80 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1</a>
+<a name="83"><span class="lineNum">      83 </span>            : ...</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : FIND_CONTOUR GRID=dens CONTOUR=0.5 FILE=mycontour.xyz</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endplumedfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : */</a>
+<a name="89"><span class="lineNum">      89 </span>            : //+ENDPLUMEDOC</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : namespace PLMD {</a>
+<a name="92"><span class="lineNum">      92 </span>            : namespace gridtools {</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : class FindContour : public ContourFindingBase {</a>
+<a name="95"><span class="lineNum">      95 </span>            : private:</a>
+<a name="96"><span class="lineNum">      96 </span>            :   bool firsttime;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   unsigned gbuffer;</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Stuff for output</a>
+<a name="99"><span class="lineNum">      99 </span>            :   OFile of;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   double lenunit;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::string fmt_xyz;</a>
+<a name="102"><span class="lineNum">     102 </span>            : public:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="104"><span class="lineNum">     104 </span>            :   explicit FindContour(const ActionOptions&amp;ao);</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   bool checkAllActive() const override { return gbuffer==0; }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   void prepareForAveraging() override;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          7 :   unsigned getNumberOfQuantities() const override { return 1 + ingrid-&gt;getDimension(); }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   void compute( const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void finishAveraging() override;</a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FindContour,&quot;FIND_CONTOUR&quot;)</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          3 : void FindContour::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          3 :   ContourFindingBase::registerKeywords( keys );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : // We want a better way of doing this bit</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;BUFFER&quot;,&quot;0&quot;,&quot;number of buffer grid points around location where grid was found on last step.  If this is zero the full grid is calculated on each step&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;file on which to output coordinates&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;UNITS&quot;,&quot;PLUMED&quot;,&quot;the units in which to print out the coordinates. PLUMED means internal PLUMED units&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;PRECISION&quot;,&quot;The number of digits in trajectory file&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 : FindContour::FindContour(const ActionOptions&amp;ao):</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   Action(ao),</a>
+<a name="126"><span class="lineNum">     126 </span>            :   ContourFindingBase(ao),</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          1 :   firsttime(true)</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : {</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   parse(&quot;BUFFER&quot;,gbuffer);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 :   if( gbuffer&gt;0 ) log.printf(&quot;  after first step a subset of only %u grid points around where the countour was found will be checked\n&quot;,gbuffer);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   std::string file; parse(&quot;FILE&quot;,file);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   if( file.length()==0 ) error(&quot;name out output file was not specified&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   std::string type=Tools::extension(file);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   log&lt;&lt;&quot;  file name &quot;&lt;&lt;file&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :   if(type!=&quot;xyz&quot;) error(&quot;can only print xyz file type with contour finding&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   fmt_xyz=&quot;%f&quot;;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   std::string precision; parse(&quot;PRECISION&quot;,precision);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :   if(precision.length()&gt;0) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :     int p; Tools::convert(precision,p);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  with precision &quot;&lt;&lt;p&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     std::string a,b;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :     Tools::convert(p+5,a);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :     Tools::convert(p,b);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :     fmt_xyz=&quot;%&quot;+a+&quot;.&quot;+b+&quot;f&quot;;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   std::string unitname; parse(&quot;UNITS&quot;,unitname);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   if(unitname!=&quot;PLUMED&quot;) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     Units myunit; myunit.setLength(unitname);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          1 :   else lenunit=1.0;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          1 :   of.link(*this); of.open(file);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   checkRead(); mydata=buildDataStashes( NULL );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          1 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 : void FindContour::prepareForAveraging() {</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   // Create a task list if first time</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :   if( firsttime ) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      16465 :     for(unsigned i=0; i&lt;ingrid-&gt;getDimension()*ingrid-&gt;getNumberOfPoints(); ++i) addTaskToList( i );</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 :   firsttime=false; deactivateAllTasks();</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   // We now need to identify the grid points that we need to search through</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   std::vector&lt;unsigned&gt; nbin( ingrid-&gt;getNbin() );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          2 :   std::vector&lt;unsigned&gt; ind( ingrid-&gt;getDimension() );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :   std::vector&lt;unsigned&gt; ones( ingrid-&gt;getDimension(), 1 );</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   unsigned num_neighbours; std::vector&lt;unsigned&gt; neighbours;</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      10978 :   for(unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     // Ensure inactive grid points are ignored</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      10976 :     if( ingrid-&gt;inactive(i) ) continue;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :     // Get the index of the current grid point</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      10976 :     ingrid-&gt;getIndices( i, ind );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      10976 :     ingrid-&gt;getNeighbors( ind, ones, num_neighbours, neighbours );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     bool cycle=false;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     307328 :     for(unsigned j=0; j&lt;num_neighbours; ++j) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     296352 :       if( ingrid-&gt;inactive( neighbours[j]) ) { cycle=true; break; }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     }</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      10976 :     if( cycle ) continue;</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :     // Get the value of a point on the grid</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">      10976 :     double val1=getFunctionValue( i ) - contour;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     bool edge=false;</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      43904 :     for(unsigned j=0; j&lt;ingrid-&gt;getDimension(); ++j) {</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :       // Make sure we don't search at the edge of the grid</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      32928 :       if( !ingrid-&gt;isPeriodic(j) &amp;&amp; (ind[j]+1)==nbin[j] ) continue;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      32928 :       else if( (ind[j]+1)==nbin[j] ) { edge=true; ind[j]=0; }</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      30968 :       else ind[j]+=1;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      32928 :       double val2=getFunctionValue( ind ) - contour;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      32928 :       if( val1*val2&lt;0 ) taskFlags[ ingrid-&gt;getDimension()*i + j ] = 1;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      32928 :       if( ingrid-&gt;isPeriodic(j) &amp;&amp; edge ) { edge=false; ind[j]=nbin[j]-1; }</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      30968 :       else ind[j]-=1;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :     }</a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          2 :   lockContributors();</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 : }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        554 : void FindContour::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   // Retrieve the initial grid point coordinates</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        554 :   unsigned gpoint = std::floor( current / ingrid-&gt;getDimension() );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        554 :   std::vector&lt;double&gt; point( ingrid-&gt;getDimension() );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        554 :   ingrid-&gt;getGridPointCoordinates( gpoint, point );</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   // Retrieve the direction we are searching for the contour</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        554 :   unsigned gdir = current%(ingrid-&gt;getDimension() );</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        554 :   std::vector&lt;double&gt; direction( ingrid-&gt;getDimension(), 0 );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        554 :   direction[gdir] = 0.999999999*ingrid-&gt;getGridSpacing()[gdir];</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   // Now find the contour</a>
+<a name="213"><span class="lineNum">     213 </span>            :   findContour( direction, point );</a>
+<a name="214"><span class="lineNum">     214 </span>            :   // And transfer to the store data vessel</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       2216 :   for(unsigned i=0; i&lt;ingrid-&gt;getDimension(); ++i) myvals.setValue( 1+i, point[i] );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        554 : }</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 : void FindContour::finishAveraging() {</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   // And update the list of active grid points</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          1 :   if( gbuffer&gt;0 ) {</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     std::vector&lt;unsigned&gt; neighbours; unsigned num_neighbours;</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :     std::vector&lt;unsigned&gt; ugrid_indices( ingrid-&gt;getDimension() );</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :     std::vector&lt;bool&gt; active( ingrid-&gt;getNumberOfPoints(), false );</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :     std::vector&lt;unsigned&gt; gbuffer_vec( ingrid-&gt;getDimension(), gbuffer );</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getCurrentNumberOfActiveTasks(); ++i) {</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :       // Get the point we are operating on</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       unsigned ipoint = std::floor( getActiveTask(i) / ingrid-&gt;getDimension() );</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :       // Get the indices of this point</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       ingrid-&gt;getIndices( ipoint, ugrid_indices );</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       // Now activate buffer region</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :       ingrid-&gt;getNeighbors( ugrid_indices, gbuffer_vec, num_neighbours, neighbours );</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :       for(unsigned n=0; n&lt;num_neighbours; ++n) active[ neighbours[n] ]=true;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :     ingrid-&gt;activateThesePoints( active );</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; point( 1 + ingrid-&gt;getDimension() );</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          1 :   of.printf(&quot;%u\n&quot;,mydata-&gt;getNumberOfStoredValues());</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          1 :   of.printf(&quot;Points found on isocontour\n&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        555 :   for(unsigned i=0; i&lt;mydata-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        554 :     mydata-&gt;retrieveSequentialValue( i, false, point ); of.printf(&quot;X&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       2216 :     for(unsigned j=0; j&lt;ingrid-&gt;getDimension(); ++j) of.printf( (&quot; &quot; + fmt_xyz).c_str(), lenunit*point[1+j] );</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        554 :     of.printf(&quot;\n&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          1 : }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : }</a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindContourSurface.cpp.func-sort-c.html b/coverage/gridtools/FindContourSurface.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b3e601176a
--- /dev/null
+++ b/coverage/gridtools/FindContourSurface.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindContourSurface.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindContourSurface.cpp<span style="font-size: 80%;"> (<a href="FindContourSurface.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FindContourSurface.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#112">_ZN4PLMD9gridtools18FindContourSurfaceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#97">_ZNK4PLMD9gridtools18FindContourSurface14checkAllActiveEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#104">_ZN4PLMD9gridtools12_GLOBAL__N_131FindContourSurfaceRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#112">_ZN4PLMD9gridtools18FindContourSurfaceC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#149">_ZN4PLMD9gridtools18FindContourSurface12clearAverageEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#182">_ZN4PLMD9gridtools18FindContourSurface15finishAveragingEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#106">_ZN4PLMD9gridtools18FindContourSurface16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#161">_ZN4PLMD9gridtools18FindContourSurface19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#96">_ZNK4PLMD9gridtools18FindContourSurface21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#209">_ZNK4PLMD9gridtools18FindContourSurface7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">588</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#104">_ZN4PLMD9gridtools12_GLOBAL__N_131FindContourSurfaceRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#104">_ZN4PLMD9gridtools12_GLOBAL__N_131FindContourSurfaceRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindContourSurface.cpp.func.html b/coverage/gridtools/FindContourSurface.cpp.func.html
new file mode 100644
index 0000000000..5a1345d06c
--- /dev/null
+++ b/coverage/gridtools/FindContourSurface.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindContourSurface.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindContourSurface.cpp<span style="font-size: 80%;"> (<a href="FindContourSurface.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FindContourSurface.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#104">_ZN4PLMD9gridtools12_GLOBAL__N_131FindContourSurfaceRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#104">_ZN4PLMD9gridtools12_GLOBAL__N_131FindContourSurfaceRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#104">_ZN4PLMD9gridtools12_GLOBAL__N_131FindContourSurfaceRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#149">_ZN4PLMD9gridtools18FindContourSurface12clearAverageEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#182">_ZN4PLMD9gridtools18FindContourSurface15finishAveragingEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#106">_ZN4PLMD9gridtools18FindContourSurface16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#161">_ZN4PLMD9gridtools18FindContourSurface19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#112">_ZN4PLMD9gridtools18FindContourSurfaceC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#112">_ZN4PLMD9gridtools18FindContourSurfaceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#97">_ZNK4PLMD9gridtools18FindContourSurface14checkAllActiveEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#96">_ZNK4PLMD9gridtools18FindContourSurface21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindContourSurface.cpp.gcov.html#209">_ZNK4PLMD9gridtools18FindContourSurface7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">588</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindContourSurface.cpp.gcov.html b/coverage/gridtools/FindContourSurface.cpp.gcov.html
new file mode 100644
index 0000000000..761396424e
--- /dev/null
+++ b/coverage/gridtools/FindContourSurface.cpp.gcov.html
@@ -0,0 +1,339 @@
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+  <title>LCOV - plumed test coverage - gridtools/FindContourSurface.cpp</title>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindContourSurface.cpp<span style="font-size: 80%;"> (source / <a href="FindContourSurface.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntry">94</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ContourFindingBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC GRIDANALYSIS FIND_CONTOUR_SURFACE</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Find an isocontour by searching along either the x, y or z direction.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : As discussed in the part of the manual on \ref Analysis PLUMED contains a number of tools that allow you to calculate</a>
+<a name="30"><span class="lineNum">      30 </span>            : a function on a grid.  The function on this grid might be a \ref HISTOGRAM as a function of a few collective variables</a>
+<a name="31"><span class="lineNum">      31 </span>            : or it might be a phase field that has been calculated using \ref MULTICOLVARDENS.  If this function has one or two input</a>
+<a name="32"><span class="lineNum">      32 </span>            : arguments it is relatively straightforward to plot the function.  If by contrast the data has a three dimensions it can be</a>
+<a name="33"><span class="lineNum">      33 </span>            : difficult to visualize.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This action provides one tool for visualizing these functions.  It can be used to search for a set of points on a contour</a>
+<a name="36"><span class="lineNum">      36 </span>            : where the function takes a particular value.  In other words, for the function \f$f(x,y,z)\f$ this action would find a set</a>
+<a name="37"><span class="lineNum">      37 </span>            : of points \f$\{x_c,y_c,z_c\}\f$ that have:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : f(x_c,y_c,z_c) - c = 0</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where \f$c\f$ is some constant value that is specified by the user.  The points on this contour are find by searching along lines</a>
+<a name="44"><span class="lineNum">      44 </span>            : that run parallel to the \f$x\f$, \f$y\f$ or \f$z\f$ axis of the simulation cell.  The result is, therefore, a two dimensional</a>
+<a name="45"><span class="lineNum">      45 </span>            : function evaluated on a grid that gives us the height of the interface as a function of two coordinates.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : It is important to note that this action can only be used to detect contours in three dimensional functions.  In addition, this action will fail to</a>
+<a name="48"><span class="lineNum">      48 </span>            : find the full set of contour  points if the contour does not have the same topology as an infinite plane.  If you are uncertain that the isocontours in your</a>
+<a name="49"><span class="lineNum">      49 </span>            : function have the appropriate topology you should use \ref FIND_CONTOUR in place of \ref FIND_CONTOUR_SURFACE.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The input shown below was used to analyze the results from a simulation of an interface between solid and molten Lennard Jones.  The interface between</a>
+<a name="55"><span class="lineNum">      55 </span>            : the solid and the liquid was set up in the plane perpendicular to the \f$z\f$ direction of the simulation cell.   The input below calculates something</a>
+<a name="56"><span class="lineNum">      56 </span>            : akin to a Willard-Chandler dividing surface \cite wcsurface between the solid phase and the liquid phase.  There are two of these interfaces within the</a>
+<a name="57"><span class="lineNum">      57 </span>            : simulation box because of the periodic boundary conditions but we were able to determine that one of these two surfaces lies in a particular part of the</a>
+<a name="58"><span class="lineNum">      58 </span>            : simulation box.  The input below detects the height profile of one of these two interfaces.  It does so by computing a phase field average of the</a>
+<a name="59"><span class="lineNum">      59 </span>            : \ref FCCUBIC symmetry function using the \ref MULTICOLVARDENS action.  Notice that we use the fact that we know roughly where the interface is when specifying</a>
+<a name="60"><span class="lineNum">      60 </span>            : how this phase field is to be calculated and specify the region over the \f$z\f$-axis in which we are going to search for the phase field in the line defining</a>
+<a name="61"><span class="lineNum">      61 </span>            : the \ref MULTICOLVARDENS.  Once we have calculated the phase field we search for contour points on the lines that run parallel to the \f$z\f$-direction of the cell</a>
+<a name="62"><span class="lineNum">      62 </span>            : box using the FIND_CONTOUR_SURFACE command.  The final result is a \f$14 \times 14\f$ grid of values for the height of the interface as a function of the \f$(x,y)\f$</a>
+<a name="63"><span class="lineNum">      63 </span>            : position.  This grid is then output to a file called contour2.dat.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : Notice that the commands below calculate the instantaneous position of the surface separating the solid and liquid and that as such the accumulated average is cleared</a>
+<a name="66"><span class="lineNum">      66 </span>            : on every step.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : UNITS NATURAL</a>
+<a name="70"><span class="lineNum">      70 </span>            : FCCUBIC ...</a>
+<a name="71"><span class="lineNum">      71 </span>            :   SPECIES=1-96000 SWITCH={CUBIC D_0=1.2 D_MAX=1.5}</a>
+<a name="72"><span class="lineNum">      72 </span>            :   ALPHA=27 PHI=0.0 THETA=-1.5708 PSI=-2.35619 LABEL=fcc</a>
+<a name="73"><span class="lineNum">      73 </span>            : ... FCCUBIC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : dens2: MULTICOLVARDENS DATA=fcc ORIGIN=1 DIR=xyz NBINS=14,14,50 ZREDUCED ZLOWER=6.0 ZUPPER=11.0 BANDWIDTH=1.0,1.0,1.0 CLEAR=1</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : ss2: FIND_CONTOUR_SURFACE GRID=dens2 CONTOUR=0.42 SEARCHDIR=z STRIDE=1 CLEAR=1</a>
+<a name="78"><span class="lineNum">      78 </span>            : DUMPGRID GRID=ss2 FILE=contour2.dat FMT=%8.4f STRIDE=1</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : */</a>
+<a name="82"><span class="lineNum">      82 </span>            : //+ENDPLUMEDOC</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : namespace PLMD {</a>
+<a name="85"><span class="lineNum">      85 </span>            : namespace gridtools {</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : class FindContourSurface : public ContourFindingBase {</a>
+<a name="88"><span class="lineNum">      88 </span>            : private:</a>
+<a name="89"><span class="lineNum">      89 </span>            :   bool firsttime;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   unsigned dir_n;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   unsigned gbuffer;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;unsigned&gt; ones;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::vector&lt;unsigned&gt; gdirs;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   std::vector&lt;double&gt; direction;</a>
+<a name="95"><span class="lineNum">      95 </span>            : public:</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="97"><span class="lineNum">      97 </span>            :   explicit FindContourSurface(const ActionOptions&amp;ao);</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         12 :   unsigned getNumberOfQuantities() const override { return 2; }</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   bool checkAllActive() const override { return gbuffer==0; }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   void clearAverage() override;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void prepareForAveraging() override;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void compute( const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void finishAveraging() override;</a>
+<a name="104"><span class="lineNum">     104 </span>            : };</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FindContourSurface,&quot;FIND_CONTOUR_SURFACE&quot;)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 : void FindContourSurface::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          3 :   ContourFindingBase::registerKeywords( keys );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;SEARCHDIR&quot;,&quot;In which directions do you wish to search for the contour.&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;BUFFER&quot;,&quot;0&quot;,&quot;number of buffer grid points around location where grid was found on last step.  If this is zero the full grid is calculated on each step&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 : FindContourSurface::FindContourSurface(const ActionOptions&amp;ao):</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   Action(ao),</a>
+<a name="116"><span class="lineNum">     116 </span>            :   ContourFindingBase(ao),</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :   firsttime(true),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   ones(ingrid-&gt;getDimension(),1)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : {</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          1 :   if( ingrid-&gt;getDimension()&lt;2 ) error(&quot;cannot find dividing surface if input grid is one dimensional&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   std::string dir; parse(&quot;SEARCHDIR&quot;,dir); parse(&quot;BUFFER&quot;,gbuffer);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :   log.printf(&quot;  calculating location of contour on %d dimensional grid \n&quot;, ingrid-&gt;getDimension()-1 );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 :   if( gbuffer&gt;0 ) log.printf(&quot;  after first step a subset of only %u grid points around where the countour was found will be checked\n&quot;,gbuffer);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          1 :   unsigned n=0; gdirs.resize( ingrid-&gt;getDimension()-1 );</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;ingrid-&gt;getDimension(); ++i) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :     if( ingrid-&gt;getComponentName(i)==dir ) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :       dir_n=i;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     } else {</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :       if( n==gdirs.size() ) error(&quot;could not find &quot; + dir + &quot; direction in input grid&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :       gdirs[n]=i; n++;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     }</a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   if( n!=(ingrid-&gt;getDimension()-1) ) error(&quot;output of grid is not understood&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Create the input from the old string</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :   std::string vstring = &quot;COMPONENTS=&quot; + getLabel() + &quot; COORDINATES=&quot; + ingrid-&gt;getComponentName( gdirs[0] );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   for(unsigned i=1; i&lt;gdirs.size(); ++i) vstring += &quot;,&quot; + ingrid-&gt;getComponentName( gdirs[i] );</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   vstring += &quot; PBC=&quot;;</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   if( ingrid-&gt;isPeriodic(gdirs[0]) ) vstring+=&quot;T&quot;;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   else vstring+=&quot;F&quot;;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   for(unsigned i=1; i&lt;gdirs.size(); ++i) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :     if( ingrid-&gt;isPeriodic(gdirs[i]) ) vstring+=&quot;,T&quot;; else vstring+=&quot;,F&quot;;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :   auto grid=createGrid( &quot;grid&quot;, vstring ); grid-&gt;setNoDerivatives();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :   setAveragingAction( std::move(grid), true );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 : }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 : void FindContourSurface::clearAverage() {</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   // Set the boundaries of the output grid</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; fspacing; std::vector&lt;unsigned&gt; snbins( ingrid-&gt;getDimension()-1 );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          3 :   std::vector&lt;std::string&gt; smin( ingrid-&gt;getDimension()-1 ), smax( ingrid-&gt;getDimension()-1 );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          9 :   for(unsigned i=0; i&lt;gdirs.size(); ++i) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         18 :     smin[i]=ingrid-&gt;getMin()[gdirs[i]]; smax[i]=ingrid-&gt;getMax()[gdirs[i]];</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          6 :     snbins[i]=ingrid-&gt;getNbin()[gdirs[i]];</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          3 :   mygrid-&gt;setBounds( smin, smax, snbins, fspacing); resizeFunctions();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          3 :   ActionWithAveraging::clearAverage();</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          6 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          3 : void FindContourSurface::prepareForAveraging() {</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   // Create a task list if first time</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   if( firsttime ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :     std::vector&lt;unsigned&gt; find( ingrid-&gt;getDimension() );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 :     std::vector&lt;unsigned&gt; ind( mygrid-&gt;getDimension() );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        197 :     for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        196 :       find.assign( find.size(), 0 ); mygrid-&gt;getIndices( i, ind );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        588 :       for(unsigned j=0; j&lt;gdirs.size(); ++j) find[gdirs[j]]=ind[j];</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :       // Current will be set equal to the start point for this grid index</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        196 :       addTaskToList( ingrid-&gt;getIndex(find) );</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     }</a>
+<a name="174"><span class="lineNum">     174 </span>            :     // And prepare the task list</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 :     deactivateAllTasks();</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        197 :     for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          1 :     lockContributors();</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     // Set the direction in which to look for the contour</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          1 :     direction.resize( ingrid-&gt;getDimension(), 0 );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :     direction[dir_n] = 0.999999999*ingrid-&gt;getGridSpacing()[dir_n];</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          3 : }</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          3 : void FindContourSurface::finishAveraging() {</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   ContourFindingBase::finishAveraging();</a>
+<a name="186"><span class="lineNum">     186 </span>            :   // And update the list of active grid points</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          3 :   if( gbuffer&gt;0 ) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; dx( ingrid-&gt;getGridSpacing() );</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; point( ingrid-&gt;getDimension() );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          3 :     std::vector&lt;double&gt; lpoint( mygrid-&gt;getDimension() );</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     std::vector&lt;unsigned&gt; neighbours; unsigned num_neighbours;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          3 :     std::vector&lt;unsigned&gt; ugrid_indices( ingrid-&gt;getDimension() );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          3 :     std::vector&lt;bool&gt; active( ingrid-&gt;getNumberOfPoints(), false );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          3 :     std::vector&lt;unsigned&gt; gbuffer_vec( ingrid-&gt;getDimension(), gbuffer );</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        591 :     for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       // Retrieve the coordinates of this grid point</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        588 :       mygrid-&gt;getGridPointCoordinates( i, lpoint );</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        588 :       point[dir_n] = mygrid-&gt;getGridElement( i, 0 );</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :       // 0.5*dx added here to prevent problems with flooring of grid points</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1764 :       for(unsigned j=0; j&lt;gdirs.size(); ++j) point[gdirs[j]]=lpoint[j] + 0.5*dx[gdirs[j]];</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        588 :       ingrid-&gt;getIndices( point, ugrid_indices );</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :       // Now activate buffer region</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        588 :       ingrid-&gt;getNeighbors( ugrid_indices, gbuffer_vec, num_neighbours, neighbours );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      16464 :       for(unsigned n=0; n&lt;num_neighbours; ++n) active[ neighbours[n] ]=true;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          3 :     ingrid-&gt;activateThesePoints( active );</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          3 :   firsttime=false;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          3 : }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        588 : void FindContourSurface::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   std::vector&lt;unsigned&gt; neighbours; unsigned num_neighbours; unsigned nfound=0; double minp=0;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        588 :   std::vector&lt;unsigned&gt; bins_n( ingrid-&gt;getNbin() ); unsigned shiftn=current;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        588 :   std::vector&lt;unsigned&gt; ind( ingrid-&gt;getDimension() ); std::vector&lt;double&gt; point( ingrid-&gt;getDimension() );</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : #ifndef NDEBUG</a>
+<a name="216"><span class="lineNum">     216 </span>            :   std::vector&lt;unsigned&gt; oind( mygrid-&gt;getDimension() ); mygrid-&gt;getIndices( current, oind );</a>
+<a name="217"><span class="lineNum">     217 </span>            : #endif</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      16749 :   for(unsigned i=0; i&lt;bins_n[dir_n]; ++i) {</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : #ifndef NDEBUG</a>
+<a name="220"><span class="lineNum">     220 </span>            :     std::vector&lt;unsigned&gt; base_ind( ingrid-&gt;getDimension() ); ingrid-&gt;getIndices( shiftn, base_ind );</a>
+<a name="221"><span class="lineNum">     221 </span>            :     for(unsigned j=0; j&lt;gdirs.size(); ++j) plumed_dbg_assert( base_ind[gdirs[j]]==oind[j] );</a>
+<a name="222"><span class="lineNum">     222 </span>            : #endif</a>
+<a name="223"><span class="lineNum">     223 </span>            :     // Ensure inactive grid points are ignored</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      16749 :     if( ingrid-&gt;inactive( shiftn ) ) { shiftn += ingrid-&gt;getStride()[dir_n]; continue; }</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     // Get the index of the current grid point</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       7857 :     ingrid-&gt;getIndices( shiftn, ind );</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     // Exit if we are at the edge of the grid</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       7857 :     if( !ingrid-&gt;isPeriodic(dir_n) &amp;&amp; (ind[dir_n]+1)==bins_n[dir_n] ) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       shiftn += ingrid-&gt;getStride()[dir_n]; continue;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :     // Ensure points with inactive neighbours are ignored</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       7857 :     ingrid-&gt;getNeighbors( ind, ones, num_neighbours, neighbours );</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     bool cycle=false;</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     179020 :     for(unsigned j=0; j&lt;num_neighbours; ++j) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">     172753 :       if( ingrid-&gt;inactive( neighbours[j]) ) { cycle=true; break; }</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     }</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       7857 :     if( cycle ) { shiftn += ingrid-&gt;getStride()[dir_n]; continue; }</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :     // Now get the function value at two points</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       6267 :     double val1=getFunctionValue( shiftn ) - contour; double val2;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">       6267 :     if( (ind[dir_n]+1)==bins_n[dir_n] ) val2 = getFunctionValue( current ) - contour;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       6267 :     else val2=getFunctionValue( shiftn + ingrid-&gt;getStride()[dir_n] ) - contour;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :     // Check if the minimum is bracketed</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">       6267 :     if( val1*val2&lt;0 ) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        588 :       ingrid-&gt;getGridPointCoordinates( shiftn, point ); findContour( direction, point );</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        588 :       minp=point[dir_n]; nfound++; break;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :     }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :     // This moves us on to the next point</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       5679 :     shiftn += ingrid-&gt;getStride()[dir_n];</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span>            :   if( nfound==0 ) {</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert( getStep(), num );</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :     error(&quot;On step &quot; + num + &quot; failed to find required grid point&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span>            :   myvals.setValue( 1, minp );</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        588 : }</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : }</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindSphericalContour.cpp.func-sort-c.html b/coverage/gridtools/FindSphericalContour.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a8e69cdc73
--- /dev/null
+++ b/coverage/gridtools/FindSphericalContour.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindSphericalContour.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindSphericalContour.cpp<span style="font-size: 80%;"> (<a href="FindSphericalContour.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FindSphericalContour.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#130">_ZN4PLMD9gridtools20FindSphericalContourC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#120">_ZN4PLMD9gridtools12_GLOBAL__N_133FindSphericalContourRegisterMe1226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#130">_ZN4PLMD9gridtools20FindSphericalContourC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#122">_ZN4PLMD9gridtools20FindSphericalContour16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#116">_ZNK4PLMD9gridtools20FindSphericalContour21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#156">_ZNK4PLMD9gridtools20FindSphericalContour7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#120">_ZN4PLMD9gridtools12_GLOBAL__N_133FindSphericalContourRegisterMe122C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#120">_ZN4PLMD9gridtools12_GLOBAL__N_133FindSphericalContourRegisterMe122D2Ev</a></td>
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+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FindSphericalContour.cpp.func.html b/coverage/gridtools/FindSphericalContour.cpp.func.html
new file mode 100644
index 0000000000..874bb861ab
--- /dev/null
+++ b/coverage/gridtools/FindSphericalContour.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FindSphericalContour.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindSphericalContour.cpp<span style="font-size: 80%;"> (<a href="FindSphericalContour.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FindSphericalContour.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#120">_ZN4PLMD9gridtools12_GLOBAL__N_133FindSphericalContourRegisterMe1226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#120">_ZN4PLMD9gridtools12_GLOBAL__N_133FindSphericalContourRegisterMe122C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#120">_ZN4PLMD9gridtools12_GLOBAL__N_133FindSphericalContourRegisterMe122D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#122">_ZN4PLMD9gridtools20FindSphericalContour16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
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+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#130">_ZN4PLMD9gridtools20FindSphericalContourC2ERKNS_13ActionOptionsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#116">_ZNK4PLMD9gridtools20FindSphericalContour21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FindSphericalContour.cpp.gcov.html#156">_ZNK4PLMD9gridtools20FindSphericalContour7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">100</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/gridtools/FindSphericalContour.cpp.gcov.html b/coverage/gridtools/FindSphericalContour.cpp.gcov.html
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FindSphericalContour.cpp<span style="font-size: 80%;"> (source / <a href="FindSphericalContour.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ContourFindingBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC GRIDANALYSIS FIND_SPHERICAL_CONTOUR</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Find an isocontour in a three dimensional grid by searching over a Fibonacci sphere.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : As discussed in the part of the manual on \ref Analysis PLUMED contains a number of tools that allow you to calculate</a>
+<a name="31"><span class="lineNum">      31 </span>            : a function on a grid.  The function on this grid might be a \ref HISTOGRAM as a function of a few collective variables</a>
+<a name="32"><span class="lineNum">      32 </span>            : or it might be a phase field that has been calculated using \ref MULTICOLVARDENS.  If this function has one or two input</a>
+<a name="33"><span class="lineNum">      33 </span>            : arguments it is relatively straightforward to plot the function.  If by contrast the data has a three dimensions it can be</a>
+<a name="34"><span class="lineNum">      34 </span>            : difficult to visualize.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This action provides one tool for visualizing these functions.  It can be used to search for a set of points on a contour</a>
+<a name="37"><span class="lineNum">      37 </span>            : where the function takes a particular value.  In other words, for the function \f$f(x,y,z)\f$ this action would find a set</a>
+<a name="38"><span class="lineNum">      38 </span>            : of points \f$\{x_c,y_c,z_c\}\f$ that have:</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            : f(x_c,y_c,z_c) - c = 0</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f]</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : where \f$c\f$ is some constant value that is specified by the user.  The points on this contour are find by searching along a</a>
+<a name="45"><span class="lineNum">      45 </span>            : set of equally spaced radii of a sphere that centered at on particular, user-specified atom or virtual atom.  To ensure that</a>
+<a name="46"><span class="lineNum">      46 </span>            : these search radii are equally spaced on the surface of the sphere the search directions are generated by using a Fibonacci</a>
+<a name="47"><span class="lineNum">      47 </span>            : spiral projected on a sphere.  In other words, the search directions are given by:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \f[</a>
+<a name="50"><span class="lineNum">      50 </span>            : \mathbf{r}_i = \left(</a>
+<a name="51"><span class="lineNum">      51 </span>            : \begin{matrix}</a>
+<a name="52"><span class="lineNum">      52 </span>            : \sqrt{1 - y^2} \cos(\phi) \\</a>
+<a name="53"><span class="lineNum">      53 </span>            : \frac{2i}{n} - 1 + \frac{1}{n}  \\</a>
+<a name="54"><span class="lineNum">      54 </span>            : \sqrt{1 - y^2} \sin(\phi)</a>
+<a name="55"><span class="lineNum">      55 </span>            : \end{matrix}</a>
+<a name="56"><span class="lineNum">      56 </span>            : \right)</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f]</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : where \f$y\f$ is the quantity second component of the vector defined above, \f$n\f$ is the number of directions to look in and \f$\phi\f$ is</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \f[</a>
+<a name="62"><span class="lineNum">      62 </span>            : \phi = \mod(i + R, n) \pi ( 3 - \sqrt{5} )</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f]</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : where \f$R\f$ is a random variable between 0 and \f$n-1\f$ that is generated during the read in of the input file and that is fixed during</a>
+<a name="66"><span class="lineNum">      66 </span>            : the whole calculation.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : It is important to note that this action can only be used to detect contours in three dimensional functions.  In addition, this action will fail to</a>
+<a name="69"><span class="lineNum">      69 </span>            : find the full set of contour  points if the contour does not have the same topology as a sphere.  If you are uncertain that the isocontours in your</a>
+<a name="70"><span class="lineNum">      70 </span>            : function have a spherical topology you should use \ref FIND_CONTOUR in place of \ref FIND_SPHERICAL_CONTOUR.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \par Examples</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : The following input demonstrates how this action can be used.  The input here is used to study the shape of a droplet that has been formed during the</a>
+<a name="75"><span class="lineNum">      75 </span>            : condensation of Lennard Jones from the vapor.  The input below achieves this by calculating the coordination numbers of all the atoms within the gas.</a>
+<a name="76"><span class="lineNum">      76 </span>            : Obviously, those atoms within the droplet will have a large value for the coordination number while the isolated atoms in the gas will have a low value.</a>
+<a name="77"><span class="lineNum">      77 </span>            : As such we can detect the sizes of the droplets by constructing a \ref CONTACT_MATRIX whose \f$ij\f$ element tells us whether atom \f$i\f$ and atom \f$j\f$</a>
+<a name="78"><span class="lineNum">      78 </span>            : have coordination number that is greater that two.  The atoms within the various droplets within the system can then be found by performing a</a>
+<a name="79"><span class="lineNum">      79 </span>            : \ref DFSCLUSTERING on this matrix to detect the connected components.  We can take the largest of these connected components and find the center of the droplet</a>
+<a name="80"><span class="lineNum">      80 </span>            : by exploiting the functionality within \ref CENTER_OF_MULTICOLVAR.  We can then construct a phase field based on the positions of the atoms in the largest</a>
+<a name="81"><span class="lineNum">      81 </span>            : cluster and the values of the coordination numbers of these atoms.  The final line in the input then finds the a set of points on the dividing surface that separates</a>
+<a name="82"><span class="lineNum">      82 </span>            : the droplet from the surrounding gas.  The value of the phase field on this isocontour is equal to 0.75.</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : \plumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : # Calculate coordination numbers</a>
+<a name="86"><span class="lineNum">      86 </span>            : c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="87"><span class="lineNum">      87 </span>            : # Select coordination numbers that are more than 2.0</a>
+<a name="88"><span class="lineNum">      88 </span>            : cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM</a>
+<a name="89"><span class="lineNum">      89 </span>            : # Build a contact matrix</a>
+<a name="90"><span class="lineNum">      90 </span>            : mat: CONTACT_MATRIX ATOMS=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="91"><span class="lineNum">      91 </span>            : # Find largest cluster</a>
+<a name="92"><span class="lineNum">      92 </span>            : dfs: DFSCLUSTERING MATRIX=mat LOWMEM</a>
+<a name="93"><span class="lineNum">      93 </span>            : clust1: CLUSTER_PROPERTIES CLUSTERS=dfs CLUSTER=1</a>
+<a name="94"><span class="lineNum">      94 </span>            : # Find center of largest cluster</a>
+<a name="95"><span class="lineNum">      95 </span>            : trans1: MTRANSFORM_MORE DATA=clust1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM</a>
+<a name="96"><span class="lineNum">      96 </span>            : cent: CENTER_OF_MULTICOLVAR DATA=trans1</a>
+<a name="97"><span class="lineNum">      97 </span>            : # Calculate the phase field of the coordination</a>
+<a name="98"><span class="lineNum">      98 </span>            : dens: MULTICOLVARDENS DATA=trans1 ORIGIN=cent DIR=xyz NBINS=30,30,30 BANDWIDTH=2.0,2.0,2.0</a>
+<a name="99"><span class="lineNum">      99 </span>            : # Find the isocontour around the nucleus</a>
+<a name="100"><span class="lineNum">     100 </span>            : sc: FIND_SPHERICAL_CONTOUR GRID=dens CONTOUR=0.85 INNER_RADIUS=10.0 OUTER_RADIUS=40.0 NPOINTS=100</a>
+<a name="101"><span class="lineNum">     101 </span>            : # And print the grid to a file</a>
+<a name="102"><span class="lineNum">     102 </span>            : GRID_TO_XYZ GRID=sc FILE=mysurface.xyz UNITS=A</a>
+<a name="103"><span class="lineNum">     103 </span>            : \endplumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : */</a>
+<a name="106"><span class="lineNum">     106 </span>            : //+ENDPLUMEDOC</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : namespace PLMD {</a>
+<a name="109"><span class="lineNum">     109 </span>            : namespace gridtools {</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : class FindSphericalContour : public ContourFindingBase {</a>
+<a name="112"><span class="lineNum">     112 </span>            : private:</a>
+<a name="113"><span class="lineNum">     113 </span>            :   unsigned nbins;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   double min, max;</a>
+<a name="115"><span class="lineNum">     115 </span>            : public:</a>
+<a name="116"><span class="lineNum">     116 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="117"><span class="lineNum">     117 </span>            :   explicit FindSphericalContour(const ActionOptions&amp;ao);</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          4 :   unsigned getNumberOfQuantities() const override { return 2; }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   void compute( const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="120"><span class="lineNum">     120 </span>            : };</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FindSphericalContour,&quot;FIND_SPHERICAL_CONTOUR&quot;)</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 : void FindSphericalContour::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   ContourFindingBase::registerKeywords( keys );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;NPOINTS&quot;,&quot;the number of points for which we are looking for the contour&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;INNER_RADIUS&quot;,&quot;the minimum radius on which to look for the contour&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;OUTER_RADIUS&quot;,&quot;the outer radius on which to look for the contour&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;NBINS&quot;,&quot;1&quot;,&quot;the number of discrete sections in which to divide the distance between the inner and outer radius when searching for a contour&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          3 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 : FindSphericalContour::FindSphericalContour(const ActionOptions&amp;ao):</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   Action(ao),</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   ContourFindingBase(ao)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : {</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   if( ingrid-&gt;getDimension()!=3 ) error(&quot;input grid must be three dimensional&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   unsigned npoints; parse(&quot;NPOINTS&quot;,npoints);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 :   log.printf(&quot;  searching for %u points on dividing surface \n&quot;,npoints);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          3 :   parse(&quot;INNER_RADIUS&quot;,min); parse(&quot;OUTER_RADIUS&quot;,max); parse(&quot;NBINS&quot;,nbins);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :   log.printf(&quot;  expecting to find dividing surface at radii between %f and %f \n&quot;,min,max);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   log.printf(&quot;  looking for contour in windows of length %f \n&quot;, (max-min)/nbins);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   // Set this here so the same set of grid points are used on every turn</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :   std::string vstring = &quot;TYPE=fibonacci COMPONENTS=&quot; + getLabel() + &quot; COORDINATES=x,y,z PBC=F,F,F&quot;;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :   auto grid=createGrid( &quot;grid&quot;, vstring ); grid-&gt;setNoDerivatives();</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   setAveragingAction( std::move(grid), true );</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   // use mygrid, since at this point grid has been moved</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :   mygrid-&gt;setupFibonacciGrid( npoints );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Create a task list</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        101 :   for(unsigned i=0; i&lt;npoints; ++i) addTaskToList( i );</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :   deactivateAllTasks();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        101 :   for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          1 :   lockContributors();</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 : }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        100 : void FindSphericalContour::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Generate contour point on inner sphere</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        100 :   std::vector&lt;double&gt; contour_point(3), direction(3), der(3), tmp(3);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   // Retrieve this contour point from grid</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        100 :   mygrid-&gt;getGridPointCoordinates( current, direction );</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   // Now setup contour point on inner sphere</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        400 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        300 :     contour_point[j] = min*direction[j];</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        300 :     direction[j] = (max-min)*direction[j] / static_cast&lt;double&gt;(nbins);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            :   bool found=false;</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        100 :   for(unsigned k=0; k&lt;nbins; ++k) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        400 :     for(unsigned j=0; j&lt;3; ++j) tmp[j] = contour_point[j] + direction[j];</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     double val1 = getDifferenceFromContour( contour_point, der );</a>
+<a name="172"><span class="lineNum">     172 </span>            :     double val2 = getDifferenceFromContour( tmp, der );</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        100 :     if( val1*val2&lt;0 ) {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :       findContour( direction, contour_point );</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        400 :       double norm=0; for(unsigned j=0; j&lt;3; ++j) norm += contour_point[j]*contour_point[j];</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        100 :       myvals.setValue( 1, std::sqrt(norm) ); found=true; break;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :     }</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;3; ++j) contour_point[j] = tmp[j];</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   if( !found ) error(&quot;range does not bracket the dividing surface&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        100 : }</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FourierTransform.cpp.func-sort-c.html b/coverage/gridtools/FourierTransform.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a182b7b4f9
--- /dev/null
+++ b/coverage/gridtools/FourierTransform.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FourierTransform.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FourierTransform.cpp<span style="font-size: 80%;"> (<a href="FourierTransform.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntryMed">83.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">70.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FourierTransform.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#82">_ZN4PLMD9gridtools16FourierTransform10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#95">_ZN4PLMD9gridtools16FourierTransformC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#81">_ZNK4PLMD9gridtools16FourierTransform7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#85">_ZN4PLMD9gridtools12_GLOBAL__N_128FourierTransformRegisterMe876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#165">_ZN4PLMD9gridtools16FourierTransform12clearAverageEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#95">_ZN4PLMD9gridtools16FourierTransformC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#87">_ZN4PLMD9gridtools16FourierTransform16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#176">_ZN4PLMD9gridtools16FourierTransform17performOperationsERKb</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#85">_ZN4PLMD9gridtools12_GLOBAL__N_128FourierTransformRegisterMe87C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#85">_ZN4PLMD9gridtools12_GLOBAL__N_128FourierTransformRegisterMe87D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FourierTransform.cpp.func.html b/coverage/gridtools/FourierTransform.cpp.func.html
new file mode 100644
index 0000000000..18732db9a7
--- /dev/null
+++ b/coverage/gridtools/FourierTransform.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FourierTransform.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FourierTransform.cpp<span style="font-size: 80%;"> (<a href="FourierTransform.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntryMed">83.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">70.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FourierTransform.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#85">_ZN4PLMD9gridtools12_GLOBAL__N_128FourierTransformRegisterMe876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#85">_ZN4PLMD9gridtools12_GLOBAL__N_128FourierTransformRegisterMe87C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#85">_ZN4PLMD9gridtools12_GLOBAL__N_128FourierTransformRegisterMe87D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#82">_ZN4PLMD9gridtools16FourierTransform10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#165">_ZN4PLMD9gridtools16FourierTransform12clearAverageEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#87">_ZN4PLMD9gridtools16FourierTransform16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#176">_ZN4PLMD9gridtools16FourierTransform17performOperationsERKb</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#95">_ZN4PLMD9gridtools16FourierTransformC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#95">_ZN4PLMD9gridtools16FourierTransformC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FourierTransform.cpp.gcov.html#81">_ZNK4PLMD9gridtools16FourierTransform7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/FourierTransform.cpp.gcov.html b/coverage/gridtools/FourierTransform.cpp.gcov.html
new file mode 100644
index 0000000000..921d143224
--- /dev/null
+++ b/coverage/gridtools/FourierTransform.cpp.gcov.html
@@ -0,0 +1,328 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/FourierTransform.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - FourierTransform.cpp<span style="font-size: 80%;"> (source / <a href="FourierTransform.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntryMed">83.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryLo">70.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &lt;iostream&gt;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;complex&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionWithInputGrid.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #ifdef __PLUMED_HAS_FFTW</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;fftw3.h&gt; // FFTW interface</a>
+<a name="28"><span class="lineNum">      28 </span>            : #endif</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace gridtools {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC GRIDANALYSIS FOURIER_TRANSFORM</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Compute the Discrete Fourier Transform (DFT) by means of FFTW of data stored on a 2D grid.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This action can operate on any other action that outputs scalar data on a two-dimensional grid.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Up to now, even if the input data are purely real the action uses a complex DFT.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : Just as a quick reference, given a 1D array \f$\mathbf{X}\f$ of size \f$n\f$, this action computes the vector \f$\mathbf{Y}\f$ given by</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : Y_k = \sum_{j=0}^{n-1} X_j e^{2\pi\, j k \sqrt{-1}/n}.</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : This can be easily extended to more than one dimension. All the other details can be found at http://www.fftw.org/doc/What-FFTW-Really-Computes.html#What-FFTW-Really-Computes.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The keyword &quot;FOURIER_PARAMETERS&quot; deserves just a note on the usage. This keyword specifies how the Fourier transform will be normalized. The keyword takes two numerical parameters (\f$a,\,b\f$) that define the normalization according to the following expression</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \f[</a>
+<a name="52"><span class="lineNum">      52 </span>            : \frac{1}{n^{(1-a)/2}} \sum_{j=0}^{n-1} X_j e^{2\pi b\, j k \sqrt{-1}/n}</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f]</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The default values of these parameters are: \f$a=1\f$ and \f$b=1\f$.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \par Examples</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The following example tells Plumed to compute the complex 2D 'backward' Discrete Fourier Transform by taking the data saved on a grid called 'density', and normalizing the output by \f$ \frac{1}{\sqrt{N_x\, N_y}}\f$, where \f$N_x\f$ and \f$N_y\f$ are the number of data on the grid (it can be the case that \f$N_x\neq N_y\f$):</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : FOURIER_TRANSFORM STRIDE=1 GRID=density FT_TYPE=complex FOURIER_PARAMETERS=0,-1</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endplumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : */</a>
+<a name="66"><span class="lineNum">      66 </span>            : //+ENDPLUMEDOC</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : class FourierTransform : public ActionWithInputGrid {</a>
+<a name="70"><span class="lineNum">      70 </span>            : private:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::string output_type;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   bool real_output, store_norm;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;int&gt; fourier_params;</a>
+<a name="74"><span class="lineNum">      74 </span>            : public:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="76"><span class="lineNum">      76 </span>            :   explicit FourierTransform(const ActionOptions&amp;ao);</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void clearAverage() override;</a>
+<a name="78"><span class="lineNum">      78 </span>            : #ifndef __PLUMED_HAS_FFTW</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void performOperations( const bool&amp; from_update ) override {}</a>
+<a name="80"><span class="lineNum">      80 </span>            : #else</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void performOperations( const bool&amp; from_update ) override;</a>
+<a name="82"><span class="lineNum">      82 </span>            : #endif</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   void compute( const unsigned&amp;, MultiValue&amp; ) const override {}</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FourierTransform,&quot;FOURIER_TRANSFORM&quot;)</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          3 : void FourierTransform::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          6 :   ActionWithInputGrid::registerKeywords( keys ); keys.remove(&quot;BANDWIDTH&quot;); keys.remove(&quot;KERNEL&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;FT_TYPE&quot;,&quot;choose what kind of data you want as output on the grid. Possible values are: ABS = compute the complex modulus of Fourier coefficients (DEFAULT); NORM = compute the norm (i.e. ABS^2) of Fourier coefficients; COMPLEX = store the FFTW complex output on the grid (as a vector).&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FOURIER_PARAMETERS&quot;,&quot;default&quot;,&quot;what kind of normalization is applied to the output and if the Fourier transform in FORWARD or BACKWARD. This keyword takes the form FOURIER_PARAMETERS=A,B, where A and B can be 0, 1 or -1. The default values are A=1 (no normalization at all) and B=1 (forward FFT). Other possible choices for A are: &quot;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :            &quot;A=-1: normalize by the number of data, &quot;</a>
+<a name="94"><span class="lineNum">      94 </span>            :            &quot;A=0: normalize by the square root of the number of data (one forward and followed by backward FFT recover the original data). &quot;);</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          3 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          1 : FourierTransform::FourierTransform(const ActionOptions&amp;ao):</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   Action(ao),</a>
+<a name="99"><span class="lineNum">      99 </span>            :   ActionWithInputGrid(ao),</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          1 :   real_output(true),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :   store_norm(false),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 :   fourier_params(2)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span>            : #ifndef __PLUMED_HAS_FFTW</a>
+<a name="105"><span class="lineNum">     105 </span>            :   error(&quot;this feature is only available if you compile PLUMED with FFTW&quot;);</a>
+<a name="106"><span class="lineNum">     106 </span>            : #else</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   if( ingrid-&gt;getDimension()!=2 ) error(&quot;fourier transform currently only works with two dimensional grids&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Get the type of FT</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   parse(&quot;FT_TYPE&quot;,output_type);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 :   if (output_type.length()==0) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  keyword FT_TYPE unset. By default output grid will contain REAL Fourier coefficients\n&quot;;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   } else if ( output_type==&quot;ABS&quot; || output_type==&quot;abs&quot;) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;  keyword FT_TYPE is '&quot;&lt;&lt; output_type &lt;&lt; &quot;' : will compute the MODULUS of Fourier coefficients\n&quot;;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   } else if ( output_type==&quot;NORM&quot; || output_type==&quot;norm&quot;) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;  keyword FT_TYPE is '&quot;&lt;&lt; output_type &lt;&lt; &quot;' : will compute the NORM of Fourier coefficients\n&quot;;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     store_norm=true;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   } else if ( output_type==&quot;COMPLEX&quot; || output_type==&quot;complex&quot; ) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  keyword FT_TYPE is '&quot;&lt;&lt; output_type &lt;&lt;&quot;' : output grid will contain the COMPLEX Fourier coefficients\n&quot;;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          1 :     real_output=false;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :   } else error(&quot;keyword FT_TYPE unrecognized!&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   // Normalize output?</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :   std::string params_str; parse(&quot;FOURIER_PARAMETERS&quot;,params_str);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :   if (params_str==&quot;default&quot;) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     fourier_params.assign( fourier_params.size(), 1 );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     log.printf(&quot;  default values of Fourier parameters A=%i, B=%i : the output will NOT be normalized and BACKWARD Fourier transform is computed \n&quot;, fourier_params[0],fourier_params[1]);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   } else {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          1 :     std::vector&lt;std::string&gt; fourier_str = Tools::getWords(params_str, &quot;\t\n ,&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :     if (fourier_str.size()&gt;2) error(&quot;FOURIER_PARAMETERS can take just two values&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          3 :     for (unsigned i=0; i&lt;fourier_str.size(); ++i) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :       Tools::convert(fourier_str[i],fourier_params[i]);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :       if (fourier_params[i]&gt;1 || fourier_params[i]&lt;-1) error(&quot;values accepted for FOURIER_PARAMETERS are only -1, 1 or 0&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     }</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :     log.printf(&quot;  Fourier parameters are A=%i, B=%i \n&quot;, fourier_params[0],fourier_params[1]);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   // Create the input from the old string</a>
+<a name="140"><span class="lineNum">     140 </span>            :   std::string vstring;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :   if (real_output) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     if (!store_norm) vstring=&quot;COMPONENTS=&quot; + getLabel() + &quot;_abs&quot;;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     else vstring=&quot;COMPONENTS=&quot; + getLabel() + &quot;_norm&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   } else vstring=&quot;COMPONENTS=&quot; + getLabel() + &quot;_real,&quot; + getLabel() + &quot;_imag&quot;;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Set COORDINATES keyword</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :   vstring += &quot; COORDINATES=&quot; + ingrid-&gt;getComponentName( 0 );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 :   for(unsigned i=1; i&lt;ingrid-&gt;getDimension(); ++i) vstring += &quot;,&quot; + ingrid-&gt;getComponentName( i );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   // Set PBC keyword</a>
+<a name="151"><span class="lineNum">     151 </span>            :   vstring += &quot; PBC=&quot;;</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :   if( ingrid-&gt;isPeriodic(0) ) vstring+=&quot;T&quot;; else vstring+=&quot;F&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :   for(unsigned i=1; i&lt;ingrid-&gt;getDimension(); ++i) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          1 :     if( ingrid-&gt;isPeriodic(i) ) vstring+=&quot;,T&quot;; else vstring+=&quot;,F&quot;;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            :   // Create a grid on which to store the fourier transform of the input grid</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          1 :   auto grid=createGrid( &quot;grid&quot;, vstring );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :   if( ingrid-&gt;noDerivatives() ) grid-&gt;setNoDerivatives();</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          1 :   setAveragingAction( std::move(grid), false );</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : #endif</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 : void FourierTransform::clearAverage() {</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   std::vector&lt;double&gt; fspacing;</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          1 :   std::vector&lt;std::string&gt; ft_min( ingrid-&gt;getMin() ), ft_max( ingrid-&gt;getMax() );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;ingrid-&gt;getDimension(); ++i) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :     Tools::convert( 0.0, ft_min[i] ); Tools::convert( 2.0*pi*ingrid-&gt;getNbin()[i]/ ingrid-&gt;getGridExtent(i), ft_max[i] );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :   mygrid-&gt;setBounds( ft_min, ft_max, ingrid-&gt;getNbin(), fspacing); resizeFunctions();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :   ActionWithAveraging::clearAverage();</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          2 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : #ifdef __PLUMED_HAS_FFTW</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          4 : void FourierTransform::performOperations( const bool&amp; from_update ) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   // Spacing of the real grid</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; g_spacing ( ingrid-&gt;getGridSpacing() );</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   // *** CHECK CORRECT k-GRID BOUNDARIES ***</a>
+<a name="184"><span class="lineNum">     184 </span>            :   //log&lt;&lt;&quot;Real grid boundaries: \n&quot;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   //    &lt;&lt;&quot;  min_x: &quot;&lt;&lt;mygrid-&gt;getMin()[0]&lt;&lt;&quot;  min_y: &quot;&lt;&lt;mygrid-&gt;getMin()[1]&lt;&lt;&quot;\n&quot;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   //    &lt;&lt;&quot;  max_x: &quot;&lt;&lt;mygrid-&gt;getMax()[0]&lt;&lt;&quot;  max_y: &quot;&lt;&lt;mygrid-&gt;getMax()[1]&lt;&lt;&quot;\n&quot;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //    &lt;&lt;&quot;K-grid boundaries:&quot;&lt;&lt;&quot;\n&quot;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   //    &lt;&lt;&quot;  min_x: &quot;&lt;&lt;ft_min[0]&lt;&lt;&quot;  min_y: &quot;&lt;&lt;ft_min[1]&lt;&lt;&quot;\n&quot;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //    &lt;&lt;&quot;  max_x: &quot;&lt;&lt;ft_max[0]&lt;&lt;&quot;  max_y: &quot;&lt;&lt;ft_max[1]&lt;&lt;&quot;\n&quot;;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Get the size of the input data arrays (to allocate FFT data)</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          4 :   size_t fft_dimension=static_cast&lt;size_t&gt;( ingrid-&gt;getNumberOfPoints() );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 :   std::vector&lt;unsigned&gt; N_input_data( ingrid-&gt;getNbin() );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;N_input_data.size(); ++i) if( !ingrid-&gt;isPeriodic(i) ) N_input_data[i]++;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   // size_t fft_dimension=1; for(unsigned i=0; i&lt;N_input_data.size(); ++i) fft_dimension*=static_cast&lt;size_t&gt;( N_input_data[i] );</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   // FFT arrays</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          4 :   std::vector&lt;std::complex&lt;double&gt; &gt; input_data(fft_dimension), fft_data(fft_dimension);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :   // Fill real input with the data on the grid</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 :   std::vector&lt;unsigned&gt; ind( ingrid-&gt;getDimension() );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      40808 :   for (unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :     // Get point indices</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      40804 :     ingrid-&gt;getIndices(i, ind);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     // Fill input data in row-major order</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      40804 :     input_data[ind[0]*N_input_data[0]+ind[1]].real( getFunctionValue( i ) );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">      40804 :     input_data[ind[0]*N_input_data[0]+ind[1]].imag( 0.0 );</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   // *** HERE is the only clear limitation: I'm computing explicitly a 2D FT. It should not happen to deal with other than two-dimensional grid ...</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          4 :   fftw_plan plan_complex = fftw_plan_dft_2d(N_input_data[0], N_input_data[1], reinterpret_cast&lt;fftw_complex*&gt;(&amp;input_data[0]), reinterpret_cast&lt;fftw_complex*&gt;(&amp;fft_data[0]), fourier_params[1], FFTW_ESTIMATE);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   // Compute FT</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          4 :   fftw_execute( plan_complex );</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // Compute the normalization constant</a>
+<a name="218"><span class="lineNum">     218 </span>            :   double norm=1.0;</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         12 :   for (unsigned i=0; i&lt;N_input_data.size(); ++i) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          8 :     norm *= pow( N_input_data[i], (1-fourier_params[0])/2 );</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   // Save FT data to output grid</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          4 :   std::vector&lt;unsigned&gt; N_out_data ( mygrid-&gt;getNbin() );</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          8 :   std::vector&lt;unsigned&gt; out_ind ( mygrid-&gt;getDimension() );</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      40808 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      40804 :     mygrid-&gt;getIndices( i, out_ind );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      40804 :     if (real_output) {</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :       double ft_value;</a>
+<a name="230"><span class="lineNum">     230 </span>            :       // Compute abs/norm and fix normalization</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :       if (!store_norm) ft_value=std::abs( fft_data[out_ind[0]*N_out_data[0]+out_ind[1]] / norm );</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :       else ft_value=std::norm( fft_data[out_ind[0]*N_out_data[0]+out_ind[1]] / norm );</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :       // Set the value</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :       mygrid-&gt;setGridElement( i, 0, ft_value );</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     } else {</a>
+<a name="236"><span class="lineNum">     236 </span>            :       double ft_value_real, ft_value_imag;</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      40804 :       ft_value_real=fft_data[out_ind[0]*N_out_data[0]+out_ind[1]].real() / norm;</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      40804 :       ft_value_imag=fft_data[out_ind[0]*N_out_data[0]+out_ind[1]].imag() / norm;</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :       // Set values</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      40804 :       mygrid-&gt;setGridElement( i, 0, ft_value_real);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">      40804 :       mygrid-&gt;setGridElement( i, 1, ft_value_imag);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     }</a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :   // Free FFTW stuff</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          4 :   fftw_destroy_plan(plan_complex);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          4 : }</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : #endif</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : } // end namespace 'gridtools'</a>
+<a name="252"><span class="lineNum">     252 </span>            : } // end namespace 'PLMD'</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridPrintingBase.cpp.func-sort-c.html b/coverage/gridtools/GridPrintingBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a55ee32159
--- /dev/null
+++ b/coverage/gridtools/GridPrintingBase.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridPrintingBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridPrintingBase.cpp<span style="font-size: 80%;"> (<a href="GridPrintingBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridPrintingBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#38">_ZN4PLMD9gridtools16GridPrintingBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#88">_ZN4PLMD9gridtools16GridPrintingBase12runFinalJobsEv</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#38">_ZN4PLMD9gridtools16GridPrintingBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#28">_ZN4PLMD9gridtools16GridPrintingBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#73">_ZN4PLMD9gridtools16GridPrintingBase6updateEv</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridPrintingBase.cpp.func.html b/coverage/gridtools/GridPrintingBase.cpp.func.html
new file mode 100644
index 0000000000..8ce898a5e8
--- /dev/null
+++ b/coverage/gridtools/GridPrintingBase.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridPrintingBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridPrintingBase.cpp<span style="font-size: 80%;"> (<a href="GridPrintingBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridPrintingBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#88">_ZN4PLMD9gridtools16GridPrintingBase12runFinalJobsEv</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#28">_ZN4PLMD9gridtools16GridPrintingBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#73">_ZN4PLMD9gridtools16GridPrintingBase6updateEv</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#38">_ZN4PLMD9gridtools16GridPrintingBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.cpp.gcov.html#38">_ZN4PLMD9gridtools16GridPrintingBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridPrintingBase.cpp.gcov.html b/coverage/gridtools/GridPrintingBase.cpp.gcov.html
new file mode 100644
index 0000000000..fd26007bee
--- /dev/null
+++ b/coverage/gridtools/GridPrintingBase.cpp.gcov.html
@@ -0,0 +1,181 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridPrintingBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridPrintingBase.cpp<span style="font-size: 80%;"> (source / <a href="GridPrintingBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;GridPrintingBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace gridtools {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         63 : void GridPrintingBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         63 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        126 :   keys.add(&quot;compulsory&quot;,&quot;GRID&quot;,&quot;the action that creates the grid you would like to output&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        126 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;0&quot;,&quot;the frequency with which the grid should be output to the file.  The default &quot;</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :            &quot;value of 0 ensures that the grid is only output at the end of the trajectory&quot;);</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        126 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;density&quot;,&quot;the file on which to write the grid.&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        126 :   keys.add(&quot;compulsory&quot;,&quot;REPLICA&quot;,&quot;0&quot;,&quot;the replica for which you would like to output this information&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        126 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;the format that should be used to output real numbers&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         63 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         57 : GridPrintingBase::GridPrintingBase(const ActionOptions&amp;ao):</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   Action(ao),</a>
+<a name="42"><span class="lineNum">      42 </span>            :   ActionPilot(ao),</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        114 :   fmt(&quot;%f&quot;),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         57 :   output_for_all_replicas(false)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         57 :   std::string mlab; parse(&quot;GRID&quot;,mlab);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         57 :   vesselbase::ActionWithVessel* mves= plumed.getActionSet().selectWithLabel&lt;vesselbase::ActionWithVessel*&gt;(mlab);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         57 :   if(!mves) error(&quot;action labelled &quot; +  mlab + &quot; does not exist or does not have vessels&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         57 :   addDependency(mves);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         57 :   for(unsigned i=0; i&lt;mves-&gt;getNumberOfVessels(); ++i) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         57 :     ingrid=dynamic_cast&lt;GridVessel*&gt;( mves-&gt;getPntrToVessel(i) );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         57 :     if( ingrid ) break;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   }</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         57 :   if( !ingrid ) error(&quot;input action does not calculate a grid&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        114 :   parse(&quot;FILE&quot;,filename);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         57 :   if(filename.length()==0) error(&quot;name out output file was not specified&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         57 :   log.printf(&quot;  outputting grid calculated by action %s to file named %s&quot;,mves-&gt;getLabel().c_str(), filename.c_str() );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        114 :   if( keywords.exists(&quot;FMT&quot;) ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        110 :     parse(&quot;FMT&quot;,fmt); log.printf(&quot; with format %s \n&quot;, fmt.c_str() );</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   } else {</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        114 :   std::string rep_data; parse(&quot;REPLICA&quot;,rep_data);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         57 :   if( rep_data==&quot;all&quot; ) output_for_all_replicas=true;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         57 :   else { preps.resize(1); Tools::convert( rep_data, preps[0] ); }</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         57 :   if( output_for_all_replicas ) log.printf(&quot;  outputting files for all replicas \n&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   else {</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         57 :     log.printf(&quot;  outputting data for replicas &quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        114 :     for(unsigned i=0; i&lt;preps.size(); ++i) log.printf(&quot;%d &quot;, preps[i] );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   }</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         57 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         68 : void GridPrintingBase::update() {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         68 :   if( !output_for_all_replicas ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         68 :     bool found=false; unsigned myrep=plumed.multi_sim_comm.Get_rank();</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         68 :     for(unsigned i=0; i&lt;preps.size(); ++i) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         68 :       if( myrep==preps[i] ) { found=true; break; }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     }</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         93 :     if( !found ) return;</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         68 :   if( getStep()==0 || getStride()==0 ) return ;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         43 :   OFile ofile; ofile.link(*this);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         43 :   ofile.setBackupString(&quot;analysis&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         43 :   ofile.open( filename ); printGrid( ofile );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         43 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         57 : void GridPrintingBase::runFinalJobs() {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         57 :   if( !output_for_all_replicas ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         57 :     bool found=false; unsigned myrep=plumed.multi_sim_comm.Get_rank();</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         62 :     for(unsigned i=0; i&lt;preps.size(); ++i) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         57 :       if( myrep==preps[i] ) { found=true; break; }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         82 :     if( !found ) return;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         52 :   if( getStride()&gt;0 ) return;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         27 :   OFile ofile; ofile.link(*this);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         27 :   ofile.open( filename ); printGrid( ofile );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         27 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridPrintingBase.h.func-sort-c.html b/coverage/gridtools/GridPrintingBase.h.func-sort-c.html
new file mode 100644
index 0000000000..e323607d01
--- /dev/null
+++ b/coverage/gridtools/GridPrintingBase.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridPrintingBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridPrintingBase.h<span style="font-size: 80%;"> (<a href="GridPrintingBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridPrintingBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.h.gcov.html#40">_ZN4PLMD9gridtools16GridPrintingBase5applyEv</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.h.gcov.html#39">_ZN4PLMD9gridtools16GridPrintingBase9calculateEv</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridPrintingBase.h.func.html b/coverage/gridtools/GridPrintingBase.h.func.html
new file mode 100644
index 0000000000..69a660ffe8
--- /dev/null
+++ b/coverage/gridtools/GridPrintingBase.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridPrintingBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridPrintingBase.h<span style="font-size: 80%;"> (<a href="GridPrintingBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridPrintingBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.h.gcov.html#40">_ZN4PLMD9gridtools16GridPrintingBase5applyEv</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridPrintingBase.h.gcov.html#39">_ZN4PLMD9gridtools16GridPrintingBase9calculateEv</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridPrintingBase.h.gcov.html b/coverage/gridtools/GridPrintingBase.h.gcov.html
new file mode 100644
index 0000000000..16f808c775
--- /dev/null
+++ b/coverage/gridtools/GridPrintingBase.h.gcov.html
@@ -0,0 +1,126 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridPrintingBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridPrintingBase.h<span style="font-size: 80%;"> (source / <a href="GridPrintingBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_GridPrintingBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_GridPrintingBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;GridVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace gridtools {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class GridPrintingBase : public ActionPilot {</a>
+<a name="33"><span class="lineNum">      33 </span>            : protected:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   GridVessel* ingrid;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   std::string fmt, filename;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   bool output_for_all_replicas;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;unsigned&gt; preps;</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit GridPrintingBase(const ActionOptions&amp;ao);</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         68 :   void calculate() override {}</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         68 :   void apply() override {}</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   void update() override;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void runFinalJobs() override;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   virtual void printGrid( OFile&amp; ofile ) const=0;</a>
+<a name="46"><span class="lineNum">      46 </span>            : };</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridSearch.h.func-sort-c.html b/coverage/gridtools/GridSearch.h.func-sort-c.html
new file mode 100644
index 0000000000..b5ee543fa7
--- /dev/null
+++ b/coverage/gridtools/GridSearch.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridSearch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridSearch.h<span style="font-size: 80%;"> (<a href="GridSearch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridSearch.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridSearch.h.gcov.html#41">_ZN4PLMD9gridtools10GridSearchINS_6dimred18SketchMapPointwiseEEC2ERKSt6vectorIdSaIdEES9_RKS5_IjSaIjEESD_PS3_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridSearch.h.gcov.html#64">_ZN4PLMD9gridtools10GridSearchINS_6dimred18SketchMapPointwiseEE8minimiseERSt6vectorIdSaIdEEMS3_FdRKS7_S8_E</a></td>
+              <td class="coverFnHi">200</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridSearch.h.func.html b/coverage/gridtools/GridSearch.h.func.html
new file mode 100644
index 0000000000..308a61038a
--- /dev/null
+++ b/coverage/gridtools/GridSearch.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridSearch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridSearch.h<span style="font-size: 80%;"> (<a href="GridSearch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridSearch.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridSearch.h.gcov.html#64">_ZN4PLMD9gridtools10GridSearchINS_6dimred18SketchMapPointwiseEE8minimiseERSt6vectorIdSaIdEEMS3_FdRKS7_S8_E</a></td>
+              <td class="coverFnHi">200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridSearch.h.gcov.html#41">_ZN4PLMD9gridtools10GridSearchINS_6dimred18SketchMapPointwiseEEC2ERKSt6vectorIdSaIdEES9_RKS5_IjSaIjEESD_PS3_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridSearch.h.gcov.html b/coverage/gridtools/GridSearch.h.gcov.html
new file mode 100644
index 0000000000..6f1c01ac8d
--- /dev/null
+++ b/coverage/gridtools/GridSearch.h.gcov.html
@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridSearch.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridSearch.h<span style="font-size: 80%;"> (source / <a href="GridSearch.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryHi">95.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_GridSearch_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_GridSearch_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/MinimiseBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;GridVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;memory&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace gridtools {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          1 : class GridSearch {</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// This is the pointer to the member function in the energy</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// calculating class that calculates the energy</a>
+<a name="38"><span class="lineNum">      38 </span>            :   typedef double(FCLASS::*engf_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der );</a>
+<a name="39"><span class="lineNum">      39 </span>            :   FCLASS* myclass_func;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   std::unique_ptr&lt;GridVessel&gt; mygrid;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::unique_ptr&lt;GridVessel&gt; myfgrid;</a>
+<a name="42"><span class="lineNum">      42 </span>            : public:</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          1 :   GridSearch( const std::vector&lt;double&gt;&amp; mmin, const std::vector&lt;double&gt;&amp; mmax, const std::vector&lt;unsigned&gt;&amp; ng, const std::vector&lt;unsigned&gt;&amp; nfg, FCLASS* funcc ) :</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          1 :     myclass_func( funcc )</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   {</a>
+<a name="46"><span class="lineNum">      46 </span>            :     // Create the grid objects</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          1 :     std::string nstr, vstring=&quot;COMPONENTS=func COORDINATES=x1&quot;;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          2 :     for(unsigned i=1; i&lt;mmin.size(); ++i) { Tools::convert(i+1,nstr); vstring += &quot;,x&quot; + nstr; }</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          2 :     vstring += &quot; PBC=F&quot;; for(unsigned i=1; i&lt;mmin.size(); ++i) vstring += &quot;,F&quot;;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 :     vesselbase::VesselOptions da(&quot;mygrid&quot;,&quot;&quot;,-1,vstring,NULL);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          1 :     Keywords keys; gridtools::GridVessel::registerKeywords( keys );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          1 :     vesselbase::VesselOptions dar( da, keys );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          2 :     mygrid=Tools::make_unique&lt;GridVessel&gt;(dar);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          2 :     if( nfg[0]&gt;0 ) myfgrid=Tools::make_unique&lt;GridVessel&gt;(dar);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :     // Now setup the min and max values for the grid</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          1 :     std::vector&lt;std::string&gt; gmin( nfg.size() ), gmax( nfg.size() ); std::vector&lt;double&gt; dummy_spacing;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;nfg.size(); ++i) { Tools::convert(mmin[i],gmin[i]); Tools::convert(mmax[i],gmax[i]); }</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          1 :     mygrid-&gt;setBounds( gmin, gmax, ng, dummy_spacing ); mygrid-&gt;resize();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          1 :     if( myfgrid ) myfgrid-&gt;setBounds( gmin, gmax, nfg, dummy_spacing );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 :   }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool minimise( std::vector&lt;double&gt;&amp; p, engf_pointer myfunc );</a>
+<a name="63"><span class="lineNum">      63 </span>            : };</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        200 : bool GridSearch&lt;FCLASS&gt;::minimise( std::vector&lt;double&gt;&amp; p, engf_pointer myfunc ) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        200 :   std::vector&lt;double&gt; der( p.size() ); std::vector&lt;double&gt; coords( p.size() );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        200 :   double initial_eng = (myclass_func-&gt;*myfunc)( p, der );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        200 :   mygrid-&gt;getGridPointCoordinates( 0, coords );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        200 :   double emin=(myclass_func-&gt;*myfunc)( coords, der );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        200 :   mygrid-&gt;setValueAndDerivatives( 0, 0, emin, der ); unsigned pmin=0;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      24200 :   for(unsigned i=1; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      24000 :     mygrid-&gt;getGridPointCoordinates( i, coords );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      24000 :     double eng = (myclass_func-&gt;*myfunc)( coords, der );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      24000 :     mygrid-&gt;setValueAndDerivatives( i, 0, eng, der );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      24000 :     if( eng&lt;emin ) { emin=eng; pmin=i; }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   }</a>
+<a name="78"><span class="lineNum">      78 </span>            :   // This prevents division by zero</a>
+<a name="79"><span class="lineNum">      79 </span>            :   mygrid-&gt;setNorm( 1.0 );</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        200 :   if( myfgrid ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        200 :     myfgrid-&gt;getGridPointCoordinates( 0, coords ); pmin=0;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        200 :     double emin=mygrid-&gt;getValueAndDerivatives( coords, 0, der );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">     520200 :     for(unsigned i=1; i&lt;myfgrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     520000 :       myfgrid-&gt;getGridPointCoordinates( i, coords );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     520000 :       double eng = mygrid-&gt;getValueAndDerivatives( coords, 0, der );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     520000 :       if( eng&lt;emin ) { emin=eng; pmin=i; }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     }</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        200 :     myfgrid-&gt;getGridPointCoordinates( pmin, coords );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        200 :     double checkEng = (myclass_func-&gt;*myfunc)( coords, der );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        200 :     if( checkEng&lt;initial_eng ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         22 :       myfgrid-&gt;getGridPointCoordinates( pmin, p );</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :       return true;</a>
+<a name="94"><span class="lineNum">      94 </span>            :     } else {</a>
+<a name="95"><span class="lineNum">      95 </span>            :       return false;</a>
+<a name="96"><span class="lineNum">      96 </span>            :     }</a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   if( emin&lt;initial_eng ) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     mygrid-&gt;getGridPointCoordinates( pmin, p );</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     return true;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   } else {</a>
+<a name="103"><span class="lineNum">     103 </span>            :     return false;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : #endif</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridToXYZ.cpp.func-sort-c.html b/coverage/gridtools/GridToXYZ.cpp.func-sort-c.html
new file mode 100644
index 0000000000..46545a2a76
--- /dev/null
+++ b/coverage/gridtools/GridToXYZ.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridToXYZ.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridToXYZ.cpp<span style="font-size: 80%;"> (<a href="GridToXYZ.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridToXYZ.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#58">_ZN4PLMD9gridtools9GridToXYZC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#48">_ZN4PLMD9gridtools12_GLOBAL__N_121GridToXYZRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#58">_ZN4PLMD9gridtools9GridToXYZC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#92">_ZNK4PLMD9gridtools9GridToXYZ9printGridERNS_5OFileE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#50">_ZN4PLMD9gridtools9GridToXYZ16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#48">_ZN4PLMD9gridtools12_GLOBAL__N_121GridToXYZRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#48">_ZN4PLMD9gridtools12_GLOBAL__N_121GridToXYZRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridToXYZ.cpp.func.html b/coverage/gridtools/GridToXYZ.cpp.func.html
new file mode 100644
index 0000000000..48dc3c35b9
--- /dev/null
+++ b/coverage/gridtools/GridToXYZ.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridToXYZ.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridToXYZ.cpp<span style="font-size: 80%;"> (<a href="GridToXYZ.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridToXYZ.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#48">_ZN4PLMD9gridtools12_GLOBAL__N_121GridToXYZRegisterMe506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#48">_ZN4PLMD9gridtools12_GLOBAL__N_121GridToXYZRegisterMe50C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#48">_ZN4PLMD9gridtools12_GLOBAL__N_121GridToXYZRegisterMe50D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#50">_ZN4PLMD9gridtools9GridToXYZ16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#58">_ZN4PLMD9gridtools9GridToXYZC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#58">_ZN4PLMD9gridtools9GridToXYZC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridToXYZ.cpp.gcov.html#92">_ZNK4PLMD9gridtools9GridToXYZ9printGridERNS_5OFileE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridToXYZ.cpp.gcov.html b/coverage/gridtools/GridToXYZ.cpp.gcov.html
new file mode 100644
index 0000000000..45eb69ad0a
--- /dev/null
+++ b/coverage/gridtools/GridToXYZ.cpp.gcov.html
@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridToXYZ.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridToXYZ.cpp<span style="font-size: 80%;"> (source / <a href="GridToXYZ.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;GridPrintingBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace gridtools {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC GRIDANALYSIS GRID_TO_XYZ</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Output the function on the grid to an xyz file</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \par Examples</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : */</a>
+<a name="38"><span class="lineNum">      38 </span>            : //+ENDPLUMEDOC</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class GridToXYZ : public GridPrintingBase {</a>
+<a name="41"><span class="lineNum">      41 </span>            : private:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double lenunit;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   unsigned mycomp;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   explicit GridToXYZ(const ActionOptions&amp;ao);</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void printGrid( OFile&amp; ofile ) const override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(GridToXYZ,&quot;GRID_TO_XYZ&quot;)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          4 : void GridToXYZ::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          4 :   GridPrintingBase::registerKeywords( keys );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;COMPONENT&quot;,&quot;if your input is a vector field use this to specify the component of the input vector field for which you wish to output&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;UNITS&quot;,&quot;PLUMED&quot;,&quot;the units in which to print out the coordinates. PLUMED means internal PLUMED units&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;, &quot;PRECISION&quot;,&quot;The number of digits in trajectory file&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          4 :   keys.remove(&quot;FMT&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          2 : GridToXYZ::GridToXYZ(const ActionOptions&amp;ao):</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   Action(ao),</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :   GridPrintingBase(ao)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          2 :   if( ingrid-&gt;getDimension()!=3 ) error(&quot;cannot print grid xyz file if grid does not contain three dimensional data&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          2 :   fmt = &quot; &quot; + fmt;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 :   if( ingrid-&gt;getNumberOfComponents()==1 ) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          2 :     mycomp=0;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   } else {</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     int tcomp=-1; parse(&quot;COMPONENT&quot;,tcomp);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :     if( tcomp&lt;0 ) error(&quot;component of vector field was not specified - use COMPONENT keyword&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :     mycomp=tcomp*(1+ingrid-&gt;getDimension()); if( ingrid-&gt;noDerivatives() ) mycomp=tcomp;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :     log.printf(&quot;  using %dth component of grid \n&quot;,tcomp );</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span>            :   fmt=&quot;%f&quot;;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          4 :   std::string precision; parse(&quot;PRECISION&quot;,precision);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          2 :   if(precision.length()&gt;0) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          2 :     int p; Tools::convert(precision,p);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  with precision &quot;&lt;&lt;p&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     std::string a,b;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          2 :     Tools::convert(p+5,a);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          2 :     Tools::convert(p,b);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :     fmt=&quot;%&quot;+a+&quot;.&quot;+b+&quot;f&quot;;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :   std::string unitname; parse(&quot;UNITS&quot;,unitname);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :   if(unitname!=&quot;PLUMED&quot;) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 :     Units myunit; myunit.setLength(unitname);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :     lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 :   }</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   else lenunit=1.0;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 : void GridToXYZ::printGrid( OFile&amp; ofile ) const {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   std::vector&lt;double&gt; point( 3 );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   ofile.printf(&quot;%u\n&quot;,ingrid-&gt;getNumberOfPoints());</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   ofile.printf(&quot;Grid converted to xyz file \n&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        246 :   for(unsigned i=0; i&lt;ingrid-&gt;getNumberOfPoints(); ++i) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        244 :     ingrid-&gt;getGridPointCoordinates( i, point );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        244 :     ofile.printf(&quot;X&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     double val;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        488 :     if( ingrid-&gt;getType()==&quot;flat&quot; ) val=1.0;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        244 :     else val=ingrid-&gt;getGridElement( i, 0 );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        976 :     for(unsigned j=0; j&lt;3; ++j) { ofile.printf( (&quot; &quot; + fmt).c_str(), val*lenunit*point[j] ); }</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        244 :     ofile.printf(&quot;\n&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          2 : }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridVessel.cpp.func-sort-c.html b/coverage/gridtools/GridVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a17ccce555
--- /dev/null
+++ b/coverage/gridtools/GridVessel.cpp.func-sort-c.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridVessel.cpp<span style="font-size: 80%;"> (<a href="GridVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">316</td>
+            <td class="headerCovTableEntry">334</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#357">_ZN4PLMD9gridtools10GridVessel14setGridElementERKSt6vectorIjSaIjEERKjRKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#353">_ZNK4PLMD9gridtools10GridVessel14getGridElementERKSt6vectorIjSaIjEERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#117">_ZN4PLMD9gridtools10GridVessel18setupFibonacciGridERKj</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#501">_ZN4PLMD9gridtools10GridVessel19activateThesePointsERKSt6vectorIbSaIbEE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#433">_ZNK4PLMD9gridtools10GridVessel12getCubeUnitsEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#429">_ZN4PLMD9gridtools10GridVessel12setCubeUnitsERKd</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#437">_ZNK4PLMD9gridtools10GridVessel14getInputStringB5cxx11Ev</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#75">_ZN4PLMD9gridtools10GridVessel16setNoDerivativesEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#515">_ZN4PLMD9gridtools10GridVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#506">_ZN4PLMD9gridtools10GridVessel8setForceERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#227">_ZNK4PLMD9gridtools10GridVessel17getFibonacciIndexERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#161">_ZN4PLMD9gridtools10GridVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">65</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#28">_ZN4PLMD9gridtools10GridVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">66</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#36">_ZN4PLMD9gridtools10GridVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">67</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#85">_ZN4PLMD9gridtools10GridVessel9setBoundsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESC_RKS2_IjSaIjEERKS2_IdSaIdEE</a></td>
+              <td class="coverFnHi">98</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#348">_ZN4PLMD9gridtools10GridVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">118</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#185">_ZN4PLMD9gridtools10GridVessel6resizeEv</a></td>
+              <td class="coverFnHi">213</td>
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+              <td class="coverFnHi">2605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#343">_ZNK4PLMD9gridtools10GridVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">15087</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#379">_ZNK4PLMD9gridtools10GridVessel12getNeighborsERKSt6vectorIdSaIdEERKS2_IjSaIjEERjRS8_</a></td>
+              <td class="coverFnHi">21514</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#333">_ZN4PLMD9gridtools10GridVessel22setValueAndDerivativesERKjS3_RKdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">24200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#398">_ZNK4PLMD9gridtools10GridVessel12getNeighborsERKSt6vectorIjSaIjEES6_RjRS4_</a></td>
+              <td class="coverFnHi">40878</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#291">_ZNK4PLMD9gridtools10GridVessel23getFibonacciCoordinatesERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">86817</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#328">_ZN4PLMD9gridtools10GridVessel14setGridElementERKjS3_RKd</a></td>
+              <td class="coverFnHi">154208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#361">_ZNK4PLMD9gridtools10GridVessel6getMinB5cxx11Ev</a></td>
+              <td class="coverFnHi">202520</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#365">_ZNK4PLMD9gridtools10GridVessel6getMaxB5cxx11Ev</a></td>
+              <td class="coverFnHi">202553</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#369">_ZNK4PLMD9gridtools10GridVessel7getNbinEv</a></td>
+              <td class="coverFnHi">203150</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#299">_ZNK4PLMD9gridtools10GridVessel18getSplineNeighborsERKjRjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">528845</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#454">_ZNK4PLMD9gridtools10GridVessel22getValueAndDerivativesERKSt6vectorIdSaIdEERKjRS4_</a></td>
+              <td class="coverFnHi">528845</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#215">_ZNK4PLMD9gridtools10GridVessel8getIndexERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">530956</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#271">_ZNK4PLMD9gridtools10GridVessel23getGridPointCoordinatesERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">665380</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#202">_ZNK4PLMD9gridtools10GridVessel10getIndicesERKSt6vectorIdSaIdEERS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">1060389</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#323">_ZNK4PLMD9gridtools10GridVessel14getGridElementERKjS3_</a></td>
+              <td class="coverFnHi">6552681</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#511">_ZNK4PLMD9gridtools10GridVessel9wasForcedEv</a></td>
+              <td class="coverFnHi">11870273</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#275">_ZNK4PLMD9gridtools10GridVessel23getGridPointCoordinatesERKjRSt6vectorIjSaIjEERS4_IdSaIdEE</a></td>
+              <td class="coverFnHi">12514073</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#286">_ZNK4PLMD9gridtools10GridVessel22getFlatGridCoordinatesERKjRSt6vectorIjSaIjEERS4_IdSaIdEE</a></td>
+              <td class="coverFnHi">13037801</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#267">_ZNK4PLMD9gridtools10GridVessel10getIndicesERKjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">15879019</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#192">_ZNK4PLMD9gridtools10GridVessel8getIndexERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">24333376</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#256">_ZNK4PLMD9gridtools10GridVessel21convertIndexToIndicesERKjRKSt6vectorIjSaIjEERS6_</a></td>
+              <td class="coverFnHi">112427817</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridVessel.cpp.func.html b/coverage/gridtools/GridVessel.cpp.func.html
new file mode 100644
index 0000000000..c4d919dd9c
--- /dev/null
+++ b/coverage/gridtools/GridVessel.cpp.func.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridVessel.cpp<span style="font-size: 80%;"> (<a href="GridVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">316</td>
+            <td class="headerCovTableEntry">334</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">24200</td>
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+              <td class="coverFnHi">17</td>
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+              <td class="coverFnHi">13037801</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#454">_ZNK4PLMD9gridtools10GridVessel22getValueAndDerivativesERKSt6vectorIdSaIdEERKjRS4_</a></td>
+              <td class="coverFnHi">528845</td>
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+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#291">_ZNK4PLMD9gridtools10GridVessel23getFibonacciCoordinatesERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">86817</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#271">_ZNK4PLMD9gridtools10GridVessel23getGridPointCoordinatesERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">665380</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#275">_ZNK4PLMD9gridtools10GridVessel23getGridPointCoordinatesERKjRSt6vectorIjSaIjEERS4_IdSaIdEE</a></td>
+              <td class="coverFnHi">12514073</td>
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+              <td class="coverFnHi">202553</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#361">_ZNK4PLMD9gridtools10GridVessel6getMinB5cxx11Ev</a></td>
+              <td class="coverFnHi">202520</td>
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+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#369">_ZNK4PLMD9gridtools10GridVessel7getNbinEv</a></td>
+              <td class="coverFnHi">203150</td>
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+              <td class="coverFnHi">530956</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#192">_ZNK4PLMD9gridtools10GridVessel8getIndexERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">24333376</td>
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+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#343">_ZNK4PLMD9gridtools10GridVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">15087</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.cpp.gcov.html#511">_ZNK4PLMD9gridtools10GridVessel9wasForcedEv</a></td>
+              <td class="coverFnHi">11870273</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridVessel.cpp.gcov.html b/coverage/gridtools/GridVessel.cpp.gcov.html
new file mode 100644
index 0000000000..a9e84392b4
--- /dev/null
+++ b/coverage/gridtools/GridVessel.cpp.gcov.html
@@ -0,0 +1,602 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridVessel.cpp<span style="font-size: 80%;"> (source / <a href="GridVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">316</td>
+            <td class="headerCovTableEntry">334</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;GridVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace gridtools {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         66 : void GridVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         66 :   AveragingVessel::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        132 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;flat&quot;,&quot;how the grid points are being generated&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        132 :   keys.add(&quot;compulsory&quot;,&quot;COMPONENTS&quot;,&quot;the names of the components in the vector&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        132 :   keys.add(&quot;compulsory&quot;,&quot;COORDINATES&quot;,&quot;the names of the coordinates of the grid&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        132 :   keys.add(&quot;compulsory&quot;,&quot;PBC&quot;,&quot;is the grid periodic in each direction or not&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         66 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         67 : GridVessel::GridVessel( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   AveragingVessel(da),</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         67 :   bounds_set(false),</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         67 :   npoints(0),</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         67 :   cube_units(1.0),</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         67 :   wasforced(false),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         67 :   noderiv(false)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        134 :   std::string geom; parse(&quot;TYPE&quot;,geom);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         67 :   if( geom==&quot;flat&quot; ) gtype=flat;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          3 :   else if( geom==&quot;fibonacci&quot; ) gtype=fibonacci;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 :   else plumed_merror( geom + &quot; is invalid geometry type&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        134 :   std::vector&lt;std::string&gt; compnames; parseVector(&quot;COMPONENTS&quot;,compnames);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         67 :   std::vector&lt;std::string&gt; coordnames; parseVector(&quot;COORDINATES&quot;,coordnames);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         67 :   if( gtype==flat ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         64 :     dimension=coordnames.size();</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         64 :     str_min.resize( dimension);  str_max.resize( dimension ); stride.resize( dimension );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         64 :     max.resize( dimension ); dx.resize( dimension ); nbin.resize( dimension ); min.resize( dimension );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          3 :   } else if( gtype==fibonacci ) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          3 :     if( coordnames.size()!=3 ) error(&quot;cannot generate fibonacci grid points on surface of sphere if not 3 input coordinates&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 :     dimension=3;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         67 :   unsigned n=0; nper=compnames.size()*( 1 + coordnames.size() );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         67 :   arg_names.resize( coordnames.size() + compnames.size()*( 1 + coordnames.size() ) );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        169 :   for(unsigned i=0; i&lt;coordnames.size(); ++i) { arg_names[n] = coordnames[i]; n++; }</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        135 :   for(unsigned i=0; i&lt;compnames.size(); ++i) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         68 :     arg_names[n]=compnames[i]; n++;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        172 :     for(unsigned j=0; j&lt;coordnames.size(); ++j) { arg_names[n] = &quot;d&quot; + compnames[i] + &quot;_&quot; + coordnames[j]; n++; }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   }</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         67 :   pbc.resize( dimension );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         67 :   std::vector&lt;std::string&gt; spbc( dimension ); parseVector(&quot;PBC&quot;,spbc);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        169 :   for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        102 :     if( spbc[i]==&quot;F&quot; ) pbc[i]=false;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         31 :     else if( spbc[i]==&quot;T&quot; ) pbc[i]=true;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :     else plumed_error();</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        134 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         19 : void GridVessel::setNoDerivatives() {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         19 :   nper = ( nper/(1+dimension) ); noderiv=true;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         19 :   std::vector&lt;std::string&gt; tnames( dimension ), cnames(nper);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         41 :   for(unsigned i=0; i&lt;dimension; ++i) tnames[i]=arg_names[i];</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         38 :   unsigned k=dimension; for(unsigned i=0; i&lt;nper; ++i) { cnames[i]=arg_names[k]; k+=(1+dimension); }</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         19 :   arg_names.resize( dimension + nper );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         41 :   for(unsigned i=0; i&lt;dimension; ++i) arg_names[i]=tnames[i];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         38 :   for(unsigned i=0; i&lt;nper; ++i) arg_names[dimension+i]=cnames[i];</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         19 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         98 : void GridVessel::setBounds( const std::vector&lt;std::string&gt;&amp; smin, const std::vector&lt;std::string&gt;&amp; smax,</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :                             const std::vector&lt;unsigned&gt;&amp; binsin, const std::vector&lt;double&gt;&amp; spacing ) {</a>
+<a name="89"><span class="lineNum">      89 </span>            :   plumed_dbg_assert( smin.size()==dimension &amp;&amp; smax.size()==dimension );</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         98 :   plumed_assert( gtype==flat &amp;&amp; (spacing.size()==dimension || binsin.size()==dimension) );</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         98 :   npoints=1; bounds_set=true;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        245 :   for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        147 :     str_min[i]=smin[i]; str_max[i]=smax[i];</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     // GB: I ignore the result here not to break test multicolvar/rt-dens-average</a>
+<a name="96"><span class="lineNum">      96 </span>            :     // where these functions were called with str_min[i] and str_max[i] as empty string</a>
+<a name="97"><span class="lineNum">      97 </span>            :     // To be checked.</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        147 :     Tools::convertNoexcept( str_min[i], min[i] );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        147 :     Tools::convertNoexcept( str_max[i], max[i] );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        147 :     if( spacing.size()==dimension &amp;&amp; binsin.size()==dimension ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         39 :       if( spacing[i]==0 ) nbin[i] = binsin[i];</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :       else {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         37 :         double range = max[i] - min[i]; nbin[i] = std::round( range / spacing[i]);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :         // This check ensures that nbins is set correctly if spacing is set the same as the number of bins</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         37 :         if( nbin[i]!=binsin[i] ) plumed_merror(&quot;mismatch between input spacing and input number of bins&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :       }</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        108 :     } else if( binsin.size()==dimension ) nbin[i]=binsin[i];</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     else if( spacing.size()==dimension ) nbin[i] = std::floor(( max[i] - min[i] ) / spacing[i]) + 1;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     else plumed_error();</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        147 :     dx[i] = ( max[i] - min[i] ) / static_cast&lt;double&gt;( nbin[i] );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        147 :     if( !pbc[i] ) { max[i] +=dx[i]; nbin[i]+=1; }</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        147 :     stride[i]=npoints;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        147 :     npoints*=nbin[i];</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   }</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         98 :   resize();  // Always resize after setting new bounds as grid size may have have changed</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         98 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          3 : void GridVessel::setupFibonacciGrid( const unsigned&amp; np ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          3 :   bounds_set=true; root5 = std::sqrt(5);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          3 :   npoints = np; golden = ( 1 + std::sqrt(5) ) / 2.0; igolden = golden - 1;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 :   fib_increment = 2*pi*igolden; log_golden2 = std::log( golden*golden );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          3 :   fib_offset = 2 / static_cast&lt;double&gt;( npoints );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 :   fib_shift = fib_offset/2 - 1;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   resize();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; icoord( dimension ), jcoord( dimension );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Find minimum distance between each pair of points</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; mindists( npoints );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        347 :   for(unsigned i=0; i&lt;npoints; ++i) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        344 :     getFibonacciCoordinates( i, icoord ); mindists[i] = 0;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      41080 :     for(unsigned j=0; j&lt;npoints; ++j) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      40736 :       if( i==j ) continue ; // Points are not neighbors to themselves</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      40392 :       getFibonacciCoordinates( j, jcoord );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :       // Calculate the dot product</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     161568 :       double dot=0; for(unsigned k=0; k&lt;dimension; ++k) dot += icoord[k]*jcoord[k];</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      40392 :       if( dot&gt;mindists[i] ) mindists[i]=dot;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :     }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   // And now take minimum of dot products</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          3 :   double min=mindists[0];</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        344 :   for(unsigned i=1; i&lt;npoints; ++i) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        341 :     if( mindists[i]&lt;min ) min=mindists[i];</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            :   double final_cutoff;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          3 :   if( getFibonacciCutoff()&lt;-1 ) final_cutoff=-1;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :   else final_cutoff = std::cos( std::acos( getFibonacciCutoff() ) + std::acos( min ) );</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   // And now construct the neighbor list</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :   fib_nlist.resize( npoints );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        347 :   for(unsigned i=0; i&lt;npoints; ++i) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        344 :     getFibonacciCoordinates( i, icoord );</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      41080 :     for(unsigned j=0; j&lt;npoints; ++j) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      40736 :       if( i==j ) continue ; // Points are not neighbors to themselves</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      40392 :       getFibonacciCoordinates( j, jcoord );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :       // Calculate the dot product</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">     161568 :       double dot=0; for(unsigned k=0; k&lt;dimension; ++k) dot += icoord[k]*jcoord[k];</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      40392 :       if( dot&gt;final_cutoff ) { fib_nlist[i].push_back(j); }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          3 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         65 : std::string GridVessel::description() {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         65 :   if( !bounds_set ) return &quot;&quot;;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::string des;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         51 :   if( gtype==flat ) {</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     des=&quot;grid of &quot;; std::string num;</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         68 :     for(unsigned i=0; i&lt;dimension-1; ++i) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         19 :       Tools::convert( nbin[i], num );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         38 :       des += num + &quot; X &quot;;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         49 :     Tools::convert( nbin[dimension-1], num );</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         49 :     des += num + &quot; equally spaced points between (&quot;;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         68 :     for(unsigned i=0; i&lt;dimension-1; ++i) des += str_min[i] + &quot;,&quot;;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         49 :     Tools::convert( nbin[dimension-1], num );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         49 :     des += str_min[dimension-1] + &quot;) and (&quot;;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         68 :     for(unsigned i=0; i&lt;dimension-1; ++i) des += str_max[i] + &quot;,&quot;;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         98 :     des += str_max[dimension-1] + &quot;)&quot;;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :   } else if( gtype==fibonacci ) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :     std::string num; Tools::convert( npoints, num );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :     des += &quot;fibonacci grid of &quot; + num + &quot; points on spherical surface&quot;;</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   return des;</a>
+<a name="185"><span class="lineNum">     185 </span>            : }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        213 : void GridVessel::resize() {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        213 :   plumed_massert( nper&gt;0, &quot;Number of datapoints at each grid point has not been set&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        213 :   if( getAction() ) resizeBuffer( getNumberOfBufferPoints()*nper + 1 + 2*getAction()-&gt;getNumberOfDerivatives() );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        213 :   setDataSize( npoints*nper ); forces.resize( npoints );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        213 :   if( active.size()!=npoints) active.resize( npoints, true );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        213 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">   24333376 : unsigned GridVessel::getIndex( const std::vector&lt;unsigned&gt;&amp; indices ) const {</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   plumed_dbg_assert( gtype==flat &amp;&amp; bounds_set &amp;&amp; indices.size()==dimension );</a>
+<a name="196"><span class="lineNum">     196 </span>            :   // indices are flattended using a column-major order</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">   24333376 :   unsigned index=indices[dimension-1];</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">   69887414 :   for(unsigned i=dimension-1; i&gt;0; --i) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">   45554038 :     index=index*nbin[i-1]+indices[i-1];</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">   24333376 :   return index;</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">    1060389 : void GridVessel::getIndices( const std::vector&lt;double&gt;&amp; point, std::vector&lt;unsigned&gt;&amp; indices ) const {</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   plumed_dbg_assert( gtype==flat &amp;&amp; bounds_set &amp;&amp; point.size()==dimension &amp;&amp; indices.size()==dimension );</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">    3196134 :   for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">    2135745 :     indices[i]=std::floor( (point[i] - min[i])/dx[i] );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">    2135745 :     if( pbc[i] ) indices[i]=indices[i]%nbin[i];</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    2090223 :     else if( indices[i]&gt;nbin[i] ) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :       std::string pp, num; Tools::convert( point[0], pp );</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       for(unsigned j=1; j&lt;point.size(); ++j) { Tools::convert( point[j], num ); pp += &quot;, &quot; + num; }</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;point (&quot; + pp + &quot;)  is outside grid range&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">    1060389 : }</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     530956 : unsigned GridVessel::getIndex( const std::vector&lt;double&gt;&amp; point ) const {</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   plumed_dbg_assert( gtype==flat &amp;&amp; bounds_set &amp;&amp; point.size()==dimension );</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">     530956 :   if( gtype==flat ) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     530956 :     std::vector&lt;unsigned&gt; indices(dimension); getIndices( point, indices );</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">     530956 :     return getIndex( indices );</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :   } else if( gtype==fibonacci ) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :     return getFibonacciIndex( point );</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   } else {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span>            : }</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         57 : unsigned GridVessel::getFibonacciIndex( const std::vector&lt;double&gt;&amp; p ) const {</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   plumed_dbg_assert( gtype==fibonacci );</a>
+<a name="231"><span class="lineNum">     231 </span>            :   // Convert input point to coordinates on cylinder</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         57 :   int k=2; double phi = std::atan2( p[2], p[0] ), sinthet2 = 1 - p[1]*p[1];</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   // Calculate power to raise golden ratio</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         57 :   if( sinthet2&lt;epsilon ) { k = 2; }</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   else {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         57 :     k = std::floor( std::log( npoints*pi*root5*sinthet2 ) / log_golden2 );</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     if( k&lt;2 ) k = 2;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         57 :   double Fk = pow( golden, k ) / root5, F0 = std::round(Fk), F1 = std::round(Fk*golden);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         57 :   Matrix&lt;double&gt; B(2,2), invB(2,2); std::vector&lt;double&gt; thisp(3);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         57 :   B(0,0) = 2*pi*((F0+1)*igolden - std::floor((F0+1)*igolden)) - fib_increment;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         57 :   B(0,1) = 2*pi*((F1+1)*igolden - std::floor((F1+1)*igolden)) - fib_increment;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         57 :   B(1,0) = -2*F0/npoints; B(1,1) = -2*F1/npoints; Invert( B, invB );</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         57 :   std::vector&lt;double&gt; vv(2), rc(2); vv[0]=-phi; vv[1] = p[1] - fib_shift;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         57 :   mult( invB, vv, rc ); std::vector&lt;int&gt; c(2); c[0]=std::floor(rc[0]); c[1]=std::floor(rc[1]);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   unsigned outind=0; double mindist = 10000000.;</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        285 :   for(int s=0; s&lt;4; ++s) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        228 :     double ttt, costheta = B(1,0)*( c[0] + s%2 ) + B(1,1)*( c[1] + s/2 ) + fib_shift;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        228 :     if( costheta&gt;1 ) ttt=1; else if( costheta&lt;-1 ) ttt=-1; else ttt=costheta;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        228 :     costheta = 2*ttt - costheta;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        228 :     unsigned i = std::floor( 0.5*npoints*(1+costheta) ); getFibonacciCoordinates( i, thisp );</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        912 :     double dist=0; for(unsigned j=0; j&lt;3; ++j) { double tmp=thisp[j]-p[j]; dist += tmp*tmp; }</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        228 :     if( dist&lt;mindist ) { outind = i; mindist = dist; }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         57 :   return outind;</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : }</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">  112427817 : void GridVessel::convertIndexToIndices( const unsigned&amp; index, const std::vector&lt;unsigned&gt;&amp; nnbin, std::vector&lt;unsigned&gt;&amp; indices ) const {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">  112427817 :   plumed_dbg_assert( gtype==flat ); unsigned kk=index; indices[0]=index%nnbin[0];</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">  220890761 :   for(unsigned i=1; i&lt;dimension-1; ++i) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">  108462944 :     kk=(kk-indices[i-1])/nnbin[i-1];</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">  108462944 :     indices[i]=kk%nnbin[i];</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   }</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">  112427817 :   if(dimension&gt;=2) { // I think this is wrong</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">  112411310 :     indices[dimension-1]=(kk-indices[dimension-2])/nnbin[dimension-2];</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :   }</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">  112427817 : }</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">   15879019 : void GridVessel::getIndices( const unsigned&amp; index, std::vector&lt;unsigned&gt;&amp; indices ) const {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">   15879019 :   plumed_dbg_assert( gtype==flat ); convertIndexToIndices( index, nbin, indices );</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">   15879019 : }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">     665380 : void GridVessel::getGridPointCoordinates( const unsigned&amp; ipoint, std::vector&lt;double&gt;&amp; x ) const {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">     665380 :   std::vector&lt;unsigned&gt; tindices( dimension ); getGridPointCoordinates( ipoint, tindices, x );</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">     665380 : }</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">   12514073 : void GridVessel::getGridPointCoordinates( const unsigned&amp; ipoint, std::vector&lt;unsigned&gt;&amp; tindices, std::vector&lt;double&gt;&amp; x ) const {</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :   plumed_dbg_assert( bounds_set &amp;&amp; x.size()==dimension &amp;&amp; tindices.size()==dimension &amp;&amp; ipoint&lt;npoints );</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">   12514073 :   if( gtype==flat ) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">   12508956 :     getFlatGridCoordinates( ipoint, tindices, x );</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       5117 :   } else if( gtype==fibonacci ) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       5117 :     getFibonacciCoordinates( ipoint, x );</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :   } else {</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">   12514073 : }</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">   13037801 : void GridVessel::getFlatGridCoordinates( const unsigned&amp; ipoint, std::vector&lt;unsigned&gt;&amp; tindices, std::vector&lt;double&gt;&amp; x ) const {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">   13037801 :   plumed_dbg_assert( gtype==flat ); getIndices( ipoint, tindices );</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">   50950445 :   for(unsigned i=0; i&lt;dimension; ++i) x[i] = min[i] + dx[i]*tindices[i];</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">   13037801 : }</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">      86817 : void GridVessel::getFibonacciCoordinates( const unsigned&amp; ipoint, std::vector&lt;double&gt;&amp; x ) const {</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   plumed_dbg_assert( gtype==fibonacci );</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">      86817 :   x[1] = (ipoint*fib_offset) + fib_shift; double r = std::sqrt( 1 - x[1]*x[1] );</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">      86817 :   double phi = ipoint*fib_increment; x[0] = r*std::cos(phi); x[2] = r*std::sin(phi);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     347268 :   double norm=0; for(unsigned j=0; j&lt;3; ++j) norm+=x[j]*x[j];</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">     347268 :   norm = std::sqrt(norm); for(unsigned j=0; j&lt;3; ++j) x[j] = x[j] / norm;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      86817 : }</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">     528845 : void GridVessel::getSplineNeighbors( const unsigned&amp; mybox, unsigned&amp; nneighbors, std::vector&lt;unsigned&gt;&amp; mysneigh ) const {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">     528845 :   plumed_dbg_assert( gtype==flat ); unsigned nneigh=unsigned(pow(2.0,int(dimension)));</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">     528845 :   if( mysneigh.size()!=nneigh ) mysneigh.resize(nneigh);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     528845 :   unsigned inind; nneighbors = 0;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">     528845 :   std::vector&lt;unsigned&gt; tmp_indices( dimension );</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">     528845 :   std::vector&lt;unsigned&gt; my_indices( dimension );</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">     528845 :   getIndices( mybox, my_indices );</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">    2677605 :   for(unsigned i=0; i&lt;nneigh; ++i) {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     unsigned tmp=i; inind=0;</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">    6513440 :     for(unsigned j=0; j&lt;dimension; ++j) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">    4364680 :       unsigned i0=tmp%2+my_indices[j]; tmp/=2;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">    4364680 :       if(!pbc[j] &amp;&amp; i0==nbin[j]) continue;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">    4323880 :       if( pbc[j] &amp;&amp; i0==nbin[j]) i0=0;</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">    4323880 :       tmp_indices[inind++]=i0;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :     }</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">    2148760 :     if(inind==dimension ) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">    2108160 :       unsigned findex=getIndex( tmp_indices );</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">    2108160 :       mysneigh[nneighbors++]=findex;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">    2108160 :       plumed_massert( active[findex], &quot;inactive grid point required for splines&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :     }</a>
+<a name="322"><span class="lineNum">     322 </span>            :   }</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">     528845 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">    6552681 : double GridVessel::getGridElement( const unsigned&amp; ipoint, const unsigned&amp; jelement ) const {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">   13105362 :   plumed_assert( bounds_set &amp;&amp; ipoint&lt;npoints &amp;&amp; jelement&lt;nper &amp;&amp; active[ipoint] );</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">    6552681 :   return getDataElement( nper*ipoint + jelement  );</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">     154208 : void GridVessel::setGridElement( const unsigned&amp; ipoint, const unsigned&amp; jelement, const double&amp; value ) {</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   plumed_dbg_assert( bounds_set &amp;&amp; ipoint&lt;npoints &amp;&amp; jelement&lt;nper );</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">     154208 :   setDataElement( nper*ipoint + jelement, value );</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">     154208 : }</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      24200 : void GridVessel::setValueAndDerivatives( const unsigned&amp; ipoint, const unsigned&amp; jelement, const double&amp; value, const std::vector&lt;double&gt;&amp; der ) {</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   plumed_dbg_assert( !noderiv &amp;&amp; jelement&lt;getNumberOfComponents() &amp;&amp; der.size()==nbin.size() );</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      72600 :   setGridElement( ipoint, jelement, value ); for(unsigned i=0; i&lt;der.size(); ++i) setGridElement( ipoint, jelement+1+i, der[i] );</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      24200 : }</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       2605 : void GridVessel::addToGridElement( const unsigned&amp; ipoint, const unsigned&amp; jelement, const double&amp; value ) {</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :   plumed_dbg_assert( bounds_set &amp;&amp; ipoint&lt;npoints &amp;&amp; jelement&lt;nper );</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       2605 :   addDataElement( nper*ipoint + jelement, value );</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">       2605 : }</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">      15087 : void GridVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :   plumed_dbg_assert( myvals.getNumberOfValues()==(nper+1) );</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">      65138 :   for(unsigned i=0; i&lt;nper; ++i) buffer[bufstart + nper*current + i] += myvals.get(i+1);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      15087 : }</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        118 : void GridVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        118 :   if( wasforced ) getFinalForces( buffer, finalForces );</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         98 :   else AveragingVessel::finish( buffer );</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        118 : }</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 : double GridVessel::getGridElement( const std::vector&lt;unsigned&gt;&amp; indices, const unsigned&amp; jelement ) const {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :   return getGridElement( getIndex( indices ), jelement );</span></a>
+<a name="357"><span class="lineNum">     357 </span>            : }</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 : void GridVessel::setGridElement( const std::vector&lt;unsigned&gt;&amp; indices, const unsigned&amp; jelement, const double&amp; value ) {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :   setGridElement( getIndex( indices ), jelement, value );</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">     202520 : std::vector&lt;std::string&gt; GridVessel::getMin() const {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">     202520 :   plumed_dbg_assert( gtype==flat ); return str_min;</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">     202553 : std::vector&lt;std::string&gt; GridVessel::getMax() const {</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">     202553 :   plumed_dbg_assert( gtype==flat ); return str_max;</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : }</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">     203150 : std::vector&lt;unsigned&gt; GridVessel::getNbin() const {</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   plumed_dbg_assert( gtype==flat &amp;&amp; bounds_set );</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">     203150 :   std::vector&lt;unsigned&gt; ngrid( dimension );</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">     605377 :   for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">     402227 :     if( !pbc[i] ) ngrid[i]=nbin[i] - 1;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      34200 :     else ngrid[i]=nbin[i];</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :   }</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">     203150 :   return ngrid;</span></a>
+<a name="379"><span class="lineNum">     379 </span>            : }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">      21514 : void GridVessel::getNeighbors( const std::vector&lt;double&gt;&amp; pp, const std::vector&lt;unsigned&gt;&amp; nneigh,</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :                                unsigned&amp; num_neighbors, std::vector&lt;unsigned&gt;&amp; neighbors ) const {</a>
+<a name="383"><span class="lineNum">     383 </span>            :   plumed_dbg_assert( bounds_set );</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      21514 :   if( gtype == flat ) {</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :     plumed_dbg_assert( nneigh.size()==dimension );</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">      21457 :     std::vector&lt;unsigned&gt; indices( dimension );</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">      85340 :     for(unsigned i=0; i&lt;dimension; ++i) indices[i] = std::floor( (pp[i]-min[i])/dx[i] );</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      21457 :     getNeighbors( indices, nneigh, num_neighbors, neighbors );</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         57 :   } else if( gtype == fibonacci ) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         57 :     unsigned find = getFibonacciIndex( pp );</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         57 :     num_neighbors = 1 + fib_nlist[find].size();</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         57 :     if( neighbors.size()&lt;num_neighbors ) neighbors.resize( num_neighbors );</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       4773 :     neighbors[0]=find; for(unsigned i=0; i&lt;fib_nlist[find].size(); ++i) neighbors[1+i] = fib_nlist[find][i];</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :   } else {</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">      21514 : }</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">      40878 : void GridVessel::getNeighbors( const std::vector&lt;unsigned&gt;&amp; indices, const std::vector&lt;unsigned&gt;&amp; nneigh,</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :                                unsigned&amp; num_neighbors, std::vector&lt;unsigned&gt;&amp; neighbors ) const {</a>
+<a name="402"><span class="lineNum">     402 </span>            :   plumed_dbg_assert( gtype==flat &amp;&amp; bounds_set &amp;&amp; nneigh.size()==dimension );</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">      40878 :   unsigned num_neigh=1; std::vector&lt;unsigned&gt; small_bin( dimension );</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">     163024 :   for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">     122146 :     small_bin[i]=(2*nneigh[i]+1);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">     122146 :     num_neigh *=small_bin[i];</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :   }</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">      40878 :   if( neighbors.size()!=num_neigh ) neighbors.resize( num_neigh );</span></a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">      40878 :   num_neighbors=0;</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">      40878 :   std::vector&lt;unsigned&gt; s_indices(dimension), t_indices(dimension);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">   96589676 :   for(unsigned index=0; index&lt;num_neigh; ++index) {</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :     bool found=true;</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">   96548798 :     convertIndexToIndices( index, small_bin, s_indices );</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">  386166232 :     for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">  289617434 :       int i0=s_indices[i]-nneigh[i]+indices[i];</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">  289617434 :       if(!pbc[i] &amp;&amp; i0&lt;0)        found=false;</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">  289617434 :       if(!pbc[i] &amp;&amp; i0&gt;=nbin[i]) found=false;</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">  289617434 :       if( pbc[i] &amp;&amp; i0&lt;0)        i0=nbin[i]-(-i0)%nbin[i];</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">  289617434 :       if( pbc[i] &amp;&amp; i0&gt;=nbin[i]) i0%=nbin[i];</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">  289617434 :       t_indices[i]=static_cast&lt;unsigned&gt;(i0);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :     }</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">   96548798 :     if( found ) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">   21093803 :       neighbors[num_neighbors]=getIndex( t_indices );</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">   21093803 :       num_neighbors++;</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :     }</a>
+<a name="428"><span class="lineNum">     428 </span>            :   }</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">      40878 : }</span></a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         11 : void GridVessel::setCubeUnits( const double&amp; units ) {</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         11 :   plumed_dbg_assert( gtype==flat ); cube_units=units;</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         11 : }</span></a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          8 : double GridVessel::getCubeUnits() const {</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          8 :   plumed_dbg_assert( gtype==flat ); return cube_units;</span></a>
+<a name="437"><span class="lineNum">     437 </span>            : }</a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         17 : std::string GridVessel::getInputString() const {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         17 :   std::string mstring=&quot;COORDINATES=&quot;+arg_names[0];</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         23 :   for(unsigned i=1; i&lt;dimension; ++i) mstring+=&quot;,&quot; + arg_names[i];</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         17 :   if( gtype==flat ) {</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     mstring += &quot; TYPE=flat PBC=&quot;;</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         17 :     if( pbc[0] ) mstring +=&quot;T&quot;;</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :     else mstring +=&quot;F&quot;;</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         23 :     for(unsigned i=1; i&lt;dimension; ++i) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          6 :       if( pbc[i] ) mstring +=&quot;,T&quot;;</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :       else mstring +=&quot;,F&quot;;</a>
+<a name="449"><span class="lineNum">     449 </span>            :     }</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :   } else if( gtype==fibonacci ) {</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :     mstring += &quot; TYPE=fibonacci&quot;;</a>
+<a name="452"><span class="lineNum">     452 </span>            :   }</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         17 :   return mstring;</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">     528845 : double GridVessel::getValueAndDerivatives( const std::vector&lt;double&gt;&amp; x, const unsigned&amp; ind, std::vector&lt;double&gt;&amp; der ) const {</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :   plumed_dbg_assert( gtype==flat &amp;&amp; der.size()==dimension &amp;&amp; !noderiv &amp;&amp; ind&lt;getNumberOfComponents() );</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">     528845 :   double X,X2,X3,value=0; der.assign(der.size(),0.0);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">     528845 :   std::vector&lt;double&gt; fd(dimension);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">     528845 :   std::vector&lt;double&gt; C(dimension);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">     528845 :   std::vector&lt;double&gt; D(dimension);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">     528845 :   std::vector&lt;double&gt; dder(dimension);</span></a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">     528845 :   std::vector&lt;unsigned&gt; nindices(dimension); unsigned n_neigh;</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">     528845 :   std::vector&lt;unsigned&gt; indices(dimension); getIndices( x, indices );</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">     528845 :   std::vector&lt;unsigned&gt; neigh; getSplineNeighbors( getIndex(indices), n_neigh, neigh );</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">     528845 :   std::vector&lt;double&gt; xfloor(dimension); getFlatGridCoordinates( getIndex(x), nindices, xfloor );</span></a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            : // loop over neighbors</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">    2637005 :   for(unsigned int ipoint=0; ipoint&lt;n_neigh; ++ipoint) {</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">    2108160 :     double grid=getGridElement(neigh[ipoint], ind*(1+dimension) );</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">    6391640 :     for(unsigned j=0; j&lt;dimension; ++j) dder[j] = getGridElement( neigh[ipoint], ind*(1+dimension) + 1 + j );</span></a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">    2108160 :     getIndices( neigh[ipoint], nindices );</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :     double ff=1.0;</a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">    6391640 :     for(unsigned j=0; j&lt;dimension; ++j) {</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :       int x0=1;</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">    4283480 :       if(nindices[j]==indices[j]) x0=0;</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">    4283480 :       double ddx=dx[j];</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">    4283480 :       X=std::fabs((x[j]-xfloor[j])/ddx-(double)x0);</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">    4283480 :       X2=X*X;</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">    4283480 :       X3=X2*X;</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :       double yy;</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">    4283480 :       if(std::fabs(grid)&lt;0.0000001) yy=0.0;</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">    4269633 :       else yy=-dder[j]/grid;</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">    6445420 :       C[j]=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*ddx;</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">    4283480 :       D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*ddx;</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">    4283480 :       D[j]*=(x0?-1.0:1.0)/ddx;</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">    4283480 :       ff*=C[j];</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :     }</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">    6391640 :     for(unsigned j=0; j&lt;dimension; ++j) {</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">    4283480 :       fd[j]=D[j];</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">   13052720 :       for(unsigned i=0; i&lt;dimension; ++i) if(i!=j) fd[j]*=C[i];</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :     }</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">    2108160 :     value+=grid*ff;</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">    6391640 :     for(unsigned j=0; j&lt;dimension; ++j) der[j]+=grid*fd[j];</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :   }</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">     528845 :   return value;</span></a>
+<a name="501"><span class="lineNum">     501 </span>            : }</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          3 : void GridVessel::activateThesePoints( const std::vector&lt;bool&gt;&amp; to_activate ) {</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :   plumed_dbg_assert( to_activate.size()==npoints );</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">      29991 :   for(unsigned i=0; i&lt;npoints; ++i) active[i]=to_activate[i];</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          3 : }</span></a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         20 : void GridVessel::setForce( const std::vector&lt;double&gt;&amp; inforces ) {</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :   plumed_dbg_assert( inforces.size()==npoints );</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">       5725 :   wasforced=true; for(unsigned i=0; i&lt;npoints; ++i) forces[i]=inforces[i];</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         20 : }</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">   11870273 : bool GridVessel::wasForced() const {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">   11870273 :   return wasforced;</span></a>
+<a name="515"><span class="lineNum">     515 </span>            : }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         20 : bool GridVessel::applyForce( std::vector&lt;double&gt;&amp; fforces ) {</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :   plumed_dbg_assert( fforces.size()==finalForces.size() );</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         20 :   if( !wasforced ) return false;</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">       3815 :   for(unsigned i=0; i&lt;finalForces.size(); ++i) fforces[i]=finalForces[i];</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         20 :   wasforced=false; return true;</span></a>
+<a name="522"><span class="lineNum">     522 </span>            : }</a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            : }</a>
+<a name="525"><span class="lineNum">     525 </span>            : }</a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridVessel.h.func-sort-c.html b/coverage/gridtools/GridVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..9fe675c91a
--- /dev/null
+++ b/coverage/gridtools/GridVessel.h.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridVessel.h<span style="font-size: 80%;"> (<a href="GridVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntryMed">89.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#186">_ZN4PLMD9gridtools10GridVessel14getFinalForcesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#279">_ZNK4PLMD9gridtools10GridVessel18getFibonacciCutoffEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#212">_ZNK4PLMD9gridtools10GridVessel13getCellVolumeEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#238">_ZNK4PLMD9gridtools10GridVessel21getNumberOfComponentsEv</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#267">_ZNK4PLMD9gridtools10GridVessel23getNumberOfBufferPointsEv</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#206">_ZNK4PLMD9gridtools10GridVessel14getGridSpacingEv</a></td>
+              <td class="coverFnHi">611</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#272">_ZNK4PLMD9gridtools10GridVessel7getTypeB5cxx11Ev</a></td>
+              <td class="coverFnHi">26251</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#255">_ZNK4PLMD9gridtools10GridVessel8inactiveERKj</a></td>
+              <td class="coverFnHi">21151408</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridVessel.h.func.html b/coverage/gridtools/GridVessel.h.func.html
new file mode 100644
index 0000000000..f38bab1bcd
--- /dev/null
+++ b/coverage/gridtools/GridVessel.h.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridVessel.h<span style="font-size: 80%;"> (<a href="GridVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntryMed">89.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#186">_ZN4PLMD9gridtools10GridVessel14getFinalForcesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#212">_ZNK4PLMD9gridtools10GridVessel13getCellVolumeEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#206">_ZNK4PLMD9gridtools10GridVessel14getGridSpacingEv</a></td>
+              <td class="coverFnHi">611</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#279">_ZNK4PLMD9gridtools10GridVessel18getFibonacciCutoffEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#238">_ZNK4PLMD9gridtools10GridVessel21getNumberOfComponentsEv</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#267">_ZNK4PLMD9gridtools10GridVessel23getNumberOfBufferPointsEv</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#272">_ZNK4PLMD9gridtools10GridVessel7getTypeB5cxx11Ev</a></td>
+              <td class="coverFnHi">26251</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridVessel.h.gcov.html#255">_ZNK4PLMD9gridtools10GridVessel8inactiveERKj</a></td>
+              <td class="coverFnHi">21151408</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/GridVessel.h.gcov.html b/coverage/gridtools/GridVessel.h.gcov.html
new file mode 100644
index 0000000000..7e06a3c2fe
--- /dev/null
+++ b/coverage/gridtools/GridVessel.h.gcov.html
@@ -0,0 +1,363 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/GridVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - GridVessel.h<span style="font-size: 80%;"> (source / <a href="GridVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntryMed">89.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_GridVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_GridVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;vesselbase/AveragingVessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace gridtools {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class GridVessel : public vesselbase::AveragingVessel {</a>
+<a name="34"><span class="lineNum">      34 </span>            :   friend class ActionWithInputGrid;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   friend class DumpGrid;</a>
+<a name="36"><span class="lineNum">      36 </span>            : private:</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// The way that grid points are constructed</a>
+<a name="38"><span class="lineNum">      38 </span>            :   enum {flat,fibonacci} gtype;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Have the minimum and maximum for the grid been set</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool bounds_set;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// The number of points in the grid</a>
+<a name="42"><span class="lineNum">      42 </span>            :   unsigned npoints;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Stuff for fibonacci grids</a>
+<a name="44"><span class="lineNum">      44 </span>            :   double root5, golden, igolden, log_golden2;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Fib increment here is equal to 2*pi*(INVERSE GOLDEN RATIO)</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double fib_offset, fib_increment, fib_shift;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;std::vector&lt;unsigned&gt; &gt; fib_nlist;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Units for Gaussian Cube file</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double cube_units;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// This flag is used to check if the user has created a valid input</a>
+<a name="51"><span class="lineNum">      51 </span>            :   bool foundprint;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// The minimum and maximum of the grid stored as doubles</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;double&gt; min, max;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// The numerical distance between adjacent grid points</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::vector&lt;unsigned&gt; stride;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The number of bins in each grid direction</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;unsigned&gt; nbin;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The grid point that was requested last by getGridPointCoordinates</a>
+<a name="59"><span class="lineNum">      59 </span>            :   unsigned currentGridPoint;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// The forces that will be output at the end of the calculation</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::vector&lt;double&gt; finalForces;</a>
+<a name="62"><span class="lineNum">      62 </span>            : protected:</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Is forced</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool wasforced;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Forces acting on grid elements</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;double&gt; forces;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Do we have derivatives</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool noderiv;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// The names of the various columns in the grid file</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt;std::string&gt; arg_names;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// The number of pieces of information we are storing for each</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// point in the grid</a>
+<a name="73"><span class="lineNum">      73 </span>            :   unsigned nper;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Is this direction periodic</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::vector&lt;bool&gt; pbc;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// The minimum and maximum in the grid stored as strings</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;std::string&gt; str_min, str_max;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// The spacing between grid points</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;double&gt; dx;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// The dimensionality of the grid</a>
+<a name="81"><span class="lineNum">      81 </span>            :   unsigned dimension;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Which grid points are we actively accumulating</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;bool&gt; active;</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// Convert a point in space the the correspoinding grid point</a>
+<a name="85"><span class="lineNum">      85 </span>            :   unsigned getIndex( const std::vector&lt;double&gt;&amp; p ) const ;</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Get the index of the closest point on the fibonacci sphere</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned getFibonacciIndex( const std::vector&lt;double&gt;&amp; p ) const ;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Get the flat grid coordinates</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void getFlatGridCoordinates( const unsigned&amp; ipoint, std::vector&lt;unsigned&gt;&amp; tindices, std::vector&lt;double&gt;&amp; x ) const ;</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// Get the coordinates on the Fibonacci grid</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void getFibonacciCoordinates( const unsigned&amp; ipoint, std::vector&lt;double&gt;&amp; x ) const ;</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// keywords</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Constructor</a>
+<a name="96"><span class="lineNum">      96 </span>            :   explicit GridVessel( const vesselbase::VesselOptions&amp; );</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Remove the derivatives</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void setNoDerivatives();</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Get the type of grid we are using</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::string getType() const ;</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Set the minimum and maximum of the grid</a>
+<a name="102"><span class="lineNum">     102 </span>            :   virtual void setBounds( const std::vector&lt;std::string&gt;&amp; smin, const std::vector&lt;std::string&gt;&amp; smax, const std::vector&lt;unsigned&gt;&amp; nbins, const std::vector&lt;double&gt;&amp; spacing );</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Get the cutoff to use for the Fibonacci spheres</a>
+<a name="104"><span class="lineNum">     104 </span>            :   virtual double getFibonacciCutoff() const ;</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Setup the grid if it is a fibonacci grid on the surface of a sphere</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void setupFibonacciGrid( const unsigned&amp; np );</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// Get a description of the grid to output to the log</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::string description() override;</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Convert an index into indices</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void convertIndexToIndices( const unsigned&amp; index, const std::vector&lt;unsigned&gt;&amp; nnbin, std::vector&lt;unsigned&gt;&amp; indices ) const ;</a>
+<a name="111"><span class="lineNum">     111 </span>            : ///  Flatten the grid and get the grid index for a point</a>
+<a name="112"><span class="lineNum">     112 </span>            :   unsigned getIndex( const std::vector&lt;unsigned&gt;&amp; indices ) const ;</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Get the indices fof a point</a>
+<a name="114"><span class="lineNum">     114 </span>            :   void getIndices( const unsigned&amp; index, std::vector&lt;unsigned&gt;&amp; indices ) const ;</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Get the indices of a particular point</a>
+<a name="116"><span class="lineNum">     116 </span>            :   void getIndices( const std::vector&lt;double&gt;&amp; point, std::vector&lt;unsigned&gt;&amp; indices ) const ;</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Operations on one of the elements of grid point i</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void setGridElement( const unsigned&amp;, const unsigned&amp;, const double&amp; );</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Add data to an element of the grid</a>
+<a name="120"><span class="lineNum">     120 </span>            :   void addToGridElement( const unsigned&amp; ipoint, const unsigned&amp; jelement, const double&amp; value );</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Operations on one of the elements of grid point specified by vector</a>
+<a name="122"><span class="lineNum">     122 </span>            :   double getGridElement( const std::vector&lt;unsigned&gt;&amp;, const unsigned&amp; ) const ;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void setGridElement( const std::vector&lt;unsigned&gt;&amp;, const unsigned&amp;, const double&amp; );</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Set the values and derivatives of a particular element</a>
+<a name="125"><span class="lineNum">     125 </span>            :   void setValueAndDerivatives( const unsigned&amp;, const unsigned&amp;, const double&amp;, const std::vector&lt;double&gt;&amp; );</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// Set the size of the buffer equal to nper*npoints</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void resize() override;</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// Get the number of points in the grid</a>
+<a name="129"><span class="lineNum">     129 </span>            :   unsigned getNumberOfPoints() const;</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// Get the coordinates for a point in the grid</a>
+<a name="131"><span class="lineNum">     131 </span>            :   void getGridPointCoordinates( const unsigned&amp;, std::vector&lt;double&gt;&amp; ) const ;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   void getGridPointCoordinates( const unsigned&amp;, std::vector&lt;unsigned&gt;&amp;, std::vector&lt;double&gt;&amp; ) const ;</a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Get the dimensionality of the function</a>
+<a name="134"><span class="lineNum">     134 </span>            :   unsigned getDimension() const ;</a>
+<a name="135"><span class="lineNum">     135 </span>            : /// Get the number of components in the vector stored on each grid point</a>
+<a name="136"><span class="lineNum">     136 </span>            :   virtual unsigned getNumberOfComponents() const ;</a>
+<a name="137"><span class="lineNum">     137 </span>            : /// Is the grid periodic in the ith direction</a>
+<a name="138"><span class="lineNum">     138 </span>            :   bool isPeriodic( const unsigned&amp; i ) const ;</a>
+<a name="139"><span class="lineNum">     139 </span>            : /// Get the number of quantities we have stored at each grid point</a>
+<a name="140"><span class="lineNum">     140 </span>            :   unsigned getNumberOfQuantities() const ;</a>
+<a name="141"><span class="lineNum">     141 </span>            : /// Get the number of grid points for each dimension</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::vector&lt;unsigned&gt; getNbin() const ;</a>
+<a name="143"><span class="lineNum">     143 </span>            : /// Get the name of the ith component</a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::string getComponentName( const unsigned&amp; i ) const ;</a>
+<a name="145"><span class="lineNum">     145 </span>            : /// Get the vector containing the minimum value of the grid in each dimension</a>
+<a name="146"><span class="lineNum">     146 </span>            :   std::vector&lt;std::string&gt; getMin() const ;</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// Get the vector containing the maximum value of the grid in each dimension</a>
+<a name="148"><span class="lineNum">     148 </span>            :   std::vector&lt;std::string&gt; getMax() const ;</a>
+<a name="149"><span class="lineNum">     149 </span>            : /// Get the number of points needed in the buffer</a>
+<a name="150"><span class="lineNum">     150 </span>            :   virtual unsigned getNumberOfBufferPoints() const ;</a>
+<a name="151"><span class="lineNum">     151 </span>            : /// Get the stride (the distance between the grid points of an index)</a>
+<a name="152"><span class="lineNum">     152 </span>            :   const std::vector&lt;unsigned&gt;&amp; getStride() const ;</a>
+<a name="153"><span class="lineNum">     153 </span>            : /// Return the volume of one of the grid cells</a>
+<a name="154"><span class="lineNum">     154 </span>            :   double getCellVolume() const ;</a>
+<a name="155"><span class="lineNum">     155 </span>            : /// Get the value of the ith grid element</a>
+<a name="156"><span class="lineNum">     156 </span>            :   virtual double getGridElement( const unsigned&amp;, const unsigned&amp; ) const ;</a>
+<a name="157"><span class="lineNum">     157 </span>            : /// Get the set of points neighouring a particular location in space</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void getNeighbors( const std::vector&lt;double&gt;&amp; pp, const std::vector&lt;unsigned&gt;&amp; nneigh,</a>
+<a name="159"><span class="lineNum">     159 </span>            :                      unsigned&amp; num_neighbours, std::vector&lt;unsigned&gt;&amp; neighbors ) const ;</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Get the neighbors for a set of indices of a point</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void getNeighbors( const std::vector&lt;unsigned&gt;&amp; indices, const std::vector&lt;unsigned&gt;&amp; nneigh,</a>
+<a name="162"><span class="lineNum">     162 </span>            :                      unsigned&amp; num_neighbors, std::vector&lt;unsigned&gt;&amp; neighbors ) const ;</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// Get the points neighboring a particular spline point</a>
+<a name="164"><span class="lineNum">     164 </span>            :   void getSplineNeighbors( const unsigned&amp; mybox, unsigned&amp; nneighbors, std::vector&lt;unsigned&gt;&amp; mysneigh ) const ;</a>
+<a name="165"><span class="lineNum">     165 </span>            : /// Get the spacing between grid points</a>
+<a name="166"><span class="lineNum">     166 </span>            :   const std::vector&lt;double&gt;&amp; getGridSpacing() const ;</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// Get the extent of the grid in one of the axis</a>
+<a name="168"><span class="lineNum">     168 </span>            :   double getGridExtent( const unsigned&amp; i ) const ;</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// Copy data from the action into the grid</a>
+<a name="170"><span class="lineNum">     170 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const override;</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// Finish the calculation</a>
+<a name="172"><span class="lineNum">     172 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="173"><span class="lineNum">     173 </span>            : /// This ensures that Gaussian cube fies are in correct units</a>
+<a name="174"><span class="lineNum">     174 </span>            :   void setCubeUnits( const double&amp; units );</a>
+<a name="175"><span class="lineNum">     175 </span>            : /// This ensures that Gaussian cube files are in correct units</a>
+<a name="176"><span class="lineNum">     176 </span>            :   double getCubeUnits() const ;</a>
+<a name="177"><span class="lineNum">     177 </span>            : /// Return a string containing the input to the grid so we can clone it</a>
+<a name="178"><span class="lineNum">     178 </span>            :   std::string getInputString() const ;</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// Does this have derivatives</a>
+<a name="180"><span class="lineNum">     180 </span>            :   bool noDerivatives() const ;</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// Get the value and derivatives at a particular location using spline interpolation</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double getValueAndDerivatives( const std::vector&lt;double&gt;&amp; x, const unsigned&amp; ind, std::vector&lt;double&gt;&amp; der ) const ;</a>
+<a name="183"><span class="lineNum">     183 </span>            : /// Deactivate all the grid points</a>
+<a name="184"><span class="lineNum">     184 </span>            :   void activateThesePoints( const std::vector&lt;bool&gt;&amp; to_activate );</a>
+<a name="185"><span class="lineNum">     185 </span>            : /// Is this point active</a>
+<a name="186"><span class="lineNum">     186 </span>            :   bool inactive( const unsigned&amp; ip ) const ;</a>
+<a name="187"><span class="lineNum">     187 </span>            : /// This retrieves the final force</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   virtual void getFinalForces( const std::vector&lt;double&gt;&amp; buffer, std::vector&lt;double&gt;&amp; finalForces ) { plumed_error(); }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : /// Apply the forces</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void setForce( const std::vector&lt;double&gt;&amp; inforces );</a>
+<a name="191"><span class="lineNum">     191 </span>            : /// Was a force added to the grid</a>
+<a name="192"><span class="lineNum">     192 </span>            :   bool wasForced() const ;</a>
+<a name="193"><span class="lineNum">     193 </span>            : /// And retrieve the forces</a>
+<a name="194"><span class="lineNum">     194 </span>            :   bool applyForce( std::vector&lt;double&gt;&amp; fforces ) override;</a>
+<a name="195"><span class="lineNum">     195 </span>            : };</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : inline</a>
+<a name="198"><span class="lineNum">     198 </span>            : unsigned GridVessel::getNumberOfQuantities() const {</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     440217 :   return nper;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : inline</a>
+<a name="203"><span class="lineNum">     203 </span>            : unsigned GridVessel::getNumberOfPoints() const {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     873010 :   return npoints;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : inline</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        611 : const std::vector&lt;double&gt;&amp; GridVessel::getGridSpacing() const {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        611 :   if( gtype==flat ) return dx;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;dont understand what spacing means for spherical grids&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : inline</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          4 : double GridVessel::getCellVolume() const {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          4 :   if( gtype==flat ) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          8 :     double myvol=1.0; for(unsigned i=0; i&lt;dimension; ++i) myvol *= dx[i];</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     return myvol;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   } else {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          1 :     return 4*pi / static_cast&lt;double&gt;( getNumberOfPoints() );</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span>            : }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : inline</a>
+<a name="224"><span class="lineNum">     224 </span>            : unsigned GridVessel::getDimension() const {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     938454 :   return dimension;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : inline</a>
+<a name="229"><span class="lineNum">     229 </span>            : bool GridVessel::isPeriodic( const unsigned&amp; i ) const {</a>
+<a name="230"><span class="lineNum">     230 </span>            :   plumed_dbg_assert( gtype==flat );</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       7859 :   return pbc[i];</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : inline</a>
+<a name="235"><span class="lineNum">     235 </span>            : std::string GridVessel::getComponentName( const unsigned&amp; i ) const {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">    1012634 :   return arg_names[i];</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : inline</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         47 : unsigned GridVessel::getNumberOfComponents() const {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         47 :   if( noderiv ) return nper;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         32 :   return nper / ( dimension + 1 );</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : inline</a>
+<a name="246"><span class="lineNum">     246 </span>            : double GridVessel::getGridExtent( const unsigned&amp; i ) const {</a>
+<a name="247"><span class="lineNum">     247 </span>            :   plumed_dbg_assert( gtype==flat );</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         40 :   return max[i] - min[i];</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : inline</a>
+<a name="252"><span class="lineNum">     252 </span>            : bool GridVessel::noDerivatives() const {</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      14312 :   return noderiv;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            : inline</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">   21151408 : bool GridVessel::inactive( const unsigned&amp; ip ) const {</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   plumed_dbg_assert( ip&lt;npoints );</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">   21151408 :   return !active[ip];</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : inline</a>
+<a name="263"><span class="lineNum">     263 </span>            : const std::vector&lt;unsigned&gt;&amp; GridVessel::getStride() const {</a>
+<a name="264"><span class="lineNum">     264 </span>            :   plumed_dbg_assert( gtype==flat );</a>
+<a name="265"><span class="lineNum">     265 </span>            :   return stride;</a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : inline</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         71 : unsigned GridVessel::getNumberOfBufferPoints() const {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        321 :   return npoints;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : inline</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      26251 : std::string GridVessel::getType() const {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      26251 :   if( gtype==flat ) return &quot;flat&quot;;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        422 :   else if( gtype==fibonacci ) return &quot;fibonacci&quot;;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : }</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            : inline</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          2 : double GridVessel::getFibonacciCutoff() const {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          2 :   return 0.0;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            : }</a>
+<a name="286"><span class="lineNum">     286 </span>            : }</a>
+<a name="287"><span class="lineNum">     287 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/HistogramOnGrid.cpp.func-sort-c.html b/coverage/gridtools/HistogramOnGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5fe487fde6
--- /dev/null
+++ b/coverage/gridtools/HistogramOnGrid.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/HistogramOnGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - HistogramOnGrid.cpp<span style="font-size: 80%;"> (<a href="HistogramOnGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">118</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HistogramOnGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#53">_ZNK4PLMD9gridtools15HistogramOnGrid18getFibonacciCutoffEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#57">_ZNK4PLMD9gridtools15HistogramOnGrid17noDiscreteKernelsEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#185">_ZN4PLMD9gridtools15HistogramOnGrid14getFinalForcesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#33">_ZN4PLMD9gridtools15HistogramOnGridC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#61">_ZN4PLMD9gridtools15HistogramOnGrid9setBoundsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESC_RKS2_IjSaIjEERKS2_IdSaIdEE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#26">_ZN4PLMD9gridtools15HistogramOnGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#202">_ZN4PLMD9gridtools15HistogramOnGrid6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#181">_ZNK4PLMD9gridtools15HistogramOnGrid15accumulateForceERKjRKdRKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnHi">5744</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#75">_ZNK4PLMD9gridtools15HistogramOnGrid21getKernelAndNeighborsERSt6vectorIdSaIdEERjRS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">23625</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#106">_ZNK4PLMD9gridtools15HistogramOnGrid9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">38461</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#176">_ZNK4PLMD9gridtools15HistogramOnGrid10accumulateERKjRKdS5_RKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnHi">40596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#96">_ZNK4PLMD9gridtools15HistogramOnGrid17getVectorOfValuesEv</a></td>
+              <td class="coverFnHi">57812</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/HistogramOnGrid.cpp.func.html b/coverage/gridtools/HistogramOnGrid.cpp.func.html
new file mode 100644
index 0000000000..70b916a5eb
--- /dev/null
+++ b/coverage/gridtools/HistogramOnGrid.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/HistogramOnGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - HistogramOnGrid.cpp<span style="font-size: 80%;"> (<a href="HistogramOnGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">118</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HistogramOnGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#185">_ZN4PLMD9gridtools15HistogramOnGrid14getFinalForcesERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#26">_ZN4PLMD9gridtools15HistogramOnGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#202">_ZN4PLMD9gridtools15HistogramOnGrid6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#61">_ZN4PLMD9gridtools15HistogramOnGrid9setBoundsERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESC_RKS2_IjSaIjEERKS2_IdSaIdEE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#33">_ZN4PLMD9gridtools15HistogramOnGridC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#176">_ZNK4PLMD9gridtools15HistogramOnGrid10accumulateERKjRKdS5_RKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnHi">40596</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#181">_ZNK4PLMD9gridtools15HistogramOnGrid15accumulateForceERKjRKdRKSt6vectorIdSaIdEERS8_</a></td>
+              <td class="coverFnHi">5744</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#96">_ZNK4PLMD9gridtools15HistogramOnGrid17getVectorOfValuesEv</a></td>
+              <td class="coverFnHi">57812</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#57">_ZNK4PLMD9gridtools15HistogramOnGrid17noDiscreteKernelsEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#53">_ZNK4PLMD9gridtools15HistogramOnGrid18getFibonacciCutoffEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#75">_ZNK4PLMD9gridtools15HistogramOnGrid21getKernelAndNeighborsERSt6vectorIdSaIdEERjRS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">23625</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.cpp.gcov.html#106">_ZNK4PLMD9gridtools15HistogramOnGrid9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">38461</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/HistogramOnGrid.cpp.gcov.html b/coverage/gridtools/HistogramOnGrid.cpp.gcov.html
new file mode 100644
index 0000000000..f7b8240ef8
--- /dev/null
+++ b/coverage/gridtools/HistogramOnGrid.cpp.gcov.html
@@ -0,0 +1,291 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/HistogramOnGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - HistogramOnGrid.cpp<span style="font-size: 80%;"> (source / <a href="HistogramOnGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">118</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;HistogramOnGrid.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace gridtools {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         65 : void HistogramOnGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         65 :   GridVessel::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        130 :   keys.add(&quot;compulsory&quot;,&quot;KERNEL&quot;,&quot;the type of kernel to use&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        130 :   keys.add(&quot;compulsory&quot;,&quot;BANDWIDTH&quot;,&quot;the bandwidths&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        130 :   keys.add(&quot;compulsory&quot;,&quot;CONCENTRATION&quot;,&quot;the concentration parameter for Von Mises-Fisher distributions&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         65 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         45 : HistogramOnGrid::HistogramOnGrid( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   GridVessel(da),</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         45 :   neigh_tot(0),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         45 :   addOneKernelAtATime(false),</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         45 :   bandwidths(dimension),</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         45 :   discrete(false)</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : {</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         90 :   if( getType()==&quot;flat&quot; ) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         86 :     parse(&quot;KERNEL&quot;,kerneltype);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         86 :     if( kerneltype==&quot;discrete&quot; || kerneltype==&quot;DISCRETE&quot; ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         10 :       discrete=true; setNoDerivatives();</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :     } else {</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         66 :       parseVector(&quot;BANDWIDTH&quot;,bandwidths);</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :     }</a>
+<a name="49"><span class="lineNum">      49 </span>            :   } else {</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 :     parse(&quot;CONCENTRATION&quot;,von_misses_concentration);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          2 :     von_misses_norm = von_misses_concentration / ( 4*pi*sinh( von_misses_concentration ) );</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   }</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         45 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          3 : double HistogramOnGrid::getFibonacciCutoff() const {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          3 :   return std::log( epsilon / von_misses_norm ) / von_misses_concentration;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         19 : bool HistogramOnGrid::noDiscreteKernels() const {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         19 :   return !discrete;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         50 : void HistogramOnGrid::setBounds( const std::vector&lt;std::string&gt;&amp; smin, const std::vector&lt;std::string&gt;&amp; smax,</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :                                  const std::vector&lt;unsigned&gt;&amp; nbins, const std::vector&lt;double&gt;&amp; spacing ) {</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         50 :   GridVessel::setBounds( smin, smax, nbins, spacing );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         50 :   if( !discrete ) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         40 :     std::vector&lt;double&gt; point(dimension,0);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         40 :     KernelFunctions kernel( point, bandwidths, kerneltype, &quot;DIAGONAL&quot;, 1.0 ); neigh_tot=1;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         80 :     nneigh=kernel.getSupport( dx ); std::vector&lt;double&gt; support( kernel.getContinuousSupport() );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        103 :     for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         63 :       if( pbc[i] &amp;&amp; 2*support[i]&gt;getGridExtent(i) ) error(&quot;bandwidth is too large for periodic grid&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         63 :       neigh_tot *= (2*nneigh[i]+1);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     }</a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         50 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      23625 : std::unique_ptr&lt;KernelFunctions&gt; HistogramOnGrid::getKernelAndNeighbors( std::vector&lt;double&gt;&amp; point, unsigned&amp; num_neigh, std::vector&lt;unsigned&gt;&amp; neighbors ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      23625 :   if( discrete ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       4222 :     plumed_assert( getType()==&quot;flat&quot; );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       4222 :     num_neigh=1; for(unsigned i=0; i&lt;dimension; ++i) point[i] += 0.5*dx[i];</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       2111 :     neighbors[0] = getIndex( point ); return NULL;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      43028 :   } else if( getType()==&quot;flat&quot; ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      21457 :     auto kernel=Tools::make_unique&lt;KernelFunctions&gt;( point, bandwidths, kerneltype, &quot;DIAGONAL&quot;, 1.0 );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : // GB: Now values is destroyed when exiting this function.</a>
+<a name="85"><span class="lineNum">      85 </span>            : // I think before there was a leak</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      21457 :     std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; values=getVectorOfValues();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      64371 :     kernel-&gt;normalize( Tools::unique2raw(values) ); getNeighbors( kernel-&gt;getCenter(), nneigh, num_neigh, neighbors );</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     return kernel;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      21571 :   } else if( getType()==&quot;fibonacci&quot; ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         57 :     getNeighbors( point, nneigh, num_neigh, neighbors );</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :     return NULL;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   } else {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span>            :   return NULL;</a>
+<a name="96"><span class="lineNum">      96 </span>            : }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     115624 : std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; HistogramOnGrid::getVectorOfValues() const {</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; vv;</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     225230 :   for(unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     167418 :     vv.emplace_back(Tools::make_unique&lt;Value&gt;());</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     167418 :     if( pbc[i] ) vv[i]-&gt;setDomain( str_min[i], str_max[i] );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      64454 :     else vv[i]-&gt;setNotPeriodic();</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      57812 :   return vv;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      38461 : void HistogramOnGrid::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      38461 :   if( addOneKernelAtATime ) {</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     plumed_dbg_assert( myvals.getNumberOfValues()==2 &amp;&amp; !wasforced );</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      14908 :     std::vector&lt;double&gt; der( dimension );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      54492 :     for(unsigned i=0; i&lt;dimension; ++i) der[i]=myvals.getDerivative( 1, i );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      14908 :     accumulate( getAction()-&gt;getPositionInCurrentTaskList(current), myvals.get(0), myvals.get(1), der, buffer );</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   } else {</a>
+<a name="115"><span class="lineNum">     115 </span>            :     plumed_dbg_assert( myvals.getNumberOfValues()==dimension+2 );</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      23553 :     std::vector&lt;double&gt; point( dimension ); double weight=myvals.get(0)*myvals.get( 1+dimension );</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      89610 :     for(unsigned i=0; i&lt;dimension; ++i) point[i]=myvals.get( 1+i );</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :     // Get the kernel</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      23553 :     unsigned num_neigh; std::vector&lt;unsigned&gt; neighbors(1);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      23553 :     std::vector&lt;double&gt; der( dimension );</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      23553 :     std::unique_ptr&lt;KernelFunctions&gt; kernel=getKernelAndNeighbors( point, num_neigh, neighbors );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      27879 :     if( !kernel &amp;&amp; getType()==&quot;flat&quot; ) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       2106 :       plumed_dbg_assert( num_neigh==1 ); der.resize(0);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       2106 :       accumulate( neighbors[0], weight, 1.0, der, buffer );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     } else {</a>
+<a name="127"><span class="lineNum">     127 </span>            :       double totwforce=0.0;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      21447 :       std::vector&lt;double&gt; intforce( 2*dimension, 0.0 );</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      21447 :       std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; vv( getVectorOfValues() );</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      21447 :       double newval; std::vector&lt;unsigned&gt; tindices( dimension ); std::vector&lt;double&gt; xx( dimension );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">   20582512 :       for(unsigned i=0; i&lt;num_neigh; ++i) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">   20561065 :         unsigned ineigh=neighbors[i];</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">   20561065 :         if( inactive( ineigh ) ) continue ;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">   11848693 :         getGridPointCoordinates( ineigh, tindices, xx );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">   11848693 :         if( kernel ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">   47354528 :           for(unsigned j=0; j&lt;dimension; ++j) vv[j]-&gt;set(xx[j]);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">   11843920 :           newval = kernel-&gt;evaluate( Tools::unique2raw(vv), der, true );</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :         } else {</a>
+<a name="140"><span class="lineNum">     140 </span>            :           // Evalulate dot product</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      19092 :           double dot=0; for(unsigned j=0; j&lt;dimension; ++j) { dot+=xx[j]*point[j]; der[j]=xx[j]; }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :           // Von misses distribution for concentration parameter</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       4773 :           newval = von_misses_norm*exp( von_misses_concentration*dot );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :           // And final derivatives</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      19092 :           for(unsigned j=0; j&lt;dimension; ++j) der[j] *= von_misses_concentration*newval;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :         }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">   11848693 :         accumulate( ineigh, weight, newval, der, buffer );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">   11848693 :         if( wasForced() ) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       5744 :           accumulateForce( ineigh, weight, der, intforce );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       5744 :           totwforce += myvals.get( 1+dimension )*newval*forces[ineigh];</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :         }</a>
+<a name="152"><span class="lineNum">     152 </span>            :       }</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      21447 :       if( wasForced() ) {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :         // Minus sign for kernel here as we are taking derivative with respect to position of center of</a>
+<a name="155"><span class="lineNum">     155 </span>            :         // kernel NOT derivative wrt to grid point</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        110 :         double pref = 1; if( kernel ) pref = -1;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        110 :         unsigned nder = getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        110 :         unsigned gridbuf = getNumberOfBufferPoints()*getNumberOfQuantities();</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        300 :         for(unsigned j=0; j&lt;dimension; ++j) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      33940 :           for(unsigned k=0; k&lt;myvals.getNumberActive(); ++k) {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :             unsigned kder=myvals.getActiveIndex(k);</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      33750 :             buffer[ bufstart + gridbuf + kder ] += pref*intforce[j]*myvals.getDerivative( j+1, kder );</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :           }</a>
+<a name="164"><span class="lineNum">     164 </span>            :         }</a>
+<a name="165"><span class="lineNum">     165 </span>            :         // Accumulate the sum of all the weights</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        110 :         buffer[ bufstart + gridbuf + nder ] += myvals.get(0);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :         // Add the derivatives of the weights into the force -- this is separate loop as weights of all parts are considered together</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      32060 :         for(unsigned k=0; k&lt;myvals.getNumberActive(); ++k) {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :           unsigned kder=myvals.getActiveIndex(k);</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      31950 :           buffer[ bufstart + gridbuf + kder ] += totwforce*myvals.getDerivative( 0, kder );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      31950 :           buffer[ bufstart + gridbuf + nder + 1 + kder ] += myvals.getDerivative( 0, kder );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :         }</a>
+<a name="173"><span class="lineNum">     173 </span>            :       }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      21447 :     }</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      23553 :   }</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      38461 : }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">      40596 : void HistogramOnGrid::accumulate( const unsigned&amp; ipoint, const double&amp; weight, const double&amp; dens, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; buffer ) const {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      40596 :   buffer[bufstart+nper*ipoint] += weight*dens;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     168672 :   if( der.size()&gt;0 ) for(unsigned j=0; j&lt;dimension; ++j) buffer[bufstart+nper*ipoint + 1 + j] += weight*der[j];</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      40596 : }</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       5744 : void HistogramOnGrid::accumulateForce( const unsigned&amp; ipoint, const double&amp; weight, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; intforce ) const {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      18414 :   for(unsigned j=0; j&lt;der.size(); ++j) intforce[j] += forces[ipoint]*weight*der[j];</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       5744 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         20 : void HistogramOnGrid::getFinalForces( const std::vector&lt;double&gt;&amp; buffer, std::vector&lt;double&gt;&amp; finalForces ) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         20 :   if( finalForces.size()!=getAction()-&gt;getNumberOfDerivatives() ) finalForces.resize( getAction()-&gt;getNumberOfDerivatives() );</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   // And the final force</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         20 :   unsigned nder = getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Derivatives due to normalization</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         20 :   unsigned gridbuf = getNumberOfBufferPoints()*getNumberOfQuantities();</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       3815 :   for(unsigned i=0; i&lt;finalForces.size(); ++i) finalForces[i] = buffer[ bufstart + gridbuf + i ];</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   // Derivatives due to normalization</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         20 :   if( !noAverage() ) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         15 :     unsigned wderstart = bufstart + gridbuf + nder; double pref=0;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       3620 :     for(unsigned ipoint=0; ipoint&lt;getNumberOfPoints(); ++ipoint) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       3605 :       pref += forces[ipoint]*buffer[ bufstart + ipoint*nper ] / buffer[wderstart];</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       3570 :     for(unsigned j=0; j&lt;finalForces.size(); ++j) finalForces[j] -= pref*buffer[ wderstart + 1 + j ];</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         20 : }</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        156 : void HistogramOnGrid::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        156 :   if( addOneKernelAtATime ) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      14975 :     for(unsigned i=0; i&lt;getAction()-&gt;getCurrentNumberOfActiveTasks(); ++i) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      69400 :       for(unsigned j=0; j&lt;nper; ++j) addDataElement( nper*getAction()-&gt;getActiveTask(i)+j, buffer[bufstart+i*nper+j] );</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :     }</a>
+<a name="209"><span class="lineNum">     209 </span>            :   } else {</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         89 :     GridVessel::finish( buffer );</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        156 : }</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/HistogramOnGrid.h.func-sort-c.html b/coverage/gridtools/HistogramOnGrid.h.func-sort-c.html
new file mode 100644
index 0000000000..dd9474e306
--- /dev/null
+++ b/coverage/gridtools/HistogramOnGrid.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/HistogramOnGrid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - HistogramOnGrid.h<span style="font-size: 80%;"> (<a href="HistogramOnGrid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HistogramOnGrid.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.h.gcov.html#62">_ZNK4PLMD9gridtools15HistogramOnGrid23getNumberOfBufferPointsEv</a></td>
+              <td class="coverFnHi">269</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/HistogramOnGrid.h.func.html b/coverage/gridtools/HistogramOnGrid.h.func.html
new file mode 100644
index 0000000000..f66ca881fd
--- /dev/null
+++ b/coverage/gridtools/HistogramOnGrid.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/HistogramOnGrid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - HistogramOnGrid.h<span style="font-size: 80%;"> (<a href="HistogramOnGrid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HistogramOnGrid.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramOnGrid.h.gcov.html#62">_ZNK4PLMD9gridtools15HistogramOnGrid23getNumberOfBufferPointsEv</a></td>
+              <td class="coverFnHi">269</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/HistogramOnGrid.h.gcov.html b/coverage/gridtools/HistogramOnGrid.h.gcov.html
new file mode 100644
index 0000000000..26686d3dd3
--- /dev/null
+++ b/coverage/gridtools/HistogramOnGrid.h.gcov.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/HistogramOnGrid.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - HistogramOnGrid.h<span style="font-size: 80%;"> (source / <a href="HistogramOnGrid.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_gridtools_HistogramOnGrid_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_gridtools_HistogramOnGrid_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;GridVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;memory&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class KernelFunctions;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace gridtools {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class HistogramOnGrid : public GridVessel {</a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   unsigned neigh_tot;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   bool addOneKernelAtATime;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::string kerneltype;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;double&gt; bandwidths;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   std::vector&lt;unsigned&gt; nneigh;</a>
+<a name="41"><span class="lineNum">      41 </span>            : protected:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   bool discrete;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   double  von_misses_norm;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   double von_misses_concentration;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="47"><span class="lineNum">      47 </span>            :   explicit HistogramOnGrid( const vesselbase::VesselOptions&amp; da );</a>
+<a name="48"><span class="lineNum">      48 </span>            :   void setBounds( const std::vector&lt;std::string&gt;&amp; smin, const std::vector&lt;std::string&gt;&amp; smax,</a>
+<a name="49"><span class="lineNum">      49 </span>            :                   const std::vector&lt;unsigned&gt;&amp; nbins, const std::vector&lt;double&gt;&amp; spacing ) override;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const override;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   virtual void accumulate( const unsigned&amp; ipoint, const double&amp; weight, const double&amp; dens, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; buffer ) const ;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   virtual void accumulateForce( const unsigned&amp; ipoint, const double&amp; weight, const std::vector&lt;double&gt;&amp; der, std::vector&lt;double&gt;&amp; intforce ) const ;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   unsigned getNumberOfBufferPoints() const override;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::unique_ptr&lt;KernelFunctions&gt; getKernelAndNeighbors( std::vector&lt;double&gt;&amp; point, unsigned&amp; num_neigh, std::vector&lt;unsigned&gt;&amp; neighbors ) const;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; getVectorOfValues() const ;</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         19 :   void addOneKernelEachTimeOnly() { addOneKernelAtATime=true; }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   void getFinalForces( const std::vector&lt;double&gt;&amp; buffer, std::vector&lt;double&gt;&amp; finalForces ) override;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   bool noDiscreteKernels() const ;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   double getFibonacciCutoff() const override;</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : inline</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        269 : unsigned HistogramOnGrid::getNumberOfBufferPoints() const {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        269 :   if( addOneKernelAtATime ) return neigh_tot;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        250 :   return GridVessel::getNumberOfBufferPoints();</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/IntegrateGrid.cpp.func-sort-c.html b/coverage/gridtools/IntegrateGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..eaf76a3ca2
--- /dev/null
+++ b/coverage/gridtools/IntegrateGrid.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/IntegrateGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - IntegrateGrid.cpp<span style="font-size: 80%;"> (<a href="IntegrateGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="IntegrateGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#48">_ZN4PLMD9gridtools13IntegrateGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools12_GLOBAL__N_125IntegrateGridRegisterMe446createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#48">_ZN4PLMD9gridtools13IntegrateGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#44">_ZN4PLMD9gridtools13IntegrateGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools12_GLOBAL__N_125IntegrateGridRegisterMe44C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools12_GLOBAL__N_125IntegrateGridRegisterMe44D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#54">_ZNK4PLMD9gridtools13IntegrateGrid7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">5705</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/IntegrateGrid.cpp.func.html b/coverage/gridtools/IntegrateGrid.cpp.func.html
new file mode 100644
index 0000000000..29109b9548
--- /dev/null
+++ b/coverage/gridtools/IntegrateGrid.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/IntegrateGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - IntegrateGrid.cpp<span style="font-size: 80%;"> (<a href="IntegrateGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="IntegrateGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools12_GLOBAL__N_125IntegrateGridRegisterMe446createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools12_GLOBAL__N_125IntegrateGridRegisterMe44C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#42">_ZN4PLMD9gridtools12_GLOBAL__N_125IntegrateGridRegisterMe44D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#44">_ZN4PLMD9gridtools13IntegrateGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#48">_ZN4PLMD9gridtools13IntegrateGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#48">_ZN4PLMD9gridtools13IntegrateGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntegrateGrid.cpp.gcov.html#54">_ZNK4PLMD9gridtools13IntegrateGrid7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">5705</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/IntegrateGrid.cpp.gcov.html b/coverage/gridtools/IntegrateGrid.cpp.gcov.html
new file mode 100644
index 0000000000..31dc6f04ce
--- /dev/null
+++ b/coverage/gridtools/IntegrateGrid.cpp.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/IntegrateGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - IntegrateGrid.cpp<span style="font-size: 80%;"> (source / <a href="IntegrateGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithIntegral.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC GRIDANALYSIS INTEGRATE_GRID</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Calculate the total integral of the function on the input grid</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : \par Examples</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : */</a>
+<a name="32"><span class="lineNum">      32 </span>            : //+ENDPLUMEDOC</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace gridtools {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class IntegrateGrid : public ActionWithIntegral {</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit IntegrateGrid(const ActionOptions&amp;ao);</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void compute( const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="42"><span class="lineNum">      42 </span>            : };</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(IntegrateGrid,&quot;INTEGRATE_GRID&quot;)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          6 : void IntegrateGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          6 :   ActionWithIntegral::registerKeywords( keys );</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          6 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 : IntegrateGrid::IntegrateGrid(const ActionOptions&amp;ao):</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   Action(ao),</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          4 :   ActionWithIntegral(ao)</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          4 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       5705 : void IntegrateGrid::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       5705 :   myvals.setValue( 0, 1.0 ); myvals.setValue( 1, getVolume()*getFunctionValue( current ) );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       5705 :   if( !doNotCalculateDerivatives() ) myvals.addDerivative( 1, current, getVolume() );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       5705 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/InterpolateGrid.cpp.func-sort-c.html b/coverage/gridtools/InterpolateGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..82d1a20d30
--- /dev/null
+++ b/coverage/gridtools/InterpolateGrid.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/InterpolateGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - InterpolateGrid.cpp<span style="font-size: 80%;"> (<a href="InterpolateGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="InterpolateGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#57">_ZN4PLMD9gridtools15InterpolateGrid10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#69">_ZN4PLMD9gridtools15InterpolateGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#60">_ZN4PLMD9gridtools12_GLOBAL__N_127InterpolateGridRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#69">_ZN4PLMD9gridtools15InterpolateGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#62">_ZN4PLMD9gridtools15InterpolateGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#97">_ZNK4PLMD9gridtools15InterpolateGrid21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#101">_ZNK4PLMD9gridtools15InterpolateGrid7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#60">_ZN4PLMD9gridtools12_GLOBAL__N_127InterpolateGridRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#60">_ZN4PLMD9gridtools12_GLOBAL__N_127InterpolateGridRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/InterpolateGrid.cpp.func.html b/coverage/gridtools/InterpolateGrid.cpp.func.html
new file mode 100644
index 0000000000..f71941e5d3
--- /dev/null
+++ b/coverage/gridtools/InterpolateGrid.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/InterpolateGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - InterpolateGrid.cpp<span style="font-size: 80%;"> (<a href="InterpolateGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="InterpolateGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#60">_ZN4PLMD9gridtools12_GLOBAL__N_127InterpolateGridRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#60">_ZN4PLMD9gridtools12_GLOBAL__N_127InterpolateGridRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#60">_ZN4PLMD9gridtools12_GLOBAL__N_127InterpolateGridRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#57">_ZN4PLMD9gridtools15InterpolateGrid10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#62">_ZN4PLMD9gridtools15InterpolateGrid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#69">_ZN4PLMD9gridtools15InterpolateGridC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#69">_ZN4PLMD9gridtools15InterpolateGridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#97">_ZNK4PLMD9gridtools15InterpolateGrid21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InterpolateGrid.cpp.gcov.html#101">_ZNK4PLMD9gridtools15InterpolateGrid7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">200</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/InterpolateGrid.cpp.gcov.html b/coverage/gridtools/InterpolateGrid.cpp.gcov.html
new file mode 100644
index 0000000000..6ec484b9bb
--- /dev/null
+++ b/coverage/gridtools/InterpolateGrid.cpp.gcov.html
@@ -0,0 +1,187 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools/InterpolateGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">gridtools</a> - InterpolateGrid.cpp<span style="font-size: 80%;"> (source / <a href="InterpolateGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionWithInputGrid.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC GRIDANALYSIS INTERPOLATE_GRID</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Interpolate a smooth function stored on a grid onto a grid with a smaller grid spacing.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : This action takes a function evaluated on a grid as input and can be used to interpolate the values of that</a>
+<a name="31"><span class="lineNum">      31 </span>            : function on to a finer grained grid.  The interpolation within this algorithm is done using splines.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \par Examples</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The input below can be used to post process a trajectory.  It calculates a \ref HISTOGRAM as a function the</a>
+<a name="36"><span class="lineNum">      36 </span>            : distance between atoms 1 and 2 using kernel density estimation.  During the calculation the values of the kernels</a>
+<a name="37"><span class="lineNum">      37 </span>            : are evaluated at 100 points on a uniform grid between 0.0 and 3.0.  Prior to outputting this function at the end of the</a>
+<a name="38"><span class="lineNum">      38 </span>            : simulation this function is interpolated onto a finer grid of 200 points between 0.0 and 3.0.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \plumedfile</a>
+<a name="41"><span class="lineNum">      41 </span>            : x: DISTANCE ATOMS=1,2</a>
+<a name="42"><span class="lineNum">      42 </span>            : hA1: HISTOGRAM ARG=x GRID_MIN=0.0 GRID_MAX=3.0 GRID_BIN=100 BANDWIDTH=0.1</a>
+<a name="43"><span class="lineNum">      43 </span>            : ii: INTERPOLATE_GRID GRID=hA1 GRID_BIN=200</a>
+<a name="44"><span class="lineNum">      44 </span>            : DUMPGRID GRID=ii FILE=histo.dat</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : namespace PLMD {</a>
+<a name="51"><span class="lineNum">      51 </span>            : namespace gridtools {</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : class InterpolateGrid : public ActionWithInputGrid {</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   explicit InterpolateGrid(const ActionOptions&amp;ao);</a>
+<a name="57"><span class="lineNum">      57 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void compute( const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(InterpolateGrid,&quot;INTERPOLATE_GRID&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 : void InterpolateGrid::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          4 :   ActionWithInputGrid::registerKeywords( keys );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;GRID_BIN&quot;,&quot;the number of bins for the grid&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;GRID_SPACING&quot;,&quot;the approximate grid spacing (to be used as an alternative or together with GRID_BIN)&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          8 :   keys.remove(&quot;KERNEL&quot;); keys.remove(&quot;BANDWIDTH&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          4 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 : InterpolateGrid::InterpolateGrid(const ActionOptions&amp;ao):</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   Action(ao),</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 :   ActionWithInputGrid(ao)</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : {</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          2 :   plumed_assert( ingrid-&gt;getNumberOfComponents()==1 );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          2 :   if( ingrid-&gt;noDerivatives() ) error(&quot;cannot interpolate a grid that does not have derivatives&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   // Create the input from the old string</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 :   auto grid=createGrid( &quot;grid&quot;, &quot;COMPONENTS=&quot; + getLabel() + &quot; &quot; + ingrid-&gt;getInputString()  );</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   // notice that createGrid also sets mygrid=grid.get()</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 :   std::vector&lt;unsigned&gt; nbin; parseVector(&quot;GRID_BIN&quot;,nbin);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; gspacing; parseVector(&quot;GRID_SPACING&quot;,gspacing);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          2 :   if( nbin.size()!=ingrid-&gt;getDimension() &amp;&amp; gspacing.size()!=ingrid-&gt;getDimension() ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :     error(&quot;GRID_BIN or GRID_SPACING must be set&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   // Need this for creation of tasks</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :   grid-&gt;setBounds( ingrid-&gt;getMin(), ingrid-&gt;getMax(), nbin, gspacing );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 :   setAveragingAction( std::move(grid), true );</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   // Now create task list</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        202 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) addTaskToList(i);</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   // And activate all tasks</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   deactivateAllTasks();</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        202 :   for(unsigned i=0; i&lt;mygrid-&gt;getNumberOfPoints(); ++i) taskFlags[i]=1;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   lockContributors();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          8 : unsigned InterpolateGrid::getNumberOfQuantities() const {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          8 :   return 2 + ingrid-&gt;getDimension();</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        200 : void InterpolateGrid::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        200 :   std::vector&lt;double&gt; pos( mygrid-&gt;getDimension() ); mygrid-&gt;getGridPointCoordinates( current, pos );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        200 :   std::vector&lt;double&gt; der( mygrid-&gt;getDimension() ); double val = getFunctionValueAndDerivatives( pos, der );</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   myvals.setValue( 0, 1.0 ); myvals.setValue(1, val );</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        400 :   for(unsigned i=0; i&lt;mygrid-&gt;getDimension(); ++i) myvals.setValue( 2+i, der[i] );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        200 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/index-sort-f.html b/coverage/gridtools/index-sort-f.html
new file mode 100644
index 0000000000..d04a946174
--- /dev/null
+++ b/coverage/gridtools/index-sort-f.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - gridtools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1183</td>
+            <td class="headerCovTableEntry">1264</td>
+            <td class="headerCovTableEntryHi">93.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">200</td>
+            <td class="headerCovTableEntryMed">85.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageOnGrid.h.gcov.html">AverageOnGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=60 height=10 alt="60.0%"><img src="../snow.png" width=40 height=10 alt="60.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithIntegral.h.gcov.html">ActionWithIntegral.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContourFindingBase.h.gcov.html">ContourFindingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContourFindingBase.cpp.gcov.html">ContourFindingBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FourierTransform.cpp.gcov.html">FourierTransform.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="83.7%"><img src="../snow.png" width=16 height=10 alt="83.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.7&nbsp;%</td>
+      <td class="coverNumMed">72 / 86</td>
+      <td class="coverPerLo">70.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindContour.cpp.gcov.html">FindContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.3%"><img src="../snow.png" width=16 height=10 alt="84.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.3&nbsp;%</td>
+      <td class="coverNumMed">75 / 89</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InterpolateGrid.cpp.gcov.html">InterpolateGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridPrintingBase.cpp.gcov.html">GridPrintingBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithIntegral.cpp.gcov.html">ActionWithIntegral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputGrid.cpp.gcov.html">ActionWithInputGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.2%"><img src="../snow.png" width=9 height=10 alt="91.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.2&nbsp;%</td>
+      <td class="coverNumHi">31 / 34</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindContourSurface.cpp.gcov.html">FindContourSurface.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">90 / 94</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpCube.cpp.gcov.html">DumpCube.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">32 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntegrateGrid.cpp.gcov.html">IntegrateGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithGrid.cpp.gcov.html">ActionWithGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">51 / 52</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridToXYZ.cpp.gcov.html">GridToXYZ.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">40 / 45</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpGrid.cpp.gcov.html">DumpGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConvertToFES.cpp.gcov.html">ConvertToFES.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">46 / 48</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindSphericalContour.cpp.gcov.html">FindSphericalContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">39 / 41</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridVessel.h.gcov.html">GridVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.3%"><img src="../snow.png" width=11 height=10 alt="89.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 28</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridVessel.cpp.gcov.html">GridVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">316 / 334</td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">37 / 39</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramOnGrid.h.gcov.html">HistogramOnGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridSearch.h.gcov.html">GridSearch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 40</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridPrintingBase.h.gcov.html">GridPrintingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputGrid.h.gcov.html">ActionWithInputGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageOnGrid.cpp.gcov.html">AverageOnGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramOnGrid.cpp.gcov.html">HistogramOnGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">118 / 120</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/index-sort-l.html b/coverage/gridtools/index-sort-l.html
new file mode 100644
index 0000000000..f0edf32e4a
--- /dev/null
+++ b/coverage/gridtools/index-sort-l.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - gridtools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1183</td>
+            <td class="headerCovTableEntry">1264</td>
+            <td class="headerCovTableEntryHi">93.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">200</td>
+            <td class="headerCovTableEntryMed">85.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageOnGrid.h.gcov.html">AverageOnGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=60 height=10 alt="60.0%"><img src="../snow.png" width=40 height=10 alt="60.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithIntegral.h.gcov.html">ActionWithIntegral.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContourFindingBase.h.gcov.html">ContourFindingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FourierTransform.cpp.gcov.html">FourierTransform.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="83.7%"><img src="../snow.png" width=16 height=10 alt="83.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.7&nbsp;%</td>
+      <td class="coverNumMed">72 / 86</td>
+      <td class="coverPerLo">70.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindContour.cpp.gcov.html">FindContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.3%"><img src="../snow.png" width=16 height=10 alt="84.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.3&nbsp;%</td>
+      <td class="coverNumMed">75 / 89</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpCube.cpp.gcov.html">DumpCube.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">32 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridToXYZ.cpp.gcov.html">GridToXYZ.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">40 / 45</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridVessel.h.gcov.html">GridVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.3%"><img src="../snow.png" width=11 height=10 alt="89.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 28</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputGrid.cpp.gcov.html">ActionWithInputGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.2%"><img src="../snow.png" width=9 height=10 alt="91.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.2&nbsp;%</td>
+      <td class="coverNumHi">31 / 34</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InterpolateGrid.cpp.gcov.html">InterpolateGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridVessel.cpp.gcov.html">GridVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">316 / 334</td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">37 / 39</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridSearch.h.gcov.html">GridSearch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 40</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindSphericalContour.cpp.gcov.html">FindSphericalContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">39 / 41</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindContourSurface.cpp.gcov.html">FindContourSurface.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">90 / 94</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConvertToFES.cpp.gcov.html">ConvertToFES.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">46 / 48</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageOnGrid.cpp.gcov.html">AverageOnGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithGrid.cpp.gcov.html">ActionWithGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">51 / 52</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramOnGrid.cpp.gcov.html">HistogramOnGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">118 / 120</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridPrintingBase.h.gcov.html">GridPrintingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramOnGrid.h.gcov.html">HistogramOnGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputGrid.h.gcov.html">ActionWithInputGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntegrateGrid.cpp.gcov.html">IntegrateGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContourFindingBase.cpp.gcov.html">ContourFindingBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithIntegral.cpp.gcov.html">ActionWithIntegral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpGrid.cpp.gcov.html">DumpGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridPrintingBase.cpp.gcov.html">GridPrintingBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/gridtools/index.html b/coverage/gridtools/index.html
new file mode 100644
index 0000000000..5ef5eca52e
--- /dev/null
+++ b/coverage/gridtools/index.html
@@ -0,0 +1,343 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - gridtools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - gridtools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1183</td>
+            <td class="headerCovTableEntry">1264</td>
+            <td class="headerCovTableEntryHi">93.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">200</td>
+            <td class="headerCovTableEntryMed">85.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithGrid.cpp.gcov.html">ActionWithGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">51 / 52</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputGrid.cpp.gcov.html">ActionWithInputGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.2%"><img src="../snow.png" width=9 height=10 alt="91.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.2&nbsp;%</td>
+      <td class="coverNumHi">31 / 34</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputGrid.h.gcov.html">ActionWithInputGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithIntegral.cpp.gcov.html">ActionWithIntegral.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithIntegral.h.gcov.html">ActionWithIntegral.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageOnGrid.cpp.gcov.html">AverageOnGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AverageOnGrid.h.gcov.html">AverageOnGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=60 height=10 alt="60.0%"><img src="../snow.png" width=40 height=10 alt="60.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+      <td class="coverPerLo">33.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContourFindingBase.cpp.gcov.html">ContourFindingBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ContourFindingBase.h.gcov.html">ContourFindingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConvertToFES.cpp.gcov.html">ConvertToFES.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">46 / 48</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpCube.cpp.gcov.html">DumpCube.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">32 / 36</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpGrid.cpp.gcov.html">DumpGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">34 / 34</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindContour.cpp.gcov.html">FindContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.3%"><img src="../snow.png" width=16 height=10 alt="84.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.3&nbsp;%</td>
+      <td class="coverNumMed">75 / 89</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindContourSurface.cpp.gcov.html">FindContourSurface.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">90 / 94</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FindSphericalContour.cpp.gcov.html">FindSphericalContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">39 / 41</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FourierTransform.cpp.gcov.html">FourierTransform.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="83.7%"><img src="../snow.png" width=16 height=10 alt="83.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.7&nbsp;%</td>
+      <td class="coverNumMed">72 / 86</td>
+      <td class="coverPerLo">70.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridPrintingBase.cpp.gcov.html">GridPrintingBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridPrintingBase.h.gcov.html">GridPrintingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridSearch.h.gcov.html">GridSearch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.0%"><img src="../snow.png" width=5 height=10 alt="95.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 40</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridToXYZ.cpp.gcov.html">GridToXYZ.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.9%"><img src="../snow.png" width=11 height=10 alt="88.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">40 / 45</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridVessel.cpp.gcov.html">GridVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">316 / 334</td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">37 / 39</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridVessel.h.gcov.html">GridVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.3%"><img src="../snow.png" width=11 height=10 alt="89.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.3&nbsp;%</td>
+      <td class="coverNumMed">25 / 28</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramOnGrid.cpp.gcov.html">HistogramOnGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">118 / 120</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramOnGrid.h.gcov.html">HistogramOnGrid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntegrateGrid.cpp.gcov.html">IntegrateGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InterpolateGrid.cpp.gcov.html">InterpolateGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">29 / 31</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/index-sort-f.html b/coverage/index-sort-f.html
new file mode 100644
index 0000000000..c1639af177
--- /dev/null
+++ b/coverage/index-sort-f.html
@@ -0,0 +1,473 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage</title>
+  <link rel="stylesheet" type="text/css" href="gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue">top level</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49880</td>
+            <td class="headerCovTableEntry">58508</td>
+            <td class="headerCovTableEntryMed">85.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5552</td>
+            <td class="headerCovTableEntry">6966</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr><td><img src="glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Directory <span class="tableHeadSort"><a href="index.html"><img src="updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="config/index.html">config</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=46 height=10 alt="46.4%"><img src="snow.png" width=54 height=10 alt="46.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">46.4&nbsp;%</td>
+      <td class="coverNumLo">64 / 138</td>
+      <td class="coverPerLo">46.0&nbsp;%</td>
+      <td class="coverNumLo">23 / 50</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="wrapper/index.html">wrapper</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=53 height=10 alt="52.7%"><img src="snow.png" width=47 height=10 alt="52.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.7&nbsp;%</td>
+      <td class="coverNumLo">247 / 469</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">144 / 252</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="manyrestraints/index.html">manyrestraints</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="81.5%"><img src="snow.png" width=18 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">75 / 92</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">18 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ves/index.html">ves</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="82.1%"><img src="snow.png" width=18 height=10 alt="82.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">5938 / 7230</td>
+      <td class="coverPerLo">70.4&nbsp;%</td>
+      <td class="coverNumLo">555 / 788</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="dimred/index.html">dimred</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=85 height=10 alt="84.8%"><img src="snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">556 / 656</td>
+      <td class="coverPerLo">73.1&nbsp;%</td>
+      <td class="coverNumLo">79 / 108</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="piv/index.html">piv</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=72 height=10 alt="71.8%"><img src="snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">428 / 596</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="crystallization/index.html">crystallization</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=84 height=10 alt="83.8%"><img src="snow.png" width=16 height=10 alt="83.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.8&nbsp;%</td>
+      <td class="coverNumMed">1015 / 1211</td>
+      <td class="coverPerMed">77.0&nbsp;%</td>
+      <td class="coverNumMed">144 / 187</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="analysis/index.html">analysis</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="88.5%"><img src="snow.png" width=12 height=10 alt="88.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.5&nbsp;%</td>
+      <td class="coverNumMed">859 / 971</td>
+      <td class="coverPerMed">77.2&nbsp;%</td>
+      <td class="coverNumMed">156 / 202</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="multicolvar/index.html">multicolvar</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=79 height=10 alt="78.6%"><img src="snow.png" width=21 height=10 alt="78.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">2377 / 3025</td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">329 / 422</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="reference/index.html">reference</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="86.1%"><img src="snow.png" width=14 height=10 alt="86.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.1&nbsp;%</td>
+      <td class="coverNumMed">668 / 776</td>
+      <td class="coverPerMed">79.3&nbsp;%</td>
+      <td class="coverNumMed">153 / 193</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pamm/index.html">pamm</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=81 height=10 alt="81.4%"><img src="snow.png" width=19 height=10 alt="81.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.4&nbsp;%</td>
+      <td class="coverNumMed">215 / 264</td>
+      <td class="coverPerMed">79.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="generic/index.html">generic</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=95 height=10 alt="94.9%"><img src="snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">1210 / 1275</td>
+      <td class="coverPerMed">79.7&nbsp;%</td>
+      <td class="coverNumMed">177 / 222</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="core/index.html">core</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="85.9%"><img src="snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">3237 / 3767</td>
+      <td class="coverPerMed">80.6&nbsp;%</td>
+      <td class="coverNumMed">431 / 535</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="tools/index.html">tools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=84 height=10 alt="83.5%"><img src="snow.png" width=16 height=10 alt="83.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.5&nbsp;%</td>
+      <td class="coverNumMed">5629 / 6739</td>
+      <td class="coverPerMed">81.4&nbsp;%</td>
+      <td class="coverNumMed">1406 / 1728</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="isdb/index.html">isdb</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="81.6%"><img src="snow.png" width=18 height=10 alt="81.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.6&nbsp;%</td>
+      <td class="coverNumMed">8645 / 10595</td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">198 / 243</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="s2cm/index.html">s2cm</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=92 height=10 alt="91.6%"><img src="snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
+      <td class="coverNumHi">152 / 166</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="adjmat/index.html">adjmat</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=89 height=10 alt="88.6%"><img src="snow.png" width=11 height=10 alt="88.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.6&nbsp;%</td>
+      <td class="coverNumMed">1038 / 1171</td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">183 / 223</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="maze/index.html">maze</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=83 height=10 alt="83.2%"><img src="snow.png" width=17 height=10 alt="83.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.2&nbsp;%</td>
+      <td class="coverNumMed">645 / 775</td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">84 / 102</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="colvar/index.html">colvar</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="94.0%"><img src="snow.png" width=6 height=10 alt="94.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.0&nbsp;%</td>
+      <td class="coverNumHi">2101 / 2235</td>
+      <td class="coverPerMed">82.5&nbsp;%</td>
+      <td class="coverNumMed">184 / 223</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="fisst/index.html">fisst</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="79.6%"><img src="snow.png" width=20 height=10 alt="79.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.6&nbsp;%</td>
+      <td class="coverNumMed">319 / 401</td>
+      <td class="coverPerMed">82.8&nbsp;%</td>
+      <td class="coverNumMed">24 / 29</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="secondarystructure/index.html">secondarystructure</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=97 height=10 alt="96.7%"><img src="snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">376 / 389</td>
+      <td class="coverPerMed">82.9&nbsp;%</td>
+      <td class="coverNumMed">29 / 35</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="setup/index.html">setup</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=98 height=10 alt="97.8%"><img src="snow.png" width=2 height=10 alt="97.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.8&nbsp;%</td>
+      <td class="coverNumHi">87 / 89</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">15 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="function/index.html">function</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="85.9%"><img src="snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">909 / 1058</td>
+      <td class="coverPerMed">84.0&nbsp;%</td>
+      <td class="coverNumMed">84 / 100</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa/index.html">sasa</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="82.0%"><img src="snow.png" width=18 height=10 alt="82.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.0&nbsp;%</td>
+      <td class="coverNumMed">998 / 1217</td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="gridtools/index.html">gridtools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="93.6%"><img src="snow.png" width=6 height=10 alt="93.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.6&nbsp;%</td>
+      <td class="coverNumHi">1183 / 1264</td>
+      <td class="coverPerMed">85.5&nbsp;%</td>
+      <td class="coverNumMed">171 / 200</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="bias/index.html">bias</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=91 height=10 alt="91.4%"><img src="snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">2393 / 2617</td>
+      <td class="coverPerMed">85.6&nbsp;%</td>
+      <td class="coverNumMed">143 / 167</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="membranefusion/index.html">membranefusion</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="88.2%"><img src="snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">456 / 517</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">18 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="funnel/index.html">funnel</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=98 height=10 alt="98.0%"><img src="snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">248 / 253</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="eds/index.html">eds</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=93 height=10 alt="92.6%"><img src="snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">452 / 488</td>
+      <td class="coverPerMed">87.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 23</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pytorch/index.html">pytorch</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=83 height=10 alt="83.1%"><img src="snow.png" width=17 height=10 alt="83.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.1&nbsp;%</td>
+      <td class="coverNumMed">54 / 65</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vatom/index.html">vatom</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=99 height=10 alt="99.1%"><img src="snow.png" width=1 height=10 alt="99.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.1&nbsp;%</td>
+      <td class="coverNumHi">221 / 223</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">21 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="annfunc/index.html">annfunc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=97 height=10 alt="97.1%"><img src="snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="mapping/index.html">mapping</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="93.7%"><img src="snow.png" width=6 height=10 alt="93.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.7&nbsp;%</td>
+      <td class="coverNumHi">758 / 809</td>
+      <td class="coverPerMed">89.0&nbsp;%</td>
+      <td class="coverNumMed">89 / 100</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vesselbase/index.html">vesselbase</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=93 height=10 alt="92.9%"><img src="snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">1141 / 1228</td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">231 / 258</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cltools/index.html">cltools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="80.0%"><img src="snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">1359 / 1699</td>
+      <td class="coverPerHi">92.0&nbsp;%</td>
+      <td class="coverNumHi">103 / 112</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logmfd/index.html">logmfd</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="87.6%"><img src="snow.png" width=12 height=10 alt="87.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.6&nbsp;%</td>
+      <td class="coverNumMed">326 / 372</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="opes/index.html">opes</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=96 height=10 alt="96.1%"><img src="snow.png" width=4 height=10 alt="96.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.1&nbsp;%</td>
+      <td class="coverNumHi">2161 / 2249</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">135 / 144</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="drr/index.html">drr</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="94.3%"><img src="snow.png" width=6 height=10 alt="94.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.3&nbsp;%</td>
+      <td class="coverNumHi">1194 / 1266</td>
+      <td class="coverPerHi">94.8&nbsp;%</td>
+      <td class="coverNumHi">92 / 97</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="main/index.html">main</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="80.0%"><img src="snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/index-sort-l.html b/coverage/index-sort-l.html
new file mode 100644
index 0000000000..f54e687b56
--- /dev/null
+++ b/coverage/index-sort-l.html
@@ -0,0 +1,473 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage</title>
+  <link rel="stylesheet" type="text/css" href="gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue">top level</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49880</td>
+            <td class="headerCovTableEntry">58508</td>
+            <td class="headerCovTableEntryMed">85.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5552</td>
+            <td class="headerCovTableEntry">6966</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr><td><img src="glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Directory <span class="tableHeadSort"><a href="index.html"><img src="updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="config/index.html">config</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=46 height=10 alt="46.4%"><img src="snow.png" width=54 height=10 alt="46.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">46.4&nbsp;%</td>
+      <td class="coverNumLo">64 / 138</td>
+      <td class="coverPerLo">46.0&nbsp;%</td>
+      <td class="coverNumLo">23 / 50</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="wrapper/index.html">wrapper</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=53 height=10 alt="52.7%"><img src="snow.png" width=47 height=10 alt="52.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.7&nbsp;%</td>
+      <td class="coverNumLo">247 / 469</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">144 / 252</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="piv/index.html">piv</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=72 height=10 alt="71.8%"><img src="snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">428 / 596</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="multicolvar/index.html">multicolvar</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=79 height=10 alt="78.6%"><img src="snow.png" width=21 height=10 alt="78.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">2377 / 3025</td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">329 / 422</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="fisst/index.html">fisst</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="79.6%"><img src="snow.png" width=20 height=10 alt="79.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.6&nbsp;%</td>
+      <td class="coverNumMed">319 / 401</td>
+      <td class="coverPerMed">82.8&nbsp;%</td>
+      <td class="coverNumMed">24 / 29</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cltools/index.html">cltools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="80.0%"><img src="snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">1359 / 1699</td>
+      <td class="coverPerHi">92.0&nbsp;%</td>
+      <td class="coverNumHi">103 / 112</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="main/index.html">main</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="80.0%"><img src="snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pamm/index.html">pamm</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=81 height=10 alt="81.4%"><img src="snow.png" width=19 height=10 alt="81.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.4&nbsp;%</td>
+      <td class="coverNumMed">215 / 264</td>
+      <td class="coverPerMed">79.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="manyrestraints/index.html">manyrestraints</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="81.5%"><img src="snow.png" width=18 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">75 / 92</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">18 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="isdb/index.html">isdb</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="81.6%"><img src="snow.png" width=18 height=10 alt="81.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.6&nbsp;%</td>
+      <td class="coverNumMed">8645 / 10595</td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">198 / 243</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa/index.html">sasa</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="82.0%"><img src="snow.png" width=18 height=10 alt="82.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.0&nbsp;%</td>
+      <td class="coverNumMed">998 / 1217</td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ves/index.html">ves</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="82.1%"><img src="snow.png" width=18 height=10 alt="82.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">5938 / 7230</td>
+      <td class="coverPerLo">70.4&nbsp;%</td>
+      <td class="coverNumLo">555 / 788</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pytorch/index.html">pytorch</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=83 height=10 alt="83.1%"><img src="snow.png" width=17 height=10 alt="83.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.1&nbsp;%</td>
+      <td class="coverNumMed">54 / 65</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="maze/index.html">maze</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=83 height=10 alt="83.2%"><img src="snow.png" width=17 height=10 alt="83.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.2&nbsp;%</td>
+      <td class="coverNumMed">645 / 775</td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">84 / 102</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="tools/index.html">tools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=84 height=10 alt="83.5%"><img src="snow.png" width=16 height=10 alt="83.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.5&nbsp;%</td>
+      <td class="coverNumMed">5629 / 6739</td>
+      <td class="coverPerMed">81.4&nbsp;%</td>
+      <td class="coverNumMed">1406 / 1728</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="crystallization/index.html">crystallization</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=84 height=10 alt="83.8%"><img src="snow.png" width=16 height=10 alt="83.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.8&nbsp;%</td>
+      <td class="coverNumMed">1015 / 1211</td>
+      <td class="coverPerMed">77.0&nbsp;%</td>
+      <td class="coverNumMed">144 / 187</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="dimred/index.html">dimred</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=85 height=10 alt="84.8%"><img src="snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">556 / 656</td>
+      <td class="coverPerLo">73.1&nbsp;%</td>
+      <td class="coverNumLo">79 / 108</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="function/index.html">function</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="85.9%"><img src="snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">909 / 1058</td>
+      <td class="coverPerMed">84.0&nbsp;%</td>
+      <td class="coverNumMed">84 / 100</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="core/index.html">core</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="85.9%"><img src="snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">3237 / 3767</td>
+      <td class="coverPerMed">80.6&nbsp;%</td>
+      <td class="coverNumMed">431 / 535</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="reference/index.html">reference</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="86.1%"><img src="snow.png" width=14 height=10 alt="86.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.1&nbsp;%</td>
+      <td class="coverNumMed">668 / 776</td>
+      <td class="coverPerMed">79.3&nbsp;%</td>
+      <td class="coverNumMed">153 / 193</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logmfd/index.html">logmfd</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="87.6%"><img src="snow.png" width=12 height=10 alt="87.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.6&nbsp;%</td>
+      <td class="coverNumMed">326 / 372</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="membranefusion/index.html">membranefusion</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="88.2%"><img src="snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">456 / 517</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">18 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="analysis/index.html">analysis</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="88.5%"><img src="snow.png" width=12 height=10 alt="88.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.5&nbsp;%</td>
+      <td class="coverNumMed">859 / 971</td>
+      <td class="coverPerMed">77.2&nbsp;%</td>
+      <td class="coverNumMed">156 / 202</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="adjmat/index.html">adjmat</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=89 height=10 alt="88.6%"><img src="snow.png" width=11 height=10 alt="88.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.6&nbsp;%</td>
+      <td class="coverNumMed">1038 / 1171</td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">183 / 223</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="bias/index.html">bias</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=91 height=10 alt="91.4%"><img src="snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">2393 / 2617</td>
+      <td class="coverPerMed">85.6&nbsp;%</td>
+      <td class="coverNumMed">143 / 167</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="s2cm/index.html">s2cm</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=92 height=10 alt="91.6%"><img src="snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
+      <td class="coverNumHi">152 / 166</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="eds/index.html">eds</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=93 height=10 alt="92.6%"><img src="snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">452 / 488</td>
+      <td class="coverPerMed">87.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 23</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vesselbase/index.html">vesselbase</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=93 height=10 alt="92.9%"><img src="snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">1141 / 1228</td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">231 / 258</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="gridtools/index.html">gridtools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="93.6%"><img src="snow.png" width=6 height=10 alt="93.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.6&nbsp;%</td>
+      <td class="coverNumHi">1183 / 1264</td>
+      <td class="coverPerMed">85.5&nbsp;%</td>
+      <td class="coverNumMed">171 / 200</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="mapping/index.html">mapping</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="93.7%"><img src="snow.png" width=6 height=10 alt="93.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.7&nbsp;%</td>
+      <td class="coverNumHi">758 / 809</td>
+      <td class="coverPerMed">89.0&nbsp;%</td>
+      <td class="coverNumMed">89 / 100</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="colvar/index.html">colvar</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="94.0%"><img src="snow.png" width=6 height=10 alt="94.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.0&nbsp;%</td>
+      <td class="coverNumHi">2101 / 2235</td>
+      <td class="coverPerMed">82.5&nbsp;%</td>
+      <td class="coverNumMed">184 / 223</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="drr/index.html">drr</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="94.3%"><img src="snow.png" width=6 height=10 alt="94.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.3&nbsp;%</td>
+      <td class="coverNumHi">1194 / 1266</td>
+      <td class="coverPerHi">94.8&nbsp;%</td>
+      <td class="coverNumHi">92 / 97</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="generic/index.html">generic</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=95 height=10 alt="94.9%"><img src="snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">1210 / 1275</td>
+      <td class="coverPerMed">79.7&nbsp;%</td>
+      <td class="coverNumMed">177 / 222</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="opes/index.html">opes</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=96 height=10 alt="96.1%"><img src="snow.png" width=4 height=10 alt="96.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.1&nbsp;%</td>
+      <td class="coverNumHi">2161 / 2249</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">135 / 144</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="secondarystructure/index.html">secondarystructure</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=97 height=10 alt="96.7%"><img src="snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">376 / 389</td>
+      <td class="coverPerMed">82.9&nbsp;%</td>
+      <td class="coverNumMed">29 / 35</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="annfunc/index.html">annfunc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=97 height=10 alt="97.1%"><img src="snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="setup/index.html">setup</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=98 height=10 alt="97.8%"><img src="snow.png" width=2 height=10 alt="97.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.8&nbsp;%</td>
+      <td class="coverNumHi">87 / 89</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">15 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="funnel/index.html">funnel</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=98 height=10 alt="98.0%"><img src="snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">248 / 253</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vatom/index.html">vatom</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=99 height=10 alt="99.1%"><img src="snow.png" width=1 height=10 alt="99.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.1&nbsp;%</td>
+      <td class="coverNumHi">221 / 223</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">21 / 24</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/index.html b/coverage/index.html
new file mode 100644
index 0000000000..2926000989
--- /dev/null
+++ b/coverage/index.html
@@ -0,0 +1,473 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage</title>
+  <link rel="stylesheet" type="text/css" href="gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue">top level</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49880</td>
+            <td class="headerCovTableEntry">58508</td>
+            <td class="headerCovTableEntryMed">85.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5552</td>
+            <td class="headerCovTableEntry">6966</td>
+            <td class="headerCovTableEntryMed">79.7 %</td>
+          </tr>
+          <tr><td><img src="glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Directory <span class="tableHeadSort"><img src="glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="adjmat/index.html">adjmat</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=89 height=10 alt="88.6%"><img src="snow.png" width=11 height=10 alt="88.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.6&nbsp;%</td>
+      <td class="coverNumMed">1038 / 1171</td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">183 / 223</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="analysis/index.html">analysis</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="88.5%"><img src="snow.png" width=12 height=10 alt="88.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.5&nbsp;%</td>
+      <td class="coverNumMed">859 / 971</td>
+      <td class="coverPerMed">77.2&nbsp;%</td>
+      <td class="coverNumMed">156 / 202</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="annfunc/index.html">annfunc</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=97 height=10 alt="97.1%"><img src="snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="bias/index.html">bias</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=91 height=10 alt="91.4%"><img src="snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">2393 / 2617</td>
+      <td class="coverPerMed">85.6&nbsp;%</td>
+      <td class="coverNumMed">143 / 167</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="cltools/index.html">cltools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="80.0%"><img src="snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">1359 / 1699</td>
+      <td class="coverPerHi">92.0&nbsp;%</td>
+      <td class="coverNumHi">103 / 112</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="colvar/index.html">colvar</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="94.0%"><img src="snow.png" width=6 height=10 alt="94.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.0&nbsp;%</td>
+      <td class="coverNumHi">2101 / 2235</td>
+      <td class="coverPerMed">82.5&nbsp;%</td>
+      <td class="coverNumMed">184 / 223</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="config/index.html">config</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=46 height=10 alt="46.4%"><img src="snow.png" width=54 height=10 alt="46.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">46.4&nbsp;%</td>
+      <td class="coverNumLo">64 / 138</td>
+      <td class="coverPerLo">46.0&nbsp;%</td>
+      <td class="coverNumLo">23 / 50</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="core/index.html">core</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="85.9%"><img src="snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">3237 / 3767</td>
+      <td class="coverPerMed">80.6&nbsp;%</td>
+      <td class="coverNumMed">431 / 535</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="crystallization/index.html">crystallization</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=84 height=10 alt="83.8%"><img src="snow.png" width=16 height=10 alt="83.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.8&nbsp;%</td>
+      <td class="coverNumMed">1015 / 1211</td>
+      <td class="coverPerMed">77.0&nbsp;%</td>
+      <td class="coverNumMed">144 / 187</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="dimred/index.html">dimred</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=85 height=10 alt="84.8%"><img src="snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">556 / 656</td>
+      <td class="coverPerLo">73.1&nbsp;%</td>
+      <td class="coverNumLo">79 / 108</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="drr/index.html">drr</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="94.3%"><img src="snow.png" width=6 height=10 alt="94.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.3&nbsp;%</td>
+      <td class="coverNumHi">1194 / 1266</td>
+      <td class="coverPerHi">94.8&nbsp;%</td>
+      <td class="coverNumHi">92 / 97</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="eds/index.html">eds</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=93 height=10 alt="92.6%"><img src="snow.png" width=7 height=10 alt="92.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.6&nbsp;%</td>
+      <td class="coverNumHi">452 / 488</td>
+      <td class="coverPerMed">87.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 23</td>
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+    <tr>
+      <td class="coverFile"><a href="fisst/index.html">fisst</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="79.6%"><img src="snow.png" width=20 height=10 alt="79.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.6&nbsp;%</td>
+      <td class="coverNumMed">319 / 401</td>
+      <td class="coverPerMed">82.8&nbsp;%</td>
+      <td class="coverNumMed">24 / 29</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="function/index.html">function</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="85.9%"><img src="snow.png" width=14 height=10 alt="85.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.9&nbsp;%</td>
+      <td class="coverNumMed">909 / 1058</td>
+      <td class="coverPerMed">84.0&nbsp;%</td>
+      <td class="coverNumMed">84 / 100</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="funnel/index.html">funnel</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=98 height=10 alt="98.0%"><img src="snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">248 / 253</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
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+      <td class="coverFile"><a href="generic/index.html">generic</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=95 height=10 alt="94.9%"><img src="snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">1210 / 1275</td>
+      <td class="coverPerMed">79.7&nbsp;%</td>
+      <td class="coverNumMed">177 / 222</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="gridtools/index.html">gridtools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="93.6%"><img src="snow.png" width=6 height=10 alt="93.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.6&nbsp;%</td>
+      <td class="coverNumHi">1183 / 1264</td>
+      <td class="coverPerMed">85.5&nbsp;%</td>
+      <td class="coverNumMed">171 / 200</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="isdb/index.html">isdb</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="81.6%"><img src="snow.png" width=18 height=10 alt="81.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.6&nbsp;%</td>
+      <td class="coverNumMed">8645 / 10595</td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">198 / 243</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="logmfd/index.html">logmfd</a></td>
+      <td class="coverBar" align="center">
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+      </td>
+      <td class="coverPerMed">87.6&nbsp;%</td>
+      <td class="coverNumMed">326 / 372</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="main/index.html">main</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=80 height=10 alt="80.0%"><img src="snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="manyrestraints/index.html">manyrestraints</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="81.5%"><img src="snow.png" width=18 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">75 / 92</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">18 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="mapping/index.html">mapping</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=94 height=10 alt="93.7%"><img src="snow.png" width=6 height=10 alt="93.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.7&nbsp;%</td>
+      <td class="coverNumHi">758 / 809</td>
+      <td class="coverPerMed">89.0&nbsp;%</td>
+      <td class="coverNumMed">89 / 100</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="maze/index.html">maze</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=83 height=10 alt="83.2%"><img src="snow.png" width=17 height=10 alt="83.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.2&nbsp;%</td>
+      <td class="coverNumMed">645 / 775</td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">84 / 102</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="membranefusion/index.html">membranefusion</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=88 height=10 alt="88.2%"><img src="snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">456 / 517</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">18 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="multicolvar/index.html">multicolvar</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=79 height=10 alt="78.6%"><img src="snow.png" width=21 height=10 alt="78.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">2377 / 3025</td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">329 / 422</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="opes/index.html">opes</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=96 height=10 alt="96.1%"><img src="snow.png" width=4 height=10 alt="96.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.1&nbsp;%</td>
+      <td class="coverNumHi">2161 / 2249</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">135 / 144</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pamm/index.html">pamm</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=81 height=10 alt="81.4%"><img src="snow.png" width=19 height=10 alt="81.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.4&nbsp;%</td>
+      <td class="coverNumMed">215 / 264</td>
+      <td class="coverPerMed">79.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="piv/index.html">piv</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=72 height=10 alt="71.8%"><img src="snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">428 / 596</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="pytorch/index.html">pytorch</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=83 height=10 alt="83.1%"><img src="snow.png" width=17 height=10 alt="83.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.1&nbsp;%</td>
+      <td class="coverNumMed">54 / 65</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="reference/index.html">reference</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=86 height=10 alt="86.1%"><img src="snow.png" width=14 height=10 alt="86.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.1&nbsp;%</td>
+      <td class="coverNumMed">668 / 776</td>
+      <td class="coverPerMed">79.3&nbsp;%</td>
+      <td class="coverNumMed">153 / 193</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="s2cm/index.html">s2cm</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=92 height=10 alt="91.6%"><img src="snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
+      <td class="coverNumHi">152 / 166</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa/index.html">sasa</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="82.0%"><img src="snow.png" width=18 height=10 alt="82.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.0&nbsp;%</td>
+      <td class="coverNumMed">998 / 1217</td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="secondarystructure/index.html">secondarystructure</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=97 height=10 alt="96.7%"><img src="snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">376 / 389</td>
+      <td class="coverPerMed">82.9&nbsp;%</td>
+      <td class="coverNumMed">29 / 35</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="setup/index.html">setup</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=98 height=10 alt="97.8%"><img src="snow.png" width=2 height=10 alt="97.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.8&nbsp;%</td>
+      <td class="coverNumHi">87 / 89</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">15 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="tools/index.html">tools</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=84 height=10 alt="83.5%"><img src="snow.png" width=16 height=10 alt="83.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.5&nbsp;%</td>
+      <td class="coverNumMed">5629 / 6739</td>
+      <td class="coverPerMed">81.4&nbsp;%</td>
+      <td class="coverNumMed">1406 / 1728</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vatom/index.html">vatom</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=99 height=10 alt="99.1%"><img src="snow.png" width=1 height=10 alt="99.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.1&nbsp;%</td>
+      <td class="coverNumHi">221 / 223</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">21 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ves/index.html">ves</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="amber.png" width=82 height=10 alt="82.1%"><img src="snow.png" width=18 height=10 alt="82.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">5938 / 7230</td>
+      <td class="coverPerLo">70.4&nbsp;%</td>
+      <td class="coverNumLo">555 / 788</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="vesselbase/index.html">vesselbase</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="emerald.png" width=93 height=10 alt="92.9%"><img src="snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">1141 / 1228</td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">231 / 258</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="wrapper/index.html">wrapper</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="ruby.png" width=53 height=10 alt="52.7%"><img src="snow.png" width=47 height=10 alt="52.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.7&nbsp;%</td>
+      <td class="coverNumLo">247 / 469</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">144 / 252</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/CS2Backbone.cpp.func-sort-c.html b/coverage/isdb/CS2Backbone.cpp.func-sort-c.html
new file mode 100644
index 0000000000..626ff949bd
--- /dev/null
+++ b/coverage/isdb/CS2Backbone.cpp.func-sort-c.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/CS2Backbone.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - CS2Backbone.cpp<span style="font-size: 80%;"> (<a href="CS2Backbone.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">918</td>
+            <td class="headerCovTableEntry">969</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CS2Backbone.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#523">_ZN4PLMD4isdb11CS2BackboneC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#851">_ZN4PLMD4isdb11CS2Backbone10init_ringsERKNS_3PDBE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#823">_ZN4PLMD4isdb11CS2Backbone10init_typesERKNS_3PDBE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1356">_ZN4PLMD4isdb11CS2Backbone13update_neighbEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1380">_ZN4PLMD4isdb11CS2Backbone23compute_ring_parametersEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1835">_ZN4PLMD4isdb11CS2Backbone6updateEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#953">_ZN4PLMD4isdb11CS2Backbone9calculateEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#523">_ZN4PLMD4isdb11CS2BackboneC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#496">_ZN4PLMD4isdb12_GLOBAL__N_124CS2BackboneRegisterMe4986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#205">_ZN4PLMD4isdb13CS2BackboneDB5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#498">_ZN4PLMD4isdb11CS2Backbone16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#641">_ZN4PLMD4isdb11CS2Backbone7init_csERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKNS_3PDBE</a></td>
+              <td class="coverFnHi">108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#451">_ZN4PLMD4isdb11CS2Backbone8RingInfoC2Ev</a></td>
+              <td class="coverFnHi">360</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#496">_ZN4PLMD4isdb12_GLOBAL__N_124CS2BackboneRegisterMe498C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#496">_ZN4PLMD4isdb12_GLOBAL__N_124CS2BackboneRegisterMe498D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#387">_ZN4PLMD4isdb13CS2BackboneDB6assignEPdRKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EEd</a></td>
+              <td class="coverFnHi">10368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#418">_ZN4PLMD4isdb11CS2Backbone13ChemicalShiftC2Ev</a></td>
+              <td class="coverFnHi">10602</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1450">_ZN4PLMD4isdb11CS2Backbone16side_chain_atomsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10602</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#175">_ZN4PLMD4isdb13CS2BackboneDB4kindERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10926</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#181">_ZN4PLMD4isdb13CS2BackboneDB9atom_kindERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10926</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#381">_ZN4PLMD4isdb13CS2BackboneDB5splitERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEc</a></td>
+              <td class="coverFnHi">20430</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#372">_ZN4PLMD4isdb13CS2BackboneDB5splitERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcRSt6vectorIS7_SaIS7_EE</a></td>
+              <td class="coverFnHi">20430</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1414">_ZN4PLMD4isdb11CS2Backbone9frag2enumERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">31806</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1762">_ZN4PLMD4isdb11CS2Backbone5isSP2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">47016</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1817">_ZN4PLMD4isdb11CS2Backbone10is_chi1_cxERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">145728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1827">_ZN4PLMD4isdb11CS2Backbone14xdist_name_mapERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3599784</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/CS2Backbone.cpp.func.html b/coverage/isdb/CS2Backbone.cpp.func.html
new file mode 100644
index 0000000000..491837178a
--- /dev/null
+++ b/coverage/isdb/CS2Backbone.cpp.func.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/CS2Backbone.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - CS2Backbone.cpp<span style="font-size: 80%;"> (<a href="CS2Backbone.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">918</td>
+            <td class="headerCovTableEntry">969</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CS2Backbone.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#851">_ZN4PLMD4isdb11CS2Backbone10init_ringsERKNS_3PDBE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#823">_ZN4PLMD4isdb11CS2Backbone10init_typesERKNS_3PDBE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1817">_ZN4PLMD4isdb11CS2Backbone10is_chi1_cxERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">145728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#418">_ZN4PLMD4isdb11CS2Backbone13ChemicalShiftC2Ev</a></td>
+              <td class="coverFnHi">10602</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1356">_ZN4PLMD4isdb11CS2Backbone13update_neighbEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1827">_ZN4PLMD4isdb11CS2Backbone14xdist_name_mapERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3599784</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#498">_ZN4PLMD4isdb11CS2Backbone16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1450">_ZN4PLMD4isdb11CS2Backbone16side_chain_atomsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10602</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1380">_ZN4PLMD4isdb11CS2Backbone23compute_ring_parametersEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1762">_ZN4PLMD4isdb11CS2Backbone5isSP2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">47016</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1835">_ZN4PLMD4isdb11CS2Backbone6updateEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#641">_ZN4PLMD4isdb11CS2Backbone7init_csERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKNS_3PDBE</a></td>
+              <td class="coverFnHi">108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#451">_ZN4PLMD4isdb11CS2Backbone8RingInfoC2Ev</a></td>
+              <td class="coverFnHi">360</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#953">_ZN4PLMD4isdb11CS2Backbone9calculateEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#1414">_ZN4PLMD4isdb11CS2Backbone9frag2enumERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">31806</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#523">_ZN4PLMD4isdb11CS2BackboneC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#523">_ZN4PLMD4isdb11CS2BackboneC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#496">_ZN4PLMD4isdb12_GLOBAL__N_124CS2BackboneRegisterMe4986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#496">_ZN4PLMD4isdb12_GLOBAL__N_124CS2BackboneRegisterMe498C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#496">_ZN4PLMD4isdb12_GLOBAL__N_124CS2BackboneRegisterMe498D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#175">_ZN4PLMD4isdb13CS2BackboneDB4kindERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10926</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#205">_ZN4PLMD4isdb13CS2BackboneDB5parseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#381">_ZN4PLMD4isdb13CS2BackboneDB5splitERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEc</a></td>
+              <td class="coverFnHi">20430</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#372">_ZN4PLMD4isdb13CS2BackboneDB5splitERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEcRSt6vectorIS7_SaIS7_EE</a></td>
+              <td class="coverFnHi">20430</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#387">_ZN4PLMD4isdb13CS2BackboneDB6assignEPdRKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS9_EEd</a></td>
+              <td class="coverFnHi">10368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CS2Backbone.cpp.gcov.html#181">_ZN4PLMD4isdb13CS2BackboneDB9atom_kindERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10926</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/CS2Backbone.cpp.gcov.html b/coverage/isdb/CS2Backbone.cpp.gcov.html
new file mode 100644
index 0000000000..94096ecf50
--- /dev/null
+++ b/coverage/isdb/CS2Backbone.cpp.gcov.html
@@ -0,0 +1,1919 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/CS2Backbone.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - CS2Backbone.cpp<span style="font-size: 80%;"> (source / <a href="CS2Backbone.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">918</td>
+            <td class="headerCovTableEntry">969</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #define cutOffNB      0.60      // buffer distance for neighbour-lists </a>
+<a name="24"><span class="lineNum">      24 </span>            : #define cutOffDist    0.50      // cut off distance for non-bonded pairwise forces</a>
+<a name="25"><span class="lineNum">      25 </span>            : #define cutOnDist     0.32      // cut off distance for non-bonded pairwise forces</a>
+<a name="26"><span class="lineNum">      26 </span>            : #define cutOffNB2     cutOffNB*cutOffNB // squared buffer distance for neighbour-lists </a>
+<a name="27"><span class="lineNum">      27 </span>            : #define cutOffDist2   cutOffDist*cutOffDist</a>
+<a name="28"><span class="lineNum">      28 </span>            : #define cutOnDist2    cutOnDist*cutOnDist</a>
+<a name="29"><span class="lineNum">      29 </span>            : #define invswitch     1.0/((cutOffDist2-cutOnDist2)*(cutOffDist2-cutOnDist2)*(cutOffDist2-cutOnDist2))</a>
+<a name="30"><span class="lineNum">      30 </span>            : #define cutOffDist4   cutOffDist2*cutOffDist2</a>
+<a name="31"><span class="lineNum">      31 </span>            : #define cutMixed      cutOffDist2*cutOffDist2*cutOffDist2 -3.*cutOffDist2*cutOffDist2*cutOnDist2</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;string&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;fstream&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;iterator&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;sstream&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace isdb {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : //+PLUMEDOC ISDB_COLVAR CS2BACKBONE</a>
+<a name="48"><span class="lineNum">      48 </span>            : /*</a>
+<a name="49"><span class="lineNum">      49 </span>            : Calculates the backbone chemical shifts for a protein.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The functional form is that of CamShift \cite Kohlhoff:2009us. The chemical shift</a>
+<a name="52"><span class="lineNum">      52 </span>            : of the selected nuclei can be saved as components. Alternatively one can calculate either</a>
+<a name="53"><span class="lineNum">      53 </span>            : the CAMSHIFT score (useful as a collective variable \cite Granata:2013dk or as a scoring</a>
+<a name="54"><span class="lineNum">      54 </span>            : function \cite Robustelli:2010dn) or a \ref METAINFERENCE score (using DOSCORE).</a>
+<a name="55"><span class="lineNum">      55 </span>            : For these two latter cases experimental chemical shifts must be provided.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : CS2BACKBONE calculation can be relatively heavy because it often uses a large number of atoms, it can</a>
+<a name="58"><span class="lineNum">      58 </span>            : be run in parallel using MPI and \ref Openmp.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : As a general rule, when using \ref CS2BACKBONE or other experimental restraints it may be better to</a>
+<a name="61"><span class="lineNum">      61 </span>            : increase the accuracy of the constraint algorithm due to the increased strain on the bonded structure.</a>
+<a name="62"><span class="lineNum">      62 </span>            : In the case of GROMACS it is safer to use lincs-iter=2 and lincs-order=6.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : In general the system for which chemical shifts are calculated must be completely included in</a>
+<a name="65"><span class="lineNum">      65 </span>            : ATOMS and a TEMPLATE pdb file for the same atoms should be provided as well in the folder DATADIR.</a>
+<a name="66"><span class="lineNum">      66 </span>            : The system is made automatically whole unless NOPBC is used, in particular if the system is made</a>
+<a name="67"><span class="lineNum">      67 </span>            : by multiple chains it is usually better to use NOPBC and make the molecule whole \ref WHOLEMOLECULES</a>
+<a name="68"><span class="lineNum">      68 </span>            : selecting an appropriate order of the atoms. The pdb file is needed to the generate a simple topology of the protein.</a>
+<a name="69"><span class="lineNum">      69 </span>            : For histidine residues in protonation states different from D the HIE/HSE HIP/HSP name should be used.</a>
+<a name="70"><span class="lineNum">      70 </span>            : GLH and ASH can be used for the alternative protonation of GLU and ASP. Non-standard amino acids and other</a>
+<a name="71"><span class="lineNum">      71 </span>            : molecules are not yet supported, but in principle they can be named UNK. If multiple chains are present</a>
+<a name="72"><span class="lineNum">      72 </span>            : the chain identifier must be in the standard PDB format, together with the TER keyword at the end of each chain.</a>
+<a name="73"><span class="lineNum">      73 </span>            : Termini groups like ACE or NME should be removed from the TEMPLATE pdb because they are not recognized by</a>
+<a name="74"><span class="lineNum">      74 </span>            : CS2BACKBONE.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : Atoms indices in the TEMPLATE file should be numbered from 1 to N where N is the number of atoms used in ATOMS.</a>
+<a name="77"><span class="lineNum">      77 </span>            : This is not a problem for simple cases where atoms goes from 1 to N but is instead something to be carefull in case</a>
+<a name="78"><span class="lineNum">      78 </span>            : that a terminal group is removed from the PDB file.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : In addition to a pdb file one needs to provide a list of chemical shifts to be calculated using one</a>
+<a name="81"><span class="lineNum">      81 </span>            : file per nucleus type (CAshifts.dat, CBshifts.dat, Cshifts.dat, Hshifts.dat, HAshifts.dat, Nshifts.dat),</a>
+<a name="82"><span class="lineNum">      82 </span>            : add only the files for the nuclei you need, but each file should include all protein residues.</a>
+<a name="83"><span class="lineNum">      83 </span>            : A chemical shift for a nucleus is calculated if a value greater than 0 is provided.</a>
+<a name="84"><span class="lineNum">      84 </span>            : For practical purposes the value can correspond to the experimental value.</a>
+<a name="85"><span class="lineNum">      85 </span>            : Residues numbers should match that used in the pdb file, but must be positive, so double check the pdb.</a>
+<a name="86"><span class="lineNum">      86 </span>            : The first and last residue of each chain should be preceded by a # character.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \verbatim</a>
+<a name="89"><span class="lineNum">      89 </span>            : CAshifts.dat:</a>
+<a name="90"><span class="lineNum">      90 </span>            : #1 0.0</a>
+<a name="91"><span class="lineNum">      91 </span>            : 2 55.5</a>
+<a name="92"><span class="lineNum">      92 </span>            : 3 58.4</a>
+<a name="93"><span class="lineNum">      93 </span>            : .</a>
+<a name="94"><span class="lineNum">      94 </span>            : .</a>
+<a name="95"><span class="lineNum">      95 </span>            : #last 0.0</a>
+<a name="96"><span class="lineNum">      96 </span>            : #first of second chain</a>
+<a name="97"><span class="lineNum">      97 </span>            : .</a>
+<a name="98"><span class="lineNum">      98 </span>            : #last of second chain</a>
+<a name="99"><span class="lineNum">      99 </span>            : \endverbatim</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : The default behavior is to store the values for the active nuclei in components (ca-#, cb-#,</a>
+<a name="102"><span class="lineNum">     102 </span>            : co-#, ha-#, hn-#, nh-# and expca-#, expcb-#, expco-#, expha-#, exphn-#, exp-nh#) with NOEXP it is possible</a>
+<a name="103"><span class="lineNum">     103 </span>            : to only store the back-calculated values, where # includes a chain and residue number.</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : One additional file is always needed in the folder DATADIR: camshift.db. This file includes all the parameters needed to</a>
+<a name="106"><span class="lineNum">     106 </span>            : calculate the chemical shifts and can be found in regtest/isdb/rt-cs2backbone/data/ .</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : Additional material and examples can be also found in the tutorial \ref isdb-1 as well as in the cs2backbone regtests</a>
+<a name="109"><span class="lineNum">     109 </span>            : in the isdb folder.</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : \par Examples</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : In this first example the chemical shifts are used to calculate a collective variable to be used</a>
+<a name="114"><span class="lineNum">     114 </span>            : in NMR driven Metadynamics \cite Granata:2013dk :</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : \plumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : #SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data</a>
+<a name="118"><span class="lineNum">     118 </span>            : whole: GROUP ATOMS=2612-2514:-1,961-1:-1,2466-962:-1,2513-2467:-1</a>
+<a name="119"><span class="lineNum">     119 </span>            : WHOLEMOLECULES ENTITY0=whole</a>
+<a name="120"><span class="lineNum">     120 </span>            : cs: CS2BACKBONE ATOMS=1-2612 DATADIR=data/ TEMPLATE=template.pdb CAMSHIFT NOPBC</a>
+<a name="121"><span class="lineNum">     121 </span>            : metad: METAD ARG=cs HEIGHT=0.5 SIGMA=0.1 PACE=200 BIASFACTOR=10</a>
+<a name="122"><span class="lineNum">     122 </span>            : PRINT ARG=cs,metad.bias FILE=COLVAR STRIDE=100</a>
+<a name="123"><span class="lineNum">     123 </span>            : \endplumedfile</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : In this second example the chemical shifts are used as replica-averaged restrained as in \cite Camilloni:2012je \cite Camilloni:2013hs .</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : \plumedfile</a>
+<a name="128"><span class="lineNum">     128 </span>            : #SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data NREPLICAS=2</a>
+<a name="129"><span class="lineNum">     129 </span>            : cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/</a>
+<a name="130"><span class="lineNum">     130 </span>            : encs: ENSEMBLE ARG=(cs\.hn-.*),(cs\.nh-.*)</a>
+<a name="131"><span class="lineNum">     131 </span>            : stcs: STATS ARG=encs.* SQDEVSUM PARARG=(cs\.exphn-.*),(cs\.expnh-.*)</a>
+<a name="132"><span class="lineNum">     132 </span>            : RESTRAINT ARG=stcs.sqdevsum AT=0 KAPPA=0 SLOPE=24</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : PRINT ARG=(cs\.hn-.*),(cs\.nh-.*) FILE=RESTRAINT STRIDE=100</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \endplumedfile</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : This third example show how to use chemical shifts to calculate a \ref METAINFERENCE score .</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : \plumedfile</a>
+<a name="141"><span class="lineNum">     141 </span>            : #SETTINGS AUXFOLDER=regtest/isdb/rt-cs2backbone/data</a>
+<a name="142"><span class="lineNum">     142 </span>            : cs: CS2BACKBONE ATOMS=1-174 DATADIR=data/ SIGMA_MEAN0=1.0 DOSCORE</a>
+<a name="143"><span class="lineNum">     143 </span>            : csbias: BIASVALUE ARG=cs.score</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : PRINT ARG=(cs\.hn-.*),(cs\.nh-.*) FILE=CS.dat STRIDE=1000</a>
+<a name="146"><span class="lineNum">     146 </span>            : PRINT ARG=cs.score FILE=BIAS STRIDE=100</a>
+<a name="147"><span class="lineNum">     147 </span>            : \endplumedfile</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : */</a>
+<a name="150"><span class="lineNum">     150 </span>            : //+ENDPLUMEDOC</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : class CS2BackboneDB {</a>
+<a name="153"><span class="lineNum">     153 </span>            :   enum { STD, GLY, PRO};</a>
+<a name="154"><span class="lineNum">     154 </span>            :   enum { HA_ATOM, H_ATOM, N_ATOM, CA_ATOM, CB_ATOM, C_ATOM };</a>
+<a name="155"><span class="lineNum">     155 </span>            :   static const unsigned aa_kind = 3;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   static const unsigned atm_kind = 6;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   static const unsigned numXtraDists = 27;</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   // ALA, ARG, ASN, ASP, CYS, GLU, GLN, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL</a>
+<a name="160"><span class="lineNum">     160 </span>            :   double c_aa[aa_kind][atm_kind][20];</a>
+<a name="161"><span class="lineNum">     161 </span>            :   double c_aa_prev[aa_kind][atm_kind][20];</a>
+<a name="162"><span class="lineNum">     162 </span>            :   double c_aa_succ[aa_kind][atm_kind][20];</a>
+<a name="163"><span class="lineNum">     163 </span>            :   double co_bb[aa_kind][atm_kind][16];</a>
+<a name="164"><span class="lineNum">     164 </span>            :   double co_sc_[aa_kind][atm_kind][20][20];</a>
+<a name="165"><span class="lineNum">     165 </span>            :   double co_xd[aa_kind][atm_kind][numXtraDists];</a>
+<a name="166"><span class="lineNum">     166 </span>            :   double co_sphere[aa_kind][atm_kind][2][8];</a>
+<a name="167"><span class="lineNum">     167 </span>            :   // for ring current effects</a>
+<a name="168"><span class="lineNum">     168 </span>            :   // Phe, Tyr, Trp_1, Trp_2, His</a>
+<a name="169"><span class="lineNum">     169 </span>            :   double co_ring[aa_kind][atm_kind][5];</a>
+<a name="170"><span class="lineNum">     170 </span>            :   // for dihedral angles</a>
+<a name="171"><span class="lineNum">     171 </span>            :   // co * (a * cos(3 * omega + c) + b * cos(omega + d))</a>
+<a name="172"><span class="lineNum">     172 </span>            :   double co_da[aa_kind][atm_kind][3];</a>
+<a name="173"><span class="lineNum">     173 </span>            :   double pars_da[aa_kind][atm_kind][3][5];</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : public:</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      10926 :   inline unsigned kind(const std::string &amp;s) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">      10926 :     if(s==&quot;GLY&quot;) return GLY;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       9324 :     else if(s==&quot;PRO&quot;) return PRO;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     return STD;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      10926 :   inline unsigned atom_kind(const std::string &amp;s) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      10926 :     if(s==&quot;HA&quot;)return HA_ATOM;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">      10872 :     else if(s==&quot;H&quot;) return H_ATOM;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       8010 :     else if(s==&quot;N&quot;) return N_ATOM;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       5148 :     else if(s==&quot;CA&quot;)return CA_ATOM;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       2160 :     else if(s==&quot;CB&quot;)return CB_ATOM;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         54 :     else if(s==&quot;C&quot;) return C_ATOM;</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :     return -1;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   unsigned get_numXtraDists() {return numXtraDists;}</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            :   //PARAMETERS</a>
+<a name="196"><span class="lineNum">     196 </span>            :   inline double * CONSTAACURR(const unsigned a_kind, const unsigned at_kind) {return c_aa[a_kind][at_kind];}</a>
+<a name="197"><span class="lineNum">     197 </span>            :   inline double * CONSTAANEXT(const unsigned a_kind, const unsigned at_kind) {return c_aa_succ[a_kind][at_kind];}</a>
+<a name="198"><span class="lineNum">     198 </span>            :   inline double * CONSTAAPREV(const unsigned a_kind, const unsigned at_kind) {return c_aa_prev[a_kind][at_kind];}</a>
+<a name="199"><span class="lineNum">     199 </span>            :   inline double * CONST_BB2(const unsigned a_kind, const unsigned at_kind) {return co_bb[a_kind][at_kind];}</a>
+<a name="200"><span class="lineNum">     200 </span>            :   inline double * CONST_SC2(const unsigned a_kind, const unsigned at_kind, unsigned res_type) { return co_sc_[a_kind][at_kind][res_type];}</a>
+<a name="201"><span class="lineNum">     201 </span>            :   inline double * CONST_XD(const unsigned a_kind, const unsigned at_kind) { return co_xd[a_kind][at_kind];}</a>
+<a name="202"><span class="lineNum">     202 </span>            :   inline double * CO_SPHERE(const unsigned a_kind, const unsigned at_kind, unsigned exp_type) { return co_sphere[a_kind][at_kind][exp_type];}</a>
+<a name="203"><span class="lineNum">     203 </span>            :   inline double * CO_RING(const unsigned a_kind, const unsigned at_kind) { return co_ring[a_kind][at_kind];}</a>
+<a name="204"><span class="lineNum">     204 </span>            :   inline double * CO_DA(const unsigned a_kind, const unsigned at_kind) { return co_da[a_kind][at_kind];}</a>
+<a name="205"><span class="lineNum">     205 </span>            :   inline double * PARS_DA(const unsigned a_kind, const unsigned at_kind, const unsigned ang_kind) { return pars_da[a_kind][at_kind][ang_kind];}</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         18 :   void parse(const std::string &amp;file, const double dscale) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         18 :     std::ifstream in;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         18 :     in.open(file.c_str());</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         18 :     if(!in) plumed_merror(&quot;Unable to open DB file: &quot; + file);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :     unsigned c_kind = 0;</a>
+<a name="213"><span class="lineNum">     213 </span>            :     unsigned c_atom = 0;</a>
+<a name="214"><span class="lineNum">     214 </span>            :     unsigned nline = 0;</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        396 :     for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;6; j++) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       6804 :         for(unsigned k=0; k&lt;20; k++) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       6480 :           c_aa[i][j][k]=0.;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       6480 :           c_aa_prev[i][j][k]=0.;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       6480 :           c_aa_succ[i][j][k]=0.;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">     136080 :           for(unsigned m=0; m&lt;20; m++) co_sc_[i][j][k][m]=0.;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :         }</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       5508 :         for(unsigned k=0; k&lt;16; k++) {co_bb[i][j][k]=0.; }</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       2916 :         for(unsigned k=0; k&lt;8; k++) { co_sphere[i][j][0][k]=0.; co_sphere[i][j][1][k]=0.; }</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       1296 :         for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        972 :           co_da[i][j][k]=0.;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       5832 :           for(unsigned l=0; l&lt;5; l++) pars_da[i][j][k][l]=0.;</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :         }</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       1944 :         for(unsigned k=0; k&lt;5; k++) co_ring[i][j][k]=0.;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       9072 :         for(unsigned k=0; k&lt;numXtraDists; k++) co_xd[i][j][k]=0.;</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :       }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      37710 :     while(!in.eof()) {</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :       std::string line;</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      37692 :       getline(in,line);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :       ++nline;</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      37692 :       if(line.compare(0,1,&quot;#&quot;)==0) continue;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :       std::vector&lt;std::string&gt; tok;</a>
+<a name="239"><span class="lineNum">     239 </span>            :       std::vector&lt;std::string&gt; tmp;</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      40860 :       tok = split(line,' ');</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">     261828 :       for(unsigned q=0; q&lt;tok.size(); q++)</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">     241398 :         if(tok[q].size()) tmp.push_back(tok[q]);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      20430 :       tok = tmp;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">      20430 :       if(tok.size()==0) continue;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      20412 :       if(tok[0]==&quot;PAR&quot;) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        324 :         c_kind = kind(tok[2]);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        324 :         c_atom = atom_kind(tok[1]);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :       }</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      20088 :       else if(tok[0]==&quot;WEIGHT&quot;) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :       }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      19764 :       else if(tok[0]==&quot;FLATBTM&quot;) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :       }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">      19440 :       else if (tok[0] == &quot;SCALEHARM&quot;) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :       }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">      19116 :       else if (tok[0] == &quot;TANHAMPLI&quot;) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :       }</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      18792 :       else if (tok[0] == &quot;ENDHARMON&quot;) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :       }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      18468 :       else if (tok[0] == &quot;MAXRCDEVI&quot;) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :       }</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      18144 :       else if (tok[0] == &quot;RANDCOIL&quot;) {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :       }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      17820 :       else if (tok[0] == &quot;CONST&quot;) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :       }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      17496 :       else if (tok[0] == &quot;CONSTAA&quot;) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        324 :         assign(c_aa[c_kind][c_atom],tok,1);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :       }</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      17172 :       else if (tok[0] == &quot;CONSTAA-1&quot;) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        324 :         assign(c_aa_prev[c_kind][c_atom],tok,1);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :       }</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">      16848 :       else if (tok[0] == &quot;CONSTAA+1&quot;) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        324 :         assign(c_aa_succ[c_kind][c_atom],tok,1);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :       }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">      16524 :       else if (tok[0] == &quot;COBB1&quot;) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :       }</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">      16200 :       else if (tok[0] == &quot;COBB2&quot;) {</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :         //angstrom to nm</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        324 :         assign(co_bb[c_kind][c_atom],tok,dscale);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :       }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      15876 :       else if (tok[0] == &quot;SPHERE1&quot;) {</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :         // angstrom^-3 to nm^-3</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        324 :         assign(co_sphere[c_kind][c_atom][0],tok,1./(dscale*dscale*dscale));</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :       }</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      15552 :       else if (tok[0] == &quot;SPHERE2&quot;) {</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :         //angstrom to nm</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        324 :         assign(co_sphere[c_kind][c_atom][1],tok,dscale);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :       }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">      15228 :       else if (tok[0] == &quot;DIHEDRALS&quot;) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        324 :         assign(co_da[c_kind][c_atom],tok,1);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :       }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">      14904 :       else if (tok[0] == &quot;RINGS&quot;) {</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :         // angstrom^-3 to nm^-3</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        324 :         assign(co_ring[c_kind][c_atom],tok,1./(dscale*dscale*dscale));</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       1944 :         for(unsigned i=1; i&lt;tok.size(); i++)</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       1620 :           co_ring[c_kind][c_atom][i-1] *= 1000;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">        324 :       }</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      14580 :       else if (tok[0] == &quot;HBONDS&quot;) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :       }</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">      14256 :       else if (tok[0] == &quot;XTRADISTS&quot;) {</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :         //angstrom to nm</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        324 :         assign(co_xd[c_kind][c_atom],tok,dscale);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :       }</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">      13932 :       else if(tok[0]==&quot;DIHEDPHI&quot;) {</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        324 :         assign(pars_da[c_kind][c_atom][0],tok,1);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :       }</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      13608 :       else if(tok[0]==&quot;DIHEDPSI&quot;) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        324 :         assign(pars_da[c_kind][c_atom][1],tok,1);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :       }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">      13284 :       else if(tok[0]==&quot;DIHEDCHI1&quot;) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        324 :         assign(pars_da[c_kind][c_atom][2],tok,1);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        324 :         continue;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :       }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :       bool ok = false;</a>
+<a name="337"><span class="lineNum">     337 </span>            :       const std::string scIdent1 [] = {&quot;COSCALA1&quot;, &quot;COSCARG1&quot;, &quot;COSCASN1&quot;, &quot;COSCASP1&quot;, &quot;COSCCYS1&quot;, &quot;COSCGLN1&quot;, &quot;COSCGLU1&quot;,</a>
+<a name="338"><span class="lineNum">     338 </span>            :                                        &quot;COSCGLY1&quot;, &quot;COSCHIS1&quot;, &quot;COSCILE1&quot;, &quot;COSCLEU1&quot;, &quot;COSCLYS1&quot;, &quot;COSCMET1&quot;, &quot;COSCPHE1&quot;,</a>
+<a name="339"><span class="lineNum">     339 </span>            :                                        &quot;COSCPRO1&quot;, &quot;COSCSER1&quot;, &quot;COSCTHR1&quot;, &quot;COSCTRP1&quot;, &quot;COSCTYR1&quot;, &quot;COSCVAL1&quot;</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">     272160 :                                       };</span></a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">     204120 :       for(unsigned scC = 0; scC &lt; 20; scC++) {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">     197640 :         if(tok[0]==scIdent1[scC]) {</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :           ok = true;</a>
+<a name="345"><span class="lineNum">     345 </span>            :           break;</a>
+<a name="346"><span class="lineNum">     346 </span>            :         }</a>
+<a name="347"><span class="lineNum">     347 </span>            :       }</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">     285120 :       if(ok) continue;</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            :       const std::string scIdent2 [] = {&quot;COSCALA2&quot;, &quot;COSCARG2&quot;, &quot;COSCASN2&quot;, &quot;COSCASP2&quot;, &quot;COSCCYS2&quot;, &quot;COSCGLN2&quot;, &quot;COSCGLU2&quot;,</a>
+<a name="351"><span class="lineNum">     351 </span>            :                                        &quot;COSCGLY2&quot;, &quot;COSCHIS2&quot;, &quot;COSCILE2&quot;, &quot;COSCLEU2&quot;, &quot;COSCLYS2&quot;, &quot;COSCMET2&quot;, &quot;COSCPHE2&quot;,</a>
+<a name="352"><span class="lineNum">     352 </span>            :                                        &quot;COSCPRO2&quot;, &quot;COSCSER2&quot;, &quot;COSCTHR2&quot;, &quot;COSCTRP2&quot;, &quot;COSCTYR2&quot;, &quot;COSCVAL2&quot;</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">     136080 :                                       };</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      68040 :       for(unsigned scC = 0; scC &lt; 20; scC++) {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">      68040 :         if(tok[0]==scIdent2[scC]) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :           //angstrom to nm</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">       6480 :           assign(co_sc_[c_kind][c_atom][scC],tok,dscale);</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :           ok = true; break;</a>
+<a name="360"><span class="lineNum">     360 </span>            :         }</a>
+<a name="361"><span class="lineNum">     361 </span>            :       }</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">     142560 :       if(ok) continue;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :       if(tok.size()) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :         std::string str_err = &quot;DB WARNING: unrecognized token: &quot; + tok[0];</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :         plumed_merror(str_err);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :       }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">     428670 :     }</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         18 :     in.close();</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         18 :   }</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : private:</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      20430 :   std::vector&lt;std::string&gt; &amp;split(const std::string &amp;s, char delim, std::vector&lt;std::string&gt; &amp;elems) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      20430 :     std::stringstream ss(s);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     std::string item;</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">     261828 :     while (getline(ss, item, delim)) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">     241398 :       elems.push_back(item);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :     }</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">      20430 :     return elems;</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">      20430 :   }</span></a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">      20430 :   std::vector&lt;std::string&gt; split(const std::string &amp;s, char delim) {</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :     std::vector&lt;std::string&gt; elems;</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      20430 :     split(s, delim, elems);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">      20430 :     return elems;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      10368 :   void assign(double * f, const std::vector&lt;std::string&gt; &amp; v, const double scale) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">     122796 :     for(unsigned i=1; i&lt;v.size(); i++) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">     112428 :       f[i-1] = scale*(atof(v[i].c_str()));</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">     112428 :       if(std::abs(f[i-1])&lt;0.000001) f[i-1]=0.;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :     }</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">      10368 :   }</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : };</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            : class CS2Backbone : public MetainferenceBase {</a>
+<a name="398"><span class="lineNum">     398 </span>            :   struct ChemicalShift {</a>
+<a name="399"><span class="lineNum">     399 </span>            :     double exp_cs;              // a reference chemical shifts</a>
+<a name="400"><span class="lineNum">     400 </span>            :     Value *comp;                // a pointer to the component</a>
+<a name="401"><span class="lineNum">     401 </span>            :     unsigned res_kind;          // residue type (STD/GLY/PRO)</a>
+<a name="402"><span class="lineNum">     402 </span>            :     unsigned atm_kind;          // nuclues (HA/CA/CB/CO/NH/HN)</a>
+<a name="403"><span class="lineNum">     403 </span>            :     unsigned res_type_prev;     // previous residue (ALA/VAL/..)</a>
+<a name="404"><span class="lineNum">     404 </span>            :     unsigned res_type_curr;     // current residue (ALA/VAL/..)</a>
+<a name="405"><span class="lineNum">     405 </span>            :     unsigned res_type_next;     // next residue (ALA/VAL/..)</a>
+<a name="406"><span class="lineNum">     406 </span>            :     std::string res_name;       // residue name</a>
+<a name="407"><span class="lineNum">     407 </span>            :     std::string nucleus;        // chemical shift</a>
+<a name="408"><span class="lineNum">     408 </span>            :     bool has_chi1;              // does we have a chi1</a>
+<a name="409"><span class="lineNum">     409 </span>            :     unsigned csatoms;           // fixed number of atoms used</a>
+<a name="410"><span class="lineNum">     410 </span>            :     unsigned totcsatoms;        // number of atoms used</a>
+<a name="411"><span class="lineNum">     411 </span>            :     unsigned res_num;           // residue number</a>
+<a name="412"><span class="lineNum">     412 </span>            :     unsigned chain;             // chain number</a>
+<a name="413"><span class="lineNum">     413 </span>            :     unsigned ipos;              // index of the atom for which we are calculating the chemical shifts</a>
+<a name="414"><span class="lineNum">     414 </span>            :     std::vector&lt;unsigned&gt; bb;        // atoms for the previous, current and next backbone</a>
+<a name="415"><span class="lineNum">     415 </span>            :     std::vector&lt;unsigned&gt; side_chain;// atoms for the current sidechain</a>
+<a name="416"><span class="lineNum">     416 </span>            :     std::vector&lt;int&gt; xd1;            // additional couple of atoms</a>
+<a name="417"><span class="lineNum">     417 </span>            :     std::vector&lt;int&gt; xd2;            // additional couple of atoms</a>
+<a name="418"><span class="lineNum">     418 </span>            :     std::vector&lt;unsigned&gt; box_nb;    // non-bonded atoms</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      10602 :     ChemicalShift():</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">      10602 :       exp_cs(0.),</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">      10602 :       comp(NULL),</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">      10602 :       res_kind(0),</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">      10602 :       atm_kind(0),</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">      10602 :       res_type_prev(0),</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">      10602 :       res_type_curr(0),</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">      10602 :       res_type_next(0),</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">      10602 :       res_name(&quot;&quot;),</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">      10602 :       nucleus(&quot;&quot;),</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">      10602 :       has_chi1(true),</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">      10602 :       csatoms(0),</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">      10602 :       totcsatoms(0),</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">      10602 :       res_num(0),</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">      10602 :       chain(0),</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">      10602 :       ipos(0)</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :     {</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">      10602 :       xd1.reserve(26);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">      10602 :       xd2.reserve(26);</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">      10602 :       box_nb.reserve(150);</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">      10602 :     }</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   };</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            :   struct RingInfo {</a>
+<a name="444"><span class="lineNum">     444 </span>            :     enum {R_PHE, R_TYR, R_TRP1, R_TRP2, R_HIS};</a>
+<a name="445"><span class="lineNum">     445 </span>            :     unsigned rtype;    // one out of five different types</a>
+<a name="446"><span class="lineNum">     446 </span>            :     unsigned atom[6];  // up to six member per ring</a>
+<a name="447"><span class="lineNum">     447 </span>            :     unsigned numAtoms; // number of ring members (5 or 6)</a>
+<a name="448"><span class="lineNum">     448 </span>            :     Vector position;   // center of ring coordinates</a>
+<a name="449"><span class="lineNum">     449 </span>            :     Vector normVect;   // ring plane normal std::vector</a>
+<a name="450"><span class="lineNum">     450 </span>            :     Vector g[6];       // std::vector of the std::vectors used for normVect</a>
+<a name="451"><span class="lineNum">     451 </span>            :     double lengthN2;   // square of length of normVect</a>
+<a name="452"><span class="lineNum">     452 </span>            :     double lengthNV;   // length of normVect</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">        360 :     RingInfo():</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">        360 :       rtype(0),</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">        360 :       numAtoms(0),</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        360 :       lengthN2(NAN),</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">       2520 :       lengthNV(NAN)</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :     {</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">       2520 :       for(unsigned i=0; i&lt;6; i++) atom[i]=0;</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">        360 :     }</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :   };</a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            :   enum aa_t {ALA, ARG, ASN, ASP, CYS, GLN, GLU, GLY, HIS, ILE, LEU, LYS, MET, PHE, PRO, SER, THR, TRP, TYR, VAL, UNK};</a>
+<a name="464"><span class="lineNum">     464 </span>            :   enum sequence_t {Np, CAp, HAp, Cp, Op, Nc, Hc, CAc, HAc, Cc, Oc, Nn, Hn, CAn, HAn, Cn, CBc, CGc};</a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span>            :   CS2BackboneDB    db;</a>
+<a name="467"><span class="lineNum">     467 </span>            :   std::vector&lt;ChemicalShift&gt; chemicalshifts;</a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span>            :   std::vector&lt;RingInfo&gt; ringInfo;</a>
+<a name="470"><span class="lineNum">     470 </span>            :   std::vector&lt;unsigned&gt; type;</a>
+<a name="471"><span class="lineNum">     471 </span>            :   std::vector&lt;unsigned&gt; res_num;</a>
+<a name="472"><span class="lineNum">     472 </span>            :   unsigned         max_cs_atoms;</a>
+<a name="473"><span class="lineNum">     473 </span>            :   unsigned         box_nupdate;</a>
+<a name="474"><span class="lineNum">     474 </span>            :   unsigned         box_count;</a>
+<a name="475"><span class="lineNum">     475 </span>            :   bool             camshift;</a>
+<a name="476"><span class="lineNum">     476 </span>            :   bool             pbc;</a>
+<a name="477"><span class="lineNum">     477 </span>            :   bool             serial;</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            :   void init_cs(const std::string &amp;file, const std::string &amp;k, const PDB &amp;pdb);</a>
+<a name="480"><span class="lineNum">     480 </span>            :   void update_neighb();</a>
+<a name="481"><span class="lineNum">     481 </span>            :   void compute_ring_parameters();</a>
+<a name="482"><span class="lineNum">     482 </span>            :   void init_types(const PDB &amp;pdb);</a>
+<a name="483"><span class="lineNum">     483 </span>            :   void init_rings(const PDB &amp;pdb);</a>
+<a name="484"><span class="lineNum">     484 </span>            :   aa_t frag2enum(const std::string &amp;aa);</a>
+<a name="485"><span class="lineNum">     485 </span>            :   std::vector&lt;std::string&gt; side_chain_atoms(const std::string &amp;s);</a>
+<a name="486"><span class="lineNum">     486 </span>            :   bool isSP2(const std::string &amp; resType, const std::string &amp; atomName);</a>
+<a name="487"><span class="lineNum">     487 </span>            :   bool is_chi1_cx(const std::string &amp; frg, const std::string &amp; atm);</a>
+<a name="488"><span class="lineNum">     488 </span>            :   void xdist_name_map(std::string &amp; name);</a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span>            : public:</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            :   explicit CS2Backbone(const ActionOptions&amp;);</a>
+<a name="493"><span class="lineNum">     493 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="494"><span class="lineNum">     494 </span>            :   void calculate() override;</a>
+<a name="495"><span class="lineNum">     495 </span>            :   void update() override;</a>
+<a name="496"><span class="lineNum">     496 </span>            : };</a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">      12540 : PLUMED_REGISTER_ACTION(CS2Backbone,&quot;CS2BACKBONE&quot;)</span></a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         20 : void CS2Backbone::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         20 :   componentsAreNotOptional(keys);</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         20 :   MetainferenceBase::registerKeywords( keys );</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         40 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         40 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         40 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;The atoms to be included in the calculation, e.g. the whole protein.&quot;);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         40 :   keys.add(&quot;compulsory&quot;,&quot;DATADIR&quot;,&quot;data/&quot;,&quot;The folder with the experimental chemical shifts.&quot;);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         40 :   keys.add(&quot;compulsory&quot;,&quot;TEMPLATE&quot;,&quot;template.pdb&quot;,&quot;A PDB file of the protein system.&quot;);</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         40 :   keys.add(&quot;compulsory&quot;,&quot;NEIGH_FREQ&quot;,&quot;20&quot;,&quot;Period in step for neighbor list update.&quot;);</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         40 :   keys.addFlag(&quot;CAMSHIFT&quot;,false,&quot;Set to TRUE if you to calculate a single CamShift score.&quot;);</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">         40 :   keys.addFlag(&quot;NOEXP&quot;,false,&quot;Set to TRUE if you don't want to have fixed components with the experimental values.&quot;);</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;ha&quot;,&quot;default&quot;,&quot;the calculated Ha hydrogen chemical shifts&quot;);</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;hn&quot;,&quot;default&quot;,&quot;the calculated H hydrogen chemical shifts&quot;);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;nh&quot;,&quot;default&quot;,&quot;the calculated N nitrogen chemical shifts&quot;);</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;ca&quot;,&quot;default&quot;,&quot;the calculated Ca carbon chemical shifts&quot;);</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;cb&quot;,&quot;default&quot;,&quot;the calculated Cb carbon chemical shifts&quot;);</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;co&quot;,&quot;default&quot;,&quot;the calculated C' carbon chemical shifts&quot;);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;expha&quot;,&quot;default&quot;,&quot;the experimental Ha hydrogen chemical shifts&quot;);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;exphn&quot;,&quot;default&quot;,&quot;the experimental H hydrogen chemical shifts&quot;);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;expnh&quot;,&quot;default&quot;,&quot;the experimental N nitrogen chemical shifts&quot;);</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;expca&quot;,&quot;default&quot;,&quot;the experimental Ca carbon chemical shifts&quot;);</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;expcb&quot;,&quot;default&quot;,&quot;the experimental Cb carbon chemical shifts&quot;);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         40 :   keys.addOutputComponent(&quot;expco&quot;,&quot;default&quot;,&quot;the experimental C' carbon chemical shifts&quot;);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         20 : }</span></a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         18 : CS2Backbone::CS2Backbone(const ActionOptions&amp;ao):</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :   PLUMED_METAINF_INIT(ao),</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         18 :   max_cs_atoms(0),</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         18 :   camshift(false),</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         18 :   pbc(true),</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         18 :   serial(false)</span></a>
+<a name="531"><span class="lineNum">     531 </span>            : {</a>
+<a name="532"><span class="lineNum">     532 </span>            :   std::vector&lt;AtomNumber&gt; used_atoms;</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         18 :   parseAtomList(&quot;ATOMS&quot;,used_atoms);</span></a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         18 :   parseFlag(&quot;CAMSHIFT&quot;,camshift);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         18 :   if(camshift&amp;&amp;getDoScore()) plumed_merror(&quot;It is not possible to use CAMSHIFT and DOSCORE at the same time&quot;);</span></a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         18 :   bool nopbc=!pbc;</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         18 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         18 :   pbc=!nopbc;</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         18 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         18 :   bool noexp=false;</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         36 :   parseFlag(&quot;NOEXP&quot;,noexp);</span></a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :   std::string stringa_data;</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         36 :   parse(&quot;DATADIR&quot;,stringa_data);</span></a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            :   std::string stringa_template;</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         18 :   parse(&quot;TEMPLATE&quot;,stringa_template);</span></a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         18 :   box_count=0;</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         18 :   box_nupdate=20;</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         18 :   parse(&quot;NEIGH_FREQ&quot;, box_nupdate);</span></a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         18 :   std::string stringadb  = stringa_data + std::string(&quot;/camshift.db&quot;);</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         36 :   std::string stringapdb = stringa_data + std::string(&quot;/&quot;) + stringa_template;</span></a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span>            :   /* Length conversion (parameters are tuned for angstrom) */</a>
+<a name="561"><span class="lineNum">     561 </span>            :   double scale=1.;</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         18 :   if(!plumed.getAtoms().usingNaturalUnits()) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         18 :     scale = 10.*atoms.getUnits().getLength();</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :   }</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         18 :   log.printf(&quot;  Initialization of the predictor ...\n&quot;);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         18 :   db.parse(stringadb,scale);</span></a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">         18 :   PDB pdb;</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">         36 :   if( !pdb.read(stringapdb,plumed.getAtoms().usingNaturalUnits(),1./scale) ) plumed_merror(&quot;missing input file &quot; + stringapdb);</span></a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span>            :   // first of all we build the list of chemical shifts we want to predict</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         18 :   log.printf(&quot;  Reading experimental data ...\n&quot;); log.flush();</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         36 :   stringadb = stringa_data + std::string(&quot;/CAshifts.dat&quot;);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         18 :   log.printf(&quot;  Initializing CA shifts %s\n&quot;, stringadb.c_str());</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         18 :   init_cs(stringadb, &quot;CA&quot;, pdb);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         36 :   stringadb = stringa_data + std::string(&quot;/CBshifts.dat&quot;);</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         18 :   log.printf(&quot;  Initializing CB shifts %s\n&quot;, stringadb.c_str());</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         18 :   init_cs(stringadb, &quot;CB&quot;, pdb);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         36 :   stringadb = stringa_data + std::string(&quot;/Cshifts.dat&quot;);</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         18 :   log.printf(&quot;  Initializing C' shifts %s\n&quot;, stringadb.c_str());</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         18 :   init_cs(stringadb, &quot;C&quot;, pdb);</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         36 :   stringadb = stringa_data + std::string(&quot;/HAshifts.dat&quot;);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         18 :   log.printf(&quot;  Initializing HA shifts %s\n&quot;, stringadb.c_str());</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         18 :   init_cs(stringadb, &quot;HA&quot;, pdb);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         36 :   stringadb = stringa_data + std::string(&quot;/Hshifts.dat&quot;);</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         18 :   log.printf(&quot;  Initializing H shifts %s\n&quot;, stringadb.c_str());</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         18 :   init_cs(stringadb, &quot;H&quot;, pdb);</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         36 :   stringadb = stringa_data + std::string(&quot;/Nshifts.dat&quot;);</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         18 :   log.printf(&quot;  Initializing N shifts %s\n&quot;, stringadb.c_str());</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         36 :   init_cs(stringadb, &quot;N&quot;, pdb);</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         18 :   if(chemicalshifts.size()==0) plumed_merror(&quot;There are no chemical shifts to calculate, there must be at least a not empty file (CA|CB|C|HA|H|N|shifts.dat)&quot;);</span></a>
+<a name="594"><span class="lineNum">     594 </span>            : </a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         18 :   init_types(pdb);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         18 :   init_rings(pdb);</span></a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         18 :   log&lt;&lt;&quot;  Bibliography &quot;</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         36 :      &lt;&lt;plumed.cite(&quot;Kohlhoff K, Robustelli P, Cavalli A, Salvatella A, Vendruscolo M, J. Am. Chem. Soc. 131, 13894 (2009)&quot;);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         23 :   if(camshift) log&lt;&lt;plumed.cite(&quot;Granata D, Camilloni C, Vendruscolo M, Laio A, Proc. Natl. Acad. Sci. USA 110, 6817 (2013)&quot;);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">         26 :   else log&lt;&lt;plumed.cite(&quot;Camilloni C, Robustelli P, De Simone A, Cavalli A, Vendruscolo M, J. Am. Chem. Soc. 134, 3968 (2012)&quot;);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         36 :   log&lt;&lt;plumed.cite(&quot;Bonomi M, Camilloni C, Bioinformatics, 33, 3999 (2017)&quot;);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         18 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">         18 :   if(camshift) {</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">          5 :     noexp = true;</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">          5 :     addValueWithDerivatives();</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">          5 :     setNotPeriodic();</span></a>
+<a name="609"><span class="lineNum">     609 </span>            :   } else {</a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">       7670 :     for(unsigned cs=0; cs&lt;chemicalshifts.size(); cs++) {</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">       7657 :       std::string num; Tools::convert(chemicalshifts[cs].res_num,num);</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">       7657 :       std::string chain_num; Tools::convert(chemicalshifts[cs].chain,chain_num);</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       7657 :       if(getDoScore()) {</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">       4712 :         addComponent(chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">       4712 :         componentIsNotPeriodic(chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">       2356 :         chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">       4712 :         setParameter(chemicalshifts[cs].exp_cs);</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :       } else {</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">      10602 :         addComponentWithDerivatives(chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">      10602 :         componentIsNotPeriodic(chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">       5301 :         chemicalshifts[cs].comp = getPntrToComponent(chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :       }</a>
+<a name="623"><span class="lineNum">     623 </span>            :     }</a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">         13 :     if(getDoScore()) Initialise(chemicalshifts.size());</span></a>
+<a name="625"><span class="lineNum">     625 </span>            :   }</a>
+<a name="626"><span class="lineNum">     626 </span>            : </a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         18 :   if(!noexp) {</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">       7670 :     for(unsigned cs=0; cs&lt;chemicalshifts.size(); cs++) {</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">       7657 :       std::string num; Tools::convert(chemicalshifts[cs].res_num,num);</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">       7657 :       std::string chain_num; Tools::convert(chemicalshifts[cs].chain,chain_num);</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">      15314 :       addComponent(&quot;exp&quot;+chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">      15314 :       componentIsNotPeriodic(&quot;exp&quot;+chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">      15314 :       Value* comp=getPntrToComponent(&quot;exp&quot;+chemicalshifts[cs].nucleus+chain_num+&quot;-&quot;+num);</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">       7657 :       comp-&gt;set(chemicalshifts[cs].exp_cs);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :     }</a>
+<a name="636"><span class="lineNum">     636 </span>            :   }</a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">         18 :   requestAtoms(used_atoms, false);</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">         18 :   setDerivatives();</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">         18 :   checkRead();</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">         36 : }</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">        108 : void CS2Backbone::init_cs(const std::string &amp;file, const std::string &amp;nucl, const PDB &amp;pdb) {</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :   // number of chains</a>
+<a name="645"><span class="lineNum">     645 </span>            :   std::vector&lt;std::string&gt; chains;</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">        108 :   pdb.getChainNames( chains );</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :   unsigned ichain=0;</a>
+<a name="648"><span class="lineNum">     648 </span>            : </a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">        108 :   std::ifstream in;</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">        108 :   in.open(file.c_str());</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">        108 :   if(!in) return;</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">        108 :   std::istream_iterator&lt;std::string&gt; iter(in), end;</span></a>
+<a name="653"><span class="lineNum">     653 </span>            :   unsigned begin=0;</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">        108 :   while(iter!=end) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">      19008 :     std::string tok = *iter;</span></a>
+<a name="657"><span class="lineNum">     657 </span>            :     ++iter;</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">      19008 :     if(tok[0]=='#') {</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :       ++iter;</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">        432 :       if(begin==1) {</span></a>
+<a name="661"><span class="lineNum">     661 </span>            :         begin=0;</a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">        216 :         ichain++;</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :       } else begin=1;</a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">        432 :       continue;</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :     }</a>
+<a name="666"><span class="lineNum">     666 </span>            :     int ro = atoi(tok.c_str());</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">      18576 :     if(ro&lt;0) plumed_merror(&quot;Residue numbers should be positive\n&quot;);</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">      18576 :     unsigned resnum = static_cast&lt;unsigned&gt; (ro);</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :     tok = *iter;</a>
+<a name="670"><span class="lineNum">     670 </span>            :     ++iter;</a>
+<a name="671"><span class="lineNum">     671 </span>            :     double cs = atof(tok.c_str());</a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">      18576 :     if(cs==0) continue;</span></a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :     unsigned fres, lres;</a>
+<a name="675"><span class="lineNum">     675 </span>            :     std::string errmsg;</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">      11070 :     pdb.getResidueRange(chains[ichain], fres, lres, errmsg);</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">      11070 :     if(resnum==fres||resnum==lres) plumed_merror(&quot;First and Last residue of each chain should be annotated as # in &quot; + file + &quot; Remember that residue numbers should match&quot;);</span></a>
+<a name="678"><span class="lineNum">     678 </span>            : </a>
+<a name="679"><span class="lineNum">     679 </span>            :     // check in the PDB for the chain/residue/atom and enable the chemical shift</a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">      11070 :     std::string RES = pdb.getResidueName(resnum, chains[ichain]);</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">      98766 :     if(RES==&quot;HIE&quot;||RES==&quot;HIP&quot;||RES==&quot;HIS&quot;||RES==&quot;HSP&quot;||RES==&quot;HSE&quot;||RES==&quot;CYS&quot;||RES==&quot;GLH&quot;||RES==&quot;ASH&quot;||RES==&quot;UNK&quot;) continue;</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">      10944 :     if(RES==&quot;GLN&quot;&amp;&amp;nucl==&quot;CB&quot;) continue;</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">      11322 :     if(RES==&quot;ILE&quot;&amp;&amp;nucl==&quot;CB&quot;) continue;</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">      10998 :     if(RES==&quot;PRO&quot;&amp;&amp;nucl==&quot;N&quot;) continue;</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">      10998 :     if(RES==&quot;PRO&quot;&amp;&amp;nucl==&quot;H&quot;) continue;</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">      10998 :     if(RES==&quot;PRO&quot;&amp;&amp;nucl==&quot;CB&quot;) continue;</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">      12240 :     if(RES==&quot;GLY&quot;&amp;&amp;nucl==&quot;HA&quot;) continue;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">      12240 :     if(RES==&quot;GLY&quot;&amp;&amp;nucl==&quot;CB&quot;) continue;</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">      10602 :     ChemicalShift tmp_cs;</span></a>
+<a name="691"><span class="lineNum">     691 </span>            : </a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">      10602 :     tmp_cs.exp_cs = cs;</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">      10602 :     if(nucl==&quot;CA&quot;)      tmp_cs.nucleus = &quot;ca-&quot;;</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">       7668 :     else if(nucl==&quot;CB&quot;) tmp_cs.nucleus = &quot;cb-&quot;;</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">       5616 :     else if(nucl==&quot;C&quot;)  tmp_cs.nucleus = &quot;co-&quot;;</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">       5616 :     else if(nucl==&quot;HA&quot;) tmp_cs.nucleus = &quot;ha-&quot;;</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">       5616 :     else if(nucl==&quot;H&quot;)  tmp_cs.nucleus = &quot;hn-&quot;;</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">       2808 :     else if(nucl==&quot;N&quot;)  tmp_cs.nucleus = &quot;nh-&quot;;</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">      10602 :     tmp_cs.chain = ichain;</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">      10602 :     tmp_cs.res_num = resnum;</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">      10602 :     tmp_cs.res_type_curr = frag2enum(RES);</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">      10602 :     tmp_cs.res_type_prev = frag2enum(pdb.getResidueName(resnum-1, chains[ichain]));</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">      10602 :     tmp_cs.res_type_next = frag2enum(pdb.getResidueName(resnum+1, chains[ichain]));</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :     tmp_cs.res_name = RES;</a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">      10602 :     tmp_cs.res_kind = db.kind(RES);</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">      10602 :     tmp_cs.atm_kind = db.atom_kind(nucl);</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">      20556 :     if(RES!=&quot;ALA&quot;&amp;&amp;RES!=&quot;GLY&quot;) {tmp_cs.bb.resize(18); tmp_cs.has_chi1=true;}</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">       2142 :     else {tmp_cs.bb.resize(16); tmp_cs.has_chi1=false;}</span></a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">      10602 :     std::vector&lt;AtomNumber&gt; res_atoms = pdb.getAtomsInResidue(resnum, chains[ichain]);</span></a>
+<a name="711"><span class="lineNum">     711 </span>            :     // find the position of the nucleus and of the other backbone atoms as well as for phi/psi/chi</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">     173268 :     for(unsigned a=0; a&lt;res_atoms.size(); a++) {</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">     162666 :       std::string AN = pdb.getAtomName(res_atoms[a]);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">     162666 :       if(nucl==&quot;HA&quot;&amp;&amp;(AN==&quot;HA&quot;||AN==&quot;HA1&quot;||AN==&quot;HA3&quot;)) tmp_cs.ipos = res_atoms[a].index();</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">     244530 :       else if(nucl==&quot;H&quot;&amp;&amp;(AN==&quot;H&quot;||AN==&quot;HN&quot;))          tmp_cs.ipos = res_atoms[a].index();</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">     202248 :       else if(nucl==&quot;N&quot;&amp;&amp;AN==&quot;N&quot;)                      tmp_cs.ipos = res_atoms[a].index();</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">     200862 :       else if(nucl==&quot;CA&quot;&amp;&amp;AN==&quot;CA&quot;)                    tmp_cs.ipos = res_atoms[a].index();</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">     188244 :       else if(nucl==&quot;CB&quot;&amp;&amp;AN==&quot;CB&quot;)                    tmp_cs.ipos = res_atoms[a].index();</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">     152064 :       else if(nucl==&quot;C&quot;&amp;&amp;AN==&quot;C&quot; )                     tmp_cs.ipos = res_atoms[a].index();</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :     }</a>
+<a name="721"><span class="lineNum">     721 </span>            : </a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">      10602 :     std::vector&lt;AtomNumber&gt; prev_res_atoms = pdb.getAtomsInResidue(resnum-1, chains[ichain]);</span></a>
+<a name="723"><span class="lineNum">     723 </span>            :     // find the position of the previous residues backbone atoms</a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">     168498 :     for(unsigned a=0; a&lt;prev_res_atoms.size(); a++) {</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">     157896 :       std::string AN = pdb.getAtomName(prev_res_atoms[a]);</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">     157896 :       if(AN==&quot;N&quot;)                             { tmp_cs.bb[Np]  = prev_res_atoms[a].index(); }</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">     147294 :       else if(AN==&quot;CA&quot;)                       { tmp_cs.bb[CAp] = prev_res_atoms[a].index(); }</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">     390690 :       else if(AN==&quot;HA&quot;||AN==&quot;HA1&quot;||AN==&quot;HA3&quot;) { tmp_cs.bb[HAp] = prev_res_atoms[a].index(); }</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">     126090 :       else if(AN==&quot;C&quot; )                       { tmp_cs.bb[Cp]  = prev_res_atoms[a].index(); }</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">     115488 :       else if(AN==&quot;O&quot; )                       { tmp_cs.bb[Op]  = prev_res_atoms[a].index(); }</span></a>
+<a name="731"><span class="lineNum">     731 </span>            :     }</a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">     173268 :     for(unsigned a=0; a&lt;res_atoms.size(); a++) {</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">     162666 :       std::string AN = pdb.getAtomName(res_atoms[a]);</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">     162666 :       if(AN==&quot;N&quot;)                                         { tmp_cs.bb[Nc]  = res_atoms[a].index(); }</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">     438282 :       else if(AN==&quot;H&quot; ||AN==&quot;HN&quot;||(AN==&quot;CD&quot;&amp;&amp;RES==&quot;PRO&quot;)) { tmp_cs.bb[Hc]  = res_atoms[a].index(); }</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">     141462 :       else if(AN==&quot;CA&quot;)                                   { tmp_cs.bb[CAc] = res_atoms[a].index(); }</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">     372870 :       else if(AN==&quot;HA&quot;||AN==&quot;HA1&quot;||AN==&quot;HA3&quot;)             { tmp_cs.bb[HAc] = res_atoms[a].index(); }</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">     120258 :       else if(AN==&quot;C&quot; )                                   { tmp_cs.bb[Cc]  = res_atoms[a].index(); }</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">     109656 :       else if(AN==&quot;O&quot; )                                   { tmp_cs.bb[Oc]  = res_atoms[a].index(); }</span></a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">     318852 :       if(RES!=&quot;ALA&quot;&amp;&amp;RES!=&quot;GLY&quot;) {</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">     145728 :         if(AN==&quot;CB&quot;) tmp_cs.bb[CBc] = res_atoms[a].index();</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">     145728 :         if(is_chi1_cx(RES,AN)) tmp_cs.bb[CGc] = res_atoms[a].index();</span></a>
+<a name="745"><span class="lineNum">     745 </span>            :       }</a>
+<a name="746"><span class="lineNum">     746 </span>            :     }</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">      10602 :     std::vector&lt;AtomNumber&gt; next_res_atoms = pdb.getAtomsInResidue(resnum+1, chains[ichain]);</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">      10602 :     std::string NRES = pdb.getResidueName(resnum+1, chains[ichain]);</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :     // find the position of the previous residues backbone atoms</a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">     168948 :     for(unsigned a=0; a&lt;next_res_atoms.size(); a++) {</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">     158346 :       std::string AN = pdb.getAtomName(next_res_atoms[a]);</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">     158346 :       if(AN==&quot;N&quot;)                                          { tmp_cs.bb[Nn]  = next_res_atoms[a].index(); }</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">     426096 :       else if(AN==&quot;H&quot; ||AN==&quot;HN&quot;||(AN==&quot;CD&quot;&amp;&amp;NRES==&quot;PRO&quot;)) { tmp_cs.bb[Hn]  = next_res_atoms[a].index(); }</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">     137142 :       else if(AN==&quot;CA&quot;)                                    { tmp_cs.bb[CAn] = next_res_atoms[a].index(); }</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">     360198 :       else if(AN==&quot;HA&quot;||AN==&quot;HA1&quot;||AN==&quot;HA3&quot;)              { tmp_cs.bb[HAn] = next_res_atoms[a].index(); }</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">     115938 :       else if(AN==&quot;C&quot; )                                    { tmp_cs.bb[Cn]  = next_res_atoms[a].index(); }</span></a>
+<a name="758"><span class="lineNum">     758 </span>            :     }</a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            :     // set sidechain atoms</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">      10602 :     std::vector&lt;std::string&gt; sc_atm = side_chain_atoms(RES);</span></a>
+<a name="762"><span class="lineNum">     762 </span>            : </a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">     141084 :     for(unsigned sc=0; sc&lt;sc_atm.size(); sc++) {</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">    2501208 :       for(unsigned aa=0; aa&lt;res_atoms.size(); aa++) {</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">    2370726 :         if(pdb.getAtomName(res_atoms[aa])==sc_atm[sc]) {</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">      99162 :           tmp_cs.side_chain.push_back(res_atoms[aa].index());</span></a>
+<a name="767"><span class="lineNum">     767 </span>            :         }</a>
+<a name="768"><span class="lineNum">     768 </span>            :       }</a>
+<a name="769"><span class="lineNum">     769 </span>            :     }</a>
+<a name="770"><span class="lineNum">     770 </span>            : </a>
+<a name="771"><span class="lineNum">     771 </span>            :     // find atoms for extra distances</a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">     286254 :     const std::string atomsP1[] =  {&quot;H&quot;, &quot;H&quot;, &quot;H&quot;, &quot;C&quot;, &quot;C&quot;, &quot;C&quot;, &quot;O&quot;, &quot;O&quot;, &quot;O&quot;, &quot;N&quot;, &quot;N&quot;, &quot;N&quot;, &quot;O&quot;, &quot;O&quot;, &quot;O&quot;, &quot;N&quot;, &quot;N&quot;, &quot;N&quot;, &quot;CG&quot;, &quot;CG&quot;, &quot;CG&quot;, &quot;CG&quot;, &quot;CG&quot;, &quot;CG&quot;, &quot;CG&quot;, &quot;CA&quot;};</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">      10602 :     const int resOffsetP1[] = { 0,   0,   0,  -1,  -1,  -1,   0,   0,   0,   1,   1,   1,   -1,  -1,  -1,  0,   0,   0,   0,    0,    0,    0,    0,    -1,   1,    -1};</span></a>
+<a name="774"><span class="lineNum">     774 </span>            : </a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">     286254 :     const std::string atomsP2[] =  {&quot;HA&quot;, &quot;C&quot;, &quot;CB&quot;, &quot;HA&quot;, &quot;C&quot;, &quot;CB&quot;, &quot;HA&quot;, &quot;N&quot;, &quot;CB&quot;, &quot;HA&quot;, &quot;N&quot;, &quot;CB&quot;, &quot;HA&quot;, &quot;N&quot;, &quot;CB&quot;, &quot;HA&quot;, &quot;N&quot;, &quot;CB&quot;, &quot;HA&quot;, &quot;N&quot;, &quot;C&quot;, &quot;C&quot;, &quot;N&quot;, &quot;CA&quot;, &quot;CA&quot;, &quot;CA&quot;};</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">      10602 :     const int resOffsetP2[] = { 0,    0,   0,    0,    0,   0,    0,    0,   0,    0,    0,   0,    -1,  -1,   -1,   -1,  -1,   -1,   0,    0,   0,   -1,  1,   0,    0,    1};</span></a>
+<a name="777"><span class="lineNum">     777 </span>            : </a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">     286254 :     for(unsigned q=0; q&lt;db.get_numXtraDists()-1; q++) {</span></a>
+<a name="779"><span class="lineNum">     779 </span>            :       std::vector&lt;AtomNumber&gt; at1;</a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">     275652 :       if(resOffsetP1[q]== 0) at1 = res_atoms;</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">     275652 :       if(resOffsetP1[q]==-1) at1 = prev_res_atoms;</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">     275652 :       if(resOffsetP1[q]==+1) at1 = next_res_atoms;</span></a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span>            :       std::vector&lt;AtomNumber&gt; at2;</a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">     275652 :       if(resOffsetP2[q]== 0) at2 = res_atoms;</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">     275652 :       if(resOffsetP2[q]==-1) at2 = prev_res_atoms;</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">     275652 :       if(resOffsetP2[q]==+1) at2 = next_res_atoms;</span></a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">     275652 :       int tmp1 = -1;</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">    2197566 :       for(unsigned a=0; a&lt;at1.size(); a++) {</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">    2181708 :         std::string name = pdb.getAtomName(at1[a]);</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">    2181708 :         xdist_name_map(name);</span></a>
+<a name="793"><span class="lineNum">     793 </span>            : </a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">    2181708 :         if(name==atomsP1[q]) {</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">     259794 :           tmp1 = at1[a].index();</span></a>
+<a name="796"><span class="lineNum">     796 </span>            :           break;</a>
+<a name="797"><span class="lineNum">     797 </span>            :         }</a>
+<a name="798"><span class="lineNum">     798 </span>            :       }</a>
+<a name="799"><span class="lineNum">     799 </span>            : </a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">     275652 :       int tmp2 = -1;</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">    1427688 :       for(unsigned a=0; a&lt;at2.size(); a++) {</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">    1418076 :         std::string name = pdb.getAtomName(at2[a]);</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">    1418076 :         xdist_name_map(name);</span></a>
+<a name="804"><span class="lineNum">     804 </span>            : </a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">    1418076 :         if(name==atomsP2[q]) {</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">     266040 :           tmp2 = at2[a].index();</span></a>
+<a name="807"><span class="lineNum">     807 </span>            :           break;</a>
+<a name="808"><span class="lineNum">     808 </span>            :         }</a>
+<a name="809"><span class="lineNum">     809 </span>            :       }</a>
+<a name="810"><span class="lineNum">     810 </span>            : </a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">     275652 :       tmp_cs.xd1.push_back(tmp1);</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">     275652 :       tmp_cs.xd2.push_back(tmp2);</span></a>
+<a name="813"><span class="lineNum">     813 </span>            :     }</a>
+<a name="814"><span class="lineNum">     814 </span>            : </a>
+<a name="815"><span class="lineNum">     815 </span>            :     // ready to add a new chemical shifts</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">      10602 :     tmp_cs.csatoms = 1 + 16 + tmp_cs.side_chain.size() + 2*tmp_cs.xd1.size();</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">      20556 :     if(tmp_cs.res_name!=&quot;ALA&quot;&amp;&amp;tmp_cs.res_name!=&quot;GLY&quot;) tmp_cs.csatoms += 2;</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">      10602 :     chemicalshifts.push_back(tmp_cs);</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">     593712 :   }</span></a>
+<a name="820"><span class="lineNum">     820 </span>            : </a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">        108 :   in.close();</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">        108 : }</span></a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span>            : // this assigns an atom-type to each atom of the pdb</a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">         18 : void CS2Backbone::init_types(const PDB &amp;pdb) {</span></a>
+<a name="826"><span class="lineNum">     826 </span>            :   enum atom_t {D_C, D_H, D_N, D_O, D_S, D_C2, D_N2, D_O2};</a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">         18 :   std::vector&lt;AtomNumber&gt; aa = pdb.getAtomNumbers();</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">      47034 :   for(unsigned i=0; i&lt;aa.size(); i++) {</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">      47016 :     unsigned frag = pdb.getResidueNumber(aa[i]);</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">      47016 :     std::string fragName = pdb.getResidueName(aa[i]);</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">      47016 :     std::string atom_name = pdb.getAtomName(aa[i]);</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">      47016 :     char atom_type = atom_name[0];</span></a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">      47016 :     if(isdigit(atom_name[0])) atom_type = atom_name[1];</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">      47016 :     res_num.push_back(frag);</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">      47016 :     unsigned t = 0;</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">      47016 :     if (!isSP2(fragName, atom_name)) {</span></a>
+<a name="837"><span class="lineNum">     837 </span>            :       if (atom_type == 'C') t = D_C;</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">        468 :       else if (atom_type == 'O') t = D_O;</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">      23256 :       else if (atom_type == 'H') t = D_H;</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">       4032 :       else if (atom_type == 'N') t = D_N;</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">        162 :       else if (atom_type == 'S') t = D_S;</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineNoCov">          0 :       else plumed_merror(&quot;Unknown atom type: &quot; + atom_name);</span></a>
+<a name="843"><span class="lineNum">     843 </span>            :     } else {</a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">      10080 :       if (atom_type == 'C') t = D_C2;</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">       4104 :       else if (atom_type == 'O') t = D_O2;</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineNoCov">          0 :       else if (atom_type == 'N') t = D_N2;</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineNoCov">          0 :       else plumed_merror(&quot;Unknown atom type: &quot; + atom_name);</span></a>
+<a name="848"><span class="lineNum">     848 </span>            :     }</a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">      47016 :     type.push_back(t);</span></a>
+<a name="850"><span class="lineNum">     850 </span>            :   }</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">         18 : }</span></a>
+<a name="852"><span class="lineNum">     852 </span>            : </a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">         18 : void CS2Backbone::init_rings(const PDB &amp;pdb)</span></a>
+<a name="854"><span class="lineNum">     854 </span>            : {</a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">        126 :   const std::string pheTyr_n[] = {&quot;CG&quot;,&quot;CD1&quot;,&quot;CE1&quot;,&quot;CZ&quot;,&quot;CE2&quot;,&quot;CD2&quot;};</span></a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">        126 :   const std::string trp1_n[]   = {&quot;CD2&quot;,&quot;CE2&quot;,&quot;CZ2&quot;,&quot;CH2&quot;,&quot;CZ3&quot;,&quot;CE3&quot;};</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">        108 :   const std::string trp2_n[]   = {&quot;CG&quot;,&quot;CD1&quot;,&quot;NE1&quot;,&quot;CE2&quot;,&quot;CD2&quot;};</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">        108 :   const std::string his_n[]    = {&quot;CG&quot;,&quot;ND1&quot;,&quot;CD2&quot;,&quot;CE1&quot;,&quot;NE2&quot;};</span></a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :   // number of chains</a>
+<a name="861"><span class="lineNum">     861 </span>            :   std::vector&lt;std::string&gt; chains;</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">         18 :   pdb.getChainNames( chains );</span></a>
+<a name="863"><span class="lineNum">     863 </span>            :   unsigned total_rings_atoms = 0;</a>
+<a name="864"><span class="lineNum">     864 </span>            : </a>
+<a name="865"><span class="lineNum">     865 </span>            :   // cycle over chains</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">         54 :   for(unsigned i=0; i&lt;chains.size(); i++) {</span></a>
+<a name="867"><span class="lineNum">     867 </span>            :     unsigned start, end;</a>
+<a name="868"><span class="lineNum">     868 </span>            :     std::string errmsg;</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">         36 :     pdb.getResidueRange( chains[i], start, end, errmsg );</span></a>
+<a name="870"><span class="lineNum">     870 </span>            :     // cycle over residues</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">       3168 :     for(unsigned res=start; res&lt;end; res++) {</span></a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">       3132 :       std::string frg = pdb.getResidueName(res, chains[i]);</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">      14364 :       if(!((frg==&quot;PHE&quot;)||(frg==&quot;TYR&quot;)||(frg==&quot;TRP&quot;)||</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">       8370 :            (frg==&quot;HIS&quot;)||(frg==&quot;HIP&quot;)||(frg==&quot;HID&quot;)||</span></a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">       5580 :            (frg==&quot;HIE&quot;)||(frg==&quot;HSD&quot;)||(frg==&quot;HSE&quot;)||</span></a>
+<a name="876"><span class="lineNum">     876 </span>            :            (frg==&quot;HSP&quot;))) continue;</a>
+<a name="877"><span class="lineNum">     877 </span>            : </a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">        342 :       std::vector&lt;AtomNumber&gt; frg_atoms = pdb.getAtomsInResidue(res,chains[i]);</span></a>
+<a name="879"><span class="lineNum">     879 </span>            : </a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">        396 :       if(frg==&quot;PHE&quot;||frg==&quot;TYR&quot;) {</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">        324 :         RingInfo ri;</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">       6840 :         for(unsigned a=0; a&lt;frg_atoms.size(); a++) {</span></a>
+<a name="883"><span class="lineNum">     883 </span>            :           unsigned atm = frg_atoms[a].index();</a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">      38808 :           for(unsigned aa=0; aa&lt;6; aa++) {</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">      34236 :             if(pdb.getAtomName(frg_atoms[a])==pheTyr_n[aa]) {</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">       1944 :               ri.atom[aa] = atm;</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">       1944 :               break;</span></a>
+<a name="888"><span class="lineNum">     888 </span>            :             }</a>
+<a name="889"><span class="lineNum">     889 </span>            :           }</a>
+<a name="890"><span class="lineNum">     890 </span>            :         }</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">        324 :         ri.numAtoms = 6;</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">        324 :         total_rings_atoms += 6;</span></a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">        324 :         if(frg==&quot;PHE&quot;) ri.rtype = RingInfo::R_PHE;</span></a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">        324 :         if(frg==&quot;TYR&quot;) ri.rtype = RingInfo::R_TYR;</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">        324 :         ringInfo.push_back(ri);</span></a>
+<a name="896"><span class="lineNum">     896 </span>            : </a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">         18 :       } else if(frg==&quot;TRP&quot;) {</span></a>
+<a name="898"><span class="lineNum">     898 </span>            :         //First ring</a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">         18 :         RingInfo ri;</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">        450 :         for(unsigned a=0; a&lt;frg_atoms.size(); a++) {</span></a>
+<a name="901"><span class="lineNum">     901 </span>            :           unsigned atm = frg_atoms[a].index();</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">       2646 :           for(unsigned aa=0; aa&lt;6; aa++) {</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">       2322 :             if(pdb.getAtomName(frg_atoms[a])==trp1_n[aa]) {</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">        108 :               ri.atom[aa] = atm;</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">        108 :               break;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :             }</a>
+<a name="907"><span class="lineNum">     907 </span>            :           }</a>
+<a name="908"><span class="lineNum">     908 </span>            :         }</a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">         18 :         ri.numAtoms = 6;</span></a>
+<a name="910"><span class="lineNum">     910 </span>            :         total_rings_atoms += 6;</a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">         18 :         ri.rtype = RingInfo::R_TRP1;</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">         18 :         ringInfo.push_back(ri);</span></a>
+<a name="913"><span class="lineNum">     913 </span>            :         //Second Ring</a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         18 :         RingInfo ri2;</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">        450 :         for(unsigned a=0; a&lt;frg_atoms.size(); a++) {</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :           unsigned atm = frg_atoms[a].index();</a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">       2322 :           for(unsigned aa=0; aa&lt;5; aa++) {</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">       1980 :             if(pdb.getAtomName(frg_atoms[a])==trp2_n[aa]) {</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">         90 :               ri2.atom[aa] = atm;</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">         90 :               break;</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :             }</a>
+<a name="922"><span class="lineNum">     922 </span>            :           }</a>
+<a name="923"><span class="lineNum">     923 </span>            :         }</a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">         18 :         ri2.numAtoms = 5;</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">         18 :         total_rings_atoms += 3;</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">         18 :         ri2.rtype = RingInfo::R_TRP2;</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">         18 :         ringInfo.push_back(ri2);</span></a>
+<a name="928"><span class="lineNum">     928 </span>            : </a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineNoCov">          0 :       } else if((frg==&quot;HIS&quot;)||(frg==&quot;HIP&quot;)||(frg==&quot;HID&quot;)||</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineNoCov">          0 :                 (frg==&quot;HIE&quot;)||(frg==&quot;HSD&quot;)||(frg==&quot;HSE&quot;)||</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :                 (frg==&quot;HSP&quot;)) {//HIS case</a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineNoCov">          0 :         RingInfo ri;</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineNoCov">          0 :         for(unsigned a=0; a&lt;frg_atoms.size(); a++) {</span></a>
+<a name="934"><span class="lineNum">     934 </span>            :           unsigned atm = frg_atoms[a].index();</a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineNoCov">          0 :           for(unsigned aa=0; aa&lt;5; aa++) {</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 :             if(pdb.getAtomName(frg_atoms[a])==his_n[aa]) {</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineNoCov">          0 :               ri.atom[aa] = atm;</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 :               break;</span></a>
+<a name="939"><span class="lineNum">     939 </span>            :             }</a>
+<a name="940"><span class="lineNum">     940 </span>            :           }</a>
+<a name="941"><span class="lineNum">     941 </span>            :         }</a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :         ri.numAtoms = 5;</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineNoCov">          0 :         total_rings_atoms += 3;</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 :         ri.rtype = RingInfo::R_HIS;</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineNoCov">          0 :         ringInfo.push_back(ri);</span></a>
+<a name="946"><span class="lineNum">     946 </span>            :       } else {</a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;Unknown Ring Fragment: &quot; + frg);</span></a>
+<a name="948"><span class="lineNum">     948 </span>            :       }</a>
+<a name="949"><span class="lineNum">     949 </span>            :     }</a>
+<a name="950"><span class="lineNum">     950 </span>            :   }</a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">      10620 :   for(unsigned cs=0; cs&lt;chemicalshifts.size(); cs++) chemicalshifts[cs].csatoms += total_rings_atoms;</span></a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">        486 : }</span></a>
+<a name="954"><span class="lineNum">     954 </span>            : </a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">         18 : void CS2Backbone::calculate()</span></a>
+<a name="956"><span class="lineNum">     956 </span>            : {</a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">         18 :   if(pbc) makeWhole();</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">         18 :   if(getExchangeStep()) box_count=0;</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">         18 :   if(box_count==0) update_neighb();</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">         18 :   compute_ring_parameters();</span></a>
+<a name="961"><span class="lineNum">     961 </span>            : </a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">         18 :   std::vector&lt;double&gt; camshift_sigma2(6);</span></a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">         18 :   camshift_sigma2[0] = 0.08; // HA</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">         18 :   camshift_sigma2[1] = 0.30; // HN</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">         18 :   camshift_sigma2[2] = 9.00; // NH</span></a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineCov">         18 :   camshift_sigma2[3] = 1.30; // CA</span></a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">         18 :   camshift_sigma2[4] = 1.56; // CB</span></a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">         18 :   camshift_sigma2[5] = 1.70; // CO</span></a>
+<a name="969"><span class="lineNum">     969 </span>            : </a>
+<a name="970"><span class="lineNum">     970 </span>            :   std::vector&lt;Vector&gt;   cs_derivs;</a>
+<a name="971"><span class="lineNum">     971 </span>            :   std::vector&lt;Vector&gt;   aa_derivs;</a>
+<a name="972"><span class="lineNum">     972 </span>            :   std::vector&lt;unsigned&gt; cs_atoms;</a>
+<a name="973"><span class="lineNum">     973 </span>            :   std::vector&lt;double&gt;   all_shifts;</a>
+<a name="974"><span class="lineNum">     974 </span>            : </a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">         18 :   cs_derivs.resize(chemicalshifts.size()*max_cs_atoms,Vector(0,0,0));</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">         18 :   cs_atoms.resize(chemicalshifts.size()*max_cs_atoms,0);</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">         18 :   all_shifts.resize(chemicalshifts.size(),0);</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">         18 :   if(camshift||getDoScore()) aa_derivs.resize(getNumberOfAtoms(),Vector(0,0,0));</span></a>
+<a name="979"><span class="lineNum">     979 </span>            : </a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">         18 :   unsigned stride = comm.Get_size();</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">         18 :   unsigned rank   = comm.Get_rank();</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">         18 :   if(serial) {</span></a>
+<a name="983"><span class="lineNum">     983 </span>            :     stride = 1;</a>
+<a name="984"><span class="lineNum">     984 </span>            :     rank   = 0;</a>
+<a name="985"><span class="lineNum">     985 </span>            :   }</a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">         18 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">         18 :   if(nt*stride*2&gt;chemicalshifts.size()) nt=1;</span></a>
+<a name="989"><span class="lineNum">     989 </span>            : </a>
+<a name="990"><span class="lineNum">     990 </span>            :   // a single loop over all chemical shifts</a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">         18 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="992"><span class="lineNum">     992 </span>            :   {</a>
+<a name="993"><span class="lineNum">     993 </span>            :     #pragma omp for schedule(dynamic)</a>
+<a name="994"><span class="lineNum">     994 </span>            :     for(unsigned cs=rank; cs&lt;chemicalshifts.size(); cs+=stride) {</a>
+<a name="995"><span class="lineNum">     995 </span>            :       const unsigned kdx=cs*max_cs_atoms;</a>
+<a name="996"><span class="lineNum">     996 </span>            :       const ChemicalShift *myfrag = &amp;chemicalshifts[cs];</a>
+<a name="997"><span class="lineNum">     997 </span>            :       const unsigned aa_kind = myfrag-&gt;res_kind;</a>
+<a name="998"><span class="lineNum">     998 </span>            :       const unsigned at_kind = myfrag-&gt;atm_kind;</a>
+<a name="999"><span class="lineNum">     999 </span>            : </a>
+<a name="1000"><span class="lineNum">    1000 </span>            :       double shift = db.CONSTAAPREV(aa_kind,at_kind)[myfrag-&gt;res_type_prev] +</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :                      db.CONSTAACURR(aa_kind,at_kind)[myfrag-&gt;res_type_curr] +</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :                      db.CONSTAANEXT(aa_kind,at_kind)[myfrag-&gt;res_type_next];</a>
+<a name="1003"><span class="lineNum">    1003 </span>            : </a>
+<a name="1004"><span class="lineNum">    1004 </span>            :       const unsigned ipos = myfrag-&gt;ipos;</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :       cs_atoms[kdx+0] = ipos;</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :       unsigned atom_counter = 1;</a>
+<a name="1007"><span class="lineNum">    1007 </span>            : </a>
+<a name="1008"><span class="lineNum">    1008 </span>            :       //BACKBONE (PREV CURR NEXT)</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :       const double * CONST_BB2 = db.CONST_BB2(aa_kind,at_kind);</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :       const unsigned bbsize = 16;</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :       for(unsigned q=0; q&lt;bbsize; q++) {</a>
+<a name="1012"><span class="lineNum">    1012 </span>            :         const double cb2q = CONST_BB2[q];</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :         if(cb2q==0.) continue;</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :         const unsigned jpos = myfrag-&gt;bb[q];</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :         if(ipos==jpos) continue;</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :         const Vector distance = delta(getPosition(jpos),getPosition(ipos));</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :         const double d = distance.modulo();</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :         const double fact = cb2q/d;</a>
+<a name="1019"><span class="lineNum">    1019 </span>            : </a>
+<a name="1020"><span class="lineNum">    1020 </span>            :         shift += cb2q*d;</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :         const Vector der = fact*distance;</a>
+<a name="1022"><span class="lineNum">    1022 </span>            : </a>
+<a name="1023"><span class="lineNum">    1023 </span>            :         cs_derivs[kdx+0] += der;</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :         cs_derivs[kdx+q+atom_counter] = -der;</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :         cs_atoms[kdx+q+atom_counter] = jpos;</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :       }</a>
+<a name="1027"><span class="lineNum">    1027 </span>            : </a>
+<a name="1028"><span class="lineNum">    1028 </span>            :       atom_counter += bbsize;</a>
+<a name="1029"><span class="lineNum">    1029 </span>            : </a>
+<a name="1030"><span class="lineNum">    1030 </span>            :       //DIHEDRAL ANGLES</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :       const double *CO_DA = db.CO_DA(aa_kind,at_kind);</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :       //Phi</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :       {</a>
+<a name="1034"><span class="lineNum">    1034 </span>            :         const Vector d0 = delta(getPosition(myfrag-&gt;bb[Nc]), getPosition(myfrag-&gt;bb[Cp]));</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :         const Vector d1 = delta(getPosition(myfrag-&gt;bb[CAc]), getPosition(myfrag-&gt;bb[Nc]));</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :         const Vector d2 = delta(getPosition(myfrag-&gt;bb[Cc]), getPosition(myfrag-&gt;bb[CAc]));</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :         Torsion t;</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :         Vector dd0, dd1, dd2;</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :         const double t_phi = t.compute(d0,d1,d2,dd0,dd1,dd2);</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :         const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,0);</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :         const double val1 = 3.*t_phi+PARS_DA[3];</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :         const double val2 = t_phi+PARS_DA[4];</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :         shift += CO_DA[0]*(PARS_DA[0]*std::cos(val1)+PARS_DA[1]*std::cos(val2)+PARS_DA[2]);</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :         const double fact = -CO_DA[0]*(+3.*PARS_DA[0]*std::sin(val1)+PARS_DA[1]*std::sin(val2));</a>
+<a name="1045"><span class="lineNum">    1045 </span>            : </a>
+<a name="1046"><span class="lineNum">    1046 </span>            :         cs_derivs[kdx+Cp+1] += fact*dd0;</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :         cs_derivs[kdx+Nc+1] += fact*(dd1-dd0);</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :         cs_derivs[kdx+CAc+1]+= fact*(dd2-dd1);</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :         cs_derivs[kdx+Cc+1] += -fact*dd2;</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :         cs_atoms[kdx+Cp+1] = myfrag-&gt;bb[Cp];</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :         cs_atoms[kdx+Nc+1] = myfrag-&gt;bb[Nc];</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :         cs_atoms[kdx+CAc+1]= myfrag-&gt;bb[CAc];</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :         cs_atoms[kdx+Cc+1] = myfrag-&gt;bb[Cc];</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :       }</a>
+<a name="1055"><span class="lineNum">    1055 </span>            : </a>
+<a name="1056"><span class="lineNum">    1056 </span>            :       //Psi</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :       {</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :         const Vector d0 = delta(getPosition(myfrag-&gt;bb[CAc]), getPosition(myfrag-&gt;bb[Nc]));</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :         const Vector d1 = delta(getPosition(myfrag-&gt;bb[Cc]), getPosition(myfrag-&gt;bb[CAc]));</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :         const Vector d2 = delta(getPosition(myfrag-&gt;bb[Nn]), getPosition(myfrag-&gt;bb[Cc]));</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :         Torsion t;</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :         Vector dd0, dd1, dd2;</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :         const double t_psi = t.compute(d0,d1,d2,dd0,dd1,dd2);</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :         const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,1);</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :         const double val1 = 3.*t_psi+PARS_DA[3];</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :         const double val2 = t_psi+PARS_DA[4];</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :         shift += CO_DA[1]*(PARS_DA[0]*std::cos(val1)+PARS_DA[1]*std::cos(val2)+PARS_DA[2]);</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :         const double fact = -CO_DA[1]*(+3.*PARS_DA[0]*std::sin(val1)+PARS_DA[1]*std::sin(val2));</a>
+<a name="1069"><span class="lineNum">    1069 </span>            : </a>
+<a name="1070"><span class="lineNum">    1070 </span>            :         cs_derivs[kdx+Nc+1] += fact*dd0;</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :         cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :         cs_derivs[kdx+Cc+1] += fact*(dd2-dd1);</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :         cs_derivs[kdx+Nn+1] += -fact*dd2;</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :         cs_atoms[kdx+Nc+1] = myfrag-&gt;bb[Nc];</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :         cs_atoms[kdx+CAc+1]= myfrag-&gt;bb[CAc];</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :         cs_atoms[kdx+Cc+1] = myfrag-&gt;bb[Cc];</a>
+<a name="1077"><span class="lineNum">    1077 </span>            :         cs_atoms[kdx+Nn+1] = myfrag-&gt;bb[Nn];</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :       }</a>
+<a name="1079"><span class="lineNum">    1079 </span>            : </a>
+<a name="1080"><span class="lineNum">    1080 </span>            :       //Chi</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :       if(myfrag-&gt;has_chi1) {</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :         const Vector d0 = delta(getPosition(myfrag-&gt;bb[CAc]), getPosition(myfrag-&gt;bb[Nc]));</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :         const Vector d1 = delta(getPosition(myfrag-&gt;bb[CBc]), getPosition(myfrag-&gt;bb[CAc]));</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :         const Vector d2 = delta(getPosition(myfrag-&gt;bb[CGc]), getPosition(myfrag-&gt;bb[CBc]));</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :         Torsion t;</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :         Vector dd0, dd1, dd2;</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :         const double t_chi1 = t.compute(d0,d1,d2,dd0,dd1,dd2);</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :         const double *PARS_DA = db.PARS_DA(aa_kind,at_kind,2);</a>
+<a name="1089"><span class="lineNum">    1089 </span>            :         const double val1 = 3.*t_chi1+PARS_DA[3];</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :         const double val2 = t_chi1+PARS_DA[4];</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :         shift += CO_DA[2]*(PARS_DA[0]*std::cos(val1)+PARS_DA[1]*std::cos(val2)+PARS_DA[2]);</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :         const double fact = -CO_DA[2]*(+3.*PARS_DA[0]*std::sin(val1)+PARS_DA[1]*std::sin(val2));</a>
+<a name="1093"><span class="lineNum">    1093 </span>            : </a>
+<a name="1094"><span class="lineNum">    1094 </span>            :         cs_derivs[kdx+Nc+1] += fact*dd0;</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :         cs_derivs[kdx+CAc+1] += fact*(dd1-dd0);</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :         cs_derivs[kdx+CBc+1] += fact*(dd2-dd1);</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :         cs_derivs[kdx+CGc+1] += -fact*dd2;</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :         cs_atoms[kdx+Nc+1]  = myfrag-&gt;bb[Nc];</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :         cs_atoms[kdx+CAc+1] = myfrag-&gt;bb[CAc];</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :         cs_atoms[kdx+CBc+1] = myfrag-&gt;bb[CBc];</a>
+<a name="1101"><span class="lineNum">    1101 </span>            :         cs_atoms[kdx+CGc+1] = myfrag-&gt;bb[CGc];</a>
+<a name="1102"><span class="lineNum">    1102 </span>            : </a>
+<a name="1103"><span class="lineNum">    1103 </span>            :         atom_counter += 2;</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :       }</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :       //END OF DIHE</a>
+<a name="1106"><span class="lineNum">    1106 </span>            : </a>
+<a name="1107"><span class="lineNum">    1107 </span>            :       //SIDE CHAIN</a>
+<a name="1108"><span class="lineNum">    1108 </span>            :       const double * CONST_SC2 = db.CONST_SC2(aa_kind,at_kind,myfrag-&gt;res_type_curr);</a>
+<a name="1109"><span class="lineNum">    1109 </span>            :       const unsigned sidsize = myfrag-&gt;side_chain.size();</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :       for(unsigned q=0; q&lt;sidsize; q++) {</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :         const double cs2q = CONST_SC2[q];</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :         if(cs2q==0.) continue;</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :         const unsigned jpos = myfrag-&gt;side_chain[q];</a>
+<a name="1114"><span class="lineNum">    1114 </span>            :         if(ipos==jpos) continue;</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :         const Vector distance = delta(getPosition(jpos),getPosition(ipos));</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :         const double d = distance.modulo();</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :         const double fact = cs2q/d;</a>
+<a name="1118"><span class="lineNum">    1118 </span>            : </a>
+<a name="1119"><span class="lineNum">    1119 </span>            :         shift += cs2q*d;</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :         const Vector der = fact*distance;</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :         cs_derivs[kdx+0] += der;</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :         cs_derivs[kdx+q+atom_counter] = -der;</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :         cs_atoms[kdx+q+atom_counter] = jpos;</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :       }</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : </a>
+<a name="1126"><span class="lineNum">    1126 </span>            :       atom_counter += sidsize;</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : </a>
+<a name="1128"><span class="lineNum">    1128 </span>            :       //EXTRA DIST</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :       const double * CONST_XD  = db.CONST_XD(aa_kind,at_kind);</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :       const unsigned xdsize=myfrag-&gt;xd1.size();</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :       for(unsigned q=0; q&lt;xdsize; q++) {</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :         const double cxdq = CONST_XD[q];</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :         if(cxdq==0.) continue;</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :         if(myfrag-&gt;xd1[q]==-1||myfrag-&gt;xd2[q]==-1) continue;</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :         const Vector distance = delta(getPosition(myfrag-&gt;xd1[q]),getPosition(myfrag-&gt;xd2[q]));</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :         const double d = distance.modulo();</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :         const double fact = cxdq/d;</a>
+<a name="1138"><span class="lineNum">    1138 </span>            : </a>
+<a name="1139"><span class="lineNum">    1139 </span>            :         shift += cxdq*d;</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :         const Vector der = fact*distance;</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :         cs_derivs[kdx+2*q+atom_counter  ] = der;</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :         cs_derivs[kdx+2*q+atom_counter+1] = -der;</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :         cs_atoms[kdx+2*q+atom_counter] = myfrag-&gt;xd2[q];</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :         cs_atoms[kdx+2*q+atom_counter+1] = myfrag-&gt;xd1[q];</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :       }</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : </a>
+<a name="1147"><span class="lineNum">    1147 </span>            :       atom_counter += 2*xdsize;</a>
+<a name="1148"><span class="lineNum">    1148 </span>            : </a>
+<a name="1149"><span class="lineNum">    1149 </span>            :       //RINGS</a>
+<a name="1150"><span class="lineNum">    1150 </span>            :       const double *rc = db.CO_RING(aa_kind,at_kind);</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :       const unsigned rsize = ringInfo.size();</a>
+<a name="1152"><span class="lineNum">    1152 </span>            :       // cycle over the list of rings</a>
+<a name="1153"><span class="lineNum">    1153 </span>            :       for(unsigned q=0; q&lt;rsize; q++) {</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :         // compute angle from ring middle point to current atom position</a>
+<a name="1155"><span class="lineNum">    1155 </span>            :         // get distance std::vector from query atom to ring center and normal std::vector to ring plane</a>
+<a name="1156"><span class="lineNum">    1156 </span>            :         const Vector n   = ringInfo[q].normVect;</a>
+<a name="1157"><span class="lineNum">    1157 </span>            :         const double nL  = ringInfo[q].lengthNV;</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :         const double inL2 = ringInfo[q].lengthN2;</a>
+<a name="1159"><span class="lineNum">    1159 </span>            : </a>
+<a name="1160"><span class="lineNum">    1160 </span>            :         const Vector d = delta(ringInfo[q].position, getPosition(ipos));</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :         const double dL2 = d.modulo2();</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :         double dL  = std::sqrt(dL2);</a>
+<a name="1163"><span class="lineNum">    1163 </span>            :         const double idL3 = 1./(dL2*dL);</a>
+<a name="1164"><span class="lineNum">    1164 </span>            : </a>
+<a name="1165"><span class="lineNum">    1165 </span>            :         const double dn    = dotProduct(d,n);</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :         const double dn2   = dn*dn;</a>
+<a name="1167"><span class="lineNum">    1167 </span>            :         const double dLnL  = dL*nL;</a>
+<a name="1168"><span class="lineNum">    1168 </span>            :         const double dL_nL = dL/nL;</a>
+<a name="1169"><span class="lineNum">    1169 </span>            : </a>
+<a name="1170"><span class="lineNum">    1170 </span>            :         const double ang2 = dn2*inL2/dL2;</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :         const double u    = 1.-3.*ang2;</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :         const double cc   = rc[ringInfo[q].rtype];</a>
+<a name="1173"><span class="lineNum">    1173 </span>            : </a>
+<a name="1174"><span class="lineNum">    1174 </span>            :         shift += cc*u*idL3;</a>
+<a name="1175"><span class="lineNum">    1175 </span>            : </a>
+<a name="1176"><span class="lineNum">    1176 </span>            :         const double fUU    = -6.*dn*inL2;</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :         const double fUQ    = fUU/dL;</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :         const Vector gradUQ = fUQ*(dL2*n - dn*d);</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :         const Vector gradVQ = (3.*dL*u)*d;</a>
+<a name="1180"><span class="lineNum">    1180 </span>            : </a>
+<a name="1181"><span class="lineNum">    1181 </span>            :         const double fact   = cc*idL3*idL3;</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :         cs_derivs[kdx+0] += fact*(gradUQ - gradVQ);</a>
+<a name="1183"><span class="lineNum">    1183 </span>            : </a>
+<a name="1184"><span class="lineNum">    1184 </span>            :         const double fU       = fUU/nL;</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :         double OneOverN = 1./6.;</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :         if(ringInfo[q].numAtoms==5) OneOverN=1./3.;</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :         const Vector factor2  = OneOverN*n;</a>
+<a name="1188"><span class="lineNum">    1188 </span>            :         const Vector factor4  = (OneOverN/dL_nL)*d;</a>
+<a name="1189"><span class="lineNum">    1189 </span>            : </a>
+<a name="1190"><span class="lineNum">    1190 </span>            :         const Vector gradV    = -OneOverN*gradVQ;</a>
+<a name="1191"><span class="lineNum">    1191 </span>            : </a>
+<a name="1192"><span class="lineNum">    1192 </span>            :         if(ringInfo[q].numAtoms==6) {</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :           // update forces on ring atoms</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :           for(unsigned at=0; at&lt;6; at++) {</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :             const Vector ab = crossProduct(d,ringInfo[q].g[at]);</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :             const Vector c  = crossProduct(n,ringInfo[q].g[at]);</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :             const Vector factor3 = 0.5*dL_nL*c;</a>
+<a name="1198"><span class="lineNum">    1198 </span>            :             const Vector factor1 = 0.5*ab;</a>
+<a name="1199"><span class="lineNum">    1199 </span>            :             const Vector gradU   = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :             cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :             cs_atoms[kdx+at+atom_counter] = ringInfo[q].atom[at];</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :           }</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :           atom_counter += 6;</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :         }  else {</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :           for(unsigned at=0; at&lt;3; at++) {</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :             const Vector ab = crossProduct(d,ringInfo[q].g[at]);</a>
+<a name="1207"><span class="lineNum">    1207 </span>            :             const Vector c  = crossProduct(n,ringInfo[q].g[at]);</a>
+<a name="1208"><span class="lineNum">    1208 </span>            :             const Vector factor3 = dL_nL*c;</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :             const Vector factor1 = ab;</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :             const Vector gradU   = fU*( dLnL*(factor1 - factor2) -dn*(factor3 - factor4) );</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :             cs_derivs[kdx+at+atom_counter] = fact*(gradU - gradV);</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :           }</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :           cs_atoms[kdx+atom_counter] = ringInfo[q].atom[0];</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :           cs_atoms[kdx+atom_counter+1] = ringInfo[q].atom[2];</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :           cs_atoms[kdx+atom_counter+2] = ringInfo[q].atom[3];</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :           atom_counter += 3;</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :         }</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :       }</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :       //END OF RINGS</a>
+<a name="1220"><span class="lineNum">    1220 </span>            : </a>
+<a name="1221"><span class="lineNum">    1221 </span>            :       //NON BOND</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :       const double * CONST_CO_SPHERE3 = db.CO_SPHERE(aa_kind,at_kind,0);</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :       const double * CONST_CO_SPHERE  = db.CO_SPHERE(aa_kind,at_kind,1);</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :       const unsigned boxsize = myfrag-&gt;box_nb.size();</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :       for(unsigned q=0; q&lt;boxsize; q++) {</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :         const unsigned jpos = myfrag-&gt;box_nb[q];</a>
+<a name="1227"><span class="lineNum">    1227 </span>            :         const Vector distance = delta(getPosition(jpos),getPosition(ipos));</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :         const double d2 = distance.modulo2();</a>
+<a name="1229"><span class="lineNum">    1229 </span>            : </a>
+<a name="1230"><span class="lineNum">    1230 </span>            :         if(d2&lt;cutOffDist2) {</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :           double factor1  = std::sqrt(d2);</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :           double dfactor1 = 1./factor1;</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :           double factor3  = dfactor1*dfactor1*dfactor1;</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :           double dfactor3 = -3.*factor3*dfactor1*dfactor1;</a>
+<a name="1235"><span class="lineNum">    1235 </span>            : </a>
+<a name="1236"><span class="lineNum">    1236 </span>            :           if(d2&gt;cutOnDist2) {</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :             const double af = cutOffDist2 - d2;</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :             const double bf = cutOffDist2 - 3.*cutOnDist2 + 2.*d2;</a>
+<a name="1239"><span class="lineNum">    1239 </span>            :             const double cf = invswitch*af;</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :             const double df = cf*af*bf;</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :             factor1 *= df;</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :             factor3 *= df;</a>
+<a name="1243"><span class="lineNum">    1243 </span>            : </a>
+<a name="1244"><span class="lineNum">    1244 </span>            :             const double d4  = d2*d2;</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :             const double af1 = 15.*cutOnDist2*d2;</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :             const double bf1 = -14.*d4;</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :             const double cf1 = -3.*cutOffDist2*cutOnDist2 + cutOffDist2*d2;</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :             const double df1 = af1+bf1+cf1;</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :             dfactor1 *= cf*(cutOffDist4+df1);</a>
+<a name="1250"><span class="lineNum">    1250 </span>            : </a>
+<a name="1251"><span class="lineNum">    1251 </span>            :             const double af3 = +2.*cutOffDist2*cutOnDist2;</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :             const double bf3 = d2*(cutOffDist2+cutOnDist2);</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :             const double cf3 = -2.*d4;</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :             const double df3 = (af3+bf3+cf3)*d2;</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :             dfactor3 *= invswitch*(cutMixed+df3);</a>
+<a name="1256"><span class="lineNum">    1256 </span>            :           }</a>
+<a name="1257"><span class="lineNum">    1257 </span>            : </a>
+<a name="1258"><span class="lineNum">    1258 </span>            :           const unsigned t = type[jpos];</a>
+<a name="1259"><span class="lineNum">    1259 </span>            :           shift += factor1*CONST_CO_SPHERE[t] + factor3*CONST_CO_SPHERE3[t] ;</a>
+<a name="1260"><span class="lineNum">    1260 </span>            :           const double fact = dfactor1*CONST_CO_SPHERE[t]+dfactor3*CONST_CO_SPHERE3[t];</a>
+<a name="1261"><span class="lineNum">    1261 </span>            :           const Vector der  = fact*distance;</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span>            :           cs_derivs[kdx+0] += der;</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :           cs_derivs[kdx+q+atom_counter] = -der;</a>
+<a name="1265"><span class="lineNum">    1265 </span>            :           cs_atoms[kdx+q+atom_counter] = jpos;</a>
+<a name="1266"><span class="lineNum">    1266 </span>            :         }</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :       }</a>
+<a name="1268"><span class="lineNum">    1268 </span>            :       //END NON BOND</a>
+<a name="1269"><span class="lineNum">    1269 </span>            : </a>
+<a name="1270"><span class="lineNum">    1270 </span>            :       atom_counter += boxsize;</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :       all_shifts[cs] = shift;</a>
+<a name="1272"><span class="lineNum">    1272 </span>            :     }</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   }</a>
+<a name="1274"><span class="lineNum">    1274 </span>            : </a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">         18 :   ++box_count;</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">         18 :   if(box_count == box_nupdate) box_count = 0;</span></a>
+<a name="1277"><span class="lineNum">    1277 </span>            : </a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">         18 :   if(!camshift) {</span></a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">         13 :     if(!serial) {</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">         13 :       if(!getDoScore()) {</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">          9 :         comm.Sum(&amp;cs_derivs[0][0], 3*cs_derivs.size());</span></a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineCov">          9 :         comm.Sum(&amp;cs_atoms[0], cs_atoms.size());</span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            :       }</a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">         13 :       comm.Sum(&amp;all_shifts[0], chemicalshifts.size());</span></a>
+<a name="1285"><span class="lineNum">    1285 </span>            :     }</a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineCov">       7670 :     for(unsigned cs=0; cs&lt;chemicalshifts.size(); cs++) {</span></a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineCov">       7657 :       Value *comp = chemicalshifts[cs].comp;</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">       7657 :       comp-&gt;set(all_shifts[cs]);</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineCov">       7657 :       if(getDoScore()) setCalcData(cs, all_shifts[cs]);</span></a>
+<a name="1290"><span class="lineNum">    1290 </span>            :       else {</a>
+<a name="1291"><span class="lineNum">    1291 </span><span class="lineCov">       5301 :         const unsigned kdx=cs*max_cs_atoms;</span></a>
+<a name="1292"><span class="lineNum">    1292 </span><span class="lineCov">       5301 :         Tensor csvirial;</span></a>
+<a name="1293"><span class="lineNum">    1293 </span><span class="lineCov">    1270127 :         for(unsigned i=0; i&lt;chemicalshifts[cs].totcsatoms; i++) {</span></a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineCov">    1264826 :           setAtomsDerivatives(comp,cs_atoms[kdx+i],cs_derivs[kdx+i]);</span></a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineCov">    1264826 :           csvirial-=Tensor(getPosition(cs_atoms[kdx+i]),cs_derivs[kdx+i]);</span></a>
+<a name="1296"><span class="lineNum">    1296 </span>            :         }</a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineCov">       5301 :         setBoxDerivatives(comp,csvirial);</span></a>
+<a name="1298"><span class="lineNum">    1298 </span>            :       }</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :     }</a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">         13 :     if(!getDoScore()) return;</span></a>
+<a name="1301"><span class="lineNum">    1301 </span>            :   }</a>
+<a name="1302"><span class="lineNum">    1302 </span>            : </a>
+<a name="1303"><span class="lineNum">    1303 </span><span class="lineCov">          9 :   double score = 0.;</span></a>
+<a name="1304"><span class="lineNum">    1304 </span>            : </a>
+<a name="1305"><span class="lineNum">    1305 </span>            :   /* Metainference */</a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">          9 :   if(getDoScore()) {</span></a>
+<a name="1307"><span class="lineNum">    1307 </span><span class="lineCov">          4 :     score = getScore();</span></a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">       1182 :     for(unsigned cs=rank; cs&lt;chemicalshifts.size(); cs+=stride) {</span></a>
+<a name="1309"><span class="lineNum">    1309 </span><span class="lineCov">       1178 :       const unsigned kdx=cs*max_cs_atoms;</span></a>
+<a name="1310"><span class="lineNum">    1310 </span>            :       const double fact = getMetaDer(cs);</a>
+<a name="1311"><span class="lineNum">    1311 </span><span class="lineCov">     282215 :       for(unsigned i=0; i&lt;chemicalshifts[cs].totcsatoms; i++) {</span></a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">     281037 :         aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;</span></a>
+<a name="1313"><span class="lineNum">    1313 </span>            :       }</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :     }</a>
+<a name="1315"><span class="lineNum">    1315 </span>            :   }</a>
+<a name="1316"><span class="lineNum">    1316 </span>            : </a>
+<a name="1317"><span class="lineNum">    1317 </span>            :   /* camshift */</a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineCov">          9 :   if(camshift) {</span></a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">       1772 :     for(unsigned cs=rank; cs&lt;chemicalshifts.size(); cs+=stride) {</span></a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">       1767 :       const unsigned kdx=cs*max_cs_atoms;</span></a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">       1767 :       score += (all_shifts[cs] - chemicalshifts[cs].exp_cs)*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];</span></a>
+<a name="1322"><span class="lineNum">    1322 </span><span class="lineCov">       1767 :       double fact = 2.0*(all_shifts[cs] - chemicalshifts[cs].exp_cs)/camshift_sigma2[chemicalshifts[cs].atm_kind];</span></a>
+<a name="1323"><span class="lineNum">    1323 </span><span class="lineCov">     423482 :       for(unsigned i=0; i&lt;chemicalshifts[cs].totcsatoms; i++) {</span></a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">     421715 :         aa_derivs[cs_atoms[kdx+i]] += cs_derivs[kdx+i]*fact;</span></a>
+<a name="1325"><span class="lineNum">    1325 </span>            :       }</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :     }</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   }</a>
+<a name="1328"><span class="lineNum">    1328 </span>            : </a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineCov">          9 :   if(!serial) {</span></a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">          9 :     comm.Sum(&amp;aa_derivs[0][0], 3*aa_derivs.size());</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineCov">          9 :     if(camshift) comm.Sum(&amp;score, 1);</span></a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   }</a>
+<a name="1333"><span class="lineNum">    1333 </span>            : </a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">          9 :   Tensor virial;</span></a>
+<a name="1335"><span class="lineNum">    1335 </span><span class="lineCov">      13069 :   for(unsigned i=rank; i&lt;getNumberOfAtoms(); i+=stride) {</span></a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineCov">      13060 :     virial += Tensor(getPosition(i), aa_derivs[i]);</span></a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   }</a>
+<a name="1338"><span class="lineNum">    1338 </span>            : </a>
+<a name="1339"><span class="lineNum">    1339 </span><span class="lineCov">          9 :   if(!serial) {</span></a>
+<a name="1340"><span class="lineNum">    1340 </span><span class="lineCov">          9 :     comm.Sum(&amp;virial[0][0], 9);</span></a>
+<a name="1341"><span class="lineNum">    1341 </span>            :   }</a>
+<a name="1342"><span class="lineNum">    1342 </span>            : </a>
+<a name="1343"><span class="lineNum">    1343 </span>            :   /* calculate final derivatives */</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :   Value* val;</a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineCov">          9 :   if(getDoScore()) {</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineCov">          4 :     val=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">          4 :     setScore(score);</span></a>
+<a name="1348"><span class="lineNum">    1348 </span>            :   } else {</a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineCov">          5 :     val=getPntrToValue();</span></a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineCov">          5 :     setValue(score);</span></a>
+<a name="1351"><span class="lineNum">    1351 </span>            :   }</a>
+<a name="1352"><span class="lineNum">    1352 </span>            : </a>
+<a name="1353"><span class="lineNum">    1353 </span>            :   /* at this point we cycle over all atoms */</a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineCov">      23517 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) setAtomsDerivatives(val, i,  aa_derivs[i]);</span></a>
+<a name="1355"><span class="lineNum">    1355 </span><span class="lineCov">          9 :   setBoxDerivatives(val,-virial);</span></a>
+<a name="1356"><span class="lineNum">    1356 </span>            : }</a>
+<a name="1357"><span class="lineNum">    1357 </span>            : </a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineCov">         18 : void CS2Backbone::update_neighb() {</span></a>
+<a name="1359"><span class="lineNum">    1359 </span>            :   // cycle over chemical shifts</a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineCov">         18 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineCov">         18 :   #pragma omp parallel for num_threads(nt)</span></a>
+<a name="1362"><span class="lineNum">    1362 </span>            :   for(unsigned cs=0; cs&lt;chemicalshifts.size(); cs++) {</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :     const unsigned boxsize = getNumberOfAtoms();</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :     chemicalshifts[cs].box_nb.clear();</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :     chemicalshifts[cs].box_nb.reserve(150);</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :     const unsigned res_curr = res_num[chemicalshifts[cs].ipos];</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :     for(unsigned bat=0; bat&lt;boxsize; bat++) {</a>
+<a name="1368"><span class="lineNum">    1368 </span>            :       const unsigned res_dist = std::abs(static_cast&lt;int&gt;(res_curr-res_num[bat]));</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :       if(res_dist&lt;2) continue;</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :       const Vector distance = delta(getPosition(bat),getPosition(chemicalshifts[cs].ipos));</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :       const double d2=distance.modulo2();</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :       if(d2&lt;cutOffNB2) chemicalshifts[cs].box_nb.push_back(bat);</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :     }</a>
+<a name="1374"><span class="lineNum">    1374 </span>            :     chemicalshifts[cs].totcsatoms = chemicalshifts[cs].csatoms + chemicalshifts[cs].box_nb.size();</a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   }</a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineCov">         18 :   max_cs_atoms=0;</span></a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">      10620 :   for(unsigned cs=0; cs&lt;chemicalshifts.size(); cs++) {</span></a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineCov">      10602 :     if(chemicalshifts[cs].totcsatoms&gt;max_cs_atoms) max_cs_atoms = chemicalshifts[cs].totcsatoms;</span></a>
+<a name="1379"><span class="lineNum">    1379 </span>            :   }</a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">         18 : }</span></a>
+<a name="1381"><span class="lineNum">    1381 </span>            : </a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineCov">         18 : void CS2Backbone::compute_ring_parameters() {</span></a>
+<a name="1383"><span class="lineNum">    1383 </span><span class="lineCov">        378 :   for(unsigned i=0; i&lt;ringInfo.size(); i++) {</span></a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineCov">        360 :     const unsigned size = ringInfo[i].numAtoms;</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineCov">        360 :     if(size==6) {</span></a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineCov">        342 :       ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[4]),getPosition(ringInfo[i].atom[2]));</span></a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineCov">        342 :       ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[5]),getPosition(ringInfo[i].atom[3]));</span></a>
+<a name="1388"><span class="lineNum">    1388 </span><span class="lineCov">        342 :       ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[4]));</span></a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineCov">        342 :       ringInfo[i].g[3] = delta(getPosition(ringInfo[i].atom[1]),getPosition(ringInfo[i].atom[5]));</span></a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineCov">        342 :       ringInfo[i].g[4] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));</span></a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineCov">        342 :       ringInfo[i].g[5] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[1]));</span></a>
+<a name="1392"><span class="lineNum">    1392 </span>            :       // ring center</a>
+<a name="1393"><span class="lineNum">    1393 </span><span class="lineCov">        342 :       Vector midP = getPosition(ringInfo[i].atom[0]);</span></a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineCov">       2052 :       for(unsigned j=1; j&lt;size; j++) midP += getPosition(ringInfo[i].atom[j]);</span></a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineCov">        342 :       ringInfo[i].position = midP/6.;</span></a>
+<a name="1396"><span class="lineNum">    1396 </span>            :       // compute normal std::vector to plane</a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">        342 :       Vector n1 = crossProduct(ringInfo[i].g[2], -ringInfo[i].g[4]);</span></a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineCov">        342 :       Vector n2 = crossProduct(ringInfo[i].g[5], -ringInfo[i].g[1]);</span></a>
+<a name="1399"><span class="lineNum">    1399 </span><span class="lineCov">        342 :       ringInfo[i].normVect = 0.5*(n1 + n2);</span></a>
+<a name="1400"><span class="lineNum">    1400 </span>            :     }  else {</a>
+<a name="1401"><span class="lineNum">    1401 </span><span class="lineCov">         18 :       ringInfo[i].g[0] = delta(getPosition(ringInfo[i].atom[3]),getPosition(ringInfo[i].atom[2]));</span></a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">         18 :       ringInfo[i].g[1] = delta(getPosition(ringInfo[i].atom[0]),getPosition(ringInfo[i].atom[3]));</span></a>
+<a name="1403"><span class="lineNum">    1403 </span><span class="lineCov">         18 :       ringInfo[i].g[2] = delta(getPosition(ringInfo[i].atom[2]),getPosition(ringInfo[i].atom[0]));</span></a>
+<a name="1404"><span class="lineNum">    1404 </span>            :       // ring center</a>
+<a name="1405"><span class="lineNum">    1405 </span><span class="lineCov">         18 :       ringInfo[i].position = (getPosition(ringInfo[i].atom[0])+getPosition(ringInfo[i].atom[2])+getPosition(ringInfo[i].atom[3]))/3.;</span></a>
+<a name="1406"><span class="lineNum">    1406 </span>            :       // ring plane normal std::vector</a>
+<a name="1407"><span class="lineNum">    1407 </span><span class="lineCov">         18 :       ringInfo[i].normVect = crossProduct(ringInfo[i].g[1],-ringInfo[i].g[2]);</span></a>
+<a name="1408"><span class="lineNum">    1408 </span>            : </a>
+<a name="1409"><span class="lineNum">    1409 </span>            :     }</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :     // calculate squared length and length of normal std::vector</a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineCov">        360 :     ringInfo[i].lengthN2 = 1./ringInfo[i].normVect.modulo2();</span></a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">        360 :     ringInfo[i].lengthNV = 1./std::sqrt(ringInfo[i].lengthN2);</span></a>
+<a name="1413"><span class="lineNum">    1413 </span>            :   }</a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineCov">         18 : }</span></a>
+<a name="1415"><span class="lineNum">    1415 </span>            : </a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineCov">      31806 : CS2Backbone::aa_t CS2Backbone::frag2enum(const std::string &amp;aa) {</span></a>
+<a name="1417"><span class="lineNum">    1417 </span>            :   aa_t type = ALA;</a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineCov">      31806 :   if (aa == &quot;ALA&quot;) type = ALA;</span></a>
+<a name="1419"><span class="lineNum">    1419 </span><span class="lineCov">      29934 :   else if (aa == &quot;ARG&quot;) type = ARG;</span></a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineCov">      28548 :   else if (aa == &quot;ASN&quot;) type = ASN;</span></a>
+<a name="1421"><span class="lineNum">    1421 </span><span class="lineCov">      26910 :   else if (aa == &quot;ASP&quot;) type = ASP;</span></a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineCov">      25380 :   else if (aa == &quot;ASH&quot;) type = ASP;</span></a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineCov">      25380 :   else if (aa == &quot;CYS&quot;) type = CYS;</span></a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineCov">      24858 :   else if (aa == &quot;CYM&quot;) type = CYS;</span></a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineCov">      24858 :   else if (aa == &quot;GLN&quot;) type = GLN;</span></a>
+<a name="1426"><span class="lineNum">    1426 </span><span class="lineCov">      24390 :   else if (aa == &quot;GLU&quot;) type = GLU;</span></a>
+<a name="1427"><span class="lineNum">    1427 </span><span class="lineCov">      22068 :   else if (aa == &quot;GLH&quot;) type = GLU;</span></a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineCov">      22068 :   else if (aa == &quot;GLY&quot;) type = GLY;</span></a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineCov">      16974 :   else if (aa == &quot;HIS&quot;) type = HIS;</span></a>
+<a name="1430"><span class="lineNum">    1430 </span><span class="lineCov">      16974 :   else if (aa == &quot;HSE&quot;) type = HIS;</span></a>
+<a name="1431"><span class="lineNum">    1431 </span><span class="lineCov">      16974 :   else if (aa == &quot;HIE&quot;) type = HIS;</span></a>
+<a name="1432"><span class="lineNum">    1432 </span><span class="lineCov">      16974 :   else if (aa == &quot;HSP&quot;) type = HIS;</span></a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineCov">      16974 :   else if (aa == &quot;HIP&quot;) type = HIS;</span></a>
+<a name="1434"><span class="lineNum">    1434 </span><span class="lineCov">      16974 :   else if (aa == &quot;HSD&quot;) type = HIS;</span></a>
+<a name="1435"><span class="lineNum">    1435 </span><span class="lineCov">      16974 :   else if (aa == &quot;HID&quot;) type = HIS;</span></a>
+<a name="1436"><span class="lineNum">    1436 </span><span class="lineCov">      16974 :   else if (aa == &quot;ILE&quot;) type = ILE;</span></a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">      15174 :   else if (aa == &quot;LEU&quot;) type = LEU;</span></a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineCov">      13536 :   else if (aa == &quot;LYS&quot;) type = LYS;</span></a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineCov">      10746 :   else if (aa == &quot;MET&quot;) type = MET;</span></a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineCov">       9936 :   else if (aa == &quot;PHE&quot;) type = PHE;</span></a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineCov">       6876 :   else if (aa == &quot;PRO&quot;) type = PRO;</span></a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineCov">       5940 :   else if (aa == &quot;SER&quot;) type = SER;</span></a>
+<a name="1443"><span class="lineNum">    1443 </span><span class="lineCov">       4302 :   else if (aa == &quot;THR&quot;) type = THR;</span></a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineCov">       2196 :   else if (aa == &quot;TRP&quot;) type = TRP;</span></a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineCov">       1980 :   else if (aa == &quot;TYR&quot;) type = TYR;</span></a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineCov">       1602 :   else if (aa == &quot;VAL&quot;) type = VAL;</span></a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineNoCov">          0 :   else if (aa == &quot;UNK&quot;) type = UNK;</span></a>
+<a name="1448"><span class="lineNum">    1448 </span><span class="lineNoCov">          0 :   else plumed_merror(&quot;Error converting std::string &quot; + aa + &quot; into amino acid index: not a valid 3-letter code&quot;);</span></a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineCov">      31806 :   return type;</span></a>
+<a name="1450"><span class="lineNum">    1450 </span>            : }</a>
+<a name="1451"><span class="lineNum">    1451 </span>            : </a>
+<a name="1452"><span class="lineNum">    1452 </span><span class="lineCov">      10602 : std::vector&lt;std::string&gt; CS2Backbone::side_chain_atoms(const std::string &amp;s) {</span></a>
+<a name="1453"><span class="lineNum">    1453 </span>            :   std::vector&lt;std::string&gt; sc;</a>
+<a name="1454"><span class="lineNum">    1454 </span>            : </a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineCov">      10602 :   if(s==&quot;ALA&quot;) {</span></a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineCov">        648 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineCov">        648 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineCov">        648 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineCov">        648 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineCov">        648 :     return sc;</span></a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineCov">       9954 :   } else if(s==&quot;ARG&quot;) {</span></a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">        468 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1463"><span class="lineNum">    1463 </span><span class="lineCov">        468 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineCov">        468 :     sc.push_back( &quot;CD&quot; );</span></a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineCov">        468 :     sc.push_back( &quot;NE&quot; );</span></a>
+<a name="1466"><span class="lineNum">    1466 </span><span class="lineCov">        468 :     sc.push_back( &quot;CZ&quot; );</span></a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">        468 :     sc.push_back( &quot;NH1&quot; );</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineCov">        468 :     sc.push_back( &quot;NH2&quot; );</span></a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineCov">        468 :     sc.push_back( &quot;NH3&quot; );</span></a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineCov">        468 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineCov">        468 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineCov">        468 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1473"><span class="lineNum">    1473 </span><span class="lineCov">        468 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineCov">        468 :     sc.push_back( &quot;HG2&quot; );</span></a>
+<a name="1475"><span class="lineNum">    1475 </span><span class="lineCov">        468 :     sc.push_back( &quot;HG3&quot; );</span></a>
+<a name="1476"><span class="lineNum">    1476 </span><span class="lineCov">        468 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">        468 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineCov">        468 :     sc.push_back( &quot;HD3&quot; );</span></a>
+<a name="1479"><span class="lineNum">    1479 </span><span class="lineCov">        468 :     sc.push_back( &quot;HE&quot; );</span></a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">        468 :     sc.push_back( &quot;HH11&quot; );</span></a>
+<a name="1481"><span class="lineNum">    1481 </span><span class="lineCov">        468 :     sc.push_back( &quot;HH12&quot; );</span></a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineCov">        468 :     sc.push_back( &quot;HH21&quot; );</span></a>
+<a name="1483"><span class="lineNum">    1483 </span><span class="lineCov">        468 :     sc.push_back( &quot;HH22&quot; );</span></a>
+<a name="1484"><span class="lineNum">    1484 </span><span class="lineCov">        468 :     sc.push_back( &quot;1HH1&quot; );</span></a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineCov">        468 :     sc.push_back( &quot;2HH1&quot; );</span></a>
+<a name="1486"><span class="lineNum">    1486 </span><span class="lineCov">        468 :     sc.push_back( &quot;1HH2&quot; );</span></a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineCov">        468 :     sc.push_back( &quot;2HH2&quot; );</span></a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineCov">        468 :     return sc;</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineCov">       9486 :   } else if(s==&quot;ASN&quot;) {</span></a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineCov">        594 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1491"><span class="lineNum">    1491 </span><span class="lineCov">        594 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1492"><span class="lineNum">    1492 </span><span class="lineCov">        594 :     sc.push_back( &quot;OD1&quot; );</span></a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineCov">        594 :     sc.push_back( &quot;ND2&quot; );</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineCov">        594 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1495"><span class="lineNum">    1495 </span><span class="lineCov">        594 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1496"><span class="lineNum">    1496 </span><span class="lineCov">        594 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineCov">        594 :     sc.push_back( &quot;HD21&quot; );</span></a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineCov">        594 :     sc.push_back( &quot;HD22&quot; );</span></a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineCov">        594 :     sc.push_back( &quot;1HD2&quot; );</span></a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineCov">        594 :     sc.push_back( &quot;2HD2&quot; );</span></a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineCov">        594 :     return sc;</span></a>
+<a name="1502"><span class="lineNum">    1502 </span><span class="lineCov">      17226 :   } else if(s==&quot;ASP&quot;||s==&quot;ASH&quot;) {</span></a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineCov">        558 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineCov">        558 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineCov">        558 :     sc.push_back( &quot;OD1&quot; );</span></a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineCov">        558 :     sc.push_back( &quot;OD2&quot; );</span></a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineCov">        558 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineCov">        558 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1509"><span class="lineNum">    1509 </span><span class="lineCov">        558 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineCov">        558 :     return sc;</span></a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineCov">      16668 :   } else if(s==&quot;CYS&quot;||s==&quot;CYM&quot;) {</span></a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1513"><span class="lineNum">    1513 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;SG&quot; );</span></a>
+<a name="1514"><span class="lineNum">    1514 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1515"><span class="lineNum">    1515 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1517"><span class="lineNum">    1517 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HG&quot; );</span></a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineNoCov">          0 :     return sc;</span></a>
+<a name="1520"><span class="lineNum">    1520 </span><span class="lineCov">       8334 :   } else if(s==&quot;GLN&quot;) {</span></a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineCov">        162 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineCov">        162 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1523"><span class="lineNum">    1523 </span><span class="lineCov">        162 :     sc.push_back( &quot;CD&quot; );</span></a>
+<a name="1524"><span class="lineNum">    1524 </span><span class="lineCov">        162 :     sc.push_back( &quot;OE1&quot; );</span></a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineCov">        162 :     sc.push_back( &quot;NE2&quot; );</span></a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineCov">        162 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineCov">        162 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1528"><span class="lineNum">    1528 </span><span class="lineCov">        162 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">        162 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1530"><span class="lineNum">    1530 </span><span class="lineCov">        162 :     sc.push_back( &quot;HG2&quot; );</span></a>
+<a name="1531"><span class="lineNum">    1531 </span><span class="lineCov">        162 :     sc.push_back( &quot;HG3&quot; );</span></a>
+<a name="1532"><span class="lineNum">    1532 </span><span class="lineCov">        162 :     sc.push_back( &quot;HE21&quot; );</span></a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineCov">        162 :     sc.push_back( &quot;HE22&quot; );</span></a>
+<a name="1534"><span class="lineNum">    1534 </span><span class="lineCov">        162 :     sc.push_back( &quot;1HE2&quot; );</span></a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineCov">        162 :     sc.push_back( &quot;2HE2&quot; );</span></a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineCov">        162 :     return sc;</span></a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineCov">      15552 :   } else if(s==&quot;GLU&quot;||s==&quot;GLH&quot;) {</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">        792 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineCov">        792 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineCov">        792 :     sc.push_back( &quot;CD&quot; );</span></a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineCov">        792 :     sc.push_back( &quot;OE1&quot; );</span></a>
+<a name="1542"><span class="lineNum">    1542 </span><span class="lineCov">        792 :     sc.push_back( &quot;OE2&quot; );</span></a>
+<a name="1543"><span class="lineNum">    1543 </span><span class="lineCov">        792 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineCov">        792 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineCov">        792 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineCov">        792 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineCov">        792 :     sc.push_back( &quot;HG2&quot; );</span></a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineCov">        792 :     sc.push_back( &quot;HG3&quot; );</span></a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineCov">        792 :     return sc;</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">       7380 :   } else if(s==&quot;GLY&quot;) {</span></a>
+<a name="1551"><span class="lineNum">    1551 </span><span class="lineCov">       1494 :     sc.push_back( &quot;HA2&quot; );</span></a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineCov">       1494 :     return sc;</span></a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineCov">      41202 :   } else if(s==&quot;HIS&quot;||s==&quot;HSE&quot;||s==&quot;HIE&quot;||s==&quot;HSD&quot;||s==&quot;HID&quot;||s==&quot;HIP&quot;||s==&quot;HSP&quot;) {</span></a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;ND1&quot; );</span></a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;CD2&quot; );</span></a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;CE1&quot; );</span></a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;NE2&quot; );</span></a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1561"><span class="lineNum">    1561 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HE1&quot; );</span></a>
+<a name="1566"><span class="lineNum">    1566 </span><span class="lineNoCov">          0 :     sc.push_back( &quot;HE2&quot; );</span></a>
+<a name="1567"><span class="lineNum">    1567 </span><span class="lineNoCov">          0 :     return sc;</span></a>
+<a name="1568"><span class="lineNum">    1568 </span><span class="lineCov">       5886 :   } else if(s==&quot;ILE&quot;) {</span></a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineCov">        540 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineCov">        540 :     sc.push_back( &quot;CG1&quot; );</span></a>
+<a name="1571"><span class="lineNum">    1571 </span><span class="lineCov">        540 :     sc.push_back( &quot;CG2&quot; );</span></a>
+<a name="1572"><span class="lineNum">    1572 </span><span class="lineCov">        540 :     sc.push_back( &quot;CD&quot; );</span></a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineCov">        540 :     sc.push_back( &quot;HB&quot; );</span></a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineCov">        540 :     sc.push_back( &quot;HG11&quot; );</span></a>
+<a name="1575"><span class="lineNum">    1575 </span><span class="lineCov">        540 :     sc.push_back( &quot;HG12&quot; );</span></a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineCov">        540 :     sc.push_back( &quot;HG21&quot; );</span></a>
+<a name="1577"><span class="lineNum">    1577 </span><span class="lineCov">        540 :     sc.push_back( &quot;HG22&quot; );</span></a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineCov">        540 :     sc.push_back( &quot;HG23&quot; );</span></a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineCov">        540 :     sc.push_back( &quot;1HG1&quot; );</span></a>
+<a name="1580"><span class="lineNum">    1580 </span><span class="lineCov">        540 :     sc.push_back( &quot;2HG1&quot; );</span></a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineCov">        540 :     sc.push_back( &quot;1HG2&quot; );</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineCov">        540 :     sc.push_back( &quot;2HG2&quot; );</span></a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineCov">        540 :     sc.push_back( &quot;3HG2&quot; );</span></a>
+<a name="1584"><span class="lineNum">    1584 </span><span class="lineCov">        540 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineCov">        540 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineCov">        540 :     sc.push_back( &quot;HD3&quot; );</span></a>
+<a name="1587"><span class="lineNum">    1587 </span><span class="lineCov">        540 :     return sc;</span></a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineCov">       5346 :   } else if(s==&quot;LEU&quot;) {</span></a>
+<a name="1589"><span class="lineNum">    1589 </span><span class="lineCov">        648 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineCov">        648 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineCov">        648 :     sc.push_back( &quot;CD1&quot; );</span></a>
+<a name="1592"><span class="lineNum">    1592 </span><span class="lineCov">        648 :     sc.push_back( &quot;CD2&quot; );</span></a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineCov">        648 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1594"><span class="lineNum">    1594 </span><span class="lineCov">        648 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1595"><span class="lineNum">    1595 </span><span class="lineCov">        648 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1596"><span class="lineNum">    1596 </span><span class="lineCov">        648 :     sc.push_back( &quot;HG&quot; );</span></a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineCov">        648 :     sc.push_back( &quot;HD11&quot; );</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineCov">        648 :     sc.push_back( &quot;HD12&quot; );</span></a>
+<a name="1599"><span class="lineNum">    1599 </span><span class="lineCov">        648 :     sc.push_back( &quot;HD13&quot; );</span></a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineCov">        648 :     sc.push_back( &quot;HD21&quot; );</span></a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineCov">        648 :     sc.push_back( &quot;HD22&quot; );</span></a>
+<a name="1602"><span class="lineNum">    1602 </span><span class="lineCov">        648 :     sc.push_back( &quot;HD23&quot; );</span></a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineCov">        648 :     sc.push_back( &quot;1HD1&quot; );</span></a>
+<a name="1604"><span class="lineNum">    1604 </span><span class="lineCov">        648 :     sc.push_back( &quot;2HD1&quot; );</span></a>
+<a name="1605"><span class="lineNum">    1605 </span><span class="lineCov">        648 :     sc.push_back( &quot;3HD1&quot; );</span></a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">        648 :     sc.push_back( &quot;1HD2&quot; );</span></a>
+<a name="1607"><span class="lineNum">    1607 </span><span class="lineCov">        648 :     sc.push_back( &quot;2HD2&quot; );</span></a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineCov">        648 :     sc.push_back( &quot;3HD2&quot; );</span></a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineCov">        648 :     return sc;</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineCov">       4698 :   } else if(s==&quot;LYS&quot;) {</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineCov">       1008 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1612"><span class="lineNum">    1612 </span><span class="lineCov">       1008 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1613"><span class="lineNum">    1613 </span><span class="lineCov">       1008 :     sc.push_back( &quot;CD&quot; );</span></a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineCov">       1008 :     sc.push_back( &quot;CE&quot; );</span></a>
+<a name="1615"><span class="lineNum">    1615 </span><span class="lineCov">       1008 :     sc.push_back( &quot;NZ&quot; );</span></a>
+<a name="1616"><span class="lineNum">    1616 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1617"><span class="lineNum">    1617 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1618"><span class="lineNum">    1618 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HG2&quot; );</span></a>
+<a name="1621"><span class="lineNum">    1621 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HG3&quot; );</span></a>
+<a name="1622"><span class="lineNum">    1622 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1623"><span class="lineNum">    1623 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HD3&quot; );</span></a>
+<a name="1625"><span class="lineNum">    1625 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HE1&quot; );</span></a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HE2&quot; );</span></a>
+<a name="1627"><span class="lineNum">    1627 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HE3&quot; );</span></a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HZ1&quot; );</span></a>
+<a name="1629"><span class="lineNum">    1629 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HZ2&quot; );</span></a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineCov">       1008 :     sc.push_back( &quot;HZ3&quot; );</span></a>
+<a name="1631"><span class="lineNum">    1631 </span><span class="lineCov">       1008 :     return sc;</span></a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineCov">       3690 :   } else if(s==&quot;MET&quot;) {</span></a>
+<a name="1633"><span class="lineNum">    1633 </span><span class="lineCov">        288 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1634"><span class="lineNum">    1634 </span><span class="lineCov">        288 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1635"><span class="lineNum">    1635 </span><span class="lineCov">        288 :     sc.push_back( &quot;SD&quot; );</span></a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineCov">        288 :     sc.push_back( &quot;CE&quot; );</span></a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineCov">        288 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1638"><span class="lineNum">    1638 </span><span class="lineCov">        288 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineCov">        288 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1640"><span class="lineNum">    1640 </span><span class="lineCov">        288 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1641"><span class="lineNum">    1641 </span><span class="lineCov">        288 :     sc.push_back( &quot;HG2&quot; );</span></a>
+<a name="1642"><span class="lineNum">    1642 </span><span class="lineCov">        288 :     sc.push_back( &quot;HG3&quot; );</span></a>
+<a name="1643"><span class="lineNum">    1643 </span><span class="lineCov">        288 :     sc.push_back( &quot;HE1&quot; );</span></a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineCov">        288 :     sc.push_back( &quot;HE2&quot; );</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineCov">        288 :     sc.push_back( &quot;HE3&quot; );</span></a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineCov">        288 :     return sc;</span></a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineCov">       3402 :   } else if(s==&quot;PHE&quot;) {</span></a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CD1&quot; );</span></a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CD2&quot; );</span></a>
+<a name="1652"><span class="lineNum">    1652 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CE1&quot; );</span></a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CE2&quot; );</span></a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineCov">       1098 :     sc.push_back( &quot;CZ&quot; );</span></a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1658"><span class="lineNum">    1658 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HD3&quot; );</span></a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HE1&quot; );</span></a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HE2&quot; );</span></a>
+<a name="1663"><span class="lineNum">    1663 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HE3&quot; );</span></a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">       1098 :     sc.push_back( &quot;HZ&quot; );</span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">       1098 :     return sc;</span></a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineCov">       2304 :   } else if(s==&quot;PRO&quot;) {</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineCov">        108 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">        108 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineCov">        108 :     sc.push_back( &quot;CD&quot; );</span></a>
+<a name="1670"><span class="lineNum">    1670 </span><span class="lineCov">        108 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineCov">        108 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1672"><span class="lineNum">    1672 </span><span class="lineCov">        108 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1673"><span class="lineNum">    1673 </span><span class="lineCov">        108 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1674"><span class="lineNum">    1674 </span><span class="lineCov">        108 :     sc.push_back( &quot;HG2&quot; );</span></a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineCov">        108 :     sc.push_back( &quot;HG3&quot; );</span></a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineCov">        108 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineCov">        108 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1678"><span class="lineNum">    1678 </span><span class="lineCov">        108 :     sc.push_back( &quot;HD3&quot; );</span></a>
+<a name="1679"><span class="lineNum">    1679 </span><span class="lineCov">        108 :     return sc;</span></a>
+<a name="1680"><span class="lineNum">    1680 </span><span class="lineCov">       2196 :   } else if(s==&quot;SER&quot;) {</span></a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineCov">        630 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineCov">        630 :     sc.push_back( &quot;OG&quot; );</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineCov">        630 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineCov">        630 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineCov">        630 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineCov">        630 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineCov">        630 :     sc.push_back( &quot;HG&quot; );</span></a>
+<a name="1688"><span class="lineNum">    1688 </span><span class="lineCov">        630 :     return sc;</span></a>
+<a name="1689"><span class="lineNum">    1689 </span><span class="lineCov">       1566 :   } else if(s==&quot;THR&quot;) {</span></a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineCov">        774 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1691"><span class="lineNum">    1691 </span><span class="lineCov">        774 :     sc.push_back( &quot;OG1&quot; );</span></a>
+<a name="1692"><span class="lineNum">    1692 </span><span class="lineCov">        774 :     sc.push_back( &quot;CG2&quot; );</span></a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineCov">        774 :     sc.push_back( &quot;HB&quot; );</span></a>
+<a name="1694"><span class="lineNum">    1694 </span><span class="lineCov">        774 :     sc.push_back( &quot;HG1&quot; );</span></a>
+<a name="1695"><span class="lineNum">    1695 </span><span class="lineCov">        774 :     sc.push_back( &quot;HG21&quot; );</span></a>
+<a name="1696"><span class="lineNum">    1696 </span><span class="lineCov">        774 :     sc.push_back( &quot;HG22&quot; );</span></a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineCov">        774 :     sc.push_back( &quot;HG23&quot; );</span></a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineCov">        774 :     sc.push_back( &quot;1HG2&quot; );</span></a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineCov">        774 :     sc.push_back( &quot;2HG2&quot; );</span></a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineCov">        774 :     sc.push_back( &quot;3HG2&quot; );</span></a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineCov">        774 :     return sc;</span></a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineCov">        792 :   } else if(s==&quot;TRP&quot;) {</span></a>
+<a name="1703"><span class="lineNum">    1703 </span><span class="lineCov">         72 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineCov">         72 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineCov">         72 :     sc.push_back( &quot;CD1&quot; );</span></a>
+<a name="1706"><span class="lineNum">    1706 </span><span class="lineCov">         72 :     sc.push_back( &quot;CD2&quot; );</span></a>
+<a name="1707"><span class="lineNum">    1707 </span><span class="lineCov">         72 :     sc.push_back( &quot;NE1&quot; );</span></a>
+<a name="1708"><span class="lineNum">    1708 </span><span class="lineCov">         72 :     sc.push_back( &quot;CE2&quot; );</span></a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineCov">         72 :     sc.push_back( &quot;CE3&quot; );</span></a>
+<a name="1710"><span class="lineNum">    1710 </span><span class="lineCov">         72 :     sc.push_back( &quot;CZ2&quot; );</span></a>
+<a name="1711"><span class="lineNum">    1711 </span><span class="lineCov">         72 :     sc.push_back( &quot;CZ3&quot; );</span></a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineCov">         72 :     sc.push_back( &quot;CH2&quot; );</span></a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineCov">         72 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineCov">         72 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineCov">         72 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineCov">         72 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1717"><span class="lineNum">    1717 </span><span class="lineCov">         72 :     sc.push_back( &quot;HE1&quot; );</span></a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineCov">         72 :     sc.push_back( &quot;HE3&quot; );</span></a>
+<a name="1719"><span class="lineNum">    1719 </span><span class="lineCov">         72 :     sc.push_back( &quot;HZ2&quot; );</span></a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineCov">         72 :     sc.push_back( &quot;HZ3&quot; );</span></a>
+<a name="1721"><span class="lineNum">    1721 </span><span class="lineCov">         72 :     sc.push_back( &quot;HH2&quot; );</span></a>
+<a name="1722"><span class="lineNum">    1722 </span><span class="lineCov">         72 :     return sc;</span></a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineCov">        720 :   } else if(s==&quot;TYR&quot;) {</span></a>
+<a name="1724"><span class="lineNum">    1724 </span><span class="lineCov">        144 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineCov">        144 :     sc.push_back( &quot;CG&quot; );</span></a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineCov">        144 :     sc.push_back( &quot;CD1&quot; );</span></a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineCov">        144 :     sc.push_back( &quot;CD2&quot; );</span></a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineCov">        144 :     sc.push_back( &quot;CE1&quot; );</span></a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineCov">        144 :     sc.push_back( &quot;CE2&quot; );</span></a>
+<a name="1730"><span class="lineNum">    1730 </span><span class="lineCov">        144 :     sc.push_back( &quot;CZ&quot; );</span></a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineCov">        144 :     sc.push_back( &quot;OH&quot; );</span></a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineCov">        144 :     sc.push_back( &quot;HB1&quot; );</span></a>
+<a name="1733"><span class="lineNum">    1733 </span><span class="lineCov">        144 :     sc.push_back( &quot;HB2&quot; );</span></a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineCov">        144 :     sc.push_back( &quot;HB3&quot; );</span></a>
+<a name="1735"><span class="lineNum">    1735 </span><span class="lineCov">        144 :     sc.push_back( &quot;HD1&quot; );</span></a>
+<a name="1736"><span class="lineNum">    1736 </span><span class="lineCov">        144 :     sc.push_back( &quot;HD2&quot; );</span></a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineCov">        144 :     sc.push_back( &quot;HD3&quot; );</span></a>
+<a name="1738"><span class="lineNum">    1738 </span><span class="lineCov">        144 :     sc.push_back( &quot;HE1&quot; );</span></a>
+<a name="1739"><span class="lineNum">    1739 </span><span class="lineCov">        144 :     sc.push_back( &quot;HE2&quot; );</span></a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">        144 :     sc.push_back( &quot;HE3&quot; );</span></a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineCov">        144 :     sc.push_back( &quot;HH&quot; );</span></a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineCov">        144 :     return sc;</span></a>
+<a name="1743"><span class="lineNum">    1743 </span><span class="lineCov">        576 :   } else if(s==&quot;VAL&quot;) {</span></a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineCov">        576 :     sc.push_back( &quot;CB&quot; );</span></a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineCov">        576 :     sc.push_back( &quot;CG1&quot; );</span></a>
+<a name="1746"><span class="lineNum">    1746 </span><span class="lineCov">        576 :     sc.push_back( &quot;CG2&quot; );</span></a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineCov">        576 :     sc.push_back( &quot;HB&quot; );</span></a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineCov">        576 :     sc.push_back( &quot;HG11&quot; );</span></a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineCov">        576 :     sc.push_back( &quot;HG12&quot; );</span></a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineCov">        576 :     sc.push_back( &quot;HG13&quot; );</span></a>
+<a name="1751"><span class="lineNum">    1751 </span><span class="lineCov">        576 :     sc.push_back( &quot;HG21&quot; );</span></a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineCov">        576 :     sc.push_back( &quot;HG22&quot; );</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineCov">        576 :     sc.push_back( &quot;HG23&quot; );</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineCov">        576 :     sc.push_back( &quot;1HG1&quot; );</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineCov">        576 :     sc.push_back( &quot;2HG1&quot; );</span></a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineCov">        576 :     sc.push_back( &quot;3HG1&quot; );</span></a>
+<a name="1757"><span class="lineNum">    1757 </span><span class="lineCov">        576 :     sc.push_back( &quot;1HG2&quot; );</span></a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineCov">        576 :     sc.push_back( &quot;2HG2&quot; );</span></a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineCov">        576 :     sc.push_back( &quot;3HG2&quot; );</span></a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineCov">        576 :     return sc;</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineNoCov">          0 :   } else plumed_merror(&quot;Sidechain atoms unknown: &quot; + s);</span></a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1763"><span class="lineNum">    1763 </span>            : </a>
+<a name="1764"><span class="lineNum">    1764 </span><span class="lineCov">      47016 : bool CS2Backbone::isSP2(const std::string &amp; resType, const std::string &amp; atomName) {</span></a>
+<a name="1765"><span class="lineNum">    1765 </span>            :   bool sp2 = false;</a>
+<a name="1766"><span class="lineNum">    1766 </span><span class="lineCov">      47016 :   if (atomName == &quot;C&quot;) return true;</span></a>
+<a name="1767"><span class="lineNum">    1767 </span><span class="lineCov">      43848 :   if (atomName == &quot;O&quot;) return true;</span></a>
+<a name="1768"><span class="lineNum">    1768 </span>            : </a>
+<a name="1769"><span class="lineNum">    1769 </span><span class="lineCov">      40716 :   if(resType == &quot;TRP&quot;) {</span></a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineCov">        396 :     if      (atomName == &quot;CG&quot;)  sp2 = true;</span></a>
+<a name="1771"><span class="lineNum">    1771 </span><span class="lineCov">        378 :     else if (atomName == &quot;CD1&quot;) sp2 = true;</span></a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineCov">        360 :     else if (atomName == &quot;CD2&quot;) sp2 = true;</span></a>
+<a name="1773"><span class="lineNum">    1773 </span><span class="lineCov">        342 :     else if (atomName == &quot;CE2&quot;) sp2 = true;</span></a>
+<a name="1774"><span class="lineNum">    1774 </span><span class="lineCov">        324 :     else if (atomName == &quot;CE3&quot;) sp2 = true;</span></a>
+<a name="1775"><span class="lineNum">    1775 </span><span class="lineCov">        306 :     else if (atomName == &quot;CZ2&quot;) sp2 = true;</span></a>
+<a name="1776"><span class="lineNum">    1776 </span><span class="lineCov">        288 :     else if (atomName == &quot;CZ3&quot;) sp2 = true;</span></a>
+<a name="1777"><span class="lineNum">    1777 </span><span class="lineCov">        270 :     else if (atomName == &quot;CH2&quot;) sp2 = true;</span></a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineCov">      40320 :   } else if (resType == &quot;ASP&quot;) {</span></a>
+<a name="1779"><span class="lineNum">    1779 </span><span class="lineCov">       1656 :     if      (atomName == &quot;CG&quot;)  sp2 = true;</span></a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineCov">       1494 :     else if (atomName == &quot;OD1&quot;) sp2 = true;</span></a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineCov">       1332 :     else if (atomName == &quot;OD2&quot;) sp2 = true;</span></a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineCov">      38664 :   } else if (resType == &quot;GLU&quot;) {</span></a>
+<a name="1783"><span class="lineNum">    1783 </span><span class="lineCov">       2844 :     if      (atomName == &quot;CD&quot;)  sp2 = true;</span></a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineCov">       2628 :     else if (atomName == &quot;OE1&quot;) sp2 = true;</span></a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineCov">       2412 :     else if (atomName == &quot;OE2&quot;) sp2 = true;</span></a>
+<a name="1786"><span class="lineNum">    1786 </span><span class="lineCov">      35820 :   } else if (resType == &quot;ARG&quot;) {</span></a>
+<a name="1787"><span class="lineNum">    1787 </span><span class="lineCov">       2772 :     if (atomName == &quot;CZ&quot;) sp2 = true;</span></a>
+<a name="1788"><span class="lineNum">    1788 </span><span class="lineCov">      33048 :   } else if (resType == &quot;HIS&quot;) {</span></a>
+<a name="1789"><span class="lineNum">    1789 </span><span class="lineNoCov">          0 :     if      (atomName == &quot;CG&quot;)  sp2 = true;</span></a>
+<a name="1790"><span class="lineNum">    1790 </span><span class="lineNoCov">          0 :     else if (atomName == &quot;ND1&quot;) sp2 = true;</span></a>
+<a name="1791"><span class="lineNum">    1791 </span><span class="lineNoCov">          0 :     else if (atomName == &quot;CD2&quot;) sp2 = true;</span></a>
+<a name="1792"><span class="lineNum">    1792 </span><span class="lineNoCov">          0 :     else if (atomName == &quot;CE1&quot;) sp2 = true;</span></a>
+<a name="1793"><span class="lineNum">    1793 </span><span class="lineNoCov">          0 :     else if (atomName == &quot;NE2&quot;) sp2 = true;</span></a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineCov">      33048 :   } else if (resType == &quot;PHE&quot;) {</span></a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineCov">       5184 :     if      (atomName == &quot;CG&quot;)  sp2 = true;</span></a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineCov">       4896 :     else if (atomName == &quot;CD1&quot;) sp2 = true;</span></a>
+<a name="1797"><span class="lineNum">    1797 </span><span class="lineCov">       4608 :     else if (atomName == &quot;CD2&quot;) sp2 = true;</span></a>
+<a name="1798"><span class="lineNum">    1798 </span><span class="lineCov">       4320 :     else if (atomName == &quot;CE1&quot;) sp2 = true;</span></a>
+<a name="1799"><span class="lineNum">    1799 </span><span class="lineCov">       4032 :     else if (atomName == &quot;CE2&quot;) sp2 = true;</span></a>
+<a name="1800"><span class="lineNum">    1800 </span><span class="lineCov">       3744 :     else if (atomName == &quot;CZ&quot;)  sp2 = true;</span></a>
+<a name="1801"><span class="lineNum">    1801 </span><span class="lineCov">      27864 :   } else if (resType == &quot;TYR&quot;) {</span></a>
+<a name="1802"><span class="lineNum">    1802 </span><span class="lineCov">        684 :     if      (atomName == &quot;CG&quot;)  sp2 = true;</span></a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineCov">        648 :     else if (atomName == &quot;CD1&quot;) sp2 = true;</span></a>
+<a name="1804"><span class="lineNum">    1804 </span><span class="lineCov">        612 :     else if (atomName == &quot;CD2&quot;) sp2 = true;</span></a>
+<a name="1805"><span class="lineNum">    1805 </span><span class="lineCov">        576 :     else if (atomName == &quot;CE1&quot;) sp2 = true;</span></a>
+<a name="1806"><span class="lineNum">    1806 </span><span class="lineCov">        540 :     else if (atomName == &quot;CE2&quot;) sp2 = true;</span></a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineCov">        504 :     else if (atomName == &quot;CZ&quot;)  sp2 = true;</span></a>
+<a name="1808"><span class="lineNum">    1808 </span><span class="lineCov">      27180 :   } else if (resType == &quot;ASN&quot;) {</span></a>
+<a name="1809"><span class="lineNum">    1809 </span><span class="lineCov">       1944 :     if      (atomName == &quot;CG&quot;)  sp2 = true;</span></a>
+<a name="1810"><span class="lineNum">    1810 </span><span class="lineCov">       1782 :     else if (atomName == &quot;OD1&quot;) sp2 = true;</span></a>
+<a name="1811"><span class="lineNum">    1811 </span><span class="lineCov">      25236 :   } else if (resType == &quot;GLN&quot;) {</span></a>
+<a name="1812"><span class="lineNum">    1812 </span><span class="lineCov">        810 :     if      (atomName == &quot;CD&quot;)  sp2 = true;</span></a>
+<a name="1813"><span class="lineNum">    1813 </span><span class="lineCov">        756 :     else if (atomName == &quot;OE1&quot;) sp2 = true;</span></a>
+<a name="1814"><span class="lineNum">    1814 </span>            :   }</a>
+<a name="1815"><span class="lineNum">    1815 </span>            : </a>
+<a name="1816"><span class="lineNum">    1816 </span>            :   return sp2;</a>
+<a name="1817"><span class="lineNum">    1817 </span>            : }</a>
+<a name="1818"><span class="lineNum">    1818 </span>            : </a>
+<a name="1819"><span class="lineNum">    1819 </span><span class="lineCov">     145728 : bool CS2Backbone::is_chi1_cx(const std::string &amp; frg, const std::string &amp; atm) {</span></a>
+<a name="1820"><span class="lineNum">    1820 </span><span class="lineCov">     145728 :   if(atm==&quot;CG&quot;)                                        return true;</span></a>
+<a name="1821"><span class="lineNum">    1821 </span><span class="lineCov">     139788 :   if((frg == &quot;CYS&quot;)&amp;&amp;(atm ==&quot;SG&quot;))                     return true;</span></a>
+<a name="1822"><span class="lineNum">    1822 </span><span class="lineCov">     288792 :   if(((frg == &quot;ILE&quot;)||(frg == &quot;VAL&quot;))&amp;&amp;(atm == &quot;CG1&quot;)) return true;</span></a>
+<a name="1823"><span class="lineNum">    1823 </span><span class="lineCov">     145602 :   if((frg == &quot;SER&quot;)&amp;&amp;(atm == &quot;OG&quot;))                    return true;</span></a>
+<a name="1824"><span class="lineNum">    1824 </span><span class="lineCov">     148878 :   if((frg == &quot;THR&quot;)&amp;&amp;(atm == &quot;OG1&quot;))                   return true;</span></a>
+<a name="1825"><span class="lineNum">    1825 </span>            : </a>
+<a name="1826"><span class="lineNum">    1826 </span>            :   return false;</a>
+<a name="1827"><span class="lineNum">    1827 </span>            : }</a>
+<a name="1828"><span class="lineNum">    1828 </span>            : </a>
+<a name="1829"><span class="lineNum">    1829 </span><span class="lineCov">    3599784 : void CS2Backbone::xdist_name_map(std::string &amp; name) {</span></a>
+<a name="1830"><span class="lineNum">    1830 </span><span class="lineCov">    7199568 :   if((name == &quot;OT1&quot;)||(name == &quot;OC1&quot;)) name = &quot;O&quot;;</span></a>
+<a name="1831"><span class="lineNum">    1831 </span><span class="lineCov">   10799352 :   else if ((name == &quot;HN&quot;) || (name == &quot;HT1&quot;) || (name == &quot;H1&quot;)) name = &quot;H&quot;;</span></a>
+<a name="1832"><span class="lineNum">    1832 </span><span class="lineCov">    7139232 :   else if ((name == &quot;CG1&quot;)|| (name == &quot;OG&quot;)||</span></a>
+<a name="1833"><span class="lineNum">    1833 </span><span class="lineCov">    7159572 :            (name == &quot;SG&quot;) || (name == &quot;OG1&quot;)) name = &quot;CG&quot;;</span></a>
+<a name="1834"><span class="lineNum">    1834 </span><span class="lineCov">    7040070 :   else if ((name == &quot;HA1&quot;)|| (name == &quot;HA3&quot;)) name = &quot;HA&quot;;</span></a>
+<a name="1835"><span class="lineNum">    1835 </span><span class="lineCov">    3599784 : }</span></a>
+<a name="1836"><span class="lineNum">    1836 </span>            : </a>
+<a name="1837"><span class="lineNum">    1837 </span><span class="lineCov">         18 : void CS2Backbone::update() {</span></a>
+<a name="1838"><span class="lineNum">    1838 </span>            :   // write status file</a>
+<a name="1839"><span class="lineNum">    1839 </span><span class="lineCov">         18 :   if(getWstride()&gt;0&amp;&amp; (getStep()%getWstride()==0 || getCPT()) ) writeStatus();</span></a>
+<a name="1840"><span class="lineNum">    1840 </span><span class="lineCov">         18 : }</span></a>
+<a name="1841"><span class="lineNum">    1841 </span>            : </a>
+<a name="1842"><span class="lineNum">    1842 </span>            : }</a>
+<a name="1843"><span class="lineNum">    1843 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Caliber.cpp.func-sort-c.html b/coverage/isdb/Caliber.cpp.func-sort-c.html
new file mode 100644
index 0000000000..70723b1e67
--- /dev/null
+++ b/coverage/isdb/Caliber.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Caliber.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Caliber.cpp<span style="font-size: 80%;"> (<a href="Caliber.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Caliber.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#232">_ZN4PLMD4isdb7Caliber14get_sigma_meanEdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#294">_ZN4PLMD4isdb7Caliber18do_regression_zeroERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#139">_ZN4PLMD4isdb7CaliberC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#121">_ZN4PLMD4isdb12_GLOBAL__N_120CaliberRegisterMe1236createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#139">_ZN4PLMD4isdb7CaliberC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#123">_ZN4PLMD4isdb7Caliber16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#254">_ZN4PLMD4isdb7Caliber17replica_averagingEdRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#310">_ZN4PLMD4isdb7Caliber9calculateEv</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#264">_ZN4PLMD4isdb7Caliber9getSplineEj</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#121">_ZN4PLMD4isdb12_GLOBAL__N_120CaliberRegisterMe123C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#121">_ZN4PLMD4isdb12_GLOBAL__N_120CaliberRegisterMe123D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Caliber.cpp.func.html b/coverage/isdb/Caliber.cpp.func.html
new file mode 100644
index 0000000000..5c6547a409
--- /dev/null
+++ b/coverage/isdb/Caliber.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Caliber.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Caliber.cpp<span style="font-size: 80%;"> (<a href="Caliber.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Caliber.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#121">_ZN4PLMD4isdb12_GLOBAL__N_120CaliberRegisterMe1236createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#121">_ZN4PLMD4isdb12_GLOBAL__N_120CaliberRegisterMe123C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#121">_ZN4PLMD4isdb12_GLOBAL__N_120CaliberRegisterMe123D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#232">_ZN4PLMD4isdb7Caliber14get_sigma_meanEdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#123">_ZN4PLMD4isdb7Caliber16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#254">_ZN4PLMD4isdb7Caliber17replica_averagingEdRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#294">_ZN4PLMD4isdb7Caliber18do_regression_zeroERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#310">_ZN4PLMD4isdb7Caliber9calculateEv</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#264">_ZN4PLMD4isdb7Caliber9getSplineEj</a></td>
+              <td class="coverFnHi">2004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#139">_ZN4PLMD4isdb7CaliberC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Caliber.cpp.gcov.html#139">_ZN4PLMD4isdb7CaliberC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Caliber.cpp.gcov.html b/coverage/isdb/Caliber.cpp.gcov.html
new file mode 100644
index 0000000000..8ff960a089
--- /dev/null
+++ b/coverage/isdb/Caliber.cpp.gcov.html
@@ -0,0 +1,423 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Caliber.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Caliber.cpp<span style="font-size: 80%;"> (source / <a href="Caliber.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;bias/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;fstream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace isdb {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC ISDB_BIAS CALIBER</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Add a time-dependent, harmonic restraint on one or more variables.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This allows implementing a maximum caliber restraint on one or more experimental time series by replica-averaged restrained simulations.</a>
+<a name="36"><span class="lineNum">      36 </span>            : See \cite Capelli:2018jt .</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The time resolved experiments are read from a text file and intermediate values are obtained by splines.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : In the following example a restraint is applied on the time evolution of a saxs spectrum</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : MOLINFO STRUCTURE=first.pdb</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : # Define saxs variable</a>
+<a name="48"><span class="lineNum">      48 </span>            : SAXS ...</a>
+<a name="49"><span class="lineNum">      49 </span>            : LABEL=saxs</a>
+<a name="50"><span class="lineNum">      50 </span>            : ATOMISTIC</a>
+<a name="51"><span class="lineNum">      51 </span>            : ATOMS=1-436</a>
+<a name="52"><span class="lineNum">      52 </span>            : QVALUE1=0.02 # Q-value at which calculate the scattering</a>
+<a name="53"><span class="lineNum">      53 </span>            : QVALUE2=0.0808</a>
+<a name="54"><span class="lineNum">      54 </span>            : QVALUE3=0.1264</a>
+<a name="55"><span class="lineNum">      55 </span>            : QVALUE4=0.1568</a>
+<a name="56"><span class="lineNum">      56 </span>            : QVALUE5=0.172</a>
+<a name="57"><span class="lineNum">      57 </span>            : QVALUE6=0.1872</a>
+<a name="58"><span class="lineNum">      58 </span>            : QVALUE7=0.2176</a>
+<a name="59"><span class="lineNum">      59 </span>            : QVALUE8=0.2328</a>
+<a name="60"><span class="lineNum">      60 </span>            : QVALUE9=0.248</a>
+<a name="61"><span class="lineNum">      61 </span>            : QVALUE10=0.2632</a>
+<a name="62"><span class="lineNum">      62 </span>            : QVALUE11=0.2936</a>
+<a name="63"><span class="lineNum">      63 </span>            : QVALUE12=0.3088</a>
+<a name="64"><span class="lineNum">      64 </span>            : QVALUE13=0.324</a>
+<a name="65"><span class="lineNum">      65 </span>            : QVALUE14=0.3544</a>
+<a name="66"><span class="lineNum">      66 </span>            : QVALUE15=0.4</a>
+<a name="67"><span class="lineNum">      67 </span>            : ... SAXS</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : #define the caliber restraint</a>
+<a name="71"><span class="lineNum">      71 </span>            : CALIBER ...</a>
+<a name="72"><span class="lineNum">      72 </span>            :   ARG=(saxs\.q_.*)</a>
+<a name="73"><span class="lineNum">      73 </span>            :   FILE=expsaxs.dat</a>
+<a name="74"><span class="lineNum">      74 </span>            :   KAPPA=10</a>
+<a name="75"><span class="lineNum">      75 </span>            :   LABEL=cal0</a>
+<a name="76"><span class="lineNum">      76 </span>            :   STRIDE=10</a>
+<a name="77"><span class="lineNum">      77 </span>            :   REGRES_ZERO=200</a>
+<a name="78"><span class="lineNum">      78 </span>            :   AVERAGING=200</a>
+<a name="79"><span class="lineNum">      79 </span>            : ... CALIBER</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endplumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : In particular the file expsaxs.dat contains the time traces for the 15 intensities at the selected scattering lengths, organized as time, q_1, etc.</a>
+<a name="83"><span class="lineNum">      83 </span>            : The strength of the bias is automatically evaluated from the standard error of the mean over AVERAGING steps and multiplied by KAPPA. This is useful when working with multiple experimental data</a>
+<a name="84"><span class="lineNum">      84 </span>            : Because \ref SAXS is usually defined in a manner that is irrespective of a scaling factor the scaling is evaluated from a linear fit every REGRES_ZERO step. Alternatively it can be given as a fixed constant as SCALE.</a>
+<a name="85"><span class="lineNum">      85 </span>            : The bias is here applied every tenth step.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : */</a>
+<a name="88"><span class="lineNum">      88 </span>            : //+ENDPLUMEDOC</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : class Caliber : public bias::Bias {</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit Caliber(const ActionOptions&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            :   void calculate();</a>
+<a name="95"><span class="lineNum">      95 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="96"><span class="lineNum">      96 </span>            : private:</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt;double&gt; time;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; var;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; dvar;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   double   mult;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   double   scale_;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   bool     master;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   unsigned replica_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   unsigned nrep_;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   // scale and offset regression</a>
+<a name="106"><span class="lineNum">     106 </span>            :   bool doregres_zero_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   int  nregres_zero_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   // force constant</a>
+<a name="109"><span class="lineNum">     109 </span>            :   unsigned optsigmamean_stride_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   std::vector&lt;double&gt; sigma_mean2_;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; sigma_mean2_last_;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;Value*&gt; x0comp;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;Value*&gt; kcomp;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;Value*&gt; mcomp;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   Value* valueScale;</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   void get_sigma_mean(const double fact, const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void replica_averaging(const double fact, std::vector&lt;double&gt; &amp;mean);</a>
+<a name="119"><span class="lineNum">     119 </span>            :   double getSpline(const unsigned iarg);</a>
+<a name="120"><span class="lineNum">     120 </span>            :   void do_regression_zero(const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="121"><span class="lineNum">     121 </span>            : };</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(Caliber,&quot;CALIBER&quot;)</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          6 : void Caliber::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          6 :   Bias::registerKeywords(keys);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          6 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         12 :   keys.addFlag(&quot;NOENSEMBLE&quot;,false,&quot;don't perform any replica-averaging&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file containing the time-resolved values&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;a force constant, this can be use to scale a constant estimated on-the-fly using AVERAGING&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;AVERAGING&quot;, &quot;Stride for calculation of the optimum kappa, if 0 only KAPPA is used.&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;TSCALE&quot;,&quot;1.0&quot;,&quot;Apply a time scaling on the experimental time scale&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;SCALE&quot;,&quot;1.0&quot;,&quot;Apply a constant scaling on the data provided as arguments&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;REGRES_ZERO&quot;,&quot;stride for regression with zero offset&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;x0&quot;,&quot;default&quot;,&quot;the instantaneous value of the center of the potential&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;mean&quot;,&quot;default&quot;,&quot;the current average value of the calculated observable&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;kappa&quot;,&quot;default&quot;,&quot;the current force constant&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;scale&quot;,&quot;REGRES_ZERO&quot;,&quot;the current scaling constant&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          6 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 : Caliber::Caliber(const ActionOptions&amp;ao):</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 :   mult(0),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          4 :   scale_(1),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          4 :   doregres_zero_(false),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :   nregres_zero_(0),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 :   optsigmamean_stride_(0)</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : {</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          8 :   parse(&quot;KAPPA&quot;,mult);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   std::string filename;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          8 :   parse(&quot;FILE&quot;,filename);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   if( filename.length()==0 ) error(&quot;No external variable file was specified&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :   unsigned averaging=0;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :   parse(&quot;AVERAGING&quot;, averaging);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          4 :   if(averaging&gt;0) optsigmamean_stride_ = averaging;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :   double tscale=1.0;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          4 :   parse(&quot;TSCALE&quot;, tscale);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :   if(tscale&lt;=0.) error(&quot;The time scale factor must be greater than 0.&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          4 :   parse(&quot;SCALE&quot;, scale_);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          4 :   if(scale_==0.) error(&quot;The time scale factor cannot be 0.&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   // regression with zero intercept</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          4 :   parse(&quot;REGRES_ZERO&quot;, nregres_zero_);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          4 :   if(nregres_zero_&gt;0) {</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     // set flag</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     doregres_zero_=true;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     log.printf(&quot;  doing regression with zero intercept with stride: %d\n&quot;, nregres_zero_);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          4 :   bool noensemble = false;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 :   parseFlag(&quot;NOENSEMBLE&quot;, noensemble);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   // set up replica stuff</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          4 :   master = (comm.Get_rank()==0);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 :   if(master) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          4 :     nrep_    = multi_sim_comm.Get_size();</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          4 :     replica_ = multi_sim_comm.Get_rank();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          4 :     if(noensemble) nrep_ = 1;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   } else {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     nrep_    = 0;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     replica_ = 0;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 :   comm.Sum(&amp;nrep_,1);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          4 :   comm.Sum(&amp;replica_,1);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   const unsigned narg = getNumberOfArguments();</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          4 :   sigma_mean2_.resize(narg,1);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          4 :   sigma_mean2_last_.resize(narg);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          8 :   for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[j].push_back(0.000001);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 :   log.printf(&quot;  Time resolved data from file %s\n&quot;,filename.c_str());</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          4 :   std::ifstream varfile(filename.c_str());</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          4 :   if(varfile.fail()) error(&quot;Cannot open &quot;+filename);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          4 :   var.resize(narg);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          4 :   dvar.resize(narg);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       2012 :   while (!varfile.eof()) {</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     double tempT, tempVar;</a>
+<a name="200"><span class="lineNum">     200 </span>            :     varfile &gt;&gt; tempT;</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       2008 :     time.push_back(tempT/tscale);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       4016 :     for(unsigned i=0; i&lt;narg; i++) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       varfile &gt;&gt; tempVar;</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       2008 :       var[i].push_back(tempVar);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          4 :   varfile.close();</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          4 :   const double deltat = time[1] - time[0];</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;narg; i++) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       2012 :     for(unsigned j=0; j&lt;var[i].size(); j++) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       2008 :       if(j==0) dvar[i].push_back((var[i][j+1] - var[i][j])/(deltat));</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       2004 :       else if(j==var[i].size()-1) dvar[i].push_back((var[i][j] - var[i][j-1])/(deltat));</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       2000 :       else dvar[i].push_back((var[i][j+1] - var[i][j-1])/(2.*deltat));</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :     }</a>
+<a name="216"><span class="lineNum">     216 </span>            :   }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;narg; i++) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          4 :     std::string num; Tools::convert(i,num);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         12 :     addComponent(&quot;x0-&quot;+num); componentIsNotPeriodic(&quot;x0-&quot;+num); x0comp.push_back(getPntrToComponent(&quot;x0-&quot;+num));</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         12 :     addComponent(&quot;kappa-&quot;+num); componentIsNotPeriodic(&quot;kappa-&quot;+num); kcomp.push_back(getPntrToComponent(&quot;kappa-&quot;+num));</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         12 :     addComponent(&quot;mean-&quot;+num); componentIsNotPeriodic(&quot;mean-&quot;+num); mcomp.push_back(getPntrToComponent(&quot;mean-&quot;+num));</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :   if(doregres_zero_) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     addComponent(&quot;scale&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :     componentIsNotPeriodic(&quot;scale&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     valueScale=getPntrToComponent(&quot;scale&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          8 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Capelli, Tiana, Camilloni, J Chem Phys, 148, 184114&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          8 : }</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 : void Caliber::get_sigma_mean(const double fact, const std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   const unsigned narg = getNumberOfArguments();</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :   const double dnrep = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   if(sigma_mean2_last_[0].size()==optsigmamean_stride_) for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_last_[i].erase(sigma_mean2_last_[i].begin());</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; sigma_mean2_now(narg,0);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   if(master) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :       double tmp = getArgument(i)-mean[i];</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :       sigma_mean2_now[i] = fact*tmp*tmp;</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :     }</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;sigma_mean2_now[0], narg);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   }</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   comm.Sum(&amp;sigma_mean2_now[0], narg);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     sigma_mean2_last_[i].push_back(sigma_mean2_now[i]/dnrep);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :     sigma_mean2_[i] = *max_element(sigma_mean2_last_[i].begin(), sigma_mean2_last_[i].end());</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       2004 : void Caliber::replica_averaging(const double fact, std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : {</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       2004 :   const unsigned narg = getNumberOfArguments();</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       2004 :   if(master) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       4008 :     for(unsigned i=0; i&lt;narg; ++i) mean[i] = fact*getArgument(i);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       2004 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       2004 :   comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       2004 : }</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       2004 : double Caliber::getSpline(const unsigned iarg)</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : {</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">       2004 :   const double deltat = time[1] - time[0];</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       2004 :   const int tindex = static_cast&lt;int&gt;(getTime()/deltat);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   unsigned start, end;</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       2004 :   start=tindex;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       2004 :   if(tindex+1&lt;var[iarg].size()) end=tindex+2;</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :   else end=var[iarg].size();</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   double value=0;</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       6012 :   for(unsigned ipoint=start; ipoint&lt;end; ++ipoint) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       4008 :     double grid=var[iarg][ipoint];</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       4008 :     double dder=dvar[iarg][ipoint];</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :     double yy=0.;</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       4008 :     if(std::abs(grid)&gt;0.0000001) yy=-dder/grid;</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            :     int x0=1;</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       4008 :     if(ipoint==tindex) x0=0;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">       4008 :     double X=std::abs((getTime()-time[tindex])/deltat-(double)x0);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       4008 :     double X2=X*X;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       4008 :     double X3=X2*X;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       4008 :     double C=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*deltat;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       4008 :     value+=grid*C;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :   }</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       2004 :   return value;</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : }</a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 : void Caliber::do_regression_zero(const std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : {</a>
+<a name="298"><span class="lineNum">     298 </span>            : // parameters[i] = scale_ * mean[i]: find scale_ with linear regression</a>
+<a name="299"><span class="lineNum">     299 </span>            :   double num = 0.0;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   double den = 0.0;</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :     num += mean[i] * getSpline(i);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :     den += mean[i] * mean[i];</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   if(den&gt;0) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 :     scale_ = num / den;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   } else {</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :     scale_ = 1.0;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   }</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       2004 : void Caliber::calculate()</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : {</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       2004 :   const unsigned narg = getNumberOfArguments();</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       2004 :   const double dnrep = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       2004 :   const double fact = 1.0/dnrep;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       2004 :   std::vector&lt;double&gt; mean(narg,0);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       2004 :   std::vector&lt;double&gt; dmean_x(narg,fact);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       2004 :   replica_averaging(fact, mean);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       2004 :   if(optsigmamean_stride_&gt;0) get_sigma_mean(fact, mean);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :   // in case of regression with zero intercept, calculate scale</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">       2004 :   if(doregres_zero_ &amp;&amp; getStep()%nregres_zero_==0) do_regression_zero(mean);</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :   double ene=0;</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">       4008 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       2004 :     const double x0 = getSpline(i);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       2004 :     const double kappa = mult*dnrep/sigma_mean2_[i];</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       2004 :     const double cv=difference(i,x0,scale_*mean[i]);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       2004 :     const double f=-kappa*cv*dmean_x[i]/scale_;</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :     setOutputForce(i,f);</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       2004 :     ene+=0.5*kappa*cv*cv;</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">       2004 :     x0comp[i]-&gt;set(x0);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">       2004 :     kcomp[i]-&gt;set(kappa);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       2004 :     mcomp[i]-&gt;set(mean[i]);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   }</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       2004 :   if(doregres_zero_) valueScale-&gt;set(scale_);</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   setBias(ene);</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       2004 : }</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            : }</a>
+<a name="345"><span class="lineNum">     345 </span>            : }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/EMMI.cpp.func-sort-c.html b/coverage/isdb/EMMI.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a848ffcfa6
--- /dev/null
+++ b/coverage/isdb/EMMI.cpp.func-sort-c.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/EMMI.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - EMMI.cpp<span style="font-size: 80%;"> (<a href="EMMI.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">593</td>
+            <td class="headerCovTableEntry">785</td>
+            <td class="headerCovTableEntryMed">75.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryMed">76.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EMMI.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#796">_ZN4PLMD4isdb4EMMI11read_statusEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1389">_ZN4PLMD4isdb4EMMI11scaleEnergyEd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#857">_ZN4PLMD4isdb4EMMI12doMonteCarloEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1398">_ZN4PLMD4isdb4EMMI12doRegressionEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1475">_ZN4PLMD4isdb4EMMI13get_annealingEx</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#936">_ZN4PLMD4isdb4EMMI15read_exp_errorsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#972">_ZN4PLMD4isdb4EMMI17read_exp_overlapsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#758">_ZN4PLMD4isdb4EMMI19write_model_overlapEx</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#842">_ZN4PLMD4isdb4EMMI8doAcceptEddd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#433">_ZN4PLMD4isdb4EMMIC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#323">_ZN4PLMD4isdb4EMMI29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#382">_ZN4PLMD4isdb12_GLOBAL__N_117EMMIRegisterMe3846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#282">_ZN4PLMD4isdb4EMMI14setDerivativesEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#298">_ZN4PLMD4isdb4EMMI17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1124">_ZN4PLMD4isdb4EMMI22calculate_useful_stuffEd</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1072">_ZN4PLMD4isdb4EMMI9get_GMM_dENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#997">_ZN4PLMD4isdb4EMMI9get_GMM_mERSt6vectorINS_10AtomNumberESaIS3_EE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#433">_ZN4PLMD4isdb4EMMIC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#384">_ZN4PLMD4isdb4EMMI16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#311">_ZN4PLMD4isdb4EMMI12lockRequestsEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#317">_ZN4PLMD4isdb4EMMI14unlockRequestsEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#340">_ZN4PLMD4isdb4EMMI5applyEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1352">_ZN4PLMD4isdb4EMMI7prepareEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#777">_ZN4PLMD4isdb4EMMI10get_medianERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#303">_ZN4PLMD4isdb4EMMI22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1056">_ZN4PLMD4isdb4EMMI11check_GMM_dERKNS_13VectorGenericILj6EEEd</a></td>
+              <td class="coverFnHi">1962</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1221">_ZN4PLMD4isdb4EMMI16get_self_overlapEj</a></td>
+              <td class="coverFnHi">1962</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#382">_ZN4PLMD4isdb12_GLOBAL__N_117EMMIRegisterMe384C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#382">_ZN4PLMD4isdb12_GLOBAL__N_117EMMIRegisterMe384D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1727">_ZN4PLMD4isdb4EMMI18calculate_MarginalEv</a></td>
+              <td class="coverFnHi">5451</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1706">_ZN4PLMD4isdb4EMMI18calculate_OutliersEv</a></td>
+              <td class="coverFnHi">5451</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1685">_ZN4PLMD4isdb4EMMI15calculate_GaussEv</a></td>
+              <td class="coverFnHi">5463</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#820">_ZN4PLMD4isdb4EMMI12print_statusEx</a></td>
+              <td class="coverFnHi">10904</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1276">_ZN4PLMD4isdb4EMMI20update_neighbor_listEv</a></td>
+              <td class="coverFnHi">16355</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1491">_ZN4PLMD4isdb4EMMI11get_weightsERdS2_S2_</a></td>
+              <td class="coverFnHi">16365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1358">_ZN4PLMD4isdb4EMMI17calculate_overlapEv</a></td>
+              <td class="coverFnHi">16365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#368">_ZN4PLMD4isdb4EMMI17setBoxDerivativesEPNS_5ValueERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">16365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1538">_ZN4PLMD4isdb4EMMI9calculateEv</a></td>
+              <td class="coverFnHi">16365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1193">_ZN4PLMD4isdb4EMMI21get_prefactor_inverseERKNS_13VectorGenericILj6EEES5_ddRS3_S6_</a></td>
+              <td class="coverFnHi">1621458</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1239">_ZN4PLMD4isdb4EMMI11get_overlapERKNS_13VectorGenericILj3EEES5_dRKNS2_ILj6EEERS3_</a></td>
+              <td class="coverFnHi">3732816</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#360">_ZN4PLMD4isdb4EMMI19setAtomsDerivativesEPNS_5ValueEjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">9844626</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1260">_ZN4PLMD4isdb4EMMI15get_exp_overlapERKNS_13VectorGenericILj3EEES5_RKNS2_ILj6EEE</a></td>
+              <td class="coverFnHi">59085036</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/EMMI.cpp.func.html b/coverage/isdb/EMMI.cpp.func.html
new file mode 100644
index 0000000000..c27510773f
--- /dev/null
+++ b/coverage/isdb/EMMI.cpp.func.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/EMMI.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - EMMI.cpp<span style="font-size: 80%;"> (<a href="EMMI.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">593</td>
+            <td class="headerCovTableEntry">785</td>
+            <td class="headerCovTableEntryMed">75.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryMed">76.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EMMI.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#382">_ZN4PLMD4isdb12_GLOBAL__N_117EMMIRegisterMe3846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#382">_ZN4PLMD4isdb12_GLOBAL__N_117EMMIRegisterMe384C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#382">_ZN4PLMD4isdb12_GLOBAL__N_117EMMIRegisterMe384D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#777">_ZN4PLMD4isdb4EMMI10get_medianERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1056">_ZN4PLMD4isdb4EMMI11check_GMM_dERKNS_13VectorGenericILj6EEEd</a></td>
+              <td class="coverFnHi">1962</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1239">_ZN4PLMD4isdb4EMMI11get_overlapERKNS_13VectorGenericILj3EEES5_dRKNS2_ILj6EEERS3_</a></td>
+              <td class="coverFnHi">3732816</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1491">_ZN4PLMD4isdb4EMMI11get_weightsERdS2_S2_</a></td>
+              <td class="coverFnHi">16365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#796">_ZN4PLMD4isdb4EMMI11read_statusEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1389">_ZN4PLMD4isdb4EMMI11scaleEnergyEd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#857">_ZN4PLMD4isdb4EMMI12doMonteCarloEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#1398">_ZN4PLMD4isdb4EMMI12doRegressionEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#311">_ZN4PLMD4isdb4EMMI12lockRequestsEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EMMI.cpp.gcov.html#820">_ZN4PLMD4isdb4EMMI12print_statusEx</a></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/EMMI.cpp.gcov.html b/coverage/isdb/EMMI.cpp.gcov.html
new file mode 100644
index 0000000000..f08a5ff26d
--- /dev/null
+++ b/coverage/isdb/EMMI.cpp.gcov.html
@@ -0,0 +1,1826 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/EMMI.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - EMMI.cpp<span style="font-size: 80%;"> (source / <a href="EMMI.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">593</td>
+            <td class="headerCovTableEntry">785</td>
+            <td class="headerCovTableEntryMed">75.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryMed">76.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;string&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;map&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;numeric&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;ctime&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace isdb {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC ISDB_COLVAR EMMI</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Calculate the fit of a structure or ensemble of structures with a cryo-EM density map.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : This action implements the multi-scale Bayesian approach to cryo-EM data fitting introduced in  Ref. \cite Hanot113951 .</a>
+<a name="46"><span class="lineNum">      46 </span>            : This method allows efficient and accurate structural modeling of cryo-electron microscopy density maps at multiple scales, from coarse-grained to atomistic resolution, by addressing the presence of random and systematic errors in the data, sample heterogeneity, data correlation, and noise correlation.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The experimental density map is fit by a Gaussian Mixture Model (GMM), which is provided as an external file specified by the keyword</a>
+<a name="49"><span class="lineNum">      49 </span>            : GMM_FILE. We are currently working on a web server to perform</a>
+<a name="50"><span class="lineNum">      50 </span>            : this operation. In the meantime, the user can request a stand-alone version of the GMM code at massimiliano.bonomi_AT_gmail.com.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : When run in single-replica mode, this action allows atomistic, flexible refinement of an individual structure into a density map.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Combined with a multi-replica framework (such as the -multi option in GROMACS), the user can model an ensemble of structures using</a>
+<a name="54"><span class="lineNum">      54 </span>            : the Metainference approach \cite Bonomi:2016ip .</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \warning</a>
+<a name="57"><span class="lineNum">      57 </span>            : To use \ref EMMI, the user should always add a \ref MOLINFO line and specify a pdb file of the system.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \note</a>
+<a name="60"><span class="lineNum">      60 </span>            : To enhance sampling in single-structure refinement, one can use a Replica Exchange Method, such as Parallel Tempering.</a>
+<a name="61"><span class="lineNum">      61 </span>            : In this case, the user should add the NO_AVER flag to the input line. To use a replica-based enhanced sampling scheme such as</a>
+<a name="62"><span class="lineNum">      62 </span>            : Parallel-Bias Metadynamics (\ref PBMETAD), one should use the REWEIGHT flag and pass the Metadynamics bias using the ARG keyword.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \note</a>
+<a name="65"><span class="lineNum">      65 </span>            : \ref EMMI can be used in combination with periodic and non-periodic systems. In the latter case, one should</a>
+<a name="66"><span class="lineNum">      66 </span>            : add the NOPBC flag to the input line</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \par Examples</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : In this example, we perform a single-structure refinement based on an experimental cryo-EM map. The map is fit with a GMM, whose</a>
+<a name="71"><span class="lineNum">      71 </span>            : parameters are listed in the file GMM_fit.dat. This file contains one line per GMM component in the following format:</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \plumedfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : #! FIELDS Id Weight Mean_0 Mean_1 Mean_2 Cov_00 Cov_01 Cov_02 Cov_11 Cov_12 Cov_22 Beta</a>
+<a name="75"><span class="lineNum">      75 </span>            :      0  2.9993805e+01   6.54628 10.37820 -0.92988  2.078920e-02 1.216254e-03 5.990827e-04 2.556246e-02 8.411835e-03 2.486254e-02  1</a>
+<a name="76"><span class="lineNum">      76 </span>            :      1  2.3468312e+01   6.56095 10.34790 -0.87808  1.879859e-02 6.636049e-03 3.682865e-04 3.194490e-02 1.750524e-03 3.017100e-02  1</a>
+<a name="77"><span class="lineNum">      77 </span>            :      ...</a>
+<a name="78"><span class="lineNum">      78 </span>            : \endplumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : To accelerate the computation of the Bayesian score, one can:</a>
+<a name="81"><span class="lineNum">      81 </span>            : - use neighbor lists, specified by the keywords NL_CUTOFF and NL_STRIDE;</a>
+<a name="82"><span class="lineNum">      82 </span>            : - calculate the restraint every other step (or more).</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : All the heavy atoms of the system are used to calculate the density map. This list can conveniently be provided</a>
+<a name="85"><span class="lineNum">      85 </span>            : using a GROMACS index file.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : The input file looks as follows:</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : \plumedfile</a>
+<a name="90"><span class="lineNum">      90 </span>            : # include pdb info</a>
+<a name="91"><span class="lineNum">      91 </span>            : MOLINFO STRUCTURE=prot.pdb</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : #  all heavy atoms</a>
+<a name="94"><span class="lineNum">      94 </span>            : protein-h: GROUP NDX_FILE=index.ndx NDX_GROUP=Protein-H</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : # create EMMI score</a>
+<a name="97"><span class="lineNum">      97 </span>            : gmm: EMMI NOPBC SIGMA_MIN=0.01 TEMP=300.0 NL_STRIDE=100 NL_CUTOFF=0.01 GMM_FILE=GMM_fit.dat ATOMS=protein-h</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : # translate into bias - apply every 2 steps</a>
+<a name="100"><span class="lineNum">     100 </span>            : emr: BIASVALUE ARG=gmm.scoreb STRIDE=2</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : PRINT ARG=emr.* FILE=COLVAR STRIDE=500 FMT=%20.10f</a>
+<a name="103"><span class="lineNum">     103 </span>            : \endplumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : */</a>
+<a name="107"><span class="lineNum">     107 </span>            : //+ENDPLUMEDOC</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : class EMMI :</a>
+<a name="110"><span class="lineNum">     110 </span>            :   public ActionAtomistic,</a>
+<a name="111"><span class="lineNum">     111 </span>            :   public ActionWithArguments,</a>
+<a name="112"><span class="lineNum">     112 </span>            :   public ActionWithValue</a>
+<a name="113"><span class="lineNum">     113 </span>            : {</a>
+<a name="114"><span class="lineNum">     114 </span>            : private:</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : // temperature in kbt</a>
+<a name="117"><span class="lineNum">     117 </span>            :   double kbt_;</a>
+<a name="118"><span class="lineNum">     118 </span>            : // model GMM - atom types</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::vector&lt;unsigned&gt; GMM_m_type_;</a>
+<a name="120"><span class="lineNum">     120 </span>            : // model GMM - list of atom sigmas - one per atom type</a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::vector&lt;double&gt; GMM_m_s_;</a>
+<a name="122"><span class="lineNum">     122 </span>            : // model GMM - list of atom weights - one per atom type</a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::vector&lt;double&gt; GMM_m_w_;</a>
+<a name="124"><span class="lineNum">     124 </span>            : // data GMM - means, weights, and covariances + beta option</a>
+<a name="125"><span class="lineNum">     125 </span>            :   std::vector&lt;Vector&gt;             GMM_d_m_;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   std::vector&lt;double&gt;             GMM_d_w_;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   std::vector&lt; VectorGeneric&lt;6&gt; &gt; GMM_d_cov_;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   std::vector&lt;int&gt;                GMM_d_beta_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector &lt; std::vector&lt;int&gt; &gt;     GMM_d_grps_;</a>
+<a name="130"><span class="lineNum">     130 </span>            : // overlaps</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::vector&lt;double&gt; ovmd_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::vector&lt;double&gt; ovdd_;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::vector&lt;double&gt; ovmd_ave_;</a>
+<a name="134"><span class="lineNum">     134 </span>            : // and derivatives</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::vector&lt;Vector&gt; ovmd_der_;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   std::vector&lt;Vector&gt; atom_der_;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   std::vector&lt;double&gt; GMMid_der_;</a>
+<a name="138"><span class="lineNum">     138 </span>            : // constants</a>
+<a name="139"><span class="lineNum">     139 </span>            :   double cfact_;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   double inv_sqrt2_, sqrt2_pi_;</a>
+<a name="141"><span class="lineNum">     141 </span>            : // metainference</a>
+<a name="142"><span class="lineNum">     142 </span>            :   unsigned nrep_;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   unsigned replica_;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::vector&lt;double&gt; sigma_min_;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   std::vector&lt;double&gt; sigma_max_;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;double&gt; dsigma_;</a>
+<a name="148"><span class="lineNum">     148 </span>            : // list of prefactors for overlap between two Gaussians</a>
+<a name="149"><span class="lineNum">     149 </span>            : // pre_fact = 1.0 / (2pi)**1.5 / std::sqrt(det_md) * Wm * Wd</a>
+<a name="150"><span class="lineNum">     150 </span>            :   std::vector&lt;double&gt; pre_fact_;</a>
+<a name="151"><span class="lineNum">     151 </span>            : // inverse of the sum of model and data covariances matrices</a>
+<a name="152"><span class="lineNum">     152 </span>            :   std::vector&lt; VectorGeneric&lt;6&gt; &gt; inv_cov_md_;</a>
+<a name="153"><span class="lineNum">     153 </span>            : // neighbor list</a>
+<a name="154"><span class="lineNum">     154 </span>            :   double   nl_cutoff_;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   unsigned nl_stride_;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   bool first_time_;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   bool no_aver_;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   std::vector&lt;unsigned&gt; nl_;</a>
+<a name="159"><span class="lineNum">     159 </span>            : // parallel stuff</a>
+<a name="160"><span class="lineNum">     160 </span>            :   unsigned size_;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   unsigned rank_;</a>
+<a name="162"><span class="lineNum">     162 </span>            : // pbc</a>
+<a name="163"><span class="lineNum">     163 </span>            :   bool pbc_;</a>
+<a name="164"><span class="lineNum">     164 </span>            : // Monte Carlo stuff</a>
+<a name="165"><span class="lineNum">     165 </span>            :   int      MCstride_;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   double   MCaccept_;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   double   MCtrials_;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   Random   random_;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   // status stuff</a>
+<a name="170"><span class="lineNum">     170 </span>            :   unsigned int statusstride_;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::string       statusfilename_;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   OFile        statusfile_;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   bool         first_status_;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   // regression</a>
+<a name="175"><span class="lineNum">     175 </span>            :   unsigned nregres_;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   double scale_;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   double scale_min_;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   double scale_max_;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   double dscale_;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   // tabulated exponential</a>
+<a name="181"><span class="lineNum">     181 </span>            :   double dpcutoff_;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double dexp_;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   unsigned nexp_;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   std::vector&lt;double&gt; tab_exp_;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   // simulated annealing</a>
+<a name="186"><span class="lineNum">     186 </span>            :   unsigned nanneal_;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   double   kanneal_;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   double   anneal_;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // prior exponent</a>
+<a name="190"><span class="lineNum">     190 </span>            :   double prior_;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   // noise type</a>
+<a name="192"><span class="lineNum">     192 </span>            :   unsigned noise_;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // total score and virial;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   double ene_;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   Tensor virial_;</a>
+<a name="196"><span class="lineNum">     196 </span>            :   // model overlap file</a>
+<a name="197"><span class="lineNum">     197 </span>            :   unsigned int ovstride_;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   std::string       ovfilename_;</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   // Reweighting additions</a>
+<a name="201"><span class="lineNum">     201 </span>            :   bool do_reweight_;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   bool first_time_w_;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   std::vector&lt;double&gt; forces;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   std::vector&lt;double&gt; forcesToApply;</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   // average weights</a>
+<a name="207"><span class="lineNum">     207 </span>            :   double decay_w_;</a>
+<a name="208"><span class="lineNum">     208 </span>            :   std::vector&lt;double&gt; average_weights_;</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : // write file with model overlap</a>
+<a name="211"><span class="lineNum">     211 </span>            :   void write_model_overlap(long long int step);</a>
+<a name="212"><span class="lineNum">     212 </span>            : // get median of std::vector</a>
+<a name="213"><span class="lineNum">     213 </span>            :   double get_median(std::vector&lt;double&gt; &amp;v);</a>
+<a name="214"><span class="lineNum">     214 </span>            : // annealing</a>
+<a name="215"><span class="lineNum">     215 </span>            :   double get_annealing(long long int step);</a>
+<a name="216"><span class="lineNum">     216 </span>            : // do regression</a>
+<a name="217"><span class="lineNum">     217 </span>            :   double scaleEnergy(double s);</a>
+<a name="218"><span class="lineNum">     218 </span>            :   double doRegression();</a>
+<a name="219"><span class="lineNum">     219 </span>            : // read and write status</a>
+<a name="220"><span class="lineNum">     220 </span>            :   void read_status();</a>
+<a name="221"><span class="lineNum">     221 </span>            :   void print_status(long long int step);</a>
+<a name="222"><span class="lineNum">     222 </span>            : // accept or reject</a>
+<a name="223"><span class="lineNum">     223 </span>            :   bool doAccept(double oldE, double newE, double kbt);</a>
+<a name="224"><span class="lineNum">     224 </span>            : // do MonteCarlo</a>
+<a name="225"><span class="lineNum">     225 </span>            :   void doMonteCarlo();</a>
+<a name="226"><span class="lineNum">     226 </span>            : // read error file</a>
+<a name="227"><span class="lineNum">     227 </span>            :   std::vector&lt;double&gt; read_exp_errors(const std::string &amp; errfile);</a>
+<a name="228"><span class="lineNum">     228 </span>            : // read experimental overlaps</a>
+<a name="229"><span class="lineNum">     229 </span>            :   std::vector&lt;double&gt; read_exp_overlaps(const std::string &amp; ovfile);</a>
+<a name="230"><span class="lineNum">     230 </span>            : // calculate model GMM weights and covariances</a>
+<a name="231"><span class="lineNum">     231 </span>            :   std::vector&lt;double&gt; get_GMM_m(std::vector&lt;AtomNumber&gt; &amp;atoms);</a>
+<a name="232"><span class="lineNum">     232 </span>            : // read data GMM file</a>
+<a name="233"><span class="lineNum">     233 </span>            :   void get_GMM_d(std::string gmm_file);</a>
+<a name="234"><span class="lineNum">     234 </span>            : // check GMM data</a>
+<a name="235"><span class="lineNum">     235 </span>            :   void check_GMM_d(const VectorGeneric&lt;6&gt; &amp;cov, double w);</a>
+<a name="236"><span class="lineNum">     236 </span>            : // auxiliary method</a>
+<a name="237"><span class="lineNum">     237 </span>            :   void calculate_useful_stuff(double reso);</a>
+<a name="238"><span class="lineNum">     238 </span>            : // get pref_fact and inv_cov_md</a>
+<a name="239"><span class="lineNum">     239 </span>            :   double get_prefactor_inverse (const VectorGeneric&lt;6&gt; &amp;GMM_cov_0, const VectorGeneric&lt;6&gt; &amp;GMM_cov_1,</a>
+<a name="240"><span class="lineNum">     240 </span>            :                                 double GMM_w_0, double GMM_w_1,</a>
+<a name="241"><span class="lineNum">     241 </span>            :                                 VectorGeneric&lt;6&gt; &amp;sum, VectorGeneric&lt;6&gt; &amp;inv_sum);</a>
+<a name="242"><span class="lineNum">     242 </span>            : // calculate self overlaps between data GMM components - ovdd_</a>
+<a name="243"><span class="lineNum">     243 </span>            :   double get_self_overlap(unsigned id);</a>
+<a name="244"><span class="lineNum">     244 </span>            : // calculate overlap between two Gaussians</a>
+<a name="245"><span class="lineNum">     245 </span>            :   double get_overlap(const Vector &amp;m_m, const Vector &amp;d_m, double pre_fact,</a>
+<a name="246"><span class="lineNum">     246 </span>            :                      const VectorGeneric&lt;6&gt; &amp;inv_cov_md, Vector &amp;ov_der);</a>
+<a name="247"><span class="lineNum">     247 </span>            : // calculate exponent of overlap for neighbor list update</a>
+<a name="248"><span class="lineNum">     248 </span>            :   double get_exp_overlap(const Vector &amp;m_m, const Vector &amp;d_m,</a>
+<a name="249"><span class="lineNum">     249 </span>            :                          const VectorGeneric&lt;6&gt; &amp;inv_cov_md);</a>
+<a name="250"><span class="lineNum">     250 </span>            : // update the neighbor list</a>
+<a name="251"><span class="lineNum">     251 </span>            :   void update_neighbor_list();</a>
+<a name="252"><span class="lineNum">     252 </span>            : // calculate overlap</a>
+<a name="253"><span class="lineNum">     253 </span>            :   void calculate_overlap();</a>
+<a name="254"><span class="lineNum">     254 </span>            : // Gaussian noise</a>
+<a name="255"><span class="lineNum">     255 </span>            :   void calculate_Gauss();</a>
+<a name="256"><span class="lineNum">     256 </span>            : // Outliers noise</a>
+<a name="257"><span class="lineNum">     257 </span>            :   void calculate_Outliers();</a>
+<a name="258"><span class="lineNum">     258 </span>            : // Marginal noise</a>
+<a name="259"><span class="lineNum">     259 </span>            :   void calculate_Marginal();</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   // See MetainferenceBase</a>
+<a name="262"><span class="lineNum">     262 </span>            :   void get_weights(double &amp;weight, double &amp;norm, double &amp;neff);</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : public:</a>
+<a name="265"><span class="lineNum">     265 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="266"><span class="lineNum">     266 </span>            :   explicit EMMI(const ActionOptions&amp;);</a>
+<a name="267"><span class="lineNum">     267 </span>            :   // needed for reweighting</a>
+<a name="268"><span class="lineNum">     268 </span>            :   void setDerivatives();</a>
+<a name="269"><span class="lineNum">     269 </span>            :   void turnOnDerivatives() override;</a>
+<a name="270"><span class="lineNum">     270 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="271"><span class="lineNum">     271 </span>            :   void lockRequests() override;</a>
+<a name="272"><span class="lineNum">     272 </span>            :   void unlockRequests() override;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a ) override;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   void apply() override;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   void setArgDerivatives(Value *v, const double &amp;d);</a>
+<a name="276"><span class="lineNum">     276 </span>            :   void setAtomsDerivatives(Value*v, const unsigned i, const Vector&amp;d);</a>
+<a name="277"><span class="lineNum">     277 </span>            :   void setBoxDerivatives(Value*v, const Tensor&amp;d);</a>
+<a name="278"><span class="lineNum">     278 </span>            : // active methods:</a>
+<a name="279"><span class="lineNum">     279 </span>            :   void prepare() override;</a>
+<a name="280"><span class="lineNum">     280 </span>            :   void calculate() override;</a>
+<a name="281"><span class="lineNum">     281 </span>            : };</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : inline</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         20 : void EMMI::setDerivatives() {</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   // Get appropriate number of derivatives</a>
+<a name="286"><span class="lineNum">     286 </span>            :   // Derivatives are first for arguments and then for atoms</a>
+<a name="287"><span class="lineNum">     287 </span>            :   unsigned nder;</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         20 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         20 :     nder = 3*getNumberOfAtoms() + 9 + getNumberOfArguments();</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   } else {</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :     nder = getNumberOfArguments();</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :   }</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            :   // Resize all derivative arrays</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         20 :   forces.resize( nder ); forcesToApply.resize( nder );</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         92 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) getPntrToComponent(i)-&gt;resizeDerivatives(nder);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         20 : }</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : inline</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         20 : void EMMI::turnOnDerivatives() {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         20 :   ActionWithValue::turnOnDerivatives();</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         20 : }</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : inline</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         72 : unsigned EMMI::getNumberOfDerivatives() {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         72 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         72 :     return 3*getNumberOfAtoms() + 9 + getNumberOfArguments();</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :   }</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :   return getNumberOfArguments();</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : }</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            : inline</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         30 : void EMMI::lockRequests() {</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :   ActionAtomistic::lockRequests();</a>
+<a name="315"><span class="lineNum">     315 </span>            :   ActionWithArguments::lockRequests();</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         30 : }</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : inline</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         30 : void EMMI::unlockRequests() {</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   ActionAtomistic::unlockRequests();</a>
+<a name="321"><span class="lineNum">     321 </span>            :   ActionWithArguments::unlockRequests();</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         30 : }</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : inline</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          9 : void EMMI::calculateNumericalDerivatives( ActionWithValue* a=NULL ) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          9 :   if( getNumberOfArguments()&gt;0 ) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :     ActionWithArguments::calculateNumericalDerivatives( a );</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :   }</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          9 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          9 :     Matrix&lt;double&gt; save_derivatives( getNumberOfComponents(), getNumberOfArguments() );</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         39 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         30 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) if(getPntrToComponent(j)-&gt;hasDerivatives()) save_derivatives(j,i)=getPntrToComponent(j)-&gt;getDerivative(i);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          9 :     calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         39 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         30 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) if(getPntrToComponent(j)-&gt;hasDerivatives()) getPntrToComponent(j)-&gt;addDerivative( i, save_derivatives(j,i) );</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     }</a>
+<a name="338"><span class="lineNum">     338 </span>            :   }</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          9 : }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : inline</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         30 : void EMMI::apply() {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         30 :   bool wasforced=false; forcesToApply.assign(forcesToApply.size(),0.0);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        162 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        132 :     if( getPntrToComponent(i)-&gt;applyForce( forces ) ) {</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :       wasforced=true;</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;forces.size(); ++i) forcesToApply[i]+=forces[i];</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :     }</a>
+<a name="349"><span class="lineNum">     349 </span>            :   }</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         30 :   if( wasforced ) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :     addForcesOnArguments( forcesToApply );</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :     if( getNumberOfAtoms()&gt;0 ) setForcesOnAtoms( forcesToApply, getNumberOfArguments() );</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :   }</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         30 : }</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            : inline</a>
+<a name="357"><span class="lineNum">     357 </span>            : void EMMI::setArgDerivatives(Value *v, const double &amp;d) {</a>
+<a name="358"><span class="lineNum">     358 </span>            :   v-&gt;addDerivative(0,d);</a>
+<a name="359"><span class="lineNum">     359 </span>            : }</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : inline</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">    9844626 : void EMMI::setAtomsDerivatives(Value*v, const unsigned i, const Vector&amp;d) {</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">    9844626 :   const unsigned noa=getNumberOfArguments();</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">    9844626 :   v-&gt;addDerivative(noa+3*i+0,d[0]);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">    9844626 :   v-&gt;addDerivative(noa+3*i+1,d[1]);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">    9844626 :   v-&gt;addDerivative(noa+3*i+2,d[2]);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">    9844626 : }</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : inline</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      16365 : void EMMI::setBoxDerivatives(Value* v,const Tensor&amp;d) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      16365 :   const unsigned noa=getNumberOfArguments();</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   const unsigned nat=getNumberOfAtoms();</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+0,d(0,0));</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+1,d(0,1));</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+2,d(0,2));</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+3,d(1,0));</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+4,d(1,1));</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+5,d(1,2));</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+6,d(2,0));</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+7,d(2,1));</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">      16365 :   v-&gt;addDerivative(noa+3*nat+8,d(2,2));</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">      16365 : }</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">      12544 : PLUMED_REGISTER_ACTION(EMMI,&quot;EMMI&quot;)</span></a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         22 : void EMMI::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         22 :   Action::registerKeywords( keys );</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         22 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         22 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         22 :   ActionWithArguments::registerKeywords( keys );</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         22 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         44 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;atoms for which we calculate the density map, typically all heavy atoms&quot;);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         44 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;GMM_FILE&quot;,&quot;file with the parameters of the GMM components&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;NL_CUTOFF&quot;,&quot;The cutoff in overlap for the neighbor list&quot;);</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;NL_STRIDE&quot;,&quot;The frequency with which we are updating the neighbor list&quot;);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA_MIN&quot;,&quot;minimum uncertainty&quot;);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;RESOLUTION&quot;, &quot;Cryo-EM map resolution&quot;);</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         44 :   keys.add(&quot;compulsory&quot;,&quot;NOISETYPE&quot;,&quot;functional form of the noise (GAUSS, OUTLIERS, MARGINAL)&quot;);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;SIGMA0&quot;,&quot;initial value of the uncertainty&quot;);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;DSIGMA&quot;,&quot;MC step for uncertainties&quot;);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;MC_STRIDE&quot;, &quot;Monte Carlo stride&quot;);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;ERR_FILE&quot;,&quot;file with experimental or GMM fit errors&quot;);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;OV_FILE&quot;,&quot;file with experimental overlaps&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;NORM_DENSITY&quot;,&quot;integral of the experimental density&quot;);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;STATUS_FILE&quot;,&quot;write a file with all the data useful for restart&quot;);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;WRITE_STRIDE&quot;,&quot;write the status to a file every N steps, this can be used for restart&quot;);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;REGRESSION&quot;,&quot;regression stride&quot;);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;REG_SCALE_MIN&quot;,&quot;regression minimum scale&quot;);</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;REG_SCALE_MAX&quot;,&quot;regression maximum scale&quot;);</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;REG_DSCALE&quot;,&quot;regression maximum scale MC move&quot;);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;SCALE&quot;,&quot;scale factor&quot;);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;ANNEAL&quot;, &quot;Length of annealing cycle&quot;);</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;ANNEAL_FACT&quot;, &quot;Annealing temperature factor&quot;);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;temperature&quot;);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;PRIOR&quot;, &quot;exponent of uncertainty prior&quot;);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;WRITE_OV_STRIDE&quot;,&quot;write model overlaps every N steps&quot;);</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;WRITE_OV&quot;,&quot;write a file with model overlaps&quot;);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;AVERAGING&quot;, &quot;Averaging window for weights&quot;);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         44 :   keys.addFlag(&quot;NO_AVER&quot;,false,&quot;don't do ensemble averaging in multi-replica mode&quot;);</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         44 :   keys.addFlag(&quot;REWEIGHT&quot;,false,&quot;simple REWEIGHT using the ARG as energy&quot;);</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         22 :   componentsAreNotOptional(keys);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;scoreb&quot;,&quot;default&quot;,&quot;Bayesian score&quot;);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;acc&quot;,   &quot;NOISETYPE&quot;,&quot;MC acceptance for uncertainty&quot;);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;scale&quot;, &quot;REGRESSION&quot;,&quot;scale factor&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;accscale&quot;, &quot;REGRESSION&quot;,&quot;MC acceptance for scale regression&quot;);</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;enescale&quot;, &quot;REGRESSION&quot;,&quot;MC energy for scale regression&quot;);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;anneal&quot;,&quot;ANNEAL&quot;,&quot;annealing factor&quot;);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;weight&quot;,       &quot;REWEIGHT&quot;,     &quot;weights of the weighted average&quot;);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;biasDer&quot;,      &quot;REWEIGHT&quot;,     &quot;derivatives with respect to the bias&quot;);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;sigma&quot;,      &quot;NOISETYPE&quot;,     &quot;uncertainty in the forward models and experiment&quot;);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         44 :   keys.addOutputComponent(&quot;neff&quot;,         &quot;default&quot;,      &quot;effective number of replicas&quot;);</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         22 : }</span></a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         20 : EMMI::EMMI(const ActionOptions&amp;ao):</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :   Action(ao),</a>
+<a name="437"><span class="lineNum">     437 </span>            :   ActionAtomistic(ao),</a>
+<a name="438"><span class="lineNum">     438 </span>            :   ActionWithArguments(ao),</a>
+<a name="439"><span class="lineNum">     439 </span>            :   ActionWithValue(ao),</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         20 :   inv_sqrt2_(0.707106781186548),</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         20 :   sqrt2_pi_(0.797884560802865),</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         20 :   first_time_(true), no_aver_(false), pbc_(true),</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         20 :   MCstride_(1), MCaccept_(0.), MCtrials_(0.),</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         40 :   statusstride_(0), first_status_(true),</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         20 :   nregres_(0), scale_(1.),</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         20 :   dpcutoff_(15.0), nexp_(1000000), nanneal_(0),</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         40 :   kanneal_(0.), anneal_(1.), prior_(1.), ovstride_(0),</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         20 :   do_reweight_(false), first_time_w_(true), decay_w_(1.)</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : {</a>
+<a name="450"><span class="lineNum">     450 </span>            :   // periodic boundary conditions</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         20 :   bool nopbc=!pbc_;</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         20 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         20 :   pbc_=!nopbc;</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            :   // list of atoms</a>
+<a name="456"><span class="lineNum">     456 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         40 :   parseAtomList(&quot;ATOMS&quot;, atoms);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            :   // file with data GMM</a>
+<a name="460"><span class="lineNum">     460 </span>            :   std::string GMM_file;</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         40 :   parse(&quot;GMM_FILE&quot;, GMM_file);</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            :   // type of data noise</a>
+<a name="464"><span class="lineNum">     464 </span>            :   std::string noise;</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         40 :   parse(&quot;NOISETYPE&quot;,noise);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         20 :   if      (noise==&quot;GAUSS&quot;)   noise_ = 0;</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         12 :   else if(noise==&quot;OUTLIERS&quot;) noise_ = 1;</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          6 :   else if(noise==&quot;MARGINAL&quot;) noise_ = 2;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :   else error(&quot;Unknown noise type!&quot;);</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            :   // minimum value for error</a>
+<a name="472"><span class="lineNum">     472 </span>            :   double sigma_min;</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         20 :   parse(&quot;SIGMA_MIN&quot;, sigma_min);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         20 :   if(sigma_min&lt;0) error(&quot;SIGMA_MIN should be greater or equal to zero&quot;);</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            :   // the following parameters must be specified with noise type 0 and 1</a>
+<a name="477"><span class="lineNum">     477 </span>            :   double sigma_ini, dsigma;</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         20 :   if(noise_!=2) {</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :     // initial value of the uncertainty</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         14 :     parse(&quot;SIGMA0&quot;, sigma_ini);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         14 :     if(sigma_ini&lt;=0) error(&quot;you must specify a positive SIGMA0&quot;);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :     // MC parameters</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         14 :     parse(&quot;DSIGMA&quot;, dsigma);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         14 :     if(dsigma&lt;0) error(&quot;you must specify a positive DSIGMA&quot;);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         14 :     parse(&quot;MC_STRIDE&quot;, MCstride_);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         14 :     if(dsigma&gt;0 &amp;&amp; MCstride_&lt;=0) error(&quot;you must specify a positive MC_STRIDE&quot;);</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     // status file parameters</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         14 :     parse(&quot;WRITE_STRIDE&quot;, statusstride_);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         14 :     if(statusstride_==0) error(&quot;you must specify a positive WRITE_STRIDE&quot;);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         28 :     parse(&quot;STATUS_FILE&quot;,  statusfilename_);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">         28 :     if(statusfilename_==&quot;&quot;) statusfilename_ = &quot;MISTATUS&quot;+getLabel();</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :     else                    statusfilename_ = statusfilename_+getLabel();</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :   }</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span>            :   // error file</a>
+<a name="496"><span class="lineNum">     496 </span>            :   std::string errfile;</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         40 :   parse(&quot;ERR_FILE&quot;, errfile);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            :   // file with experimental overlaps</a>
+<a name="500"><span class="lineNum">     500 </span>            :   std::string ovfile;</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         20 :   parse(&quot;OV_FILE&quot;, ovfile);</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            :   // integral of the experimetal density</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         20 :   double norm_d = 0.0;</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         20 :   parse(&quot;NORM_DENSITY&quot;, norm_d);</span></a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span>            :   // temperature</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         20 :   double temp=0.0;</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         20 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :   // convert temp to kbt</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         20 :   if(temp&gt;0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :   else kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            :   // exponent of uncertainty prior</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         20 :   parse(&quot;PRIOR&quot;,prior_);</span></a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span>            :   // simulated annealing stuff</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         20 :   parse(&quot;ANNEAL&quot;, nanneal_);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         20 :   parse(&quot;ANNEAL_FACT&quot;, kanneal_);</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         20 :   if(nanneal_&gt;0 &amp;&amp; kanneal_&lt;=1.0) error(&quot;with ANNEAL, ANNEAL_FACT must be greater than 1&quot;);</span></a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span>            :   // regression stride</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         20 :   parse(&quot;REGRESSION&quot;,nregres_);</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :   // other regression parameters</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         20 :   if(nregres_&gt;0) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :     parse(&quot;REG_SCALE_MIN&quot;,scale_min_);</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :     parse(&quot;REG_SCALE_MAX&quot;,scale_max_);</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 :     parse(&quot;REG_DSCALE&quot;,dscale_);</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :     // checks</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :     if(scale_max_&lt;=scale_min_) error(&quot;with REGRESSION, REG_SCALE_MAX must be greater than REG_SCALE_MIN&quot;);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :     if(dscale_&lt;=0.) error(&quot;with REGRESSION, REG_DSCALE must be positive&quot;);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :   }</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            :   // scale factor</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         20 :   parse(&quot;SCALE&quot;, scale_);</span></a>
+<a name="536"><span class="lineNum">     536 </span>            : </a>
+<a name="537"><span class="lineNum">     537 </span>            :   // read map resolution</a>
+<a name="538"><span class="lineNum">     538 </span>            :   double reso;</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         20 :   parse(&quot;RESOLUTION&quot;, reso);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         20 :   if(reso&lt;=0.) error(&quot;RESOLUTION should be strictly positive&quot;);</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span>            :   // neighbor list stuff</a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         20 :   parse(&quot;NL_CUTOFF&quot;,nl_cutoff_);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         20 :   if(nl_cutoff_&lt;=0.0) error(&quot;NL_CUTOFF should be explicitly specified and positive&quot;);</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         20 :   parse(&quot;NL_STRIDE&quot;,nl_stride_);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         20 :   if(nl_stride_==0) error(&quot;NL_STRIDE should be explicitly specified and positive&quot;);</span></a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            :   // averaging or not</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         20 :   parseFlag(&quot;NO_AVER&quot;,no_aver_);</span></a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span>            :   // write overlap file</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         20 :   parse(&quot;WRITE_OV_STRIDE&quot;, ovstride_);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         20 :   parse(&quot;WRITE_OV&quot;, ovfilename_);</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         20 :   if(ovstride_&gt;0 &amp;&amp; ovfilename_==&quot;&quot;) error(&quot;With WRITE_OV_STRIDE you must specify WRITE_OV&quot;);</span></a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            :   // set parallel stuff</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         20 :   size_=comm.Get_size();</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         20 :   rank_=comm.Get_rank();</span></a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span>            :   // get number of replicas</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">         20 :   if(rank_==0) {</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         14 :     if(no_aver_) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         12 :       nrep_ = 1;</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :     } else {</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          2 :       nrep_ = multi_sim_comm.Get_size();</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :     }</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         14 :     replica_ = multi_sim_comm.Get_rank();</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :   } else {</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          6 :     nrep_ = 0;</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">          6 :     replica_ = 0;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :   }</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         20 :   comm.Sum(&amp;nrep_,1);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         20 :   comm.Sum(&amp;replica_,1);</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span>            :   // Reweighting flag</a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         20 :   parseFlag(&quot;REWEIGHT&quot;, do_reweight_);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         20 :   if(do_reweight_&amp;&amp;getNumberOfArguments()!=1) error(&quot;To REWEIGHT one must provide one single bias as an argument&quot;);</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         20 :   if(do_reweight_&amp;&amp;no_aver_) error(&quot;REWEIGHT cannot be used with NO_AVER&quot;);</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         20 :   if(do_reweight_&amp;&amp;nrep_&lt;2) error(&quot;REWEIGHT can only be used in parallel with 2 or more replicas&quot;);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         20 :   if(!getRestart()) average_weights_.resize(nrep_, 1./static_cast&lt;double&gt;(nrep_));</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :   else average_weights_.resize(nrep_, 0.);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         20 :   unsigned averaging=0;</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         20 :   parse(&quot;AVERAGING&quot;, averaging);</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         20 :   if(averaging&gt;0) {</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">          2 :     decay_w_ = 1./static_cast&lt;double&gt; (averaging);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :   }</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         20 :   checkRead();</span></a>
+<a name="590"><span class="lineNum">     590 </span>            : </a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         20 :   log.printf(&quot;  atoms involved : &quot;);</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">      10876 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         20 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         20 :   log.printf(&quot;  GMM data file : %s\n&quot;, GMM_file.c_str());</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         20 :   if(no_aver_) log.printf(&quot;  without ensemble averaging\n&quot;);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         20 :   log.printf(&quot;  type of data noise : %s\n&quot;, noise.c_str());</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">         20 :   log.printf(&quot;  neighbor list cutoff : %lf\n&quot;, nl_cutoff_);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         20 :   log.printf(&quot;  neighbor list stride : %u\n&quot;,  nl_stride_);</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         20 :   log.printf(&quot;  minimum uncertainty : %f\n&quot;,sigma_min);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         20 :   log.printf(&quot;  scale factor : %lf\n&quot;,scale_);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">         20 :   if(nregres_&gt;0) {</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :     log.printf(&quot;  regression stride : %u\n&quot;, nregres_);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :     log.printf(&quot;  regression minimum scale : %lf\n&quot;, scale_min_);</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :     log.printf(&quot;  regression maximum scale : %lf\n&quot;, scale_max_);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 :     log.printf(&quot;  regression maximum scale MC move : %lf\n&quot;, dscale_);</span></a>
+<a name="606"><span class="lineNum">     606 </span>            :   }</a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         20 :   if(noise_!=2) {</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">         14 :     log.printf(&quot;  initial value of the uncertainty : %f\n&quot;,sigma_ini);</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         14 :     log.printf(&quot;  max MC move in uncertainty : %f\n&quot;,dsigma);</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         14 :     log.printf(&quot;  MC stride : %u\n&quot;, MCstride_);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         14 :     log.printf(&quot;  reading/writing to status file : %s\n&quot;,statusfilename_.c_str());</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         14 :     log.printf(&quot;  with stride : %u\n&quot;,statusstride_);</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :   }</a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         20 :   if(errfile.size()&gt;0) log.printf(&quot;  reading experimental errors from file : %s\n&quot;, errfile.c_str());</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         20 :   if(ovfile.size()&gt;0)  log.printf(&quot;  reading experimental overlaps from file : %s\n&quot;, ovfile.c_str());</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         20 :   log.printf(&quot;  temperature of the system in energy unit : %f\n&quot;,kbt_);</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         20 :   log.printf(&quot;  prior exponent : %f\n&quot;,prior_);</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         20 :   log.printf(&quot;  number of replicas for averaging: %u\n&quot;,nrep_);</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         20 :   log.printf(&quot;  id of the replica : %u\n&quot;,replica_);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         20 :   if(nanneal_&gt;0) {</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :     log.printf(&quot;  length of annealing cycle : %u\n&quot;,nanneal_);</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :     log.printf(&quot;  annealing factor : %f\n&quot;,kanneal_);</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :   }</a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">         20 :   if(ovstride_&gt;0) {</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineNoCov">          0 :     log.printf(&quot;  stride for writing model overlaps : %u\n&quot;,ovstride_);</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :     log.printf(&quot;  file for writing model overlaps : %s\n&quot;, ovfilename_.c_str());</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :   }</a>
+<a name="628"><span class="lineNum">     628 </span>            : </a>
+<a name="629"><span class="lineNum">     629 </span>            :   // set constant quantity before calculating stuff</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         20 :   cfact_ = 1.0/pow( 2.0*pi, 1.5 );</span></a>
+<a name="631"><span class="lineNum">     631 </span>            : </a>
+<a name="632"><span class="lineNum">     632 </span>            :   // calculate model GMM constant parameters</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">         20 :   std::vector&lt;double&gt; GMM_m_w = get_GMM_m(atoms);</span></a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            :   // read data GMM parameters</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         20 :   get_GMM_d(GMM_file);</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">         20 :   log.printf(&quot;  number of GMM components : %u\n&quot;, static_cast&lt;unsigned&gt;(GMM_d_m_.size()));</span></a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            :   // normalize atom weight map</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">         40 :   if(norm_d &lt;= 0.0) norm_d = accumulate(GMM_d_w_.begin(), GMM_d_w_.end(), 0.0);</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :   double norm_m = accumulate(GMM_m_w.begin(),  GMM_m_w.end(),  0.0);</a>
+<a name="642"><span class="lineNum">     642 </span>            :   // renormalization</a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">        100 :   for(unsigned i=0; i&lt;GMM_m_w_.size(); ++i) GMM_m_w_[i] *= norm_d / norm_m;</span></a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span>            :   // read experimental errors</a>
+<a name="646"><span class="lineNum">     646 </span>            :   std::vector&lt;double&gt; exp_err;</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         20 :   if(errfile.size()&gt;0) exp_err = read_exp_errors(errfile);</span></a>
+<a name="648"><span class="lineNum">     648 </span>            : </a>
+<a name="649"><span class="lineNum">     649 </span>            :   // get self overlaps between data GMM components</a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         20 :   if(ovfile.size()&gt;0) {</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 :     ovdd_ = read_exp_overlaps(ovfile);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :   } else {</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">       1982 :     for(unsigned i=0; i&lt;GMM_d_m_.size(); ++i) {</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">       1962 :       double ov = get_self_overlap(i);</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">       1962 :       ovdd_.push_back(ov);</span></a>
+<a name="656"><span class="lineNum">     656 </span>            :     }</a>
+<a name="657"><span class="lineNum">     657 </span>            :   }</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">         20 :   log.printf(&quot;  number of GMM groups : %u\n&quot;, static_cast&lt;unsigned&gt;(GMM_d_grps_.size()));</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :   // cycle on GMM groups</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         40 :   for(unsigned Gid=0; Gid&lt;GMM_d_grps_.size(); ++Gid) {</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         20 :     log.printf(&quot;    group %d\n&quot;, Gid);</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :     // calculate median overlap and experimental error</a>
+<a name="664"><span class="lineNum">     664 </span>            :     std::vector&lt;double&gt; ovdd;</a>
+<a name="665"><span class="lineNum">     665 </span>            :     std::vector&lt;double&gt; err;</a>
+<a name="666"><span class="lineNum">     666 </span>            :     // cycle on the group members</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">       1982 :     for(unsigned i=0; i&lt;GMM_d_grps_[Gid].size(); ++i) {</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :       // GMM id</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">       1962 :       int GMMid = GMM_d_grps_[Gid][i];</span></a>
+<a name="670"><span class="lineNum">     670 </span>            :       // add to experimental error</a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">       1962 :       if(errfile.size()&gt;0) err.push_back(exp_err[GMMid]);</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">       1962 :       else                 err.push_back(0.);</span></a>
+<a name="673"><span class="lineNum">     673 </span>            :       // add to GMM overlap</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">       1962 :       ovdd.push_back(ovdd_[GMMid]);</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :     }</a>
+<a name="676"><span class="lineNum">     676 </span>            :     // calculate median quantities</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         20 :     double ovdd_m = get_median(ovdd);</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         20 :     double err_m  = get_median(err);</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :     // print out statistics</a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         20 :     log.printf(&quot;     # of members : %zu\n&quot;, GMM_d_grps_[Gid].size());</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         20 :     log.printf(&quot;     median overlap : %lf\n&quot;, ovdd_m);</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         20 :     log.printf(&quot;     median error : %lf\n&quot;, err_m);</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :     // add minimum value of sigma for this group of GMMs</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         20 :     sigma_min_.push_back(std::sqrt(err_m*err_m+sigma_min*ovdd_m*sigma_min*ovdd_m));</span></a>
+<a name="685"><span class="lineNum">     685 </span>            :     // these are only needed with Gaussian and Outliers noise models</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         20 :     if(noise_!=2) {</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :       // set dsigma</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         14 :       dsigma_.push_back(dsigma * ovdd_m);</span></a>
+<a name="689"><span class="lineNum">     689 </span>            :       // set sigma max</a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         14 :       sigma_max_.push_back(10.0*ovdd_m + sigma_min_[Gid] + dsigma_[Gid]);</span></a>
+<a name="691"><span class="lineNum">     691 </span>            :       // initialize sigma</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         28 :       sigma_.push_back(std::max(sigma_min_[Gid],std::min(sigma_ini*ovdd_m,sigma_max_[Gid])));</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :     }</a>
+<a name="694"><span class="lineNum">     694 </span>            :   }</a>
+<a name="695"><span class="lineNum">     695 </span>            : </a>
+<a name="696"><span class="lineNum">     696 </span>            :   // read status file if restarting</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         20 :   if(getRestart() &amp;&amp; noise_!=2) read_status();</span></a>
+<a name="698"><span class="lineNum">     698 </span>            : </a>
+<a name="699"><span class="lineNum">     699 </span>            :   // calculate auxiliary stuff</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         20 :   calculate_useful_stuff(reso);</span></a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            :   // prepare data and derivative std::vectors</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         20 :   ovmd_.resize(ovdd_.size());</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">         20 :   ovmd_ave_.resize(ovdd_.size());</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         20 :   atom_der_.resize(GMM_m_type_.size());</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">         20 :   GMMid_der_.resize(ovdd_.size());</span></a>
+<a name="707"><span class="lineNum">     707 </span>            : </a>
+<a name="708"><span class="lineNum">     708 </span>            :   // clear things that are no longer needed</a>
+<a name="709"><span class="lineNum">     709 </span>            :   GMM_d_cov_.clear();</a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            :   // add components</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">         40 :   addComponentWithDerivatives(&quot;scoreb&quot;); componentIsNotPeriodic(&quot;scoreb&quot;);</span></a>
+<a name="713"><span class="lineNum">     713 </span>            : </a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">         48 :   if(noise_!=2) {addComponent(&quot;acc&quot;); componentIsNotPeriodic(&quot;acc&quot;);}</span></a>
+<a name="715"><span class="lineNum">     715 </span>            : </a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">         20 :   if(nregres_&gt;0) {</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :     addComponent(&quot;scale&quot;);     componentIsNotPeriodic(&quot;scale&quot;);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineNoCov">          0 :     addComponent(&quot;accscale&quot;);  componentIsNotPeriodic(&quot;accscale&quot;);</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :     addComponent(&quot;enescale&quot;);  componentIsNotPeriodic(&quot;enescale&quot;);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :   }</a>
+<a name="721"><span class="lineNum">     721 </span>            : </a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">         20 :   if(nanneal_&gt;0) {addComponent(&quot;anneal&quot;); componentIsNotPeriodic(&quot;anneal&quot;);}</span></a>
+<a name="723"><span class="lineNum">     723 </span>            : </a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">         20 :   if(do_reweight_) {</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">          2 :     addComponent(&quot;biasDer&quot;);</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">          2 :     componentIsNotPeriodic(&quot;biasDer&quot;);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">          2 :     addComponent(&quot;weight&quot;);</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">          4 :     componentIsNotPeriodic(&quot;weight&quot;);</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :   }</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">         20 :   addComponent(&quot;neff&quot;);</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">         20 :   componentIsNotPeriodic(&quot;neff&quot;);</span></a>
+<a name="733"><span class="lineNum">     733 </span>            : </a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">         34 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         14 :     std::string num; Tools::convert(i, num);</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">         28 :     addComponent(&quot;sigma-&quot;+num); componentIsNotPeriodic(&quot;sigma-&quot;+num);</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">         28 :     getPntrToComponent(&quot;sigma-&quot;+num)-&gt;set(sigma_[i]);</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :   }</a>
+<a name="739"><span class="lineNum">     739 </span>            : </a>
+<a name="740"><span class="lineNum">     740 </span>            :   // initialize random seed</a>
+<a name="741"><span class="lineNum">     741 </span>            :   unsigned iseed;</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">         20 :   if(rank_==0) iseed = time(NULL)+replica_;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">          6 :   else iseed = 0;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">         20 :   comm.Sum(&amp;iseed, 1);</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">         20 :   random_.setSeed(-iseed);</span></a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span>            :   // request the atoms</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">         20 :   requestAtoms(atoms);</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">         20 :   setDerivatives();</span></a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            :   // print bibliography</a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">         40 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;);</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         40 :   log&lt;&lt;plumed.cite(&quot;Hanot, Bonomi, Greenberg, Sali, Nilges, Vendruscolo, Pellarin, bioRxiv doi: 10.1101/113951 (2017)&quot;);</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">         40 :   log&lt;&lt;plumed.cite(&quot;Bonomi, Pellarin, Vendruscolo, Biophys. J. 114, 1604 (2018)&quot;);</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">         22 :   if(do_reweight_) log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)&quot;);</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">         22 :   if(!no_aver_ &amp;&amp; nrep_&gt;1)log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)&quot;);</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">         20 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">         20 : }</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineNoCov">          0 : void EMMI::write_model_overlap(long long int step)</span></a>
+<a name="761"><span class="lineNum">     761 </span>            : {</a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :   OFile ovfile;</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineNoCov">          0 :   ovfile.link(*this);</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineNoCov">          0 :   std::string num; Tools::convert(step,num);</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineNoCov">          0 :   std::string name = ovfilename_+&quot;-&quot;+num;</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineNoCov">          0 :   ovfile.open(name);</span></a>
+<a name="767"><span class="lineNum">     767 </span>            :   ovfile.setHeavyFlush();</a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineNoCov">          0 :   ovfile.fmtField(&quot;%10.7e &quot;);</span></a>
+<a name="769"><span class="lineNum">     769 </span>            : // write overlaps</a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineNoCov">          0 :   for(int i=0; i&lt;ovmd_.size(); ++i) {</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineNoCov">          0 :     ovfile.printField(&quot;Model&quot;, ovmd_[i]);</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineNoCov">          0 :     ovfile.printField(&quot;ModelScaled&quot;, scale_ * ovmd_[i]);</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineNoCov">          0 :     ovfile.printField(&quot;Data&quot;, ovdd_[i]);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineNoCov">          0 :     ovfile.printField();</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :   }</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineNoCov">          0 :   ovfile.close();</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">         40 : double EMMI::get_median(std::vector&lt;double&gt; &amp;v)</span></a>
+<a name="780"><span class="lineNum">     780 </span>            : {</a>
+<a name="781"><span class="lineNum">     781 </span>            : // dimension of std::vector</a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">         40 :   unsigned size = v.size();</span></a>
+<a name="783"><span class="lineNum">     783 </span>            : // in case of only one entry</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">         40 :   if (size==1) {</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineNoCov">          0 :     return v[0];</span></a>
+<a name="786"><span class="lineNum">     786 </span>            :   } else {</a>
+<a name="787"><span class="lineNum">     787 </span>            :     // reorder std::vector</a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">         40 :     sort(v.begin(), v.end());</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :     // odd or even?</a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">         40 :     if (size%2==0) {</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">          4 :       return (v[size/2-1]+v[size/2])/2.0;</span></a>
+<a name="792"><span class="lineNum">     792 </span>            :     } else {</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">         36 :       return v[size/2];</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :     }</a>
+<a name="795"><span class="lineNum">     795 </span>            :   }</a>
+<a name="796"><span class="lineNum">     796 </span>            : }</a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 : void EMMI::read_status()</span></a>
+<a name="799"><span class="lineNum">     799 </span>            : {</a>
+<a name="800"><span class="lineNum">     800 </span>            :   double MDtime;</a>
+<a name="801"><span class="lineNum">     801 </span>            : // open file</a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineNoCov">          0 :   auto ifile = Tools::make_unique&lt;IFile&gt;();</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineNoCov">          0 :   ifile-&gt;link(*this);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineNoCov">          0 :   if(ifile-&gt;FileExist(statusfilename_)) {</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineNoCov">          0 :     ifile-&gt;open(statusfilename_);</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineNoCov">          0 :     while(ifile-&gt;scanField(&quot;MD_time&quot;, MDtime)) {</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="808"><span class="lineNum">     808 </span>            :         // convert i to std::string</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineNoCov">          0 :         std::string num; Tools::convert(i,num);</span></a>
+<a name="810"><span class="lineNum">     810 </span>            :         // read entries</a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineNoCov">          0 :         ifile-&gt;scanField(&quot;s&quot;+num, sigma_[i]);</span></a>
+<a name="812"><span class="lineNum">     812 </span>            :       }</a>
+<a name="813"><span class="lineNum">     813 </span>            :       // new line</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineNoCov">          0 :       ifile-&gt;scanField();</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :     }</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineNoCov">          0 :     ifile-&gt;close();</span></a>
+<a name="817"><span class="lineNum">     817 </span>            :   } else {</a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineNoCov">          0 :     error(&quot;Cannot find status file &quot;+statusfilename_+&quot;\n&quot;);</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :   }</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="821"><span class="lineNum">     821 </span>            : </a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">      10904 : void EMMI::print_status(long long int step)</span></a>
+<a name="823"><span class="lineNum">     823 </span>            : {</a>
+<a name="824"><span class="lineNum">     824 </span>            : // if first time open the file</a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">      10904 :   if(first_status_) {</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         14 :     first_status_ = false;</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">         14 :     statusfile_.link(*this);</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         14 :     statusfile_.open(statusfilename_);</span></a>
+<a name="829"><span class="lineNum">     829 </span>            :     statusfile_.setHeavyFlush();</a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">         28 :     statusfile_.fmtField(&quot;%6.3e &quot;);</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :   }</a>
+<a name="832"><span class="lineNum">     832 </span>            : // write fields</a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">      10904 :   double MDtime = static_cast&lt;double&gt;(step)*getTimeStep();</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">      10904 :   statusfile_.printField(&quot;MD_time&quot;, MDtime);</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">      21808 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :     // convert i to std::string</a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">      10904 :     std::string num; Tools::convert(i,num);</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :     // print entry</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">      21808 :     statusfile_.printField(&quot;s&quot;+num, sigma_[i]);</span></a>
+<a name="840"><span class="lineNum">     840 </span>            :   }</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">      10904 :   statusfile_.printField();</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">      10904 : }</span></a>
+<a name="843"><span class="lineNum">     843 </span>            : </a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineNoCov">          0 : bool EMMI::doAccept(double oldE, double newE, double kbt) {</span></a>
+<a name="845"><span class="lineNum">     845 </span>            :   bool accept = false;</a>
+<a name="846"><span class="lineNum">     846 </span>            :   // calculate delta energy</a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineNoCov">          0 :   double delta = ( newE - oldE ) / kbt;</span></a>
+<a name="848"><span class="lineNum">     848 </span>            :   // if delta is negative always accept move</a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :   if( delta &lt; 0.0 ) {</span></a>
+<a name="850"><span class="lineNum">     850 </span>            :     accept = true;</a>
+<a name="851"><span class="lineNum">     851 </span>            :   } else {</a>
+<a name="852"><span class="lineNum">     852 </span>            :     // otherwise extract random number</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :     double s = random_.RandU01();</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) { accept = true; }</span></a>
+<a name="855"><span class="lineNum">     855 </span>            :   }</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineNoCov">          0 :   return accept;</span></a>
+<a name="857"><span class="lineNum">     857 </span>            : }</a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineNoCov">          0 : void EMMI::doMonteCarlo()</span></a>
+<a name="860"><span class="lineNum">     860 </span>            : {</a>
+<a name="861"><span class="lineNum">     861 </span>            :   // extract random GMM group</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineNoCov">          0 :   unsigned nGMM = static_cast&lt;unsigned&gt;(std::floor(random_.RandU01()*static_cast&lt;double&gt;(GMM_d_grps_.size())));</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineNoCov">          0 :   if(nGMM==GMM_d_grps_.size()) nGMM -= 1;</span></a>
+<a name="864"><span class="lineNum">     864 </span>            : </a>
+<a name="865"><span class="lineNum">     865 </span>            :   // generate random move</a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineNoCov">          0 :   double shift = dsigma_[nGMM] * ( 2.0 * random_.RandU01() - 1.0 );</span></a>
+<a name="867"><span class="lineNum">     867 </span>            :   // new sigma</a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineNoCov">          0 :   double new_s = sigma_[nGMM] + shift;</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :   // check boundaries</a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineNoCov">          0 :   if(new_s &gt; sigma_max_[nGMM]) {new_s = 2.0 * sigma_max_[nGMM] - new_s;}</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :   if(new_s &lt; sigma_min_[nGMM]) {new_s = 2.0 * sigma_min_[nGMM] - new_s;}</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :   // old s2</a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineNoCov">          0 :   double old_inv_s2 = 1.0 / sigma_[nGMM] / sigma_[nGMM];</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :   // new s2</a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineNoCov">          0 :   double new_inv_s2 = 1.0 / new_s / new_s;</span></a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span>            :   // cycle on GMM group and calculate old and new energy</a>
+<a name="878"><span class="lineNum">     878 </span>            :   double old_ene = 0.0;</a>
+<a name="879"><span class="lineNum">     879 </span>            :   double new_ene = 0.0;</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :   double ng = static_cast&lt;double&gt;(GMM_d_grps_[nGMM].size());</span></a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span>            :   // in case of Gaussian noise</a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineNoCov">          0 :   if(noise_==0) {</span></a>
+<a name="884"><span class="lineNum">     884 </span>            :     double chi2 = 0.0;</a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;GMM_d_grps_[nGMM].size(); ++i) {</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :       // id GMM component</a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :       int GMMid = GMM_d_grps_[nGMM][i];</span></a>
+<a name="888"><span class="lineNum">     888 </span>            :       // deviation</a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineNoCov">          0 :       double dev = ( scale_*ovmd_ave_[GMMid]-ovdd_[GMMid] );</span></a>
+<a name="890"><span class="lineNum">     890 </span>            :       // add to chi2</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineNoCov">          0 :       chi2 += dev * dev;</span></a>
+<a name="892"><span class="lineNum">     892 </span>            :     }</a>
+<a name="893"><span class="lineNum">     893 </span>            :     // final energy calculation: add normalization and prior</a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineNoCov">          0 :     old_ene = 0.5 * kbt_ * ( chi2 * old_inv_s2 - (ng+prior_) * std::log(old_inv_s2) );</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineNoCov">          0 :     new_ene = 0.5 * kbt_ * ( chi2 * new_inv_s2 - (ng+prior_) * std::log(new_inv_s2) );</span></a>
+<a name="896"><span class="lineNum">     896 </span>            :   }</a>
+<a name="897"><span class="lineNum">     897 </span>            : </a>
+<a name="898"><span class="lineNum">     898 </span>            :   // in case of Outliers noise</a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineNoCov">          0 :   if(noise_==1) {</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;GMM_d_grps_[nGMM].size(); ++i) {</span></a>
+<a name="901"><span class="lineNum">     901 </span>            :       // id GMM component</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineNoCov">          0 :       int GMMid = GMM_d_grps_[nGMM][i];</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :       // calculate deviation</a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineNoCov">          0 :       double dev = ( scale_*ovmd_ave_[GMMid]-ovdd_[GMMid] );</span></a>
+<a name="905"><span class="lineNum">     905 </span>            :       // add to energies</a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineNoCov">          0 :       old_ene += std::log1p( 0.5 * dev * dev * old_inv_s2);</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineNoCov">          0 :       new_ene += std::log1p( 0.5 * dev * dev * new_inv_s2);</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :     }</a>
+<a name="909"><span class="lineNum">     909 </span>            :     // final energy calculation: add normalization and prior</a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineNoCov">          0 :     old_ene = kbt_ * ( old_ene + (ng+prior_) * std::log(sigma_[nGMM]) );</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineNoCov">          0 :     new_ene = kbt_ * ( new_ene + (ng+prior_) * std::log(new_s) );</span></a>
+<a name="912"><span class="lineNum">     912 </span>            :   }</a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span>            :   // increment number of trials</a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineNoCov">          0 :   MCtrials_ += 1.0;</span></a>
+<a name="916"><span class="lineNum">     916 </span>            : </a>
+<a name="917"><span class="lineNum">     917 </span>            :   // accept or reject</a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineNoCov">          0 :   bool accept = doAccept(old_ene/anneal_, new_ene/anneal_, kbt_);</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :   if(accept) {</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineNoCov">          0 :     sigma_[nGMM] = new_s;</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineNoCov">          0 :     MCaccept_ += 1.0;</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :   }</a>
+<a name="923"><span class="lineNum">     923 </span>            :   // local communication</a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineNoCov">          0 :   if(rank_!=0) {</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;sigma_.size(); ++i) sigma_[i] = 0.0;</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineNoCov">          0 :     MCaccept_ = 0.0;</span></a>
+<a name="927"><span class="lineNum">     927 </span>            :   }</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineNoCov">          0 :   if(size_&gt;1) {</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;sigma_[0], sigma_.size());</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;MCaccept_, 1);</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :   }</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span>            :   // update sigma output</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :   std::string num; Tools::convert(nGMM, num);</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineNoCov">          0 :   getPntrToComponent(&quot;sigma-&quot;+num)-&gt;set(sigma_[nGMM]);</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="937"><span class="lineNum">     937 </span>            : </a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 : std::vector&lt;double&gt; EMMI::read_exp_errors(const std::string &amp; errfile)</span></a>
+<a name="939"><span class="lineNum">     939 </span>            : {</a>
+<a name="940"><span class="lineNum">     940 </span>            :   int nexp, idcomp;</a>
+<a name="941"><span class="lineNum">     941 </span>            :   double err;</a>
+<a name="942"><span class="lineNum">     942 </span>            :   std::vector&lt;double&gt; exp_err;</a>
+<a name="943"><span class="lineNum">     943 </span>            : // open file</a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 :   IFile *ifile = new IFile();</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineNoCov">          0 :   if(ifile-&gt;FileExist(errfile)) {</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineNoCov">          0 :     ifile-&gt;open(errfile);</span></a>
+<a name="947"><span class="lineNum">     947 </span>            :     // scan for number of experimental errors</a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineNoCov">          0 :     ifile-&gt;scanField(&quot;Nexp&quot;, nexp);</span></a>
+<a name="949"><span class="lineNum">     949 </span>            :     // cycle on GMM components</a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineNoCov">          0 :     while(ifile-&gt;scanField(&quot;Id&quot;,idcomp)) {</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :       // total experimental error</a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineNoCov">          0 :       double err_tot = 0.0;</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :       // cycle on number of experimental overlaps</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;nexp; ++i) {</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineNoCov">          0 :         std::string ss; Tools::convert(i,ss);</span></a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineNoCov">          0 :         ifile-&gt;scanField(&quot;Err&quot;+ss, err);</span></a>
+<a name="957"><span class="lineNum">     957 </span>            :         // add to total error</a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineNoCov">          0 :         err_tot += err*err;</span></a>
+<a name="959"><span class="lineNum">     959 </span>            :       }</a>
+<a name="960"><span class="lineNum">     960 </span>            :       // new line</a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineNoCov">          0 :       ifile-&gt;scanField();</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :       // calculate RMSE</a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineNoCov">          0 :       err_tot = std::sqrt(err_tot/static_cast&lt;double&gt;(nexp));</span></a>
+<a name="964"><span class="lineNum">     964 </span>            :       // add to global</a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineNoCov">          0 :       exp_err.push_back(err_tot);</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :     }</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineNoCov">          0 :     ifile-&gt;close();</span></a>
+<a name="968"><span class="lineNum">     968 </span>            :   } else {</a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineNoCov">          0 :     error(&quot;Cannot find ERR_FILE &quot;+errfile+&quot;\n&quot;);</span></a>
+<a name="970"><span class="lineNum">     970 </span>            :   }</a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineNoCov">          0 :   return exp_err;</span></a>
+<a name="972"><span class="lineNum">     972 </span>            : }</a>
+<a name="973"><span class="lineNum">     973 </span>            : </a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineNoCov">          0 : std::vector&lt;double&gt; EMMI::read_exp_overlaps(const std::string &amp; ovfile)</span></a>
+<a name="975"><span class="lineNum">     975 </span>            : {</a>
+<a name="976"><span class="lineNum">     976 </span>            :   int idcomp;</a>
+<a name="977"><span class="lineNum">     977 </span>            :   double ov;</a>
+<a name="978"><span class="lineNum">     978 </span>            :   std::vector&lt;double&gt; ovdd;</a>
+<a name="979"><span class="lineNum">     979 </span>            : // open file</a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :   IFile *ifile = new IFile();</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 :   if(ifile-&gt;FileExist(ovfile)) {</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineNoCov">          0 :     ifile-&gt;open(ovfile);</span></a>
+<a name="983"><span class="lineNum">     983 </span>            :     // cycle on GMM components</a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineNoCov">          0 :     while(ifile-&gt;scanField(&quot;Id&quot;,idcomp)) {</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :       // read experimental overlap</a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineNoCov">          0 :       ifile-&gt;scanField(&quot;Overlap&quot;, ov);</span></a>
+<a name="987"><span class="lineNum">     987 </span>            :       // add to ovdd</a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineNoCov">          0 :       ovdd.push_back(ov);</span></a>
+<a name="989"><span class="lineNum">     989 </span>            :       // new line</a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineNoCov">          0 :       ifile-&gt;scanField();</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :     }</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineNoCov">          0 :     ifile-&gt;close();</span></a>
+<a name="993"><span class="lineNum">     993 </span>            :   } else {</a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineNoCov">          0 :     error(&quot;Cannot find OV_FILE &quot;+ovfile+&quot;\n&quot;);</span></a>
+<a name="995"><span class="lineNum">     995 </span>            :   }</a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineNoCov">          0 :   return ovdd;</span></a>
+<a name="997"><span class="lineNum">     997 </span>            : }</a>
+<a name="998"><span class="lineNum">     998 </span>            : </a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">         20 : std::vector&lt;double&gt; EMMI::get_GMM_m(std::vector&lt;AtomNumber&gt; &amp;atoms)</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            : {</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   // list of weights - one per atom</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :   std::vector&lt;double&gt; GMM_m_w;</a>
+<a name="1003"><span class="lineNum">    1003 </span>            : </a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">         20 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            :   // map of atom types to A and B coefficients of scattering factor</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :   // f(s) = A * exp(-B*s**2)</a>
+<a name="1007"><span class="lineNum">    1007 </span>            :   // B is in Angstrom squared</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :   // map between an atom type and an index</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   std::map&lt;std::string, unsigned&gt; type_map;</a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">         20 :   type_map[&quot;C&quot;]=0;</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">         20 :   type_map[&quot;O&quot;]=1;</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">         20 :   type_map[&quot;N&quot;]=2;</span></a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">         20 :   type_map[&quot;S&quot;]=3;</span></a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   // fill in sigma std::vector</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">         20 :   GMM_m_s_.push_back(0.01*15.146);  // type 0</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">         20 :   GMM_m_s_.push_back(0.01*8.59722); // type 1</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">         20 :   GMM_m_s_.push_back(0.01*11.1116); // type 2</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">         20 :   GMM_m_s_.push_back(0.01*15.8952); // type 3</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   // fill in weight std::vector</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">         20 :   GMM_m_w_.push_back(2.49982); // type 0</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">         20 :   GMM_m_w_.push_back(1.97692); // type 1</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">         20 :   GMM_m_w_.push_back(2.20402); // type 2</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">         20 :   GMM_m_w_.push_back(5.14099); // type 3</span></a>
+<a name="1024"><span class="lineNum">    1024 </span>            : </a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   // check if MOLINFO line is present</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">         20 :   if( moldat ) {</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">         20 :     log&lt;&lt;&quot;  MOLINFO DATA found with label &quot; &lt;&lt;moldat-&gt;getLabel()&lt;&lt;&quot;, using proper atom names\n&quot;;</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">      10876 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            :       // get atom name</a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">      10856 :       std::string name = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :       char type;</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :       // get atom type</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">      10856 :       char first = name.at(0);</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :       // GOLDEN RULE: type is first letter, if not a number</a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">      10856 :       if (!isdigit(first)) {</span></a>
+<a name="1036"><span class="lineNum">    1036 </span>            :         type = first;</a>
+<a name="1037"><span class="lineNum">    1037 </span>            :         // otherwise is the second</a>
+<a name="1038"><span class="lineNum">    1038 </span>            :       } else {</a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineNoCov">          0 :         type = name.at(1);</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :       }</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :       // check if key in map</a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">      10856 :       std::string type_s = std::string(1,type);</span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">      10856 :       if(type_map.find(type_s) != type_map.end()) {</span></a>
+<a name="1044"><span class="lineNum">    1044 </span>            :         // save atom type</a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">      10856 :         GMM_m_type_.push_back(type_map[type_s]);</span></a>
+<a name="1046"><span class="lineNum">    1046 </span>            :         // this will be normalized in the final density</a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">      10856 :         GMM_m_w.push_back(GMM_m_w_[type_map[type_s]]);</span></a>
+<a name="1048"><span class="lineNum">    1048 </span>            :       } else {</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineNoCov">          0 :         error(&quot;Wrong atom type &quot;+type_s+&quot; from atom name &quot;+name+&quot;\n&quot;);</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :       }</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     }</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   } else {</a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineNoCov">          0 :     error(&quot;MOLINFO DATA not found\n&quot;);</span></a>
+<a name="1054"><span class="lineNum">    1054 </span>            :   }</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">         20 :   return GMM_m_w;</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            : }</a>
+<a name="1057"><span class="lineNum">    1057 </span>            : </a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">       1962 : void EMMI::check_GMM_d(const VectorGeneric&lt;6&gt; &amp;cov, double w)</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            : {</a>
+<a name="1060"><span class="lineNum">    1060 </span>            : </a>
+<a name="1061"><span class="lineNum">    1061 </span>            : // check if positive defined, by calculating the 3 leading principal minors</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">       1962 :   double pm1 = cov[0];</span></a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">       1962 :   double pm2 = cov[0]*cov[3]-cov[1]*cov[1];</span></a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">       1962 :   double pm3 = cov[0]*(cov[3]*cov[5]-cov[4]*cov[4])-cov[1]*(cov[1]*cov[5]-cov[4]*cov[2])+cov[2]*(cov[1]*cov[4]-cov[3]*cov[2]);</span></a>
+<a name="1065"><span class="lineNum">    1065 </span>            : // apply Sylvester’s criterion</a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">       1962 :   if(pm1&lt;=0.0 || pm2&lt;=0.0 || pm3&lt;=0.0)</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineNoCov">          0 :     error(&quot;check data GMM: covariance matrix is not positive defined&quot;);</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            : </a>
+<a name="1069"><span class="lineNum">    1069 </span>            : // check if weight is positive</a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">       1962 :   if(w&lt;=0) error(&quot;check data GMM: weight must be positive&quot;);</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">       1962 : }</span></a>
+<a name="1072"><span class="lineNum">    1072 </span>            : </a>
+<a name="1073"><span class="lineNum">    1073 </span>            : // read GMM data file in PLUMED format:</a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">         20 : void EMMI::get_GMM_d(std::string GMM_file)</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            : {</a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">         20 :   VectorGeneric&lt;6&gt; cov;</span></a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span>            : // open file</a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">         20 :   auto ifile=Tools::make_unique&lt;IFile&gt;();</span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">         20 :   if(ifile-&gt;FileExist(GMM_file)) {</span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">         20 :     ifile-&gt;open(GMM_file);</span></a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     int idcomp;</a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">       3964 :     while(ifile-&gt;scanField(&quot;Id&quot;,idcomp)) {</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :       int beta;</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :       double w, m0, m1, m2;</a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Weight&quot;,w);</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Mean_0&quot;,m0);</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Mean_1&quot;,m1);</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Mean_2&quot;,m2);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Cov_00&quot;,cov[0]);</span></a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Cov_01&quot;,cov[1]);</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Cov_02&quot;,cov[2]);</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Cov_11&quot;,cov[3]);</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Cov_12&quot;,cov[4]);</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">       3924 :       ifile-&gt;scanField(&quot;Cov_22&quot;,cov[5]);</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">       1962 :       ifile-&gt;scanField(&quot;Beta&quot;,beta);</span></a>
+<a name="1097"><span class="lineNum">    1097 </span>            :       // check input</a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">       1962 :       check_GMM_d(cov, w);</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            :       // check beta</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">       1962 :       if(beta&lt;0) error(&quot;Beta must be positive!&quot;);</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            :       // center of the Gaussian</a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">       1962 :       GMM_d_m_.push_back(Vector(m0,m1,m2));</span></a>
+<a name="1103"><span class="lineNum">    1103 </span>            :       // covariance matrix</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">       1962 :       GMM_d_cov_.push_back(cov);</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            :       // weight</a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">       1962 :       GMM_d_w_.push_back(w);</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            :       // beta</a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">       1962 :       GMM_d_beta_.push_back(beta);</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            :       // new line</a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">       1962 :       ifile-&gt;scanField();</span></a>
+<a name="1111"><span class="lineNum">    1111 </span>            :     }</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   } else {</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineNoCov">          0 :     error(&quot;Cannot find GMM_FILE &quot;+GMM_file+&quot;\n&quot;);</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            :   }</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   // now create a set from beta (unique set of values)</a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">         20 :   std::set&lt;int&gt; bu(GMM_d_beta_.begin(), GMM_d_beta_.end());</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :   // now prepare the group std::vector</a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">         20 :   GMM_d_grps_.resize(bu.size());</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :   // and fill it in</a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">       1982 :   for(unsigned i=0; i&lt;GMM_d_beta_.size(); ++i) {</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">       1962 :     if(GMM_d_beta_[i]&gt;=GMM_d_grps_.size()) error(&quot;Check Beta values&quot;);</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">       1962 :     GMM_d_grps_[GMM_d_beta_[i]].push_back(i);</span></a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   }</a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">         20 : }</span></a>
+<a name="1125"><span class="lineNum">    1125 </span>            : </a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">         20 : void EMMI::calculate_useful_stuff(double reso)</span></a>
+<a name="1127"><span class="lineNum">    1127 </span>            : {</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   // We use the following definition for resolution:</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   // the Fourier transform of the density distribution in real space</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :   // f(s) falls to 1/e of its maximum value at wavenumber 1/resolution</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :   // i.e. from f(s) = A * exp(-B*s**2) -&gt; Res = std::sqrt(B).</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :   // average value of B</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :   double Bave = 0.0;</a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">      10876 :   for(unsigned i=0; i&lt;GMM_m_type_.size(); ++i) {</span></a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">      10856 :     Bave += GMM_m_s_[GMM_m_type_[i]];</span></a>
+<a name="1136"><span class="lineNum">    1136 </span>            :   }</a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">         20 :   Bave /= static_cast&lt;double&gt;(GMM_m_type_.size());</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   // calculate blur factor</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :   double blur = 0.0;</a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineCov">         20 :   if(reso*reso&gt;Bave) blur = reso*reso-Bave;</span></a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineCov">         36 :   else warning(&quot;PLUMED should not be used with maps at resolution better than 0.3 nm&quot;);</span></a>
+<a name="1142"><span class="lineNum">    1142 </span>            :   // add blur to B</a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">        100 :   for(unsigned i=0; i&lt;GMM_m_s_.size(); ++i) GMM_m_s_[i] += blur;</span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   // calculate average resolution</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   double ave_res = 0.0;</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">      10876 :   for(unsigned i=0; i&lt;GMM_m_type_.size(); ++i) {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">      10856 :     ave_res += std::sqrt(GMM_m_s_[GMM_m_type_[i]]);</span></a>
+<a name="1148"><span class="lineNum">    1148 </span>            :   }</a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">         20 :   ave_res = ave_res / static_cast&lt;double&gt;(GMM_m_type_.size());</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">         20 :   log.printf(&quot;  experimental map resolution : %3.2f\n&quot;, reso);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">         20 :   log.printf(&quot;  predicted map resolution : %3.2f\n&quot;, ave_res);</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">         20 :   log.printf(&quot;  blur factor : %f\n&quot;, blur);</span></a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   // now calculate useful stuff</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">         20 :   VectorGeneric&lt;6&gt; cov, sum, inv_sum;</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :   // cycle on all atoms types (4 for the moment)</a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">        100 :   for(unsigned i=0; i&lt;GMM_m_s_.size(); ++i) {</span></a>
+<a name="1157"><span class="lineNum">    1157 </span>            :     // the Gaussian in density (real) space is the FT of scattering factor</a>
+<a name="1158"><span class="lineNum">    1158 </span>            :     // f(r) = A * (pi/B)**1.5 * exp(-pi**2/B*r**2)</a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineCov">         80 :     double s = std::sqrt ( 0.5 * GMM_m_s_[i] ) / pi;</span></a>
+<a name="1160"><span class="lineNum">    1160 </span>            :     // covariance matrix for spherical Gaussian</a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">         80 :     cov[0]=s*s; cov[1]=0.0; cov[2]=0.0;</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">         80 :     cov[3]=s*s; cov[4]=0.0;</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">         80 :     cov[5]=s*s;</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     // cycle on all data GMM</a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">       7928 :     for(unsigned j=0; j&lt;GMM_d_m_.size(); ++j) {</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            :       // we need the sum of the covariance matrices</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">      54936 :       for(unsigned k=0; k&lt;6; ++k) sum[k] = cov[k] + GMM_d_cov_[j][k];</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :       // and to calculate its determinant</a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">       7848 :       double det = sum[0]*(sum[3]*sum[5]-sum[4]*sum[4]);</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">       7848 :       det -= sum[1]*(sum[1]*sum[5]-sum[4]*sum[2]);</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineCov">       7848 :       det += sum[2]*(sum[1]*sum[4]-sum[3]*sum[2]);</span></a>
+<a name="1172"><span class="lineNum">    1172 </span>            :       // calculate prefactor - model weights are already normalized</a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineCov">       7848 :       double pre_fact =  cfact_ / std::sqrt(det) * GMM_d_w_[j] * GMM_m_w_[i];</span></a>
+<a name="1174"><span class="lineNum">    1174 </span>            :       // and its inverse</a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineCov">       7848 :       inv_sum[0] = (sum[3]*sum[5] - sum[4]*sum[4])/det;</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">       7848 :       inv_sum[1] = (sum[2]*sum[4] - sum[1]*sum[5])/det;</span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">       7848 :       inv_sum[2] = (sum[1]*sum[4] - sum[2]*sum[3])/det;</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">       7848 :       inv_sum[3] = (sum[0]*sum[5] - sum[2]*sum[2])/det;</span></a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineCov">       7848 :       inv_sum[4] = (sum[2]*sum[1] - sum[0]*sum[4])/det;</span></a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineCov">       7848 :       inv_sum[5] = (sum[0]*sum[3] - sum[1]*sum[1])/det;</span></a>
+<a name="1181"><span class="lineNum">    1181 </span>            :       // now we store the prefactor</a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">       7848 :       pre_fact_.push_back(pre_fact);</span></a>
+<a name="1183"><span class="lineNum">    1183 </span>            :       // and the inverse of the sum</a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineCov">       7848 :       inv_cov_md_.push_back(inv_sum);</span></a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     }</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   }</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :   // tabulate exponential</a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">         20 :   dexp_ = dpcutoff_ / static_cast&lt;double&gt; (nexp_-1);</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">   20000020 :   for(unsigned i=0; i&lt;nexp_; ++i) {</span></a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineCov">   20000000 :     tab_exp_.push_back(std::exp(-static_cast&lt;double&gt;(i) * dexp_));</span></a>
+<a name="1191"><span class="lineNum">    1191 </span>            :   }</a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineCov">         20 : }</span></a>
+<a name="1193"><span class="lineNum">    1193 </span>            : </a>
+<a name="1194"><span class="lineNum">    1194 </span>            : // get prefactors</a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineCov">    1621458 : double EMMI::get_prefactor_inverse</span></a>
+<a name="1196"><span class="lineNum">    1196 </span>            : (const VectorGeneric&lt;6&gt; &amp;GMM_cov_0, const VectorGeneric&lt;6&gt; &amp;GMM_cov_1,</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :  double GMM_w_0, double GMM_w_1,</a>
+<a name="1198"><span class="lineNum">    1198 </span>            :  VectorGeneric&lt;6&gt; &amp;sum, VectorGeneric&lt;6&gt; &amp;inv_sum)</a>
+<a name="1199"><span class="lineNum">    1199 </span>            : {</a>
+<a name="1200"><span class="lineNum">    1200 </span>            : // we need the sum of the covariance matrices</a>
+<a name="1201"><span class="lineNum">    1201 </span><span class="lineCov">   11350206 :   for(unsigned k=0; k&lt;6; ++k) sum[k] = GMM_cov_0[k] + GMM_cov_1[k];</span></a>
+<a name="1202"><span class="lineNum">    1202 </span>            : </a>
+<a name="1203"><span class="lineNum">    1203 </span>            : // and to calculate its determinant</a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineCov">    1621458 :   double det = sum[0]*(sum[3]*sum[5]-sum[4]*sum[4]);</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">    1621458 :   det -= sum[1]*(sum[1]*sum[5]-sum[4]*sum[2]);</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">    1621458 :   det += sum[2]*(sum[1]*sum[4]-sum[3]*sum[2]);</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            : </a>
+<a name="1208"><span class="lineNum">    1208 </span>            : // the prefactor is</a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">    1621458 :   double pre_fact =  cfact_ / std::sqrt(det) * GMM_w_0 * GMM_w_1;</span></a>
+<a name="1210"><span class="lineNum">    1210 </span>            : </a>
+<a name="1211"><span class="lineNum">    1211 </span>            : // and its inverse</a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineCov">    1621458 :   inv_sum[0] = (sum[3]*sum[5] - sum[4]*sum[4])/det;</span></a>
+<a name="1213"><span class="lineNum">    1213 </span><span class="lineCov">    1621458 :   inv_sum[1] = (sum[2]*sum[4] - sum[1]*sum[5])/det;</span></a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineCov">    1621458 :   inv_sum[2] = (sum[1]*sum[4] - sum[2]*sum[3])/det;</span></a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineCov">    1621458 :   inv_sum[3] = (sum[0]*sum[5] - sum[2]*sum[2])/det;</span></a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineCov">    1621458 :   inv_sum[4] = (sum[2]*sum[1] - sum[0]*sum[4])/det;</span></a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">    1621458 :   inv_sum[5] = (sum[0]*sum[3] - sum[1]*sum[1])/det;</span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            : </a>
+<a name="1219"><span class="lineNum">    1219 </span>            : // return pre-factor</a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">    1621458 :   return pre_fact;</span></a>
+<a name="1221"><span class="lineNum">    1221 </span>            : }</a>
+<a name="1222"><span class="lineNum">    1222 </span>            : </a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">       1962 : double EMMI::get_self_overlap(unsigned id)</span></a>
+<a name="1224"><span class="lineNum">    1224 </span>            : {</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :   double ov_tot = 0.0;</a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">       1962 :   VectorGeneric&lt;6&gt; sum, inv_sum;</span></a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">       1962 :   Vector ov_der;</span></a>
+<a name="1228"><span class="lineNum">    1228 </span>            : // start loop</a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">    1623420 :   for(unsigned i=0; i&lt;GMM_d_m_.size(); ++i) {</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :     // call auxiliary method</a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">    1621458 :     double pre_fact = get_prefactor_inverse(GMM_d_cov_[id], GMM_d_cov_[i],</span></a>
+<a name="1232"><span class="lineNum">    1232 </span><span class="lineCov">    1621458 :                                             GMM_d_w_[id],   GMM_d_w_[i], sum, inv_sum);</span></a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     // add overlap to ov_tot</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">    1621458 :     ov_tot += get_overlap(GMM_d_m_[id], GMM_d_m_[i], pre_fact, inv_sum, ov_der);</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            :   }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            : // and return it</a>
+<a name="1237"><span class="lineNum">    1237 </span><span class="lineCov">       1962 :   return ov_tot;</span></a>
+<a name="1238"><span class="lineNum">    1238 </span>            : }</a>
+<a name="1239"><span class="lineNum">    1239 </span>            : </a>
+<a name="1240"><span class="lineNum">    1240 </span>            : // get overlap and derivatives</a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineCov">    3732816 : double EMMI::get_overlap(const Vector &amp;m_m, const Vector &amp;d_m, double pre_fact,</span></a>
+<a name="1242"><span class="lineNum">    1242 </span>            :                          const VectorGeneric&lt;6&gt; &amp;inv_cov_md, Vector &amp;ov_der)</a>
+<a name="1243"><span class="lineNum">    1243 </span>            : {</a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">    3732816 :   Vector md;</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :   // calculate std::vector difference m_m-d_m with/without pbc</a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">    3732816 :   if(pbc_) md = pbcDistance(d_m, m_m);</span></a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">    3732816 :   else     md = delta(d_m, m_m);</span></a>
+<a name="1248"><span class="lineNum">    1248 </span>            :   // calculate product of transpose of md and inv_cov_md</a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">    3732816 :   double p_x = md[0]*inv_cov_md[0]+md[1]*inv_cov_md[1]+md[2]*inv_cov_md[2];</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">    3732816 :   double p_y = md[0]*inv_cov_md[1]+md[1]*inv_cov_md[3]+md[2]*inv_cov_md[4];</span></a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineCov">    3732816 :   double p_z = md[0]*inv_cov_md[2]+md[1]*inv_cov_md[4]+md[2]*inv_cov_md[5];</span></a>
+<a name="1252"><span class="lineNum">    1252 </span>            :   // calculate product of prod and md</a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineCov">    3732816 :   double ov = md[0]*p_x+md[1]*p_y+md[2]*p_z;</span></a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   // final calculation</a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineCov">    3732816 :   ov = pre_fact * std::exp(-0.5*ov);</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            :   // derivatives</a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">    3732816 :   ov_der = ov * Vector(p_x, p_y, p_z);</span></a>
+<a name="1258"><span class="lineNum">    1258 </span><span class="lineCov">    3732816 :   return ov;</span></a>
+<a name="1259"><span class="lineNum">    1259 </span>            : }</a>
+<a name="1260"><span class="lineNum">    1260 </span>            : </a>
+<a name="1261"><span class="lineNum">    1261 </span>            : // get the exponent of the overlap</a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineCov">   59085036 : double EMMI::get_exp_overlap(const Vector &amp;m_m, const Vector &amp;d_m,</span></a>
+<a name="1263"><span class="lineNum">    1263 </span>            :                              const VectorGeneric&lt;6&gt; &amp;inv_cov_md)</a>
+<a name="1264"><span class="lineNum">    1264 </span>            : {</a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineCov">   59085036 :   Vector md;</span></a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   // calculate std::vector difference m_m-d_m with/without pbc</a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineCov">   59085036 :   if(pbc_) md = pbcDistance(d_m, m_m);</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineCov">   59085036 :   else     md = delta(d_m, m_m);</span></a>
+<a name="1269"><span class="lineNum">    1269 </span>            :   // calculate product of transpose of md and inv_cov_md</a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineCov">   59085036 :   double p_x = md[0]*inv_cov_md[0]+md[1]*inv_cov_md[1]+md[2]*inv_cov_md[2];</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">   59085036 :   double p_y = md[0]*inv_cov_md[1]+md[1]*inv_cov_md[3]+md[2]*inv_cov_md[4];</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineCov">   59085036 :   double p_z = md[0]*inv_cov_md[2]+md[1]*inv_cov_md[4]+md[2]*inv_cov_md[5];</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   // calculate product of prod and md</a>
+<a name="1274"><span class="lineNum">    1274 </span><span class="lineCov">   59085036 :   double ov = md[0]*p_x+md[1]*p_y+md[2]*p_z;</span></a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">   59085036 :   return ov;</span></a>
+<a name="1276"><span class="lineNum">    1276 </span>            : }</a>
+<a name="1277"><span class="lineNum">    1277 </span>            : </a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">      16355 : void EMMI::update_neighbor_list()</span></a>
+<a name="1279"><span class="lineNum">    1279 </span>            : {</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :   // dimension of GMM and atom std::vectors</a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">      16355 :   unsigned GMM_d_size = GMM_d_m_.size();</span></a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineCov">      16355 :   unsigned GMM_m_size = GMM_m_type_.size();</span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   // local neighbor list</a>
+<a name="1284"><span class="lineNum">    1284 </span>            :   std::vector &lt; unsigned &gt; nl_l;</a>
+<a name="1285"><span class="lineNum">    1285 </span>            :   // clear old neighbor list</a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineCov">      16355 :   nl_.clear();</span></a>
+<a name="1287"><span class="lineNum">    1287 </span>            : </a>
+<a name="1288"><span class="lineNum">    1288 </span>            :   // cycle on GMM components - in parallel</a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineCov">     116273 :   for(unsigned id=rank_; id&lt;GMM_d_size; id+=size_) {</span></a>
+<a name="1290"><span class="lineNum">    1290 </span>            :     // overlap lists and map</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     std::vector&lt;double&gt; ov_l;</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :     std::map&lt;double, unsigned&gt; ov_m;</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :     // total overlap with id</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :     double ov_tot = 0.0;</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :     // cycle on all atoms</a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineCov">   59184954 :     for(unsigned im=0; im&lt;GMM_m_size; ++im) {</span></a>
+<a name="1297"><span class="lineNum">    1297 </span>            :       // get index in auxiliary lists</a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineCov">   59085036 :       unsigned kaux = GMM_m_type_[im] * GMM_d_size + id;</span></a>
+<a name="1299"><span class="lineNum">    1299 </span>            :       // calculate exponent of overlap</a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">   59085036 :       double expov = get_exp_overlap(GMM_d_m_[id], getPosition(im), inv_cov_md_[kaux]);</span></a>
+<a name="1301"><span class="lineNum">    1301 </span>            :       // get index of 0.5*expov in tabulated exponential</a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineCov">   59085036 :       unsigned itab = static_cast&lt;unsigned&gt; (round( 0.5*expov/dexp_ ));</span></a>
+<a name="1303"><span class="lineNum">    1303 </span>            :       // check boundaries and skip atom in case</a>
+<a name="1304"><span class="lineNum">    1304 </span><span class="lineCov">   59085036 :       if(itab &gt;= tab_exp_.size()) continue;</span></a>
+<a name="1305"><span class="lineNum">    1305 </span>            :       // in case calculate overlap</a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">    4133388 :       double ov = pre_fact_[kaux] * tab_exp_[itab];</span></a>
+<a name="1307"><span class="lineNum">    1307 </span>            :       // add to list</a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">    4133388 :       ov_l.push_back(ov);</span></a>
+<a name="1309"><span class="lineNum">    1309 </span>            :       // and map to retrieve atom index</a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineCov">    4133388 :       ov_m[ov] = im;</span></a>
+<a name="1311"><span class="lineNum">    1311 </span>            :       // increase ov_tot</a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">    4133388 :       ov_tot += ov;</span></a>
+<a name="1313"><span class="lineNum">    1313 </span>            :     }</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :     // check if zero size -&gt; ov_tot = 0</a>
+<a name="1315"><span class="lineNum">    1315 </span><span class="lineCov">      99918 :     if(ov_l.size()==0) continue;</span></a>
+<a name="1316"><span class="lineNum">    1316 </span>            :     // define cutoff</a>
+<a name="1317"><span class="lineNum">    1317 </span><span class="lineCov">      99842 :     double ov_cut = ov_tot * nl_cutoff_;</span></a>
+<a name="1318"><span class="lineNum">    1318 </span>            :     // sort ov_l in ascending order</a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">      99842 :     std::sort(ov_l.begin(), ov_l.end());</span></a>
+<a name="1320"><span class="lineNum">    1320 </span>            :     // integrate ov_l</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :     double res = 0.0;</a>
+<a name="1322"><span class="lineNum">    1322 </span><span class="lineCov">    2146102 :     for(unsigned i=0; i&lt;ov_l.size(); ++i) {</span></a>
+<a name="1323"><span class="lineNum">    1323 </span><span class="lineCov">    2146102 :       res += ov_l[i];</span></a>
+<a name="1324"><span class="lineNum">    1324 </span>            :       // if exceeding the cutoff for overlap, stop</a>
+<a name="1325"><span class="lineNum">    1325 </span><span class="lineCov">    2146102 :       if(res &gt;= ov_cut) break;</span></a>
+<a name="1326"><span class="lineNum">    1326 </span>            :       else ov_m.erase(ov_l[i]);</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :     }</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :     // now add atoms to neighborlist</a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineCov">    2186970 :     for(std::map&lt;double, unsigned&gt;::iterator it=ov_m.begin(); it!=ov_m.end(); ++it)</span></a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">    2087128 :       nl_l.push_back(id*GMM_m_size+it-&gt;second);</span></a>
+<a name="1331"><span class="lineNum">    1331 </span>            :     // end cycle on GMM components in parallel</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   }</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :   // find total dimension of neighborlist</a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">      16355 :   std::vector &lt;int&gt; recvcounts(size_, 0);</span></a>
+<a name="1335"><span class="lineNum">    1335 </span><span class="lineCov">      16355 :   recvcounts[rank_] = nl_l.size();</span></a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineCov">      16355 :   comm.Sum(&amp;recvcounts[0], size_);</span></a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   int tot_size = accumulate(recvcounts.begin(), recvcounts.end(), 0);</a>
+<a name="1338"><span class="lineNum">    1338 </span>            :   // resize neighbor stuff</a>
+<a name="1339"><span class="lineNum">    1339 </span><span class="lineCov">      16355 :   nl_.resize(tot_size);</span></a>
+<a name="1340"><span class="lineNum">    1340 </span>            :   // calculate std::vector of displacement</a>
+<a name="1341"><span class="lineNum">    1341 </span><span class="lineCov">      16355 :   std::vector&lt;int&gt; disp(size_);</span></a>
+<a name="1342"><span class="lineNum">    1342 </span><span class="lineCov">      16355 :   disp[0] = 0;</span></a>
+<a name="1343"><span class="lineNum">    1343 </span>            :   int rank_size = 0;</a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineCov">      27257 :   for(unsigned i=0; i&lt;size_-1; ++i) {</span></a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineCov">      10902 :     rank_size += recvcounts[i];</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineCov">      10902 :     disp[i+1] = rank_size;</span></a>
+<a name="1347"><span class="lineNum">    1347 </span>            :   }</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :   // Allgather neighbor list</a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineCov">      16355 :   comm.Allgatherv(&amp;nl_l[0], recvcounts[rank_], &amp;nl_[0], &amp;recvcounts[0], &amp;disp[0]);</span></a>
+<a name="1350"><span class="lineNum">    1350 </span>            :   // now resize derivatives</a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineCov">      16355 :   ovmd_der_.resize(tot_size);</span></a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">      16355 : }</span></a>
+<a name="1353"><span class="lineNum">    1353 </span>            : </a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineCov">         30 : void EMMI::prepare()</span></a>
+<a name="1355"><span class="lineNum">    1355 </span>            : {</a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineCov">         30 :   if(getExchangeStep()) first_time_=true;</span></a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineCov">         30 : }</span></a>
+<a name="1358"><span class="lineNum">    1358 </span>            : </a>
+<a name="1359"><span class="lineNum">    1359 </span>            : // overlap calculator</a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineCov">      16365 : void EMMI::calculate_overlap() {</span></a>
+<a name="1361"><span class="lineNum">    1361 </span>            : </a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineCov">      16365 :   if(first_time_ || getExchangeStep() || getStep()%nl_stride_==0) {</span></a>
+<a name="1363"><span class="lineNum">    1363 </span><span class="lineCov">      16355 :     update_neighbor_list();</span></a>
+<a name="1364"><span class="lineNum">    1364 </span><span class="lineCov">      16355 :     first_time_=false;</span></a>
+<a name="1365"><span class="lineNum">    1365 </span>            :   }</a>
+<a name="1366"><span class="lineNum">    1366 </span>            : </a>
+<a name="1367"><span class="lineNum">    1367 </span>            :   // clean temporary std::vectors</a>
+<a name="1368"><span class="lineNum">    1368 </span><span class="lineCov">     174342 :   for(unsigned i=0; i&lt;ovmd_.size(); ++i)     ovmd_[i] = 0.0;</span></a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineCov">    3168864 :   for(unsigned i=0; i&lt;ovmd_der_.size(); ++i) ovmd_der_[i] = Vector(0,0,0);</span></a>
+<a name="1370"><span class="lineNum">    1370 </span>            : </a>
+<a name="1371"><span class="lineNum">    1371 </span>            :   // we have to cycle over all model and data GMM components in the neighbor list</a>
+<a name="1372"><span class="lineNum">    1372 </span><span class="lineCov">      16365 :   unsigned GMM_d_size = GMM_d_m_.size();</span></a>
+<a name="1373"><span class="lineNum">    1373 </span><span class="lineCov">      16365 :   unsigned GMM_m_size = GMM_m_type_.size();</span></a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineCov">    2127723 :   for(unsigned i=rank_; i&lt;nl_.size(); i=i+size_) {</span></a>
+<a name="1375"><span class="lineNum">    1375 </span>            :     // get data (id) and atom (im) indexes</a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineCov">    2111358 :     unsigned id = nl_[i] / GMM_m_size;</span></a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">    2111358 :     unsigned im = nl_[i] % GMM_m_size;</span></a>
+<a name="1378"><span class="lineNum">    1378 </span>            :     // get index in auxiliary lists</a>
+<a name="1379"><span class="lineNum">    1379 </span><span class="lineCov">    2111358 :     unsigned kaux = GMM_m_type_[im] * GMM_d_size + id;</span></a>
+<a name="1380"><span class="lineNum">    1380 </span>            :     // add overlap with im component of model GMM</a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineCov">    2111358 :     ovmd_[id] += get_overlap(GMM_d_m_[id], getPosition(im), pre_fact_[kaux],</span></a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineCov">    2111358 :                              inv_cov_md_[kaux], ovmd_der_[i]);</span></a>
+<a name="1383"><span class="lineNum">    1383 </span>            :   }</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :   // communicate stuff</a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineCov">      16365 :   if(size_&gt;1) {</span></a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineCov">      10902 :     comm.Sum(&amp;ovmd_[0], ovmd_.size());</span></a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineCov">      10902 :     comm.Sum(&amp;ovmd_der_[0][0], 3*ovmd_der_.size());</span></a>
+<a name="1388"><span class="lineNum">    1388 </span>            :   }</a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineCov">      16365 : }</span></a>
+<a name="1390"><span class="lineNum">    1390 </span>            : </a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineNoCov">          0 : double EMMI::scaleEnergy(double s)</span></a>
+<a name="1392"><span class="lineNum">    1392 </span>            : {</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :   double ene = 0.0;</a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ovdd_.size(); ++i) {</span></a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineNoCov">          0 :     ene += std::log( abs ( s * ovmd_ave_[i] - ovdd_[i] ) );</span></a>
+<a name="1396"><span class="lineNum">    1396 </span>            :   }</a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineNoCov">          0 :   return ene;</span></a>
+<a name="1398"><span class="lineNum">    1398 </span>            : }</a>
+<a name="1399"><span class="lineNum">    1399 </span>            : </a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineNoCov">          0 : double EMMI::doRegression()</span></a>
+<a name="1401"><span class="lineNum">    1401 </span>            : {</a>
+<a name="1402"><span class="lineNum">    1402 </span>            : // standard MC parameters</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :   unsigned MCsteps = 100000;</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :   double kbtmin = 1.0;</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :   double kbtmax = 10.0;</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :   unsigned ncold = 5000;</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :   unsigned nhot = 2000;</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :   double MCacc = 0.0;</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :   double kbt, ebest, scale_best;</a>
+<a name="1410"><span class="lineNum">    1410 </span>            : </a>
+<a name="1411"><span class="lineNum">    1411 </span>            : // initial value of scale factor and energy</a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineNoCov">          0 :   double scale = random_.RandU01() * ( scale_max_ - scale_min_ ) + scale_min_;</span></a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineNoCov">          0 :   double ene = scaleEnergy(scale);</span></a>
+<a name="1414"><span class="lineNum">    1414 </span>            : // set best energy</a>
+<a name="1415"><span class="lineNum">    1415 </span><span class="lineNoCov">          0 :   ebest = ene;</span></a>
+<a name="1416"><span class="lineNum">    1416 </span>            : </a>
+<a name="1417"><span class="lineNum">    1417 </span>            : // MC loop</a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineNoCov">          0 :   for(unsigned istep=0; istep&lt;MCsteps; ++istep) {</span></a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     // get temperature</a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineNoCov">          0 :     if(istep%(ncold+nhot)&lt;ncold) kbt = kbtmin;</span></a>
+<a name="1421"><span class="lineNum">    1421 </span>            :     else kbt = kbtmax;</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     // propose move in scale</a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineNoCov">          0 :     double ds = dscale_ * ( 2.0 * random_.RandU01() - 1.0 );</span></a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineNoCov">          0 :     double new_scale = scale + ds;</span></a>
+<a name="1425"><span class="lineNum">    1425 </span>            :     // check boundaries</a>
+<a name="1426"><span class="lineNum">    1426 </span><span class="lineNoCov">          0 :     if(new_scale &gt; scale_max_) {new_scale = 2.0 * scale_max_ - new_scale;}</span></a>
+<a name="1427"><span class="lineNum">    1427 </span><span class="lineNoCov">          0 :     if(new_scale &lt; scale_min_) {new_scale = 2.0 * scale_min_ - new_scale;}</span></a>
+<a name="1428"><span class="lineNum">    1428 </span>            :     // new energy</a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineNoCov">          0 :     double new_ene = scaleEnergy(new_scale);</span></a>
+<a name="1430"><span class="lineNum">    1430 </span>            :     // accept or reject</a>
+<a name="1431"><span class="lineNum">    1431 </span><span class="lineNoCov">          0 :     bool accept = doAccept(ene, new_ene, kbt);</span></a>
+<a name="1432"><span class="lineNum">    1432 </span>            :     // in case of acceptance</a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineNoCov">          0 :     if(accept) {</span></a>
+<a name="1434"><span class="lineNum">    1434 </span>            :       scale = new_scale;</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :       ene = new_ene;</a>
+<a name="1436"><span class="lineNum">    1436 </span><span class="lineNoCov">          0 :       MCacc += 1.0;</span></a>
+<a name="1437"><span class="lineNum">    1437 </span>            :     }</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :     // save best</a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineNoCov">          0 :     if(ene&lt;ebest) {</span></a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineNoCov">          0 :       ebest = ene;</span></a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineNoCov">          0 :       scale_best = scale;</span></a>
+<a name="1442"><span class="lineNum">    1442 </span>            :     }</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :   }</a>
+<a name="1444"><span class="lineNum">    1444 </span>            : // calculate acceptance</a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineNoCov">          0 :   double accscale = MCacc / static_cast&lt;double&gt;(MCsteps);</span></a>
+<a name="1446"><span class="lineNum">    1446 </span>            : // global communication</a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineNoCov">          0 :   if(!no_aver_ &amp;&amp; nrep_&gt;1) {</span></a>
+<a name="1448"><span class="lineNum">    1448 </span><span class="lineNoCov">          0 :     if(replica_!=0) {</span></a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineNoCov">          0 :       scale_best = 0.0;</span></a>
+<a name="1450"><span class="lineNum">    1450 </span><span class="lineNoCov">          0 :       ebest = 0.0;</span></a>
+<a name="1451"><span class="lineNum">    1451 </span><span class="lineNoCov">          0 :       accscale = 0.0;</span></a>
+<a name="1452"><span class="lineNum">    1452 </span>            :     }</a>
+<a name="1453"><span class="lineNum">    1453 </span><span class="lineNoCov">          0 :     if(rank_==0) {</span></a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineNoCov">          0 :       multi_sim_comm.Sum(&amp;scale_best, 1);</span></a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineNoCov">          0 :       multi_sim_comm.Sum(&amp;ebest, 1);</span></a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineNoCov">          0 :       multi_sim_comm.Sum(&amp;accscale, 1);</span></a>
+<a name="1457"><span class="lineNum">    1457 </span>            :     }</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :   }</a>
+<a name="1459"><span class="lineNum">    1459 </span>            :   // local communication</a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineNoCov">          0 :   if(rank_!=0) {</span></a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineNoCov">          0 :     scale_best = 0.0;</span></a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineNoCov">          0 :     ebest = 0.0;</span></a>
+<a name="1463"><span class="lineNum">    1463 </span><span class="lineNoCov">          0 :     accscale = 0.0;</span></a>
+<a name="1464"><span class="lineNum">    1464 </span>            :   }</a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineNoCov">          0 :   if(size_&gt;1) {</span></a>
+<a name="1466"><span class="lineNum">    1466 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;scale_best, 1);</span></a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;ebest, 1);</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;accscale, 1);</span></a>
+<a name="1469"><span class="lineNum">    1469 </span>            :   }</a>
+<a name="1470"><span class="lineNum">    1470 </span>            : // set scale parameters</a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineNoCov">          0 :   getPntrToComponent(&quot;accscale&quot;)-&gt;set(accscale);</span></a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineNoCov">          0 :   getPntrToComponent(&quot;enescale&quot;)-&gt;set(ebest);</span></a>
+<a name="1473"><span class="lineNum">    1473 </span>            : // return scale value</a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineNoCov">          0 :   return scale_best;</span></a>
+<a name="1475"><span class="lineNum">    1475 </span>            : }</a>
+<a name="1476"><span class="lineNum">    1476 </span>            : </a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineNoCov">          0 : double EMMI::get_annealing(long long int step)</span></a>
+<a name="1478"><span class="lineNum">    1478 </span>            : {</a>
+<a name="1479"><span class="lineNum">    1479 </span>            : // default no annealing</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :   double fact = 1.0;</a>
+<a name="1481"><span class="lineNum">    1481 </span>            : // position in annealing cycle</a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineNoCov">          0 :   unsigned nc = step%(4*nanneal_);</span></a>
+<a name="1483"><span class="lineNum">    1483 </span>            : // useful doubles</a>
+<a name="1484"><span class="lineNum">    1484 </span><span class="lineNoCov">          0 :   double ncd = static_cast&lt;double&gt;(nc);</span></a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineNoCov">          0 :   double nn  = static_cast&lt;double&gt;(nanneal_);</span></a>
+<a name="1486"><span class="lineNum">    1486 </span>            : // set fact</a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineNoCov">          0 :   if(nc&gt;=nanneal_   &amp;&amp; nc&lt;2*nanneal_) fact = (kanneal_-1.0) / nn * ( ncd - nn ) + 1.0;</span></a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineNoCov">          0 :   if(nc&gt;=2*nanneal_ &amp;&amp; nc&lt;3*nanneal_) fact = kanneal_;</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineNoCov">          0 :   if(nc&gt;=3*nanneal_)                  fact = (1.0-kanneal_) / nn * ( ncd - 3.0*nn) + kanneal_;</span></a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineNoCov">          0 :   return fact;</span></a>
+<a name="1491"><span class="lineNum">    1491 </span>            : }</a>
+<a name="1492"><span class="lineNum">    1492 </span>            : </a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineCov">      16365 : void EMMI::get_weights(double &amp;weight, double &amp;norm, double &amp;neff)</span></a>
+<a name="1494"><span class="lineNum">    1494 </span>            : {</a>
+<a name="1495"><span class="lineNum">    1495 </span><span class="lineCov">      16365 :   const double dnrep = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="1496"><span class="lineNum">    1496 </span>            :   // calculate the weights either from BIAS</a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineCov">      16365 :   if(do_reweight_) {</span></a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineCov">         12 :     std::vector&lt;double&gt; bias(nrep_,0);</span></a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineCov">         12 :     if(rank_==0) {</span></a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineCov">         12 :       bias[replica_] = getArgument(0);</span></a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineCov">         12 :       if(nrep_&gt;1) multi_sim_comm.Sum(&amp;bias[0], nrep_);</span></a>
+<a name="1502"><span class="lineNum">    1502 </span>            :     }</a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineCov">         12 :     comm.Sum(&amp;bias[0], nrep_);</span></a>
+<a name="1504"><span class="lineNum">    1504 </span>            : </a>
+<a name="1505"><span class="lineNum">    1505 </span>            :     // accumulate weights</a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineCov">         12 :     if(!first_time_w_) {</span></a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineCov">         30 :       for(unsigned i=0; i&lt;nrep_; ++i) {</span></a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineCov">         20 :         const double delta=bias[i]-average_weights_[i];</span></a>
+<a name="1509"><span class="lineNum">    1509 </span>            :         // FIXME: multiplying by fractional decay here causes problems with numerical derivatives,</a>
+<a name="1510"><span class="lineNum">    1510 </span>            :         // probably because we're making several calls to calculate(), causing accumulation</a>
+<a name="1511"><span class="lineNum">    1511 </span>            :         // of epsilons. Maybe we can work on a temporary copy of the action instead?</a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineCov">         20 :         average_weights_[i]+=decay_w_*delta;</span></a>
+<a name="1513"><span class="lineNum">    1513 </span>            :       }</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :     } else {</a>
+<a name="1515"><span class="lineNum">    1515 </span><span class="lineCov">          2 :       first_time_w_ = false;</span></a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;nrep_; ++i) average_weights_[i] = bias[i];</span></a>
+<a name="1517"><span class="lineNum">    1517 </span>            :     }</a>
+<a name="1518"><span class="lineNum">    1518 </span>            : </a>
+<a name="1519"><span class="lineNum">    1519 </span>            :     // set average back into bias and set norm to one</a>
+<a name="1520"><span class="lineNum">    1520 </span><span class="lineCov">         12 :     const double maxbias = *(std::max_element(average_weights_.begin(), average_weights_.end()));</span></a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineCov">         36 :     for(unsigned i=0; i&lt;nrep_; ++i) bias[i] = std::exp((average_weights_[i]-maxbias)/kbt_);</span></a>
+<a name="1522"><span class="lineNum">    1522 </span>            :     // set local weight, norm and weight variance</a>
+<a name="1523"><span class="lineNum">    1523 </span><span class="lineCov">         12 :     weight = bias[replica_];</span></a>
+<a name="1524"><span class="lineNum">    1524 </span>            :     double w2=0.;</a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineCov">         36 :     for(unsigned i=0; i&lt;nrep_; ++i) {</span></a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineCov">         24 :       w2 += bias[i]*bias[i];</span></a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineCov">         24 :       norm += bias[i];</span></a>
+<a name="1528"><span class="lineNum">    1528 </span>            :     }</a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">         12 :     neff = norm*norm/w2;</span></a>
+<a name="1530"><span class="lineNum">    1530 </span><span class="lineCov">         24 :     getPntrToComponent(&quot;weight&quot;)-&gt;set(weight/norm);</span></a>
+<a name="1531"><span class="lineNum">    1531 </span>            :   } else {</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :     // or arithmetic ones</a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineCov">      16353 :     neff = dnrep;</span></a>
+<a name="1534"><span class="lineNum">    1534 </span><span class="lineCov">      16353 :     weight = 1.0;</span></a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineCov">      16353 :     norm = dnrep;</span></a>
+<a name="1536"><span class="lineNum">    1536 </span>            :   }</a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineCov">      16365 :   getPntrToComponent(&quot;neff&quot;)-&gt;set(neff);</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">      16365 : }</span></a>
+<a name="1539"><span class="lineNum">    1539 </span>            : </a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineCov">      16365 : void EMMI::calculate()</span></a>
+<a name="1541"><span class="lineNum">    1541 </span>            : {</a>
+<a name="1542"><span class="lineNum">    1542 </span>            : </a>
+<a name="1543"><span class="lineNum">    1543 </span>            : // calculate CV</a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineCov">      16365 :   calculate_overlap();</span></a>
+<a name="1545"><span class="lineNum">    1545 </span>            : </a>
+<a name="1546"><span class="lineNum">    1546 </span>            :   // rescale factor for ensemble average</a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineCov">      16365 :   double weight = 0.;</span></a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineCov">      16365 :   double neff = 0.;</span></a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineCov">      16365 :   double norm = 0.;</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">      16365 :   get_weights(weight, norm, neff);</span></a>
+<a name="1551"><span class="lineNum">    1551 </span>            : </a>
+<a name="1552"><span class="lineNum">    1552 </span>            :   // in case of ensemble averaging, calculate average overlap</a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineCov">      16365 :   if(!no_aver_ &amp;&amp; nrep_&gt;1) {</span></a>
+<a name="1554"><span class="lineNum">    1554 </span>            :     // if master node, calculate average across replicas</a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineCov">         12 :     if(rank_==0) {</span></a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineCov">      10812 :       for(unsigned i=0; i&lt;ovmd_.size(); ++i) ovmd_ave_[i] = weight / norm * ovmd_[i];</span></a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineCov">         12 :       multi_sim_comm.Sum(&amp;ovmd_ave_[0], ovmd_ave_.size());</span></a>
+<a name="1558"><span class="lineNum">    1558 </span>            :     } else {</a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;ovmd_ave_.size(); ++i) ovmd_ave_[i] = 0.0;</span></a>
+<a name="1560"><span class="lineNum">    1560 </span>            :     }</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :     // local communication</a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineCov">         12 :     if(size_&gt;1) comm.Sum(&amp;ovmd_ave_[0], ovmd_ave_.size());</span></a>
+<a name="1563"><span class="lineNum">    1563 </span>            :   } else {</a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineCov">     163530 :     for(unsigned i=0; i&lt;ovmd_.size(); ++i) ovmd_ave_[i] = ovmd_[i];</span></a>
+<a name="1565"><span class="lineNum">    1565 </span>            :   }</a>
+<a name="1566"><span class="lineNum">    1566 </span>            : </a>
+<a name="1567"><span class="lineNum">    1567 </span>            :   // get time step</a>
+<a name="1568"><span class="lineNum">    1568 </span><span class="lineCov">      16365 :   long long int step = getStep();</span></a>
+<a name="1569"><span class="lineNum">    1569 </span>            : </a>
+<a name="1570"><span class="lineNum">    1570 </span>            :   // do regression</a>
+<a name="1571"><span class="lineNum">    1571 </span><span class="lineCov">      16365 :   if(nregres_&gt;0) {</span></a>
+<a name="1572"><span class="lineNum">    1572 </span><span class="lineNoCov">          0 :     if(step%nregres_==0 &amp;&amp; !getExchangeStep()) scale_ = doRegression();</span></a>
+<a name="1573"><span class="lineNum">    1573 </span>            :     // set scale component</a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;scale&quot;)-&gt;set(scale_);</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            :   }</a>
+<a name="1576"><span class="lineNum">    1576 </span>            : </a>
+<a name="1577"><span class="lineNum">    1577 </span>            :   // write model overlap to file</a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineCov">      16365 :   if(ovstride_&gt;0 &amp;&amp; step%ovstride_==0) write_model_overlap(step);</span></a>
+<a name="1579"><span class="lineNum">    1579 </span>            : </a>
+<a name="1580"><span class="lineNum">    1580 </span>            :   // clear energy and virial</a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineCov">      16365 :   ene_ = 0.0;</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineCov">      16365 :   virial_.zero();</span></a>
+<a name="1583"><span class="lineNum">    1583 </span>            : </a>
+<a name="1584"><span class="lineNum">    1584 </span>            :   // Gaussian noise</a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineCov">      16365 :   if(noise_==0) calculate_Gauss();</span></a>
+<a name="1586"><span class="lineNum">    1586 </span>            : </a>
+<a name="1587"><span class="lineNum">    1587 </span>            :   // Outliers noise</a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineCov">      16365 :   if(noise_==1) calculate_Outliers();</span></a>
+<a name="1589"><span class="lineNum">    1589 </span>            : </a>
+<a name="1590"><span class="lineNum">    1590 </span>            :   // Marginal noise</a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineCov">      16365 :   if(noise_==2) calculate_Marginal();</span></a>
+<a name="1592"><span class="lineNum">    1592 </span>            : </a>
+<a name="1593"><span class="lineNum">    1593 </span>            :   // get annealing rescale factor</a>
+<a name="1594"><span class="lineNum">    1594 </span><span class="lineCov">      16365 :   if(nanneal_&gt;0) {</span></a>
+<a name="1595"><span class="lineNum">    1595 </span><span class="lineNoCov">          0 :     anneal_ = get_annealing(step);</span></a>
+<a name="1596"><span class="lineNum">    1596 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;anneal&quot;)-&gt;set(anneal_);</span></a>
+<a name="1597"><span class="lineNum">    1597 </span>            :   }</a>
+<a name="1598"><span class="lineNum">    1598 </span>            : </a>
+<a name="1599"><span class="lineNum">    1599 </span>            :   // annealing rescale</a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineCov">      16365 :   ene_ /= anneal_;</span></a>
+<a name="1601"><span class="lineNum">    1601 </span>            : </a>
+<a name="1602"><span class="lineNum">    1602 </span><span class="lineCov">      16365 :   std::vector&lt;double&gt; GMMid_der_av_(GMMid_der_.size(), 0.0);</span></a>
+<a name="1603"><span class="lineNum">    1603 </span>            :   // in case of ensemble averaging</a>
+<a name="1604"><span class="lineNum">    1604 </span><span class="lineCov">      16365 :   if(!no_aver_ &amp;&amp; nrep_&gt;1) {</span></a>
+<a name="1605"><span class="lineNum">    1605 </span>            :     // if master node, sum der_GMMid derivatives and ene</a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">         12 :     if(rank_==0) {</span></a>
+<a name="1607"><span class="lineNum">    1607 </span><span class="lineCov">      10812 :       for(unsigned i=0; i&lt;GMMid_der_.size(); ++i) {</span></a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineCov">      10800 :         GMMid_der_av_[i] = (weight / norm) * GMMid_der_[i];</span></a>
+<a name="1609"><span class="lineNum">    1609 </span>            :       }</a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineCov">         12 :       multi_sim_comm.Sum(&amp;GMMid_der_av_[0], GMMid_der_av_.size());</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineCov">         12 :       multi_sim_comm.Sum(&amp;ene_, 1);</span></a>
+<a name="1612"><span class="lineNum">    1612 </span>            :     } else {</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :       // set der_GMMid derivatives and energy to zero</a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;GMMid_der_av_.size(); ++i) GMMid_der_av_[i]=0.0;</span></a>
+<a name="1615"><span class="lineNum">    1615 </span><span class="lineNoCov">          0 :       ene_ = 0.0;</span></a>
+<a name="1616"><span class="lineNum">    1616 </span>            :     }</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :     // local communication</a>
+<a name="1618"><span class="lineNum">    1618 </span><span class="lineCov">         12 :     if(size_&gt;1) {</span></a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineNoCov">          0 :       comm.Sum(&amp;GMMid_der_av_[0], GMMid_der_av_.size());</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineNoCov">          0 :       comm.Sum(&amp;ene_, 1);</span></a>
+<a name="1621"><span class="lineNum">    1621 </span>            :     }</a>
+<a name="1622"><span class="lineNum">    1622 </span>            :   } else {</a>
+<a name="1623"><span class="lineNum">    1623 </span><span class="lineCov">     163530 :     for (unsigned i = 0; i &lt; GMMid_der_.size(); ++i) {</span></a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineCov">     147177 :       GMMid_der_av_[i] = GMMid_der_[i];</span></a>
+<a name="1625"><span class="lineNum">    1625 </span>            :     }</a>
+<a name="1626"><span class="lineNum">    1626 </span>            :   }</a>
+<a name="1627"><span class="lineNum">    1627 </span>            : </a>
+<a name="1628"><span class="lineNum">    1628 </span>            :   // clean temporary std::vector</a>
+<a name="1629"><span class="lineNum">    1629 </span><span class="lineCov">    9860991 :   for(unsigned i=0; i&lt;atom_der_.size(); ++i) atom_der_[i] = Vector(0,0,0);</span></a>
+<a name="1630"><span class="lineNum">    1630 </span>            : </a>
+<a name="1631"><span class="lineNum">    1631 </span>            :   // get derivatives of bias with respect to atoms</a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineCov">    2127723 :   for(unsigned i=rank_; i&lt;nl_.size(); i=i+size_) {</span></a>
+<a name="1633"><span class="lineNum">    1633 </span>            :     // get indexes of data and model component</a>
+<a name="1634"><span class="lineNum">    1634 </span><span class="lineCov">    2111358 :     unsigned id = nl_[i] / GMM_m_type_.size();</span></a>
+<a name="1635"><span class="lineNum">    1635 </span><span class="lineCov">    2111358 :     unsigned im = nl_[i] % GMM_m_type_.size();</span></a>
+<a name="1636"><span class="lineNum">    1636 </span>            :     // chain rule + replica normalization</a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineCov">    2111358 :     Vector tot_der = GMMid_der_av_[id] * ovmd_der_[i] * scale_ / anneal_;</span></a>
+<a name="1638"><span class="lineNum">    1638 </span><span class="lineCov">    2111358 :     Vector pos;</span></a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineCov">    2111358 :     if(pbc_) pos = pbcDistance(GMM_d_m_[id], getPosition(im)) + GMM_d_m_[id];</span></a>
+<a name="1640"><span class="lineNum">    1640 </span><span class="lineCov">    2111358 :     else     pos = getPosition(im);</span></a>
+<a name="1641"><span class="lineNum">    1641 </span>            :     // increment derivatives and virial</a>
+<a name="1642"><span class="lineNum">    1642 </span><span class="lineCov">    2111358 :     atom_der_[im] += tot_der;</span></a>
+<a name="1643"><span class="lineNum">    1643 </span><span class="lineCov">    2111358 :     virial_ += Tensor(pos, -tot_der);</span></a>
+<a name="1644"><span class="lineNum">    1644 </span>            :   }</a>
+<a name="1645"><span class="lineNum">    1645 </span>            : </a>
+<a name="1646"><span class="lineNum">    1646 </span>            :   // communicate local derivatives and virial</a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineCov">      16365 :   if(size_&gt;1) {</span></a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">      10902 :     comm.Sum(&amp;atom_der_[0][0], 3*atom_der_.size());</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">      10902 :     comm.Sum(virial_);</span></a>
+<a name="1650"><span class="lineNum">    1650 </span>            :   }</a>
+<a name="1651"><span class="lineNum">    1651 </span>            : </a>
+<a name="1652"><span class="lineNum">    1652 </span>            :   // set derivatives, virial, and score</a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineCov">    9860991 :   for(unsigned i=0; i&lt;atom_der_.size(); ++i) setAtomsDerivatives(getPntrToComponent(&quot;scoreb&quot;), i, atom_der_[i]);</span></a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineCov">      16365 :   setBoxDerivatives(getPntrToComponent(&quot;scoreb&quot;), virial_);</span></a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineCov">      16365 :   getPntrToComponent(&quot;scoreb&quot;)-&gt;set(ene_);</span></a>
+<a name="1656"><span class="lineNum">    1656 </span>            : </a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">      16365 :   if (do_reweight_) {</span></a>
+<a name="1658"><span class="lineNum">    1658 </span>            :     double w_tmp = 0.;</a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineCov">      10812 :     for (unsigned i = 0; i &lt; ovmd_.size(); ++i) {</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">      10800 :       w_tmp += (ovmd_[i] - ovmd_ave_[i]) * GMMid_der_[i];</span></a>
+<a name="1661"><span class="lineNum">    1661 </span>            :     }</a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineCov">         12 :     w_tmp *= scale_ * (weight / norm) / kbt_ * decay_w_;</span></a>
+<a name="1663"><span class="lineNum">    1663 </span>            : </a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">         12 :     setArgDerivatives(getPntrToComponent(&quot;scoreb&quot;), w_tmp);</span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">         24 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(w_tmp);</span></a>
+<a name="1666"><span class="lineNum">    1666 </span>            :   }</a>
+<a name="1667"><span class="lineNum">    1667 </span>            : </a>
+<a name="1668"><span class="lineNum">    1668 </span>            :   // This part is needed only for Gaussian and Outliers noise models</a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineCov">      16365 :   if(noise_!=2) {</span></a>
+<a name="1670"><span class="lineNum">    1670 </span>            : </a>
+<a name="1671"><span class="lineNum">    1671 </span>            :     // do Montecarlo</a>
+<a name="1672"><span class="lineNum">    1672 </span><span class="lineCov">      10914 :     if(dsigma_[0]&gt;0 &amp;&amp; step%MCstride_==0 &amp;&amp; !getExchangeStep()) doMonteCarlo();</span></a>
+<a name="1673"><span class="lineNum">    1673 </span>            : </a>
+<a name="1674"><span class="lineNum">    1674 </span>            :     // print status</a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineCov">      10914 :     if(step%statusstride_==0) print_status(step);</span></a>
+<a name="1676"><span class="lineNum">    1676 </span>            : </a>
+<a name="1677"><span class="lineNum">    1677 </span>            :     // calculate acceptance ratio</a>
+<a name="1678"><span class="lineNum">    1678 </span><span class="lineCov">      10914 :     double acc = MCaccept_ / MCtrials_;</span></a>
+<a name="1679"><span class="lineNum">    1679 </span>            : </a>
+<a name="1680"><span class="lineNum">    1680 </span>            :     // set value</a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineCov">      21828 :     getPntrToComponent(&quot;acc&quot;)-&gt;set(acc);</span></a>
+<a name="1682"><span class="lineNum">    1682 </span>            : </a>
+<a name="1683"><span class="lineNum">    1683 </span>            :   }</a>
+<a name="1684"><span class="lineNum">    1684 </span>            : </a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineCov">      16365 : }</span></a>
+<a name="1686"><span class="lineNum">    1686 </span>            : </a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineCov">       5463 : void EMMI::calculate_Gauss()</span></a>
+<a name="1688"><span class="lineNum">    1688 </span>            : {</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :   // cycle on all the GMM groups</a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineCov">      10926 :   for(unsigned i=0; i&lt;GMM_d_grps_.size(); ++i) {</span></a>
+<a name="1691"><span class="lineNum">    1691 </span>            :     double eneg = 0.0;</a>
+<a name="1692"><span class="lineNum">    1692 </span>            :     // cycle on all the members of the group</a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineCov">      65322 :     for(unsigned j=0; j&lt;GMM_d_grps_[i].size(); ++j) {</span></a>
+<a name="1694"><span class="lineNum">    1694 </span>            :       // id of the GMM component</a>
+<a name="1695"><span class="lineNum">    1695 </span><span class="lineCov">      59859 :       int GMMid = GMM_d_grps_[i][j];</span></a>
+<a name="1696"><span class="lineNum">    1696 </span>            :       // calculate deviation</a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineCov">      59859 :       double dev = ( scale_*ovmd_ave_[GMMid]-ovdd_[GMMid] ) / sigma_[i];</span></a>
+<a name="1698"><span class="lineNum">    1698 </span>            :       // add to group energy</a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineCov">      59859 :       eneg += 0.5 * dev * dev;</span></a>
+<a name="1700"><span class="lineNum">    1700 </span>            :       // store derivative for later</a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineCov">      59859 :       GMMid_der_[GMMid] = kbt_ * dev / sigma_[i];</span></a>
+<a name="1702"><span class="lineNum">    1702 </span>            :     }</a>
+<a name="1703"><span class="lineNum">    1703 </span>            :     // add to total energy along with normalizations and prior</a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineCov">       5463 :     ene_ += kbt_ * ( eneg + (static_cast&lt;double&gt;(GMM_d_grps_[i].size())+prior_) * std::log(sigma_[i]) );</span></a>
+<a name="1705"><span class="lineNum">    1705 </span>            :   }</a>
+<a name="1706"><span class="lineNum">    1706 </span><span class="lineCov">       5463 : }</span></a>
+<a name="1707"><span class="lineNum">    1707 </span>            : </a>
+<a name="1708"><span class="lineNum">    1708 </span><span class="lineCov">       5451 : void EMMI::calculate_Outliers()</span></a>
+<a name="1709"><span class="lineNum">    1709 </span>            : {</a>
+<a name="1710"><span class="lineNum">    1710 </span>            :   // cycle on all the GMM groups</a>
+<a name="1711"><span class="lineNum">    1711 </span><span class="lineCov">      10902 :   for(unsigned i=0; i&lt;GMM_d_grps_.size(); ++i) {</span></a>
+<a name="1712"><span class="lineNum">    1712 </span>            :     // cycle on all the members of the group</a>
+<a name="1713"><span class="lineNum">    1713 </span>            :     double eneg = 0.0;</a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineCov">      54510 :     for(unsigned j=0; j&lt;GMM_d_grps_[i].size(); ++j) {</span></a>
+<a name="1715"><span class="lineNum">    1715 </span>            :       // id of the GMM component</a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineCov">      49059 :       int GMMid = GMM_d_grps_[i][j];</span></a>
+<a name="1717"><span class="lineNum">    1717 </span>            :       // calculate deviation</a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineCov">      49059 :       double dev = ( scale_*ovmd_ave_[GMMid]-ovdd_[GMMid] ) / sigma_[i];</span></a>
+<a name="1719"><span class="lineNum">    1719 </span>            :       // add to group energy</a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineCov">      49059 :       eneg += std::log1p( 0.5 * dev * dev );</span></a>
+<a name="1721"><span class="lineNum">    1721 </span>            :       // store derivative for later</a>
+<a name="1722"><span class="lineNum">    1722 </span><span class="lineCov">      49059 :       GMMid_der_[GMMid] = kbt_ / ( 1.0 + 0.5 * dev * dev ) * dev / sigma_[i];</span></a>
+<a name="1723"><span class="lineNum">    1723 </span>            :     }</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :     // add to total energy along with normalizations and prior</a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineCov">       5451 :     ene_ += kbt_ * ( eneg + (static_cast&lt;double&gt;(GMM_d_grps_[i].size())+prior_) * std::log(sigma_[i]) );</span></a>
+<a name="1726"><span class="lineNum">    1726 </span>            :   }</a>
+<a name="1727"><span class="lineNum">    1727 </span><span class="lineCov">       5451 : }</span></a>
+<a name="1728"><span class="lineNum">    1728 </span>            : </a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineCov">       5451 : void EMMI::calculate_Marginal()</span></a>
+<a name="1730"><span class="lineNum">    1730 </span>            : {</a>
+<a name="1731"><span class="lineNum">    1731 </span>            :   // cycle on all the GMM groups</a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineCov">      10902 :   for(unsigned i=0; i&lt;GMM_d_grps_.size(); ++i) {</span></a>
+<a name="1733"><span class="lineNum">    1733 </span>            :     // cycle on all the members of the group</a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineCov">      54510 :     for(unsigned j=0; j&lt;GMM_d_grps_[i].size(); ++j) {</span></a>
+<a name="1735"><span class="lineNum">    1735 </span>            :       // id of the GMM component</a>
+<a name="1736"><span class="lineNum">    1736 </span><span class="lineCov">      49059 :       int GMMid = GMM_d_grps_[i][j];</span></a>
+<a name="1737"><span class="lineNum">    1737 </span>            :       // calculate deviation</a>
+<a name="1738"><span class="lineNum">    1738 </span><span class="lineCov">      49059 :       double dev = ( scale_*ovmd_ave_[GMMid]-ovdd_[GMMid] );</span></a>
+<a name="1739"><span class="lineNum">    1739 </span>            :       // calculate errf</a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">      49059 :       double errf = erf ( dev * inv_sqrt2_ / sigma_min_[i] );</span></a>
+<a name="1741"><span class="lineNum">    1741 </span>            :       // add to group energy</a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineCov">      49059 :       ene_ += -kbt_ * std::log ( 0.5 / dev * errf ) ;</span></a>
+<a name="1743"><span class="lineNum">    1743 </span>            :       // store derivative for later</a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineCov">      49059 :       GMMid_der_[GMMid] = - kbt_/errf*sqrt2_pi_*std::exp(-0.5*dev*dev/sigma_min_[i]/sigma_min_[i])/sigma_min_[i]+kbt_/dev;</span></a>
+<a name="1745"><span class="lineNum">    1745 </span>            :     }</a>
+<a name="1746"><span class="lineNum">    1746 </span>            :   }</a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineCov">       5451 : }</span></a>
+<a name="1748"><span class="lineNum">    1748 </span>            : </a>
+<a name="1749"><span class="lineNum">    1749 </span>            : }</a>
+<a name="1750"><span class="lineNum">    1750 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/FretEfficiency.cpp.func-sort-c.html b/coverage/isdb/FretEfficiency.cpp.func-sort-c.html
new file mode 100644
index 0000000000..969e6a3976
--- /dev/null
+++ b/coverage/isdb/FretEfficiency.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/FretEfficiency.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - FretEfficiency.cpp<span style="font-size: 80%;"> (<a href="FretEfficiency.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FretEfficiency.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#99">_ZN4PLMD4isdb14FretEfficiencyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#91">_ZN4PLMD4isdb12_GLOBAL__N_126FretEfficiencyRegisterMe936createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#99">_ZN4PLMD4isdb14FretEfficiencyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#93">_ZN4PLMD4isdb14FretEfficiency16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#129">_ZN4PLMD4isdb14FretEfficiency9calculateEv</a></td>
+              <td class="coverFnHi">238</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#91">_ZN4PLMD4isdb12_GLOBAL__N_126FretEfficiencyRegisterMe93C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#91">_ZN4PLMD4isdb12_GLOBAL__N_126FretEfficiencyRegisterMe93D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/FretEfficiency.cpp.func.html b/coverage/isdb/FretEfficiency.cpp.func.html
new file mode 100644
index 0000000000..54f1dc473f
--- /dev/null
+++ b/coverage/isdb/FretEfficiency.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/FretEfficiency.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - FretEfficiency.cpp<span style="font-size: 80%;"> (<a href="FretEfficiency.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FretEfficiency.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#91">_ZN4PLMD4isdb12_GLOBAL__N_126FretEfficiencyRegisterMe936createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#91">_ZN4PLMD4isdb12_GLOBAL__N_126FretEfficiencyRegisterMe93C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#91">_ZN4PLMD4isdb12_GLOBAL__N_126FretEfficiencyRegisterMe93D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#93">_ZN4PLMD4isdb14FretEfficiency16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#129">_ZN4PLMD4isdb14FretEfficiency9calculateEv</a></td>
+              <td class="coverFnHi">238</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#99">_ZN4PLMD4isdb14FretEfficiencyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FretEfficiency.cpp.gcov.html#99">_ZN4PLMD4isdb14FretEfficiencyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/FretEfficiency.cpp.gcov.html b/coverage/isdb/FretEfficiency.cpp.gcov.html
new file mode 100644
index 0000000000..c71a5275df
--- /dev/null
+++ b/coverage/isdb/FretEfficiency.cpp.gcov.html
@@ -0,0 +1,231 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/FretEfficiency.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - FretEfficiency.cpp<span style="font-size: 80%;"> (source / <a href="FretEfficiency.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;colvar/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace isdb {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC ISDB_COLVAR FRET</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Calculates the FRET efficiency between a pair of atoms.</a>
+<a name="36"><span class="lineNum">      36 </span>            : The efficiency is calculated using the Forster relation:</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : E=\frac{1}{1+(R/R_0)^6}</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f]</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : where \f$R\f$ is the distance and \f$R_0\f$ is the Forster radius.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : By default the distance is computed taking into account periodic</a>
+<a name="45"><span class="lineNum">      45 </span>            : boundary conditions. This behavior can be changed with the NOPBC flag.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \par Examples</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The following input tells plumed to print the FRET efficiencies</a>
+<a name="51"><span class="lineNum">      51 </span>            : calculated as a function of the distance between atoms 3 and 5 and</a>
+<a name="52"><span class="lineNum">      52 </span>            : the distance between atoms 2 and 4.</a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : fe1:  FRET ATOMS=3,5 R0=5.5</a>
+<a name="55"><span class="lineNum">      55 </span>            : fe2:  FRET ATOMS=2,4 R0=5.5</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=fe1,fe2</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The following input computes the FRET efficiency calculated on the</a>
+<a name="60"><span class="lineNum">      60 </span>            : terminal atoms of a polymer</a>
+<a name="61"><span class="lineNum">      61 </span>            : of 100 atoms and keeps it at a value around 0.5.</a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : WHOLEMOLECULES ENTITY0=1-100</a>
+<a name="64"><span class="lineNum">      64 </span>            : fe: FRET ATOMS=1,100 R0=5.5 NOPBC</a>
+<a name="65"><span class="lineNum">      65 </span>            : RESTRAINT ARG=fe KAPPA=100 AT=0.5</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : Notice that NOPBC is used</a>
+<a name="69"><span class="lineNum">      69 </span>            : to be sure that if the distance is larger than half the simulation</a>
+<a name="70"><span class="lineNum">      70 </span>            : box the distance is compute properly. Also notice that, since many MD</a>
+<a name="71"><span class="lineNum">      71 </span>            : codes break molecules across cell boundary, it might be necessary to</a>
+<a name="72"><span class="lineNum">      72 </span>            : use the \ref WHOLEMOLECULES keyword (also notice that it should be</a>
+<a name="73"><span class="lineNum">      73 </span>            : _before_ FRET).</a>
+<a name="74"><span class="lineNum">      74 </span>            : Just be sure that the ordered list provide to WHOLEMOLECULES has the following</a>
+<a name="75"><span class="lineNum">      75 </span>            : properties:</a>
+<a name="76"><span class="lineNum">      76 </span>            : - Consecutive atoms should be closer than half-cell throughout the entire simulation.</a>
+<a name="77"><span class="lineNum">      77 </span>            : - Atoms required later for the distance (e.g. 1 and 100) should be included in the list</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : class FretEfficiency : public Colvar {</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool pbc;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   double R0_;</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit FretEfficiency(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            : // active methods:</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void calculate() override;</a>
+<a name="91"><span class="lineNum">      91 </span>            : };</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      12532 : PLUMED_REGISTER_ACTION(FretEfficiency,&quot;FRET&quot;)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         16 : void FretEfficiency::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         16 :   Colvar::registerKeywords( keys );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         32 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the pair of atom that we are calculating the distance between&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         32 :   keys.add(&quot;compulsory&quot;,&quot;R0&quot;,&quot;The value of the Forster radius.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         16 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         14 : FretEfficiency::FretEfficiency(const ActionOptions&amp;ao):</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         14 :   pbc(true)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : {</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         28 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         14 :   if(atoms.size()!=2)</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     error(&quot;Number of specified atoms should be 2&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         14 :   parse(&quot;R0&quot;,R0_);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         14 :   bool nopbc=!pbc;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         14 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         14 :   pbc=!nopbc;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         14 :   checkRead();</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         14 :   log.printf(&quot;  between atoms %d %d\n&quot;,atoms[0].serial(),atoms[1].serial());</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         14 :   log.printf(&quot;  with Forster radius set to %lf\n&quot;,R0_);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         14 :   if(pbc) log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   else    log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         28 :   log &lt;&lt; &quot; Bibliography&quot; &lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         14 :   addValueWithDerivatives();</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         14 :   setNotPeriodic();</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         14 :   requestAtoms(atoms);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         14 : }</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : // calculator</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        238 : void FretEfficiency::calculate() {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        238 :   if(pbc) makeWhole();</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        238 :   Vector distance=delta(getPosition(0),getPosition(1));</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        238 :   const double dist_mod=distance.modulo();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        238 :   const double inv_dist_mod=1.0/dist_mod;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        238 :   const double ratiosix=std::pow(dist_mod/R0_,6);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        238 :   const double fret_eff = 1.0/(1.0+ratiosix);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        238 :   const double der = -6.0*fret_eff*fret_eff*ratiosix*inv_dist_mod;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        238 :   setAtomsDerivatives(0,-inv_dist_mod*der*distance);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        238 :   setAtomsDerivatives(1, inv_dist_mod*der*distance);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        238 :   setBoxDerivativesNoPbc();</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        238 :   setValue(fret_eff);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        238 : }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Jcoupling.cpp.func-sort-c.html b/coverage/isdb/Jcoupling.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0e877cc292
--- /dev/null
+++ b/coverage/isdb/Jcoupling.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Jcoupling.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Jcoupling.cpp<span style="font-size: 80%;"> (<a href="Jcoupling.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">160</td>
+            <td class="headerCovTableEntry">172</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Jcoupling.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#124">_ZN4PLMD4isdb9JCouplingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#104">_ZN4PLMD4isdb12_GLOBAL__N_122JCouplingRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#124">_ZN4PLMD4isdb9JCouplingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#106">_ZN4PLMD4isdb9JCoupling16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#386">_ZN4PLMD4isdb9JCoupling6updateEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#293">_ZN4PLMD4isdb9JCoupling9calculateEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#104">_ZN4PLMD4isdb12_GLOBAL__N_122JCouplingRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#104">_ZN4PLMD4isdb12_GLOBAL__N_122JCouplingRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Jcoupling.cpp.func.html b/coverage/isdb/Jcoupling.cpp.func.html
new file mode 100644
index 0000000000..6cd5227bd9
--- /dev/null
+++ b/coverage/isdb/Jcoupling.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Jcoupling.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Jcoupling.cpp<span style="font-size: 80%;"> (<a href="Jcoupling.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">160</td>
+            <td class="headerCovTableEntry">172</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Jcoupling.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#104">_ZN4PLMD4isdb12_GLOBAL__N_122JCouplingRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#104">_ZN4PLMD4isdb12_GLOBAL__N_122JCouplingRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#104">_ZN4PLMD4isdb12_GLOBAL__N_122JCouplingRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#106">_ZN4PLMD4isdb9JCoupling16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#386">_ZN4PLMD4isdb9JCoupling6updateEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#293">_ZN4PLMD4isdb9JCoupling9calculateEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#124">_ZN4PLMD4isdb9JCouplingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Jcoupling.cpp.gcov.html#124">_ZN4PLMD4isdb9JCouplingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Jcoupling.cpp.gcov.html b/coverage/isdb/Jcoupling.cpp.gcov.html
new file mode 100644
index 0000000000..ebed60cb74
--- /dev/null
+++ b/coverage/isdb/Jcoupling.cpp.gcov.html
@@ -0,0 +1,470 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Jcoupling.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Jcoupling.cpp<span style="font-size: 80%;"> (source / <a href="Jcoupling.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">160</td>
+            <td class="headerCovTableEntry">172</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace isdb {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC ISDB_COLVAR JCOUPLING</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculates 3J coupling constants for a dihedral angle.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : The J-coupling between two atoms is given by the Karplus relation:</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \f[</a>
+<a name="37"><span class="lineNum">      37 </span>            : ^3J(\theta)=A\cos^2(\theta+\Delta\theta)+B\cos(\theta+\Delta\theta)+C</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f]</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : where \f$A\f$, \f$B\f$ and \f$C\f$ are the Karplus parameters and \f$\Delta\theta\f$ is an additional constant</a>
+<a name="41"><span class="lineNum">      41 </span>            : added on to the dihedral angle \f$\theta\f$. The Karplus parameters are determined empirically and are dependent</a>
+<a name="42"><span class="lineNum">      42 </span>            : on the type of J-coupling.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This collective variable computes the J-couplings for a set of atoms defining a dihedral angle. You can specify</a>
+<a name="45"><span class="lineNum">      45 </span>            : the atoms involved using the \ref MOLINFO notation. You can also specify the experimental couplings using the</a>
+<a name="46"><span class="lineNum">      46 </span>            :  COUPLING keywords. These will be included in the output. You must choose the type of</a>
+<a name="47"><span class="lineNum">      47 </span>            : coupling using the type keyword, you can also supply custom Karplus parameters using TYPE=CUSTOM and the A, B, C</a>
+<a name="48"><span class="lineNum">      48 </span>            : and SHIFT keywords. You will need to make sure you are using the correct dihedral angle:</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : - Ha-N: \f$\psi\f$</a>
+<a name="51"><span class="lineNum">      51 </span>            : - Ha-HN: \f$\phi\f$</a>
+<a name="52"><span class="lineNum">      52 </span>            : - N-C\f$\gamma\f$: \f$\chi_1\f$</a>
+<a name="53"><span class="lineNum">      53 </span>            : - CO-C\f$\gamma\f$: \f$\chi_1\f$</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : J-couplings can be used to calculate a Metainference score using the internal keyword DOSCORE and all the options</a>
+<a name="56"><span class="lineNum">      56 </span>            : of \ref METAINFERENCE .</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : In the following example we calculate the Ha-N J-coupling from a set of atoms involved in</a>
+<a name="61"><span class="lineNum">      61 </span>            : dihedral \f$\psi\f$ angles in the peptide backbone. We also add the experimental data points and compute</a>
+<a name="62"><span class="lineNum">      62 </span>            : the correlation and other measures and finally print the results.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="66"><span class="lineNum">      66 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=peptide.pdb</a>
+<a name="67"><span class="lineNum">      67 </span>            : WHOLEMOLECULES ENTITY0=1-111</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : JCOUPLING ...</a>
+<a name="70"><span class="lineNum">      70 </span>            :     TYPE=HAN</a>
+<a name="71"><span class="lineNum">      71 </span>            :     ATOMS1=@psi-2 COUPLING1=-0.49</a>
+<a name="72"><span class="lineNum">      72 </span>            :     ATOMS2=@psi-4 COUPLING2=-0.54</a>
+<a name="73"><span class="lineNum">      73 </span>            :     ATOMS3=@psi-5 COUPLING3=-0.53</a>
+<a name="74"><span class="lineNum">      74 </span>            :     ATOMS4=@psi-7 COUPLING4=-0.39</a>
+<a name="75"><span class="lineNum">      75 </span>            :     ATOMS5=@psi-8 COUPLING5=-0.39</a>
+<a name="76"><span class="lineNum">      76 </span>            :     LABEL=jhan</a>
+<a name="77"><span class="lineNum">      77 </span>            : ... JCOUPLING</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : jhanst: STATS ARG=(jhan\.j-.*) PARARG=(jhan\.exp-.*)</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : PRINT ARG=jhanst.*,jhan.* FILE=COLVAR STRIDE=100</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endplumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : */</a>
+<a name="85"><span class="lineNum">      85 </span>            : //+ENDPLUMEDOC</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : class JCoupling :</a>
+<a name="88"><span class="lineNum">      88 </span>            :   public MetainferenceBase</a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            : private:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   bool pbc;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   enum { HAN, HAHN, CCG, NCG, CUSTOM };</a>
+<a name="93"><span class="lineNum">      93 </span>            :   unsigned ncoupl_;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   double ka_;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   double kb_;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   double kc_;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   double kshift_;</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : public:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit JCoupling(const ActionOptions&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void calculate() override;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void update() override;</a>
+<a name="104"><span class="lineNum">     104 </span>            : };</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(JCoupling, &quot;JCOUPLING&quot;)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          8 : void JCoupling::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          8 :   componentsAreNotOptional(keys);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          8 :   MetainferenceBase::registerKeywords(keys);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         16 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;, &quot;ATOMS&quot;, &quot;the 4 atoms involved in each of the bonds for which you wish to calculate the J-coupling. &quot;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one J-coupling will be &quot;</a>
+<a name="114"><span class="lineNum">     114 </span>            :            &quot;calculated for each ATOMS keyword you specify.&quot;);</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         16 :   keys.reset_style(&quot;ATOMS&quot;, &quot;atoms&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;, &quot;TYPE&quot;, &quot;Type of J-coupling to compute (HAN,HAHN,CCG,NCG,CUSTOM)&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;, &quot;A&quot;, &quot;Karplus parameter A&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;, &quot;B&quot;, &quot;Karplus parameter B&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;, &quot;C&quot;, &quot;Karplus parameter C&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;, &quot;SHIFT&quot;, &quot;Angle shift in radians&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;, &quot;COUPLING&quot;, &quot;Add an experimental value for each coupling&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         16 :   keys.addOutputComponent(&quot;j&quot;, &quot;default&quot;, &quot;the calculated J-coupling&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         16 :   keys.addOutputComponent(&quot;exp&quot;, &quot;COUPLING&quot;, &quot;the experimental J-coupling&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          6 : JCoupling::JCoupling(const ActionOptions&amp;ao):</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   PLUMED_METAINF_INIT(ao),</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   pbc(true)</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : {</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          6 :   bool nopbc = !pbc;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          6 :   parseFlag(&quot;NOPBC&quot;, nopbc);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          6 :   pbc =! nopbc;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   // Read in the atoms</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::vector&lt;AtomNumber&gt; t, atoms;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          6 :   for (int i = 1; ; ++i) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         68 :     parseAtomList(&quot;ATOMS&quot;, i, t );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         34 :     if (t.empty()) {</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :       break;</a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         28 :     if (t.size() != 4) {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :       std::string ss;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :       Tools::convert(i, ss);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :       error(&quot;ATOMS&quot; + ss + &quot; keyword has the wrong number of atoms&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :     // This makes the distance calculation easier later on (see Torsion implementation)</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         28 :     atoms.push_back(t[0]);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         28 :     atoms.push_back(t[1]);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         28 :     atoms.push_back(t[1]);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         28 :     atoms.push_back(t[2]);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         28 :     atoms.push_back(t[2]);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         28 :     atoms.push_back(t[3]);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         28 :     t.resize(0);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         28 :   }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            :   // We now have 6 atoms per datapoint</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          6 :   ncoupl_ = atoms.size()/6;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            :   // Parse J-Coupling type, this will determine the Karplus parameters</a>
+<a name="162"><span class="lineNum">     162 </span>            :   unsigned jtype_ = CUSTOM;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   std::string string_type;</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         12 :   parse(&quot;TYPE&quot;, string_type);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          6 :   if(string_type == &quot;HAN&quot;) {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     jtype_ = HAN;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          5 :   } else if(string_type == &quot;HAHN&quot;) {</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     jtype_ = HAHN;</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :   } else if(string_type == &quot;CCG&quot;) {</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     jtype_ = CCG;</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          1 :   } else if(string_type == &quot;NCG&quot;) {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     jtype_ = NCG;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   } else if(string_type == &quot;CUSTOM&quot;) {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     jtype_ = CUSTOM;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   } else {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     error(&quot;Unknown J-coupling type!&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   // Optionally add an experimental value (like with RDCs)</a>
+<a name="180"><span class="lineNum">     180 </span>            :   std::vector&lt;double&gt; coupl;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          6 :   coupl.resize( ncoupl_ );</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   unsigned ntarget=0;</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         13 :   for(unsigned i=0; i&lt;ncoupl_; ++i) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         24 :     if( !parseNumbered( &quot;COUPLING&quot;, i+1, coupl[i] ) ) break;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          7 :     ntarget++;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span>            :   bool addcoupling=false;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          6 :   if(ntarget!=ncoupl_ &amp;&amp; ntarget!=0) error(&quot;found wrong number of COUPLING values&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          6 :   if(ntarget==ncoupl_) addcoupling=true;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          6 :   if(getDoScore()&amp;&amp;!addcoupling) error(&quot;with DOSCORE you need to set the COUPLING values&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   // For custom types we allow use of custom Karplus parameters</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          6 :   if (jtype_ == CUSTOM) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     parse(&quot;A&quot;, ka_);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     parse(&quot;B&quot;, kb_);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     parse(&quot;C&quot;, kc_);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     parse(&quot;SHIFT&quot;, kshift_);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          6 :   log &lt;&lt; &quot;  Bibliography &quot;;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         12 :   log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   // Set Karplus parameters</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          6 :   switch (jtype_) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          1 :   case HAN:</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          1 :     ka_ = -0.88;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          1 :     kb_ = -0.61;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          1 :     kc_ = -0.27;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          1 :     kshift_ = pi / 3.0;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          2 :     log &lt;&lt; plumed.cite(&quot;Wang A C, Bax A, J. Am. Chem. Soc. 117, 1810 (1995)&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          1 :     log.printf(&quot;  J-coupling type is HAN, with A: %f, B: %f, C: %f, angle shift: %f\n&quot;, ka_, kb_, kc_, kshift_);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     break;</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          3 :   case HAHN:</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          3 :     ka_ = 7.09;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          3 :     kb_ = -1.42;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          3 :     kc_ = 1.55;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          3 :     kshift_ = -pi / 3.0;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          6 :     log &lt;&lt; plumed.cite(&quot;Hu J-S, Bax A, J. Am. Chem. Soc. 119, 6360 (1997)&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          3 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          3 :     log.printf(&quot;  J-coupling type is HAHN, with A: %f, B: %f, C: %f, angle shift: %f\n&quot;, ka_, kb_, kc_, kshift_);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     break;</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          1 :   case CCG:</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          1 :     ka_ = 2.31;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          1 :     kb_ = -0.87;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          1 :     kc_ = 0.55;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          1 :     kshift_ = (2.0 * pi) / 3.0;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          2 :     log &lt;&lt; plumed.cite(&quot;Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          1 :     log.printf(&quot;  J-coupling type is CCG, with A: %f, B: %f, C: %f, angle shift: %f\n&quot;, ka_, kb_, kc_, kshift_);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     break;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          1 :   case NCG:</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          1 :     ka_ = 1.29;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          1 :     kb_ = -0.49;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          1 :     kc_ = 0.37;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          1 :     kshift_ = 0.0;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          2 :     log &lt;&lt; plumed.cite(&quot;Perez C, Löhr F, Rüterjans H, Schmidt J, J. Am. Chem. Soc. 123, 7081 (2001)&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          1 :     log.printf(&quot;  J-coupling type is NCG, with A: %f, B: %f, C: %f, angle shift: %f\n&quot;, ka_, kb_, kc_, kshift_);</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :     break;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   case CUSTOM:</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :     log.printf(&quot;  J-coupling type is custom, with A: %f, B: %f, C: %f, angle shift: %f\n&quot;, ka_, kb_, kc_, kshift_);</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :     break;</a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         34 :   for (unsigned i = 0; i &lt; ncoupl_; ++i) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         28 :     log.printf(&quot;  The %uth J-Coupling is calculated from atoms : %d %d %d %d.&quot;,</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         28 :                i+1, atoms[6*i].serial(), atoms[6*i+1].serial(), atoms[6*i+3].serial(), atoms[6*i+5].serial());</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         28 :     if (addcoupling) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          7 :       log.printf(&quot; Experimental J-Coupling is %f.&quot;, coupl[i]);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     }</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         28 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          6 :   if (pbc) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :     log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   } else {</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          6 :     log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          6 :   if(!getDoScore()) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         26 :     for (unsigned i = 0; i &lt; ncoupl_; i++) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         21 :       std::string num; Tools::convert(i, num);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         21 :       addComponentWithDerivatives(&quot;j-&quot; + num);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         42 :       componentIsNotPeriodic(&quot;j-&quot; + num);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   } else {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          8 :     for (unsigned i = 0; i &lt; ncoupl_; i++) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          7 :       std::string num; Tools::convert(i, num);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          7 :       addComponent(&quot;j-&quot; + num);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         14 :       componentIsNotPeriodic(&quot;j-&quot; + num);</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span>            :   }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          6 :   if (addcoupling||getDoScore()) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          8 :     for (unsigned i = 0; i &lt; ncoupl_; i++) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          7 :       std::string num; Tools::convert(i, num);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          7 :       addComponent(&quot;exp-&quot; + num);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          7 :       componentIsNotPeriodic(&quot;exp-&quot; + num);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          7 :       Value* comp = getPntrToComponent(&quot;exp-&quot; + num);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          7 :       comp-&gt;set(coupl[i]);</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     }</a>
+<a name="284"><span class="lineNum">     284 </span>            :   }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          6 :   requestAtoms(atoms, false);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          6 :   if(getDoScore()) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          1 :     setParameters(coupl);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          1 :     Initialise(ncoupl_);</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          6 :   setDerivatives();</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          6 :   checkRead();</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          6 : }</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         16 : void JCoupling::calculate()</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : {</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         16 :   if (pbc) makeWhole();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         16 :   std::vector&lt;Vector&gt; deriv(ncoupl_*6);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         16 :   std::vector&lt;double&gt; j(ncoupl_,0.);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         16 :   #pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   {</a>
+<a name="303"><span class="lineNum">     303 </span>            :     #pragma omp for</a>
+<a name="304"><span class="lineNum">     304 </span>            :     // Loop through atoms, with steps of 6 atoms (one iteration per datapoint)</a>
+<a name="305"><span class="lineNum">     305 </span>            :     for (unsigned r=0; r&lt;ncoupl_; r++) {</a>
+<a name="306"><span class="lineNum">     306 </span>            :       // Index is the datapoint index</a>
+<a name="307"><span class="lineNum">     307 </span>            :       unsigned a0 = 6*r;</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :       // 6 atoms -&gt; 3 vectors</a>
+<a name="310"><span class="lineNum">     310 </span>            :       Vector d0 = delta(getPosition(a0+1), getPosition(a0));</a>
+<a name="311"><span class="lineNum">     311 </span>            :       Vector d1 = delta(getPosition(a0+3), getPosition(a0+2));</a>
+<a name="312"><span class="lineNum">     312 </span>            :       Vector d2 = delta(getPosition(a0+5), getPosition(a0+4));</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :       // Calculate dihedral with 3 vectors, get the derivatives</a>
+<a name="315"><span class="lineNum">     315 </span>            :       Vector dd0, dd1, dd2;</a>
+<a name="316"><span class="lineNum">     316 </span>            :       PLMD::Torsion t;</a>
+<a name="317"><span class="lineNum">     317 </span>            :       double torsion = t.compute(d0, d1, d2, dd0, dd1, dd2);</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :       // Calculate the Karplus relation and its derivative</a>
+<a name="320"><span class="lineNum">     320 </span>            :       double theta = torsion + kshift_;</a>
+<a name="321"><span class="lineNum">     321 </span>            :       double cos_theta = std::cos(theta);</a>
+<a name="322"><span class="lineNum">     322 </span>            :       double sin_theta = std::sin(theta);</a>
+<a name="323"><span class="lineNum">     323 </span>            :       j[r] = ka_*cos_theta*cos_theta + kb_*cos_theta + kc_;</a>
+<a name="324"><span class="lineNum">     324 </span>            :       double derj = -2.*ka_*sin_theta*cos_theta - kb_*sin_theta;</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            :       dd0 *= derj;</a>
+<a name="327"><span class="lineNum">     327 </span>            :       dd1 *= derj;</a>
+<a name="328"><span class="lineNum">     328 </span>            :       dd2 *= derj;</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :       if(getDoScore()) setCalcData(r, j[r]);</a>
+<a name="331"><span class="lineNum">     331 </span>            :       deriv[a0] =  dd0;</a>
+<a name="332"><span class="lineNum">     332 </span>            :       deriv[a0+1] = -dd0;</a>
+<a name="333"><span class="lineNum">     333 </span>            :       deriv[a0+2] =  dd1;</a>
+<a name="334"><span class="lineNum">     334 </span>            :       deriv[a0+3] = -dd1;</a>
+<a name="335"><span class="lineNum">     335 </span>            :       deriv[a0+4] =  dd2;</a>
+<a name="336"><span class="lineNum">     336 </span>            :       deriv[a0+5] = -dd2;</a>
+<a name="337"><span class="lineNum">     337 </span>            :     }</a>
+<a name="338"><span class="lineNum">     338 </span>            :   }</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         16 :   if(getDoScore()) {</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :     /* Metainference */</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          6 :     double score = getScore();</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :     setScore(score);</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            :     /* calculate final derivatives */</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          6 :     Tensor virial;</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          6 :     Value* val=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         48 :     for (unsigned r=0; r&lt;ncoupl_; r++) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         42 :       const unsigned a0 = 6*r;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         42 :       setAtomsDerivatives(val, a0, deriv[a0]*getMetaDer(r));</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         42 :       setAtomsDerivatives(val, a0+1, deriv[a0+1]*getMetaDer(r));</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         42 :       setAtomsDerivatives(val, a0+2, deriv[a0+2]*getMetaDer(r));</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         42 :       setAtomsDerivatives(val, a0+3, deriv[a0+3]*getMetaDer(r));</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         42 :       setAtomsDerivatives(val, a0+4, deriv[a0+4]*getMetaDer(r));</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         42 :       setAtomsDerivatives(val, a0+5, deriv[a0+5]*getMetaDer(r));</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         42 :       virial-=Tensor(getPosition(a0), deriv[a0]*getMetaDer(r));</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         42 :       virial-=Tensor(getPosition(a0+1), deriv[a0+1]*getMetaDer(r));</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         42 :       virial-=Tensor(getPosition(a0+2), deriv[a0+2]*getMetaDer(r));</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         42 :       virial-=Tensor(getPosition(a0+3), deriv[a0+3]*getMetaDer(r));</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         42 :       virial-=Tensor(getPosition(a0+4), deriv[a0+4]*getMetaDer(r));</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         42 :       virial-=Tensor(getPosition(a0+5), deriv[a0+5]*getMetaDer(r));</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :     }</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          6 :     setBoxDerivatives(val, virial);</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   } else {</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         66 :     for (unsigned r=0; r&lt;ncoupl_; r++) {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         56 :       const unsigned a0 = 6*r;</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         56 :       std::string num; Tools::convert(r,num);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         56 :       Value* val=getPntrToComponent(&quot;j-&quot;+num);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         56 :       val-&gt;set(j[r]);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         56 :       setAtomsDerivatives(val, a0, deriv[a0]);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         56 :       setAtomsDerivatives(val, a0+1, deriv[a0+1]);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         56 :       setAtomsDerivatives(val, a0+2, deriv[a0+2]);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         56 :       setAtomsDerivatives(val, a0+3, deriv[a0+3]);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         56 :       setAtomsDerivatives(val, a0+4, deriv[a0+4]);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         56 :       setAtomsDerivatives(val, a0+5, deriv[a0+5]);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         56 :       Tensor virial;</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         56 :       virial-=Tensor(getPosition(a0), deriv[a0]);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         56 :       virial-=Tensor(getPosition(a0+1), deriv[a0+1]);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         56 :       virial-=Tensor(getPosition(a0+2), deriv[a0+2]);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         56 :       virial-=Tensor(getPosition(a0+3), deriv[a0+3]);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         56 :       virial-=Tensor(getPosition(a0+4), deriv[a0+4]);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         56 :       virial-=Tensor(getPosition(a0+5), deriv[a0+5]);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         56 :       setBoxDerivatives(val, virial);</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :     }</a>
+<a name="385"><span class="lineNum">     385 </span>            :   }</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         16 : }</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         16 : void JCoupling::update() {</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   // write status file</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         16 :   if(getWstride()&gt;0&amp;&amp; (getStep()%getWstride()==0 || getCPT()) ) writeStatus();</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         16 : }</span></a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span>            : }</a>
+<a name="394"><span class="lineNum">     394 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Metainference.cpp.func-sort-c.html b/coverage/isdb/Metainference.cpp.func-sort-c.html
new file mode 100644
index 0000000000..204404af80
--- /dev/null
+++ b/coverage/isdb/Metainference.cpp.func-sort-c.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Metainference.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Metainference.cpp<span style="font-size: 80%;"> (<a href="Metainference.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">741</td>
+            <td class="headerCovTableEntry">880</td>
+            <td class="headerCovTableEntryMed">84.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Metainference.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#1669">_ZN4PLMD4isdb13Metainference18do_regression_zeroERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#337">_ZN4PLMD4isdb13MetainferenceC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#915">_ZN4PLMD4isdb13MetainferenceD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#1432">_ZN4PLMD4isdb13Metainference16getEnergyForceGJERKSt6vectorIdSaIdEES6_S6_</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#1492">_ZN4PLMD4isdb13Metainference19getEnergyForceMIGENERKSt6vectorIdSaIdEES6_S6_</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
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+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/isdb/Metainference.cpp.func.html b/coverage/isdb/Metainference.cpp.func.html
new file mode 100644
index 0000000000..105c85025d
--- /dev/null
+++ b/coverage/isdb/Metainference.cpp.func.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Metainference.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Metainference.cpp<span style="font-size: 80%;"> (<a href="Metainference.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">741</td>
+            <td class="headerCovTableEntry">880</td>
+            <td class="headerCovTableEntryMed">84.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Metainference.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFnHi">178</td>
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+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#1685">_ZN4PLMD4isdb13Metainference9calculateEv</a></td>
+              <td class="coverFnHi">178</td>
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+              <td class="coverFnHi">19</td>
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+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#915">_ZN4PLMD4isdb13MetainferenceD1Ev</a></td>
+              <td class="coverFnHi">19</td>
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+    <tr>
+              <td class="coverFn"><a href="Metainference.cpp.gcov.html#915">_ZN4PLMD4isdb13MetainferenceD2Ev</a></td>
+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Metainference.cpp.gcov.html b/coverage/isdb/Metainference.cpp.gcov.html
new file mode 100644
index 0000000000..f7d675f36a
--- /dev/null
+++ b/coverage/isdb/Metainference.cpp.gcov.html
@@ -0,0 +1,1881 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Metainference.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Metainference.cpp<span style="font-size: 80%;"> (source / <a href="Metainference.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">741</td>
+            <td class="headerCovTableEntry">880</td>
+            <td class="headerCovTableEntryMed">84.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;bias/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;chrono&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;numeric&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : #ifndef M_PI</a>
+<a name="35"><span class="lineNum">      35 </span>            : #define M_PI           3.14159265358979323846</a>
+<a name="36"><span class="lineNum">      36 </span>            : #endif</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace isdb {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC ISDB_BIAS METAINFERENCE</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Calculates the Metainference energy for a set of experimental data.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Metainference \cite Bonomi:2016ip is a Bayesian framework</a>
+<a name="46"><span class="lineNum">      46 </span>            : to model heterogeneous systems by integrating prior information with noisy, ensemble-averaged data.</a>
+<a name="47"><span class="lineNum">      47 </span>            : Metainference models a system and quantifies the level of noise in the data by considering a set of replicas of the system.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Calculated experimental data are given in input as ARG while reference experimental values</a>
+<a name="50"><span class="lineNum">      50 </span>            : can be given either from fixed components of other actions using PARARG or as numbers using</a>
+<a name="51"><span class="lineNum">      51 </span>            : PARAMETERS. The default behavior is that of averaging the data over the available replicas,</a>
+<a name="52"><span class="lineNum">      52 </span>            : if this is not wanted the keyword NOENSEMBLE prevent this averaging.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : Metadynamics Metainference \cite Bonomi:2016ge or more in general biased Metainference requires the knowledge of</a>
+<a name="55"><span class="lineNum">      55 </span>            : biasing potential in order to calculate the weighted average. In this case the value of the bias</a>
+<a name="56"><span class="lineNum">      56 </span>            : can be provided as the last argument in ARG and adding the keyword REWEIGHT. To avoid the noise</a>
+<a name="57"><span class="lineNum">      57 </span>            : resulting from the instantaneous value of the bias the weight of each replica can be averaged</a>
+<a name="58"><span class="lineNum">      58 </span>            : over a give time using the keyword AVERAGING.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The data can be averaged by using multiple replicas and weighted for a bias if present.</a>
+<a name="61"><span class="lineNum">      61 </span>            : The functional form of Metainference can be chosen among four variants selected</a>
+<a name="62"><span class="lineNum">      62 </span>            : with NOISE=GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC which correspond to modelling the noise for</a>
+<a name="63"><span class="lineNum">      63 </span>            : the arguments as a single gaussian common to all the data points, a gaussian per data</a>
+<a name="64"><span class="lineNum">      64 </span>            : point, a single long-tailed gaussian common to all the data points, a log-tailed</a>
+<a name="65"><span class="lineNum">      65 </span>            :  gaussian per data point or using two distinct noises as for the most general formulation of Metainference.</a>
+<a name="66"><span class="lineNum">      66 </span>            : In this latter case the noise of the replica-averaging is gaussian (one per data point) and the noise for</a>
+<a name="67"><span class="lineNum">      67 </span>            : the comparison with the experimental data can chosen using the keyword LIKELIHOOD</a>
+<a name="68"><span class="lineNum">      68 </span>            : between gaussian or log-normal (one per data point), furthermore the evolution of the estimated average</a>
+<a name="69"><span class="lineNum">      69 </span>            : over an infinite number of replicas is driven by DFTILDE.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : As for Metainference theory there are two sigma values: SIGMA_MEAN0 represent the</a>
+<a name="72"><span class="lineNum">      72 </span>            : error of calculating an average quantity using a finite set of replica and should</a>
+<a name="73"><span class="lineNum">      73 </span>            : be set as small as possible following the guidelines for replica-averaged simulations</a>
+<a name="74"><span class="lineNum">      74 </span>            : in the framework of the Maximum Entropy Principle. Alternatively, this can be obtained</a>
+<a name="75"><span class="lineNum">      75 </span>            : automatically using the internal sigma mean optimization as introduced in \cite Lohr:2017gc</a>
+<a name="76"><span class="lineNum">      76 </span>            : (OPTSIGMAMEAN=SEM), in this second case sigma_mean is estimated from the maximum standard error</a>
+<a name="77"><span class="lineNum">      77 </span>            : of the mean either over the simulation or over a defined time using the keyword AVERAGING.</a>
+<a name="78"><span class="lineNum">      78 </span>            : SIGMA_BIAS is an uncertainty parameter, sampled by a MC algorithm in the bounded interval</a>
+<a name="79"><span class="lineNum">      79 </span>            : defined by SIGMA_MIN and SIGMA_MAX. The initial value is set at SIGMA0. The MC move is a</a>
+<a name="80"><span class="lineNum">      80 </span>            : random displacement of maximum value equal to DSIGMA. If the number of data point is</a>
+<a name="81"><span class="lineNum">      81 </span>            : too large and the acceptance rate drops it is possible to make the MC move over mutually</a>
+<a name="82"><span class="lineNum">      82 </span>            : exclusive, random subset of size MC_CHUNKSIZE and run more than one move setting MC_STEPS</a>
+<a name="83"><span class="lineNum">      83 </span>            : in such a way that MC_CHUNKSIZE*MC_STEPS will cover all the data points.</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : Calculated and experimental data can be compared modulo a scaling factor and/or an offset</a>
+<a name="86"><span class="lineNum">      86 </span>            : using SCALEDATA and/or ADDOFFSET, the sampling is obtained by a MC algorithm either using</a>
+<a name="87"><span class="lineNum">      87 </span>            : a flat or a gaussian prior setting it with SCALE_PRIOR or OFFSET_PRIOR.</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : \par Examples</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : In the following example we calculate a set of \ref RDC, take the replica-average of</a>
+<a name="92"><span class="lineNum">      92 </span>            : them and comparing them with a set of experimental values. RDCs are compared with</a>
+<a name="93"><span class="lineNum">      93 </span>            : the experimental data but for a multiplication factor SCALE that is also sampled by</a>
+<a name="94"><span class="lineNum">      94 </span>            : MC on-the-fly</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \plumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : RDC ...</a>
+<a name="98"><span class="lineNum">      98 </span>            : LABEL=rdc</a>
+<a name="99"><span class="lineNum">      99 </span>            : SCALE=0.0001</a>
+<a name="100"><span class="lineNum">     100 </span>            : GYROM=-72.5388</a>
+<a name="101"><span class="lineNum">     101 </span>            : ATOMS1=22,23</a>
+<a name="102"><span class="lineNum">     102 </span>            : ATOMS2=25,27</a>
+<a name="103"><span class="lineNum">     103 </span>            : ATOMS3=29,31</a>
+<a name="104"><span class="lineNum">     104 </span>            : ATOMS4=33,34</a>
+<a name="105"><span class="lineNum">     105 </span>            : ... RDC</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : METAINFERENCE ...</a>
+<a name="108"><span class="lineNum">     108 </span>            : ARG=rdc.*</a>
+<a name="109"><span class="lineNum">     109 </span>            : NOISETYPE=MGAUSS</a>
+<a name="110"><span class="lineNum">     110 </span>            : PARAMETERS=1.9190,2.9190,3.9190,4.9190</a>
+<a name="111"><span class="lineNum">     111 </span>            : SCALEDATA SCALE0=1 SCALE_MIN=0.1 SCALE_MAX=3 DSCALE=0.01</a>
+<a name="112"><span class="lineNum">     112 </span>            : SIGMA0=0.01 SIGMA_MIN=0.00001 SIGMA_MAX=3 DSIGMA=0.01</a>
+<a name="113"><span class="lineNum">     113 </span>            : SIGMA_MEAN0=0.001</a>
+<a name="114"><span class="lineNum">     114 </span>            : LABEL=spe</a>
+<a name="115"><span class="lineNum">     115 </span>            : ... METAINFERENCE</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : PRINT ARG=spe.bias FILE=BIAS STRIDE=1</a>
+<a name="118"><span class="lineNum">     118 </span>            : \endplumedfile</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : in the following example instead of using one uncertainty parameter per data point we use</a>
+<a name="121"><span class="lineNum">     121 </span>            : a single uncertainty value in a long-tailed gaussian to take into account for outliers, furthermore</a>
+<a name="122"><span class="lineNum">     122 </span>            : the data are weighted for the bias applied to other variables of the system.</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : \plumedfile</a>
+<a name="125"><span class="lineNum">     125 </span>            : RDC ...</a>
+<a name="126"><span class="lineNum">     126 </span>            : LABEL=rdc</a>
+<a name="127"><span class="lineNum">     127 </span>            : SCALE=0.0001</a>
+<a name="128"><span class="lineNum">     128 </span>            : GYROM=-72.5388</a>
+<a name="129"><span class="lineNum">     129 </span>            : ATOMS1=22,23</a>
+<a name="130"><span class="lineNum">     130 </span>            : ATOMS2=25,27</a>
+<a name="131"><span class="lineNum">     131 </span>            : ATOMS3=29,31</a>
+<a name="132"><span class="lineNum">     132 </span>            : ATOMS4=33,34</a>
+<a name="133"><span class="lineNum">     133 </span>            : ... RDC</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : cv1: TORSION ATOMS=1,2,3,4</a>
+<a name="136"><span class="lineNum">     136 </span>            : cv2: TORSION ATOMS=2,3,4,5</a>
+<a name="137"><span class="lineNum">     137 </span>            : mm: METAD ARG=cv1,cv2 HEIGHT=0.5 SIGMA=0.3,0.3 PACE=200 BIASFACTOR=8 WALKERS_MPI</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : METAINFERENCE ...</a>
+<a name="140"><span class="lineNum">     140 </span>            : #SETTINGS NREPLICAS=2</a>
+<a name="141"><span class="lineNum">     141 </span>            : ARG=rdc.*,mm.bias</a>
+<a name="142"><span class="lineNum">     142 </span>            : REWEIGHT</a>
+<a name="143"><span class="lineNum">     143 </span>            : NOISETYPE=OUTLIERS</a>
+<a name="144"><span class="lineNum">     144 </span>            : PARAMETERS=1.9190,2.9190,3.9190,4.9190</a>
+<a name="145"><span class="lineNum">     145 </span>            : SCALEDATA SCALE0=1 SCALE_MIN=0.1 SCALE_MAX=3 DSCALE=0.01</a>
+<a name="146"><span class="lineNum">     146 </span>            : SIGMA0=0.01 SIGMA_MIN=0.00001 SIGMA_MAX=3 DSIGMA=0.01</a>
+<a name="147"><span class="lineNum">     147 </span>            : SIGMA_MEAN0=0.001</a>
+<a name="148"><span class="lineNum">     148 </span>            : LABEL=spe</a>
+<a name="149"><span class="lineNum">     149 </span>            : ... METAINFERENCE</a>
+<a name="150"><span class="lineNum">     150 </span>            : \endplumedfile</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : (See also \ref RDC, \ref PBMETAD).</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : */</a>
+<a name="155"><span class="lineNum">     155 </span>            : //+ENDPLUMEDOC</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : class Metainference : public bias::Bias</a>
+<a name="158"><span class="lineNum">     158 </span>            : {</a>
+<a name="159"><span class="lineNum">     159 </span>            :   // experimental values</a>
+<a name="160"><span class="lineNum">     160 </span>            :   std::vector&lt;double&gt; parameters;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   // noise type</a>
+<a name="162"><span class="lineNum">     162 </span>            :   unsigned noise_type_;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   enum { GAUSS, MGAUSS, OUTLIERS, MOUTLIERS, GENERIC };</a>
+<a name="164"><span class="lineNum">     164 </span>            :   unsigned gen_likelihood_;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   enum { LIKE_GAUSS, LIKE_LOGN };</a>
+<a name="166"><span class="lineNum">     166 </span>            :   // scale is data scaling factor</a>
+<a name="167"><span class="lineNum">     167 </span>            :   // noise type</a>
+<a name="168"><span class="lineNum">     168 </span>            :   unsigned scale_prior_;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   enum { SC_GAUSS, SC_FLAT };</a>
+<a name="170"><span class="lineNum">     170 </span>            :   bool   doscale_;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   double scale_;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   double scale_mu_;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   double scale_min_;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   double scale_max_;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   double Dscale_;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   // scale is data scaling factor</a>
+<a name="177"><span class="lineNum">     177 </span>            :   // noise type</a>
+<a name="178"><span class="lineNum">     178 </span>            :   unsigned offset_prior_;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   bool   dooffset_;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   double offset_;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   double offset_mu_;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double offset_min_;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   double offset_max_;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   double Doffset_;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   // scale and offset regression</a>
+<a name="186"><span class="lineNum">     186 </span>            :   bool doregres_zero_;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   int  nregres_zero_;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   // sigma is data uncertainty</a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   std::vector&lt;double&gt; sigma_min_;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   std::vector&lt;double&gt; sigma_max_;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   std::vector&lt;double&gt; Dsigma_;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // sigma_mean is uncertainty in the mean estimate</a>
+<a name="194"><span class="lineNum">     194 </span>            :   std::vector&lt;double&gt; sigma_mean2_;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   // this is the estimator of the mean value per replica for generic metainference</a>
+<a name="196"><span class="lineNum">     196 </span>            :   std::vector&lt;double&gt; ftilde_;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   double Dftilde_;</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // temperature in kbt</a>
+<a name="200"><span class="lineNum">     200 </span>            :   double   kbt_;</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   // Monte Carlo stuff</a>
+<a name="203"><span class="lineNum">     203 </span>            :   std::vector&lt;Random&gt; random;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   unsigned MCsteps_;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   long long unsigned MCaccept_;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   long long unsigned MCacceptScale_;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   long long unsigned MCacceptFT_;</a>
+<a name="208"><span class="lineNum">     208 </span>            :   long long unsigned MCtrial_;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   unsigned MCchunksize_;</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   // output</a>
+<a name="212"><span class="lineNum">     212 </span>            :   Value*   valueScale;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   Value*   valueOffset;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   Value*   valueAccept;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   Value*   valueAcceptScale;</a>
+<a name="216"><span class="lineNum">     216 </span>            :   Value*   valueAcceptFT;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   std::vector&lt;Value*&gt; valueSigma;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   std::vector&lt;Value*&gt; valueSigmaMean;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   std::vector&lt;Value*&gt; valueFtilde;</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   // restart</a>
+<a name="222"><span class="lineNum">     222 </span>            :   unsigned write_stride_;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   OFile    sfile_;</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   // others</a>
+<a name="226"><span class="lineNum">     226 </span>            :   bool         firstTime;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   std::vector&lt;bool&gt; firstTimeW;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   bool     master;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   bool     do_reweight_;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   unsigned do_optsigmamean_;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   unsigned nrep_;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   unsigned replica_;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   unsigned narg;</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   // selector</a>
+<a name="236"><span class="lineNum">     236 </span>            :   std::string selector_;</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            :   // optimize sigma mean</a>
+<a name="239"><span class="lineNum">     239 </span>            :   std::vector&lt; std::vector &lt; std::vector &lt;double&gt; &gt; &gt; sigma_mean2_last_;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   unsigned optsigmamean_stride_;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   // optimize sigma max</a>
+<a name="242"><span class="lineNum">     242 </span>            :   unsigned N_optimized_step_;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   unsigned optimized_step_;</a>
+<a name="244"><span class="lineNum">     244 </span>            :   bool sigmamax_opt_done_;</a>
+<a name="245"><span class="lineNum">     245 </span>            :   std::vector&lt;double&gt; sigma_max_est_;</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :   // average weights</a>
+<a name="248"><span class="lineNum">     248 </span>            :   unsigned                   average_weights_stride_;</a>
+<a name="249"><span class="lineNum">     249 </span>            :   std::vector&lt; std::vector &lt;double&gt; &gt;  average_weights_;</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :   double getEnergyMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;ftilde, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="252"><span class="lineNum">     252 </span>            :                         const double scale, const double offset);</a>
+<a name="253"><span class="lineNum">     253 </span>            :   double getEnergySP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="254"><span class="lineNum">     254 </span>            :                      const double scale, const double offset);</a>
+<a name="255"><span class="lineNum">     255 </span>            :   double getEnergySPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="256"><span class="lineNum">     256 </span>            :                       const double scale, const double offset);</a>
+<a name="257"><span class="lineNum">     257 </span>            :   double getEnergyGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="258"><span class="lineNum">     258 </span>            :                      const double scale, const double offset);</a>
+<a name="259"><span class="lineNum">     259 </span>            :   double getEnergyGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="260"><span class="lineNum">     260 </span>            :                       const double scale, const double offset);</a>
+<a name="261"><span class="lineNum">     261 </span>            :   void moveTilde(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy);</a>
+<a name="262"><span class="lineNum">     262 </span>            :   void moveScaleOffset(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy);</a>
+<a name="263"><span class="lineNum">     263 </span>            :   void moveSigmas(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy, const unsigned i, const std::vector&lt;unsigned&gt; &amp;indices, bool &amp;breaknow);</a>
+<a name="264"><span class="lineNum">     264 </span>            :   double doMonteCarlo(const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="265"><span class="lineNum">     265 </span>            :   void getEnergyForceMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="266"><span class="lineNum">     266 </span>            :   void getEnergyForceSP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="267"><span class="lineNum">     267 </span>            :   void getEnergyForceSPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="268"><span class="lineNum">     268 </span>            :   void getEnergyForceGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="269"><span class="lineNum">     269 </span>            :   void getEnergyForceGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="270"><span class="lineNum">     270 </span>            :   void get_weights(const unsigned iselect, double &amp;weight, double &amp;norm, double &amp;neff);</a>
+<a name="271"><span class="lineNum">     271 </span>            :   void replica_averaging(const double weight, const double norm, std::vector&lt;double&gt; &amp;mean, std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="272"><span class="lineNum">     272 </span>            :   void get_sigma_mean(const unsigned iselect, const double weight, const double norm, const double neff, const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="273"><span class="lineNum">     273 </span>            :   void writeStatus();</a>
+<a name="274"><span class="lineNum">     274 </span>            :   void do_regression_zero(const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : public:</a>
+<a name="277"><span class="lineNum">     277 </span>            :   explicit Metainference(const ActionOptions&amp;);</a>
+<a name="278"><span class="lineNum">     278 </span>            :   ~Metainference();</a>
+<a name="279"><span class="lineNum">     279 </span>            :   void calculate() override;</a>
+<a name="280"><span class="lineNum">     280 </span>            :   void update() override;</a>
+<a name="281"><span class="lineNum">     281 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="282"><span class="lineNum">     282 </span>            : };</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">      12542 : PLUMED_REGISTER_ACTION(Metainference,&quot;METAINFERENCE&quot;)</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         21 : void Metainference::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         21 :   Bias::registerKeywords(keys);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         21 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;PARARG&quot;,&quot;reference values for the experimental data, these can be provided as arguments without derivatives&quot;);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;PARAMETERS&quot;,&quot;reference values for the experimental data&quot;);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         42 :   keys.addFlag(&quot;NOENSEMBLE&quot;,false,&quot;don't perform any replica-averaging&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         42 :   keys.addFlag(&quot;REWEIGHT&quot;,false,&quot;simple REWEIGHT using the latest ARG as energy&quot;);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;AVERAGING&quot;, &quot;Stride for calculation of averaged weights and sigma_mean&quot;);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;NOISETYPE&quot;,&quot;MGAUSS&quot;,&quot;functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)&quot;);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;LIKELIHOOD&quot;,&quot;GAUSS&quot;,&quot;the likelihood for the GENERIC metainference model, GAUSS or LOGN&quot;);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;DFTILDE&quot;,&quot;0.1&quot;,&quot;fraction of sigma_mean used to evolve ftilde&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         42 :   keys.addFlag(&quot;SCALEDATA&quot;,false,&quot;Set to TRUE if you want to sample a scaling factor common to all values and replicas&quot;);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;SCALE0&quot;,&quot;1.0&quot;,&quot;initial value of the scaling factor&quot;);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;SCALE_PRIOR&quot;,&quot;FLAT&quot;,&quot;either FLAT or GAUSSIAN&quot;);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;SCALE_MIN&quot;,&quot;minimum value of the scaling factor&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;SCALE_MAX&quot;,&quot;maximum value of the scaling factor&quot;);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;DSCALE&quot;,&quot;maximum MC move of the scaling factor&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         42 :   keys.addFlag(&quot;ADDOFFSET&quot;,false,&quot;Set to TRUE if you want to sample an offset common to all values and replicas&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET0&quot;,&quot;0.0&quot;,&quot;initial value of the offset&quot;);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET_PRIOR&quot;,&quot;FLAT&quot;,&quot;either FLAT or GAUSSIAN&quot;);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;OFFSET_MIN&quot;,&quot;minimum value of the offset&quot;);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;OFFSET_MAX&quot;,&quot;maximum value of the offset&quot;);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;DOFFSET&quot;,&quot;maximum MC move of the offset&quot;);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;REGRES_ZERO&quot;,&quot;stride for regression with zero offset&quot;);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA0&quot;,&quot;1.0&quot;,&quot;initial value of the uncertainty parameter&quot;);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA_MIN&quot;,&quot;0.0&quot;,&quot;minimum value of the uncertainty parameter&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA_MAX&quot;,&quot;10.&quot;,&quot;maximum value of the uncertainty parameter&quot;);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;DSIGMA&quot;,&quot;maximum MC move of the uncertainty parameter&quot;);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;OPTSIGMAMEAN&quot;,&quot;NONE&quot;,&quot;Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly&quot;);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MEAN0&quot;,&quot;starting value for the uncertainty in the mean estimate&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MAX_STEPS&quot;, &quot;Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used&quot;);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - this is only needed if code doesn't pass the temperature to plumed&quot;);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;MC_STEPS&quot;,&quot;number of MC steps&quot;);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;MC_CHUNKSIZE&quot;,&quot;MC chunksize&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;STATUS_FILE&quot;,&quot;write a file with all the data useful for restart/continuation of Metainference&quot;);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         42 :   keys.add(&quot;compulsory&quot;,&quot;WRITE_STRIDE&quot;,&quot;10000&quot;,&quot;write the status to a file every N steps, this can be used for restart/continuation&quot;);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;SELECTOR&quot;,&quot;name of selector&quot;);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         42 :   keys.add(&quot;optional&quot;,&quot;NSELECT&quot;,&quot;range of values for selector [0, N-1]&quot;);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         21 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;sigma&quot;,        &quot;default&quot;,      &quot;uncertainty parameter&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;sigmaMean&quot;,    &quot;default&quot;,      &quot;uncertainty in the mean estimate&quot;);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;neff&quot;,         &quot;default&quot;,      &quot;effective number of replicas&quot;);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;acceptSigma&quot;,  &quot;default&quot;,      &quot;MC acceptance for sigma values&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;acceptScale&quot;,  &quot;SCALEDATA&quot;,    &quot;MC acceptance for scale value&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;acceptFT&quot;,     &quot;GENERIC&quot;,      &quot;MC acceptance for general metainference f tilde value&quot;);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;weight&quot;,       &quot;REWEIGHT&quot;,     &quot;weights of the weighted average&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;biasDer&quot;,      &quot;REWEIGHT&quot;,     &quot;derivatives with respect to the bias&quot;);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;scale&quot;,        &quot;SCALEDATA&quot;,    &quot;scale parameter&quot;);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;offset&quot;,       &quot;ADDOFFSET&quot;,    &quot;offset parameter&quot;);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         42 :   keys.addOutputComponent(&quot;ftilde&quot;,       &quot;GENERIC&quot;,      &quot;ensemble average estimator&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         21 : }</span></a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         19 : Metainference::Metainference(const ActionOptions&amp;ao):</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         19 :   doscale_(false),</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         19 :   scale_(1.),</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         19 :   scale_mu_(0),</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         19 :   scale_min_(1),</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         19 :   scale_max_(-1),</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         19 :   Dscale_(-1),</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         19 :   dooffset_(false),</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         19 :   offset_(0.),</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         19 :   offset_mu_(0),</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         19 :   offset_min_(1),</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         19 :   offset_max_(-1),</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         19 :   Doffset_(-1),</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         19 :   doregres_zero_(false),</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         19 :   nregres_zero_(0),</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         19 :   Dftilde_(0.1),</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         19 :   random(3),</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         19 :   MCsteps_(1),</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         19 :   MCaccept_(0),</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         19 :   MCacceptScale_(0),</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         19 :   MCacceptFT_(0),</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         19 :   MCtrial_(0),</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         19 :   MCchunksize_(0),</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         19 :   write_stride_(0),</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         19 :   firstTime(true),</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         19 :   do_reweight_(false),</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         19 :   do_optsigmamean_(0),</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         19 :   optsigmamean_stride_(0),</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         19 :   N_optimized_step_(0),</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         19 :   optimized_step_(0),</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         19 :   sigmamax_opt_done_(false),</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         19 :   average_weights_stride_(1)</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : {</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         19 :   bool noensemble = false;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         19 :   parseFlag(&quot;NOENSEMBLE&quot;, noensemble);</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            :   // set up replica stuff</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         19 :   master = (comm.Get_rank()==0);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         19 :   if(master) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         11 :     nrep_    = multi_sim_comm.Get_size();</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         11 :     replica_ = multi_sim_comm.Get_rank();</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         11 :     if(noensemble) nrep_ = 1;</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   } else {</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          8 :     nrep_    = 0;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          8 :     replica_ = 0;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :   }</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         19 :   comm.Sum(&amp;nrep_,1);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         19 :   comm.Sum(&amp;replica_,1);</span></a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         19 :   unsigned nsel = 1;</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         19 :   parse(&quot;SELECTOR&quot;, selector_);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         38 :   parse(&quot;NSELECT&quot;, nsel);</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   // do checks</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         19 :   if(selector_.length()&gt;0 &amp;&amp; nsel&lt;=1) error(&quot;With SELECTOR active, NSELECT must be greater than 1&quot;);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         19 :   if(selector_.length()==0 &amp;&amp; nsel&gt;1) error(&quot;With NSELECT greater than 1, you must specify SELECTOR&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   // initialise firstTimeW</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         19 :   firstTimeW.resize(nsel, true);</span></a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            :   // reweight implies a different number of arguments (the latest one must always be the bias)</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         19 :   parseFlag(&quot;REWEIGHT&quot;, do_reweight_);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         19 :   if(do_reweight_&amp;&amp;nrep_&lt;2) error(&quot;REWEIGHT can only be used in parallel with 2 or more replicas&quot;);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         34 :   if(!getRestart()) average_weights_.resize(nsel, std::vector&lt;double&gt; (nrep_, 1./static_cast&lt;double&gt;(nrep_)));</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          8 :   else average_weights_.resize(nsel, std::vector&lt;double&gt; (nrep_, 0.));</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         19 :   narg = getNumberOfArguments();</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         19 :   if(do_reweight_) narg--;</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         19 :   unsigned averaging=0;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         19 :   parse(&quot;AVERAGING&quot;, averaging);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         19 :   if(averaging&gt;0) {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :     average_weights_stride_ = averaging;</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :     optsigmamean_stride_    = averaging;</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :   }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         38 :   parseVector(&quot;PARAMETERS&quot;,parameters);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">         19 :   if(parameters.size()!=static_cast&lt;unsigned&gt;(narg)&amp;&amp;!parameters.empty())</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :     error(&quot;Size of PARAMETERS array should be either 0 or the same as of the number of arguments in ARG1&quot;);</span></a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            :   std::vector&lt;Value*&gt; arg2;</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         38 :   parseArgumentList(&quot;PARARG&quot;,arg2);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         19 :   if(!arg2.empty()) {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">          4 :     if(parameters.size()&gt;0) error(&quot;It is not possible to use PARARG and PARAMETERS together&quot;);</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          4 :     if(arg2.size()!=narg) error(&quot;Size of PARARG array should be the same as number for arguments in ARG&quot;);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">       2360 :     for(unsigned i=0; i&lt;arg2.size(); i++) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">       2356 :       parameters.push_back(arg2[i]-&gt;get());</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">       2356 :       if(arg2[i]-&gt;hasDerivatives()==true) error(&quot;PARARG can only accept arguments without derivatives&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     }</a>
+<a name="427"><span class="lineNum">     427 </span>            :   }</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         19 :   if(parameters.size()!=narg)</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :     error(&quot;PARARG or PARAMETERS arrays should include the same number of elements as the arguments in ARG&quot;);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :   std::string stringa_noise;</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         38 :   parse(&quot;NOISETYPE&quot;,stringa_noise);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         19 :   if(stringa_noise==&quot;GAUSS&quot;)           noise_type_ = GAUSS;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         18 :   else if(stringa_noise==&quot;MGAUSS&quot;)     noise_type_ = MGAUSS;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         10 :   else if(stringa_noise==&quot;OUTLIERS&quot;)   noise_type_ = OUTLIERS;</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          5 :   else if(stringa_noise==&quot;MOUTLIERS&quot;)  noise_type_ = MOUTLIERS;</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          1 :   else if(stringa_noise==&quot;GENERIC&quot;)    noise_type_ = GENERIC;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :   else error(&quot;Unknown noise type!&quot;);</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         19 :   if(noise_type_== GENERIC) {</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :     std::string stringa_like;</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          2 :     parse(&quot;LIKELIHOOD&quot;,stringa_like);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          1 :     if(stringa_like==&quot;GAUSS&quot;) gen_likelihood_ = LIKE_GAUSS;</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :     else if(stringa_like==&quot;LOGN&quot;) gen_likelihood_ = LIKE_LOGN;</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     else error(&quot;Unknown likelihood type!&quot;);</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          2 :     parse(&quot;DFTILDE&quot;,Dftilde_);</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   }</a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         38 :   parse(&quot;WRITE_STRIDE&quot;,write_stride_);</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :   std::string status_file_name_;</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         38 :   parse(&quot;STATUS_FILE&quot;,status_file_name_);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">         38 :   if(status_file_name_==&quot;&quot;) status_file_name_ = &quot;MISTATUS&quot;+getLabel();</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :   else                      status_file_name_ = status_file_name_+getLabel();</span></a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   std::string stringa_optsigma;</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         38 :   parse(&quot;OPTSIGMAMEAN&quot;, stringa_optsigma);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         19 :   if(stringa_optsigma==&quot;NONE&quot;)      do_optsigmamean_=0;</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :   else if(stringa_optsigma==&quot;SEM&quot;)  do_optsigmamean_=1;</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :   else if(stringa_optsigma==&quot;SEM_MAX&quot;)  do_optsigmamean_=2;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         19 :   unsigned aver_max_steps=0;</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         19 :   parse(&quot;SIGMA_MAX_STEPS&quot;, aver_max_steps);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         19 :   if(aver_max_steps==0&amp;&amp;do_optsigmamean_==2) aver_max_steps=averaging*2000;</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         19 :   if(aver_max_steps&gt;0&amp;&amp;do_optsigmamean_&lt;2) error(&quot;SIGMA_MAX_STEPS can only be used together with OPTSIGMAMEAN=SEM_MAX&quot;);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         19 :   if(aver_max_steps&gt;0&amp;&amp;do_optsigmamean_==2) N_optimized_step_=aver_max_steps;</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         19 :   if(aver_max_steps&gt;0&amp;&amp;aver_max_steps&lt;averaging) error(&quot;SIGMA_MAX_STEPS must be greater than AVERAGING&quot;);</span></a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            :   // resize std::vector for sigma_mean history</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         19 :   sigma_mean2_last_.resize(nsel);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         38 :   for(unsigned i=0; i&lt;nsel; i++) sigma_mean2_last_[i].resize(narg);</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span>            :   std::vector&lt;double&gt; read_sigma_mean_;</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         19 :   parseVector(&quot;SIGMA_MEAN0&quot;,read_sigma_mean_);</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         19 :   if(do_optsigmamean_==0 &amp;&amp; read_sigma_mean_.size()==0 &amp;&amp; !getRestart())</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :     error(&quot;If you don't use OPTSIGMAMEAN and you are not RESTARTING then you MUST SET SIGMA_MEAN0&quot;);</span></a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         19 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         13 :     if(read_sigma_mean_.size()==narg) {</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :       sigma_mean2_.resize(narg);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; i++) sigma_mean2_[i]=read_sigma_mean_[i]*read_sigma_mean_[i];</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         13 :     } else if(read_sigma_mean_.size()==1) {</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         13 :       sigma_mean2_.resize(narg,read_sigma_mean_[0]*read_sigma_mean_[0]);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :     } else if(read_sigma_mean_.size()==0) {</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :       sigma_mean2_.resize(narg,0.000001);</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     } else {</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA_MEAN0 can accept either one single value or as many values as the arguments (with NOISETYPE=MGAUSS|MOUTLIERS)&quot;);</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :     }</a>
+<a name="490"><span class="lineNum">     490 </span>            :     // set the initial value for the history</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">       2416 :     for(unsigned i=0; i&lt;nsel; i++) for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[i][j].push_back(sigma_mean2_[j]);</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :   } else {</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          6 :     if(read_sigma_mean_.size()==1) {</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          6 :       sigma_mean2_.resize(1, read_sigma_mean_[0]*read_sigma_mean_[0]);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineNoCov">          0 :     } else if(read_sigma_mean_.size()==0) {</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :       sigma_mean2_.resize(1, 0.000001);</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :     } else {</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :       error(&quot;If you want to use more than one SIGMA_MEAN0 you should use NOISETYPE=MGAUSS|MOUTLIERS&quot;);</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :     }</a>
+<a name="500"><span class="lineNum">     500 </span>            :     // set the initial value for the history</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         37 :     for(unsigned i=0; i&lt;nsel; i++) for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[i][j].push_back(sigma_mean2_[0]);</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :   }</a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         19 :   parseFlag(&quot;SCALEDATA&quot;, doscale_);</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         19 :   if(doscale_) {</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     std::string stringa_noise;</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         24 :     parse(&quot;SCALE_PRIOR&quot;,stringa_noise);</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         12 :     if(stringa_noise==&quot;GAUSSIAN&quot;)  scale_prior_ = SC_GAUSS;</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         12 :     else if(stringa_noise==&quot;FLAT&quot;) scale_prior_ = SC_FLAT;</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :     else error(&quot;Unknown SCALE_PRIOR type!&quot;);</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         12 :     parse(&quot;SCALE0&quot;,scale_);</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         12 :     parse(&quot;DSCALE&quot;,Dscale_);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         12 :     if(Dscale_&lt;0.) error(&quot;DSCALE must be set when using SCALEDATA&quot;);</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         12 :     if(scale_prior_==SC_GAUSS) {</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :       scale_mu_=scale_;</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :     } else {</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         12 :       parse(&quot;SCALE_MIN&quot;,scale_min_);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         12 :       parse(&quot;SCALE_MAX&quot;,scale_max_);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         12 :       if(scale_max_&lt;scale_min_) error(&quot;SCALE_MAX and SCALE_MIN must be set when using SCALE_PRIOR=FLAT&quot;);</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :     }</a>
+<a name="521"><span class="lineNum">     521 </span>            :   }</a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         19 :   parseFlag(&quot;ADDOFFSET&quot;, dooffset_);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         19 :   if(dooffset_) {</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :     std::string stringa_noise;</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">          4 :     parse(&quot;OFFSET_PRIOR&quot;,stringa_noise);</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">          2 :     if(stringa_noise==&quot;GAUSSIAN&quot;)  offset_prior_ = SC_GAUSS;</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">          2 :     else if(stringa_noise==&quot;FLAT&quot;) offset_prior_ = SC_FLAT;</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :     else error(&quot;Unknown OFFSET_PRIOR type!&quot;);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          2 :     parse(&quot;OFFSET0&quot;,offset_);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">          2 :     parse(&quot;DOFFSET&quot;,Doffset_);</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">          2 :     if(offset_prior_==SC_GAUSS) {</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :       offset_mu_=offset_;</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :       if(Doffset_&lt;0.) error(&quot;DOFFSET must be set when using OFFSET_PRIOR=GAUSS&quot;);</span></a>
+<a name="535"><span class="lineNum">     535 </span>            :     } else {</a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          2 :       parse(&quot;OFFSET_MIN&quot;,offset_min_);</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          2 :       parse(&quot;OFFSET_MAX&quot;,offset_max_);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          2 :       if(Doffset_&lt;0) Doffset_ = 0.05*(offset_max_ - offset_min_);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">          2 :       if(offset_max_&lt;offset_min_) error(&quot;OFFSET_MAX and OFFSET_MIN must be set when using OFFSET_PRIOR=FLAT&quot;);</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :     }</a>
+<a name="541"><span class="lineNum">     541 </span>            :   }</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            :   // regression with zero intercept</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         19 :   parse(&quot;REGRES_ZERO&quot;, nregres_zero_);</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         19 :   if(nregres_zero_&gt;0) {</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :     // set flag</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 :     doregres_zero_=true;</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :     // check if already sampling scale and offset</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :     if(doscale_)  error(&quot;REGRES_ZERO and SCALEDATA are mutually exclusive&quot;);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :     if(dooffset_) error(&quot;REGRES_ZERO and ADDOFFSET are mutually exclusive&quot;);</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :   }</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span>            :   std::vector&lt;double&gt; readsigma;</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         19 :   parseVector(&quot;SIGMA0&quot;,readsigma);</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         19 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma.size()&gt;1)</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         19 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         13 :     sigma_.resize(readsigma.size());</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         13 :     sigma_=readsigma;</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">          6 :   } else sigma_.resize(1, readsigma[0]);</span></a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span>            :   std::vector&lt;double&gt; readsigma_min;</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         19 :   parseVector(&quot;SIGMA_MIN&quot;,readsigma_min);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         19 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma_min.size()&gt;1)</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         19 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         13 :     sigma_min_.resize(readsigma_min.size());</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         13 :     sigma_min_=readsigma_min;</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          6 :   } else sigma_min_.resize(1, readsigma_min[0]);</span></a>
+<a name="570"><span class="lineNum">     570 </span>            : </a>
+<a name="571"><span class="lineNum">     571 </span>            :   std::vector&lt;double&gt; readsigma_max;</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         19 :   parseVector(&quot;SIGMA_MAX&quot;,readsigma_max);</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         19 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma_max.size()&gt;1)</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         19 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         13 :     sigma_max_.resize(readsigma_max.size());</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         13 :     sigma_max_=readsigma_max;</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">          6 :   } else sigma_max_.resize(1, readsigma_max[0]);</span></a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         19 :   if(sigma_max_.size()!=sigma_min_.size()) error(&quot;The number of values for SIGMA_MIN and SIGMA_MAX must be the same&quot;);</span></a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span>            :   std::vector&lt;double&gt; read_dsigma;</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         19 :   parseVector(&quot;DSIGMA&quot;,read_dsigma);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         19 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma_max.size()&gt;1)</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         19 :   if(read_dsigma.size()&gt;0) {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         19 :     Dsigma_.resize(read_dsigma.size());</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         19 :     Dsigma_=read_dsigma;</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :   } else {</a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :     Dsigma_.resize(sigma_max_.size(), -1.);</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :     /* in this case Dsigma is initialised after reading the restart file if present */</a>
+<a name="592"><span class="lineNum">     592 </span>            :   }</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span>            :   // monte carlo stuff</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         19 :   parse(&quot;MC_STEPS&quot;,MCsteps_);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         19 :   parse(&quot;MC_CHUNKSIZE&quot;, MCchunksize_);</span></a>
+<a name="597"><span class="lineNum">     597 </span>            :   // get temperature</a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         19 :   double temp=0.0;</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         19 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         19 :   if(temp&gt;0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :   else kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         19 :   if(kbt_==0.0) error(&quot;Unless the MD engine passes the temperature to plumed, you must specify it using TEMP&quot;);</span></a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         19 :   checkRead();</span></a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            :   // set sigma_bias</a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         19 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">         13 :     if(sigma_.size()==1) {</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         13 :       double tmp = sigma_[0];</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         13 :       sigma_.resize(narg, tmp);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :     } else if(sigma_.size()&gt;1&amp;&amp;sigma_.size()!=narg) {</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA0 can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :     }</a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         13 :     if(sigma_min_.size()==1) {</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         13 :       double tmp = sigma_min_[0];</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         13 :       sigma_min_.resize(narg, tmp);</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :     } else if(sigma_min_.size()&gt;1&amp;&amp;sigma_min_.size()!=narg) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA_MIN can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="619"><span class="lineNum">     619 </span>            :     }</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         13 :     if(sigma_max_.size()==1) {</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">         13 :       double tmp = sigma_max_[0];</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         13 :       sigma_max_.resize(narg, tmp);</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineNoCov">          0 :     } else if(sigma_max_.size()&gt;1&amp;&amp;sigma_max_.size()!=narg) {</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA_MAX can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="625"><span class="lineNum">     625 </span>            :     }</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         13 :     if(Dsigma_.size()==1) {</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         13 :       double tmp = Dsigma_[0];</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         13 :       Dsigma_.resize(narg, tmp);</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :     } else if(Dsigma_.size()&gt;1&amp;&amp;Dsigma_.size()!=narg) {</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :       error(&quot;DSIGMA can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="631"><span class="lineNum">     631 </span>            :     }</a>
+<a name="632"><span class="lineNum">     632 </span>            :   }</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">         19 :   sigma_max_est_.resize(sigma_max_.size(), 0.);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         19 :   IFile restart_sfile;</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">         19 :   restart_sfile.link(*this);</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">         19 :   if(getRestart()&amp;&amp;restart_sfile.FileExist(status_file_name_)) {</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">          4 :     firstTime = false;</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">          8 :     for(unsigned i=0; i&lt;nsel; i++) firstTimeW[i] = false;</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">          4 :     restart_sfile.open(status_file_name_);</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">          4 :     log.printf(&quot;  Restarting from %s\n&quot;, status_file_name_.c_str());</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :     double dummy;</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">          8 :     if(restart_sfile.scanField(&quot;time&quot;,dummy)) {</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :       // check for syncronisation</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">          4 :       std::vector&lt;double&gt; dummy_time(nrep_,0);</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          4 :       if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">          2 :         dummy_time[replica_] = dummy;</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          2 :         multi_sim_comm.Sum(dummy_time);</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :       }</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          4 :       comm.Sum(dummy_time);</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">          8 :       for(unsigned i=1; i&lt;nrep_; i++) {</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">          4 :         std::string msg = &quot;METAINFERENCE restart files &quot; + status_file_name_ + &quot;  are not in sync&quot;;</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">          4 :         if(dummy_time[i]!=dummy_time[0]) plumed_merror(msg);</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :       }</a>
+<a name="656"><span class="lineNum">     656 </span>            :       // nsel</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">          8 :       for(unsigned i=0; i&lt;sigma_mean2_last_.size(); i++) {</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :         std::string msg_i;</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">          4 :         Tools::convert(i,msg_i);</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :         // narg</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">          4 :         if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         20 :           for(unsigned j=0; j&lt;narg; ++j) {</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :             std::string msg_j;</a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         16 :             Tools::convert(j,msg_j);</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">         16 :             std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="666"><span class="lineNum">     666 </span>            :             double read_sm;</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         16 :             restart_sfile.scanField(&quot;sigmaMean_&quot;+msg,read_sm);</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">         16 :             sigma_mean2_last_[i][j][0] = read_sm*read_sm;</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :           }</a>
+<a name="670"><span class="lineNum">     670 </span>            :         }</a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">          4 :         if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :           double read_sm;</a>
+<a name="673"><span class="lineNum">     673 </span>            :           std::string msg_j;</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :           Tools::convert(0,msg_j);</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :           std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :           restart_sfile.scanField(&quot;sigmaMean_&quot;+msg,read_sm);</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :           for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[i][j][0] = read_sm*read_sm;</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :         }</a>
+<a name="679"><span class="lineNum">     679 </span>            :       }</a>
+<a name="680"><span class="lineNum">     680 </span>            : </a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         20 :       for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="682"><span class="lineNum">     682 </span>            :         std::string msg;</a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">         16 :         Tools::convert(i,msg);</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         32 :         restart_sfile.scanField(&quot;sigma_&quot;+msg,sigma_[i]);</span></a>
+<a name="685"><span class="lineNum">     685 </span>            :       }</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         20 :       for(unsigned i=0; i&lt;sigma_max_.size(); ++i) {</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :         std::string msg;</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         16 :         Tools::convert(i,msg);</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">         16 :         restart_sfile.scanField(&quot;sigma_max_&quot;+msg,sigma_max_[i]);</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         16 :         sigmamax_opt_done_=true;</span></a>
+<a name="691"><span class="lineNum">     691 </span>            :       }</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">          4 :       if(noise_type_==GENERIC) {</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;ftilde_.size(); ++i) {</span></a>
+<a name="694"><span class="lineNum">     694 </span>            :           std::string msg;</a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :           Tools::convert(i,msg);</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :           restart_sfile.scanField(&quot;ftilde_&quot;+msg,ftilde_[i]);</span></a>
+<a name="697"><span class="lineNum">     697 </span>            :         }</a>
+<a name="698"><span class="lineNum">     698 </span>            :       }</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">          4 :       restart_sfile.scanField(&quot;scale0_&quot;,scale_);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">          4 :       restart_sfile.scanField(&quot;offset0_&quot;,offset_);</span></a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">          8 :       for(unsigned i=0; i&lt;nsel; i++) {</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :         std::string msg;</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">          4 :         Tools::convert(i,msg);</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :         double tmp_w;</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">          4 :         restart_sfile.scanField(&quot;weight_&quot;+msg,tmp_w);</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">          4 :         if(master) {</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">          2 :           average_weights_[i][replica_] = tmp_w;</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">          2 :           if(nrep_&gt;1) multi_sim_comm.Sum(&amp;average_weights_[i][0], nrep_);</span></a>
+<a name="710"><span class="lineNum">     710 </span>            :         }</a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">          4 :         comm.Sum(&amp;average_weights_[i][0], nrep_);</span></a>
+<a name="712"><span class="lineNum">     712 </span>            :       }</a>
+<a name="713"><span class="lineNum">     713 </span>            : </a>
+<a name="714"><span class="lineNum">     714 </span>            :     }</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">          4 :     restart_sfile.scanField();</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">          4 :     restart_sfile.close();</span></a>
+<a name="717"><span class="lineNum">     717 </span>            :   }</a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            :   /* If DSIGMA is not yet initialised do it now */</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_max_.size(); i++) if(Dsigma_[i]==-1) Dsigma_[i] = 0.05*(sigma_max_[i] - sigma_min_[i]);</span></a>
+<a name="721"><span class="lineNum">     721 </span>            : </a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">         19 :   switch(noise_type_) {</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">          1 :   case GENERIC:</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">          1 :     log.printf(&quot;  with general metainference &quot;);</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">          1 :     if(gen_likelihood_==LIKE_GAUSS) log.printf(&quot; and a gaussian likelihood\n&quot;);</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :     else if(gen_likelihood_==LIKE_LOGN) log.printf(&quot; and a log-normal likelihood\n&quot;);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">          1 :     log.printf(&quot;  ensemble average parameter sampled with a step %lf of sigma_mean\n&quot;, Dftilde_);</span></a>
+<a name="728"><span class="lineNum">     728 </span>            :     break;</a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">          1 :   case GAUSS:</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">          1 :     log.printf(&quot;  with gaussian noise and a single noise parameter for all the data\n&quot;);</span></a>
+<a name="731"><span class="lineNum">     731 </span>            :     break;</a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">          8 :   case MGAUSS:</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">          8 :     log.printf(&quot;  with gaussian noise and a noise parameter for each data point\n&quot;);</span></a>
+<a name="734"><span class="lineNum">     734 </span>            :     break;</a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">          5 :   case OUTLIERS:</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">          5 :     log.printf(&quot;  with long tailed gaussian noise and a single noise parameter for all the data\n&quot;);</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :     break;</a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">          4 :   case MOUTLIERS:</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">          4 :     log.printf(&quot;  with long tailed gaussian noise and a noise parameter for each data point\n&quot;);</span></a>
+<a name="740"><span class="lineNum">     740 </span>            :     break;</a>
+<a name="741"><span class="lineNum">     741 </span>            :   }</a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">         19 :   if(doscale_) {</span></a>
+<a name="744"><span class="lineNum">     744 </span>            :     // check that the scale value is the same for all replicas</a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">         12 :     std::vector&lt;double&gt; dummy_scale(nrep_,0);</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">         12 :     if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">          6 :       dummy_scale[replica_] = scale_;</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">          6 :       multi_sim_comm.Sum(dummy_scale);</span></a>
+<a name="749"><span class="lineNum">     749 </span>            :     }</a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">         12 :     comm.Sum(dummy_scale);</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">         24 :     for(unsigned i=1; i&lt;nrep_; i++) {</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">         12 :       std::string msg = &quot;The SCALE value must be the same for all replicas: check your input or restart file&quot;;</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         12 :       if(dummy_scale[i]!=dummy_scale[0]) plumed_merror(msg);</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :     }</a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">         12 :     log.printf(&quot;  sampling a common scaling factor with:\n&quot;);</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">         12 :     log.printf(&quot;    initial scale parameter %f\n&quot;,scale_);</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">         12 :     if(scale_prior_==SC_GAUSS) {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :       log.printf(&quot;    gaussian prior with mean %f and width %f\n&quot;,scale_mu_,Dscale_);</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :     }</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">         12 :     if(scale_prior_==SC_FLAT) {</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">         12 :       log.printf(&quot;    flat prior between %f - %f\n&quot;,scale_min_,scale_max_);</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">         12 :       log.printf(&quot;    maximum MC move of scale parameter %f\n&quot;,Dscale_);</span></a>
+<a name="763"><span class="lineNum">     763 </span>            :     }</a>
+<a name="764"><span class="lineNum">     764 </span>            :   }</a>
+<a name="765"><span class="lineNum">     765 </span>            : </a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">         19 :   if(dooffset_) {</span></a>
+<a name="767"><span class="lineNum">     767 </span>            :     // check that the offset value is the same for all replicas</a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">          2 :     std::vector&lt;double&gt; dummy_offset(nrep_,0);</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">          2 :     if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineNoCov">          0 :       dummy_offset[replica_] = offset_;</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineNoCov">          0 :       multi_sim_comm.Sum(dummy_offset);</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :     }</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">          2 :     comm.Sum(dummy_offset);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">          2 :     for(unsigned i=1; i&lt;nrep_; i++) {</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineNoCov">          0 :       std::string msg = &quot;The OFFSET value must be the same for all replicas: check your input or restart file&quot;;</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineNoCov">          0 :       if(dummy_offset[i]!=dummy_offset[0]) plumed_merror(msg);</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :     }</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">          2 :     log.printf(&quot;  sampling a common offset with:\n&quot;);</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">          2 :     log.printf(&quot;    initial offset parameter %f\n&quot;,offset_);</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">          2 :     if(offset_prior_==SC_GAUSS) {</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineNoCov">          0 :       log.printf(&quot;    gaussian prior with mean %f and width %f\n&quot;,offset_mu_,Doffset_);</span></a>
+<a name="782"><span class="lineNum">     782 </span>            :     }</a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">          2 :     if(offset_prior_==SC_FLAT) {</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">          2 :       log.printf(&quot;    flat prior between %f - %f\n&quot;,offset_min_,offset_max_);</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">          2 :       log.printf(&quot;    maximum MC move of offset parameter %f\n&quot;,Doffset_);</span></a>
+<a name="786"><span class="lineNum">     786 </span>            :     }</a>
+<a name="787"><span class="lineNum">     787 </span>            :   }</a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">         19 :   if(doregres_zero_)</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineNoCov">          0 :     log.printf(&quot;  doing regression with zero intercept with stride: %d\n&quot;, nregres_zero_);</span></a>
+<a name="791"><span class="lineNum">     791 </span>            : </a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">         19 :   log.printf(&quot;  number of experimental data points %u\n&quot;,narg);</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">         19 :   log.printf(&quot;  number of replicas %u\n&quot;,nrep_);</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">         19 :   log.printf(&quot;  initial data uncertainties&quot;);</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;, sigma_[i]);</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">         19 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">         19 :   log.printf(&quot;  minimum data uncertainties&quot;);</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,sigma_min_[i]);</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">         19 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">         19 :   log.printf(&quot;  maximum data uncertainties&quot;);</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,sigma_max_[i]);</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">         19 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">         19 :   log.printf(&quot;  maximum MC move of data uncertainties&quot;);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,Dsigma_[i]);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">         19 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">         19 :   log.printf(&quot;  temperature of the system %f\n&quot;,kbt_);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">         19 :   log.printf(&quot;  MC steps %u\n&quot;,MCsteps_);</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">         19 :   log.printf(&quot;  initial standard errors of the mean&quot;);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_mean2_.size(); ++i) log.printf(&quot; %f&quot;, std::sqrt(sigma_mean2_[i]));</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">         19 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         19 :   if(do_reweight_) {</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         16 :     addComponent(&quot;biasDer&quot;);</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         16 :     componentIsNotPeriodic(&quot;biasDer&quot;);</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">         16 :     addComponent(&quot;weight&quot;);</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">         32 :     componentIsNotPeriodic(&quot;weight&quot;);</span></a>
+<a name="817"><span class="lineNum">     817 </span>            :   }</a>
+<a name="818"><span class="lineNum">     818 </span>            : </a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">         19 :   addComponent(&quot;neff&quot;);</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         19 :   componentIsNotPeriodic(&quot;neff&quot;);</span></a>
+<a name="821"><span class="lineNum">     821 </span>            : </a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">         19 :   if(doscale_ || doregres_zero_) {</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">         12 :     addComponent(&quot;scale&quot;);</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">         12 :     componentIsNotPeriodic(&quot;scale&quot;);</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">         12 :     valueScale=getPntrToComponent(&quot;scale&quot;);</span></a>
+<a name="826"><span class="lineNum">     826 </span>            :   }</a>
+<a name="827"><span class="lineNum">     827 </span>            : </a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         19 :   if(dooffset_) {</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">          2 :     addComponent(&quot;offset&quot;);</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">          2 :     componentIsNotPeriodic(&quot;offset&quot;);</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">          2 :     valueOffset=getPntrToComponent(&quot;offset&quot;);</span></a>
+<a name="832"><span class="lineNum">     832 </span>            :   }</a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">         19 :   if(dooffset_||doscale_) {</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">         14 :     addComponent(&quot;acceptScale&quot;);</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;acceptScale&quot;);</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">         14 :     valueAcceptScale=getPntrToComponent(&quot;acceptScale&quot;);</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :   }</a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">         19 :   if(noise_type_==GENERIC) {</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">          1 :     addComponent(&quot;acceptFT&quot;);</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">          1 :     componentIsNotPeriodic(&quot;acceptFT&quot;);</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">          1 :     valueAcceptFT=getPntrToComponent(&quot;acceptFT&quot;);</span></a>
+<a name="844"><span class="lineNum">     844 </span>            :   }</a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">         19 :   addComponent(&quot;acceptSigma&quot;);</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">         19 :   componentIsNotPeriodic(&quot;acceptSigma&quot;);</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">         19 :   valueAccept=getPntrToComponent(&quot;acceptSigma&quot;);</span></a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">         19 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">       2403 :     for(unsigned i=0; i&lt;sigma_mean2_.size(); ++i) {</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">       2390 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">       4780 :       addComponent(&quot;sigmaMean-&quot;+num); componentIsNotPeriodic(&quot;sigmaMean-&quot;+num);</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">       2390 :       valueSigmaMean.push_back(getPntrToComponent(&quot;sigmaMean-&quot;+num));</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">       2390 :       getPntrToComponent(&quot;sigmaMean-&quot;+num)-&gt;set(std::sqrt(sigma_mean2_[i]));</span></a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">       4780 :       addComponent(&quot;sigma-&quot;+num); componentIsNotPeriodic(&quot;sigma-&quot;+num);</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">       2390 :       valueSigma.push_back(getPntrToComponent(&quot;sigma-&quot;+num));</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">       2390 :       getPntrToComponent(&quot;sigma-&quot;+num)-&gt;set(sigma_[i]);</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">       2390 :       if(noise_type_==GENERIC) {</span></a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">          4 :         addComponent(&quot;ftilde-&quot;+num); componentIsNotPeriodic(&quot;ftilde-&quot;+num);</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">          2 :         valueFtilde.push_back(getPntrToComponent(&quot;ftilde-&quot;+num));</span></a>
+<a name="862"><span class="lineNum">     862 </span>            :       }</a>
+<a name="863"><span class="lineNum">     863 </span>            :     }</a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">         13 :   } else {</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">         12 :     addComponent(&quot;sigmaMean&quot;); componentIsNotPeriodic(&quot;sigmaMean&quot;);</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">          6 :     valueSigmaMean.push_back(getPntrToComponent(&quot;sigmaMean&quot;));</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">          6 :     getPntrToComponent(&quot;sigmaMean&quot;)-&gt;set(std::sqrt(sigma_mean2_[0]));</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">         12 :     addComponent(&quot;sigma&quot;); componentIsNotPeriodic(&quot;sigma&quot;);</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">          6 :     valueSigma.push_back(getPntrToComponent(&quot;sigma&quot;));</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">         12 :     getPntrToComponent(&quot;sigma&quot;)-&gt;set(sigma_[0]);</span></a>
+<a name="871"><span class="lineNum">     871 </span>            :   }</a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span>            :   // initialize random seed</a>
+<a name="874"><span class="lineNum">     874 </span>            :   unsigned iseed;</a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">         19 :   if(master) {</span></a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">         11 :     auto ts = std::chrono::time_point_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::steady_clock::now()).time_since_epoch().count();</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">         11 :     iseed = static_cast&lt;unsigned&gt;(ts)+replica_;</span></a>
+<a name="878"><span class="lineNum">     878 </span>            :   } else {</a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">          8 :     iseed = 0;</span></a>
+<a name="880"><span class="lineNum">     880 </span>            :   }</a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">         19 :   comm.Sum(&amp;iseed, 1);</span></a>
+<a name="882"><span class="lineNum">     882 </span>            :   // this is used for ftilde and sigma both the move and the acceptance</a>
+<a name="883"><span class="lineNum">     883 </span>            :   // this is different for each replica</a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         19 :   random[0].setSeed(-iseed);</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">         19 :   if(doscale_||dooffset_) {</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :     // in this case we want the same seed everywhere</a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">         14 :     auto ts = std::chrono::time_point_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::steady_clock::now()).time_since_epoch().count();</span></a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineCov">         14 :     iseed = static_cast&lt;unsigned&gt;(ts);</span></a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">         14 :     if(master&amp;&amp;nrep_&gt;1) multi_sim_comm.Bcast(iseed,0);</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">         14 :     comm.Bcast(iseed,0);</span></a>
+<a name="891"><span class="lineNum">     891 </span>            :     // this is used for scale and offset sampling and acceptance</a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">         14 :     random[1].setSeed(-iseed);</span></a>
+<a name="893"><span class="lineNum">     893 </span>            :   }</a>
+<a name="894"><span class="lineNum">     894 </span>            :   // this is used for random chunk of sigmas, and it is different for each replica</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">         19 :   if(master) {</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">         11 :     auto ts = std::chrono::time_point_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::steady_clock::now()).time_since_epoch().count();</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">         11 :     iseed = static_cast&lt;unsigned&gt;(ts)+replica_;</span></a>
+<a name="898"><span class="lineNum">     898 </span>            :   } else {</a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">          8 :     iseed = 0;</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :   }</a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">         19 :   comm.Sum(&amp;iseed, 1);</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">         19 :   random[2].setSeed(-iseed);</span></a>
+<a name="903"><span class="lineNum">     903 </span>            : </a>
+<a name="904"><span class="lineNum">     904 </span>            :   // outfile stuff</a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">         19 :   if(write_stride_&gt;0) {</span></a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">         19 :     sfile_.link(*this);</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">         19 :     sfile_.open(status_file_name_);</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :   }</a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">         38 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)&quot;);</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">         35 :   if(do_reweight_) log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)&quot;);</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">         19 :   if(do_optsigmamean_&gt;0) log&lt;&lt;plumed.cite(&quot;Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)&quot;);</span></a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">         38 :   log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;);</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         19 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">         38 : }</span></a>
+<a name="916"><span class="lineNum">     916 </span>            : </a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">         38 : Metainference::~Metainference()</span></a>
+<a name="918"><span class="lineNum">     918 </span>            : {</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">         19 :   if(sfile_.isOpen()) sfile_.close();</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">        114 : }</span></a>
+<a name="921"><span class="lineNum">     921 </span>            : </a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">        156 : double Metainference::getEnergySP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="923"><span class="lineNum">     923 </span>            :                                   const double scale, const double offset)</a>
+<a name="924"><span class="lineNum">     924 </span>            : {</a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">        156 :   const double scale2 = scale*scale;</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">        156 :   const double sm2    = sigma_mean2_[0];</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">        156 :   const double ss2    = sigma[0]*sigma[0] + scale2*sm2;</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">        156 :   const double sss    = sigma[0]*sigma[0] + sm2;</span></a>
+<a name="929"><span class="lineNum">     929 </span>            : </a>
+<a name="930"><span class="lineNum">     930 </span>            :   double ene = 0.0;</a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">        156 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="932"><span class="lineNum">     932 </span>            :   {</a>
+<a name="933"><span class="lineNum">     933 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="934"><span class="lineNum">     934 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="935"><span class="lineNum">     935 </span>            :       const double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="936"><span class="lineNum">     936 </span>            :       const double a2 = 0.5*dev*dev + ss2;</a>
+<a name="937"><span class="lineNum">     937 </span>            :       if(sm2 &gt; 0.0) {</a>
+<a name="938"><span class="lineNum">     938 </span>            :         ene += std::log(2.0*a2/(1.0-std::exp(-a2/sm2)));</a>
+<a name="939"><span class="lineNum">     939 </span>            :       }</a>
+<a name="940"><span class="lineNum">     940 </span>            :       else {</a>
+<a name="941"><span class="lineNum">     941 </span>            :         ene += std::log(2.0*a2);</a>
+<a name="942"><span class="lineNum">     942 </span>            :       }</a>
+<a name="943"><span class="lineNum">     943 </span>            :     }</a>
+<a name="944"><span class="lineNum">     944 </span>            :   }</a>
+<a name="945"><span class="lineNum">     945 </span>            :   // add one single Jeffrey's prior and one normalisation per data point</a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">        156 :   ene += 0.5*std::log(sss) + static_cast&lt;double&gt;(narg)*0.5*std::log(0.5*M_PI*M_PI/ss2);</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">        156 :   if(doscale_ || doregres_zero_) ene += 0.5*std::log(sss);</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">        156 :   if(dooffset_) ene += 0.5*std::log(sss);</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">        156 :   return kbt_ * ene;</span></a>
+<a name="950"><span class="lineNum">     950 </span>            : }</a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">        144 : double Metainference::getEnergySPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :                                    const double scale, const double offset)</a>
+<a name="954"><span class="lineNum">     954 </span>            : {</a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">        144 :   const double scale2 = scale*scale;</span></a>
+<a name="956"><span class="lineNum">     956 </span>            :   double ene = 0.0;</a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">        144 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="958"><span class="lineNum">     958 </span>            :   {</a>
+<a name="959"><span class="lineNum">     959 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="960"><span class="lineNum">     960 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="961"><span class="lineNum">     961 </span>            :       const double sm2 = sigma_mean2_[i];</a>
+<a name="962"><span class="lineNum">     962 </span>            :       const double ss2 = sigma[i]*sigma[i] + scale2*sm2;</a>
+<a name="963"><span class="lineNum">     963 </span>            :       const double sss = sigma[i]*sigma[i] + sm2;</a>
+<a name="964"><span class="lineNum">     964 </span>            :       const double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="965"><span class="lineNum">     965 </span>            :       const double a2  = 0.5*dev*dev + ss2;</a>
+<a name="966"><span class="lineNum">     966 </span>            :       if(sm2 &gt; 0.0) {</a>
+<a name="967"><span class="lineNum">     967 </span>            :         ene += 0.5*std::log(sss) + 0.5*std::log(0.5*M_PI*M_PI/ss2) + std::log(2.0*a2/(1.0-std::exp(-a2/sm2)));</a>
+<a name="968"><span class="lineNum">     968 </span>            :       }</a>
+<a name="969"><span class="lineNum">     969 </span>            :       else {</a>
+<a name="970"><span class="lineNum">     970 </span>            :         ene += 0.5*std::log(sss) + 0.5*std::log(0.5*M_PI*M_PI/ss2) + std::log(2.0*a2);</a>
+<a name="971"><span class="lineNum">     971 </span>            :       }</a>
+<a name="972"><span class="lineNum">     972 </span>            :       if(doscale_ || doregres_zero_)  ene += 0.5*std::log(sss);</a>
+<a name="973"><span class="lineNum">     973 </span>            :       if(dooffset_) ene += 0.5*std::log(sss);</a>
+<a name="974"><span class="lineNum">     974 </span>            :     }</a>
+<a name="975"><span class="lineNum">     975 </span>            :   }</a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">        144 :   return kbt_ * ene;</span></a>
+<a name="977"><span class="lineNum">     977 </span>            : }</a>
+<a name="978"><span class="lineNum">     978 </span>            : </a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">         48 : double Metainference::getEnergyMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;ftilde, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="980"><span class="lineNum">     980 </span>            :                                      const double scale, const double offset)</a>
+<a name="981"><span class="lineNum">     981 </span>            : {</a>
+<a name="982"><span class="lineNum">     982 </span>            :   double ene = 0.0;</a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">         48 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="984"><span class="lineNum">     984 </span>            :   {</a>
+<a name="985"><span class="lineNum">     985 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="986"><span class="lineNum">     986 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="987"><span class="lineNum">     987 </span>            :       const double inv_sb2  = 1./(sigma[i]*sigma[i]);</a>
+<a name="988"><span class="lineNum">     988 </span>            :       const double inv_sm2  = 1./sigma_mean2_[i];</a>
+<a name="989"><span class="lineNum">     989 </span>            :       double devb = 0;</a>
+<a name="990"><span class="lineNum">     990 </span>            :       if(gen_likelihood_==LIKE_GAUSS)     devb = scale*ftilde[i]-parameters[i]+offset;</a>
+<a name="991"><span class="lineNum">     991 </span>            :       else if(gen_likelihood_==LIKE_LOGN) devb = std::log(scale*ftilde[i]/parameters[i]);</a>
+<a name="992"><span class="lineNum">     992 </span>            :       double devm = mean[i] - ftilde[i];</a>
+<a name="993"><span class="lineNum">     993 </span>            :       // deviation + normalisation + jeffrey</a>
+<a name="994"><span class="lineNum">     994 </span>            :       double normb = 0.;</a>
+<a name="995"><span class="lineNum">     995 </span>            :       if(gen_likelihood_==LIKE_GAUSS)     normb = -0.5*std::log(0.5/M_PI*inv_sb2);</a>
+<a name="996"><span class="lineNum">     996 </span>            :       else if(gen_likelihood_==LIKE_LOGN) normb = -0.5*std::log(0.5/M_PI*inv_sb2/(parameters[i]*parameters[i]));</a>
+<a name="997"><span class="lineNum">     997 </span>            :       const double normm         = -0.5*std::log(0.5/M_PI*inv_sm2);</a>
+<a name="998"><span class="lineNum">     998 </span>            :       const double jeffreys      = -0.5*std::log(2.*inv_sb2);</a>
+<a name="999"><span class="lineNum">     999 </span>            :       ene += 0.5*devb*devb*inv_sb2 + 0.5*devm*devm*inv_sm2 + normb + normm + jeffreys;</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :       if(doscale_ || doregres_zero_)  ene += jeffreys;</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :       if(dooffset_) ene += jeffreys;</a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     }</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   }</a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">         48 :   return kbt_ * ene;</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            : }</a>
+<a name="1006"><span class="lineNum">    1006 </span>            : </a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">         36 : double Metainference::getEnergyGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            :                                   const double scale, const double offset)</a>
+<a name="1009"><span class="lineNum">    1009 </span>            : {</a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">         36 :   const double scale2  = scale*scale;</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">         36 :   const double inv_s2  = 1./(sigma[0]*sigma[0] + scale2*sigma_mean2_[0]);</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">         36 :   const double inv_sss = 1./(sigma[0]*sigma[0] + sigma_mean2_[0]);</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   double ene = 0.0;</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">         36 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            :   {</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="1018"><span class="lineNum">    1018 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :       double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="1020"><span class="lineNum">    1020 </span>            :       ene += 0.5*dev*dev*inv_s2;</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :     }</a>
+<a name="1022"><span class="lineNum">    1022 </span>            :   }</a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">         36 :   const double normalisation = -0.5*std::log(0.5/M_PI*inv_s2);</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">         36 :   const double jeffreys = -0.5*std::log(2.*inv_sss);</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   // add Jeffrey's prior in case one sigma for all data points + one normalisation per datapoint</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">         36 :   ene += jeffreys + static_cast&lt;double&gt;(narg)*normalisation;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">         36 :   if(doscale_ || doregres_zero_)  ene += jeffreys;</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">         36 :   if(dooffset_) ene += jeffreys;</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            : </a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">         36 :   return kbt_ * ene;</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            : }</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : </a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">        152 : double Metainference::getEnergyGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :                                    const double scale, const double offset)</a>
+<a name="1035"><span class="lineNum">    1035 </span>            : {</a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">        152 :   const double scale2 = scale*scale;</span></a>
+<a name="1037"><span class="lineNum">    1037 </span>            : </a>
+<a name="1038"><span class="lineNum">    1038 </span>            :   double ene = 0.0;</a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">        152 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   {</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :       const double inv_s2  = 1./(sigma[i]*sigma[i] + scale2*sigma_mean2_[i]);</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :       const double inv_sss = 1./(sigma[i]*sigma[i] + sigma_mean2_[i]);</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :       double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :       // deviation + normalisation + jeffrey</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :       const double normalisation = -0.5*std::log(0.5/M_PI*inv_s2);</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :       const double jeffreys      = -0.5*std::log(2.*inv_sss);</a>
+<a name="1049"><span class="lineNum">    1049 </span>            :       ene += 0.5*dev*dev*inv_s2 + normalisation + jeffreys;</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :       if(doscale_ || doregres_zero_)  ene += jeffreys;</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :       if(dooffset_) ene += jeffreys;</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :     }</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   }</a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">        152 :   return kbt_ * ene;</span></a>
+<a name="1055"><span class="lineNum">    1055 </span>            : }</a>
+<a name="1056"><span class="lineNum">    1056 </span>            : </a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">         12 : void Metainference::moveTilde(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy)</span></a>
+<a name="1058"><span class="lineNum">    1058 </span>            : {</a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; new_ftilde(sigma_.size());</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">         12 :   new_ftilde = ftilde_;</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            : </a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   // change all tildes</a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">         36 :   for(unsigned j=0; j&lt;sigma_.size(); j++) {</span></a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">         24 :     const double r3 = random[0].Gaussian();</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">         24 :     const double ds3 = Dftilde_*std::sqrt(sigma_mean2_[j])*r3;</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">         24 :     new_ftilde[j] = ftilde_[j] + ds3;</span></a>
+<a name="1067"><span class="lineNum">    1067 </span>            :   }</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :   // calculate new energy</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">         12 :   double new_energy = getEnergyMIGEN(mean_,new_ftilde,sigma_,scale_,offset_);</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            : </a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   // accept or reject</a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         12 :   const double delta = ( new_energy - old_energy ) / kbt_;</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :   // if delta is negative always accept move</a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">         12 :   if( delta &lt;= 0.0 ) {</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">         12 :     old_energy = new_energy;</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">         12 :     ftilde_ = new_ftilde;</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">         12 :     MCacceptFT_++;</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     // otherwise extract random number</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :   } else {</a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineNoCov">          0 :     const double s = random[0].RandU01();</span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) {</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineNoCov">          0 :       old_energy = new_energy;</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineNoCov">          0 :       ftilde_ = new_ftilde;</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineNoCov">          0 :       MCacceptFT_++;</span></a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     }</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :   }</a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">         12 : }</span></a>
+<a name="1088"><span class="lineNum">    1088 </span>            : </a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">        168 : void Metainference::moveScaleOffset(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy)</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            : {</a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">        168 :   double new_scale = scale_;</span></a>
+<a name="1092"><span class="lineNum">    1092 </span>            : </a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">        168 :   if(doscale_) {</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineCov">        144 :     if(scale_prior_==SC_FLAT) {</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">        144 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">        144 :       const double ds1 = Dscale_*r1;</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">        144 :       new_scale += ds1;</span></a>
+<a name="1098"><span class="lineNum">    1098 </span>            :       // check boundaries</a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">        144 :       if(new_scale &gt; scale_max_) {new_scale = 2.0 * scale_max_ - new_scale;}</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">        144 :       if(new_scale &lt; scale_min_) {new_scale = 2.0 * scale_min_ - new_scale;}</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            :     } else {</a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineNoCov">          0 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineNoCov">          0 :       const double ds1 = 0.5*(scale_mu_-new_scale)+Dscale_*std::exp(1)/M_PI*r1;</span></a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineNoCov">          0 :       new_scale += ds1;</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            :     }</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   }</a>
+<a name="1107"><span class="lineNum">    1107 </span>            : </a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">        168 :   double new_offset = offset_;</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">        168 :   if(dooffset_) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">         24 :     if(offset_prior_==SC_FLAT) {</span></a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineCov">         24 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">         24 :       const double ds1 = Doffset_*r1;</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">         24 :       new_offset += ds1;</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            :       // check boundaries</a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">         24 :       if(new_offset &gt; offset_max_) {new_offset = 2.0 * offset_max_ - new_offset;}</span></a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineCov">         24 :       if(new_offset &lt; offset_min_) {new_offset = 2.0 * offset_min_ - new_offset;}</span></a>
+<a name="1118"><span class="lineNum">    1118 </span>            :     } else {</a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineNoCov">          0 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineNoCov">          0 :       const double ds1 = 0.5*(offset_mu_-new_offset)+Doffset_*std::exp(1)/M_PI*r1;</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineNoCov">          0 :       new_offset += ds1;</span></a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     }</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   }</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : </a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   // calculate new energy</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :   double new_energy = 0.;</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : </a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">        168 :   switch(noise_type_) {</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">         12 :   case GAUSS:</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">         12 :     new_energy = getEnergyGJ(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="1131"><span class="lineNum">    1131 </span>            :     break;</a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">         48 :   case MGAUSS:</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">         48 :     new_energy = getEnergyGJE(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     break;</a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">         48 :   case OUTLIERS:</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">         48 :     new_energy = getEnergySP(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span>            :     break;</a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">         48 :   case MOUTLIERS:</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">         48 :     new_energy = getEnergySPE(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            :     break;</a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">         12 :     new_energy = getEnergyMIGEN(mean_,ftilde_,sigma_,new_scale,new_offset);</span></a>
+<a name="1143"><span class="lineNum">    1143 </span>            :     break;</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : </a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   // for the scale/offset we need to consider the total energy</a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">        168 :   std::vector&lt;double&gt; totenergies(2);</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">        168 :   if(master) {</span></a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">         96 :     totenergies[0] = old_energy;</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">         96 :     totenergies[1] = new_energy;</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">         96 :     if(nrep_&gt;1) multi_sim_comm.Sum(totenergies);</span></a>
+<a name="1152"><span class="lineNum">    1152 </span>            :   } else {</a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineCov">         72 :     totenergies[0] = 0;</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">         72 :     totenergies[1] = 0;</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :   }</a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">        168 :   comm.Sum(totenergies);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span>            : </a>
+<a name="1158"><span class="lineNum">    1158 </span>            :   // accept or reject</a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineCov">        168 :   const double delta = ( totenergies[1] - totenergies[0] ) / kbt_;</span></a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   // if delta is negative always accept move</a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">        168 :   if( delta &lt;= 0.0 ) {</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">        168 :     old_energy = new_energy;</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">        168 :     scale_ = new_scale;</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">        168 :     offset_ = new_offset;</span></a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">        168 :     MCacceptScale_++;</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            :     // otherwise extract random number</a>
+<a name="1167"><span class="lineNum">    1167 </span>            :   } else {</a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineNoCov">          0 :     double s = random[1].RandU01();</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) {</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineNoCov">          0 :       old_energy = new_energy;</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :       scale_ = new_scale;</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :       offset_ = new_offset;</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineNoCov">          0 :       MCacceptScale_++;</span></a>
+<a name="1174"><span class="lineNum">    1174 </span>            :     }</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :   }</a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">        168 : }</span></a>
+<a name="1177"><span class="lineNum">    1177 </span>            : </a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">        178 : void Metainference::moveSigmas(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy, const unsigned i, const std::vector&lt;unsigned&gt; &amp;indices, bool &amp;breaknow)</span></a>
+<a name="1179"><span class="lineNum">    1179 </span>            : {</a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineCov">        178 :   std::vector&lt;double&gt; new_sigma(sigma_.size());</span></a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineCov">        178 :   new_sigma = sigma_;</span></a>
+<a name="1182"><span class="lineNum">    1182 </span>            : </a>
+<a name="1183"><span class="lineNum">    1183 </span>            :   // change MCchunksize_ sigmas</a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineCov">        178 :   if (MCchunksize_ &gt; 0) {</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineNoCov">          0 :     if ((MCchunksize_ * i) &gt;= sigma_.size()) {</span></a>
+<a name="1186"><span class="lineNum">    1186 </span>            :       // This means we are not moving any sigma, so we should break immediately</a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineNoCov">          0 :       breaknow = true;</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :     }</a>
+<a name="1189"><span class="lineNum">    1189 </span>            : </a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     // change random sigmas</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;MCchunksize_; j++) {</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :       const unsigned shuffle_index = j + MCchunksize_ * i;</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineNoCov">          0 :       if (shuffle_index &gt;= sigma_.size()) {</span></a>
+<a name="1194"><span class="lineNum">    1194 </span>            :         // Going any further will segfault but we should still evaluate the sigmas we changed</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :         break;</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :       }</a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineNoCov">          0 :       const unsigned index = indices[shuffle_index];</span></a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineNoCov">          0 :       const double r2 = random[0].Gaussian();</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :       const double ds2 = Dsigma_[index]*r2;</span></a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineNoCov">          0 :       new_sigma[index] = sigma_[index] + ds2;</span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            :       // check boundaries</a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineNoCov">          0 :       if(new_sigma[index] &gt; sigma_max_[index]) {new_sigma[index] = 2.0 * sigma_max_[index] - new_sigma[index];}</span></a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineNoCov">          0 :       if(new_sigma[index] &lt; sigma_min_[index]) {new_sigma[index] = 2.0 * sigma_min_[index] - new_sigma[index];}</span></a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     }</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :   } else {</a>
+<a name="1206"><span class="lineNum">    1206 </span>            :     // change all sigmas</a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">       3008 :     for(unsigned j=0; j&lt;sigma_.size(); j++) {</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">       2830 :       const double r2 = random[0].Gaussian();</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">       2830 :       const double ds2 = Dsigma_[j]*r2;</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">       2830 :       new_sigma[j] = sigma_[j] + ds2;</span></a>
+<a name="1211"><span class="lineNum">    1211 </span>            :       // check boundaries</a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineCov">       2830 :       if(new_sigma[j] &gt; sigma_max_[j]) {new_sigma[j] = 2.0 * sigma_max_[j] - new_sigma[j];}</span></a>
+<a name="1213"><span class="lineNum">    1213 </span><span class="lineCov">       2830 :       if(new_sigma[j] &lt; sigma_min_[j]) {new_sigma[j] = 2.0 * sigma_min_[j] - new_sigma[j];}</span></a>
+<a name="1214"><span class="lineNum">    1214 </span>            :     }</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :   }</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">        178 :   if (breaknow) {</span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            :     // We didnt move any sigmas, so no sense in evaluating anything</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :     return;</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :   }</a>
+<a name="1221"><span class="lineNum">    1221 </span>            : </a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   // calculate new energy</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   double new_energy = 0.;</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">        178 :   switch(noise_type_) {</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">         12 :   case GAUSS:</span></a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">         12 :     new_energy = getEnergyGJ(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="1227"><span class="lineNum">    1227 </span>            :     break;</a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">         52 :   case MGAUSS:</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">         52 :     new_energy = getEnergyGJE(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :     break;</a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">         54 :   case OUTLIERS:</span></a>
+<a name="1232"><span class="lineNum">    1232 </span><span class="lineCov">         54 :     new_energy = getEnergySP(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="1233"><span class="lineNum">    1233 </span>            :     break;</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">         48 :   case MOUTLIERS:</span></a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineCov">         48 :     new_energy = getEnergySPE(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     break;</a>
+<a name="1237"><span class="lineNum">    1237 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">         12 :     new_energy = getEnergyMIGEN(mean_,ftilde_,new_sigma,scale_,offset_);</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            :     break;</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :   }</a>
+<a name="1241"><span class="lineNum">    1241 </span>            : </a>
+<a name="1242"><span class="lineNum">    1242 </span>            :   // accept or reject</a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">        178 :   const double delta = ( new_energy - old_energy ) / kbt_;</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            :   // if delta is negative always accept move</a>
+<a name="1245"><span class="lineNum">    1245 </span><span class="lineCov">        178 :   if( delta &lt;= 0.0 ) {</span></a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">        178 :     old_energy = new_energy;</span></a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">        178 :     sigma_ = new_sigma;</span></a>
+<a name="1248"><span class="lineNum">    1248 </span><span class="lineCov">        178 :     MCaccept_++;</span></a>
+<a name="1249"><span class="lineNum">    1249 </span>            :     // otherwise extract random number</a>
+<a name="1250"><span class="lineNum">    1250 </span>            :   } else {</a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineNoCov">          0 :     const double s = random[0].RandU01();</span></a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) {</span></a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineNoCov">          0 :       old_energy = new_energy;</span></a>
+<a name="1254"><span class="lineNum">    1254 </span><span class="lineNoCov">          0 :       sigma_ = new_sigma;</span></a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineNoCov">          0 :       MCaccept_++;</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            :     }</a>
+<a name="1257"><span class="lineNum">    1257 </span>            :   }</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : }</a>
+<a name="1259"><span class="lineNum">    1259 </span>            : </a>
+<a name="1260"><span class="lineNum">    1260 </span><span class="lineCov">        178 : double Metainference::doMonteCarlo(const std::vector&lt;double&gt; &amp;mean_)</span></a>
+<a name="1261"><span class="lineNum">    1261 </span>            : {</a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   // calculate old energy with the updated coordinates</a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">        178 :   double old_energy=0.;</span></a>
+<a name="1264"><span class="lineNum">    1264 </span>            : </a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineCov">        178 :   switch(noise_type_) {</span></a>
+<a name="1266"><span class="lineNum">    1266 </span><span class="lineCov">         12 :   case GAUSS:</span></a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineCov">         12 :     old_energy = getEnergyGJ(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineCov">         12 :     break;</span></a>
+<a name="1269"><span class="lineNum">    1269 </span><span class="lineCov">         52 :   case MGAUSS:</span></a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineCov">         52 :     old_energy = getEnergyGJE(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">         52 :     break;</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineCov">         54 :   case OUTLIERS:</span></a>
+<a name="1273"><span class="lineNum">    1273 </span><span class="lineCov">         54 :     old_energy = getEnergySP(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1274"><span class="lineNum">    1274 </span><span class="lineCov">         54 :     break;</span></a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">         48 :   case MOUTLIERS:</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">         48 :     old_energy = getEnergySPE(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineCov">         48 :     break;</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">         12 :     old_energy = getEnergyMIGEN(mean_,ftilde_,sigma_,scale_,offset_);</span></a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">         12 :     break;</span></a>
+<a name="1281"><span class="lineNum">    1281 </span>            :   }</a>
+<a name="1282"><span class="lineNum">    1282 </span>            : </a>
+<a name="1283"><span class="lineNum">    1283 </span>            :   // do not run MC if this is a replica-exchange trial</a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">        178 :   if(!getExchangeStep()) {</span></a>
+<a name="1285"><span class="lineNum">    1285 </span>            : </a>
+<a name="1286"><span class="lineNum">    1286 </span>            :     // Create std::vector of random sigma indices</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :     std::vector&lt;unsigned&gt; indices;</a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">        178 :     if (MCchunksize_ &gt; 0) {</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineNoCov">          0 :       for (unsigned j=0; j&lt;sigma_.size(); j++) {</span></a>
+<a name="1290"><span class="lineNum">    1290 </span><span class="lineNoCov">          0 :         indices.push_back(j);</span></a>
+<a name="1291"><span class="lineNum">    1291 </span>            :       }</a>
+<a name="1292"><span class="lineNum">    1292 </span><span class="lineNoCov">          0 :       random[2].Shuffle(indices);</span></a>
+<a name="1293"><span class="lineNum">    1293 </span>            :     }</a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineCov">        178 :     bool breaknow = false;</span></a>
+<a name="1295"><span class="lineNum">    1295 </span>            : </a>
+<a name="1296"><span class="lineNum">    1296 </span>            :     // cycle on MC steps</a>
+<a name="1297"><span class="lineNum">    1297 </span><span class="lineCov">        356 :     for(unsigned i=0; i&lt;MCsteps_; ++i) {</span></a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineCov">        178 :       MCtrial_++;</span></a>
+<a name="1299"><span class="lineNum">    1299 </span>            :       // propose move for ftilde</a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">        178 :       if(noise_type_==GENERIC) moveTilde(mean_, old_energy);</span></a>
+<a name="1301"><span class="lineNum">    1301 </span>            :       // propose move for scale and/or offset</a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineCov">        178 :       if(doscale_||dooffset_) moveScaleOffset(mean_, old_energy);</span></a>
+<a name="1303"><span class="lineNum">    1303 </span>            :       // propose move for sigma</a>
+<a name="1304"><span class="lineNum">    1304 </span><span class="lineCov">        178 :       moveSigmas(mean_, old_energy, i, indices, breaknow);</span></a>
+<a name="1305"><span class="lineNum">    1305 </span>            :       // exit from the loop if this is the case</a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">        178 :       if(breaknow) break;</span></a>
+<a name="1307"><span class="lineNum">    1307 </span>            :     }</a>
+<a name="1308"><span class="lineNum">    1308 </span>            : </a>
+<a name="1309"><span class="lineNum">    1309 </span>            :     /* save the result of the sampling */</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :     /* ftilde */</a>
+<a name="1311"><span class="lineNum">    1311 </span><span class="lineCov">        178 :     if(noise_type_==GENERIC) {</span></a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">         12 :       double accept = static_cast&lt;double&gt;(MCacceptFT_) / static_cast&lt;double&gt;(MCtrial_);</span></a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineCov">         12 :       valueAcceptFT-&gt;set(accept);</span></a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineCov">         36 :       for(unsigned i=0; i&lt;sigma_.size(); i++) valueFtilde[i]-&gt;set(ftilde_[i]);</span></a>
+<a name="1315"><span class="lineNum">    1315 </span>            :     }</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :     /* scale and offset */</a>
+<a name="1317"><span class="lineNum">    1317 </span><span class="lineCov">        178 :     if(doscale_ || doregres_zero_) valueScale-&gt;set(scale_);</span></a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineCov">        178 :     if(dooffset_) valueOffset-&gt;set(offset_);</span></a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">        178 :     if(doscale_||dooffset_) {</span></a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">        168 :       double accept = static_cast&lt;double&gt;(MCacceptScale_) / static_cast&lt;double&gt;(MCtrial_);</span></a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">        168 :       valueAcceptScale-&gt;set(accept);</span></a>
+<a name="1322"><span class="lineNum">    1322 </span>            :     }</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :     /* sigmas */</a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">       3008 :     for(unsigned i=0; i&lt;sigma_.size(); i++) valueSigma[i]-&gt;set(sigma_[i]);</span></a>
+<a name="1325"><span class="lineNum">    1325 </span><span class="lineCov">        178 :     double accept = static_cast&lt;double&gt;(MCaccept_) / static_cast&lt;double&gt;(MCtrial_);</span></a>
+<a name="1326"><span class="lineNum">    1326 </span><span class="lineCov">        178 :     valueAccept-&gt;set(accept);</span></a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   }</a>
+<a name="1328"><span class="lineNum">    1328 </span>            : </a>
+<a name="1329"><span class="lineNum">    1329 </span>            :   // here we sum the score over the replicas to get the full metainference score that we save as a bias</a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">        178 :   if(master) {</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineCov">        104 :     if(nrep_&gt;1) multi_sim_comm.Sum(old_energy);</span></a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   } else {</a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineCov">         74 :     old_energy=0;</span></a>
+<a name="1334"><span class="lineNum">    1334 </span>            :   }</a>
+<a name="1335"><span class="lineNum">    1335 </span><span class="lineCov">        178 :   comm.Sum(old_energy);</span></a>
+<a name="1336"><span class="lineNum">    1336 </span>            : </a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   // this is the energy with current coordinates and parameters</a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineCov">        178 :   return old_energy;</span></a>
+<a name="1339"><span class="lineNum">    1339 </span>            : }</a>
+<a name="1340"><span class="lineNum">    1340 </span>            : </a>
+<a name="1341"><span class="lineNum">    1341 </span>            : /*</a>
+<a name="1342"><span class="lineNum">    1342 </span>            :    In the following energy-force functions we don't add the normalisation and the jeffreys priors</a>
+<a name="1343"><span class="lineNum">    1343 </span>            :    because they are not needed for the forces, the correct MetaInference energy is the one calculated</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :    in the Monte-Carlo</a>
+<a name="1345"><span class="lineNum">    1345 </span>            : */</a>
+<a name="1346"><span class="lineNum">    1346 </span>            : </a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">         54 : void Metainference::getEnergyForceSP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1348"><span class="lineNum">    1348 </span>            :                                      const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1349"><span class="lineNum">    1349 </span>            : {</a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineCov">         54 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineCov">         54 :   const double sm2    = sigma_mean2_[0];</span></a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">         54 :   const double ss2    = sigma_[0]*sigma_[0] + scale2*sm2;</span></a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineCov">         54 :   std::vector&lt;double&gt; f(narg,0);</span></a>
+<a name="1354"><span class="lineNum">    1354 </span>            : </a>
+<a name="1355"><span class="lineNum">    1355 </span><span class="lineCov">         54 :   if(master) {</span></a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineCov">         30 :     #pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="1357"><span class="lineNum">    1357 </span>            :     {</a>
+<a name="1358"><span class="lineNum">    1358 </span>            :       #pragma omp for</a>
+<a name="1359"><span class="lineNum">    1359 </span>            :       for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :         const double dev = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :         const double a2 = 0.5*dev*dev + ss2;</a>
+<a name="1362"><span class="lineNum">    1362 </span>            :         if(sm2 &gt; 0.0) {</a>
+<a name="1363"><span class="lineNum">    1363 </span>            :           const double t = std::exp(-a2/sm2);</a>
+<a name="1364"><span class="lineNum">    1364 </span>            :           const double dt = 1./t;</a>
+<a name="1365"><span class="lineNum">    1365 </span>            :           const double dit = 1./(1.-dt);</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :           f[i] = -scale_*dev*(dit/sm2 + 1./a2);</a>
+<a name="1367"><span class="lineNum">    1367 </span>            :         }</a>
+<a name="1368"><span class="lineNum">    1368 </span>            :         else {</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :           f[i] = -scale_*dev*(1./a2);</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :         }</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :       }</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :     }</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :     // collect contribution to forces and energy from other replicas</a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineCov">         30 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1375"><span class="lineNum">    1375 </span>            :   }</a>
+<a name="1376"><span class="lineNum">    1376 </span>            :   // intra-replica summation</a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">         54 :   comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1378"><span class="lineNum">    1378 </span>            : </a>
+<a name="1379"><span class="lineNum">    1379 </span>            :   double w_tmp = 0.;</a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">        288 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineCov">        234 :     setOutputForce(i, kbt_*f[i]*dmean_x[i]);</span></a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineCov">        234 :     w_tmp += kbt_*f[i]*dmean_b[i];</span></a>
+<a name="1383"><span class="lineNum">    1383 </span>            :   }</a>
+<a name="1384"><span class="lineNum">    1384 </span>            : </a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineCov">         54 :   if(do_reweight_) {</span></a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineCov">         48 :     setOutputForce(narg, w_tmp);</span></a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineCov">         96 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(-w_tmp);</span></a>
+<a name="1388"><span class="lineNum">    1388 </span>            :   }</a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineCov">         54 : }</span></a>
+<a name="1390"><span class="lineNum">    1390 </span>            : </a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineCov">         48 : void Metainference::getEnergyForceSPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1392"><span class="lineNum">    1392 </span>            :                                       const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1393"><span class="lineNum">    1393 </span>            : {</a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineCov">         48 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineCov">         48 :   std::vector&lt;double&gt; f(narg,0);</span></a>
+<a name="1396"><span class="lineNum">    1396 </span>            : </a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">         48 :   if(master) {</span></a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineCov">         24 :     #pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="1399"><span class="lineNum">    1399 </span>            :     {</a>
+<a name="1400"><span class="lineNum">    1400 </span>            :       #pragma omp for</a>
+<a name="1401"><span class="lineNum">    1401 </span>            :       for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :         const double sm2 = sigma_mean2_[i];</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :         const double ss2 = sigma_[i]*sigma_[i] + scale2*sm2;</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :         const double dev = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :         const double a2  = 0.5*dev*dev + ss2;</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :         if(sm2 &gt; 0.0) {</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :           const double t   = std::exp(-a2/sm2);</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :           const double dt  = 1./t;</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :           const double dit = 1./(1.-dt);</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :           f[i] = -scale_*dev*(dit/sm2 + 1./a2);</a>
+<a name="1411"><span class="lineNum">    1411 </span>            :         }</a>
+<a name="1412"><span class="lineNum">    1412 </span>            :         else {</a>
+<a name="1413"><span class="lineNum">    1413 </span>            :           f[i] = -scale_*dev*(1./a2);</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :         }</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :       }</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :     }</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :     // collect contribution to forces and energy from other replicas</a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineCov">         24 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1419"><span class="lineNum">    1419 </span>            :   }</a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineCov">         48 :   comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1421"><span class="lineNum">    1421 </span>            : </a>
+<a name="1422"><span class="lineNum">    1422 </span>            :   double w_tmp = 0.;</a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineCov">        240 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineCov">        192 :     setOutputForce(i, kbt_ * dmean_x[i] * f[i]);</span></a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineCov">        192 :     w_tmp += kbt_ * dmean_b[i] *f[i];</span></a>
+<a name="1426"><span class="lineNum">    1426 </span>            :   }</a>
+<a name="1427"><span class="lineNum">    1427 </span>            : </a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineCov">         48 :   if(do_reweight_) {</span></a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineCov">         48 :     setOutputForce(narg, w_tmp);</span></a>
+<a name="1430"><span class="lineNum">    1430 </span><span class="lineCov">         96 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(-w_tmp);</span></a>
+<a name="1431"><span class="lineNum">    1431 </span>            :   }</a>
+<a name="1432"><span class="lineNum">    1432 </span><span class="lineCov">         48 : }</span></a>
+<a name="1433"><span class="lineNum">    1433 </span>            : </a>
+<a name="1434"><span class="lineNum">    1434 </span><span class="lineCov">         12 : void Metainference::getEnergyForceGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1435"><span class="lineNum">    1435 </span>            :                                      const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1436"><span class="lineNum">    1436 </span>            : {</a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">         12 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineCov">         12 :   double inv_s2=0.;</span></a>
+<a name="1439"><span class="lineNum">    1439 </span>            : </a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineCov">         12 :   if(master) {</span></a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineCov">         12 :     inv_s2 = 1./(sigma_[0]*sigma_[0] + scale2*sigma_mean2_[0]);</span></a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineCov">         12 :     if(nrep_&gt;1) multi_sim_comm.Sum(inv_s2);</span></a>
+<a name="1443"><span class="lineNum">    1443 </span>            :   }</a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineCov">         12 :   comm.Sum(inv_s2);</span></a>
+<a name="1445"><span class="lineNum">    1445 </span>            : </a>
+<a name="1446"><span class="lineNum">    1446 </span>            :   double w_tmp = 0.;</a>
+<a name="1447"><span class="lineNum">    1447 </span><span class="lineCov">         12 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(w_tmp)</span></a>
+<a name="1448"><span class="lineNum">    1448 </span>            :   {</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :     #pragma omp for reduction( + : w_tmp)</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :       const double dev = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :       const double mult = dev*scale_*inv_s2;</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :       setOutputForce(i, -kbt_*dmean_x[i]*mult);</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :       w_tmp += kbt_*dmean_b[i]*mult;</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :     }</a>
+<a name="1456"><span class="lineNum">    1456 </span>            :   }</a>
+<a name="1457"><span class="lineNum">    1457 </span>            : </a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineCov">         12 :   if(do_reweight_) {</span></a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineNoCov">          0 :     setOutputForce(narg, -w_tmp);</span></a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(w_tmp);</span></a>
+<a name="1461"><span class="lineNum">    1461 </span>            :   }</a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">         12 : }</span></a>
+<a name="1463"><span class="lineNum">    1463 </span>            : </a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineCov">         52 : void Metainference::getEnergyForceGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1465"><span class="lineNum">    1465 </span>            :                                       const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1466"><span class="lineNum">    1466 </span>            : {</a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">         52 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineCov">         52 :   std::vector&lt;double&gt; inv_s2(sigma_.size(),0.);</span></a>
+<a name="1469"><span class="lineNum">    1469 </span>            : </a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineCov">         52 :   if(master) {</span></a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineCov">       1300 :     for(unsigned i=0; i&lt;sigma_.size(); ++i) inv_s2[i] = 1./(sigma_[i]*sigma_[i] + scale2*sigma_mean2_[i]);</span></a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineCov">         26 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;inv_s2[0],sigma_.size());</span></a>
+<a name="1473"><span class="lineNum">    1473 </span>            :   }</a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineCov">         52 :   comm.Sum(&amp;inv_s2[0],sigma_.size());</span></a>
+<a name="1475"><span class="lineNum">    1475 </span>            : </a>
+<a name="1476"><span class="lineNum">    1476 </span>            :   double w_tmp = 0.;</a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">         52 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(w_tmp)</span></a>
+<a name="1478"><span class="lineNum">    1478 </span>            :   {</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :     #pragma omp for reduction( + : w_tmp)</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1481"><span class="lineNum">    1481 </span>            :       const double dev  = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1482"><span class="lineNum">    1482 </span>            :       const double mult = dev*scale_*inv_s2[i];</a>
+<a name="1483"><span class="lineNum">    1483 </span>            :       setOutputForce(i, -kbt_*dmean_x[i]*mult);</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :       w_tmp += kbt_*dmean_b[i]*mult;</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :     }</a>
+<a name="1486"><span class="lineNum">    1486 </span>            :   }</a>
+<a name="1487"><span class="lineNum">    1487 </span>            : </a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineCov">         52 :   if(do_reweight_) {</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineCov">         52 :     setOutputForce(narg, -w_tmp);</span></a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineCov">        104 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(w_tmp);</span></a>
+<a name="1491"><span class="lineNum">    1491 </span>            :   }</a>
+<a name="1492"><span class="lineNum">    1492 </span><span class="lineCov">         52 : }</span></a>
+<a name="1493"><span class="lineNum">    1493 </span>            : </a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineCov">         12 : void Metainference::getEnergyForceMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b)</span></a>
+<a name="1495"><span class="lineNum">    1495 </span>            : {</a>
+<a name="1496"><span class="lineNum">    1496 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; inv_s2(sigma_.size(),0.);</span></a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; dev(sigma_.size(),0.);</span></a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; dev2(sigma_.size(),0.);</span></a>
+<a name="1499"><span class="lineNum">    1499 </span>            : </a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineCov">         36 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineCov">         24 :     inv_s2[i]   = 1./sigma_mean2_[i];</span></a>
+<a name="1502"><span class="lineNum">    1502 </span><span class="lineCov">         24 :     if(master) {</span></a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineCov">         24 :       dev[i]  = (mean[i]-ftilde_[i]);</span></a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineCov">         24 :       dev2[i] = dev[i]*dev[i];</span></a>
+<a name="1505"><span class="lineNum">    1505 </span>            :     }</a>
+<a name="1506"><span class="lineNum">    1506 </span>            :   }</a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineCov">         12 :   if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineNoCov">          0 :     multi_sim_comm.Sum(&amp;dev[0],dev.size());</span></a>
+<a name="1509"><span class="lineNum">    1509 </span><span class="lineNoCov">          0 :     multi_sim_comm.Sum(&amp;dev2[0],dev2.size());</span></a>
+<a name="1510"><span class="lineNum">    1510 </span>            :   }</a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineCov">         12 :   comm.Sum(&amp;dev[0],dev.size());</span></a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineCov">         12 :   comm.Sum(&amp;dev2[0],dev2.size());</span></a>
+<a name="1513"><span class="lineNum">    1513 </span>            : </a>
+<a name="1514"><span class="lineNum">    1514 </span>            :   double dene_b = 0.;</a>
+<a name="1515"><span class="lineNum">    1515 </span><span class="lineCov">         12 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(dene_b)</span></a>
+<a name="1516"><span class="lineNum">    1516 </span>            :   {</a>
+<a name="1517"><span class="lineNum">    1517 </span>            :     #pragma omp for reduction( + : dene_b)</a>
+<a name="1518"><span class="lineNum">    1518 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1519"><span class="lineNum">    1519 </span>            :       const double dene_x  = kbt_*inv_s2[i]*dmean_x[i]*dev[i];</a>
+<a name="1520"><span class="lineNum">    1520 </span>            :       dene_b += kbt_*inv_s2[i]*dmean_b[i]*dev[i];</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :       setOutputForce(i, -dene_x);</a>
+<a name="1522"><span class="lineNum">    1522 </span>            :     }</a>
+<a name="1523"><span class="lineNum">    1523 </span>            :   }</a>
+<a name="1524"><span class="lineNum">    1524 </span>            : </a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineCov">         12 :   if(do_reweight_) {</span></a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineNoCov">          0 :     setOutputForce(narg, -dene_b);</span></a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(dene_b);</span></a>
+<a name="1528"><span class="lineNum">    1528 </span>            :   }</a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">         12 : }</span></a>
+<a name="1530"><span class="lineNum">    1530 </span>            : </a>
+<a name="1531"><span class="lineNum">    1531 </span><span class="lineCov">        178 : void Metainference::get_weights(const unsigned iselect, double &amp;weight, double &amp;norm, double &amp;neff)</span></a>
+<a name="1532"><span class="lineNum">    1532 </span>            : {</a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineCov">        178 :   const double dnrep = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="1534"><span class="lineNum">    1534 </span>            :   // calculate the weights either from BIAS</a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineCov">        178 :   if(do_reweight_) {</span></a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineCov">        148 :     std::vector&lt;double&gt; bias(nrep_,0);</span></a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineCov">        148 :     if(master) {</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">         74 :       bias[replica_] = getArgument(narg);</span></a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineCov">         74 :       if(nrep_&gt;1) multi_sim_comm.Sum(&amp;bias[0], nrep_);</span></a>
+<a name="1540"><span class="lineNum">    1540 </span>            :     }</a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineCov">        148 :     comm.Sum(&amp;bias[0], nrep_);</span></a>
+<a name="1542"><span class="lineNum">    1542 </span>            : </a>
+<a name="1543"><span class="lineNum">    1543 </span>            :     // accumulate weights</a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineCov">        148 :     const double decay = 1./static_cast&lt;double&gt; (average_weights_stride_);</span></a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineCov">        148 :     if(!firstTimeW[iselect]) {</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineCov">        408 :       for(unsigned i=0; i&lt;nrep_; ++i) {</span></a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineCov">        272 :         const double delta=bias[i]-average_weights_[iselect][i];</span></a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineCov">        272 :         average_weights_[iselect][i]+=decay*delta;</span></a>
+<a name="1549"><span class="lineNum">    1549 </span>            :       }</a>
+<a name="1550"><span class="lineNum">    1550 </span>            :     } else {</a>
+<a name="1551"><span class="lineNum">    1551 </span>            :       firstTimeW[iselect] = false;</a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineCov">         36 :       for(unsigned i=0; i&lt;nrep_; ++i) average_weights_[iselect][i] = bias[i];</span></a>
+<a name="1553"><span class="lineNum">    1553 </span>            :     }</a>
+<a name="1554"><span class="lineNum">    1554 </span>            : </a>
+<a name="1555"><span class="lineNum">    1555 </span>            :     // set average back into bias and set norm to one</a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineCov">        148 :     const double maxbias = *(std::max_element(average_weights_[iselect].begin(), average_weights_[iselect].end()));</span></a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineCov">        444 :     for(unsigned i=0; i&lt;nrep_; ++i) bias[i] = std::exp((average_weights_[iselect][i]-maxbias)/kbt_);</span></a>
+<a name="1558"><span class="lineNum">    1558 </span>            :     // set local weight, norm and weight variance</a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineCov">        148 :     weight = bias[replica_];</span></a>
+<a name="1560"><span class="lineNum">    1560 </span>            :     double w2=0.;</a>
+<a name="1561"><span class="lineNum">    1561 </span><span class="lineCov">        444 :     for(unsigned i=0; i&lt;nrep_; ++i) {</span></a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineCov">        296 :       w2 += bias[i]*bias[i];</span></a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineCov">        296 :       norm += bias[i];</span></a>
+<a name="1564"><span class="lineNum">    1564 </span>            :     }</a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineCov">        148 :     neff = norm*norm/w2;</span></a>
+<a name="1566"><span class="lineNum">    1566 </span><span class="lineCov">        296 :     getPntrToComponent(&quot;weight&quot;)-&gt;set(weight/norm);</span></a>
+<a name="1567"><span class="lineNum">    1567 </span>            :   } else {</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :     // or arithmetic ones</a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineCov">         30 :     neff = dnrep;</span></a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineCov">         30 :     weight = 1.0;</span></a>
+<a name="1571"><span class="lineNum">    1571 </span><span class="lineCov">         30 :     norm = dnrep;</span></a>
+<a name="1572"><span class="lineNum">    1572 </span>            :   }</a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineCov">        178 :   getPntrToComponent(&quot;neff&quot;)-&gt;set(neff);</span></a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineCov">        178 : }</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            : </a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineCov">        178 : void Metainference::get_sigma_mean(const unsigned iselect, const double weight, const double norm, const double neff, const std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="1577"><span class="lineNum">    1577 </span>            : {</a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineCov">        178 :   const double dnrep    = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineCov">        178 :   std::vector&lt;double&gt; sigma_mean2_tmp(sigma_mean2_.size(), 0.);</span></a>
+<a name="1580"><span class="lineNum">    1580 </span>            : </a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineCov">        178 :   if(do_optsigmamean_&gt;0) {</span></a>
+<a name="1582"><span class="lineNum">    1582 </span>            :     // remove first entry of the history std::vector</a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineNoCov">          0 :     if(sigma_mean2_last_[iselect][0].size()==optsigmamean_stride_&amp;&amp;optsigmamean_stride_&gt;0)</span></a>
+<a name="1584"><span class="lineNum">    1584 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_last_[iselect][i].erase(sigma_mean2_last_[iselect][i].begin());</span></a>
+<a name="1585"><span class="lineNum">    1585 </span>            :     /* this is the current estimate of sigma mean for each argument</a>
+<a name="1586"><span class="lineNum">    1586 </span>            :        there is one of this per argument in any case  because it is</a>
+<a name="1587"><span class="lineNum">    1587 </span>            :        the maximum among these to be used in case of GAUSS/OUTLIER */</a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineNoCov">          0 :     std::vector&lt;double&gt; sigma_mean2_now(narg,0);</span></a>
+<a name="1589"><span class="lineNum">    1589 </span><span class="lineNoCov">          0 :     if(master) {</span></a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_now[i] = weight*(getArgument(i)-mean[i])*(getArgument(i)-mean[i]);</span></a>
+<a name="1591"><span class="lineNum">    1591 </span><span class="lineNoCov">          0 :       if(nrep_&gt;1) multi_sim_comm.Sum(&amp;sigma_mean2_now[0], narg);</span></a>
+<a name="1592"><span class="lineNum">    1592 </span>            :     }</a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineNoCov">          0 :     comm.Sum(&amp;sigma_mean2_now[0], narg);</span></a>
+<a name="1594"><span class="lineNum">    1594 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_now[i] *= 1.0/(neff-1.)/norm;</span></a>
+<a name="1595"><span class="lineNum">    1595 </span>            : </a>
+<a name="1596"><span class="lineNum">    1596 </span>            :     // add sigma_mean2 to history</a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineNoCov">          0 :     if(optsigmamean_stride_&gt;0) {</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_last_[iselect][i].push_back(sigma_mean2_now[i]);</span></a>
+<a name="1599"><span class="lineNum">    1599 </span>            :     } else {</a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) if(sigma_mean2_now[i] &gt; sigma_mean2_last_[iselect][i][0]) sigma_mean2_last_[iselect][i][0] = sigma_mean2_now[i];</span></a>
+<a name="1601"><span class="lineNum">    1601 </span>            :     }</a>
+<a name="1602"><span class="lineNum">    1602 </span>            : </a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineNoCov">          0 :     if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="1604"><span class="lineNum">    1604 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1605"><span class="lineNum">    1605 </span>            :         /* set to the maximum in history std::vector */</a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineNoCov">          0 :         sigma_mean2_tmp[i] = *max_element(sigma_mean2_last_[iselect][i].begin(), sigma_mean2_last_[iselect][i].end());</span></a>
+<a name="1607"><span class="lineNum">    1607 </span>            :         /* the standard error of the mean */</a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineNoCov">          0 :         valueSigmaMean[i]-&gt;set(std::sqrt(sigma_mean2_tmp[i]));</span></a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineNoCov">          0 :         if(noise_type_==GENERIC) {</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineNoCov">          0 :           sigma_min_[i] = std::sqrt(sigma_mean2_tmp[i]);</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineNoCov">          0 :           if(sigma_[i] &lt; sigma_min_[i]) sigma_[i] = sigma_min_[i];</span></a>
+<a name="1612"><span class="lineNum">    1612 </span>            :         }</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :       }</a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineNoCov">          0 :     } else if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="1615"><span class="lineNum">    1615 </span>            :       // find maximum for each data point</a>
+<a name="1616"><span class="lineNum">    1616 </span>            :       std::vector &lt;double&gt; max_values;</a>
+<a name="1617"><span class="lineNum">    1617 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) max_values.push_back(*max_element(sigma_mean2_last_[iselect][i].begin(), sigma_mean2_last_[iselect][i].end()));</span></a>
+<a name="1618"><span class="lineNum">    1618 </span>            :       // find maximum across data points</a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineNoCov">          0 :       const double max_now = *max_element(max_values.begin(), max_values.end());</span></a>
+<a name="1620"><span class="lineNum">    1620 </span>            :       // set new value</a>
+<a name="1621"><span class="lineNum">    1621 </span><span class="lineNoCov">          0 :       sigma_mean2_tmp[0] = max_now;</span></a>
+<a name="1622"><span class="lineNum">    1622 </span><span class="lineNoCov">          0 :       valueSigmaMean[0]-&gt;set(std::sqrt(sigma_mean2_tmp[0]));</span></a>
+<a name="1623"><span class="lineNum">    1623 </span>            :     }</a>
+<a name="1624"><span class="lineNum">    1624 </span>            :     // endif sigma mean optimization</a>
+<a name="1625"><span class="lineNum">    1625 </span>            :     // start sigma max optimization</a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineNoCov">          0 :     if(do_optsigmamean_&gt;1&amp;&amp;!sigmamax_opt_done_) {</span></a>
+<a name="1627"><span class="lineNum">    1627 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;sigma_max_.size(); i++) {</span></a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineNoCov">          0 :         if(sigma_max_est_[i]&lt;sigma_mean2_tmp[i]&amp;&amp;optimized_step_&gt;optsigmamean_stride_) sigma_max_est_[i]=sigma_mean2_tmp[i];</span></a>
+<a name="1629"><span class="lineNum">    1629 </span>            :         // ready to set once and for all the value of sigma_max</a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineNoCov">          0 :         if(optimized_step_==N_optimized_step_) {</span></a>
+<a name="1631"><span class="lineNum">    1631 </span><span class="lineNoCov">          0 :           sigmamax_opt_done_=true;</span></a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineNoCov">          0 :           for(unsigned i=0; i&lt;sigma_max_.size(); i++) {</span></a>
+<a name="1633"><span class="lineNum">    1633 </span><span class="lineNoCov">          0 :             sigma_max_[i]=std::sqrt(sigma_max_est_[i]*dnrep);</span></a>
+<a name="1634"><span class="lineNum">    1634 </span><span class="lineNoCov">          0 :             Dsigma_[i] = 0.05*(sigma_max_[i] - sigma_min_[i]);</span></a>
+<a name="1635"><span class="lineNum">    1635 </span><span class="lineNoCov">          0 :             if(sigma_[i]&gt;sigma_max_[i]) sigma_[i]=sigma_max_[i];</span></a>
+<a name="1636"><span class="lineNum">    1636 </span>            :           }</a>
+<a name="1637"><span class="lineNum">    1637 </span>            :         }</a>
+<a name="1638"><span class="lineNum">    1638 </span>            :       }</a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineNoCov">          0 :       optimized_step_++;</span></a>
+<a name="1640"><span class="lineNum">    1640 </span>            :     }</a>
+<a name="1641"><span class="lineNum">    1641 </span>            :     // end sigma max optimization</a>
+<a name="1642"><span class="lineNum">    1642 </span>            :   } else {</a>
+<a name="1643"><span class="lineNum">    1643 </span><span class="lineCov">        178 :     if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineCov">       2876 :       for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineCov">       2764 :         sigma_mean2_tmp[i] = sigma_mean2_last_[iselect][i][0];</span></a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineCov">       2764 :         valueSigmaMean[i]-&gt;set(std::sqrt(sigma_mean2_tmp[i]));</span></a>
+<a name="1647"><span class="lineNum">    1647 </span>            :       }</a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">         66 :     } else if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">         66 :       sigma_mean2_tmp[0] = sigma_mean2_last_[iselect][0][0];</span></a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineCov">         66 :       valueSigmaMean[0]-&gt;set(std::sqrt(sigma_mean2_tmp[0]));</span></a>
+<a name="1651"><span class="lineNum">    1651 </span>            :     }</a>
+<a name="1652"><span class="lineNum">    1652 </span>            :   }</a>
+<a name="1653"><span class="lineNum">    1653 </span>            : </a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineCov">        178 :   sigma_mean2_ = sigma_mean2_tmp;</span></a>
+<a name="1655"><span class="lineNum">    1655 </span><span class="lineCov">        178 : }</span></a>
+<a name="1656"><span class="lineNum">    1656 </span>            : </a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">        178 : void Metainference::replica_averaging(const double weight, const double norm, std::vector&lt;double&gt; &amp;mean, std::vector&lt;double&gt; &amp;dmean_b)</span></a>
+<a name="1658"><span class="lineNum">    1658 </span>            : {</a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineCov">        178 :   if(master) {</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">       1660 :     for(unsigned i=0; i&lt;narg; ++i) mean[i] = weight/norm*getArgument(i);</span></a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineCov">        104 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="1662"><span class="lineNum">    1662 </span>            :   }</a>
+<a name="1663"><span class="lineNum">    1663 </span><span class="lineCov">        178 :   comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="1664"><span class="lineNum">    1664 </span>            :   // set the derivative of the mean with respect to the bias</a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">       3200 :   for(unsigned i=0; i&lt;narg; ++i) dmean_b[i] = weight/norm/kbt_*(getArgument(i)-mean[i])/static_cast&lt;double&gt;(average_weights_stride_);</span></a>
+<a name="1666"><span class="lineNum">    1666 </span>            : </a>
+<a name="1667"><span class="lineNum">    1667 </span>            :   // this is only for generic metainference</a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">        178 :   if(firstTime) {ftilde_ = mean; firstTime = false;}</span></a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineCov">        178 : }</span></a>
+<a name="1670"><span class="lineNum">    1670 </span>            : </a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineNoCov">          0 : void Metainference::do_regression_zero(const std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="1672"><span class="lineNum">    1672 </span>            : {</a>
+<a name="1673"><span class="lineNum">    1673 </span>            : // parameters[i] = scale_ * mean[i]: find scale_ with linear regression</a>
+<a name="1674"><span class="lineNum">    1674 </span>            :   double num = 0.0;</a>
+<a name="1675"><span class="lineNum">    1675 </span>            :   double den = 0.0;</a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;parameters.size(); ++i) {</span></a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineNoCov">          0 :     num += mean[i] * parameters[i];</span></a>
+<a name="1678"><span class="lineNum">    1678 </span><span class="lineNoCov">          0 :     den += mean[i] * mean[i];</span></a>
+<a name="1679"><span class="lineNum">    1679 </span>            :   }</a>
+<a name="1680"><span class="lineNum">    1680 </span><span class="lineNoCov">          0 :   if(den&gt;0) {</span></a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineNoCov">          0 :     scale_ = num / den;</span></a>
+<a name="1682"><span class="lineNum">    1682 </span>            :   } else {</a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineNoCov">          0 :     scale_ = 1.0;</span></a>
+<a name="1684"><span class="lineNum">    1684 </span>            :   }</a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1686"><span class="lineNum">    1686 </span>            : </a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineCov">        178 : void Metainference::calculate()</span></a>
+<a name="1688"><span class="lineNum">    1688 </span>            : {</a>
+<a name="1689"><span class="lineNum">    1689 </span>            :   // get step</a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineCov">        178 :   const long long int step = getStep();</span></a>
+<a name="1691"><span class="lineNum">    1691 </span>            : </a>
+<a name="1692"><span class="lineNum">    1692 </span>            :   unsigned iselect = 0;</a>
+<a name="1693"><span class="lineNum">    1693 </span>            :   // set the value of selector for  REM-like stuff</a>
+<a name="1694"><span class="lineNum">    1694 </span><span class="lineCov">        178 :   if(selector_.length()&gt;0) iselect = static_cast&lt;unsigned&gt;(plumed.passMap[selector_]);</span></a>
+<a name="1695"><span class="lineNum">    1695 </span>            : </a>
+<a name="1696"><span class="lineNum">    1696 </span>            :   /* 1) collect weights */</a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineCov">        178 :   double weight = 0.;</span></a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineCov">        178 :   double neff = 0.;</span></a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineCov">        178 :   double norm = 0.;</span></a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineCov">        178 :   get_weights(iselect, weight, norm, neff);</span></a>
+<a name="1701"><span class="lineNum">    1701 </span>            : </a>
+<a name="1702"><span class="lineNum">    1702 </span>            :   /* 2) calculate average */</a>
+<a name="1703"><span class="lineNum">    1703 </span><span class="lineCov">        178 :   std::vector&lt;double&gt; mean(narg,0);</span></a>
+<a name="1704"><span class="lineNum">    1704 </span>            :   // this is the derivative of the mean with respect to the argument</a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineCov">        178 :   std::vector&lt;double&gt; dmean_x(narg,weight/norm);</span></a>
+<a name="1706"><span class="lineNum">    1706 </span>            :   // this is the derivative of the mean with respect to the bias</a>
+<a name="1707"><span class="lineNum">    1707 </span><span class="lineCov">        178 :   std::vector&lt;double&gt; dmean_b(narg,0);</span></a>
+<a name="1708"><span class="lineNum">    1708 </span>            :   // calculate it</a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineCov">        178 :   replica_averaging(weight, norm, mean, dmean_b);</span></a>
+<a name="1710"><span class="lineNum">    1710 </span>            : </a>
+<a name="1711"><span class="lineNum">    1711 </span>            :   /* 3) calculates parameters */</a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineCov">        178 :   get_sigma_mean(iselect, weight, norm, neff, mean);</span></a>
+<a name="1713"><span class="lineNum">    1713 </span>            : </a>
+<a name="1714"><span class="lineNum">    1714 </span>            :   // in case of regression with zero intercept, calculate scale</a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineCov">        178 :   if(doregres_zero_ &amp;&amp; step%nregres_zero_==0) do_regression_zero(mean);</span></a>
+<a name="1716"><span class="lineNum">    1716 </span>            : </a>
+<a name="1717"><span class="lineNum">    1717 </span>            :   /* 4) run monte carlo */</a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineCov">        178 :   double ene = doMonteCarlo(mean);</span></a>
+<a name="1719"><span class="lineNum">    1719 </span>            : </a>
+<a name="1720"><span class="lineNum">    1720 </span>            :   // calculate bias and forces</a>
+<a name="1721"><span class="lineNum">    1721 </span><span class="lineCov">        178 :   switch(noise_type_) {</span></a>
+<a name="1722"><span class="lineNum">    1722 </span><span class="lineCov">         12 :   case GAUSS:</span></a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineCov">         12 :     getEnergyForceGJ(mean, dmean_x, dmean_b);</span></a>
+<a name="1724"><span class="lineNum">    1724 </span>            :     break;</a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineCov">         52 :   case MGAUSS:</span></a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineCov">         52 :     getEnergyForceGJE(mean, dmean_x, dmean_b);</span></a>
+<a name="1727"><span class="lineNum">    1727 </span>            :     break;</a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineCov">         54 :   case OUTLIERS:</span></a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineCov">         54 :     getEnergyForceSP(mean, dmean_x, dmean_b);</span></a>
+<a name="1730"><span class="lineNum">    1730 </span>            :     break;</a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineCov">         48 :   case MOUTLIERS:</span></a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineCov">         48 :     getEnergyForceSPE(mean, dmean_x, dmean_b);</span></a>
+<a name="1733"><span class="lineNum">    1733 </span>            :     break;</a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1735"><span class="lineNum">    1735 </span><span class="lineCov">         12 :     getEnergyForceMIGEN(mean, dmean_x, dmean_b);</span></a>
+<a name="1736"><span class="lineNum">    1736 </span>            :     break;</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :   }</a>
+<a name="1738"><span class="lineNum">    1738 </span>            : </a>
+<a name="1739"><span class="lineNum">    1739 </span>            :   setBias(ene);</a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">        178 : }</span></a>
+<a name="1741"><span class="lineNum">    1741 </span>            : </a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineCov">         19 : void Metainference::writeStatus()</span></a>
+<a name="1743"><span class="lineNum">    1743 </span>            : {</a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineCov">         19 :   sfile_.rewind();</span></a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineCov">         19 :   sfile_.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="1746"><span class="lineNum">    1746 </span>            :   //nsel</a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineCov">         38 :   for(unsigned i=0; i&lt;sigma_mean2_last_.size(); i++) {</span></a>
+<a name="1748"><span class="lineNum">    1748 </span>            :     std::string msg_i,msg_j;</a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineCov">         19 :     Tools::convert(i,msg_i);</span></a>
+<a name="1750"><span class="lineNum">    1750 </span>            :     std::vector &lt;double&gt; max_values;</a>
+<a name="1751"><span class="lineNum">    1751 </span>            :     //narg</a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineCov">       2434 :     for(unsigned j=0; j&lt;narg; ++j) {</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineCov">       2415 :       Tools::convert(j,msg_j);</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineCov">       2415 :       std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineCov">       2415 :       if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineCov">       7170 :         sfile_.printField(&quot;sigmaMean_&quot;+msg,std::sqrt(*max_element(sigma_mean2_last_[i][j].begin(), sigma_mean2_last_[i][j].end())));</span></a>
+<a name="1757"><span class="lineNum">    1757 </span>            :       } else {</a>
+<a name="1758"><span class="lineNum">    1758 </span>            :         // find maximum for each data point</a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineCov">         50 :         max_values.push_back(*max_element(sigma_mean2_last_[i][j].begin(), sigma_mean2_last_[i][j].end()));</span></a>
+<a name="1760"><span class="lineNum">    1760 </span>            :       }</a>
+<a name="1761"><span class="lineNum">    1761 </span>            :     }</a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineCov">         19 :     if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="1763"><span class="lineNum">    1763 </span>            :       // find maximum across data points</a>
+<a name="1764"><span class="lineNum">    1764 </span><span class="lineCov">          6 :       const double max_now = std::sqrt(*max_element(max_values.begin(), max_values.end()));</span></a>
+<a name="1765"><span class="lineNum">    1765 </span><span class="lineCov">          6 :       Tools::convert(0,msg_j);</span></a>
+<a name="1766"><span class="lineNum">    1766 </span><span class="lineCov">          6 :       std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="1767"><span class="lineNum">    1767 </span><span class="lineCov">         12 :       sfile_.printField(&quot;sigmaMean_&quot;+msg, max_now);</span></a>
+<a name="1768"><span class="lineNum">    1768 </span>            :     }</a>
+<a name="1769"><span class="lineNum">    1769 </span>            :   }</a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="1771"><span class="lineNum">    1771 </span>            :     std::string msg;</a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineCov">       2396 :     Tools::convert(i,msg);</span></a>
+<a name="1773"><span class="lineNum">    1773 </span><span class="lineCov">       4792 :     sfile_.printField(&quot;sigma_&quot;+msg,sigma_[i]);</span></a>
+<a name="1774"><span class="lineNum">    1774 </span>            :   }</a>
+<a name="1775"><span class="lineNum">    1775 </span><span class="lineCov">       2415 :   for(unsigned i=0; i&lt;sigma_max_.size(); ++i) {</span></a>
+<a name="1776"><span class="lineNum">    1776 </span>            :     std::string msg;</a>
+<a name="1777"><span class="lineNum">    1777 </span><span class="lineCov">       2396 :     Tools::convert(i,msg);</span></a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineCov">       4792 :     sfile_.printField(&quot;sigma_max_&quot;+msg,sigma_max_[i]);</span></a>
+<a name="1779"><span class="lineNum">    1779 </span>            :   }</a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineCov">         19 :   if(noise_type_==GENERIC) {</span></a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;ftilde_.size(); ++i) {</span></a>
+<a name="1782"><span class="lineNum">    1782 </span>            :       std::string msg;</a>
+<a name="1783"><span class="lineNum">    1783 </span><span class="lineCov">          2 :       Tools::convert(i,msg);</span></a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineCov">          4 :       sfile_.printField(&quot;ftilde_&quot;+msg,ftilde_[i]);</span></a>
+<a name="1785"><span class="lineNum">    1785 </span>            :     }</a>
+<a name="1786"><span class="lineNum">    1786 </span>            :   }</a>
+<a name="1787"><span class="lineNum">    1787 </span><span class="lineCov">         19 :   sfile_.printField(&quot;scale0_&quot;,scale_);</span></a>
+<a name="1788"><span class="lineNum">    1788 </span><span class="lineCov">         19 :   sfile_.printField(&quot;offset0_&quot;,offset_);</span></a>
+<a name="1789"><span class="lineNum">    1789 </span><span class="lineCov">         38 :   for(unsigned i=0; i&lt;average_weights_.size(); i++) {</span></a>
+<a name="1790"><span class="lineNum">    1790 </span>            :     std::string msg_i;</a>
+<a name="1791"><span class="lineNum">    1791 </span><span class="lineCov">         19 :     Tools::convert(i,msg_i);</span></a>
+<a name="1792"><span class="lineNum">    1792 </span><span class="lineCov">         38 :     sfile_.printField(&quot;weight_&quot;+msg_i,average_weights_[i][replica_]);</span></a>
+<a name="1793"><span class="lineNum">    1793 </span>            :   }</a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineCov">         19 :   sfile_.printField();</span></a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineCov">         19 :   sfile_.flush();</span></a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineCov">         19 : }</span></a>
+<a name="1797"><span class="lineNum">    1797 </span>            : </a>
+<a name="1798"><span class="lineNum">    1798 </span><span class="lineCov">        178 : void Metainference::update() {</span></a>
+<a name="1799"><span class="lineNum">    1799 </span>            :   // write status file</a>
+<a name="1800"><span class="lineNum">    1800 </span><span class="lineCov">        178 :   if(write_stride_&gt;0&amp;&amp; (getStep()%write_stride_==0 || getCPT()) ) writeStatus();</span></a>
+<a name="1801"><span class="lineNum">    1801 </span><span class="lineCov">        178 : }</span></a>
+<a name="1802"><span class="lineNum">    1802 </span>            : </a>
+<a name="1803"><span class="lineNum">    1803 </span>            : }</a>
+<a name="1804"><span class="lineNum">    1804 </span>            : }</a>
+<a name="1805"><span class="lineNum">    1805 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/MetainferenceBase.cpp.func-sort-c.html b/coverage/isdb/MetainferenceBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c25e0fb620
--- /dev/null
+++ b/coverage/isdb/MetainferenceBase.cpp.func-sort-c.html
@@ -0,0 +1,184 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/MetainferenceBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - MetainferenceBase.cpp<span style="font-size: 80%;"> (<a href="MetainferenceBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">757</td>
+            <td class="headerCovTableEntry">888</td>
+            <td class="headerCovTableEntryMed">85.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/isdb/MetainferenceBase.cpp.func.html b/coverage/isdb/MetainferenceBase.cpp.func.html
new file mode 100644
index 0000000000..662cadcc94
--- /dev/null
+++ b/coverage/isdb/MetainferenceBase.cpp.func.html
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/MetainferenceBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
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+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">757</td>
+            <td class="headerCovTableEntry">888</td>
+            <td class="headerCovTableEntryMed">85.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
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+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MetainferenceBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFn"><a href="MetainferenceBase.cpp.gcov.html#1261">_ZN4PLMD4isdb17MetainferenceBase19getEnergyForceMIGENERKSt6vectorIdSaIdEES6_S6_</a></td>
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+    <tr>
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+              <td class="coverFnHi">2225</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.cpp.gcov.html#824">_ZN4PLMD4isdb17MetainferenceBase9moveTildeERKSt6vectorIdSaIdEERd</a></td>
+              <td class="coverFnHi">12</td>
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+    <tr>
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+              <td class="coverFnLo">0</td>
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+    <tr>
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+              <td class="coverFnHi">96</td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/MetainferenceBase.cpp.gcov.html b/coverage/isdb/MetainferenceBase.cpp.gcov.html
new file mode 100644
index 0000000000..9bd239a1eb
--- /dev/null
+++ b/coverage/isdb/MetainferenceBase.cpp.gcov.html
@@ -0,0 +1,1639 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/MetainferenceBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - MetainferenceBase.cpp<span style="font-size: 80%;"> (source / <a href="MetainferenceBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">757</td>
+            <td class="headerCovTableEntry">888</td>
+            <td class="headerCovTableEntryMed">85.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;chrono&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;numeric&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #ifndef M_PI</a>
+<a name="28"><span class="lineNum">      28 </span>            : #define M_PI           3.14159265358979323846</a>
+<a name="29"><span class="lineNum">      29 </span>            : #endif</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace isdb {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        112 : void MetainferenceBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        112 :   Action::registerKeywords(keys);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        112 :   ActionAtomistic::registerKeywords(keys);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        112 :   ActionWithValue::registerKeywords(keys);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        112 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        112 :   componentsAreNotOptional(keys);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        112 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        224 :   keys.addFlag(&quot;DOSCORE&quot;,false,&quot;activate metainference&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        224 :   keys.addFlag(&quot;NOENSEMBLE&quot;,false,&quot;don't perform any replica-averaging&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        224 :   keys.addFlag(&quot;REWEIGHT&quot;,false,&quot;simple REWEIGHT using the ARG as energy&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;AVERAGING&quot;, &quot;Stride for calculation of averaged weights and sigma_mean&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;NOISETYPE&quot;,&quot;MGAUSS&quot;,&quot;functional form of the noise (GAUSS,MGAUSS,OUTLIERS,MOUTLIERS,GENERIC)&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;LIKELIHOOD&quot;,&quot;GAUSS&quot;,&quot;the likelihood for the GENERIC metainference model, GAUSS or LOGN&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;DFTILDE&quot;,&quot;0.1&quot;,&quot;fraction of sigma_mean used to evolve ftilde&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        224 :   keys.addFlag(&quot;SCALEDATA&quot;,false,&quot;Set to TRUE if you want to sample a scaling factor common to all values and replicas&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;SCALE0&quot;,&quot;1.0&quot;,&quot;initial value of the scaling factor&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;SCALE_PRIOR&quot;,&quot;FLAT&quot;,&quot;either FLAT or GAUSSIAN&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;SCALE_MIN&quot;,&quot;minimum value of the scaling factor&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;SCALE_MAX&quot;,&quot;maximum value of the scaling factor&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;DSCALE&quot;,&quot;maximum MC move of the scaling factor&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        224 :   keys.addFlag(&quot;ADDOFFSET&quot;,false,&quot;Set to TRUE if you want to sample an offset common to all values and replicas&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET0&quot;,&quot;0.0&quot;,&quot;initial value of the offset&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET_PRIOR&quot;,&quot;FLAT&quot;,&quot;either FLAT or GAUSSIAN&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;OFFSET_MIN&quot;,&quot;minimum value of the offset&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;OFFSET_MAX&quot;,&quot;maximum value of the offset&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;DOFFSET&quot;,&quot;maximum MC move of the offset&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;REGRES_ZERO&quot;,&quot;stride for regression with zero offset&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA0&quot;,&quot;1.0&quot;,&quot;initial value of the uncertainty parameter&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA_MIN&quot;,&quot;0.0&quot;,&quot;minimum value of the uncertainty parameter&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA_MAX&quot;,&quot;10.&quot;,&quot;maximum value of the uncertainty parameter&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;DSIGMA&quot;,&quot;maximum MC move of the uncertainty parameter&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;OPTSIGMAMEAN&quot;,&quot;NONE&quot;,&quot;Set to NONE/SEM to manually set sigma mean, or to estimate it on the fly&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MEAN0&quot;,&quot;starting value for the uncertainty in the mean estimate&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MAX_STEPS&quot;, &quot;Number of steps used to optimise SIGMA_MAX, before that the SIGMA_MAX value is used&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - this is only needed if code doesn't pass the temperature to plumed&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;MC_STEPS&quot;,&quot;number of MC steps&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;MC_CHUNKSIZE&quot;,&quot;MC chunksize&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;STATUS_FILE&quot;,&quot;write a file with all the data useful for restart/continuation of Metainference&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        224 :   keys.add(&quot;compulsory&quot;,&quot;WRITE_STRIDE&quot;,&quot;10000&quot;,&quot;write the status to a file every N steps, this can be used for restart/continuation&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;SELECTOR&quot;,&quot;name of selector&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        224 :   keys.add(&quot;optional&quot;,&quot;NSELECT&quot;,&quot;range of values for selector [0, N-1]&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        112 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;score&quot;,        &quot;default&quot;,      &quot;the Metainference score&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;sigma&quot;,        &quot;default&quot;,      &quot;uncertainty parameter&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;sigmaMean&quot;,    &quot;default&quot;,      &quot;uncertainty in the mean estimate&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;neff&quot;,         &quot;default&quot;,      &quot;effective number of replicas&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;acceptSigma&quot;,  &quot;default&quot;,      &quot;MC acceptance for sigma values&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;acceptScale&quot;,  &quot;SCALEDATA&quot;,    &quot;MC acceptance for scale value&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;acceptFT&quot;,     &quot;GENERIC&quot;,      &quot;MC acceptance for general metainference f tilde value&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;weight&quot;,       &quot;REWEIGHT&quot;,     &quot;weights of the weighted average&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;biasDer&quot;,      &quot;REWEIGHT&quot;,     &quot;derivatives with respect to the bias&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;scale&quot;,        &quot;SCALEDATA&quot;,    &quot;scale parameter&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;offset&quot;,       &quot;ADDOFFSET&quot;,    &quot;offset parameter&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        224 :   keys.addOutputComponent(&quot;ftilde&quot;,       &quot;GENERIC&quot;,      &quot;ensemble average estimator&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        112 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         96 : MetainferenceBase::MetainferenceBase(const ActionOptions&amp;ao):</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   Action(ao),</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ActionAtomistic(ao),</a>
+<a name="93"><span class="lineNum">      93 </span>            :   ActionWithArguments(ao),</a>
+<a name="94"><span class="lineNum">      94 </span>            :   ActionWithValue(ao),</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         96 :   doscore_(false),</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         96 :   write_stride_(0),</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         96 :   narg(0),</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         96 :   doscale_(false),</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         96 :   scale_(1.),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         96 :   scale_mu_(0),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         96 :   scale_min_(1),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         96 :   scale_max_(-1),</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         96 :   Dscale_(-1),</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         96 :   dooffset_(false),</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         96 :   offset_(0.),</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         96 :   offset_mu_(0),</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         96 :   offset_min_(1),</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         96 :   offset_max_(-1),</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         96 :   Doffset_(-1),</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         96 :   doregres_zero_(false),</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         96 :   nregres_zero_(0),</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         96 :   Dftilde_(0.1),</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         96 :   random(3),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         96 :   MCsteps_(1),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         96 :   MCaccept_(0),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         96 :   MCacceptScale_(0),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         96 :   MCacceptFT_(0),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         96 :   MCtrial_(0),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         96 :   MCchunksize_(0),</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         96 :   firstTime(true),</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         96 :   do_reweight_(false),</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         96 :   do_optsigmamean_(0),</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         96 :   nsel_(1),</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         96 :   iselect(0),</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         96 :   optsigmamean_stride_(0),</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         96 :   N_optimized_step_(0),</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         96 :   optimized_step_(0),</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         96 :   sigmamax_opt_done_(false),</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         96 :   decay_w_(1.)</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : {</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         96 :   parseFlag(&quot;DOSCORE&quot;, doscore_);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         96 :   bool noensemble = false;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         96 :   parseFlag(&quot;NOENSEMBLE&quot;, noensemble);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // set up replica stuff</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         96 :   master = (comm.Get_rank()==0);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         96 :   if(master) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         61 :     nrep_    = multi_sim_comm.Get_size();</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         61 :     replica_ = multi_sim_comm.Get_rank();</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         61 :     if(noensemble) nrep_ = 1;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   } else {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         35 :     nrep_    = 0;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         35 :     replica_ = 0;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         96 :   comm.Sum(&amp;nrep_,1);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         96 :   comm.Sum(&amp;replica_,1);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         96 :   parse(&quot;SELECTOR&quot;, selector_);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        192 :   parse(&quot;NSELECT&quot;, nsel_);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   // do checks</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         96 :   if(selector_.length()&gt;0 &amp;&amp; nsel_&lt;=1) error(&quot;With SELECTOR active, NSELECT must be greater than 1&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         96 :   if(selector_.length()==0 &amp;&amp; nsel_&gt;1) error(&quot;With NSELECT greater than 1, you must specify SELECTOR&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   // initialise firstTimeW</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         96 :   firstTimeW.resize(nsel_, true);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            :   // reweight implies a different number of arguments (the latest one must always be the bias)</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         96 :   parseFlag(&quot;REWEIGHT&quot;, do_reweight_);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         96 :   if(do_reweight_&amp;&amp;getNumberOfArguments()!=1) error(&quot;To REWEIGHT one must provide one single bias as an argument&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         96 :   if(do_reweight_&amp;&amp;nrep_&lt;2) error(&quot;REWEIGHT can only be used in parallel with 2 or more replicas&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        191 :   if(!getRestart()) average_weights_.resize(nsel_, std::vector&lt;double&gt; (nrep_, 1./static_cast&lt;double&gt;(nrep_)));</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   else average_weights_.resize(nsel_, std::vector&lt;double&gt; (nrep_, 0.));</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         96 :   unsigned averaging=0;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         96 :   parse(&quot;AVERAGING&quot;, averaging);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         96 :   if(averaging&gt;0) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     decay_w_ = 1./static_cast&lt;double&gt; (averaging);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     optsigmamean_stride_ = averaging;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   std::string stringa_noise;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        192 :   parse(&quot;NOISETYPE&quot;,stringa_noise);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         96 :   if(stringa_noise==&quot;GAUSS&quot;)           noise_type_ = GAUSS;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         89 :   else if(stringa_noise==&quot;MGAUSS&quot;)     noise_type_ = MGAUSS;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         10 :   else if(stringa_noise==&quot;OUTLIERS&quot;)   noise_type_ = OUTLIERS;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          9 :   else if(stringa_noise==&quot;MOUTLIERS&quot;)  noise_type_ = MOUTLIERS;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :   else if(stringa_noise==&quot;GENERIC&quot;)    noise_type_ = GENERIC;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   else error(&quot;Unknown noise type!&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         96 :   if(noise_type_== GENERIC) {</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     std::string stringa_like;</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :     parse(&quot;LIKELIHOOD&quot;,stringa_like);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :     if(stringa_like==&quot;GAUSS&quot;) gen_likelihood_ = LIKE_GAUSS;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     else if(stringa_like==&quot;LOGN&quot;) gen_likelihood_ = LIKE_LOGN;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     else error(&quot;Unknown likelihood type!&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :     parse(&quot;DFTILDE&quot;,Dftilde_);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         96 :   parse(&quot;WRITE_STRIDE&quot;,write_stride_);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        192 :   parse(&quot;STATUS_FILE&quot;,status_file_name_);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        192 :   if(status_file_name_==&quot;&quot;) status_file_name_ = &quot;MISTATUS&quot;+getLabel();</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   else                      status_file_name_ = status_file_name_+getLabel();</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   std::string stringa_optsigma;</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        192 :   parse(&quot;OPTSIGMAMEAN&quot;, stringa_optsigma);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         96 :   if(stringa_optsigma==&quot;NONE&quot;)      do_optsigmamean_=0;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          4 :   else if(stringa_optsigma==&quot;SEM&quot;)  do_optsigmamean_=1;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :   else if(stringa_optsigma==&quot;SEM_MAX&quot;)  do_optsigmamean_=2;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         96 :   unsigned aver_max_steps=0;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         96 :   parse(&quot;SIGMA_MAX_STEPS&quot;, aver_max_steps);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         96 :   if(aver_max_steps==0&amp;&amp;do_optsigmamean_==2) aver_max_steps=averaging*2000;</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         96 :   if(aver_max_steps&gt;0&amp;&amp;do_optsigmamean_&lt;2) error(&quot;SIGMA_MAX_STEPS can only be used together with OPTSIGMAMEAN=SEM_MAX&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         96 :   if(aver_max_steps&gt;0&amp;&amp;do_optsigmamean_==2) N_optimized_step_=aver_max_steps;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         96 :   if(aver_max_steps&gt;0&amp;&amp;aver_max_steps&lt;averaging) error(&quot;SIGMA_MAX_STEPS must be greater than AVERAGING&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   std::vector&lt;double&gt; read_sigma_mean_;</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         96 :   parseVector(&quot;SIGMA_MEAN0&quot;,read_sigma_mean_);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         96 :   if(do_optsigmamean_==0 &amp;&amp; read_sigma_mean_.size()==0 &amp;&amp; !getRestart() &amp;&amp; doscore_)</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :     error(&quot;If you don't use OPTSIGMAMEAN and you are not RESTARTING then you MUST SET SIGMA_MEAN0&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         96 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         88 :     if(read_sigma_mean_.size()&gt;0) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         23 :       sigma_mean2_.resize(read_sigma_mean_.size());</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         46 :       for(unsigned i=0; i&lt;read_sigma_mean_.size(); i++) sigma_mean2_[i]=read_sigma_mean_[i]*read_sigma_mean_[i];</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     } else {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         65 :       sigma_mean2_.resize(1,0.000001);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :     }</a>
+<a name="221"><span class="lineNum">     221 </span>            :   } else {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          8 :     if(read_sigma_mean_.size()==1) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          8 :       sigma_mean2_.resize(1, read_sigma_mean_[0]*read_sigma_mean_[0]);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :     } else if(read_sigma_mean_.size()==0) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :       sigma_mean2_.resize(1, 0.000001);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :     } else {</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       error(&quot;If you want to use more than one SIGMA_MEAN0 you should use NOISETYPE=MGAUSS|MOUTLIERS&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         96 :   parseFlag(&quot;SCALEDATA&quot;, doscale_);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         96 :   if(doscale_) {</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     std::string stringa_noise;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         24 :     parse(&quot;SCALE_PRIOR&quot;,stringa_noise);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         12 :     if(stringa_noise==&quot;GAUSSIAN&quot;)  scale_prior_ = SC_GAUSS;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         12 :     else if(stringa_noise==&quot;FLAT&quot;) scale_prior_ = SC_FLAT;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :     else error(&quot;Unknown SCALE_PRIOR type!&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         12 :     parse(&quot;SCALE0&quot;,scale_);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         12 :     parse(&quot;DSCALE&quot;,Dscale_);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         12 :     if(Dscale_&lt;0.) error(&quot;DSCALE must be set when using SCALEDATA&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         12 :     if(scale_prior_==SC_GAUSS) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :       scale_mu_=scale_;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     } else {</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         12 :       parse(&quot;SCALE_MIN&quot;,scale_min_);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         12 :       parse(&quot;SCALE_MAX&quot;,scale_max_);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         12 :       if(scale_max_&lt;scale_min_) error(&quot;SCALE_MAX and SCALE_MIN must be set when using SCALE_PRIOR=FLAT&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :     }</a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         96 :   parseFlag(&quot;ADDOFFSET&quot;, dooffset_);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         96 :   if(dooffset_) {</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     std::string stringa_noise;</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          4 :     parse(&quot;OFFSET_PRIOR&quot;,stringa_noise);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          2 :     if(stringa_noise==&quot;GAUSSIAN&quot;)  offset_prior_ = SC_GAUSS;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          2 :     else if(stringa_noise==&quot;FLAT&quot;) offset_prior_ = SC_FLAT;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :     else error(&quot;Unknown OFFSET_PRIOR type!&quot;);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          2 :     parse(&quot;OFFSET0&quot;,offset_);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          2 :     parse(&quot;DOFFSET&quot;,Doffset_);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          2 :     if(offset_prior_==SC_GAUSS) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :       offset_mu_=offset_;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :       if(Doffset_&lt;0.) error(&quot;DOFFSET must be set when using OFFSET_PRIOR=GAUSS&quot;);</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :     } else {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          2 :       parse(&quot;OFFSET_MIN&quot;,offset_min_);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          2 :       parse(&quot;OFFSET_MAX&quot;,offset_max_);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          2 :       if(Doffset_&lt;0) Doffset_ = 0.05*(offset_max_ - offset_min_);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          2 :       if(offset_max_&lt;offset_min_) error(&quot;OFFSET_MAX and OFFSET_MIN must be set when using OFFSET_PRIOR=FLAT&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   // regression with zero intercept</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         96 :   parse(&quot;REGRES_ZERO&quot;, nregres_zero_);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         96 :   if(nregres_zero_&gt;0) {</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     // set flag</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :     doregres_zero_=true;</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :     // check if already sampling scale and offset</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     if(doscale_)  error(&quot;REGRES_ZERO and SCALEDATA are mutually exclusive&quot;);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :     if(dooffset_) error(&quot;REGRES_ZERO and ADDOFFSET are mutually exclusive&quot;);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :   }</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :   std::vector&lt;double&gt; readsigma;</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         96 :   parseVector(&quot;SIGMA0&quot;,readsigma);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         96 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma.size()&gt;1)</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         96 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         88 :     sigma_.resize(readsigma.size());</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         88 :     sigma_=readsigma;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          8 :   } else sigma_.resize(1, readsigma[0]);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   std::vector&lt;double&gt; readsigma_min;</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         96 :   parseVector(&quot;SIGMA_MIN&quot;,readsigma_min);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         96 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma_min.size()&gt;1)</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         96 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         88 :     sigma_min_.resize(readsigma_min.size());</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         88 :     sigma_min_=readsigma_min;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          8 :   } else sigma_min_.resize(1, readsigma_min[0]);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :   std::vector&lt;double&gt; readsigma_max;</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         96 :   parseVector(&quot;SIGMA_MAX&quot;,readsigma_max);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         96 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma_max.size()&gt;1)</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         96 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         88 :     sigma_max_.resize(readsigma_max.size());</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         88 :     sigma_max_=readsigma_max;</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          8 :   } else sigma_max_.resize(1, readsigma_max[0]);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         96 :   if(sigma_max_.size()!=sigma_min_.size()) error(&quot;The number of values for SIGMA_MIN and SIGMA_MAX must be the same&quot;);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            :   std::vector&lt;double&gt; read_dsigma;</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         96 :   parseVector(&quot;DSIGMA&quot;,read_dsigma);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         96 :   if((noise_type_!=MGAUSS&amp;&amp;noise_type_!=MOUTLIERS&amp;&amp;noise_type_!=GENERIC)&amp;&amp;readsigma_max.size()&gt;1)</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :     error(&quot;If you want to use more than one SIGMA you should use NOISETYPE=MGAUSS|MOUTLIERS|GENERIC&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         96 :   if(read_dsigma.size()&gt;0) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         31 :     Dsigma_.resize(read_dsigma.size());</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         31 :     Dsigma_=read_dsigma;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :   } else {</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         65 :     Dsigma_.resize(sigma_max_.size(), -1.);</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :     /* in this case Dsigma is initialised after reading the restart file if present */</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :   // monte carlo stuff</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         96 :   parse(&quot;MC_STEPS&quot;,MCsteps_);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         96 :   parse(&quot;MC_CHUNKSIZE&quot;, MCchunksize_);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   // get temperature</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         96 :   double temp=0.0;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         96 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         96 :   if(temp&gt;0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         65 :   else kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         96 :   if(kbt_==0.0&amp;&amp;doscore_) error(&quot;Unless the MD engine passes the temperature to plumed, you must specify it using TEMP&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            :   // initialize random seed</a>
+<a name="332"><span class="lineNum">     332 </span>            :   unsigned iseed;</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         96 :   if(master) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         61 :     auto ts = std::chrono::time_point_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::steady_clock::now()).time_since_epoch().count();</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         61 :     iseed = static_cast&lt;unsigned&gt;(ts)+replica_;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   } else {</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         35 :     iseed = 0;</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   }</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         96 :   comm.Sum(&amp;iseed, 1);</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :   // this is used for ftilde and sigma both the move and the acceptance</a>
+<a name="341"><span class="lineNum">     341 </span>            :   // this is different for each replica</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         96 :   random[0].setSeed(-iseed);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         96 :   if(doscale_||dooffset_) {</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :     // in this case we want the same seed everywhere</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         14 :     auto ts = std::chrono::time_point_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::steady_clock::now()).time_since_epoch().count();</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         14 :     iseed = static_cast&lt;unsigned&gt;(ts);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         14 :     if(master&amp;&amp;nrep_&gt;1) multi_sim_comm.Bcast(iseed,0);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         14 :     comm.Bcast(iseed,0);</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :     // this is used for scale and offset sampling and acceptance</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         14 :     random[1].setSeed(-iseed);</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :   }</a>
+<a name="352"><span class="lineNum">     352 </span>            :   // this is used for random chunk of sigmas, and it is different for each replica</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         96 :   if(master) {</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         61 :     auto ts = std::chrono::time_point_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::steady_clock::now()).time_since_epoch().count();</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         61 :     iseed = static_cast&lt;unsigned&gt;(ts)+replica_;</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :   } else {</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         35 :     iseed = 0;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   }</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         96 :   comm.Sum(&amp;iseed, 1);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         96 :   random[2].setSeed(-iseed);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   // outfile stuff</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         96 :   if(write_stride_&gt;0&amp;&amp;doscore_) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         31 :     sfile_.link(*this);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         31 :     sfile_.open(status_file_name_);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   }</a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         96 : }</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         96 : MetainferenceBase::~MetainferenceBase()</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : {</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         96 :   if(sfile_.isOpen()) sfile_.close();</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        480 : }</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         31 : void MetainferenceBase::Initialise(const unsigned input)</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : {</a>
+<a name="377"><span class="lineNum">     377 </span>            :   setNarg(input);</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         31 :   if(narg!=parameters.size()) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :     std::string num1; Tools::convert(parameters.size(),num1);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     std::string num2; Tools::convert(narg,num2);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :     std::string msg = &quot;The number of experimental values &quot; + num1 +&quot; must be the same of the calculated values &quot; + num2;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :     error(msg);</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :   }</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            :   // resize std::vector for sigma_mean history</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         31 :   sigma_mean2_last_.resize(nsel_);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         62 :   for(unsigned i=0; i&lt;nsel_; i++) sigma_mean2_last_[i].resize(narg);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         31 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         23 :     if(sigma_mean2_.size()==1) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         23 :       double tmp = sigma_mean2_[0];</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         23 :       sigma_mean2_.resize(narg, tmp);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :     } else if(sigma_mean2_.size()&gt;1&amp;&amp;sigma_mean2_.size()!=narg) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA_MEAN0 can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :     }</a>
+<a name="395"><span class="lineNum">     395 </span>            :     // set the initial value for the history</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       2516 :     for(unsigned i=0; i&lt;nsel_; i++) for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[i][j].push_back(sigma_mean2_[j]);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   } else {</a>
+<a name="398"><span class="lineNum">     398 </span>            :     // set the initial value for the history</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         43 :     for(unsigned i=0; i&lt;nsel_; i++) for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[i][j].push_back(sigma_mean2_[0]);</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :   }</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            :   // set sigma_bias</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         31 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         23 :     if(sigma_.size()==1) {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         23 :       double tmp = sigma_[0];</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         23 :       sigma_.resize(narg, tmp);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :     } else if(sigma_.size()&gt;1&amp;&amp;sigma_.size()!=narg) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA0 can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     }</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         23 :     if(sigma_min_.size()==1) {</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         23 :       double tmp = sigma_min_[0];</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         23 :       sigma_min_.resize(narg, tmp);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :     } else if(sigma_min_.size()&gt;1&amp;&amp;sigma_min_.size()!=narg) {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA_MIN can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :     }</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         23 :     if(sigma_max_.size()==1) {</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         23 :       double tmp = sigma_max_[0];</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         23 :       sigma_max_.resize(narg, tmp);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :     } else if(sigma_max_.size()&gt;1&amp;&amp;sigma_max_.size()!=narg) {</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :       error(&quot;SIGMA_MAX can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :     }</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         23 :     if(Dsigma_.size()==1) {</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         23 :       double tmp = Dsigma_[0];</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         23 :       Dsigma_.resize(narg, tmp);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :     } else if(Dsigma_.size()&gt;1&amp;&amp;Dsigma_.size()!=narg) {</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :       error(&quot;DSIGMA can accept either one single value or as many values as the number of arguments (with NOISETYPE=MGAUSS|MOUTLIERS|GENERIC)&quot;);</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :     }</a>
+<a name="428"><span class="lineNum">     428 </span>            :   }</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         31 :   sigma_max_est_.resize(sigma_max_.size(), 0.);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         31 :   IFile restart_sfile;</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         31 :   restart_sfile.link(*this);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         31 :   if(getRestart()&amp;&amp;restart_sfile.FileExist(status_file_name_)) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          1 :     firstTime = false;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          2 :     for(unsigned i=0; i&lt;nsel_; i++) firstTimeW[i] = false;</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          1 :     restart_sfile.open(status_file_name_);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          1 :     log.printf(&quot;  Restarting from %s\n&quot;, status_file_name_.c_str());</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     double dummy;</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          2 :     if(restart_sfile.scanField(&quot;time&quot;,dummy)) {</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :       // check for syncronisation</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          1 :       std::vector&lt;double&gt; dummy_time(nrep_,0);</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          1 :       if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :         dummy_time[replica_] = dummy;</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :         multi_sim_comm.Sum(dummy_time);</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :       }</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          1 :       comm.Sum(dummy_time);</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">          1 :       for(unsigned i=1; i&lt;nrep_; i++) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 :         std::string msg = &quot;METAINFERENCE restart files &quot; + status_file_name_ + &quot;  are not in sync&quot;;</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :         if(dummy_time[i]!=dummy_time[0]) plumed_merror(msg);</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :       }</a>
+<a name="452"><span class="lineNum">     452 </span>            :       // nsel</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">          2 :       for(unsigned i=0; i&lt;sigma_mean2_last_.size(); i++) {</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :         std::string msg_i;</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          1 :         Tools::convert(i,msg_i);</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :         // narg</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">          1 :         if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineNoCov">          0 :           for(unsigned j=0; j&lt;narg; ++j) {</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :             std::string msg_j;</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :             Tools::convert(j,msg_j);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :             std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :             double read_sm;</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :             restart_sfile.scanField(&quot;sigmaMean_&quot;+msg,read_sm);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :             sigma_mean2_last_[i][j][0] = read_sm*read_sm;</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :           }</a>
+<a name="466"><span class="lineNum">     466 </span>            :         }</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          1 :         if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :           double read_sm;</a>
+<a name="469"><span class="lineNum">     469 </span>            :           std::string msg_j;</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          1 :           Tools::convert(0,msg_j);</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          1 :           std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          1 :           restart_sfile.scanField(&quot;sigmaMean_&quot;+msg,read_sm);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          8 :           for(unsigned j=0; j&lt;narg; j++) sigma_mean2_last_[i][j][0] = read_sm*read_sm;</span></a>
+<a name="474"><span class="lineNum">     474 </span>            :         }</a>
+<a name="475"><span class="lineNum">     475 </span>            :       }</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          2 :       for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :         std::string msg;</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          1 :         Tools::convert(i,msg);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          2 :         restart_sfile.scanField(&quot;sigma_&quot;+msg,sigma_[i]);</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :       }</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          2 :       for(unsigned i=0; i&lt;sigma_max_.size(); ++i) {</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :         std::string msg;</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          1 :         Tools::convert(i,msg);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          1 :         restart_sfile.scanField(&quot;sigma_max_&quot;+msg,sigma_max_[i]);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          1 :         sigmamax_opt_done_=true;</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :       }</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          1 :       if(noise_type_==GENERIC) {</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;ftilde_.size(); ++i) {</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :           std::string msg;</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineNoCov">          0 :           Tools::convert(i,msg);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :           restart_sfile.scanField(&quot;ftilde_&quot;+msg,ftilde_[i]);</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :         }</a>
+<a name="494"><span class="lineNum">     494 </span>            :       }</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          1 :       restart_sfile.scanField(&quot;scale0_&quot;,scale_);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          1 :       restart_sfile.scanField(&quot;offset0_&quot;,offset_);</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          2 :       for(unsigned i=0; i&lt;nsel_; i++) {</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :         std::string msg;</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          1 :         Tools::convert(i,msg);</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :         double tmp_w;</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          1 :         restart_sfile.scanField(&quot;weight_&quot;+msg,tmp_w);</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          1 :         if(master) {</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          1 :           average_weights_[i][replica_] = tmp_w;</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          1 :           if(nrep_&gt;1) multi_sim_comm.Sum(&amp;average_weights_[i][0], nrep_);</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :         }</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          1 :         comm.Sum(&amp;average_weights_[i][0], nrep_);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :       }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            :     }</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">          1 :     restart_sfile.scanField();</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">          1 :     restart_sfile.close();</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :   }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :   /* If DSIGMA is not yet initialised do it now */</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_max_.size(); i++) if(Dsigma_[i]==-1) Dsigma_[i] = 0.05*(sigma_max_[i] - sigma_min_[i]);</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         31 :   addComponentWithDerivatives(&quot;score&quot;);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         31 :   componentIsNotPeriodic(&quot;score&quot;);</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         31 :   valueScore=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="521"><span class="lineNum">     521 </span>            : </a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         31 :   if(do_reweight_) {</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         22 :     addComponent(&quot;biasDer&quot;);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         22 :     componentIsNotPeriodic(&quot;biasDer&quot;);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         22 :     addComponent(&quot;weight&quot;);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         44 :     componentIsNotPeriodic(&quot;weight&quot;);</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :   }</a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         31 :   addComponent(&quot;neff&quot;);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         31 :   componentIsNotPeriodic(&quot;neff&quot;);</span></a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         31 :   if(doscale_ || doregres_zero_) {</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">         12 :     addComponent(&quot;scale&quot;);</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">         12 :     componentIsNotPeriodic(&quot;scale&quot;);</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         12 :     valueScale=getPntrToComponent(&quot;scale&quot;);</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :   }</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         31 :   if(dooffset_) {</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">          2 :     addComponent(&quot;offset&quot;);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">          2 :     componentIsNotPeriodic(&quot;offset&quot;);</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">          2 :     valueOffset=getPntrToComponent(&quot;offset&quot;);</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :   }</a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         31 :   if(dooffset_||doscale_) {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         14 :     addComponent(&quot;acceptScale&quot;);</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;acceptScale&quot;);</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         14 :     valueAcceptScale=getPntrToComponent(&quot;acceptScale&quot;);</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :   }</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         31 :   if(noise_type_==GENERIC) {</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          1 :     addComponent(&quot;acceptFT&quot;);</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          1 :     componentIsNotPeriodic(&quot;acceptFT&quot;);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          1 :     valueAcceptFT=getPntrToComponent(&quot;acceptFT&quot;);</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :   }</a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">         31 :   addComponent(&quot;acceptSigma&quot;);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         31 :   componentIsNotPeriodic(&quot;acceptSigma&quot;);</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         31 :   valueAccept=getPntrToComponent(&quot;acceptSigma&quot;);</span></a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         31 :   if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">       2493 :     for(unsigned i=0; i&lt;sigma_mean2_.size(); ++i) {</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">       2470 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">       4940 :       addComponent(&quot;sigmaMean-&quot;+num); componentIsNotPeriodic(&quot;sigmaMean-&quot;+num);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">       2470 :       valueSigmaMean.push_back(getPntrToComponent(&quot;sigmaMean-&quot;+num));</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">       2470 :       getPntrToComponent(&quot;sigmaMean-&quot;+num)-&gt;set(std::sqrt(sigma_mean2_[i]));</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">       4940 :       addComponent(&quot;sigma-&quot;+num); componentIsNotPeriodic(&quot;sigma-&quot;+num);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">       2470 :       valueSigma.push_back(getPntrToComponent(&quot;sigma-&quot;+num));</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">       2470 :       getPntrToComponent(&quot;sigma-&quot;+num)-&gt;set(sigma_[i]);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">       2470 :       if(noise_type_==GENERIC) {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">          4 :         addComponent(&quot;ftilde-&quot;+num); componentIsNotPeriodic(&quot;ftilde-&quot;+num);</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">          2 :         valueFtilde.push_back(getPntrToComponent(&quot;ftilde-&quot;+num));</span></a>
+<a name="572"><span class="lineNum">     572 </span>            :       }</a>
+<a name="573"><span class="lineNum">     573 </span>            :     }</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         23 :   } else {</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         16 :     addComponent(&quot;sigmaMean&quot;); componentIsNotPeriodic(&quot;sigmaMean&quot;);</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">          8 :     valueSigmaMean.push_back(getPntrToComponent(&quot;sigmaMean&quot;));</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">          8 :     getPntrToComponent(&quot;sigmaMean&quot;)-&gt;set(std::sqrt(sigma_mean2_[0]));</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         16 :     addComponent(&quot;sigma&quot;); componentIsNotPeriodic(&quot;sigma&quot;);</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          8 :     valueSigma.push_back(getPntrToComponent(&quot;sigma&quot;));</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         16 :     getPntrToComponent(&quot;sigma&quot;)-&gt;set(sigma_[0]);</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :   }</a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         31 :   switch(noise_type_) {</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">          1 :   case GENERIC:</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">          1 :     log.printf(&quot;  with general metainference &quot;);</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">          1 :     if(gen_likelihood_==LIKE_GAUSS) log.printf(&quot; and a gaussian likelihood\n&quot;);</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineNoCov">          0 :     else if(gen_likelihood_==LIKE_LOGN) log.printf(&quot; and a log-normal likelihood\n&quot;);</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">          1 :     log.printf(&quot;  ensemble average parameter sampled with a step %lf of sigma_mean\n&quot;, Dftilde_);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :     break;</a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">          7 :   case GAUSS:</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">          7 :     log.printf(&quot;  with gaussian noise and a single noise parameter for all the data\n&quot;);</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :     break;</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         14 :   case MGAUSS:</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         14 :     log.printf(&quot;  with gaussian noise and a noise parameter for each data point\n&quot;);</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :     break;</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">          1 :   case OUTLIERS:</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          1 :     log.printf(&quot;  with long tailed gaussian noise and a single noise parameter for all the data\n&quot;);</span></a>
+<a name="598"><span class="lineNum">     598 </span>            :     break;</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">          8 :   case MOUTLIERS:</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">          8 :     log.printf(&quot;  with long tailed gaussian noise and a noise parameter for each data point\n&quot;);</span></a>
+<a name="601"><span class="lineNum">     601 </span>            :     break;</a>
+<a name="602"><span class="lineNum">     602 </span>            :   }</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         31 :   if(doscale_) {</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :     // check that the scale value is the same for all replicas</a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">         12 :     std::vector&lt;double&gt; dummy_scale(nrep_,0);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         12 :     if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">          6 :       dummy_scale[replica_] = scale_;</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">          6 :       multi_sim_comm.Sum(dummy_scale);</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :     }</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         12 :     comm.Sum(dummy_scale);</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         24 :     for(unsigned i=1; i&lt;nrep_; i++) {</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">         12 :       std::string msg = &quot;The SCALE value must be the same for all replicas: check your input or restart file&quot;;</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         12 :       if(dummy_scale[i]!=dummy_scale[0]) plumed_merror(msg);</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :     }</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         12 :     log.printf(&quot;  sampling a common scaling factor with:\n&quot;);</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         12 :     log.printf(&quot;    initial scale parameter %f\n&quot;,scale_);</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         12 :     if(scale_prior_==SC_GAUSS) {</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :       log.printf(&quot;    gaussian prior with mean %f and width %f\n&quot;,scale_mu_,Dscale_);</span></a>
+<a name="620"><span class="lineNum">     620 </span>            :     }</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">         12 :     if(scale_prior_==SC_FLAT) {</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         12 :       log.printf(&quot;    flat prior between %f - %f\n&quot;,scale_min_,scale_max_);</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         12 :       log.printf(&quot;    maximum MC move of scale parameter %f\n&quot;,Dscale_);</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :     }</a>
+<a name="625"><span class="lineNum">     625 </span>            :   }</a>
+<a name="626"><span class="lineNum">     626 </span>            : </a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         31 :   if(dooffset_) {</span></a>
+<a name="628"><span class="lineNum">     628 </span>            :     // check that the offset value is the same for all replicas</a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">          2 :     std::vector&lt;double&gt; dummy_offset(nrep_,0);</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">          2 :     if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :       dummy_offset[replica_] = offset_;</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :       multi_sim_comm.Sum(dummy_offset);</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :     }</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">          2 :     comm.Sum(dummy_offset);</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">          2 :     for(unsigned i=1; i&lt;nrep_; i++) {</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :       std::string msg = &quot;The OFFSET value must be the same for all replicas: check your input or restart file&quot;;</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :       if(dummy_offset[i]!=dummy_offset[0]) plumed_merror(msg);</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :     }</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">          2 :     log.printf(&quot;  sampling a common offset with:\n&quot;);</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">          2 :     log.printf(&quot;    initial offset parameter %f\n&quot;,offset_);</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">          2 :     if(offset_prior_==SC_GAUSS) {</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :       log.printf(&quot;    gaussian prior with mean %f and width %f\n&quot;,offset_mu_,Doffset_);</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :     }</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">          2 :     if(offset_prior_==SC_FLAT) {</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">          2 :       log.printf(&quot;    flat prior between %f - %f\n&quot;,offset_min_,offset_max_);</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">          2 :       log.printf(&quot;    maximum MC move of offset parameter %f\n&quot;,Doffset_);</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :     }</a>
+<a name="648"><span class="lineNum">     648 </span>            :   }</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         31 :   if(doregres_zero_)</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 :     log.printf(&quot;  doing regression with zero intercept with stride: %d\n&quot;, nregres_zero_);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">         31 :   log.printf(&quot;  number of experimental data points %u\n&quot;,narg);</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">         31 :   log.printf(&quot;  number of replicas %u\n&quot;,nrep_);</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         31 :   log.printf(&quot;  initial data uncertainties&quot;);</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;, sigma_[i]);</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">         31 :   log.printf(&quot;  minimum data uncertainties&quot;);</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,sigma_min_[i]);</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         31 :   log.printf(&quot;  maximum data uncertainties&quot;);</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,sigma_max_[i]);</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         31 :   log.printf(&quot;  maximum MC move of data uncertainties&quot;);</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,Dsigma_[i]);</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         31 :   log.printf(&quot;  temperature of the system %f\n&quot;,kbt_);</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">         31 :   log.printf(&quot;  MC steps %u\n&quot;,MCsteps_);</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">         31 :   log.printf(&quot;  initial standard errors of the mean&quot;);</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_mean2_.size(); ++i) log.printf(&quot; %f&quot;, std::sqrt(sigma_mean2_[i]));</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">         31 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="672"><span class="lineNum">     672 </span>            : </a>
+<a name="673"><span class="lineNum">     673 </span>            :   //resize the number of metainference derivatives and the number of back-calculated data</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">         31 :   metader_.resize(narg, 0.);</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">         31 :   calc_data_.resize(narg, 0.);</span></a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         62 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Cavalli, Vendruscolo, Sci. Adv. 2, e150117 (2016)&quot;);</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         53 :   if(do_reweight_) log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Vendruscolo, Sci. Rep. 6, 31232 (2016)&quot;);</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">         35 :   if(do_optsigmamean_&gt;0) log&lt;&lt;plumed.cite(&quot;Loehr, Jussupow, Camilloni, J. Chem. Phys. 146, 165102 (2017)&quot;);</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         62 :   log&lt;&lt;plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;);</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         31 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         31 : }</span></a>
+<a name="683"><span class="lineNum">     683 </span>            : </a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineNoCov">          0 : void MetainferenceBase::Selector()</span></a>
+<a name="685"><span class="lineNum">     685 </span>            : {</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :   iselect = 0;</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :   // set the value of selector for  REM-like stuff</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :   if(selector_.length()&gt;0) iselect = static_cast&lt;unsigned&gt;(plumed.passMap[selector_]);</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         12 : double MetainferenceBase::getEnergySP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="692"><span class="lineNum">     692 </span>            :                                       const double scale, const double offset)</a>
+<a name="693"><span class="lineNum">     693 </span>            : {</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">         12 :   const double scale2 = scale*scale;</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">         12 :   const double sm2    = sigma_mean2_[0];</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">         12 :   const double ss2    = sigma[0]*sigma[0] + scale2*sm2;</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         12 :   const double sss    = sigma[0]*sigma[0] + sm2;</span></a>
+<a name="698"><span class="lineNum">     698 </span>            : </a>
+<a name="699"><span class="lineNum">     699 </span>            :   double ene = 0.0;</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         12 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="701"><span class="lineNum">     701 </span>            :   {</a>
+<a name="702"><span class="lineNum">     702 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="703"><span class="lineNum">     703 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="704"><span class="lineNum">     704 </span>            :       const double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="705"><span class="lineNum">     705 </span>            :       const double a2 = 0.5*dev*dev + ss2;</a>
+<a name="706"><span class="lineNum">     706 </span>            :       if(sm2 &gt; 0.0) {</a>
+<a name="707"><span class="lineNum">     707 </span>            :         ene += std::log(2.0*a2/(1.0-std::exp(-a2/sm2)));</a>
+<a name="708"><span class="lineNum">     708 </span>            :       }</a>
+<a name="709"><span class="lineNum">     709 </span>            :       else {</a>
+<a name="710"><span class="lineNum">     710 </span>            :         ene += std::log(2.0*a2);</a>
+<a name="711"><span class="lineNum">     711 </span>            :       }</a>
+<a name="712"><span class="lineNum">     712 </span>            :     }</a>
+<a name="713"><span class="lineNum">     713 </span>            :   }</a>
+<a name="714"><span class="lineNum">     714 </span>            :   // add one single Jeffrey's prior and one normalisation per data point</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">         12 :   ene += 0.5*std::log(sss) + static_cast&lt;double&gt;(narg)*0.5*std::log(0.5*M_PI*M_PI/ss2);</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">         12 :   if(doscale_ || doregres_zero_) ene += 0.5*std::log(sss);</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">         12 :   if(dooffset_) ene += 0.5*std::log(sss);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">         12 :   return kbt_ * ene;</span></a>
+<a name="719"><span class="lineNum">     719 </span>            : }</a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">       5328 : double MetainferenceBase::getEnergySPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="722"><span class="lineNum">     722 </span>            :                                        const double scale, const double offset)</a>
+<a name="723"><span class="lineNum">     723 </span>            : {</a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">       5328 :   const double scale2 = scale*scale;</span></a>
+<a name="725"><span class="lineNum">     725 </span>            :   double ene = 0.0;</a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">       5328 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="727"><span class="lineNum">     727 </span>            :   {</a>
+<a name="728"><span class="lineNum">     728 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="729"><span class="lineNum">     729 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="730"><span class="lineNum">     730 </span>            :       const double sm2 = sigma_mean2_[i];</a>
+<a name="731"><span class="lineNum">     731 </span>            :       const double ss2 = sigma[i]*sigma[i] + scale2*sm2;</a>
+<a name="732"><span class="lineNum">     732 </span>            :       const double sss = sigma[i]*sigma[i] + sm2;</a>
+<a name="733"><span class="lineNum">     733 </span>            :       const double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="734"><span class="lineNum">     734 </span>            :       const double a2  = 0.5*dev*dev + ss2;</a>
+<a name="735"><span class="lineNum">     735 </span>            :       if(sm2 &gt; 0.0) {</a>
+<a name="736"><span class="lineNum">     736 </span>            :         ene += 0.5*std::log(sss) + 0.5*std::log(0.5*M_PI*M_PI/ss2) + std::log(2.0*a2/(1.0-std::exp(-a2/sm2)));</a>
+<a name="737"><span class="lineNum">     737 </span>            :       }</a>
+<a name="738"><span class="lineNum">     738 </span>            :       else {</a>
+<a name="739"><span class="lineNum">     739 </span>            :         ene += 0.5*std::log(sss) + 0.5*std::log(0.5*M_PI*M_PI/ss2) + std::log(2.0*a2);</a>
+<a name="740"><span class="lineNum">     740 </span>            :       }</a>
+<a name="741"><span class="lineNum">     741 </span>            :       if(doscale_ || doregres_zero_)  ene += 0.5*std::log(sss);</a>
+<a name="742"><span class="lineNum">     742 </span>            :       if(dooffset_) ene += 0.5*std::log(sss);</a>
+<a name="743"><span class="lineNum">     743 </span>            :     }</a>
+<a name="744"><span class="lineNum">     744 </span>            :   }</a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">       5328 :   return kbt_ * ene;</span></a>
+<a name="746"><span class="lineNum">     746 </span>            : }</a>
+<a name="747"><span class="lineNum">     747 </span>            : </a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">         48 : double MetainferenceBase::getEnergyMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;ftilde, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="749"><span class="lineNum">     749 </span>            :     const double scale, const double offset)</a>
+<a name="750"><span class="lineNum">     750 </span>            : {</a>
+<a name="751"><span class="lineNum">     751 </span>            :   double ene = 0.0;</a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">         48 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="753"><span class="lineNum">     753 </span>            :   {</a>
+<a name="754"><span class="lineNum">     754 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="755"><span class="lineNum">     755 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="756"><span class="lineNum">     756 </span>            :       const double inv_sb2  = 1./(sigma[i]*sigma[i]);</a>
+<a name="757"><span class="lineNum">     757 </span>            :       const double inv_sm2  = 1./sigma_mean2_[i];</a>
+<a name="758"><span class="lineNum">     758 </span>            :       double devb = 0;</a>
+<a name="759"><span class="lineNum">     759 </span>            :       if(gen_likelihood_==LIKE_GAUSS)     devb = scale*ftilde[i]-parameters[i]+offset;</a>
+<a name="760"><span class="lineNum">     760 </span>            :       else if(gen_likelihood_==LIKE_LOGN) devb = std::log(scale*ftilde[i]/parameters[i]);</a>
+<a name="761"><span class="lineNum">     761 </span>            :       double devm = mean[i] - ftilde[i];</a>
+<a name="762"><span class="lineNum">     762 </span>            :       // deviation + normalisation + jeffrey</a>
+<a name="763"><span class="lineNum">     763 </span>            :       double normb = 0.;</a>
+<a name="764"><span class="lineNum">     764 </span>            :       if(gen_likelihood_==LIKE_GAUSS)     normb = -0.5*std::log(0.5/M_PI*inv_sb2);</a>
+<a name="765"><span class="lineNum">     765 </span>            :       else if(gen_likelihood_==LIKE_LOGN) normb = -0.5*std::log(0.5/M_PI*inv_sb2/(parameters[i]*parameters[i]));</a>
+<a name="766"><span class="lineNum">     766 </span>            :       const double normm         = -0.5*std::log(0.5/M_PI*inv_sm2);</a>
+<a name="767"><span class="lineNum">     767 </span>            :       const double jeffreys      = -0.5*std::log(2.*inv_sb2);</a>
+<a name="768"><span class="lineNum">     768 </span>            :       ene += 0.5*devb*devb*inv_sb2 + 0.5*devm*devm*inv_sm2 + normb + normm + jeffreys;</a>
+<a name="769"><span class="lineNum">     769 </span>            :       if(doscale_ || doregres_zero_)  ene += jeffreys;</a>
+<a name="770"><span class="lineNum">     770 </span>            :       if(dooffset_) ene += jeffreys;</a>
+<a name="771"><span class="lineNum">     771 </span>            :     }</a>
+<a name="772"><span class="lineNum">     772 </span>            :   }</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">         48 :   return kbt_ * ene;</span></a>
+<a name="774"><span class="lineNum">     774 </span>            : }</a>
+<a name="775"><span class="lineNum">     775 </span>            : </a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">        554 : double MetainferenceBase::getEnergyGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :                                       const double scale, const double offset)</a>
+<a name="778"><span class="lineNum">     778 </span>            : {</a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">        554 :   const double scale2  = scale*scale;</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">        554 :   const double inv_s2  = 1./(sigma[0]*sigma[0] + scale2*sigma_mean2_[0]);</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">        554 :   const double inv_sss = 1./(sigma[0]*sigma[0] + sigma_mean2_[0]);</span></a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            :   double ene = 0.0;</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">        554 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="785"><span class="lineNum">     785 </span>            :   {</a>
+<a name="786"><span class="lineNum">     786 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="787"><span class="lineNum">     787 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="788"><span class="lineNum">     788 </span>            :       double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="789"><span class="lineNum">     789 </span>            :       ene += 0.5*dev*dev*inv_s2;</a>
+<a name="790"><span class="lineNum">     790 </span>            :     }</a>
+<a name="791"><span class="lineNum">     791 </span>            :   }</a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">        554 :   const double normalisation = -0.5*std::log(0.5/M_PI*inv_s2);</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">        554 :   const double jeffreys = -0.5*std::log(2.*inv_sss);</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :   // add Jeffrey's prior in case one sigma for all data points + one normalisation per datapoint</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">        554 :   ene += jeffreys + static_cast&lt;double&gt;(narg)*normalisation;</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">        554 :   if(doscale_ || doregres_zero_)  ene += jeffreys;</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">        554 :   if(dooffset_) ene += jeffreys;</span></a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">        554 :   return kbt_ * ene;</span></a>
+<a name="800"><span class="lineNum">     800 </span>            : }</a>
+<a name="801"><span class="lineNum">     801 </span>            : </a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">        368 : double MetainferenceBase::getEnergyGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</span></a>
+<a name="803"><span class="lineNum">     803 </span>            :                                        const double scale, const double offset)</a>
+<a name="804"><span class="lineNum">     804 </span>            : {</a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">        368 :   const double scale2 = scale*scale;</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span>            :   double ene = 0.0;</a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">        368 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(ene)</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :   {</a>
+<a name="810"><span class="lineNum">     810 </span>            :     #pragma omp for reduction( + : ene)</a>
+<a name="811"><span class="lineNum">     811 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="812"><span class="lineNum">     812 </span>            :       const double inv_s2  = 1./(sigma[i]*sigma[i] + scale2*sigma_mean2_[i]);</a>
+<a name="813"><span class="lineNum">     813 </span>            :       const double inv_sss = 1./(sigma[i]*sigma[i] + sigma_mean2_[i]);</a>
+<a name="814"><span class="lineNum">     814 </span>            :       double dev = scale*mean[i]-parameters[i]+offset;</a>
+<a name="815"><span class="lineNum">     815 </span>            :       // deviation + normalisation + jeffrey</a>
+<a name="816"><span class="lineNum">     816 </span>            :       const double normalisation = -0.5*std::log(0.5/M_PI*inv_s2);</a>
+<a name="817"><span class="lineNum">     817 </span>            :       const double jeffreys      = -0.5*std::log(2.*inv_sss);</a>
+<a name="818"><span class="lineNum">     818 </span>            :       ene += 0.5*dev*dev*inv_s2 + normalisation + jeffreys;</a>
+<a name="819"><span class="lineNum">     819 </span>            :       if(doscale_ || doregres_zero_)  ene += jeffreys;</a>
+<a name="820"><span class="lineNum">     820 </span>            :       if(dooffset_) ene += jeffreys;</a>
+<a name="821"><span class="lineNum">     821 </span>            :     }</a>
+<a name="822"><span class="lineNum">     822 </span>            :   }</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">        368 :   return kbt_ * ene;</span></a>
+<a name="824"><span class="lineNum">     824 </span>            : }</a>
+<a name="825"><span class="lineNum">     825 </span>            : </a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         12 : void MetainferenceBase::moveTilde(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy)</span></a>
+<a name="827"><span class="lineNum">     827 </span>            : {</a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; new_ftilde(sigma_.size());</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">         12 :   new_ftilde = ftilde_;</span></a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span>            :   // change all tildes</a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">         36 :   for(unsigned j=0; j&lt;sigma_.size(); j++) {</span></a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">         24 :     const double r3 = random[0].Gaussian();</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">         24 :     const double ds3 = Dftilde_*std::sqrt(sigma_mean2_[j])*r3;</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">         24 :     new_ftilde[j] = ftilde_[j] + ds3;</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :   }</a>
+<a name="837"><span class="lineNum">     837 </span>            :   // calculate new energy</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">         12 :   double new_energy = getEnergyMIGEN(mean_,new_ftilde,sigma_,scale_,offset_);</span></a>
+<a name="839"><span class="lineNum">     839 </span>            : </a>
+<a name="840"><span class="lineNum">     840 </span>            :   // accept or reject</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">         12 :   const double delta = ( new_energy - old_energy ) / kbt_;</span></a>
+<a name="842"><span class="lineNum">     842 </span>            :   // if delta is negative always accept move</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         12 :   if( delta &lt;= 0.0 ) {</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">         12 :     old_energy = new_energy;</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">         12 :     ftilde_ = new_ftilde;</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">         12 :     MCacceptFT_++;</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :     // otherwise extract random number</a>
+<a name="848"><span class="lineNum">     848 </span>            :   } else {</a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :     const double s = random[0].RandU01();</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) {</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineNoCov">          0 :       old_energy = new_energy;</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineNoCov">          0 :       ftilde_ = new_ftilde;</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :       MCacceptFT_++;</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :     }</a>
+<a name="855"><span class="lineNum">     855 </span>            :   }</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">         12 : }</span></a>
+<a name="857"><span class="lineNum">     857 </span>            : </a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">       1848 : void MetainferenceBase::moveScaleOffset(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy)</span></a>
+<a name="859"><span class="lineNum">     859 </span>            : {</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">       1848 :   double new_scale = scale_;</span></a>
+<a name="861"><span class="lineNum">     861 </span>            : </a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">       1848 :   if(doscale_) {</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">       1824 :     if(scale_prior_==SC_FLAT) {</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">       1824 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">       1824 :       const double ds1 = Dscale_*r1;</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">       1824 :       new_scale += ds1;</span></a>
+<a name="867"><span class="lineNum">     867 </span>            :       // check boundaries</a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">       1824 :       if(new_scale &gt; scale_max_) {new_scale = 2.0 * scale_max_ - new_scale;}</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">       1824 :       if(new_scale &lt; scale_min_) {new_scale = 2.0 * scale_min_ - new_scale;}</span></a>
+<a name="870"><span class="lineNum">     870 </span>            :     } else {</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineNoCov">          0 :       const double ds1 = 0.5*(scale_mu_-new_scale)+Dscale_*std::exp(1)/M_PI*r1;</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineNoCov">          0 :       new_scale += ds1;</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :     }</a>
+<a name="875"><span class="lineNum">     875 </span>            :   }</a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">       1848 :   double new_offset = offset_;</span></a>
+<a name="878"><span class="lineNum">     878 </span>            : </a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">       1848 :   if(dooffset_) {</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">         24 :     if(offset_prior_==SC_FLAT) {</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">         24 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">         24 :       const double ds1 = Doffset_*r1;</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">         24 :       new_offset += ds1;</span></a>
+<a name="884"><span class="lineNum">     884 </span>            :       // check boundaries</a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">         24 :       if(new_offset &gt; offset_max_) {new_offset = 2.0 * offset_max_ - new_offset;}</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">         24 :       if(new_offset &lt; offset_min_) {new_offset = 2.0 * offset_min_ - new_offset;}</span></a>
+<a name="887"><span class="lineNum">     887 </span>            :     } else {</a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineNoCov">          0 :       const double r1 = random[1].Gaussian();</span></a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineNoCov">          0 :       const double ds1 = 0.5*(offset_mu_-new_offset)+Doffset_*std::exp(1)/M_PI*r1;</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineNoCov">          0 :       new_offset += ds1;</span></a>
+<a name="891"><span class="lineNum">     891 </span>            :     }</a>
+<a name="892"><span class="lineNum">     892 </span>            :   }</a>
+<a name="893"><span class="lineNum">     893 </span>            : </a>
+<a name="894"><span class="lineNum">     894 </span>            :   // calculate new energy</a>
+<a name="895"><span class="lineNum">     895 </span>            :   double new_energy = 0.;</a>
+<a name="896"><span class="lineNum">     896 </span>            : </a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">       1848 :   switch(noise_type_) {</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">         12 :   case GAUSS:</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">         12 :     new_energy = getEnergyGJ(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :     break;</a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">         48 :   case MGAUSS:</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">         48 :     new_energy = getEnergyGJE(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :     break;</a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineNoCov">          0 :   case OUTLIERS:</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineNoCov">          0 :     new_energy = getEnergySP(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :     break;</a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">       1776 :   case MOUTLIERS:</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">       1776 :     new_energy = getEnergySPE(mean_,sigma_,new_scale,new_offset);</span></a>
+<a name="909"><span class="lineNum">     909 </span>            :     break;</a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">         12 :     new_energy = getEnergyMIGEN(mean_,ftilde_,sigma_,new_scale,new_offset);</span></a>
+<a name="912"><span class="lineNum">     912 </span>            :     break;</a>
+<a name="913"><span class="lineNum">     913 </span>            :   }</a>
+<a name="914"><span class="lineNum">     914 </span>            : </a>
+<a name="915"><span class="lineNum">     915 </span>            :   // for the scale/offset we need to consider the total energy</a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">       1848 :   std::vector&lt;double&gt; totenergies(2);</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">       1848 :   if(master) {</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">        936 :     totenergies[0] = old_energy;</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">        936 :     totenergies[1] = new_energy;</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">        936 :     if(nrep_&gt;1) multi_sim_comm.Sum(totenergies);</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :   } else {</a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">        912 :     totenergies[0] = 0;</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">        912 :     totenergies[1] = 0;</span></a>
+<a name="924"><span class="lineNum">     924 </span>            :   }</a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">       1848 :   comm.Sum(totenergies);</span></a>
+<a name="926"><span class="lineNum">     926 </span>            : </a>
+<a name="927"><span class="lineNum">     927 </span>            :   // accept or reject</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">       1848 :   const double delta = ( totenergies[1] - totenergies[0] ) / kbt_;</span></a>
+<a name="929"><span class="lineNum">     929 </span>            :   // if delta is negative always accept move</a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">       1848 :   if( delta &lt;= 0.0 ) {</span></a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">       1848 :     old_energy = new_energy;</span></a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">       1848 :     scale_ = new_scale;</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">       1848 :     offset_ = new_offset;</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">       1848 :     MCacceptScale_++;</span></a>
+<a name="935"><span class="lineNum">     935 </span>            :     // otherwise extract random number</a>
+<a name="936"><span class="lineNum">     936 </span>            :   } else {</a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineNoCov">          0 :     double s = random[1].RandU01();</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) {</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineNoCov">          0 :       old_energy = new_energy;</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineNoCov">          0 :       scale_ = new_scale;</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineNoCov">          0 :       offset_ = new_offset;</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :       MCacceptScale_++;</span></a>
+<a name="943"><span class="lineNum">     943 </span>            :     }</a>
+<a name="944"><span class="lineNum">     944 </span>            :   }</a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">       1848 : }</span></a>
+<a name="946"><span class="lineNum">     946 </span>            : </a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">       2225 : void MetainferenceBase::moveSigmas(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy, const unsigned i, const std::vector&lt;unsigned&gt; &amp;indices, bool &amp;breaknow)</span></a>
+<a name="948"><span class="lineNum">     948 </span>            : {</a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">       2225 :   std::vector&lt;double&gt; new_sigma(sigma_.size());</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">       2225 :   new_sigma = sigma_;</span></a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span>            :   // change MCchunksize_ sigmas</a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">       2225 :   if (MCchunksize_ &gt; 0) {</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineNoCov">          0 :     if ((MCchunksize_ * i) &gt;= sigma_.size()) {</span></a>
+<a name="955"><span class="lineNum">     955 </span>            :       // This means we are not moving any sigma, so we should break immediately</a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineNoCov">          0 :       breaknow = true;</span></a>
+<a name="957"><span class="lineNum">     957 </span>            :     }</a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span>            :     // change random sigmas</a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;MCchunksize_; j++) {</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineNoCov">          0 :       const unsigned shuffle_index = j + MCchunksize_ * i;</span></a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineNoCov">          0 :       if (shuffle_index &gt;= sigma_.size()) {</span></a>
+<a name="963"><span class="lineNum">     963 </span>            :         // Going any further will segfault but we should still evaluate the sigmas we changed</a>
+<a name="964"><span class="lineNum">     964 </span>            :         break;</a>
+<a name="965"><span class="lineNum">     965 </span>            :       }</a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineNoCov">          0 :       const unsigned index = indices[shuffle_index];</span></a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineNoCov">          0 :       const double r2 = random[0].Gaussian();</span></a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineNoCov">          0 :       const double ds2 = Dsigma_[index]*r2;</span></a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineNoCov">          0 :       new_sigma[index] = sigma_[index] + ds2;</span></a>
+<a name="970"><span class="lineNum">     970 </span>            :       // check boundaries</a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineNoCov">          0 :       if(new_sigma[index] &gt; sigma_max_[index]) {new_sigma[index] = 2.0 * sigma_max_[index] - new_sigma[index];}</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineNoCov">          0 :       if(new_sigma[index] &lt; sigma_min_[index]) {new_sigma[index] = 2.0 * sigma_min_[index] - new_sigma[index];}</span></a>
+<a name="973"><span class="lineNum">     973 </span>            :     }</a>
+<a name="974"><span class="lineNum">     974 </span>            :   } else {</a>
+<a name="975"><span class="lineNum">     975 </span>            :     // change all sigmas</a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">      13486 :     for(unsigned j=0; j&lt;sigma_.size(); j++) {</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">      11261 :       const double r2 = random[0].Gaussian();</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">      11261 :       const double ds2 = Dsigma_[j]*r2;</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">      11261 :       new_sigma[j] = sigma_[j] + ds2;</span></a>
+<a name="980"><span class="lineNum">     980 </span>            :       // check boundaries</a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">      11261 :       if(new_sigma[j] &gt; sigma_max_[j]) {new_sigma[j] = 2.0 * sigma_max_[j] - new_sigma[j];}</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">      11261 :       if(new_sigma[j] &lt; sigma_min_[j]) {new_sigma[j] = 2.0 * sigma_min_[j] - new_sigma[j];}</span></a>
+<a name="983"><span class="lineNum">     983 </span>            :     }</a>
+<a name="984"><span class="lineNum">     984 </span>            :   }</a>
+<a name="985"><span class="lineNum">     985 </span>            : </a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">       2225 :   if (breaknow) {</span></a>
+<a name="987"><span class="lineNum">     987 </span>            :     // We didnt move any sigmas, so no sense in evaluating anything</a>
+<a name="988"><span class="lineNum">     988 </span>            :     return;</a>
+<a name="989"><span class="lineNum">     989 </span>            :   }</a>
+<a name="990"><span class="lineNum">     990 </span>            : </a>
+<a name="991"><span class="lineNum">     991 </span>            :   // calculate new energy</a>
+<a name="992"><span class="lineNum">     992 </span>            :   double new_energy = 0.;</a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">       2225 :   switch(noise_type_) {</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">        271 :   case GAUSS:</span></a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">        271 :     new_energy = getEnergyGJ(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="996"><span class="lineNum">     996 </span>            :     break;</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">        160 :   case MGAUSS:</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">        160 :     new_energy = getEnergyGJE(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="999"><span class="lineNum">     999 </span>            :     break;</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">          6 :   case OUTLIERS:</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">          6 :     new_energy = getEnergySP(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            :     break;</a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">       1776 :   case MOUTLIERS:</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">       1776 :     new_energy = getEnergySPE(mean_,new_sigma,scale_,offset_);</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            :     break;</a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">         12 :     new_energy = getEnergyMIGEN(mean_,ftilde_,new_sigma,scale_,offset_);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            :     break;</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   }</a>
+<a name="1010"><span class="lineNum">    1010 </span>            : </a>
+<a name="1011"><span class="lineNum">    1011 </span>            :   // accept or reject</a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">       2225 :   const double delta = ( new_energy - old_energy ) / kbt_;</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :   // if delta is negative always accept move</a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">       2225 :   if( delta &lt;= 0.0 ) {</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">       2225 :     old_energy = new_energy;</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">       2225 :     sigma_ = new_sigma;</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">       2225 :     MCaccept_++;</span></a>
+<a name="1018"><span class="lineNum">    1018 </span>            :     // otherwise extract random number</a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   } else {</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineNoCov">          0 :     const double s = random[0].RandU01();</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) {</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineNoCov">          0 :       old_energy = new_energy;</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineNoCov">          0 :       sigma_ = new_sigma;</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineNoCov">          0 :       MCaccept_++;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :     }</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :   }</a>
+<a name="1027"><span class="lineNum">    1027 </span>            : }</a>
+<a name="1028"><span class="lineNum">    1028 </span>            : </a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">       2225 : double MetainferenceBase::doMonteCarlo(const std::vector&lt;double&gt; &amp;mean_)</span></a>
+<a name="1030"><span class="lineNum">    1030 </span>            : {</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   // calculate old energy with the updated coordinates</a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">       2225 :   double old_energy=0.;</span></a>
+<a name="1033"><span class="lineNum">    1033 </span>            : </a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">       2225 :   switch(noise_type_) {</span></a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">        271 :   case GAUSS:</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">        271 :     old_energy = getEnergyGJ(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">        271 :     break;</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">        160 :   case MGAUSS:</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">        160 :     old_energy = getEnergyGJE(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">        160 :     break;</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">          6 :   case OUTLIERS:</span></a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">          6 :     old_energy = getEnergySP(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">          6 :     break;</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">       1776 :   case MOUTLIERS:</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">       1776 :     old_energy = getEnergySPE(mean_,sigma_,scale_,offset_);</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">       1776 :     break;</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">         12 :     old_energy = getEnergyMIGEN(mean_,ftilde_,sigma_,scale_,offset_);</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">         12 :     break;</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :   }</a>
+<a name="1051"><span class="lineNum">    1051 </span>            : </a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   // do not run MC if this is a replica-exchange trial</a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">       2225 :   if(!getExchangeStep()) {</span></a>
+<a name="1054"><span class="lineNum">    1054 </span>            : </a>
+<a name="1055"><span class="lineNum">    1055 </span>            :     // Create std::vector of random sigma indices</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :     std::vector&lt;unsigned&gt; indices;</a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">       2225 :     if (MCchunksize_ &gt; 0) {</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineNoCov">          0 :       for (unsigned j=0; j&lt;sigma_.size(); j++) {</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineNoCov">          0 :         indices.push_back(j);</span></a>
+<a name="1060"><span class="lineNum">    1060 </span>            :       }</a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineNoCov">          0 :       random[2].Shuffle(indices);</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     }</a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">       2225 :     bool breaknow = false;</span></a>
+<a name="1064"><span class="lineNum">    1064 </span>            : </a>
+<a name="1065"><span class="lineNum">    1065 </span>            :     // cycle on MC steps</a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">       4450 :     for(unsigned i=0; i&lt;MCsteps_; ++i) {</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">       2225 :       MCtrial_++;</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            :       // propose move for ftilde</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">       2225 :       if(noise_type_==GENERIC) moveTilde(mean_, old_energy);</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            :       // propose move for scale and/or offset</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">       2225 :       if(doscale_||dooffset_) moveScaleOffset(mean_, old_energy);</span></a>
+<a name="1072"><span class="lineNum">    1072 </span>            :       // propose move for sigma</a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">       2225 :       moveSigmas(mean_, old_energy, i, indices, breaknow);</span></a>
+<a name="1074"><span class="lineNum">    1074 </span>            :       // exit from the loop if this is the case</a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">       2225 :       if(breaknow) break;</span></a>
+<a name="1076"><span class="lineNum">    1076 </span>            :     }</a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     /* save the result of the sampling */</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     /* ftilde */</a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">       2225 :     if(noise_type_==GENERIC) {</span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">         12 :       double accept = static_cast&lt;double&gt;(MCacceptFT_) / static_cast&lt;double&gt;(MCtrial_);</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">         12 :       valueAcceptFT-&gt;set(accept);</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">         36 :       for(unsigned i=0; i&lt;sigma_.size(); i++) valueFtilde[i]-&gt;set(ftilde_[i]);</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :     }</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     /* scale and offset */</a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">       2225 :     if(doscale_ || doregres_zero_) valueScale-&gt;set(scale_);</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">       2225 :     if(dooffset_) valueOffset-&gt;set(offset_);</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">       2225 :     if(doscale_||dooffset_) {</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">       1848 :       double accept = static_cast&lt;double&gt;(MCacceptScale_) / static_cast&lt;double&gt;(MCtrial_);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineCov">       1848 :       valueAcceptScale-&gt;set(accept);</span></a>
+<a name="1091"><span class="lineNum">    1091 </span>            :     }</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :     /* sigmas */</a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">      13486 :     for(unsigned i=0; i&lt;sigma_.size(); i++) valueSigma[i]-&gt;set(sigma_[i]);</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineCov">       2225 :     double accept = static_cast&lt;double&gt;(MCaccept_) / static_cast&lt;double&gt;(MCtrial_);</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">       2225 :     valueAccept-&gt;set(accept);</span></a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   }</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : </a>
+<a name="1098"><span class="lineNum">    1098 </span>            :   // here we sum the score over the replicas to get the full metainference score that we save as a bias</a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">       2225 :   if(master) {</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">       1227 :     if(nrep_&gt;1) multi_sim_comm.Sum(old_energy);</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            :   } else {</a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">        998 :     old_energy=0;</span></a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   }</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">       2225 :   comm.Sum(old_energy);</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            : </a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   // this is the energy with current coordinates and parameters</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">       2225 :   return old_energy;</span></a>
+<a name="1108"><span class="lineNum">    1108 </span>            : }</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span>            : /*</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :    In the following energy-force functions we don't add the normalisation and the jeffreys priors</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :    because they are not needed for the forces, the correct MetaInference energy is the one calculated</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :    in the Monte-Carlo</a>
+<a name="1114"><span class="lineNum">    1114 </span>            : */</a>
+<a name="1115"><span class="lineNum">    1115 </span>            : </a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">          6 : void MetainferenceBase::getEnergyForceSP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1118"><span class="lineNum">    1118 </span>            : {</a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">          6 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">          6 :   const double sm2    = sigma_mean2_[0];</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">          6 :   const double ss2    = sigma_[0]*sigma_[0] + scale2*sm2;</span></a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">          6 :   std::vector&lt;double&gt; f(narg,0);</span></a>
+<a name="1123"><span class="lineNum">    1123 </span>            : </a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">          6 :   if(master) {</span></a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">          6 :     #pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="1126"><span class="lineNum">    1126 </span>            :     {</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :       #pragma omp for</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :       for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1129"><span class="lineNum">    1129 </span>            :         const double dev = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :         const double a2 = 0.5*dev*dev + ss2;</a>
+<a name="1131"><span class="lineNum">    1131 </span>            :         if(sm2 &gt; 0.0) {</a>
+<a name="1132"><span class="lineNum">    1132 </span>            :           const double t = std::exp(-a2/sm2);</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :           const double dt = 1./t;</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :           const double dit = 1./(1.-dt);</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :           f[i] = -scale_*dev*(dit/sm2 + 1./a2);</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :         }</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :         else {</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :           f[i] = -scale_*dev*(1./a2);</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :         }</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :       }</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :     }</a>
+<a name="1142"><span class="lineNum">    1142 </span>            :     // collect contribution to forces and energy from other replicas</a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">          6 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   // intra-replica summation</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">          6 :   comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1147"><span class="lineNum">    1147 </span>            : </a>
+<a name="1148"><span class="lineNum">    1148 </span>            :   double w_tmp = 0.;</a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">         48 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">         42 :     setMetaDer(i, -kbt_*f[i]*dmean_x[i]);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">         42 :     w_tmp += kbt_*f[i]*dmean_b[i];</span></a>
+<a name="1152"><span class="lineNum">    1152 </span>            :   }</a>
+<a name="1153"><span class="lineNum">    1153 </span>            : </a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">          6 :   if(do_reweight_) {</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineNoCov">          0 :     setArgDerivatives(valueScore, -w_tmp);</span></a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(-w_tmp);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span>            :   }</a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">          6 : }</span></a>
+<a name="1159"><span class="lineNum">    1159 </span>            : </a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">       1776 : void MetainferenceBase::getEnergyForceSPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1161"><span class="lineNum">    1161 </span>            :     const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1162"><span class="lineNum">    1162 </span>            : {</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">       1776 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">       1776 :   std::vector&lt;double&gt; f(narg,0);</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            : </a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">       1776 :   if(master) {</span></a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">        888 :     #pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :     {</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :       #pragma omp for</a>
+<a name="1170"><span class="lineNum">    1170 </span>            :       for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1171"><span class="lineNum">    1171 </span>            :         const double sm2 = sigma_mean2_[i];</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :         const double ss2 = sigma_[i]*sigma_[i] + scale2*sm2;</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :         const double dev = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1174"><span class="lineNum">    1174 </span>            :         const double a2  = 0.5*dev*dev + ss2;</a>
+<a name="1175"><span class="lineNum">    1175 </span>            :         if(sm2 &gt; 0.0) {</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :           const double t   = std::exp(-a2/sm2);</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :           const double dt  = 1./t;</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :           const double dit = 1./(1.-dt);</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :           f[i] = -scale_*dev*(dit/sm2 + 1./a2);</a>
+<a name="1180"><span class="lineNum">    1180 </span>            :         }</a>
+<a name="1181"><span class="lineNum">    1181 </span>            :         else {</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :           f[i] = -scale_*dev*(1./a2);</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :         }</a>
+<a name="1184"><span class="lineNum">    1184 </span>            :       }</a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     }</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :     // collect contribution to forces and energy from other replicas</a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">        888 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :   }</a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">       1776 :   comm.Sum(&amp;f[0],narg);</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            : </a>
+<a name="1191"><span class="lineNum">    1191 </span>            :   double w_tmp = 0.;</a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineCov">       8880 :   for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineCov">       7104 :     setMetaDer(i, -kbt_ * dmean_x[i] * f[i]);</span></a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineCov">       7104 :     w_tmp += kbt_ * dmean_b[i] *f[i];</span></a>
+<a name="1195"><span class="lineNum">    1195 </span>            :   }</a>
+<a name="1196"><span class="lineNum">    1196 </span>            : </a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineCov">       1776 :   if(do_reweight_) {</span></a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineCov">       1776 :     setArgDerivatives(valueScore, -w_tmp);</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineCov">       3552 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(-w_tmp);</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            :   }</a>
+<a name="1201"><span class="lineNum">    1201 </span><span class="lineCov">       1776 : }</span></a>
+<a name="1202"><span class="lineNum">    1202 </span>            : </a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineCov">        271 : void MetainferenceBase::getEnergyForceGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1204"><span class="lineNum">    1204 </span>            :     const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1205"><span class="lineNum">    1205 </span>            : {</a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">        271 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">        271 :   double inv_s2=0.;</span></a>
+<a name="1208"><span class="lineNum">    1208 </span>            : </a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">        271 :   if(master) {</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">        229 :     inv_s2 = 1./(sigma_[0]*sigma_[0] + scale2*sigma_mean2_[0]);</span></a>
+<a name="1211"><span class="lineNum">    1211 </span><span class="lineCov">        229 :     if(nrep_&gt;1) multi_sim_comm.Sum(inv_s2);</span></a>
+<a name="1212"><span class="lineNum">    1212 </span>            :   }</a>
+<a name="1213"><span class="lineNum">    1213 </span><span class="lineCov">        271 :   comm.Sum(inv_s2);</span></a>
+<a name="1214"><span class="lineNum">    1214 </span>            : </a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineCov">        271 :   double w_tmp = 0.;</span></a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineCov">        271 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(w_tmp)</span></a>
+<a name="1217"><span class="lineNum">    1217 </span>            :   {</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :     #pragma omp for reduction( + : w_tmp)</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :       const double dev = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :       const double mult = dev*scale_*inv_s2;</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :       setMetaDer(i, kbt_*dmean_x[i]*mult);</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :       w_tmp += kbt_*dmean_b[i]*mult;</a>
+<a name="1224"><span class="lineNum">    1224 </span>            :     }</a>
+<a name="1225"><span class="lineNum">    1225 </span>            :   }</a>
+<a name="1226"><span class="lineNum">    1226 </span>            : </a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">        271 :   if(do_reweight_) {</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">         84 :     setArgDerivatives(valueScore, w_tmp);</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">        168 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(w_tmp);</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   }</a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">        271 : }</span></a>
+<a name="1232"><span class="lineNum">    1232 </span>            : </a>
+<a name="1233"><span class="lineNum">    1233 </span><span class="lineCov">        160 : void MetainferenceBase::getEnergyForceGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x,</span></a>
+<a name="1234"><span class="lineNum">    1234 </span>            :     const std::vector&lt;double&gt; &amp;dmean_b)</a>
+<a name="1235"><span class="lineNum">    1235 </span>            : {</a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineCov">        160 :   const double scale2 = scale_*scale_;</span></a>
+<a name="1237"><span class="lineNum">    1237 </span><span class="lineCov">        160 :   std::vector&lt;double&gt; inv_s2(sigma_.size(),0.);</span></a>
+<a name="1238"><span class="lineNum">    1238 </span>            : </a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineCov">        160 :   if(master) {</span></a>
+<a name="1240"><span class="lineNum">    1240 </span><span class="lineCov">       2044 :     for(unsigned i=0; i&lt;sigma_.size(); ++i) inv_s2[i] = 1./(sigma_[i]*sigma_[i] + scale2*sigma_mean2_[i]);</span></a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineCov">         92 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;inv_s2[0],sigma_.size());</span></a>
+<a name="1242"><span class="lineNum">    1242 </span>            :   }</a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">        160 :   comm.Sum(&amp;inv_s2[0],sigma_.size());</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            : </a>
+<a name="1245"><span class="lineNum">    1245 </span><span class="lineCov">        160 :   double w_tmp = 0.;</span></a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">        160 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(w_tmp)</span></a>
+<a name="1247"><span class="lineNum">    1247 </span>            :   {</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :     #pragma omp for reduction( + : w_tmp)</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1250"><span class="lineNum">    1250 </span>            :       const double dev  = scale_*mean[i]-parameters[i]+offset_;</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :       const double mult = dev*scale_*inv_s2[i];</a>
+<a name="1252"><span class="lineNum">    1252 </span>            :       setMetaDer(i, kbt_*dmean_x[i]*mult);</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :       w_tmp += kbt_*dmean_b[i]*mult;</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :     }</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :   }</a>
+<a name="1256"><span class="lineNum">    1256 </span>            : </a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">        160 :   if(do_reweight_) {</span></a>
+<a name="1258"><span class="lineNum">    1258 </span><span class="lineCov">         76 :     setArgDerivatives(valueScore, w_tmp);</span></a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineCov">        152 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(w_tmp);</span></a>
+<a name="1260"><span class="lineNum">    1260 </span>            :   }</a>
+<a name="1261"><span class="lineNum">    1261 </span><span class="lineCov">        160 : }</span></a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">         12 : void MetainferenceBase::getEnergyForceMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b)</span></a>
+<a name="1264"><span class="lineNum">    1264 </span>            : {</a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; inv_s2(sigma_.size(),0.);</span></a>
+<a name="1266"><span class="lineNum">    1266 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; dev(sigma_.size(),0.);</span></a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; dev2(sigma_.size(),0.);</span></a>
+<a name="1268"><span class="lineNum">    1268 </span>            : </a>
+<a name="1269"><span class="lineNum">    1269 </span><span class="lineCov">         36 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineCov">         24 :     inv_s2[i]   = 1./sigma_mean2_[i];</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">         24 :     if(master) {</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineCov">         24 :       dev[i]  = (mean[i]-ftilde_[i]);</span></a>
+<a name="1273"><span class="lineNum">    1273 </span><span class="lineCov">         24 :       dev2[i] = dev[i]*dev[i];</span></a>
+<a name="1274"><span class="lineNum">    1274 </span>            :     }</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :   }</a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">         12 :   if(master&amp;&amp;nrep_&gt;1) {</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineNoCov">          0 :     multi_sim_comm.Sum(&amp;dev[0],dev.size());</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineNoCov">          0 :     multi_sim_comm.Sum(&amp;dev2[0],dev2.size());</span></a>
+<a name="1279"><span class="lineNum">    1279 </span>            :   }</a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">         12 :   comm.Sum(&amp;dev[0],dev.size());</span></a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">         12 :   comm.Sum(&amp;dev2[0],dev2.size());</span></a>
+<a name="1282"><span class="lineNum">    1282 </span>            : </a>
+<a name="1283"><span class="lineNum">    1283 </span><span class="lineCov">         12 :   double dene_b = 0.;</span></a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">         12 :   #pragma omp parallel num_threads(OpenMP::getNumThreads()) shared(dene_b)</span></a>
+<a name="1285"><span class="lineNum">    1285 </span>            :   {</a>
+<a name="1286"><span class="lineNum">    1286 </span>            :     #pragma omp for reduction( + : dene_b)</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :     for(unsigned i=0; i&lt;narg; ++i) {</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :       const double dene_x  = kbt_*inv_s2[i]*dmean_x[i]*dev[i];</a>
+<a name="1289"><span class="lineNum">    1289 </span>            :       dene_b += kbt_*inv_s2[i]*dmean_b[i]*dev[i];</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :       setMetaDer(i, dene_x);</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     }</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :   }</a>
+<a name="1293"><span class="lineNum">    1293 </span>            : </a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineCov">         12 :   if(do_reweight_) {</span></a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineNoCov">          0 :     setArgDerivatives(valueScore, dene_b);</span></a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;biasDer&quot;)-&gt;set(dene_b);</span></a>
+<a name="1297"><span class="lineNum">    1297 </span>            :   }</a>
+<a name="1298"><span class="lineNum">    1298 </span><span class="lineCov">         12 : }</span></a>
+<a name="1299"><span class="lineNum">    1299 </span>            : </a>
+<a name="1300"><span class="lineNum">    1300 </span><span class="lineCov">       2225 : void MetainferenceBase::get_weights(double &amp;weight, double &amp;norm, double &amp;neff)</span></a>
+<a name="1301"><span class="lineNum">    1301 </span>            : {</a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineCov">       2225 :   const double dnrep = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="1303"><span class="lineNum">    1303 </span>            :   // calculate the weights either from BIAS</a>
+<a name="1304"><span class="lineNum">    1304 </span><span class="lineCov">       2225 :   if(do_reweight_) {</span></a>
+<a name="1305"><span class="lineNum">    1305 </span><span class="lineCov">       1936 :     std::vector&lt;double&gt; bias(nrep_,0);</span></a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">       1936 :     if(master) {</span></a>
+<a name="1307"><span class="lineNum">    1307 </span><span class="lineCov">        980 :       bias[replica_] = getArgument(0);</span></a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">        980 :       if(nrep_&gt;1) multi_sim_comm.Sum(&amp;bias[0], nrep_);</span></a>
+<a name="1309"><span class="lineNum">    1309 </span>            :     }</a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineCov">       1936 :     comm.Sum(&amp;bias[0], nrep_);</span></a>
+<a name="1311"><span class="lineNum">    1311 </span>            : </a>
+<a name="1312"><span class="lineNum">    1312 </span>            :     // accumulate weights</a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineCov">       1936 :     if(!firstTimeW[iselect]) {</span></a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineCov">       5742 :       for(unsigned i=0; i&lt;nrep_; ++i) {</span></a>
+<a name="1315"><span class="lineNum">    1315 </span><span class="lineCov">       3828 :         const double delta=bias[i]-average_weights_[iselect][i];</span></a>
+<a name="1316"><span class="lineNum">    1316 </span><span class="lineCov">       3828 :         average_weights_[iselect][i]+=decay_w_*delta;</span></a>
+<a name="1317"><span class="lineNum">    1317 </span>            :       }</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :     } else {</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :       firstTimeW[iselect] = false;</a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">         66 :       for(unsigned i=0; i&lt;nrep_; ++i) average_weights_[iselect][i] = bias[i];</span></a>
+<a name="1321"><span class="lineNum">    1321 </span>            :     }</a>
+<a name="1322"><span class="lineNum">    1322 </span>            : </a>
+<a name="1323"><span class="lineNum">    1323 </span>            :     // set average back into bias and set norm to one</a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">       1936 :     const double maxbias = *(std::max_element(average_weights_[iselect].begin(), average_weights_[iselect].end()));</span></a>
+<a name="1325"><span class="lineNum">    1325 </span><span class="lineCov">       5808 :     for(unsigned i=0; i&lt;nrep_; ++i) bias[i] = std::exp((average_weights_[iselect][i]-maxbias)/kbt_);</span></a>
+<a name="1326"><span class="lineNum">    1326 </span>            :     // set local weight, norm and weight variance</a>
+<a name="1327"><span class="lineNum">    1327 </span><span class="lineCov">       1936 :     weight = bias[replica_];</span></a>
+<a name="1328"><span class="lineNum">    1328 </span>            :     double w2=0.;</a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineCov">       5808 :     for(unsigned i=0; i&lt;nrep_; ++i) {</span></a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">       3872 :       w2 += bias[i]*bias[i];</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineCov">       3872 :       norm += bias[i];</span></a>
+<a name="1332"><span class="lineNum">    1332 </span>            :     }</a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineCov">       1936 :     neff = norm*norm/w2;</span></a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">       3872 :     getPntrToComponent(&quot;weight&quot;)-&gt;set(weight/norm);</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            :   } else {</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :     // or arithmetic ones</a>
+<a name="1337"><span class="lineNum">    1337 </span><span class="lineCov">        289 :     neff = dnrep;</span></a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineCov">        289 :     weight = 1.0;</span></a>
+<a name="1339"><span class="lineNum">    1339 </span><span class="lineCov">        289 :     norm = dnrep;</span></a>
+<a name="1340"><span class="lineNum">    1340 </span>            :   }</a>
+<a name="1341"><span class="lineNum">    1341 </span><span class="lineCov">       2225 :   getPntrToComponent(&quot;neff&quot;)-&gt;set(neff);</span></a>
+<a name="1342"><span class="lineNum">    1342 </span><span class="lineCov">       2225 : }</span></a>
+<a name="1343"><span class="lineNum">    1343 </span>            : </a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineCov">       2225 : void MetainferenceBase::get_sigma_mean(const double weight, const double norm, const double neff, const std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="1345"><span class="lineNum">    1345 </span>            : {</a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineCov">       2225 :   const double dnrep    = static_cast&lt;double&gt;(nrep_);</span></a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">       2225 :   std::vector&lt;double&gt; sigma_mean2_tmp(sigma_mean2_.size());</span></a>
+<a name="1348"><span class="lineNum">    1348 </span>            : </a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineCov">       2225 :   if(do_optsigmamean_&gt;0) {</span></a>
+<a name="1350"><span class="lineNum">    1350 </span>            :     // remove first entry of the history std::vector</a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineCov">         84 :     if(sigma_mean2_last_[iselect][0].size()==optsigmamean_stride_&amp;&amp;optsigmamean_stride_&gt;0)</span></a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_last_[iselect][i].erase(sigma_mean2_last_[iselect][i].begin());</span></a>
+<a name="1353"><span class="lineNum">    1353 </span>            :     /* this is the current estimate of sigma mean for each argument</a>
+<a name="1354"><span class="lineNum">    1354 </span>            :        there is one of this per argument in any case  because it is</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :        the maximum among these to be used in case of GAUSS/OUTLIER */</a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineCov">         84 :     std::vector&lt;double&gt; sigma_mean2_now(narg,0);</span></a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineCov">         84 :     if(master) {</span></a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineCov">        672 :       for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_now[i] = weight*(calc_data_[i]-mean[i])*(calc_data_[i]-mean[i]);</span></a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineCov">         42 :       if(nrep_&gt;1) multi_sim_comm.Sum(&amp;sigma_mean2_now[0], narg);</span></a>
+<a name="1360"><span class="lineNum">    1360 </span>            :     }</a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineCov">         84 :     comm.Sum(&amp;sigma_mean2_now[0], narg);</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineCov">       1344 :     for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_now[i] *= 1.0/(neff-1.)/norm;</span></a>
+<a name="1363"><span class="lineNum">    1363 </span>            : </a>
+<a name="1364"><span class="lineNum">    1364 </span>            :     // add sigma_mean2 to history</a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineCov">         84 :     if(optsigmamean_stride_&gt;0) {</span></a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) sigma_mean2_last_[iselect][i].push_back(sigma_mean2_now[i]);</span></a>
+<a name="1367"><span class="lineNum">    1367 </span>            :     } else {</a>
+<a name="1368"><span class="lineNum">    1368 </span><span class="lineCov">       1344 :       for(unsigned i=0; i&lt;narg; ++i) if(sigma_mean2_now[i] &gt; sigma_mean2_last_[iselect][i][0]) sigma_mean2_last_[iselect][i][0] = sigma_mean2_now[i];</span></a>
+<a name="1369"><span class="lineNum">    1369 </span>            :     }</a>
+<a name="1370"><span class="lineNum">    1370 </span>            : </a>
+<a name="1371"><span class="lineNum">    1371 </span><span class="lineCov">         84 :     if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="1372"><span class="lineNum">    1372 </span><span class="lineCov">       1344 :       for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1373"><span class="lineNum">    1373 </span>            :         /* set to the maximum in history std::vector */</a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineCov">       1260 :         sigma_mean2_tmp[i] = *max_element(sigma_mean2_last_[iselect][i].begin(), sigma_mean2_last_[iselect][i].end());</span></a>
+<a name="1375"><span class="lineNum">    1375 </span>            :         /* the standard error of the mean */</a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineCov">       1260 :         valueSigmaMean[i]-&gt;set(std::sqrt(sigma_mean2_tmp[i]));</span></a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">       1260 :         if(noise_type_==GENERIC) {</span></a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineNoCov">          0 :           sigma_min_[i] = std::sqrt(sigma_mean2_tmp[i]);</span></a>
+<a name="1379"><span class="lineNum">    1379 </span><span class="lineNoCov">          0 :           if(sigma_[i] &lt; sigma_min_[i]) sigma_[i] = sigma_min_[i];</span></a>
+<a name="1380"><span class="lineNum">    1380 </span>            :         }</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :       }</a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineNoCov">          0 :     } else if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="1383"><span class="lineNum">    1383 </span>            :       // find maximum for each data point</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :       std::vector &lt;double&gt; max_values;</a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;narg; ++i) max_values.push_back(*max_element(sigma_mean2_last_[iselect][i].begin(), sigma_mean2_last_[iselect][i].end()));</span></a>
+<a name="1386"><span class="lineNum">    1386 </span>            :       // find maximum across data points</a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineNoCov">          0 :       const double max_now = *max_element(max_values.begin(), max_values.end());</span></a>
+<a name="1388"><span class="lineNum">    1388 </span>            :       // set new value</a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineNoCov">          0 :       sigma_mean2_tmp[0] = max_now;</span></a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineNoCov">          0 :       valueSigmaMean[0]-&gt;set(std::sqrt(sigma_mean2_tmp[0]));</span></a>
+<a name="1391"><span class="lineNum">    1391 </span>            :     }</a>
+<a name="1392"><span class="lineNum">    1392 </span>            :     // endif sigma mean optimization</a>
+<a name="1393"><span class="lineNum">    1393 </span>            :     // start sigma max optimization</a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineCov">         84 :     if(do_optsigmamean_&gt;1&amp;&amp;!sigmamax_opt_done_) {</span></a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;sigma_max_.size(); i++) {</span></a>
+<a name="1396"><span class="lineNum">    1396 </span><span class="lineNoCov">          0 :         if(sigma_max_est_[i]&lt;sigma_mean2_tmp[i]&amp;&amp;optimized_step_&gt;optsigmamean_stride_) sigma_max_est_[i]=sigma_mean2_tmp[i];</span></a>
+<a name="1397"><span class="lineNum">    1397 </span>            :         // ready to set once and for all the value of sigma_max</a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineNoCov">          0 :         if(optimized_step_==N_optimized_step_) {</span></a>
+<a name="1399"><span class="lineNum">    1399 </span><span class="lineNoCov">          0 :           sigmamax_opt_done_=true;</span></a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineNoCov">          0 :           for(unsigned i=0; i&lt;sigma_max_.size(); i++) {</span></a>
+<a name="1401"><span class="lineNum">    1401 </span><span class="lineNoCov">          0 :             sigma_max_[i]=std::sqrt(sigma_max_est_[i]*dnrep);</span></a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineNoCov">          0 :             Dsigma_[i] = 0.05*(sigma_max_[i] - sigma_min_[i]);</span></a>
+<a name="1403"><span class="lineNum">    1403 </span><span class="lineNoCov">          0 :             if(sigma_[i]&gt;sigma_max_[i]) sigma_[i]=sigma_max_[i];</span></a>
+<a name="1404"><span class="lineNum">    1404 </span>            :           }</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :         }</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :       }</a>
+<a name="1407"><span class="lineNum">    1407 </span><span class="lineNoCov">          0 :       optimized_step_++;</span></a>
+<a name="1408"><span class="lineNum">    1408 </span>            :     }</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :     // end sigma max optimization</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :   } else {</a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineCov">       2141 :     if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">      11588 :       for(unsigned i=0; i&lt;narg; ++i) {</span></a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineCov">       9724 :         sigma_mean2_tmp[i] = sigma_mean2_last_[iselect][i][0];</span></a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineCov">       9724 :         valueSigmaMean[i]-&gt;set(std::sqrt(sigma_mean2_tmp[i]));</span></a>
+<a name="1415"><span class="lineNum">    1415 </span>            :       }</a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineCov">        277 :     } else if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineCov">        277 :       sigma_mean2_tmp[0] = sigma_mean2_last_[iselect][0][0];</span></a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineCov">        277 :       valueSigmaMean[0]-&gt;set(std::sqrt(sigma_mean2_tmp[0]));</span></a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     }</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :   }</a>
+<a name="1421"><span class="lineNum">    1421 </span>            : </a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineCov">       2225 :   sigma_mean2_ = sigma_mean2_tmp;</span></a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineCov">       2225 : }</span></a>
+<a name="1424"><span class="lineNum">    1424 </span>            : </a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineCov">       2225 : void MetainferenceBase::replica_averaging(const double weight, const double norm, std::vector&lt;double&gt; &amp;mean, std::vector&lt;double&gt; &amp;dmean_b)</span></a>
+<a name="1426"><span class="lineNum">    1426 </span>            : {</a>
+<a name="1427"><span class="lineNum">    1427 </span><span class="lineCov">       2225 :   if(master) {</span></a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineCov">       7472 :     for(unsigned i=0; i&lt;narg; ++i) mean[i] = weight/norm*calc_data_[i];</span></a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineCov">       1227 :     if(nrep_&gt;1) multi_sim_comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="1430"><span class="lineNum">    1430 </span>            :   }</a>
+<a name="1431"><span class="lineNum">    1431 </span><span class="lineCov">       2225 :   comm.Sum(&amp;mean[0], narg);</span></a>
+<a name="1432"><span class="lineNum">    1432 </span>            :   // set the derivative of the mean with respect to the bias</a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineCov">      14052 :   for(unsigned i=0; i&lt;narg; ++i) dmean_b[i] = weight/norm/kbt_*(calc_data_[i]-mean[i])*decay_w_;</span></a>
+<a name="1434"><span class="lineNum">    1434 </span>            : </a>
+<a name="1435"><span class="lineNum">    1435 </span>            :   // this is only for generic metainference</a>
+<a name="1436"><span class="lineNum">    1436 </span><span class="lineCov">       2225 :   if(firstTime) {ftilde_ = mean; firstTime = false;}</span></a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">       2225 : }</span></a>
+<a name="1438"><span class="lineNum">    1438 </span>            : </a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineNoCov">          0 : void MetainferenceBase::do_regression_zero(const std::vector&lt;double&gt; &amp;mean)</span></a>
+<a name="1440"><span class="lineNum">    1440 </span>            : {</a>
+<a name="1441"><span class="lineNum">    1441 </span>            : // parameters[i] = scale_ * mean[i]: find scale_ with linear regression</a>
+<a name="1442"><span class="lineNum">    1442 </span>            :   double num = 0.0;</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :   double den = 0.0;</a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;parameters.size(); ++i) {</span></a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineNoCov">          0 :     num += mean[i] * parameters[i];</span></a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineNoCov">          0 :     den += mean[i] * mean[i];</span></a>
+<a name="1447"><span class="lineNum">    1447 </span>            :   }</a>
+<a name="1448"><span class="lineNum">    1448 </span><span class="lineNoCov">          0 :   if(den&gt;0) {</span></a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineNoCov">          0 :     scale_ = num / den;</span></a>
+<a name="1450"><span class="lineNum">    1450 </span>            :   } else {</a>
+<a name="1451"><span class="lineNum">    1451 </span><span class="lineNoCov">          0 :     scale_ = 1.0;</span></a>
+<a name="1452"><span class="lineNum">    1452 </span>            :   }</a>
+<a name="1453"><span class="lineNum">    1453 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="1454"><span class="lineNum">    1454 </span>            : </a>
+<a name="1455"><span class="lineNum">    1455 </span><span class="lineCov">       2225 : double MetainferenceBase::getScore()</span></a>
+<a name="1456"><span class="lineNum">    1456 </span>            : {</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :   /* Metainference */</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :   /* 1) collect weights */</a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineCov">       2225 :   double weight = 0.;</span></a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineCov">       2225 :   double neff = 0.;</span></a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineCov">       2225 :   double norm = 0.;</span></a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">       2225 :   get_weights(weight, norm, neff);</span></a>
+<a name="1463"><span class="lineNum">    1463 </span>            : </a>
+<a name="1464"><span class="lineNum">    1464 </span>            :   /* 2) calculate average */</a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineCov">       2225 :   std::vector&lt;double&gt; mean(getNarg(),0);</span></a>
+<a name="1466"><span class="lineNum">    1466 </span>            :   // this is the derivative of the mean with respect to the argument</a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">       2225 :   std::vector&lt;double&gt; dmean_x(getNarg(),weight/norm);</span></a>
+<a name="1468"><span class="lineNum">    1468 </span>            :   // this is the derivative of the mean with respect to the bias</a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineCov">       2225 :   std::vector&lt;double&gt; dmean_b(getNarg(),0);</span></a>
+<a name="1470"><span class="lineNum">    1470 </span>            :   // calculate it</a>
+<a name="1471"><span class="lineNum">    1471 </span><span class="lineCov">       2225 :   replica_averaging(weight, norm, mean, dmean_b);</span></a>
+<a name="1472"><span class="lineNum">    1472 </span>            : </a>
+<a name="1473"><span class="lineNum">    1473 </span>            :   /* 3) calculates parameters */</a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineCov">       2225 :   get_sigma_mean(weight, norm, neff, mean);</span></a>
+<a name="1475"><span class="lineNum">    1475 </span>            : </a>
+<a name="1476"><span class="lineNum">    1476 </span>            :   // in case of regression with zero intercept, calculate scale</a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">       2225 :   if(doregres_zero_ &amp;&amp; getStep()%nregres_zero_==0) do_regression_zero(mean);</span></a>
+<a name="1478"><span class="lineNum">    1478 </span>            : </a>
+<a name="1479"><span class="lineNum">    1479 </span>            :   /* 4) run monte carlo */</a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">       2225 :   double ene = doMonteCarlo(mean);</span></a>
+<a name="1481"><span class="lineNum">    1481 </span>            : </a>
+<a name="1482"><span class="lineNum">    1482 </span>            :   // calculate bias and forces</a>
+<a name="1483"><span class="lineNum">    1483 </span><span class="lineCov">       2225 :   switch(noise_type_) {</span></a>
+<a name="1484"><span class="lineNum">    1484 </span><span class="lineCov">        271 :   case GAUSS:</span></a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineCov">        271 :     getEnergyForceGJ(mean, dmean_x, dmean_b);</span></a>
+<a name="1486"><span class="lineNum">    1486 </span>            :     break;</a>
+<a name="1487"><span class="lineNum">    1487 </span><span class="lineCov">        160 :   case MGAUSS:</span></a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineCov">        160 :     getEnergyForceGJE(mean, dmean_x, dmean_b);</span></a>
+<a name="1489"><span class="lineNum">    1489 </span>            :     break;</a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineCov">          6 :   case OUTLIERS:</span></a>
+<a name="1491"><span class="lineNum">    1491 </span><span class="lineCov">          6 :     getEnergyForceSP(mean, dmean_x, dmean_b);</span></a>
+<a name="1492"><span class="lineNum">    1492 </span>            :     break;</a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineCov">       1776 :   case MOUTLIERS:</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineCov">       1776 :     getEnergyForceSPE(mean, dmean_x, dmean_b);</span></a>
+<a name="1495"><span class="lineNum">    1495 </span>            :     break;</a>
+<a name="1496"><span class="lineNum">    1496 </span><span class="lineCov">         12 :   case GENERIC:</span></a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineCov">         12 :     getEnergyForceMIGEN(mean, dmean_x, dmean_b);</span></a>
+<a name="1498"><span class="lineNum">    1498 </span>            :     break;</a>
+<a name="1499"><span class="lineNum">    1499 </span>            :   }</a>
+<a name="1500"><span class="lineNum">    1500 </span>            : </a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineCov">       2225 :   return ene;</span></a>
+<a name="1502"><span class="lineNum">    1502 </span>            : }</a>
+<a name="1503"><span class="lineNum">    1503 </span>            : </a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineCov">         96 : void MetainferenceBase::writeStatus()</span></a>
+<a name="1505"><span class="lineNum">    1505 </span>            : {</a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineCov">         96 :   if(!doscore_) return;</span></a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineCov">         31 :   sfile_.rewind();</span></a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineCov">         31 :   sfile_.printField(&quot;time&quot;,getTimeStep()*getStep());</span></a>
+<a name="1509"><span class="lineNum">    1509 </span>            :   //nsel</a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineCov">         62 :   for(unsigned i=0; i&lt;sigma_mean2_last_.size(); i++) {</span></a>
+<a name="1511"><span class="lineNum">    1511 </span>            :     std::string msg_i,msg_j;</a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineCov">         31 :     Tools::convert(i,msg_i);</span></a>
+<a name="1513"><span class="lineNum">    1513 </span>            :     std::vector &lt;double&gt; max_values;</a>
+<a name="1514"><span class="lineNum">    1514 </span>            :     //narg</a>
+<a name="1515"><span class="lineNum">    1515 </span><span class="lineCov">       2528 :     for(unsigned j=0; j&lt;narg; ++j) {</span></a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">       2497 :       Tools::convert(j,msg_j);</span></a>
+<a name="1517"><span class="lineNum">    1517 </span><span class="lineCov">       2497 :       std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineCov">       2497 :       if(noise_type_==MGAUSS||noise_type_==MOUTLIERS||noise_type_==GENERIC) {</span></a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineCov">       7410 :         sfile_.printField(&quot;sigmaMean_&quot;+msg,std::sqrt(*max_element(sigma_mean2_last_[i][j].begin(), sigma_mean2_last_[i][j].end())));</span></a>
+<a name="1520"><span class="lineNum">    1520 </span>            :       } else {</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :         // find maximum for each data point</a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineCov">         54 :         max_values.push_back(*max_element(sigma_mean2_last_[i][j].begin(), sigma_mean2_last_[i][j].end()));</span></a>
+<a name="1523"><span class="lineNum">    1523 </span>            :       }</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :     }</a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineCov">         31 :     if(noise_type_==GAUSS||noise_type_==OUTLIERS) {</span></a>
+<a name="1526"><span class="lineNum">    1526 </span>            :       // find maximum across data points</a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineCov">          8 :       const double max_now = std::sqrt(*max_element(max_values.begin(), max_values.end()));</span></a>
+<a name="1528"><span class="lineNum">    1528 </span><span class="lineCov">          8 :       Tools::convert(0,msg_j);</span></a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">          8 :       std::string msg = msg_i+&quot;_&quot;+msg_j;</span></a>
+<a name="1530"><span class="lineNum">    1530 </span><span class="lineCov">         16 :       sfile_.printField(&quot;sigmaMean_&quot;+msg, max_now);</span></a>
+<a name="1531"><span class="lineNum">    1531 </span>            :     }</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :   }</a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_.size(); ++i) {</span></a>
+<a name="1534"><span class="lineNum">    1534 </span>            :     std::string msg;</a>
+<a name="1535"><span class="lineNum">    1535 </span><span class="lineCov">       2478 :     Tools::convert(i,msg);</span></a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineCov">       4956 :     sfile_.printField(&quot;sigma_&quot;+msg,sigma_[i]);</span></a>
+<a name="1537"><span class="lineNum">    1537 </span>            :   }</a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">       2509 :   for(unsigned i=0; i&lt;sigma_max_.size(); ++i) {</span></a>
+<a name="1539"><span class="lineNum">    1539 </span>            :     std::string msg;</a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineCov">       2478 :     Tools::convert(i,msg);</span></a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineCov">       4956 :     sfile_.printField(&quot;sigma_max_&quot;+msg,sigma_max_[i]);</span></a>
+<a name="1542"><span class="lineNum">    1542 </span>            :   }</a>
+<a name="1543"><span class="lineNum">    1543 </span><span class="lineCov">         31 :   if(noise_type_==GENERIC) {</span></a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;ftilde_.size(); ++i) {</span></a>
+<a name="1545"><span class="lineNum">    1545 </span>            :       std::string msg;</a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineCov">          2 :       Tools::convert(i,msg);</span></a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineCov">          4 :       sfile_.printField(&quot;ftilde_&quot;+msg,ftilde_[i]);</span></a>
+<a name="1548"><span class="lineNum">    1548 </span>            :     }</a>
+<a name="1549"><span class="lineNum">    1549 </span>            :   }</a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">         31 :   sfile_.printField(&quot;scale0_&quot;,scale_);</span></a>
+<a name="1551"><span class="lineNum">    1551 </span><span class="lineCov">         31 :   sfile_.printField(&quot;offset0_&quot;,offset_);</span></a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineCov">         62 :   for(unsigned i=0; i&lt;average_weights_.size(); i++) {</span></a>
+<a name="1553"><span class="lineNum">    1553 </span>            :     std::string msg_i;</a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineCov">         31 :     Tools::convert(i,msg_i);</span></a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineCov">         62 :     sfile_.printField(&quot;weight_&quot;+msg_i,average_weights_[i][replica_]);</span></a>
+<a name="1556"><span class="lineNum">    1556 </span>            :   }</a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineCov">         31 :   sfile_.printField();</span></a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineCov">         31 :   sfile_.flush();</span></a>
+<a name="1559"><span class="lineNum">    1559 </span>            : }</a>
+<a name="1560"><span class="lineNum">    1560 </span>            : </a>
+<a name="1561"><span class="lineNum">    1561 </span>            : }</a>
+<a name="1562"><span class="lineNum">    1562 </span>            : }</a>
+<a name="1563"><span class="lineNum">    1563 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/MetainferenceBase.h.func-sort-c.html b/coverage/isdb/MetainferenceBase.h.func-sort-c.html
new file mode 100644
index 0000000000..bb27b46a1f
--- /dev/null
+++ b/coverage/isdb/MetainferenceBase.h.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/MetainferenceBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - MetainferenceBase.h<span style="font-size: 80%;"> (<a href="MetainferenceBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MetainferenceBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#263">_ZN4PLMD4isdb17MetainferenceBase13setParametersERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#319">_ZN4PLMD4isdb17MetainferenceBase29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#278">_ZN4PLMD4isdb17MetainferenceBase14setDerivativesEv</a></td>
+              <td class="coverFnHi">96</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#307">_ZN4PLMD4isdb17MetainferenceBase12lockRequestsEv</a></td>
+              <td class="coverFnHi">701</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#313">_ZN4PLMD4isdb17MetainferenceBase14unlockRequestsEv</a></td>
+              <td class="coverFnHi">701</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#336">_ZN4PLMD4isdb17MetainferenceBase5applyEv</a></td>
+              <td class="coverFnHi">701</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#364">_ZN4PLMD4isdb17MetainferenceBase17setBoxDerivativesEPNS_5ValueERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">11848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#356">_ZN4PLMD4isdb17MetainferenceBase19setAtomsDerivativesEPNS_5ValueEjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">2375432</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#294">_ZN4PLMD4isdb17MetainferenceBase17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">3480147</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#299">_ZN4PLMD4isdb17MetainferenceBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4099241332</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/MetainferenceBase.h.func.html b/coverage/isdb/MetainferenceBase.h.func.html
new file mode 100644
index 0000000000..6a74fa3849
--- /dev/null
+++ b/coverage/isdb/MetainferenceBase.h.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/MetainferenceBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - MetainferenceBase.h<span style="font-size: 80%;"> (<a href="MetainferenceBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MetainferenceBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#307">_ZN4PLMD4isdb17MetainferenceBase12lockRequestsEv</a></td>
+              <td class="coverFnHi">701</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#263">_ZN4PLMD4isdb17MetainferenceBase13setParametersERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#278">_ZN4PLMD4isdb17MetainferenceBase14setDerivativesEv</a></td>
+              <td class="coverFnHi">96</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#313">_ZN4PLMD4isdb17MetainferenceBase14unlockRequestsEv</a></td>
+              <td class="coverFnHi">701</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#364">_ZN4PLMD4isdb17MetainferenceBase17setBoxDerivativesEPNS_5ValueERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">11848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#294">_ZN4PLMD4isdb17MetainferenceBase17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">3480147</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#356">_ZN4PLMD4isdb17MetainferenceBase19setAtomsDerivativesEPNS_5ValueEjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">2375432</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#299">_ZN4PLMD4isdb17MetainferenceBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">4099241332</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#319">_ZN4PLMD4isdb17MetainferenceBase29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetainferenceBase.h.gcov.html#336">_ZN4PLMD4isdb17MetainferenceBase5applyEv</a></td>
+              <td class="coverFnHi">701</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/MetainferenceBase.h.gcov.html b/coverage/isdb/MetainferenceBase.h.gcov.html
new file mode 100644
index 0000000000..cf82b2ba65
--- /dev/null
+++ b/coverage/isdb/MetainferenceBase.h.gcov.html
@@ -0,0 +1,461 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/MetainferenceBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - MetainferenceBase.h<span style="font-size: 80%;"> (source / <a href="MetainferenceBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_isdb_MetainferenceBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_isdb_MetainferenceBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #define PLUMED_METAINF_INIT(ao) Action(ao),MetainferenceBase(ao)</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace isdb {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : /**</a>
+<a name="38"><span class="lineNum">      38 </span>            : \ingroup INHERIT</a>
+<a name="39"><span class="lineNum">      39 </span>            : This is the abstract base class to use for implementing new ISDB Metainference actions, within it there is</a>
+<a name="40"><span class="lineNum">      40 </span>            : information as to how to go about implementing a new Metainference action.</a>
+<a name="41"><span class="lineNum">      41 </span>            : */</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : class MetainferenceBase :</a>
+<a name="44"><span class="lineNum">      44 </span>            :   public ActionAtomistic,</a>
+<a name="45"><span class="lineNum">      45 </span>            :   public ActionWithArguments,</a>
+<a name="46"><span class="lineNum">      46 </span>            :   public ActionWithValue</a>
+<a name="47"><span class="lineNum">      47 </span>            : {</a>
+<a name="48"><span class="lineNum">      48 </span>            : private:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::vector&lt;double&gt; forces;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;double&gt; forcesToApply;</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   // activate metainference</a>
+<a name="53"><span class="lineNum">      53 </span>            :   bool doscore_;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   unsigned write_stride_;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // number of experimental data</a>
+<a name="56"><span class="lineNum">      56 </span>            :   unsigned narg;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   // experimental data</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::vector&lt;double&gt; parameters;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   // metainference derivatives</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;double&gt; metader_;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   // vector of back-calculated experimental data</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;double&gt; calc_data_;</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   // noise type</a>
+<a name="65"><span class="lineNum">      65 </span>            :   unsigned noise_type_;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   enum { GAUSS, MGAUSS, OUTLIERS, MOUTLIERS, GENERIC };</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned gen_likelihood_;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   enum { LIKE_GAUSS, LIKE_LOGN };</a>
+<a name="69"><span class="lineNum">      69 </span>            :   bool   doscale_;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   unsigned scale_prior_;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   enum { SC_GAUSS, SC_FLAT };</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double scale_;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double scale_mu_;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   double scale_min_;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double scale_max_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   double Dscale_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   // scale is data scaling factor</a>
+<a name="78"><span class="lineNum">      78 </span>            :   // noise type</a>
+<a name="79"><span class="lineNum">      79 </span>            :   unsigned offset_prior_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool   dooffset_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double offset_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   double offset_mu_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   double offset_min_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   double offset_max_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   double Doffset_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   // scale and offset regression</a>
+<a name="87"><span class="lineNum">      87 </span>            :   bool doregres_zero_;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   int  nregres_zero_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   // sigma is data uncertainty</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;double&gt; sigma_min_;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;double&gt; sigma_max_;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::vector&lt;double&gt; Dsigma_;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   // sigma_mean is uncertainty in the mean estimate</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::vector&lt;double&gt; sigma_mean2_;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   // this is the estimator of the mean value per replica for generic metainference</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt;double&gt; ftilde_;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   double Dftilde_;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   // temperature in kbt</a>
+<a name="101"><span class="lineNum">     101 </span>            :   double   kbt_;</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   // Monte Carlo stuff</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;Random&gt; random;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   unsigned MCsteps_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   long long unsigned MCaccept_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   long long unsigned MCacceptScale_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   long long unsigned MCacceptFT_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   long long unsigned MCtrial_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   unsigned MCchunksize_;</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   // output</a>
+<a name="113"><span class="lineNum">     113 </span>            :   Value*   valueScore;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   Value*   valueScale;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   Value*   valueOffset;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   Value*   valueAccept;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   Value*   valueAcceptScale;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   Value*   valueAcceptFT;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::vector&lt;Value*&gt; valueSigma;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::vector&lt;Value*&gt; valueSigmaMean;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::vector&lt;Value*&gt; valueFtilde;</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   // restart</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::string status_file_name_;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   OFile    sfile_;</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // others</a>
+<a name="128"><span class="lineNum">     128 </span>            :   bool     firstTime;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector&lt;bool&gt; firstTimeW;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   bool     master;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool     do_reweight_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   unsigned do_optsigmamean_;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   unsigned nrep_;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   unsigned replica_;</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // selector</a>
+<a name="137"><span class="lineNum">     137 </span>            :   unsigned nsel_;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   std::string selector_;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   unsigned iselect;</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // optimize sigma mean</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::vector&lt; std::vector &lt; std::vector &lt;double&gt; &gt; &gt; sigma_mean2_last_;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   unsigned optsigmamean_stride_;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   // optimize sigma max</a>
+<a name="145"><span class="lineNum">     145 </span>            :   unsigned N_optimized_step_;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   unsigned optimized_step_;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   bool sigmamax_opt_done_;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   std::vector&lt;double&gt; sigma_max_est_;</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   // average weights</a>
+<a name="151"><span class="lineNum">     151 </span>            :   double decay_w_;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   std::vector&lt; std::vector &lt;double&gt; &gt;  average_weights_;</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   double getEnergyMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;ftilde, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="155"><span class="lineNum">     155 </span>            :                         const double scale, const double offset);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   double getEnergySP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="157"><span class="lineNum">     157 </span>            :                      const double scale, const double offset);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   double getEnergySPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="159"><span class="lineNum">     159 </span>            :                       const double scale, const double offset);</a>
+<a name="160"><span class="lineNum">     160 </span>            :   double getEnergyGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="161"><span class="lineNum">     161 </span>            :                      const double scale, const double offset);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   double getEnergyGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;sigma,</a>
+<a name="163"><span class="lineNum">     163 </span>            :                       const double scale, const double offset);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   void setMetaDer(const unsigned index, const double der);</a>
+<a name="165"><span class="lineNum">     165 </span>            :   void getEnergyForceSP(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="166"><span class="lineNum">     166 </span>            :   void getEnergyForceSPE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   void getEnergyForceGJ(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="168"><span class="lineNum">     168 </span>            :   void getEnergyForceGJE(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="169"><span class="lineNum">     169 </span>            :   void getEnergyForceMIGEN(const std::vector&lt;double&gt; &amp;mean, const std::vector&lt;double&gt; &amp;dmean_x, const std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="170"><span class="lineNum">     170 </span>            :   double getCalcData(const unsigned index);</a>
+<a name="171"><span class="lineNum">     171 </span>            :   void get_weights(double &amp;weight, double &amp;norm, double &amp;neff);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   void replica_averaging(const double weight, const double norm, std::vector&lt;double&gt; &amp;mean, std::vector&lt;double&gt; &amp;dmean_b);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   void get_sigma_mean(const double weight, const double norm, const double neff, const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="174"><span class="lineNum">     174 </span>            :   void do_regression_zero(const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void moveTilde(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy);</a>
+<a name="176"><span class="lineNum">     176 </span>            :   void moveScaleOffset(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy);</a>
+<a name="177"><span class="lineNum">     177 </span>            :   void moveSigmas(const std::vector&lt;double&gt; &amp;mean_, double &amp;old_energy, const unsigned i, const std::vector&lt;unsigned&gt; &amp;indices, bool &amp;breaknow);</a>
+<a name="178"><span class="lineNum">     178 </span>            :   double doMonteCarlo(const std::vector&lt;double&gt; &amp;mean);</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : public:</a>
+<a name="181"><span class="lineNum">     181 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="182"><span class="lineNum">     182 </span>            :   explicit MetainferenceBase(const ActionOptions&amp;);</a>
+<a name="183"><span class="lineNum">     183 </span>            :   ~MetainferenceBase();</a>
+<a name="184"><span class="lineNum">     184 </span>            :   void Initialise(const unsigned input);</a>
+<a name="185"><span class="lineNum">     185 </span>            :   void Selector();</a>
+<a name="186"><span class="lineNum">     186 </span>            :   unsigned getNarg();</a>
+<a name="187"><span class="lineNum">     187 </span>            :   void setNarg(const unsigned input);</a>
+<a name="188"><span class="lineNum">     188 </span>            :   void setParameters(const std::vector&lt;double&gt;&amp; input);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   void setParameter(const double input);</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void setCalcData(const unsigned index, const double datum);</a>
+<a name="191"><span class="lineNum">     191 </span>            :   void setCalcData(const std::vector&lt;double&gt;&amp; data);</a>
+<a name="192"><span class="lineNum">     192 </span>            :   bool getDoScore();</a>
+<a name="193"><span class="lineNum">     193 </span>            :   unsigned getWstride();</a>
+<a name="194"><span class="lineNum">     194 </span>            :   double getScore();</a>
+<a name="195"><span class="lineNum">     195 </span>            :   void setScore(const double score);</a>
+<a name="196"><span class="lineNum">     196 </span>            :   void setDerivatives();</a>
+<a name="197"><span class="lineNum">     197 </span>            :   double getMetaDer(const unsigned index);</a>
+<a name="198"><span class="lineNum">     198 </span>            :   void writeStatus();</a>
+<a name="199"><span class="lineNum">     199 </span>            :   void turnOnDerivatives() override;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   void lockRequests() override;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   void unlockRequests() override;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a ) override;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   void apply() override;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   void setArgDerivatives(Value *v, const double &amp;d);</a>
+<a name="206"><span class="lineNum">     206 </span>            :   void setAtomsDerivatives(Value*v, const unsigned i, const Vector&amp;d);</a>
+<a name="207"><span class="lineNum">     207 </span>            :   void setBoxDerivatives(Value*v, const Tensor&amp;d);</a>
+<a name="208"><span class="lineNum">     208 </span>            : };</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : inline</a>
+<a name="211"><span class="lineNum">     211 </span>            : void MetainferenceBase::setNarg(const unsigned input)</a>
+<a name="212"><span class="lineNum">     212 </span>            : {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         31 :   narg = input;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : inline</a>
+<a name="217"><span class="lineNum">     217 </span>            : bool MetainferenceBase::getDoScore()</a>
+<a name="218"><span class="lineNum">     218 </span>            : {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      22234 :   return doscore_;</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : inline</a>
+<a name="223"><span class="lineNum">     223 </span>            : unsigned MetainferenceBase::getWstride()</a>
+<a name="224"><span class="lineNum">     224 </span>            : {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       1402 :   return write_stride_;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : inline</a>
+<a name="229"><span class="lineNum">     229 </span>            : unsigned MetainferenceBase::getNarg()</a>
+<a name="230"><span class="lineNum">     230 </span>            : {</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       2225 :   return narg;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : inline</a>
+<a name="235"><span class="lineNum">     235 </span>            : void MetainferenceBase::setMetaDer(const unsigned index, const double der)</a>
+<a name="236"><span class="lineNum">     236 </span>            : {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       7146 :   metader_[index] = der;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : inline</a>
+<a name="241"><span class="lineNum">     241 </span>            : double MetainferenceBase::getMetaDer(const unsigned index)</a>
+<a name="242"><span class="lineNum">     242 </span>            : {</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">     909788 :   return metader_[index];</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : inline</a>
+<a name="247"><span class="lineNum">     247 </span>            : double MetainferenceBase::getCalcData(const unsigned index)</a>
+<a name="248"><span class="lineNum">     248 </span>            : {</a>
+<a name="249"><span class="lineNum">     249 </span>            :   return calc_data_[index];</a>
+<a name="250"><span class="lineNum">     250 </span>            : }</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : inline</a>
+<a name="253"><span class="lineNum">     253 </span>            : void MetainferenceBase::setCalcData(const unsigned index, const double datum)</a>
+<a name="254"><span class="lineNum">     254 </span>            : {</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">       3868 :   calc_data_[index] = datum;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       3868 : }</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : inline</a>
+<a name="259"><span class="lineNum">     259 </span>            : void MetainferenceBase::setCalcData(const std::vector&lt;double&gt;&amp; data)</a>
+<a name="260"><span class="lineNum">     260 </span>            : {</a>
+<a name="261"><span class="lineNum">     261 </span>            :   for(unsigned i=0; i&lt;data.size(); i++) calc_data_[i] = data[i];</a>
+<a name="262"><span class="lineNum">     262 </span>            : }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : inline</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         27 : void MetainferenceBase::setParameters(const std::vector&lt;double&gt;&amp; input) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        168 :   for(unsigned i=0; i&lt;input.size(); i++) parameters.push_back(input[i]);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         27 : }</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            : inline</a>
+<a name="270"><span class="lineNum">     270 </span>            : void MetainferenceBase::setParameter(const double input) {</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       2356 :   parameters.push_back(input);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       2356 : }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : inline</a>
+<a name="275"><span class="lineNum">     275 </span>            : void MetainferenceBase::setScore(const double score) {</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       2225 :   valueScore-&gt;set(score);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       2225 : }</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : inline</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         96 : void MetainferenceBase::setDerivatives() {</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   // Get appropriate number of derivatives</a>
+<a name="282"><span class="lineNum">     282 </span>            :   // Derivatives are first for arguments and then for atoms</a>
+<a name="283"><span class="lineNum">     283 </span>            :   unsigned nder;</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         96 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         96 :     nder = 3*getNumberOfAtoms() + 9 + getNumberOfArguments();</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   } else {</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     nder = getNumberOfArguments();</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   }</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            :   // Resize all derivative arrays</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         96 :   forces.resize( nder ); forcesToApply.resize( nder );</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">      21216 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) getPntrToComponent(i)-&gt;resizeDerivatives(nder);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         96 : }</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : inline</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">    3480147 : void MetainferenceBase::turnOnDerivatives() {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">    3480147 :   ActionWithValue::turnOnDerivatives();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">    3480147 : }</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : inline</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov"> 4099241332 : unsigned MetainferenceBase::getNumberOfDerivatives() {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov"> 4099241332 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov"> 4099241332 :     return 3*getNumberOfAtoms() + 9 + getNumberOfArguments();</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   return getNumberOfArguments();</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : }</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : inline</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        701 : void MetainferenceBase::lockRequests() {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   ActionAtomistic::lockRequests();</a>
+<a name="311"><span class="lineNum">     311 </span>            :   ActionWithArguments::lockRequests();</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        701 : }</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : inline</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        701 : void MetainferenceBase::unlockRequests() {</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :   ActionAtomistic::unlockRequests();</a>
+<a name="317"><span class="lineNum">     317 </span>            :   ActionWithArguments::unlockRequests();</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        701 : }</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            : inline</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         75 : void MetainferenceBase::calculateNumericalDerivatives( ActionWithValue* a=NULL ) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         75 :   if( getNumberOfArguments()&gt;0 ) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         48 :     ActionWithArguments::calculateNumericalDerivatives( a );</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   }</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         75 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         75 :     Matrix&lt;double&gt; save_derivatives( getNumberOfComponents(), getNumberOfArguments() );</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">       1293 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       2322 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) if(getPntrToComponent(j)-&gt;hasDerivatives()) save_derivatives(j,i)=getPntrToComponent(j)-&gt;getDerivative(i);</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :     }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         75 :     calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       1293 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       2322 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) if(getPntrToComponent(j)-&gt;hasDerivatives()) getPntrToComponent(j)-&gt;addDerivative( i, save_derivatives(j,i) );</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span>            :   }</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         75 : }</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            : inline</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        701 : void MetainferenceBase::apply() {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">        701 :   bool wasforced=false; forcesToApply.assign(forcesToApply.size(),0.0);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      32738 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      32037 :     if( getPntrToComponent(i)-&gt;applyForce( forces ) ) {</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :       wasforced=true;</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">   41664408 :       for(unsigned i=0; i&lt;forces.size(); ++i) forcesToApply[i]+=forces[i];</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :     }</a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">        701 :   if( wasforced ) {</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">        350 :     addForcesOnArguments( forcesToApply );</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        350 :     if( getNumberOfAtoms()&gt;0 ) setForcesOnAtoms( forcesToApply, getNumberOfArguments() );</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :   }</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        701 : }</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            : inline</a>
+<a name="353"><span class="lineNum">     353 </span>            : void MetainferenceBase::setArgDerivatives(Value *v, const double &amp;d) {</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        160 :   v-&gt;addDerivative(0,d);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : inline</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">    2375432 : void MetainferenceBase::setAtomsDerivatives(Value*v, const unsigned i, const Vector&amp;d) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">    2375432 :   const unsigned noa=getNumberOfArguments();</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">    2375432 :   v-&gt;addDerivative(noa+3*i+0,d[0]);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">    2375432 :   v-&gt;addDerivative(noa+3*i+1,d[1]);</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">    2375432 :   v-&gt;addDerivative(noa+3*i+2,d[2]);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">    2375432 : }</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            : inline</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">      11848 : void MetainferenceBase::setBoxDerivatives(Value* v,const Tensor&amp;d) {</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">      11848 :   const unsigned noa=getNumberOfArguments();</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   const unsigned nat=getNumberOfAtoms();</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+0,d(0,0));</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+1,d(0,1));</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+2,d(0,2));</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+3,d(1,0));</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+4,d(1,1));</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+5,d(1,2));</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+6,d(2,0));</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+7,d(2,1));</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">      11848 :   v-&gt;addDerivative(noa+3*nat+8,d(2,2));</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">      11848 : }</span></a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            : }</a>
+<a name="382"><span class="lineNum">     382 </span>            : }</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            : #endif</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/NOE.cpp.func-sort-c.html b/coverage/isdb/NOE.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8a2fef313f
--- /dev/null
+++ b/coverage/isdb/NOE.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/NOE.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - NOE.cpp<span style="font-size: 80%;"> (<a href="NOE.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="NOE.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#99">_ZN4PLMD4isdb3NOEC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#80">_ZN4PLMD4isdb12_GLOBAL__N_115NOERegisterMe826createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#99">_ZN4PLMD4isdb3NOEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#82">_ZN4PLMD4isdb3NOE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#266">_ZN4PLMD4isdb3NOE6updateEv</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#197">_ZN4PLMD4isdb3NOE9calculateEv</a></td>
+              <td class="coverFnHi">456</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#80">_ZN4PLMD4isdb12_GLOBAL__N_115NOERegisterMe82C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#80">_ZN4PLMD4isdb12_GLOBAL__N_115NOERegisterMe82D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/NOE.cpp.func.html b/coverage/isdb/NOE.cpp.func.html
new file mode 100644
index 0000000000..55717b3694
--- /dev/null
+++ b/coverage/isdb/NOE.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/NOE.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - NOE.cpp<span style="font-size: 80%;"> (<a href="NOE.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="NOE.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#80">_ZN4PLMD4isdb12_GLOBAL__N_115NOERegisterMe826createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#80">_ZN4PLMD4isdb12_GLOBAL__N_115NOERegisterMe82C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#80">_ZN4PLMD4isdb12_GLOBAL__N_115NOERegisterMe82D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#82">_ZN4PLMD4isdb3NOE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#266">_ZN4PLMD4isdb3NOE6updateEv</a></td>
+              <td class="coverFnHi">132</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#197">_ZN4PLMD4isdb3NOE9calculateEv</a></td>
+              <td class="coverFnHi">456</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#99">_ZN4PLMD4isdb3NOEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NOE.cpp.gcov.html#99">_ZN4PLMD4isdb3NOEC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/NOE.cpp.gcov.html b/coverage/isdb/NOE.cpp.gcov.html
new file mode 100644
index 0000000000..3acd681ddd
--- /dev/null
+++ b/coverage/isdb/NOE.cpp.gcov.html
@@ -0,0 +1,350 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/NOE.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - NOE.cpp<span style="font-size: 80%;"> (source / <a href="NOE.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntryHi">98.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;memory&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace isdb {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC ISDB_COLVAR NOE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculates NOE intensities as sums of 1/r^6, also averaging over multiple equivalent atoms</a>
+<a name="34"><span class="lineNum">      34 </span>            :  or ambiguous NOE.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : Each NOE is defined by two groups containing the same number of atoms, distances are</a>
+<a name="37"><span class="lineNum">      37 </span>            : calculated in pairs, transformed in 1/r^6, summed and saved as components.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : NOE() = (\frac{1}{N_{eq}}\sum_j^{N_{eq}} (\frac{1}{r_j^6}))</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : NOE can be used to calculate a Metainference score over one or more replicas using the intrinsic implementation</a>
+<a name="44"><span class="lineNum">      44 </span>            : of \ref METAINFERENCE that is activated by DOSCORE.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : In the following examples three noes are defined, the first is calculated based on the distances</a>
+<a name="48"><span class="lineNum">      48 </span>            : of atom 1-2 and 3-2; the second is defined by the distance 5-7 and the third by the distances</a>
+<a name="49"><span class="lineNum">      49 </span>            : 4-15,4-16,8-15,8-16. \ref METAINFERENCE is activated using DOSCORE.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : NOE ...</a>
+<a name="53"><span class="lineNum">      53 </span>            : GROUPA1=1,3 GROUPB1=2,2 NOEDIST1=0.6</a>
+<a name="54"><span class="lineNum">      54 </span>            : GROUPA2=5 GROUPB2=7 NOEDIST2=0.6</a>
+<a name="55"><span class="lineNum">      55 </span>            : GROUPA3=4,4,8,8 GROUPB3=15,16,15,16 NOEDIST3=0.6</a>
+<a name="56"><span class="lineNum">      56 </span>            : DOSCORE</a>
+<a name="57"><span class="lineNum">      57 </span>            : SIGMA_MEAN0=1</a>
+<a name="58"><span class="lineNum">      58 </span>            : LABEL=noes</a>
+<a name="59"><span class="lineNum">      59 </span>            : ... NOE</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : PRINT ARG=noes.* FILE=colvar</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : */</a>
+<a name="65"><span class="lineNum">      65 </span>            : //+ENDPLUMEDOC</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : class NOE :</a>
+<a name="68"><span class="lineNum">      68 </span>            :   public MetainferenceBase</a>
+<a name="69"><span class="lineNum">      69 </span>            : {</a>
+<a name="70"><span class="lineNum">      70 </span>            : private:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   bool             pbc;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;unsigned&gt; nga;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::unique_ptr&lt;NeighborList&gt; nl;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   unsigned         tot_size;</a>
+<a name="75"><span class="lineNum">      75 </span>            : public:</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="77"><span class="lineNum">      77 </span>            :   explicit NOE(const ActionOptions&amp;);</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void calculate() override;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void update() override;</a>
+<a name="80"><span class="lineNum">      80 </span>            : };</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      12526 : PLUMED_REGISTER_ACTION(NOE,&quot;NOE&quot;)</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         13 : void NOE::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         13 :   componentsAreNotOptional(keys);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         13 :   MetainferenceBase::registerKeywords(keys);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         26 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         26 :   keys.add(&quot;numbered&quot;,&quot;GROUPA&quot;,&quot;the atoms involved in each of the contacts you wish to calculate. &quot;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :            &quot;Keywords like GROUPA1, GROUPA2, GROUPA3,... should be listed and one contact will be &quot;</a>
+<a name="90"><span class="lineNum">      90 </span>            :            &quot;calculated for each ATOM keyword you specify.&quot;);</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         26 :   keys.add(&quot;numbered&quot;,&quot;GROUPB&quot;,&quot;the atoms involved in each of the contacts you wish to calculate. &quot;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :            &quot;Keywords like GROUPB1, GROUPB2, GROUPB3,... should be listed and one contact will be &quot;</a>
+<a name="93"><span class="lineNum">      93 </span>            :            &quot;calculated for each ATOM keyword you specify.&quot;);</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         26 :   keys.reset_style(&quot;GROUPA&quot;,&quot;atoms&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         26 :   keys.reset_style(&quot;GROUPB&quot;,&quot;atoms&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         26 :   keys.add(&quot;numbered&quot;,&quot;NOEDIST&quot;,&quot;Add an experimental value for each NOE.&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         26 :   keys.addOutputComponent(&quot;noe&quot;,&quot;default&quot;,&quot;the # NOE&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         26 :   keys.addOutputComponent(&quot;exp&quot;,&quot;NOEDIST&quot;,&quot;the # NOE experimental distance&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         13 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         11 : NOE::NOE(const ActionOptions&amp;ao):</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   PLUMED_METAINF_INIT(ao),</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         11 :   pbc(true)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : {</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         11 :   bool nopbc=!pbc;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         11 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         11 :   pbc=!nopbc;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Read in the atoms</a>
+<a name="110"><span class="lineNum">     110 </span>            :   std::vector&lt;AtomNumber&gt; t, ga_lista, gb_lista;</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         22 :   for(int i=1;; ++i ) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         66 :     parseAtomList(&quot;GROUPA&quot;, i, t );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         33 :     if( t.empty() ) break;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         55 :     for(unsigned j=0; j&lt;t.size(); j++) ga_lista.push_back(t[j]);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         22 :     nga.push_back(t.size());</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         22 :     t.resize(0);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         22 :   }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   std::vector&lt;unsigned&gt; ngb;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         22 :   for(int i=1;; ++i ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         66 :     parseAtomList(&quot;GROUPB&quot;, i, t );</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         33 :     if( t.empty() ) break;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         55 :     for(unsigned j=0; j&lt;t.size(); j++) gb_lista.push_back(t[j]);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         22 :     ngb.push_back(t.size());</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         22 :     if(ngb[i-1]!=nga[i-1]) error(&quot;The same number of atoms is expected for the same GROUPA-GROUPB couple&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         22 :     t.resize(0);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         22 :   }</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         11 :   if(nga.size()!=ngb.size()) error(&quot;There should be the same number of GROUPA and GROUPB keywords&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Create neighbour lists</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         22 :   nl=Tools::make_unique&lt;NeighborList&gt;(ga_lista,gb_lista,false,true,pbc,getPbc(),comm);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Optionally add an experimental value (like with RDCs)</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::vector&lt;double&gt; noedist;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         11 :   noedist.resize( nga.size() );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   unsigned ntarget=0;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         29 :   for(unsigned i=0; i&lt;nga.size(); ++i) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         40 :     if( !parseNumbered( &quot;NOEDIST&quot;, i+1, noedist[i] ) ) break;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         18 :     ntarget++;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   bool addexp=false;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         11 :   if(ntarget!=nga.size() &amp;&amp; ntarget!=0) error(&quot;found wrong number of NOEDIST values&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         11 :   if(ntarget==nga.size()) addexp=true;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         11 :   if(getDoScore()&amp;&amp;!addexp) error(&quot;with DOSCORE you need to set the NOEDIST values&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   // Output details of all contacts</a>
+<a name="145"><span class="lineNum">     145 </span>            :   unsigned index=0;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         33 :   for(unsigned i=0; i&lt;nga.size(); ++i) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         22 :     log.printf(&quot;  The %uth NOE is calculated using %u equivalent couples of atoms\n&quot;, i, nga[i]);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         55 :     for(unsigned j=0; j&lt;nga[i]; j++) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         33 :       log.printf(&quot;    couple %u is %d %d.\n&quot;, j, ga_lista[index].serial(), gb_lista[index].serial() );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         33 :       index++;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     }</a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         11 :   tot_size = index;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         11 :   if(pbc)      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   else         log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         22 :   log &lt;&lt; &quot; Bibliography&quot; &lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         11 :   if(!getDoScore()) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         21 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         14 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         14 :       addComponentWithDerivatives(&quot;noe-&quot;+num);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         28 :       componentIsNotPeriodic(&quot;noe-&quot;+num);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     }</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          7 :     if(addexp) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         15 :       for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         10 :         std::string num; Tools::convert(i,num);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         10 :         addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         10 :         componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         10 :         Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         10 :         comp-&gt;set(noedist[i]);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :       }</a>
+<a name="174"><span class="lineNum">     174 </span>            :     }</a>
+<a name="175"><span class="lineNum">     175 </span>            :   } else {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         12 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          8 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          8 :       addComponent(&quot;noe-&quot;+num);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         16 :       componentIsNotPeriodic(&quot;noe-&quot;+num);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         12 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          8 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          8 :       addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          8 :       componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          8 :       Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          8 :       comp-&gt;set(noedist[i]);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     }</a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         11 :   requestAtoms(nl-&gt;getFullAtomList(), false);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         11 :   if(getDoScore()) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          4 :     setParameters(noedist);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 :     Initialise(nga.size());</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         11 :   setDerivatives();</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         11 :   checkRead();</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         11 : }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        456 : void NOE::calculate()</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : {</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        456 :   const unsigned ngasz=nga.size();</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        456 :   std::vector&lt;Vector&gt; deriv(tot_size, Vector{0,0,0});</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        456 :   #pragma omp parallel for num_threads(OpenMP::getNumThreads())</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   for(unsigned i=0; i&lt;ngasz; i++) {</a>
+<a name="206"><span class="lineNum">     206 </span>            :     Tensor dervir;</a>
+<a name="207"><span class="lineNum">     207 </span>            :     double noe=0;</a>
+<a name="208"><span class="lineNum">     208 </span>            :     unsigned index=0;</a>
+<a name="209"><span class="lineNum">     209 </span>            :     for(unsigned k=0; k&lt;i; k++) index+=nga[k];</a>
+<a name="210"><span class="lineNum">     210 </span>            :     std::string num; Tools::convert(i,num);</a>
+<a name="211"><span class="lineNum">     211 </span>            :     Value* val=getPntrToComponent(&quot;noe-&quot;+num);</a>
+<a name="212"><span class="lineNum">     212 </span>            :     // cycle over equivalent atoms</a>
+<a name="213"><span class="lineNum">     213 </span>            :     for(unsigned j=0; j&lt;nga[i]; j++) {</a>
+<a name="214"><span class="lineNum">     214 </span>            :       const unsigned i0=nl-&gt;getClosePair(index+j).first;</a>
+<a name="215"><span class="lineNum">     215 </span>            :       const unsigned i1=nl-&gt;getClosePair(index+j).second;</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :       Vector distance;</a>
+<a name="218"><span class="lineNum">     218 </span>            :       if(pbc) distance=pbcDistance(getPosition(i0),getPosition(i1));</a>
+<a name="219"><span class="lineNum">     219 </span>            :       else    distance=delta(getPosition(i0),getPosition(i1));</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :       const double ir2=1./distance.modulo2();</a>
+<a name="222"><span class="lineNum">     222 </span>            :       const double ir6=ir2*ir2*ir2;</a>
+<a name="223"><span class="lineNum">     223 </span>            :       const double ir8=6*ir6*ir2;</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :       noe += ir6;</a>
+<a name="226"><span class="lineNum">     226 </span>            :       deriv[index+j] = ir8*distance;</a>
+<a name="227"><span class="lineNum">     227 </span>            :       if(!getDoScore()) {</a>
+<a name="228"><span class="lineNum">     228 </span>            :         dervir += Tensor(distance, deriv[index+j]);</a>
+<a name="229"><span class="lineNum">     229 </span>            :         setAtomsDerivatives(val, i0,  deriv[index+j]);</a>
+<a name="230"><span class="lineNum">     230 </span>            :         setAtomsDerivatives(val, i1, -deriv[index+j]);</a>
+<a name="231"><span class="lineNum">     231 </span>            :       }</a>
+<a name="232"><span class="lineNum">     232 </span>            :     }</a>
+<a name="233"><span class="lineNum">     233 </span>            :     val-&gt;set(noe);</a>
+<a name="234"><span class="lineNum">     234 </span>            :     if(!getDoScore()) {</a>
+<a name="235"><span class="lineNum">     235 </span>            :       setBoxDerivatives(val, dervir);</a>
+<a name="236"><span class="lineNum">     236 </span>            :     } else setCalcData(i, noe);</a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        456 :   if(getDoScore()) {</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :     /* Metainference */</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         48 :     Tensor dervir;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         48 :     double score = getScore();</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     setScore(score);</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :     /* calculate final derivatives */</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         48 :     Value* val=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        144 :     for(unsigned i=0; i&lt;ngasz; i++) {</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :       unsigned index=0;</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        144 :       for(unsigned k=0; k&lt;i; k++) index+=nga[k];</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :       // cycle over equivalent atoms</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        240 :       for(unsigned j=0; j&lt;nga[i]; j++) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        144 :         const unsigned i0=nl-&gt;getClosePair(index+j).first;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        144 :         const unsigned i1=nl-&gt;getClosePair(index+j).second;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        144 :         Vector distance;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        144 :         if(pbc) distance=pbcDistance(getPosition(i0),getPosition(i1));</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :         else    distance=delta(getPosition(i0),getPosition(i1));</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        144 :         dervir += Tensor(distance,deriv[index+j]*getMetaDer(i));</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        144 :         setAtomsDerivatives(val, i0,  deriv[index+j]*getMetaDer(i));</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        144 :         setAtomsDerivatives(val, i1, -deriv[index+j]*getMetaDer(i));</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :       }</a>
+<a name="263"><span class="lineNum">     263 </span>            :     }</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         48 :     setBoxDerivatives(val, dervir);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        456 : }</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        132 : void NOE::update() {</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   // write status file</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        132 :   if(getWstride()&gt;0&amp;&amp; (getStep()%getWstride()==0 || getCPT()) ) writeStatus();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        132 : }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : }</a>
+<a name="274"><span class="lineNum">     274 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/PRE.cpp.func-sort-c.html b/coverage/isdb/PRE.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2b060d3df4
--- /dev/null
+++ b/coverage/isdb/PRE.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/PRE.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - PRE.cpp<span style="font-size: 80%;"> (<a href="PRE.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">129</td>
+            <td class="headerCovTableEntryHi">92.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PRE.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#109">_ZN4PLMD4isdb3PREC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#87">_ZN4PLMD4isdb12_GLOBAL__N_115PRERegisterMe896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#109">_ZN4PLMD4isdb3PREC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#89">_ZN4PLMD4isdb3PRE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#332">_ZN4PLMD4isdb3PRE6updateEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#247">_ZN4PLMD4isdb3PRE9calculateEv</a></td>
+              <td class="coverFnHi">350</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#87">_ZN4PLMD4isdb12_GLOBAL__N_115PRERegisterMe89C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#87">_ZN4PLMD4isdb12_GLOBAL__N_115PRERegisterMe89D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/PRE.cpp.func.html b/coverage/isdb/PRE.cpp.func.html
new file mode 100644
index 0000000000..aa3ce36632
--- /dev/null
+++ b/coverage/isdb/PRE.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/PRE.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - PRE.cpp<span style="font-size: 80%;"> (<a href="PRE.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">129</td>
+            <td class="headerCovTableEntryHi">92.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PRE.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#87">_ZN4PLMD4isdb12_GLOBAL__N_115PRERegisterMe896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#87">_ZN4PLMD4isdb12_GLOBAL__N_115PRERegisterMe89C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#87">_ZN4PLMD4isdb12_GLOBAL__N_115PRERegisterMe89D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#89">_ZN4PLMD4isdb3PRE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#332">_ZN4PLMD4isdb3PRE6updateEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#247">_ZN4PLMD4isdb3PRE9calculateEv</a></td>
+              <td class="coverFnHi">350</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#109">_ZN4PLMD4isdb3PREC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PRE.cpp.gcov.html#109">_ZN4PLMD4isdb3PREC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/PRE.cpp.gcov.html b/coverage/isdb/PRE.cpp.gcov.html
new file mode 100644
index 0000000000..198238148e
--- /dev/null
+++ b/coverage/isdb/PRE.cpp.gcov.html
@@ -0,0 +1,416 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/PRE.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - PRE.cpp<span style="font-size: 80%;"> (source / <a href="PRE.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">129</td>
+            <td class="headerCovTableEntryHi">92.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;memory&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace isdb {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC ISDB_COLVAR PRE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculates the Paramagnetic Resonance Enhancement intensity ratio between a spin label atom and a list of atoms .</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The reference atom for the spin label is added with SPINLABEL, the affected atom(s)</a>
+<a name="36"><span class="lineNum">      36 </span>            : are give as numbered GROUPA1, GROUPA2, ...</a>
+<a name="37"><span class="lineNum">      37 </span>            : The additional parameters needed for the calculation are given as INEPT, the inept</a>
+<a name="38"><span class="lineNum">      38 </span>            : time, TAUC the correlation time, OMEGA, the Larmor frequency and RTWO for the relaxation</a>
+<a name="39"><span class="lineNum">      39 </span>            : time.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \ref METAINFERENCE can be activated using DOSCORE and the other relevant keywords.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : In the following example five PRE intensities are calculated using the distance between the</a>
+<a name="46"><span class="lineNum">      46 </span>            : oxygen of the spin label and the backbone hydrogen atoms. Omega is the NMR frequency, RTWO the</a>
+<a name="47"><span class="lineNum">      47 </span>            : R2 for the hydrogen atoms, INEPT of 8 ms for the experiment and a TAUC of 1.21 ns</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : PRE ...</a>
+<a name="51"><span class="lineNum">      51 </span>            : LABEL=HN_pre</a>
+<a name="52"><span class="lineNum">      52 </span>            : INEPT=8</a>
+<a name="53"><span class="lineNum">      53 </span>            : TAUC=1.21</a>
+<a name="54"><span class="lineNum">      54 </span>            : OMEGA=900</a>
+<a name="55"><span class="lineNum">      55 </span>            : SPINLABEL=1818</a>
+<a name="56"><span class="lineNum">      56 </span>            : GROUPA1=86  RTWO1=0.0120272827</a>
+<a name="57"><span class="lineNum">      57 </span>            : GROUPA2=177 RTWO2=0.0263953158</a>
+<a name="58"><span class="lineNum">      58 </span>            : GROUPA3=285 RTWO3=0.0058899829</a>
+<a name="59"><span class="lineNum">      59 </span>            : GROUPA4=335 RTWO4=0.0102072646</a>
+<a name="60"><span class="lineNum">      60 </span>            : GROUPA5=451 RTWO5=0.0086341843</a>
+<a name="61"><span class="lineNum">      61 </span>            : ... PRE</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : PRINT ARG=HN_pre.* FILE=PRE.dat STRIDE=1</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \endplumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : //+ENDPLUMEDOC</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : class PRE :</a>
+<a name="71"><span class="lineNum">      71 </span>            :   public MetainferenceBase</a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span>            : private:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   bool             pbc;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool             doratio;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   double           constant;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   double           inept;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::vector&lt;double&gt;   rtwo;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;unsigned&gt; nga;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::unique_ptr&lt;NeighborList&gt; nl;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   unsigned         tot_size;</a>
+<a name="82"><span class="lineNum">      82 </span>            : public:</a>
+<a name="83"><span class="lineNum">      83 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="84"><span class="lineNum">      84 </span>            :   explicit PRE(const ActionOptions&amp;);</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void calculate() override;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void update() override;</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(PRE,&quot;PRE&quot;)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 : void PRE::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          6 :   componentsAreNotOptional(keys);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          6 :   MetainferenceBase::registerKeywords(keys);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         12 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         12 :   keys.addFlag(&quot;NORATIO&quot;,false,&quot;Set to TRUE if you want to compute PRE without Intensity Ratio&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;INEPT&quot;,&quot;is the INEPT time (in ms).&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;TAUC&quot;,&quot;is the correlation time (in ns) for this electron-nuclear interaction.&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;OMEGA&quot;,&quot;is the Larmor frequency of the nuclear spin (in MHz).&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         12 :   keys.add(&quot;atoms&quot;,&quot;SPINLABEL&quot;,&quot;The atom to be used as the paramagnetic center.&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;GROUPA&quot;,&quot;the atoms involved in each of the contacts you wish to calculate. &quot;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :            &quot;Keywords like GROUPA1, GROUPA2, GROUPA3,... should be listed and one contact will be &quot;</a>
+<a name="102"><span class="lineNum">     102 </span>            :            &quot;calculated for each ATOM keyword you specify.&quot;);</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         12 :   keys.reset_style(&quot;GROUPA&quot;,&quot;atoms&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;RTWO&quot;,&quot;The relaxation of the atom/atoms in the corresponding GROUPA of atoms. &quot;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :            &quot;Keywords like RTWO1, RTWO2, RTWO3,... should be listed.&quot;);</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;PREINT&quot;,&quot;Add an experimental value for each PRE.&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;pre&quot;,&quot;default&quot;,&quot;the # PRE&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;exp&quot;,&quot;PREINT&quot;,&quot;the # PRE experimental intensity&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          6 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          4 : PRE::PRE(const ActionOptions&amp;ao):</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   PLUMED_METAINF_INIT(ao),</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 :   pbc(true),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          4 :   doratio(true)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : {</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          4 :   bool nopbc=!pbc;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          4 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          4 :   pbc=!nopbc;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          4 :   bool noratio=!doratio;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          4 :   parseFlag(&quot;NORATIO&quot;,noratio);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          4 :   doratio=!noratio;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   parseAtomList(&quot;SPINLABEL&quot;,atom);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          4 :   if(atom.size()!=1) error(&quot;Number of specified atom should be 1&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Read in the atoms</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector&lt;AtomNumber&gt; t, ga_lista, gb_lista;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         12 :   for(int i=1;; ++i ) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         32 :     parseAtomList(&quot;GROUPA&quot;, i, t );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         16 :     if( t.empty() ) break;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         28 :     for(unsigned j=0; j&lt;t.size(); j++) {ga_lista.push_back(t[j]); gb_lista.push_back(atom[0]);}</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         12 :     nga.push_back(t.size());</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         12 :     t.resize(0);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         12 :   }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Read in reference values</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :   rtwo.resize( nga.size() );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          4 :   if(doratio) {</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     unsigned ntarget=0;</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;nga.size(); ++i) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          8 :       if( !parseNumbered( &quot;RTWO&quot;, i+1, rtwo[i] ) ) break;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :       ntarget++;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :     }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :     if( ntarget==0 ) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 :       parse(&quot;RTWO&quot;,rtwo[0]);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         12 :       for(unsigned i=1; i&lt;nga.size(); ++i) rtwo[i]=rtwo[0];</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     } else if( ntarget!=nga.size() ) error(&quot;found wrong number of RTWO values&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   double tauc=0.;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :   parse(&quot;TAUC&quot;,tauc);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :   if(tauc==0.) error(&quot;TAUC must be set&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :   double omega=0.;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          4 :   parse(&quot;OMEGA&quot;,omega);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :   if(omega==0.) error(&quot;OMEGA must be set&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          4 :   inept=0.;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          4 :   if(doratio) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          4 :     parse(&quot;INEPT&quot;,inept);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          4 :     if(inept==0.) error(&quot;INEPT must be set&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          4 :     inept *= 0.001; // ms2s</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   const double ns2s   = 0.000000001;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   const double MHz2Hz = 1000000.;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   const double Kappa  = 12300000000.00; // this is 1/15*S*(S+1)*gamma^2*g^2*beta^2</a>
+<a name="170"><span class="lineNum">     170 </span>            :   // where gamma is the nuclear gyromagnetic ratio,</a>
+<a name="171"><span class="lineNum">     171 </span>            :   // g is the electronic g factor, and beta is the Bohr magneton</a>
+<a name="172"><span class="lineNum">     172 </span>            :   // in nm^6/s^2</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 :   constant = (4.*tauc*ns2s+(3.*tauc*ns2s)/(1+omega*omega*MHz2Hz*MHz2Hz*tauc*tauc*ns2s*ns2s))*Kappa;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            :   // Optionally add an experimental value (like with RDCs)</a>
+<a name="176"><span class="lineNum">     176 </span>            :   std::vector&lt;double&gt; exppre;</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 :   exppre.resize( nga.size() );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   unsigned ntarget=0;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;nga.size(); ++i) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         16 :     if( !parseNumbered( &quot;PREINT&quot;, i+1, exppre[i] ) ) break;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          6 :     ntarget++;</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span>            :   bool addexp=false;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :   if(ntarget!=nga.size() &amp;&amp; ntarget!=0) error(&quot;found wrong number of PREINT values&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 :   if(ntarget==nga.size()) addexp=true;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          4 :   if(getDoScore()&amp;&amp;!addexp) error(&quot;with DOSCORE you need to set the PREINT values&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   // Create neighbour lists</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          8 :   nl=Tools::make_unique&lt;NeighborList&gt;(gb_lista,ga_lista,false,true,pbc,getPbc(),comm);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Output details of all contacts</a>
+<a name="192"><span class="lineNum">     192 </span>            :   unsigned index=0;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         16 :   for(unsigned i=0; i&lt;nga.size(); ++i) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         12 :     log.printf(&quot;  The %uth PRE is calculated using %u equivalent atoms:\n&quot;, i, nga[i]);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         12 :     log.printf(&quot;    %d&quot;, ga_lista[index].serial());</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         12 :     index++;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         16 :     for(unsigned j=1; j&lt;nga[i]; j++) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          4 :       log.printf(&quot; %d&quot;, ga_lista[index].serial());</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          4 :       index++;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         12 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          4 :   tot_size = index;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          4 :   if(pbc)      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :   else         log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          8 :   log &lt;&lt; &quot; Bibliography&quot; &lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          4 :   if(!getDoScore()) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          8 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          6 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          6 :       addComponentWithDerivatives(&quot;pre-&quot;+num);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         12 :       componentIsNotPeriodic(&quot;pre-&quot;+num);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :     }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          2 :     if(addexp) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :         std::string num; Tools::convert(i,num);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :         addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :         componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :         Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :         comp-&gt;set(exppre[i]);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :       }</a>
+<a name="224"><span class="lineNum">     224 </span>            :     }</a>
+<a name="225"><span class="lineNum">     225 </span>            :   } else {</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          8 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          6 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          6 :       addComponent(&quot;pre-&quot;+num);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         12 :       componentIsNotPeriodic(&quot;pre-&quot;+num);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          8 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          6 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          6 :       addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          6 :       componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          6 :       Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          6 :       comp-&gt;set(exppre[i]);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     }</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          4 :   requestAtoms(nl-&gt;getFullAtomList(), false);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          4 :   if(getDoScore()) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          2 :     setParameters(exppre);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          2 :     Initialise(nga.size());</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   }</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          4 :   setDerivatives();</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          4 : }</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        350 : void PRE::calculate()</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : {</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        350 :   std::vector&lt;Vector&gt; deriv(tot_size, Vector{0,0,0});</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        350 :   std::vector&lt;double&gt; fact(nga.size(), 0.);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :   // cycle over the number of PRE</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        350 :   #pragma omp parallel for num_threads(OpenMP::getNumThreads())</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   for(unsigned i=0; i&lt;nga.size(); i++) {</a>
+<a name="257"><span class="lineNum">     257 </span>            :     Tensor dervir;</a>
+<a name="258"><span class="lineNum">     258 </span>            :     double pre=0;</a>
+<a name="259"><span class="lineNum">     259 </span>            :     unsigned index=0;</a>
+<a name="260"><span class="lineNum">     260 </span>            :     for(unsigned k=0; k&lt;i; k++) index+=nga[k];</a>
+<a name="261"><span class="lineNum">     261 </span>            :     const double c_aver=constant/static_cast&lt;double&gt;(nga[i]);</a>
+<a name="262"><span class="lineNum">     262 </span>            :     std::string num; Tools::convert(i,num);</a>
+<a name="263"><span class="lineNum">     263 </span>            :     Value* val=getPntrToComponent(&quot;pre-&quot;+num);</a>
+<a name="264"><span class="lineNum">     264 </span>            :     // cycle over equivalent atoms</a>
+<a name="265"><span class="lineNum">     265 </span>            :     for(unsigned j=0; j&lt;nga[i]; j++) {</a>
+<a name="266"><span class="lineNum">     266 </span>            :       // the first atom is always the same (the paramagnetic group)</a>
+<a name="267"><span class="lineNum">     267 </span>            :       const unsigned i0=nl-&gt;getClosePair(index+j).first;</a>
+<a name="268"><span class="lineNum">     268 </span>            :       const unsigned i1=nl-&gt;getClosePair(index+j).second;</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :       Vector distance;</a>
+<a name="271"><span class="lineNum">     271 </span>            :       if(pbc) distance=pbcDistance(getPosition(i0),getPosition(i1));</a>
+<a name="272"><span class="lineNum">     272 </span>            :       else    distance=delta(getPosition(i0),getPosition(i1));</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :       const double r2=distance.modulo2();</a>
+<a name="275"><span class="lineNum">     275 </span>            :       const double r6=r2*r2*r2;</a>
+<a name="276"><span class="lineNum">     276 </span>            :       const double r8=r6*r2;</a>
+<a name="277"><span class="lineNum">     277 </span>            :       const double tmpir6=c_aver/r6;</a>
+<a name="278"><span class="lineNum">     278 </span>            :       const double tmpir8=-6.*c_aver/r8;</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :       pre += tmpir6;</a>
+<a name="281"><span class="lineNum">     281 </span>            :       deriv[index+j] = -tmpir8*distance;</a>
+<a name="282"><span class="lineNum">     282 </span>            :       if(!getDoScore()) dervir   +=  Tensor(distance,deriv[index+j]);</a>
+<a name="283"><span class="lineNum">     283 </span>            :     }</a>
+<a name="284"><span class="lineNum">     284 </span>            :     double tmpratio;</a>
+<a name="285"><span class="lineNum">     285 </span>            :     if(!doratio) {</a>
+<a name="286"><span class="lineNum">     286 </span>            :       tmpratio = pre ; //prova a caso per vedere se lui da problemi</a>
+<a name="287"><span class="lineNum">     287 </span>            :       fact[i] = 1.; //prova a caso per vedere se lui da problemi</a>
+<a name="288"><span class="lineNum">     288 </span>            :     } else {</a>
+<a name="289"><span class="lineNum">     289 </span>            :       tmpratio = rtwo[i]*std::exp(-pre*inept) / (rtwo[i]+pre);</a>
+<a name="290"><span class="lineNum">     290 </span>            :       fact[i] = -tmpratio*(inept+1./(rtwo[i]+pre));</a>
+<a name="291"><span class="lineNum">     291 </span>            :     }</a>
+<a name="292"><span class="lineNum">     292 </span>            :     const double ratio = tmpratio;</a>
+<a name="293"><span class="lineNum">     293 </span>            :     val-&gt;set(ratio) ;</a>
+<a name="294"><span class="lineNum">     294 </span>            :     if(!getDoScore()) {</a>
+<a name="295"><span class="lineNum">     295 </span>            :       setBoxDerivatives(val, fact[i]*dervir);</a>
+<a name="296"><span class="lineNum">     296 </span>            :       for(unsigned j=0; j&lt;nga[i]; j++) {</a>
+<a name="297"><span class="lineNum">     297 </span>            :         const unsigned i0=nl-&gt;getClosePair(index+j).first;</a>
+<a name="298"><span class="lineNum">     298 </span>            :         const unsigned i1=nl-&gt;getClosePair(index+j).second;</a>
+<a name="299"><span class="lineNum">     299 </span>            :         setAtomsDerivatives(val, i0,  fact[i]*deriv[index+j]);</a>
+<a name="300"><span class="lineNum">     300 </span>            :         setAtomsDerivatives(val, i1, -fact[i]*deriv[index+j]);</a>
+<a name="301"><span class="lineNum">     301 </span>            :       }</a>
+<a name="302"><span class="lineNum">     302 </span>            :     } else setCalcData(i, ratio);</a>
+<a name="303"><span class="lineNum">     303 </span>            :   }</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        350 :   if(getDoScore()) {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     /* Metainference */</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">        175 :     Tensor dervir;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">        175 :     double score = getScore();</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :     setScore(score);</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :     /* calculate final derivatives */</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        175 :     Value* val=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        700 :     for(unsigned i=0; i&lt;nga.size(); i++) {</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :       unsigned index=0;</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       1050 :       for(unsigned k=0; k&lt;i; k++) index+=nga[k];</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :       // cycle over equivalent atoms</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       1225 :       for(unsigned j=0; j&lt;nga[i]; j++) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        700 :         const unsigned i0=nl-&gt;getClosePair(index+j).first;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        700 :         const unsigned i1=nl-&gt;getClosePair(index+j).second;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        700 :         Vector distance;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        700 :         if(pbc) distance=pbcDistance(getPosition(i0),getPosition(i1));</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :         else    distance=delta(getPosition(i0),getPosition(i1));</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        700 :         dervir += Tensor(distance,fact[i]*deriv[index+j]*getMetaDer(i));</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">        700 :         setAtomsDerivatives(val, i0,  fact[i]*deriv[index+j]*getMetaDer(i));</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">        700 :         setAtomsDerivatives(val, i1, -fact[i]*deriv[index+j]*getMetaDer(i));</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :       }</a>
+<a name="329"><span class="lineNum">     329 </span>            :     }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">        175 :     setBoxDerivatives(val, dervir);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   }</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        350 : }</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         20 : void PRE::update() {</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :   // write status file</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         20 :   if(getWstride()&gt;0&amp;&amp; (getStep()%getWstride()==0 || getCPT()) ) writeStatus();</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         20 : }</span></a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : }</a>
+<a name="340"><span class="lineNum">     340 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/RDC.cpp.func-sort-c.html b/coverage/isdb/RDC.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f9f080dd2d
--- /dev/null
+++ b/coverage/isdb/RDC.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/RDC.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - RDC.cpp<span style="font-size: 80%;"> (<a href="RDC.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">182</td>
+            <td class="headerCovTableEntryHi">94.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RDC.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#219">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe2216createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#243">_ZN4PLMD4isdb3RDCC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#367">_ZN4PLMD4isdb3RDC6do_svdEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#218">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe2206createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
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+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#243">_ZN4PLMD4isdb3RDCC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
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+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#221">_ZN4PLMD4isdb3RDC16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">33</td>
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+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#513">_ZN4PLMD4isdb3RDC6updateEv</a></td>
+              <td class="coverFnHi">327</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#439">_ZN4PLMD4isdb3RDC9calculateEv</a></td>
+              <td class="coverFnHi">2172</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#218">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe220C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#218">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe220D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#219">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe221C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#219">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe221D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/RDC.cpp.func.html b/coverage/isdb/RDC.cpp.func.html
new file mode 100644
index 0000000000..51f6e0635d
--- /dev/null
+++ b/coverage/isdb/RDC.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/RDC.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - RDC.cpp<span style="font-size: 80%;"> (<a href="RDC.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">182</td>
+            <td class="headerCovTableEntryHi">94.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="RDC.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#218">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe2206createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#218">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe220C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#218">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe220D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="RDC.cpp.gcov.html#219">_ZN4PLMD4isdb12_GLOBAL__N_116RDCRegisterMe2216createERKNS_13ActionOptionsE</a></td>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</html>
diff --git a/coverage/isdb/RDC.cpp.gcov.html b/coverage/isdb/RDC.cpp.gcov.html
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+  <title>LCOV - plumed test coverage - isdb/RDC.cpp</title>
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+</head>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - RDC.cpp<span style="font-size: 80%;"> (source / <a href="RDC.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">171</td>
+            <td class="headerCovTableEntry">182</td>
+            <td class="headerCovTableEntryHi">94.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #ifdef __PLUMED_HAS_GSL</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;gsl/gsl_vector.h&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;gsl/gsl_matrix.h&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;gsl/gsl_linalg.h&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;gsl/gsl_blas.h&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #endif</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace isdb {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC ISDB_COLVAR RDC</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculates the (Residual) Dipolar Coupling between two atoms.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The Dipolar Coupling between two nuclei depends on the \f$\theta\f$ angle between</a>
+<a name="41"><span class="lineNum">      41 </span>            : the inter-nuclear vector and the external magnetic field.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : D=D_{max}0.5(3\cos^2(\theta)-1)</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : where</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \f[</a>
+<a name="50"><span class="lineNum">      50 </span>            : D_{max}=-\mu_0\gamma_1\gamma_2h/(8\pi^3r^3)</a>
+<a name="51"><span class="lineNum">      51 </span>            : \f]</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : that is the maximal value of the dipolar coupling for the two nuclear spins with gyromagnetic ratio \f$\gamma\f$.</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f$\mu\f$ is the magnetic constant and h is the Planck constant.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : Common Gyromagnetic Ratios (C.G.S)</a>
+<a name="57"><span class="lineNum">      57 </span>            : - H(1) 26.7513</a>
+<a name="58"><span class="lineNum">      58 </span>            : - C(13) 6.7261</a>
+<a name="59"><span class="lineNum">      59 </span>            : - N(15) -2.7116</a>
+<a name="60"><span class="lineNum">      60 </span>            : and their products (this is what is given in input using the keyword GYROM)</a>
+<a name="61"><span class="lineNum">      61 </span>            : - N-H -72.5388</a>
+<a name="62"><span class="lineNum">      62 </span>            : - C-H 179.9319</a>
+<a name="63"><span class="lineNum">      63 </span>            : - C-N -18.2385</a>
+<a name="64"><span class="lineNum">      64 </span>            : - C-C 45.2404</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : In isotropic media DCs average to zero because of the rotational</a>
+<a name="67"><span class="lineNum">      67 </span>            : averaging, but when the rotational symmetry is broken, either through the introduction of an alignment medium or for molecules</a>
+<a name="68"><span class="lineNum">      68 </span>            : with highly anisotropic paramagnetic susceptibility, then the average of the DCs is not zero and it is possible to measure a Residual Dipolar Coupling (RDCs).</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : This collective variable calculates the Dipolar Coupling for a set of couple of atoms using</a>
+<a name="71"><span class="lineNum">      71 </span>            : the above definition.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : In a standard MD simulation the average over time of the DC should then be zero. If one wants to model the meaning of a set of measured RDCs it is possible to try to solve the following problem: &quot;what is the distribution of structures and orientations that reproduce the measured RDCs&quot;.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : This collective variable can then be use to break the rotational symmetry of a simulation by imposing that the average of the DCs over the conformational ensemble must be equal to the measured RDCs \cite Camilloni:2015ka . Since measured RDCs are also a function of the fraction of aligned molecules in the sample it is better to compare them modulo a constant or looking at the correlation.</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : Alternatively if the molecule is rigid it is possible to use the experimental data to calculate the alignment tensor and the use that to back calculate the RDCs, this is what is usually call the Single Value Decomposition approach. In this case the code rely on the</a>
+<a name="78"><span class="lineNum">      78 </span>            : a set of function from the GNU Scientific Library (GSL). (With SVD forces are not currently implemented).</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : Replica-Averaged simulations can be performed using RDCs, \ref ENSEMBLE, \ref STATS and \ref RESTRAINT .</a>
+<a name="81"><span class="lineNum">      81 </span>            : \ref METAINFERENCE can be activated using DOSCORE and the other relevant keywords.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : Additional material and examples can be also found in the tutorial \ref isdb-1</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : \par Examples</a>
+<a name="86"><span class="lineNum">      86 </span>            : In the following example five N-H RDCs are defined and averaged over multiple replicas,</a>
+<a name="87"><span class="lineNum">      87 </span>            : their correlation is then calculated with respect to a set of experimental data and restrained.</a>
+<a name="88"><span class="lineNum">      88 </span>            : In addition, and only for analysis purposes, the same RDCs each single conformation are calculated</a>
+<a name="89"><span class="lineNum">      89 </span>            : using a Single Value Decomposition algorithm, then averaged and again compared with the experimental data.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \plumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : #SETTINGS NREPLICAS=2</a>
+<a name="93"><span class="lineNum">      93 </span>            : RDC ...</a>
+<a name="94"><span class="lineNum">      94 </span>            : GYROM=-72.5388</a>
+<a name="95"><span class="lineNum">      95 </span>            : SCALE=0.001</a>
+<a name="96"><span class="lineNum">      96 </span>            : ATOMS1=20,21</a>
+<a name="97"><span class="lineNum">      97 </span>            : ATOMS2=37,38</a>
+<a name="98"><span class="lineNum">      98 </span>            : ATOMS3=56,57</a>
+<a name="99"><span class="lineNum">      99 </span>            : ATOMS4=76,77</a>
+<a name="100"><span class="lineNum">     100 </span>            : ATOMS5=92,93</a>
+<a name="101"><span class="lineNum">     101 </span>            : LABEL=nh</a>
+<a name="102"><span class="lineNum">     102 </span>            : ... RDC</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : erdc: ENSEMBLE ARG=nh.*</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : st: STATS ARG=erdc.* PARAMETERS=8.17,-8.271,-10.489,-9.871,-9.152</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : rdce: RESTRAINT ARG=st.corr KAPPA=0. SLOPE=-25000.0 AT=1.</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : RDC ...</a>
+<a name="111"><span class="lineNum">     111 </span>            : GYROM=-72.5388</a>
+<a name="112"><span class="lineNum">     112 </span>            : SVD</a>
+<a name="113"><span class="lineNum">     113 </span>            : ATOMS1=20,21 COUPLING1=8.17</a>
+<a name="114"><span class="lineNum">     114 </span>            : ATOMS2=37,38 COUPLING2=-8.271</a>
+<a name="115"><span class="lineNum">     115 </span>            : ATOMS3=56,57 COUPLING3=-10.489</a>
+<a name="116"><span class="lineNum">     116 </span>            : ATOMS4=76,77 COUPLING4=-9.871</a>
+<a name="117"><span class="lineNum">     117 </span>            : ATOMS5=92,93 COUPLING5=-9.152</a>
+<a name="118"><span class="lineNum">     118 </span>            : LABEL=svd</a>
+<a name="119"><span class="lineNum">     119 </span>            : ... RDC</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : esvd: ENSEMBLE ARG=(svd\.rdc-.*)</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : st_svd: STATS ARG=esvd.* PARAMETERS=8.17,-8.271,-10.489,-9.871,-9.152</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : PRINT ARG=st.corr,st_svd.corr,rdce.bias FILE=colvar</a>
+<a name="126"><span class="lineNum">     126 </span>            : \endplumedfile</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : */</a>
+<a name="129"><span class="lineNum">     129 </span>            : //+ENDPLUMEDOC</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : //+PLUMEDOC ISDB_COLVAR PCS</a>
+<a name="132"><span class="lineNum">     132 </span>            : /*</a>
+<a name="133"><span class="lineNum">     133 </span>            : Calculates the Pseudo-contact shift of a nucleus determined by the presence of a metal ion susceptible to anisotropic magnetization.</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : The PCS of an atomic nucleus depends on the \f$\theta\f$ angle between the vector from the spin-label to the nucleus</a>
+<a name="136"><span class="lineNum">     136 </span>            :  and the external magnetic field and the module of the vector itself \cite Camilloni:2015jf . While in principle the averaging</a>
+<a name="137"><span class="lineNum">     137 </span>            : resulting from the tumbling should remove the pseudo-contact shift, in presence of the NMR magnetic field the magnetically anisotropic molecule bound to system will break the rotational symmetry does resulting in measurable values for the PCS and RDC.</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : PCS values can also be calculated using a Single Value Decomposition approach, in this case the code rely on the</a>
+<a name="140"><span class="lineNum">     140 </span>            : a set of function from the GNU Scientific Library (GSL). (With SVD forces are not currently implemented).</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : Replica-Averaged simulations can be performed using PCS values, \ref ENSEMBLE, \ref STATS and \ref RESTRAINT .</a>
+<a name="143"><span class="lineNum">     143 </span>            : Metainference simulations can be performed with this CV and \ref METAINFERENCE .</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : \par Examples</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : In the following example five PCS values are defined and their correlation with</a>
+<a name="148"><span class="lineNum">     148 </span>            : respect to a set of experimental data is calculated and restrained. In addition,</a>
+<a name="149"><span class="lineNum">     149 </span>            : and only for analysis purposes, the same PCS values are calculated using a Single Value</a>
+<a name="150"><span class="lineNum">     150 </span>            : Decomposition algorithm.</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : \plumedfile</a>
+<a name="153"><span class="lineNum">     153 </span>            : PCS ...</a>
+<a name="154"><span class="lineNum">     154 </span>            : ATOMS1=20,21</a>
+<a name="155"><span class="lineNum">     155 </span>            : ATOMS2=20,38</a>
+<a name="156"><span class="lineNum">     156 </span>            : ATOMS3=20,57</a>
+<a name="157"><span class="lineNum">     157 </span>            : ATOMS4=20,77</a>
+<a name="158"><span class="lineNum">     158 </span>            : ATOMS5=20,93</a>
+<a name="159"><span class="lineNum">     159 </span>            : LABEL=nh</a>
+<a name="160"><span class="lineNum">     160 </span>            : ... PCS</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : enh: ENSEMBLE ARG=nh.*</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : st: STATS ARG=enh.* PARAMETERS=8.17,-8.271,-10.489,-9.871,-9.152</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : pcse: RESTRAINT ARG=st.corr KAPPA=0. SLOPE=-25000.0 AT=1.</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : PRINT ARG=st.corr,pcse.bias FILE=colvar</a>
+<a name="169"><span class="lineNum">     169 </span>            : \endplumedfile</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : */</a>
+<a name="172"><span class="lineNum">     172 </span>            : //+ENDPLUMEDOC</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : class RDC :</a>
+<a name="175"><span class="lineNum">     175 </span>            :   public MetainferenceBase</a>
+<a name="176"><span class="lineNum">     176 </span>            : {</a>
+<a name="177"><span class="lineNum">     177 </span>            : private:</a>
+<a name="178"><span class="lineNum">     178 </span>            :   double         Const;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   double         mu_s;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   double         scale;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   std::vector&lt;double&gt; coupl;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   bool           svd;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   bool           pbc;</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : #ifdef __PLUMED_HAS_GSL</a>
+<a name="186"><span class="lineNum">     186 </span>            : /// Auxiliary class to delete a gsl_vector.</a>
+<a name="187"><span class="lineNum">     187 </span>            : /// If used somewhere else we can move it.</a>
+<a name="188"><span class="lineNum">     188 </span>            :   struct gsl_vector_deleter {</a>
+<a name="189"><span class="lineNum">     189 </span>            :     void operator()(gsl_vector* p) {</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         25 :       gsl_vector_free(p);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         25 :     }</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   };</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : /// unique_ptr to a gsl_vector.</a>
+<a name="195"><span class="lineNum">     195 </span>            : /// Gets deleted when going out of scope.</a>
+<a name="196"><span class="lineNum">     196 </span>            :   typedef std::unique_ptr&lt;gsl_vector,gsl_vector_deleter&gt; gsl_vector_unique_ptr;</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : /// Auxiliary class to delete a gsl_matrix.</a>
+<a name="199"><span class="lineNum">     199 </span>            : /// If used somewhere else we can move it.</a>
+<a name="200"><span class="lineNum">     200 </span>            :   struct gsl_matrix_deleter {</a>
+<a name="201"><span class="lineNum">     201 </span>            :     void operator()(gsl_matrix* p) {</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         15 :       gsl_matrix_free(p);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         15 :     }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   };</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : /// unique_ptr to a gsl_matrix.</a>
+<a name="207"><span class="lineNum">     207 </span>            : /// Gets deleted when going out of scope.</a>
+<a name="208"><span class="lineNum">     208 </span>            :   typedef std::unique_ptr&lt;gsl_matrix,gsl_matrix_deleter&gt; gsl_matrix_unique_ptr;</a>
+<a name="209"><span class="lineNum">     209 </span>            : #endif</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            :   void do_svd();</a>
+<a name="213"><span class="lineNum">     213 </span>            : public:</a>
+<a name="214"><span class="lineNum">     214 </span>            :   explicit RDC(const ActionOptions&amp;);</a>
+<a name="215"><span class="lineNum">     215 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="216"><span class="lineNum">     216 </span>            :   void calculate() override;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   void update() override;</a>
+<a name="218"><span class="lineNum">     218 </span>            : };</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      12562 : PLUMED_REGISTER_ACTION(RDC,&quot;RDC&quot;)</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(RDC,&quot;PCS&quot;)</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         33 : void RDC::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         33 :   componentsAreNotOptional(keys);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         33 :   MetainferenceBase::registerKeywords(keys);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         66 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         66 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the couple of atoms involved in each of the bonds for which you wish to calculate the RDC. &quot;</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one dipolar coupling will be &quot;</a>
+<a name="229"><span class="lineNum">     229 </span>            :            &quot;calculated for each ATOMS keyword you specify.&quot;);</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         66 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         66 :   keys.add(&quot;compulsory&quot;,&quot;GYROM&quot;,&quot;1.&quot;,&quot;Add the product of the gyromagnetic constants for the bond. &quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         66 :   keys.add(&quot;compulsory&quot;,&quot;SCALE&quot;,&quot;1.&quot;,&quot;Add the scaling factor to take into account concentration and other effects. &quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         66 :   keys.addFlag(&quot;SVD&quot;,false,&quot;Set to TRUE if you want to back calculate using Single Value Decomposition (need GSL at compilation time).&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         66 :   keys.add(&quot;numbered&quot;,&quot;COUPLING&quot;,&quot;Add an experimental value for each coupling (needed by SVD and useful for \\ref STATS).&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;rdc&quot;,&quot;default&quot;,&quot;the calculated # RDC&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;exp&quot;,&quot;SVD/COUPLING&quot;,&quot;the experimental # RDC&quot;);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;Sxx&quot;,&quot;SVD&quot;,&quot;Tensor component&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;Syy&quot;,&quot;SVD&quot;,&quot;Tensor component&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;Szz&quot;,&quot;SVD&quot;,&quot;Tensor component&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;Sxy&quot;,&quot;SVD&quot;,&quot;Tensor component&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;Sxz&quot;,&quot;SVD&quot;,&quot;Tensor component&quot;);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         66 :   keys.addOutputComponent(&quot;Syz&quot;,&quot;SVD&quot;,&quot;Tensor component&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         33 : }</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         29 : RDC::RDC(const ActionOptions&amp;ao):</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   PLUMED_METAINF_INIT(ao),</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         29 :   Const(1.),</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         29 :   mu_s(1.),</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         29 :   scale(1.),</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         29 :   pbc(true)</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : {</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         29 :   bool nopbc=!pbc;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         29 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         29 :   pbc=!nopbc;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            :   const double RDCConst = 0.3356806;</a>
+<a name="257"><span class="lineNum">     257 </span>            :   const double PCSConst = 1.0;</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         29 :   if( getName().find(&quot;RDC&quot;)!=std::string::npos) { Const *= RDCConst; }</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :   else if( getName().find(&quot;PCS&quot;)!=std::string::npos) { Const *= PCSConst; }</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :   // Read in the atoms</a>
+<a name="263"><span class="lineNum">     263 </span>            :   std::vector&lt;AtomNumber&gt; t, atoms;</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         29 :   for(int i=1;; ++i ) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        292 :     parseAtomList(&quot;ATOMS&quot;, i, t );</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        146 :     if( t.empty() ) break;</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        117 :     if( t.size()!=2 ) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :       std::string ss; Tools::convert(i,ss);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :       error(&quot;ATOMS&quot; + ss + &quot; keyword has the wrong number of atoms&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        117 :     atoms.push_back(t[0]);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        117 :     atoms.push_back(t[1]);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        117 :     t.resize(0);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        117 :   }</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         29 :   const unsigned ndata = atoms.size()/2;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   // Read in GYROMAGNETIC constants</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         29 :   parse(&quot;GYROM&quot;, mu_s);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         29 :   if(mu_s==0.) error(&quot;GYROM cannot be 0&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   // Read in SCALING factors</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         29 :   parse(&quot;SCALE&quot;, scale);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         29 :   if(scale==0.) error(&quot;SCALE cannot be 0&quot;);</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         29 :   svd=false;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         29 :   parseFlag(&quot;SVD&quot;,svd);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            : #ifndef __PLUMED_HAS_GSL</a>
+<a name="289"><span class="lineNum">     289 </span>            :   if(svd) error(&quot;You CANNOT use SVD without GSL. Recompile PLUMED with GSL!\n&quot;);</a>
+<a name="290"><span class="lineNum">     290 </span>            : #endif</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         29 :   if(svd&amp;&amp;getDoScore()) error(&quot;It is not possible to use SVD and METAINFERENCE together&quot;);</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            :   // Optionally add an experimental value</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         29 :   coupl.resize( ndata );</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   unsigned ntarget=0;</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         82 :   for(unsigned i=0; i&lt;ndata; ++i) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">        138 :     if( !parseNumbered( &quot;COUPLING&quot;, i+1, coupl[i] ) ) break;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         53 :     ntarget++;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   }</a>
+<a name="300"><span class="lineNum">     300 </span>            :   bool addexp=false;</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         29 :   if(ntarget!=ndata &amp;&amp; ntarget!=0) error(&quot;found wrong number of COUPLING values&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         29 :   if(ntarget==ndata) addexp=true;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         29 :   if(getDoScore()&amp;&amp;!addexp) error(&quot;with DOSCORE you need to set the COUPLING values&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         29 :   if(svd&amp;&amp;!addexp) error(&quot;with SVD you need to set the COUPLING values&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   // Output details of all contacts</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         29 :   log.printf(&quot;  Gyromagnetic moment is %f. Scaling factor is %f.&quot;,mu_s,scale);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        146 :   for(unsigned i=0; i&lt;ndata; ++i) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        117 :     log.printf(&quot;  The %uth Bond Dipolar Coupling is calculated from atoms : %d %d.&quot;, i+1, atoms[2*i].serial(), atoms[2*i+1].serial());</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        117 :     if(addexp) log.printf(&quot; Experimental coupling is %f.&quot;, coupl[i]);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        117 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :   }</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         29 :   log&lt;&lt;&quot;  Bibliography &quot;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         58 :      &lt;&lt;plumed.cite(&quot;Camilloni C, Vendruscolo M, J. Phys. Chem. B 119, 653 (2015)&quot;)</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         87 :      &lt;&lt;plumed.cite(&quot;Camilloni C, Vendruscolo M, Biochemistry 54, 7470 (2015)&quot;);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         58 :   log&lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         29 :   if(!getDoScore()&amp;&amp;!svd) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         80 :     for(unsigned i=0; i&lt;ndata; i++) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         64 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         64 :       addComponentWithDerivatives(&quot;rdc-&quot;+num);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        128 :       componentIsNotPeriodic(&quot;rdc-&quot;+num);</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         16 :     if(addexp) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;ndata; i++) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :         std::string num; Tools::convert(i,num);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :         addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :         componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :         Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :         comp-&gt;set(coupl[i]);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :       }</a>
+<a name="335"><span class="lineNum">     335 </span>            :     }</a>
+<a name="336"><span class="lineNum">     336 </span>            :   } else {</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         66 :     for(unsigned i=0; i&lt;ndata; i++) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         53 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         53 :       addComponentWithDerivatives(&quot;rdc-&quot;+num);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">        106 :       componentIsNotPeriodic(&quot;rdc-&quot;+num);</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :     }</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         66 :     for(unsigned i=0; i&lt;ndata; i++) {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         53 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         53 :       addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         53 :       componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         53 :       Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         53 :       comp-&gt;set(coupl[i]);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :     }</a>
+<a name="349"><span class="lineNum">     349 </span>            :   }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         29 :   if(svd) {</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          2 :     addComponent(&quot;Sxx&quot;); componentIsNotPeriodic(&quot;Sxx&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          2 :     addComponent(&quot;Syy&quot;); componentIsNotPeriodic(&quot;Syy&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          2 :     addComponent(&quot;Szz&quot;); componentIsNotPeriodic(&quot;Szz&quot;);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          2 :     addComponent(&quot;Sxy&quot;); componentIsNotPeriodic(&quot;Sxy&quot;);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          2 :     addComponent(&quot;Sxz&quot;); componentIsNotPeriodic(&quot;Sxz&quot;);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          3 :     addComponent(&quot;Syz&quot;); componentIsNotPeriodic(&quot;Syz&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   }</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         29 :   requestAtoms(atoms, false);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         29 :   if(getDoScore()) {</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         12 :     setParameters(coupl);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         12 :     Initialise(coupl.size());</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   }</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         29 :   setDerivatives();</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         29 :   checkRead();</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         29 : }</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          5 : void RDC::do_svd()</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : {</a>
+<a name="371"><span class="lineNum">     371 </span>            : #ifdef __PLUMED_HAS_GSL</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          5 :   gsl_vector_unique_ptr rdc_vec(gsl_vector_alloc(coupl.size())),</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          5 :                         S(gsl_vector_alloc(5)),</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          5 :                         Stmp(gsl_vector_alloc(5)),</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          5 :                         work(gsl_vector_alloc(5)),</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          5 :                         bc(gsl_vector_alloc(coupl.size()));</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          5 :   gsl_matrix_unique_ptr coef_mat(gsl_matrix_alloc(coupl.size(),5)),</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">          5 :                         A(gsl_matrix_alloc(coupl.size(),5)),</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">          5 :                         V(gsl_matrix_alloc(5,5));</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          5 :   gsl_matrix_set_zero(coef_mat.get());</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          5 :   gsl_vector_set_zero(bc.get());</span></a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span>            :   unsigned index=0;</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">          5 :   std::vector&lt;double&gt; dmax(coupl.size());</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         30 :   for(unsigned r=0; r&lt;getNumberOfAtoms(); r+=2) {</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         25 :     Vector  distance;</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         25 :     if(pbc) distance = pbcDistance(getPosition(r),getPosition(r+1));</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :     else    distance = delta(getPosition(r),getPosition(r+1));</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         25 :     double d    = distance.modulo();</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         25 :     double d2   = d*d;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         25 :     double d3   = d2*d;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         25 :     double id3  = 1./d3;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         25 :     double max  = -Const*mu_s*scale;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         25 :     dmax[index] = id3*max;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         25 :     double mu_x = distance[0]/d;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         25 :     double mu_y = distance[1]/d;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         25 :     double mu_z = distance[2]/d;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         25 :     gsl_vector_set(rdc_vec.get(),index,coupl[index]/dmax[index]);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         25 :     gsl_matrix_set(coef_mat.get(),index,0,gsl_matrix_get(coef_mat.get(),index,0)+(mu_x*mu_x-mu_z*mu_z));</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         25 :     gsl_matrix_set(coef_mat.get(),index,1,gsl_matrix_get(coef_mat.get(),index,1)+(mu_y*mu_y-mu_z*mu_z));</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         25 :     gsl_matrix_set(coef_mat.get(),index,2,gsl_matrix_get(coef_mat.get(),index,2)+(2.0*mu_x*mu_y));</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         25 :     gsl_matrix_set(coef_mat.get(),index,3,gsl_matrix_get(coef_mat.get(),index,3)+(2.0*mu_x*mu_z));</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         25 :     gsl_matrix_set(coef_mat.get(),index,4,gsl_matrix_get(coef_mat.get(),index,4)+(2.0*mu_y*mu_z));</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         25 :     index++;</span></a>
+<a name="407"><span class="lineNum">     407 </span>            :   }</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          5 :   gsl_matrix_memcpy(A.get(),coef_mat.get());</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">          5 :   gsl_linalg_SV_decomp(A.get(), V.get(), Stmp.get(), work.get());</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">          5 :   gsl_linalg_SV_solve(A.get(), V.get(), Stmp.get(), rdc_vec.get(), S.get());</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :   /* tensor */</a>
+<a name="412"><span class="lineNum">     412 </span>            :   Value* tensor;</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          5 :   tensor=getPntrToComponent(&quot;Sxx&quot;);</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          5 :   double Sxx = gsl_vector_get(S.get(),0);</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   tensor-&gt;set(Sxx);</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          5 :   tensor=getPntrToComponent(&quot;Syy&quot;);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">          5 :   double Syy = gsl_vector_get(S.get(),1);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :   tensor-&gt;set(Syy);</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          5 :   tensor=getPntrToComponent(&quot;Szz&quot;);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          5 :   double Szz = -Sxx-Syy;</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :   tensor-&gt;set(Szz);</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          5 :   tensor=getPntrToComponent(&quot;Sxy&quot;);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">          5 :   double Sxy = gsl_vector_get(S.get(),2);</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :   tensor-&gt;set(Sxy);</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          5 :   tensor=getPntrToComponent(&quot;Sxz&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          5 :   double Sxz = gsl_vector_get(S.get(),3);</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :   tensor-&gt;set(Sxz);</a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          5 :   tensor=getPntrToComponent(&quot;Syz&quot;);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          5 :   double Syz = gsl_vector_get(S.get(),4);</span></a>
+<a name="430"><span class="lineNum">     430 </span>            :   tensor-&gt;set(Syz);</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">          5 :   gsl_blas_dgemv(CblasNoTrans, 1.0, coef_mat.get(), S.get(), 0., bc.get());</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         30 :   for(index=0; index&lt;coupl.size(); index++) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         25 :     double rdc = gsl_vector_get(bc.get(),index)*dmax[index];</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         25 :     Value* val=getPntrToComponent(index);</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :     val-&gt;set(rdc);</a>
+<a name="437"><span class="lineNum">     437 </span>            :   }</a>
+<a name="438"><span class="lineNum">     438 </span>            : #endif</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          5 : }</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">       2172 : void RDC::calculate()</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : {</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">       2172 :   if(svd) {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">          5 :     do_svd();</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          5 :     return;</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :   }</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">       2167 :   const double max  = -Const*scale*mu_s;</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   const unsigned N=getNumberOfAtoms();</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">       2167 :   std::vector&lt;Vector&gt; dRDC(N/2, Vector{0.,0.,0.});</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            :   /* RDC Calculations and forces */</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">       2167 :   #pragma omp parallel num_threads(OpenMP::getNumThreads())</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :   {</a>
+<a name="455"><span class="lineNum">     455 </span>            :     #pragma omp for</a>
+<a name="456"><span class="lineNum">     456 </span>            :     for(unsigned r=0; r&lt;N; r+=2)</a>
+<a name="457"><span class="lineNum">     457 </span>            :     {</a>
+<a name="458"><span class="lineNum">     458 </span>            :       const unsigned index=r/2;</a>
+<a name="459"><span class="lineNum">     459 </span>            :       Vector  distance;</a>
+<a name="460"><span class="lineNum">     460 </span>            :       if(pbc) distance   = pbcDistance(getPosition(r),getPosition(r+1));</a>
+<a name="461"><span class="lineNum">     461 </span>            :       else    distance   = delta(getPosition(r),getPosition(r+1));</a>
+<a name="462"><span class="lineNum">     462 </span>            :       const double d2    = distance.modulo2();</a>
+<a name="463"><span class="lineNum">     463 </span>            :       const double ind   = 1./std::sqrt(d2);</a>
+<a name="464"><span class="lineNum">     464 </span>            :       const double ind2  = 1./d2;</a>
+<a name="465"><span class="lineNum">     465 </span>            :       const double ind3  = ind2*ind;</a>
+<a name="466"><span class="lineNum">     466 </span>            :       const double x2    = distance[0]*distance[0]*ind2;</a>
+<a name="467"><span class="lineNum">     467 </span>            :       const double y2    = distance[1]*distance[1]*ind2;</a>
+<a name="468"><span class="lineNum">     468 </span>            :       const double z2    = distance[2]*distance[2]*ind2;</a>
+<a name="469"><span class="lineNum">     469 </span>            :       const double dmax  = ind3*max;</a>
+<a name="470"><span class="lineNum">     470 </span>            :       const double ddmax = dmax*ind2;</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :       const double rdc   = 0.5*dmax*(3.*z2-1.);</a>
+<a name="473"><span class="lineNum">     473 </span>            :       const double prod_xy = (x2+y2-4.*z2);</a>
+<a name="474"><span class="lineNum">     474 </span>            :       const double prod_z =  (3.*x2 + 3.*y2 - 2.*z2);</a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            :       dRDC[index] = -1.5*ddmax*distance;</a>
+<a name="477"><span class="lineNum">     477 </span>            :       dRDC[index][0] *= prod_xy;</a>
+<a name="478"><span class="lineNum">     478 </span>            :       dRDC[index][1] *= prod_xy;</a>
+<a name="479"><span class="lineNum">     479 </span>            :       dRDC[index][2] *= prod_z;</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            :       std::string num; Tools::convert(index,num);</a>
+<a name="482"><span class="lineNum">     482 </span>            :       Value* val=getPntrToComponent(&quot;rdc-&quot;+num);</a>
+<a name="483"><span class="lineNum">     483 </span>            :       val-&gt;set(rdc);</a>
+<a name="484"><span class="lineNum">     484 </span>            :       if(!getDoScore()) {</a>
+<a name="485"><span class="lineNum">     485 </span>            :         setBoxDerivatives(val, Tensor(distance,dRDC[index]));</a>
+<a name="486"><span class="lineNum">     486 </span>            :         setAtomsDerivatives(val, r,  dRDC[index]);</a>
+<a name="487"><span class="lineNum">     487 </span>            :         setAtomsDerivatives(val, r+1, -dRDC[index]);</a>
+<a name="488"><span class="lineNum">     488 </span>            :       } else setCalcData(index, rdc);</a>
+<a name="489"><span class="lineNum">     489 </span>            :     }</a>
+<a name="490"><span class="lineNum">     490 </span>            :   }</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">       2167 :   if(getDoScore()) {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :     /* Metainference */</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">       1824 :     Tensor dervir;</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">       1824 :     double score = getScore();</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :     setScore(score);</a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span>            :     /* calculate final derivatives */</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">       1824 :     Value* val=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">       9120 :     for(unsigned r=0; r&lt;N; r+=2)</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :     {</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">       7296 :       const unsigned index=r/2;</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">       7296 :       Vector  distance;</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">       7296 :       if(pbc) distance   = pbcDistance(getPosition(r),getPosition(r+1));</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :       else    distance   = delta(getPosition(r),getPosition(r+1));</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">       7296 :       const Vector der = dRDC[index]*getMetaDer(index);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">       7296 :       dervir += Tensor(distance, der);</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">       7296 :       setAtomsDerivatives(val, r,  der);</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">       7296 :       setAtomsDerivatives(val, r+1, -der);</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :     }</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">       1824 :     setBoxDerivatives(val, dervir);</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :   }</a>
+<a name="513"><span class="lineNum">     513 </span>            : }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        327 : void RDC::update() {</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :   // write status file</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">        327 :   if(getWstride()&gt;0&amp;&amp; (getStep()%getWstride()==0 || getCPT()) ) writeStatus();</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">        327 : }</span></a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            : }</a>
+<a name="521"><span class="lineNum">     521 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Rescale.cpp.func-sort-c.html b/coverage/isdb/Rescale.cpp.func-sort-c.html
new file mode 100644
index 0000000000..aa148ccaf3
--- /dev/null
+++ b/coverage/isdb/Rescale.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Rescale.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Rescale.cpp<span style="font-size: 80%;"> (<a href="Rescale.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntryLo">11.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Rescale.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
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+</body>
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diff --git a/coverage/isdb/Rescale.cpp.func.html b/coverage/isdb/Rescale.cpp.func.html
new file mode 100644
index 0000000000..3dd6f941d5
--- /dev/null
+++ b/coverage/isdb/Rescale.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Rescale.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Rescale.cpp<span style="font-size: 80%;"> (<a href="Rescale.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntryLo">11.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Rescale.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#160">_ZN4PLMD4isdb12_GLOBAL__N_120RescaleRegisterMe1626createERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#160">_ZN4PLMD4isdb12_GLOBAL__N_120RescaleRegisterMe162D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#412">_ZN4PLMD4isdb7Rescale10print_biasEx</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#366">_ZN4PLMD4isdb7Rescale12doMonteCarloEjdSt6vectorIdSaIdEES4_</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#162">_ZN4PLMD4isdb7Rescale16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#350">_ZN4PLMD4isdb7Rescale8doAcceptEdd</a></td>
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+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#438">_ZN4PLMD4isdb7Rescale9calculateEv</a></td>
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+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#306">_ZN4PLMD4isdb7Rescale9read_biasEv</a></td>
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+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#184">_ZN4PLMD4isdb7RescaleC1ERKNS_13ActionOptionsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#301">_ZN4PLMD4isdb7RescaleD0Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#301">_ZN4PLMD4isdb7RescaleD1Ev</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Rescale.cpp.gcov.html#301">_ZN4PLMD4isdb7RescaleD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Rescale.cpp.gcov.html b/coverage/isdb/Rescale.cpp.gcov.html
new file mode 100644
index 0000000000..6a864e1d96
--- /dev/null
+++ b/coverage/isdb/Rescale.cpp.gcov.html
@@ -0,0 +1,592 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Rescale.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Rescale.cpp<span style="font-size: 80%;"> (source / <a href="Rescale.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntryLo">11.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : /*</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : */</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;bias/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;ctime&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace isdb {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : //+PLUMEDOC ISDB_BIAS RESCALE</a>
+<a name="38"><span class="lineNum">      38 </span>            : /*</a>
+<a name="39"><span class="lineNum">      39 </span>            : Scales the value of an another action, being a Collective Variable or a Bias.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The rescaling factor is determined by a parameter defined on a logarithmic grid of dimension NBIN in the range</a>
+<a name="42"><span class="lineNum">      42 </span>            : from 1 to MAX_RESCALE. The current value of the rescaling parameter is stored and shared across</a>
+<a name="43"><span class="lineNum">      43 </span>            : other actions using a \ref SELECTOR. A Monte Carlo procedure is used to update the value</a>
+<a name="44"><span class="lineNum">      44 </span>            : of the rescaling factor every MC_STRIDE steps of molecular dynamics. Well-tempered metadynamics, defined by the</a>
+<a name="45"><span class="lineNum">      45 </span>            : parameters W0 and BIASFACTOR, is used to enhance the sampling in the space of the rescaling factor.</a>
+<a name="46"><span class="lineNum">      46 </span>            : The well-tempered metadynamics bias potential is written to the file BFILE every BSTRIDE steps and read</a>
+<a name="47"><span class="lineNum">      47 </span>            : when restarting the simulation using the directive \ref RESTART.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \note</a>
+<a name="50"><span class="lineNum">      50 </span>            : Additional arguments not to be scaled, one for each bin in the rescaling parameter ladder, can be</a>
+<a name="51"><span class="lineNum">      51 </span>            : provided at the end of the ARG list. The number of such arguments is specified by the option NOT_RESCALED.</a>
+<a name="52"><span class="lineNum">      52 </span>            : These arguments will be not be scaled, but they will be</a>
+<a name="53"><span class="lineNum">      53 </span>            : considered as bias potentials and used in the computation of the Metropolis</a>
+<a name="54"><span class="lineNum">      54 </span>            : acceptance probability when proposing a move in the rescaling parameter. See example below.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \note</a>
+<a name="57"><span class="lineNum">      57 </span>            : If PLUMED is running in a multiple-replica framework (for example using the -multi option in GROMACS),</a>
+<a name="58"><span class="lineNum">      58 </span>            : the arguments will be summed across replicas, unless the NOT_SHARED option is used. Also, the value of the</a>
+<a name="59"><span class="lineNum">      59 </span>            : \ref SELECTOR will be shared and thus will be the same in all replicas.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \par Examples</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : In this example we use \ref RESCALE to implement a simulated-tempering like approach.</a>
+<a name="64"><span class="lineNum">      64 </span>            : The total potential energy of the system is scaled by a parameter defined on a logarithmic grid</a>
+<a name="65"><span class="lineNum">      65 </span>            : of 5 bins in the range from 1 to 1.5.</a>
+<a name="66"><span class="lineNum">      66 </span>            : A well-tempered metadynamics bias potential is used to ensure diffusion in the space of the rescaling</a>
+<a name="67"><span class="lineNum">      67 </span>            : parameter.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : ene: ENERGY</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : SELECTOR NAME=GAMMA VALUE=0</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : RESCALE ...</a>
+<a name="75"><span class="lineNum">      75 </span>            : LABEL=res ARG=ene TEMP=300</a>
+<a name="76"><span class="lineNum">      76 </span>            : SELECTOR=GAMMA MAX_RESCALE=1.5 NBIN=5</a>
+<a name="77"><span class="lineNum">      77 </span>            : W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat</a>
+<a name="78"><span class="lineNum">      78 </span>            : ...</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : PRINT FILE=COLVAR ARG=* STRIDE=100</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endplumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : In this second example, we add to the simulated-tempering approach introduced above</a>
+<a name="84"><span class="lineNum">      84 </span>            : one Parallel Bias metadynamics simulation (see \ref PBMETAD) for each value of the rescaling parameter.</a>
+<a name="85"><span class="lineNum">      85 </span>            : At each moment of the simulation, only one of the \ref PBMETAD</a>
+<a name="86"><span class="lineNum">      86 </span>            : actions is activated, based on the current value of the associated \ref SELECTOR.</a>
+<a name="87"><span class="lineNum">      87 </span>            : The \ref PBMETAD bias potentials are not scaled, but just used in the calculation of</a>
+<a name="88"><span class="lineNum">      88 </span>            : the Metropolis acceptance probability when proposing a move in the rescaling parameter.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \plumedfile</a>
+<a name="91"><span class="lineNum">      91 </span>            : ene: ENERGY</a>
+<a name="92"><span class="lineNum">      92 </span>            : d: DISTANCE ATOMS=1,2</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : SELECTOR NAME=GAMMA VALUE=0</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : pbmetad0: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=0 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.0</a>
+<a name="97"><span class="lineNum">      97 </span>            : pbmetad1: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=1 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.1</a>
+<a name="98"><span class="lineNum">      98 </span>            : pbmetad2: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=2 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.2</a>
+<a name="99"><span class="lineNum">      99 </span>            : pbmetad3: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=3 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.3</a>
+<a name="100"><span class="lineNum">     100 </span>            : pbmetad4: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=4 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.4</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : RESCALE ...</a>
+<a name="103"><span class="lineNum">     103 </span>            : LABEL=res TEMP=300</a>
+<a name="104"><span class="lineNum">     104 </span>            : ARG=ene,pbmetad0.bias,pbmetad1.bias,pbmetad2.bias,pbmetad3.bias,pbmetad4.bias</a>
+<a name="105"><span class="lineNum">     105 </span>            : SELECTOR=GAMMA MAX_RESCALE=1.5 NOT_RESCALED=5 NBIN=5</a>
+<a name="106"><span class="lineNum">     106 </span>            : W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat</a>
+<a name="107"><span class="lineNum">     107 </span>            : ...</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : PRINT FILE=COLVAR ARG=* STRIDE=100</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endplumedfile</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : */</a>
+<a name="115"><span class="lineNum">     115 </span>            : //+ENDPLUMEDOC</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : class Rescale : public bias::Bias</a>
+<a name="118"><span class="lineNum">     118 </span>            : {</a>
+<a name="119"><span class="lineNum">     119 </span>            :   // gamma parameter</a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::vector&lt;double&gt; gamma_;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   double         w0_;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   double         biasf_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::vector&lt;double&gt; bias_;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::vector&lt;double&gt; expo_;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   std::vector&lt;unsigned&gt; shared_;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   unsigned nores_;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   // bias</a>
+<a name="128"><span class="lineNum">     128 </span>            :   unsigned int   Biasstride_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   unsigned int   Biaspace_;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   std::string         Biasfilename_;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool           first_bias_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   OFile          Biasfile_;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // temperature in kbt</a>
+<a name="134"><span class="lineNum">     134 </span>            :   double kbt_;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   // Monte Carlo stuff</a>
+<a name="136"><span class="lineNum">     136 </span>            :   unsigned MCsteps_;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   unsigned MCstride_;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   long long int MCfirst_;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   long long unsigned MCaccgamma_;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   // replica stuff</a>
+<a name="141"><span class="lineNum">     141 </span>            :   unsigned nrep_;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   unsigned replica_;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   // selector</a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::string selector_;</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Monte Carlo</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void doMonteCarlo(unsigned igamma, double oldE, std::vector&lt;double&gt; args, std::vector&lt;double&gt; bargs);</a>
+<a name="148"><span class="lineNum">     148 </span>            :   unsigned proposeMove(unsigned x, unsigned xmin, unsigned xmax);</a>
+<a name="149"><span class="lineNum">     149 </span>            :   bool doAccept(double oldE, double newE);</a>
+<a name="150"><span class="lineNum">     150 </span>            :   // read and print bias</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void read_bias();</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void print_bias(long long int step);</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : public:</a>
+<a name="155"><span class="lineNum">     155 </span>            :   explicit Rescale(const ActionOptions&amp;);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   ~Rescale();</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void calculate();</a>
+<a name="158"><span class="lineNum">     158 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="159"><span class="lineNum">     159 </span>            : };</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(Rescale,&quot;RESCALE&quot;)</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 : void Rescale::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   Bias::registerKeywords(keys);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;TEMP&quot;,&quot;temperature&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;SELECTOR&quot;, &quot;name of the SELECTOR used for rescaling&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;MAX_RESCALE&quot;,&quot;maximum values for rescaling&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;NBIN&quot;,&quot;number of bins for gamma grid&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;W0&quot;, &quot;initial bias height&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BIASFACTOR&quot;, &quot;bias factor&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BSTRIDE&quot;, &quot;stride for writing bias&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BFILE&quot;, &quot;file name for bias&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;NOT_SHARED&quot;,   &quot;list of arguments (from 1 to N) not summed across replicas&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;NOT_RESCALED&quot;, &quot;these last N arguments will not be scaled&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;MC_STEPS&quot;,&quot;number of MC steps&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;MC_STRIDE&quot;,&quot;MC stride&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;PACE&quot;, &quot;Pace for adding bias, in MC stride unit&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :   componentsAreNotOptional(keys);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :   keys.addOutputComponent(&quot;igamma&quot;,  &quot;default&quot;,&quot;gamma parameter&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :   keys.addOutputComponent(&quot;accgamma&quot;,&quot;default&quot;,&quot;MC acceptance for gamma&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          4 :   keys.addOutputComponent(&quot;wtbias&quot;,  &quot;default&quot;,&quot;well-tempered bias&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 : }</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 : Rescale::Rescale(const ActionOptions&amp;ao):</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   nores_(0), Biaspace_(1), first_bias_(true),</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :   MCsteps_(1), MCstride_(1), MCfirst_(-1), MCaccgamma_(0)</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : {</a>
+<a name="191"><span class="lineNum">     191 </span>            :   // set up replica stuff</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :   if(comm.Get_rank()==0) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     nrep_    = multi_sim_comm.Get_size();</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     replica_ = multi_sim_comm.Get_rank();</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   } else {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     nrep_    = 0;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     replica_ = 0;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   comm.Sum(&amp;nrep_,1);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :   comm.Sum(&amp;replica_,1);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   // wt-parameters</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :   parse(&quot;W0&quot;, w0_);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   parse(&quot;BIASFACTOR&quot;, biasf_);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   // selector name</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :   parse(&quot;SELECTOR&quot;, selector_);</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :   // number of bins for gamma ladder</a>
+<a name="210"><span class="lineNum">     210 </span>            :   unsigned nbin;</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :   parse(&quot;NBIN&quot;, nbin);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            :   // number of bias</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :   parse(&quot;NOT_RESCALED&quot;, nores_);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   if(nores_&gt;0 &amp;&amp; nores_!=nbin) error(&quot;The number of non scaled arguments must be equal to either 0 or the number of bins&quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // maximum value of rescale</a>
+<a name="218"><span class="lineNum">     218 </span>            :   std::vector&lt;double&gt; max_rescale;</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   parseVector(&quot;MAX_RESCALE&quot;, max_rescale);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   // check dimension of max_rescale</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :   if(max_rescale.size()!=(getNumberOfArguments()-nores_))</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :     error(&quot;Size of MAX_RESCALE array must be equal to the number of arguments that will to be scaled&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   // calculate exponents</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :   double igamma_max = static_cast&lt;double&gt;(nbin);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;max_rescale.size(); ++i)</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :     expo_.push_back(std::log(max_rescale[i])/std::log(igamma_max));</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :   // allocate gamma grid and set bias to zero</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;nbin; ++i) {</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     // bias grid</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     bias_.push_back(0.0);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     // gamma ladder</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :     double gamma = std::exp( static_cast&lt;double&gt;(i) / static_cast&lt;double&gt;(nbin-1) * std::log(igamma_max) );</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :     gamma_.push_back(gamma);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :   }</a>
+<a name="237"><span class="lineNum">     237 </span>            :   // print bias to file</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :   parse(&quot;BSTRIDE&quot;, Biasstride_);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   parse(&quot;BFILE&quot;,   Biasfilename_);</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            :   // create vectors of shared arguments</a>
+<a name="242"><span class="lineNum">     242 </span>            :   // by default they are all shared</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) shared_.push_back(1);</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   // share across replicas or not</a>
+<a name="245"><span class="lineNum">     245 </span>            :   std::vector&lt;unsigned&gt; not_shared;</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   parseVector(&quot;NOT_SHARED&quot;, not_shared);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   // and change the non-shared</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;not_shared.size(); ++i) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :     if((not_shared[i]-1)&gt;=(getNumberOfArguments()-nores_) &amp;&amp; nrep_&gt;1)</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :       error(&quot;NOT_RESCALED args must always be shared when using multiple replicas&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     if((not_shared[i]-1)&gt;=getNumberOfArguments())</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :       error(&quot;NOT_SHARED args should be lower than total number of arguments&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :     shared_[not_shared[i]-1] = 0;</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            :   // monte carlo stuff</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   parse(&quot;MC_STEPS&quot;,MCsteps_);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :   parse(&quot;MC_STRIDE&quot;,MCstride_);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   // adjust for multiple-time steps</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :   MCstride_ *= getStride();</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   // read bias deposition pace</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :   parse(&quot;PACE&quot;, Biaspace_);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   // multiply by MCstride</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   Biaspace_ *= MCstride_;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :   // get temperature</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :   double temp=0.0;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :   if(temp&gt;0.0) kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :   else kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :   log.printf(&quot;  temperature of the system in energy unit %f\n&quot;,kbt_);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   log.printf(&quot;  name of the SELECTOR use for this action %s\n&quot;,selector_.c_str());</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :   log.printf(&quot;  number of bins in grid %u\n&quot;,nbin);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :   log.printf(&quot;  number of arguments that will not be scaled %u\n&quot;,nores_);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   if(nrep_&gt;1) log&lt;&lt;&quot;  number of arguments that will not be summed across replicas &quot;&lt;&lt;not_shared.size()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   log.printf(&quot;  biasfactor %f\n&quot;,biasf_);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :   log.printf(&quot;  initial hills height %f\n&quot;,w0_);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :   log.printf(&quot;  stride to write bias to file %u\n&quot;,Biasstride_);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :   log.printf(&quot;  write bias to file : %s\n&quot;,Biasfilename_.c_str());</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :   log.printf(&quot;  number of replicas %u\n&quot;,nrep_);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :   log.printf(&quot;  number of MC steps %d\n&quot;,MCsteps_);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :   log.printf(&quot;  do MC every %d steps\n&quot;, MCstride_);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :   log &lt;&lt; &quot; Bibliography&quot; &lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :   // add components</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   addComponent(&quot;igamma&quot;);   componentIsNotPeriodic(&quot;igamma&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :   addComponent(&quot;accgamma&quot;); componentIsNotPeriodic(&quot;accgamma&quot;);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :   addComponent(&quot;wtbias&quot;);   componentIsNotPeriodic(&quot;wtbias&quot;);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   // initialize random seed</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :   srand (time(NULL));</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :   // read bias if restarting</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   if(getRestart()) read_bias();</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 : Rescale::~Rescale()</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   Biasfile_.close();</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 : void Rescale::read_bias()</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : {</a>
+<a name="310"><span class="lineNum">     310 </span>            : // open file</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :   auto ifile=Tools::make_unique&lt;IFile&gt;();</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :   ifile-&gt;link(*this);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :   if(ifile-&gt;FileExist(Biasfilename_)) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :     ifile-&gt;open(Biasfilename_);</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :     // read all the lines, store last value of bias</a>
+<a name="316"><span class="lineNum">     316 </span>            :     double MDtime;</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :     while(ifile-&gt;scanField(&quot;MD_time&quot;,MDtime)) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;bias_.size(); ++i) {</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :         // convert i to string</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :         std::stringstream ss;</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :         ss &lt;&lt; i;</a>
+<a name="322"><span class="lineNum">     322 </span>            :         // label</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :         std::string label = &quot;b&quot; + ss.str();</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :         // read entry</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :         ifile-&gt;scanField(label, bias_[i]);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :       // new line</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :       ifile-&gt;scanField();</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :     }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :     ifile-&gt;close();</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   } else {</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :     error(&quot;Cannot find bias file &quot;+Biasfilename_+&quot;\n&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 : unsigned Rescale::proposeMove(unsigned x, unsigned xmin, unsigned xmax)</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : {</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :   int xmin_i = static_cast&lt;int&gt;(xmin);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :   int xmax_i = static_cast&lt;int&gt;(xmax);</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :   int dx;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :   int r = rand() % 2;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :   if( r % 2 == 0 ) dx = +1;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   else             dx = -1;</a>
+<a name="344"><span class="lineNum">     344 </span>            : // new index, integer</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   int x_new = static_cast&lt;int&gt;(x) + dx;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : // check boundaries</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :   if(x_new &gt;= xmax_i) x_new = xmax_i-1;</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :   if(x_new &lt;  xmin_i) x_new = xmin_i;</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   return static_cast&lt;unsigned&gt;(x_new);</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : }</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 : bool Rescale::doAccept(double oldE, double newE)</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : {</a>
+<a name="354"><span class="lineNum">     354 </span>            :   bool accept = false;</a>
+<a name="355"><span class="lineNum">     355 </span>            :   // calculate delta energy</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :   double delta = ( newE - oldE ) / kbt_;</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   // if delta is negative always accept move</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   if( delta &lt; 0.0 ) {</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :     accept = true;</a>
+<a name="360"><span class="lineNum">     360 </span>            :   } else {</a>
+<a name="361"><span class="lineNum">     361 </span>            :     // otherwise extract random number</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :     double s = static_cast&lt;double&gt;(rand()) / RAND_MAX;</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :     if( s &lt; std::exp(-delta) ) { accept = true; }</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   }</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :   return accept;</span></a>
+<a name="366"><span class="lineNum">     366 </span>            : }</a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 : void Rescale::doMonteCarlo(unsigned igamma, double oldE,</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :                            std::vector&lt;double&gt; args, std::vector&lt;double&gt; bargs)</a>
+<a name="370"><span class="lineNum">     370 </span>            : {</a>
+<a name="371"><span class="lineNum">     371 </span>            :   double oldB, newB;</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            : // cycle on MC steps</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;MCsteps_; ++i) {</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :     // propose move in igamma</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :     unsigned new_igamma = proposeMove(igamma, 0, gamma_.size());</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :     // calculate new energy</a>
+<a name="378"><span class="lineNum">     378 </span>            :     double newE = 0.0;</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;args.size(); ++j) {</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :       // calculate energy term</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :       double fact = 1.0/pow(gamma_[new_igamma], expo_[j]) - 1.0;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :       newE += args[j] * fact;</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     }</a>
+<a name="384"><span class="lineNum">     384 </span>            :     // calculate contributions from non-rescaled terms</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :     if(bargs.size()&gt;0) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :       oldB = bias_[igamma]+bargs[igamma];</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :       newB = bias_[new_igamma]+bargs[new_igamma];</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :     } else {</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :       oldB = bias_[igamma];</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :       newB = bias_[new_igamma];</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     }</a>
+<a name="392"><span class="lineNum">     392 </span>            :     // accept or reject</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :     bool accept = doAccept(oldE+oldB, newE+newB);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :     if(accept) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :       igamma = new_igamma;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :       oldE = newE;</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :       MCaccgamma_++;</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :     }</a>
+<a name="399"><span class="lineNum">     399 </span>            :   }</a>
+<a name="400"><span class="lineNum">     400 </span>            : // send values of gamma to all replicas</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :   if(comm.Get_rank()==0) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :     if(multi_sim_comm.Get_rank()!=0) igamma = 0;</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :     multi_sim_comm.Sum(&amp;igamma, 1);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :   } else {</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :     igamma = 0;</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :   }</a>
+<a name="407"><span class="lineNum">     407 </span>            : // local communication</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :   comm.Sum(&amp;igamma, 1);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            : // set the value of gamma into passMap</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :   plumed.passMap[selector_]=static_cast&lt;double&gt;(igamma);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 : void Rescale::print_bias(long long int step)</span></a>
+<a name="415"><span class="lineNum">     415 </span>            : {</a>
+<a name="416"><span class="lineNum">     416 </span>            : // if first time open the file</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :   if(first_bias_) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :     first_bias_ = false;</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :     Biasfile_.link(*this);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :     Biasfile_.open(Biasfilename_);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :     Biasfile_.setHeavyFlush();</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :     Biasfile_.fmtField(&quot;%30.5f&quot;);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :   }</a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            : // write fields</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 :   double MDtime = static_cast&lt;double&gt;(step)*getTimeStep();</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :   Biasfile_.printField(&quot;MD_time&quot;, MDtime);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;bias_.size(); ++i) {</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :     // convert i to string</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :     std::stringstream ss;</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :     ss &lt;&lt; i;</a>
+<a name="432"><span class="lineNum">     432 </span>            :     // label</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :     std::string label = &quot;b&quot; + ss.str();</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :     // print entry</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :     Biasfile_.printField(label, bias_[i]);</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :   Biasfile_.printField();</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 : void Rescale::calculate()</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : {</a>
+<a name="442"><span class="lineNum">     442 </span>            :   // get the current value of the selector</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :   unsigned igamma = static_cast&lt;unsigned&gt;(plumed.passMap[selector_]);</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span>            :   // collect data from other replicas</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; all_args(getNumberOfArguments(), 0.0);</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   // first calculate arguments</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;all_args.size(); ++i) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 :     double arg = getArgument(i);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :     // sum shared arguments across replicas</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :     if(shared_[i]==1) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :       if(comm.Get_rank()==0) multi_sim_comm.Sum(arg);</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :       else                   arg = 0.0;</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :       if(comm.Get_size()&gt;1)  comm.Sum(arg);</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :     }</a>
+<a name="456"><span class="lineNum">     456 </span>            :     // put into all_args</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :     all_args[i] = arg;</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :   }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   // now separate terms that should be rescaled</a>
+<a name="461"><span class="lineNum">     461 </span>            :   std::vector&lt;double&gt; args;</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :   if(getNumberOfArguments()-nores_&gt;0) args.resize(getNumberOfArguments()-nores_);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;args.size(); ++i)  args[i]  = all_args[i];</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :   // and terms that should not</a>
+<a name="465"><span class="lineNum">     465 </span>            :   std::vector&lt;double&gt; bargs;</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :   if(nores_&gt;0) bargs.resize(nores_);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;bargs.size(); ++i) bargs[i] = all_args[i+args.size()];</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span>            :   // calculate energy and forces, only on rescaled terms</a>
+<a name="470"><span class="lineNum">     470 </span>            :   double ene = 0.0;</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;args.size(); ++i) {</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :     // calculate energy term</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :     double fact = 1.0/pow(gamma_[igamma], expo_[i]) - 1.0;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :     ene += args[i] * fact;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :     // add force</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :     setOutputForce(i, -fact);</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :   }</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            :   // set to zero on the others</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;bargs.size(); ++i) setOutputForce(i+args.size(), 0.0);</span></a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span>            :   // set value of the bias</a>
+<a name="483"><span class="lineNum">     483 </span>            :   setBias(ene);</a>
+<a name="484"><span class="lineNum">     484 </span>            :   // set value of the wt-bias</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :   getPntrToComponent(&quot;wtbias&quot;)-&gt;set(bias_[igamma]);</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :   // set values of gamma</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :   getPntrToComponent(&quot;igamma&quot;)-&gt;set(igamma);</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   // get time step</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :   long long int step = getStep();</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineNoCov">          0 :   if(MCfirst_==-1) MCfirst_=step;</span></a>
+<a name="491"><span class="lineNum">     491 </span>            :   // calculate gamma acceptance</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :   double MCtrials = std::floor(static_cast&lt;double&gt;(step-MCfirst_) / static_cast&lt;double&gt;(MCstride_))+1.0;</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :   double accgamma = static_cast&lt;double&gt;(MCaccgamma_) / static_cast&lt;double&gt;(MCsteps_) / MCtrials;</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :   getPntrToComponent(&quot;accgamma&quot;)-&gt;set(accgamma);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            :   // do MC at the right time step</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :   if(step%MCstride_==0&amp;&amp;!getExchangeStep()) doMonteCarlo(igamma, ene, args, bargs);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span>            :   // add well-tempered like bias</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :   if(step%Biaspace_==0) {</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :     // get updated igamma</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 :     unsigned igamma = static_cast&lt;unsigned&gt;(plumed.passMap[selector_]);</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :     // add &quot;Gaussian&quot;</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :     double kbDT = kbt_ * ( biasf_ - 1.0 );</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :     bias_[igamma] += w0_ * std::exp(-bias_[igamma] / kbDT);</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :   }</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span>            :   // print bias</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :   if(step%Biasstride_==0) print_bias(step);</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            : }</a>
+<a name="515"><span class="lineNum">     515 </span>            : }</a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/SAXS.cpp.func-sort-c.html b/coverage/isdb/SAXS.cpp.func-sort-c.html
new file mode 100644
index 0000000000..135486e517
--- /dev/null
+++ b/coverage/isdb/SAXS.cpp.func-sort-c.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/SAXS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - SAXS.cpp<span style="font-size: 80%;"> (<a href="SAXS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4808</td>
+            <td class="headerCovTableEntry">6005</td>
+            <td class="headerCovTableEntryMed">80.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SAXS.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#821">_ZN4PLMD4isdb4SAXS13calculate_gpuERSt6vectorINS_13VectorGenericILj3EEESaIS4_EES7_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#342">_ZN4PLMD4isdb4SAXSC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#6337">_ZN4PLMD4isdb4SAXS16calculateAFFsansERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IeSaIeEESaIS9_EEd</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#6230">_ZN4PLMD4isdb4SAXS12calculateAFFERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IeSaIeEESaIS9_EEd</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#5235">_ZN4PLMD4isdb4SAXS21getOnebeadparam_sansDERKNS_3PDBERKSt6vectorINS_10AtomNumberESaIS6_EERS5_IS5_IeSaIeEESaISC_EESF_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#3976">_ZN4PLMD4isdb4SAXS21getOnebeadparam_sansHERKNS_3PDBERKSt6vectorINS_10AtomNumberESaIS6_EERS5_IS5_IeSaIeEESaISC_EESF_SF_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#315">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe3176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#2716">_ZN4PLMD4isdb4SAXS15getOnebeadparamERKNS_3PDBERKSt6vectorINS_10AtomNumberESaIS6_EERS5_IS5_IeSaIeEESaISC_EESF_SF_S5_IjSaIjEE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#777">_ZN4PLMD4isdb4SAXS14sasa_calculateERSt6vectorIbSaIbEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#1316">_ZN4PLMD4isdb4SAXS17getMartiniFFparamERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IeSaIeEESaIS9_EE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#756">_ZN4PLMD4isdb4SAXS9calcNlistERSt6vectorIS2_IiSaIiEESaIS4_EE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#7410">_ZN4PLMD4isdb4SAXS13readLCPOparamERKSt6vectorIS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESaISA_EEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#6408">_ZN4PLMD4isdb4SAXS14setupLCPOparamB5cxx11Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#1220">_ZN4PLMD4isdb4SAXS17getOnebeadMappingERKNS_3PDBERKSt6vectorINS_10AtomNumberESaIS6_EE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#314">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe3166createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#342">_ZN4PLMD4isdb4SAXSC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#317">_ZN4PLMD4isdb4SAXS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#938">_ZN4PLMD4isdb4SAXS13calculate_cpuERSt6vectorINS_13VectorGenericILj3EEESaIS4_EES7_</a></td>
+              <td class="coverFnHi">188</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#1215">_ZN4PLMD4isdb4SAXS6updateEv</a></td>
+              <td class="coverFnHi">188</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#1005">_ZN4PLMD4isdb4SAXS9calculateEv</a></td>
+              <td class="coverFnHi">188</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#314">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe316C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#314">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe316D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#315">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe317C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#315">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe317D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/SAXS.cpp.func.html b/coverage/isdb/SAXS.cpp.func.html
new file mode 100644
index 0000000000..b43ac1b16a
--- /dev/null
+++ b/coverage/isdb/SAXS.cpp.func.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/SAXS.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - SAXS.cpp<span style="font-size: 80%;"> (<a href="SAXS.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4808</td>
+            <td class="headerCovTableEntry">6005</td>
+            <td class="headerCovTableEntryMed">80.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SAXS.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#314">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe3166createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#314">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe316C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#314">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe316D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#315">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe3176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#315">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe317C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#315">_ZN4PLMD4isdb12_GLOBAL__N_117SAXSRegisterMe317D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#6230">_ZN4PLMD4isdb4SAXS12calculateAFFERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IeSaIeEESaIS9_EEd</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#938">_ZN4PLMD4isdb4SAXS13calculate_cpuERSt6vectorINS_13VectorGenericILj3EEESaIS4_EES7_</a></td>
+              <td class="coverFnHi">188</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#821">_ZN4PLMD4isdb4SAXS13calculate_gpuERSt6vectorINS_13VectorGenericILj3EEESaIS4_EES7_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#7410">_ZN4PLMD4isdb4SAXS13readLCPOparamERKSt6vectorIS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EESaISA_EEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#777">_ZN4PLMD4isdb4SAXS14sasa_calculateERSt6vectorIbSaIbEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#6408">_ZN4PLMD4isdb4SAXS14setupLCPOparamB5cxx11Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#2716">_ZN4PLMD4isdb4SAXS15getOnebeadparamERKNS_3PDBERKSt6vectorINS_10AtomNumberESaIS6_EERS5_IS5_IeSaIeEESaISC_EESF_SF_S5_IjSaIjEE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#6337">_ZN4PLMD4isdb4SAXS16calculateAFFsansERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IeSaIeEESaIS9_EEd</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#317">_ZN4PLMD4isdb4SAXS16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#1316">_ZN4PLMD4isdb4SAXS17getMartiniFFparamERKSt6vectorINS_10AtomNumberESaIS3_EERS2_IS2_IeSaIeEESaIS9_EE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SAXS.cpp.gcov.html#1220">_ZN4PLMD4isdb4SAXS17getOnebeadMappingERKNS_3PDBERKSt6vectorINS_10AtomNumberESaIS6_EE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
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+  <br>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
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+</html>
diff --git a/coverage/isdb/SAXS.cpp.gcov.html b/coverage/isdb/SAXS.cpp.gcov.html
new file mode 100644
index 0000000000..fa3073c423
--- /dev/null
+++ b/coverage/isdb/SAXS.cpp.gcov.html
@@ -0,0 +1,7532 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <title>LCOV - plumed test coverage - isdb/SAXS.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - SAXS.cpp<span style="font-size: 80%;"> (source / <a href="SAXS.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4808</td>
+            <td class="headerCovTableEntry">6005</td>
+            <td class="headerCovTableEntryMed">80.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : /*</a>
+<a name="23"><span class="lineNum">      23 </span>            :  This class was originally written by Alexander Jussupow</a>
+<a name="24"><span class="lineNum">      24 </span>            :  Arrayfire implementation by Alexander Jussupow and CC</a>
+<a name="25"><span class="lineNum">      25 </span>            :  Extension for the middleman algorithm (now removed) by Max Muehlbauer</a>
+<a name="26"><span class="lineNum">      26 </span>            :  Refactoring for hySAXS Martini form factors for Nucleic Acids by Cristina Paissoni</a>
+<a name="27"><span class="lineNum">      27 </span>            :  Refactoring for hySAS OneBead form factors with solvent correction by Federico Ballabio and Riccardo Capelli</a>
+<a name="28"><span class="lineNum">      28 </span>            : */</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;MetainferenceBase.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/MolDataClass.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;map&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &lt;iterator&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &lt;iostream&gt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &lt;algorithm&gt;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &lt;cctype&gt;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : #ifdef __PLUMED_HAS_ARRAYFIRE</a>
+<a name="46"><span class="lineNum">      46 </span>            : #include &lt;arrayfire.h&gt;</a>
+<a name="47"><span class="lineNum">      47 </span>            : #include &lt;af/util.h&gt;</a>
+<a name="48"><span class="lineNum">      48 </span>            : #ifdef __PLUMED_HAS_ARRAYFIRE_CUDA</a>
+<a name="49"><span class="lineNum">      49 </span>            : #include &lt;cuda_runtime.h&gt;</a>
+<a name="50"><span class="lineNum">      50 </span>            : #include &lt;cublas_v2.h&gt;</a>
+<a name="51"><span class="lineNum">      51 </span>            : #include &lt;af/cuda.h&gt;</a>
+<a name="52"><span class="lineNum">      52 </span>            : #elif __PLUMED_HAS_ARRAYFIRE_OCL</a>
+<a name="53"><span class="lineNum">      53 </span>            : #include &lt;af/opencl.h&gt;</a>
+<a name="54"><span class="lineNum">      54 </span>            : #endif</a>
+<a name="55"><span class="lineNum">      55 </span>            : #endif</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : #ifndef M_PI</a>
+<a name="58"><span class="lineNum">      58 </span>            : #define M_PI           3.14159265358979323846</a>
+<a name="59"><span class="lineNum">      59 </span>            : #endif</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace PLMD {</a>
+<a name="62"><span class="lineNum">      62 </span>            : namespace isdb {</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : //+PLUMEDOC ISDB_COLVAR SAXS</a>
+<a name="65"><span class="lineNum">      65 </span>            : /*</a>
+<a name="66"><span class="lineNum">      66 </span>            : Calculates SAXS intensity.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : SAXS intensities are calculated for a set of scattering vectors using QVALUE keywords numbered from 1.</a>
+<a name="69"><span class="lineNum">      69 </span>            : Form factors can be assigned either by polynomial expansion of any order by using the PARAMETERS keywords, or</a>
+<a name="70"><span class="lineNum">      70 </span>            : automatically matched to atoms using the ATOMISTIC flag by reading a PDB file. Alternatively to the atomistic</a>
+<a name="71"><span class="lineNum">      71 </span>            : representation, two types of coarse-grained mapping are available:</a>
+<a name="72"><span class="lineNum">      72 </span>            : - MARTINI.</a>
+<a name="73"><span class="lineNum">      73 </span>            : - ONEBEAD.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : Whether for PARAMETERS, ATOMISTIC, and ONEBEAD the user must provide an all-atom PDB file via MOLINFO before the</a>
+<a name="76"><span class="lineNum">      76 </span>            : SAXS instruction. MARTINI requires a mapping scheme consisting of a PDB file that contains both the all-atom</a>
+<a name="77"><span class="lineNum">      77 </span>            : and MARTINI representations, and a bead position file (e.g., bead1: CENTER ATOMS=1,5,7,11,12 WEIGHTS=14,12,12,</a>
+<a name="78"><span class="lineNum">      78 </span>            : 12,16).</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : ONEBEAD scheme consists in a single-bead per amino acid residue or three-bead for nucleic acid residue (one for</a>
+<a name="81"><span class="lineNum">      81 </span>            : the phosphate group, one for the pentose sugar, one for the nucleobase). PLUMED creates a virtual bead on which</a>
+<a name="82"><span class="lineNum">      82 </span>            : the SAXS calculations are performed, centred on the COM of all atoms belonging to the bead. It is possible to</a>
+<a name="83"><span class="lineNum">      83 </span>            : account for the contribution of the solvation layer to the SAXS intensity by adding a correction term for the</a>
+<a name="84"><span class="lineNum">      84 </span>            : solvent accessible beads only: the form factors of the amino acids / phosphate groups / pentose sugars /</a>
+<a name="85"><span class="lineNum">      85 </span>            : nucleobases with a SASA (computed via LCPO algorithm) greater than a threshold are corrected according to an</a>
+<a name="86"><span class="lineNum">      86 </span>            : electron density term. Both the surface cut-off threshold and the electron density term can be set by the user</a>
+<a name="87"><span class="lineNum">      87 </span>            : with the SASA_CUTOFF and SOLVATION_CORRECTION keywords. Moreover, SASA stride calculation can be modified using</a>
+<a name="88"><span class="lineNum">      88 </span>            : SOLVATION_STRIDE, which is set to 100 steps by default.</a>
+<a name="89"><span class="lineNum">      89 </span>            : ONEBEAD requires an additional PDB file to perform mapping conversion, which must be provided via TEMPLATE</a>
+<a name="90"><span class="lineNum">      90 </span>            : keyword. This PDB file should only include the atoms for which the SAXS intensity will be computed.</a>
+<a name="91"><span class="lineNum">      91 </span>            : The AMBER OL3 (RNA) and OL15 (DNA) naming is required for nucleic acids.</a>
+<a name="92"><span class="lineNum">      92 </span>            : Two additional bead types are available for DNA and RNA besides phosphate group, pentose sugar, and nucleobase:</a>
+<a name="93"><span class="lineNum">      93 </span>            : - 5'-end pentose sugar capped with an hydroxyl moiety at C5' (the residue name in the PDB must be followed by</a>
+<a name="94"><span class="lineNum">      94 </span>            : &quot;5&quot;, e.g., DC5 or C5 for cytosine in DNA and RNA, respectively);</a>
+<a name="95"><span class="lineNum">      95 </span>            : - 3'-end pentose sugar capped with an hydroxyl moiety at C3' (the residue name in the PDB must be followed by</a>
+<a name="96"><span class="lineNum">      96 </span>            : &quot;3&quot;, e.g., DC3 or C3 for cytosine in DNA and RNA, respectively).</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : Experimental reference intensities can be added using the EXPINT keywords. All these values must be normalised</a>
+<a name="99"><span class="lineNum">      99 </span>            : to the SAXS intensity at q = 0. To facilitate this operation, the SCALE_EXPINT keyword can be used to provide</a>
+<a name="100"><span class="lineNum">     100 </span>            : the intensity at q = 0. Each EXPINT is divided by SCALE_EXPINT.</a>
+<a name="101"><span class="lineNum">     101 </span>            : The maximum QVALUE for ONEBEAD is set to 0.3 inverse angstroms.</a>
+<a name="102"><span class="lineNum">     102 </span>            : The solvent density, that by default is set to 0.334 electrons per cubic angstrom (bulk water), can be modified</a>
+<a name="103"><span class="lineNum">     103 </span>            : using the SOLVDENS keyword.</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : By default SAXS is calculated using Debye on CPU, by adding the GPU flag it is possible to solve the equation on</a>
+<a name="106"><span class="lineNum">     106 </span>            : a GPU if the ARRAYFIRE libraries are installed and correctly linked.</a>
+<a name="107"><span class="lineNum">     107 </span>            : \ref METAINFERENCE can be activated using DOSCORE and the other relevant keywords.</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : \par Examples</a>
+<a name="110"><span class="lineNum">     110 </span>            : in the following example the SAXS intensities are calculated using single-bead per residue approximation, with a</a>
+<a name="111"><span class="lineNum">     111 </span>            : SASA threshold of 1 square nanometer and a solvation term of 0.04. Each experimental intensity is divided by</a>
+<a name="112"><span class="lineNum">     112 </span>            : 1.4002, which is the corresponding theoretical intensity value at q = 0. The form factors are selected according</a>
+<a name="113"><span class="lineNum">     113 </span>            : to the PDB file specified by TEMPLATE keyword.</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : \plumedfile</a>
+<a name="116"><span class="lineNum">     116 </span>            : MOLINFO STRUCTURE=template_AA.pdb</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : SAXS ...</a>
+<a name="119"><span class="lineNum">     119 </span>            : LABEL=SAXS</a>
+<a name="120"><span class="lineNum">     120 </span>            : ATOMS=1-355</a>
+<a name="121"><span class="lineNum">     121 </span>            : ONEBEAD</a>
+<a name="122"><span class="lineNum">     122 </span>            : TEMPLATE=template_AA.pdb</a>
+<a name="123"><span class="lineNum">     123 </span>            : SOLVDENS=0.334</a>
+<a name="124"><span class="lineNum">     124 </span>            : SOLVATION_CORRECTION=0.04</a>
+<a name="125"><span class="lineNum">     125 </span>            : SOLVATION_STRIDE=1</a>
+<a name="126"><span class="lineNum">     126 </span>            : SASA_CUTOFF=1.0</a>
+<a name="127"><span class="lineNum">     127 </span>            : SCALE_EXPINT=1.4002</a>
+<a name="128"><span class="lineNum">     128 </span>            : QVALUE1=0.03 EXPINT1=1.0902</a>
+<a name="129"><span class="lineNum">     129 </span>            : QVALUE2=0.06 EXPINT2=0.790632</a>
+<a name="130"><span class="lineNum">     130 </span>            : QVALUE3=0.09 EXPINT3=0.453808</a>
+<a name="131"><span class="lineNum">     131 </span>            : QVALUE4=0.12 EXPINT4=0.254737</a>
+<a name="132"><span class="lineNum">     132 </span>            : QVALUE5=0.15 EXPINT5=0.154928</a>
+<a name="133"><span class="lineNum">     133 </span>            : QVALUE6=0.18 EXPINT6=0.0921503</a>
+<a name="134"><span class="lineNum">     134 </span>            : QVALUE7=0.21 EXPINT7=0.052633</a>
+<a name="135"><span class="lineNum">     135 </span>            : QVALUE8=0.24 EXPINT8=0.0276557</a>
+<a name="136"><span class="lineNum">     136 </span>            : QVALUE9=0.27 EXPINT9=0.0122775</a>
+<a name="137"><span class="lineNum">     137 </span>            : QVALUE10=0.30 EXPINT10=0.00880634</a>
+<a name="138"><span class="lineNum">     138 </span>            : ... SAXS</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : PRINT ARG=(SAXS\.q-.*),(SAXS\.exp-.*) FILE=saxsdata STRIDE=1</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : \endplumedfile</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : */</a>
+<a name="145"><span class="lineNum">     145 </span>            : //+ENDPLUMEDOC</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : //+PLUMEDOC ISDB_COLVAR SANS</a>
+<a name="148"><span class="lineNum">     148 </span>            : /*</a>
+<a name="149"><span class="lineNum">     149 </span>            : Calculates SANS intensity.</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : SANS intensities are calculated for a set of scattering vectors using QVALUE keywords numbered from 1.</a>
+<a name="152"><span class="lineNum">     152 </span>            : Form factors are automatically assigned to atoms using the ATOMISTIC flag by reading a PDB file or, alternatively,</a>
+<a name="153"><span class="lineNum">     153 </span>            : a ONEBEAD coarse-grained implementation is available.</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : Both for ATOMISTIC and ONEBEAD the user must provide an all-atom PDB file via MOLINFO before the SANS instruction.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : ONEBEAD scheme consists in a single-bead per amino acid residue or three-bead for nucleic acid residue (one for</a>
+<a name="158"><span class="lineNum">     158 </span>            : the phosphate group, one for the pentose sugar, one for the nucleobase). PLUMED creates a virtual bead on which</a>
+<a name="159"><span class="lineNum">     159 </span>            : the SANS calculations are performed, centred on the COM of all atoms belonging to the bead. It is possible to</a>
+<a name="160"><span class="lineNum">     160 </span>            : account for the contribution of the solvation layer to the SAXS intensity by adding a correction term for the</a>
+<a name="161"><span class="lineNum">     161 </span>            : solvent accessible beads only: the form factors of the amino acids / phosphate groups / pentose sugars /</a>
+<a name="162"><span class="lineNum">     162 </span>            : nucleobases with a SASA (computed via LCPO algorithm) greater than a threshold are corrected according to an</a>
+<a name="163"><span class="lineNum">     163 </span>            : electron density term. Both the surface cut-off threshold and the electron density term can be set by the user</a>
+<a name="164"><span class="lineNum">     164 </span>            : with the SASA_CUTOFF and SOLVATION_CORRECTION keywords. Moreover, SASA stride calculation can be modified using</a>
+<a name="165"><span class="lineNum">     165 </span>            : SOLVATION_STRIDE, which is set to 100 steps by default. The deuteration of the solvent-exposed residues is chosen</a>
+<a name="166"><span class="lineNum">     166 </span>            : with a probability equal to the deuterium concentration in the buffer. The deuterated residues are updated with a</a>
+<a name="167"><span class="lineNum">     167 </span>            : stride equal to SOLVATION_STRIDE. The fraction of deuterated water can be set with DEUTER_CONC, the default value</a>
+<a name="168"><span class="lineNum">     168 </span>            : is 0.</a>
+<a name="169"><span class="lineNum">     169 </span>            : ONEBEAD requires an additional PDB file to perform mapping conversion, which must be provided via TEMPLATE</a>
+<a name="170"><span class="lineNum">     170 </span>            : keyword. This PDB file should only include the atoms for which the SANS intensity will be computed.</a>
+<a name="171"><span class="lineNum">     171 </span>            : The AMBER OL3 (RNA) and OL15 (DNA) naming is required for nucleic acids.</a>
+<a name="172"><span class="lineNum">     172 </span>            : Two additional bead types are available for DNA and RNA besides phosphate group, pentose sugar, and nucleobase:</a>
+<a name="173"><span class="lineNum">     173 </span>            : - 5'-end pentose sugar capped with an hydroxyl moiety at C5' (the residue name in the PDB must be followed by &quot;5&quot;,</a>
+<a name="174"><span class="lineNum">     174 </span>            : e.g., DC5 or C5 for cytosine in DNA and RNA, respectively);</a>
+<a name="175"><span class="lineNum">     175 </span>            : - 3'-end pentose sugar capped with an hydroxyl moiety at C3' (the residue name in the PDB must be followed by &quot;3&quot;,</a>
+<a name="176"><span class="lineNum">     176 </span>            : e.g., DC3 or C3 for cytosine in DNA and RNA, respectively).</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : PLEASE NOTE: at the moment, we DO NOT explicitly take into account deuterated residues in the ATOMISTIC</a>
+<a name="179"><span class="lineNum">     179 </span>            : representation, but we correct the solvent contribution via the DEUTER_CONC keyword.</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : Experimental reference intensities can be added using the EXPINT keywords. All these values must be normalised</a>
+<a name="182"><span class="lineNum">     182 </span>            : to the SANS intensity at q = 0. To facilitate this operation, the SCALE_EXPINT keyword can be used to provide</a>
+<a name="183"><span class="lineNum">     183 </span>            : the intensity at q = 0. Each EXPINT is divided by SCALE_EXPINT.</a>
+<a name="184"><span class="lineNum">     184 </span>            : The maximum QVALUE for ONEBEAD is set to 0.3 inverse angstroms.</a>
+<a name="185"><span class="lineNum">     185 </span>            : The solvent density, that by default is set to 0.334 electrons per cubic angstrom (bulk water), can be modified</a>
+<a name="186"><span class="lineNum">     186 </span>            : using the SOLVDENS keyword.</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : By default SANS is calculated using Debye on CPU, by adding the GPU flag it is possible to solve the equation on a</a>
+<a name="189"><span class="lineNum">     189 </span>            : GPU if the ARRAYFIRE libraries are installed and correctly linked.</a>
+<a name="190"><span class="lineNum">     190 </span>            : \ref METAINFERENCE can be activated using DOSCORE and the other relevant keywords.</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : \par Examples</a>
+<a name="193"><span class="lineNum">     193 </span>            : in the following example the SANS intensities are calculated at atomistic resolution. The form factors are assigned</a>
+<a name="194"><span class="lineNum">     194 </span>            : according to the PDB file specified in the MOLINFO. Each experimental intensity is divided by 1.4002, which is the</a>
+<a name="195"><span class="lineNum">     195 </span>            : corresponding theoretical intensity value at q = 0. The deuterated water fraction is set to 48%.</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : \plumedfile</a>
+<a name="198"><span class="lineNum">     198 </span>            : MOLINFO STRUCTURE=template_AA.pdb</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : SANS ...</a>
+<a name="201"><span class="lineNum">     201 </span>            : LABEL=SANS</a>
+<a name="202"><span class="lineNum">     202 </span>            : ATOMS=1-355</a>
+<a name="203"><span class="lineNum">     203 </span>            : ATOMISTIC</a>
+<a name="204"><span class="lineNum">     204 </span>            : SCALE_EXPINT=1.4002</a>
+<a name="205"><span class="lineNum">     205 </span>            : DEUTER_CONC=0.48</a>
+<a name="206"><span class="lineNum">     206 </span>            : QVALUE1=0.03 EXPINT1=1.0902</a>
+<a name="207"><span class="lineNum">     207 </span>            : QVALUE2=0.06 EXPINT2=0.790632</a>
+<a name="208"><span class="lineNum">     208 </span>            : QVALUE3=0.09 EXPINT3=0.453808</a>
+<a name="209"><span class="lineNum">     209 </span>            : QVALUE4=0.12 EXPINT4=0.254737</a>
+<a name="210"><span class="lineNum">     210 </span>            : QVALUE5=0.15 EXPINT5=0.154928</a>
+<a name="211"><span class="lineNum">     211 </span>            : QVALUE6=0.18 EXPINT6=0.0921503</a>
+<a name="212"><span class="lineNum">     212 </span>            : QVALUE7=0.21 EXPINT7=0.052633</a>
+<a name="213"><span class="lineNum">     213 </span>            : QVALUE8=0.24 EXPINT8=0.0276557</a>
+<a name="214"><span class="lineNum">     214 </span>            : QVALUE9=0.27 EXPINT9=0.0122775</a>
+<a name="215"><span class="lineNum">     215 </span>            : QVALUE10=0.30 EXPINT10=0.00880634</a>
+<a name="216"><span class="lineNum">     216 </span>            : ... SANS</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : PRINT ARG=(SANS\.q-.*),(SANS\.exp-.*) FILE=sansdata STRIDE=1</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : \endplumedfile</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : */</a>
+<a name="223"><span class="lineNum">     223 </span>            : //+ENDPLUMEDOC</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : class SAXS :</a>
+<a name="226"><span class="lineNum">     226 </span>            :   public MetainferenceBase</a>
+<a name="227"><span class="lineNum">     227 </span>            : {</a>
+<a name="228"><span class="lineNum">     228 </span>            : private:</a>
+<a name="229"><span class="lineNum">     229 </span>            :   enum { H, C, N, O, P, S, NTT };</a>
+<a name="230"><span class="lineNum">     230 </span>            :   enum { ALA_BB, ARG_BB, ARG_SC1, ARG_SC2, ASN_BB, ASN_SC1, ASP_BB, ASP_SC1, CYS_BB, CYS_SC1,</a>
+<a name="231"><span class="lineNum">     231 </span>            :          GLN_BB, GLN_SC1, GLU_BB, GLU_SC1, GLY_BB, HIS_BB, HIS_SC1, HIS_SC2, HIS_SC3, ILE_BB,</a>
+<a name="232"><span class="lineNum">     232 </span>            :          ILE_SC1, LEU_BB, LEU_SC1, LYS_BB, LYS_SC1, LYS_SC2, MET_BB, MET_SC1, PHE_BB, PHE_SC1,</a>
+<a name="233"><span class="lineNum">     233 </span>            :          PHE_SC2, PHE_SC3, PRO_BB, PRO_SC1, SER_BB, SER_SC1, THR_BB, THR_SC1, TRP_BB, TRP_SC1,</a>
+<a name="234"><span class="lineNum">     234 </span>            :          TRP_SC2, TRP_SC3, TRP_SC4, TYR_BB, TYR_SC1, TYR_SC2, TYR_SC3, VAL_BB, VAL_SC1, A_BB1,</a>
+<a name="235"><span class="lineNum">     235 </span>            :          A_BB2, A_BB3, A_SC1, A_SC2, A_SC3, A_SC4, A_3TE, A_5TE, A_TE3, A_TE5, C_BB1, C_BB2,</a>
+<a name="236"><span class="lineNum">     236 </span>            :          C_BB3, C_SC1, C_SC2, C_SC3, C_3TE, C_5TE, C_TE3, C_TE5, G_BB1, G_BB2, G_BB3, G_SC1,</a>
+<a name="237"><span class="lineNum">     237 </span>            :          G_SC2, G_SC3, G_SC4, G_3TE, G_5TE, G_TE3, G_TE5, U_BB1, U_BB2, U_BB3, U_SC1, U_SC2,</a>
+<a name="238"><span class="lineNum">     238 </span>            :          U_SC3, U_3TE, U_5TE, U_TE3, U_TE5, DA_BB1, DA_BB2, DA_BB3, DA_SC1, DA_SC2, DA_SC3,</a>
+<a name="239"><span class="lineNum">     239 </span>            :          DA_SC4, DA_3TE, DA_5TE, DA_TE3, DA_TE5, DC_BB1, DC_BB2, DC_BB3, DC_SC1, DC_SC2, DC_SC3,</a>
+<a name="240"><span class="lineNum">     240 </span>            :          DC_3TE, DC_5TE, DC_TE3, DC_TE5, DG_BB1, DG_BB2, DG_BB3, DG_SC1, DG_SC2, DG_SC3, DG_SC4,</a>
+<a name="241"><span class="lineNum">     241 </span>            :          DG_3TE, DG_5TE, DG_TE3, DG_TE5, DT_BB1, DT_BB2, DT_BB3, DT_SC1, DT_SC2, DT_SC3, DT_3TE,</a>
+<a name="242"><span class="lineNum">     242 </span>            :          DT_5TE, DT_TE3, DT_TE5, NMARTINI</a>
+<a name="243"><span class="lineNum">     243 </span>            :        };</a>
+<a name="244"><span class="lineNum">     244 </span>            :   enum { TRP, TYR, PHE, HIS, HIP, ARG, LYS, CYS, ASP, GLU, ILE, LEU, MET, ASN, PRO, GLN, SER, THR, VAL, ALA, GLY,</a>
+<a name="245"><span class="lineNum">     245 </span>            :          BASE_A, BASE_C, BASE_T, BASE_G, BASE_U,</a>
+<a name="246"><span class="lineNum">     246 </span>            :          BB_DNA, BB_DNA_5, BB_DNA_3,</a>
+<a name="247"><span class="lineNum">     247 </span>            :          BB_RNA, BB_RNA_5, BB_RNA_3,</a>
+<a name="248"><span class="lineNum">     248 </span>            :          BB_PO2,</a>
+<a name="249"><span class="lineNum">     249 </span>            :          NONEBEAD</a>
+<a name="250"><span class="lineNum">     250 </span>            :        };</a>
+<a name="251"><span class="lineNum">     251 </span>            :   bool saxs;</a>
+<a name="252"><span class="lineNum">     252 </span>            :   bool pbc;</a>
+<a name="253"><span class="lineNum">     253 </span>            :   bool serial;</a>
+<a name="254"><span class="lineNum">     254 </span>            :   bool gpu;</a>
+<a name="255"><span class="lineNum">     255 </span>            :   bool onebead;</a>
+<a name="256"><span class="lineNum">     256 </span>            :   bool isFirstStep;</a>
+<a name="257"><span class="lineNum">     257 </span>            :   int  deviceid;</a>
+<a name="258"><span class="lineNum">     258 </span>            :   unsigned nres;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   std::vector&lt;unsigned&gt; atoi;</a>
+<a name="260"><span class="lineNum">     260 </span>            :   std::vector&lt;unsigned&gt; atoms_per_bead;</a>
+<a name="261"><span class="lineNum">     261 </span>            :   std::vector&lt;double&gt;   atoms_masses;</a>
+<a name="262"><span class="lineNum">     262 </span>            :   std::vector&lt;double&gt;   q_list;</a>
+<a name="263"><span class="lineNum">     263 </span>            :   std::vector&lt;double&gt;   FF_rank;</a>
+<a name="264"><span class="lineNum">     264 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_vacuum;</a>
+<a name="265"><span class="lineNum">     265 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_solv;</a>
+<a name="266"><span class="lineNum">     266 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_mixed;</a>
+<a name="267"><span class="lineNum">     267 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   std::vector&lt;std::vector&lt;float&gt; &gt;  FFf_value;</a>
+<a name="269"><span class="lineNum">     269 </span>            :   // SANS:</a>
+<a name="270"><span class="lineNum">     270 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_vacuum_H;</a>
+<a name="271"><span class="lineNum">     271 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_solv_H;</a>
+<a name="272"><span class="lineNum">     272 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_mixed_H;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_vacuum_D;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; FF_value_mixed_D;</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; LCPOparam;</a>
+<a name="277"><span class="lineNum">     277 </span>            :   std::vector&lt;unsigned&gt; residue_atom;</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :   double rho, rho_corr, sasa_cutoff;</a>
+<a name="280"><span class="lineNum">     280 </span>            :   double deuter_conc;</a>
+<a name="281"><span class="lineNum">     281 </span>            :   unsigned solv_stride;</a>
+<a name="282"><span class="lineNum">     282 </span>            :   std::vector&lt;double&gt; Iq0_vac;</a>
+<a name="283"><span class="lineNum">     283 </span>            :   std::vector&lt;double&gt; Iq0_solv;</a>
+<a name="284"><span class="lineNum">     284 </span>            :   std::vector&lt;double&gt; Iq0_mix;</a>
+<a name="285"><span class="lineNum">     285 </span>            :   double Iq0;</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :   // SANS:</a>
+<a name="288"><span class="lineNum">     288 </span>            :   std::vector&lt;double&gt; Iq0_vac_H;</a>
+<a name="289"><span class="lineNum">     289 </span>            :   std::vector&lt;double&gt; Iq0_solv_H;</a>
+<a name="290"><span class="lineNum">     290 </span>            :   std::vector&lt;double&gt; Iq0_mix_H;</a>
+<a name="291"><span class="lineNum">     291 </span>            :   std::vector&lt;double&gt; Iq0_vac_D;</a>
+<a name="292"><span class="lineNum">     292 </span>            :   std::vector&lt;double&gt; Iq0_mix_D;</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            :   void calculate_gpu(std::vector&lt;Vector&gt; &amp;pos, std::vector&lt;Vector&gt; &amp;deriv);</a>
+<a name="295"><span class="lineNum">     295 </span>            :   void calculate_cpu(std::vector&lt;Vector&gt; &amp;pos, std::vector&lt;Vector&gt; &amp;deriv);</a>
+<a name="296"><span class="lineNum">     296 </span>            :   void getMartiniFFparam(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter);</a>
+<a name="297"><span class="lineNum">     297 </span>            :   void getOnebeadparam(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_vac, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_mix, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_solv, std::vector&lt;unsigned&gt; residue_atom);</a>
+<a name="298"><span class="lineNum">     298 </span>            :   unsigned getOnebeadMapping(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms);</a>
+<a name="299"><span class="lineNum">     299 </span>            :   double calculateAFF(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;FF_tmp, const double rho);</a>
+<a name="300"><span class="lineNum">     300 </span>            :   std::map&lt;std::string, std::vector&lt;double&gt; &gt; setupLCPOparam();</a>
+<a name="301"><span class="lineNum">     301 </span>            :   void readLCPOparam(const std::vector&lt;std::vector&lt;std::string&gt; &gt; &amp;AtomResidueName, unsigned natoms);</a>
+<a name="302"><span class="lineNum">     302 </span>            :   void calcNlist(std::vector&lt;std::vector&lt;int&gt; &gt; &amp;Nlist);</a>
+<a name="303"><span class="lineNum">     303 </span>            :   void sasa_calculate(std::vector&lt;bool&gt; &amp;solv_res);</a>
+<a name="304"><span class="lineNum">     304 </span>            :   // SANS:</a>
+<a name="305"><span class="lineNum">     305 </span>            :   void getOnebeadparam_sansH(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_vac_H, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_mix_H, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_solv_H);</a>
+<a name="306"><span class="lineNum">     306 </span>            :   void getOnebeadparam_sansD(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_vac_D, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_mix_D);</a>
+<a name="307"><span class="lineNum">     307 </span>            :   double calculateAFFsans(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;FF_tmp, const double deuter_conc);</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : public:</a>
+<a name="310"><span class="lineNum">     310 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="311"><span class="lineNum">     311 </span>            :   explicit SAXS(const ActionOptions&amp;);</a>
+<a name="312"><span class="lineNum">     312 </span>            :   void calculate() override;</a>
+<a name="313"><span class="lineNum">     313 </span>            :   void update() override;</a>
+<a name="314"><span class="lineNum">     314 </span>            : };</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      12548 : PLUMED_REGISTER_ACTION(SAXS,&quot;SAXS&quot;)</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(SAXS,&quot;SANS&quot;)</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         32 : void SAXS::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         32 :   componentsAreNotOptional(keys);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         32 :   MetainferenceBase::registerKeywords(keys);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         64 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         64 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;DEVICEID&quot;,&quot;-1&quot;,&quot;Identifier of the GPU to be used&quot;);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         64 :   keys.addFlag(&quot;GPU&quot;,false,&quot;calculate SAXS using ARRAYFIRE on an accelerator device&quot;);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         64 :   keys.addFlag(&quot;ATOMISTIC&quot;,false,&quot;calculate SAXS for an atomistic model&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         64 :   keys.addFlag(&quot;MARTINI&quot;,false,&quot;calculate SAXS for a Martini model&quot;);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         64 :   keys.addFlag(&quot;ONEBEAD&quot;,false,&quot;calculate SAXS for a single bead model&quot;);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;TEMPLATE&quot;,&quot;template.pdb&quot;,&quot;A PDB file is required for ONEBEAD mapping&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         64 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;The atoms to be included in the calculation, e.g. the whole protein&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         64 :   keys.add(&quot;numbered&quot;,&quot;QVALUE&quot;,&quot;Selected scattering lengths in inverse angstroms are given as QVALUE1, QVALUE2, ...&quot;);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         64 :   keys.add(&quot;numbered&quot;,&quot;PARAMETERS&quot;,&quot;Used parameter Keywords like PARAMETERS1, PARAMETERS2. These are used to calculate the form factor for the \\f$i\\f$th atom/bead&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;DEUTER_CONC&quot;,&quot;0.&quot;,&quot;Fraction of deuterated solvent&quot;);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;SOLVDENS&quot;,&quot;0.334&quot;,&quot;Density of the solvent to be used for the correction of atomistic form factors&quot;);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;SOLVATION_CORRECTION&quot;,&quot;0.0&quot;,&quot;Hydration layer electron density correction (ONEBEAD only)&quot;);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;SASA_CUTOFF&quot;,&quot;1.0&quot;,&quot;SASA value to consider a residue as exposed to the solvent (ONEBEAD only)&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         64 :   keys.add(&quot;numbered&quot;,&quot;EXPINT&quot;,&quot;Add an experimental value for each q value&quot;);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;SOLVATION_STRIDE&quot;,&quot;100&quot;,&quot;Number of steps between every new residues solvation estimation via LCPO (ONEBEAD only)&quot;);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;SCALE_EXPINT&quot;,&quot;1.0&quot;,&quot;Scaling value for experimental data normalization&quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         64 :   keys.addOutputComponent(&quot;q&quot;,&quot;default&quot;,&quot;the # SAXS of q&quot;);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         64 :   keys.addOutputComponent(&quot;exp&quot;,&quot;EXPINT&quot;,&quot;the # experimental intensity&quot;);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         32 : }</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         28 : SAXS::SAXS(const ActionOptions&amp;ao):</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   PLUMED_METAINF_INIT(ao),</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         28 :   saxs(true),</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         28 :   pbc(true),</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         28 :   serial(false),</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         28 :   gpu(false),</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         28 :   onebead(false),</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         28 :   isFirstStep(true),</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         28 :   deviceid(-1)</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : {</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         28 :   if( getName().find(&quot;SAXS&quot;)!=std::string::npos) { saxs=true; }</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          6 :   else if( getName().find(&quot;SANS&quot;)!=std::string::npos) { saxs=false; }</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         56 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         28 :   unsigned size = atoms.size();</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         28 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         28 :   bool nopbc=!pbc;</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         28 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         28 :   pbc=!nopbc;</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         28 :   if(pbc)      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         16 :   else         log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         28 :   parseFlag(&quot;GPU&quot;,gpu);</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : #ifndef  __PLUMED_HAS_ARRAYFIRE</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         28 :   if(gpu) error(&quot;To use the GPU mode PLUMED must be compiled with ARRAYFIRE&quot;);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : #endif</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         28 :   parse(&quot;DEVICEID&quot;,deviceid);</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : #ifdef  __PLUMED_HAS_ARRAYFIRE</a>
+<a name="376"><span class="lineNum">     376 </span>            :   if(gpu&amp;&amp;comm.Get_rank()==0) {</a>
+<a name="377"><span class="lineNum">     377 </span>            :     // if not set try to check the one set by the API</a>
+<a name="378"><span class="lineNum">     378 </span>            :     if(deviceid==-1) deviceid=plumed.getGpuDeviceId();</a>
+<a name="379"><span class="lineNum">     379 </span>            :     // if still not set use 0</a>
+<a name="380"><span class="lineNum">     380 </span>            :     if(deviceid==-1) deviceid=0;</a>
+<a name="381"><span class="lineNum">     381 </span>            : #ifdef  __PLUMED_HAS_ARRAYFIRE_CUDA</a>
+<a name="382"><span class="lineNum">     382 </span>            :     af::setDevice(afcu::getNativeId(deviceid));</a>
+<a name="383"><span class="lineNum">     383 </span>            : #elif   __PLUMED_HAS_ARRAYFIRE_OCL</a>
+<a name="384"><span class="lineNum">     384 </span>            :     af::setDevice(afcl::getNativeId(deviceid));</a>
+<a name="385"><span class="lineNum">     385 </span>            : #else</a>
+<a name="386"><span class="lineNum">     386 </span>            :     af::setDevice(deviceid);</a>
+<a name="387"><span class="lineNum">     387 </span>            : #endif</a>
+<a name="388"><span class="lineNum">     388 </span>            :     af::info();</a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span>            : #endif</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         28 :   bool atomistic=false;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         28 :   parseFlag(&quot;ATOMISTIC&quot;,atomistic);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         28 :   if(atomistic) log.printf(&quot;  using ATOMISTIC form factors\n&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         28 :   bool martini=false;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         28 :   parseFlag(&quot;MARTINI&quot;,martini);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         28 :   if(martini) log.printf(&quot;  using MARTINI form factors\n&quot;);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         28 :   onebead=false;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         28 :   parseFlag(&quot;ONEBEAD&quot;,onebead);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         28 :   if(onebead) log.printf(&quot;  using ONEBEAD form factors\n&quot;);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         28 :   if(martini&amp;&amp;atomistic) error(&quot;You cannot use MARTINI and ATOMISTIC at the same time&quot;);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         28 :   if(martini&amp;&amp;onebead) error(&quot;You cannot use MARTINI and ONEBEAD at the same time&quot;);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         28 :   if(onebead&amp;&amp;atomistic) error(&quot;You cannot use ONEBEAD and ATOMISTIC at the same time&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         28 :   if((martini)&amp;&amp;(!saxs)) error(&quot;MARTINI cannot be used with SANS&quot;);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         28 :   if((!atomistic)&amp;&amp;(!martini)&amp;&amp;(!onebead)&amp;&amp;(!saxs)) error(&quot;External PARAMETERS cannot be used with SANS&quot;);</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :   unsigned ntarget=0;</a>
+<a name="409"><span class="lineNum">     409 </span>            :   for(unsigned i=0;; ++i) {</a>
+<a name="410"><span class="lineNum">     410 </span>            :     double t_list;</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        608 :     if( !parseNumbered( &quot;QVALUE&quot;, i+1, t_list) ) break;</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">        276 :     if(t_list&lt;=0.) error(&quot;QVALUE cannot be less or equal to zero!\n&quot;);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">        276 :     if(onebead&amp;&amp;t_list&gt;0.3) error(&quot;ONEBEAD mapping QVALUE must be smaller or equal to 0.3&quot;);</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">        276 :     q_list.push_back(t_list);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        276 :     ntarget++;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        276 :   }</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :   const unsigned numq = ntarget;</a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        304 :   for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">        276 :     if(q_list[i]==0.) error(&quot;it is not possible to set q=0\n&quot;);</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        276 :     if(i&gt;0&amp;&amp;q_list[i]&lt;q_list[i-1]) error(&quot;QVALUE must be in ascending order&quot;);</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        276 :     log.printf(&quot;  my q: %lf \n&quot;,q_list[i]);</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :   }</a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         28 :   rho = 0.334;</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         28 :   parse(&quot;SOLVDENS&quot;, rho);</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         28 :   log.printf(&quot;  Solvent density: %lf\n&quot;, rho);</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         28 :   double scale_expint=1.;</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         28 :   parse(&quot;SCALE_EXPINT&quot;,scale_expint);</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         28 :   double correction = 0.00;</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         28 :   parse(&quot;SOLVATION_CORRECTION&quot;, correction);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         28 :   rho_corr=rho-correction;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         28 :   if(onebead) log.printf(&quot;  Solvation density contribution: %lf\n&quot;, correction);</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         28 :   if((atomistic||martini)&amp;&amp;(rho_corr!=rho)) log.printf(&quot;  Solvation density contribution is taken into account in ONEBEAD only\n&quot;);</span></a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">         28 :   solv_stride = 100;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         28 :   parse(&quot;SOLVATION_STRIDE&quot;, solv_stride);</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         28 :   if(solv_stride &lt; 1.) error(&quot;SOLVATION_STRIDE must be greater than 0&quot;);</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         28 :   if(onebead&amp;&amp;(rho_corr!=rho)) log.printf(&quot;  SASA calculation stride: %u\n&quot;, solv_stride);</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         28 :   sasa_cutoff = 1.0;</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         28 :   parse(&quot;SASA_CUTOFF&quot;, sasa_cutoff);</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         28 :   if(sasa_cutoff &lt;= 0.) error(&quot;SASA_CUTOFF must be greater than 0&quot;);</span></a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         28 :   deuter_conc = 0.;</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         28 :   parse(&quot;DEUTER_CONC&quot;, deuter_conc);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         28 :   if(deuter_conc &lt; 0. || deuter_conc &gt; 1.) error(&quot;DEUTER_CONC must be in 0-1 range&quot;);</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">         28 :   if ((atomistic||onebead)&amp;&amp;(!saxs)) log.printf(&quot;  Solvent deuterium fraction: %lf/1.000000\n&quot;, deuter_conc);</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         28 :   PDB pdb;</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         28 :   if(onebead) {</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :     std::string template_name;</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         10 :     parse(&quot;TEMPLATE&quot;,template_name);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">         10 :     log.printf(&quot;  Template for ONEBEAD mapping conversion: %s\n&quot;, template_name.c_str());</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         20 :     if( !pdb.read(template_name,plumed.getAtoms().usingNaturalUnits(),1.) ) plumed_merror(&quot;missing input file &quot; + template_name);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :   }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   // Here we perform the preliminary mapping for onebead representation</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         28 :   if(onebead) {</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         10 :     LCPOparam.resize(size);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         10 :     nres = getOnebeadMapping(pdb, atoms);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         10 :     if(saxs) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          6 :       Iq0_vac.resize(nres);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          6 :       Iq0_solv.resize(nres);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          6 :       Iq0_mix.resize(nres);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :     } else { // SANS</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          4 :       Iq0_vac_H.resize(nres);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          4 :       Iq0_solv_H.resize(nres);</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          4 :       Iq0_mix_H.resize(nres);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          4 :       Iq0_vac_D.resize(nres);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          4 :       Iq0_mix_D.resize(nres);</span></a>
+<a name="474"><span class="lineNum">     474 </span>            :     }</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         10 :     atoi.resize(nres);</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :   } else {</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">         18 :     atoi.resize(size);</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :   }</a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         28 :   Iq0=0;</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp;</a>
+<a name="482"><span class="lineNum">     482 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_vac;</a>
+<a name="483"><span class="lineNum">     483 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_mix;</a>
+<a name="484"><span class="lineNum">     484 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_solv;</a>
+<a name="485"><span class="lineNum">     485 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; parameter;</a>
+<a name="486"><span class="lineNum">     486 </span>            :   // SANS</a>
+<a name="487"><span class="lineNum">     487 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_vac_H;</a>
+<a name="488"><span class="lineNum">     488 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_mix_H;</a>
+<a name="489"><span class="lineNum">     489 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_solv_H;</a>
+<a name="490"><span class="lineNum">     490 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_vac_D;</a>
+<a name="491"><span class="lineNum">     491 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; FF_tmp_mix_D;</a>
+<a name="492"><span class="lineNum">     492 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_H;</a>
+<a name="493"><span class="lineNum">     493 </span>            :   std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_D;</a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">         28 :   if(!atomistic&amp;&amp;!martini&amp;&amp;!onebead) {</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :     // read in parameter std::vector</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          4 :     parameter.resize(size);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :     ntarget=0;</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         36 :     for(unsigned i=0; i&lt;size; ++i) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         64 :       if( !parseNumberedVector( &quot;PARAMETERS&quot;, i+1, parameter[i]) ) break;</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         32 :       ntarget++;</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :     }</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          4 :     if( ntarget!=size ) error(&quot;found wrong number of parameter std::vectors&quot;);</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          4 :     FF_tmp.resize(numq,std::vector&lt;long double&gt;(size));</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         36 :     for(unsigned i=0; i&lt;size; ++i) {</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         32 :       atoi[i]=i;</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        128 :       for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">        480 :         for(unsigned j=0; j&lt;parameter[i].size(); ++j) {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">        384 :           FF_tmp[k][i]+= parameter[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :         }</a>
+<a name="511"><span class="lineNum">     511 </span>            :       }</a>
+<a name="512"><span class="lineNum">     512 </span>            :     }</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         36 :     for(unsigned i=0; i&lt;size; ++i) Iq0+=parameter[i][0];</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          4 :     Iq0 *= Iq0;</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         28 :   } else if(onebead) {</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         10 :     if(saxs) {</span></a>
+<a name="517"><span class="lineNum">     517 </span>            :       // read in parameter std::vector</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">          6 :       FF_tmp_vac.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          6 :       FF_tmp_mix.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">          6 :       FF_tmp_solv.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">          6 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_vac(NONEBEAD);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">          6 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_mix(NONEBEAD);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">          6 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_solv(NONEBEAD);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          6 :       getOnebeadparam(pdb, atoms, parameter_vac, parameter_mix, parameter_solv,residue_atom);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">        204 :       for(unsigned i=0; i&lt;NONEBEAD; ++i) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">       1980 :         for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">      14256 :           for(unsigned j=0; j&lt;parameter_vac[i].size(); ++j) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">      12474 :             FF_tmp_vac[k][i]+= parameter_vac[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :           }</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">      14256 :           for(unsigned j=0; j&lt;parameter_mix[i].size(); ++j) {</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">      12474 :             FF_tmp_mix[k][i]+= parameter_mix[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :           }</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">      14256 :           for(unsigned j=0; j&lt;parameter_solv[i].size(); ++j) {</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">      12474 :             FF_tmp_solv[k][i]+= parameter_solv[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="535"><span class="lineNum">     535 </span>            :           }</a>
+<a name="536"><span class="lineNum">     536 </span>            :         }</a>
+<a name="537"><span class="lineNum">     537 </span>            :       }</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">       1294 :       for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">       1288 :         Iq0_vac[i]=parameter_vac[atoi[i]][0];</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">       1288 :         Iq0_mix[i]=parameter_mix[atoi[i]][0];</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">       1288 :         Iq0_solv[i]=parameter_solv[atoi[i]][0];</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :       }</a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">          6 :     } else { // SANS</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :       // read in parameter std::vector</a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">          4 :       FF_tmp_vac_H.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">          4 :       FF_tmp_mix_H.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">          4 :       FF_tmp_solv_H.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">          4 :       FF_tmp_vac_D.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">          4 :       FF_tmp_mix_D.resize(numq,std::vector&lt;long double&gt;(NONEBEAD));</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">          4 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_vac_H(NONEBEAD);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          4 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_mix_H(NONEBEAD);</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          4 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_solv_H(NONEBEAD);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          4 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_vac_D(NONEBEAD);</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">          4 :       std::vector&lt;std::vector&lt;long double&gt; &gt; parameter_mix_D(NONEBEAD);</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">          4 :       getOnebeadparam_sansH(pdb, atoms, parameter_vac_H, parameter_mix_H, parameter_solv_H);</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">          4 :       getOnebeadparam_sansD(pdb, atoms, parameter_vac_D, parameter_mix_D);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        136 :       for(unsigned i=0; i&lt;NONEBEAD; ++i) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">       1320 :         for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">       9504 :           for(unsigned j=0; j&lt;parameter_vac_H[i].size(); ++j) { // same number of parameters</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">       8316 :             FF_tmp_vac_H[k][i]+= parameter_vac_H[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">       8316 :             FF_tmp_vac_D[k][i]+= parameter_vac_D[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :           }</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">       9504 :           for(unsigned j=0; j&lt;parameter_mix_H[i].size(); ++j) {</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">       8316 :             FF_tmp_mix_H[k][i]+= parameter_mix_H[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">       8316 :             FF_tmp_mix_D[k][i]+= parameter_mix_D[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :           }</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">       9504 :           for(unsigned j=0; j&lt;parameter_solv_H[i].size(); ++j) {</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">       8316 :             FF_tmp_solv_H[k][i]+= parameter_solv_H[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :           }</a>
+<a name="570"><span class="lineNum">     570 </span>            :         }</a>
+<a name="571"><span class="lineNum">     571 </span>            :       }</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">        880 :       for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        876 :         Iq0_vac_H[i]=parameter_vac_H[atoi[i]][0];</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        876 :         Iq0_mix_H[i]=parameter_mix_H[atoi[i]][0];</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        876 :         Iq0_solv_H[i]=parameter_solv_H[atoi[i]][0];</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">        876 :         Iq0_vac_D[i]=parameter_vac_D[atoi[i]][0];</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        876 :         Iq0_mix_D[i]=parameter_mix_D[atoi[i]][0];</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :       }</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          4 :     }</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         14 :   } else if(martini) {</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :     // read in parameter std::vector</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">          8 :     FF_tmp.resize(numq,std::vector&lt;long double&gt;(NMARTINI));</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">          8 :     parameter.resize(NMARTINI);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">          8 :     getMartiniFFparam(atoms, parameter);</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">       1072 :     for(unsigned i=0; i&lt;NMARTINI; ++i) {</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">      17024 :       for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">     127680 :         for(unsigned j=0; j&lt;parameter[i].size(); ++j) {</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">     111720 :           FF_tmp[k][i]+= parameter[i][j]*std::pow(static_cast&lt;long double&gt;(q_list[k]),j);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :         }</a>
+<a name="590"><span class="lineNum">     590 </span>            :       }</a>
+<a name="591"><span class="lineNum">     591 </span>            :     }</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">       8400 :     for(unsigned i=0; i&lt;size; ++i) Iq0+=parameter[atoi[i]][0];</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">          8 :     Iq0 *= Iq0;</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          6 :   } else if(atomistic) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          6 :     FF_tmp.resize(numq,std::vector&lt;long double&gt;(NTT));</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">          6 :     if(saxs) Iq0=calculateAFF(atoms, FF_tmp, rho);</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          2 :     else Iq0=calculateAFFsans(atoms, FF_tmp, deuter_conc);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">          6 :     Iq0 *= Iq0;</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :   }</a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span>            :   std::vector&lt;double&gt; expint;</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         28 :   expint.resize( numq );</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :   ntarget=0;</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        160 :   for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        296 :     if( !parseNumbered( &quot;EXPINT&quot;, i+1, expint[i] ) ) break;</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">        132 :     ntarget++;</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :   }</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">        160 :   std::transform(expint.begin(), expint.begin() + ntarget, expint.begin(), [scale_expint](double x) { return x / scale_expint; });</span></a>
+<a name="609"><span class="lineNum">     609 </span>            :   bool exp=false;</a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         28 :   if(ntarget!=numq &amp;&amp; ntarget!=0) error(&quot;found wrong number of EXPINT values&quot;);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         28 :   if(ntarget==numq) exp=true;</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         28 :   if(getDoScore()&amp;&amp;!exp) error(&quot;with DOSCORE you need to set the EXPINT values&quot;);</span></a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         28 :   if(!gpu) {</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         28 :     FF_rank.resize(numq);</span></a>
+<a name="616"><span class="lineNum">     616 </span>            :     unsigned n_atom_types;</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         28 :     if(onebead) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         10 :       FF_value.resize(nres,std::vector&lt;double&gt;(numq));</span></a>
+<a name="619"><span class="lineNum">     619 </span>            :       n_atom_types=NONEBEAD;</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         10 :       if(saxs) {</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">          6 :         FF_value_vacuum.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">          6 :         FF_value_solv.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         12 :         FF_value_mixed.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :       } else {</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">          4 :         FF_value_vacuum_H.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">          4 :         FF_value_solv_H.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">          4 :         FF_value_mixed_H.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">          4 :         FF_value_vacuum_D.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">          8 :         FF_value_mixed_D.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :       }</a>
+<a name="631"><span class="lineNum">     631 </span>            :     } else {</a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">         36 :       FF_value.resize(size,std::vector&lt;double&gt;(numq));</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :     }</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">        304 :     for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">        276 :       if(!onebead) {</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">     316710 :         for(unsigned i=0; i&lt;size; ++i) FF_value[i][k] = static_cast&lt;double&gt;(FF_tmp[k][atoi[i]])/(std::sqrt(Iq0));</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">     316710 :         for(unsigned i=0; i&lt;size; ++i) FF_rank[k] += FF_value[i][k]*FF_value[i][k];</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :       } else {</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">         90 :         if(saxs) {</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">       1836 :           for(unsigned i=0; i&lt;n_atom_types; ++i) {</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">       1782 :             FF_value_vacuum[i][k] = static_cast&lt;double&gt;(FF_tmp_vac[k][i]);</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">       1782 :             FF_value_mixed[i][k] = static_cast&lt;double&gt;(FF_tmp_mix[k][i]);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">       1782 :             FF_value_solv[i][k] = static_cast&lt;double&gt;(FF_tmp_solv[k][i]);</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :           }</a>
+<a name="645"><span class="lineNum">     645 </span>            :         } else { // SANS</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">       1224 :           for(unsigned i=0; i&lt;n_atom_types; ++i) {</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">       1188 :             FF_value_vacuum_H[i][k] = static_cast&lt;double&gt;(FF_tmp_vac_H[k][i]);</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">       1188 :             FF_value_mixed_H[i][k] = static_cast&lt;double&gt;(FF_tmp_mix_H[k][i]);</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">       1188 :             FF_value_solv_H[i][k] = static_cast&lt;double&gt;(FF_tmp_solv_H[k][i]);</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">       1188 :             FF_value_vacuum_D[i][k] = static_cast&lt;double&gt;(FF_tmp_vac_D[k][i]);</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">       1188 :             FF_value_mixed_D[i][k] = static_cast&lt;double&gt;(FF_tmp_mix_D[k][i]);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :           }</a>
+<a name="653"><span class="lineNum">     653 </span>            :         }</a>
+<a name="654"><span class="lineNum">     654 </span>            :       }</a>
+<a name="655"><span class="lineNum">     655 </span>            :     }</a>
+<a name="656"><span class="lineNum">     656 </span>            :   } else {</a>
+<a name="657"><span class="lineNum">     657 </span>            :     unsigned n_atom_types;</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 :     if(onebead) {</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineNoCov">          0 :       FFf_value.resize(numq,std::vector&lt;float&gt;(nres));</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :       n_atom_types=NONEBEAD;</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :       if(saxs) {</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :         FF_value_vacuum.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :         FF_value_solv.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :         FF_value_mixed.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :       } else { // SANS</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :         FF_value_vacuum_H.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :         FF_value_solv_H.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :         FF_value_mixed_H.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :         FF_value_vacuum_D.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :         FF_value_mixed_D.resize(n_atom_types,std::vector&lt;double&gt;(numq));</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :       }</a>
+<a name="672"><span class="lineNum">     672 </span>            :     } else {</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :       FFf_value.resize(numq,std::vector&lt;float&gt;(size));</span></a>
+<a name="674"><span class="lineNum">     674 </span>            :     }</a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :     for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :       if(!onebead) {</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;size; ++i) {</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :           FFf_value[k][i] = static_cast&lt;float&gt;(FF_tmp[k][atoi[i]])/(std::sqrt(Iq0));</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :         }</a>
+<a name="680"><span class="lineNum">     680 </span>            :       } else {</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :         if(saxs) {</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :           for(unsigned i=0; i&lt;n_atom_types; ++i) {</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :             FF_value_vacuum[i][k] = static_cast&lt;double&gt;(FF_tmp_vac[k][i]);</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineNoCov">          0 :             FF_value_mixed[i][k] = static_cast&lt;double&gt;(FF_tmp_mix[k][i]);</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :             FF_value_solv[i][k] = static_cast&lt;double&gt;(FF_tmp_solv[k][i]);</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :           }</a>
+<a name="687"><span class="lineNum">     687 </span>            :         } else { // SANS</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :           for(unsigned i=0; i&lt;n_atom_types; ++i) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :             FF_value_vacuum_H[i][k] = static_cast&lt;double&gt;(FF_tmp_vac_H[k][i]);</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :             FF_value_mixed_H[i][k] = static_cast&lt;double&gt;(FF_tmp_mix_H[k][i]);</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :             FF_value_solv_H[i][k] = static_cast&lt;double&gt;(FF_tmp_solv_H[k][i]);</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 :             FF_value_vacuum_D[i][k] = static_cast&lt;double&gt;(FF_tmp_vac_D[k][i]);</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :             FF_value_mixed_D[i][k] = static_cast&lt;double&gt;(FF_tmp_mix_D[k][i]);</span></a>
+<a name="694"><span class="lineNum">     694 </span>            :           }</a>
+<a name="695"><span class="lineNum">     695 </span>            :         }</a>
+<a name="696"><span class="lineNum">     696 </span>            :       }</a>
+<a name="697"><span class="lineNum">     697 </span>            :     }</a>
+<a name="698"><span class="lineNum">     698 </span>            :   }</a>
+<a name="699"><span class="lineNum">     699 </span>            : </a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         28 :   if(!getDoScore()) {</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">        224 :     for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">        204 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">        204 :       addComponentWithDerivatives(&quot;q-&quot;+num);</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">        408 :       componentIsNotPeriodic(&quot;q-&quot;+num);</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :     }</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">         20 :     if(exp) {</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         64 :       for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">         60 :         std::string num; Tools::convert(i,num);</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         60 :         addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">         60 :         componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">         60 :         Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">         60 :         comp-&gt;set(expint[i]);</span></a>
+<a name="713"><span class="lineNum">     713 </span>            :       }</a>
+<a name="714"><span class="lineNum">     714 </span>            :     }</a>
+<a name="715"><span class="lineNum">     715 </span>            :   } else {</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">         80 :     for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">         72 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">         72 :       addComponent(&quot;q-&quot;+num);</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">        144 :       componentIsNotPeriodic(&quot;q-&quot;+num);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :     }</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">         80 :     for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">         72 :       std::string num; Tools::convert(i,num);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">         72 :       addComponent(&quot;exp-&quot;+num);</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">         72 :       componentIsNotPeriodic(&quot;exp-&quot;+num);</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">         72 :       Value* comp=getPntrToComponent(&quot;exp-&quot;+num);</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">         72 :       comp-&gt;set(expint[i]);</span></a>
+<a name="727"><span class="lineNum">     727 </span>            :     }</a>
+<a name="728"><span class="lineNum">     728 </span>            :   }</a>
+<a name="729"><span class="lineNum">     729 </span>            : </a>
+<a name="730"><span class="lineNum">     730 </span>            :   // convert units to nm^-1</a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">        304 :   for(unsigned i=0; i&lt;numq; ++i) {</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">        276 :     q_list[i]=q_list[i]*10.0;    // factor 10 to convert from A^-1 to nm^-1</span></a>
+<a name="733"><span class="lineNum">     733 </span>            :   }</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">         28 :   log&lt;&lt;&quot;  Bibliography &quot;;</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         28 :   if(martini) {</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">         16 :     log&lt;&lt;plumed.cite(&quot;Niebling, Björling, Westenhoff, J Appl Crystallogr 47, 1190–1198 (2014).&quot;);</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">         16 :     log&lt;&lt;plumed.cite(&quot;Paissoni, Jussupow, Camilloni, J Appl Crystallogr 52, 394-402 (2019).&quot;);</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :   }</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">         28 :   if(atomistic) {</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">         12 :     log&lt;&lt;plumed.cite(&quot;Fraser, MacRae, Suzuki, J. Appl. Crystallogr., 11, 693–694 (1978).&quot;);</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">         12 :     log&lt;&lt;plumed.cite(&quot;Brown, Fox, Maslen, O'Keefe, Willis, International Tables for Crystallography C, 554–595 (International Union of Crystallography, 2006).&quot;);</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :   }</a>
+<a name="743"><span class="lineNum">     743 </span>            : </a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">         56 :   log&lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;);</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">         28 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">         28 :   requestAtoms(atoms, false);</span></a>
+<a name="748"><span class="lineNum">     748 </span>            : </a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">         28 :   if(getDoScore()) {</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">          8 :     setParameters(expint);</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">          8 :     Initialise(numq);</span></a>
+<a name="752"><span class="lineNum">     752 </span>            :   }</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         28 :   setDerivatives();</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">         28 :   checkRead();</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">         56 : }</span></a>
+<a name="756"><span class="lineNum">     756 </span>            : </a>
+<a name="757"><span class="lineNum">     757 </span>            : // calculates SASA neighbor list</a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">          8 : void SAXS::calcNlist(std::vector&lt;std::vector&lt;int&gt; &gt; &amp;Nlist)</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : {</a>
+<a name="760"><span class="lineNum">     760 </span>            :   unsigned natoms = getNumberOfAtoms();</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">      28596 :   for(unsigned i = 0; i &lt; natoms; ++i) {</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">      28588 :     if (LCPOparam[i].size()&gt;0) {</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">   24279400 :       for (unsigned j = 0; j &lt; i; ++j) {</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">   24266020 :         if (LCPOparam[j].size()&gt;0) {</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">   11213664 :           double Delta_ij_mod = modulo(delta(getPosition(i), getPosition(j)))*10.;</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">   11213664 :           double overlapD = LCPOparam[i][0]+LCPOparam[j][0];</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">   11213664 :           if(Delta_ij_mod &lt; overlapD) {</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">     259140 :             Nlist.at(i).push_back(j);</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">     259140 :             Nlist.at(j).push_back(i);</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :           }</a>
+<a name="771"><span class="lineNum">     771 </span>            :         }</a>
+<a name="772"><span class="lineNum">     772 </span>            :       }</a>
+<a name="773"><span class="lineNum">     773 </span>            :     }</a>
+<a name="774"><span class="lineNum">     774 </span>            :   }</a>
+<a name="775"><span class="lineNum">     775 </span>            : </a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">          8 : }</span></a>
+<a name="777"><span class="lineNum">     777 </span>            : </a>
+<a name="778"><span class="lineNum">     778 </span>            : // calculates SASA according to LCPO algorithm</a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">          8 : void SAXS::sasa_calculate(std::vector&lt;bool&gt; &amp;solv_res)</span></a>
+<a name="780"><span class="lineNum">     780 </span>            : {</a>
+<a name="781"><span class="lineNum">     781 </span>            :   unsigned natoms = getNumberOfAtoms();</a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">          8 :   std::vector&lt;std::vector&lt;int&gt; &gt; Nlist(natoms);</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">          8 :   calcNlist(Nlist);</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">          8 :   std::vector&lt;double&gt; sasares(nres, 0.);</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">      28596 :   for(unsigned i = 0; i &lt; natoms; ++i) {</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">      28588 :     if(LCPOparam[i].size()&gt;1) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">      13380 :       if(LCPOparam[i][1]&gt;0.0) {</span></a>
+<a name="788"><span class="lineNum">     788 </span>            :         double Aij = 0.0;</a>
+<a name="789"><span class="lineNum">     789 </span>            :         double Aijk = 0.0;</a>
+<a name="790"><span class="lineNum">     790 </span>            :         double Ajk = 0.0;</a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">      13380 :         double ri = LCPOparam[i][0];</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">      13380 :         double S1 = 4.*M_PI*ri*ri;</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">     531660 :         for (unsigned j = 0; j &lt; Nlist[i].size(); ++j) {</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">     518280 :           double d_ij = modulo(delta( getPosition(i), getPosition(Nlist[i][j]) ))*10.;</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">     518280 :           double rj = LCPOparam[Nlist[i][j]][0];</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">     518280 :           double Aijt = (2.*M_PI*ri*(ri-d_ij/2.-((ri*ri-rj*rj)/(2.*d_ij))));</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :           double Ajkt = 0.0;</a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">   22258568 :           for (unsigned k = 0; k &lt; Nlist[Nlist[i][j]].size(); ++k) {</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">   21740288 :             if (std::find (Nlist[i].begin(), Nlist[i].end(), Nlist[Nlist[i][j]][k]) !=  Nlist[i].end()) {</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">   11186016 :               double d_jk = modulo(delta( getPosition(Nlist[i][j]), getPosition(Nlist[Nlist[i][j]][k]) ))*10.;</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">   11186016 :               double rk = LCPOparam[Nlist[Nlist[i][j]][k]][0];</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">   11186016 :               double sjk =  (2.*M_PI*rj*(rj-d_jk/2.-((rj*rj-rk*rk)/(2.*d_jk))));</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">   11186016 :               Ajkt += sjk;</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :             }</a>
+<a name="805"><span class="lineNum">     805 </span>            :           }</a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">     518280 :           Aijk += (Aijt * Ajkt);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">     518280 :           Aij += Aijt;</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">     518280 :           Ajk += Ajkt;</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :         }</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">      13380 :         double sasai = (LCPOparam[i][1]*S1+LCPOparam[i][2]*Aij+LCPOparam[i][3]*Ajk+LCPOparam[i][4]*Aijk);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">      13380 :         if (sasai &gt; 0 ) {</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">      10420 :           sasares[residue_atom[i]] += sasai/100.;</span></a>
+<a name="813"><span class="lineNum">     813 </span>            :         }</a>
+<a name="814"><span class="lineNum">     814 </span>            :       }</a>
+<a name="815"><span class="lineNum">     815 </span>            :     }</a>
+<a name="816"><span class="lineNum">     816 </span>            :   }</a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">       1760 :   for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">       1752 :     if(sasares[i]&gt;sasa_cutoff) solv_res[i] = 1;</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :     else solv_res[i] = 0;</a>
+<a name="820"><span class="lineNum">     820 </span>            :   }</a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">          8 : }</span></a>
+<a name="822"><span class="lineNum">     822 </span>            : </a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 : void SAXS::calculate_gpu(std::vector&lt;Vector&gt; &amp;pos, std::vector&lt;Vector&gt; &amp;deriv)</span></a>
+<a name="824"><span class="lineNum">     824 </span>            : {</a>
+<a name="825"><span class="lineNum">     825 </span>            : #ifdef __PLUMED_HAS_ARRAYFIRE</a>
+<a name="826"><span class="lineNum">     826 </span>            :   unsigned size;</a>
+<a name="827"><span class="lineNum">     827 </span>            :   if(onebead) size = nres;</a>
+<a name="828"><span class="lineNum">     828 </span>            :   else size = getNumberOfAtoms();</a>
+<a name="829"><span class="lineNum">     829 </span>            :   const unsigned numq = q_list.size();</a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span>            :   std::vector&lt;float&gt; sum;</a>
+<a name="832"><span class="lineNum">     832 </span>            :   sum.resize(numq);</a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span>            :   std::vector&lt;float&gt; dd;</a>
+<a name="835"><span class="lineNum">     835 </span>            :   dd.resize(size*3*numq);</a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            :   // on gpu only the master rank run the calculation</a>
+<a name="838"><span class="lineNum">     838 </span>            :   if(comm.Get_rank()==0) {</a>
+<a name="839"><span class="lineNum">     839 </span>            :     std::vector&lt;float&gt; posi;</a>
+<a name="840"><span class="lineNum">     840 </span>            :     posi.resize(3*size);</a>
+<a name="841"><span class="lineNum">     841 </span>            :     #pragma omp parallel for num_threads(OpenMP::getNumThreads())</a>
+<a name="842"><span class="lineNum">     842 </span>            :     for (unsigned i=0; i&lt;size; ++i) {</a>
+<a name="843"><span class="lineNum">     843 </span>            :       const Vector tmp = pos[i];</a>
+<a name="844"><span class="lineNum">     844 </span>            :       posi[3*i]   = static_cast&lt;float&gt;(tmp[0]);</a>
+<a name="845"><span class="lineNum">     845 </span>            :       posi[3*i+1] = static_cast&lt;float&gt;(tmp[1]);</a>
+<a name="846"><span class="lineNum">     846 </span>            :       posi[3*i+2] = static_cast&lt;float&gt;(tmp[2]);</a>
+<a name="847"><span class="lineNum">     847 </span>            :     }</a>
+<a name="848"><span class="lineNum">     848 </span>            : </a>
+<a name="849"><span class="lineNum">     849 </span>            :     // create array a and b containing atomic coordinates</a>
+<a name="850"><span class="lineNum">     850 </span>            : #ifdef  __PLUMED_HAS_ARRAYFIRE_CUDA</a>
+<a name="851"><span class="lineNum">     851 </span>            :     af::setDevice(afcu::getNativeId(deviceid));</a>
+<a name="852"><span class="lineNum">     852 </span>            : #elif   __PLUMED_HAS_ARRAYFIRE_OCL</a>
+<a name="853"><span class="lineNum">     853 </span>            :     af::setDevice(afcl::getNativeId(deviceid));</a>
+<a name="854"><span class="lineNum">     854 </span>            : #else</a>
+<a name="855"><span class="lineNum">     855 </span>            :     af::setDevice(deviceid);</a>
+<a name="856"><span class="lineNum">     856 </span>            : #endif</a>
+<a name="857"><span class="lineNum">     857 </span>            :     // 3,size,1,1</a>
+<a name="858"><span class="lineNum">     858 </span>            :     af::array pos_a = af::array(3, size, &amp;posi.front());</a>
+<a name="859"><span class="lineNum">     859 </span>            :     // size,3,1,1</a>
+<a name="860"><span class="lineNum">     860 </span>            :     pos_a = af::moddims(pos_a.T(), size, 3, 1);</a>
+<a name="861"><span class="lineNum">     861 </span>            :     // size,3,1,1</a>
+<a name="862"><span class="lineNum">     862 </span>            :     af::array pos_b = pos_a(af::span, af::span);</a>
+<a name="863"><span class="lineNum">     863 </span>            :     // size,1,3,1</a>
+<a name="864"><span class="lineNum">     864 </span>            :     pos_a = af::moddims(pos_a, size, 1, 3);</a>
+<a name="865"><span class="lineNum">     865 </span>            :     // 1,size,3,1</a>
+<a name="866"><span class="lineNum">     866 </span>            :     pos_b = af::moddims(pos_b, 1, size, 3);</a>
+<a name="867"><span class="lineNum">     867 </span>            : </a>
+<a name="868"><span class="lineNum">     868 </span>            :     // size,size,3,1</a>
+<a name="869"><span class="lineNum">     869 </span>            :     af::array pos_a_t = af::tile(pos_a, 1, size, 1);</a>
+<a name="870"><span class="lineNum">     870 </span>            :     // size,size,3,1: for some reason we need this</a>
+<a name="871"><span class="lineNum">     871 </span>            :     pos_a_t = af::moddims(pos_a_t, size, size, 3);</a>
+<a name="872"><span class="lineNum">     872 </span>            :     // size,size,3,1</a>
+<a name="873"><span class="lineNum">     873 </span>            :     af::array pos_b_t = af::tile(pos_b, size, 1, 1);</a>
+<a name="874"><span class="lineNum">     874 </span>            :     // size,size,3,1: for some reason we need this</a>
+<a name="875"><span class="lineNum">     875 </span>            :     pos_b_t = af::moddims(pos_b_t, size, size, 3);</a>
+<a name="876"><span class="lineNum">     876 </span>            :     // size,size,3,1</a>
+<a name="877"><span class="lineNum">     877 </span>            :     af::array xyz_dist = pos_a_t - pos_b_t;</a>
+<a name="878"><span class="lineNum">     878 </span>            :     // size,size,1,1</a>
+<a name="879"><span class="lineNum">     879 </span>            :     af::array square = af::sum(xyz_dist*xyz_dist,2);</a>
+<a name="880"><span class="lineNum">     880 </span>            :     // size,size,1,1</a>
+<a name="881"><span class="lineNum">     881 </span>            :     af::array dist_sqrt = af::sqrt(square);</a>
+<a name="882"><span class="lineNum">     882 </span>            :     // replace the zero of square with one to avoid nan in the derivatives (the number does not matter because this are multiplied by zero)</a>
+<a name="883"><span class="lineNum">     883 </span>            :     af::replace(square,!(af::iszero(square)),1.);</a>
+<a name="884"><span class="lineNum">     884 </span>            :     // size,size,3,1</a>
+<a name="885"><span class="lineNum">     885 </span>            :     xyz_dist = xyz_dist / af::tile(square, 1, 1, 3);</a>
+<a name="886"><span class="lineNum">     886 </span>            :     // numq,1,1,1</a>
+<a name="887"><span class="lineNum">     887 </span>            :     af::array sum_device   = af::constant(0, numq, f32);</a>
+<a name="888"><span class="lineNum">     888 </span>            :     // numq,size,3,1</a>
+<a name="889"><span class="lineNum">     889 </span>            :     af::array deriv_device = af::constant(0, numq, size, 3, f32);</a>
+<a name="890"><span class="lineNum">     890 </span>            : </a>
+<a name="891"><span class="lineNum">     891 </span>            :     for (unsigned k=0; k&lt;numq; ++k) {</a>
+<a name="892"><span class="lineNum">     892 </span>            :       // calculate FF matrix</a>
+<a name="893"><span class="lineNum">     893 </span>            :       // size,1,1,1</a>
+<a name="894"><span class="lineNum">     894 </span>            :       af::array AFF_value(size, &amp;FFf_value[k].front());</a>
+<a name="895"><span class="lineNum">     895 </span>            :       // size,size,1,1</a>
+<a name="896"><span class="lineNum">     896 </span>            :       af::array FFdist_mod = af::tile(AFF_value(af::span), 1, size)*af::transpose(af::tile(AFF_value(af::span), 1, size));</a>
+<a name="897"><span class="lineNum">     897 </span>            : </a>
+<a name="898"><span class="lineNum">     898 </span>            :       // get q</a>
+<a name="899"><span class="lineNum">     899 </span>            :       const float qvalue = static_cast&lt;float&gt;(q_list[k]);</a>
+<a name="900"><span class="lineNum">     900 </span>            :       // size,size,1,1</a>
+<a name="901"><span class="lineNum">     901 </span>            :       af::array dist_q = qvalue*dist_sqrt;</a>
+<a name="902"><span class="lineNum">     902 </span>            :       // size,size,1</a>
+<a name="903"><span class="lineNum">     903 </span>            :       af::array dist_sin = af::sin(dist_q)/dist_q;</a>
+<a name="904"><span class="lineNum">     904 </span>            :       af::replace(dist_sin,!(af::isNaN(dist_sin)),1.);</a>
+<a name="905"><span class="lineNum">     905 </span>            :       // 1,1,1,1</a>
+<a name="906"><span class="lineNum">     906 </span>            :       sum_device(k) = af::sum(af::flat(dist_sin)*af::flat(FFdist_mod));</a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span>            :       // size,size,1,1</a>
+<a name="909"><span class="lineNum">     909 </span>            :       af::array tmp = FFdist_mod*(dist_sin - af::cos(dist_q));</a>
+<a name="910"><span class="lineNum">     910 </span>            :       // size,size,3,1</a>
+<a name="911"><span class="lineNum">     911 </span>            :       af::array dd_all = af::tile(tmp, 1, 1, 3)*xyz_dist;</a>
+<a name="912"><span class="lineNum">     912 </span>            :       // it should become 1,size,3</a>
+<a name="913"><span class="lineNum">     913 </span>            :       deriv_device(k, af::span, af::span) = af::sum(dd_all,0);</a>
+<a name="914"><span class="lineNum">     914 </span>            :     }</a>
+<a name="915"><span class="lineNum">     915 </span>            : </a>
+<a name="916"><span class="lineNum">     916 </span>            :     // read out results</a>
+<a name="917"><span class="lineNum">     917 </span>            :     sum_device.host(&amp;sum.front());</a>
+<a name="918"><span class="lineNum">     918 </span>            : </a>
+<a name="919"><span class="lineNum">     919 </span>            :     deriv_device = af::reorder(deriv_device, 2, 1, 0);</a>
+<a name="920"><span class="lineNum">     920 </span>            :     deriv_device = af::flat(deriv_device);</a>
+<a name="921"><span class="lineNum">     921 </span>            :     deriv_device.host(&amp;dd.front());</a>
+<a name="922"><span class="lineNum">     922 </span>            :   }</a>
+<a name="923"><span class="lineNum">     923 </span>            : </a>
+<a name="924"><span class="lineNum">     924 </span>            :   comm.Bcast(dd, 0);</a>
+<a name="925"><span class="lineNum">     925 </span>            :   comm.Bcast(sum, 0);</a>
+<a name="926"><span class="lineNum">     926 </span>            : </a>
+<a name="927"><span class="lineNum">     927 </span>            :   for(unsigned k=0; k&lt;numq; ++k) {</a>
+<a name="928"><span class="lineNum">     928 </span>            :     std::string num; Tools::convert(k,num);</a>
+<a name="929"><span class="lineNum">     929 </span>            :     Value* val=getPntrToComponent(&quot;q-&quot;+num);</a>
+<a name="930"><span class="lineNum">     930 </span>            :     val-&gt;set(sum[k]);</a>
+<a name="931"><span class="lineNum">     931 </span>            :     if(getDoScore()) setCalcData(k, sum[k]);</a>
+<a name="932"><span class="lineNum">     932 </span>            :     for(unsigned i=0; i&lt;size; ++i) {</a>
+<a name="933"><span class="lineNum">     933 </span>            :       const unsigned di = k*size*3+i*3;</a>
+<a name="934"><span class="lineNum">     934 </span>            :       deriv[k*size+i] = Vector(2.*dd[di+0],2.*dd[di+1],2.*dd[di+2]);</a>
+<a name="935"><span class="lineNum">     935 </span>            :     }</a>
+<a name="936"><span class="lineNum">     936 </span>            :   }</a>
+<a name="937"><span class="lineNum">     937 </span>            : #endif</a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="939"><span class="lineNum">     939 </span>            : </a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">        188 : void SAXS::calculate_cpu(std::vector&lt;Vector&gt; &amp;pos, std::vector&lt;Vector&gt; &amp;deriv)</span></a>
+<a name="941"><span class="lineNum">     941 </span>            : {</a>
+<a name="942"><span class="lineNum">     942 </span>            :   unsigned size;</a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">        188 :   if(onebead) size = nres;</span></a>
+<a name="944"><span class="lineNum">     944 </span>            :   else size = getNumberOfAtoms();</a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">        188 :   const unsigned numq = q_list.size();</span></a>
+<a name="946"><span class="lineNum">     946 </span>            : </a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">        188 :   unsigned stride = comm.Get_size();</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">        188 :   unsigned rank   = comm.Get_rank();</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">        188 :   if(serial) {</span></a>
+<a name="950"><span class="lineNum">     950 </span>            :     stride = 1;</a>
+<a name="951"><span class="lineNum">     951 </span>            :     rank   = 0;</a>
+<a name="952"><span class="lineNum">     952 </span>            :   }</a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">        188 :   std::vector&lt;double&gt; sum(numq,0);</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">        188 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">        188 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="956"><span class="lineNum">     956 </span>            :   {</a>
+<a name="957"><span class="lineNum">     957 </span>            :     std::vector&lt;Vector&gt; omp_deriv(deriv.size());</a>
+<a name="958"><span class="lineNum">     958 </span>            :     std::vector&lt;double&gt; omp_sum(numq,0);</a>
+<a name="959"><span class="lineNum">     959 </span>            :     #pragma omp for nowait</a>
+<a name="960"><span class="lineNum">     960 </span>            :     for (unsigned i=rank; i&lt;size-1; i+=stride) {</a>
+<a name="961"><span class="lineNum">     961 </span>            :       Vector posi = pos[i];</a>
+<a name="962"><span class="lineNum">     962 </span>            :       for (unsigned j=i+1; j&lt;size ; ++j) {</a>
+<a name="963"><span class="lineNum">     963 </span>            :         Vector c_distances = delta(posi,pos[j]);</a>
+<a name="964"><span class="lineNum">     964 </span>            :         double m_distances = c_distances.modulo();</a>
+<a name="965"><span class="lineNum">     965 </span>            :         c_distances = c_distances/m_distances/m_distances;</a>
+<a name="966"><span class="lineNum">     966 </span>            :         for (unsigned k=0; k&lt;numq; ++k) {</a>
+<a name="967"><span class="lineNum">     967 </span>            :           unsigned kdx=k*size;</a>
+<a name="968"><span class="lineNum">     968 </span>            :           double qdist = q_list[k]*m_distances;</a>
+<a name="969"><span class="lineNum">     969 </span>            :           double FFF = 2.*FF_value[i][k]*FF_value[j][k];</a>
+<a name="970"><span class="lineNum">     970 </span>            :           double tsq = std::sin(qdist)/qdist;</a>
+<a name="971"><span class="lineNum">     971 </span>            :           double tcq = std::cos(qdist);</a>
+<a name="972"><span class="lineNum">     972 </span>            :           double tmp = FFF*(tcq-tsq);</a>
+<a name="973"><span class="lineNum">     973 </span>            :           Vector dd  = c_distances*tmp;</a>
+<a name="974"><span class="lineNum">     974 </span>            :           if(nt&gt;1) {</a>
+<a name="975"><span class="lineNum">     975 </span>            :             omp_deriv[kdx+i] -=dd;</a>
+<a name="976"><span class="lineNum">     976 </span>            :             omp_deriv[kdx+j] +=dd;</a>
+<a name="977"><span class="lineNum">     977 </span>            :             omp_sum[k] += FFF*tsq;</a>
+<a name="978"><span class="lineNum">     978 </span>            :           } else {</a>
+<a name="979"><span class="lineNum">     979 </span>            :             deriv[kdx+i] -= dd;</a>
+<a name="980"><span class="lineNum">     980 </span>            :             deriv[kdx+j] += dd;</a>
+<a name="981"><span class="lineNum">     981 </span>            :             sum[k] += FFF*tsq;</a>
+<a name="982"><span class="lineNum">     982 </span>            :           }</a>
+<a name="983"><span class="lineNum">     983 </span>            :         }</a>
+<a name="984"><span class="lineNum">     984 </span>            :       }</a>
+<a name="985"><span class="lineNum">     985 </span>            :     }</a>
+<a name="986"><span class="lineNum">     986 </span>            :     #pragma omp critical</a>
+<a name="987"><span class="lineNum">     987 </span>            :     if(nt&gt;1) {</a>
+<a name="988"><span class="lineNum">     988 </span>            :       for(unsigned i=0; i&lt;deriv.size(); ++i) deriv[i]+=omp_deriv[i];</a>
+<a name="989"><span class="lineNum">     989 </span>            :       for(unsigned k=0; k&lt;numq; ++k) sum[k]+=omp_sum[k];</a>
+<a name="990"><span class="lineNum">     990 </span>            :     }</a>
+<a name="991"><span class="lineNum">     991 </span>            :   }</a>
+<a name="992"><span class="lineNum">     992 </span>            : </a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">        188 :   if(!serial) {</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">        186 :     comm.Sum(&amp;deriv[0][0], 3*deriv.size());</span></a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">        186 :     comm.Sum(&amp;sum[0], numq);</span></a>
+<a name="996"><span class="lineNum">     996 </span>            :   }</a>
+<a name="997"><span class="lineNum">     997 </span>            : </a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">       1904 :   for (unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">       1716 :     sum[k]+=FF_rank[k];</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">       1716 :     std::string num; Tools::convert(k,num);</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">       1716 :     Value* val=getPntrToComponent(&quot;q-&quot;+num);</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">       1716 :     val-&gt;set(sum[k]);</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">       1716 :     if(getDoScore()) setCalcData(k, sum[k]);</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :   }</a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">        188 : }</span></a>
+<a name="1006"><span class="lineNum">    1006 </span>            : </a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">        188 : void SAXS::calculate()</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            : {</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">        188 :   if(pbc) makeWhole();</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            : </a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">        188 :   const size_t size = getNumberOfAtoms();</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :   const size_t numq = q_list.size();</a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   // these are the derivatives associated to the coarse graining</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">        188 :   std::vector&lt;Vector&gt; aa_deriv(size);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   size_t beads_size = size;</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">        188 :   if(onebead) beads_size = nres;</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   // these are the derivatives particle,q</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">        188 :   std::vector&lt;Vector&gt; bd_deriv(numq*beads_size);</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            : </a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">        188 :   std::vector&lt;Vector&gt; beads_pos(beads_size);</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">        188 :   if(onebead) {</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">       2174 :     for(unsigned resid=0; resid&lt;nres; resid++) {</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :       double sum_mass = 0.;</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">       2164 :       Vector sum_pos = Vector(0,0,0);</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">    7693792 :       for(unsigned atom_id=0; atom_id&lt;size; atom_id++) {</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">    7691628 :         if(residue_atom[atom_id] == resid) {</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">      35466 :           aa_deriv[atom_id] = Vector(atoms_masses[atom_id],atoms_masses[atom_id],atoms_masses[atom_id]);</span></a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">      35466 :           sum_pos += atoms_masses[atom_id] * getPosition(atom_id); // getPosition(first_atom+atom_id)</span></a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">      35466 :           sum_mass += atoms_masses[atom_id];</span></a>
+<a name="1032"><span class="lineNum">    1032 </span>            :         }</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :       }</a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">       2164 :       beads_pos[resid] = sum_pos/sum_mass;</span></a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">    7693792 :       for(unsigned atom_id=0; atom_id&lt;size; atom_id++) {</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">    7691628 :         if(residue_atom[atom_id] == resid) {</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">      35466 :           aa_deriv[atom_id] /= sum_mass;</span></a>
+<a name="1038"><span class="lineNum">    1038 </span>            :         }</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :       }</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :     }</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :     // SASA</a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">         10 :     std::vector&lt;bool&gt; solv_res(nres, 0);</span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">         10 :     if(saxs) {</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">          6 :       if(getStep()%solv_stride == 0 || isFirstStep) {</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">          6 :         isFirstStep = 0;</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">          6 :         if(rho_corr!=rho) sasa_calculate(solv_res);</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">          6 :         Iq0=0.;</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">       1294 :         for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">       1288 :           if(solv_res[i] == 1 ) {</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">        182 :             Iq0 += std::sqrt((Iq0_vac[i]+(rho_corr*rho_corr)*Iq0_solv[i]-rho_corr*Iq0_mix[i]));</span></a>
+<a name="1051"><span class="lineNum">    1051 </span>            :           } else {</a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">       1106 :             Iq0 += std::sqrt((Iq0_vac[i]+(rho*rho)*Iq0_solv[i]-rho*Iq0_mix[i]));</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            :           }</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :         }</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :         // Form Factors</a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">         60 :         for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">      11646 :           for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">      11592 :             if(!gpu) {</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">      11592 :               if(solv_res[i] == 0) { // buried</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">       9954 :                 FF_value[i][k] = std::sqrt(std::fabs(FF_value_vacuum[atoi[i]][k] + rho*rho*FF_value_solv[atoi[i]][k] - rho*FF_value_mixed[atoi[i]][k]))/Iq0;</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            :               } else { // surface</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">       1638 :                 FF_value[i][k] = std::sqrt(std::fabs(FF_value_vacuum[atoi[i]][k] + rho_corr*rho_corr*FF_value_solv[atoi[i]][k] - rho_corr*FF_value_mixed[atoi[i]][k]))/Iq0;</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            :               }</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :             } else {</a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineNoCov">          0 :               if(solv_res[i] == 0) { // buried</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineNoCov">          0 :                 FFf_value[k][i] = static_cast&lt;float&gt;(std::sqrt(std::fabs(FF_value_vacuum[atoi[i]][k] + rho*rho*FF_value_solv[atoi[i]][k] - rho*FF_value_mixed[atoi[i]][k]))/Iq0);</span></a>
+<a name="1067"><span class="lineNum">    1067 </span>            :               } else { // surface</a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineNoCov">          0 :                 FFf_value[k][i] = static_cast&lt;float&gt;(std::sqrt(std::fabs(FF_value_vacuum[atoi[i]][k] + rho_corr*rho_corr*FF_value_solv[atoi[i]][k] - rho_corr*FF_value_mixed[atoi[i]][k]))/Iq0);</span></a>
+<a name="1069"><span class="lineNum">    1069 </span>            :               }</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :             }</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :           }</a>
+<a name="1072"><span class="lineNum">    1072 </span>            :         }</a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">          6 :         if(!gpu) {</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">         60 :           for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">         54 :             FF_rank[k]=0.;</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">      11646 :             for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">      11592 :               FF_rank[k]+=FF_value[i][k]*FF_value[i][k];</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            :             }</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :           }</a>
+<a name="1080"><span class="lineNum">    1080 </span>            :         }</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :       }</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     } else { // SANS</a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">          4 :       std::vector&lt;bool&gt; deut_res(nres, 0);</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">          4 :       double solv_sc_length = 0.1*(0.580 + 2.*((1. - deuter_conc) * (-0.374) + deuter_conc * 0.667)); // per water electron (10 electrons)</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">          4 :       double rho_sans = rho * solv_sc_length;</span></a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">          4 :       double rho_sans_corr = rho_corr * solv_sc_length;</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">          4 :       if(getStep()%solv_stride == 0 || isFirstStep) {</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">          4 :         isFirstStep = 0;</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">          4 :         if(deuter_conc!=0.||rho != rho_corr) sasa_calculate(solv_res);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineCov">          4 :         Iq0=0.;</span></a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">        880 :         for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">        876 :           if(solv_res[i] == 1 ) {</span></a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">        182 :             if(rand()/RAND_MAX&lt;deuter_conc) {</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineNoCov">          0 :               Iq0 += std::sqrt(std::fabs(Iq0_vac_D[i] + rho_sans_corr*rho_sans_corr*Iq0_solv_H[i] - rho_sans_corr*Iq0_mix_D[i]));</span></a>
+<a name="1095"><span class="lineNum">    1095 </span>            :               deut_res[i] = 1;</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :             } else {</a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">        182 :               Iq0 += std::sqrt(std::fabs(Iq0_vac_H[i] + rho_sans_corr*rho_sans_corr*Iq0_solv_H[i] - rho_sans_corr*Iq0_mix_H[i]));</span></a>
+<a name="1098"><span class="lineNum">    1098 </span>            :             }</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :           } else {</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">        694 :             Iq0 += std::sqrt(std::fabs(Iq0_vac_H[i] + rho_sans*rho_sans*Iq0_solv_H[i] - rho_sans*Iq0_mix_H[i]));</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            :           }</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :         }</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :         // Form Factors</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">         40 :         for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">       7920 :           for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">       7884 :             if(!gpu) {</span></a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">       7884 :               if(solv_res[i] == 0) { // hydrogen</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">       6246 :                 FF_value[i][k] = std::sqrt(std::fabs(FF_value_vacuum_H[atoi[i]][k] + rho_sans*rho_sans*FF_value_solv_H[atoi[i]][k] - rho_sans*FF_value_mixed_H[atoi[i]][k]))/Iq0;</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            :               } else {</a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">       1638 :                 if(deut_res[i] == 0) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">       1638 :                   FF_value[i][k] = std::sqrt(std::fabs(FF_value_vacuum_H[atoi[i]][k] + rho_sans_corr*rho_sans_corr*FF_value_solv_H[atoi[i]][k] - rho_sans_corr*FF_value_mixed_H[atoi[i]][k]))/Iq0;</span></a>
+<a name="1112"><span class="lineNum">    1112 </span>            :                 } else {</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineNoCov">          0 :                   FF_value[i][k] = std::sqrt(std::fabs(FF_value_vacuum_D[atoi[i]][k] + rho_sans_corr*rho_sans_corr*FF_value_solv_H[atoi[i]][k] - rho_sans_corr*FF_value_mixed_D[atoi[i]][k]))/Iq0;</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            :                 }</a>
+<a name="1115"><span class="lineNum">    1115 </span>            :               }</a>
+<a name="1116"><span class="lineNum">    1116 </span>            :             } else {</a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineNoCov">          0 :               if(solv_res[i] == 0) { // hydrogen</span></a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineNoCov">          0 :                 FFf_value[k][i] = static_cast&lt;float&gt;(std::sqrt(std::fabs(FF_value_vacuum_H[atoi[i]][k] + rho_sans*rho_sans*FF_value_solv_H[atoi[i]][k] - rho_sans*FF_value_mixed_H[atoi[i]][k]))/Iq0);</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :               } else {</a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineNoCov">          0 :                 if(deut_res[i] == 0) {</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineNoCov">          0 :                   FFf_value[k][i] = static_cast&lt;float&gt;(std::sqrt(std::fabs(FF_value_vacuum_H[atoi[i]][k] + rho_sans_corr*rho_sans_corr*FF_value_solv_H[atoi[i]][k] - rho_sans_corr*FF_value_mixed_H[atoi[i]][k]))/Iq0);</span></a>
+<a name="1122"><span class="lineNum">    1122 </span>            :                 } else {</a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineNoCov">          0 :                   FFf_value[k][i] = static_cast&lt;float&gt;(std::sqrt(std::fabs(FF_value_vacuum_D[atoi[i]][k] + rho_sans_corr*rho_sans_corr*FF_value_solv_H[atoi[i]][k] - rho_sans_corr*FF_value_mixed_D[atoi[i]][k]))/Iq0);</span></a>
+<a name="1124"><span class="lineNum">    1124 </span>            :                 }</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :               }</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :             }</a>
+<a name="1127"><span class="lineNum">    1127 </span>            :           }</a>
+<a name="1128"><span class="lineNum">    1128 </span>            :         }</a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">          4 :         if(!gpu) {</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">         40 :           for(unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">         36 :             FF_rank[k]=0.;</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">       7920 :             for(unsigned i=0; i&lt;nres; ++i) {</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">       7884 :               FF_rank[k]+=FF_value[i][k]*FF_value[i][k];</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            :             }</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :           }</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :         }</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :       }</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :     }</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :     // not ONEBEAD</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   } else {</a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineCov">      58814 :     for(unsigned i=0; i&lt;size; ++i) {</span></a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">      58636 :       beads_pos[i] = getPosition(i);</span></a>
+<a name="1143"><span class="lineNum">    1143 </span>            :     }</a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">        356 :     aa_deriv = std::vector&lt;Vector&gt;(size,(Vector(1,1,1)));</span></a>
+<a name="1145"><span class="lineNum">    1145 </span>            :   }</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : </a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">        188 :   if(gpu) calculate_gpu(beads_pos, bd_deriv);</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">        188 :   else calculate_cpu(beads_pos, bd_deriv);</span></a>
+<a name="1149"><span class="lineNum">    1149 </span>            : </a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">        188 :   if(getDoScore()) {</span></a>
+<a name="1151"><span class="lineNum">    1151 </span>            :     /* Metainference */</a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">        168 :     double score = getScore();</span></a>
+<a name="1153"><span class="lineNum">    1153 </span>            :     setScore(score);</a>
+<a name="1154"><span class="lineNum">    1154 </span>            :   }</a>
+<a name="1155"><span class="lineNum">    1155 </span>            : </a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">       1904 :   for (unsigned k=0; k&lt;numq; ++k) {</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">       1716 :     const unsigned kdx=k*beads_size;</span></a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">       1716 :     Tensor deriv_box;</span></a>
+<a name="1159"><span class="lineNum">    1159 </span>            :     Value* val;</a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">       1716 :     if(!getDoScore()) {</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">        204 :       std::string num; Tools::convert(k,num);</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">        204 :       val=getPntrToComponent(&quot;q-&quot;+num);</span></a>
+<a name="1163"><span class="lineNum">    1163 </span>            : </a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">        204 :       if(onebead) {</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            :         unsigned atom_id=0;</a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">      19566 :         for(unsigned i=0; i&lt;beads_size; ++i) {</span></a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">     338670 :           for(unsigned j=0; j&lt;atoms_per_bead[i]; ++j) {</span></a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineCov">     319194 :             setAtomsDerivatives(val, atom_id, Vector(aa_deriv[atom_id][0]*bd_deriv[kdx+i][0], \</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">     319194 :                                 aa_deriv[atom_id][1]*bd_deriv[kdx+i][1], \</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">     319194 :                                 aa_deriv[atom_id][2]*bd_deriv[kdx+i][2]) );</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineCov">     319194 :             deriv_box += Tensor(getPosition(atom_id),Vector(aa_deriv[atom_id][0]*bd_deriv[kdx+i][0], \</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineCov">     319194 :                                 aa_deriv[atom_id][1]*bd_deriv[kdx+i][1], \</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineCov">     638388 :                                 aa_deriv[atom_id][2]*bd_deriv[kdx+i][2]) );</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineCov">     319194 :             atom_id++;</span></a>
+<a name="1175"><span class="lineNum">    1175 </span>            :           }</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :         }</a>
+<a name="1177"><span class="lineNum">    1177 </span>            :       } else {</a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">     295242 :         for(unsigned i=0; i&lt;beads_size; ++i) {</span></a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineCov">     295128 :           setAtomsDerivatives(val, i, Vector(bd_deriv[kdx+i][0], \</span></a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineCov">     295128 :                                              bd_deriv[kdx+i][1], \</span></a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineCov">     295128 :                                              bd_deriv[kdx+i][2]) );</span></a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">     590256 :           deriv_box += Tensor(getPosition(i),Vector(bd_deriv[kdx+i][0], \</span></a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineCov">     295128 :                               bd_deriv[kdx+i][1], \</span></a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineCov">     590256 :                               bd_deriv[kdx+i][2]) );</span></a>
+<a name="1185"><span class="lineNum">    1185 </span>            :         }</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :       }</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :     } else {</a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">       1512 :       val=getPntrToComponent(&quot;score&quot;);</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">       1512 :       if(onebead) {</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            :         unsigned atom_id=0;</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;beads_size; ++i) {</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :           for(unsigned j=0; j&lt;atoms_per_bead[i]; ++j) {</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineNoCov">          0 :             setAtomsDerivatives(val, atom_id, Vector(aa_deriv[atom_id][0]*bd_deriv[kdx+i][0]*getMetaDer(k),</span></a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineNoCov">          0 :                                 aa_deriv[atom_id][1]*bd_deriv[kdx+i][1]*getMetaDer(k),</span></a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineNoCov">          0 :                                 aa_deriv[atom_id][2]*bd_deriv[kdx+i][2]*getMetaDer(k)) );</span></a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineNoCov">          0 :             deriv_box += Tensor(getPosition(atom_id),Vector(aa_deriv[atom_id][0]*bd_deriv[kdx+i][0]*getMetaDer(k),</span></a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineNoCov">          0 :                                 aa_deriv[atom_id][1]*bd_deriv[kdx+i][1]*getMetaDer(k),</span></a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineNoCov">          0 :                                 aa_deriv[atom_id][2]*bd_deriv[kdx+i][2]*getMetaDer(k)) );</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :             atom_id++;</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            :           }</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :         }</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :       } else {</a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineCov">     450828 :         for(unsigned i=0; i&lt;beads_size; ++i) {</span></a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineCov">     449316 :           setAtomsDerivatives(val, i, Vector(bd_deriv[kdx+i][0]*getMetaDer(k),</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">     449316 :                                              bd_deriv[kdx+i][1]*getMetaDer(k),</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">     449316 :                                              bd_deriv[kdx+i][2]*getMetaDer(k)) );</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">     898632 :           deriv_box += Tensor(getPosition(i),Vector(bd_deriv[kdx+i][0]*getMetaDer(k),</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">     449316 :                               bd_deriv[kdx+i][1]*getMetaDer(k),</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineCov">     898632 :                               bd_deriv[kdx+i][2]*getMetaDer(k)) );</span></a>
+<a name="1210"><span class="lineNum">    1210 </span>            :         }</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :       }</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :     }</a>
+<a name="1213"><span class="lineNum">    1213 </span><span class="lineCov">       1716 :     setBoxDerivatives(val, -deriv_box);</span></a>
+<a name="1214"><span class="lineNum">    1214 </span>            :   }</a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineCov">        188 : }</span></a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">        188 : void SAXS::update() {</span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   // write status file</a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">        188 :   if(getWstride()&gt;0&amp;&amp; (getStep()%getWstride()==0 || getCPT()) ) writeStatus();</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">        188 : }</span></a>
+<a name="1221"><span class="lineNum">    1221 </span>            : </a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">         10 : unsigned SAXS::getOnebeadMapping(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms) {</span></a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">         10 :   std::vector&lt;std::string&gt; chains; pdb.getChainNames( chains );</span></a>
+<a name="1224"><span class="lineNum">    1224 </span>            :   std::vector&lt;std::vector&lt;std::string&gt; &gt; AtomResidueName;</a>
+<a name="1225"><span class="lineNum">    1225 </span>            : </a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">         10 :   atoms_masses.resize(atoms.size());</span></a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">         10 :   residue_atom.resize(atoms.size());</span></a>
+<a name="1228"><span class="lineNum">    1228 </span>            : </a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   // cycle over chains</a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineCov">         24 :   for(unsigned i=0; i&lt;chains.size(); ++i) {</span></a>
+<a name="1231"><span class="lineNum">    1231 </span>            :     unsigned start, end;</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :     std::string errmsg;</a>
+<a name="1233"><span class="lineNum">    1233 </span><span class="lineCov">         14 :     pdb.getResidueRange(chains[i], start, end, errmsg);</span></a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">         14 :     AtomResidueName.resize(2);</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            :     // cycle over residues</a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineCov">       2110 :     for(unsigned res=start; res&lt;=end; res++) {</span></a>
+<a name="1237"><span class="lineNum">    1237 </span><span class="lineCov">       2096 :       std::string Rname = pdb.getResidueName(res, chains[i]);</span></a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">       2096 :       Rname.erase(std::remove_if(Rname.begin(), Rname.end(), ::isspace),Rname.end());</span></a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineCov">       2096 :       std::vector&lt;AtomNumber&gt; res_atoms = pdb.getAtomsInResidue(res, chains[i]);</span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            :       unsigned first_time=1;</a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineCov">       2096 :       std::vector&lt;std::vector&lt;unsigned&gt; &gt; tmp_residue_atom; tmp_residue_atom.resize(3);</span></a>
+<a name="1242"><span class="lineNum">    1242 </span>            :       // cycle over atoms</a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">      37562 :       for(unsigned a=0; a&lt;res_atoms.size(); a++) {</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            :         // operations shared among all beads</a>
+<a name="1245"><span class="lineNum">    1245 </span><span class="lineCov">      35466 :         std::string Aname=pdb.getAtomName(res_atoms[a]);</span></a>
+<a name="1246"><span class="lineNum">    1246 </span><span class="lineCov">      35466 :         AtomResidueName[0].push_back(Aname);</span></a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">      35466 :         AtomResidueName[1].push_back(Rname);</span></a>
+<a name="1248"><span class="lineNum">    1248 </span>            :         char type;</a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">      35466 :         char first = Aname.at(0);</span></a>
+<a name="1250"><span class="lineNum">    1250 </span>            :         // We assume that element symbol is first letter, if not a number</a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineCov">      35466 :         if (!isdigit(first)) {</span></a>
+<a name="1252"><span class="lineNum">    1252 </span>            :           type = first;</a>
+<a name="1253"><span class="lineNum">    1253 </span>            :           // otherwise is the second</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :         } else {</a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineNoCov">          0 :           type = Aname.at(1);</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            :         }</a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">      35466 :         if (type == 'H') atoms_masses[res_atoms[a].index()] = 1.008;</span></a>
+<a name="1258"><span class="lineNum">    1258 </span><span class="lineCov">      10384 :         else if(type == 'C') atoms_masses[res_atoms[a].index()] = 12.011;</span></a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineCov">       2772 :         else if(type == 'N') atoms_masses[res_atoms[a].index()] = 14.007;</span></a>
+<a name="1260"><span class="lineNum">    1260 </span><span class="lineCov">       3270 :         else if(type == 'O') atoms_masses[res_atoms[a].index()] = 15.999;</span></a>
+<a name="1261"><span class="lineNum">    1261 </span><span class="lineCov">         90 :         else if(type == 'S') atoms_masses[res_atoms[a].index()] = 32.065;</span></a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineCov">         32 :         else if(type == 'P') atoms_masses[res_atoms[a].index()] = 30.974;</span></a>
+<a name="1263"><span class="lineNum">    1263 </span>            :         else {</a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineNoCov">          0 :           error(&quot;Unknown element in mass extraction\n&quot;);</span></a>
+<a name="1265"><span class="lineNum">    1265 </span>            :         }</a>
+<a name="1266"><span class="lineNum">    1266 </span><span class="lineCov">      70932 :         if(pdb.allowedResidue(&quot;protein&quot;,Rname)) {</span></a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineCov">      34390 :           if(first_time) {</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineCov">       2060 :             atoms_per_bead.push_back(res_atoms.size());</span></a>
+<a name="1269"><span class="lineNum">    1269 </span>            :             first_time = 0;</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :           }</a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">      34390 :           residue_atom[res_atoms[a].index()] = atoms_per_bead.size()-1;</span></a>
+<a name="1272"><span class="lineNum">    1272 </span>            :         } else {</a>
+<a name="1273"><span class="lineNum">    1273 </span>            :           // check for nucleic acids</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :           // Pentose bead</a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">       4840 :           if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  || Aname==&quot;O3'&quot;  ||</span></a>
+<a name="1276"><span class="lineNum">    1276 </span><span class="lineCov">       3940 :               Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  ||</span></a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineCov">       3076 :               Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; ||</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">       2660 :               Aname==&quot;H2'2&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; ||</span></a>
+<a name="1279"><span class="lineNum">    1279 </span><span class="lineCov">       3536 :               Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot;  ||</span></a>
+<a name="1280"><span class="lineNum">    1280 </span>            :               Aname==&quot;H3T&quot; ) {</a>
+<a name="1281"><span class="lineNum">    1281 </span><span class="lineCov">        584 :             tmp_residue_atom[0].push_back(res_atoms[a].index());</span></a>
+<a name="1282"><span class="lineNum">    1282 </span>            :           }</a>
+<a name="1283"><span class="lineNum">    1283 </span>            :           // Nucleobase bead</a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">       2172 :           else if(Aname==&quot;N1&quot;  || Aname==&quot;N2&quot;  || Aname==&quot;N3&quot;  || Aname==&quot;N4&quot;  || Aname==&quot;N6&quot;  ||</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineCov">       1884 :                   Aname==&quot;N7&quot;  || Aname==&quot;N9&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;C4&quot;  || Aname==&quot;C5&quot;  ||</span></a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineCov">       1272 :                   Aname==&quot;C6&quot;  || Aname==&quot;C7&quot;  || Aname==&quot;C8&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;O4&quot;  ||</span></a>
+<a name="1287"><span class="lineNum">    1287 </span><span class="lineCov">        912 :                   Aname==&quot;O6&quot;  || Aname==&quot;H1&quot;  || Aname==&quot;H2&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H5&quot;  ||</span></a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineCov">        480 :                   Aname==&quot;H6&quot;  || Aname==&quot;H8&quot;  || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; || Aname==&quot;H41&quot; ||</span></a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineCov">        972 :                   Aname==&quot;H42&quot; || Aname==&quot;H61&quot; || Aname==&quot;H62&quot; || Aname==&quot;H71&quot; || Aname==&quot;H72&quot; ||</span></a>
+<a name="1290"><span class="lineNum">    1290 </span>            :                   Aname==&quot;H73&quot; ) {</a>
+<a name="1291"><span class="lineNum">    1291 </span><span class="lineCov">        396 :             tmp_residue_atom[1].push_back(res_atoms[a].index());</span></a>
+<a name="1292"><span class="lineNum">    1292 </span>            :           }</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :           // PO2 bead</a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineCov">         96 :           else if(Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; || Aname==&quot;O1P&quot; ||</span></a>
+<a name="1295"><span class="lineNum">    1295 </span><span class="lineCov">         96 :                   Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="1296"><span class="lineNum">    1296 </span><span class="lineCov">         96 :             tmp_residue_atom[2].push_back(res_atoms[a].index());</span></a>
+<a name="1297"><span class="lineNum">    1297 </span>            :           }</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :           // error</a>
+<a name="1299"><span class="lineNum">    1299 </span><span class="lineNoCov">          0 :           else error(&quot;Atom name &quot;+Aname+&quot; cannot be indexed to any bead. Check the PDB.&quot;);</span></a>
+<a name="1300"><span class="lineNum">    1300 </span>            :         }</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :       }</a>
+<a name="1302"><span class="lineNum">    1302 </span><span class="lineCov">       4192 :       if(!pdb.allowedResidue(&quot;protein&quot;,Rname)) {</span></a>
+<a name="1303"><span class="lineNum">    1303 </span><span class="lineCov">         36 :         atoms_per_bead.push_back(tmp_residue_atom[0].size());</span></a>
+<a name="1304"><span class="lineNum">    1304 </span><span class="lineCov">        620 :         for(unsigned tmp_i=0; tmp_i&lt;tmp_residue_atom[0].size(); tmp_i++) residue_atom[tmp_residue_atom[0][tmp_i]]=atoms_per_bead.size()-1;</span></a>
+<a name="1305"><span class="lineNum">    1305 </span><span class="lineCov">         36 :         atoms_per_bead.push_back(tmp_residue_atom[1].size());</span></a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">        432 :         for(unsigned tmp_i=0; tmp_i&lt;tmp_residue_atom[1].size(); tmp_i++) residue_atom[tmp_residue_atom[1][tmp_i]]=atoms_per_bead.size()-1;</span></a>
+<a name="1307"><span class="lineNum">    1307 </span><span class="lineCov">         36 :         if(tmp_residue_atom[2].size()&gt;0) {</span></a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">         32 :           atoms_per_bead.push_back(tmp_residue_atom[2].size());</span></a>
+<a name="1309"><span class="lineNum">    1309 </span><span class="lineCov">        128 :           for(unsigned tmp_i=0; tmp_i&lt;tmp_residue_atom[2].size(); tmp_i++) residue_atom[tmp_residue_atom[2][tmp_i]]=atoms_per_bead.size()-1;</span></a>
+<a name="1310"><span class="lineNum">    1310 </span>            :         }</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :       }</a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">       2096 :     }</span></a>
+<a name="1313"><span class="lineNum">    1313 </span>            :   }</a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineCov">         10 :   readLCPOparam(AtomResidueName, atoms.size());</span></a>
+<a name="1315"><span class="lineNum">    1315 </span><span class="lineCov">         10 :   return atoms_per_bead.size();</span></a>
+<a name="1316"><span class="lineNum">    1316 </span><span class="lineCov">         10 : }</span></a>
+<a name="1317"><span class="lineNum">    1317 </span>            : </a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineCov">          8 : void SAXS::getMartiniFFparam(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter)</span></a>
+<a name="1319"><span class="lineNum">    1319 </span>            : {</a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(9.045);</span></a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(-0.098114);</span></a>
+<a name="1322"><span class="lineNum">    1322 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(7.54281);</span></a>
+<a name="1323"><span class="lineNum">    1323 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(-1.97438);</span></a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(-8.32689);</span></a>
+<a name="1325"><span class="lineNum">    1325 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(6.09318);</span></a>
+<a name="1326"><span class="lineNum">    1326 </span><span class="lineCov">          8 :   parameter[ALA_BB].push_back(-1.18913);</span></a>
+<a name="1327"><span class="lineNum">    1327 </span>            : </a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(10.729);</span></a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(-0.0392574);</span></a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(1.15382);</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(-0.155999);</span></a>
+<a name="1332"><span class="lineNum">    1332 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(-2.43619);</span></a>
+<a name="1333"><span class="lineNum">    1333 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(1.72922);</span></a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">          8 :   parameter[ARG_BB].push_back(-0.33799);</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            : </a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(-2.796);</span></a>
+<a name="1337"><span class="lineNum">    1337 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(0.472403);</span></a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(8.07424);</span></a>
+<a name="1339"><span class="lineNum">    1339 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(4.37299);</span></a>
+<a name="1340"><span class="lineNum">    1340 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(-10.7398);</span></a>
+<a name="1341"><span class="lineNum">    1341 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(4.95677);</span></a>
+<a name="1342"><span class="lineNum">    1342 </span><span class="lineCov">          8 :   parameter[ARG_SC1].push_back(-0.725797);</span></a>
+<a name="1343"><span class="lineNum">    1343 </span>            : </a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(15.396);</span></a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(0.0636736);</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(-1.258);</span></a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(1.93135);</span></a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(-4.45031);</span></a>
+<a name="1349"><span class="lineNum">    1349 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(2.49356);</span></a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineCov">          8 :   parameter[ARG_SC2].push_back(-0.410721);</span></a>
+<a name="1351"><span class="lineNum">    1351 </span>            : </a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(10.738);</span></a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(-0.0402162);</span></a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(1.03007);</span></a>
+<a name="1355"><span class="lineNum">    1355 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(-0.254174);</span></a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(-2.12015);</span></a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(1.55535);</span></a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineCov">          8 :   parameter[ASN_BB].push_back(-0.30963);</span></a>
+<a name="1359"><span class="lineNum">    1359 </span>            : </a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(9.249);</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(-0.0148678);</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(5.52169);</span></a>
+<a name="1363"><span class="lineNum">    1363 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(0.00853212);</span></a>
+<a name="1364"><span class="lineNum">    1364 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(-6.71992);</span></a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(3.93622);</span></a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineCov">          8 :   parameter[ASN_SC1].push_back(-0.64973);</span></a>
+<a name="1367"><span class="lineNum">    1367 </span>            : </a>
+<a name="1368"><span class="lineNum">    1368 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(10.695);</span></a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(-0.0410247);</span></a>
+<a name="1370"><span class="lineNum">    1370 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(1.03656);</span></a>
+<a name="1371"><span class="lineNum">    1371 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(-0.298558);</span></a>
+<a name="1372"><span class="lineNum">    1372 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(-2.06064);</span></a>
+<a name="1373"><span class="lineNum">    1373 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(1.53495);</span></a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineCov">          8 :   parameter[ASP_BB].push_back(-0.308365);</span></a>
+<a name="1375"><span class="lineNum">    1375 </span>            : </a>
+<a name="1376"><span class="lineNum">    1376 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(9.476);</span></a>
+<a name="1377"><span class="lineNum">    1377 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(-0.0254664);</span></a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(5.57899);</span></a>
+<a name="1379"><span class="lineNum">    1379 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(-0.395027);</span></a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(-5.9407);</span></a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(3.48836);</span></a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineCov">          8 :   parameter[ASP_SC1].push_back(-0.569402);</span></a>
+<a name="1383"><span class="lineNum">    1383 </span>            : </a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(10.698);</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(-0.0233493);</span></a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(1.18257);</span></a>
+<a name="1387"><span class="lineNum">    1387 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(0.0684464);</span></a>
+<a name="1388"><span class="lineNum">    1388 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(-2.792);</span></a>
+<a name="1389"><span class="lineNum">    1389 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(1.88995);</span></a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineCov">          8 :   parameter[CYS_BB].push_back(-0.360229);</span></a>
+<a name="1391"><span class="lineNum">    1391 </span>            : </a>
+<a name="1392"><span class="lineNum">    1392 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(8.199);</span></a>
+<a name="1393"><span class="lineNum">    1393 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(-0.0261569);</span></a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(6.79677);</span></a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(-0.343845);</span></a>
+<a name="1396"><span class="lineNum">    1396 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(-5.03578);</span></a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(2.7076);</span></a>
+<a name="1398"><span class="lineNum">    1398 </span><span class="lineCov">          8 :   parameter[CYS_SC1].push_back(-0.420714);</span></a>
+<a name="1399"><span class="lineNum">    1399 </span>            : </a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(10.728);</span></a>
+<a name="1401"><span class="lineNum">    1401 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(-0.0391984);</span></a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(1.09264);</span></a>
+<a name="1403"><span class="lineNum">    1403 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(-0.261555);</span></a>
+<a name="1404"><span class="lineNum">    1404 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(-2.21245);</span></a>
+<a name="1405"><span class="lineNum">    1405 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(1.62071);</span></a>
+<a name="1406"><span class="lineNum">    1406 </span><span class="lineCov">          8 :   parameter[GLN_BB].push_back(-0.322325);</span></a>
+<a name="1407"><span class="lineNum">    1407 </span>            : </a>
+<a name="1408"><span class="lineNum">    1408 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(8.317);</span></a>
+<a name="1409"><span class="lineNum">    1409 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(-0.229045);</span></a>
+<a name="1410"><span class="lineNum">    1410 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(12.6338);</span></a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(-7.6719);</span></a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(-5.8376);</span></a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(5.53784);</span></a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineCov">          8 :   parameter[GLN_SC1].push_back(-1.12604);</span></a>
+<a name="1415"><span class="lineNum">    1415 </span>            : </a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(10.694);</span></a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(-0.0521961);</span></a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(1.11153);</span></a>
+<a name="1419"><span class="lineNum">    1419 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(-0.491995);</span></a>
+<a name="1420"><span class="lineNum">    1420 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(-1.86236);</span></a>
+<a name="1421"><span class="lineNum">    1421 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(1.45332);</span></a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineCov">          8 :   parameter[GLU_BB].push_back(-0.29708);</span></a>
+<a name="1423"><span class="lineNum">    1423 </span>            : </a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(8.544);</span></a>
+<a name="1425"><span class="lineNum">    1425 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(-0.249555);</span></a>
+<a name="1426"><span class="lineNum">    1426 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(12.8031);</span></a>
+<a name="1427"><span class="lineNum">    1427 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(-8.42696);</span></a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(-4.66486);</span></a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(4.90004);</span></a>
+<a name="1430"><span class="lineNum">    1430 </span><span class="lineCov">          8 :   parameter[GLU_SC1].push_back(-1.01204);</span></a>
+<a name="1431"><span class="lineNum">    1431 </span>            : </a>
+<a name="1432"><span class="lineNum">    1432 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(9.977);</span></a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(-0.0285799);</span></a>
+<a name="1434"><span class="lineNum">    1434 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(1.84236);</span></a>
+<a name="1435"><span class="lineNum">    1435 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(-0.0315192);</span></a>
+<a name="1436"><span class="lineNum">    1436 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(-2.88326);</span></a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(1.87323);</span></a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineCov">          8 :   parameter[GLY_BB].push_back(-0.345773);</span></a>
+<a name="1439"><span class="lineNum">    1439 </span>            : </a>
+<a name="1440"><span class="lineNum">    1440 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(10.721);</span></a>
+<a name="1441"><span class="lineNum">    1441 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(-0.0379337);</span></a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(1.06028);</span></a>
+<a name="1443"><span class="lineNum">    1443 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(-0.236143);</span></a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(-2.17819);</span></a>
+<a name="1445"><span class="lineNum">    1445 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(1.58357);</span></a>
+<a name="1446"><span class="lineNum">    1446 </span><span class="lineCov">          8 :   parameter[HIS_BB].push_back(-0.31345);</span></a>
+<a name="1447"><span class="lineNum">    1447 </span>            : </a>
+<a name="1448"><span class="lineNum">    1448 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(-0.424);</span></a>
+<a name="1449"><span class="lineNum">    1449 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(0.665176);</span></a>
+<a name="1450"><span class="lineNum">    1450 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(3.4369);</span></a>
+<a name="1451"><span class="lineNum">    1451 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(2.93795);</span></a>
+<a name="1452"><span class="lineNum">    1452 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(-5.18288);</span></a>
+<a name="1453"><span class="lineNum">    1453 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(2.12381);</span></a>
+<a name="1454"><span class="lineNum">    1454 </span><span class="lineCov">          8 :   parameter[HIS_SC1].push_back(-0.284224);</span></a>
+<a name="1455"><span class="lineNum">    1455 </span>            : </a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(5.363);</span></a>
+<a name="1457"><span class="lineNum">    1457 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(-0.0176945);</span></a>
+<a name="1458"><span class="lineNum">    1458 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(2.9506);</span></a>
+<a name="1459"><span class="lineNum">    1459 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(-0.387018);</span></a>
+<a name="1460"><span class="lineNum">    1460 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(-1.83951);</span></a>
+<a name="1461"><span class="lineNum">    1461 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(0.9703);</span></a>
+<a name="1462"><span class="lineNum">    1462 </span><span class="lineCov">          8 :   parameter[HIS_SC2].push_back(-0.1458);</span></a>
+<a name="1463"><span class="lineNum">    1463 </span>            : </a>
+<a name="1464"><span class="lineNum">    1464 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(5.784);</span></a>
+<a name="1465"><span class="lineNum">    1465 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(-0.0293129);</span></a>
+<a name="1466"><span class="lineNum">    1466 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(2.74167);</span></a>
+<a name="1467"><span class="lineNum">    1467 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(-0.520875);</span></a>
+<a name="1468"><span class="lineNum">    1468 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(-1.62949);</span></a>
+<a name="1469"><span class="lineNum">    1469 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(0.902379);</span></a>
+<a name="1470"><span class="lineNum">    1470 </span><span class="lineCov">          8 :   parameter[HIS_SC3].push_back(-0.139957);</span></a>
+<a name="1471"><span class="lineNum">    1471 </span>            : </a>
+<a name="1472"><span class="lineNum">    1472 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(10.699);</span></a>
+<a name="1473"><span class="lineNum">    1473 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(-0.0188962);</span></a>
+<a name="1474"><span class="lineNum">    1474 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(1.217);</span></a>
+<a name="1475"><span class="lineNum">    1475 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(0.242481);</span></a>
+<a name="1476"><span class="lineNum">    1476 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(-3.13898);</span></a>
+<a name="1477"><span class="lineNum">    1477 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(2.07916);</span></a>
+<a name="1478"><span class="lineNum">    1478 </span><span class="lineCov">          8 :   parameter[ILE_BB].push_back(-0.392574);</span></a>
+<a name="1479"><span class="lineNum">    1479 </span>            : </a>
+<a name="1480"><span class="lineNum">    1480 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(-4.448);</span></a>
+<a name="1481"><span class="lineNum">    1481 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(1.20996);</span></a>
+<a name="1482"><span class="lineNum">    1482 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(11.5141);</span></a>
+<a name="1483"><span class="lineNum">    1483 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(6.98895);</span></a>
+<a name="1484"><span class="lineNum">    1484 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(-19.1948);</span></a>
+<a name="1485"><span class="lineNum">    1485 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(9.89207);</span></a>
+<a name="1486"><span class="lineNum">    1486 </span><span class="lineCov">          8 :   parameter[ILE_SC1].push_back(-1.60877);</span></a>
+<a name="1487"><span class="lineNum">    1487 </span>            : </a>
+<a name="1488"><span class="lineNum">    1488 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(10.692);</span></a>
+<a name="1489"><span class="lineNum">    1489 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(-0.0414917);</span></a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(1.1077);</span></a>
+<a name="1491"><span class="lineNum">    1491 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(-0.288062);</span></a>
+<a name="1492"><span class="lineNum">    1492 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(-2.17187);</span></a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(1.59879);</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineCov">          8 :   parameter[LEU_BB].push_back(-0.318545);</span></a>
+<a name="1495"><span class="lineNum">    1495 </span>            : </a>
+<a name="1496"><span class="lineNum">    1496 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(-4.448);</span></a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(2.1063);</span></a>
+<a name="1498"><span class="lineNum">    1498 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(6.72381);</span></a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(14.6954);</span></a>
+<a name="1500"><span class="lineNum">    1500 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(-23.7197);</span></a>
+<a name="1501"><span class="lineNum">    1501 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(10.7247);</span></a>
+<a name="1502"><span class="lineNum">    1502 </span><span class="lineCov">          8 :   parameter[LEU_SC1].push_back(-1.59146);</span></a>
+<a name="1503"><span class="lineNum">    1503 </span>            : </a>
+<a name="1504"><span class="lineNum">    1504 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(10.706);</span></a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(-0.0468629);</span></a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(1.09477);</span></a>
+<a name="1507"><span class="lineNum">    1507 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(-0.432751);</span></a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(-1.94335);</span></a>
+<a name="1509"><span class="lineNum">    1509 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(1.49109);</span></a>
+<a name="1510"><span class="lineNum">    1510 </span><span class="lineCov">          8 :   parameter[LYS_BB].push_back(-0.302589);</span></a>
+<a name="1511"><span class="lineNum">    1511 </span>            : </a>
+<a name="1512"><span class="lineNum">    1512 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(-2.796);</span></a>
+<a name="1513"><span class="lineNum">    1513 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(0.508044);</span></a>
+<a name="1514"><span class="lineNum">    1514 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(7.91436);</span></a>
+<a name="1515"><span class="lineNum">    1515 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(4.54097);</span></a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(-10.8051);</span></a>
+<a name="1517"><span class="lineNum">    1517 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(4.96204);</span></a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineCov">          8 :   parameter[LYS_SC1].push_back(-0.724414);</span></a>
+<a name="1519"><span class="lineNum">    1519 </span>            : </a>
+<a name="1520"><span class="lineNum">    1520 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(3.070);</span></a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(-0.0101448);</span></a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(4.67994);</span></a>
+<a name="1523"><span class="lineNum">    1523 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(-0.792529);</span></a>
+<a name="1524"><span class="lineNum">    1524 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(-2.09142);</span></a>
+<a name="1525"><span class="lineNum">    1525 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(1.02933);</span></a>
+<a name="1526"><span class="lineNum">    1526 </span><span class="lineCov">          8 :   parameter[LYS_SC2].push_back(-0.137787);</span></a>
+<a name="1527"><span class="lineNum">    1527 </span>            : </a>
+<a name="1528"><span class="lineNum">    1528 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(10.671);</span></a>
+<a name="1529"><span class="lineNum">    1529 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(-0.0433724);</span></a>
+<a name="1530"><span class="lineNum">    1530 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(1.13784);</span></a>
+<a name="1531"><span class="lineNum">    1531 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(-0.40768);</span></a>
+<a name="1532"><span class="lineNum">    1532 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(-2.00555);</span></a>
+<a name="1533"><span class="lineNum">    1533 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(1.51673);</span></a>
+<a name="1534"><span class="lineNum">    1534 </span><span class="lineCov">          8 :   parameter[MET_BB].push_back(-0.305547);</span></a>
+<a name="1535"><span class="lineNum">    1535 </span>            : </a>
+<a name="1536"><span class="lineNum">    1536 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(5.85);</span></a>
+<a name="1537"><span class="lineNum">    1537 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(-0.0485798);</span></a>
+<a name="1538"><span class="lineNum">    1538 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(17.0391);</span></a>
+<a name="1539"><span class="lineNum">    1539 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(-3.65327);</span></a>
+<a name="1540"><span class="lineNum">    1540 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(-13.174);</span></a>
+<a name="1541"><span class="lineNum">    1541 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(8.68286);</span></a>
+<a name="1542"><span class="lineNum">    1542 </span><span class="lineCov">          8 :   parameter[MET_SC1].push_back(-1.56095);</span></a>
+<a name="1543"><span class="lineNum">    1543 </span>            : </a>
+<a name="1544"><span class="lineNum">    1544 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(10.741);</span></a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(-0.0317275);</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(1.15599);</span></a>
+<a name="1547"><span class="lineNum">    1547 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(0.0276187);</span></a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(-2.74757);</span></a>
+<a name="1549"><span class="lineNum">    1549 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(1.88783);</span></a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">          8 :   parameter[PHE_BB].push_back(-0.363525);</span></a>
+<a name="1551"><span class="lineNum">    1551 </span>            : </a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(-0.636);</span></a>
+<a name="1553"><span class="lineNum">    1553 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(0.527882);</span></a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(6.77612);</span></a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(3.18508);</span></a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(-8.92826);</span></a>
+<a name="1557"><span class="lineNum">    1557 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(4.29752);</span></a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineCov">          8 :   parameter[PHE_SC1].push_back(-0.65187);</span></a>
+<a name="1559"><span class="lineNum">    1559 </span>            : </a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(-0.424);</span></a>
+<a name="1561"><span class="lineNum">    1561 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(0.389174);</span></a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(4.11761);</span></a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(2.29527);</span></a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(-4.7652);</span></a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(1.97023);</span></a>
+<a name="1566"><span class="lineNum">    1566 </span><span class="lineCov">          8 :   parameter[PHE_SC2].push_back(-0.262318);</span></a>
+<a name="1567"><span class="lineNum">    1567 </span>            : </a>
+<a name="1568"><span class="lineNum">    1568 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(-0.424);</span></a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(0.38927);</span></a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(4.11708);</span></a>
+<a name="1571"><span class="lineNum">    1571 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(2.29623);</span></a>
+<a name="1572"><span class="lineNum">    1572 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(-4.76592);</span></a>
+<a name="1573"><span class="lineNum">    1573 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(1.97055);</span></a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineCov">          8 :   parameter[PHE_SC3].push_back(-0.262381);</span></a>
+<a name="1575"><span class="lineNum">    1575 </span>            : </a>
+<a name="1576"><span class="lineNum">    1576 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(11.434);</span></a>
+<a name="1577"><span class="lineNum">    1577 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(-0.033323);</span></a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(0.472014);</span></a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(-0.290854);</span></a>
+<a name="1580"><span class="lineNum">    1580 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(-1.81409);</span></a>
+<a name="1581"><span class="lineNum">    1581 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(1.39751);</span></a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineCov">          8 :   parameter[PRO_BB].push_back(-0.280407);</span></a>
+<a name="1583"><span class="lineNum">    1583 </span>            : </a>
+<a name="1584"><span class="lineNum">    1584 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(-2.796);</span></a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(0.95668);</span></a>
+<a name="1586"><span class="lineNum">    1586 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(6.84197);</span></a>
+<a name="1587"><span class="lineNum">    1587 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(6.43774);</span></a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(-12.5068);</span></a>
+<a name="1589"><span class="lineNum">    1589 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(5.64597);</span></a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineCov">          8 :   parameter[PRO_SC1].push_back(-0.825206);</span></a>
+<a name="1591"><span class="lineNum">    1591 </span>            : </a>
+<a name="1592"><span class="lineNum">    1592 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(10.699);</span></a>
+<a name="1593"><span class="lineNum">    1593 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(-0.0325828);</span></a>
+<a name="1594"><span class="lineNum">    1594 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(1.20329);</span></a>
+<a name="1595"><span class="lineNum">    1595 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(-0.0674351);</span></a>
+<a name="1596"><span class="lineNum">    1596 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(-2.60749);</span></a>
+<a name="1597"><span class="lineNum">    1597 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(1.80318);</span></a>
+<a name="1598"><span class="lineNum">    1598 </span><span class="lineCov">          8 :   parameter[SER_BB].push_back(-0.346803);</span></a>
+<a name="1599"><span class="lineNum">    1599 </span>            : </a>
+<a name="1600"><span class="lineNum">    1600 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(3.298);</span></a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(-0.0366801);</span></a>
+<a name="1602"><span class="lineNum">    1602 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(5.11077);</span></a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(-1.46774);</span></a>
+<a name="1604"><span class="lineNum">    1604 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(-1.48421);</span></a>
+<a name="1605"><span class="lineNum">    1605 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(0.800326);</span></a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">          8 :   parameter[SER_SC1].push_back(-0.108314);</span></a>
+<a name="1607"><span class="lineNum">    1607 </span>            : </a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(10.697);</span></a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(-0.0242955);</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(1.24671);</span></a>
+<a name="1611"><span class="lineNum">    1611 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(0.146423);</span></a>
+<a name="1612"><span class="lineNum">    1612 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(-2.97429);</span></a>
+<a name="1613"><span class="lineNum">    1613 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(1.97513);</span></a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineCov">          8 :   parameter[THR_BB].push_back(-0.371479);</span></a>
+<a name="1615"><span class="lineNum">    1615 </span>            : </a>
+<a name="1616"><span class="lineNum">    1616 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(2.366);</span></a>
+<a name="1617"><span class="lineNum">    1617 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(0.0297604);</span></a>
+<a name="1618"><span class="lineNum">    1618 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(11.9216);</span></a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(-9.32503);</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(1.9396);</span></a>
+<a name="1621"><span class="lineNum">    1621 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(0.0804861);</span></a>
+<a name="1622"><span class="lineNum">    1622 </span><span class="lineCov">          8 :   parameter[THR_SC1].push_back(-0.0302721);</span></a>
+<a name="1623"><span class="lineNum">    1623 </span>            : </a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(10.689);</span></a>
+<a name="1625"><span class="lineNum">    1625 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(-0.0265879);</span></a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(1.17819);</span></a>
+<a name="1627"><span class="lineNum">    1627 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(0.0386457);</span></a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(-2.75634);</span></a>
+<a name="1629"><span class="lineNum">    1629 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(1.88065);</span></a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineCov">          8 :   parameter[TRP_BB].push_back(-0.360217);</span></a>
+<a name="1631"><span class="lineNum">    1631 </span>            : </a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(0.084);</span></a>
+<a name="1633"><span class="lineNum">    1633 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(0.752407);</span></a>
+<a name="1634"><span class="lineNum">    1634 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(5.3802);</span></a>
+<a name="1635"><span class="lineNum">    1635 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(4.09281);</span></a>
+<a name="1636"><span class="lineNum">    1636 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(-9.28029);</span></a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(4.45923);</span></a>
+<a name="1638"><span class="lineNum">    1638 </span><span class="lineCov">          8 :   parameter[TRP_SC1].push_back(-0.689008);</span></a>
+<a name="1639"><span class="lineNum">    1639 </span>            : </a>
+<a name="1640"><span class="lineNum">    1640 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(5.739);</span></a>
+<a name="1641"><span class="lineNum">    1641 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(0.0298492);</span></a>
+<a name="1642"><span class="lineNum">    1642 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(4.60446);</span></a>
+<a name="1643"><span class="lineNum">    1643 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(1.34463);</span></a>
+<a name="1644"><span class="lineNum">    1644 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(-5.69968);</span></a>
+<a name="1645"><span class="lineNum">    1645 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(2.84924);</span></a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineCov">          8 :   parameter[TRP_SC2].push_back(-0.433781);</span></a>
+<a name="1647"><span class="lineNum">    1647 </span>            : </a>
+<a name="1648"><span class="lineNum">    1648 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(-0.424);</span></a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(0.388576);</span></a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(4.11859);</span></a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(2.29485);</span></a>
+<a name="1652"><span class="lineNum">    1652 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(-4.76255);</span></a>
+<a name="1653"><span class="lineNum">    1653 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(1.96849);</span></a>
+<a name="1654"><span class="lineNum">    1654 </span><span class="lineCov">          8 :   parameter[TRP_SC3].push_back(-0.262015);</span></a>
+<a name="1655"><span class="lineNum">    1655 </span>            : </a>
+<a name="1656"><span class="lineNum">    1656 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(-0.424);</span></a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(0.387685);</span></a>
+<a name="1658"><span class="lineNum">    1658 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(4.12153);</span></a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(2.29144);</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(-4.7589);</span></a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(1.96686);</span></a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineCov">          8 :   parameter[TRP_SC4].push_back(-0.261786);</span></a>
+<a name="1663"><span class="lineNum">    1663 </span>            : </a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(10.689);</span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(-0.0193526);</span></a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(1.18241);</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(0.207318);</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(-3.0041);</span></a>
+<a name="1669"><span class="lineNum">    1669 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(1.99335);</span></a>
+<a name="1670"><span class="lineNum">    1670 </span><span class="lineCov">          8 :   parameter[TYR_BB].push_back(-0.376482);</span></a>
+<a name="1671"><span class="lineNum">    1671 </span>            : </a>
+<a name="1672"><span class="lineNum">    1672 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(-0.636);</span></a>
+<a name="1673"><span class="lineNum">    1673 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(0.528902);</span></a>
+<a name="1674"><span class="lineNum">    1674 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(6.78168);</span></a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(3.17769);</span></a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(-8.93667);</span></a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(4.30692);</span></a>
+<a name="1678"><span class="lineNum">    1678 </span><span class="lineCov">          8 :   parameter[TYR_SC1].push_back(-0.653993);</span></a>
+<a name="1679"><span class="lineNum">    1679 </span>            : </a>
+<a name="1680"><span class="lineNum">    1680 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(-0.424);</span></a>
+<a name="1681"><span class="lineNum">    1681 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(0.388811);</span></a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(4.11851);</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(2.29545);</span></a>
+<a name="1684"><span class="lineNum">    1684 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(-4.7668);</span></a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(1.97131);</span></a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineCov">          8 :   parameter[TYR_SC2].push_back(-0.262534);</span></a>
+<a name="1687"><span class="lineNum">    1687 </span>            : </a>
+<a name="1688"><span class="lineNum">    1688 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(4.526);</span></a>
+<a name="1689"><span class="lineNum">    1689 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(-0.00381305);</span></a>
+<a name="1690"><span class="lineNum">    1690 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(5.8567);</span></a>
+<a name="1691"><span class="lineNum">    1691 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(-0.214086);</span></a>
+<a name="1692"><span class="lineNum">    1692 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(-4.63649);</span></a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(2.52869);</span></a>
+<a name="1694"><span class="lineNum">    1694 </span><span class="lineCov">          8 :   parameter[TYR_SC3].push_back(-0.39894);</span></a>
+<a name="1695"><span class="lineNum">    1695 </span>            : </a>
+<a name="1696"><span class="lineNum">    1696 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(10.691);</span></a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(-0.0162929);</span></a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(1.24446);</span></a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(0.307914);</span></a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(-3.27446);</span></a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(2.14788);</span></a>
+<a name="1702"><span class="lineNum">    1702 </span><span class="lineCov">          8 :   parameter[VAL_BB].push_back(-0.403259);</span></a>
+<a name="1703"><span class="lineNum">    1703 </span>            : </a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(-3.516);</span></a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(1.62307);</span></a>
+<a name="1706"><span class="lineNum">    1706 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(5.43064);</span></a>
+<a name="1707"><span class="lineNum">    1707 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(9.28809);</span></a>
+<a name="1708"><span class="lineNum">    1708 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(-14.9927);</span></a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(6.6133);</span></a>
+<a name="1710"><span class="lineNum">    1710 </span><span class="lineCov">          8 :   parameter[VAL_SC1].push_back(-0.964977);</span></a>
+<a name="1711"><span class="lineNum">    1711 </span>            : </a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(32.88500000);</span></a>
+<a name="1713"><span class="lineNum">    1713 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(0.08339900);</span></a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(-7.36054400);</span></a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(2.19220300);</span></a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(-3.56523400);</span></a>
+<a name="1717"><span class="lineNum">    1717 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(2.33326900);</span></a>
+<a name="1718"><span class="lineNum">    1718 </span><span class="lineCov">          8 :   parameter[A_BB1].push_back(-0.39785500);</span></a>
+<a name="1719"><span class="lineNum">    1719 </span>            : </a>
+<a name="1720"><span class="lineNum">    1720 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(3.80600000);</span></a>
+<a name="1721"><span class="lineNum">    1721 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(-0.10727600);</span></a>
+<a name="1722"><span class="lineNum">    1722 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(9.58854100);</span></a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(-6.23740500);</span></a>
+<a name="1724"><span class="lineNum">    1724 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(-0.48267300);</span></a>
+<a name="1725"><span class="lineNum">    1725 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(1.14119500);</span></a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineCov">          8 :   parameter[A_BB2].push_back(-0.21385600);</span></a>
+<a name="1727"><span class="lineNum">    1727 </span>            : </a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(3.59400000);</span></a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(0.04537300);</span></a>
+<a name="1730"><span class="lineNum">    1730 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(9.59178900);</span></a>
+<a name="1731"><span class="lineNum">    1731 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(-1.29202200);</span></a>
+<a name="1732"><span class="lineNum">    1732 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(-7.10851000);</span></a>
+<a name="1733"><span class="lineNum">    1733 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(4.05571200);</span></a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineCov">          8 :   parameter[A_BB3].push_back(-0.63372500);</span></a>
+<a name="1735"><span class="lineNum">    1735 </span>            : </a>
+<a name="1736"><span class="lineNum">    1736 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(6.67100000);</span></a>
+<a name="1737"><span class="lineNum">    1737 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(-0.00855300);</span></a>
+<a name="1738"><span class="lineNum">    1738 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(1.63222400);</span></a>
+<a name="1739"><span class="lineNum">    1739 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(-0.06466200);</span></a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(-1.48694200);</span></a>
+<a name="1741"><span class="lineNum">    1741 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(0.78544600);</span></a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineCov">          8 :   parameter[A_SC1].push_back(-0.12083500);</span></a>
+<a name="1743"><span class="lineNum">    1743 </span>            : </a>
+<a name="1744"><span class="lineNum">    1744 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(5.95100000);</span></a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(-0.02606600);</span></a>
+<a name="1746"><span class="lineNum">    1746 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(2.54399900);</span></a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(-0.48436900);</span></a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(-1.55357400);</span></a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(0.86466900);</span></a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineCov">          8 :   parameter[A_SC2].push_back(-0.13509000);</span></a>
+<a name="1751"><span class="lineNum">    1751 </span>            : </a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(11.39400000);</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(0.00871300);</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(-0.23891300);</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(0.48919400);</span></a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(-1.75289400);</span></a>
+<a name="1757"><span class="lineNum">    1757 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(0.99267500);</span></a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineCov">          8 :   parameter[A_SC3].push_back(-0.16291300);</span></a>
+<a name="1759"><span class="lineNum">    1759 </span>            : </a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(6.45900000);</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(0.01990600);</span></a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(4.17970400);</span></a>
+<a name="1763"><span class="lineNum">    1763 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(0.97629900);</span></a>
+<a name="1764"><span class="lineNum">    1764 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(-5.03297800);</span></a>
+<a name="1765"><span class="lineNum">    1765 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(2.55576700);</span></a>
+<a name="1766"><span class="lineNum">    1766 </span><span class="lineCov">          8 :   parameter[A_SC4].push_back(-0.39150500);</span></a>
+<a name="1767"><span class="lineNum">    1767 </span>            : </a>
+<a name="1768"><span class="lineNum">    1768 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(4.23000000);</span></a>
+<a name="1769"><span class="lineNum">    1769 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(0.00064800);</span></a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(0.92124600);</span></a>
+<a name="1771"><span class="lineNum">    1771 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(0.08064300);</span></a>
+<a name="1772"><span class="lineNum">    1772 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(-0.39054400);</span></a>
+<a name="1773"><span class="lineNum">    1773 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(0.12429100);</span></a>
+<a name="1774"><span class="lineNum">    1774 </span><span class="lineCov">          8 :   parameter[A_3TE].push_back(-0.01122700);</span></a>
+<a name="1775"><span class="lineNum">    1775 </span>            : </a>
+<a name="1776"><span class="lineNum">    1776 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(4.23000000);</span></a>
+<a name="1777"><span class="lineNum">    1777 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(0.00039300);</span></a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(0.92305100);</span></a>
+<a name="1779"><span class="lineNum">    1779 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(0.07747500);</span></a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(-0.38792100);</span></a>
+<a name="1781"><span class="lineNum">    1781 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(0.12323800);</span></a>
+<a name="1782"><span class="lineNum">    1782 </span><span class="lineCov">          8 :   parameter[A_5TE].push_back(-0.01106600);</span></a>
+<a name="1783"><span class="lineNum">    1783 </span>            : </a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(7.82400000);</span></a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(-0.04881000);</span></a>
+<a name="1786"><span class="lineNum">    1786 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(8.21557900);</span></a>
+<a name="1787"><span class="lineNum">    1787 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(-0.89491400);</span></a>
+<a name="1788"><span class="lineNum">    1788 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(-9.54293700);</span></a>
+<a name="1789"><span class="lineNum">    1789 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(6.33122200);</span></a>
+<a name="1790"><span class="lineNum">    1790 </span><span class="lineCov">          8 :   parameter[A_TE3].push_back(-1.16672900);</span></a>
+<a name="1791"><span class="lineNum">    1791 </span>            : </a>
+<a name="1792"><span class="lineNum">    1792 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(8.03600000);</span></a>
+<a name="1793"><span class="lineNum">    1793 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(0.01641200);</span></a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(5.14902200);</span></a>
+<a name="1795"><span class="lineNum">    1795 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(0.83419700);</span></a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(-7.59068300);</span></a>
+<a name="1797"><span class="lineNum">    1797 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(4.52063200);</span></a>
+<a name="1798"><span class="lineNum">    1798 </span><span class="lineCov">          8 :   parameter[A_TE5].push_back(-0.78260800);</span></a>
+<a name="1799"><span class="lineNum">    1799 </span>            : </a>
+<a name="1800"><span class="lineNum">    1800 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(32.88500000);</span></a>
+<a name="1801"><span class="lineNum">    1801 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(0.08311100);</span></a>
+<a name="1802"><span class="lineNum">    1802 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(-7.35432100);</span></a>
+<a name="1803"><span class="lineNum">    1803 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(2.18610000);</span></a>
+<a name="1804"><span class="lineNum">    1804 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(-3.55788300);</span></a>
+<a name="1805"><span class="lineNum">    1805 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(2.32918700);</span></a>
+<a name="1806"><span class="lineNum">    1806 </span><span class="lineCov">          8 :   parameter[C_BB1].push_back(-0.39720000);</span></a>
+<a name="1807"><span class="lineNum">    1807 </span>            : </a>
+<a name="1808"><span class="lineNum">    1808 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(3.80600000);</span></a>
+<a name="1809"><span class="lineNum">    1809 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(-0.10808100);</span></a>
+<a name="1810"><span class="lineNum">    1810 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(9.61612600);</span></a>
+<a name="1811"><span class="lineNum">    1811 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(-6.28595400);</span></a>
+<a name="1812"><span class="lineNum">    1812 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(-0.45187000);</span></a>
+<a name="1813"><span class="lineNum">    1813 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(1.13326000);</span></a>
+<a name="1814"><span class="lineNum">    1814 </span><span class="lineCov">          8 :   parameter[C_BB2].push_back(-0.21320300);</span></a>
+<a name="1815"><span class="lineNum">    1815 </span>            : </a>
+<a name="1816"><span class="lineNum">    1816 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(3.59400000);</span></a>
+<a name="1817"><span class="lineNum">    1817 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(0.04484200);</span></a>
+<a name="1818"><span class="lineNum">    1818 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(9.61919800);</span></a>
+<a name="1819"><span class="lineNum">    1819 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(-1.33582800);</span></a>
+<a name="1820"><span class="lineNum">    1820 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(-7.07200400);</span></a>
+<a name="1821"><span class="lineNum">    1821 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(4.03952900);</span></a>
+<a name="1822"><span class="lineNum">    1822 </span><span class="lineCov">          8 :   parameter[C_BB3].push_back(-0.63098200);</span></a>
+<a name="1823"><span class="lineNum">    1823 </span>            : </a>
+<a name="1824"><span class="lineNum">    1824 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(5.95100000);</span></a>
+<a name="1825"><span class="lineNum">    1825 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(-0.02911300);</span></a>
+<a name="1826"><span class="lineNum">    1826 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(2.59700400);</span></a>
+<a name="1827"><span class="lineNum">    1827 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(-0.55507700);</span></a>
+<a name="1828"><span class="lineNum">    1828 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(-1.56344600);</span></a>
+<a name="1829"><span class="lineNum">    1829 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(0.88956200);</span></a>
+<a name="1830"><span class="lineNum">    1830 </span><span class="lineCov">          8 :   parameter[C_SC1].push_back(-0.14061300);</span></a>
+<a name="1831"><span class="lineNum">    1831 </span>            : </a>
+<a name="1832"><span class="lineNum">    1832 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(11.62100000);</span></a>
+<a name="1833"><span class="lineNum">    1833 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(0.01366100);</span></a>
+<a name="1834"><span class="lineNum">    1834 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(-0.25959200);</span></a>
+<a name="1835"><span class="lineNum">    1835 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(0.48918300);</span></a>
+<a name="1836"><span class="lineNum">    1836 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(-1.52550500);</span></a>
+<a name="1837"><span class="lineNum">    1837 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(0.83644100);</span></a>
+<a name="1838"><span class="lineNum">    1838 </span><span class="lineCov">          8 :   parameter[C_SC2].push_back(-0.13407300);</span></a>
+<a name="1839"><span class="lineNum">    1839 </span>            : </a>
+<a name="1840"><span class="lineNum">    1840 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(5.01900000);</span></a>
+<a name="1841"><span class="lineNum">    1841 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(-0.03276100);</span></a>
+<a name="1842"><span class="lineNum">    1842 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(5.53776900);</span></a>
+<a name="1843"><span class="lineNum">    1843 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(-0.95105000);</span></a>
+<a name="1844"><span class="lineNum">    1844 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(-3.71130800);</span></a>
+<a name="1845"><span class="lineNum">    1845 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(2.16146000);</span></a>
+<a name="1846"><span class="lineNum">    1846 </span><span class="lineCov">          8 :   parameter[C_SC3].push_back(-0.34918600);</span></a>
+<a name="1847"><span class="lineNum">    1847 </span>            : </a>
+<a name="1848"><span class="lineNum">    1848 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(4.23000000);</span></a>
+<a name="1849"><span class="lineNum">    1849 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(0.00057300);</span></a>
+<a name="1850"><span class="lineNum">    1850 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(0.92174800);</span></a>
+<a name="1851"><span class="lineNum">    1851 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(0.07964500);</span></a>
+<a name="1852"><span class="lineNum">    1852 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(-0.38965700);</span></a>
+<a name="1853"><span class="lineNum">    1853 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(0.12392500);</span></a>
+<a name="1854"><span class="lineNum">    1854 </span><span class="lineCov">          8 :   parameter[C_3TE].push_back(-0.01117000);</span></a>
+<a name="1855"><span class="lineNum">    1855 </span>            : </a>
+<a name="1856"><span class="lineNum">    1856 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(4.23000000);</span></a>
+<a name="1857"><span class="lineNum">    1857 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(0.00071000);</span></a>
+<a name="1858"><span class="lineNum">    1858 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(0.92082800);</span></a>
+<a name="1859"><span class="lineNum">    1859 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(0.08150600);</span></a>
+<a name="1860"><span class="lineNum">    1860 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(-0.39127000);</span></a>
+<a name="1861"><span class="lineNum">    1861 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(0.12455900);</span></a>
+<a name="1862"><span class="lineNum">    1862 </span><span class="lineCov">          8 :   parameter[C_5TE].push_back(-0.01126300);</span></a>
+<a name="1863"><span class="lineNum">    1863 </span>            : </a>
+<a name="1864"><span class="lineNum">    1864 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(7.82400000);</span></a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(-0.05848300);</span></a>
+<a name="1866"><span class="lineNum">    1866 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(8.29319900);</span></a>
+<a name="1867"><span class="lineNum">    1867 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(-1.12563800);</span></a>
+<a name="1868"><span class="lineNum">    1868 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(-9.42197600);</span></a>
+<a name="1869"><span class="lineNum">    1869 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(6.35441700);</span></a>
+<a name="1870"><span class="lineNum">    1870 </span><span class="lineCov">          8 :   parameter[C_TE3].push_back(-1.18356900);</span></a>
+<a name="1871"><span class="lineNum">    1871 </span>            : </a>
+<a name="1872"><span class="lineNum">    1872 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(8.03600000);</span></a>
+<a name="1873"><span class="lineNum">    1873 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(0.00493500);</span></a>
+<a name="1874"><span class="lineNum">    1874 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(4.92622000);</span></a>
+<a name="1875"><span class="lineNum">    1875 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(0.64810700);</span></a>
+<a name="1876"><span class="lineNum">    1876 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(-7.05100000);</span></a>
+<a name="1877"><span class="lineNum">    1877 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(4.26064400);</span></a>
+<a name="1878"><span class="lineNum">    1878 </span><span class="lineCov">          8 :   parameter[C_TE5].push_back(-0.74819100);</span></a>
+<a name="1879"><span class="lineNum">    1879 </span>            : </a>
+<a name="1880"><span class="lineNum">    1880 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(32.88500000);</span></a>
+<a name="1881"><span class="lineNum">    1881 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(0.08325400);</span></a>
+<a name="1882"><span class="lineNum">    1882 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(-7.35736000);</span></a>
+<a name="1883"><span class="lineNum">    1883 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(2.18914800);</span></a>
+<a name="1884"><span class="lineNum">    1884 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(-3.56154800);</span></a>
+<a name="1885"><span class="lineNum">    1885 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(2.33120600);</span></a>
+<a name="1886"><span class="lineNum">    1886 </span><span class="lineCov">          8 :   parameter[G_BB1].push_back(-0.39752300);</span></a>
+<a name="1887"><span class="lineNum">    1887 </span>            : </a>
+<a name="1888"><span class="lineNum">    1888 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(3.80600000);</span></a>
+<a name="1889"><span class="lineNum">    1889 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(-0.10788300);</span></a>
+<a name="1890"><span class="lineNum">    1890 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(9.60930800);</span></a>
+<a name="1891"><span class="lineNum">    1891 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(-6.27402500);</span></a>
+<a name="1892"><span class="lineNum">    1892 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(-0.46192700);</span></a>
+<a name="1893"><span class="lineNum">    1893 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(1.13737000);</span></a>
+<a name="1894"><span class="lineNum">    1894 </span><span class="lineCov">          8 :   parameter[G_BB2].push_back(-0.21383100);</span></a>
+<a name="1895"><span class="lineNum">    1895 </span>            : </a>
+<a name="1896"><span class="lineNum">    1896 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(3.59400000);</span></a>
+<a name="1897"><span class="lineNum">    1897 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(0.04514500);</span></a>
+<a name="1898"><span class="lineNum">    1898 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(9.61234700);</span></a>
+<a name="1899"><span class="lineNum">    1899 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(-1.31542100);</span></a>
+<a name="1900"><span class="lineNum">    1900 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(-7.09150500);</span></a>
+<a name="1901"><span class="lineNum">    1901 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(4.04706200);</span></a>
+<a name="1902"><span class="lineNum">    1902 </span><span class="lineCov">          8 :   parameter[G_BB3].push_back(-0.63201000);</span></a>
+<a name="1903"><span class="lineNum">    1903 </span>            : </a>
+<a name="1904"><span class="lineNum">    1904 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(6.67100000);</span></a>
+<a name="1905"><span class="lineNum">    1905 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(-0.00863200);</span></a>
+<a name="1906"><span class="lineNum">    1906 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(1.63252300);</span></a>
+<a name="1907"><span class="lineNum">    1907 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(-0.06567200);</span></a>
+<a name="1908"><span class="lineNum">    1908 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(-1.48680500);</span></a>
+<a name="1909"><span class="lineNum">    1909 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(0.78565600);</span></a>
+<a name="1910"><span class="lineNum">    1910 </span><span class="lineCov">          8 :   parameter[G_SC1].push_back(-0.12088900);</span></a>
+<a name="1911"><span class="lineNum">    1911 </span>            : </a>
+<a name="1912"><span class="lineNum">    1912 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(11.39400000);</span></a>
+<a name="1913"><span class="lineNum">    1913 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(0.00912200);</span></a>
+<a name="1914"><span class="lineNum">    1914 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(-0.22869000);</span></a>
+<a name="1915"><span class="lineNum">    1915 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(0.49616400);</span></a>
+<a name="1916"><span class="lineNum">    1916 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(-1.75039000);</span></a>
+<a name="1917"><span class="lineNum">    1917 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(0.98649200);</span></a>
+<a name="1918"><span class="lineNum">    1918 </span><span class="lineCov">          8 :   parameter[G_SC2].push_back(-0.16141600);</span></a>
+<a name="1919"><span class="lineNum">    1919 </span>            : </a>
+<a name="1920"><span class="lineNum">    1920 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(10.90100000);</span></a>
+<a name="1921"><span class="lineNum">    1921 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(0.02208700);</span></a>
+<a name="1922"><span class="lineNum">    1922 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(0.17032800);</span></a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(0.73280800);</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(-1.95292000);</span></a>
+<a name="1925"><span class="lineNum">    1925 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(0.98357600);</span></a>
+<a name="1926"><span class="lineNum">    1926 </span><span class="lineCov">          8 :   parameter[G_SC3].push_back(-0.14790900);</span></a>
+<a name="1927"><span class="lineNum">    1927 </span>            : </a>
+<a name="1928"><span class="lineNum">    1928 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(6.45900000);</span></a>
+<a name="1929"><span class="lineNum">    1929 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(0.02023700);</span></a>
+<a name="1930"><span class="lineNum">    1930 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(4.17655400);</span></a>
+<a name="1931"><span class="lineNum">    1931 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(0.98731800);</span></a>
+<a name="1932"><span class="lineNum">    1932 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(-5.04352800);</span></a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(2.56059400);</span></a>
+<a name="1934"><span class="lineNum">    1934 </span><span class="lineCov">          8 :   parameter[G_SC4].push_back(-0.39234300);</span></a>
+<a name="1935"><span class="lineNum">    1935 </span>            : </a>
+<a name="1936"><span class="lineNum">    1936 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(4.23000000);</span></a>
+<a name="1937"><span class="lineNum">    1937 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(0.00066300);</span></a>
+<a name="1938"><span class="lineNum">    1938 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(0.92118800);</span></a>
+<a name="1939"><span class="lineNum">    1939 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(0.08062700);</span></a>
+<a name="1940"><span class="lineNum">    1940 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(-0.39041600);</span></a>
+<a name="1941"><span class="lineNum">    1941 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(0.12419400);</span></a>
+<a name="1942"><span class="lineNum">    1942 </span><span class="lineCov">          8 :   parameter[G_3TE].push_back(-0.01120500);</span></a>
+<a name="1943"><span class="lineNum">    1943 </span>            : </a>
+<a name="1944"><span class="lineNum">    1944 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(4.23000000);</span></a>
+<a name="1945"><span class="lineNum">    1945 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(0.00062800);</span></a>
+<a name="1946"><span class="lineNum">    1946 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(0.92133500);</span></a>
+<a name="1947"><span class="lineNum">    1947 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(0.08029900);</span></a>
+<a name="1948"><span class="lineNum">    1948 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(-0.39015300);</span></a>
+<a name="1949"><span class="lineNum">    1949 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(0.12411600);</span></a>
+<a name="1950"><span class="lineNum">    1950 </span><span class="lineCov">          8 :   parameter[G_5TE].push_back(-0.01119900);</span></a>
+<a name="1951"><span class="lineNum">    1951 </span>            : </a>
+<a name="1952"><span class="lineNum">    1952 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(7.82400000);</span></a>
+<a name="1953"><span class="lineNum">    1953 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(-0.05177400);</span></a>
+<a name="1954"><span class="lineNum">    1954 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(8.34606700);</span></a>
+<a name="1955"><span class="lineNum">    1955 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(-1.02936300);</span></a>
+<a name="1956"><span class="lineNum">    1956 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(-9.55211900);</span></a>
+<a name="1957"><span class="lineNum">    1957 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(6.37776600);</span></a>
+<a name="1958"><span class="lineNum">    1958 </span><span class="lineCov">          8 :   parameter[G_TE3].push_back(-1.17898000);</span></a>
+<a name="1959"><span class="lineNum">    1959 </span>            : </a>
+<a name="1960"><span class="lineNum">    1960 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(8.03600000);</span></a>
+<a name="1961"><span class="lineNum">    1961 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(0.00525100);</span></a>
+<a name="1962"><span class="lineNum">    1962 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(4.71070600);</span></a>
+<a name="1963"><span class="lineNum">    1963 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(0.66746900);</span></a>
+<a name="1964"><span class="lineNum">    1964 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(-6.72538700);</span></a>
+<a name="1965"><span class="lineNum">    1965 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(4.03644100);</span></a>
+<a name="1966"><span class="lineNum">    1966 </span><span class="lineCov">          8 :   parameter[G_TE5].push_back(-0.70605700);</span></a>
+<a name="1967"><span class="lineNum">    1967 </span>            : </a>
+<a name="1968"><span class="lineNum">    1968 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(32.88500000);</span></a>
+<a name="1969"><span class="lineNum">    1969 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(0.08321400);</span></a>
+<a name="1970"><span class="lineNum">    1970 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(-7.35634900);</span></a>
+<a name="1971"><span class="lineNum">    1971 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(2.18826800);</span></a>
+<a name="1972"><span class="lineNum">    1972 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(-3.56047400);</span></a>
+<a name="1973"><span class="lineNum">    1973 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(2.33064700);</span></a>
+<a name="1974"><span class="lineNum">    1974 </span><span class="lineCov">          8 :   parameter[U_BB1].push_back(-0.39744000);</span></a>
+<a name="1975"><span class="lineNum">    1975 </span>            : </a>
+<a name="1976"><span class="lineNum">    1976 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(3.80600000);</span></a>
+<a name="1977"><span class="lineNum">    1977 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(-0.10773100);</span></a>
+<a name="1978"><span class="lineNum">    1978 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(9.60099900);</span></a>
+<a name="1979"><span class="lineNum">    1979 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(-6.26131900);</span></a>
+<a name="1980"><span class="lineNum">    1980 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(-0.46668300);</span></a>
+<a name="1981"><span class="lineNum">    1981 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(1.13698100);</span></a>
+<a name="1982"><span class="lineNum">    1982 </span><span class="lineCov">          8 :   parameter[U_BB2].push_back(-0.21351600);</span></a>
+<a name="1983"><span class="lineNum">    1983 </span>            : </a>
+<a name="1984"><span class="lineNum">    1984 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(3.59400000);</span></a>
+<a name="1985"><span class="lineNum">    1985 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(0.04544300);</span></a>
+<a name="1986"><span class="lineNum">    1986 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(9.59625900);</span></a>
+<a name="1987"><span class="lineNum">    1987 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(-1.29222200);</span></a>
+<a name="1988"><span class="lineNum">    1988 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(-7.11143200);</span></a>
+<a name="1989"><span class="lineNum">    1989 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(4.05687700);</span></a>
+<a name="1990"><span class="lineNum">    1990 </span><span class="lineCov">          8 :   parameter[U_BB3].push_back(-0.63382800);</span></a>
+<a name="1991"><span class="lineNum">    1991 </span>            : </a>
+<a name="1992"><span class="lineNum">    1992 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(5.95100000);</span></a>
+<a name="1993"><span class="lineNum">    1993 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(-0.02924500);</span></a>
+<a name="1994"><span class="lineNum">    1994 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(2.59668700);</span></a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(-0.56118700);</span></a>
+<a name="1996"><span class="lineNum">    1996 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(-1.56477100);</span></a>
+<a name="1997"><span class="lineNum">    1997 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(0.89265100);</span></a>
+<a name="1998"><span class="lineNum">    1998 </span><span class="lineCov">          8 :   parameter[U_SC1].push_back(-0.14130800);</span></a>
+<a name="1999"><span class="lineNum">    1999 </span>            : </a>
+<a name="2000"><span class="lineNum">    2000 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(10.90100000);</span></a>
+<a name="2001"><span class="lineNum">    2001 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(0.02178900);</span></a>
+<a name="2002"><span class="lineNum">    2002 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(0.18839000);</span></a>
+<a name="2003"><span class="lineNum">    2003 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(0.72223100);</span></a>
+<a name="2004"><span class="lineNum">    2004 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(-1.92581600);</span></a>
+<a name="2005"><span class="lineNum">    2005 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(0.96654300);</span></a>
+<a name="2006"><span class="lineNum">    2006 </span><span class="lineCov">          8 :   parameter[U_SC2].push_back(-0.14501300);</span></a>
+<a name="2007"><span class="lineNum">    2007 </span>            : </a>
+<a name="2008"><span class="lineNum">    2008 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(5.24600000);</span></a>
+<a name="2009"><span class="lineNum">    2009 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(-0.04586500);</span></a>
+<a name="2010"><span class="lineNum">    2010 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(5.89978100);</span></a>
+<a name="2011"><span class="lineNum">    2011 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(-1.50664700);</span></a>
+<a name="2012"><span class="lineNum">    2012 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(-3.17054400);</span></a>
+<a name="2013"><span class="lineNum">    2013 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(1.93717100);</span></a>
+<a name="2014"><span class="lineNum">    2014 </span><span class="lineCov">          8 :   parameter[U_SC3].push_back(-0.31701000);</span></a>
+<a name="2015"><span class="lineNum">    2015 </span>            : </a>
+<a name="2016"><span class="lineNum">    2016 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(4.23000000);</span></a>
+<a name="2017"><span class="lineNum">    2017 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(0.00067500);</span></a>
+<a name="2018"><span class="lineNum">    2018 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(0.92102300);</span></a>
+<a name="2019"><span class="lineNum">    2019 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(0.08100800);</span></a>
+<a name="2020"><span class="lineNum">    2020 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(-0.39084300);</span></a>
+<a name="2021"><span class="lineNum">    2021 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(0.12441900);</span></a>
+<a name="2022"><span class="lineNum">    2022 </span><span class="lineCov">          8 :   parameter[U_3TE].push_back(-0.01124900);</span></a>
+<a name="2023"><span class="lineNum">    2023 </span>            : </a>
+<a name="2024"><span class="lineNum">    2024 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(4.23000000);</span></a>
+<a name="2025"><span class="lineNum">    2025 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(0.00059000);</span></a>
+<a name="2026"><span class="lineNum">    2026 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(0.92154600);</span></a>
+<a name="2027"><span class="lineNum">    2027 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(0.07968200);</span></a>
+<a name="2028"><span class="lineNum">    2028 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(-0.38950100);</span></a>
+<a name="2029"><span class="lineNum">    2029 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(0.12382500);</span></a>
+<a name="2030"><span class="lineNum">    2030 </span><span class="lineCov">          8 :   parameter[U_5TE].push_back(-0.01115100);</span></a>
+<a name="2031"><span class="lineNum">    2031 </span>            : </a>
+<a name="2032"><span class="lineNum">    2032 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(7.82400000);</span></a>
+<a name="2033"><span class="lineNum">    2033 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(-0.02968100);</span></a>
+<a name="2034"><span class="lineNum">    2034 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(7.93783200);</span></a>
+<a name="2035"><span class="lineNum">    2035 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(-0.33078100);</span></a>
+<a name="2036"><span class="lineNum">    2036 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(-10.14120200);</span></a>
+<a name="2037"><span class="lineNum">    2037 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(6.63334700);</span></a>
+<a name="2038"><span class="lineNum">    2038 </span><span class="lineCov">          8 :   parameter[U_TE3].push_back(-1.22111200);</span></a>
+<a name="2039"><span class="lineNum">    2039 </span>            : </a>
+<a name="2040"><span class="lineNum">    2040 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(8.03600000);</span></a>
+<a name="2041"><span class="lineNum">    2041 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(-0.00909700);</span></a>
+<a name="2042"><span class="lineNum">    2042 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(4.33193500);</span></a>
+<a name="2043"><span class="lineNum">    2043 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(0.43416500);</span></a>
+<a name="2044"><span class="lineNum">    2044 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(-5.80831400);</span></a>
+<a name="2045"><span class="lineNum">    2045 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(3.52438800);</span></a>
+<a name="2046"><span class="lineNum">    2046 </span><span class="lineCov">          8 :   parameter[U_TE5].push_back(-0.62382400);</span></a>
+<a name="2047"><span class="lineNum">    2047 </span>            : </a>
+<a name="2048"><span class="lineNum">    2048 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(32.88500000);</span></a>
+<a name="2049"><span class="lineNum">    2049 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(0.08179900);</span></a>
+<a name="2050"><span class="lineNum">    2050 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(-7.31735900);</span></a>
+<a name="2051"><span class="lineNum">    2051 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(2.15614500);</span></a>
+<a name="2052"><span class="lineNum">    2052 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(-3.52263200);</span></a>
+<a name="2053"><span class="lineNum">    2053 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(2.30604700);</span></a>
+<a name="2054"><span class="lineNum">    2054 </span><span class="lineCov">          8 :   parameter[DA_BB1].push_back(-0.39270100);</span></a>
+<a name="2055"><span class="lineNum">    2055 </span>            : </a>
+<a name="2056"><span class="lineNum">    2056 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(3.80600000);</span></a>
+<a name="2057"><span class="lineNum">    2057 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(-0.10597700);</span></a>
+<a name="2058"><span class="lineNum">    2058 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(9.52537500);</span></a>
+<a name="2059"><span class="lineNum">    2059 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(-6.12991000);</span></a>
+<a name="2060"><span class="lineNum">    2060 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(-0.54092600);</span></a>
+<a name="2061"><span class="lineNum">    2061 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(1.15429100);</span></a>
+<a name="2062"><span class="lineNum">    2062 </span><span class="lineCov">          8 :   parameter[DA_BB2].push_back(-0.21503500);</span></a>
+<a name="2063"><span class="lineNum">    2063 </span>            : </a>
+<a name="2064"><span class="lineNum">    2064 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(-1.35600000);</span></a>
+<a name="2065"><span class="lineNum">    2065 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(0.58928300);</span></a>
+<a name="2066"><span class="lineNum">    2066 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(6.71894100);</span></a>
+<a name="2067"><span class="lineNum">    2067 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(4.14050900);</span></a>
+<a name="2068"><span class="lineNum">    2068 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(-9.65859900);</span></a>
+<a name="2069"><span class="lineNum">    2069 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(4.43185000);</span></a>
+<a name="2070"><span class="lineNum">    2070 </span><span class="lineCov">          8 :   parameter[DA_BB3].push_back(-0.64657300);</span></a>
+<a name="2071"><span class="lineNum">    2071 </span>            : </a>
+<a name="2072"><span class="lineNum">    2072 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(6.67100000);</span></a>
+<a name="2073"><span class="lineNum">    2073 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(-0.00871400);</span></a>
+<a name="2074"><span class="lineNum">    2074 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(1.63289100);</span></a>
+<a name="2075"><span class="lineNum">    2075 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(-0.06637700);</span></a>
+<a name="2076"><span class="lineNum">    2076 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(-1.48632900);</span></a>
+<a name="2077"><span class="lineNum">    2077 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(0.78551800);</span></a>
+<a name="2078"><span class="lineNum">    2078 </span><span class="lineCov">          8 :   parameter[DA_SC1].push_back(-0.12087300);</span></a>
+<a name="2079"><span class="lineNum">    2079 </span>            : </a>
+<a name="2080"><span class="lineNum">    2080 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(5.95100000);</span></a>
+<a name="2081"><span class="lineNum">    2081 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(-0.02634300);</span></a>
+<a name="2082"><span class="lineNum">    2082 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(2.54864300);</span></a>
+<a name="2083"><span class="lineNum">    2083 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(-0.49015800);</span></a>
+<a name="2084"><span class="lineNum">    2084 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(-1.55386900);</span></a>
+<a name="2085"><span class="lineNum">    2085 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(0.86630200);</span></a>
+<a name="2086"><span class="lineNum">    2086 </span><span class="lineCov">          8 :   parameter[DA_SC2].push_back(-0.13546200);</span></a>
+<a name="2087"><span class="lineNum">    2087 </span>            : </a>
+<a name="2088"><span class="lineNum">    2088 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(11.39400000);</span></a>
+<a name="2089"><span class="lineNum">    2089 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(0.00859500);</span></a>
+<a name="2090"><span class="lineNum">    2090 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(-0.25471400);</span></a>
+<a name="2091"><span class="lineNum">    2091 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(0.48718800);</span></a>
+<a name="2092"><span class="lineNum">    2092 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(-1.74520000);</span></a>
+<a name="2093"><span class="lineNum">    2093 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(0.99246200);</span></a>
+<a name="2094"><span class="lineNum">    2094 </span><span class="lineCov">          8 :   parameter[DA_SC3].push_back(-0.16351900);</span></a>
+<a name="2095"><span class="lineNum">    2095 </span>            : </a>
+<a name="2096"><span class="lineNum">    2096 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(6.45900000);</span></a>
+<a name="2097"><span class="lineNum">    2097 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(0.01991800);</span></a>
+<a name="2098"><span class="lineNum">    2098 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(4.17962300);</span></a>
+<a name="2099"><span class="lineNum">    2099 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(0.97469100);</span></a>
+<a name="2100"><span class="lineNum">    2100 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(-5.02950400);</span></a>
+<a name="2101"><span class="lineNum">    2101 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(2.55371800);</span></a>
+<a name="2102"><span class="lineNum">    2102 </span><span class="lineCov">          8 :   parameter[DA_SC4].push_back(-0.39113400);</span></a>
+<a name="2103"><span class="lineNum">    2103 </span>            : </a>
+<a name="2104"><span class="lineNum">    2104 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(4.23000000);</span></a>
+<a name="2105"><span class="lineNum">    2105 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(0.00062600);</span></a>
+<a name="2106"><span class="lineNum">    2106 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(0.92142000);</span></a>
+<a name="2107"><span class="lineNum">    2107 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(0.08016400);</span></a>
+<a name="2108"><span class="lineNum">    2108 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(-0.39000300);</span></a>
+<a name="2109"><span class="lineNum">    2109 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(0.12402500);</span></a>
+<a name="2110"><span class="lineNum">    2110 </span><span class="lineCov">          8 :   parameter[DA_3TE].push_back(-0.01117900);</span></a>
+<a name="2111"><span class="lineNum">    2111 </span>            : </a>
+<a name="2112"><span class="lineNum">    2112 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(4.23000000);</span></a>
+<a name="2113"><span class="lineNum">    2113 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(0.00055500);</span></a>
+<a name="2114"><span class="lineNum">    2114 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(0.92183900);</span></a>
+<a name="2115"><span class="lineNum">    2115 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(0.07907600);</span></a>
+<a name="2116"><span class="lineNum">    2116 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(-0.38895100);</span></a>
+<a name="2117"><span class="lineNum">    2117 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(0.12359600);</span></a>
+<a name="2118"><span class="lineNum">    2118 </span><span class="lineCov">          8 :   parameter[DA_5TE].push_back(-0.01111600);</span></a>
+<a name="2119"><span class="lineNum">    2119 </span>            : </a>
+<a name="2120"><span class="lineNum">    2120 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(2.87400000);</span></a>
+<a name="2121"><span class="lineNum">    2121 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(0.00112900);</span></a>
+<a name="2122"><span class="lineNum">    2122 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(12.51167200);</span></a>
+<a name="2123"><span class="lineNum">    2123 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(-7.67548000);</span></a>
+<a name="2124"><span class="lineNum">    2124 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(-2.02234000);</span></a>
+<a name="2125"><span class="lineNum">    2125 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(2.50837100);</span></a>
+<a name="2126"><span class="lineNum">    2126 </span><span class="lineCov">          8 :   parameter[DA_TE3].push_back(-0.49458500);</span></a>
+<a name="2127"><span class="lineNum">    2127 </span>            : </a>
+<a name="2128"><span class="lineNum">    2128 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(8.03600000);</span></a>
+<a name="2129"><span class="lineNum">    2129 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(0.00473100);</span></a>
+<a name="2130"><span class="lineNum">    2130 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(4.65554400);</span></a>
+<a name="2131"><span class="lineNum">    2131 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(0.66424100);</span></a>
+<a name="2132"><span class="lineNum">    2132 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(-6.62131300);</span></a>
+<a name="2133"><span class="lineNum">    2133 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(3.96107400);</span></a>
+<a name="2134"><span class="lineNum">    2134 </span><span class="lineCov">          8 :   parameter[DA_TE5].push_back(-0.69075800);</span></a>
+<a name="2135"><span class="lineNum">    2135 </span>            : </a>
+<a name="2136"><span class="lineNum">    2136 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(32.88500000);</span></a>
+<a name="2137"><span class="lineNum">    2137 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(0.08189900);</span></a>
+<a name="2138"><span class="lineNum">    2138 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(-7.32493500);</span></a>
+<a name="2139"><span class="lineNum">    2139 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(2.15976900);</span></a>
+<a name="2140"><span class="lineNum">    2140 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(-3.52612100);</span></a>
+<a name="2141"><span class="lineNum">    2141 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(2.31058600);</span></a>
+<a name="2142"><span class="lineNum">    2142 </span><span class="lineCov">          8 :   parameter[DC_BB1].push_back(-0.39402700);</span></a>
+<a name="2143"><span class="lineNum">    2143 </span>            : </a>
+<a name="2144"><span class="lineNum">    2144 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(3.80600000);</span></a>
+<a name="2145"><span class="lineNum">    2145 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(-0.10559800);</span></a>
+<a name="2146"><span class="lineNum">    2146 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(9.52527700);</span></a>
+<a name="2147"><span class="lineNum">    2147 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(-6.12131700);</span></a>
+<a name="2148"><span class="lineNum">    2148 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(-0.54899400);</span></a>
+<a name="2149"><span class="lineNum">    2149 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(1.15592900);</span></a>
+<a name="2150"><span class="lineNum">    2150 </span><span class="lineCov">          8 :   parameter[DC_BB2].push_back(-0.21494500);</span></a>
+<a name="2151"><span class="lineNum">    2151 </span>            : </a>
+<a name="2152"><span class="lineNum">    2152 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(-1.35600000);</span></a>
+<a name="2153"><span class="lineNum">    2153 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(0.55525700);</span></a>
+<a name="2154"><span class="lineNum">    2154 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(6.80305500);</span></a>
+<a name="2155"><span class="lineNum">    2155 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(4.05924700);</span></a>
+<a name="2156"><span class="lineNum">    2156 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(-9.61034700);</span></a>
+<a name="2157"><span class="lineNum">    2157 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(4.41253800);</span></a>
+<a name="2158"><span class="lineNum">    2158 </span><span class="lineCov">          8 :   parameter[DC_BB3].push_back(-0.64315100);</span></a>
+<a name="2159"><span class="lineNum">    2159 </span>            : </a>
+<a name="2160"><span class="lineNum">    2160 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(5.95100000);</span></a>
+<a name="2161"><span class="lineNum">    2161 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(-0.02899900);</span></a>
+<a name="2162"><span class="lineNum">    2162 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(2.59587800);</span></a>
+<a name="2163"><span class="lineNum">    2163 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(-0.55388300);</span></a>
+<a name="2164"><span class="lineNum">    2164 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(-1.56395100);</span></a>
+<a name="2165"><span class="lineNum">    2165 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(0.88967400);</span></a>
+<a name="2166"><span class="lineNum">    2166 </span><span class="lineCov">          8 :   parameter[DC_SC1].push_back(-0.14062500);</span></a>
+<a name="2167"><span class="lineNum">    2167 </span>            : </a>
+<a name="2168"><span class="lineNum">    2168 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(11.62100000);</span></a>
+<a name="2169"><span class="lineNum">    2169 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(0.01358100);</span></a>
+<a name="2170"><span class="lineNum">    2170 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(-0.24913000);</span></a>
+<a name="2171"><span class="lineNum">    2171 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(0.48787200);</span></a>
+<a name="2172"><span class="lineNum">    2172 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(-1.52867300);</span></a>
+<a name="2173"><span class="lineNum">    2173 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(0.83694900);</span></a>
+<a name="2174"><span class="lineNum">    2174 </span><span class="lineCov">          8 :   parameter[DC_SC2].push_back(-0.13395300);</span></a>
+<a name="2175"><span class="lineNum">    2175 </span>            : </a>
+<a name="2176"><span class="lineNum">    2176 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(5.01900000);</span></a>
+<a name="2177"><span class="lineNum">    2177 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(-0.03298400);</span></a>
+<a name="2178"><span class="lineNum">    2178 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(5.54242800);</span></a>
+<a name="2179"><span class="lineNum">    2179 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(-0.96081500);</span></a>
+<a name="2180"><span class="lineNum">    2180 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(-3.71051600);</span></a>
+<a name="2181"><span class="lineNum">    2181 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(2.16500200);</span></a>
+<a name="2182"><span class="lineNum">    2182 </span><span class="lineCov">          8 :   parameter[DC_SC3].push_back(-0.35023400);</span></a>
+<a name="2183"><span class="lineNum">    2183 </span>            : </a>
+<a name="2184"><span class="lineNum">    2184 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(4.23000000);</span></a>
+<a name="2185"><span class="lineNum">    2185 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(0.00055700);</span></a>
+<a name="2186"><span class="lineNum">    2186 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(0.92181400);</span></a>
+<a name="2187"><span class="lineNum">    2187 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(0.07924000);</span></a>
+<a name="2188"><span class="lineNum">    2188 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(-0.38916400);</span></a>
+<a name="2189"><span class="lineNum">    2189 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(0.12369900);</span></a>
+<a name="2190"><span class="lineNum">    2190 </span><span class="lineCov">          8 :   parameter[DC_3TE].push_back(-0.01113300);</span></a>
+<a name="2191"><span class="lineNum">    2191 </span>            : </a>
+<a name="2192"><span class="lineNum">    2192 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(4.23000000);</span></a>
+<a name="2193"><span class="lineNum">    2193 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(0.00066500);</span></a>
+<a name="2194"><span class="lineNum">    2194 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(0.92103900);</span></a>
+<a name="2195"><span class="lineNum">    2195 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(0.08064600);</span></a>
+<a name="2196"><span class="lineNum">    2196 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(-0.39034900);</span></a>
+<a name="2197"><span class="lineNum">    2197 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(0.12417600);</span></a>
+<a name="2198"><span class="lineNum">    2198 </span><span class="lineCov">          8 :   parameter[DC_5TE].push_back(-0.01120600);</span></a>
+<a name="2199"><span class="lineNum">    2199 </span>            : </a>
+<a name="2200"><span class="lineNum">    2200 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(2.87400000);</span></a>
+<a name="2201"><span class="lineNum">    2201 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(-0.05235500);</span></a>
+<a name="2202"><span class="lineNum">    2202 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(13.09201200);</span></a>
+<a name="2203"><span class="lineNum">    2203 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(-9.48128200);</span></a>
+<a name="2204"><span class="lineNum">    2204 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(-0.14958600);</span></a>
+<a name="2205"><span class="lineNum">    2205 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(1.75537200);</span></a>
+<a name="2206"><span class="lineNum">    2206 </span><span class="lineCov">          8 :   parameter[DC_TE3].push_back(-0.39347500);</span></a>
+<a name="2207"><span class="lineNum">    2207 </span>            : </a>
+<a name="2208"><span class="lineNum">    2208 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(8.03600000);</span></a>
+<a name="2209"><span class="lineNum">    2209 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(-0.00513600);</span></a>
+<a name="2210"><span class="lineNum">    2210 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(4.67705700);</span></a>
+<a name="2211"><span class="lineNum">    2211 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(0.48333300);</span></a>
+<a name="2212"><span class="lineNum">    2212 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(-6.34511000);</span></a>
+<a name="2213"><span class="lineNum">    2213 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(3.83388500);</span></a>
+<a name="2214"><span class="lineNum">    2214 </span><span class="lineCov">          8 :   parameter[DC_TE5].push_back(-0.67367800);</span></a>
+<a name="2215"><span class="lineNum">    2215 </span>            : </a>
+<a name="2216"><span class="lineNum">    2216 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(32.88500000);</span></a>
+<a name="2217"><span class="lineNum">    2217 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(0.08182900);</span></a>
+<a name="2218"><span class="lineNum">    2218 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(-7.32133900);</span></a>
+<a name="2219"><span class="lineNum">    2219 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(2.15767900);</span></a>
+<a name="2220"><span class="lineNum">    2220 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(-3.52369700);</span></a>
+<a name="2221"><span class="lineNum">    2221 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(2.30839600);</span></a>
+<a name="2222"><span class="lineNum">    2222 </span><span class="lineCov">          8 :   parameter[DG_BB1].push_back(-0.39348300);</span></a>
+<a name="2223"><span class="lineNum">    2223 </span>            : </a>
+<a name="2224"><span class="lineNum">    2224 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(3.80600000);</span></a>
+<a name="2225"><span class="lineNum">    2225 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(-0.10618100);</span></a>
+<a name="2226"><span class="lineNum">    2226 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(9.54169000);</span></a>
+<a name="2227"><span class="lineNum">    2227 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(-6.15177600);</span></a>
+<a name="2228"><span class="lineNum">    2228 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(-0.53462400);</span></a>
+<a name="2229"><span class="lineNum">    2229 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(1.15581300);</span></a>
+<a name="2230"><span class="lineNum">    2230 </span><span class="lineCov">          8 :   parameter[DG_BB2].push_back(-0.21567000);</span></a>
+<a name="2231"><span class="lineNum">    2231 </span>            : </a>
+<a name="2232"><span class="lineNum">    2232 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(-1.35600000);</span></a>
+<a name="2233"><span class="lineNum">    2233 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(0.57489100);</span></a>
+<a name="2234"><span class="lineNum">    2234 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(6.75164700);</span></a>
+<a name="2235"><span class="lineNum">    2235 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(4.11300900);</span></a>
+<a name="2236"><span class="lineNum">    2236 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(-9.63394600);</span></a>
+<a name="2237"><span class="lineNum">    2237 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(4.41675400);</span></a>
+<a name="2238"><span class="lineNum">    2238 </span><span class="lineCov">          8 :   parameter[DG_BB3].push_back(-0.64339900);</span></a>
+<a name="2239"><span class="lineNum">    2239 </span>            : </a>
+<a name="2240"><span class="lineNum">    2240 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(6.67100000);</span></a>
+<a name="2241"><span class="lineNum">    2241 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(-0.00886600);</span></a>
+<a name="2242"><span class="lineNum">    2242 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(1.63333000);</span></a>
+<a name="2243"><span class="lineNum">    2243 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(-0.06892100);</span></a>
+<a name="2244"><span class="lineNum">    2244 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(-1.48683500);</span></a>
+<a name="2245"><span class="lineNum">    2245 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(0.78670800);</span></a>
+<a name="2246"><span class="lineNum">    2246 </span><span class="lineCov">          8 :   parameter[DG_SC1].push_back(-0.12113900);</span></a>
+<a name="2247"><span class="lineNum">    2247 </span>            : </a>
+<a name="2248"><span class="lineNum">    2248 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(11.39400000);</span></a>
+<a name="2249"><span class="lineNum">    2249 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(0.00907900);</span></a>
+<a name="2250"><span class="lineNum">    2250 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(-0.22475500);</span></a>
+<a name="2251"><span class="lineNum">    2251 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(0.49535100);</span></a>
+<a name="2252"><span class="lineNum">    2252 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(-1.75324900);</span></a>
+<a name="2253"><span class="lineNum">    2253 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(0.98767400);</span></a>
+<a name="2254"><span class="lineNum">    2254 </span><span class="lineCov">          8 :   parameter[DG_SC2].push_back(-0.16150800);</span></a>
+<a name="2255"><span class="lineNum">    2255 </span>            : </a>
+<a name="2256"><span class="lineNum">    2256 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(10.90100000);</span></a>
+<a name="2257"><span class="lineNum">    2257 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(0.02207600);</span></a>
+<a name="2258"><span class="lineNum">    2258 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(0.17932200);</span></a>
+<a name="2259"><span class="lineNum">    2259 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(0.73253200);</span></a>
+<a name="2260"><span class="lineNum">    2260 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(-1.95554900);</span></a>
+<a name="2261"><span class="lineNum">    2261 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(0.98339900);</span></a>
+<a name="2262"><span class="lineNum">    2262 </span><span class="lineCov">          8 :   parameter[DG_SC3].push_back(-0.14763600);</span></a>
+<a name="2263"><span class="lineNum">    2263 </span>            : </a>
+<a name="2264"><span class="lineNum">    2264 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(6.45900000);</span></a>
+<a name="2265"><span class="lineNum">    2265 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(0.02018400);</span></a>
+<a name="2266"><span class="lineNum">    2266 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(4.17705400);</span></a>
+<a name="2267"><span class="lineNum">    2267 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(0.98531700);</span></a>
+<a name="2268"><span class="lineNum">    2268 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(-5.04354900);</span></a>
+<a name="2269"><span class="lineNum">    2269 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(2.56123700);</span></a>
+<a name="2270"><span class="lineNum">    2270 </span><span class="lineCov">          8 :   parameter[DG_SC4].push_back(-0.39249300);</span></a>
+<a name="2271"><span class="lineNum">    2271 </span>            : </a>
+<a name="2272"><span class="lineNum">    2272 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(4.23000000);</span></a>
+<a name="2273"><span class="lineNum">    2273 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(0.00061700);</span></a>
+<a name="2274"><span class="lineNum">    2274 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(0.92140100);</span></a>
+<a name="2275"><span class="lineNum">    2275 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(0.08016400);</span></a>
+<a name="2276"><span class="lineNum">    2276 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(-0.39003500);</span></a>
+<a name="2277"><span class="lineNum">    2277 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(0.12406900);</span></a>
+<a name="2278"><span class="lineNum">    2278 </span><span class="lineCov">          8 :   parameter[DG_3TE].push_back(-0.01119200);</span></a>
+<a name="2279"><span class="lineNum">    2279 </span>            : </a>
+<a name="2280"><span class="lineNum">    2280 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(4.23000000);</span></a>
+<a name="2281"><span class="lineNum">    2281 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(0.00064900);</span></a>
+<a name="2282"><span class="lineNum">    2282 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(0.92110500);</span></a>
+<a name="2283"><span class="lineNum">    2283 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(0.08031500);</span></a>
+<a name="2284"><span class="lineNum">    2284 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(-0.38997000);</span></a>
+<a name="2285"><span class="lineNum">    2285 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(0.12401200);</span></a>
+<a name="2286"><span class="lineNum">    2286 </span><span class="lineCov">          8 :   parameter[DG_5TE].push_back(-0.01118100);</span></a>
+<a name="2287"><span class="lineNum">    2287 </span>            : </a>
+<a name="2288"><span class="lineNum">    2288 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(2.87400000);</span></a>
+<a name="2289"><span class="lineNum">    2289 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(0.00182000);</span></a>
+<a name="2290"><span class="lineNum">    2290 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(12.41507000);</span></a>
+<a name="2291"><span class="lineNum">    2291 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(-7.47384800);</span></a>
+<a name="2292"><span class="lineNum">    2292 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(-2.11864700);</span></a>
+<a name="2293"><span class="lineNum">    2293 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(2.50112600);</span></a>
+<a name="2294"><span class="lineNum">    2294 </span><span class="lineCov">          8 :   parameter[DG_TE3].push_back(-0.48652200);</span></a>
+<a name="2295"><span class="lineNum">    2295 </span>            : </a>
+<a name="2296"><span class="lineNum">    2296 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(8.03600000);</span></a>
+<a name="2297"><span class="lineNum">    2297 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(0.00676400);</span></a>
+<a name="2298"><span class="lineNum">    2298 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(4.65989200);</span></a>
+<a name="2299"><span class="lineNum">    2299 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(0.78482500);</span></a>
+<a name="2300"><span class="lineNum">    2300 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(-6.86460600);</span></a>
+<a name="2301"><span class="lineNum">    2301 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(4.11675400);</span></a>
+<a name="2302"><span class="lineNum">    2302 </span><span class="lineCov">          8 :   parameter[DG_TE5].push_back(-0.72249100);</span></a>
+<a name="2303"><span class="lineNum">    2303 </span>            : </a>
+<a name="2304"><span class="lineNum">    2304 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(32.88500000);</span></a>
+<a name="2305"><span class="lineNum">    2305 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(0.08220100);</span></a>
+<a name="2306"><span class="lineNum">    2306 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(-7.33006800);</span></a>
+<a name="2307"><span class="lineNum">    2307 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(2.16636500);</span></a>
+<a name="2308"><span class="lineNum">    2308 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(-3.53465700);</span></a>
+<a name="2309"><span class="lineNum">    2309 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(2.31447600);</span></a>
+<a name="2310"><span class="lineNum">    2310 </span><span class="lineCov">          8 :   parameter[DT_BB1].push_back(-0.39445400);</span></a>
+<a name="2311"><span class="lineNum">    2311 </span>            : </a>
+<a name="2312"><span class="lineNum">    2312 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(3.80600000);</span></a>
+<a name="2313"><span class="lineNum">    2313 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(-0.10723000);</span></a>
+<a name="2314"><span class="lineNum">    2314 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(9.56675000);</span></a>
+<a name="2315"><span class="lineNum">    2315 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(-6.20236100);</span></a>
+<a name="2316"><span class="lineNum">    2316 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(-0.49550400);</span></a>
+<a name="2317"><span class="lineNum">    2317 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(1.14300600);</span></a>
+<a name="2318"><span class="lineNum">    2318 </span><span class="lineCov">          8 :   parameter[DT_BB2].push_back(-0.21420000);</span></a>
+<a name="2319"><span class="lineNum">    2319 </span>            : </a>
+<a name="2320"><span class="lineNum">    2320 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(-1.35600000);</span></a>
+<a name="2321"><span class="lineNum">    2321 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(0.56737900);</span></a>
+<a name="2322"><span class="lineNum">    2322 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(6.76595400);</span></a>
+<a name="2323"><span class="lineNum">    2323 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(4.08976100);</span></a>
+<a name="2324"><span class="lineNum">    2324 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(-9.61512500);</span></a>
+<a name="2325"><span class="lineNum">    2325 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(4.40975100);</span></a>
+<a name="2326"><span class="lineNum">    2326 </span><span class="lineCov">          8 :   parameter[DT_BB3].push_back(-0.64239800);</span></a>
+<a name="2327"><span class="lineNum">    2327 </span>            : </a>
+<a name="2328"><span class="lineNum">    2328 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(5.95100000);</span></a>
+<a name="2329"><span class="lineNum">    2329 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(-0.02926500);</span></a>
+<a name="2330"><span class="lineNum">    2330 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(2.59630300);</span></a>
+<a name="2331"><span class="lineNum">    2331 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(-0.56152200);</span></a>
+<a name="2332"><span class="lineNum">    2332 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(-1.56532600);</span></a>
+<a name="2333"><span class="lineNum">    2333 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(0.89322800);</span></a>
+<a name="2334"><span class="lineNum">    2334 </span><span class="lineCov">          8 :   parameter[DT_SC1].push_back(-0.14142900);</span></a>
+<a name="2335"><span class="lineNum">    2335 </span>            : </a>
+<a name="2336"><span class="lineNum">    2336 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(10.90100000);</span></a>
+<a name="2337"><span class="lineNum">    2337 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(0.02183400);</span></a>
+<a name="2338"><span class="lineNum">    2338 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(0.19463000);</span></a>
+<a name="2339"><span class="lineNum">    2339 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(0.72393000);</span></a>
+<a name="2340"><span class="lineNum">    2340 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(-1.93199500);</span></a>
+<a name="2341"><span class="lineNum">    2341 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(0.96856300);</span></a>
+<a name="2342"><span class="lineNum">    2342 </span><span class="lineCov">          8 :   parameter[DT_SC2].push_back(-0.14512600);</span></a>
+<a name="2343"><span class="lineNum">    2343 </span>            : </a>
+<a name="2344"><span class="lineNum">    2344 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(4.31400000);</span></a>
+<a name="2345"><span class="lineNum">    2345 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(-0.07745600);</span></a>
+<a name="2346"><span class="lineNum">    2346 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(12.49820300);</span></a>
+<a name="2347"><span class="lineNum">    2347 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(-7.64994200);</span></a>
+<a name="2348"><span class="lineNum">    2348 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(-3.00359600);</span></a>
+<a name="2349"><span class="lineNum">    2349 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(3.26263300);</span></a>
+<a name="2350"><span class="lineNum">    2350 </span><span class="lineCov">          8 :   parameter[DT_SC3].push_back(-0.64498600);</span></a>
+<a name="2351"><span class="lineNum">    2351 </span>            : </a>
+<a name="2352"><span class="lineNum">    2352 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(4.23000000);</span></a>
+<a name="2353"><span class="lineNum">    2353 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(0.00062000);</span></a>
+<a name="2354"><span class="lineNum">    2354 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(0.92141100);</span></a>
+<a name="2355"><span class="lineNum">    2355 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(0.08030900);</span></a>
+<a name="2356"><span class="lineNum">    2356 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(-0.39021500);</span></a>
+<a name="2357"><span class="lineNum">    2357 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(0.12414000);</span></a>
+<a name="2358"><span class="lineNum">    2358 </span><span class="lineCov">          8 :   parameter[DT_3TE].push_back(-0.01120100);</span></a>
+<a name="2359"><span class="lineNum">    2359 </span>            : </a>
+<a name="2360"><span class="lineNum">    2360 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(4.23000000);</span></a>
+<a name="2361"><span class="lineNum">    2361 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(0.00063700);</span></a>
+<a name="2362"><span class="lineNum">    2362 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(0.92130800);</span></a>
+<a name="2363"><span class="lineNum">    2363 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(0.08026900);</span></a>
+<a name="2364"><span class="lineNum">    2364 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(-0.39007500);</span></a>
+<a name="2365"><span class="lineNum">    2365 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(0.12406600);</span></a>
+<a name="2366"><span class="lineNum">    2366 </span><span class="lineCov">          8 :   parameter[DT_5TE].push_back(-0.01118800);</span></a>
+<a name="2367"><span class="lineNum">    2367 </span>            : </a>
+<a name="2368"><span class="lineNum">    2368 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(2.87400000);</span></a>
+<a name="2369"><span class="lineNum">    2369 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(-0.00251200);</span></a>
+<a name="2370"><span class="lineNum">    2370 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(12.43576400);</span></a>
+<a name="2371"><span class="lineNum">    2371 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(-7.55343800);</span></a>
+<a name="2372"><span class="lineNum">    2372 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(-2.07363500);</span></a>
+<a name="2373"><span class="lineNum">    2373 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(2.51279300);</span></a>
+<a name="2374"><span class="lineNum">    2374 </span><span class="lineCov">          8 :   parameter[DT_TE3].push_back(-0.49437100);</span></a>
+<a name="2375"><span class="lineNum">    2375 </span>            : </a>
+<a name="2376"><span class="lineNum">    2376 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(8.03600000);</span></a>
+<a name="2377"><span class="lineNum">    2377 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(0.00119900);</span></a>
+<a name="2378"><span class="lineNum">    2378 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(4.91762300);</span></a>
+<a name="2379"><span class="lineNum">    2379 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(0.65637000);</span></a>
+<a name="2380"><span class="lineNum">    2380 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(-7.23392500);</span></a>
+<a name="2381"><span class="lineNum">    2381 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(4.44636600);</span></a>
+<a name="2382"><span class="lineNum">    2382 </span><span class="lineCov">          8 :   parameter[DT_TE5].push_back(-0.79467800);</span></a>
+<a name="2383"><span class="lineNum">    2383 </span>            : </a>
+<a name="2384"><span class="lineNum">    2384 </span><span class="lineCov">          8 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="2385"><span class="lineNum">    2385 </span><span class="lineCov">          8 :   if( moldat ) {</span></a>
+<a name="2386"><span class="lineNum">    2386 </span><span class="lineCov">       8400 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="2387"><span class="lineNum">    2387 </span><span class="lineCov">       8392 :       std::string Aname = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="2388"><span class="lineNum">    2388 </span><span class="lineCov">       8392 :       std::string Rname = moldat-&gt;getResidueName(atoms[i]);</span></a>
+<a name="2389"><span class="lineNum">    2389 </span><span class="lineCov">       8392 :       if(Rname==&quot;ALA&quot;) {</span></a>
+<a name="2390"><span class="lineNum">    2390 </span><span class="lineCov">         72 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2391"><span class="lineNum">    2391 </span><span class="lineCov">         72 :           atoi[i]=ALA_BB;</span></a>
+<a name="2392"><span class="lineNum">    2392 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2393"><span class="lineNum">    2393 </span><span class="lineCov">       8320 :       } else if(Rname==&quot;ARG&quot;) {</span></a>
+<a name="2394"><span class="lineNum">    2394 </span><span class="lineCov">        420 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2395"><span class="lineNum">    2395 </span><span class="lineCov">        140 :           atoi[i]=ARG_BB;</span></a>
+<a name="2396"><span class="lineNum">    2396 </span><span class="lineCov">        280 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2397"><span class="lineNum">    2397 </span><span class="lineCov">        140 :           atoi[i]=ARG_SC1;</span></a>
+<a name="2398"><span class="lineNum">    2398 </span><span class="lineCov">        140 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2399"><span class="lineNum">    2399 </span><span class="lineCov">        140 :           atoi[i]=ARG_SC2;</span></a>
+<a name="2400"><span class="lineNum">    2400 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2401"><span class="lineNum">    2401 </span><span class="lineCov">       7900 :       } else if(Rname==&quot;ASN&quot;) {</span></a>
+<a name="2402"><span class="lineNum">    2402 </span><span class="lineCov">        240 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2403"><span class="lineNum">    2403 </span><span class="lineCov">        120 :           atoi[i]=ASN_BB;</span></a>
+<a name="2404"><span class="lineNum">    2404 </span><span class="lineCov">        120 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2405"><span class="lineNum">    2405 </span><span class="lineCov">        120 :           atoi[i]=ASN_SC1;</span></a>
+<a name="2406"><span class="lineNum">    2406 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2407"><span class="lineNum">    2407 </span><span class="lineCov">       7660 :       } else if(Rname==&quot;ASP&quot;) {</span></a>
+<a name="2408"><span class="lineNum">    2408 </span><span class="lineCov">        368 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2409"><span class="lineNum">    2409 </span><span class="lineCov">        184 :           atoi[i]=ASP_BB;</span></a>
+<a name="2410"><span class="lineNum">    2410 </span><span class="lineCov">        184 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2411"><span class="lineNum">    2411 </span><span class="lineCov">        184 :           atoi[i]=ASP_SC1;</span></a>
+<a name="2412"><span class="lineNum">    2412 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2413"><span class="lineNum">    2413 </span><span class="lineCov">       7292 :       } else if(Rname==&quot;CYS&quot;) {</span></a>
+<a name="2414"><span class="lineNum">    2414 </span><span class="lineCov">         16 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2415"><span class="lineNum">    2415 </span><span class="lineCov">          8 :           atoi[i]=CYS_BB;</span></a>
+<a name="2416"><span class="lineNum">    2416 </span><span class="lineCov">          8 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2417"><span class="lineNum">    2417 </span><span class="lineCov">          8 :           atoi[i]=CYS_SC1;</span></a>
+<a name="2418"><span class="lineNum">    2418 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2419"><span class="lineNum">    2419 </span><span class="lineCov">       7276 :       } else if(Rname==&quot;GLN&quot;) {</span></a>
+<a name="2420"><span class="lineNum">    2420 </span><span class="lineCov">        224 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2421"><span class="lineNum">    2421 </span><span class="lineCov">        112 :           atoi[i]=GLN_BB;</span></a>
+<a name="2422"><span class="lineNum">    2422 </span><span class="lineCov">        112 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2423"><span class="lineNum">    2423 </span><span class="lineCov">        112 :           atoi[i]=GLN_SC1;</span></a>
+<a name="2424"><span class="lineNum">    2424 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2425"><span class="lineNum">    2425 </span><span class="lineCov">       7052 :       } else if(Rname==&quot;GLU&quot;) {</span></a>
+<a name="2426"><span class="lineNum">    2426 </span><span class="lineCov">        480 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2427"><span class="lineNum">    2427 </span><span class="lineCov">        240 :           atoi[i]=GLU_BB;</span></a>
+<a name="2428"><span class="lineNum">    2428 </span><span class="lineCov">        240 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2429"><span class="lineNum">    2429 </span><span class="lineCov">        240 :           atoi[i]=GLU_SC1;</span></a>
+<a name="2430"><span class="lineNum">    2430 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2431"><span class="lineNum">    2431 </span><span class="lineCov">       6572 :       } else if(Rname==&quot;GLY&quot;) {</span></a>
+<a name="2432"><span class="lineNum">    2432 </span><span class="lineCov">        116 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2433"><span class="lineNum">    2433 </span><span class="lineCov">        116 :           atoi[i]=GLY_BB;</span></a>
+<a name="2434"><span class="lineNum">    2434 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2435"><span class="lineNum">    2435 </span><span class="lineCov">       6456 :       } else if(Rname==&quot;HIS&quot;) {</span></a>
+<a name="2436"><span class="lineNum">    2436 </span><span class="lineCov">        576 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2437"><span class="lineNum">    2437 </span><span class="lineCov">        144 :           atoi[i]=HIS_BB;</span></a>
+<a name="2438"><span class="lineNum">    2438 </span><span class="lineCov">        432 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2439"><span class="lineNum">    2439 </span><span class="lineCov">        144 :           atoi[i]=HIS_SC1;</span></a>
+<a name="2440"><span class="lineNum">    2440 </span><span class="lineCov">        288 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2441"><span class="lineNum">    2441 </span><span class="lineCov">        144 :           atoi[i]=HIS_SC2;</span></a>
+<a name="2442"><span class="lineNum">    2442 </span><span class="lineCov">        144 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2443"><span class="lineNum">    2443 </span><span class="lineCov">        144 :           atoi[i]=HIS_SC3;</span></a>
+<a name="2444"><span class="lineNum">    2444 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2445"><span class="lineNum">    2445 </span><span class="lineCov">       5880 :       } else if(Rname==&quot;ILE&quot;) {</span></a>
+<a name="2446"><span class="lineNum">    2446 </span><span class="lineCov">        584 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2447"><span class="lineNum">    2447 </span><span class="lineCov">        292 :           atoi[i]=ILE_BB;</span></a>
+<a name="2448"><span class="lineNum">    2448 </span><span class="lineCov">        292 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2449"><span class="lineNum">    2449 </span><span class="lineCov">        292 :           atoi[i]=ILE_SC1;</span></a>
+<a name="2450"><span class="lineNum">    2450 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2451"><span class="lineNum">    2451 </span><span class="lineCov">       5296 :       } else if(Rname==&quot;LEU&quot;) {</span></a>
+<a name="2452"><span class="lineNum">    2452 </span><span class="lineCov">        448 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2453"><span class="lineNum">    2453 </span><span class="lineCov">        224 :           atoi[i]=LEU_BB;</span></a>
+<a name="2454"><span class="lineNum">    2454 </span><span class="lineCov">        224 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2455"><span class="lineNum">    2455 </span><span class="lineCov">        224 :           atoi[i]=LEU_SC1;</span></a>
+<a name="2456"><span class="lineNum">    2456 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2457"><span class="lineNum">    2457 </span><span class="lineCov">       4848 :       } else if(Rname==&quot;LYS&quot;) {</span></a>
+<a name="2458"><span class="lineNum">    2458 </span><span class="lineCov">        792 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2459"><span class="lineNum">    2459 </span><span class="lineCov">        264 :           atoi[i]=LYS_BB;</span></a>
+<a name="2460"><span class="lineNum">    2460 </span><span class="lineCov">        528 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2461"><span class="lineNum">    2461 </span><span class="lineCov">        264 :           atoi[i]=LYS_SC1;</span></a>
+<a name="2462"><span class="lineNum">    2462 </span><span class="lineCov">        264 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2463"><span class="lineNum">    2463 </span><span class="lineCov">        264 :           atoi[i]=LYS_SC2;</span></a>
+<a name="2464"><span class="lineNum">    2464 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2465"><span class="lineNum">    2465 </span><span class="lineCov">       4056 :       } else if(Rname==&quot;MET&quot;) {</span></a>
+<a name="2466"><span class="lineNum">    2466 </span><span class="lineCov">         80 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2467"><span class="lineNum">    2467 </span><span class="lineCov">         40 :           atoi[i]=MET_BB;</span></a>
+<a name="2468"><span class="lineNum">    2468 </span><span class="lineCov">         40 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2469"><span class="lineNum">    2469 </span><span class="lineCov">         40 :           atoi[i]=MET_SC1;</span></a>
+<a name="2470"><span class="lineNum">    2470 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2471"><span class="lineNum">    2471 </span><span class="lineCov">       3976 :       } else if(Rname==&quot;PHE&quot;) {</span></a>
+<a name="2472"><span class="lineNum">    2472 </span><span class="lineCov">        512 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2473"><span class="lineNum">    2473 </span><span class="lineCov">        128 :           atoi[i]=PHE_BB;</span></a>
+<a name="2474"><span class="lineNum">    2474 </span><span class="lineCov">        384 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2475"><span class="lineNum">    2475 </span><span class="lineCov">        128 :           atoi[i]=PHE_SC1;</span></a>
+<a name="2476"><span class="lineNum">    2476 </span><span class="lineCov">        256 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2477"><span class="lineNum">    2477 </span><span class="lineCov">        128 :           atoi[i]=PHE_SC2;</span></a>
+<a name="2478"><span class="lineNum">    2478 </span><span class="lineCov">        128 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2479"><span class="lineNum">    2479 </span><span class="lineCov">        128 :           atoi[i]=PHE_SC3;</span></a>
+<a name="2480"><span class="lineNum">    2480 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2481"><span class="lineNum">    2481 </span><span class="lineCov">       3464 :       } else if(Rname==&quot;PRO&quot;) {</span></a>
+<a name="2482"><span class="lineNum">    2482 </span><span class="lineCov">        128 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2483"><span class="lineNum">    2483 </span><span class="lineCov">         64 :           atoi[i]=PRO_BB;</span></a>
+<a name="2484"><span class="lineNum">    2484 </span><span class="lineCov">         64 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2485"><span class="lineNum">    2485 </span><span class="lineCov">         64 :           atoi[i]=PRO_SC1;</span></a>
+<a name="2486"><span class="lineNum">    2486 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2487"><span class="lineNum">    2487 </span><span class="lineCov">       3336 :       } else if(Rname==&quot;SER&quot;) {</span></a>
+<a name="2488"><span class="lineNum">    2488 </span><span class="lineCov">        248 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2489"><span class="lineNum">    2489 </span><span class="lineCov">        124 :           atoi[i]=SER_BB;</span></a>
+<a name="2490"><span class="lineNum">    2490 </span><span class="lineCov">        124 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2491"><span class="lineNum">    2491 </span><span class="lineCov">        124 :           atoi[i]=SER_SC1;</span></a>
+<a name="2492"><span class="lineNum">    2492 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2493"><span class="lineNum">    2493 </span><span class="lineCov">       3088 :       } else if(Rname==&quot;THR&quot;) {</span></a>
+<a name="2494"><span class="lineNum">    2494 </span><span class="lineCov">        288 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2495"><span class="lineNum">    2495 </span><span class="lineCov">        144 :           atoi[i]=THR_BB;</span></a>
+<a name="2496"><span class="lineNum">    2496 </span><span class="lineCov">        144 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2497"><span class="lineNum">    2497 </span><span class="lineCov">        144 :           atoi[i]=THR_SC1;</span></a>
+<a name="2498"><span class="lineNum">    2498 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2499"><span class="lineNum">    2499 </span><span class="lineCov">       2800 :       } else if(Rname==&quot;TRP&quot;) {</span></a>
+<a name="2500"><span class="lineNum">    2500 </span><span class="lineNoCov">          0 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2501"><span class="lineNum">    2501 </span><span class="lineNoCov">          0 :           atoi[i]=TRP_BB;</span></a>
+<a name="2502"><span class="lineNum">    2502 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2503"><span class="lineNum">    2503 </span><span class="lineNoCov">          0 :           atoi[i]=TRP_SC1;</span></a>
+<a name="2504"><span class="lineNum">    2504 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2505"><span class="lineNum">    2505 </span><span class="lineNoCov">          0 :           atoi[i]=TRP_SC2;</span></a>
+<a name="2506"><span class="lineNum">    2506 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2507"><span class="lineNum">    2507 </span><span class="lineNoCov">          0 :           atoi[i]=TRP_SC3;</span></a>
+<a name="2508"><span class="lineNum">    2508 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC4&quot;) {</span></a>
+<a name="2509"><span class="lineNum">    2509 </span><span class="lineNoCov">          0 :           atoi[i]=TRP_SC4;</span></a>
+<a name="2510"><span class="lineNum">    2510 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2511"><span class="lineNum">    2511 </span><span class="lineCov">       2800 :       } else if(Rname==&quot;TYR&quot;) {</span></a>
+<a name="2512"><span class="lineNum">    2512 </span><span class="lineCov">        544 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2513"><span class="lineNum">    2513 </span><span class="lineCov">        136 :           atoi[i]=TYR_BB;</span></a>
+<a name="2514"><span class="lineNum">    2514 </span><span class="lineCov">        408 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2515"><span class="lineNum">    2515 </span><span class="lineCov">        136 :           atoi[i]=TYR_SC1;</span></a>
+<a name="2516"><span class="lineNum">    2516 </span><span class="lineCov">        272 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2517"><span class="lineNum">    2517 </span><span class="lineCov">        136 :           atoi[i]=TYR_SC2;</span></a>
+<a name="2518"><span class="lineNum">    2518 </span><span class="lineCov">        136 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2519"><span class="lineNum">    2519 </span><span class="lineCov">        136 :           atoi[i]=TYR_SC3;</span></a>
+<a name="2520"><span class="lineNum">    2520 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2521"><span class="lineNum">    2521 </span><span class="lineCov">       2256 :       } else if(Rname==&quot;VAL&quot;) {</span></a>
+<a name="2522"><span class="lineNum">    2522 </span><span class="lineCov">        288 :         if(Aname==&quot;BB&quot;) {</span></a>
+<a name="2523"><span class="lineNum">    2523 </span><span class="lineCov">        144 :           atoi[i]=VAL_BB;</span></a>
+<a name="2524"><span class="lineNum">    2524 </span><span class="lineCov">        144 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2525"><span class="lineNum">    2525 </span><span class="lineCov">        144 :           atoi[i]=VAL_SC1;</span></a>
+<a name="2526"><span class="lineNum">    2526 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2527"><span class="lineNum">    2527 </span><span class="lineCov">       1968 :       } else if(Rname==&quot;  A&quot;) {</span></a>
+<a name="2528"><span class="lineNum">    2528 </span><span class="lineNoCov">          0 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2529"><span class="lineNum">    2529 </span><span class="lineNoCov">          0 :           atoi[i]=A_BB1;</span></a>
+<a name="2530"><span class="lineNum">    2530 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2531"><span class="lineNum">    2531 </span><span class="lineNoCov">          0 :           atoi[i]=A_BB2;</span></a>
+<a name="2532"><span class="lineNum">    2532 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2533"><span class="lineNum">    2533 </span><span class="lineNoCov">          0 :           atoi[i]=A_BB3;</span></a>
+<a name="2534"><span class="lineNum">    2534 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2535"><span class="lineNum">    2535 </span><span class="lineNoCov">          0 :           atoi[i]=A_SC1;</span></a>
+<a name="2536"><span class="lineNum">    2536 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2537"><span class="lineNum">    2537 </span><span class="lineNoCov">          0 :           atoi[i]=A_SC2;</span></a>
+<a name="2538"><span class="lineNum">    2538 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2539"><span class="lineNum">    2539 </span><span class="lineNoCov">          0 :           atoi[i]=A_SC3;</span></a>
+<a name="2540"><span class="lineNum">    2540 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC4&quot;) {</span></a>
+<a name="2541"><span class="lineNum">    2541 </span><span class="lineNoCov">          0 :           atoi[i]=A_SC4;</span></a>
+<a name="2542"><span class="lineNum">    2542 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2543"><span class="lineNum">    2543 </span><span class="lineNoCov">          0 :           atoi[i]=A_3TE;</span></a>
+<a name="2544"><span class="lineNum">    2544 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2545"><span class="lineNum">    2545 </span><span class="lineNoCov">          0 :           atoi[i]=A_5TE;</span></a>
+<a name="2546"><span class="lineNum">    2546 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2547"><span class="lineNum">    2547 </span><span class="lineNoCov">          0 :           atoi[i]=A_TE3;</span></a>
+<a name="2548"><span class="lineNum">    2548 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2549"><span class="lineNum">    2549 </span><span class="lineNoCov">          0 :           atoi[i]=A_TE5;</span></a>
+<a name="2550"><span class="lineNum">    2550 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2551"><span class="lineNum">    2551 </span><span class="lineCov">       1968 :       } else if(Rname==&quot;  C&quot;) {</span></a>
+<a name="2552"><span class="lineNum">    2552 </span><span class="lineNoCov">          0 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2553"><span class="lineNum">    2553 </span><span class="lineNoCov">          0 :           atoi[i]=C_BB1;</span></a>
+<a name="2554"><span class="lineNum">    2554 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2555"><span class="lineNum">    2555 </span><span class="lineNoCov">          0 :           atoi[i]=C_BB2;</span></a>
+<a name="2556"><span class="lineNum">    2556 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2557"><span class="lineNum">    2557 </span><span class="lineNoCov">          0 :           atoi[i]=C_BB3;</span></a>
+<a name="2558"><span class="lineNum">    2558 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2559"><span class="lineNum">    2559 </span><span class="lineNoCov">          0 :           atoi[i]=C_SC1;</span></a>
+<a name="2560"><span class="lineNum">    2560 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2561"><span class="lineNum">    2561 </span><span class="lineNoCov">          0 :           atoi[i]=C_SC2;</span></a>
+<a name="2562"><span class="lineNum">    2562 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2563"><span class="lineNum">    2563 </span><span class="lineNoCov">          0 :           atoi[i]=C_SC3;</span></a>
+<a name="2564"><span class="lineNum">    2564 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2565"><span class="lineNum">    2565 </span><span class="lineNoCov">          0 :           atoi[i]=C_3TE;</span></a>
+<a name="2566"><span class="lineNum">    2566 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2567"><span class="lineNum">    2567 </span><span class="lineNoCov">          0 :           atoi[i]=C_5TE;</span></a>
+<a name="2568"><span class="lineNum">    2568 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2569"><span class="lineNum">    2569 </span><span class="lineNoCov">          0 :           atoi[i]=C_TE3;</span></a>
+<a name="2570"><span class="lineNum">    2570 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2571"><span class="lineNum">    2571 </span><span class="lineNoCov">          0 :           atoi[i]=C_TE5;</span></a>
+<a name="2572"><span class="lineNum">    2572 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2573"><span class="lineNum">    2573 </span><span class="lineCov">       1968 :       } else if(Rname==&quot;  G&quot;) {</span></a>
+<a name="2574"><span class="lineNum">    2574 </span><span class="lineNoCov">          0 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2575"><span class="lineNum">    2575 </span><span class="lineNoCov">          0 :           atoi[i]=G_BB1;</span></a>
+<a name="2576"><span class="lineNum">    2576 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2577"><span class="lineNum">    2577 </span><span class="lineNoCov">          0 :           atoi[i]=G_BB2;</span></a>
+<a name="2578"><span class="lineNum">    2578 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2579"><span class="lineNum">    2579 </span><span class="lineNoCov">          0 :           atoi[i]=G_BB3;</span></a>
+<a name="2580"><span class="lineNum">    2580 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2581"><span class="lineNum">    2581 </span><span class="lineNoCov">          0 :           atoi[i]=G_SC1;</span></a>
+<a name="2582"><span class="lineNum">    2582 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2583"><span class="lineNum">    2583 </span><span class="lineNoCov">          0 :           atoi[i]=G_SC2;</span></a>
+<a name="2584"><span class="lineNum">    2584 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2585"><span class="lineNum">    2585 </span><span class="lineNoCov">          0 :           atoi[i]=G_SC3;</span></a>
+<a name="2586"><span class="lineNum">    2586 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC4&quot;) {</span></a>
+<a name="2587"><span class="lineNum">    2587 </span><span class="lineNoCov">          0 :           atoi[i]=G_SC4;</span></a>
+<a name="2588"><span class="lineNum">    2588 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2589"><span class="lineNum">    2589 </span><span class="lineNoCov">          0 :           atoi[i]=G_3TE;</span></a>
+<a name="2590"><span class="lineNum">    2590 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2591"><span class="lineNum">    2591 </span><span class="lineNoCov">          0 :           atoi[i]=G_5TE;</span></a>
+<a name="2592"><span class="lineNum">    2592 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2593"><span class="lineNum">    2593 </span><span class="lineNoCov">          0 :           atoi[i]=G_TE3;</span></a>
+<a name="2594"><span class="lineNum">    2594 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2595"><span class="lineNum">    2595 </span><span class="lineNoCov">          0 :           atoi[i]=G_TE5;</span></a>
+<a name="2596"><span class="lineNum">    2596 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2597"><span class="lineNum">    2597 </span><span class="lineCov">       1968 :       } else if(Rname==&quot;  U&quot;) {</span></a>
+<a name="2598"><span class="lineNum">    2598 </span><span class="lineNoCov">          0 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2599"><span class="lineNum">    2599 </span><span class="lineNoCov">          0 :           atoi[i]=U_BB1;</span></a>
+<a name="2600"><span class="lineNum">    2600 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2601"><span class="lineNum">    2601 </span><span class="lineNoCov">          0 :           atoi[i]=U_BB2;</span></a>
+<a name="2602"><span class="lineNum">    2602 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2603"><span class="lineNum">    2603 </span><span class="lineNoCov">          0 :           atoi[i]=U_BB3;</span></a>
+<a name="2604"><span class="lineNum">    2604 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2605"><span class="lineNum">    2605 </span><span class="lineNoCov">          0 :           atoi[i]=U_SC1;</span></a>
+<a name="2606"><span class="lineNum">    2606 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2607"><span class="lineNum">    2607 </span><span class="lineNoCov">          0 :           atoi[i]=U_SC2;</span></a>
+<a name="2608"><span class="lineNum">    2608 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2609"><span class="lineNum">    2609 </span><span class="lineNoCov">          0 :           atoi[i]=U_SC3;</span></a>
+<a name="2610"><span class="lineNum">    2610 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2611"><span class="lineNum">    2611 </span><span class="lineNoCov">          0 :           atoi[i]=U_3TE;</span></a>
+<a name="2612"><span class="lineNum">    2612 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2613"><span class="lineNum">    2613 </span><span class="lineNoCov">          0 :           atoi[i]=U_5TE;</span></a>
+<a name="2614"><span class="lineNum">    2614 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2615"><span class="lineNum">    2615 </span><span class="lineNoCov">          0 :           atoi[i]=U_TE3;</span></a>
+<a name="2616"><span class="lineNum">    2616 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2617"><span class="lineNum">    2617 </span><span class="lineNoCov">          0 :           atoi[i]=U_TE5;</span></a>
+<a name="2618"><span class="lineNum">    2618 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2619"><span class="lineNum">    2619 </span><span class="lineCov">       1968 :       } else if(Rname==&quot; DA&quot;) {</span></a>
+<a name="2620"><span class="lineNum">    2620 </span><span class="lineCov">        696 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2621"><span class="lineNum">    2621 </span><span class="lineCov">         96 :           atoi[i]=DA_BB1;</span></a>
+<a name="2622"><span class="lineNum">    2622 </span><span class="lineCov">        600 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2623"><span class="lineNum">    2623 </span><span class="lineCov">         96 :           atoi[i]=DA_BB2;</span></a>
+<a name="2624"><span class="lineNum">    2624 </span><span class="lineCov">        504 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2625"><span class="lineNum">    2625 </span><span class="lineCov">         96 :           atoi[i]=DA_BB3;</span></a>
+<a name="2626"><span class="lineNum">    2626 </span><span class="lineCov">        408 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2627"><span class="lineNum">    2627 </span><span class="lineCov">        100 :           atoi[i]=DA_SC1;</span></a>
+<a name="2628"><span class="lineNum">    2628 </span><span class="lineCov">        308 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2629"><span class="lineNum">    2629 </span><span class="lineCov">        100 :           atoi[i]=DA_SC2;</span></a>
+<a name="2630"><span class="lineNum">    2630 </span><span class="lineCov">        208 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2631"><span class="lineNum">    2631 </span><span class="lineCov">        100 :           atoi[i]=DA_SC3;</span></a>
+<a name="2632"><span class="lineNum">    2632 </span><span class="lineCov">        108 :         } else if(Aname==&quot;SC4&quot;) {</span></a>
+<a name="2633"><span class="lineNum">    2633 </span><span class="lineCov">        100 :           atoi[i]=DA_SC4;</span></a>
+<a name="2634"><span class="lineNum">    2634 </span><span class="lineCov">          8 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2635"><span class="lineNum">    2635 </span><span class="lineNoCov">          0 :           atoi[i]=DA_3TE;</span></a>
+<a name="2636"><span class="lineNum">    2636 </span><span class="lineCov">          8 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2637"><span class="lineNum">    2637 </span><span class="lineNoCov">          0 :           atoi[i]=DA_5TE;</span></a>
+<a name="2638"><span class="lineNum">    2638 </span><span class="lineCov">          8 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2639"><span class="lineNum">    2639 </span><span class="lineCov">          4 :           atoi[i]=DA_TE3;</span></a>
+<a name="2640"><span class="lineNum">    2640 </span><span class="lineCov">          4 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2641"><span class="lineNum">    2641 </span><span class="lineCov">          4 :           atoi[i]=DA_TE5;</span></a>
+<a name="2642"><span class="lineNum">    2642 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2643"><span class="lineNum">    2643 </span><span class="lineCov">       1272 :       } else if(Rname==&quot; DC&quot;) {</span></a>
+<a name="2644"><span class="lineNum">    2644 </span><span class="lineCov">        312 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2645"><span class="lineNum">    2645 </span><span class="lineCov">         52 :           atoi[i]=DC_BB1;</span></a>
+<a name="2646"><span class="lineNum">    2646 </span><span class="lineCov">        260 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2647"><span class="lineNum">    2647 </span><span class="lineCov">         52 :           atoi[i]=DC_BB2;</span></a>
+<a name="2648"><span class="lineNum">    2648 </span><span class="lineCov">        208 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2649"><span class="lineNum">    2649 </span><span class="lineCov">         52 :           atoi[i]=DC_BB3;</span></a>
+<a name="2650"><span class="lineNum">    2650 </span><span class="lineCov">        156 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2651"><span class="lineNum">    2651 </span><span class="lineCov">         52 :           atoi[i]=DC_SC1;</span></a>
+<a name="2652"><span class="lineNum">    2652 </span><span class="lineCov">        104 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2653"><span class="lineNum">    2653 </span><span class="lineCov">         52 :           atoi[i]=DC_SC2;</span></a>
+<a name="2654"><span class="lineNum">    2654 </span><span class="lineCov">         52 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2655"><span class="lineNum">    2655 </span><span class="lineCov">         52 :           atoi[i]=DC_SC3;</span></a>
+<a name="2656"><span class="lineNum">    2656 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2657"><span class="lineNum">    2657 </span><span class="lineNoCov">          0 :           atoi[i]=DC_3TE;</span></a>
+<a name="2658"><span class="lineNum">    2658 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2659"><span class="lineNum">    2659 </span><span class="lineNoCov">          0 :           atoi[i]=DC_5TE;</span></a>
+<a name="2660"><span class="lineNum">    2660 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2661"><span class="lineNum">    2661 </span><span class="lineNoCov">          0 :           atoi[i]=DC_TE3;</span></a>
+<a name="2662"><span class="lineNum">    2662 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2663"><span class="lineNum">    2663 </span><span class="lineNoCov">          0 :           atoi[i]=DC_TE5;</span></a>
+<a name="2664"><span class="lineNum">    2664 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2665"><span class="lineNum">    2665 </span><span class="lineCov">        960 :       } else if(Rname==&quot; DG&quot;) {</span></a>
+<a name="2666"><span class="lineNum">    2666 </span><span class="lineCov">        364 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2667"><span class="lineNum">    2667 </span><span class="lineCov">         52 :           atoi[i]=DG_BB1;</span></a>
+<a name="2668"><span class="lineNum">    2668 </span><span class="lineCov">        312 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2669"><span class="lineNum">    2669 </span><span class="lineCov">         52 :           atoi[i]=DG_BB2;</span></a>
+<a name="2670"><span class="lineNum">    2670 </span><span class="lineCov">        260 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2671"><span class="lineNum">    2671 </span><span class="lineCov">         52 :           atoi[i]=DG_BB3;</span></a>
+<a name="2672"><span class="lineNum">    2672 </span><span class="lineCov">        208 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2673"><span class="lineNum">    2673 </span><span class="lineCov">         52 :           atoi[i]=DG_SC1;</span></a>
+<a name="2674"><span class="lineNum">    2674 </span><span class="lineCov">        156 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2675"><span class="lineNum">    2675 </span><span class="lineCov">         52 :           atoi[i]=DG_SC2;</span></a>
+<a name="2676"><span class="lineNum">    2676 </span><span class="lineCov">        104 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2677"><span class="lineNum">    2677 </span><span class="lineCov">         52 :           atoi[i]=DG_SC3;</span></a>
+<a name="2678"><span class="lineNum">    2678 </span><span class="lineCov">         52 :         } else if(Aname==&quot;SC4&quot;) {</span></a>
+<a name="2679"><span class="lineNum">    2679 </span><span class="lineCov">         52 :           atoi[i]=DG_SC4;</span></a>
+<a name="2680"><span class="lineNum">    2680 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2681"><span class="lineNum">    2681 </span><span class="lineNoCov">          0 :           atoi[i]=DG_3TE;</span></a>
+<a name="2682"><span class="lineNum">    2682 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2683"><span class="lineNum">    2683 </span><span class="lineNoCov">          0 :           atoi[i]=DG_5TE;</span></a>
+<a name="2684"><span class="lineNum">    2684 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2685"><span class="lineNum">    2685 </span><span class="lineNoCov">          0 :           atoi[i]=DG_TE3;</span></a>
+<a name="2686"><span class="lineNum">    2686 </span><span class="lineNoCov">          0 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2687"><span class="lineNum">    2687 </span><span class="lineNoCov">          0 :           atoi[i]=DG_TE5;</span></a>
+<a name="2688"><span class="lineNum">    2688 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2689"><span class="lineNum">    2689 </span><span class="lineCov">        596 :       } else if(Rname==&quot; DT&quot;) {</span></a>
+<a name="2690"><span class="lineNum">    2690 </span><span class="lineCov">        596 :         if(Aname==&quot;BB1&quot;) {</span></a>
+<a name="2691"><span class="lineNum">    2691 </span><span class="lineCov">         96 :           atoi[i]=DT_BB1;</span></a>
+<a name="2692"><span class="lineNum">    2692 </span><span class="lineCov">        500 :         } else if(Aname==&quot;BB2&quot;) {</span></a>
+<a name="2693"><span class="lineNum">    2693 </span><span class="lineCov">         96 :           atoi[i]=DT_BB2;</span></a>
+<a name="2694"><span class="lineNum">    2694 </span><span class="lineCov">        404 :         } else if(Aname==&quot;BB3&quot;) {</span></a>
+<a name="2695"><span class="lineNum">    2695 </span><span class="lineCov">         96 :           atoi[i]=DT_BB3;</span></a>
+<a name="2696"><span class="lineNum">    2696 </span><span class="lineCov">        308 :         } else if(Aname==&quot;SC1&quot;) {</span></a>
+<a name="2697"><span class="lineNum">    2697 </span><span class="lineCov">        100 :           atoi[i]=DT_SC1;</span></a>
+<a name="2698"><span class="lineNum">    2698 </span><span class="lineCov">        208 :         } else if(Aname==&quot;SC2&quot;) {</span></a>
+<a name="2699"><span class="lineNum">    2699 </span><span class="lineCov">        100 :           atoi[i]=DT_SC2;</span></a>
+<a name="2700"><span class="lineNum">    2700 </span><span class="lineCov">        108 :         } else if(Aname==&quot;SC3&quot;) {</span></a>
+<a name="2701"><span class="lineNum">    2701 </span><span class="lineCov">        100 :           atoi[i]=DT_SC3;</span></a>
+<a name="2702"><span class="lineNum">    2702 </span><span class="lineCov">          8 :         } else if(Aname==&quot;3TE&quot;) {</span></a>
+<a name="2703"><span class="lineNum">    2703 </span><span class="lineNoCov">          0 :           atoi[i]=DT_3TE;</span></a>
+<a name="2704"><span class="lineNum">    2704 </span><span class="lineCov">          8 :         } else if(Aname==&quot;5TE&quot;) {</span></a>
+<a name="2705"><span class="lineNum">    2705 </span><span class="lineNoCov">          0 :           atoi[i]=DT_5TE;</span></a>
+<a name="2706"><span class="lineNum">    2706 </span><span class="lineCov">          8 :         } else if(Aname==&quot;TE3&quot;) {</span></a>
+<a name="2707"><span class="lineNum">    2707 </span><span class="lineCov">          4 :           atoi[i]=DT_TE3;</span></a>
+<a name="2708"><span class="lineNum">    2708 </span><span class="lineCov">          4 :         } else if(Aname==&quot;TE5&quot;) {</span></a>
+<a name="2709"><span class="lineNum">    2709 </span><span class="lineCov">          4 :           atoi[i]=DT_TE5;</span></a>
+<a name="2710"><span class="lineNum">    2710 </span><span class="lineNoCov">          0 :         } else error(&quot;Atom name not known: &quot;+Aname);</span></a>
+<a name="2711"><span class="lineNum">    2711 </span><span class="lineNoCov">          0 :       } else error(&quot;Residue not known: &quot;+Rname);</span></a>
+<a name="2712"><span class="lineNum">    2712 </span>            :     }</a>
+<a name="2713"><span class="lineNum">    2713 </span>            :   } else {</a>
+<a name="2714"><span class="lineNum">    2714 </span><span class="lineNoCov">          0 :     error(&quot;MOLINFO DATA not found\n&quot;);</span></a>
+<a name="2715"><span class="lineNum">    2715 </span>            :   }</a>
+<a name="2716"><span class="lineNum">    2716 </span><span class="lineCov">          8 : }</span></a>
+<a name="2717"><span class="lineNum">    2717 </span>            : </a>
+<a name="2718"><span class="lineNum">    2718 </span><span class="lineCov">          6 : void SAXS::getOnebeadparam(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_vac, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_mix, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_solv, std::vector&lt;unsigned&gt; residue_atom)</span></a>
+<a name="2719"><span class="lineNum">    2719 </span>            : {</a>
+<a name="2720"><span class="lineNum">    2720 </span>            : </a>
+<a name="2721"><span class="lineNum">    2721 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(60737.60249988003);</span></a>
+<a name="2722"><span class="lineNum">    2722 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(-77.75716755173752);</span></a>
+<a name="2723"><span class="lineNum">    2723 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(-205962.98557711052);</span></a>
+<a name="2724"><span class="lineNum">    2724 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(-62013.46984155453);</span></a>
+<a name="2725"><span class="lineNum">    2725 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(680710.7592231638);</span></a>
+<a name="2726"><span class="lineNum">    2726 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(-681336.8777362367);</span></a>
+<a name="2727"><span class="lineNum">    2727 </span><span class="lineCov">          6 :   parameter_solv[TRP].push_back(211473.65530642506);</span></a>
+<a name="2728"><span class="lineNum">    2728 </span>            : </a>
+<a name="2729"><span class="lineNum">    2729 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(46250.80359987982);</span></a>
+<a name="2730"><span class="lineNum">    2730 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(-45.8287864681578);</span></a>
+<a name="2731"><span class="lineNum">    2731 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(-143872.91752817619);</span></a>
+<a name="2732"><span class="lineNum">    2732 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(-39049.68736409533);</span></a>
+<a name="2733"><span class="lineNum">    2733 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(441321.71874090104);</span></a>
+<a name="2734"><span class="lineNum">    2734 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(-434478.0972346327);</span></a>
+<a name="2735"><span class="lineNum">    2735 </span><span class="lineCov">          6 :   parameter_solv[TYR].push_back(133179.3694641212);</span></a>
+<a name="2736"><span class="lineNum">    2736 </span>            : </a>
+<a name="2737"><span class="lineNum">    2737 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(42407.164900118914);</span></a>
+<a name="2738"><span class="lineNum">    2738 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(-159.1980754191431);</span></a>
+<a name="2739"><span class="lineNum">    2739 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(-123847.86192757386);</span></a>
+<a name="2740"><span class="lineNum">    2740 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(-41797.69041575073);</span></a>
+<a name="2741"><span class="lineNum">    2741 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(380283.7035277073);</span></a>
+<a name="2742"><span class="lineNum">    2742 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(-361432.67247521743);</span></a>
+<a name="2743"><span class="lineNum">    2743 </span><span class="lineCov">          6 :   parameter_solv[PHE].push_back(107750.64978068044);</span></a>
+<a name="2744"><span class="lineNum">    2744 </span>            : </a>
+<a name="2745"><span class="lineNum">    2745 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(24473.47360011923);</span></a>
+<a name="2746"><span class="lineNum">    2746 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(-111.64156672747428);</span></a>
+<a name="2747"><span class="lineNum">    2747 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(-65826.16993707925);</span></a>
+<a name="2748"><span class="lineNum">    2748 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(-23305.91329798928);</span></a>
+<a name="2749"><span class="lineNum">    2749 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(194795.11911635034);</span></a>
+<a name="2750"><span class="lineNum">    2750 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(-180454.49458095312);</span></a>
+<a name="2751"><span class="lineNum">    2751 </span><span class="lineCov">          6 :   parameter_solv[HIP].push_back(52699.374196745615);</span></a>
+<a name="2752"><span class="lineNum">    2752 </span>            : </a>
+<a name="2753"><span class="lineNum">    2753 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(34106.70239988039);</span></a>
+<a name="2754"><span class="lineNum">    2754 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(152.7472727640246);</span></a>
+<a name="2755"><span class="lineNum">    2755 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(-117086.49392248681);</span></a>
+<a name="2756"><span class="lineNum">    2756 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(-19664.229479267167);</span></a>
+<a name="2757"><span class="lineNum">    2757 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(364454.0909203641);</span></a>
+<a name="2758"><span class="lineNum">    2758 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(-382075.8018312776);</span></a>
+<a name="2759"><span class="lineNum">    2759 </span><span class="lineCov">          6 :   parameter_solv[ARG].push_back(122775.75036605193);</span></a>
+<a name="2760"><span class="lineNum">    2760 </span>            : </a>
+<a name="2761"><span class="lineNum">    2761 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(32292.090000118922);</span></a>
+<a name="2762"><span class="lineNum">    2762 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(-111.97371180593888);</span></a>
+<a name="2763"><span class="lineNum">    2763 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(-91953.10997619898);</span></a>
+<a name="2764"><span class="lineNum">    2764 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(-30690.807047993283);</span></a>
+<a name="2765"><span class="lineNum">    2765 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(282092.40760143084);</span></a>
+<a name="2766"><span class="lineNum">    2766 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(-269503.2592457489);</span></a>
+<a name="2767"><span class="lineNum">    2767 </span><span class="lineCov">          6 :   parameter_solv[LYS].push_back(80777.81552915688);</span></a>
+<a name="2768"><span class="lineNum">    2768 </span>            : </a>
+<a name="2769"><span class="lineNum">    2769 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(11352.902500119093);</span></a>
+<a name="2770"><span class="lineNum">    2770 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(-45.5226331859686);</span></a>
+<a name="2771"><span class="lineNum">    2771 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(-20925.085562607524);</span></a>
+<a name="2772"><span class="lineNum">    2772 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(-5662.685408989286);</span></a>
+<a name="2773"><span class="lineNum">    2773 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(38559.10376731146);</span></a>
+<a name="2774"><span class="lineNum">    2774 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(-27885.23426006181);</span></a>
+<a name="2775"><span class="lineNum">    2775 </span><span class="lineCov">          6 :   parameter_solv[CYS].push_back(6280.15058191397);</span></a>
+<a name="2776"><span class="lineNum">    2776 </span>            : </a>
+<a name="2777"><span class="lineNum">    2777 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(13511.73760011933);</span></a>
+<a name="2778"><span class="lineNum">    2778 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(-59.929111107656595);</span></a>
+<a name="2779"><span class="lineNum">    2779 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(-25849.869639655575);</span></a>
+<a name="2780"><span class="lineNum">    2780 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(-7541.669448872824);</span></a>
+<a name="2781"><span class="lineNum">    2781 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(50760.92045144903);</span></a>
+<a name="2782"><span class="lineNum">    2782 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(-37677.87583269734);</span></a>
+<a name="2783"><span class="lineNum">    2783 </span><span class="lineCov">          6 :   parameter_solv[ASP].push_back(8745.7056219399);</span></a>
+<a name="2784"><span class="lineNum">    2784 </span>            : </a>
+<a name="2785"><span class="lineNum">    2785 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(20443.280400119456);</span></a>
+<a name="2786"><span class="lineNum">    2786 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(-113.77561814283207);</span></a>
+<a name="2787"><span class="lineNum">    2787 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(-45587.79314626863);</span></a>
+<a name="2788"><span class="lineNum">    2788 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(-16187.556837331254);</span></a>
+<a name="2789"><span class="lineNum">    2789 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(112609.65830609271);</span></a>
+<a name="2790"><span class="lineNum">    2790 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(-93362.05323205091);</span></a>
+<a name="2791"><span class="lineNum">    2791 </span><span class="lineCov">          6 :   parameter_solv[GLU].push_back(24519.557866124724);</span></a>
+<a name="2792"><span class="lineNum">    2792 </span>            : </a>
+<a name="2793"><span class="lineNum">    2793 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(27858.948100119596);</span></a>
+<a name="2794"><span class="lineNum">    2794 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(-159.27355145839834);</span></a>
+<a name="2795"><span class="lineNum">    2795 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(-61571.43463039565);</span></a>
+<a name="2796"><span class="lineNum">    2796 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(-21324.879474559468);</span></a>
+<a name="2797"><span class="lineNum">    2797 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(144070.7572894681);</span></a>
+<a name="2798"><span class="lineNum">    2798 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(-115021.81959095894);</span></a>
+<a name="2799"><span class="lineNum">    2799 </span><span class="lineCov">          6 :   parameter_solv[ILE].push_back(28939.085108838968);</span></a>
+<a name="2800"><span class="lineNum">    2800 </span>            : </a>
+<a name="2801"><span class="lineNum">    2801 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(27858.948100119596);</span></a>
+<a name="2802"><span class="lineNum">    2802 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(-165.61892007509647);</span></a>
+<a name="2803"><span class="lineNum">    2803 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(-62564.568746500125);</span></a>
+<a name="2804"><span class="lineNum">    2804 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(-22465.332149768525);</span></a>
+<a name="2805"><span class="lineNum">    2805 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(151616.79489291538);</span></a>
+<a name="2806"><span class="lineNum">    2806 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(-122905.6119395393);</span></a>
+<a name="2807"><span class="lineNum">    2807 </span><span class="lineCov">          6 :   parameter_solv[LEU].push_back(31436.664377885514);</span></a>
+<a name="2808"><span class="lineNum">    2808 </span>            : </a>
+<a name="2809"><span class="lineNum">    2809 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(25609.60090011981);</span></a>
+<a name="2810"><span class="lineNum">    2810 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(-135.38857843066708);</span></a>
+<a name="2811"><span class="lineNum">    2811 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(-67771.01108177133);</span></a>
+<a name="2812"><span class="lineNum">    2812 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(-25228.934337676077);</span></a>
+<a name="2813"><span class="lineNum">    2813 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(199649.95030712147);</span></a>
+<a name="2814"><span class="lineNum">    2814 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(-182251.94895101967);</span></a>
+<a name="2815"><span class="lineNum">    2815 </span><span class="lineCov">          6 :   parameter_solv[MET].push_back(52502.88444247481);</span></a>
+<a name="2816"><span class="lineNum">    2816 </span>            : </a>
+<a name="2817"><span class="lineNum">    2817 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(14376.010000119095);</span></a>
+<a name="2818"><span class="lineNum">    2818 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(-67.65579048748472);</span></a>
+<a name="2819"><span class="lineNum">    2819 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(-28302.87809850141);</span></a>
+<a name="2820"><span class="lineNum">    2820 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(-8577.439830985548);</span></a>
+<a name="2821"><span class="lineNum">    2821 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(57532.879075695324);</span></a>
+<a name="2822"><span class="lineNum">    2822 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(-43261.79286366774);</span></a>
+<a name="2823"><span class="lineNum">    2823 </span><span class="lineCov">          6 :   parameter_solv[ASN].push_back(10186.448634149085);</span></a>
+<a name="2824"><span class="lineNum">    2824 </span>            : </a>
+<a name="2825"><span class="lineNum">    2825 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(16866.21690011944);</span></a>
+<a name="2826"><span class="lineNum">    2826 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(-70.84327801054884);</span></a>
+<a name="2827"><span class="lineNum">    2827 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(-31465.84064925844);</span></a>
+<a name="2828"><span class="lineNum">    2828 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(-8653.3693368317);</span></a>
+<a name="2829"><span class="lineNum">    2829 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(58032.28250733714);</span></a>
+<a name="2830"><span class="lineNum">    2830 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(-41521.01146771431);</span></a>
+<a name="2831"><span class="lineNum">    2831 </span><span class="lineCov">          6 :   parameter_solv[PRO].push_back(9184.530596102064);</span></a>
+<a name="2832"><span class="lineNum">    2832 </span>            : </a>
+<a name="2833"><span class="lineNum">    2833 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(21503.289600119);</span></a>
+<a name="2834"><span class="lineNum">    2834 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(-121.30164008960246);</span></a>
+<a name="2835"><span class="lineNum">    2835 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(-50468.580981118175);</span></a>
+<a name="2836"><span class="lineNum">    2836 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(-18462.49098408308);</span></a>
+<a name="2837"><span class="lineNum">    2837 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(132718.44904081387);</span></a>
+<a name="2838"><span class="lineNum">    2838 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(-113787.22666510186);</span></a>
+<a name="2839"><span class="lineNum">    2839 </span><span class="lineCov">          6 :   parameter_solv[GLN].push_back(30920.348610969988);</span></a>
+<a name="2840"><span class="lineNum">    2840 </span>            : </a>
+<a name="2841"><span class="lineNum">    2841 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(9181.472400119354);</span></a>
+<a name="2842"><span class="lineNum">    2842 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(-28.77519915767741);</span></a>
+<a name="2843"><span class="lineNum">    2843 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(-15205.543144104717);</span></a>
+<a name="2844"><span class="lineNum">    2844 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(-3377.782176346411);</span></a>
+<a name="2845"><span class="lineNum">    2845 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(23345.555771001076);</span></a>
+<a name="2846"><span class="lineNum">    2846 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(-15312.694356014094);</span></a>
+<a name="2847"><span class="lineNum">    2847 </span><span class="lineCov">          6 :   parameter_solv[SER].push_back(3013.8428466148);</span></a>
+<a name="2848"><span class="lineNum">    2848 </span>            : </a>
+<a name="2849"><span class="lineNum">    2849 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(15020.953600119403);</span></a>
+<a name="2850"><span class="lineNum">    2850 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(-61.91004832631006);</span></a>
+<a name="2851"><span class="lineNum">    2851 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(-27814.537889259853);</span></a>
+<a name="2852"><span class="lineNum">    2852 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(-7532.227289701552);</span></a>
+<a name="2853"><span class="lineNum">    2853 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(50586.30566118166);</span></a>
+<a name="2854"><span class="lineNum">    2854 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(-35943.866131120165);</span></a>
+<a name="2855"><span class="lineNum">    2855 </span><span class="lineCov">          6 :   parameter_solv[THR].push_back(7880.093558764326);</span></a>
+<a name="2856"><span class="lineNum">    2856 </span>            : </a>
+<a name="2857"><span class="lineNum">    2857 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(19647.628900119355);</span></a>
+<a name="2858"><span class="lineNum">    2858 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(-89.04983250107853);</span></a>
+<a name="2859"><span class="lineNum">    2859 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(-38050.09958470928);</span></a>
+<a name="2860"><span class="lineNum">    2860 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(-10921.427112288537);</span></a>
+<a name="2861"><span class="lineNum">    2861 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(72774.32322962297);</span></a>
+<a name="2862"><span class="lineNum">    2862 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(-52689.060152305225);</span></a>
+<a name="2863"><span class="lineNum">    2863 </span><span class="lineCov">          6 :   parameter_solv[VAL].push_back(11806.492503632868);</span></a>
+<a name="2864"><span class="lineNum">    2864 </span>            : </a>
+<a name="2865"><span class="lineNum">    2865 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(7515.156100119276);</span></a>
+<a name="2866"><span class="lineNum">    2866 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(-20.226381685697746);</span></a>
+<a name="2867"><span class="lineNum">    2867 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(-11761.841094237716);</span></a>
+<a name="2868"><span class="lineNum">    2868 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(-2341.4929468980367);</span></a>
+<a name="2869"><span class="lineNum">    2869 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(16545.385777961936);</span></a>
+<a name="2870"><span class="lineNum">    2870 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(-10397.175253025776);</span></a>
+<a name="2871"><span class="lineNum">    2871 </span><span class="lineCov">          6 :   parameter_solv[ALA].push_back(1921.5264606725107);</span></a>
+<a name="2872"><span class="lineNum">    2872 </span>            : </a>
+<a name="2873"><span class="lineNum">    2873 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(3594.002500119159);</span></a>
+<a name="2874"><span class="lineNum">    2874 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(-6.910836154887606);</span></a>
+<a name="2875"><span class="lineNum">    2875 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(-4937.354220666574);</span></a>
+<a name="2876"><span class="lineNum">    2876 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(-785.4549468992149);</span></a>
+<a name="2877"><span class="lineNum">    2877 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(5852.854429532936);</span></a>
+<a name="2878"><span class="lineNum">    2878 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(-3391.2927115487832);</span></a>
+<a name="2879"><span class="lineNum">    2879 </span><span class="lineCov">          6 :   parameter_solv[GLY].push_back(552.3280571490722);</span></a>
+<a name="2880"><span class="lineNum">    2880 </span>            : </a>
+<a name="2881"><span class="lineNum">    2881 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(22888.664100119073);</span></a>
+<a name="2882"><span class="lineNum">    2882 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(-133.86265270962434);</span></a>
+<a name="2883"><span class="lineNum">    2883 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(-57533.51591635819);</span></a>
+<a name="2884"><span class="lineNum">    2884 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(-21767.293192014684);</span></a>
+<a name="2885"><span class="lineNum">    2885 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(161255.14120001195);</span></a>
+<a name="2886"><span class="lineNum">    2886 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(-142176.64081149307);</span></a>
+<a name="2887"><span class="lineNum">    2887 </span><span class="lineCov">          6 :   parameter_solv[HIS].push_back(39642.61185646193);</span></a>
+<a name="2888"><span class="lineNum">    2888 </span>            : </a>
+<a name="2889"><span class="lineNum">    2889 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(48294.0117571196);</span></a>
+<a name="2890"><span class="lineNum">    2890 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(-205.45879626487798);</span></a>
+<a name="2891"><span class="lineNum">    2891 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(-148816.1858118254);</span></a>
+<a name="2892"><span class="lineNum">    2892 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(-54968.030079609875);</span></a>
+<a name="2893"><span class="lineNum">    2893 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(491793.79967057955);</span></a>
+<a name="2894"><span class="lineNum">    2894 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(-476312.9117969879);</span></a>
+<a name="2895"><span class="lineNum">    2895 </span><span class="lineCov">          6 :   parameter_mix[TRP].push_back(144159.96165644142);</span></a>
+<a name="2896"><span class="lineNum">    2896 </span>            : </a>
+<a name="2897"><span class="lineNum">    2897 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(36984.20240312081);</span></a>
+<a name="2898"><span class="lineNum">    2898 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(-83.86380083812203);</span></a>
+<a name="2899"><span class="lineNum">    2899 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(-108820.52211887162);</span></a>
+<a name="2900"><span class="lineNum">    2900 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(-33934.69818901515);</span></a>
+<a name="2901"><span class="lineNum">    2901 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(341504.736372253);</span></a>
+<a name="2902"><span class="lineNum">    2902 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(-334008.1748614056);</span></a>
+<a name="2903"><span class="lineNum">    2903 </span><span class="lineCov">          6 :   parameter_mix[TYR].push_back(102033.08077851454);</span></a>
+<a name="2904"><span class="lineNum">    2904 </span>            : </a>
+<a name="2905"><span class="lineNum">    2905 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(32119.469231338233);</span></a>
+<a name="2906"><span class="lineNum">    2906 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(-172.96940450568917);</span></a>
+<a name="2907"><span class="lineNum">    2907 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(-85831.4326887122);</span></a>
+<a name="2908"><span class="lineNum">    2908 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(-33193.32405438845);</span></a>
+<a name="2909"><span class="lineNum">    2909 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(262940.64471909316);</span></a>
+<a name="2910"><span class="lineNum">    2910 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(-243540.06898907054);</span></a>
+<a name="2911"><span class="lineNum">    2911 </span><span class="lineCov">          6 :   parameter_mix[PHE].push_back(71084.54387480798);</span></a>
+<a name="2912"><span class="lineNum">    2912 </span>            : </a>
+<a name="2913"><span class="lineNum">    2913 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(22833.36414923898);</span></a>
+<a name="2914"><span class="lineNum">    2914 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(-134.0493955562186);</span></a>
+<a name="2915"><span class="lineNum">    2915 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(-55325.55607328898);</span></a>
+<a name="2916"><span class="lineNum">    2916 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(-21898.314938881984);</span></a>
+<a name="2917"><span class="lineNum">    2917 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(159995.6912885654);</span></a>
+<a name="2918"><span class="lineNum">    2918 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(-142968.19796084083);</span></a>
+<a name="2919"><span class="lineNum">    2919 </span><span class="lineCov">          6 :   parameter_mix[HIP].push_back(40417.44581470003);</span></a>
+<a name="2920"><span class="lineNum">    2920 </span>            : </a>
+<a name="2921"><span class="lineNum">    2921 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(31385.401600920715);</span></a>
+<a name="2922"><span class="lineNum">    2922 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(36.114094042884254);</span></a>
+<a name="2923"><span class="lineNum">    2923 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(-103730.44467490204);</span></a>
+<a name="2924"><span class="lineNum">    2924 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(-27036.249157905615);</span></a>
+<a name="2925"><span class="lineNum">    2925 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(347011.0339314942);</span></a>
+<a name="2926"><span class="lineNum">    2926 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(-358879.9736802336);</span></a>
+<a name="2927"><span class="lineNum">    2927 </span><span class="lineCov">          6 :   parameter_mix[ARG].push_back(114432.18361399164);</span></a>
+<a name="2928"><span class="lineNum">    2928 </span>            : </a>
+<a name="2929"><span class="lineNum">    2929 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(25511.35812671878);</span></a>
+<a name="2930"><span class="lineNum">    2930 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(-130.4381491986372);</span></a>
+<a name="2931"><span class="lineNum">    2931 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(-69258.61236879184);</span></a>
+<a name="2932"><span class="lineNum">    2932 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(-27066.36783798707);</span></a>
+<a name="2933"><span class="lineNum">    2933 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(220092.65231165203);</span></a>
+<a name="2934"><span class="lineNum">    2934 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(-207794.5056092443);</span></a>
+<a name="2935"><span class="lineNum">    2935 </span><span class="lineCov">          6 :   parameter_mix[LYS].push_back(61665.57004630315);</span></a>
+<a name="2936"><span class="lineNum">    2936 </span>            : </a>
+<a name="2937"><span class="lineNum">    2937 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(11505.517261618916);</span></a>
+<a name="2938"><span class="lineNum">    2938 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(-33.60468076978334);</span></a>
+<a name="2939"><span class="lineNum">    2939 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(-18328.882710004465);</span></a>
+<a name="2940"><span class="lineNum">    2940 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(-3956.9113649567626);</span></a>
+<a name="2941"><span class="lineNum">    2941 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(27546.35146501212);</span></a>
+<a name="2942"><span class="lineNum">    2942 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(-18024.826330595406);</span></a>
+<a name="2943"><span class="lineNum">    2943 </span><span class="lineCov">          6 :   parameter_mix[CYS].push_back(3551.2207387570024);</span></a>
+<a name="2944"><span class="lineNum">    2944 </span>            : </a>
+<a name="2945"><span class="lineNum">    2945 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(13713.858501879382);</span></a>
+<a name="2946"><span class="lineNum">    2946 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(-51.33286241257164);</span></a>
+<a name="2947"><span class="lineNum">    2947 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(-23807.8549764091);</span></a>
+<a name="2948"><span class="lineNum">    2948 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(-6153.667315935503);</span></a>
+<a name="2949"><span class="lineNum">    2949 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(41296.118377286424);</span></a>
+<a name="2950"><span class="lineNum">    2950 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(-28740.28391184026);</span></a>
+<a name="2951"><span class="lineNum">    2951 </span><span class="lineCov">          6 :   parameter_mix[ASP].push_back(6132.671533319127);</span></a>
+<a name="2952"><span class="lineNum">    2952 </span>            : </a>
+<a name="2953"><span class="lineNum">    2953 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(19156.03660739947);</span></a>
+<a name="2954"><span class="lineNum">    2954 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(-110.90600703589246);</span></a>
+<a name="2955"><span class="lineNum">    2955 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(-40319.3351514524);</span></a>
+<a name="2956"><span class="lineNum">    2956 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(-14679.813393816446);</span></a>
+<a name="2957"><span class="lineNum">    2957 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(96769.28565573556);</span></a>
+<a name="2958"><span class="lineNum">    2958 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(-77909.09315520026);</span></a>
+<a name="2959"><span class="lineNum">    2959 </span><span class="lineCov">          6 :   parameter_mix[GLU].push_back(19770.047062759568);</span></a>
+<a name="2960"><span class="lineNum">    2960 </span>            : </a>
+<a name="2961"><span class="lineNum">    2961 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(20693.06215917923);</span></a>
+<a name="2962"><span class="lineNum">    2962 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(-102.87208880594848);</span></a>
+<a name="2963"><span class="lineNum">    2963 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(-41080.44036311675);</span></a>
+<a name="2964"><span class="lineNum">    2964 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(-12874.439649378206);</span></a>
+<a name="2965"><span class="lineNum">    2965 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(84947.33147117581);</span></a>
+<a name="2966"><span class="lineNum">    2966 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(-63779.07871450237);</span></a>
+<a name="2967"><span class="lineNum">    2967 </span><span class="lineCov">          6 :   parameter_mix[ILE].push_back(14938.919981690511);</span></a>
+<a name="2968"><span class="lineNum">    2968 </span>            : </a>
+<a name="2969"><span class="lineNum">    2969 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(20693.062159179233);</span></a>
+<a name="2970"><span class="lineNum">    2970 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(-114.09539845409269);</span></a>
+<a name="2971"><span class="lineNum">    2971 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(-42417.3431074524);</span></a>
+<a name="2972"><span class="lineNum">    2972 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(-14393.801090829746);</span></a>
+<a name="2973"><span class="lineNum">    2973 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(93640.48403643962);</span></a>
+<a name="2974"><span class="lineNum">    2974 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(-71990.10354816525);</span></a>
+<a name="2975"><span class="lineNum">    2975 </span><span class="lineCov">          6 :   parameter_mix[LEU].push_back(17299.01082057651);</span></a>
+<a name="2976"><span class="lineNum">    2976 </span>            : </a>
+<a name="2977"><span class="lineNum">    2977 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(22400.800002738917);</span></a>
+<a name="2978"><span class="lineNum">    2978 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(-138.14469221559762);</span></a>
+<a name="2979"><span class="lineNum">    2979 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(-53013.97694299946);</span></a>
+<a name="2980"><span class="lineNum">    2980 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(-21079.899452619244);</span></a>
+<a name="2981"><span class="lineNum">    2981 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(148607.1089339919);</span></a>
+<a name="2982"><span class="lineNum">    2982 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(-129827.63962878387);</span></a>
+<a name="2983"><span class="lineNum">    2983 </span><span class="lineCov">          6 :   parameter_mix[MET].push_back(35882.3297822684);</span></a>
+<a name="2984"><span class="lineNum">    2984 </span>            : </a>
+<a name="2985"><span class="lineNum">    2985 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(14384.287416519475);</span></a>
+<a name="2986"><span class="lineNum">    2986 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(-55.24976731179147);</span></a>
+<a name="2987"><span class="lineNum">    2987 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(-25372.978199926372);</span></a>
+<a name="2988"><span class="lineNum">    2988 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(-6646.452004616925);</span></a>
+<a name="2989"><span class="lineNum">    2989 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(44594.5027556148);</span></a>
+<a name="2990"><span class="lineNum">    2990 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(-31202.511764907107);</span></a>
+<a name="2991"><span class="lineNum">    2991 </span><span class="lineCov">          6 :   parameter_mix[ASN].push_back(6703.764135873442);</span></a>
+<a name="2992"><span class="lineNum">    2992 </span>            : </a>
+<a name="2993"><span class="lineNum">    2993 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(13503.797145659117);</span></a>
+<a name="2994"><span class="lineNum">    2994 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(-38.58316011847087);</span></a>
+<a name="2995"><span class="lineNum">    2995 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(-21446.17847324053);</span></a>
+<a name="2996"><span class="lineNum">    2996 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(-4480.55896170459);</span></a>
+<a name="2997"><span class="lineNum">    2997 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(31274.287350083254);</span></a>
+<a name="2998"><span class="lineNum">    2998 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(-19984.249229169505);</span></a>
+<a name="2999"><span class="lineNum">    2999 </span><span class="lineCov">          6 :   parameter_mix[PRO].push_back(3782.272312712745);</span></a>
+<a name="3000"><span class="lineNum">    3000 </span>            : </a>
+<a name="3001"><span class="lineNum">    3001 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(19938.23724683901);</span></a>
+<a name="3002"><span class="lineNum">    3002 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(-121.24884503048865);</span></a>
+<a name="3003"><span class="lineNum">    3003 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(-43928.589472297834);</span></a>
+<a name="3004"><span class="lineNum">    3004 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(-16805.069757865473);</span></a>
+<a name="3005"><span class="lineNum">    3005 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(112831.61348476357);</span></a>
+<a name="3006"><span class="lineNum">    3006 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(-93979.08819184235);</span></a>
+<a name="3007"><span class="lineNum">    3007 </span><span class="lineCov">          6 :   parameter_mix[GLN].push_back(24741.563493163732);</span></a>
+<a name="3008"><span class="lineNum">    3008 </span>            : </a>
+<a name="3009"><span class="lineNum">    3009 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(8813.67020471935);</span></a>
+<a name="3010"><span class="lineNum">    3010 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(-18.291615317790175);</span></a>
+<a name="3011"><span class="lineNum">    3011 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(-12585.074732466266);</span></a>
+<a name="3012"><span class="lineNum">    3012 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(-2064.454891600786);</span></a>
+<a name="3013"><span class="lineNum">    3013 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(15273.905065790364);</span></a>
+<a name="3014"><span class="lineNum">    3014 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(-8813.056005263466);</span></a>
+<a name="3015"><span class="lineNum">    3015 </span><span class="lineCov">          6 :   parameter_mix[SER].push_back(1404.9812302289881);</span></a>
+<a name="3016"><span class="lineNum">    3016 </span>            : </a>
+<a name="3017"><span class="lineNum">    3017 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(13233.997179639062);</span></a>
+<a name="3018"><span class="lineNum">    3018 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(-39.40454157416847);</span></a>
+<a name="3019"><span class="lineNum">    3019 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(-21430.58717233547);</span></a>
+<a name="3020"><span class="lineNum">    3020 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(-4566.332853710876);</span></a>
+<a name="3021"><span class="lineNum">    3021 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(31717.497780073558);</span></a>
+<a name="3022"><span class="lineNum">    3022 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(-20299.614304281313);</span></a>
+<a name="3023"><span class="lineNum">    3023 </span><span class="lineCov">          6 :   parameter_mix[THR].push_back(3837.207224537505);</span></a>
+<a name="3024"><span class="lineNum">    3024 </span>            : </a>
+<a name="3025"><span class="lineNum">    3025 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(15135.438016299158);</span></a>
+<a name="3026"><span class="lineNum">    3026 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(-51.415141550353205);</span></a>
+<a name="3027"><span class="lineNum">    3027 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(-25859.078442379723);</span></a>
+<a name="3028"><span class="lineNum">    3028 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(-6007.697291593915);</span></a>
+<a name="3029"><span class="lineNum">    3029 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(40997.969600345634);</span></a>
+<a name="3030"><span class="lineNum">    3030 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(-27036.257386814148);</span></a>
+<a name="3031"><span class="lineNum">    3031 </span><span class="lineCov">          6 :   parameter_mix[VAL].push_back(5328.922363811635);</span></a>
+<a name="3032"><span class="lineNum">    3032 </span>            : </a>
+<a name="3033"><span class="lineNum">    3033 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(6586.942863819189);</span></a>
+<a name="3034"><span class="lineNum">    3034 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(-10.96713559950907);</span></a>
+<a name="3035"><span class="lineNum">    3035 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(-8758.836131731925);</span></a>
+<a name="3036"><span class="lineNum">    3036 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(-1223.1723720922605);</span></a>
+<a name="3037"><span class="lineNum">    3037 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(9475.182453543037);</span></a>
+<a name="3038"><span class="lineNum">    3038 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(-5124.611191433804);</span></a>
+<a name="3039"><span class="lineNum">    3039 </span><span class="lineCov">          6 :   parameter_mix[ALA].push_back(721.7625962949869);</span></a>
+<a name="3040"><span class="lineNum">    3040 </span>            : </a>
+<a name="3041"><span class="lineNum">    3041 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(3596.0718542192762);</span></a>
+<a name="3042"><span class="lineNum">    3042 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(-4.079285964028122);</span></a>
+<a name="3043"><span class="lineNum">    3043 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(-4089.4217504382686);</span></a>
+<a name="3044"><span class="lineNum">    3044 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(-450.9650932154967);</span></a>
+<a name="3045"><span class="lineNum">    3045 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(3737.026778223427);</span></a>
+<a name="3046"><span class="lineNum">    3046 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(-1862.9856575810572);</span></a>
+<a name="3047"><span class="lineNum">    3047 </span><span class="lineCov">          6 :   parameter_mix[GLY].push_back(222.97288276257262);</span></a>
+<a name="3048"><span class="lineNum">    3048 </span>            : </a>
+<a name="3049"><span class="lineNum">    3049 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(21779.124723299232);</span></a>
+<a name="3050"><span class="lineNum">    3050 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(-131.4603421188538);</span></a>
+<a name="3051"><span class="lineNum">    3051 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(-49068.74667421681);</span></a>
+<a name="3052"><span class="lineNum">    3052 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(-18685.909496392127);</span></a>
+<a name="3053"><span class="lineNum">    3053 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(127724.60792384286);</span></a>
+<a name="3054"><span class="lineNum">    3054 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(-107419.22159440348);</span></a>
+<a name="3055"><span class="lineNum">    3055 </span><span class="lineCov">          6 :   parameter_mix[HIS].push_back(28577.228634530744);</span></a>
+<a name="3056"><span class="lineNum">    3056 </span>            : </a>
+<a name="3057"><span class="lineNum">    3057 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(9599.949107368187);</span></a>
+<a name="3058"><span class="lineNum">    3058 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(-66.35331786175249);</span></a>
+<a name="3059"><span class="lineNum">    3059 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(-26311.640290970638);</span></a>
+<a name="3060"><span class="lineNum">    3060 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(-11577.314600529338);</span></a>
+<a name="3061"><span class="lineNum">    3061 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(85847.52554160352);</span></a>
+<a name="3062"><span class="lineNum">    3062 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(-79417.17065742958);</span></a>
+<a name="3063"><span class="lineNum">    3063 </span><span class="lineCov">          6 :   parameter_vac[TRP].push_back(23090.348430572863);</span></a>
+<a name="3064"><span class="lineNum">    3064 </span>            : </a>
+<a name="3065"><span class="lineNum">    3065 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(7393.553846412945);</span></a>
+<a name="3066"><span class="lineNum">    3066 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(-27.51954035778316);</span></a>
+<a name="3067"><span class="lineNum">    3067 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(-20329.10485615286);</span></a>
+<a name="3068"><span class="lineNum">    3068 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(-7444.276340508767);</span></a>
+<a name="3069"><span class="lineNum">    3069 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(66343.22315132803);</span></a>
+<a name="3070"><span class="lineNum">    3070 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(-64470.58721639446);</span></a>
+<a name="3071"><span class="lineNum">    3071 </span><span class="lineCov">          6 :   parameter_vac[TYR].push_back(19614.63563898146);</span></a>
+<a name="3072"><span class="lineNum">    3072 </span>            : </a>
+<a name="3073"><span class="lineNum">    3073 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(6081.874997705279);</span></a>
+<a name="3074"><span class="lineNum">    3074 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(-40.474695969500104);</span></a>
+<a name="3075"><span class="lineNum">    3075 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(-14354.627390498901);</span></a>
+<a name="3076"><span class="lineNum">    3076 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(-6156.69750315959);</span></a>
+<a name="3077"><span class="lineNum">    3077 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(42580.84239395237);</span></a>
+<a name="3078"><span class="lineNum">    3078 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(-37704.09749809582);</span></a>
+<a name="3079"><span class="lineNum">    3079 </span><span class="lineCov">          6 :   parameter_vac[PHE].push_back(10543.005717478625);</span></a>
+<a name="3080"><span class="lineNum">    3080 </span>            : </a>
+<a name="3081"><span class="lineNum">    3081 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(5325.791987063724);</span></a>
+<a name="3082"><span class="lineNum">    3082 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(-35.512112257530156);</span></a>
+<a name="3083"><span class="lineNum">    3083 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(-11488.443296477566);</span></a>
+<a name="3084"><span class="lineNum">    3084 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(-4916.724935318093);</span></a>
+<a name="3085"><span class="lineNum">    3085 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(32134.338675979947);</span></a>
+<a name="3086"><span class="lineNum">    3086 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(-27388.387595464188);</span></a>
+<a name="3087"><span class="lineNum">    3087 </span><span class="lineCov">          6 :   parameter_vac[HIP].push_back(7359.899986748838);</span></a>
+<a name="3088"><span class="lineNum">    3088 </span>            : </a>
+<a name="3089"><span class="lineNum">    3089 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(7220.306892248294);</span></a>
+<a name="3090"><span class="lineNum">    3090 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(-20.65912886190997);</span></a>
+<a name="3091"><span class="lineNum">    3091 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(-22700.70129646048);</span></a>
+<a name="3092"><span class="lineNum">    3092 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(-8696.901551172636);</span></a>
+<a name="3093"><span class="lineNum">    3093 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(83641.36257312517);</span></a>
+<a name="3094"><span class="lineNum">    3094 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(-85237.33676336925);</span></a>
+<a name="3095"><span class="lineNum">    3095 </span><span class="lineCov">          6 :   parameter_vac[ARG].push_back(26899.162688310953);</span></a>
+<a name="3096"><span class="lineNum">    3096 </span>            : </a>
+<a name="3097"><span class="lineNum">    3097 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(5038.613120729022);</span></a>
+<a name="3098"><span class="lineNum">    3098 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(-34.08366887546492);</span></a>
+<a name="3099"><span class="lineNum">    3099 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(-12812.921120433106);</span></a>
+<a name="3100"><span class="lineNum">    3100 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(-5843.761329082788);</span></a>
+<a name="3101"><span class="lineNum">    3101 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(42419.08427856609);</span></a>
+<a name="3102"><span class="lineNum">    3102 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(-39460.49038159249);</span></a>
+<a name="3103"><span class="lineNum">    3103 </span><span class="lineCov">          6 :   parameter_vac[LYS].push_back(11542.320830663035);</span></a>
+<a name="3104"><span class="lineNum">    3104 </span>            : </a>
+<a name="3105"><span class="lineNum">    3105 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(2915.0458981763995);</span></a>
+<a name="3106"><span class="lineNum">    3106 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(-5.380571839804511);</span></a>
+<a name="3107"><span class="lineNum">    3107 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(-3865.366285883624);</span></a>
+<a name="3108"><span class="lineNum">    3108 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(-602.3275271136284);</span></a>
+<a name="3109"><span class="lineNum">    3109 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(4524.133086072617);</span></a>
+<a name="3110"><span class="lineNum">    3110 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(-2537.87137720241);</span></a>
+<a name="3111"><span class="lineNum">    3111 </span><span class="lineCov">          6 :   parameter_vac[CYS].push_back(381.52870758240016);</span></a>
+<a name="3112"><span class="lineNum">    3112 </span>            : </a>
+<a name="3113"><span class="lineNum">    3113 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(3479.750728224898);</span></a>
+<a name="3114"><span class="lineNum">    3114 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(-10.33897891836596);</span></a>
+<a name="3115"><span class="lineNum">    3115 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(-5382.628188436401);</span></a>
+<a name="3116"><span class="lineNum">    3116 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(-1183.8060939576694);</span></a>
+<a name="3117"><span class="lineNum">    3117 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(8100.082378727997);</span></a>
+<a name="3118"><span class="lineNum">    3118 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(-5162.630696148773);</span></a>
+<a name="3119"><span class="lineNum">    3119 </span><span class="lineCov">          6 :   parameter_vac[ASP].push_back(958.993022379732);</span></a>
+<a name="3120"><span class="lineNum">    3120 </span>            : </a>
+<a name="3121"><span class="lineNum">    3121 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(4487.461543955491);</span></a>
+<a name="3122"><span class="lineNum">    3122 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(-26.671865751817936);</span></a>
+<a name="3123"><span class="lineNum">    3123 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(-8829.738168429001);</span></a>
+<a name="3124"><span class="lineNum">    3124 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(-3297.668395415257);</span></a>
+<a name="3125"><span class="lineNum">    3125 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(20686.457747123466);</span></a>
+<a name="3126"><span class="lineNum">    3126 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(-16030.814134196151);</span></a>
+<a name="3127"><span class="lineNum">    3127 </span><span class="lineCov">          6 :   parameter_vac[GLU].push_back(3858.4457728083275);</span></a>
+<a name="3128"><span class="lineNum">    3128 </span>            : </a>
+<a name="3129"><span class="lineNum">    3129 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(3842.5968201937776);</span></a>
+<a name="3130"><span class="lineNum">    3130 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(-13.848165050578492);</span></a>
+<a name="3131"><span class="lineNum">    3131 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(-6480.062699452774);</span></a>
+<a name="3132"><span class="lineNum">    3132 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(-1636.3888925440413);</span></a>
+<a name="3133"><span class="lineNum">    3133 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(10967.333210698738);</span></a>
+<a name="3134"><span class="lineNum">    3134 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(-7483.704914714421);</span></a>
+<a name="3135"><span class="lineNum">    3135 </span><span class="lineCov">          6 :   parameter_vac[ILE].push_back(1548.5696047594895);</span></a>
+<a name="3136"><span class="lineNum">    3136 </span>            : </a>
+<a name="3137"><span class="lineNum">    3137 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(3842.5968201937785);</span></a>
+<a name="3138"><span class="lineNum">    3138 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(-16.2745108270949);</span></a>
+<a name="3139"><span class="lineNum">    3139 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(-6807.110269770606);</span></a>
+<a name="3140"><span class="lineNum">    3140 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(-1926.6303434106014);</span></a>
+<a name="3141"><span class="lineNum">    3141 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(12577.952756390941);</span></a>
+<a name="3142"><span class="lineNum">    3142 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(-8829.40489330961);</span></a>
+<a name="3143"><span class="lineNum">    3143 </span><span class="lineCov">          6 :   parameter_vac[LEU].push_back(1882.919316016889);</span></a>
+<a name="3144"><span class="lineNum">    3144 </span>            : </a>
+<a name="3145"><span class="lineNum">    3145 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(4898.512892967389);</span></a>
+<a name="3146"><span class="lineNum">    3146 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(-30.588244886468207);</span></a>
+<a name="3147"><span class="lineNum">    3147 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(-10159.093665859045);</span></a>
+<a name="3148"><span class="lineNum">    3148 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(-4025.0261508449653);</span></a>
+<a name="3149"><span class="lineNum">    3149 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(26007.394369425827);</span></a>
+<a name="3150"><span class="lineNum">    3150 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(-21199.218680206573);</span></a>
+<a name="3151"><span class="lineNum">    3151 </span><span class="lineCov">          6 :   parameter_vac[MET].push_back(5423.004225853842);</span></a>
+<a name="3152"><span class="lineNum">    3152 </span>            : </a>
+<a name="3153"><span class="lineNum">    3153 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(3598.1423998115492);</span></a>
+<a name="3154"><span class="lineNum">    3154 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(-10.357995638888545);</span></a>
+<a name="3155"><span class="lineNum">    3155 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(-5565.603011562138);</span></a>
+<a name="3156"><span class="lineNum">    3156 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(-1190.3294930971967);</span></a>
+<a name="3157"><span class="lineNum">    3157 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(8227.920711951123);</span></a>
+<a name="3158"><span class="lineNum">    3158 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(-5222.61541118056);</span></a>
+<a name="3159"><span class="lineNum">    3159 </span><span class="lineCov">          6 :   parameter_vac[ASN].push_back(968.593406702772);</span></a>
+<a name="3160"><span class="lineNum">    3160 </span>            : </a>
+<a name="3161"><span class="lineNum">    3161 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(2702.925890807494);</span></a>
+<a name="3162"><span class="lineNum">    3162 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(-4.11690159421177);</span></a>
+<a name="3163"><span class="lineNum">    3163 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(-3395.325331307625);</span></a>
+<a name="3164"><span class="lineNum">    3164 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(-458.95242128002894);</span></a>
+<a name="3165"><span class="lineNum">    3165 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(3584.3640448715823);</span></a>
+<a name="3166"><span class="lineNum">    3166 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(-1921.4140769384692);</span></a>
+<a name="3167"><span class="lineNum">    3167 </span><span class="lineCov">          6 :   parameter_vac[PRO].push_back(267.08577848319516);</span></a>
+<a name="3168"><span class="lineNum">    3168 </span>            : </a>
+<a name="3169"><span class="lineNum">    3169 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(4621.773132292556);</span></a>
+<a name="3170"><span class="lineNum">    3170 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(-29.511778489038818);</span></a>
+<a name="3171"><span class="lineNum">    3171 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(-9486.077450010192);</span></a>
+<a name="3172"><span class="lineNum">    3172 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(-3768.5756897489828);</span></a>
+<a name="3173"><span class="lineNum">    3173 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(23828.07111260487);</span></a>
+<a name="3174"><span class="lineNum">    3174 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(-19110.205836780202);</span></a>
+<a name="3175"><span class="lineNum">    3175 </span><span class="lineCov">          6 :   parameter_vac[GLN].push_back(4791.718204894083);</span></a>
+<a name="3176"><span class="lineNum">    3176 </span>            : </a>
+<a name="3177"><span class="lineNum">    3177 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(2115.1504654043965);</span></a>
+<a name="3178"><span class="lineNum">    3178 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(-2.4158378234251234);</span></a>
+<a name="3179"><span class="lineNum">    3179 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(-2488.1131972903822);</span></a>
+<a name="3180"><span class="lineNum">    3180 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(-263.64072945387693);</span></a>
+<a name="3181"><span class="lineNum">    3181 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(2251.376687850687);</span></a>
+<a name="3182"><span class="lineNum">    3182 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(-1066.0790768852626);</span></a>
+<a name="3183"><span class="lineNum">    3183 </span><span class="lineCov">          6 :   parameter_vac[SER].push_back(105.5155397911316);</span></a>
+<a name="3184"><span class="lineNum">    3184 </span>            : </a>
+<a name="3185"><span class="lineNum">    3185 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(2914.9061707158835);</span></a>
+<a name="3186"><span class="lineNum">    3186 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(-5.032844592364407);</span></a>
+<a name="3187"><span class="lineNum">    3187 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(-3903.2546253886653);</span></a>
+<a name="3188"><span class="lineNum">    3188 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(-559.4734271244915);</span></a>
+<a name="3189"><span class="lineNum">    3189 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(4315.044828297787);</span></a>
+<a name="3190"><span class="lineNum">    3190 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(-2331.211908177365);</span></a>
+<a name="3191"><span class="lineNum">    3191 </span><span class="lineCov">          6 :   parameter_vac[THR].push_back(323.76849758109853);</span></a>
+<a name="3192"><span class="lineNum">    3192 </span>            : </a>
+<a name="3193"><span class="lineNum">    3193 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(2914.8744247581953);</span></a>
+<a name="3194"><span class="lineNum">    3194 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(-5.847217106105881);</span></a>
+<a name="3195"><span class="lineNum">    3195 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(-4096.370479502377);</span></a>
+<a name="3196"><span class="lineNum">    3196 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(-655.2917606620404);</span></a>
+<a name="3197"><span class="lineNum">    3197 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(4888.77261250007);</span></a>
+<a name="3198"><span class="lineNum">    3198 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(-2765.7552774385167);</span></a>
+<a name="3199"><span class="lineNum">    3199 </span><span class="lineCov">          6 :   parameter_vac[VAL].push_back(421.9081598033515);</span></a>
+<a name="3200"><span class="lineNum">    3200 </span>            : </a>
+<a name="3201"><span class="lineNum">    3201 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(1443.3438146824446);</span></a>
+<a name="3202"><span class="lineNum">    3202 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(-1.1234573178567506);</span></a>
+<a name="3203"><span class="lineNum">    3203 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(-1492.4547663363514);</span></a>
+<a name="3204"><span class="lineNum">    3204 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(-121.47935619968672);</span></a>
+<a name="3205"><span class="lineNum">    3205 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(1139.689871538201);</span></a>
+<a name="3206"><span class="lineNum">    3206 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(-483.8336547914466);</span></a>
+<a name="3207"><span class="lineNum">    3207 </span><span class="lineCov">          6 :   parameter_vac[ALA].push_back(32.48231950404626);</span></a>
+<a name="3208"><span class="lineNum">    3208 </span>            : </a>
+<a name="3209"><span class="lineNum">    3209 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(899.5356000422925);</span></a>
+<a name="3210"><span class="lineNum">    3210 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(-0.5200880084066986);</span></a>
+<a name="3211"><span class="lineNum">    3211 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(-787.5892053280859);</span></a>
+<a name="3212"><span class="lineNum">    3212 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(-56.07596224884467);</span></a>
+<a name="3213"><span class="lineNum">    3213 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(546.4212287680981);</span></a>
+<a name="3214"><span class="lineNum">    3214 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(-222.2667666932616);</span></a>
+<a name="3215"><span class="lineNum">    3215 </span><span class="lineCov">          6 :   parameter_vac[GLY].push_back(12.474587265791476);</span></a>
+<a name="3216"><span class="lineNum">    3216 </span>            : </a>
+<a name="3217"><span class="lineNum">    3217 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(5180.842705000207);</span></a>
+<a name="3218"><span class="lineNum">    3218 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(-29.578973475252766);</span></a>
+<a name="3219"><span class="lineNum">    3219 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(-10323.417251934066);</span></a>
+<a name="3220"><span class="lineNum">    3220 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(-3788.977215582307);</span></a>
+<a name="3221"><span class="lineNum">    3221 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(24427.720792289427);</span></a>
+<a name="3222"><span class="lineNum">    3222 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(-19307.35836837878);</span></a>
+<a name="3223"><span class="lineNum">    3223 </span><span class="lineCov">          6 :   parameter_vac[HIS].push_back(4780.831414992477);</span></a>
+<a name="3224"><span class="lineNum">    3224 </span>            : </a>
+<a name="3225"><span class="lineNum">    3225 </span>            :   // NUCLEIC ACIDS</a>
+<a name="3226"><span class="lineNum">    3226 </span>            : </a>
+<a name="3227"><span class="lineNum">    3227 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(575.5201001192197);</span></a>
+<a name="3228"><span class="lineNum">    3228 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(-0.6126595489733868);</span></a>
+<a name="3229"><span class="lineNum">    3229 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(-623.3371092254897);</span></a>
+<a name="3230"><span class="lineNum">    3230 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(-68.05795957022156);</span></a>
+<a name="3231"><span class="lineNum">    3231 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(561.8052621243662);</span></a>
+<a name="3232"><span class="lineNum">    3232 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(-283.39573309540344);</span></a>
+<a name="3233"><span class="lineNum">    3233 </span><span class="lineCov">          6 :   parameter_solv[BB_PO2].push_back(35.55001698010027);</span></a>
+<a name="3234"><span class="lineNum">    3234 </span>            : </a>
+<a name="3235"><span class="lineNum">    3235 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(21211.009600118316);</span></a>
+<a name="3236"><span class="lineNum">    3236 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(-90.18805990529991);</span></a>
+<a name="3237"><span class="lineNum">    3237 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(-39731.1337351215);</span></a>
+<a name="3238"><span class="lineNum">    3238 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(-10920.373563712878);</span></a>
+<a name="3239"><span class="lineNum">    3239 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(72882.21702424977);</span></a>
+<a name="3240"><span class="lineNum">    3240 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(-51747.487078112754);</span></a>
+<a name="3241"><span class="lineNum">    3241 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA].push_back(11308.67842901876);</span></a>
+<a name="3242"><span class="lineNum">    3242 </span>            : </a>
+<a name="3243"><span class="lineNum">    3243 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(22737.624100119025);</span></a>
+<a name="3244"><span class="lineNum">    3244 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(-102.72714886664163);</span></a>
+<a name="3245"><span class="lineNum">    3245 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(-43685.329677789705);</span></a>
+<a name="3246"><span class="lineNum">    3246 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(-12564.259374093454);</span></a>
+<a name="3247"><span class="lineNum">    3247 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(83454.87540484876);</span></a>
+<a name="3248"><span class="lineNum">    3248 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(-60367.15652138888);</span></a>
+<a name="3249"><span class="lineNum">    3249 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_5].push_back(13507.33372986899);</span></a>
+<a name="3250"><span class="lineNum">    3250 </span>            : </a>
+<a name="3251"><span class="lineNum">    3251 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(22737.62410011902);</span></a>
+<a name="3252"><span class="lineNum">    3252 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(-101.57816684452263);</span></a>
+<a name="3253"><span class="lineNum">    3253 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(-43488.53670557616);</span></a>
+<a name="3254"><span class="lineNum">    3254 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(-12345.056184958417);</span></a>
+<a name="3255"><span class="lineNum">    3255 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(81963.5236411489);</span></a>
+<a name="3256"><span class="lineNum">    3256 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(-58791.59443618196);</span></a>
+<a name="3257"><span class="lineNum">    3257 </span><span class="lineCov">          6 :   parameter_solv[BB_DNA_3].push_back(13003.199362335576);</span></a>
+<a name="3258"><span class="lineNum">    3258 </span>            : </a>
+<a name="3259"><span class="lineNum">    3259 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(23953.752900120977);</span></a>
+<a name="3260"><span class="lineNum">    3260 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(-117.35779348824401);</span></a>
+<a name="3261"><span class="lineNum">    3261 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(-47644.41735332837);</span></a>
+<a name="3262"><span class="lineNum">    3262 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(-14641.556643789863);</span></a>
+<a name="3263"><span class="lineNum">    3263 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(96893.48627050382);</span></a>
+<a name="3264"><span class="lineNum">    3264 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(-72249.62534169314);</span></a>
+<a name="3265"><span class="lineNum">    3265 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA].push_back(16792.05552105538);</span></a>
+<a name="3266"><span class="lineNum">    3266 </span>            : </a>
+<a name="3267"><span class="lineNum">    3267 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(25574.406400119024);</span></a>
+<a name="3268"><span class="lineNum">    3268 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(-131.99642772933734);</span></a>
+<a name="3269"><span class="lineNum">    3269 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(-52136.51404531249);</span></a>
+<a name="3270"><span class="lineNum">    3270 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(-16682.14273917604);</span></a>
+<a name="3271"><span class="lineNum">    3271 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(110278.019216394);</span></a>
+<a name="3272"><span class="lineNum">    3272 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(-83715.92027818545);</span></a>
+<a name="3273"><span class="lineNum">    3273 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_5].push_back(19875.891337706045);</span></a>
+<a name="3274"><span class="lineNum">    3274 </span>            : </a>
+<a name="3275"><span class="lineNum">    3275 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(25574.406400119024);</span></a>
+<a name="3276"><span class="lineNum">    3276 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(-127.96875237036166);</span></a>
+<a name="3277"><span class="lineNum">    3277 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(-51407.183917584385);</span></a>
+<a name="3278"><span class="lineNum">    3278 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(-15922.900669975606);</span></a>
+<a name="3279"><span class="lineNum">    3279 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(105078.58889106264);</span></a>
+<a name="3280"><span class="lineNum">    3280 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(-78289.16276190648);</span></a>
+<a name="3281"><span class="lineNum">    3281 </span><span class="lineCov">          6 :   parameter_solv[BB_RNA_3].push_back(18156.83214344118);</span></a>
+<a name="3282"><span class="lineNum">    3282 </span>            : </a>
+<a name="3283"><span class="lineNum">    3283 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(13282.562500119211);</span></a>
+<a name="3284"><span class="lineNum">    3284 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(-76.45124168404048);</span></a>
+<a name="3285"><span class="lineNum">    3285 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(-28376.06994108963);</span></a>
+<a name="3286"><span class="lineNum">    3286 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(-9972.910773722022);</span></a>
+<a name="3287"><span class="lineNum">    3287 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(65873.86341939073);</span></a>
+<a name="3288"><span class="lineNum">    3288 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(-52064.33492910885);</span></a>
+<a name="3289"><span class="lineNum">    3289 </span><span class="lineCov">          6 :   parameter_solv[BASE_A].push_back(12931.608989412513);</span></a>
+<a name="3290"><span class="lineNum">    3290 </span>            : </a>
+<a name="3291"><span class="lineNum">    3291 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(10600.76160011891);</span></a>
+<a name="3292"><span class="lineNum">    3292 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(-49.1670871249108);</span></a>
+<a name="3293"><span class="lineNum">    3293 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(-20239.818742072875);</span></a>
+<a name="3294"><span class="lineNum">    3294 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(-6020.278780090207);</span></a>
+<a name="3295"><span class="lineNum">    3295 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(39632.13288981881);</span></a>
+<a name="3296"><span class="lineNum">    3296 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(-28954.779736165576);</span></a>
+<a name="3297"><span class="lineNum">    3297 </span><span class="lineCov">          6 :   parameter_solv[BASE_C].push_back(6551.541109526305);</span></a>
+<a name="3298"><span class="lineNum">    3298 </span>            : </a>
+<a name="3299"><span class="lineNum">    3299 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(15470.384400119934);</span></a>
+<a name="3300"><span class="lineNum">    3300 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(-93.8013620200972);</span></a>
+<a name="3301"><span class="lineNum">    3301 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(-36188.29687013545);</span></a>
+<a name="3302"><span class="lineNum">    3302 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(-13717.685098209471);</span></a>
+<a name="3303"><span class="lineNum">    3303 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(95658.18473657136);</span></a>
+<a name="3304"><span class="lineNum">    3304 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(-81262.37811451119);</span></a>
+<a name="3305"><span class="lineNum">    3305 </span><span class="lineCov">          6 :   parameter_solv[BASE_G].push_back(21841.903930943085);</span></a>
+<a name="3306"><span class="lineNum">    3306 </span>            : </a>
+<a name="3307"><span class="lineNum">    3307 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(17210.81610011936);</span></a>
+<a name="3308"><span class="lineNum">    3308 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(-93.10189802920208);</span></a>
+<a name="3309"><span class="lineNum">    3309 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(-36466.51927689957);</span></a>
+<a name="3310"><span class="lineNum">    3310 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(-12425.55615716932);</span></a>
+<a name="3311"><span class="lineNum">    3311 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(83847.427808925);</span></a>
+<a name="3312"><span class="lineNum">    3312 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(-66735.64997846584);</span></a>
+<a name="3313"><span class="lineNum">    3313 </span><span class="lineCov">          6 :   parameter_solv[BASE_T].push_back(16757.3463987507);</span></a>
+<a name="3314"><span class="lineNum">    3314 </span>            : </a>
+<a name="3315"><span class="lineNum">    3315 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(10909.802500119395);</span></a>
+<a name="3316"><span class="lineNum">    3316 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(-46.17712672768298);</span></a>
+<a name="3317"><span class="lineNum">    3317 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(-20149.67695512526);</span></a>
+<a name="3318"><span class="lineNum">    3318 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(-5590.242961204435);</span></a>
+<a name="3319"><span class="lineNum">    3319 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(37169.2740983132);</span></a>
+<a name="3320"><span class="lineNum">    3320 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(-26475.631627167604);</span></a>
+<a name="3321"><span class="lineNum">    3321 </span><span class="lineCov">          6 :   parameter_solv[BASE_U].push_back(5808.201015156168);</span></a>
+<a name="3322"><span class="lineNum">    3322 </span>            : </a>
+<a name="3323"><span class="lineNum">    3323 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(1487.2888381188868);</span></a>
+<a name="3324"><span class="lineNum">    3324 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(-0.6155376265599789);</span></a>
+<a name="3325"><span class="lineNum">    3325 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(-1181.5076027691764);</span></a>
+<a name="3326"><span class="lineNum">    3326 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(-66.25027450710594);</span></a>
+<a name="3327"><span class="lineNum">    3327 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(697.0421991965113);</span></a>
+<a name="3328"><span class="lineNum">    3328 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(-261.8559466354847);</span></a>
+<a name="3329"><span class="lineNum">    3329 </span><span class="lineCov">          6 :   parameter_mix[BB_PO2].push_back(9.974337082362194);</span></a>
+<a name="3330"><span class="lineNum">    3330 </span>            : </a>
+<a name="3331"><span class="lineNum">    3331 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(17766.29474499878);</span></a>
+<a name="3332"><span class="lineNum">    3332 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(-48.97330188566253);</span></a>
+<a name="3333"><span class="lineNum">    3333 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(-28199.563596327207);</span></a>
+<a name="3334"><span class="lineNum">    3334 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(-5623.82085602494);</span></a>
+<a name="3335"><span class="lineNum">    3335 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(39646.22954828498);</span></a>
+<a name="3336"><span class="lineNum">    3336 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(-24658.81157651943);</span></a>
+<a name="3337"><span class="lineNum">    3337 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA].push_back(4453.73906293146);</span></a>
+<a name="3338"><span class="lineNum">    3338 </span>            : </a>
+<a name="3339"><span class="lineNum">    3339 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(18696.09744203927);</span></a>
+<a name="3340"><span class="lineNum">    3340 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(-56.29408880833802);</span></a>
+<a name="3341"><span class="lineNum">    3341 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(-30486.108599707608);</span></a>
+<a name="3342"><span class="lineNum">    3342 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(-6524.195857141158);</span></a>
+<a name="3343"><span class="lineNum">    3343 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(45280.80142686446);</span></a>
+<a name="3344"><span class="lineNum">    3344 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(-29007.98616567993);</span></a>
+<a name="3345"><span class="lineNum">    3345 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_5].push_back(5488.566965501818);</span></a>
+<a name="3346"><span class="lineNum">    3346 </span>            : </a>
+<a name="3347"><span class="lineNum">    3347 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(18696.097442039274);</span></a>
+<a name="3348"><span class="lineNum">    3348 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(-55.5645003501971);</span></a>
+<a name="3349"><span class="lineNum">    3349 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(-30422.262113654506);</span></a>
+<a name="3350"><span class="lineNum">    3350 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(-6409.659659309089);</span></a>
+<a name="3351"><span class="lineNum">    3351 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(44605.76043515699);</span></a>
+<a name="3352"><span class="lineNum">    3352 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(-28295.62152988411);</span></a>
+<a name="3353"><span class="lineNum">    3353 </span><span class="lineCov">          6 :   parameter_mix[BB_DNA_3].push_back(5262.5765863484);</span></a>
+<a name="3354"><span class="lineNum">    3354 </span>            : </a>
+<a name="3355"><span class="lineNum">    3355 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(21356.177105457366);</span></a>
+<a name="3356"><span class="lineNum">    3356 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(-76.73490647754872);</span></a>
+<a name="3357"><span class="lineNum">    3357 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(-36845.234814782816);</span></a>
+<a name="3358"><span class="lineNum">    3358 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(-9066.559625582728);</span></a>
+<a name="3359"><span class="lineNum">    3359 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(61167.998793390485);</span></a>
+<a name="3360"><span class="lineNum">    3360 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(-41467.23384423218);</span></a>
+<a name="3361"><span class="lineNum">    3361 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA].push_back(8518.937793863257);</span></a>
+<a name="3362"><span class="lineNum">    3362 </span>            : </a>
+<a name="3363"><span class="lineNum">    3363 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(22386.63276427916);</span></a>
+<a name="3364"><span class="lineNum">    3364 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(-85.70426456933487);</span></a>
+<a name="3365"><span class="lineNum">    3365 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(-39490.50298502025);</span></a>
+<a name="3366"><span class="lineNum">    3366 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(-10223.702594972712);</span></a>
+<a name="3367"><span class="lineNum">    3367 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(68450.60459618448);</span></a>
+<a name="3368"><span class="lineNum">    3368 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(-47409.91098159006);</span></a>
+<a name="3369"><span class="lineNum">    3369 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_5].push_back(10031.136138513202);</span></a>
+<a name="3370"><span class="lineNum">    3370 </span>            : </a>
+<a name="3371"><span class="lineNum">    3371 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(22386.63276427916);</span></a>
+<a name="3372"><span class="lineNum">    3372 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(-81.93760812351479);</span></a>
+<a name="3373"><span class="lineNum">    3373 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(-39031.70571520093);</span></a>
+<a name="3374"><span class="lineNum">    3374 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(-9666.316086142708);</span></a>
+<a name="3375"><span class="lineNum">    3375 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(65120.07128126262);</span></a>
+<a name="3376"><span class="lineNum">    3376 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(-44110.13603681317);</span></a>
+<a name="3377"><span class="lineNum">    3377 </span><span class="lineCov">          6 :   parameter_mix[BB_RNA_3].push_back(9036.76498256983);</span></a>
+<a name="3378"><span class="lineNum">    3378 </span>            : </a>
+<a name="3379"><span class="lineNum">    3379 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(15897.31116611889);</span></a>
+<a name="3380"><span class="lineNum">    3380 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(-67.86385832953485);</span></a>
+<a name="3381"><span class="lineNum">    3381 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(-28851.754660951636);</span></a>
+<a name="3382"><span class="lineNum">    3382 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(-8144.431687170413);</span></a>
+<a name="3383"><span class="lineNum">    3383 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(53606.39082954489);</span></a>
+<a name="3384"><span class="lineNum">    3384 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(-38083.51243782253);</span></a>
+<a name="3385"><span class="lineNum">    3385 </span><span class="lineCov">          6 :   parameter_mix[BASE_A].push_back(8293.47107993253);</span></a>
+<a name="3386"><span class="lineNum">    3386 </span>            : </a>
+<a name="3387"><span class="lineNum">    3387 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(11733.2828871599);</span></a>
+<a name="3388"><span class="lineNum">    3388 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(-38.76775400274115);</span></a>
+<a name="3389"><span class="lineNum">    3389 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(-19318.84666423464);</span></a>
+<a name="3390"><span class="lineNum">    3390 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(-4507.915522704176);</span></a>
+<a name="3391"><span class="lineNum">    3391 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(30576.57671286052);</span></a>
+<a name="3392"><span class="lineNum">    3392 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(-20132.46696910844);</span></a>
+<a name="3393"><span class="lineNum">    3393 </span><span class="lineCov">          6 :   parameter_mix[BASE_C].push_back(3947.8727087996162);</span></a>
+<a name="3394"><span class="lineNum">    3394 </span>            : </a>
+<a name="3395"><span class="lineNum">    3395 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(19146.612417237808);</span></a>
+<a name="3396"><span class="lineNum">    3396 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(-102.37046638004914);</span></a>
+<a name="3397"><span class="lineNum">    3397 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(-38718.96478190546);</span></a>
+<a name="3398"><span class="lineNum">    3398 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(-13238.106081860074);</span></a>
+<a name="3399"><span class="lineNum">    3399 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(87309.07460288722);</span></a>
+<a name="3400"><span class="lineNum">    3400 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(-68364.82442984737);</span></a>
+<a name="3401"><span class="lineNum">    3401 </span><span class="lineCov">          6 :   parameter_mix[BASE_G].push_back(16815.362401369);</span></a>
+<a name="3402"><span class="lineNum">    3402 </span>            : </a>
+<a name="3403"><span class="lineNum">    3403 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(17050.440260819163);</span></a>
+<a name="3404"><span class="lineNum">    3404 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(-76.33750600643376);</span></a>
+<a name="3405"><span class="lineNum">    3405 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(-31849.539096715005);</span></a>
+<a name="3406"><span class="lineNum">    3406 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(-9484.498992751434);</span></a>
+<a name="3407"><span class="lineNum">    3407 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(62881.895771680494);</span></a>
+<a name="3408"><span class="lineNum">    3408 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(-46531.948557759024);</span></a>
+<a name="3409"><span class="lineNum">    3409 </span><span class="lineCov">          6 :   parameter_mix[BASE_T].push_back(10734.196329884822);</span></a>
+<a name="3410"><span class="lineNum">    3410 </span>            : </a>
+<a name="3411"><span class="lineNum">    3411 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(11904.095265219023);</span></a>
+<a name="3412"><span class="lineNum">    3412 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(-34.67511054915295);</span></a>
+<a name="3413"><span class="lineNum">    3413 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(-18842.275003104005);</span></a>
+<a name="3414"><span class="lineNum">    3414 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(-3993.1174764890684);</span></a>
+<a name="3415"><span class="lineNum">    3415 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(27663.625106762345);</span></a>
+<a name="3416"><span class="lineNum">    3416 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(-17577.387831701515);</span></a>
+<a name="3417"><span class="lineNum">    3417 </span><span class="lineCov">          6 :   parameter_mix[BASE_U].push_back(3273.183903219142);</span></a>
+<a name="3418"><span class="lineNum">    3418 </span>            : </a>
+<a name="3419"><span class="lineNum">    3419 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(960.8822037291127);</span></a>
+<a name="3420"><span class="lineNum">    3420 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(-0.09312135742159174);</span></a>
+<a name="3421"><span class="lineNum">    3421 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(-469.39643497461844);</span></a>
+<a name="3422"><span class="lineNum">    3422 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(-9.779346709041985);</span></a>
+<a name="3423"><span class="lineNum">    3423 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(162.1581550003227);</span></a>
+<a name="3424"><span class="lineNum">    3424 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(-37.06686233305618);</span></a>
+<a name="3425"><span class="lineNum">    3425 </span><span class="lineCov">          6 :   parameter_vac[BB_PO2].push_back(-4.695586672655664);</span></a>
+<a name="3426"><span class="lineNum">    3426 </span>            : </a>
+<a name="3427"><span class="lineNum">    3427 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(3720.2522996838984);</span></a>
+<a name="3428"><span class="lineNum">    3428 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(-5.4229642176938);</span></a>
+<a name="3429"><span class="lineNum">    3429 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(-4800.897672711981);</span></a>
+<a name="3430"><span class="lineNum">    3430 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(-597.2274673070993);</span></a>
+<a name="3431"><span class="lineNum">    3431 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(4825.908840953665);</span></a>
+<a name="3432"><span class="lineNum">    3432 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(-2451.397454446564);</span></a>
+<a name="3433"><span class="lineNum">    3433 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA].push_back(294.93071756645685);</span></a>
+<a name="3434"><span class="lineNum">    3434 </span>            : </a>
+<a name="3435"><span class="lineNum">    3435 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(3843.234214262163);</span></a>
+<a name="3436"><span class="lineNum">    3436 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(-6.423078416284452);</span></a>
+<a name="3437"><span class="lineNum">    3437 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(-5112.1216386963115);</span></a>
+<a name="3438"><span class="lineNum">    3438 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(-713.8373583426668);</span></a>
+<a name="3439"><span class="lineNum">    3439 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(5547.545382516269);</span></a>
+<a name="3440"><span class="lineNum">    3440 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(-2973.5659871174225);</span></a>
+<a name="3441"><span class="lineNum">    3441 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_5].push_back(407.2789106630427);</span></a>
+<a name="3442"><span class="lineNum">    3442 </span>            : </a>
+<a name="3443"><span class="lineNum">    3443 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(3843.234214262163);</span></a>
+<a name="3444"><span class="lineNum">    3444 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(-6.268636561475645);</span></a>
+<a name="3445"><span class="lineNum">    3445 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(-5103.192931218086);</span></a>
+<a name="3446"><span class="lineNum">    3446 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(-693.8705734390547);</span></a>
+<a name="3447"><span class="lineNum">    3447 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(5443.979645097035);</span></a>
+<a name="3448"><span class="lineNum">    3448 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(-2871.4337477324893);</span></a>
+<a name="3449"><span class="lineNum">    3449 </span><span class="lineCov">          6 :   parameter_vac[BB_DNA_3].push_back(377.3062915349831);</span></a>
+<a name="3450"><span class="lineNum">    3450 </span>            : </a>
+<a name="3451"><span class="lineNum">    3451 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(4760.071443398374);</span></a>
+<a name="3452"><span class="lineNum">    3452 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(-11.0990475402486);</span></a>
+<a name="3453"><span class="lineNum">    3453 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(-6934.713566418421);</span></a>
+<a name="3454"><span class="lineNum">    3454 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(-1256.5202524085096);</span></a>
+<a name="3455"><span class="lineNum">    3455 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(9024.962587066922);</span></a>
+<a name="3456"><span class="lineNum">    3456 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(-5386.842667932241);</span></a>
+<a name="3457"><span class="lineNum">    3457 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA].push_back(907.42947751372);</span></a>
+<a name="3458"><span class="lineNum">    3458 </span>            : </a>
+<a name="3459"><span class="lineNum">    3459 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(4899.051406033406);</span></a>
+<a name="3460"><span class="lineNum">    3460 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(-12.279240472628238);</span></a>
+<a name="3461"><span class="lineNum">    3461 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(-7276.273570813667);</span></a>
+<a name="3462"><span class="lineNum">    3462 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(-1400.9520839250868);</span></a>
+<a name="3463"><span class="lineNum">    3463 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(9912.215823228895);</span></a>
+<a name="3464"><span class="lineNum">    3464 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(-6079.2565270404075);</span></a>
+<a name="3465"><span class="lineNum">    3465 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_5].push_back(1073.53428175472);</span></a>
+<a name="3466"><span class="lineNum">    3466 </span>            : </a>
+<a name="3467"><span class="lineNum">    3467 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(4899.051406033406);</span></a>
+<a name="3468"><span class="lineNum">    3468 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(-11.642804195148194);</span></a>
+<a name="3469"><span class="lineNum">    3469 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(-7213.774619570996);</span></a>
+<a name="3470"><span class="lineNum">    3470 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(-1317.4463949342964);</span></a>
+<a name="3471"><span class="lineNum">    3471 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(9450.928929264686);</span></a>
+<a name="3472"><span class="lineNum">    3472 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(-5643.856117200917);</span></a>
+<a name="3473"><span class="lineNum">    3473 </span><span class="lineCov">          6 :   parameter_vac[BB_RNA_3].push_back(949.4698817407918);</span></a>
+<a name="3474"><span class="lineNum">    3474 </span>            : </a>
+<a name="3475"><span class="lineNum">    3475 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(4756.697028810353);</span></a>
+<a name="3476"><span class="lineNum">    3476 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(-12.158940746852812);</span></a>
+<a name="3477"><span class="lineNum">    3477 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(-7106.473423744205);</span></a>
+<a name="3478"><span class="lineNum">    3478 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(-1376.295184173137);</span></a>
+<a name="3479"><span class="lineNum">    3479 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(9747.132255557788);</span></a>
+<a name="3480"><span class="lineNum">    3480 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(-5900.026637038756);</span></a>
+<a name="3481"><span class="lineNum">    3481 </span><span class="lineCov">          6 :   parameter_vac[BASE_A].push_back(1004.6226388342955);</span></a>
+<a name="3482"><span class="lineNum">    3482 </span>            : </a>
+<a name="3483"><span class="lineNum">    3483 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(3246.698975674651);</span></a>
+<a name="3484"><span class="lineNum">    3484 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(-6.125036521218687);</span></a>
+<a name="3485"><span class="lineNum">    3485 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(-4280.666521437201);</span></a>
+<a name="3486"><span class="lineNum">    3486 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(-684.0183580843932);</span></a>
+<a name="3487"><span class="lineNum">    3487 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(5077.062889522692);</span></a>
+<a name="3488"><span class="lineNum">    3488 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(-2870.3239317750963);</span></a>
+<a name="3489"><span class="lineNum">    3489 </span><span class="lineCov">          6 :   parameter_vac[BASE_C].push_back(434.51551177863547);</span></a>
+<a name="3490"><span class="lineNum">    3490 </span>            : </a>
+<a name="3491"><span class="lineNum">    3491 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(5924.105658596052);</span></a>
+<a name="3492"><span class="lineNum">    3492 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(-23.097956587232552);</span></a>
+<a name="3493"><span class="lineNum">    3493 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(-10149.526301285418);</span></a>
+<a name="3494"><span class="lineNum">    3494 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(-2752.9166169522528);</span></a>
+<a name="3495"><span class="lineNum">    3495 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(18239.32985385683);</span></a>
+<a name="3496"><span class="lineNum">    3496 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(-12749.277858800957);</span></a>
+<a name="3497"><span class="lineNum">    3497 </span><span class="lineCov">          6 :   parameter_vac[BASE_G].push_back(2715.354663787367);</span></a>
+<a name="3498"><span class="lineNum">    3498 </span>            : </a>
+<a name="3499"><span class="lineNum">    3499 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(4222.889713694404);</span></a>
+<a name="3500"><span class="lineNum">    3500 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(-12.15861456306705);</span></a>
+<a name="3501"><span class="lineNum">    3501 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(-6395.50289789404);</span></a>
+<a name="3502"><span class="lineNum">    3502 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(-1421.3942549301012);</span></a>
+<a name="3503"><span class="lineNum">    3503 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(9757.061008720135);</span></a>
+<a name="3504"><span class="lineNum">    3504 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(-6399.630933839126);</span></a>
+<a name="3505"><span class="lineNum">    3505 </span><span class="lineCov">          6 :   parameter_vac[BASE_T].push_back(1258.9874225605438);</span></a>
+<a name="3506"><span class="lineNum">    3506 </span>            : </a>
+<a name="3507"><span class="lineNum">    3507 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(3247.251361465539);</span></a>
+<a name="3508"><span class="lineNum">    3508 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(-5.211020853261115);</span></a>
+<a name="3509"><span class="lineNum">    3509 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(-4125.165310360279);</span></a>
+<a name="3510"><span class="lineNum">    3510 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(-575.1860235473902);</span></a>
+<a name="3511"><span class="lineNum">    3511 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(4457.6562621371495);</span></a>
+<a name="3512"><span class="lineNum">    3512 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(-2368.7250146912766);</span></a>
+<a name="3513"><span class="lineNum">    3513 </span><span class="lineCov">          6 :   parameter_vac[BASE_U].push_back(313.23997718445014);</span></a>
+<a name="3514"><span class="lineNum">    3514 </span>            : </a>
+<a name="3515"><span class="lineNum">    3515 </span><span class="lineCov">      21178 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="3516"><span class="lineNum">    3516 </span><span class="lineCov">      21172 :     std::string Aname = pdb.getAtomName(atoms[i]);</span></a>
+<a name="3517"><span class="lineNum">    3517 </span><span class="lineCov">      21172 :     std::string Rname = pdb.getResidueName(atoms[i]);</span></a>
+<a name="3518"><span class="lineNum">    3518 </span><span class="lineCov">      21172 :     Rname.erase(std::remove_if(Rname.begin(), Rname.end(), ::isspace),Rname.end());</span></a>
+<a name="3519"><span class="lineNum">    3519 </span><span class="lineCov">      21172 :     if(Rname==&quot;ALA&quot;) {</span></a>
+<a name="3520"><span class="lineNum">    3520 </span><span class="lineCov">       1098 :       atoi[residue_atom[i]]=ALA;</span></a>
+<a name="3521"><span class="lineNum">    3521 </span><span class="lineCov">      20074 :     } else if(Rname==&quot;ARG&quot;) {</span></a>
+<a name="3522"><span class="lineNum">    3522 </span><span class="lineCov">       1296 :       atoi[residue_atom[i]]=ARG;</span></a>
+<a name="3523"><span class="lineNum">    3523 </span><span class="lineCov">      18778 :     } else if(Rname==&quot;ASN&quot;) {</span></a>
+<a name="3524"><span class="lineNum">    3524 </span><span class="lineCov">       1080 :       atoi[residue_atom[i]]=ASN;</span></a>
+<a name="3525"><span class="lineNum">    3525 </span><span class="lineCov">      17698 :     } else if(Rname==&quot;ASP&quot;) {</span></a>
+<a name="3526"><span class="lineNum">    3526 </span><span class="lineCov">        936 :       atoi[residue_atom[i]]=ASP;</span></a>
+<a name="3527"><span class="lineNum">    3527 </span><span class="lineCov">      16762 :     } else if(Rname==&quot;CYS&quot;) {</span></a>
+<a name="3528"><span class="lineNum">    3528 </span><span class="lineCov">         72 :       atoi[residue_atom[i]]=CYS;</span></a>
+<a name="3529"><span class="lineNum">    3529 </span><span class="lineCov">      16690 :     } else if(Rname==&quot;GLN&quot;) {</span></a>
+<a name="3530"><span class="lineNum">    3530 </span><span class="lineCov">       1596 :       atoi[residue_atom[i]]=GLN;</span></a>
+<a name="3531"><span class="lineNum">    3531 </span><span class="lineCov">      15094 :     } else if(Rname==&quot;GLU&quot;) {</span></a>
+<a name="3532"><span class="lineNum">    3532 </span><span class="lineCov">        714 :       atoi[residue_atom[i]]=GLU;</span></a>
+<a name="3533"><span class="lineNum">    3533 </span><span class="lineCov">      14380 :     } else if(Rname==&quot;GLY&quot;) {</span></a>
+<a name="3534"><span class="lineNum">    3534 </span><span class="lineCov">        972 :       atoi[residue_atom[i]]=GLY;</span></a>
+<a name="3535"><span class="lineNum">    3535 </span><span class="lineCov">      13408 :     } else if(Rname==&quot;HIS&quot;) {</span></a>
+<a name="3536"><span class="lineNum">    3536 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="3537"><span class="lineNum">    3537 </span><span class="lineCov">      13408 :     } else if(Rname==&quot;HID&quot;) {</span></a>
+<a name="3538"><span class="lineNum">    3538 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="3539"><span class="lineNum">    3539 </span><span class="lineCov">      13408 :     } else if(Rname==&quot;HIE&quot;) {</span></a>
+<a name="3540"><span class="lineNum">    3540 </span><span class="lineCov">        216 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="3541"><span class="lineNum">    3541 </span><span class="lineCov">      13192 :     } else if(Rname==&quot;HIP&quot;) {</span></a>
+<a name="3542"><span class="lineNum">    3542 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIP;</span></a>
+<a name="3543"><span class="lineNum">    3543 </span>            :       // CHARMM NAMING FOR PROTONATION STATES OF HISTIDINE</a>
+<a name="3544"><span class="lineNum">    3544 </span><span class="lineCov">      13192 :     } else if(Rname==&quot;HSD&quot;) {</span></a>
+<a name="3545"><span class="lineNum">    3545 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="3546"><span class="lineNum">    3546 </span><span class="lineCov">      13192 :     } else if(Rname==&quot;HSE&quot;) {</span></a>
+<a name="3547"><span class="lineNum">    3547 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="3548"><span class="lineNum">    3548 </span><span class="lineCov">      13192 :     } else if(Rname==&quot;HSP&quot;) {</span></a>
+<a name="3549"><span class="lineNum">    3549 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIP;</span></a>
+<a name="3550"><span class="lineNum">    3550 </span><span class="lineCov">      13192 :     } else if(Rname==&quot;ILE&quot;) {</span></a>
+<a name="3551"><span class="lineNum">    3551 </span><span class="lineCov">       1296 :       atoi[residue_atom[i]]=ILE;</span></a>
+<a name="3552"><span class="lineNum">    3552 </span><span class="lineCov">      11896 :     } else if(Rname==&quot;LEU&quot;) {</span></a>
+<a name="3553"><span class="lineNum">    3553 </span><span class="lineCov">       2280 :       atoi[residue_atom[i]]=LEU;</span></a>
+<a name="3554"><span class="lineNum">    3554 </span><span class="lineCov">       9616 :     } else if(Rname==&quot;LYS&quot;) {</span></a>
+<a name="3555"><span class="lineNum">    3555 </span><span class="lineCov">       1560 :       atoi[residue_atom[i]]=LYS;</span></a>
+<a name="3556"><span class="lineNum">    3556 </span><span class="lineCov">       8056 :     } else if(Rname==&quot;MET&quot;) {</span></a>
+<a name="3557"><span class="lineNum">    3557 </span><span class="lineCov">        912 :       atoi[residue_atom[i]]=MET;</span></a>
+<a name="3558"><span class="lineNum">    3558 </span><span class="lineCov">       7144 :     } else if(Rname==&quot;PHE&quot;) {</span></a>
+<a name="3559"><span class="lineNum">    3559 </span><span class="lineCov">       1512 :       atoi[residue_atom[i]]=PHE;</span></a>
+<a name="3560"><span class="lineNum">    3560 </span><span class="lineCov">       5632 :     } else if(Rname==&quot;PRO&quot;) {</span></a>
+<a name="3561"><span class="lineNum">    3561 </span><span class="lineCov">       1122 :       atoi[residue_atom[i]]=PRO;</span></a>
+<a name="3562"><span class="lineNum">    3562 </span><span class="lineCov">       4510 :     } else if(Rname==&quot;SER&quot;) {</span></a>
+<a name="3563"><span class="lineNum">    3563 </span><span class="lineCov">        792 :       atoi[residue_atom[i]]=SER;</span></a>
+<a name="3564"><span class="lineNum">    3564 </span><span class="lineCov">       3718 :     } else if(Rname==&quot;THR&quot;) {</span></a>
+<a name="3565"><span class="lineNum">    3565 </span><span class="lineCov">        756 :       atoi[residue_atom[i]]=THR;</span></a>
+<a name="3566"><span class="lineNum">    3566 </span><span class="lineCov">       2962 :     } else if(Rname==&quot;TRP&quot;) {</span></a>
+<a name="3567"><span class="lineNum">    3567 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=TRP;</span></a>
+<a name="3568"><span class="lineNum">    3568 </span><span class="lineCov">       2962 :     } else if(Rname==&quot;TYR&quot;) {</span></a>
+<a name="3569"><span class="lineNum">    3569 </span><span class="lineCov">        792 :       atoi[residue_atom[i]]=TYR;</span></a>
+<a name="3570"><span class="lineNum">    3570 </span><span class="lineCov">       2170 :     } else if(Rname==&quot;VAL&quot;) {</span></a>
+<a name="3571"><span class="lineNum">    3571 </span><span class="lineCov">       1632 :       atoi[residue_atom[i]]=VAL;</span></a>
+<a name="3572"><span class="lineNum">    3572 </span>            :     }</a>
+<a name="3573"><span class="lineNum">    3573 </span>            :     // NUCLEIC ACIDS</a>
+<a name="3574"><span class="lineNum">    3574 </span>            :     // nucleobases are not automatically populated as an additional check on the health of the PDB.</a>
+<a name="3575"><span class="lineNum">    3575 </span>            :     // RNA - G</a>
+<a name="3576"><span class="lineNum">    3576 </span><span class="lineCov">        538 :     else if(Rname==&quot;G&quot;) {</span></a>
+<a name="3577"><span class="lineNum">    3577 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3578"><span class="lineNum">    3578 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3579"><span class="lineNum">    3579 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3580"><span class="lineNum">    3580 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3581"><span class="lineNum">    3581 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3582"><span class="lineNum">    3582 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3583"><span class="lineNum">    3583 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3584"><span class="lineNum">    3584 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3585"><span class="lineNum">    3585 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3586"><span class="lineNum">    3586 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="3587"><span class="lineNum">    3587 </span><span class="lineNoCov">          0 :       } else if( Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3588"><span class="lineNum">    3588 </span><span class="lineNoCov">          0 :                  Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="3589"><span class="lineNum">    3589 </span><span class="lineNoCov">          0 :                  Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="3590"><span class="lineNum">    3590 </span><span class="lineNoCov">          0 :                  Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="3591"><span class="lineNum">    3591 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="3592"><span class="lineNum">    3592 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3593"><span class="lineNum">    3593 </span>            :       // RNA - G3</a>
+<a name="3594"><span class="lineNum">    3594 </span><span class="lineCov">        538 :     } else if(Rname==&quot;G3&quot;) {</span></a>
+<a name="3595"><span class="lineNum">    3595 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3596"><span class="lineNum">    3596 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3597"><span class="lineNum">    3597 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3598"><span class="lineNum">    3598 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3599"><span class="lineNum">    3599 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3600"><span class="lineNum">    3600 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3601"><span class="lineNum">    3601 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3602"><span class="lineNum">    3602 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3603"><span class="lineNum">    3603 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="3604"><span class="lineNum">    3604 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="3605"><span class="lineNum">    3605 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3606"><span class="lineNum">    3606 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="3607"><span class="lineNum">    3607 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="3608"><span class="lineNum">    3608 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="3609"><span class="lineNum">    3609 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="3610"><span class="lineNum">    3610 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3611"><span class="lineNum">    3611 </span>            :       // RNA - G5</a>
+<a name="3612"><span class="lineNum">    3612 </span><span class="lineCov">        538 :     } else if(Rname==&quot;G5&quot;) {</span></a>
+<a name="3613"><span class="lineNum">    3613 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3614"><span class="lineNum">    3614 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3615"><span class="lineNum">    3615 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3616"><span class="lineNum">    3616 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3617"><span class="lineNum">    3617 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="3618"><span class="lineNum">    3618 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3619"><span class="lineNum">    3619 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="3620"><span class="lineNum">    3620 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3621"><span class="lineNum">    3621 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="3622"><span class="lineNum">    3622 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="3623"><span class="lineNum">    3623 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="3624"><span class="lineNum">    3624 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="3625"><span class="lineNum">    3625 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3626"><span class="lineNum">    3626 </span>            :       // RNA - U</a>
+<a name="3627"><span class="lineNum">    3627 </span><span class="lineCov">        538 :     } else if(Rname==&quot;U&quot;) {</span></a>
+<a name="3628"><span class="lineNum">    3628 </span><span class="lineCov">       1554 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3629"><span class="lineNum">    3629 </span><span class="lineCov">       1176 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3630"><span class="lineNum">    3630 </span><span class="lineCov">         42 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3631"><span class="lineNum">    3631 </span><span class="lineCov">       1372 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3632"><span class="lineNum">    3632 </span><span class="lineCov">       1148 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3633"><span class="lineNum">    3633 </span><span class="lineCov">        924 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3634"><span class="lineNum">    3634 </span><span class="lineCov">        714 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3635"><span class="lineNum">    3635 </span><span class="lineCov">        644 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3636"><span class="lineNum">    3636 </span><span class="lineCov">        840 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3637"><span class="lineNum">    3637 </span><span class="lineCov">        224 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="3638"><span class="lineNum">    3638 </span><span class="lineCov">        476 :       } else if( Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3639"><span class="lineNum">    3639 </span><span class="lineCov">        252 :                  Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="3640"><span class="lineNum">    3640 </span><span class="lineCov">        196 :                  Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="3641"><span class="lineNum">    3641 </span><span class="lineCov">        154 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="3642"><span class="lineNum">    3642 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3643"><span class="lineNum">    3643 </span>            :       // RNA - U3</a>
+<a name="3644"><span class="lineNum">    3644 </span><span class="lineCov">        118 :     } else if(Rname==&quot;U3&quot;) {</span></a>
+<a name="3645"><span class="lineNum">    3645 </span><span class="lineCov">        230 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3646"><span class="lineNum">    3646 </span><span class="lineCov">        174 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3647"><span class="lineNum">    3647 </span><span class="lineCov">          6 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3648"><span class="lineNum">    3648 </span><span class="lineCov">        204 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3649"><span class="lineNum">    3649 </span><span class="lineCov">        172 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3650"><span class="lineNum">    3650 </span><span class="lineCov">        140 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3651"><span class="lineNum">    3651 </span><span class="lineCov">        110 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3652"><span class="lineNum">    3652 </span><span class="lineCov">         94 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3653"><span class="lineNum">    3653 </span><span class="lineCov">         78 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="3654"><span class="lineNum">    3654 </span><span class="lineCov">         34 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="3655"><span class="lineNum">    3655 </span><span class="lineCov">         68 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3656"><span class="lineNum">    3656 </span><span class="lineCov">         36 :                 Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="3657"><span class="lineNum">    3657 </span><span class="lineCov">         28 :                 Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="3658"><span class="lineNum">    3658 </span><span class="lineCov">         22 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="3659"><span class="lineNum">    3659 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3660"><span class="lineNum">    3660 </span>            :       // RNA - U5</a>
+<a name="3661"><span class="lineNum">    3661 </span><span class="lineCov">         56 :     } else if(Rname==&quot;U5&quot;) {</span></a>
+<a name="3662"><span class="lineNum">    3662 </span><span class="lineCov">        204 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3663"><span class="lineNum">    3663 </span><span class="lineCov">        172 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3664"><span class="lineNum">    3664 </span><span class="lineCov">        140 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3665"><span class="lineNum">    3665 </span><span class="lineCov">        108 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3666"><span class="lineNum">    3666 </span><span class="lineCov">         88 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="3667"><span class="lineNum">    3667 </span><span class="lineCov">         78 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3668"><span class="lineNum">    3668 </span><span class="lineCov">         34 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="3669"><span class="lineNum">    3669 </span><span class="lineCov">         68 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3670"><span class="lineNum">    3670 </span><span class="lineCov">         36 :                 Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="3671"><span class="lineNum">    3671 </span><span class="lineCov">         28 :                 Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="3672"><span class="lineNum">    3672 </span><span class="lineCov">         22 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="3673"><span class="lineNum">    3673 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3674"><span class="lineNum">    3674 </span>            :       // RNA - A</a>
+<a name="3675"><span class="lineNum">    3675 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A&quot;) {</span></a>
+<a name="3676"><span class="lineNum">    3676 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3677"><span class="lineNum">    3677 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3678"><span class="lineNum">    3678 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3679"><span class="lineNum">    3679 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3680"><span class="lineNum">    3680 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3681"><span class="lineNum">    3681 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3682"><span class="lineNum">    3682 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3683"><span class="lineNum">    3683 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3684"><span class="lineNum">    3684 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3685"><span class="lineNum">    3685 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="3686"><span class="lineNum">    3686 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="3687"><span class="lineNum">    3687 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="3688"><span class="lineNum">    3688 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="3689"><span class="lineNum">    3689 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="3690"><span class="lineNum">    3690 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="3691"><span class="lineNum">    3691 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3692"><span class="lineNum">    3692 </span>            :       // RNA - A3</a>
+<a name="3693"><span class="lineNum">    3693 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A3&quot;) {</span></a>
+<a name="3694"><span class="lineNum">    3694 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3695"><span class="lineNum">    3695 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3696"><span class="lineNum">    3696 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3697"><span class="lineNum">    3697 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3698"><span class="lineNum">    3698 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3699"><span class="lineNum">    3699 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3700"><span class="lineNum">    3700 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3701"><span class="lineNum">    3701 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3702"><span class="lineNum">    3702 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="3703"><span class="lineNum">    3703 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="3704"><span class="lineNum">    3704 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="3705"><span class="lineNum">    3705 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="3706"><span class="lineNum">    3706 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="3707"><span class="lineNum">    3707 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="3708"><span class="lineNum">    3708 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="3709"><span class="lineNum">    3709 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3710"><span class="lineNum">    3710 </span>            :       // RNA - A5</a>
+<a name="3711"><span class="lineNum">    3711 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A5&quot;) {</span></a>
+<a name="3712"><span class="lineNum">    3712 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3713"><span class="lineNum">    3713 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3714"><span class="lineNum">    3714 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3715"><span class="lineNum">    3715 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3716"><span class="lineNum">    3716 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="3717"><span class="lineNum">    3717 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3718"><span class="lineNum">    3718 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="3719"><span class="lineNum">    3719 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="3720"><span class="lineNum">    3720 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="3721"><span class="lineNum">    3721 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="3722"><span class="lineNum">    3722 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="3723"><span class="lineNum">    3723 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="3724"><span class="lineNum">    3724 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3725"><span class="lineNum">    3725 </span>            :       // RNA - C</a>
+<a name="3726"><span class="lineNum">    3726 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C&quot;) {</span></a>
+<a name="3727"><span class="lineNum">    3727 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3728"><span class="lineNum">    3728 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3729"><span class="lineNum">    3729 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3730"><span class="lineNum">    3730 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3731"><span class="lineNum">    3731 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3732"><span class="lineNum">    3732 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3733"><span class="lineNum">    3733 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3734"><span class="lineNum">    3734 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3735"><span class="lineNum">    3735 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3736"><span class="lineNum">    3736 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="3737"><span class="lineNum">    3737 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="3738"><span class="lineNum">    3738 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="3739"><span class="lineNum">    3739 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="3740"><span class="lineNum">    3740 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="3741"><span class="lineNum">    3741 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3742"><span class="lineNum">    3742 </span>            :       // RNA - C3</a>
+<a name="3743"><span class="lineNum">    3743 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C3&quot;) {</span></a>
+<a name="3744"><span class="lineNum">    3744 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3745"><span class="lineNum">    3745 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3746"><span class="lineNum">    3746 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3747"><span class="lineNum">    3747 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3748"><span class="lineNum">    3748 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3749"><span class="lineNum">    3749 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3750"><span class="lineNum">    3750 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="3751"><span class="lineNum">    3751 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="3752"><span class="lineNum">    3752 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="3753"><span class="lineNum">    3753 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="3754"><span class="lineNum">    3754 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="3755"><span class="lineNum">    3755 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="3756"><span class="lineNum">    3756 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="3757"><span class="lineNum">    3757 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="3758"><span class="lineNum">    3758 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3759"><span class="lineNum">    3759 </span>            :       // RNA - C5</a>
+<a name="3760"><span class="lineNum">    3760 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C5&quot;) {</span></a>
+<a name="3761"><span class="lineNum">    3761 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3762"><span class="lineNum">    3762 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="3763"><span class="lineNum">    3763 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="3764"><span class="lineNum">    3764 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3765"><span class="lineNum">    3765 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="3766"><span class="lineNum">    3766 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="3767"><span class="lineNum">    3767 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="3768"><span class="lineNum">    3768 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="3769"><span class="lineNum">    3769 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="3770"><span class="lineNum">    3770 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="3771"><span class="lineNum">    3771 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="3772"><span class="lineNum">    3772 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3773"><span class="lineNum">    3773 </span>            :       // DNA - G</a>
+<a name="3774"><span class="lineNum">    3774 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG&quot;) {</span></a>
+<a name="3775"><span class="lineNum">    3775 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3776"><span class="lineNum">    3776 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3777"><span class="lineNum">    3777 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3778"><span class="lineNum">    3778 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3779"><span class="lineNum">    3779 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3780"><span class="lineNum">    3780 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3781"><span class="lineNum">    3781 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3782"><span class="lineNum">    3782 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="3783"><span class="lineNum">    3783 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="3784"><span class="lineNum">    3784 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="3785"><span class="lineNum">    3785 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3786"><span class="lineNum">    3786 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="3787"><span class="lineNum">    3787 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="3788"><span class="lineNum">    3788 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="3789"><span class="lineNum">    3789 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="3790"><span class="lineNum">    3790 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3791"><span class="lineNum">    3791 </span>            :       // DNA - G3</a>
+<a name="3792"><span class="lineNum">    3792 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG3&quot;) {</span></a>
+<a name="3793"><span class="lineNum">    3793 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3794"><span class="lineNum">    3794 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3795"><span class="lineNum">    3795 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3796"><span class="lineNum">    3796 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3797"><span class="lineNum">    3797 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3798"><span class="lineNum">    3798 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3799"><span class="lineNum">    3799 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="3800"><span class="lineNum">    3800 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3801"><span class="lineNum">    3801 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="3802"><span class="lineNum">    3802 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="3803"><span class="lineNum">    3803 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3804"><span class="lineNum">    3804 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="3805"><span class="lineNum">    3805 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="3806"><span class="lineNum">    3806 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="3807"><span class="lineNum">    3807 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="3808"><span class="lineNum">    3808 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3809"><span class="lineNum">    3809 </span>            :       // DNA - G5</a>
+<a name="3810"><span class="lineNum">    3810 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG5&quot;) {</span></a>
+<a name="3811"><span class="lineNum">    3811 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3812"><span class="lineNum">    3812 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="3813"><span class="lineNum">    3813 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3814"><span class="lineNum">    3814 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3815"><span class="lineNum">    3815 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3816"><span class="lineNum">    3816 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="3817"><span class="lineNum">    3817 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="3818"><span class="lineNum">    3818 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="3819"><span class="lineNum">    3819 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="3820"><span class="lineNum">    3820 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="3821"><span class="lineNum">    3821 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="3822"><span class="lineNum">    3822 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="3823"><span class="lineNum">    3823 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3824"><span class="lineNum">    3824 </span>            :       // DNA - T</a>
+<a name="3825"><span class="lineNum">    3825 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT&quot;) {</span></a>
+<a name="3826"><span class="lineNum">    3826 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3827"><span class="lineNum">    3827 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3828"><span class="lineNum">    3828 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3829"><span class="lineNum">    3829 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3830"><span class="lineNum">    3830 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3831"><span class="lineNum">    3831 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3832"><span class="lineNum">    3832 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3833"><span class="lineNum">    3833 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="3834"><span class="lineNum">    3834 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="3835"><span class="lineNum">    3835 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="3836"><span class="lineNum">    3836 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="3837"><span class="lineNum">    3837 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="3838"><span class="lineNum">    3838 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="3839"><span class="lineNum">    3839 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="3840"><span class="lineNum">    3840 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="3841"><span class="lineNum">    3841 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3842"><span class="lineNum">    3842 </span>            :       // DNA - T3</a>
+<a name="3843"><span class="lineNum">    3843 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT3&quot;) {</span></a>
+<a name="3844"><span class="lineNum">    3844 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3845"><span class="lineNum">    3845 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3846"><span class="lineNum">    3846 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3847"><span class="lineNum">    3847 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3848"><span class="lineNum">    3848 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3849"><span class="lineNum">    3849 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3850"><span class="lineNum">    3850 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="3851"><span class="lineNum">    3851 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3852"><span class="lineNum">    3852 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="3853"><span class="lineNum">    3853 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="3854"><span class="lineNum">    3854 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="3855"><span class="lineNum">    3855 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="3856"><span class="lineNum">    3856 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="3857"><span class="lineNum">    3857 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="3858"><span class="lineNum">    3858 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="3859"><span class="lineNum">    3859 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3860"><span class="lineNum">    3860 </span>            :       // DNA - T5</a>
+<a name="3861"><span class="lineNum">    3861 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT5&quot;) {</span></a>
+<a name="3862"><span class="lineNum">    3862 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3863"><span class="lineNum">    3863 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="3864"><span class="lineNum">    3864 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3865"><span class="lineNum">    3865 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3866"><span class="lineNum">    3866 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3867"><span class="lineNum">    3867 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="3868"><span class="lineNum">    3868 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="3869"><span class="lineNum">    3869 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="3870"><span class="lineNum">    3870 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="3871"><span class="lineNum">    3871 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="3872"><span class="lineNum">    3872 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="3873"><span class="lineNum">    3873 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="3874"><span class="lineNum">    3874 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3875"><span class="lineNum">    3875 </span>            :       // DNA - A</a>
+<a name="3876"><span class="lineNum">    3876 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA&quot;) {</span></a>
+<a name="3877"><span class="lineNum">    3877 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3878"><span class="lineNum">    3878 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3879"><span class="lineNum">    3879 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3880"><span class="lineNum">    3880 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3881"><span class="lineNum">    3881 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3882"><span class="lineNum">    3882 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3883"><span class="lineNum">    3883 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3884"><span class="lineNum">    3884 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="3885"><span class="lineNum">    3885 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="3886"><span class="lineNum">    3886 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="3887"><span class="lineNum">    3887 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="3888"><span class="lineNum">    3888 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="3889"><span class="lineNum">    3889 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="3890"><span class="lineNum">    3890 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="3891"><span class="lineNum">    3891 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="3892"><span class="lineNum">    3892 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3893"><span class="lineNum">    3893 </span>            :       // DNA - A3</a>
+<a name="3894"><span class="lineNum">    3894 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA3&quot;) {</span></a>
+<a name="3895"><span class="lineNum">    3895 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3896"><span class="lineNum">    3896 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3897"><span class="lineNum">    3897 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3898"><span class="lineNum">    3898 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3899"><span class="lineNum">    3899 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3900"><span class="lineNum">    3900 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3901"><span class="lineNum">    3901 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="3902"><span class="lineNum">    3902 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3903"><span class="lineNum">    3903 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="3904"><span class="lineNum">    3904 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="3905"><span class="lineNum">    3905 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="3906"><span class="lineNum">    3906 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="3907"><span class="lineNum">    3907 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="3908"><span class="lineNum">    3908 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="3909"><span class="lineNum">    3909 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="3910"><span class="lineNum">    3910 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3911"><span class="lineNum">    3911 </span>            :       // DNA - A5</a>
+<a name="3912"><span class="lineNum">    3912 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA5&quot;) {</span></a>
+<a name="3913"><span class="lineNum">    3913 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3914"><span class="lineNum">    3914 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="3915"><span class="lineNum">    3915 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3916"><span class="lineNum">    3916 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3917"><span class="lineNum">    3917 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3918"><span class="lineNum">    3918 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="3919"><span class="lineNum">    3919 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="3920"><span class="lineNum">    3920 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="3921"><span class="lineNum">    3921 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="3922"><span class="lineNum">    3922 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="3923"><span class="lineNum">    3923 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="3924"><span class="lineNum">    3924 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="3925"><span class="lineNum">    3925 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3926"><span class="lineNum">    3926 </span>            :       // DNA - C</a>
+<a name="3927"><span class="lineNum">    3927 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC&quot;) {</span></a>
+<a name="3928"><span class="lineNum">    3928 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3929"><span class="lineNum">    3929 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3930"><span class="lineNum">    3930 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3931"><span class="lineNum">    3931 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3932"><span class="lineNum">    3932 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3933"><span class="lineNum">    3933 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3934"><span class="lineNum">    3934 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3935"><span class="lineNum">    3935 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="3936"><span class="lineNum">    3936 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="3937"><span class="lineNum">    3937 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="3938"><span class="lineNum">    3938 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="3939"><span class="lineNum">    3939 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="3940"><span class="lineNum">    3940 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="3941"><span class="lineNum">    3941 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="3942"><span class="lineNum">    3942 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3943"><span class="lineNum">    3943 </span>            :       // DNA - C3</a>
+<a name="3944"><span class="lineNum">    3944 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC3&quot;) {</span></a>
+<a name="3945"><span class="lineNum">    3945 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="3946"><span class="lineNum">    3946 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="3947"><span class="lineNum">    3947 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="3948"><span class="lineNum">    3948 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3949"><span class="lineNum">    3949 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="3950"><span class="lineNum">    3950 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3951"><span class="lineNum">    3951 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="3952"><span class="lineNum">    3952 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3953"><span class="lineNum">    3953 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="3954"><span class="lineNum">    3954 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="3955"><span class="lineNum">    3955 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="3956"><span class="lineNum">    3956 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="3957"><span class="lineNum">    3957 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="3958"><span class="lineNum">    3958 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="3959"><span class="lineNum">    3959 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3960"><span class="lineNum">    3960 </span>            :       // DNA - C5</a>
+<a name="3961"><span class="lineNum">    3961 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC5&quot;) {</span></a>
+<a name="3962"><span class="lineNum">    3962 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="3963"><span class="lineNum">    3963 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="3964"><span class="lineNum">    3964 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="3965"><span class="lineNum">    3965 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="3966"><span class="lineNum">    3966 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="3967"><span class="lineNum">    3967 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="3968"><span class="lineNum">    3968 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="3969"><span class="lineNum">    3969 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="3970"><span class="lineNum">    3970 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="3971"><span class="lineNum">    3971 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="3972"><span class="lineNum">    3972 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="3973"><span class="lineNum">    3973 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="3974"><span class="lineNum">    3974 </span><span class="lineNoCov">          0 :     } else error(&quot;Residue not known: &quot;+Rname);</span></a>
+<a name="3975"><span class="lineNum">    3975 </span>            :   }</a>
+<a name="3976"><span class="lineNum">    3976 </span><span class="lineCov">          6 : }</span></a>
+<a name="3977"><span class="lineNum">    3977 </span>            : </a>
+<a name="3978"><span class="lineNum">    3978 </span><span class="lineCov">          4 : void SAXS::getOnebeadparam_sansH(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_vac_H, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_mix_H, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_solv_H)</span></a>
+<a name="3979"><span class="lineNum">    3979 </span>            : {</a>
+<a name="3980"><span class="lineNum">    3980 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(60737.60249988011);</span></a>
+<a name="3981"><span class="lineNum">    3981 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(-77.77344118516487);</span></a>
+<a name="3982"><span class="lineNum">    3982 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(-205962.80436572764);</span></a>
+<a name="3983"><span class="lineNum">    3983 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(-62014.18523271781);</span></a>
+<a name="3984"><span class="lineNum">    3984 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(680712.0512548896);</span></a>
+<a name="3985"><span class="lineNum">    3985 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(-681337.967312983);</span></a>
+<a name="3986"><span class="lineNum">    3986 </span><span class="lineCov">          4 :   parameter_solv_H[TRP].push_back(211474.00338118695);</span></a>
+<a name="3987"><span class="lineNum">    3987 </span>            : </a>
+<a name="3988"><span class="lineNum">    3988 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(46250.803599880084);</span></a>
+<a name="3989"><span class="lineNum">    3989 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(-45.827646837514614);</span></a>
+<a name="3990"><span class="lineNum">    3990 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(-143872.94597686914);</span></a>
+<a name="3991"><span class="lineNum">    3991 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(-39049.51580628132);</span></a>
+<a name="3992"><span class="lineNum">    3992 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(441321.31246635393);</span></a>
+<a name="3993"><span class="lineNum">    3993 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(-434477.6826175059);</span></a>
+<a name="3994"><span class="lineNum">    3994 </span><span class="lineCov">          4 :   parameter_solv_H[TYR].push_back(133179.21673104732);</span></a>
+<a name="3995"><span class="lineNum">    3995 </span>            : </a>
+<a name="3996"><span class="lineNum">    3996 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(42407.164900118914);</span></a>
+<a name="3997"><span class="lineNum">    3997 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(-159.20054549009086);</span></a>
+<a name="3998"><span class="lineNum">    3998 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(-123847.83591352346);</span></a>
+<a name="3999"><span class="lineNum">    3999 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(-41797.78884558073);</span></a>
+<a name="4000"><span class="lineNum">    4000 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(380283.87543872406);</span></a>
+<a name="4001"><span class="lineNum">    4001 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(-361432.81356389285);</span></a>
+<a name="4002"><span class="lineNum">    4002 </span><span class="lineCov">          4 :   parameter_solv_H[PHE].push_back(107750.69385054041);</span></a>
+<a name="4003"><span class="lineNum">    4003 </span>            : </a>
+<a name="4004"><span class="lineNum">    4004 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(24473.473600119047);</span></a>
+<a name="4005"><span class="lineNum">    4005 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(-111.6412807124612);</span></a>
+<a name="4006"><span class="lineNum">    4006 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(-65826.17293437096);</span></a>
+<a name="4007"><span class="lineNum">    4007 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(-23305.902022201855);</span></a>
+<a name="4008"><span class="lineNum">    4008 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(194795.09953510275);</span></a>
+<a name="4009"><span class="lineNum">    4009 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(-180454.47859494278);</span></a>
+<a name="4010"><span class="lineNum">    4010 </span><span class="lineCov">          4 :   parameter_solv_H[HIP].push_back(52699.36922660704);</span></a>
+<a name="4011"><span class="lineNum">    4011 </span>            : </a>
+<a name="4012"><span class="lineNum">    4012 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(34106.70239988039);</span></a>
+<a name="4013"><span class="lineNum">    4013 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(152.74468231268114);</span></a>
+<a name="4014"><span class="lineNum">    4014 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(-117086.46040369231);</span></a>
+<a name="4015"><span class="lineNum">    4015 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(-19664.37512726012);</span></a>
+<a name="4016"><span class="lineNum">    4016 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(364454.3721646173);</span></a>
+<a name="4017"><span class="lineNum">    4017 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(-382076.05102190404);</span></a>
+<a name="4018"><span class="lineNum">    4018 </span><span class="lineCov">          4 :   parameter_solv_H[ARG].push_back(122775.83306003918);</span></a>
+<a name="4019"><span class="lineNum">    4019 </span>            : </a>
+<a name="4020"><span class="lineNum">    4020 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(32292.09000011877);</span></a>
+<a name="4021"><span class="lineNum">    4021 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(-111.97888350941923);</span></a>
+<a name="4022"><span class="lineNum">    4022 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(-91953.05212591762);</span></a>
+<a name="4023"><span class="lineNum">    4023 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(-30691.03615444628);</span></a>
+<a name="4024"><span class="lineNum">    4024 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(282092.82233263896);</span></a>
+<a name="4025"><span class="lineNum">    4025 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(-269503.6095978623);</span></a>
+<a name="4026"><span class="lineNum">    4026 </span><span class="lineCov">          4 :   parameter_solv_H[LYS].push_back(80777.92760273012);</span></a>
+<a name="4027"><span class="lineNum">    4027 </span>            : </a>
+<a name="4028"><span class="lineNum">    4028 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(11352.902500119093);</span></a>
+<a name="4029"><span class="lineNum">    4029 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(-45.52255488723637);</span></a>
+<a name="4030"><span class="lineNum">    4030 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(-20925.086525675117);</span></a>
+<a name="4031"><span class="lineNum">    4031 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(-5662.681335644281);</span></a>
+<a name="4032"><span class="lineNum">    4032 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(38559.09602816144);</span></a>
+<a name="4033"><span class="lineNum">    4033 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(-27885.22747486708);</span></a>
+<a name="4034"><span class="lineNum">    4034 </span><span class="lineCov">          4 :   parameter_solv_H[CYS].push_back(6280.148346561226);</span></a>
+<a name="4035"><span class="lineNum">    4035 </span>            : </a>
+<a name="4036"><span class="lineNum">    4036 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(13511.73760011933);</span></a>
+<a name="4037"><span class="lineNum">    4037 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(-59.92934247210642);</span></a>
+<a name="4038"><span class="lineNum">    4038 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(-25849.867077822244);</span></a>
+<a name="4039"><span class="lineNum">    4039 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(-7541.679510407563);</span></a>
+<a name="4040"><span class="lineNum">    4040 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(50760.93853987092);</span></a>
+<a name="4041"><span class="lineNum">    4041 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(-37677.89102528413);</span></a>
+<a name="4042"><span class="lineNum">    4042 </span><span class="lineCov">          4 :   parameter_solv_H[ASP].push_back(8745.710458140105);</span></a>
+<a name="4043"><span class="lineNum">    4043 </span>            : </a>
+<a name="4044"><span class="lineNum">    4044 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(20443.280400119456);</span></a>
+<a name="4045"><span class="lineNum">    4045 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(-113.77513581661388);</span></a>
+<a name="4046"><span class="lineNum">    4046 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(-45587.79863958479);</span></a>
+<a name="4047"><span class="lineNum">    4047 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(-16187.534798976243);</span></a>
+<a name="4048"><span class="lineNum">    4048 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(112609.61802147207);</span></a>
+<a name="4049"><span class="lineNum">    4049 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(-93362.01894077536);</span></a>
+<a name="4050"><span class="lineNum">    4050 </span><span class="lineCov">          4 :   parameter_solv_H[GLU].push_back(24519.546829431332);</span></a>
+<a name="4051"><span class="lineNum">    4051 </span>            : </a>
+<a name="4052"><span class="lineNum">    4052 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(27858.948100119596);</span></a>
+<a name="4053"><span class="lineNum">    4053 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(-159.27394962770595);</span></a>
+<a name="4054"><span class="lineNum">    4054 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(-61571.43025249802);</span></a>
+<a name="4055"><span class="lineNum">    4055 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(-21324.89659912433);</span></a>
+<a name="4056"><span class="lineNum">    4056 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(144070.7880009225);</span></a>
+<a name="4057"><span class="lineNum">    4057 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(-115021.84534734003);</span></a>
+<a name="4058"><span class="lineNum">    4058 </span><span class="lineCov">          4 :   parameter_solv_H[ILE].push_back(28939.093300284097);</span></a>
+<a name="4059"><span class="lineNum">    4059 </span>            : </a>
+<a name="4060"><span class="lineNum">    4060 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(27858.948100119596);</span></a>
+<a name="4061"><span class="lineNum">    4061 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(-165.61872365361);</span></a>
+<a name="4062"><span class="lineNum">    4062 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(-62564.5706162518);</span></a>
+<a name="4063"><span class="lineNum">    4063 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(-22465.325666767214);</span></a>
+<a name="4064"><span class="lineNum">    4064 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(151616.7844050042);</span></a>
+<a name="4065"><span class="lineNum">    4065 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(-122905.60389771541);</span></a>
+<a name="4066"><span class="lineNum">    4066 </span><span class="lineCov">          4 :   parameter_solv_H[LEU].push_back(31436.66201442061);</span></a>
+<a name="4067"><span class="lineNum">    4067 </span>            : </a>
+<a name="4068"><span class="lineNum">    4068 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(25609.60090011981);</span></a>
+<a name="4069"><span class="lineNum">    4069 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(-135.38816369794569);</span></a>
+<a name="4070"><span class="lineNum">    4070 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(-67771.01548433342);</span></a>
+<a name="4071"><span class="lineNum">    4071 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(-25228.91756660071);</span></a>
+<a name="4072"><span class="lineNum">    4072 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(199649.92084565928);</span></a>
+<a name="4073"><span class="lineNum">    4073 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(-182251.9246506795);</span></a>
+<a name="4074"><span class="lineNum">    4074 </span><span class="lineCov">          4 :   parameter_solv_H[MET].push_back(52502.876819125115);</span></a>
+<a name="4075"><span class="lineNum">    4075 </span>            : </a>
+<a name="4076"><span class="lineNum">    4076 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(14376.010000119095);</span></a>
+<a name="4077"><span class="lineNum">    4077 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(-67.65587848183215);</span></a>
+<a name="4078"><span class="lineNum">    4078 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(-28302.877059425664);</span></a>
+<a name="4079"><span class="lineNum">    4079 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(-8577.444107282141);</span></a>
+<a name="4080"><span class="lineNum">    4080 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(57532.88704197217);</span></a>
+<a name="4081"><span class="lineNum">    4081 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(-43261.79974462857);</span></a>
+<a name="4082"><span class="lineNum">    4082 </span><span class="lineCov">          4 :   parameter_solv_H[ASN].push_back(10186.450874679671);</span></a>
+<a name="4083"><span class="lineNum">    4083 </span>            : </a>
+<a name="4084"><span class="lineNum">    4084 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(16866.21690011944);</span></a>
+<a name="4085"><span class="lineNum">    4085 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(-70.84312112734995);</span></a>
+<a name="4086"><span class="lineNum">    4086 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(-31465.8423531932);</span></a>
+<a name="4087"><span class="lineNum">    4087 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(-8653.362744540535);</span></a>
+<a name="4088"><span class="lineNum">    4088 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(58032.27079924916);</span></a>
+<a name="4089"><span class="lineNum">    4089 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(-41521.001733021694);</span></a>
+<a name="4090"><span class="lineNum">    4090 </span><span class="lineCov">          4 :   parameter_solv_H[PRO].push_back(9184.527523759205);</span></a>
+<a name="4091"><span class="lineNum">    4091 </span>            : </a>
+<a name="4092"><span class="lineNum">    4092 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(21503.289600119);</span></a>
+<a name="4093"><span class="lineNum">    4093 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(-121.3012777474678);</span></a>
+<a name="4094"><span class="lineNum">    4094 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(-50468.58503443957);</span></a>
+<a name="4095"><span class="lineNum">    4095 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(-18462.47495329696);</span></a>
+<a name="4096"><span class="lineNum">    4096 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(132718.42007501892);</span></a>
+<a name="4097"><span class="lineNum">    4097 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(-113787.20224345029);</span></a>
+<a name="4098"><span class="lineNum">    4098 </span><span class="lineCov">          4 :   parameter_solv_H[GLN].push_back(30920.340813688686);</span></a>
+<a name="4099"><span class="lineNum">    4099 </span>            : </a>
+<a name="4100"><span class="lineNum">    4100 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(9181.47240011935);</span></a>
+<a name="4101"><span class="lineNum">    4101 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(-28.775273124392083);</span></a>
+<a name="4102"><span class="lineNum">    4102 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(-15205.54229808512);</span></a>
+<a name="4103"><span class="lineNum">    4103 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(-3377.785599913673);</span></a>
+<a name="4104"><span class="lineNum">    4104 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(23345.562090489493);</span></a>
+<a name="4105"><span class="lineNum">    4105 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(-15312.699787471944);</span></a>
+<a name="4106"><span class="lineNum">    4106 </span><span class="lineCov">          4 :   parameter_solv_H[SER].push_back(3013.844610647712);</span></a>
+<a name="4107"><span class="lineNum">    4107 </span>            : </a>
+<a name="4108"><span class="lineNum">    4108 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(15020.953600119403);</span></a>
+<a name="4109"><span class="lineNum">    4109 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(-61.909951810375105);</span></a>
+<a name="4110"><span class="lineNum">    4110 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(-27814.538986050964);</span></a>
+<a name="4111"><span class="lineNum">    4111 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(-7532.222992514079);</span></a>
+<a name="4112"><span class="lineNum">    4112 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(50586.29804970814);</span></a>
+<a name="4113"><span class="lineNum">    4113 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(-35943.85986777198);</span></a>
+<a name="4114"><span class="lineNum">    4114 </span><span class="lineCov">          4 :   parameter_solv_H[THR].push_back(7880.091610023207);</span></a>
+<a name="4115"><span class="lineNum">    4115 </span>            : </a>
+<a name="4116"><span class="lineNum">    4116 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(19647.628900119355);</span></a>
+<a name="4117"><span class="lineNum">    4117 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(-89.04968136833762);</span></a>
+<a name="4118"><span class="lineNum">    4118 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(-38050.10118919102);</span></a>
+<a name="4119"><span class="lineNum">    4119 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(-10921.421066774372);</span></a>
+<a name="4120"><span class="lineNum">    4120 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(72774.31277743122);</span></a>
+<a name="4121"><span class="lineNum">    4121 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(-52689.05168504517);</span></a>
+<a name="4122"><span class="lineNum">    4122 </span><span class="lineCov">          4 :   parameter_solv_H[VAL].push_back(11806.48989635518);</span></a>
+<a name="4123"><span class="lineNum">    4123 </span>            : </a>
+<a name="4124"><span class="lineNum">    4124 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(7515.156100119273);</span></a>
+<a name="4125"><span class="lineNum">    4125 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(-20.226317591188526);</span></a>
+<a name="4126"><span class="lineNum">    4126 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(-11761.841775007797);</span></a>
+<a name="4127"><span class="lineNum">    4127 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(-2341.4903622033885);</span></a>
+<a name="4128"><span class="lineNum">    4128 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(16545.381259883452);</span></a>
+<a name="4129"><span class="lineNum">    4129 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(-10397.171546969075);</span></a>
+<a name="4130"><span class="lineNum">    4130 </span><span class="lineCov">          4 :   parameter_solv_H[ALA].push_back(1921.5253045340198);</span></a>
+<a name="4131"><span class="lineNum">    4131 </span>            : </a>
+<a name="4132"><span class="lineNum">    4132 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(3594.002500119159);</span></a>
+<a name="4133"><span class="lineNum">    4133 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(-6.910832388009796);</span></a>
+<a name="4134"><span class="lineNum">    4134 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(-4937.3542895091905);</span></a>
+<a name="4135"><span class="lineNum">    4135 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(-785.4545979203357);</span></a>
+<a name="4136"><span class="lineNum">    4136 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(5852.853693316741);</span></a>
+<a name="4137"><span class="lineNum">    4137 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(-3391.2920205126734);</span></a>
+<a name="4138"><span class="lineNum">    4138 </span><span class="lineCov">          4 :   parameter_solv_H[GLY].push_back(552.3278183161507);</span></a>
+<a name="4139"><span class="lineNum">    4139 </span>            : </a>
+<a name="4140"><span class="lineNum">    4140 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(22888.664100119073);</span></a>
+<a name="4141"><span class="lineNum">    4141 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(-133.86281863999585);</span></a>
+<a name="4142"><span class="lineNum">    4142 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(-57533.51412287858);</span></a>
+<a name="4143"><span class="lineNum">    4143 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(-21767.300111408193);</span></a>
+<a name="4144"><span class="lineNum">    4144 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(161255.15347073504);</span></a>
+<a name="4145"><span class="lineNum">    4145 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(-142176.65100718598);</span></a>
+<a name="4146"><span class="lineNum">    4146 </span><span class="lineCov">          4 :   parameter_solv_H[HIS].push_back(39642.61507384587);</span></a>
+<a name="4147"><span class="lineNum">    4147 </span>            : </a>
+<a name="4148"><span class="lineNum">    4148 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(2974.6515001192306);</span></a>
+<a name="4149"><span class="lineNum">    4149 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(-18.361939022074825);</span></a>
+<a name="4150"><span class="lineNum">    4150 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(-7284.637435770752);</span></a>
+<a name="4151"><span class="lineNum">    4151 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(-2945.7969900381895);</span></a>
+<a name="4152"><span class="lineNum">    4152 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(21235.01878657283);</span></a>
+<a name="4153"><span class="lineNum">    4153 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(-18909.7406035548);</span></a>
+<a name="4154"><span class="lineNum">    4154 </span><span class="lineCov">          4 :   parameter_mix_H[TRP].push_back(5324.324204245179);</span></a>
+<a name="4155"><span class="lineNum">    4155 </span>            : </a>
+<a name="4156"><span class="lineNum">    4156 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(2029.7362801192114);</span></a>
+<a name="4157"><span class="lineNum">    4157 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(-6.983186065527884);</span></a>
+<a name="4158"><span class="lineNum">    4158 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(-5041.996113037476);</span></a>
+<a name="4159"><span class="lineNum">    4159 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(-1744.5213085724158);</span></a>
+<a name="4160"><span class="lineNum">    4160 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(15329.420227814338);</span></a>
+<a name="4161"><span class="lineNum">    4161 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(-14648.322529889958);</span></a>
+<a name="4162"><span class="lineNum">    4162 </span><span class="lineCov">          4 :   parameter_mix_H[TYR].push_back(4405.608657083287);</span></a>
+<a name="4163"><span class="lineNum">    4163 </span>            : </a>
+<a name="4164"><span class="lineNum">    4164 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(1704.6885401192117);</span></a>
+<a name="4165"><span class="lineNum">    4165 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(-10.077274979133408);</span></a>
+<a name="4166"><span class="lineNum">    4166 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(-3769.440088334303);</span></a>
+<a name="4167"><span class="lineNum">    4167 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(-1574.6255694551546);</span></a>
+<a name="4168"><span class="lineNum">    4168 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(10996.32497868798);</span></a>
+<a name="4169"><span class="lineNum">    4169 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(-9840.68281283696);</span></a>
+<a name="4170"><span class="lineNum">    4170 </span><span class="lineCov">          4 :   parameter_mix_H[PHE].push_back(2792.098605716682);</span></a>
+<a name="4171"><span class="lineNum">    4171 </span>            : </a>
+<a name="4172"><span class="lineNum">    4172 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(1376.0462401192394);</span></a>
+<a name="4173"><span class="lineNum">    4173 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(-8.576320475413144);</span></a>
+<a name="4174"><span class="lineNum">    4174 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(-2796.8327726392167);</span></a>
+<a name="4175"><span class="lineNum">    4175 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(-1165.0473128576);</span></a>
+<a name="4176"><span class="lineNum">    4176 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(7495.063650365717);</span></a>
+<a name="4177"><span class="lineNum">    4177 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(-6331.20422098132);</span></a>
+<a name="4178"><span class="lineNum">    4178 </span><span class="lineCov">          4 :   parameter_mix_H[HIP].push_back(1692.637366093312);</span></a>
+<a name="4179"><span class="lineNum">    4179 </span>            : </a>
+<a name="4180"><span class="lineNum">    4180 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(1280.940480119178);</span></a>
+<a name="4181"><span class="lineNum">    4181 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(-7.411214928783748);</span></a>
+<a name="4182"><span class="lineNum">    4182 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(-3747.6200569785033);</span></a>
+<a name="4183"><span class="lineNum">    4183 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(-1766.5282176004569);</span></a>
+<a name="4184"><span class="lineNum">    4184 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(14307.817638456267);</span></a>
+<a name="4185"><span class="lineNum">    4185 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(-14297.104122885643);</span></a>
+<a name="4186"><span class="lineNum">    4186 </span><span class="lineCov">          4 :   parameter_mix_H[ARG].push_back(4450.526244207772);</span></a>
+<a name="4187"><span class="lineNum">    4187 </span>            : </a>
+<a name="4188"><span class="lineNum">    4188 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(570.7272001192143);</span></a>
+<a name="4189"><span class="lineNum">    4189 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(-5.371742288956095);</span></a>
+<a name="4190"><span class="lineNum">    4190 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(-1255.9868267793006);</span></a>
+<a name="4191"><span class="lineNum">    4191 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(-748.3071074443138);</span></a>
+<a name="4192"><span class="lineNum">    4192 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(4534.824932304509);</span></a>
+<a name="4193"><span class="lineNum">    4193 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(-4125.307867230812);</span></a>
+<a name="4194"><span class="lineNum">    4194 </span><span class="lineCov">          4 :   parameter_mix_H[LYS].push_back(1178.781491068295);</span></a>
+<a name="4195"><span class="lineNum">    4195 </span>            : </a>
+<a name="4196"><span class="lineNum">    4196 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(410.21750011921864);</span></a>
+<a name="4197"><span class="lineNum">    4197 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(-0.7655651758449595);</span></a>
+<a name="4198"><span class="lineNum">    4198 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(-523.8897033718782);</span></a>
+<a name="4199"><span class="lineNum">    4199 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(-89.88478273744425);</span></a>
+<a name="4200"><span class="lineNum">    4200 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(655.3313542467919);</span></a>
+<a name="4201"><span class="lineNum">    4201 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(-407.87897719750896);</span></a>
+<a name="4202"><span class="lineNum">    4202 </span><span class="lineCov">          4 :   parameter_mix_H[CYS].push_back(76.50541508448237);</span></a>
+<a name="4203"><span class="lineNum">    4203 </span>            : </a>
+<a name="4204"><span class="lineNum">    4204 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(893.6531201192147);</span></a>
+<a name="4205"><span class="lineNum">    4205 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(-3.0756255172248874);</span></a>
+<a name="4206"><span class="lineNum">    4206 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(-1453.1760425275006);</span></a>
+<a name="4207"><span class="lineNum">    4207 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(-365.0424824614137);</span></a>
+<a name="4208"><span class="lineNum">    4208 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(2443.570600976796);</span></a>
+<a name="4209"><span class="lineNum">    4209 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(-1679.8996339740277);</span></a>
+<a name="4210"><span class="lineNum">    4210 </span><span class="lineCov">          4 :   parameter_mix_H[ASP].push_back(352.33054461512455);</span></a>
+<a name="4211"><span class="lineNum">    4211 </span>            : </a>
+<a name="4212"><span class="lineNum">    4212 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(1075.4955601191884);</span></a>
+<a name="4213"><span class="lineNum">    4213 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(-6.917429973203965);</span></a>
+<a name="4214"><span class="lineNum">    4214 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(-2262.861870389347);</span></a>
+<a name="4215"><span class="lineNum">    4215 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(-909.8078514527992);</span></a>
+<a name="4216"><span class="lineNum">    4216 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(5841.923857549836);</span></a>
+<a name="4217"><span class="lineNum">    4217 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(-4784.620969556751);</span></a>
+<a name="4218"><span class="lineNum">    4218 </span><span class="lineCov">          4 :   parameter_mix_H[GLU].push_back(1230.873134652953);</span></a>
+<a name="4219"><span class="lineNum">    4219 </span>            : </a>
+<a name="4220"><span class="lineNum">    4220 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(466.0127201192081);</span></a>
+<a name="4221"><span class="lineNum">    4221 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(-0.9323443258150218);</span></a>
+<a name="4222"><span class="lineNum">    4222 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(-576.7178005955719);</span></a>
+<a name="4223"><span class="lineNum">    4223 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(-103.03003361062478);</span></a>
+<a name="4224"><span class="lineNum">    4224 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(706.4269951176641);</span></a>
+<a name="4225"><span class="lineNum">    4225 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(-420.4412859632717);</span></a>
+<a name="4226"><span class="lineNum">    4226 </span><span class="lineCov">          4 :   parameter_mix_H[ILE].push_back(71.53175726608731);</span></a>
+<a name="4227"><span class="lineNum">    4227 </span>            : </a>
+<a name="4228"><span class="lineNum">    4228 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(466.0127201192081);</span></a>
+<a name="4229"><span class="lineNum">    4229 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(-1.9793605752606065);</span></a>
+<a name="4230"><span class="lineNum">    4230 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(-718.3988478701591);</span></a>
+<a name="4231"><span class="lineNum">    4231 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(-227.36409339012113);</span></a>
+<a name="4232"><span class="lineNum">    4232 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(1389.2058254917304);</span></a>
+<a name="4233"><span class="lineNum">    4233 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(-990.0033118748643);</span></a>
+<a name="4234"><span class="lineNum">    4234 </span><span class="lineCov">          4 :   parameter_mix_H[LEU].push_back(213.15736815883042);</span></a>
+<a name="4235"><span class="lineNum">    4235 </span>            : </a>
+<a name="4236"><span class="lineNum">    4236 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(562.9855401192196);</span></a>
+<a name="4237"><span class="lineNum">    4237 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(-3.7994094933771643);</span></a>
+<a name="4238"><span class="lineNum">    4238 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(-1139.6331862451661);</span></a>
+<a name="4239"><span class="lineNum">    4239 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(-516.6313269725724);</span></a>
+<a name="4240"><span class="lineNum">    4240 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(3268.957245190869);</span></a>
+<a name="4241"><span class="lineNum">    4241 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(-2809.178864807947);</span></a>
+<a name="4242"><span class="lineNum">    4242 </span><span class="lineCov">          4 :   parameter_mix_H[MET].push_back(761.4832732100416);</span></a>
+<a name="4243"><span class="lineNum">    4243 </span>            : </a>
+<a name="4244"><span class="lineNum">    4244 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(828.7488001191887);</span></a>
+<a name="4245"><span class="lineNum">    4245 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(-2.1275493073799625);</span></a>
+<a name="4246"><span class="lineNum">    4246 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(-1222.248291388804);</span></a>
+<a name="4247"><span class="lineNum">    4247 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(-238.94210659613537);</span></a>
+<a name="4248"><span class="lineNum">    4248 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(1660.8322402171973);</span></a>
+<a name="4249"><span class="lineNum">    4249 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(-1008.7934996077323);</span></a>
+<a name="4250"><span class="lineNum">    4250 </span><span class="lineCov">          4 :   parameter_mix_H[ASN].push_back(173.6082238625797);</span></a>
+<a name="4251"><span class="lineNum">    4251 </span>            : </a>
+<a name="4252"><span class="lineNum">    4252 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(578.4409801192146);</span></a>
+<a name="4253"><span class="lineNum">    4253 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(-0.5379505780909722);</span></a>
+<a name="4254"><span class="lineNum">    4254 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(-648.146493857212);</span></a>
+<a name="4255"><span class="lineNum">    4255 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(-56.67223895342921);</span></a>
+<a name="4256"><span class="lineNum">    4256 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(509.88860586987437);</span></a>
+<a name="4257"><span class="lineNum">    4257 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(-214.57871784725265);</span></a>
+<a name="4258"><span class="lineNum">    4258 </span><span class="lineCov">          4 :   parameter_mix_H[PRO].push_back(11.99659463759968);</span></a>
+<a name="4259"><span class="lineNum">    4259 </span>            : </a>
+<a name="4260"><span class="lineNum">    4260 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(989.2334401191976);</span></a>
+<a name="4261"><span class="lineNum">    4261 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(-6.307760694331967);</span></a>
+<a name="4262"><span class="lineNum">    4262 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(-1971.7067150503622);</span></a>
+<a name="4263"><span class="lineNum">    4263 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(-791.333088386235);</span></a>
+<a name="4264"><span class="lineNum">    4264 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(4900.009768434847);</span></a>
+<a name="4265"><span class="lineNum">    4265 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(-3909.7740976374153);</span></a>
+<a name="4266"><span class="lineNum">    4266 </span><span class="lineCov">          4 :   parameter_mix_H[GLN].push_back(975.4952613244343);</span></a>
+<a name="4267"><span class="lineNum">    4267 </span>            : </a>
+<a name="4268"><span class="lineNum">    4268 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(426.39900011920196);</span></a>
+<a name="4269"><span class="lineNum">    4269 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(-0.42304498358319664);</span></a>
+<a name="4270"><span class="lineNum">    4270 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(-484.2066027682147);</span></a>
+<a name="4271"><span class="lineNum">    4271 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(-45.38968988754228);</span></a>
+<a name="4272"><span class="lineNum">    4272 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(401.3420977115044);</span></a>
+<a name="4273"><span class="lineNum">    4273 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(-178.0861461692512);</span></a>
+<a name="4274"><span class="lineNum">    4274 </span><span class="lineCov">          4 :   parameter_mix_H[SER].push_back(13.540349238730284);</span></a>
+<a name="4275"><span class="lineNum">    4275 </span>            : </a>
+<a name="4276"><span class="lineNum">    4276 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(525.0470401191992);</span></a>
+<a name="4277"><span class="lineNum">    4277 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(-0.7419102811534484);</span></a>
+<a name="4278"><span class="lineNum">    4278 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(-652.7134808154495);</span></a>
+<a name="4279"><span class="lineNum">    4279 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(-80.39481224407903);</span></a>
+<a name="4280"><span class="lineNum">    4280 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(641.5487902728123);</span></a>
+<a name="4281"><span class="lineNum">    4281 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(-320.4227667104819);</span></a>
+<a name="4282"><span class="lineNum">    4282 </span><span class="lineCov">          4 :   parameter_mix_H[THR].push_back(36.03558531183942);</span></a>
+<a name="4283"><span class="lineNum">    4283 </span>            : </a>
+<a name="4284"><span class="lineNum">    4284 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(414.6228601192123);</span></a>
+<a name="4285"><span class="lineNum">    4285 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(-0.35889335250521337);</span></a>
+<a name="4286"><span class="lineNum">    4286 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(-453.11631644097474);</span></a>
+<a name="4287"><span class="lineNum">    4287 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(-36.402101097644284);</span></a>
+<a name="4288"><span class="lineNum">    4288 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(336.24049431626804);</span></a>
+<a name="4289"><span class="lineNum">    4289 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(-127.42235327515239);</span></a>
+<a name="4290"><span class="lineNum">    4290 </span><span class="lineCov">          4 :   parameter_mix_H[VAL].push_back(0.8013280923923705);</span></a>
+<a name="4291"><span class="lineNum">    4291 </span>            : </a>
+<a name="4292"><span class="lineNum">    4292 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(285.21010011920816);</span></a>
+<a name="4293"><span class="lineNum">    4293 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(-0.1573012439142169);</span></a>
+<a name="4294"><span class="lineNum">    4294 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(-282.8945838800694);</span></a>
+<a name="4295"><span class="lineNum">    4295 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(-16.32030056827785);</span></a>
+<a name="4296"><span class="lineNum">    4296 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(178.065895049598);</span></a>
+<a name="4297"><span class="lineNum">    4297 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(-60.27423229179658);</span></a>
+<a name="4298"><span class="lineNum">    4298 </span><span class="lineCov">          4 :   parameter_mix_H[ALA].push_back(-1.4695219304131588);</span></a>
+<a name="4299"><span class="lineNum">    4299 </span>            : </a>
+<a name="4300"><span class="lineNum">    4300 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(207.18720011920414);</span></a>
+<a name="4301"><span class="lineNum">    4301 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(-0.1036587134183235);</span></a>
+<a name="4302"><span class="lineNum">    4302 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(-185.70794948240638);</span></a>
+<a name="4303"><span class="lineNum">    4303 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(-11.008101039836257);</span></a>
+<a name="4304"><span class="lineNum">    4304 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(115.30600405624061);</span></a>
+<a name="4305"><span class="lineNum">    4305 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(-42.46629718037158);</span></a>
+<a name="4306"><span class="lineNum">    4306 </span><span class="lineCov">          4 :   parameter_mix_H[GLY].push_back(0.9238928987070913);</span></a>
+<a name="4307"><span class="lineNum">    4307 </span>            : </a>
+<a name="4308"><span class="lineNum">    4308 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(1443.9117601192354);</span></a>
+<a name="4309"><span class="lineNum">    4309 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(-7.478618745973115);</span></a>
+<a name="4310"><span class="lineNum">    4310 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(-2715.0835155803215);</span></a>
+<a name="4311"><span class="lineNum">    4311 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(-918.5243015382779);</span></a>
+<a name="4312"><span class="lineNum">    4312 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(5821.6258431396);</span></a>
+<a name="4313"><span class="lineNum">    4313 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(-4415.32722209556);</span></a>
+<a name="4314"><span class="lineNum">    4314 </span><span class="lineCov">          4 :   parameter_mix_H[HIS].push_back(1044.7044029209756);</span></a>
+<a name="4315"><span class="lineNum">    4315 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(36.42122511920832);</span></a>
+<a name="4316"><span class="lineNum">    4316 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(-0.36925500341767903);</span></a>
+<a name="4317"><span class="lineNum">    4317 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(-51.34228792835503);</span></a>
+<a name="4318"><span class="lineNum">    4318 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(-34.10021080004831);</span></a>
+<a name="4319"><span class="lineNum">    4319 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(132.647034983933);</span></a>
+<a name="4320"><span class="lineNum">    4320 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(-82.89152328934257);</span></a>
+<a name="4321"><span class="lineNum">    4321 </span><span class="lineCov">          4 :   parameter_vac_H[TRP].push_back(13.029994092013231);</span></a>
+<a name="4322"><span class="lineNum">    4322 </span>            : </a>
+<a name="4323"><span class="lineNum">    4323 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(22.268961119209557);</span></a>
+<a name="4324"><span class="lineNum">    4324 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(-0.1995573892347673);</span></a>
+<a name="4325"><span class="lineNum">    4325 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(-36.54202179838511);</span></a>
+<a name="4326"><span class="lineNum">    4326 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(-23.820801043096694);</span></a>
+<a name="4327"><span class="lineNum">    4327 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(127.46799692275353);</span></a>
+<a name="4328"><span class="lineNum">    4328 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(-107.63783234245744);</span></a>
+<a name="4329"><span class="lineNum">    4329 </span><span class="lineCov">          4 :   parameter_vac_H[TYR].push_back(28.180858902960775);</span></a>
+<a name="4330"><span class="lineNum">    4330 </span>            : </a>
+<a name="4331"><span class="lineNum">    4331 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(17.131321119209627);</span></a>
+<a name="4332"><span class="lineNum">    4332 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(-0.15766725674246446);</span></a>
+<a name="4333"><span class="lineNum">    4333 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(-19.19964432024534);</span></a>
+<a name="4334"><span class="lineNum">    4334 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(-12.34326882843138);</span></a>
+<a name="4335"><span class="lineNum">    4335 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(38.17216645824474);</span></a>
+<a name="4336"><span class="lineNum">    4336 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(-11.245288857407298);</span></a>
+<a name="4337"><span class="lineNum">    4337 </span><span class="lineCov">          4 :   parameter_vac_H[PHE].push_back(-3.8114731300899343);</span></a>
+<a name="4338"><span class="lineNum">    4338 </span>            : </a>
+<a name="4339"><span class="lineNum">    4339 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(19.34240411920875);</span></a>
+<a name="4340"><span class="lineNum">    4340 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(-0.13533410292592593);</span></a>
+<a name="4341"><span class="lineNum">    4341 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(-25.924121027387276);</span></a>
+<a name="4342"><span class="lineNum">    4342 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(-12.36586927492752);</span></a>
+<a name="4343"><span class="lineNum">    4343 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(56.75268702111191);</span></a>
+<a name="4344"><span class="lineNum">    4344 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(-31.126240293638094);</span></a>
+<a name="4345"><span class="lineNum">    4345 </span><span class="lineCov">          4 :   parameter_vac_H[HIP].push_back(2.749811579250848);</span></a>
+<a name="4346"><span class="lineNum">    4346 </span>            : </a>
+<a name="4347"><span class="lineNum">    4347 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(12.027024119209557);</span></a>
+<a name="4348"><span class="lineNum">    4348 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(-0.41927538341868287);</span></a>
+<a name="4349"><span class="lineNum">    4349 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(-22.137566939867042);</span></a>
+<a name="4350"><span class="lineNum">    4350 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(-43.22615008762667);</span></a>
+<a name="4351"><span class="lineNum">    4351 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(165.77466655520323);</span></a>
+<a name="4352"><span class="lineNum">    4352 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(-140.68664871425898);</span></a>
+<a name="4353"><span class="lineNum">    4353 </span><span class="lineCov">          4 :   parameter_vac_H[ARG].push_back(36.67401195170306);</span></a>
+<a name="4354"><span class="lineNum">    4354 </span>            : </a>
+<a name="4355"><span class="lineNum">    4355 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(2.5217441192093717);</span></a>
+<a name="4356"><span class="lineNum">    4356 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(-0.0032825476242835413);</span></a>
+<a name="4357"><span class="lineNum">    4357 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(14.019071697737793);</span></a>
+<a name="4358"><span class="lineNum">    4358 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(7.8634074595069245);</span></a>
+<a name="4359"><span class="lineNum">    4359 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(-82.44639716451474);</span></a>
+<a name="4360"><span class="lineNum">    4360 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(94.32937851921197);</span></a>
+<a name="4361"><span class="lineNum">    4361 </span><span class="lineCov">          4 :   parameter_vac_H[LYS].push_back(-32.324473823417);</span></a>
+<a name="4362"><span class="lineNum">    4362 </span>            : </a>
+<a name="4363"><span class="lineNum">    4363 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(3.705624880856525);</span></a>
+<a name="4364"><span class="lineNum">    4364 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(0.005214780840206113);</span></a>
+<a name="4365"><span class="lineNum">    4365 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(1.25680902661715);</span></a>
+<a name="4366"><span class="lineNum">    4366 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(0.5779209425501814);</span></a>
+<a name="4367"><span class="lineNum">    4367 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(-3.716408071089366);</span></a>
+<a name="4368"><span class="lineNum">    4368 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(2.3947518943233117);</span></a>
+<a name="4369"><span class="lineNum">    4369 </span><span class="lineCov">          4 :   parameter_vac_H[CYS].push_back(-0.40204949737133333);</span></a>
+<a name="4370"><span class="lineNum">    4370 </span>            : </a>
+<a name="4371"><span class="lineNum">    4371 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(14.776336119209605);</span></a>
+<a name="4372"><span class="lineNum">    4372 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(-0.037351220316916435);</span></a>
+<a name="4373"><span class="lineNum">    4373 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(-18.556358387626286);</span></a>
+<a name="4374"><span class="lineNum">    4374 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(-4.1737354794552886);</span></a>
+<a name="4375"><span class="lineNum">    4375 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(28.424721213037405);</span></a>
+<a name="4376"><span class="lineNum">    4376 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(-17.51389895324883);</span></a>
+<a name="4377"><span class="lineNum">    4377 </span><span class="lineCov">          4 :   parameter_vac_H[ASP].push_back(2.9729111724708597);</span></a>
+<a name="4378"><span class="lineNum">    4378 </span>            : </a>
+<a name="4379"><span class="lineNum">    4379 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(14.145121119208973);</span></a>
+<a name="4380"><span class="lineNum">    4380 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(-0.11468766098213011);</span></a>
+<a name="4381"><span class="lineNum">    4381 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(-26.272637652294613);</span></a>
+<a name="4382"><span class="lineNum">    4382 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(-13.769758826440151);</span></a>
+<a name="4383"><span class="lineNum">    4383 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(80.4575683578491);</span></a>
+<a name="4384"><span class="lineNum">    4384 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(-64.19346347075);</span></a>
+<a name="4385"><span class="lineNum">    4385 </span><span class="lineCov">          4 :   parameter_vac_H[GLU].push_back(15.545440117656236);</span></a>
+<a name="4386"><span class="lineNum">    4386 </span>            : </a>
+<a name="4387"><span class="lineNum">    4387 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(1.9488158808808775);</span></a>
+<a name="4388"><span class="lineNum">    4388 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(0.05873132133874459);</span></a>
+<a name="4389"><span class="lineNum">    4389 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(12.032778845884135);</span></a>
+<a name="4390"><span class="lineNum">    4390 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(7.148416980612881);</span></a>
+<a name="4391"><span class="lineNum">    4391 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(-41.87377843832961);</span></a>
+<a name="4392"><span class="lineNum">    4392 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(33.96120749582283);</span></a>
+<a name="4393"><span class="lineNum">    4393 </span><span class="lineCov">          4 :   parameter_vac_H[ILE].push_back(-8.362535852631256);</span></a>
+<a name="4394"><span class="lineNum">    4394 </span>            : </a>
+<a name="4395"><span class="lineNum">    4395 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(1.9488158808977816);</span></a>
+<a name="4396"><span class="lineNum">    4396 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(0.0778305500414777);</span></a>
+<a name="4397"><span class="lineNum">    4397 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(12.333370614594);</span></a>
+<a name="4398"><span class="lineNum">    4398 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(9.449427967560764);</span></a>
+<a name="4399"><span class="lineNum">    4399 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(-52.65457680603262);</span></a>
+<a name="4400"><span class="lineNum">    4400 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(44.681877289399615);</span></a>
+<a name="4401"><span class="lineNum">    4401 </span><span class="lineCov">          4 :   parameter_vac_H[LEU].push_back(-11.460498338671227);</span></a>
+<a name="4402"><span class="lineNum">    4402 </span>            : </a>
+<a name="4403"><span class="lineNum">    4403 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(3.0940808808117652);</span></a>
+<a name="4404"><span class="lineNum">    4404 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(0.04903755678213222);</span></a>
+<a name="4405"><span class="lineNum">    4405 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(8.981927022922049);</span></a>
+<a name="4406"><span class="lineNum">    4406 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(8.654862771879014);</span></a>
+<a name="4407"><span class="lineNum">    4407 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(-57.09889409156816);</span></a>
+<a name="4408"><span class="lineNum">    4408 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(58.87704775164829);</span></a>
+<a name="4409"><span class="lineNum">    4409 </span><span class="lineCov">          4 :   parameter_vac_H[MET].push_back(-18.60431990258862);</span></a>
+<a name="4410"><span class="lineNum">    4410 </span>            : </a>
+<a name="4411"><span class="lineNum">    4411 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(11.943936119209074);</span></a>
+<a name="4412"><span class="lineNum">    4412 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(-0.0005000836239497835);</span></a>
+<a name="4413"><span class="lineNum">    4413 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(-9.581236453763157);</span></a>
+<a name="4414"><span class="lineNum">    4414 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(0.16244025786232308);</span></a>
+<a name="4415"><span class="lineNum">    4415 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(2.9276580099749574);</span></a>
+<a name="4416"><span class="lineNum">    4416 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(2.133535783835143);</span></a>
+<a name="4417"><span class="lineNum">    4417 </span><span class="lineCov">          4 :   parameter_vac_H[ASN].push_back(-1.5709968820975018);</span></a>
+<a name="4418"><span class="lineNum">    4418 </span>            : </a>
+<a name="4419"><span class="lineNum">    4419 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(4.9595288808229245);</span></a>
+<a name="4420"><span class="lineNum">    4420 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(0.017853932680793515);</span></a>
+<a name="4421"><span class="lineNum">    4421 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(4.5421559293101605);</span></a>
+<a name="4422"><span class="lineNum">    4422 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(2.008455612787203);</span></a>
+<a name="4423"><span class="lineNum">    4423 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(-12.444117841318494);</span></a>
+<a name="4424"><span class="lineNum">    4424 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(8.511723688836447);</span></a>
+<a name="4425"><span class="lineNum">    4425 </span><span class="lineCov">          4 :   parameter_vac_H[PRO].push_back(-1.6337543903496765);</span></a>
+<a name="4426"><span class="lineNum">    4426 </span>            : </a>
+<a name="4427"><span class="lineNum">    4427 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(11.377129119208574);</span></a>
+<a name="4428"><span class="lineNum">    4428 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(-0.0674805307761209);</span></a>
+<a name="4429"><span class="lineNum">    4429 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(-16.56692720411458);</span></a>
+<a name="4430"><span class="lineNum">    4430 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(-6.477707440126834);</span></a>
+<a name="4431"><span class="lineNum">    4431 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(34.78232259512621);</span></a>
+<a name="4432"><span class="lineNum">    4432 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(-19.450886909938312);</span></a>
+<a name="4433"><span class="lineNum">    4433 </span><span class="lineCov">          4 :   parameter_vac_H[GLN].push_back(1.944286925108988);</span></a>
+<a name="4434"><span class="lineNum">    4434 </span>            : </a>
+<a name="4435"><span class="lineNum">    4435 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(4.95062488096605);</span></a>
+<a name="4436"><span class="lineNum">    4436 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(0.004676435440506079);</span></a>
+<a name="4437"><span class="lineNum">    4437 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(-0.1896653085608564);</span></a>
+<a name="4438"><span class="lineNum">    4438 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(0.5142284931977218);</span></a>
+<a name="4439"><span class="lineNum">    4439 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(-2.8946087252759893);</span></a>
+<a name="4440"><span class="lineNum">    4440 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(2.1031239401634836);</span></a>
+<a name="4441"><span class="lineNum">    4441 </span><span class="lineCov">          4 :   parameter_vac_H[SER].push_back(-0.38226443516361713);</span></a>
+<a name="4442"><span class="lineNum">    4442 </span>            : </a>
+<a name="4443"><span class="lineNum">    4443 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(4.588163880808971);</span></a>
+<a name="4444"><span class="lineNum">    4444 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(0.018587905993982613);</span></a>
+<a name="4445"><span class="lineNum">    4445 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(3.5289861308270214);</span></a>
+<a name="4446"><span class="lineNum">    4446 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(2.0780583604591567);</span></a>
+<a name="4447"><span class="lineNum">    4447 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(-12.3802007068414);</span></a>
+<a name="4448"><span class="lineNum">    4448 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(8.720986674116094);</span></a>
+<a name="4449"><span class="lineNum">    4449 </span><span class="lineCov">          4 :   parameter_vac_H[THR].push_back(-1.683256475122275);</span></a>
+<a name="4450"><span class="lineNum">    4450 </span>            : </a>
+<a name="4451"><span class="lineNum">    4451 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(2.187440880853519);</span></a>
+<a name="4452"><span class="lineNum">    4452 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(0.028351524826584255);</span></a>
+<a name="4453"><span class="lineNum">    4453 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(8.36584512491955);</span></a>
+<a name="4454"><span class="lineNum">    4454 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(3.1686206615123926);</span></a>
+<a name="4455"><span class="lineNum">    4455 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(-19.81959917770108);</span></a>
+<a name="4456"><span class="lineNum">    4456 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(13.293003038570571);</span></a>
+<a name="4457"><span class="lineNum">    4457 </span><span class="lineCov">          4 :   parameter_vac_H[VAL].push_back(-2.4595257726774125);</span></a>
+<a name="4458"><span class="lineNum">    4458 </span>            : </a>
+<a name="4459"><span class="lineNum">    4459 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(2.7060248808167935);</span></a>
+<a name="4460"><span class="lineNum">    4460 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(0.004618897267213416);</span></a>
+<a name="4461"><span class="lineNum">    4461 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(2.4990261487383947);</span></a>
+<a name="4462"><span class="lineNum">    4462 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(0.49579332664340864);</span></a>
+<a name="4463"><span class="lineNum">    4463 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(-3.850400071630347);</span></a>
+<a name="4464"><span class="lineNum">    4464 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(1.9501161562030942);</span></a>
+<a name="4465"><span class="lineNum">    4465 </span><span class="lineCov">          4 :   parameter_vac_H[ALA].push_back(-0.18332582719788362);</span></a>
+<a name="4466"><span class="lineNum">    4466 </span>            : </a>
+<a name="4467"><span class="lineNum">    4467 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(2.985983880876256);</span></a>
+<a name="4468"><span class="lineNum">    4468 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(0.0005033131808079042);</span></a>
+<a name="4469"><span class="lineNum">    4469 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(-0.42250170279962684);</span></a>
+<a name="4470"><span class="lineNum">    4470 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(0.05620517453257455);</span></a>
+<a name="4471"><span class="lineNum">    4471 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(-0.16801962822020733);</span></a>
+<a name="4472"><span class="lineNum">    4472 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(0.23635459648780555);</span></a>
+<a name="4473"><span class="lineNum">    4473 </span><span class="lineCov">          4 :   parameter_vac_H[GLY].push_back(-0.06585244715658795);</span></a>
+<a name="4474"><span class="lineNum">    4474 </span>            : </a>
+<a name="4475"><span class="lineNum">    4475 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(22.77198411920933);</span></a>
+<a name="4476"><span class="lineNum">    4476 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(-0.06607491006655417);</span></a>
+<a name="4477"><span class="lineNum">    4477 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(-27.277710268717247);</span></a>
+<a name="4478"><span class="lineNum">    4478 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(-5.674444390934355);</span></a>
+<a name="4479"><span class="lineNum">    4479 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(33.4059567406171);</span></a>
+<a name="4480"><span class="lineNum">    4480 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(-11.60826210271092);</span></a>
+<a name="4481"><span class="lineNum">    4481 </span><span class="lineCov">          4 :   parameter_vac_H[HIS].push_back(-1.7359607560773076);</span></a>
+<a name="4482"><span class="lineNum">    4482 </span>            : </a>
+<a name="4483"><span class="lineNum">    4483 </span>            :   // NUCLEIC ACIDS</a>
+<a name="4484"><span class="lineNum">    4484 </span>            : </a>
+<a name="4485"><span class="lineNum">    4485 </span>            :   // BB_PO2 H and D parameters are identical as there is no H or D in the bead.</a>
+<a name="4486"><span class="lineNum">    4486 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(575.5201001192197);</span></a>
+<a name="4487"><span class="lineNum">    4487 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(-0.6126595489733864);</span></a>
+<a name="4488"><span class="lineNum">    4488 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(-623.3371092254899);</span></a>
+<a name="4489"><span class="lineNum">    4489 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(-68.05795957022144);</span></a>
+<a name="4490"><span class="lineNum">    4490 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(561.8052621243661);</span></a>
+<a name="4491"><span class="lineNum">    4491 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(-283.39573309540276);</span></a>
+<a name="4492"><span class="lineNum">    4492 </span><span class="lineCov">          4 :   parameter_solv_H[BB_PO2].push_back(35.550016980100295);</span></a>
+<a name="4493"><span class="lineNum">    4493 </span>            : </a>
+<a name="4494"><span class="lineNum">    4494 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA].push_back(21211.009600118316);</span></a>
+<a name="4495"><span class="lineNum">    4495 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA].push_back(-90.18805990529991);</span></a>
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+<a name="4500"><span class="lineNum">    4500 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA].push_back(11308.678429018755);</span></a>
+<a name="4501"><span class="lineNum">    4501 </span>            : </a>
+<a name="4502"><span class="lineNum">    4502 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_5].push_back(22737.624100119025);</span></a>
+<a name="4503"><span class="lineNum">    4503 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_5].push_back(-102.72714886664161);</span></a>
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+<a name="4507"><span class="lineNum">    4507 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_5].push_back(-60367.15652138887);</span></a>
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+<a name="4509"><span class="lineNum">    4509 </span>            : </a>
+<a name="4510"><span class="lineNum">    4510 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_3].push_back(22737.62410011902);</span></a>
+<a name="4511"><span class="lineNum">    4511 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_3].push_back(-101.57816684452251);</span></a>
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+<a name="4515"><span class="lineNum">    4515 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_3].push_back(-58791.59443618196);</span></a>
+<a name="4516"><span class="lineNum">    4516 </span><span class="lineCov">          4 :   parameter_solv_H[BB_DNA_3].push_back(13003.199362335583);</span></a>
+<a name="4517"><span class="lineNum">    4517 </span>            : </a>
+<a name="4518"><span class="lineNum">    4518 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA].push_back(23953.752900120977);</span></a>
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+<a name="4524"><span class="lineNum">    4524 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA].push_back(16792.055521055358);</span></a>
+<a name="4525"><span class="lineNum">    4525 </span>            : </a>
+<a name="4526"><span class="lineNum">    4526 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_5].push_back(25574.406400119024);</span></a>
+<a name="4527"><span class="lineNum">    4527 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_5].push_back(-131.99642772933734);</span></a>
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+<a name="4530"><span class="lineNum">    4530 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_5].push_back(110278.01921639398);</span></a>
+<a name="4531"><span class="lineNum">    4531 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_5].push_back(-83715.92027818544);</span></a>
+<a name="4532"><span class="lineNum">    4532 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_5].push_back(19875.89133770605);</span></a>
+<a name="4533"><span class="lineNum">    4533 </span>            : </a>
+<a name="4534"><span class="lineNum">    4534 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_3].push_back(25574.406400119027);</span></a>
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+<a name="4536"><span class="lineNum">    4536 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_3].push_back(-51407.18391758439);</span></a>
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+<a name="4538"><span class="lineNum">    4538 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_3].push_back(105078.5888910626);</span></a>
+<a name="4539"><span class="lineNum">    4539 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_3].push_back(-78289.16276190645);</span></a>
+<a name="4540"><span class="lineNum">    4540 </span><span class="lineCov">          4 :   parameter_solv_H[BB_RNA_3].push_back(18156.832143441192);</span></a>
+<a name="4541"><span class="lineNum">    4541 </span>            : </a>
+<a name="4542"><span class="lineNum">    4542 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_A].push_back(13282.562500119211);</span></a>
+<a name="4543"><span class="lineNum">    4543 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_A].push_back(-76.45124168404048);</span></a>
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+<a name="4547"><span class="lineNum">    4547 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_A].push_back(-52064.33492910885);</span></a>
+<a name="4548"><span class="lineNum">    4548 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_A].push_back(12931.608989412513);</span></a>
+<a name="4549"><span class="lineNum">    4549 </span>            : </a>
+<a name="4550"><span class="lineNum">    4550 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_C].push_back(10600.76160011891);</span></a>
+<a name="4551"><span class="lineNum">    4551 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_C].push_back(-49.1670871249108);</span></a>
+<a name="4552"><span class="lineNum">    4552 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_C].push_back(-20239.818742072875);</span></a>
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+<a name="4555"><span class="lineNum">    4555 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_C].push_back(-28954.779736165576);</span></a>
+<a name="4556"><span class="lineNum">    4556 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_C].push_back(6551.541109526305);</span></a>
+<a name="4557"><span class="lineNum">    4557 </span>            : </a>
+<a name="4558"><span class="lineNum">    4558 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(15470.384400119934);</span></a>
+<a name="4559"><span class="lineNum">    4559 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(-93.8013620200972);</span></a>
+<a name="4560"><span class="lineNum">    4560 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(-36188.29687013545);</span></a>
+<a name="4561"><span class="lineNum">    4561 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(-13717.685098209471);</span></a>
+<a name="4562"><span class="lineNum">    4562 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(95658.18473657136);</span></a>
+<a name="4563"><span class="lineNum">    4563 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(-81262.37811451119);</span></a>
+<a name="4564"><span class="lineNum">    4564 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_G].push_back(21841.903930943085);</span></a>
+<a name="4565"><span class="lineNum">    4565 </span>            : </a>
+<a name="4566"><span class="lineNum">    4566 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(17210.81610011936);</span></a>
+<a name="4567"><span class="lineNum">    4567 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(-93.10189802920208);</span></a>
+<a name="4568"><span class="lineNum">    4568 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(-36466.51927689957);</span></a>
+<a name="4569"><span class="lineNum">    4569 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(-12425.55615716932);</span></a>
+<a name="4570"><span class="lineNum">    4570 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(83847.427808925);</span></a>
+<a name="4571"><span class="lineNum">    4571 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(-66735.64997846584);</span></a>
+<a name="4572"><span class="lineNum">    4572 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_T].push_back(16757.3463987507);</span></a>
+<a name="4573"><span class="lineNum">    4573 </span>            : </a>
+<a name="4574"><span class="lineNum">    4574 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(10909.802500119395);</span></a>
+<a name="4575"><span class="lineNum">    4575 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(-46.17712672768298);</span></a>
+<a name="4576"><span class="lineNum">    4576 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(-20149.67695512526);</span></a>
+<a name="4577"><span class="lineNum">    4577 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(-5590.242961204435);</span></a>
+<a name="4578"><span class="lineNum">    4578 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(37169.2740983132);</span></a>
+<a name="4579"><span class="lineNum">    4579 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(-26475.631627167604);</span></a>
+<a name="4580"><span class="lineNum">    4580 </span><span class="lineCov">          4 :   parameter_solv_H[BASE_U].push_back(5808.201015156168);</span></a>
+<a name="4581"><span class="lineNum">    4581 </span>            : </a>
+<a name="4582"><span class="lineNum">    4582 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(80.12660011920252);</span></a>
+<a name="4583"><span class="lineNum">    4583 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(-0.0278885551982023);</span></a>
+<a name="4584"><span class="lineNum">    4584 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(-60.532194918222984);</span></a>
+<a name="4585"><span class="lineNum">    4585 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(-2.976882903409687);</span></a>
+<a name="4586"><span class="lineNum">    4586 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(33.30645116638125);</span></a>
+<a name="4587"><span class="lineNum">    4587 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(-11.601573219761374);</span></a>
+<a name="4588"><span class="lineNum">    4588 </span><span class="lineCov">          4 :   parameter_mix_H[BB_PO2].push_back(0.12551046492022422);</span></a>
+<a name="4589"><span class="lineNum">    4589 </span>            : </a>
+<a name="4590"><span class="lineNum">    4590 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(712.7621601191935);</span></a>
+<a name="4591"><span class="lineNum">    4591 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(-0.3228709821198571);</span></a>
+<a name="4592"><span class="lineNum">    4592 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(-784.5118228559945);</span></a>
+<a name="4593"><span class="lineNum">    4593 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(-27.196125702249613);</span></a>
+<a name="4594"><span class="lineNum">    4594 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(410.0185035102729);</span></a>
+<a name="4595"><span class="lineNum">    4595 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(-54.453513369320355);</span></a>
+<a name="4596"><span class="lineNum">    4596 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA].push_back(-44.85506789237683);</span></a>
+<a name="4597"><span class="lineNum">    4597 </span>            : </a>
+<a name="4598"><span class="lineNum">    4598 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(625.175339965785);</span></a>
+<a name="4599"><span class="lineNum">    4599 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(0.2691706617748245);</span></a>
+<a name="4600"><span class="lineNum">    4600 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(-582.8721350420001);</span></a>
+<a name="4601"><span class="lineNum">    4601 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(46.512408351374326);</span></a>
+<a name="4602"><span class="lineNum">    4602 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(-58.93886949899108);</span></a>
+<a name="4603"><span class="lineNum">    4603 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(307.29720336085046);</span></a>
+<a name="4604"><span class="lineNum">    4604 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_5].push_back(-131.71996309259953);</span></a>
+<a name="4605"><span class="lineNum">    4605 </span>            : </a>
+<a name="4606"><span class="lineNum">    4606 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(625.1753399401266);</span></a>
+<a name="4607"><span class="lineNum">    4607 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(0.08763234414546289);</span></a>
+<a name="4608"><span class="lineNum">    4608 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(-606.8067575087485);</span></a>
+<a name="4609"><span class="lineNum">    4609 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(20.84427254872218);</span></a>
+<a name="4610"><span class="lineNum">    4610 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(92.53523123608991);</span></a>
+<a name="4611"><span class="lineNum">    4611 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(162.04688035654937);</span></a>
+<a name="4612"><span class="lineNum">    4612 </span><span class="lineCov">          4 :   parameter_mix_H[BB_DNA_3].push_back(-89.13571774638052);</span></a>
+<a name="4613"><span class="lineNum">    4613 </span>            : </a>
+<a name="4614"><span class="lineNum">    4614 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(936.9775801191857);</span></a>
+<a name="4615"><span class="lineNum">    4615 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(-1.3233686929680253);</span></a>
+<a name="4616"><span class="lineNum">    4616 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(-1212.1627155263773);</span></a>
+<a name="4617"><span class="lineNum">    4617 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(-141.35324744384351);</span></a>
+<a name="4618"><span class="lineNum">    4618 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(1155.8281658363026);</span></a>
+<a name="4619"><span class="lineNum">    4619 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(-548.9340055857343);</span></a>
+<a name="4620"><span class="lineNum">    4620 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA].push_back(50.81734777881503);</span></a>
+<a name="4621"><span class="lineNum">    4621 </span>            : </a>
+<a name="4622"><span class="lineNum">    4622 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(848.5355201165631);</span></a>
+<a name="4623"><span class="lineNum">    4623 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(-0.49570338490120175);</span></a>
+<a name="4624"><span class="lineNum">    4624 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(-976.1033073783973);</span></a>
+<a name="4625"><span class="lineNum">    4625 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(-32.943532187986605);</span></a>
+<a name="4626"><span class="lineNum">    4626 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(475.66177061923884);</span></a>
+<a name="4627"><span class="lineNum">    4627 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(17.51955845824258);</span></a>
+<a name="4628"><span class="lineNum">    4628 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_5].push_back(-96.74451972314769);</span></a>
+<a name="4629"><span class="lineNum">    4629 </span>            : </a>
+<a name="4630"><span class="lineNum">    4630 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(848.5355201192122);</span></a>
+<a name="4631"><span class="lineNum">    4631 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(-0.8301109354355396);</span></a>
+<a name="4632"><span class="lineNum">    4632 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(-1019.9524389785406);</span></a>
+<a name="4633"><span class="lineNum">    4633 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(-84.1388451424885);</span></a>
+<a name="4634"><span class="lineNum">    4634 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(787.1277245040931);</span></a>
+<a name="4635"><span class="lineNum">    4635 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(-294.67807432795627);</span></a>
+<a name="4636"><span class="lineNum">    4636 </span><span class="lineCov">          4 :   parameter_mix_H[BB_RNA_3].push_back(-1.3214626461251089);</span></a>
+<a name="4637"><span class="lineNum">    4637 </span>            : </a>
+<a name="4638"><span class="lineNum">    4638 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(1504.9345001191857);</span></a>
+<a name="4639"><span class="lineNum">    4639 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(-3.5306888452552663);</span></a>
+<a name="4640"><span class="lineNum">    4640 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(-2234.3933572775572);</span></a>
+<a name="4641"><span class="lineNum">    4641 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(-380.0255208494757);</span></a>
+<a name="4642"><span class="lineNum">    4642 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(2726.27802432048);</span></a>
+<a name="4643"><span class="lineNum">    4643 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(-1490.8825754968443);</span></a>
+<a name="4644"><span class="lineNum">    4644 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_A].push_back(199.7501110740159);</span></a>
+<a name="4645"><span class="lineNum">    4645 </span>            : </a>
+<a name="4646"><span class="lineNum">    4646 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(939.8188801192172);</span></a>
+<a name="4647"><span class="lineNum">    4647 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(-1.489638186262854);</span></a>
+<a name="4648"><span class="lineNum">    4648 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(-1244.5515798554075);</span></a>
+<a name="4649"><span class="lineNum">    4649 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(-161.3972705672055);</span></a>
+<a name="4650"><span class="lineNum">    4650 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(1276.3568466722545);</span></a>
+<a name="4651"><span class="lineNum">    4651 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(-643.3057776225742);</span></a>
+<a name="4652"><span class="lineNum">    4652 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_C].push_back(72.75963113826273);</span></a>
+<a name="4653"><span class="lineNum">    4653 </span>            : </a>
+<a name="4654"><span class="lineNum">    4654 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(1768.434840119199);</span></a>
+<a name="4655"><span class="lineNum">    4655 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(-6.505347007077434);</span></a>
+<a name="4656"><span class="lineNum">    4656 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(-2919.3856777898427);</span></a>
+<a name="4657"><span class="lineNum">    4657 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(-701.2456464463938);</span></a>
+<a name="4658"><span class="lineNum">    4658 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(4464.594230284102);</span></a>
+<a name="4659"><span class="lineNum">    4659 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(-2733.138521295608);</span></a>
+<a name="4660"><span class="lineNum">    4660 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_G].push_back(458.1177706235891);</span></a>
+<a name="4661"><span class="lineNum">    4661 </span>            : </a>
+<a name="4662"><span class="lineNum">    4662 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(1179.3981001192033);</span></a>
+<a name="4663"><span class="lineNum">    4663 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(-3.2037849252756527);</span></a>
+<a name="4664"><span class="lineNum">    4664 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(-1821.255498763799);</span></a>
+<a name="4665"><span class="lineNum">    4665 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(-371.01993266441303);</span></a>
+<a name="4666"><span class="lineNum">    4666 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(2604.074226688971);</span></a>
+<a name="4667"><span class="lineNum">    4667 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(-1648.1965787713084);</span></a>
+<a name="4668"><span class="lineNum">    4668 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_T].push_back(307.2962186436368);</span></a>
+<a name="4669"><span class="lineNum">    4669 </span>            : </a>
+<a name="4670"><span class="lineNum">    4670 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(956.3442001192266);</span></a>
+<a name="4671"><span class="lineNum">    4671 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(-1.724458000760567);</span></a>
+<a name="4672"><span class="lineNum">    4672 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(-1287.9746970192687);</span></a>
+<a name="4673"><span class="lineNum">    4673 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(-192.74748379510373);</span></a>
+<a name="4674"><span class="lineNum">    4674 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(1459.0789258833893);</span></a>
+<a name="4675"><span class="lineNum">    4675 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(-810.0763075080915);</span></a>
+<a name="4676"><span class="lineNum">    4676 </span><span class="lineCov">          4 :   parameter_mix_H[BASE_U].push_back(119.81810290248339);</span></a>
+<a name="4677"><span class="lineNum">    4677 </span>            : </a>
+<a name="4678"><span class="lineNum">    4678 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(2.7889001116093275);</span></a>
+<a name="4679"><span class="lineNum">    4679 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(-0.00011178884266113128);</span></a>
+<a name="4680"><span class="lineNum">    4680 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(-1.1702605818380667);</span></a>
+<a name="4681"><span class="lineNum">    4681 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(-0.011278044036819933);</span></a>
+<a name="4682"><span class="lineNum">    4682 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(0.3214006584089025);</span></a>
+<a name="4683"><span class="lineNum">    4683 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(-0.04097165983591666);</span></a>
+<a name="4684"><span class="lineNum">    4684 </span><span class="lineCov">          4 :   parameter_vac_H[BB_PO2].push_back(-0.017525098100539722);</span></a>
+<a name="4685"><span class="lineNum">    4685 </span>            : </a>
+<a name="4686"><span class="lineNum">    4686 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(5.987809026456476);</span></a>
+<a name="4687"><span class="lineNum">    4687 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(9.945454528827912e-05);</span></a>
+<a name="4688"><span class="lineNum">    4688 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(-1.1884708569330031);</span></a>
+<a name="4689"><span class="lineNum">    4689 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(-0.007457733256362841);</span></a>
+<a name="4690"><span class="lineNum">    4690 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(0.05666858781418339);</span></a>
+<a name="4691"><span class="lineNum">    4691 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(-0.15158797629971757);</span></a>
+<a name="4692"><span class="lineNum">    4692 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA].push_back(0.11642340861329734);</span></a>
+<a name="4693"><span class="lineNum">    4693 </span>            : </a>
+<a name="4694"><span class="lineNum">    4694 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(4.297328944539055);</span></a>
+<a name="4695"><span class="lineNum">    4695 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(0.0014793971885106831);</span></a>
+<a name="4696"><span class="lineNum">    4696 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(1.3961088365255605);</span></a>
+<a name="4697"><span class="lineNum">    4697 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(0.08974639858979384);</span></a>
+<a name="4698"><span class="lineNum">    4698 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(-1.5198099705167643);</span></a>
+<a name="4699"><span class="lineNum">    4699 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(-0.12127122359433733);</span></a>
+<a name="4700"><span class="lineNum">    4700 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_5].push_back(0.4134601046223601);</span></a>
+<a name="4701"><span class="lineNum">    4701 </span>            : </a>
+<a name="4702"><span class="lineNum">    4702 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(4.297328886488132);</span></a>
+<a name="4703"><span class="lineNum">    4703 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(0.0041802954281271905);</span></a>
+<a name="4704"><span class="lineNum">    4704 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(1.6065462295705266);</span></a>
+<a name="4705"><span class="lineNum">    4705 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(0.4399805535688805);</span></a>
+<a name="4706"><span class="lineNum">    4706 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(-3.3806711791929804);</span></a>
+<a name="4707"><span class="lineNum">    4707 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(1.6729551563628675);</span></a>
+<a name="4708"><span class="lineNum">    4708 </span><span class="lineCov">          4 :   parameter_vac_H[BB_DNA_3].push_back(-0.10911063067909885);</span></a>
+<a name="4709"><span class="lineNum">    4709 </span>            : </a>
+<a name="4710"><span class="lineNum">    4710 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(9.162728984394093);</span></a>
+<a name="4711"><span class="lineNum">    4711 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(0.00019952321584579868);</span></a>
+<a name="4712"><span class="lineNum">    4712 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(-4.744748946331966);</span></a>
+<a name="4713"><span class="lineNum">    4713 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(0.025106563403946364);</span></a>
+<a name="4714"><span class="lineNum">    4714 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(1.2302956694109803);</span></a>
+<a name="4715"><span class="lineNum">    4715 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(0.12359062278096915);</span></a>
+<a name="4716"><span class="lineNum">    4716 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA].push_back(-0.1725633367685285);</span></a>
+<a name="4717"><span class="lineNum">    4717 </span>            : </a>
+<a name="4718"><span class="lineNum">    4718 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(7.038408898671503);</span></a>
+<a name="4719"><span class="lineNum">    4719 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(0.005106788424920148);</span></a>
+<a name="4720"><span class="lineNum">    4720 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(-0.8981588221803118);</span></a>
+<a name="4721"><span class="lineNum">    4721 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(0.4922588155214312);</span></a>
+<a name="4722"><span class="lineNum">    4722 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(-2.6667853454023644);</span></a>
+<a name="4723"><span class="lineNum">    4723 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(1.533316567240718);</span></a>
+<a name="4724"><span class="lineNum">    4724 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_5].push_back(-0.07199604869737707);</span></a>
+<a name="4725"><span class="lineNum">    4725 </span>            : </a>
+<a name="4726"><span class="lineNum">    4726 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(7.038408892621863);</span></a>
+<a name="4727"><span class="lineNum">    4727 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(0.002993083907266898);</span></a>
+<a name="4728"><span class="lineNum">    4728 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(-1.3626596831098492);</span></a>
+<a name="4729"><span class="lineNum">    4729 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(0.3138856961130113);</span></a>
+<a name="4730"><span class="lineNum">    4730 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(-1.684185014289391);</span></a>
+<a name="4731"><span class="lineNum">    4731 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(1.1862168720864616);</span></a>
+<a name="4732"><span class="lineNum">    4732 </span><span class="lineCov">          4 :   parameter_vac_H[BB_RNA_3].push_back(-0.1443894172417523);</span></a>
+<a name="4733"><span class="lineNum">    4733 </span>            : </a>
+<a name="4734"><span class="lineNum">    4734 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(42.62784088079008);</span></a>
+<a name="4735"><span class="lineNum">    4735 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(0.02302908536431516);</span></a>
+<a name="4736"><span class="lineNum">    4736 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(-33.22707177297222);</span></a>
+<a name="4737"><span class="lineNum">    4737 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(2.6853748424439834);</span></a>
+<a name="4738"><span class="lineNum">    4738 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(-1.6632902891624768);</span></a>
+<a name="4739"><span class="lineNum">    4739 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(11.905766349515268);</span></a>
+<a name="4740"><span class="lineNum">    4740 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_A].push_back(-4.547083454788805);</span></a>
+<a name="4741"><span class="lineNum">    4741 </span>            : </a>
+<a name="4742"><span class="lineNum">    4742 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(20.83009588079022);</span></a>
+<a name="4743"><span class="lineNum">    4743 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(0.017055822321768378);</span></a>
+<a name="4744"><span class="lineNum">    4744 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(-8.349634734370916);</span></a>
+<a name="4745"><span class="lineNum">    4745 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(1.9324634367723073);</span></a>
+<a name="4746"><span class="lineNum">    4746 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(-8.435199734060882);</span></a>
+<a name="4747"><span class="lineNum">    4747 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(8.272798368731268);</span></a>
+<a name="4748"><span class="lineNum">    4748 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_C].push_back(-1.986671440757263);</span></a>
+<a name="4749"><span class="lineNum">    4749 </span>            : </a>
+<a name="4750"><span class="lineNum">    4750 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(50.53788088079374);</span></a>
+<a name="4751"><span class="lineNum">    4751 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(0.024035597617780367);</span></a>
+<a name="4752"><span class="lineNum">    4752 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(-47.94916639302998);</span></a>
+<a name="4753"><span class="lineNum">    4753 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(3.143375731466498);</span></a>
+<a name="4754"><span class="lineNum">    4754 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(4.297009866708155);</span></a>
+<a name="4755"><span class="lineNum">    4755 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(15.855448505050578);</span></a>
+<a name="4756"><span class="lineNum">    4756 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_G].push_back(-7.827484135873966);</span></a>
+<a name="4757"><span class="lineNum">    4757 </span>            : </a>
+<a name="4758"><span class="lineNum">    4758 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(20.20502488079069);</span></a>
+<a name="4759"><span class="lineNum">    4759 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(0.033659966153300002);</span></a>
+<a name="4760"><span class="lineNum">    4760 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(-6.057999187718758);</span></a>
+<a name="4761"><span class="lineNum">    4761 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(4.146969282504351);</span></a>
+<a name="4762"><span class="lineNum">    4762 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(-20.664315319574357);</span></a>
+<a name="4763"><span class="lineNum">    4763 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(19.982178623201648);</span></a>
+<a name="4764"><span class="lineNum">    4764 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_T].push_back(-5.440921587349456);</span></a>
+<a name="4765"><span class="lineNum">    4765 </span>            : </a>
+<a name="4766"><span class="lineNum">    4766 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(20.958084119209754);</span></a>
+<a name="4767"><span class="lineNum">    4767 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(-0.005164660707148803);</span></a>
+<a name="4768"><span class="lineNum">    4768 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(-14.53831312442302);</span></a>
+<a name="4769"><span class="lineNum">    4769 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(-0.5276995756310442);</span></a>
+<a name="4770"><span class="lineNum">    4770 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(7.060900707522138);</span></a>
+<a name="4771"><span class="lineNum">    4771 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(-1.8988408480951036);</span></a>
+<a name="4772"><span class="lineNum">    4772 </span><span class="lineCov">          4 :   parameter_vac_H[BASE_U].push_back(-0.215000567681094);</span></a>
+<a name="4773"><span class="lineNum">    4773 </span>            : </a>
+<a name="4774"><span class="lineNum">    4774 </span><span class="lineCov">      14298 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="4775"><span class="lineNum">    4775 </span><span class="lineCov">      14294 :     std::string Aname = pdb.getAtomName(atoms[i]);</span></a>
+<a name="4776"><span class="lineNum">    4776 </span><span class="lineCov">      14294 :     std::string Rname = pdb.getResidueName(atoms[i]);</span></a>
+<a name="4777"><span class="lineNum">    4777 </span><span class="lineCov">      14294 :     Rname.erase(std::remove_if(Rname.begin(), Rname.end(), ::isspace),Rname.end());</span></a>
+<a name="4778"><span class="lineNum">    4778 </span><span class="lineCov">      14294 :     if(Rname==&quot;ALA&quot;) {</span></a>
+<a name="4779"><span class="lineNum">    4779 </span><span class="lineCov">        732 :       atoi[residue_atom[i]]=ALA;</span></a>
+<a name="4780"><span class="lineNum">    4780 </span><span class="lineCov">      13562 :     } else if(Rname==&quot;ARG&quot;) {</span></a>
+<a name="4781"><span class="lineNum">    4781 </span><span class="lineCov">        864 :       atoi[residue_atom[i]]=ARG;</span></a>
+<a name="4782"><span class="lineNum">    4782 </span><span class="lineCov">      12698 :     } else if(Rname==&quot;ASN&quot;) {</span></a>
+<a name="4783"><span class="lineNum">    4783 </span><span class="lineCov">        720 :       atoi[residue_atom[i]]=ASN;</span></a>
+<a name="4784"><span class="lineNum">    4784 </span><span class="lineCov">      11978 :     } else if(Rname==&quot;ASP&quot;) {</span></a>
+<a name="4785"><span class="lineNum">    4785 </span><span class="lineCov">        624 :       atoi[residue_atom[i]]=ASP;</span></a>
+<a name="4786"><span class="lineNum">    4786 </span><span class="lineCov">      11354 :     } else if(Rname==&quot;CYS&quot;) {</span></a>
+<a name="4787"><span class="lineNum">    4787 </span><span class="lineCov">         48 :       atoi[residue_atom[i]]=CYS;</span></a>
+<a name="4788"><span class="lineNum">    4788 </span><span class="lineCov">      11306 :     } else if(Rname==&quot;GLN&quot;) {</span></a>
+<a name="4789"><span class="lineNum">    4789 </span><span class="lineCov">       1064 :       atoi[residue_atom[i]]=GLN;</span></a>
+<a name="4790"><span class="lineNum">    4790 </span><span class="lineCov">      10242 :     } else if(Rname==&quot;GLU&quot;) {</span></a>
+<a name="4791"><span class="lineNum">    4791 </span><span class="lineCov">        476 :       atoi[residue_atom[i]]=GLU;</span></a>
+<a name="4792"><span class="lineNum">    4792 </span><span class="lineCov">       9766 :     } else if(Rname==&quot;GLY&quot;) {</span></a>
+<a name="4793"><span class="lineNum">    4793 </span><span class="lineCov">        648 :       atoi[residue_atom[i]]=GLY;</span></a>
+<a name="4794"><span class="lineNum">    4794 </span><span class="lineCov">       9118 :     } else if(Rname==&quot;HIS&quot;) {</span></a>
+<a name="4795"><span class="lineNum">    4795 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="4796"><span class="lineNum">    4796 </span><span class="lineCov">       9118 :     } else if(Rname==&quot;HID&quot;) {</span></a>
+<a name="4797"><span class="lineNum">    4797 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="4798"><span class="lineNum">    4798 </span><span class="lineCov">       9118 :     } else if(Rname==&quot;HIE&quot;) {</span></a>
+<a name="4799"><span class="lineNum">    4799 </span><span class="lineCov">        144 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="4800"><span class="lineNum">    4800 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HIP&quot;) {</span></a>
+<a name="4801"><span class="lineNum">    4801 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIP;</span></a>
+<a name="4802"><span class="lineNum">    4802 </span>            :       // CHARMM NAMING FOR PROTONATION STATES OF HISTIDINE</a>
+<a name="4803"><span class="lineNum">    4803 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HSD&quot;) {</span></a>
+<a name="4804"><span class="lineNum">    4804 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="4805"><span class="lineNum">    4805 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HSE&quot;) {</span></a>
+<a name="4806"><span class="lineNum">    4806 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="4807"><span class="lineNum">    4807 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HSP&quot;) {</span></a>
+<a name="4808"><span class="lineNum">    4808 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIP;</span></a>
+<a name="4809"><span class="lineNum">    4809 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;ILE&quot;) {</span></a>
+<a name="4810"><span class="lineNum">    4810 </span><span class="lineCov">        864 :       atoi[residue_atom[i]]=ILE;</span></a>
+<a name="4811"><span class="lineNum">    4811 </span><span class="lineCov">       8110 :     } else if(Rname==&quot;LEU&quot;) {</span></a>
+<a name="4812"><span class="lineNum">    4812 </span><span class="lineCov">       1520 :       atoi[residue_atom[i]]=LEU;</span></a>
+<a name="4813"><span class="lineNum">    4813 </span><span class="lineCov">       6590 :     } else if(Rname==&quot;LYS&quot;) {</span></a>
+<a name="4814"><span class="lineNum">    4814 </span><span class="lineCov">       1040 :       atoi[residue_atom[i]]=LYS;</span></a>
+<a name="4815"><span class="lineNum">    4815 </span><span class="lineCov">       5550 :     } else if(Rname==&quot;MET&quot;) {</span></a>
+<a name="4816"><span class="lineNum">    4816 </span><span class="lineCov">        608 :       atoi[residue_atom[i]]=MET;</span></a>
+<a name="4817"><span class="lineNum">    4817 </span><span class="lineCov">       4942 :     } else if(Rname==&quot;PHE&quot;) {</span></a>
+<a name="4818"><span class="lineNum">    4818 </span><span class="lineCov">       1008 :       atoi[residue_atom[i]]=PHE;</span></a>
+<a name="4819"><span class="lineNum">    4819 </span><span class="lineCov">       3934 :     } else if(Rname==&quot;PRO&quot;) {</span></a>
+<a name="4820"><span class="lineNum">    4820 </span><span class="lineCov">        748 :       atoi[residue_atom[i]]=PRO;</span></a>
+<a name="4821"><span class="lineNum">    4821 </span><span class="lineCov">       3186 :     } else if(Rname==&quot;SER&quot;) {</span></a>
+<a name="4822"><span class="lineNum">    4822 </span><span class="lineCov">        528 :       atoi[residue_atom[i]]=SER;</span></a>
+<a name="4823"><span class="lineNum">    4823 </span><span class="lineCov">       2658 :     } else if(Rname==&quot;THR&quot;) {</span></a>
+<a name="4824"><span class="lineNum">    4824 </span><span class="lineCov">        504 :       atoi[residue_atom[i]]=THR;</span></a>
+<a name="4825"><span class="lineNum">    4825 </span><span class="lineCov">       2154 :     } else if(Rname==&quot;TRP&quot;) {</span></a>
+<a name="4826"><span class="lineNum">    4826 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=TRP;</span></a>
+<a name="4827"><span class="lineNum">    4827 </span><span class="lineCov">       2154 :     } else if(Rname==&quot;TYR&quot;) {</span></a>
+<a name="4828"><span class="lineNum">    4828 </span><span class="lineCov">        528 :       atoi[residue_atom[i]]=TYR;</span></a>
+<a name="4829"><span class="lineNum">    4829 </span><span class="lineCov">       1626 :     } else if(Rname==&quot;VAL&quot;) {</span></a>
+<a name="4830"><span class="lineNum">    4830 </span><span class="lineCov">       1088 :       atoi[residue_atom[i]]=VAL;</span></a>
+<a name="4831"><span class="lineNum">    4831 </span>            :     }</a>
+<a name="4832"><span class="lineNum">    4832 </span>            :     // NUCLEIC ACIDS</a>
+<a name="4833"><span class="lineNum">    4833 </span>            :     // nucleobases are not automatically populated as an additional check on the health of the PDB.</a>
+<a name="4834"><span class="lineNum">    4834 </span>            :     // RNA - G</a>
+<a name="4835"><span class="lineNum">    4835 </span><span class="lineCov">        538 :     else if(Rname==&quot;G&quot;) {</span></a>
+<a name="4836"><span class="lineNum">    4836 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4837"><span class="lineNum">    4837 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4838"><span class="lineNum">    4838 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4839"><span class="lineNum">    4839 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4840"><span class="lineNum">    4840 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4841"><span class="lineNum">    4841 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4842"><span class="lineNum">    4842 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4843"><span class="lineNum">    4843 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4844"><span class="lineNum">    4844 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4845"><span class="lineNum">    4845 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="4846"><span class="lineNum">    4846 </span><span class="lineNoCov">          0 :       } else if( Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="4847"><span class="lineNum">    4847 </span><span class="lineNoCov">          0 :                  Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="4848"><span class="lineNum">    4848 </span><span class="lineNoCov">          0 :                  Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="4849"><span class="lineNum">    4849 </span><span class="lineNoCov">          0 :                  Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="4850"><span class="lineNum">    4850 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="4851"><span class="lineNum">    4851 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4852"><span class="lineNum">    4852 </span>            :       // RNA - G3</a>
+<a name="4853"><span class="lineNum">    4853 </span><span class="lineCov">        538 :     } else if(Rname==&quot;G3&quot;) {</span></a>
+<a name="4854"><span class="lineNum">    4854 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4855"><span class="lineNum">    4855 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4856"><span class="lineNum">    4856 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4857"><span class="lineNum">    4857 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4858"><span class="lineNum">    4858 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4859"><span class="lineNum">    4859 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4860"><span class="lineNum">    4860 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4861"><span class="lineNum">    4861 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4862"><span class="lineNum">    4862 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="4863"><span class="lineNum">    4863 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="4864"><span class="lineNum">    4864 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="4865"><span class="lineNum">    4865 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="4866"><span class="lineNum">    4866 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="4867"><span class="lineNum">    4867 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="4868"><span class="lineNum">    4868 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="4869"><span class="lineNum">    4869 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4870"><span class="lineNum">    4870 </span>            :       // RNA - G5</a>
+<a name="4871"><span class="lineNum">    4871 </span><span class="lineCov">        538 :     } else if(Rname==&quot;G5&quot;) {</span></a>
+<a name="4872"><span class="lineNum">    4872 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4873"><span class="lineNum">    4873 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4874"><span class="lineNum">    4874 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4875"><span class="lineNum">    4875 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="4876"><span class="lineNum">    4876 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="4877"><span class="lineNum">    4877 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4878"><span class="lineNum">    4878 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="4879"><span class="lineNum">    4879 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="4880"><span class="lineNum">    4880 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="4881"><span class="lineNum">    4881 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="4882"><span class="lineNum">    4882 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="4883"><span class="lineNum">    4883 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="4884"><span class="lineNum">    4884 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4885"><span class="lineNum">    4885 </span>            :       // RNA - U</a>
+<a name="4886"><span class="lineNum">    4886 </span><span class="lineCov">        538 :     } else if(Rname==&quot;U&quot;) {</span></a>
+<a name="4887"><span class="lineNum">    4887 </span><span class="lineCov">       1554 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4888"><span class="lineNum">    4888 </span><span class="lineCov">       1176 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4889"><span class="lineNum">    4889 </span><span class="lineCov">         42 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4890"><span class="lineNum">    4890 </span><span class="lineCov">       1372 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4891"><span class="lineNum">    4891 </span><span class="lineCov">       1148 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4892"><span class="lineNum">    4892 </span><span class="lineCov">        924 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4893"><span class="lineNum">    4893 </span><span class="lineCov">        714 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4894"><span class="lineNum">    4894 </span><span class="lineCov">        644 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4895"><span class="lineNum">    4895 </span><span class="lineCov">        840 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4896"><span class="lineNum">    4896 </span><span class="lineCov">        224 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="4897"><span class="lineNum">    4897 </span><span class="lineCov">        476 :       } else if( Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="4898"><span class="lineNum">    4898 </span><span class="lineCov">        252 :                  Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="4899"><span class="lineNum">    4899 </span><span class="lineCov">        196 :                  Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="4900"><span class="lineNum">    4900 </span><span class="lineCov">        154 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="4901"><span class="lineNum">    4901 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4902"><span class="lineNum">    4902 </span>            :       // RNA - U3</a>
+<a name="4903"><span class="lineNum">    4903 </span><span class="lineCov">        118 :     } else if(Rname==&quot;U3&quot;) {</span></a>
+<a name="4904"><span class="lineNum">    4904 </span><span class="lineCov">        230 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4905"><span class="lineNum">    4905 </span><span class="lineCov">        174 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4906"><span class="lineNum">    4906 </span><span class="lineCov">          6 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4907"><span class="lineNum">    4907 </span><span class="lineCov">        204 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4908"><span class="lineNum">    4908 </span><span class="lineCov">        172 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4909"><span class="lineNum">    4909 </span><span class="lineCov">        140 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4910"><span class="lineNum">    4910 </span><span class="lineCov">        110 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4911"><span class="lineNum">    4911 </span><span class="lineCov">         94 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4912"><span class="lineNum">    4912 </span><span class="lineCov">         78 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="4913"><span class="lineNum">    4913 </span><span class="lineCov">         34 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="4914"><span class="lineNum">    4914 </span><span class="lineCov">         68 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="4915"><span class="lineNum">    4915 </span><span class="lineCov">         36 :                 Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="4916"><span class="lineNum">    4916 </span><span class="lineCov">         28 :                 Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="4917"><span class="lineNum">    4917 </span><span class="lineCov">         22 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="4918"><span class="lineNum">    4918 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4919"><span class="lineNum">    4919 </span>            :       // RNA - U5</a>
+<a name="4920"><span class="lineNum">    4920 </span><span class="lineCov">         56 :     } else if(Rname==&quot;U5&quot;) {</span></a>
+<a name="4921"><span class="lineNum">    4921 </span><span class="lineCov">        204 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4922"><span class="lineNum">    4922 </span><span class="lineCov">        172 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4923"><span class="lineNum">    4923 </span><span class="lineCov">        140 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4924"><span class="lineNum">    4924 </span><span class="lineCov">        108 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="4925"><span class="lineNum">    4925 </span><span class="lineCov">         88 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="4926"><span class="lineNum">    4926 </span><span class="lineCov">         78 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4927"><span class="lineNum">    4927 </span><span class="lineCov">         34 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="4928"><span class="lineNum">    4928 </span><span class="lineCov">         68 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="4929"><span class="lineNum">    4929 </span><span class="lineCov">         36 :                 Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="4930"><span class="lineNum">    4930 </span><span class="lineCov">         28 :                 Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="4931"><span class="lineNum">    4931 </span><span class="lineCov">         22 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="4932"><span class="lineNum">    4932 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4933"><span class="lineNum">    4933 </span>            :       // RNA - A</a>
+<a name="4934"><span class="lineNum">    4934 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A&quot;) {</span></a>
+<a name="4935"><span class="lineNum">    4935 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4936"><span class="lineNum">    4936 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4937"><span class="lineNum">    4937 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4938"><span class="lineNum">    4938 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4939"><span class="lineNum">    4939 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4940"><span class="lineNum">    4940 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4941"><span class="lineNum">    4941 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4942"><span class="lineNum">    4942 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4943"><span class="lineNum">    4943 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4944"><span class="lineNum">    4944 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="4945"><span class="lineNum">    4945 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="4946"><span class="lineNum">    4946 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="4947"><span class="lineNum">    4947 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="4948"><span class="lineNum">    4948 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="4949"><span class="lineNum">    4949 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="4950"><span class="lineNum">    4950 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4951"><span class="lineNum">    4951 </span>            :       // RNA - A3</a>
+<a name="4952"><span class="lineNum">    4952 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A3&quot;) {</span></a>
+<a name="4953"><span class="lineNum">    4953 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4954"><span class="lineNum">    4954 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4955"><span class="lineNum">    4955 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4956"><span class="lineNum">    4956 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4957"><span class="lineNum">    4957 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4958"><span class="lineNum">    4958 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4959"><span class="lineNum">    4959 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4960"><span class="lineNum">    4960 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4961"><span class="lineNum">    4961 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="4962"><span class="lineNum">    4962 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="4963"><span class="lineNum">    4963 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="4964"><span class="lineNum">    4964 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="4965"><span class="lineNum">    4965 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="4966"><span class="lineNum">    4966 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="4967"><span class="lineNum">    4967 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="4968"><span class="lineNum">    4968 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4969"><span class="lineNum">    4969 </span>            :       // RNA - A5</a>
+<a name="4970"><span class="lineNum">    4970 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A5&quot;) {</span></a>
+<a name="4971"><span class="lineNum">    4971 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4972"><span class="lineNum">    4972 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4973"><span class="lineNum">    4973 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4974"><span class="lineNum">    4974 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="4975"><span class="lineNum">    4975 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="4976"><span class="lineNum">    4976 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4977"><span class="lineNum">    4977 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="4978"><span class="lineNum">    4978 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="4979"><span class="lineNum">    4979 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="4980"><span class="lineNum">    4980 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="4981"><span class="lineNum">    4981 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="4982"><span class="lineNum">    4982 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="4983"><span class="lineNum">    4983 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="4984"><span class="lineNum">    4984 </span>            :       // RNA - C</a>
+<a name="4985"><span class="lineNum">    4985 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C&quot;) {</span></a>
+<a name="4986"><span class="lineNum">    4986 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="4987"><span class="lineNum">    4987 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="4988"><span class="lineNum">    4988 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="4989"><span class="lineNum">    4989 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="4990"><span class="lineNum">    4990 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="4991"><span class="lineNum">    4991 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="4992"><span class="lineNum">    4992 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="4993"><span class="lineNum">    4993 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="4994"><span class="lineNum">    4994 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="4995"><span class="lineNum">    4995 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="4996"><span class="lineNum">    4996 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="4997"><span class="lineNum">    4997 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="4998"><span class="lineNum">    4998 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="4999"><span class="lineNum">    4999 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5000"><span class="lineNum">    5000 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5001"><span class="lineNum">    5001 </span>            :       // RNA - C3</a>
+<a name="5002"><span class="lineNum">    5002 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C3&quot;) {</span></a>
+<a name="5003"><span class="lineNum">    5003 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5004"><span class="lineNum">    5004 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5005"><span class="lineNum">    5005 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5006"><span class="lineNum">    5006 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5007"><span class="lineNum">    5007 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5008"><span class="lineNum">    5008 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5009"><span class="lineNum">    5009 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5010"><span class="lineNum">    5010 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5011"><span class="lineNum">    5011 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="5012"><span class="lineNum">    5012 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="5013"><span class="lineNum">    5013 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="5014"><span class="lineNum">    5014 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="5015"><span class="lineNum">    5015 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="5016"><span class="lineNum">    5016 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5017"><span class="lineNum">    5017 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5018"><span class="lineNum">    5018 </span>            :       // RNA - C5</a>
+<a name="5019"><span class="lineNum">    5019 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C5&quot;) {</span></a>
+<a name="5020"><span class="lineNum">    5020 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5021"><span class="lineNum">    5021 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5022"><span class="lineNum">    5022 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5023"><span class="lineNum">    5023 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5024"><span class="lineNum">    5024 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="5025"><span class="lineNum">    5025 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5026"><span class="lineNum">    5026 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="5027"><span class="lineNum">    5027 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="5028"><span class="lineNum">    5028 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="5029"><span class="lineNum">    5029 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="5030"><span class="lineNum">    5030 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5031"><span class="lineNum">    5031 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5032"><span class="lineNum">    5032 </span>            :       // DNA - G</a>
+<a name="5033"><span class="lineNum">    5033 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG&quot;) {</span></a>
+<a name="5034"><span class="lineNum">    5034 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5035"><span class="lineNum">    5035 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5036"><span class="lineNum">    5036 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5037"><span class="lineNum">    5037 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5038"><span class="lineNum">    5038 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5039"><span class="lineNum">    5039 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5040"><span class="lineNum">    5040 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5041"><span class="lineNum">    5041 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="5042"><span class="lineNum">    5042 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="5043"><span class="lineNum">    5043 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="5044"><span class="lineNum">    5044 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5045"><span class="lineNum">    5045 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="5046"><span class="lineNum">    5046 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="5047"><span class="lineNum">    5047 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="5048"><span class="lineNum">    5048 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="5049"><span class="lineNum">    5049 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5050"><span class="lineNum">    5050 </span>            :       // DNA - G3</a>
+<a name="5051"><span class="lineNum">    5051 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG3&quot;) {</span></a>
+<a name="5052"><span class="lineNum">    5052 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5053"><span class="lineNum">    5053 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5054"><span class="lineNum">    5054 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5055"><span class="lineNum">    5055 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5056"><span class="lineNum">    5056 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5057"><span class="lineNum">    5057 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5058"><span class="lineNum">    5058 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="5059"><span class="lineNum">    5059 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5060"><span class="lineNum">    5060 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="5061"><span class="lineNum">    5061 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="5062"><span class="lineNum">    5062 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5063"><span class="lineNum">    5063 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="5064"><span class="lineNum">    5064 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="5065"><span class="lineNum">    5065 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="5066"><span class="lineNum">    5066 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="5067"><span class="lineNum">    5067 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5068"><span class="lineNum">    5068 </span>            :       // DNA - G5</a>
+<a name="5069"><span class="lineNum">    5069 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG5&quot;) {</span></a>
+<a name="5070"><span class="lineNum">    5070 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5071"><span class="lineNum">    5071 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="5072"><span class="lineNum">    5072 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5073"><span class="lineNum">    5073 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5074"><span class="lineNum">    5074 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5075"><span class="lineNum">    5075 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="5076"><span class="lineNum">    5076 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="5077"><span class="lineNum">    5077 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5078"><span class="lineNum">    5078 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="5079"><span class="lineNum">    5079 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="5080"><span class="lineNum">    5080 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="5081"><span class="lineNum">    5081 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="5082"><span class="lineNum">    5082 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5083"><span class="lineNum">    5083 </span>            :       // DNA - T</a>
+<a name="5084"><span class="lineNum">    5084 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT&quot;) {</span></a>
+<a name="5085"><span class="lineNum">    5085 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5086"><span class="lineNum">    5086 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5087"><span class="lineNum">    5087 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5088"><span class="lineNum">    5088 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5089"><span class="lineNum">    5089 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5090"><span class="lineNum">    5090 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5091"><span class="lineNum">    5091 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5092"><span class="lineNum">    5092 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="5093"><span class="lineNum">    5093 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="5094"><span class="lineNum">    5094 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="5095"><span class="lineNum">    5095 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="5096"><span class="lineNum">    5096 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="5097"><span class="lineNum">    5097 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="5098"><span class="lineNum">    5098 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="5099"><span class="lineNum">    5099 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="5100"><span class="lineNum">    5100 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5101"><span class="lineNum">    5101 </span>            :       // DNA - T3</a>
+<a name="5102"><span class="lineNum">    5102 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT3&quot;) {</span></a>
+<a name="5103"><span class="lineNum">    5103 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5104"><span class="lineNum">    5104 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5105"><span class="lineNum">    5105 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5106"><span class="lineNum">    5106 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5107"><span class="lineNum">    5107 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5108"><span class="lineNum">    5108 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5109"><span class="lineNum">    5109 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="5110"><span class="lineNum">    5110 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5111"><span class="lineNum">    5111 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="5112"><span class="lineNum">    5112 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="5113"><span class="lineNum">    5113 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="5114"><span class="lineNum">    5114 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="5115"><span class="lineNum">    5115 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="5116"><span class="lineNum">    5116 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="5117"><span class="lineNum">    5117 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="5118"><span class="lineNum">    5118 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5119"><span class="lineNum">    5119 </span>            :       // DNA - T5</a>
+<a name="5120"><span class="lineNum">    5120 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT5&quot;) {</span></a>
+<a name="5121"><span class="lineNum">    5121 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5122"><span class="lineNum">    5122 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="5123"><span class="lineNum">    5123 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5124"><span class="lineNum">    5124 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5125"><span class="lineNum">    5125 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5126"><span class="lineNum">    5126 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="5127"><span class="lineNum">    5127 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="5128"><span class="lineNum">    5128 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="5129"><span class="lineNum">    5129 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="5130"><span class="lineNum">    5130 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="5131"><span class="lineNum">    5131 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="5132"><span class="lineNum">    5132 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="5133"><span class="lineNum">    5133 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5134"><span class="lineNum">    5134 </span>            :       // DNA - A</a>
+<a name="5135"><span class="lineNum">    5135 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA&quot;) {</span></a>
+<a name="5136"><span class="lineNum">    5136 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5137"><span class="lineNum">    5137 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5138"><span class="lineNum">    5138 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5139"><span class="lineNum">    5139 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5140"><span class="lineNum">    5140 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5141"><span class="lineNum">    5141 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5142"><span class="lineNum">    5142 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5143"><span class="lineNum">    5143 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="5144"><span class="lineNum">    5144 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="5145"><span class="lineNum">    5145 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="5146"><span class="lineNum">    5146 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="5147"><span class="lineNum">    5147 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="5148"><span class="lineNum">    5148 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="5149"><span class="lineNum">    5149 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="5150"><span class="lineNum">    5150 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="5151"><span class="lineNum">    5151 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5152"><span class="lineNum">    5152 </span>            :       // DNA - A3</a>
+<a name="5153"><span class="lineNum">    5153 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA3&quot;) {</span></a>
+<a name="5154"><span class="lineNum">    5154 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5155"><span class="lineNum">    5155 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5156"><span class="lineNum">    5156 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5157"><span class="lineNum">    5157 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5158"><span class="lineNum">    5158 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5159"><span class="lineNum">    5159 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5160"><span class="lineNum">    5160 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="5161"><span class="lineNum">    5161 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5162"><span class="lineNum">    5162 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="5163"><span class="lineNum">    5163 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="5164"><span class="lineNum">    5164 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="5165"><span class="lineNum">    5165 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="5166"><span class="lineNum">    5166 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="5167"><span class="lineNum">    5167 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="5168"><span class="lineNum">    5168 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="5169"><span class="lineNum">    5169 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5170"><span class="lineNum">    5170 </span>            :       // DNA - A5</a>
+<a name="5171"><span class="lineNum">    5171 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA5&quot;) {</span></a>
+<a name="5172"><span class="lineNum">    5172 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5173"><span class="lineNum">    5173 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="5174"><span class="lineNum">    5174 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5175"><span class="lineNum">    5175 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5176"><span class="lineNum">    5176 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5177"><span class="lineNum">    5177 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="5178"><span class="lineNum">    5178 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="5179"><span class="lineNum">    5179 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="5180"><span class="lineNum">    5180 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="5181"><span class="lineNum">    5181 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="5182"><span class="lineNum">    5182 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="5183"><span class="lineNum">    5183 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="5184"><span class="lineNum">    5184 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5185"><span class="lineNum">    5185 </span>            :       // DNA - C</a>
+<a name="5186"><span class="lineNum">    5186 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC&quot;) {</span></a>
+<a name="5187"><span class="lineNum">    5187 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5188"><span class="lineNum">    5188 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5189"><span class="lineNum">    5189 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5190"><span class="lineNum">    5190 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5191"><span class="lineNum">    5191 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5192"><span class="lineNum">    5192 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5193"><span class="lineNum">    5193 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5194"><span class="lineNum">    5194 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="5195"><span class="lineNum">    5195 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="5196"><span class="lineNum">    5196 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="5197"><span class="lineNum">    5197 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="5198"><span class="lineNum">    5198 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="5199"><span class="lineNum">    5199 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="5200"><span class="lineNum">    5200 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5201"><span class="lineNum">    5201 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5202"><span class="lineNum">    5202 </span>            :       // DNA - C3</a>
+<a name="5203"><span class="lineNum">    5203 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC3&quot;) {</span></a>
+<a name="5204"><span class="lineNum">    5204 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5205"><span class="lineNum">    5205 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5206"><span class="lineNum">    5206 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5207"><span class="lineNum">    5207 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5208"><span class="lineNum">    5208 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="5209"><span class="lineNum">    5209 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5210"><span class="lineNum">    5210 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="5211"><span class="lineNum">    5211 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5212"><span class="lineNum">    5212 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="5213"><span class="lineNum">    5213 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="5214"><span class="lineNum">    5214 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="5215"><span class="lineNum">    5215 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="5216"><span class="lineNum">    5216 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="5217"><span class="lineNum">    5217 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5218"><span class="lineNum">    5218 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5219"><span class="lineNum">    5219 </span>            :       // DNA - C5</a>
+<a name="5220"><span class="lineNum">    5220 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC5&quot;) {</span></a>
+<a name="5221"><span class="lineNum">    5221 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5222"><span class="lineNum">    5222 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="5223"><span class="lineNum">    5223 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="5224"><span class="lineNum">    5224 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5225"><span class="lineNum">    5225 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="5226"><span class="lineNum">    5226 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="5227"><span class="lineNum">    5227 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="5228"><span class="lineNum">    5228 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="5229"><span class="lineNum">    5229 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="5230"><span class="lineNum">    5230 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="5231"><span class="lineNum">    5231 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5232"><span class="lineNum">    5232 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5233"><span class="lineNum">    5233 </span><span class="lineNoCov">          0 :     } else error(&quot;Residue not known: &quot;+Rname);</span></a>
+<a name="5234"><span class="lineNum">    5234 </span>            :   }</a>
+<a name="5235"><span class="lineNum">    5235 </span><span class="lineCov">          4 : }</span></a>
+<a name="5236"><span class="lineNum">    5236 </span>            : </a>
+<a name="5237"><span class="lineNum">    5237 </span><span class="lineCov">          4 : void SAXS::getOnebeadparam_sansD(const PDB &amp;pdb, const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_vac_D, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;parameter_mix_D)</span></a>
+<a name="5238"><span class="lineNum">    5238 </span>            : { // parameter_solv is identical in SAXS/SANS_H/SANS_D since it depends exclusively on param_v. For that reason we kept param_solv only in SAXS and SANS_H.</a>
+<a name="5239"><span class="lineNum">    5239 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(8105.740500119327);</span></a>
+<a name="5240"><span class="lineNum">    5240 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(-41.785616935469804);</span></a>
+<a name="5241"><span class="lineNum">    5241 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(-25456.92790554363);</span></a>
+<a name="5242"><span class="lineNum">    5242 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(-10058.20599969184);</span></a>
+<a name="5243"><span class="lineNum">    5243 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(86171.76479108425);</span></a>
+<a name="5244"><span class="lineNum">    5244 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(-83227.63139882773);</span></a>
+<a name="5245"><span class="lineNum">    5245 </span><span class="lineCov">          4 :   parameter_mix_D[TRP].push_back(25121.390436258724);</span></a>
+<a name="5246"><span class="lineNum">    5246 </span>            : </a>
+<a name="5247"><span class="lineNum">    5247 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(6059.530560118732);</span></a>
+<a name="5248"><span class="lineNum">    5248 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(-24.522695525705736);</span></a>
+<a name="5249"><span class="lineNum">    5249 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(-17180.858815360847);</span></a>
+<a name="5250"><span class="lineNum">    5250 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(-5990.1358528219325);</span></a>
+<a name="5251"><span class="lineNum">    5251 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(52936.46126637543);</span></a>
+<a name="5252"><span class="lineNum">    5252 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(-50150.0042622683);</span></a>
+<a name="5253"><span class="lineNum">    5253 </span><span class="lineCov">          4 :   parameter_mix_D[TYR].push_back(14914.553672440441);</span></a>
+<a name="5254"><span class="lineNum">    5254 </span>            : </a>
+<a name="5255"><span class="lineNum">    5255 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(5563.404880119222);</span></a>
+<a name="5256"><span class="lineNum">    5256 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(-33.609784645922794);</span></a>
+<a name="5257"><span class="lineNum">    5257 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(-14576.935030777448);</span></a>
+<a name="5258"><span class="lineNum">    5258 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(-5759.170105553782);</span></a>
+<a name="5259"><span class="lineNum">    5259 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(43316.895956549866);</span></a>
+<a name="5260"><span class="lineNum">    5260 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(-39106.58694570862);</span></a>
+<a name="5261"><span class="lineNum">    5261 </span><span class="lineCov">          4 :   parameter_mix_D[PHE].push_back(11143.375742877468);</span></a>
+<a name="5262"><span class="lineNum">    5262 </span>            : </a>
+<a name="5263"><span class="lineNum">    5263 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(3981.7108801192553);</span></a>
+<a name="5264"><span class="lineNum">    5264 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(-23.788371565946427);</span></a>
+<a name="5265"><span class="lineNum">    5265 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(-9471.73953776056);</span></a>
+<a name="5266"><span class="lineNum">    5266 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(-3690.3981577198365);</span></a>
+<a name="5267"><span class="lineNum">    5267 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(26365.958584217453);</span></a>
+<a name="5268"><span class="lineNum">    5268 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(-23067.58974902849);</span></a>
+<a name="5269"><span class="lineNum">    5269 </span><span class="lineCov">          4 :   parameter_mix_D[HIP].push_back(6390.507451097114);</span></a>
+<a name="5270"><span class="lineNum">    5270 </span>            : </a>
+<a name="5271"><span class="lineNum">    5271 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(6279.489359881259);</span></a>
+<a name="5272"><span class="lineNum">    5272 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(1.2061878338083583);</span></a>
+<a name="5273"><span class="lineNum">    5273 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(-20305.413937989913);</span></a>
+<a name="5274"><span class="lineNum">    5274 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(-5621.666335222669);</span></a>
+<a name="5275"><span class="lineNum">    5275 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(67341.96785520067);</span></a>
+<a name="5276"><span class="lineNum">    5276 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(-68849.15464591733);</span></a>
+<a name="5277"><span class="lineNum">    5277 </span><span class="lineCov">          4 :   parameter_mix_D[ARG].push_back(21773.0630363882);</span></a>
+<a name="5278"><span class="lineNum">    5278 </span>            : </a>
+<a name="5279"><span class="lineNum">    5279 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(5434.487400119193);</span></a>
+<a name="5280"><span class="lineNum">    5280 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(-29.32356328987909);</span></a>
+<a name="5281"><span class="lineNum">    5281 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(-14363.66155749977);</span></a>
+<a name="5282"><span class="lineNum">    5282 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(-5650.383128516514);</span></a>
+<a name="5283"><span class="lineNum">    5283 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(44573.73888236887);</span></a>
+<a name="5284"><span class="lineNum">    5284 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(-41515.980945300485);</span></a>
+<a name="5285"><span class="lineNum">    5285 </span><span class="lineCov">          4 :   parameter_mix_D[LYS].push_back(12181.965046747513);</span></a>
+<a name="5286"><span class="lineNum">    5286 </span>            : </a>
+<a name="5287"><span class="lineNum">    5287 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(1519.4030001192032);</span></a>
+<a name="5288"><span class="lineNum">    5288 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(-3.564386334921097);</span></a>
+<a name="5289"><span class="lineNum">    5289 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(-2275.813167459516);</span></a>
+<a name="5290"><span class="lineNum">    5290 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(-409.54431591328125);</span></a>
+<a name="5291"><span class="lineNum">    5291 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(2969.5412742839258);</span></a>
+<a name="5292"><span class="lineNum">    5292 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(-1798.3157146799638);</span></a>
+<a name="5293"><span class="lineNum">    5293 </span><span class="lineCov">          4 :   parameter_mix_D[CYS].push_back(314.568167888235);</span></a>
+<a name="5294"><span class="lineNum">    5294 </span>            : </a>
+<a name="5295"><span class="lineNum">    5295 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(1861.6998401191709);</span></a>
+<a name="5296"><span class="lineNum">    5296 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(-5.349780637260551);</span></a>
+<a name="5297"><span class="lineNum">    5297 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(-2960.36741510377);</span></a>
+<a name="5298"><span class="lineNum">    5298 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(-621.8270745040523);</span></a>
+<a name="5299"><span class="lineNum">    5299 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(4334.798300452934);</span></a>
+<a name="5300"><span class="lineNum">    5300 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(-2776.8560521554878);</span></a>
+<a name="5301"><span class="lineNum">    5301 </span><span class="lineCov">          4 :   parameter_mix_D[ASP].push_back(527.9777182094936);</span></a>
+<a name="5302"><span class="lineNum">    5302 </span>            : </a>
+<a name="5303"><span class="lineNum">    5303 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(2861.6017201192253);</span></a>
+<a name="5304"><span class="lineNum">    5304 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(-13.146456903921809);</span></a>
+<a name="5305"><span class="lineNum">    5305 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(-5393.408563875243);</span></a>
+<a name="5306"><span class="lineNum">    5306 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(-1646.460570818364);</span></a>
+<a name="5307"><span class="lineNum">    5307 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(10884.544923253858);</span></a>
+<a name="5308"><span class="lineNum">    5308 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(-8159.923373048856);</span></a>
+<a name="5309"><span class="lineNum">    5309 </span><span class="lineCov">          4 :   parameter_mix_D[GLU].push_back(1914.545660397314);</span></a>
+<a name="5310"><span class="lineNum">    5310 </span>            : </a>
+<a name="5311"><span class="lineNum">    5311 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(4288.585540119189);</span></a>
+<a name="5312"><span class="lineNum">    5312 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(-19.937215352880365);</span></a>
+<a name="5313"><span class="lineNum">    5313 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(-8324.540144463375);</span></a>
+<a name="5314"><span class="lineNum">    5314 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(-2431.835931316717);</span></a>
+<a name="5315"><span class="lineNum">    5315 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(16079.9912986194);</span></a>
+<a name="5316"><span class="lineNum">    5316 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(-11637.693060394462);</span></a>
+<a name="5317"><span class="lineNum">    5317 </span><span class="lineCov">          4 :   parameter_mix_D[ILE].push_back(2600.8258068480495);</span></a>
+<a name="5318"><span class="lineNum">    5318 </span>            : </a>
+<a name="5319"><span class="lineNum">    5319 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(4288.585540119186);</span></a>
+<a name="5320"><span class="lineNum">    5320 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(-21.50343599461759);</span></a>
+<a name="5321"><span class="lineNum">    5321 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(-8479.703435720274);</span></a>
+<a name="5322"><span class="lineNum">    5322 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(-2647.8693829269596);</span></a>
+<a name="5323"><span class="lineNum">    5323 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(17297.18115838578);</span></a>
+<a name="5324"><span class="lineNum">    5324 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(-12826.972408323161);</span></a>
+<a name="5325"><span class="lineNum">    5325 </span><span class="lineCov">          4 :   parameter_mix_D[LEU].push_back(2953.1262521615645);</span></a>
+<a name="5326"><span class="lineNum">    5326 </span>            : </a>
+<a name="5327"><span class="lineNum">    5327 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(3561.6276801191552);</span></a>
+<a name="5328"><span class="lineNum">    5328 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(-22.19323392975885);</span></a>
+<a name="5329"><span class="lineNum">    5329 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(-8348.33907053846);</span></a>
+<a name="5330"><span class="lineNum">    5330 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(-3323.053272414289);</span></a>
+<a name="5331"><span class="lineNum">    5331 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(23153.238909304255);</span></a>
+<a name="5332"><span class="lineNum">    5332 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(-20091.960440908682);</span></a>
+<a name="5333"><span class="lineNum">    5333 </span><span class="lineCov">          4 :   parameter_mix_D[MET].push_back(5518.759669687693);</span></a>
+<a name="5334"><span class="lineNum">    5334 </span>            : </a>
+<a name="5335"><span class="lineNum">    5335 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(2326.5396001192003);</span></a>
+<a name="5336"><span class="lineNum">    5336 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(-8.634908921289112);</span></a>
+<a name="5337"><span class="lineNum">    5337 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(-4057.4552636749636);</span></a>
+<a name="5338"><span class="lineNum">    5338 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(-1032.743130124821);</span></a>
+<a name="5339"><span class="lineNum">    5339 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(6957.141592429445);</span></a>
+<a name="5340"><span class="lineNum">    5340 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(-4808.265318722317);</span></a>
+<a name="5341"><span class="lineNum">    5341 </span><span class="lineCov">          4 :   parameter_mix_D[ASN].push_back(1016.3944815533755);</span></a>
+<a name="5342"><span class="lineNum">    5342 </span>            : </a>
+<a name="5343"><span class="lineNum">    5343 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(2471.1663601191985);</span></a>
+<a name="5344"><span class="lineNum">    5344 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(-6.360795284260088);</span></a>
+<a name="5345"><span class="lineNum">    5345 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(-3825.4533158429153);</span></a>
+<a name="5346"><span class="lineNum">    5346 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(-728.7164844824666);</span></a>
+<a name="5347"><span class="lineNum">    5347 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(5195.036303827973);</span></a>
+<a name="5348"><span class="lineNum">    5348 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(-3183.733716480742);</span></a>
+<a name="5349"><span class="lineNum">    5349 </span><span class="lineCov">          4 :   parameter_mix_D[PRO].push_back(563.2376162754107);</span></a>
+<a name="5350"><span class="lineNum">    5350 </span>            : </a>
+<a name="5351"><span class="lineNum">    5351 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(3431.669280119236);</span></a>
+<a name="5352"><span class="lineNum">    5352 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(-19.412747205646166);</span></a>
+<a name="5353"><span class="lineNum">    5353 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(-7298.017973002134);</span></a>
+<a name="5354"><span class="lineNum">    5354 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(-2659.3014182337706);</span></a>
+<a name="5355"><span class="lineNum">    5355 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(17890.76595805173);</span></a>
+<a name="5356"><span class="lineNum">    5356 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(-14684.603067192957);</span></a>
+<a name="5357"><span class="lineNum">    5357 </span><span class="lineCov">          4 :   parameter_mix_D[GLN].push_back(3814.338335151394);</span></a>
+<a name="5358"><span class="lineNum">    5358 </span>            : </a>
+<a name="5359"><span class="lineNum">    5359 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(1423.885200119192);</span></a>
+<a name="5360"><span class="lineNum">    5360 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(-2.586428606204385);</span></a>
+<a name="5361"><span class="lineNum">    5361 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(-1966.7369507188134);</span></a>
+<a name="5362"><span class="lineNum">    5362 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(-289.17277383434106);</span></a>
+<a name="5363"><span class="lineNum">    5363 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(2209.478296043199);</span></a>
+<a name="5364"><span class="lineNum">    5364 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(-1216.1521614944);</span></a>
+<a name="5365"><span class="lineNum">    5365 </span><span class="lineCov">          4 :   parameter_mix_D[SER].push_back(177.0615931546754);</span></a>
+<a name="5366"><span class="lineNum">    5366 </span>            : </a>
+<a name="5367"><span class="lineNum">    5367 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(2311.2364801191825);</span></a>
+<a name="5368"><span class="lineNum">    5368 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(-6.258071321531929);</span></a>
+<a name="5369"><span class="lineNum">    5369 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(-3656.295629081312);</span></a>
+<a name="5370"><span class="lineNum">    5370 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(-716.4013890357804);</span></a>
+<a name="5371"><span class="lineNum">    5371 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(5071.656317108832);</span></a>
+<a name="5372"><span class="lineNum">    5372 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(-3125.8076789667816);</span></a>
+<a name="5373"><span class="lineNum">    5373 </span><span class="lineCov">          4 :   parameter_mix_D[THR].push_back(555.9775741081131);</span></a>
+<a name="5374"><span class="lineNum">    5374 </span>            : </a>
+<a name="5375"><span class="lineNum">    5375 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(3041.128320119224);</span></a>
+<a name="5376"><span class="lineNum">    5376 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(-9.314034190716423);</span></a>
+<a name="5377"><span class="lineNum">    5377 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(-5075.684780220629);</span></a>
+<a name="5378"><span class="lineNum">    5378 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(-1070.7083380665008);</span></a>
+<a name="5379"><span class="lineNum">    5379 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(7455.654515006894);</span></a>
+<a name="5380"><span class="lineNum">    5380 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(-4701.19187164774);</span></a>
+<a name="5381"><span class="lineNum">    5381 </span><span class="lineCov">          4 :   parameter_mix_D[VAL].push_back(863.4906179388547);</span></a>
+<a name="5382"><span class="lineNum">    5382 </span>            : </a>
+<a name="5383"><span class="lineNum">    5383 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(1187.65300011922);</span></a>
+<a name="5384"><span class="lineNum">    5384 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(-1.7011187932116822);</span></a>
+<a name="5385"><span class="lineNum">    5385 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(-1521.0113615359212);</span></a>
+<a name="5386"><span class="lineNum">    5386 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(-187.93745840575576);</span></a>
+<a name="5387"><span class="lineNum">    5387 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(1514.6745873304449);</span></a>
+<a name="5388"><span class="lineNum">    5388 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(-775.3890045113897);</span></a>
+<a name="5389"><span class="lineNum">    5389 </span><span class="lineCov">          4 :   parameter_mix_D[ALA].push_back(96.41428177656567);</span></a>
+<a name="5390"><span class="lineNum">    5390 </span>            : </a>
+<a name="5391"><span class="lineNum">    5391 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(581.6349001192067);</span></a>
+<a name="5392"><span class="lineNum">    5392 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(-0.5877833598361395);</span></a>
+<a name="5393"><span class="lineNum">    5393 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(-640.0421286186524);</span></a>
+<a name="5394"><span class="lineNum">    5394 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(-64.58515074152534);</span></a>
+<a name="5395"><span class="lineNum">    5395 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(551.9509853583185);</span></a>
+<a name="5396"><span class="lineNum">    5396 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(-264.1522021146006);</span></a>
+<a name="5397"><span class="lineNum">    5397 </span><span class="lineCov">          4 :   parameter_mix_D[GLY].push_back(28.36986478439301);</span></a>
+<a name="5398"><span class="lineNum">    5398 </span>            : </a>
+<a name="5399"><span class="lineNum">    5399 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(3648.812220119277);</span></a>
+<a name="5400"><span class="lineNum">    5400 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(-22.703075403555548);</span></a>
+<a name="5401"><span class="lineNum">    5401 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(-8260.235189881098);</span></a>
+<a name="5402"><span class="lineNum">    5402 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(-3190.3176569039265);</span></a>
+<a name="5403"><span class="lineNum">    5403 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(21589.074332364213);</span></a>
+<a name="5404"><span class="lineNum">    5404 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(-18108.640157613925);</span></a>
+<a name="5405"><span class="lineNum">    5405 </span><span class="lineCov">          4 :   parameter_mix_D[HIS].push_back(4801.237639634437);</span></a>
+<a name="5406"><span class="lineNum">    5406 </span>            : </a>
+<a name="5407"><span class="lineNum">    5407 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(270.43802511921314);</span></a>
+<a name="5408"><span class="lineNum">    5408 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(-2.196022464340772);</span></a>
+<a name="5409"><span class="lineNum">    5409 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(-780.9546710244318);</span></a>
+<a name="5410"><span class="lineNum">    5410 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(-371.1573508312626);</span></a>
+<a name="5411"><span class="lineNum">    5411 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(2668.7678731652445);</span></a>
+<a name="5412"><span class="lineNum">    5412 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(-2478.2920954223678);</span></a>
+<a name="5413"><span class="lineNum">    5413 </span><span class="lineCov">          4 :   parameter_vac_D[TRP].push_back(722.3731624901676);</span></a>
+<a name="5414"><span class="lineNum">    5414 </span>            : </a>
+<a name="5415"><span class="lineNum">    5415 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(198.471744119211);</span></a>
+<a name="5416"><span class="lineNum">    5416 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(-1.236792846228289);</span></a>
+<a name="5417"><span class="lineNum">    5417 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(-508.0448711054671);</span></a>
+<a name="5418"><span class="lineNum">    5418 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(-210.55908129481216);</span></a>
+<a name="5419"><span class="lineNum">    5419 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(1558.3884734212413);</span></a>
+<a name="5420"><span class="lineNum">    5420 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(-1418.36319255665);</span></a>
+<a name="5421"><span class="lineNum">    5421 </span><span class="lineCov">          4 :   parameter_vac_D[TYR].push_back(407.21567613893296);</span></a>
+<a name="5422"><span class="lineNum">    5422 </span>            : </a>
+<a name="5423"><span class="lineNum">    5423 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(182.46606411921402);</span></a>
+<a name="5424"><span class="lineNum">    5424 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(-1.2708008333861447);</span></a>
+<a name="5425"><span class="lineNum">    5425 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(-424.50905926426054);</span></a>
+<a name="5426"><span class="lineNum">    5426 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(-177.97207825696387);</span></a>
+<a name="5427"><span class="lineNum">    5427 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(1180.839971941918);</span></a>
+<a name="5428"><span class="lineNum">    5428 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(-1004.004765231886);</span></a>
+<a name="5429"><span class="lineNum">    5429 </span><span class="lineCov">          4 :   parameter_vac_D[PHE].push_back(269.34384064610344);</span></a>
+<a name="5430"><span class="lineNum">    5430 </span>            : </a>
+<a name="5431"><span class="lineNum">    5431 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(161.95107611920753);</span></a>
+<a name="5432"><span class="lineNum">    5432 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(-0.9661246983835707);</span></a>
+<a name="5433"><span class="lineNum">    5433 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(-332.04673226423995);</span></a>
+<a name="5434"><span class="lineNum">    5434 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(-125.41755194926544);</span></a>
+<a name="5435"><span class="lineNum">    5435 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(808.705672166199);</span></a>
+<a name="5436"><span class="lineNum">    5436 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(-648.8340711218191);</span></a>
+<a name="5437"><span class="lineNum">    5437 </span><span class="lineCov">          4 :   parameter_vac_D[HIP].push_back(163.71251277400307);</span></a>
+<a name="5438"><span class="lineNum">    5438 </span>            : </a>
+<a name="5439"><span class="lineNum">    5439 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(289.0340011192071);</span></a>
+<a name="5440"><span class="lineNum">    5440 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(-1.4195753436279361);</span></a>
+<a name="5441"><span class="lineNum">    5441 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(-836.3864005546434);</span></a>
+<a name="5442"><span class="lineNum">    5442 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(-346.7081039129904);</span></a>
+<a name="5443"><span class="lineNum">    5443 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(2922.003491580559);</span></a>
+<a name="5444"><span class="lineNum">    5444 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(-2864.816533173085);</span></a>
+<a name="5445"><span class="lineNum">    5445 </span><span class="lineCov">          4 :   parameter_vac_D[ARG].push_back(877.9525045072293);</span></a>
+<a name="5446"><span class="lineNum">    5446 </span>            : </a>
+<a name="5447"><span class="lineNum">    5447 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(228.64464111920753);</span></a>
+<a name="5448"><span class="lineNum">    5448 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(-1.686580749083617);</span></a>
+<a name="5449"><span class="lineNum">    5449 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(-544.8870548339771);</span></a>
+<a name="5450"><span class="lineNum">    5450 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(-252.11087773186324);</span></a>
+<a name="5451"><span class="lineNum">    5451 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(1693.784850493428);</span></a>
+<a name="5452"><span class="lineNum">    5452 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(-1514.2375008160348);</span></a>
+<a name="5453"><span class="lineNum">    5453 </span><span class="lineCov">          4 :   parameter_vac_D[LYS].push_back(427.0713155512121);</span></a>
+<a name="5454"><span class="lineNum">    5454 </span>            : </a>
+<a name="5455"><span class="lineNum">    5455 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(50.836900116324315);</span></a>
+<a name="5456"><span class="lineNum">    5456 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(-0.040204572899665315);</span></a>
+<a name="5457"><span class="lineNum">    5457 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(-55.592868149339424);</span></a>
+<a name="5458"><span class="lineNum">    5458 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(-4.341359624977117);</span></a>
+<a name="5459"><span class="lineNum">    5459 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(41.55290573185214);</span></a>
+<a name="5460"><span class="lineNum">    5460 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(-17.248208429078456);</span></a>
+<a name="5461"><span class="lineNum">    5461 </span><span class="lineCov">          4 :   parameter_vac_D[CYS].push_back(1.0736187172140528);</span></a>
+<a name="5462"><span class="lineNum">    5462 </span>            : </a>
+<a name="5463"><span class="lineNum">    5463 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(64.12806411920792);</span></a>
+<a name="5464"><span class="lineNum">    5464 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(-0.08245818875074411);</span></a>
+<a name="5465"><span class="lineNum">    5465 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(-78.95500211069523);</span></a>
+<a name="5466"><span class="lineNum">    5466 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(-9.030157332821238);</span></a>
+<a name="5467"><span class="lineNum">    5467 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(74.72033164806712);</span></a>
+<a name="5468"><span class="lineNum">    5468 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(-36.71042192737952);</span></a>
+<a name="5469"><span class="lineNum">    5469 </span><span class="lineCov">          4 :   parameter_vac_D[ASP].push_back(4.0989206257493676);</span></a>
+<a name="5470"><span class="lineNum">    5470 </span>            : </a>
+<a name="5471"><span class="lineNum">    5471 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(100.14004911920799);</span></a>
+<a name="5472"><span class="lineNum">    5472 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(-0.28685123265362006);</span></a>
+<a name="5473"><span class="lineNum">    5473 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(-152.44619103423773);</span></a>
+<a name="5474"><span class="lineNum">    5474 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(-32.99432901288321);</span></a>
+<a name="5475"><span class="lineNum">    5475 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(225.5853175183811);</span></a>
+<a name="5476"><span class="lineNum">    5476 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(-144.8489352831419);</span></a>
+<a name="5477"><span class="lineNum">    5477 </span><span class="lineCov">          4 :   parameter_vac_D[GLU].push_back(27.49692658880534);</span></a>
+<a name="5478"><span class="lineNum">    5478 </span>            : </a>
+<a name="5479"><span class="lineNum">    5479 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(165.04540911921134);</span></a>
+<a name="5480"><span class="lineNum">    5480 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(-0.5061553029227089);</span></a>
+<a name="5481"><span class="lineNum">    5481 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(-275.1890586090823);</span></a>
+<a name="5482"><span class="lineNum">    5482 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(-57.288063177375356);</span></a>
+<a name="5483"><span class="lineNum">    5483 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(398.9780357099449);</span></a>
+<a name="5484"><span class="lineNum">    5484 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(-245.42678814428692);</span></a>
+<a name="5485"><span class="lineNum">    5485 </span><span class="lineCov">          4 :   parameter_vac_D[ILE].push_back(42.72941025472001);</span></a>
+<a name="5486"><span class="lineNum">    5486 </span>            : </a>
+<a name="5487"><span class="lineNum">    5487 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(165.04540911921134);</span></a>
+<a name="5488"><span class="lineNum">    5488 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(-0.580034983510499);</span></a>
+<a name="5489"><span class="lineNum">    5489 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(-281.30910057877514);</span></a>
+<a name="5490"><span class="lineNum">    5490 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(-66.19427345166183);</span></a>
+<a name="5491"><span class="lineNum">    5491 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(445.19214155995115);</span></a>
+<a name="5492"><span class="lineNum">    5492 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(-287.0653610399624);</span></a>
+<a name="5493"><span class="lineNum">    5493 </span><span class="lineCov">          4 :   parameter_vac_D[LEU].push_back(53.86626261066706);</span></a>
+<a name="5494"><span class="lineNum">    5494 </span>            : </a>
+<a name="5495"><span class="lineNum">    5495 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(123.83238411920684);</span></a>
+<a name="5496"><span class="lineNum">    5496 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(-0.7698672022751385);</span></a>
+<a name="5497"><span class="lineNum">    5497 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(-251.2481622173618);</span></a>
+<a name="5498"><span class="lineNum">    5498 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(-100.67742019193848);</span></a>
+<a name="5499"><span class="lineNum">    5499 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(641.1563254731632);</span></a>
+<a name="5500"><span class="lineNum">    5500 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(-524.8742634212379);</span></a>
+<a name="5501"><span class="lineNum">    5501 </span><span class="lineCov">          4 :   parameter_vac_D[MET].push_back(135.36487813767542);</span></a>
+<a name="5502"><span class="lineNum">    5502 </span>            : </a>
+<a name="5503"><span class="lineNum">    5503 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(94.12880411921148);</span></a>
+<a name="5504"><span class="lineNum">    5504 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(-0.22986194121078912);</span></a>
+<a name="5505"><span class="lineNum">    5505 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(-138.78769705028003);</span></a>
+<a name="5506"><span class="lineNum">    5506 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(-25.896846049402594);</span></a>
+<a name="5507"><span class="lineNum">    5507 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(184.55609781654326);</span></a>
+<a name="5508"><span class="lineNum">    5508 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(-110.14043851975404);</span></a>
+<a name="5509"><span class="lineNum">    5509 </span><span class="lineCov">          4 :   parameter_vac_D[ASN].push_back(18.388834098004153);</span></a>
+<a name="5510"><span class="lineNum">    5510 </span>            : </a>
+<a name="5511"><span class="lineNum">    5511 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(90.51619611920745);</span></a>
+<a name="5512"><span class="lineNum">    5512 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(-0.0977238494110807);</span></a>
+<a name="5513"><span class="lineNum">    5513 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(-109.43531311067846);</span></a>
+<a name="5514"><span class="lineNum">    5514 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(-10.592981104983805);</span></a>
+<a name="5515"><span class="lineNum">    5515 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(93.64863466237733);</span></a>
+<a name="5516"><span class="lineNum">    5516 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(-42.348197720920865);</span></a>
+<a name="5517"><span class="lineNum">    5517 </span><span class="lineCov">          4 :   parameter_vac_D[PRO].push_back(3.5854078482704574);</span></a>
+<a name="5518"><span class="lineNum">    5518 </span>            : </a>
+<a name="5519"><span class="lineNum">    5519 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(136.91340111920806);</span></a>
+<a name="5520"><span class="lineNum">    5520 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(-0.7259026842220699);</span></a>
+<a name="5521"><span class="lineNum">    5521 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(-257.0347011897067);</span></a>
+<a name="5522"><span class="lineNum">    5522 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(-89.99600255417684);</span></a>
+<a name="5523"><span class="lineNum">    5523 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(570.3890595917421);</span></a>
+<a name="5524"><span class="lineNum">    5524 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(-438.8977029769549);</span></a>
+<a name="5525"><span class="lineNum">    5525 </span><span class="lineCov">          4 :   parameter_vac_D[GLN].push_back(105.48846039376491);</span></a>
+<a name="5526"><span class="lineNum">    5526 </span>            : </a>
+<a name="5527"><span class="lineNum">    5527 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(55.20490011583253);</span></a>
+<a name="5528"><span class="lineNum">    5528 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(-0.038078030710377984);</span></a>
+<a name="5529"><span class="lineNum">    5529 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(-58.79085960838952);</span></a>
+<a name="5530"><span class="lineNum">    5530 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(-4.067364063406562);</span></a>
+<a name="5531"><span class="lineNum">    5531 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(41.319899403658475);</span></a>
+<a name="5532"><span class="lineNum">    5532 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(-15.865682241288962);</span></a>
+<a name="5533"><span class="lineNum">    5533 </span><span class="lineCov">          4 :   parameter_vac_D[SER].push_back(0.5028409006168431);</span></a>
+<a name="5534"><span class="lineNum">    5534 </span>            : </a>
+<a name="5535"><span class="lineNum">    5535 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(88.90604111920842);</span></a>
+<a name="5536"><span class="lineNum">    5536 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(-0.11566717587697625);</span></a>
+<a name="5537"><span class="lineNum">    5537 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(-114.4541243837681);</span></a>
+<a name="5538"><span class="lineNum">    5538 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(-12.541537413808342);</span></a>
+<a name="5539"><span class="lineNum">    5539 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(106.4974738790947);</span></a>
+<a name="5540"><span class="lineNum">    5540 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(-50.15009912825225);</span></a>
+<a name="5541"><span class="lineNum">    5541 </span><span class="lineCov">          4 :   parameter_vac_D[THR].push_back(4.719349514074467);</span></a>
+<a name="5542"><span class="lineNum">    5542 </span>            : </a>
+<a name="5543"><span class="lineNum">    5543 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(117.67910411920792);</span></a>
+<a name="5544"><span class="lineNum">    5544 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(-0.18187311248567883);</span></a>
+<a name="5545"><span class="lineNum">    5545 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(-162.8697844894754);</span></a>
+<a name="5546"><span class="lineNum">    5546 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(-19.769248288711825);</span></a>
+<a name="5547"><span class="lineNum">    5547 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(162.59270939168965);</span></a>
+<a name="5548"><span class="lineNum">    5548 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(-79.37261506441627);</span></a>
+<a name="5549"><span class="lineNum">    5549 </span><span class="lineCov">          4 :   parameter_vac_D[VAL].push_back(8.230771959393175);</span></a>
+<a name="5550"><span class="lineNum">    5550 </span>            : </a>
+<a name="5551"><span class="lineNum">    5551 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(46.92250011448002);</span></a>
+<a name="5552"><span class="lineNum">    5552 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(-0.020339064649444412);</span></a>
+<a name="5553"><span class="lineNum">    5553 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(-44.41584945233503);</span></a>
+<a name="5554"><span class="lineNum">    5554 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(-2.1483754537886113);</span></a>
+<a name="5555"><span class="lineNum">    5555 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(25.713667829058785);</span></a>
+<a name="5556"><span class="lineNum">    5556 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(-8.222782061575268);</span></a>
+<a name="5557"><span class="lineNum">    5557 </span><span class="lineCov">          4 :   parameter_vac_D[ALA].push_back(-0.2521732728817875);</span></a>
+<a name="5558"><span class="lineNum">    5558 </span>            : </a>
+<a name="5559"><span class="lineNum">    5559 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(23.532201119209795);</span></a>
+<a name="5560"><span class="lineNum">    5560 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(-0.00628609590047614);</span></a>
+<a name="5561"><span class="lineNum">    5561 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(-17.28421910139733);</span></a>
+<a name="5562"><span class="lineNum">    5562 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(-0.6641226821159686);</span></a>
+<a name="5563"><span class="lineNum">    5563 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(8.536119110048007);</span></a>
+<a name="5564"><span class="lineNum">    5564 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(-2.5438638688361466);</span></a>
+<a name="5565"><span class="lineNum">    5565 </span><span class="lineCov">          4 :   parameter_vac_D[GLY].push_back(-0.11165675928832643);</span></a>
+<a name="5566"><span class="lineNum">    5566 </span>            : </a>
+<a name="5567"><span class="lineNum">    5567 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(145.41948111920982);</span></a>
+<a name="5568"><span class="lineNum">    5568 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(-0.8548328183368781);</span></a>
+<a name="5569"><span class="lineNum">    5569 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(-290.8653238004162);</span></a>
+<a name="5570"><span class="lineNum">    5570 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(-107.85375269366395);</span></a>
+<a name="5571"><span class="lineNum">    5571 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(685.7025818759361);</span></a>
+<a name="5572"><span class="lineNum">    5572 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(-538.2592043545858);</span></a>
+<a name="5573"><span class="lineNum">    5573 </span><span class="lineCov">          4 :   parameter_vac_D[HIS].push_back(132.17357375729733);</span></a>
+<a name="5574"><span class="lineNum">    5574 </span>            : </a>
+<a name="5575"><span class="lineNum">    5575 </span>            :   // NUCLEIC ACIDS</a>
+<a name="5576"><span class="lineNum">    5576 </span>            : </a>
+<a name="5577"><span class="lineNum">    5577 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(80.12660011920252);</span></a>
+<a name="5578"><span class="lineNum">    5578 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(-0.02788855519820236);</span></a>
+<a name="5579"><span class="lineNum">    5579 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(-60.53219491822279);</span></a>
+<a name="5580"><span class="lineNum">    5580 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(-2.9768829034096806);</span></a>
+<a name="5581"><span class="lineNum">    5581 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(33.30645116638123);</span></a>
+<a name="5582"><span class="lineNum">    5582 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(-11.601573219761375);</span></a>
+<a name="5583"><span class="lineNum">    5583 </span><span class="lineCov">          4 :   parameter_mix_D[BB_PO2].push_back(0.12551046492022438);</span></a>
+<a name="5584"><span class="lineNum">    5584 </span>            : </a>
+<a name="5585"><span class="lineNum">    5585 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(2835.3195201193003);</span></a>
+<a name="5586"><span class="lineNum">    5586 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(-7.954301723608173);</span></a>
+<a name="5587"><span class="lineNum">    5587 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(-4509.325563460958);</span></a>
+<a name="5588"><span class="lineNum">    5588 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(-909.1870692311344);</span></a>
+<a name="5589"><span class="lineNum">    5589 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(6375.156903893768);</span></a>
+<a name="5590"><span class="lineNum">    5590 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(-3956.4787847570715);</span></a>
+<a name="5591"><span class="lineNum">    5591 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA].push_back(708.9872879613656);</span></a>
+<a name="5592"><span class="lineNum">    5592 </span>            : </a>
+<a name="5593"><span class="lineNum">    5593 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(3136.73358011921);</span></a>
+<a name="5594"><span class="lineNum">    5594 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(-10.023435855160427);</span></a>
+<a name="5595"><span class="lineNum">    5595 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(-5208.921666368173);</span></a>
+<a name="5596"><span class="lineNum">    5596 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(-1160.4403539440214);</span></a>
+<a name="5597"><span class="lineNum">    5597 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(7962.598421448727);</span></a>
+<a name="5598"><span class="lineNum">    5598 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(-5149.059857691847);</span></a>
+<a name="5599"><span class="lineNum">    5599 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_5].push_back(984.5217027570121);</span></a>
+<a name="5600"><span class="lineNum">    5600 </span>            : </a>
+<a name="5601"><span class="lineNum">    5601 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(3136.73358011921);</span></a>
+<a name="5602"><span class="lineNum">    5602 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(-9.618834865806274);</span></a>
+<a name="5603"><span class="lineNum">    5603 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(-5164.249220443828);</span></a>
+<a name="5604"><span class="lineNum">    5604 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(-1103.2721475326382);</span></a>
+<a name="5605"><span class="lineNum">    5605 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(7633.46089052312);</span></a>
+<a name="5606"><span class="lineNum">    5606 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(-4826.171688395644);</span></a>
+<a name="5607"><span class="lineNum">    5607 </span><span class="lineCov">          4 :   parameter_mix_D[BB_DNA_3].push_back(888.1820863683546);</span></a>
+<a name="5608"><span class="lineNum">    5608 </span>            : </a>
+<a name="5609"><span class="lineNum">    5609 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(3192.5955601188807);</span></a>
+<a name="5610"><span class="lineNum">    5610 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(-11.475781582628308);</span></a>
+<a name="5611"><span class="lineNum">    5611 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(-5486.264576931735);</span></a>
+<a name="5612"><span class="lineNum">    5612 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(-1344.2878288415961);</span></a>
+<a name="5613"><span class="lineNum">    5613 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(9035.26109892441);</span></a>
+<a name="5614"><span class="lineNum">    5614 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(-6068.471909763036);</span></a>
+<a name="5615"><span class="lineNum">    5615 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA].push_back(1226.3696076463866);</span></a>
+<a name="5616"><span class="lineNum">    5616 </span>            : </a>
+<a name="5617"><span class="lineNum">    5617 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(3512.1630401192215);</span></a>
+<a name="5618"><span class="lineNum">    5618 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(-14.191020069433975);</span></a>
+<a name="5619"><span class="lineNum">    5619 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(-6293.687102187508);</span></a>
+<a name="5620"><span class="lineNum">    5620 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(-1689.3688494490984);</span></a>
+<a name="5621"><span class="lineNum">    5621 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(11193.448566821942);</span></a>
+<a name="5622"><span class="lineNum">    5622 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(-7806.9064399949375);</span></a>
+<a name="5623"><span class="lineNum">    5623 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_5].push_back(1662.4594983069844);</span></a>
+<a name="5624"><span class="lineNum">    5624 </span>            : </a>
+<a name="5625"><span class="lineNum">    5625 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(3512.1630401192215);</span></a>
+<a name="5626"><span class="lineNum">    5626 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(-12.978118135595812);</span></a>
+<a name="5627"><span class="lineNum">    5627 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(-6149.290195451877);</span></a>
+<a name="5628"><span class="lineNum">    5628 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(-1515.8309761505627);</span></a>
+<a name="5629"><span class="lineNum">    5629 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(10176.605450440278);</span></a>
+<a name="5630"><span class="lineNum">    5630 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(-6813.250569884159);</span></a>
+<a name="5631"><span class="lineNum">    5631 </span><span class="lineCov">          4 :   parameter_mix_D[BB_RNA_3].push_back(1366.823518955858);</span></a>
+<a name="5632"><span class="lineNum">    5632 </span>            : </a>
+<a name="5633"><span class="lineNum">    5633 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(2464.736500119229);</span></a>
+<a name="5634"><span class="lineNum">    5634 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(-12.127452038444783);</span></a>
+<a name="5635"><span class="lineNum">    5635 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(-4710.661256689607);</span></a>
+<a name="5636"><span class="lineNum">    5636 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(-1462.6964141954452);</span></a>
+<a name="5637"><span class="lineNum">    5637 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(9451.725575888277);</span></a>
+<a name="5638"><span class="lineNum">    5638 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(-6883.018479948857);</span></a>
+<a name="5639"><span class="lineNum">    5639 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_A].push_back(1540.1526599737797);</span></a>
+<a name="5640"><span class="lineNum">    5640 </span>            : </a>
+<a name="5641"><span class="lineNum">    5641 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(1797.2697601191685);</span></a>
+<a name="5642"><span class="lineNum">    5642 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(-5.963855532295215);</span></a>
+<a name="5643"><span class="lineNum">    5643 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(-2955.077717756034);</span></a>
+<a name="5644"><span class="lineNum">    5644 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(-689.4543508746372);</span></a>
+<a name="5645"><span class="lineNum">    5645 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(4665.914740532565);</span></a>
+<a name="5646"><span class="lineNum">    5646 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(-3051.4605913706982);</span></a>
+<a name="5647"><span class="lineNum">    5647 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_C].push_back(590.2201952719585);</span></a>
+<a name="5648"><span class="lineNum">    5648 </span>            : </a>
+<a name="5649"><span class="lineNum">    5649 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(2804.271480119049);</span></a>
+<a name="5650"><span class="lineNum">    5650 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(-16.928072935469974);</span></a>
+<a name="5651"><span class="lineNum">    5651 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(-5989.82519987899);</span></a>
+<a name="5652"><span class="lineNum">    5652 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(-2275.490326521775);</span></a>
+<a name="5653"><span class="lineNum">    5653 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(15007.832401865428);</span></a>
+<a name="5654"><span class="lineNum">    5654 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(-12287.520690325606);</span></a>
+<a name="5655"><span class="lineNum">    5655 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_G].push_back(3172.98306575258);</span></a>
+<a name="5656"><span class="lineNum">    5656 </span>            : </a>
+<a name="5657"><span class="lineNum">    5657 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(2545.0860001192113);</span></a>
+<a name="5658"><span class="lineNum">    5658 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(-10.975141620541738);</span></a>
+<a name="5659"><span class="lineNum">    5659 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(-4636.058358764447);</span></a>
+<a name="5660"><span class="lineNum">    5660 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(-1340.3746388296138);</span></a>
+<a name="5661"><span class="lineNum">    5661 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(8850.604320505428);</span></a>
+<a name="5662"><span class="lineNum">    5662 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(-6421.852532013674);</span></a>
+<a name="5663"><span class="lineNum">    5663 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_T].push_back(1443.371517335904);</span></a>
+<a name="5664"><span class="lineNum">    5664 </span>            : </a>
+<a name="5665"><span class="lineNum">    5665 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(1608.7389001192062);</span></a>
+<a name="5666"><span class="lineNum">    5666 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(-3.9816849036181434);</span></a>
+<a name="5667"><span class="lineNum">    5667 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(-2411.056432130769);</span></a>
+<a name="5668"><span class="lineNum">    5668 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(-451.8236361945487);</span></a>
+<a name="5669"><span class="lineNum">    5669 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(3220.4418252803644);</span></a>
+<a name="5670"><span class="lineNum">    5670 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(-1944.2515577994325);</span></a>
+<a name="5671"><span class="lineNum">    5671 </span><span class="lineCov">          4 :   parameter_mix_D[BASE_U].push_back(332.9259542628691);</span></a>
+<a name="5672"><span class="lineNum">    5672 </span>            : </a>
+<a name="5673"><span class="lineNum">    5673 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(2.7889001116093284);</span></a>
+<a name="5674"><span class="lineNum">    5674 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(-0.00011178884266113128);</span></a>
+<a name="5675"><span class="lineNum">    5675 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(-1.1702605818380654);</span></a>
+<a name="5676"><span class="lineNum">    5676 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(-0.011278044036819927);</span></a>
+<a name="5677"><span class="lineNum">    5677 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(0.3214006584089024);</span></a>
+<a name="5678"><span class="lineNum">    5678 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(-0.04097165983591666);</span></a>
+<a name="5679"><span class="lineNum">    5679 </span><span class="lineCov">          4 :   parameter_vac_D[BB_PO2].push_back(-0.017525098100539684);</span></a>
+<a name="5680"><span class="lineNum">    5680 </span>            : </a>
+<a name="5681"><span class="lineNum">    5681 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(94.75075611920529);</span></a>
+<a name="5682"><span class="lineNum">    5682 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(-0.13973533952241124);</span></a>
+<a name="5683"><span class="lineNum">    5683 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(-123.45402430039046);</span></a>
+<a name="5684"><span class="lineNum">    5684 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(-15.19494522082691);</span></a>
+<a name="5685"><span class="lineNum">    5685 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(123.34749914811465);</span></a>
+<a name="5686"><span class="lineNum">    5686 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(-61.038507985345504);</span></a>
+<a name="5687"><span class="lineNum">    5687 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA].push_back(6.601587478585944);</span></a>
+<a name="5688"><span class="lineNum">    5688 </span>            : </a>
+<a name="5689"><span class="lineNum">    5689 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(108.18080111920679);</span></a>
+<a name="5690"><span class="lineNum">    5690 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(-0.2055953690887981);</span></a>
+<a name="5691"><span class="lineNum">    5691 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(-150.7924892157235);</span></a>
+<a name="5692"><span class="lineNum">    5692 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(-22.700459516383198);</span></a>
+<a name="5693"><span class="lineNum">    5693 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(172.2599851655527);</span></a>
+<a name="5694"><span class="lineNum">    5694 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(-93.4983124807692);</span></a>
+<a name="5695"><span class="lineNum">    5695 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_5].push_back(12.867661230942868);</span></a>
+<a name="5696"><span class="lineNum">    5696 </span>            : </a>
+<a name="5697"><span class="lineNum">    5697 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(108.18080111920537);</span></a>
+<a name="5698"><span class="lineNum">    5698 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(-0.18263717534168372);</span></a>
+<a name="5699"><span class="lineNum">    5699 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(-148.5918817744255);</span></a>
+<a name="5700"><span class="lineNum">    5700 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(-19.90799847398835);</span></a>
+<a name="5701"><span class="lineNum">    5701 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(157.55184203379557);</span></a>
+<a name="5702"><span class="lineNum">    5702 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(-80.28471270058103);</span></a>
+<a name="5703"><span class="lineNum">    5703 </span><span class="lineCov">          4 :   parameter_vac_D[BB_DNA_3].push_back(9.313712500298278);</span></a>
+<a name="5704"><span class="lineNum">    5704 </span>            : </a>
+<a name="5705"><span class="lineNum">    5705 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(106.37859611922117);</span></a>
+<a name="5706"><span class="lineNum">    5706 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(-0.2380766148121975);</span></a>
+<a name="5707"><span class="lineNum">    5707 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(-153.74131338570024);</span></a>
+<a name="5708"><span class="lineNum">    5708 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(-26.415436217574932);</span></a>
+<a name="5709"><span class="lineNum">    5709 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(191.90585451112776);</span></a>
+<a name="5710"><span class="lineNum">    5710 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(-109.61737794316868);</span></a>
+<a name="5711"><span class="lineNum">    5711 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA].push_back(16.663804191332204);</span></a>
+<a name="5712"><span class="lineNum">    5712 </span>            : </a>
+<a name="5713"><span class="lineNum">    5713 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(120.58236111920618);</span></a>
+<a name="5714"><span class="lineNum">    5714 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(-0.340258533619014);</span></a>
+<a name="5715"><span class="lineNum">    5715 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(-186.08333929996334);</span></a>
+<a name="5716"><span class="lineNum">    5716 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(-38.493337147644795);</span></a>
+<a name="5717"><span class="lineNum">    5717 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(266.2262415641144);</span></a>
+<a name="5718"><span class="lineNum">    5718 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(-164.73088478359585);</span></a>
+<a name="5719"><span class="lineNum">    5719 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_5].push_back(29.07014157680879);</span></a>
+<a name="5720"><span class="lineNum">    5720 </span>            : </a>
+<a name="5721"><span class="lineNum">    5721 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(120.5823611192099);</span></a>
+<a name="5722"><span class="lineNum">    5722 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(-0.274146129206928);</span></a>
+<a name="5723"><span class="lineNum">    5723 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(-179.24499182395388);</span></a>
+<a name="5724"><span class="lineNum">    5724 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(-30.315729372259426);</span></a>
+<a name="5725"><span class="lineNum">    5725 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(222.2645581367648);</span></a>
+<a name="5726"><span class="lineNum">    5726 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(-125.13581171514033);</span></a>
+<a name="5727"><span class="lineNum">    5727 </span><span class="lineCov">          4 :   parameter_vac_D[BB_RNA_3].push_back(18.350308154920107);</span></a>
+<a name="5728"><span class="lineNum">    5728 </span>            : </a>
+<a name="5729"><span class="lineNum">    5729 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(114.34024911921);</span></a>
+<a name="5730"><span class="lineNum">    5730 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(-0.4136665918383359);</span></a>
+<a name="5731"><span class="lineNum">    5731 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(-192.33138384655922);</span></a>
+<a name="5732"><span class="lineNum">    5732 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(-46.74428306691412);</span></a>
+<a name="5733"><span class="lineNum">    5733 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(312.9511030981905);</span></a>
+<a name="5734"><span class="lineNum">    5734 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(-199.6349962647333);</span></a>
+<a name="5735"><span class="lineNum">    5735 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_A].push_back(36.15938693202153);</span></a>
+<a name="5736"><span class="lineNum">    5736 </span>            : </a>
+<a name="5737"><span class="lineNum">    5737 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(76.17798411921166);</span></a>
+<a name="5738"><span class="lineNum">    5738 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(-0.1444475142707445);</span></a>
+<a name="5739"><span class="lineNum">    5739 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(-102.66873668949485);</span></a>
+<a name="5740"><span class="lineNum">    5740 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(-15.813768367725821);</span></a>
+<a name="5741"><span class="lineNum">    5741 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(119.63436338715553);</span></a>
+<a name="5742"><span class="lineNum">    5742 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(-64.22251971660583);</span></a>
+<a name="5743"><span class="lineNum">    5743 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_C].push_back(8.351952332828862);</span></a>
+<a name="5744"><span class="lineNum">    5744 </span>            : </a>
+<a name="5745"><span class="lineNum">    5745 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(127.08052911921965);</span></a>
+<a name="5746"><span class="lineNum">    5746 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(-0.7137457014712297);</span></a>
+<a name="5747"><span class="lineNum">    5747 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(-239.67686838772786);</span></a>
+<a name="5748"><span class="lineNum">    5748 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(-88.53661981200943);</span></a>
+<a name="5749"><span class="lineNum">    5749 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(556.7254485453866);</span></a>
+<a name="5750"><span class="lineNum">    5750 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(-432.0234649577737);</span></a>
+<a name="5751"><span class="lineNum">    5751 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_G].push_back(104.407200463848);</span></a>
+<a name="5752"><span class="lineNum">    5752 </span>            : </a>
+<a name="5753"><span class="lineNum">    5753 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(94.09000011920868);</span></a>
+<a name="5754"><span class="lineNum">    5754 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(-0.27147149980458524);</span></a>
+<a name="5755"><span class="lineNum">    5755 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(-143.65649702254174);</span></a>
+<a name="5756"><span class="lineNum">    5756 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(-30.861235738371892);</span></a>
+<a name="5757"><span class="lineNum">    5757 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(212.3643014774958);</span></a>
+<a name="5758"><span class="lineNum">    5758 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(-133.06675501066275);</span></a>
+<a name="5759"><span class="lineNum">    5759 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_T].push_back(23.951588200687073);</span></a>
+<a name="5760"><span class="lineNum">    5760 </span>            : </a>
+<a name="5761"><span class="lineNum">    5761 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(59.30540111665979);</span></a>
+<a name="5762"><span class="lineNum">    5762 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(-0.06146929846591808);</span></a>
+<a name="5763"><span class="lineNum">    5763 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(-67.43680950211682);</span></a>
+<a name="5764"><span class="lineNum">    5764 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(-6.625289749170134);</span></a>
+<a name="5765"><span class="lineNum">    5765 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(58.37012229348065);</span></a>
+<a name="5766"><span class="lineNum">    5766 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(-26.23044613101723);</span></a>
+<a name="5767"><span class="lineNum">    5767 </span><span class="lineCov">          4 :   parameter_vac_D[BASE_U].push_back(2.061238351422343);</span></a>
+<a name="5768"><span class="lineNum">    5768 </span>            : </a>
+<a name="5769"><span class="lineNum">    5769 </span><span class="lineCov">      14298 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="5770"><span class="lineNum">    5770 </span><span class="lineCov">      14294 :     std::string Aname = pdb.getAtomName(atoms[i]);</span></a>
+<a name="5771"><span class="lineNum">    5771 </span><span class="lineCov">      14294 :     std::string Rname = pdb.getResidueName(atoms[i]);</span></a>
+<a name="5772"><span class="lineNum">    5772 </span><span class="lineCov">      14294 :     Rname.erase(std::remove_if(Rname.begin(), Rname.end(), ::isspace),Rname.end());</span></a>
+<a name="5773"><span class="lineNum">    5773 </span><span class="lineCov">      14294 :     if(Rname==&quot;ALA&quot;) {</span></a>
+<a name="5774"><span class="lineNum">    5774 </span><span class="lineCov">        732 :       atoi[residue_atom[i]]=ALA;</span></a>
+<a name="5775"><span class="lineNum">    5775 </span><span class="lineCov">      13562 :     } else if(Rname==&quot;ARG&quot;) {</span></a>
+<a name="5776"><span class="lineNum">    5776 </span><span class="lineCov">        864 :       atoi[residue_atom[i]]=ARG;</span></a>
+<a name="5777"><span class="lineNum">    5777 </span><span class="lineCov">      12698 :     } else if(Rname==&quot;ASN&quot;) {</span></a>
+<a name="5778"><span class="lineNum">    5778 </span><span class="lineCov">        720 :       atoi[residue_atom[i]]=ASN;</span></a>
+<a name="5779"><span class="lineNum">    5779 </span><span class="lineCov">      11978 :     } else if(Rname==&quot;ASP&quot;) {</span></a>
+<a name="5780"><span class="lineNum">    5780 </span><span class="lineCov">        624 :       atoi[residue_atom[i]]=ASP;</span></a>
+<a name="5781"><span class="lineNum">    5781 </span><span class="lineCov">      11354 :     } else if(Rname==&quot;CYS&quot;) {</span></a>
+<a name="5782"><span class="lineNum">    5782 </span><span class="lineCov">         48 :       atoi[residue_atom[i]]=CYS;</span></a>
+<a name="5783"><span class="lineNum">    5783 </span><span class="lineCov">      11306 :     } else if(Rname==&quot;GLN&quot;) {</span></a>
+<a name="5784"><span class="lineNum">    5784 </span><span class="lineCov">       1064 :       atoi[residue_atom[i]]=GLN;</span></a>
+<a name="5785"><span class="lineNum">    5785 </span><span class="lineCov">      10242 :     } else if(Rname==&quot;GLU&quot;) {</span></a>
+<a name="5786"><span class="lineNum">    5786 </span><span class="lineCov">        476 :       atoi[residue_atom[i]]=GLU;</span></a>
+<a name="5787"><span class="lineNum">    5787 </span><span class="lineCov">       9766 :     } else if(Rname==&quot;GLY&quot;) {</span></a>
+<a name="5788"><span class="lineNum">    5788 </span><span class="lineCov">        648 :       atoi[residue_atom[i]]=GLY;</span></a>
+<a name="5789"><span class="lineNum">    5789 </span><span class="lineCov">       9118 :     } else if(Rname==&quot;HIS&quot;) {</span></a>
+<a name="5790"><span class="lineNum">    5790 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="5791"><span class="lineNum">    5791 </span><span class="lineCov">       9118 :     } else if(Rname==&quot;HID&quot;) {</span></a>
+<a name="5792"><span class="lineNum">    5792 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="5793"><span class="lineNum">    5793 </span><span class="lineCov">       9118 :     } else if(Rname==&quot;HIE&quot;) {</span></a>
+<a name="5794"><span class="lineNum">    5794 </span><span class="lineCov">        144 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="5795"><span class="lineNum">    5795 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HIP&quot;) {</span></a>
+<a name="5796"><span class="lineNum">    5796 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIP;</span></a>
+<a name="5797"><span class="lineNum">    5797 </span>            :       // CHARMM NAMING FOR PROTONATION STATES OF HISTIDINE</a>
+<a name="5798"><span class="lineNum">    5798 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HSD&quot;) {</span></a>
+<a name="5799"><span class="lineNum">    5799 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="5800"><span class="lineNum">    5800 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HSE&quot;) {</span></a>
+<a name="5801"><span class="lineNum">    5801 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIS;</span></a>
+<a name="5802"><span class="lineNum">    5802 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;HSP&quot;) {</span></a>
+<a name="5803"><span class="lineNum">    5803 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=HIP;</span></a>
+<a name="5804"><span class="lineNum">    5804 </span><span class="lineCov">       8974 :     } else if(Rname==&quot;ILE&quot;) {</span></a>
+<a name="5805"><span class="lineNum">    5805 </span><span class="lineCov">        864 :       atoi[residue_atom[i]]=ILE;</span></a>
+<a name="5806"><span class="lineNum">    5806 </span><span class="lineCov">       8110 :     } else if(Rname==&quot;LEU&quot;) {</span></a>
+<a name="5807"><span class="lineNum">    5807 </span><span class="lineCov">       1520 :       atoi[residue_atom[i]]=LEU;</span></a>
+<a name="5808"><span class="lineNum">    5808 </span><span class="lineCov">       6590 :     } else if(Rname==&quot;LYS&quot;) {</span></a>
+<a name="5809"><span class="lineNum">    5809 </span><span class="lineCov">       1040 :       atoi[residue_atom[i]]=LYS;</span></a>
+<a name="5810"><span class="lineNum">    5810 </span><span class="lineCov">       5550 :     } else if(Rname==&quot;MET&quot;) {</span></a>
+<a name="5811"><span class="lineNum">    5811 </span><span class="lineCov">        608 :       atoi[residue_atom[i]]=MET;</span></a>
+<a name="5812"><span class="lineNum">    5812 </span><span class="lineCov">       4942 :     } else if(Rname==&quot;PHE&quot;) {</span></a>
+<a name="5813"><span class="lineNum">    5813 </span><span class="lineCov">       1008 :       atoi[residue_atom[i]]=PHE;</span></a>
+<a name="5814"><span class="lineNum">    5814 </span><span class="lineCov">       3934 :     } else if(Rname==&quot;PRO&quot;) {</span></a>
+<a name="5815"><span class="lineNum">    5815 </span><span class="lineCov">        748 :       atoi[residue_atom[i]]=PRO;</span></a>
+<a name="5816"><span class="lineNum">    5816 </span><span class="lineCov">       3186 :     } else if(Rname==&quot;SER&quot;) {</span></a>
+<a name="5817"><span class="lineNum">    5817 </span><span class="lineCov">        528 :       atoi[residue_atom[i]]=SER;</span></a>
+<a name="5818"><span class="lineNum">    5818 </span><span class="lineCov">       2658 :     } else if(Rname==&quot;THR&quot;) {</span></a>
+<a name="5819"><span class="lineNum">    5819 </span><span class="lineCov">        504 :       atoi[residue_atom[i]]=THR;</span></a>
+<a name="5820"><span class="lineNum">    5820 </span><span class="lineCov">       2154 :     } else if(Rname==&quot;TRP&quot;) {</span></a>
+<a name="5821"><span class="lineNum">    5821 </span><span class="lineNoCov">          0 :       atoi[residue_atom[i]]=TRP;</span></a>
+<a name="5822"><span class="lineNum">    5822 </span><span class="lineCov">       2154 :     } else if(Rname==&quot;TYR&quot;) {</span></a>
+<a name="5823"><span class="lineNum">    5823 </span><span class="lineCov">        528 :       atoi[residue_atom[i]]=TYR;</span></a>
+<a name="5824"><span class="lineNum">    5824 </span><span class="lineCov">       1626 :     } else if(Rname==&quot;VAL&quot;) {</span></a>
+<a name="5825"><span class="lineNum">    5825 </span><span class="lineCov">       1088 :       atoi[residue_atom[i]]=VAL;</span></a>
+<a name="5826"><span class="lineNum">    5826 </span>            :     }</a>
+<a name="5827"><span class="lineNum">    5827 </span>            :     // NUCLEIC ACIDS</a>
+<a name="5828"><span class="lineNum">    5828 </span>            :     // nucleobases are not automatically populated as an additional check on the health of the PDB.</a>
+<a name="5829"><span class="lineNum">    5829 </span>            :     // RNA - G</a>
+<a name="5830"><span class="lineNum">    5830 </span><span class="lineCov">        538 :     else if(Rname==&quot;G&quot;) {</span></a>
+<a name="5831"><span class="lineNum">    5831 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5832"><span class="lineNum">    5832 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5833"><span class="lineNum">    5833 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5834"><span class="lineNum">    5834 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5835"><span class="lineNum">    5835 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5836"><span class="lineNum">    5836 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5837"><span class="lineNum">    5837 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5838"><span class="lineNum">    5838 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5839"><span class="lineNum">    5839 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5840"><span class="lineNum">    5840 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="5841"><span class="lineNum">    5841 </span><span class="lineNoCov">          0 :       } else if( Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5842"><span class="lineNum">    5842 </span><span class="lineNoCov">          0 :                  Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="5843"><span class="lineNum">    5843 </span><span class="lineNoCov">          0 :                  Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="5844"><span class="lineNum">    5844 </span><span class="lineNoCov">          0 :                  Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="5845"><span class="lineNum">    5845 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="5846"><span class="lineNum">    5846 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5847"><span class="lineNum">    5847 </span>            :       // RNA - G3</a>
+<a name="5848"><span class="lineNum">    5848 </span><span class="lineCov">        538 :     } else if(Rname==&quot;G3&quot;) {</span></a>
+<a name="5849"><span class="lineNum">    5849 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5850"><span class="lineNum">    5850 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5851"><span class="lineNum">    5851 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5852"><span class="lineNum">    5852 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5853"><span class="lineNum">    5853 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5854"><span class="lineNum">    5854 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5855"><span class="lineNum">    5855 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5856"><span class="lineNum">    5856 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5857"><span class="lineNum">    5857 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="5858"><span class="lineNum">    5858 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="5859"><span class="lineNum">    5859 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5860"><span class="lineNum">    5860 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="5861"><span class="lineNum">    5861 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="5862"><span class="lineNum">    5862 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="5863"><span class="lineNum">    5863 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="5864"><span class="lineNum">    5864 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5865"><span class="lineNum">    5865 </span>            :       // RNA - G5</a>
+<a name="5866"><span class="lineNum">    5866 </span><span class="lineCov">        538 :     } else if(Rname==&quot;G5&quot;) {</span></a>
+<a name="5867"><span class="lineNum">    5867 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5868"><span class="lineNum">    5868 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5869"><span class="lineNum">    5869 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5870"><span class="lineNum">    5870 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5871"><span class="lineNum">    5871 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="5872"><span class="lineNum">    5872 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5873"><span class="lineNum">    5873 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="5874"><span class="lineNum">    5874 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5875"><span class="lineNum">    5875 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="5876"><span class="lineNum">    5876 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="5877"><span class="lineNum">    5877 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="5878"><span class="lineNum">    5878 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="5879"><span class="lineNum">    5879 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5880"><span class="lineNum">    5880 </span>            :       // RNA - U</a>
+<a name="5881"><span class="lineNum">    5881 </span><span class="lineCov">        538 :     } else if(Rname==&quot;U&quot;) {</span></a>
+<a name="5882"><span class="lineNum">    5882 </span><span class="lineCov">       1554 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5883"><span class="lineNum">    5883 </span><span class="lineCov">       1176 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5884"><span class="lineNum">    5884 </span><span class="lineCov">         42 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5885"><span class="lineNum">    5885 </span><span class="lineCov">       1372 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5886"><span class="lineNum">    5886 </span><span class="lineCov">       1148 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5887"><span class="lineNum">    5887 </span><span class="lineCov">        924 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5888"><span class="lineNum">    5888 </span><span class="lineCov">        714 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5889"><span class="lineNum">    5889 </span><span class="lineCov">        644 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5890"><span class="lineNum">    5890 </span><span class="lineCov">        840 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5891"><span class="lineNum">    5891 </span><span class="lineCov">        224 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="5892"><span class="lineNum">    5892 </span><span class="lineCov">        476 :       } else if( Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5893"><span class="lineNum">    5893 </span><span class="lineCov">        252 :                  Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="5894"><span class="lineNum">    5894 </span><span class="lineCov">        196 :                  Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="5895"><span class="lineNum">    5895 </span><span class="lineCov">        154 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="5896"><span class="lineNum">    5896 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5897"><span class="lineNum">    5897 </span>            :       // RNA - U3</a>
+<a name="5898"><span class="lineNum">    5898 </span><span class="lineCov">        118 :     } else if(Rname==&quot;U3&quot;) {</span></a>
+<a name="5899"><span class="lineNum">    5899 </span><span class="lineCov">        230 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5900"><span class="lineNum">    5900 </span><span class="lineCov">        174 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5901"><span class="lineNum">    5901 </span><span class="lineCov">          6 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5902"><span class="lineNum">    5902 </span><span class="lineCov">        204 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5903"><span class="lineNum">    5903 </span><span class="lineCov">        172 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5904"><span class="lineNum">    5904 </span><span class="lineCov">        140 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5905"><span class="lineNum">    5905 </span><span class="lineCov">        110 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5906"><span class="lineNum">    5906 </span><span class="lineCov">         94 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5907"><span class="lineNum">    5907 </span><span class="lineCov">         78 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="5908"><span class="lineNum">    5908 </span><span class="lineCov">         34 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="5909"><span class="lineNum">    5909 </span><span class="lineCov">         68 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5910"><span class="lineNum">    5910 </span><span class="lineCov">         36 :                 Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="5911"><span class="lineNum">    5911 </span><span class="lineCov">         28 :                 Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="5912"><span class="lineNum">    5912 </span><span class="lineCov">         22 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="5913"><span class="lineNum">    5913 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5914"><span class="lineNum">    5914 </span>            :       // RNA - U5</a>
+<a name="5915"><span class="lineNum">    5915 </span><span class="lineCov">         56 :     } else if(Rname==&quot;U5&quot;) {</span></a>
+<a name="5916"><span class="lineNum">    5916 </span><span class="lineCov">        204 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5917"><span class="lineNum">    5917 </span><span class="lineCov">        172 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5918"><span class="lineNum">    5918 </span><span class="lineCov">        140 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5919"><span class="lineNum">    5919 </span><span class="lineCov">        108 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5920"><span class="lineNum">    5920 </span><span class="lineCov">         88 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="5921"><span class="lineNum">    5921 </span><span class="lineCov">         78 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5922"><span class="lineNum">    5922 </span><span class="lineCov">         34 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="5923"><span class="lineNum">    5923 </span><span class="lineCov">         68 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="5924"><span class="lineNum">    5924 </span><span class="lineCov">         36 :                 Aname==&quot;C4&quot; || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot; || Aname==&quot;C6&quot; ||</span></a>
+<a name="5925"><span class="lineNum">    5925 </span><span class="lineCov">         28 :                 Aname==&quot;H3&quot; || Aname==&quot;H5&quot;  || Aname==&quot;H6&quot;) {</span></a>
+<a name="5926"><span class="lineNum">    5926 </span><span class="lineCov">         22 :         atoi[residue_atom[i]]=BASE_U;</span></a>
+<a name="5927"><span class="lineNum">    5927 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5928"><span class="lineNum">    5928 </span>            :       // RNA - A</a>
+<a name="5929"><span class="lineNum">    5929 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A&quot;) {</span></a>
+<a name="5930"><span class="lineNum">    5930 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5931"><span class="lineNum">    5931 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5932"><span class="lineNum">    5932 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5933"><span class="lineNum">    5933 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5934"><span class="lineNum">    5934 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5935"><span class="lineNum">    5935 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5936"><span class="lineNum">    5936 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5937"><span class="lineNum">    5937 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5938"><span class="lineNum">    5938 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5939"><span class="lineNum">    5939 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="5940"><span class="lineNum">    5940 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="5941"><span class="lineNum">    5941 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="5942"><span class="lineNum">    5942 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="5943"><span class="lineNum">    5943 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="5944"><span class="lineNum">    5944 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="5945"><span class="lineNum">    5945 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5946"><span class="lineNum">    5946 </span>            :       // RNA - A3</a>
+<a name="5947"><span class="lineNum">    5947 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A3&quot;) {</span></a>
+<a name="5948"><span class="lineNum">    5948 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5949"><span class="lineNum">    5949 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5950"><span class="lineNum">    5950 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5951"><span class="lineNum">    5951 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5952"><span class="lineNum">    5952 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5953"><span class="lineNum">    5953 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5954"><span class="lineNum">    5954 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5955"><span class="lineNum">    5955 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5956"><span class="lineNum">    5956 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="5957"><span class="lineNum">    5957 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="5958"><span class="lineNum">    5958 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="5959"><span class="lineNum">    5959 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="5960"><span class="lineNum">    5960 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="5961"><span class="lineNum">    5961 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="5962"><span class="lineNum">    5962 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="5963"><span class="lineNum">    5963 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5964"><span class="lineNum">    5964 </span>            :       // RNA - A5</a>
+<a name="5965"><span class="lineNum">    5965 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;A5&quot;) {</span></a>
+<a name="5966"><span class="lineNum">    5966 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5967"><span class="lineNum">    5967 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5968"><span class="lineNum">    5968 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5969"><span class="lineNum">    5969 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="5970"><span class="lineNum">    5970 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="5971"><span class="lineNum">    5971 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5972"><span class="lineNum">    5972 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="5973"><span class="lineNum">    5973 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="5974"><span class="lineNum">    5974 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="5975"><span class="lineNum">    5975 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="5976"><span class="lineNum">    5976 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="5977"><span class="lineNum">    5977 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="5978"><span class="lineNum">    5978 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5979"><span class="lineNum">    5979 </span>            :       // RNA - C</a>
+<a name="5980"><span class="lineNum">    5980 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C&quot;) {</span></a>
+<a name="5981"><span class="lineNum">    5981 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5982"><span class="lineNum">    5982 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="5983"><span class="lineNum">    5983 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="5984"><span class="lineNum">    5984 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="5985"><span class="lineNum">    5985 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="5986"><span class="lineNum">    5986 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="5987"><span class="lineNum">    5987 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="5988"><span class="lineNum">    5988 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO5'&quot; || Aname==&quot;HO3'&quot; || Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="5989"><span class="lineNum">    5989 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="5990"><span class="lineNum">    5990 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA;</span></a>
+<a name="5991"><span class="lineNum">    5991 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="5992"><span class="lineNum">    5992 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="5993"><span class="lineNum">    5993 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="5994"><span class="lineNum">    5994 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="5995"><span class="lineNum">    5995 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="5996"><span class="lineNum">    5996 </span>            :       // RNA - C3</a>
+<a name="5997"><span class="lineNum">    5997 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C3&quot;) {</span></a>
+<a name="5998"><span class="lineNum">    5998 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="5999"><span class="lineNum">    5999 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6000"><span class="lineNum">    6000 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6001"><span class="lineNum">    6001 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot; || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6002"><span class="lineNum">    6002 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot; || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="6003"><span class="lineNum">    6003 </span><span class="lineNoCov">          0 :                 Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot; || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="6004"><span class="lineNum">    6004 </span><span class="lineNoCov">          0 :                 Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;H3T&quot;  ||</span></a>
+<a name="6005"><span class="lineNum">    6005 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'1&quot; || Aname==&quot;HO3'&quot;|| Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; ||</span></a>
+<a name="6006"><span class="lineNum">    6006 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ) {</span></a>
+<a name="6007"><span class="lineNum">    6007 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_3;</span></a>
+<a name="6008"><span class="lineNum">    6008 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="6009"><span class="lineNum">    6009 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="6010"><span class="lineNum">    6010 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="6011"><span class="lineNum">    6011 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="6012"><span class="lineNum">    6012 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6013"><span class="lineNum">    6013 </span>            :       // RNA - C5</a>
+<a name="6014"><span class="lineNum">    6014 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;C5&quot;) {</span></a>
+<a name="6015"><span class="lineNum">    6015 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6016"><span class="lineNum">    6016 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;O2'&quot;  || Aname==&quot;C2'&quot;  ||</span></a>
+<a name="6017"><span class="lineNum">    6017 </span><span class="lineNoCov">          0 :           Aname==&quot;C1'&quot;  || Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  ||</span></a>
+<a name="6018"><span class="lineNum">    6018 </span><span class="lineNoCov">          0 :           Aname==&quot;H3'&quot;  || Aname==&quot;H2'&quot;  || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6019"><span class="lineNum">    6019 </span><span class="lineNoCov">          0 :           Aname==&quot;HO2'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;HO'2&quot; ||</span></a>
+<a name="6020"><span class="lineNum">    6020 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'1&quot; || Aname==&quot;H5T&quot; ) {</span></a>
+<a name="6021"><span class="lineNum">    6021 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_RNA_5;</span></a>
+<a name="6022"><span class="lineNum">    6022 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="6023"><span class="lineNum">    6023 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="6024"><span class="lineNum">    6024 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="6025"><span class="lineNum">    6025 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="6026"><span class="lineNum">    6026 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6027"><span class="lineNum">    6027 </span>            :       // DNA - G</a>
+<a name="6028"><span class="lineNum">    6028 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG&quot;) {</span></a>
+<a name="6029"><span class="lineNum">    6029 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6030"><span class="lineNum">    6030 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6031"><span class="lineNum">    6031 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6032"><span class="lineNum">    6032 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6033"><span class="lineNum">    6033 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6034"><span class="lineNum">    6034 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6035"><span class="lineNum">    6035 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6036"><span class="lineNum">    6036 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="6037"><span class="lineNum">    6037 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="6038"><span class="lineNum">    6038 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="6039"><span class="lineNum">    6039 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="6040"><span class="lineNum">    6040 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="6041"><span class="lineNum">    6041 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="6042"><span class="lineNum">    6042 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="6043"><span class="lineNum">    6043 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="6044"><span class="lineNum">    6044 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6045"><span class="lineNum">    6045 </span>            :       // DNA - G3</a>
+<a name="6046"><span class="lineNum">    6046 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG3&quot;) {</span></a>
+<a name="6047"><span class="lineNum">    6047 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6048"><span class="lineNum">    6048 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6049"><span class="lineNum">    6049 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6050"><span class="lineNum">    6050 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6051"><span class="lineNum">    6051 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6052"><span class="lineNum">    6052 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6053"><span class="lineNum">    6053 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="6054"><span class="lineNum">    6054 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6055"><span class="lineNum">    6055 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="6056"><span class="lineNum">    6056 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="6057"><span class="lineNum">    6057 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="6058"><span class="lineNum">    6058 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="6059"><span class="lineNum">    6059 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="6060"><span class="lineNum">    6060 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="6061"><span class="lineNum">    6061 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="6062"><span class="lineNum">    6062 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6063"><span class="lineNum">    6063 </span>            :       // DNA - G5</a>
+<a name="6064"><span class="lineNum">    6064 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DG5&quot;) {</span></a>
+<a name="6065"><span class="lineNum">    6065 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6066"><span class="lineNum">    6066 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="6067"><span class="lineNum">    6067 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6068"><span class="lineNum">    6068 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6069"><span class="lineNum">    6069 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6070"><span class="lineNum">    6070 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="6071"><span class="lineNum">    6071 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="6072"><span class="lineNum">    6072 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot;  || Aname==&quot;N2&quot; || Aname==&quot;N3&quot; ||</span></a>
+<a name="6073"><span class="lineNum">    6073 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;O6&quot; ||</span></a>
+<a name="6074"><span class="lineNum">    6074 </span><span class="lineNoCov">          0 :                 Aname==&quot;N7&quot; || Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H1&quot; ||</span></a>
+<a name="6075"><span class="lineNum">    6075 </span><span class="lineNoCov">          0 :                 Aname==&quot;H8&quot; || Aname==&quot;H21&quot; || Aname==&quot;H22&quot; ) {</span></a>
+<a name="6076"><span class="lineNum">    6076 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_G;</span></a>
+<a name="6077"><span class="lineNum">    6077 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6078"><span class="lineNum">    6078 </span>            :       // DNA - T</a>
+<a name="6079"><span class="lineNum">    6079 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT&quot;) {</span></a>
+<a name="6080"><span class="lineNum">    6080 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6081"><span class="lineNum">    6081 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6082"><span class="lineNum">    6082 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6083"><span class="lineNum">    6083 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6084"><span class="lineNum">    6084 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6085"><span class="lineNum">    6085 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6086"><span class="lineNum">    6086 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6087"><span class="lineNum">    6087 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="6088"><span class="lineNum">    6088 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="6089"><span class="lineNum">    6089 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="6090"><span class="lineNum">    6090 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="6091"><span class="lineNum">    6091 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="6092"><span class="lineNum">    6092 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="6093"><span class="lineNum">    6093 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="6094"><span class="lineNum">    6094 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="6095"><span class="lineNum">    6095 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6096"><span class="lineNum">    6096 </span>            :       // DNA - T3</a>
+<a name="6097"><span class="lineNum">    6097 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT3&quot;) {</span></a>
+<a name="6098"><span class="lineNum">    6098 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6099"><span class="lineNum">    6099 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6100"><span class="lineNum">    6100 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6101"><span class="lineNum">    6101 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6102"><span class="lineNum">    6102 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6103"><span class="lineNum">    6103 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6104"><span class="lineNum">    6104 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="6105"><span class="lineNum">    6105 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6106"><span class="lineNum">    6106 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="6107"><span class="lineNum">    6107 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="6108"><span class="lineNum">    6108 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="6109"><span class="lineNum">    6109 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="6110"><span class="lineNum">    6110 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="6111"><span class="lineNum">    6111 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="6112"><span class="lineNum">    6112 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="6113"><span class="lineNum">    6113 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6114"><span class="lineNum">    6114 </span>            :       // DNA - T5</a>
+<a name="6115"><span class="lineNum">    6115 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DT5&quot;) {</span></a>
+<a name="6116"><span class="lineNum">    6116 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6117"><span class="lineNum">    6117 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="6118"><span class="lineNum">    6118 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6119"><span class="lineNum">    6119 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6120"><span class="lineNum">    6120 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6121"><span class="lineNum">    6121 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="6122"><span class="lineNum">    6122 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="6123"><span class="lineNum">    6123 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot;  || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot;  ||</span></a>
+<a name="6124"><span class="lineNum">    6124 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot;  || Aname==&quot;O4&quot;  || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot;  ||</span></a>
+<a name="6125"><span class="lineNum">    6125 </span><span class="lineNoCov">          0 :                 Aname==&quot;C7&quot;  || Aname==&quot;H3&quot;  || Aname==&quot;H6&quot;  || Aname==&quot;H71&quot; ||</span></a>
+<a name="6126"><span class="lineNum">    6126 </span><span class="lineNoCov">          0 :                 Aname==&quot;H72&quot; || Aname==&quot;H73&quot; ) {</span></a>
+<a name="6127"><span class="lineNum">    6127 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_T;</span></a>
+<a name="6128"><span class="lineNum">    6128 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6129"><span class="lineNum">    6129 </span>            :       // DNA - A</a>
+<a name="6130"><span class="lineNum">    6130 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA&quot;) {</span></a>
+<a name="6131"><span class="lineNum">    6131 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6132"><span class="lineNum">    6132 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6133"><span class="lineNum">    6133 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6134"><span class="lineNum">    6134 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6135"><span class="lineNum">    6135 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6136"><span class="lineNum">    6136 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6137"><span class="lineNum">    6137 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6138"><span class="lineNum">    6138 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="6139"><span class="lineNum">    6139 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="6140"><span class="lineNum">    6140 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="6141"><span class="lineNum">    6141 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="6142"><span class="lineNum">    6142 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="6143"><span class="lineNum">    6143 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="6144"><span class="lineNum">    6144 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="6145"><span class="lineNum">    6145 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="6146"><span class="lineNum">    6146 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6147"><span class="lineNum">    6147 </span>            :       // DNA - A3</a>
+<a name="6148"><span class="lineNum">    6148 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA3&quot;) {</span></a>
+<a name="6149"><span class="lineNum">    6149 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6150"><span class="lineNum">    6150 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6151"><span class="lineNum">    6151 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6152"><span class="lineNum">    6152 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6153"><span class="lineNum">    6153 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6154"><span class="lineNum">    6154 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6155"><span class="lineNum">    6155 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="6156"><span class="lineNum">    6156 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6157"><span class="lineNum">    6157 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="6158"><span class="lineNum">    6158 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="6159"><span class="lineNum">    6159 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="6160"><span class="lineNum">    6160 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="6161"><span class="lineNum">    6161 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="6162"><span class="lineNum">    6162 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="6163"><span class="lineNum">    6163 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="6164"><span class="lineNum">    6164 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6165"><span class="lineNum">    6165 </span>            :       // DNA - A5</a>
+<a name="6166"><span class="lineNum">    6166 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DA5&quot;) {</span></a>
+<a name="6167"><span class="lineNum">    6167 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6168"><span class="lineNum">    6168 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="6169"><span class="lineNum">    6169 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6170"><span class="lineNum">    6170 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6171"><span class="lineNum">    6171 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6172"><span class="lineNum">    6172 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="6173"><span class="lineNum">    6173 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="6174"><span class="lineNum">    6174 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot;  || Aname==&quot;C2&quot; || Aname==&quot;N3&quot; || Aname==&quot;C4&quot; ||</span></a>
+<a name="6175"><span class="lineNum">    6175 </span><span class="lineNoCov">          0 :                 Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; || Aname==&quot;N6&quot; || Aname==&quot;N7&quot; ||</span></a>
+<a name="6176"><span class="lineNum">    6176 </span><span class="lineNoCov">          0 :                 Aname==&quot;C8&quot;  || Aname==&quot;N9&quot; || Aname==&quot;H2&quot; || Aname==&quot;H8&quot; ||</span></a>
+<a name="6177"><span class="lineNum">    6177 </span><span class="lineNoCov">          0 :                 Aname==&quot;H61&quot; || Aname==&quot;H62&quot; ) {</span></a>
+<a name="6178"><span class="lineNum">    6178 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_A;</span></a>
+<a name="6179"><span class="lineNum">    6179 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6180"><span class="lineNum">    6180 </span>            :       // DNA - C</a>
+<a name="6181"><span class="lineNum">    6181 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC&quot;) {</span></a>
+<a name="6182"><span class="lineNum">    6182 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6183"><span class="lineNum">    6183 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6184"><span class="lineNum">    6184 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6185"><span class="lineNum">    6185 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6186"><span class="lineNum">    6186 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6187"><span class="lineNum">    6187 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6188"><span class="lineNum">    6188 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6189"><span class="lineNum">    6189 </span><span class="lineNoCov">          0 :                 Aname==&quot;HO3'&quot; || Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; ||</span></a>
+<a name="6190"><span class="lineNum">    6190 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'2&quot; || Aname==&quot;H5T&quot;  || Aname==&quot;H3T&quot; ) {</span></a>
+<a name="6191"><span class="lineNum">    6191 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA;</span></a>
+<a name="6192"><span class="lineNum">    6192 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="6193"><span class="lineNum">    6193 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="6194"><span class="lineNum">    6194 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="6195"><span class="lineNum">    6195 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="6196"><span class="lineNum">    6196 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6197"><span class="lineNum">    6197 </span>            :       // DNA - C3</a>
+<a name="6198"><span class="lineNum">    6198 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC3&quot;) {</span></a>
+<a name="6199"><span class="lineNum">    6199 </span><span class="lineNoCov">          0 :       if( Aname==&quot;P&quot;   || Aname==&quot;OP1&quot; || Aname==&quot;OP2&quot; || Aname==&quot;OP3&quot; ||</span></a>
+<a name="6200"><span class="lineNum">    6200 </span><span class="lineNoCov">          0 :           Aname==&quot;O1P&quot; || Aname==&quot;O2P&quot; || Aname==&quot;O3P&quot; ) {</span></a>
+<a name="6201"><span class="lineNum">    6201 </span><span class="lineNoCov">          0 :         atoi [residue_atom[i]]=BB_PO2;</span></a>
+<a name="6202"><span class="lineNum">    6202 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6203"><span class="lineNum">    6203 </span><span class="lineNoCov">          0 :                 Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  || Aname==&quot;C1'&quot;  ||</span></a>
+<a name="6204"><span class="lineNum">    6204 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6205"><span class="lineNum">    6205 </span><span class="lineNoCov">          0 :                 Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO3'&quot; ||</span></a>
+<a name="6206"><span class="lineNum">    6206 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6207"><span class="lineNum">    6207 </span>            :                 Aname==&quot;H3T&quot; ) {</a>
+<a name="6208"><span class="lineNum">    6208 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_3;</span></a>
+<a name="6209"><span class="lineNum">    6209 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="6210"><span class="lineNum">    6210 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="6211"><span class="lineNum">    6211 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="6212"><span class="lineNum">    6212 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="6213"><span class="lineNum">    6213 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6214"><span class="lineNum">    6214 </span>            :       // DNA - C5</a>
+<a name="6215"><span class="lineNum">    6215 </span><span class="lineNoCov">          0 :     } else if(Rname==&quot;DC5&quot;) {</span></a>
+<a name="6216"><span class="lineNum">    6216 </span><span class="lineNoCov">          0 :       if( Aname==&quot;O5'&quot;  || Aname==&quot;C5'&quot;  || Aname==&quot;O4'&quot;  || Aname==&quot;C4'&quot;  ||</span></a>
+<a name="6217"><span class="lineNum">    6217 </span><span class="lineNoCov">          0 :           Aname==&quot;O3'&quot;  || Aname==&quot;C3'&quot;  || Aname==&quot;C2'&quot;  ||  Aname==&quot;C1'&quot; ||</span></a>
+<a name="6218"><span class="lineNum">    6218 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'&quot;  || Aname==&quot;H5''&quot; || Aname==&quot;H4'&quot;  || Aname==&quot;H3'&quot;  ||</span></a>
+<a name="6219"><span class="lineNum">    6219 </span><span class="lineNoCov">          0 :           Aname==&quot;H2'&quot;  || Aname==&quot;H2''&quot; || Aname==&quot;H1'&quot;  || Aname==&quot;HO5'&quot; ||</span></a>
+<a name="6220"><span class="lineNum">    6220 </span><span class="lineNoCov">          0 :           Aname==&quot;H5'1&quot; || Aname==&quot;H5'2&quot; || Aname==&quot;H2'1&quot; || Aname==&quot;H2'2&quot; ||</span></a>
+<a name="6221"><span class="lineNum">    6221 </span>            :           Aname==&quot;H5T&quot; ) {</a>
+<a name="6222"><span class="lineNum">    6222 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BB_DNA_5;</span></a>
+<a name="6223"><span class="lineNum">    6223 </span><span class="lineNoCov">          0 :       } else if(Aname==&quot;N1&quot; || Aname==&quot;C2&quot; || Aname==&quot;O2&quot;  || Aname==&quot;N3&quot; ||</span></a>
+<a name="6224"><span class="lineNum">    6224 </span><span class="lineNoCov">          0 :                 Aname==&quot;C4&quot; || Aname==&quot;N4&quot; || Aname==&quot;C5&quot;  || Aname==&quot;C6&quot; ||</span></a>
+<a name="6225"><span class="lineNum">    6225 </span><span class="lineNoCov">          0 :                 Aname==&quot;H5&quot; || Aname==&quot;H6&quot; || Aname==&quot;H41&quot; || Aname==&quot;H42&quot; ) {</span></a>
+<a name="6226"><span class="lineNum">    6226 </span><span class="lineNoCov">          0 :         atoi[residue_atom[i]]=BASE_C;</span></a>
+<a name="6227"><span class="lineNum">    6227 </span><span class="lineNoCov">          0 :       } else error(&quot;Atom name &quot;+Aname+&quot; is not defined for residue &quot;+Rname+&quot;. Check the PDB.&quot;);</span></a>
+<a name="6228"><span class="lineNum">    6228 </span><span class="lineNoCov">          0 :     } else error(&quot;Residue not known: &quot;+Rname);</span></a>
+<a name="6229"><span class="lineNum">    6229 </span>            :   }</a>
+<a name="6230"><span class="lineNum">    6230 </span><span class="lineCov">          4 : }</span></a>
+<a name="6231"><span class="lineNum">    6231 </span>            : </a>
+<a name="6232"><span class="lineNum">    6232 </span><span class="lineCov">          4 : double SAXS::calculateAFF(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;FF_tmp, const double rho)</span></a>
+<a name="6233"><span class="lineNum">    6233 </span>            : {</a>
+<a name="6234"><span class="lineNum">    6234 </span>            :   std::map&lt;std::string, unsigned&gt; AA_map;</a>
+<a name="6235"><span class="lineNum">    6235 </span><span class="lineCov">          4 :   AA_map[&quot;H&quot;] = H;</span></a>
+<a name="6236"><span class="lineNum">    6236 </span><span class="lineCov">          4 :   AA_map[&quot;C&quot;] = C;</span></a>
+<a name="6237"><span class="lineNum">    6237 </span><span class="lineCov">          4 :   AA_map[&quot;N&quot;] = N;</span></a>
+<a name="6238"><span class="lineNum">    6238 </span><span class="lineCov">          4 :   AA_map[&quot;O&quot;] = O;</span></a>
+<a name="6239"><span class="lineNum">    6239 </span><span class="lineCov">          4 :   AA_map[&quot;P&quot;] = P;</span></a>
+<a name="6240"><span class="lineNum">    6240 </span><span class="lineCov">          4 :   AA_map[&quot;S&quot;] = S;</span></a>
+<a name="6241"><span class="lineNum">    6241 </span>            : </a>
+<a name="6242"><span class="lineNum">    6242 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; param_a;</a>
+<a name="6243"><span class="lineNum">    6243 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; param_b;</a>
+<a name="6244"><span class="lineNum">    6244 </span>            :   std::vector&lt;double&gt; param_c;</a>
+<a name="6245"><span class="lineNum">    6245 </span>            :   std::vector&lt;double&gt; param_v;</a>
+<a name="6246"><span class="lineNum">    6246 </span>            : </a>
+<a name="6247"><span class="lineNum">    6247 </span><span class="lineCov">          4 :   param_a.resize(NTT, std::vector&lt;double&gt;(5));</span></a>
+<a name="6248"><span class="lineNum">    6248 </span><span class="lineCov">          4 :   param_b.resize(NTT, std::vector&lt;double&gt;(5));</span></a>
+<a name="6249"><span class="lineNum">    6249 </span><span class="lineCov">          4 :   param_c.resize(NTT);</span></a>
+<a name="6250"><span class="lineNum">    6250 </span><span class="lineCov">          4 :   param_v.resize(NTT);</span></a>
+<a name="6251"><span class="lineNum">    6251 </span>            : </a>
+<a name="6252"><span class="lineNum">    6252 </span><span class="lineCov">          4 :   param_a[H][0] = 0.493002; param_b[H][0] = 10.5109; param_c[H] = 0.003038;</span></a>
+<a name="6253"><span class="lineNum">    6253 </span><span class="lineCov">          4 :   param_a[H][1] = 0.322912; param_b[H][1] = 26.1257; param_v[H] = 5.15;</span></a>
+<a name="6254"><span class="lineNum">    6254 </span><span class="lineCov">          4 :   param_a[H][2] = 0.140191; param_b[H][2] = 3.14236;</span></a>
+<a name="6255"><span class="lineNum">    6255 </span><span class="lineCov">          4 :   param_a[H][3] = 0.040810; param_b[H][3] = 57.7997;</span></a>
+<a name="6256"><span class="lineNum">    6256 </span><span class="lineCov">          4 :   param_a[H][4] = 0.0;      param_b[H][4] = 1.0;</span></a>
+<a name="6257"><span class="lineNum">    6257 </span>            : </a>
+<a name="6258"><span class="lineNum">    6258 </span><span class="lineCov">          4 :   param_a[C][0] = 2.31000; param_b[C][0] = 20.8439; param_c[C] = 0.215600;</span></a>
+<a name="6259"><span class="lineNum">    6259 </span><span class="lineCov">          4 :   param_a[C][1] = 1.02000; param_b[C][1] = 10.2075; param_v[C] = 16.44;</span></a>
+<a name="6260"><span class="lineNum">    6260 </span><span class="lineCov">          4 :   param_a[C][2] = 1.58860; param_b[C][2] = 0.56870;</span></a>
+<a name="6261"><span class="lineNum">    6261 </span><span class="lineCov">          4 :   param_a[C][3] = 0.86500; param_b[C][3] = 51.6512;</span></a>
+<a name="6262"><span class="lineNum">    6262 </span><span class="lineCov">          4 :   param_a[C][4] = 0.0;     param_b[C][4] = 1.0;</span></a>
+<a name="6263"><span class="lineNum">    6263 </span>            : </a>
+<a name="6264"><span class="lineNum">    6264 </span><span class="lineCov">          4 :   param_a[N][0] = 12.2126; param_b[N][0] = 0.00570; param_c[N] = -11.529;</span></a>
+<a name="6265"><span class="lineNum">    6265 </span><span class="lineCov">          4 :   param_a[N][1] = 3.13220; param_b[N][1] = 9.89330; param_v[N] = 2.49;</span></a>
+<a name="6266"><span class="lineNum">    6266 </span><span class="lineCov">          4 :   param_a[N][2] = 2.01250; param_b[N][2] = 28.9975;</span></a>
+<a name="6267"><span class="lineNum">    6267 </span><span class="lineCov">          4 :   param_a[N][3] = 1.16630; param_b[N][3] = 0.58260;</span></a>
+<a name="6268"><span class="lineNum">    6268 </span><span class="lineCov">          4 :   param_a[N][4] = 0.0;     param_b[N][4] = 1.0;</span></a>
+<a name="6269"><span class="lineNum">    6269 </span>            : </a>
+<a name="6270"><span class="lineNum">    6270 </span><span class="lineCov">          4 :   param_a[O][0] = 3.04850; param_b[O][0] = 13.2771; param_c[O] = 0.250800 ;</span></a>
+<a name="6271"><span class="lineNum">    6271 </span><span class="lineCov">          4 :   param_a[O][1] = 2.28680; param_b[O][1] = 5.70110; param_v[O] = 9.13;</span></a>
+<a name="6272"><span class="lineNum">    6272 </span><span class="lineCov">          4 :   param_a[O][2] = 1.54630; param_b[O][2] = 0.32390;</span></a>
+<a name="6273"><span class="lineNum">    6273 </span><span class="lineCov">          4 :   param_a[O][3] = 0.86700; param_b[O][3] = 32.9089;</span></a>
+<a name="6274"><span class="lineNum">    6274 </span><span class="lineCov">          4 :   param_a[O][4] = 0.0;     param_b[O][4] = 1.0;</span></a>
+<a name="6275"><span class="lineNum">    6275 </span>            : </a>
+<a name="6276"><span class="lineNum">    6276 </span><span class="lineCov">          4 :   param_a[P][0] = 6.43450; param_b[P][0] = 1.90670; param_c[P] = 1.11490;</span></a>
+<a name="6277"><span class="lineNum">    6277 </span><span class="lineCov">          4 :   param_a[P][1] = 4.17910; param_b[P][1] = 27.1570; param_v[P] = 5.73;</span></a>
+<a name="6278"><span class="lineNum">    6278 </span><span class="lineCov">          4 :   param_a[P][2] = 1.78000; param_b[P][2] = 0.52600;</span></a>
+<a name="6279"><span class="lineNum">    6279 </span><span class="lineCov">          4 :   param_a[P][3] = 1.49080; param_b[P][3] = 68.1645;</span></a>
+<a name="6280"><span class="lineNum">    6280 </span><span class="lineCov">          4 :   param_a[P][4] = 0.0;     param_b[P][4] = 1.0;</span></a>
+<a name="6281"><span class="lineNum">    6281 </span>            : </a>
+<a name="6282"><span class="lineNum">    6282 </span><span class="lineCov">          4 :   param_a[S][0] = 6.90530; param_b[S][0] = 1.46790; param_c[S] = 0.866900;</span></a>
+<a name="6283"><span class="lineNum">    6283 </span><span class="lineCov">          4 :   param_a[S][1] = 5.20340; param_b[S][1] = 22.2151; param_v[S] = 19.86;</span></a>
+<a name="6284"><span class="lineNum">    6284 </span><span class="lineCov">          4 :   param_a[S][2] = 1.43790; param_b[S][2] = 0.25360;</span></a>
+<a name="6285"><span class="lineNum">    6285 </span><span class="lineCov">          4 :   param_a[S][3] = 1.58630; param_b[S][3] = 56.1720;</span></a>
+<a name="6286"><span class="lineNum">    6286 </span><span class="lineCov">          4 :   param_a[S][4] = 0.0;     param_b[S][4] = 1.0;</span></a>
+<a name="6287"><span class="lineNum">    6287 </span>            : </a>
+<a name="6288"><span class="lineNum">    6288 </span><span class="lineCov">          4 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="6289"><span class="lineNum">    6289 </span>            : </a>
+<a name="6290"><span class="lineNum">    6290 </span>            :   double Iq0=0.;</a>
+<a name="6291"><span class="lineNum">    6291 </span><span class="lineCov">          4 :   if( moldat ) {</span></a>
+<a name="6292"><span class="lineNum">    6292 </span>            :     // cycle over the atom types</a>
+<a name="6293"><span class="lineNum">    6293 </span><span class="lineCov">         28 :     for(unsigned i=0; i&lt;NTT; ++i) {</span></a>
+<a name="6294"><span class="lineNum">    6294 </span><span class="lineCov">         24 :       const double volr = std::pow(param_v[i], (2.0/3.0)) /(4. * M_PI);</span></a>
+<a name="6295"><span class="lineNum">    6295 </span>            :       // cycle over q</a>
+<a name="6296"><span class="lineNum">    6296 </span><span class="lineCov">        240 :       for(unsigned k=0; k&lt;q_list.size(); ++k) {</span></a>
+<a name="6297"><span class="lineNum">    6297 </span><span class="lineCov">        216 :         const double q = q_list[k];</span></a>
+<a name="6298"><span class="lineNum">    6298 </span><span class="lineCov">        216 :         const double s = q / (4. * M_PI);</span></a>
+<a name="6299"><span class="lineNum">    6299 </span><span class="lineCov">        216 :         FF_tmp[k][i] = param_c[i];</span></a>
+<a name="6300"><span class="lineNum">    6300 </span>            :         // SUM [a_i * EXP( - b_i * (q/4pi)^2 )] Waasmaier and Kirfel (1995)</a>
+<a name="6301"><span class="lineNum">    6301 </span><span class="lineCov">       1080 :         for(unsigned j=0; j&lt;4; ++j) {</span></a>
+<a name="6302"><span class="lineNum">    6302 </span><span class="lineCov">        864 :           FF_tmp[k][i] += param_a[i][j]*std::exp(-param_b[i][j]*s*s);</span></a>
+<a name="6303"><span class="lineNum">    6303 </span>            :         }</a>
+<a name="6304"><span class="lineNum">    6304 </span>            :         // subtract solvation: rho * v_i * EXP( (- v_i^(2/3) / (4pi)) * q^2  ) // since  D in Fraser 1978 is 2*s</a>
+<a name="6305"><span class="lineNum">    6305 </span><span class="lineCov">        216 :         FF_tmp[k][i] -= rho*param_v[i]*std::exp(-volr*q*q);</span></a>
+<a name="6306"><span class="lineNum">    6306 </span>            :       }</a>
+<a name="6307"><span class="lineNum">    6307 </span>            :     }</a>
+<a name="6308"><span class="lineNum">    6308 </span>            :     // cycle over the atoms to assign the atom type and calculate I0</a>
+<a name="6309"><span class="lineNum">    6309 </span><span class="lineCov">      14298 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="6310"><span class="lineNum">    6310 </span>            :       // get atom name</a>
+<a name="6311"><span class="lineNum">    6311 </span><span class="lineCov">      14294 :       std::string name = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="6312"><span class="lineNum">    6312 </span>            :       char type;</a>
+<a name="6313"><span class="lineNum">    6313 </span>            :       // get atom type</a>
+<a name="6314"><span class="lineNum">    6314 </span><span class="lineCov">      14294 :       char first = name.at(0);</span></a>
+<a name="6315"><span class="lineNum">    6315 </span>            :       // GOLDEN RULE: type is first letter, if not a number</a>
+<a name="6316"><span class="lineNum">    6316 </span><span class="lineCov">      14294 :       if (!isdigit(first)) {</span></a>
+<a name="6317"><span class="lineNum">    6317 </span>            :         type = first;</a>
+<a name="6318"><span class="lineNum">    6318 </span>            :         // otherwise is the second</a>
+<a name="6319"><span class="lineNum">    6319 </span>            :       } else {</a>
+<a name="6320"><span class="lineNum">    6320 </span><span class="lineNoCov">          0 :         type = name.at(1);</span></a>
+<a name="6321"><span class="lineNum">    6321 </span>            :       }</a>
+<a name="6322"><span class="lineNum">    6322 </span><span class="lineCov">      14294 :       std::string type_s = std::string(1,type);</span></a>
+<a name="6323"><span class="lineNum">    6323 </span><span class="lineCov">      14294 :       if(AA_map.find(type_s) != AA_map.end()) {</span></a>
+<a name="6324"><span class="lineNum">    6324 </span><span class="lineCov">      14294 :         const unsigned index=AA_map[type_s];</span></a>
+<a name="6325"><span class="lineNum">    6325 </span><span class="lineCov">      14294 :         atoi[i] = AA_map[type_s];</span></a>
+<a name="6326"><span class="lineNum">    6326 </span><span class="lineCov">      71470 :         for(unsigned j=0; j&lt;4; ++j) Iq0 += param_a[index][j];</span></a>
+<a name="6327"><span class="lineNum">    6327 </span><span class="lineCov">      14294 :         Iq0 = Iq0 -rho*param_v[index] + param_c[index];</span></a>
+<a name="6328"><span class="lineNum">    6328 </span>            :       } else {</a>
+<a name="6329"><span class="lineNum">    6329 </span><span class="lineNoCov">          0 :         error(&quot;Wrong atom type &quot;+type_s+&quot; from atom name &quot;+name+&quot;\n&quot;);</span></a>
+<a name="6330"><span class="lineNum">    6330 </span>            :       }</a>
+<a name="6331"><span class="lineNum">    6331 </span>            :     }</a>
+<a name="6332"><span class="lineNum">    6332 </span>            :   } else {</a>
+<a name="6333"><span class="lineNum">    6333 </span><span class="lineNoCov">          0 :     error(&quot;MOLINFO DATA not found\n&quot;);</span></a>
+<a name="6334"><span class="lineNum">    6334 </span>            :   }</a>
+<a name="6335"><span class="lineNum">    6335 </span>            : </a>
+<a name="6336"><span class="lineNum">    6336 </span><span class="lineCov">          4 :   return Iq0;</span></a>
+<a name="6337"><span class="lineNum">    6337 </span><span class="lineCov">          4 : }</span></a>
+<a name="6338"><span class="lineNum">    6338 </span>            : </a>
+<a name="6339"><span class="lineNum">    6339 </span><span class="lineCov">          2 : double SAXS::calculateAFFsans(const std::vector&lt;AtomNumber&gt; &amp;atoms, std::vector&lt;std::vector&lt;long double&gt; &gt; &amp;FF_tmp, const double deuter_conc)</span></a>
+<a name="6340"><span class="lineNum">    6340 </span>            : {</a>
+<a name="6341"><span class="lineNum">    6341 </span>            :   std::map&lt;std::string, unsigned&gt; AA_map;</a>
+<a name="6342"><span class="lineNum">    6342 </span><span class="lineCov">          2 :   AA_map[&quot;H&quot;] = H;</span></a>
+<a name="6343"><span class="lineNum">    6343 </span><span class="lineCov">          2 :   AA_map[&quot;C&quot;] = C;</span></a>
+<a name="6344"><span class="lineNum">    6344 </span><span class="lineCov">          2 :   AA_map[&quot;N&quot;] = N;</span></a>
+<a name="6345"><span class="lineNum">    6345 </span><span class="lineCov">          2 :   AA_map[&quot;O&quot;] = O;</span></a>
+<a name="6346"><span class="lineNum">    6346 </span><span class="lineCov">          2 :   AA_map[&quot;P&quot;] = P;</span></a>
+<a name="6347"><span class="lineNum">    6347 </span><span class="lineCov">          2 :   AA_map[&quot;S&quot;] = S;</span></a>
+<a name="6348"><span class="lineNum">    6348 </span>            : </a>
+<a name="6349"><span class="lineNum">    6349 </span>            :   std::vector&lt;double&gt; param_b;</a>
+<a name="6350"><span class="lineNum">    6350 </span>            :   std::vector&lt;double&gt; param_v;</a>
+<a name="6351"><span class="lineNum">    6351 </span>            : </a>
+<a name="6352"><span class="lineNum">    6352 </span><span class="lineCov">          2 :   param_b.resize(NTT);</span></a>
+<a name="6353"><span class="lineNum">    6353 </span><span class="lineCov">          2 :   param_v.resize(NTT);</span></a>
+<a name="6354"><span class="lineNum">    6354 </span>            : </a>
+<a name="6355"><span class="lineNum">    6355 </span><span class="lineCov">          2 :   param_b[H] = -0.374; param_v[H] = 5.15;</span></a>
+<a name="6356"><span class="lineNum">    6356 </span>            :   // param_b[D] = 0.667;</a>
+<a name="6357"><span class="lineNum">    6357 </span><span class="lineCov">          2 :   param_b[C] =  0.665;  param_v[C] = 16.44;</span></a>
+<a name="6358"><span class="lineNum">    6358 </span><span class="lineCov">          2 :   param_b[N] =  0.94;   param_v[N] = 2.49;</span></a>
+<a name="6359"><span class="lineNum">    6359 </span><span class="lineCov">          2 :   param_b[O] =  0.580;  param_v[O] = 9.13;</span></a>
+<a name="6360"><span class="lineNum">    6360 </span><span class="lineCov">          2 :   param_b[P] =  0.51;   param_v[P] = 5.73;</span></a>
+<a name="6361"><span class="lineNum">    6361 </span><span class="lineCov">          2 :   param_b[S] =  0.28;   param_v[S] = 19.86;</span></a>
+<a name="6362"><span class="lineNum">    6362 </span>            : </a>
+<a name="6363"><span class="lineNum">    6363 </span><span class="lineCov">          2 :   double solv_sc_length = 0.1*(param_b[O] + 2.*((1. - deuter_conc) * param_b[H] + deuter_conc * 0.667)); // per water electron (10 electrons)</span></a>
+<a name="6364"><span class="lineNum">    6364 </span>            : </a>
+<a name="6365"><span class="lineNum">    6365 </span><span class="lineCov">          2 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="6366"><span class="lineNum">    6366 </span>            : </a>
+<a name="6367"><span class="lineNum">    6367 </span>            :   double Iq0=0.;</a>
+<a name="6368"><span class="lineNum">    6368 </span><span class="lineCov">          2 :   if( moldat ) {</span></a>
+<a name="6369"><span class="lineNum">    6369 </span>            :     // cycle over the atom types</a>
+<a name="6370"><span class="lineNum">    6370 </span><span class="lineCov">         14 :     for(unsigned i=0; i&lt;NTT; ++i) {</span></a>
+<a name="6371"><span class="lineNum">    6371 </span><span class="lineCov">         12 :       double volr = std::pow(param_v[i], (2.0/3.0)) /(4. * M_PI);</span></a>
+<a name="6372"><span class="lineNum">    6372 </span>            :       // cycle over q</a>
+<a name="6373"><span class="lineNum">    6373 </span><span class="lineCov">        120 :       for(unsigned k=0; k&lt;q_list.size(); ++k) {</span></a>
+<a name="6374"><span class="lineNum">    6374 </span><span class="lineCov">        108 :         const double q = q_list[k];</span></a>
+<a name="6375"><span class="lineNum">    6375 </span><span class="lineCov">        108 :         FF_tmp[k][i] = param_b[i];</span></a>
+<a name="6376"><span class="lineNum">    6376 </span>            :         // subtract solvation: rho * v_i * EXP( (- v_i^(2/3) / (4pi)) * q^2  ) // since  D in Fraser 1978 is 2*s</a>
+<a name="6377"><span class="lineNum">    6377 </span><span class="lineCov">        108 :         FF_tmp[k][i] -= solv_sc_length*rho*param_v[i]*std::exp(-volr*q*q);</span></a>
+<a name="6378"><span class="lineNum">    6378 </span>            :       }</a>
+<a name="6379"><span class="lineNum">    6379 </span>            :     }</a>
+<a name="6380"><span class="lineNum">    6380 </span>            :     // cycle over the atoms to assign the atom type and calculate I0</a>
+<a name="6381"><span class="lineNum">    6381 </span><span class="lineCov">       6880 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="6382"><span class="lineNum">    6382 </span>            :       // get atom name</a>
+<a name="6383"><span class="lineNum">    6383 </span><span class="lineCov">       6878 :       std::string name = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="6384"><span class="lineNum">    6384 </span>            :       char type;</a>
+<a name="6385"><span class="lineNum">    6385 </span>            :       // get atom type</a>
+<a name="6386"><span class="lineNum">    6386 </span><span class="lineCov">       6878 :       char first = name.at(0);</span></a>
+<a name="6387"><span class="lineNum">    6387 </span>            :       // GOLDEN RULE: type is first letter, if not a number</a>
+<a name="6388"><span class="lineNum">    6388 </span><span class="lineCov">       6878 :       if (!isdigit(first)) {</span></a>
+<a name="6389"><span class="lineNum">    6389 </span>            :         type = first;</a>
+<a name="6390"><span class="lineNum">    6390 </span>            :         // otherwise is the second</a>
+<a name="6391"><span class="lineNum">    6391 </span>            :       } else {</a>
+<a name="6392"><span class="lineNum">    6392 </span><span class="lineNoCov">          0 :         type = name.at(1);</span></a>
+<a name="6393"><span class="lineNum">    6393 </span>            :       }</a>
+<a name="6394"><span class="lineNum">    6394 </span><span class="lineCov">       6878 :       std::string type_s = std::string(1,type);</span></a>
+<a name="6395"><span class="lineNum">    6395 </span><span class="lineCov">       6878 :       if(AA_map.find(type_s) != AA_map.end()) {</span></a>
+<a name="6396"><span class="lineNum">    6396 </span><span class="lineCov">       6878 :         const unsigned index=AA_map[type_s];</span></a>
+<a name="6397"><span class="lineNum">    6397 </span><span class="lineCov">       6878 :         atoi[i] = AA_map[type_s];</span></a>
+<a name="6398"><span class="lineNum">    6398 </span><span class="lineCov">       6878 :         Iq0 += param_b[index]-solv_sc_length*rho*param_v[index];</span></a>
+<a name="6399"><span class="lineNum">    6399 </span>            :       } else {</a>
+<a name="6400"><span class="lineNum">    6400 </span><span class="lineNoCov">          0 :         error(&quot;Wrong atom type &quot;+type_s+&quot; from atom name &quot;+name+&quot;\n&quot;);</span></a>
+<a name="6401"><span class="lineNum">    6401 </span>            :       }</a>
+<a name="6402"><span class="lineNum">    6402 </span>            :     }</a>
+<a name="6403"><span class="lineNum">    6403 </span>            :   } else {</a>
+<a name="6404"><span class="lineNum">    6404 </span><span class="lineNoCov">          0 :     error(&quot;MOLINFO DATA not found\n&quot;);</span></a>
+<a name="6405"><span class="lineNum">    6405 </span>            :   }</a>
+<a name="6406"><span class="lineNum">    6406 </span>            : </a>
+<a name="6407"><span class="lineNum">    6407 </span><span class="lineCov">          2 :   return Iq0;</span></a>
+<a name="6408"><span class="lineNum">    6408 </span>            : }</a>
+<a name="6409"><span class="lineNum">    6409 </span>            : </a>
+<a name="6410"><span class="lineNum">    6410 </span><span class="lineCov">         10 : std::map&lt;std::string, std::vector&lt;double&gt; &gt; SAXS::setupLCPOparam() {</span></a>
+<a name="6411"><span class="lineNum">    6411 </span>            :   std::map&lt;std::string, std::vector&lt;double&gt; &gt; lcpomap;</a>
+<a name="6412"><span class="lineNum">    6412 </span>            : </a>
+<a name="6413"><span class="lineNum">    6413 </span>            :   // We arbitrarily set OC1/OT1 as the charged oxygen.</a>
+<a name="6414"><span class="lineNum">    6414 </span>            : </a>
+<a name="6415"><span class="lineNum">    6415 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6416"><span class="lineNum">    6416 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6417"><span class="lineNum">    6417 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6418"><span class="lineNum">    6418 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6419"><span class="lineNum">    6419 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_CB&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6420"><span class="lineNum">    6420 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6421"><span class="lineNum">    6421 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6422"><span class="lineNum">    6422 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6423"><span class="lineNum">    6423 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6424"><span class="lineNum">    6424 </span><span class="lineCov">         10 :   lcpomap[&quot;ALA_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6425"><span class="lineNum">    6425 </span>            : </a>
+<a name="6426"><span class="lineNum">    6426 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6427"><span class="lineNum">    6427 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6428"><span class="lineNum">    6428 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6429"><span class="lineNum">    6429 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6430"><span class="lineNum">    6430 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6431"><span class="lineNum">    6431 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6432"><span class="lineNum">    6432 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OD1&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6433"><span class="lineNum">    6433 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OD2&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6434"><span class="lineNum">    6434 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6435"><span class="lineNum">    6435 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6436"><span class="lineNum">    6436 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6437"><span class="lineNum">    6437 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6438"><span class="lineNum">    6438 </span><span class="lineCov">         10 :   lcpomap[&quot;ASP_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6439"><span class="lineNum">    6439 </span>            : </a>
+<a name="6440"><span class="lineNum">    6440 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6441"><span class="lineNum">    6441 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6442"><span class="lineNum">    6442 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6443"><span class="lineNum">    6443 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6444"><span class="lineNum">    6444 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6445"><span class="lineNum">    6445 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6446"><span class="lineNum">    6446 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_OD1&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6447"><span class="lineNum">    6447 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_ND2&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="6448"><span class="lineNum">    6448 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6449"><span class="lineNum">    6449 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6450"><span class="lineNum">    6450 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6451"><span class="lineNum">    6451 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6452"><span class="lineNum">    6452 </span><span class="lineCov">         10 :   lcpomap[&quot;ASN_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6453"><span class="lineNum">    6453 </span>            : </a>
+<a name="6454"><span class="lineNum">    6454 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6455"><span class="lineNum">    6455 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6456"><span class="lineNum">    6456 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6457"><span class="lineNum">    6457 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6458"><span class="lineNum">    6458 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6459"><span class="lineNum">    6459 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6460"><span class="lineNum">    6460 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_CD&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6461"><span class="lineNum">    6461 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_NE&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6462"><span class="lineNum">    6462 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_NH1&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="6463"><span class="lineNum">    6463 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_NH2&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="6464"><span class="lineNum">    6464 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_CZ&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6465"><span class="lineNum">    6465 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6466"><span class="lineNum">    6466 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6467"><span class="lineNum">    6467 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6468"><span class="lineNum">    6468 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6469"><span class="lineNum">    6469 </span><span class="lineCov">         10 :   lcpomap[&quot;ARG_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6470"><span class="lineNum">    6470 </span>            : </a>
+<a name="6471"><span class="lineNum">    6471 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6472"><span class="lineNum">    6472 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6473"><span class="lineNum">    6473 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6474"><span class="lineNum">    6474 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6475"><span class="lineNum">    6475 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6476"><span class="lineNum">    6476 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_SG&quot;] = { 1.9,  0.54581,  -0.19477,  -0.0012873,  0.00029247};</span></a>
+<a name="6477"><span class="lineNum">    6477 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6478"><span class="lineNum">    6478 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6479"><span class="lineNum">    6479 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6480"><span class="lineNum">    6480 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6481"><span class="lineNum">    6481 </span><span class="lineCov">         10 :   lcpomap[&quot;CYS_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6482"><span class="lineNum">    6482 </span>            : </a>
+<a name="6483"><span class="lineNum">    6483 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6484"><span class="lineNum">    6484 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6485"><span class="lineNum">    6485 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6486"><span class="lineNum">    6486 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6487"><span class="lineNum">    6487 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6488"><span class="lineNum">    6488 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6489"><span class="lineNum">    6489 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_CD&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6490"><span class="lineNum">    6490 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OE1&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6491"><span class="lineNum">    6491 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OE2&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6492"><span class="lineNum">    6492 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6493"><span class="lineNum">    6493 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6494"><span class="lineNum">    6494 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6495"><span class="lineNum">    6495 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6496"><span class="lineNum">    6496 </span><span class="lineCov">         10 :   lcpomap[&quot;GLU_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6497"><span class="lineNum">    6497 </span>            : </a>
+<a name="6498"><span class="lineNum">    6498 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6499"><span class="lineNum">    6499 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6500"><span class="lineNum">    6500 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6501"><span class="lineNum">    6501 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6502"><span class="lineNum">    6502 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6503"><span class="lineNum">    6503 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6504"><span class="lineNum">    6504 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_CD&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6505"><span class="lineNum">    6505 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_OE1&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6506"><span class="lineNum">    6506 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_NE2&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="6507"><span class="lineNum">    6507 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6508"><span class="lineNum">    6508 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6509"><span class="lineNum">    6509 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6510"><span class="lineNum">    6510 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6511"><span class="lineNum">    6511 </span><span class="lineCov">         10 :   lcpomap[&quot;GLN_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6512"><span class="lineNum">    6512 </span>            : </a>
+<a name="6513"><span class="lineNum">    6513 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6514"><span class="lineNum">    6514 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_CA&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6515"><span class="lineNum">    6515 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6516"><span class="lineNum">    6516 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6517"><span class="lineNum">    6517 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6518"><span class="lineNum">    6518 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6519"><span class="lineNum">    6519 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6520"><span class="lineNum">    6520 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6521"><span class="lineNum">    6521 </span><span class="lineCov">         10 :   lcpomap[&quot;GLY_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6522"><span class="lineNum">    6522 </span>            : </a>
+<a name="6523"><span class="lineNum">    6523 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6524"><span class="lineNum">    6524 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6525"><span class="lineNum">    6525 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6526"><span class="lineNum">    6526 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6527"><span class="lineNum">    6527 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6528"><span class="lineNum">    6528 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6529"><span class="lineNum">    6529 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6530"><span class="lineNum">    6530 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6531"><span class="lineNum">    6531 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6532"><span class="lineNum">    6532 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6533"><span class="lineNum">    6533 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6534"><span class="lineNum">    6534 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6535"><span class="lineNum">    6535 </span><span class="lineCov">         10 :   lcpomap[&quot;HIS_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6536"><span class="lineNum">    6536 </span>            : </a>
+<a name="6537"><span class="lineNum">    6537 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6538"><span class="lineNum">    6538 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6539"><span class="lineNum">    6539 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6540"><span class="lineNum">    6540 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6541"><span class="lineNum">    6541 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6542"><span class="lineNum">    6542 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6543"><span class="lineNum">    6543 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6544"><span class="lineNum">    6544 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6545"><span class="lineNum">    6545 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6546"><span class="lineNum">    6546 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6547"><span class="lineNum">    6547 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6548"><span class="lineNum">    6548 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6549"><span class="lineNum">    6549 </span><span class="lineCov">         10 :   lcpomap[&quot;HIE_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6550"><span class="lineNum">    6550 </span>            : </a>
+<a name="6551"><span class="lineNum">    6551 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6552"><span class="lineNum">    6552 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6553"><span class="lineNum">    6553 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6554"><span class="lineNum">    6554 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6555"><span class="lineNum">    6555 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6556"><span class="lineNum">    6556 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6557"><span class="lineNum">    6557 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6558"><span class="lineNum">    6558 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6559"><span class="lineNum">    6559 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6560"><span class="lineNum">    6560 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6561"><span class="lineNum">    6561 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6562"><span class="lineNum">    6562 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6563"><span class="lineNum">    6563 </span><span class="lineCov">         10 :   lcpomap[&quot;HSE_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6564"><span class="lineNum">    6564 </span>            : </a>
+<a name="6565"><span class="lineNum">    6565 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6566"><span class="lineNum">    6566 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6567"><span class="lineNum">    6567 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6568"><span class="lineNum">    6568 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6569"><span class="lineNum">    6569 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6570"><span class="lineNum">    6570 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6571"><span class="lineNum">    6571 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6572"><span class="lineNum">    6572 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6573"><span class="lineNum">    6573 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6574"><span class="lineNum">    6574 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6575"><span class="lineNum">    6575 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6576"><span class="lineNum">    6576 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6577"><span class="lineNum">    6577 </span><span class="lineCov">         10 :   lcpomap[&quot;HID_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6578"><span class="lineNum">    6578 </span>            : </a>
+<a name="6579"><span class="lineNum">    6579 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6580"><span class="lineNum">    6580 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6581"><span class="lineNum">    6581 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6582"><span class="lineNum">    6582 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6583"><span class="lineNum">    6583 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6584"><span class="lineNum">    6584 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6585"><span class="lineNum">    6585 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6586"><span class="lineNum">    6586 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6587"><span class="lineNum">    6587 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6588"><span class="lineNum">    6588 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6589"><span class="lineNum">    6589 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6590"><span class="lineNum">    6590 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6591"><span class="lineNum">    6591 </span><span class="lineCov">         10 :   lcpomap[&quot;HSD_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6592"><span class="lineNum">    6592 </span>            : </a>
+<a name="6593"><span class="lineNum">    6593 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6594"><span class="lineNum">    6594 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6595"><span class="lineNum">    6595 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6596"><span class="lineNum">    6596 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6597"><span class="lineNum">    6597 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6598"><span class="lineNum">    6598 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6599"><span class="lineNum">    6599 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6600"><span class="lineNum">    6600 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6601"><span class="lineNum">    6601 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6602"><span class="lineNum">    6602 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6603"><span class="lineNum">    6603 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6604"><span class="lineNum">    6604 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6605"><span class="lineNum">    6605 </span><span class="lineCov">         10 :   lcpomap[&quot;HIP_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6606"><span class="lineNum">    6606 </span>            : </a>
+<a name="6607"><span class="lineNum">    6607 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6608"><span class="lineNum">    6608 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6609"><span class="lineNum">    6609 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6610"><span class="lineNum">    6610 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6611"><span class="lineNum">    6611 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6612"><span class="lineNum">    6612 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6613"><span class="lineNum">    6613 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6614"><span class="lineNum">    6614 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6615"><span class="lineNum">    6615 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6616"><span class="lineNum">    6616 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6617"><span class="lineNum">    6617 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6618"><span class="lineNum">    6618 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6619"><span class="lineNum">    6619 </span><span class="lineCov">         10 :   lcpomap[&quot;HSP_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6620"><span class="lineNum">    6620 </span>            : </a>
+<a name="6621"><span class="lineNum">    6621 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6622"><span class="lineNum">    6622 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6623"><span class="lineNum">    6623 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6624"><span class="lineNum">    6624 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6625"><span class="lineNum">    6625 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_CB&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6626"><span class="lineNum">    6626 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_CG2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6627"><span class="lineNum">    6627 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_CG1&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6628"><span class="lineNum">    6628 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_CD1&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6629"><span class="lineNum">    6629 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_CD&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6630"><span class="lineNum">    6630 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6631"><span class="lineNum">    6631 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6632"><span class="lineNum">    6632 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6633"><span class="lineNum">    6633 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6634"><span class="lineNum">    6634 </span><span class="lineCov">         10 :   lcpomap[&quot;ILE_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6635"><span class="lineNum">    6635 </span>            : </a>
+<a name="6636"><span class="lineNum">    6636 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6637"><span class="lineNum">    6637 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6638"><span class="lineNum">    6638 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6639"><span class="lineNum">    6639 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6640"><span class="lineNum">    6640 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6641"><span class="lineNum">    6641 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_CG&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6642"><span class="lineNum">    6642 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_CD1&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6643"><span class="lineNum">    6643 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_CD2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6644"><span class="lineNum">    6644 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6645"><span class="lineNum">    6645 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6646"><span class="lineNum">    6646 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6647"><span class="lineNum">    6647 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6648"><span class="lineNum">    6648 </span><span class="lineCov">         10 :   lcpomap[&quot;LEU_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6649"><span class="lineNum">    6649 </span>            : </a>
+<a name="6650"><span class="lineNum">    6650 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6651"><span class="lineNum">    6651 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6652"><span class="lineNum">    6652 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6653"><span class="lineNum">    6653 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6654"><span class="lineNum">    6654 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6655"><span class="lineNum">    6655 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6656"><span class="lineNum">    6656 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_CD&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6657"><span class="lineNum">    6657 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_CE&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6658"><span class="lineNum">    6658 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_NZ&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="6659"><span class="lineNum">    6659 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6660"><span class="lineNum">    6660 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6661"><span class="lineNum">    6661 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6662"><span class="lineNum">    6662 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6663"><span class="lineNum">    6663 </span><span class="lineCov">         10 :   lcpomap[&quot;LYS_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6664"><span class="lineNum">    6664 </span>            : </a>
+<a name="6665"><span class="lineNum">    6665 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6666"><span class="lineNum">    6666 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6667"><span class="lineNum">    6667 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6668"><span class="lineNum">    6668 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6669"><span class="lineNum">    6669 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6670"><span class="lineNum">    6670 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6671"><span class="lineNum">    6671 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_SD&quot;] = { 1.9,  0.54581,  -0.19477,  -0.0012873,  0.00029247};</span></a>
+<a name="6672"><span class="lineNum">    6672 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_CE&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6673"><span class="lineNum">    6673 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6674"><span class="lineNum">    6674 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6675"><span class="lineNum">    6675 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6676"><span class="lineNum">    6676 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6677"><span class="lineNum">    6677 </span><span class="lineCov">         10 :   lcpomap[&quot;MET_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6678"><span class="lineNum">    6678 </span>            : </a>
+<a name="6679"><span class="lineNum">    6679 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6680"><span class="lineNum">    6680 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6681"><span class="lineNum">    6681 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6682"><span class="lineNum">    6682 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6683"><span class="lineNum">    6683 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6684"><span class="lineNum">    6684 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6685"><span class="lineNum">    6685 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CD1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6686"><span class="lineNum">    6686 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6687"><span class="lineNum">    6687 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CZ&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6688"><span class="lineNum">    6688 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CE2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6689"><span class="lineNum">    6689 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6690"><span class="lineNum">    6690 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6691"><span class="lineNum">    6691 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6692"><span class="lineNum">    6692 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6693"><span class="lineNum">    6693 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6694"><span class="lineNum">    6694 </span><span class="lineCov">         10 :   lcpomap[&quot;PHE_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6695"><span class="lineNum">    6695 </span>            : </a>
+<a name="6696"><span class="lineNum">    6696 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6697"><span class="lineNum">    6697 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6698"><span class="lineNum">    6698 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6699"><span class="lineNum">    6699 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6700"><span class="lineNum">    6700 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6701"><span class="lineNum">    6701 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6702"><span class="lineNum">    6702 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_CD&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6703"><span class="lineNum">    6703 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6704"><span class="lineNum">    6704 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6705"><span class="lineNum">    6705 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6706"><span class="lineNum">    6706 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6707"><span class="lineNum">    6707 </span><span class="lineCov">         10 :   lcpomap[&quot;PRO_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6708"><span class="lineNum">    6708 </span>            : </a>
+<a name="6709"><span class="lineNum">    6709 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6710"><span class="lineNum">    6710 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6711"><span class="lineNum">    6711 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6712"><span class="lineNum">    6712 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6713"><span class="lineNum">    6713 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6714"><span class="lineNum">    6714 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_OG&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6715"><span class="lineNum">    6715 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6716"><span class="lineNum">    6716 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6717"><span class="lineNum">    6717 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6718"><span class="lineNum">    6718 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6719"><span class="lineNum">    6719 </span><span class="lineCov">         10 :   lcpomap[&quot;SER_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6720"><span class="lineNum">    6720 </span>            : </a>
+<a name="6721"><span class="lineNum">    6721 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6722"><span class="lineNum">    6722 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6723"><span class="lineNum">    6723 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6724"><span class="lineNum">    6724 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6725"><span class="lineNum">    6725 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_CB&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6726"><span class="lineNum">    6726 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_CG2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6727"><span class="lineNum">    6727 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_OG1&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6728"><span class="lineNum">    6728 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6729"><span class="lineNum">    6729 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6730"><span class="lineNum">    6730 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6731"><span class="lineNum">    6731 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6732"><span class="lineNum">    6732 </span><span class="lineCov">         10 :   lcpomap[&quot;THR_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6733"><span class="lineNum">    6733 </span>            : </a>
+<a name="6734"><span class="lineNum">    6734 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6735"><span class="lineNum">    6735 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6736"><span class="lineNum">    6736 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6737"><span class="lineNum">    6737 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6738"><span class="lineNum">    6738 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6739"><span class="lineNum">    6739 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6740"><span class="lineNum">    6740 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CD1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6741"><span class="lineNum">    6741 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_NE1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="6742"><span class="lineNum">    6742 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CE2&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6743"><span class="lineNum">    6743 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CZ2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6744"><span class="lineNum">    6744 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CH2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6745"><span class="lineNum">    6745 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CZ3&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6746"><span class="lineNum">    6746 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CE3&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6747"><span class="lineNum">    6747 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_CD2&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6748"><span class="lineNum">    6748 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6749"><span class="lineNum">    6749 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6750"><span class="lineNum">    6750 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6751"><span class="lineNum">    6751 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6752"><span class="lineNum">    6752 </span><span class="lineCov">         10 :   lcpomap[&quot;TRP_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6753"><span class="lineNum">    6753 </span>            : </a>
+<a name="6754"><span class="lineNum">    6754 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_N&quot;] = { 1.65,  0.062577,  -0.017874,  -8.312e-05,  1.9849e-05};</span></a>
+<a name="6755"><span class="lineNum">    6755 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6756"><span class="lineNum">    6756 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6757"><span class="lineNum">    6757 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6758"><span class="lineNum">    6758 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="6759"><span class="lineNum">    6759 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6760"><span class="lineNum">    6760 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CD1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6761"><span class="lineNum">    6761 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6762"><span class="lineNum">    6762 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CZ&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6763"><span class="lineNum">    6763 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_OH&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="6764"><span class="lineNum">    6764 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CE2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6765"><span class="lineNum">    6765 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="6766"><span class="lineNum">    6766 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6767"><span class="lineNum">    6767 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6768"><span class="lineNum">    6768 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6769"><span class="lineNum">    6769 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6770"><span class="lineNum">    6770 </span><span class="lineCov">         10 :   lcpomap[&quot;TYR_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6771"><span class="lineNum">    6771 </span>            : </a>
+<a name="6772"><span class="lineNum">    6772 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_N&quot;] = { 1.65,  0.062577,  -0.017874,  -8.312e-05,  1.9849e-05};</span></a>
+<a name="6773"><span class="lineNum">    6773 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6774"><span class="lineNum">    6774 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="6775"><span class="lineNum">    6775 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6776"><span class="lineNum">    6776 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_CB&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="6777"><span class="lineNum">    6777 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_CG1&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6778"><span class="lineNum">    6778 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_CG2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="6779"><span class="lineNum">    6779 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_OC1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6780"><span class="lineNum">    6780 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_OC2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6781"><span class="lineNum">    6781 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_OT1&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6782"><span class="lineNum">    6782 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_OT2&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="6783"><span class="lineNum">    6783 </span><span class="lineCov">         10 :   lcpomap[&quot;VAL_OXT&quot;] = { 1.6,  0.88857,  -0.33421,  -0.0018683,  0.00049372};</span></a>
+<a name="6784"><span class="lineNum">    6784 </span>            : </a>
+<a name="6785"><span class="lineNum">    6785 </span>            :   // nucleic acids - WARNING: ONLY AMBER (OL3-rna/ol15-dna) FORMAT</a>
+<a name="6786"><span class="lineNum">    6786 </span>            : </a>
+<a name="6787"><span class="lineNum">    6787 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6788"><span class="lineNum">    6788 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C2&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6789"><span class="lineNum">    6789 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6790"><span class="lineNum">    6790 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6791"><span class="lineNum">    6791 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6792"><span class="lineNum">    6792 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6793"><span class="lineNum">    6793 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6794"><span class="lineNum">    6794 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6795"><span class="lineNum">    6795 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6796"><span class="lineNum">    6796 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6797"><span class="lineNum">    6797 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6798"><span class="lineNum">    6798 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6799"><span class="lineNum">    6799 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_N6&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6800"><span class="lineNum">    6800 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6801"><span class="lineNum">    6801 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6802"><span class="lineNum">    6802 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6803"><span class="lineNum">    6803 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6804"><span class="lineNum">    6804 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6805"><span class="lineNum">    6805 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6806"><span class="lineNum">    6806 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6807"><span class="lineNum">    6807 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6808"><span class="lineNum">    6808 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6809"><span class="lineNum">    6809 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6810"><span class="lineNum">    6810 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6811"><span class="lineNum">    6811 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6812"><span class="lineNum">    6812 </span><span class="lineCov">         10 :   lcpomap[&quot;A3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6813"><span class="lineNum">    6813 </span>            : </a>
+<a name="6814"><span class="lineNum">    6814 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6815"><span class="lineNum">    6815 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C2&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6816"><span class="lineNum">    6816 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6817"><span class="lineNum">    6817 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6818"><span class="lineNum">    6818 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6819"><span class="lineNum">    6819 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6820"><span class="lineNum">    6820 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6821"><span class="lineNum">    6821 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6822"><span class="lineNum">    6822 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6823"><span class="lineNum">    6823 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6824"><span class="lineNum">    6824 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6825"><span class="lineNum">    6825 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6826"><span class="lineNum">    6826 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_N6&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6827"><span class="lineNum">    6827 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6828"><span class="lineNum">    6828 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6829"><span class="lineNum">    6829 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6830"><span class="lineNum">    6830 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6831"><span class="lineNum">    6831 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6832"><span class="lineNum">    6832 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6833"><span class="lineNum">    6833 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6834"><span class="lineNum">    6834 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6835"><span class="lineNum">    6835 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6836"><span class="lineNum">    6836 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6837"><span class="lineNum">    6837 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6838"><span class="lineNum">    6838 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6839"><span class="lineNum">    6839 </span><span class="lineCov">         10 :   lcpomap[&quot;A5_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6840"><span class="lineNum">    6840 </span>            : </a>
+<a name="6841"><span class="lineNum">    6841 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6842"><span class="lineNum">    6842 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C2&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6843"><span class="lineNum">    6843 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6844"><span class="lineNum">    6844 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6845"><span class="lineNum">    6845 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6846"><span class="lineNum">    6846 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6847"><span class="lineNum">    6847 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6848"><span class="lineNum">    6848 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6849"><span class="lineNum">    6849 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6850"><span class="lineNum">    6850 </span><span class="lineCov">         10 :   lcpomap[&quot;A_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6851"><span class="lineNum">    6851 </span><span class="lineCov">         10 :   lcpomap[&quot;A_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6852"><span class="lineNum">    6852 </span><span class="lineCov">         10 :   lcpomap[&quot;A_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6853"><span class="lineNum">    6853 </span><span class="lineCov">         10 :   lcpomap[&quot;A_N6&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6854"><span class="lineNum">    6854 </span><span class="lineCov">         10 :   lcpomap[&quot;A_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6855"><span class="lineNum">    6855 </span><span class="lineCov">         10 :   lcpomap[&quot;A_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6856"><span class="lineNum">    6856 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6857"><span class="lineNum">    6857 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6858"><span class="lineNum">    6858 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6859"><span class="lineNum">    6859 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6860"><span class="lineNum">    6860 </span><span class="lineCov">         10 :   lcpomap[&quot;A_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6861"><span class="lineNum">    6861 </span><span class="lineCov">         10 :   lcpomap[&quot;A_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6862"><span class="lineNum">    6862 </span><span class="lineCov">         10 :   lcpomap[&quot;A_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6863"><span class="lineNum">    6863 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6864"><span class="lineNum">    6864 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6865"><span class="lineNum">    6865 </span><span class="lineCov">         10 :   lcpomap[&quot;A_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6866"><span class="lineNum">    6866 </span><span class="lineCov">         10 :   lcpomap[&quot;A_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6867"><span class="lineNum">    6867 </span>            : </a>
+<a name="6868"><span class="lineNum">    6868 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6869"><span class="lineNum">    6869 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6870"><span class="lineNum">    6870 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6871"><span class="lineNum">    6871 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6872"><span class="lineNum">    6872 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6873"><span class="lineNum">    6873 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6874"><span class="lineNum">    6874 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6875"><span class="lineNum">    6875 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6876"><span class="lineNum">    6876 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6877"><span class="lineNum">    6877 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6878"><span class="lineNum">    6878 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6879"><span class="lineNum">    6879 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_N4&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6880"><span class="lineNum">    6880 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="6881"><span class="lineNum">    6881 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6882"><span class="lineNum">    6882 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6883"><span class="lineNum">    6883 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6884"><span class="lineNum">    6884 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6885"><span class="lineNum">    6885 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6886"><span class="lineNum">    6886 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6887"><span class="lineNum">    6887 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6888"><span class="lineNum">    6888 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6889"><span class="lineNum">    6889 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6890"><span class="lineNum">    6890 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6891"><span class="lineNum">    6891 </span><span class="lineCov">         10 :   lcpomap[&quot;C3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6892"><span class="lineNum">    6892 </span>            : </a>
+<a name="6893"><span class="lineNum">    6893 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6894"><span class="lineNum">    6894 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6895"><span class="lineNum">    6895 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6896"><span class="lineNum">    6896 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6897"><span class="lineNum">    6897 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6898"><span class="lineNum">    6898 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6899"><span class="lineNum">    6899 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6900"><span class="lineNum">    6900 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6901"><span class="lineNum">    6901 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6902"><span class="lineNum">    6902 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6903"><span class="lineNum">    6903 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6904"><span class="lineNum">    6904 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_N4&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6905"><span class="lineNum">    6905 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="6906"><span class="lineNum">    6906 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6907"><span class="lineNum">    6907 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6908"><span class="lineNum">    6908 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6909"><span class="lineNum">    6909 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6910"><span class="lineNum">    6910 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6911"><span class="lineNum">    6911 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6912"><span class="lineNum">    6912 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6913"><span class="lineNum">    6913 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6914"><span class="lineNum">    6914 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6915"><span class="lineNum">    6915 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6916"><span class="lineNum">    6916 </span><span class="lineCov">         10 :   lcpomap[&quot;C5_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6917"><span class="lineNum">    6917 </span>            : </a>
+<a name="6918"><span class="lineNum">    6918 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6919"><span class="lineNum">    6919 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6920"><span class="lineNum">    6920 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6921"><span class="lineNum">    6921 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6922"><span class="lineNum">    6922 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6923"><span class="lineNum">    6923 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6924"><span class="lineNum">    6924 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6925"><span class="lineNum">    6925 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6926"><span class="lineNum">    6926 </span><span class="lineCov">         10 :   lcpomap[&quot;C_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6927"><span class="lineNum">    6927 </span><span class="lineCov">         10 :   lcpomap[&quot;C_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6928"><span class="lineNum">    6928 </span><span class="lineCov">         10 :   lcpomap[&quot;C_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6929"><span class="lineNum">    6929 </span><span class="lineCov">         10 :   lcpomap[&quot;C_N4&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6930"><span class="lineNum">    6930 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="6931"><span class="lineNum">    6931 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6932"><span class="lineNum">    6932 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6933"><span class="lineNum">    6933 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6934"><span class="lineNum">    6934 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6935"><span class="lineNum">    6935 </span><span class="lineCov">         10 :   lcpomap[&quot;C_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6936"><span class="lineNum">    6936 </span><span class="lineCov">         10 :   lcpomap[&quot;C_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6937"><span class="lineNum">    6937 </span><span class="lineCov">         10 :   lcpomap[&quot;C_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6938"><span class="lineNum">    6938 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6939"><span class="lineNum">    6939 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6940"><span class="lineNum">    6940 </span><span class="lineCov">         10 :   lcpomap[&quot;C_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6941"><span class="lineNum">    6941 </span><span class="lineCov">         10 :   lcpomap[&quot;C_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6942"><span class="lineNum">    6942 </span>            : </a>
+<a name="6943"><span class="lineNum">    6943 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6944"><span class="lineNum">    6944 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C2&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6945"><span class="lineNum">    6945 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6946"><span class="lineNum">    6946 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6947"><span class="lineNum">    6947 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6948"><span class="lineNum">    6948 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6949"><span class="lineNum">    6949 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6950"><span class="lineNum">    6950 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6951"><span class="lineNum">    6951 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6952"><span class="lineNum">    6952 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6953"><span class="lineNum">    6953 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6954"><span class="lineNum">    6954 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6955"><span class="lineNum">    6955 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_N6&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6956"><span class="lineNum">    6956 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6957"><span class="lineNum">    6957 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6958"><span class="lineNum">    6958 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6959"><span class="lineNum">    6959 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6960"><span class="lineNum">    6960 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6961"><span class="lineNum">    6961 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6962"><span class="lineNum">    6962 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6963"><span class="lineNum">    6963 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6964"><span class="lineNum">    6964 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6965"><span class="lineNum">    6965 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6966"><span class="lineNum">    6966 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6967"><span class="lineNum">    6967 </span><span class="lineCov">         10 :   lcpomap[&quot;DA3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6968"><span class="lineNum">    6968 </span>            : </a>
+<a name="6969"><span class="lineNum">    6969 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6970"><span class="lineNum">    6970 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C2&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6971"><span class="lineNum">    6971 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6972"><span class="lineNum">    6972 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6973"><span class="lineNum">    6973 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6974"><span class="lineNum">    6974 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6975"><span class="lineNum">    6975 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6976"><span class="lineNum">    6976 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6977"><span class="lineNum">    6977 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="6978"><span class="lineNum">    6978 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6979"><span class="lineNum">    6979 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6980"><span class="lineNum">    6980 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6981"><span class="lineNum">    6981 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_N6&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="6982"><span class="lineNum">    6982 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="6983"><span class="lineNum">    6983 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="6984"><span class="lineNum">    6984 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6985"><span class="lineNum">    6985 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6986"><span class="lineNum">    6986 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="6987"><span class="lineNum">    6987 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6988"><span class="lineNum">    6988 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6989"><span class="lineNum">    6989 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6990"><span class="lineNum">    6990 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="6991"><span class="lineNum">    6991 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6992"><span class="lineNum">    6992 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="6993"><span class="lineNum">    6993 </span><span class="lineCov">         10 :   lcpomap[&quot;DA5_P&quot;]   = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="6994"><span class="lineNum">    6994 </span>            : </a>
+<a name="6995"><span class="lineNum">    6995 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6996"><span class="lineNum">    6996 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C2&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="6997"><span class="lineNum">    6997 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="6998"><span class="lineNum">    6998 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="6999"><span class="lineNum">    6999 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7000"><span class="lineNum">    7000 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7001"><span class="lineNum">    7001 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7002"><span class="lineNum">    7002 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7003"><span class="lineNum">    7003 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7004"><span class="lineNum">    7004 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7005"><span class="lineNum">    7005 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7006"><span class="lineNum">    7006 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7007"><span class="lineNum">    7007 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_N6&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7008"><span class="lineNum">    7008 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7009"><span class="lineNum">    7009 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7010"><span class="lineNum">    7010 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7011"><span class="lineNum">    7011 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7012"><span class="lineNum">    7012 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7013"><span class="lineNum">    7013 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7014"><span class="lineNum">    7014 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7015"><span class="lineNum">    7015 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7016"><span class="lineNum">    7016 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7017"><span class="lineNum">    7017 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7018"><span class="lineNum">    7018 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7019"><span class="lineNum">    7019 </span><span class="lineCov">         10 :   lcpomap[&quot;DA_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7020"><span class="lineNum">    7020 </span>            : </a>
+<a name="7021"><span class="lineNum">    7021 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7022"><span class="lineNum">    7022 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7023"><span class="lineNum">    7023 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7024"><span class="lineNum">    7024 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7025"><span class="lineNum">    7025 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7026"><span class="lineNum">    7026 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7027"><span class="lineNum">    7027 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7028"><span class="lineNum">    7028 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7029"><span class="lineNum">    7029 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7030"><span class="lineNum">    7030 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7031"><span class="lineNum">    7031 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7032"><span class="lineNum">    7032 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_N4&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7033"><span class="lineNum">    7033 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7034"><span class="lineNum">    7034 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7035"><span class="lineNum">    7035 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7036"><span class="lineNum">    7036 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7037"><span class="lineNum">    7037 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7038"><span class="lineNum">    7038 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7039"><span class="lineNum">    7039 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7040"><span class="lineNum">    7040 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7041"><span class="lineNum">    7041 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7042"><span class="lineNum">    7042 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7043"><span class="lineNum">    7043 </span><span class="lineCov">         10 :   lcpomap[&quot;DC3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7044"><span class="lineNum">    7044 </span>            : </a>
+<a name="7045"><span class="lineNum">    7045 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7046"><span class="lineNum">    7046 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7047"><span class="lineNum">    7047 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7048"><span class="lineNum">    7048 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7049"><span class="lineNum">    7049 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7050"><span class="lineNum">    7050 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7051"><span class="lineNum">    7051 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7052"><span class="lineNum">    7052 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7053"><span class="lineNum">    7053 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7054"><span class="lineNum">    7054 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7055"><span class="lineNum">    7055 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7056"><span class="lineNum">    7056 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_N4&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7057"><span class="lineNum">    7057 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7058"><span class="lineNum">    7058 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7059"><span class="lineNum">    7059 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7060"><span class="lineNum">    7060 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7061"><span class="lineNum">    7061 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7062"><span class="lineNum">    7062 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7063"><span class="lineNum">    7063 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7064"><span class="lineNum">    7064 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7065"><span class="lineNum">    7065 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7066"><span class="lineNum">    7066 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7067"><span class="lineNum">    7067 </span><span class="lineCov">         10 :   lcpomap[&quot;DC5_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7068"><span class="lineNum">    7068 </span>            : </a>
+<a name="7069"><span class="lineNum">    7069 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7070"><span class="lineNum">    7070 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7071"><span class="lineNum">    7071 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7072"><span class="lineNum">    7072 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7073"><span class="lineNum">    7073 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7074"><span class="lineNum">    7074 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7075"><span class="lineNum">    7075 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7076"><span class="lineNum">    7076 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7077"><span class="lineNum">    7077 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7078"><span class="lineNum">    7078 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7079"><span class="lineNum">    7079 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7080"><span class="lineNum">    7080 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_N4&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7081"><span class="lineNum">    7081 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7082"><span class="lineNum">    7082 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7083"><span class="lineNum">    7083 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7084"><span class="lineNum">    7084 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7085"><span class="lineNum">    7085 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7086"><span class="lineNum">    7086 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7087"><span class="lineNum">    7087 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7088"><span class="lineNum">    7088 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7089"><span class="lineNum">    7089 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7090"><span class="lineNum">    7090 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7091"><span class="lineNum">    7091 </span><span class="lineCov">         10 :   lcpomap[&quot;DC_P&quot;]   = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7092"><span class="lineNum">    7092 </span>            : </a>
+<a name="7093"><span class="lineNum">    7093 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7094"><span class="lineNum">    7094 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7095"><span class="lineNum">    7095 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7096"><span class="lineNum">    7096 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7097"><span class="lineNum">    7097 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7098"><span class="lineNum">    7098 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7099"><span class="lineNum">    7099 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7100"><span class="lineNum">    7100 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7101"><span class="lineNum">    7101 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7102"><span class="lineNum">    7102 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7103"><span class="lineNum">    7103 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7104"><span class="lineNum">    7104 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_N2&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7105"><span class="lineNum">    7105 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7106"><span class="lineNum">    7106 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7107"><span class="lineNum">    7107 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7108"><span class="lineNum">    7108 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7109"><span class="lineNum">    7109 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7110"><span class="lineNum">    7110 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7111"><span class="lineNum">    7111 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O6&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7112"><span class="lineNum">    7112 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7113"><span class="lineNum">    7113 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7114"><span class="lineNum">    7114 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7115"><span class="lineNum">    7115 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7116"><span class="lineNum">    7116 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7117"><span class="lineNum">    7117 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7118"><span class="lineNum">    7118 </span><span class="lineCov">         10 :   lcpomap[&quot;DG3_P&quot;]   = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7119"><span class="lineNum">    7119 </span>            : </a>
+<a name="7120"><span class="lineNum">    7120 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7121"><span class="lineNum">    7121 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7122"><span class="lineNum">    7122 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7123"><span class="lineNum">    7123 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7124"><span class="lineNum">    7124 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7125"><span class="lineNum">    7125 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7126"><span class="lineNum">    7126 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7127"><span class="lineNum">    7127 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7128"><span class="lineNum">    7128 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7129"><span class="lineNum">    7129 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7130"><span class="lineNum">    7130 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7131"><span class="lineNum">    7131 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_N2&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7132"><span class="lineNum">    7132 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7133"><span class="lineNum">    7133 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7134"><span class="lineNum">    7134 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7135"><span class="lineNum">    7135 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7136"><span class="lineNum">    7136 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7137"><span class="lineNum">    7137 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7138"><span class="lineNum">    7138 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O6&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7139"><span class="lineNum">    7139 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7140"><span class="lineNum">    7140 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7141"><span class="lineNum">    7141 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7142"><span class="lineNum">    7142 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7143"><span class="lineNum">    7143 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7144"><span class="lineNum">    7144 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7145"><span class="lineNum">    7145 </span><span class="lineCov">         10 :   lcpomap[&quot;DG5_P&quot;]   = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7146"><span class="lineNum">    7146 </span>            : </a>
+<a name="7147"><span class="lineNum">    7147 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7148"><span class="lineNum">    7148 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7149"><span class="lineNum">    7149 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7150"><span class="lineNum">    7150 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7151"><span class="lineNum">    7151 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7152"><span class="lineNum">    7152 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7153"><span class="lineNum">    7153 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7154"><span class="lineNum">    7154 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7155"><span class="lineNum">    7155 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7156"><span class="lineNum">    7156 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7157"><span class="lineNum">    7157 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7158"><span class="lineNum">    7158 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_N2&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7159"><span class="lineNum">    7159 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7160"><span class="lineNum">    7160 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7161"><span class="lineNum">    7161 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7162"><span class="lineNum">    7162 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7163"><span class="lineNum">    7163 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7164"><span class="lineNum">    7164 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7165"><span class="lineNum">    7165 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O6&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7166"><span class="lineNum">    7166 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7167"><span class="lineNum">    7167 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7168"><span class="lineNum">    7168 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7169"><span class="lineNum">    7169 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7170"><span class="lineNum">    7170 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7171"><span class="lineNum">    7171 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7172"><span class="lineNum">    7172 </span><span class="lineCov">         10 :   lcpomap[&quot;DG_P&quot;]   = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7173"><span class="lineNum">    7173 </span>            : </a>
+<a name="7174"><span class="lineNum">    7174 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7175"><span class="lineNum">    7175 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7176"><span class="lineNum">    7176 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7177"><span class="lineNum">    7177 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7178"><span class="lineNum">    7178 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7179"><span class="lineNum">    7179 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7180"><span class="lineNum">    7180 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7181"><span class="lineNum">    7181 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7182"><span class="lineNum">    7182 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7183"><span class="lineNum">    7183 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_C7&quot;]  = { 1.7,  0.77887, -0.28063, -1.2968e-03, 3.9328e-04 };</span></a>
+<a name="7184"><span class="lineNum">    7184 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7185"><span class="lineNum">    7185 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7186"><span class="lineNum">    7186 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7187"><span class="lineNum">    7187 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7188"><span class="lineNum">    7188 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O4&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7189"><span class="lineNum">    7189 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7190"><span class="lineNum">    7190 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7191"><span class="lineNum">    7191 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7192"><span class="lineNum">    7192 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7193"><span class="lineNum">    7193 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7194"><span class="lineNum">    7194 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7195"><span class="lineNum">    7195 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7196"><span class="lineNum">    7196 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7197"><span class="lineNum">    7197 </span><span class="lineCov">         10 :   lcpomap[&quot;DT3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7198"><span class="lineNum">    7198 </span>            : </a>
+<a name="7199"><span class="lineNum">    7199 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7200"><span class="lineNum">    7200 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7201"><span class="lineNum">    7201 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7202"><span class="lineNum">    7202 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7203"><span class="lineNum">    7203 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7204"><span class="lineNum">    7204 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7205"><span class="lineNum">    7205 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7206"><span class="lineNum">    7206 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7207"><span class="lineNum">    7207 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7208"><span class="lineNum">    7208 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_C7&quot;]  = { 1.7,  0.77887, -0.28063, -1.2968e-03, 3.9328e-04 };</span></a>
+<a name="7209"><span class="lineNum">    7209 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7210"><span class="lineNum">    7210 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7211"><span class="lineNum">    7211 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7212"><span class="lineNum">    7212 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7213"><span class="lineNum">    7213 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O4&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7214"><span class="lineNum">    7214 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7215"><span class="lineNum">    7215 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7216"><span class="lineNum">    7216 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7217"><span class="lineNum">    7217 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7218"><span class="lineNum">    7218 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7219"><span class="lineNum">    7219 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7220"><span class="lineNum">    7220 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7221"><span class="lineNum">    7221 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7222"><span class="lineNum">    7222 </span><span class="lineCov">         10 :   lcpomap[&quot;DT5_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7223"><span class="lineNum">    7223 </span>            : </a>
+<a name="7224"><span class="lineNum">    7224 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7225"><span class="lineNum">    7225 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7226"><span class="lineNum">    7226 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C2'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7227"><span class="lineNum">    7227 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7228"><span class="lineNum">    7228 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7229"><span class="lineNum">    7229 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7230"><span class="lineNum">    7230 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7231"><span class="lineNum">    7231 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7232"><span class="lineNum">    7232 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7233"><span class="lineNum">    7233 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_C7&quot;]  = { 1.7,  0.77887, -0.28063, -1.2968e-03, 3.9328e-04 };</span></a>
+<a name="7234"><span class="lineNum">    7234 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7235"><span class="lineNum">    7235 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7236"><span class="lineNum">    7236 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7237"><span class="lineNum">    7237 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7238"><span class="lineNum">    7238 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O4&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7239"><span class="lineNum">    7239 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7240"><span class="lineNum">    7240 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7241"><span class="lineNum">    7241 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7242"><span class="lineNum">    7242 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7243"><span class="lineNum">    7243 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7244"><span class="lineNum">    7244 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7245"><span class="lineNum">    7245 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7246"><span class="lineNum">    7246 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7247"><span class="lineNum">    7247 </span><span class="lineCov">         10 :   lcpomap[&quot;DT_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7248"><span class="lineNum">    7248 </span>            : </a>
+<a name="7249"><span class="lineNum">    7249 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7250"><span class="lineNum">    7250 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C2&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7251"><span class="lineNum">    7251 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7252"><span class="lineNum">    7252 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7253"><span class="lineNum">    7253 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C4&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7254"><span class="lineNum">    7254 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7255"><span class="lineNum">    7255 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C5&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7256"><span class="lineNum">    7256 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7257"><span class="lineNum">    7257 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C6&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7258"><span class="lineNum">    7258 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_C8&quot;] = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7259"><span class="lineNum">    7259 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_N1&quot;] = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7260"><span class="lineNum">    7260 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_N2&quot;] = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7261"><span class="lineNum">    7261 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_N3&quot;] = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7262"><span class="lineNum">    7262 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_N7&quot;] = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7263"><span class="lineNum">    7263 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_N9&quot;] = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7264"><span class="lineNum">    7264 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7265"><span class="lineNum">    7265 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7266"><span class="lineNum">    7266 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7267"><span class="lineNum">    7267 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7268"><span class="lineNum">    7268 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O6&quot;] = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7269"><span class="lineNum">    7269 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7270"><span class="lineNum">    7270 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7271"><span class="lineNum">    7271 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7272"><span class="lineNum">    7272 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7273"><span class="lineNum">    7273 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7274"><span class="lineNum">    7274 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7275"><span class="lineNum">    7275 </span><span class="lineCov">         10 :   lcpomap[&quot;G3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7276"><span class="lineNum">    7276 </span>            : </a>
+<a name="7277"><span class="lineNum">    7277 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7278"><span class="lineNum">    7278 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C2&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7279"><span class="lineNum">    7279 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7280"><span class="lineNum">    7280 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7281"><span class="lineNum">    7281 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C4&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7282"><span class="lineNum">    7282 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7283"><span class="lineNum">    7283 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C5&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7284"><span class="lineNum">    7284 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7285"><span class="lineNum">    7285 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C6&quot;] = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7286"><span class="lineNum">    7286 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_C8&quot;] = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7287"><span class="lineNum">    7287 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_N1&quot;] = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7288"><span class="lineNum">    7288 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_N2&quot;] = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7289"><span class="lineNum">    7289 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_N3&quot;] = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7290"><span class="lineNum">    7290 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_N7&quot;] = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7291"><span class="lineNum">    7291 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_N9&quot;] = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7292"><span class="lineNum">    7292 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7293"><span class="lineNum">    7293 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7294"><span class="lineNum">    7294 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7295"><span class="lineNum">    7295 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7296"><span class="lineNum">    7296 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O6&quot;] = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7297"><span class="lineNum">    7297 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7298"><span class="lineNum">    7298 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7299"><span class="lineNum">    7299 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7300"><span class="lineNum">    7300 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7301"><span class="lineNum">    7301 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7302"><span class="lineNum">    7302 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7303"><span class="lineNum">    7303 </span><span class="lineCov">         10 :   lcpomap[&quot;G5_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7304"><span class="lineNum">    7304 </span>            : </a>
+<a name="7305"><span class="lineNum">    7305 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7306"><span class="lineNum">    7306 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7307"><span class="lineNum">    7307 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7308"><span class="lineNum">    7308 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7309"><span class="lineNum">    7309 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7310"><span class="lineNum">    7310 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7311"><span class="lineNum">    7311 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C5&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7312"><span class="lineNum">    7312 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7313"><span class="lineNum">    7313 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C6&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7314"><span class="lineNum">    7314 </span><span class="lineCov">         10 :   lcpomap[&quot;G_C8&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7315"><span class="lineNum">    7315 </span><span class="lineCov">         10 :   lcpomap[&quot;G_N1&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7316"><span class="lineNum">    7316 </span><span class="lineCov">         10 :   lcpomap[&quot;G_N2&quot;]  = { 1.65,  0.73511, -0.22116, -8.9148e-04, 2.523e-04 };</span></a>
+<a name="7317"><span class="lineNum">    7317 </span><span class="lineCov">         10 :   lcpomap[&quot;G_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7318"><span class="lineNum">    7318 </span><span class="lineCov">         10 :   lcpomap[&quot;G_N7&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7319"><span class="lineNum">    7319 </span><span class="lineCov">         10 :   lcpomap[&quot;G_N9&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7320"><span class="lineNum">    7320 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7321"><span class="lineNum">    7321 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7322"><span class="lineNum">    7322 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7323"><span class="lineNum">    7323 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7324"><span class="lineNum">    7324 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O6&quot;] = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7325"><span class="lineNum">    7325 </span><span class="lineCov">         10 :   lcpomap[&quot;G_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7326"><span class="lineNum">    7326 </span><span class="lineCov">         10 :   lcpomap[&quot;G_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7327"><span class="lineNum">    7327 </span><span class="lineCov">         10 :   lcpomap[&quot;G_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7328"><span class="lineNum">    7328 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7329"><span class="lineNum">    7329 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7330"><span class="lineNum">    7330 </span><span class="lineCov">         10 :   lcpomap[&quot;G_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7331"><span class="lineNum">    7331 </span><span class="lineCov">         10 :   lcpomap[&quot;G_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7332"><span class="lineNum">    7332 </span>            : </a>
+<a name="7333"><span class="lineNum">    7333 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7334"><span class="lineNum">    7334 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7335"><span class="lineNum">    7335 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7336"><span class="lineNum">    7336 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7337"><span class="lineNum">    7337 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7338"><span class="lineNum">    7338 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7339"><span class="lineNum">    7339 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7340"><span class="lineNum">    7340 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7341"><span class="lineNum">    7341 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7342"><span class="lineNum">    7342 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7343"><span class="lineNum">    7343 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7344"><span class="lineNum">    7344 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7345"><span class="lineNum">    7345 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7346"><span class="lineNum">    7346 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O3'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7347"><span class="lineNum">    7347 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O4&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7348"><span class="lineNum">    7348 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7349"><span class="lineNum">    7349 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7350"><span class="lineNum">    7350 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7351"><span class="lineNum">    7351 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7352"><span class="lineNum">    7352 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7353"><span class="lineNum">    7353 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7354"><span class="lineNum">    7354 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7355"><span class="lineNum">    7355 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7356"><span class="lineNum">    7356 </span><span class="lineCov">         10 :   lcpomap[&quot;U3_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7357"><span class="lineNum">    7357 </span>            : </a>
+<a name="7358"><span class="lineNum">    7358 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7359"><span class="lineNum">    7359 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7360"><span class="lineNum">    7360 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7361"><span class="lineNum">    7361 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7362"><span class="lineNum">    7362 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7363"><span class="lineNum">    7363 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7364"><span class="lineNum">    7364 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7365"><span class="lineNum">    7365 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7366"><span class="lineNum">    7366 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7367"><span class="lineNum">    7367 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7368"><span class="lineNum">    7368 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7369"><span class="lineNum">    7369 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7370"><span class="lineNum">    7370 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7371"><span class="lineNum">    7371 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7372"><span class="lineNum">    7372 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O4&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7373"><span class="lineNum">    7373 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7374"><span class="lineNum">    7374 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7375"><span class="lineNum">    7375 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7376"><span class="lineNum">    7376 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7377"><span class="lineNum">    7377 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7378"><span class="lineNum">    7378 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7379"><span class="lineNum">    7379 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7380"><span class="lineNum">    7380 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7381"><span class="lineNum">    7381 </span><span class="lineCov">         10 :   lcpomap[&quot;U5_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7382"><span class="lineNum">    7382 </span>            : </a>
+<a name="7383"><span class="lineNum">    7383 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C1'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7384"><span class="lineNum">    7384 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C2&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7385"><span class="lineNum">    7385 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C2'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7386"><span class="lineNum">    7386 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C3'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7387"><span class="lineNum">    7387 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C4&quot;]  = { 1.7,  0.070344, -0.019015, -2.2009e-05, 1.6875e-05 };</span></a>
+<a name="7388"><span class="lineNum">    7388 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C4'&quot;] = { 1.7,  0.23348, -0.072627, -2.0079e-04, 7.967e-05 };</span></a>
+<a name="7389"><span class="lineNum">    7389 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C5&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7390"><span class="lineNum">    7390 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C5'&quot;] = { 1.7,  0.56482, -0.19608, -1.0219e-03, 2.658e-04 };</span></a>
+<a name="7391"><span class="lineNum">    7391 </span><span class="lineCov">         10 :   lcpomap[&quot;U_C6&quot;]  = { 1.7,  0.51245, -0.15966, -1.9781e-04, 1.6392e-04 };</span></a>
+<a name="7392"><span class="lineNum">    7392 </span><span class="lineCov">         10 :   lcpomap[&quot;U_N1&quot;]  = { 1.65,  0.062577, -0.017874, -8.312e-05, 1.9849e-05 };</span></a>
+<a name="7393"><span class="lineNum">    7393 </span><span class="lineCov">         10 :   lcpomap[&quot;U_N3&quot;]  = { 1.65,  0.41102, -0.12254, -7.5448e-05, 1.1804e-04 };</span></a>
+<a name="7394"><span class="lineNum">    7394 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O2&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7395"><span class="lineNum">    7395 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O2'&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7396"><span class="lineNum">    7396 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O3'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7397"><span class="lineNum">    7397 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O4&quot;]  = { 1.6,  0.68563, -0.1868, -1.35573e-03, 2.3743e-04 };</span></a>
+<a name="7398"><span class="lineNum">    7398 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O4'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7399"><span class="lineNum">    7399 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O5'&quot;] = { 1.6,  0.49392, -0.16038, -1.5512e-04, 1.6453e-04 };</span></a>
+<a name="7400"><span class="lineNum">    7400 </span><span class="lineCov">         10 :   lcpomap[&quot;U_OP1&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7401"><span class="lineNum">    7401 </span><span class="lineCov">         10 :   lcpomap[&quot;U_OP2&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7402"><span class="lineNum">    7402 </span><span class="lineCov">         10 :   lcpomap[&quot;U_OP3&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7403"><span class="lineNum">    7403 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O1P&quot;] = { 1.6,  0.77914, -0.25262, -1.6056e-03, 3.5071e-04 };</span></a>
+<a name="7404"><span class="lineNum">    7404 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O2P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7405"><span class="lineNum">    7405 </span><span class="lineCov">         10 :   lcpomap[&quot;U_O3P&quot;] = { 1.6,  0.88857, -0.33421, -1.8683e-03, 4.9372e-04 };</span></a>
+<a name="7406"><span class="lineNum">    7406 </span><span class="lineCov">         10 :   lcpomap[&quot;U_P&quot;] = { 1.9,  0.03873,  -0.0089339, 8.3582e-06,  3.0381e-06};</span></a>
+<a name="7407"><span class="lineNum">    7407 </span>            : </a>
+<a name="7408"><span class="lineNum">    7408 </span><span class="lineCov">         10 :   return lcpomap;</span></a>
+<a name="7409"><span class="lineNum">    7409 </span>            : }</a>
+<a name="7410"><span class="lineNum">    7410 </span>            : </a>
+<a name="7411"><span class="lineNum">    7411 </span>            : // assigns LCPO parameters to each atom reading from database</a>
+<a name="7412"><span class="lineNum">    7412 </span><span class="lineCov">         10 : void SAXS::readLCPOparam(const std::vector&lt;std::vector&lt;std::string&gt; &gt; &amp;AtomResidueName, unsigned natoms)</span></a>
+<a name="7413"><span class="lineNum">    7413 </span>            : {</a>
+<a name="7414"><span class="lineNum">    7414 </span><span class="lineCov">         10 :   std::map&lt;std::string, std::vector&lt;double&gt; &gt; lcpomap = setupLCPOparam();</span></a>
+<a name="7415"><span class="lineNum">    7415 </span>            : </a>
+<a name="7416"><span class="lineNum">    7416 </span><span class="lineCov">      35476 :   for(unsigned i=0; i&lt;natoms; ++i)</span></a>
+<a name="7417"><span class="lineNum">    7417 </span>            :   {</a>
+<a name="7418"><span class="lineNum">    7418 </span><span class="lineCov">      35466 :     if ((AtomResidueName[0][i][0]=='O') || (AtomResidueName[0][i][0]=='N') || (AtomResidueName[0][i][0]=='C') || (AtomResidueName[0][i][0]=='S' || (AtomResidueName[0][i][0]=='P'))) {</span></a>
+<a name="7419"><span class="lineNum">    7419 </span><span class="lineCov">      16548 :       std::string identifier = AtomResidueName[1][i]+&quot;_&quot;+AtomResidueName[0][i];</span></a>
+<a name="7420"><span class="lineNum">    7420 </span><span class="lineCov">      16548 :       std::vector&lt;double&gt; LCPOparamVector = lcpomap.at(identifier);</span></a>
+<a name="7421"><span class="lineNum">    7421 </span>            :       double rs = 0.14;</a>
+<a name="7422"><span class="lineNum">    7422 </span><span class="lineCov">      16548 :       LCPOparam[i].push_back(LCPOparamVector[0]+rs*10.);</span></a>
+<a name="7423"><span class="lineNum">    7423 </span><span class="lineCov">      16548 :       LCPOparam[i].push_back(LCPOparamVector[1]);</span></a>
+<a name="7424"><span class="lineNum">    7424 </span><span class="lineCov">      16548 :       LCPOparam[i].push_back(LCPOparamVector[2]);</span></a>
+<a name="7425"><span class="lineNum">    7425 </span><span class="lineCov">      16548 :       LCPOparam[i].push_back(LCPOparamVector[3]);</span></a>
+<a name="7426"><span class="lineNum">    7426 </span><span class="lineCov">      16548 :       LCPOparam[i].push_back(LCPOparamVector[4]);</span></a>
+<a name="7427"><span class="lineNum">    7427 </span>            :     }</a>
+<a name="7428"><span class="lineNum">    7428 </span>            :   }</a>
+<a name="7429"><span class="lineNum">    7429 </span>            : </a>
+<a name="7430"><span class="lineNum">    7430 </span><span class="lineCov">      35476 :   for(unsigned i=0; i&lt;natoms; ++i) {</span></a>
+<a name="7431"><span class="lineNum">    7431 </span><span class="lineCov">      35466 :     if (LCPOparam[i].size()==0 ) {</span></a>
+<a name="7432"><span class="lineNum">    7432 </span><span class="lineCov">      18918 :       if ((AtomResidueName[0][i][0]=='O') || (AtomResidueName[0][i][0]=='N') || (AtomResidueName[0][i][0]=='C') || (AtomResidueName[0][i][0]=='S') || (AtomResidueName[0][i][0]=='P')) {</span></a>
+<a name="7433"><span class="lineNum">    7433 </span><span class="lineNoCov">          0 :         std::cout &lt;&lt; &quot;Could not find LCPO paramaters for atom &quot; &lt;&lt; AtomResidueName[0][i] &lt;&lt; &quot; of residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; std::endl;</span></a>
+<a name="7434"><span class="lineNum">    7434 </span><span class="lineNoCov">          0 :         error (&quot;missing LCPO parameters\n&quot;);</span></a>
+<a name="7435"><span class="lineNum">    7435 </span>            :       }</a>
+<a name="7436"><span class="lineNum">    7436 </span>            :     }</a>
+<a name="7437"><span class="lineNum">    7437 </span>            :   }</a>
+<a name="7438"><span class="lineNum">    7438 </span>            : </a>
+<a name="7439"><span class="lineNum">    7439 </span><span class="lineCov">         10 :   if (AtomResidueName[0][0] == &quot;N&quot;) {</span></a>
+<a name="7440"><span class="lineNum">    7440 </span><span class="lineCov">         10 :     LCPOparam[0][1] = 7.3511e-01;</span></a>
+<a name="7441"><span class="lineNum">    7441 </span><span class="lineCov">         10 :     LCPOparam[0][2] = -2.2116e-01;</span></a>
+<a name="7442"><span class="lineNum">    7442 </span><span class="lineCov">         10 :     LCPOparam[0][3] = -8.9148e-04;</span></a>
+<a name="7443"><span class="lineNum">    7443 </span><span class="lineCov">         10 :     LCPOparam[0][4] = 2.5230e-04;</span></a>
+<a name="7444"><span class="lineNum">    7444 </span>            :   }</a>
+<a name="7445"><span class="lineNum">    7445 </span>            : </a>
+<a name="7446"><span class="lineNum">    7446 </span><span class="lineCov">         10 :   if (AtomResidueName[0][natoms-1] == &quot;O&quot;) {</span></a>
+<a name="7447"><span class="lineNum">    7447 </span><span class="lineNoCov">          0 :     LCPOparam[natoms-1][1] = 8.8857e-01;</span></a>
+<a name="7448"><span class="lineNum">    7448 </span><span class="lineNoCov">          0 :     LCPOparam[natoms-1][2] = -3.3421e-01;</span></a>
+<a name="7449"><span class="lineNum">    7449 </span><span class="lineNoCov">          0 :     LCPOparam[natoms-1][3] = -1.8683e-03;</span></a>
+<a name="7450"><span class="lineNum">    7450 </span><span class="lineNoCov">          0 :     LCPOparam[natoms-1][4] = 4.9372e-04;</span></a>
+<a name="7451"><span class="lineNum">    7451 </span>            :   }</a>
+<a name="7452"><span class="lineNum">    7452 </span><span class="lineCov">         10 : }</span></a>
+<a name="7453"><span class="lineNum">    7453 </span>            : </a>
+<a name="7454"><span class="lineNum">    7454 </span>            : </a>
+<a name="7455"><span class="lineNum">    7455 </span>            : }//namespace isdb</a>
+<a name="7456"><span class="lineNum">    7456 </span>            : }//namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Select.cpp.func-sort-c.html b/coverage/isdb/Select.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f726e4d16d
--- /dev/null
+++ b/coverage/isdb/Select.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Select.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Select.cpp<span style="font-size: 80%;"> (<a href="Select.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Select.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#85">_ZN4PLMD4isdb6SelectC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#77">_ZN4PLMD4isdb12_GLOBAL__N_118SelectRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#85">_ZN4PLMD4isdb6SelectC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#79">_ZN4PLMD4isdb6Select16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#99">_ZN4PLMD4isdb6Select9calculateEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#77">_ZN4PLMD4isdb12_GLOBAL__N_118SelectRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#77">_ZN4PLMD4isdb12_GLOBAL__N_118SelectRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Select.cpp.func.html b/coverage/isdb/Select.cpp.func.html
new file mode 100644
index 0000000000..caa799c0e4
--- /dev/null
+++ b/coverage/isdb/Select.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Select.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Select.cpp<span style="font-size: 80%;"> (<a href="Select.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Select.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#77">_ZN4PLMD4isdb12_GLOBAL__N_118SelectRegisterMe796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#77">_ZN4PLMD4isdb12_GLOBAL__N_118SelectRegisterMe79C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#77">_ZN4PLMD4isdb12_GLOBAL__N_118SelectRegisterMe79D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#79">_ZN4PLMD4isdb6Select16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#99">_ZN4PLMD4isdb6Select9calculateEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#85">_ZN4PLMD4isdb6SelectC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Select.cpp.gcov.html#85">_ZN4PLMD4isdb6SelectC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Select.cpp.gcov.html b/coverage/isdb/Select.cpp.gcov.html
new file mode 100644
index 0000000000..48270d9b5d
--- /dev/null
+++ b/coverage/isdb/Select.cpp.gcov.html
@@ -0,0 +1,194 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Select.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Select.cpp<span style="font-size: 80%;"> (source / <a href="Select.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : /*</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : */</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;function/Function.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;function/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace isdb {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC ISDB_FUNCTION SELECT</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Selects an argument based on the value of a SELECTOR.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : You should read the documentation for \ref SELECTOR to understand this action better.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : In this example we use a simulated-tempering like approach activated by the \ref RESCALE action.</a>
+<a name="41"><span class="lineNum">      41 </span>            : For each value of the scale parameter, we perform an independent Parallel Bias Metadynamics</a>
+<a name="42"><span class="lineNum">      42 </span>            : simulation (see \ref PBMETAD). At each moment of the simulation, only one of the \ref PBMETAD</a>
+<a name="43"><span class="lineNum">      43 </span>            : actions is activated, based on the current value of the associated \ref SELECTOR.</a>
+<a name="44"><span class="lineNum">      44 </span>            : The \ref SELECT action can then be used to print out the value of the (active) \ref PBMETAD bias potential.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : ene:  ENERGY</a>
+<a name="48"><span class="lineNum">      48 </span>            : d: DISTANCE ATOMS=1,2</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : SELECTOR NAME=GAMMA VALUE=0</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : pbmetad0: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=0 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.0</a>
+<a name="53"><span class="lineNum">      53 </span>            : pbmetad1: PBMETAD ARG=d SELECTOR=GAMMA SELECTOR_ID=1 SIGMA=0.1 PACE=500 HEIGHT=1 BIASFACTOR=8 FILE=HILLS.1</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : RESCALE ...</a>
+<a name="56"><span class="lineNum">      56 </span>            : LABEL=res ARG=ene,pbmetad0.bias,pbmetad1.bias TEMP=300</a>
+<a name="57"><span class="lineNum">      57 </span>            : SELECTOR=GAMMA MAX_RESCALE=1.2 NOT_RESCALED=2 NBIN=2</a>
+<a name="58"><span class="lineNum">      58 </span>            : W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat</a>
+<a name="59"><span class="lineNum">      59 </span>            : ...</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : pbactive: SELECT ARG=pbmetad0.bias,pbmetad1.bias SELECTOR=GAMMA</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : PRINT ARG=pbactive STRIDE=100 FILE=COLVAR</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : //+ENDPLUMEDOC</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : class Select : public function::Function</a>
+<a name="70"><span class="lineNum">      70 </span>            : {</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::string selector_;</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : public:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit Select(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void calculate();</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="77"><span class="lineNum">      77 </span>            : };</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Select,&quot;SELECT&quot;)</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 : void Select::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   Function::registerKeywords(keys);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;SELECTOR&quot;,&quot;name of the variable used to select&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 : Select::Select(const ActionOptions&amp;ao):</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :   Action(ao), Function(ao)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // name of selector</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   parse(&quot;SELECTOR&quot;, selector_);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   log.printf(&quot;  select based on %s\n&quot;,selector_.c_str());</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          4 :   log &lt;&lt; &quot; Bibliography&quot; &lt;&lt; plumed.cite(&quot;Bonomi, Camilloni, Bioinformatics, 33, 3999 (2017)&quot;) &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          8 : void Select::calculate()</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : {</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          8 :   unsigned iselect = static_cast&lt;unsigned&gt;(plumed.passMap[selector_]);</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :   // check if iselect is smaller than the number of arguments</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          8 :   if(iselect&gt;=getNumberOfArguments()) error(&quot;the value of the SELECTOR is greater than the number of arguments!&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // put all the derivatives to zero</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         24 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) setDerivative(i, 0.0);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   // set value and derivative for selected argument</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 :   setValue(getArgument(iselect));</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          8 :   setDerivative(iselect, 1.0);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          8 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Selector.cpp.func-sort-c.html b/coverage/isdb/Selector.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c7889bfd54
--- /dev/null
+++ b/coverage/isdb/Selector.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Selector.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Selector.cpp<span style="font-size: 80%;"> (<a href="Selector.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Selector.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#67">_ZN4PLMD4isdb8Selector5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#66">_ZN4PLMD4isdb8Selector9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#70">_ZN4PLMD4isdb12_GLOBAL__N_120SelectorRegisterMe726createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#78">_ZN4PLMD4isdb8SelectorC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#72">_ZN4PLMD4isdb8Selector16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#70">_ZN4PLMD4isdb12_GLOBAL__N_120SelectorRegisterMe72C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#70">_ZN4PLMD4isdb12_GLOBAL__N_120SelectorRegisterMe72D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Selector.cpp.func.html b/coverage/isdb/Selector.cpp.func.html
new file mode 100644
index 0000000000..64c880605b
--- /dev/null
+++ b/coverage/isdb/Selector.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Selector.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Selector.cpp<span style="font-size: 80%;"> (<a href="Selector.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Selector.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#70">_ZN4PLMD4isdb12_GLOBAL__N_120SelectorRegisterMe726createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#70">_ZN4PLMD4isdb12_GLOBAL__N_120SelectorRegisterMe72C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#70">_ZN4PLMD4isdb12_GLOBAL__N_120SelectorRegisterMe72D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#72">_ZN4PLMD4isdb8Selector16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#67">_ZN4PLMD4isdb8Selector5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#66">_ZN4PLMD4isdb8Selector9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Selector.cpp.gcov.html#78">_ZN4PLMD4isdb8SelectorC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/Selector.cpp.gcov.html b/coverage/isdb/Selector.cpp.gcov.html
new file mode 100644
index 0000000000..a79ec374ca
--- /dev/null
+++ b/coverage/isdb/Selector.cpp.gcov.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb/Selector.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">isdb</a> - Selector.cpp<span style="font-size: 80%;"> (source / <a href="Selector.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace isdb {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC ISDB_GENERIC SELECTOR</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Defines a variable (of the type double) inside the PLUMED code that can be used and modified by other actions.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : A \ref SELECTOR can be used for example to activate or modify a bias based on its current value.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \par Examples</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : A typical example is the simulated-tempering like approach activated by \ref RESCALE.</a>
+<a name="39"><span class="lineNum">      39 </span>            : In this example the total potential energy of the system is scaled</a>
+<a name="40"><span class="lineNum">      40 </span>            : by a parameter defined on a grid of dimension NBIN in the range from 1 to MAX_RESCALE.</a>
+<a name="41"><span class="lineNum">      41 </span>            : The value of the scaling parameter is determined by the current value of the \ref SELECTOR GAMMA.</a>
+<a name="42"><span class="lineNum">      42 </span>            : The value of the \ref SELECTOR is updated by a MC protocol inside the \ref RESCALE class.</a>
+<a name="43"><span class="lineNum">      43 </span>            : A well-tempered metadynamics potential is used to enhance sampling in the \ref SELECTOR space.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : ene:  ENERGY</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : SELECTOR NAME=GAMMA VALUE=0</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : RESCALE ...</a>
+<a name="51"><span class="lineNum">      51 </span>            : LABEL=res ARG=ene TEMP=300</a>
+<a name="52"><span class="lineNum">      52 </span>            : SELECTOR=GAMMA MAX_RESCALE=1.2 NBIN=2</a>
+<a name="53"><span class="lineNum">      53 </span>            : W0=1000 BIASFACTOR=100.0 BSTRIDE=2000 BFILE=bias.dat</a>
+<a name="54"><span class="lineNum">      54 </span>            : ...</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT FILE=COLVAR ARG=* STRIDE=100</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : */</a>
+<a name="60"><span class="lineNum">      60 </span>            : //+ENDPLUMEDOC</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : class Selector:</a>
+<a name="63"><span class="lineNum">      63 </span>            :   public Action</a>
+<a name="64"><span class="lineNum">      64 </span>            : {</a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="67"><span class="lineNum">      67 </span>            :   explicit Selector(const ActionOptions&amp;ao);</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Selector,&quot;SELECTOR&quot;)</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          4 : void Selector::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          4 :   Action::registerKeywords(keys);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;NAME&quot;,&quot;name of the SELECTOR&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;VALUE&quot;,&quot;set (initial) value of the SELECTOR&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 : }</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          2 : Selector::Selector(const ActionOptions&amp;ao):</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          2 :   Action(ao)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : {</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::string name;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          2 :   parse(&quot;NAME&quot;, name);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   double value;</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :   parse(&quot;VALUE&quot;, value);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          2 :   plumed.passMap[name] = value;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/index-sort-f.html b/coverage/isdb/index-sort-f.html
new file mode 100644
index 0000000000..cf84fd360c
--- /dev/null
+++ b/coverage/isdb/index-sort-f.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - isdb</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8645</td>
+            <td class="headerCovTableEntry">10595</td>
+            <td class="headerCovTableEntryMed">81.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">198</td>
+            <td class="headerCovTableEntry">243</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Rescale.cpp.gcov.html">Rescale.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="11.6%"><img src="../snow.png" width=88 height=10 alt="11.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">11.6&nbsp;%</td>
+      <td class="coverNumLo">22 / 190</td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Selector.cpp.gcov.html">Selector.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Caliber.cpp.gcov.html">Caliber.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 146</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EMMI.cpp.gcov.html">EMMI.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.5%"><img src="../snow.png" width=24 height=10 alt="75.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.5&nbsp;%</td>
+      <td class="coverNumMed">593 / 785</td>
+      <td class="coverPerMed">76.2&nbsp;%</td>
+      <td class="coverNumMed">32 / 42</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetainferenceBase.cpp.gcov.html">MetainferenceBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.2%"><img src="../snow.png" width=15 height=10 alt="85.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.2&nbsp;%</td>
+      <td class="coverNumMed">757 / 888</td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">23 / 28</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RDC.cpp.gcov.html">RDC.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.0%"><img src="../snow.png" width=6 height=10 alt="94.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.0&nbsp;%</td>
+      <td class="coverNumHi">171 / 182</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FretEfficiency.cpp.gcov.html">FretEfficiency.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">36 / 38</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Select.cpp.gcov.html">Select.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NOE.cpp.gcov.html">NOE.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">102 / 104</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Jcoupling.cpp.gcov.html">Jcoupling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.0%"><img src="../snow.png" width=7 height=10 alt="93.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">160 / 172</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PRE.cpp.gcov.html">PRE.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.2%"><img src="../snow.png" width=8 height=10 alt="92.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.2&nbsp;%</td>
+      <td class="coverNumHi">119 / 129</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Metainference.cpp.gcov.html">Metainference.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.2%"><img src="../snow.png" width=16 height=10 alt="84.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.2&nbsp;%</td>
+      <td class="coverNumMed">741 / 880</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SAXS.cpp.gcov.html">SAXS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.1%"><img src="../snow.png" width=20 height=10 alt="80.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.1&nbsp;%</td>
+      <td class="coverNumMed">4808 / 6005</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CS2Backbone.cpp.gcov.html">CS2Backbone.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">918 / 969</td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetainferenceBase.h.gcov.html">MetainferenceBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">70 / 72</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/index-sort-l.html b/coverage/isdb/index-sort-l.html
new file mode 100644
index 0000000000..78adde9b05
--- /dev/null
+++ b/coverage/isdb/index-sort-l.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - isdb</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8645</td>
+            <td class="headerCovTableEntry">10595</td>
+            <td class="headerCovTableEntryMed">81.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">198</td>
+            <td class="headerCovTableEntry">243</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Rescale.cpp.gcov.html">Rescale.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="11.6%"><img src="../snow.png" width=88 height=10 alt="11.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">11.6&nbsp;%</td>
+      <td class="coverNumLo">22 / 190</td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EMMI.cpp.gcov.html">EMMI.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.5%"><img src="../snow.png" width=24 height=10 alt="75.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.5&nbsp;%</td>
+      <td class="coverNumMed">593 / 785</td>
+      <td class="coverPerMed">76.2&nbsp;%</td>
+      <td class="coverNumMed">32 / 42</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Caliber.cpp.gcov.html">Caliber.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 146</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SAXS.cpp.gcov.html">SAXS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.1%"><img src="../snow.png" width=20 height=10 alt="80.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.1&nbsp;%</td>
+      <td class="coverNumMed">4808 / 6005</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Metainference.cpp.gcov.html">Metainference.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.2%"><img src="../snow.png" width=16 height=10 alt="84.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.2&nbsp;%</td>
+      <td class="coverNumMed">741 / 880</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetainferenceBase.cpp.gcov.html">MetainferenceBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.2%"><img src="../snow.png" width=15 height=10 alt="85.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.2&nbsp;%</td>
+      <td class="coverNumMed">757 / 888</td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">23 / 28</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Selector.cpp.gcov.html">Selector.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PRE.cpp.gcov.html">PRE.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.2%"><img src="../snow.png" width=8 height=10 alt="92.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.2&nbsp;%</td>
+      <td class="coverNumHi">119 / 129</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Jcoupling.cpp.gcov.html">Jcoupling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.0%"><img src="../snow.png" width=7 height=10 alt="93.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">160 / 172</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RDC.cpp.gcov.html">RDC.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.0%"><img src="../snow.png" width=6 height=10 alt="94.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.0&nbsp;%</td>
+      <td class="coverNumHi">171 / 182</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FretEfficiency.cpp.gcov.html">FretEfficiency.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">36 / 38</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CS2Backbone.cpp.gcov.html">CS2Backbone.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">918 / 969</td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetainferenceBase.h.gcov.html">MetainferenceBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">70 / 72</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NOE.cpp.gcov.html">NOE.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">102 / 104</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Select.cpp.gcov.html">Select.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/isdb/index.html b/coverage/isdb/index.html
new file mode 100644
index 0000000000..2edeb3bb4f
--- /dev/null
+++ b/coverage/isdb/index.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - isdb</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - isdb</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8645</td>
+            <td class="headerCovTableEntry">10595</td>
+            <td class="headerCovTableEntryMed">81.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">198</td>
+            <td class="headerCovTableEntry">243</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CS2Backbone.cpp.gcov.html">CS2Backbone.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">918 / 969</td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">25 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Caliber.cpp.gcov.html">Caliber.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 146</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EMMI.cpp.gcov.html">EMMI.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.5%"><img src="../snow.png" width=24 height=10 alt="75.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.5&nbsp;%</td>
+      <td class="coverNumMed">593 / 785</td>
+      <td class="coverPerMed">76.2&nbsp;%</td>
+      <td class="coverNumMed">32 / 42</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FretEfficiency.cpp.gcov.html">FretEfficiency.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">36 / 38</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Jcoupling.cpp.gcov.html">Jcoupling.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.0%"><img src="../snow.png" width=7 height=10 alt="93.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">160 / 172</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Metainference.cpp.gcov.html">Metainference.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.2%"><img src="../snow.png" width=16 height=10 alt="84.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.2&nbsp;%</td>
+      <td class="coverNumMed">741 / 880</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 30</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetainferenceBase.cpp.gcov.html">MetainferenceBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.2%"><img src="../snow.png" width=15 height=10 alt="85.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.2&nbsp;%</td>
+      <td class="coverNumMed">757 / 888</td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">23 / 28</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetainferenceBase.h.gcov.html">MetainferenceBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">70 / 72</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NOE.cpp.gcov.html">NOE.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.1%"><img src="../snow.png" width=2 height=10 alt="98.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.1&nbsp;%</td>
+      <td class="coverNumHi">102 / 104</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PRE.cpp.gcov.html">PRE.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.2%"><img src="../snow.png" width=8 height=10 alt="92.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.2&nbsp;%</td>
+      <td class="coverNumHi">119 / 129</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RDC.cpp.gcov.html">RDC.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.0%"><img src="../snow.png" width=6 height=10 alt="94.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.0&nbsp;%</td>
+      <td class="coverNumHi">171 / 182</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Rescale.cpp.gcov.html">Rescale.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=12 height=10 alt="11.6%"><img src="../snow.png" width=88 height=10 alt="11.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">11.6&nbsp;%</td>
+      <td class="coverNumLo">22 / 190</td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SAXS.cpp.gcov.html">SAXS.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.1%"><img src="../snow.png" width=20 height=10 alt="80.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.1&nbsp;%</td>
+      <td class="coverNumMed">4808 / 6005</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">22 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Select.cpp.gcov.html">Select.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Selector.cpp.gcov.html">Selector.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">12 / 14</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/logmfd/LogMFD.cpp.func-sort-c.html b/coverage/logmfd/LogMFD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c2689500c2
--- /dev/null
+++ b/coverage/logmfd/LogMFD.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - logmfd/LogMFD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">logmfd</a> - LogMFD.cpp<span style="font-size: 80%;"> (<a href="LogMFD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">372</td>
+            <td class="headerCovTableEntryMed">87.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LogMFD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#559">_ZN4PLMD6logmfd6LogMFDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#456">_ZN4PLMD6logmfd12_GLOBAL__N_119LogMFDRegisterMe4586createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#559">_ZN4PLMD6logmfd6LogMFDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#461">_ZN4PLMD6logmfd6LogMFD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1105">_ZN4PLMD6logmfd6LogMFD8updateVSEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1032">_ZN4PLMD6logmfd6LogMFD9updateNVEEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1053">_ZN4PLMD6logmfd6LogMFD9updateNVTEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1135">_ZN4PLMD6logmfd6LogMFD10updateWorkEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1148">_ZN4PLMD6logmfd6LogMFD13calcMeanForceEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1241">_ZN4PLMD6logmfd6LogMFD8calcClogEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1214">_ZN4PLMD6logmfd6LogMFD8calcFlogEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1201">_ZN4PLMD6logmfd6LogMFD8calcEkinEv</a></td>
+              <td class="coverFnHi">83</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#932">_ZN4PLMD6logmfd6LogMFD6updateEv</a></td>
+              <td class="coverFnHi">1500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#765">_ZN4PLMD6logmfd6LogMFD9calculateEv</a></td>
+              <td class="coverFnHi">1500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#456">_ZN4PLMD6logmfd12_GLOBAL__N_119LogMFDRegisterMe458C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#456">_ZN4PLMD6logmfd12_GLOBAL__N_119LogMFDRegisterMe458D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/logmfd/LogMFD.cpp.func.html b/coverage/logmfd/LogMFD.cpp.func.html
new file mode 100644
index 0000000000..b765b583a2
--- /dev/null
+++ b/coverage/logmfd/LogMFD.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - logmfd/LogMFD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">logmfd</a> - LogMFD.cpp<span style="font-size: 80%;"> (<a href="LogMFD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">372</td>
+            <td class="headerCovTableEntryMed">87.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LogMFD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#456">_ZN4PLMD6logmfd12_GLOBAL__N_119LogMFDRegisterMe4586createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#456">_ZN4PLMD6logmfd12_GLOBAL__N_119LogMFDRegisterMe458C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#456">_ZN4PLMD6logmfd12_GLOBAL__N_119LogMFDRegisterMe458D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1135">_ZN4PLMD6logmfd6LogMFD10updateWorkEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1148">_ZN4PLMD6logmfd6LogMFD13calcMeanForceEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#461">_ZN4PLMD6logmfd6LogMFD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#932">_ZN4PLMD6logmfd6LogMFD6updateEv</a></td>
+              <td class="coverFnHi">1500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1241">_ZN4PLMD6logmfd6LogMFD8calcClogEv</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1201">_ZN4PLMD6logmfd6LogMFD8calcEkinEv</a></td>
+              <td class="coverFnHi">83</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1214">_ZN4PLMD6logmfd6LogMFD8calcFlogEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1105">_ZN4PLMD6logmfd6LogMFD8updateVSEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#765">_ZN4PLMD6logmfd6LogMFD9calculateEv</a></td>
+              <td class="coverFnHi">1500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1032">_ZN4PLMD6logmfd6LogMFD9updateNVEEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#1053">_ZN4PLMD6logmfd6LogMFD9updateNVTEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#559">_ZN4PLMD6logmfd6LogMFDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LogMFD.cpp.gcov.html#559">_ZN4PLMD6logmfd6LogMFDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/logmfd/LogMFD.cpp.gcov.html b/coverage/logmfd/LogMFD.cpp.gcov.html
new file mode 100644
index 0000000000..b9900f1547
--- /dev/null
+++ b/coverage/logmfd/LogMFD.cpp.gcov.html
@@ -0,0 +1,1324 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - logmfd/LogMFD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">logmfd</a> - LogMFD.cpp<span style="font-size: 80%;"> (source / <a href="LogMFD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">372</td>
+            <td class="headerCovTableEntryMed">87.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019</a>
+<a name="3"><span class="lineNum">       3 </span>            : National Institute of Advanced Industrial Science and Technology (AIST), Japan.</a>
+<a name="4"><span class="lineNum">       4 </span>            : This file contains module for LogMFD method proposed by Tetsuya Morishita(AIST).</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : The LogMFD module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            : (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            : The LogMFD module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : //+PLUMEDOC LOGMFDMOD_BIAS LOGMFD</a>
+<a name="21"><span class="lineNum">      21 </span>            : /*</a>
+<a name="22"><span class="lineNum">      22 </span>            : Used to perform LogMFD, LogPD, and TAMD/d-AFED.</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : \section LogMFD LogMFD</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : Consider a physical system of \f$N_q\f$ particles, for which the Hamiltonian is given as</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : \f[</a>
+<a name="29"><span class="lineNum">      29 </span>            :   {H_{\rm MD}}\left( {\bf{\Gamma}} \right) = \sum\limits_{j = 1}^{{N_q}} {\frac{{{\bf{p}}_j^2}}{{2{m_j}}}}  + \Phi \left( {\bf{q}} \right)</a>
+<a name="30"><span class="lineNum">      30 </span>            : \f]</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : where \f${\bf q}_j\f$, \f${\bf p}_j\f$ (\f$\bf{\Gamma}={\bf q},{\bf p}\f$), and \f$m_j\f$ are the position, momentum, and mass of particle \f$j\f$ respectively,</a>
+<a name="33"><span class="lineNum">      33 </span>            : and \f$\Phi\f$ is the potential energy function for \f${\bf q}\f$.</a>
+<a name="34"><span class="lineNum">      34 </span>            : The free energy \f$F({\bf X})\f$ as a function of a set of \f$N\f$ collective variables (CVs) is given as</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \f{eqnarray*}{</a>
+<a name="37"><span class="lineNum">      37 </span>            :   F\left( {{\bf X}} \right) &amp;=&amp;  - {k_B}T\log \int {\exp \left[ { - \beta {H_{\rm MD}}} \right]\prod\limits_{i = 1}^N {\delta \left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)} d{\bf{\Gamma }}} \\</a>
+<a name="38"><span class="lineNum">      38 </span>            :   &amp;\simeq&amp;  - {k_B}T\log \int {\exp \left[ { - \beta \left\{ {{H_{\rm MD}} + \sum\limits_i^N {\frac{{{K_i}}}{2}{{\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)}^2}} } \right\}} \right]} d{\bf{\Gamma }}</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f}</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : where \f$\bf{s}\f$ are the CVs, \f$k_B\f$ is Boltzmann constant, \f$\beta=1/k_BT\f$,</a>
+<a name="42"><span class="lineNum">      42 </span>            : and \f$K_i\f$ is the spring constant which is large enough to invoke</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \f[</a>
+<a name="45"><span class="lineNum">      45 </span>            :  \delta \left( x \right) = \lim_{k \to \infty } \sqrt {\beta k/2\pi} \exp \left( -\beta kx^2/2 \right)</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : In mean-force dynamics, \f${\bf X}\f$ are treated as fictitious dynamical variables, which are associated with the following Hamiltonian,</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \f[</a>
+<a name="51"><span class="lineNum">      51 </span>            :  {H_{\rm log}} = \sum\limits_{i = 1}^N {\frac{{P_{{X_i}}^2}}{{2{M_i}}} + \Psi \left( {{\bf X}} \right)}</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f]</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : where \f${P_{{X_i}}}\f$  and \f$M_i\f$ are the momentum and mass of \f$X_i\f$, respectively, and \f$\Psi\f$ is the potential function for \f${\bf X}\f$.</a>
+<a name="55"><span class="lineNum">      55 </span>            : We assume that \f$\Psi\f$ is a functional of \f$F({\bf X})\f$; \f$Ψ[F({\bf X})]\f$. The simplest form of \f$\Psi\f$ is \f$\Psi = F({\bf X})\f$,</a>
+<a name="56"><span class="lineNum">      56 </span>            : which corresponds to TAMD/d-AFED \cite AbramsJ2008, \cite Maragliano2006 (or the extended Lagrangian dynamics in the limit of the adiabatic decoupling between \f$\bf{q}\f$ and \f${\bf X}\f$).</a>
+<a name="57"><span class="lineNum">      57 </span>            :  In the case of LogMFD, the following form of \f$\Psi\f$ is introduced \cite MorishitaLogMFD;</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \f[</a>
+<a name="61"><span class="lineNum">      61 </span>            :   {\Psi _{\rm log}}\left( {{\bf X}} \right) = \gamma \log \left[ {\alpha F\left( {{\bf X}} \right) + 1} \right]</a>
+<a name="62"><span class="lineNum">      62 </span>            : \f]</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : where \f$\alpha\f$ (ALPHA) and \f$\gamma\f$ (GAMMA) are positive parameters. The logarithmic form of \f$\Psi_{\rm log}\f$ ensures the dynamics of \f${\bf X}\f$ on a much smoother energy surface [i.e., \f$\Psi_{\rm log}({\bf X})\f$] than \f$F({\bf X})\f$, thus enhancing the sampling in the \f${\bf X}\f$-space. The parameters \f$\alpha\f$ and \f$\gamma\f$ determine the degree of flatness of \f$\Psi_{\rm log}\f$, but adjusting only \f$\alpha\f$ is normally sufficient to have a relatively flat surface (with keeping the relation \f$\gamma=1/\alpha\f$).</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : The equation of motion for \f$X_i\f$ in LogMFD (no thermostat) is</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \f[</a>
+<a name="69"><span class="lineNum">      69 </span>            :  {M_i}{\ddot X_i} =  - \left( {\frac{{\alpha \gamma }}{{\alpha F + 1}}} \right)\frac{{\partial F}}{{\partial {X_i}}}</a>
+<a name="70"><span class="lineNum">      70 </span>            : \f]</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : where \f$-\partial F/\partial X_i\f$  is evaluated as a canonical average under the condition that \f${\bf X}\f$ is fixed;</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \f{eqnarray*}{</a>
+<a name="75"><span class="lineNum">      75 </span>            :  - \frac{{\partial F}}{{\partial {X_i}}} &amp;\simeq&amp; \frac{1}{Z}\int {{K_i}\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)\exp \left[ { - \beta \left\{ {{H_{\rm MD}} + \sum\limits_i^N {\frac{{{K_i}}}{2}{{\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)}^2}} } \right\}} \right]} d{\bf{\Gamma }}\\</a>
+<a name="76"><span class="lineNum">      76 </span>            :  &amp;\equiv&amp; {\left\langle {{K_i}\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)} \right\rangle _{{\bf X}}}</a>
+<a name="77"><span class="lineNum">      77 </span>            : \f}</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : where</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \f[</a>
+<a name="82"><span class="lineNum">      82 </span>            :  Z = \int {\exp \left[ { - \beta \left\{ {{H_{\rm MD}} + \sum\limits_i^N {\frac{{{K_i}}}{2}{{\left( {{s_i}\left( {{\bf q}} \right) - {X_i}} \right)}^2}} } \right\}} \right]} d{\bf{\Gamma }}</a>
+<a name="83"><span class="lineNum">      83 </span>            : \f]</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The mean-force (MF) is practically evaluated by performing a shot-time canonical MD run of \f$N_m\f$ steps each time \f${\bf X}\f$ is updated according to the equation of motion for \f${\bf X}\f$.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : If the canonical average for the MF is effectively converged, the dynamical variables \f${\bf q}\f$ and \f${\bf X}\f$ are decoupled and they evolve adiabatically, which can be exploited for the on-the-fly evaluation of \f$F({\bf X})\f$. I.e., \f$H_{\rm log}\f$ should be a constant of motion in this case, thus \f$F({\bf X})\f$ can be evaluated each time \f${\bf X}\f$ is updated as</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \f[</a>
+<a name="91"><span class="lineNum">      91 </span>            :  F\left( {{{\bf X}}\left( t \right)} \right) = \frac{1}{\alpha} \left[</a>
+<a name="92"><span class="lineNum">      92 </span>            :   \exp \frac{1}{\gamma} \left\{ \left( H_{\rm log} - \sum_i \frac{P_{X_i}^2}{2M_i} \right) \right\} - 1 \right]</a>
+<a name="93"><span class="lineNum">      93 </span>            : \f]</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : This means that \f$F({\bf X})\f$ can be constructed without post processing (on-the-fly free energy reconstruction). Note that the on-the-fly free energy reconstruction is also possible in TAMD/d-AFED if the Hamiltonian-like conserved quantity is available (e.g., the Nose-Hoover type dynamics).</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : \section LogPD LogPD</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : The accuracy in the MF is critical to the on-the-fly free energy reconstruction. To improve the evaluation of the MF, parallel-dynamics (PD) is incorporated into LogMFD, leading to logarithmic parallel-dynamics (LogPD) \cite MorishitaLogPD.</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : In PD, the MF is evaluated by a non-equilibrium path-ensemble based on the Crooks-Jarzynski non-equilibrium work relation. To this end, multiple replicas of the MD system which run in parallel are introduced. The CVs [\f${\bf s}({\bf q})\f$] in each replica is restrained to the same value of \f${\bf X}(t)\f$. A canonical MD run with \f$N_m\f$ steps is performed in each replica, then the MF on \f$X_i\f$ is evaluated using the MD trajectories from all replicas.</a>
+<a name="107"><span class="lineNum">     107 </span>            : The MF is practically calculated as</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : \f[</a>
+<a name="111"><span class="lineNum">     111 </span>            :  - \frac{{\partial F}}{{\partial {X_i}}} = \sum\limits_{k = 1}^{{N_r}} {{W_k}} \sum\limits_{n = 1}^{{N_m}} {\frac{1}{{{N_m}}}{K_i}\left[ {{s_i}\left( {{{\bf q}}_n^k} \right) - {X_i}} \right]}</a>
+<a name="112"><span class="lineNum">     112 </span>            : \f]</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : where \f${\bf q}^k_n\f$  indicates the \f${\bf q}\f$-configuration at time step \f$n\f$ in the \f$N_m\f$-step shot-time MD run in the \f$k\f$th replica among \f$N_r\f$ replicas. \f$W_k\f$ is given as</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : \f[</a>
+<a name="119"><span class="lineNum">     119 </span>            :  {W_k} = \frac{{{e^{ - \beta {w_k}\left( t \right)}}}}{{\sum\limits_{k=1}^{{N_r}} {{e^{ - \beta {w_k}\left( t \right)}}} }}</a>
+<a name="120"><span class="lineNum">     120 </span>            : \f]</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : where</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : \f[</a>
+<a name="127"><span class="lineNum">     127 </span>            :  {w_k}\left( t \right) = \int\limits_{{X_0}}^{X\left( t \right)} {\sum\limits_{i=1}^N {\frac{{\partial H_{\rm MD}^k}}{{\partial {X_i}}}d{X_i}} }</a>
+<a name="128"><span class="lineNum">     128 </span>            : \f]</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : \f[</a>
+<a name="131"><span class="lineNum">     131 </span>            :  H_{\rm MD}^k\left( {{\bf{\Gamma }},{{\bf X}}} \right) = {H_{\rm MD}}\left( {{{\bf{\Gamma }}^k}} \right) + \sum\limits_{i = 1}^N {\frac{{{K_i}}}{2}{{\left( {s_i^k - {X_i}} \right)}^2}}</a>
+<a name="132"><span class="lineNum">     132 </span>            : \f]</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : and \f$s^k_i\f$ is the \f$i\f$th CV in the \f$k\f$th replica.</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \f$W_k\f$ comes from the Crooks-Jarzynski non-equilibrium work relation by which we can evaluate an equilibrium ensemble average from a set of non-equilibrium trajectories. Note that, to avoid possible numerical errors in the exponential function, the following form of \f$W_k\f$ is instead used in PLUMED,</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : \f[</a>
+<a name="139"><span class="lineNum">     139 </span>            :  {W_k}\left( t \right) = \frac{{\exp \left[ { - \beta \left\{ {{w_k}\left( t \right) - {w_{\min }}\left( t \right)} \right\}} \right]}}{{\sum\nolimits_k {\exp \left[ { - \beta \left\{ {{w_k}\left( t \right) - {w_{\min }}\left( t \right)} \right\}} \right]} }}</a>
+<a name="140"><span class="lineNum">     140 </span>            : \f]</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : where</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : \f[</a>
+<a name="145"><span class="lineNum">     145 </span>            :  {w_{\min }}\left( t \right) = {\rm Min}_k\left[ {{w_k}\left( t \right)} \right]</a>
+<a name="146"><span class="lineNum">     146 </span>            : \f]</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : With the MF evaluated using the PD approach, free energy profiles can be reconstructed more efficiently (requiring less elapsed computing time) in LogPD than with a single MD system in LogMFD. In the case that there exist more than one stable state separated by high energy barriers in the hidden subspace orthogonal to the CV-subspace, LogPD is particularly of use to incorporate all the contributions from such hidden states with appropriate weights (in the limit \f$N_r\to\infty\f$ ).</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : Note that LogPD calculations should always be initiated with an equilibrium \f${\bf q}\f$-configuration in each replica, because the Crooks-Jarzynski non-equilibrium work relation is invoked. Also note that LogPD is currently available only with Gromacs, while LogMFD can be performed with LAMMPS, Gromacs, Quantum Espresso, NAMD, and so on.</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : \section Thermostat Using LogMFD/PD with a thermostat</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : Introducing a thermostat on \f${\bf X}\f$ is often recommended in LogMFD/PD to maintain the adiabatic decoupling between \f${\bf q}\f$ and \f${\bf X}\f$. In the framework of the LogMFD approach, the Nose-Hoover type thermostat and the Gaussian isokinetic (velocity scaling) thermostat can be used to control the kinetic energy of \f${\bf X}\f$.</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : \subsection Nose-Hoover Nose-Hoover LogMFD/PD</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : The equation of motion for \f$X_i\f$ coupled to a Nose-Hoover thermostat variable \f$\eta\f$ (single heat bath) is</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : \f[</a>
+<a name="162"><span class="lineNum">     162 </span>            :  {M_i}{\ddot X_i} =  - \left( {\frac{{\alpha \gamma }}{{\alpha F + 1}}} \right)\frac{{\partial F}}{{\partial {X_i}}} - {M_i}{\dot X_i}\dot \eta</a>
+<a name="163"><span class="lineNum">     163 </span>            : \f]</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : The equation of motion for \f$\eta\f$ is</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : \f[</a>
+<a name="168"><span class="lineNum">     168 </span>            :  Q\ddot \eta  = \sum\limits_{i = 1}^N {\frac{{P_{{X_i}}^2}}{{{M_i}}} - N{k_B}T}</a>
+<a name="169"><span class="lineNum">     169 </span>            : \f]</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : where \f$N\f$ is the number of the CVs. Since the following pseudo-Hamiltonian is a constant of motion in Nose-Hoover LogMFD/PD,</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : \f[</a>
+<a name="174"><span class="lineNum">     174 </span>            :  H_{\rm log}^{\rm NH} = \sum\limits_{i = 1}^N {\frac{{P_{{X_i}}^2}}{{2{M_i}}} + \gamma \log \left[ {\alpha F\left( {{\bf X}} \right) + 1} \right] + \frac{1}{2}Q{{\dot \eta }^2} + N{k_B}T\eta}</a>
+<a name="175"><span class="lineNum">     175 </span>            : \f]</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : \f$F({\bf X}(t))\f$ is obtained at each MFD step as</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : \f[</a>
+<a name="180"><span class="lineNum">     180 </span>            :  F\left( {{{\bf X}}\left( t \right)} \right) = \frac{1}{\alpha }\left[ {\exp \left\{ {{{ \frac{1}{\gamma} \left( {H_{\rm log}^{\rm NH} - \sum_i {\frac{{P_{{X_i}}^2}}{{2{M_i}}}}  - \frac{1}{2}Q{{\dot \eta }^2} - N{k_B}T\eta} \right)}  }} \right\} - 1} \right]</a>
+<a name="181"><span class="lineNum">     181 </span>            : \f]</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : \subsection VS Velocity scaling LogMFD/PD</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : The velocity scaling algorithm (which is equivalent to the Gaussian isokinetic dynamics in the limit \f$\Delta t\to 0\f$) can also be employed to control the velocity of \f${\bf X}\f$, \f$\bf{V}_x\f$.</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : The following algorithm is introduced to perform isokinetic LogMFD calculations \cite MorishitaVsLogMFD;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : \f{eqnarray*}{</a>
+<a name="192"><span class="lineNum">     192 </span>            : {V_{{X_i}}}\left( {{t_{n + 1}}} \right)</a>
+<a name="193"><span class="lineNum">     193 </span>            : &amp;=&amp;</a>
+<a name="194"><span class="lineNum">     194 </span>            :  V_{X_i}^\prime \left( {{t_n}} \right) + \Delta t \left[</a>
+<a name="195"><span class="lineNum">     195 </span>            :   { - \left( {\frac{{\alpha \gamma }}{{\alpha F\left( {{t_n}} \right) + 1}}} \right)</a>
+<a name="196"><span class="lineNum">     196 </span>            :   \frac{{\partial F\left( {{t_n}} \right)}}{{\partial {X_i}}}}</a>
+<a name="197"><span class="lineNum">     197 </span>            :  \right]\\</a>
+<a name="198"><span class="lineNum">     198 </span>            : S\left( {{t_{n + 1}}} \right)</a>
+<a name="199"><span class="lineNum">     199 </span>            : &amp;=&amp;</a>
+<a name="200"><span class="lineNum">     200 </span>            :  \sqrt {\frac{{N{k_B}T}}{{\sum\limits_i {{M_i}V_{{X_i}}^2\left( {{t_{n + 1}}} \right)} }}} \\</a>
+<a name="201"><span class="lineNum">     201 </span>            : {V_{{X_i}}}^\prime \left( {{t_{n + 1}}} \right)</a>
+<a name="202"><span class="lineNum">     202 </span>            : &amp;=&amp;</a>
+<a name="203"><span class="lineNum">     203 </span>            : S\left( {{t_{n + 1}}} \right){V_{{X_i}}}\left( {{t_{n + 1}}} \right)\\</a>
+<a name="204"><span class="lineNum">     204 </span>            : {X_i}\left( {{t_{n + 1}}} \right)</a>
+<a name="205"><span class="lineNum">     205 </span>            : &amp;=&amp;</a>
+<a name="206"><span class="lineNum">     206 </span>            : {X_i}\left( {{t_n}} \right) + \Delta t V_{X_i}^\prime \left( {{t_{n + 1}}} \right)\\</a>
+<a name="207"><span class="lineNum">     207 </span>            : {\Psi_{\rm log}}\left( {{t_{n + 1}}} \right)</a>
+<a name="208"><span class="lineNum">     208 </span>            : &amp;=&amp;</a>
+<a name="209"><span class="lineNum">     209 </span>            : N{k_B}T\log S\left( {{t_{n + 1}}} \right) + {\Psi_{\rm log}}\left( {{t_n}} \right)\\</a>
+<a name="210"><span class="lineNum">     210 </span>            : F\left( {{t_{n + 1}}} \right)</a>
+<a name="211"><span class="lineNum">     211 </span>            : &amp;=&amp;</a>
+<a name="212"><span class="lineNum">     212 </span>            : \frac{1}{\alpha} \left[</a>
+<a name="213"><span class="lineNum">     213 </span>            :   \exp \left\{ \Psi_{\rm log} \left( t_{n+1} \right) / \gamma \right\} - 1</a>
+<a name="214"><span class="lineNum">     214 </span>            : \right]</a>
+<a name="215"><span class="lineNum">     215 </span>            : \f}</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : Note that \f$V_{X_i}^\prime\left( {{t_0}} \right)\f$ is assumed to be initially given, which meets the following relation,</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            : \f[</a>
+<a name="220"><span class="lineNum">     220 </span>            :   \sum\limits_{i = 1}^N M_i V_{X_i}^{\prime 2} \left( t_0 \right)  = N{k_B}{T}</a>
+<a name="221"><span class="lineNum">     221 </span>            : \f]</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : It should be stressed that, in the same way as in the NVE and Nose-Hoover LogMFD/PD, \f$F({\bf X}(t))\f$ can be evaluated at each MFD step (on-the-fly free energy reconstruction) in Velocity Scaling LogMFD/PD.</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : \par Examples</a>
+<a name="227"><span class="lineNum">     227 </span>            : \section Examples Examples</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : \subsection Example-LoGMFD Example of LogMFD</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : The following input file tells plumed to restrain collective variables</a>
+<a name="232"><span class="lineNum">     232 </span>            : to the fictitious dynamical variables in LogMFD/PD.</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : plumed.dat</a>
+<a name="235"><span class="lineNum">     235 </span>            : \plumedfile</a>
+<a name="236"><span class="lineNum">     236 </span>            : UNITS TIME=fs LENGTH=1.0 ENERGY=kcal/mol MASS=1.0 CHARGE=1.0</a>
+<a name="237"><span class="lineNum">     237 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="238"><span class="lineNum">     238 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : # LogMFD</a>
+<a name="241"><span class="lineNum">     241 </span>            : LOGMFD ...</a>
+<a name="242"><span class="lineNum">     242 </span>            : LABEL=logmfd</a>
+<a name="243"><span class="lineNum">     243 </span>            : ARG=phi,psi</a>
+<a name="244"><span class="lineNum">     244 </span>            : KAPPA=1000.0,1000.0</a>
+<a name="245"><span class="lineNum">     245 </span>            : DELTA_T=1.0</a>
+<a name="246"><span class="lineNum">     246 </span>            : INTERVAL=200</a>
+<a name="247"><span class="lineNum">     247 </span>            : TEMP=300.0</a>
+<a name="248"><span class="lineNum">     248 </span>            : FLOG=2.0</a>
+<a name="249"><span class="lineNum">     249 </span>            : MFICT=5000000,5000000</a>
+<a name="250"><span class="lineNum">     250 </span>            : VFICT=3.5e-4,3.5e-4</a>
+<a name="251"><span class="lineNum">     251 </span>            : ALPHA=4.0</a>
+<a name="252"><span class="lineNum">     252 </span>            : THERMOSTAT=NVE</a>
+<a name="253"><span class="lineNum">     253 </span>            : FICT_MAX=3.15,3.15</a>
+<a name="254"><span class="lineNum">     254 </span>            : FICT_MIN=-3.15,-3.15</a>
+<a name="255"><span class="lineNum">     255 </span>            : ... LOGMFD</a>
+<a name="256"><span class="lineNum">     256 </span>            : \endplumedfile</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : To submit this simulation with Gromacs, use the following command line</a>
+<a name="259"><span class="lineNum">     259 </span>            : to execute a LogMFD run with Gromacs-MD.</a>
+<a name="260"><span class="lineNum">     260 </span>            : Here topol.tpr is the input file</a>
+<a name="261"><span class="lineNum">     261 </span>            : which contains atomic coordinates and Gromacs parameters.</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : \verbatim</a>
+<a name="264"><span class="lineNum">     264 </span>            : gmx_mpi mdrun -s topol.tpr -plumed</a>
+<a name="265"><span class="lineNum">     265 </span>            : \endverbatim</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : This command will output files named logmfd.out and replica.out.</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            : The output file logmfd.out records free energy and all fictitious dynamical variables at every MFD step.</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : logmfd.out</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : \verbatim</a>
+<a name="274"><span class="lineNum">     274 </span>            : # LogMFD</a>
+<a name="275"><span class="lineNum">     275 </span>            : # CVs : phi psi</a>
+<a name="276"><span class="lineNum">     276 </span>            : # Mass for CV particles : 5000000.000000 5000000.000000</a>
+<a name="277"><span class="lineNum">     277 </span>            : # Mass for thermostat   :   11923.224809</a>
+<a name="278"><span class="lineNum">     278 </span>            : # 1:iter_mfd, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,</a>
+<a name="279"><span class="lineNum">     279 </span>            : # 6:phi_fict(t), 7:phi_vfict(t), 8:phi_force(t),</a>
+<a name="280"><span class="lineNum">     280 </span>            : # 9:psi_fict(t), 10:psi_vfict(t), 11:psi_force(t),</a>
+<a name="281"><span class="lineNum">     281 </span>            :        0       2.000000     308.221983       0.000000       0.000000      -2.442363       0.000350       5.522717       2.426650       0.000350       7.443177</a>
+<a name="282"><span class="lineNum">     282 </span>            :        1       1.995466     308.475775       0.000000       0.000000      -2.442013       0.000350      -4.406246       2.427000       0.000350      11.531345</a>
+<a name="283"><span class="lineNum">     283 </span>            :        2       1.992970     308.615664       0.000000       0.000000      -2.441663       0.000350      -3.346513       2.427350       0.000350      15.763196</a>
+<a name="284"><span class="lineNum">     284 </span>            :        3       1.988619     308.859946       0.000000       0.000000      -2.441313       0.000350       6.463092       2.427701       0.000351       6.975422</a>
+<a name="285"><span class="lineNum">     285 </span>            : ...</a>
+<a name="286"><span class="lineNum">     286 </span>            : \endverbatim</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : The output file replica.out records all collective variables at every MFD step.</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : replica.out</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            : \verbatim</a>
+<a name="293"><span class="lineNum">     293 </span>            :  Replica No. 0 of 1.</a>
+<a name="294"><span class="lineNum">     294 </span>            : # 1:iter_mfd, 2:work, 3:weight,</a>
+<a name="295"><span class="lineNum">     295 </span>            : # 4:phi(q)</a>
+<a name="296"><span class="lineNum">     296 </span>            : # 5:psi(q)</a>
+<a name="297"><span class="lineNum">     297 </span>            :        0    0.000000e+00     1.000000e+00       -2.436841       2.434093</a>
+<a name="298"><span class="lineNum">     298 </span>            :        1   -4.539972e-03     1.000000e+00       -2.446420       2.438531</a>
+<a name="299"><span class="lineNum">     299 </span>            :        2   -7.038516e-03     1.000000e+00       -2.445010       2.443114</a>
+<a name="300"><span class="lineNum">     300 </span>            :        3   -1.139672e-02     1.000000e+00       -2.434850       2.434677</a>
+<a name="301"><span class="lineNum">     301 </span>            : ...</a>
+<a name="302"><span class="lineNum">     302 </span>            : \endverbatim</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : \subsection Example-LogPD Example of LogPD</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            : Use the following command line to execute a LogPD run using two MD replicas (note that only Gromacs is currently available for LogPD).</a>
+<a name="307"><span class="lineNum">     307 </span>            : Here 0/topol.tpr and 1/topol.tpr are the input files,</a>
+<a name="308"><span class="lineNum">     308 </span>            : each containing the atomic coordinates for the corresponding replica and Gromacs parameters. All the directories, 0/ and 1/, should contain the same plumed.dat.</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : \verbatim</a>
+<a name="311"><span class="lineNum">     311 </span>            : mpirun -np 2 gmx_mpi mdrun -s topol -plumed -multidir 0 1</a>
+<a name="312"><span class="lineNum">     312 </span>            : \endverbatim</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : This command will output files named logmfd.out in 0/, and replica.out.0 and replica.out.1 in 0/ and 1/, respectively.</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : The output file logmfd.out records free energy and all fictitious dynamical variables at every MFD step.</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : logmfd.out</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            : \verbatim</a>
+<a name="321"><span class="lineNum">     321 </span>            : # LogPD, replica parallel of LogMFD</a>
+<a name="322"><span class="lineNum">     322 </span>            : # number of replica : 2</a>
+<a name="323"><span class="lineNum">     323 </span>            : # CVs : phi psi</a>
+<a name="324"><span class="lineNum">     324 </span>            : # Mass for CV particles : 5000000.000000 5000000.000000</a>
+<a name="325"><span class="lineNum">     325 </span>            : # Mass for thermostat   :   11923.224809</a>
+<a name="326"><span class="lineNum">     326 </span>            : # 1:iter_mfd, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,</a>
+<a name="327"><span class="lineNum">     327 </span>            : # 6:phi_fict(t), 7:phi_vfict(t), 8:phi_force(t),</a>
+<a name="328"><span class="lineNum">     328 </span>            : # 9:psi_fict(t), 10:psi_vfict(t), 11:psi_force(t),</a>
+<a name="329"><span class="lineNum">     329 </span>            :        0       2.000000     308.221983       0.000000       0.000000      -2.417903       0.000350       4.930899       2.451475       0.000350      -3.122024</a>
+<a name="330"><span class="lineNum">     330 </span>            :        1       1.999367     308.257404       0.000000       0.000000      -2.417552       0.000350       0.851133       2.451825       0.000350      -1.552718</a>
+<a name="331"><span class="lineNum">     331 </span>            :        2       1.999612     308.243683       0.000000       0.000000      -2.417202       0.000350      -1.588175       2.452175       0.000350       1.601274</a>
+<a name="332"><span class="lineNum">     332 </span>            :        3       1.999608     308.243922       0.000000       0.000000      -2.416852       0.000350       4.267745       2.452525       0.000350      -4.565621</a>
+<a name="333"><span class="lineNum">     333 </span>            : ...</a>
+<a name="334"><span class="lineNum">     334 </span>            : \endverbatim</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            : The output file replica.out.0 records all collective variables and the Jarzynski weight of replica No.0 at every MFD step.</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : replica.out.0</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : \verbatim</a>
+<a name="342"><span class="lineNum">     342 </span>            : # Replica No. 0 of 2.</a>
+<a name="343"><span class="lineNum">     343 </span>            : # 1:iter_mfd, 2:work, 3:weight,</a>
+<a name="344"><span class="lineNum">     344 </span>            : # 4:phi(q)</a>
+<a name="345"><span class="lineNum">     345 </span>            : # 5:psi(q)</a>
+<a name="346"><span class="lineNum">     346 </span>            :        0    0.000000e+00     5.000000e-01       -2.412607       2.446191</a>
+<a name="347"><span class="lineNum">     347 </span>            :        1   -4.649101e-06     4.994723e-01       -2.421403       2.451318</a>
+<a name="348"><span class="lineNum">     348 </span>            :        2    1.520985e-03     4.983996e-01       -2.420269       2.455049</a>
+<a name="349"><span class="lineNum">     349 </span>            :        3    1.588855e-03     4.983392e-01       -2.411081       2.447394</a>
+<a name="350"><span class="lineNum">     350 </span>            : ...</a>
+<a name="351"><span class="lineNum">     351 </span>            : \endverbatim</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            : The output file replica.out.1 records all collective variables and the Jarzynski weight of replica No.1 at every MFD step.</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : replica.out.1</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span>            : \verbatim</a>
+<a name="358"><span class="lineNum">     358 </span>            : # Replica No. 1 of 2.</a>
+<a name="359"><span class="lineNum">     359 </span>            : # 1:iter_mfd, 2:work, 3:weight,</a>
+<a name="360"><span class="lineNum">     360 </span>            : # 4:phi(q)</a>
+<a name="361"><span class="lineNum">     361 </span>            : # 5:psi(q)</a>
+<a name="362"><span class="lineNum">     362 </span>            :        0    0.000000e+00     5.000000e-01       -2.413336       2.450516</a>
+<a name="363"><span class="lineNum">     363 </span>            :        1   -1.263077e-03     5.005277e-01       -2.412009       2.449229</a>
+<a name="364"><span class="lineNum">     364 </span>            :        2   -2.295444e-03     5.016004e-01       -2.417322       2.452512</a>
+<a name="365"><span class="lineNum">     365 </span>            :        3   -2.371507e-03     5.016608e-01       -2.414078       2.448521</a>
+<a name="366"><span class="lineNum">     366 </span>            : ...</a>
+<a name="367"><span class="lineNum">     367 </span>            : \endverbatim</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : */</a>
+<a name="370"><span class="lineNum">     370 </span>            : //+ENDPLUMEDOC</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="373"><span class="lineNum">     373 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="374"><span class="lineNum">     374 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="375"><span class="lineNum">     375 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : #include &lt;iostream&gt;</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            : using namespace std;</a>
+<a name="380"><span class="lineNum">     380 </span>            : using namespace PLMD;</a>
+<a name="381"><span class="lineNum">     381 </span>            : using namespace bias;</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            : namespace PLMD {</a>
+<a name="384"><span class="lineNum">     384 </span>            : namespace logmfd {</a>
+<a name="385"><span class="lineNum">     385 </span>            : /**</a>
+<a name="386"><span class="lineNum">     386 </span>            :    \brief class for LogMFD parameters, variables and subroutines.</a>
+<a name="387"><span class="lineNum">     387 </span>            :  */</a>
+<a name="388"><span class="lineNum">     388 </span>            : class LogMFD : public Bias {</a>
+<a name="389"><span class="lineNum">     389 </span>            :   bool firsttime;               ///&lt; flag that indicates first MFD step or not.</a>
+<a name="390"><span class="lineNum">     390 </span>            :   int    step_initial;          ///&lt; initial MD step.</a>
+<a name="391"><span class="lineNum">     391 </span>            :   int    interval;              ///&lt; input parameter, period of MD steps when fictitious dynamical variables are evolved.</a>
+<a name="392"><span class="lineNum">     392 </span>            :   double delta_t;               ///&lt; input parameter, one time step of MFD when fictitious dynamical variables are evolved.</a>
+<a name="393"><span class="lineNum">     393 </span>            :   string thermostat;            ///&lt; input parameter, type of thermostat for canonical dyanamics.</a>
+<a name="394"><span class="lineNum">     394 </span>            :   double kbt;                   ///&lt; k_B*temperature</a>
+<a name="395"><span class="lineNum">     395 </span>            :   double kbtpd;                   ///&lt; k_B*temperature for PD</a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :   int    TAMD;                  ///&lt; input parameter, perform TAMD instead of LogMFD.</a>
+<a name="398"><span class="lineNum">     398 </span>            :   double alpha;                 ///&lt; input parameter, alpha parameter for LogMFD.</a>
+<a name="399"><span class="lineNum">     399 </span>            :   double gamma;                 ///&lt; input parameter, gamma parameter for LogMFD.</a>
+<a name="400"><span class="lineNum">     400 </span>            :   std::vector&lt;double&gt; kappa;    ///&lt; input parameter, strength of the harmonic restraining potential.</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            :   std::vector&lt;double&gt; fict_max; ///&lt; input parameter, maximum of each fictitous dynamical variable.</a>
+<a name="403"><span class="lineNum">     403 </span>            :   std::vector&lt;double&gt; fict_min; ///&lt; input parameter, minimum of each fictitous dynamical variable.</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            :   std::vector&lt;double&gt;  fict;    ///&lt; current values of each fictitous dynamical variable.</a>
+<a name="407"><span class="lineNum">     407 </span>            :   std::vector&lt;double&gt; vfict;    ///&lt; current velocity of each fictitous dynamical variable.</a>
+<a name="408"><span class="lineNum">     408 </span>            :   std::vector&lt;double&gt; mfict;    ///&lt; mass of each fictitous dynamical variable.</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :   double xeta;                  ///&lt; current eta variable of thermostat.</a>
+<a name="411"><span class="lineNum">     411 </span>            :   double veta;                  ///&lt; current velocity of eta variable of thermostat.</a>
+<a name="412"><span class="lineNum">     412 </span>            :   double meta;                  ///&lt; mass of eta variable of thermostat.</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :   double phivs;                 ///&lt; potential used in VS method</a>
+<a name="415"><span class="lineNum">     415 </span>            :   double work;                  ///&lt; current works done by fictitious dynamical variables in this replica.</a>
+<a name="416"><span class="lineNum">     416 </span>            :   double weight;                ///&lt; current weight of this replica.</a>
+<a name="417"><span class="lineNum">     417 </span>            :   double flog;                  ///&lt; current free energy</a>
+<a name="418"><span class="lineNum">     418 </span>            :   double hlog;                  ///&lt; value invariant</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   struct {</a>
+<a name="421"><span class="lineNum">     421 </span>            :     std::vector&lt;double&gt;  fict;</a>
+<a name="422"><span class="lineNum">     422 </span>            :     std::vector&lt;double&gt; vfict;</a>
+<a name="423"><span class="lineNum">     423 </span>            :     std::vector&lt;double&gt; ffict;</a>
+<a name="424"><span class="lineNum">     424 </span>            :     double xeta;</a>
+<a name="425"><span class="lineNum">     425 </span>            :     double veta;</a>
+<a name="426"><span class="lineNum">     426 </span>            :     double phivs;</a>
+<a name="427"><span class="lineNum">     427 </span>            :     double work;</a>
+<a name="428"><span class="lineNum">     428 </span>            :     double weight;</a>
+<a name="429"><span class="lineNum">     429 </span>            :   } backup;</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            :   std::vector&lt;double&gt; ffict;    ///&lt; current force of each fictitous dynamical variable.</a>
+<a name="432"><span class="lineNum">     432 </span>            :   std::vector&lt;double&gt; fict_ave; ///&lt; averaged values of each collective variable.</a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span>            :   std::vector&lt;Value*&gt;  fictValue; ///&lt; pointers to fictitious dynamical variables</a>
+<a name="435"><span class="lineNum">     435 </span>            :   std::vector&lt;Value*&gt; vfictValue; ///&lt; pointers to velocity of fictitious dynamical variables</a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            : public:</a>
+<a name="438"><span class="lineNum">     438 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span>            :   explicit LogMFD(const ActionOptions&amp;);</a>
+<a name="441"><span class="lineNum">     441 </span>            :   void calculate();</a>
+<a name="442"><span class="lineNum">     442 </span>            :   void update();</a>
+<a name="443"><span class="lineNum">     443 </span>            :   void updateNVE();</a>
+<a name="444"><span class="lineNum">     444 </span>            :   void updateNVT();</a>
+<a name="445"><span class="lineNum">     445 </span>            :   void updateVS();</a>
+<a name="446"><span class="lineNum">     446 </span>            :   void updateWork();</a>
+<a name="447"><span class="lineNum">     447 </span>            :   void calcMeanForce();</a>
+<a name="448"><span class="lineNum">     448 </span>            :   double calcEkin();</a>
+<a name="449"><span class="lineNum">     449 </span>            :   double calcFlog();</a>
+<a name="450"><span class="lineNum">     450 </span>            :   double calcClog();</a>
+<a name="451"><span class="lineNum">     451 </span>            : </a>
+<a name="452"><span class="lineNum">     452 </span>            : private:</a>
+<a name="453"><span class="lineNum">     453 </span>            :   double sgn( double x ) {</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">         55 :     return x&gt;0.0 ? 1.0 : x&lt;0.0 ? -1.0 : 0.0;</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :   }</a>
+<a name="456"><span class="lineNum">     456 </span>            : };</a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(LogMFD,&quot;LOGMFD&quot;)</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            : /**</a>
+<a name="461"><span class="lineNum">     461 </span>            :    \brief instruction of parameters for Plumed manual.</a>
+<a name="462"><span class="lineNum">     462 </span>            : */</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          5 : void LogMFD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">          5 :   Bias::registerKeywords(keys);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          5 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;INTERVAL&quot;,</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :            &quot;Period of MD steps (\\f$N_m\\f$) to update fictitious dynamical variables.&quot; );</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;DELTA_T&quot;,</span></a>
+<a name="469"><span class="lineNum">     469 </span>            :            &quot;Time step for the fictitious dynamical variables (DELTA_T=1 often works).&quot; );</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;THERMOSTAT&quot;,</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :            &quot;Type of thermostat for the fictitious dynamical variables. NVE, NVT, VS are available.&quot; );</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :            &quot;Target temperature for the fictitious dynamical variables in LogMFD/PD. &quot;</a>
+<a name="474"><span class="lineNum">     474 </span>            :            &quot;It is recommended to set TEMP to be the same as &quot;</a>
+<a name="475"><span class="lineNum">     475 </span>            :            &quot;the temperature of the MD system in any thermostated LogMFD/PD run. &quot;</a>
+<a name="476"><span class="lineNum">     476 </span>            :            &quot;If not provided, it will be taken from the temperature of the MD system (Gromacs only).&quot; );</a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;TAMD&quot;,</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :            &quot;When TAMD=1, TAMD/d-AFED calculations can be performed instead of LogMFD. Otherwise, the LogMFD protocol is switched on (default).&quot; );</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;ALPHA&quot;,</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :            &quot;Alpha parameter for LogMFD. &quot;</a>
+<a name="483"><span class="lineNum">     483 </span>            :            &quot;If not provided or provided as 0, it will be taken as 1/gamma. &quot;</a>
+<a name="484"><span class="lineNum">     484 </span>            :            &quot;If gamma is also not provided, Alpha is set as 4, which is a sensible value when the unit of kcal/mol is used.&quot; );</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;GAMMA&quot;,</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :            &quot;Gamma parameter for LogMFD. &quot;</a>
+<a name="487"><span class="lineNum">     487 </span>            :            &quot;If not provided or provided as 0, it will be taken as 1/alpha. &quot;</a>
+<a name="488"><span class="lineNum">     488 </span>            :            &quot;If alpha is also not provided, Gamma is set as 0.25, which is a sensible value when the unit of kcal/mol is used.&quot; );</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :            &quot;Spring constant of the harmonic restraining potential.&quot; );</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;FICT_MAX&quot;,</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :            &quot;Maximum values reachable for the fictitious dynamical variables. The variables will elastically bounce back at the boundary (mirror boundary).&quot; );</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;FICT_MIN&quot;,</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :            &quot;Minimum values reachable for the fictitious dynamical variables. The variables will elastically bounce back at the boundary (mirror boundary).&quot; );</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;FICT&quot;,</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :            &quot;The initial values of the fictitious dynamical variables. &quot;</a>
+<a name="499"><span class="lineNum">     499 </span>            :            &quot;If not provided, they are set equal to their corresponding CVs for the initial atomic configuration.&quot; );</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;VFICT&quot;,</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :            &quot;The initial velocities of the fictitious dynamical variables. &quot;</a>
+<a name="502"><span class="lineNum">     502 </span>            :            &quot;If not provided, they will be taken as 0. &quot;</a>
+<a name="503"><span class="lineNum">     503 </span>            :            &quot;If THERMOSTAT=VS, they are instead automatically adjusted according to TEMP. &quot;  );</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;MFICT&quot;,</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :            &quot;Masses of each fictitious dynamical variable. &quot;</a>
+<a name="506"><span class="lineNum">     506 </span>            :            &quot;If not provided, they will be taken as 10000.&quot; );</a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;XETA&quot;,</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :            &quot;The initial eta variable of the Nose-Hoover thermostat &quot;</a>
+<a name="510"><span class="lineNum">     510 </span>            :            &quot;for the fictitious dynamical variables. &quot;</a>
+<a name="511"><span class="lineNum">     511 </span>            :            &quot;If not provided, it will be taken as 0.&quot; );</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;VETA&quot;,</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :            &quot;The initial velocity of eta variable. &quot;</a>
+<a name="514"><span class="lineNum">     514 </span>            :            &quot;If not provided, it will be taken as 0.&quot; );</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;META&quot;,</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :            &quot;Mass of eta variable. &quot;</a>
+<a name="517"><span class="lineNum">     517 </span>            :            &quot;If not provided, it will be taken as \\f$N*kb*T*100*100\\f$.&quot; );</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;FLOG&quot;,</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :            &quot;The initial free energy value in the LogMFD/PD run.&quot;</a>
+<a name="521"><span class="lineNum">     521 </span>            :            &quot;The origin of the free energy profile is adjusted by FLOG to &quot;</a>
+<a name="522"><span class="lineNum">     522 </span>            :            &quot;realize \\f$F({\\bf X}(t)) &gt; 0\\f$ at any \\f${\\bf X}(t)\\f$, &quot;</a>
+<a name="523"><span class="lineNum">     523 </span>            :            &quot;resulting in enhanced barrier-crossing. &quot;</a>
+<a name="524"><span class="lineNum">     524 </span>            :            &quot;(The value of \\f$H_{\\rm log}\\f$ is automatically &quot;</a>
+<a name="525"><span class="lineNum">     525 </span>            :            &quot;set according to FLOG). &quot;</a>
+<a name="526"><span class="lineNum">     526 </span>            :            &quot;In fact, \\f$F({\\bf X}(t))\\f$ is correctly &quot;</a>
+<a name="527"><span class="lineNum">     527 </span>            :            &quot;estimated in PLUMED even when \\f$F({\\bf X}(t)) &lt; 0\\f$ in &quot;</a>
+<a name="528"><span class="lineNum">     528 </span>            :            &quot;the LogMFD/PD run.&quot; );</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;WORK&quot;,</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :            &quot;The initial value of the work done by fictitious dynamical &quot;</a>
+<a name="532"><span class="lineNum">     532 </span>            :            &quot;variables in each replica. &quot;</a>
+<a name="533"><span class="lineNum">     533 </span>            :            &quot;If not provided, it will be taken as 0.&quot;);</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;TEMPPD&quot;,</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :            &quot;Temperature of the Boltzmann factor in the Jarzynski weight in LogPD (Gromacs only). &quot;</a>
+<a name="537"><span class="lineNum">     537 </span>            :            &quot;TEMPPD should be the same as the &quot;</a>
+<a name="538"><span class="lineNum">     538 </span>            :            &quot;temperature of the MD system, while TEMP may be (in principle) different from it. &quot;</a>
+<a name="539"><span class="lineNum">     539 </span>            :            &quot;If not provided, TEMPPD is set to be the same value as TEMP.&quot; );</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">          5 :   componentsAreNotOptional(keys);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         10 :   keys.addOutputComponent(&quot;_fict&quot;,&quot;default&quot;,</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :                           &quot;For example, the fictitious collective variable for LogMFD is specified as &quot;</a>
+<a name="544"><span class="lineNum">     544 </span>            :                           &quot;ARG=dist12 and LABEL=logmfd in LOGMFD section in Plumed input file, &quot;</a>
+<a name="545"><span class="lineNum">     545 </span>            :                           &quot;the associated fictitious dynamical variable can be specified as &quot;</a>
+<a name="546"><span class="lineNum">     546 </span>            :                           &quot;PRINT ARG=dist12,logmfd.dist12_fict FILE=COLVAR&quot;);</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         10 :   keys.addOutputComponent(&quot;_vfict&quot;,&quot;default&quot;,</span></a>
+<a name="548"><span class="lineNum">     548 </span>            :                           &quot;For example, the fictitious collective variable for LogMFD is specified as &quot;</a>
+<a name="549"><span class="lineNum">     549 </span>            :                           &quot;ARG=dist12 and LABEL=logmfd in LOGMFD section in Plumed input file, the &quot;</a>
+<a name="550"><span class="lineNum">     550 </span>            :                           &quot;velocity of the associated fictitious dynamical variable can be specified as &quot;</a>
+<a name="551"><span class="lineNum">     551 </span>            :                           &quot;PRINT ARG=dist12,logmfd.dist12_vfict FILE=COLVAR&quot;);</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          5 : }</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            : /**</a>
+<a name="556"><span class="lineNum">     556 </span>            :    \brief constructor of LogMFD class</a>
+<a name="557"><span class="lineNum">     557 </span>            :    \details This constructor initializes all parameters and variables,</a>
+<a name="558"><span class="lineNum">     558 </span>            :    reads input file and set value of parameters and initial value of variables,</a>
+<a name="559"><span class="lineNum">     559 </span>            :    and writes messages as Plumed log.</a>
+<a name="560"><span class="lineNum">     560 </span>            : */</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">          3 : LogMFD::LogMFD( const ActionOptions&amp; ao ):</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :   PLUMED_BIAS_INIT(ao),</a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">          3 :   firsttime(true),</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">          3 :   step_initial(0),</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          3 :   interval(10),</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">          3 :   delta_t(1.0),</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">          6 :   thermostat(&quot;NVE&quot;),</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">          3 :   kbt(-1.0),</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          3 :   kbtpd(-1.0),</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">          3 :   TAMD(0),</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">          3 :   alpha(0.0),</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">          3 :   gamma(0.0),</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">          3 :   kappa(getNumberOfArguments(),0.0),</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">          3 :   fict_max(getNumberOfArguments(),0.0),</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">          3 :   fict_min(getNumberOfArguments(),0.0),</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">          3 :   fict (getNumberOfArguments(),-999.0), // -999 means no initial values given in plumed.dat</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">          3 :   vfict(getNumberOfArguments(),0.0),</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">          3 :   mfict(getNumberOfArguments(),10000.0),</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          3 :   xeta(0.0),</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">          3 :   veta(0.0),</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">          3 :   meta(0.0),</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">          3 :   flog(0.0),</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">          3 :   hlog(0.0),</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">          3 :   phivs(0.0),</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">          3 :   work(0.0),</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">          3 :   weight(0.0),</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">          3 :   ffict(getNumberOfArguments(),0.0),</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">          3 :   fict_ave(getNumberOfArguments(),0.0),</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">          3 :   fictValue(getNumberOfArguments(),NULL),</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">          9 :   vfictValue(getNumberOfArguments(),NULL)</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : {</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">          3 :   backup.fict.resize(getNumberOfArguments(),0.0);</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">          3 :   backup.vfict.resize(getNumberOfArguments(),0.0);</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          3 :   backup.ffict.resize(getNumberOfArguments(),0.0);</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          3 :   backup.xeta = 0.0;</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">          3 :   backup.veta = 0.0;</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          3 :   backup.phivs = 0.0;</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">          3 :   backup.work = 0.0;</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">          3 :   backup.weight = 0.0;</span></a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">          3 :   parse(&quot;INTERVAL&quot;,interval);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">          3 :   parse(&quot;DELTA_T&quot;,delta_t);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">          3 :   parse(&quot;THERMOSTAT&quot;,thermostat);</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">          3 :   parse(&quot;TEMP&quot;,kbt); // read as temperature</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">          3 :   parse(&quot;TEMPPD&quot;,kbtpd); // read as temperature</span></a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">          3 :   parse(&quot;TAMD&quot;,TAMD);</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">          3 :   parse(&quot;ALPHA&quot;,alpha);</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">          3 :   parse(&quot;GAMMA&quot;,gamma);</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">          3 :   parseVector(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="611"><span class="lineNum">     611 </span>            : </a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">          3 :   parseVector(&quot;FICT_MAX&quot;,fict_max);</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">          3 :   parseVector(&quot;FICT_MIN&quot;,fict_min);</span></a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">          3 :   parseVector(&quot;FICT&quot;,fict);</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">          3 :   parseVector(&quot;VFICT&quot;,vfict);</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">          3 :   parseVector(&quot;MFICT&quot;,mfict);</span></a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">          3 :   parse(&quot;XETA&quot;,xeta);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">          3 :   parse(&quot;VETA&quot;,veta);</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">          3 :   parse(&quot;META&quot;,meta);</span></a>
+<a name="622"><span class="lineNum">     622 </span>            : </a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">          3 :   parse(&quot;FLOG&quot;,flog);</span></a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span>            :   // read initial value of work for each replica of LogPD</a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">          3 :   if( multi_sim_comm.Get_size()&gt;1 ) {</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :     vector&lt;double&gt; vwork(multi_sim_comm.Get_size(),0.0);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :     parseVector(&quot;WORK&quot;,vwork);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :     // initial work of this replica</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :     work = vwork[multi_sim_comm.Get_rank()];</span></a>
+<a name="631"><span class="lineNum">     631 </span>            :   }</a>
+<a name="632"><span class="lineNum">     632 </span>            :   else {</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">          3 :     work = 0.0;</span></a>
+<a name="634"><span class="lineNum">     634 </span>            :   }</a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">          3 :   if( kbt&gt;=0.0 ) {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">          3 :     kbt *= plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :   }</a>
+<a name="639"><span class="lineNum">     639 </span>            :   else {</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :     kbt = plumed.getAtoms().getKbT();</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :   }</a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">          3 :   if( kbtpd&gt;=0.0 ) {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :     kbtpd *= plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :   }</a>
+<a name="646"><span class="lineNum">     646 </span>            :   else {</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          3 :     kbtpd = kbt;</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :   }</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          3 :   if( meta == 0.0 ) {</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          2 :     const double nkt = getNumberOfArguments()*kbt;</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">          2 :     meta = nkt*100.0*100.0;</span></a>
+<a name="653"><span class="lineNum">     653 </span>            :   }</a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">          3 :   if(alpha == 0.0 &amp;&amp; gamma == 0.0) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineNoCov">          0 :     alpha = 4.0;</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 :     gamma = 1 / alpha;</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :   }</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">          3 :   else if(alpha != 0.0 &amp;&amp; gamma == 0.0) {</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">          3 :     gamma = 1 / alpha;</span></a>
+<a name="661"><span class="lineNum">     661 </span>            :   }</a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :   else if(alpha == 0.0 &amp;&amp; gamma != 0.0) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :     alpha = 1 / gamma;</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :   }</a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="667"><span class="lineNum">     667 </span>            : </a>
+<a name="668"><span class="lineNum">     668 </span>            :   // output messaages to Plumed's log file</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">          3 :   if( multi_sim_comm.Get_size()&gt;1 ) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :     if( TAMD ) {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :       log.printf(&quot;TAMD-PD, replica parallel of TAMD, no logarithmic flattening.\n&quot;);</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :     }</a>
+<a name="673"><span class="lineNum">     673 </span>            :     else {</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :       log.printf(&quot;LogPD, replica parallel of LogMFD.\n&quot;);</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :     }</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :     log.printf(&quot;number of replica : %d.\n&quot;, multi_sim_comm.Get_size() );</span></a>
+<a name="677"><span class="lineNum">     677 </span>            :   }</a>
+<a name="678"><span class="lineNum">     678 </span>            :   else {</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">          3 :     if( TAMD ) {</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :       log.printf(&quot;TAMD, no logarithmic flattening.\n&quot;);</span></a>
+<a name="681"><span class="lineNum">     681 </span>            :     }</a>
+<a name="682"><span class="lineNum">     682 </span>            :     else {</a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">          3 :       log.printf(&quot;LogMFD, logarithmic flattening.\n&quot;);</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :     }</a>
+<a name="685"><span class="lineNum">     685 </span>            :   }</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">          3 :   log.printf(&quot;  with harmonic force constant      &quot;);</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;kappa.size(); i++) log.printf(&quot; %f&quot;,kappa[i]);</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">          3 :   log.printf(&quot;  with interval of cv(ideal) update &quot;);</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">          3 :   log.printf(&quot; %d&quot;, interval);</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">          3 :   log.printf(&quot;  with time step of cv(ideal) update &quot;);</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">          3 :   log.printf(&quot; %f&quot;, delta_t);</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="698"><span class="lineNum">     698 </span>            : </a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">          3 :   if( !TAMD ) {</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">          3 :     log.printf(&quot;  with alpha, gamma                 &quot;);</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">          3 :     log.printf(&quot; %f %f&quot;, alpha, gamma);</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">          3 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :   }</a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">          3 :   log.printf(&quot;  with Thermostat for cv(ideal)     &quot;);</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">          3 :   log.printf(&quot; %s&quot;, thermostat.c_str());</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">          3 :   log.printf(&quot;  with initial free energy          &quot;);</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">          3 :   log.printf(&quot; %f&quot;, flog);</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">          3 :   log.printf(&quot;  with mass of cv(ideal)&quot;);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;mfict.size(); i++) log.printf(&quot; %f&quot;, mfict[i]);</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">          3 :   log.printf(&quot;  with initial value of cv(ideal)&quot;);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;fict.size(); i++) log.printf(&quot; %f&quot;, fict[i]);</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            : </a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">          3 :   log.printf(&quot;  with initial velocity of cv(ideal)&quot;);</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;vfict.size(); i++) log.printf(&quot; %f&quot;, vfict[i]);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="724"><span class="lineNum">     724 </span>            : </a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">          3 :   log.printf(&quot;  with maximum value of cv(ideal)    &quot;);</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;fict_max.size(); i++) log.printf(&quot; %f&quot;,fict_max[i]);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">          3 :   log.printf(&quot;  with minimum value of cv(ideal)    &quot;);</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;fict_min.size(); i++) log.printf(&quot; %f&quot;,fict_min[i]);</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">          3 :   log.printf(&quot;  and kbt                           &quot;);</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">          3 :   log.printf(&quot; %f\n&quot;,kbt);</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">          3 :   log.printf(&quot; kbt for PD %f\n&quot;,kbtpd);</span></a>
+<a name="736"><span class="lineNum">     736 </span>            : </a>
+<a name="737"><span class="lineNum">     737 </span>            :   // setup Value* variables</a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;getNumberOfArguments(); i++) {</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">          3 :     std::string comp = getPntrToArgument(i)-&gt;getName()+&quot;_fict&quot;;</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">          3 :     addComponentWithDerivatives(comp);</span></a>
+<a name="741"><span class="lineNum">     741 </span>            : </a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">          3 :     if(getPntrToArgument(i)-&gt;isPeriodic()) {</span></a>
+<a name="743"><span class="lineNum">     743 </span>            :       std::string a,b;</a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :       getPntrToArgument(i)-&gt;getDomain(a,b);</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :       componentIsPeriodic(comp,a,b);</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :     }</a>
+<a name="747"><span class="lineNum">     747 </span>            :     else {</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">          3 :       componentIsNotPeriodic(comp);</span></a>
+<a name="749"><span class="lineNum">     749 </span>            :     }</a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">          3 :     fictValue[i] = getPntrToComponent(comp);</span></a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">          3 :     comp = getPntrToArgument(i)-&gt;getName()+&quot;_vfict&quot;;</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">          3 :     addComponent(comp);</span></a>
+<a name="754"><span class="lineNum">     754 </span>            : </a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">          3 :     componentIsNotPeriodic(comp);</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">          3 :     vfictValue[i] = getPntrToComponent(comp);</span></a>
+<a name="757"><span class="lineNum">     757 </span>            :   }</a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">          3 : }</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            : /**</a>
+<a name="761"><span class="lineNum">     761 </span>            :    \brief calculate forces for fictitious variables at every MD steps.</a>
+<a name="762"><span class="lineNum">     762 </span>            :    \details This function calculates initial values of fictitious variables</a>
+<a name="763"><span class="lineNum">     763 </span>            :    and write header messages to LogMFD log files at the first MFD step,</a>
+<a name="764"><span class="lineNum">     764 </span>            :    calculates restraining fources comes from difference between the fictitious variable</a>
+<a name="765"><span class="lineNum">     765 </span>            :    and collective variable at every MD steps.</a>
+<a name="766"><span class="lineNum">     766 </span>            : */</a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       1500 : void LogMFD::calculate() {</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">       1500 :   if( firsttime ) {</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">          3 :     firsttime = false;</span></a>
+<a name="770"><span class="lineNum">     770 </span>            : </a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">          3 :     step_initial = getStep();</span></a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            :     // set initial values of fictitious variables if they were not specified.</a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">          3 :       if( fict[i] != -999.0 ) continue; // -999 means no initial values given in plumed.dat</span></a>
+<a name="776"><span class="lineNum">     776 </span>            : </a>
+<a name="777"><span class="lineNum">     777 </span>            :       // use the collective variables as the initial of the fictitious variable.</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineNoCov">          0 :       fict[i] = getArgument(i);</span></a>
+<a name="779"><span class="lineNum">     779 </span>            : </a>
+<a name="780"><span class="lineNum">     780 </span>            :       // average values of fictitious variables by all replica.</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineNoCov">          0 :       if( multi_sim_comm.Get_size()&gt;1 ) {</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineNoCov">          0 :         multi_sim_comm.Sum(fict[i]);</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineNoCov">          0 :         fict[i] /= multi_sim_comm.Get_size();</span></a>
+<a name="784"><span class="lineNum">     784 </span>            :       }</a>
+<a name="785"><span class="lineNum">     785 </span>            :     }</a>
+<a name="786"><span class="lineNum">     786 </span>            : </a>
+<a name="787"><span class="lineNum">     787 </span>            :     // initialize accumulation value to zero</a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">          3 :       fict_ave[i] = 0.0;</span></a>
+<a name="790"><span class="lineNum">     790 </span>            :     }</a>
+<a name="791"><span class="lineNum">     791 </span>            : </a>
+<a name="792"><span class="lineNum">     792 </span>            :     // calculate invariant for NVE</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">          3 :     if(thermostat == &quot;NVE&quot;) {</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :       // kinetic energy</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">          1 :       const double ekin = calcEkin();</span></a>
+<a name="796"><span class="lineNum">     796 </span>            :       // potential energy</a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">          1 :       const double pot = TAMD ? flog : sgn(flog)*gamma * std::log1p( alpha*fabs(flog) );</span></a>
+<a name="798"><span class="lineNum">     798 </span>            :       // invariant</a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">          1 :       hlog = pot + ekin;</span></a>
+<a name="800"><span class="lineNum">     800 </span>            :     }</a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">          2 :     else if(thermostat == &quot;NVT&quot;) {</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">          1 :       const double nkt = getNumberOfArguments()*kbt;</span></a>
+<a name="803"><span class="lineNum">     803 </span>            :       // kinetic energy</a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">          1 :       const double ekin = calcEkin();</span></a>
+<a name="805"><span class="lineNum">     805 </span>            :       // bath energy</a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">          1 :       const double ekin_bath = 0.5*veta*veta*meta + xeta*nkt;</span></a>
+<a name="807"><span class="lineNum">     807 </span>            :       // potential energy</a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">          1 :       const double pot = TAMD ? flog : sgn(flog)*gamma * std::log1p( alpha*fabs(flog) );</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :       // invariant</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">          1 :       hlog = pot + ekin + ekin_bath;</span></a>
+<a name="811"><span class="lineNum">     811 </span>            :     }</a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">          1 :     else if(thermostat == &quot;VS&quot;) {</span></a>
+<a name="813"><span class="lineNum">     813 </span>            :       // kinetic energy</a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">          1 :       const double ekin = calcEkin();</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">          1 :       if( ekin == 0.0 ) { // this means VFICT is not given.</span></a>
+<a name="816"><span class="lineNum">     816 </span>            :         // initial velocities</a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">          2 :         for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">          1 :           vfict[i] = sqrt(kbt/mfict[i]);</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :         }</a>
+<a name="820"><span class="lineNum">     820 </span>            :       }</a>
+<a name="821"><span class="lineNum">     821 </span>            :       else {</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineNoCov">          0 :         const double nkt = getNumberOfArguments()*kbt;</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 :         const double svs = sqrt(nkt/ekin/2);</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineNoCov">          0 :           vfict[i] *= svs; // scale velocities</span></a>
+<a name="826"><span class="lineNum">     826 </span>            :         }</a>
+<a name="827"><span class="lineNum">     827 </span>            :       }</a>
+<a name="828"><span class="lineNum">     828 </span>            :       // initial VS potential</a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">          1 :       phivs = TAMD ? flog : sgn(flog)* gamma*std::log1p( alpha*fabs(flog) );</span></a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span>            :       // invariant</a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">          1 :       hlog = 0.0;</span></a>
+<a name="833"><span class="lineNum">     833 </span>            :     }</a>
+<a name="834"><span class="lineNum">     834 </span>            : </a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">          3 :     weight = 1.0; // for replica parallel</span></a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            :     // open LogMFD's log file</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">          3 :     if( multi_sim_comm.Get_rank()==0 &amp;&amp; comm.Get_rank()==0 ) {</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">          3 :       FILE *outlog = std::fopen(&quot;logmfd.out&quot;, &quot;w&quot;);</span></a>
+<a name="840"><span class="lineNum">     840 </span>            : </a>
+<a name="841"><span class="lineNum">     841 </span>            :       // output messages to LogMFD's log file</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">          3 :       if( multi_sim_comm.Get_size()&gt;1 ) {</span></a>
+<a name="843"><span class="lineNum">     843 </span>            :         fprintf(outlog, &quot;# LogPD, replica parallel of LogMFD\n&quot;);</a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineNoCov">          0 :         fprintf(outlog, &quot;# number of replica : %d\n&quot;, multi_sim_comm.Get_size() );</span></a>
+<a name="845"><span class="lineNum">     845 </span>            :       }</a>
+<a name="846"><span class="lineNum">     846 </span>            :       else {</a>
+<a name="847"><span class="lineNum">     847 </span>            :         fprintf(outlog, &quot;# LogMFD\n&quot;);</a>
+<a name="848"><span class="lineNum">     848 </span>            :       }</a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span>            :       fprintf(outlog, &quot;# CVs :&quot;);</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :         fprintf(outlog, &quot; %s&quot;,  getPntrToArgument(i)-&gt;getName().c_str() );</a>
+<a name="853"><span class="lineNum">     853 </span>            :       }</a>
+<a name="854"><span class="lineNum">     854 </span>            :       fprintf(outlog, &quot;\n&quot;);</a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span>            :       fprintf(outlog, &quot;# Mass for CV particles :&quot;);</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">          3 :         fprintf(outlog, &quot;%15.6f&quot;, mfict[i]);</span></a>
+<a name="859"><span class="lineNum">     859 </span>            :       }</a>
+<a name="860"><span class="lineNum">     860 </span>            :       fprintf(outlog, &quot;\n&quot;);</a>
+<a name="861"><span class="lineNum">     861 </span>            : </a>
+<a name="862"><span class="lineNum">     862 </span>            :       fprintf(outlog, &quot;# Mass for thermostat   :&quot;);</a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">          3 :       fprintf(outlog, &quot;%15.6f&quot;, meta);</span></a>
+<a name="864"><span class="lineNum">     864 </span>            :       fprintf(outlog, &quot;\n&quot;);</a>
+<a name="865"><span class="lineNum">     865 </span>            :       fprintf(outlog, &quot;# 1:iter_mfd, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,\n&quot;);</a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">          3 :         fprintf(outlog, &quot;# %u:%s_fict(t), %u:%s_vfict(t), %u:%s_force(t),\n&quot;,</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :                 6+i*3, getPntrToArgument(i)-&gt;getName().c_str(),</a>
+<a name="870"><span class="lineNum">     870 </span>            :                 7+i*3, getPntrToArgument(i)-&gt;getName().c_str(),</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">          3 :                 8+i*3, getPntrToArgument(i)-&gt;getName().c_str() );</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :       }</a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">          3 :       fclose(outlog);</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :     }</a>
+<a name="875"><span class="lineNum">     875 </span>            : </a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">          3 :     if( comm.Get_rank()==0 ) {</span></a>
+<a name="877"><span class="lineNum">     877 </span>            :       // the number of replica is added to file name to distingwish replica.</a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">          3 :       FILE *outlog2 = fopen(&quot;replica.out&quot;, &quot;w&quot;);</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">          6 :       fprintf(outlog2, &quot;# Replica No. %d of %d.\n&quot;,</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">          3 :               multi_sim_comm.Get_rank(), multi_sim_comm.Get_size() );</span></a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span>            :       fprintf(outlog2, &quot;# 1:iter_mfd, 2:work, 3:weight,\n&quot;);</a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">          3 :         fprintf(outlog2, &quot;# %u:%s(q)\n&quot;,</span></a>
+<a name="885"><span class="lineNum">     885 </span>            :                 4+i, getPntrToArgument(i)-&gt;getName().c_str() );</a>
+<a name="886"><span class="lineNum">     886 </span>            :       }</a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">          3 :       fclose(outlog2);</span></a>
+<a name="888"><span class="lineNum">     888 </span>            :     }</a>
+<a name="889"><span class="lineNum">     889 </span>            : </a>
+<a name="890"><span class="lineNum">     890 </span>            :     // output messages to Plumed's log file</a>
+<a name="891"><span class="lineNum">     891 </span>            :     //    log.printf(&quot;LOGMFD thermostat parameters Xeta Veta Meta&quot;);</a>
+<a name="892"><span class="lineNum">     892 </span>            :     //    log.printf(&quot; %f %f %f&quot;, xeta, veta, meta);</a>
+<a name="893"><span class="lineNum">     893 </span>            :     //    log.printf(&quot;\n&quot;);</a>
+<a name="894"><span class="lineNum">     894 </span>            :     //    log.printf(&quot;# 1:iter_mfd, 2:Flog, 3:2*Ekin/gkb[K], 4:eta, 5:Veta,&quot;);</a>
+<a name="895"><span class="lineNum">     895 </span>            :     //    log.printf(&quot;# 6:X1(t), 7:V1(t), 8:F1(t), 9:X2(t), 10:V2(t), 11:F2(t), ...&quot;);</a>
+<a name="896"><span class="lineNum">     896 </span>            : </a>
+<a name="897"><span class="lineNum">     897 </span>            :   } // firsttime</a>
+<a name="898"><span class="lineNum">     898 </span>            : </a>
+<a name="899"><span class="lineNum">     899 </span>            :   // calculate force for fictitious variable</a>
+<a name="900"><span class="lineNum">     900 </span>            :   double ene=0.0;</a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">       3000 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="902"><span class="lineNum">     902 </span>            :     // difference between fictitious variable and collective variable.</a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">       1500 :     const double diff = difference(i,fict[i],getArgument(i));</span></a>
+<a name="904"><span class="lineNum">     904 </span>            :     // restraining force.</a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">       1500 :     const double f = -kappa[i]*diff;</span></a>
+<a name="906"><span class="lineNum">     906 </span>            :     setOutputForce(i,f);</a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span>            :     // restraining energy.</a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">       1500 :     ene += 0.5*kappa[i]*diff*diff;</span></a>
+<a name="910"><span class="lineNum">     910 </span>            : </a>
+<a name="911"><span class="lineNum">     911 </span>            :     // accumulate force, later it will be averaged.</a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">       1500 :     ffict[i] += -f;</span></a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span>            :     // accumulate varience of collective variable, later it will be averaged.</a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">       1500 :     fict_ave[i] += diff;</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :   }</a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span>            :   setBias(ene);</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">       3000 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="920"><span class="lineNum">     920 </span>            :     // correct fict so that it is inside [min:max].</a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">       1500 :     double tmp = fict[i];</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">       1500 :     fict[i] = fictValue[i]-&gt;bringBackInPbc(fict[i]);</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">       1500 :     fictValue[i]-&gt;set(fict[i]);</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">       1500 :     vfictValue[i]-&gt;set(vfict[i]);</span></a>
+<a name="925"><span class="lineNum">     925 </span>            :   }</a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">       1500 : } // calculate</span></a>
+<a name="927"><span class="lineNum">     927 </span>            : </a>
+<a name="928"><span class="lineNum">     928 </span>            : /**</a>
+<a name="929"><span class="lineNum">     929 </span>            :    \brief update fictitious variables.</a>
+<a name="930"><span class="lineNum">     930 </span>            :    \details This function manages evolution of fictitious variables.</a>
+<a name="931"><span class="lineNum">     931 </span>            :    This function calculates mean force, updates fictitious variables by one MFD step,</a>
+<a name="932"><span class="lineNum">     932 </span>            :    bounces back variables, updates free energy, and record logs.</a>
+<a name="933"><span class="lineNum">     933 </span>            : */</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">       1500 : void LogMFD::update() {</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">       1500 :   if( (getStep()-step_initial)%interval != interval-1 ) return;</span></a>
+<a name="936"><span class="lineNum">     936 </span>            : </a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">         30 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">         15 :     backup.fict[i]  =  fict[i];</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">         15 :     backup.vfict[i] = vfict[i];</span></a>
+<a name="940"><span class="lineNum">     940 </span>            :   }</a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">         15 :   backup.xeta = xeta;</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">         15 :   backup.veta = veta;</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">         15 :   backup.phivs = phivs;</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">         15 :   backup.work = work;</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">         15 :   backup.weight = weight;</span></a>
+<a name="946"><span class="lineNum">     946 </span>            : </a>
+<a name="947"><span class="lineNum">     947 </span>            :   // calc mean force for fictitious variables</a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">         15 :   calcMeanForce();</span></a>
+<a name="949"><span class="lineNum">     949 </span>            : </a>
+<a name="950"><span class="lineNum">     950 </span>            :   // record log for fictitious variables</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">         15 :   if( multi_sim_comm.Get_rank()==0 &amp;&amp; comm.Get_rank()==0 ) {</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">         15 :     const double ekin = calcEkin();</span></a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">         15 :     const double temp = 2.0*ekin/getNumberOfArguments()/plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="954"><span class="lineNum">     954 </span>            : </a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">         15 :     FILE *outlog = std::fopen(&quot;logmfd.out&quot;, &quot;a&quot;);</span></a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">         15 :     fprintf(outlog, &quot;%*d&quot;, 8, (int)(getStep()-step_initial)/interval);</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">         15 :     fprintf(outlog, &quot;%15.6f&quot;, flog);</span></a>
+<a name="958"><span class="lineNum">     958 </span>            :     fprintf(outlog, &quot;%15.6f&quot;, temp);</a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">         15 :     fprintf(outlog, &quot;%15.6f&quot;, xeta);</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">         15 :     fprintf(outlog, &quot;%15.6f&quot;, veta);</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">         30 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">         15 :       fprintf(outlog, &quot;%15.6f&quot;, fict[i]);</span></a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">         15 :       fprintf(outlog, &quot;%15.6f&quot;, vfict[i]);</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">         15 :       fprintf(outlog, &quot;%15.6f&quot;, ffict[i]);</span></a>
+<a name="965"><span class="lineNum">     965 </span>            :     }</a>
+<a name="966"><span class="lineNum">     966 </span>            :     fprintf(outlog,&quot; \n&quot;);</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">         15 :     fclose(outlog);</span></a>
+<a name="968"><span class="lineNum">     968 </span>            :   }</a>
+<a name="969"><span class="lineNum">     969 </span>            : </a>
+<a name="970"><span class="lineNum">     970 </span>            :   // record log for collective variables</a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">         15 :   if( comm.Get_rank()==0 ) {</span></a>
+<a name="972"><span class="lineNum">     972 </span>            :     // the number of replica is added to file name to distingwish replica.</a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">         15 :     FILE *outlog2 = fopen(&quot;replica.out&quot;, &quot;a&quot;);</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">         15 :     fprintf(outlog2, &quot;%*d&quot;, 8, (int)(getStep()-step_initial)/interval);</span></a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">         15 :     fprintf(outlog2, &quot;%16.6e &quot;, work);</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">         15 :     fprintf(outlog2, &quot;%16.6e &quot;, weight);</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">         30 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">         15 :       fprintf(outlog2, &quot;%15.6f&quot;, fict_ave[i]);</span></a>
+<a name="979"><span class="lineNum">     979 </span>            :     }</a>
+<a name="980"><span class="lineNum">     980 </span>            :     fprintf(outlog2,&quot; \n&quot;);</a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">         15 :     fclose(outlog2);</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :   }</a>
+<a name="983"><span class="lineNum">     983 </span>            : </a>
+<a name="984"><span class="lineNum">     984 </span>            :   // update fictitious variables</a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">         15 :   if(thermostat == &quot;NVE&quot;) {</span></a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">          5 :     updateNVE();</span></a>
+<a name="987"><span class="lineNum">     987 </span>            :   }</a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">         10 :   else if(thermostat == &quot;NVT&quot;) {</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">          5 :     updateNVT();</span></a>
+<a name="990"><span class="lineNum">     990 </span>            :   }</a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">          5 :   else if(thermostat == &quot;VS&quot;) {</span></a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">          5 :     updateVS();</span></a>
+<a name="993"><span class="lineNum">     993 </span>            :   }</a>
+<a name="994"><span class="lineNum">     994 </span>            : </a>
+<a name="995"><span class="lineNum">     995 </span>            :   // update work done by fictitious dynamical variables</a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">         15 :   updateWork();</span></a>
+<a name="997"><span class="lineNum">     997 </span>            : </a>
+<a name="998"><span class="lineNum">     998 </span>            :   // check boundary</a>
+<a name="999"><span class="lineNum">     999 </span>            :   bool reject = false;</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">         30 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">         15 :     if( fict[i] &lt; fict_min[i] || fict_max[i] &lt; fict[i] ) {</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            :       reject = true;</a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineNoCov">          0 :       backup.vfict[i] *= -1.0;</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :     }</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :   }</a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">         15 :   if( reject ) {</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineNoCov">          0 :       fict[i] = backup.fict[i];</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineNoCov">          0 :       vfict[i] = backup.vfict[i];</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            :     }</a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineNoCov">          0 :     xeta = backup.xeta;</span></a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineNoCov">          0 :     veta = backup.veta;</span></a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineNoCov">          0 :     phivs = backup.phivs;</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineNoCov">          0 :     work = backup.work;</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineNoCov">          0 :     weight = backup.weight;</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            :   }</a>
+<a name="1017"><span class="lineNum">    1017 </span>            : </a>
+<a name="1018"><span class="lineNum">    1018 </span>            :   // update free energy</a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">         15 :   flog = calcFlog();</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span>            :   // reset mean force</a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">         30 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">         15 :     ffict[i] = 0.0;</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">         15 :     fict_ave[i] = 0.0;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :   }</a>
+<a name="1026"><span class="lineNum">    1026 </span>            : </a>
+<a name="1027"><span class="lineNum">    1027 </span>            : } // update</a>
+<a name="1028"><span class="lineNum">    1028 </span>            : </a>
+<a name="1029"><span class="lineNum">    1029 </span>            : /**</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :    \brief update fictitious variables by NVE mechanics.</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :    \details This function updates ficitious variables by one NVE-MFD step using mean forces</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :    and flattening coefficient and free energy.</a>
+<a name="1033"><span class="lineNum">    1033 </span>            :  */</a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">          5 : void LogMFD::updateNVE() {</span></a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">          5 :   const double dt = delta_t;</span></a>
+<a name="1036"><span class="lineNum">    1036 </span>            : </a>
+<a name="1037"><span class="lineNum">    1037 </span>            :   // get latest free energy and flattening coefficient</a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">          5 :   flog = calcFlog();</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">          5 :   const double clog = calcClog();</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            : </a>
+<a name="1041"><span class="lineNum">    1041 </span>            :   // update all ficitious variables by one MFD step</a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">         10 :   for( unsigned i=0; i&lt;getNumberOfArguments(); ++i ) {</span></a>
+<a name="1043"><span class="lineNum">    1043 </span>            :     // update velocity (full step)</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">          5 :     vfict[i]+=clog*ffict[i]*dt/mfict[i];</span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     // update position (full step)</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :     fict[i]+=vfict[i]*dt;</a>
+<a name="1047"><span class="lineNum">    1047 </span>            :   }</a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">          5 : } // updateNVE</span></a>
+<a name="1049"><span class="lineNum">    1049 </span>            : </a>
+<a name="1050"><span class="lineNum">    1050 </span>            : /**</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :    \brief update fictitious variables by NVT mechanics.</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :    \details This function updates ficitious variables by one NVT-MFD step using mean forces</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :    and flattening coefficient and free energy.</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :  */</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">          5 : void LogMFD::updateNVT() {</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">          5 :   const double dt = delta_t;</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">          5 :   const double nkt = getNumberOfArguments()*kbt;</span></a>
+<a name="1058"><span class="lineNum">    1058 </span>            : </a>
+<a name="1059"><span class="lineNum">    1059 </span>            :   // backup vfict</a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">          5 :     backup.vfict[i] = vfict[i];</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   }</a>
+<a name="1063"><span class="lineNum">    1063 </span>            : </a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   const int niter=5;</a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">         30 :   for(unsigned j=0; j&lt;niter; ++j) {</span></a>
+<a name="1066"><span class="lineNum">    1066 </span>            :     // get latest free energy and flattening coefficient</a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">         25 :     flog = calcFlog();</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">         25 :     const double clog = calcClog();</span></a>
+<a name="1069"><span class="lineNum">    1069 </span>            : </a>
+<a name="1070"><span class="lineNum">    1070 </span>            :     // restore vfict from backup.vfict</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         50 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         25 :       vfict[i] = backup.vfict[i];</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :     }</a>
+<a name="1074"><span class="lineNum">    1074 </span>            : </a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     // evolve vfict from backup.vfict by dt/2</a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">         50 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">         25 :       vfict[i] *= exp(-0.25*dt*veta);</span></a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">         25 :       vfict[i] += 0.5*dt*clog*ffict[i]/mfict[i];</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">         25 :       vfict[i] *= exp(-0.25*dt*veta);</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :     }</a>
+<a name="1081"><span class="lineNum">    1081 </span>            :   }</a>
+<a name="1082"><span class="lineNum">    1082 </span>            : </a>
+<a name="1083"><span class="lineNum">    1083 </span>            :   // get latest free energy and flattening coefficient</a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">          5 :   flog = calcFlog();</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">          5 :   const double clog = calcClog();</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            : </a>
+<a name="1087"><span class="lineNum">    1087 </span>            :   // evolve vfict by dt/2, and evolve fict by dt</a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">          5 :     vfict[i] *= exp(-0.25*dt*veta);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineCov">          5 :     vfict[i] += 0.5*dt*clog*ffict[i]/mfict[i];</span></a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineCov">          5 :     vfict[i] *= exp(-0.25*dt*veta);</span></a>
+<a name="1092"><span class="lineNum">    1092 </span><span class="lineCov">          5 :     fict[i]  += dt*vfict[i];</span></a>
+<a name="1093"><span class="lineNum">    1093 </span>            :   }</a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   // evolve xeta and veta by dt</a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">          5 :   xeta += 0.5*dt*veta;</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">          5 :   const double ekin = calcEkin();</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">          5 :   veta += dt*(2.0*ekin-nkt)/meta;</span></a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">          5 :   xeta += 0.5*dt*veta;</span></a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">          5 : } // updateNVT</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            : </a>
+<a name="1102"><span class="lineNum">    1102 </span>            : /**</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :    \brief update fictitious variables by VS mechanics.</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :    \details This function updates ficitious variables by one VS-MFD step using mean forces</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :    and flattening coefficient and free energy.</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :  */</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">          5 : void LogMFD::updateVS() {</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">          5 :   const double dt = delta_t;</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineCov">          5 :   const double nkt = getNumberOfArguments()*kbt;</span></a>
+<a name="1110"><span class="lineNum">    1110 </span>            : </a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   // get latest free energy and flattening coefficient</a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineCov">          5 :   flog = calcFlog();</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">          5 :   const double clog = calcClog();</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            : </a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            :     // update velocity (full step)</a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineCov">          5 :     vfict[i] += clog*ffict[i]*dt/mfict[i];</span></a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   }</a>
+<a name="1119"><span class="lineNum">    1119 </span>            : </a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">          5 :   const double ekin = calcEkin();</span></a>
+<a name="1121"><span class="lineNum">    1121 </span><span class="lineCov">          5 :   const double svs = sqrt(nkt/ekin/2);</span></a>
+<a name="1122"><span class="lineNum">    1122 </span>            : </a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1124"><span class="lineNum">    1124 </span>            :     // update position (full step)</a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">          5 :     vfict[i] *= svs;</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">          5 :     fict[i] += vfict[i]*dt;</span></a>
+<a name="1127"><span class="lineNum">    1127 </span>            :   }</a>
+<a name="1128"><span class="lineNum">    1128 </span>            : </a>
+<a name="1129"><span class="lineNum">    1129 </span>            :   // evolve VS potential</a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">          5 :   phivs += nkt*std::log(svs);</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">          5 : } // updateVS</span></a>
+<a name="1132"><span class="lineNum">    1132 </span>            : </a>
+<a name="1133"><span class="lineNum">    1133 </span>            : /**</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :    \brief update work done by fictious variables.</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :    \details This function updates work done by ficitious variables.</a>
+<a name="1136"><span class="lineNum">    1136 </span>            :  */</a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">         15 : void LogMFD::updateWork() {</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   // accumulate work, it was initialized as 0.0</a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">         30 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineCov">         15 :     work -= backup.ffict[i] * vfict[i] * delta_t;</span></a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   }</a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">         15 : } // updateWork</span></a>
+<a name="1143"><span class="lineNum">    1143 </span>            : </a>
+<a name="1144"><span class="lineNum">    1144 </span>            : /**</a>
+<a name="1145"><span class="lineNum">    1145 </span>            :    \brief calculate mean force for fictitious variables.</a>
+<a name="1146"><span class="lineNum">    1146 </span>            :    \details This function calculates mean forces by averaging forces accumulated during one MFD step,</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :    update work variables done by fictitious variables by one MFD step,</a>
+<a name="1148"><span class="lineNum">    1148 </span>            :    calculate weight variable of this replica for LogPD.</a>
+<a name="1149"><span class="lineNum">    1149 </span>            : */</a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">         15 : void LogMFD::calcMeanForce() {</span></a>
+<a name="1151"><span class="lineNum">    1151 </span>            :   // cale temporal mean force for each CV</a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">         30 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineCov">         15 :     ffict[i] /= interval;</span></a>
+<a name="1154"><span class="lineNum">    1154 </span>            :     // backup force of replica</a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">         15 :     backup.ffict[i] = ffict[i];</span></a>
+<a name="1156"><span class="lineNum">    1156 </span>            :     // average of diff (getArgument(i)-fict[i])</a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">         15 :     fict_ave[i] /= interval;</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :     // average of getArgument(i)</a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineCov">         15 :     fict_ave[i] += fict[i];</span></a>
+<a name="1160"><span class="lineNum">    1160 </span>            : </a>
+<a name="1161"><span class="lineNum">    1161 </span>            :     // correct fict_ave so that it is inside [min:max].</a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">         15 :     fict_ave[i] = fictValue[i]-&gt;bringBackInPbc(fict_ave[i]);</span></a>
+<a name="1163"><span class="lineNum">    1163 </span>            :   }</a>
+<a name="1164"><span class="lineNum">    1164 </span>            : </a>
+<a name="1165"><span class="lineNum">    1165 </span>            :   // for replica parallel</a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">         15 :   if( multi_sim_comm.Get_size()&gt;1 ) {</span></a>
+<a name="1167"><span class="lineNum">    1167 </span>            :     // find the minimum work among all replicas</a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineNoCov">          0 :     double work_min = work;</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineNoCov">          0 :     multi_sim_comm.Min(work_min);</span></a>
+<a name="1170"><span class="lineNum">    1170 </span>            : </a>
+<a name="1171"><span class="lineNum">    1171 </span>            :     // weight of this replica.</a>
+<a name="1172"><span class="lineNum">    1172 </span>            :     // here, work is reduced by work_min to avoid all exp(-work/kbt)s disconverge</a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineNoCov">          0 :     if( kbtpd == 0.0 ) {</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineNoCov">          0 :       weight = work==work_min ? 1.0 : 0.0;</span></a>
+<a name="1175"><span class="lineNum">    1175 </span>            :     }</a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     else {</a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineNoCov">          0 :       weight = exp(-(work-work_min)/kbtpd);</span></a>
+<a name="1178"><span class="lineNum">    1178 </span>            :     }</a>
+<a name="1179"><span class="lineNum">    1179 </span>            : </a>
+<a name="1180"><span class="lineNum">    1180 </span>            :     // normalize the weight</a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineNoCov">          0 :     double sum_weight = weight;</span></a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineNoCov">          0 :     multi_sim_comm.Sum(sum_weight);</span></a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineNoCov">          0 :     weight /= sum_weight;</span></a>
+<a name="1184"><span class="lineNum">    1184 </span>            : </a>
+<a name="1185"><span class="lineNum">    1185 </span>            :     // weighting force of this replica</a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineNoCov">          0 :       ffict[i] *= weight;</span></a>
+<a name="1188"><span class="lineNum">    1188 </span>            :     }</a>
+<a name="1189"><span class="lineNum">    1189 </span>            : </a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     // averaged mean forces of all replica.</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :       multi_sim_comm.Sum(ffict[i]);</span></a>
+<a name="1193"><span class="lineNum">    1193 </span>            :     }</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :     // now, mean force is obtained.</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :   }</a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineCov">         15 : } // calcMeanForce</span></a>
+<a name="1197"><span class="lineNum">    1197 </span>            : </a>
+<a name="1198"><span class="lineNum">    1198 </span>            : /**</a>
+<a name="1199"><span class="lineNum">    1199 </span>            :    \brief calculate kinetic energy of fictitious variables.</a>
+<a name="1200"><span class="lineNum">    1200 </span>            :    \retval kinetic energy.</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :    \details This function calculates sum of kinetic energy of all fictitious variables.</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :  */</a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineCov">         83 : double LogMFD::calcEkin() {</span></a>
+<a name="1204"><span class="lineNum">    1204 </span>            :   double ekin=0.0;</a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">        166 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">         83 :     ekin += mfict[i]*vfict[i]*vfict[i]*0.5;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            :   }</a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineCov">         83 :   return ekin;</span></a>
+<a name="1209"><span class="lineNum">    1209 </span>            : } // calcEkin</a>
+<a name="1210"><span class="lineNum">    1210 </span>            : </a>
+<a name="1211"><span class="lineNum">    1211 </span>            : /**</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :    \brief calculate free energy of fictitious variables.</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :    \retval free energy.</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :    \details This function calculates free energy by using invariant of canonical mechanics.</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :  */</a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineCov">         55 : double LogMFD::calcFlog() {</span></a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">         55 :   const double nkt = getNumberOfArguments()*kbt;</span></a>
+<a name="1218"><span class="lineNum">    1218 </span><span class="lineCov">         55 :   const double ekin = calcEkin();</span></a>
+<a name="1219"><span class="lineNum">    1219 </span>            :   double pot;</a>
+<a name="1220"><span class="lineNum">    1220 </span>            : </a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineCov">         55 :   if (thermostat == &quot;NVE&quot;) {</span></a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">         10 :     pot = hlog - ekin;</span></a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   }</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">         45 :   else if (thermostat == &quot;NVT&quot;) {</span></a>
+<a name="1225"><span class="lineNum">    1225 </span><span class="lineCov">         35 :     const double ekin_bath = 0.5*veta*veta*meta+xeta*nkt;</span></a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">         35 :     pot = hlog - ekin - ekin_bath;</span></a>
+<a name="1227"><span class="lineNum">    1227 </span>            :   }</a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">         10 :   else if (thermostat == &quot;VS&quot;) {</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">         10 :     pot = phivs;</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   }</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :   else {</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :     pot = 0.0; // never occurs</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :   }</a>
+<a name="1234"><span class="lineNum">    1234 </span>            : </a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineCov">        110 :   return TAMD ? pot : sgn(pot)*expm1(fabs(pot)/gamma)/alpha;</span></a>
+<a name="1236"><span class="lineNum">    1236 </span>            : } // calcFlog</a>
+<a name="1237"><span class="lineNum">    1237 </span>            : </a>
+<a name="1238"><span class="lineNum">    1238 </span>            : /**</a>
+<a name="1239"><span class="lineNum">    1239 </span>            :    \brief calculate coefficient for flattening.</a>
+<a name="1240"><span class="lineNum">    1240 </span>            :    \retval flattering coefficient.</a>
+<a name="1241"><span class="lineNum">    1241 </span>            :    \details This function returns 1.0 for TAMD, flattening coefficient for LogMFD.</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :  */</a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">         40 : double LogMFD::calcClog() {</span></a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">         40 :   return TAMD ? 1.0 : alpha*gamma/(alpha*fabs(flog)+1.0);</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            : } // calcClog</a>
+<a name="1246"><span class="lineNum">    1246 </span>            : </a>
+<a name="1247"><span class="lineNum">    1247 </span>            : } // logmfd</a>
+<a name="1248"><span class="lineNum">    1248 </span>            : } // PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/logmfd/index-sort-f.html b/coverage/logmfd/index-sort-f.html
new file mode 100644
index 0000000000..5ee58809fb
--- /dev/null
+++ b/coverage/logmfd/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - logmfd</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - logmfd</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">372</td>
+            <td class="headerCovTableEntryMed">87.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LogMFD.cpp.gcov.html">LogMFD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.6%"><img src="../snow.png" width=12 height=10 alt="87.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.6&nbsp;%</td>
+      <td class="coverNumMed">326 / 372</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/logmfd/index-sort-l.html b/coverage/logmfd/index-sort-l.html
new file mode 100644
index 0000000000..74cecfbd7e
--- /dev/null
+++ b/coverage/logmfd/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - logmfd</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - logmfd</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">372</td>
+            <td class="headerCovTableEntryMed">87.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LogMFD.cpp.gcov.html">LogMFD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.6%"><img src="../snow.png" width=12 height=10 alt="87.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.6&nbsp;%</td>
+      <td class="coverNumMed">326 / 372</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/logmfd/index.html b/coverage/logmfd/index.html
new file mode 100644
index 0000000000..460736a869
--- /dev/null
+++ b/coverage/logmfd/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - logmfd</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - logmfd</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">372</td>
+            <td class="headerCovTableEntryMed">87.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LogMFD.cpp.gcov.html">LogMFD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.6%"><img src="../snow.png" width=12 height=10 alt="87.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.6&nbsp;%</td>
+      <td class="coverNumMed">326 / 372</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/main/index-sort-f.html b/coverage/main/index-sort-f.html
new file mode 100644
index 0000000000..d2af481463
--- /dev/null
+++ b/coverage/main/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - main</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - main</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="main.cpp.gcov.html">main.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/main/index-sort-l.html b/coverage/main/index-sort-l.html
new file mode 100644
index 0000000000..4c30e14d6d
--- /dev/null
+++ b/coverage/main/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - main</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - main</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="main.cpp.gcov.html">main.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/main/index.html b/coverage/main/index.html
new file mode 100644
index 0000000000..28abb0a6a3
--- /dev/null
+++ b/coverage/main/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - main</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - main</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="main.cpp.gcov.html">main.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/main/main.cpp.func-sort-c.html b/coverage/main/main.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3e951c08ea
--- /dev/null
+++ b/coverage/main/main.cpp.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - main/main.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">main</a> - main.cpp<span style="font-size: 80%;"> (<a href="main.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="main.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="main.cpp.gcov.html#34">main</a></td>
+              <td class="coverFnHi">4133</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/main/main.cpp.func.html b/coverage/main/main.cpp.func.html
new file mode 100644
index 0000000000..716c8fc773
--- /dev/null
+++ b/coverage/main/main.cpp.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - main/main.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">main</a> - main.cpp<span style="font-size: 80%;"> (<a href="main.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="main.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="main.cpp.gcov.html#34">main</a></td>
+              <td class="coverFnHi">4133</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/main/main.cpp.gcov.html b/coverage/main/main.cpp.gcov.html
new file mode 100644
index 0000000000..1f7da47226
--- /dev/null
+++ b/coverage/main/main.cpp.gcov.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - main/main.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">main</a> - main.cpp<span style="font-size: 80%;"> (source / <a href="main.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;wrapper/Plumed.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;cstring&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;mpi.h&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #endif</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : /**</a>
+<a name="30"><span class="lineNum">      30 </span>            :   This main uses only the interface published in</a>
+<a name="31"><span class="lineNum">      31 </span>            :   Plumed.h. The object file generated from this .cpp</a>
+<a name="32"><span class="lineNum">      32 </span>            :   is the only part of the plumed library that should</a>
+<a name="33"><span class="lineNum">      33 </span>            :   not be linked with external MD codes, so as</a>
+<a name="34"><span class="lineNum">      34 </span>            :   to avoid linker error.</a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       4133 : int main(int argc,char**argv) {</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="38"><span class="lineNum">      38 </span>            :   bool nompi=false;</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       8566 :   for(unsigned iarg=1; iarg&lt;argc; iarg++) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       7928 :     if(!std::strcmp(argv[iarg],&quot;--no-mpi&quot;)) nompi=true;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       7928 :     if(!std::strcmp(argv[iarg],&quot;--mpi&quot;))    nompi=false;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : // stop at first non-option</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       7928 :     if(argv[iarg] &amp;&amp; argv[iarg][0]!='-') break;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   }</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       4133 :   if(!nompi) MPI_Init(&amp;argc,&amp;argv);</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : #endif</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       4133 :   int ret=0;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            :   try {</a>
+<a name="50"><span class="lineNum">      50 </span>            :     PLMD::Plumed p;</a>
+<a name="51"><span class="lineNum">      51 </span>            :     p.cmd(&quot;CLTool setArgc&quot;,&amp;argc);</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       4133 :     p.cmd(&quot;CLTool setArgv&quot;,argv);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       4133 :     if(!nompi) {</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :       MPI_Comm comm;</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        338 :       MPI_Comm_dup(MPI_COMM_WORLD,&amp;comm);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :       p.cmd(&quot;CLTool setMPIComm&quot;,&amp;comm);</a>
+<a name="58"><span class="lineNum">      58 </span>            :     }</a>
+<a name="59"><span class="lineNum">      59 </span>            : #endif</a>
+<a name="60"><span class="lineNum">      60 </span>            :     p.cmd(&quot;CLTool run&quot;,&amp;ret);</a>
+<a name="61"><span class="lineNum">      61 </span>            : // end block deletes p also in case an exception occurs</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   } catch(...) {</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : // exception is rethrown and results in a call to terminate</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :     throw;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       4133 :   if(!nompi) MPI_Finalize();</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : #endif</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       4133 :   return ret;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/LWalls.cpp.func-sort-c.html b/coverage/manyrestraints/LWalls.cpp.func-sort-c.html
new file mode 100644
index 0000000000..335fd41d19
--- /dev/null
+++ b/coverage/manyrestraints/LWalls.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/LWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - LWalls.cpp<span style="font-size: 80%;"> (<a href="LWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LWalls.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#69">_ZN4PLMD14manyrestraints12_GLOBAL__N_118LWallsRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#80">_ZN4PLMD14manyrestraints6LWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#80">_ZN4PLMD14manyrestraints6LWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#92">_ZNK4PLMD14manyrestraints6LWalls13calcPotentialERKdRd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#71">_ZN4PLMD14manyrestraints6LWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#69">_ZN4PLMD14manyrestraints12_GLOBAL__N_118LWallsRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#69">_ZN4PLMD14manyrestraints12_GLOBAL__N_118LWallsRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/LWalls.cpp.func.html b/coverage/manyrestraints/LWalls.cpp.func.html
new file mode 100644
index 0000000000..28038e57ce
--- /dev/null
+++ b/coverage/manyrestraints/LWalls.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/LWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - LWalls.cpp<span style="font-size: 80%;"> (<a href="LWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LWalls.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#69">_ZN4PLMD14manyrestraints12_GLOBAL__N_118LWallsRegisterMe716createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#69">_ZN4PLMD14manyrestraints12_GLOBAL__N_118LWallsRegisterMe71C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#69">_ZN4PLMD14manyrestraints12_GLOBAL__N_118LWallsRegisterMe71D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#71">_ZN4PLMD14manyrestraints6LWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#80">_ZN4PLMD14manyrestraints6LWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#80">_ZN4PLMD14manyrestraints6LWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LWalls.cpp.gcov.html#92">_ZNK4PLMD14manyrestraints6LWalls13calcPotentialERKdRd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/LWalls.cpp.gcov.html b/coverage/manyrestraints/LWalls.cpp.gcov.html
new file mode 100644
index 0000000000..69af9e7a1c
--- /dev/null
+++ b/coverage/manyrestraints/LWalls.cpp.gcov.html
@@ -0,0 +1,184 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/LWalls.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - LWalls.cpp<span style="font-size: 80%;"> (source / <a href="LWalls.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">42.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ManyRestraintsBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace manyrestraints {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC MCOLVARB LWALLS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Add LOWER_WALLS restraints on all the multicolvar values</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This action takes the set of values calculated by the colvar specified by label in the DATA</a>
+<a name="33"><span class="lineNum">      33 </span>            : keyword and places a restraint on each quantity, \f$x\f$, with the following functional form:</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \f$</a>
+<a name="36"><span class="lineNum">      36 </span>            :   k((x-a+o)/s)^e</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f$</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$k\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s\f$ (EPS) a rescaling factor and</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f$e\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFF = 0.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : The following set of commands can be used to stop any of the 800 atoms in group A from moving more than 2.46425 nm</a>
+<a name="45"><span class="lineNum">      45 </span>            : in the z direction from atom 34137.  This is done by adding a lower wall on the z-distance between all the atoms in</a>
+<a name="46"><span class="lineNum">      46 </span>            : group A and the position of 34137.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \plumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : l: ZDISTANCES GROUPA=1-800 GROUPB=34137 NOPBC</a>
+<a name="50"><span class="lineNum">      50 </span>            : LWALLS DATA=l AT=2.46465 KAPPA=150.0 EXP=2 EPS=1 OFFSET=0 LABEL=lwall</a>
+<a name="51"><span class="lineNum">      51 </span>            : \endplumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : */</a>
+<a name="55"><span class="lineNum">      55 </span>            : //+ENDPLUMEDOC</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : class LWalls : public ManyRestraintsBase {</a>
+<a name="59"><span class="lineNum">      59 </span>            : private:</a>
+<a name="60"><span class="lineNum">      60 </span>            :   double at;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   double kappa;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double exp;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double eps;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double offset;</a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="67"><span class="lineNum">      67 </span>            :   explicit LWalls( const ActionOptions&amp; );</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double calcPotential( const double&amp; val, double&amp; df ) const override;</a>
+<a name="69"><span class="lineNum">      69 </span>            : };</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(LWalls,&quot;LWALLS&quot;)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 : void LWalls::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          2 :   ManyRestraintsBase::registerKeywords( keys );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;the radius of the sphere&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;the force constant for the wall.  The k_i in the expression for a wall.&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET&quot;,&quot;0.0&quot;,&quot;the offset for the start of the wall.  The o_i in the expression for a wall.&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;EXP&quot;,&quot;2.0&quot;,&quot;the powers for the walls.  The e_i in the expression for a wall.&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;EPS&quot;,&quot;1.0&quot;,&quot;the values for s_i in the expression for a wall&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          2 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 : LWalls::LWalls(const ActionOptions&amp; ao):</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   Action(ao),</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   ManyRestraintsBase(ao)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : {</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   parse(&quot;AT&quot;,at);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   parse(&quot;OFFSET&quot;,offset);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :   parse(&quot;EPS&quot;,eps);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   parse(&quot;EXP&quot;,exp);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   parse(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 : double LWalls::calcPotential( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   double uscale = (val - at + offset)/eps;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   if( uscale &lt; 0. ) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     double power = pow( uscale, exp );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     df = ( kappa / eps ) * exp * power / uscale;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     return kappa*power;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   return 0.0;</a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/ManyRestraintsBase.cpp.func-sort-c.html b/coverage/manyrestraints/ManyRestraintsBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..17899a46d1
--- /dev/null
+++ b/coverage/manyrestraints/ManyRestraintsBase.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/ManyRestraintsBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - ManyRestraintsBase.cpp<span style="font-size: 80%;"> (<a href="ManyRestraintsBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ManyRestraintsBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#37">_ZN4PLMD14manyrestraints18ManyRestraintsBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#37">_ZN4PLMD14manyrestraints18ManyRestraintsBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#26">_ZN4PLMD14manyrestraints18ManyRestraintsBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#87">_ZN4PLMD14manyrestraints18ManyRestraintsBase5applyEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#63">_ZN4PLMD14manyrestraints18ManyRestraintsBase28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">740</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#68">_ZNK4PLMD14manyrestraints18ManyRestraintsBase27transformBridgedDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">14800</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/ManyRestraintsBase.cpp.func.html b/coverage/manyrestraints/ManyRestraintsBase.cpp.func.html
new file mode 100644
index 0000000000..38264a68ba
--- /dev/null
+++ b/coverage/manyrestraints/ManyRestraintsBase.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/ManyRestraintsBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - ManyRestraintsBase.cpp<span style="font-size: 80%;"> (<a href="ManyRestraintsBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ManyRestraintsBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#26">_ZN4PLMD14manyrestraints18ManyRestraintsBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#63">_ZN4PLMD14manyrestraints18ManyRestraintsBase28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">740</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#87">_ZN4PLMD14manyrestraints18ManyRestraintsBase5applyEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#37">_ZN4PLMD14manyrestraints18ManyRestraintsBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#37">_ZN4PLMD14manyrestraints18ManyRestraintsBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.cpp.gcov.html#68">_ZNK4PLMD14manyrestraints18ManyRestraintsBase27transformBridgedDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">14800</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/ManyRestraintsBase.cpp.gcov.html b/coverage/manyrestraints/ManyRestraintsBase.cpp.gcov.html
new file mode 100644
index 0000000000..4f9b47d3fb
--- /dev/null
+++ b/coverage/manyrestraints/ManyRestraintsBase.cpp.gcov.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/ManyRestraintsBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - ManyRestraintsBase.cpp<span style="font-size: 80%;"> (source / <a href="ManyRestraintsBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ManyRestraintsBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/Vessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace manyrestraints {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          6 : void ManyRestraintsBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          6 :   Action::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">          6 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          6 :   ActionWithVessel::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          6 :   ActionWithInputVessel::registerKeywords( keys );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          6 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         12 :   keys.add(&quot;hidden&quot;,&quot;STRIDE&quot;,&quot;the frequency with which the forces due to the bias should be calculated.  This can be used to correctly set up multistep algorithms&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          6 :   keys.remove(&quot;TOL&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;bias&quot;,&quot;default&quot;,&quot;the instantaneous value of the bias potentials&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          6 : }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          2 : ManyRestraintsBase::ManyRestraintsBase(const ActionOptions&amp; ao):</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   Action(ao),</a>
+<a name="41"><span class="lineNum">      41 </span>            :   ActionWithValue(ao),</a>
+<a name="42"><span class="lineNum">      42 </span>            :   ActionPilot(ao),</a>
+<a name="43"><span class="lineNum">      43 </span>            :   ActionWithVessel(ao),</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          2 :   ActionWithInputVessel(ao)</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span>            :   // Read in the vessel we are action on</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          2 :   readArgument(&quot;bridge&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          2 :   aves=dynamic_cast&lt;ActionWithVessel*&gt;( getDependencies()[0] );</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 :   plumed_assert( getDependencies().size()==1 &amp;&amp; aves );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          2 :   log.printf(&quot;  adding restraints on variables calculated by %s action with label %s\n&quot;,</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          2 :              aves-&gt;getName().c_str(),aves-&gt;getLabel().c_str());</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            :   // Add a task list in order to avoid problems</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;aves-&gt;getFullNumberOfTasks(); ++i) addTaskToList( aves-&gt;getTaskCode(i) );</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   // And turn on the derivatives (note problems here because of ActionWithValue)</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          2 :   turnOnDerivatives(); needsDerivatives();</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            :   // Now create the vessel</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          2 :   std::string fake_input=&quot;LABEL=bias&quot;;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 :   addVessel( &quot;SUM&quot;, fake_input, 0 );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :   readVesselKeywords();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        740 : void ManyRestraintsBase::doJobsRequiredBeforeTaskList() {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        740 :   ActionWithVessel::doJobsRequiredBeforeTaskList();</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        740 :   ActionWithValue::clearDerivatives();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        740 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      14800 : void ManyRestraintsBase::transformBridgedDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) const {</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   outvals.setValue( 0, invals.get(0) );</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   // Get the potential</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      14800 :   double dval=0, val=calcPotential( invals.get(1), dval );</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            :   outvals.setValue( 1, val );</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     236800 :   for(unsigned i=0; i&lt;invals.getNumberActive(); ++i) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     222000 :     unsigned jder=invals.getActiveIndex(i);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     222000 :     outvals.addDerivative( 1, jder, dval*invals.getDerivative( 1, jder ) );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   // Now update the outvals derivatives lists</a>
+<a name="83"><span class="lineNum">      83 </span>            :   outvals.emptyActiveMembers();</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">     236800 :   for(unsigned j=0; j&lt;invals.getNumberActive(); ++j) outvals.updateIndex( invals.getActiveIndex(j) );</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   outvals.completeUpdate();</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      14800 :   return;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         10 : void ManyRestraintsBase::apply() {</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   plumed_dbg_assert( getNumberOfComponents()==1 );</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         10 :   getPntrToComponent(0)-&gt;addForce( -1.0*getStride() );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         10 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/ManyRestraintsBase.h.func-sort-c.html b/coverage/manyrestraints/ManyRestraintsBase.h.func-sort-c.html
new file mode 100644
index 0000000000..0920bfd182
--- /dev/null
+++ b/coverage/manyrestraints/ManyRestraintsBase.h.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/ManyRestraintsBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - ManyRestraintsBase.h<span style="font-size: 80%;"> (<a href="ManyRestraintsBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ManyRestraintsBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#44">_ZN4PLMD14manyrestraints18ManyRestraintsBase10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#60">_ZNK4PLMD14manyrestraints18ManyRestraintsBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#58">_ZN4PLMD14manyrestraints18ManyRestraintsBase9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#50">_ZN4PLMD14manyrestraints18ManyRestraintsBase16clearDerivativesEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#63">_ZN4PLMD14manyrestraints18ManyRestraintsBase17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#67">_ZN4PLMD14manyrestraints18ManyRestraintsBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">14828</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/ManyRestraintsBase.h.func.html b/coverage/manyrestraints/ManyRestraintsBase.h.func.html
new file mode 100644
index 0000000000..d02cb9c78f
--- /dev/null
+++ b/coverage/manyrestraints/ManyRestraintsBase.h.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/ManyRestraintsBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - ManyRestraintsBase.h<span style="font-size: 80%;"> (<a href="ManyRestraintsBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ManyRestraintsBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#44">_ZN4PLMD14manyrestraints18ManyRestraintsBase10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#50">_ZN4PLMD14manyrestraints18ManyRestraintsBase16clearDerivativesEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#63">_ZN4PLMD14manyrestraints18ManyRestraintsBase17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#67">_ZN4PLMD14manyrestraints18ManyRestraintsBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">14828</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#58">_ZN4PLMD14manyrestraints18ManyRestraintsBase9calculateEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ManyRestraintsBase.h.gcov.html#60">_ZNK4PLMD14manyrestraints18ManyRestraintsBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/ManyRestraintsBase.h.gcov.html b/coverage/manyrestraints/ManyRestraintsBase.h.gcov.html
new file mode 100644
index 0000000000..5c4d099ba0
--- /dev/null
+++ b/coverage/manyrestraints/ManyRestraintsBase.h.gcov.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/ManyRestraintsBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - ManyRestraintsBase.h<span style="font-size: 80%;"> (source / <a href="ManyRestraintsBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_manyrestraints_ManyRestraintsBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_manyrestraints_ManyRestraintsBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;vesselbase/ActionWithInputVessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace manyrestraints {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class ManyRestraintsBase :</a>
+<a name="35"><span class="lineNum">      35 </span>            :   public ActionWithValue,</a>
+<a name="36"><span class="lineNum">      36 </span>            :   public ActionPilot,</a>
+<a name="37"><span class="lineNum">      37 </span>            :   public vesselbase::ActionWithVessel,</a>
+<a name="38"><span class="lineNum">      38 </span>            :   public vesselbase::ActionWithInputVessel</a>
+<a name="39"><span class="lineNum">      39 </span>            : {</a>
+<a name="40"><span class="lineNum">      40 </span>            : private:</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Pointer to underlying action with vessel</a>
+<a name="42"><span class="lineNum">      42 </span>            :   vesselbase::ActionWithVessel* aves;</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit ManyRestraintsBase(const ActionOptions&amp;);</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Routines that have to be defined so as not to have problems with virtual methods</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void deactivate_task( const unsigned &amp; task_index ) {};</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Don't actually clear the derivatives when this is called from plumed main.</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// They are calculated inside another action and clearing them would be bad</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         10 :   void clearDerivatives() override {}</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Do jobs required before tasks are undertaken</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void doJobsRequiredBeforeTaskList() override;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// This actually does the calculation</a>
+<a name="56"><span class="lineNum">      56 </span>            :   void transformBridgedDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) const override;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Calculate the potential</a>
+<a name="58"><span class="lineNum">      58 </span>            :   virtual double calcPotential( const double&amp; val, double&amp; df ) const=0;</a>
+<a name="59"><span class="lineNum">      59 </span>            : // Calculate does nothing</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          5 :   void calculate() override {};</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : /// This should never be called</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override { plumed_error(); }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Deactivate task now does nothing</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void apply() override;</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         10 :   void applyBridgeForces( const std::vector&lt;double&gt;&amp; bb ) override { plumed_assert( bb.size()==0 ); }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : inline</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      14828 : unsigned ManyRestraintsBase::getNumberOfDerivatives() {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      14828 :   return aves-&gt;getNumberOfDerivatives();</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/UWalls.cpp.func-sort-c.html b/coverage/manyrestraints/UWalls.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a3be726c82
--- /dev/null
+++ b/coverage/manyrestraints/UWalls.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/UWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - UWalls.cpp<span style="font-size: 80%;"> (<a href="UWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="UWalls.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#84">_ZN4PLMD14manyrestraints6UWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD14manyrestraints12_GLOBAL__N_118UWallsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#84">_ZN4PLMD14manyrestraints6UWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#75">_ZN4PLMD14manyrestraints6UWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD14manyrestraints12_GLOBAL__N_118UWallsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD14manyrestraints12_GLOBAL__N_118UWallsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#96">_ZNK4PLMD14manyrestraints6UWalls13calcPotentialERKdRd</a></td>
+              <td class="coverFnHi">14800</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/UWalls.cpp.func.html b/coverage/manyrestraints/UWalls.cpp.func.html
new file mode 100644
index 0000000000..b94d3860a3
--- /dev/null
+++ b/coverage/manyrestraints/UWalls.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/UWalls.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - UWalls.cpp<span style="font-size: 80%;"> (<a href="UWalls.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="UWalls.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD14manyrestraints12_GLOBAL__N_118UWallsRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD14manyrestraints12_GLOBAL__N_118UWallsRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#73">_ZN4PLMD14manyrestraints12_GLOBAL__N_118UWallsRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#75">_ZN4PLMD14manyrestraints6UWalls16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#84">_ZN4PLMD14manyrestraints6UWallsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#84">_ZN4PLMD14manyrestraints6UWallsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="UWalls.cpp.gcov.html#96">_ZNK4PLMD14manyrestraints6UWalls13calcPotentialERKdRd</a></td>
+              <td class="coverFnHi">14800</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/UWalls.cpp.gcov.html b/coverage/manyrestraints/UWalls.cpp.gcov.html
new file mode 100644
index 0000000000..a51bccdf56
--- /dev/null
+++ b/coverage/manyrestraints/UWalls.cpp.gcov.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints/UWalls.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">manyrestraints</a> - UWalls.cpp<span style="font-size: 80%;"> (source / <a href="UWalls.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ManyRestraintsBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace manyrestraints {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : //+PLUMEDOC MCOLVARB UWALLS</a>
+<a name="29"><span class="lineNum">      29 </span>            : /*</a>
+<a name="30"><span class="lineNum">      30 </span>            : Add UPPER_WALL restraints on all the multicolvar values</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : This action takes the set of values calculated by the colvar specified by label in the DATA</a>
+<a name="33"><span class="lineNum">      33 </span>            : keyword and places a restraint on each quantity, \f$x\f$, with the following functional form:</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \f$</a>
+<a name="36"><span class="lineNum">      36 </span>            :   k((x-a+o)/s)^e</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f$</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$k\f$ (KAPPA) is an energy constant in internal unit of the code, \f$s\f$ (EPS) a rescaling factor and</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f$e\f$ (EXP) the exponent determining the power law. By default: EXP = 2, EPS = 1.0, OFF = 0.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : The following set of commands can be used to stop a cluster composed of 20 atoms subliming.  The position of</a>
+<a name="45"><span class="lineNum">      45 </span>            : the center of mass of the cluster is calculated by the \ref COM command labelled c1.  The \ref DISTANCES</a>
+<a name="46"><span class="lineNum">      46 </span>            : command labelled d1 is then used to calculate the distance between each of the 20 atoms in the cluster</a>
+<a name="47"><span class="lineNum">      47 </span>            : and the center of mass of the cluster.  These distances are then passed to the UWALLS command, which adds</a>
+<a name="48"><span class="lineNum">      48 </span>            : a \ref UPPER_WALLS restraint on each of them and thereby prevents each of them from moving very far from the center</a>
+<a name="49"><span class="lineNum">      49 </span>            : of mass of the cluster.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : COM ATOMS=1-20 LABEL=c1</a>
+<a name="53"><span class="lineNum">      53 </span>            : DISTANCES GROUPA=c1 GROUPB=1-20 LABEL=d1</a>
+<a name="54"><span class="lineNum">      54 </span>            : UWALLS DATA=d1 AT=2.5 KAPPA=0.2 LABEL=sr</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : class UWalls : public ManyRestraintsBase {</a>
+<a name="63"><span class="lineNum">      63 </span>            : private:</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double at;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double kappa;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double exp;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double eps;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double offset;</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit UWalls( const ActionOptions&amp; );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double calcPotential( const double&amp; val, double&amp; df ) const override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(UWalls,&quot;UWALLS&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          4 : void UWalls::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 :   ManyRestraintsBase::registerKeywords( keys );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;the radius of the sphere&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;the force constant for the wall.  The k_i in the expression for a wall.&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET&quot;,&quot;0.0&quot;,&quot;the offset for the start of the wall.  The o_i in the expression for a wall.&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;EXP&quot;,&quot;2.0&quot;,&quot;the powers for the walls.  The e_i in the expression for a wall.&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;EPS&quot;,&quot;1.0&quot;,&quot;the values for s_i in the expression for a wall&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 : UWalls::UWalls(const ActionOptions&amp; ao):</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   Action(ao),</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          2 :   ManyRestraintsBase(ao)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          2 :   parse(&quot;AT&quot;,at);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   parse(&quot;OFFSET&quot;,offset);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 :   parse(&quot;EPS&quot;,eps);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   parse(&quot;EXP&quot;,exp);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   parse(&quot;KAPPA&quot;,kappa);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      14800 : double UWalls::calcPotential( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      14800 :   double uscale = (val - at + offset)/eps;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      14800 :   if( uscale &gt; 0. ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1036 :     double power = pow( uscale, exp );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       1036 :     df = ( kappa / eps ) * exp * power / uscale;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1036 :     return kappa*power;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   return 0.0;</a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/index-sort-f.html b/coverage/manyrestraints/index-sort-f.html
new file mode 100644
index 0000000000..8caa68d2eb
--- /dev/null
+++ b/coverage/manyrestraints/index-sort-f.html
@@ -0,0 +1,123 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - manyrestraints</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LWalls.cpp.gcov.html">LWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=38 height=10 alt="37.5%"><img src="../snow.png" width=62 height=10 alt="37.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">9 / 24</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ManyRestraintsBase.h.gcov.html">ManyRestraintsBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="71.4%"><img src="../snow.png" width=29 height=10 alt="71.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ManyRestraintsBase.cpp.gcov.html">ManyRestraintsBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UWalls.cpp.gcov.html">UWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/index-sort-l.html b/coverage/manyrestraints/index-sort-l.html
new file mode 100644
index 0000000000..28712fdf2b
--- /dev/null
+++ b/coverage/manyrestraints/index-sort-l.html
@@ -0,0 +1,123 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - manyrestraints</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LWalls.cpp.gcov.html">LWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=38 height=10 alt="37.5%"><img src="../snow.png" width=62 height=10 alt="37.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">9 / 24</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ManyRestraintsBase.h.gcov.html">ManyRestraintsBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="71.4%"><img src="../snow.png" width=29 height=10 alt="71.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UWalls.cpp.gcov.html">UWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ManyRestraintsBase.cpp.gcov.html">ManyRestraintsBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/manyrestraints/index.html b/coverage/manyrestraints/index.html
new file mode 100644
index 0000000000..c92166cb82
--- /dev/null
+++ b/coverage/manyrestraints/index.html
@@ -0,0 +1,123 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - manyrestraints</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - manyrestraints</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LWalls.cpp.gcov.html">LWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=38 height=10 alt="37.5%"><img src="../snow.png" width=62 height=10 alt="37.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">9 / 24</td>
+      <td class="coverPerLo">42.9&nbsp;%</td>
+      <td class="coverNumLo">3 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ManyRestraintsBase.cpp.gcov.html">ManyRestraintsBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ManyRestraintsBase.h.gcov.html">ManyRestraintsBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="71.4%"><img src="../snow.png" width=29 height=10 alt="71.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="UWalls.cpp.gcov.html">UWalls.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/AdaptivePath.cpp.func-sort-c.html b/coverage/mapping/AdaptivePath.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5e2f6813d7
--- /dev/null
+++ b/coverage/mapping/AdaptivePath.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/AdaptivePath.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - AdaptivePath.cpp<span style="font-size: 80%;"> (<a href="AdaptivePath.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AdaptivePath.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#124">_ZN4PLMD7mapping12AdaptivePathC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#124">_ZN4PLMD7mapping12AdaptivePathC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#111">_ZN4PLMD7mapping12_GLOBAL__N_125AdaptivePathRegisterMe1136createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#113">_ZN4PLMD7mapping12AdaptivePath16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#202">_ZN4PLMD7mapping12AdaptivePath6updateEv</a></td>
+              <td class="coverFnHi">101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#183">_ZN4PLMD7mapping12AdaptivePath9calculateEv</a></td>
+              <td class="coverFnHi">101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#106">_ZN4PLMD7mapping12AdaptivePath9getLambdaEv</a></td>
+              <td class="coverFnHi">101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#187">_ZNK4PLMD7mapping12AdaptivePath11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">2020</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#198">_ZNK4PLMD7mapping12AdaptivePath11transformHDERKdRd</a></td>
+              <td class="coverFnHi">2020</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#111">_ZN4PLMD7mapping12_GLOBAL__N_125AdaptivePathRegisterMe113C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#111">_ZN4PLMD7mapping12_GLOBAL__N_125AdaptivePathRegisterMe113D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/AdaptivePath.cpp.func.html b/coverage/mapping/AdaptivePath.cpp.func.html
new file mode 100644
index 0000000000..8fd6e7e805
--- /dev/null
+++ b/coverage/mapping/AdaptivePath.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/AdaptivePath.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - AdaptivePath.cpp<span style="font-size: 80%;"> (<a href="AdaptivePath.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AdaptivePath.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#113">_ZN4PLMD7mapping12AdaptivePath16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#202">_ZN4PLMD7mapping12AdaptivePath6updateEv</a></td>
+              <td class="coverFnHi">101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#183">_ZN4PLMD7mapping12AdaptivePath9calculateEv</a></td>
+              <td class="coverFnHi">101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#106">_ZN4PLMD7mapping12AdaptivePath9getLambdaEv</a></td>
+              <td class="coverFnHi">101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#124">_ZN4PLMD7mapping12AdaptivePathC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#124">_ZN4PLMD7mapping12AdaptivePathC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#111">_ZN4PLMD7mapping12_GLOBAL__N_125AdaptivePathRegisterMe1136createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#111">_ZN4PLMD7mapping12_GLOBAL__N_125AdaptivePathRegisterMe113C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#111">_ZN4PLMD7mapping12_GLOBAL__N_125AdaptivePathRegisterMe113D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#187">_ZNK4PLMD7mapping12AdaptivePath11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">2020</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AdaptivePath.cpp.gcov.html#198">_ZNK4PLMD7mapping12AdaptivePath11transformHDERKdRd</a></td>
+              <td class="coverFnHi">2020</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/AdaptivePath.cpp.gcov.html b/coverage/mapping/AdaptivePath.cpp.gcov.html
new file mode 100644
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/AdaptivePath.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+<body>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - AdaptivePath.cpp<span style="font-size: 80%;"> (source / <a href="AdaptivePath.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Mapping.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TrigonometricPathVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;PathReparameterization.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/Direction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC COLVAR ADAPTIVE_PATH</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Compute path collective variables that adapt to the lowest free energy path connecting states A and B.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The Path Collective Variables developed by Branduardi and co-workers \cite brand07 allow one</a>
+<a name="36"><span class="lineNum">      36 </span>            : to compute the progress along a high-dimensional path and the distance from the high-dimensional</a>
+<a name="37"><span class="lineNum">      37 </span>            : path.  The progress along the path (s) is computed using:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : s = i_2 + \textrm{sign}(i_2-i_1) \frac{ \sqrt{( \mathbf{v}_1\cdot\mathbf{v}_2 )^2 - |\mathbf{v}_3|^2(|\mathbf{v}_1|^2 - |\mathbf{v}_2|^2) } }{2|\mathbf{v}_3|^2} - \frac{\mathbf{v}_1\cdot\mathbf{v}_3 - |\mathbf{v}_3|^2}{2|\mathbf{v}_3|^2}</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : In this expression \f$\mathbf{v}_1\f$ and \f$\mathbf{v}_3\f$ are the vectors connecting the current position to the closest and second closest node of the path,</a>
+<a name="44"><span class="lineNum">      44 </span>            : respectfully and \f$i_1\f$ and \f$i_2\f$ are the projections of the closest and second closest frames of the path. \f$\mathbf{v}_2\f$, meanwhile, is the</a>
+<a name="45"><span class="lineNum">      45 </span>            : vector connecting the closest frame to the second closest frame.  The distance from the path, \f$z\f$ is calculated using:</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            : z = \sqrt{ \left[ |\mathbf{v}_1|^2 - |\mathbf{v}_2| \left( \frac{ \sqrt{( \mathbf{v}_1\cdot\mathbf{v}_2 )^2 - |\mathbf{v}_3|^2(|\mathbf{v}_1|^2 - |\mathbf{v}_2|^2) } }{2|\mathbf{v}_3|^2} - \frac{\mathbf{v}_1\cdot\mathbf{v}_3 - |\mathbf{v}_3|^2}{2|\mathbf{v}_3|^2} \right) \right]^2 }</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f]</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : Notice that these are the definitions of \f$s\f$ and \f$z\f$ that are used by \ref PATH when the GPATH option is employed.  The reason for this is that</a>
+<a name="52"><span class="lineNum">      52 </span>            : the adaptive path method implemented in this action was inspired by the work of Diaz and Ensing in which these formula were used \cite BerndAdaptivePath.</a>
+<a name="53"><span class="lineNum">      53 </span>            : To learn more about how the path is adapted we strongly recommend reading this paper.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \par Examples</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : The input below provides an example that shows how the adaptive path works. The path is updated every 50 steps of</a>
+<a name="58"><span class="lineNum">      58 </span>            : MD based on the data accumulated during the preceding 50 time steps.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : d1: DISTANCE ATOMS=1,2 COMPONENTS</a>
+<a name="62"><span class="lineNum">      62 </span>            : pp: ADAPTIVE_PATH TYPE=EUCLIDEAN FIXED=2,5 UPDATE=50 WFILE=out-path.pdb WSTRIDE=50 REFERENCE=mypath.pdb</a>
+<a name="63"><span class="lineNum">      63 </span>            : PRINT ARG=d1.x,d1.y,pp.* FILE=colvar</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : In the case above the distance between frames is calculated based on the \f$x\f$ and \f$y\f$ components of the vector connecting</a>
+<a name="67"><span class="lineNum">      67 </span>            : atoms 1 and 2.  As such an extract from the input reference path (mypath.pdb) would look as follows:</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \auxfile{mypath.pdb}</a>
+<a name="70"><span class="lineNum">      70 </span>            : REMARK ARG=d1.x,d1.y d1.x=1.12 d1.y=-.60</a>
+<a name="71"><span class="lineNum">      71 </span>            : END</a>
+<a name="72"><span class="lineNum">      72 </span>            : REMARK ARG=d1.x,d1.y d1.x=.99 d1.y=-.45</a>
+<a name="73"><span class="lineNum">      73 </span>            : END</a>
+<a name="74"><span class="lineNum">      74 </span>            : REMARK ARG=d1.x,d1.y d1.x=.86 d1.y=-.30</a>
+<a name="75"><span class="lineNum">      75 </span>            : END</a>
+<a name="76"><span class="lineNum">      76 </span>            : REMARK ARG=d1.x,d1.y d1.x=.73 d1.y=-.15</a>
+<a name="77"><span class="lineNum">      77 </span>            : END</a>
+<a name="78"><span class="lineNum">      78 </span>            : REMARK ARG=d1.x,d1.y d1.x=.60 d1.y=0</a>
+<a name="79"><span class="lineNum">      79 </span>            : END</a>
+<a name="80"><span class="lineNum">      80 </span>            : REMARK ARG=d1.x,d1.y d1.x=.47 d1.y=.15</a>
+<a name="81"><span class="lineNum">      81 </span>            : END</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endauxfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : Notice that one can also use RMSD frames in place of arguments like those above.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : */</a>
+<a name="87"><span class="lineNum">      87 </span>            : //+ENDPLUMEDOC</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : namespace PLMD {</a>
+<a name="90"><span class="lineNum">      90 </span>            : namespace mapping {</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : class AdaptivePath : public Mapping {</a>
+<a name="93"><span class="lineNum">      93 </span>            : private:</a>
+<a name="94"><span class="lineNum">      94 </span>            :   OFile pathfile;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::string ofmt;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   double fadefact, tolerance;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   unsigned update_str, wstride;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;unsigned&gt; fixedn;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   TrigonometricPathVessel* mypathv;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;double&gt; wsum;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   Direction displacement,displacement2;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;Direction&gt; pdisplacements;</a>
+<a name="103"><span class="lineNum">     103 </span>            : public:</a>
+<a name="104"><span class="lineNum">     104 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="105"><span class="lineNum">     105 </span>            :   explicit AdaptivePath(const ActionOptions&amp;);</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void calculate() override;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        101 :   double getLambda() override { return 0.0; }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   double transformHD( const double&amp; dist, double&amp; df ) const override;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void update() override;</a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(AdaptivePath,&quot;ADAPTIVE_PATH&quot;)</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          3 : void AdaptivePath::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          3 :   Mapping::registerKeywords( keys ); keys.remove(&quot;PROPERTY&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FIXED&quot;,&quot;the positions in the list of input frames of the two path nodes whose positions remain fixed during the path optimization&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;HALFLIFE&quot;,&quot;-1&quot;,&quot;the number of MD steps after which a previously measured path distance weighs only 50% in the average. This option may increase convergence by allowing to forget the memory of a bad initial guess path. The default is to set this to infinity&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;UPDATE&quot;,&quot;the frequency with which the path should be updated&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;TOLERANCE&quot;,&quot;1E-6&quot;,&quot;the tolerance to use for the path updating algorithm that makes all frames equidistant&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;WFILE&quot;,&quot;file on which to write out the path&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;FMT&quot;,&quot;%f&quot;,&quot;the format to use for output files&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;WSTRIDE&quot;,&quot;frequency with which to write out the path&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 : AdaptivePath::AdaptivePath(const ActionOptions&amp; ao):</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   Action(ao),</a>
+<a name="128"><span class="lineNum">     128 </span>            :   Mapping(ao),</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          1 :   fixedn(2),</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   displacement(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)),</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          3 :   displacement2(ReferenceConfigurationOptions(&quot;DIRECTION&quot;))</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : {</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   setLowMemOption( true ); parseVector(&quot;FIXED&quot;,fixedn);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   if( fixedn[0]&lt;1 || fixedn[1]&gt;getNumberOfReferencePoints() ) error(&quot;fixed nodes must be in range from 0 to number of nodes&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   if( fixedn[0]&gt;=fixedn[1] ) error(&quot;invalid selection for fixed nodes first index provided must be smaller than second index&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   log.printf(&quot;  fixing position of frames numbered %u and %u \n&quot;,fixedn[0],fixedn[1]);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :   fixedn[0]--; fixedn[1]--;   // Set fixed notes with c++ indexing starting from zero</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :   parse(&quot;UPDATE&quot;,update_str); if( update_str&lt;1 ) error(&quot;update frequency for path should be greater than or equal to one&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 :   log.printf(&quot;  updating path every %u MD steps \n&quot;,update_str);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :   double halflife; parse(&quot;HALFLIFE&quot;,halflife);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   if( halflife&lt;0 ) fadefact=1.0;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   else {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :     fadefact = exp( -0.693147180559945 / static_cast&lt;double&gt;(halflife) );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     log.printf(&quot;  weight of contribution to frame halves every %f steps \n&quot;,halflife);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :   // Create the list of tasks (and reset projections of frames)</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 :   PDB mypdb; mypdb.setAtomNumbers( getAbsoluteIndexes() ); mypdb.addBlockEnd( getAbsoluteIndexes().size() );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   std::vector&lt;std::string&gt; argument_names( getNumberOfArguments() );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) argument_names[i] = getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :   if( argument_names.size()&gt;0 ) mypdb.setArgumentNames( argument_names );</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :   displacement.read( mypdb ); displacement2.read( mypdb );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         21 :   for(int i=0; i&lt;getNumberOfReferencePoints(); ++i) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         40 :     addTaskToList( i ); pdisplacements.push_back( Direction(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)) );</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         40 :     property.find(&quot;spath&quot;)-&gt;second[i] = static_cast&lt;double&gt;( i - static_cast&lt;int&gt;(fixedn[0]) ) / static_cast&lt;double&gt;( fixedn[1] - fixedn[0] );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         20 :     pdisplacements[i].read( mypdb ); wsum.push_back( 0.0 );</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :   plumed_assert( getPropertyValue( fixedn[0], &quot;spath&quot; )==0.0 &amp;&amp; getPropertyValue( fixedn[1], &quot;spath&quot; )==1.0 );</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   // And activate them all</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          1 :   deactivateAllTasks();</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         21 :   for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :   lockContributors();</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            :   // Setup the vessel to hold the trig path</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :   std::string input; addVessel(&quot;GPATH&quot;, input, -1 );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 :   readVesselKeywords();</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   // Check that there is only one vessel - the one holding the trig path</a>
+<a name="169"><span class="lineNum">     169 </span>            :   plumed_dbg_assert( getNumberOfVessels()==1 );</a>
+<a name="170"><span class="lineNum">     170 </span>            :   // Retrieve the path vessel</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          1 :   mypathv = dynamic_cast&lt;TrigonometricPathVessel*&gt;( getPntrToVessel(0) );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :   plumed_assert( mypathv );</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // Information for write out</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          2 :   std::string wfilename; parse(&quot;WFILE&quot;,wfilename);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 :   if( wfilename.length()&gt;0 ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :     wstride=0; parse(&quot;WSTRIDE&quot;,wstride); parse(&quot;FMT&quot;,ofmt);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :     pathfile.link(*this); pathfile.open( wfilename ); pathfile.setHeavyFlush();</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          1 :     if( wstride&lt;update_str ) error(&quot;makes no sense to write out path more frequently than update stride&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :     log.printf(&quot;  writing path out every %u steps to file named %s with format %s \n&quot;,wstride,wfilename.c_str(),ofmt.c_str());</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Diaz Leines and Ensing, Phys. Rev. Lett. 109, 020601 (2012)&quot;)&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          1 : }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        101 : void AdaptivePath::calculate() {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        101 :   runAllTasks();</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        101 : }</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       2020 : void AdaptivePath::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   // This builds a pack to hold the derivatives</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       2020 :   ReferenceValuePack mypack( getNumberOfArguments(), getNumberOfAtoms(), myvals );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       2020 :   finishPackSetup( current, mypack );</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   // Calculate the distance from the frame</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       2020 :   double val=calculateDistanceFunction( current, mypack, true );</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   // Put the element value in element zero</a>
+<a name="196"><span class="lineNum">     196 </span>            :   myvals.setValue( 0, val ); myvals.setValue( 1, 1.0 );</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       2020 :   return;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       2020 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       2020 : double AdaptivePath::transformHD( const double&amp; dist, double&amp; df ) const {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       2020 :   df=1.0; return dist;</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        101 : void AdaptivePath::update() {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        101 :   double weight2 = -1.*mypathv-&gt;dx;</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        101 :   double weight1 = 1.0 + mypathv-&gt;dx;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        101 :   if( weight1&gt;1.0 ) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     weight1=1.0; weight2=0.0;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        101 :   } else if( weight2&gt;1.0 ) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :     weight1=0.0; weight2=1.0;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span>            :   // Add projections to dispalcement accumulators</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        101 :   ReferenceConfiguration* myref = getReferenceConfiguration( mypathv-&gt;iclose1 );</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        101 :   myref-&gt;extractDisplacementVector( getPositions(), getArguments(), mypathv-&gt;cargs, false, displacement );</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        101 :   getReferenceConfiguration( mypathv-&gt;iclose2 )-&gt;extractDisplacementVector( myref-&gt;getReferencePositions(), getArguments(), myref-&gt;getReferenceArguments(), false, displacement2 );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        101 :   displacement.addDirection( -mypathv-&gt;dx, displacement2 );</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        101 :   pdisplacements[mypathv-&gt;iclose1].addDirection( weight1, displacement );</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        101 :   pdisplacements[mypathv-&gt;iclose2].addDirection( weight2, displacement );</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   // Update weight accumulators</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        101 :   wsum[mypathv-&gt;iclose1] *= fadefact;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        101 :   wsum[mypathv-&gt;iclose2] *= fadefact;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        101 :   wsum[mypathv-&gt;iclose1] += weight1;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        101 :   wsum[mypathv-&gt;iclose2] += weight2;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   // This does the update of the path if it is time to</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        101 :   if( (getStep()&gt;0) &amp;&amp; (getStep()%update_str==0) ) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          2 :     wsum[fixedn[0]]=wsum[fixedn[1]]=0.;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         42 :     for(unsigned inode=0; inode&lt;getNumberOfReferencePoints(); ++inode) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         40 :       if( wsum[inode]&gt;0 ) {</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :         // First displace the node by the weighted direction</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          6 :         getReferenceConfiguration( inode )-&gt;displaceReferenceConfiguration( 1./wsum[inode], pdisplacements[inode] );</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :         // Reset the displacement</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          6 :         pdisplacements[inode].zeroDirection();</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :       }</a>
+<a name="235"><span class="lineNum">     235 </span>            :     }</a>
+<a name="236"><span class="lineNum">     236 </span>            :     // Now ensure all the nodes of the path are equally spaced</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          2 :     PathReparameterization myspacings( getPbc(), getArguments(), getAllReferenceConfigurations() );</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          2 :     myspacings.reparameterize( fixedn[0], fixedn[1], tolerance );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :   }</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        101 :   if( (getStep()&gt;0) &amp;&amp; (getStep()%wstride==0) ) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 :     pathfile&lt;&lt;&quot;# PATH AT STEP &quot;&lt;&lt;getStep();</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          2 :     pathfile.printf(&quot; TIME %f \n&quot;,getTime());</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt;&gt;&amp; myconfs=getAllReferenceConfigurations();</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :     auto* mymoldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          2 :     std::vector&lt;std::string&gt; argument_names( getNumberOfArguments() );</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          6 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) argument_names[i] = getPntrToArgument(i)-&gt;getName();</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          2 :     PDB mypdb; mypdb.setArgumentNames( argument_names );</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         42 :     for(unsigned i=0; i&lt;myconfs.size(); ++i) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         80 :       pathfile.printf(&quot;REMARK TYPE=%s\n&quot;, myconfs[i]-&gt;getName().c_str() );</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         40 :       mypdb.setAtomPositions( myconfs[i]-&gt;getReferencePositions() );</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        120 :       for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) mypdb.setArgumentValue( getPntrToArgument(j)-&gt;getName(), myconfs[i]-&gt;getReferenceArgument(j) );</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         40 :       mypdb.print( atoms.getUnits().getLength()/0.1, mymoldat, pathfile, ofmt );</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          2 :     pathfile.flush();</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          2 :   }</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        101 : }</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : }</a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Mapping.cpp.func-sort-c.html b/coverage/mapping/Mapping.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4130e98933
--- /dev/null
+++ b/coverage/mapping/Mapping.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Mapping.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Mapping.cpp<span style="font-size: 80%;"> (<a href="Mapping.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntryMed">78.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Mapping.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#146">_ZN4PLMD7mapping7Mapping15getArgumentNameB5cxx11ERj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#185">_ZN4PLMD7mapping7Mapping29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#142">_ZN4PLMD7mapping7Mapping9getLambdaEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#46">_ZN4PLMD7mapping7MappingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#46">_ZN4PLMD7mapping7MappingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#74">_ZZN4PLMD7mapping7MappingC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#32">_ZN4PLMD7mapping7Mapping16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#137">_ZN4PLMD7mapping7Mapping17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#201">_ZN4PLMD7mapping7Mapping5applyEv</a></td>
+              <td class="coverFnHi">5015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#181">_ZN4PLMD7mapping7Mapping25getReferenceConfigurationERKj</a></td>
+              <td class="coverFnHi">13175</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#156">_ZNK4PLMD7mapping7Mapping15finishPackSetupERKjRNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">172372</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#167">_ZNK4PLMD7mapping7Mapping25calculateDistanceFunctionERKjRNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">172372</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Mapping.cpp.func.html b/coverage/mapping/Mapping.cpp.func.html
new file mode 100644
index 0000000000..bfc45d1a18
--- /dev/null
+++ b/coverage/mapping/Mapping.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Mapping.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Mapping.cpp<span style="font-size: 80%;"> (<a href="Mapping.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntryMed">78.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Mapping.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#146">_ZN4PLMD7mapping7Mapping15getArgumentNameB5cxx11ERj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#32">_ZN4PLMD7mapping7Mapping16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#137">_ZN4PLMD7mapping7Mapping17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#181">_ZN4PLMD7mapping7Mapping25getReferenceConfigurationERKj</a></td>
+              <td class="coverFnHi">13175</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#185">_ZN4PLMD7mapping7Mapping29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#201">_ZN4PLMD7mapping7Mapping5applyEv</a></td>
+              <td class="coverFnHi">5015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#142">_ZN4PLMD7mapping7Mapping9getLambdaEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#46">_ZN4PLMD7mapping7MappingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#46">_ZN4PLMD7mapping7MappingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#156">_ZNK4PLMD7mapping7Mapping15finishPackSetupERKjRNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">172372</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#167">_ZNK4PLMD7mapping7Mapping25calculateDistanceFunctionERKjRNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">172372</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.cpp.gcov.html#74">_ZZN4PLMD7mapping7MappingC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Mapping.cpp.gcov.html b/coverage/mapping/Mapping.cpp.gcov.html
new file mode 100644
index 0000000000..d8965900e4
--- /dev/null
+++ b/coverage/mapping/Mapping.cpp.gcov.html
@@ -0,0 +1,289 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Mapping.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Mapping.cpp<span style="font-size: 80%;"> (source / <a href="Mapping.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntryMed">78.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Mapping.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/Vessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/ReferenceAtoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace mapping {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         16 : void Mapping::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         16 :   Action::registerKeywords( keys );</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         16 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         16 :   ActionWithArguments::registerKeywords( keys );</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         16 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         16 :   vesselbase::ActionWithVessel::registerKeywords( keys );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         32 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a pdb file containing the set of reference configurations&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         32 :   keys.add(&quot;compulsory&quot;,&quot;PROPERTY&quot;,&quot;the property to be used in the index. This should be in the REMARK of the reference&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         32 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;OPTIMAL-FAST&quot;,&quot;the manner in which distances are calculated. More information on the different &quot;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :            &quot;metrics that are available in PLUMED can be found in the section of the manual on &quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            :            &quot;\\ref dists&quot;);</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         32 :   keys.addFlag(&quot;DISABLE_CHECKS&quot;,false,&quot;disable checks on reference input structures.&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         16 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         10 : Mapping::Mapping(const ActionOptions&amp;ao):</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   Action(ao),</a>
+<a name="50"><span class="lineNum">      50 </span>            :   ActionAtomistic(ao),</a>
+<a name="51"><span class="lineNum">      51 </span>            :   ActionWithArguments(ao),</a>
+<a name="52"><span class="lineNum">      52 </span>            :   ActionWithValue(ao),</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         10 :   ActionWithVessel(ao)</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // Read the input</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         10 :   std::string mtype; parse(&quot;TYPE&quot;,mtype);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         10 :   bool skipchecks; parseFlag(&quot;DISABLE_CHECKS&quot;,skipchecks);</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            :   // Read the properties we require</a>
+<a name="60"><span class="lineNum">      60 </span>            :   bool ispath=false;</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         20 :   if( keywords.exists(&quot;PROPERTY&quot;) ) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          6 :     std::vector&lt;std::string&gt; propnames; parseVector(&quot;PROPERTY&quot;,propnames);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          3 :     if(propnames.size()==0) error(&quot;no properties were specified&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          9 :     for(unsigned i=0; i&lt;propnames.size(); ++i) property.insert( std::pair&lt;std::string,std::vector&lt;double&gt; &gt;( propnames[i], std::vector&lt;double&gt;() ) );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          3 :   } else {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         14 :     property.insert( std::pair&lt;std::string,std::vector&lt;double&gt; &gt;( &quot;spath&quot;, std::vector&lt;double&gt;() ) ); ispath=true;</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            :   // Open reference file</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         10 :   std::string reference; parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         10 :   FILE* fp=this-&gt;fopen(reference.c_str(),&quot;r&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         10 :   if(!fp) error(&quot;could not open reference file &quot; + reference );</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   // call fclose when exiting this block</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         10 :   auto deleter=[this](FILE* f) { this-&gt;fclose(f); };</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   // Read all reference configurations</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool do_read=true; unsigned nfram=0; double wnorm=0., ww;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        426 :   while (do_read) {</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :     // Read the pdb file</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        852 :     PDB mypdb; do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :     // Break if we are done</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        426 :     if( !do_read ) break ;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     // Check for required properties</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        416 :     if( !ispath ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :       double prop;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        378 :       for(std::map&lt;std::string,std::vector&lt;double&gt; &gt;::iterator it=property.begin(); it!=property.end(); ++it) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        252 :         if( !mypdb.getArgumentValue( it-&gt;first, prop ) ) error(&quot;pdb input does not have contain property named &quot; + it-&gt;first );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        252 :         it-&gt;second.push_back(prop);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :       }</a>
+<a name="93"><span class="lineNum">      93 </span>            :     } else {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        580 :       property.find(&quot;spath&quot;)-&gt;second.push_back( myframes.size()+1 );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span>            :     // Fix argument names</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        416 :     expandArgKeywordInPDB( mypdb );</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :     // And read the frame</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        416 :     myframes.emplace_back( metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, mypdb ) );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        832 :     if( !mypdb.getArgumentValue( &quot;WEIGHT&quot;, ww ) ) ww=1.0;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        416 :     weights.push_back( ww ); wnorm+=ww; nfram++;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        426 :   }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         10 :   if(nfram==0 ) error(&quot;no reference configurations were specified&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         10 :   log.printf(&quot;  found %u configurations in file %s\n&quot;,nfram,reference.c_str() );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        426 :   for(unsigned i=0; i&lt;weights.size(); ++i) weights[i] = weights[i]/wnorm;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Finish the setup of the mapping object</a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Get the arguments and atoms that are required</a>
+<a name="110"><span class="lineNum">     110 </span>            :   std::vector&lt;AtomNumber&gt; atoms; std::vector&lt;std::string&gt; args;</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        426 :   for(unsigned i=0; i&lt;myframes.size(); ++i) { myframes[i]-&gt;getAtomRequests( atoms, skipchecks ); myframes[i]-&gt;getArgumentRequests( args, skipchecks ); }</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         10 :   std::vector&lt;Value*&gt; req_args; interpretArgumentList( args, req_args );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         10 :   if( req_args.size()&gt;0 &amp;&amp; atoms.size()&gt;0 ) error(&quot;cannot mix atoms and arguments&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         10 :   if( req_args.size()&gt;0 ) requestArguments( req_args );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         10 :   if( atoms.size()&gt;0 ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          8 :     log.printf(&quot;  found %zu atoms in input \n&quot;,atoms.size());</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          8 :     log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        112 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        104 :       if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        104 :       log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          8 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          8 :     requestAtoms( atoms );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            :   // Duplicate all frames (duplicates are used by sketch-map)</a>
+<a name="126"><span class="lineNum">     126 </span>            :   // mymap-&gt;duplicateFrameList();</a>
+<a name="127"><span class="lineNum">     127 </span>            :   // fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );</a>
+<a name="128"><span class="lineNum">     128 </span>            :   // plumed_assert( !mymap-&gt;mappingNeedsSetup() );</a>
+<a name="129"><span class="lineNum">     129 </span>            :   // Resize all derivative arrays</a>
+<a name="130"><span class="lineNum">     130 </span>            :   // mymap-&gt;setNumberOfAtomsAndArguments( atoms.size(), args.size() );</a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Resize forces array</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         10 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :     forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   } else {</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          2 :     forcesToApply.resize( getNumberOfArguments() );</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         30 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         19 : void Mapping::turnOnDerivatives() {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         19 :   ActionWithValue::turnOnDerivatives();</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         19 :   needsDerivatives();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         19 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 : double Mapping::getLambda() {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;lambda is not defined in this mapping type&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 : std::string Mapping::getArgumentName( unsigned&amp; iarg ) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   if( iarg &lt; getNumberOfArguments() ) return getPntrToArgument(iarg)-&gt;getName();</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   unsigned iatom=iarg - getNumberOfArguments();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   std::string atnum; Tools::convert( getAbsoluteIndex(iatom).serial(),atnum);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   unsigned icomp=iatom%3;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   if(icomp==0) return &quot;pos&quot; + atnum + &quot;x&quot;;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :   if(icomp==1) return &quot;pos&quot; + atnum + &quot;y&quot;;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :   return &quot;pos&quot; + atnum + &quot;z&quot;;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">     172372 : void Mapping::finishPackSetup( const unsigned&amp; ifunc, ReferenceValuePack&amp; mypack ) const {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   mypack.setValIndex(0);</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">     172372 :   unsigned nargs2=myframes[ifunc]-&gt;getNumberOfReferenceArguments();</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     172372 :   unsigned nat2=myframes[ifunc]-&gt;getNumberOfReferencePositions();</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     172372 :   if( mypack.getNumberOfAtoms()!=nat2 || mypack.getNumberOfArguments()!=nargs2 ) mypack.resize( nargs2, nat2 );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     172372 :   if( nat2&gt;0 ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     137592 :     ReferenceAtoms* myat2=dynamic_cast&lt;ReferenceAtoms*&gt;( myframes[ifunc].get() ); plumed_dbg_assert( myat2 );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">    1926288 :     for(unsigned i=0; i&lt;nat2; ++i) mypack.setAtomIndex( i, myat2-&gt;getAtomIndex(i) );</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">     172372 : }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     172372 : double Mapping::calculateDistanceFunction( const unsigned&amp; ifunc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   // Calculate the distance</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     172372 :   double dd = myframes[ifunc]-&gt;calculate( getPositions(), getPbc(), getArguments(), myder, squared );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   // Transform distance by whatever</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     172372 :   double df, ff=transformHD( dd, df ); myder.scaleAllDerivatives( df );</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   // And the virial</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     172372 :   if( getNumberOfAtoms()&gt;0 &amp;&amp; !myder.virialWasSet() ) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     137592 :     Tensor tvir; tvir.zero();</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">    1926288 :     for(unsigned i=0; i&lt;myder.getNumberOfAtoms(); ++i) tvir +=-1.0*Tensor( getPosition( myder.getAtomIndex(i) ), myder.getAtomDerivative(i) );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     137592 :     myder.addBoxDerivatives( tvir );</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     172372 :   return ff;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      13175 : ReferenceConfiguration* Mapping::getReferenceConfiguration( const unsigned&amp; ifunc ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      13175 :   return myframes[ifunc].get();</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 : void Mapping::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   if( getNumberOfArguments()&gt;0 ) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     ActionWithArguments::calculateNumericalDerivatives( a );</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     Matrix&lt;double&gt; save_derivatives( getNumberOfComponents(), getNumberOfArguments() );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) save_derivatives(j,i)=getPntrToComponent(j)-&gt;getDerivative(i);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     }</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) getPntrToComponent(j)-&gt;addDerivative( i, save_derivatives(j,i) );</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     }</a>
+<a name="200"><span class="lineNum">     200 </span>            :   }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       5015 : void Mapping::apply() {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       5015 :   if( getForcesFromVessels( forcesToApply ) ) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :     addForcesOnArguments( forcesToApply );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :     if( getNumberOfAtoms()&gt;0 ) setForcesOnAtoms( forcesToApply, getNumberOfArguments() );</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       5015 : }</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Mapping.h.func-sort-c.html b/coverage/mapping/Mapping.h.func-sort-c.html
new file mode 100644
index 0000000000..cc492e1106
--- /dev/null
+++ b/coverage/mapping/Mapping.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Mapping.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Mapping.h<span style="font-size: 80%;"> (<a href="Mapping.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Mapping.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#82">_ZN4PLMD7mapping7Mapping10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#112">_ZN4PLMD7mapping7Mapping12lockRequestsEv</a></td>
+              <td class="coverFnHi">5015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#118">_ZN4PLMD7mapping7Mapping14unlockRequestsEv</a></td>
+              <td class="coverFnHi">5015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#105">_ZN4PLMD7mapping7Mapping22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">20192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#124">_ZNK4PLMD7mapping7Mapping16getPropertyValueERKjRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">30972</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Mapping.h.func.html b/coverage/mapping/Mapping.h.func.html
new file mode 100644
index 0000000000..ce5aaf3306
--- /dev/null
+++ b/coverage/mapping/Mapping.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Mapping.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Mapping.h<span style="font-size: 80%;"> (<a href="Mapping.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Mapping.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#82">_ZN4PLMD7mapping7Mapping10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#112">_ZN4PLMD7mapping7Mapping12lockRequestsEv</a></td>
+              <td class="coverFnHi">5015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#118">_ZN4PLMD7mapping7Mapping14unlockRequestsEv</a></td>
+              <td class="coverFnHi">5015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#105">_ZN4PLMD7mapping7Mapping22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">20192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mapping.h.gcov.html#124">_ZNK4PLMD7mapping7Mapping16getPropertyValueERKjRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">30972</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Mapping.h.gcov.html b/coverage/mapping/Mapping.h.gcov.html
new file mode 100644
index 0000000000..0e9381e85e
--- /dev/null
+++ b/coverage/mapping/Mapping.h.gcov.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Mapping.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Mapping.h<span style="font-size: 80%;"> (source / <a href="Mapping.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_mapping_Mapping_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_mapping_Mapping_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;map&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;memory&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class PDB;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace mapping {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class Mapping :</a>
+<a name="41"><span class="lineNum">      41 </span>            :   public ActionAtomistic,</a>
+<a name="42"><span class="lineNum">      42 </span>            :   public ActionWithArguments,</a>
+<a name="43"><span class="lineNum">      43 </span>            :   public ActionWithValue,</a>
+<a name="44"><span class="lineNum">      44 </span>            :   public vesselbase::ActionWithVessel</a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span>            :   friend class PropertyMap;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   friend class TrigonometricPathVessel;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   friend class AdaptivePath;</a>
+<a name="49"><span class="lineNum">      49 </span>            : private:</a>
+<a name="50"><span class="lineNum">      50 </span>            : //  The derivative wrt to the distance from the frame</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;double&gt; dfframes;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// This holds all the reference information</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt; &gt; myframes;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// The forces on each of the derivatives (used in apply)</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::vector&lt;double&gt; forcesToApply;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The weights of the various configurations</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;double&gt; weights;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The list of properties in the property map</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::map&lt;std::string,std::vector&lt;double&gt; &gt; property;</a>
+<a name="60"><span class="lineNum">      60 </span>            : protected:</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// The (transformed) distance from each frame</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;double&gt; fframes;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Get the number of frames in the path</a>
+<a name="64"><span class="lineNum">      64 </span>            :   unsigned getNumberOfReferencePoints() const;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Finish the setup of the referenceValuePack by transferring atoms and args</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void finishPackSetup( const unsigned&amp; ifunc, ReferenceValuePack&amp; mypack ) const ;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Calculate the value of the distance from the ith frame</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double calculateDistanceFunction( const unsigned&amp; ifunc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const ;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Get the value of the weight</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double getWeight( const unsigned&amp; weight ) const ;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Return the vector of refernece configurations</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt;&gt;&amp; getAllReferenceConfigurations();</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Return a pointer to one of the reference configurations</a>
+<a name="74"><span class="lineNum">      74 </span>            :   ReferenceConfiguration* getReferenceConfiguration( const unsigned&amp; ifunc );</a>
+<a name="75"><span class="lineNum">      75 </span>            : public:</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="77"><span class="lineNum">      77 </span>            :   explicit Mapping(const ActionOptions&amp;);</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Overload the virtual functions that appear in both ActionAtomistic and ActionWithArguments</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void turnOnDerivatives() override;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void lockRequests() override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void unlockRequests() override;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Distance from a point is never periodic</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Get the number of derivatives for this action</a>
+<a name="86"><span class="lineNum">      86 </span>            :   unsigned getNumberOfDerivatives() override;  // N.B. This is replacing the virtual function in ActionWithValue</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Get the value of lambda for paths and property maps</a>
+<a name="88"><span class="lineNum">      88 </span>            :   virtual double getLambda();</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// This does the transformation of the distance by whatever function is required</a>
+<a name="90"><span class="lineNum">      90 </span>            :   virtual double transformHD( const double&amp; dist, double&amp; df ) const=0;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Get the number of properties we are projecting onto</a>
+<a name="92"><span class="lineNum">      92 </span>            :   unsigned getNumberOfProperties() const ;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Get the name of the ith argument</a>
+<a name="94"><span class="lineNum">      94 </span>            :   std::string getArgumentName( unsigned&amp; iarg );</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Get the value of the ith property for the current frame</a>
+<a name="96"><span class="lineNum">      96 </span>            :   double getPropertyValue( const unsigned&amp; current, const std::string&amp; name ) const ;</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Apply the forces</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void apply() override;</a>
+<a name="99"><span class="lineNum">      99 </span>            : };</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : inline</a>
+<a name="102"><span class="lineNum">     102 </span>            : unsigned Mapping::getNumberOfReferencePoints() const {</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        469 :   return myframes.size();</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : inline</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      20192 : unsigned Mapping::getNumberOfDerivatives() {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   unsigned nat=getNumberOfAtoms();</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      20192 :   if(nat&gt;0) return 3*nat + 9 + getNumberOfArguments();</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       2612 :   return getNumberOfArguments();</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : inline</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       5015 : void Mapping::lockRequests() {</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   ActionWithArguments::lockRequests();</a>
+<a name="116"><span class="lineNum">     116 </span>            :   ActionAtomistic::lockRequests();</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       5015 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : inline</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       5015 : void Mapping::unlockRequests() {</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   ActionWithArguments::unlockRequests();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   ActionAtomistic::unlockRequests();</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       5015 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : inline</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      30972 : double Mapping::getPropertyValue( const unsigned&amp; cur, const std::string&amp; name ) const {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      30972 :   return property.find(name)-&gt;second[cur];</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : inline</a>
+<a name="131"><span class="lineNum">     131 </span>            : double Mapping::getWeight( const unsigned&amp; current ) const {</a>
+<a name="132"><span class="lineNum">     132 </span>            :   return weights[current];</a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : inline</a>
+<a name="136"><span class="lineNum">     136 </span>            : std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt;&gt;&amp; Mapping::getAllReferenceConfigurations() {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :   return myframes;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : inline</a>
+<a name="141"><span class="lineNum">     141 </span>            : unsigned Mapping::getNumberOfProperties() const {</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          3 :   return property.size();</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PCAVars.cpp.func-sort-c.html b/coverage/mapping/PCAVars.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6251e5e275
--- /dev/null
+++ b/coverage/mapping/PCAVars.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PCAVars.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PCAVars.cpp<span style="font-size: 80%;"> (<a href="PCAVars.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PCAVars.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#424">_ZN4PLMD7mapping7PCAVars29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#211">_ZN4PLMD7mapping7PCAVarsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#195">_ZN4PLMD7mapping12_GLOBAL__N_120PCAVarsRegisterMe1976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#211">_ZN4PLMD7mapping7PCAVarsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#232">_ZZN4PLMD7mapping7PCAVarsC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#197">_ZN4PLMD7mapping7PCAVars16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#336">_ZN4PLMD7mapping7PCAVars22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#343">_ZN4PLMD7mapping7PCAVars12lockRequestsEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#348">_ZN4PLMD7mapping7PCAVars14unlockRequestsEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#440">_ZN4PLMD7mapping7PCAVars5applyEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#353">_ZN4PLMD7mapping7PCAVars9calculateEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#195">_ZN4PLMD7mapping12_GLOBAL__N_120PCAVarsRegisterMe197C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#195">_ZN4PLMD7mapping12_GLOBAL__N_120PCAVarsRegisterMe197D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PCAVars.cpp.func.html b/coverage/mapping/PCAVars.cpp.func.html
new file mode 100644
index 0000000000..c30eb62bfc
--- /dev/null
+++ b/coverage/mapping/PCAVars.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PCAVars.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PCAVars.cpp<span style="font-size: 80%;"> (<a href="PCAVars.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PCAVars.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#195">_ZN4PLMD7mapping12_GLOBAL__N_120PCAVarsRegisterMe1976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#195">_ZN4PLMD7mapping12_GLOBAL__N_120PCAVarsRegisterMe197C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#195">_ZN4PLMD7mapping12_GLOBAL__N_120PCAVarsRegisterMe197D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#343">_ZN4PLMD7mapping7PCAVars12lockRequestsEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#348">_ZN4PLMD7mapping7PCAVars14unlockRequestsEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#197">_ZN4PLMD7mapping7PCAVars16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#336">_ZN4PLMD7mapping7PCAVars22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#424">_ZN4PLMD7mapping7PCAVars29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#440">_ZN4PLMD7mapping7PCAVars5applyEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#353">_ZN4PLMD7mapping7PCAVars9calculateEv</a></td>
+              <td class="coverFnHi">55</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#211">_ZN4PLMD7mapping7PCAVarsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#211">_ZN4PLMD7mapping7PCAVarsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PCAVars.cpp.gcov.html#232">_ZZN4PLMD7mapping7PCAVarsC4ERKNS_13ActionOptionsEENKUlP8_IO_FILEE_clES6_</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PCAVars.cpp.gcov.html b/coverage/mapping/PCAVars.cpp.gcov.html
new file mode 100644
index 0000000000..50d25de4f6
--- /dev/null
+++ b/coverage/mapping/PCAVars.cpp.gcov.html
@@ -0,0 +1,535 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PCAVars.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PCAVars.cpp<span style="font-size: 80%;"> (source / <a href="PCAVars.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;reference/Direction.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC COLVAR PCAVARS</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Projection on principal component eigenvectors or other high dimensional linear subspace</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The collective variables described in \ref dists allow one to calculate the distance between the</a>
+<a name="36"><span class="lineNum">      36 </span>            : instantaneous structure adopted by the system and some high-dimensional, reference configuration.  The</a>
+<a name="37"><span class="lineNum">      37 </span>            : problem with doing this is that, as one gets further and further from the reference configuration, the</a>
+<a name="38"><span class="lineNum">      38 </span>            : distance from it becomes a progressively poorer and poorer collective variable.  This happens because</a>
+<a name="39"><span class="lineNum">      39 </span>            : the ``number&quot; of structures at a distance \f$d\f$ from a reference configuration is proportional to \f$d^N\f$ in</a>
+<a name="40"><span class="lineNum">      40 </span>            : an \f$N\f$ dimensional space.  Consequently, when \f$d\f$ is small the distance from the reference configuration</a>
+<a name="41"><span class="lineNum">      41 </span>            : may well be a good collective variable.  However, when \f$d\f$ is large it is unlikely that the distance from the reference</a>
+<a name="42"><span class="lineNum">      42 </span>            : structure is a good CV.  When the distance is large there will almost certainly be markedly different</a>
+<a name="43"><span class="lineNum">      43 </span>            : configuration that have the same CV value and hence barriers in transverse degrees of</a>
+<a name="44"><span class="lineNum">      44 </span>            : freedom.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : For these reasons dimensionality reduction is often employed so a projection \f$\mathbf{s}\f$ of a high-dimensional configuration</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f$\mathbf{X}\f$ in a lower dimensionality space using a function:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \f[</a>
+<a name="50"><span class="lineNum">      50 </span>            : \mathbf{s} = F(\mathbf{X}-\mathbf{X}^{ref})</a>
+<a name="51"><span class="lineNum">      51 </span>            : \f]</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : where here we have introduced some high-dimensional reference configuration \f$\mathbf{X}^{ref}\f$.  By far the simplest way to</a>
+<a name="54"><span class="lineNum">      54 </span>            : do this is to use some linear operator for \f$F\f$.  That is to say we find a low-dimensional projection</a>
+<a name="55"><span class="lineNum">      55 </span>            : by rotating the basis vectors using some linear algebra:</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \f[</a>
+<a name="58"><span class="lineNum">      58 </span>            : \mathbf{s}_i = \sum_k A_{ik} ( X_{k} - X_{k}^{ref} )</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f]</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : Here \f$A\f$ is a \f$d\f$ by \f$D\f$ matrix where \f$D\f$ is the dimensionality of the high dimensional space and \f$d\f$ is</a>
+<a name="62"><span class="lineNum">      62 </span>            : the dimensionality of the lower dimensional subspace.  In plumed when this kind of projection you can use the majority</a>
+<a name="63"><span class="lineNum">      63 </span>            : of the metrics detailed on \ref dists to calculate the displacement, \f$\mathbf{X}-\mathbf{X}^{ref}\f$, from the reference configuration.</a>
+<a name="64"><span class="lineNum">      64 </span>            : The matrix \f$A\f$ can be found by various means including principal component analysis and normal mode analysis.  In both these methods the</a>
+<a name="65"><span class="lineNum">      65 </span>            : rows of \f$A\f$ would be the principle eigenvectors of a square matrix.  For PCA the covariance while for normal modes the Hessian.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \bug It is not possible to use the \ref DRMSD metric with this variable.  You can get around this by listing the set of distances you wish to calculate for your DRMSD in the plumed file explicitly and using the EUCLIDEAN metric.  MAHALONOBIS and NORM-EUCLIDEAN also do not work with this variable but using these options makes little sense when projecting on a linear subspace.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \par Examples</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : The following input calculates a projection on a linear subspace where the displacements</a>
+<a name="72"><span class="lineNum">      72 </span>            : from the reference configuration are calculated using the OPTIMAL metric.  Consequently,</a>
+<a name="73"><span class="lineNum">      73 </span>            : both translation of the center of mass of the atoms and rotation of the reference</a>
+<a name="74"><span class="lineNum">      74 </span>            : frame are removed from these displacements.  The matrix \f$A\f$ and the reference</a>
+<a name="75"><span class="lineNum">      75 </span>            : configuration \f$R^{ref}\f$ are specified in the pdb input file reference.pdb and the</a>
+<a name="76"><span class="lineNum">      76 </span>            : value of all projections (and the residual) are output to a file called colvar2.</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : PCAVARS REFERENCE=reference.pdb TYPE=OPTIMAL LABEL=pca2</a>
+<a name="80"><span class="lineNum">      80 </span>            : PRINT ARG=pca2.* FILE=colvar2</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endplumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : The reference configurations can be specified using a pdb file.  The first configuration that you provide is the reference configuration,</a>
+<a name="84"><span class="lineNum">      84 </span>            : which is referred to in the above as \f$X^{ref}\f$ subsequent configurations give the directions of row vectors that are contained in</a>
+<a name="85"><span class="lineNum">      85 </span>            : the matrix \f$A\f$ above.  These directions can be specified by specifying a second configuration - in this case a vector will</a>
+<a name="86"><span class="lineNum">      86 </span>            : be constructed by calculating the displacement of this second configuration from the reference configuration.  A pdb input prepared</a>
+<a name="87"><span class="lineNum">      87 </span>            : in this way would look as follows:</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : \auxfile{reference.pdb}</a>
+<a name="90"><span class="lineNum">      90 </span>            : REMARK TYPE=OPTIMAL</a>
+<a name="91"><span class="lineNum">      91 </span>            : ATOM      2  CH3 ACE     1      12.932 -14.718  -6.016  1.00  1.00</a>
+<a name="92"><span class="lineNum">      92 </span>            : ATOM      5  C   ACE     1      21.312  -9.928  -5.946  1.00  1.00</a>
+<a name="93"><span class="lineNum">      93 </span>            : ATOM      9  CA  ALA     2      19.462 -11.088  -8.986  1.00  1.00</a>
+<a name="94"><span class="lineNum">      94 </span>            : ATOM     13  HB2 ALA     2      21.112 -10.688 -12.476  1.00  1.00</a>
+<a name="95"><span class="lineNum">      95 </span>            : ATOM     15  C   ALA     2      19.422   7.978 -14.536  1.00  1.00</a>
+<a name="96"><span class="lineNum">      96 </span>            : ATOM     20 HH31 NME     3      20.122  -9.928 -17.746  1.00  1.00</a>
+<a name="97"><span class="lineNum">      97 </span>            : ATOM     21 HH32 NME     3      18.572 -13.148 -16.346  1.00  1.00</a>
+<a name="98"><span class="lineNum">      98 </span>            : END</a>
+<a name="99"><span class="lineNum">      99 </span>            : REMARK TYPE=OPTIMAL</a>
+<a name="100"><span class="lineNum">     100 </span>            : ATOM      2  CH3 ACE     1      13.932 -14.718  -6.016  1.00  1.00</a>
+<a name="101"><span class="lineNum">     101 </span>            : ATOM      5  C   ACE     1      20.312  -9.928  -5.946  1.00  1.00</a>
+<a name="102"><span class="lineNum">     102 </span>            : ATOM      9  CA  ALA     2      18.462 -11.088  -8.986  1.00  1.00</a>
+<a name="103"><span class="lineNum">     103 </span>            : ATOM     13  HB2 ALA     2      20.112 -11.688 -12.476  1.00  1.00</a>
+<a name="104"><span class="lineNum">     104 </span>            : ATOM     15  C   ALA     2      19.422   7.978 -12.536  1.00  1.00</a>
+<a name="105"><span class="lineNum">     105 </span>            : ATOM     20 HH31 NME     3      20.122  -9.928 -17.746  1.00  1.00</a>
+<a name="106"><span class="lineNum">     106 </span>            : ATOM     21 HH32 NME     3      18.572 -13.148 -16.346  1.00  1.00</a>
+<a name="107"><span class="lineNum">     107 </span>            : END</a>
+<a name="108"><span class="lineNum">     108 </span>            : \endauxfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : Alternatively, the second configuration can specify the components of \f$A\f$ explicitly.  In this case you need to include the</a>
+<a name="111"><span class="lineNum">     111 </span>            : keyword TYPE=DIRECTION in the remarks to the pdb as shown below.</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : \verbatim</a>
+<a name="114"><span class="lineNum">     114 </span>            : ATOM      2  CH3 ACE     1      12.932 -14.718  -6.016  1.00  1.00</a>
+<a name="115"><span class="lineNum">     115 </span>            : ATOM      5  C   ACE     1      21.312  -9.928  -5.946  1.00  1.00</a>
+<a name="116"><span class="lineNum">     116 </span>            : ATOM      9  CA  ALA     2      19.462 -11.088  -8.986  1.00  1.00</a>
+<a name="117"><span class="lineNum">     117 </span>            : ATOM     13  HB2 ALA     2      21.112 -10.688 -12.476  1.00  1.00</a>
+<a name="118"><span class="lineNum">     118 </span>            : ATOM     15  C   ALA     2      19.422   7.978 -14.536  1.00  1.00</a>
+<a name="119"><span class="lineNum">     119 </span>            : ATOM     20 HH31 NME     3      20.122  -9.928 -17.746  1.00  1.00</a>
+<a name="120"><span class="lineNum">     120 </span>            : ATOM     21 HH32 NME     3      18.572 -13.148 -16.346  1.00  1.00</a>
+<a name="121"><span class="lineNum">     121 </span>            : END</a>
+<a name="122"><span class="lineNum">     122 </span>            : REMARK TYPE=DIRECTION</a>
+<a name="123"><span class="lineNum">     123 </span>            : ATOM      2  CH3 ACE     1      0.1414  0.3334 -0.0302  1.00  0.00</a>
+<a name="124"><span class="lineNum">     124 </span>            : ATOM      5  C   ACE     1      0.0893 -0.1095 -0.1434  1.00  0.00</a>
+<a name="125"><span class="lineNum">     125 </span>            : ATOM      9  CA  ALA     2      0.0207 -0.321   0.0321  1.00  0.00</a>
+<a name="126"><span class="lineNum">     126 </span>            : ATOM     13  HB2 ALA     2      0.0317 -0.6085  0.0783  1.00  0.00</a>
+<a name="127"><span class="lineNum">     127 </span>            : ATOM     15  C   ALA     2      0.1282 -0.4792  0.0797  1.00  0.00</a>
+<a name="128"><span class="lineNum">     128 </span>            : ATOM     20 HH31 NME     3      0.0053 -0.465   0.0309  1.00  0.00</a>
+<a name="129"><span class="lineNum">     129 </span>            : ATOM     21 HH32 NME     3     -0.1019 -0.4261 -0.0082  1.00  0.00</a>
+<a name="130"><span class="lineNum">     130 </span>            : END</a>
+<a name="131"><span class="lineNum">     131 </span>            : \endverbatim</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : If your metric involves arguments the labels of these arguments in your plumed input file should be specified in the REMARKS</a>
+<a name="134"><span class="lineNum">     134 </span>            : for each of the frames of your path.  An input file in this case might look like this:</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \verbatim</a>
+<a name="137"><span class="lineNum">     137 </span>            : DESCRIPTION: a pca eigenvector specified using the start point and direction in the HD space.</a>
+<a name="138"><span class="lineNum">     138 </span>            : REMARK WEIGHT=1.0</a>
+<a name="139"><span class="lineNum">     139 </span>            : REMARK ARG=d1,d2</a>
+<a name="140"><span class="lineNum">     140 </span>            : REMARK d1=1.0 d2=1.0</a>
+<a name="141"><span class="lineNum">     141 </span>            : END</a>
+<a name="142"><span class="lineNum">     142 </span>            : REMARK TYPE=DIRECTION</a>
+<a name="143"><span class="lineNum">     143 </span>            : REMARK ARG=d1,d2</a>
+<a name="144"><span class="lineNum">     144 </span>            : REMARK d1=0.1 d2=0.25</a>
+<a name="145"><span class="lineNum">     145 </span>            : END</a>
+<a name="146"><span class="lineNum">     146 </span>            : \endverbatim</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : Here we are working with the EUCLIDEAN metric and notice that we have specified the components of \f$A\f$ using DIRECTION.</a>
+<a name="149"><span class="lineNum">     149 </span>            : Consequently, the values of d1 and d2 in the second frame above do not specify a particular coordinate in the high-dimensional</a>
+<a name="150"><span class="lineNum">     150 </span>            : space as in they do in the first frame.  Instead these values are the coefficients that can be used to construct a linear combination of d1 and d2.</a>
+<a name="151"><span class="lineNum">     151 </span>            : If we wanted to specify the direction in this metric using the start and end point of the vector we would write:</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : \verbatim</a>
+<a name="154"><span class="lineNum">     154 </span>            : DESCRIPTION: a pca eigenvector specified using the start and end point of a vector in the HD space.</a>
+<a name="155"><span class="lineNum">     155 </span>            : REMARK WEIGHT=1.0</a>
+<a name="156"><span class="lineNum">     156 </span>            : REMARK ARG=d1,d2</a>
+<a name="157"><span class="lineNum">     157 </span>            : REMARK d1=1.0 d2=1.0</a>
+<a name="158"><span class="lineNum">     158 </span>            : END</a>
+<a name="159"><span class="lineNum">     159 </span>            : REMARK ARG=d1,d2</a>
+<a name="160"><span class="lineNum">     160 </span>            : REMARK d1=1.1 d2=1.25</a>
+<a name="161"><span class="lineNum">     161 </span>            : END</a>
+<a name="162"><span class="lineNum">     162 </span>            : \endverbatim</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : */</a>
+<a name="165"><span class="lineNum">     165 </span>            : //+ENDPLUMEDOC</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : namespace PLMD {</a>
+<a name="168"><span class="lineNum">     168 </span>            : namespace mapping {</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : class PCAVars :</a>
+<a name="171"><span class="lineNum">     171 </span>            :   public ActionWithValue,</a>
+<a name="172"><span class="lineNum">     172 </span>            :   public ActionAtomistic,</a>
+<a name="173"><span class="lineNum">     173 </span>            :   public ActionWithArguments</a>
+<a name="174"><span class="lineNum">     174 </span>            : {</a>
+<a name="175"><span class="lineNum">     175 </span>            : private:</a>
+<a name="176"><span class="lineNum">     176 </span>            : /// The holders for the derivatives</a>
+<a name="177"><span class="lineNum">     177 </span>            :   MultiValue myvals;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   ReferenceValuePack mypack;</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// The position of the reference configuration (the one we align to)</a>
+<a name="180"><span class="lineNum">     180 </span>            :   std::unique_ptr&lt;ReferenceConfiguration&gt; myref;</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// The eigenvectors we are interested in</a>
+<a name="182"><span class="lineNum">     182 </span>            :   std::vector&lt;Direction&gt; directions;</a>
+<a name="183"><span class="lineNum">     183 </span>            : /// Stuff for applying forces</a>
+<a name="184"><span class="lineNum">     184 </span>            :   std::vector&lt;double&gt; forces, forcesToApply;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   bool nopbc;</a>
+<a name="186"><span class="lineNum">     186 </span>            : public:</a>
+<a name="187"><span class="lineNum">     187 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="188"><span class="lineNum">     188 </span>            :   explicit PCAVars(const ActionOptions&amp;);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void lockRequests() override;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   void unlockRequests() override;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a ) override;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   void calculate() override;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   void apply() override;</a>
+<a name="195"><span class="lineNum">     195 </span>            : };</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(PCAVars,&quot;PCAVARS&quot;)</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          7 : void PCAVars::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          7 :   Action::registerKeywords( keys );</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          7 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          7 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          7 :   ActionWithArguments::registerKeywords( keys );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          7 :   componentsAreNotOptional(keys); keys.use(&quot;ARG&quot;);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         14 :   keys.addOutputComponent(&quot;eig&quot;,&quot;default&quot;,&quot;the projections on each eigenvalue are stored on values labeled eig-1, eig-2, ...&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         14 :   keys.addOutputComponent(&quot;residual&quot;,&quot;default&quot;,&quot;the distance of the configuration from the linear subspace defined &quot;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :                           &quot;by the vectors, eig-1, eig2, ... that are contained in the rows of A.&quot;);</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;REFERENCE&quot;,&quot;a pdb file containing the reference configuration and configurations that define the directions for each eigenvector&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;OPTIMAL&quot;,&quot;The method we are using for alignment to the reference structure&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         14 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          7 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          5 : PCAVars::PCAVars(const ActionOptions&amp; ao):</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   Action(ao),</a>
+<a name="215"><span class="lineNum">     215 </span>            :   ActionWithValue(ao),</a>
+<a name="216"><span class="lineNum">     216 </span>            :   ActionAtomistic(ao),</a>
+<a name="217"><span class="lineNum">     217 </span>            :   ActionWithArguments(ao),</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         10 :   myvals(1,0),</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          5 :   mypack(0,0,myvals),</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         10 :   nopbc(false)</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : {</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   // What type of distance are we calculating</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          5 :   std::string mtype; parse(&quot;TYPE&quot;,mtype);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         10 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   // Open reference file</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         10 :   std::string reference; parse(&quot;REFERENCE&quot;,reference);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          5 :   FILE* fp=this-&gt;fopen(reference.c_str(),&quot;r&quot;);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          5 :   if(!fp) error(&quot;could not open reference file &quot; + reference );</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :   // call fclose when exiting this block</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          5 :   auto deleter=[this](FILE* f) { this-&gt;fclose(f); };</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   // Read all reference configurations</a>
+<a name="238"><span class="lineNum">     238 </span>            :   // MultiReferenceBase myframes( &quot;&quot;, false );</a>
+<a name="239"><span class="lineNum">     239 </span>            :   std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt; &gt; myframes;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   bool do_read=true; unsigned nfram=0;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         20 :   while (do_read) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         20 :     PDB mypdb;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     // Read the pdb file</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         40 :     do_read=mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :     // Fix argument names</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         20 :     if(do_read) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         15 :       if( nfram==0 ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         10 :         myref=metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, mypdb );</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          5 :         Direction* tdir = dynamic_cast&lt;Direction*&gt;( myref.get() );</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          5 :         if( tdir ) error(&quot;first frame should be reference configuration - not direction of vector&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          5 :         if( !myref-&gt;pcaIsEnabledForThisReference() ) error(&quot;can't do PCA with reference type &quot; + mtype );</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :         // std::vector&lt;std::string&gt; remarks( mypdb.getRemark() ); std::string rtype;</a>
+<a name="253"><span class="lineNum">     253 </span>            :         // bool found=Tools::parse( remarks, &quot;TYPE&quot;, rtype );</a>
+<a name="254"><span class="lineNum">     254 </span>            :         // if(!found){ std::vector&lt;std::string&gt; newrem(1); newrem[0]=&quot;TYPE=&quot;+mtype; mypdb.addRemark(newrem); }</a>
+<a name="255"><span class="lineNum">     255 </span>            :         // myframes.push_back( metricRegister().create&lt;ReferenceConfiguration&gt;( &quot;&quot;, mypdb ) );</a>
+<a name="256"><span class="lineNum">     256 </span>            :       } else {</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         10 :         auto mymsd = metricRegister().create&lt;ReferenceConfiguration&gt;( &quot;&quot;, mypdb );</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         10 :         myframes.emplace_back( std::move(mymsd) );</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         10 :       }</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         15 :       nfram++;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     } else {</a>
+<a name="262"><span class="lineNum">     262 </span>            :       break;</a>
+<a name="263"><span class="lineNum">     263 </span>            :     }</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         20 :   }</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          5 :   if( nfram&lt;=1 ) error(&quot;no eigenvectors were specified&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          5 :   log.printf(&quot;  found %u eigenvectors in file %s \n&quot;,nfram-1,reference.c_str() );</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :   // Finish the setup of the mapping object</a>
+<a name="270"><span class="lineNum">     270 </span>            :   // Get the arguments and atoms that are required</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          5 :   std::vector&lt;AtomNumber&gt; atoms; myref-&gt;getAtomRequests( atoms, false );</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          5 :   std::vector&lt;std::string&gt; args; myref-&gt;getArgumentRequests( args, false );</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          5 :   if( atoms.size()&gt;0 ) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          5 :     log.printf(&quot;  found %zu atoms in input \n&quot;,atoms.size());</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          5 :     log.printf(&quot;  with indices : &quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         40 :     for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         35 :       if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         35 :       log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :     }</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          5 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   }</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          5 :   requestAtoms( atoms ); std::vector&lt;Value*&gt; req_args;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          5 :   interpretArgumentList( args, req_args ); requestArguments( req_args );</span></a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            :   // And now check that the atoms/arguments are the same in all the eigenvalues</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;myframes.size(); ++i) { myframes[i]-&gt;getAtomRequests( atoms, false ); myframes[i]-&gt;getArgumentRequests( args, false ); }</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   // Setup the derivative pack</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          5 :   if( atoms.size()&gt;0 ) myvals.resize( 1, args.size() + 3*atoms.size() + 9 );</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :   else myvals.resize( 1, args.size() );</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          5 :   mypack.resize( args.size(), atoms.size() );</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         40 :   for(unsigned i=0; i&lt;atoms.size(); ++i) mypack.setAtomIndex( i, i );</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   /// This sets up all the storage data required by PCA in the pack</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          5 :   myref-&gt;setupPCAStorage( mypack );</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   // Check there are no periodic arguments</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          5 :   for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :     if( getPntrToArgument(i)-&gt;isPeriodic() ) error(&quot;cannot use periodic variables in pca projections&quot;);</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   }</a>
+<a name="300"><span class="lineNum">     300 </span>            :   // Work out if the user wants to normalise the input vector</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          5 :   checkRead();</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          5 :   if(nopbc) log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          4 :   else      log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :   // Resize the matrices that will hold our eivenvectors</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          5 :   PDB mypdb; mypdb.setAtomNumbers( atoms ); mypdb.addBlockEnd( atoms.size() );</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          5 :   if( args.size()&gt;0 ) mypdb.setArgumentNames( args );</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   // Resize the matrices that will hold our eivenvectors</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;myframes.size(); ++i) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         20 :     directions.push_back( Direction(ReferenceConfigurationOptions(&quot;DIRECTION&quot;))); directions[i].read( mypdb );</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   }</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :   // Create fake periodic boundary condition (these would only be used for DRMSD which is not allowed)</a>
+<a name="315"><span class="lineNum">     315 </span>            :   // Now calculate the eigenvectors</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;myframes.size(); ++i) {</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     // Calculate distance from reference configuration</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         10 :     myframes[i]-&gt;extractDisplacementVector( myref-&gt;getReferencePositions(), getArguments(), myref-&gt;getReferenceArguments(), true, directions[i] );</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :     // Create a component to store the output</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         10 :     std::string num; Tools::convert( i+1, num );</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         30 :     addComponentWithDerivatives(&quot;eig-&quot;+num); componentIsNotPeriodic(&quot;eig-&quot;+num);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   }</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         15 :   addComponentWithDerivatives(&quot;residual&quot;); componentIsNotPeriodic(&quot;residual&quot;);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :   // Get appropriate number of derivatives</a>
+<a name="326"><span class="lineNum">     326 </span>            :   unsigned nder;</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          5 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          5 :     nder = 3*getNumberOfAtoms() + 9 + getNumberOfArguments();</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   } else {</a>
+<a name="330"><span class="lineNum">     330 </span>            :     nder = getNumberOfArguments();</a>
+<a name="331"><span class="lineNum">     331 </span>            :   }</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   // Resize all derivative arrays</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          5 :   forces.resize( nder ); forcesToApply.resize( nder );</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         20 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) getPntrToComponent(i)-&gt;resizeDerivatives(nder);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         20 : }</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         36 : unsigned PCAVars::getNumberOfDerivatives() {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         36 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         36 :     return 3*getNumberOfAtoms() + 9 + getNumberOfArguments();</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :   }</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :   return getNumberOfArguments();</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         55 : void PCAVars::lockRequests() {</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :   ActionWithArguments::lockRequests();</a>
+<a name="347"><span class="lineNum">     347 </span>            :   ActionAtomistic::lockRequests();</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         55 : }</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         55 : void PCAVars::unlockRequests() {</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :   ActionWithArguments::unlockRequests();</a>
+<a name="352"><span class="lineNum">     352 </span>            :   ActionAtomistic::unlockRequests();</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         55 : }</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         55 : void PCAVars::calculate() {</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         55 :   if(!nopbc &amp;&amp; getNumberOfAtoms()&gt;0) makeWhole();</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            :   // Clear the reference value pack</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         55 :   mypack.clear();</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :   // Calculate distance between instaneous configuration and reference</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         55 :   double dist = myref-&gt;calculate( getPositions(), getPbc(), getArguments(), mypack, true );</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            :   // Start accumulating residual by adding derivatives of distance</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         55 :   Value* resid=getPntrToComponent( getNumberOfComponents()-1 ); unsigned nargs=getNumberOfArguments();</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         55 :   for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) resid-&gt;addDerivative( j, mypack.getArgumentDerivative(j) );</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        440 :   for(unsigned j=0; j&lt;getNumberOfAtoms(); ++j) {</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        385 :     Vector ader=mypack.getAtomDerivative( j );</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">       1540 :     for(unsigned k=0; k&lt;3; ++k) resid-&gt;addDerivative( nargs +3*j+k, ader[k] );</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span>            :   // Retrieve the values of all arguments</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         55 :   std::vector&lt;double&gt; args( getNumberOfArguments() ); for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) args[i]=getArgument(i);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            :   // Now calculate projections on pca vectors</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         55 :   Vector adif, ader; Tensor fvir, tvir;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        165 :   for(int i=0; i&lt;getNumberOfComponents()-1; ++i) { // One less component as we also have residual</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        110 :     double proj=myref-&gt;projectDisplacementOnVector( directions[i], getArguments(), args, mypack );</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :     // And now accumulate derivatives</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        110 :     Value* eid=getPntrToComponent(i);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        110 :     for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) eid-&gt;addDerivative( j, mypack.getArgumentDerivative(j) );</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        110 :     if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        110 :       tvir.zero();</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        880 :       for(unsigned j=0; j&lt;getNumberOfAtoms(); ++j) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        770 :         Vector myader=mypack.getAtomDerivative(j);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       3080 :         for(unsigned k=0; k&lt;3; ++k) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       2310 :           eid-&gt;addDerivative( nargs + 3*j+k, myader[k] );</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       2310 :           resid-&gt;addDerivative( nargs + 3*j+k, -2*proj*myader[k] );</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :         }</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        770 :         tvir += -1.0*Tensor( getPosition(j), myader );</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :       }</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        440 :       for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       1320 :         for(unsigned k=0; k&lt;3; ++k) eid-&gt;addDerivative( nargs + 3*getNumberOfAtoms() + 3*j + k, tvir(j,k) );</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :       }</a>
+<a name="394"><span class="lineNum">     394 </span>            :     }</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">        110 :     dist -= proj*proj; // Subtract square from total squared distance to get residual squared</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :     // Derivatives of residual</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        110 :     for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) resid-&gt;addDerivative( j, -2*proj*eid-&gt;getDerivative(j) );</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :     // for(unsigned j=0;j&lt;getNumberOfArguments();++j) resid-&gt;addDerivative( j, -2*proj*arg_eigv(i,j) );</a>
+<a name="399"><span class="lineNum">     399 </span>            :     // And set final value</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        110 :     getPntrToComponent(i)-&gt;set( proj );</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   }</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         55 :   dist=std::sqrt(dist);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   resid-&gt;set( dist );</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            :   // Take square root of residual derivatives</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         55 :   double prefactor = 0.5 / dist;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         55 :   for(unsigned j=0; j&lt;getNumberOfArguments(); ++j) resid-&gt;setDerivative( j, prefactor*resid-&gt;getDerivative(j) );</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">        440 :   for(unsigned j=0; j&lt;getNumberOfAtoms(); ++j) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">       1540 :     for(unsigned k=0; k&lt;3; ++k) resid-&gt;setDerivative( nargs + 3*j+k, prefactor*resid-&gt;getDerivative( nargs+3*j+k ) );</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            :   // And finally virial for residual</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         55 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         55 :     tvir.zero();</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        440 :     for(unsigned j=0; j&lt;getNumberOfAtoms(); ++j) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       1540 :       Vector ader; for(unsigned k=0; k&lt;3; ++k) ader[k]=resid-&gt;getDerivative( nargs + 3*j+k );</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">        385 :       tvir += -1.0*Tensor( getPosition(j), ader );</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :     }</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        220 :     for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">        660 :       for(unsigned k=0; k&lt;3; ++k) resid-&gt;addDerivative( nargs + 3*getNumberOfAtoms() + 3*j + k, tvir(j,k) );</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :     }</a>
+<a name="422"><span class="lineNum">     422 </span>            :   }</a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         55 : }</span></a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineNoCov">          0 : void PCAVars::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :   if( getNumberOfArguments()&gt;0 ) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :     ActionWithArguments::calculateNumericalDerivatives( a );</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :   }</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :   if( getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :     Matrix&lt;double&gt; save_derivatives( getNumberOfComponents(), getNumberOfArguments() );</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) save_derivatives(j,i)=getPntrToComponent(j)-&gt;getDerivative(i);</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :     }</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :     calculateAtomicNumericalDerivatives( a, getNumberOfArguments() );</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :     for(int j=0; j&lt;getNumberOfComponents(); ++j) {</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) getPntrToComponent(j)-&gt;addDerivative( i, save_derivatives(j,i) );</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :     }</a>
+<a name="439"><span class="lineNum">     439 </span>            :   }</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         55 : void PCAVars::apply() {</span></a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         55 :   bool wasforced=false; forcesToApply.assign(forcesToApply.size(),0.0);</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        220 :   for(int i=0; i&lt;getNumberOfComponents(); ++i) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        165 :     if( getPntrToComponent(i)-&gt;applyForce( forces ) ) {</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :       wasforced=true;</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;forces.size(); ++i) forcesToApply[i]+=forces[i];</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :     }</a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         55 :   if( wasforced ) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :     addForcesOnArguments( forcesToApply );</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :     if( getNumberOfAtoms()&gt;0 ) setForcesOnAtoms( forcesToApply, getNumberOfArguments() );</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">         55 : }</span></a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span>            : }</a>
+<a name="459"><span class="lineNum">     459 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Path.cpp.func-sort-c.html b/coverage/mapping/Path.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9b06ca95fd
--- /dev/null
+++ b/coverage/mapping/Path.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Path.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Path.cpp<span style="font-size: 80%;"> (<a href="Path.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Path.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#145">_ZN4PLMD7mapping4PathC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#137">_ZN4PLMD7mapping12_GLOBAL__N_117PathRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#145">_ZN4PLMD7mapping4PathC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#139">_ZN4PLMD7mapping4Path16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#137">_ZN4PLMD7mapping12_GLOBAL__N_117PathRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#137">_ZN4PLMD7mapping12_GLOBAL__N_117PathRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Path.cpp.func.html b/coverage/mapping/Path.cpp.func.html
new file mode 100644
index 0000000000..145954f253
--- /dev/null
+++ b/coverage/mapping/Path.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Path.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Path.cpp<span style="font-size: 80%;"> (<a href="Path.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Path.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#137">_ZN4PLMD7mapping12_GLOBAL__N_117PathRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#137">_ZN4PLMD7mapping12_GLOBAL__N_117PathRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#137">_ZN4PLMD7mapping12_GLOBAL__N_117PathRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#139">_ZN4PLMD7mapping4Path16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#145">_ZN4PLMD7mapping4PathC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Path.cpp.gcov.html#145">_ZN4PLMD7mapping4PathC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/Path.cpp.gcov.html b/coverage/mapping/Path.cpp.gcov.html
new file mode 100644
index 0000000000..ff6cb268a7
--- /dev/null
+++ b/coverage/mapping/Path.cpp.gcov.html
@@ -0,0 +1,241 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/Path.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - Path.cpp<span style="font-size: 80%;"> (source / <a href="Path.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC COLVAR PATH</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Path collective variables with a more flexible framework for the distance metric being used.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : The Path Collective Variables developed by Branduardi and co-workers \cite brand07 allow one</a>
+<a name="30"><span class="lineNum">      30 </span>            : to compute the progress along a high-dimensional path and the distance from the high-dimensional</a>
+<a name="31"><span class="lineNum">      31 </span>            : path.  The progress along the path (s) is computed using:</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \f[</a>
+<a name="34"><span class="lineNum">      34 </span>            : s = \frac{ \sum_{i=1}^N i \exp( -\lambda R[X - X_i] ) }{ \sum_{i=1}^N \exp( -\lambda R[X - X_i] ) }</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f]</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : while the distance from the path (z) is measured using:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : z = -\frac{1}{\lambda} \ln\left[ \sum_{i=1}^N \exp( -\lambda R[X - X_i] ) \right]</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : In these expressions \f$N\f$ high-dimensional frames (\f$X_i\f$) are used to describe the path in the high-dimensional</a>
+<a name="44"><span class="lineNum">      44 </span>            : space. The two expressions above are then functions of the distances from each of the high-dimensional frames \f$R[X - X_i]\f$.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Within PLUMED there are multiple ways to define the distance from a high-dimensional configuration.  You could calculate</a>
+<a name="46"><span class="lineNum">      46 </span>            : the RMSD distance or you could calculate the amount by which a set of collective variables change.  As such this implementation</a>
+<a name="47"><span class="lineNum">      47 </span>            : of the path CV allows one to use all the difference distance metrics that are discussed in \ref dists. This is as opposed to</a>
+<a name="48"><span class="lineNum">      48 </span>            : the alternative implementation of path (\ref PATHMSD) which is a bit faster but which only allows one to use the RMSD distance.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The \f$s\f$ and \f$z\f$ variables are calculated using the above formulas by default.  However, there is an alternative method</a>
+<a name="51"><span class="lineNum">      51 </span>            : of calculating these collective variables, which is detailed in \cite bernd-path.  This alternative method uses the tools of</a>
+<a name="52"><span class="lineNum">      52 </span>            : geometry (as opposed to algebra, which is used in the equations above).  In this alternative formula the progress along the path</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f$s\f$ is calculated using:</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \f[</a>
+<a name="56"><span class="lineNum">      56 </span>            : s = i_2 + \textrm{sign}(i_2-i_1) \frac{ \sqrt{( \mathbf{v}_1\cdot\mathbf{v}_2 )^2 - |\mathbf{v}_3|^2(|\mathbf{v}_1|^2 - |\mathbf{v}_2|^2) } }{2|\mathbf{v}_3|^2} - \frac{\mathbf{v}_1\cdot\mathbf{v}_3 - |\mathbf{v}_3|^2}{2|\mathbf{v}_3|^2}</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f]</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : where \f$\mathbf{v}_1\f$ and \f$\mathbf{v}_3\f$ are the vectors connecting the current position to the closest and second closest node of the path,</a>
+<a name="60"><span class="lineNum">      60 </span>            : respectfully and \f$i_1\f$ and \f$i_2\f$ are the projections of the closest and second closest frames of the path. \f$\mathbf{v}_2\f$, meanwhile, is the</a>
+<a name="61"><span class="lineNum">      61 </span>            : vector connecting the closest frame to the second closest frame.  The distance from the path, \f$z\f$ is calculated using:</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \f[</a>
+<a name="64"><span class="lineNum">      64 </span>            : z = \sqrt{ \left[ |\mathbf{v}_1|^2 - |\mathbf{v}_2| \left( \frac{ \sqrt{( \mathbf{v}_1\cdot\mathbf{v}_2 )^2 - |\mathbf{v}_3|^2(|\mathbf{v}_1|^2 - |\mathbf{v}_2|^2) } }{2|\mathbf{v}_3|^2} - \frac{\mathbf{v}_1\cdot\mathbf{v}_3 - |\mathbf{v}_3|^2}{2|\mathbf{v}_3|^2} \right) \right]^2 }</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f]</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : The symbols here are as they were for \f$s\f$.  If you would like to use these equations to calculate \f$s\f$ and \f$z\f$ then you should use the GPATH flag.</a>
+<a name="68"><span class="lineNum">      68 </span>            : The values of \f$s\f$ and \f$z\f$ can then be referenced using the gspath and gzpath labels.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : In the example below the path is defined using RMSD distance from frames.</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : p1: PATH REFERENCE=file.pdb TYPE=OPTIMAL LAMBDA=500.0</a>
+<a name="76"><span class="lineNum">      76 </span>            : PRINT ARG=p1.spath,p1.zpath STRIDE=1 FILE=colvar FMT=%8.4f</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endplumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : The reference frames in the path are defined in the pdb file shown below.  In this frame</a>
+<a name="80"><span class="lineNum">      80 </span>            : each configuration in the path is separated by a line containing just the word END.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : \auxfile{file.pdb}</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00</a>
+<a name="84"><span class="lineNum">      84 </span>            : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00</a>
+<a name="85"><span class="lineNum">      85 </span>            : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00</a>
+<a name="86"><span class="lineNum">      86 </span>            : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00</a>
+<a name="87"><span class="lineNum">      87 </span>            : END</a>
+<a name="88"><span class="lineNum">      88 </span>            : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00</a>
+<a name="89"><span class="lineNum">      89 </span>            : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00</a>
+<a name="90"><span class="lineNum">      90 </span>            : ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00</a>
+<a name="91"><span class="lineNum">      91 </span>            : ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00</a>
+<a name="92"><span class="lineNum">      92 </span>            : END</a>
+<a name="93"><span class="lineNum">      93 </span>            : ATOM      1  CL  ALA     1      -2.990   0.383   2.277  1.00  1.00</a>
+<a name="94"><span class="lineNum">      94 </span>            : ATOM      5  CLP ALA     1      -1.664  -0.085   1.831  1.00  1.00</a>
+<a name="95"><span class="lineNum">      95 </span>            : ATOM      6  OL  ALA     1      -0.987  -0.835   2.533  1.00  1.00</a>
+<a name="96"><span class="lineNum">      96 </span>            : ATOM      7  NL  ALA     1      -1.227   0.364   0.646  1.00  1.00</a>
+<a name="97"><span class="lineNum">      97 </span>            : END</a>
+<a name="98"><span class="lineNum">      98 </span>            : \endauxfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : In the example below the path is defined using the values of two torsional angles (t1 and t2).</a>
+<a name="101"><span class="lineNum">     101 </span>            : In addition, the \f$s\f$ and \f$z\f$ are calculated using the geometric expressions described</a>
+<a name="102"><span class="lineNum">     102 </span>            : above rather than the algebraic expressions that are used by default.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : \plumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : t1: TORSION ATOMS=5,7,9,15</a>
+<a name="106"><span class="lineNum">     106 </span>            : t2: TORSION ATOMS=7,9,15,17</a>
+<a name="107"><span class="lineNum">     107 </span>            : pp: PATH TYPE=EUCLIDEAN REFERENCE=epath.pdb GPATH NOSPATH NOZPATH</a>
+<a name="108"><span class="lineNum">     108 </span>            : PRINT ARG=pp.* FILE=colvar</a>
+<a name="109"><span class="lineNum">     109 </span>            : \endplumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : Notice that the LAMBDA parameter is not required here as we are not calculating \f$s\f$ and \f$s\f$</a>
+<a name="112"><span class="lineNum">     112 </span>            : using the algebraic formulas defined earlier.  The positions of the frames in the path are defined</a>
+<a name="113"><span class="lineNum">     113 </span>            : in the file epath.pdb.  An extract from this file looks as shown below.</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : \auxfile{epath.pdb}</a>
+<a name="116"><span class="lineNum">     116 </span>            : REMARK ARG=t1,t2 t1=-4.25053  t2=3.88053</a>
+<a name="117"><span class="lineNum">     117 </span>            : END</a>
+<a name="118"><span class="lineNum">     118 </span>            : REMARK ARG=t1,t2 t1=-4.11     t2=3.75</a>
+<a name="119"><span class="lineNum">     119 </span>            : END</a>
+<a name="120"><span class="lineNum">     120 </span>            : REMARK ARG=t1,t2 t1=-3.96947  t2=3.61947</a>
+<a name="121"><span class="lineNum">     121 </span>            : END</a>
+<a name="122"><span class="lineNum">     122 </span>            : \endauxfile</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : The remarks in this pdb file tell PLUMED the labels that are being used to define the position in the</a>
+<a name="125"><span class="lineNum">     125 </span>            : high dimensional space and the values that these arguments have at each point on the path.</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : */</a>
+<a name="128"><span class="lineNum">     128 </span>            : //+ENDPLUMEDOC</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : namespace PLMD {</a>
+<a name="131"><span class="lineNum">     131 </span>            : namespace mapping {</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : class Path : public PathBase {</a>
+<a name="134"><span class="lineNum">     134 </span>            : public:</a>
+<a name="135"><span class="lineNum">     135 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="136"><span class="lineNum">     136 </span>            :   explicit Path(const ActionOptions&amp;);</a>
+<a name="137"><span class="lineNum">     137 </span>            : };</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(Path,&quot;PATH&quot;)</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          8 : void Path::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          8 :   PathBase::registerKeywords( keys ); keys.remove(&quot;PROPERTY&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         16 :   keys.addFlag(&quot;NOSPATH&quot;,false,&quot;do not calculate the spath position&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         16 :   keys.remove(&quot;LOWMEM&quot;); keys.use(&quot;GPATH&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          8 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          6 : Path::Path(const ActionOptions&amp; ao):</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   Action(ao),</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          6 :   PathBase(ao)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : {</a>
+<a name="151"><span class="lineNum">     151 </span>            :   setLowMemOption( true );</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         12 :   bool nos; parseFlag(&quot;NOSPATH&quot;,nos);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::string empty;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          6 :   if(!nos) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :     if( getLambda()==0 ) error(&quot;you must set LAMBDA parameter in order to calculate spath position.  Use LAMBDA/NOSPATH keyword&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     empty=&quot;LABEL=spath&quot;;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          8 :     addVessel(&quot;SPATH&quot;,empty,0);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          6 :   readVesselKeywords();</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          6 :   checkRead();</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          6 : }</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathBase.cpp.func-sort-c.html b/coverage/mapping/PathBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6abd5fa502
--- /dev/null
+++ b/coverage/mapping/PathBase.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathBase.cpp<span style="font-size: 80%;"> (<a href="PathBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PathBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#32">_ZN4PLMD7mapping8PathBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#32">_ZN4PLMD7mapping8PathBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#26">_ZN4PLMD7mapping8PathBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#55">_ZN4PLMD7mapping8PathBase9getLambdaEv</a></td>
+              <td class="coverFnHi">1103</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#59">_ZN4PLMD7mapping8PathBase9calculateEv</a></td>
+              <td class="coverFnHi">4914</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#64">_ZNK4PLMD7mapping8PathBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">170352</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#75">_ZNK4PLMD7mapping8PathBase11transformHDERKdRd</a></td>
+              <td class="coverFnHi">170352</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathBase.cpp.func.html b/coverage/mapping/PathBase.cpp.func.html
new file mode 100644
index 0000000000..c16e394b19
--- /dev/null
+++ b/coverage/mapping/PathBase.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathBase.cpp<span style="font-size: 80%;"> (<a href="PathBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PathBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#26">_ZN4PLMD7mapping8PathBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#59">_ZN4PLMD7mapping8PathBase9calculateEv</a></td>
+              <td class="coverFnHi">4914</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#55">_ZN4PLMD7mapping8PathBase9getLambdaEv</a></td>
+              <td class="coverFnHi">1103</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#32">_ZN4PLMD7mapping8PathBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#32">_ZN4PLMD7mapping8PathBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#64">_ZNK4PLMD7mapping8PathBase11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">170352</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathBase.cpp.gcov.html#75">_ZNK4PLMD7mapping8PathBase11transformHDERKdRd</a></td>
+              <td class="coverFnHi">170352</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathBase.cpp.gcov.html b/coverage/mapping/PathBase.cpp.gcov.html
new file mode 100644
index 0000000000..c779418837
--- /dev/null
+++ b/coverage/mapping/PathBase.cpp.gcov.html
@@ -0,0 +1,161 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathBase.cpp<span style="font-size: 80%;"> (source / <a href="PathBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace mapping {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         13 : void PathBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         13 :   Mapping::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         26 :   keys.add(&quot;compulsory&quot;,&quot;LAMBDA&quot;,&quot;0&quot;,&quot;the value of the lambda parameter for paths&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         26 :   keys.addFlag(&quot;NOZPATH&quot;,false,&quot;do not calculate the zpath position&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         13 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          9 : PathBase::PathBase(const ActionOptions&amp; ao):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   Action(ao),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          9 :   Mapping(ao)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span>            :   setLowMemOption( true );</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          9 :   weightHasDerivatives=true;</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          9 :   bool noz; parseFlag(&quot;NOZPATH&quot;,noz);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          9 :   parse(&quot;LAMBDA&quot;,lambda);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            :   // Create the list of tasks</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        405 :   for(unsigned i=0; i&lt;getNumberOfReferencePoints(); ++i) addTaskToList( i );</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   // And activate them all</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          9 :   deactivateAllTasks();</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        405 :   for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          9 :   lockContributors();</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          9 :   std::string empty=&quot;LABEL=zpath&quot;;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          9 :   if(!noz) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          7 :     if( lambda==0 ) error(&quot;you must set LAMDBA value in order to calculate ZPATH coordinate.  Use LAMBDA/NOZPATH keyword&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         14 :     addVessel(&quot;ZPATH&quot;,empty,0);</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   }</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          9 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1103 : double PathBase::getLambda() {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       1103 :   return lambda;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       4914 : void PathBase::calculate() {</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   // Loop over all frames is now performed by ActionWithVessel</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       4914 :   runAllTasks();</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4914 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     170352 : void PathBase::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   // This builds a pack to hold the derivatives</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     170352 :   ReferenceValuePack mypack( getNumberOfArguments(), getNumberOfAtoms(), myvals );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     170352 :   finishPackSetup( current, mypack );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Calculate the distance from the frame</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     170352 :   double val=calculateDistanceFunction( current, mypack, true );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   // Put the element value in element zero</a>
+<a name="73"><span class="lineNum">      73 </span>            :   myvals.setValue( 0, val ); myvals.setValue( 1, 1.0 );</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     170352 :   return;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     170352 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     170352 : double PathBase::transformHD( const double&amp; dist, double&amp; df ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     170352 :   if( lambda==0 ) { df=1; return dist; }</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     114660 :   double val = exp( -dist*lambda );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     114660 :   df = -lambda*val;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     114660 :   return val;</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathReparameterization.cpp.func-sort-c.html b/coverage/mapping/PathReparameterization.cpp.func-sort-c.html
new file mode 100644
index 0000000000..eb702e513a
--- /dev/null
+++ b/coverage/mapping/PathReparameterization.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathReparameterization.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathReparameterization.cpp<span style="font-size: 80%;"> (<a href="PathReparameterization.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PathReparameterization.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#129">_ZN4PLMD7mapping22PathReparameterization14reparameterizeERKiS3_RKd</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#25">_ZN4PLMD7mapping22PathReparameterizationC2ERKNS_3PbcERKSt6vectorIPNS_5ValueESaIS7_EERS5_ISt10unique_ptrINS_22ReferenceConfigurationESt14default_deleteISD_EESaISG_EE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#63">_ZN4PLMD7mapping22PathReparameterization18reparameterizePartERKiS3_RKdS5_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#48">_ZN4PLMD7mapping22PathReparameterization23calcCurrentPathSpacingsERKiS3_</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#42">_ZNK4PLMD7mapping22PathReparameterization7loopEndERKiS3_S3_</a></td>
+              <td class="coverFnHi">1741</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathReparameterization.cpp.func.html b/coverage/mapping/PathReparameterization.cpp.func.html
new file mode 100644
index 0000000000..7217185de6
--- /dev/null
+++ b/coverage/mapping/PathReparameterization.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathReparameterization.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathReparameterization.cpp<span style="font-size: 80%;"> (<a href="PathReparameterization.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PathReparameterization.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#129">_ZN4PLMD7mapping22PathReparameterization14reparameterizeERKiS3_RKd</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#63">_ZN4PLMD7mapping22PathReparameterization18reparameterizePartERKiS3_RKdS5_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#48">_ZN4PLMD7mapping22PathReparameterization23calcCurrentPathSpacingsERKiS3_</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#25">_ZN4PLMD7mapping22PathReparameterizationC2ERKNS_3PbcERKSt6vectorIPNS_5ValueESaIS7_EERS5_ISt10unique_ptrINS_22ReferenceConfigurationESt14default_deleteISD_EESaISG_EE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathReparameterization.cpp.gcov.html#42">_ZNK4PLMD7mapping22PathReparameterization7loopEndERKiS3_S3_</a></td>
+              <td class="coverFnHi">1741</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathReparameterization.cpp.gcov.html b/coverage/mapping/PathReparameterization.cpp.gcov.html
new file mode 100644
index 0000000000..e0f63ed7ea
--- /dev/null
+++ b/coverage/mapping/PathReparameterization.cpp.gcov.html
@@ -0,0 +1,222 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathReparameterization.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathReparameterization.cpp<span style="font-size: 80%;"> (source / <a href="PathReparameterization.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathReparameterization.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace mapping {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">          4 : PathReparameterization::PathReparameterization( const Pbc&amp; ipbc, const std::vector&lt;Value*&gt;&amp; iargs, std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt;&gt;&amp; pp ):</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          4 :   mydpack( 1, pp[0]-&gt;getNumberOfReferenceArguments() + 3*pp[0]-&gt;getNumberOfReferencePositions() + 9 ),</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          4 :   mypack( pp[0]-&gt;getNumberOfReferenceArguments(), pp[0]-&gt;getNumberOfReferencePositions(), mydpack ),</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">          8 :   mydir(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)),</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          4 :   pbc(ipbc),</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          4 :   args(iargs),</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          4 :   mypath(pp),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          4 :   len(pp.size()),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          4 :   sumlen(pp.size()),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          4 :   sfrac(pp.size()),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          8 :   MAXCYCLES(100)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          4 :   mypdb.setAtomNumbers(  pp[0]-&gt;getAbsoluteIndexes() ); mypdb.addBlockEnd( pp[0]-&gt;getAbsoluteIndexes().size() );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          4 :   if( pp[0]-&gt;getArgumentNames().size()&gt;0 ) mypdb.setArgumentNames( pp[0]-&gt;getArgumentNames() );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          4 :   mydir.read( mypdb ); mydir.zeroDirection(); pp[0]-&gt;setupPCAStorage( mypack );</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          4 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       1741 : bool PathReparameterization::loopEnd( const int&amp; index, const int&amp; end, const int&amp; inc ) const {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1741 :   if( inc&gt;0 &amp;&amp; index&lt;end ) return false;</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        270 :   else if( inc&lt;0 &amp;&amp; index&gt;end ) return false;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   return true;</a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         71 : void PathReparameterization::calcCurrentPathSpacings( const int&amp; istart, const int&amp; iend ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   plumed_dbg_assert( istart&lt;len.size() &amp;&amp; iend&lt;len.size() );</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         71 :   len[istart] = sumlen[istart]=0;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   //printf(&quot;HELLO PATH SPACINGS ARE CURRENTLY \n&quot;);</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            :   // Get the spacings given we can go forward and backwards</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         71 :   int incr=1; if( istart&gt;iend ) { incr=-1; }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        657 :   for(int i=istart+incr; loopEnd(i,iend+incr,incr)==false; i+=incr) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        586 :     len[i] = mypath[i-incr]-&gt;calc( mypath[i]-&gt;getReferencePositions(), pbc, args, mypath[i]-&gt;getReferenceArguments(), mypack, false );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        586 :     sumlen[i] = sumlen[i-incr] + len[i];</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :     //printf(&quot;FRAME %d TO FRAME %d EQUALS %f : %f \n&quot;,i-incr,i,len[i],sumlen[i] );</a>
+<a name="62"><span class="lineNum">      62 </span>            :   }</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         71 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         10 : void PathReparameterization::reparameterizePart( const int&amp; istart, const int&amp; iend, const double&amp; target, const double&amp; TOL ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         10 :   calcCurrentPathSpacings( istart, iend ); unsigned cfin;</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   // If a target separation is set we fix where we want the nodes</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         10 :   int incr=1; if( istart&gt;iend ) { incr=-1; }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         10 :   if( target&gt;0 ) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          6 :     if( iend&gt;istart ) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         19 :       for(unsigned i=istart; i&lt;iend+1; ++i) sfrac[i] = target*(i-istart);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     } else {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         14 :       for(int i=istart-1; i&gt;iend-1; --i) sfrac[i]=target*(istart-i);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 :     cfin = iend+incr;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   } else {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 :     cfin = iend;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;Direction&gt; newpath;</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        170 :   for(unsigned i=0; i&lt;mypath.size(); ++i) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        320 :     newpath.push_back( Direction(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)) ); newpath[i].read( mypdb );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   double prevsum=0.;</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         71 :   for(unsigned iter=0; iter&lt;MAXCYCLES; ++iter) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         71 :     if( std::fabs(sumlen[iend] - prevsum)&lt;=TOL ) break ;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     prevsum = sumlen[iend];</a>
+<a name="90"><span class="lineNum">      90 </span>            :     // If no target is set we redistribute length</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         61 :     if( target&lt;0 ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         49 :       plumed_assert( istart&lt;iend );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         49 :       double dr = sumlen[iend] / static_cast&lt;double&gt;( iend - istart );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        531 :       for(unsigned i=istart; i&lt;iend; ++i) sfrac[i] = dr*(i-istart);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :     // Now compute positions of new nodes in path</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        542 :     for(int i=istart+incr; loopEnd(i,cfin,incr)==false; i+=incr) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        481 :       int k = istart;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       2567 :       while( !((sumlen[k] &lt; sfrac[i]) &amp;&amp; (sumlen[k+incr]&gt;=sfrac[i])) ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       2093 :         k+=incr;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       2093 :         if( cfin==iend &amp;&amp; k&gt;= iend+1 ) plumed_merror(&quot;path reparameterization error&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       2093 :         else if( cfin==(iend+1) &amp;&amp; k&gt;=iend ) { k=iend-1; break; }</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       2090 :         else if( cfin==(iend-1) &amp;&amp; k&lt;=iend ) { k=iend+1; break; }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :       }</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        481 :       double dr = (sfrac[i]-sumlen[k])/len[k+incr];</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :       // Calculate the displacement between the appropriate points</a>
+<a name="108"><span class="lineNum">     108 </span>            :       // double dd = mypath[k]-&gt;calc( mypath[k+incr]-&gt;getReferencePositions(), pbc, args, mypath[k+incr]-&gt;getReferenceArguments(), mypack, true );</a>
+<a name="109"><span class="lineNum">     109 </span>            :       // Copy the reference configuration from the configuration to a tempory direction</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        481 :       newpath[i].setDirection( mypath[k]-&gt;getReferencePositions(), mypath[k]-&gt;getReferenceArguments() );</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :       // Get the displacement of the path</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        481 :       mypath[k]-&gt;extractDisplacementVector( mypath[k+incr]-&gt;getReferencePositions(), args, mypath[k+incr]-&gt;getReferenceArguments(), false, mydir );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :       // Set our direction equal to the displacement</a>
+<a name="114"><span class="lineNum">     114 </span>            :       // mydir.setDirection( mypack );</a>
+<a name="115"><span class="lineNum">     115 </span>            :       // Shift the reference configuration by this amount</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        481 :       newpath[i].displaceReferenceConfiguration( dr, mydir );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :     // Copy the positions of the new path to the new paths</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        542 :     for(int i=istart+incr; loopEnd(i,cfin,incr)==false; i+=incr) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        481 :       mypdb.setAtomPositions( newpath[i].getReferencePositions() );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       1415 :       for(unsigned j=0; j&lt;newpath[i].getNumberOfReferenceArguments(); ++j) mypdb.setArgumentValue( mypath[i]-&gt;getArgumentNames()[j], newpath[i].getReferenceArgument(j) );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        481 :       mypath[i]-&gt;read( mypdb );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :     }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :     // Recompute the separations between frames</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         61 :     calcCurrentPathSpacings( istart, iend );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         10 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 : void PathReparameterization::reparameterize( const int&amp; ifix1, const int&amp; ifix2, const double&amp; TOL ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   plumed_dbg_assert( ifix1&lt;ifix2 );</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // First reparameterize the part between the fixed frames</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 :   reparameterizePart( ifix1, ifix2, -1.0, TOL );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Get the separation between frames which we will use to set the remaining frames</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   double target = sumlen[ifix2] / ( ifix2 - ifix1 );</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   // And reparameterize the beginning and end of the path</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          4 :   if( ifix1&gt;0 ) reparameterizePart( ifix1, 0, target, TOL );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :   if( ifix2&lt;(mypath.size()-1) ) reparameterizePart( ifix2, mypath.size()-1, target, TOL );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : //  calcCurrentPathSpacings( 0, mypath.size()-1 );</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathTools.cpp.func-sort-c.html b/coverage/mapping/PathTools.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3cbe226a07
--- /dev/null
+++ b/coverage/mapping/PathTools.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathTools.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathTools.cpp<span style="font-size: 80%;"> (<a href="PathTools.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntry">125</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PathTools.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#137">_ZN4PLMD7mapping9PathTools4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#109">_ZNK4PLMD7mapping9PathTools11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#114">_ZN4PLMD7mapping12_GLOBAL__N_119PathToolsRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#131">_ZN4PLMD7mapping9PathToolsC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#114">_ZN4PLMD7mapping12_GLOBAL__N_119PathToolsRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#114">_ZN4PLMD7mapping12_GLOBAL__N_119PathToolsRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#116">_ZN4PLMD7mapping9PathTools16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathTools.cpp.func.html b/coverage/mapping/PathTools.cpp.func.html
new file mode 100644
index 0000000000..8a98db2a6b
--- /dev/null
+++ b/coverage/mapping/PathTools.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathTools.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathTools.cpp<span style="font-size: 80%;"> (<a href="PathTools.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntry">125</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PathTools.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#114">_ZN4PLMD7mapping12_GLOBAL__N_119PathToolsRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#114">_ZN4PLMD7mapping12_GLOBAL__N_119PathToolsRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#137">_ZN4PLMD7mapping9PathTools4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
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+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#131">_ZN4PLMD7mapping9PathToolsC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">8</td>
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+              <td class="coverFn"><a href="PathTools.cpp.gcov.html#109">_ZNK4PLMD7mapping9PathTools11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PathTools.cpp.gcov.html b/coverage/mapping/PathTools.cpp.gcov.html
new file mode 100644
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--- /dev/null
+++ b/coverage/mapping/PathTools.cpp.gcov.html
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PathTools.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PathTools.cpp<span style="font-size: 80%;"> (source / <a href="PathTools.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntry">125</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;cltools/CLTool.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;cltools/CLToolRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;reference/ReferenceConfiguration.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;PathReparameterization.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstdio&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;string&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;vector&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;iostream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace mapping {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC TOOLS pathtools</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : pathtools can be used to construct paths from pdb data</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : The path CVs in PLUMED are curvilinear coordinates through a high dimensional vector space.</a>
+<a name="43"><span class="lineNum">      43 </span>            : Enhanced sampling calculations are often run using the progress along the paths and the distance from the path as CVs</a>
+<a name="44"><span class="lineNum">      44 </span>            : as this provides a convenient way of defining a reaction coordinate for a complicated process.  This method is explained</a>
+<a name="45"><span class="lineNum">      45 </span>            : in the documentation for \ref PATH.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The path itself is an ordered set of equally-spaced, high-dimensional frames the way in which these frames</a>
+<a name="48"><span class="lineNum">      48 </span>            : should be constructed will depend on the problem in hand.  In other words, you will need to understand the reaction</a>
+<a name="49"><span class="lineNum">      49 </span>            : you wish to study in order to select a sensible set of frames to use in your path CV.  This tool provides two</a>
+<a name="50"><span class="lineNum">      50 </span>            : methods that may be useful when it comes to constructing paths; namely:</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : - A tool that takes in an initial guess path in which the frames are not equally spaced.  This tool adjusts the positions</a>
+<a name="53"><span class="lineNum">      53 </span>            : of the frames in order to make them equally spaced so that they can be used as the basis for a path CV.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : - A tool that takes two frames as input and that allows you to return a linear path connecting these two frames.  The</a>
+<a name="56"><span class="lineNum">      56 </span>            : output from this method may be useful as an initial guess path.  It is arguable that a linear path rather defeats the</a>
+<a name="57"><span class="lineNum">      57 </span>            : purpose of the path CV method, however, as the whole purpose is to be able to define non-linear paths.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : Notice that you can use these two methods and take advantage of all the ways of measuring \ref dists that are available within</a>
+<a name="60"><span class="lineNum">      60 </span>            : PLUMED. The way you do this with each of these tools described above is explained in the example below.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \par Examples</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The example below shows how you can take a set of unequally spaced frames from a pdb file named in_path.pdb</a>
+<a name="65"><span class="lineNum">      65 </span>            : and use pathtools to make them equally spaced so that they can be used as the basis for a path CV.  The file</a>
+<a name="66"><span class="lineNum">      66 </span>            : containing this final path is named final_path.pdb.</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \verbatim</a>
+<a name="69"><span class="lineNum">      69 </span>            : plumed pathtools --path in_path.pdb --metric EUCLIDEAN --out final_path.pdb</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endverbatim</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The example below shows how can create an initial linear path connecting the two pdb frames in start.pdb and</a>
+<a name="73"><span class="lineNum">      73 </span>            : end.pdb.  In this case the path output to path.pdb will consist of 6 frames: the initial and final frames that</a>
+<a name="74"><span class="lineNum">      74 </span>            : were contained in start.pdb and end.pdb as well as four equally spaced frames along the vector connecting</a>
+<a name="75"><span class="lineNum">      75 </span>            : start.pdb to end.pdb.</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : \verbatim</a>
+<a name="78"><span class="lineNum">      78 </span>            : plumed pathtools --start start.pdb --end end.pdb --nframes 4 --metric OPTIMAL --out path.pdb</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endverbatim</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : Often the idea with path collective variables is to create a path connecting some initial state A to some final state B.  You would</a>
+<a name="82"><span class="lineNum">      82 </span>            : in this case have representative configurations from your A and B states defined in the input files to pathtools</a>
+<a name="83"><span class="lineNum">      83 </span>            : that we have called start.pdb and end.pdb in the example above.  Furthermore, it may be useful to have a few frames</a>
+<a name="84"><span class="lineNum">      84 </span>            : before your start frame and after your end frame.  You can use path tools to create these extended paths as shown below.</a>
+<a name="85"><span class="lineNum">      85 </span>            : In this case the final path would now consist of 8 frames.  Four of these frames would lie on the vector connecting state</a>
+<a name="86"><span class="lineNum">      86 </span>            : A to state B, there would be one frame each at start.pdb and end.pdb as well as one frame just before start.pdb and one</a>
+<a name="87"><span class="lineNum">      87 </span>            : frame just after end.pdb.  All these frames would be equally spaced.</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : \verbatim</a>
+<a name="90"><span class="lineNum">      90 </span>            : plumed pathtools --start start.pdb --end end.pdb --nframes 4 --metric OPTIMAL --out path.pdb --nframes-before-start 2 --nframes-after-end 2</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endverbatim</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : Notice also that when you re-parameterize paths you must choose two frames to fix.  Generally you chose to fix the states</a>
+<a name="94"><span class="lineNum">      94 </span>            : that are representative of your states A and B.  By default pathtools will fix the first and last frames.  You can, however,</a>
+<a name="95"><span class="lineNum">      95 </span>            : change the states to fix by taking advantage of the fixed flag as shown below.</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : \verbatim</a>
+<a name="98"><span class="lineNum">      98 </span>            : plumed pathtools --path inpath.pdb --metric EUCLIDEAN --out outpath.pdb --fixed 2,12</a>
+<a name="99"><span class="lineNum">      99 </span>            : \endverbatim</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : */</a>
+<a name="102"><span class="lineNum">     102 </span>            : //+ENDPLUMEDOC</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : class PathTools :</a>
+<a name="105"><span class="lineNum">     105 </span>            :   public CLTool</a>
+<a name="106"><span class="lineNum">     106 </span>            : {</a>
+<a name="107"><span class="lineNum">     107 </span>            : public:</a>
+<a name="108"><span class="lineNum">     108 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="109"><span class="lineNum">     109 </span>            :   explicit PathTools(const CLToolOptions&amp; co );</a>
+<a name="110"><span class="lineNum">     110 </span>            :   int main(FILE* in, FILE*out,Communicator&amp; pc);</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          4 :   std::string description()const {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          4 :     return &quot;print out a description of the keywords for an action in html&quot;;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      12512 : PLUMED_REGISTER_CLTOOL(PathTools,&quot;pathtools&quot;)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       4168 : void PathTools::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       8336 :   keys.add(&quot;atoms&quot;,&quot;--start&quot;,&quot;a pdb file that contains the structure for the initial frame of your path&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       8336 :   keys.add(&quot;atoms&quot;,&quot;--end&quot;,&quot;a pdb file that contains the structure for the final frame of your path&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       8336 :   keys.add(&quot;atoms-1&quot;,&quot;--path&quot;,&quot;a pdb file that contains an initial path in which the frames are not equally spaced&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--fixed&quot;,&quot;0&quot;,&quot;the frames to fix when constructing the path using --path&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--metric&quot;,&quot;the measure to use to calculate the distance between frames&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--out&quot;,&quot;the name of the file on which to output your path&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--arg-fmt&quot;,&quot;%f&quot;,&quot;the format to use for argument values in your frames&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--tolerance&quot;,&quot;1E-4&quot;,&quot;the tolerance to use for the algorithm that is used to re-parameterize the path&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--nframes-before-start&quot;,&quot;1&quot;,&quot;the number of frames to include in the path before the first frame&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--nframes&quot;,&quot;1&quot;,&quot;the number of frames between the start and end frames in your path&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;--nframes-after-end&quot;,&quot;1&quot;,&quot;the number of frames to put after the last frame of your path&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       4168 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 : PathTools::PathTools(const CLToolOptions&amp; co ):</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          8 :   CLTool(co)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : {</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :   inputdata=commandline;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          8 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 : int PathTools::main(FILE* in, FILE*out,Communicator&amp; pc) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          8 :   std::string mtype; parse(&quot;--metric&quot;,mtype);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          8 :   std::string ifilename; parse(&quot;--path&quot;,ifilename);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          8 :   std::string ofmt; parse(&quot;--arg-fmt&quot;,ofmt);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          8 :   std::string ofilename; parse(&quot;--out&quot;,ofilename);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          4 :   if( ifilename.length()&gt;0 ) {</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :     std::fprintf(out,&quot;Reparameterising path in file named %s so that all frames are equally spaced \n&quot;,ifilename.c_str() );</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 :     FILE* fp=std::fopen(ifilename.c_str(),&quot;r&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : // call fclose when fp goes out of scope</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :     auto deleter=[](FILE* f) { if(f) std::fclose(f); };</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="150"><span class="lineNum">     150 </span>            :     bool do_read=true; std::vector&lt;std::unique_ptr&lt;ReferenceConfiguration&gt;&gt; frames;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         24 :     while (do_read) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         22 :       PDB mypdb;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       // Read the pdb file</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         22 :       do_read=mypdb.readFromFilepointer(fp,false,0.1);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         22 :       if( do_read ) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         20 :         auto mymsd(metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, mypdb ));</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         20 :         frames.emplace_back( std::move(mymsd) );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         20 :       }</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         22 :     }</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          4 :     std::vector&lt;unsigned&gt; fixed; parseVector(&quot;--fixed&quot;,fixed);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :     if( fixed.size()==1 ) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :       if( fixed[0]!=0 ) error(&quot;input to --fixed should be two integers&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :       fixed.resize(2); fixed[0]=0; fixed[1]=frames.size()-1;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :     } else if( fixed.size()==2 ) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          1 :       if( fixed[0]&gt;(frames.size()-1) || fixed[1]&gt;(frames.size()-1) ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :         error(&quot;input to --fixed should be two numbers between 0 and the number of frames-1&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :       }</a>
+<a name="168"><span class="lineNum">     168 </span>            :     } else {</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       error(&quot;input to --fixed should be two integers&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span>            :     std::vector&lt;AtomNumber&gt; atoms; std::vector&lt;std::string&gt; arg_names;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         22 :     for(unsigned i=0; i&lt;frames.size(); ++i) {</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :       frames[i]-&gt;getAtomRequests( atoms);</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         20 :       frames[i]-&gt;getArgumentRequests( arg_names );</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            :     // Generate stuff to reparameterize</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :     Pbc fake_pbc; std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; vals;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;frames[0]-&gt;getNumberOfReferenceArguments(); ++i) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :       vals.emplace_back(Tools::make_unique&lt;Value&gt;()); vals[vals.size()-1]-&gt;setNotPeriodic();</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :     // temporary pointes used to make the conversion once</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :     auto vals_ptr=Tools::unique2raw(vals);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     // And reparameterize</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          2 :     PathReparameterization myparam( fake_pbc, vals_ptr, frames );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     // And make all points equally spaced</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          4 :     double tol; parse(&quot;--tolerance&quot;,tol); myparam.reparameterize( fixed[0], fixed[1], tol );</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :     // Output data on spacings</a>
+<a name="191"><span class="lineNum">     191 </span>            :     double mean=0;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          2 :     MultiValue myvpack( 1, frames[0]-&gt;getNumberOfReferenceArguments() + 3*frames[0]-&gt;getNumberOfReferencePositions() + 9 );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 :     ReferenceValuePack mypack( frames[0]-&gt;getNumberOfReferenceArguments(), frames[0]-&gt;getNumberOfReferencePositions(), myvpack );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         20 :     for(unsigned i=1; i&lt;frames.size(); ++i) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         18 :       double len = frames[i]-&gt;calc( frames[i-1]-&gt;getReferencePositions(), fake_pbc, vals_ptr, frames[i-1]-&gt;getReferenceArguments(), mypack, false );</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       printf(&quot;FINAL DISTANCE BETWEEN FRAME %u AND %u IS %f \n&quot;,i-1,i,len );</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         18 :       mean+=len*len;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :     printf(&quot;SUGGESTED LAMBDA PARAMETER IS THUS %f \n&quot;,2.3/(mean/static_cast&lt;double&gt;( frames.size()-1 )) );</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :     // Delete all the frames</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :     OFile ofile; ofile.open(ofilename);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          2 :     std::vector&lt;std::string&gt; argnames; frames[0]-&gt;getArgumentRequests( argnames );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          2 :     std::vector&lt;AtomNumber&gt; atindices; frames[0]-&gt;getAtomRequests( atindices );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          2 :     PDB mypdb; mypdb.setAtomNumbers( atindices ); mypdb.setArgumentNames( argnames );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         22 :     for(unsigned i=0; i&lt;frames.size(); ++i) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         20 :       mypdb.setAtomPositions( frames[i]-&gt;getReferencePositions() );</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         40 :       for(unsigned j=0; j&lt;argnames.size(); ++j) mypdb.setArgumentValue( argnames[j], frames[i]-&gt;getReferenceArguments()[j] );</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         20 :       ofile.printf(&quot;REMARK TYPE=%s\n&quot;,mtype.c_str() );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         20 :       mypdb.print( 10, NULL, ofile, ofmt );</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     }</a>
+<a name="212"><span class="lineNum">     212 </span>            :     // Delete the vals as we don't need them</a>
+<a name="213"><span class="lineNum">     213 </span>            :     // for(unsigned i=0; i&lt;vals.size(); ++i) delete vals[i];</a>
+<a name="214"><span class="lineNum">     214 </span>            :     // Return as we are done</a>
+<a name="215"><span class="lineNum">     215 </span>            :     return 0;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         10 :   }</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : // Read initial frame</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          2 :   std::string istart; parse(&quot;--start&quot;,istart);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          2 :   PDB mystartpdb;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 :     FILE* fp2=std::fopen(istart.c_str(),&quot;r&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : // call fclose when fp goes out of scope</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          2 :     auto deleter=[](FILE* f) { std::fclose(f); };</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp2,deleter);</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          2 :     if( istart.length()==0 ) error(&quot;input is missing use --istart + --iend or --path&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          2 :     if( !mystartpdb.readFromFilepointer(fp2,false,0.1) ) error(&quot;could not read fila &quot; + istart);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          2 :   auto sframe=metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, mystartpdb );</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : // Read final frame</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          2 :   std::string iend; parse(&quot;--end&quot;,iend);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 :   PDB myendpdb;</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   {</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          2 :     FILE* fp1=std::fopen(iend.c_str(),&quot;r&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : // call fclose when fp goes out of scope</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          2 :     auto deleter=[](FILE* f) { std::fclose(f); };</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :     std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp1,deleter);</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :     if( iend.length()==0 ) error(&quot;input is missing using --istart + --iend or --path&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          2 :     if( !myendpdb.readFromFilepointer(fp1,false,0.1) ) error(&quot;could not read fila &quot; + iend);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          2 :   auto eframe=metricRegister().create&lt;ReferenceConfiguration&gt;( mtype, myendpdb );</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : // Get atoms and arg requests</a>
+<a name="245"><span class="lineNum">     245 </span>            :   std::vector&lt;AtomNumber&gt; atoms; std::vector&lt;std::string&gt; arg_names;</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          2 :   sframe-&gt;getAtomRequests( atoms); eframe-&gt;getAtomRequests( atoms);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          2 :   sframe-&gt;getArgumentRequests( arg_names ); eframe-&gt;getArgumentRequests( arg_names );</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : // Now read in the rest of the instructions</a>
+<a name="250"><span class="lineNum">     250 </span>            :   unsigned nbefore, nbetween, nafter;</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          6 :   parse(&quot;--nframes-before-start&quot;,nbefore); parse(&quot;--nframes&quot;,nbetween); parse(&quot;--nframes-after-end&quot;,nafter);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 :   nbetween++;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   std::fprintf(out,&quot;Generating linear path connecting structure in file named %s to structure in file named %s \n&quot;,istart.c_str(),iend.c_str() );</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          2 :   std::fprintf(out,&quot;A path consisting of %u equally-spaced frames before the initial structure, %u frames between the initial and final structures &quot;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :                &quot;and %u frames after the final structure will be created \n&quot;,nbefore,nbetween,nafter);</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : // Create a vector of arguments to use for calculating displacements</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          2 :   Pbc fpbc;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; args;</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;eframe-&gt;getNumberOfReferenceArguments(); ++i) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          2 :     args.emplace_back(Tools::make_unique&lt;Value&gt;()); args[args.size()-1]-&gt;setNotPeriodic();</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   // convert pointer once:</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          2 :   auto args_ptr=Tools::unique2raw(args);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : // Calculate the distance between the start and the end</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          2 :   MultiValue myvpack( 1, sframe-&gt;getNumberOfReferenceArguments() + 3*sframe-&gt;getNumberOfReferencePositions() + 9);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          2 :   ReferenceValuePack mypack( sframe-&gt;getNumberOfReferenceArguments(), sframe-&gt;getNumberOfReferencePositions(), myvpack );</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          2 :   sframe-&gt;calc( eframe-&gt;getReferencePositions(), fpbc, args_ptr, eframe-&gt;getReferenceArguments(), mypack, false );</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : // And the spacing between frames</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :   double delr = 1.0 / static_cast&lt;double&gt;( nbetween );</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : // Calculate the vector connecting the start to the end</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          2 :   PDB mypdb; mypdb.setAtomNumbers( sframe-&gt;getAbsoluteIndexes() ); mypdb.addBlockEnd( sframe-&gt;getAbsoluteIndexes().size() );</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          2 :   if( sframe-&gt;getArgumentNames().size()&gt;0 ) mypdb.setArgumentNames( sframe-&gt;getArgumentNames() );</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          4 :   Direction mydir(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)); sframe-&gt;setupPCAStorage( mypack ); mydir.read( mypdb ); mydir.zeroDirection();</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          2 :   sframe-&gt;extractDisplacementVector( eframe-&gt;getReferencePositions(), args_ptr, eframe-&gt;getReferenceArguments(), false, mydir );</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : // Now create frames</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          2 :   OFile ofile; ofile.open(ofilename); unsigned nframes=0;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          4 :   Direction pos(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)); pos.read( mypdb );</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          4 :   for(int i=0; i&lt;nbefore; ++i) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          2 :     pos.setDirection( sframe-&gt;getReferencePositions(), sframe-&gt;getReferenceArguments() );</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          2 :     pos.displaceReferenceConfiguration( -i*delr, mydir );</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          2 :     mypdb.setAtomPositions( pos.getReferencePositions() );</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          4 :     for(unsigned j=0; j&lt;pos.getReferenceArguments().size(); ++j) mypdb.setArgumentValue( sframe-&gt;getArgumentNames()[j], pos.getReferenceArgument(j) );</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          2 :     ofile.printf(&quot;REMARK TYPE=%s\n&quot;,mtype.c_str() );</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          2 :     mypdb.print( 10, NULL, ofile, ofmt ); nframes++;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          8 :   for(unsigned i=1; i&lt;nbetween; ++i) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          6 :     pos.setDirection( sframe-&gt;getReferencePositions(), sframe-&gt;getReferenceArguments() );</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          6 :     pos.displaceReferenceConfiguration( i*delr, mydir );</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          6 :     mypdb.setAtomPositions( pos.getReferencePositions() );</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         16 :     for(unsigned j=0; j&lt;pos.getReferenceArguments().size(); ++j) mypdb.setArgumentValue( sframe-&gt;getArgumentNames()[j], pos.getReferenceArgument(j) );</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          6 :     ofile.printf(&quot;REMARK TYPE=%s\n&quot;,mtype.c_str() );</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          6 :     mypdb.print( 10, NULL, ofile, ofmt ); nframes++;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          7 :   for(unsigned i=0; i&lt;nafter; ++i) {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          5 :     pos.setDirection( eframe-&gt;getReferencePositions(), eframe-&gt;getReferenceArguments() );</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          5 :     pos.displaceReferenceConfiguration( i*delr, mydir );</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          5 :     mypdb.setAtomPositions( pos.getReferencePositions() );</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         13 :     for(unsigned j=0; j&lt;pos.getReferenceArguments().size(); ++j) mypdb.setArgumentValue( sframe-&gt;getArgumentNames()[j], pos.getReferenceArgument(j) );</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          5 :     ofile.printf(&quot;REMARK TYPE=%s\n&quot;,mtype.c_str() );</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          5 :     mypdb.print( 10, NULL, ofile, ofmt ); nframes++;</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :   }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          2 :   ofile.close(); return 0;</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         10 : }</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : } // End of namespace</a>
+<a name="311"><span class="lineNum">     311 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PropertyMap.cpp.func-sort-c.html b/coverage/mapping/PropertyMap.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b89721c405
--- /dev/null
+++ b/coverage/mapping/PropertyMap.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PropertyMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PropertyMap.cpp<span style="font-size: 80%;"> (<a href="PropertyMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PropertyMap.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#110">_ZN4PLMD7mapping11PropertyMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#110">_ZN4PLMD7mapping11PropertyMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#102">_ZN4PLMD7mapping12_GLOBAL__N_124PropertyMapRegisterMe1046createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#104">_ZN4PLMD7mapping11PropertyMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#102">_ZN4PLMD7mapping12_GLOBAL__N_124PropertyMapRegisterMe104C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#102">_ZN4PLMD7mapping12_GLOBAL__N_124PropertyMapRegisterMe104D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PropertyMap.cpp.func.html b/coverage/mapping/PropertyMap.cpp.func.html
new file mode 100644
index 0000000000..533430ba11
--- /dev/null
+++ b/coverage/mapping/PropertyMap.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PropertyMap.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PropertyMap.cpp<span style="font-size: 80%;"> (<a href="PropertyMap.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PropertyMap.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#104">_ZN4PLMD7mapping11PropertyMap16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#110">_ZN4PLMD7mapping11PropertyMapC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#110">_ZN4PLMD7mapping11PropertyMapC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#102">_ZN4PLMD7mapping12_GLOBAL__N_124PropertyMapRegisterMe1046createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#102">_ZN4PLMD7mapping12_GLOBAL__N_124PropertyMapRegisterMe104C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PropertyMap.cpp.gcov.html#102">_ZN4PLMD7mapping12_GLOBAL__N_124PropertyMapRegisterMe104D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/PropertyMap.cpp.gcov.html b/coverage/mapping/PropertyMap.cpp.gcov.html
new file mode 100644
index 0000000000..3425971c87
--- /dev/null
+++ b/coverage/mapping/PropertyMap.cpp.gcov.html
@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/PropertyMap.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - PropertyMap.cpp<span style="font-size: 80%;"> (source / <a href="PropertyMap.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PathBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC COLVAR GPROPERTYMAP</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Property maps but with a more flexible framework for the distance metric being used.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : This colvar calculates a property map using the formalism developed by Spiwok \cite Spiwok:2011ce.</a>
+<a name="30"><span class="lineNum">      30 </span>            : In essence if you have the value of some property, \f$X_i\f$, that it takes at a set of high-dimensional</a>
+<a name="31"><span class="lineNum">      31 </span>            : positions then you calculate the value of the property at some arbitrary point in the high-dimensional space</a>
+<a name="32"><span class="lineNum">      32 </span>            : using:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i  \exp(-\lambda D_i(x))}</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Within PLUMED there are multiple ways to define the distance from a high-dimensional configuration, \f$D_i\f$.  You could calculate</a>
+<a name="39"><span class="lineNum">      39 </span>            : the RMSD distance or you could calculate the amount by which a set of collective variables change.  As such this implementation</a>
+<a name="40"><span class="lineNum">      40 </span>            : of the property map allows one to use all the different distance metric that are discussed in \ref dists. This is as opposed to</a>
+<a name="41"><span class="lineNum">      41 </span>            : the alternative implementation \ref PROPERTYMAP which is a bit faster but which only allows one to use the RMSD distance.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The input shown below can be used to calculate the interpolated values of two properties called X and Y based on the values</a>
+<a name="46"><span class="lineNum">      46 </span>            : that these properties take at a set of reference configurations and using the formula above.  For this input the distances</a>
+<a name="47"><span class="lineNum">      47 </span>            : between the reference configurations and the instantaneous configurations are calculated using the OPTIMAL metric that is</a>
+<a name="48"><span class="lineNum">      48 </span>            : discussed at length in the manual pages on \ref RMSD.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \plumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : p2: GPROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087</a>
+<a name="52"><span class="lineNum">      52 </span>            : PRINT ARG=p2.X,p2.Y,p2.zpath STRIDE=1 FILE=colvar</a>
+<a name="53"><span class="lineNum">      53 </span>            : \endplumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The additional input file for this calculation, which contains the reference frames and the values of X and Y at these reference</a>
+<a name="56"><span class="lineNum">      56 </span>            : points has the following format.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \auxfile{allv.pdb}</a>
+<a name="59"><span class="lineNum">      59 </span>            : REMARK X=1 Y=2</a>
+<a name="60"><span class="lineNum">      60 </span>            : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00</a>
+<a name="61"><span class="lineNum">      61 </span>            : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00</a>
+<a name="62"><span class="lineNum">      62 </span>            : ATOM      6  OL  ALA     1      -1.177  -0.889   2.401  1.00  1.00</a>
+<a name="63"><span class="lineNum">      63 </span>            : ATOM      7  NL  ALA     1      -1.313   0.341   0.529  1.00  1.00</a>
+<a name="64"><span class="lineNum">      64 </span>            : ATOM      8  HL  ALA     1      -1.845   0.961  -0.011  1.00  1.00</a>
+<a name="65"><span class="lineNum">      65 </span>            : ATOM      9  CA  ALA     1      -0.003  -0.019   0.021  1.00  1.00</a>
+<a name="66"><span class="lineNum">      66 </span>            : ATOM     10  HA  ALA     1       0.205  -1.051   0.259  1.00  1.00</a>
+<a name="67"><span class="lineNum">      67 </span>            : ATOM     11  CB  ALA     1       0.009   0.135  -1.509  1.00  1.00</a>
+<a name="68"><span class="lineNum">      68 </span>            : ATOM     15  CRP ALA     1       1.121   0.799   0.663  1.00  1.00</a>
+<a name="69"><span class="lineNum">      69 </span>            : ATOM     16  OR  ALA     1       1.723   1.669   0.043  1.00  1.00</a>
+<a name="70"><span class="lineNum">      70 </span>            : ATOM     17  NR  ALA     1       1.423   0.519   1.941  1.00  1.00</a>
+<a name="71"><span class="lineNum">      71 </span>            : ATOM     18  HR  ALA     1       0.873  -0.161   2.413  1.00  1.00</a>
+<a name="72"><span class="lineNum">      72 </span>            : ATOM     19  CR  ALA     1       2.477   1.187   2.675  1.00  1.00</a>
+<a name="73"><span class="lineNum">      73 </span>            : END</a>
+<a name="74"><span class="lineNum">      74 </span>            : FIXED</a>
+<a name="75"><span class="lineNum">      75 </span>            : REMARK X=2 Y=3</a>
+<a name="76"><span class="lineNum">      76 </span>            : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00</a>
+<a name="77"><span class="lineNum">      77 </span>            : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00</a>
+<a name="78"><span class="lineNum">      78 </span>            : ATOM      6  OL  ALA     1      -1.201  -0.849   2.425  1.00  1.00</a>
+<a name="79"><span class="lineNum">      79 </span>            : ATOM      7  NL  ALA     1      -1.296   0.337   0.534  1.00  1.00</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOM      8  HL  ALA     1      -1.807   0.951  -0.044  1.00  1.00</a>
+<a name="81"><span class="lineNum">      81 </span>            : ATOM      9  CA  ALA     1       0.009  -0.067   0.033  1.00  1.00</a>
+<a name="82"><span class="lineNum">      82 </span>            : ATOM     10  HA  ALA     1       0.175  -1.105   0.283  1.00  1.00</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM     11  CB  ALA     1       0.027   0.046  -1.501  1.00  1.00</a>
+<a name="84"><span class="lineNum">      84 </span>            : ATOM     15  CRP ALA     1       1.149   0.725   0.654  1.00  1.00</a>
+<a name="85"><span class="lineNum">      85 </span>            : ATOM     16  OR  ALA     1       1.835   1.491  -0.011  1.00  1.00</a>
+<a name="86"><span class="lineNum">      86 </span>            : ATOM     17  NR  ALA     1       1.380   0.537   1.968  1.00  1.00</a>
+<a name="87"><span class="lineNum">      87 </span>            : ATOM     18  HR  ALA     1       0.764  -0.060   2.461  1.00  1.00</a>
+<a name="88"><span class="lineNum">      88 </span>            : ATOM     19  CR  ALA     1       2.431   1.195   2.683  1.00  1.00</a>
+<a name="89"><span class="lineNum">      89 </span>            : END</a>
+<a name="90"><span class="lineNum">      90 </span>            : \endauxfile</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : */</a>
+<a name="93"><span class="lineNum">      93 </span>            : //+ENDPLUMEDOC</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : namespace PLMD {</a>
+<a name="96"><span class="lineNum">      96 </span>            : namespace mapping {</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : class PropertyMap : public PathBase {</a>
+<a name="99"><span class="lineNum">      99 </span>            : public:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit PropertyMap(const ActionOptions&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            : };</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(PropertyMap,&quot;GPROPERTYMAP&quot;)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          5 : void PropertyMap::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          5 :   PathBase::registerKeywords( keys );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          5 :   ActionWithValue::useCustomisableComponents( keys );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         10 :   keys.addFlag(&quot;NOMAPPING&quot;,false,&quot;do not calculate the position on the manifold&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          5 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 : PropertyMap::PropertyMap(const ActionOptions&amp; ao):</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   Action(ao),</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 :   PathBase(ao)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : {</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          6 :   bool nos; parseFlag(&quot;NOMAPPING&quot;,nos);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   std::string empty;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          3 :   if(!nos) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          9 :     for(std::map&lt;std::string,std::vector&lt;double&gt; &gt;::iterator it=property.begin(); it!=property.end(); ++it) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         18 :       empty=&quot;LABEL=&quot;+it-&gt;first; addVessel( &quot;SPATH&quot;, empty, 0 );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     }</a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 :   readVesselKeywords();</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          3 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/SpathVessel.cpp.func-sort-c.html b/coverage/mapping/SpathVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..30a18e8b8a
--- /dev/null
+++ b/coverage/mapping/SpathVessel.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/SpathVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - SpathVessel.cpp<span style="font-size: 80%;"> (<a href="SpathVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SpathVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#42">_ZN4PLMD7mapping11SpathVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#65">_ZN4PLMD7mapping11SpathVessel16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#51">_ZN4PLMD7mapping11SpathVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#40">_ZN4PLMD7mapping12_GLOBAL__N_121SpathVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#46">_ZN4PLMD7mapping11SpathVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#40">_ZN4PLMD7mapping12_GLOBAL__N_121SpathVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#40">_ZN4PLMD7mapping12_GLOBAL__N_121SpathVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#69">_ZN4PLMD7mapping11SpathVessel7prepareEv</a></td>
+              <td class="coverFnHi">5460</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#73">_ZNK4PLMD7mapping11SpathVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">27391</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/SpathVessel.cpp.func.html b/coverage/mapping/SpathVessel.cpp.func.html
new file mode 100644
index 0000000000..e76485b78a
--- /dev/null
+++ b/coverage/mapping/SpathVessel.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/SpathVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - SpathVessel.cpp<span style="font-size: 80%;"> (<a href="SpathVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SpathVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#46">_ZN4PLMD7mapping11SpathVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#42">_ZN4PLMD7mapping11SpathVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#65">_ZN4PLMD7mapping11SpathVessel16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#69">_ZN4PLMD7mapping11SpathVessel7prepareEv</a></td>
+              <td class="coverFnHi">5460</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#51">_ZN4PLMD7mapping11SpathVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#40">_ZN4PLMD7mapping12_GLOBAL__N_121SpathVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#40">_ZN4PLMD7mapping12_GLOBAL__N_121SpathVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#40">_ZN4PLMD7mapping12_GLOBAL__N_121SpathVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SpathVessel.cpp.gcov.html#73">_ZNK4PLMD7mapping11SpathVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">27391</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/SpathVessel.cpp.gcov.html b/coverage/mapping/SpathVessel.cpp.gcov.html
new file mode 100644
index 0000000000..17eb48d809
--- /dev/null
+++ b/coverage/mapping/SpathVessel.cpp.gcov.html
@@ -0,0 +1,163 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/SpathVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - SpathVessel.cpp<span style="font-size: 80%;"> (source / <a href="SpathVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;vesselbase/VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Mapping.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace mapping {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class SpathVessel : public vesselbase::FunctionVessel {</a>
+<a name="30"><span class="lineNum">      30 </span>            : private:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   bool foundoneclose;</a>
+<a name="32"><span class="lineNum">      32 </span>            :   Mapping* mymap;</a>
+<a name="33"><span class="lineNum">      33 </span>            : public:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="35"><span class="lineNum">      35 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   explicit SpathVessel( const vesselbase::VesselOptions&amp; da );</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::string value_descriptor() override;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   void prepare() override;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_index ) const override;</a>
+<a name="40"><span class="lineNum">      40 </span>            : };</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      12514 : PLUMED_REGISTER_VESSEL(SpathVessel,&quot;SPATH&quot;)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         10 : void SpathVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         10 :   FunctionVessel::registerKeywords(keys);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         10 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       4168 : void SpathVessel::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;SPATH&quot;,&quot;docs should not appear&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;spath&quot;,&quot;SPATH&quot;,&quot;the position on the path&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       4168 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         10 : SpathVessel::SpathVessel( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   FunctionVessel(da),</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         10 :   foundoneclose(false)</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         10 :   mymap=dynamic_cast&lt;Mapping*&gt;( getAction() );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         10 :   plumed_massert( mymap, &quot;SpathVessel can only be used with mappings&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   // Retrieve the index of the property in the underlying mapping</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         10 :   usetol=true; norm=true;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        430 :   for(unsigned i=0; i&lt;mymap-&gt;getFullNumberOfTasks(); ++i) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        420 :     if( mymap-&gt;getTaskCode(i)!=mymap-&gt;getPositionInFullTaskList(i) ) error(&quot;mismatched tasks and codes&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         10 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         10 : std::string SpathVessel::value_descriptor() {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         10 :   return &quot;the position on the path&quot;;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       5460 : void SpathVessel::prepare() {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       5460 :   foundoneclose=false;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       5460 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      27391 : void SpathVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_index ) const {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      27391 :   double pp=mymap-&gt;getPropertyValue( current, getLabel() ), weight=myvals.get(0);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      27391 :   if( weight&lt;getTolerance() ) return;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      27391 :   unsigned nderivatives=getFinalValue()-&gt;getNumberOfDerivatives();</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      27391 :   buffer[bufstart] += weight*pp; buffer[bufstart+1+nderivatives] += weight;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      27391 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      23478 :     myvals.chainRule( 0, 0, 1, 0, pp, bufstart, buffer );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      23478 :     myvals.chainRule( 0, 1, 1, 0, 1.0, bufstart, buffer );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/TrigonometricPathVessel.cpp.func-sort-c.html b/coverage/mapping/TrigonometricPathVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3499ae76b3
--- /dev/null
+++ b/coverage/mapping/TrigonometricPathVessel.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/TrigonometricPathVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - TrigonometricPathVessel.cpp<span style="font-size: 80%;"> (<a href="TrigonometricPathVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TrigonometricPathVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#27">_ZN4PLMD7mapping12_GLOBAL__N_133TrigonometricPathVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#83">_ZN4PLMD7mapping23TrigonometricPathVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#29">_ZN4PLMD7mapping23TrigonometricPathVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping23TrigonometricPathVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#87">_ZN4PLMD7mapping23TrigonometricPathVessel6resizeEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#211">_ZN4PLMD7mapping23TrigonometricPathVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#95">_ZN4PLMD7mapping23TrigonometricPathVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#27">_ZN4PLMD7mapping12_GLOBAL__N_133TrigonometricPathVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#27">_ZN4PLMD7mapping12_GLOBAL__N_133TrigonometricPathVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#33">_ZN4PLMD7mapping23TrigonometricPathVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/TrigonometricPathVessel.cpp.func.html b/coverage/mapping/TrigonometricPathVessel.cpp.func.html
new file mode 100644
index 0000000000..89967151da
--- /dev/null
+++ b/coverage/mapping/TrigonometricPathVessel.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/TrigonometricPathVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - TrigonometricPathVessel.cpp<span style="font-size: 80%;"> (<a href="TrigonometricPathVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TrigonometricPathVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#27">_ZN4PLMD7mapping12_GLOBAL__N_133TrigonometricPathVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#27">_ZN4PLMD7mapping12_GLOBAL__N_133TrigonometricPathVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#27">_ZN4PLMD7mapping12_GLOBAL__N_133TrigonometricPathVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#211">_ZN4PLMD7mapping23TrigonometricPathVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#83">_ZN4PLMD7mapping23TrigonometricPathVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#33">_ZN4PLMD7mapping23TrigonometricPathVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#29">_ZN4PLMD7mapping23TrigonometricPathVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#95">_ZN4PLMD7mapping23TrigonometricPathVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#87">_ZN4PLMD7mapping23TrigonometricPathVessel6resizeEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TrigonometricPathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping23TrigonometricPathVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/TrigonometricPathVessel.cpp.gcov.html b/coverage/mapping/TrigonometricPathVessel.cpp.gcov.html
new file mode 100644
index 0000000000..d54eb6c735
--- /dev/null
+++ b/coverage/mapping/TrigonometricPathVessel.cpp.gcov.html
@@ -0,0 +1,305 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/TrigonometricPathVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - TrigonometricPathVessel.cpp<span style="font-size: 80%;"> (source / <a href="TrigonometricPathVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;TrigonometricPathVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace mapping {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">      12507 : PLUMED_REGISTER_VESSEL(TrigonometricPathVessel,&quot;GPATH&quot;)</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          3 : void TrigonometricPathVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          3 :   StoreDataVessel::registerKeywords(keys);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          3 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       4168 : void TrigonometricPathVessel::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;GPATH&quot;,&quot;calculate the position on the path using trigonometry&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;gspath&quot;,&quot;GPATH&quot;,&quot;the position on the path calculated using trigonometry&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;gzpath&quot;,&quot;GPATH&quot;,&quot;the distance from the path calculated using trigonometry&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       4168 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          3 : TrigonometricPathVessel::TrigonometricPathVessel( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   StoreDataVessel(da),</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          6 :   projdir(ReferenceConfigurationOptions(&quot;DIRECTION&quot;)),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          3 :   mydpack1( 1, getAction()-&gt;getNumberOfDerivatives() ),</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          3 :   mydpack2( 1, getAction()-&gt;getNumberOfDerivatives() ),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          3 :   mydpack3( 1, getAction()-&gt;getNumberOfDerivatives() ),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          3 :   mypack1( 0, 0, mydpack1 ),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          3 :   mypack2( 0, 0, mydpack2 ),</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          9 :   mypack3( 0, 0, mydpack3 )</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          3 :   mymap=dynamic_cast&lt;Mapping*&gt;( getAction() );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          3 :   plumed_massert( mymap, &quot;Trigonometric path vessel can only be used with mappings&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   // Retrieve the index of the property in the underlying mapping</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 :   if( mymap-&gt;getNumberOfProperties()!=1 ) error(&quot;cannot use trigonometric paths when there are multiple properties&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        125 :   for(unsigned i=0; i&lt;mymap-&gt;getFullNumberOfTasks(); ++i) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        122 :     if( mymap-&gt;getTaskCode(i)!=mymap-&gt;getPositionInFullTaskList(i) ) error(&quot;mismatched tasks and codes&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   }</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          6 :   mymap-&gt;addComponentWithDerivatives(&quot;gspath&quot;); mymap-&gt;componentIsNotPeriodic(&quot;gspath&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          3 :   sp=mymap-&gt;copyOutput( mymap-&gt;getNumberOfComponents()-1 ); sp-&gt;resizeDerivatives( mymap-&gt;getNumberOfDerivatives() );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          6 :   mymap-&gt;addComponentWithDerivatives(&quot;gzpath&quot;); mymap-&gt;componentIsNotPeriodic(&quot;gzpath&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          3 :   zp=mymap-&gt;copyOutput( mymap-&gt;getNumberOfComponents()-1 ); zp-&gt;resizeDerivatives( mymap-&gt;getNumberOfDerivatives() );</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   // Check we have PCA</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          3 :   ReferenceConfiguration* ref0=mymap-&gt;getReferenceConfiguration(0);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        125 :   for(unsigned i=0; i&lt;mymap-&gt;getFullNumberOfTasks(); ++i) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        122 :     if( !(mymap-&gt;getReferenceConfiguration(i))-&gt;pcaIsEnabledForThisReference() ) error(&quot;pca must be implemented in order to use trigometric path&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        244 :     if( ref0-&gt;getName()!=(mymap-&gt;getReferenceConfiguration(i))-&gt;getName() ) error(&quot;cannot use mixed metrics&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        122 :     if( mymap-&gt;getNumberOfAtoms()!=(mymap-&gt;getReferenceConfiguration(i))-&gt;getNumberOfReferencePositions() ) error(&quot;all frames must use the same set of atoms&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        122 :     if( mymap-&gt;getNumberOfArguments()!=(mymap-&gt;getReferenceConfiguration(i))-&gt;getNumberOfReferenceArguments() ) error(&quot;all frames must use the same set of arguments&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          3 :   cargs.resize( mymap-&gt;getNumberOfArguments() ); std::vector&lt;std::string&gt; argument_names( mymap-&gt;getNumberOfArguments() );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          7 :   for(unsigned i=0; i&lt;mymap-&gt;getNumberOfArguments(); ++i) argument_names[i] = (mymap-&gt;getPntrToArgument(i))-&gt;getName();</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          3 :   PDB mypdb; mypdb.setAtomNumbers( mymap-&gt;getAbsoluteIndexes() ); mypdb.addBlockEnd( mymap-&gt;getAbsoluteIndexes().size() );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          3 :   if( argument_names.size()&gt;0 ) mypdb.setArgumentNames( argument_names );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          3 :   projdir.read( mypdb );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          3 :   mypack1.resize( mymap-&gt;getNumberOfArguments(), mymap-&gt;getNumberOfAtoms() ); ref0-&gt;setupPCAStorage( mypack1 );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          3 :   mypack2.resize( mymap-&gt;getNumberOfArguments(), mymap-&gt;getNumberOfAtoms() ); ref0-&gt;setupPCAStorage( mypack2 );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 :   mypack3.resize( mymap-&gt;getNumberOfArguments(), mymap-&gt;getNumberOfAtoms() );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         16 :   for(unsigned i=0; i&lt;mymap-&gt;getNumberOfAtoms(); ++i) { mypack1.setAtomIndex(i,i); mypack2.setAtomIndex(i,i); mypack3.setAtomIndex(i,i); }</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          3 :   mypack1_stashd_atoms.resize( mymap-&gt;getNumberOfAtoms() ); mypack1_stashd_args.resize( mymap-&gt;getNumberOfArguments() );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          3 : }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          3 : std::string TrigonometricPathVessel::description() {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          3 :   return &quot;values gspath and gzpath contain the position on and distance from the path calculated using trigonometry&quot;;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          7 : void TrigonometricPathVessel::resize() {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          7 :   StoreDataVessel::resize();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          7 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          4 :     unsigned nderivatives=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          8 :     sp-&gt;resizeDerivatives( nderivatives ); zp-&gt;resizeDerivatives( nderivatives );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          7 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1193 : void TrigonometricPathVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   // Store the data calculated during mpi loop</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       1193 :   StoreDataVessel::finish( buffer );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   // Get current value of all arguments</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       2487 :   for(unsigned i=0; i&lt;cargs.size(); ++i) cargs[i]=mymap-&gt;getArgument(i);</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   // Determine closest and second closest point to current position</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       1193 :   double lambda=mymap-&gt;getLambda();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1193 :   std::vector&lt;double&gt; dist( getNumberOfComponents() ), dist2( getNumberOfComponents() );;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1193 :   retrieveSequentialValue( 0, false, dist );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1193 :   retrieveSequentialValue( 1, false, dist2 );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1193 :   iclose1=getStoreIndex(0); iclose2=getStoreIndex(1);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1193 :   double mindist1=dist[0], mindist2=dist2[0];</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       1193 :   if( lambda&gt;0.0 ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     mindist1=-std::log( dist[0] ) / lambda;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     mindist2=-std::log( dist2[0] ) / lambda;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1193 :   if( mindist2&lt;mindist1 ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     double tmp=mindist1; mindist1=mindist2; mindist2=tmp;</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        866 :     iclose1=getStoreIndex(1); iclose2=getStoreIndex(0);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      56519 :   for(unsigned i=2; i&lt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      55326 :     retrieveSequentialValue( i, false, dist );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      55326 :     double ndist=dist[0];</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      55326 :     if( lambda&gt;0.0 ) ndist=-std::log( dist[0] ) / lambda;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      55326 :     if( ndist&lt;mindist1 ) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      19737 :       mindist2=mindist1; iclose2=iclose1;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      19737 :       mindist1=ndist; iclose1=getStoreIndex(i);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      35589 :     } else if( ndist&lt;mindist2 ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       1062 :       mindist2=ndist; iclose2=getStoreIndex(i);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     }</a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span>            :   // And find third closest point</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       1193 :   int isign = iclose1 - iclose2;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   if( isign&gt;1 ) isign=1; else if( isign&lt;-1 ) isign=-1;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       1193 :   int iclose3 = iclose1 + isign; double v2v2;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   // We now have to compute vectors connecting the three closest points to the</a>
+<a name="134"><span class="lineNum">     134 </span>            :   // new point</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1193 :   double v1v1 = (mymap-&gt;getReferenceConfiguration( iclose1 ))-&gt;calculate( mymap-&gt;getPositions(), mymap-&gt;getPbc(), mymap-&gt;getArguments(), mypack1, true );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1193 :   double v3v3 = (mymap-&gt;getReferenceConfiguration( iclose2 ))-&gt;calculate( mymap-&gt;getPositions(), mymap-&gt;getPbc(), mymap-&gt;getArguments(), mypack3, true );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1193 :   if( iclose3&lt;0 || iclose3&gt;=mymap-&gt;getFullNumberOfTasks() ) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         31 :     ReferenceConfiguration* conf2=mymap-&gt;getReferenceConfiguration( iclose1 );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         62 :     v2v2=(mymap-&gt;getReferenceConfiguration( iclose2 ))-&gt;calc( conf2-&gt;getReferencePositions(), mymap-&gt;getPbc(), mymap-&gt;getArguments(),</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         31 :          conf2-&gt;getReferenceArguments(), mypack2, true );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         62 :     (mymap-&gt;getReferenceConfiguration( iclose2 ))-&gt;extractDisplacementVector( conf2-&gt;getReferencePositions(), mymap-&gt;getArguments(),</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         62 :         conf2-&gt;getReferenceArguments(), false, projdir );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   } else {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       1162 :     ReferenceConfiguration* conf2=mymap-&gt;getReferenceConfiguration( iclose3 );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       2324 :     v2v2=(mymap-&gt;getReferenceConfiguration( iclose1 ))-&gt;calc( conf2-&gt;getReferencePositions(), mymap-&gt;getPbc(), mymap-&gt;getArguments(),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1162 :          conf2-&gt;getReferenceArguments(), mypack2, true );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       2324 :     (mymap-&gt;getReferenceConfiguration( iclose1 ))-&gt;extractDisplacementVector( conf2-&gt;getReferencePositions(), mymap-&gt;getArguments(),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       2324 :         conf2-&gt;getReferenceArguments(), false, projdir );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Stash derivatives of v1v1</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       2487 :   for(unsigned i=0; i&lt;mymap-&gt;getNumberOfArguments(); ++i) mypack1_stashd_args[i]=mypack1.getArgumentDerivative(i);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       1193 :   if( mymap-&gt;getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        546 :     ReferenceAtoms* at = dynamic_cast&lt;ReferenceAtoms*&gt;( mymap-&gt;getReferenceConfiguration( iclose1 ) );</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     const std::vector&lt;double&gt; &amp; displace( at-&gt;getDisplace() );</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       7644 :     for(unsigned i=0; i&lt;mymap-&gt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       7098 :       mypack1_stashd_atoms[i]=mypack1.getAtomDerivative(i); mypack1.getAtomsDisplacementVector()[i] /= displace[i];</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :     }</a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   // Calculate the dot product of v1 with v2</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1193 :   double v1v2 = (mymap-&gt;getReferenceConfiguration(iclose1))-&gt;projectDisplacementOnVector( projdir, mymap-&gt;getArguments(), cargs, mypack1 );</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   // This computes s value</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       1193 :   double spacing = mymap-&gt;getPropertyValue( iclose1, (mymap-&gt;property.begin())-&gt;first ) - mymap-&gt;getPropertyValue( iclose2, (mymap-&gt;property.begin())-&gt;first );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       1193 :   double root = sqrt( v1v2*v1v2 - v2v2 * ( v1v1 - v3v3) );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       1193 :   dx = 0.5 * ( (root + v1v2) / v2v2 - 1.);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1193 :   double path_s = mymap-&gt;getPropertyValue(iclose1, (mymap-&gt;property.begin())-&gt;first ) + spacing * dx; sp-&gt;set( path_s );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       1193 :   double fact = 0.25*spacing / v2v2;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   // Derivative of s wrt arguments</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       2487 :   for(unsigned i=0; i&lt;mymap-&gt;getNumberOfArguments(); ++i) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1294 :     sp-&gt;setDerivative( i, fact*( mypack2.getArgumentDerivative(i) + (v2v2 * (-mypack1_stashd_args[i] + mypack3.getArgumentDerivative(i))</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       1294 :                                  + v1v2*mypack2.getArgumentDerivative(i) )/root ) );</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span>            :   // Derivative of s wrt atoms</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1193 :   unsigned narg=mymap-&gt;getNumberOfArguments(); Tensor vir; vir.zero(); fact = 0.5*spacing / v2v2;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1193 :   if( mymap-&gt;getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       7644 :     for(unsigned i=0; i&lt;mymap-&gt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       7098 :       Vector ader = fact*(( v1v2*mypack1.getAtomDerivative(i) + 0.5*v2v2*(-mypack1_stashd_atoms[i] + mypack3.getAtomDerivative(i) ) )/root + mypack1.getAtomDerivative(i) );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      28392 :       for(unsigned k=0; k&lt;3; ++k) sp-&gt;setDerivative( narg+3*i+k, ader[k] );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       7098 :       vir-=Tensor( mymap-&gt;getPosition(i), ader );</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     }</a>
+<a name="182"><span class="lineNum">     182 </span>            :     // Set the virial</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        546 :     unsigned nbase=narg+3*mymap-&gt;getNumberOfAtoms();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       7098 :     for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) sp-&gt;setDerivative( nbase+3*i+j, vir(i,j) );</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span>            :   // Now compute z value</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       1193 :   ReferenceConfiguration* conf2=mymap-&gt;getReferenceConfiguration( iclose1 );</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       2386 :   double v4v4=(mymap-&gt;getReferenceConfiguration( iclose2 ))-&gt;calc( conf2-&gt;getReferencePositions(), mymap-&gt;getPbc(), mymap-&gt;getArguments(),</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       1193 :               conf2-&gt;getReferenceArguments(), mypack2, true );</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   // Extract vector connecting frames</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       2386 :   (mymap-&gt;getReferenceConfiguration( iclose2 ))-&gt;extractDisplacementVector( conf2-&gt;getReferencePositions(), mymap-&gt;getArguments(),</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1193 :       conf2-&gt;getReferenceArguments(), false, projdir );</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   // Calculate projection of vector on line connnecting frames</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1193 :   double proj = (mymap-&gt;getReferenceConfiguration(iclose1))-&gt;projectDisplacementOnVector( projdir, mymap-&gt;getArguments(), cargs, mypack1 );</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1193 :   double path_z = v1v1 + dx*dx*v4v4 - 2*dx*proj;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   // Derivatives for z path</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       2386 :   path_z = sqrt(path_z); zp-&gt;set( path_z ); vir.zero();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       2487 :   for(unsigned i=0; i&lt;mymap-&gt;getNumberOfArguments(); ++i) zp-&gt;setDerivative( i, (mypack1_stashd_args[i] - 2*dx*mypack1.getArgumentDerivative(i))/(2.0*path_z) );</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Derivative wrt atoms</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1193 :   if( mymap-&gt;getNumberOfAtoms()&gt;0 ) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       7644 :     for(unsigned i=0; i&lt;mymap-&gt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      28392 :       Vector dxder; for(unsigned k=0; k&lt;3; ++k) dxder[k] = ( 2*v4v4*dx - 2*proj )*spacing*sp-&gt;getDerivative( narg + 3*i+k );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       7098 :       Vector ader = ( mypack1_stashd_atoms[i] - 2.*dx*mypack1.getAtomDerivative(i) + dxder )/ (2.0*path_z);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      28392 :       for(unsigned k=0; k&lt;3; ++k) zp-&gt;setDerivative( narg+3*i+k, ader[k] );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       7098 :       vir-=Tensor( mymap-&gt;getPosition(i), ader );</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     }</a>
+<a name="207"><span class="lineNum">     207 </span>            :     // Set the virial</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        546 :     unsigned nbase=narg+3*mymap-&gt;getNumberOfAtoms();</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       7098 :     for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) zp-&gt;setDerivative( nbase+3*i+j, vir(i,j) );</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       1193 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1193 : bool TrigonometricPathVessel::applyForce( std::vector&lt;double&gt;&amp; forces ) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1193 :   std::vector&lt;double&gt; tmpforce( forces.size(), 0.0 );</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1193 :   forces.assign(forces.size(),0.0); bool wasforced=false;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1193 :   if( sp-&gt;applyForce( tmpforce ) ) {</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     wasforced=true;</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;forces.size(); ++j) forces[j]+=tmpforce[j];</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   }</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       1193 :   tmpforce.assign(forces.size(),0.0);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       1193 :   if( zp-&gt;applyForce( tmpforce ) ) {</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     wasforced=true;</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;forces.size(); ++j) forces[j]+=tmpforce[j];</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       1193 :   return wasforced;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : }</a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/ZpathVessel.cpp.func-sort-c.html b/coverage/mapping/ZpathVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e76e508681
--- /dev/null
+++ b/coverage/mapping/ZpathVessel.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/ZpathVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - ZpathVessel.cpp<span style="font-size: 80%;"> (<a href="ZpathVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ZpathVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#41">_ZN4PLMD7mapping11ZpathVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#58">_ZN4PLMD7mapping11ZpathVessel16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#50">_ZN4PLMD7mapping11ZpathVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping12_GLOBAL__N_121ZpathVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#66">_ZN4PLMD7mapping11ZpathVessel14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">3822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#45">_ZN4PLMD7mapping11ZpathVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping12_GLOBAL__N_121ZpathVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping12_GLOBAL__N_121ZpathVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#62">_ZNK4PLMD7mapping11ZpathVessel13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">19565</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/mapping/ZpathVessel.cpp.func.html b/coverage/mapping/ZpathVessel.cpp.func.html
new file mode 100644
index 0000000000..407b3772e1
--- /dev/null
+++ b/coverage/mapping/ZpathVessel.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/ZpathVessel.cpp - functions</title>
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+</head>
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - ZpathVessel.cpp<span style="font-size: 80%;"> (<a href="ZpathVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#66">_ZN4PLMD7mapping11ZpathVessel14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">3822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#45">_ZN4PLMD7mapping11ZpathVessel14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#41">_ZN4PLMD7mapping11ZpathVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#58">_ZN4PLMD7mapping11ZpathVessel16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#50">_ZN4PLMD7mapping11ZpathVesselC2ERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping12_GLOBAL__N_121ZpathVesselRegisterMe6createERKNS_10vesselbase13VesselOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping12_GLOBAL__N_121ZpathVesselRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#39">_ZN4PLMD7mapping12_GLOBAL__N_121ZpathVesselRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ZpathVessel.cpp.gcov.html#62">_ZNK4PLMD7mapping11ZpathVessel13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">19565</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/mapping/ZpathVessel.cpp.gcov.html b/coverage/mapping/ZpathVessel.cpp.gcov.html
new file mode 100644
index 0000000000..983d625b64
--- /dev/null
+++ b/coverage/mapping/ZpathVessel.cpp.gcov.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping/ZpathVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">mapping</a> - ZpathVessel.cpp<span style="font-size: 80%;"> (source / <a href="ZpathVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;vesselbase/VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;vesselbase/FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Mapping.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace mapping {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class ZpathVessel : public vesselbase::FunctionVessel {</a>
+<a name="30"><span class="lineNum">      30 </span>            : private:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   double invlambda;</a>
+<a name="32"><span class="lineNum">      32 </span>            : public:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="34"><span class="lineNum">      34 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="35"><span class="lineNum">      35 </span>            :   explicit ZpathVessel( const vesselbase::VesselOptions&amp; da );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::string value_descriptor() override;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   double finalTransform( const double&amp; val, double&amp; dv ) override;</a>
+<a name="39"><span class="lineNum">      39 </span>            : };</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      12511 : PLUMED_REGISTER_VESSEL(ZpathVessel,&quot;ZPATH&quot;)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          7 : void ZpathVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          7 :   FunctionVessel::registerKeywords(keys);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          7 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       4168 : void ZpathVessel::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;ZPATH&quot;,&quot;calculate the distance from the low dimensionality manifold&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;zpath&quot;,&quot;ZPATH&quot;,&quot;the distance from the path&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       4168 : }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          7 : ZpathVessel::ZpathVessel( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          7 :   FunctionVessel(da)</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          7 :   Mapping* mymap=dynamic_cast&lt;Mapping*&gt;( getAction() );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          7 :   plumed_massert( mymap, &quot;ZpathVessel should only be used with mappings&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          7 :   invlambda = 1.0 / mymap-&gt;getLambda(); usetol=true;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          7 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          7 : std::string ZpathVessel::value_descriptor() {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          7 :   return &quot;the distance from the low-dimensional manifold&quot;;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      19565 : double ZpathVessel::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      19565 :   dv=0.0; return 1.0;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       3822 : double ZpathVessel::finalTransform( const double&amp; val, double&amp; dv ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       3822 :   dv = -invlambda / val;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       3822 :   return -invlambda*std::log( val );</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/index-sort-f.html b/coverage/mapping/index-sort-f.html
new file mode 100644
index 0000000000..4f91576b4c
--- /dev/null
+++ b/coverage/mapping/index-sort-f.html
@@ -0,0 +1,203 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - mapping</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">758</td>
+            <td class="headerCovTableEntry">809</td>
+            <td class="headerCovTableEntryHi">93.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryMed">89.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mapping.cpp.gcov.html">Mapping.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.1%"><img src="../snow.png" width=22 height=10 alt="78.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.1&nbsp;%</td>
+      <td class="coverNumMed">82 / 105</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mapping.h.gcov.html">Mapping.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Path.cpp.gcov.html">Path.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PropertyMap.cpp.gcov.html">PropertyMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCAVars.cpp.gcov.html">PCAVars.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">127 / 144</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathBase.cpp.gcov.html">PathBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdaptivePath.cpp.gcov.html">AdaptivePath.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">100 / 104</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathReparameterization.cpp.gcov.html">PathReparameterization.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">65 / 65</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathTools.cpp.gcov.html">PathTools.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">123 / 125</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ZpathVessel.cpp.gcov.html">ZpathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SpathVessel.cpp.gcov.html">SpathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TrigonometricPathVessel.cpp.gcov.html">TrigonometricPathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.1%"><img src="../snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/index-sort-l.html b/coverage/mapping/index-sort-l.html
new file mode 100644
index 0000000000..f6dc7a7b41
--- /dev/null
+++ b/coverage/mapping/index-sort-l.html
@@ -0,0 +1,203 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - mapping</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">758</td>
+            <td class="headerCovTableEntry">809</td>
+            <td class="headerCovTableEntryHi">93.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryMed">89.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mapping.cpp.gcov.html">Mapping.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.1%"><img src="../snow.png" width=22 height=10 alt="78.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.1&nbsp;%</td>
+      <td class="coverNumMed">82 / 105</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCAVars.cpp.gcov.html">PCAVars.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">127 / 144</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mapping.h.gcov.html">Mapping.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdaptivePath.cpp.gcov.html">AdaptivePath.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">100 / 104</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TrigonometricPathVessel.cpp.gcov.html">TrigonometricPathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.1%"><img src="../snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathTools.cpp.gcov.html">PathTools.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">123 / 125</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Path.cpp.gcov.html">Path.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PropertyMap.cpp.gcov.html">PropertyMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ZpathVessel.cpp.gcov.html">ZpathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SpathVessel.cpp.gcov.html">SpathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathBase.cpp.gcov.html">PathBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathReparameterization.cpp.gcov.html">PathReparameterization.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">65 / 65</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/mapping/index.html b/coverage/mapping/index.html
new file mode 100644
index 0000000000..8ba2b02e61
--- /dev/null
+++ b/coverage/mapping/index.html
@@ -0,0 +1,203 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - mapping</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - mapping</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">758</td>
+            <td class="headerCovTableEntry">809</td>
+            <td class="headerCovTableEntryHi">93.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">100</td>
+            <td class="headerCovTableEntryMed">89.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AdaptivePath.cpp.gcov.html">AdaptivePath.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">100 / 104</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mapping.cpp.gcov.html">Mapping.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=78 height=10 alt="78.1%"><img src="../snow.png" width=22 height=10 alt="78.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.1&nbsp;%</td>
+      <td class="coverNumMed">82 / 105</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mapping.h.gcov.html">Mapping.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PCAVars.cpp.gcov.html">PCAVars.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">127 / 144</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Path.cpp.gcov.html">Path.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathBase.cpp.gcov.html">PathBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">35 / 35</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathReparameterization.cpp.gcov.html">PathReparameterization.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">65 / 65</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PathTools.cpp.gcov.html">PathTools.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">123 / 125</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PropertyMap.cpp.gcov.html">PropertyMap.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SpathVessel.cpp.gcov.html">SpathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">29 / 29</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TrigonometricPathVessel.cpp.gcov.html">TrigonometricPathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.1%"><img src="../snow.png" width=3 height=10 alt="97.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">134 / 138</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">10 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ZpathVessel.cpp.gcov.html">ZpathVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Loss.cpp.func-sort-c.html b/coverage/maze/Loss.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6e0f0602d4
--- /dev/null
+++ b/coverage/maze/Loss.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Loss.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Loss.cpp<span style="font-size: 80%;"> (<a href="Loss.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Loss.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#72">_ZN4PLMD4maze4LossC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#60">_ZN4PLMD4maze12_GLOBAL__N_116LossRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#72">_ZN4PLMD4maze4LossC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#62">_ZN4PLMD4maze4Loss16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#60">_ZN4PLMD4maze12_GLOBAL__N_116LossRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#60">_ZN4PLMD4maze12_GLOBAL__N_116LossRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#98">_ZN4PLMD4maze4Loss7pairingEd</a></td>
+              <td class="coverFnHi">15290970</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/maze/Loss.cpp.func.html b/coverage/maze/Loss.cpp.func.html
new file mode 100644
index 0000000000..fbd08ebd9d
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+++ b/coverage/maze/Loss.cpp.func.html
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+  <title>LCOV - plumed test coverage - maze/Loss.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Loss.cpp<span style="font-size: 80%;"> (<a href="Loss.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Loss.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#60">_ZN4PLMD4maze12_GLOBAL__N_116LossRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#60">_ZN4PLMD4maze12_GLOBAL__N_116LossRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#60">_ZN4PLMD4maze12_GLOBAL__N_116LossRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#62">_ZN4PLMD4maze4Loss16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#98">_ZN4PLMD4maze4Loss7pairingEd</a></td>
+              <td class="coverFnHi">15290970</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#72">_ZN4PLMD4maze4LossC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.cpp.gcov.html#72">_ZN4PLMD4maze4LossC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
+</html>
diff --git a/coverage/maze/Loss.cpp.gcov.html b/coverage/maze/Loss.cpp.gcov.html
new file mode 100644
index 0000000000..692f2715db
--- /dev/null
+++ b/coverage/maze/Loss.cpp.gcov.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Loss.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Loss.cpp<span style="font-size: 80%;"> (source / <a href="Loss.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Loss.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="26"><span class="lineNum">      26 </span>            :  */</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Loss.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace maze {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC MAZE_LOSS MAZE_LOSS</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : Define a coarse-grained loss function describing interactions in a</a>
+<a name="37"><span class="lineNum">      37 </span>            : ligand-protein complex, which is minimized during the simulation to</a>
+<a name="38"><span class="lineNum">      38 </span>            : obtain ligand unbinding pathways.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The loss function is the following:</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : \mathcal{L}=</a>
+<a name="43"><span class="lineNum">      43 </span>            : \sum_{i=1}^{N_p}</a>
+<a name="44"><span class="lineNum">      44 </span>            : r_i^{-\alpha}\text{e}^{-\beta r_i^{-\gamma}},</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : where \f$N_p\f$ is the number of ligand-protein atom pairs, \f$r\f$</a>
+<a name="47"><span class="lineNum">      47 </span>            : is a re-scaled distance between the \f$i\f$th pair, and \f$\alpha,</a>
+<a name="48"><span class="lineNum">      48 </span>            : \beta, \gamma\f$ are the positive parameters defined in that order by</a>
+<a name="49"><span class="lineNum">      49 </span>            : the PARAMS keyword.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \par Examples</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : The loss function can be defined in the following way:</a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : l: MAZE_LOSS PARAMS=1,1,1</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // Registers the LOSS action.</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(Loss, &quot;MAZE_LOSS&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         10 : void Loss::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         10 :   Colvar::registerKeywords(keys);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         20 :   keys.add(</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :     &quot;compulsory&quot;,</a>
+<a name="69"><span class="lineNum">      69 </span>            :     &quot;PARAMS&quot;,</a>
+<a name="70"><span class="lineNum">      70 </span>            :     &quot;Parameters for the loss function.&quot;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   );</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         10 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          8 : Loss::Loss(const ActionOptions&amp; ao)</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          8 :   : PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : {</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         16 :   if (keywords.exists(&quot;PARAMS&quot;)) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         16 :     parseVector(&quot;PARAMS&quot;, params_);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 :     plumed_massert(</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :       params_.size() == 3,</a>
+<a name="82"><span class="lineNum">      82 </span>            :       &quot;maze&gt; PARAMS should be of size 3: alpha, beta, gamma\n&quot;</a>
+<a name="83"><span class="lineNum">      83 </span>            :     );</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          8 :     plumed_massert(</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :       params_[0] &gt; 0 &amp;&amp; params_[1] &gt; 0 &amp;&amp; params_[2] &gt; 0,</a>
+<a name="87"><span class="lineNum">      87 </span>            :       &quot;maze&gt; Each parameter should be positive\n&quot;</a>
+<a name="88"><span class="lineNum">      88 </span>            :     );</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          8 :     log.printf(&quot;maze&gt; \t Loss parsed with parameters: &quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         32 :     for (size_t i = 0; i &lt; params_.size(); ++i) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         24 :       log.printf(&quot;%f &quot;, params_[i]);</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :     }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          8 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          8 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">   15290970 : double Loss::pairing(double distance) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">   15290970 :   double alpha = params_[0];</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">   15290970 :   double beta = params_[1];</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">   15290970 :   double gamma = params_[2];</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">   15290970 :   if (atoms.getUnits().getLengthString() == &quot;nm&quot;) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">   15171840 :     distance *= 10.0;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">   15290970 :   return pow(distance, -alpha) * exp(-beta * pow(distance, gamma));</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : } // namespace maze</a>
+<a name="113"><span class="lineNum">     113 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Loss.h.func-sort-c.html b/coverage/maze/Loss.h.func-sort-c.html
new file mode 100644
index 0000000000..f41cd992bf
--- /dev/null
+++ b/coverage/maze/Loss.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Loss.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Loss.h<span style="font-size: 80%;"> (<a href="Loss.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Loss.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.h.gcov.html#74">_ZN4PLMD4maze4Loss9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.h.gcov.html#57">_ZN4PLMD4maze4LossD0Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.h.gcov.html#57">_ZN4PLMD4maze4LossD1Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Loss.h.func.html b/coverage/maze/Loss.h.func.html
new file mode 100644
index 0000000000..f9f5e16d7a
--- /dev/null
+++ b/coverage/maze/Loss.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Loss.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Loss.h<span style="font-size: 80%;"> (<a href="Loss.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Loss.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.h.gcov.html#74">_ZN4PLMD4maze4Loss9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.h.gcov.html#57">_ZN4PLMD4maze4LossD0Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Loss.h.gcov.html#57">_ZN4PLMD4maze4LossD1Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Loss.h.gcov.html b/coverage/maze/Loss.h.gcov.html
new file mode 100644
index 0000000000..520cec3591
--- /dev/null
+++ b/coverage/maze/Loss.h.gcov.html
@@ -0,0 +1,162 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Loss.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Loss.h<span style="font-size: 80%;"> (source / <a href="Loss.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_maze_Loss_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_maze_Loss_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /**</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @file Loss.h</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;Core.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace maze {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : /**</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * @class Loss Loss.h &quot;maze/Loss.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * @brief Loss function describes a score between a ligand-protein conformation.</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * Loss function must be defined for an optimizer as it minimizes a loss</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * of a ligand-protein conformation in order to simulate the ligand-protein</a>
+<a name="45"><span class="lineNum">      45 </span>            :  * dissociation process.</a>
+<a name="46"><span class="lineNum">      46 </span>            :  */</a>
+<a name="47"><span class="lineNum">      47 </span>            : class Loss: public colvar::Colvar {</a>
+<a name="48"><span class="lineNum">      48 </span>            : public:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   /**</a>
+<a name="50"><span class="lineNum">      50 </span>            :    * PLMD constructor.</a>
+<a name="51"><span class="lineNum">      51 </span>            :    *</a>
+<a name="52"><span class="lineNum">      52 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;.</a>
+<a name="53"><span class="lineNum">      53 </span>            :    */</a>
+<a name="54"><span class="lineNum">      54 </span>            :   explicit Loss(const ActionOptions&amp; ao);</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   /**</a>
+<a name="57"><span class="lineNum">      57 </span>            :    * Destructor.</a>
+<a name="58"><span class="lineNum">      58 </span>            :    */</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         16 :   ~Loss() { /* Nothing to do. */ }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   /**</a>
+<a name="62"><span class="lineNum">      62 </span>            :    * Register PLMD keywords.</a>
+<a name="63"><span class="lineNum">      63 </span>            :    *</a>
+<a name="64"><span class="lineNum">      64 </span>            :    * @param[in] keys Keywords.</a>
+<a name="65"><span class="lineNum">      65 </span>            :    */</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   /**</a>
+<a name="69"><span class="lineNum">      69 </span>            :    * Calculate a loss of a single pair of ligand-protein atoms.</a>
+<a name="70"><span class="lineNum">      70 </span>            :    *</a>
+<a name="71"><span class="lineNum">      71 </span>            :    * @param[in] distance Distance between atoms in the pair.</a>
+<a name="72"><span class="lineNum">      72 </span>            :    */</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double pairing(double distance);</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            :   // Required by the Colvar class.</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   void calculate() override { /* Nothing to do. */ }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : protected:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   //! Parameters of the loss function.</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;double&gt; params_;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : } // namespace maze</a>
+<a name="84"><span class="lineNum">      84 </span>            : } // namespace PLMD</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : #endif // __PLUMED_maze_Loss_h</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Member.h.func-sort-c.html b/coverage/maze/Member.h.func-sort-c.html
new file mode 100644
index 0000000000..91b4b137d8
--- /dev/null
+++ b/coverage/maze/Member.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Member.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Member.h<span style="font-size: 80%;"> (<a href="Member.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Member.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Member.h.gcov.html#46">_ZN4PLMD4maze6MemberC2Ev</a></td>
+              <td class="coverFnHi">334</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Member.h.gcov.html#57">_ZN4PLMD4maze7compareERNS0_6MemberES2_</a></td>
+              <td class="coverFnHi">406</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Member.h.func.html b/coverage/maze/Member.h.func.html
new file mode 100644
index 0000000000..3c4977b4e1
--- /dev/null
+++ b/coverage/maze/Member.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Member.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Member.h<span style="font-size: 80%;"> (<a href="Member.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Member.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Member.h.gcov.html#46">_ZN4PLMD4maze6MemberC2Ev</a></td>
+              <td class="coverFnHi">334</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Member.h.gcov.html#57">_ZN4PLMD4maze7compareERNS0_6MemberES2_</a></td>
+              <td class="coverFnHi">406</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Member.h.gcov.html b/coverage/maze/Member.h.gcov.html
new file mode 100644
index 0000000000..a5adde6f67
--- /dev/null
+++ b/coverage/maze/Member.h.gcov.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Member.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Member.h<span style="font-size: 80%;"> (source / <a href="Member.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_maze_Member_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_maze_Member_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /**</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @file Member.h</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;Core.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace maze {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /**</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * @class Member Member.h &quot;maze/Member.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            :  *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * @brief Defines the encoding for a ligand conformation.</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * The Member class is required by some optimizers. Ligand conformations are</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * encoded by a Cartesian translation relative to a ligand conformation from</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * the MD simulation. Each translation has a loss (score) which tells how</a>
+<a name="44"><span class="lineNum">      44 </span>            :  * preferred is the encoding w.r.t. a chosen loss function.</a>
+<a name="45"><span class="lineNum">      45 </span>            :  */</a>
+<a name="46"><span class="lineNum">      46 </span>            : struct Member {</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        334 :   Member()</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        334 :     : score(-1),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        334 :       translation({0, 0, 0}) { /* Nothing to do. */ }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   //! Value of the loss function.</a>
+<a name="53"><span class="lineNum">      53 </span>            :   double score;</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            :   //! Encoding of a ligand conformation, i.e., its translation.</a>
+<a name="56"><span class="lineNum">      56 </span>            :   Vector translation;</a>
+<a name="57"><span class="lineNum">      57 </span>            : };</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        406 : inline bool compare(Member&amp; m, Member&amp; n) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        406 :   return m.score &gt; n.score;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : } // namespace maze</a>
+<a name="64"><span class="lineNum">      64 </span>            : } // namespace PLMD</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : #endif // __PLUMED_maze_Member_h</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Memetic.cpp.func-sort-c.html b/coverage/maze/Memetic.cpp.func-sort-c.html
new file mode 100644
index 0000000000..76306bcbfd
--- /dev/null
+++ b/coverage/maze/Memetic.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Memetic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Memetic.cpp<span style="font-size: 80%;"> (<a href="Memetic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Memetic.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#141">_ZN4PLMD4maze7MemeticC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#81">_ZN4PLMD4maze12_GLOBAL__N_119MemeticRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#141">_ZN4PLMD4maze7MemeticC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#83">_ZN4PLMD4maze7Memetic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#272">_ZN4PLMD4maze7Memetic8optimizeEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#81">_ZN4PLMD4maze12_GLOBAL__N_119MemeticRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#81">_ZN4PLMD4maze12_GLOBAL__N_119MemeticRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Memetic.cpp.func.html b/coverage/maze/Memetic.cpp.func.html
new file mode 100644
index 0000000000..2265b5bd65
--- /dev/null
+++ b/coverage/maze/Memetic.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Memetic.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Memetic.cpp<span style="font-size: 80%;"> (<a href="Memetic.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Memetic.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">2</td>
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+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#81">_ZN4PLMD4maze12_GLOBAL__N_119MemeticRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#83">_ZN4PLMD4maze7Memetic16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#272">_ZN4PLMD4maze7Memetic8optimizeEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#141">_ZN4PLMD4maze7MemeticC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.cpp.gcov.html#141">_ZN4PLMD4maze7MemeticC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Memetic.cpp.gcov.html b/coverage/maze/Memetic.cpp.gcov.html
new file mode 100644
index 0000000000..4d6daac636
--- /dev/null
+++ b/coverage/maze/Memetic.cpp.gcov.html
@@ -0,0 +1,358 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Memetic.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Memetic.cpp<span style="font-size: 80%;"> (source / <a href="Memetic.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Memetic.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="26"><span class="lineNum">      26 </span>            :  */</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Memetic.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace maze {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC MAZE_OPTIMIZER MAZE_MEMETIC_SAMPLING</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculates the biasing direction along which the ligand unbinds by</a>
+<a name="37"><span class="lineNum">      37 </span>            : minimizing the \ref MAZE_LOSS function. The optimal biasing direction is</a>
+<a name="38"><span class="lineNum">      38 </span>            : determined by performing a population-based memetics search with local</a>
+<a name="39"><span class="lineNum">      39 </span>            : heuristics.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : Every optimizer implemented in the maze module needs a loss function as</a>
+<a name="44"><span class="lineNum">      44 </span>            : an argument, and it should be passed using the \ref MAZE_LOSS keyword.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : MAZE_MEMETIC_SAMPLING ...</a>
+<a name="48"><span class="lineNum">      48 </span>            :   LABEL=ma</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            :   LOSS=l</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   N_ITER=10</a>
+<a name="53"><span class="lineNum">      53 </span>            :   OPTIMIZER_STRIDE=200</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            :   CAPACITY=20</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            :   LOCAL_SEARCH_ON</a>
+<a name="58"><span class="lineNum">      58 </span>            :   N_LOCAL_ITER=10</a>
+<a name="59"><span class="lineNum">      59 </span>            :   LOCAL_SEARCH_RATE=0.1</a>
+<a name="60"><span class="lineNum">      60 </span>            :   LOCAL_SEARCH_TYPE=stochastic_hill_climbing</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            :   MUTATION_RATE=0.1</a>
+<a name="63"><span class="lineNum">      63 </span>            :   MATING_RATE=0.7</a>
+<a name="64"><span class="lineNum">      64 </span>            :   CAUCHY_ALPHA=0</a>
+<a name="65"><span class="lineNum">      65 </span>            :   CAUCHY_BETA=0.1</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            :   LIGAND=2635-2646</a>
+<a name="68"><span class="lineNum">      68 </span>            :   PROTEIN=1-2634</a>
+<a name="69"><span class="lineNum">      69 </span>            : ... MAZE_MEMETIC_SAMPLING</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : As shown above, each optimizer should be provided with the LIGAND and</a>
+<a name="73"><span class="lineNum">      73 </span>            : the PROTEIN keywords.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : The neighbor list can be turned on by providing the NLIST keyword.</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : /**</a>
+<a name="81"><span class="lineNum">      81 </span>            :  * Register MAZE_MEMETIC_SAMPLING.</a>
+<a name="82"><span class="lineNum">      82 </span>            :  */</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Memetic, &quot;MAZE_MEMETIC_SAMPLING&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 : void Memetic::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          4 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     &quot;compulsory&quot;,</a>
+<a name="90"><span class="lineNum">      90 </span>            :     &quot;CAPACITY&quot;,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     &quot;Sampling set size.&quot;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   );</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     &quot;compulsory&quot;,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     &quot;MUTATION_RATE&quot;,</a>
+<a name="97"><span class="lineNum">      97 </span>            :     &quot;Probability of mutation.&quot;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   );</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     &quot;compulsory&quot;,</a>
+<a name="102"><span class="lineNum">     102 </span>            :     &quot;MATING_RATE&quot;,</a>
+<a name="103"><span class="lineNum">     103 </span>            :     &quot;Probability of mating.&quot;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   );</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     &quot;compulsory&quot;,</a>
+<a name="108"><span class="lineNum">     108 </span>            :     &quot;CAUCHY_ALPHA&quot;,</a>
+<a name="109"><span class="lineNum">     109 </span>            :     &quot;Mean of Cauchy distribution for sampling.&quot;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   );</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     &quot;compulsory&quot;,</a>
+<a name="114"><span class="lineNum">     114 </span>            :     &quot;CAUCHY_BETA&quot;,</a>
+<a name="115"><span class="lineNum">     115 </span>            :     &quot;Spread of Cauchy distribution for sampling.&quot;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   );</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          8 :   keys.addFlag(</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     &quot;LOCAL_SEARCH_ON&quot;,</a>
+<a name="120"><span class="lineNum">     120 </span>            :     false,</a>
+<a name="121"><span class="lineNum">     121 </span>            :     &quot;Turn local search on.&quot;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   );</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     &quot;optional&quot;,</a>
+<a name="126"><span class="lineNum">     126 </span>            :     &quot;N_LOCAL_ITER&quot;,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     &quot;Number of local search iterations.&quot;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   );</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     &quot;optional&quot;,</a>
+<a name="132"><span class="lineNum">     132 </span>            :     &quot;LOCAL_SEARCH_RATE&quot;,</a>
+<a name="133"><span class="lineNum">     133 </span>            :     &quot;Rate of mutation in local search.&quot;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   );</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :   keys.add(</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     &quot;optional&quot;,</a>
+<a name="138"><span class="lineNum">     138 </span>            :     &quot;LOCAL_SEARCH_TYPE&quot;,</a>
+<a name="139"><span class="lineNum">     139 </span>            :     &quot;Type of local search.&quot;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   );</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 : Memetic::Memetic(const ActionOptions&amp; ao)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   : PLUMED_OPT_INIT(ao),</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :     bound_(true),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 :     score_worst_(0),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :     score_best_(0),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :     adaptation_(true),</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :     coding_len_(3),</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :     local_search_on_(false)</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : {</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          2 :   log.printf(&quot;maze&gt; Memetic sampling.\n&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :   if (keywords.exists(&quot;CAPACITY&quot;)) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :     parse(&quot;CAPACITY&quot;, capacity_);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :     plumed_massert(</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :       capacity_ &gt; 0,</a>
+<a name="159"><span class="lineNum">     159 </span>            :       &quot;maze&gt; CAPACITY should be explicitly specified and positive.\n&quot;</a>
+<a name="160"><span class="lineNum">     160 </span>            :     );</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          2 :     log.printf(</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :       &quot;maze&gt; CAPACITY read: %u.\n&quot;,</a>
+<a name="164"><span class="lineNum">     164 </span>            :       capacity_</a>
+<a name="165"><span class="lineNum">     165 </span>            :     );</a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          4 :   if (keywords.exists(&quot;MUTATION_RATE&quot;)) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :     parse(&quot;MUTATION_RATE&quot;, mutation_rate_);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :     plumed_massert(</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :       mutation_rate_ &gt; 0 &amp;&amp; mutation_rate_ &lt;= 1,</a>
+<a name="173"><span class="lineNum">     173 </span>            :       &quot;maze&gt; MUTATION_RATE should be in [0, 1).\n&quot;</a>
+<a name="174"><span class="lineNum">     174 </span>            :     );</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :     log.printf(</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :       &quot;maze&gt; MUTATION_RATE read: %f.\n&quot;,</a>
+<a name="178"><span class="lineNum">     178 </span>            :       mutation_rate_</a>
+<a name="179"><span class="lineNum">     179 </span>            :     );</a>
+<a name="180"><span class="lineNum">     180 </span>            :   }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :   if (keywords.exists(&quot;MATING_RATE&quot;)) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :     parse(&quot;MATING_RATE&quot;, mating_rate_);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          2 :     plumed_massert(</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :       mating_rate_ &gt; 0 &amp;&amp; mating_rate_ &lt;= 1,</a>
+<a name="187"><span class="lineNum">     187 </span>            :       &quot;maze&gt; MATING_RATE should be in [0, 1).\n&quot;</a>
+<a name="188"><span class="lineNum">     188 </span>            :     );</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          2 :     log.printf(</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       &quot;maze&gt; MATING_RATE read: %f.\n&quot;,</a>
+<a name="192"><span class="lineNum">     192 </span>            :       mating_rate_</a>
+<a name="193"><span class="lineNum">     193 </span>            :     );</a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          4 :   if (keywords.exists(&quot;CAUCHY_ALPHA&quot;)) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          2 :     parse(&quot;CAUCHY_ALPHA&quot;, cauchy_mean_alpha_);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :     log.printf(</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :       &quot;maze&gt; CAUCHY_ALPHA read: %f.\n&quot;,</a>
+<a name="201"><span class="lineNum">     201 </span>            :       cauchy_mean_alpha_</a>
+<a name="202"><span class="lineNum">     202 </span>            :     );</a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          4 :   if (keywords.exists(&quot;CAUCHY_BETA&quot;)) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          2 :     parse(&quot;CAUCHY_BETA&quot;, cauchy_mean_beta_);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :     plumed_massert(</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :       cauchy_mean_beta_ &gt; 0,</a>
+<a name="210"><span class="lineNum">     210 </span>            :       &quot;maze&gt; CAUCHY_BETA should be explicitly specified and positive.\n&quot;</a>
+<a name="211"><span class="lineNum">     211 </span>            :     );</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          2 :     log.printf(</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :       &quot;maze&gt; CAUCHY_BETA read: %f.\n&quot;,</a>
+<a name="215"><span class="lineNum">     215 </span>            :       cauchy_mean_beta_</a>
+<a name="216"><span class="lineNum">     216 </span>            :     );</a>
+<a name="217"><span class="lineNum">     217 </span>            :   }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          4 :   if (keywords.exists(&quot;LOCAL_SEARCH_ON&quot;)) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          2 :     parseFlag(&quot;LOCAL_SEARCH_ON&quot;, local_search_on_);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 :     log.printf(&quot;maze&gt; LOCAL_SEARCH_ON enabled: %d.\n&quot;, local_search_on_);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          2 :   if (local_search_on_) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          1 :     parse(&quot;N_LOCAL_ITER&quot;, n_local_iterations_);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :       n_local_iterations_ &gt; 0,</a>
+<a name="230"><span class="lineNum">     230 </span>            :       &quot;maze&gt; N_LOCAL_ITER should be explicitly specified and positive.\n&quot;</a>
+<a name="231"><span class="lineNum">     231 </span>            :     );</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :       &quot;maze&gt; N_LOCAL_ITER read: %u.\n&quot;,</a>
+<a name="235"><span class="lineNum">     235 </span>            :       n_local_iterations_</a>
+<a name="236"><span class="lineNum">     236 </span>            :     );</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          1 :     parse(&quot;LOCAL_SEARCH_RATE&quot;, local_search_rate_);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :       local_search_rate_ &gt; 0 &amp;&amp; local_search_rate_ &lt;= 1,</a>
+<a name="242"><span class="lineNum">     242 </span>            :       &quot;maze&gt; LOCAL_SEARCH_RATE should be in [0, 1).\n&quot;</a>
+<a name="243"><span class="lineNum">     243 </span>            :     );</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :       &quot;maze&gt; LOCAL_SEARCH_RATE read: %f.\n&quot;,</a>
+<a name="247"><span class="lineNum">     247 </span>            :       local_search_rate_</a>
+<a name="248"><span class="lineNum">     248 </span>            :     );</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :     parse(&quot;LOCAL_SEARCH_TYPE&quot;, local_search_type_);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :       local_search_type_ == &quot;stochastic_hill_climbing&quot; ||</a>
+<a name="254"><span class="lineNum">     254 </span>            :       local_search_type_ == &quot;adaptive_random_search&quot;,</a>
+<a name="255"><span class="lineNum">     255 </span>            :       &quot;maze&gt; LOCAL_SEARCH_TYPE should be: &quot;</a>
+<a name="256"><span class="lineNum">     256 </span>            :       &quot;stochastic_hill_climbing, or adaptive_random_search.\n&quot;</a>
+<a name="257"><span class="lineNum">     257 </span>            :     );</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :       &quot;maze&gt; LOCAL_SEARCH_TYPE read: %s.\n&quot;,</a>
+<a name="261"><span class="lineNum">     261 </span>            :       local_search_type_.c_str()</a>
+<a name="262"><span class="lineNum">     262 </span>            :     );</a>
+<a name="263"><span class="lineNum">     263 </span>            :   }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          2 :   set_n_global_iterations(n_iter_);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          4 :   set_label(&quot;MEMETIC_SAMPLING&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :   start_step_0();</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 : }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          6 : void Memetic::optimize() {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          6 :   Vector t = solve();</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :   set_opt(t);</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          6 :   set_opt_value(score());</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          6 : }</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : } // namespace maze</a>
+<a name="282"><span class="lineNum">     282 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Memetic.h.func-sort-c.html b/coverage/maze/Memetic.h.func-sort-c.html
new file mode 100644
index 0000000000..81c84f825d
--- /dev/null
+++ b/coverage/maze/Memetic.h.func-sort-c.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Memetic.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Memetic.h<span style="font-size: 80%;"> (<a href="Memetic.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntryLo">55.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">65.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Memetic.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#357">_ZN4PLMD4maze7Memetic10score_meanEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#505">_ZN4PLMD4maze7Memetic12luus_jaakolaERNS0_6MemberERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#512">_ZN4PLMD4maze7Memetic22adaptive_random_searchERNS0_6MemberERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#455">_ZN4PLMD4maze7Memetic28random_restart_hill_climbingERNS0_6MemberERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#478">_ZN4PLMD4maze7Memetic9annealingERNS0_6MemberERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#404">_ZN4PLMD4maze7Memetic9crossoverERNS0_6MemberES3_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#685">_ZNK4PLMD4maze7Memetic12print_statusEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#318">_ZN4PLMD4maze7Memetic18initialize_membersEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#689">_ZN4PLMD4maze7Memetic5solveEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#439">_ZN4PLMD4maze7Memetic24stochastic_hill_climbingERNS0_6MemberERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#584">_ZN4PLMD4maze7Memetic12local_searchERSt6vectorINS0_6MemberESaIS3_EE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#339">_ZN4PLMD4maze7Memetic12sort_membersEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#332">_ZN4PLMD4maze7Memetic13score_membersEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#367">_ZN4PLMD4maze7Memetic18selection_rouletteEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#605">_ZN4PLMD4maze7Memetic6matingERSt6vectorINS0_6MemberESaIS3_EE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#430">_ZN4PLMD4maze7Memetic8mutationERSt6vectorINS0_6MemberESaIS3_EE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#641">_ZN4PLMD4maze7Memetic13create_codingEv</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#648">_ZN4PLMD4maze7Memetic13out_of_boundsEd</a></td>
+              <td class="coverFnHi">81</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#421">_ZN4PLMD4maze7Memetic8mutationERNS0_6MemberE</a></td>
+              <td class="coverFnHi">81</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#654">_ZN4PLMD4maze7Memetic12score_memberERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">260</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Memetic.h.func.html b/coverage/maze/Memetic.h.func.html
new file mode 100644
index 0000000000..fc439c8127
--- /dev/null
+++ b/coverage/maze/Memetic.h.func.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Memetic.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Memetic.h<span style="font-size: 80%;"> (<a href="Memetic.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntryLo">55.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">65.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Memetic.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#357">_ZN4PLMD4maze7Memetic10score_meanEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#584">_ZN4PLMD4maze7Memetic12local_searchERSt6vectorINS0_6MemberESaIS3_EE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#505">_ZN4PLMD4maze7Memetic12luus_jaakolaERNS0_6MemberERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Memetic.h.gcov.html#654">_ZN4PLMD4maze7Memetic12score_memberERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">260</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="Memetic.h.gcov.html#685">_ZNK4PLMD4maze7Memetic12print_statusEv</a></td>
+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Memetic.h.gcov.html b/coverage/maze/Memetic.h.gcov.html
new file mode 100644
index 0000000000..4f8919ca86
--- /dev/null
+++ b/coverage/maze/Memetic.h.gcov.html
@@ -0,0 +1,882 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Memetic.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Memetic.h<span style="font-size: 80%;"> (source / <a href="Memetic.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntryLo">55.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryLo">65.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_maze_Memetic_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_maze_Memetic_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /**</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @file Memetic.h</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;Core.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;Member.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace maze {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : /**</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * @class Memetic Memetic.h &quot;maze/Memetic.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            :  *</a>
+<a name="43"><span class="lineNum">      43 </span>            :  * @brief Memetic algorithms for the optimization of the loss function.</a>
+<a name="44"><span class="lineNum">      44 </span>            :  */</a>
+<a name="45"><span class="lineNum">      45 </span>            : class Memetic: public Optimizer {</a>
+<a name="46"><span class="lineNum">      46 </span>            : public:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   /**</a>
+<a name="48"><span class="lineNum">      48 </span>            :    * PLMD constructor.</a>
+<a name="49"><span class="lineNum">      49 </span>            :    *</a>
+<a name="50"><span class="lineNum">      50 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;.</a>
+<a name="51"><span class="lineNum">      51 </span>            :    */</a>
+<a name="52"><span class="lineNum">      52 </span>            :   explicit Memetic(const ActionOptions&amp; ao);</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            :   /**</a>
+<a name="55"><span class="lineNum">      55 </span>            :    * Registers PLMD keywords.</a>
+<a name="56"><span class="lineNum">      56 </span>            :    *</a>
+<a name="57"><span class="lineNum">      57 </span>            :    * @param[in] keys Keywords.</a>
+<a name="58"><span class="lineNum">      58 </span>            :    */</a>
+<a name="59"><span class="lineNum">      59 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   /**</a>
+<a name="62"><span class="lineNum">      62 </span>            :    * Each class deriving from Optimizer needs to override this function.</a>
+<a name="63"><span class="lineNum">      63 </span>            :    */</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void optimize() override;</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : private:</a>
+<a name="67"><span class="lineNum">      67 </span>            :   /**</a>
+<a name="68"><span class="lineNum">      68 </span>            :    * Create a set of translations relative to the ligand, each translation</a>
+<a name="69"><span class="lineNum">      69 </span>            :    * encodes a probable biasing direction.</a>
+<a name="70"><span class="lineNum">      70 </span>            :    */</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void initialize_members();</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   /**</a>
+<a name="74"><span class="lineNum">      74 </span>            :    * Score each translation by the loss function.</a>
+<a name="75"><span class="lineNum">      75 </span>            :    */</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void score_members();</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   /**</a>
+<a name="79"><span class="lineNum">      79 </span>            :    * Calculate the mean score.</a>
+<a name="80"><span class="lineNum">      80 </span>            :    */</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double score_mean();</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   /**</a>
+<a name="84"><span class="lineNum">      84 </span>            :    * Sort the population using heaps, required for finding a minimum of the loss</a>
+<a name="85"><span class="lineNum">      85 </span>            :    * function.</a>
+<a name="86"><span class="lineNum">      86 </span>            :    */</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void sort_members();</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   /**</a>
+<a name="90"><span class="lineNum">      90 </span>            :    * Encode a ligand conformation.</a>
+<a name="91"><span class="lineNum">      91 </span>            :    */</a>
+<a name="92"><span class="lineNum">      92 </span>            :   Vector create_coding();</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   /**</a>
+<a name="95"><span class="lineNum">      95 </span>            :    * Check if the vector length is out of bounds.</a>
+<a name="96"><span class="lineNum">      96 </span>            :    *</a>
+<a name="97"><span class="lineNum">      97 </span>            :    * @param[in] v Vector length.</a>
+<a name="98"><span class="lineNum">      98 </span>            :    */</a>
+<a name="99"><span class="lineNum">      99 </span>            :   bool out_of_bounds(double v);</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   /**</a>
+<a name="102"><span class="lineNum">     102 </span>            :    * Score a single member.</a>
+<a name="103"><span class="lineNum">     103 </span>            :    *</a>
+<a name="104"><span class="lineNum">     104 </span>            :    * @param[in] v Member's translation.</a>
+<a name="105"><span class="lineNum">     105 </span>            :    */</a>
+<a name="106"><span class="lineNum">     106 </span>            :   double score_member(const Vector&amp; v);</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   /**</a>
+<a name="109"><span class="lineNum">     109 </span>            :    * Print a status.</a>
+<a name="110"><span class="lineNum">     110 </span>            :    */</a>
+<a name="111"><span class="lineNum">     111 </span>            :   void print_status() const;</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   /**</a>
+<a name="114"><span class="lineNum">     114 </span>            :    * Select a new population using the roulette selection.</a>
+<a name="115"><span class="lineNum">     115 </span>            :    */</a>
+<a name="116"><span class="lineNum">     116 </span>            :   void selection_roulette();</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   /**</a>
+<a name="119"><span class="lineNum">     119 </span>            :    * Perform mating in the population.</a>
+<a name="120"><span class="lineNum">     120 </span>            :    *</a>
+<a name="121"><span class="lineNum">     121 </span>            :    * @param[in,out] members Population.</a>
+<a name="122"><span class="lineNum">     122 </span>            :    */</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void mating(std::vector&lt;Member&gt;&amp; members);</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   /**</a>
+<a name="126"><span class="lineNum">     126 </span>            :    * Mate two members.</a>
+<a name="127"><span class="lineNum">     127 </span>            :    *</a>
+<a name="128"><span class="lineNum">     128 </span>            :    * @param[in,out] m1 1st member.</a>
+<a name="129"><span class="lineNum">     129 </span>            :    * @param[in,out] m2 2nd member.</a>
+<a name="130"><span class="lineNum">     130 </span>            :    */</a>
+<a name="131"><span class="lineNum">     131 </span>            :   void crossover(Member&amp; m1, Member&amp; m2);</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   /**</a>
+<a name="134"><span class="lineNum">     134 </span>            :    * Mutate a member.</a>
+<a name="135"><span class="lineNum">     135 </span>            :    *</a>
+<a name="136"><span class="lineNum">     136 </span>            :    * @param[in,out] m Member.</a>
+<a name="137"><span class="lineNum">     137 </span>            :    */</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void mutation(Member&amp; m);</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   /**</a>
+<a name="141"><span class="lineNum">     141 </span>            :    * Mutate the population.</a>
+<a name="142"><span class="lineNum">     142 </span>            :    *</a>
+<a name="143"><span class="lineNum">     143 </span>            :    * @param[in,out] members Population.</a>
+<a name="144"><span class="lineNum">     144 </span>            :    */</a>
+<a name="145"><span class="lineNum">     145 </span>            :   void mutation(std::vector&lt;Member&gt;&amp; members);</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : protected:</a>
+<a name="148"><span class="lineNum">     148 </span>            :   /**</a>
+<a name="149"><span class="lineNum">     149 </span>            :    * Local searches to improve global solutions.</a>
+<a name="150"><span class="lineNum">     150 </span>            :    */</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   /**</a>
+<a name="153"><span class="lineNum">     153 </span>            :    * Stochastic hill climbing.</a>
+<a name="154"><span class="lineNum">     154 </span>            :    *</a>
+<a name="155"><span class="lineNum">     155 </span>            :    * Neighbors with better or equal cost should be accepted, allowing the</a>
+<a name="156"><span class="lineNum">     156 </span>            :    * technique to navigate across plateaus in the response surface.</a>
+<a name="157"><span class="lineNum">     157 </span>            :    *</a>
+<a name="158"><span class="lineNum">     158 </span>            :    * @param[in,out] m Member.</a>
+<a name="159"><span class="lineNum">     159 </span>            :    * @param[in] params None.</a>
+<a name="160"><span class="lineNum">     160 </span>            :    */</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void stochastic_hill_climbing(</a>
+<a name="162"><span class="lineNum">     162 </span>            :     Member&amp; m,</a>
+<a name="163"><span class="lineNum">     163 </span>            :     /* none */ const std::vector&lt;double&gt;&amp; params = {}</a>
+<a name="164"><span class="lineNum">     164 </span>            :   );</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   /**</a>
+<a name="167"><span class="lineNum">     167 </span>            :    * Random-restart hill climbing.</a>
+<a name="168"><span class="lineNum">     168 </span>            :    *</a>
+<a name="169"><span class="lineNum">     169 </span>            :    * The algorithm can be restarted and repeated a number of  times after it</a>
+<a name="170"><span class="lineNum">     170 </span>            :    * converges to provide an improved result.</a>
+<a name="171"><span class="lineNum">     171 </span>            :    *</a>
+<a name="172"><span class="lineNum">     172 </span>            :    * @param[in,out] m Member.</a>
+<a name="173"><span class="lineNum">     173 </span>            :    * @param[in] params Number of restarts.</a>
+<a name="174"><span class="lineNum">     174 </span>            :    */</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void random_restart_hill_climbing(</a>
+<a name="176"><span class="lineNum">     176 </span>            :     Member&amp; m,</a>
+<a name="177"><span class="lineNum">     177 </span>            :     /* n_restarts */ const std::vector&lt;double&gt;&amp; params = {10}</a>
+<a name="178"><span class="lineNum">     178 </span>            :   );</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   /**</a>
+<a name="181"><span class="lineNum">     181 </span>            :    * Solis-Wets random walk.</a>
+<a name="182"><span class="lineNum">     182 </span>            :    *</a>
+<a name="183"><span class="lineNum">     183 </span>            :    * Adaptive random search algorithm was designed to address the limitations of</a>
+<a name="184"><span class="lineNum">     184 </span>            :    * the fixed step size. The strategy for adaptive random search is to</a>
+<a name="185"><span class="lineNum">     185 </span>            :    * continually approximate the optimal step size required to reach the global</a>
+<a name="186"><span class="lineNum">     186 </span>            :    * optimum in the search space. This is achieved by trialling and adopting</a>
+<a name="187"><span class="lineNum">     187 </span>            :    * smaller or larger step sizes only if they result in an improvement in the</a>
+<a name="188"><span class="lineNum">     188 </span>            :    * search performance.</a>
+<a name="189"><span class="lineNum">     189 </span>            :    *</a>
+<a name="190"><span class="lineNum">     190 </span>            :    * Very large step sizes are trialled with a much lower frequency. This</a>
+<a name="191"><span class="lineNum">     191 </span>            :    * strategy of preferring large moves is intended to allow the technique to</a>
+<a name="192"><span class="lineNum">     192 </span>            :    * escape local optima. Smaller step sizes are adopted if no improvement is</a>
+<a name="193"><span class="lineNum">     193 </span>            :    * made for an extended period.</a>
+<a name="194"><span class="lineNum">     194 </span>            :    *</a>
+<a name="195"><span class="lineNum">     195 </span>            :    * @param[in,out] m Member.</a>
+<a name="196"><span class="lineNum">     196 </span>            :    * @param[in] params</a>
+<a name="197"><span class="lineNum">     197 </span>            :    */</a>
+<a name="198"><span class="lineNum">     198 </span>            :   void adaptive_random_search(</a>
+<a name="199"><span class="lineNum">     199 </span>            :     Member&amp; m,</a>
+<a name="200"><span class="lineNum">     200 </span>            :     /* */ const std::vector&lt;double&gt;&amp; params = {1.0, 1.e-5, 2.0, 2.0, 3.0, 3.0}</a>
+<a name="201"><span class="lineNum">     201 </span>            :   );</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   /**</a>
+<a name="204"><span class="lineNum">     204 </span>            :    * Luus–Jaakola heuristics.</a>
+<a name="205"><span class="lineNum">     205 </span>            :    *</a>
+<a name="206"><span class="lineNum">     206 </span>            :    * @param[in,out] m Member.</a>
+<a name="207"><span class="lineNum">     207 </span>            :    * @param[in] params Bounds.</a>
+<a name="208"><span class="lineNum">     208 </span>            :    */</a>
+<a name="209"><span class="lineNum">     209 </span>            :   void luus_jaakola(</a>
+<a name="210"><span class="lineNum">     210 </span>            :     Member&amp; m,</a>
+<a name="211"><span class="lineNum">     211 </span>            :     /* bounds */ const std::vector&lt;double&gt;&amp; params</a>
+<a name="212"><span class="lineNum">     212 </span>            :   );</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            :   /**</a>
+<a name="215"><span class="lineNum">     215 </span>            :    * Local annealing.</a>
+<a name="216"><span class="lineNum">     216 </span>            :    *</a>
+<a name="217"><span class="lineNum">     217 </span>            :    * @param[in,out] m Member.</a>
+<a name="218"><span class="lineNum">     218 </span>            :    * @param[in] params T, alpha.</a>
+<a name="219"><span class="lineNum">     219 </span>            :    */</a>
+<a name="220"><span class="lineNum">     220 </span>            :   void annealing(</a>
+<a name="221"><span class="lineNum">     221 </span>            :     Member&amp; m,</a>
+<a name="222"><span class="lineNum">     222 </span>            :     /* T, alpha */const std::vector&lt;double&gt;&amp; params = {300.0, 0.95}</a>
+<a name="223"><span class="lineNum">     223 </span>            :   );</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   /**</a>
+<a name="226"><span class="lineNum">     226 </span>            :    * Apply local search to members.</a>
+<a name="227"><span class="lineNum">     227 </span>            :    *</a>
+<a name="228"><span class="lineNum">     228 </span>            :    * @param[in,out] members Population.</a>
+<a name="229"><span class="lineNum">     229 </span>            :    */</a>
+<a name="230"><span class="lineNum">     230 </span>            :   void local_search(std::vector&lt;Member&gt;&amp; members);</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : protected:</a>
+<a name="233"><span class="lineNum">     233 </span>            :   /**</a>
+<a name="234"><span class="lineNum">     234 </span>            :    * Return an optimal biasing direction.</a>
+<a name="235"><span class="lineNum">     235 </span>            :    */</a>
+<a name="236"><span class="lineNum">     236 </span>            :   Vector solve();</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : public:</a>
+<a name="239"><span class="lineNum">     239 </span>            :   /**</a>
+<a name="240"><span class="lineNum">     240 </span>            :    * Setters and getters.</a>
+<a name="241"><span class="lineNum">     241 </span>            :    */</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   unsigned int get_capacity() const;</a>
+<a name="244"><span class="lineNum">     244 </span>            :   void set_capacity(unsigned int);</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :   unsigned int get_coding_len() const;</a>
+<a name="247"><span class="lineNum">     247 </span>            :   void set_coding_len(unsigned int);</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   unsigned int get_n_local_iterations() const;</a>
+<a name="250"><span class="lineNum">     250 </span>            :   void set_n_local_iterations(unsigned int);</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :   unsigned int get_n_global_iterations() const;</a>
+<a name="253"><span class="lineNum">     253 </span>            :   void set_n_global_iterations(unsigned int);</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   double get_mutation_rate() const;</a>
+<a name="256"><span class="lineNum">     256 </span>            :   void set_mutation_rate(double);</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   double get_mating_rate() const;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   void set_mating_rate(double);</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   double get_cauchy_mean() const;</a>
+<a name="262"><span class="lineNum">     262 </span>            :   void set_cauchy_mean(double);</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   double get_cauchy_spread() const;</a>
+<a name="265"><span class="lineNum">     265 </span>            :   void set_cauchy_spread(double);</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            :   bool is_local_search_on() const;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   void local_search_on();</a>
+<a name="269"><span class="lineNum">     269 </span>            :   void local_search_off();</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   double get_local_search_rate() const;</a>
+<a name="272"><span class="lineNum">     272 </span>            :   void set_local_search_rate(double);</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   std::string get_local_search_type() const;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   void set_local_search_type(const std::string&amp;);</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            : protected:</a>
+<a name="278"><span class="lineNum">     278 </span>            :   //! Population</a>
+<a name="279"><span class="lineNum">     279 </span>            :   std::vector&lt;Member&gt; members_;</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            :   //! Bound</a>
+<a name="282"><span class="lineNum">     282 </span>            :   double bound_;</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   //! Scores</a>
+<a name="285"><span class="lineNum">     285 </span>            :   double score_worst_;</a>
+<a name="286"><span class="lineNum">     286 </span>            :   double score_best_;</a>
+<a name="287"><span class="lineNum">     287 </span>            :   Member member_best_;</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   //! If a local search is performed</a>
+<a name="290"><span class="lineNum">     290 </span>            :   bool adaptation_;</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            : protected:</a>
+<a name="293"><span class="lineNum">     293 </span>            :   //! Size of population</a>
+<a name="294"><span class="lineNum">     294 </span>            :   unsigned int capacity_;</a>
+<a name="295"><span class="lineNum">     295 </span>            :   //! Length of coding</a>
+<a name="296"><span class="lineNum">     296 </span>            :   unsigned int coding_len_;</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :   //! Number of local search iterations</a>
+<a name="299"><span class="lineNum">     299 </span>            :   unsigned int n_local_iterations_;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   //! Number of global search iterations, doomsday</a>
+<a name="301"><span class="lineNum">     301 </span>            :   unsigned int n_global_iterations_;</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            :   //! Probability of mutation</a>
+<a name="304"><span class="lineNum">     304 </span>            :   double mutation_rate_;</a>
+<a name="305"><span class="lineNum">     305 </span>            :   //! Probability of mating</a>
+<a name="306"><span class="lineNum">     306 </span>            :   double mating_rate_;</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            :   //! Mean and spread of cauchy sampler</a>
+<a name="309"><span class="lineNum">     309 </span>            :   double cauchy_mean_alpha_;</a>
+<a name="310"><span class="lineNum">     310 </span>            :   double cauchy_mean_beta_;</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            :   //! If local search is employed in sampling</a>
+<a name="313"><span class="lineNum">     313 </span>            :   bool local_search_on_;</a>
+<a name="314"><span class="lineNum">     314 </span>            :   //! Rate of local mutation</a>
+<a name="315"><span class="lineNum">     315 </span>            :   double local_search_rate_;</a>
+<a name="316"><span class="lineNum">     316 </span>            :   //! Type of local search, stochastic_hill_climbing or adaptive_random_search</a>
+<a name="317"><span class="lineNum">     317 </span>            :   std::string local_search_type_;</a>
+<a name="318"><span class="lineNum">     318 </span>            : };</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          6 : void Memetic::initialize_members() {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          6 :   members_.clear();</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          6 :   members_.resize(capacity_);</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         42 :   for (size_t i = 0; i &lt; capacity_; ++i) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         36 :     Member m{};</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         36 :     m.score=0;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         36 :     m.translation=create_coding();</span></a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         36 :     members_.at(i) = m;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   }</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          6 : }</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         30 : void Memetic::score_members() {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        210 :   for (size_t i = 0; i &lt; members_.size(); ++i) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        180 :     double s = score_member(members_[i].translation);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        180 :     members_[i].score=s;</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   }</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         30 : }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         30 : void Memetic::sort_members() {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         30 :   std::make_heap(</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :     members_.begin(),</a>
+<a name="344"><span class="lineNum">     344 </span>            :     members_.end(),</a>
+<a name="345"><span class="lineNum">     345 </span>            :     compare</a>
+<a name="346"><span class="lineNum">     346 </span>            :   );</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         30 :   std::sort_heap(</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :     members_.begin(),</a>
+<a name="350"><span class="lineNum">     350 </span>            :     members_.end(),</a>
+<a name="351"><span class="lineNum">     351 </span>            :     compare</a>
+<a name="352"><span class="lineNum">     352 </span>            :   );</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         30 :   member_best_ = members_[capacity_ - 1];</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         30 :   score_best_ = members_[capacity_ - 1].score;</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         30 :   score_worst_ = members_[0].score;</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         30 : }</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 : double Memetic::score_mean() {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :   auto acc = [](double s, const Member&amp; m) { return s + m.score; };</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            :   return std::accumulate(</a>
+<a name="363"><span class="lineNum">     363 </span>            :            members_.begin(),</a>
+<a name="364"><span class="lineNum">     364 </span>            :            members_.end(),</a>
+<a name="365"><span class="lineNum">     365 </span>            :            0.0,</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :            acc) / capacity_;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         30 : void Memetic::selection_roulette() {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         30 :   std::vector&lt;Member&gt; sel(members_);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         30 :   std::vector&lt;double&gt; rel_scores(capacity_, 0.0);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        210 :   for (std::size_t i = 0; i &lt; capacity_; ++i) {</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        180 :     double r = 1.0 / (members_[i].score + 0.01);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        180 :     rel_scores.at(i) = r;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         30 :   std::vector&lt;double&gt; cum_sum(capacity_, 0.0);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         30 :   std::partial_sum(</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :     rel_scores.begin(),</a>
+<a name="381"><span class="lineNum">     381 </span>            :     rel_scores.end(),</a>
+<a name="382"><span class="lineNum">     382 </span>            :     cum_sum.begin(),</a>
+<a name="383"><span class="lineNum">     383 </span>            :     std::plus&lt;double&gt;()</a>
+<a name="384"><span class="lineNum">     384 </span>            :   );</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         30 :   double sum = cum_sum.back();</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :   members_.clear();</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         30 :   members_.resize(capacity_);</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   int chosen = -1;</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        210 :   for (size_t j = 0; j &lt; capacity_; ++j) {</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :     double probability=rnd::next_double(sum);</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        641 :     for (size_t i = 0; i &lt; cum_sum.size(); ++i) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        641 :       if (cum_sum[i] &gt; probability) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">        180 :         chosen = i;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        360 :         members_.at(j).score = sel.at(chosen).score;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        180 :         members_.at(j).translation = sel.at(chosen).translation;</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        180 :         break;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :       }</a>
+<a name="402"><span class="lineNum">     402 </span>            :     }</a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         30 : }</span></a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineNoCov">          0 : void Memetic::crossover(Member&amp; s1, Member&amp; s2) {</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :   size_t i = rnd::next_int(1, coding_len_ - 1);</span></a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :   Member z1(s1);</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :   Member z2(s2);</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :   for (size_t j = i; j &lt; coding_len_; ++j) {</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :     z1.translation[j] = s2.translation[j];</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :     z2.translation[j] = s1.translation[j];</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :   if (!out_of_bounds(z1.translation.modulo()) &amp;&amp; !out_of_bounds(z2.translation.modulo())) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :     s1 = z1;</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :     s2 = z2;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         81 : void Memetic::mutation(Member&amp; m) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         81 :   int which = rnd::next_int(coding_len_);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         81 :   double v = rnd::next_cauchy(cauchy_mean_alpha_, cauchy_mean_beta_);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         81 :   m.translation[which] += v;</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         81 :   if (out_of_bounds(m.translation.modulo())) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         32 :     m.translation[which] -= v;</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :   }</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         81 : }</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         30 : void Memetic::mutation(std::vector&lt;Member&gt;&amp; m) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        210 :   for (std::vector&lt;Member&gt;::iterator it = m.begin(), end = m.end(); it != end; ++it) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        180 :     double r = rnd::next_double();</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">        180 :     if (r &lt; mutation_rate_) {</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          1 :       mutation(*it);</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :     }</a>
+<a name="438"><span class="lineNum">     438 </span>            :   }</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         30 : }</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          8 : void Memetic::stochastic_hill_climbing(</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :   Member&amp; m,</a>
+<a name="443"><span class="lineNum">     443 </span>            :   const std::vector&lt;double&gt;&amp; params)</a>
+<a name="444"><span class="lineNum">     444 </span>            : {</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         88 :   for (std::size_t i = 0; i &lt; n_local_iterations_; ++i) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         80 :     Member n;</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         80 :     n.translation = m.translation;</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         80 :     mutation(n);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         80 :     double score_n = score_member(n.translation);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         80 :     if (m.score &gt; score_n) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         35 :       m.translation = n.translation;</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     }</a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          8 : }</span></a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 : void Memetic::random_restart_hill_climbing(</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :   Member&amp; m,</a>
+<a name="459"><span class="lineNum">     459 </span>            :   const std::vector&lt;double&gt;&amp; params)</a>
+<a name="460"><span class="lineNum">     460 </span>            : {</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :   unsigned int n_restarts = static_cast&lt;int&gt;(params[0]);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :   std::vector&lt;Member&gt; s(n_restarts);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   unsigned int ndx = 0;</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :   double min = m.score;</span></a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :   for (std::size_t r = 0; r &lt; n_restarts; ++r) {</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :     Member n = m;</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :     stochastic_hill_climbing(n);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :     s[r] = n;</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :     if (min &gt; n.score) {</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :       min = n.score;</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :       ndx = r;</span></a>
+<a name="474"><span class="lineNum">     474 </span>            :     }</a>
+<a name="475"><span class="lineNum">     475 </span>            :   }</a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   m = s[ndx];</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 : void Memetic::annealing(</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :   Member&amp; m,</a>
+<a name="482"><span class="lineNum">     482 </span>            :   const std::vector&lt;double&gt;&amp; params)</a>
+<a name="483"><span class="lineNum">     483 </span>            : {</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineNoCov">          0 :   double T = params[0];</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :   double alpha = params[1];</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :   for (std::size_t i = 0; i &lt; n_local_iterations_; ++i) {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :     Member n = m;</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :     mutation(n);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineNoCov">          0 :     double score_n = score_member(n.translation);</span></a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span>            :     double probability = std::min(</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :                            1.0,</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :                            std::exp(-(score_n - m.score) / T)</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineNoCov">          0 :                          );</span></a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :     double r = rnd::next_double();</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :     if (r &lt; probability) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :       m = n;</span></a>
+<a name="501"><span class="lineNum">     501 </span>            :     }</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :     T *= alpha;</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :   }</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 : void Memetic::luus_jaakola(</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   Member&amp; m,</a>
+<a name="509"><span class="lineNum">     509 </span>            :   const std::vector&lt;double&gt;&amp; params)</a>
+<a name="510"><span class="lineNum">     510 </span>            : {</a>
+<a name="511"><span class="lineNum">     511 </span>            :   /* TODO */</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 : void Memetic::adaptive_random_search(</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :   Member&amp; m,</a>
+<a name="516"><span class="lineNum">     516 </span>            :   const std::vector&lt;double&gt;&amp; params)</a>
+<a name="517"><span class="lineNum">     517 </span>            : {</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :   double rho_start = params[0];</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :   double rho_lower_bound = params[1];</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   double ex = params[2];</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :   double ct = params[3];</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 :   int s_ex = static_cast&lt;int&gt;(params[4]);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :   int f_ct = static_cast&lt;int&gt;(params[5]);</span></a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            :   unsigned int k = 0;</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   Vector xk = m.translation;</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :   int ns = 0;</a>
+<a name="528"><span class="lineNum">     528 </span>            :   int nf = 0;</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :   Vector bk;</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :   bk.zero();</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :   double rho_k = rho_start;</a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :   while (rho_k &gt; rho_lower_bound &amp;&amp; k &lt; n_local_iterations_) {</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :     if (ns &gt;= s_ex) {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :       rho_k *= ex;</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :     }</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :     else if (nf &gt;= f_ct) {</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :       rho_k *= ct;</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :     }</a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :     std::vector&lt;double&gt; chiv = rnd::next_double(-rho_k, rho_k, 3);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :     Vector chi = tls::vector2Vector(chiv);</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     Vector tmp;</span></a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :     for (unsigned int i = 0; i &lt; 3; ++i) {</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :       tmp[i] = 2.0 * (xk[i] - chi[i]);</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :     }</a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 :     double score_chi = score_member(chi);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 :     double score_xk = score_member(xk);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :     double score_tmp = score_member(tmp);</span></a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :     if (score_chi &lt; score_xk) {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :       ns++;</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :       nf = 0;</a>
+<a name="556"><span class="lineNum">     556 </span>            : </a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :       for (unsigned int i = 0; i &lt; 3; i++) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineNoCov">          0 :         bk[i] = 0.2 * bk[i] + 0.4 * (chi[i] - xk[i]);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :         xk[i] = chi[i];</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :       }</a>
+<a name="561"><span class="lineNum">     561 </span>            :     }</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :     else if (score_tmp &lt; score_xk &amp;&amp; score_xk &lt;= score_chi) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineNoCov">          0 :       ns++;</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :       nf = 0;</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineNoCov">          0 :       for (unsigned int i = 0; i &lt; 3; i++) {</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineNoCov">          0 :         bk[i] = bk[i] - 0.4 * (chi[i] - xk[i]);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineNoCov">          0 :         xk[i] = 2.0 * xk[i] - chi[i];</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :       }</a>
+<a name="570"><span class="lineNum">     570 </span>            :     }</a>
+<a name="571"><span class="lineNum">     571 </span>            :     else {</a>
+<a name="572"><span class="lineNum">     572 </span>            :       ns = 0;</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :       nf++;</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :       for (unsigned int i = 0; i &lt; 3; i++) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :         bk[i] = 0.5 * bk[i];</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :       }</a>
+<a name="578"><span class="lineNum">     578 </span>            :     }</a>
+<a name="579"><span class="lineNum">     579 </span>            : </a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :     k++;</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :   }</a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :   m.translation = xk;</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         30 : void Memetic::local_search(std::vector&lt;Member&gt;&amp; m) {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         30 :   adaptation_ = true;</span></a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         30 :   if (local_search_on_) {</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">        105 :     for (std::size_t i = 0; i &lt; capacity_; ++i) {</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         90 :       double probability = rnd::next_double();</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         90 :       if (probability &lt; local_search_rate_) {</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          8 :         if (local_search_type_ == &quot;stochastic_hill_climbing&quot;)</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         16 :           stochastic_hill_climbing(m[i]);</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :         else if (local_search_type_ == &quot;adaptive_random_search&quot;)</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :           adaptive_random_search(m[i]);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :         else if (local_search_type_ == &quot;random_restart_hill_climbing&quot;)</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 :           random_restart_hill_climbing(m[i]);</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :       }</a>
+<a name="601"><span class="lineNum">     601 </span>            :     }</a>
+<a name="602"><span class="lineNum">     602 </span>            :   }</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         30 :   adaptation_ = false;</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">         30 : }</span></a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">         30 : void Memetic::mating(std::vector&lt;Member&gt;&amp; m) {</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :   std::vector&lt;Member&gt; offspring;</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">        120 :   while (m.size() != 0) {</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         90 :     int j = rnd::next_int(m.size());</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         90 :     int i = rnd::next_int(m.size());</span></a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">        120 :     while (i == j) {</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         30 :       j=rnd::next_int(m.size());</span></a>
+<a name="616"><span class="lineNum">     616 </span>            :     }</a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         90 :     Member m1 = m[i];</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         90 :     Member m2 = m[j];</span></a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">         90 :     if (i &gt; j) {</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :       m.erase(m.begin() + i);</a>
+<a name="623"><span class="lineNum">     623 </span>            :       m.erase(m.begin() + j);</a>
+<a name="624"><span class="lineNum">     624 </span>            :     }</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         46 :     else if (j &gt; i) {</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :       m.erase(m.begin() + j);</a>
+<a name="627"><span class="lineNum">     627 </span>            :       m.erase(m.begin() + i);</a>
+<a name="628"><span class="lineNum">     628 </span>            :     }</a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         90 :     double probability = rnd::next_double();</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         90 :     if (probability &lt; mating_rate_) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :       crossover(m1, m2);</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :     }</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">         90 :     offspring.push_back(m1);</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         90 :     offspring.push_back(m2);</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :   }</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">         30 :   m = offspring;</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :   offspring.clear();</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">         30 : }</span></a>
+<a name="642"><span class="lineNum">     642 </span>            : </a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">         36 : Vector Memetic::create_coding() {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">         36 :   double s = sampling_radius();</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :   double r = rnd::next_double(s);</a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         36 :   return rnd::next_plmd_vector(r);</span></a>
+<a name="648"><span class="lineNum">     648 </span>            : }</a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         81 : bool Memetic::out_of_bounds(double v) {</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         81 :   double s = sampling_radius();</span></a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">         81 :   return v &gt; s;</span></a>
+<a name="654"><span class="lineNum">     654 </span>            : }</a>
+<a name="655"><span class="lineNum">     655 </span>            : </a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">        260 : double Memetic::score_member(const Vector&amp; coding) {</span></a>
+<a name="657"><span class="lineNum">     657 </span>            :   double action = 0;</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">        260 :   Vector distance;</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">        260 :   const unsigned nl_size = neighbor_list_-&gt;size();</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">        260 :   Vector dev = coding;</span></a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">        260 :   #pragma omp parallel num_threads(get_n_threads_openmp())</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :   {</a>
+<a name="664"><span class="lineNum">     664 </span>            :     #pragma omp for reduction(+:action)</a>
+<a name="665"><span class="lineNum">     665 </span>            :     for (unsigned int i = 0; i &lt; nl_size; i++) {</a>
+<a name="666"><span class="lineNum">     666 </span>            :       unsigned i0 = neighbor_list_-&gt;getClosePair(i).first;</a>
+<a name="667"><span class="lineNum">     667 </span>            :       unsigned i1 = neighbor_list_-&gt;getClosePair(i).second;</a>
+<a name="668"><span class="lineNum">     668 </span>            : </a>
+<a name="669"><span class="lineNum">     669 </span>            :       if (getAbsoluteIndex(i0) == getAbsoluteIndex(i1)) {</a>
+<a name="670"><span class="lineNum">     670 </span>            :         continue;</a>
+<a name="671"><span class="lineNum">     671 </span>            :       }</a>
+<a name="672"><span class="lineNum">     672 </span>            : </a>
+<a name="673"><span class="lineNum">     673 </span>            :       if (pbc_) {</a>
+<a name="674"><span class="lineNum">     674 </span>            :         distance = pbcDistance(getPosition(i0) + dev, getPosition(i1));</a>
+<a name="675"><span class="lineNum">     675 </span>            :       }</a>
+<a name="676"><span class="lineNum">     676 </span>            :       else {</a>
+<a name="677"><span class="lineNum">     677 </span>            :         distance = delta(getPosition(i0) + dev, getPosition(i1));</a>
+<a name="678"><span class="lineNum">     678 </span>            :       }</a>
+<a name="679"><span class="lineNum">     679 </span>            : </a>
+<a name="680"><span class="lineNum">     680 </span>            :       action += pairing(distance.modulo());</a>
+<a name="681"><span class="lineNum">     681 </span>            :     }</a>
+<a name="682"><span class="lineNum">     682 </span>            :   }</a>
+<a name="683"><span class="lineNum">     683 </span>            : </a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">        260 :   return action;</span></a>
+<a name="685"><span class="lineNum">     685 </span>            : }</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 : void Memetic::print_status() const {</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :   log.printf(&quot;Lowest score: %f \n&quot;, score_best_);</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">          6 : Vector Memetic::solve() {</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">          6 :   initialize_members();</span></a>
+<a name="693"><span class="lineNum">     693 </span>            : </a>
+<a name="694"><span class="lineNum">     694 </span>            :   size_t epoch = 0;</a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">         36 :   while (epoch &lt; n_global_iterations_) {</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">         30 :     score_members();</span></a>
+<a name="697"><span class="lineNum">     697 </span>            : </a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">         30 :     selection_roulette();</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         30 :     mating(members_);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         30 :     mutation(members_);</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">         30 :     local_search(members_);</span></a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         30 :     sort_members();</span></a>
+<a name="704"><span class="lineNum">     704 </span>            : </a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         30 :     epoch++;</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :   }</a>
+<a name="707"><span class="lineNum">     707 </span>            : </a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">          6 :   return member_best_.translation / member_best_.translation.modulo();</span></a>
+<a name="709"><span class="lineNum">     709 </span>            : }</a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            : inline unsigned int Memetic::get_capacity() const {</a>
+<a name="712"><span class="lineNum">     712 </span>            :   return capacity_;</a>
+<a name="713"><span class="lineNum">     713 </span>            : }</a>
+<a name="714"><span class="lineNum">     714 </span>            : </a>
+<a name="715"><span class="lineNum">     715 </span>            : inline void Memetic::set_capacity(unsigned int capacity) {</a>
+<a name="716"><span class="lineNum">     716 </span>            :   capacity_ = capacity;</a>
+<a name="717"><span class="lineNum">     717 </span>            : }</a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            : inline unsigned int Memetic::get_coding_len() const {</a>
+<a name="720"><span class="lineNum">     720 </span>            :   return coding_len_;</a>
+<a name="721"><span class="lineNum">     721 </span>            : }</a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            : inline void Memetic::set_coding_len(unsigned int coding_len) {</a>
+<a name="724"><span class="lineNum">     724 </span>            :   coding_len_ = coding_len;</a>
+<a name="725"><span class="lineNum">     725 </span>            : }</a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span>            : inline unsigned int Memetic::get_n_global_iterations() const {</a>
+<a name="728"><span class="lineNum">     728 </span>            :   return n_global_iterations_;</a>
+<a name="729"><span class="lineNum">     729 </span>            : }</a>
+<a name="730"><span class="lineNum">     730 </span>            : </a>
+<a name="731"><span class="lineNum">     731 </span>            : inline void Memetic::set_n_global_iterations(unsigned int n_global_iterations) {</a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">          2 :   n_global_iterations_ = n_global_iterations;</span></a>
+<a name="733"><span class="lineNum">     733 </span>            : }</a>
+<a name="734"><span class="lineNum">     734 </span>            : </a>
+<a name="735"><span class="lineNum">     735 </span>            : inline unsigned int Memetic::get_n_local_iterations() const {</a>
+<a name="736"><span class="lineNum">     736 </span>            :   return n_local_iterations_;</a>
+<a name="737"><span class="lineNum">     737 </span>            : }</a>
+<a name="738"><span class="lineNum">     738 </span>            : </a>
+<a name="739"><span class="lineNum">     739 </span>            : inline void Memetic::set_n_local_iterations(unsigned int n_local_iterations) {</a>
+<a name="740"><span class="lineNum">     740 </span>            :   n_local_iterations_ = n_local_iterations;</a>
+<a name="741"><span class="lineNum">     741 </span>            : }</a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span>            : inline double Memetic::get_mating_rate() const {</a>
+<a name="744"><span class="lineNum">     744 </span>            :   return mating_rate_;</a>
+<a name="745"><span class="lineNum">     745 </span>            : }</a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span>            : inline void Memetic::set_mating_rate(double mating_rate) {</a>
+<a name="748"><span class="lineNum">     748 </span>            :   mating_rate_ = mating_rate;</a>
+<a name="749"><span class="lineNum">     749 </span>            : }</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            : inline double Memetic::get_mutation_rate() const {</a>
+<a name="752"><span class="lineNum">     752 </span>            :   return mutation_rate_;</a>
+<a name="753"><span class="lineNum">     753 </span>            : }</a>
+<a name="754"><span class="lineNum">     754 </span>            : </a>
+<a name="755"><span class="lineNum">     755 </span>            : inline void Memetic::set_mutation_rate(double mutation_rate) {</a>
+<a name="756"><span class="lineNum">     756 </span>            :   mutation_rate_ = mutation_rate;</a>
+<a name="757"><span class="lineNum">     757 </span>            : }</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            : inline double Memetic::get_cauchy_mean() const {</a>
+<a name="760"><span class="lineNum">     760 </span>            :   return cauchy_mean_alpha_;</a>
+<a name="761"><span class="lineNum">     761 </span>            : }</a>
+<a name="762"><span class="lineNum">     762 </span>            : </a>
+<a name="763"><span class="lineNum">     763 </span>            : inline void Memetic::set_cauchy_mean(double cauchy_mean_alpha) {</a>
+<a name="764"><span class="lineNum">     764 </span>            :   cauchy_mean_alpha_ = cauchy_mean_alpha;</a>
+<a name="765"><span class="lineNum">     765 </span>            : }</a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            : inline double Memetic::get_cauchy_spread() const {</a>
+<a name="768"><span class="lineNum">     768 </span>            :   return cauchy_mean_beta_;</a>
+<a name="769"><span class="lineNum">     769 </span>            : }</a>
+<a name="770"><span class="lineNum">     770 </span>            : </a>
+<a name="771"><span class="lineNum">     771 </span>            : inline void Memetic::set_cauchy_spread(double cauchy_mean_beta) {</a>
+<a name="772"><span class="lineNum">     772 </span>            :   cauchy_mean_beta_ = cauchy_mean_beta;</a>
+<a name="773"><span class="lineNum">     773 </span>            : }</a>
+<a name="774"><span class="lineNum">     774 </span>            : </a>
+<a name="775"><span class="lineNum">     775 </span>            : inline bool Memetic::is_local_search_on() const {</a>
+<a name="776"><span class="lineNum">     776 </span>            :   return local_search_on_;</a>
+<a name="777"><span class="lineNum">     777 </span>            : }</a>
+<a name="778"><span class="lineNum">     778 </span>            : </a>
+<a name="779"><span class="lineNum">     779 </span>            : inline void Memetic::local_search_on() {</a>
+<a name="780"><span class="lineNum">     780 </span>            :   local_search_on_ = true;</a>
+<a name="781"><span class="lineNum">     781 </span>            : }</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            : inline void Memetic::local_search_off() {</a>
+<a name="784"><span class="lineNum">     784 </span>            :   local_search_on_ = false;</a>
+<a name="785"><span class="lineNum">     785 </span>            : }</a>
+<a name="786"><span class="lineNum">     786 </span>            : </a>
+<a name="787"><span class="lineNum">     787 </span>            : inline double Memetic::get_local_search_rate() const {</a>
+<a name="788"><span class="lineNum">     788 </span>            :   return local_search_rate_;</a>
+<a name="789"><span class="lineNum">     789 </span>            : }</a>
+<a name="790"><span class="lineNum">     790 </span>            : </a>
+<a name="791"><span class="lineNum">     791 </span>            : inline void Memetic::set_local_search_rate(double local_search_rate) {</a>
+<a name="792"><span class="lineNum">     792 </span>            :   local_search_rate_ = local_search_rate;</a>
+<a name="793"><span class="lineNum">     793 </span>            : }</a>
+<a name="794"><span class="lineNum">     794 </span>            : </a>
+<a name="795"><span class="lineNum">     795 </span>            : inline std::string Memetic::get_local_search_type() const {</a>
+<a name="796"><span class="lineNum">     796 </span>            :   return local_search_type_;</a>
+<a name="797"><span class="lineNum">     797 </span>            : }</a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span>            : inline void Memetic::set_local_search_type(const std::string&amp; local_search_type) {</a>
+<a name="800"><span class="lineNum">     800 </span>            :   local_search_type_ = local_search_type;</a>
+<a name="801"><span class="lineNum">     801 </span>            : }</a>
+<a name="802"><span class="lineNum">     802 </span>            : </a>
+<a name="803"><span class="lineNum">     803 </span>            : } // namespace maze</a>
+<a name="804"><span class="lineNum">     804 </span>            : } // namespace PLMD</a>
+<a name="805"><span class="lineNum">     805 </span>            : </a>
+<a name="806"><span class="lineNum">     806 </span>            : #endif // __PLUMED_maze_Memetic_h</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Optimizer.cpp.func-sort-c.html b/coverage/maze/Optimizer.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9ca97e88d1
--- /dev/null
+++ b/coverage/maze/Optimizer.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer.cpp<span style="font-size: 80%;"> (<a href="Optimizer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">162</td>
+            <td class="headerCovTableEntry">180</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Optimizer.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#138">_ZN4PLMD4maze9OptimizerC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#373">_ZNK4PLMD4maze9Optimizer14center_of_massEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#138">_ZN4PLMD4maze9OptimizerC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#34">_ZN4PLMD4maze9Optimizer16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#389">_ZN4PLMD4maze9Optimizer7prepareEv</a></td>
+              <td class="coverFnHi">210</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#482">_ZN4PLMD4maze9Optimizer9calculateEv</a></td>
+              <td class="coverFnHi">210</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#445">_ZN4PLMD4maze9Optimizer9update_nlEv</a></td>
+              <td class="coverFnHi">210</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#415">_ZN4PLMD4maze9Optimizer5scoreEv</a></td>
+              <td class="coverFnHi">226</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#451">_ZN4PLMD4maze9Optimizer15sampling_radiusEv</a></td>
+              <td class="coverFnHi">330</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#369">_ZNK4PLMD4maze9Optimizer7pairingEd</a></td>
+              <td class="coverFnHi">15290970</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Optimizer.cpp.func.html b/coverage/maze/Optimizer.cpp.func.html
new file mode 100644
index 0000000000..a0cda782e0
--- /dev/null
+++ b/coverage/maze/Optimizer.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer.cpp<span style="font-size: 80%;"> (<a href="Optimizer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">162</td>
+            <td class="headerCovTableEntry">180</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Optimizer.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#451">_ZN4PLMD4maze9Optimizer15sampling_radiusEv</a></td>
+              <td class="coverFnHi">330</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#34">_ZN4PLMD4maze9Optimizer16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#415">_ZN4PLMD4maze9Optimizer5scoreEv</a></td>
+              <td class="coverFnHi">226</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#389">_ZN4PLMD4maze9Optimizer7prepareEv</a></td>
+              <td class="coverFnHi">210</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#482">_ZN4PLMD4maze9Optimizer9calculateEv</a></td>
+              <td class="coverFnHi">210</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#445">_ZN4PLMD4maze9Optimizer9update_nlEv</a></td>
+              <td class="coverFnHi">210</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#138">_ZN4PLMD4maze9OptimizerC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#138">_ZN4PLMD4maze9OptimizerC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#373">_ZNK4PLMD4maze9Optimizer14center_of_massEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#369">_ZNK4PLMD4maze9Optimizer7pairingEd</a></td>
+              <td class="coverFnHi">15290970</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/maze/Optimizer.cpp.gcov.html b/coverage/maze/Optimizer.cpp.gcov.html
new file mode 100644
index 0000000000..fb83d95aba
--- /dev/null
+++ b/coverage/maze/Optimizer.cpp.gcov.html
@@ -0,0 +1,586 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer.cpp<span style="font-size: 80%;"> (source / <a href="Optimizer.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">162</td>
+            <td class="headerCovTableEntry">180</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Optimizer.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  */</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace maze {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         17 : void Optimizer::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         17 :   Colvar::registerKeywords(keys);</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         34 :   keys.addFlag(</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :     &quot;SERIAL&quot;,</a>
+<a name="41"><span class="lineNum">      41 </span>            :     false,</a>
+<a name="42"><span class="lineNum">      42 </span>            :     &quot;Perform the simulation in serial -- used only for debugging purposes, &quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            :     &quot;should not be used otherwise.&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   );</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         34 :   keys.addFlag(</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :     &quot;PAIR&quot;,</a>
+<a name="48"><span class="lineNum">      48 </span>            :     false,</a>
+<a name="49"><span class="lineNum">      49 </span>            :     &quot;Pair only the 1st element of the 1st group with the 1st element in the &quot;</a>
+<a name="50"><span class="lineNum">      50 </span>            :     &quot;second, etc.&quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   );</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         34 :   keys.addFlag(</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :     &quot;NLIST&quot;,</a>
+<a name="55"><span class="lineNum">      55 </span>            :     false,</a>
+<a name="56"><span class="lineNum">      56 </span>            :     &quot;Use a neighbor list of ligand-protein atom pairs to speed up the &quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            :     &quot;calculating of the distances.&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   );</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :     &quot;optional&quot;,</a>
+<a name="62"><span class="lineNum">      62 </span>            :     &quot;NL_CUTOFF&quot;,</a>
+<a name="63"><span class="lineNum">      63 </span>            :     &quot;Neighbor list cut-off for the distances of ligand-protein atom pairs.&quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   );</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     &quot;optional&quot;,</a>
+<a name="68"><span class="lineNum">      68 </span>            :     &quot;NL_STRIDE&quot;,</a>
+<a name="69"><span class="lineNum">      69 </span>            :     &quot;Update stride for the ligand-protein atom pairs in the neighbor list.&quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   );</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     &quot;compulsory&quot;,</a>
+<a name="74"><span class="lineNum">      74 </span>            :     &quot;N_ITER&quot;,</a>
+<a name="75"><span class="lineNum">      75 </span>            :     &quot;Number of optimization steps. Required only for optimizers, do not pass &quot;</a>
+<a name="76"><span class="lineNum">      76 </span>            :     &quot;this keyword to the fake optimizers (results in crash) , e.g., random &quot;</a>
+<a name="77"><span class="lineNum">      77 </span>            :     &quot;walk, steered MD, or random acceleration MD.&quot;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   );</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :     &quot;optional&quot;,</a>
+<a name="82"><span class="lineNum">      82 </span>            :     &quot;LOSS&quot;,</a>
+<a name="83"><span class="lineNum">      83 </span>            :     &quot;Loss function describing ligand-protein interactions required by every &quot;</a>
+<a name="84"><span class="lineNum">      84 </span>            :     &quot;optimizer.&quot;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   );</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     &quot;atoms&quot;,</a>
+<a name="89"><span class="lineNum">      89 </span>            :     &quot;LIGAND&quot;,</a>
+<a name="90"><span class="lineNum">      90 </span>            :     &quot;Indices of ligand atoms.&quot;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   );</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :     &quot;atoms&quot;,</a>
+<a name="95"><span class="lineNum">      95 </span>            :     &quot;PROTEIN&quot;,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     &quot;Indices of protein atoms.&quot;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   );</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         34 :   keys.add(</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :     &quot;compulsory&quot;,</a>
+<a name="101"><span class="lineNum">     101 </span>            :     &quot;OPTIMIZER_STRIDE&quot;,</a>
+<a name="102"><span class="lineNum">     102 </span>            :     &quot;Optimizer stride. Sets up a callback function that launches the &quot;</a>
+<a name="103"><span class="lineNum">     103 </span>            :     &quot;optimization process every OPTIMIZER_STRIDE.&quot;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   );</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         17 :   componentsAreNotOptional(keys);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         34 :   keys.addOutputComponent(</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     &quot;x&quot;,</a>
+<a name="110"><span class="lineNum">     110 </span>            :     &quot;default&quot;,</a>
+<a name="111"><span class="lineNum">     111 </span>            :     &quot;Optimal biasing direction; x component.&quot;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   );</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         34 :   keys.addOutputComponent(</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     &quot;y&quot;,</a>
+<a name="116"><span class="lineNum">     116 </span>            :     &quot;default&quot;,</a>
+<a name="117"><span class="lineNum">     117 </span>            :     &quot;Optimal biasing direction; y component.&quot;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   );</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         34 :   keys.addOutputComponent(</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     &quot;z&quot;,</a>
+<a name="122"><span class="lineNum">     122 </span>            :     &quot;default&quot;,</a>
+<a name="123"><span class="lineNum">     123 </span>            :     &quot;Optimal biasing direction; z component.&quot;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   );</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         34 :   keys.addOutputComponent(</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     &quot;loss&quot;,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     &quot;default&quot;,</a>
+<a name="129"><span class="lineNum">     129 </span>            :     &quot;Loss function value defined by the provided pairing function.&quot;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   );</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         34 :   keys.addOutputComponent(</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     &quot;sr&quot;,</a>
+<a name="134"><span class="lineNum">     134 </span>            :     &quot;default&quot;,</a>
+<a name="135"><span class="lineNum">     135 </span>            :     &quot;Sampling radius. Reduces sampling to the local proximity of the ligand &quot;</a>
+<a name="136"><span class="lineNum">     136 </span>            :     &quot;position.&quot;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   );</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         17 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          7 : Optimizer::Optimizer(const ActionOptions&amp; ao)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   : PLUMED_COLVAR_INIT(ao),</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          7 :     first_step_(true),</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          7 :     opt_value_(0.0),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          7 :     pbc_(true),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          7 :     sampling_r_(0.0),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          7 :     serial_(false),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          7 :     validate_list_(true),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          7 :     first_time_(true)</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : {</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          7 :   parseFlag(&quot;SERIAL&quot;, serial_);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         14 :   if (keywords.exists(&quot;LOSS&quot;)) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          7 :     std::vector&lt;std::string&gt; loss_labels(0);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         14 :     parseVector(&quot;LOSS&quot;, loss_labels);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          7 :     plumed_massert(</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       loss_labels.size() &gt; 0,</a>
+<a name="158"><span class="lineNum">     158 </span>            :       &quot;maze&gt; Something went wrong with the LOSS keyword.\n&quot;</a>
+<a name="159"><span class="lineNum">     159 </span>            :     );</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          7 :     std::string error_msg = &quot;&quot;;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          7 :     vec_loss_ = tls::get_pointers_labels&lt;Loss*&gt;(</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :                   loss_labels,</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          7 :                   plumed.getActionSet(),</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :                   error_msg</a>
+<a name="166"><span class="lineNum">     166 </span>            :                 );</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          7 :     if (error_msg.size() &gt; 0) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       plumed_merror(</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :         &quot;maze&gt; Error in the LOSS keyword &quot; + getName() + &quot;: &quot; + error_msg</a>
+<a name="171"><span class="lineNum">     171 </span>            :       );</a>
+<a name="172"><span class="lineNum">     172 </span>            :     }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          7 :     loss_ = vec_loss_[0];</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          7 :     log.printf(&quot;maze&gt; Loss function linked to the optimizer.\n&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          7 :   }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         14 :   if (keywords.exists(&quot;N_ITER&quot;)) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :     parse(&quot;N_ITER&quot;, n_iter_);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          3 :     plumed_massert(</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :       n_iter_ &gt; 0,</a>
+<a name="183"><span class="lineNum">     183 </span>            :       &quot;maze&gt; N_ITER should be explicitly specified and positive.\n&quot;</a>
+<a name="184"><span class="lineNum">     184 </span>            :     );</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          3 :     log.printf(</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :       &quot;maze&gt; Optimizer will run %u iterations once launched.\n&quot;,</a>
+<a name="188"><span class="lineNum">     188 </span>            :       n_iter_</a>
+<a name="189"><span class="lineNum">     189 </span>            :     );</a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   std::vector&lt;AtomNumber&gt; ga_list, gb_list;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          7 :   parseAtomList(&quot;LIGAND&quot;, ga_list);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          7 :   parseAtomList(&quot;PROTEIN&quot;, gb_list);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          7 :   bool nopbc = !pbc_;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          7 :   parseFlag(&quot;NOPBC&quot;, nopbc);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          7 :   bool do_pair = false;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          7 :   parseFlag(&quot;PAIR&quot;, do_pair);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          7 :   nl_stride_ = 0;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          7 :   bool do_neigh = false;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          7 :   parseFlag(&quot;NLIST&quot;, do_neigh);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          7 :   if (do_neigh) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         14 :     if (keywords.exists(&quot;NL_CUTOFF&quot;)) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          7 :       parse(&quot;NL_CUTOFF&quot;, nl_cutoff_);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          7 :       plumed_massert(</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :         nl_cutoff_ &gt; 0,</a>
+<a name="212"><span class="lineNum">     212 </span>            :         &quot;maze&gt; NL_CUTOFF should be explicitly specified and positive.\n&quot;</a>
+<a name="213"><span class="lineNum">     213 </span>            :       );</a>
+<a name="214"><span class="lineNum">     214 </span>            :     }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         14 :     if (keywords.exists(&quot;NL_STRIDE&quot;)) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          7 :       parse(&quot;NL_STRIDE&quot;, nl_stride_);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          7 :       plumed_massert(</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :         nl_stride_ &gt; 0,</a>
+<a name="221"><span class="lineNum">     221 </span>            :         &quot;maze&gt; NL_STRIDE should be explicitly specified and positive.\n&quot;</a>
+<a name="222"><span class="lineNum">     222 </span>            :       );</a>
+<a name="223"><span class="lineNum">     223 </span>            :     }</a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          7 :   if (gb_list.size() &gt; 0) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          7 :     if (do_neigh) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          7 :       neighbor_list_ = Tools::make_unique&lt;NeighborList&gt;(</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :                          ga_list,</a>
+<a name="230"><span class="lineNum">     230 </span>            :                          gb_list,</a>
+<a name="231"><span class="lineNum">     231 </span>            :                          serial_,</a>
+<a name="232"><span class="lineNum">     232 </span>            :                          do_pair,</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          7 :                          pbc_,</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :                          getPbc(),</a>
+<a name="235"><span class="lineNum">     235 </span>            :                          comm,</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          7 :                          nl_cutoff_,</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          7 :                          nl_stride_</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :                        );</a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span>            :     else {</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :       neighbor_list_=Tools::make_unique&lt;NeighborList&gt;(</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :                        ga_list,</a>
+<a name="243"><span class="lineNum">     243 </span>            :                        gb_list,</a>
+<a name="244"><span class="lineNum">     244 </span>            :                        serial_,</a>
+<a name="245"><span class="lineNum">     245 </span>            :                        do_pair,</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :                        pbc_,</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :                        getPbc(),</a>
+<a name="248"><span class="lineNum">     248 </span>            :                        comm</a>
+<a name="249"><span class="lineNum">     249 </span>            :                      );</a>
+<a name="250"><span class="lineNum">     250 </span>            :     }</a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span>            :   else {</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :     if (do_neigh) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       neighbor_list_ = Tools::make_unique&lt;NeighborList&gt;(</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :                          ga_list,</a>
+<a name="256"><span class="lineNum">     256 </span>            :                          serial_,</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :                          pbc_,</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :                          getPbc(),</a>
+<a name="259"><span class="lineNum">     259 </span>            :                          comm,</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :                          nl_cutoff_,</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :                          nl_stride_</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :                        );</a>
+<a name="263"><span class="lineNum">     263 </span>            :     }</a>
+<a name="264"><span class="lineNum">     264 </span>            :     else {</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :       neighbor_list_=Tools::make_unique&lt;NeighborList&gt;(</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :                        ga_list,</a>
+<a name="267"><span class="lineNum">     267 </span>            :                        serial_,</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :                        pbc_,</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :                        getPbc(),</a>
+<a name="270"><span class="lineNum">     270 </span>            :                        comm</a>
+<a name="271"><span class="lineNum">     271 </span>            :                      );</a>
+<a name="272"><span class="lineNum">     272 </span>            :     }</a>
+<a name="273"><span class="lineNum">     273 </span>            :   }</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          7 :   requestAtoms(neighbor_list_-&gt;getFullAtomList());</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          7 :   log.printf(</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     &quot;maze&gt; Loss will be calculated between two groups of %u and %u atoms.\n&quot;,</a>
+<a name="279"><span class="lineNum">     279 </span>            :     static_cast&lt;unsigned&gt;(ga_list.size()),</a>
+<a name="280"><span class="lineNum">     280 </span>            :     static_cast&lt;unsigned&gt;(gb_list.size())</a>
+<a name="281"><span class="lineNum">     281 </span>            :   );</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          7 :   log.printf(</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :     &quot;maze&gt; First group (LIGAND): from %d to %d.\n&quot;,</a>
+<a name="285"><span class="lineNum">     285 </span>            :     ga_list[0].serial(),</a>
+<a name="286"><span class="lineNum">     286 </span>            :     ga_list[ga_list.size()-1].serial()</a>
+<a name="287"><span class="lineNum">     287 </span>            :   );</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          7 :   if (gb_list.size() &gt; 0) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          7 :     log.printf(</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :       &quot;maze&gt; Second group (PROTEIN): from %d to %d.\n&quot;,</a>
+<a name="292"><span class="lineNum">     292 </span>            :       gb_list[0].serial(),</a>
+<a name="293"><span class="lineNum">     293 </span>            :       gb_list[gb_list.size()-1].serial()</a>
+<a name="294"><span class="lineNum">     294 </span>            :     );</a>
+<a name="295"><span class="lineNum">     295 </span>            :   }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          7 :   if (pbc_) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          7 :     log.printf(&quot;maze&gt; Using periodic boundary conditions.\n&quot;);</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   }</a>
+<a name="300"><span class="lineNum">     300 </span>            :   else {</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :     log.printf(&quot;maze&gt; Without periodic boundary conditions.\n&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          7 :   if (do_pair) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :     log.printf(&quot;maze&gt; With PAIR option.\n&quot;);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          7 :   if (do_neigh) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          7 :     log.printf(</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :       &quot;maze&gt; Using neighbor lists updated every %d steps and cutoff %f.\n&quot;,</a>
+<a name="311"><span class="lineNum">     311 </span>            :       nl_stride_,</a>
+<a name="312"><span class="lineNum">     312 </span>            :       nl_cutoff_</a>
+<a name="313"><span class="lineNum">     313 </span>            :     );</a>
+<a name="314"><span class="lineNum">     314 </span>            :   }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            :   // OpenMP</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          7 :   stride_ = comm.Get_size();</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          7 :   rank_ = comm.Get_rank();</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          7 :   n_threads_ = OpenMP::getNumThreads();</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          7 :   unsigned int nn = neighbor_list_-&gt;size();</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          7 :   if (n_threads_ * stride_ * 10 &gt; nn) {</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :     n_threads_ = nn / stride_ / 10;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :   }</a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          7 :   if (n_threads_ == 0) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :     n_threads_ = 1;</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   }</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         14 :   if (keywords.exists(&quot;OPTIMIZER_STRIDE&quot;)) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          7 :     parse(&quot;OPTIMIZER_STRIDE&quot;, optimizer_stride_);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          7 :     plumed_massert(</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :       optimizer_stride_,</a>
+<a name="336"><span class="lineNum">     336 </span>            :       &quot;maze&gt; OPTIMIZER_STRIDE should be explicitly specified and positive.\n&quot;</a>
+<a name="337"><span class="lineNum">     337 </span>            :     );</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          7 :     log.printf(</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :       &quot;maze&gt; Launching optimization every %u steps.\n&quot;,</a>
+<a name="341"><span class="lineNum">     341 </span>            :       optimizer_stride_</a>
+<a name="342"><span class="lineNum">     342 </span>            :     );</a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          7 :   rnd::randomize();</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          7 :   opt_.zero();</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          7 :   addComponentWithDerivatives(&quot;x&quot;);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          7 :   componentIsNotPeriodic(&quot;x&quot;);</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          7 :   addComponentWithDerivatives(&quot;y&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          7 :   componentIsNotPeriodic(&quot;y&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          7 :   addComponentWithDerivatives(&quot;z&quot;);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          7 :   componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          7 :   addComponent(&quot;loss&quot;);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          7 :   componentIsNotPeriodic(&quot;loss&quot;);</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          7 :   addComponent(&quot;sr&quot;);</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          7 :   componentIsNotPeriodic(&quot;sr&quot;);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          7 :   value_x_ = getPntrToComponent(&quot;x&quot;);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          7 :   value_y_ = getPntrToComponent(&quot;y&quot;);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          7 :   value_z_ = getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          7 :   value_action_ = getPntrToComponent(&quot;loss&quot;);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          7 :   value_sampling_radius_ = getPntrToComponent(&quot;sr&quot;);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          7 : }</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">   15290970 : double Optimizer::pairing(double distance) const {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">   15290970 :   return loss_-&gt;pairing(distance);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          6 : Vector Optimizer::center_of_mass() const {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          6 :   const unsigned nl_size = neighbor_list_-&gt;size();</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          6 :   Vector center_of_mass;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">          6 :   center_of_mass.zero();</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :   double mass = 0;</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">     189654 :   for (unsigned int i = 0; i &lt; nl_size; ++i) {</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">     189648 :     unsigned int i0 = neighbor_list_-&gt;getClosePair(i).first;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">     189648 :     center_of_mass += getPosition(i0) * getMass(i0);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">     189648 :     mass += getMass(i0);</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :   }</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">          6 :   return center_of_mass / mass;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : }</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        210 : void Optimizer::prepare() {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        210 :   if (neighbor_list_-&gt;getStride() &gt; 0) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        210 :     if (first_time_ || (getStep() % neighbor_list_-&gt;getStride() == 0)) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          7 :       requestAtoms(neighbor_list_-&gt;getFullAtomList());</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          7 :       validate_list_ = true;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          7 :       first_time_ = false;</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :     }</a>
+<a name="399"><span class="lineNum">     399 </span>            :     else {</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        203 :       requestAtoms(neighbor_list_-&gt;getReducedAtomList());</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">        203 :       validate_list_ = false;</span></a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">        203 :       if (getExchangeStep()) {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :         plumed_merror(</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :           &quot;maze&gt; Neighbor lists should be updated on exchange steps -- choose &quot;</a>
+<a name="407"><span class="lineNum">     407 </span>            :           &quot;an NL_STRIDE which divides the exchange stride.\n&quot;);</a>
+<a name="408"><span class="lineNum">     408 </span>            :       }</a>
+<a name="409"><span class="lineNum">     409 </span>            :     }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        210 :     if (getExchangeStep()) {</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :       first_time_ = true;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :     }</a>
+<a name="414"><span class="lineNum">     414 </span>            :   }</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        210 : }</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">        226 : double Optimizer::score() {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">        226 :   const unsigned nl_size = neighbor_list_-&gt;size();</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        226 :   Vector distance;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   double function = 0;</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        226 :   #pragma omp parallel num_threads(n_threads_)</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :   {</a>
+<a name="424"><span class="lineNum">     424 </span>            :     #pragma omp for reduction(+:function)</a>
+<a name="425"><span class="lineNum">     425 </span>            :     for(unsigned int i = 0; i &lt; nl_size; i++) {</a>
+<a name="426"><span class="lineNum">     426 </span>            :       unsigned i0 = neighbor_list_-&gt;getClosePair(i).first;</a>
+<a name="427"><span class="lineNum">     427 </span>            :       unsigned i1 = neighbor_list_-&gt;getClosePair(i).second;</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            :       if (getAbsoluteIndex(i0) == getAbsoluteIndex(i1)) {</a>
+<a name="430"><span class="lineNum">     430 </span>            :         continue;</a>
+<a name="431"><span class="lineNum">     431 </span>            :       }</a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :       if (pbc_) {</a>
+<a name="434"><span class="lineNum">     434 </span>            :         distance = pbcDistance(getPosition(i0), getPosition(i1));</a>
+<a name="435"><span class="lineNum">     435 </span>            :       }</a>
+<a name="436"><span class="lineNum">     436 </span>            :       else {</a>
+<a name="437"><span class="lineNum">     437 </span>            :         distance = delta(getPosition(i0), getPosition(i1));</a>
+<a name="438"><span class="lineNum">     438 </span>            :       }</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span>            :       function += pairing(distance.modulo());</a>
+<a name="441"><span class="lineNum">     441 </span>            :     }</a>
+<a name="442"><span class="lineNum">     442 </span>            :   }</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">        226 :   return function;</span></a>
+<a name="445"><span class="lineNum">     445 </span>            : }</a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        210 : void Optimizer::update_nl() {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        210 :   if (neighbor_list_-&gt;getStride() &gt; 0 &amp;&amp; validate_list_) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          7 :     neighbor_list_-&gt;update(getPositions());</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        210 : }</span></a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">        330 : double Optimizer::sampling_radius()</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : {</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">        330 :   const unsigned nl_size=neighbor_list_-&gt;size();</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        330 :   Vector d;</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :   double min=std::numeric_limits&lt;int&gt;::max();</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">    8642790 :   for (unsigned int i = 0; i &lt; nl_size; ++i) {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">    8642460 :     unsigned i0 = neighbor_list_-&gt;getClosePair(i).first;</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">    8642460 :     unsigned i1 = neighbor_list_-&gt;getClosePair(i).second;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">    8642460 :     if (getAbsoluteIndex(i0) == getAbsoluteIndex(i1)) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :     }</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">    8642460 :     if (pbc_) {</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">    8642460 :       d = pbcDistance(getPosition(i0), getPosition(i1));</span></a>
+<a name="469"><span class="lineNum">     469 </span>            :     }</a>
+<a name="470"><span class="lineNum">     470 </span>            :     else {</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :       d = delta(getPosition(i0), getPosition(i1));</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :     }</a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">    8642460 :     double dist = d.modulo();</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">    8642460 :     if(dist &lt; min) {</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :       min = dist;</a>
+<a name="478"><span class="lineNum">     478 </span>            :     }</a>
+<a name="479"><span class="lineNum">     479 </span>            :   }</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">        330 :   return min;</span></a>
+<a name="482"><span class="lineNum">     482 </span>            : }</a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        210 : void Optimizer::calculate() {</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">        210 :   update_nl();</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        210 :   if (getStep() % optimizer_stride_ == 0 &amp;&amp; !first_step_) {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         19 :     optimize();</span></a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         19 :     value_x_-&gt;set(opt_[0]);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">         19 :     value_y_-&gt;set(opt_[1]);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         19 :     value_z_-&gt;set(opt_[2]);</span></a>
+<a name="493"><span class="lineNum">     493 </span>            : </a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         19 :     value_action_-&gt;set(score());</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">         19 :     value_sampling_radius_-&gt;set(sampling_radius());</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :   }</a>
+<a name="497"><span class="lineNum">     497 </span>            :   else {</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">        191 :     first_step_=false;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        191 :     value_x_-&gt;set(opt_[0]);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        191 :     value_y_-&gt;set(opt_[1]);</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        191 :     value_z_-&gt;set(opt_[2]);</span></a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        191 :     value_action_-&gt;set(score());</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        191 :     value_sampling_radius_-&gt;set(sampling_radius());</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :   }</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        210 : }</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : </a>
+<a name="509"><span class="lineNum">     509 </span>            : } // namespace maze</a>
+<a name="510"><span class="lineNum">     510 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Optimizer.h.func-sort-c.html b/coverage/maze/Optimizer.h.func-sort-c.html
new file mode 100644
index 0000000000..997fb74e81
--- /dev/null
+++ b/coverage/maze/Optimizer.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer.h<span style="font-size: 80%;"> (<a href="Optimizer.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Optimizer.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#66">_ZN4PLMD4maze9OptimizerD2Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Optimizer.h.func.html b/coverage/maze/Optimizer.h.func.html
new file mode 100644
index 0000000000..0dca17eb8a
--- /dev/null
+++ b/coverage/maze/Optimizer.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer.h<span style="font-size: 80%;"> (<a href="Optimizer.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+    </tr>
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+              <td class="coverFn"><a href="Optimizer.h.gcov.html#66">_ZN4PLMD4maze9OptimizerD2Ev</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
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diff --git a/coverage/maze/Optimizer.h.gcov.html b/coverage/maze/Optimizer.h.gcov.html
new file mode 100644
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer.h<span style="font-size: 80%;"> (source / <a href="Optimizer.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_maze_Optimizer_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_maze_Optimizer_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /**</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @file Optimizer.h</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;Core.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;Loss.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &lt;memory&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : #define PLUMED_OPT_INIT(ao) Action(ao), Optimizer(ao)</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace maze {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : /**</a>
+<a name="48"><span class="lineNum">      48 </span>            :  * @ingroup INHERIT</a>
+<a name="49"><span class="lineNum">      49 </span>            :  *</a>
+<a name="50"><span class="lineNum">      50 </span>            :  * @class Optimizer Optimizer.h &quot;maze/Optimizer.h&quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :  *</a>
+<a name="52"><span class="lineNum">      52 </span>            :  * @brief Base class for implementing optimizers for ligand unbinding.</a>
+<a name="53"><span class="lineNum">      53 </span>            :  *</a>
+<a name="54"><span class="lineNum">      54 </span>            :  * An optimizer is defined as a colvar that can be passed to Optimizer_Bias.</a>
+<a name="55"><span class="lineNum">      55 </span>            :  */</a>
+<a name="56"><span class="lineNum">      56 </span>            : class Optimizer: public colvar::Colvar {</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   /**</a>
+<a name="59"><span class="lineNum">      59 </span>            :    * PLMD constructor.</a>
+<a name="60"><span class="lineNum">      60 </span>            :    *</a>
+<a name="61"><span class="lineNum">      61 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;</a>
+<a name="62"><span class="lineNum">      62 </span>            :    */</a>
+<a name="63"><span class="lineNum">      63 </span>            :   explicit Optimizer(const ActionOptions&amp;);</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   /**</a>
+<a name="66"><span class="lineNum">      66 </span>            :    * Destructor.</a>
+<a name="67"><span class="lineNum">      67 </span>            :    */</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          7 :   ~Optimizer() { /* Nothing to do. */ }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   /**</a>
+<a name="71"><span class="lineNum">      71 </span>            :    * Registers PLMD keywords.</a>
+<a name="72"><span class="lineNum">      72 </span>            :    *</a>
+<a name="73"><span class="lineNum">      73 </span>            :    * @param[in] keys PLMD keywords</a>
+<a name="74"><span class="lineNum">      74 </span>            :    */</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :   /**</a>
+<a name="78"><span class="lineNum">      78 </span>            :    * The pairing function needs to be overridden by a specific optimizer.</a>
+<a name="79"><span class="lineNum">      79 </span>            :    *</a>
+<a name="80"><span class="lineNum">      80 </span>            :    * @param[in] distance distance between a pair of atoms</a>
+<a name="81"><span class="lineNum">      81 </span>            :    */</a>
+<a name="82"><span class="lineNum">      82 </span>            :   virtual double pairing(double distance) const;</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   /**</a>
+<a name="85"><span class="lineNum">      85 </span>            :    * Optimal values needed for biasing are computed by methods overridding the</a>
+<a name="86"><span class="lineNum">      86 </span>            :    * optimize function.</a>
+<a name="87"><span class="lineNum">      87 </span>            :    */</a>
+<a name="88"><span class="lineNum">      88 </span>            :   virtual void optimize() = 0;</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   /**</a>
+<a name="91"><span class="lineNum">      91 </span>            :    * Calculate the optimal direction of pulling.</a>
+<a name="92"><span class="lineNum">      92 </span>            :    */</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void calculate();</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   /**</a>
+<a name="96"><span class="lineNum">      96 </span>            :    * Prepare the neighbor list.</a>
+<a name="97"><span class="lineNum">      97 </span>            :    */</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void prepare();</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   /**</a>
+<a name="101"><span class="lineNum">     101 </span>            :    * Score a ligand-protein configuration.</a>
+<a name="102"><span class="lineNum">     102 </span>            :    *</a>
+<a name="103"><span class="lineNum">     103 </span>            :    * @return score</a>
+<a name="104"><span class="lineNum">     104 </span>            :    */</a>
+<a name="105"><span class="lineNum">     105 </span>            :   double score();</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   /**</a>
+<a name="108"><span class="lineNum">     108 </span>            :    * Calculate sampling radius as the minimal distance between two groups in</a>
+<a name="109"><span class="lineNum">     109 </span>            :    * neighbors list.</a>
+<a name="110"><span class="lineNum">     110 </span>            :    *</a>
+<a name="111"><span class="lineNum">     111 </span>            :    * @return minimal distance of ligand-protein atom pairs</a>
+<a name="112"><span class="lineNum">     112 </span>            :    */</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double sampling_radius();</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   /**</a>
+<a name="116"><span class="lineNum">     116 </span>            :    * Load new positions of atoms in the neighbor list.</a>
+<a name="117"><span class="lineNum">     117 </span>            :    */</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void update_nl();</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   /**</a>
+<a name="121"><span class="lineNum">     121 </span>            :    * Calculate the center of mass.</a>
+<a name="122"><span class="lineNum">     122 </span>            :    *</a>
+<a name="123"><span class="lineNum">     123 </span>            :    * @return center of mass</a>
+<a name="124"><span class="lineNum">     124 </span>            :    */</a>
+<a name="125"><span class="lineNum">     125 </span>            :   Vector center_of_mass() const;</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : public:</a>
+<a name="128"><span class="lineNum">     128 </span>            :   /**</a>
+<a name="129"><span class="lineNum">     129 </span>            :    * Getters and setters.</a>
+<a name="130"><span class="lineNum">     130 </span>            :    */</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::string get_label() const;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void set_label(const std::string&amp;);</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   // Start optimizer at time = 0.</a>
+<a name="136"><span class="lineNum">     136 </span>            :   void start_step_0();</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   // Start optimizer at time = optimizer stride.</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void start_step_stride();</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   Vector get_opt() const;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void set_opt(Vector);</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   double get_opt_value() const;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   void set_opt_value(double);</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   unsigned int get_optimizer_stride() const;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   void set_optimizer_stride(unsigned int);</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   bool is_pbc_on() const;</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void pbc_on();</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void pbc_off();</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   unsigned int get_n_iterations() const;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void set_n_iterations(unsigned int);</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   double get_sampling_radius() const;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void set_sampling_radius(double);</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   unsigned int get_rank_openmp() const;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void set_rank_openmp(unsigned int);</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   unsigned int get_stride_openmp() const;</a>
+<a name="164"><span class="lineNum">     164 </span>            :   void set_stride_openmp(unsigned int);</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            :   unsigned int get_n_threads_openmp() const;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   void set_n_threads_openmp(unsigned int);</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   unsigned int get_nl_stride() const;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   void set_nl_stride(unsigned int);</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   double get_nl_cutofff() const;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   void set_nl_cutoff(double);</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : protected:</a>
+<a name="176"><span class="lineNum">     176 </span>            :   //! Optimizer label.</a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::string label_;</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   //! Start either at time =  0 or time = optimizer stride.</a>
+<a name="180"><span class="lineNum">     180 </span>            :   bool first_step_;</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :   //! Biasing direction.</a>
+<a name="183"><span class="lineNum">     183 </span>            :   Vector opt_;</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   //! Current loss function value.</a>
+<a name="186"><span class="lineNum">     186 </span>            :   double opt_value_;</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   //! Optimizer stride.</a>
+<a name="189"><span class="lineNum">     189 </span>            :   unsigned int optimizer_stride_;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   //! Periodic boundary conditions.</a>
+<a name="192"><span class="lineNum">     192 </span>            :   bool pbc_;</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            :   //! Number of global iterations.</a>
+<a name="195"><span class="lineNum">     195 </span>            :   unsigned int n_iter_;</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   //! Sampling radius.</a>
+<a name="198"><span class="lineNum">     198 </span>            :   double sampling_r_;</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   /**</a>
+<a name="201"><span class="lineNum">     201 </span>            :    * OpenMP</a>
+<a name="202"><span class="lineNum">     202 </span>            :    */</a>
+<a name="203"><span class="lineNum">     203 </span>            :   unsigned int rank_;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   unsigned int stride_;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   unsigned int n_threads_;</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   //! Neighbor list of ligand-protein atom pairs.</a>
+<a name="208"><span class="lineNum">     208 </span>            :   std::unique_ptr&lt;NeighborList&gt; neighbor_list_;</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            :   //! Neighbor list cut-off.</a>
+<a name="211"><span class="lineNum">     211 </span>            :   double nl_cutoff_;</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            :   //! Neighbor list stride.</a>
+<a name="214"><span class="lineNum">     214 </span>            :   int nl_stride_;</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : private:</a>
+<a name="217"><span class="lineNum">     217 </span>            :   bool serial_;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   bool validate_list_;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   bool first_time_;</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            :   //! Pointer to the loss function.</a>
+<a name="222"><span class="lineNum">     222 </span>            :   Loss* loss_;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   std::vector&lt;Loss*&gt; vec_loss_;</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : public:</a>
+<a name="226"><span class="lineNum">     226 </span>            :   /*</a>
+<a name="227"><span class="lineNum">     227 </span>            :    * Pointers to PLMD components.</a>
+<a name="228"><span class="lineNum">     228 </span>            :    */</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            :   //! Biased cv.</a>
+<a name="231"><span class="lineNum">     231 </span>            :   Value* value_x_;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   Value* value_y_;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   Value* value_z_;</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   //! Loss value.</a>
+<a name="236"><span class="lineNum">     236 </span>            :   Value* value_action_;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   //! Sampling radiues value.</a>
+<a name="238"><span class="lineNum">     238 </span>            :   Value* value_sampling_radius_;</a>
+<a name="239"><span class="lineNum">     239 </span>            : };</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : /*</a>
+<a name="242"><span class="lineNum">     242 </span>            :  * Getters and setters.</a>
+<a name="243"><span class="lineNum">     243 </span>            :  */</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : inline void Optimizer::set_nl_cutoff(double nl_cutoff) {</a>
+<a name="246"><span class="lineNum">     246 </span>            :   nl_cutoff_=nl_cutoff;</a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : inline double Optimizer::get_nl_cutofff() const {</a>
+<a name="250"><span class="lineNum">     250 </span>            :   return nl_cutoff_;</a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : inline void Optimizer::set_nl_stride(unsigned int nl_stride) {</a>
+<a name="254"><span class="lineNum">     254 </span>            :   nl_stride_=nl_stride;</a>
+<a name="255"><span class="lineNum">     255 </span>            : }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : inline unsigned int Optimizer::get_nl_stride() const {</a>
+<a name="258"><span class="lineNum">     258 </span>            :   return nl_stride_;</a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : inline void Optimizer::set_n_threads_openmp(unsigned int n_threads) {</a>
+<a name="262"><span class="lineNum">     262 </span>            :   n_threads_=n_threads;</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : inline unsigned int Optimizer::get_n_threads_openmp() const {</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        290 :   return n_threads_;</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            : inline void Optimizer::set_stride_openmp(unsigned int stride) {</a>
+<a name="270"><span class="lineNum">     270 </span>            :   stride_=stride;</a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : inline unsigned int Optimizer::get_stride_openmp() const {</a>
+<a name="274"><span class="lineNum">     274 </span>            :   return stride_;</a>
+<a name="275"><span class="lineNum">     275 </span>            : }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            : inline void Optimizer::set_rank_openmp(unsigned int rank) {</a>
+<a name="278"><span class="lineNum">     278 </span>            :   rank_=rank;</a>
+<a name="279"><span class="lineNum">     279 </span>            : }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : inline unsigned int Optimizer::get_rank_openmp() const {</a>
+<a name="282"><span class="lineNum">     282 </span>            :   return rank_;</a>
+<a name="283"><span class="lineNum">     283 </span>            : }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            : inline void Optimizer::set_sampling_radius(double sampling_r) {</a>
+<a name="286"><span class="lineNum">     286 </span>            :   sampling_r_=sampling_r;</a>
+<a name="287"><span class="lineNum">     287 </span>            : }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : inline double Optimizer::get_sampling_radius() const {</a>
+<a name="290"><span class="lineNum">     290 </span>            :   return sampling_r_;</a>
+<a name="291"><span class="lineNum">     291 </span>            : }</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            : inline void Optimizer::set_n_iterations(unsigned int n_iter) {</a>
+<a name="294"><span class="lineNum">     294 </span>            :   n_iter_=n_iter;</a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : inline unsigned int Optimizer::get_n_iterations() const {</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         33 :   return n_iter_;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : }</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : inline void Optimizer::pbc_off() {</a>
+<a name="302"><span class="lineNum">     302 </span>            :   pbc_=false;</a>
+<a name="303"><span class="lineNum">     303 </span>            : }</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            : inline void Optimizer::pbc_on() {</a>
+<a name="306"><span class="lineNum">     306 </span>            :   pbc_=true;</a>
+<a name="307"><span class="lineNum">     307 </span>            : }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : inline bool Optimizer::is_pbc_on() const {</a>
+<a name="310"><span class="lineNum">     310 </span>            :   return pbc_==true;</a>
+<a name="311"><span class="lineNum">     311 </span>            : }</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : inline void Optimizer::set_optimizer_stride(unsigned int optimizer_stride) {</a>
+<a name="314"><span class="lineNum">     314 </span>            :   optimizer_stride_=optimizer_stride;</a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : inline unsigned int Optimizer::get_optimizer_stride() const {</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          1 :   return optimizer_stride_;</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : inline void Optimizer::set_opt_value(double opt_value) {</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         46 :   opt_value_=opt_value;</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         30 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            : inline double Optimizer::get_opt_value() const {</a>
+<a name="326"><span class="lineNum">     326 </span>            :   return opt_value_;</a>
+<a name="327"><span class="lineNum">     327 </span>            : }</a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            : inline void Optimizer::set_opt(Vector opt) {</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         44 :   opt_=opt;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            : }</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            : inline Vector Optimizer::get_opt() const {</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          3 :   return opt_;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span>            : inline void Optimizer::set_label(const std::string&amp; label) {</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          7 :   label_=label;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          7 : }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : inline std::string Optimizer::get_label() const {</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          1 :   return label_;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            : inline void Optimizer::start_step_0() {</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          5 :   first_step_=false;</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : }</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            : inline void Optimizer::start_step_stride() {</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          2 :   first_step_=true;</span></a>
+<a name="351"><span class="lineNum">     351 </span>            : }</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            : } // namespace maze</a>
+<a name="354"><span class="lineNum">     354 </span>            : } // namespace PLMD</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span>            : #endif // __PLUMED_maze_Optimizer_h</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Optimizer_Bias.cpp.func-sort-c.html b/coverage/maze/Optimizer_Bias.cpp.func-sort-c.html
new file mode 100644
index 0000000000..214284741a
--- /dev/null
+++ b/coverage/maze/Optimizer_Bias.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer_Bias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer_Bias.cpp<span style="font-size: 80%;"> (<a href="Optimizer_Bias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">98</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Optimizer_Bias.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#259">_ZN4PLMD4maze13OptimizerBiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#196">_ZN4PLMD4maze12_GLOBAL__N_126OptimizerBiasRegisterMe1986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#259">_ZN4PLMD4maze13OptimizerBiasC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#119">_ZN4PLMD4maze13OptimizerBiasD0Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#119">_ZN4PLMD4maze13OptimizerBiasD1Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#198">_ZN4PLMD4maze13OptimizerBias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#376">_ZN4PLMD4maze13OptimizerBias9calculateEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#196">_ZN4PLMD4maze12_GLOBAL__N_126OptimizerBiasRegisterMe198C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#196">_ZN4PLMD4maze12_GLOBAL__N_126OptimizerBiasRegisterMe198D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Optimizer_Bias.cpp.func.html b/coverage/maze/Optimizer_Bias.cpp.func.html
new file mode 100644
index 0000000000..832786d652
--- /dev/null
+++ b/coverage/maze/Optimizer_Bias.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Optimizer_Bias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer_Bias.cpp<span style="font-size: 80%;"> (<a href="Optimizer_Bias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">98</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Optimizer_Bias.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#196">_ZN4PLMD4maze12_GLOBAL__N_126OptimizerBiasRegisterMe1986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#196">_ZN4PLMD4maze12_GLOBAL__N_126OptimizerBiasRegisterMe198C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
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+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#259">_ZN4PLMD4maze13OptimizerBiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#119">_ZN4PLMD4maze13OptimizerBiasD0Ev</a></td>
+              <td class="coverFnHi">1</td>
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+    <tr>
+              <td class="coverFn"><a href="Optimizer_Bias.cpp.gcov.html#119">_ZN4PLMD4maze13OptimizerBiasD1Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</html>
diff --git a/coverage/maze/Optimizer_Bias.cpp.gcov.html b/coverage/maze/Optimizer_Bias.cpp.gcov.html
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+  <title>LCOV - plumed test coverage - maze/Optimizer_Bias.cpp</title>
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Optimizer_Bias.cpp<span style="font-size: 80%;"> (source / <a href="Optimizer_Bias.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">98</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Optimizer_Bias.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @code</a>
+<a name="29"><span class="lineNum">      29 </span>            :  * @article{rydzewski2018finding,</a>
+<a name="30"><span class="lineNum">      30 </span>            :  *   title={Finding Multiple Reaction Pathways of Ligand Unbinding},</a>
+<a name="31"><span class="lineNum">      31 </span>            :  *   author={Rydzewski, J and Valsson, O},</a>
+<a name="32"><span class="lineNum">      32 </span>            :  *   journal={arXiv preprint arXiv:1808.08089},</a>
+<a name="33"><span class="lineNum">      33 </span>            :  *   year={2018}</a>
+<a name="34"><span class="lineNum">      34 </span>            :  * }</a>
+<a name="35"><span class="lineNum">      35 </span>            :  * @endcode</a>
+<a name="36"><span class="lineNum">      36 </span>            :  */</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : namespace PLMD {</a>
+<a name="47"><span class="lineNum">      47 </span>            : namespace maze {</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : //+PLUMEDOC MAZE_BIAS MAZE_OPTIMIZER_BIAS</a>
+<a name="50"><span class="lineNum">      50 </span>            : /*</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : Biases the ligand along the direction calculated by the chosen MAZE_OPTIMIZER.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : OptimizerBias is a class deriving from Bias, and it is used to adaptively</a>
+<a name="55"><span class="lineNum">      55 </span>            : bias a ligand-protein system toward an optimal solution found by the chosen</a>
+<a name="56"><span class="lineNum">      56 </span>            : \ref MAZE_OPTIMIZER.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : Remember to define the loss function (\ref MAZE_LOSS) and the optimizer</a>
+<a name="59"><span class="lineNum">      59 </span>            : (\ref MAZE_OPTIMIZER) prior to the adaptive bias for the optimizer.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The adaptive bias potential is the following:</a>
+<a name="62"><span class="lineNum">      62 </span>            : \f[</a>
+<a name="63"><span class="lineNum">      63 </span>            :   V({\bf x}_t)=\alpha</a>
+<a name="64"><span class="lineNum">      64 </span>            :     \left(wt -</a>
+<a name="65"><span class="lineNum">      65 </span>            :       ({\bf x} - {\bf x}^*_{t-\tau})</a>
+<a name="66"><span class="lineNum">      66 </span>            :       \cdot</a>
+<a name="67"><span class="lineNum">      67 </span>            :       \frac{{\bf x}^*_t - {\bf x}_t}{\|{\bf x}^*_t-{\bf x}_t\|}</a>
+<a name="68"><span class="lineNum">      68 </span>            :     \right)^2,</a>
+<a name="69"><span class="lineNum">      69 </span>            : \f]</a>
+<a name="70"><span class="lineNum">      70 </span>            : where \f${\bf x}^*_t\f$ is the optimal solution at time \f$t\f$, \f$w\f$ is the</a>
+<a name="71"><span class="lineNum">      71 </span>            : biasing rate, \f$\tau\f$ is the interval at which the loss function is minimized,</a>
+<a name="72"><span class="lineNum">      72 </span>            : and \f$\alpha\f$ is a scaled force constant.</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \par Examples</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : In the following example the bias potential biases a ligand atom (which have to be</a>
+<a name="77"><span class="lineNum">      77 </span>            : given as an argument) with the biasing rate equal to 0.02 A/ps, and the biasing</a>
+<a name="78"><span class="lineNum">      78 </span>            : constant equal to 3.6 kcal/(mol A). It also takes an optimizer (see</a>
+<a name="79"><span class="lineNum">      79 </span>            : \ref MAZE_OPTIMIZER).</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \plumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : UNITS LENGTH=A TIME=ps ENERGY=kcal/mol</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : p: POSITION ATOM=2635 NOPBC</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : MAZE_OPTIMIZER_BIAS ...</a>
+<a name="87"><span class="lineNum">      87 </span>            :   LABEL=bias</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   ARG=p.x,p.y,p.z</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   BIASING_RATE=0.02</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ALPHA=3.6</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   OPTIMIZER=opt</a>
+<a name="95"><span class="lineNum">      95 </span>            : ... MAZE_OPTIMIZER_BIAS</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endplumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : */</a>
+<a name="99"><span class="lineNum">      99 </span>            : //+ENDPLUMEDOC</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : /**</a>
+<a name="102"><span class="lineNum">     102 </span>            :  * @class OptimizerBias OptimizerBias.cpp &quot;maze/OptimizerBias.cpp&quot;</a>
+<a name="103"><span class="lineNum">     103 </span>            :  *</a>
+<a name="104"><span class="lineNum">     104 </span>            :  * @brief Adaptive bias for the maze optimizers.</a>
+<a name="105"><span class="lineNum">     105 </span>            :  *</a>
+<a name="106"><span class="lineNum">     106 </span>            :  * OptimizerBias is a class deriving from Bias, and it is used to adaptively</a>
+<a name="107"><span class="lineNum">     107 </span>            :  * bias a system toward an optimal solution found by an optimizer.</a>
+<a name="108"><span class="lineNum">     108 </span>            :  */</a>
+<a name="109"><span class="lineNum">     109 </span>            : class OptimizerBias: public bias::Bias {</a>
+<a name="110"><span class="lineNum">     110 </span>            : public:</a>
+<a name="111"><span class="lineNum">     111 </span>            :   /**</a>
+<a name="112"><span class="lineNum">     112 </span>            :    * Standard PLUMED2 constructor.</a>
+<a name="113"><span class="lineNum">     113 </span>            :    *</a>
+<a name="114"><span class="lineNum">     114 </span>            :    * @param ao ActionOptions&amp;.</a>
+<a name="115"><span class="lineNum">     115 </span>            :    */</a>
+<a name="116"><span class="lineNum">     116 </span>            :   explicit OptimizerBias(const ActionOptions&amp; ao);</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   /**</a>
+<a name="119"><span class="lineNum">     119 </span>            :    * Destructor.</a>
+<a name="120"><span class="lineNum">     120 </span>            :    */</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          3 :   ~OptimizerBias() { /* Nothing to do. */ }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            :   /**</a>
+<a name="124"><span class="lineNum">     124 </span>            :    * Register PLUMED2 keywords.</a>
+<a name="125"><span class="lineNum">     125 </span>            :    *</a>
+<a name="126"><span class="lineNum">     126 </span>            :    * @param keys Keywords.</a>
+<a name="127"><span class="lineNum">     127 </span>            :    */</a>
+<a name="128"><span class="lineNum">     128 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :   /**</a>
+<a name="131"><span class="lineNum">     131 </span>            :    * Calculate the adaptive biasing potential for ligand unbinding.</a>
+<a name="132"><span class="lineNum">     132 </span>            :    */</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void calculate();</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : private:</a>
+<a name="136"><span class="lineNum">     136 </span>            :   /**</a>
+<a name="137"><span class="lineNum">     137 </span>            :    * Biased collective variable with Cartesian components, i.e., position,</a>
+<a name="138"><span class="lineNum">     138 </span>            :    * center of mass.</a>
+<a name="139"><span class="lineNum">     139 </span>            :    */</a>
+<a name="140"><span class="lineNum">     140 </span>            :   std::vector&lt;Value*&gt; args_;</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   /**</a>
+<a name="143"><span class="lineNum">     143 </span>            :    * Pointer to the optimizer used to minimize the collective variable for</a>
+<a name="144"><span class="lineNum">     144 </span>            :    * ligand unbinding.</a>
+<a name="145"><span class="lineNum">     145 </span>            :    */</a>
+<a name="146"><span class="lineNum">     146 </span>            :   Optimizer* optimizer_;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;Optimizer*&gt; opt_pntrs_;</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   //! Adaptive bias potential and the corresponding force.</a>
+<a name="150"><span class="lineNum">     150 </span>            :   double bias_;</a>
+<a name="151"><span class="lineNum">     151 </span>            :   double force_;</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   /*</a>
+<a name="154"><span class="lineNum">     154 </span>            :    * Parameters of the adaptive biasing potential:</a>
+<a name="155"><span class="lineNum">     155 </span>            :    *  alpha_            rescaled force constant</a>
+<a name="156"><span class="lineNum">     156 </span>            :    *  biasing_speed     biasing rate</a>
+<a name="157"><span class="lineNum">     157 </span>            :    *  biasing_stride    biasing stride</a>
+<a name="158"><span class="lineNum">     158 </span>            :    *  biasing_direction biasing direction</a>
+<a name="159"><span class="lineNum">     159 </span>            :    */</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            :   //! Rescaled force constant.</a>
+<a name="162"><span class="lineNum">     162 </span>            :   double alpha_;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //! Biasing rate.</a>
+<a name="164"><span class="lineNum">     164 </span>            :   double biasing_speed_;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   //! Biasing stride.</a>
+<a name="166"><span class="lineNum">     166 </span>            :   int biasing_stride_;</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   /**</a>
+<a name="169"><span class="lineNum">     169 </span>            :    * Biasing direction is approximated by an optimal solution found by an</a>
+<a name="170"><span class="lineNum">     170 </span>            :    * optimizer.</a>
+<a name="171"><span class="lineNum">     171 </span>            :    */</a>
+<a name="172"><span class="lineNum">     172 </span>            :   Vector biasing_direction_;</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   //! Total distance traveled by biased atoms.</a>
+<a name="175"><span class="lineNum">     175 </span>            :   double total_distance_;</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            :   //! Previous value of the collective variable.</a>
+<a name="178"><span class="lineNum">     178 </span>            :   Vector cv0_;</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   /*</a>
+<a name="181"><span class="lineNum">     181 </span>            :    * Pointers to PLUMED2 output components.</a>
+<a name="182"><span class="lineNum">     182 </span>            :    */</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            :   //! Biased collective variable components.</a>
+<a name="185"><span class="lineNum">     185 </span>            :   Value* value_dir_x_;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   Value* value_dir_y_;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   Value* value_dir_z_;</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   //! Values of the bias and its force.</a>
+<a name="190"><span class="lineNum">     190 </span>            :   Value* value_bias_;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   Value* value_force_;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   //! Total distance.</a>
+<a name="194"><span class="lineNum">     194 </span>            :   Value* value_total_distance_;</a>
+<a name="195"><span class="lineNum">     195 </span>            : };</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : // Register OPTIMIZER_BIAS as a keyword for PLUMED2 input files.</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(OptimizerBias, &quot;MAZE_OPTIMIZER_BIAS&quot;)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          3 : void OptimizerBias::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          3 :   Bias::registerKeywords(keys);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          3 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     &quot;compulsory&quot;,</a>
+<a name="207"><span class="lineNum">     207 </span>            :     &quot;BIASING_RATE&quot;,</a>
+<a name="208"><span class="lineNum">     208 </span>            :     &quot;Biasing rate.&quot;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   );</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     &quot;compulsory&quot;,</a>
+<a name="213"><span class="lineNum">     213 </span>            :     &quot;ALPHA&quot;,</a>
+<a name="214"><span class="lineNum">     214 </span>            :     &quot;Rescaled force constant.&quot;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   );</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     &quot;compulsory&quot;,</a>
+<a name="219"><span class="lineNum">     219 </span>            :     &quot;OPTIMIZER&quot;,</a>
+<a name="220"><span class="lineNum">     220 </span>            :     &quot;Optimization technique to minimize the collective variable for ligand\</a>
+<a name="221"><span class="lineNum">     221 </span>            :      unbinding: RANDOM_WALK,\</a>
+<a name="222"><span class="lineNum">     222 </span>            :                 STEERED_MD,\</a>
+<a name="223"><span class="lineNum">     223 </span>            :                 RANDOM_ACCELERATION_MD,\</a>
+<a name="224"><span class="lineNum">     224 </span>            :                 SIMULATED_ANNEALING,\</a>
+<a name="225"><span class="lineNum">     225 </span>            :                 MEMETIC_SAMPLING&quot;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   );</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          3 :   componentsAreNotOptional(keys);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     &quot;force2&quot;,</a>
+<a name="232"><span class="lineNum">     232 </span>            :     &quot;default&quot;,</a>
+<a name="233"><span class="lineNum">     233 </span>            :     &quot;Square of the biasing force.&quot;</a>
+<a name="234"><span class="lineNum">     234 </span>            :   );</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     &quot;x&quot;,</a>
+<a name="238"><span class="lineNum">     238 </span>            :     &quot;default&quot;,</a>
+<a name="239"><span class="lineNum">     239 </span>            :     &quot;Optimal biasing direction: x component.&quot;</a>
+<a name="240"><span class="lineNum">     240 </span>            :   );</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     &quot;y&quot;,</a>
+<a name="244"><span class="lineNum">     244 </span>            :     &quot;default&quot;,</a>
+<a name="245"><span class="lineNum">     245 </span>            :     &quot;Optimal biasing direction: y component.&quot;</a>
+<a name="246"><span class="lineNum">     246 </span>            :   );</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :     &quot;z&quot;,</a>
+<a name="250"><span class="lineNum">     250 </span>            :     &quot;default&quot;,</a>
+<a name="251"><span class="lineNum">     251 </span>            :     &quot;Optimal biasing direction: z component.&quot;</a>
+<a name="252"><span class="lineNum">     252 </span>            :   );</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     &quot;tdist&quot;,</a>
+<a name="256"><span class="lineNum">     256 </span>            :     &quot;default&quot;,</a>
+<a name="257"><span class="lineNum">     257 </span>            :     &quot;Total distance traveled by biased atoms.&quot;</a>
+<a name="258"><span class="lineNum">     258 </span>            :   );</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          3 : }</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          1 : OptimizerBias::OptimizerBias(const ActionOptions&amp; ao)</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   : PLUMED_BIAS_INIT(ao),</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          1 :     bias_(0.0),</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          1 :     force_(0.0),</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          1 :     total_distance_(0.0)</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : {</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          1 :   log.printf(</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :     &quot;maze&gt; You are using the maze module of PLUMED2,\</a>
+<a name="269"><span class="lineNum">     269 </span>            :     please read and cite &quot;</a>
+<a name="270"><span class="lineNum">     270 </span>            :   );</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :   log &lt;&lt; plumed.cite(&quot;Rydzewski J. and Valsson O., arXiv:1808.08089, 2018&quot;);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          1 :   args_ = getArguments();</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          1 :   log.printf(</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :     &quot;maze&gt; Number of args %zu\n&quot;,</a>
+<a name="278"><span class="lineNum">     278 </span>            :     args_.size()</a>
+<a name="279"><span class="lineNum">     279 </span>            :   );</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          1 :   if (!args_.empty()) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          1 :     log.printf(&quot;maze&gt; With arguments&quot;);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          4 :     for (unsigned i = 0; i &lt; args_.size(); i++) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          3 :       log.printf(&quot; %s&quot;, args_[i]-&gt;getName().c_str());</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          1 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :   }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          2 :   if (keywords.exists(&quot;ALPHA&quot;)) {</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          1 :     parse(&quot;ALPHA&quot;, alpha_);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :       alpha_&gt;0,</a>
+<a name="294"><span class="lineNum">     294 </span>            :       &quot;maze&gt; ALPHA should be explicitly specified and positive.\n&quot;</a>
+<a name="295"><span class="lineNum">     295 </span>            :     );</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :       &quot;maze&gt; ALPHA read: %f [kcal/mol/A].\n&quot;,</a>
+<a name="299"><span class="lineNum">     299 </span>            :       alpha_</a>
+<a name="300"><span class="lineNum">     300 </span>            :     );</a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          2 :   if (keywords.exists(&quot;BIASING_RATE&quot;)) {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          1 :     parse(&quot;BIASING_RATE&quot;, biasing_speed_);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :       biasing_speed_&gt;0,</a>
+<a name="308"><span class="lineNum">     308 </span>            :       &quot;maze&gt; BIASING_RATE should be explicitly specified and positive.\n&quot;</a>
+<a name="309"><span class="lineNum">     309 </span>            :     );</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :       &quot;maze&gt; BIASING_RATE read: %f [A/ps].\n&quot;,</a>
+<a name="313"><span class="lineNum">     313 </span>            :       biasing_speed_</a>
+<a name="314"><span class="lineNum">     314 </span>            :     );</a>
+<a name="315"><span class="lineNum">     315 </span>            :   }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          2 :   if (keywords.exists(&quot;OPTIMIZER&quot;)) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          1 :     std::vector&lt;std::string&gt; opt_labels(0);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          2 :     parseVector(&quot;OPTIMIZER&quot;, opt_labels);</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :       opt_labels.size() &gt; 0,</a>
+<a name="323"><span class="lineNum">     323 </span>            :       &quot;maze&gt; Problem with OPTIMIZER keyword.\n&quot;</a>
+<a name="324"><span class="lineNum">     324 </span>            :     );</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          1 :     std::string error_msg = &quot;&quot;;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          2 :     opt_pntrs_ = tls::get_pointers_labels&lt;Optimizer*&gt;(</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :                    opt_labels,</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          1 :                    plumed.getActionSet(),</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :                    error_msg</a>
+<a name="331"><span class="lineNum">     331 </span>            :                  );</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          1 :     if (error_msg.size() &gt; 0) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :       plumed_merror(</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :         &quot;maze&gt; Error in keyword OPTIMIZER of &quot; + getName() + &quot;: &quot; + error_msg</a>
+<a name="336"><span class="lineNum">     336 </span>            :       );</a>
+<a name="337"><span class="lineNum">     337 </span>            :     }</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          1 :     optimizer_ = opt_pntrs_[0];</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :       &quot;maze&gt; Optimizer linked: %s.\n&quot;,</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :       optimizer_-&gt;get_label().c_str()</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :     );</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          1 :     biasing_stride_=optimizer_-&gt;get_optimizer_stride();</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          1 :   }</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          1 :   addComponent(&quot;force2&quot;);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          1 :   addComponent(&quot;x&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;x&quot;);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          1 :   addComponent(&quot;y&quot;);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;y&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          1 :   addComponent(&quot;z&quot;);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;z&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          1 :   addComponent(&quot;tdist&quot;);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;tdist&quot;);</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          1 :   biasing_direction_.zero();</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          1 :   cv0_.zero();</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          1 :   value_bias_ = getPntrToComponent(&quot;bias&quot;);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          1 :   value_force_ = getPntrToComponent(&quot;force2&quot;);</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">          1 :   value_dir_x_ = getPntrToComponent(&quot;x&quot;);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          1 :   value_dir_y_ = getPntrToComponent(&quot;y&quot;);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          1 :   value_dir_z_ = getPntrToComponent(&quot;z&quot;);</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          1 :   value_total_distance_=getPntrToComponent(&quot;tdist&quot;);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          1 : }</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         30 : void OptimizerBias::calculate() {</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   // Unpack arguments and optimizers.</a>
+<a name="380"><span class="lineNum">     380 </span>            :   Vector cv(</a>
+<a name="381"><span class="lineNum">     381 </span>            :     args_[0]-&gt;get(),</a>
+<a name="382"><span class="lineNum">     382 </span>            :     args_[1]-&gt;get(),</a>
+<a name="383"><span class="lineNum">     383 </span>            :     args_[2]-&gt;get()</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         30 :   );</span></a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            :   Vector opt_direction(</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         30 :     optimizer_-&gt;value_x_-&gt;get(),</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         30 :     optimizer_-&gt;value_y_-&gt;get(),</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         30 :     optimizer_-&gt;value_z_-&gt;get()</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         30 :   );</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         30 :   if (getStep() == 0) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          1 :     cv0_=cv;</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :   }</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   /*</a>
+<a name="397"><span class="lineNum">     397 </span>            :    * For details see a paper by Rydzewski and Valsson.</a>
+<a name="398"><span class="lineNum">     398 </span>            :    */</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         30 :   double dot = dotProduct(cv - cv0_, biasing_direction_);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         30 :   double delta_cv = biasing_speed_ * getTime() - (dot + total_distance_);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         30 :   double sign = tls::sgn(delta_cv);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         30 :   bias_ = alpha_ * delta_cv * delta_cv;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         30 :   force_ = 2.0 * sign * alpha_ * fabs(delta_cv);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         30 :   if (getStep() % biasing_stride_ == 0) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          3 :     biasing_direction_ = opt_direction;</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">          3 :     cv0_ = cv;</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">          3 :     total_distance_ += dot;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :   }</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span>            :   /*</a>
+<a name="414"><span class="lineNum">     414 </span>            :    * Return the biasing force to MD engine.</a>
+<a name="415"><span class="lineNum">     415 </span>            :    */</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         30 :   setOutputForce(0, force_ * biasing_direction_[0]);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         30 :   setOutputForce(1, force_ * biasing_direction_[1]);</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         30 :   setOutputForce(2, force_ * biasing_direction_[2]);</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   /*</a>
+<a name="421"><span class="lineNum">     421 </span>            :    * Set values for PLUMED2 outputs.</a>
+<a name="422"><span class="lineNum">     422 </span>            :    */</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         30 :   value_bias_-&gt;set(bias_);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         30 :   value_force_-&gt;set(force_);</span></a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         30 :   value_total_distance_-&gt;set(total_distance_);</span></a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         30 :   value_dir_x_-&gt;set(biasing_direction_[0]);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         30 :   value_dir_y_-&gt;set(biasing_direction_[1]);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         30 :   value_dir_z_-&gt;set(biasing_direction_[2]);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         30 : }</span></a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            : } // namespace maze</a>
+<a name="434"><span class="lineNum">     434 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_Acceleration_MD.cpp.func-sort-c.html b/coverage/maze/Random_Acceleration_MD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ae21fb9673
--- /dev/null
+++ b/coverage/maze/Random_Acceleration_MD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_Acceleration_MD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_Acceleration_MD.cpp<span style="font-size: 80%;"> (<a href="Random_Acceleration_MD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Random_Acceleration_MD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#136">_ZN4PLMD4maze22Random_Acceleration_MDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#110">_ZN4PLMD4maze12_GLOBAL__N_135Random_Acceleration_MDRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#136">_ZN4PLMD4maze22Random_Acceleration_MDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#175">_ZN4PLMD4maze22Random_Acceleration_MD8optimizeEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#112">_ZN4PLMD4maze22Random_Acceleration_MD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#110">_ZN4PLMD4maze12_GLOBAL__N_135Random_Acceleration_MDRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#110">_ZN4PLMD4maze12_GLOBAL__N_135Random_Acceleration_MDRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_Acceleration_MD.cpp.func.html b/coverage/maze/Random_Acceleration_MD.cpp.func.html
new file mode 100644
index 0000000000..715878e892
--- /dev/null
+++ b/coverage/maze/Random_Acceleration_MD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_Acceleration_MD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_Acceleration_MD.cpp<span style="font-size: 80%;"> (<a href="Random_Acceleration_MD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Random_Acceleration_MD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#110">_ZN4PLMD4maze12_GLOBAL__N_135Random_Acceleration_MDRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#110">_ZN4PLMD4maze12_GLOBAL__N_135Random_Acceleration_MDRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#110">_ZN4PLMD4maze12_GLOBAL__N_135Random_Acceleration_MDRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#112">_ZN4PLMD4maze22Random_Acceleration_MD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#175">_ZN4PLMD4maze22Random_Acceleration_MD8optimizeEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#136">_ZN4PLMD4maze22Random_Acceleration_MDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Acceleration_MD.cpp.gcov.html#136">_ZN4PLMD4maze22Random_Acceleration_MDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_Acceleration_MD.cpp.gcov.html b/coverage/maze/Random_Acceleration_MD.cpp.gcov.html
new file mode 100644
index 0000000000..728b01d54f
--- /dev/null
+++ b/coverage/maze/Random_Acceleration_MD.cpp.gcov.html
@@ -0,0 +1,279 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_Acceleration_MD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_Acceleration_MD.cpp<span style="font-size: 80%;"> (source / <a href="Random_Acceleration_MD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Random_Acceleration_MD.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  */</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace maze {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC MAZE_OPTIMIZER MAZE_RANDOM_ACCELERATION_MD</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Performs random acceleration MD within the protein matrix.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Every optimizer implemented in the maze module needs a loss function as</a>
+<a name="43"><span class="lineNum">      43 </span>            : an argument, and it should be passed using the \ref MAZE_LOSS keyword.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \plumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : MAZE_RANDOM_ACCELERATION_MD ...</a>
+<a name="47"><span class="lineNum">      47 </span>            :   LABEL=rw</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            :   OPTIMIZER_STRIDE=_</a>
+<a name="50"><span class="lineNum">      50 </span>            :   LOSS=l</a>
+<a name="51"><span class="lineNum">      51 </span>            :   RMIN=_</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            :   LIGAND=2635-2646</a>
+<a name="54"><span class="lineNum">      54 </span>            :   PROTEIN=1-2634</a>
+<a name="55"><span class="lineNum">      55 </span>            : ... MAZE_RANDOM_ACCELERATION_MD</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : As shown above, each optimizer should be provided with the LIGAND and</a>
+<a name="59"><span class="lineNum">      59 </span>            : the PROTEIN keywords.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : */</a>
+<a name="62"><span class="lineNum">      62 </span>            : //+ENDPLUMEDOC</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : /**</a>
+<a name="65"><span class="lineNum">      65 </span>            :  * @class Random_Acceleration_MD Random_Acceleration_MD.cpp</a>
+<a name="66"><span class="lineNum">      66 </span>            :  *  &quot;maze/Random_Acceleration_MD.cpp&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :  *</a>
+<a name="68"><span class="lineNum">      68 </span>            :  * @brief Perform RAMD simulation.</a>
+<a name="69"><span class="lineNum">      69 </span>            :  */</a>
+<a name="70"><span class="lineNum">      70 </span>            : class Random_Acceleration_MD: public Optimizer {</a>
+<a name="71"><span class="lineNum">      71 </span>            : public:</a>
+<a name="72"><span class="lineNum">      72 </span>            :   /**</a>
+<a name="73"><span class="lineNum">      73 </span>            :    * PLMD constructor.</a>
+<a name="74"><span class="lineNum">      74 </span>            :    *</a>
+<a name="75"><span class="lineNum">      75 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;</a>
+<a name="76"><span class="lineNum">      76 </span>            :    */</a>
+<a name="77"><span class="lineNum">      77 </span>            :   explicit Random_Acceleration_MD(const ActionOptions&amp;);</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   /**</a>
+<a name="80"><span class="lineNum">      80 </span>            :    * Registers PLMD keywords.</a>
+<a name="81"><span class="lineNum">      81 </span>            :    *</a>
+<a name="82"><span class="lineNum">      82 </span>            :    * @param[in] keys PLMD keywords</a>
+<a name="83"><span class="lineNum">      83 </span>            :    */</a>
+<a name="84"><span class="lineNum">      84 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   /**</a>
+<a name="87"><span class="lineNum">      87 </span>            :    * Each class deriving from Optimizer needs to override this function.</a>
+<a name="88"><span class="lineNum">      88 </span>            :    */</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void optimize() override;</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : private:</a>
+<a name="92"><span class="lineNum">      92 </span>            :   //! Threshold distance that the ligand needs to pass.</a>
+<a name="93"><span class="lineNum">      93 </span>            :   double r_min_;</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            :   //! Total distance.</a>
+<a name="96"><span class="lineNum">      96 </span>            :   double total_dist_;</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   //! Distance.</a>
+<a name="99"><span class="lineNum">      99 </span>            :   double dist_;</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   //! Ligand center of mass.</a>
+<a name="102"><span class="lineNum">     102 </span>            :   Vector com_;</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   //! PLMD value for distance.</a>
+<a name="105"><span class="lineNum">     105 </span>            :   Value* value_dist_;</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   //! PLMD value for total distance.</a>
+<a name="108"><span class="lineNum">     108 </span>            :   Value* value_total_dist_;</a>
+<a name="109"><span class="lineNum">     109 </span>            : };</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : // Register MAZE_RANDOM_ACCELERATION_MD.</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Random_Acceleration_MD, &quot;MAZE_RANDOM_ACCELERATION_MD&quot;)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 : void Random_Acceleration_MD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          3 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          3 :   keys.remove(&quot;N_ITER&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     &quot;compulsory&quot;,</a>
+<a name="121"><span class="lineNum">     121 </span>            :     &quot;R_MIN&quot;,</a>
+<a name="122"><span class="lineNum">     122 </span>            :     &quot;Minimal distance traveled before sampling a new direction of biasing.&quot;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   );</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     &quot;dist&quot;,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     &quot;default&quot;,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     &quot;Distance traveled in one sampling interval.&quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   );</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     &quot;tdist&quot;,</a>
+<a name="133"><span class="lineNum">     133 </span>            :     &quot;default&quot;,</a>
+<a name="134"><span class="lineNum">     134 </span>            :     &quot;Total distance traveled by biased atoms.&quot;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   );</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 : Random_Acceleration_MD::Random_Acceleration_MD(const ActionOptions&amp; ao)</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   : PLUMED_OPT_INIT(ao),</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :     total_dist_(0.0),</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :     dist_(0.0) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   log.printf(&quot;maze&gt; Random accelerated molecular dynamics.\n&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   if(keywords.exists(&quot;R_MIN&quot;)) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :     parse(&quot;R_MIN&quot;, r_min_);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :       r_min_ &gt; 0,</a>
+<a name="149"><span class="lineNum">     149 </span>            :       &quot;maze&gt; R_MIN should be explicitly specified and positive.\n&quot;</a>
+<a name="150"><span class="lineNum">     150 </span>            :     );</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       &quot;maze&gt; R_MIN read: %f [A].\n&quot;,</a>
+<a name="154"><span class="lineNum">     154 </span>            :       r_min_</a>
+<a name="155"><span class="lineNum">     155 </span>            :     );</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :   set_label(&quot;RANDOM_ACCELERATION_MD&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          1 :   set_opt(rnd::next_plmd_vector());</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   set_opt_value(0.0);</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   start_step_stride();</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :   com_ = center_of_mass();</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :   addComponent(&quot;dist&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;dist&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 :   value_dist_ = getPntrToComponent(&quot;dist&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :   addComponent(&quot;tdist&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;tdist&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :   value_total_dist_ = getPntrToComponent(&quot;tdist&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 : void Random_Acceleration_MD::optimize() {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          2 :   Vector c = center_of_mass();</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :   Vector d;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :   if (pbc_) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :     d = pbcDistance(c, com_);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   else {</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     d = delta(c, com_);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :   dist_ = d.modulo();</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :   total_dist_ += dist_;</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          2 :   if(dist_ &lt; r_min_) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     set_opt(rnd::next_plmd_vector());</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 :   set_opt_value(score());</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          2 :   com_ = c;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          2 :   value_dist_-&gt;set(dist_);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :   value_total_dist_-&gt;set(total_dist_);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          2 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : } // namespace maze</a>
+<a name="203"><span class="lineNum">     203 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_MT.cpp.func-sort-c.html b/coverage/maze/Random_MT.cpp.func-sort-c.html
new file mode 100644
index 0000000000..70697a23a0
--- /dev/null
+++ b/coverage/maze/Random_MT.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_MT.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_MT.cpp<span style="font-size: 80%;"> (<a href="Random_MT.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Random_MT.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#64">_ZN4PLMD4maze3rnd8next_intEii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#72">_ZN4PLMD4maze3rnd11next_cauchyEdd</a></td>
+              <td class="coverFnHi">81</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#40">_ZN4PLMD4maze3rnd11next_doubleEdd</a></td>
+              <td class="coverFnHi">246</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#56">_ZN4PLMD4maze3rnd8next_intEi</a></td>
+              <td class="coverFnHi">291</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#48">_ZN4PLMD4maze3rnd11next_doubleEv</a></td>
+              <td class="coverFnHi">536</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#34">_ZN4PLMD4maze3rnd6mt_engEv</a></td>
+              <td class="coverFnHi">1161</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_MT.cpp.func.html b/coverage/maze/Random_MT.cpp.func.html
new file mode 100644
index 0000000000..b581a5d03d
--- /dev/null
+++ b/coverage/maze/Random_MT.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_MT.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_MT.cpp<span style="font-size: 80%;"> (<a href="Random_MT.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Random_MT.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#72">_ZN4PLMD4maze3rnd11next_cauchyEdd</a></td>
+              <td class="coverFnHi">81</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#40">_ZN4PLMD4maze3rnd11next_doubleEdd</a></td>
+              <td class="coverFnHi">246</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#48">_ZN4PLMD4maze3rnd11next_doubleEv</a></td>
+              <td class="coverFnHi">536</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#34">_ZN4PLMD4maze3rnd6mt_engEv</a></td>
+              <td class="coverFnHi">1161</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#56">_ZN4PLMD4maze3rnd8next_intEi</a></td>
+              <td class="coverFnHi">291</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.cpp.gcov.html#64">_ZN4PLMD4maze3rnd8next_intEii</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_MT.cpp.gcov.html b/coverage/maze/Random_MT.cpp.gcov.html
new file mode 100644
index 0000000000..f06fd89b3d
--- /dev/null
+++ b/coverage/maze/Random_MT.cpp.gcov.html
@@ -0,0 +1,157 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_MT.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_MT.cpp<span style="font-size: 80%;"> (source / <a href="Random_MT.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Random_MT.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @brief Dummy cpp file.</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;Random_MT.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace maze {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       1161 : std::mt19937_64&amp; rnd::mt_eng() {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       1168 :   static std::mt19937_64 mt{};</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       1161 :   return mt;</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : }</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        246 : double rnd::next_double(double f, double e) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        246 :   static std::uniform_real_distribution&lt;double&gt; dist_double(f, e);</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::uniform_real_distribution&lt;double&gt;::param_type p(f, e);</a>
+<a name="45"><span class="lineNum">      45 </span>            :   dist_double.param(p);</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        246 :   return dist_double(mt_eng());</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        536 : double rnd::next_double() {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        536 :   static std::uniform_real_distribution&lt;double&gt; dist_double(0, 1);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::uniform_real_distribution&lt;double&gt;::param_type p(0, 1);</a>
+<a name="53"><span class="lineNum">      53 </span>            :   dist_double.param(p);</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        536 :   return dist_double(mt_eng());</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        291 : int rnd::next_int(int e) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        291 :   static std::uniform_int_distribution&lt;int&gt; dist_int(0, e-1);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        291 :   std::uniform_int_distribution&lt;int&gt;::param_type p(0, e-1);</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   dist_int.param(p);</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        291 :   return dist_int(mt_eng());</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 : int rnd::next_int(int f, int e) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   static std::uniform_int_distribution&lt;int&gt; dist_int(f, e-1);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   std::uniform_int_distribution&lt;int&gt;::param_type p(f, e-1);</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   dist_int.param(p);</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   return dist_int(mt_eng());</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         81 : double rnd::next_cauchy(double m, double s) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         81 :   static std::cauchy_distribution&lt;double&gt; dist_cauchy(m, s);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         81 :   return dist_cauchy(mt_eng());</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : } // namespace maze</a>
+<a name="81"><span class="lineNum">      81 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_MT.h.func-sort-c.html b/coverage/maze/Random_MT.h.func-sort-c.html
new file mode 100644
index 0000000000..2decaa8f1a
--- /dev/null
+++ b/coverage/maze/Random_MT.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_MT.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_MT.h<span style="font-size: 80%;"> (<a href="Random_MT.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryLo">70.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Random_MT.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#112">_ZN4PLMD4maze3rnd11next_doubleEddm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#147">_ZN4PLMD4maze3rnd9randomizeEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#97">_ZN4PLMD4maze3rnd16next_plmd_vectorEd</a></td>
+              <td class="coverFnHi">66</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#121">_ZN4PLMD4maze3rnd16next_plmd_vectorEv</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_MT.h.func.html b/coverage/maze/Random_MT.h.func.html
new file mode 100644
index 0000000000..732c33b0b4
--- /dev/null
+++ b/coverage/maze/Random_MT.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_MT.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_MT.h<span style="font-size: 80%;"> (<a href="Random_MT.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryLo">70.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Random_MT.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#112">_ZN4PLMD4maze3rnd11next_doubleEddm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#97">_ZN4PLMD4maze3rnd16next_plmd_vectorEd</a></td>
+              <td class="coverFnHi">66</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#121">_ZN4PLMD4maze3rnd16next_plmd_vectorEv</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_MT.h.gcov.html#147">_ZN4PLMD4maze3rnd9randomizeEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_MT.h.gcov.html b/coverage/maze/Random_MT.h.gcov.html
new file mode 100644
index 0000000000..50e971afe4
--- /dev/null
+++ b/coverage/maze/Random_MT.h.gcov.html
@@ -0,0 +1,232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_MT.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_MT.h<span style="font-size: 80%;"> (source / <a href="Random_MT.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryLo">70.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_maze_Random_MT_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_maze_Random_MT_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /**</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @file Random_MT.h</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;Core.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace maze {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /**</a>
+<a name="37"><span class="lineNum">      37 </span>            :  * @class rnd Random_MT.h &quot;maze/Random_MT.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            :  *</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * @brief Mersenne Twister sampler for random variables.</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * Supports generating integers, doubles, and std::vectors and PLMD::Vectors</a>
+<a name="42"><span class="lineNum">      42 </span>            :  * within a given range.</a>
+<a name="43"><span class="lineNum">      43 </span>            :  */</a>
+<a name="44"><span class="lineNum">      44 </span>            : class rnd {</a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   /**</a>
+<a name="47"><span class="lineNum">      47 </span>            :    * Initialize MT sampler engine based on std::mt19937_64.</a>
+<a name="48"><span class="lineNum">      48 </span>            :    */</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static std::mt19937_64&amp; mt_eng();</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            :   /**</a>
+<a name="52"><span class="lineNum">      52 </span>            :    * Feed a random seed.</a>
+<a name="53"><span class="lineNum">      53 </span>            :    */</a>
+<a name="54"><span class="lineNum">      54 </span>            :   static void randomize();</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   /**</a>
+<a name="57"><span class="lineNum">      57 </span>            :    * Returns a random double from the Cauchy distribution.</a>
+<a name="58"><span class="lineNum">      58 </span>            :    *</a>
+<a name="59"><span class="lineNum">      59 </span>            :    * @param m mean</a>
+<a name="60"><span class="lineNum">      60 </span>            :    * @param s spread</a>
+<a name="61"><span class="lineNum">      61 </span>            :    */</a>
+<a name="62"><span class="lineNum">      62 </span>            :   static double next_cauchy(double m, double s);</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   /**</a>
+<a name="65"><span class="lineNum">      65 </span>            :    * Returns a random int from the uniform distribution from a [f, e) range.</a>
+<a name="66"><span class="lineNum">      66 </span>            :    *</a>
+<a name="67"><span class="lineNum">      67 </span>            :    * @param f begin</a>
+<a name="68"><span class="lineNum">      68 </span>            :    * @param e end</a>
+<a name="69"><span class="lineNum">      69 </span>            :    */</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static int next_int(int f, int e);</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static int next_int(int e);</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   /**</a>
+<a name="74"><span class="lineNum">      74 </span>            :    * Returns a random double from the uniform distribution from a [f, e) range.</a>
+<a name="75"><span class="lineNum">      75 </span>            :    */</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static double next_double(double f, double e);</a>
+<a name="77"><span class="lineNum">      77 </span>            :   static double next_double(double e);</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static double next_double();</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   /**</a>
+<a name="81"><span class="lineNum">      81 </span>            :    * Returns a random vector&lt;double&gt; from the uniform distribution from a [f, e)</a>
+<a name="82"><span class="lineNum">      82 </span>            :    * range of length n.</a>
+<a name="83"><span class="lineNum">      83 </span>            :    */</a>
+<a name="84"><span class="lineNum">      84 </span>            :   static std::vector&lt;double&gt; next_double(double f, double e, std::size_t n);</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   /**</a>
+<a name="87"><span class="lineNum">      87 </span>            :    * Returns a random PLMD::Vector of length r.</a>
+<a name="88"><span class="lineNum">      88 </span>            :    */</a>
+<a name="89"><span class="lineNum">      89 </span>            :   static Vector next_plmd_vector();</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static Vector next_plmd_vector(double r);</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   /**</a>
+<a name="93"><span class="lineNum">      93 </span>            :    * Returns a random std::vector of length r.</a>
+<a name="94"><span class="lineNum">      94 </span>            :    */</a>
+<a name="95"><span class="lineNum">      95 </span>            :   static std::vector&lt;double&gt; next_std_vector();</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static std::vector&lt;double&gt; next_std_vector(double r);</a>
+<a name="97"><span class="lineNum">      97 </span>            : };</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         66 : inline Vector rnd::next_plmd_vector(double r) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         66 :   return next_plmd_vector() * r;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : inline std::vector&lt;double&gt; rnd::next_std_vector(double r) {</a>
+<a name="104"><span class="lineNum">     104 </span>            :   double t = next_double() * 2.0 * pi;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   double p = next_double() * pi;</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   return std::vector&lt;double&gt; {</a>
+<a name="108"><span class="lineNum">     108 </span>            :     r * std::sin(p) * std::cos(t),</a>
+<a name="109"><span class="lineNum">     109 </span>            :     r * std::sin(t) * std::sin(p),</a>
+<a name="110"><span class="lineNum">     110 </span>            :     r * std::cos(p)</a>
+<a name="111"><span class="lineNum">     111 </span>            :   };</a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 : inline std::vector&lt;double&gt; rnd::next_double(double f, double e, size_t n) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; t(n);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :   for (std::size_t i=0; i &lt; n; ++i) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     t[i] = next_double(f, e);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   return t;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         73 : inline Vector rnd::next_plmd_vector() {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         73 :   double t = next_double() * 2.0 * pi;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         73 :   double p = next_double() * pi;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   return Vector(</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         73 :            std::sin(p) * std::cos(t),</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         73 :            std::sin(t) * std::sin(p),</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :            std::cos(p)</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         73 :          );</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : inline std::vector&lt;double&gt; rnd::next_std_vector() {</a>
+<a name="135"><span class="lineNum">     135 </span>            :   double t = next_double() * 2.0 * pi;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   double p = next_double() * pi;</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   return std::vector&lt;double&gt; {</a>
+<a name="139"><span class="lineNum">     139 </span>            :     std::sin(p) * std::cos(t),</a>
+<a name="140"><span class="lineNum">     140 </span>            :     std::sin(t) * std::sin(p),</a>
+<a name="141"><span class="lineNum">     141 </span>            :     std::cos(p)</a>
+<a name="142"><span class="lineNum">     142 </span>            :   };</a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : inline double rnd::next_double(double e) {</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        246 :   return next_double(0, e);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          7 : inline void rnd::randomize() {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          7 :   mt_eng().seed(time(0));</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          7 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : } // namespace maze</a>
+<a name="154"><span class="lineNum">     154 </span>            : } // namespace PLMD</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : #endif // __PLUMED_maze_Random_MT_h</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_Walk.cpp.func-sort-c.html b/coverage/maze/Random_Walk.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3780d40ef2
--- /dev/null
+++ b/coverage/maze/Random_Walk.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_Walk.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_Walk.cpp<span style="font-size: 80%;"> (<a href="Random_Walk.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Random_Walk.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#103">_ZN4PLMD4maze11Random_WalkC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#103">_ZN4PLMD4maze11Random_WalkC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#95">_ZN4PLMD4maze12_GLOBAL__N_123Random_WalkRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#97">_ZN4PLMD4maze11Random_Walk16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#116">_ZN4PLMD4maze11Random_Walk8optimizeEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#95">_ZN4PLMD4maze12_GLOBAL__N_123Random_WalkRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#95">_ZN4PLMD4maze12_GLOBAL__N_123Random_WalkRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_Walk.cpp.func.html b/coverage/maze/Random_Walk.cpp.func.html
new file mode 100644
index 0000000000..7338dcd347
--- /dev/null
+++ b/coverage/maze/Random_Walk.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_Walk.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_Walk.cpp<span style="font-size: 80%;"> (<a href="Random_Walk.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Random_Walk.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#97">_ZN4PLMD4maze11Random_Walk16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#116">_ZN4PLMD4maze11Random_Walk8optimizeEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#103">_ZN4PLMD4maze11Random_WalkC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#103">_ZN4PLMD4maze11Random_WalkC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#95">_ZN4PLMD4maze12_GLOBAL__N_123Random_WalkRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#95">_ZN4PLMD4maze12_GLOBAL__N_123Random_WalkRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random_Walk.cpp.gcov.html#95">_ZN4PLMD4maze12_GLOBAL__N_123Random_WalkRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Random_Walk.cpp.gcov.html b/coverage/maze/Random_Walk.cpp.gcov.html
new file mode 100644
index 0000000000..7d08da1239
--- /dev/null
+++ b/coverage/maze/Random_Walk.cpp.gcov.html
@@ -0,0 +1,200 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Random_Walk.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Random_Walk.cpp<span style="font-size: 80%;"> (source / <a href="Random_Walk.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Random_Walk.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  */</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace maze {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC MAZE_OPTIMIZER MAZE_RANDOM_WALK</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Fake optimizer that can be used for debugging.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : This is dummy optimizer that can be used for debugging and monitoring</a>
+<a name="41"><span class="lineNum">      41 </span>            : purposes. It returns a random direction of biasing, changed every</a>
+<a name="42"><span class="lineNum">      42 </span>            : OPTIMIZER_STRIDE.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : Performs a random walk within the protein matrix.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : Every optimizer implemented in the maze module needs a loss function as</a>
+<a name="49"><span class="lineNum">      49 </span>            : an argument, and it should be passed using the \ref MAZE_LOSS keyword.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : MAZE_RANDOM_WALK ...</a>
+<a name="53"><span class="lineNum">      53 </span>            :   LABEL=rw</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            :   LOSS=l</a>
+<a name="56"><span class="lineNum">      56 </span>            :   OPTIMIZER_STRIDE=200</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   LIGAND=2635-2646</a>
+<a name="59"><span class="lineNum">      59 </span>            :   PROTEIN=1-2634</a>
+<a name="60"><span class="lineNum">      60 </span>            : ... MAZE_RANDOM_WALK</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : As shown above, each optimizer should be provided with the LIGAND and</a>
+<a name="64"><span class="lineNum">      64 </span>            : the PROTEIN keywords.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : //+ENDPLUMEDOC</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : /**</a>
+<a name="70"><span class="lineNum">      70 </span>            :  * @class Random_Walk Random_Walk.cpp &quot;maze/Random_Walk.cpp&quot;</a>
+<a name="71"><span class="lineNum">      71 </span>            :  *</a>
+<a name="72"><span class="lineNum">      72 </span>            :  * @brief Perform a random walk within the protein matrix.</a>
+<a name="73"><span class="lineNum">      73 </span>            :  */</a>
+<a name="74"><span class="lineNum">      74 </span>            : class Random_Walk: public Optimizer {</a>
+<a name="75"><span class="lineNum">      75 </span>            : public:</a>
+<a name="76"><span class="lineNum">      76 </span>            :   /**</a>
+<a name="77"><span class="lineNum">      77 </span>            :    * PLMD constructor.</a>
+<a name="78"><span class="lineNum">      78 </span>            :    *</a>
+<a name="79"><span class="lineNum">      79 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;</a>
+<a name="80"><span class="lineNum">      80 </span>            :    */</a>
+<a name="81"><span class="lineNum">      81 </span>            :   explicit Random_Walk(const ActionOptions&amp; ao);</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   /**</a>
+<a name="84"><span class="lineNum">      84 </span>            :    * Registers PLMD keywords.</a>
+<a name="85"><span class="lineNum">      85 </span>            :    *</a>
+<a name="86"><span class="lineNum">      86 </span>            :    * @param[in] keys PLMD keywords</a>
+<a name="87"><span class="lineNum">      87 </span>            :    */</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   /**</a>
+<a name="91"><span class="lineNum">      91 </span>            :    * Each class deriving from Optimizer needs to override this function.</a>
+<a name="92"><span class="lineNum">      92 </span>            :    */</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void optimize() override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : // Register MAZE_RANDOM_WALK.</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Random_Walk, &quot;MAZE_RANDOM_WALK&quot;)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          4 : void Random_Walk::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          4 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :   keys.remove(&quot;N_ITER&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 : Random_Walk::Random_Walk(const ActionOptions&amp; ao)</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   : PLUMED_OPT_INIT(ao)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 :   log.printf(&quot;maze&gt; Fake optimizer that returns a next step as random,\</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     can be used to monitor loss, and for debugging and regtests purposes.\n&quot;);</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          4 :   set_label(&quot;RANDOM_WALK&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   start_step_0();</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          2 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 : void Random_Walk::optimize() {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          6 :   set_opt(rnd::next_plmd_vector());</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          6 :   set_opt_value(score());</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : } // namespace maze</a>
+<a name="124"><span class="lineNum">     124 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Simulated_Annealing.cpp.func-sort-c.html b/coverage/maze/Simulated_Annealing.cpp.func-sort-c.html
new file mode 100644
index 0000000000..87b4820aa9
--- /dev/null
+++ b/coverage/maze/Simulated_Annealing.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Simulated_Annealing.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Simulated_Annealing.cpp<span style="font-size: 80%;"> (<a href="Simulated_Annealing.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Simulated_Annealing.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#143">_ZN4PLMD4maze19Simulated_AnnealingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#118">_ZN4PLMD4maze12_GLOBAL__N_132Simulated_AnnealingRegisterMe1206createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
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+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#143">_ZN4PLMD4maze19Simulated_AnnealingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#120">_ZN4PLMD4maze19Simulated_Annealing16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#200">_ZN4PLMD4maze19Simulated_Annealing8optimizeEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#182">_ZN4PLMD4maze19Simulated_Annealing20decrease_probabilityEj</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#118">_ZN4PLMD4maze12_GLOBAL__N_132Simulated_AnnealingRegisterMe120C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#118">_ZN4PLMD4maze12_GLOBAL__N_132Simulated_AnnealingRegisterMe120D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/maze/Simulated_Annealing.cpp.func.html b/coverage/maze/Simulated_Annealing.cpp.func.html
new file mode 100644
index 0000000000..78d6acc3b5
--- /dev/null
+++ b/coverage/maze/Simulated_Annealing.cpp.func.html
@@ -0,0 +1,104 @@
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+  <title>LCOV - plumed test coverage - maze/Simulated_Annealing.cpp - functions</title>
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+
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Simulated_Annealing.cpp<span style="font-size: 80%;"> (<a href="Simulated_Annealing.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#118">_ZN4PLMD4maze12_GLOBAL__N_132Simulated_AnnealingRegisterMe1206createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#118">_ZN4PLMD4maze12_GLOBAL__N_132Simulated_AnnealingRegisterMe120C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#118">_ZN4PLMD4maze12_GLOBAL__N_132Simulated_AnnealingRegisterMe120D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#120">_ZN4PLMD4maze19Simulated_Annealing16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#182">_ZN4PLMD4maze19Simulated_Annealing20decrease_probabilityEj</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#200">_ZN4PLMD4maze19Simulated_Annealing8optimizeEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#143">_ZN4PLMD4maze19Simulated_AnnealingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Simulated_Annealing.cpp.gcov.html#143">_ZN4PLMD4maze19Simulated_AnnealingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/maze/Simulated_Annealing.cpp.gcov.html b/coverage/maze/Simulated_Annealing.cpp.gcov.html
new file mode 100644
index 0000000000..6c1c2eedb7
--- /dev/null
+++ b/coverage/maze/Simulated_Annealing.cpp.gcov.html
@@ -0,0 +1,351 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
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+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Simulated_Annealing.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Simulated_Annealing.cpp<span style="font-size: 80%;"> (source / <a href="Simulated_Annealing.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Simulated_Annealing.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  */</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace maze {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC MAZE_OPTIMIZER MAZE_SIMULATED_ANNEALING</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculates the biasing direction along which the ligand unbinds by minimizing</a>
+<a name="39"><span class="lineNum">      39 </span>            : the \ref MAZE_LOSS function. The optimal biasing direction is determined by</a>
+<a name="40"><span class="lineNum">      40 </span>            : performing simulated annealing.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : Every optimizer implemented in the maze module needs a loss function as an</a>
+<a name="45"><span class="lineNum">      45 </span>            : argument, and it should be passed using the \ref MAZE_LOSS keyword.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : In the following example simulated annealing is launched for 1000 iterations</a>
+<a name="48"><span class="lineNum">      48 </span>            : as the optimizer for the loss function every 200 ps. The geometric cooling</a>
+<a name="49"><span class="lineNum">      49 </span>            : scheme is used.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : UNITS LENGTH=A TIME=ps ENERGY=kcal/mol</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : MAZE_SIMULATED_ANNEALING ...</a>
+<a name="55"><span class="lineNum">      55 </span>            :   LABEL=sa</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            :   LOSS=l</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            :   N_ITER=1000</a>
+<a name="60"><span class="lineNum">      60 </span>            :   OPTIMIZER_STRIDE=200</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            :   PROBABILITY_DECREASER=300</a>
+<a name="63"><span class="lineNum">      63 </span>            :   COOLING=0.95</a>
+<a name="64"><span class="lineNum">      64 </span>            :   COOLING_TYPE=geometric</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            :   LIGAND=2635-2646</a>
+<a name="67"><span class="lineNum">      67 </span>            :   PROTEIN=1-2634</a>
+<a name="68"><span class="lineNum">      68 </span>            : ... MAZE_SIMULATED_ANNEALING</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : As shown above, each optimizer should be provided with the LIGAND and</a>
+<a name="72"><span class="lineNum">      72 </span>            : the PROTEIN keywords.</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : */</a>
+<a name="75"><span class="lineNum">      75 </span>            : //+ENDPLUMEDOC</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : /**</a>
+<a name="78"><span class="lineNum">      78 </span>            :  * @class Simulated_Annealing Simulated_Annealing.cpp &quot;maze/Simulated_Annealing.cpp&quot;</a>
+<a name="79"><span class="lineNum">      79 </span>            :  *</a>
+<a name="80"><span class="lineNum">      80 </span>            :  * @brief Perform simulated annealing to compute an optimal bias direction.</a>
+<a name="81"><span class="lineNum">      81 </span>            :  */</a>
+<a name="82"><span class="lineNum">      82 </span>            : class Simulated_Annealing: public Optimizer {</a>
+<a name="83"><span class="lineNum">      83 </span>            : public:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   /**</a>
+<a name="85"><span class="lineNum">      85 </span>            :    * PLMD constructor.</a>
+<a name="86"><span class="lineNum">      86 </span>            :    *</a>
+<a name="87"><span class="lineNum">      87 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;.</a>
+<a name="88"><span class="lineNum">      88 </span>            :    */</a>
+<a name="89"><span class="lineNum">      89 </span>            :   explicit Simulated_Annealing(const ActionOptions&amp; ao);</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            :   /**</a>
+<a name="92"><span class="lineNum">      92 </span>            :    * Register PLMD keywords.</a>
+<a name="93"><span class="lineNum">      93 </span>            :    *</a>
+<a name="94"><span class="lineNum">      94 </span>            :    * @param[in] keys Keywords.</a>
+<a name="95"><span class="lineNum">      95 </span>            :    */</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   /**</a>
+<a name="99"><span class="lineNum">      99 </span>            :    * Each class deriving from Optimizer needs to override this function.</a>
+<a name="100"><span class="lineNum">     100 </span>            :    */</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void optimize() override;</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            :   /**</a>
+<a name="104"><span class="lineNum">     104 </span>            :    * Reduce the temperature parameter.</a>
+<a name="105"><span class="lineNum">     105 </span>            :    */</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void decrease_probability(unsigned int);</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : private:</a>
+<a name="109"><span class="lineNum">     109 </span>            :   //! Temperature parameter.</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double probability_decreaser_;</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   //! Cooling factor.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double cooling_factor_;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   //! Cooling scheme.</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::string cooling_scheme_;</a>
+<a name="117"><span class="lineNum">     117 </span>            : };</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : // Register MAZE_SIMULATED_ANNEALING.</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Simulated_Annealing, &quot;MAZE_SIMULATED_ANNEALING&quot;)</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 : void Simulated_Annealing::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          3 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     &quot;compulsory&quot;,</a>
+<a name="127"><span class="lineNum">     127 </span>            :     &quot;PROBABILITY_DECREASER&quot;,</a>
+<a name="128"><span class="lineNum">     128 </span>            :     &quot;Temperature-like parameter that is decreased during optimization to modify &quot;</a>
+<a name="129"><span class="lineNum">     129 </span>            :     &quot;the Metropolis-Hastings acceptance probability.&quot;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   );</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     &quot;compulsory&quot;,</a>
+<a name="134"><span class="lineNum">     134 </span>            :     &quot;COOLING&quot;,</a>
+<a name="135"><span class="lineNum">     135 </span>            :     &quot;Reduction factor for PROBABILITY_DECREASER, should be in (0, 1].&quot;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   );</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     &quot;compulsory&quot;,</a>
+<a name="140"><span class="lineNum">     140 </span>            :     &quot;COOLING_SCHEME&quot;,</a>
+<a name="141"><span class="lineNum">     141 </span>            :     &quot;Cooling scheme: geometric.&quot;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   );</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 : Simulated_Annealing::Simulated_Annealing(const ActionOptions&amp; ao)</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   : PLUMED_OPT_INIT(ao)</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : {</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :   log.printf(&quot;maze&gt; Simulated annealing optimizer.\n&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :   if(keywords.exists(&quot;COOLING&quot;)) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          1 :     parse(&quot;COOLING&quot;, cooling_factor_);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :       cooling_factor_ &gt; 0 &amp;&amp; cooling_factor_ &lt;= 1,</a>
+<a name="155"><span class="lineNum">     155 </span>            :       &quot;maze&gt; COOLING should be in (0, 1]; preferably 0.95.\n&quot;</a>
+<a name="156"><span class="lineNum">     156 </span>            :     );</a>
+<a name="157"><span class="lineNum">     157 </span>            :   }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :   if(keywords.exists(&quot;PROBABILITY_DECREASER&quot;)) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :     parse(&quot;PROBABILITY_DECREASER&quot;, probability_decreaser_);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :     plumed_massert(</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :       probability_decreaser_ &gt; 0,</a>
+<a name="164"><span class="lineNum">     164 </span>            :       &quot;maze&gt; PROBABILITY_DECREASER should be explicitly specified and positive.\n&quot;);</a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   if(keywords.exists(&quot;COOLING_SCHEME&quot;)) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :     parse(&quot;COOLING_SCHEME&quot;, cooling_scheme_);</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 :     log.printf(</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :       &quot;maze&gt; COOLING_SCHEME read: %s.\n&quot;,</a>
+<a name="172"><span class="lineNum">     172 </span>            :       cooling_scheme_.c_str()</a>
+<a name="173"><span class="lineNum">     173 </span>            :     );</a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   set_label(&quot;SIMULATED_ANNEALING&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   // Calculate an optimal direction at the beginning of the MD simulation.</a>
+<a name="179"><span class="lineNum">     179 </span>            :   start_step_0();</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          1 : }</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         30 : void Simulated_Annealing::decrease_probability(unsigned int time) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         30 :   if (cooling_scheme_ == &quot;linear&quot;) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     probability_decreaser_ -= time * cooling_factor_;</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         30 :   else if (cooling_scheme_ == &quot;exponential&quot;) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     probability_decreaser_ *= pow(cooling_factor_, time);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         30 :   else if (cooling_scheme_ == &quot;geometric&quot;) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         30 :     probability_decreaser_ *= cooling_factor_;</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   else if (cooling_scheme_ == &quot;logarithmic&quot;) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     probability_decreaser_ = cooling_factor_ / std::log(time + 1);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   else if (cooling_scheme_ == &quot;hoffman&quot;) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :     probability_decreaser_ = (cooling_factor_ - 1) / std::log(time);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         30 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          3 : void Simulated_Annealing::optimize() {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          3 :   sampling_r_ = sampling_radius();</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   double rad_s;</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          3 :   const unsigned nl_size = neighbor_list_-&gt;size();</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          3 :   Vector distance, distance_next;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         33 :   for (unsigned int iter=0; iter &lt; get_n_iterations(); ++iter) {</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     double action = 0;</a>
+<a name="211"><span class="lineNum">     211 </span>            :     double action_next = 0;</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         30 :     rad_s = rnd::next_double(sampling_r_);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         30 :     Vector dev = rnd::next_plmd_vector(rad_s);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         30 :     #pragma omp parallel num_threads(get_n_threads_openmp())</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     {</a>
+<a name="218"><span class="lineNum">     218 </span>            :       #pragma omp for reduction(+:action_next, action)</a>
+<a name="219"><span class="lineNum">     219 </span>            :       for (unsigned int i=0; i &lt; nl_size; i++) {</a>
+<a name="220"><span class="lineNum">     220 </span>            :         unsigned i0 = neighbor_list_-&gt;getClosePair(i).first;</a>
+<a name="221"><span class="lineNum">     221 </span>            :         unsigned i1 = neighbor_list_-&gt;getClosePair(i).second;</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :         if (getAbsoluteIndex(i0) == getAbsoluteIndex(i1)) {</a>
+<a name="224"><span class="lineNum">     224 </span>            :           continue;</a>
+<a name="225"><span class="lineNum">     225 </span>            :         }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            :         if (pbc_) {</a>
+<a name="228"><span class="lineNum">     228 </span>            :           distance = pbcDistance(</a>
+<a name="229"><span class="lineNum">     229 </span>            :                        getPosition(i0) + get_opt(),</a>
+<a name="230"><span class="lineNum">     230 </span>            :                        getPosition(i1)</a>
+<a name="231"><span class="lineNum">     231 </span>            :                      );</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :           distance_next = pbcDistance(</a>
+<a name="234"><span class="lineNum">     234 </span>            :                             getPosition(i0) + dev,</a>
+<a name="235"><span class="lineNum">     235 </span>            :                             getPosition(i1)</a>
+<a name="236"><span class="lineNum">     236 </span>            :                           );</a>
+<a name="237"><span class="lineNum">     237 </span>            :         }</a>
+<a name="238"><span class="lineNum">     238 </span>            :         else {</a>
+<a name="239"><span class="lineNum">     239 </span>            :           distance = delta(</a>
+<a name="240"><span class="lineNum">     240 </span>            :                        getPosition(i0) + get_opt(),</a>
+<a name="241"><span class="lineNum">     241 </span>            :                        getPosition(i1)</a>
+<a name="242"><span class="lineNum">     242 </span>            :                      );</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            :           distance_next = delta(</a>
+<a name="245"><span class="lineNum">     245 </span>            :                             getPosition(i0) + dev,</a>
+<a name="246"><span class="lineNum">     246 </span>            :                             getPosition(i1)</a>
+<a name="247"><span class="lineNum">     247 </span>            :                           );</a>
+<a name="248"><span class="lineNum">     248 </span>            :         }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            :         action += pairing(distance.modulo());</a>
+<a name="251"><span class="lineNum">     251 </span>            :         action_next += pairing(distance_next.modulo());</a>
+<a name="252"><span class="lineNum">     252 </span>            :       }</a>
+<a name="253"><span class="lineNum">     253 </span>            :     }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :     double p = std::min(</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         60 :                  1.0,</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         30 :                  std::exp(-(action_next - action) / probability_decreaser_)</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         30 :                );</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         30 :     double r = rnd::next_double();</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         30 :     if (r &lt; p) {</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :       set_opt(dev);</a>
+<a name="264"><span class="lineNum">     264 </span>            :       set_opt_value(action_next);</a>
+<a name="265"><span class="lineNum">     265 </span>            :     }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         30 :     decrease_probability(iter);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          3 :   Vector s = get_opt() / modulo(get_opt());</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :   set_opt(s);</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          3 : }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : } // namespace maze</a>
+<a name="275"><span class="lineNum">     275 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Steered_MD.cpp.func-sort-c.html b/coverage/maze/Steered_MD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..43eea29da9
--- /dev/null
+++ b/coverage/maze/Steered_MD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Steered_MD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Steered_MD.cpp<span style="font-size: 80%;"> (<a href="Steered_MD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Steered_MD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#123">_ZN4PLMD4maze10Steered_MDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#123">_ZN4PLMD4maze10Steered_MDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#103">_ZN4PLMD4maze12_GLOBAL__N_123Steered_MDRegisterMe1056createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#152">_ZN4PLMD4maze10Steered_MD8optimizeEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#105">_ZN4PLMD4maze10Steered_MD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#103">_ZN4PLMD4maze12_GLOBAL__N_123Steered_MDRegisterMe105C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#103">_ZN4PLMD4maze12_GLOBAL__N_123Steered_MDRegisterMe105D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Steered_MD.cpp.func.html b/coverage/maze/Steered_MD.cpp.func.html
new file mode 100644
index 0000000000..98187d553c
--- /dev/null
+++ b/coverage/maze/Steered_MD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Steered_MD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Steered_MD.cpp<span style="font-size: 80%;"> (<a href="Steered_MD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Steered_MD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#105">_ZN4PLMD4maze10Steered_MD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#152">_ZN4PLMD4maze10Steered_MD8optimizeEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#123">_ZN4PLMD4maze10Steered_MDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#123">_ZN4PLMD4maze10Steered_MDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#103">_ZN4PLMD4maze12_GLOBAL__N_123Steered_MDRegisterMe1056createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#103">_ZN4PLMD4maze12_GLOBAL__N_123Steered_MDRegisterMe105C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Steered_MD.cpp.gcov.html#103">_ZN4PLMD4maze12_GLOBAL__N_123Steered_MDRegisterMe105D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/maze/Steered_MD.cpp.gcov.html b/coverage/maze/Steered_MD.cpp.gcov.html
new file mode 100644
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Steered_MD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Steered_MD.cpp<span style="font-size: 80%;"> (source / <a href="Steered_MD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /**</a>
+<a name="24"><span class="lineNum">      24 </span>            :  * @file Steered_MD.cpp</a>
+<a name="25"><span class="lineNum">      25 </span>            :  *</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @author J. Rydzewski (jr@fizyka.umk.pl)</a>
+<a name="27"><span class="lineNum">      27 </span>            :  */</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace maze {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC MAZE_OPTIMIZER MAZE_STEERED_MD</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Performs a linear unbinding along a predefined biasing direction that</a>
+<a name="39"><span class="lineNum">      39 </span>            : needs to be provided using the PULLING keyword.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : Every optimizer implemented in the maze module needs a loss function as</a>
+<a name="44"><span class="lineNum">      44 </span>            : an argument, and it should be passed using the \ref MAZE_LOSS keyword.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : MAZE_STEERED_MD ...</a>
+<a name="48"><span class="lineNum">      48 </span>            :   LABEL=smd</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            :   LOSS=l</a>
+<a name="51"><span class="lineNum">      51 </span>            :   PULLING=0.3,0.3,0.3</a>
+<a name="52"><span class="lineNum">      52 </span>            :   OPTIMIZER_STRIDE=_</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            :   LIGAND=2635-2646</a>
+<a name="55"><span class="lineNum">      55 </span>            :   PROTEIN=1-2634</a>
+<a name="56"><span class="lineNum">      56 </span>            : ... MAZE_STEERED_MD</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : As shown above, each optimizer should be provided with the LIGAND and</a>
+<a name="60"><span class="lineNum">      60 </span>            : the PROTEIN keywords.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : */</a>
+<a name="63"><span class="lineNum">      63 </span>            : //+ENDPLUMEDOC</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : /**</a>
+<a name="66"><span class="lineNum">      66 </span>            :  * @class Steered_MD Steered_MD.cpp &quot;maze/Steered_MD.cpp&quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :  * @brief Performs steered MD simulation.</a>
+<a name="68"><span class="lineNum">      68 </span>            :  */</a>
+<a name="69"><span class="lineNum">      69 </span>            : class Steered_MD: public Optimizer {</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   /**</a>
+<a name="72"><span class="lineNum">      72 </span>            :    * PLMD constructor.</a>
+<a name="73"><span class="lineNum">      73 </span>            :    *</a>
+<a name="74"><span class="lineNum">      74 </span>            :    * @param[in] ao PLMD::ActionOptions&amp;</a>
+<a name="75"><span class="lineNum">      75 </span>            :    */</a>
+<a name="76"><span class="lineNum">      76 </span>            :   explicit Steered_MD(const ActionOptions&amp; ao);</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   /**</a>
+<a name="79"><span class="lineNum">      79 </span>            :    * Registers PLMD keywords.</a>
+<a name="80"><span class="lineNum">      80 </span>            :    *</a>
+<a name="81"><span class="lineNum">      81 </span>            :    * @param[in] keys PLMD keywords</a>
+<a name="82"><span class="lineNum">      82 </span>            :    */</a>
+<a name="83"><span class="lineNum">      83 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            :   /**</a>
+<a name="86"><span class="lineNum">      86 </span>            :    * Each class deriving from Optimizer needs to override this function.</a>
+<a name="87"><span class="lineNum">      87 </span>            :    */</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void optimize() override;</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : private:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   //! Total distance traveled by the ligand.</a>
+<a name="92"><span class="lineNum">      92 </span>            :   double total_dist_;</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            :   //! Ligand center of mass.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   Vector com_;</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   //! Constant direction of biasing.</a>
+<a name="98"><span class="lineNum">      98 </span>            :   Vector pulling_;</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :   //! PLMD::Value of total distance.</a>
+<a name="101"><span class="lineNum">     101 </span>            :   Value* value_total_dist_;</a>
+<a name="102"><span class="lineNum">     102 </span>            : };</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : // Register MAZE_STEERED_MD.</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Steered_MD, &quot;MAZE_STEERED_MD&quot;)</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          3 : void Steered_MD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :   keys.remove(&quot;N_ITER&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          6 :   keys.add(</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     &quot;compulsory&quot;,</a>
+<a name="114"><span class="lineNum">     114 </span>            :     &quot;PULLING&quot;,</a>
+<a name="115"><span class="lineNum">     115 </span>            :     &quot;Constant biasing direction.&quot;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   );</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 :   keys.addOutputComponent(</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     &quot;tdist&quot;,</a>
+<a name="120"><span class="lineNum">     120 </span>            :     &quot;default&quot;,</a>
+<a name="121"><span class="lineNum">     121 </span>            :     &quot;Total distance traveled by biased atoms.&quot;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   );</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          3 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 : Steered_MD::Steered_MD(const ActionOptions&amp; ao)</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   : PLUMED_OPT_INIT(ao),</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          1 :     total_dist_(0.0)</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          1 :   log.printf(&quot;maze&gt; Steered MD.\n&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :   if (keywords.exists(&quot;PULLING&quot;)) {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     std::vector&lt;double&gt; v;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          1 :     parseVector(&quot;PULLING&quot;, v);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :     pulling_ = tls::vector2Vector(v);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :     log.printf(&quot;maze&gt; PULLING read.\n&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :   set_label(&quot;STEERED_MD&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   set_opt(pulling_);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   set_opt_value(0.0);</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   start_step_stride();</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 :   com_ = center_of_mass();</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 :   addComponent(&quot;tdist&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   componentIsNotPeriodic(&quot;tdist&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          1 :   value_total_dist_ = getPntrToComponent(&quot;tdist&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 : }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          2 : void Steered_MD::optimize() {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   Vector c = center_of_mass();</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :   Vector d;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          2 :   if (pbc_) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :     d = pbcDistance(c, com_);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            :   else {</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     d = delta(c, com_);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   double dist = d.modulo();</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :   total_dist_ += dist;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   set_opt(pulling_);</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :   set_opt_value(score());</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :   com_ = c;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 :   value_total_dist_-&gt;set(total_dist_);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 : }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : } // namespace maze</a>
+<a name="176"><span class="lineNum">     176 </span>            : } // namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Tools.h.func-sort-c.html b/coverage/maze/Tools.h.func-sort-c.html
new file mode 100644
index 0000000000..0d9295d906
--- /dev/null
+++ b/coverage/maze/Tools.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Tools.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Tools.h<span style="font-size: 80%;"> (<a href="Tools.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Tools.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#121">_ZN4PLMD4maze3tls13vector2VectorIdEENS_13VectorGenericILj3EEERKSt6vectorIT_SaIS6_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#157">_ZN4PLMD4maze3tls19get_pointers_labelsIPNS0_9OptimizerEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#157">_ZN4PLMD4maze3tls19get_pointers_labelsIPNS0_4LossEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#128">_ZN4PLMD4maze3tls3sgnIdEEiT_</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Tools.h.func.html b/coverage/maze/Tools.h.func.html
new file mode 100644
index 0000000000..7f5f84a1ee
--- /dev/null
+++ b/coverage/maze/Tools.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Tools.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Tools.h<span style="font-size: 80%;"> (<a href="Tools.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Tools.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#121">_ZN4PLMD4maze3tls13vector2VectorIdEENS_13VectorGenericILj3EEERKSt6vectorIT_SaIS6_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#157">_ZN4PLMD4maze3tls19get_pointers_labelsIPNS0_4LossEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#157">_ZN4PLMD4maze3tls19get_pointers_labelsIPNS0_9OptimizerEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tools.h.gcov.html#128">_ZN4PLMD4maze3tls3sgnIdEEiT_</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/Tools.h.gcov.html b/coverage/maze/Tools.h.gcov.html
new file mode 100644
index 0000000000..bddcdcc2c6
--- /dev/null
+++ b/coverage/maze/Tools.h.gcov.html
@@ -0,0 +1,256 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze/Tools.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">maze</a> - Tools.h<span style="font-size: 80%;"> (source / <a href="Tools.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2019 Jakub Rydzewski (jr@fizyka.umk.pl). All rights reserved.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : See http://www.maze-code.github.io for more information.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            : This file is part of maze.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : maze is free software: you can redistribute it and/or modify it under the</a>
+<a name="9"><span class="lineNum">       9 </span>            : terms of the GNU Lesser General Public License as published by the Free</a>
+<a name="10"><span class="lineNum">      10 </span>            : Software Foundation, either version 3 of the License, or (at your option)</a>
+<a name="11"><span class="lineNum">      11 </span>            : any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : maze is distributed in the hope that it will be useful, but WITHOUT ANY</a>
+<a name="14"><span class="lineNum">      14 </span>            : WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS</a>
+<a name="15"><span class="lineNum">      15 </span>            : FOR A PARTICULAR PURPOSE.</a>
+<a name="16"><span class="lineNum">      16 </span>            : </a>
+<a name="17"><span class="lineNum">      17 </span>            : See the GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            : along with maze. If not, see &lt;https://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_maze_Tools_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_maze_Tools_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /**</a>
+<a name="26"><span class="lineNum">      26 </span>            :  * @file Tools.h</a>
+<a name="27"><span class="lineNum">      27 </span>            :  *</a>
+<a name="28"><span class="lineNum">      28 </span>            :  * @author J. Rydzewski</a>
+<a name="29"><span class="lineNum">      29 </span>            :  */</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;Core.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace maze {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : /**</a>
+<a name="39"><span class="lineNum">      39 </span>            :  * @class tls Tools.h &quot;maze/Tools.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :  *</a>
+<a name="41"><span class="lineNum">      41 </span>            :  * @brief Helper functions.</a>
+<a name="42"><span class="lineNum">      42 </span>            :  */</a>
+<a name="43"><span class="lineNum">      43 </span>            : class tls {</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   template&lt;typename T&gt; static int sgn(T val);</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            :   template&lt;typename T&gt;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   static std::vector&lt;std::string&gt; get_labels_actions(const ActionSet&amp;);</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            :   template&lt;typename T&gt;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   static T get_pointer_label(</a>
+<a name="52"><span class="lineNum">      52 </span>            :     const std::string&amp;,</a>
+<a name="53"><span class="lineNum">      53 </span>            :     const ActionSet&amp;, std::string&amp;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   );</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   template&lt;typename T&gt;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   static std::vector&lt;T&gt; get_pointers_labels(</a>
+<a name="58"><span class="lineNum">      58 </span>            :     const std::vector&lt;std::string&gt;&amp;,</a>
+<a name="59"><span class="lineNum">      59 </span>            :     const ActionSet&amp;, std::string&amp;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   );</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            :   template&lt;typename T&gt;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   static std::vector&lt;T&gt; Vector2vector(const Vector&amp;);</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            :   template&lt;typename T&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static Vector vector2Vector(const std::vector&lt;T&gt;&amp;);</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   template&lt;typename T&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   static T vector_l(const std::vector&lt;T&gt;&amp;);</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            :   template&lt;typename T&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   static std::vector&lt;T&gt; vector_n(const std::vector&lt;T&gt;&amp;);</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   template&lt;typename T&gt;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static T mean(const std::vector&lt;T&gt;&amp;);</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :   template&lt;typename T&gt;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static T std(const std::vector&lt;T&gt;&amp;);</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   struct delete_ptr {</a>
+<a name="81"><span class="lineNum">      81 </span>            :     template&lt;typename T&gt; void operator()(T t) {</a>
+<a name="82"><span class="lineNum">      82 </span>            :       delete t;</a>
+<a name="83"><span class="lineNum">      83 </span>            :     }</a>
+<a name="84"><span class="lineNum">      84 </span>            :   };</a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : template&lt;typename T&gt;</a>
+<a name="88"><span class="lineNum">      88 </span>            : T tls::std(const std::vector&lt;T&gt;&amp; v) {</a>
+<a name="89"><span class="lineNum">      89 </span>            :   T m=mean(v);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   T sq_sum=std::inner_product(v.begin(), v.end(), v.begin(), 0.0);</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   return std::sqrt(sq_sum/v.size()-m*m);</a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : template&lt;typename T&gt;</a>
+<a name="96"><span class="lineNum">      96 </span>            : T tls::mean(const std::vector&lt;T&gt;&amp; v) {</a>
+<a name="97"><span class="lineNum">      97 </span>            :   return std::accumulate(v.begin(), v.end(), 0.0)/v.size();</a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : template&lt;typename T&gt;</a>
+<a name="101"><span class="lineNum">     101 </span>            : T tls::vector_l(const std::vector&lt;T&gt;&amp; v) {</a>
+<a name="102"><span class="lineNum">     102 </span>            :   return std::sqrt(std::inner_product(v.begin(), v.end(), v.begin(), 0.0));</a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : template&lt;typename T&gt;</a>
+<a name="106"><span class="lineNum">     106 </span>            : std::vector&lt;T&gt; tls::vector_n(const std::vector&lt;T&gt;&amp; v) {</a>
+<a name="107"><span class="lineNum">     107 </span>            :   double l=vector_l(v);</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt;double&gt; n;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   for(std::size_t i=0; i&lt;v.size(); ++i)</a>
+<a name="110"><span class="lineNum">     110 </span>            :     n.push_back(v[i]/l);</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   return n;</a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : template&lt;typename T&gt;</a>
+<a name="116"><span class="lineNum">     116 </span>            : std::vector&lt;T&gt; tls::Vector2vector(const Vector&amp; v) {</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;T&gt; t= {v[0], v[1], v[2]};</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   return t;</a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : template&lt;typename T&gt;</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 : Vector tls::vector2Vector(const std::vector&lt;T&gt;&amp; v) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 :   Vector t(v[0], v[1], v[2]);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   return t;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : template&lt;typename T&gt;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         30 : int tls::sgn(T val) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         30 :   return (T(0)&lt;val)-(val&lt;T(0));</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : template&lt;typename T&gt;</a>
+<a name="135"><span class="lineNum">     135 </span>            : std::vector&lt;std::string&gt; tls::get_labels_actions(const ActionSet&amp; actionset) {</a>
+<a name="136"><span class="lineNum">     136 </span>            :   std::vector&lt;std::string&gt; action_str(0);</a>
+<a name="137"><span class="lineNum">     137 </span>            :   std::vector&lt;T&gt; action_pntrs=actionset.select&lt;T&gt;();</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   for(unsigned int i=0; i&lt;action_pntrs.size(); i++)</a>
+<a name="140"><span class="lineNum">     140 </span>            :     action_str.push_back(action_pntrs[i]-&gt;getLabel());</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   return action_str;</a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : template&lt;typename T&gt; T</a>
+<a name="146"><span class="lineNum">     146 </span>            : tls::get_pointer_label(</a>
+<a name="147"><span class="lineNum">     147 </span>            :   const std::string&amp; action_label,</a>
+<a name="148"><span class="lineNum">     148 </span>            :   const ActionSet&amp; actionset,</a>
+<a name="149"><span class="lineNum">     149 </span>            :   std::string&amp; error_msg) {</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   std::vector&lt;std::string&gt; action_labels(1);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   action_labels[0]=action_label;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   std::vector&lt;T&gt; action_pntrs=get_pointers_labels&lt;T&gt;(action_labels, actionset, error_msg);</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   return action_pntrs[0];</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : template&lt;typename T&gt;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          8 : std::vector&lt;T&gt; tls::get_pointers_labels(</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   const std::vector&lt;std::string&gt;&amp; action_labels,</a>
+<a name="161"><span class="lineNum">     161 </span>            :   const ActionSet&amp; actionset,</a>
+<a name="162"><span class="lineNum">     162 </span>            :   std::string&amp; error_msg) {</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          8 :   std::vector&lt;T&gt; action_pntrs(action_labels.size(), NULL);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   error_msg=&quot;&quot;;</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          8 :   std::vector&lt;std::string&gt; missing(0);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         16 :   for(unsigned int i=0; i&lt;action_labels.size(); i++) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :     action_pntrs[i]=actionset.selectWithLabel&lt;T&gt;(action_labels[i]);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          8 :     if(action_pntrs[i]==NULL)</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :       missing.push_back(action_labels[i]);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          8 :   return action_pntrs;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          8 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : } // namespace maze</a>
+<a name="178"><span class="lineNum">     178 </span>            : } // namespace PLMD</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : #endif // __PLUMED_maze_Tools_h</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/index-sort-f.html b/coverage/maze/index-sort-f.html
new file mode 100644
index 0000000000..b864391810
--- /dev/null
+++ b/coverage/maze/index-sort-f.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - maze</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">645</td>
+            <td class="headerCovTableEntry">775</td>
+            <td class="headerCovTableEntryMed">83.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Memetic.h.gcov.html">Memetic.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="55.2%"><img src="../snow.png" width=45 height=10 alt="55.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.2&nbsp;%</td>
+      <td class="coverNumLo">111 / 201</td>
+      <td class="coverPerLo">65.0&nbsp;%</td>
+      <td class="coverNumLo">13 / 20</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Loss.h.gcov.html">Loss.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_MT.h.gcov.html">Random_MT.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.6%"><img src="../snow.png" width=29 height=10 alt="70.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.6&nbsp;%</td>
+      <td class="coverNumLo">12 / 17</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_MT.cpp.gcov.html">Random_MT.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">16 / 20</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_Acceleration_MD.cpp.gcov.html">Random_Acceleration_MD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">40 / 42</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_Walk.cpp.gcov.html">Random_Walk.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Steered_MD.cpp.gcov.html">Steered_MD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 33</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Loss.cpp.gcov.html">Loss.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Memetic.cpp.gcov.html">Memetic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Simulated_Annealing.cpp.gcov.html">Simulated_Annealing.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.0%"><img src="../snow.png" width=12 height=10 alt="88.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">44 / 50</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer_Bias.cpp.gcov.html">Optimizer_Bias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 98</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.cpp.gcov.html">Optimizer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=90 height=10 alt="90.0%"><img src="../snow.png" width=10 height=10 alt="90.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">162 / 180</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.h.gcov.html">Optimizer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Member.h.gcov.html">Member.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tools.h.gcov.html">Tools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/index-sort-l.html b/coverage/maze/index-sort-l.html
new file mode 100644
index 0000000000..351d8e6da8
--- /dev/null
+++ b/coverage/maze/index-sort-l.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - maze</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">645</td>
+            <td class="headerCovTableEntry">775</td>
+            <td class="headerCovTableEntryMed">83.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Loss.h.gcov.html">Loss.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Memetic.h.gcov.html">Memetic.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="55.2%"><img src="../snow.png" width=45 height=10 alt="55.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.2&nbsp;%</td>
+      <td class="coverNumLo">111 / 201</td>
+      <td class="coverPerLo">65.0&nbsp;%</td>
+      <td class="coverNumLo">13 / 20</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_MT.h.gcov.html">Random_MT.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.6%"><img src="../snow.png" width=29 height=10 alt="70.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.6&nbsp;%</td>
+      <td class="coverNumLo">12 / 17</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_MT.cpp.gcov.html">Random_MT.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">16 / 20</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Simulated_Annealing.cpp.gcov.html">Simulated_Annealing.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.0%"><img src="../snow.png" width=12 height=10 alt="88.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">44 / 50</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.cpp.gcov.html">Optimizer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=90 height=10 alt="90.0%"><img src="../snow.png" width=10 height=10 alt="90.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">162 / 180</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tools.h.gcov.html">Tools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_Acceleration_MD.cpp.gcov.html">Random_Acceleration_MD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">40 / 42</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Steered_MD.cpp.gcov.html">Steered_MD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 33</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer_Bias.cpp.gcov.html">Optimizer_Bias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 98</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Member.h.gcov.html">Member.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.h.gcov.html">Optimizer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_Walk.cpp.gcov.html">Random_Walk.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Loss.cpp.gcov.html">Loss.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Memetic.cpp.gcov.html">Memetic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/maze/index.html b/coverage/maze/index.html
new file mode 100644
index 0000000000..dbe08449e8
--- /dev/null
+++ b/coverage/maze/index.html
@@ -0,0 +1,233 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - maze</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - maze</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">645</td>
+            <td class="headerCovTableEntry">775</td>
+            <td class="headerCovTableEntryMed">83.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Loss.cpp.gcov.html">Loss.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Loss.h.gcov.html">Loss.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Member.h.gcov.html">Member.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Memetic.cpp.gcov.html">Memetic.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">61 / 61</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Memetic.h.gcov.html">Memetic.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="55.2%"><img src="../snow.png" width=45 height=10 alt="55.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.2&nbsp;%</td>
+      <td class="coverNumLo">111 / 201</td>
+      <td class="coverPerLo">65.0&nbsp;%</td>
+      <td class="coverNumLo">13 / 20</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.cpp.gcov.html">Optimizer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=90 height=10 alt="90.0%"><img src="../snow.png" width=10 height=10 alt="90.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">162 / 180</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.h.gcov.html">Optimizer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer_Bias.cpp.gcov.html">Optimizer_Bias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 98</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_Acceleration_MD.cpp.gcov.html">Random_Acceleration_MD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">40 / 42</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_MT.cpp.gcov.html">Random_MT.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">16 / 20</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_MT.h.gcov.html">Random_MT.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.6%"><img src="../snow.png" width=29 height=10 alt="70.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.6&nbsp;%</td>
+      <td class="coverNumLo">12 / 17</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random_Walk.cpp.gcov.html">Random_Walk.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Simulated_Annealing.cpp.gcov.html">Simulated_Annealing.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.0%"><img src="../snow.png" width=12 height=10 alt="88.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">44 / 50</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Steered_MD.cpp.gcov.html">Steered_MD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 33</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tools.h.gcov.html">Tools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/FusionPoreExpansionP.cpp.func-sort-c.html b/coverage/membranefusion/FusionPoreExpansionP.cpp.func-sort-c.html
new file mode 100644
index 0000000000..386a1c3c75
--- /dev/null
+++ b/coverage/membranefusion/FusionPoreExpansionP.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion/FusionPoreExpansionP.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - FusionPoreExpansionP.cpp<span style="font-size: 80%;"> (<a href="FusionPoreExpansionP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntry">158</td>
+            <td class="headerCovTableEntryMed">87.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FusionPoreExpansionP.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion20fusionPoreExpansionPC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#83">_ZN4PLMD14membranefusion12_GLOBAL__N_132fusionPoreExpansionPRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion20fusionPoreExpansionPC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#85">_ZN4PLMD14membranefusion20fusionPoreExpansionP16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#209">_ZN4PLMD14membranefusion20fusionPoreExpansionP9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#83">_ZN4PLMD14membranefusion12_GLOBAL__N_132fusionPoreExpansionPRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#83">_ZN4PLMD14membranefusion12_GLOBAL__N_132fusionPoreExpansionPRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/FusionPoreExpansionP.cpp.func.html b/coverage/membranefusion/FusionPoreExpansionP.cpp.func.html
new file mode 100644
index 0000000000..cfc2fc6b6d
--- /dev/null
+++ b/coverage/membranefusion/FusionPoreExpansionP.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion/FusionPoreExpansionP.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - FusionPoreExpansionP.cpp<span style="font-size: 80%;"> (<a href="FusionPoreExpansionP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntry">158</td>
+            <td class="headerCovTableEntryMed">87.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FusionPoreExpansionP.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#83">_ZN4PLMD14membranefusion12_GLOBAL__N_132fusionPoreExpansionPRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#83">_ZN4PLMD14membranefusion12_GLOBAL__N_132fusionPoreExpansionPRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#83">_ZN4PLMD14membranefusion12_GLOBAL__N_132fusionPoreExpansionPRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#85">_ZN4PLMD14membranefusion20fusionPoreExpansionP16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#209">_ZN4PLMD14membranefusion20fusionPoreExpansionP9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion20fusionPoreExpansionPC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreExpansionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion20fusionPoreExpansionPC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/FusionPoreExpansionP.cpp.gcov.html b/coverage/membranefusion/FusionPoreExpansionP.cpp.gcov.html
new file mode 100644
index 0000000000..fbba739b69
--- /dev/null
+++ b/coverage/membranefusion/FusionPoreExpansionP.cpp.gcov.html
@@ -0,0 +1,681 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion/FusionPoreExpansionP.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - FusionPoreExpansionP.cpp<span style="font-size: 80%;"> (source / <a href="FusionPoreExpansionP.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntry">158</td>
+            <td class="headerCovTableEntryMed">87.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2022.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : CVs originally developed by the Jochen Hub group from the University of Saarland (Germany)</a>
+<a name="5"><span class="lineNum">       5 </span>            : and adapted and implemented in PLUMED by Ary Lautaro Di Bartolo and Diego Masone from the</a>
+<a name="6"><span class="lineNum">       6 </span>            : National University of Cuyo (Argentina).</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : The membranefusion module is free software: you can redistribute it and/or modify</a>
+<a name="9"><span class="lineNum">       9 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="10"><span class="lineNum">      10 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="11"><span class="lineNum">      11 </span>            : (at your option) any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : The membranefusion module is distributed in the hope that it will be useful,</a>
+<a name="14"><span class="lineNum">      14 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="15"><span class="lineNum">      15 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="16"><span class="lineNum">      16 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="17"><span class="lineNum">      17 </span>            : </a>
+<a name="18"><span class="lineNum">      18 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="19"><span class="lineNum">      19 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="20"><span class="lineNum">      20 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;cmath&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #ifdef _OPENMP</a>
+<a name="25"><span class="lineNum">      25 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;omp.h&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #endif</a>
+<a name="28"><span class="lineNum">      28 </span>            : #endif</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD</a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace membranefusion</a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MEMBRANEFUSIONMOD_COLVAR FUSIONPOREEXPANSIONP</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : A CV for inducing the expansion of a fusion pore from a nucleated fusion pore.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculate the collective variable designed by Hub \cite Hub2021  and implemented into PLUMED by Masone and collaborators.</a>
+<a name="39"><span class="lineNum">      39 </span>            : This CV is capable of inducing the expansion of the fusion pore from a nucleated fusion pore.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : \xi_e = \frac{R(r) - R_0}{R_0}</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Where \f$\xi_e\f$ is the CV, \f$R_0\f$ is a normalization constant that makes zero the initial value of \f$\xi_e\f$, and</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f$R(r)\f$ is the approximate radius of the fusion pore, which is defined by the number of waters and phosphateoxygens</a>
+<a name="47"><span class="lineNum">      47 </span>            : beads within a horizontal layer in the center of both membranes.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : This example induces the expansion of a nucleated fusion pore (\f$\xi_e = 0.75\f$) from a just nucleated fusion pore (\f$\xi_e = 0.00\f$).</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : lMem: GROUP ATOMS=1-10752,21505-22728,23953-24420 #All the lower membrane beads.</a>
+<a name="55"><span class="lineNum">      55 </span>            : uMem: GROUP ATOMS=10753-21504,22729-23952,24421-24888 #All the upper membrane beads.</a>
+<a name="56"><span class="lineNum">      56 </span>            : tails: GROUP ATOMS=8-23948:12,12-23952:12,23966-24884:18,23970-24888:18 #All the lipid tails beads (from the lower and upper membrane).</a>
+<a name="57"><span class="lineNum">      57 </span>            : waters: GROUP ATOMS=24889-56589  #All the water beads.</a>
+<a name="58"><span class="lineNum">      58 </span>            : po4: GROUP ATOMS=2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : fusionPoreExpansion: FUSIONPOREEXPANSIONP UMEMBRANE=uMem LMEMBRANE=lMem TAILS=tails WATERS=waters PHOSPHATEOXYGENS=po4 NSMEM=85 D=7.0 R0=0.57</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : MOVINGRESTRAINT ...</a>
+<a name="63"><span class="lineNum">      63 </span>            :     ARG=fusionPoreExpansion</a>
+<a name="64"><span class="lineNum">      64 </span>            :     STEP0=0 AT0=0.0 KAPPA0=10000.0</a>
+<a name="65"><span class="lineNum">      65 </span>            :     STEP1=500000 AT1=0.75 KAPPA1=10000.0</a>
+<a name="66"><span class="lineNum">      66 </span>            : ...</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : PRINT ARG=fusionPoreExpansion FILE=COLVAR STRIDE=1</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : class fusionPoreExpansionP : public Colvar</a>
+<a name="75"><span class="lineNum">      75 </span>            : {</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::vector&lt;AtomNumber&gt; UMEM, LMEM, TAILS, WATERS, POXYGENS;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;double&gt; NSMEM, DSMEM, HMEM, VO, D, H, RMAX, R0, XCYL, YCYL;</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : public:</a>
+<a name="80"><span class="lineNum">      80 </span>            :   explicit fusionPoreExpansionP(const ActionOptions &amp;);</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void calculate() override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   static void registerKeywords(Keywords &amp;keys);</a>
+<a name="83"><span class="lineNum">      83 </span>            : };</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(fusionPoreExpansionP, &quot;FUSIONPOREEXPANSIONP&quot;)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 : void fusionPoreExpansionP::registerKeywords(Keywords &amp;keys)</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          3 :   Colvar::registerKeywords(keys);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;UMEMBRANE&quot;, &quot;all the beads of the upper membrane.&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;LMEMBRANE&quot;, &quot;all the beads of the lower membrane.&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;TAILS&quot;, &quot;all the tail beads of the system.&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;WATERS&quot;, &quot;all the water beads of the system.&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;PHOSPHATEOXYGENS&quot;, &quot;all the lipid phosphateoxygens beads of the system.&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;NSMEM&quot;, &quot;the number of slices of the membrane fusion cylinder.&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;DSMEM&quot;, &quot;( default=0.1 ) thickness of the slices of the membrane fusion cylinder.&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;HMEM&quot;, &quot;( default=0.25 ) parameter of the step function θ(x,h) for the membrane fusion.&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;VO&quot;, &quot;( default=0.076879 ) beads' molecular volume.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;D&quot;, &quot;horizontal layer thickness, it depends on the Z separation of the membranes.&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;H&quot;, &quot;( default=0.1 ) parameter of the step function θ(x,h) for the fusion pore expansion.&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;RMAX&quot;, &quot;( default=2.5 ) to avoid effects of membrane undulations in large membranes (more than 256 lipids).&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;R0&quot;, &quot;normalization constant that makes 0 the initial value of the CV.&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;XCYL&quot;, &quot;X coordinate of the fixed cylinder, if not present this will be calculated.&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;YCYL&quot;, &quot;X coordinate of the fixed cylinder, if not present this will be calculated.&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          3 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 : fusionPoreExpansionP::fusionPoreExpansionP(const ActionOptions &amp;ao) : PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   parseAtomList(&quot;UMEMBRANE&quot;, UMEM);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :   if (UMEM.size() == 0)</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     error(&quot;UMEMBRANE has not any atom specified.&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   parseAtomList(&quot;LMEMBRANE&quot;, LMEM);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   if (LMEM.size() == 0)</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     error(&quot;LMEMBRANE has not any atom specified.&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   parseAtomList(&quot;TAILS&quot;, TAILS);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   if (TAILS.size() == 0)</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     error(&quot;TAILS has not any atom specified.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   parseAtomList(&quot;WATERS&quot;, WATERS);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 :   if (WATERS.size() == 0)</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     error(&quot;WATERS has not any atom specified.&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   parseAtomList(&quot;PHOSPHATEOXYGENS&quot;, POXYGENS);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   if (POXYGENS.size() == 0)</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     error(&quot;PHOSPHATEOXYGENS has not any atom specified.&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :   parseVector(&quot;NSMEM&quot;, NSMEM);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   if (NSMEM.size() &gt; 1)</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     error(&quot;NSMEM cannot take more than one value.&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   parseVector(&quot;DSMEM&quot;, DSMEM);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   if (DSMEM.size() &gt; 1)</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     error(&quot;DSMEM cannot take more than one value.&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   if (DSMEM.size() == 0)</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     DSMEM.push_back(0.1);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :   parseVector(&quot;HMEM&quot;, HMEM);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :   if (HMEM.size() &gt; 1)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     error(&quot;HMEM cannot take more than one value.&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          1 :   if (HMEM.size() == 0)</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     HMEM.push_back(0.25);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :   parseVector(&quot;VO&quot;, VO);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   if (VO.size() &gt; 1)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     error(&quot;VO cannot take more than one value.&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :   if (VO.size() == 0)</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     VO.push_back(0.076879);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          2 :   parseVector(&quot;D&quot;, D);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :   if (D.size() &gt; 1)</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :     error(&quot;D cannot take more than one value.&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   parseVector(&quot;H&quot;, H);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   if (H.size() &gt; 1)</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     error(&quot;H cannot take more than one value.&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :   if (H.size() == 0)</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     H.push_back(0.1);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :   parseVector(&quot;RMAX&quot;, RMAX);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   if (RMAX.size() &gt; 1)</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     error(&quot;RMAX cannot take more than one value.&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   if (RMAX.size() == 0)</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     RMAX.push_back(2.5);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   parseVector(&quot;R0&quot;, R0);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :   if (R0.size() &gt; 1)</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     error(&quot;R0 cannot take more than one value.&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :   parseVector(&quot;XCYL&quot;, XCYL);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :   if (XCYL.size() &gt; 1)</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     error(&quot;XCYL cannot take more than one value.&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :   if (XCYL.size() == 0)</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 :     XCYL.push_back(-1.0);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   parseVector(&quot;YCYL&quot;, YCYL);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :   if (YCYL.size() &gt; 1)</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     error(&quot;YCYL cannot take more than one value.&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :   if (YCYL.size() == 0)</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          1 :     YCYL.push_back(-1.0);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">      12445 :   for (unsigned i = 0; i &lt; UMEM.size(); i++)</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      12444 :     atoms.push_back(UMEM[i]);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      12445 :   for (unsigned i = 0; i &lt; LMEM.size(); i++)</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   {</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      12444 :     atoms.push_back(LMEM[i]);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       4097 :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       4096 :     atoms.push_back(TAILS[i]);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      31800 :   for (unsigned i = 0; i &lt; WATERS.size(); i++)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      31799 :     atoms.push_back(WATERS[i]);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       2049 :   for (unsigned i = 0; i &lt; POXYGENS.size(); i++)</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       2048 :     atoms.push_back(POXYGENS[i]);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          1 :   addValueWithDerivatives();</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          1 :   setNotPeriodic();</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          1 :   requestAtoms(atoms);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          1 : }</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          4 : void fusionPoreExpansionP::calculate()</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : {</a>
+<a name="213"><span class="lineNum">     213 </span>            :   /*************************</a>
+<a name="214"><span class="lineNum">     214 </span>            :   *                        *</a>
+<a name="215"><span class="lineNum">     215 </span>            :   *         System         *</a>
+<a name="216"><span class="lineNum">     216 </span>            :   *                        *</a>
+<a name="217"><span class="lineNum">     217 </span>            :   **************************/</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :   // Box dimensions.</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          4 :   double Lx = getBox()[0][0], Ly = getBox()[1][1], Lz = getBox()[2][2];</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   // Z center of the upper membrane (uMem) and lower membrane (lMem) for systems with PBC: https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions .</a>
+<a name="223"><span class="lineNum">     223 </span>            :   double ZuMem, ZuMemcos = 0.0, ZuMemsin = 0.0, uMemAngle, ZlMem, ZlMemcos = 0.0, ZlMemsin = 0.0, lMemAngle;</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : #ifdef _OPENMP</a>
+<a name="226"><span class="lineNum">     226 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          4 :   #pragma omp parallel for private(uMemAngle, lMemAngle) reduction(+:ZuMemcos, ZuMemsin, ZlMemcos, ZlMemsin)</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : #endif</a>
+<a name="229"><span class="lineNum">     229 </span>            : #endif</a>
+<a name="230"><span class="lineNum">     230 </span>            :   for (unsigned i = 0; i &lt; UMEM.size(); i++)</a>
+<a name="231"><span class="lineNum">     231 </span>            :   {</a>
+<a name="232"><span class="lineNum">     232 </span>            :     uMemAngle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i)))[2];</a>
+<a name="233"><span class="lineNum">     233 </span>            :     lMemAngle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + UMEM.size())))[2];</a>
+<a name="234"><span class="lineNum">     234 </span>            :     ZuMemcos += cos(uMemAngle);</a>
+<a name="235"><span class="lineNum">     235 </span>            :     ZuMemsin += sin(uMemAngle);</a>
+<a name="236"><span class="lineNum">     236 </span>            :     ZlMemcos += cos(lMemAngle);</a>
+<a name="237"><span class="lineNum">     237 </span>            :     ZlMemsin += sin(lMemAngle);</a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          4 :   ZuMemcos = ZuMemcos / UMEM.size();</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          4 :   ZuMemsin = ZuMemsin / UMEM.size();</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          4 :   ZuMem = Lz * (atan2(-ZuMemsin, -ZuMemcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          4 :   ZlMemcos = ZlMemcos / UMEM.size();</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          4 :   ZlMemsin = ZlMemsin / UMEM.size();</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          4 :   ZlMem = Lz * (atan2(-ZlMemsin, -ZlMemcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :   // Z center of the boths membranes (upper and lower).</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          4 :   double ZMems = (ZuMem + ZlMem) / 2.0;</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   /**************************</a>
+<a name="250"><span class="lineNum">     250 </span>            :   *                         *</a>
+<a name="251"><span class="lineNum">     251 </span>            :   *   Xcyl_Mem &amp; Ycyl_Mem   *</a>
+<a name="252"><span class="lineNum">     252 </span>            :   *                         *</a>
+<a name="253"><span class="lineNum">     253 </span>            :   ***************************/</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   // Quantity of beads of the membranes.</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          4 :   unsigned membraneBeads = UMEM.size() + LMEM.size();</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // Z distance from the lipid tail to the geometric center of both membranes.</a>
+<a name="259"><span class="lineNum">     259 </span>            :   double ZTailDistance;</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   // Z position of the first slice.</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          4 :   double firstSliceZ_Mem = ZMems + (0.0 + 0.5 - NSMEM[0] / 2.0) * DSMEM[0];</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   // Z distance between the first slice and the Z center of the membrane.</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          4 :   double firstSliceZDist_Mem = pbcDistance(Vector(0.0, 0.0, firstSliceZ_Mem), Vector(0.0, 0.0, ZMems))[2];</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            :   // Position in the cylinder.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   double PositionS_Mem;</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   // Slices to analyze per particle.</a>
+<a name="271"><span class="lineNum">     271 </span>            :   unsigned s1_Mem, s2_Mem;</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   // Eq. 7 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; faxial_Mem(TAILS.size() * NSMEM[0]);</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; Fs_Mem(NSMEM[0]);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :   // Eq. 11 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; ws_Mem(NSMEM[0]);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="283"><span class="lineNum">     283 </span>            :   double W_Mem = 0.0;</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            :   // Eq. 21 and 22 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; sx_Mem(NSMEM[0]), sy_Mem(NSMEM[0]), cx_Mem(NSMEM[0]), cy_Mem(NSMEM[0]);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="289"><span class="lineNum">     289 </span>            :   double Xsc_Mem = 0.0, Xcc_Mem = 0.0, Ysc_Mem = 0.0, Ycc_Mem = 0.0;</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :   // Aux.</a>
+<a name="292"><span class="lineNum">     292 </span>            :   double x, aux;</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            :   // Scaled position of the lipid tail respect the origin of coordinates.</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          4 :   Vector TailPosition;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : #ifdef _OPENMP</a>
+<a name="298"><span class="lineNum">     298 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="299"><span class="lineNum">     299 </span>            :   #pragma omp declare reduction(vec_double_plus : std::vector&lt;double&gt; : \</a>
+<a name="300"><span class="lineNum">     300 </span>            :   std::transform(omp_out.begin(), omp_out.end(), omp_in.begin(), omp_out.begin(), std::plus&lt;double&gt;())) \</a>
+<a name="301"><span class="lineNum">     301 </span>            :   initializer(omp_priv = decltype(omp_orig)(omp_orig.size()))</a>
+<a name="302"><span class="lineNum">     302 </span>            : #endif</a>
+<a name="303"><span class="lineNum">     303 </span>            : #endif</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span>            : #ifdef _OPENMP</a>
+<a name="306"><span class="lineNum">     306 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          4 :   #pragma omp parallel for private(ZTailDistance, PositionS_Mem, TailPosition, x, aux, s1_Mem, s2_Mem) reduction(vec_double_plus:Fs_Mem, sx_Mem, sy_Mem, cx_Mem, cy_Mem)</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : #endif</a>
+<a name="309"><span class="lineNum">     309 </span>            : #endif</a>
+<a name="310"><span class="lineNum">     310 </span>            :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</a>
+<a name="311"><span class="lineNum">     311 </span>            :   {</a>
+<a name="312"><span class="lineNum">     312 </span>            :     ZTailDistance = pbcDistance(Vector(0.0, 0.0, ZMems), getPosition(i + membraneBeads))[2];</a>
+<a name="313"><span class="lineNum">     313 </span>            :     PositionS_Mem = (ZTailDistance + firstSliceZDist_Mem) / DSMEM[0];</a>
+<a name="314"><span class="lineNum">     314 </span>            :     // If the following condition is met the particle is in the Z space of the cylinder.</a>
+<a name="315"><span class="lineNum">     315 </span>            :     if ((PositionS_Mem &gt;= (-0.5 - HMEM[0])) &amp;&amp; (PositionS_Mem &lt;= (NSMEM[0] + 0.5 - 1.0 + HMEM[0])))</a>
+<a name="316"><span class="lineNum">     316 </span>            :     {</a>
+<a name="317"><span class="lineNum">     317 </span>            :       //Defining the slices to analyze each particle.</a>
+<a name="318"><span class="lineNum">     318 </span>            :       if (PositionS_Mem &lt; 1)</a>
+<a name="319"><span class="lineNum">     319 </span>            :       {</a>
+<a name="320"><span class="lineNum">     320 </span>            :         s1_Mem = 0;</a>
+<a name="321"><span class="lineNum">     321 </span>            :         s2_Mem = 2;</a>
+<a name="322"><span class="lineNum">     322 </span>            :       }</a>
+<a name="323"><span class="lineNum">     323 </span>            :       else if (PositionS_Mem &lt;= (NSMEM[0] - 2.0))</a>
+<a name="324"><span class="lineNum">     324 </span>            :       {</a>
+<a name="325"><span class="lineNum">     325 </span>            :         s1_Mem = floor(PositionS_Mem) - 1;</a>
+<a name="326"><span class="lineNum">     326 </span>            :         s2_Mem = floor(PositionS_Mem) + 1;</a>
+<a name="327"><span class="lineNum">     327 </span>            :       }</a>
+<a name="328"><span class="lineNum">     328 </span>            :       else</a>
+<a name="329"><span class="lineNum">     329 </span>            :       {</a>
+<a name="330"><span class="lineNum">     330 </span>            :         s1_Mem = NSMEM[0] - 3;</a>
+<a name="331"><span class="lineNum">     331 </span>            :         s2_Mem = NSMEM[0] - 1;</a>
+<a name="332"><span class="lineNum">     332 </span>            :       }</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            :       TailPosition = getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + membraneBeads)));</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            :       for (unsigned s = s1_Mem; s &lt;= s2_Mem; s++)</a>
+<a name="337"><span class="lineNum">     337 </span>            :       {</a>
+<a name="338"><span class="lineNum">     338 </span>            :         x = (ZTailDistance - (s + 0.5 - NSMEM[0] / 2.0) * DSMEM[0]) * 2.0 / DSMEM[0];</a>
+<a name="339"><span class="lineNum">     339 </span>            :         if (!((x &lt;= -1.0 - HMEM[0]) || (x &gt;= 1.0 + HMEM[0])))</a>
+<a name="340"><span class="lineNum">     340 </span>            :         {</a>
+<a name="341"><span class="lineNum">     341 </span>            :           if (((-1.0 + HMEM[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - HMEM[0])))</a>
+<a name="342"><span class="lineNum">     342 </span>            :           {</a>
+<a name="343"><span class="lineNum">     343 </span>            :             faxial_Mem[i + TAILS.size() * s] = 1.0;</a>
+<a name="344"><span class="lineNum">     344 </span>            :             Fs_Mem[s] += 1.0;</a>
+<a name="345"><span class="lineNum">     345 </span>            :             sx_Mem[s] += sin(2.0 * M_PI * TailPosition[0]);</a>
+<a name="346"><span class="lineNum">     346 </span>            :             sy_Mem[s] += sin(2.0 * M_PI * TailPosition[1]);</a>
+<a name="347"><span class="lineNum">     347 </span>            :             cx_Mem[s] += cos(2.0 * M_PI * TailPosition[0]);</a>
+<a name="348"><span class="lineNum">     348 </span>            :             cy_Mem[s] += cos(2.0 * M_PI * TailPosition[1]);</a>
+<a name="349"><span class="lineNum">     349 </span>            :           }</a>
+<a name="350"><span class="lineNum">     350 </span>            :           else if (((1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + HMEM[0])))</a>
+<a name="351"><span class="lineNum">     351 </span>            :           {</a>
+<a name="352"><span class="lineNum">     352 </span>            :             aux = 0.5 - ((3.0 * x - 3.0) / (4.0 * HMEM[0])) + (pow((x - 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="353"><span class="lineNum">     353 </span>            :             faxial_Mem[i + TAILS.size() * s] = aux;</a>
+<a name="354"><span class="lineNum">     354 </span>            :             Fs_Mem[s] += aux;</a>
+<a name="355"><span class="lineNum">     355 </span>            :             sx_Mem[s] += aux * sin(2.0 * M_PI * TailPosition[0]);</a>
+<a name="356"><span class="lineNum">     356 </span>            :             sy_Mem[s] += aux * sin(2.0 * M_PI * TailPosition[1]);</a>
+<a name="357"><span class="lineNum">     357 </span>            :             cx_Mem[s] += aux * cos(2.0 * M_PI * TailPosition[0]);</a>
+<a name="358"><span class="lineNum">     358 </span>            :             cy_Mem[s] += aux * cos(2.0 * M_PI * TailPosition[1]);</a>
+<a name="359"><span class="lineNum">     359 </span>            :           }</a>
+<a name="360"><span class="lineNum">     360 </span>            :           else if (((-1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + HMEM[0])))</a>
+<a name="361"><span class="lineNum">     361 </span>            :           {</a>
+<a name="362"><span class="lineNum">     362 </span>            :             aux = 0.5 + ((3.0 * x + 3.0) / (4.0 * HMEM[0])) - (pow((x + 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="363"><span class="lineNum">     363 </span>            :             faxial_Mem[i + TAILS.size() * s] = aux;</a>
+<a name="364"><span class="lineNum">     364 </span>            :             Fs_Mem[s] += aux;</a>
+<a name="365"><span class="lineNum">     365 </span>            :             sx_Mem[s] += (aux * sin(2.0 * M_PI * TailPosition[0]));</a>
+<a name="366"><span class="lineNum">     366 </span>            :             sy_Mem[s] += (aux * sin(2.0 * M_PI * TailPosition[1]));</a>
+<a name="367"><span class="lineNum">     367 </span>            :             cx_Mem[s] += (aux * cos(2.0 * M_PI * TailPosition[0]));</a>
+<a name="368"><span class="lineNum">     368 </span>            :             cy_Mem[s] += (aux * cos(2.0 * M_PI * TailPosition[1]));</a>
+<a name="369"><span class="lineNum">     369 </span>            :           }</a>
+<a name="370"><span class="lineNum">     370 </span>            :         }</a>
+<a name="371"><span class="lineNum">     371 </span>            :       }</a>
+<a name="372"><span class="lineNum">     372 </span>            :     }</a>
+<a name="373"><span class="lineNum">     373 </span>            :   }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        344 :   for (unsigned s = 0; s &lt; NSMEM[0]; s++)</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   {</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        340 :     if (Fs_Mem[s] != 0.0)</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :     {</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        340 :       ws_Mem[s] = tanh(Fs_Mem[s]);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        340 :       W_Mem += ws_Mem[s];</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        340 :       sx_Mem[s] = sx_Mem[s] / Fs_Mem[s];</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        340 :       sy_Mem[s] = sy_Mem[s] / Fs_Mem[s];</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        340 :       cx_Mem[s] = cx_Mem[s] / Fs_Mem[s];</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        340 :       cy_Mem[s] = cy_Mem[s] / Fs_Mem[s];</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        340 :       Xsc_Mem += sx_Mem[s] * ws_Mem[s];</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        340 :       Ysc_Mem += sy_Mem[s] * ws_Mem[s];</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        340 :       Xcc_Mem += cx_Mem[s] * ws_Mem[s];</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        340 :       Ycc_Mem += cy_Mem[s] * ws_Mem[s];</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :     }</a>
+<a name="390"><span class="lineNum">     390 </span>            :   }</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          4 :   Xsc_Mem = Xsc_Mem / W_Mem;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          4 :   Ysc_Mem = Ysc_Mem / W_Mem;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          4 :   Xcc_Mem = Xcc_Mem / W_Mem;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          4 :   Ycc_Mem = Ycc_Mem / W_Mem;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span>            :   // Eq. 12 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="398"><span class="lineNum">     398 </span>            :   double Xcyl_Mem, Ycyl_Mem;</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          4 :   if ((XCYL[0] &gt; 0.0) &amp;&amp; (YCYL[0] &gt; 0.0))</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   {</a>
+<a name="402"><span class="lineNum">     402 </span>            :     Xcyl_Mem = XCYL[0];</a>
+<a name="403"><span class="lineNum">     403 </span>            :     Ycyl_Mem = YCYL[0];</a>
+<a name="404"><span class="lineNum">     404 </span>            :   }</a>
+<a name="405"><span class="lineNum">     405 </span>            :   else</a>
+<a name="406"><span class="lineNum">     406 </span>            :   {</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          4 :     Xcyl_Mem = (atan2(-Xsc_Mem, -Xcc_Mem) + M_PI) * Lx / (2 * M_PI);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          4 :     Ycyl_Mem = (atan2(-Ysc_Mem, -Ycc_Mem) + M_PI) * Ly / (2 * M_PI);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :   }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            :   /*************************</a>
+<a name="412"><span class="lineNum">     412 </span>            :   *                        *</a>
+<a name="413"><span class="lineNum">     413 </span>            :   *         Xi_Exp         *</a>
+<a name="414"><span class="lineNum">     414 </span>            :   *                        *</a>
+<a name="415"><span class="lineNum">     415 </span>            :   **************************/</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   // Quantity of beads that could participate in the calculation of the Xi_Chain</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          4 :   unsigned chainBeads = WATERS.size() + POXYGENS.size();</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            :   // Quantity of beads that don't participate in the calculation of the Xi_Chain</a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">          4 :   unsigned noChainBeads = (UMEM.size() * 2) + TAILS.size();</span></a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span>            :   // Center of the cylinder. X and Y are calculated (or defined), Z is the Z component of the geometric center of the membranes.</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          4 :   Vector xyzCyl = pbcDistance(Vector(0.0, 0.0, 0.0), Vector(Xcyl_Mem, Ycyl_Mem, ZMems));</span></a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            :   // Estimation of RO with the Hub 2021 JCTC method. Only needed for the expansion.</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          4 :   double RO = R0[0];</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            :   // Number of polar atoms inside the horizontal layer. Eq. 3 Hub 2021 JCTC.</a>
+<a name="430"><span class="lineNum">     430 </span>            :   double np = 0.0, fz, fr, fz_prime, fr_prime;</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            :   // Derivative of np. Eq. 8 Hub 2021 JCTC.</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; d_np_dx(chainBeads), d_np_dy(chainBeads), d_np_dz(chainBeads);</span></a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :   // Pore radius of the defect. Eq. 2 Hub 2021 JCTC.</a>
+<a name="436"><span class="lineNum">     436 </span>            :   double poreR = 1.0;</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            :   // Z center of the Membrane in the RMAX radius.</a>
+<a name="439"><span class="lineNum">     439 </span>            :   double ZMemRMAX, ZMemRMAXcos = 0.0, ZMemRMAXsin = 0.0, countAux = 0.0, auxcos, auxsin;</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            :   ZMemRMAX = ZMems;</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            :   // The curvature of large membranes (1024 lipids) makes the Z-center of the membranes not to be representative</a>
+<a name="444"><span class="lineNum">     444 </span>            :   // in some sectors, particularly in the region of ​​the defect.</a>
+<a name="445"><span class="lineNum">     445 </span>            :   //</a>
+<a name="446"><span class="lineNum">     446 </span>            :   // To solve this, the center Z of the membranes in the defect sector is calculated and used to calculate</a>
+<a name="447"><span class="lineNum">     447 </span>            :   // the number of polar atoms within the horizontal layer AND in the radious of the defect.</a>
+<a name="448"><span class="lineNum">     448 </span>            :   //</a>
+<a name="449"><span class="lineNum">     449 </span>            :   // ________       | |       ________</a>
+<a name="450"><span class="lineNum">     450 </span>            :   // ________ \_____| |______/ _______&lt;-- Top membrane.</a>
+<a name="451"><span class="lineNum">     451 </span>            :   //         \______|P|_______/</a>
+<a name="452"><span class="lineNum">     452 </span>            :   //                |O|</a>
+<a name="453"><span class="lineNum">     453 </span>            :   //                | |               &lt;-- Z-center of the membranes in the region of the defect.</a>
+<a name="454"><span class="lineNum">     454 </span>            :   //          ______|R|_______        &lt;-- Z-center of the membranes</a>
+<a name="455"><span class="lineNum">     455 </span>            :   //         / _____|E|______ \ </a>
+<a name="456"><span class="lineNum">     456 </span>            :   //        / /     | |      \ \ </a>
+<a name="457"><span class="lineNum">     457 </span>            :   // ______/ /      | |       \ \______</a>
+<a name="458"><span class="lineNum">     458 </span>            :   // _______/                  \_______&lt;-- Bottom membrane.</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   // Center of mass for systems with PBC: https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          4 :   Vector MemCylDistances, distCylinder;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            :   double angle, ri;</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            : #ifdef _OPENMP</a>
+<a name="465"><span class="lineNum">     465 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          4 :   #pragma omp parallel for private(MemCylDistances, x, angle, auxcos, auxsin) reduction(+:ZMemRMAXcos, ZMemRMAXsin, countAux)</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : #endif</a>
+<a name="468"><span class="lineNum">     468 </span>            : #endif</a>
+<a name="469"><span class="lineNum">     469 </span>            :   for (unsigned i = 0; i &lt; membraneBeads; i++)</a>
+<a name="470"><span class="lineNum">     470 </span>            : {</a>
+<a name="471"><span class="lineNum">     471 </span>            :   MemCylDistances = pbcDistance(xyzCyl, pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i)));</a>
+<a name="472"><span class="lineNum">     472 </span>            :     x = sqrt(pow(MemCylDistances[0], 2) + pow(MemCylDistances[1], 2)) / RMAX[0];</a>
+<a name="473"><span class="lineNum">     473 </span>            :     if (!((x &lt;= -1.0 - H[0]) || (x &gt;= 1.0 + H[0])))</a>
+<a name="474"><span class="lineNum">     474 </span>            :     {</a>
+<a name="475"><span class="lineNum">     475 </span>            :       angle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i)))[2];</a>
+<a name="476"><span class="lineNum">     476 </span>            :       auxcos = cos(angle);</a>
+<a name="477"><span class="lineNum">     477 </span>            :       auxsin = sin(angle);</a>
+<a name="478"><span class="lineNum">     478 </span>            :       if (((-1.0 + H[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - H[0])))</a>
+<a name="479"><span class="lineNum">     479 </span>            :       {</a>
+<a name="480"><span class="lineNum">     480 </span>            :         ZMemRMAXcos += 1.0 * auxcos;</a>
+<a name="481"><span class="lineNum">     481 </span>            :         ZMemRMAXsin += 1.0 * auxsin;</a>
+<a name="482"><span class="lineNum">     482 </span>            :         countAux += 1.0;</a>
+<a name="483"><span class="lineNum">     483 </span>            :       }</a>
+<a name="484"><span class="lineNum">     484 </span>            :       else if (((1.0 - H[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + H[0])))</a>
+<a name="485"><span class="lineNum">     485 </span>            :       {</a>
+<a name="486"><span class="lineNum">     486 </span>            :         ZMemRMAXcos += (0.5 - 0.75 * (x - 1.0) / H[0] + 0.25 * pow((x - 1.0), 3) / pow(H[0], 3)) * auxcos;</a>
+<a name="487"><span class="lineNum">     487 </span>            :         ZMemRMAXsin += (0.5 - 0.75 * (x - 1.0) / H[0] + 0.25 * pow((x - 1.0), 3) / pow(H[0], 3)) * auxsin;</a>
+<a name="488"><span class="lineNum">     488 </span>            :         countAux += (0.5 - 0.75 * (x - 1.0) / H[0] + 0.25 * pow((x - 1.0), 3) / pow(H[0], 3));</a>
+<a name="489"><span class="lineNum">     489 </span>            :       }</a>
+<a name="490"><span class="lineNum">     490 </span>            :       else if (((-1.0 - H[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + H[0])))</a>
+<a name="491"><span class="lineNum">     491 </span>            :       {</a>
+<a name="492"><span class="lineNum">     492 </span>            :         ZMemRMAXcos += (0.5 + 0.75 * (x + 1.0) / H[0] - 0.25 * pow((x + 1.0), 3) / pow(H[0], 3)) * auxcos;</a>
+<a name="493"><span class="lineNum">     493 </span>            :         ZMemRMAXsin += (0.5 + 0.75 * (x + 1.0) / H[0] - 0.25 * pow((x + 1.0), 3) / pow(H[0], 3)) * auxsin;</a>
+<a name="494"><span class="lineNum">     494 </span>            :         countAux += (0.5 + 0.75 * (x + 1.0) / H[0] - 0.25 * pow((x + 1.0), 3) / pow(H[0], 3));</a>
+<a name="495"><span class="lineNum">     495 </span>            :       }</a>
+<a name="496"><span class="lineNum">     496 </span>            :     }</a>
+<a name="497"><span class="lineNum">     497 </span>            :   }</a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          4 :   ZMemRMAXcos = ZMemRMAXcos / countAux;</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          4 :   ZMemRMAXsin = ZMemRMAXsin / countAux;</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          4 :   ZMemRMAX = Lz * (atan2(-ZMemRMAXsin, -ZMemRMAXcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          4 :   xyzCyl = pbcDistance(Vector(0.0, 0.0, 0.0), Vector(Xcyl_Mem, Ycyl_Mem, ZMemRMAX));</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            : #ifdef _OPENMP</a>
+<a name="506"><span class="lineNum">     506 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          4 :   #pragma omp parallel for private(distCylinder, fz, fz_prime, fr, fr_prime, ri, x) reduction(+:np)</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : #endif</a>
+<a name="509"><span class="lineNum">     509 </span>            : #endif</a>
+<a name="510"><span class="lineNum">     510 </span>            :   for (unsigned i = 0; i &lt; chainBeads; i++)</a>
+<a name="511"><span class="lineNum">     511 </span>            : {</a>
+<a name="512"><span class="lineNum">     512 </span>            :   distCylinder = pbcDistance(xyzCyl, pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + noChainBeads)));</a>
+<a name="513"><span class="lineNum">     513 </span>            :     fz = 0.0;</a>
+<a name="514"><span class="lineNum">     514 </span>            :     fz_prime = 0.0;</a>
+<a name="515"><span class="lineNum">     515 </span>            :     fr = 0.0;</a>
+<a name="516"><span class="lineNum">     516 </span>            :     fr_prime = 0.0;</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            :     ri = sqrt(pow(distCylinder[0], 2) + pow(distCylinder[1], 2));</a>
+<a name="519"><span class="lineNum">     519 </span>            :     x = ri / RMAX[0];</a>
+<a name="520"><span class="lineNum">     520 </span>            :     if (!((x &lt;= -1.0 - H[0]) || (x &gt;= 1.0 + H[0])))</a>
+<a name="521"><span class="lineNum">     521 </span>            :     {</a>
+<a name="522"><span class="lineNum">     522 </span>            :       if (((-1.0 + H[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - H[0])))</a>
+<a name="523"><span class="lineNum">     523 </span>            :       {</a>
+<a name="524"><span class="lineNum">     524 </span>            :         fr = 1.0;</a>
+<a name="525"><span class="lineNum">     525 </span>            :       }</a>
+<a name="526"><span class="lineNum">     526 </span>            :       else if (((1.0 - H[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + H[0])))</a>
+<a name="527"><span class="lineNum">     527 </span>            :       {</a>
+<a name="528"><span class="lineNum">     528 </span>            :         fr = 0.5 - 0.75 * (x - 1.0) / H[0] + 0.25 * pow((x - 1.0), 3) / pow(H[0], 3);</a>
+<a name="529"><span class="lineNum">     529 </span>            :         fr_prime = (-0.75 / H[0] + 0.75 * pow((x - 1.0), 2) / pow(H[0], 3)) / (RMAX[0] * ri);</a>
+<a name="530"><span class="lineNum">     530 </span>            :       }</a>
+<a name="531"><span class="lineNum">     531 </span>            :       else if (((-1.0 - H[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + H[0])))</a>
+<a name="532"><span class="lineNum">     532 </span>            :       {</a>
+<a name="533"><span class="lineNum">     533 </span>            :         fr = 0.5 + 0.75 * (x + 1.0) / H[0] - 0.25 * pow((x + 1.0), 3) / pow(H[0], 3);</a>
+<a name="534"><span class="lineNum">     534 </span>            :         fr_prime = (0.75 / H[0] - 0.75 * pow((x + 1), 2) / pow(H[0], 3)) / (RMAX[0] * ri);</a>
+<a name="535"><span class="lineNum">     535 </span>            :       }</a>
+<a name="536"><span class="lineNum">     536 </span>            : </a>
+<a name="537"><span class="lineNum">     537 </span>            :       x = distCylinder[2] * 2.0 / D[0];</a>
+<a name="538"><span class="lineNum">     538 </span>            :       if (!((x &lt;= -1.0 - H[0]) || (x &gt;= 1.0 + H[0])))</a>
+<a name="539"><span class="lineNum">     539 </span>            :       {</a>
+<a name="540"><span class="lineNum">     540 </span>            :         if (((-1.0 + H[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - H[0])))</a>
+<a name="541"><span class="lineNum">     541 </span>            :         {</a>
+<a name="542"><span class="lineNum">     542 </span>            :           fz = 1.0;</a>
+<a name="543"><span class="lineNum">     543 </span>            :         }</a>
+<a name="544"><span class="lineNum">     544 </span>            :         else if (((1.0 - H[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + H[0])))</a>
+<a name="545"><span class="lineNum">     545 </span>            :         {</a>
+<a name="546"><span class="lineNum">     546 </span>            :           fz = 0.5 - 0.75 * (x - 1.0) / H[0] + 0.25 * pow((x - 1.0), 3) / pow(H[0], 3);</a>
+<a name="547"><span class="lineNum">     547 </span>            :           fz_prime = (-0.75 / H[0] + 0.75 * pow((x - 1.0), 2) / pow(H[0], 3)) * 2.0 / D[0];</a>
+<a name="548"><span class="lineNum">     548 </span>            :         }</a>
+<a name="549"><span class="lineNum">     549 </span>            :         else if (((-1.0 - H[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + H[0])))</a>
+<a name="550"><span class="lineNum">     550 </span>            :         {</a>
+<a name="551"><span class="lineNum">     551 </span>            :           fz = 0.5 + 0.75 * (x + 1.0) / H[0] - 0.25 * pow((x + 1.0), 3) / pow(H[0], 3);</a>
+<a name="552"><span class="lineNum">     552 </span>            :           fz_prime = (0.75 / H[0] - 0.75 * pow((x + 1), 2) / pow(H[0], 3)) * 2.0 / D[0];</a>
+<a name="553"><span class="lineNum">     553 </span>            :         }</a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            :         np += fz * fr;</a>
+<a name="556"><span class="lineNum">     556 </span>            :         d_np_dx[i] = fz * fr_prime * distCylinder[0];</a>
+<a name="557"><span class="lineNum">     557 </span>            :         d_np_dy[i] = fz * fr_prime * distCylinder[1];</a>
+<a name="558"><span class="lineNum">     558 </span>            :         d_np_dz[i] = fz_prime * fr;</a>
+<a name="559"><span class="lineNum">     559 </span>            :       }</a>
+<a name="560"><span class="lineNum">     560 </span>            :     }</a>
+<a name="561"><span class="lineNum">     561 </span>            :   }</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">          4 :   poreR = sqrt(np * VO[0] / (M_PI * D[0]));</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :   // This is the CV that describes the Pore Expansion.</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          4 :   double Xi_Exp = (poreR - RO) / RO;</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            :   // Derivatives vector.</a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">          4 :   std::vector&lt;Vector&gt; derivatives(chainBeads);</span></a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span>            :   // Aux for the derivatives calculations. Eq. 7 Hub 2021 JCTC.</a>
+<a name="571"><span class="lineNum">     571 </span>            :   double fact2 = 0.0;</a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">          4 :   if (poreR != 0.0)</span></a>
+<a name="574"><span class="lineNum">     574 </span>            : {</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">          4 :   fact2 = VO[0] / (2.0 * M_PI * RO * D[0] * poreR);</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :   }</a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span>            :   // Distances from the oxygens to center of the cylinder.</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          4 :   std::vector&lt;Vector&gt; CylDistances(chainBeads);</span></a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            : #ifdef _OPENMP</a>
+<a name="582"><span class="lineNum">     582 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">          4 :   #pragma omp parallel for</span></a>
+<a name="584"><span class="lineNum">     584 </span>            : #endif</a>
+<a name="585"><span class="lineNum">     585 </span>            : #endif</a>
+<a name="586"><span class="lineNum">     586 </span>            :   for (unsigned i = 0; i &lt; chainBeads; i++)</a>
+<a name="587"><span class="lineNum">     587 </span>            : {</a>
+<a name="588"><span class="lineNum">     588 </span>            :   derivatives[i][0] = fact2 * d_np_dx[i];</a>
+<a name="589"><span class="lineNum">     589 </span>            :     derivatives[i][1] = fact2 * d_np_dy[i];</a>
+<a name="590"><span class="lineNum">     590 </span>            :     derivatives[i][2] = fact2 * d_np_dz[i];</a>
+<a name="591"><span class="lineNum">     591 </span>            :     CylDistances[i] = pbcDistance(xyzCyl, pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + noChainBeads)));</a>
+<a name="592"><span class="lineNum">     592 </span>            :   }</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          4 :   Tensor virial;</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">     135392 :   for (unsigned i = 0; i &lt; chainBeads; i++)</span></a>
+<a name="596"><span class="lineNum">     596 </span>            : {</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">     135388 :   setAtomsDerivatives((i + noChainBeads), derivatives[i]);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">     135388 :     virial -= Tensor(CylDistances[i], derivatives[i]);</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :   }</a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">          4 :   setValue(Xi_Exp);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">          4 :   setBoxDerivatives(virial);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">          4 : }</span></a>
+<a name="604"><span class="lineNum">     604 </span>            : }</a>
+<a name="605"><span class="lineNum">     605 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/FusionPoreNucleationP.cpp.func-sort-c.html b/coverage/membranefusion/FusionPoreNucleationP.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5dc19cd8b8
--- /dev/null
+++ b/coverage/membranefusion/FusionPoreNucleationP.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion/FusionPoreNucleationP.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - FusionPoreNucleationP.cpp<span style="font-size: 80%;"> (<a href="FusionPoreNucleationP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">184</td>
+            <td class="headerCovTableEntry">208</td>
+            <td class="headerCovTableEntryMed">88.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FusionPoreNucleationP.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#109">_ZN4PLMD14membranefusion21fusionPoreNucleationPC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#86">_ZN4PLMD14membranefusion12_GLOBAL__N_133fusionPoreNucleationPRegisterMe886createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#109">_ZN4PLMD14membranefusion21fusionPoreNucleationPC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#88">_ZN4PLMD14membranefusion21fusionPoreNucleationP16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#222">_ZN4PLMD14membranefusion21fusionPoreNucleationP9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#86">_ZN4PLMD14membranefusion12_GLOBAL__N_133fusionPoreNucleationPRegisterMe88C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#86">_ZN4PLMD14membranefusion12_GLOBAL__N_133fusionPoreNucleationPRegisterMe88D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/membranefusion/FusionPoreNucleationP.cpp.func.html b/coverage/membranefusion/FusionPoreNucleationP.cpp.func.html
new file mode 100644
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+
+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - FusionPoreNucleationP.cpp<span style="font-size: 80%;"> (<a href="FusionPoreNucleationP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">184</td>
+            <td class="headerCovTableEntry">208</td>
+            <td class="headerCovTableEntryMed">88.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#86">_ZN4PLMD14membranefusion12_GLOBAL__N_133fusionPoreNucleationPRegisterMe886createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#86">_ZN4PLMD14membranefusion12_GLOBAL__N_133fusionPoreNucleationPRegisterMe88C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#86">_ZN4PLMD14membranefusion12_GLOBAL__N_133fusionPoreNucleationPRegisterMe88D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#88">_ZN4PLMD14membranefusion21fusionPoreNucleationP16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#222">_ZN4PLMD14membranefusion21fusionPoreNucleationP9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#109">_ZN4PLMD14membranefusion21fusionPoreNucleationPC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FusionPoreNucleationP.cpp.gcov.html#109">_ZN4PLMD14membranefusion21fusionPoreNucleationPC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/membranefusion/FusionPoreNucleationP.cpp.gcov.html b/coverage/membranefusion/FusionPoreNucleationP.cpp.gcov.html
new file mode 100644
index 0000000000..d4c8100da0
--- /dev/null
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - FusionPoreNucleationP.cpp<span style="font-size: 80%;"> (source / <a href="FusionPoreNucleationP.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">184</td>
+            <td class="headerCovTableEntry">208</td>
+            <td class="headerCovTableEntryMed">88.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
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+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2022.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : CVs originally developed by the Jochen Hub group from the University of Saarland (Germany)</a>
+<a name="5"><span class="lineNum">       5 </span>            : and adapted and implemented in PLUMED by Ary Lautaro Di Bartolo and Diego Masone from the</a>
+<a name="6"><span class="lineNum">       6 </span>            : National University of Cuyo (Argentina).</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : The membranefusion module is free software: you can redistribute it and/or modify</a>
+<a name="9"><span class="lineNum">       9 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="10"><span class="lineNum">      10 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="11"><span class="lineNum">      11 </span>            : (at your option) any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : The membranefusion module is distributed in the hope that it will be useful,</a>
+<a name="14"><span class="lineNum">      14 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="15"><span class="lineNum">      15 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="16"><span class="lineNum">      16 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="17"><span class="lineNum">      17 </span>            : </a>
+<a name="18"><span class="lineNum">      18 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="19"><span class="lineNum">      19 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="20"><span class="lineNum">      20 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;cmath&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #ifdef _OPENMP</a>
+<a name="25"><span class="lineNum">      25 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;omp.h&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #endif</a>
+<a name="28"><span class="lineNum">      28 </span>            : #endif</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD</a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace membranefusion</a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MEMBRANEFUSIONMOD_COLVAR FUSIONPORENUCLEATIONP</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : A CV for inducing the nucleation of the fusion pore from a hemifusion stalk.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculate the collective variable designed by Hub and collaborators \cite Hub2017 and</a>
+<a name="39"><span class="lineNum">      39 </span>            : implemented into PLUMED by Masone and collaborators.</a>
+<a name="40"><span class="lineNum">      40 </span>            : This CV is capable of inducing the nucleation of the fusion pore from a hemifusion stalk.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : \xi_n = \frac{1}{N_{sn}} \sum_{s=0}^{N_{sn}-1} \delta_{sn} (N_{sn}^{(p)})</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : Where \f$\xi_n\f$ is the CV, \f$N_{sn}\f$ is the number of slices of the cylinder that make up the CV,</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f$\delta_{sn}\f$ is a continuos function in the interval [0 1] (\f$\delta_{sf} = 0\f$ for no beads in the slice s, and</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f$\delta_{sf} = 1\f$ for 1 or more beads in the slice s) and \f$N_{sf}^{(p)}\f$ accounts for the number of water and</a>
+<a name="49"><span class="lineNum">      49 </span>            : phosphateoxygens beads within the slice s.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \par Examples</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : This example induces the nucleation of the fusion pore (\f$\xi_n = 1.0\f$) from a hemifusion stalk (\f$\xi_n = 0.2\f$).</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \plumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : lMem: GROUP ATOMS=1-10752,21505-22728,23953-24420 #All the lower membrane beads.</a>
+<a name="58"><span class="lineNum">      58 </span>            : uMem: GROUP ATOMS=10753-21504,22729-23952,24421-24888 #All the upper membrane beads.</a>
+<a name="59"><span class="lineNum">      59 </span>            : tails: GROUP ATOMS=8-23948:12,12-23952:12,23966-24884:18,23970-24888:18 #All the lipid tails beads (from the lower and upper membrane).</a>
+<a name="60"><span class="lineNum">      60 </span>            : waters: GROUP ATOMS=24889-56490 #All the water beads.</a>
+<a name="61"><span class="lineNum">      61 </span>            : po4: GROUP ATOMS=2-23942:12,23957-24875:18 #All the lipid phosphateoxygens beads.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : fusionPoreNucleation: FUSIONPORENUCLEATIONP UMEMBRANE=uMem LMEMBRANE=lMem TAILS=tails WATERS=waters PHOSPHATEOXYGENS=po4 NSMEM=85 NS=45</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : MOVINGRESTRAINT ...</a>
+<a name="66"><span class="lineNum">      66 </span>            :     ARG=fusionPoreNucleation</a>
+<a name="67"><span class="lineNum">      67 </span>            :     STEP0=0 AT0=0.2 KAPPA0=10000.0</a>
+<a name="68"><span class="lineNum">      68 </span>            :     STEP1=500000 AT1=1.0 KAPPA1=10000.0</a>
+<a name="69"><span class="lineNum">      69 </span>            : ...</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : PRINT ARG=fusionPoreNucleation FILE=COLVAR STRIDE=1</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \endplumedfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : class fusionPoreNucleationP : public Colvar</a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;AtomNumber&gt; UMEM, LMEM, TAILS, WATERS, POXYGENS;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;double&gt; NSMEM, DSMEM, HMEM, NS, DS, HCH, RCYL, ZETA, ONEOVERS2C2CUTOFF, XCYL, YCYL;</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : public:</a>
+<a name="83"><span class="lineNum">      83 </span>            :   explicit fusionPoreNucleationP(const ActionOptions &amp;);</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void calculate() override;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   static void registerKeywords(Keywords &amp;keys);</a>
+<a name="86"><span class="lineNum">      86 </span>            : };</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(fusionPoreNucleationP, &quot;FUSIONPORENUCLEATIONP&quot;)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          3 : void fusionPoreNucleationP::registerKeywords(Keywords &amp;keys)</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : {</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          3 :   Colvar::registerKeywords(keys);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;UMEMBRANE&quot;, &quot;all the beads of the upper membrane.&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;LMEMBRANE&quot;, &quot;all the beads of the lower membrane.&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;TAILS&quot;, &quot;all the tail beads of the system.&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;WATERS&quot;, &quot;all the water beads of the system.&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;PHOSPHATEOXYGENS&quot;, &quot;all the lipid phosphateoxygens beads of the system.&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;NSMEM&quot;, &quot;the number of slices of the membrane fusion cylinder.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;DSMEM&quot;, &quot;( default=0.1 ) thickness of the slices of the membrane fusion cylinder.&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;HMEM&quot;, &quot;( default=0.25 ) parameter of the step function θ(x,h) for the membrane fusion.&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;NS&quot;, &quot;the number of slices of the membrane-spanning cylinder in such a way that when the bilayers are flat and parallel the CV is equal to 0.2.&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;DS&quot;, &quot;( default=0.25 ) thickness of the slices of the membrane-spanning cylinder.&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;HCH&quot;, &quot;( default=0.25 ) parameter of the step function θ(x,h) for the CV.&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;RCYL&quot;, &quot;( default=0.8 ) the radius of the membrane-spanning cylinder.&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;ZETA&quot;, &quot;( default=0.75 ) parameter of the switch function ψ(x,ζ).&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;ONEOVERS2C2CUTOFF&quot;, &quot;( default=500 ) cut off large values for the derivative of the atan2 function to avoid violate energy.&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;XCYL&quot;, &quot;X coordinate of the fixed cylinder, if not present this will be calculated.&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;YCYL&quot;, &quot;X coordinate of the fixed cylinder, if not present this will be calculated.&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          3 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 : fusionPoreNucleationP::fusionPoreNucleationP(const ActionOptions &amp;ao) : PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : {</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   parseAtomList(&quot;UMEMBRANE&quot;, UMEM);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   if (UMEM.size() == 0)</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     error(&quot;UMEMBRANE has not any atom specified.&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   parseAtomList(&quot;LMEMBRANE&quot;, LMEM);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   if (LMEM.size() == 0)</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     error(&quot;LMEMBRANE has not any atom specified.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   parseAtomList(&quot;TAILS&quot;, TAILS);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 :   if (TAILS.size() == 0)</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     error(&quot;TAILS has not any atom specified.&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   parseAtomList(&quot;WATERS&quot;, WATERS);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   if (WATERS.size() == 0)</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     error(&quot;WATERS has not any atom specified.&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :   parseAtomList(&quot;PHOSPHATEOXYGENS&quot;, POXYGENS);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   if (POXYGENS.size() == 0)</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     error(&quot;PHOSPHATEOXYGENS has not any atom specified.&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   parseVector(&quot;NSMEM&quot;, NSMEM);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   if (NSMEM.size() &gt; 1)</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     error(&quot;NSMEM cannot take more than one value.&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :   parseVector(&quot;DSMEM&quot;, DSMEM);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   if (DSMEM.size() &gt; 1)</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     error(&quot;DSMEM cannot take more than one value.&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :   if (DSMEM.size() == 0)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     DSMEM.push_back(0.1);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 :   parseVector(&quot;HMEM&quot;, HMEM);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :   if (HMEM.size() &gt; 1)</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     error(&quot;HMEM cannot take more than one value.&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   if (HMEM.size() == 0)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     HMEM.push_back(0.25);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   parseVector(&quot;NS&quot;, NS);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   if (NS.size() &gt; 1)</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     error(&quot;NS cannot take more than one value.&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :   parseVector(&quot;DS&quot;, DS);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          1 :   if (DS.size() &gt; 1)</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     error(&quot;DS cannot take more than one value.&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   if (DS.size() == 0)</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     DS.push_back(0.25);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :   parseVector(&quot;HCH&quot;, HCH);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :   if (HCH.size() &gt; 1)</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     error(&quot;H cannot take more than one value.&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   if (HCH.size() == 0)</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     HCH.push_back(0.25);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   parseVector(&quot;RCYL&quot;, RCYL);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :   if (RCYL.size() &gt; 1)</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     error(&quot;RCYL cannot take more than one value.&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :   if (RCYL.size() == 0)</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     RCYL.push_back(0.8);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :   parseVector(&quot;ZETA&quot;, ZETA);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :   if (ZETA.size() &gt; 1)</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     error(&quot;ZETA cannot take more than one value.&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          1 :   if (ZETA.size() == 0)</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     ZETA.push_back(0.75);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   parseVector(&quot;ONEOVERS2C2CUTOFF&quot;, ONEOVERS2C2CUTOFF);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :   if (ONEOVERS2C2CUTOFF.size() &gt; 1)</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     error(&quot;ONEOVERS2C2CUTOFF cannot take more than one value.&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :   if (ONEOVERS2C2CUTOFF.size() == 0)</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          1 :     ONEOVERS2C2CUTOFF.push_back(500);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :   parseVector(&quot;XCYL&quot;, XCYL);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :   if (XCYL.size() &gt; 1)</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     error(&quot;XCYL cannot take more than one value.&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          1 :   if (XCYL.size() == 0)</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          1 :     XCYL.push_back(-1.0);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :   parseVector(&quot;YCYL&quot;, YCYL);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          1 :   if (YCYL.size() &gt; 1)</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     error(&quot;YCYL cannot take more than one value.&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          1 :   if (YCYL.size() == 0)</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          1 :     YCYL.push_back(-1.0);</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      12445 :   for (unsigned i = 0; i &lt; UMEM.size(); i++)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      12444 :     atoms.push_back(UMEM[i]);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      12445 :   for (unsigned i = 0; i &lt; LMEM.size(); i++)</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      12444 :     atoms.push_back(LMEM[i]);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       4097 :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       4096 :     atoms.push_back(TAILS[i]);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      31603 :   for (unsigned i = 0; i &lt; WATERS.size(); i++)</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      31602 :     atoms.push_back(WATERS[i]);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       2049 :   for (unsigned i = 0; i &lt; POXYGENS.size(); i++)</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   {</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       2048 :     atoms.push_back(POXYGENS[i]);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          1 :   addValueWithDerivatives();</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          1 :   setNotPeriodic();</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          1 :   requestAtoms(atoms);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          1 : }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          4 : void fusionPoreNucleationP::calculate()</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : {</a>
+<a name="226"><span class="lineNum">     226 </span>            :   /*************************</a>
+<a name="227"><span class="lineNum">     227 </span>            :   *                        *</a>
+<a name="228"><span class="lineNum">     228 </span>            :   *         System         *</a>
+<a name="229"><span class="lineNum">     229 </span>            :   *                        *</a>
+<a name="230"><span class="lineNum">     230 </span>            :   **************************/</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            :   // Box dimensions.</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          4 :   double Lx = getBox()[0][0], Ly = getBox()[1][1], Lz = getBox()[2][2];</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            :   // Z center of the upper membrane (uMem) and lower membrane (lMem) for systems with PBC: https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions .</a>
+<a name="236"><span class="lineNum">     236 </span>            :   double ZuMem, ZuMemcos = 0.0, ZuMemsin = 0.0, uMemAngle, ZlMem, ZlMemcos = 0.0, ZlMemsin = 0.0, lMemAngle;</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : #ifdef _OPENMP</a>
+<a name="239"><span class="lineNum">     239 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          4 :   #pragma omp parallel for private(uMemAngle, lMemAngle) reduction(+:ZuMemcos, ZuMemsin, ZlMemcos, ZlMemsin)</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : #endif</a>
+<a name="242"><span class="lineNum">     242 </span>            : #endif</a>
+<a name="243"><span class="lineNum">     243 </span>            :   for (unsigned i = 0; i &lt; UMEM.size(); i++)</a>
+<a name="244"><span class="lineNum">     244 </span>            :   {</a>
+<a name="245"><span class="lineNum">     245 </span>            :     uMemAngle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i)))[2];</a>
+<a name="246"><span class="lineNum">     246 </span>            :     lMemAngle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + UMEM.size())))[2];</a>
+<a name="247"><span class="lineNum">     247 </span>            :     ZuMemcos += cos(uMemAngle);</a>
+<a name="248"><span class="lineNum">     248 </span>            :     ZuMemsin += sin(uMemAngle);</a>
+<a name="249"><span class="lineNum">     249 </span>            :     ZlMemcos += cos(lMemAngle);</a>
+<a name="250"><span class="lineNum">     250 </span>            :     ZlMemsin += sin(lMemAngle);</a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          4 :   ZuMemcos = ZuMemcos / UMEM.size();</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          4 :   ZuMemsin = ZuMemsin / UMEM.size();</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          4 :   ZuMem = Lz * (atan2(-ZuMemsin, -ZuMemcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          4 :   ZlMemcos = ZlMemcos / UMEM.size();</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          4 :   ZlMemsin = ZlMemsin / UMEM.size();</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          4 :   ZlMem = Lz * (atan2(-ZlMemsin, -ZlMemcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            :   // Z center of the boths membranes (upper and lower).</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          4 :   double ZMems = (ZuMem + ZlMem) / 2.0;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            :   /**************************</a>
+<a name="263"><span class="lineNum">     263 </span>            :   *                         *</a>
+<a name="264"><span class="lineNum">     264 </span>            :   *   Xcyl_Mem &amp; Ycyl_Mem   *</a>
+<a name="265"><span class="lineNum">     265 </span>            :   *                         *</a>
+<a name="266"><span class="lineNum">     266 </span>            :   ***************************/</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   // Quantity of beads of the membranes.</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          4 :   unsigned membraneBeads = UMEM.size() + LMEM.size();</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   // Z distance from the lipid tail to the geometric center of both membranes.</a>
+<a name="272"><span class="lineNum">     272 </span>            :   double ZTailDistance;</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   // Z position of the first slice.</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          4 :   double firstSliceZ_Mem = ZMems + (0.0 + 0.5 - NSMEM[0] / 2.0) * DSMEM[0];</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :   // Z distance between the first slice and the Z center of the membrane.</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          4 :   double firstSliceZDist_Mem = pbcDistance(Vector(0.0, 0.0, firstSliceZ_Mem), Vector(0.0, 0.0, ZMems))[2];</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :   // Position in the cylinder.</a>
+<a name="281"><span class="lineNum">     281 </span>            :   double PositionS_Mem;</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            :   // Slices to analyze per particle.</a>
+<a name="284"><span class="lineNum">     284 </span>            :   unsigned s1_Mem, s2_Mem;</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :   // Eq. 7 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; faxial_Mem(TAILS.size() * NSMEM[0]);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; Fs_Mem(NSMEM[0]);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            :   // Eq. 11 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; ws_Mem(NSMEM[0]);</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="296"><span class="lineNum">     296 </span>            :   double W_Mem = 0.0;</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :   // Eq. 21 and 22 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; sx_Mem(NSMEM[0]), sy_Mem(NSMEM[0]), cx_Mem(NSMEM[0]), cy_Mem(NSMEM[0]);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="302"><span class="lineNum">     302 </span>            :   double Xsc_Mem = 0.0, Xcc_Mem = 0.0, Ysc_Mem = 0.0, Ycc_Mem = 0.0;</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   // Aux.</a>
+<a name="305"><span class="lineNum">     305 </span>            :   double x, aux;</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   // Scaled position of the lipid tail respect the origin of coordinates.</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          4 :   Vector TailPosition;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : #ifdef _OPENMP</a>
+<a name="311"><span class="lineNum">     311 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="312"><span class="lineNum">     312 </span>            :   #pragma omp declare reduction(vec_double_plus : std::vector&lt;double&gt; : \</a>
+<a name="313"><span class="lineNum">     313 </span>            :   std::transform(omp_out.begin(), omp_out.end(), omp_in.begin(), omp_out.begin(), std::plus&lt;double&gt;())) \</a>
+<a name="314"><span class="lineNum">     314 </span>            :   initializer(omp_priv = decltype(omp_orig)(omp_orig.size()))</a>
+<a name="315"><span class="lineNum">     315 </span>            : #endif</a>
+<a name="316"><span class="lineNum">     316 </span>            : #endif</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : #ifdef _OPENMP</a>
+<a name="319"><span class="lineNum">     319 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :   #pragma omp parallel for private(ZTailDistance, PositionS_Mem, s1_Mem, s2_Mem, TailPosition, x, aux) reduction(vec_double_plus:Fs_Mem, sx_Mem, sy_Mem, cx_Mem, cy_Mem)</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : #endif</a>
+<a name="322"><span class="lineNum">     322 </span>            : #endif</a>
+<a name="323"><span class="lineNum">     323 </span>            :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</a>
+<a name="324"><span class="lineNum">     324 </span>            :   {</a>
+<a name="325"><span class="lineNum">     325 </span>            :     ZTailDistance = pbcDistance(Vector(0.0, 0.0, ZMems), getPosition(i + membraneBeads))[2];</a>
+<a name="326"><span class="lineNum">     326 </span>            :     PositionS_Mem = (ZTailDistance + firstSliceZDist_Mem) / DSMEM[0];</a>
+<a name="327"><span class="lineNum">     327 </span>            :     // If the following condition is met the particle is in the Z space of the cylinder.</a>
+<a name="328"><span class="lineNum">     328 </span>            :     if ((PositionS_Mem &gt;= (-0.5 - HMEM[0])) &amp;&amp; (PositionS_Mem &lt;= (NSMEM[0] + 0.5 - 1.0 + HMEM[0])))</a>
+<a name="329"><span class="lineNum">     329 </span>            :     {</a>
+<a name="330"><span class="lineNum">     330 </span>            :       //Defining the slices to analyze each particle.</a>
+<a name="331"><span class="lineNum">     331 </span>            :       if (PositionS_Mem &lt; 1)</a>
+<a name="332"><span class="lineNum">     332 </span>            :       {</a>
+<a name="333"><span class="lineNum">     333 </span>            :         s1_Mem = 0;</a>
+<a name="334"><span class="lineNum">     334 </span>            :         s2_Mem = 2;</a>
+<a name="335"><span class="lineNum">     335 </span>            :       }</a>
+<a name="336"><span class="lineNum">     336 </span>            :       else if (PositionS_Mem &lt;= (NSMEM[0] - 2.0))</a>
+<a name="337"><span class="lineNum">     337 </span>            :       {</a>
+<a name="338"><span class="lineNum">     338 </span>            :         s1_Mem = floor(PositionS_Mem) - 1;</a>
+<a name="339"><span class="lineNum">     339 </span>            :         s2_Mem = floor(PositionS_Mem) + 1;</a>
+<a name="340"><span class="lineNum">     340 </span>            :       }</a>
+<a name="341"><span class="lineNum">     341 </span>            :       else</a>
+<a name="342"><span class="lineNum">     342 </span>            :       {</a>
+<a name="343"><span class="lineNum">     343 </span>            :         s1_Mem = NSMEM[0] - 3;</a>
+<a name="344"><span class="lineNum">     344 </span>            :         s2_Mem = NSMEM[0] - 1;</a>
+<a name="345"><span class="lineNum">     345 </span>            :       }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :       TailPosition = getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + membraneBeads)));</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            :       for (unsigned s = s1_Mem; s &lt;= s2_Mem; s++)</a>
+<a name="350"><span class="lineNum">     350 </span>            :       {</a>
+<a name="351"><span class="lineNum">     351 </span>            :         x = (ZTailDistance - (s + 0.5 - NSMEM[0] / 2.0) * DSMEM[0]) * 2.0 / DSMEM[0];</a>
+<a name="352"><span class="lineNum">     352 </span>            :         if (!((x &lt;= -1.0 - HMEM[0]) || (x &gt;= 1.0 + HMEM[0])))</a>
+<a name="353"><span class="lineNum">     353 </span>            :         {</a>
+<a name="354"><span class="lineNum">     354 </span>            :           if (((-1.0 + HMEM[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - HMEM[0])))</a>
+<a name="355"><span class="lineNum">     355 </span>            :           {</a>
+<a name="356"><span class="lineNum">     356 </span>            :             faxial_Mem[i + TAILS.size() * s] = 1.0;</a>
+<a name="357"><span class="lineNum">     357 </span>            :             Fs_Mem[s] += 1.0;</a>
+<a name="358"><span class="lineNum">     358 </span>            :             sx_Mem[s] += sin(2.0 * M_PI * TailPosition[0]);</a>
+<a name="359"><span class="lineNum">     359 </span>            :             sy_Mem[s] += sin(2.0 * M_PI * TailPosition[1]);</a>
+<a name="360"><span class="lineNum">     360 </span>            :             cx_Mem[s] += cos(2.0 * M_PI * TailPosition[0]);</a>
+<a name="361"><span class="lineNum">     361 </span>            :             cy_Mem[s] += cos(2.0 * M_PI * TailPosition[1]);</a>
+<a name="362"><span class="lineNum">     362 </span>            :           }</a>
+<a name="363"><span class="lineNum">     363 </span>            :           else if (((1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + HMEM[0])))</a>
+<a name="364"><span class="lineNum">     364 </span>            :           {</a>
+<a name="365"><span class="lineNum">     365 </span>            :             aux = 0.5 - ((3.0 * x - 3.0) / (4.0 * HMEM[0])) + (pow((x - 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="366"><span class="lineNum">     366 </span>            :             faxial_Mem[i + TAILS.size() * s] = aux;</a>
+<a name="367"><span class="lineNum">     367 </span>            :             Fs_Mem[s] += aux;</a>
+<a name="368"><span class="lineNum">     368 </span>            :             sx_Mem[s] += aux * sin(2.0 * M_PI * TailPosition[0]);</a>
+<a name="369"><span class="lineNum">     369 </span>            :             sy_Mem[s] += aux * sin(2.0 * M_PI * TailPosition[1]);</a>
+<a name="370"><span class="lineNum">     370 </span>            :             cx_Mem[s] += aux * cos(2.0 * M_PI * TailPosition[0]);</a>
+<a name="371"><span class="lineNum">     371 </span>            :             cy_Mem[s] += aux * cos(2.0 * M_PI * TailPosition[1]);</a>
+<a name="372"><span class="lineNum">     372 </span>            :           }</a>
+<a name="373"><span class="lineNum">     373 </span>            :           else if (((-1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + HMEM[0])))</a>
+<a name="374"><span class="lineNum">     374 </span>            :           {</a>
+<a name="375"><span class="lineNum">     375 </span>            :             aux = 0.5 + ((3.0 * x + 3.0) / (4.0 * HMEM[0])) - (pow((x + 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="376"><span class="lineNum">     376 </span>            :             faxial_Mem[i + TAILS.size() * s] = aux;</a>
+<a name="377"><span class="lineNum">     377 </span>            :             Fs_Mem[s] += aux;</a>
+<a name="378"><span class="lineNum">     378 </span>            :             sx_Mem[s] += (aux * sin(2.0 * M_PI * TailPosition[0]));</a>
+<a name="379"><span class="lineNum">     379 </span>            :             sy_Mem[s] += (aux * sin(2.0 * M_PI * TailPosition[1]));</a>
+<a name="380"><span class="lineNum">     380 </span>            :             cx_Mem[s] += (aux * cos(2.0 * M_PI * TailPosition[0]));</a>
+<a name="381"><span class="lineNum">     381 </span>            :             cy_Mem[s] += (aux * cos(2.0 * M_PI * TailPosition[1]));</a>
+<a name="382"><span class="lineNum">     382 </span>            :           }</a>
+<a name="383"><span class="lineNum">     383 </span>            :         }</a>
+<a name="384"><span class="lineNum">     384 </span>            :       }</a>
+<a name="385"><span class="lineNum">     385 </span>            :     }</a>
+<a name="386"><span class="lineNum">     386 </span>            :   }</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        344 :   for (unsigned s = 0; s &lt; NSMEM[0]; s++)</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   {</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        340 :     if (Fs_Mem[s] != 0.0)</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :     {</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        339 :       ws_Mem[s] = tanh(Fs_Mem[s]);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        339 :       W_Mem += ws_Mem[s];</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        339 :       sx_Mem[s] = sx_Mem[s] / Fs_Mem[s];</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">        339 :       sy_Mem[s] = sy_Mem[s] / Fs_Mem[s];</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        339 :       cx_Mem[s] = cx_Mem[s] / Fs_Mem[s];</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        339 :       cy_Mem[s] = cy_Mem[s] / Fs_Mem[s];</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        339 :       Xsc_Mem += sx_Mem[s] * ws_Mem[s];</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">        339 :       Ysc_Mem += sy_Mem[s] * ws_Mem[s];</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        339 :       Xcc_Mem += cx_Mem[s] * ws_Mem[s];</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">        339 :       Ycc_Mem += cy_Mem[s] * ws_Mem[s];</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :     }</a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          4 :   Xsc_Mem = Xsc_Mem / W_Mem;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          4 :   Ysc_Mem = Ysc_Mem / W_Mem;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          4 :   Xcc_Mem = Xcc_Mem / W_Mem;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          4 :   Ycc_Mem = Ycc_Mem / W_Mem;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :   // Eq. 12 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="411"><span class="lineNum">     411 </span>            :   double Xcyl_Mem, Ycyl_Mem;</a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          4 :   if ((XCYL[0] &gt; 0.0) &amp;&amp; (YCYL[0] &gt; 0.0))</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :   {</a>
+<a name="415"><span class="lineNum">     415 </span>            :     Xcyl_Mem = XCYL[0];</a>
+<a name="416"><span class="lineNum">     416 </span>            :     Ycyl_Mem = YCYL[0];</a>
+<a name="417"><span class="lineNum">     417 </span>            :   }</a>
+<a name="418"><span class="lineNum">     418 </span>            :   else</a>
+<a name="419"><span class="lineNum">     419 </span>            :   {</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          4 :     Xcyl_Mem = (atan2(-Xsc_Mem, -Xcc_Mem) + M_PI) * Lx / (2 * M_PI);</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">          4 :     Ycyl_Mem = (atan2(-Ysc_Mem, -Ycc_Mem) + M_PI) * Ly / (2 * M_PI);</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :   }</a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span>            :   /*************************</a>
+<a name="425"><span class="lineNum">     425 </span>            :   *                        *</a>
+<a name="426"><span class="lineNum">     426 </span>            :   *        Xi_n            *</a>
+<a name="427"><span class="lineNum">     427 </span>            :   *                        *</a>
+<a name="428"><span class="lineNum">     428 </span>            :   **************************/</a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span>            :   // Eq. 1 Hub &amp; Awasthi JCTC 2017. This is the CV that describes de Pore Nucleation.</a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">          4 :   double Xi_n = 0.0;</span></a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span>            :   // Quantity of beads that could participate in the calculation of the Xi_Chain</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          4 :   unsigned chainBeads = WATERS.size() + POXYGENS.size();</span></a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            :   // Quantity of beads that don't participate in the calculation of the Xi_Chain</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          4 :   unsigned noChainBeads = (UMEM.size() * 2) + TAILS.size();</span></a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span>            :   // Z Distances from the oxygens to the geometric center of the membranes.</a>
+<a name="440"><span class="lineNum">     440 </span>            :   double ZMemDistance;</a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            :   // Scaled positions of the oxygens to respect of the origin of coordinates.</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          4 :   Vector Position;</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span>            :   // Distance from the water/phosphate group to the defect cylinder.</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          4 :   Vector distCylinder;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            :   // Center of the cylinder. XY components are calculated (or defined), Z is the Z geometric center of the membranes of the system.</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          4 :   Vector xyzCyl_Mem = pbcDistance(Vector(0.0, 0.0, 0.0), Vector(Xcyl_Mem, Ycyl_Mem, ZMems));</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            :   // Average of the radius of the water and lipid cylinder.</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          4 :   double RCYLAVERAGE = RCYL[0] * (1 + HCH[0]);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span>            :   // Conditions.</a>
+<a name="455"><span class="lineNum">     455 </span>            :   bool condition1, condition2, condition3;</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   // Z position of the first slice.</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          4 :   double firstSliceZ = ZMems + (0.0 + 0.5 - NS[0] / 2.0) * DS[0];</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   // Z distance between the first slice and the Z center of the membrane.</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          4 :   double firstSliceZDist = pbcDistance(Vector(0.0, 0.0, firstSliceZ), Vector(0.0, 0.0, ZMems))[2];</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            :   // Position in the cylinder.</a>
+<a name="464"><span class="lineNum">     464 </span>            :   double PositionS;</a>
+<a name="465"><span class="lineNum">     465 </span>            : </a>
+<a name="466"><span class="lineNum">     466 </span>            :   // Mark the particles to analyze.</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; analyzeThisParticle(chainBeads);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span>            :   // Slices to analyze per particle.</a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          4 :   std::vector&lt;unsigned&gt; s1(chainBeads), s2(chainBeads);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span>            :   // Eq. 7 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; faxial(chainBeads * NS[0]);</span></a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            :   // Eq. 16 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; d_faxial_dz(chainBeads * NS[0]);</span></a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; Fs(NS[0]);</span></a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            :   // Eq. 11 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; ws(NS[0]);</span></a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="485"><span class="lineNum">     485 </span>            :   double W = 0.0;</a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span>            :   // Eq. 21 and 22 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; sx(NS[0]), sy(NS[0]), cx(NS[0]), cy(NS[0]);</span></a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="491"><span class="lineNum">     491 </span>            :   double Xsc = 0.0, Xcc = 0.0, Ysc = 0.0, Ycc = 0.0;</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            : #ifdef _OPENMP</a>
+<a name="494"><span class="lineNum">     494 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          4 :   #pragma omp parallel for private(distCylinder, aux, condition1, condition2, condition3, ZMemDistance, PositionS, Position, x) reduction(vec_double_plus:Fs, sx, sy, cx, cy)</span></a>
+<a name="496"><span class="lineNum">     496 </span>            : #endif</a>
+<a name="497"><span class="lineNum">     497 </span>            : #endif</a>
+<a name="498"><span class="lineNum">     498 </span>            :   for (unsigned i = 0; i &lt; chainBeads; i++)</a>
+<a name="499"><span class="lineNum">     499 </span>            : {</a>
+<a name="500"><span class="lineNum">     500 </span>            :   distCylinder = pbcDistance(xyzCyl_Mem, pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + noChainBeads)));</a>
+<a name="501"><span class="lineNum">     501 </span>            :     aux = sqrt(pow(distCylinder[0], 2) + pow(distCylinder[1], 2));</a>
+<a name="502"><span class="lineNum">     502 </span>            :     condition1 = ((aux / RCYLAVERAGE) &lt; 1.0);</a>
+<a name="503"><span class="lineNum">     503 </span>            :     condition2 = ((pbcDistance(Vector(0.0, 0.0, ZuMem), getPosition(i + noChainBeads))[2] &gt; 0) &amp;&amp; (aux / RCYLAVERAGE) &lt; 2.0);</a>
+<a name="504"><span class="lineNum">     504 </span>            :     condition3 = ((pbcDistance(getPosition(i + noChainBeads), Vector(0.0, 0.0, ZlMem))[2] &gt; 0) &amp;&amp; (aux / RCYLAVERAGE) &lt; 2.0);</a>
+<a name="505"><span class="lineNum">     505 </span>            :     if (condition1 || condition2 || condition3)</a>
+<a name="506"><span class="lineNum">     506 </span>            :     {</a>
+<a name="507"><span class="lineNum">     507 </span>            :       ZMemDistance = pbcDistance(Vector(0.0, 0.0, ZMems), getPosition(i + noChainBeads))[2];</a>
+<a name="508"><span class="lineNum">     508 </span>            :       PositionS = (ZMemDistance + firstSliceZDist) / DS[0];</a>
+<a name="509"><span class="lineNum">     509 </span>            :       // If the following condition is met the particle is in the Z space of the cylinder.</a>
+<a name="510"><span class="lineNum">     510 </span>            :       if ((PositionS &gt;= (-0.5 - HCH[0])) &amp;&amp; (PositionS &lt;= (NS[0] + 0.5 - 1.0 + HCH[0])))</a>
+<a name="511"><span class="lineNum">     511 </span>            :       {</a>
+<a name="512"><span class="lineNum">     512 </span>            :         analyzeThisParticle[i] = 1.0;</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            :         //Defining the slices to analyze each particle.</a>
+<a name="515"><span class="lineNum">     515 </span>            :         if (PositionS &lt; 1)</a>
+<a name="516"><span class="lineNum">     516 </span>            :         {</a>
+<a name="517"><span class="lineNum">     517 </span>            :           s1[i] = 0;</a>
+<a name="518"><span class="lineNum">     518 </span>            :           s2[i] = 2;</a>
+<a name="519"><span class="lineNum">     519 </span>            :         }</a>
+<a name="520"><span class="lineNum">     520 </span>            :         else if (PositionS &lt;= (NS[0] - 2.0))</a>
+<a name="521"><span class="lineNum">     521 </span>            :         {</a>
+<a name="522"><span class="lineNum">     522 </span>            :           s1[i] = floor(PositionS) - 1;</a>
+<a name="523"><span class="lineNum">     523 </span>            :           s2[i] = floor(PositionS) + 1;</a>
+<a name="524"><span class="lineNum">     524 </span>            :         }</a>
+<a name="525"><span class="lineNum">     525 </span>            :         else</a>
+<a name="526"><span class="lineNum">     526 </span>            :         {</a>
+<a name="527"><span class="lineNum">     527 </span>            :           s1[i] = NS[0] - 3;</a>
+<a name="528"><span class="lineNum">     528 </span>            :           s2[i] = NS[0] - 1;</a>
+<a name="529"><span class="lineNum">     529 </span>            :         }</a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            :         Position = getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + noChainBeads)));</a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span>            :         for (unsigned s = s1[i]; s &lt;= s2[i]; s++)</a>
+<a name="534"><span class="lineNum">     534 </span>            :         {</a>
+<a name="535"><span class="lineNum">     535 </span>            :           x = (ZMemDistance - (s + 0.5 - NS[0] / 2.0) * DS[0]) * 2.0 / DS[0];</a>
+<a name="536"><span class="lineNum">     536 </span>            :           if (!((x &lt;= -1.0 - HCH[0]) || (x &gt;= 1.0 + HCH[0])))</a>
+<a name="537"><span class="lineNum">     537 </span>            :           {</a>
+<a name="538"><span class="lineNum">     538 </span>            :             if (((-1.0 + HCH[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - HCH[0])))</a>
+<a name="539"><span class="lineNum">     539 </span>            :             {</a>
+<a name="540"><span class="lineNum">     540 </span>            :               faxial[i + chainBeads * s] = 1.0;</a>
+<a name="541"><span class="lineNum">     541 </span>            :               Fs[s] += 1.0;</a>
+<a name="542"><span class="lineNum">     542 </span>            :               sx[s] += sin(2.0 * M_PI * Position[0]);</a>
+<a name="543"><span class="lineNum">     543 </span>            :               sy[s] += sin(2.0 * M_PI * Position[1]);</a>
+<a name="544"><span class="lineNum">     544 </span>            :               cx[s] += cos(2.0 * M_PI * Position[0]);</a>
+<a name="545"><span class="lineNum">     545 </span>            :               cy[s] += cos(2.0 * M_PI * Position[1]);</a>
+<a name="546"><span class="lineNum">     546 </span>            :             }</a>
+<a name="547"><span class="lineNum">     547 </span>            :             else if (((1.0 - HCH[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + HCH[0])))</a>
+<a name="548"><span class="lineNum">     548 </span>            :             {</a>
+<a name="549"><span class="lineNum">     549 </span>            :               aux = 0.5 - ((3.0 * x - 3.0) / (4.0 * HCH[0])) + (pow((x - 1.0), 3) / (4.0 * pow(HCH[0], 3)));</a>
+<a name="550"><span class="lineNum">     550 </span>            :               faxial[i + chainBeads * s] = aux;</a>
+<a name="551"><span class="lineNum">     551 </span>            :               d_faxial_dz[i + chainBeads * s] = ((-3.0 / (4.0 * HCH[0])) + ((3.0 * pow((x - 1), 2)) / (4.0 * pow(HCH[0], 3)))) * 2.0 / DS[0];</a>
+<a name="552"><span class="lineNum">     552 </span>            :               Fs[s] += aux;</a>
+<a name="553"><span class="lineNum">     553 </span>            :               sx[s] += aux * sin(2.0 * M_PI * Position[0]);</a>
+<a name="554"><span class="lineNum">     554 </span>            :               sy[s] += aux * sin(2.0 * M_PI * Position[1]);</a>
+<a name="555"><span class="lineNum">     555 </span>            :               cx[s] += aux * cos(2.0 * M_PI * Position[0]);</a>
+<a name="556"><span class="lineNum">     556 </span>            :               cy[s] += aux * cos(2.0 * M_PI * Position[1]);</a>
+<a name="557"><span class="lineNum">     557 </span>            :             }</a>
+<a name="558"><span class="lineNum">     558 </span>            :             else if (((-1.0 - HCH[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + HCH[0])))</a>
+<a name="559"><span class="lineNum">     559 </span>            :             {</a>
+<a name="560"><span class="lineNum">     560 </span>            :               aux = 0.5 + ((3.0 * x + 3.0) / (4.0 * HCH[0])) - (pow((x + 1.0), 3) / (4.0 * pow(HCH[0], 3)));</a>
+<a name="561"><span class="lineNum">     561 </span>            :               faxial[i + chainBeads * s] = aux;</a>
+<a name="562"><span class="lineNum">     562 </span>            :               d_faxial_dz[i + chainBeads * s] = ((3.0 / (4.0 * HCH[0])) - ((3.0 * pow((x + 1), 2)) / (4.0 * pow(HCH[0], 3)))) * 2.0 / DS[0];</a>
+<a name="563"><span class="lineNum">     563 </span>            :               Fs[s] += aux;</a>
+<a name="564"><span class="lineNum">     564 </span>            :               sx[s] += (aux * sin(2.0 * M_PI * Position[0]));</a>
+<a name="565"><span class="lineNum">     565 </span>            :               sy[s] += (aux * sin(2.0 * M_PI * Position[1]));</a>
+<a name="566"><span class="lineNum">     566 </span>            :               cx[s] += (aux * cos(2.0 * M_PI * Position[0]));</a>
+<a name="567"><span class="lineNum">     567 </span>            :               cy[s] += (aux * cos(2.0 * M_PI * Position[1]));</a>
+<a name="568"><span class="lineNum">     568 </span>            :             }</a>
+<a name="569"><span class="lineNum">     569 </span>            :           }</a>
+<a name="570"><span class="lineNum">     570 </span>            :         }</a>
+<a name="571"><span class="lineNum">     571 </span>            :       }</a>
+<a name="572"><span class="lineNum">     572 </span>            :     }</a>
+<a name="573"><span class="lineNum">     573 </span>            :   }</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        184 :   for (unsigned s = 0; s &lt; NS[0]; s++)</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :   {</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        180 :     if (Fs[s] != 0.0)</span></a>
+<a name="578"><span class="lineNum">     578 </span>            :     {</a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         49 :       ws[s] = tanh(Fs[s]);</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         49 :       W += ws[s];</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         49 :       sx[s] = sx[s] / Fs[s];</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         49 :       sy[s] = sy[s] / Fs[s];</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         49 :       cx[s] = cx[s] / Fs[s];</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         49 :       cy[s] = cy[s] / Fs[s];</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         49 :       Xsc += sx[s] * ws[s];</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         49 :       Ysc += sy[s] * ws[s];</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         49 :       Xcc += cx[s] * ws[s];</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         49 :       Ycc += cy[s] * ws[s];</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :     }</a>
+<a name="590"><span class="lineNum">     590 </span>            :   }</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">          4 :   Xsc = Xsc / W;</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">          4 :   Ysc = Ysc / W;</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">          4 :   Xcc = Xcc / W;</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">          4 :   Ycc = Ycc / W;</span></a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            :   // Eq. 12 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="598"><span class="lineNum">     598 </span>            :   double Xcyl, Ycyl;</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span>            :   Xcyl = Xcyl_Mem;</a>
+<a name="601"><span class="lineNum">     601 </span>            :   Ycyl = Ycyl_Mem;</a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span>            :   // Eq. 25, 26 and 27 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="604"><span class="lineNum">     604 </span>            :   double d_sx_dx, d_sx_dz, d_sy_dy, d_sy_dz, d_cx_dx, d_cx_dz, d_cy_dy, d_cy_dz;</a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span>            :   // Eq. 29 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="607"><span class="lineNum">     607 </span>            :   double d_ws_dz;</a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            :   // Eq. 31, 32 and 33 Hub &amp; Awasthi JCTC 2017</a>
+<a name="610"><span class="lineNum">     610 </span>            :   double d_Xsc_dx, d_Xsc_dz, d_Xcc_dx, d_Xcc_dz, d_Ysc_dy, d_Ysc_dz, d_Ycc_dy, d_Ycc_dz;</a>
+<a name="611"><span class="lineNum">     611 </span>            : </a>
+<a name="612"><span class="lineNum">     612 </span>            :   // Center of the cylinder. X and Y are calculated (or defined), Z is the Z component of the geometric center of the membranes.</a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">          4 :   Vector xyzCyl = pbcDistance(Vector(0.0, 0.0, 0.0), Vector(Xcyl, Ycyl, ZMems));</span></a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span>            :   // Distances from the oxygens to center of the cylinder.</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">          4 :   std::vector&lt;Vector&gt; CylDistances(chainBeads);</span></a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span>            :   // Modulo of the XY distances from the oxygens to the center of the cylinder.</a>
+<a name="619"><span class="lineNum">     619 </span>            :   double ri;</a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span>            :   // Eq. 8 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="622"><span class="lineNum">     622 </span>            :   double fradial;</a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            :   // Eq. 15 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; d_fradial_dx(chainBeads), d_fradial_dy(chainBeads);</span></a>
+<a name="626"><span class="lineNum">     626 </span>            : </a>
+<a name="627"><span class="lineNum">     627 </span>            :   // Eq. 35, 36, 37 and 38 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; d_Xcyl_dx(chainBeads), d_Xcyl_dz(chainBeads), d_Ycyl_dy(chainBeads), d_Ycyl_dz(chainBeads);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            :   // To avoid rare instabilities auxX and auxY are truncated at a configurable value (default 500).</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">          4 :   double auxX = (1 / (pow(Xsc, 2) + pow(Xcc, 2))), auxY = (1 / (pow(Ysc, 2) + pow(Ycc, 2)));</span></a>
+<a name="632"><span class="lineNum">     632 </span>            : </a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">          4 :   if (auxX &gt; ONEOVERS2C2CUTOFF[0])</span></a>
+<a name="634"><span class="lineNum">     634 </span>            :   {</a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineNoCov">          0 :     auxX = Lx * ONEOVERS2C2CUTOFF[0] / (2 * M_PI);</span></a>
+<a name="636"><span class="lineNum">     636 </span>            :   }</a>
+<a name="637"><span class="lineNum">     637 </span>            :   else</a>
+<a name="638"><span class="lineNum">     638 </span>            :   {</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">          4 :     auxX = Lx * auxX / (2 * M_PI);</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :   }</a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">          4 :   if (auxY &gt; ONEOVERS2C2CUTOFF[0])</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :   {</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :     auxY = Ly * ONEOVERS2C2CUTOFF[0] / (2 * M_PI);</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :   }</a>
+<a name="646"><span class="lineNum">     646 </span>            :   else</a>
+<a name="647"><span class="lineNum">     647 </span>            :   {</a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">          4 :     auxY = Ly * auxY / (2 * M_PI);</span></a>
+<a name="649"><span class="lineNum">     649 </span>            :   }</a>
+<a name="650"><span class="lineNum">     650 </span>            : </a>
+<a name="651"><span class="lineNum">     651 </span>            :   //Number of oxygens within the slice s of the membrane-spanning cylinder.</a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; Nsp(NS[0]), psi(NS[0]), d_psi(NS[0]);</span></a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span>            :   // Eq. 3 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">          4 :   double b = (ZETA[0] / (1.0 - ZETA[0])), c = ((1.0 - ZETA[0]) * exp(b));</span></a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            :   // Eq. 19 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; fradial_d_faxial_dz(chainBeads * NS[0]);</span></a>
+<a name="659"><span class="lineNum">     659 </span>            : </a>
+<a name="660"><span class="lineNum">     660 </span>            :   // Eq. 20 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; Axs(NS[0]), Ays(NS[0]);</span></a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span>            : #ifdef _OPENMP</a>
+<a name="664"><span class="lineNum">     664 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">          4 :   #pragma omp parallel for private(d_Xsc_dx,d_Xcc_dx,d_Ysc_dy,d_Ycc_dy,d_Xsc_dz,d_Xcc_dz,d_Ysc_dz,d_Ycc_dz,d_sx_dx,d_sy_dy,d_cx_dx,d_cy_dy,d_sx_dz,d_sy_dz,d_cx_dz,d_cy_dz,d_ws_dz,ri,x,fradial) reduction(vec_double_plus: Nsp, Axs, Ays)</span></a>
+<a name="666"><span class="lineNum">     666 </span>            : #endif</a>
+<a name="667"><span class="lineNum">     667 </span>            : #endif</a>
+<a name="668"><span class="lineNum">     668 </span>            :   for (unsigned i = 0; i &lt; chainBeads; i++)</a>
+<a name="669"><span class="lineNum">     669 </span>            : {</a>
+<a name="670"><span class="lineNum">     670 </span>            :   CylDistances[i] = pbcDistance(xyzCyl, pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + noChainBeads)));</a>
+<a name="671"><span class="lineNum">     671 </span>            :     if (analyzeThisParticle[i])</a>
+<a name="672"><span class="lineNum">     672 </span>            :     {</a>
+<a name="673"><span class="lineNum">     673 </span>            :       Position = getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + noChainBeads)));</a>
+<a name="674"><span class="lineNum">     674 </span>            :       d_Xsc_dx = 0.0;</a>
+<a name="675"><span class="lineNum">     675 </span>            :       d_Xcc_dx = 0.0;</a>
+<a name="676"><span class="lineNum">     676 </span>            :       d_Ysc_dy = 0.0;</a>
+<a name="677"><span class="lineNum">     677 </span>            :       d_Ycc_dy = 0.0;</a>
+<a name="678"><span class="lineNum">     678 </span>            :       d_Xsc_dz = 0.0;</a>
+<a name="679"><span class="lineNum">     679 </span>            :       d_Xcc_dz = 0.0;</a>
+<a name="680"><span class="lineNum">     680 </span>            :       d_Ysc_dz = 0.0;</a>
+<a name="681"><span class="lineNum">     681 </span>            :       d_Ycc_dz = 0.0;</a>
+<a name="682"><span class="lineNum">     682 </span>            :       for (unsigned s = s1[i]; s &lt;= s2[i]; s++)</a>
+<a name="683"><span class="lineNum">     683 </span>            :       {</a>
+<a name="684"><span class="lineNum">     684 </span>            :         if (Fs[s] != 0.0)</a>
+<a name="685"><span class="lineNum">     685 </span>            :         {</a>
+<a name="686"><span class="lineNum">     686 </span>            :           d_sx_dx = faxial[i + chainBeads * s] * 2.0 * M_PI * cos(2.0 * M_PI * Position[0]) / (Lx * Fs[s]);</a>
+<a name="687"><span class="lineNum">     687 </span>            :           d_sy_dy = faxial[i + chainBeads * s] * 2.0 * M_PI * cos(2.0 * M_PI * Position[1]) / (Ly * Fs[s]);</a>
+<a name="688"><span class="lineNum">     688 </span>            :           d_cx_dx = -faxial[i + chainBeads * s] * 2.0 * M_PI * sin(2.0 * M_PI * Position[0]) / (Lx * Fs[s]);</a>
+<a name="689"><span class="lineNum">     689 </span>            :           d_cy_dy = -faxial[i + chainBeads * s] * 2.0 * M_PI * sin(2.0 * M_PI * Position[1]) / (Ly * Fs[s]);</a>
+<a name="690"><span class="lineNum">     690 </span>            :           d_Xsc_dx += ws[s] * d_sx_dx / W;</a>
+<a name="691"><span class="lineNum">     691 </span>            :           d_Xcc_dx += ws[s] * d_cx_dx / W;</a>
+<a name="692"><span class="lineNum">     692 </span>            :           d_Ysc_dy += ws[s] * d_sy_dy / W;</a>
+<a name="693"><span class="lineNum">     693 </span>            :           d_Ycc_dy += ws[s] * d_cy_dy / W;</a>
+<a name="694"><span class="lineNum">     694 </span>            : </a>
+<a name="695"><span class="lineNum">     695 </span>            :           d_sx_dz = d_faxial_dz[i + chainBeads * s] * (sin(2.0 * M_PI * Position[0]) - sx[s]) / Fs[s];</a>
+<a name="696"><span class="lineNum">     696 </span>            :           d_sy_dz = d_faxial_dz[i + chainBeads * s] * (sin(2.0 * M_PI * Position[1]) - sy[s]) / Fs[s];</a>
+<a name="697"><span class="lineNum">     697 </span>            :           d_cx_dz = d_faxial_dz[i + chainBeads * s] * (cos(2.0 * M_PI * Position[0]) - cx[s]) / Fs[s];</a>
+<a name="698"><span class="lineNum">     698 </span>            :           d_cy_dz = d_faxial_dz[i + chainBeads * s] * (cos(2.0 * M_PI * Position[1]) - cy[s]) / Fs[s];</a>
+<a name="699"><span class="lineNum">     699 </span>            :           d_ws_dz = (1 - pow(ws[s], 2)) * d_faxial_dz[i + chainBeads * s];</a>
+<a name="700"><span class="lineNum">     700 </span>            :           d_Xsc_dz += (ws[s] * d_sx_dz + d_ws_dz * (sx[s] - Xsc)) / W;</a>
+<a name="701"><span class="lineNum">     701 </span>            :           d_Xcc_dz += (ws[s] * d_cx_dz + d_ws_dz * (cx[s] - Xcc)) / W;</a>
+<a name="702"><span class="lineNum">     702 </span>            :           d_Ysc_dz += (ws[s] * d_sy_dz + d_ws_dz * (sy[s] - Ysc)) / W;</a>
+<a name="703"><span class="lineNum">     703 </span>            :           d_Ycc_dz += (ws[s] * d_cy_dz + d_ws_dz * (cy[s] - Ycc)) / W;</a>
+<a name="704"><span class="lineNum">     704 </span>            :         }</a>
+<a name="705"><span class="lineNum">     705 </span>            :       }</a>
+<a name="706"><span class="lineNum">     706 </span>            :       d_Xcyl_dx[i] = auxX * (-Xsc * d_Xcc_dx + Xcc * d_Xsc_dx);</a>
+<a name="707"><span class="lineNum">     707 </span>            :       d_Xcyl_dz[i] = auxX * (-Xsc * d_Xcc_dz + Xcc * d_Xsc_dz);</a>
+<a name="708"><span class="lineNum">     708 </span>            :       d_Ycyl_dy[i] = auxY * (-Ysc * d_Ycc_dy + Ycc * d_Ysc_dy);</a>
+<a name="709"><span class="lineNum">     709 </span>            :       d_Ycyl_dz[i] = auxY * (-Ysc * d_Ycc_dz + Ycc * d_Ysc_dz);</a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            :       ri = sqrt(pow(CylDistances[i][0], 2) + pow(CylDistances[i][1], 2));</a>
+<a name="712"><span class="lineNum">     712 </span>            :       x = ri / RCYL[0];</a>
+<a name="713"><span class="lineNum">     713 </span>            :       if (!((x &lt;= -1.0 - HCH[0]) || (x &gt;= 1.0 + HCH[0])))</a>
+<a name="714"><span class="lineNum">     714 </span>            :       {</a>
+<a name="715"><span class="lineNum">     715 </span>            :         if (((-1.0 + HCH[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - HCH[0])))</a>
+<a name="716"><span class="lineNum">     716 </span>            :         {</a>
+<a name="717"><span class="lineNum">     717 </span>            :           fradial = 1.0;</a>
+<a name="718"><span class="lineNum">     718 </span>            :         }</a>
+<a name="719"><span class="lineNum">     719 </span>            :         else if (((1.0 - HCH[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + HCH[0])))</a>
+<a name="720"><span class="lineNum">     720 </span>            :         {</a>
+<a name="721"><span class="lineNum">     721 </span>            :           fradial = 0.5 - ((3.0 * x - 3.0) / (4.0 * HCH[0])) + (pow((x - 1.0), 3) / (4.0 * pow(HCH[0], 3)));</a>
+<a name="722"><span class="lineNum">     722 </span>            :           d_fradial_dx[i] = ((-3.0 / (4.0 * HCH[0])) + ((3.0 * pow((x - 1), 2)) / (4.0 * pow(HCH[0], 3)))) * CylDistances[i][0] / (RCYL[0] * ri);</a>
+<a name="723"><span class="lineNum">     723 </span>            :           d_fradial_dy[i] = ((-3.0 / (4.0 * HCH[0])) + ((3.0 * pow((x - 1), 2)) / (4.0 * pow(HCH[0], 3)))) * CylDistances[i][1] / (RCYL[0] * ri);</a>
+<a name="724"><span class="lineNum">     724 </span>            :         }</a>
+<a name="725"><span class="lineNum">     725 </span>            :         else if (((-1.0 - HCH[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + HCH[0])))</a>
+<a name="726"><span class="lineNum">     726 </span>            :         {</a>
+<a name="727"><span class="lineNum">     727 </span>            :           fradial = 0.5 + ((3.0 * x + 3.0) / (4.0 * HCH[0])) - (pow((x + 1.0), 3) / (4.0 * pow(HCH[0], 3)));</a>
+<a name="728"><span class="lineNum">     728 </span>            :           d_fradial_dx[i] = ((3.0 / (4.0 * HCH[0])) - ((3.0 * pow((x + 1), 2)) / (4.0 * pow(HCH[0], 3)))) * CylDistances[i][0] / (RCYL[0] * ri);</a>
+<a name="729"><span class="lineNum">     729 </span>            :           d_fradial_dy[i] = ((3.0 / (4.0 * HCH[0])) - ((3.0 * pow((x + 1), 2)) / (4.0 * pow(HCH[0], 3)))) * CylDistances[i][1] / (RCYL[0] * ri);</a>
+<a name="730"><span class="lineNum">     730 </span>            :         }</a>
+<a name="731"><span class="lineNum">     731 </span>            : </a>
+<a name="732"><span class="lineNum">     732 </span>            :         for (unsigned s = s1[i]; s &lt;= s2[i]; s++)</a>
+<a name="733"><span class="lineNum">     733 </span>            :         {</a>
+<a name="734"><span class="lineNum">     734 </span>            :           Nsp[s] += fradial * faxial[i + chainBeads * s];</a>
+<a name="735"><span class="lineNum">     735 </span>            :           Axs[s] += faxial[i + chainBeads * s] * d_fradial_dx[i];</a>
+<a name="736"><span class="lineNum">     736 </span>            :           Ays[s] += faxial[i + chainBeads * s] * d_fradial_dy[i];</a>
+<a name="737"><span class="lineNum">     737 </span>            :           fradial_d_faxial_dz[i + chainBeads * s] = fradial * d_faxial_dz[i + chainBeads * s];</a>
+<a name="738"><span class="lineNum">     738 </span>            :         }</a>
+<a name="739"><span class="lineNum">     739 </span>            :       }</a>
+<a name="740"><span class="lineNum">     740 </span>            :     }</a>
+<a name="741"><span class="lineNum">     741 </span>            :   }</a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">        184 :   for (unsigned s = 0; s &lt; NS[0]; s++)</span></a>
+<a name="744"><span class="lineNum">     744 </span>            :   {</a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">        180 :     if (Nsp[s] &lt;= 1.0)</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :     {</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">        149 :       psi[s] = ZETA[0] * Nsp[s];</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">        149 :       d_psi[s] = ZETA[0];</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">        149 :       Xi_n += psi[s];</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :     }</a>
+<a name="751"><span class="lineNum">     751 </span>            :     else</a>
+<a name="752"><span class="lineNum">     752 </span>            :     {</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         31 :       psi[s] = 1.0 - c * exp(-b * Nsp[s]);</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">         31 :       d_psi[s] = b * c * exp(-b * Nsp[s]);</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">         31 :       Xi_n += psi[s];</span></a>
+<a name="756"><span class="lineNum">     756 </span>            :     }</a>
+<a name="757"><span class="lineNum">     757 </span>            :   }</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">          4 :   Xi_n = Xi_n / NS[0];</span></a>
+<a name="760"><span class="lineNum">     760 </span>            : </a>
+<a name="761"><span class="lineNum">     761 </span>            :   // Eq. 18 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; faxial_d_fradial_dx(chainBeads * NS[0]), faxial_d_fradial_dy(chainBeads * NS[0]), faxial_d_fradial_dz(chainBeads * NS[0]);</span></a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span>            :   // Eq. 13 Hub &amp; Awasthi JCTC 2017 modified to considere the Heaviside_Chain step function (this only affect during the transition).</a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">          4 :   std::vector&lt;Vector&gt; derivatives_Chain(chainBeads);</span></a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            : #ifdef _OPENMP</a>
+<a name="768"><span class="lineNum">     768 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">          4 :   #pragma omp parallel for private(aux)</span></a>
+<a name="770"><span class="lineNum">     770 </span>            : #endif</a>
+<a name="771"><span class="lineNum">     771 </span>            : #endif</a>
+<a name="772"><span class="lineNum">     772 </span>            :   for (unsigned i = 0; i &lt; chainBeads; i++)</a>
+<a name="773"><span class="lineNum">     773 </span>            : {</a>
+<a name="774"><span class="lineNum">     774 </span>            :   if (analyzeThisParticle[i])</a>
+<a name="775"><span class="lineNum">     775 </span>            :     {</a>
+<a name="776"><span class="lineNum">     776 </span>            :       for (unsigned s = s1[i]; s &lt;= s2[i]; s++)</a>
+<a name="777"><span class="lineNum">     777 </span>            :       {</a>
+<a name="778"><span class="lineNum">     778 </span>            :         if (faxial[i + chainBeads * s])</a>
+<a name="779"><span class="lineNum">     779 </span>            :         {</a>
+<a name="780"><span class="lineNum">     780 </span>            :           faxial_d_fradial_dx[i + chainBeads * s] = faxial[i + chainBeads * s] * d_fradial_dx[i] - d_Xcyl_dx[i] * Axs[s];</a>
+<a name="781"><span class="lineNum">     781 </span>            :           faxial_d_fradial_dy[i + chainBeads * s] = faxial[i + chainBeads * s] * d_fradial_dy[i] - d_Ycyl_dy[i] * Ays[s];</a>
+<a name="782"><span class="lineNum">     782 </span>            :           faxial_d_fradial_dz[i + chainBeads * s] = -d_Xcyl_dz[i] * Axs[s] - d_Ycyl_dz[i] * Ays[s];</a>
+<a name="783"><span class="lineNum">     783 </span>            :         }</a>
+<a name="784"><span class="lineNum">     784 </span>            :       }</a>
+<a name="785"><span class="lineNum">     785 </span>            : </a>
+<a name="786"><span class="lineNum">     786 </span>            :       for (unsigned s = s1[i]; s &lt;= s2[i]; s++)</a>
+<a name="787"><span class="lineNum">     787 </span>            :       {</a>
+<a name="788"><span class="lineNum">     788 </span>            :         aux = d_psi[s] / NS[0];</a>
+<a name="789"><span class="lineNum">     789 </span>            :         derivatives_Chain[i][0] += aux * faxial_d_fradial_dx[i + chainBeads * s];</a>
+<a name="790"><span class="lineNum">     790 </span>            :         derivatives_Chain[i][1] += aux * faxial_d_fradial_dy[i + chainBeads * s];</a>
+<a name="791"><span class="lineNum">     791 </span>            :         derivatives_Chain[i][2] += aux * (faxial_d_fradial_dz[i + chainBeads * s] + fradial_d_faxial_dz[i + chainBeads * s]);</a>
+<a name="792"><span class="lineNum">     792 </span>            :       }</a>
+<a name="793"><span class="lineNum">     793 </span>            :     }</a>
+<a name="794"><span class="lineNum">     794 </span>            :   }</a>
+<a name="795"><span class="lineNum">     795 </span>            : </a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">          4 :   Tensor virial;</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">     134604 :   for (unsigned i = 0; i &lt; chainBeads; i++)</span></a>
+<a name="798"><span class="lineNum">     798 </span>            : {</a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">     134600 :   setAtomsDerivatives((i + noChainBeads), derivatives_Chain[i]);</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">     134600 :     virial -= Tensor(CylDistances[i], derivatives_Chain[i]);</span></a>
+<a name="801"><span class="lineNum">     801 </span>            :   }</a>
+<a name="802"><span class="lineNum">     802 </span>            : </a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">          4 :   setValue(Xi_n);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">          4 :   setBoxDerivatives(virial);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">          4 : }</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : }</a>
+<a name="807"><span class="lineNum">     807 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/MemFusionP.cpp.func-sort-c.html b/coverage/membranefusion/MemFusionP.cpp.func-sort-c.html
new file mode 100644
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+
+<html lang="en">
+
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+  <title>LCOV - plumed test coverage - membranefusion/MemFusionP.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - MemFusionP.cpp<span style="font-size: 80%;"> (<a href="MemFusionP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryMed">88.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MemFusionP.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion10memFusionPC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion10memFusionPC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#87">_ZN4PLMD14membranefusion12_GLOBAL__N_122memFusionPRegisterMe896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#89">_ZN4PLMD14membranefusion10memFusionP16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#186">_ZN4PLMD14membranefusion10memFusionP9calculateEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#87">_ZN4PLMD14membranefusion12_GLOBAL__N_122memFusionPRegisterMe89C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#87">_ZN4PLMD14membranefusion12_GLOBAL__N_122memFusionPRegisterMe89D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
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diff --git a/coverage/membranefusion/MemFusionP.cpp.func.html b/coverage/membranefusion/MemFusionP.cpp.func.html
new file mode 100644
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - MemFusionP.cpp<span style="font-size: 80%;"> (<a href="MemFusionP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryMed">88.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MemFusionP.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#89">_ZN4PLMD14membranefusion10memFusionP16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#186">_ZN4PLMD14membranefusion10memFusionP9calculateEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion10memFusionPC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#105">_ZN4PLMD14membranefusion10memFusionPC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#87">_ZN4PLMD14membranefusion12_GLOBAL__N_122memFusionPRegisterMe896createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#87">_ZN4PLMD14membranefusion12_GLOBAL__N_122memFusionPRegisterMe89C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MemFusionP.cpp.gcov.html#87">_ZN4PLMD14membranefusion12_GLOBAL__N_122memFusionPRegisterMe89D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/membranefusion/MemFusionP.cpp.gcov.html b/coverage/membranefusion/MemFusionP.cpp.gcov.html
new file mode 100644
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--- /dev/null
+++ b/coverage/membranefusion/MemFusionP.cpp.gcov.html
@@ -0,0 +1,684 @@
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+  <title>LCOV - plumed test coverage - membranefusion/MemFusionP.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">membranefusion</a> - MemFusionP.cpp<span style="font-size: 80%;"> (source / <a href="MemFusionP.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">134</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryMed">88.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2022.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : CVs originally developed by the Jochen Hub group from the University of Saarland (Germany)</a>
+<a name="5"><span class="lineNum">       5 </span>            : and adapted and implemented in PLUMED by Ary Lautaro Di Bartolo and Diego Masone from the</a>
+<a name="6"><span class="lineNum">       6 </span>            : National University of Cuyo (Argentina).</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : The membranefusion module is free software: you can redistribute it and/or modify</a>
+<a name="9"><span class="lineNum">       9 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="10"><span class="lineNum">      10 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="11"><span class="lineNum">      11 </span>            : (at your option) any later version.</a>
+<a name="12"><span class="lineNum">      12 </span>            : </a>
+<a name="13"><span class="lineNum">      13 </span>            : The membranefusion module is distributed in the hope that it will be useful,</a>
+<a name="14"><span class="lineNum">      14 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="15"><span class="lineNum">      15 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="16"><span class="lineNum">      16 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="17"><span class="lineNum">      17 </span>            : </a>
+<a name="18"><span class="lineNum">      18 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="19"><span class="lineNum">      19 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="20"><span class="lineNum">      20 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;cmath&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #ifdef _OPENMP</a>
+<a name="25"><span class="lineNum">      25 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;omp.h&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #endif</a>
+<a name="28"><span class="lineNum">      28 </span>            : #endif</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD</a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace membranefusion</a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MEMBRANEFUSIONMOD_COLVAR MEMFUSIONP</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculate a CV that can induce the formation of the hemifusion stalk between two initially flat and planar bilayers.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculate the collective variable designed by Hub and collaborators \cite Hub2017 and</a>
+<a name="39"><span class="lineNum">      39 </span>            : implemented into PLUMED by Masone and collaborators \cite DiBartolo2022 .</a>
+<a name="40"><span class="lineNum">      40 </span>            : This CV is capable of inducing the formation of the hemifusion stalk between two initially flat and planar bilayers</a>
+<a name="41"><span class="lineNum">      41 </span>            : surrounded by water molecules.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : \xi_f = \frac{1}{N_{sf}} \sum_{s=0}^{N_{sf}-1} \delta_{sf} (N_{sf}^{(p)})</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Where \f$\xi_f\f$ is the CV, \f$N_{sf}\f$ is the number of slices of the cylinder that make up the CV,</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f$\delta_{sf}\f$ is a continuos function in the interval [0 1] (\f$\delta_{sf} = 0\f$ for no beads in the slice s, and</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f$\delta_{sf} = 1\f$ for 1 or more beads in the slice s) and \f$N_{sf}^{(p)}\f$ accounts for the number of tail beads</a>
+<a name="50"><span class="lineNum">      50 </span>            : within the slice s.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : This example induces a hemifusion stalk (\f$\xi_f = 0.85\f$) from a pair of initially flat membranes (\f$\xi_f = 0.2\f$).</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : lMem: GROUP ATOMS=1-12288 #All the lower membrane beads.</a>
+<a name="58"><span class="lineNum">      58 </span>            : uMem: GROUP ATOMS=12289-24576 #All the upper membrane beads.</a>
+<a name="59"><span class="lineNum">      59 </span>            : tails: GROUP ATOMS=8-24572:12,12-24576:12 #All the lipid tails beads (from the lower and upper membrane).</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : memFusion: MEMFUSIONP UMEMBRANE=uMem LMEMBRANE=lMem TAILS=tails NSMEM=70 DSMEM=0.1 HMEM=0.25 RCYLMEM=1.75 ZETAMEM=0.5</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : MOVINGRESTRAINT ...</a>
+<a name="64"><span class="lineNum">      64 </span>            :     ARG=memFusion</a>
+<a name="65"><span class="lineNum">      65 </span>            :     STEP0=0 AT0=0.2 KAPPA0=10000.0</a>
+<a name="66"><span class="lineNum">      66 </span>            :     STEP1=500000 AT1=0.85 KAPPA1=10000.0</a>
+<a name="67"><span class="lineNum">      67 </span>            : ...</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : PRINT ARG=memFusion FILE=COLVAR STRIDE=1</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \endplumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : You can test this CV with another example in this &lt;a href=&quot;https://github.com/lautarodibartolo/MemFusion/tree/main/ExampleParallel&quot;&gt;GitHub folder&lt;/a&gt;.</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : class memFusionP : public Colvar</a>
+<a name="79"><span class="lineNum">      79 </span>            : {</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;AtomNumber&gt; UMEM, LMEM, TAILS;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;double&gt; NSMEM, DSMEM, HMEM, RCYLMEM, ZETAMEM, ONEOVERS2C2CUTOFF, XCYL, YCYL;</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : public:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   explicit memFusionP(const ActionOptions &amp;);</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void calculate() override;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static void registerKeywords(Keywords &amp;keys);</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(memFusionP, &quot;MEMFUSIONP&quot;)</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          3 : void memFusionP::registerKeywords(Keywords &amp;keys)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          3 :   Colvar::registerKeywords(keys);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;UMEMBRANE&quot;, &quot;all the beads of the upper membrane&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;LMEMBRANE&quot;, &quot;all the beads of the lower membrane&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;, &quot;TAILS&quot;, &quot;all the tail beads of the system&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;, &quot;NSMEM&quot;, &quot;the number of slices of the membrane fusion cylinder in such a way that when the bilayers are flat and parallel the CV is equal to 0.2.&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;DSMEM&quot;, &quot;( default=0.1) thickness of the slices of the membrane fusion cylinder.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;HMEM&quot;, &quot;( default=0.25 ) parameter of the step function θ(x,h) for the membrane fusion.&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;RCYLMEM&quot;, &quot;( default=1.75 ) the radius of the membrane fusion cylinder.&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;ZETAMEM&quot;, &quot;( default=0.5 ) occupation factor.&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;ONEOVERS2C2CUTOFF&quot;, &quot;( default=500 ) cut off large values for the derivative of the atan2 function.&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;XCYL&quot;, &quot;X coordinate of the fixed cylinder, if not present this will be calculated.&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;, &quot;YCYL&quot;, &quot;Y coordinate of the fixed cylinder, if not present this will be calculated.&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          3 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 : memFusionP::memFusionP(const ActionOptions &amp;ao) : PLUMED_COLVAR_INIT(ao)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   parseAtomList(&quot;UMEMBRANE&quot;, UMEM);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :   if (UMEM.size() == 0)</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     error(&quot;UMEMBRANE has not any atom specified.&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   parseAtomList(&quot;LMEMBRANE&quot;, LMEM);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   if (LMEM.size() == 0)</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     error(&quot;LMEMBRANE has not any atom specified.&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   parseAtomList(&quot;TAILS&quot;, TAILS);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   if (TAILS.size() == 0)</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     error(&quot;TAILS has not any atom specified.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   parseVector(&quot;NSMEM&quot;, NSMEM);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          1 :   if (NSMEM.size() &gt; 1)</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     error(&quot;NSMEM cannot take more than one value.&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   parseVector(&quot;DSMEM&quot;, DSMEM);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   if (DSMEM.size() &gt; 1)</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     error(&quot;DSMEM cannot take more than one value.&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          1 :   if (DSMEM.size() == 0)</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     DSMEM.push_back(0.1);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :   parseVector(&quot;HMEM&quot;, HMEM);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 :   if (HMEM.size() &gt; 1)</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     error(&quot;HMEM cannot take more than one value.&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :   if (HMEM.size() == 0)</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     HMEM.push_back(0.25);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :   parseVector(&quot;RCYLMEM&quot;, RCYLMEM);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   if (RCYLMEM.size() &gt; 1)</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     error(&quot;RCYLMEM cannot take more than one value.&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :   if (RCYLMEM.size() == 0)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     RCYLMEM.push_back(1.75);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 :   parseVector(&quot;ZETAMEM&quot;, ZETAMEM);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :   if (ZETAMEM.size() &gt; 1)</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     error(&quot;ZETA cannot take more than one value.&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   if (ZETAMEM.size() == 0)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     ZETAMEM.push_back(0.5);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   parseVector(&quot;ONEOVERS2C2CUTOFF&quot;, ONEOVERS2C2CUTOFF);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   if (ONEOVERS2C2CUTOFF.size() &gt; 1)</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     error(&quot;ONEOVERS2C2CUTOFF cannot take more than one value.&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :   if (ONEOVERS2C2CUTOFF.size() == 0)</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :     ONEOVERS2C2CUTOFF.push_back(500);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   parseVector(&quot;XCYL&quot;, XCYL);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   if (XCYL.size() &gt; 1)</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     error(&quot;XCYL cannot take more than one value.&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :   if (XCYL.size() == 0)</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          1 :     XCYL.push_back(-1.0);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :   parseVector(&quot;YCYL&quot;, YCYL);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   if (YCYL.size() &gt; 1)</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     error(&quot;YCYL cannot take more than one value.&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   if (YCYL.size() == 0)</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          1 :     YCYL.push_back(-1.0);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      12289 :   for (unsigned i = 0; i &lt; UMEM.size(); i++)</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   {</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      12288 :     atoms.push_back(UMEM[i]);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      12289 :   for (unsigned i = 0; i &lt; LMEM.size(); i++)</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      12288 :     atoms.push_back(LMEM[i]);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   }</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       4097 :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   {</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       4096 :     atoms.push_back(TAILS[i]);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          1 :   addValueWithDerivatives();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :   setNotPeriodic();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          1 :   requestAtoms(atoms);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          1 : }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          3 : void memFusionP::calculate()</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : {</a>
+<a name="190"><span class="lineNum">     190 </span>            :   /**************************</a>
+<a name="191"><span class="lineNum">     191 </span>            :    *                        *</a>
+<a name="192"><span class="lineNum">     192 </span>            :    *         System         *</a>
+<a name="193"><span class="lineNum">     193 </span>            :    *                        *</a>
+<a name="194"><span class="lineNum">     194 </span>            :    **************************/</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   // Box dimensions.</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          3 :   double Lx = getBox()[0][0], Ly = getBox()[1][1], Lz = getBox()[2][2];</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Z center of the upper membrane (uMem) and lower membrane (lMem) for systems with PBC: https://en.wikipedia.org/wiki/Center_of_mass#Systems_with_periodic_boundary_conditions .</a>
+<a name="200"><span class="lineNum">     200 </span>            :   double ZuMem, ZuMemcos = 0.0, ZuMemsin = 0.0, uMemAngle, ZlMem, ZlMemcos = 0.0, ZlMemsin = 0.0, lMemAngle;</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : #ifdef _OPENMP</a>
+<a name="203"><span class="lineNum">     203 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          3 :   #pragma omp parallel for private(uMemAngle, lMemAngle) reduction(+:ZuMemcos, ZuMemsin, ZlMemcos, ZlMemsin)</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : #endif</a>
+<a name="206"><span class="lineNum">     206 </span>            : #endif</a>
+<a name="207"><span class="lineNum">     207 </span>            :   for (unsigned i = 0; i &lt; UMEM.size(); i++)</a>
+<a name="208"><span class="lineNum">     208 </span>            :   {</a>
+<a name="209"><span class="lineNum">     209 </span>            :     uMemAngle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i)))[2];</a>
+<a name="210"><span class="lineNum">     210 </span>            :     lMemAngle = 2.0 * M_PI * getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + UMEM.size())))[2];</a>
+<a name="211"><span class="lineNum">     211 </span>            :     ZuMemcos += cos(uMemAngle);</a>
+<a name="212"><span class="lineNum">     212 </span>            :     ZuMemsin += sin(uMemAngle);</a>
+<a name="213"><span class="lineNum">     213 </span>            :     ZlMemcos += cos(lMemAngle);</a>
+<a name="214"><span class="lineNum">     214 </span>            :     ZlMemsin += sin(lMemAngle);</a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          3 :   ZuMemcos = ZuMemcos / UMEM.size();</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          3 :   ZuMemsin = ZuMemsin / UMEM.size();</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          3 :   ZlMemcos = ZlMemcos / UMEM.size();</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          3 :   ZlMemsin = ZlMemsin / UMEM.size();</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          3 :   ZuMem = Lz * (atan2(-ZuMemsin, -ZuMemcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          3 :   ZlMem = Lz * (atan2(-ZlMemsin, -ZlMemcos) + M_PI) / (2.0 * M_PI);</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            :   // Z center of the boths membranes (upper and lower).</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          3 :   double ZMems = (ZuMem + ZlMem) / 2.0;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   /*************************</a>
+<a name="229"><span class="lineNum">     229 </span>            :    *                        *</a>
+<a name="230"><span class="lineNum">     230 </span>            :    *         Xi_Mem         *</a>
+<a name="231"><span class="lineNum">     231 </span>            :    *                        *</a>
+<a name="232"><span class="lineNum">     232 </span>            :    **************************/</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            :   // Quantity of beads of the membranes.</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          3 :   unsigned membraneBeads = UMEM.size() + LMEM.size();</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   // Z distance from the lipid tail to the geometric center of both membranes.</a>
+<a name="238"><span class="lineNum">     238 </span>            :   double ZTailDistance;</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   // Z position of the first slice.</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          3 :   double firstSliceZ_Mem = ZMems + (0.0 + 0.5 - NSMEM[0] / 2.0) * DSMEM[0];</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   // Z distance between the first slice and the Z center of the membrane.</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          3 :   double firstSliceZDist_Mem = pbcDistance(Vector(0.0, 0.0, firstSliceZ_Mem), Vector(0.0, 0.0, ZMems))[2];</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :   // Position in the cylinder.</a>
+<a name="247"><span class="lineNum">     247 </span>            :   double PositionS_Mem;</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   // Slices to analyze per particle.</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          3 :   std::vector&lt;unsigned&gt; s1_Mem(TAILS.size()), s2_Mem(TAILS.size());</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            :   // Mark the particles to analyze.</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; analyzeThisParticle_Mem(TAILS.size());</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :   // Eq. 7 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; faxial_Mem(TAILS.size() * NSMEM[0]);</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // Eq. 16 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; d_faxial_Mem_dz(TAILS.size() * NSMEM[0]);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; Fs_Mem(NSMEM[0]);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            :   // Eq. 11 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; ws_Mem(NSMEM[0]);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   double W_Mem = 0.0;</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   // Eq. 21 and 22 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; sx_Mem(NSMEM[0]), sy_Mem(NSMEM[0]), cx_Mem(NSMEM[0]), cy_Mem(NSMEM[0]);</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   // Eq. 10 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="274"><span class="lineNum">     274 </span>            :   double Xsc_Mem = 0.0, Xcc_Mem = 0.0, Ysc_Mem = 0.0, Ycc_Mem = 0.0;</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :   // Aux.</a>
+<a name="277"><span class="lineNum">     277 </span>            :   double x, aux;</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            :   // Scaled position of the lipid tail respect the origin of coordinates.</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          3 :   Vector TailPosition;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            :   // Thanks stack overflow.</a>
+<a name="283"><span class="lineNum">     283 </span>            : #ifdef _OPENMP</a>
+<a name="284"><span class="lineNum">     284 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="285"><span class="lineNum">     285 </span>            :   #pragma omp declare reduction(vec_double_plus : std::vector&lt;double&gt; : \</a>
+<a name="286"><span class="lineNum">     286 </span>            :   std::transform(omp_out.begin(), omp_out.end(), omp_in.begin(), omp_out.begin(), std::plus&lt;double&gt;())) \</a>
+<a name="287"><span class="lineNum">     287 </span>            :   initializer(omp_priv = decltype(omp_orig)(omp_orig.size()))</a>
+<a name="288"><span class="lineNum">     288 </span>            : #endif</a>
+<a name="289"><span class="lineNum">     289 </span>            : #endif</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : #ifdef _OPENMP</a>
+<a name="292"><span class="lineNum">     292 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          3 :   #pragma omp parallel for private(ZTailDistance, PositionS_Mem, TailPosition, x, aux) reduction(vec_double_plus:Fs_Mem, sx_Mem, sy_Mem, cx_Mem, cy_Mem)</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : #endif</a>
+<a name="295"><span class="lineNum">     295 </span>            : #endif</a>
+<a name="296"><span class="lineNum">     296 </span>            :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</a>
+<a name="297"><span class="lineNum">     297 </span>            :   {</a>
+<a name="298"><span class="lineNum">     298 </span>            :     ZTailDistance = pbcDistance(Vector(0.0, 0.0, ZMems), getPosition(i + membraneBeads))[2];</a>
+<a name="299"><span class="lineNum">     299 </span>            :     PositionS_Mem = (ZTailDistance + firstSliceZDist_Mem) / DSMEM[0];</a>
+<a name="300"><span class="lineNum">     300 </span>            :     // If the following condition is met the particle is in the Z space of the cylinder.</a>
+<a name="301"><span class="lineNum">     301 </span>            :     if ((PositionS_Mem &gt;= (-0.5 - HMEM[0])) &amp;&amp; (PositionS_Mem &lt;= (NSMEM[0] + 0.5 - 1.0 + HMEM[0])))</a>
+<a name="302"><span class="lineNum">     302 </span>            :     {</a>
+<a name="303"><span class="lineNum">     303 </span>            :       analyzeThisParticle_Mem[i] = 1.0;</a>
+<a name="304"><span class="lineNum">     304 </span>            :       // Defining the slices to analyze each particle.</a>
+<a name="305"><span class="lineNum">     305 </span>            :       if (PositionS_Mem &lt; 1)</a>
+<a name="306"><span class="lineNum">     306 </span>            :       {</a>
+<a name="307"><span class="lineNum">     307 </span>            :         s1_Mem[i] = 0;</a>
+<a name="308"><span class="lineNum">     308 </span>            :         s2_Mem[i] = 2;</a>
+<a name="309"><span class="lineNum">     309 </span>            :       }</a>
+<a name="310"><span class="lineNum">     310 </span>            :       else if (PositionS_Mem &lt;= (NSMEM[0] - 2.0))</a>
+<a name="311"><span class="lineNum">     311 </span>            :       {</a>
+<a name="312"><span class="lineNum">     312 </span>            :         s1_Mem[i] = floor(PositionS_Mem) - 1;</a>
+<a name="313"><span class="lineNum">     313 </span>            :         s2_Mem[i] = floor(PositionS_Mem) + 1;</a>
+<a name="314"><span class="lineNum">     314 </span>            :       }</a>
+<a name="315"><span class="lineNum">     315 </span>            :       else</a>
+<a name="316"><span class="lineNum">     316 </span>            :       {</a>
+<a name="317"><span class="lineNum">     317 </span>            :         s1_Mem[i] = NSMEM[0] - 3;</a>
+<a name="318"><span class="lineNum">     318 </span>            :         s2_Mem[i] = NSMEM[0] - 1;</a>
+<a name="319"><span class="lineNum">     319 </span>            :       }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :       TailPosition = getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + membraneBeads)));</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            :       for (unsigned s = s1_Mem[i]; s &lt;= s2_Mem[i]; s++)</a>
+<a name="324"><span class="lineNum">     324 </span>            :       {</a>
+<a name="325"><span class="lineNum">     325 </span>            :         x = (ZTailDistance - (s + 0.5 - NSMEM[0] / 2.0) * DSMEM[0]) * 2.0 / DSMEM[0];</a>
+<a name="326"><span class="lineNum">     326 </span>            :         if (!((x &lt;= -1.0 - HMEM[0]) || (x &gt;= 1.0 + HMEM[0])))</a>
+<a name="327"><span class="lineNum">     327 </span>            :         {</a>
+<a name="328"><span class="lineNum">     328 </span>            :           if (((-1.0 + HMEM[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - HMEM[0])))</a>
+<a name="329"><span class="lineNum">     329 </span>            :           {</a>
+<a name="330"><span class="lineNum">     330 </span>            :             faxial_Mem[i + TAILS.size() * s] = 1.0;</a>
+<a name="331"><span class="lineNum">     331 </span>            :             Fs_Mem[s] += 1.0;</a>
+<a name="332"><span class="lineNum">     332 </span>            :             sx_Mem[s] += sin(2.0 * M_PI * TailPosition[0]);</a>
+<a name="333"><span class="lineNum">     333 </span>            :             sy_Mem[s] += sin(2.0 * M_PI * TailPosition[1]);</a>
+<a name="334"><span class="lineNum">     334 </span>            :             cx_Mem[s] += cos(2.0 * M_PI * TailPosition[0]);</a>
+<a name="335"><span class="lineNum">     335 </span>            :             cy_Mem[s] += cos(2.0 * M_PI * TailPosition[1]);</a>
+<a name="336"><span class="lineNum">     336 </span>            :           }</a>
+<a name="337"><span class="lineNum">     337 </span>            :           else if (((1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + HMEM[0])))</a>
+<a name="338"><span class="lineNum">     338 </span>            :           {</a>
+<a name="339"><span class="lineNum">     339 </span>            :             aux = 0.5 - ((3.0 * x - 3.0) / (4.0 * HMEM[0])) + (pow((x - 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="340"><span class="lineNum">     340 </span>            :             faxial_Mem[i + TAILS.size() * s] = aux;</a>
+<a name="341"><span class="lineNum">     341 </span>            :             d_faxial_Mem_dz[i + TAILS.size() * s] = ((-3.0 / (4.0 * HMEM[0])) + ((3.0 * pow((x - 1), 2)) / (4.0 * pow(HMEM[0], 3)))) * 2.0 / DSMEM[0];</a>
+<a name="342"><span class="lineNum">     342 </span>            :             Fs_Mem[s] += aux;</a>
+<a name="343"><span class="lineNum">     343 </span>            :             sx_Mem[s] += aux * sin(2.0 * M_PI * TailPosition[0]);</a>
+<a name="344"><span class="lineNum">     344 </span>            :             sy_Mem[s] += aux * sin(2.0 * M_PI * TailPosition[1]);</a>
+<a name="345"><span class="lineNum">     345 </span>            :             cx_Mem[s] += aux * cos(2.0 * M_PI * TailPosition[0]);</a>
+<a name="346"><span class="lineNum">     346 </span>            :             cy_Mem[s] += aux * cos(2.0 * M_PI * TailPosition[1]);</a>
+<a name="347"><span class="lineNum">     347 </span>            :           }</a>
+<a name="348"><span class="lineNum">     348 </span>            :           else if (((-1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + HMEM[0])))</a>
+<a name="349"><span class="lineNum">     349 </span>            :           {</a>
+<a name="350"><span class="lineNum">     350 </span>            :             aux = 0.5 + ((3.0 * x + 3.0) / (4.0 * HMEM[0])) - (pow((x + 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="351"><span class="lineNum">     351 </span>            :             faxial_Mem[i + TAILS.size() * s] = aux;</a>
+<a name="352"><span class="lineNum">     352 </span>            :             d_faxial_Mem_dz[i + TAILS.size() * s] = ((3.0 / (4.0 * HMEM[0])) - ((3.0 * pow((x + 1), 2)) / (4.0 * pow(HMEM[0], 3)))) * 2.0 / DSMEM[0];</a>
+<a name="353"><span class="lineNum">     353 </span>            :             Fs_Mem[s] += aux;</a>
+<a name="354"><span class="lineNum">     354 </span>            :             sx_Mem[s] += (aux * sin(2.0 * M_PI * TailPosition[0]));</a>
+<a name="355"><span class="lineNum">     355 </span>            :             sy_Mem[s] += (aux * sin(2.0 * M_PI * TailPosition[1]));</a>
+<a name="356"><span class="lineNum">     356 </span>            :             cx_Mem[s] += (aux * cos(2.0 * M_PI * TailPosition[0]));</a>
+<a name="357"><span class="lineNum">     357 </span>            :             cy_Mem[s] += (aux * cos(2.0 * M_PI * TailPosition[1]));</a>
+<a name="358"><span class="lineNum">     358 </span>            :           }</a>
+<a name="359"><span class="lineNum">     359 </span>            :         }</a>
+<a name="360"><span class="lineNum">     360 </span>            :       }</a>
+<a name="361"><span class="lineNum">     361 </span>            :     }</a>
+<a name="362"><span class="lineNum">     362 </span>            :   }</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        213 :   for (unsigned s = 0; s &lt; NSMEM[0]; s++)</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :   {</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        210 :     if (Fs_Mem[s] != 0.0)</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :     {</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        106 :       ws_Mem[s] = tanh(Fs_Mem[s]);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        106 :       W_Mem += ws_Mem[s];</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        106 :       sx_Mem[s] = sx_Mem[s] / Fs_Mem[s];</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        106 :       sy_Mem[s] = sy_Mem[s] / Fs_Mem[s];</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        106 :       cx_Mem[s] = cx_Mem[s] / Fs_Mem[s];</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        106 :       cy_Mem[s] = cy_Mem[s] / Fs_Mem[s];</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        106 :       Xsc_Mem += sx_Mem[s] * ws_Mem[s];</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        106 :       Ysc_Mem += sy_Mem[s] * ws_Mem[s];</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        106 :       Xcc_Mem += cx_Mem[s] * ws_Mem[s];</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        106 :       Ycc_Mem += cy_Mem[s] * ws_Mem[s];</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :     }</a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          3 :   Xsc_Mem = Xsc_Mem / W_Mem;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          3 :   Ysc_Mem = Ysc_Mem / W_Mem;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          3 :   Xcc_Mem = Xcc_Mem / W_Mem;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          3 :   Ycc_Mem = Ycc_Mem / W_Mem;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            :   // Eq. 12 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="387"><span class="lineNum">     387 </span>            :   double Xcyl_Mem, Ycyl_Mem;</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">          3 :   if ((XCYL[0] &gt; 0.0) &amp;&amp; (YCYL[0] &gt; 0.0))</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :   {</a>
+<a name="391"><span class="lineNum">     391 </span>            :     Xcyl_Mem = XCYL[0];</a>
+<a name="392"><span class="lineNum">     392 </span>            :     Ycyl_Mem = YCYL[0];</a>
+<a name="393"><span class="lineNum">     393 </span>            :   }</a>
+<a name="394"><span class="lineNum">     394 </span>            :   else</a>
+<a name="395"><span class="lineNum">     395 </span>            :   {</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          3 :     Xcyl_Mem = (atan2(-Xsc_Mem, -Xcc_Mem) + M_PI) * Lx / (2 * M_PI);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          3 :     Ycyl_Mem = (atan2(-Ysc_Mem, -Ycc_Mem) + M_PI) * Ly / (2 * M_PI);</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   }</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :   // Eq. 25, 26 and 27 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="401"><span class="lineNum">     401 </span>            :   double d_sx_Mem_dx, d_sx_Mem_dz, d_sy_Mem_dy, d_sy_Mem_dz, d_cx_Mem_dx, d_cx_Mem_dz, d_cy_Mem_dy, d_cy_Mem_dz;</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            :   // Eq. 29 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="404"><span class="lineNum">     404 </span>            :   double d_ws_Mem_dz;</a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            :   // Eq. 31, 32 and 33 Hub &amp; Awasthi JCTC 2017</a>
+<a name="407"><span class="lineNum">     407 </span>            :   double d_Xsc_Mem_dx, d_Xsc_Mem_dz, d_Xcc_Mem_dx, d_Xcc_Mem_dz, d_Ysc_Mem_dy, d_Ysc_Mem_dz, d_Ycc_Mem_dy, d_Ycc_Mem_dz;</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            :   // Center of the cylinder. XY components are calculated (or defined), Z is the Z geometric center of the membranes of the system.</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">          3 :   Vector xyzCyl_Mem = pbcDistance(Vector(0.0, 0.0, 0.0), Vector(Xcyl_Mem, Ycyl_Mem, ZMems));</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            :   // Distances from the lipid tails to center of the cylinder.</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          3 :   std::vector&lt;Vector&gt; CylDistances_Mem(TAILS.size());</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            :   // XY distance from the lipid tails to the center of the cylinder.</a>
+<a name="416"><span class="lineNum">     416 </span>            :   double ri_Mem;</a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span>            :   // Eq. 8 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="419"><span class="lineNum">     419 </span>            :   double fradial_Mem = 0;</a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            :   // Eq. 15 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; d_fradial_Mem_dx(TAILS.size()), d_fradial_Mem_dy(TAILS.size());</span></a>
+<a name="423"><span class="lineNum">     423 </span>            : </a>
+<a name="424"><span class="lineNum">     424 </span>            :   // Eq. 35, 36, 37 and 38 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; d_Xcyl_Mem_dx(TAILS.size()), d_Xcyl_Mem_dz(TAILS.size()), d_Ycyl_Mem_dy(TAILS.size()), d_Ycyl_Mem_dz(TAILS.size());</span></a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :   // To avoid rare instabilities auxX_Mem and auxY_Mem are truncated at a configurable value (default = 500).</a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          3 :   double auxX_Mem = (1 / (pow(Xsc_Mem, 2) + pow(Xcc_Mem, 2))), auxY_Mem = (1 / (pow(Ysc_Mem, 2) + pow(Ycc_Mem, 2)));</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          3 :   if (auxX_Mem &gt; ONEOVERS2C2CUTOFF[0])</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :   {</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :     auxX_Mem = Lx * ONEOVERS2C2CUTOFF[0] / (2 * M_PI);</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :   }</a>
+<a name="434"><span class="lineNum">     434 </span>            :   else</a>
+<a name="435"><span class="lineNum">     435 </span>            :   {</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          3 :     auxX_Mem = Lx * auxX_Mem / (2 * M_PI);</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :   }</a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          3 :   if (auxY_Mem &gt; ONEOVERS2C2CUTOFF[0])</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   {</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineNoCov">          0 :     auxY_Mem = Ly * ONEOVERS2C2CUTOFF[0] / (2 * M_PI);</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :   }</a>
+<a name="443"><span class="lineNum">     443 </span>            :   else</a>
+<a name="444"><span class="lineNum">     444 </span>            :   {</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          3 :     auxY_Mem = Ly * auxY_Mem / (2 * M_PI);</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :   }</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            :   // Number of lipid tails within the slice s of the membranes cylinder.</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; Nsp_Mem(NSMEM[0]), psi_Mem(NSMEM[0]), d_psi_Mem(NSMEM[0]);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            :   // Eq. 3 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          3 :   double b_Mem = (ZETAMEM[0] / (1.0 - ZETAMEM[0])), c_Mem = ((1.0 - ZETAMEM[0]) * exp(b_Mem));</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span>            :   // Eq. 19 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; fradial_Mem_d_faxial_Mem_dz(TAILS.size() * NSMEM[0]);</span></a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   // Eq. 20 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; Axs_Mem(NSMEM[0]), Ays_Mem(NSMEM[0]);</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            :   // Eq. 1 Hub &amp; Awasthi JCTC 2017. This is the CV that describes de Pore Nucleation.</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          3 :   double Xi_Mem = 0.0;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            : #ifdef _OPENMP</a>
+<a name="464"><span class="lineNum">     464 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          3 :   #pragma omp parallel for private(TailPosition,d_Xsc_Mem_dx,d_Xcc_Mem_dx,d_Ysc_Mem_dy,d_Ycc_Mem_dy,d_Xsc_Mem_dz,d_Xcc_Mem_dz,d_Ysc_Mem_dz,d_Ycc_Mem_dz,d_sx_Mem_dx,d_sy_Mem_dy,d_cx_Mem_dx,d_cy_Mem_dy,d_sx_Mem_dz,d_sy_Mem_dz,d_cx_Mem_dz,d_cy_Mem_dz,d_ws_Mem_dz,ri_Mem,x,fradial_Mem) reduction(vec_double_plus: Nsp_Mem, Axs_Mem, Ays_Mem)</span></a>
+<a name="466"><span class="lineNum">     466 </span>            : #endif</a>
+<a name="467"><span class="lineNum">     467 </span>            : #endif</a>
+<a name="468"><span class="lineNum">     468 </span>            :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</a>
+<a name="469"><span class="lineNum">     469 </span>            :   {</a>
+<a name="470"><span class="lineNum">     470 </span>            :     if (analyzeThisParticle_Mem[i])</a>
+<a name="471"><span class="lineNum">     471 </span>            :     {</a>
+<a name="472"><span class="lineNum">     472 </span>            :       TailPosition = getPbc().realToScaled(pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + membraneBeads)));</a>
+<a name="473"><span class="lineNum">     473 </span>            :       d_Xsc_Mem_dx = 0.0;</a>
+<a name="474"><span class="lineNum">     474 </span>            :       d_Xcc_Mem_dx = 0.0;</a>
+<a name="475"><span class="lineNum">     475 </span>            :       d_Ysc_Mem_dy = 0.0;</a>
+<a name="476"><span class="lineNum">     476 </span>            :       d_Ycc_Mem_dy = 0.0;</a>
+<a name="477"><span class="lineNum">     477 </span>            :       d_Xsc_Mem_dz = 0.0;</a>
+<a name="478"><span class="lineNum">     478 </span>            :       d_Xcc_Mem_dz = 0.0;</a>
+<a name="479"><span class="lineNum">     479 </span>            :       d_Ysc_Mem_dz = 0.0;</a>
+<a name="480"><span class="lineNum">     480 </span>            :       d_Ycc_Mem_dz = 0.0;</a>
+<a name="481"><span class="lineNum">     481 </span>            :       for (unsigned s = s1_Mem[i]; s &lt;= s2_Mem[i]; s++)</a>
+<a name="482"><span class="lineNum">     482 </span>            :       {</a>
+<a name="483"><span class="lineNum">     483 </span>            :         if (Fs_Mem[s] != 0.0)</a>
+<a name="484"><span class="lineNum">     484 </span>            :         {</a>
+<a name="485"><span class="lineNum">     485 </span>            :           d_sx_Mem_dx = faxial_Mem[i + TAILS.size() * s] * 2.0 * M_PI * cos(2.0 * M_PI * TailPosition[0]) / (Lx * Fs_Mem[s]);</a>
+<a name="486"><span class="lineNum">     486 </span>            :           d_sy_Mem_dy = faxial_Mem[i + TAILS.size() * s] * 2.0 * M_PI * cos(2.0 * M_PI * TailPosition[1]) / (Ly * Fs_Mem[s]);</a>
+<a name="487"><span class="lineNum">     487 </span>            :           d_cx_Mem_dx = -faxial_Mem[i + TAILS.size() * s] * 2.0 * M_PI * sin(2.0 * M_PI * TailPosition[0]) / (Lx * Fs_Mem[s]);</a>
+<a name="488"><span class="lineNum">     488 </span>            :           d_cy_Mem_dy = -faxial_Mem[i + TAILS.size() * s] * 2.0 * M_PI * sin(2.0 * M_PI * TailPosition[1]) / (Ly * Fs_Mem[s]);</a>
+<a name="489"><span class="lineNum">     489 </span>            :           d_Xsc_Mem_dx += ws_Mem[s] * d_sx_Mem_dx / W_Mem;</a>
+<a name="490"><span class="lineNum">     490 </span>            :           d_Xcc_Mem_dx += ws_Mem[s] * d_cx_Mem_dx / W_Mem;</a>
+<a name="491"><span class="lineNum">     491 </span>            :           d_Ysc_Mem_dy += ws_Mem[s] * d_sy_Mem_dy / W_Mem;</a>
+<a name="492"><span class="lineNum">     492 </span>            :           d_Ycc_Mem_dy += ws_Mem[s] * d_cy_Mem_dy / W_Mem;</a>
+<a name="493"><span class="lineNum">     493 </span>            : </a>
+<a name="494"><span class="lineNum">     494 </span>            :           d_sx_Mem_dz = d_faxial_Mem_dz[i + TAILS.size() * s] * (sin(2.0 * M_PI * TailPosition[0]) - sx_Mem[s]) / Fs_Mem[s];</a>
+<a name="495"><span class="lineNum">     495 </span>            :           d_sy_Mem_dz = d_faxial_Mem_dz[i + TAILS.size() * s] * (sin(2.0 * M_PI * TailPosition[1]) - sy_Mem[s]) / Fs_Mem[s];</a>
+<a name="496"><span class="lineNum">     496 </span>            :           d_cx_Mem_dz = d_faxial_Mem_dz[i + TAILS.size() * s] * (cos(2.0 * M_PI * TailPosition[0]) - cx_Mem[s]) / Fs_Mem[s];</a>
+<a name="497"><span class="lineNum">     497 </span>            :           d_cy_Mem_dz = d_faxial_Mem_dz[i + TAILS.size() * s] * (cos(2.0 * M_PI * TailPosition[1]) - cy_Mem[s]) / Fs_Mem[s];</a>
+<a name="498"><span class="lineNum">     498 </span>            :           d_ws_Mem_dz = (1 - pow(ws_Mem[s], 2)) * d_faxial_Mem_dz[i + TAILS.size() * s];</a>
+<a name="499"><span class="lineNum">     499 </span>            :           d_Xsc_Mem_dz += (ws_Mem[s] * d_sx_Mem_dz + d_ws_Mem_dz * (sx_Mem[s] - Xsc_Mem)) / W_Mem;</a>
+<a name="500"><span class="lineNum">     500 </span>            :           d_Xcc_Mem_dz += (ws_Mem[s] * d_cx_Mem_dz + d_ws_Mem_dz * (cx_Mem[s] - Xcc_Mem)) / W_Mem;</a>
+<a name="501"><span class="lineNum">     501 </span>            :           d_Ysc_Mem_dz += (ws_Mem[s] * d_sy_Mem_dz + d_ws_Mem_dz * (sy_Mem[s] - Ysc_Mem)) / W_Mem;</a>
+<a name="502"><span class="lineNum">     502 </span>            :           d_Ycc_Mem_dz += (ws_Mem[s] * d_cy_Mem_dz + d_ws_Mem_dz * (cy_Mem[s] - Ycc_Mem)) / W_Mem;</a>
+<a name="503"><span class="lineNum">     503 </span>            :         }</a>
+<a name="504"><span class="lineNum">     504 </span>            :       }</a>
+<a name="505"><span class="lineNum">     505 </span>            :       d_Xcyl_Mem_dx[i] = auxX_Mem * (-Xsc_Mem * d_Xcc_Mem_dx + Xcc_Mem * d_Xsc_Mem_dx);</a>
+<a name="506"><span class="lineNum">     506 </span>            :       d_Xcyl_Mem_dz[i] = auxX_Mem * (-Xsc_Mem * d_Xcc_Mem_dz + Xcc_Mem * d_Xsc_Mem_dz);</a>
+<a name="507"><span class="lineNum">     507 </span>            :       d_Ycyl_Mem_dy[i] = auxY_Mem * (-Ysc_Mem * d_Ycc_Mem_dy + Ycc_Mem * d_Ysc_Mem_dy);</a>
+<a name="508"><span class="lineNum">     508 </span>            :       d_Ycyl_Mem_dz[i] = auxY_Mem * (-Ysc_Mem * d_Ycc_Mem_dz + Ycc_Mem * d_Ysc_Mem_dz);</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            :       CylDistances_Mem[i] = pbcDistance(xyzCyl_Mem, pbcDistance(Vector(0.0, 0.0, 0.0), getPosition(i + membraneBeads)));</a>
+<a name="511"><span class="lineNum">     511 </span>            :       ri_Mem = sqrt(pow(CylDistances_Mem[i][0], 2) + pow(CylDistances_Mem[i][1], 2));</a>
+<a name="512"><span class="lineNum">     512 </span>            :       x = ri_Mem / RCYLMEM[0];</a>
+<a name="513"><span class="lineNum">     513 </span>            :       if (!((x &lt;= -1.0 - HMEM[0]) || (x &gt;= 1.0 + HMEM[0])))</a>
+<a name="514"><span class="lineNum">     514 </span>            :       {</a>
+<a name="515"><span class="lineNum">     515 </span>            :         if (((-1.0 + HMEM[0]) &lt;= x) &amp;&amp; (x &lt;= (1.0 - HMEM[0])))</a>
+<a name="516"><span class="lineNum">     516 </span>            :         {</a>
+<a name="517"><span class="lineNum">     517 </span>            :           fradial_Mem = 1.0;</a>
+<a name="518"><span class="lineNum">     518 </span>            :         }</a>
+<a name="519"><span class="lineNum">     519 </span>            :         else if (((1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (1.0 + HMEM[0])))</a>
+<a name="520"><span class="lineNum">     520 </span>            :         {</a>
+<a name="521"><span class="lineNum">     521 </span>            :           fradial_Mem = 0.5 - ((3.0 * x - 3.0) / (4.0 * HMEM[0])) + (pow((x - 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="522"><span class="lineNum">     522 </span>            :           d_fradial_Mem_dx[i] = ((-3.0 / (4.0 * HMEM[0])) + ((3.0 * pow((x - 1), 2)) / (4.0 * pow(HMEM[0], 3)))) * CylDistances_Mem[i][0] / (RCYLMEM[0] * ri_Mem);</a>
+<a name="523"><span class="lineNum">     523 </span>            :           d_fradial_Mem_dy[i] = ((-3.0 / (4.0 * HMEM[0])) + ((3.0 * pow((x - 1), 2)) / (4.0 * pow(HMEM[0], 3)))) * CylDistances_Mem[i][1] / (RCYLMEM[0] * ri_Mem);</a>
+<a name="524"><span class="lineNum">     524 </span>            :         }</a>
+<a name="525"><span class="lineNum">     525 </span>            :         else if (((-1.0 - HMEM[0]) &lt; x) &amp;&amp; (x &lt; (-1.0 + HMEM[0])))</a>
+<a name="526"><span class="lineNum">     526 </span>            :         {</a>
+<a name="527"><span class="lineNum">     527 </span>            :           fradial_Mem = 0.5 + ((3.0 * x + 3.0) / (4.0 * HMEM[0])) - (pow((x + 1.0), 3) / (4.0 * pow(HMEM[0], 3)));</a>
+<a name="528"><span class="lineNum">     528 </span>            :           d_fradial_Mem_dx[i] = ((3.0 / (4.0 * HMEM[0])) - ((3.0 * pow((x + 1), 2)) / (4.0 * pow(HMEM[0], 3)))) * CylDistances_Mem[i][0] / (RCYLMEM[0] * ri_Mem);</a>
+<a name="529"><span class="lineNum">     529 </span>            :           d_fradial_Mem_dy[i] = ((3.0 / (4.0 * HMEM[0])) - ((3.0 * pow((x + 1), 2)) / (4.0 * pow(HMEM[0], 3)))) * CylDistances_Mem[i][1] / (RCYLMEM[0] * ri_Mem);</a>
+<a name="530"><span class="lineNum">     530 </span>            :         }</a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span>            :         for (unsigned s = s1_Mem[i]; s &lt;= s2_Mem[i]; s++)</a>
+<a name="533"><span class="lineNum">     533 </span>            :         {</a>
+<a name="534"><span class="lineNum">     534 </span>            :           Nsp_Mem[s] += fradial_Mem * faxial_Mem[i + TAILS.size() * s];</a>
+<a name="535"><span class="lineNum">     535 </span>            :           Axs_Mem[s] += faxial_Mem[i + TAILS.size() * s] * d_fradial_Mem_dx[i];</a>
+<a name="536"><span class="lineNum">     536 </span>            :           Ays_Mem[s] += faxial_Mem[i + TAILS.size() * s] * d_fradial_Mem_dy[i];</a>
+<a name="537"><span class="lineNum">     537 </span>            :           fradial_Mem_d_faxial_Mem_dz[i + TAILS.size() * s] = fradial_Mem * d_faxial_Mem_dz[i + TAILS.size() * s];</a>
+<a name="538"><span class="lineNum">     538 </span>            :         }</a>
+<a name="539"><span class="lineNum">     539 </span>            :       }</a>
+<a name="540"><span class="lineNum">     540 </span>            :     }</a>
+<a name="541"><span class="lineNum">     541 </span>            :   }</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">        213 :   for (unsigned s = 0; s &lt; NSMEM[0]; s++)</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :   {</a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">        210 :     if (Nsp_Mem[s] &lt;= 1.0)</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :     {</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">        166 :       psi_Mem[s] = ZETAMEM[0] * Nsp_Mem[s];</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        166 :       d_psi_Mem[s] = ZETAMEM[0];</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">        166 :       Xi_Mem += psi_Mem[s];</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :     }</a>
+<a name="551"><span class="lineNum">     551 </span>            :     else</a>
+<a name="552"><span class="lineNum">     552 </span>            :     {</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         44 :       psi_Mem[s] = 1.0 - c_Mem * exp(-b_Mem * Nsp_Mem[s]);</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         44 :       d_psi_Mem[s] = b_Mem * c_Mem * exp(-b_Mem * Nsp_Mem[s]);</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         44 :       Xi_Mem += psi_Mem[s];</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :     }</a>
+<a name="557"><span class="lineNum">     557 </span>            :   }</a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">          3 :   Xi_Mem = Xi_Mem / NSMEM[0];</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            :   // Eq. 18 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">          3 :   std::vector&lt;double&gt; faxial_Mem_d_fradial_Mem_dx(TAILS.size() * NSMEM[0]), faxial_Mem_d_fradial_Mem_dy(TAILS.size() * NSMEM[0]), faxial_Mem_d_fradial_Mem_dz(TAILS.size() * NSMEM[0]);</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span>            :   // Eq. 13 Hub &amp; Awasthi JCTC 2017.</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">          3 :   std::vector&lt;Vector&gt; derivatives_Mem(TAILS.size());</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            : #ifdef _OPENMP</a>
+<a name="568"><span class="lineNum">     568 </span>            : #if _OPENMP &gt;= 201307</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          3 :   #pragma omp parallel for private(aux)</span></a>
+<a name="570"><span class="lineNum">     570 </span>            : #endif</a>
+<a name="571"><span class="lineNum">     571 </span>            : #endif</a>
+<a name="572"><span class="lineNum">     572 </span>            :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</a>
+<a name="573"><span class="lineNum">     573 </span>            :   {</a>
+<a name="574"><span class="lineNum">     574 </span>            :     if (analyzeThisParticle_Mem[i])</a>
+<a name="575"><span class="lineNum">     575 </span>            :     {</a>
+<a name="576"><span class="lineNum">     576 </span>            :       for (unsigned s = s1_Mem[i]; s &lt;= s2_Mem[i]; s++)</a>
+<a name="577"><span class="lineNum">     577 </span>            :       {</a>
+<a name="578"><span class="lineNum">     578 </span>            :         if (faxial_Mem[i + TAILS.size() * s])</a>
+<a name="579"><span class="lineNum">     579 </span>            :         {</a>
+<a name="580"><span class="lineNum">     580 </span>            :           faxial_Mem_d_fradial_Mem_dx[i + TAILS.size() * s] = faxial_Mem[i + TAILS.size() * s] * d_fradial_Mem_dx[i] - d_Xcyl_Mem_dx[i] * Axs_Mem[s];</a>
+<a name="581"><span class="lineNum">     581 </span>            :           faxial_Mem_d_fradial_Mem_dy[i + TAILS.size() * s] = faxial_Mem[i + TAILS.size() * s] * d_fradial_Mem_dy[i] - d_Ycyl_Mem_dy[i] * Ays_Mem[s];</a>
+<a name="582"><span class="lineNum">     582 </span>            :           faxial_Mem_d_fradial_Mem_dz[i + TAILS.size() * s] = -d_Xcyl_Mem_dz[i] * Axs_Mem[s] - d_Ycyl_Mem_dz[i] * Ays_Mem[s];</a>
+<a name="583"><span class="lineNum">     583 </span>            :         }</a>
+<a name="584"><span class="lineNum">     584 </span>            :       }</a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span>            :       for (unsigned s = s1_Mem[i]; s &lt;= s2_Mem[i]; s++)</a>
+<a name="587"><span class="lineNum">     587 </span>            :       {</a>
+<a name="588"><span class="lineNum">     588 </span>            :         aux = d_psi_Mem[s] / NSMEM[0];</a>
+<a name="589"><span class="lineNum">     589 </span>            :         derivatives_Mem[i][0] += aux * faxial_Mem_d_fradial_Mem_dx[i + TAILS.size() * s];</a>
+<a name="590"><span class="lineNum">     590 </span>            :         derivatives_Mem[i][1] += aux * faxial_Mem_d_fradial_Mem_dy[i + TAILS.size() * s];</a>
+<a name="591"><span class="lineNum">     591 </span>            :         derivatives_Mem[i][2] += aux * (faxial_Mem_d_fradial_Mem_dz[i + TAILS.size() * s] + fradial_Mem_d_faxial_Mem_dz[i + TAILS.size() * s]);</a>
+<a name="592"><span class="lineNum">     592 </span>            :       }</a>
+<a name="593"><span class="lineNum">     593 </span>            :     }</a>
+<a name="594"><span class="lineNum">     594 </span>            :   }</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            :   // Derivatives and virial for the Xi_Mem.</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">          3 :   Tensor virial;</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">      12291 :   for (unsigned i = 0; i &lt; TAILS.size(); i++)</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :   {</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">      12288 :     setAtomsDerivatives((i + membraneBeads), derivatives_Mem[i]);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">      12288 :     virial -= Tensor(CylDistances_Mem[i], derivatives_Mem[i]);</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :   }</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">          3 :   setValue(Xi_Mem);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">          3 :   setBoxDerivatives(virial);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">          3 : }</span></a>
+<a name="607"><span class="lineNum">     607 </span>            : }</a>
+<a name="608"><span class="lineNum">     608 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/index-sort-f.html b/coverage/membranefusion/index-sort-f.html
new file mode 100644
index 0000000000..c06c2d6b13
--- /dev/null
+++ b/coverage/membranefusion/index-sort-f.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - membranefusion</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">456</td>
+            <td class="headerCovTableEntry">517</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FusionPoreNucleationP.cpp.gcov.html">FusionPoreNucleationP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.5%"><img src="../snow.png" width=12 height=10 alt="88.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.5&nbsp;%</td>
+      <td class="coverNumMed">184 / 208</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MemFusionP.cpp.gcov.html">MemFusionP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.7%"><img src="../snow.png" width=11 height=10 alt="88.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.7&nbsp;%</td>
+      <td class="coverNumMed">134 / 151</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FusionPoreExpansionP.cpp.gcov.html">FusionPoreExpansionP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.3%"><img src="../snow.png" width=13 height=10 alt="87.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.3&nbsp;%</td>
+      <td class="coverNumMed">138 / 158</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/index-sort-l.html b/coverage/membranefusion/index-sort-l.html
new file mode 100644
index 0000000000..753b272d19
--- /dev/null
+++ b/coverage/membranefusion/index-sort-l.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - membranefusion</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">456</td>
+            <td class="headerCovTableEntry">517</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FusionPoreExpansionP.cpp.gcov.html">FusionPoreExpansionP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.3%"><img src="../snow.png" width=13 height=10 alt="87.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.3&nbsp;%</td>
+      <td class="coverNumMed">138 / 158</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FusionPoreNucleationP.cpp.gcov.html">FusionPoreNucleationP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.5%"><img src="../snow.png" width=12 height=10 alt="88.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.5&nbsp;%</td>
+      <td class="coverNumMed">184 / 208</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MemFusionP.cpp.gcov.html">MemFusionP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.7%"><img src="../snow.png" width=11 height=10 alt="88.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.7&nbsp;%</td>
+      <td class="coverNumMed">134 / 151</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/membranefusion/index.html b/coverage/membranefusion/index.html
new file mode 100644
index 0000000000..92996868e4
--- /dev/null
+++ b/coverage/membranefusion/index.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - membranefusion</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - membranefusion</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">456</td>
+            <td class="headerCovTableEntry">517</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FusionPoreExpansionP.cpp.gcov.html">FusionPoreExpansionP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.3%"><img src="../snow.png" width=13 height=10 alt="87.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.3&nbsp;%</td>
+      <td class="coverNumMed">138 / 158</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FusionPoreNucleationP.cpp.gcov.html">FusionPoreNucleationP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.5%"><img src="../snow.png" width=12 height=10 alt="88.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.5&nbsp;%</td>
+      <td class="coverNumMed">184 / 208</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MemFusionP.cpp.gcov.html">MemFusionP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.7%"><img src="../snow.png" width=11 height=10 alt="88.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.7&nbsp;%</td>
+      <td class="coverNumMed">134 / 151</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/ActionVolume.cpp.func-sort-c.html b/coverage/multicolvar/ActionVolume.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3044bfb005
--- /dev/null
+++ b/coverage/multicolvar/ActionVolume.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/ActionVolume.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - ActionVolume.cpp<span style="font-size: 80%;"> (<a href="ActionVolume.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionVolume.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#35">_ZN4PLMD11multicolvar12ActionVolumeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#35">_ZN4PLMD11multicolvar12ActionVolumeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#25">_ZN4PLMD11multicolvar12ActionVolume16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#60">_ZNK4PLMD11multicolvar12ActionVolume19calculateAllVolumesERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">69358</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#72">_ZNK4PLMD11multicolvar12ActionVolume18inVolumeOfInterestERKj</a></td>
+              <td class="coverFnHi">148129</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/ActionVolume.cpp.func.html b/coverage/multicolvar/ActionVolume.cpp.func.html
new file mode 100644
index 0000000000..dc0f848f24
--- /dev/null
+++ b/coverage/multicolvar/ActionVolume.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/ActionVolume.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - ActionVolume.cpp<span style="font-size: 80%;"> (<a href="ActionVolume.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionVolume.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#25">_ZN4PLMD11multicolvar12ActionVolume16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#35">_ZN4PLMD11multicolvar12ActionVolumeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#35">_ZN4PLMD11multicolvar12ActionVolumeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#72">_ZNK4PLMD11multicolvar12ActionVolume18inVolumeOfInterestERKj</a></td>
+              <td class="coverFnHi">148129</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.cpp.gcov.html#60">_ZNK4PLMD11multicolvar12ActionVolume19calculateAllVolumesERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">69358</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/ActionVolume.cpp.gcov.html b/coverage/multicolvar/ActionVolume.cpp.gcov.html
new file mode 100644
index 0000000000..6df3c0ba08
--- /dev/null
+++ b/coverage/multicolvar/ActionVolume.cpp.gcov.html
@@ -0,0 +1,160 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/ActionVolume.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - ActionVolume.cpp<span style="font-size: 80%;"> (source / <a href="ActionVolume.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace multicolvar {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         40 : void ActionVolume::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         40 :   VolumeGradientBase::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        120 :   if( keys.reserved(&quot;VMEAN&quot;) ) keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        120 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MORE_THAN&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        120 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;SUM&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         80 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;the width of the function to be used for kernel density estimation&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         80 :   keys.add(&quot;compulsory&quot;,&quot;KERNEL&quot;,&quot;gaussian&quot;,&quot;the type of kernel function to be used&quot;);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         80 :   keys.addFlag(&quot;OUTSIDE&quot;,false,&quot;calculate quantities for colvars that are on atoms outside the region of interest&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         40 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         28 : ActionVolume::ActionVolume(const ActionOptions&amp;ao):</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   Action(ao),</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         28 :   VolumeGradientBase(ao)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span>            :   // Find number of quantities</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         28 :   if( getPntrToMultiColvar()-&gt;isDensity() ) nquantities=2;                           // Value + weight</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         17 :   else if( getPntrToMultiColvar()-&gt;getNumberOfQuantities()==2 ) nquantities=2;       // Value + weight</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          2 :   else nquantities = 1 + getPntrToMultiColvar()-&gt;getNumberOfQuantities()-2 + 1;      // Norm  + vector + weight</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            :   // Output some nice information</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         28 :   std::string functype=getPntrToMultiColvar()-&gt;getName();</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        279 :   std::transform( functype.begin(), functype.end(), functype.begin(), [](unsigned char c) { return std::tolower(c); } );</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         28 :   log.printf(&quot;  calculating %s inside region of insterest\n&quot;,functype.c_str() );</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         28 :   parseFlag(&quot;OUTSIDE&quot;,not_in); sigma=0.0;</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         81 :   if( keywords.exists(&quot;SIGMA&quot;) ) parse(&quot;SIGMA&quot;,sigma);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         84 :   if( keywords.exists(&quot;KERNEL&quot;) ) parse(&quot;KERNEL&quot;,kerneltype);</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         28 :   if( getPntrToMultiColvar()-&gt;isDensity() ) {</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :     std::string input;</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         22 :     addVessel( &quot;SUM&quot;, input, -1 );  // -1 here means that this value will be named getLabel()</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   }</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         28 :   readVesselKeywords();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         28 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      69358 : void ActionVolume::calculateAllVolumes( const unsigned&amp; curr, MultiValue&amp; outvals ) const {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      69358 :   Vector catom_pos=getPntrToMultiColvar()-&gt;getCentralAtomPos( curr );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      69358 :   double weight; Vector wdf; Tensor vir; std::vector&lt;Vector&gt; refders( getNumberOfAtoms() );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      69358 :   weight=calculateNumberInside( catom_pos, wdf, vir, refders );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      69358 :   if( not_in ) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       4000 :     weight = 1.0 - weight; wdf *= -1.; vir *=-1;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       8000 :     for(unsigned i=0; i&lt;refders.size(); ++i) refders[i]*=-1;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   }</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      69358 :   setNumberInVolume( 0, curr, weight, wdf, vir, refders, outvals );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      69358 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     148129 : bool ActionVolume::inVolumeOfInterest( const unsigned&amp; curr ) const {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     148129 :   Vector catom_pos=getPntrToMultiColvar()-&gt;getCentralAtomPos( curr );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     148129 :   Vector wdf; Tensor vir; std::vector&lt;Vector&gt; refders( getNumberOfAtoms() );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     148129 :   double weight=calculateNumberInside( catom_pos, wdf, vir, refders );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     148129 :   if( not_in ) weight = 1.0 - weight;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     148129 :   if( weight&lt;getTolerance() ) return false;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   return true;</a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/ActionVolume.h.func-sort-c.html b/coverage/multicolvar/ActionVolume.h.func-sort-c.html
new file mode 100644
index 0000000000..7d1212eee6
--- /dev/null
+++ b/coverage/multicolvar/ActionVolume.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/ActionVolume.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - ActionVolume.h<span style="font-size: 80%;"> (<a href="ActionVolume.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionVolume.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.h.gcov.html#64">_ZNK4PLMD11multicolvar12ActionVolume21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">71213</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/ActionVolume.h.func.html b/coverage/multicolvar/ActionVolume.h.func.html
new file mode 100644
index 0000000000..6b63d2c4f7
--- /dev/null
+++ b/coverage/multicolvar/ActionVolume.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/ActionVolume.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - ActionVolume.h<span style="font-size: 80%;"> (<a href="ActionVolume.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionVolume.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionVolume.h.gcov.html#64">_ZNK4PLMD11multicolvar12ActionVolume21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">71213</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/ActionVolume.h.gcov.html b/coverage/multicolvar/ActionVolume.h.gcov.html
new file mode 100644
index 0000000000..6d54d6f098
--- /dev/null
+++ b/coverage/multicolvar/ActionVolume.h.gcov.html
@@ -0,0 +1,163 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/ActionVolume.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - ActionVolume.h<span style="font-size: 80%;"> (source / <a href="ActionVolume.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_ActionVolume_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_ActionVolume_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VolumeGradientBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace multicolvar {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /**</a>
+<a name="32"><span class="lineNum">      32 </span>            : \ingroup INHERIT</a>
+<a name="33"><span class="lineNum">      33 </span>            : This is the abstract base class to use for implementing a new way of defining a particular region of the simulation</a>
+<a name="34"><span class="lineNum">      34 </span>            : box. You can use this to calculate the number of atoms inside that part or the average value of a quantity like the</a>
+<a name="35"><span class="lineNum">      35 </span>            : coordination number inside that part of the cell.</a>
+<a name="36"><span class="lineNum">      36 </span>            : */</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class ActionVolume : public VolumeGradientBase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Number of quantities in use in this colvar</a>
+<a name="41"><span class="lineNum">      41 </span>            :   unsigned nquantities;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// The value of sigma</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double sigma;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Are we interested in the area outside the colvar</a>
+<a name="45"><span class="lineNum">      45 </span>            :   bool not_in;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// The kernel type for this histogram</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::string kerneltype;</a>
+<a name="48"><span class="lineNum">      48 </span>            : protected:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double getSigma() const ;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string getKernelType() const ;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit ActionVolume(const ActionOptions&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Get the number of quantities that are calculated each time</a>
+<a name="55"><span class="lineNum">      55 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Calculate whats in the volume</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void calculateAllVolumes( const unsigned&amp; curr, MultiValue&amp; outvals ) const override;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// This calculates whether or not a particular is inside the box of interest</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// this is used for neighbour list with volumes</a>
+<a name="60"><span class="lineNum">      60 </span>            :   bool inVolumeOfInterest( const unsigned&amp; curr ) const ;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   virtual double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const=0;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned getCentralAtomElementIndex();</a>
+<a name="63"><span class="lineNum">      63 </span>            : };</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : inline</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      71213 : unsigned ActionVolume::getNumberOfQuantities() const {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      71213 :   return nquantities;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : inline</a>
+<a name="71"><span class="lineNum">      71 </span>            : double ActionVolume::getSigma() const {</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      98014 :   return sigma;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : inline</a>
+<a name="76"><span class="lineNum">      76 </span>            : std::string ActionVolume::getKernelType() const {</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      58014 :   return kerneltype;</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : inline</a>
+<a name="81"><span class="lineNum">      81 </span>            : unsigned ActionVolume::getCentralAtomElementIndex() {</a>
+<a name="82"><span class="lineNum">      82 </span>            :   return 1;</a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AlphaBeta.cpp.func-sort-c.html b/coverage/multicolvar/AlphaBeta.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4a13f43da9
--- /dev/null
+++ b/coverage/multicolvar/AlphaBeta.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AlphaBeta.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AlphaBeta.cpp<span style="font-size: 80%;"> (<a href="AlphaBeta.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryMed">87.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AlphaBeta.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#101">_ZN4PLMD11multicolvar9AlphaBeta10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#122">_ZN4PLMD11multicolvar9AlphaBetaC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#104">_ZN4PLMD11multicolvar12_GLOBAL__N_122AlphaBetaRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#122">_ZN4PLMD11multicolvar9AlphaBetaC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#106">_ZN4PLMD11multicolvar9AlphaBeta16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#176">_ZNK4PLMD11multicolvar9AlphaBeta7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#104">_ZN4PLMD11multicolvar12_GLOBAL__N_122AlphaBetaRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#104">_ZN4PLMD11multicolvar12_GLOBAL__N_122AlphaBetaRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AlphaBeta.cpp.func.html b/coverage/multicolvar/AlphaBeta.cpp.func.html
new file mode 100644
index 0000000000..abefb58fd4
--- /dev/null
+++ b/coverage/multicolvar/AlphaBeta.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AlphaBeta.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AlphaBeta.cpp<span style="font-size: 80%;"> (<a href="AlphaBeta.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryMed">87.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AlphaBeta.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#104">_ZN4PLMD11multicolvar12_GLOBAL__N_122AlphaBetaRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#104">_ZN4PLMD11multicolvar12_GLOBAL__N_122AlphaBetaRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#104">_ZN4PLMD11multicolvar12_GLOBAL__N_122AlphaBetaRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#101">_ZN4PLMD11multicolvar9AlphaBeta10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#106">_ZN4PLMD11multicolvar9AlphaBeta16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#122">_ZN4PLMD11multicolvar9AlphaBetaC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#122">_ZN4PLMD11multicolvar9AlphaBetaC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaBeta.cpp.gcov.html#176">_ZNK4PLMD11multicolvar9AlphaBeta7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AlphaBeta.cpp.gcov.html b/coverage/multicolvar/AlphaBeta.cpp.gcov.html
new file mode 100644
index 0000000000..2c342d2ca9
--- /dev/null
+++ b/coverage/multicolvar/AlphaBeta.cpp.gcov.html
@@ -0,0 +1,280 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AlphaBeta.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AlphaBeta.cpp<span style="font-size: 80%;"> (source / <a href="AlphaBeta.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntryMed">87.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace multicolvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC COLVAR ALPHABETA</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Measures a distance including pbc between the instantaneous values of a set of torsional angles and set of reference values.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This colvar calculates the following quantity.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : s = \frac{1}{2} \sum_i \left[ 1 + \cos( \phi_i - \phi_i^{\textrm{Ref}} ) \right]</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where the \f$\phi_i\f$ values are the instantaneous values for the \ref TORSION angles of interest.</a>
+<a name="44"><span class="lineNum">      44 </span>            : The \f$\phi_i^{\textrm{Ref}}\f$ values are the user-specified reference values for the torsional angles.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The following provides an example of the input for an alpha beta similarity.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \plumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : ALPHABETA ...</a>
+<a name="52"><span class="lineNum">      52 </span>            : ATOMS1=168,170,172,188 REFERENCE1=3.14</a>
+<a name="53"><span class="lineNum">      53 </span>            : ATOMS2=170,172,188,190 REFERENCE2=3.14</a>
+<a name="54"><span class="lineNum">      54 </span>            : ATOMS3=188,190,192,230 REFERENCE3=3.14</a>
+<a name="55"><span class="lineNum">      55 </span>            : LABEL=ab</a>
+<a name="56"><span class="lineNum">      56 </span>            : ... ALPHABETA</a>
+<a name="57"><span class="lineNum">      57 </span>            : PRINT ARG=ab FILE=colvar STRIDE=10</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endplumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : Because all the reference values are the same we can calculate the same quantity using</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : ALPHABETA ...</a>
+<a name="64"><span class="lineNum">      64 </span>            : ATOMS1=168,170,172,188 REFERENCE=3.14</a>
+<a name="65"><span class="lineNum">      65 </span>            : ATOMS2=170,172,188,190</a>
+<a name="66"><span class="lineNum">      66 </span>            : ATOMS3=188,190,192,230</a>
+<a name="67"><span class="lineNum">      67 </span>            : LABEL=ab</a>
+<a name="68"><span class="lineNum">      68 </span>            : ... ALPHABETA</a>
+<a name="69"><span class="lineNum">      69 </span>            : PRINT ARG=ab FILE=colvar STRIDE=10</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : Writing out the atoms involved in all the torsion angles in this way can be rather tedious. Thankfully if you are working with protein you</a>
+<a name="73"><span class="lineNum">      73 </span>            : can avoid this by using the \ref MOLINFO command.  PLUMED uses the pdb file that you provide to this command to learn</a>
+<a name="74"><span class="lineNum">      74 </span>            : about the topology of the protein molecule.  This means that you can specify torsion angles using the following syntax:</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \plumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="78"><span class="lineNum">      78 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb</a>
+<a name="79"><span class="lineNum">      79 </span>            : ALPHABETA ...</a>
+<a name="80"><span class="lineNum">      80 </span>            : ATOMS1=@phi-3 REFERENCE=3.14</a>
+<a name="81"><span class="lineNum">      81 </span>            : ATOMS2=@psi-3</a>
+<a name="82"><span class="lineNum">      82 </span>            : ATOMS3=@phi-4</a>
+<a name="83"><span class="lineNum">      83 </span>            : LABEL=ab</a>
+<a name="84"><span class="lineNum">      84 </span>            : ... ALPHABETA</a>
+<a name="85"><span class="lineNum">      85 </span>            : PRINT ARG=ab FILE=colvar STRIDE=10</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endplumedfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.</a>
+<a name="89"><span class="lineNum">      89 </span>            : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the fourth residue of the protein.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : */</a>
+<a name="93"><span class="lineNum">      93 </span>            : //+ENDPLUMEDOC</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : class AlphaBeta : public MultiColvarBase {</a>
+<a name="96"><span class="lineNum">      96 </span>            : private:</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt;double&gt; target;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;double&gt; coefficient;</a>
+<a name="99"><span class="lineNum">      99 </span>            : public:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit AlphaBeta(const ActionOptions&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : };</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(AlphaBeta,&quot;ALPHABETA&quot;)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 : void AlphaBeta::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          3 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          6 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the alpha-beta variables you wish to calculate. &quot;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one alpha-beta values will be &quot;</a>
+<a name="112"><span class="lineNum">     112 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="113"><span class="lineNum">     113 </span>            :            &quot;specify the indices of four atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="114"><span class="lineNum">     114 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          6 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          6 :   keys.add(&quot;numbered&quot;,&quot;REFERENCE&quot;,&quot;the reference values for each of the torsional angles.  If you use a single REFERENCE value the &quot;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :            &quot;same reference value is used for all torsional angles&quot;);</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          6 :   keys.add(&quot;numbered&quot;,&quot;COEFFICIENT&quot;,&quot;the coefficient for each of the torsional angles.  If you use a single COEFFICIENT value the &quot;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :            &quot;same reference value is used for all torsional angles&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          6 :   keys.reset_style(&quot;REFERENCE&quot;,&quot;compulsory&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 :   keys.reset_style(&quot;COEFFICIENT&quot;,&quot;optional&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 : AlphaBeta::AlphaBeta(const ActionOptions&amp;ao):</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   Action(ao),</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   MultiColvarBase(ao)</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : {</a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Read in the atoms</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   readAtomsLikeKeyword( &quot;ATOMS&quot;, 4, all_atoms );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // Resize target</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          1 :   target.resize( getFullNumberOfTasks() );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   // Resize coeff</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :   coefficient.resize( getFullNumberOfTasks(), 1.0);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Setup central atom indices</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :   std::vector&lt;bool&gt; catom_ind(4, false);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   catom_ind[1]=catom_ind[2]=true;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 :   setAtomsForCentralAtom( catom_ind );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // Read in reference values</a>
+<a name="142"><span class="lineNum">     142 </span>            :   unsigned ntarget=0;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :   for(unsigned i=0; i&lt;target.size(); ++i) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :     if( !parseNumbered( &quot;REFERENCE&quot;, i+1, target[i] ) ) break;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     ntarget++;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          1 :   if( ntarget==0 ) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :     parse(&quot;REFERENCE&quot;,target[0]);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          8 :     for(unsigned i=1; i&lt;target.size(); ++i) target[i]=target[0];</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   } else if( ntarget!=target.size() ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     error(&quot;found wrong number of REFERENCE values&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   // Read in reference values</a>
+<a name="155"><span class="lineNum">     155 </span>            :   unsigned ncoefficient=0;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   for(unsigned i=0; i&lt;coefficient.size(); ++i) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :     if( !parseNumbered( &quot;COEFFICIENT&quot;, i+1, coefficient[i] ) ) break;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     ncoefficient++;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          1 :   if( ncoefficient==0 ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          1 :     parse(&quot;COEFFICIENT&quot;,coefficient[0]);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          8 :     for(unsigned i=1; i&lt;coefficient.size(); ++i) coefficient[i]=coefficient[0];</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   } else if( ncoefficient !=coefficient.size() ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     error(&quot;found wrong number of COEFFICIENT values&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   // And setup the ActionWithVessel</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :   if( getNumberOfVessels()==0 ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     std::string fake_input;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 :     addVessel( &quot;SUM&quot;, fake_input, -1 );  // -1 here means that this value will be named getLabel()</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          1 :     readVesselKeywords();  // This makes sure resizing is done</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // And check everything has been read in correctly</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 : }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         40 : double AlphaBeta::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         40 :   const Vector d0=getSeparation(myatoms.getPosition(1),myatoms.getPosition(0));</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         40 :   const Vector d1=getSeparation(myatoms.getPosition(2),myatoms.getPosition(1));</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         40 :   const Vector d2=getSeparation(myatoms.getPosition(3),myatoms.getPosition(2));</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         40 :   Vector dd0,dd1,dd2;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   PLMD::Torsion t;</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         40 :   const double value  = t.compute(d0,d1,d2,dd0,dd1,dd2);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         40 :   const double svalue = -0.5*coefficient[tindex]*std::sin(value-target[tindex]);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         40 :   const double cvalue = coefficient[tindex]*(1.+std::cos(value-target[tindex]));</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         40 :   dd0 *= svalue;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         40 :   dd1 *= svalue;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         40 :   dd2 *= svalue;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         40 :   addAtomDerivatives(1, 0, dd0, myatoms);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         40 :   addAtomDerivatives(1, 1, dd1-dd0, myatoms);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         40 :   addAtomDerivatives(1, 2, dd2-dd1, myatoms);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         40 :   addAtomDerivatives(1, 3, -dd2, myatoms);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         40 :   myatoms.addBoxDerivatives(1, -(extProduct(d0,dd0)+extProduct(d1,dd1)+extProduct(d2,dd2)));</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         40 :   return 0.5*cvalue;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : }</a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Angles.cpp.func-sort-c.html b/coverage/multicolvar/Angles.cpp.func-sort-c.html
new file mode 100644
index 0000000000..90233b03b7
--- /dev/null
+++ b/coverage/multicolvar/Angles.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Angles.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Angles.cpp<span style="font-size: 80%;"> (<a href="Angles.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntryMed">84.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Angles.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#130">_ZN4PLMD11multicolvar6AnglesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_119AnglesRegisterMe1016createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#130">_ZN4PLMD11multicolvar6AnglesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#101">_ZN4PLMD11multicolvar6Angles16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#96">_ZN4PLMD11multicolvar6Angles10isPeriodicEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_119AnglesRegisterMe101C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_119AnglesRegisterMe101D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#201">_ZNK4PLMD11multicolvar6Angles7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">26964</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#178">_ZNK4PLMD11multicolvar6Angles15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">48510</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Angles.cpp.func.html b/coverage/multicolvar/Angles.cpp.func.html
new file mode 100644
index 0000000000..c9a7c33fb9
--- /dev/null
+++ b/coverage/multicolvar/Angles.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Angles.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Angles.cpp<span style="font-size: 80%;"> (<a href="Angles.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntryMed">84.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Angles.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_119AnglesRegisterMe1016createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_119AnglesRegisterMe101C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_119AnglesRegisterMe101D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#96">_ZN4PLMD11multicolvar6Angles10isPeriodicEv</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#101">_ZN4PLMD11multicolvar6Angles16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#130">_ZN4PLMD11multicolvar6AnglesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#130">_ZN4PLMD11multicolvar6AnglesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#178">_ZNK4PLMD11multicolvar6Angles15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">48510</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angles.cpp.gcov.html#201">_ZNK4PLMD11multicolvar6Angles7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">26964</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Angles.cpp.gcov.html b/coverage/multicolvar/Angles.cpp.gcov.html
new file mode 100644
index 0000000000..fab502540d
--- /dev/null
+++ b/coverage/multicolvar/Angles.cpp.gcov.html
@@ -0,0 +1,296 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Angles.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Angles.cpp<span style="font-size: 80%;"> (source / <a href="Angles.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntryMed">84.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Angle.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace multicolvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MCOLVAR ANGLES</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculate functions of the distribution of angles .</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : You can use this command to calculate functions such as:</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            :  f(x) = \sum_{ijk} g( \theta_{ijk} )</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f]</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : Alternatively you can use this command to calculate functions such as:</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            : f(x) = \sum_{ijk} s(r_{ij})s(r_{jk}) g(\theta_{ijk})</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : where \f$s(r)\f$ is a \ref switchingfunction.  This second form means that you can</a>
+<a name="51"><span class="lineNum">      51 </span>            : use this to calculate functions of the angles in the first coordination sphere of</a>
+<a name="52"><span class="lineNum">      52 </span>            : an atom / molecule \cite lj-recon.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \par Examples</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The following example instructs plumed to find the average of two angles and to</a>
+<a name="57"><span class="lineNum">      57 </span>            : print it to a file</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \plumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : ANGLES ATOMS1=1,2,3 ATOMS2=4,5,6 MEAN LABEL=a1</a>
+<a name="61"><span class="lineNum">      61 </span>            : PRINT ARG=a1.mean FILE=colvar</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The following example tells plumed to calculate all angles involving</a>
+<a name="65"><span class="lineNum">      65 </span>            : at least one atom from GROUPA and two atoms from GROUPB in which the distances</a>
+<a name="66"><span class="lineNum">      66 </span>            : are less than 1.0. The number of angles between \f$\frac{\pi}{4}\f$ and</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f$\frac{3\pi}{4}\f$ is then output</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : ANGLES GROUPA=1-10 GROUPB=11-100 BETWEEN={GAUSSIAN LOWER=0.25pi UPPER=0.75pi} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1</a>
+<a name="71"><span class="lineNum">      71 </span>            : PRINT ARG=a1.between FILE=colvar</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : This final example instructs plumed to calculate all the angles in the first coordination</a>
+<a name="75"><span class="lineNum">      75 </span>            : spheres of the atoms. The bins for a normalized histogram of the distribution is then output</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : \plumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : ANGLES GROUP=1-38 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=pi NBINS=20} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1</a>
+<a name="79"><span class="lineNum">      79 </span>            : PRINT ARG=a1.* FILE=colvar</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endplumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : */</a>
+<a name="83"><span class="lineNum">      83 </span>            : //+ENDPLUMEDOC</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : class Angles : public MultiColvarBase {</a>
+<a name="86"><span class="lineNum">      86 </span>            : private:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   bool use_sf;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   double rcut2_1, rcut2_2;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   SwitchingFunction sf1;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   SwitchingFunction sf2;</a>
+<a name="91"><span class="lineNum">      91 </span>            : public:</a>
+<a name="92"><span class="lineNum">      92 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit Angles(const ActionOptions&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Updates neighbor list</a>
+<a name="95"><span class="lineNum">      95 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; ) const override;</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="97"><span class="lineNum">      97 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; ) const override;</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   bool isPeriodic() override { return false; }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : };</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Angles,&quot;ANGLES&quot;)</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 : void Angles::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          4 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          8 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MORE_THAN&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   // Could also add Region here in theory</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the angles you wish to calculate. &quot;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one angle will be &quot;</a>
+<a name="110"><span class="lineNum">     110 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="111"><span class="lineNum">     111 </span>            :            &quot;provide the indices of three atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="112"><span class="lineNum">     112 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          8 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate angles for each distinct set of three atoms in the group&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;A group of central atoms about which angles should be calculated&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;When used in conjunction with GROUPA this keyword instructs plumed &quot;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :            &quot;to calculate all distinct angles involving one atom from GROUPA &quot;</a>
+<a name="118"><span class="lineNum">     118 </span>            :            &quot;and two atoms from GROUPB. The atom from GROUPA is the central atom.&quot;);</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-3&quot;,&quot;GROUPC&quot;,&quot;This must be used in conjunction with GROUPA and GROUPB.  All angles &quot;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :            &quot;involving one atom from GROUPA, one atom from GROUPB and one atom from &quot;</a>
+<a name="121"><span class="lineNum">     121 </span>            :            &quot;GROUPC are calculated. The GROUPA atoms are assumed to be the central &quot;</a>
+<a name="122"><span class="lineNum">     122 </span>            :            &quot;atoms&quot;);</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;A switching function that ensures that only angles between atoms that &quot;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :            &quot;are within a certain fixed cutoff are calculated. The following provides &quot;</a>
+<a name="125"><span class="lineNum">     125 </span>            :            &quot;information on the \\ref switchingfunction that are available.&quot;);</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;SWITCHA&quot;,&quot;A switching function on the distance between the atoms in group A and the atoms in &quot;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :            &quot;group B&quot;);</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;SWITCHB&quot;,&quot;A switching function on the distance between the atoms in group A and the atoms in &quot;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;group B&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          4 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 : Angles::Angles(const ActionOptions&amp;ao):</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   Action(ao),</a>
+<a name="134"><span class="lineNum">     134 </span>            :   MultiColvarBase(ao),</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          2 :   use_sf(false)</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   std::string sfinput,errors; parse(&quot;SWITCH&quot;,sfinput);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :   if( sfinput.length()&gt;0 ) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :     use_sf=true;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :     weightHasDerivatives=true;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :     sf1.set(sfinput,errors);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 :     sf2.set(sfinput,errors);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          4 :     log.printf(&quot;  only calculating angles for atoms separated by less than %s\n&quot;, sf1.description().c_str() );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   } else {</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     parse(&quot;SWITCHA&quot;,sfinput);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :     if(sfinput.length()&gt;0) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :       use_sf=true;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :       weightHasDerivatives=true;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :       sf1.set(sfinput,errors);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCHA keyword : &quot; + errors );</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :       sfinput.clear(); parse(&quot;SWITCHB&quot;,sfinput);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :       if(sfinput.length()==0) error(&quot;found SWITCHA keyword without SWITCHB&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :       sf2.set(sfinput,errors);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCHB keyword : &quot; + errors );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :       log.printf(&quot;  only calculating angles when the distance between GROUPA and GROUPB atoms is less than %s\n&quot;, sf1.description().c_str() );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :       log.printf(&quot;  only calculating angles when the distance between GROUPA and GROUPC atoms is less than %s\n&quot;, sf2.description().c_str() );</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            :   // Read in the atoms</a>
+<a name="162"><span class="lineNum">     162 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          4 :   readGroupKeywords( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, &quot;GROUPC&quot;, false, true, all_atoms );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 3, all_atoms );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   // Set cutoff for link cells</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :   if( use_sf ) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          2 :     setLinkCellCutoff( sf1.get_dmax() );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :     rcut2_1=sf1.get_dmax()*sf1.get_dmax();</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :     rcut2_2=sf2.get_dmax()*sf2.get_dmax();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :   // And check everything has been read in correctly</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   // Setup stuff for central atom</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   std::vector&lt;bool&gt; catom_ind(3, false); catom_ind[0]=true;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   setAtomsForCentralAtom( catom_ind );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          2 : }</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      48510 : double Angles::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      48510 :   if(!use_sf) return 1.0;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      48510 :   Vector dij=getSeparation( myatoms.getPosition(0), myatoms.getPosition(2) );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      48510 :   Vector dik=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   double w1, w2, dw1, dw2, wtot;</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">      48510 :   double ldij = dij.modulo2(), ldik = dik.modulo2();</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      48510 :   if( use_sf ) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      48510 :     if( ldij&gt;rcut2_1 || ldik&gt;rcut2_2 ) return 0.0;</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      48510 :   w1=sf1.calculateSqr( ldij, dw1 );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      48510 :   w2=sf2.calculateSqr( ldik, dw2 );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      48510 :   wtot=w1*w2; dw1*=weight*w2; dw2*=weight*w1;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      48510 :   addAtomDerivatives( 0, 1, dw2*dik, myatoms );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      48510 :   addAtomDerivatives( 0, 0, -dw1*dij - dw2*dik, myatoms );</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      48510 :   addAtomDerivatives( 0, 2, dw1*dij, myatoms );</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      48510 :   myatoms.addBoxDerivatives( 0, (-dw1)*Tensor(dij,dij) + (-dw2)*Tensor(dik,dik) );</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      48510 :   return wtot;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      26964 : double Angles::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      26964 :   Vector dij=getSeparation( myatoms.getPosition(0), myatoms.getPosition(2) );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      26964 :   Vector dik=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      26964 :   Vector ddij,ddik; PLMD::Angle a;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">      26964 :   double angle=a.compute(dij,dik,ddij,ddik);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            :   // And finish the calculation</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">      26964 :   addAtomDerivatives( 1, 1, ddik, myatoms );</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      26964 :   addAtomDerivatives( 1, 0, - ddik - ddij, myatoms );</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      26964 :   addAtomDerivatives( 1, 2, ddij, myatoms );</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      26964 :   myatoms.addBoxDerivatives( 1, -(Tensor(dij,ddij)+Tensor(dik,ddik)) );</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      26964 :   return angle;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            : }</a>
+<a name="220"><span class="lineNum">     220 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AtomValuePack.cpp.func-sort-c.html b/coverage/multicolvar/AtomValuePack.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8466d97dd7
--- /dev/null
+++ b/coverage/multicolvar/AtomValuePack.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AtomValuePack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AtomValuePack.cpp<span style="font-size: 80%;"> (<a href="AtomValuePack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AtomValuePack.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#42">_ZN4PLMD11multicolvar13AtomValuePack23setupAtomsFromLinkCellsERKSt6vectorIjSaIjEERKNS_13VectorGenericILj3EEERKNS_9LinkCellsE</a></td>
+              <td class="coverFnHi">220663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#27">_ZN4PLMD11multicolvar13AtomValuePackC2ERNS_10MultiValueEPKNS0_15MultiColvarBaseE</a></td>
+              <td class="coverFnHi">448077</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#55">_ZN4PLMD11multicolvar13AtomValuePack18updateUsingIndicesEv</a></td>
+              <td class="coverFnHi">516365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#79">_ZN4PLMD11multicolvar13AtomValuePack17addComDerivativesERKiRKNS_13VectorGenericILj3EEERKNS0_9CatomPackE</a></td>
+              <td class="coverFnHi">905762</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AtomValuePack.cpp.func.html b/coverage/multicolvar/AtomValuePack.cpp.func.html
new file mode 100644
index 0000000000..b1b7db1262
--- /dev/null
+++ b/coverage/multicolvar/AtomValuePack.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AtomValuePack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AtomValuePack.cpp<span style="font-size: 80%;"> (<a href="AtomValuePack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AtomValuePack.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#79">_ZN4PLMD11multicolvar13AtomValuePack17addComDerivativesERKiRKNS_13VectorGenericILj3EEERKNS0_9CatomPackE</a></td>
+              <td class="coverFnHi">905762</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#55">_ZN4PLMD11multicolvar13AtomValuePack18updateUsingIndicesEv</a></td>
+              <td class="coverFnHi">516365</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#42">_ZN4PLMD11multicolvar13AtomValuePack23setupAtomsFromLinkCellsERKSt6vectorIjSaIjEERKNS_13VectorGenericILj3EEERKNS_9LinkCellsE</a></td>
+              <td class="coverFnHi">220663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.cpp.gcov.html#27">_ZN4PLMD11multicolvar13AtomValuePackC2ERNS_10MultiValueEPKNS0_15MultiColvarBaseE</a></td>
+              <td class="coverFnHi">448077</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AtomValuePack.cpp.gcov.html b/coverage/multicolvar/AtomValuePack.cpp.gcov.html
new file mode 100644
index 0000000000..a84c0adb11
--- /dev/null
+++ b/coverage/multicolvar/AtomValuePack.cpp.gcov.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AtomValuePack.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AtomValuePack.cpp<span style="font-size: 80%;"> (source / <a href="AtomValuePack.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CatomPack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/LinkCells.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace multicolvar {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     448077 : AtomValuePack::AtomValuePack( MultiValue&amp; vals, MultiColvarBase const * mcolv ):</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">     448077 :   myvals(vals),</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">     448077 :   mycolv(mcolv),</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     448077 :   natoms(0),</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     448077 :   indices( vals.getIndices() ),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     448077 :   sort_vector( vals.getSortIndices() ),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     448077 :   myatoms( vals.getAtomVector() )</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : {</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     448077 :   if( indices.size()!=mcolv-&gt;getNumberOfAtoms() ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      23864 :     indices.resize( mcolv-&gt;getNumberOfAtoms() );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">      23864 :     sort_vector.resize( mcolv-&gt;getNumberOfAtoms() );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      23864 :     myatoms.resize( mcolv-&gt;getNumberOfAtoms() );</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   }</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">     448077 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">     220663 : unsigned AtomValuePack::setupAtomsFromLinkCells( const std::vector&lt;unsigned&gt;&amp; cind, const Vector&amp; cpos, const LinkCells&amp; linkcells ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">     220663 :   if( cells_required.size()!=linkcells.getNumberOfCells() ) cells_required.resize( linkcells.getNumberOfCells() );</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   // Build the list of cells that we need</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">     220663 :   unsigned ncells_required=0; linkcells.addRequiredCells( linkcells.findMyCell( cpos ), ncells_required, cells_required );</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   // Now build the list of atoms we need</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     481142 :   natoms=cind.size(); for(unsigned i=0; i&lt;natoms; ++i) indices[i]=cind[i];</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">     220663 :   linkcells.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : //  linkcells.retrieveNeighboringAtoms( cpos, natoms, indices );</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">  404345371 :   for(unsigned i=0; i&lt;natoms; ++i) myatoms[i]=mycolv-&gt;getPositionOfAtomForLinkCells( indices[i] ) - cpos;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     220663 :   if( mycolv-&gt;usesPbc() ) mycolv-&gt;applyPbc( myatoms, natoms );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">     220663 :   return natoms;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">     516365 : void AtomValuePack::updateUsingIndices() {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">     516365 :   if( myvals.updateComplete() ) return;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned jactive=0;</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">  402807162 :   for(unsigned i=0; i&lt;natoms; ++i) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">  402492393 :     unsigned base=3*indices[i];</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">  402492393 :     if( myvals.isActive( base ) ) { sort_vector[jactive]=indices[i]; jactive++; }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     314769 :   std::sort( sort_vector.begin(), sort_vector.begin()+jactive );</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     314769 :   myvals.emptyActiveMembers();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    4413816 :   for(unsigned i=0; i&lt;jactive; ++i) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">    4099047 :     unsigned base=3*sort_vector[i]; // indices[i];</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    4099047 :     myvals.putIndexInActiveArray( base );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    4099047 :     myvals.putIndexInActiveArray( base + 1 );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    4099047 :     myvals.putIndexInActiveArray( base + 2 );</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   }</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     314769 :   unsigned nvir=3*mycolv-&gt;getNumberOfAtoms();</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     314769 :   if( myvals.isActive( nvir ) ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">    2060650 :     for(unsigned i=0; i&lt;9; ++i) myvals.putIndexInActiveArray( nvir + i );</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   }</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     314769 :   myvals.completeUpdate();</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     905762 : void AtomValuePack::addComDerivatives( const int&amp; ind, const Vector&amp; der, const CatomPack&amp; catom_der ) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     905762 :   if( ind&lt;0 ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     104392 :     for(unsigned ider=0; ider&lt;catom_der.getNumberOfAtomsWithDerivatives(); ++ider) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      54660 :       unsigned jder=3*catom_der.getIndex(ider);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      54660 :       myvals.addTemporyDerivative( jder+0, catom_der.getDerivative(ider,0,der) );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      54660 :       myvals.addTemporyDerivative( jder+1, catom_der.getDerivative(ider,1,der) );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      54660 :       myvals.addTemporyDerivative( jder+2, catom_der.getDerivative(ider,2,der) );</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     }</a>
+<a name="89"><span class="lineNum">      89 </span>            :   } else {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">    1716988 :     for(unsigned ider=0; ider&lt;catom_der.getNumberOfAtomsWithDerivatives(); ++ider) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     860958 :       unsigned jder=3*catom_der.getIndex(ider);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">     860958 :       myvals.addDerivative( ind, jder+0, catom_der.getDerivative(ider,0,der) );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     860958 :       myvals.addDerivative( ind, jder+1, catom_der.getDerivative(ider,1,der) );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     860958 :       myvals.addDerivative( ind, jder+2, catom_der.getDerivative(ider,2,der) );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     905762 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AtomValuePack.h.func-sort-c.html b/coverage/multicolvar/AtomValuePack.h.func-sort-c.html
new file mode 100644
index 0000000000..92228d382d
--- /dev/null
+++ b/coverage/multicolvar/AtomValuePack.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AtomValuePack.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AtomValuePack.h<span style="font-size: 80%;"> (<a href="AtomValuePack.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AtomValuePack.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#200">_ZN4PLMD11multicolvar13AtomValuePack17updateDynamicListEv</a></td>
+              <td class="coverFnHi">141871</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#126">_ZN4PLMD11multicolvar13AtomValuePack7setAtomERKjS3_</a></td>
+              <td class="coverFnHi">571749</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#188">_ZN4PLMD11multicolvar13AtomValuePack24addTemporyBoxDerivativesERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">2283013</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#180">_ZN4PLMD11multicolvar13AtomValuePack26addTemporyAtomsDerivativesERKjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">4516294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#194">_ZN4PLMD11multicolvar13AtomValuePack17addBoxDerivativesERKjRKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">56357934</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#172">_ZN4PLMD11multicolvar13AtomValuePack19addAtomsDerivativesERKjS3_RKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">111743475</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#136">_ZNK4PLMD11multicolvar13AtomValuePack16getAbsoluteIndexERKj</a></td>
+              <td class="coverFnHi">117937031</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AtomValuePack.h.func.html b/coverage/multicolvar/AtomValuePack.h.func.html
new file mode 100644
index 0000000000..3903d80ea9
--- /dev/null
+++ b/coverage/multicolvar/AtomValuePack.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AtomValuePack.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AtomValuePack.h<span style="font-size: 80%;"> (<a href="AtomValuePack.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AtomValuePack.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#194">_ZN4PLMD11multicolvar13AtomValuePack17addBoxDerivativesERKjRKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">56357934</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#200">_ZN4PLMD11multicolvar13AtomValuePack17updateDynamicListEv</a></td>
+              <td class="coverFnHi">141871</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#172">_ZN4PLMD11multicolvar13AtomValuePack19addAtomsDerivativesERKjS3_RKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">111743475</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#188">_ZN4PLMD11multicolvar13AtomValuePack24addTemporyBoxDerivativesERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">2283013</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#180">_ZN4PLMD11multicolvar13AtomValuePack26addTemporyAtomsDerivativesERKjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">4516294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#126">_ZN4PLMD11multicolvar13AtomValuePack7setAtomERKjS3_</a></td>
+              <td class="coverFnHi">571749</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomValuePack.h.gcov.html#136">_ZNK4PLMD11multicolvar13AtomValuePack16getAbsoluteIndexERKj</a></td>
+              <td class="coverFnHi">117937031</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/AtomValuePack.h.gcov.html b/coverage/multicolvar/AtomValuePack.h.gcov.html
new file mode 100644
index 0000000000..1f8cf8139c
--- /dev/null
+++ b/coverage/multicolvar/AtomValuePack.h.gcov.html
@@ -0,0 +1,291 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/AtomValuePack.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - AtomValuePack.h<span style="font-size: 80%;"> (source / <a href="AtomValuePack.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">95.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_AtomValuePack_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_AtomValuePack_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/MultiValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class LinkCells;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace multicolvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class CatomPack;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     448023 : class AtomValuePack {</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   friend class MultiColvarBase;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   friend class LocalAverage;</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Copy of the values that we are adding to</a>
+<a name="41"><span class="lineNum">      41 </span>            :   MultiValue&amp; myvals;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Copy of the underlying multicolvar</a>
+<a name="43"><span class="lineNum">      43 </span>            :   MultiColvarBase const * mycolv;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Number of atoms at the moment</a>
+<a name="45"><span class="lineNum">      45 </span>            :   unsigned natoms;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Atom indices</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;unsigned&gt;&amp; indices;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// This is used to sort the atom indices</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::vector&lt;unsigned&gt;&amp; sort_vector;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// This holds atom positions</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;Vector&gt;&amp; myatoms;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// This is stuff for link cells</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;unsigned&gt; cells_required;</a>
+<a name="54"><span class="lineNum">      54 </span>            : ///</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void addAtomsDerivatives( const unsigned&amp;, const unsigned&amp;, const Vector&amp; );</a>
+<a name="56"><span class="lineNum">      56 </span>            : ///</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void addTemporyAtomsDerivatives( const unsigned&amp; jder, const Vector&amp; der );</a>
+<a name="58"><span class="lineNum">      58 </span>            : public:</a>
+<a name="59"><span class="lineNum">      59 </span>            :   AtomValuePack( MultiValue&amp; vals, MultiColvarBase const * mcolv );</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Set the number of atoms</a>
+<a name="61"><span class="lineNum">      61 </span>            :   void setNumberOfAtoms( const unsigned&amp; );</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Set the index for one of the atoms</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void setIndex( const unsigned&amp;, const unsigned&amp; );</a>
+<a name="64"><span class="lineNum">      64 </span>            : ///</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void setAtomIndex( const unsigned&amp; j, const unsigned&amp; ind );</a>
+<a name="66"><span class="lineNum">      66 </span>            : ///</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void setAtom( const unsigned&amp; j, const unsigned&amp; ind );</a>
+<a name="68"><span class="lineNum">      68 </span>            : ///</a>
+<a name="69"><span class="lineNum">      69 </span>            :   unsigned setupAtomsFromLinkCells( const std::vector&lt;unsigned&gt;&amp; cind, const Vector&amp; cpos, const LinkCells&amp; linkcells );</a>
+<a name="70"><span class="lineNum">      70 </span>            : ///</a>
+<a name="71"><span class="lineNum">      71 </span>            :   unsigned getIndex( const unsigned&amp; j ) const ;</a>
+<a name="72"><span class="lineNum">      72 </span>            : ///</a>
+<a name="73"><span class="lineNum">      73 </span>            :   unsigned getNumberOfAtoms() const ;</a>
+<a name="74"><span class="lineNum">      74 </span>            : ///</a>
+<a name="75"><span class="lineNum">      75 </span>            :   unsigned getNumberOfDerivatives() const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Get the position of the ith atom</a>
+<a name="77"><span class="lineNum">      77 </span>            :   Vector&amp; getPosition( const unsigned&amp; );</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Get the absolute index of the ith atom in the list</a>
+<a name="79"><span class="lineNum">      79 </span>            :   AtomNumber getAbsoluteIndex( const unsigned&amp; j ) const ;</a>
+<a name="80"><span class="lineNum">      80 </span>            : ///</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void setValue( const unsigned&amp;, const double&amp; );</a>
+<a name="82"><span class="lineNum">      82 </span>            : ///</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void addValue( const unsigned&amp; ival, const double&amp; vv );</a>
+<a name="84"><span class="lineNum">      84 </span>            : ///</a>
+<a name="85"><span class="lineNum">      85 </span>            :   double getValue( const unsigned&amp; ) const ;</a>
+<a name="86"><span class="lineNum">      86 </span>            : ///</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void addBoxDerivatives( const unsigned&amp;, const Tensor&amp; );</a>
+<a name="88"><span class="lineNum">      88 </span>            : ///</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void addTemporyBoxDerivatives( const Tensor&amp; vir );</a>
+<a name="90"><span class="lineNum">      90 </span>            : ///</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void updateUsingIndices();</a>
+<a name="92"><span class="lineNum">      92 </span>            : ///</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void updateDynamicList();</a>
+<a name="94"><span class="lineNum">      94 </span>            : ///</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void addComDerivatives( const int&amp;, const Vector&amp;, const CatomPack&amp; );</a>
+<a name="96"><span class="lineNum">      96 </span>            : ///</a>
+<a name="97"><span class="lineNum">      97 </span>            :   MultiValue&amp; getUnderlyingMultiValue();</a>
+<a name="98"><span class="lineNum">      98 </span>            : ///</a>
+<a name="99"><span class="lineNum">      99 </span>            :   void addDerivative( const unsigned&amp;, const unsigned&amp;, const double&amp; );</a>
+<a name="100"><span class="lineNum">     100 </span>            : };</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : inline</a>
+<a name="103"><span class="lineNum">     103 </span>            : void AtomValuePack::setNumberOfAtoms( const unsigned&amp; nat ) {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">     230894 :   natoms=nat;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : inline</a>
+<a name="108"><span class="lineNum">     108 </span>            : unsigned AtomValuePack::getNumberOfAtoms() const {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">  524950726 :   return natoms;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : inline</a>
+<a name="113"><span class="lineNum">     113 </span>            : unsigned AtomValuePack::getNumberOfDerivatives() const {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        110 :   return myvals.getNumberOfDerivatives();</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : inline</a>
+<a name="118"><span class="lineNum">     118 </span>            : void AtomValuePack::setIndex( const unsigned&amp; j, const unsigned&amp; ind ) {</a>
+<a name="119"><span class="lineNum">     119 </span>            :   plumed_dbg_assert( j&lt;natoms ); indices[j]=ind;</a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : inline</a>
+<a name="123"><span class="lineNum">     123 </span>            : void AtomValuePack::setAtomIndex( const unsigned&amp; j, const unsigned&amp; ind ) {</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     605398 :   plumed_dbg_assert( j&lt;natoms ); indices[j]=ind;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : inline</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">     571749 : void AtomValuePack::setAtom( const unsigned&amp; j, const unsigned&amp; ind ) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     571749 :   setAtomIndex( j, ind ); myatoms[j]=mycolv-&gt;getPositionOfAtomForLinkCells( ind );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     571749 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : inline</a>
+<a name="133"><span class="lineNum">     133 </span>            : unsigned AtomValuePack::getIndex( const unsigned&amp; j ) const {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">  679827770 :   plumed_dbg_assert( j&lt;natoms ); return indices[j];</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : inline</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">  117937031 : AtomNumber AtomValuePack::getAbsoluteIndex( const unsigned&amp; j ) const {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">  117937031 :   plumed_dbg_assert( j&lt;natoms ); unsigned jatom=indices[j];</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">  117937031 :   if( mycolv-&gt;atom_lab[jatom].first&gt;0 ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     unsigned mmc=mycolv-&gt;atom_lab[jatom].first - 1;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     return (mycolv-&gt;mybasemulticolvars[mmc])-&gt;getAbsoluteIndexOfCentralAtom( mycolv-&gt;atom_lab[jatom].second );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">  117937031 :   return mycolv-&gt;getAbsoluteIndex( mycolv-&gt;atom_lab[jatom].second );</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : inline</a>
+<a name="148"><span class="lineNum">     148 </span>            : Vector&amp; AtomValuePack::getPosition( const unsigned&amp; iatom ) {</a>
+<a name="149"><span class="lineNum">     149 </span>            :   plumed_dbg_assert( iatom&lt;natoms );</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">  142087490 :   return myatoms[iatom];</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : inline</a>
+<a name="154"><span class="lineNum">     154 </span>            : void AtomValuePack::setValue( const unsigned&amp; ival, const double&amp; vv ) {</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">     695731 :   myvals.setValue( ival, vv );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : inline</a>
+<a name="159"><span class="lineNum">     159 </span>            : void AtomValuePack::addValue( const unsigned&amp; ival, const double&amp; vv ) {</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   62235725 :   myvals.addValue( ival, vv );</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : inline</a>
+<a name="164"><span class="lineNum">     164 </span>            : double AtomValuePack::getValue( const unsigned&amp; ival ) const {</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">    3392234 :   return myvals.get( ival );</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : inline</a>
+<a name="169"><span class="lineNum">     169 </span>            : void AtomValuePack::addDerivative( const unsigned&amp; ival, const unsigned&amp; jder, const double&amp; der ) {</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">   37930230 :   myvals.addDerivative( ival, jder, der );</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : inline</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">  111743475 : void AtomValuePack::addAtomsDerivatives( const unsigned&amp; ival, const unsigned&amp; jder, const Vector&amp; der ) {</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   plumed_dbg_assert( jder&lt;natoms );</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">  111743475 :   myvals.addDerivative( ival, 3*indices[jder] + 0, der[0] );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">  111743475 :   myvals.addDerivative( ival, 3*indices[jder] + 1, der[1] );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">  111743475 :   myvals.addDerivative( ival, 3*indices[jder] + 2, der[2] );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">  111743475 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : inline</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    4516294 : void AtomValuePack::addTemporyAtomsDerivatives( const unsigned&amp; jder, const Vector&amp; der ) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   plumed_dbg_assert( jder&lt;natoms );</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">    4516294 :   myvals.addTemporyDerivative( 3*indices[jder] + 0, der[0] );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">    4516294 :   myvals.addTemporyDerivative( 3*indices[jder] + 1, der[1] );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">    4516294 :   myvals.addTemporyDerivative( 3*indices[jder] + 2, der[2] );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">    4516294 : }</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : inline</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">    2283013 : void AtomValuePack::addTemporyBoxDerivatives( const Tensor&amp; vir ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">    2283013 :   unsigned nvir=3*mycolv-&gt;getNumberOfAtoms();</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">   29679169 :   for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) myvals.addTemporyDerivative( nvir + 3*i+j, vir(i,j) );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">    2283013 : }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : inline</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">   56357934 : void AtomValuePack::addBoxDerivatives( const unsigned&amp; ival, const Tensor&amp; vir ) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">   56357934 :   unsigned nvir=3*mycolv-&gt;getNumberOfAtoms();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">  732653142 :   for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) myvals.addDerivative( ival, nvir + 3*i+j, vir(i,j) );</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">   56357934 : }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : inline</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     141871 : void AtomValuePack::updateDynamicList() {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     141871 :   if( myvals.updateComplete() ) return;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   myvals.updateDynamicList();</a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : inline</a>
+<a name="208"><span class="lineNum">     208 </span>            : MultiValue&amp; AtomValuePack::getUnderlyingMultiValue() {</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    4742586 :   return myvals;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            : }</a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : #endif</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Bridge.cpp.func-sort-c.html b/coverage/multicolvar/Bridge.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4054a6e98c
--- /dev/null
+++ b/coverage/multicolvar/Bridge.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Bridge.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Bridge.cpp<span style="font-size: 80%;"> (<a href="Bridge.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryMed">79.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Bridge.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#68">_ZN4PLMD11multicolvar6Bridge10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#86">_ZN4PLMD11multicolvar6BridgeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#71">_ZN4PLMD11multicolvar12_GLOBAL__N_118BridgeRegisterMe736createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#86">_ZN4PLMD11multicolvar6BridgeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#73">_ZN4PLMD11multicolvar6Bridge16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#134">_ZNK4PLMD11multicolvar6Bridge7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">537</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#71">_ZN4PLMD11multicolvar12_GLOBAL__N_118BridgeRegisterMe73C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#71">_ZN4PLMD11multicolvar12_GLOBAL__N_118BridgeRegisterMe73D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Bridge.cpp.func.html b/coverage/multicolvar/Bridge.cpp.func.html
new file mode 100644
index 0000000000..6d4c899be5
--- /dev/null
+++ b/coverage/multicolvar/Bridge.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Bridge.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Bridge.cpp<span style="font-size: 80%;"> (<a href="Bridge.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryMed">79.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Bridge.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#71">_ZN4PLMD11multicolvar12_GLOBAL__N_118BridgeRegisterMe736createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#71">_ZN4PLMD11multicolvar12_GLOBAL__N_118BridgeRegisterMe73C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#71">_ZN4PLMD11multicolvar12_GLOBAL__N_118BridgeRegisterMe73D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#68">_ZN4PLMD11multicolvar6Bridge10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#73">_ZN4PLMD11multicolvar6Bridge16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#86">_ZN4PLMD11multicolvar6BridgeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#86">_ZN4PLMD11multicolvar6BridgeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Bridge.cpp.gcov.html#134">_ZNK4PLMD11multicolvar6Bridge7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">537</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Bridge.cpp.gcov.html b/coverage/multicolvar/Bridge.cpp.gcov.html
new file mode 100644
index 0000000000..e4773110df
--- /dev/null
+++ b/coverage/multicolvar/Bridge.cpp.gcov.html
@@ -0,0 +1,231 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Bridge.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Bridge.cpp<span style="font-size: 80%;"> (source / <a href="Bridge.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryMed">79.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace multicolvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC MCOLVAR BRIDGE</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Calculate the number of atoms that bridge two parts of a structure</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This quantity calculates:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            :  f(x) = \sum_{ijk} s_A(r_{ij})s_B(r_{ik})</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where the sum over \f$i\f$ is over all the ``bridging atoms&quot; and</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f$s_A\f$ and \f$s_B\f$ are \ref switchingfunction.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The following example instructs plumed to calculate the number of water molecules</a>
+<a name="49"><span class="lineNum">      49 </span>            : that are bridging between atoms 1-10 and atoms 11-20 and to print the value</a>
+<a name="50"><span class="lineNum">      50 </span>            : to a file</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : w1: BRIDGE BRIDGING_ATOMS=100-200 GROUPA=1-10 GROUPB=11-20 SWITCH={RATIONAL R_0=0.2}</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=w1 FILE=colvar</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : */</a>
+<a name="58"><span class="lineNum">      58 </span>            : //+ENDPLUMEDOC</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : class Bridge : public MultiColvarBase {</a>
+<a name="61"><span class="lineNum">      61 </span>            : private:</a>
+<a name="62"><span class="lineNum">      62 </span>            :   Vector dij, dik;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   SwitchingFunction sf1;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   SwitchingFunction sf2;</a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="67"><span class="lineNum">      67 </span>            :   explicit Bridge(const ActionOptions&amp;);</a>
+<a name="68"><span class="lineNum">      68 </span>            : // active methods:</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : };</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(Bridge,&quot;BRIDGE&quot;)</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         10 : void Bridge::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         10 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         20 :   keys.add(&quot;atoms-2&quot;,&quot;BRIDGING_ATOMS&quot;,&quot;The list of atoms that can form the bridge between the two interesting parts &quot;</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :            &quot;of the structure.&quot;);</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         20 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;The list of atoms that are in the first interesting part of the structure&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         20 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;The list of atoms that are in the second interesting part of the structure&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;The parameters of the two \\ref switchingfunction in the above formula&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;,&quot;SWITCHA&quot;,&quot;The \\ref switchingfunction on the distance between bridging atoms and the atoms in &quot;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :            &quot;group A&quot;);</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;,&quot;SWITCHB&quot;,&quot;The \\ref switchingfunction on the distance between the bridging atoms and the atoms in &quot;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :            &quot;group B&quot;);</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         10 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          8 : Bridge::Bridge(const ActionOptions&amp;ao):</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   Action(ao),</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          8 :   MultiColvarBase(ao)</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : {</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // Read in the atoms</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         16 :   readThreeGroups(&quot;GROUPA&quot;,&quot;GROUPB&quot;,&quot;BRIDGING_ATOMS&quot;,false,true,all_atoms);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   // Setup the multicolvar base</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          8 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Setup Central atom atoms</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          8 :   std::vector&lt;bool&gt; catom_ind(3, false); catom_ind[0]=true;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          8 :   setAtomsForCentralAtom( catom_ind );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         16 :   std::string sfinput,errors; parse(&quot;SWITCH&quot;,sfinput);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          8 :   if( sfinput.length()&gt;0 ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          8 :     sf1.set(sfinput,errors);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          8 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          8 :     sf2.set(sfinput,errors);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          8 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   } else {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     parse(&quot;SWITCHA&quot;,sfinput);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     if(sfinput.length()&gt;0) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :       weightHasDerivatives=true;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :       sf1.set(sfinput,errors);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCHA keyword : &quot; + errors );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       sfinput.clear(); parse(&quot;SWITCHB&quot;,sfinput);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :       if(sfinput.length()==0) error(&quot;found SWITCHA keyword without SWITCHB&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :       sf2.set(sfinput,errors);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCHB keyword : &quot; + errors );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     } else {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :       error(&quot;missing definition of switching functions&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     }</a>
+<a name="120"><span class="lineNum">     120 </span>            :   }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          8 :   log.printf(&quot;  distance between bridging atoms and atoms in GROUPA must be less than %s\n&quot;,sf1.description().c_str());</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          8 :   log.printf(&quot;  distance between bridging atoms and atoms in GROUPB must be less than %s\n&quot;,sf2.description().c_str());</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   // Setup link cells</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   setLinkCellCutoff( sf1.get_dmax() + sf2.get_dmax() );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // And setup the ActionWithVessel</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          8 :   if( getNumberOfVessels()!=0 ) error(&quot;should not have vessels for this action&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::string fake_input;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :   addVessel( &quot;SUM&quot;, fake_input, -1 );  // -1 here means that this value will be named getLabel()</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          8 :   readVesselKeywords();</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // And check everything has been read in correctly</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          8 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        537 : double Bridge::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   double tot=0;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      21359 :   for(unsigned i=2; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      20822 :     Vector dij=getSeparation( myatoms.getPosition(i), myatoms.getPosition(0) );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      20822 :     double dw1, w1=sf1.calculateSqr( dij.modulo2(), dw1 );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      20822 :     Vector dik=getSeparation( myatoms.getPosition(i), myatoms.getPosition(1) );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      20822 :     double dw2, w2=sf2.calculateSqr( dik.modulo2(), dw2 );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      20822 :     tot += w1*w2;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :     // And finish the calculation</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      20822 :     addAtomDerivatives( 1, 0,  w2*dw1*dij, myatoms );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      20822 :     addAtomDerivatives( 1, 1,  w1*dw2*dik, myatoms );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      20822 :     addAtomDerivatives( 1, i, -w1*dw2*dik-w2*dw1*dij, myatoms );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      20822 :     myatoms.addBoxDerivatives( 1, w1*(-dw2)*Tensor(dik,dik)+w2*(-dw1)*Tensor(dij,dij) );</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        537 :   return tot;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/BridgedMultiColvarFunction.cpp.func-sort-c.html b/coverage/multicolvar/BridgedMultiColvarFunction.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4511084a11
--- /dev/null
+++ b/coverage/multicolvar/BridgedMultiColvarFunction.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/BridgedMultiColvarFunction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - BridgedMultiColvarFunction.cpp<span style="font-size: 80%;"> (<a href="BridgedMultiColvarFunction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BridgedMultiColvarFunction.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#113">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction15deactivate_taskERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#33">_ZN4PLMD11multicolvar26BridgedMultiColvarFunctionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#99">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#109">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction10isPeriodicEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#33">_ZN4PLMD11multicolvar26BridgedMultiColvarFunctionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#51">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#87">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#28">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#117">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction18getCentralAtomPackERKjS3_RNS0_9CatomPackE</a></td>
+              <td class="coverFnHi">11462</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#76">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">13042</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#59">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction27transformBridgedDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">100985</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/BridgedMultiColvarFunction.cpp.func.html b/coverage/multicolvar/BridgedMultiColvarFunction.cpp.func.html
new file mode 100644
index 0000000000..6d02128116
--- /dev/null
+++ b/coverage/multicolvar/BridgedMultiColvarFunction.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/BridgedMultiColvarFunction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - BridgedMultiColvarFunction.cpp<span style="font-size: 80%;"> (<a href="BridgedMultiColvarFunction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BridgedMultiColvarFunction.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#109">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction10isPeriodicEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#113">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction15deactivate_taskERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#28">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#99">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">21</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#51">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#117">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction18getCentralAtomPackERKjS3_RNS0_9CatomPackE</a></td>
+              <td class="coverFnHi">11462</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#87">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#33">_ZN4PLMD11multicolvar26BridgedMultiColvarFunctionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#33">_ZN4PLMD11multicolvar26BridgedMultiColvarFunctionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#76">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">13042</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.cpp.gcov.html#59">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction27transformBridgedDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">100985</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/BridgedMultiColvarFunction.cpp.gcov.html b/coverage/multicolvar/BridgedMultiColvarFunction.cpp.gcov.html
new file mode 100644
index 0000000000..1e942f0dbd
--- /dev/null
+++ b/coverage/multicolvar/BridgedMultiColvarFunction.cpp.gcov.html
@@ -0,0 +1,200 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/BridgedMultiColvarFunction.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - BridgedMultiColvarFunction.cpp<span style="font-size: 80%;"> (source / <a href="BridgedMultiColvarFunction.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;BridgedMultiColvarFunction.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CatomPack.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace multicolvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         70 : void BridgedMultiColvarFunction::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         70 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        140 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;The multicolvar that calculates the set of base quantities that we are interested in&quot;);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         70 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         44 : BridgedMultiColvarFunction::BridgedMultiColvarFunction(const ActionOptions&amp;ao):</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   Action(ao),</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         44 :   MultiColvarBase(ao)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         44 :   std::string mlab; parse(&quot;DATA&quot;,mlab);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         44 :   mycolv = plumed.getActionSet().selectWithLabel&lt;MultiColvarBase*&gt;(mlab);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         44 :   if(!mycolv) error(&quot;action labeled &quot; + mlab + &quot; does not exist or is not a multicolvar&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            :   // When using numerical derivatives here we must use numerical derivatives</a>
+<a name="44"><span class="lineNum">      44 </span>            :   // in base multicolvar</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         44 :   if( checkNumericalDerivatives() ) mycolv-&gt;useNumericalDerivatives();</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         44 :   myBridgeVessel = mycolv-&gt;addBridgingVessel( this ); addDependency(mycolv);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         44 :   weightHasDerivatives=true; usespecies=mycolv-&gt;usespecies;</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   // Number of tasks is the same as the number in the underlying MultiColvar</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      20060 :   for(unsigned i=0; i&lt;mycolv-&gt;getFullNumberOfTasks(); ++i) addTaskToList( mycolv-&gt;getTaskCode(i) );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         44 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         45 : void BridgedMultiColvarFunction::turnOnDerivatives() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         45 :   BridgedMultiColvarFunction* check = dynamic_cast&lt;BridgedMultiColvarFunction*&gt;( mycolv );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         45 :   if( check ) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :     if( check-&gt;getNumberOfAtoms()&gt;0 ) error(&quot;cannot calculate required derivatives of this quantity&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         45 :   MultiColvarBase::turnOnDerivatives();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         45 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">     100985 : void BridgedMultiColvarFunction::transformBridgedDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) const {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     100985 :   completeTask( current, invals, outvals );</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            :   // Now update the outvals derivatives lists</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     100985 :   if( derivativesAreRequired() ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :     outvals.emptyActiveMembers();</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      94076 :     if( mycolv-&gt;isDensity() ) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     173680 :       for(unsigned j=0; j&lt;3; ++j) outvals.putIndexInActiveArray( 3*current+j );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     434200 :       for(unsigned j=invals.getNumberOfDerivatives()-9; j&lt;invals.getNumberOfDerivatives(); ++j) outvals.putIndexInActiveArray(j);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     } else {</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    3766585 :       for(unsigned j=0; j&lt;invals.getNumberActive(); ++j) outvals.putIndexInActiveArray( invals.getActiveIndex(j) );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :     }</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">     342431 :     for(unsigned j=invals.getNumberOfDerivatives(); j&lt;outvals.getNumberOfDerivatives(); ++j) outvals.putIndexInActiveArray( j );</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :     outvals.completeUpdate();</a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     100985 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      13042 : void BridgedMultiColvarFunction::performTask( const unsigned&amp; taskIndex, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   // This allows us to speed up the code as we don't need to reallocate memory on every call of perform task</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      13042 :   MultiValue&amp; invals=myBridgeVessel-&gt;getTemporyMultiValue();</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      26080 :   if( invals.getNumberOfValues()!=mycolv-&gt;getNumberOfQuantities() ||</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      13038 :       invals.getNumberOfDerivatives()!=mycolv-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :     invals.resize( mycolv-&gt;getNumberOfQuantities(), mycolv-&gt;getNumberOfDerivatives() );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      13042 :   invals.clearAll(); mycolv-&gt;performTask( taskIndex, current, invals );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      13042 :   transformBridgedDerivatives( taskIndex, invals, myvals );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      13042 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         60 : void BridgedMultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         60 :   if(!a) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         60 :     a=dynamic_cast&lt;ActionWithValue*&gt;(this);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         60 :     plumed_massert(a,&quot;cannot compute numerical derivatives for an action without values&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         60 :   if( myBridgeVessel ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         60 :     myBridgeVessel-&gt;completeNumericalDerivatives();</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   } else {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     error(&quot;numerical derivatives are not implemented&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         60 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         21 : void BridgedMultiColvarFunction::applyBridgeForces( const std::vector&lt;double&gt;&amp; bb ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         21 :   if( getNumberOfAtoms()==0 ) return ;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;Vector&gt;&amp; f( modifyForces() );</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         42 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         21 :     f[i][0]+=bb[3*i+0]; f[i][1]+=bb[3*i+1]; f[i][2]+=bb[3*i+2];</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   }</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         21 :   applyForces();</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         34 : bool BridgedMultiColvarFunction::isPeriodic() {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         34 :   return mycolv-&gt;isPeriodic();</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 : void BridgedMultiColvarFunction::deactivate_task( const unsigned&amp; taskno ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;This should never be called&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      11462 : void BridgedMultiColvarFunction::getCentralAtomPack( const unsigned&amp; basn, const unsigned&amp; curr, CatomPack&amp; mypack ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      11462 :   return mycolv-&gt;getCentralAtomPack( basn, curr, mypack );</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/BridgedMultiColvarFunction.h.func-sort-c.html b/coverage/multicolvar/BridgedMultiColvarFunction.h.func-sort-c.html
new file mode 100644
index 0000000000..a330292b45
--- /dev/null
+++ b/coverage/multicolvar/BridgedMultiColvarFunction.h.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/BridgedMultiColvarFunction.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - BridgedMultiColvarFunction.h<span style="font-size: 80%;"> (<a href="BridgedMultiColvarFunction.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">52.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">58.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BridgedMultiColvarFunction.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#109">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17isCurrentlyActiveERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#134">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#139">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#119">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#83">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#94">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#129">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#65">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction9calculateEv</a></td>
+              <td class="coverFnHi">725</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#54">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction16clearDerivativesEv</a></td>
+              <td class="coverFnHi">785</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#78">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction5applyEv</a></td>
+              <td class="coverFnHi">785</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#124">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17getCentralAtomPosERKj</a></td>
+              <td class="coverFnHi">78336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#104">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">128406</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/BridgedMultiColvarFunction.h.func.html b/coverage/multicolvar/BridgedMultiColvarFunction.h.func.html
new file mode 100644
index 0000000000..f4f50bd730
--- /dev/null
+++ b/coverage/multicolvar/BridgedMultiColvarFunction.h.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/BridgedMultiColvarFunction.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - BridgedMultiColvarFunction.h<span style="font-size: 80%;"> (<a href="BridgedMultiColvarFunction.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">52.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">58.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BridgedMultiColvarFunction.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#54">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction16clearDerivativesEv</a></td>
+              <td class="coverFnHi">785</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#124">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17getCentralAtomPosERKj</a></td>
+              <td class="coverFnHi">78336</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#109">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction17isCurrentlyActiveERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#104">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">128406</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#78">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction5applyEv</a></td>
+              <td class="coverFnHi">785</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#65">_ZN4PLMD11multicolvar26BridgedMultiColvarFunction9calculateEv</a></td>
+              <td class="coverFnHi">725</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#134">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#94">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#139">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#129">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#119">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgedMultiColvarFunction.h.gcov.html#83">_ZNK4PLMD11multicolvar26BridgedMultiColvarFunction7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/BridgedMultiColvarFunction.h.gcov.html b/coverage/multicolvar/BridgedMultiColvarFunction.h.gcov.html
new file mode 100644
index 0000000000..596e31db27
--- /dev/null
+++ b/coverage/multicolvar/BridgedMultiColvarFunction.h.gcov.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/BridgedMultiColvarFunction.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - BridgedMultiColvarFunction.h<span style="font-size: 80%;"> (source / <a href="BridgedMultiColvarFunction.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryLo">52.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">58.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_BridgedMultiColvarFunction_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_BridgedMultiColvarFunction_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/BridgeVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace multicolvar {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class BridgedMultiColvarFunction : public MultiColvarBase {</a>
+<a name="32"><span class="lineNum">      32 </span>            :   friend class MultiColvarBase;</a>
+<a name="33"><span class="lineNum">      33 </span>            :   friend class MultiColvarFunction;</a>
+<a name="34"><span class="lineNum">      34 </span>            : private:</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// This is used for storing positions properly</a>
+<a name="36"><span class="lineNum">      36 </span>            :   Vector tmp_p;</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// The action that is calculating the colvars of interest</a>
+<a name="38"><span class="lineNum">      38 </span>            :   MultiColvarBase* mycolv;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// The vessel that bridges</a>
+<a name="40"><span class="lineNum">      40 </span>            :   vesselbase::BridgeVessel* myBridgeVessel;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Everything for controlling the updating of neighbor lists</a>
+<a name="42"><span class="lineNum">      42 </span>            :   bool firsttime;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   int updateFreq;</a>
+<a name="44"><span class="lineNum">      44 </span>            : protected:</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Deactivate all the atoms in the list</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void deactivateAllAtoms();</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Activate the nth atom in the list</a>
+<a name="48"><span class="lineNum">      48 </span>            :   void setAtomActive( const unsigned&amp; n );</a>
+<a name="49"><span class="lineNum">      49 </span>            : public:</a>
+<a name="50"><span class="lineNum">      50 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit BridgedMultiColvarFunction(const ActionOptions&amp;);</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Get a pointer to the base multicolvar</a>
+<a name="53"><span class="lineNum">      53 </span>            :   MultiColvarBase* getPntrToMultiColvar() const ;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Don't actually clear the derivatives when this is called from plumed main.</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// They are calculated inside another action and clearing them would be bad</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        785 :   void clearDerivatives() override {}</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Check nothing impossible being done with derivatives</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void turnOnDerivatives() override;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Get the number of derivatives for this action</a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Get the size of the atoms with derivatives array</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned getSizeOfAtomsWithDerivatives();</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Is the output quantity periodic</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool isPeriodic() override;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Routines that have to be defined so as not to have problems with virtual methods</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void deactivate_task( const unsigned&amp; taskno );</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        725 :   void calculate() override {}</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : /// This does the task</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void transformBridgedDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) const override;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   virtual void completeTask( const unsigned&amp; curr, MultiValue&amp; invals, MultiValue&amp; outvals ) const=0;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Get the central atom position</a>
+<a name="73"><span class="lineNum">      73 </span>            :   Vector retrieveCentralAtomPos();</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Get the index of the central atom</a>
+<a name="75"><span class="lineNum">      75 </span>            :   AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned&amp; i ) const override;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Get indicecs involved in this colvar</a>
+<a name="77"><span class="lineNum">      77 </span>            :   const std::vector&lt;AtomNumber&gt; &amp; getAbsoluteIndexes()const override;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// We need our own calculate numerical derivatives here</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        785 :   void apply() override {};</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Is this atom currently being copied</a>
+<a name="82"><span class="lineNum">      82 </span>            :   bool isCurrentlyActive( const unsigned&amp; ) override;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// This should not be called</a>
+<a name="84"><span class="lineNum">      84 </span>            :   Vector calculateCentralAtomPosition() { plumed_error(); }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myvals ) const override { plumed_error(); }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   Vector getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const override;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void getIndexList( const unsigned&amp; ntotal, const unsigned&amp; jstore, const unsigned&amp; maxder, std::vector&lt;unsigned&gt;&amp; indices );</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void applyBridgeForces( const std::vector&lt;double&gt;&amp; bb ) override;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   Vector getCentralAtomPos( const unsigned&amp; curr ) override;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void normalizeVector( std::vector&lt;double&gt;&amp; vals ) const override;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void normalizeVectorDerivatives( MultiValue&amp; myvals ) const override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void getCentralAtomPack( const unsigned&amp; basn, const unsigned&amp; curr, CatomPack&amp; mypack ) override;</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : inline</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          5 : const std::vector&lt;AtomNumber&gt; &amp; BridgedMultiColvarFunction::getAbsoluteIndexes() const {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          5 :   return mycolv-&gt;getAbsoluteIndexes();</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : inline</a>
+<a name="101"><span class="lineNum">     101 </span>            : MultiColvarBase* BridgedMultiColvarFunction::getPntrToMultiColvar() const {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     889857 :   return mycolv;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : inline</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">     128406 : unsigned BridgedMultiColvarFunction::getNumberOfDerivatives() {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">     128406 :   return mycolv-&gt;getNumberOfDerivatives() + 3*getNumberOfAtoms();</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : inline</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 : bool BridgedMultiColvarFunction::isCurrentlyActive( const unsigned&amp; code ) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   return mycolv-&gt;isCurrentlyActive( code );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : inline</a>
+<a name="116"><span class="lineNum">     116 </span>            : unsigned BridgedMultiColvarFunction::getSizeOfAtomsWithDerivatives() {</a>
+<a name="117"><span class="lineNum">     117 </span>            :   return mycolv-&gt;getNumberOfAtoms();</a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : inline</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 : Vector BridgedMultiColvarFunction::getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :   return mycolv-&gt;getPositionOfAtomForLinkCells(iatom);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : inline</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      78336 : Vector BridgedMultiColvarFunction::getCentralAtomPos( const unsigned&amp; curr ) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      78336 :   return mycolv-&gt;getCentralAtomPos( curr );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : inline</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        156 : AtomNumber BridgedMultiColvarFunction::getAbsoluteIndexOfCentralAtom(const unsigned&amp; i) const {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        156 :   return mycolv-&gt;getAbsoluteIndexOfCentralAtom(i);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : inline</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 : void BridgedMultiColvarFunction::normalizeVector( std::vector&lt;double&gt;&amp; vals ) const {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :   mycolv-&gt;normalizeVector( vals );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : inline</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : void BridgedMultiColvarFunction::normalizeVectorDerivatives( MultiValue&amp; myvals ) const {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   mycolv-&gt;normalizeVectorDerivatives( myvals );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CatomPack.cpp.func-sort-c.html b/coverage/multicolvar/CatomPack.cpp.func-sort-c.html
new file mode 100644
index 0000000000..161279033a
--- /dev/null
+++ b/coverage/multicolvar/CatomPack.cpp.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CatomPack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CatomPack.cpp<span style="font-size: 80%;"> (<a href="CatomPack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CatomPack.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CatomPack.cpp.gcov.html#25">_ZN4PLMD11multicolvar9CatomPack6resizeERKj</a></td>
+              <td class="coverFnHi">114577</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CatomPack.cpp.func.html b/coverage/multicolvar/CatomPack.cpp.func.html
new file mode 100644
index 0000000000..74fdac2154
--- /dev/null
+++ b/coverage/multicolvar/CatomPack.cpp.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CatomPack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CatomPack.cpp<span style="font-size: 80%;"> (<a href="CatomPack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CatomPack.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CatomPack.cpp.gcov.html#25">_ZN4PLMD11multicolvar9CatomPack6resizeERKj</a></td>
+              <td class="coverFnHi">114577</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CatomPack.cpp.gcov.html b/coverage/multicolvar/CatomPack.cpp.gcov.html
new file mode 100644
index 0000000000..8ef85619ca
--- /dev/null
+++ b/coverage/multicolvar/CatomPack.cpp.gcov.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CatomPack.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CatomPack.cpp<span style="font-size: 80%;"> (source / <a href="CatomPack.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;CatomPack.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace multicolvar {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">     114577 : void CatomPack::resize( const unsigned&amp; size ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">     114577 :   indices.resize(size); derivs.resize(size);</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     114577 : }</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : }</a>
+<a name="32"><span class="lineNum">      32 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CatomPack.h.func-sort-c.html b/coverage/multicolvar/CatomPack.h.func-sort-c.html
new file mode 100644
index 0000000000..2c112295d9
--- /dev/null
+++ b/coverage/multicolvar/CatomPack.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CatomPack.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CatomPack.h<span style="font-size: 80%;"> (<a href="CatomPack.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CatomPack.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CatomPack.h.gcov.html#51">_ZN4PLMD11multicolvar9CatomPack13setDerivativeERKjRKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">638690</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CatomPack.h.gcov.html#68">_ZNK4PLMD11multicolvar9CatomPack13getDerivativeERKjS3_RKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">3179913</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CatomPack.h.func.html b/coverage/multicolvar/CatomPack.h.func.html
new file mode 100644
index 0000000000..d0d92403d8
--- /dev/null
+++ b/coverage/multicolvar/CatomPack.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CatomPack.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CatomPack.h<span style="font-size: 80%;"> (<a href="CatomPack.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CatomPack.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CatomPack.h.gcov.html#51">_ZN4PLMD11multicolvar9CatomPack13setDerivativeERKjRKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">638690</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CatomPack.h.gcov.html#68">_ZNK4PLMD11multicolvar9CatomPack13getDerivativeERKjS3_RKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">3179913</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CatomPack.h.gcov.html b/coverage/multicolvar/CatomPack.h.gcov.html
new file mode 100644
index 0000000000..f24cf4131f
--- /dev/null
+++ b/coverage/multicolvar/CatomPack.h.gcov.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CatomPack.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CatomPack.h<span style="font-size: 80%;"> (source / <a href="CatomPack.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_CatomPack_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_CatomPack_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tensor.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace multicolvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     114695 : class CatomPack {</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : private:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   std::vector&lt;unsigned&gt; indices;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::vector&lt;Tensor&gt; derivs;</a>
+<a name="37"><span class="lineNum">      37 </span>            : public:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   void resize( const unsigned&amp; );</a>
+<a name="39"><span class="lineNum">      39 </span>            :   void setIndex( const unsigned&amp;, const unsigned&amp; );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void setDerivative( const unsigned&amp;, const Tensor&amp; );</a>
+<a name="41"><span class="lineNum">      41 </span>            :   unsigned getNumberOfAtomsWithDerivatives() const ;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   unsigned getIndex( const unsigned&amp; ) const ;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double getDerivative( const unsigned&amp;, const unsigned&amp;, const Vector&amp; ) const ;</a>
+<a name="44"><span class="lineNum">      44 </span>            : };</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : inline</a>
+<a name="47"><span class="lineNum">      47 </span>            : void CatomPack::setIndex( const unsigned&amp; jind, const unsigned&amp; ind ) {</a>
+<a name="48"><span class="lineNum">      48 </span>            :   plumed_dbg_assert( jind&lt;indices.size() );</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     638690 :   indices[jind]=ind;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : inline</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     638690 : void CatomPack::setDerivative( const unsigned&amp; jind, const Tensor&amp; der ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   plumed_dbg_assert( jind&lt;indices.size() );</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">     638690 :   derivs[jind]=der;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     638690 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : inline</a>
+<a name="59"><span class="lineNum">      59 </span>            : unsigned CatomPack::getNumberOfAtomsWithDerivatives() const {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">    2683868 :   return indices.size();</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : inline</a>
+<a name="64"><span class="lineNum">      64 </span>            : unsigned CatomPack::getIndex( const unsigned&amp; jind ) const {</a>
+<a name="65"><span class="lineNum">      65 </span>            :   plumed_dbg_assert( jind&lt;indices.size() );</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">    1058157 :   return indices[jind];</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : inline</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    3179913 : double CatomPack::getDerivative( const unsigned&amp; iatom, const unsigned&amp; jcomp, const Vector&amp; df ) const {</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   plumed_dbg_assert( iatom&lt;indices.size() );</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    3179913 :   return df[jcomp]*derivs[iatom](jcomp,0) + df[jcomp]*derivs[iatom](jcomp,1) + df[jcomp]*derivs[iatom](jcomp,2);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CenterOfMultiColvar.cpp.func-sort-c.html b/coverage/multicolvar/CenterOfMultiColvar.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5fda8969c3
--- /dev/null
+++ b/coverage/multicolvar/CenterOfMultiColvar.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CenterOfMultiColvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CenterOfMultiColvar.cpp<span style="font-size: 80%;"> (<a href="CenterOfMultiColvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CenterOfMultiColvar.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#102">_ZN4PLMD11multicolvar19CenterOfMultiColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#94">_ZN4PLMD11multicolvar12_GLOBAL__N_131CenterOfMultiColvarRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#102">_ZN4PLMD11multicolvar19CenterOfMultiColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#129">_ZN4PLMD11multicolvar19CenterOfMultiColvar9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#96">_ZN4PLMD11multicolvar19CenterOfMultiColvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#94">_ZN4PLMD11multicolvar12_GLOBAL__N_131CenterOfMultiColvarRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#94">_ZN4PLMD11multicolvar12_GLOBAL__N_131CenterOfMultiColvarRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CenterOfMultiColvar.cpp.func.html b/coverage/multicolvar/CenterOfMultiColvar.cpp.func.html
new file mode 100644
index 0000000000..acdef07fc6
--- /dev/null
+++ b/coverage/multicolvar/CenterOfMultiColvar.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CenterOfMultiColvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CenterOfMultiColvar.cpp<span style="font-size: 80%;"> (<a href="CenterOfMultiColvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CenterOfMultiColvar.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#94">_ZN4PLMD11multicolvar12_GLOBAL__N_131CenterOfMultiColvarRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#94">_ZN4PLMD11multicolvar12_GLOBAL__N_131CenterOfMultiColvarRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#94">_ZN4PLMD11multicolvar12_GLOBAL__N_131CenterOfMultiColvarRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#96">_ZN4PLMD11multicolvar19CenterOfMultiColvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#129">_ZN4PLMD11multicolvar19CenterOfMultiColvar9calculateEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#102">_ZN4PLMD11multicolvar19CenterOfMultiColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CenterOfMultiColvar.cpp.gcov.html#102">_ZN4PLMD11multicolvar19CenterOfMultiColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CenterOfMultiColvar.cpp.gcov.html b/coverage/multicolvar/CenterOfMultiColvar.cpp.gcov.html
new file mode 100644
index 0000000000..d685fe9072
--- /dev/null
+++ b/coverage/multicolvar/CenterOfMultiColvar.cpp.gcov.html
@@ -0,0 +1,297 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CenterOfMultiColvar.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CenterOfMultiColvar.cpp<span style="font-size: 80%;"> (source / <a href="CenterOfMultiColvar.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryHi">96.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionWithVirtualAtom.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;CatomPack.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;BridgedMultiColvarFunction.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;vesselbase/StoreDataVessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VATOM CENTER_OF_MULTICOLVAR</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculate a a weighted average position based on the value of some multicolvar.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This action calculates the position of a new virtual atom using the following formula:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : x_\alpha = \frac{1}{2\pi} \arctan \left[ \frac{ \sum_i w_i f_i \sin\left( 2\pi x_{i,\alpha} \right) }{ \sum_i w_i f_i \cos\left( 2\pi x_{i,\alpha} \right) } \right]</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : Where in this expression the \f$w_i\f$ values are a set of weights calculated within a multicolvar</a>
+<a name="42"><span class="lineNum">      42 </span>            : action and the \f$f_i\f$ are the values of the multicolvar functions. The \f$x_{i,\alpha}\f$ values are</a>
+<a name="43"><span class="lineNum">      43 </span>            : the positions (in scaled coordinates) associated with each of the multicolvars calculated.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \bug The virial contribution for this type of virtual atom is not currently evaluated so do not use in bias functions unless the volume of the cell is fixed</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \par Examples</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Lets suppose that you are examining the formation of liquid droplets from gas.  You may want to</a>
+<a name="50"><span class="lineNum">      50 </span>            : determine the center of mass of any of the droplets formed.  In doing this calculation you recognize that</a>
+<a name="51"><span class="lineNum">      51 </span>            : the atoms in the liquid droplets will have a higher coordination number than those in the surrounding gas.</a>
+<a name="52"><span class="lineNum">      52 </span>            : As you want to calculate the position of the droplets you thus recognize that these atoms with high coordination</a>
+<a name="53"><span class="lineNum">      53 </span>            : numbers should have a high weight in the weighted average you are using to calculate the position of the droplet.</a>
+<a name="54"><span class="lineNum">      54 </span>            : You can thus calculate the position of the droplet using an input like the one shown below:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : c1: COORDINATIONNUMBER LOWMEM SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}</a>
+<a name="58"><span class="lineNum">      58 </span>            : cc: CENTER_OF_MULTICOLVAR DATA=c1</a>
+<a name="59"><span class="lineNum">      59 </span>            : \endplumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The first line here calculates the coordination numbers of all the atoms in the system.  The virtual atom then uses the values</a>
+<a name="62"><span class="lineNum">      62 </span>            : of the coordination numbers calculated by the action labelled c1 when it calculates the Berry Phase average described above.</a>
+<a name="63"><span class="lineNum">      63 </span>            : (N.B. the \f$w_i\f$ in the above expression are all set equal to 1 in this case)</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : The above input is fine we can, however, refine this somewhat by making use of a multicolvar transform action as shown below:</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \plumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}</a>
+<a name="69"><span class="lineNum">      69 </span>            : cf: MTRANSFORM_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM</a>
+<a name="70"><span class="lineNum">      70 </span>            : cc: CENTER_OF_MULTICOLVAR DATA=cf</a>
+<a name="71"><span class="lineNum">      71 </span>            : \endplumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : This input once again calculates the coordination numbers of all the atoms in the system.  The middle line then transforms these</a>
+<a name="74"><span class="lineNum">      74 </span>            : coordination numbers to numbers between 0 and 1.  Essentially any atom with a coordination number larger than 2.0 is given a weight</a>
+<a name="75"><span class="lineNum">      75 </span>            : of one and below this value the transformed value decays to zero.  It is these transformed coordination numbers that are used to calculate</a>
+<a name="76"><span class="lineNum">      76 </span>            : the Berry phase average described in the previous section.</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : */</a>
+<a name="79"><span class="lineNum">      79 </span>            : //+ENDPLUMEDOC</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : namespace PLMD {</a>
+<a name="82"><span class="lineNum">      82 </span>            : namespace multicolvar {</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : class CenterOfMultiColvar : public ActionWithVirtualAtom {</a>
+<a name="86"><span class="lineNum">      86 </span>            : private:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned comp;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   vesselbase::StoreDataVessel* mystash;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   MultiColvarBase* mycolv;</a>
+<a name="90"><span class="lineNum">      90 </span>            : public:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="92"><span class="lineNum">      92 </span>            :   explicit CenterOfMultiColvar(const ActionOptions&amp;ao);</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void calculate() override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(CenterOfMultiColvar,&quot;CENTER_OF_MULTICOLVAR&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          5 : void CenterOfMultiColvar::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          5 :   ActionWithVirtualAtom::registerKeywords(keys);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;find the average value for a multicolvar&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;COMPONENT&quot;,&quot;if your input multicolvar is a vector then specify which component you would like to use in calculating the weight&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          5 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          3 : CenterOfMultiColvar::CenterOfMultiColvar(const ActionOptions&amp;ao):</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   Action(ao),</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          3 :   ActionWithVirtualAtom(ao)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 :   std::string mlab; parse(&quot;DATA&quot;,mlab);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          3 :   mycolv= plumed.getActionSet().selectWithLabel&lt;MultiColvarBase*&gt;(mlab);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :   if(!mycolv) error(&quot;action labelled &quot; +  mlab + &quot; does not exist or does not have vessels&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   // Copy the atoms from the input multicolvar</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 :   BridgedMultiColvarFunction* mybr=dynamic_cast&lt;BridgedMultiColvarFunction*&gt;( mycolv );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          3 :   if( mybr ) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :     requestAtoms( (mybr-&gt;getPntrToMultiColvar())-&gt;getAbsoluteIndexes() ); comp=1;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   } else {</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :     if( mycolv-&gt;getNumberOfQuantities()&gt;5 ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :       int incomp=-1; parse(&quot;COMPONENT&quot;,incomp);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :       if( incomp&lt;0 ) error(&quot;vector input but component was not specified&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :       comp=incomp;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     } else {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          1 :       comp=1;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :     }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :     requestAtoms( mycolv-&gt;getAbsoluteIndexes () );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            :   // We need the derivatives</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          3 :   mycolv-&gt;turnOnDerivatives(); addDependency(mycolv);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   mystash = mycolv-&gt;buildDataStashes( NULL );</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          3 :   log.printf(&quot;  building center of mass based on weights calculated in multicolvar action named %s \n&quot;,mycolv-&gt;getLabel().c_str() );</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 : void CenterOfMultiColvar::calculate() {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // Retrieve the periodic boundary conditions</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   const Pbc&amp; pbc=mycolv-&gt;getPbc();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 :   if( !pbc.isOrthorombic() ) error(&quot;Berry phase does not work for non orthorhombic cells&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Create a multivalue to store the derivatives</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   MultiValue myvals( 7, mycolv-&gt;getNumberOfDerivatives() ); myvals.clearAll();</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 :   MultiValue tvals( mycolv-&gt;getNumberOfQuantities(), mycolv-&gt;getNumberOfDerivatives() );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :   tvals.clearAll();</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // Now loop over all active multicolvars</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :   Vector stmp, ctmp, scom, ccom, sder, cder;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 :   scom.zero(); ccom.zero(); double norm=0;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; cvals( mycolv-&gt;getNumberOfQuantities() );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1818 :   for(unsigned i=0; i&lt;mystash-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     // Retrieve value and derivatives</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1814 :     mystash-&gt;retrieveSequentialValue( i, false, cvals );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       1814 :     mystash-&gt;retrieveDerivatives( mycolv-&gt;getPositionInFullTaskList(i), false, tvals );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     // Convert position into fractionals</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       1814 :     Vector fpos = pbc.realToScaled( mycolv-&gt;getCentralAtomPos( mycolv-&gt;getPositionInFullTaskList(i) ) );</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     // Now accumulate Berry phase averages</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       7256 :     for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       5442 :       stmp[j] = std::sin( 2*pi*fpos[j] ); ctmp[j] = std::cos( 2*pi*fpos[j] );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       5442 :       scom[j] += cvals[0]*cvals[comp]*stmp[j]; ccom[j] += cvals[0]*cvals[comp]*ctmp[j];</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       5442 :       double icell = 1.0 / getPbc().getBox().getRow(j).modulo();</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       5442 :       sder[j] = 2*pi*icell*cvals[0]*cvals[comp]*std::cos( 2*pi*fpos[j] );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       5442 :       cder[j]=-2*pi*icell*cvals[0]*cvals[comp]*std::sin( 2*pi*fpos[j] );</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :     }</a>
+<a name="159"><span class="lineNum">     159 </span>            :     // Now accumulate derivatives</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    1623560 :     for(unsigned k=0; k&lt;tvals.getNumberActive(); ++k) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    1621746 :       unsigned icomp=tvals.getActiveIndex(k);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">    1621746 :       myvals.addDerivative( 0, icomp, cvals[0]*tvals.getDerivative( comp, icomp ) + cvals[comp]*tvals.getDerivative( 0, icomp ) );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">    6486984 :       for(unsigned k=0; k&lt;3; ++k) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">    4865238 :         myvals.addDerivative( 1+k, icomp, stmp[k]*( cvals[0]*tvals.getDerivative( comp, icomp ) +</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">    4865238 :                               cvals[comp]*tvals.getDerivative( 0, icomp ) ) );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">    4865238 :         myvals.addDerivative( 4+k, icomp, ctmp[k]*( cvals[0]*tvals.getDerivative( comp, icomp ) +</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">    4865238 :                               cvals[comp]*tvals.getDerivative( 0, icomp ) ) );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :       }</a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span>            :     // Get the central atom pack</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1814 :     CatomPack mypack; mycolv-&gt;getCentralAtomPack( 0, mycolv-&gt;getPositionInFullTaskList(i), mypack );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       3628 :     for(unsigned j=0; j&lt;mypack.getNumberOfAtomsWithDerivatives(); ++j) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       1814 :       unsigned jder=3*mypack.getIndex(j);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :       // Derivatives of sine</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1814 :       myvals.addDerivative( 1, jder+0, mypack.getDerivative(j, 0, sder) );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1814 :       myvals.addDerivative( 2, jder+1, mypack.getDerivative(j, 1, sder) );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       1814 :       myvals.addDerivative( 3, jder+2, mypack.getDerivative(j, 2, sder) );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :       // Derivatives of cosine</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       1814 :       myvals.addDerivative( 4, jder+0, mypack.getDerivative(j, 0, cder) );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       1814 :       myvals.addDerivative( 5, jder+1, mypack.getDerivative(j, 1, cder) );</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       1814 :       myvals.addDerivative( 6, jder+2, mypack.getDerivative(j, 2, cder) );</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       1814 :     norm += cvals[0]*cvals[comp]; tvals.clearAll();</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // And now finish Berry phase average</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :   scom /= norm; ccom /=norm; Vector cpos;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         16 :   for(unsigned j=0; j&lt;3; ++j) cpos[j] = std::atan2( scom[j], ccom[j] ) / (2*pi);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          4 :   Vector cart_pos = pbc.scaledToReal( cpos );</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   setPosition(cart_pos); setMass(1.0);   // This could be much cleverer but not without changing many things in PLMED</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            :   // And derivatives</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 :   Vector tander; myvals.updateDynamicList(); double inv_weight = 1.0 / norm;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         16 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         12 :     double tmp = scom[j] / ccom[j];</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         12 :     tander[j] = getPbc().getBox().getRow(j).modulo() / (2*pi*( 1 + tmp*tmp ));</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       5578 :   for(unsigned i=0; i&lt;myvals.getNumberActive(); ++i) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       5574 :     unsigned ider=myvals.getActiveIndex(i);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      22296 :     for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      16722 :       double sderv = inv_weight*myvals.getDerivative(1+j,ider) - inv_weight*scom[j]*myvals.getDerivative(0,ider);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      16722 :       double cderv = inv_weight*myvals.getDerivative(4+j,ider) - inv_weight*ccom[j]*myvals.getDerivative(0,ider);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      16722 :       myvals.setDerivative( 1+j, ider, tander[j]*(sderv/ccom[j]  - scom[j]*cderv/(ccom[j]*ccom[j])) );</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       //if( j==2 ) std::printf(&quot;DERIV %d %10.4f %10.4f %10.4f %10.4f \n&quot;,i,myvals.getDerivative(0,ider),sderv,cderv,myvals.getDerivative(1+j,ider ) );</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   // Atom derivatives</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          4 :   std::vector&lt;Tensor&gt; fderiv( getNumberOfAtoms() );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       2052 :   for(unsigned j=0; j&lt;getNumberOfAtoms(); ++j) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       8192 :     for(unsigned k=0; k&lt;3; ++k) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      22758 :       if( myvals.isActive(3*j+k) ) for(unsigned n=0; n&lt;3; ++n) fderiv[j](k,n) = myvals.getDerivative( 1+n, 3*j+k );</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       2424 :       else for(unsigned n=0; n&lt;3; ++n) fderiv[j](k,n) = 0;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :     }</a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            :   setAtomsDerivatives( fderiv );</a>
+<a name="217"><span class="lineNum">     217 </span>            :   // Box derivatives?</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          4 : }</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : }</a>
+<a name="221"><span class="lineNum">     221 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CoordinationNumbers.cpp.func-sort-c.html b/coverage/multicolvar/CoordinationNumbers.cpp.func-sort-c.html
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CoordinationNumbers.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CoordinationNumbers.cpp<span style="font-size: 80%;"> (<a href="CoordinationNumbers.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoordinationNumbers.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#113">_ZN4PLMD11multicolvar19CoordinationNumbersC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#93">_ZN4PLMD11multicolvar12_GLOBAL__N_131CoordinationNumbersRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#113">_ZN4PLMD11multicolvar19CoordinationNumbersC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#95">_ZN4PLMD11multicolvar19CoordinationNumbers16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#90">_ZN4PLMD11multicolvar19CoordinationNumbers10isPeriodicEv</a></td>
+              <td class="coverFnHi">856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#93">_ZN4PLMD11multicolvar12_GLOBAL__N_131CoordinationNumbersRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#93">_ZN4PLMD11multicolvar12_GLOBAL__N_131CoordinationNumbersRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#154">_ZNK4PLMD11multicolvar19CoordinationNumbers7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">37088</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CoordinationNumbers.cpp.func.html b/coverage/multicolvar/CoordinationNumbers.cpp.func.html
new file mode 100644
index 0000000000..8862c9a2f8
--- /dev/null
+++ b/coverage/multicolvar/CoordinationNumbers.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CoordinationNumbers.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CoordinationNumbers.cpp<span style="font-size: 80%;"> (<a href="CoordinationNumbers.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CoordinationNumbers.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#93">_ZN4PLMD11multicolvar12_GLOBAL__N_131CoordinationNumbersRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#93">_ZN4PLMD11multicolvar12_GLOBAL__N_131CoordinationNumbersRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#93">_ZN4PLMD11multicolvar12_GLOBAL__N_131CoordinationNumbersRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#90">_ZN4PLMD11multicolvar19CoordinationNumbers10isPeriodicEv</a></td>
+              <td class="coverFnHi">856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#95">_ZN4PLMD11multicolvar19CoordinationNumbers16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">54</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#113">_ZN4PLMD11multicolvar19CoordinationNumbersC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">52</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#113">_ZN4PLMD11multicolvar19CoordinationNumbersC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoordinationNumbers.cpp.gcov.html#154">_ZNK4PLMD11multicolvar19CoordinationNumbers7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">37088</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/CoordinationNumbers.cpp.gcov.html b/coverage/multicolvar/CoordinationNumbers.cpp.gcov.html
new file mode 100644
index 0000000000..6ffb7dd3ee
--- /dev/null
+++ b/coverage/multicolvar/CoordinationNumbers.cpp.gcov.html
@@ -0,0 +1,260 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/CoordinationNumbers.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - CoordinationNumbers.cpp<span style="font-size: 80%;"> (source / <a href="CoordinationNumbers.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace multicolvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MCOLVAR COORDINATIONNUMBER</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculate the coordination numbers of atoms so that you can then calculate functions of the distribution of</a>
+<a name="37"><span class="lineNum">      37 </span>            :  coordination numbers such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : So that the calculated coordination numbers have continuous derivatives the following function is used:</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : s = \frac{ 1 - \left(\frac{r-d_0}{r_0}\right)^n } { 1 - \left(\frac{r-d_0}{r_0}\right)^m }</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : If R_POWER is set, this will use the product of pairwise distance</a>
+<a name="46"><span class="lineNum">      46 </span>            : raised to the R_POWER with the coordination number function defined</a>
+<a name="47"><span class="lineNum">      47 </span>            : above. This was used in White and Voth \cite white2014efficient as a</a>
+<a name="48"><span class="lineNum">      48 </span>            : way of indirectly biasing radial distribution functions. Note that in</a>
+<a name="49"><span class="lineNum">      49 </span>            : that reference this function is referred to as moments of coordination</a>
+<a name="50"><span class="lineNum">      50 </span>            : number, but here we call them powers to distinguish from the existing</a>
+<a name="51"><span class="lineNum">      51 </span>            : MOMENTS keyword of Multicolvars.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \par Examples</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The following input tells plumed to calculate the coordination numbers of atoms 1-100 with themselves.</a>
+<a name="56"><span class="lineNum">      56 </span>            : The minimum coordination number is then calculated.</a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 MIN={BETA=0.1}</a>
+<a name="59"><span class="lineNum">      59 </span>            : \endplumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The following input tells plumed to calculate how many atoms from 1-100 are within 3.0 of each of the atoms</a>
+<a name="62"><span class="lineNum">      62 </span>            : from 101-110.  In the first 101 is the central atom, in the second 102 is the central atom and so on.  The</a>
+<a name="63"><span class="lineNum">      63 </span>            : number of coordination numbers more than 6 is then computed.</a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : COORDINATIONNUMBER SPECIESA=101-110 SPECIESB=1-100 R_0=3.0 MORE_THAN={RATIONAL R_0=6.0 NN=6 MM=12 D_0=0}</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : The following input tells plumed to calculate the mean coordination number of all atoms with themselves</a>
+<a name="69"><span class="lineNum">      69 </span>            : and its powers. An explicit cutoff is set for each of 8.</a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : cn0: COORDINATIONNUMBER SPECIES=1-10 SWITCH={RATIONAL R_0=1.0 D_MAX=8} MEAN</a>
+<a name="72"><span class="lineNum">      72 </span>            : cn1: COORDINATIONNUMBER SPECIES=1-10 SWITCH={RATIONAL R_0=1.0 D_MAX=8} R_POWER=1 MEAN</a>
+<a name="73"><span class="lineNum">      73 </span>            : cn2: COORDINATIONNUMBER SPECIES=1-10 SWITCH={RATIONAL R_0=1.0 D_MAX=8} R_POWER=2 MEAN</a>
+<a name="74"><span class="lineNum">      74 </span>            : PRINT ARG=cn0.mean,cn1.mean,cn2.mean STRIDE=1 FILE=cn_out</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class CoordinationNumbers : public MultiColvarBase {</a>
+<a name="82"><span class="lineNum">      82 </span>            : private:</a>
+<a name="83"><span class="lineNum">      83 </span>            :   double rcut2;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   int r_power;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit CoordinationNumbers(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            : // active methods:</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        856 :   bool isPeriodic() override { return false; }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      12608 : PLUMED_REGISTER_ACTION(CoordinationNumbers,&quot;COORDINATIONNUMBER&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         54 : void CoordinationNumbers::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         54 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        162 :   keys.use(&quot;SPECIES&quot;); keys.use(&quot;SPECIESA&quot;); keys.use(&quot;SPECIESB&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        108 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        108 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        108 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        108 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        108 :   keys.add(&quot;optional&quot;,&quot;R_POWER&quot;,&quot;Multiply the coordination number function by a power of r, &quot;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :            &quot;as done in White and Voth (see note above, default: no)&quot;);</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        108 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="108"><span class="lineNum">     108 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        216 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MAX&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        216 :   keys.use(&quot;MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        162 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         54 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         52 : CoordinationNumbers::CoordinationNumbers(const ActionOptions&amp;ao):</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   Action(ao),</a>
+<a name="117"><span class="lineNum">     117 </span>            :   MultiColvarBase(ao),</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         52 :   r_power(0)</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : {</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   // Read in the switching function</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        104 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         52 :   if(sw.length()&gt;0) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         50 :     switchingFunction.set(sw,errors);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         50 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   } else {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          4 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          4 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   }</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         52 :   log.printf(&quot;  coordination of central atom and those within %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   //get cutoff of switching function</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         52 :   double rcut = switchingFunction.get_dmax();</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   //parse power</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         52 :   parse(&quot;R_POWER&quot;, r_power);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         52 :   if(r_power &gt; 0) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :     log.printf(&quot;  Multiplying switching function by r^%d\n&quot;, r_power);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 :     double offset = switchingFunction.calculate(rcut*0.9999, rcut2) * std::pow(rcut*0.9999, r_power);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          4 :     log.printf(&quot;  You will have a discontinuous jump of %f to 0 near the cutoff of your switching function. &quot;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :                &quot;Consider setting D_MAX or reducing R_POWER if this is large\n&quot;, offset);</a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            :   // Set the link cell cutoff</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         52 :   setLinkCellCutoff( rcut );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         52 :   rcut2 = rcut * rcut;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   // And setup the ActionWithVessel</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         52 :   std::vector&lt;AtomNumber&gt; all_atoms; setupMultiColvarBase( all_atoms ); checkRead();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         52 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      37088 : double CoordinationNumbers::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   // Calculate the coordination number</a>
+<a name="158"><span class="lineNum">     158 </span>            :   double dfunc, sw, d, raised;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    3822803 :   for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     Vector&amp; distance=myatoms.getPosition(i);</a>
+<a name="161"><span class="lineNum">     161 </span>            :     double d2;</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">    7107372 :     if ( (d2=distance[0]*distance[0])&lt;rcut2 &amp;&amp;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">    3321657 :          (d2+=distance[1]*distance[1])&lt;rcut2 &amp;&amp;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">    6676366 :          (d2+=distance[2]*distance[2])&lt;rcut2 &amp;&amp;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :          d2&gt;epsilon ) {</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">    2633753 :       sw = switchingFunction.calculateSqr( d2, dfunc );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">    2633753 :       if(r_power &gt; 0) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      19350 :         d = std::sqrt(d2); raised = std::pow( d, r_power - 1 );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      19350 :         accumulateSymmetryFunction( 1, i, sw * raised * d,</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      19350 :                                     (dfunc * d * raised + sw * r_power * raised / d) * distance,</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      38700 :                                     (-dfunc * d * raised - sw * r_power * raised / d) * Tensor(distance, distance),</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :                                     myatoms );</a>
+<a name="174"><span class="lineNum">     174 </span>            :       } else {</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">    2614403 :         accumulateSymmetryFunction( 1, i, sw, (dfunc)*distance, (-dfunc)*Tensor(distance,distance), myatoms );</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :       }</a>
+<a name="177"><span class="lineNum">     177 </span>            :     }</a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      37088 :   return myatoms.getValue(1);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Density.cpp.func-sort-c.html b/coverage/multicolvar/Density.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6dc65e932f
--- /dev/null
+++ b/coverage/multicolvar/Density.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Density.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Density.cpp<span style="font-size: 80%;"> (<a href="Density.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">70.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Density.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#89">_ZN4PLMD11multicolvar7Density12getIndexListERKjS3_S3_RSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#97">_ZN4PLMD11multicolvar7Density15getValueForTaskERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#73">_ZN4PLMD11multicolvar7DensityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#58">_ZNK4PLMD11multicolvar7Density28hasDifferentiableOrientationEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#56">_ZN4PLMD11multicolvar7Density10isPeriodicEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#66">_ZN4PLMD11multicolvar12_GLOBAL__N_119DensityRegisterMe686createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#73">_ZN4PLMD11multicolvar7DensityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#68">_ZN4PLMD11multicolvar7Density16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#66">_ZN4PLMD11multicolvar12_GLOBAL__N_119DensityRegisterMe68C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#66">_ZN4PLMD11multicolvar12_GLOBAL__N_119DensityRegisterMe68D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#85">_ZNK4PLMD11multicolvar7Density7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15955</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#57">_ZNK4PLMD11multicolvar7Density9isDensityEv</a></td>
+              <td class="coverFnHi">200727</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Density.cpp.func.html b/coverage/multicolvar/Density.cpp.func.html
new file mode 100644
index 0000000000..3be65320d3
--- /dev/null
+++ b/coverage/multicolvar/Density.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Density.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Density.cpp<span style="font-size: 80%;"> (<a href="Density.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">70.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Density.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#66">_ZN4PLMD11multicolvar12_GLOBAL__N_119DensityRegisterMe686createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#66">_ZN4PLMD11multicolvar12_GLOBAL__N_119DensityRegisterMe68C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#66">_ZN4PLMD11multicolvar12_GLOBAL__N_119DensityRegisterMe68D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#56">_ZN4PLMD11multicolvar7Density10isPeriodicEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#89">_ZN4PLMD11multicolvar7Density12getIndexListERKjS3_S3_RSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#97">_ZN4PLMD11multicolvar7Density15getValueForTaskERKjRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#68">_ZN4PLMD11multicolvar7Density16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#73">_ZN4PLMD11multicolvar7DensityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#73">_ZN4PLMD11multicolvar7DensityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#58">_ZNK4PLMD11multicolvar7Density28hasDifferentiableOrientationEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#85">_ZNK4PLMD11multicolvar7Density7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15955</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Density.cpp.gcov.html#57">_ZNK4PLMD11multicolvar7Density9isDensityEv</a></td>
+              <td class="coverFnHi">200727</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Density.cpp.gcov.html b/coverage/multicolvar/Density.cpp.gcov.html
new file mode 100644
index 0000000000..d738372d70
--- /dev/null
+++ b/coverage/multicolvar/Density.cpp.gcov.html
@@ -0,0 +1,181 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Density.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Density.cpp<span style="font-size: 80%;"> (source / <a href="Density.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryLo">70.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace multicolvar {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC MCOLVAR DENSITY</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Calculate functions of the density of atoms as a function of the box.  This allows one to calculate</a>
+<a name="35"><span class="lineNum">      35 </span>            :  the number of atoms in half the box.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The following example calculates the number of atoms in one half of the simulation box.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : DENSITY SPECIES=1-100 LABEL=d</a>
+<a name="43"><span class="lineNum">      43 </span>            : AROUND ATOM=101 DATA=d SIGMA=0.1 XLOWER=0.0 XUPPER=0.5 LABEL=d1</a>
+<a name="44"><span class="lineNum">      44 </span>            : PRINT ARG=d1.* FILE=colvar1 FMT=%8.4f</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : class Density : public MultiColvarBase {</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="54"><span class="lineNum">      54 </span>            :   explicit Density(const ActionOptions&amp;);</a>
+<a name="55"><span class="lineNum">      55 </span>            : // active methods:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   /// Returns the number of coordinates of the field</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :   bool isPeriodic() override { return false; }</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">     200727 :   bool isDensity() const override { return true; }</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :   bool hasDifferentiableOrientation() const override { return true; }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : //  void addOrientationDerivativesToBase( const unsigned&amp; iatom, const unsigned&amp; jstore, const unsigned&amp; base_cv_no,</a>
+<a name="62"><span class="lineNum">      62 </span>            : //                                        const std::vector&lt;double&gt;&amp; weight, MultiColvarFunction* func ){}</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void getIndexList( const unsigned&amp; ntotal, const unsigned&amp; jstore, const unsigned&amp; maxder, std::vector&lt;unsigned&gt;&amp; indices );</a>
+<a name="64"><span class="lineNum">      64 </span>            : //  unsigned getNumberOfQuantities();</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void getValueForTask( const unsigned&amp; iatom, std::vector&lt;double&gt;&amp; vals );</a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      12526 : PLUMED_REGISTER_ACTION(Density,&quot;DENSITY&quot;)</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         13 : void Density::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         13 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         13 :   keys.use(&quot;SPECIES&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         13 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         11 : Density::Density(const ActionOptions&amp;ao):</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   Action(ao),</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         11 :   MultiColvarBase(ao)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         11 :   std::vector&lt;AtomNumber&gt; all_atoms; parseMultiColvarAtomList(&quot;SPECIES&quot;, -1, all_atoms);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         11 :   ablocks.resize(1); ablocks[0].resize( atom_lab.size() );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        489 :   for(unsigned i=0; i&lt;atom_lab.size(); ++i) { addTaskToList(i); ablocks[0][i]=i; }</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         11 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   // And check everything has been read in correctly</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         11 :   checkRead();</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         11 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      15955 : double Density::compute( const unsigned&amp; tindex, AtomValuePack&amp; myvals ) const {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      15955 :   return 1.0;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 : void Density::getIndexList( const unsigned&amp; ntotal, const unsigned&amp; jstore, const unsigned&amp; maxder, std::vector&lt;unsigned&gt;&amp; indices ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :   indices[jstore]=0;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : // unsigned Density::getNumberOfQuantities(){</a>
+<a name="96"><span class="lineNum">      96 </span>            : //    return 2;</a>
+<a name="97"><span class="lineNum">      97 </span>            : // }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 : void Density::getValueForTask( const unsigned&amp; iatom, std::vector&lt;double&gt;&amp; vals ) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   plumed_dbg_assert( vals.size()==2 ); vals[0]=vals[1]=1.0;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DihedralCorrelation.cpp.func-sort-c.html b/coverage/multicolvar/DihedralCorrelation.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5ff9bdc542
--- /dev/null
+++ b/coverage/multicolvar/DihedralCorrelation.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DihedralCorrelation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DihedralCorrelation.cpp<span style="font-size: 80%;"> (<a href="DihedralCorrelation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DihedralCorrelation.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#87">_ZN4PLMD11multicolvar19DihedralCorrelation10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#102">_ZN4PLMD11multicolvar19DihedralCorrelationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#90">_ZN4PLMD11multicolvar12_GLOBAL__N_131DihedralCorrelationRegisterMe926createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#102">_ZN4PLMD11multicolvar19DihedralCorrelationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#92">_ZN4PLMD11multicolvar19DihedralCorrelation16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#126">_ZNK4PLMD11multicolvar19DihedralCorrelation7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">590</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#90">_ZN4PLMD11multicolvar12_GLOBAL__N_131DihedralCorrelationRegisterMe92C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#90">_ZN4PLMD11multicolvar12_GLOBAL__N_131DihedralCorrelationRegisterMe92D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DihedralCorrelation.cpp.func.html b/coverage/multicolvar/DihedralCorrelation.cpp.func.html
new file mode 100644
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DihedralCorrelation.cpp<span style="font-size: 80%;"> (<a href="DihedralCorrelation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
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+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#90">_ZN4PLMD11multicolvar12_GLOBAL__N_131DihedralCorrelationRegisterMe926createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#90">_ZN4PLMD11multicolvar12_GLOBAL__N_131DihedralCorrelationRegisterMe92C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
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+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#90">_ZN4PLMD11multicolvar12_GLOBAL__N_131DihedralCorrelationRegisterMe92D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#87">_ZN4PLMD11multicolvar19DihedralCorrelation10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#92">_ZN4PLMD11multicolvar19DihedralCorrelation16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#102">_ZN4PLMD11multicolvar19DihedralCorrelationC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#102">_ZN4PLMD11multicolvar19DihedralCorrelationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DihedralCorrelation.cpp.gcov.html#126">_ZNK4PLMD11multicolvar19DihedralCorrelation7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">590</td>
+            </tr>
+  </table>
+  <br>
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diff --git a/coverage/multicolvar/DihedralCorrelation.cpp.gcov.html b/coverage/multicolvar/DihedralCorrelation.cpp.gcov.html
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DihedralCorrelation.cpp<span style="font-size: 80%;"> (source / <a href="DihedralCorrelation.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace multicolvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC COLVAR DIHCOR</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Measures the degree of similarity between dihedral angles.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This colvar calculates the following quantity.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : s = \frac{1}{2} \sum_i \left[ 1 + \cos( \phi_i - \psi_i ) \right]</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where the \f$\phi_i\f$ and \f$\psi\f$ values and the instantaneous values for the \ref TORSION angles of interest.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The following provides an example input for the DIHCOR action</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : DIHCOR ...</a>
+<a name="51"><span class="lineNum">      51 </span>            :   ATOMS1=1,2,3,4,5,6,7,8</a>
+<a name="52"><span class="lineNum">      52 </span>            :   ATOMS2=5,6,7,8,9,10,11,12</a>
+<a name="53"><span class="lineNum">      53 </span>            :   LABEL=dih</a>
+<a name="54"><span class="lineNum">      54 </span>            : ... DIHCOR</a>
+<a name="55"><span class="lineNum">      55 </span>            : PRINT ARG=dih FILE=colvar STRIDE=10</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : In the above input we are calculating the correlation between the torsion angle involving atoms 1, 2, 3 and 4 and the torsion angle</a>
+<a name="59"><span class="lineNum">      59 </span>            : involving atoms 5, 6, 7 and 8.  This is then added to the correlation between the torsion angle involving atoms 5, 6, 7 and 8 and the</a>
+<a name="60"><span class="lineNum">      60 </span>            : correlation angle involving atoms 9, 10, 11 and 12.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : Writing out the atoms involved in all the torsion angles in this way can be rather tedious. Thankfully if you are working with protein you</a>
+<a name="63"><span class="lineNum">      63 </span>            : can avoid this by using the \ref MOLINFO command.  PLUMED uses the pdb file that you provide to this command to learn</a>
+<a name="64"><span class="lineNum">      64 </span>            : about the topology of the protein molecule.  This means that you can specify torsion angles using the following syntax:</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="68"><span class="lineNum">      68 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb</a>
+<a name="69"><span class="lineNum">      69 </span>            : dih: DIHCOR ...</a>
+<a name="70"><span class="lineNum">      70 </span>            : ATOMS1=@phi-3,@psi-3</a>
+<a name="71"><span class="lineNum">      71 </span>            : ATOMS2=@psi-3,@phi-4</a>
+<a name="72"><span class="lineNum">      72 </span>            : ATOMS3=@phi-4,@psi-4</a>
+<a name="73"><span class="lineNum">      73 </span>            : ...</a>
+<a name="74"><span class="lineNum">      74 </span>            : PRINT ARG=dih FILE=colvar STRIDE=10</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.</a>
+<a name="78"><span class="lineNum">      78 </span>            : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the fourth residue of the protein.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : */</a>
+<a name="81"><span class="lineNum">      81 </span>            : //+ENDPLUMEDOC</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : class DihedralCorrelation : public MultiColvarBase {</a>
+<a name="84"><span class="lineNum">      84 </span>            : private:</a>
+<a name="85"><span class="lineNum">      85 </span>            : public:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="87"><span class="lineNum">      87 </span>            :   explicit DihedralCorrelation(const ActionOptions&amp;);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : };</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(DihedralCorrelation,&quot;DIHCOR&quot;)</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          4 : void DihedralCorrelation::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the dihedral correlation values you wish to calculate. &quot;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one dihedral correlation will be &quot;</a>
+<a name="98"><span class="lineNum">      98 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="99"><span class="lineNum">      99 </span>            :            &quot;specify the indices of 8 atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="100"><span class="lineNum">     100 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          8 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          2 : DihedralCorrelation::DihedralCorrelation(const ActionOptions&amp;ao):</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   Action(ao),</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   MultiColvarBase(ao)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : {</a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Read in the atoms</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   readAtomsLikeKeyword( &quot;ATOMS&quot;, 8, all_atoms );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   // Stuff for central atoms</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   std::vector&lt;bool&gt; catom_ind(8, false);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          6 :   catom_ind[1]=catom_ind[2]=catom_ind[5]=catom_ind[6]=true;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   setAtomsForCentralAtom( catom_ind );</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   // And setup the ActionWithVessel</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   if( getNumberOfVessels()==0 ) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     std::string fake_input;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :     addVessel( &quot;SUM&quot;, fake_input, -1 );  // -1 here means that this value will be named getLabel()</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :     readVesselKeywords();  // This makes sure resizing is done</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   // And check everything has been read in correctly</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        590 : double DihedralCorrelation::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        590 :   const Vector d10=getSeparation(myatoms.getPosition(1),myatoms.getPosition(0));</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        590 :   const Vector d11=getSeparation(myatoms.getPosition(2),myatoms.getPosition(1));</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        590 :   const Vector d12=getSeparation(myatoms.getPosition(3),myatoms.getPosition(2));</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        590 :   Vector dd10,dd11,dd12;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   PLMD::Torsion t1;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        590 :   const double phi1  = t1.compute(d10,d11,d12,dd10,dd11,dd12);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        590 :   const Vector d20=getSeparation(myatoms.getPosition(5),myatoms.getPosition(4));</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        590 :   const Vector d21=getSeparation(myatoms.getPosition(6),myatoms.getPosition(5));</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        590 :   const Vector d22=getSeparation(myatoms.getPosition(7),myatoms.getPosition(6));</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        590 :   Vector dd20,dd21,dd22;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   PLMD::Torsion t2;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        590 :   const double phi2 = t2.compute( d20, d21, d22, dd20, dd21, dd22 );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   // Calculate value</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        590 :   const double diff = phi2 - phi1;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        590 :   const double value = 0.5*(1.+std::cos(diff));</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   // Derivatives wrt phi1</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        590 :   const double dval = 0.5*std::sin(diff);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        590 :   dd10 *= dval;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        590 :   dd11 *= dval;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        590 :   dd12 *= dval;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   // And add</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 0, dd10, myatoms );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 1, dd11-dd10, myatoms );</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 2, dd12-dd11, myatoms );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 3, -dd12, myatoms );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        590 :   myatoms.addBoxDerivatives  (1, -(extProduct(d10,dd10)+extProduct(d11,dd11)+extProduct(d12,dd12)));</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Derivative wrt phi2</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        590 :   dd20 *= -dval;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        590 :   dd21 *= -dval;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        590 :   dd22 *= -dval;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   // And add</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 4, dd20, myatoms );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 5, dd21-dd20, myatoms );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 6, dd22-dd21, myatoms );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        590 :   addAtomDerivatives(1, 7, -dd22, myatoms );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        590 :   myatoms.addBoxDerivatives(1, -(extProduct(d20,dd20)+extProduct(d21,dd21)+extProduct(d22,dd22)));</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        590 :   return value;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DistanceFromContour.cpp.func-sort-c.html b/coverage/multicolvar/DistanceFromContour.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f2da78578e
--- /dev/null
+++ b/coverage/multicolvar/DistanceFromContour.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DistanceFromContour.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DistanceFromContour.cpp<span style="font-size: 80%;"> (<a href="DistanceFromContour.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">131</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntryMed">86.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DistanceFromContour.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#91">_ZN4PLMD11multicolvar19DistanceFromContour10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#121">_ZN4PLMD11multicolvar19DistanceFromContourC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_132DistanceFromContourRegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#121">_ZN4PLMD11multicolvar19DistanceFromContourC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#100">_ZN4PLMD11multicolvar19DistanceFromContour16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#335">_ZN4PLMD11multicolvar19DistanceFromContour5applyEv</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#192">_ZN4PLMD11multicolvar19DistanceFromContour9calculateEv</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#290">_ZN4PLMD11multicolvar19DistanceFromContour24getDifferenceFromContourERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">3115</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#301">_ZNK4PLMD11multicolvar19DistanceFromContour7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">3115</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#88">_ZNK4PLMD11multicolvar19DistanceFromContour9isDensityEv</a></td>
+              <td class="coverFnHi">3115</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_132DistanceFromContourRegisterMe100C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_132DistanceFromContourRegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#188">_ZNK4PLMD11multicolvar19DistanceFromContour21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">6230</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DistanceFromContour.cpp.func.html b/coverage/multicolvar/DistanceFromContour.cpp.func.html
new file mode 100644
index 0000000000..f74a809c2e
--- /dev/null
+++ b/coverage/multicolvar/DistanceFromContour.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DistanceFromContour.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DistanceFromContour.cpp<span style="font-size: 80%;"> (<a href="DistanceFromContour.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">131</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntryMed">86.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DistanceFromContour.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_132DistanceFromContourRegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_132DistanceFromContourRegisterMe100C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_132DistanceFromContourRegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#91">_ZN4PLMD11multicolvar19DistanceFromContour10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#100">_ZN4PLMD11multicolvar19DistanceFromContour16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#290">_ZN4PLMD11multicolvar19DistanceFromContour24getDifferenceFromContourERKSt6vectorIdSaIdEERS4_</a></td>
+              <td class="coverFnHi">3115</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#335">_ZN4PLMD11multicolvar19DistanceFromContour5applyEv</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#192">_ZN4PLMD11multicolvar19DistanceFromContour9calculateEv</a></td>
+              <td class="coverFnHi">137</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#121">_ZN4PLMD11multicolvar19DistanceFromContourC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#121">_ZN4PLMD11multicolvar19DistanceFromContourC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#188">_ZNK4PLMD11multicolvar19DistanceFromContour21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">6230</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#301">_ZNK4PLMD11multicolvar19DistanceFromContour7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">3115</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DistanceFromContour.cpp.gcov.html#88">_ZNK4PLMD11multicolvar19DistanceFromContour9isDensityEv</a></td>
+              <td class="coverFnHi">3115</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DistanceFromContour.cpp.gcov.html b/coverage/multicolvar/DistanceFromContour.cpp.gcov.html
new file mode 100644
index 0000000000..d263c8d2c2
--- /dev/null
+++ b/coverage/multicolvar/DistanceFromContour.cpp.gcov.html
@@ -0,0 +1,418 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DistanceFromContour.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DistanceFromContour.cpp<span style="font-size: 80%;"> (source / <a href="DistanceFromContour.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">131</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntryMed">86.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/RootFindingBase.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;vesselbase/ValueVessel.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR DISTANCE_FROM_CONTOUR</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate the perpendicular distance from a Willard-Chandler dividing surface.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Suppose that you have calculated a multicolvar.  By doing so you have calculated a</a>
+<a name="34"><span class="lineNum">      34 </span>            : set of colvars, \f$s_i\f$, and each of these colvars has a well defined position in</a>
+<a name="35"><span class="lineNum">      35 </span>            : space \f$(x_i,y_i,z_i)\f$.  You can use this information to calculate a phase-field</a>
+<a name="36"><span class="lineNum">      36 </span>            : model of the colvar density using:</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : p(x,y,x) = \sum_{i} s_i K\left[\frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right]</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f]</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : In this expression \f$\sigma_x, \sigma_y\f$ and \f$\sigma_z\f$ are bandwidth parameters and</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f$K\f$ is one of the \ref kernelfunctions.  This is what is done within \ref MULTICOLVARDENS</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The Willard-Chandler surface is a surface of constant density in the above phase field \f$p(x,y,z)\f$.</a>
+<a name="46"><span class="lineNum">      46 </span>            : In other words, it is a set of points, \f$(x',y',z')\f$, in your box which have:</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : p(x',y',z') = \rho</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : where \f$\rho\f$ is some target density.  This action calculates the distance projected on the \f$x, y\f$ or</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f$z\f$ axis between the position of some test particle and this surface of constant field density.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \par Examples</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : In this example atoms 2-100 are assumed to be concentrated along some part of the \f$z\f$ axis so that you</a>
+<a name="58"><span class="lineNum">      58 </span>            : an interface between a liquid/solid and the vapor.  The quantity dc measures the distance between the</a>
+<a name="59"><span class="lineNum">      59 </span>            : surface at which the density of 2-100 atoms is equal to 0.2 and the position of the test particle atom 1.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : dens: DENSITY SPECIES=2-100</a>
+<a name="63"><span class="lineNum">      63 </span>            : dc: DISTANCE_FROM_CONTOUR DATA=dens ATOM=1 BANDWIDTH=0.5,0.5,0.5 DIR=z CONTOUR=0.2</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : //+ENDPLUMEDOC</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace PLMD {</a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace multicolvar {</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : class DistanceFromContour : public MultiColvarBase {</a>
+<a name="73"><span class="lineNum">      73 </span>            : private:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   unsigned dir;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool derivTime;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   double rcut2;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   double contour;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   double pbc_param;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::string kerneltype;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; pval;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;double&gt; bw, pos1, pos2, dirv, dirv2;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;double&gt; forces;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;unsigned&gt; perp_dirs;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   vesselbase::ValueVessel* myvalue_vessel;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   vesselbase::ValueVessel* myderiv_vessel;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   RootFindingBase&lt;DistanceFromContour&gt; mymin;</a>
+<a name="87"><span class="lineNum">      87 </span>            : public:</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="89"><span class="lineNum">      89 </span>            :   explicit DistanceFromContour( const ActionOptions&amp; );</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       3115 :   bool isDensity() const override { return true; }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   void calculate() override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   double getDifferenceFromContour( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der );</a>
+<a name="96"><span class="lineNum">      96 </span>            : // We need an apply action as we are using an independent value</a>
+<a name="97"><span class="lineNum">      97 </span>            :   void apply() override;</a>
+<a name="98"><span class="lineNum">      98 </span>            : };</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(DistanceFromContour,&quot;DISTANCE_FROM_CONTOUR&quot;)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          3 : void DistanceFromContour::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          3 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;dist1&quot;,&quot;default&quot;,&quot;the distance between the reference atom and the nearest contour&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;dist2&quot;,&quot;default&quot;,&quot;the distance between the reference atom and the other contour&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;qdist&quot;,&quot;default&quot;,&quot;the differentiable (squared) distance between the two contours (see above)&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;thickness&quot;,&quot;default&quot;,&quot;the distance between the two contours on the line from the reference atom&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;The input base multicolvar which is being used to calculate the contour&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;,&quot;ATOM&quot;,&quot;The atom whose perpendicular distance we are calculating from the contour&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;BANDWIDTH&quot;,&quot;the bandwidths for kernel density estimation&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;KERNEL&quot;,&quot;gaussian&quot;,&quot;the kernel function you are using.  More details on  the kernels available &quot;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :            &quot;in plumed plumed can be found in \\ref kernelfunctions.&quot;);</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;DIR&quot;,&quot;the direction perpendicular to the contour that you are looking for&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;CONTOUR&quot;,&quot;the value we would like for the contour&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;TOLERANCE&quot;,&quot;0.1&quot;,&quot;this parameter is used to manage periodic boundary conditions.  The problem &quot;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :            &quot;here is that we can be between contours even when we are not within the membrane &quot;</a>
+<a name="117"><span class="lineNum">     117 </span>            :            &quot;because of periodic boundary conditions.  When we are in the contour, however, we &quot;</a>
+<a name="118"><span class="lineNum">     118 </span>            :            &quot;should have it so that the sums of the absolute values of the distances to the two &quot;</a>
+<a name="119"><span class="lineNum">     119 </span>            :            &quot;contours is approximately the distance between the two contours.  There can be numerical errors in these calculations, however, so &quot;</a>
+<a name="120"><span class="lineNum">     120 </span>            :            &quot;we specify a small tolerance here&quot;);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          3 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 : DistanceFromContour::DistanceFromContour( const ActionOptions&amp; ao ):</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   Action(ao),</a>
+<a name="125"><span class="lineNum">     125 </span>            :   MultiColvarBase(ao),</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :   derivTime(false),</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          1 :   bw(3),</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          1 :   pos1(3,0.0),</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          1 :   pos2(3,0.0),</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   dirv(3,0.0),</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 :   dirv2(3,0.0),</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          1 :   perp_dirs(2),</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          2 :   mymin(this)</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : {</a>
+<a name="135"><span class="lineNum">     135 </span>            :   // Read in the multicolvar/atoms</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   std::vector&lt;AtomNumber&gt; all_atoms; parse(&quot;TOLERANCE&quot;,pbc_param);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          1 :   bool read2 = parseMultiColvarAtomList(&quot;DATA&quot;, -1, all_atoms);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          1 :   if( !read2 ) error(&quot;missing DATA keyword&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          1 :   bool read1 = parseMultiColvarAtomList(&quot;ATOM&quot;, -1, all_atoms);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          1 :   if( !read1 ) error(&quot;missing ATOM keyword&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :   if( all_atoms.size()!=1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   // Read in the center of the binding object</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :   log.printf(&quot;  computing distance of atom %d from contour \n&quot;,all_atoms[0].serial() );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :   setupMultiColvarBase( all_atoms ); forces.resize( 3*getNumberOfAtoms() + 9 );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :   if( getNumberOfBaseMultiColvars()!=1 ) error(&quot;should only be one input multicolvar&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   // Get the direction</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :   std::string ldir; parse(&quot;DIR&quot;,ldir );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 :   if( ldir==&quot;x&quot; ) { dir=0; perp_dirs[0]=1; perp_dirs[1]=2; dirv[0]=1; dirv2[0]=-1; }</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :   else if( ldir==&quot;y&quot; ) { dir=1; perp_dirs[0]=0; perp_dirs[1]=2; dirv[1]=1; dirv2[1]=-1; }</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          1 :   else if( ldir==&quot;z&quot; ) { dir=2; perp_dirs[0]=0; perp_dirs[1]=1; dirv[2]=1; dirv2[2]=-1; }</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   else error(ldir + &quot; is not a valid direction use x, y or z&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            :   // Read in details of phase field construction</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          3 :   parseVector(&quot;BANDWIDTH&quot;,bw); parse(&quot;KERNEL&quot;,kerneltype); parse(&quot;CONTOUR&quot;,contour);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :   log.printf(&quot;  searching for contour in %s direction at %f in phase field for multicolvar %s \n&quot;,ldir.c_str(), contour, mybasemulticolvars[0]-&gt;getLabel().c_str() );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          1 :   log.printf(&quot;  constructing phase field using %s kernels with bandwidth (%f, %f, %f) \n&quot;,kerneltype.c_str(), bw[0], bw[1], bw[2] );</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Now create a task list</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          2 :   for(unsigned i=0; i&lt;mybasemulticolvars[0]-&gt;getFullNumberOfTasks(); ++i) addTaskToList(i);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   // And a cutoff</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; pp( bw.size(),0 );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   KernelFunctions kernel( pp, bw, kerneltype, &quot;DIAGONAL&quot;, 1.0 );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   double rcut = kernel.getCutoff( bw[0] );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   for(unsigned j=1; j&lt;bw.size(); ++j) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :     if( kernel.getCutoff(bw[j])&gt;rcut ) rcut=kernel.getCutoff(bw[j]);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :   rcut2=rcut*rcut;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   // Create the values</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :   addComponent(&quot;thickness&quot;); componentIsNotPeriodic(&quot;thickness&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :   addComponent(&quot;dist1&quot;); componentIsNotPeriodic(&quot;dist1&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 :   addComponent(&quot;dist2&quot;); componentIsNotPeriodic(&quot;dist2&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          3 :   addComponentWithDerivatives(&quot;qdist&quot;); componentIsNotPeriodic(&quot;qdist&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   // Create sum vessels</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          1 :   std::string fake_input; std::string deriv_input=&quot;COMPONENT=2&quot;;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 :   if( mybasemulticolvars[0]-&gt;isDensity() ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :     addVessel( &quot;SUM&quot;, fake_input, -1 ); addVessel( &quot;SUM&quot;, deriv_input, -1 );</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   } else {</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :     addVessel( &quot;MEAN&quot;, fake_input, -1 ); addVessel( &quot;MEAN&quot;, deriv_input, -1 );</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   }</a>
+<a name="181"><span class="lineNum">     181 </span>            :   // And convert to a value vessel so we can get the final value</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          1 :   myvalue_vessel = dynamic_cast&lt;vesselbase::ValueVessel*&gt;( getPntrToVessel(0) );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          1 :   myderiv_vessel = dynamic_cast&lt;vesselbase::ValueVessel*&gt;( getPntrToVessel(1) );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :   plumed_assert( myvalue_vessel &amp;&amp; myderiv_vessel ); resizeFunctions();</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // Create the vector of values that holds the position</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;3; ++i) pval.emplace_back( Tools::make_unique&lt;Value&gt;() );</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          1 : }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       6230 : unsigned DistanceFromContour::getNumberOfQuantities() const {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       6230 :   return 3;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        137 : void DistanceFromContour::calculate() {</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   // Check box is orthorhombic</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        137 :   if( !getPbc().isOrthorombic() ) error(&quot;cell box must be orthorhombic&quot;);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :   // The nanoparticle is at the origin of our coordinate system</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        137 :   pos1[0]=pos1[1]=pos1[2]=0.0; pos2[0]=pos2[1]=pos2[2]=0.0;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :   // Set bracket as center of mass of membrane in active region</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        137 :   deactivateAllTasks();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        137 :   Vector myvec = getSeparation( getPosition(getNumberOfAtoms()-1), getPosition(0) ); pos2[dir]=myvec[dir];</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        137 :   taskFlags[0]=1; double mindist = myvec.modulo2();</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        137 :   for(unsigned j=1; j&lt;getNumberOfAtoms()-1; ++j) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :     Vector distance=getSeparation( getPosition(getNumberOfAtoms()-1), getPosition(j) );</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     double d2;</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :     if( (d2=distance[perp_dirs[0]]*distance[perp_dirs[0]])&lt;rcut2 &amp;&amp;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :         (d2+=distance[perp_dirs[1]]*distance[perp_dirs[1]])&lt;rcut2 ) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :       d2+=distance[dir]*distance[dir];</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       if( d2&lt;mindist &amp;&amp; std::fabs(distance[dir])&gt;epsilon ) { pos2[dir]=distance[dir]; mindist = d2; }</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       taskFlags[j]=1;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        137 :   lockContributors(); derivTime=false;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   // pos1 position of the nanoparticle, in the first time</a>
+<a name="217"><span class="lineNum">     217 </span>            :   // pos2 is the position of the closer atom in the membrane with respect the nanoparticle</a>
+<a name="218"><span class="lineNum">     218 </span>            :   // fa = distance between pos1 and the contour</a>
+<a name="219"><span class="lineNum">     219 </span>            :   // fb = distance between pos2 and the contour</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        137 :   std::vector&lt;double&gt; faked(3);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        137 :   double fa = getDifferenceFromContour( pos1, faked );</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        137 :   double fb = getDifferenceFromContour( pos2, faked );</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        137 :   if( fa*fb&gt;0 ) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :     unsigned maxtries = std::floor( ( getBox()(dir,dir) ) / bw[dir] );</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;maxtries; ++i) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :       double sign=(pos2[dir]&gt;0)? -1 : +1; // If the nanoparticle is inside the membrane push it out</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       pos1[dir] += sign*bw[dir]; fa = getDifferenceFromContour( pos1, faked );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :       if( fa*fb&lt;0 ) break;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :       // if fa*fb is less than zero the new pos 1 is outside the contour</a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span>            :   }</a>
+<a name="232"><span class="lineNum">     232 </span>            :   // Set direction for contour search</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        137 :   dirv[dir] = pos2[dir] - pos1[dir];</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   // Bracket for second root starts in center of membrane</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        137 :   double fc = getDifferenceFromContour( pos2, faked );</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        137 :   if( fc*fb&gt;0 ) {</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     // first time is true, because fc=fb</a>
+<a name="238"><span class="lineNum">     238 </span>            :     // push pos2 from its initial position inside the membrane towards the second contourn</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        137 :     unsigned maxtries = std::floor( ( getBox()(dir,dir) ) / bw[dir] );</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        230 :     for(unsigned i=0; i&lt;maxtries; ++i) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        230 :       double sign=(dirv[dir]&gt;0)? +1 : -1;</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        230 :       pos2[dir] += sign*bw[dir]; fc = getDifferenceFromContour( pos2, faked );</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        230 :       if( fc*fb&lt;0 ) break;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :     }</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        137 :     dirv2[dir] = ( pos1[dir] + dirv[dir] ) - pos2[dir];</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   // Now do a search for the two contours</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        137 :   mymin.lsearch( dirv, pos1, &amp;DistanceFromContour::getDifferenceFromContour );</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   // Save the first value</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        137 :   Vector root1; root1.zero(); root1[dir] = pval[dir]-&gt;get();</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        137 :   mymin.lsearch( dirv2, pos2, &amp;DistanceFromContour::getDifferenceFromContour );</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   // Calculate the separation between the two roots using PBC</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        137 :   Vector root2; root2.zero(); root2[dir]=pval[dir]-&gt;get();</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        137 :   Vector sep = getSeparation( root1, root2 ); double spacing = std::fabs( sep[dir] ); plumed_assert( spacing&gt;epsilon );</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        137 :   getPntrToComponent(&quot;thickness&quot;)-&gt;set( spacing );</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            :   // Make sure the sign is right</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        137 :   double predir=(root1[dir]*root2[dir]&lt;0)? -1 : 1;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   // This deals with periodic boundary conditions - if we are inside the membrane the sum of the absolute</a>
+<a name="261"><span class="lineNum">     261 </span>            :   // distances from the contours should add up to the spacing.  When this is not the case we must be outside</a>
+<a name="262"><span class="lineNum">     262 </span>            :   // the contour</a>
+<a name="263"><span class="lineNum">     263 </span>            :   // if( predir==-1 &amp;&amp; (std::fabs(root1[dir])+std::fabs(root2[dir]))&gt;(spacing+pbc_param) ) predir=1;</a>
+<a name="264"><span class="lineNum">     264 </span>            :   // Set the final value to root that is closest to the &quot;origin&quot; = position of atom</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        137 :   if( std::fabs(root1[dir])&lt;std::fabs(root2[dir]) ) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        137 :     getPntrToComponent(&quot;dist1&quot;)-&gt;set( predir*std::fabs(root1[dir]) );</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        274 :     getPntrToComponent(&quot;dist2&quot;)-&gt;set( std::fabs(root2[dir]) );</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   } else {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;dist1&quot;)-&gt;set( predir*std::fabs(root2[dir]) );</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;dist2&quot;)-&gt;set( std::fabs(root1[dir]) );</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        137 :   getPntrToComponent(&quot;qdist&quot;)-&gt;set( root2[dir]*root1[dir] );</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   // Now calculate the derivatives</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        137 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        137 :     Value* ival=myvalue_vessel-&gt;getFinalValue(); ival-&gt;clearDerivatives();</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        548 :     std::vector&lt;double&gt; root1v(3); for(unsigned i=0; i&lt;3; ++i) root1v[i]=root1[i];</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        137 :     derivTime=true; std::vector&lt;double&gt; der(3); getDifferenceFromContour( root1v, der ); double prefactor;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        137 :     if( mybasemulticolvars[0]-&gt;isDensity() ) prefactor = root2[dir] / myderiv_vessel-&gt;getOutputValue();</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :     else plumed_error();</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        137 :     Value* val=getPntrToComponent(&quot;qdist&quot;);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       2192 :     for(unsigned i=0; i&lt;val-&gt;getNumberOfDerivatives(); ++i) val-&gt;setDerivative( i, -prefactor*ival-&gt;getDerivative(i) );</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     ival-&gt;clearDerivatives();</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        548 :     std::vector&lt;double&gt; root2v(3); for(unsigned i=0; i&lt;3; ++i) root2v[i]=root2[i];</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        137 :     getDifferenceFromContour( root2v, der );</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">        137 :     if( mybasemulticolvars[0]-&gt;isDensity() ) prefactor = root1[dir] / myderiv_vessel-&gt;getOutputValue();</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     else plumed_error();</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       2192 :     for(unsigned i=0; i&lt;val-&gt;getNumberOfDerivatives(); ++i) val-&gt;addDerivative( i, -prefactor*ival-&gt;getDerivative(i) );</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        137 : }</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       3115 : double DistanceFromContour::getDifferenceFromContour( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der ) {</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   std::string min, max;</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      12460 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       9345 :     Tools::convert( -0.5*getBox()(j,j), min );</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       9345 :     Tools::convert( +0.5*getBox()(j,j), max );</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       9345 :     pval[j]-&gt;setDomain( min, max ); pval[j]-&gt;set( x[j] );</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :   }</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       3115 :   runAllTasks();</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       6230 :   return myvalue_vessel-&gt;getOutputValue() - contour;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       3115 : double DistanceFromContour::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       3115 :   Vector distance = getSeparation( getPosition(getNumberOfAtoms()-1), myatoms.getPosition(0) );</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">      12460 :   std::vector&lt;double&gt; pp(3), der(3,0); for(unsigned j=0; j&lt;3; ++j) pp[j] = distance[j];</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   // convert the pointer once</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       3115 :   auto pval_ptr=Tools::unique2raw(pval);</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            :   // Now create the kernel and evaluate</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       3115 :   KernelFunctions kernel( pp, bw, kerneltype, &quot;DIAGONAL&quot;, 1.0 );</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       3115 :   kernel.normalize( pval_ptr ); double newval = kernel.evaluate( pval_ptr, der, true );</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       3115 :   if( mybasemulticolvars[0]-&gt;isDensity() ) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       3115 :     if( !doNotCalculateDerivatives() &amp;&amp; derivTime ) {</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :       MultiValue&amp; myvals=myatoms.getUnderlyingMultiValue();</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        274 :       Vector vder; unsigned basen=myvals.getNumberOfDerivatives() - 12;</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       1096 :       for(unsigned i=0; i&lt;3; ++i) {</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        822 :         vder[i]=der[i]; myvals.addDerivative( 1, basen+i, vder[i] );</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :       }</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        274 :       myatoms.setValue( 2, der[dir] );</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        274 :       addAtomDerivatives( 1, 0, -vder, myatoms );</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        274 :       myatoms.addBoxDerivatives( 1, Tensor(vder,distance) );</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :     }</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       3115 :     myatoms.setValue( 0, 1.0 ); return newval;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            :   // This does the stuff for averaging</a>
+<a name="329"><span class="lineNum">     329 </span>            :   myatoms.setValue( 0, newval );</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            :   // This gets the average if we are using a phase field</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; cvals( mybasemulticolvars[0]-&gt;getNumberOfQuantities() );</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :   mybasedata[0]-&gt;retrieveValueWithIndex( tindex, false, cvals );</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :   return newval*cvals[0]*cvals[1];</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        137 : void DistanceFromContour::apply() {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        274 :   if( getPntrToComponent(&quot;qdist&quot;)-&gt;applyForce( forces ) ) setForcesOnAtoms( forces );</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">        137 : }</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            : }</a>
+<a name="342"><span class="lineNum">     342 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Distances.cpp.func-sort-c.html b/coverage/multicolvar/Distances.cpp.func-sort-c.html
new file mode 100644
index 0000000000..076b8c56ab
--- /dev/null
+++ b/coverage/multicolvar/Distances.cpp.func-sort-c.html
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+  <title>LCOV - plumed test coverage - multicolvar/Distances.cpp - functions</title>
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+<body>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Distances.cpp<span style="font-size: 80%;"> (<a href="Distances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Distances.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#153">_ZN4PLMD11multicolvar9DistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_122DistancesRegisterMe1356createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">51</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#153">_ZN4PLMD11multicolvar9DistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">51</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#135">_ZN4PLMD11multicolvar9Distances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">53</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#130">_ZN4PLMD11multicolvar9Distances10isPeriodicEv</a></td>
+              <td class="coverFnHi">111</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_122DistancesRegisterMe135C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_122DistancesRegisterMe135D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#194">_ZNK4PLMD11multicolvar9Distances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15275</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Distances.cpp.func.html b/coverage/multicolvar/Distances.cpp.func.html
new file mode 100644
index 0000000000..70c6495141
--- /dev/null
+++ b/coverage/multicolvar/Distances.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Distances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Distances.cpp<span style="font-size: 80%;"> (<a href="Distances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Distances.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_122DistancesRegisterMe1356createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">51</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_122DistancesRegisterMe135C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_122DistancesRegisterMe135D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#130">_ZN4PLMD11multicolvar9Distances10isPeriodicEv</a></td>
+              <td class="coverFnHi">111</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#135">_ZN4PLMD11multicolvar9Distances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">53</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#153">_ZN4PLMD11multicolvar9DistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">51</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#153">_ZN4PLMD11multicolvar9DistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Distances.cpp.gcov.html#194">_ZNK4PLMD11multicolvar9Distances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15275</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Distances.cpp.gcov.html b/coverage/multicolvar/Distances.cpp.gcov.html
new file mode 100644
index 0000000000..b4acb84319
--- /dev/null
+++ b/coverage/multicolvar/Distances.cpp.gcov.html
@@ -0,0 +1,287 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Distances.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Distances.cpp<span style="font-size: 80%;"> (source / <a href="Distances.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/LessThan.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;vesselbase/Between.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace multicolvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MCOLVAR DISTANCES</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculate the distances between one or many pairs of atoms.  You can then calculate functions of the distribution of</a>
+<a name="37"><span class="lineNum">      37 </span>            :  distances such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2 and to</a>
+<a name="42"><span class="lineNum">      42 </span>            : print the minimum for these two distances.</a>
+<a name="43"><span class="lineNum">      43 </span>            : \plumedfile</a>
+<a name="44"><span class="lineNum">      44 </span>            : d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="45"><span class="lineNum">      45 </span>            : PRINT ARG=d1.min</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : (See also \ref PRINT).</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The following input tells plumed to calculate the distances between atoms 3 and 5 and between atoms 1 and 2</a>
+<a name="50"><span class="lineNum">      50 </span>            : and then to calculate the number of these distances that are less than 0.1 nm.  The number of distances</a>
+<a name="51"><span class="lineNum">      51 </span>            : less than 0.1nm is then printed to a file.</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : d1: DISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=d1.lessthan</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : (See also \ref PRINT \ref switchingfunction).</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The following input tells plumed to calculate all the distances between atoms 1, 2 and 3 (i.e. the distances between atoms</a>
+<a name="59"><span class="lineNum">      59 </span>            : 1 and 2, atoms 1 and 3 and atoms 2 and 3).  The average of these distances is then calculated.</a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : d1: DISTANCES GROUP=1-3 MEAN</a>
+<a name="62"><span class="lineNum">      62 </span>            : PRINT ARG=d1.mean</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endplumedfile</a>
+<a name="64"><span class="lineNum">      64 </span>            : (See also \ref PRINT)</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : The following input tells plumed to calculate all the distances between the atoms in GROUPA and the atoms in GROUPB.</a>
+<a name="67"><span class="lineNum">      67 </span>            : In other words the distances between atoms 1 and 2 and the distance between atoms 1 and 3.  The number of distances</a>
+<a name="68"><span class="lineNum">      68 </span>            : more than 0.1 is then printed to a file.</a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : d1: DISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}</a>
+<a name="71"><span class="lineNum">      71 </span>            : PRINT ARG=d1.morethan</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : (See also \ref PRINT \ref switchingfunction)</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \par Calculating minimum distances</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : To calculate and print the minimum distance between two groups of atoms you use the following commands</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : d1: DISTANCES GROUPA=1-10 GROUPB=11-20 MIN={BETA=500.}</a>
+<a name="82"><span class="lineNum">      82 </span>            : PRINT ARG=d1.min FILE=colvar STRIDE=10</a>
+<a name="83"><span class="lineNum">      83 </span>            : \endplumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : (see \ref DISTANCES and \ref PRINT)</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : In order to ensure that the minimum value has continuous derivatives we use the following function:</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \f[</a>
+<a name="89"><span class="lineNum">      89 </span>            : s = \frac{\beta}{ \log \sum_i \exp\left( \frac{\beta}{s_i} \right) }</a>
+<a name="90"><span class="lineNum">      90 </span>            : \f]</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : where \f$\beta\f$ is a user specified parameter.</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : This input is used rather than a separate MINDIST colvar so that the same routine and the same input style can be</a>
+<a name="95"><span class="lineNum">      95 </span>            : used to calculate minimum coordination numbers (see \ref COORDINATIONNUMBER), minimum</a>
+<a name="96"><span class="lineNum">      96 </span>            : angles (see \ref ANGLES) and many other variables.</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : This new way of calculating mindist is part of plumed 2's multicolvar functionality.  These special actions</a>
+<a name="99"><span class="lineNum">      99 </span>            : allow you to calculate multiple functions of a distribution of simple collective variables.  As an example you</a>
+<a name="100"><span class="lineNum">     100 </span>            : can calculate the number of distances less than 1.0, the minimum distance, the number of distances more than</a>
+<a name="101"><span class="lineNum">     101 </span>            : 2.0 and the number of distances between 1.0 and 2.0 by using the following command:</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : \plumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : d1: DISTANCES ...</a>
+<a name="105"><span class="lineNum">     105 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="106"><span class="lineNum">     106 </span>            :  LESS_THAN={RATIONAL R_0=1.0}</a>
+<a name="107"><span class="lineNum">     107 </span>            :  MORE_THAN={RATIONAL R_0=2.0}</a>
+<a name="108"><span class="lineNum">     108 </span>            :  BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}</a>
+<a name="109"><span class="lineNum">     109 </span>            :  MIN={BETA=500.}</a>
+<a name="110"><span class="lineNum">     110 </span>            : ...</a>
+<a name="111"><span class="lineNum">     111 </span>            : PRINT ARG=d1.lessthan,d1.morethan,d1.between,d1.min FILE=colvar STRIDE=10</a>
+<a name="112"><span class="lineNum">     112 </span>            : \endplumedfile</a>
+<a name="113"><span class="lineNum">     113 </span>            : (see \ref DISTANCES and \ref PRINT)</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : A calculation performed this way is fast because the expensive part of the calculation - the calculation of all the distances - is only</a>
+<a name="116"><span class="lineNum">     116 </span>            : done once per step.  Furthermore, it can be made faster by using the TOL keyword to discard those distance that make only a small contributions</a>
+<a name="117"><span class="lineNum">     117 </span>            : to the final values together with the NL_STRIDE keyword, which ensures that the distances that make only a small contribution to the final values aren't</a>
+<a name="118"><span class="lineNum">     118 </span>            : calculated at every step.</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : */</a>
+<a name="121"><span class="lineNum">     121 </span>            : //+ENDPLUMEDOC</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : class Distances : public MultiColvarBase {</a>
+<a name="125"><span class="lineNum">     125 </span>            : private:</a>
+<a name="126"><span class="lineNum">     126 </span>            : public:</a>
+<a name="127"><span class="lineNum">     127 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="128"><span class="lineNum">     128 </span>            :   explicit Distances(const ActionOptions&amp;);</a>
+<a name="129"><span class="lineNum">     129 </span>            : // active methods:</a>
+<a name="130"><span class="lineNum">     130 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="131"><span class="lineNum">     131 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        111 :   bool isPeriodic() override { return false; }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : };</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      12606 : PLUMED_REGISTER_ACTION(Distances,&quot;DISTANCES&quot;)</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         53 : void Distances::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         53 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        159 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        212 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LESS_THAN&quot;); // keys.use(&quot;DHENERGY&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        212 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        106 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the distances you wish to calculate. &quot;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one distance will be &quot;</a>
+<a name="144"><span class="lineNum">     144 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="145"><span class="lineNum">     145 </span>            :            &quot;specify the indices of two atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="146"><span class="lineNum">     146 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        106 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        106 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate the distance between each distinct pair of atoms in the group&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        106 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all &quot;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :            &quot;the atoms in GROUPB. This must be used in conjunction with GROUPB.&quot;);</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        106 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all the atoms &quot;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :            &quot;in GROUPB. This must be used in conjunction with GROUPA.&quot;);</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         53 : }</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         51 : Distances::Distances(const ActionOptions&amp;ao):</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   Action(ao),</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         51 :   MultiColvarBase(ao)</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : {</a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Read in the atoms</a>
+<a name="160"><span class="lineNum">     160 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        102 :   readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         86 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 2, all_atoms );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         51 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   // And check everything has been read in correctly</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         51 :   checkRead();</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   // Now check if we can use link cells</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         51 :   if( getNumberOfVessels()&gt;0 ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     bool use_link=false; double rcut;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         49 :     vesselbase::LessThan* lt=dynamic_cast&lt;vesselbase::LessThan*&gt;( getPntrToVessel(0) );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         49 :     if( lt ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         16 :       use_link=true; rcut=lt-&gt;getCutoff();</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     } else {</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         33 :       vesselbase::Between* bt=dynamic_cast&lt;vesselbase::Between*&gt;( getPntrToVessel(0) );</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         33 :       if( bt ) { use_link=true; rcut=bt-&gt;getCutoff(); }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :     }</a>
+<a name="177"><span class="lineNum">     177 </span>            :     if( use_link ) {</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         76 :       for(unsigned i=1; i&lt;getNumberOfVessels(); ++i) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         30 :         vesselbase::LessThan* lt2=dynamic_cast&lt;vesselbase::LessThan*&gt;( getPntrToVessel(i) );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         30 :         vesselbase::Between* bt=dynamic_cast&lt;vesselbase::Between*&gt;( getPntrToVessel(i) );</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         30 :         if( lt2 ) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :           double tcut=lt2-&gt;getCutoff();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :           if( tcut&gt;rcut ) rcut=tcut;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         30 :         } else if( bt ) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         30 :           double tcut=bt-&gt;getCutoff();</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         30 :           if( tcut&gt;rcut ) rcut=tcut;</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :         } else {</a>
+<a name="188"><span class="lineNum">     188 </span>            :           use_link=false;</a>
+<a name="189"><span class="lineNum">     189 </span>            :         }</a>
+<a name="190"><span class="lineNum">     190 </span>            :       }</a>
+<a name="191"><span class="lineNum">     191 </span>            :     }</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         49 :     if( use_link ) setLinkCellCutoff( rcut );</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         51 : }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      15275 : double Distances::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      15275 :   Vector distance;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      15275 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      15275 :   const double value=distance.modulo();</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      15275 :   const double invvalue=1.0/value;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   // And finish the calculation</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      15275 :   addAtomDerivatives( 1, 0,-invvalue*distance, myatoms );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      15275 :   addAtomDerivatives( 1, 1, invvalue*distance, myatoms );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      15275 :   myatoms.addBoxDerivatives( 1, -invvalue*Tensor(distance,distance) );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      15275 :   return value;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DumpMultiColvar.cpp.func-sort-c.html b/coverage/multicolvar/DumpMultiColvar.cpp.func-sort-c.html
new file mode 100644
index 0000000000..18dd8113af
--- /dev/null
+++ b/coverage/multicolvar/DumpMultiColvar.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DumpMultiColvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DumpMultiColvar.cpp<span style="font-size: 80%;"> (<a href="DumpMultiColvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">93.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DumpMultiColvar.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#76">_ZN4PLMD11multicolvar15DumpMultiColvar29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#95">_ZN4PLMD11multicolvar15DumpMultiColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#176">_ZN4PLMD11multicolvar15DumpMultiColvarD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_127DumpMultiColvarRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#95">_ZN4PLMD11multicolvar15DumpMultiColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#176">_ZN4PLMD11multicolvar15DumpMultiColvarD0Ev</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#176">_ZN4PLMD11multicolvar15DumpMultiColvarD1Ev</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#83">_ZN4PLMD11multicolvar15DumpMultiColvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#77">_ZN4PLMD11multicolvar15DumpMultiColvar5applyEv</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#144">_ZN4PLMD11multicolvar15DumpMultiColvar6updateEv</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#75">_ZN4PLMD11multicolvar15DumpMultiColvar9calculateEv</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_127DumpMultiColvarRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_127DumpMultiColvarRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DumpMultiColvar.cpp.func.html b/coverage/multicolvar/DumpMultiColvar.cpp.func.html
new file mode 100644
index 0000000000..e8eff39ca1
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+++ b/coverage/multicolvar/DumpMultiColvar.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DumpMultiColvar.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DumpMultiColvar.cpp<span style="font-size: 80%;"> (<a href="DumpMultiColvar.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">93.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DumpMultiColvar.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_127DumpMultiColvarRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_127DumpMultiColvarRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_127DumpMultiColvarRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#83">_ZN4PLMD11multicolvar15DumpMultiColvar16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#76">_ZN4PLMD11multicolvar15DumpMultiColvar29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#77">_ZN4PLMD11multicolvar15DumpMultiColvar5applyEv</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#144">_ZN4PLMD11multicolvar15DumpMultiColvar6updateEv</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#75">_ZN4PLMD11multicolvar15DumpMultiColvar9calculateEv</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#95">_ZN4PLMD11multicolvar15DumpMultiColvarC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#95">_ZN4PLMD11multicolvar15DumpMultiColvarC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#176">_ZN4PLMD11multicolvar15DumpMultiColvarD0Ev</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#176">_ZN4PLMD11multicolvar15DumpMultiColvarD1Ev</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DumpMultiColvar.cpp.gcov.html#176">_ZN4PLMD11multicolvar15DumpMultiColvarD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/DumpMultiColvar.cpp.gcov.html b/coverage/multicolvar/DumpMultiColvar.cpp.gcov.html
new file mode 100644
index 0000000000..fbbac437b3
--- /dev/null
+++ b/coverage/multicolvar/DumpMultiColvar.cpp.gcov.html
@@ -0,0 +1,259 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/DumpMultiColvar.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - DumpMultiColvar.cpp<span style="font-size: 80%;"> (source / <a href="DumpMultiColvar.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntry">72</td>
+            <td class="headerCovTableEntryHi">93.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstdio&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;vesselbase/ActionWithInputVessel.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;vesselbase/StoreDataVessel.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD</a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace multicolvar {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC PRINTANALYSIS DUMPMULTICOLVAR</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Dump atom positions and multicolvar on a file.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : In this examples we calculate the distances between the  atoms of the first and the second</a>
+<a name="48"><span class="lineNum">      48 </span>            : group and we write them in the file MULTICOLVAR.xyz. For each couple it writes the</a>
+<a name="49"><span class="lineNum">      49 </span>            : coordinates of their geometric center and their distance.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : pos:   GROUP ATOMS=220,221,235,236,247,248,438,439,450,451,534,535</a>
+<a name="53"><span class="lineNum">      53 </span>            : neg:   GROUP ATOMS=65,68,138,182,185,267,270,291,313,316,489,583,621,711</a>
+<a name="54"><span class="lineNum">      54 </span>            : DISTANCES GROUPA=pos GROUPB=neg LABEL=slt</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : DUMPMULTICOLVAR DATA=slt FILE=MULTICOLVAR.xyz</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : (see also \ref DISTANCES)</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : */</a>
+<a name="62"><span class="lineNum">      62 </span>            : //+ENDPLUMEDOC</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : class DumpMultiColvar:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   public ActionPilot,</a>
+<a name="66"><span class="lineNum">      66 </span>            :   public ActionAtomistic,</a>
+<a name="67"><span class="lineNum">      67 </span>            :   public vesselbase::ActionWithInputVessel</a>
+<a name="68"><span class="lineNum">      68 </span>            : {</a>
+<a name="69"><span class="lineNum">      69 </span>            :   OFile of;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double lenunit;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   MultiColvarBase* mycolv;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::string fmt_xyz;</a>
+<a name="73"><span class="lineNum">      73 </span>            : public:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit DumpMultiColvar(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ~DumpMultiColvar();</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         74 :   void calculate() override {}</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   void calculateNumericalDerivatives( ActionWithValue* vv ) override { plumed_error(); }</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         74 :   void apply() override {}</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   void update() override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12548 : PLUMED_REGISTER_ACTION(DumpMultiColvar,&quot;DUMPMULTICOLVAR&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         24 : void DumpMultiColvar::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         24 :   Action::registerKeywords( keys );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         24 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         24 :   ActionPilot::registerKeywords( keys );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         24 :   ActionWithInputVessel::registerKeywords( keys );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the atoms should be output&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;, &quot;FILE&quot;, &quot;file on which to output coordinates&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;, &quot;UNITS&quot;,&quot;PLUMED&quot;,&quot;the units in which to print out the coordinates. PLUMED means internal PLUMED units&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         48 :   keys.add(&quot;optional&quot;,&quot;PRECISION&quot;,&quot;The number of digits in trajectory file&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         48 :   keys.add(&quot;atoms&quot;,&quot;ORIGIN&quot;,&quot;You can use this keyword to specify the position of an atom as an origin. The positions output will then be displayed relative to that origin&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         24 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         22 : DumpMultiColvar::DumpMultiColvar(const ActionOptions&amp;ao):</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   Action(ao),</a>
+<a name="99"><span class="lineNum">      99 </span>            :   ActionPilot(ao),</a>
+<a name="100"><span class="lineNum">     100 </span>            :   ActionAtomistic(ao),</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         22 :   ActionWithInputVessel(ao)</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : {</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         44 :   readArgument(&quot;store&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         22 :   mycolv = dynamic_cast&lt;MultiColvarBase*&gt;( getDependencies()[0] );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         22 :   plumed_assert( getDependencies().size()==1 );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         22 :   if(!mycolv) error(&quot;action labeled &quot; + getDependencies()[0]-&gt;getLabel() + &quot; is not a multicolvar&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         22 :   log.printf(&quot;  printing colvars calculated by action %s \n&quot;,mycolv-&gt;getLabel().c_str() );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         44 :   parseAtomList(&quot;ORIGIN&quot;,atom);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         22 :   if( atom.size()&gt;1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         22 :   if( atom.size()==1 ) log.printf(&quot;  origin is at position of atom : %d\n&quot;,atom[0].serial() );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         44 :   std::string file; parse(&quot;FILE&quot;,file);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         22 :   if(file.length()==0) error(&quot;name out output file was not specified&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         22 :   std::string type=Tools::extension(file);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         22 :   log&lt;&lt;&quot;  file name &quot;&lt;&lt;file&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         22 :   if(type!=&quot;xyz&quot;) error(&quot;can only print xyz file type with DUMPMULTICOLVAR&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   fmt_xyz=&quot;%f&quot;;</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         44 :   std::string precision; parse(&quot;PRECISION&quot;,precision);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         22 :   if(precision.length()&gt;0) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         11 :     int p; Tools::convert(precision,p);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         11 :     log&lt;&lt;&quot;  with precision &quot;&lt;&lt;p&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     std::string a,b;</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         11 :     Tools::convert(p+5,a);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         11 :     Tools::convert(p,b);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         22 :     fmt_xyz=&quot;%&quot;+a+&quot;.&quot;+b+&quot;f&quot;;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         44 :   std::string unitname; parse(&quot;UNITS&quot;,unitname);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         22 :   if(unitname!=&quot;PLUMED&quot;) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :     Units myunit; myunit.setLength(unitname);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          1 :     lenunit=plumed.getAtoms().getUnits().getLength()/myunit.getLength();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          1 :   }</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         21 :   else lenunit=1.0;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         22 :   checkRead();</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         22 :   of.link(*this);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         22 :   of.open(file);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         22 :   log.printf(&quot;  printing atom positions in %s units \n&quot;, unitname.c_str() );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         22 :   requestAtoms(atom); addDependency( mycolv );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         22 : }</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         74 : void DumpMultiColvar::update() {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         74 :   of.printf(&quot;%u\n&quot;,mycolv-&gt;getCurrentNumberOfActiveTasks());</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         74 :   const Tensor &amp; t(mycolv-&gt;getPbc().getBox());</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         74 :   if(mycolv-&gt;getPbc().isOrthorombic()) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        148 :     of.printf((&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot;\n&quot;).c_str(),lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   } else {</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     of.printf((&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot;\n&quot;).c_str(),</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :               lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :               lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :               lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :              );</a>
+<a name="157"><span class="lineNum">     157 </span>            :   }</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         74 :   vesselbase::StoreDataVessel* stash=dynamic_cast&lt;vesselbase::StoreDataVessel*&gt;( getPntrToArgument() );</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   plumed_dbg_assert( stash );</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         74 :   std::vector&lt;double&gt; cvals( mycolv-&gt;getNumberOfQuantities() );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">      13974 :   for(unsigned i=0; i&lt;mycolv-&gt;getCurrentNumberOfActiveTasks(); ++i) {</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     const char* defname=&quot;X&quot;;</a>
+<a name="163"><span class="lineNum">     163 </span>            :     const char* name=defname;</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      13900 :     Vector apos = mycolv-&gt;getCentralAtomPos( mycolv-&gt;getPositionInFullTaskList(i) );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      13900 :     if( getNumberOfAtoms()&gt;0 ) apos=pbcDistance( getPosition(0), apos );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      27800 :     of.printf((&quot;%s &quot;+fmt_xyz+&quot; &quot;+fmt_xyz+&quot; &quot;+fmt_xyz).c_str(),name,lenunit*apos[0],lenunit*apos[1],lenunit*apos[2]);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      13900 :     stash-&gt;retrieveSequentialValue( i, true, cvals );</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      13900 :     if( mycolv-&gt;weightWithDerivatives() ) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       2370 :       for(unsigned j=0; j&lt;cvals.size(); ++j) of.printf((&quot; &quot;+fmt_xyz).c_str(),cvals[j]);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     } else {</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      27884 :       for(unsigned j=1; j&lt;cvals.size(); ++j) of.printf((&quot; &quot;+fmt_xyz).c_str(),cvals[j]);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      13900 :     of.printf(&quot;\n&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         74 : }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         44 : DumpMultiColvar::~DumpMultiColvar() {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         44 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : }</a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterBetween.cpp.func-sort-c.html b/coverage/multicolvar/FilterBetween.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9726156405
--- /dev/null
+++ b/coverage/multicolvar/FilterBetween.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterBetween.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterBetween.cpp<span style="font-size: 80%;"> (<a href="FilterBetween.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryMed">82.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FilterBetween.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#145">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe1476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#157">_ZN4PLMD11multicolvar13FilterBetweenC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#144">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe1466createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#157">_ZN4PLMD11multicolvar13FilterBetweenC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#147">_ZN4PLMD11multicolvar13FilterBetween16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#186">_ZNK4PLMD11multicolvar13FilterBetween11applyFilterERKdRd</a></td>
+              <td class="coverFnHi">735</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#144">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe146C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#144">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe146D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#145">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe147C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#145">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe147D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterBetween.cpp.func.html b/coverage/multicolvar/FilterBetween.cpp.func.html
new file mode 100644
index 0000000000..f069a5fcb6
--- /dev/null
+++ b/coverage/multicolvar/FilterBetween.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterBetween.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterBetween.cpp<span style="font-size: 80%;"> (<a href="FilterBetween.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryMed">82.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FilterBetween.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#144">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe1466createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#144">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe146C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#144">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe146D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#145">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe1476createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#145">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe147C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#145">_ZN4PLMD11multicolvar12_GLOBAL__N_126FilterBetweenRegisterMe147D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#147">_ZN4PLMD11multicolvar13FilterBetween16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#157">_ZN4PLMD11multicolvar13FilterBetweenC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#157">_ZN4PLMD11multicolvar13FilterBetweenC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterBetween.cpp.gcov.html#186">_ZNK4PLMD11multicolvar13FilterBetween11applyFilterERKdRd</a></td>
+              <td class="coverFnHi">735</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterBetween.cpp.gcov.html b/coverage/multicolvar/FilterBetween.cpp.gcov.html
new file mode 100644
index 0000000000..4a065905e3
--- /dev/null
+++ b/coverage/multicolvar/FilterBetween.cpp.gcov.html
@@ -0,0 +1,270 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterBetween.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterBetween.cpp<span style="font-size: 80%;"> (source / <a href="FilterBetween.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntryMed">82.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;MultiColvarFilter.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MTRANSFORMS MTRANSFORM_BETWEEN</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : This action can be used to transform the colvar values calculated by a MultiColvar using a histogram bead</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : In this action each colvar, \f$s_i\f$, calculated by MultiColvar is transformed by a \ref histogrambead function that</a>
+<a name="31"><span class="lineNum">      31 </span>            : is equal to one if the colvar is within a certain range and which is equal to zero otherwise.  In other words, we</a>
+<a name="32"><span class="lineNum">      32 </span>            : compute:</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : \f[</a>
+<a name="35"><span class="lineNum">      35 </span>            : f_i = \int_a^b K\left( \frac{s-s_i}{w} \right)</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f]</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : where \f$a, b\f$ and \f$w\f$ are parameters.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : It is important to understand the distinction between what is done here and what is done by \ref MFILTER_BETWEEN.</a>
+<a name="41"><span class="lineNum">      41 </span>            : In \ref MFILTER_BETWEEN a weight, \f$w_i\f$ for the colvar is calculated using the \ref histogrambead.  If one calculates the</a>
+<a name="42"><span class="lineNum">      42 </span>            : MEAN for \ref MFILTER_BETWEEN one is thus calculating:</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \f[</a>
+<a name="45"><span class="lineNum">      45 </span>            : \mu = \frac{ \sum_i f_i s_i }{ \sum_i f_i}</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : In this action by contrast the colvar is being transformed by the \ref histogrambead.  If one thus calculates a MEAN for</a>
+<a name="49"><span class="lineNum">      49 </span>            : this action one computes:</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \f[</a>
+<a name="52"><span class="lineNum">      52 </span>            : \mu = \frac{ \sum_{i=1}^N f_i }{ N }</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f]</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : In other words, you are calculating the mean for the transformed colvar.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \par Examples</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The following input gives an example of how a \ref MTRANSFORM_BETWEEN action can be used to duplicate</a>
+<a name="60"><span class="lineNum">      60 </span>            : functionality that is elsewhere in PLUMED.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : DISTANCES ...</a>
+<a name="64"><span class="lineNum">      64 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="65"><span class="lineNum">      65 </span>            :  LABEL=d1</a>
+<a name="66"><span class="lineNum">      66 </span>            : ... DISTANCES</a>
+<a name="67"><span class="lineNum">      67 </span>            : MTRANSFORM_BETWEEN DATA=d1 LOWER=1.0 UPPER=2.0 SMEAR=0.5</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : In this case you can achieve the same result by using:</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : DISTANCES ...</a>
+<a name="74"><span class="lineNum">      74 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="75"><span class="lineNum">      75 </span>            :  BETWEEN={GAUSSIAN LOWER=1.0 UPPER=2.0}</a>
+<a name="76"><span class="lineNum">      76 </span>            : ... DISTANCES</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endplumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : (see \ref DISTANCES)</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : The advantage of \ref MTRANSFORM_BETWEEN comes, however, if you want to use transformed colvars as input</a>
+<a name="81"><span class="lineNum">      81 </span>            : for \ref MULTICOLVARDENS</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : */</a>
+<a name="84"><span class="lineNum">      84 </span>            : //+ENDPLUMEDOC</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : //+PLUMEDOC MFILTERS MFILTER_BETWEEN</a>
+<a name="87"><span class="lineNum">      87 </span>            : /*</a>
+<a name="88"><span class="lineNum">      88 </span>            : This action can be used to filter the colvar values calculated by a multicolvar so that one can compute the mean and so on for only those multicolvars within a certain range.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : This action can be used to create a dynamic group of atom based on the value of a multicolvar.</a>
+<a name="91"><span class="lineNum">      91 </span>            : In this action a multicolvar is within the dynamic group if its value lies in a particular range.</a>
+<a name="92"><span class="lineNum">      92 </span>            : In actuality a weight, \f$w_i\f$  is ascribed to each colvar, \f$s_i\f$ calculated by a multicolvar</a>
+<a name="93"><span class="lineNum">      93 </span>            : and this weight measures the degree to which a colvar is a member of the group.  This weight is</a>
+<a name="94"><span class="lineNum">      94 </span>            : calculated using a \ref histogrambead so it is given by:</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \f[</a>
+<a name="97"><span class="lineNum">      97 </span>            : w_i = \int_a^b K\left( \frac{s - s_i}{w} \right)</a>
+<a name="98"><span class="lineNum">      98 </span>            : \f]</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : where \f$a, b\f$ and \f$w\f$ are parameters.  If one calculates a function of the set of multicolvars</a>
+<a name="101"><span class="lineNum">     101 </span>            : these weights are included in the calculation.  As such if one calculates the MEAN, \f$\mu\f$ of a filtered</a>
+<a name="102"><span class="lineNum">     102 </span>            : multicolvar what is computed is the following:</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : \f[</a>
+<a name="105"><span class="lineNum">     105 </span>            : \mu = \frac{ \sum_i w_i s_i }{ \sum_i w_i}</a>
+<a name="106"><span class="lineNum">     106 </span>            : \f]</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : One is thus calculating the mean for those colvars that are within the range of interest.</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : \par Examples</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : The example shown below calculates the mean for those distances that are between 0 and 3 nm in length</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : \plumedfile</a>
+<a name="115"><span class="lineNum">     115 </span>            : DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1</a>
+<a name="116"><span class="lineNum">     116 </span>            : MFILTER_BETWEEN DATA=d1 LOWER=0 UPPER=3.0 SMEAR=0.0001 MEAN LABEL=d4</a>
+<a name="117"><span class="lineNum">     117 </span>            : \endplumedfile</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : More complicated things can be done by using the label of a filter as input to a new multicolvar as shown</a>
+<a name="120"><span class="lineNum">     120 </span>            : in the example below.  Here the coordination numbers of all atoms are computed.  The atoms with a coordination</a>
+<a name="121"><span class="lineNum">     121 </span>            : number between 4 and 6 are then identified using the filter.  This reduced list of atoms is then used as input</a>
+<a name="122"><span class="lineNum">     122 </span>            : to a second coordination number calculation.  This second coordination number thus measures the number of atoms</a>
+<a name="123"><span class="lineNum">     123 </span>            : 4-6 coordinated atoms each of the 4-6 coordination atoms is bound to.</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : \plumedfile</a>
+<a name="126"><span class="lineNum">     126 </span>            : c1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="127"><span class="lineNum">     127 </span>            : cf: MFILTER_BETWEEN DATA=c1 LOWER=4 UPPER=6 SMEAR=0.5 LOWMEM</a>
+<a name="128"><span class="lineNum">     128 </span>            : c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}</a>
+<a name="129"><span class="lineNum">     129 </span>            : \endplumedfile</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : */</a>
+<a name="132"><span class="lineNum">     132 </span>            : //+ENDPLUMEDOC</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : namespace PLMD {</a>
+<a name="135"><span class="lineNum">     135 </span>            : namespace multicolvar {</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : class FilterBetween : public MultiColvarFilter {</a>
+<a name="138"><span class="lineNum">     138 </span>            : private:</a>
+<a name="139"><span class="lineNum">     139 </span>            :   HistogramBead hb;</a>
+<a name="140"><span class="lineNum">     140 </span>            : public:</a>
+<a name="141"><span class="lineNum">     141 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="142"><span class="lineNum">     142 </span>            :   explicit FilterBetween(const ActionOptions&amp; ao);</a>
+<a name="143"><span class="lineNum">     143 </span>            :   double applyFilter( const double&amp; val, double&amp; df ) const override;</a>
+<a name="144"><span class="lineNum">     144 </span>            : };</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(FilterBetween,&quot;MFILTER_BETWEEN&quot;)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(FilterBetween,&quot;MTRANSFORM_BETWEEN&quot;)</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          7 : void FilterBetween::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          7 :   MultiColvarFilter::registerKeywords( keys );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;LOWER&quot;,&quot;the lower boundary for the range of interest&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;UPPER&quot;,&quot;the upper boundary for the range of interest&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;SMEAR&quot;,&quot;0.5&quot;,&quot;the amount by which to smear the value for kernel density estimation&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         14 :   keys.add(&quot;optional&quot;,&quot;BEAD&quot;,&quot;This keywords is used if you want to employ an alternative to the function defined above. &quot;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :            &quot;The following provides information on the \\ref histogrambead that are available. &quot;</a>
+<a name="156"><span class="lineNum">     156 </span>            :            &quot;When this keyword is present you no longer need the LOWER, UPPER and SMEAR keywords.&quot;);</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          7 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          3 : FilterBetween::FilterBetween(const ActionOptions&amp; ao):</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   Action(ao),</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          3 :   MultiColvarFilter(ao)</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : {</a>
+<a name="163"><span class="lineNum">     163 </span>            :   // Read in the switching function</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          6 :   std::string sw, errors; parse(&quot;BEAD&quot;,sw);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          3 :   if( getPntrToMultiColvar()-&gt;isPeriodic() ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     std::string min, max; getPntrToMultiColvar()-&gt;retrieveDomain( min, max );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     double mlow, mhigh; Tools::convert( min,mlow ); Tools::convert( max, mhigh);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     hb.isPeriodic( mlow, mhigh );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   } else {</a>
+<a name="170"><span class="lineNum">     170 </span>            :     hb.isNotPeriodic();</a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          3 :   if(sw.length()&gt;0) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :     hb.set(sw,errors);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     if( errors.length()!=0 ) error(&quot;problem reading BEAD keyword : &quot; + errors );</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   } else {</a>
+<a name="177"><span class="lineNum">     177 </span>            :     double l, u, s; std::string ll, uu, ss;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          9 :     parse(&quot;LOWER&quot;,l); parse(&quot;UPPER&quot;,u); parse(&quot;SMEAR&quot;,s);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :     Tools::convert(l,ll); Tools::convert(u,uu); Tools::convert(s,ss);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          6 :     sw=&quot;GAUSSIAN LOWER=&quot; + ll + &quot; UPPER=&quot; + uu + &quot; SMEAR=&quot; + ss;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          3 :     hb.set(sw,errors); plumed_massert(errors.length()==0,&quot;problems with bead&quot; + errors);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :   log.printf(&quot;  filtering colvar values and focussing only on those values in range %s\n&quot;,( hb.description() ).c_str() );</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          3 : }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        735 : double FilterBetween::applyFilter( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        735 :   double f = hb.calculate( val, df );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        735 :   return f;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterLessThan.cpp.func-sort-c.html b/coverage/multicolvar/FilterLessThan.cpp.func-sort-c.html
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--- /dev/null
+++ b/coverage/multicolvar/FilterLessThan.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterLessThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterLessThan.cpp<span style="font-size: 80%;"> (<a href="FilterLessThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FilterLessThan.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#133">_ZN4PLMD11multicolvar10FilterLessC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#120">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe1226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#133">_ZN4PLMD11multicolvar10FilterLessC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#119">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe1216createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#122">_ZN4PLMD11multicolvar10FilterLess16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#154">_ZNK4PLMD11multicolvar10FilterLess11applyFilterERKdRd</a></td>
+              <td class="coverFnHi">2486</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#119">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe121C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#119">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe121D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#120">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe122C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#120">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe122D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterLessThan.cpp.func.html b/coverage/multicolvar/FilterLessThan.cpp.func.html
new file mode 100644
index 0000000000..2c54d2a7c8
--- /dev/null
+++ b/coverage/multicolvar/FilterLessThan.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterLessThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterLessThan.cpp<span style="font-size: 80%;"> (<a href="FilterLessThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FilterLessThan.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#122">_ZN4PLMD11multicolvar10FilterLess16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#133">_ZN4PLMD11multicolvar10FilterLessC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#133">_ZN4PLMD11multicolvar10FilterLessC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#119">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe1216createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#119">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe121C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#119">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe121D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#120">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe1226createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#120">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe122C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#120">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterLessRegisterMe122D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterLessThan.cpp.gcov.html#154">_ZNK4PLMD11multicolvar10FilterLess11applyFilterERKdRd</a></td>
+              <td class="coverFnHi">2486</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterLessThan.cpp.gcov.html b/coverage/multicolvar/FilterLessThan.cpp.gcov.html
new file mode 100644
index 0000000000..fb02877a61
--- /dev/null
+++ b/coverage/multicolvar/FilterLessThan.cpp.gcov.html
@@ -0,0 +1,238 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterLessThan.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterLessThan.cpp<span style="font-size: 80%;"> (source / <a href="FilterLessThan.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;MultiColvarFilter.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MTRANSFORMS MTRANSFORM_LESS</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : This action can be used to transform the colvar values calculated by a multicovar using a switching function</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : In this action each colvar, \f$s_i\f$, calculated by \ref mcolv is transformed by a \ref switchingfunction function that</a>
+<a name="31"><span class="lineNum">      31 </span>            : is equal to one if the colvar is less than a certain target value and which is equal to zero otherwise.</a>
+<a name="32"><span class="lineNum">      32 </span>            : It is important to understand the distinction between what is done here and what is done by \ref MFILTER_LESS.</a>
+<a name="33"><span class="lineNum">      33 </span>            : In \ref MFILTER_LESS a weight, \f$w_i\f$ for the colvar is calculated using the \ref switchingfunction.  If one calculates the</a>
+<a name="34"><span class="lineNum">      34 </span>            : MEAN for \ref MFILTER_LESS one is thus calculating:</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \f[</a>
+<a name="37"><span class="lineNum">      37 </span>            : \mu = \frac{ \sum_i \sigma(s_i) s_i }{\sum_i \simga(s_i) }</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f]</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : where \f$\sigma\f$ is the \ref switchingfunction.  In this action by contrast the colvar is being transformed by</a>
+<a name="41"><span class="lineNum">      41 </span>            : the \ref switchingfunction.  If one thus calculates a MEAN for this action one computes:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : \mu = \frac{ \sum_{i=1}^N \simga(s_i) }{ N }</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : In other words, you are calculating the mean for the transformed colvar.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The following input gives an example of how a MTRANSFORM_LESS action can be used to duplicate</a>
+<a name="52"><span class="lineNum">      52 </span>            : functionality that is elsewhere in PLUMED.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : DISTANCES ...</a>
+<a name="56"><span class="lineNum">      56 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="57"><span class="lineNum">      57 </span>            :  LABEL=d1</a>
+<a name="58"><span class="lineNum">      58 </span>            : ... DISTANCES</a>
+<a name="59"><span class="lineNum">      59 </span>            : MTRANSFORM_LESS DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : In this case you can achieve the same result by using:</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : DISTANCES ...</a>
+<a name="66"><span class="lineNum">      66 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="67"><span class="lineNum">      67 </span>            :  LESS_THAN={GAUSSIAN D_0=1.5 R_0=0.00001}</a>
+<a name="68"><span class="lineNum">      68 </span>            : ... DISTANCES</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : (see \ref DISTANCES)</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The advantage of MTRANSFORM_LESS comes, however, if you want to use transformed colvars as input</a>
+<a name="73"><span class="lineNum">      73 </span>            : for \ref MULTICOLVARDENS</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : //+PLUMEDOC MFILTERS MFILTER_LESS</a>
+<a name="79"><span class="lineNum">      79 </span>            : /*</a>
+<a name="80"><span class="lineNum">      80 </span>            : This action can be used to filter the distribution of colvar values in a multicolvar so that one can compute the mean and so on for only those multicolvars less than a tolerance.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : This action can be used to create a dynamic group of atom based on the value of a multicolvar.</a>
+<a name="83"><span class="lineNum">      83 </span>            : In this action a multicolvar is within the dynamic group if its value is less than a target.</a>
+<a name="84"><span class="lineNum">      84 </span>            : In actuality a weight, \f$w_i\f$ is ascribed to each colvar, \f$s_i\f$ calculated by a multicolvar</a>
+<a name="85"><span class="lineNum">      85 </span>            : and this weight measures the degree to which a colvar is a member of the group.  This weight is a number</a>
+<a name="86"><span class="lineNum">      86 </span>            : between 0 and 1 that is calculated using a \ref switchingfunction , \f$\sigma\f$.</a>
+<a name="87"><span class="lineNum">      87 </span>            : If one calculates a function of the set of multicolvars</a>
+<a name="88"><span class="lineNum">      88 </span>            : these weights are included in the calculation.  As such if one calculates the MEAN, \f$\mu\f$ of a filtered</a>
+<a name="89"><span class="lineNum">      89 </span>            : multicolvar what is computed is the following:</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \f[</a>
+<a name="92"><span class="lineNum">      92 </span>            : \mu = \frac{ \sum_i w_i s_i }{ \sum_i w_i}</a>
+<a name="93"><span class="lineNum">      93 </span>            : \f]</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : One is thus calculating the mean for those colvars that are less than the target.</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : \par Examples</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : The example shown below calculates the mean for those distances that less than 1.5 nm in length</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : \plumedfile</a>
+<a name="102"><span class="lineNum">     102 </span>            : DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1</a>
+<a name="103"><span class="lineNum">     103 </span>            : MFILTER_LESS DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001} MEAN LABEL=d4</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endplumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : */</a>
+<a name="107"><span class="lineNum">     107 </span>            : //+ENDPLUMEDOC</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : namespace PLMD {</a>
+<a name="110"><span class="lineNum">     110 </span>            : namespace multicolvar {</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : class FilterLess : public MultiColvarFilter {</a>
+<a name="113"><span class="lineNum">     113 </span>            : private:</a>
+<a name="114"><span class="lineNum">     114 </span>            :   SwitchingFunction sf;</a>
+<a name="115"><span class="lineNum">     115 </span>            : public:</a>
+<a name="116"><span class="lineNum">     116 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="117"><span class="lineNum">     117 </span>            :   explicit FilterLess(const ActionOptions&amp; ao);</a>
+<a name="118"><span class="lineNum">     118 </span>            :   double applyFilter( const double&amp; val, double&amp; df ) const override;</a>
+<a name="119"><span class="lineNum">     119 </span>            : };</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(FilterLess,&quot;MFILTER_LESS&quot;)</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(FilterLess,&quot;MTRANSFORM_LESS&quot;)</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 : void FilterLess::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   MultiColvarFilter::registerKeywords( keys );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function &quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="132"><span class="lineNum">     132 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 : FilterLess::FilterLess(const ActionOptions&amp; ao):</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   Action(ao),</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   MultiColvarFilter(ao)</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   // Read in the switching function</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          8 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :   if(sw.length()&gt;0) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :     sf.set(sw,errors);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   } else {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     sf.set(nn,mm,r_0,d_0);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          4 :   log.printf(&quot;  filtering colvar values and focussing only on those less than %s\n&quot;,( sf.description() ).c_str() );</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       2486 : double FilterLess::applyFilter( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       2486 :   double f = sf.calculate( val, df ); df*=val;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       2486 :   return f;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterMoreThan.cpp.func-sort-c.html b/coverage/multicolvar/FilterMoreThan.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ce2601c29c
--- /dev/null
+++ b/coverage/multicolvar/FilterMoreThan.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterMoreThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterMoreThan.cpp<span style="font-size: 80%;"> (<a href="FilterMoreThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FilterMoreThan.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#150">_ZN4PLMD11multicolvar10FilterMoreC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#137">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#136">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe1386createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#150">_ZN4PLMD11multicolvar10FilterMoreC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#139">_ZN4PLMD11multicolvar10FilterMore16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#136">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe138C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#136">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe138D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#137">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#137">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#171">_ZNK4PLMD11multicolvar10FilterMore11applyFilterERKdRd</a></td>
+              <td class="coverFnHi">16806</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterMoreThan.cpp.func.html b/coverage/multicolvar/FilterMoreThan.cpp.func.html
new file mode 100644
index 0000000000..59264c01dd
--- /dev/null
+++ b/coverage/multicolvar/FilterMoreThan.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterMoreThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterMoreThan.cpp<span style="font-size: 80%;"> (<a href="FilterMoreThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FilterMoreThan.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#139">_ZN4PLMD11multicolvar10FilterMore16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#150">_ZN4PLMD11multicolvar10FilterMoreC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#150">_ZN4PLMD11multicolvar10FilterMoreC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#136">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe1386createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#136">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe138C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#136">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe138D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#137">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#137">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#137">_ZN4PLMD11multicolvar12_GLOBAL__N_123FilterMoreRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FilterMoreThan.cpp.gcov.html#171">_ZNK4PLMD11multicolvar10FilterMore11applyFilterERKdRd</a></td>
+              <td class="coverFnHi">16806</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/FilterMoreThan.cpp.gcov.html b/coverage/multicolvar/FilterMoreThan.cpp.gcov.html
new file mode 100644
index 0000000000..5b2f271ed5
--- /dev/null
+++ b/coverage/multicolvar/FilterMoreThan.cpp.gcov.html
@@ -0,0 +1,255 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/FilterMoreThan.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - FilterMoreThan.cpp<span style="font-size: 80%;"> (source / <a href="FilterMoreThan.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">81.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;MultiColvarFilter.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC MTRANSFORMS MTRANSFORM_MORE</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : This action can be used to transform the colvar values calculated by a multicolvar using one minus a switching function</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : In this action each colvar, \f$s_i\f$, calculated by \ref mcolv is transformed by a \ref switchingfunction function that</a>
+<a name="31"><span class="lineNum">      31 </span>            : is equal to one if the colvar is greater than a certain target value and which is equal to zero otherwise.</a>
+<a name="32"><span class="lineNum">      32 </span>            : It is important to understand the distinction between what is done here and what is done by \ref MFILTER_MORE.</a>
+<a name="33"><span class="lineNum">      33 </span>            : In \ref MFILTER_MORE a weight, \f$w_i\f$ for the colvar is calculated using the \ref histogrambead.  If one calculates the</a>
+<a name="34"><span class="lineNum">      34 </span>            : MEAN for \ref MFILTER_MORE one is thus calculating:</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \f[</a>
+<a name="37"><span class="lineNum">      37 </span>            : \mu = \frac{ \sum_i [1 - \sigma(s_i) ] s_i }{\sum_i [1 - \sigma(s_i)] }</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f]</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : where \f$\sigma\f$ is the \ref switchingfunction.  In this action by contrast the colvar is being transformed by the \ref switchingfunction.</a>
+<a name="41"><span class="lineNum">      41 </span>            : If one thus calculates a MEAN for this action one computes:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : \mu = \frac{ \sum_{i=1}^N 1 - \sigma(s_i) }{ N }</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : In other words, you are calculating the mean for the transformed colvar.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The following input gives an example of how a MTRANSFORM_MORE action can be used to duplicate</a>
+<a name="52"><span class="lineNum">      52 </span>            : functionality that is elsewhere in PLUMED.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : DISTANCES ...</a>
+<a name="56"><span class="lineNum">      56 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="57"><span class="lineNum">      57 </span>            :  LABEL=d1</a>
+<a name="58"><span class="lineNum">      58 </span>            : ... DISTANCES</a>
+<a name="59"><span class="lineNum">      59 </span>            : MTRANSFORM_MORE DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001}</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endplumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : In this case you can achieve the same result by using:</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \plumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : DISTANCES ...</a>
+<a name="66"><span class="lineNum">      66 </span>            :  GROUPA=1-10 GROUPB=11-20</a>
+<a name="67"><span class="lineNum">      67 </span>            :  MORE_THAN={GAUSSIAN D_0=1.5 R_0=0.00001}</a>
+<a name="68"><span class="lineNum">      68 </span>            : ... DISTANCES</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : (see \ref DISTANCES)</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The advantage of MTRANSFORM_MORE comes, however, if you want to use transformed colvars as input</a>
+<a name="73"><span class="lineNum">      73 </span>            : for \ref MULTICOLVARDENS</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : //+PLUMEDOC MFILTERS MFILTER_MORE</a>
+<a name="79"><span class="lineNum">      79 </span>            : /*</a>
+<a name="80"><span class="lineNum">      80 </span>            : This action can be used to filter the distribution of colvar values in a multicolvar so that one can compute the mean and so on for only those multicolvars more than a tolerance.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : This action can be used to create a dynamic group of atom based on the value of a multicolvar.</a>
+<a name="83"><span class="lineNum">      83 </span>            : In this action a multicolvar is within the dynamic group if its value is greater than a target.</a>
+<a name="84"><span class="lineNum">      84 </span>            : In actuality a weight, \f$w_i\f$  is ascribed to each colvar, \f$s_i\f$ calculated by a multicolvar</a>
+<a name="85"><span class="lineNum">      85 </span>            : and this weight measures the degree to which a colvar is a member of the group.  This weight is</a>
+<a name="86"><span class="lineNum">      86 </span>            : calculated using a \ref switchingfunction , \f$\sigma\f$ so it is given by:</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \f[</a>
+<a name="89"><span class="lineNum">      89 </span>            : w_i = 1 - \sigma(s_i)</a>
+<a name="90"><span class="lineNum">      90 </span>            : \f]</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : If one calculates a function of the set of multicolvars</a>
+<a name="93"><span class="lineNum">      93 </span>            : these weights are included in the calculation.  As such if one calculates the MEAN, \f$\mu\f$ of a filtered</a>
+<a name="94"><span class="lineNum">      94 </span>            : multicolvar what is computed is the following:</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \f[</a>
+<a name="97"><span class="lineNum">      97 </span>            : \mu = \frac{ \sum_i w_i s_i }{ \sum_i w_i}</a>
+<a name="98"><span class="lineNum">      98 </span>            : \f]</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : One is thus calculating the mean for those colvars that are greater than the target.</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : \par Examples</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The example shown below calculates the mean for those distances that greater than 1.5 nm in length</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : \plumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : DISTANCES GROUPA=1 GROUPB=2-50 MEAN LABEL=d1</a>
+<a name="108"><span class="lineNum">     108 </span>            : MFILTER_MORE DATA=d1 SWITCH={GAUSSIAN D_0=1.5 R_0=0.00001} MEAN LABEL=d4</a>
+<a name="109"><span class="lineNum">     109 </span>            : \endplumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : More complicated things can be done by using the label of a filter as input to a new multicolvar as shown</a>
+<a name="112"><span class="lineNum">     112 </span>            : in the example below.  Here the coordination numbers of all atoms are computed.  The atoms with a coordination</a>
+<a name="113"><span class="lineNum">     113 </span>            : number greater than 2 are then identified using the filter.  This reduced list of atoms is then used as input</a>
+<a name="114"><span class="lineNum">     114 </span>            : to a second coordination number calculation.  This second coordination number thus measures the number of</a>
+<a name="115"><span class="lineNum">     115 </span>            : two-coordinated atoms that each of the two-coordinated atoms is bound to.</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : \plumedfile</a>
+<a name="118"><span class="lineNum">     118 </span>            : c1: COORDINATIONNUMBER SPECIES=1-150 SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0}</a>
+<a name="119"><span class="lineNum">     119 </span>            : cf: MFILTER_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM</a>
+<a name="120"><span class="lineNum">     120 </span>            : c2: COORDINATIONNUMBER SPECIES=cf SWITCH={EXP D_0=4.0 R_0=0.5 D_MAX=6.0} MORE_THAN={RATIONAL D_0=2.0 R_0=0.1}</a>
+<a name="121"><span class="lineNum">     121 </span>            : \endplumedfile</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : */</a>
+<a name="124"><span class="lineNum">     124 </span>            : //+ENDPLUMEDOC</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : namespace PLMD {</a>
+<a name="127"><span class="lineNum">     127 </span>            : namespace multicolvar {</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : class FilterMore : public MultiColvarFilter {</a>
+<a name="130"><span class="lineNum">     130 </span>            : private:</a>
+<a name="131"><span class="lineNum">     131 </span>            :   SwitchingFunction sf;</a>
+<a name="132"><span class="lineNum">     132 </span>            : public:</a>
+<a name="133"><span class="lineNum">     133 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="134"><span class="lineNum">     134 </span>            :   explicit FilterMore(const ActionOptions&amp; ao);</a>
+<a name="135"><span class="lineNum">     135 </span>            :   double applyFilter( const double&amp; val, double&amp; df ) const override;</a>
+<a name="136"><span class="lineNum">     136 </span>            : };</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(FilterMore,&quot;MFILTER_MORE&quot;)</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(FilterMore,&quot;MTRANSFORM_MORE&quot;)</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         11 : void FilterMore::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         11 :   MultiColvarFilter::registerKeywords( keys );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="149"><span class="lineNum">     149 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         11 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          7 : FilterMore::FilterMore(const ActionOptions&amp; ao):</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   Action(ao),</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          7 :   MultiColvarFilter(ao)</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : {</a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Read in the switching function</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         14 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          7 :   if(sw.length()&gt;0) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          7 :     sf.set(sw,errors);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          7 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   } else {</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     sf.set(nn,mm,r_0,d_0);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          7 :   log.printf(&quot;  filtering colvar values and focussing only on those more than %s\n&quot;,( sf.description() ).c_str() );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          7 :   checkRead();</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          7 : }</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      16806 : double FilterMore::applyFilter( const double&amp; val, double&amp; df ) const {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      16806 :   double f = 1.0 - sf.calculate( val, df ); df*=-val;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      16806 :   return f;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/InPlaneDistances.cpp.func-sort-c.html b/coverage/multicolvar/InPlaneDistances.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6112995fdb
--- /dev/null
+++ b/coverage/multicolvar/InPlaneDistances.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/InPlaneDistances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - InPlaneDistances.cpp<span style="font-size: 80%;"> (<a href="InPlaneDistances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryLo">21.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="InPlaneDistances.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#70">_ZN4PLMD11multicolvar12_GLOBAL__N_128InPlaneDistancesRegisterMe726createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#67">_ZN4PLMD11multicolvar16InPlaneDistances10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#82">_ZN4PLMD11multicolvar16InPlaneDistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#82">_ZN4PLMD11multicolvar16InPlaneDistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#129">_ZNK4PLMD11multicolvar16InPlaneDistances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#72">_ZN4PLMD11multicolvar16InPlaneDistances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#70">_ZN4PLMD11multicolvar12_GLOBAL__N_128InPlaneDistancesRegisterMe72C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#70">_ZN4PLMD11multicolvar12_GLOBAL__N_128InPlaneDistancesRegisterMe72D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/InPlaneDistances.cpp.func.html b/coverage/multicolvar/InPlaneDistances.cpp.func.html
new file mode 100644
index 0000000000..8e90f35b96
--- /dev/null
+++ b/coverage/multicolvar/InPlaneDistances.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/InPlaneDistances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - InPlaneDistances.cpp<span style="font-size: 80%;"> (<a href="InPlaneDistances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryLo">21.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="InPlaneDistances.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#70">_ZN4PLMD11multicolvar12_GLOBAL__N_128InPlaneDistancesRegisterMe726createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#70">_ZN4PLMD11multicolvar12_GLOBAL__N_128InPlaneDistancesRegisterMe72C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#70">_ZN4PLMD11multicolvar12_GLOBAL__N_128InPlaneDistancesRegisterMe72D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#67">_ZN4PLMD11multicolvar16InPlaneDistances10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#72">_ZN4PLMD11multicolvar16InPlaneDistances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#82">_ZN4PLMD11multicolvar16InPlaneDistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#82">_ZN4PLMD11multicolvar16InPlaneDistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="InPlaneDistances.cpp.gcov.html#129">_ZNK4PLMD11multicolvar16InPlaneDistances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/InPlaneDistances.cpp.gcov.html b/coverage/multicolvar/InPlaneDistances.cpp.gcov.html
new file mode 100644
index 0000000000..3539f3ff88
--- /dev/null
+++ b/coverage/multicolvar/InPlaneDistances.cpp.gcov.html
@@ -0,0 +1,223 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/InPlaneDistances.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - InPlaneDistances.cpp<span style="font-size: 80%;"> (source / <a href="InPlaneDistances.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryLo">21.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;vesselbase/LessThan.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;vesselbase/Between.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Angle.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;string&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cmath&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace multicolvar {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC MCOLVAR INPLANEDISTANCES</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : Calculate distances in the plane perpendicular to an axis</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : Each quantity calculated in this CV uses the positions of two atoms, this indices of which are specified using the VECTORSTART and VECTOREND keywords, to specify the</a>
+<a name="41"><span class="lineNum">      41 </span>            : orientation of a vector, \f$\mathbf{n}\f$.  The perpendicular distance between this vector and the position of some third atom is then computed using:</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            :  x_j = |\mathbf{r}_{j}| \sin (\theta_j)</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : where \f$\mathbf{r}_j\f$ is the distance between one of the two atoms that define the vector \f$\mathbf{n}\f$ and a third atom (atom \f$j\f$) and where \f$\theta_j\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : is the angle between the vector \f$\mathbf{n}\f$ and the vector \f$\mathbf{r}_{j}\f$.  The \f$x_j\f$ values for each of the atoms specified using the GROUP keyword are calculated.</a>
+<a name="47"><span class="lineNum">      47 </span>            : Keywords such as MORE_THAN and LESS_THAN can then be used to calculate the number of these quantities that are more or less than a given cutoff.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The following input can be used to calculate the number of atoms that have indices greater than 3 and less than 101 that</a>
+<a name="52"><span class="lineNum">      52 </span>            : are within a cylinder with a radius of 0.3 nm that has its long axis aligned with the vector connecting atoms 1 and 2.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : d1: INPLANEDISTANCES VECTORSTART=1 VECTOREND=2 GROUP=3-100 LESS_THAN={RATIONAL D_0=0.2 R_0=0.1}</a>
+<a name="56"><span class="lineNum">      56 </span>            : PRINT ARG=d1.lessthan FILE=colvar</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : */</a>
+<a name="61"><span class="lineNum">      61 </span>            : //+ENDPLUMEDOC</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : class InPlaneDistances : public MultiColvarBase {</a>
+<a name="64"><span class="lineNum">      64 </span>            : public:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="66"><span class="lineNum">      66 </span>            :   explicit InPlaneDistances(const ActionOptions&amp;);</a>
+<a name="67"><span class="lineNum">      67 </span>            : // active methods:</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double compute(const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(InPlaneDistances,&quot;INPLANEDISTANCES&quot;)</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          2 : void InPlaneDistances::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          2 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          8 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          8 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          4 :   keys.add(&quot;atoms&quot;,&quot;VECTORSTART&quot;,&quot;The first atom position that is used to define the normal to the plane of interest&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          4 :   keys.add(&quot;atoms&quot;,&quot;VECTOREND&quot;,&quot;The second atom position that is used to define the normal to the plane of interest&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 :   keys.add(&quot;atoms-2&quot;,&quot;GROUP&quot;,&quot;The set of atoms for which you wish to calculate the in plane distance &quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          2 : }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 : InPlaneDistances::InPlaneDistances(const ActionOptions&amp;ao):</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Action(ao),</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   MultiColvarBase(ao)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span>            :   // Read in the atoms</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   readThreeGroups(&quot;GROUP&quot;,&quot;VECTORSTART&quot;,&quot;VECTOREND&quot;,false,false,all_atoms);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   // Setup the multicolvar base</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   setupMultiColvarBase( all_atoms ); readVesselKeywords();</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   // Check atoms are OK</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   if( getFullNumberOfTasks()!=getNumberOfAtoms()-2 ) error(&quot;you should specify one atom for VECTORSTART and one atom for VECTOREND only&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   // And check everything has been read in correctly</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : // Now check if we can use link cells</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   if( getNumberOfVessels()&gt;0 ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     bool use_link=false; double rcut;</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :     vesselbase::LessThan* lt=dynamic_cast&lt;vesselbase::LessThan*&gt;( getPntrToVessel(0) );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     if( lt ) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :       use_link=true; rcut=lt-&gt;getCutoff();</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :     } else {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :       vesselbase::Between* bt=dynamic_cast&lt;vesselbase::Between*&gt;( getPntrToVessel(0) );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :       if( bt ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :         use_link=true; rcut=bt-&gt;getCutoff();</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :       }</a>
+<a name="111"><span class="lineNum">     111 </span>            :     }</a>
+<a name="112"><span class="lineNum">     112 </span>            :     if( use_link ) {</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       for(unsigned i=1; i&lt;getNumberOfVessels(); ++i) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :         vesselbase::LessThan* lt2=dynamic_cast&lt;vesselbase::LessThan*&gt;( getPntrToVessel(i) );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :         vesselbase::Between* bt=dynamic_cast&lt;vesselbase::Between*&gt;( getPntrToVessel(i) );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :         if( lt2 ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :           double tcut=lt2-&gt;getCutoff();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :           if( tcut&gt;rcut ) rcut=tcut;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :         } else if( bt ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :           double tcut=bt-&gt;getCutoff();</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :           if( tcut&gt;rcut ) rcut=tcut;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :         } else {</a>
+<a name="123"><span class="lineNum">     123 </span>            :           use_link=false;</a>
+<a name="124"><span class="lineNum">     124 </span>            :         }</a>
+<a name="125"><span class="lineNum">     125 </span>            :       }</a>
+<a name="126"><span class="lineNum">     126 </span>            :     }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     if( use_link ) setLinkCellCutoff( rcut );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 : double InPlaneDistances::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   Vector normal=getSeparation( myatoms.getPosition(1), myatoms.getPosition(2) );</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :   Vector dir=getSeparation( myatoms.getPosition(1), myatoms.getPosition(0) );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   PLMD::Angle a; Vector ddij, ddik; double angle=a.compute(normal,dir,ddij,ddik);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :   double sangle=std::sin(angle), cangle=std::cos(angle);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :   double dd=dir.modulo(), invdd=1.0/dd, val=dd*sangle;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   addAtomDerivatives( 1, 0, dd*cangle*ddik + sangle*invdd*dir, myatoms );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   addAtomDerivatives( 1, 1, -dd*cangle*(ddik+ddij) - sangle*invdd*dir, myatoms );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   addAtomDerivatives( 1, 2, dd*cangle*ddij, myatoms );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   myatoms.addBoxDerivatives( 1, -dd*cangle*(Tensor(normal,ddij)+Tensor(dir,ddik)) - sangle*invdd*Tensor(dir,dir) );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   return val;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/LocalAverage.cpp.func-sort-c.html b/coverage/multicolvar/LocalAverage.cpp.func-sort-c.html
new file mode 100644
index 0000000000..82cf03c33a
--- /dev/null
+++ b/coverage/multicolvar/LocalAverage.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/LocalAverage.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - LocalAverage.cpp<span style="font-size: 80%;"> (<a href="LocalAverage.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryMed">79.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LocalAverage.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#121">_ZN4PLMD11multicolvar12LocalAverageC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#96">_ZNK4PLMD11multicolvar12LocalAverage15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#98">_ZN4PLMD11multicolvar12LocalAverage10isPeriodicEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#121">_ZN4PLMD11multicolvar12LocalAverageC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#101">_ZN4PLMD11multicolvar12_GLOBAL__N_125LocalAverageRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#103">_ZN4PLMD11multicolvar12LocalAverage16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#143">_ZNK4PLMD11multicolvar12LocalAverage21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#147">_ZNK4PLMD11multicolvar12LocalAverage7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">1004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#101">_ZN4PLMD11multicolvar12_GLOBAL__N_125LocalAverageRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#101">_ZN4PLMD11multicolvar12_GLOBAL__N_125LocalAverageRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/LocalAverage.cpp.func.html b/coverage/multicolvar/LocalAverage.cpp.func.html
new file mode 100644
index 0000000000..a2b68ab649
--- /dev/null
+++ b/coverage/multicolvar/LocalAverage.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/LocalAverage.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - LocalAverage.cpp<span style="font-size: 80%;"> (<a href="LocalAverage.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryMed">79.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LocalAverage.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#98">_ZN4PLMD11multicolvar12LocalAverage10isPeriodicEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#103">_ZN4PLMD11multicolvar12LocalAverage16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#121">_ZN4PLMD11multicolvar12LocalAverageC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#121">_ZN4PLMD11multicolvar12LocalAverageC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#101">_ZN4PLMD11multicolvar12_GLOBAL__N_125LocalAverageRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#101">_ZN4PLMD11multicolvar12_GLOBAL__N_125LocalAverageRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#101">_ZN4PLMD11multicolvar12_GLOBAL__N_125LocalAverageRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#96">_ZNK4PLMD11multicolvar12LocalAverage15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#143">_ZNK4PLMD11multicolvar12LocalAverage21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LocalAverage.cpp.gcov.html#147">_ZNK4PLMD11multicolvar12LocalAverage7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">1004</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/LocalAverage.cpp.gcov.html b/coverage/multicolvar/LocalAverage.cpp.gcov.html
new file mode 100644
index 0000000000..0539c02e95
--- /dev/null
+++ b/coverage/multicolvar/LocalAverage.cpp.gcov.html
@@ -0,0 +1,406 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/LocalAverage.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - LocalAverage.cpp<span style="font-size: 80%;"> (source / <a href="LocalAverage.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryMed">79.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC MCOLVARF LOCAL_AVERAGE</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Calculate averages over spherical regions centered on atoms</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : As is explained in &lt;a href=&quot;http://www.youtube.com/watch?v=iDvZmbWE5ps&quot;&gt; this video &lt;/a&gt; certain multicolvars</a>
+<a name="32"><span class="lineNum">      32 </span>            : calculate one scalar quantity or one vector for each of the atoms in the system.  For example</a>
+<a name="33"><span class="lineNum">      33 </span>            : \ref COORDINATIONNUMBER measures the coordination number of each of the atoms in the system and \ref Q4 measures</a>
+<a name="34"><span class="lineNum">      34 </span>            : the fourth order Steinhardt parameter for each of the atoms in the system.  These quantities provide tell us something about</a>
+<a name="35"><span class="lineNum">      35 </span>            : the disposition of the atoms in the first coordination sphere of each of the atoms of interest.  Lechner and Dellago \cite dellago-q6</a>
+<a name="36"><span class="lineNum">      36 </span>            : have suggested that one can probe local order in a system by taking the average value of such symmetry functions over</a>
+<a name="37"><span class="lineNum">      37 </span>            : the atoms within a spherical cutoff of each of these atoms in the systems.  When this is done with Steinhardt parameters</a>
+<a name="38"><span class="lineNum">      38 </span>            : they claim this gives a coordinate that is better able to distinguish solid and liquid configurations of Lennard-Jones atoms.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : You can calculate such locally averaged quantities within plumed by using the LOCAL_AVERAGE command.  This command calculates</a>
+<a name="41"><span class="lineNum">      41 </span>            : the following atom-centered quantities:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : s_i = \frac{ c_i + \sum_j \sigma(r_{ij})c_j }{ 1 + \sum_j \sigma(r_{ij}) }</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : where the \f$c_i\f$ and \f$c_j\f$ values can be for any one of the symmetry functions that can be calculated using plumed</a>
+<a name="48"><span class="lineNum">      48 </span>            : multicolvars.  The function \f$\sigma( r_{ij} )\f$ is a \ref switchingfunction that acts on the distance between</a>
+<a name="49"><span class="lineNum">      49 </span>            : atoms \f$i\f$ and \f$j\f$.  Lechner and Dellago suggest that the parameters of this function should be set so that it the function is equal to one</a>
+<a name="50"><span class="lineNum">      50 </span>            : when atom \f$j\f$ is in the first coordination sphere of atom \f$i\f$ and is zero otherwise.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The \f$s_i\f$ quantities calculated using the above command can be again thought of as atom-centered symmetry functions.  They</a>
+<a name="53"><span class="lineNum">      53 </span>            : thus operate much like multicolvars.  You can thus calculate properties of the distribution of \f$s_i\f$ values using MEAN, LESS_THAN, HISTOGRAM</a>
+<a name="54"><span class="lineNum">      54 </span>            : and so on.  You can also probe the value of these averaged variables in regions of the box by using the command in tandem with the</a>
+<a name="55"><span class="lineNum">      55 </span>            : \ref AROUND command.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \par Examples</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : This example input calculates the coordination numbers for all the atoms in the system.  These coordination numbers are then averaged over</a>
+<a name="60"><span class="lineNum">      60 </span>            : spherical regions.  The number of averaged coordination numbers that are greater than 4 is then output to a file.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : COORDINATIONNUMBER SPECIES=1-64 D_0=1.3 R_0=0.2 LABEL=d1</a>
+<a name="64"><span class="lineNum">      64 </span>            : LOCAL_AVERAGE SPECIES=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MORE_THAN={RATIONAL R_0=4} LABEL=la</a>
+<a name="65"><span class="lineNum">      65 </span>            : PRINT ARG=la.* FILE=colvar</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : This example input calculates the \f$q_4\f$ (see \ref Q4) vectors for each of the atoms in the system.  These vectors are then averaged</a>
+<a name="69"><span class="lineNum">      69 </span>            : component by component over a spherical region.  The average value for this quantity is then output to a file.  This calculates the</a>
+<a name="70"><span class="lineNum">      70 </span>            : quantities that were used in the paper by Lechner and Dellago \cite dellago-q6</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : Q4 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q4</a>
+<a name="74"><span class="lineNum">      74 </span>            : LOCAL_AVERAGE SPECIES=q4 SWITCH={RATIONAL D_0=1.3 R_0=0.2} MEAN LABEL=la</a>
+<a name="75"><span class="lineNum">      75 </span>            : PRINT ARG=la.* FILE=colvar</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : */</a>
+<a name="79"><span class="lineNum">      79 </span>            : //+ENDPLUMEDOC</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : namespace PLMD {</a>
+<a name="82"><span class="lineNum">      82 </span>            : namespace multicolvar {</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : class LocalAverage : public MultiColvarBase {</a>
+<a name="85"><span class="lineNum">      85 </span>            : private:</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Cutoff</a>
+<a name="87"><span class="lineNum">      87 </span>            :   double rcut2;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// The switching function that tells us if atoms are close enough together</a>
+<a name="89"><span class="lineNum">      89 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="90"><span class="lineNum">      90 </span>            : public:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="92"><span class="lineNum">      92 </span>            :   explicit LocalAverage(const ActionOptions&amp;);</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// We have to overwrite this here</a>
+<a name="94"><span class="lineNum">      94 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Actually do the calculation</a>
+<a name="96"><span class="lineNum">      96 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// We overwrite this in order to have dumpmulticolvar working for local average</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   void normalizeVector( std::vector&lt;double&gt;&amp; vals ) const override {}</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Is the variable periodic</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          3 :   bool isPeriodic() override { return false; }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : };</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(LocalAverage,&quot;LOCAL_AVERAGE&quot;)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          6 : void LocalAverage::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          6 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="113"><span class="lineNum">     113 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         18 :   keys.use(&quot;SPECIES&quot;); keys.use(&quot;SPECIESA&quot;); keys.use(&quot;SPECIESB&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         24 :   keys.remove(&quot;LOWMEM&quot;); keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         18 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         12 :   keys.addFlag(&quot;LOWMEM&quot;,false,&quot;lower the memory requirements&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         18 :   if( keys.reserved(&quot;VMEAN&quot;) ) keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         18 :   if( keys.reserved(&quot;VSUM&quot;) ) keys.use(&quot;VSUM&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          6 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 : LocalAverage::LocalAverage(const ActionOptions&amp; ao):</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   Action(ao),</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          4 :   MultiColvarBase(ao)</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          4 :   if( getNumberOfBaseMultiColvars()&gt;1 ) error(&quot;local average with more than one base colvar makes no sense&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Read in the switching function</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          8 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          4 :   if(sw.length()&gt;0) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 :     switchingFunction.set(sw,errors);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   } else {</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :   log.printf(&quot;  averaging over central molecule and those within %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          4 :   rcut2 = switchingFunction.get_dmax()*switchingFunction.get_dmax();</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :   setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :   std::vector&lt;AtomNumber&gt; all_atoms; setupMultiColvarBase( all_atoms );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          4 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         71 : unsigned LocalAverage::getNumberOfQuantities() const {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         71 :   return getBaseMultiColvar(0)-&gt;getNumberOfQuantities();</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1004 : double LocalAverage::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   double sw, dfunc; MultiValue&amp; myvals = myatoms.getUnderlyingMultiValue();</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       1004 :   std::vector&lt;double&gt; values( getBaseMultiColvar(0)-&gt;getNumberOfQuantities() );</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       1004 :   getInputData( 0, false, myatoms, values );</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   myvals.addTemporyValue( values[0] );</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       1004 :   if( values.size()&gt;2 ) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      27108 :     for(unsigned j=2; j&lt;values.size(); ++j) myatoms.addValue( j, values[0]*values[j] );</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   } else {</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     myatoms.addValue( 1, values[0]*values[1] );</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1004 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       1004 :     MultiValue&amp; myder=getInputDerivatives( 0, false, myatoms );</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            :     // Convert input atom to local index</a>
+<a name="165"><span class="lineNum">     165 </span>            :     unsigned katom = myatoms.getIndex( 0 ); plumed_dbg_assert( katom&lt;atom_lab.size() ); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="166"><span class="lineNum">     166 </span>            :     // Find base colvar</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1004 :     unsigned mmc=atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     // Get start of indices for this atom</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1004 :     unsigned basen=0; for(unsigned i=0; i&lt;mmc; ++i) basen+=mybasemulticolvars[i]-&gt;getNumberOfDerivatives() - 9;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     plumed_dbg_assert( basen%3==0 ); // Check the number of atoms is consistent with input derivatives</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       1004 :     unsigned virbas = myvals.getNumberOfDerivatives()-9;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       1004 :     if( values.size()&gt;2 ) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      49505 :       for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :         unsigned jder=myder.getActiveIndex(j);</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      48501 :         if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      39465 :           unsigned kder=basen+jder;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    1065555 :           for(unsigned k=2; k&lt;values.size(); ++k) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">    1026090 :             myatoms.addDerivative( k, kder, values[0]*myder.getDerivative(k,jder) );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">    1026090 :             myatoms.addDerivative( k, kder, values[k]*myder.getDerivative(0,jder) );</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :           }</a>
+<a name="182"><span class="lineNum">     182 </span>            :         } else {</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       9036 :           unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     243972 :           for(unsigned k=2; k&lt;values.size(); ++k) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">     234936 :             myatoms.addDerivative( k, kder, values[0]*myder.getDerivative(k,jder) );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     234936 :             myatoms.addDerivative( k, kder, values[k]*myder.getDerivative(0,jder) );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :           }</a>
+<a name="188"><span class="lineNum">     188 </span>            :         }</a>
+<a name="189"><span class="lineNum">     189 </span>            :       }</a>
+<a name="190"><span class="lineNum">     190 </span>            :     } else {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :         unsigned jder=myder.getActiveIndex(j);</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :         if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :           unsigned kder=basen+jder;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :           myatoms.addDerivative( 1, kder, values[0]*myder.getDerivative(1,jder) );</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :           myatoms.addDerivative( 1, kder, values[1]*myder.getDerivative(0,jder) );</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :         } else {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :           unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :           myatoms.addDerivative( 1, kder, values[0]*myder.getDerivative(1,jder) );</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :           myatoms.addDerivative( 1, kder, values[1]*myder.getDerivative(0,jder) );</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :         }</a>
+<a name="202"><span class="lineNum">     202 </span>            :       }</a>
+<a name="203"><span class="lineNum">     203 </span>            :     }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      49505 :     for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :       unsigned jder=myder.getActiveIndex(j);</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      48501 :       if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      39465 :         unsigned kder=basen+jder;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">      39465 :         myvals.addTemporyDerivative( kder, myder.getDerivative(0, jder) );</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :       } else {</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       9036 :         unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       9036 :         myvals.addTemporyDerivative( kder, myder.getDerivative(0, jder) );</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :       }</a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1004 :     myder.clearAll();</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     274074 :   for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     Vector&amp; distance=myatoms.getPosition(i);  // getSeparation( myatoms.getPosition(0), myatoms.getPosition(i) );</a>
+<a name="219"><span class="lineNum">     219 </span>            :     double d2;</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     363595 :     if ( (d2=distance[0]*distance[0])&lt;rcut2 &amp;&amp;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      90525 :          (d2+=distance[1]*distance[1])&lt;rcut2 &amp;&amp;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">     305390 :          (d2+=distance[2]*distance[2])&lt;rcut2 &amp;&amp;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :          d2&gt;epsilon) {</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      14639 :       sw = switchingFunction.calculateSqr( d2, dfunc );</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      14639 :       getInputData( i, false, myatoms, values );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      14639 :       if( values.size()&gt;2 ) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">     395253 :         for(unsigned j=2; j&lt;values.size(); ++j) myatoms.addValue( j, sw*values[0]*values[j] );</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       } else {</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :         myatoms.addValue( 1, sw*values[0]*values[1] );</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :       }</a>
+<a name="233"><span class="lineNum">     233 </span>            :       myvals.addTemporyValue(sw);</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      14639 :       if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      14639 :         Tensor vir(distance,distance);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      14639 :         MultiValue&amp; myder=getInputDerivatives( i, false, myatoms );</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            :         // Convert input atom to local index</a>
+<a name="240"><span class="lineNum">     240 </span>            :         unsigned katom = myatoms.getIndex( i ); plumed_dbg_assert( katom&lt;atom_lab.size() ); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="241"><span class="lineNum">     241 </span>            :         // Find base colvar</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">      14639 :         unsigned mmc=atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :         // Get start of indices for this atom</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">      19559 :         unsigned basen=0; for(unsigned j=0; j&lt;mmc; ++j) basen+=mybasemulticolvars[j]-&gt;getNumberOfDerivatives() - 9;</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :         plumed_dbg_assert( basen%3==0 ); // Check the number of atoms is consistent with input derivatives</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      14639 :         unsigned virbas = myvals.getNumberOfDerivatives()-9;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">      14639 :         if( values.size()&gt;2 ) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">    1424993 :           for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :             unsigned jder=myder.getActiveIndex(j);</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">    1410354 :             if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">    1278603 :               unsigned kder=basen+jder;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">   34522281 :               for(unsigned k=2; k&lt;values.size(); ++k) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">   33243678 :                 myatoms.addDerivative( k, kder, sw*values[0]*myder.getDerivative(k,jder) );</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">   33243678 :                 myatoms.addDerivative( k, kder, sw*values[k]*myder.getDerivative(0,jder) );</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :               }</a>
+<a name="257"><span class="lineNum">     257 </span>            :             } else {</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">     131751 :               unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">    3557277 :               for(unsigned k=2; k&lt;values.size(); ++k) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">    3425526 :                 myatoms.addDerivative( k, kder, sw*values[0]*myder.getDerivative(k,jder) );</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">    3425526 :                 myatoms.addDerivative( k, kder, sw*values[k]*myder.getDerivative(0,jder) );</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :               }</a>
+<a name="263"><span class="lineNum">     263 </span>            :             }</a>
+<a name="264"><span class="lineNum">     264 </span>            :           }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">     395253 :           for(unsigned k=2; k&lt;values.size(); ++k) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">     380614 :             addAtomDerivatives( k, 0, (-dfunc)*values[0]*values[k]*distance, myatoms );</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">     380614 :             addAtomDerivatives( k, i, (+dfunc)*values[0]*values[k]*distance, myatoms );</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">     380614 :             myatoms.addBoxDerivatives( k, (-dfunc)*values[0]*values[k]*vir );</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :           }</a>
+<a name="270"><span class="lineNum">     270 </span>            :         } else {</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :           for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :             unsigned jder=myder.getActiveIndex(j);</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :             if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :               unsigned kder=basen+jder;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :               myatoms.addDerivative( 1, kder, sw*values[0]*myder.getDerivative(1,jder) );</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :               myatoms.addDerivative( 1, kder, sw*values[1]*myder.getDerivative(0,jder) );</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :             } else {</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :               unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :               myatoms.addDerivative( 1, kder, sw*values[0]*myder.getDerivative(1,jder) );</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :               myatoms.addDerivative( 1, kder, sw*values[1]*myder.getDerivative(0,jder) );</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :             }</a>
+<a name="282"><span class="lineNum">     282 </span>            :           }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :           addAtomDerivatives( 1, 0, (-dfunc)*values[0]*values[1]*distance, myatoms );</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :           addAtomDerivatives( 1, i, (+dfunc)*values[0]*values[1]*distance, myatoms );</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :           myatoms.addBoxDerivatives( 1, (-dfunc)*values[0]*values[1]*vir );</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :         }</a>
+<a name="287"><span class="lineNum">     287 </span>            :         // And the bit we use to average the vector</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      14639 :         addAtomDerivatives( -1, 0, (-dfunc)*values[0]*distance, myatoms );</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">      14639 :         addAtomDerivatives( -1, i, (+dfunc)*values[0]*distance, myatoms );</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">    1424993 :         for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :           unsigned jder=myder.getActiveIndex(j);</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">    1410354 :           if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">    1278603 :             unsigned kder=basen+jder;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">    1278603 :             myvals.addTemporyDerivative( kder, sw*myder.getDerivative(0, jder) );</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :           } else {</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">     131751 :             unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     131751 :             myvals.addTemporyDerivative( kder, sw*myder.getDerivative(0, jder) );</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :           }</a>
+<a name="299"><span class="lineNum">     299 </span>            :         }</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">      14639 :         myatoms.addTemporyBoxDerivatives( (-dfunc)*values[0]*vir );</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">      14639 :         myder.clearAll();</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :       }</a>
+<a name="303"><span class="lineNum">     303 </span>            :     }</a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            :   // Set the tempory weight</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       1004 :   updateActiveAtoms( myatoms );</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       1004 :   if( values.size()&gt;2) {</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :     double norm=0;</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      27108 :     for(unsigned i=2; i&lt;values.size(); ++i) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      26104 :       myvals.quotientRule( i, i );</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :       // Calculate length of vector</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">      26104 :       norm+=myvals.get(i)*myvals.get(i);</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :     }</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       1004 :     norm=sqrt(norm); myatoms.setValue(1, norm); double inorm = 1.0 / norm;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">     132755 :     for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     131751 :       unsigned jder=myvals.getActiveIndex(j);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">    3557277 :       for(unsigned i=2; i&lt;values.size(); ++i) {</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">    3425526 :         myvals.addDerivative( 1, jder, myvals.get(i)*inorm*myvals.getDerivative(i,jder) );</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :       }</a>
+<a name="321"><span class="lineNum">     321 </span>            :     }</a>
+<a name="322"><span class="lineNum">     322 </span>            :   } else {</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     myvals.quotientRule( 1, 1 );</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       1004 :   return myatoms.getValue(1);</span></a>
+<a name="327"><span class="lineNum">     327 </span>            : }</a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            : }</a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarBase.cpp.func-sort-c.html b/coverage/multicolvar/MultiColvarBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9abdecc7a2
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarBase.cpp.func-sort-c.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarBase.cpp<span style="font-size: 80%;"> (<a href="MultiColvarBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">583</td>
+            <td class="headerCovTableEntry">652</td>
+            <td class="headerCovTableEntryMed">89.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.cpp.gcov.html#72">_ZN4PLMD11multicolvar15MultiColvarBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.cpp.gcov.html#340">_ZN4PLMD11multicolvar15MultiColvarBase9buildSetsEv</a></td>
+              <td class="coverFnHi">4</td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarBase.cpp.gcov.html b/coverage/multicolvar/MultiColvarBase.cpp.gcov.html
new file mode 100644
index 0000000000..b9f915f2c3
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarBase.cpp.gcov.html
@@ -0,0 +1,1164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarBase.cpp<span style="font-size: 80%;"> (source / <a href="MultiColvarBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">583</td>
+            <td class="headerCovTableEntry">652</td>
+            <td class="headerCovTableEntryMed">89.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;MultiColvarFilter.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;vesselbase/Vessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;vesselbase/BridgeVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;vector&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;string&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;limits&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace multicolvar {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        501 : void MultiColvarBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        501 :   Action::registerKeywords( keys );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        501 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        501 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       1002 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        501 :   ActionWithVessel::registerKeywords( keys );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       1002 :   keys.add(&quot;hidden&quot;,&quot;NL_STRIDE&quot;,&quot;the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities &quot;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :            &quot;that contributed less than TOL at the previous neighbor list update step are ignored.&quot;);</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        501 :   keys.setComponentsIntroduction(&quot;When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in &quot;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :                                  &quot;regular collective variables.  The label is used to reference the full set of quantities calculated by &quot;</a>
+<a name="48"><span class="lineNum">      48 </span>            :                                  &quot;the action.  This is usual when using \\ref multicolvarfunction. Generally when doing this the previously calculated &quot;</a>
+<a name="49"><span class="lineNum">      49 </span>            :                                  &quot;multicolvar will be referenced using the DATA keyword rather than ARG.\n\n&quot;</a>
+<a name="50"><span class="lineNum">      50 </span>            :                                  &quot;This Action can be used to calculate the following scalar quantities directly.  These quantities are calculated by &quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :                                  &quot;employing the keywords listed below. &quot;</a>
+<a name="52"><span class="lineNum">      52 </span>            :                                  &quot;These quantities can then be referenced elsewhere in the input file by using this Action's label &quot;</a>
+<a name="53"><span class="lineNum">      53 </span>            :                                  &quot;followed by a dot and the name of the quantity. Some of them can be calculated multiple times &quot;</a>
+<a name="54"><span class="lineNum">      54 </span>            :                                  &quot;with different parameters.  In this case the quantities calculated can be referenced elsewhere in the &quot;</a>
+<a name="55"><span class="lineNum">      55 </span>            :                                  &quot;input by using the name of the quantity followed by a numerical identifier &quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            :                                  &quot;e.g. &lt;em&gt;label&lt;/em&gt;.lessthan-1, &lt;em&gt;label&lt;/em&gt;.lessthan-2 etc.  When doing this and, for clarity we have &quot;</a>
+<a name="57"><span class="lineNum">      57 </span>            :                                  &quot;made it so that the user can set a particular label for each of the components. As such by using the LABEL keyword in the description of the keyword &quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            :                                  &quot;input you can customize the component name&quot;);</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       1002 :   keys.reserve(&quot;atoms-3&quot;,&quot;SPECIES&quot;,&quot;this keyword is used for colvars such as coordination number. In that context it specifies that plumed should calculate &quot;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :                &quot;one coordination number for each of the atoms specified.  Each of these coordination numbers specifies how many of the &quot;</a>
+<a name="61"><span class="lineNum">      61 </span>            :                &quot;other specified atoms are within a certain cutoff of the central atom.  You can specify the atoms here as another multicolvar &quot;</a>
+<a name="62"><span class="lineNum">      62 </span>            :                &quot;action or using a MultiColvarFilter or ActionVolume action.  When you do so the quantity is calculated for those atoms specified &quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            :                &quot;in the previous multicolvar.  This is useful if you would like to calculate the Steinhardt parameter for those atoms that have a &quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            :                &quot;coordination number more than four for example&quot;);</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1002 :   keys.reserve(&quot;atoms-4&quot;,&quot;SPECIESA&quot;,&quot;this keyword is used for colvars such as the coordination number.  In that context it species that plumed should calculate &quot;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :                &quot;one coordination number for each of the atoms specified in SPECIESA.  Each of these coordination numbers specifies how many &quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :                &quot;of the atoms specifies using SPECIESB is within the specified cutoff.  As with the species keyword the input can also be specified &quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            :                &quot;using the label of another multicolvar&quot;);</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1002 :   keys.reserve(&quot;atoms-4&quot;,&quot;SPECIESB&quot;,&quot;this keyword is used for colvars such as the coordination number.  It must appear with SPECIESA.  For a full explanation see &quot;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :                &quot;the documentation for that keyword&quot;);</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1002 :   keys.add(&quot;hidden&quot;,&quot;ALL_INPUT_SAME_TYPE&quot;,&quot;remove this keyword to remove certain checks in the input on the sanity of your input file.  See code for details&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        501 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        351 : MultiColvarBase::MultiColvarBase(const ActionOptions&amp;ao):</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   Action(ao),</a>
+<a name="76"><span class="lineNum">      76 </span>            :   ActionAtomistic(ao),</a>
+<a name="77"><span class="lineNum">      77 </span>            :   ActionWithValue(ao),</a>
+<a name="78"><span class="lineNum">      78 </span>            :   ActionWithVessel(ao),</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        351 :   usepbc(false),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        351 :   allthirdblockintasks(false),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        351 :   uselinkforthree(false),</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        351 :   linkcells(comm),</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        351 :   threecells(comm),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        351 :   setup_completed(false),</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        351 :   atomsWereRetrieved(false),</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        351 :   matsums(false),</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        351 :   usespecies(false),</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        702 :   nblock(0)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        702 :   if( keywords.exists(&quot;NOPBC&quot;) ) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        351 :     bool nopbc=!usepbc; parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        351 :     usepbc=!nopbc;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        702 :   if( keywords.exists(&quot;SPECIESA&quot;) ) { matsums=usespecies=true; }</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        351 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         48 : void MultiColvarBase::readAtomsLikeKeyword( const std::string &amp; key, const int&amp; natoms, std::vector&lt;AtomNumber&gt;&amp; all_atoms ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         48 :   plumed_assert( !usespecies );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         48 :   if( all_atoms.size()&gt;0 ) return;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;AtomNumber&gt; t;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         48 :   for(int i=1;; ++i ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        970 :     parseAtomList(key, i, t );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        970 :     if( t.empty() ) break;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        922 :     log.printf(&quot;  Colvar %d is calculated from atoms : &quot;, i);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       3450 :     for(unsigned j=0; j&lt;t.size(); ++j) log.printf(&quot;%d &quot;,t[j].serial() );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        922 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        922 :     if( i==1 &amp;&amp; natoms&lt;0 ) { ablocks.resize(t.size()); }</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        916 :     else if( i==1 ) ablocks.resize(natoms);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        922 :     if( t.size()!=ablocks.size() ) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :       std::string ss; Tools::convert(i,ss);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :       error(key + ss + &quot; keyword has the wrong number of atoms&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     }</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       3450 :     for(unsigned j=0; j&lt;ablocks.size(); ++j) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       2528 :       ablocks[j].push_back( ablocks.size()*(i-1)+j ); all_atoms.push_back( t[j] );</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       2528 :       atom_lab.push_back( std::pair&lt;unsigned,unsigned&gt;( 0, ablocks.size()*(i-1)+j ) );</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     }</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        922 :     t.resize(0);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        922 :   }</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         48 :   if( all_atoms.size()&gt;0 ) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         48 :     nblock=0;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        970 :     for(unsigned i=0; i&lt;ablocks[0].size(); ++i) addTaskToList( i );</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        471 : bool MultiColvarBase::parseMultiColvarAtomList(const std::string&amp; key, const int&amp; num, std::vector&lt;AtomNumber&gt;&amp; t) {</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector&lt;std::string&gt; mlabs;</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        471 :   if( num&lt;0 ) parseVector(key,mlabs);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   else parseNumberedVector(key,num,mlabs);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        471 :   if( mlabs.size()==0 ) return false;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        323 :   std::string mname; unsigned found_mcolv=mlabs.size();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        450 :   for(unsigned i=0; i&lt;mlabs.size(); ++i) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        328 :     MultiColvarBase* mycolv = plumed.getActionSet().selectWithLabel&lt;MultiColvarBase*&gt;(mlabs[i]);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        328 :     if(!mycolv) { found_mcolv=i; break; }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     // Check all base multicolvars are of same type</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        127 :     if( i==0 ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        122 :       mname = mycolv-&gt;getName();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        244 :       if( keywords.exists(&quot;ALL_INPUT_SAME_TYPE&quot;) &amp;&amp; mycolv-&gt;isPeriodic() ) error(&quot;multicolvar functions don't work with this multicolvar&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     } else {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         10 :       if( keywords.exists(&quot;ALL_INPUT_SAME_TYPE&quot;) &amp;&amp; mname!=mycolv-&gt;getName() ) error(&quot;All input multicolvars must be of same type&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :     }</a>
+<a name="146"><span class="lineNum">     146 </span>            :     // And track which variable stores each colvar</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">    4458438 :     for(unsigned j=0; j&lt;mycolv-&gt;getFullNumberOfTasks(); ++j) atom_lab.push_back( std::pair&lt;unsigned,unsigned&gt;( mybasemulticolvars.size()+1, j ) );</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     // And store the multicolvar base</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        127 :     mybasemulticolvars.push_back( mycolv );</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     // And create a basedata stash</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        127 :     mybasedata.push_back( mybasemulticolvars[mybasemulticolvars.size()-1]-&gt;buildDataStashes( this ) );</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :     // Check if weight has derivatives</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        127 :     if( mybasemulticolvars[ mybasemulticolvars.size()-1 ]-&gt;weightHasDerivatives ) weightHasDerivatives=true;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        127 :     plumed_assert( mybasemulticolvars.size()==mybasedata.size() );</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Have we conventional atoms to read in</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        323 :   if( found_mcolv==0 ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        201 :     std::vector&lt;AtomNumber&gt; tt; ActionAtomistic::interpretAtomList( mlabs, tt );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      89846 :     for(unsigned i=0; i&lt;tt.size(); ++i) { atom_lab.push_back( std::pair&lt;unsigned,unsigned&gt;( 0, t.size() + i ) ); }</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        201 :     log.printf(&quot;  keyword %s takes atoms : &quot;, key.c_str() );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">      89846 :     for(unsigned i=0; i&lt;tt.size(); ++i) { t.push_back( tt[i] ); log.printf(&quot;%d &quot;,tt[i].serial() ); }</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        201 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        122 :   } else if( found_mcolv==mlabs.size() ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        122 :     if( checkNumericalDerivatives() ) error(&quot;cannot use NUMERICAL_DERIVATIVES keyword with dynamic groups as input&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        122 :     log.printf(&quot;  keyword %s takes dynamic groups of atoms constructed from multicolvars labelled : &quot;, key.c_str() );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        249 :     for(unsigned i=0; i&lt;mlabs.size(); ++i) log.printf(&quot;%s &quot;,mlabs[i].c_str() );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        122 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :   } else if( found_mcolv&lt;mlabs.size() ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     error(&quot;cannot mix multicolvar input and atom input in one line&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            :   return true;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        471 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         76 : void MultiColvarBase::readTwoGroups( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, std::vector&lt;AtomNumber&gt;&amp; all_atoms ) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         76 :   plumed_dbg_assert( keywords.exists(key0) &amp;&amp; keywords.exists(key1) &amp;&amp; keywords.exists(key2) ); ablocks.resize( 2 );</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         76 :   if( parseMultiColvarAtomList(key0,-1,all_atoms) ) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         78 :     nblock=atom_lab.size(); for(unsigned i=0; i&lt;2; ++i) ablocks[i].resize(nblock);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         26 :     resizeBookeepingArray( nblock, nblock );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       5486 :     for(unsigned i=0; i&lt;nblock; ++i) ablocks[0][i]=ablocks[1][i]=i;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       5460 :     for(unsigned i=1; i&lt;nblock; ++i) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    4216329 :       for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">    4210895 :         bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">    4210895 :         addTaskToList( i*nblock + j );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">    4210895 :         bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :       }</a>
+<a name="187"><span class="lineNum">     187 </span>            :     }</a>
+<a name="188"><span class="lineNum">     188 </span>            :   } else {</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         50 :     parseMultiColvarAtomList(key1,-1,all_atoms);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         67 :     ablocks[0].resize( atom_lab.size() ); for(unsigned i=0; i&lt;ablocks[0].size(); ++i) ablocks[0][i]=i;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         50 :     parseMultiColvarAtomList(key2,-1,all_atoms);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1119 :     ablocks[1].resize( atom_lab.size() - ablocks[0].size() ); for(unsigned i=0; i&lt;ablocks[1].size(); ++i) ablocks[1][i]=ablocks[0].size() + i;</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         50 :     if( ablocks[0].size()&gt;ablocks[1].size() ) nblock = ablocks[0].size();</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         50 :     else nblock=ablocks[1].size();</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         50 :     resizeBookeepingArray( ablocks[0].size(), ablocks[1].size() );</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         67 :     for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       1126 :       for(unsigned j=0; j&lt;ablocks[1].size(); ++j) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1109 :         bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1109 :         if( atom_lab[ablocks[0][i]].first&gt;0 &amp;&amp; atom_lab[ablocks[1][j]].first&gt;0 ) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :           if( mybasemulticolvars[atom_lab[ablocks[0][i]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[1][j]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :               atom_lab[ablocks[0][i]].second!=atom_lab[ablocks[1][j]].second ) addTaskToList( i*nblock + j );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       1109 :         } else if( all_atoms[atom_lab[ablocks[0][i]].second]!=all_atoms[atom_lab[ablocks[1][j]].second] ) addTaskToList( i*nblock + j );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       1109 :         bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :       }</a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         76 : }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         12 : void MultiColvarBase::readGroupKeywords( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, const std::string&amp; key3,</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     const bool&amp; no_third_dim_accum, const bool&amp; symmetric, std::vector&lt;AtomNumber&gt;&amp; all_atoms ) {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         12 :   plumed_dbg_assert( keywords.exists(key0) &amp;&amp; keywords.exists(key1) &amp;&amp; keywords.exists(key2) &amp;&amp; keywords.exists(key3) ); ablocks.resize( 3 );</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         12 :   if( parseMultiColvarAtomList(key0,-1,all_atoms) ) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         10 :     if( no_third_dim_accum ) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         10 :       nblock=atom_lab.size(); ablocks[0].resize(nblock); ablocks[1].resize( nblock );</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       1481 :       for(unsigned i=0; i&lt;ablocks[0].size(); ++i) ablocks[0][i]=ablocks[1][i]=i;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         10 :       resizeBookeepingArray( nblock, nblock );</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         10 :       if( symmetric ) {</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :         // This ensures that later parts of the code don't switch off allthirdblockintasks</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       1343 :         for(unsigned i=0; i&lt;nblock; ++i) { bookeeping(i,i).first=0; bookeeping(i,i).second=1; }</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       1337 :         for(unsigned i=1; i&lt;nblock; ++i) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     222447 :           for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     221116 :             bookeeping(j,i).first=bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">     221116 :             addTaskToList( i*nblock + j );</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">     221116 :             bookeeping(j,i).second=bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :           }</a>
+<a name="229"><span class="lineNum">     229 </span>            :         }</a>
+<a name="230"><span class="lineNum">     230 </span>            :       } else {</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        138 :         for(unsigned i=0; i&lt;nblock; ++i) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       8344 :           for(unsigned j=0; j&lt;nblock; ++j) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       8210 :             if( i==j ) continue ;</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       8076 :             bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       8076 :             addTaskToList( i*nblock + j );</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       8076 :             bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :           }</a>
+<a name="238"><span class="lineNum">     238 </span>            :         }</a>
+<a name="239"><span class="lineNum">     239 </span>            :       }</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         10 :       if( !parseMultiColvarAtomList(key3,-1,all_atoms) ) error(&quot;missing required keyword &quot; + key3 + &quot; in input&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         10 :       ablocks[2].resize( atom_lab.size() - ablocks[0].size() );</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">      49845 :       for(unsigned i=0; i&lt;ablocks[2].size(); ++i) ablocks[2][i]=ablocks[0].size() + i;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     } else {</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :       nblock=atom_lab.size(); for(unsigned i=0; i&lt;3; ++i) ablocks[i].resize(nblock);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :       resizeBookeepingArray( nblock, nblock );</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;nblock; ++i) { ablocks[0][i]=i; ablocks[1][i]=i; ablocks[2][i]=i; }</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :       if( symmetric ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :         for(unsigned i=2; i&lt;nblock; ++i) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :           for(unsigned j=1; j&lt;i; ++j) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :             bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :             for(unsigned k=0; k&lt;j; ++k) addTaskToList( i*nblock*nblock + j*nblock + k );</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :             bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :           }</a>
+<a name="254"><span class="lineNum">     254 </span>            :         }</a>
+<a name="255"><span class="lineNum">     255 </span>            :       } else {</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;nblock; ++i) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :           for(unsigned j=0; j&lt;nblock; ++j) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :             if( i==j ) continue;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :             bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :             for(unsigned k=0; k&lt;nblock; ++k) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :               if( i!=k &amp;&amp; j!=k ) addTaskToList( i*nblock*nblock + j*nblock + k );</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :             }</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :             bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :           }</a>
+<a name="265"><span class="lineNum">     265 </span>            :         }</a>
+<a name="266"><span class="lineNum">     266 </span>            :       }</a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   } else {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          2 :     readThreeGroups( key1, key2, key3, true, no_third_dim_accum, all_atoms );</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         12 : }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         10 : void MultiColvarBase::readThreeGroups( const std::string&amp; key1, const std::string&amp; key2, const std::string&amp; key3,</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :                                        const bool&amp; allow2, const bool&amp; no_third_dim_accum, std::vector&lt;AtomNumber&gt;&amp; all_atoms ) {</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         10 :   plumed_dbg_assert( keywords.exists(key1) &amp;&amp; keywords.exists(key2) &amp;&amp; keywords.exists(key3) ); ablocks.resize( 3 );</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         10 :   bool readkey1=parseMultiColvarAtomList(key1,-1,all_atoms);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         31 :   ablocks[0].resize( atom_lab.size() ); for(unsigned i=0; i&lt;ablocks[0].size(); ++i) ablocks[0][i]=i;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         10 :   bool readkey2=parseMultiColvarAtomList(key2,-1,all_atoms);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         10 :   if( !readkey1 &amp;&amp; !readkey2 ) return ;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        225 :   ablocks[1].resize( atom_lab.size() - ablocks[0].size() ); for(unsigned i=0; i&lt;ablocks[1].size(); ++i) ablocks[1][i]=ablocks[0].size() + i;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         10 :   resizeBookeepingArray( ablocks[0].size(), ablocks[1].size() );</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         10 :   bool readkey3=parseMultiColvarAtomList(key3,-1,all_atoms);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         10 :   if( !readkey3 &amp;&amp; !allow2 ) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     error(&quot;missing atom specification &quot; + key3);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         10 :   } else if( !readkey3 ) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          2 :     if( ablocks[1].size()&gt;ablocks[0].size() ) nblock=ablocks[1].size();</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :     else nblock=ablocks[0].size();</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          2 :     ablocks[2].resize( ablocks[1].size() );</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        200 :     for(unsigned i=0; i&lt;ablocks[1].size(); ++i) ablocks[2][i]=ablocks[0].size() + i;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        198 :       for(unsigned j=1; j&lt;ablocks[1].size(); ++j) {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        196 :         bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       9898 :         for(unsigned k=0; k&lt;j; ++k) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       9702 :           if( atom_lab[ablocks[0][i]].first&gt;0 &amp;&amp; atom_lab[ablocks[1][j]].first&gt;0 &amp;&amp; atom_lab[ablocks[2][k]].first&gt;0 ) {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :             if( mybasemulticolvars[atom_lab[ablocks[0][i]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[1][j]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :                 mybasemulticolvars[atom_lab[ablocks[0][i]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[2][k]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :                 mybasemulticolvars[atom_lab[ablocks[1][j]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[2][k]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :                 atom_lab[ablocks[0][i]].second!=atom_lab[ablocks[1][j]].second &amp;&amp; atom_lab[ablocks[0][i]].second!=atom_lab[ablocks[2][k]].second &amp;&amp;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :                 atom_lab[ablocks[1][j]].second!=atom_lab[ablocks[2][k]].second )  addTaskToList( nblock*nblock*i + nblock*j + k );</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       9702 :           } else if( all_atoms[atom_lab[ablocks[0][i]].second]!=all_atoms[atom_lab[ablocks[1][j]].second] &amp;&amp;</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       9702 :                      all_atoms[atom_lab[ablocks[0][i]].second]!=all_atoms[atom_lab[ablocks[2][k]].second] &amp;&amp;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       9702 :                      all_atoms[atom_lab[ablocks[1][j]].second]!=all_atoms[atom_lab[ablocks[2][k]].second] ) addTaskToList( nblock*nblock*i + nblock*j + k );</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :         }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">        196 :         bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :       }</a>
+<a name="310"><span class="lineNum">     310 </span>            :     }</a>
+<a name="311"><span class="lineNum">     311 </span>            :   } else {</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          8 :     ablocks[2].resize( atom_lab.size() - ablocks[1].size() - ablocks[0].size() );</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       3182 :     for(unsigned i=0; i&lt;ablocks[2].size(); ++i) ablocks[2][i] = ablocks[0].size() + ablocks[1].size() + i;</span></a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          8 :     if( ablocks[1].size()&gt;ablocks[0].size() ) nblock=ablocks[1].size();</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          8 :     else nblock=ablocks[0].size();</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          8 :     if( ablocks[2].size()&gt;nblock ) nblock=ablocks[2].size();</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          8 :     unsigned  kcount; if( no_third_dim_accum ) kcount=1; else kcount=ablocks[2].size();</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         27 :     for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        128 :       for(unsigned j=0; j&lt;ablocks[1].size(); ++j) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        109 :         bookeeping(i,j).first=getFullNumberOfTasks();</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        218 :         for(unsigned k=0; k&lt;kcount; ++k) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        109 :           if( no_third_dim_accum ) addTaskToList( nblock*i + j  );</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :           else if( atom_lab[ablocks[0][i]].first&gt;0 &amp;&amp; atom_lab[ablocks[1][j]].first&gt;0 &amp;&amp; atom_lab[ablocks[2][k]].first&gt;0 ) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :             if( mybasemulticolvars[atom_lab[ablocks[0][i]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[1][j]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :                 mybasemulticolvars[atom_lab[ablocks[0][i]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[2][k]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :                 mybasemulticolvars[atom_lab[ablocks[1][j]].first-1]-&gt;getLabel()!=mybasemulticolvars[atom_lab[ablocks[2][k]].first-1]-&gt;getLabel() &amp;&amp;</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :                 atom_lab[ablocks[0][i]].second!=atom_lab[ablocks[1][j]].second &amp;&amp; atom_lab[ablocks[0][i]].second!=atom_lab[ablocks[2][k]].second &amp;&amp;</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :                 atom_lab[ablocks[1][j]].second!=atom_lab[ablocks[2][k]].second ) addTaskToList( nblock*nblock*i + nblock*j + k );</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :           } else if( all_atoms[atom_lab[ablocks[0][i]].second]!=all_atoms[atom_lab[ablocks[1][j]].second] &amp;&amp;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :                      all_atoms[atom_lab[ablocks[0][i]].second]!=all_atoms[atom_lab[ablocks[2][k]].second] &amp;&amp;</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :                      all_atoms[atom_lab[ablocks[1][j]].second]!=all_atoms[atom_lab[ablocks[2][k]].second] ) addTaskToList( nblock*nblock*i + nblock*j + k );</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :         }</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        109 :         bookeeping(i,j).second=getFullNumberOfTasks();</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :       }</a>
+<a name="338"><span class="lineNum">     338 </span>            :     }</a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span>            : }</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          4 : void MultiColvarBase::buildSets() {</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   std::vector&lt;AtomNumber&gt; fake_atoms;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          8 :   if( !parseMultiColvarAtomList(&quot;DATA&quot;,-1,fake_atoms) ) error(&quot;missing DATA keyword&quot;);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          4 :   if( fake_atoms.size()&gt;0 ) error(&quot;no atoms should appear in the specification for this object.  Input should be other multicolvars&quot;);</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          4 :   nblock = mybasemulticolvars[0]-&gt;getFullNumberOfTasks();</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         11 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          7 :     if( mybasemulticolvars[i]-&gt;getFullNumberOfTasks()!=nblock ) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :       error(&quot;mismatch between numbers of tasks in various base multicolvars&quot;);</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :     }</a>
+<a name="352"><span class="lineNum">     352 </span>            :   }</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          4 :   ablocks.resize( mybasemulticolvars.size() ); usespecies=false;</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         11 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          7 :     ablocks[i].resize( nblock );</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         27 :     for(unsigned j=0; j&lt;nblock; ++j) ablocks[i][j]=i*nblock+j;</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   }</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;nblock; ++i) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         11 :     if( mybasemulticolvars.size()&lt;4 ) {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         11 :       unsigned cvcode=0, tmpc=1;</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         31 :       for(unsigned j=0; j&lt;ablocks.size(); ++j) { cvcode += i*tmpc; tmpc *= nblock; }</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         11 :       addTaskToList( cvcode );</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :     } else {</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :       addTaskToList( i );</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :     }</a>
+<a name="366"><span class="lineNum">     366 </span>            :   }</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          4 :   mybasedata[0]-&gt;resizeTemporyMultiValues( mybasemulticolvars.size() ); setupMultiColvarBase( fake_atoms );</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          4 : }</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">   12512702 : void MultiColvarBase::addTaskToList( const unsigned&amp; taskCode ) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">   12512702 :   plumed_assert( getNumberOfVessels()==0 );</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">   12512702 :   ActionWithVessel::addTaskToList( taskCode );</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">   12512702 : }</span></a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         96 : void MultiColvarBase::resizeBookeepingArray( const unsigned&amp; num1, const unsigned&amp; num2 ) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         96 :   bookeeping.resize( num1, num2 );</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">       7065 :   for(unsigned i=0; i&lt;num1; ++i) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">    8887414 :     for(unsigned j=0; j&lt;num2; ++j) { bookeeping(i,j).first=0; bookeeping(i,j).second=0; }</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         96 : }</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        309 : void MultiColvarBase::setupMultiColvarBase( const std::vector&lt;AtomNumber&gt;&amp; atoms ) {</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        309 :   if( !matsums &amp;&amp; atom_lab.size()==0 ) error(&quot;No atoms have been read in&quot;);</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="385"><span class="lineNum">     385 </span>            :   // Setup decoder array</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        309 :   if( !usespecies &amp;&amp; nblock&gt;0 ) {</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         63 :     ncentral=ablocks.size(); use_for_central_atom.resize( ablocks.size(), true );</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         63 :     numberForCentralAtom = 1.0 / static_cast&lt;double&gt;( ablocks.size() );</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         63 :     if( ablocks.size()==3 ) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         20 :       allthirdblockintasks=uselinkforthree=true;</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       1512 :       for(unsigned i=0; i&lt;bookeeping.nrows(); ++i) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">     453578 :         for(unsigned j=0; j&lt;bookeeping.ncols(); ++j) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">     452086 :           unsigned ntper = bookeeping(i,j).second - bookeeping(i,j).first;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">     452086 :           if( i==j &amp;&amp; ntper==0 ) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        136 :             continue;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">     451950 :           } else if( ntper == 1 &amp;&amp; allthirdblockintasks ) {</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">     451756 :             allthirdblockintasks=true;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">        194 :           } else if( ntper != ablocks[2].size() ) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        194 :             allthirdblockintasks=uselinkforthree=false;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :           } else {</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :             allthirdblockintasks=false;</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :           }</a>
+<a name="404"><span class="lineNum">     404 </span>            :         }</a>
+<a name="405"><span class="lineNum">     405 </span>            :       }</a>
+<a name="406"><span class="lineNum">     406 </span>            :     }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         63 :     if( allthirdblockintasks ) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         18 :       decoder.resize(2); plumed_assert( ablocks.size()==3 );</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :       // Check if number of atoms is too large</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         18 :       if( std::pow( double(nblock), 2.0 )&gt;std::numeric_limits&lt;unsigned&gt;::max() ) error(&quot;number of atoms in groups is too big for PLUMED to handle&quot;);</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :     } else {</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         45 :       decoder.resize( ablocks.size() );</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :       // Check if number of atoms is too large</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">         45 :       if( std::pow( double(nblock), double(ablocks.size()) )&gt;std::numeric_limits&lt;unsigned&gt;::max() ) error(&quot;number of atoms in groups is too big for PLUMED to handle&quot;);</span></a>
+<a name="416"><span class="lineNum">     416 </span>            :     }</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">        190 :     unsigned code=1; for(unsigned i=0; i&lt;decoder.size(); ++i) { decoder[decoder.size()-1-i]=code; code *= nblock; }</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">        246 :   } else if( !usespecies ) {</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         87 :     ncentral=ablocks.size(); use_for_central_atom.resize( ablocks.size(), true );</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         87 :     numberForCentralAtom = 1.0 / static_cast&lt;double&gt;( ablocks.size() );</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        318 :   } else if( keywords.exists(&quot;SPECIESA&quot;) ) {</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        101 :     plumed_assert( atom_lab.size()==0 &amp;&amp; all_atoms.size()==0 );</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        101 :     ablocks.resize( 1 ); bool readspecies=parseMultiColvarAtomList(&quot;SPECIES&quot;, -1, all_atoms);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        101 :     if( readspecies ) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">      41493 :       ablocks[0].resize( atom_lab.size() ); for(unsigned i=0; i&lt;atom_lab.size(); ++i) { addTaskToList(i); ablocks[0][i]=i; }</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     } else {</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         40 :       if( !parseMultiColvarAtomList(&quot;SPECIESA&quot;, -1, all_atoms) ) error(&quot;missing SPECIES/SPECIESA keyword&quot;);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         20 :       unsigned nat1=atom_lab.size();</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         40 :       if( !parseMultiColvarAtomList(&quot;SPECIESB&quot;, -1, all_atoms) ) error(&quot;missing SPECIESB keyword&quot;);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         20 :       unsigned nat2=atom_lab.size() - nat1;</span></a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        759 :       for(unsigned i=0; i&lt;nat1; ++i) addTaskToList(i);</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         20 :       ablocks[0].resize( nat2 );</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">       3726 :       for(unsigned i=0; i&lt;nat2; ++i) {</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :         bool found=false; unsigned inum=0;</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">     288729 :         for(unsigned j=0; j&lt;nat1; ++j) {</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">     285201 :           if( atom_lab[nat1+i].first&gt;0 &amp;&amp; atom_lab[j].first&gt;0 ) {</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">     252720 :             if( atom_lab[nat1+i].first==atom_lab[j].first &amp;&amp;</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :                 mybasemulticolvars[atom_lab[nat1+i].first-1]-&gt;getAbsoluteIndexOfCentralAtom(atom_lab[nat1+i].second)==</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">     252720 :                 mybasemulticolvars[atom_lab[j].first-1]-&gt;getAbsoluteIndexOfCentralAtom(atom_lab[j].second) ) { found=true; inum=j; break; }</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">      32481 :           } else if( atom_lab[nat1+i].first&gt;0 ) {</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineNoCov">          0 :             if( mybasemulticolvars[atom_lab[nat1+i].first-1]-&gt;getAbsoluteIndexOfCentralAtom(atom_lab[nat1+i].second)==</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :                 all_atoms[atom_lab[j].second] ) { found=true; inum=nat1 + i; break; }</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">      32481 :           } else if( atom_lab[j].first&gt;0 ) {</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :             if( all_atoms[atom_lab[nat1+i].second]==</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :                 mybasemulticolvars[atom_lab[j].first-1]-&gt;getAbsoluteIndexOfCentralAtom(atom_lab[j].second) ) { found=true; inum=nat1+i; break; }</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">      32481 :           } else if( all_atoms[atom_lab[nat1+i].second]==all_atoms[atom_lab[j].second] ) { found=true; inum=j; break; }</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :         }</a>
+<a name="449"><span class="lineNum">     449 </span>            :         // This prevents mistakes being made in colvar setup</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">        178 :         if( found ) { ablocks[0][i]=inum; }</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">       3528 :         else { ablocks[0][i]=nat1 + i; }</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :       }</a>
+<a name="453"><span class="lineNum">     453 </span>            :     }</a>
+<a name="454"><span class="lineNum">     454 </span>            :   }</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">        309 :   if( mybasemulticolvars.size()&gt;0 ) {</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        246 :     for(unsigned i=0; i&lt;mybasedata.size(); ++i) {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        127 :       mybasedata[i]-&gt;resizeTemporyMultiValues(2); mybasemulticolvars[i]-&gt;my_tmp_capacks.resize(2);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :     }</a>
+<a name="459"><span class="lineNum">     459 </span>            :   }</a>
+<a name="460"><span class="lineNum">     460 </span>            : </a>
+<a name="461"><span class="lineNum">     461 </span>            :   // Copy lists of atoms involved from base multicolvars</a>
+<a name="462"><span class="lineNum">     462 </span>            :   std::vector&lt;AtomNumber&gt; tmp_atoms;</a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">        436 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        127 :     tmp_atoms=mybasemulticolvars[i]-&gt;getAbsoluteIndexes();</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">     416316 :     for(unsigned j=0; j&lt;tmp_atoms.size(); ++j) all_atoms.push_back( tmp_atoms[j] );</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :   }</a>
+<a name="467"><span class="lineNum">     467 </span>            :   // Copy atom lists from input</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">      59576 :   for(unsigned i=0; i&lt;atoms.size(); ++i) all_atoms.push_back( atoms[i] );</span></a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            :   // Now make sure we get all the atom positions</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">        309 :   ActionAtomistic::requestAtoms( all_atoms );</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :   // And setup dependencies</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">        436 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) addDependency( mybasemulticolvars[i] );</span></a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            :   // Setup underlying ActionWithVessel</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">        309 :   readVesselKeywords();</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">        309 : }</span></a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         19 : void MultiColvarBase::setAtomsForCentralAtom( const std::vector&lt;bool&gt;&amp; catom_ind ) {</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         19 :   unsigned nat=0; plumed_assert( catom_ind.size()==ablocks.size() );</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         89 :   for(unsigned i=0; i&lt;catom_ind.size(); ++i) {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         70 :     use_for_central_atom[i]=catom_ind[i];</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         70 :     if( use_for_central_atom[i] ) nat++;</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :   }</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         19 :   plumed_dbg_assert( nat&gt;0 ); ncentral=nat;</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         19 :   numberForCentralAtom = 1.0 / static_cast&lt;double&gt;( nat );</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">         19 : }</span></a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">        429 : void MultiColvarBase::turnOnDerivatives() {</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        429 :   ActionWithValue::turnOnDerivatives();</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        429 :   needsDerivatives();</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        429 :   forcesToApply.resize( getNumberOfDerivatives() );</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        429 : }</span></a>
+<a name="494"><span class="lineNum">     494 </span>            : </a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">        192 : void MultiColvarBase::setLinkCellCutoff( const double&amp; lcut, double tcut ) {</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">        192 :   plumed_assert( usespecies || ablocks.size()&lt;4 );</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">        192 :   if( tcut&lt;0 ) tcut=lcut;</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        192 :   if( !linkcells.enabled() ) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        192 :     linkcells.setCutoff( lcut );</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        192 :     threecells.setCutoff( tcut );</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :   } else {</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :     if( lcut&gt;linkcells.getCutoff() ) linkcells.setCutoff( lcut );</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :     if( tcut&gt;threecells.getCutoff() ) threecells.setCutoff( tcut );</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :   }</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">        192 : }</span></a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">          8 : double MultiColvarBase::getLinkCellCutoff()  const {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          8 :   return linkcells.getCutoff();</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">       1939 : void MultiColvarBase::setupLinkCells() {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">       1939 :   if( (!usespecies &amp;&amp; nblock==0) || !linkcells.enabled() ) return ;</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :   // Retrieve any atoms that haven't already been retrieved</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">       1319 :   for(std::vector&lt;MultiColvarBase*&gt;::iterator p=mybasemulticolvars.begin(); p!=mybasemulticolvars.end(); ++p) {</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        203 :     (*p)-&gt;retrieveAtoms();</span></a>
+<a name="517"><span class="lineNum">     517 </span>            :   }</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">       1116 :   retrieveAtoms();</span></a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            :   unsigned iblock;</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">       1116 :   if( usespecies ) {</span></a>
+<a name="522"><span class="lineNum">     522 </span>            :     iblock=0;</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">        217 :   } else if( ablocks.size()&lt;4 ) {</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :     iblock=1;</a>
+<a name="525"><span class="lineNum">     525 </span>            :   } else {</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :   }</a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span>            :   // Count number of currently active atoms</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">       1116 :   nactive_atoms=0;</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">     387954 :   for(unsigned i=0; i&lt;ablocks[iblock].size(); ++i) {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">     386838 :     if( isCurrentlyActive( ablocks[iblock][i] ) ) nactive_atoms++;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">       1116 :   if( nactive_atoms&gt;0 ) {</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">       1116 :     std::vector&lt;Vector&gt; ltmp_pos( nactive_atoms );</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">       1116 :     std::vector&lt;unsigned&gt; ltmp_ind( nactive_atoms );</span></a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">       1116 :     nactive_atoms=0;</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">       1116 :     if( usespecies ) {</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">     366639 :       for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">     365740 :         if( !isCurrentlyActive( ablocks[0][i] ) ) continue;</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">     365644 :         ltmp_ind[nactive_atoms]=ablocks[0][i];</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">     365644 :         ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ltmp_ind[nactive_atoms] );</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">     365644 :         nactive_atoms++;</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :       }</a>
+<a name="547"><span class="lineNum">     547 </span>            :     } else {</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">      21315 :       for(unsigned i=0; i&lt;ablocks[1].size(); ++i) {</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">      21098 :         if( !isCurrentlyActive( ablocks[1][i] ) ) continue;</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">      16178 :         ltmp_ind[nactive_atoms]=i;</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">      16178 :         ltmp_pos[nactive_atoms]=getPositionOfAtomForLinkCells( ablocks[1][i] );</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">      16178 :         nactive_atoms++;</span></a>
+<a name="553"><span class="lineNum">     553 </span>            :       }</a>
+<a name="554"><span class="lineNum">     554 </span>            :     }</a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            :     // Build the lists for the link cells</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">       1116 :     linkcells.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span>            : }</a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">       4628 : void MultiColvarBase::setupNonUseSpeciesLinkCells( const unsigned&amp; my_always_active ) {</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">       4628 :   plumed_assert( !usespecies );</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">       4628 :   if( nblock==0 || !linkcells.enabled() ) return ;</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">        210 :   deactivateAllTasks();</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :   std::vector&lt;unsigned&gt; requiredlinkcells;</a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">        210 :   if( !uselinkforthree &amp;&amp; nactive_atoms&gt;0 ) {</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :     // Get some parallel info</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">        156 :     unsigned stride=comm.Get_size();</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">        156 :     unsigned rank=comm.Get_rank();</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">        156 :     if( serialCalculation() ) { stride=1; rank=0; }</span></a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span>            :     // Ensure we only do tasks where atoms are in appropriate link cells</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        156 :     std::vector&lt;unsigned&gt; linked_atoms( 1+ablocks[1].size() );</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">       5757 :     for(unsigned i=rank; i&lt;ablocks[0].size(); i+=stride) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">       5601 :       if( !isCurrentlyActive( ablocks[0][i] ) ) continue;</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">       2622 :       unsigned natomsper=1; linked_atoms[0]=my_always_active;  // Note we always check atom 0 because it is simpler than changing LinkCells.cpp</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">       2622 :       linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), requiredlinkcells, natomsper, linked_atoms );</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">     205705 :       for(unsigned j=0; j&lt;natomsper; ++j) {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">     353118 :         for(unsigned k=bookeeping(i,linked_atoms[j]).first; k&lt;bookeeping(i,linked_atoms[j]).second; ++k) taskFlags[k]=1;</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :       }</a>
+<a name="582"><span class="lineNum">     582 </span>            :     }</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">        210 :   } else if( nactive_atoms&gt;0 ) {</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :     // Get some parallel info</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         54 :     unsigned stride=comm.Get_size();</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">         54 :     unsigned rank=comm.Get_rank();</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         54 :     if( serialCalculation() ) { stride=1; rank=0; }</span></a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span>            :     unsigned nactive_three=0;</a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">      66599 :     for(unsigned i=0; i&lt;ablocks[2].size(); ++i) {</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">      66545 :       if( isCurrentlyActive( ablocks[2][i] ) ) nactive_three++;</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :     }</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         54 :     std::vector&lt;Vector&gt; lttmp_pos( nactive_three );</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         54 :     std::vector&lt;unsigned&gt; lttmp_ind( nactive_three );</span></a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span>            :     nactive_three=0;</a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         54 :     if( allthirdblockintasks ) {</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">      66599 :       for(unsigned i=0; i&lt;ablocks[2].size(); ++i) {</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">      66545 :         if( !isCurrentlyActive( ablocks[2][i] ) ) continue;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">      66545 :         lttmp_ind[nactive_three]=ablocks[2][i];</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">      66545 :         lttmp_pos[nactive_three]=getPositionOfAtomForLinkCells( ablocks[2][i] );</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">      66545 :         nactive_three++;</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :       }</a>
+<a name="605"><span class="lineNum">     605 </span>            :     } else {</a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;ablocks[2].size(); ++i) {</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :         if( !isCurrentlyActive( ablocks[2][i] ) ) continue;</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :         lttmp_ind[nactive_three]=i;</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :         lttmp_pos[nactive_three]=getPositionOfAtomForLinkCells( ablocks[2][i] );</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 :         nactive_three++;</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :       }</a>
+<a name="612"><span class="lineNum">     612 </span>            :     }</a>
+<a name="613"><span class="lineNum">     613 </span>            :     // Build the list of the link cells</a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         54 :     threecells.buildCellLists( lttmp_pos, lttmp_ind, getPbc() );</span></a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span>            :     // Ensure we only do tasks where atoms are in appropriate link cells</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">         54 :     std::vector&lt;unsigned&gt; linked_atoms( 1+ablocks[1].size() );</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         54 :     std::vector&lt;unsigned&gt; tlinked_atoms( 1+ablocks[2].size() );</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        633 :     for(unsigned i=rank; i&lt;ablocks[0].size(); i+=stride) {</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">        579 :       if( !isCurrentlyActive( ablocks[0][i] ) ) continue;</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">        579 :       unsigned natomsper=1; linked_atoms[0]=my_always_active;  // Note we always check atom 0 because it is simpler than changing LinkCells.cpp</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        579 :       linkcells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), requiredlinkcells, natomsper, linked_atoms );</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        579 :       if( allthirdblockintasks ) {</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">      71832 :         for(unsigned j=0; j&lt;natomsper; ++j) {</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">     142372 :           for(unsigned k=bookeeping(i,linked_atoms[j]).first; k&lt;bookeeping(i,linked_atoms[j]).second; ++k) taskFlags[k]=1;</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :         }</a>
+<a name="627"><span class="lineNum">     627 </span>            :       } else {</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :         unsigned ntatomsper=1; tlinked_atoms[0]=lttmp_ind[0];</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :         threecells.retrieveNeighboringAtoms( getPositionOfAtomForLinkCells( ablocks[0][i] ), requiredlinkcells, ntatomsper, tlinked_atoms );</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;natomsper; ++j) {</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :           for(unsigned k=0; k&lt;ntatomsper; ++k) taskFlags[bookeeping(i,linked_atoms[j]).first+tlinked_atoms[k]]=1;</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :         }</a>
+<a name="633"><span class="lineNum">     633 </span>            :       }</a>
+<a name="634"><span class="lineNum">     634 </span>            :     }</a>
+<a name="635"><span class="lineNum">     635 </span>            :   }</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">        210 :   if( !serialCalculation() ) comm.Sum( taskFlags );</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">        210 :   lockContributors();</span></a>
+<a name="638"><span class="lineNum">     638 </span>            : }</a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">     245988 : void MultiColvarBase::decodeIndexToAtoms( const unsigned&amp; taskCode, std::vector&lt;unsigned&gt;&amp; atoms ) const {</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :   plumed_dbg_assert( !usespecies &amp;&amp; nblock&gt;0 );</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">     245988 :   if( atoms.size()!=decoder.size() ) atoms.resize( decoder.size() );</span></a>
+<a name="643"><span class="lineNum">     643 </span>            : </a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">     245988 :   unsigned scode = taskCode;</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">     786464 :   for(unsigned i=0; i&lt;decoder.size(); ++i) {</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">     540476 :     unsigned ind=( scode / decoder[i] );</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">     540476 :     atoms[i] = ablocks[i][ind];</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">     540476 :     scode -= ind*decoder[i];</span></a>
+<a name="649"><span class="lineNum">     649 </span>            :   }</a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">     245988 : }</span></a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">     451503 : bool MultiColvarBase::setupCurrentAtomList( const unsigned&amp; taskCode, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">     451503 :   if( isDensity() ) {</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">      19070 :     myatoms.setNumberOfAtoms( 1 ); myatoms.setAtom( 0, taskCode ); return true;</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">     432433 :   } else if( usespecies ) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">     180847 :     std::vector&lt;unsigned&gt; task_atoms(1); task_atoms[0]=taskCode;</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">     180847 :     unsigned natomsper=myatoms.setupAtomsFromLinkCells( task_atoms, getPositionOfAtomForLinkCells( taskCode ), linkcells );</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">     180847 :     return natomsper&gt;1;</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">     251586 :   } else if( matsums ) {</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :     myatoms.setNumberOfAtoms( getNumberOfAtoms() );</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">      52798 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) myatoms.setAtom( i, i );</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">     251145 :   } else if( allthirdblockintasks ) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">      39816 :     plumed_dbg_assert( ablocks.size()==3 ); std::vector&lt;unsigned&gt; atoms(2); decodeIndexToAtoms( taskCode, atoms );</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">      39816 :     myatoms.setupAtomsFromLinkCells( atoms, getPositionOfAtomForLinkCells( atoms[0] ), threecells );</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">     211329 :   } else if( nblock&gt;0 ) {</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">     179551 :     std::vector&lt;unsigned&gt; atoms( ablocks.size() );</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">     179551 :     decodeIndexToAtoms( taskCode, atoms ); myatoms.setNumberOfAtoms( ablocks.size() );</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">     587153 :     for(unsigned i=0; i&lt;ablocks.size(); ++i) myatoms.setAtom( i, atoms[i] );</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :   } else {</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">      31778 :     myatoms.setNumberOfAtoms( ablocks.size() );</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">     124498 :     for(unsigned i=0; i&lt;ablocks.size(); ++i) myatoms.setAtom( i, ablocks[i][taskCode] );</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :   }</a>
+<a name="673"><span class="lineNum">     673 </span>            :   return true;</a>
+<a name="674"><span class="lineNum">     674 </span>            : }</a>
+<a name="675"><span class="lineNum">     675 </span>            : </a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">       9074 : void MultiColvarBase::setupActiveTaskSet( std::vector&lt;unsigned&gt;&amp; active_tasks, const std::string&amp; input_label ) {</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">       9074 :   if( !setup_completed ) {</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :     bool justVolumes=false;</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">       1931 :     if( usespecies ) {</span></a>
+<a name="680"><span class="lineNum">     680 </span>            :       justVolumes=true;</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">       1438 :       for(unsigned i=0; i&lt;getNumberOfVessels(); ++i) {</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">       1318 :         vesselbase::StoreDataVessel* mys=dynamic_cast&lt;vesselbase::StoreDataVessel*&gt;( getPntrToVessel(i) );</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">       1318 :         if( mys ) continue;</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">        810 :         vesselbase::BridgeVessel* myb=dynamic_cast&lt;vesselbase::BridgeVessel*&gt;( getPntrToVessel(i) );</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">        810 :         if( !myb ) { justVolumes=false; break; }</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         38 :         ActionVolume* myv=dynamic_cast&lt;ActionVolume*&gt;( myb-&gt;getOutputAction() );</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">         38 :         if( !myv ) { justVolumes=false; break; }</span></a>
+<a name="688"><span class="lineNum">     688 </span>            :       }</a>
+<a name="689"><span class="lineNum">     689 </span>            :     }</a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">       1931 :     deactivateAllTasks();</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">       1931 :     if( justVolumes &amp;&amp; mydata ) {</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         88 :       if( mydata-&gt;getNumberOfDataUsers()==0 ) justVolumes=false;</span></a>
+<a name="693"><span class="lineNum">     693 </span>            : </a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">        137 :       for(unsigned i=0; i&lt;mydata-&gt;getNumberOfDataUsers(); ++i) {</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">         49 :         MultiColvarBase* myu=dynamic_cast&lt;MultiColvarBase*&gt;( mydata-&gt;getDataUser(i) );</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">         49 :         if( myu ) {</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         49 :           myu-&gt;setupActiveTaskSet( taskFlags, getLabel() );</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :         } else {</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :           for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="700"><span class="lineNum">     700 </span>            :         }</a>
+<a name="701"><span class="lineNum">     701 </span>            :       }</a>
+<a name="702"><span class="lineNum">     702 </span>            :     }</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">       1931 :     if( justVolumes ) {</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">        160 :       for(unsigned j=0; j&lt;getNumberOfVessels(); ++j) {</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         80 :         vesselbase::BridgeVessel* myb=dynamic_cast&lt;vesselbase::BridgeVessel*&gt;( getPntrToVessel(j) );</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">         80 :         if( !myb ) continue ;</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         32 :         ActionVolume* myv=dynamic_cast&lt;ActionVolume*&gt;( myb-&gt;getOutputAction() );</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">         32 :         if( !myv ) continue ;</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         32 :         myv-&gt;retrieveAtoms(); myv-&gt;setupRegions();</span></a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">     148161 :         for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) {</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">     148129 :           if( myv-&gt;inVolumeOfInterest(i) ) taskFlags[i]=1;</span></a>
+<a name="713"><span class="lineNum">     713 </span>            :         }</a>
+<a name="714"><span class="lineNum">     714 </span>            :       }</a>
+<a name="715"><span class="lineNum">     715 </span>            :     } else {</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">    4886702 :       for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="717"><span class="lineNum">     717 </span>            :     }</a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            :     // Now activate all this class</a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">       1931 :     lockContributors();</span></a>
+<a name="721"><span class="lineNum">     721 </span>            :     // Setup the link cells</a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">       1931 :     setupLinkCells();</span></a>
+<a name="723"><span class="lineNum">     723 </span>            :     // Ensures that setup is not performed multiple times during one cycle</a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">       1931 :     setup_completed=true;</span></a>
+<a name="725"><span class="lineNum">     725 </span>            :   }</a>
+<a name="726"><span class="lineNum">     726 </span>            : </a>
+<a name="727"><span class="lineNum">     727 </span>            :   // And activate the tasks in input action</a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">       9074 :   if( getLabel()!=input_label ) {</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :     int input_code=-1;</a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">         61 :     for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">         61 :       if( mybasemulticolvars[i]-&gt;getLabel()==input_label ) { input_code=i+1; break; }</span></a>
+<a name="732"><span class="lineNum">     732 </span>            :     }</a>
+<a name="733"><span class="lineNum">     733 </span>            : </a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">         49 :     MultiValue my_tvals( getNumberOfQuantities(), getNumberOfDerivatives() );</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         49 :     AtomValuePack mytmp_atoms( my_tvals, this );</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">     148234 :     for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) {</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">     148185 :       if( !taskIsCurrentlyActive(i) ) continue;</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">       3529 :       setupCurrentAtomList( getTaskCode(i), mytmp_atoms );</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">     254796 :       for(unsigned j=0; j&lt;mytmp_atoms.getNumberOfAtoms(); ++j) {</span></a>
+<a name="740"><span class="lineNum">     740 </span>            :         unsigned itask=mytmp_atoms.getIndex(j);</a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">     251267 :         if( atom_lab[itask].first==input_code ) active_tasks[ atom_lab[itask].second ]=1;</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :       }</a>
+<a name="743"><span class="lineNum">     743 </span>            :     }</a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">         49 :   }</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">       9074 : }</span></a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">        467 : bool MultiColvarBase::filtersUsedAsInput() {</span></a>
+<a name="748"><span class="lineNum">     748 </span>            :   bool inputAreFilters=false;</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">        728 :   for(unsigned i=0; i&lt;mybasemulticolvars.size(); ++i) {</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">        261 :     MultiColvarFilter* myfilt=dynamic_cast&lt;MultiColvarFilter*&gt;( mybasemulticolvars[i] );</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">        261 :     if( myfilt || mybasemulticolvars[i]-&gt;filtersUsedAsInput() ) inputAreFilters=true;</span></a>
+<a name="752"><span class="lineNum">     752 </span>            :   }</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">        467 :   return inputAreFilters;</span></a>
+<a name="754"><span class="lineNum">     754 </span>            : }</a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">       9025 : void MultiColvarBase::calculate() {</span></a>
+<a name="757"><span class="lineNum">     757 </span>            :   // Recursive function that sets up tasks</a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">       9025 :   setupActiveTaskSet( taskFlags, getLabel() );</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            :   // Check for filters and rerun setup of link cells if there are any</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">       9025 :   if( mybasemulticolvars.size()&gt;0 &amp;&amp; filtersUsedAsInput() ) setupLinkCells();</span></a>
+<a name="762"><span class="lineNum">     762 </span>            : </a>
+<a name="763"><span class="lineNum">     763 </span>            :   //  Setup the link cells if we are not using species</a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">       9025 :   if( !usespecies &amp;&amp; ablocks.size()&gt;1 ) {</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :     // This loop finds the first active atom, which is always checked because</a>
+<a name="766"><span class="lineNum">     766 </span>            :     // of a peculiarity in linkcells</a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       4628 :     unsigned first_active=std::numeric_limits&lt;unsigned&gt;::max();</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">       4762 :     for(unsigned i=0; i&lt;ablocks[0].size(); ++i) {</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">       4762 :       if( !isCurrentlyActive( ablocks[1][i] ) ) continue;</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :       else {</a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">       4628 :         first_active=i; break;</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :       }</a>
+<a name="773"><span class="lineNum">     773 </span>            :     }</a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">       4628 :     setupNonUseSpeciesLinkCells( first_active );</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :   }</a>
+<a name="776"><span class="lineNum">     776 </span>            :   // And run all tasks</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">       9025 :   runAllTasks();</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">       9025 : }</span></a>
+<a name="779"><span class="lineNum">     779 </span>            : </a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">        213 : void MultiColvarBase::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">        213 :   if( mybasemulticolvars.size()&gt;0 ) plumed_merror(&quot;cannot calculate numerical derivatives for this quantity&quot;);</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">        213 :   calculateAtomicNumericalDerivatives( this, 0 );</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">        213 : }</span></a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">       2960 : void MultiColvarBase::prepare() {</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">       2960 :   setup_completed=false; atomsWereRetrieved=false;</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">       2960 : }</span></a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">       6550 : void MultiColvarBase::retrieveAtoms() {</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">       6550 :   if( !atomsWereRetrieved ) { ActionAtomistic::retrieveAtoms(); atomsWereRetrieved=true; }</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">       6550 : }</span></a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">      38245 : void MultiColvarBase::mergeInputDerivatives( const unsigned&amp; ival, const unsigned&amp; start, const unsigned&amp; end,</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :     const unsigned&amp; jatom, const std::vector&lt;double&gt;&amp; der,</a>
+<a name="795"><span class="lineNum">     795 </span>            :     MultiValue&amp; myder, AtomValuePack&amp; myatoms ) const {</a>
+<a name="796"><span class="lineNum">     796 </span>            :   MultiValue&amp; myvals=myatoms.getUnderlyingMultiValue();</a>
+<a name="797"><span class="lineNum">     797 </span>            :   plumed_dbg_assert( ival&lt;myatoms.getUnderlyingMultiValue().getNumberOfValues() );</a>
+<a name="798"><span class="lineNum">     798 </span>            :   plumed_dbg_assert( start&lt;myder.getNumberOfValues() &amp;&amp; end&lt;=myder.getNumberOfValues() );</a>
+<a name="799"><span class="lineNum">     799 </span>            :   plumed_dbg_assert( der.size()==myder.getNumberOfValues() &amp;&amp; jatom&lt;myatoms.getNumberOfAtoms() );</a>
+<a name="800"><span class="lineNum">     800 </span>            :   // Convert input atom to local index</a>
+<a name="801"><span class="lineNum">     801 </span>            :   unsigned katom = myatoms.getIndex( jatom ); plumed_dbg_assert( katom&lt;atom_lab.size() ); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="802"><span class="lineNum">     802 </span>            :   // Find base colvar</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">      38245 :   unsigned mmc=atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="804"><span class="lineNum">     804 </span>            :   // Get start of indices for this atom</a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">      38855 :   unsigned basen=0; for(unsigned i=0; i&lt;mmc; ++i) basen+=mybasemulticolvars[i]-&gt;getNumberOfDerivatives() - 9;</span></a>
+<a name="806"><span class="lineNum">     806 </span>            :   plumed_dbg_assert( basen%3==0 ); // Check the number of atoms is consistent with input derivatives</a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">      38245 :   unsigned virbas = myvals.getNumberOfDerivatives()-9;</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">    4805851 :   for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :     unsigned jder=myder.getActiveIndex(j);</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">    4767606 :     if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">    4434561 :       unsigned kder=basen+jder;</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">  110197260 :       for(unsigned icomp=start; icomp&lt;end; ++icomp) {</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">  105762699 :         myvals.addDerivative( ival, kder, der[icomp]*myder.getDerivative( icomp, jder ) );</span></a>
+<a name="814"><span class="lineNum">     814 </span>            :       }</a>
+<a name="815"><span class="lineNum">     815 </span>            :     } else {</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">     333045 :       unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">    7551360 :       for(unsigned icomp=start; icomp&lt;end; ++icomp) {</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">    7218315 :         myvals.addDerivative( ival, kder, der[icomp]*myder.getDerivative( icomp, jder ) );</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :       }</a>
+<a name="820"><span class="lineNum">     820 </span>            :     }</a>
+<a name="821"><span class="lineNum">     821 </span>            :   }</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">      38245 : }</span></a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        106 : void MultiColvarBase::splitInputDerivatives( const unsigned&amp; ival, const unsigned&amp; start, const unsigned&amp; end,</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :     const unsigned&amp; jatom, const std::vector&lt;double&gt;&amp; der,</a>
+<a name="826"><span class="lineNum">     826 </span>            :     MultiValue&amp; myder, AtomValuePack&amp; myatoms ) const {</a>
+<a name="827"><span class="lineNum">     827 </span>            :   MultiValue&amp; myvals=myatoms.getUnderlyingMultiValue();</a>
+<a name="828"><span class="lineNum">     828 </span>            :   plumed_dbg_assert( ival&lt;myder.getNumberOfValues() );</a>
+<a name="829"><span class="lineNum">     829 </span>            :   plumed_dbg_assert( start&lt;myvals.getNumberOfValues() &amp;&amp; end&lt;=myvals.getNumberOfValues() );</a>
+<a name="830"><span class="lineNum">     830 </span>            :   plumed_dbg_assert( der.size()==myatoms.getUnderlyingMultiValue().getNumberOfValues() &amp;&amp; jatom&lt;myatoms.getNumberOfAtoms() );</a>
+<a name="831"><span class="lineNum">     831 </span>            :   // Convert input atom to local index</a>
+<a name="832"><span class="lineNum">     832 </span>            :   unsigned katom = myatoms.getIndex( jatom ); plumed_dbg_assert( katom&lt;atom_lab.size() ); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="833"><span class="lineNum">     833 </span>            :   // Find base colvar</a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">        106 :   unsigned mmc=atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="835"><span class="lineNum">     835 </span>            :   // Get start of indices for this atom</a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">        154 :   unsigned basen=0; for(unsigned i=0; i&lt;mmc; ++i) basen+=mybasemulticolvars[i]-&gt;getNumberOfDerivatives() - 9;</span></a>
+<a name="837"><span class="lineNum">     837 </span>            :   plumed_dbg_assert( basen%3==0 ); // Check the number of atoms is consistent with input derivatives</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">        106 :   unsigned virbas = myvals.getNumberOfDerivatives()-9;</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">      19534 :   for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="840"><span class="lineNum">     840 </span>            :     unsigned jder=myder.getActiveIndex(j);</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">      19428 :     if( jder&lt;mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives()-9 ) {</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">      18474 :       unsigned kder=basen+jder; plumed_assert( kder&lt;myvals.getNumberOfDerivatives() );</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">      39942 :       for(unsigned icomp=start; icomp&lt;end; ++icomp) {</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">      21468 :         myvals.addDerivative( icomp, kder, der[icomp]*myder.getDerivative( ival, jder ) );</span></a>
+<a name="845"><span class="lineNum">     845 </span>            :       }</a>
+<a name="846"><span class="lineNum">     846 </span>            :     } else {</a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">        954 :       unsigned kder=virbas + (jder - mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() + 9);</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">       3942 :       for(unsigned icomp=start; icomp&lt;end; ++icomp) {</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">       2988 :         myvals.addDerivative( icomp, kder, der[icomp]*myder.getDerivative( ival, jder ) );</span></a>
+<a name="850"><span class="lineNum">     850 </span>            :       }</a>
+<a name="851"><span class="lineNum">     851 </span>            :     }</a>
+<a name="852"><span class="lineNum">     852 </span>            :   }</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">        106 : }</span></a>
+<a name="854"><span class="lineNum">     854 </span>            : </a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">     905762 : void MultiColvarBase::addComDerivatives( const int&amp; ival, const unsigned&amp; iatom, const Vector&amp; der, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="856"><span class="lineNum">     856 </span>            :   plumed_dbg_assert( ival&lt;static_cast&lt;int&gt;(myatoms.getUnderlyingMultiValue().getNumberOfValues()) &amp;&amp; iatom&lt;myatoms.getNumberOfAtoms() );</a>
+<a name="857"><span class="lineNum">     857 </span>            :   // Convert input atom to local index</a>
+<a name="858"><span class="lineNum">     858 </span>            :   unsigned katom = myatoms.getIndex( iatom ); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="859"><span class="lineNum">     859 </span>            :   // Find base colvar</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">     905762 :   unsigned mmc = atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">     905762 :   if( usespecies &amp;&amp; iatom==0 ) { myatoms.addComDerivatives( ival, der, mybasemulticolvars[mmc]-&gt;my_tmp_capacks[0] ); return; }</span></a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span>            :   // Get start of indices for this atom</a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">     646526 :   unsigned basen=0; for(unsigned i=0; i&lt;mmc; ++i) basen+=(mybasemulticolvars[i]-&gt;getNumberOfDerivatives() - 9) / 3;</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">     489261 :   mybasemulticolvars[mmc]-&gt;getCentralAtomPack( basen, atom_lab[katom].second, mybasemulticolvars[mmc]-&gt;my_tmp_capacks[1] );</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">     489261 :   myatoms.addComDerivatives( ival, der, mybasemulticolvars[mmc]-&gt;my_tmp_capacks[1] );</span></a>
+<a name="867"><span class="lineNum">     867 </span>            : }</a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">    1122658 : void MultiColvarBase::getInputData( const unsigned&amp; ind, const bool&amp; normed,</span></a>
+<a name="870"><span class="lineNum">     870 </span>            :                                     const multicolvar::AtomValuePack&amp; myatoms,</a>
+<a name="871"><span class="lineNum">     871 </span>            :                                     std::vector&lt;double&gt;&amp; orient ) const {</a>
+<a name="872"><span class="lineNum">     872 </span>            :   // Converint input atom to local index</a>
+<a name="873"><span class="lineNum">     873 </span>            :   unsigned katom = myatoms.getIndex(ind); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="874"><span class="lineNum">     874 </span>            :   // Find base colvar</a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">    1122658 :   unsigned mmc = atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="876"><span class="lineNum">     876 </span>            :   // Check if orient is the correct size</a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">    1122658 :   if( orient.size()!=mybasemulticolvars[mmc]-&gt;getNumberOfQuantities() ) orient.resize( mybasemulticolvars[mmc]-&gt;getNumberOfQuantities() );</span></a>
+<a name="878"><span class="lineNum">     878 </span>            :   // Retrieve the value</a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">    1122658 :   mybasedata[mmc]-&gt;retrieveValueWithIndex( atom_lab[katom].second, normed, orient );</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">    1122658 : }</span></a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">      53063 : MultiValue&amp; MultiColvarBase::getInputDerivatives( const unsigned&amp; iatom, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="883"><span class="lineNum">     883 </span>            :   // Converint input atom to local index</a>
+<a name="884"><span class="lineNum">     884 </span>            :   unsigned katom = myatoms.getIndex(iatom); plumed_dbg_assert( atom_lab[katom].first&gt;0 );</a>
+<a name="885"><span class="lineNum">     885 </span>            :   // Find base colvar</a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">      53063 :   unsigned mmc = atom_lab[katom].first - 1; plumed_dbg_assert( mybasemulticolvars[mmc]-&gt;taskIsCurrentlyActive( atom_lab[katom].second ) );</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">      53063 :   if( usespecies &amp;&amp; !normed &amp;&amp; iatom==0 ) return mybasedata[mmc]-&gt;getTemporyMultiValue(0);</span></a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">      51265 :   unsigned oval=0; if( iatom&gt;0 ) oval=1;</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">      51265 :   MultiValue&amp; myder=mybasedata[mmc]-&gt;getTemporyMultiValue(oval);</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">     102491 :   if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]-&gt;getNumberOfQuantities() ||</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">      51226 :       myder.getNumberOfDerivatives()!=mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">         39 :     myder.resize( mybasemulticolvars[mmc]-&gt;getNumberOfQuantities(), mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() );</span></a>
+<a name="894"><span class="lineNum">     894 </span>            :   }</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">      51265 :   mybasedata[mmc]-&gt;retrieveDerivatives( atom_lab[katom].second, normed, myder );</span></a>
+<a name="896"><span class="lineNum">     896 </span>            :   return myder;</a>
+<a name="897"><span class="lineNum">     897 </span>            : }</a>
+<a name="898"><span class="lineNum">     898 </span>            : </a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">   64365841 : void MultiColvarBase::accumulateSymmetryFunction( const int&amp; ival, const unsigned&amp; iatom, const double&amp; val, const Vector&amp; der, const Tensor&amp; vir, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :   plumed_dbg_assert( usespecies ); unsigned katom=myatoms.getIndex(0), jatom=myatoms.getIndex(iatom);</a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">   64365841 :   double weight0=1.0; if( atom_lab[katom].first&gt;0 ) weight0=mybasedata[atom_lab[katom].first-1]-&gt;retrieveWeightWithIndex( atom_lab[katom].second );</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">   64365841 :   double weighti=1.0; if( atom_lab[jatom].first&gt;0 ) weighti=mybasedata[atom_lab[jatom].first-1]-&gt;retrieveWeightWithIndex( atom_lab[jatom].second );</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :   // Accumulate the value</a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">   64365841 :   if( ival&lt;0 ) myatoms.getUnderlyingMultiValue().addTemporyValue( weight0*weighti*val );</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">   61628941 :   else myatoms.addValue( ival, weight0*weighti*val );</span></a>
+<a name="906"><span class="lineNum">     906 </span>            : </a>
+<a name="907"><span class="lineNum">     907 </span>            :   // Return if we don't need derivatives</a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">   64365841 :   if( doNotCalculateDerivatives() ) return ;</span></a>
+<a name="909"><span class="lineNum">     909 </span>            :   // And virial</a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">   57992318 :   if( ival&lt;0 ) myatoms.addTemporyBoxDerivatives( weight0*weighti*vir );</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">   55734171 :   else myatoms.addBoxDerivatives( ival, weight0*weighti*vir );</span></a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span>            :   // Add derivatives of central atom</a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">   57992318 :   if( atom_lab[katom].first&gt;0 ) {</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">        794 :     addComDerivatives( ival, 0, -weight0*weighti*der, myatoms );</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">        794 :     std::vector&lt;double&gt; tmpder( mybasemulticolvars[atom_lab[katom].first - 1]-&gt;getNumberOfQuantities(), 0. );</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">        794 :     tmpder[0]=weighti*val; mergeInputDerivatives( ival, 0, 1, 0, tmpder, getInputDerivatives(0, false, myatoms), myatoms );</span></a>
+<a name="918"><span class="lineNum">     918 </span>            :   } else {</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">   57991524 :     if( ival&lt;0 ) myatoms.addTemporyAtomsDerivatives( 0, -der );</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">   55733377 :     else myatoms.addAtomsDerivatives( ival, 0, -der );</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :   }</a>
+<a name="922"><span class="lineNum">     922 </span>            :   // Add derivatives of atom in coordination sphere</a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">   57992318 :   if( atom_lab[jatom].first&gt;0 ) {</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">        794 :     addComDerivatives( ival, iatom, weight0*weighti*der, myatoms );</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">        794 :     std::vector&lt;double&gt; tmpder( mybasemulticolvars[atom_lab[katom].first - 1]-&gt;getNumberOfQuantities(), 0. );</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">        794 :     tmpder[0]=weight0*val; mergeInputDerivatives( ival, 0, 1, iatom, tmpder, getInputDerivatives(iatom, false, myatoms), myatoms );</span></a>
+<a name="927"><span class="lineNum">     927 </span>            :   } else {</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">   57991524 :     if( ival&lt;0 ) myatoms.addTemporyAtomsDerivatives( iatom, der );</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">   55733377 :     else myatoms.addAtomsDerivatives( ival, iatom, der );</span></a>
+<a name="930"><span class="lineNum">     930 </span>            :   }</a>
+<a name="931"><span class="lineNum">     931 </span>            : }</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">    1428471 : void MultiColvarBase::addAtomDerivatives( const int&amp; ival, const unsigned&amp; iatom, const Vector&amp; der, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">    1428471 :   if( doNotCalculateDerivatives() ) return ;</span></a>
+<a name="935"><span class="lineNum">     935 </span>            :   unsigned jatom=myatoms.getIndex(iatom);</a>
+<a name="936"><span class="lineNum">     936 </span>            : </a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">    1180895 :   if( atom_lab[jatom].first&gt;0 ) {</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">     904174 :     addComDerivatives( ival, iatom, der, myatoms );</span></a>
+<a name="939"><span class="lineNum">     939 </span>            :   } else {</a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">     276721 :     if( ival&lt;0 ) myatoms.addTemporyAtomsDerivatives( iatom, der );</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">     276721 :     else myatoms.addAtomsDerivatives( ival, iatom, der );</span></a>
+<a name="942"><span class="lineNum">     942 </span>            :   }</a>
+<a name="943"><span class="lineNum">     943 </span>            : }</a>
+<a name="944"><span class="lineNum">     944 </span>            : </a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">     242860 : double MultiColvarBase::calculateWeight( const unsigned&amp; current, const double&amp; weight, AtomValuePack&amp; myvals ) const {</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">     242860 :   return 1.0;</span></a>
+<a name="947"><span class="lineNum">     947 </span>            : }</a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">     447974 : void MultiColvarBase::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">     447974 :   AtomValuePack myatoms( myvals, this );</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :   // Retrieve the atom list</a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">     447974 :   if( !setupCurrentAtomList( current, myatoms ) ) return;</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :   // Get weight due to dynamic groups</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">     447854 :   double weight = 1.0;</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">     447854 :   if( !matsums ) {</span></a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">  386210280 :     for(unsigned i=0; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">  385940036 :       if( atom_lab[myatoms.getIndex(i)].first==0 ) continue;</span></a>
+<a name="958"><span class="lineNum">     958 </span>            :       // Only need to do first two atoms for things like TopologyMatrix, HbondMatrix, Bridge and so on</a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">     244017 :       if( allthirdblockintasks &amp;&amp; i&gt;1 ) break;</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">     244017 :       unsigned mmc = atom_lab[myatoms.getIndex(i)].first - 1;</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">     244017 :       weight *= mybasedata[mmc]-&gt;retrieveWeightWithIndex( atom_lab[myatoms.getIndex(i)].second );</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :     }</a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">     177610 :   } else if( usespecies ) {</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">     177169 :     if( atom_lab[myatoms.getIndex(0)].first&gt;0 ) {</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">       9073 :       if( mybasedata[atom_lab[myatoms.getIndex(0)].first-1]-&gt;retrieveWeightWithIndex( atom_lab[myatoms.getIndex(0)].second )&lt;epsilon ) weight=0.;</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :     }</a>
+<a name="967"><span class="lineNum">     967 </span>            :   }</a>
+<a name="968"><span class="lineNum">     968 </span>            :   // Do a quick check on the size of this contribution</a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">     447854 :   double multweight = calculateWeight( current, weight, myatoms );</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">     447854 :   if( weight*multweight&lt;getTolerance() ) {</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">     121536 :     updateActiveAtoms( myatoms );</span></a>
+<a name="972"><span class="lineNum">     972 </span>            :     return;</a>
+<a name="973"><span class="lineNum">     973 </span>            :   }</a>
+<a name="974"><span class="lineNum">     974 </span>            :   myatoms.setValue( 0, weight*multweight );</a>
+<a name="975"><span class="lineNum">     975 </span>            :   // Deal with derivatives of weights due to dynamic groups</a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">     326318 :   if( !matsums &amp;&amp; !doNotCalculateDerivatives() &amp;&amp; mybasemulticolvars.size()&gt;0 ) {</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">      39416 :     MultiValue&amp; outder=myatoms.getUnderlyingMultiValue(); MultiValue myder(0,0);</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">     115123 :     for(unsigned i=0; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="979"><span class="lineNum">     979 </span>            :       // Neglect any atoms without differentiable weights</a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">      75707 :       if( atom_lab[myatoms.getIndex(i)].first==0 ) continue;</span></a>
+<a name="981"><span class="lineNum">     981 </span>            : </a>
+<a name="982"><span class="lineNum">     982 </span>            :       // Retrieve derivatives</a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">      75707 :       unsigned mmc = atom_lab[myatoms.getIndex(i)].first - 1;</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">      75707 :       if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]-&gt;getNumberOfQuantities() || myder.getNumberOfDerivatives()!=mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">      39416 :         myder.resize( mybasemulticolvars[mmc]-&gt;getNumberOfQuantities(), mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() );</span></a>
+<a name="986"><span class="lineNum">     986 </span>            :       }</a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">      75707 :       mybasedata[mmc]-&gt;retrieveDerivatives( atom_lab[myatoms.getIndex(i)].second, false, myder );</span></a>
+<a name="988"><span class="lineNum">     988 </span>            : </a>
+<a name="989"><span class="lineNum">     989 </span>            :       // Retrieve the prefactor (product of all other weights)</a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">      75707 :       double prefactor = multweight*weight / mybasedata[mmc]-&gt;retrieveWeightWithIndex( atom_lab[myatoms.getIndex(i)].second );</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :       // And accumulate the derivatives</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineCov">    2927141 :       for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) { unsigned jder=myder.getActiveIndex(j); outder.addDerivative( 0, jder, prefactor*myder.getDerivative(0,jder) ); }</span></a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">      75707 :       myder.clearAll();</span></a>
+<a name="994"><span class="lineNum">     994 </span>            :     }</a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">      39416 :   }</span></a>
+<a name="996"><span class="lineNum">     996 </span>            :   // Retrieve derivative stuff for central atom</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">     326318 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">     206915 :     if( usespecies &amp;&amp; mybasemulticolvars.size()&gt;0 &amp;&amp; atom_lab[myatoms.getIndex(0)].first&gt;0 ) {</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">       1610 :       unsigned mmc = atom_lab[0].first - 1;</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">       1610 :       MultiValue&amp; myder=mybasedata[mmc]-&gt;getTemporyMultiValue(0);</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">       3208 :       if( myder.getNumberOfValues()!=mybasemulticolvars[mmc]-&gt;getNumberOfQuantities() ||</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">       1598 :           myder.getNumberOfDerivatives()!=mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">         12 :         myder.resize( mybasemulticolvars[mmc]-&gt;getNumberOfQuantities(), mybasemulticolvars[mmc]-&gt;getNumberOfDerivatives() );</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :       }</a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">       1610 :       mybasedata[mmc]-&gt;retrieveDerivatives( atom_lab[myatoms.getIndex(0)].second, false, myder );</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">       1610 :       unsigned basen=0; for(unsigned i=0; i&lt;mmc; ++i) basen+=mybasemulticolvars[i]-&gt;getNumberOfDerivatives() - 9;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">       1610 :       mybasemulticolvars[mmc]-&gt;getCentralAtomPack( basen, atom_lab[myatoms.getIndex(0)].second,  mybasemulticolvars[mmc]-&gt;my_tmp_capacks[0] );</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            :     }</a>
+<a name="1009"><span class="lineNum">    1009 </span>            :   }</a>
+<a name="1010"><span class="lineNum">    1010 </span>            :   // Compute everything</a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">     326318 :   double vv=compute( task_index, myatoms ); updateActiveAtoms( myatoms );</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :   myatoms.setValue( 1, vv );</a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">     326318 :   return;</span></a>
+<a name="1014"><span class="lineNum">    1014 </span>            : }</a>
+<a name="1015"><span class="lineNum">    1015 </span>            : </a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">     658236 : void MultiColvarBase::updateActiveAtoms( AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">     658236 :   if( mybasemulticolvars.size()==0 ) myatoms.updateUsingIndices();</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">     141871 :   else myatoms.updateDynamicList();</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">     658236 : }</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">    2753935 : Vector MultiColvarBase::getCentralAtomPos( const unsigned&amp; taskIndex ) {</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">    2753935 :   unsigned curr=getTaskCode( taskIndex );</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            : </a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">    2753935 :   if( usespecies || isDensity() ) {</span></a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineCov">    1459946 :     return getPositionOfAtomForLinkCells(curr);</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">    1293989 :   } else if( nblock&gt;0 ) {</span></a>
+<a name="1027"><span class="lineNum">    1027 </span>            :     // double factor=1.0/static_cast&lt;double&gt;( ablocks.size() );</a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">       2130 :     Vector mypos; mypos.zero();</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">       2130 :     std::vector&lt;unsigned&gt; atoms( ablocks.size() ); decodeIndexToAtoms( curr, atoms );</span></a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">       6390 :     for(unsigned i=0; i&lt;ablocks.size(); ++i) {</span></a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">       4260 :       if( use_for_central_atom[i] ) mypos+=numberForCentralAtom*getPositionOfAtomForLinkCells(atoms[i]);</span></a>
+<a name="1032"><span class="lineNum">    1032 </span>            :     }</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">       2130 :     return mypos;</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :   } else {</a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">    1291859 :     Vector mypos; mypos.zero();</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">    5138646 :     for(unsigned i=0; i&lt;ablocks.size(); ++i) {</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">    3846787 :       if( use_for_central_atom[i] ) mypos+=numberForCentralAtom*getPositionOfAtomForLinkCells(ablocks[i][curr]);</span></a>
+<a name="1038"><span class="lineNum">    1038 </span>            :     }</a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">    1291859 :     return mypos;</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :   }</a>
+<a name="1041"><span class="lineNum">    1041 </span>            : }</a>
+<a name="1042"><span class="lineNum">    1042 </span>            : </a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">     605410 : void MultiColvarBase::getCentralAtomPack( const unsigned&amp; basn, const unsigned&amp; taskIndex, CatomPack&amp; mypack ) {</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">     605410 :   unsigned curr=getTaskCode( taskIndex );</span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            : </a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">     605410 :   if(usespecies) {</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">     464996 :     if( mypack.getNumberOfAtomsWithDerivatives()!=1 ) mypack.resize(1);</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">     464996 :     mypack.setIndex( 0, basn + curr );</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">     464996 :     mypack.setDerivative( 0, Tensor::identity() );</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">     140414 :   } else if( nblock&gt;0 ) {</span></a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineNoCov">          0 :     if( mypack.getNumberOfAtomsWithDerivatives()!=ncentral ) mypack.resize(ncentral);</span></a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineNoCov">          0 :     unsigned k=0;</span></a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineNoCov">          0 :     std::vector&lt;unsigned&gt; atoms( ablocks.size() ); decodeIndexToAtoms( curr, atoms );</span></a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;ablocks.size(); ++i) {</span></a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineNoCov">          0 :       if( use_for_central_atom[i] ) {</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineNoCov">          0 :         mypack.setIndex( k, basn + atoms[i] );</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineNoCov">          0 :         mypack.setDerivative( k, numberForCentralAtom*Tensor::identity() );</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineNoCov">          0 :         k++;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :       }</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     }</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :   } else {</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">     140414 :     if( mypack.getNumberOfAtomsWithDerivatives()!=ncentral ) mypack.resize(ncentral);</span></a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">     140414 :     unsigned k=0;</span></a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">     316748 :     for(unsigned i=0; i&lt;ablocks.size(); ++i) {</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">     176334 :       if( use_for_central_atom[i] ) {</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">     173694 :         mypack.setIndex( k, basn + ablocks[i][curr] );</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">     173694 :         mypack.setDerivative( k, numberForCentralAtom*Tensor::identity() );</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">     173694 :         k++;</span></a>
+<a name="1069"><span class="lineNum">    1069 </span>            :       }</a>
+<a name="1070"><span class="lineNum">    1070 </span>            :     }</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :   }</a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">     605410 : }</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            : </a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">  121150993 : Vector MultiColvarBase::getSeparation( const Vector&amp; vec1, const Vector&amp; vec2 ) const {</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">  121150993 :   if(usepbc) { return pbcDistance( vec1, vec2 ); }</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineNoCov">          0 :   else { return delta( vec1, vec2 ); }</span></a>
+<a name="1077"><span class="lineNum">    1077 </span>            : }</a>
+<a name="1078"><span class="lineNum">    1078 </span>            : </a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">     220663 : void MultiColvarBase::applyPbc(std::vector&lt;Vector&gt;&amp; dlist, unsigned int max_index) const {</span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">     220663 :   if (usepbc) pbcApply(dlist, max_index);</span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">     220663 : }</span></a>
+<a name="1082"><span class="lineNum">    1082 </span>            : </a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">       1995 : void MultiColvarBase::apply() {</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">       1995 :   if( getForcesFromVessels( forcesToApply ) ) setForcesOnAtoms( forcesToApply );</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">       1995 : }</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            : </a>
+<a name="1087"><span class="lineNum">    1087 </span>            : }</a>
+<a name="1088"><span class="lineNum">    1088 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarBase.h.func-sort-c.html b/coverage/multicolvar/MultiColvarBase.h.func-sort-c.html
new file mode 100644
index 0000000000..a9b84a8ba5
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarBase.h.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarBase.h<span style="font-size: 80%;"> (<a href="MultiColvarBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">85.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#199">_ZN4PLMD11multicolvar15MultiColvarBase22doNotCalculateDirectorEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#197">_ZNK4PLMD11multicolvar15MultiColvarBase28hasDifferentiableOrientationEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#222">_ZNK4PLMD11multicolvar15MultiColvarBase29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#148">_ZN4PLMD11multicolvar15MultiColvarBaseD2Ev</a></td>
+              <td class="coverFnHi">351</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#159">_ZNK4PLMD11multicolvar15MultiColvarBase10threadSafeEv</a></td>
+              <td class="coverFnHi">4462</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#213">_ZN4PLMD11multicolvar15MultiColvarBase17isCurrentlyActiveERKj</a></td>
+              <td class="coverFnHi">917709</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#193">_ZNK4PLMD11multicolvar15MultiColvarBase9isDensityEv</a></td>
+              <td class="coverFnHi">1814681</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#243">_ZN4PLMD11multicolvar15MultiColvarBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">8911890</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#253">_ZNK4PLMD11multicolvar15MultiColvarBase25doNotCalculateDerivativesEv</a></td>
+              <td class="coverFnHi">69061330</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#233">_ZNK4PLMD11multicolvar15MultiColvarBase29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnHi">408156345</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarBase.h.func.html b/coverage/multicolvar/MultiColvarBase.h.func.html
new file mode 100644
index 0000000000..7abf0e73b3
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarBase.h.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarBase.h<span style="font-size: 80%;"> (<a href="MultiColvarBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">85.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiColvarBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#213">_ZN4PLMD11multicolvar15MultiColvarBase17isCurrentlyActiveERKj</a></td>
+              <td class="coverFnHi">917709</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#199">_ZN4PLMD11multicolvar15MultiColvarBase22doNotCalculateDirectorEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#243">_ZN4PLMD11multicolvar15MultiColvarBase22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">8911890</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#148">_ZN4PLMD11multicolvar15MultiColvarBaseD2Ev</a></td>
+              <td class="coverFnHi">351</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#159">_ZNK4PLMD11multicolvar15MultiColvarBase10threadSafeEv</a></td>
+              <td class="coverFnHi">4462</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#253">_ZNK4PLMD11multicolvar15MultiColvarBase25doNotCalculateDerivativesEv</a></td>
+              <td class="coverFnHi">69061330</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#197">_ZNK4PLMD11multicolvar15MultiColvarBase28hasDifferentiableOrientationEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#222">_ZNK4PLMD11multicolvar15MultiColvarBase29getAbsoluteIndexOfCentralAtomERKj</a></td>
+              <td class="coverFnHi">156</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#233">_ZNK4PLMD11multicolvar15MultiColvarBase29getPositionOfAtomForLinkCellsERKj</a></td>
+              <td class="coverFnHi">408156345</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarBase.h.gcov.html#193">_ZNK4PLMD11multicolvar15MultiColvarBase9isDensityEv</a></td>
+              <td class="coverFnHi">1814681</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarBase.h.gcov.html b/coverage/multicolvar/MultiColvarBase.h.gcov.html
new file mode 100644
index 0000000000..41e3b80824
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarBase.h.gcov.html
@@ -0,0 +1,350 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarBase.h<span style="font-size: 80%;"> (source / <a href="MultiColvarBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryMed">85.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_MultiColvarBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_MultiColvarBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/DynamicList.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/LinkCells.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;vesselbase/StoreDataVessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;CatomPack.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;vector&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace multicolvar {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class AtomValuePack;</a>
+<a name="38"><span class="lineNum">      38 </span>            : class BridgedMultiColvarFunction;</a>
+<a name="39"><span class="lineNum">      39 </span>            : class ActionVolume;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class MultiColvarBase :</a>
+<a name="42"><span class="lineNum">      42 </span>            :   public ActionAtomistic,</a>
+<a name="43"><span class="lineNum">      43 </span>            :   public ActionWithValue,</a>
+<a name="44"><span class="lineNum">      44 </span>            :   public vesselbase::ActionWithVessel</a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span>            :   friend class BridgedMultiColvarFunction;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   friend class VolumeGradientBase;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   friend class MultiColvarFilter;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   friend class AtomValuePack;</a>
+<a name="50"><span class="lineNum">      50 </span>            : private:</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Use periodic boundary conditions</a>
+<a name="52"><span class="lineNum">      52 </span>            :   bool usepbc;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// The forces we are going to apply to things</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;double&gt; forcesToApply;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// We use this to say that all the atoms in the third block should are in the tasks</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool allthirdblockintasks;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// In certain cases we can make three atom link cells faster</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool uselinkforthree;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Number of atoms that are active on this step</a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned nactive_atoms;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Stuff for link cells - this is used to make coordination number like variables faster</a>
+<a name="62"><span class="lineNum">      62 </span>            :   LinkCells linkcells;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Link cells for third block of atoms</a>
+<a name="64"><span class="lineNum">      64 </span>            :   LinkCells threecells;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Number of atoms that are being used for central atom position</a>
+<a name="66"><span class="lineNum">      66 </span>            :   unsigned ncentral;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Bool vector telling us which atoms are required to calculate central atom position</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;bool&gt; use_for_central_atom;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Vector of tempory holders for central atom values</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt;CatomPack&gt; my_tmp_capacks;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// 1/number of atoms involved in central atoms</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double numberForCentralAtom;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Ensures that setup is only performed once per loop</a>
+<a name="74"><span class="lineNum">      74 </span>            :   bool setup_completed;</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Ensures that retrieving of atoms is only done once per calculation loop</a>
+<a name="76"><span class="lineNum">      76 </span>            :   bool atomsWereRetrieved;</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Add derivatives of center of mass position</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void addComDerivatives( const int&amp; ival, const unsigned&amp; iatom, const Vector&amp; der, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="79"><span class="lineNum">      79 </span>            : protected:</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// This is used to keep track of what is calculated where</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt; std::pair&lt;unsigned,unsigned&gt; &gt; atom_lab;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// The vessels in these multicolvars in which the data is stored</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;vesselbase::StoreDataVessel*&gt; mybasedata;</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// The multicolvars from which we construct these quantities</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;MultiColvarBase*&gt; mybasemulticolvars;</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// This remembers where the boundaries are for the tasks. It makes link cells work fast</a>
+<a name="87"><span class="lineNum">      87 </span>            :   Matrix&lt;std::pair&lt;unsigned,unsigned&gt; &gt; bookeeping;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Function that recursively checks if filters have been used in the input to a multicolvar</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// we need this to ensure that setupLinkCells is run in calculate with some actions</a>
+<a name="90"><span class="lineNum">      90 </span>            :   bool filtersUsedAsInput();</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// This resizes the arrays that are used for link cell update</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void resizeBookeepingArray( const unsigned&amp; num1, const unsigned&amp; num2 );</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Are we doing sums of matrix rows</a>
+<a name="94"><span class="lineNum">      94 </span>            :   bool matsums;</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Using the species keyword to read in atoms</a>
+<a name="96"><span class="lineNum">      96 </span>            :   bool usespecies;</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Number of atoms in each block</a>
+<a name="98"><span class="lineNum">      98 </span>            :   unsigned nblock;</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// This is used when turning cvcodes into atom numbers</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;unsigned&gt; decoder;</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Blocks of atom numbers</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; ablocks;</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Add a task to the list of tasks</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void addTaskToList( const unsigned&amp; taskCode );</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Finish setting up the multicolvar base</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void setupMultiColvarBase( const std::vector&lt;AtomNumber&gt;&amp; atoms );</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// This routine take the vector of input derivatives and adds all the vectors to ivalth output derivatives</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// In other words end-start sets of derivatives come in and one set of derivatives come out</a>
+<a name="109"><span class="lineNum">     109 </span>            :   void mergeInputDerivatives( const unsigned&amp; ival, const unsigned&amp; start, const unsigned&amp; end, const unsigned&amp; jatom,</a>
+<a name="110"><span class="lineNum">     110 </span>            :                               const std::vector&lt;double&gt;&amp; der, MultiValue&amp; myder, AtomValuePack&amp; myatoms ) const ;</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// This routine take the ith set of input derivatives and adds it to each of the (end-start) output derivatives</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// In other words one set of derivatives comes in and end-start sets of derivatives come out</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void splitInputDerivatives( const unsigned&amp; ival, const unsigned&amp; start, const unsigned&amp; end,</a>
+<a name="114"><span class="lineNum">     114 </span>            :                               const unsigned&amp; jatom, const std::vector&lt;double&gt;&amp; der,</a>
+<a name="115"><span class="lineNum">     115 </span>            :                               MultiValue&amp; myder, AtomValuePack&amp; myatoms ) const ;</a>
+<a name="116"><span class="lineNum">     116 </span>            : /// This is used to accumulate functions of the coordination sphere.  Ensures weights are taken into account</a>
+<a name="117"><span class="lineNum">     117 </span>            :   void accumulateSymmetryFunction( const int&amp; ival, const unsigned&amp; iatom, const double&amp; val, const Vector&amp; der, const Tensor&amp; vir, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="118"><span class="lineNum">     118 </span>            : /// Set which atoms are to be used to calculate the central atom position</a>
+<a name="119"><span class="lineNum">     119 </span>            :   void setAtomsForCentralAtom( const std::vector&lt;bool&gt;&amp; catom_ind );</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// Set the value of the cutoff for the link cells</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void setLinkCellCutoff( const double&amp; lcut, double tcut=-1.0 );</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// Setup the link cells and neighbour list stuff</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void setupActiveTaskSet( std::vector&lt;unsigned&gt;&amp; active_tasks, const std::string&amp; input_label );</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Setup link cells in order to make this calculation faster</a>
+<a name="125"><span class="lineNum">     125 </span>            :   void setupLinkCells();</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// Get the cutoff for the link cells</a>
+<a name="127"><span class="lineNum">     127 </span>            :   double getLinkCellCutoff()  const ;</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// This does setup of link cell stuff that is specific to the non-use of the usespecies keyword</a>
+<a name="129"><span class="lineNum">     129 </span>            :   void setupNonUseSpeciesLinkCells( const unsigned&amp; );</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// This sets up the list of atoms that are involved in this colvar</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool setupCurrentAtomList( const unsigned&amp; taskCode, AtomValuePack&amp; myatoms ) const ;</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Decode indices if there are 2 or 3 atoms involved</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void decodeIndexToAtoms( const unsigned&amp; taskCode, std::vector&lt;unsigned&gt;&amp; atoms ) const ;</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Read in some atoms</a>
+<a name="135"><span class="lineNum">     135 </span>            :   bool parseMultiColvarAtomList(const std::string&amp; key, const int&amp; num, std::vector&lt;AtomNumber&gt;&amp; t);</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Read in ATOMS keyword</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void readAtomsLikeKeyword( const std::string &amp; key, const int&amp; natoms, std::vector&lt;AtomNumber&gt;&amp; all_atoms );</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Read in two groups of atoms and setup multicolvars to calculate</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void readTwoGroups( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, std::vector&lt;AtomNumber&gt;&amp; all_atoms );</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Read in three groups of atoms</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void readGroupKeywords( const std::string&amp; key0, const std::string&amp; key1, const std::string&amp; key2, const std::string&amp; key3,</a>
+<a name="142"><span class="lineNum">     142 </span>            :                           const bool&amp; no_third_dim_accum, const bool&amp; symmetric, std::vector&lt;AtomNumber&gt;&amp; all_atoms );</a>
+<a name="143"><span class="lineNum">     143 </span>            : /// Read in three groups of atoms and construct CVs involving at least one</a>
+<a name="144"><span class="lineNum">     144 </span>            :   void readThreeGroups( const std::string&amp; key1, const std::string&amp; key2, const std::string&amp; key3,</a>
+<a name="145"><span class="lineNum">     145 </span>            :                         const bool&amp; allow2, const bool&amp; no_third_dim_accum, std::vector&lt;AtomNumber&gt;&amp; all_atoms );</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Build sets by taking one multicolvar from each base</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void buildSets();</a>
+<a name="148"><span class="lineNum">     148 </span>            : public:</a>
+<a name="149"><span class="lineNum">     149 </span>            :   explicit MultiColvarBase(const ActionOptions&amp;);</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       1404 :   ~MultiColvarBase() {}</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Turn on the derivatives</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void turnOnDerivatives() override;</a>
+<a name="154"><span class="lineNum">     154 </span>            : /// Get the separation between a pair of vectors</a>
+<a name="155"><span class="lineNum">     155 </span>            :   Vector getSeparation( const Vector&amp; vec1, const Vector&amp; vec2 ) const ;</a>
+<a name="156"><span class="lineNum">     156 </span>            : /// Do we use pbc to calculate this quantity</a>
+<a name="157"><span class="lineNum">     157 </span>            :   bool usesPbc() const ;</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// Apply PBCs over a set of distance vectors</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void applyPbc(std::vector&lt;Vector&gt;&amp; dlist, unsigned max_index=0) const;</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Is it safe to use multithreading</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       4462 :   bool threadSafe() const override { return !(mybasemulticolvars.size()&gt;0); }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : /// Do some setup before the calculation</a>
+<a name="163"><span class="lineNum">     163 </span>            :   void prepare() override;</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// This is overwritten here in order to make sure that we do not retrieve atoms multiple times</a>
+<a name="165"><span class="lineNum">     165 </span>            :   void retrieveAtoms() override;</a>
+<a name="166"><span class="lineNum">     166 </span>            : /// Do the calculation</a>
+<a name="167"><span class="lineNum">     167 </span>            :   void calculate() override;</a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Calculate numerical derivatives</a>
+<a name="169"><span class="lineNum">     169 </span>            :   void calculateNumericalDerivatives( ActionWithValue* a=NULL ) override;</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// Perform one of the tasks</a>
+<a name="171"><span class="lineNum">     171 </span>            :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="172"><span class="lineNum">     172 </span>            : /// Update the active atoms</a>
+<a name="173"><span class="lineNum">     173 </span>            :   virtual void updateActiveAtoms( AtomValuePack&amp; myatoms ) const ;</a>
+<a name="174"><span class="lineNum">     174 </span>            : /// This gets the position of an atom for the link cell setup</a>
+<a name="175"><span class="lineNum">     175 </span>            :   virtual Vector getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const ;</a>
+<a name="176"><span class="lineNum">     176 </span>            : /// Get the absolute index of the central atom</a>
+<a name="177"><span class="lineNum">     177 </span>            :   virtual AtomNumber getAbsoluteIndexOfCentralAtom( const unsigned&amp; i ) const ;</a>
+<a name="178"><span class="lineNum">     178 </span>            : /// This is replaced once we have a function to calculate the cv</a>
+<a name="179"><span class="lineNum">     179 </span>            :   virtual double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const=0;</a>
+<a name="180"><span class="lineNum">     180 </span>            : /// Apply the forces from this action</a>
+<a name="181"><span class="lineNum">     181 </span>            :   void apply() override;</a>
+<a name="182"><span class="lineNum">     182 </span>            : /// Get the number of derivatives for this action</a>
+<a name="183"><span class="lineNum">     183 </span>            :   unsigned getNumberOfDerivatives() override;  // N.B. This is replacing the virtual function in ActionWithValue</a>
+<a name="184"><span class="lineNum">     184 </span>            : /// Checks if an task is being performed at the present time</a>
+<a name="185"><span class="lineNum">     185 </span>            :   virtual bool isCurrentlyActive( const unsigned&amp; code );</a>
+<a name="186"><span class="lineNum">     186 </span>            : /// Add some derivatives to a particular component of a particular atom</a>
+<a name="187"><span class="lineNum">     187 </span>            :   void addAtomDerivatives( const int&amp;, const unsigned&amp;, const Vector&amp;, multicolvar::AtomValuePack&amp; ) const ;</a>
+<a name="188"><span class="lineNum">     188 </span>            : ///</a>
+<a name="189"><span class="lineNum">     189 </span>            :   virtual void getCentralAtomPack( const unsigned&amp; basn, const unsigned&amp; curr, CatomPack&amp; mypack);</a>
+<a name="190"><span class="lineNum">     190 </span>            : /// Get the index where the central atom is stored</a>
+<a name="191"><span class="lineNum">     191 </span>            :   virtual Vector getCentralAtomPos( const unsigned&amp; curr );</a>
+<a name="192"><span class="lineNum">     192 </span>            : /// You can use this to screen contributions that are very small so we can avoid expensive (and pointless) calculations</a>
+<a name="193"><span class="lineNum">     193 </span>            :   virtual double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; myatoms ) const ;</a>
+<a name="194"><span class="lineNum">     194 </span>            : /// Is this a density?</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">    1814681 :   virtual bool isDensity() const { return false; }</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : /// Is the iatom'th stored value currently active</a>
+<a name="197"><span class="lineNum">     197 </span>            :   bool storedValueIsActive( const unsigned&amp; iatom );</a>
+<a name="198"><span class="lineNum">     198 </span>            : /// This is true if multicolvar is calculating a vector or if the multicolvar is the density</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   virtual bool hasDifferentiableOrientation() const { return false; }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : /// This makes sure we are not calculating the director when we do LocalAverage</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   virtual void doNotCalculateDirector() {}</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : /// Ensure that derivatives are only calculated when needed</a>
+<a name="203"><span class="lineNum">     203 </span>            :   bool doNotCalculateDerivatives() const override;</a>
+<a name="204"><span class="lineNum">     204 </span>            : /// Get the icolv th base multicolvar</a>
+<a name="205"><span class="lineNum">     205 </span>            :   MultiColvarBase* getBaseMultiColvar( const unsigned&amp; icolv ) const ;</a>
+<a name="206"><span class="lineNum">     206 </span>            : /// Get the number of base multicolvars</a>
+<a name="207"><span class="lineNum">     207 </span>            :   unsigned getNumberOfBaseMultiColvars() const ;</a>
+<a name="208"><span class="lineNum">     208 </span>            : /// Get an input data</a>
+<a name="209"><span class="lineNum">     209 </span>            :   virtual void getInputData( const unsigned&amp; ind, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms, std::vector&lt;double&gt;&amp; orient ) const ;</a>
+<a name="210"><span class="lineNum">     210 </span>            : /// Retrieve the input derivatives</a>
+<a name="211"><span class="lineNum">     211 </span>            :   virtual MultiValue&amp; getInputDerivatives( const unsigned&amp; iatom, const bool&amp; normed, const multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="212"><span class="lineNum">     212 </span>            : };</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : inline</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">     917709 : bool MultiColvarBase::isCurrentlyActive( const unsigned&amp; code ) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     917709 :   if( setup_completed &amp;&amp; atom_lab[code].first&gt;0 ) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      17644 :     unsigned mmc=atom_lab[code].first - 1;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      17644 :     return mybasedata[mmc]-&gt;storedValueIsActive( atom_lab[code].second );</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   }</a>
+<a name="220"><span class="lineNum">     220 </span>            :   return true;</a>
+<a name="221"><span class="lineNum">     221 </span>            : }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : inline</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        156 : AtomNumber MultiColvarBase::getAbsoluteIndexOfCentralAtom( const unsigned&amp; iatom ) const {</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   plumed_dbg_assert( iatom&lt;atom_lab.size() );</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        156 :   if( atom_lab[iatom].first&gt;0  ) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :     unsigned mmc=atom_lab[iatom].first - 1;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     return mybasemulticolvars[mmc]-&gt;getAbsoluteIndexOfCentralAtom( atom_lab[iatom].second );</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            :   plumed_dbg_assert( usespecies );</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        156 :   return ActionAtomistic::getAbsoluteIndex( atom_lab[getTaskCode(iatom)].second );</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : inline</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">  408156345 : Vector MultiColvarBase::getPositionOfAtomForLinkCells( const unsigned&amp; iatom ) const {</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :   plumed_dbg_assert( iatom&lt;atom_lab.size() );</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">  408156345 :   if( atom_lab[iatom].first&gt;0  ) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">    2487982 :     unsigned mmc=atom_lab[iatom].first - 1;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">    2487982 :     return mybasemulticolvars[mmc]-&gt;getCentralAtomPos( atom_lab[iatom].second );</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   }</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">  405668363 :   return ActionAtomistic::getPosition( atom_lab[iatom].second );</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : inline</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    8911890 : unsigned MultiColvarBase::getNumberOfDerivatives() {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">    8911890 :   return 3*getNumberOfAtoms()+9;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : inline</a>
+<a name="250"><span class="lineNum">     250 </span>            : bool MultiColvarBase::usesPbc() const {</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">     220663 :   return usepbc;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : inline</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">   69061330 : bool MultiColvarBase::doNotCalculateDerivatives() const {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">   69061330 :   if( !dertime ) return true;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">   68373610 :   return ActionWithValue::doNotCalculateDerivatives();</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            : inline</a>
+<a name="261"><span class="lineNum">     261 </span>            : unsigned MultiColvarBase::getNumberOfBaseMultiColvars() const {</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        178 :   return mybasemulticolvars.size();</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : inline</a>
+<a name="266"><span class="lineNum">     266 </span>            : MultiColvarBase* MultiColvarBase::getBaseMultiColvar( const unsigned&amp; icolv ) const {</a>
+<a name="267"><span class="lineNum">     267 </span>            :   plumed_dbg_assert( icolv&lt;mybasemulticolvars.size() );</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      25010 :   return mybasemulticolvars[icolv];</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarCombine.cpp.func-sort-c.html b/coverage/multicolvar/MultiColvarCombine.cpp.func-sort-c.html
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+++ b/coverage/multicolvar/MultiColvarCombine.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarCombine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarCombine.cpp<span style="font-size: 80%;"> (<a href="MultiColvarCombine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarCombine.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#61">_ZN4PLMD11multicolvar18MultiColvarCombineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#51">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarCombineRegisterMe536createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#48">_ZN4PLMD11multicolvar18MultiColvarCombine10isPeriodicEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#61">_ZN4PLMD11multicolvar18MultiColvarCombineC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#53">_ZN4PLMD11multicolvar18MultiColvarCombine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#76">_ZNK4PLMD11multicolvar18MultiColvarCombine7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#51">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarCombineRegisterMe53C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#51">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarCombineRegisterMe53D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarCombine.cpp.func.html b/coverage/multicolvar/MultiColvarCombine.cpp.func.html
new file mode 100644
index 0000000000..272984ce7e
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarCombine.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarCombine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarCombine.cpp<span style="font-size: 80%;"> (<a href="MultiColvarCombine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiColvarCombine.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#51">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarCombineRegisterMe536createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#51">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarCombineRegisterMe53C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#51">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarCombineRegisterMe53D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#48">_ZN4PLMD11multicolvar18MultiColvarCombine10isPeriodicEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#53">_ZN4PLMD11multicolvar18MultiColvarCombine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#61">_ZN4PLMD11multicolvar18MultiColvarCombineC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#61">_ZN4PLMD11multicolvar18MultiColvarCombineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarCombine.cpp.gcov.html#76">_ZNK4PLMD11multicolvar18MultiColvarCombine7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarCombine.cpp.gcov.html b/coverage/multicolvar/MultiColvarCombine.cpp.gcov.html
new file mode 100644
index 0000000000..83bef3c4e2
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarCombine.cpp.gcov.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarCombine.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarCombine.cpp<span style="font-size: 80%;"> (source / <a href="MultiColvarCombine.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC MCOLVARF MCOLV_COMBINE</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate linear combinations of multiple multicolvars</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \par Examples</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span>            : //+ENDPLUMEDOC</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace multicolvar {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class MultiColvarCombine : public MultiColvarBase {</a>
+<a name="42"><span class="lineNum">      42 </span>            : private:</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;double&gt; coeff;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="46"><span class="lineNum">      46 </span>            :   explicit MultiColvarCombine(const ActionOptions&amp;);</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Actually do the calculation</a>
+<a name="48"><span class="lineNum">      48 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Is the variable periodic</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :   bool isPeriodic() override { return false; }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : };</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(MultiColvarCombine,&quot;MCOLV_COMBINE&quot;)</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          3 : void MultiColvarCombine::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          3 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;the multicolvars you are calculating linear combinations for&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;COEFFICIENTS&quot;,&quot;1.0&quot;,&quot;the coefficients to use for the various multicolvars&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         15 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;SUM&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;HISTOGRAM&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         21 :   keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;); keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          3 : }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          1 : MultiColvarCombine::MultiColvarCombine(const ActionOptions&amp; ao):</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   Action(ao),</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          1 :   MultiColvarBase(ao)</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          1 :   buildSets();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          2 :     if( mybasemulticolvars[i]-&gt;weightWithDerivatives() ) error(&quot;cannot combine multicolvars with weights&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   }</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 :   coeff.resize( getNumberOfBaseMultiColvars() );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          1 :   parseVector(&quot;COEFFICIENTS&quot;,coeff);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          1 :   log.printf(&quot;  coefficients of multicolvars %f&quot;, coeff[0] );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          2 :   for(unsigned i=1; i&lt;coeff.size(); ++i) log.printf(&quot;, %f&quot;, coeff[i] );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          1 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          1 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         15 : double MultiColvarCombine::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         15 :   double dot=0; std::vector&lt;double&gt; tval(2);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         45 :   for(unsigned i=0; i&lt;coeff.size(); ++i) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         30 :     getInputData( i, false, myatoms, tval );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         30 :     dot += coeff[i]*tval[1];</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         15 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         15 :     std::vector&lt;double&gt; cc(2);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         45 :     for(unsigned i=0; i&lt;coeff.size(); ++i) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         30 :       cc[1]=coeff[i]; MultiValue&amp; myder=getInputDerivatives( i, false, myatoms );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         30 :       splitInputDerivatives( 1, 1, 2, i, cc, myder, myatoms );</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     }</a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         15 :   return dot;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarDensity.cpp.func-sort-c.html b/coverage/multicolvar/MultiColvarDensity.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9b5924a91a
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarDensity.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarDensity.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarDensity.cpp<span style="font-size: 80%;"> (<a href="MultiColvarDensity.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">116</td>
+            <td class="headerCovTableEntry">139</td>
+            <td class="headerCovTableEntryMed">83.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarDensity.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#98">_ZN4PLMD11multicolvar18MultiColvarDensity10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#132">_ZN4PLMD11multicolvar18MultiColvarDensityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#105">_ZN4PLMD11multicolvar12_GLOBAL__N_131MultiColvarDensityRegisterMe1076createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#132">_ZN4PLMD11multicolvar18MultiColvarDensityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#107">_ZN4PLMD11multicolvar18MultiColvarDensity16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#249">_ZN4PLMD11multicolvar18MultiColvarDensity12clearAverageEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#272">_ZN4PLMD11multicolvar18MultiColvarDensity19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#102">_ZN4PLMD11multicolvar18MultiColvarDensity5applyEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#245">_ZNK4PLMD11multicolvar18MultiColvarDensity21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#105">_ZN4PLMD11multicolvar12_GLOBAL__N_131MultiColvarDensityRegisterMe107C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#105">_ZN4PLMD11multicolvar12_GLOBAL__N_131MultiColvarDensityRegisterMe107D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#286">_ZNK4PLMD11multicolvar18MultiColvarDensity7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">21152</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarDensity.cpp.func.html b/coverage/multicolvar/MultiColvarDensity.cpp.func.html
new file mode 100644
index 0000000000..c9b2742eed
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarDensity.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarDensity.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarDensity.cpp<span style="font-size: 80%;"> (<a href="MultiColvarDensity.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">116</td>
+            <td class="headerCovTableEntry">139</td>
+            <td class="headerCovTableEntryMed">83.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiColvarDensity.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#105">_ZN4PLMD11multicolvar12_GLOBAL__N_131MultiColvarDensityRegisterMe1076createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#105">_ZN4PLMD11multicolvar12_GLOBAL__N_131MultiColvarDensityRegisterMe107C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#105">_ZN4PLMD11multicolvar12_GLOBAL__N_131MultiColvarDensityRegisterMe107D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#98">_ZN4PLMD11multicolvar18MultiColvarDensity10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#249">_ZN4PLMD11multicolvar18MultiColvarDensity12clearAverageEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#107">_ZN4PLMD11multicolvar18MultiColvarDensity16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#272">_ZN4PLMD11multicolvar18MultiColvarDensity19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#102">_ZN4PLMD11multicolvar18MultiColvarDensity5applyEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#132">_ZN4PLMD11multicolvar18MultiColvarDensityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#132">_ZN4PLMD11multicolvar18MultiColvarDensityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#245">_ZNK4PLMD11multicolvar18MultiColvarDensity21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarDensity.cpp.gcov.html#286">_ZNK4PLMD11multicolvar18MultiColvarDensity7computeERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">21152</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarDensity.cpp.gcov.html b/coverage/multicolvar/MultiColvarDensity.cpp.gcov.html
new file mode 100644
index 0000000000..c5d7cc9265
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarDensity.cpp.gcov.html
@@ -0,0 +1,374 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarDensity.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarDensity.cpp<span style="font-size: 80%;"> (source / <a href="MultiColvarDensity.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">116</td>
+            <td class="headerCovTableEntry">139</td>
+            <td class="headerCovTableEntryMed">83.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;gridtools/ActionWithGrid.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace multicolvar {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC GRIDCALC MULTICOLVARDENS</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Evaluate the average value of a multicolvar on a grid.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : This keyword allows one to construct a phase field representation for a symmetry function from</a>
+<a name="40"><span class="lineNum">      40 </span>            : an atomistic description.  If each atom has an associated order parameter, \f$\phi_i\f$ then a</a>
+<a name="41"><span class="lineNum">      41 </span>            : smooth phase field function \f$\phi(r)\f$ can be computed using:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : \phi(\mathbf{r}) = \frac{\sum_i K(\mathbf{r}-\mathbf{r}_i) \phi_i }{ \sum_i K(\mathbf{r} - \mathbf{r}_i )}</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : where \f$\mathbf{r}_i\f$ is the position of atom \f$i\f$, the sums run over all the atoms input</a>
+<a name="48"><span class="lineNum">      48 </span>            : and \f$K(\mathbf{r} - \mathbf{r}_i)\f$ is one of the \ref kernelfunctions implemented in plumed.</a>
+<a name="49"><span class="lineNum">      49 </span>            : This action calculates the above function on a grid, which can then be used in the input to further</a>
+<a name="50"><span class="lineNum">      50 </span>            : actions.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The following example shows perhaps the simplest way in which this action can be used.  The following</a>
+<a name="55"><span class="lineNum">      55 </span>            : input computes the density of atoms at each point on the grid and outputs this quantity to a file.  In</a>
+<a name="56"><span class="lineNum">      56 </span>            : other words this input instructs plumed to calculate \f$\rho(\mathbf{r}) = \sum_i K(\mathbf{r} - \mathbf{r}_i )\f$</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \plumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : dens: DENSITY SPECIES=1-100</a>
+<a name="60"><span class="lineNum">      60 </span>            : grid: MULTICOLVARDENS DATA=dens ORIGIN=1 DIR=xyz NBINS=100,100,100 BANDWIDTH=0.05,0.05,0.05 STRIDE=1</a>
+<a name="61"><span class="lineNum">      61 </span>            : DUMPGRID GRID=grid STRIDE=500 FILE=density</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : In the above example density is added to the grid on every step.  The PRINT_GRID instruction thus tells PLUMED to</a>
+<a name="65"><span class="lineNum">      65 </span>            : output the average density at each point on the grid every 500 steps of simulation.  Notice that the that grid output</a>
+<a name="66"><span class="lineNum">      66 </span>            : on step 1000 is an average over all 1000 frames of the trajectory.  If you would like to analyze these two blocks</a>
+<a name="67"><span class="lineNum">      67 </span>            : of data separately you must use the CLEAR flag.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : This second example computes an order parameter (in this case \ref FCCUBIC) and constructs a phase field model</a>
+<a name="70"><span class="lineNum">      70 </span>            : for this order parameter using the equation above.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : fcc: FCCUBIC SPECIES=1-5184 SWITCH={CUBIC D_0=1.2 D_MAX=1.5} ALPHA=27</a>
+<a name="74"><span class="lineNum">      74 </span>            : dens: MULTICOLVARDENS DATA=fcc ORIGIN=1 DIR=xyz NBINS=14,14,28 BANDWIDTH=1.0,1.0,1.0 STRIDE=1 CLEAR=1</a>
+<a name="75"><span class="lineNum">      75 </span>            : DUMPCUBE GRID=dens STRIDE=1 FILE=dens.cube</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : In this example the phase field model is computed and output to a file on every step of the simulation.  Furthermore,</a>
+<a name="79"><span class="lineNum">      79 </span>            : because the CLEAR=1 keyword is set on the MULTICOLVARDENS line each Gaussian cube file output is a phase field</a>
+<a name="80"><span class="lineNum">      80 </span>            : model for a particular trajectory frame. The average value accumulated thus far is cleared at the start of every single</a>
+<a name="81"><span class="lineNum">      81 </span>            : timestep and there is no averaging over trajectory frames in this case.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : */</a>
+<a name="84"><span class="lineNum">      84 </span>            : //+ENDPLUMEDOC</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : class MultiColvarDensity : public gridtools::ActionWithGrid {</a>
+<a name="87"><span class="lineNum">      87 </span>            :   bool fractional;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   MultiColvarBase* mycolv;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;unsigned&gt; nbins;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;double&gt; gspacing;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;bool&gt; confined;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;double&gt; cmin, cmax;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   vesselbase::StoreDataVessel* stash;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   Vector origin;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::vector&lt;unsigned&gt; directions;</a>
+<a name="96"><span class="lineNum">      96 </span>            : public:</a>
+<a name="97"><span class="lineNum">      97 </span>            :   explicit MultiColvarDensity(const ActionOptions&amp;);</a>
+<a name="98"><span class="lineNum">      98 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="99"><span class="lineNum">      99 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   void clearAverage() override;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void prepareForAveraging() override;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void compute( const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         34 :   void apply() override {}</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : };</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      12526 : PLUMED_REGISTER_ACTION(MultiColvarDensity,&quot;MULTICOLVARDENS&quot;)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         13 : void MultiColvarDensity::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         13 :   gridtools::ActionWithGrid::registerKeywords( keys );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         26 :   keys.add(&quot;atoms&quot;,&quot;ORIGIN&quot;,&quot;we will use the position of this atom as the origin&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         26 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;the multicolvar which you would like to calculate the density profile for&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         26 :   keys.add(&quot;compulsory&quot;,&quot;DIR&quot;,&quot;the direction in which to calculate the density profile&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;NBINS&quot;,&quot;the number of bins to use to represent the density profile&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;SPACING&quot;,&quot;the approximate grid spacing (to be used as an alternative or together with NBINS)&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         26 :   keys.addFlag(&quot;FRACTIONAL&quot;,false,&quot;use fractional coordinates for the various axes&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         26 :   keys.addFlag(&quot;XREDUCED&quot;,false,&quot;limit the calculation of the density/average to a portion of the z-axis only&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;XLOWER&quot;,&quot;this is required if you are using XREDUCED. It specifies the lower bound for the region of the x-axis that for &quot;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :            &quot;which you are calculating the density/average&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;XUPPER&quot;,&quot;this is required if you are using XREDUCED. It specifies the upper bound for the region of the x-axis that for &quot;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :            &quot;which you are calculating the density/average&quot;);</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         26 :   keys.addFlag(&quot;YREDUCED&quot;,false,&quot;limit the calculation of the density/average to a portion of the y-axis only&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;YLOWER&quot;,&quot;this is required if you are using YREDUCED. It specifies the lower bound for the region of the y-axis that for &quot;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :            &quot;which you are calculating the density/average&quot;);</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;YUPPER&quot;,&quot;this is required if you are using YREDUCED. It specifies the upper bound for the region of the y-axis that for &quot;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :            &quot;which you are calculating the density/average&quot;);</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         26 :   keys.addFlag(&quot;ZREDUCED&quot;,false,&quot;limit the calculation of the density/average to a portion of the z-axis only&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;ZLOWER&quot;,&quot;this is required if you are using ZREDUCED. It specifies the lower bound for the region of the z-axis that for &quot;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;which you are calculating the density/average&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;ZUPPER&quot;,&quot;this is required if you are using ZREDUCED. It specifies the upper bound for the region of the z-axis that for &quot;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :            &quot;which you are calculating the density/average&quot;);</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         13 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         11 : MultiColvarDensity::MultiColvarDensity(const ActionOptions&amp;ao):</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   Action(ao),</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         11 :   ActionWithGrid(ao)</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : {</a>
+<a name="138"><span class="lineNum">     138 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         22 :   parseAtomList(&quot;ORIGIN&quot;,atom);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         11 :   if( atom.size()!=1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         11 :   log.printf(&quot;  origin is at position of atom : %d\n&quot;,atom[0].serial() );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         11 :   std::string mlab; parse(&quot;DATA&quot;,mlab);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         11 :   mycolv = plumed.getActionSet().selectWithLabel&lt;MultiColvarBase*&gt;(mlab);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         11 :   if(!mycolv) error(&quot;action labelled &quot; +  mlab + &quot; does not exist or is not a MultiColvar&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         11 :   stash = mycolv-&gt;buildDataStashes( NULL );</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         22 :   parseFlag(&quot;FRACTIONAL&quot;,fractional);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         11 :   std::string direction; parse(&quot;DIR&quot;,direction);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         11 :   log.printf(&quot;  calculating for %s density profile along &quot;, mycolv-&gt;getLabel().c_str() );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         11 :   if( direction==&quot;x&quot; ) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          8 :     log.printf(&quot;x axis&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          8 :     directions.resize(1); directions[0]=0;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          3 :   } else if( direction==&quot;y&quot; ) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :     log.printf(&quot;y axis&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :     directions.resize(1); directions[0]=1;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 :   } else if( direction==&quot;z&quot; ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     log.printf(&quot;z axis&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     directions.resize(1); directions[0]=2;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          3 :   } else if( direction==&quot;xy&quot; ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     log.printf(&quot;x and y axes&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     directions.resize(2); directions[0]=0; directions[1]=1;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          3 :   } else if( direction==&quot;xz&quot; ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     log.printf(&quot;x and z axes&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     directions.resize(2); directions[0]=0; directions[1]=2;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          3 :   } else if( direction==&quot;yz&quot; ) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     log.printf(&quot;y and z axis&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     directions.resize(2); directions[0]=1; directions[1]=2;</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          3 :   } else if( direction==&quot;xyz&quot; ) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          3 :     log.printf(&quot;x, y and z axes&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          3 :     directions.resize(3); directions[0]=0; directions[1]=1; directions[2]=2;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   } else {</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     error( direction + &quot; is not valid gradient direction&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         11 :   log.printf(&quot; for colvars calculated by action %s \n&quot;,mycolv-&gt;getLabel().c_str() );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         33 :   parseVector(&quot;NBINS&quot;,nbins); parseVector(&quot;SPACING&quot;,gspacing);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         11 :   if( nbins.size()!=directions.size() &amp;&amp; gspacing.size()!=directions.size() ) error(&quot;NBINS or SPACING must be set&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         11 :   confined.resize( directions.size() ); cmin.resize( directions.size(), 0 ); cmax.resize( directions.size(), 0 );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         28 :   for(unsigned i=0; i&lt;directions.size(); ++i) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         17 :     if( directions[i]==0 ) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         22 :       bool tflag; parseFlag(&quot;XREDUCED&quot;,tflag); confined[i]=tflag;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         11 :       if( confined[i] ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :         cmin[i]=cmax[i]=0.0; parse(&quot;XLOWER&quot;,cmin[i]); parse(&quot;XUPPER&quot;,cmax[i]);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :         if( fractional ) error(&quot;XREDUCED is incompatible with FRACTIONAL&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :         if( std::abs(cmin[i]-cmax[i])&lt;epsilon ) error(&quot;range set for x axis makes no sense&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :         log.printf(&quot;  confining calculation in x direction to between %f and %f \n&quot;,cmin[i],cmax[i]);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :       }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          6 :     } else if( directions[i]==1 ) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          6 :       bool tflag; parseFlag(&quot;YREDUCED&quot;,tflag); confined[i]=tflag;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          3 :       if( confined[i] ) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :         cmin[i]=cmax[i]=0.0; parse(&quot;YLOWER&quot;,cmin[i]); parse(&quot;YUPPER&quot;,cmax[i]);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :         if( fractional ) error(&quot;YREDUCED is incompatible with FRACTIONAL&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :         if( std::abs(cmin[i]-cmax[i])&lt;epsilon ) error(&quot;range set for y axis makes no sense&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :         log.printf(&quot;  confining calculation in y direction to between %f and %f \n&quot;,cmin[i],cmax[i]);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       }</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          3 :     } else if( directions[i]==2 ) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          6 :       bool tflag; parseFlag(&quot;ZREDUCED&quot;,tflag); confined[i]=tflag;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          3 :       if( confined[i] ) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          2 :         cmin[i]=cmax[i]=0.0; parse(&quot;ZLOWER&quot;,cmin[i]); parse(&quot;ZUPPER&quot;,cmax[i]);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          1 :         if( fractional ) error(&quot;ZREDUCED is incompatible with FRACTIONAL&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          1 :         if( std::abs(cmin[i]-cmax[i])&lt;epsilon ) error(&quot;range set for z axis search makes no sense&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          1 :         log.printf(&quot;  confining calculation in z direction to between %f and %f \n&quot;,cmin[i],cmax[i]);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       }</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   std::string vstring;</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         11 :   if( confined[0] ) vstring +=&quot;PBC=F&quot;;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   else vstring += &quot; PBC=T&quot;;</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         17 :   for(unsigned i=1; i&lt;directions.size(); ++i) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          6 :     if( confined[i] ) vstring += &quot;,F&quot;;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     else vstring += &quot;,T&quot;;</a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         22 :   vstring +=&quot; COMPONENTS=&quot; + mycolv-&gt;getLabel() + &quot;.dens&quot;;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   vstring +=&quot; COORDINATES=&quot;;</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         11 :   if( directions[0]==0 ) vstring+=&quot;x&quot;;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :   else if( directions[0]==1 ) vstring+=&quot;y&quot;;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   else if( directions[0]==2 ) vstring+=&quot;z&quot;;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         17 :   for(unsigned i=1; i&lt;directions.size(); ++i) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          6 :     if( directions[i]==0 ) vstring+=&quot;,x&quot;;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          6 :     else if( directions[i]==1 ) vstring+=&quot;,y&quot;;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          3 :     else if( directions[i]==2 ) vstring+=&quot;,z&quot;;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span>            :   // Create a task list</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      10899 :   for(unsigned i=0; i&lt;mycolv-&gt;getFullNumberOfTasks(); ++i) addTaskToList(i);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   // And create the grid</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         11 :   std::unique_ptr&lt;gridtools::GridVessel&gt; grid;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         14 :   if( mycolv-&gt;isDensity() ) grid=createGrid( &quot;histogram&quot;, vstring );</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         16 :   else grid=createGrid( &quot;average&quot;, vstring );</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   // cppcheck-suppress danglingLifetime</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         11 :   mygrid=grid.get();</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   // And finish the grid setup</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         11 :   setAveragingAction( std::move(grid), true );</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :   // Enusre units for cube files are set correctly</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         11 :   if( !fractional ) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         11 :     if( plumed.getAtoms().usingNaturalUnits() ) mygrid-&gt;setCubeUnits( 1.0/0.5292 );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          1 :     else mygrid-&gt;setCubeUnits( plumed.getAtoms().getUnits().getLength()/.05929 );</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         11 :   checkRead(); requestAtoms(atom);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   // Stupid dependencies cleared by requestAtoms - why GBussi why? That's got me so many times</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         11 :   addDependency( mycolv );</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         22 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         62 : unsigned MultiColvarDensity::getNumberOfQuantities() const {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         62 :   return directions.size() + 2;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         18 : void MultiColvarDensity::clearAverage() {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         18 :   std::vector&lt;double&gt; min(directions.size()), max(directions.size());</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         18 :   std::vector&lt;std::string&gt; gmin(directions.size()), gmax(directions.size());;</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         46 :   for(unsigned i=0; i&lt;directions.size(); ++i) { min[i]=-0.5; max[i]=0.5; }</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         18 :   if( !fractional ) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         18 :     if( !mycolv-&gt;getPbc().isOrthorombic() ) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :       error(&quot;I think that density profiles with non-orthorhombic cells don't work.  If you want it have a look and see if you can work it out&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :     }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         46 :     for(unsigned i=0; i&lt;directions.size(); ++i) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         28 :       if( !confined[i] ) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         25 :         min[i]*=mycolv-&gt;getBox()(directions[i],directions[i]);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         25 :         max[i]*=mycolv-&gt;getBox()(directions[i],directions[i]);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :       } else {</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          3 :         min[i]=cmin[i]; max[i]=cmax[i];</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :       }</a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         46 :   for(unsigned i=0; i&lt;directions.size(); ++i) { Tools::convert(min[i],gmin[i]); Tools::convert(max[i],gmax[i]); }</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         18 :   ActionWithAveraging::clearAverage();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         18 :   mygrid-&gt;setBounds( gmin, gmax, nbins, gspacing ); resizeFunctions();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         36 : }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         26 : void MultiColvarDensity::prepareForAveraging() {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         62 :   for(unsigned i=0; i&lt;directions.size(); ++i) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         36 :     if( confined[i] ) continue;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         33 :     std::string max; Tools::convert( 0.5*mycolv-&gt;getBox()(directions[i],directions[i]), max );</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         33 :     if( max!=mygrid-&gt;getMax()[i] ) error(&quot;box size should be fixed.  Use FRACTIONAL&quot;);</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   }</a>
+<a name="280"><span class="lineNum">     280 </span>            :   // Ensure we only work with active multicolvars</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         26 :   deactivateAllTasks();</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">      21178 :   for(unsigned i=0; i&lt;stash-&gt;getNumberOfStoredValues(); ++i) taskFlags[i]=1;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         26 :   lockContributors();</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   // Retrieve the origin</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         26 :   origin = getPosition(0);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         26 : }</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      21152 : void MultiColvarDensity::compute( const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">      21152 :   std::vector&lt;double&gt; cvals( mycolv-&gt;getNumberOfQuantities() ); stash-&gt;retrieveSequentialValue( current, false, cvals );</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">      21152 :   Vector fpos, apos = pbcDistance( origin, mycolv-&gt;getCentralAtomPos( mycolv-&gt;getPositionInFullTaskList(current) ) );</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">      21152 :   if( fractional ) { fpos = getPbc().realToScaled( apos ); } else { fpos=apos; }</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">      84566 :   myvals.setValue( 0, cweight*cvals[0] ); for(unsigned j=0; j&lt;directions.size(); ++j) myvals.setValue( 1+j, fpos[ directions[j] ] );</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      21152 :   myvals.setValue( 1+directions.size(), cvals[1] );</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">      21152 : }</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : }</a>
+<a name="298"><span class="lineNum">     298 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarFilter.cpp.func-sort-c.html b/coverage/multicolvar/MultiColvarFilter.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ba529dcc47
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarFilter.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarFilter.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarFilter.cpp<span style="font-size: 80%;"> (<a href="MultiColvarFilter.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryMed">82.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarFilter.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#87">_ZN4PLMD11multicolvar17MultiColvarFilter15addBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#32">_ZN4PLMD11multicolvar17MultiColvarFilterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#32">_ZN4PLMD11multicolvar17MultiColvarFilterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#25">_ZN4PLMD11multicolvar17MultiColvarFilter16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#47">_ZN4PLMD11multicolvar17MultiColvarFilter28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#52">_ZNK4PLMD11multicolvar17MultiColvarFilter12completeTaskERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">20027</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarFilter.cpp.func.html b/coverage/multicolvar/MultiColvarFilter.cpp.func.html
new file mode 100644
index 0000000000..132ee702da
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarFilter.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarFilter.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarFilter.cpp<span style="font-size: 80%;"> (<a href="MultiColvarFilter.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryMed">82.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiColvarFilter.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#87">_ZN4PLMD11multicolvar17MultiColvarFilter15addBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#25">_ZN4PLMD11multicolvar17MultiColvarFilter16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#47">_ZN4PLMD11multicolvar17MultiColvarFilter28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#32">_ZN4PLMD11multicolvar17MultiColvarFilterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#32">_ZN4PLMD11multicolvar17MultiColvarFilterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.cpp.gcov.html#52">_ZNK4PLMD11multicolvar17MultiColvarFilter12completeTaskERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">20027</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarFilter.cpp.gcov.html b/coverage/multicolvar/MultiColvarFilter.cpp.gcov.html
new file mode 100644
index 0000000000..ec2b1c45b4
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarFilter.cpp.gcov.html
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarFilter.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarFilter.cpp<span style="font-size: 80%;"> (source / <a href="MultiColvarFilter.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntryMed">82.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarFilter.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace multicolvar {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         26 : void MultiColvarFilter::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         26 :   BridgedMultiColvarFunction::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         78 :   if( keys.reserved(&quot;VMEAN&quot;) ) keys.use(&quot;VMEAN&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        104 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MOMENTS&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         78 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         26 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         14 : MultiColvarFilter::MultiColvarFilter(const ActionOptions&amp;ao):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   Action(ao),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         14 :   BridgedMultiColvarFunction(ao)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         14 :   if( getPntrToMultiColvar()-&gt;isDensity() ) error(&quot;filtering/transforming density makes no sense&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         14 :   if( getName().find(&quot;MFILTER&quot;)!=std::string::npos ) filter=true;</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   else {</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          1 :     plumed_assert( getName().find(&quot;MTRANSFORM&quot;)!=std::string::npos );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          1 :     filter=false;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   }</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         14 :   readVesselKeywords();</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         14 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         46 : void MultiColvarFilter::doJobsRequiredBeforeTaskList() {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         46 :   ActionWithValue::clearDerivatives();</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         46 :   ActionWithVessel::doJobsRequiredBeforeTaskList();</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         46 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      20027 : void MultiColvarFilter::completeTask( const unsigned&amp; curr, MultiValue&amp; invals, MultiValue&amp; outvals ) const {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      20027 :   invals.copyValues( outvals );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      20027 :   if( derivativesAreRequired() ) invals.copyDerivatives( outvals );</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   // Retrieve the value of the multicolvar and apply filter</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      20027 :   double val=invals.get(1), df, weight=applyFilter( val, df );</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   // Now propegate derivatives</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      20027 :   if( filter &amp;&amp; !getPntrToMultiColvar()-&gt;weightHasDerivatives ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     outvals.setValue( 0, weight );</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      18447 :     if( derivativesAreRequired() ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">    2268072 :       for(unsigned i=0; i&lt;invals.getNumberActive(); ++i) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">    2253501 :         unsigned jder=invals.getActiveIndex(i);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">    2253501 :         outvals.addDerivative( 0, jder, df*invals.getDerivative(1, jder ) );</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :       }</a>
+<a name="69"><span class="lineNum">      69 </span>            :     }</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       1580 :   } else if( filter ) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :     double ww=outvals.get(0); outvals.setValue( 0, ww*weight );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :     if( derivativesAreRequired() ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;outvals.getNumberActive(); ++i) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :         unsigned ider=outvals.getActiveIndex(i);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :         outvals.setDerivative( 0, ider, weight*outvals.getDerivative(1,ider) + ww*df*outvals.getDerivative(0,ider) );</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :       }</a>
+<a name="77"><span class="lineNum">      77 </span>            :     }</a>
+<a name="78"><span class="lineNum">      78 </span>            :   } else {</a>
+<a name="79"><span class="lineNum">      79 </span>            :     outvals.setValue( 1, weight );</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       1580 :     if( derivativesAreRequired() ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      80912 :       for(unsigned i=0; i&lt;invals.getNumberActive(); ++i) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      79332 :         unsigned jder=invals.getActiveIndex(i);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      79332 :         outvals.setDerivative( 1, jder, df*invals.getDerivative(1, jder ) );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :       }</a>
+<a name="85"><span class="lineNum">      85 </span>            :     }</a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      20027 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 : void MultiColvarFilter::addBridgeForces( const std::vector&lt;double&gt;&amp; bb ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   plumed_dbg_assert( bb.size()==0 );</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarFilter.h.func-sort-c.html b/coverage/multicolvar/MultiColvarFilter.h.func-sort-c.html
new file mode 100644
index 0000000000..a645d18201
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarFilter.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarFilter.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarFilter.h<span style="font-size: 80%;"> (<a href="MultiColvarFilter.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarFilter.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.h.gcov.html#55">_ZNK4PLMD11multicolvar17MultiColvarFilter21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">28192</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarFilter.h.func.html b/coverage/multicolvar/MultiColvarFilter.h.func.html
new file mode 100644
index 0000000000..c8ff4d4120
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarFilter.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarFilter.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarFilter.h<span style="font-size: 80%;"> (<a href="MultiColvarFilter.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiColvarFilter.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarFilter.h.gcov.html#55">_ZNK4PLMD11multicolvar17MultiColvarFilter21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">28192</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarFilter.h.gcov.html b/coverage/multicolvar/MultiColvarFilter.h.gcov.html
new file mode 100644
index 0000000000..a20e5014b4
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarFilter.h.gcov.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarFilter.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarFilter.h<span style="font-size: 80%;"> (source / <a href="MultiColvarFilter.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_MultiColvarFilter_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_MultiColvarFilter_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;BridgedMultiColvarFunction.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace multicolvar {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /**</a>
+<a name="32"><span class="lineNum">      32 </span>            : \ingroup INHERIT</a>
+<a name="33"><span class="lineNum">      33 </span>            : This is the abstract base class to use for implementing a new way of filtering collective variable values</a>
+<a name="34"><span class="lineNum">      34 </span>            : to see whether or not they are within a certain range</a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class MultiColvarFilter : public BridgedMultiColvarFunction {</a>
+<a name="38"><span class="lineNum">      38 </span>            : private:</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Are we doing a filtering of the coordinates or a transoformation</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool filter;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit MultiColvarFilter(const ActionOptions&amp;);</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Do everything required to setup the derivatives</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void doJobsRequiredBeforeTaskList() override;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Get the number of quantities in the colvar</a>
+<a name="47"><span class="lineNum">      47 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Actually do what we are asked</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void completeTask( const unsigned&amp; curr, MultiValue&amp; invals, MultiValue&amp; outvals ) const override;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Do the filtering</a>
+<a name="51"><span class="lineNum">      51 </span>            :   virtual double applyFilter( const double&amp; val, double&amp; df ) const=0;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Just checks there are no bridging forces</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void addBridgeForces( const std::vector&lt;double&gt;&amp; bb );</a>
+<a name="54"><span class="lineNum">      54 </span>            : };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : inline</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      28192 : unsigned MultiColvarFilter::getNumberOfQuantities() const {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      28192 :   return getPntrToMultiColvar()-&gt;getNumberOfQuantities();</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarProduct.cpp.func-sort-c.html b/coverage/multicolvar/MultiColvarProduct.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4bd4ba4242
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarProduct.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarProduct.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarProduct.cpp<span style="font-size: 80%;"> (<a href="MultiColvarProduct.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiColvarProduct.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#59">_ZN4PLMD11multicolvar18MultiColvarProductC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#50">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarProductRegisterMe526createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#47">_ZN4PLMD11multicolvar18MultiColvarProduct10isPeriodicEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#59">_ZN4PLMD11multicolvar18MultiColvarProductC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#52">_ZN4PLMD11multicolvar18MultiColvarProduct16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#69">_ZNK4PLMD11multicolvar18MultiColvarProduct7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#50">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarProductRegisterMe52C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#50">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarProductRegisterMe52D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarProduct.cpp.func.html b/coverage/multicolvar/MultiColvarProduct.cpp.func.html
new file mode 100644
index 0000000000..5bf7482c40
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarProduct.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarProduct.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarProduct.cpp<span style="font-size: 80%;"> (<a href="MultiColvarProduct.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiColvarProduct.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#50">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarProductRegisterMe526createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#50">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarProductRegisterMe52C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#50">_ZN4PLMD11multicolvar12_GLOBAL__N_130MultiColvarProductRegisterMe52D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#47">_ZN4PLMD11multicolvar18MultiColvarProduct10isPeriodicEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#52">_ZN4PLMD11multicolvar18MultiColvarProduct16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#59">_ZN4PLMD11multicolvar18MultiColvarProductC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#59">_ZN4PLMD11multicolvar18MultiColvarProductC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiColvarProduct.cpp.gcov.html#69">_ZNK4PLMD11multicolvar18MultiColvarProduct7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/MultiColvarProduct.cpp.gcov.html b/coverage/multicolvar/MultiColvarProduct.cpp.gcov.html
new file mode 100644
index 0000000000..a9693574c4
--- /dev/null
+++ b/coverage/multicolvar/MultiColvarProduct.cpp.gcov.html
@@ -0,0 +1,165 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/MultiColvarProduct.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - MultiColvarProduct.cpp<span style="font-size: 80%;"> (source / <a href="MultiColvarProduct.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC MCOLVARF MCOLV_PRODUCT</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Calculate a product of multiple multicolvars</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \par Examples</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span>            : //+ENDPLUMEDOC</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace multicolvar {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class MultiColvarProduct : public MultiColvarBase {</a>
+<a name="42"><span class="lineNum">      42 </span>            : private:</a>
+<a name="43"><span class="lineNum">      43 </span>            : public:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="45"><span class="lineNum">      45 </span>            :   explicit MultiColvarProduct(const ActionOptions&amp;);</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Actually do the calculation</a>
+<a name="47"><span class="lineNum">      47 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Is the variable periodic</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :   bool isPeriodic() override { return false; }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : };</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(MultiColvarProduct,&quot;MCOLV_PRODUCT&quot;)</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 : void MultiColvarProduct::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          3 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;the multicolvars you are calculating the product of&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         15 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;SUM&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;HISTOGRAM&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         21 :   keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;); keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          3 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          1 : MultiColvarProduct::MultiColvarProduct(const ActionOptions&amp; ao):</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   Action(ao),</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          1 :   MultiColvarBase(ao)</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : {</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          1 :   buildSets();</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 :     if( mybasemulticolvars[i]-&gt;weightWithDerivatives() ) error(&quot;cannot take product of multicolvars with weights&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          1 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         15 : double MultiColvarProduct::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         15 :   double dot=1; std::vector&lt;double&gt; tval(2);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         45 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         30 :     getInputData( i, false, myatoms, tval );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         30 :     dot *= tval[1];</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         15 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         15 :     std::vector&lt;double&gt; cc(2);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         45 :     for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         30 :       getInputData( i, false, myatoms, cc ); cc[1] = dot / cc[1];</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         30 :       MultiValue&amp; myder=getInputDerivatives( i, false, myatoms );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         30 :       splitInputDerivatives( 1, 1, 2, i, cc, myder, myatoms );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :     }</a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         15 :   return dot;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/NumberOfLinks.cpp.func-sort-c.html b/coverage/multicolvar/NumberOfLinks.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d87ef73182
--- /dev/null
+++ b/coverage/multicolvar/NumberOfLinks.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/NumberOfLinks.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - NumberOfLinks.cpp<span style="font-size: 80%;"> (<a href="NumberOfLinks.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="NumberOfLinks.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#81">_ZN4PLMD11multicolvar13NumberOfLinks10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#103">_ZN4PLMD11multicolvar13NumberOfLinksC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#84">_ZN4PLMD11multicolvar12_GLOBAL__N_125NumberOfLinksRegisterMe866createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#103">_ZN4PLMD11multicolvar13NumberOfLinksC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#86">_ZN4PLMD11multicolvar13NumberOfLinks16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#84">_ZN4PLMD11multicolvar12_GLOBAL__N_125NumberOfLinksRegisterMe86C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#84">_ZN4PLMD11multicolvar12_GLOBAL__N_125NumberOfLinksRegisterMe86D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#136">_ZNK4PLMD11multicolvar13NumberOfLinks15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">8064</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#148">_ZNK4PLMD11multicolvar13NumberOfLinks7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">8064</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/NumberOfLinks.cpp.func.html b/coverage/multicolvar/NumberOfLinks.cpp.func.html
new file mode 100644
index 0000000000..cb7286dbca
--- /dev/null
+++ b/coverage/multicolvar/NumberOfLinks.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/NumberOfLinks.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - NumberOfLinks.cpp<span style="font-size: 80%;"> (<a href="NumberOfLinks.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="NumberOfLinks.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#84">_ZN4PLMD11multicolvar12_GLOBAL__N_125NumberOfLinksRegisterMe866createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#84">_ZN4PLMD11multicolvar12_GLOBAL__N_125NumberOfLinksRegisterMe86C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#84">_ZN4PLMD11multicolvar12_GLOBAL__N_125NumberOfLinksRegisterMe86D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#81">_ZN4PLMD11multicolvar13NumberOfLinks10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#86">_ZN4PLMD11multicolvar13NumberOfLinks16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#103">_ZN4PLMD11multicolvar13NumberOfLinksC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#103">_ZN4PLMD11multicolvar13NumberOfLinksC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#136">_ZNK4PLMD11multicolvar13NumberOfLinks15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">8064</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NumberOfLinks.cpp.gcov.html#148">_ZNK4PLMD11multicolvar13NumberOfLinks7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">8064</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/NumberOfLinks.cpp.gcov.html b/coverage/multicolvar/NumberOfLinks.cpp.gcov.html
new file mode 100644
index 0000000000..15e03e89d1
--- /dev/null
+++ b/coverage/multicolvar/NumberOfLinks.cpp.gcov.html
@@ -0,0 +1,251 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/NumberOfLinks.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - NumberOfLinks.cpp<span style="font-size: 80%;"> (source / <a href="NumberOfLinks.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC MCOLVARF NLINKS</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculate number of pairs of atoms/molecules that are linked</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : In its simplest guise this coordinate calculates a coordination number.  Each pair</a>
+<a name="35"><span class="lineNum">      35 </span>            : of atoms is assumed &quot;linked&quot; if they are within some cutoff of each other.  In more</a>
+<a name="36"><span class="lineNum">      36 </span>            : complex applications each entity is a vector and this quantity measures whether</a>
+<a name="37"><span class="lineNum">      37 </span>            : pairs of vectors are (a) within a certain cutoff and (b) if the two vectors have</a>
+<a name="38"><span class="lineNum">      38 </span>            : similar orientations.  The vectors on individual atoms could be Steinhardt parameters</a>
+<a name="39"><span class="lineNum">      39 </span>            : (see \ref Q3, \ref Q4 and \ref Q6) or they could describe some internal vector in a molecule.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The following calculates how many bonds there are in a system containing 64 atoms and outputs</a>
+<a name="44"><span class="lineNum">      44 </span>            : this quantity to a file.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \plumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : DENSITY SPECIES=1-64 LABEL=d1</a>
+<a name="48"><span class="lineNum">      48 </span>            : NLINKS GROUP=d1 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=dd FILE=colvar</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The following calculates how many pairs of neighboring atoms in a system containing 64 atoms have</a>
+<a name="53"><span class="lineNum">      53 </span>            : similar dispositions for the atoms in their coordination sphere.  This calculation uses the</a>
+<a name="54"><span class="lineNum">      54 </span>            : dot product of the Q6 vectors on adjacent atoms to measure whether or not two atoms have the same</a>
+<a name="55"><span class="lineNum">      55 </span>            : ``orientation&quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : Q6 SPECIES=1-64 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=q6</a>
+<a name="59"><span class="lineNum">      59 </span>            : NLINKS GROUP=q6 SWITCH={RATIONAL D_0=1.3 R_0=0.2} LABEL=dd</a>
+<a name="60"><span class="lineNum">      60 </span>            : PRINT ARG=dd FILE=colvar</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : */</a>
+<a name="64"><span class="lineNum">      64 </span>            : //+ENDPLUMEDOC</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace PLMD {</a>
+<a name="67"><span class="lineNum">      67 </span>            : namespace multicolvar {</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : class NumberOfLinks : public MultiColvarBase {</a>
+<a name="70"><span class="lineNum">      70 </span>            : private:</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// The values of the quantities in the dot products</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;double&gt; orient0, orient1;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// The switching function that tells us if atoms are close enough together</a>
+<a name="74"><span class="lineNum">      74 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="75"><span class="lineNum">      75 </span>            : public:</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="77"><span class="lineNum">      77 </span>            :   explicit NumberOfLinks(const ActionOptions&amp;);</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Do the stuff with the switching functions</a>
+<a name="79"><span class="lineNum">      79 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Actually do the calculation</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Is the variable periodic</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : };</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(NumberOfLinks,&quot;NLINKS&quot;)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          6 : void NumberOfLinks::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          6 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         12 :   keys.add(&quot;atoms&quot;,&quot;GROUP&quot;,&quot;&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-1&quot;,&quot;GROUPA&quot;,&quot;&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-1&quot;,&quot;GROUPB&quot;,&quot;&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;The n parameter of the switching function &quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;The m parameter of the switching function; 0 implies 2*NN&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;The r_0 parameter of the switching function&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;This keyword is used if you want to employ an alternative to the continuous switching function defined above. &quot;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :            &quot;The following provides information on the \\ref switchingfunction that are available. &quot;</a>
+<a name="99"><span class="lineNum">      99 </span>            :            &quot;When this keyword is present you no longer need the NN, MM, D_0 and R_0 keywords.&quot;);</a>
+<a name="100"><span class="lineNum">     100 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   keys.remove(&quot;LOWMEM&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         12 :   keys.addFlag(&quot;LOWMEM&quot;,false,&quot;lower the memory requirements&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 : NumberOfLinks::NumberOfLinks(const ActionOptions&amp; ao):</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   Action(ao),</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          4 :   MultiColvarBase(ao)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : {</a>
+<a name="109"><span class="lineNum">     109 </span>            :   // The weight of this does have derivatives</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          4 :   weightHasDerivatives=true;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   // Read in the switching function</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          8 :   std::string sw, errors; parse(&quot;SWITCH&quot;,sw);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          4 :   if(sw.length()&gt;0) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          4 :     switchingFunction.set(sw,errors);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   } else {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     double r_0=-1.0, d_0; int nn, mm;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     parse(&quot;NN&quot;,nn); parse(&quot;MM&quot;,mm);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     parse(&quot;R_0&quot;,r_0); parse(&quot;D_0&quot;,d_0);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     if( r_0&lt;0.0 ) error(&quot;you must set a value for R_0&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     switchingFunction.set(nn,mm,r_0,d_0);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          8 :   log.printf(&quot;  calculating number of links with atoms separation of %s\n&quot;,( switchingFunction.description() ).c_str() );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          8 :   std::vector&lt;AtomNumber&gt; all_atoms; readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          4 :   setupMultiColvarBase( all_atoms ); setLinkCellCutoff( switchingFunction.get_dmax() );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          4 :     if( !getBaseMultiColvar(i)-&gt;hasDifferentiableOrientation() ) error(&quot;cannot use multicolvar of type &quot; + getBaseMultiColvar(i)-&gt;getName() );</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   // Create holders for the collective variable</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          4 :   readVesselKeywords();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   plumed_assert( getNumberOfVessels()==0 );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 :   std::string input; addVessel( &quot;SUM&quot;, input, -1 );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   readVesselKeywords();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       8064 : double NumberOfLinks::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       8064 :   Vector distance = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       8064 :   double dfunc, sw = switchingFunction.calculateSqr( distance.modulo2(), dfunc );</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       8064 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       8064 :     addAtomDerivatives( 0, 0, (-dfunc)*weight*distance, myatoms );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       8064 :     addAtomDerivatives( 0, 1, (dfunc)*weight*distance, myatoms );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       8064 :     myatoms.addBoxDerivatives( 0, (-dfunc)*weight*Tensor(distance,distance) );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       8064 :   return sw;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       8064 : double NumberOfLinks::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       8064 :   if( getBaseMultiColvar(0)-&gt;getNumberOfQuantities()&lt;3 ) return 1.0;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       8064 :   unsigned ncomp=getBaseMultiColvar(0)-&gt;getNumberOfQuantities();</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       8064 :   std::vector&lt;double&gt; orient0( ncomp ), orient1( ncomp );</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       8064 :   getInputData( 0, true, myatoms, orient0 );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       8064 :   getInputData( 1, true, myatoms, orient1 );</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   double dot=0;</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">     185472 :   for(unsigned k=2; k&lt;orient0.size(); ++k) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     177408 :     dot+=orient0[k]*orient1[k];</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       8064 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       8064 :     MultiValue&amp; myder0=getInputDerivatives( 0, true, myatoms );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       8064 :     mergeInputDerivatives( 1, 2, orient1.size(), 0, orient1, myder0, myatoms );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       8064 :     MultiValue&amp; myder1=getInputDerivatives( 1, true, myatoms );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       8064 :     mergeInputDerivatives( 1, 2, orient0.size(), 1, orient0, myder1, myatoms );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   return dot;</a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Torsions.cpp.func-sort-c.html b/coverage/multicolvar/Torsions.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8c65bf6809
--- /dev/null
+++ b/coverage/multicolvar/Torsions.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Torsions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Torsions.cpp<span style="font-size: 80%;"> (<a href="Torsions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Torsions.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#96">_ZN4PLMD11multicolvar8TorsionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#83">_ZN4PLMD11multicolvar12_GLOBAL__N_120TorsionsRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#80">_ZN4PLMD11multicolvar8Torsions14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#96">_ZN4PLMD11multicolvar8TorsionsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#85">_ZN4PLMD11multicolvar8Torsions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#79">_ZN4PLMD11multicolvar8Torsions10isPeriodicEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#113">_ZNK4PLMD11multicolvar8Torsions7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#83">_ZN4PLMD11multicolvar12_GLOBAL__N_120TorsionsRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#83">_ZN4PLMD11multicolvar12_GLOBAL__N_120TorsionsRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Torsions.cpp.func.html b/coverage/multicolvar/Torsions.cpp.func.html
new file mode 100644
index 0000000000..76ea07327b
--- /dev/null
+++ b/coverage/multicolvar/Torsions.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Torsions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Torsions.cpp<span style="font-size: 80%;"> (<a href="Torsions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Torsions.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#83">_ZN4PLMD11multicolvar12_GLOBAL__N_120TorsionsRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#83">_ZN4PLMD11multicolvar12_GLOBAL__N_120TorsionsRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#83">_ZN4PLMD11multicolvar12_GLOBAL__N_120TorsionsRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#79">_ZN4PLMD11multicolvar8Torsions10isPeriodicEv</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#80">_ZN4PLMD11multicolvar8Torsions14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#85">_ZN4PLMD11multicolvar8Torsions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#96">_ZN4PLMD11multicolvar8TorsionsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#96">_ZN4PLMD11multicolvar8TorsionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsions.cpp.gcov.html#113">_ZNK4PLMD11multicolvar8Torsions7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/Torsions.cpp.gcov.html b/coverage/multicolvar/Torsions.cpp.gcov.html
new file mode 100644
index 0000000000..0331c95ea6
--- /dev/null
+++ b/coverage/multicolvar/Torsions.cpp.gcov.html
@@ -0,0 +1,211 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/Torsions.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - Torsions.cpp<span style="font-size: 80%;"> (source / <a href="Torsions.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace multicolvar {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC MCOLVAR TORSIONS</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Calculate whether or not a set of torsional angles are within a particular range.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The following provides an example of the input for the TORSIONS command</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : TORSIONS ...</a>
+<a name="43"><span class="lineNum">      43 </span>            : ATOMS1=168,170,172,188</a>
+<a name="44"><span class="lineNum">      44 </span>            : ATOMS2=170,172,188,190</a>
+<a name="45"><span class="lineNum">      45 </span>            : ATOMS3=188,190,192,230</a>
+<a name="46"><span class="lineNum">      46 </span>            : BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="47"><span class="lineNum">      47 </span>            : LABEL=ab</a>
+<a name="48"><span class="lineNum">      48 </span>            : ... TORSIONS</a>
+<a name="49"><span class="lineNum">      49 </span>            : PRINT ARG=ab.* FILE=colvar STRIDE=10</a>
+<a name="50"><span class="lineNum">      50 </span>            : \endplumedfile</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : Writing out the atoms involved in all the torsion angles in this way can be rather tedious. Thankfully if you are working with protein you</a>
+<a name="53"><span class="lineNum">      53 </span>            : can avoid this by using the \ref MOLINFO command.  PLUMED uses the pdb file that you provide to this command to learn</a>
+<a name="54"><span class="lineNum">      54 </span>            : about the topology of the protein molecule.  This means that you can specify torsion angles using the following syntax:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \plumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="58"><span class="lineNum">      58 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=myprotein.pdb</a>
+<a name="59"><span class="lineNum">      59 </span>            : TORSIONS ...</a>
+<a name="60"><span class="lineNum">      60 </span>            : ATOMS1=@phi-3</a>
+<a name="61"><span class="lineNum">      61 </span>            : ATOMS2=@psi-3</a>
+<a name="62"><span class="lineNum">      62 </span>            : ATOMS3=@phi-4</a>
+<a name="63"><span class="lineNum">      63 </span>            : BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="64"><span class="lineNum">      64 </span>            : LABEL=ab</a>
+<a name="65"><span class="lineNum">      65 </span>            : ... TORSIONS</a>
+<a name="66"><span class="lineNum">      66 </span>            : PRINT ARG=ab.* FILE=colvar STRIDE=10</a>
+<a name="67"><span class="lineNum">      67 </span>            : \endplumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : Here, \@phi-3 tells plumed that you would like to calculate the \f$\phi\f$ angle in the third residue of the protein.</a>
+<a name="70"><span class="lineNum">      70 </span>            : Similarly \@psi-4 tells plumed that you want to calculate the \f$\psi\f$ angle of the fourth residue of the protein.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : */</a>
+<a name="74"><span class="lineNum">      74 </span>            : //+ENDPLUMEDOC</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : class Torsions : public MultiColvarBase {</a>
+<a name="77"><span class="lineNum">      77 </span>            : public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="79"><span class="lineNum">      79 </span>            :   explicit Torsions(const ActionOptions&amp;);</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          5 :   bool isPeriodic() override { return true; }</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          2 :   void retrieveDomain( std::string&amp; min, std::string&amp; max ) override { min=&quot;-pi&quot;; max=&quot;pi&quot;; }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : };</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Torsions,&quot;TORSIONS&quot;)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          4 : void Torsions::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          4 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the torsion angles you wish to calculate. &quot;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one torsion will be &quot;</a>
+<a name="91"><span class="lineNum">      91 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="92"><span class="lineNum">      92 </span>            :            &quot;provide the indices of four atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="93"><span class="lineNum">      93 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          8 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          8 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          4 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 : Torsions::Torsions(const ActionOptions&amp;ao):</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   Action(ao),</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   MultiColvarBase(ao)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span>            :   // Read in the atoms</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          2 :   int natoms=4; std::vector&lt;AtomNumber&gt; all_atoms;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          2 :   readAtomsLikeKeyword( &quot;ATOMS&quot;, natoms, all_atoms );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   std::vector&lt;bool&gt; catom_ind(4, false);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          2 :   catom_ind[1]=catom_ind[2]=true;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 :   setAtomsForCentralAtom( catom_ind );</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   // Read in the vessels</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   readVesselKeywords();</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   // And check everything has been read in correctly</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         36 : double Torsions::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         36 :   Vector d0,d1,d2;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         36 :   d0=getSeparation(myatoms.getPosition(1),myatoms.getPosition(0));</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         36 :   d1=getSeparation(myatoms.getPosition(2),myatoms.getPosition(1));</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         36 :   d2=getSeparation(myatoms.getPosition(3),myatoms.getPosition(2));</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         36 :   Vector dd0,dd1,dd2; PLMD::Torsion t;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         36 :   double value  = t.compute(d0,d1,d2,dd0,dd1,dd2);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         36 :   addAtomDerivatives(1,0,dd0,myatoms);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         36 :   addAtomDerivatives(1,1,dd1-dd0,myatoms);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         36 :   addAtomDerivatives(1,2,dd2-dd1,myatoms);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         36 :   addAtomDerivatives(1,3,-dd2,myatoms);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         36 :   myatoms.addBoxDerivatives  (1, -(extProduct(d0,dd0)+extProduct(d1,dd1)+extProduct(d2,dd2)));</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         36 :   return value;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeAround.cpp.func-sort-c.html b/coverage/multicolvar/VolumeAround.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c3b27ce1db
--- /dev/null
+++ b/coverage/multicolvar/VolumeAround.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeAround.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeAround.cpp<span style="font-size: 80%;"> (<a href="VolumeAround.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeAround.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#94">_ZN4PLMD11multicolvar12VolumeAroundC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#94">_ZN4PLMD11multicolvar12VolumeAroundC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_124VolumeAroundRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#83">_ZN4PLMD11multicolvar12VolumeAround16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#114">_ZN4PLMD11multicolvar12VolumeAround12setupRegionsEv</a></td>
+              <td class="coverFnHi">317</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_124VolumeAroundRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_124VolumeAroundRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#116">_ZNK4PLMD11multicolvar12VolumeAround21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">56393</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeAround.cpp.func.html b/coverage/multicolvar/VolumeAround.cpp.func.html
new file mode 100644
index 0000000000..ee7dc6a1de
--- /dev/null
+++ b/coverage/multicolvar/VolumeAround.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeAround.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeAround.cpp<span style="font-size: 80%;"> (<a href="VolumeAround.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeAround.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#114">_ZN4PLMD11multicolvar12VolumeAround12setupRegionsEv</a></td>
+              <td class="coverFnHi">317</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#83">_ZN4PLMD11multicolvar12VolumeAround16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#94">_ZN4PLMD11multicolvar12VolumeAroundC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#94">_ZN4PLMD11multicolvar12VolumeAroundC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_124VolumeAroundRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_124VolumeAroundRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_124VolumeAroundRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeAround.cpp.gcov.html#116">_ZNK4PLMD11multicolvar12VolumeAround21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">56393</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeAround.cpp.gcov.html b/coverage/multicolvar/VolumeAround.cpp.gcov.html
new file mode 100644
index 0000000000..af72f4b0d2
--- /dev/null
+++ b/coverage/multicolvar/VolumeAround.cpp.gcov.html
@@ -0,0 +1,230 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeAround.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeAround.cpp<span style="font-size: 80%;"> (source / <a href="VolumeAround.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC VOLUMES AROUND</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three</a>
+<a name="31"><span class="lineNum">      31 </span>            : dimensional space. For example, if we have the coordination numbers for all the atoms in the</a>
+<a name="32"><span class="lineNum">      32 </span>            : system each coordination number can be assumed to lie on the position of the central atom.</a>
+<a name="33"><span class="lineNum">      33 </span>            : Because each base quantity can be assigned to a particular point in space we can calculate functions of the</a>
+<a name="34"><span class="lineNum">      34 </span>            : distribution of base quantities in a particular part of the box by using:</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \f[</a>
+<a name="37"><span class="lineNum">      37 </span>            : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) w(x_i,y_i,z_i) }{ \sum_i w(x_i,y_i,z_i) }</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f]</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (x_i,y_i,z_i)\f$.</a>
+<a name="41"><span class="lineNum">      41 </span>            : The function \f$ w(x_i,y_i,z_i) \f$ measures whether or not the system is in the subregion of interest. It</a>
+<a name="42"><span class="lineNum">      42 </span>            : is equal to:</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \f[</a>
+<a name="45"><span class="lineNum">      45 </span>            : w(x_i,y_i,z_i) = \int_{xl}^{xu} \int_{yl}^{yu} \int_{zl}^{zu} \textrm{d}x\textrm{d}y\textrm{d}z K\left( \frac{x - x_i}{\sigma} \right)K\left( \frac{y - y_i}{\sigma} \right)K\left( \frac{z - z_i}{\sigma} \right)</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.</a>
+<a name="49"><span class="lineNum">      49 </span>            : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : When AROUND is used with the \ref DENSITY action the number of atoms in the specified region is calculated</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \par Examples</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The following commands tell plumed to calculate the average coordination number for the atoms</a>
+<a name="56"><span class="lineNum">      56 </span>            : that have x (in fractional coordinates) within 2.0 nm of the com of mass c1. The final value will be labeled s.mean.</a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : COM ATOMS=1-100 LABEL=c1</a>
+<a name="59"><span class="lineNum">      59 </span>            : COORDINATIONNUMBER SPECIES=1-100 R_0=1.0 LABEL=c</a>
+<a name="60"><span class="lineNum">      60 </span>            : AROUND DATA=c ATOM=c1 XLOWER=-2.0 XUPPER=2.0 SIGMA=0.1 MEAN LABEL=s</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : */</a>
+<a name="64"><span class="lineNum">      64 </span>            : //+ENDPLUMEDOC</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : namespace PLMD {</a>
+<a name="67"><span class="lineNum">      67 </span>            : namespace multicolvar {</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : class VolumeAround : public ActionVolume {</a>
+<a name="70"><span class="lineNum">      70 </span>            : private:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   Vector origin;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   bool dox, doy, doz;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double xlow, xhigh;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   double ylow, yhigh;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double zlow, zhigh;</a>
+<a name="76"><span class="lineNum">      76 </span>            : public:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="78"><span class="lineNum">      78 </span>            :   explicit VolumeAround(const ActionOptions&amp; ao);</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void setupRegions() override;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12548 : PLUMED_REGISTER_ACTION(VolumeAround,&quot;AROUND&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         24 : void VolumeAround::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         24 :   ActionVolume::registerKeywords( keys );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         48 :   keys.add(&quot;atoms&quot;,&quot;ATOM&quot;,&quot;the atom whose vicinity we are interested in examining&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;XLOWER&quot;,&quot;0.0&quot;,&quot;the lower boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;XUPPER&quot;,&quot;0.0&quot;,&quot;the upper boundary in x relative to the x coordinate of the atom (0 indicates use full extent of box).&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;YLOWER&quot;,&quot;0.0&quot;,&quot;the lower boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;YUPPER&quot;,&quot;0.0&quot;,&quot;the upper boundary in y relative to the y coordinate of the atom (0 indicates use full extent of box).&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;ZLOWER&quot;,&quot;0.0&quot;,&quot;the lower boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         48 :   keys.add(&quot;compulsory&quot;,&quot;ZUPPER&quot;,&quot;0.0&quot;,&quot;the upper boundary in z relative to the z coordinate of the atom (0 indicates use full extent of box).&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         24 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         22 : VolumeAround::VolumeAround(const ActionOptions&amp; ao):</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   Action(ao),</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         22 :   ActionVolume(ao)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : {</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         44 :   parseAtomList(&quot;ATOM&quot;,atom);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         22 :   if( atom.size()!=1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         22 :   log.printf(&quot;  boundaries for region are calculated based on positions of atom : %d\n&quot;,atom[0].serial() );</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         44 :   dox=true; parse(&quot;XLOWER&quot;,xlow); parse(&quot;XUPPER&quot;,xhigh);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         44 :   doy=true; parse(&quot;YLOWER&quot;,ylow); parse(&quot;YUPPER&quot;,yhigh);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         44 :   doz=true; parse(&quot;ZLOWER&quot;,zlow); parse(&quot;ZUPPER&quot;,zhigh);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         22 :   if( xlow==0.0 &amp;&amp; xhigh==0.0 ) dox=false;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         22 :   if( ylow==0.0 &amp;&amp; yhigh==0.0 ) doy=false;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         22 :   if( zlow==0.0 &amp;&amp; zhigh==0.0 ) doz=false;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         22 :   if( !dox &amp;&amp; !doy &amp;&amp; !doz ) error(&quot;no subregion defined use XLOWER, XUPPER, YLOWER, YUPPER, ZLOWER, ZUPPER&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         22 :   log.printf(&quot;  boundaries for region (region of interest about atom) : x %f %f, y %f %f, z %f %f \n&quot;,xlow,xhigh,ylow,yhigh,zlow,zhigh);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         22 :   checkRead(); requestAtoms(atom);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         22 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        317 : void VolumeAround::setupRegions() { }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      56393 : double VolumeAround::calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   // Setup the histogram bead</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     112786 :   HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   // Calculate position of atom wrt to origin</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      56393 :   Vector fpos=pbcDistance( getPosition(0), cpos );</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   double xcontr, ycontr, zcontr, xder, yder, zder;</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      56393 :   if( dox ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      32393 :     bead.set( xlow, xhigh, getSigma() );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      32393 :     xcontr=bead.calculate( fpos[0], xder );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   } else {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      24000 :     xcontr=1.; xder=0.;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      56393 :   if( doy ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      32000 :     bead.set( ylow, yhigh, getSigma() );</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      32000 :     ycontr=bead.calculate( fpos[1], yder );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   } else {</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      24393 :     ycontr=1.; yder=0.;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      56393 :   if( doz ) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      32000 :     bead.set( zlow, zhigh, getSigma() );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      32000 :     zcontr=bead.calculate( fpos[2], zder );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   } else {</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      24393 :     zcontr=1.; zder=0.;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      56393 :   derivatives[0]=xder*ycontr*zcontr;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      56393 :   derivatives[1]=xcontr*yder*zcontr;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      56393 :   derivatives[2]=xcontr*ycontr*zder;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Add derivatives wrt to position of origin atom</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      56393 :   refders[0] = -derivatives;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   // Add virial contribution</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      56393 :   vir -= Tensor(fpos,derivatives);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      56393 :   return xcontr*ycontr*zcontr;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeBetweenContours.cpp.func-sort-c.html b/coverage/multicolvar/VolumeBetweenContours.cpp.func-sort-c.html
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index 0000000000..4b70c67558
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@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeBetweenContours.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeBetweenContours.cpp<span style="font-size: 80%;"> (<a href="VolumeBetweenContours.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryLo">14.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeBetweenContours.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#76">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInEnvelopeRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#114">_ZN4PLMD11multicolvar16VolumeInEnvelope12setupRegionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#85">_ZN4PLMD11multicolvar16VolumeInEnvelopeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#85">_ZN4PLMD11multicolvar16VolumeInEnvelopeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#119">_ZNK4PLMD11multicolvar16VolumeInEnvelope21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#78">_ZN4PLMD11multicolvar16VolumeInEnvelope16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#76">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInEnvelopeRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#76">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInEnvelopeRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeBetweenContours.cpp.func.html b/coverage/multicolvar/VolumeBetweenContours.cpp.func.html
new file mode 100644
index 0000000000..6440133614
--- /dev/null
+++ b/coverage/multicolvar/VolumeBetweenContours.cpp.func.html
@@ -0,0 +1,104 @@
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeBetweenContours.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeBetweenContours.cpp<span style="font-size: 80%;"> (<a href="VolumeBetweenContours.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryLo">14.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeBetweenContours.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#76">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInEnvelopeRegisterMe786createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#76">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInEnvelopeRegisterMe78C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#76">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInEnvelopeRegisterMe78D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#114">_ZN4PLMD11multicolvar16VolumeInEnvelope12setupRegionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#78">_ZN4PLMD11multicolvar16VolumeInEnvelope16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#85">_ZN4PLMD11multicolvar16VolumeInEnvelopeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#85">_ZN4PLMD11multicolvar16VolumeInEnvelopeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeBetweenContours.cpp.gcov.html#119">_ZNK4PLMD11multicolvar16VolumeInEnvelope21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeBetweenContours.cpp.gcov.html b/coverage/multicolvar/VolumeBetweenContours.cpp.gcov.html
new file mode 100644
index 0000000000..f845e2e4ba
--- /dev/null
+++ b/coverage/multicolvar/VolumeBetweenContours.cpp.gcov.html
@@ -0,0 +1,222 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeBetweenContours.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeBetweenContours.cpp<span style="font-size: 80%;"> (source / <a href="VolumeBetweenContours.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryLo">14.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">37.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;memory&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC VOLUMES INENVELOPE</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a region where the density of a certain type of atom is high.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This collective variable can be used to determine whether colvars are within region where the density</a>
+<a name="34"><span class="lineNum">      34 </span>            : of a particular atom is high.  This is achieved by calculating the following function at the point where</a>
+<a name="35"><span class="lineNum">      35 </span>            : the atom is located \f$(x,y,z)\f$:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : w_j = 1 - \sigma\left[ \sum_{i=1}^N K\left( \frac{x-x_i}{\sigma_x},\frac{y-y_i}{\sigma_y},\frac{z-z_i}{\sigma_z} \right) \right]</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : Here \f$\sigma\f$ is a \ref switchingfunction and \f$K\f$ is a \ref kernelfunctions.  The sum runs over the atoms</a>
+<a name="42"><span class="lineNum">      42 </span>            : specified using the ATOMS keyword and a \f$w_j\f$ value is calculated for each of the central atoms of the input</a>
+<a name="43"><span class="lineNum">      43 </span>            : multicolvar.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \par Examples</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The input below calculates a density field from the positions of atoms 1-14400.  The number of the atoms</a>
+<a name="48"><span class="lineNum">      48 </span>            : that are specified in the DENSITY action that are within a region where the density field is greater than</a>
+<a name="49"><span class="lineNum">      49 </span>            : 2.0 is then calculated.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : d1: DENSITY SPECIES=14401-74134:3 LOWMEM</a>
+<a name="53"><span class="lineNum">      53 </span>            : fi: INENVELOPE DATA=d1 ATOMS=1-14400 CONTOUR={RATIONAL D_0=2.0 R_0=1.0} BANDWIDTH=0.1,0.1,0.1 LOWMEM</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=fi FILE=colvar</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : */</a>
+<a name="58"><span class="lineNum">      58 </span>            : //+ENDPLUMEDOC</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : namespace PLMD {</a>
+<a name="61"><span class="lineNum">      61 </span>            : namespace multicolvar {</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : class VolumeInEnvelope : public ActionVolume {</a>
+<a name="64"><span class="lineNum">      64 </span>            : private:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   LinkCells mylinks;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::unique_ptr&lt;KernelFunctions&gt; kernel;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; pos;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;Vector&gt; ltmp_pos;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;unsigned&gt; ltmp_ind;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   SwitchingFunction sfunc;</a>
+<a name="71"><span class="lineNum">      71 </span>            : public:</a>
+<a name="72"><span class="lineNum">      72 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="73"><span class="lineNum">      73 </span>            :   explicit VolumeInEnvelope(const ActionOptions&amp; ao);</a>
+<a name="74"><span class="lineNum">      74 </span>            :   void setupRegions() override;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const override;</a>
+<a name="76"><span class="lineNum">      76 </span>            : };</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(VolumeInEnvelope,&quot;INENVELOPE&quot;)</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          2 : void VolumeInEnvelope::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          2 :   ActionVolume::registerKeywords( keys ); keys.remove(&quot;SIGMA&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the atom whose positions we are constructing a field from&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BANDWIDTH&quot;,&quot;the bandwidths for kernel density estimation&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;CONTOUR&quot;,&quot;a switching function that tells PLUMED how large the density should be&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 : VolumeInEnvelope::VolumeInEnvelope(const ActionOptions&amp; ao):</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   Action(ao),</a>
+<a name="89"><span class="lineNum">      89 </span>            :   ActionVolume(ao),</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   mylinks(comm)</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : {</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :   std::vector&lt;AtomNumber&gt; atoms; parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   log.printf(&quot;  creating density field from atoms : &quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot;%d &quot;,atoms[i].serial() );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :   log.printf(&quot;\n&quot;); ltmp_ind.resize( atoms.size() ); ltmp_pos.resize( atoms.size() );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;atoms.size(); ++i) ltmp_ind[i]=i;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   std::string sw, errors; parse(&quot;CONTOUR&quot;,sw);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   if(sw.length()==0) error(&quot;missing CONTOURkeyword&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   sfunc.set(sw,errors);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   if( errors.length()!=0 ) error(&quot;problem reading RADIUS keyword : &quot; + errors );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   log.printf(&quot;  density at atom must be larger than %s \n&quot;, ( sfunc.description() ).c_str() );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; pp(3,0.0), bandwidth(3); parseVector(&quot;BANDWIDTH&quot;,bandwidth);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   log.printf(&quot;  using %s kernel with bandwidths %f %f %f \n&quot;,getKernelType().c_str(),bandwidth[0],bandwidth[1],bandwidth[2] );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   kernel=Tools::make_unique&lt;KernelFunctions&gt;( pp, bandwidth, getKernelType(), &quot;DIAGONAL&quot;, 1.0 );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;3; ++i) { pos.emplace_back(Tools::make_unique&lt;Value&gt;()); pos[i]-&gt;setNotPeriodic(); }</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; csupport( kernel-&gt;getContinuousSupport() );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :   double maxs = csupport[0];</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   for(unsigned i=1; i&lt;csupport.size(); ++i) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     if( csupport[i]&gt;maxs ) maxs = csupport[i];</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   checkRead(); requestAtoms(atoms); mylinks.setCutoff( maxs );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 : void VolumeInEnvelope::setupRegions() {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ltmp_ind.size(); ++i) { ltmp_pos[i]=getPosition(i); }</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   mylinks.buildCellLists( ltmp_pos, ltmp_ind, getPbc() );</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 : double VolumeInEnvelope::calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :   unsigned ncells_required=0, natoms=1; std::vector&lt;unsigned&gt; cells_required( mylinks.getNumberOfCells() ), indices( 1 + getNumberOfAtoms() );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :   mylinks.addRequiredCells( mylinks.findMyCell( cpos ), ncells_required, cells_required );</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :   indices[0]=getNumberOfAtoms(); mylinks.retrieveAtomsInCells( ncells_required, cells_required, natoms, indices );</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   double value=0; std::vector&lt;double&gt; der(3); Vector tder;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   // convert pointer once</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   auto pos_ptr=Tools::unique2raw(pos);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :   for(unsigned i=1; i&lt;natoms; ++i) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     Vector dist = getSeparation( cpos, getPosition( indices[i] ) );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;3; ++j) pos[j]-&gt;set( dist[j] );</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     value += kernel-&gt;evaluate( pos_ptr, der, true );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :       derivatives[j] -= der[j]; refders[ indices[i] ][j] += der[j]; tder[j]=der[j];</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :     }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     vir -= Tensor( tder, dist );</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   double deriv, fval = sfunc.calculate( value, deriv );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   derivatives *= -deriv*value; vir *= -deriv*value;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   for(unsigned i=1; i&lt;natoms; ++i) refders[ indices[i] ] *= -deriv*value;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   return 1.0 - fval;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeCavity.cpp.func-sort-c.html b/coverage/multicolvar/VolumeCavity.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5046c8dd05
--- /dev/null
+++ b/coverage/multicolvar/VolumeCavity.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeCavity.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeCavity.cpp<span style="font-size: 80%;"> (<a href="VolumeCavity.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntry">214</td>
+            <td class="headerCovTableEntryMed">79.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeCavity.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#135">_ZN4PLMD11multicolvar12VolumeCavityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#177">_ZN4PLMD11multicolvar12VolumeCavityD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#135">_ZN4PLMD11multicolvar12VolumeCavityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#177">_ZN4PLMD11multicolvar12VolumeCavityD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#177">_ZN4PLMD11multicolvar12VolumeCavityD1Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#125">_ZN4PLMD11multicolvar12_GLOBAL__N_125VolumeCavityRegisterMe1276createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#127">_ZN4PLMD11multicolvar12VolumeCavity16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#319">_ZN4PLMD11multicolvar12VolumeCavity6updateEv</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#180">_ZN4PLMD11multicolvar12VolumeCavity12setupRegionsEv</a></td>
+              <td class="coverFnHi">1620</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#355">_ZNK4PLMD11multicolvar12VolumeCavity21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">1620</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#125">_ZN4PLMD11multicolvar12_GLOBAL__N_125VolumeCavityRegisterMe127C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#125">_ZN4PLMD11multicolvar12_GLOBAL__N_125VolumeCavityRegisterMe127D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeCavity.cpp.func.html b/coverage/multicolvar/VolumeCavity.cpp.func.html
new file mode 100644
index 0000000000..8e9359fd1e
--- /dev/null
+++ b/coverage/multicolvar/VolumeCavity.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeCavity.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeCavity.cpp<span style="font-size: 80%;"> (<a href="VolumeCavity.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntry">214</td>
+            <td class="headerCovTableEntryMed">79.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeCavity.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#180">_ZN4PLMD11multicolvar12VolumeCavity12setupRegionsEv</a></td>
+              <td class="coverFnHi">1620</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#127">_ZN4PLMD11multicolvar12VolumeCavity16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#319">_ZN4PLMD11multicolvar12VolumeCavity6updateEv</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#135">_ZN4PLMD11multicolvar12VolumeCavityC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#135">_ZN4PLMD11multicolvar12VolumeCavityC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#177">_ZN4PLMD11multicolvar12VolumeCavityD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#177">_ZN4PLMD11multicolvar12VolumeCavityD1Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#177">_ZN4PLMD11multicolvar12VolumeCavityD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#125">_ZN4PLMD11multicolvar12_GLOBAL__N_125VolumeCavityRegisterMe1276createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#125">_ZN4PLMD11multicolvar12_GLOBAL__N_125VolumeCavityRegisterMe127C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#125">_ZN4PLMD11multicolvar12_GLOBAL__N_125VolumeCavityRegisterMe127D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeCavity.cpp.gcov.html#355">_ZNK4PLMD11multicolvar12VolumeCavity21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">1620</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeCavity.cpp.gcov.html b/coverage/multicolvar/VolumeCavity.cpp.gcov.html
new file mode 100644
index 0000000000..901b462153
--- /dev/null
+++ b/coverage/multicolvar/VolumeCavity.cpp.gcov.html
@@ -0,0 +1,488 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeCavity.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeCavity.cpp<span style="font-size: 80%;"> (source / <a href="VolumeCavity.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntry">214</td>
+            <td class="headerCovTableEntryMed">79.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC VOLUMES CAVITY</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a box defined by the positions of four atoms.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three</a>
+<a name="34"><span class="lineNum">      34 </span>            : dimensional space. For example, if we have the coordination numbers for all the atoms in the</a>
+<a name="35"><span class="lineNum">      35 </span>            : system each coordination number can be assumed to lie on the position of the central atom.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Because each base quantity can be assigned to a particular point in space we can calculate functions of the</a>
+<a name="37"><span class="lineNum">      37 </span>            : distribution of base quantities in a particular part of the box by using:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) w(u_i,v_i,w_i) }{ \sum_i w(u_i,v_i,w_i) }</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (u_i,v_i,z_i)\f$.</a>
+<a name="44"><span class="lineNum">      44 </span>            : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Notice that here (at variance with what is done in \ref AROUND) we have transformed from the usual \f$(x_i,y_i,z_i)\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : position to a position in \f$ (u_i,v_i,z_i)\f$.  This is done using a rotation matrix as follows:</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : \left(</a>
+<a name="50"><span class="lineNum">      50 </span>            : \begin{matrix}</a>
+<a name="51"><span class="lineNum">      51 </span>            :  u_i \\</a>
+<a name="52"><span class="lineNum">      52 </span>            :  v_i \\</a>
+<a name="53"><span class="lineNum">      53 </span>            :  w_i</a>
+<a name="54"><span class="lineNum">      54 </span>            : \end{matrix}</a>
+<a name="55"><span class="lineNum">      55 </span>            : \right) = \mathbf{R}</a>
+<a name="56"><span class="lineNum">      56 </span>            : \left(</a>
+<a name="57"><span class="lineNum">      57 </span>            : \begin{matrix}</a>
+<a name="58"><span class="lineNum">      58 </span>            :  x_i - x_o \\</a>
+<a name="59"><span class="lineNum">      59 </span>            :  y_i - y_o \\</a>
+<a name="60"><span class="lineNum">      60 </span>            :  z_i - z_o</a>
+<a name="61"><span class="lineNum">      61 </span>            : \end{matrix}</a>
+<a name="62"><span class="lineNum">      62 </span>            : \right)</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f]</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : where \f$\mathbf{R}\f$ is a rotation matrix that is calculated by constructing a set of three orthonormal vectors from the</a>
+<a name="66"><span class="lineNum">      66 </span>            : reference positions specified by the user. The first of these unit vectors points from the first reference atom to the second.</a>
+<a name="67"><span class="lineNum">      67 </span>            : The second is then the normal to the plane containing atoms 1,2 and 3 and the the third is the unit vector orthogonal to</a>
+<a name="68"><span class="lineNum">      68 </span>            : these first two vectors.  \f$(x_o,y_o,z_o)\f$, meanwhile, specifies the position of the first reference atom.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : In the previous function \f$ w(u_i,v_i,w_i) \f$ measures whether or not the system is in the subregion of interest. It</a>
+<a name="71"><span class="lineNum">      71 </span>            : is equal to:</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \f[</a>
+<a name="74"><span class="lineNum">      74 </span>            : w(u_i,v_i,w_i) = \int_{0}^{u'} \int_{0}^{v'} \int_{0}^{w'} \textrm{d}u\textrm{d}v\textrm{d}w</a>
+<a name="75"><span class="lineNum">      75 </span>            :    K\left( \frac{u - u_i}{\sigma} \right)K\left( \frac{v - v_i}{\sigma} \right)K\left( \frac{w - w_i}{\sigma} \right)</a>
+<a name="76"><span class="lineNum">      76 </span>            : \f]</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.</a>
+<a name="79"><span class="lineNum">      79 </span>            : The vector connecting atom 1 to atom 4 is used to define the extent of the box in each of the \f$u\f$, \f$v\f$ and \f$w\f$</a>
+<a name="80"><span class="lineNum">      80 </span>            : directions.  Essentially the vector connecting atom 1 to atom 4 is projected onto the three unit vectors</a>
+<a name="81"><span class="lineNum">      81 </span>            : described above and the resulting projections determine the \f$u'\f$, \f$v'\f$ and \f$w'\f$ parameters in the above expression.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \par Examples</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The following commands tell plumed to calculate the number of atoms in an ion channel in a protein.</a>
+<a name="86"><span class="lineNum">      86 </span>            : The extent of the channel is calculated from the positions of atoms 1, 4, 5 and 11. The final value will be labeled cav.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \plumedfile</a>
+<a name="89"><span class="lineNum">      89 </span>            : d1: DENSITY SPECIES=20-500</a>
+<a name="90"><span class="lineNum">      90 </span>            : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endplumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water</a>
+<a name="94"><span class="lineNum">      94 </span>            : molecules in the protein channel described above.  The average coordination number and the number of coordination</a>
+<a name="95"><span class="lineNum">      95 </span>            : numbers more than 4 is then calculated.  The values of these two quantities are given the labels cav.mean and cav.morethan</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : \plumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : d1: COORDINATIONNUMBER SPECIES=20-500 R_0=0.1</a>
+<a name="99"><span class="lineNum">      99 </span>            : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav</a>
+<a name="100"><span class="lineNum">     100 </span>            : \endplumedfile</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : */</a>
+<a name="103"><span class="lineNum">     103 </span>            : //+ENDPLUMEDOC</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : namespace PLMD {</a>
+<a name="106"><span class="lineNum">     106 </span>            : namespace multicolvar {</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : class VolumeCavity : public ActionVolume {</a>
+<a name="109"><span class="lineNum">     109 </span>            : private:</a>
+<a name="110"><span class="lineNum">     110 </span>            :   bool boxout;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   OFile boxfile;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   double lenunit;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double jacob_det;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   double len_bi, len_cross, len_perp, sigma;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   Vector origin, bi, cross, perp;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::vector&lt;Vector&gt; dlbi, dlcross, dlperp;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;Tensor&gt; dbi, dcross, dperp;</a>
+<a name="118"><span class="lineNum">     118 </span>            : public:</a>
+<a name="119"><span class="lineNum">     119 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="120"><span class="lineNum">     120 </span>            :   explicit VolumeCavity(const ActionOptions&amp; ao);</a>
+<a name="121"><span class="lineNum">     121 </span>            :   ~VolumeCavity();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   void setupRegions() override;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void update() override;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const override;</a>
+<a name="125"><span class="lineNum">     125 </span>            : };</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(VolumeCavity,&quot;CAVITY&quot;)</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          4 : void VolumeCavity::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          4 :   ActionVolume::registerKeywords( keys );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the positions of four atoms that define spatial extent of the cavity&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          8 :   keys.addFlag(&quot;PRINT_BOX&quot;,false,&quot;write out the positions of the corners of the box to an xyz file&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;the file on which to write out the box coordinates&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;UNITS&quot;,&quot;( default=nm ) the units in which to write out the corners of the box&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 : }</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 : VolumeCavity::VolumeCavity(const ActionOptions&amp; ao):</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   Action(ao),</a>
+<a name="139"><span class="lineNum">     139 </span>            :   ActionVolume(ao),</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :   boxout(false),</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :   lenunit(1.0),</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          2 :   dlbi(4),</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 :   dlcross(4),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :   dlperp(4),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :   dbi(3),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 :   dcross(3),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 :   dperp(3)</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : {</a>
+<a name="149"><span class="lineNum">     149 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          4 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          2 :   if( atoms.size()!=4 ) error(&quot;number of atoms should be equal to four&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          2 :   log.printf(&quot;  boundaries for region are calculated based on positions of atoms : &quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot;%d &quot;,atoms[i].serial() );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          2 :   boxout=false; parseFlag(&quot;PRINT_BOX&quot;,boxout);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          2 :   if(boxout) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     std::string boxfname; parse(&quot;FILE&quot;,boxfname);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     if(boxfname.length()==0) error(&quot;no name for box file specified&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     std::string unitname; parse(&quot;UNITS&quot;,unitname);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     if ( unitname.length()&gt;0 ) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :       Units u; u.setLength(unitname);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :       lenunit=plumed.getAtoms().getUnits().getLength()/u.getLength();</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     } else {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :       unitname=&quot;nm&quot;;</a>
+<a name="167"><span class="lineNum">     167 </span>            :     }</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     boxfile.link(*this);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     boxfile.open( boxfname );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     log.printf(&quot;  printing box coordinates on file named %s in %s \n&quot;,boxfname.c_str(), unitname.c_str() );</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :   requestAtoms(atoms);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   // We have to readd the dependency because requestAtoms removes it</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   addDependency( getPntrToMultiColvar() );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 : }</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          4 : VolumeCavity::~VolumeCavity() {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          4 : }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       1620 : void VolumeCavity::setupRegions() {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   // Make some space for things</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       1620 :   Vector d1, d2, d3;</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            :   // Retrieve the sigma value</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       1620 :   sigma=getSigma();</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   // Set the position of the origin</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       1620 :   origin=getPosition(0);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Get two vectors</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1620 :   d1 = pbcDistance(origin,getPosition(1));</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       1620 :   double d1l=d1.modulo();</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1620 :   d2 = pbcDistance(origin,getPosition(2));</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   // Find the vector connecting the origin to the top corner of</a>
+<a name="197"><span class="lineNum">     197 </span>            :   // the subregion</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       1620 :   d3 = pbcDistance(origin,getPosition(3));</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   // Create a set of unit vectors</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1620 :   bi = d1 / d1l; len_bi=dotProduct( d3, bi );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       1620 :   cross = crossProduct( d1, d2 ); double crossmod=cross.modulo();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       1620 :   cross = cross / crossmod; len_cross=dotProduct( d3, cross );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       1620 :   perp = crossProduct( cross, bi ); len_perp=dotProduct( d3, perp );</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            :   // Calculate derivatives of box shape with respect to atoms</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       1620 :   double d1l3=d1l*d1l*d1l;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       1620 :   dbi[0](0,0) = ( -(d1[1]*d1[1]+d1[2]*d1[2])/d1l3 );   // dx/dx</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1620 :   dbi[0](0,1) = (  d1[0]*d1[1]/d1l3 );                 // dx/dy</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       1620 :   dbi[0](0,2) = (  d1[0]*d1[2]/d1l3 );                 // dx/dz</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       1620 :   dbi[0](1,0) = (  d1[1]*d1[0]/d1l3 );                 // dy/dx</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       1620 :   dbi[0](1,1) = ( -(d1[0]*d1[0]+d1[2]*d1[2])/d1l3 );   // dy/dy</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1620 :   dbi[0](1,2) = (  d1[1]*d1[2]/d1l3 );</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1620 :   dbi[0](2,0) = (  d1[2]*d1[0]/d1l3 );</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1620 :   dbi[0](2,1) = (  d1[2]*d1[1]/d1l3 );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1620 :   dbi[0](2,2) = ( -(d1[1]*d1[1]+d1[0]*d1[0])/d1l3 );</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       1620 :   dbi[1](0,0) = ( (d1[1]*d1[1]+d1[2]*d1[2])/d1l3 );</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1620 :   dbi[1](0,1) = ( -d1[0]*d1[1]/d1l3 );</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       1620 :   dbi[1](0,2) = ( -d1[0]*d1[2]/d1l3 );</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       1620 :   dbi[1](1,0) = ( -d1[1]*d1[0]/d1l3 );</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       1620 :   dbi[1](1,1) = ( (d1[0]*d1[0]+d1[2]*d1[2])/d1l3 );</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       1620 :   dbi[1](1,2) = ( -d1[1]*d1[2]/d1l3 );</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       1620 :   dbi[1](2,0) = ( -d1[2]*d1[0]/d1l3 );</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       1620 :   dbi[1](2,1) = ( -d1[2]*d1[1]/d1l3 );</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       1620 :   dbi[1](2,2) = ( (d1[1]*d1[1]+d1[0]*d1[0])/d1l3 );</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       1620 :   dbi[2].zero();</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       1620 :   Tensor tcderiv; double cmod3=crossmod*crossmod*crossmod; Vector ucross=crossmod*cross;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       1620 :   tcderiv.setCol( 0, crossProduct( d1, Vector(-1.0,0.0,0.0) ) + crossProduct( Vector(-1.0,0.0,0.0), d2 ) );</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       1620 :   tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,-1.0,0.0) ) + crossProduct( Vector(0.0,-1.0,0.0), d2 ) );</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       1620 :   tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,-1.0) ) + crossProduct( Vector(0.0,0.0,-1.0), d2 ) );</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">       1620 :   dcross[0](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dx/dx</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       1620 :   dcross[0](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dx/dy</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       1620 :   dcross[0](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dx/dz</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       1620 :   dcross[0](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dy/dx</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       1620 :   dcross[0](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dy/dy</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       1620 :   dcross[0](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dy/dz</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       1620 :   dcross[0](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dz/dx</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       1620 :   dcross[0](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dz/dy</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       1620 :   dcross[0](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dz/dz</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       1620 :   tcderiv.setCol( 0, crossProduct( Vector(1.0,0.0,0.0), d2 ) );</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">       1620 :   tcderiv.setCol( 1, crossProduct( Vector(0.0,1.0,0.0), d2 ) );</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">       1620 :   tcderiv.setCol( 2, crossProduct( Vector(0.0,0.0,1.0), d2 ) );</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">       1620 :   dcross[1](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dx/dx</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       1620 :   dcross[1](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dx/dy</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       1620 :   dcross[1](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dx/dz</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       1620 :   dcross[1](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dy/dx</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       1620 :   dcross[1](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dy/dy</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       1620 :   dcross[1](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dy/dz</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       1620 :   dcross[1](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dz/dx</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       1620 :   dcross[1](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dz/dy</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       1620 :   dcross[1](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dz/dz</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       1620 :   tcderiv.setCol( 0, crossProduct( d1, Vector(1.0,0.0,0.0) ) );</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       1620 :   tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,1.0,0.0) ) );</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       1620 :   tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,1.0) ) );</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       1620 :   dcross[2](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dx/dx</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       1620 :   dcross[2](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dx/dy</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       1620 :   dcross[2](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dx/dz</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       1620 :   dcross[2](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dy/dx</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       1620 :   dcross[2](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dy/dy</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       1620 :   dcross[2](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dy/dz</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       1620 :   dcross[2](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dz/dx</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       1620 :   dcross[2](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dz/dy</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       1620 :   dcross[2](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dz/dz</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       1620 :   dperp[0].setCol( 0, ( crossProduct( dcross[0].getCol(0), bi ) + crossProduct( cross, dbi[0].getCol(0) ) ) );</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       1620 :   dperp[0].setCol( 1, ( crossProduct( dcross[0].getCol(1), bi ) + crossProduct( cross, dbi[0].getCol(1) ) ) );</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       1620 :   dperp[0].setCol( 2, ( crossProduct( dcross[0].getCol(2), bi ) + crossProduct( cross, dbi[0].getCol(2) ) ) );</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">       1620 :   dperp[1].setCol( 0, ( crossProduct( dcross[1].getCol(0), bi ) + crossProduct( cross, dbi[1].getCol(0) ) ) );</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       1620 :   dperp[1].setCol( 1, ( crossProduct( dcross[1].getCol(1), bi ) + crossProduct( cross, dbi[1].getCol(1) ) ) );</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1620 :   dperp[1].setCol( 2, ( crossProduct( dcross[1].getCol(2), bi ) + crossProduct( cross, dbi[1].getCol(2) ) ) );</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       1620 :   dperp[2].setCol( 0, ( crossProduct( dcross[2].getCol(0), bi ) ) );</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       1620 :   dperp[2].setCol( 1, ( crossProduct( dcross[2].getCol(1), bi ) ) );</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       1620 :   dperp[2].setCol( 2, ( crossProduct( dcross[2].getCol(2), bi ) ) );</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            :   // Ensure that all lengths are positive</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       1620 :   if( len_bi&lt;0 ) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :     bi=-bi; len_bi=-len_bi;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; ++i) dbi[i]*=-1.0;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">       1620 :   if( len_cross&lt;0 ) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     cross=-cross; len_cross=-len_cross;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; ++i) dcross[i]*=-1.0;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       1620 :   if( len_perp&lt;0 ) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :     perp=-perp; len_perp=-len_perp;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; ++i) dperp[i]*=-1.0;</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       1620 :   if( len_bi&lt;=0 || len_cross&lt;=0 || len_perp&lt;=0 ) plumed_merror(&quot;Invalid box coordinates&quot;);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :   // Now derivatives of lengths</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       1620 :   Tensor dd3( Tensor::identity() );</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1620 :   dlbi[0] = matmul(d3,dbi[0]) - matmul(bi,dd3);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       1620 :   dlbi[1] = matmul(d3,dbi[1]);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1620 :   dlbi[2] = matmul(d3,dbi[2]);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       1620 :   dlbi[3] = matmul(bi,dd3);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       1620 :   dlcross[0] = matmul(d3,dcross[0]) - matmul(cross,dd3);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       1620 :   dlcross[1] = matmul(d3,dcross[1]);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       1620 :   dlcross[2] = matmul(d3,dcross[2]);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       1620 :   dlcross[3] = matmul(cross,dd3);</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       1620 :   dlperp[0] = matmul(d3,dperp[0]) - matmul(perp,dd3);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1620 :   dlperp[1] = matmul(d3,dperp[1]);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">       1620 :   dlperp[2] = matmul(d3,dperp[2]);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       1620 :   dlperp[3] = matmul(perp,dd3);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            :   // Need to calculate the jacobian</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       1620 :   Tensor jacob;</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       1620 :   jacob(0,0)=bi[0]; jacob(1,0)=bi[1]; jacob(2,0)=bi[2];</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       1620 :   jacob(0,1)=cross[0]; jacob(1,1)=cross[1]; jacob(2,1)=cross[2];</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       1620 :   jacob(0,2)=perp[0]; jacob(1,2)=perp[1]; jacob(2,2)=perp[2];</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       1620 :   jacob_det = std::fabs( jacob.determinant() );</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       1620 : }</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        120 : void VolumeCavity::update() {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        120 :   if(boxout) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;%d\n&quot;,8);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :     const Tensor &amp; t(getPbc().getBox());</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :     if(getPbc().isOrthorombic()) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :       boxfile.printf(&quot; %f %f %f\n&quot;,lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     } else {</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :       boxfile.printf(&quot; %f %f %f %f %f %f %f %f %f\n&quot;,</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :                      lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :                      lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :                      lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :                     );</a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*origin[0],lenunit*origin[1],lenunit*origin[2]);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :     Vector ut, vt, wt;</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :     ut = origin + len_bi*bi;</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :     vt = origin + len_cross*cross;</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :     wt = origin + len_perp*perp;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(ut[0]), lenunit*(ut[1]), lenunit*(ut[2]) );</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]), lenunit*(vt[1]), lenunit*(vt[2]) );</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(wt[0]), lenunit*(wt[1]), lenunit*(wt[2]) );</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]+len_bi*bi[0]),</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :                    lenunit*(vt[1]+len_bi*bi[1]),</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :                    lenunit*(vt[2]+len_bi*bi[2]) );</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(ut[0]+len_perp*perp[0]),</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :                    lenunit*(ut[1]+len_perp*perp[1]),</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :                    lenunit*(ut[2]+len_perp*perp[2]) );</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]+len_perp*perp[0]),</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :                    lenunit*(vt[1]+len_perp*perp[1]),</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :                    lenunit*(vt[2]+len_perp*perp[2]) );</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]+len_perp*perp[0]+len_bi*bi[0]),</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :                    lenunit*(vt[1]+len_perp*perp[1]+len_bi*bi[1]),</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :                    lenunit*(vt[2]+len_perp*perp[2]+len_bi*bi[2]) );</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :   }</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        120 : }</span></a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       1620 : double VolumeCavity::calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; rderiv ) const {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   // Setup the histogram bead</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">       3240 :   HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            :   // Calculate distance of atom from origin of new coordinate frame</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       1620 :   Vector datom=pbcDistance( origin, cpos );</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :   double ucontr, uder, vcontr, vder, wcontr, wder;</a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            :   // Calculate contribution from integral along bi</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">       1620 :   bead.set( 0, len_bi, sigma );</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">       1620 :   double upos=dotProduct( datom, bi );</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">       1620 :   ucontr=bead.calculate( upos, uder );</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">       1620 :   double udlen=bead.uboundDerivative( upos );</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       1620 :   double uder2 = bead.lboundDerivative( upos ) - udlen;</span></a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            :   // Calculate contribution from integral along cross</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">       1620 :   bead.set( 0, len_cross, sigma );</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">       1620 :   double vpos=dotProduct( datom, cross );</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">       1620 :   vcontr=bead.calculate( vpos, vder );</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">       1620 :   double vdlen=bead.uboundDerivative( vpos );</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">       1620 :   double vder2 = bead.lboundDerivative( vpos ) - vdlen;</span></a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :   // Calculate contribution from integral along perp</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">       1620 :   bead.set( 0, len_perp, sigma );</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       1620 :   double wpos=dotProduct( datom, perp );</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       1620 :   wcontr=bead.calculate( wpos, wder );</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       1620 :   double wdlen=bead.uboundDerivative( wpos );</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       1620 :   double wder2 = bead.lboundDerivative( wpos ) - wdlen;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       1620 :   Vector dfd; dfd[0]=uder*vcontr*wcontr; dfd[1]=ucontr*vder*wcontr; dfd[2]=ucontr*vcontr*wder;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       1620 :   derivatives[0] = (dfd[0]*bi[0]+dfd[1]*cross[0]+dfd[2]*perp[0]);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       1620 :   derivatives[1] = (dfd[0]*bi[1]+dfd[1]*cross[1]+dfd[2]*perp[1]);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">       1620 :   derivatives[2] = (dfd[0]*bi[2]+dfd[1]*cross[2]+dfd[2]*perp[2]);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">       1620 :   double tot = ucontr*vcontr*wcontr*jacob_det;</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            :   // Add reference atom derivatives</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       1620 :   dfd[0]=uder2*vcontr*wcontr; dfd[1]=ucontr*vder2*wcontr; dfd[2]=ucontr*vcontr*wder2;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       1620 :   Vector dfld; dfld[0]=udlen*vcontr*wcontr; dfld[1]=ucontr*vdlen*wcontr; dfld[2]=ucontr*vcontr*wdlen;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       1620 :   rderiv[0] = dfd[0]*matmul(datom,dbi[0]) + dfd[1]*matmul(datom,dcross[0]) + dfd[2]*matmul(datom,dperp[0]) +</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       3240 :               dfld[0]*dlbi[0] + dfld[1]*dlcross[0] + dfld[2]*dlperp[0] - derivatives;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">       1620 :   rderiv[1] = dfd[0]*matmul(datom,dbi[1]) + dfd[1]*matmul(datom,dcross[1]) + dfd[2]*matmul(datom,dperp[1]) +</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       3240 :               dfld[0]*dlbi[1] + dfld[1]*dlcross[1] + dfld[2]*dlperp[1];</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       1620 :   rderiv[2] = dfd[0]*matmul(datom,dbi[2]) + dfd[1]*matmul(datom,dcross[2]) + dfd[2]*matmul(datom,dperp[2]) +</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       3240 :               dfld[0]*dlbi[2] + dfld[1]*dlcross[2] + dfld[2]*dlperp[2];</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       1620 :   rderiv[3] = dfld[0]*dlbi[3] + dfld[1]*dlcross[3] + dfld[2]*dlperp[3];</span></a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       1620 :   vir.zero(); vir-=Tensor( cpos,derivatives );</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       8100 :   for(unsigned i=0; i&lt;4; ++i) {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       6480 :     vir -= Tensor( getPosition(i), rderiv[i] );</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :   }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">       1620 :   return tot;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            : }</a>
+<a name="412"><span class="lineNum">     412 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeGradientBase.cpp.func-sort-c.html b/coverage/multicolvar/VolumeGradientBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..091234ebd3
--- /dev/null
+++ b/coverage/multicolvar/VolumeGradientBase.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeGradientBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeGradientBase.cpp<span style="font-size: 80%;"> (<a href="VolumeGradientBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">78.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeGradientBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#141">_ZN4PLMD11multicolvar18VolumeGradientBase15addBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#32">_ZN4PLMD11multicolvar18VolumeGradientBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#38">_ZN4PLMD11multicolvar18VolumeGradientBase12requestAtomsERKSt6vectorINS_10AtomNumberESaIS3_EE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#32">_ZN4PLMD11multicolvar18VolumeGradientBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#28">_ZN4PLMD11multicolvar18VolumeGradientBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#53">_ZN4PLMD11multicolvar18VolumeGradientBase28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">2239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#59">_ZNK4PLMD11multicolvar18VolumeGradientBase12completeTaskERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">80958</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#70">_ZNK4PLMD11multicolvar18VolumeGradientBase17setNumberInVolumeERKjS3_RKdRKNS_13VectorGenericILj3EEERKNS_13TensorGenericILj3ELj3EEERKSt6vectorIS7_SaIS7_EERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">115758</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeGradientBase.cpp.func.html b/coverage/multicolvar/VolumeGradientBase.cpp.func.html
new file mode 100644
index 0000000000..57e80c57c0
--- /dev/null
+++ b/coverage/multicolvar/VolumeGradientBase.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeGradientBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeGradientBase.cpp<span style="font-size: 80%;"> (<a href="VolumeGradientBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">78.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeGradientBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#38">_ZN4PLMD11multicolvar18VolumeGradientBase12requestAtomsERKSt6vectorINS_10AtomNumberESaIS3_EE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#141">_ZN4PLMD11multicolvar18VolumeGradientBase15addBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#28">_ZN4PLMD11multicolvar18VolumeGradientBase16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#53">_ZN4PLMD11multicolvar18VolumeGradientBase28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">2239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#32">_ZN4PLMD11multicolvar18VolumeGradientBaseC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#32">_ZN4PLMD11multicolvar18VolumeGradientBaseC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#59">_ZNK4PLMD11multicolvar18VolumeGradientBase12completeTaskERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">80958</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.cpp.gcov.html#70">_ZNK4PLMD11multicolvar18VolumeGradientBase17setNumberInVolumeERKjS3_RKdRKNS_13VectorGenericILj3EEERKNS_13TensorGenericILj3ELj3EEERKSt6vectorIS7_SaIS7_EERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">115758</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeGradientBase.cpp.gcov.html b/coverage/multicolvar/VolumeGradientBase.cpp.gcov.html
new file mode 100644
index 0000000000..53df6c8265
--- /dev/null
+++ b/coverage/multicolvar/VolumeGradientBase.cpp.gcov.html
@@ -0,0 +1,229 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeGradientBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeGradientBase.cpp<span style="font-size: 80%;"> (source / <a href="VolumeGradientBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryMed">78.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VolumeGradientBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CatomPack.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace multicolvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         44 : void VolumeGradientBase::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         44 :   BridgedMultiColvarFunction::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         44 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         30 : VolumeGradientBase::VolumeGradientBase(const ActionOptions&amp;ao):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   Action(ao),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         30 :   BridgedMultiColvarFunction(ao)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         30 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         30 : void VolumeGradientBase::requestAtoms( const std::vector&lt;AtomNumber&gt;&amp; atoms ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         30 :   ActionAtomistic::requestAtoms(atoms); bridgeVariable=3*atoms.size();</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   std::map&lt;std::string,bool&gt; checklabs;</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         33 :   for(const auto &amp; p : getDependencies() ) checklabs.insert(std::pair&lt;std::string,bool&gt;(p-&gt;getLabel(),false));</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        102 :   for(const auto &amp; p : plumed.getActionSet() ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        102 :     if( p-&gt;getLabel()==getPntrToMultiColvar()-&gt;getLabel() ) break;</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          3 :     if( checklabs.count(p-&gt;getLabel()) ) checklabs[p-&gt;getLabel()]=true;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   }</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         33 :   for(const auto &amp; p : checklabs ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          3 :     if( !p.second ) error(&quot;the input for the virtual atoms used in the input for this action must appear in the input file before the input multicolvar&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   }</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         30 :   addDependency( getPntrToMultiColvar() );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         30 :   tmpforces.resize( 3*atoms.size()+9 );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         30 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       2239 : void VolumeGradientBase::doJobsRequiredBeforeTaskList() {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       2239 :   ActionWithValue::clearDerivatives();</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       2239 :   retrieveAtoms(); setupRegions();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       2239 :   ActionWithVessel::doJobsRequiredBeforeTaskList();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       2239 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      80958 : void VolumeGradientBase::completeTask( const unsigned&amp; curr, MultiValue&amp; invals, MultiValue&amp; outvals ) const {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      80958 :   if( getPntrToMultiColvar()-&gt;isDensity() ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     outvals.setValue(0, 1.0); outvals.setValue(1, 1.0);</a>
+<a name="64"><span class="lineNum">      64 </span>            :   } else {</a>
+<a name="65"><span class="lineNum">      65 </span>            :     // Copy derivatives of the colvar and the value of the colvar</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      37538 :     invals.copyValues( outvals );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      37538 :     if( derivativesAreRequired() ) invals.copyDerivatives( outvals );</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      80958 :   calculateAllVolumes( curr, outvals );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      80958 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">     115758 : void VolumeGradientBase::setNumberInVolume( const unsigned&amp; ivol, const unsigned&amp; curr, const double&amp; weight,</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     const Vector&amp; wdf, const Tensor&amp; virial, const std::vector&lt;Vector&gt;&amp; refders,</a>
+<a name="74"><span class="lineNum">      74 </span>            :     MultiValue&amp; outvals ) const {</a>
+<a name="75"><span class="lineNum">      75 </span>            :   MultiColvarBase* mcolv=getPntrToMultiColvar();</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     115758 :   if( !mcolv-&gt;weightHasDerivatives ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     outvals.setValue(ivol, weight );</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     115758 :     if( derivativesAreRequired() ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     112725 :       CatomPack catom; mcolv-&gt;getCentralAtomPack( 0, curr, catom );</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     253450 :       for(unsigned i=0; i&lt;catom.getNumberOfAtomsWithDerivatives(); ++i) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     140725 :         unsigned jatom=3*catom.getIndex(i);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     140725 :         outvals.addDerivative( ivol, jatom+0, catom.getDerivative(i,0,wdf) );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     140725 :         outvals.addDerivative( ivol, jatom+1, catom.getDerivative(i,1,wdf) );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">     140725 :         outvals.addDerivative( ivol, jatom+2, catom.getDerivative(i,2,wdf) );</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :       }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     112725 :       unsigned nmder=getPntrToMultiColvar()-&gt;getNumberOfDerivatives();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    1465425 :       for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, virial(i,j) );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     230310 :       for(unsigned i=0; i&lt;refders.size(); ++i) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     117585 :         unsigned iatom=nmder+3*i;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     117585 :         outvals.addDerivative( ivol, iatom+0, refders[i][0] );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">     117585 :         outvals.addDerivative( ivol, iatom+1, refders[i][1] );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     117585 :         outvals.addDerivative( ivol, iatom+2, refders[i][2] );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :       }</a>
+<a name="95"><span class="lineNum">      95 </span>            :     }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   } else if(ivol==0) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     if( derivativesAreRequired() ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;This needs testing&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : #if 0</a>
+<a name="101"><span class="lineNum">     101 </span>            :       CatomPack catom; mcolv-&gt;getCentralAtomPack( 0, curr, catom );</a>
+<a name="102"><span class="lineNum">     102 </span>            :       for(unsigned i=0; i&lt;catom.getNumberOfAtomsWithDerivatives(); ++i) {</a>
+<a name="103"><span class="lineNum">     103 </span>            :         unsigned jatom=3*catom.getIndex(i);</a>
+<a name="104"><span class="lineNum">     104 </span>            :         outvals.addDerivative( ivol, jatom+0, weight*outvals.getDerivative(ivol,jatom+0) + ww*catom.getDerivative(i,0,wdf) );</a>
+<a name="105"><span class="lineNum">     105 </span>            :         outvals.addDerivative( ivol, jatom+1, weight*outvals.getDerivative(ivol,jatom+1) + ww*catom.getDerivative(i,1,wdf) );</a>
+<a name="106"><span class="lineNum">     106 </span>            :         outvals.addDerivative( ivol, jatom+2, weight*outvals.getDerivative(ivol,jatom+2) + ww*catom.getDerivative(i,2,wdf) );</a>
+<a name="107"><span class="lineNum">     107 </span>            :       }</a>
+<a name="108"><span class="lineNum">     108 </span>            :       unsigned nmder=getPntrToMultiColvar()-&gt;getNumberOfDerivatives();</a>
+<a name="109"><span class="lineNum">     109 </span>            :       for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );</a>
+<a name="110"><span class="lineNum">     110 </span>            :       for(unsigned i=0; i&lt;refders.size(); ++i) {</a>
+<a name="111"><span class="lineNum">     111 </span>            :         unsigned iatom=nmder+3*i;</a>
+<a name="112"><span class="lineNum">     112 </span>            :         outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );</a>
+<a name="113"><span class="lineNum">     113 </span>            :         outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );</a>
+<a name="114"><span class="lineNum">     114 </span>            :         outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );</a>
+<a name="115"><span class="lineNum">     115 </span>            :       }</a>
+<a name="116"><span class="lineNum">     116 </span>            : #endif</a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   } else {</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     double ww=outvals.get(0); outvals.setValue(ivol,ww*weight);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     if( derivativesAreRequired() ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;This needs testing&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : #if 0</a>
+<a name="123"><span class="lineNum">     123 </span>            :       CatomPack catom; mcolv-&gt;getCentralAtomPack( 0, curr, catom );</a>
+<a name="124"><span class="lineNum">     124 </span>            :       for(unsigned i=0; i&lt;catom.getNumberOfAtomsWithDerivatives(); ++i) {</a>
+<a name="125"><span class="lineNum">     125 </span>            :         unsigned jatom=3*catom.getIndex(i);</a>
+<a name="126"><span class="lineNum">     126 </span>            :         outvals.addDerivative( ivol, jatom+0, ww*catom.getDerivative(i,0,wdf) );</a>
+<a name="127"><span class="lineNum">     127 </span>            :         outvals.addDerivative( ivol, jatom+1, ww*catom.getDerivative(i,1,wdf) );</a>
+<a name="128"><span class="lineNum">     128 </span>            :         outvals.addDerivative( ivol, jatom+2, ww*catom.getDerivative(i,2,wdf) );</a>
+<a name="129"><span class="lineNum">     129 </span>            :       }</a>
+<a name="130"><span class="lineNum">     130 </span>            :       unsigned nmder=getPntrToMultiColvar()-&gt;getNumberOfDerivatives();</a>
+<a name="131"><span class="lineNum">     131 </span>            :       for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) outvals.addDerivative( ivol, nmder-9+3*i+j, ww*virial(i,j) );</a>
+<a name="132"><span class="lineNum">     132 </span>            :       for(unsigned i=0; i&lt;refders.size(); ++i) {</a>
+<a name="133"><span class="lineNum">     133 </span>            :         unsigned iatom=nmder+3*i;</a>
+<a name="134"><span class="lineNum">     134 </span>            :         outvals.addDerivative( ivol, iatom+0, ww*refders[i][0] );</a>
+<a name="135"><span class="lineNum">     135 </span>            :         outvals.addDerivative( ivol, iatom+1, ww*refders[i][1] );</a>
+<a name="136"><span class="lineNum">     136 </span>            :         outvals.addDerivative( ivol, iatom+2, ww*refders[i][2] );</a>
+<a name="137"><span class="lineNum">     137 </span>            :       }</a>
+<a name="138"><span class="lineNum">     138 </span>            : #endif</a>
+<a name="139"><span class="lineNum">     139 </span>            :     }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">     115758 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : void VolumeGradientBase::addBridgeForces( const std::vector&lt;double&gt;&amp; bb ) {</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   plumed_dbg_assert( bb.size()==tmpforces.size()-9 );</a>
+<a name="145"><span class="lineNum">     145 </span>            :   // Forces on local atoms</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;bb.size(); ++i) tmpforces[i]=bb[i];</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   // Virial contribution is zero</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   for(unsigned i=bb.size(); i&lt;bb.size()+9; ++i) tmpforces[i]=0.0;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   setForcesOnAtoms( tmpforces, 0 );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeGradientBase.h.func-sort-c.html b/coverage/multicolvar/VolumeGradientBase.h.func-sort-c.html
new file mode 100644
index 0000000000..459d95dc55
--- /dev/null
+++ b/coverage/multicolvar/VolumeGradientBase.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeGradientBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeGradientBase.h<span style="font-size: 80%;"> (<a href="VolumeGradientBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeGradientBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.h.gcov.html#77">_ZNK4PLMD11multicolvar18VolumeGradientBase11getPositionEi</a></td>
+              <td class="coverFnHi">240427</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeGradientBase.h.func.html b/coverage/multicolvar/VolumeGradientBase.h.func.html
new file mode 100644
index 0000000000..61fafd8c57
--- /dev/null
+++ b/coverage/multicolvar/VolumeGradientBase.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeGradientBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeGradientBase.h<span style="font-size: 80%;"> (<a href="VolumeGradientBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeGradientBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeGradientBase.h.gcov.html#77">_ZNK4PLMD11multicolvar18VolumeGradientBase11getPositionEi</a></td>
+              <td class="coverFnHi">240427</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeGradientBase.h.gcov.html b/coverage/multicolvar/VolumeGradientBase.h.gcov.html
new file mode 100644
index 0000000000..825ba4d00d
--- /dev/null
+++ b/coverage/multicolvar/VolumeGradientBase.h.gcov.html
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeGradientBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeGradientBase.h<span style="font-size: 80%;"> (source / <a href="VolumeGradientBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_multicolvar_VolumeGradientBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_multicolvar_VolumeGradientBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;BridgedMultiColvarFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace multicolvar {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class VolumeGradientBase : public BridgedMultiColvarFunction {</a>
+<a name="31"><span class="lineNum">      31 </span>            :   friend class MultiColvarBase;</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// This is used to store forces temporarily in apply</a>
+<a name="34"><span class="lineNum">      34 </span>            :   std::vector&lt;double&gt; tmpforces;</a>
+<a name="35"><span class="lineNum">      35 </span>            : protected:</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Get the cell box</a>
+<a name="37"><span class="lineNum">      37 </span>            :   const Tensor &amp; getBox() const;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Get reference to Pbc</a>
+<a name="39"><span class="lineNum">      39 </span>            :   const Pbc &amp; getPbc() const;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Calculate distance between two points</a>
+<a name="41"><span class="lineNum">      41 </span>            :   Vector pbcDistance( const Vector&amp; v1, const Vector&amp; v2) const;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Get position of atom</a>
+<a name="43"><span class="lineNum">      43 </span>            :   Vector getPosition( int iatom ) const ;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Request the atoms</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void requestAtoms( const std::vector&lt;AtomNumber&gt;&amp; atoms );</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Set the number in the volume</a>
+<a name="47"><span class="lineNum">      47 </span>            :   void setNumberInVolume( const unsigned&amp;, const unsigned&amp;, const double&amp;, const Vector&amp;, const Tensor&amp;, const std::vector&lt;Vector&gt;&amp;, MultiValue&amp; ) const ;</a>
+<a name="48"><span class="lineNum">      48 </span>            : public:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="50"><span class="lineNum">      50 </span>            :   explicit VolumeGradientBase(const ActionOptions&amp;);</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Do jobs required before tasks are undertaken</a>
+<a name="52"><span class="lineNum">      52 </span>            :   void doJobsRequiredBeforeTaskList() override;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Actually do what we are asked</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void completeTask( const unsigned&amp; curr, MultiValue&amp; invals, MultiValue&amp; outvals ) const override;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Calculate what is in the volumes</a>
+<a name="56"><span class="lineNum">      56 </span>            :   virtual void calculateAllVolumes( const unsigned&amp; curr, MultiValue&amp; outvals ) const=0;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Setup the regions that this is based on</a>
+<a name="58"><span class="lineNum">      58 </span>            :   virtual void setupRegions()=0;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Forces here are applied through the bridge</a>
+<a name="60"><span class="lineNum">      60 </span>            :   void addBridgeForces( const std::vector&lt;double&gt;&amp; bb );</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : inline</a>
+<a name="64"><span class="lineNum">      64 </span>            : const Tensor &amp; VolumeGradientBase::getBox()const {</a>
+<a name="65"><span class="lineNum">      65 </span>            :   return getPntrToMultiColvar()-&gt;getBox();</a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : inline</a>
+<a name="69"><span class="lineNum">      69 </span>            : const Pbc &amp; VolumeGradientBase::getPbc() const {</a>
+<a name="70"><span class="lineNum">      70 </span>            :   return getPntrToMultiColvar()-&gt;getPbc();</a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : inline</a>
+<a name="74"><span class="lineNum">      74 </span>            : Vector VolumeGradientBase::pbcDistance( const Vector&amp; v1, const Vector&amp; v2) const {</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     233947 :   return getPntrToMultiColvar()-&gt;pbcDistance(v1,v2);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : inline</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     240427 : Vector VolumeGradientBase::getPosition( int iatom ) const {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     240427 :   if( !checkNumericalDerivatives() ) return ActionAtomistic::getPosition(iatom);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : // This is for numerical derivatives of quantity wrt to the local atoms</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      12480 :   Vector tmp_p = ActionAtomistic::getPosition(iatom);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12480 :   if( bridgeVariable&lt;3*getNumberOfAtoms() ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       5760 :     if( static_cast&lt;int&gt;(bridgeVariable)&gt;=3*iatom &amp;&amp; static_cast&lt;int&gt;(bridgeVariable)&lt;(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span>            : // This makes sure that numerical derivatives of virial are calculated correctly</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      12480 :   tmp_p = ActionAtomistic::getPbc().realToScaled( tmp_p );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      12480 :   tmp_p = getPbc().scaledToReal( tmp_p );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      12480 :   return tmp_p;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeInCylinder.cpp.func-sort-c.html b/coverage/multicolvar/VolumeInCylinder.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4862032408
--- /dev/null
+++ b/coverage/multicolvar/VolumeInCylinder.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeInCylinder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeInCylinder.cpp<span style="font-size: 80%;"> (<a href="VolumeInCylinder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">95.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeInCylinder.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#97">_ZN4PLMD11multicolvar16VolumeInCylinderC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#85">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInCylinderRegisterMe876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#97">_ZN4PLMD11multicolvar16VolumeInCylinderC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#87">_ZN4PLMD11multicolvar16VolumeInCylinder16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#131">_ZN4PLMD11multicolvar16VolumeInCylinder12setupRegionsEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#133">_ZNK4PLMD11multicolvar16VolumeInCylinder21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">4000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#85">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInCylinderRegisterMe87C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#85">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInCylinderRegisterMe87D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeInCylinder.cpp.func.html b/coverage/multicolvar/VolumeInCylinder.cpp.func.html
new file mode 100644
index 0000000000..148d2eedef
--- /dev/null
+++ b/coverage/multicolvar/VolumeInCylinder.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeInCylinder.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeInCylinder.cpp<span style="font-size: 80%;"> (<a href="VolumeInCylinder.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">95.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeInCylinder.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#85">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInCylinderRegisterMe876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#85">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInCylinderRegisterMe87C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#85">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeInCylinderRegisterMe87D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#131">_ZN4PLMD11multicolvar16VolumeInCylinder12setupRegionsEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#87">_ZN4PLMD11multicolvar16VolumeInCylinder16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#97">_ZN4PLMD11multicolvar16VolumeInCylinderC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#97">_ZN4PLMD11multicolvar16VolumeInCylinderC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInCylinder.cpp.gcov.html#133">_ZNK4PLMD11multicolvar16VolumeInCylinder21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">4000</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeInCylinder.cpp.gcov.html b/coverage/multicolvar/VolumeInCylinder.cpp.gcov.html
new file mode 100644
index 0000000000..04f4508fd2
--- /dev/null
+++ b/coverage/multicolvar/VolumeInCylinder.cpp.gcov.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeInCylinder.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeInCylinder.cpp<span style="font-size: 80%;"> (source / <a href="VolumeInCylinder.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">95.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC VOLUMES INCYLINDER</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three</a>
+<a name="32"><span class="lineNum">      32 </span>            : dimensional space. For example, if we have the coordination numbers for all the atoms in the</a>
+<a name="33"><span class="lineNum">      33 </span>            : system each coordination number can be assumed to lie on the position of the central atom.</a>
+<a name="34"><span class="lineNum">      34 </span>            : Because each base quantity can be assigned to a particular point in space we can calculate functions of the</a>
+<a name="35"><span class="lineNum">      35 </span>            : distribution of base quantities in a particular part of the box by using:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) \sigma(r_{xy}) }{ \sum_i \sigma(r_{xy}) }</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (x_i,y_i,z_i)\f$.</a>
+<a name="42"><span class="lineNum">      42 </span>            : The function \f$\sigma\f$ is a \ref switchingfunction that acts on the distance between the point at which the</a>
+<a name="43"><span class="lineNum">      43 </span>            : collective is located \f$(x_i,y_i,z_i)\f$ and the position of the atom that was specified using the ORIGIN keyword</a>
+<a name="44"><span class="lineNum">      44 </span>            : projected in the xy plane if DIRECTION=z is used.  In other words:</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f[</a>
+<a name="46"><span class="lineNum">      46 </span>            : r_{xy} = sqrt{ ( x_i - x_0)^2 + ( y_i - y_0)^2 }</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f]</a>
+<a name="48"><span class="lineNum">      48 </span>            : In short this function, \f$\sigma(r_{xy})\f$, measures whether or not the CV is within a cylinder that</a>
+<a name="49"><span class="lineNum">      49 </span>            : runs along the axis specified using the DIRECTION keyword and that is centered on the position of the atom specified using</a>
+<a name="50"><span class="lineNum">      50 </span>            : ORIGIN.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : When INCYLINDER is used with the \ref DENSITY action the number of atoms in the specified region is calculated</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \par Examples</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The input below can be use to calculate the average coordination numbers for those atoms that are within a cylindrical tube</a>
+<a name="59"><span class="lineNum">      59 </span>            : of radius 1.5 nm that is centered on the position of atom 101 and that has its long axis parallel to the z-axis.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}</a>
+<a name="63"><span class="lineNum">      63 </span>            : d2: INCYLINDER ATOM=101 DATA=c1 DIRECTION=Z RADIUS={TANH R_0=1.5} SIGMA=0.1 LOWER=-0.1 UPPER=0.1 MEAN</a>
+<a name="64"><span class="lineNum">      64 </span>            : PRINT ARG=d2.* FILE=colvar</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endplumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : //+ENDPLUMEDOC</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace PLMD {</a>
+<a name="71"><span class="lineNum">      71 </span>            : namespace multicolvar {</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : class VolumeInCylinder : public ActionVolume {</a>
+<a name="74"><span class="lineNum">      74 </span>            : private:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool docylinder;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   Vector origin;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   HistogramBead bead;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::vector&lt;unsigned&gt; dir;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="80"><span class="lineNum">      80 </span>            : public:</a>
+<a name="81"><span class="lineNum">      81 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="82"><span class="lineNum">      82 </span>            :   explicit VolumeInCylinder (const ActionOptions&amp; ao);</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void setupRegions() override;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const override;</a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(VolumeInCylinder,&quot;INCYLINDER&quot;)</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          3 : void VolumeInCylinder::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          3 :   ActionVolume::registerKeywords( keys );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          6 :   keys.add(&quot;atoms&quot;,&quot;ATOM&quot;,&quot;the atom whose vicinity we are interested in examining&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;DIRECTION&quot;,&quot;the direction of the long axis of the cylinder. Must be x, y or z&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;RADIUS&quot;,&quot;a switching function that gives the extent of the cylinder in the plane perpendicular to the direction&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;LOWER&quot;,&quot;0.0&quot;,&quot;the lower boundary on the direction parallel to the long axis of the cylinder&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;UPPER&quot;,&quot;0.0&quot;,&quot;the upper boundary on the direction parallel to the long axis of the cylinder&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 :   keys.reset_style(&quot;SIGMA&quot;,&quot;optional&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          3 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          1 : VolumeInCylinder::VolumeInCylinder(const ActionOptions&amp; ao):</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   Action(ao),</a>
+<a name="101"><span class="lineNum">     101 </span>            :   ActionVolume(ao),</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 :   docylinder(false)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 :   parseAtomList(&quot;ATOM&quot;,atom);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :   if( atom.size()!=1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   log.printf(&quot;  center of cylinder is at position of atom : %d\n&quot;,atom[0].serial() );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   std::string sdir; parse(&quot;DIRECTION&quot;,sdir);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :   if( sdir==&quot;X&quot;) {dir.push_back(1); dir.push_back(2); dir.push_back(0); }</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          1 :   else if( sdir==&quot;Y&quot;) {dir.push_back(0); dir.push_back(2); dir.push_back(1); }</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          1 :   else if( sdir==&quot;Z&quot;) {dir.push_back(0); dir.push_back(1); dir.push_back(2); }</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   else { error(sdir + &quot;is not a valid direction.  Should be X, Y or Z&quot;); }</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :   log.printf(&quot;  cylinder's long axis is along %s axis\n&quot;,sdir.c_str() );</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          2 :   std::string sw, errors; parse(&quot;RADIUS&quot;,sw);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          1 :   if(sw.length()==0) error(&quot;missing RADIUS keyword&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          1 :   switchingFunction.set(sw,errors);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          1 :   if( errors.length()!=0 ) error(&quot;problem reading RADIUS keyword : &quot; + errors );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          1 :   log.printf(&quot;  radius of cylinder is given by %s \n&quot;, ( switchingFunction.description() ).c_str() );</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   double min, max; parse(&quot;LOWER&quot;,min); parse(&quot;UPPER&quot;,max);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :   if( min!=0.0 ||  max!=0.0 ) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          1 :     if( min&gt;max ) error(&quot;minimum of cylinder should be less than maximum&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          1 :     docylinder=true;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          1 :     log.printf(&quot;  cylinder extends from %f to %f along the %s axis\n&quot;,min,max,sdir.c_str() );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :     bead.isNotPeriodic(); bead.setKernelType( getKernelType() ); bead.set( min, max, getSigma() );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          1 :   checkRead(); requestAtoms(atom);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          1 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         20 : void VolumeInCylinder::setupRegions() { }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       4000 : double VolumeInCylinder::calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const {</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   // Calculate position of atom wrt to origin</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       4000 :   Vector fpos=pbcDistance( getPosition(0), cpos );</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   double vcylinder, dcylinder;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       4000 :   if( docylinder ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       4000 :     vcylinder=bead.calculate( fpos[dir[2]], dcylinder );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   } else {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     vcylinder=1.0; dcylinder=0.0;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       4000 :   const double dd = fpos[dir[0]]*fpos[dir[0]] + fpos[dir[1]]*fpos[dir[1]];</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       4000 :   double dfunc, vswitch = switchingFunction.calculateSqr( dd, dfunc );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       4000 :   derivatives.zero(); double value=vswitch*vcylinder;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       4000 :   derivatives[dir[0]]=vcylinder*dfunc*fpos[dir[0]];</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       4000 :   derivatives[dir[1]]=vcylinder*dfunc*fpos[dir[1]];</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       4000 :   derivatives[dir[2]]=vswitch*dcylinder;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   // Add derivatives wrt to position of origin atom</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       4000 :   refders[0] = -derivatives;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   // Add virial contribution</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       4000 :   vir -= Tensor(fpos,derivatives);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       4000 :   return value;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeInSphere.cpp.func-sort-c.html b/coverage/multicolvar/VolumeInSphere.cpp.func-sort-c.html
new file mode 100644
index 0000000000..bad5c82864
--- /dev/null
+++ b/coverage/multicolvar/VolumeInSphere.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeInSphere.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeInSphere.cpp<span style="font-size: 80%;"> (<a href="VolumeInSphere.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeInSphere.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#90">_ZN4PLMD11multicolvar14VolumeInSphereC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_126VolumeInSphereRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#90">_ZN4PLMD11multicolvar14VolumeInSphereC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#83">_ZN4PLMD11multicolvar14VolumeInSphere16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#108">_ZN4PLMD11multicolvar14VolumeInSphere12setupRegionsEv</a></td>
+              <td class="coverFnHi">82</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_126VolumeInSphereRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_126VolumeInSphereRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#110">_ZNK4PLMD11multicolvar14VolumeInSphere21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">155474</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeInSphere.cpp.func.html b/coverage/multicolvar/VolumeInSphere.cpp.func.html
new file mode 100644
index 0000000000..dbde18b7cd
--- /dev/null
+++ b/coverage/multicolvar/VolumeInSphere.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeInSphere.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeInSphere.cpp<span style="font-size: 80%;"> (<a href="VolumeInSphere.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeInSphere.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_126VolumeInSphereRegisterMe836createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_126VolumeInSphereRegisterMe83C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#81">_ZN4PLMD11multicolvar12_GLOBAL__N_126VolumeInSphereRegisterMe83D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#108">_ZN4PLMD11multicolvar14VolumeInSphere12setupRegionsEv</a></td>
+              <td class="coverFnHi">82</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#83">_ZN4PLMD11multicolvar14VolumeInSphere16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#90">_ZN4PLMD11multicolvar14VolumeInSphereC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#90">_ZN4PLMD11multicolvar14VolumeInSphereC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeInSphere.cpp.gcov.html#110">_ZNK4PLMD11multicolvar14VolumeInSphere21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnHi">155474</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeInSphere.cpp.gcov.html b/coverage/multicolvar/VolumeInSphere.cpp.gcov.html
new file mode 100644
index 0000000000..f9816d2050
--- /dev/null
+++ b/coverage/multicolvar/VolumeInSphere.cpp.gcov.html
@@ -0,0 +1,199 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeInSphere.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeInSphere.cpp<span style="font-size: 80%;"> (source / <a href="VolumeInSphere.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC VOLUMES INSPHERE</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : This quantity can be used to calculate functions of the distribution of collective variables for the atoms that lie in a particular, user-specified part of of the cell.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three</a>
+<a name="32"><span class="lineNum">      32 </span>            : dimensional space. For example, if we have the coordination numbers for all the atoms in the</a>
+<a name="33"><span class="lineNum">      33 </span>            : system each coordination number can be assumed to lie on the position of the central atom.</a>
+<a name="34"><span class="lineNum">      34 </span>            : Because each base quantity can be assigned to a particular point in space we can calculate functions of the</a>
+<a name="35"><span class="lineNum">      35 </span>            : distribution of base quantities in a particular part of the box by using:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) \sigma(r) }{ \sum_i \sigma(r) }</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (x_i,y_i,z_i)\f$.</a>
+<a name="42"><span class="lineNum">      42 </span>            : The function \f$\sigma\f$ is a \ref switchingfunction that acts on the distance between the point at which the</a>
+<a name="43"><span class="lineNum">      43 </span>            : collective is located \f$(x_i,y_i,z_i)\f$ and the position of the atom that was specified using the ORIGIN keyword.</a>
+<a name="44"><span class="lineNum">      44 </span>            : In other words:</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f[</a>
+<a name="46"><span class="lineNum">      46 </span>            : r = sqrt{ ( x_i - x_0)^2 + ( y_i - y_0)^2 + ( z_i - z_0)^2}</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f]</a>
+<a name="48"><span class="lineNum">      48 </span>            : In short this function, \f$\sigma(r_{xy})\f$, measures whether or not the CV is within a sphere that is</a>
+<a name="49"><span class="lineNum">      49 </span>            : centered on the position of the atom specified using the keyword ORIGIN.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : When INCYLINDER is used with the \ref DENSITY action the number of atoms in the specified region is calculated</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : \par Examples</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : The input below can be use to calculate the average coordination numbers for those atoms that are within a sphere</a>
+<a name="58"><span class="lineNum">      58 </span>            : of radius 1.5 nm that is centered on the position of atom 101.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : c1: COORDINATIONNUMBER SPECIES=1-100 SWITCH={RATIONAL R_0=0.1}</a>
+<a name="62"><span class="lineNum">      62 </span>            : d2: INSPHERE ATOM=101 DATA=c1 RADIUS={TANH R_0=1.5} MEAN</a>
+<a name="63"><span class="lineNum">      63 </span>            : PRINT ARG=d2.* FILE=colvar</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : //+ENDPLUMEDOC</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : namespace PLMD {</a>
+<a name="70"><span class="lineNum">      70 </span>            : namespace multicolvar {</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : class VolumeInSphere : public ActionVolume {</a>
+<a name="73"><span class="lineNum">      73 </span>            : private:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   Vector origin;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   SwitchingFunction switchingFunction;</a>
+<a name="76"><span class="lineNum">      76 </span>            : public:</a>
+<a name="77"><span class="lineNum">      77 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="78"><span class="lineNum">      78 </span>            :   explicit VolumeInSphere(const ActionOptions&amp; ao);</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void setupRegions() override;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(VolumeInSphere,&quot;INSPHERE&quot;)</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          5 : void VolumeInSphere::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          5 :   ActionVolume::registerKeywords( keys );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         10 :   keys.add(&quot;atoms&quot;,&quot;ATOM&quot;,&quot;the atom whose vicinity we are interested in examining&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;RADIUS&quot;,&quot;the switching function that tells us the extent of the spherical region of interest&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          5 :   keys.remove(&quot;SIGMA&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          5 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          3 : VolumeInSphere::VolumeInSphere(const ActionOptions&amp; ao):</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   Action(ao),</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          3 :   ActionVolume(ao)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : {</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::vector&lt;AtomNumber&gt; atom;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   parseAtomList(&quot;ATOM&quot;,atom);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          3 :   if( atom.size()!=1 ) error(&quot;should only be one atom specified&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          3 :   log.printf(&quot;  center of sphere is at position of atom : %d\n&quot;,atom[0].serial() );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          6 :   std::string sw, errors; parse(&quot;RADIUS&quot;,sw);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          3 :   if(sw.length()==0) error(&quot;missing RADIUS keyword&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          3 :   switchingFunction.set(sw,errors);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          3 :   if( errors.length()!=0 ) error(&quot;problem reading RADIUS keyword : &quot; + errors );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          3 :   log.printf(&quot;  radius of sphere is given by %s \n&quot;, ( switchingFunction.description() ).c_str() );</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          3 :   checkRead(); requestAtoms(atom);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         82 : void VolumeInSphere::setupRegions() { }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     155474 : double VolumeInSphere::calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   // Calculate position of atom wrt to origin</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     155474 :   Vector fpos=pbcDistance( getPosition(0), cpos );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     155474 :   double dfunc, value = switchingFunction.calculateSqr( fpos.modulo2(), dfunc );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     155474 :   derivatives.zero(); derivatives = dfunc*fpos; refders[0] = -derivatives;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   // Add a virial contribution</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     155474 :   vir -= Tensor(fpos,derivatives);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     155474 :   return value;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeTetrapore.cpp.func-sort-c.html b/coverage/multicolvar/VolumeTetrapore.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b47f297620
--- /dev/null
+++ b/coverage/multicolvar/VolumeTetrapore.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeTetrapore.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeTetrapore.cpp<span style="font-size: 80%;"> (<a href="VolumeTetrapore.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">232</td>
+            <td class="headerCovTableEntryLo">3.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VolumeTetrapore.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeTetraporeRegisterMe1356createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#188">_ZN4PLMD11multicolvar15VolumeTetrapore12setupRegionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#354">_ZN4PLMD11multicolvar15VolumeTetrapore6updateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#143">_ZN4PLMD11multicolvar15VolumeTetraporeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#143">_ZN4PLMD11multicolvar15VolumeTetraporeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#185">_ZN4PLMD11multicolvar15VolumeTetraporeD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#185">_ZN4PLMD11multicolvar15VolumeTetraporeD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#185">_ZN4PLMD11multicolvar15VolumeTetraporeD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#390">_ZNK4PLMD11multicolvar15VolumeTetrapore21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#135">_ZN4PLMD11multicolvar15VolumeTetrapore16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeTetraporeRegisterMe135C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeTetraporeRegisterMe135D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeTetrapore.cpp.func.html b/coverage/multicolvar/VolumeTetrapore.cpp.func.html
new file mode 100644
index 0000000000..2049cf47be
--- /dev/null
+++ b/coverage/multicolvar/VolumeTetrapore.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeTetrapore.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeTetrapore.cpp<span style="font-size: 80%;"> (<a href="VolumeTetrapore.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">232</td>
+            <td class="headerCovTableEntryLo">3.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VolumeTetrapore.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeTetraporeRegisterMe1356createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeTetraporeRegisterMe135C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#133">_ZN4PLMD11multicolvar12_GLOBAL__N_128VolumeTetraporeRegisterMe135D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#188">_ZN4PLMD11multicolvar15VolumeTetrapore12setupRegionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#135">_ZN4PLMD11multicolvar15VolumeTetrapore16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#354">_ZN4PLMD11multicolvar15VolumeTetrapore6updateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#143">_ZN4PLMD11multicolvar15VolumeTetraporeC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#143">_ZN4PLMD11multicolvar15VolumeTetraporeC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#185">_ZN4PLMD11multicolvar15VolumeTetraporeD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#185">_ZN4PLMD11multicolvar15VolumeTetraporeD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#185">_ZN4PLMD11multicolvar15VolumeTetraporeD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VolumeTetrapore.cpp.gcov.html#390">_ZNK4PLMD11multicolvar15VolumeTetrapore21calculateNumberInsideERKNS_13VectorGenericILj3EEERS3_RNS_13TensorGenericILj3ELj3EEERSt6vectorIS3_SaIS3_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/VolumeTetrapore.cpp.gcov.html b/coverage/multicolvar/VolumeTetrapore.cpp.gcov.html
new file mode 100644
index 0000000000..0d7c5d45a5
--- /dev/null
+++ b/coverage/multicolvar/VolumeTetrapore.cpp.gcov.html
@@ -0,0 +1,523 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/VolumeTetrapore.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - VolumeTetrapore.cpp<span style="font-size: 80%;"> (source / <a href="VolumeTetrapore.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">232</td>
+            <td class="headerCovTableEntryLo">3.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">25.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Units.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ActionVolume.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC VOLUMES TETRAHEDRALPORE</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : This quantity can be used to calculate functions of the distribution of collective variables for the atoms lie that lie in a box defined by the positions of four atoms at the corners of a tetrahedron.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Each of the base quantities calculated by a multicolvar can can be assigned to a particular point in three</a>
+<a name="34"><span class="lineNum">      34 </span>            : dimensional space. For example, if we have the coordination numbers for all the atoms in the</a>
+<a name="35"><span class="lineNum">      35 </span>            : system each coordination number can be assumed to lie on the position of the central atom.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Because each base quantity can be assigned to a particular point in space we can calculate functions of the</a>
+<a name="37"><span class="lineNum">      37 </span>            : distribution of base quantities in a particular part of the box by using:</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : \overline{s}_{\tau} = \frac{ \sum_i f(s_i) w(u_i,v_i,w_i) }{ \sum_i w(u_i,v_i,w_i) }</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : where the sum is over the collective variables, \f$s_i\f$, each of which can be thought to be at \f$ (u_i,v_i,z_i)\f$.</a>
+<a name="44"><span class="lineNum">      44 </span>            : The function \f$(s_i)\f$ can be any of the usual LESS_THAN, MORE_THAN, WITHIN etc that are used in all other multicolvars.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Notice that here (at variance with what is done in \ref AROUND) we have transformed from the usual \f$(x_i,y_i,z_i)\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : position to a position in \f$ (u_i,v_i,z_i)\f$.  This is done using a rotation matrix as follows:</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : \left(</a>
+<a name="50"><span class="lineNum">      50 </span>            : \begin{matrix}</a>
+<a name="51"><span class="lineNum">      51 </span>            :  u_i \\</a>
+<a name="52"><span class="lineNum">      52 </span>            :  v_i \\</a>
+<a name="53"><span class="lineNum">      53 </span>            :  w_i</a>
+<a name="54"><span class="lineNum">      54 </span>            : \end{matrix}</a>
+<a name="55"><span class="lineNum">      55 </span>            : \right) = \mathbf{R}</a>
+<a name="56"><span class="lineNum">      56 </span>            : \left(</a>
+<a name="57"><span class="lineNum">      57 </span>            : \begin{matrix}</a>
+<a name="58"><span class="lineNum">      58 </span>            :  x_i - x_o \\</a>
+<a name="59"><span class="lineNum">      59 </span>            :  y_i - y_o \\</a>
+<a name="60"><span class="lineNum">      60 </span>            :  z_i - z_o</a>
+<a name="61"><span class="lineNum">      61 </span>            : \end{matrix}</a>
+<a name="62"><span class="lineNum">      62 </span>            : \right)</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f]</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : where \f$\mathbf{R}\f$ is a rotation matrix that is calculated by constructing a set of three orthonormal vectors from the</a>
+<a name="66"><span class="lineNum">      66 </span>            : reference positions specified by the user.  Initially unit vectors are found by calculating the bisector, \f$\mathbf{b}\f$, and</a>
+<a name="67"><span class="lineNum">      67 </span>            : cross product, \f$\mathbf{c}\f$, of the vectors connecting atoms 1 and 2.  A third unit vector, \f$\mathbf{p}\f$ is then found by taking the cross</a>
+<a name="68"><span class="lineNum">      68 </span>            : product between the cross product calculated during the first step, \f$\mathbf{c}\f$ and the bisector, \f$\mathbf{b}\f$.  From this</a>
+<a name="69"><span class="lineNum">      69 </span>            : second cross product \f$\mathbf{p}\f$ and the bisector \f$\mathbf{b}\f$ two new vectors are calculated using:</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \f[</a>
+<a name="72"><span class="lineNum">      72 </span>            : v_1 = \cos\left(\frac{\pi}{4}\right)\mathbf{b} + \sin\left(\frac{\pi}{4}\right)\mathbf{p} \qquad \textrm{and} \qquad</a>
+<a name="73"><span class="lineNum">      73 </span>            : v_2 = \cos\left(\frac{\pi}{4}\right)\mathbf{b} - \sin\left(\frac{\pi}{4}\right)\mathbf{p}</a>
+<a name="74"><span class="lineNum">      74 </span>            : \f]</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : In the previous function \f$ w(u_i,v_i,w_i) \f$ measures whether or not the system is in the subregion of interest. It</a>
+<a name="77"><span class="lineNum">      77 </span>            : is equal to:</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : \f[</a>
+<a name="80"><span class="lineNum">      80 </span>            : w(u_i,v_i,w_i) = \int_{0}^{u'} \int_{0}^{v'} \int_{0}^{w'} \textrm{d}u\textrm{d}v\textrm{d}w</a>
+<a name="81"><span class="lineNum">      81 </span>            :    K\left( \frac{u - u_i}{\sigma} \right)K\left( \frac{v - v_i}{\sigma} \right)K\left( \frac{w - w_i}{\sigma} \right)</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f]</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : where \f$K\f$ is one of the kernel functions described on \ref histogrambead and \f$\sigma\f$ is a bandwidth parameter.</a>
+<a name="85"><span class="lineNum">      85 </span>            : The values of \f$u'\f$ and \f$v'\f$ are found by finding the projections of the vectors connecting atoms 1 and 2 and 1</a>
+<a name="86"><span class="lineNum">      86 </span>            : and 3 \f$v_1\f$ and \f$v_2\f$.  This gives four projections: the largest two projections are used in the remainder of</a>
+<a name="87"><span class="lineNum">      87 </span>            : the calculations.  \f$w'\f$ is calculated by taking the projection of the vector connecting atoms 1 and 4 on the vector</a>
+<a name="88"><span class="lineNum">      88 </span>            : \f$\mathbf{c}\f$.  Notice that the manner by which this box is constructed differs from the way this is done in \ref CAVITY.</a>
+<a name="89"><span class="lineNum">      89 </span>            : This is in fact the only point of difference between these two actions.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \par Examples</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : The following commands tell plumed to calculate the number of atom inside a tetrahedral cavity.  The extent of the tetrahedral</a>
+<a name="94"><span class="lineNum">      94 </span>            : cavity is calculated from the positions of atoms 1, 4, 5, and 11,  The final value will be labeled cav.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \plumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : d1: DENSITY SPECIES=20-500</a>
+<a name="98"><span class="lineNum">      98 </span>            : TETRAHEDRALPORE DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 LABEL=cav</a>
+<a name="99"><span class="lineNum">      99 </span>            : \endplumedfile</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : The following command tells plumed to calculate the coordination numbers (with other water molecules) for the water</a>
+<a name="102"><span class="lineNum">     102 </span>            : molecules in the tetrahedral cavity described above.  The average coordination number and the number of coordination</a>
+<a name="103"><span class="lineNum">     103 </span>            : numbers more than 4 is then calculated.  The values of these two quantities are given the labels cav.mean and cav.morethan</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : \plumedfile</a>
+<a name="106"><span class="lineNum">     106 </span>            : d1: COORDINATIONNUMBER SPECIES=20-500 R_0=0.1</a>
+<a name="107"><span class="lineNum">     107 </span>            : CAVITY DATA=d1 ATOMS=1,4,5,11 SIGMA=0.1 MEAN MORE_THAN={RATIONAL R_0=4} LABEL=cav</a>
+<a name="108"><span class="lineNum">     108 </span>            : \endplumedfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : */</a>
+<a name="111"><span class="lineNum">     111 </span>            : //+ENDPLUMEDOC</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : namespace PLMD {</a>
+<a name="114"><span class="lineNum">     114 </span>            : namespace multicolvar {</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : class VolumeTetrapore : public ActionVolume {</a>
+<a name="117"><span class="lineNum">     117 </span>            : private:</a>
+<a name="118"><span class="lineNum">     118 </span>            :   bool boxout;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   OFile boxfile;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   double lenunit;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   double jacob_det;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   double len_bi, len_cross, len_perp, sigma;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   Vector origin, bi, cross, perp;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::vector&lt;Vector&gt; dlbi, dlcross, dlperp;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   std::vector&lt;Tensor&gt; dbi, dcross, dperp;</a>
+<a name="126"><span class="lineNum">     126 </span>            : public:</a>
+<a name="127"><span class="lineNum">     127 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="128"><span class="lineNum">     128 </span>            :   explicit VolumeTetrapore(const ActionOptions&amp; ao);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   ~VolumeTetrapore();</a>
+<a name="130"><span class="lineNum">     130 </span>            :   void setupRegions() override;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   void update() override;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   double calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; refders ) const override;</a>
+<a name="133"><span class="lineNum">     133 </span>            : };</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(VolumeTetrapore,&quot;TETRAHEDRALPORE&quot;)</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 : void VolumeTetrapore::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :   ActionVolume::registerKeywords( keys );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the positions of four atoms that define spatial extent of the cavity&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          4 :   keys.addFlag(&quot;PRINT_BOX&quot;,false,&quot;write out the positions of the corners of the box to an xyz file&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;the file on which to write out the box coordinates&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 :   keys.add(&quot;optional&quot;,&quot;UNITS&quot;,&quot;( default=nm ) the units in which to write out the corners of the box&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          2 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 : VolumeTetrapore::VolumeTetrapore(const ActionOptions&amp; ao):</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   Action(ao),</a>
+<a name="147"><span class="lineNum">     147 </span>            :   ActionVolume(ao),</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   boxout(false),</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   lenunit(1.0),</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   dlbi(4),</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   dlcross(4),</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   dlperp(4),</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   dbi(3),</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :   dcross(3),</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :   dperp(3)</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : {</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :   if( atoms.size()!=4 ) error(&quot;number of atoms should be equal to four&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   log.printf(&quot;  boundaries for region are calculated based on positions of atoms : &quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot;%d &quot;,atoms[i].serial() );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :   boxout=false; parseFlag(&quot;PRINT_BOX&quot;,boxout);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   if(boxout) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     std::string boxfname; parse(&quot;FILE&quot;,boxfname);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     if(boxfname.length()==0) error(&quot;no name for box file specified&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     std::string unitname; parse(&quot;UNITS&quot;,unitname);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     if ( unitname.length()&gt;0 ) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :       Units u; u.setLength(unitname);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :       lenunit=plumed.getAtoms().getUnits().getLength()/u.getLength();</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     } else {</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :       unitname=&quot;nm&quot;;</a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     boxfile.link(*this);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     boxfile.open( boxfname );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     log.printf(&quot;  printing box coordinates on file named %s in %s \n&quot;,boxfname.c_str(), unitname.c_str() );</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   requestAtoms(atoms);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   // We have to readd the dependency because requestAtoms removes it</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :   addDependency( getPntrToMultiColvar() );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 : VolumeTetrapore::~VolumeTetrapore() {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 : void VolumeTetrapore::setupRegions() {</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Make some space for things</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :   Vector d1, d2, d3;</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            :   // Retrieve the sigma value</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   sigma=getSigma();</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   // Set the position of the origin</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   origin=getPosition(0);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            :   // Get two vectors</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :   d1 = pbcDistance(origin,getPosition(1));</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   d2 = pbcDistance(origin,getPosition(2));</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   // Find the vector connecting the origin to the top corner of</a>
+<a name="204"><span class="lineNum">     204 </span>            :   // the subregion</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :   d3 = pbcDistance(origin,getPosition(3));</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            :   // Create a set of unit vectors</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :   Vector bisector = d1 + d2; double bmod=bisector.modulo(); bisector=bisector/bmod;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            :   // bi = d1 / d1l; len_bi=dotProduct( d3, bi );</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :   cross = crossProduct( d1, d2 ); double crossmod=cross.modulo();</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   cross = cross / crossmod; len_cross=dotProduct( d3, cross );</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   Vector truep = crossProduct( cross, bisector );</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   // These are our true vectors 45 degrees from bisector</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   bi = std::cos(pi/4.0)*bisector + std::sin(pi/4.0)*truep;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   perp = std::cos(pi/4.0)*bisector - std::sin(pi/4.0)*truep;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :   // And the lengths of the various parts average distance to opposite corners of tetetrahedron</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :   len_bi = dotProduct( d1, bi ); double len_bi2 = dotProduct( d2, bi ); unsigned lbi=1;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :   if( len_bi2&gt;len_bi ) { len_bi=len_bi2; lbi=2; }</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :   len_perp = dotProduct( d1, perp ); double len_perp2 = dotProduct( d2, perp ); unsigned lpi=1;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :   if( len_perp2&gt;len_perp ) { len_perp=len_perp2; lpi=2; }</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :   plumed_assert( lbi!=lpi );</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :   Tensor tcderiv; double cmod3=crossmod*crossmod*crossmod; Vector ucross=crossmod*cross;</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 0, crossProduct( d1, Vector(-1.0,0.0,0.0) ) + crossProduct( Vector(-1.0,0.0,0.0), d2 ) );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,-1.0,0.0) ) + crossProduct( Vector(0.0,-1.0,0.0), d2 ) );</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,-1.0) ) + crossProduct( Vector(0.0,0.0,-1.0), d2 ) );</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :   dcross[0](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dx/dx</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   dcross[0](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dx/dy</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :   dcross[0](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dx/dz</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :   dcross[0](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dy/dx</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :   dcross[0](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dy/dy</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   dcross[0](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dy/dz</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   dcross[0](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dz/dx</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :   dcross[0](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dz/dy</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :   dcross[0](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dz/dz</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 0, crossProduct( Vector(1.0,0.0,0.0), d2 ) );</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 1, crossProduct( Vector(0.0,1.0,0.0), d2 ) );</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 2, crossProduct( Vector(0.0,0.0,1.0), d2 ) );</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   dcross[1](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dx/dx</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :   dcross[1](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dx/dy</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :   dcross[1](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dx/dz</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   dcross[1](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dy/dx</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :   dcross[1](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dy/dy</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   dcross[1](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dy/dz</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   dcross[1](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dz/dx</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :   dcross[1](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dz/dy</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :   dcross[1](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dz/dz</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 0, crossProduct( d1, Vector(1.0,0.0,0.0) ) );</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 1, crossProduct( d1, Vector(0.0,1.0,0.0) ) );</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :   tcderiv.setCol( 2, crossProduct( d1, Vector(0.0,0.0,1.0) ) );</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :   dcross[2](0,0)=( tcderiv(0,0)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dx/dx</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   dcross[2](0,1)=( tcderiv(0,1)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dx/dy</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :   dcross[2](0,2)=( tcderiv(0,2)/crossmod - ucross[0]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dx/dz</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :   dcross[2](1,0)=( tcderiv(1,0)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dy/dx</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :   dcross[2](1,1)=( tcderiv(1,1)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dy/dy</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   dcross[2](1,2)=( tcderiv(1,2)/crossmod - ucross[1]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dy/dz</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :   dcross[2](2,0)=( tcderiv(2,0)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,0) + ucross[1]*tcderiv(1,0) + ucross[2]*tcderiv(2,0))/cmod3 );    // dz/dx</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :   dcross[2](2,1)=( tcderiv(2,1)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,1) + ucross[1]*tcderiv(1,1) + ucross[2]*tcderiv(2,1))/cmod3 );    // dz/dy</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   dcross[2](2,2)=( tcderiv(2,2)/crossmod - ucross[2]*(ucross[0]*tcderiv(0,2) + ucross[1]*tcderiv(1,2) + ucross[2]*tcderiv(2,2))/cmod3 );    // dz/dz</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :   std::vector&lt;Tensor&gt; dbisector(3);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :   double bmod3=bmod*bmod*bmod; Vector ubisector=bmod*bisector;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :   dbisector[0](0,0)= -2.0/bmod + 2*ubisector[0]*ubisector[0]/bmod3;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :   dbisector[0](0,1)= 2*ubisector[0]*ubisector[1]/bmod3;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :   dbisector[0](0,2)= 2*ubisector[0]*ubisector[2]/bmod3;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :   dbisector[0](1,0)= 2*ubisector[1]*ubisector[0]/bmod3;</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :   dbisector[0](1,1)= -2.0/bmod + 2*ubisector[1]*ubisector[1]/bmod3;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :   dbisector[0](1,2)= 2*ubisector[1]*ubisector[2]/bmod3;</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :   dbisector[0](2,0)= 2*ubisector[2]*ubisector[0]/bmod3;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   dbisector[0](2,1)= 2*ubisector[2]*ubisector[1]/bmod3;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :   dbisector[0](2,2)= -2.0/bmod + 2*ubisector[2]*ubisector[2]/bmod3;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   dbisector[1](0,0)= 1.0/bmod - ubisector[0]*ubisector[0]/bmod3;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   dbisector[1](0,1)= -ubisector[0]*ubisector[1]/bmod3;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :   dbisector[1](0,2)= -ubisector[0]*ubisector[2]/bmod3;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :   dbisector[1](1,0)= -ubisector[1]*ubisector[0]/bmod3;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :   dbisector[1](1,1)= 1.0/bmod - ubisector[1]*ubisector[1]/bmod3;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :   dbisector[1](1,2)= -ubisector[1]*ubisector[2]/bmod3;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :   dbisector[1](2,0)= -ubisector[2]*ubisector[0]/bmod3;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :   dbisector[1](2,1)= -ubisector[2]*ubisector[1]/bmod3;</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   dbisector[1](2,2)=1.0/bmod - ubisector[2]*ubisector[2]/bmod3;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :   dbisector[2](0,0)=1.0/bmod - ubisector[0]*ubisector[0]/bmod3;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :   dbisector[2](0,1)= -ubisector[0]*ubisector[1]/bmod3;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :   dbisector[2](0,2)= -ubisector[0]*ubisector[2]/bmod3;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   dbisector[2](1,0)= -ubisector[1]*ubisector[0]/bmod3;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   dbisector[2](1,1)=1.0/bmod - ubisector[1]*ubisector[1]/bmod3;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :   dbisector[2](1,2)= -ubisector[1]*ubisector[2]/bmod3;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :   dbisector[2](2,0)= -ubisector[2]*ubisector[0]/bmod3;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :   dbisector[2](2,1)= -ubisector[2]*ubisector[1]/bmod3;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :   dbisector[2](2,2)=1.0/bmod - ubisector[2]*ubisector[2]/bmod3;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :   std::vector&lt;Tensor&gt; dtruep(3);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :   dtruep[0].setCol( 0, ( crossProduct( dcross[0].getCol(0), bisector ) + crossProduct( cross, dbisector[0].getCol(0) ) ) );</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   dtruep[0].setCol( 1, ( crossProduct( dcross[0].getCol(1), bisector ) + crossProduct( cross, dbisector[0].getCol(1) ) ) );</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :   dtruep[0].setCol( 2, ( crossProduct( dcross[0].getCol(2), bisector ) + crossProduct( cross, dbisector[0].getCol(2) ) ) );</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :   dtruep[1].setCol( 0, ( crossProduct( dcross[1].getCol(0), bisector ) + crossProduct( cross, dbisector[1].getCol(0) ) ) );</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :   dtruep[1].setCol( 1, ( crossProduct( dcross[1].getCol(1), bisector ) + crossProduct( cross, dbisector[1].getCol(1) ) ) );</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   dtruep[1].setCol( 2, ( crossProduct( dcross[1].getCol(2), bisector ) + crossProduct( cross, dbisector[1].getCol(2) ) ) );</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :   dtruep[2].setCol( 0, ( crossProduct( dcross[2].getCol(0), bisector ) + crossProduct( cross, dbisector[2].getCol(0) ) ) );</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :   dtruep[2].setCol( 1, ( crossProduct( dcross[2].getCol(1), bisector ) + crossProduct( cross, dbisector[2].getCol(1) ) ) );</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :   dtruep[2].setCol( 2, ( crossProduct( dcross[2].getCol(2), bisector ) + crossProduct( cross, dbisector[2].getCol(2) ) ) );</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :   // Now convert these to the derivatives of the true axis</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;3; ++i) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     dbi[i] = std::cos(pi/4.0)*dbisector[i] + std::sin(pi/4.0)*dtruep[i];</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :     dperp[i] = std::cos(pi/4.0)*dbisector[i] - std::sin(pi/4.0)*dtruep[i];</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :   }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :   // Ensure that all lengths are positive</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :   if( len_bi&lt;0 ) {</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :     bi=-bi; len_bi=-len_bi;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; ++i) dbi[i]*=-1.0;</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :   }</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :   if( len_cross&lt;0 ) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     cross=-cross; len_cross=-len_cross;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; ++i) dcross[i]*=-1.0;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :   }</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :   if( len_perp&lt;0 ) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :     perp=-perp; len_perp=-len_perp;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; ++i) dperp[i]*=-1.0;</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   }</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :   if( len_bi&lt;=0 || len_cross&lt;=0 || len_perp&lt;=0 ) plumed_merror(&quot;Invalid box coordinates&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            :   // Now derivatives of lengths</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :   Tensor dd3( Tensor::identity() ); Vector ddb2=d1; if( lbi==2 ) ddb2=d2;</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :   dlbi[1].zero(); dlbi[2].zero(); dlbi[3].zero();</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :   dlbi[0] = matmul(ddb2,dbi[0]) - matmul(bi,dd3);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :   dlbi[lbi] = matmul(ddb2,dbi[lbi]) + matmul(bi,dd3);  // Derivative wrt d1</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :   dlcross[0] = matmul(d3,dcross[0]) - matmul(cross,dd3);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineNoCov">          0 :   dlcross[1] = matmul(d3,dcross[1]);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :   dlcross[2] = matmul(d3,dcross[2]);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :   dlcross[3] = matmul(cross,dd3);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :   ddb2=d1; if( lpi==2 ) ddb2=d2;</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :   dlperp[1].zero(); dlperp[2].zero(); dlperp[3].zero();</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   dlperp[0] = matmul(ddb2,dperp[0]) - matmul( perp, dd3 );</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   dlperp[lpi] = matmul(ddb2,dperp[lpi]) + matmul(perp, dd3);</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            :   // Need to calculate the jacobian</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   Tensor jacob;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :   jacob(0,0)=bi[0]; jacob(1,0)=bi[1]; jacob(2,0)=bi[2];</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :   jacob(0,1)=cross[0]; jacob(1,1)=cross[1]; jacob(2,1)=cross[2];</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :   jacob(0,2)=perp[0]; jacob(1,2)=perp[1]; jacob(2,2)=perp[2];</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :   jacob_det = std::fabs( jacob.determinant() );</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 : void VolumeTetrapore::update() {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :   if(boxout) {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;%d\n&quot;,8);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :     const Tensor &amp; t(getPbc().getBox());</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :     if(getPbc().isOrthorombic()) {</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :       boxfile.printf(&quot; %f %f %f\n&quot;,lenunit*t(0,0),lenunit*t(1,1),lenunit*t(2,2));</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :     } else {</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :       boxfile.printf(&quot; %f %f %f %f %f %f %f %f %f\n&quot;,</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :                      lenunit*t(0,0),lenunit*t(0,1),lenunit*t(0,2),</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :                      lenunit*t(1,0),lenunit*t(1,1),lenunit*t(1,2),</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :                      lenunit*t(2,0),lenunit*t(2,1),lenunit*t(2,2)</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :                     );</a>
+<a name="368"><span class="lineNum">     368 </span>            :     }</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*origin[0],lenunit*origin[1],lenunit*origin[2]);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :     Vector ut, vt, wt;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :     ut = origin + len_bi*bi;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     vt = origin + len_cross*cross;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :     wt = origin + len_perp*perp;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(ut[0]), lenunit*(ut[1]), lenunit*(ut[2]) );</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]), lenunit*(vt[1]), lenunit*(vt[2]) );</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(wt[0]), lenunit*(wt[1]), lenunit*(wt[2]) );</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]+len_bi*bi[0]),</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :                    lenunit*(vt[1]+len_bi*bi[1]),</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :                    lenunit*(vt[2]+len_bi*bi[2]) );</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(ut[0]+len_perp*perp[0]),</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :                    lenunit*(ut[1]+len_perp*perp[1]),</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :                    lenunit*(ut[2]+len_perp*perp[2]) );</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]+len_perp*perp[0]),</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :                    lenunit*(vt[1]+len_perp*perp[1]),</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :                    lenunit*(vt[2]+len_perp*perp[2]) );</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :     boxfile.printf(&quot;AR %f %f %f \n&quot;,lenunit*(vt[0]+len_perp*perp[0]+len_bi*bi[0]),</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :                    lenunit*(vt[1]+len_perp*perp[1]+len_bi*bi[1]),</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :                    lenunit*(vt[2]+len_perp*perp[2]+len_bi*bi[2]) );</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 : double VolumeTetrapore::calculateNumberInside( const Vector&amp; cpos, Vector&amp; derivatives, Tensor&amp; vir, std::vector&lt;Vector&gt;&amp; rderiv ) const {</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   // Setup the histogram bead</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :   HistogramBead bead; bead.isNotPeriodic(); bead.setKernelType( getKernelType() );</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   // Calculate distance of atom from origin of new coordinate frame</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :   Vector datom=pbcDistance( origin, cpos );</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   double ucontr, uder, vcontr, vder, wcontr, wder;</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            :   // Calculate contribution from integral along bi</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :   bead.set( 0, len_bi, sigma );</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :   double upos=dotProduct( datom, bi );</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :   ucontr=bead.calculate( upos, uder );</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 :   double udlen=bead.uboundDerivative( upos );</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :   double uder2 = bead.lboundDerivative( upos ) - udlen;</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   // Calculate contribution from integral along cross</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :   bead.set( 0, len_cross, sigma );</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :   double vpos=dotProduct( datom, cross );</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :   vcontr=bead.calculate( vpos, vder );</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :   double vdlen=bead.uboundDerivative( vpos );</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 :   double vder2 = bead.lboundDerivative( vpos ) - vdlen;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :   // Calculate contribution from integral along perp</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 :   bead.set( 0, len_perp, sigma );</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :   double wpos=dotProduct( datom, perp );</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :   wcontr=bead.calculate( wpos, wder );</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :   double wdlen=bead.uboundDerivative( wpos );</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :   double wder2 = bead.lboundDerivative( wpos ) - wdlen;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :   Vector dfd; dfd[0]=uder*vcontr*wcontr; dfd[1]=ucontr*vder*wcontr; dfd[2]=ucontr*vcontr*wder;</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :   derivatives[0] = (dfd[0]*bi[0]+dfd[1]*cross[0]+dfd[2]*perp[0]);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :   derivatives[1] = (dfd[0]*bi[1]+dfd[1]*cross[1]+dfd[2]*perp[1]);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :   derivatives[2] = (dfd[0]*bi[2]+dfd[1]*cross[2]+dfd[2]*perp[2]);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :   double tot = ucontr*vcontr*wcontr*jacob_det;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            :   // Add reference atom derivatives</a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 :   dfd[0]=uder2*vcontr*wcontr; dfd[1]=ucontr*vder2*wcontr; dfd[2]=ucontr*vcontr*wder2;</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :   Vector dfld; dfld[0]=udlen*vcontr*wcontr; dfld[1]=ucontr*vdlen*wcontr; dfld[2]=ucontr*vcontr*wdlen;</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :   rderiv[0] = dfd[0]*matmul(datom,dbi[0]) + dfd[1]*matmul(datom,dcross[0]) + dfd[2]*matmul(datom,dperp[0]) +</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :               dfld[0]*dlbi[0] + dfld[1]*dlcross[0] + dfld[2]*dlperp[0] - derivatives;</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :   rderiv[1] = dfd[0]*matmul(datom,dbi[1]) + dfd[1]*matmul(datom,dcross[1]) + dfd[2]*matmul(datom,dperp[1]) +</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :               dfld[0]*dlbi[1] + dfld[1]*dlcross[1] + dfld[2]*dlperp[1];</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :   rderiv[2] = dfd[0]*matmul(datom,dbi[2]) + dfd[1]*matmul(datom,dcross[2]) + dfd[2]*matmul(datom,dperp[2]) +</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :               dfld[0]*dlbi[2] + dfld[1]*dlcross[2] + dfld[2]*dlperp[2];</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :   rderiv[3] = dfld[0]*dlbi[3] + dfld[1]*dlcross[3] + dfld[2]*dlperp[3];</span></a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :   vir.zero(); vir-=Tensor( cpos,derivatives );</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;4; ++i) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :     vir -= Tensor( getPosition(i), rderiv[i] );</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   }</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :   return tot;</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : }</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            : }</a>
+<a name="447"><span class="lineNum">     447 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XAngle.cpp.func-sort-c.html b/coverage/multicolvar/XAngle.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a3d1c48f74
--- /dev/null
+++ b/coverage/multicolvar/XAngle.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XAngle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XAngle.cpp<span style="font-size: 80%;"> (<a href="XAngle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="XAngle.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#122">_ZN4PLMD11multicolvar7XAnglesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#97">_ZN4PLMD11multicolvar12_GLOBAL__N_119XAnglesRegisterMe996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe1016createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#94">_ZN4PLMD11multicolvar7XAngles10isPeriodicEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#122">_ZN4PLMD11multicolvar7XAnglesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#101">_ZN4PLMD11multicolvar7XAngles16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#162">_ZNK4PLMD11multicolvar7XAngles7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#151">_ZNK4PLMD11multicolvar7XAngles15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">110</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#97">_ZN4PLMD11multicolvar12_GLOBAL__N_119XAnglesRegisterMe99C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#97">_ZN4PLMD11multicolvar12_GLOBAL__N_119XAnglesRegisterMe99D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe100C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe101C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe101D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XAngle.cpp.func.html b/coverage/multicolvar/XAngle.cpp.func.html
new file mode 100644
index 0000000000..bb2b3df4d3
--- /dev/null
+++ b/coverage/multicolvar/XAngle.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XAngle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XAngle.cpp<span style="font-size: 80%;"> (<a href="XAngle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="XAngle.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#97">_ZN4PLMD11multicolvar12_GLOBAL__N_119XAnglesRegisterMe996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#97">_ZN4PLMD11multicolvar12_GLOBAL__N_119XAnglesRegisterMe99C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#97">_ZN4PLMD11multicolvar12_GLOBAL__N_119XAnglesRegisterMe99D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe1006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe100C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#98">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe100D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe1016createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe101C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#99">_ZN4PLMD11multicolvar12_GLOBAL__N_120XAnglesRegisterMe101D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#94">_ZN4PLMD11multicolvar7XAngles10isPeriodicEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#101">_ZN4PLMD11multicolvar7XAngles16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#122">_ZN4PLMD11multicolvar7XAnglesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#122">_ZN4PLMD11multicolvar7XAnglesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#151">_ZNK4PLMD11multicolvar7XAngles15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">110</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XAngle.cpp.gcov.html#162">_ZNK4PLMD11multicolvar7XAngles7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XAngle.cpp.gcov.html b/coverage/multicolvar/XAngle.cpp.gcov.html
new file mode 100644
index 0000000000..7a2757e468
--- /dev/null
+++ b/coverage/multicolvar/XAngle.cpp.gcov.html
@@ -0,0 +1,253 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XAngle.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XAngle.cpp<span style="font-size: 80%;"> (source / <a href="XAngle.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntryHi">98.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Angle.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace multicolvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MCOLVAR XANGLES</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculate the angles between the vector connecting two atoms and the x axis.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The following input tells plumed to calculate the angles between the x-axis and the vector connecting atom 3 to atom 5 and between the x-axis</a>
+<a name="41"><span class="lineNum">      41 </span>            : and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then</a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : XANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1</a>
+<a name="44"><span class="lineNum">      44 </span>            : PRINT ARG=d1.min</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : (See also \ref PRINT).</a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : //+PLUMEDOC MCOLVAR YANGLES</a>
+<a name="51"><span class="lineNum">      51 </span>            : /*</a>
+<a name="52"><span class="lineNum">      52 </span>            : Calculate the angles between the vector connecting two atoms and the y axis.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \par Examples</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The following input tells plumed to calculate the angles between the y-axis and the vector connecting atom 3 to atom 5 and between the y-axis</a>
+<a name="57"><span class="lineNum">      57 </span>            : and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then</a>
+<a name="58"><span class="lineNum">      58 </span>            : \plumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : YANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1</a>
+<a name="60"><span class="lineNum">      60 </span>            : PRINT ARG=d1.min</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : (See also \ref PRINT).</a>
+<a name="63"><span class="lineNum">      63 </span>            : */</a>
+<a name="64"><span class="lineNum">      64 </span>            : //+ENDPLUMEDOC</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : //+PLUMEDOC MCOLVAR ZANGLES</a>
+<a name="67"><span class="lineNum">      67 </span>            : /*</a>
+<a name="68"><span class="lineNum">      68 </span>            : Calculate the angles between the vector connecting two atoms and the z axis.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The following input tells plumed to calculate the angles between the z-axis and the vector connecting atom 3 to atom 5 and between the z-axis</a>
+<a name="73"><span class="lineNum">      73 </span>            : and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then</a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : ZANGLES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1} LABEL=d1</a>
+<a name="76"><span class="lineNum">      76 </span>            : PRINT ARG=d1.min</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endplumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : (See also \ref PRINT).</a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : class XAngles : public MultiColvarBase {</a>
+<a name="85"><span class="lineNum">      85 </span>            : private:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   bool use_sf;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned myc;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   SwitchingFunction sf1;</a>
+<a name="89"><span class="lineNum">      89 </span>            : public:</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit XAngles(const ActionOptions&amp;);</a>
+<a name="92"><span class="lineNum">      92 </span>            : // active methods:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; ) const override;</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          3 :   bool isPeriodic() override { return false; }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : };</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(XAngles,&quot;XANGLES&quot;)</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XAngles,&quot;YANGLES&quot;)</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(XAngles,&quot;ZANGLES&quot;)</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          9 : void XAngles::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          9 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         18 :   keys.use(&quot;MAX&quot;); keys.use(&quot;ALT_MIN&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         27 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         18 :   keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         36 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         18 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the angles you wish to calculate. &quot;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one angle will be &quot;</a>
+<a name="111"><span class="lineNum">     111 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="112"><span class="lineNum">     112 </span>            :            &quot;specify the indices of two atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="113"><span class="lineNum">     113 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         18 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         18 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate the distance between each distinct pair of atoms in the group&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         18 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all &quot;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :            &quot;the atoms in GROUPB. This must be used in conjunction with GROUPB.&quot;);</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         18 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all the atoms &quot;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :            &quot;in GROUPB. This must be used in conjunction with GROUPA.&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         18 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;A switching function that ensures that only angles are only computed when atoms are within &quot;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :            &quot;are within a certain fixed cutoff. The following provides information on the \\ref switchingfunction that are available.&quot;);</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          9 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 : XAngles::XAngles(const ActionOptions&amp;ao):</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   Action(ao),</a>
+<a name="126"><span class="lineNum">     126 </span>            :   MultiColvarBase(ao),</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   use_sf(false)</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :   if( getName().find(&quot;X&quot;)!=std::string::npos) myc=0;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   else if( getName().find(&quot;Y&quot;)!=std::string::npos) myc=1;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :   else if( getName().find(&quot;Z&quot;)!=std::string::npos) myc=2;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   else plumed_error();</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   // Read in switching function</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          6 :   std::string sfinput, errors; parse(&quot;SWITCH&quot;,sfinput);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 :   if( sfinput.length()&gt;0 ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :     use_sf=true; weightHasDerivatives=true;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :     sf1.set(sfinput,errors);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :     log.printf(&quot;  only calculating angles for atoms separated by less than %s\n&quot;, sf1.description().c_str() );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :     setLinkCellCutoff( sf1.get_dmax() );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   // Read in the atoms</a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          6 :   readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          4 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 2, all_atoms );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   // And check everything has been read in correctly</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        110 : double XAngles::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        110 :   if(!use_sf) return 1.0;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        100 :   Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        100 :   double dw, w = sf1.calculateSqr( distance.modulo2(), dw );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        100 :   addAtomDerivatives( 0, 0, (-dw)*distance, myatoms );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        100 :   addAtomDerivatives( 0, 1, (+dw)*distance, myatoms );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        100 :   myatoms.addBoxDerivatives( 0, (-dw)*Tensor(distance,distance) );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        100 :   return w;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         50 : double XAngles::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         50 :   Vector ddij, ddik, axis, distance; axis.zero(); axis[myc]=1;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         50 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         50 :   PLMD::Angle a; double angle=a.compute( distance, axis, ddij, ddik );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         50 :   addAtomDerivatives( 1, 0, -ddij, myatoms );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         50 :   addAtomDerivatives( 1, 1, ddij, myatoms );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         50 :   myatoms.addBoxDerivatives( 1, -Tensor( distance,ddij ) );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         50 :   return angle;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XDistances.cpp.func-sort-c.html b/coverage/multicolvar/XDistances.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8f88d81512
--- /dev/null
+++ b/coverage/multicolvar/XDistances.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XDistances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XDistances.cpp<span style="font-size: 80%;"> (<a href="XDistances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">41.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="XDistances.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#180">_ZN4PLMD11multicolvar10XDistances10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#206">_ZN4PLMD11multicolvar10XDistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#206">_ZN4PLMD11multicolvar10XDistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
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+              <td class="coverFnLo">0</td>
+            </tr>
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+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#184">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe1866createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#224">_ZNK4PLMD11multicolvar10XDistances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#187">_ZN4PLMD11multicolvar10XDistances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#183">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe185C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#183">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe185D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#184">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe186C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#184">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe186D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#185">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe187C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#185">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe187D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XDistances.cpp.func.html b/coverage/multicolvar/XDistances.cpp.func.html
new file mode 100644
index 0000000000..ddfada878e
--- /dev/null
+++ b/coverage/multicolvar/XDistances.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XDistances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XDistances.cpp<span style="font-size: 80%;"> (<a href="XDistances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">41.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="XDistances.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#180">_ZN4PLMD11multicolvar10XDistances10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#187">_ZN4PLMD11multicolvar10XDistances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#206">_ZN4PLMD11multicolvar10XDistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#206">_ZN4PLMD11multicolvar10XDistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#183">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe1856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#183">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe185C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#183">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe185D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#184">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe1866createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#184">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe186C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#184">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe186D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#185">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe1876createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#185">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe187C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#185">_ZN4PLMD11multicolvar12_GLOBAL__N_123XDistancesRegisterMe187D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XDistances.cpp.gcov.html#224">_ZNK4PLMD11multicolvar10XDistances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XDistances.cpp.gcov.html b/coverage/multicolvar/XDistances.cpp.gcov.html
new file mode 100644
index 0000000000..5759f11a7e
--- /dev/null
+++ b/coverage/multicolvar/XDistances.cpp.gcov.html
@@ -0,0 +1,317 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XDistances.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XDistances.cpp<span style="font-size: 80%;"> (source / <a href="XDistances.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryLo">41.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace multicolvar {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC MCOLVAR XDISTANCES</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Calculate the x components of the vectors connecting one or many pairs of atoms.</a>
+<a name="35"><span class="lineNum">      35 </span>            : You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and</a>
+<a name="40"><span class="lineNum">      40 </span>            : the x-component of the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then</a>
+<a name="41"><span class="lineNum">      41 </span>            : printed</a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : d1: XDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="44"><span class="lineNum">      44 </span>            : PRINT ARG=d1.min</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : (See also \ref PRINT).</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The following input tells plumed to calculate the x-component of the vector connecting atom 3 to atom 5 and</a>
+<a name="50"><span class="lineNum">      50 </span>            : the x-component of the vector connecting atom 1 to atom 2.  The number of values that are</a>
+<a name="51"><span class="lineNum">      51 </span>            : less than 0.1nm is then printed to a file.</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : d1: XDISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT ARG=d1.lessthan</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : (See also \ref PRINT \ref switchingfunction).</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The following input tells plumed to calculate the x-components of all the distinct vectors that can be created</a>
+<a name="59"><span class="lineNum">      59 </span>            : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).</a>
+<a name="60"><span class="lineNum">      60 </span>            : The average of these quantities is then calculated.</a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : d1: XDISTANCES GROUP=1-3 MEAN</a>
+<a name="63"><span class="lineNum">      63 </span>            : PRINT ARG=d1.mean</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endplumedfile</a>
+<a name="65"><span class="lineNum">      65 </span>            : (See also \ref PRINT)</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.</a>
+<a name="68"><span class="lineNum">      68 </span>            : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3.  The number of values</a>
+<a name="69"><span class="lineNum">      69 </span>            : more than 0.1 is then printed to a file.</a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : d1: XDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}</a>
+<a name="72"><span class="lineNum">      72 </span>            : PRINT ARG=d1.morethan</a>
+<a name="73"><span class="lineNum">      73 </span>            : \endplumedfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : (See also \ref PRINT \ref switchingfunction)</a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : //+ENDPLUMEDOC</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : //+PLUMEDOC MCOLVAR YDISTANCES</a>
+<a name="79"><span class="lineNum">      79 </span>            : /*</a>
+<a name="80"><span class="lineNum">      80 </span>            : Calculate the y components of the vectors connecting one or many pairs of atoms.</a>
+<a name="81"><span class="lineNum">      81 </span>            : You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \par Examples</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and</a>
+<a name="86"><span class="lineNum">      86 </span>            : the y-component of the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then</a>
+<a name="87"><span class="lineNum">      87 </span>            : printed</a>
+<a name="88"><span class="lineNum">      88 </span>            : \plumedfile</a>
+<a name="89"><span class="lineNum">      89 </span>            : d1: YDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="90"><span class="lineNum">      90 </span>            : PRINT ARG=d1.min</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endplumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : (See also \ref PRINT).</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : The following input tells plumed to calculate the y-component of the vector connecting atom 3 to atom 5 and</a>
+<a name="96"><span class="lineNum">      96 </span>            : the y-component of the vector connecting atom 1 to atom 2.  The number of values that are</a>
+<a name="97"><span class="lineNum">      97 </span>            : less than 0.1nm is then printed to a file.</a>
+<a name="98"><span class="lineNum">      98 </span>            : \plumedfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : d1: YDISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}</a>
+<a name="100"><span class="lineNum">     100 </span>            : PRINT ARG=d1.lessthan</a>
+<a name="101"><span class="lineNum">     101 </span>            : \endplumedfile</a>
+<a name="102"><span class="lineNum">     102 </span>            : (See also \ref PRINT \ref switchingfunction).</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The following input tells plumed to calculate the y-components of all the distinct vectors that can be created</a>
+<a name="105"><span class="lineNum">     105 </span>            : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).</a>
+<a name="106"><span class="lineNum">     106 </span>            : The average of these quantities is then calculated.</a>
+<a name="107"><span class="lineNum">     107 </span>            : \plumedfile</a>
+<a name="108"><span class="lineNum">     108 </span>            : d1: YDISTANCES GROUP=1-3 MEAN</a>
+<a name="109"><span class="lineNum">     109 </span>            : PRINT ARG=d1.mean</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endplumedfile</a>
+<a name="111"><span class="lineNum">     111 </span>            : (See also \ref PRINT)</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.</a>
+<a name="114"><span class="lineNum">     114 </span>            : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3.  The number of values</a>
+<a name="115"><span class="lineNum">     115 </span>            : more than 0.1 is then printed to a file.</a>
+<a name="116"><span class="lineNum">     116 </span>            : \plumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : d1: YDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}</a>
+<a name="118"><span class="lineNum">     118 </span>            : PRINT ARG=d1.morethan</a>
+<a name="119"><span class="lineNum">     119 </span>            : \endplumedfile</a>
+<a name="120"><span class="lineNum">     120 </span>            : (See also \ref PRINT \ref switchingfunction)</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : */</a>
+<a name="123"><span class="lineNum">     123 </span>            : //+ENDPLUMEDOC</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : //+PLUMEDOC MCOLVAR ZDISTANCES</a>
+<a name="126"><span class="lineNum">     126 </span>            : /*</a>
+<a name="127"><span class="lineNum">     127 </span>            : Calculate the z components of the vectors connecting one or many pairs of atoms.</a>
+<a name="128"><span class="lineNum">     128 </span>            : You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : \par Examples</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and</a>
+<a name="133"><span class="lineNum">     133 </span>            : the z-component of the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then</a>
+<a name="134"><span class="lineNum">     134 </span>            : printed</a>
+<a name="135"><span class="lineNum">     135 </span>            : \plumedfile</a>
+<a name="136"><span class="lineNum">     136 </span>            : d1: ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="137"><span class="lineNum">     137 </span>            : PRINT ARG=d1.min</a>
+<a name="138"><span class="lineNum">     138 </span>            : \endplumedfile</a>
+<a name="139"><span class="lineNum">     139 </span>            : (See also \ref PRINT).</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : The following input tells plumed to calculate the z-component of the vector connecting atom 3 to atom 5 and</a>
+<a name="143"><span class="lineNum">     143 </span>            : the z-component of the vector connecting atom 1 to atom 2.  The number of values that are</a>
+<a name="144"><span class="lineNum">     144 </span>            : less than 0.1nm is then printed to a file.</a>
+<a name="145"><span class="lineNum">     145 </span>            : \plumedfile</a>
+<a name="146"><span class="lineNum">     146 </span>            : d1: ZDISTANCES ATOMS1=3,5 ATOMS2=1,2 LESS_THAN={RATIONAL R_0=0.1}</a>
+<a name="147"><span class="lineNum">     147 </span>            : PRINT ARG=d1.lessthan</a>
+<a name="148"><span class="lineNum">     148 </span>            : \endplumedfile</a>
+<a name="149"><span class="lineNum">     149 </span>            : (See also \ref PRINT \ref switchingfunction).</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : The following input tells plumed to calculate the z-components of all the distinct vectors that can be created</a>
+<a name="152"><span class="lineNum">     152 </span>            : between atoms 1, 2 and 3 (i.e. the vectors between atoms 1 and 2, atoms 1 and 3 and atoms 2 and 3).</a>
+<a name="153"><span class="lineNum">     153 </span>            : The average of these quantities is then calculated.</a>
+<a name="154"><span class="lineNum">     154 </span>            : \plumedfile</a>
+<a name="155"><span class="lineNum">     155 </span>            : d1: ZDISTANCES GROUP=1-3 MEAN</a>
+<a name="156"><span class="lineNum">     156 </span>            : PRINT ARG=d1.mean</a>
+<a name="157"><span class="lineNum">     157 </span>            : \endplumedfile</a>
+<a name="158"><span class="lineNum">     158 </span>            : (See also \ref PRINT)</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : The following input tells plumed to calculate all the vectors connecting the the atoms in GROUPA to the atoms in GROUPB.</a>
+<a name="161"><span class="lineNum">     161 </span>            : In other words the vector between atoms 1 and 2 and the vector between atoms 1 and 3.  The number of values</a>
+<a name="162"><span class="lineNum">     162 </span>            : more than 0.1 is then printed to a file.</a>
+<a name="163"><span class="lineNum">     163 </span>            : \plumedfile</a>
+<a name="164"><span class="lineNum">     164 </span>            : d1: ZDISTANCES GROUPA=1 GROUPB=2,3 MORE_THAN={RATIONAL R_0=0.1}</a>
+<a name="165"><span class="lineNum">     165 </span>            : PRINT ARG=d1.morethan</a>
+<a name="166"><span class="lineNum">     166 </span>            : \endplumedfile</a>
+<a name="167"><span class="lineNum">     167 </span>            : (See also \ref PRINT \ref switchingfunction)</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : */</a>
+<a name="170"><span class="lineNum">     170 </span>            : //+ENDPLUMEDOC</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : class XDistances : public MultiColvarBase {</a>
+<a name="174"><span class="lineNum">     174 </span>            : private:</a>
+<a name="175"><span class="lineNum">     175 </span>            :   unsigned myc;</a>
+<a name="176"><span class="lineNum">     176 </span>            : public:</a>
+<a name="177"><span class="lineNum">     177 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="178"><span class="lineNum">     178 </span>            :   explicit XDistances(const ActionOptions&amp;);</a>
+<a name="179"><span class="lineNum">     179 </span>            : // active methods:</a>
+<a name="180"><span class="lineNum">     180 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : };</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XDistances,&quot;XDISTANCES&quot;)</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XDistances,&quot;YDISTANCES&quot;)</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XDistances,&quot;ZDISTANCES&quot;)</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          6 : void XDistances::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          6 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         12 :   keys.use(&quot;MAX&quot;); keys.use(&quot;ALT_MIN&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         18 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;LESS_THAN&quot;);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         12 :   keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         24 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the distances you wish to calculate. &quot;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one distance will be &quot;</a>
+<a name="197"><span class="lineNum">     197 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="198"><span class="lineNum">     198 </span>            :            &quot;specify the indices of two atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="199"><span class="lineNum">     199 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         12 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate the distance between each distinct pair of atoms in the group&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all &quot;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :            &quot;the atoms in GROUPB. This must be used in conjunction with GROUPB.&quot;);</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all the atoms &quot;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :            &quot;in GROUPB. This must be used in conjunction with GROUPA.&quot;);</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          6 : }</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 : XDistances::XDistances(const ActionOptions&amp;ao):</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   Action(ao),</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   MultiColvarBase(ao)</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   if( getName().find(&quot;X&quot;)!=std::string::npos) myc=0;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   else if( getName().find(&quot;Y&quot;)!=std::string::npos) myc=1;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :   else if( getName().find(&quot;Z&quot;)!=std::string::npos) myc=2;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   else plumed_error();</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   // Read in the atoms</a>
+<a name="218"><span class="lineNum">     218 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 2, all_atoms );</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   // And check everything has been read in correctly</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 : double XDistances::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   Vector distance;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :   const double value=distance[myc];</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   Vector myvec; myvec.zero();</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   // And finish the calculation</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :   myvec[myc]=+1; addAtomDerivatives( 1, 1, myvec, myatoms );</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :   myvec[myc]=-1; addAtomDerivatives( 1, 0, myvec, myatoms );</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   myatoms.addBoxDerivatives( 1, Tensor(distance,myvec) );</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :   return value;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : }</a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XYDistances.cpp.func-sort-c.html b/coverage/multicolvar/XYDistances.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7f5e7a3272
--- /dev/null
+++ b/coverage/multicolvar/XYDistances.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XYDistances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XYDistances.cpp<span style="font-size: 80%;"> (<a href="XYDistances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="XYDistances.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#105">_ZN4PLMD11multicolvar11XYDistances10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#130">_ZN4PLMD11multicolvar11XYDistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#130">_ZN4PLMD11multicolvar11XYDistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#108">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#109">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe1116createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#110">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#151">_ZNK4PLMD11multicolvar11XYDistances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#112">_ZN4PLMD11multicolvar11XYDistances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#108">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#108">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#109">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe111C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#109">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe111D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#110">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#110">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XYDistances.cpp.func.html b/coverage/multicolvar/XYDistances.cpp.func.html
new file mode 100644
index 0000000000..cf5e2b66da
--- /dev/null
+++ b/coverage/multicolvar/XYDistances.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XYDistances.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XYDistances.cpp<span style="font-size: 80%;"> (<a href="XYDistances.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="XYDistances.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#105">_ZN4PLMD11multicolvar11XYDistances10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#112">_ZN4PLMD11multicolvar11XYDistances16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#130">_ZN4PLMD11multicolvar11XYDistancesC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#130">_ZN4PLMD11multicolvar11XYDistancesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#108">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#108">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#108">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#109">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe1116createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#109">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe111C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#109">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe111D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#110">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#110">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#110">_ZN4PLMD11multicolvar12_GLOBAL__N_124XYDistancesRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYDistances.cpp.gcov.html#151">_ZNK4PLMD11multicolvar11XYDistances7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XYDistances.cpp.gcov.html b/coverage/multicolvar/XYDistances.cpp.gcov.html
new file mode 100644
index 0000000000..370b8824dc
--- /dev/null
+++ b/coverage/multicolvar/XYDistances.cpp.gcov.html
@@ -0,0 +1,245 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XYDistances.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XYDistances.cpp<span style="font-size: 80%;"> (source / <a href="XYDistances.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryLo">35.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace multicolvar {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC MCOLVAR XYDISTANCES</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Calculate distance between a pair of atoms neglecting the z-component.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3</a>
+<a name="41"><span class="lineNum">      41 </span>            : to atom 5 projected in the xy-plane and the projection of the length of the vector</a>
+<a name="42"><span class="lineNum">      42 </span>            : the vector connecting atom 1 to atom 2 in the xy-plane.  The minimum of these two quantities is then</a>
+<a name="43"><span class="lineNum">      43 </span>            : printed</a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : d1: XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="46"><span class="lineNum">      46 </span>            : PRINT ARG=d1.min</a>
+<a name="47"><span class="lineNum">      47 </span>            : \endplumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : (See also \ref PRINT).</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : */</a>
+<a name="51"><span class="lineNum">      51 </span>            : //+ENDPLUMEDOC</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : //+PLUMEDOC MCOLVAR XZDISTANCES</a>
+<a name="54"><span class="lineNum">      54 </span>            : /*</a>
+<a name="55"><span class="lineNum">      55 </span>            : Calculate distance between a pair of atoms neglecting the y-component.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : You can then calculate functions of the distribution of</a>
+<a name="58"><span class="lineNum">      58 </span>            : values such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \par Examples</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3</a>
+<a name="63"><span class="lineNum">      63 </span>            : to atom 5 projected in the xz-plane and the projection of the length of the vector</a>
+<a name="64"><span class="lineNum">      64 </span>            : the vector connecting atom 1 to atom 2 in the xz-plane.  The minimum of these two quantities is then</a>
+<a name="65"><span class="lineNum">      65 </span>            : printed</a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : d1: XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="68"><span class="lineNum">      68 </span>            : PRINT ARG=d1.min</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : (See also \ref PRINT).</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : */</a>
+<a name="73"><span class="lineNum">      73 </span>            : //+ENDPLUMEDOC</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : //+PLUMEDOC MCOLVAR YZDISTANCES</a>
+<a name="76"><span class="lineNum">      76 </span>            : /*</a>
+<a name="77"><span class="lineNum">      77 </span>            : Calculate distance between a pair of atoms neglecting the x-component.</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : You can then calculate functions of the distribution of</a>
+<a name="80"><span class="lineNum">      80 </span>            : values such as the minimum, the number less than a certain quantity and so on.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : \par Examples</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3</a>
+<a name="85"><span class="lineNum">      85 </span>            : to atom 5 in the yz-plane and the projection of the length of the vector</a>
+<a name="86"><span class="lineNum">      86 </span>            : the vector connecting atom 1 to atom 2 in the yz-plane.  The minimum of these two quantities is then</a>
+<a name="87"><span class="lineNum">      87 </span>            : printed</a>
+<a name="88"><span class="lineNum">      88 </span>            : \plumedfile</a>
+<a name="89"><span class="lineNum">      89 </span>            : d1: YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}</a>
+<a name="90"><span class="lineNum">      90 </span>            : PRINT ARG=d1.min</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endplumedfile</a>
+<a name="92"><span class="lineNum">      92 </span>            : (See also \ref PRINT).</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : */</a>
+<a name="95"><span class="lineNum">      95 </span>            : //+ENDPLUMEDOC</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : class XYDistances : public MultiColvarBase {</a>
+<a name="99"><span class="lineNum">      99 </span>            : private:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   unsigned myc1, myc2;</a>
+<a name="101"><span class="lineNum">     101 </span>            : public:</a>
+<a name="102"><span class="lineNum">     102 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="103"><span class="lineNum">     103 </span>            :   explicit XYDistances(const ActionOptions&amp;);</a>
+<a name="104"><span class="lineNum">     104 </span>            : // active methods:</a>
+<a name="105"><span class="lineNum">     105 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : };</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYDistances,&quot;XYDISTANCES&quot;)</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYDistances,&quot;XZDISTANCES&quot;)</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYDistances,&quot;YZDISTANCES&quot;)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          6 : void XYDistances::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          6 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         12 :   keys.use(&quot;MAX&quot;); keys.use(&quot;ALT_MIN&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         30 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         24 :   keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the distances you wish to calculate. &quot;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one distance will be &quot;</a>
+<a name="121"><span class="lineNum">     121 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="122"><span class="lineNum">     122 </span>            :            &quot;specify the indices of two atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="123"><span class="lineNum">     123 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         12 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate the distance between each distinct pair of atoms in the group&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all &quot;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :            &quot;the atoms in GROUPB. This must be used in conjunction with GROUPB.&quot;);</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         12 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all the atoms &quot;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :            &quot;in GROUPB. This must be used in conjunction with GROUPA.&quot;);</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          6 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 : XYDistances::XYDistances(const ActionOptions&amp;ao):</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   Action(ao),</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   MultiColvarBase(ao)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : {</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :   if( getName().find(&quot;XY&quot;)!=std::string::npos) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     myc1=0; myc2=1;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   } else if( getName().find(&quot;XZ&quot;)!=std::string::npos) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     myc1=0; myc2=2;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   } else if( getName().find(&quot;YZ&quot;)!=std::string::npos) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     myc1=1; myc2=2;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   } else plumed_error();</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   // Read in the atoms</a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :   readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 2, all_atoms );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   // And check everything has been read in correctly</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   checkRead();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 : double XYDistances::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :   Vector distance;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   const double value=std::sqrt(distance[myc1]*distance[myc1] + distance[myc2]*distance[myc2] );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   const double invvalue=1.0/value;</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :   Vector myvec; myvec.zero();</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   // And finish the calculation</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   myvec[myc1]=+invvalue*distance[myc1]; myvec[myc2]=+invvalue*distance[myc2]; addAtomDerivatives( 1, 1, myvec, myatoms  );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :   myvec[myc1]=-invvalue*distance[myc1]; myvec[myc2]=-invvalue*distance[myc2]; addAtomDerivatives( 1, 0, myvec, myatoms );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   myatoms.addBoxDerivatives( 1, Tensor(distance,myvec) );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   return value;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : }</a>
+<a name="168"><span class="lineNum">     168 </span>            : }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XYTorsion.cpp.func-sort-c.html b/coverage/multicolvar/XYTorsion.cpp.func-sort-c.html
new file mode 100644
index 0000000000..541841ae5e
--- /dev/null
+++ b/coverage/multicolvar/XYTorsion.cpp.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XYTorsion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XYTorsion.cpp<span style="font-size: 80%;"> (<a href="XYTorsion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="XYTorsion.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#147">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#148">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#149">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1516createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#150">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1526createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#175">_ZN4PLMD11multicolvar9XYTorsionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#152">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#144">_ZN4PLMD11multicolvar9XYTorsion14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">1</td>
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+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#151">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1536createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#143">_ZN4PLMD11multicolvar9XYTorsion10isPeriodicEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#175">_ZN4PLMD11multicolvar9XYTorsionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#154">_ZN4PLMD11multicolvar9XYTorsion16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#218">_ZNK4PLMD11multicolvar9XYTorsion7computeERKjRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#207">_ZNK4PLMD11multicolvar9XYTorsion15calculateWeightERKjRKdRNS0_13AtomValuePackE</a></td>
+              <td class="coverFnHi">110</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#147">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe149C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#147">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe149D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#148">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe150C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#148">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe150D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#149">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe151C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#149">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe151D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#150">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe152C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#150">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe152D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#151">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe153C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#151">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe153D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#152">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe154C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#152">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe154D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XYTorsion.cpp.func.html b/coverage/multicolvar/XYTorsion.cpp.func.html
new file mode 100644
index 0000000000..1fdaf3a6c2
--- /dev/null
+++ b/coverage/multicolvar/XYTorsion.cpp.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XYTorsion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XYTorsion.cpp<span style="font-size: 80%;"> (<a href="XYTorsion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="XYTorsion.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#147">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1496createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#147">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe149C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#147">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe149D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="XYTorsion.cpp.gcov.html#148">_ZN4PLMD11multicolvar12_GLOBAL__N_122XYTorsionRegisterMe1506createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">4168</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/XYTorsion.cpp.gcov.html b/coverage/multicolvar/XYTorsion.cpp.gcov.html
new file mode 100644
index 0000000000..61d69c5151
--- /dev/null
+++ b/coverage/multicolvar/XYTorsion.cpp.gcov.html
@@ -0,0 +1,310 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar/XYTorsion.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">multicolvar</a> - XYTorsion.cpp<span style="font-size: 80%;"> (source / <a href="XYTorsion.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Torsion.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace multicolvar {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC MCOLVAR XYTORSIONS</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Calculate the torsional angle around the x axis from the positive y direction.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : The following input tells plumed to calculate the angle around the x direction between the positive y-axis and the vector connecting atom 3 to atom 5 and</a>
+<a name="41"><span class="lineNum">      41 </span>            : the angle around the x direction between the positive y axis and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output</a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : d1: XYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="44"><span class="lineNum">      44 </span>            : PRINT ARG=d1.between</a>
+<a name="45"><span class="lineNum">      45 </span>            : \endplumedfile</a>
+<a name="46"><span class="lineNum">      46 </span>            : (See also \ref PRINT).</a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : //+ENDPLUMEDOC</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : //+PLUMEDOC MCOLVAR XZTORSIONS</a>
+<a name="51"><span class="lineNum">      51 </span>            : /*</a>
+<a name="52"><span class="lineNum">      52 </span>            : Calculate the torsional angle around the x axis from the positive z direction.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \par Examples</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The following input tells plumed to calculate the angle around the x direction between the positive z-axis and the vector connecting atom 3 to atom 5 and</a>
+<a name="57"><span class="lineNum">      57 </span>            : the angle around the x direction between the positive z direction and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output</a>
+<a name="58"><span class="lineNum">      58 </span>            : \plumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : d1: XZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="60"><span class="lineNum">      60 </span>            : PRINT ARG=d1.*</a>
+<a name="61"><span class="lineNum">      61 </span>            : \endplumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : (See also \ref PRINT).</a>
+<a name="63"><span class="lineNum">      63 </span>            : */</a>
+<a name="64"><span class="lineNum">      64 </span>            : //+ENDPLUMEDOC</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : //+PLUMEDOC MCOLVAR YXTORSIONS</a>
+<a name="67"><span class="lineNum">      67 </span>            : /*</a>
+<a name="68"><span class="lineNum">      68 </span>            : Calculate the torsional angle around the y axis from the positive x direction.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : The following input tells plumed to calculate the angle around the y direction between the positive x-direction and the vector connecting atom 3 to atom 5 and</a>
+<a name="73"><span class="lineNum">      73 </span>            : the angle around the y direction between the positive x axis and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output</a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : d1: YXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="76"><span class="lineNum">      76 </span>            : PRINT ARG=d1.*</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endplumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : (See also \ref PRINT).</a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : //+PLUMEDOC MCOLVAR YZTORSIONS</a>
+<a name="83"><span class="lineNum">      83 </span>            : /*</a>
+<a name="84"><span class="lineNum">      84 </span>            : Calculate the torsional angle around the y axis from the positive z direction.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : \par Examples</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : The following input tells plumed to calculate the angle around the y direction between the positive z-direction and the vector connecting atom 3 to atom 5 and</a>
+<a name="89"><span class="lineNum">      89 </span>            : the angle around the y direction between the positive z direction and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output</a>
+<a name="90"><span class="lineNum">      90 </span>            : \plumedfile</a>
+<a name="91"><span class="lineNum">      91 </span>            : d1: YZTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="92"><span class="lineNum">      92 </span>            : PRINT ARG=d1.*</a>
+<a name="93"><span class="lineNum">      93 </span>            : \endplumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : (See also \ref PRINT).</a>
+<a name="95"><span class="lineNum">      95 </span>            : */</a>
+<a name="96"><span class="lineNum">      96 </span>            : //+ENDPLUMEDOC</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : //+PLUMEDOC MCOLVAR ZXTORSIONS</a>
+<a name="99"><span class="lineNum">      99 </span>            : /*</a>
+<a name="100"><span class="lineNum">     100 </span>            : Calculate the torsional angle around the z axis from the positive x direction.</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : \par Examples</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : The following input tells plumed to calculate the angle around the z direction between the positive x-direction and the vector connecting atom 3 to atom 5 and</a>
+<a name="105"><span class="lineNum">     105 </span>            : the angle around the z direction between the positive x-direction and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output</a>
+<a name="106"><span class="lineNum">     106 </span>            : \plumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : d1: ZXTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="108"><span class="lineNum">     108 </span>            : PRINT ARG=d1.*</a>
+<a name="109"><span class="lineNum">     109 </span>            : \endplumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : (See also \ref PRINT).</a>
+<a name="111"><span class="lineNum">     111 </span>            : */</a>
+<a name="112"><span class="lineNum">     112 </span>            : //+ENDPLUMEDOC</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : //+PLUMEDOC MCOLVAR ZYTORSIONS</a>
+<a name="115"><span class="lineNum">     115 </span>            : /*</a>
+<a name="116"><span class="lineNum">     116 </span>            : Calculate the torsional angle around the z axis from the positive y direction.</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : \par Examples</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : The following input tells plumed to calculate the angle around the z direction between the positive y-axis and the vector connecting atom 3 to atom 5 and</a>
+<a name="121"><span class="lineNum">     121 </span>            : the angle around the z direction between the positive y axis and the vector connecting atom 1 to atom 2.  The minimum of these two quantities is then output</a>
+<a name="122"><span class="lineNum">     122 </span>            : \plumedfile</a>
+<a name="123"><span class="lineNum">     123 </span>            : d1: ZYTORSIONS ATOMS1=3,5 ATOMS2=1,2 BETWEEN={GAUSSIAN LOWER=0 UPPER=pi SMEAR=0.1}</a>
+<a name="124"><span class="lineNum">     124 </span>            : PRINT ARG=d1.*</a>
+<a name="125"><span class="lineNum">     125 </span>            : \endplumedfile</a>
+<a name="126"><span class="lineNum">     126 </span>            : (See also \ref PRINT).</a>
+<a name="127"><span class="lineNum">     127 </span>            : */</a>
+<a name="128"><span class="lineNum">     128 </span>            : //+ENDPLUMEDOC</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : class XYTorsion : public MultiColvarBase {</a>
+<a name="134"><span class="lineNum">     134 </span>            : private:</a>
+<a name="135"><span class="lineNum">     135 </span>            :   bool use_sf;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   unsigned myc1, myc2;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   SwitchingFunction sf1;</a>
+<a name="138"><span class="lineNum">     138 </span>            : public:</a>
+<a name="139"><span class="lineNum">     139 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="140"><span class="lineNum">     140 </span>            :   explicit XYTorsion(const ActionOptions&amp;);</a>
+<a name="141"><span class="lineNum">     141 </span>            : // active methods:</a>
+<a name="142"><span class="lineNum">     142 </span>            :   double compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const override;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   double calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; ) const override;</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 :   bool isPeriodic() override { return true; }</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          1 :   void retrieveDomain( std::string&amp; min, std::string&amp; max) override { min=&quot;-pi&quot;; max=&quot;pi&quot;; }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : };</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYTorsion,&quot;XYTORSIONS&quot;)</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYTorsion,&quot;XZTORSIONS&quot;)</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYTorsion,&quot;YXTORSIONS&quot;)</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      12504 : PLUMED_REGISTER_ACTION(XYTorsion,&quot;YZTORSIONS&quot;)</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(XYTorsion,&quot;ZXTORSIONS&quot;)</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(XYTorsion,&quot;ZYTORSIONS&quot;)</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         15 : void XYTorsion::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         15 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         30 :   keys.use(&quot;MAX&quot;); keys.use(&quot;ALT_MIN&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         30 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MIN&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         30 :   keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         45 :   keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         30 :   keys.add(&quot;numbered&quot;,&quot;ATOMS&quot;,&quot;the atoms involved in each of the torsion angles you wish to calculate. &quot;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :            &quot;Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one torsion will be &quot;</a>
+<a name="164"><span class="lineNum">     164 </span>            :            &quot;calculated for each ATOM keyword you specify (all ATOM keywords should &quot;</a>
+<a name="165"><span class="lineNum">     165 </span>            :            &quot;specify the indices of two atoms).  The eventual number of quantities calculated by this &quot;</a>
+<a name="166"><span class="lineNum">     166 </span>            :            &quot;action will depend on what functions of the distribution you choose to calculate.&quot;);</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         30 :   keys.reset_style(&quot;ATOMS&quot;,&quot;atoms&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         30 :   keys.add(&quot;atoms-1&quot;,&quot;GROUP&quot;,&quot;Calculate the distance between each distinct pair of atoms in the group&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         30 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPA&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all &quot;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :            &quot;the atoms in GROUPB. This must be used in conjunction with GROUPB.&quot;);</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         30 :   keys.add(&quot;atoms-2&quot;,&quot;GROUPB&quot;,&quot;Calculate the distances between all the atoms in GROUPA and all the atoms &quot;</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :            &quot;in GROUPB. This must be used in conjunction with GROUPA.&quot;);</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         30 :   keys.add(&quot;optional&quot;,&quot;SWITCH&quot;,&quot;A switching function that ensures that only angles are only computed when atoms are within &quot;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :            &quot;are within a certain fixed cutoff. The following provides information on the \\ref switchingfunction that are available.&quot;);</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         15 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 : XYTorsion::XYTorsion(const ActionOptions&amp;ao):</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   Action(ao),</a>
+<a name="179"><span class="lineNum">     179 </span>            :   MultiColvarBase(ao),</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          3 :   use_sf(false)</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          3 :   if( getName().find(&quot;XY&quot;)!=std::string::npos) { myc1=0; myc2=1; }</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :   else if( getName().find(&quot;XZ&quot;)!=std::string::npos) { myc1=0; myc2=2; }</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          3 :   else if( getName().find(&quot;YX&quot;)!=std::string::npos) { myc1=1; myc2=0; }</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          3 :   else if( getName().find(&quot;YZ&quot;)!=std::string::npos) { myc1=1; myc2=2; }</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          3 :   else if( getName().find(&quot;ZX&quot;)!=std::string::npos) { myc1=2; myc2=0; }</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          1 :   else if( getName().find(&quot;ZY&quot;)!=std::string::npos) { myc1=2; myc2=1; }</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   else plumed_error();</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   // Read in switching function</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          6 :   std::string sfinput, errors; parse(&quot;SWITCH&quot;,sfinput);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          3 :   if( sfinput.length()&gt;0 ) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 :     use_sf=true; weightHasDerivatives=true;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          2 :     sf1.set(sfinput,errors);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 :     if( errors.length()!=0 ) error(&quot;problem reading SWITCH keyword : &quot; + errors );</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          2 :     log.printf(&quot;  only calculating angles for atoms separated by less than %s\n&quot;, sf1.description().c_str() );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          2 :     setLinkCellCutoff( sf1.get_dmax() );</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   // Read in the atoms</a>
+<a name="201"><span class="lineNum">     201 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          6 :   readTwoGroups( &quot;GROUP&quot;, &quot;GROUPA&quot;, &quot;GROUPB&quot;, all_atoms );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          4 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( &quot;ATOMS&quot;, 2, all_atoms );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          3 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   // And check everything has been read in correctly</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          3 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        110 : double XYTorsion::calculateWeight( const unsigned&amp; taskCode, const double&amp; weight, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        110 :   if(!use_sf) return 1.0;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        100 :   Vector distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        100 :   double dw, w = sf1.calculateSqr( distance.modulo2(), dw );</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        100 :   addAtomDerivatives( 0, 0, (-dw)*distance, myatoms );</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        100 :   addAtomDerivatives( 0, 1, (+dw)*distance, myatoms );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        100 :   myatoms.addBoxDerivatives( 0, (-dw)*Tensor(distance,distance) );</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        100 :   return w;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         50 : double XYTorsion::compute( const unsigned&amp; tindex, AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         50 :   Vector dd0, dd1, dd2, axis, rot, distance;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         50 :   axis.zero(); rot.zero(); rot[myc1]=1; axis[myc2]=1;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         50 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         50 :   PLMD::Torsion t; double torsion=t.compute( distance, rot, axis, dd0, dd1, dd2 );</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         50 :   addAtomDerivatives( 1, 0, -dd0, myatoms );</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         50 :   addAtomDerivatives( 1, 1, dd0, myatoms );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         50 :   myatoms.addBoxDerivatives( 1, -extProduct(distance,dd0) );</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         50 :   return torsion;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/index-sort-f.html b/coverage/multicolvar/index-sort-f.html
new file mode 100644
index 0000000000..ba7ca3a8c8
--- /dev/null
+++ b/coverage/multicolvar/index-sort-f.html
@@ -0,0 +1,523 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - multicolvar</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2377</td>
+            <td class="headerCovTableEntry">3025</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">329</td>
+            <td class="headerCovTableEntry">422</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeTetrapore.cpp.gcov.html">VolumeTetrapore.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=3 height=10 alt="3.4%"><img src="../snow.png" width=97 height=10 alt="3.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">3.4&nbsp;%</td>
+      <td class="coverNumLo">8 / 232</td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InPlaneDistances.cpp.gcov.html">InPlaneDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=21 height=10 alt="21.3%"><img src="../snow.png" width=79 height=10 alt="21.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">21.3&nbsp;%</td>
+      <td class="coverNumLo">10 / 47</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeBetweenContours.cpp.gcov.html">VolumeBetweenContours.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=14 height=10 alt="14.0%"><img src="../snow.png" width=86 height=10 alt="14.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">14.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 50</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XYDistances.cpp.gcov.html">XYDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=36 height=10 alt="35.9%"><img src="../snow.png" width=64 height=10 alt="35.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">14 / 39</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XDistances.cpp.gcov.html">XDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=42 height=10 alt="41.7%"><img src="../snow.png" width=58 height=10 alt="41.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">41.7&nbsp;%</td>
+      <td class="coverNumLo">15 / 36</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgedMultiColvarFunction.h.gcov.html">BridgedMultiColvarFunction.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=52 height=10 alt="52.2%"><img src="../snow.png" width=48 height=10 alt="52.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 23</td>
+      <td class="coverPerLo">58.3&nbsp;%</td>
+      <td class="coverNumLo">7 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarFilter.cpp.gcov.html">MultiColvarFilter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.5%"><img src="../snow.png" width=18 height=10 alt="82.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.5&nbsp;%</td>
+      <td class="coverNumMed">33 / 40</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Density.cpp.gcov.html">Density.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.8%"><img src="../snow.png" width=29 height=10 alt="70.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.8&nbsp;%</td>
+      <td class="coverNumLo">17 / 24</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlphaBeta.cpp.gcov.html">AlphaBeta.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.9%"><img src="../snow.png" width=12 height=10 alt="87.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.9&nbsp;%</td>
+      <td class="coverNumMed">51 / 58</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bridge.cpp.gcov.html">Bridge.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.2%"><img src="../snow.png" width=21 height=10 alt="79.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.2&nbsp;%</td>
+      <td class="coverNumMed">42 / 53</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DihedralCorrelation.cpp.gcov.html">DihedralCorrelation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 50</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeGradientBase.cpp.gcov.html">VolumeGradientBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.9%"><img src="../snow.png" width=21 height=10 alt="78.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.9&nbsp;%</td>
+      <td class="coverNumMed">45 / 57</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpMultiColvar.cpp.gcov.html">DumpMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.1%"><img src="../snow.png" width=7 height=10 alt="93.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.1&nbsp;%</td>
+      <td class="coverNumHi">67 / 72</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">10 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NumberOfLinks.cpp.gcov.html">NumberOfLinks.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.5%"><img src="../snow.png" width=11 height=10 alt="89.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">51 / 57</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionVolume.cpp.gcov.html">ActionVolume.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterBetween.cpp.gcov.html">FilterBetween.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.8%"><img src="../snow.png" width=17 height=10 alt="82.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.8&nbsp;%</td>
+      <td class="coverNumMed">24 / 29</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterLessThan.cpp.gcov.html">FilterLessThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.5%"><img src="../snow.png" width=19 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">22 / 27</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarBase.h.gcov.html">MultiColvarBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.2%"><img src="../snow.png" width=15 height=10 alt="85.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.2&nbsp;%</td>
+      <td class="coverNumMed">23 / 27</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalAverage.cpp.gcov.html">LocalAverage.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.3%"><img src="../snow.png" width=21 height=10 alt="79.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.3&nbsp;%</td>
+      <td class="coverNumMed">107 / 135</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XYTorsion.cpp.gcov.html">XYTorsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">58 / 59</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgedMultiColvarFunction.cpp.gcov.html">BridgedMultiColvarFunction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">52 / 56</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarDensity.cpp.gcov.html">MultiColvarDensity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.5%"><img src="../snow.png" width=17 height=10 alt="83.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.5&nbsp;%</td>
+      <td class="coverNumMed">116 / 139</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeCavity.cpp.gcov.html">VolumeCavity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.4%"><img src="../snow.png" width=21 height=10 alt="79.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.4&nbsp;%</td>
+      <td class="coverNumMed">170 / 214</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DistanceFromContour.cpp.gcov.html">DistanceFromContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.2%"><img src="../snow.png" width=14 height=10 alt="86.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.2&nbsp;%</td>
+      <td class="coverNumMed">131 / 152</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CenterOfMultiColvar.cpp.gcov.html">CenterOfMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">77 / 80</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XAngle.cpp.gcov.html">XAngle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 51</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeInSphere.cpp.gcov.html">VolumeInSphere.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeInCylinder.cpp.gcov.html">VolumeInCylinder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.9%"><img src="../snow.png" width=4 height=10 alt="95.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.9&nbsp;%</td>
+      <td class="coverNumHi">47 / 49</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Distances.cpp.gcov.html">Distances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">43 / 45</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeAround.cpp.gcov.html">VolumeAround.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">48 / 48</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoordinationNumbers.cpp.gcov.html">CoordinationNumbers.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 50</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarCombine.cpp.gcov.html">MultiColvarCombine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarProduct.cpp.gcov.html">MultiColvarProduct.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angles.cpp.gcov.html">Angles.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.0%"><img src="../snow.png" width=16 height=10 alt="84.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.0&nbsp;%</td>
+      <td class="coverNumMed">63 / 75</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsions.cpp.gcov.html">Torsions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">33 / 33</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterMoreThan.cpp.gcov.html">FilterMoreThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.5%"><img src="../snow.png" width=19 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">22 / 27</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarBase.cpp.gcov.html">MultiColvarBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.4%"><img src="../snow.png" width=11 height=10 alt="89.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.4&nbsp;%</td>
+      <td class="coverNumMed">583 / 652</td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">40 / 41</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionVolume.h.gcov.html">ActionVolume.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarFilter.h.gcov.html">MultiColvarFilter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeGradientBase.h.gcov.html">VolumeGradientBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CatomPack.cpp.gcov.html">CatomPack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CatomPack.h.gcov.html">CatomPack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomValuePack.cpp.gcov.html">AtomValuePack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 49</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomValuePack.h.gcov.html">AtomValuePack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">39 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/index-sort-l.html b/coverage/multicolvar/index-sort-l.html
new file mode 100644
index 0000000000..efdd9b2995
--- /dev/null
+++ b/coverage/multicolvar/index-sort-l.html
@@ -0,0 +1,523 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - multicolvar</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2377</td>
+            <td class="headerCovTableEntry">3025</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">329</td>
+            <td class="headerCovTableEntry">422</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeTetrapore.cpp.gcov.html">VolumeTetrapore.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=3 height=10 alt="3.4%"><img src="../snow.png" width=97 height=10 alt="3.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">3.4&nbsp;%</td>
+      <td class="coverNumLo">8 / 232</td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeBetweenContours.cpp.gcov.html">VolumeBetweenContours.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=14 height=10 alt="14.0%"><img src="../snow.png" width=86 height=10 alt="14.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">14.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 50</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InPlaneDistances.cpp.gcov.html">InPlaneDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=21 height=10 alt="21.3%"><img src="../snow.png" width=79 height=10 alt="21.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">21.3&nbsp;%</td>
+      <td class="coverNumLo">10 / 47</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XYDistances.cpp.gcov.html">XYDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=36 height=10 alt="35.9%"><img src="../snow.png" width=64 height=10 alt="35.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">14 / 39</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XDistances.cpp.gcov.html">XDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=42 height=10 alt="41.7%"><img src="../snow.png" width=58 height=10 alt="41.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">41.7&nbsp;%</td>
+      <td class="coverNumLo">15 / 36</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgedMultiColvarFunction.h.gcov.html">BridgedMultiColvarFunction.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=52 height=10 alt="52.2%"><img src="../snow.png" width=48 height=10 alt="52.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 23</td>
+      <td class="coverPerLo">58.3&nbsp;%</td>
+      <td class="coverNumLo">7 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Density.cpp.gcov.html">Density.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.8%"><img src="../snow.png" width=29 height=10 alt="70.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.8&nbsp;%</td>
+      <td class="coverNumLo">17 / 24</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeGradientBase.cpp.gcov.html">VolumeGradientBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.9%"><img src="../snow.png" width=21 height=10 alt="78.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.9&nbsp;%</td>
+      <td class="coverNumMed">45 / 57</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bridge.cpp.gcov.html">Bridge.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.2%"><img src="../snow.png" width=21 height=10 alt="79.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.2&nbsp;%</td>
+      <td class="coverNumMed">42 / 53</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalAverage.cpp.gcov.html">LocalAverage.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.3%"><img src="../snow.png" width=21 height=10 alt="79.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.3&nbsp;%</td>
+      <td class="coverNumMed">107 / 135</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeCavity.cpp.gcov.html">VolumeCavity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.4%"><img src="../snow.png" width=21 height=10 alt="79.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.4&nbsp;%</td>
+      <td class="coverNumMed">170 / 214</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterLessThan.cpp.gcov.html">FilterLessThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.5%"><img src="../snow.png" width=19 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">22 / 27</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterMoreThan.cpp.gcov.html">FilterMoreThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.5%"><img src="../snow.png" width=19 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">22 / 27</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarFilter.cpp.gcov.html">MultiColvarFilter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.5%"><img src="../snow.png" width=18 height=10 alt="82.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.5&nbsp;%</td>
+      <td class="coverNumMed">33 / 40</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterBetween.cpp.gcov.html">FilterBetween.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.8%"><img src="../snow.png" width=17 height=10 alt="82.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.8&nbsp;%</td>
+      <td class="coverNumMed">24 / 29</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarDensity.cpp.gcov.html">MultiColvarDensity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.5%"><img src="../snow.png" width=17 height=10 alt="83.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.5&nbsp;%</td>
+      <td class="coverNumMed">116 / 139</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angles.cpp.gcov.html">Angles.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.0%"><img src="../snow.png" width=16 height=10 alt="84.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.0&nbsp;%</td>
+      <td class="coverNumMed">63 / 75</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarBase.h.gcov.html">MultiColvarBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.2%"><img src="../snow.png" width=15 height=10 alt="85.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.2&nbsp;%</td>
+      <td class="coverNumMed">23 / 27</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DistanceFromContour.cpp.gcov.html">DistanceFromContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.2%"><img src="../snow.png" width=14 height=10 alt="86.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.2&nbsp;%</td>
+      <td class="coverNumMed">131 / 152</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlphaBeta.cpp.gcov.html">AlphaBeta.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.9%"><img src="../snow.png" width=12 height=10 alt="87.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.9&nbsp;%</td>
+      <td class="coverNumMed">51 / 58</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NumberOfLinks.cpp.gcov.html">NumberOfLinks.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.5%"><img src="../snow.png" width=11 height=10 alt="89.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">51 / 57</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarBase.cpp.gcov.html">MultiColvarBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.4%"><img src="../snow.png" width=11 height=10 alt="89.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.4&nbsp;%</td>
+      <td class="coverNumMed">583 / 652</td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">40 / 41</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgedMultiColvarFunction.cpp.gcov.html">BridgedMultiColvarFunction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">52 / 56</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpMultiColvar.cpp.gcov.html">DumpMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.1%"><img src="../snow.png" width=7 height=10 alt="93.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.1&nbsp;%</td>
+      <td class="coverNumHi">67 / 72</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">10 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomValuePack.h.gcov.html">AtomValuePack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">39 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Distances.cpp.gcov.html">Distances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">43 / 45</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeInCylinder.cpp.gcov.html">VolumeInCylinder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.9%"><img src="../snow.png" width=4 height=10 alt="95.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.9&nbsp;%</td>
+      <td class="coverNumHi">47 / 49</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CenterOfMultiColvar.cpp.gcov.html">CenterOfMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">77 / 80</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DihedralCorrelation.cpp.gcov.html">DihedralCorrelation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 50</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XAngle.cpp.gcov.html">XAngle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 51</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XYTorsion.cpp.gcov.html">XYTorsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">58 / 59</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarFilter.h.gcov.html">MultiColvarFilter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CatomPack.cpp.gcov.html">CatomPack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionVolume.h.gcov.html">ActionVolume.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeGradientBase.h.gcov.html">VolumeGradientBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CatomPack.h.gcov.html">CatomPack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeInSphere.cpp.gcov.html">VolumeInSphere.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarProduct.cpp.gcov.html">MultiColvarProduct.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarCombine.cpp.gcov.html">MultiColvarCombine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsions.cpp.gcov.html">Torsions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">33 / 33</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionVolume.cpp.gcov.html">ActionVolume.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeAround.cpp.gcov.html">VolumeAround.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">48 / 48</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomValuePack.cpp.gcov.html">AtomValuePack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 49</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoordinationNumbers.cpp.gcov.html">CoordinationNumbers.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 50</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/multicolvar/index.html b/coverage/multicolvar/index.html
new file mode 100644
index 0000000000..124f123d6e
--- /dev/null
+++ b/coverage/multicolvar/index.html
@@ -0,0 +1,523 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - multicolvar</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - multicolvar</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2377</td>
+            <td class="headerCovTableEntry">3025</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">329</td>
+            <td class="headerCovTableEntry">422</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionVolume.cpp.gcov.html">ActionVolume.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionVolume.h.gcov.html">ActionVolume.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlphaBeta.cpp.gcov.html">AlphaBeta.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.9%"><img src="../snow.png" width=12 height=10 alt="87.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.9&nbsp;%</td>
+      <td class="coverNumMed">51 / 58</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angles.cpp.gcov.html">Angles.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.0%"><img src="../snow.png" width=16 height=10 alt="84.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.0&nbsp;%</td>
+      <td class="coverNumMed">63 / 75</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomValuePack.cpp.gcov.html">AtomValuePack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 49</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomValuePack.h.gcov.html">AtomValuePack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.1%"><img src="../snow.png" width=5 height=10 alt="95.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.1&nbsp;%</td>
+      <td class="coverNumHi">39 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Bridge.cpp.gcov.html">Bridge.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.2%"><img src="../snow.png" width=21 height=10 alt="79.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.2&nbsp;%</td>
+      <td class="coverNumMed">42 / 53</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgedMultiColvarFunction.cpp.gcov.html">BridgedMultiColvarFunction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">52 / 56</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgedMultiColvarFunction.h.gcov.html">BridgedMultiColvarFunction.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=52 height=10 alt="52.2%"><img src="../snow.png" width=48 height=10 alt="52.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 23</td>
+      <td class="coverPerLo">58.3&nbsp;%</td>
+      <td class="coverNumLo">7 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CatomPack.cpp.gcov.html">CatomPack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CatomPack.h.gcov.html">CatomPack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CenterOfMultiColvar.cpp.gcov.html">CenterOfMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.2%"><img src="../snow.png" width=4 height=10 alt="96.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.2&nbsp;%</td>
+      <td class="coverNumHi">77 / 80</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoordinationNumbers.cpp.gcov.html">CoordinationNumbers.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 50</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Density.cpp.gcov.html">Density.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="70.8%"><img src="../snow.png" width=29 height=10 alt="70.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.8&nbsp;%</td>
+      <td class="coverNumLo">17 / 24</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DihedralCorrelation.cpp.gcov.html">DihedralCorrelation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 50</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DistanceFromContour.cpp.gcov.html">DistanceFromContour.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.2%"><img src="../snow.png" width=14 height=10 alt="86.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.2&nbsp;%</td>
+      <td class="coverNumMed">131 / 152</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Distances.cpp.gcov.html">Distances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">43 / 45</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DumpMultiColvar.cpp.gcov.html">DumpMultiColvar.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.1%"><img src="../snow.png" width=7 height=10 alt="93.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.1&nbsp;%</td>
+      <td class="coverNumHi">67 / 72</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">10 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterBetween.cpp.gcov.html">FilterBetween.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.8%"><img src="../snow.png" width=17 height=10 alt="82.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.8&nbsp;%</td>
+      <td class="coverNumMed">24 / 29</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterLessThan.cpp.gcov.html">FilterLessThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.5%"><img src="../snow.png" width=19 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">22 / 27</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FilterMoreThan.cpp.gcov.html">FilterMoreThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.5%"><img src="../snow.png" width=19 height=10 alt="81.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.5&nbsp;%</td>
+      <td class="coverNumMed">22 / 27</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="InPlaneDistances.cpp.gcov.html">InPlaneDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=21 height=10 alt="21.3%"><img src="../snow.png" width=79 height=10 alt="21.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">21.3&nbsp;%</td>
+      <td class="coverNumLo">10 / 47</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LocalAverage.cpp.gcov.html">LocalAverage.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.3%"><img src="../snow.png" width=21 height=10 alt="79.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.3&nbsp;%</td>
+      <td class="coverNumMed">107 / 135</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarBase.cpp.gcov.html">MultiColvarBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.4%"><img src="../snow.png" width=11 height=10 alt="89.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.4&nbsp;%</td>
+      <td class="coverNumMed">583 / 652</td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">40 / 41</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarBase.h.gcov.html">MultiColvarBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.2%"><img src="../snow.png" width=15 height=10 alt="85.2%"></td></tr></table>
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+      <td class="coverPerMed">85.2&nbsp;%</td>
+      <td class="coverNumMed">23 / 27</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarCombine.cpp.gcov.html">MultiColvarCombine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarDensity.cpp.gcov.html">MultiColvarDensity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.5%"><img src="../snow.png" width=17 height=10 alt="83.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.5&nbsp;%</td>
+      <td class="coverNumMed">116 / 139</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarFilter.cpp.gcov.html">MultiColvarFilter.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.5%"><img src="../snow.png" width=18 height=10 alt="82.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.5&nbsp;%</td>
+      <td class="coverNumMed">33 / 40</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarFilter.h.gcov.html">MultiColvarFilter.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiColvarProduct.cpp.gcov.html">MultiColvarProduct.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NumberOfLinks.cpp.gcov.html">NumberOfLinks.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.5%"><img src="../snow.png" width=11 height=10 alt="89.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">51 / 57</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsions.cpp.gcov.html">Torsions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">33 / 33</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeAround.cpp.gcov.html">VolumeAround.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">48 / 48</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeBetweenContours.cpp.gcov.html">VolumeBetweenContours.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=14 height=10 alt="14.0%"><img src="../snow.png" width=86 height=10 alt="14.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">14.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 50</td>
+      <td class="coverPerLo">37.5&nbsp;%</td>
+      <td class="coverNumLo">3 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeCavity.cpp.gcov.html">VolumeCavity.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="79.4%"><img src="../snow.png" width=21 height=10 alt="79.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">79.4&nbsp;%</td>
+      <td class="coverNumMed">170 / 214</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeGradientBase.cpp.gcov.html">VolumeGradientBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.9%"><img src="../snow.png" width=21 height=10 alt="78.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.9&nbsp;%</td>
+      <td class="coverNumMed">45 / 57</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeGradientBase.h.gcov.html">VolumeGradientBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeInCylinder.cpp.gcov.html">VolumeInCylinder.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.9%"><img src="../snow.png" width=4 height=10 alt="95.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.9&nbsp;%</td>
+      <td class="coverNumHi">47 / 49</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeInSphere.cpp.gcov.html">VolumeInSphere.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VolumeTetrapore.cpp.gcov.html">VolumeTetrapore.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=3 height=10 alt="3.4%"><img src="../snow.png" width=97 height=10 alt="3.4%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">3.4&nbsp;%</td>
+      <td class="coverNumLo">8 / 232</td>
+      <td class="coverPerLo">25.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XAngle.cpp.gcov.html">XAngle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.0%"><img src="../snow.png" width=2 height=10 alt="98.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 51</td>
+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">13 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XDistances.cpp.gcov.html">XDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=42 height=10 alt="41.7%"><img src="../snow.png" width=58 height=10 alt="41.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">41.7&nbsp;%</td>
+      <td class="coverNumLo">15 / 36</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XYDistances.cpp.gcov.html">XYDistances.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=36 height=10 alt="35.9%"><img src="../snow.png" width=64 height=10 alt="35.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">35.9&nbsp;%</td>
+      <td class="coverNumLo">14 / 39</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">7 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="XYTorsion.cpp.gcov.html">XYTorsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
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+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">58 / 59</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">20 / 25</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVcustom.cpp.func-sort-c.html b/coverage/opes/ECVcustom.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d25f249e4e
--- /dev/null
+++ b/coverage/opes/ECVcustom.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVcustom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVcustom.cpp<span style="font-size: 80%;"> (<a href="ECVcustom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryHi">92.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ECVcustom.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#95">_ZN4PLMD4opes9ECVcustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#211">_ZN4PLMD4opes9ECVcustom15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#219">_ZN4PLMD4opes9ECVcustom16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#83">_ZN4PLMD4opes12_GLOBAL__N_121ECVcustomRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#204">_ZN4PLMD4opes9ECVcustom8initECVsEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#95">_ZN4PLMD4opes9ECVcustomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#161">_ZNK4PLMD4opes9ECVcustom10getIndex_kEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#172">_ZNK4PLMD4opes9ECVcustom10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#147">_ZN4PLMD4opes9ECVcustom13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#154">_ZN4PLMD4opes9ECVcustom16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#85">_ZN4PLMD4opes9ECVcustom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#140">_ZN4PLMD4opes9ECVcustom13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#83">_ZN4PLMD4opes12_GLOBAL__N_121ECVcustomRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#83">_ZN4PLMD4opes12_GLOBAL__N_121ECVcustomRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVcustom.cpp.func.html b/coverage/opes/ECVcustom.cpp.func.html
new file mode 100644
index 0000000000..08ddd039d6
--- /dev/null
+++ b/coverage/opes/ECVcustom.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVcustom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVcustom.cpp<span style="font-size: 80%;"> (<a href="ECVcustom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryHi">92.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#83">_ZN4PLMD4opes12_GLOBAL__N_121ECVcustomRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#83">_ZN4PLMD4opes12_GLOBAL__N_121ECVcustomRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#83">_ZN4PLMD4opes12_GLOBAL__N_121ECVcustomRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#140">_ZN4PLMD4opes9ECVcustom13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#147">_ZN4PLMD4opes9ECVcustom13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">4</td>
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+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#211">_ZN4PLMD4opes9ECVcustom15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#154">_ZN4PLMD4opes9ECVcustom16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#219">_ZN4PLMD4opes9ECVcustom16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#85">_ZN4PLMD4opes9ECVcustom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#204">_ZN4PLMD4opes9ECVcustom8initECVsEv</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#95">_ZN4PLMD4opes9ECVcustomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#95">_ZN4PLMD4opes9ECVcustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#161">_ZNK4PLMD4opes9ECVcustom10getIndex_kEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVcustom.cpp.gcov.html#172">_ZNK4PLMD4opes9ECVcustom10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVcustom.cpp.gcov.html b/coverage/opes/ECVcustom.cpp.gcov.html
new file mode 100644
index 0000000000..5d704f5ac8
--- /dev/null
+++ b/coverage/opes/ECVcustom.cpp.gcov.html
@@ -0,0 +1,314 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVcustom.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVcustom.cpp<span style="font-size: 80%;"> (source / <a href="ECVcustom.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">101</td>
+            <td class="headerCovTableEntryHi">92.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : </a>
+<a name="22"><span class="lineNum">      22 </span>            : namespace PLMD {</a>
+<a name="23"><span class="lineNum">      23 </span>            : namespace opes {</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC OPES_EXPANSION_CV ECV_CUSTOM</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Use some given CVs as a set of expansion collective variables (ECVs).</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : This can be useful e.g. for quickly testing new ECVs, but from a performance point of view it is probably better to implement a new ECV class.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : By default the ARGs are expeted to be energies, \f$\Delta U_i\f$, and are then multiplied by the inverse temperature \f$\beta\f$</a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            :   \Delta u_i=\beta \Delta U_i\, .</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : Use the DIMENSIONLESS flag to avoid this multiplication.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : The flag ADD_P0 adds also the unbiased distribution to the target.</a>
+<a name="38"><span class="lineNum">      38 </span>            : It is possible to specify a BARRIER as in \ref ECV_UMBRELLAS_LINE, to avoid a too high initial bias.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \plumedfile</a>
+<a name="43"><span class="lineNum">      43 </span>            : ene: ENERGY</a>
+<a name="44"><span class="lineNum">      44 </span>            : t1: CUSTOM PERIODIC=NO ARG=ene FUNC=(300/500-1)*x</a>
+<a name="45"><span class="lineNum">      45 </span>            : t2: CUSTOM PERIODIC=NO ARG=ene FUNC=(300/1000-1)*x</a>
+<a name="46"><span class="lineNum">      46 </span>            : ecv: ECV_CUSTOM ARG=t1,t2 TEMP=300 ADD_P0</a>
+<a name="47"><span class="lineNum">      47 </span>            : opes: OPES_EXPANDED ARG=ecv.* PACE=500</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : It is equivalent to the following:</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : ene: ENERGY</a>
+<a name="54"><span class="lineNum">      54 </span>            : ecv: ECV_MULTITHERMAL ARG=ene TEMP=300 TEMP_SET_ALL=300,500,1000</a>
+<a name="55"><span class="lineNum">      55 </span>            : opes: OPES_EXPANDED ARG=ecv.* PACE=500</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : //+ENDPLUMEDOC</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : class ECVcustom :</a>
+<a name="62"><span class="lineNum">      62 </span>            :   public ExpansionCVs</a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span>            : private:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   unsigned P0_contribution_;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double barrier_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double beta0_;</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; ECVs_;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; derECVs_;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void initECVs();</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : public:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit ECVcustom(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void calculateECVs(const double *) override;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   const double * getPntrToECVs(unsigned) override;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   const double * getPntrToDerECVs(unsigned) override;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; getIndex_k() const override;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;std::string&gt; getLambdas() const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) override;</a>
+<a name="83"><span class="lineNum">      83 </span>            : };</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(ECVcustom,&quot;ECV_CUSTOM&quot;)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          4 : void ECVcustom::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          4 :   ExpansionCVs::registerKeywords(keys);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          4 :   keys.remove(&quot;ARG&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;the labels of the single ECVs. \\f$\\Delta U_i\\f$, in energy units&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          8 :   keys.addFlag(&quot;ADD_P0&quot;,false,&quot;add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          8 :   keys.addFlag(&quot;DIMENSIONLESS&quot;,false,&quot;consider ARG as dimensionless rather than an energy, thus do not multiply it by \\f$\\beta\\f$&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;BARRIER&quot;,&quot;a guess of the free energy barrier to be overcome (better to stay higher than lower)&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          4 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 : ECVcustom::ECVcustom(const ActionOptions&amp;ao)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   : Action(ao)</a>
+<a name="99"><span class="lineNum">      99 </span>            :   , ExpansionCVs(ao)</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   , beta0_(1./kbt_)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span>            : //set beta0_</a>
+<a name="103"><span class="lineNum">     103 </span>            :   bool dimensionless;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          2 :   parseFlag(&quot;DIMENSIONLESS&quot;,dimensionless);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 :   if(dimensionless)</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     beta0_=1;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : //set P0_contribution_</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   bool add_P0=false;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   parseFlag(&quot;ADD_P0&quot;,add_P0);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :   if(add_P0)</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :     P0_contribution_=1;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   else</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     P0_contribution_=0;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : //set barrier_</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   barrier_=std::numeric_limits&lt;double&gt;::infinity();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   parse(&quot;BARRIER&quot;,barrier_);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : //set ECVs stuff</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :   totNumECVs_=getNumberOfArguments()+P0_contribution_;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :   ECVs_.resize(getNumberOfArguments(),std::vector&lt;double&gt;(totNumECVs_));</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   derECVs_.resize(getNumberOfArguments(),std::vector&lt;double&gt;(totNumECVs_));</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          6 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          4 :     derECVs_[j][j+P0_contribution_]=beta0_; //always constant</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : //print some info</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   if(dimensionless)</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     log.printf(&quot; -- DIMENSIONLESS: the ARG is not multiplied by beta\n&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :   if(barrier_!=std::numeric_limits&lt;double&gt;::infinity())</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     log.printf(&quot;  guess for free energy BARRIER = %g\n&quot;,barrier_);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     if(dimensionless)</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :       log.printf(&quot;    also the BARRIER is considered to be DIMENSIONLESS\n&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          2 :   if(P0_contribution_==1)</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          2 :     log.printf(&quot; -- ADD_P0: the target includes also the unbiased probability itself\n&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         91 : void ECVcustom::calculateECVs(const double * cv)</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        273 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        182 :     ECVs_[j][j+P0_contribution_]=beta0_*cv[j];</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   //derivative is constant</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         91 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          4 : const double * ECVcustom::getPntrToECVs(unsigned j)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : {</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          4 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :   plumed_massert(j&lt;getNumberOfArguments(),getName()+&quot; has fewer CVs&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :   return &amp;ECVs_[j][0];</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 : const double * ECVcustom::getPntrToDerECVs(unsigned j)</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : {</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          4 :   plumed_massert(j&lt;getNumberOfArguments(),getName()+&quot; has fewer CVs&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          4 :   return &amp;derECVs_[j][0];</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 : std::vector&lt; std::vector&lt;unsigned&gt; &gt; ECVcustom::getIndex_k() const</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : {</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   plumed_massert(isReady_ &amp;&amp; totNumECVs_&gt;0,&quot;cannot access getIndex_k() of ECV before initialization&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; index_k(totNumECVs_,std::vector&lt;unsigned&gt;(getNumberOfArguments()));</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          8 :   for(unsigned k=0; k&lt;totNumECVs_; k++)</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         18 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         12 :       if(k==j+P0_contribution_)</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          4 :         index_k[k][j]=k;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :   return index_k;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 : std::vector&lt;std::string&gt; ECVcustom::getLambdas() const</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   std::vector&lt;std::string&gt; lambdas(totNumECVs_);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   if(P0_contribution_==1)</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   {</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :     std::ostringstream subs;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :     subs&lt;&lt;&quot;P0&quot;;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :     for(unsigned j=1; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :       subs&lt;&lt;&quot;_P0&quot;;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :     lambdas[0]=subs.str();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :   }</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          6 :   for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++)</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   {</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :     const unsigned kk=k-P0_contribution_;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          4 :     std::ostringstream subs;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : //the getLambdas method is const, so it complains if one tries to access a non-const pointer, hence the const_cast</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          4 :     if(kk==0)</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :       subs&lt;&lt;const_cast&lt;ECVcustom *&gt;(this)-&gt;getPntrToArgument(kk)-&gt;getName();</a>
+<a name="192"><span class="lineNum">     192 </span>            :     else</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 :       subs&lt;&lt;&quot;NaN&quot;;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          8 :     for(unsigned j=1; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          4 :       if(kk==j)</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          2 :         subs&lt;&lt;&quot;_&quot;&lt;&lt;const_cast&lt;ECVcustom *&gt;(this)-&gt;getPntrToArgument(kk)-&gt;getName();</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :       else</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :         subs&lt;&lt;&quot;_NaN&quot;;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          4 :     lambdas[k]=subs.str();</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          4 :   }</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          2 :   return lambdas;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          2 : void ECVcustom::initECVs()</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :   plumed_massert(!isReady_,&quot;initialization should not be called twice&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          2 :   isReady_=true;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          2 :   log.printf(&quot;  *%4u ECVs for %s\n&quot;,totNumECVs_,getName().c_str());</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          1 : void ECVcustom::initECVs_observ(const std::vector&lt;double&gt;&amp; all_obs_cvs,const unsigned ncv,const unsigned index_j)</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : {</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          1 :   initECVs();</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          1 :   calculateECVs(&amp;all_obs_cvs[index_j]);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          3 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          4 :     ECVs_[j][j+P0_contribution_]=std::min(barrier_*beta0_,ECVs_[j][j+P0_contribution_]);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          1 : }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          1 : void ECVcustom::initECVs_restart(const std::vector&lt;std::string&gt;&amp; lambdas)</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : {</a>
+<a name="223"><span class="lineNum">     223 </span>            :   std::size_t pos=0;</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          2 :   for(unsigned j=0; j&lt;getNumberOfArguments()-1; j++)</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          1 :     pos=lambdas[0].find(&quot;_&quot;,pos+1); //checking only lambdas[0] is hopefully enough</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          1 :   plumed_massert(pos&lt;lambdas[0].length(),&quot;this should not happen, fewer '_' than expected in &quot;+getName());</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          1 :   pos=lambdas[0].find(&quot;_&quot;,pos+1);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          1 :   plumed_massert(pos&gt;lambdas[0].length(),&quot;this should not happen, more '_' than expected in &quot;+getName());</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          1 :   std::vector&lt;std::string&gt; myLambdas=getLambdas();</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          1 :   plumed_massert(myLambdas.size()==lambdas.size(),&quot;RESTART - mismatch in number of &quot;+getName());</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          1 :   plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),&quot;RESTART - mismatch in lambda values of &quot;+getName());</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          1 :   initECVs();</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          1 : }</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVlinear.cpp.func-sort-c.html b/coverage/opes/ECVlinear.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e96ba57e66
--- /dev/null
+++ b/coverage/opes/ECVlinear.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVlinear.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVlinear.cpp<span style="font-size: 80%;"> (<a href="ECVlinear.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ECVlinear.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#109">_ZN4PLMD4opes9ECVlinearC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#249">_ZN4PLMD4opes9ECVlinear16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#231">_ZN4PLMD4opes9ECVlinear15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#93">_ZN4PLMD4opes12_GLOBAL__N_121ECVlinearRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#194">_ZN4PLMD4opes9ECVlinear13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#201">_ZN4PLMD4opes9ECVlinear16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#221">_ZN4PLMD4opes9ECVlinear8initECVsEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#109">_ZN4PLMD4opes9ECVlinearC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#208">_ZNK4PLMD4opes9ECVlinear10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#95">_ZN4PLMD4opes9ECVlinear16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#187">_ZN4PLMD4opes9ECVlinear13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">182</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#93">_ZN4PLMD4opes12_GLOBAL__N_121ECVlinearRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#93">_ZN4PLMD4opes12_GLOBAL__N_121ECVlinearRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVlinear.cpp.func.html b/coverage/opes/ECVlinear.cpp.func.html
new file mode 100644
index 0000000000..b84da6a072
--- /dev/null
+++ b/coverage/opes/ECVlinear.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVlinear.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVlinear.cpp<span style="font-size: 80%;"> (<a href="ECVlinear.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ECVlinear.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#93">_ZN4PLMD4opes12_GLOBAL__N_121ECVlinearRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#93">_ZN4PLMD4opes12_GLOBAL__N_121ECVlinearRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#93">_ZN4PLMD4opes12_GLOBAL__N_121ECVlinearRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#187">_ZN4PLMD4opes9ECVlinear13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">182</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#194">_ZN4PLMD4opes9ECVlinear13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#231">_ZN4PLMD4opes9ECVlinear15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#201">_ZN4PLMD4opes9ECVlinear16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#249">_ZN4PLMD4opes9ECVlinear16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#95">_ZN4PLMD4opes9ECVlinear16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#221">_ZN4PLMD4opes9ECVlinear8initECVsEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#109">_ZN4PLMD4opes9ECVlinearC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#109">_ZN4PLMD4opes9ECVlinearC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVlinear.cpp.gcov.html#208">_ZNK4PLMD4opes9ECVlinear10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVlinear.cpp.gcov.html b/coverage/opes/ECVlinear.cpp.gcov.html
new file mode 100644
index 0000000000..8d44c8fd59
--- /dev/null
+++ b/coverage/opes/ECVlinear.cpp.gcov.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVlinear.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVlinear.cpp<span style="font-size: 80%;"> (source / <a href="ECVlinear.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryHi">95.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : </a>
+<a name="22"><span class="lineNum">      22 </span>            : namespace PLMD {</a>
+<a name="23"><span class="lineNum">      23 </span>            : namespace opes {</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC OPES_EXPANSION_CV ECV_LINEAR</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Linear expansion, according to a parameter lambda.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : This can be used e.g. for thermodynamic integration, or for multibaric simulations, in which case lambda=pressure.</a>
+<a name="30"><span class="lineNum">      30 </span>            : It can also be used for multithermal simulations, but for simplicity it is more convenient to use \ref ECV_MULTITHERMAL.</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : The difference in Hamiltonian \f$\Delta U\f$ is expected as ARG.</a>
+<a name="33"><span class="lineNum">      33 </span>            : \f[</a>
+<a name="34"><span class="lineNum">      34 </span>            :   \Delta u_\lambda=\beta \lambda \Delta U\, .</a>
+<a name="35"><span class="lineNum">      35 </span>            : \f]</a>
+<a name="36"><span class="lineNum">      36 </span>            : Use the DIMENSIONLESS flag to avoid multiplying for the inverse temperature \f$\beta\f$.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : By defauly the needed steps in lambda are automatically guessed from few initial unbiased MD steps, as descibed in \cite Invernizzi2020unified.</a>
+<a name="39"><span class="lineNum">      39 </span>            : Otherwise one can set this number with LAMBDA_STEPS.</a>
+<a name="40"><span class="lineNum">      40 </span>            : In both cases the steps will be uniformly distriuted.</a>
+<a name="41"><span class="lineNum">      41 </span>            : Finally, one can use instead the keyword LAMBDA_SET_ALL and explicitly provide each lambda value.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \par Examples</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Typical multibaric simulation:</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \plumedfile</a>
+<a name="48"><span class="lineNum">      48 </span>            : vol: VOLUME</a>
+<a name="49"><span class="lineNum">      49 </span>            : ecv: ECV_LINEAR ...</a>
+<a name="50"><span class="lineNum">      50 </span>            :   ARG=vol</a>
+<a name="51"><span class="lineNum">      51 </span>            :   TEMP=300</a>
+<a name="52"><span class="lineNum">      52 </span>            :   LAMBDA=0.06022140857*2000 #2 kbar</a>
+<a name="53"><span class="lineNum">      53 </span>            :   LAMBDA_MIN=0.06022140857  #1 bar</a>
+<a name="54"><span class="lineNum">      54 </span>            :   LAMBDA_MAX=0.06022140857*4000 #4 kbar</a>
+<a name="55"><span class="lineNum">      55 </span>            : ...</a>
+<a name="56"><span class="lineNum">      56 </span>            : opes: OPES_EXPANDED ARG=ecv.vol PACE=500</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : Typical thermodynamic integration:</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : DeltaU: EXTRACV NAME=energy_difference</a>
+<a name="63"><span class="lineNum">      63 </span>            : ecv: ECV_LINEAR ARG=DeltaU TEMP=300</a>
+<a name="64"><span class="lineNum">      64 </span>            : opes: OPES_EXPANDED ARG=ecv.* PACE=100</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endplumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : Notice that by defauly LAMBDA=0, LAMBDA_MIN=0 and LAMBDA_MAX=1, which is the typical case for thermodynamic integration.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : */</a>
+<a name="70"><span class="lineNum">      70 </span>            : //+ENDPLUMEDOC</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : class ECVlinear :</a>
+<a name="73"><span class="lineNum">      73 </span>            :   public ExpansionCVs</a>
+<a name="74"><span class="lineNum">      74 </span>            : {</a>
+<a name="75"><span class="lineNum">      75 </span>            : private:</a>
+<a name="76"><span class="lineNum">      76 </span>            :   bool todoAutomatic_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool geom_spacing_;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   double beta0_;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   double lambda0_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;double&gt; ECVs_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;double&gt; derECVs_; //beta0*(lambda_k-lambda0)</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void initECVs();</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   explicit ECVlinear(const ActionOptions&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void calculateECVs(const double *) override;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   const double * getPntrToECVs(unsigned) override;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   const double * getPntrToDerECVs(unsigned) override;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;std::string&gt; getLambdas() const override;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) override;</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(ECVlinear,&quot;ECV_LINEAR&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 : void ECVlinear::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : {</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 :   ExpansionCVs::registerKeywords(keys);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          6 :   keys.remove(&quot;ARG&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;the label of the Hamiltonian difference. \\f$\\Delta U\\f$&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;LAMBDA&quot;,&quot;0&quot;,&quot;the lambda at which the underlying simulation runs&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;LAMBDA_MIN&quot;,&quot;( default=0 ) the minimum of the lambda range&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;LAMBDA_MAX&quot;,&quot;( default=1 ) the maximum of the lambda range&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;LAMBDA_STEPS&quot;,&quot;uniformly place the lambda values, for a total of LAMBDA_STEPS&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;LAMBDA_SET_ALL&quot;,&quot;manually set all the lamdbas&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         12 :   keys.addFlag(&quot;DIMENSIONLESS&quot;,false,&quot;ARG is considered dimensionless rather than an energy, thus is not multiplied by \\f$\\beta\\f$&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   keys.addFlag(&quot;GEOM_SPACING&quot;,false,&quot;use geometrical spacing in lambda instead of linear spacing&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          6 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          4 : ECVlinear::ECVlinear(const ActionOptions&amp;ao)</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   : Action(ao)</a>
+<a name="113"><span class="lineNum">     113 </span>            :   , ExpansionCVs(ao)</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          4 :   , todoAutomatic_(false)</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          4 :   , beta0_(1./kbt_)</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          4 :   plumed_massert(getNumberOfArguments()==1,&quot;only DeltaU should be given as ARG&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : //set beta0_</a>
+<a name="120"><span class="lineNum">     120 </span>            :   bool dimensionless;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          4 :   parseFlag(&quot;DIMENSIONLESS&quot;,dimensionless);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          4 :   if(dimensionless)</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :     beta0_=1;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : //parse lambda info</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          4 :   parse(&quot;LAMBDA&quot;,lambda0_);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   const double myNone=std::numeric_limits&lt;double&gt;::lowest(); //quiet_NaN is not supported by some intel compiler</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          4 :   double lambda_min=myNone;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          4 :   double lambda_max=myNone;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          4 :   parse(&quot;LAMBDA_MIN&quot;,lambda_min);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 :   parse(&quot;LAMBDA_MAX&quot;,lambda_max);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          4 :   unsigned lambda_steps=0;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   parse(&quot;LAMBDA_STEPS&quot;,lambda_steps);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::vector&lt;double&gt; lambdas;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   parseVector(&quot;LAMBDA_SET_ALL&quot;,lambdas);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 :   parseFlag(&quot;GEOM_SPACING&quot;,geom_spacing_);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : //set the diff vector using lambdas</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :   if(lambdas.size()&gt;0)</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          1 :     plumed_massert(lambda_steps==0,&quot;cannot set both LAMBDA_STEPS and LAMBDA_SET_ALL&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          1 :     plumed_massert(lambda_min==myNone &amp;&amp; lambda_max==myNone,&quot;cannot set both LAMBDA_SET_ALL and LAMBDA_MIN/MAX&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          1 :     plumed_massert(lambdas.size()&gt;=2,&quot;set at least 2 lambdas with LAMBDA_SET_ALL&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :     for(unsigned k=0; k&lt;lambdas.size()-1; k++)</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          3 :       plumed_massert(lambdas[k]&lt;=lambdas[k+1],&quot;LAMBDA_SET_ALL must be properly ordered&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          1 :     lambda_min=lambdas[0];</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          1 :     lambda_max=lambdas[lambdas.size()-1];</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          1 :     derECVs_.resize(lambdas.size());</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          5 :     for(unsigned k=0; k&lt;derECVs_.size(); k++)</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          4 :       derECVs_[k]=beta0_*(lambdas[k]-lambda0_);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span>            :   else</a>
+<a name="155"><span class="lineNum">     155 </span>            :   { //get LAMBDA_MIN and LAMBDA_MAX</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          3 :     if(lambda_min==myNone)</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     {</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :       lambda_min=0;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :       log.printf(&quot;  no LAMBDA_MIN provided, using LAMBDA_MIN = %g\n&quot;,lambda_min);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          3 :     if(lambda_max==myNone)</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     {</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          1 :       lambda_max=1;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :       log.printf(&quot;  no LAMBDA_MAX provided, using LAMBDA_MAX = %g\n&quot;,lambda_max);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     }</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          3 :     plumed_massert(lambda_max&gt;=lambda_min,&quot;LAMBDA_MAX should be bigger than LAMBDA_MIN&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          3 :     derECVs_.resize(2);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          3 :     derECVs_[0]=beta0_*(lambda_min-lambda0_);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          3 :     derECVs_[1]=beta0_*(lambda_max-lambda0_);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          3 :     if(lambda_min==lambda_max &amp;&amp; lambda_steps==0)</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :       lambda_steps=1;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          3 :     if(lambda_steps&gt;0)</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :       derECVs_=getSteps(derECVs_[0],derECVs_[1],lambda_steps,&quot;LAMBDA&quot;,geom_spacing_,beta0_*lambda0_);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     else</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          2 :       todoAutomatic_=true;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          4 :   if(lambda0_&lt;lambda_min || lambda0_&gt;lambda_max)</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          1 :     log.printf(&quot; +++ WARNING +++ running at LAMBDA=%g which is outside the chosen lambda range\n&quot;,lambda0_);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : //print some info</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :   log.printf(&quot;  running at LAMBDA=%g\n&quot;,lambda0_);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :   log.printf(&quot;  targeting a lambda range from LAMBDA_MIN=%g to LAMBDA_MAX=%g\n&quot;,lambda_min,lambda_max);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          4 :   if(dimensionless)</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :     log.printf(&quot; -- DIMENSIONLESS: the ARG is not multiplied by beta\n&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 :   if(geom_spacing_)</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          1 :     log.printf(&quot; -- GEOM_SPACING: lambdas will be geometrically spaced\n&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 : }</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        182 : void ECVlinear::calculateECVs(const double * DeltaU)</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1587 :   for(unsigned k=0; k&lt;derECVs_.size(); k++)</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1405 :     ECVs_[k]=derECVs_[k]*DeltaU[0];</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : // derivatives never change: derECVs_k=beta0*(lambda_k-lambda0)</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        182 : }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          4 : const double * ECVlinear::getPntrToECVs(unsigned j)</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          4 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          4 :   plumed_massert(j==0,getName()+&quot; has only one CV, the DeltaU&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          4 :   return &amp;ECVs_[0];</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          4 : const double * ECVlinear::getPntrToDerECVs(unsigned j)</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : {</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          4 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          4 :   plumed_massert(j==0,getName()+&quot; has only one CV, the DeltaU&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          4 :   return &amp;derECVs_[0];</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          4 : std::vector&lt;std::string&gt; ECVlinear::getLambdas() const</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          4 :   plumed_massert(!todoAutomatic_,&quot;cannot access lambdas before initializing them&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          4 :   std::vector&lt;std::string&gt; lambdas(derECVs_.size());</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         35 :   for(unsigned k=0; k&lt;derECVs_.size(); k++)</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   {</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         31 :     std::ostringstream subs;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         31 :     subs&lt;&lt;derECVs_[k]/beta0_+lambda0_; //lambda_k</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         31 :     lambdas[k]=subs.str();</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         31 :   }</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          4 :   return lambdas;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          4 : void ECVlinear::initECVs()</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :   plumed_massert(!isReady_,&quot;initialization should not be called twice&quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          4 :   plumed_massert(!todoAutomatic_,&quot;this should not happen&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          4 :   totNumECVs_=derECVs_.size();</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          4 :   ECVs_.resize(derECVs_.size());</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          4 :   isReady_=true;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          4 :   log.printf(&quot;  *%4lu lambdas for %s\n&quot;,derECVs_.size(),getName().c_str());</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          4 : }</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          3 : void ECVlinear::initECVs_observ(const std::vector&lt;double&gt;&amp; all_obs_cvs,const unsigned ncv,const unsigned index_j)</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : {</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          3 :   if(todoAutomatic_) //estimate the steps in lambda from observations</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :   {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          1 :     plumed_massert(all_obs_cvs.size()%ncv==0 &amp;&amp; index_j&lt;ncv,&quot;initECVs_observ parameters are inconsistent&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          1 :     std::vector&lt;double&gt; obs_cv(all_obs_cvs.size()/ncv); //copy only useful observation (would be better not to copy...)</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         11 :     for(unsigned t=0; t&lt;obs_cv.size(); t++)</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         10 :       obs_cv[t]=all_obs_cvs[t*ncv+index_j];</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          1 :     const unsigned lambda_steps=estimateNumSteps(derECVs_[0],derECVs_[1],obs_cv,&quot;LAMBDA&quot;);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          1 :     if(beta0_!=1)</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :       log.printf(&quot;    (spacing is in beta0 units)\n&quot;);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :     derECVs_=getSteps(derECVs_[0],derECVs_[1],lambda_steps,&quot;LAMBDA&quot;,geom_spacing_,beta0_*lambda0_);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          1 :     todoAutomatic_=false;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          3 :   initECVs();</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          3 :   calculateECVs(&amp;all_obs_cvs[index_j]);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          3 : }</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          1 : void ECVlinear::initECVs_restart(const std::vector&lt;std::string&gt;&amp; lambdas)</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : {</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          1 :   std::size_t pos=lambdas[0].find(&quot;_&quot;);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          1 :   plumed_massert(pos==std::string::npos,&quot;this should not happen, only one CV is used in &quot;+getName());</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          1 :   if(todoAutomatic_)</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   {</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          2 :     derECVs_=getSteps(derECVs_[0],derECVs_[1],lambdas.size(),&quot;LAMBDA&quot;,geom_spacing_,beta0_*lambda0_);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          1 :     todoAutomatic_=false;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 :   std::vector&lt;std::string&gt; myLambdas=getLambdas();</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          1 :   plumed_massert(myLambdas.size()==lambdas.size(),&quot;RESTART - mismatch in number of &quot;+getName());</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          1 :   plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),&quot;RESTART - mismatch in lambda values of &quot;+getName());</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          1 :   initECVs();</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          1 : }</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+<a name="268"><span class="lineNum">     268 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVmultiThermal.cpp.func-sort-c.html b/coverage/opes/ECVmultiThermal.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4ca92e0a20
--- /dev/null
+++ b/coverage/opes/ECVmultiThermal.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVmultiThermal.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVmultiThermal.cpp<span style="font-size: 80%;"> (<a href="ECVmultiThermal.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">108</td>
+            <td class="headerCovTableEntry">113</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ECVmultiThermal.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#115">_ZN4PLMD4opes15ECVmultiThermalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#251">_ZN4PLMD4opes15ECVmultiThermal16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#234">_ZN4PLMD4opes15ECVmultiThermal15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#101">_ZN4PLMD4opes12_GLOBAL__N_128ECVmultiThermalRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#196">_ZN4PLMD4opes15ECVmultiThermal13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#203">_ZN4PLMD4opes15ECVmultiThermal16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
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+              <td class="coverFnHi">11</td>
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+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#210">_ZNK4PLMD4opes15ECVmultiThermal10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#103">_ZN4PLMD4opes15ECVmultiThermal16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#189">_ZN4PLMD4opes15ECVmultiThermal13calculateECVsEPKd</a></td>
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+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#101">_ZN4PLMD4opes12_GLOBAL__N_128ECVmultiThermalRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#101">_ZN4PLMD4opes12_GLOBAL__N_128ECVmultiThermalRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/opes/ECVmultiThermal.cpp.func.html b/coverage/opes/ECVmultiThermal.cpp.func.html
new file mode 100644
index 0000000000..ba3555e13f
--- /dev/null
+++ b/coverage/opes/ECVmultiThermal.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVmultiThermal.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVmultiThermal.cpp<span style="font-size: 80%;"> (<a href="ECVmultiThermal.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">108</td>
+            <td class="headerCovTableEntry">113</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ECVmultiThermal.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#101">_ZN4PLMD4opes12_GLOBAL__N_128ECVmultiThermalRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#101">_ZN4PLMD4opes12_GLOBAL__N_128ECVmultiThermalRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#101">_ZN4PLMD4opes12_GLOBAL__N_128ECVmultiThermalRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#189">_ZN4PLMD4opes15ECVmultiThermal13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">586</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#196">_ZN4PLMD4opes15ECVmultiThermal13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#234">_ZN4PLMD4opes15ECVmultiThermal15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#203">_ZN4PLMD4opes15ECVmultiThermal16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#251">_ZN4PLMD4opes15ECVmultiThermal16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#103">_ZN4PLMD4opes15ECVmultiThermal16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#224">_ZN4PLMD4opes15ECVmultiThermal8initECVsEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#115">_ZN4PLMD4opes15ECVmultiThermalC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#115">_ZN4PLMD4opes15ECVmultiThermalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermal.cpp.gcov.html#210">_ZNK4PLMD4opes15ECVmultiThermal10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVmultiThermal.cpp.gcov.html b/coverage/opes/ECVmultiThermal.cpp.gcov.html
new file mode 100644
index 0000000000..f3f632f685
--- /dev/null
+++ b/coverage/opes/ECVmultiThermal.cpp.gcov.html
@@ -0,0 +1,346 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVmultiThermal.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVmultiThermal.cpp<span style="font-size: 80%;"> (source / <a href="ECVmultiThermal.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">108</td>
+            <td class="headerCovTableEntry">113</td>
+            <td class="headerCovTableEntryHi">95.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace opes {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC OPES_EXPANSION_CV ECV_MULTITHERMAL</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Expand a simulation to sample multiple temperatures simultaneously.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : The internal energy \f$U\f$ of of the system should be used as ARG.</a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            :   \Delta u_{\beta'}=(\beta'-\beta) U\, ,</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : where \f$\beta'\f$ are the temperatures to be sampled and \f$\beta\f$ is the temperature at which the simulation is conducted.</a>
+<a name="36"><span class="lineNum">      36 </span>            : In case of fixed volume, the internal energy is simply the potential energy given by the \ref ENERGY colvar\f$U=E\f$, and you will run a multicanonical simulation.</a>
+<a name="37"><span class="lineNum">      37 </span>            : If instead the simulation is at fixed pressure \f$p\f$, the contribution of the volume must be added \f$U=E+pV\f$ (see example below).</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : By defauly the needed steps in temperatures are automatically guessed from few initial unbiased MD steps, as descibed in \cite Invernizzi2020unified.</a>
+<a name="40"><span class="lineNum">      40 </span>            : Otherwise you can manually set this number with TEMP_STEPS.</a>
+<a name="41"><span class="lineNum">      41 </span>            : In both cases the steps will be geometrically spaced in temperature.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Use instead the keyword NO_GEOM_SPACING for a linear spacing in the inverse temperature (beta), that typically increases the focus on lower temperatures.</a>
+<a name="43"><span class="lineNum">      43 </span>            : Finally, you can use instead the keyword TEMP_SET_ALL and explicitly provide each temperature.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : You can reweight the resulting simulation at any temperature in the chosen range, using e.g. \ref REWEIGHT_TEMP_PRESS.</a>
+<a name="46"><span class="lineNum">      46 </span>            : A similar target distribution can be sampled using \ref TD_MULTICANONICAL.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : Fixed volume, multicanonical simulation:</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : ene: ENERGY</a>
+<a name="55"><span class="lineNum">      55 </span>            : ecv: ECV_MULTITHERMAL ARG=ene TEMP=300 TEMP_MIN=300 TEMP_MAX=800</a>
+<a name="56"><span class="lineNum">      56 </span>            : opes: OPES_EXPANDED ARG=ecv.ene PACE=500</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : which, if your MD code passes the temperature to PLUMED, is equivalent to:</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : ene: ENERGY</a>
+<a name="63"><span class="lineNum">      63 </span>            : ecv: ECV_MULTITHERMAL ARG=ene TEMP_MAX=800</a>
+<a name="64"><span class="lineNum">      64 </span>            : opes: OPES_EXPANDED ARG=ecv.ene PACE=500</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endplumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : If instead the pressure is fixed and the volume changes, you shuld calculate the internal energy first, \f$U=E+pV\f$</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : ene: ENERGY</a>
+<a name="71"><span class="lineNum">      71 </span>            : vol: VOLUME</a>
+<a name="72"><span class="lineNum">      72 </span>            : intEne: CUSTOM PERIODIC=NO ARG=ene,vol FUNC=x+0.06022140857*y</a>
+<a name="73"><span class="lineNum">      73 </span>            : ecv: ECV_MULTITHERMAL ARG=intEne TEMP_MAX=800</a>
+<a name="74"><span class="lineNum">      74 </span>            : opes: OPES_EXPANDED ARG=ecv.intEne PACE=500</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : Notice that \f$p=0.06022140857\f$ corresponds to 1 bar when using the default PLUMED units.</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : class ECVmultiThermal :</a>
+<a name="83"><span class="lineNum">      83 </span>            :   public ExpansionCVs</a>
+<a name="84"><span class="lineNum">      84 </span>            : {</a>
+<a name="85"><span class="lineNum">      85 </span>            : private:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   bool todoAutomatic_;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   bool geom_spacing_;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;double&gt; ECVs_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;double&gt; derECVs_; //(beta_k-beta0) or (temp0/temp_k-1)/kbt</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void initECVs();</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit ECVmultiThermal(const ActionOptions&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void calculateECVs(const double *) override;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   const double * getPntrToECVs(unsigned) override;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   const double * getPntrToDerECVs(unsigned) override;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt;std::string&gt; getLambdas() const override;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) override;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) override;</a>
+<a name="101"><span class="lineNum">     101 </span>            : };</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      12526 : PLUMED_REGISTER_ACTION(ECVmultiThermal,&quot;ECV_MULTITHERMAL&quot;)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         13 : void ECVmultiThermal::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         13 :   ExpansionCVs::registerKeywords(keys);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         13 :   keys.remove(&quot;ARG&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         26 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;the label of the internal energy of the system. If volume is fixed it is calculated by the \\ref ENERGY colvar&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;TEMP_MIN&quot;,&quot;the minimum of the temperature range&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;TEMP_MAX&quot;,&quot;the maximum of the temperature range&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;TEMP_STEPS&quot;,&quot;the number of steps in temperature&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         26 :   keys.add(&quot;optional&quot;,&quot;TEMP_SET_ALL&quot;,&quot;manually set all the temperatures&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         26 :   keys.addFlag(&quot;NO_GEOM_SPACING&quot;,false,&quot;do not use geometrical spacing in temperature, but instead linear spacing in inverse temperature&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         13 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         11 : ECVmultiThermal::ECVmultiThermal(const ActionOptions&amp;ao)</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   : Action(ao)</a>
+<a name="119"><span class="lineNum">     119 </span>            :   , ExpansionCVs(ao)</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         11 :   , todoAutomatic_(false)</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : {</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         11 :   plumed_massert(getNumberOfArguments()==1,&quot;only the internal energy should be given as ARG&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : //set temp0</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         11 :   const double temp0=kbt_/plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : //parse temp range</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         11 :   double temp_min=-1;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         11 :   double temp_max=-1;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         11 :   parse(&quot;TEMP_MIN&quot;,temp_min);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         11 :   parse(&quot;TEMP_MAX&quot;,temp_max);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         11 :   unsigned temp_steps=0;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         22 :   parse(&quot;TEMP_STEPS&quot;,temp_steps);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::vector&lt;double&gt; temps;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         11 :   parseVector(&quot;TEMP_SET_ALL&quot;,temps);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         11 :   parseFlag(&quot;NO_GEOM_SPACING&quot;,geom_spacing_);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         11 :   geom_spacing_=!geom_spacing_;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         11 :   checkRead();</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : //set the intermediate temperatures</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         11 :   if(temps.size()&gt;0)</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 :     plumed_massert(temp_steps==0,&quot;cannot set both TEMP_STEPS and TEMP_SET_ALL&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          2 :     plumed_massert(temp_min==-1 &amp;&amp; temp_max==-1,&quot;cannot set both TEMP_SET_ALL and TEMP_MIN/MAX&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 :     plumed_massert(temps.size()&gt;=2,&quot;set at least 2 temperatures&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :     temp_min=temps[0];</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :     temp_max=temps[temps.size()-1];</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :     derECVs_.resize(temps.size());</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         10 :     for(unsigned k=0; k&lt;derECVs_.size(); k++)</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     {</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          8 :       derECVs_[k]=(temp0/temps[k]-1.)/kbt_;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          8 :       if(k&lt;derECVs_.size()-1)</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          6 :         plumed_massert(temps[k]&lt;=temps[k+1],&quot;TEMP_SET_ALL must be properly ordered&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            :   else</a>
+<a name="158"><span class="lineNum">     158 </span>            :   { //get TEMP_MIN and TEMP_MAX</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          9 :     plumed_massert(temp_min!=-1 || temp_max!=-1,&quot;TEMP_MIN, TEMP_MAX or both, should be set&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          9 :     if(temp_min==-1)</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :     {</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          2 :       temp_min=temp0;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :       log.printf(&quot;  no TEMP_MIN provided, using TEMP_MIN=TEMP\n&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          9 :     if(temp_max==-1)</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       temp_max=temp0;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :       log.printf(&quot;  no TEMP_MAX provided, using TEMP_MAX=TEMP\n&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          9 :     plumed_massert(temp_max&gt;=temp_min,&quot;TEMP_MAX should be bigger than TEMP_MIN&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          9 :     derECVs_.resize(2);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          9 :     derECVs_[0]=(temp0/temp_min-1.)/kbt_;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 :     derECVs_[1]=(temp0/temp_max-1.)/kbt_;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          9 :     if(temp_min==temp_max &amp;&amp; temp_steps==0)</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :       temp_steps=1;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          9 :     if(temp_steps&gt;0)</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         14 :       derECVs_=getSteps(derECVs_[0],derECVs_[1],temp_steps,&quot;TEMP&quot;,geom_spacing_,1./kbt_);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     else</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :       todoAutomatic_=true;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   }</a>
+<a name="181"><span class="lineNum">     181 </span>            :   const double tol=1e-3; //if temp is taken from MD engine it might be numerically slightly different</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         11 :   if(temp0&lt;(1-tol)*temp_min || temp0&gt;(1+tol)*temp_max)</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ running at TEMP=%g which is outside the chosen temperature range\n&quot;,temp0);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : //print some info</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         11 :   log.printf(&quot;  targeting a temperature range from TEMP_MIN=%g to TEMP_MAX=%g\n&quot;,temp_min,temp_max);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         11 :   if(!geom_spacing_)</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          1 :     log.printf(&quot; -- NO_GEOM_SPACING: inverse temperatures will be linearly spaced\n&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         11 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        586 : void ECVmultiThermal::calculateECVs(const double * ene)</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : {</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       3618 :   for(unsigned k=0; k&lt;derECVs_.size(); k++)</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       3032 :     ECVs_[k]=derECVs_[k]*ene[0];</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : // derivatives never change: derECVs_k=(beta_k-beta0)</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        586 : }</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         11 : const double * ECVmultiThermal::getPntrToECVs(unsigned j)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         11 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         11 :   plumed_massert(j==0,getName()+&quot; has only one CV, the ENERGY&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         11 :   return &amp;ECVs_[0];</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         11 : const double * ECVmultiThermal::getPntrToDerECVs(unsigned j)</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : {</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         11 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         11 :   plumed_massert(j==0,getName()+&quot; has only one CV, the ENERGY&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         11 :   return &amp;derECVs_[0];</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         11 : std::vector&lt;std::string&gt; ECVmultiThermal::getLambdas() const</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : {</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         11 :   plumed_massert(!todoAutomatic_,&quot;cannot access lambdas before initializing them&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         11 :   const double temp0=kbt_/plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         11 :   std::vector&lt;std::string&gt; lambdas(derECVs_.size());</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         70 :   for(unsigned k=0; k&lt;derECVs_.size(); k++)</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         59 :     std::ostringstream subs;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         59 :     subs&lt;&lt;temp0/(derECVs_[k]*kbt_+1); //temp_k</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         59 :     lambdas[k]=subs.str();</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         59 :   }</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         11 :   return lambdas;</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         11 : void ECVmultiThermal::initECVs()</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : {</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         11 :   plumed_massert(!isReady_,&quot;initialization should not be called twice&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         11 :   plumed_massert(!todoAutomatic_,&quot;this should not happen&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         11 :   totNumECVs_=derECVs_.size();</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         11 :   ECVs_.resize(derECVs_.size());</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         11 :   isReady_=true;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         11 :   log.printf(&quot;  *%4lu temperatures for %s\n&quot;,derECVs_.size(),getName().c_str());</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         11 : }</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          8 : void ECVmultiThermal::initECVs_observ(const std::vector&lt;double&gt;&amp; all_obs_cvs,const unsigned ncv,const unsigned index_j)</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : {</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          8 :   if(todoAutomatic_) //estimate the steps in beta from observations</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   {</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          1 :     plumed_massert(all_obs_cvs.size()%ncv==0 &amp;&amp; index_j&lt;ncv,&quot;initECVs_observ parameters are inconsistent&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          1 :     std::vector&lt;double&gt; obs_ene(all_obs_cvs.size()/ncv); //copy only useful observation (would be better not to copy...)</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         11 :     for(unsigned t=0; t&lt;obs_ene.size(); t++)</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         10 :       obs_ene[t]=all_obs_cvs[t*ncv+index_j];</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          1 :     const unsigned temp_steps=estimateNumSteps(derECVs_[0],derECVs_[1],obs_ene,&quot;TEMP&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          1 :     log.printf(&quot;    (spacing is in beta, not in temperature)\n&quot;);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          2 :     derECVs_=getSteps(derECVs_[0],derECVs_[1],temp_steps,&quot;TEMP&quot;,geom_spacing_,1./kbt_);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          1 :     todoAutomatic_=false;</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          8 :   initECVs();</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          8 :   calculateECVs(&amp;all_obs_cvs[index_j]);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          8 : }</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          3 : void ECVmultiThermal::initECVs_restart(const std::vector&lt;std::string&gt;&amp; lambdas)</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : {</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          3 :   std::size_t pos=lambdas[0].find(&quot;_&quot;);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          3 :   plumed_massert(pos==std::string::npos,&quot;this should not happen, only one CV is used in &quot;+getName());</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          3 :   if(todoAutomatic_)</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   {</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          2 :     derECVs_=getSteps(derECVs_[0],derECVs_[1],lambdas.size(),&quot;TEMP&quot;,geom_spacing_,1./kbt_);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 :     todoAutomatic_=false;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          3 :   std::vector&lt;std::string&gt; myLambdas=getLambdas();</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          3 :   plumed_massert(myLambdas.size()==lambdas.size(),&quot;RESTART - mismatch in number of &quot;+getName());</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          3 :   plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),&quot;RESTART - mismatch in lambda values of &quot;+getName());</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          3 :   initECVs();</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          3 : }</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+<a name="270"><span class="lineNum">     270 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVmultiThermalBaric.cpp.func-sort-c.html b/coverage/opes/ECVmultiThermalBaric.cpp.func-sort-c.html
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+++ b/coverage/opes/ECVmultiThermalBaric.cpp.func-sort-c.html
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVmultiThermalBaric.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVmultiThermalBaric.cpp<span style="font-size: 80%;"> (<a href="ECVmultiThermalBaric.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">264</td>
+            <td class="headerCovTableEntry">273</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ECVmultiThermalBaric.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#132">_ZN4PLMD4opes20ECVmultiThermalBaricC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#489">_ZN4PLMD4opes20ECVmultiThermalBaric16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#461">_ZN4PLMD4opes20ECVmultiThermalBaric15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#108">_ZN4PLMD4opes12_GLOBAL__N_133ECVmultiThermalBaricRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#420">_ZN4PLMD4opes20ECVmultiThermalBaric8initECVsEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#132">_ZN4PLMD4opes20ECVmultiThermalBaricC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#364">_ZNK4PLMD4opes20ECVmultiThermalBaric10getIndex_kEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#110">_ZN4PLMD4opes20ECVmultiThermalBaric16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#344">_ZN4PLMD4opes20ECVmultiThermalBaric13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#354">_ZN4PLMD4opes20ECVmultiThermalBaric16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#395">_ZNK4PLMD4opes20ECVmultiThermalBaric10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#496">_ZZN4PLMD4opes20ECVmultiThermalBaric16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEENKUljE_clEj</a></td>
+              <td class="coverFnHi">230</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#335">_ZN4PLMD4opes20ECVmultiThermalBaric13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">463</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#108">_ZN4PLMD4opes12_GLOBAL__N_133ECVmultiThermalBaricRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#108">_ZN4PLMD4opes12_GLOBAL__N_133ECVmultiThermalBaricRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVmultiThermalBaric.cpp.func.html b/coverage/opes/ECVmultiThermalBaric.cpp.func.html
new file mode 100644
index 0000000000..534e506483
--- /dev/null
+++ b/coverage/opes/ECVmultiThermalBaric.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVmultiThermalBaric.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVmultiThermalBaric.cpp<span style="font-size: 80%;"> (<a href="ECVmultiThermalBaric.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">264</td>
+            <td class="headerCovTableEntry">273</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ECVmultiThermalBaric.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#108">_ZN4PLMD4opes12_GLOBAL__N_133ECVmultiThermalBaricRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#108">_ZN4PLMD4opes12_GLOBAL__N_133ECVmultiThermalBaricRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#108">_ZN4PLMD4opes12_GLOBAL__N_133ECVmultiThermalBaricRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#335">_ZN4PLMD4opes20ECVmultiThermalBaric13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">463</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#344">_ZN4PLMD4opes20ECVmultiThermalBaric13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#461">_ZN4PLMD4opes20ECVmultiThermalBaric15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#354">_ZN4PLMD4opes20ECVmultiThermalBaric16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#489">_ZN4PLMD4opes20ECVmultiThermalBaric16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#110">_ZN4PLMD4opes20ECVmultiThermalBaric16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#420">_ZN4PLMD4opes20ECVmultiThermalBaric8initECVsEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#132">_ZN4PLMD4opes20ECVmultiThermalBaricC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#132">_ZN4PLMD4opes20ECVmultiThermalBaricC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#364">_ZNK4PLMD4opes20ECVmultiThermalBaric10getIndex_kEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#395">_ZNK4PLMD4opes20ECVmultiThermalBaric10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVmultiThermalBaric.cpp.gcov.html#496">_ZZN4PLMD4opes20ECVmultiThermalBaric16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEENKUljE_clEj</a></td>
+              <td class="coverFnHi">230</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVmultiThermalBaric.cpp.gcov.html b/coverage/opes/ECVmultiThermalBaric.cpp.gcov.html
new file mode 100644
index 0000000000..de68a2b4fd
--- /dev/null
+++ b/coverage/opes/ECVmultiThermalBaric.cpp.gcov.html
@@ -0,0 +1,608 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVmultiThermalBaric.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVmultiThermalBaric.cpp<span style="font-size: 80%;"> (source / <a href="ECVmultiThermalBaric.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">264</td>
+            <td class="headerCovTableEntry">273</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace opes {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : //+PLUMEDOC OPES_EXPANSION_CV ECV_MULTITHERMAL_MULTIBARIC</a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : Expand a simulation to sample multiple temperatures and pressures.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : The potential \ref ENERGY, \f$E\f$, and the \ref VOLUME, \f$V\f$, of the system should be used as ARG.</a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            :   \Delta u_{\beta',p'}=(\beta'-\beta) E + (\beta' p' -\beta p) V\, ,</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : where \f$\beta', p'\f$ are the temperatures and pressures to be sampled, while \f$\beta, p\f$ is the temperature and pressure at which the simulation is conducted.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : If instead you wish to sample multiple temperatures and a single pressure, you should use \ref ECV_MULTITHERMAL with as ARG the internal energy \f$U=E+pV\f$.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The TEMP_STEPS and PRESSURE_STEPS are automatically guessed from the initial unbiased steps (see OBSERVATION_STEPS in \ref OPES_EXPANDED), unless explicitly set.</a>
+<a name="40"><span class="lineNum">      40 </span>            : The algorithm for this guess is described in \cite Invernizzi2020unified should provide a rough estimate useful for most applications.</a>
+<a name="41"><span class="lineNum">      41 </span>            : The pressures are uniformely spaced, while the temperatures steps are geometrically spaced.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Use instead the keyword NO_GEOM_SPACING for a linear spacing in inverse temperature (beta).</a>
+<a name="43"><span class="lineNum">      43 </span>            : For more detailed control you can use instead TEMP_SET_ALL and/or PRESSURE_SET_ALL to explicitly set all of them.</a>
+<a name="44"><span class="lineNum">      44 </span>            : The temperatures and pressures are then combined in a 2D grid.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : You can use CUT_CORNER to avoid a high-temperature/low-pressure region.</a>
+<a name="47"><span class="lineNum">      47 </span>            : This can be useful e.g. to increase the temperature for greater ergodicity, while avoiding water to vaporize, as in Ref.\cite Invernizzi2020unified.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : You can reweight the resulting simulation at any temperature and pressure in chosen target, using e.g. \ref REWEIGHT_TEMP_PRESS.</a>
+<a name="50"><span class="lineNum">      50 </span>            : A similar target distribution can be sampled using \ref TD_MULTITHERMAL_MULTIBARIC.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : ene: ENERGY</a>
+<a name="56"><span class="lineNum">      56 </span>            : vol: VOLUME</a>
+<a name="57"><span class="lineNum">      57 </span>            : ecv: ECV_MULTITHERMAL_MULTIBARIC ...</a>
+<a name="58"><span class="lineNum">      58 </span>            :   ARG=ene,vol</a>
+<a name="59"><span class="lineNum">      59 </span>            :   TEMP=500</a>
+<a name="60"><span class="lineNum">      60 </span>            :   TEMP_MIN=270</a>
+<a name="61"><span class="lineNum">      61 </span>            :   TEMP_MAX=800</a>
+<a name="62"><span class="lineNum">      62 </span>            :   PRESSURE=0.06022140857*2000 #2 kbar</a>
+<a name="63"><span class="lineNum">      63 </span>            :   PRESSURE_MIN=0.06022140857  #1 bar</a>
+<a name="64"><span class="lineNum">      64 </span>            :   PRESSURE_MAX=0.06022140857*4000 #4 kbar</a>
+<a name="65"><span class="lineNum">      65 </span>            :   CUT_CORNER=500,0.06022140857,800,0.06022140857*1000</a>
+<a name="66"><span class="lineNum">      66 </span>            : ...</a>
+<a name="67"><span class="lineNum">      67 </span>            : opes: OPES_EXPANDED ARG=ecv.* FILE=DeltaF.data PACE=500 WALKERS_MPI</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : Notice that \f$p=0.06022140857\f$ corresponds to 1 bar only when using the default PLUMED units.</a>
+<a name="71"><span class="lineNum">      71 </span>            : If you modify them via the \ref UNITS command, then the pressure has to be rescaled accordingly.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : */</a>
+<a name="74"><span class="lineNum">      74 </span>            : //+ENDPLUMEDOC</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : class ECVmultiThermalBaric :</a>
+<a name="77"><span class="lineNum">      77 </span>            :   public ExpansionCVs</a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span>            : private:</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool todoAutomatic_beta_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   bool todoAutomatic_pres_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   bool geom_spacing_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   double pres0_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;double&gt; pres_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;double&gt; ECVs_beta_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;double&gt; ECVs_pres_;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   std::vector&lt;double&gt; derECVs_beta_; //(beta_k-beta0) or (temp0/temp_k-1)/kbt</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;double&gt; derECVs_pres_; //(beta_k*pres_kk-beta0*pres0) or (temp0/temp_k*pres_kk-pres0)/kbt</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void initECVs();</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : //CUT_CORNER stuff</a>
+<a name="92"><span class="lineNum">      92 </span>            :   double coeff_;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   double pres_low_;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   double kB_temp_low_;</a>
+<a name="95"><span class="lineNum">      95 </span>            : //SET_ALL_TEMP_PRESSURE stuff</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::vector&lt;std::string&gt; custom_lambdas_;</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : public:</a>
+<a name="99"><span class="lineNum">      99 </span>            :   explicit ECVmultiThermalBaric(const ActionOptions&amp;);</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void calculateECVs(const double *) override;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   const double * getPntrToECVs(unsigned) override;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   const double * getPntrToDerECVs(unsigned) override;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; getIndex_k() const override;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;std::string&gt; getLambdas() const override;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) override;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) override;</a>
+<a name="108"><span class="lineNum">     108 </span>            : };</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(ECVmultiThermalBaric,&quot;ECV_MULTITHERMAL_MULTIBARIC&quot;)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         11 : void ECVmultiThermalBaric::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         11 :   ExpansionCVs::registerKeywords(keys);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         11 :   keys.remove(&quot;ARG&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;the labels of the potential energy and of the volume of the system. You can calculate them with \\ref ENERGY and \\ref VOLUME respectively&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : //temperature</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;TEMP_MIN&quot;,&quot;the minimum of the temperature range&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;TEMP_MAX&quot;,&quot;the maximum of the temperature range&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;TEMP_STEPS&quot;,&quot;the number of steps in temperature&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;TEMP_SET_ALL&quot;,&quot;manually set all the temperatures&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         22 :   keys.addFlag(&quot;NO_GEOM_SPACING&quot;,false,&quot;do not use geometrical spacing in temperature, but instead linear spacing in inverse temperature&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : //pressure</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;PRESSURE&quot;,&quot;pressure. Use the proper units&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;PRESSURE_MIN&quot;,&quot;the minimum of the pressure range&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;PRESSURE_MAX&quot;,&quot;the maximum of the pressure range&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;PRESSURE_STEPS&quot;,&quot;the number of steps in pressure&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;PRESSURE_SET_ALL&quot;,&quot;manually set all the pressures&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : //other</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;SET_ALL_TEMP_PRESSURE&quot;,&quot;manually set all the target temperature_pressure pairs. An underscore separates temperature and pressure, while different points are comma-separated, e.g.: temp1_pres1,temp1_pres2,...&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;CUT_CORNER&quot;,&quot;avoid region of high temperature and low pressure. Exclude all points below a line in the temperature-pressure plane, defined by two points: \\f$T_{\\text{low}},P_{\\text{low}},T_{\\text{high}},P_{\\text{high}}\\f$&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         11 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          9 : ECVmultiThermalBaric::ECVmultiThermalBaric(const ActionOptions&amp;ao)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   : Action(ao)</a>
+<a name="136"><span class="lineNum">     136 </span>            :   , ExpansionCVs(ao)</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          9 :   , todoAutomatic_beta_(false)</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          9 :   , todoAutomatic_pres_(false)</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          9 :   , coeff_(0)</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          9 :   , pres_low_(0)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          9 :   , kB_temp_low_(0)</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          9 :   plumed_massert(getNumberOfArguments()==2,&quot;ENERGY and VOLUME should be given as ARG&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : //set temp0</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          9 :   const double kB=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :   const double temp0=kbt_/kB;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : //parse temp range</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          9 :   double temp_min=-1;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          9 :   double temp_max=-1;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          9 :   parse(&quot;TEMP_MIN&quot;,temp_min);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          9 :   parse(&quot;TEMP_MAX&quot;,temp_max);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          9 :   unsigned temp_steps=0;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         18 :   parse(&quot;TEMP_STEPS&quot;,temp_steps);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   std::vector&lt;double&gt; temps;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          9 :   parseVector(&quot;TEMP_SET_ALL&quot;,temps);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          9 :   parseFlag(&quot;NO_GEOM_SPACING&quot;,geom_spacing_);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          9 :   geom_spacing_=!geom_spacing_;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : //parse pressures</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          9 :   parse(&quot;PRESSURE&quot;,pres0_);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   const double myNone=std::numeric_limits&lt;double&gt;::lowest(); //quiet_NaN is not supported by some intel compiler</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          9 :   double pres_min=myNone; //-1 might be a meaningful pressure</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          9 :   double pres_max=myNone;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          9 :   parse(&quot;PRESSURE_MIN&quot;,pres_min);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          9 :   parse(&quot;PRESSURE_MAX&quot;,pres_max);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          9 :   unsigned pres_steps=0;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          9 :   parse(&quot;PRESSURE_STEPS&quot;,pres_steps);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         18 :   parseVector(&quot;PRESSURE_SET_ALL&quot;,pres_);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : //other</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::vector&lt;double&gt; cut_corner;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          9 :   parseVector(&quot;CUT_CORNER&quot;,cut_corner);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 :   parseVector(&quot;SET_ALL_TEMP_PRESSURE&quot;,custom_lambdas_);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          9 :   if(custom_lambdas_.size()&gt;0)</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   {</a>
+<a name="179"><span class="lineNum">     179 </span>            :     //make sure no incompatible options are used</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :     plumed_massert(temps.size()==0,&quot;cannot set both SET_ALL_TEMP_PRESSURE and TEMP_SET_ALL&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :     plumed_massert(pres_.size()==0,&quot;cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_SET_ALL&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :     plumed_massert(temp_steps==0,&quot;cannot set both SET_ALL_TEMP_PRESSURE and TEMP_STEPS&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :     plumed_massert(pres_steps==0,&quot;cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_STEPS&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :     plumed_massert(temp_min==-1 &amp;&amp; temp_max==-1,&quot;cannot set both SET_ALL_TEMP_PRESSURE and TEMP_MIN/MAX&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          2 :     plumed_massert(pres_min==myNone &amp;&amp; pres_max==myNone,&quot;cannot set both SET_ALL_TEMP_PRESSURE and PRESSURE_MIN/MAX&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          2 :     plumed_massert(cut_corner.size()==0,&quot;cannot set both SET_ALL_TEMP_PRESSURE and CUT_CORNER&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : //setup the target temperature-pressure grid</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :     derECVs_beta_.resize(custom_lambdas_.size());</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :     derECVs_pres_.resize(custom_lambdas_.size());</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          2 :     const std::string error_msg=&quot;SET_ALL_TEMP_PRESSURE: two underscore-separated values are expected for each comma-separated point, cannot understand: &quot;;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         22 :     for(unsigned i=0; i&lt;custom_lambdas_.size(); i++)</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     {</a>
+<a name="193"><span class="lineNum">     193 </span>            :       try</a>
+<a name="194"><span class="lineNum">     194 </span>            :       {</a>
+<a name="195"><span class="lineNum">     195 </span>            :         std::size_t pos1;</a>
+<a name="196"><span class="lineNum">     196 </span>            :         const double temp_i=std::stod(custom_lambdas_[i],&amp;pos1);</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         20 :         plumed_massert(pos1+1&lt;custom_lambdas_[i].size(),error_msg+custom_lambdas_[i]);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         20 :         plumed_massert(custom_lambdas_[i][pos1]=='_',error_msg+custom_lambdas_[i]);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :         std::size_t pos2;</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         20 :         const double pres_i=std::stod(custom_lambdas_[i].substr(pos1+1),&amp;pos2);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         20 :         plumed_massert(pos1+1+pos2==custom_lambdas_[i].size(),error_msg+custom_lambdas_[i]);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         20 :         derECVs_beta_[i]=(temp0/temp_i-1.)/kbt_;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         20 :         derECVs_pres_[i]=(temp0/temp_i*pres_i-pres0_)/kbt_;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :       }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       catch (std::exception &amp;ex)</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :       {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :         plumed_merror(error_msg+custom_lambdas_[i]);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     }</a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span>            :   else</a>
+<a name="213"><span class="lineNum">     213 </span>            :   {</a>
+<a name="214"><span class="lineNum">     214 </span>            :     //set the intermediate temperatures</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          7 :     if(temps.size()&gt;0)</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :     {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          1 :       plumed_massert(temp_steps==0,&quot;cannot set both TEMP_STEPS and TEMP_SET_ALL&quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 :       plumed_massert(temp_min==-1 &amp;&amp; temp_max==-1,&quot;cannot set both TEMP_SET_ALL and TEMP_MIN/MAX&quot;);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          1 :       plumed_massert(temps.size()&gt;=2,&quot;set at least 2 temperatures&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          1 :       temp_min=temps[0];</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          1 :       temp_max=temps[temps.size()-1];</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          1 :       derECVs_beta_.resize(temps.size());</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          5 :       for(unsigned k=0; k&lt;derECVs_beta_.size(); k++)</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :       {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :         derECVs_beta_[k]=(temp0/temps[k]-1.)/kbt_;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          4 :         if(k&lt;derECVs_beta_.size()-1)</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          3 :           plumed_massert(temps[k]&lt;=temps[k+1],&quot;TEMP_SET_ALL must be properly ordered&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :       }</a>
+<a name="229"><span class="lineNum">     229 </span>            :     }</a>
+<a name="230"><span class="lineNum">     230 </span>            :     else</a>
+<a name="231"><span class="lineNum">     231 </span>            :     { //get TEMP_MIN and TEMP_MAX</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          6 :       if(temp_min==-1)</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :       {</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :         temp_min=temp0;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :         log.printf(&quot;  no TEMP_MIN provided, using TEMP_MIN=TEMP\n&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :       }</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          6 :       if(temp_max==-1)</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :       {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          1 :         temp_max=temp0;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          1 :         log.printf(&quot;  no TEMP_MAX provided, using TEMP_MAX=TEMP\n&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :       }</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          6 :       plumed_massert(temp_max&gt;=temp_min,&quot;TEMP_MAX should be bigger than TEMP_MIN&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          6 :       derECVs_beta_.resize(2);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          6 :       derECVs_beta_[0]=(temp0/temp_min-1.)/kbt_;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          6 :       derECVs_beta_[1]=(temp0/temp_max-1.)/kbt_;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          6 :       if(temp_min==temp_max &amp;&amp; temp_steps==0)</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :         temp_steps=1;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          6 :       if(temp_steps&gt;0)</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          4 :         derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,&quot;TEMP&quot;,geom_spacing_,1./kbt_);</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :       else</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          4 :         todoAutomatic_beta_=true;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     }</a>
+<a name="253"><span class="lineNum">     253 </span>            :     const double tol=1e-3; //if temp is taken from MD engine it might be numerically slightly different</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          7 :     if(temp0&lt;(1-tol)*temp_min || temp0&gt;(1+tol)*temp_max)</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          1 :       log.printf(&quot; +++ WARNING +++ running at TEMP=%g which is outside the chosen temperature range\n&quot;,temp0);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :     //set the intermediate pressures</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          7 :     if(pres_.size()&gt;0)</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :     {</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 :       plumed_massert(pres_steps==0,&quot;cannot set both PRESSURE_STEPS and PRESSURE_SET_ALL&quot;);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          1 :       plumed_massert(pres_min==myNone &amp;&amp; pres_max==myNone,&quot;cannot set both PRESSURE_SET_ALL and PRESSURE_MIN/MAX&quot;);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          1 :       plumed_massert(pres_.size()&gt;=2,&quot;set at least 2 pressures&quot;);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          6 :       for(unsigned kk=0; kk&lt;pres_.size()-1; kk++)</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          5 :         plumed_massert(pres_[kk]&lt;=pres_[kk+1],&quot;PRESSURE_SET_ALL must be properly ordered&quot;);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          1 :       pres_min=pres_[0];</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          1 :       pres_max=pres_[pres_.size()-1];</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :     else</a>
+<a name="269"><span class="lineNum">     269 </span>            :     { //get PRESSURE_MIN and PRESSURE_MAX</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          6 :       if(pres_min==myNone)</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :       {</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          3 :         pres_min=pres0_;</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          3 :         log.printf(&quot;  no PRESSURE_MIN provided, using PRESSURE_MIN=PRESSURE\n&quot;);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :       }</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          6 :       if(pres_max==myNone)</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :       {</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          2 :         pres_max=pres0_;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          2 :         log.printf(&quot;  no PRESSURE_MAX provided, using PRESSURE_MAX=PRESSURE\n&quot;);</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :       }</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          6 :       plumed_massert(pres_max&gt;=pres_min,&quot;PRESSURE_MAX should be bigger than PRESSURE_MIN&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          6 :       if(pres_min==pres_max &amp;&amp; pres_steps==0)</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :         pres_steps=1;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          6 :       if(pres_steps&gt;0)</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          4 :         pres_=getSteps(pres_min,pres_max,pres_steps,&quot;PRESSURE&quot;,false,0);</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :       else</a>
+<a name="286"><span class="lineNum">     286 </span>            :       {</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          4 :         pres_.resize(2);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          4 :         pres_[0]=pres_min;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          4 :         pres_[1]=pres_max;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          4 :         todoAutomatic_pres_=true;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :       }</a>
+<a name="292"><span class="lineNum">     292 </span>            :     }</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          7 :     if(pres0_&lt;pres_min || pres0_&gt;pres_max)</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 :       log.printf(&quot; +++ WARNING +++ running at PRESSURE=%g which is outside the chosen pressure range\n&quot;,pres0_);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            :     //set CUT_CORNER</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          7 :     std::string cc_usage(&quot;CUT_CORNER=temp_low,pres_low,temp_high,pres_high&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          7 :     if(cut_corner.size()==4)</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :     {</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          6 :       const double temp_low=cut_corner[0];</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          6 :       const double pres_low=cut_corner[1];</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          6 :       const double temp_high=cut_corner[2];</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          6 :       const double pres_high=cut_corner[3];</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          6 :       plumed_massert(temp_low&lt;temp_high,&quot;temp_low=&quot;+std::to_string(temp_low)+&quot; should be smaller than temp_high=&quot;+std::to_string(temp_high)+&quot;, &quot;+cc_usage);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          6 :       plumed_massert(temp_low&gt;=temp_min &amp;&amp; temp_low&lt;=temp_max,&quot;temp_low=&quot;+std::to_string(temp_low)+&quot; is out of temperature range. &quot;+cc_usage);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          6 :       plumed_massert(temp_high&gt;=temp_min &amp;&amp; temp_high&lt;=temp_max,&quot;temp_high=&quot;+std::to_string(temp_high)+&quot; is out of temperature range. &quot;+cc_usage);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          6 :       plumed_massert(pres_low&lt;pres_high,&quot;pres_low=&quot;+std::to_string(pres_low)+&quot; should be smaller than pres_high=&quot;+std::to_string(pres_high)+&quot;, &quot;+cc_usage);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          6 :       plumed_massert(pres_low&gt;=pres_min &amp;&amp; pres_low&lt;=pres_max,&quot;pres_low=&quot;+std::to_string(pres_low)+&quot; is out of pressure range. &quot;+cc_usage);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          6 :       plumed_massert(pres_high&gt;=pres_min &amp;&amp; pres_high&lt;=pres_max,&quot;pres_high=&quot;+std::to_string(pres_high)+&quot; is out of pressure range. &quot;+cc_usage);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          6 :       kB_temp_low_=kB*temp_low;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          6 :       coeff_=(pres_high-pres_low)/(temp_high-temp_low)/kB;</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          6 :       plumed_massert(coeff_!=0,&quot;this should not be possible&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          6 :       const double small_value=(temp_high-pres_low)/1e4;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          6 :       pres_low_=pres_low-small_value; //make sure pres_max is included</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          6 :       plumed_massert(pres_max&gt;=coeff_*(kB*temp_max-kB_temp_low_)+pres_low_,&quot;please chose a pres_high slightly smaller than PRESSURE_MAX in &quot;+cc_usage);</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :     }</a>
+<a name="317"><span class="lineNum">     317 </span>            :     else</a>
+<a name="318"><span class="lineNum">     318 </span>            :     {</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          1 :       plumed_massert(cut_corner.size()==0,&quot;expected 4 values: &quot;+cc_usage);</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :     }</a>
+<a name="321"><span class="lineNum">     321 </span>            :   }</a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            : //print some info</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          9 :   log.printf(&quot;  running at TEMP=%g and PRESSURE=%g\n&quot;,temp0,pres0_);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          9 :   log.printf(&quot;  targeting a temperature range from TEMP_MIN=%g to TEMP_MAX=%g\n&quot;,temp_min,temp_max);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          9 :   if(temp_min==temp_max)</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          2 :     log.printf(&quot; +++ WARNING +++ if you only need a multibaric simulation it is more efficient to set it up with ECV_LINEAR\n&quot;);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          9 :   log.printf(&quot;   and a pressure range from PRESSURE_MIN=%g to PRESSURE_MAX=%g\n&quot;,pres_min,pres_max);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          9 :   if(pres_min==pres_max)</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          2 :     log.printf(&quot; +++ WARNING +++ if you only need a multithermal simulation it is more efficient to set it up with ECV_MULTITHERMAL\n&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          9 :   if(!geom_spacing_)</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          1 :     log.printf(&quot; -- NO_GEOM_SPACING: inverse temperatures will be linearly spaced\n&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          9 :   if(coeff_!=0)</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          6 :     log.printf(&quot; -- CUT_CORNER: ignoring some high temperature and low pressure values\n&quot;);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          9 : }</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        463 : void ECVmultiThermalBaric::calculateECVs(const double * ene_vol)</span></a>
+<a name="338"><span class="lineNum">     338 </span>            : {</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       5925 :   for(unsigned k=0; k&lt;derECVs_beta_.size(); k++)</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       5462 :     ECVs_beta_[k]=derECVs_beta_[k]*ene_vol[0];</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      50075 :   for(unsigned i=0; i&lt;derECVs_pres_.size(); i++)</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">      49612 :     ECVs_pres_[i]=derECVs_pres_[i]*ene_vol[1];</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : // derivatives are constant, as usual in linear expansions</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        463 : }</span></a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         18 : const double * ECVmultiThermalBaric::getPntrToECVs(unsigned j)</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : {</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         18 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         18 :   plumed_massert(j==0 || j==1,getName()+&quot; has only two CVs, the ENERGY and the VOLUME&quot;);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         18 :   if(j==0)</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          9 :     return &amp;ECVs_beta_[0];</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   else //if (j==1)</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          9 :     return &amp;ECVs_pres_[0];</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         18 : const double * ECVmultiThermalBaric::getPntrToDerECVs(unsigned j)</span></a>
+<a name="357"><span class="lineNum">     357 </span>            : {</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         18 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         18 :   plumed_massert(j==0 || j==1,getName()+&quot; has only two CVs, the ENERGY and the VOLUME&quot;);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         18 :   if(j==0)</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          9 :     return &amp;derECVs_beta_[0];</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :   else //if (j==1)</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          9 :     return &amp;derECVs_pres_[0];</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : }</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          9 : std::vector&lt; std::vector&lt;unsigned&gt; &gt; ECVmultiThermalBaric::getIndex_k() const</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : {</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          9 :   plumed_massert(isReady_ &amp;&amp; totNumECVs_&gt;0,&quot;cannot access getIndex_k() of ECV before initialization&quot;);</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; index_k;</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          9 :   if(custom_lambdas_.size()&gt;0)</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :   { //same as default getIndex_k() function</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          2 :     plumed_massert(totNumECVs_==custom_lambdas_.size(),&quot;this should not happen&quot;);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         22 :     for(unsigned i=0; i&lt;totNumECVs_; i++)</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         40 :       index_k.emplace_back(std::vector&lt;unsigned&gt; {i,i});</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :   }</a>
+<a name="376"><span class="lineNum">     376 </span>            :   else</a>
+<a name="377"><span class="lineNum">     377 </span>            :   {</a>
+<a name="378"><span class="lineNum">     378 </span>            :     unsigned i=0;</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        146 :     for(unsigned k=0; k&lt;derECVs_beta_.size(); k++)</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :     {</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        139 :       const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">        139 :       const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       2594 :       for(unsigned kk=0; kk&lt;pres_.size(); kk++)</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :       {</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       2455 :         if(coeff_==0 || pres_[kk]&gt;=line_k) //important to be inclusive, thus &gt;=, not just &gt;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :         {</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">       2254 :           index_k.emplace_back(std::vector&lt;unsigned&gt; {k,i});</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       2254 :           i++;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :         }</a>
+<a name="390"><span class="lineNum">     390 </span>            :       }</a>
+<a name="391"><span class="lineNum">     391 </span>            :     }</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          7 :     plumed_massert(totNumECVs_==index_k.size(),&quot;this should not happen, is something wrong with CUT_CORNER ?&quot;);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   }</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          9 :   return index_k;</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="396"><span class="lineNum">     396 </span>            : </a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         18 : std::vector&lt;std::string&gt; ECVmultiThermalBaric::getLambdas() const</span></a>
+<a name="398"><span class="lineNum">     398 </span>            : {</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         18 :   if(custom_lambdas_.size()&gt;0)</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          4 :     return custom_lambdas_;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         14 :   plumed_massert(!todoAutomatic_beta_ &amp;&amp; !todoAutomatic_pres_,&quot;cannot access lambdas before initializing them&quot;);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   std::vector&lt;std::string&gt; lambdas;</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         14 :   const double kB=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">        292 :   for(unsigned k=0; k&lt;derECVs_beta_.size(); k++)</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :   {</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">        278 :     const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">        278 :     const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">       5188 :     for(unsigned kk=0; kk&lt;pres_.size(); kk++)</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :     {</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       4910 :       if(coeff_==0 || pres_[kk]&gt;=line_k)</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :       {</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">       4508 :         std::ostringstream subs;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">       4508 :         subs&lt;&lt;kB_temp_k/kB&lt;&lt;&quot;_&quot;&lt;&lt;pres_[kk];</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">       4508 :         lambdas.emplace_back(subs.str());</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       4508 :       }</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :     }</a>
+<a name="418"><span class="lineNum">     418 </span>            :   }</a>
+<a name="419"><span class="lineNum">     419 </span>            :   return lambdas;</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         14 : }</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          9 : void ECVmultiThermalBaric::initECVs()</span></a>
+<a name="423"><span class="lineNum">     423 </span>            : {</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          9 :   plumed_massert(!isReady_,&quot;initialization should not be called twice&quot;);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          9 :   plumed_massert(!todoAutomatic_beta_ &amp;&amp; !todoAutomatic_pres_,&quot;this should not happen&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          9 :   totNumECVs_=getLambdas().size(); //slow, but runs only once</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          9 :   if(custom_lambdas_.size()&gt;0)</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :   {</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          2 :     log.printf(&quot;  *%4lu temperatures for %s\n&quot;,derECVs_beta_.size(),getName().c_str());</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          2 :     log.printf(&quot;  *%4lu beta-pressures for %s\n&quot;,derECVs_pres_.size(),getName().c_str());</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">          2 :     log.printf(&quot;    -- SET_ALL_TEMP_PRESSURE: total number of temp-pres points is %u\n&quot;,totNumECVs_);</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :   }</a>
+<a name="433"><span class="lineNum">     433 </span>            :   else</a>
+<a name="434"><span class="lineNum">     434 </span>            :   {</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          7 :     plumed_massert(derECVs_beta_.size()*pres_.size()&gt;=totNumECVs_,&quot;this should not happen, is something wrong with CUT_CORNER ?&quot;);</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">          7 :     derECVs_pres_.resize(totNumECVs_); //pres is mixed with temp (beta*p*V), thus we need to store all possible</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :     //initialize the derECVs.</a>
+<a name="438"><span class="lineNum">     438 </span>            :     //this could be done before and one could avoid storing also beta0, beta_k, etc. but this way the code should be more readable</a>
+<a name="439"><span class="lineNum">     439 </span>            :     unsigned i=0;</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        146 :     for(unsigned k=0; k&lt;derECVs_beta_.size(); k++)</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :     {</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">        139 :       const double kB_temp_k=kbt_/(derECVs_beta_[k]*kbt_+1);</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">        139 :       const double line_k=coeff_*(kB_temp_k-kB_temp_low_)+pres_low_;</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">       2594 :       for(unsigned kk=0; kk&lt;pres_.size(); kk++)</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :       {</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">       2455 :         if(coeff_==0 || pres_[kk]&gt;=line_k)</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :         {</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">       2254 :           derECVs_pres_[i]=(pres_[kk]/kB_temp_k-pres0_/kbt_);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">       2254 :           i++;</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :         }</a>
+<a name="451"><span class="lineNum">     451 </span>            :       }</a>
+<a name="452"><span class="lineNum">     452 </span>            :     }</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">          7 :     log.printf(&quot;  *%4lu temperatures for %s\n&quot;,derECVs_beta_.size(),getName().c_str());</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          7 :     log.printf(&quot;  *%4lu pressures for %s\n&quot;,pres_.size(),getName().c_str());</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          7 :     if(coeff_!=0)</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          6 :       log.printf(&quot;    -- CUT_CORNER: %lu temp-pres points were excluded, thus total is %u\n&quot;,derECVs_beta_.size()*pres_.size()-totNumECVs_,totNumECVs_);</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :   }</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          9 :   ECVs_beta_.resize(derECVs_beta_.size());</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          9 :   ECVs_pres_.resize(derECVs_pres_.size());</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          9 :   isReady_=true;</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          9 : }</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          6 : void ECVmultiThermalBaric::initECVs_observ(const std::vector&lt;double&gt;&amp; all_obs_cvs,const unsigned ncv,const unsigned index_j)</span></a>
+<a name="464"><span class="lineNum">     464 </span>            : {</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          6 :   if(todoAutomatic_beta_) //estimate the steps in beta from observations</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :   {</a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          2 :     plumed_massert(all_obs_cvs.size()%ncv==0 &amp;&amp; index_j&lt;ncv,&quot;initECVs_observ parameters are inconsistent&quot;);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          2 :     std::vector&lt;double&gt; obs_ene(all_obs_cvs.size()/ncv); //copy only useful observations</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         17 :     for(unsigned t=0; t&lt;obs_ene.size(); t++)</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         15 :       obs_ene[t]=all_obs_cvs[t*ncv+index_j]+pres0_*all_obs_cvs[t*ncv+index_j+1]; //U=E+pV</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          2 :     const unsigned temp_steps=estimateNumSteps(derECVs_beta_[0],derECVs_beta_[1],obs_ene,&quot;TEMP&quot;);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          2 :     log.printf(&quot;    (spacing is on beta, not on temperature)\n&quot;);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          4 :     derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,&quot;TEMP&quot;,geom_spacing_,1./kbt_);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          2 :     todoAutomatic_beta_=false;</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :   }</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          6 :   if(todoAutomatic_pres_) //estimate the steps in pres from observations</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :   {</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          2 :     plumed_massert(all_obs_cvs.size()%ncv==0 &amp;&amp; index_j+1&lt;ncv,&quot;initECVs_observ parameters are inconsistent&quot;);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          2 :     std::vector&lt;double&gt; obs_vol(all_obs_cvs.size()/ncv); //copy only useful observations</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">         17 :     for(unsigned t=0; t&lt;obs_vol.size(); t++)</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         15 :       obs_vol[t]=all_obs_cvs[t*ncv+index_j+1];</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          2 :     const unsigned pres_steps=estimateNumSteps((pres_[0]-pres0_)/kbt_,(pres_[1]-pres0_)/kbt_,obs_vol,&quot;PRESSURE&quot;);</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          2 :     log.printf(&quot;    (spacing is in beta0 units)\n&quot;);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          4 :     pres_=getSteps(pres_[0],pres_[1],pres_steps,&quot;PRESSURE&quot;,false,0);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          2 :     todoAutomatic_pres_=false;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :   }</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          6 :   initECVs();</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          6 :   calculateECVs(&amp;all_obs_cvs[index_j]);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          6 : }</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          3 : void ECVmultiThermalBaric::initECVs_restart(const std::vector&lt;std::string&gt;&amp; lambdas)</span></a>
+<a name="492"><span class="lineNum">     492 </span>            : {</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          3 :   std::size_t pos=lambdas[0].find(&quot;_&quot;);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          3 :   plumed_massert(pos!=std::string::npos,&quot;this should not happen, two CVs are used in &quot;+getName()+&quot;, not less&quot;);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          3 :   pos=lambdas[0].find(&quot;_&quot;,pos+1);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          3 :   plumed_massert(pos==std::string::npos,&quot;this should not happen, two CVs are used in &quot;+getName()+&quot;, not more&quot;);</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">        230 :   auto getPres=[&amp;lambdas](const unsigned i) {return lambdas[i].substr(lambdas[i].find(&quot;_&quot;)+1);};</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          3 :   if(todoAutomatic_pres_)</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :   {</a>
+<a name="501"><span class="lineNum">     501 </span>            :     unsigned pres_steps=1;</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          2 :     std::string pres_min=getPres(0);</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         20 :     for(unsigned i=1; i&lt;lambdas.size(); i++) //pres is second, thus increas by 1</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :     {</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         20 :       if(getPres(i)==pres_min)</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :         break;</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         18 :       pres_steps++;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :     }</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          4 :     pres_=getSteps(pres_[0],pres_[1],pres_steps,&quot;PRESSURE&quot;,false,0);</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">          2 :     todoAutomatic_pres_=false;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   }</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">          3 :   if(todoAutomatic_beta_)</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :   {</a>
+<a name="514"><span class="lineNum">     514 </span>            :     unsigned temp_steps=1;</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">          2 :     std::string pres_max=getPres(pres_.size()-1);</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        208 :     for(unsigned i=pres_.size(); i&lt;lambdas.size(); i++)</span></a>
+<a name="517"><span class="lineNum">     517 </span>            :     { //even if CUT_CORNER, the max pressures are all present, for each temp</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">        206 :       if(getPres(i)==pres_max)</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         24 :         temp_steps++;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :     }</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">          4 :     derECVs_beta_=getSteps(derECVs_beta_[0],derECVs_beta_[1],temp_steps,&quot;TEMP&quot;,geom_spacing_,1./kbt_);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">          2 :     todoAutomatic_beta_=false;</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :   }</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          3 :   std::vector&lt;std::string&gt; myLambdas=getLambdas();</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          3 :   plumed_assert(myLambdas.size()==lambdas.size())&lt;&lt;&quot;RESTART - mismatch in number of &quot;&lt;&lt;getName()&lt;&lt;&quot;.\nFrom &quot;&lt;&lt;lambdas.size()&lt;&lt;&quot; labels &quot;&lt;&lt;derECVs_beta_.size()&lt;&lt;&quot; temperatures and &quot;&lt;&lt;pres_.size()&lt;&lt;&quot; pressures were found, for a total of &quot;&lt;&lt;myLambdas.size()&lt;&lt;&quot; estimated steps.\nCheck if the CUT_CORNER or the SET_ALL_TEMP_PRESSURE options are consistent\n&quot;;</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">          3 :   plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),&quot;RESTART - mismatch in lambda values of &quot;+getName());</span></a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">          3 :   initECVs();</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">          3 : }</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            : }</a>
+<a name="532"><span class="lineNum">     532 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVumbrellasFile.cpp.func-sort-c.html b/coverage/opes/ECVumbrellasFile.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ccae2a5bc3
--- /dev/null
+++ b/coverage/opes/ECVumbrellasFile.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVumbrellasFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVumbrellasFile.cpp<span style="font-size: 80%;"> (<a href="ECVumbrellasFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ECVumbrellasFile.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#106">_ZN4PLMD4opes16ECVumbrellasFileC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#276">_ZN4PLMD4opes16ECVumbrellasFile16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#266">_ZN4PLMD4opes16ECVumbrellasFile15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#94">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasFileRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#259">_ZN4PLMD4opes16ECVumbrellasFile8initECVsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#106">_ZN4PLMD4opes16ECVumbrellasFileC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#236">_ZNK4PLMD4opes16ECVumbrellasFile10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#96">_ZN4PLMD4opes16ECVumbrellasFile16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#222">_ZN4PLMD4opes16ECVumbrellasFile13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#229">_ZN4PLMD4opes16ECVumbrellasFile16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#184">_ZN4PLMD4opes16ECVumbrellasFile13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">131</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#94">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasFileRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#94">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasFileRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVumbrellasFile.cpp.func.html b/coverage/opes/ECVumbrellasFile.cpp.func.html
new file mode 100644
index 0000000000..644d420521
--- /dev/null
+++ b/coverage/opes/ECVumbrellasFile.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVumbrellasFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVumbrellasFile.cpp<span style="font-size: 80%;"> (<a href="ECVumbrellasFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ECVumbrellasFile.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#94">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasFileRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#94">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasFileRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#94">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasFileRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#184">_ZN4PLMD4opes16ECVumbrellasFile13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">131</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#222">_ZN4PLMD4opes16ECVumbrellasFile13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#266">_ZN4PLMD4opes16ECVumbrellasFile15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#229">_ZN4PLMD4opes16ECVumbrellasFile16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#276">_ZN4PLMD4opes16ECVumbrellasFile16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#96">_ZN4PLMD4opes16ECVumbrellasFile16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#259">_ZN4PLMD4opes16ECVumbrellasFile8initECVsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#106">_ZN4PLMD4opes16ECVumbrellasFileC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#106">_ZN4PLMD4opes16ECVumbrellasFileC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasFile.cpp.gcov.html#236">_ZNK4PLMD4opes16ECVumbrellasFile10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVumbrellasFile.cpp.gcov.html b/coverage/opes/ECVumbrellasFile.cpp.gcov.html
new file mode 100644
index 0000000000..82bb8b4d33
--- /dev/null
+++ b/coverage/opes/ECVumbrellasFile.cpp.gcov.html
@@ -0,0 +1,371 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVumbrellasFile.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVumbrellasFile.cpp<span style="font-size: 80%;"> (source / <a href="ECVumbrellasFile.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">121</td>
+            <td class="headerCovTableEntryHi">98.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : namespace PLMD {</a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace opes {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : //+PLUMEDOC OPES_EXPANSION_CV ECV_UMBRELLAS_FILE</a>
+<a name="27"><span class="lineNum">      27 </span>            : /*</a>
+<a name="28"><span class="lineNum">      28 </span>            : Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location.</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : Any set of collective variables \f$\mathbf{s}\f$ can be used as ARG.</a>
+<a name="31"><span class="lineNum">      31 </span>            : The positions \f$\mathbf{s}_i\f$ and dimension \f$\mathbf{\sigma}_i\f$ of the umbrellas are read from file.</a>
+<a name="32"><span class="lineNum">      32 </span>            : \f[</a>
+<a name="33"><span class="lineNum">      33 </span>            :   \Delta u_{\mathbf{s}_i}(\mathbf{s})=\sum_j^{\text{dim}}\frac{([s]_j-[s_i]_j)^2}{2[\sigma_i]_j^2}\, .</a>
+<a name="34"><span class="lineNum">      34 </span>            : \f]</a>
+<a name="35"><span class="lineNum">      35 </span>            : Notice that \f$\mathbf{\sigma}_i\f$ is diagonal, thus only one SIGMA per CV has to be specified for each umbrella.</a>
+<a name="36"><span class="lineNum">      36 </span>            : You can choose the umbrellas manually, or place them on a grid, or along a path, similar to \ref PATH.</a>
+<a name="37"><span class="lineNum">      37 </span>            : They must cover all the CV space that one wishes to sample.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The first column of the umbrellas file is always ignored and must be called &quot;time&quot;.</a>
+<a name="40"><span class="lineNum">      40 </span>            : You can also use as input file a STATE file from an earlier \ref OPES_METAD run (or an \ref OPES_MEAD_EXPLORE run, if you combine it with other ECVs).</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Similarly to \ref ECV_UMBRELLAS_LINE, you should set the flag ADD_P0 if you think your umbrellas might not properly cover all the CV region relevant for the unbiased distribution.</a>
+<a name="43"><span class="lineNum">      43 </span>            : You can also use BARRIER to set the maximum barrier height to be explored, and avoid huge biases at the beginning of your simulation.</a>
+<a name="44"><span class="lineNum">      44 </span>            : See also Appendix B of Ref.\cite Invernizzi2020unified for more details on these last two options.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \plumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : cv1: DISTANCE ATOMS=1,2</a>
+<a name="50"><span class="lineNum">      50 </span>            : cv2: DISTANCE ATOMS=3,4</a>
+<a name="51"><span class="lineNum">      51 </span>            : cv3: DISTANCE ATOMS=4,1</a>
+<a name="52"><span class="lineNum">      52 </span>            : ecv: ECV_UMBRELLAS_FILE ARG=cv1,cv2,cv3 FILE=Umbrellas.data ADD_P0 BARRIER=70</a>
+<a name="53"><span class="lineNum">      53 </span>            : opes: OPES_EXPANDED ARG=ecv.* PACE=500</a>
+<a name="54"><span class="lineNum">      54 </span>            : PRINT FILE=COLVAR STRIDE=500 ARG=cv1,cv2,cv3,opes.bias</a>
+<a name="55"><span class="lineNum">      55 </span>            : \endplumedfile</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : The umbrellas file might look like this:</a>
+<a name="58"><span class="lineNum">      58 </span>            : \auxfile{Umbrellas.data}</a>
+<a name="59"><span class="lineNum">      59 </span>            : #! FIELDS time cv1 cv2 cv3 sigma_cv1 sigma_cv2 sigma_cv3</a>
+<a name="60"><span class="lineNum">      60 </span>            : 1  1.17958  2.93697  1.06109  0.19707  0.28275  0.32427</a>
+<a name="61"><span class="lineNum">      61 </span>            : 2  2.04023  2.69714  1.84770  0.22307  0.25933  0.31783</a>
+<a name="62"><span class="lineNum">      62 </span>            : 3  1.99693  1.10299  1.13351  0.19517  0.26260  0.37427</a>
+<a name="63"><span class="lineNum">      63 </span>            : 4  1.15954  1.37447  2.25975  0.20096  0.27168  0.33353</a>
+<a name="64"><span class="lineNum">      64 </span>            : 5  1.10126  2.45936  2.40260  0.19747  0.24215  0.35523</a>
+<a name="65"><span class="lineNum">      65 </span>            : \endauxfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : //+ENDPLUMEDOC</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : class ECVumbrellasFile :</a>
+<a name="71"><span class="lineNum">      71 </span>            :   public ExpansionCVs</a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span>            : private:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   double barrier_;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   unsigned P0_contribution_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   bool lower_only_;</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; centers_;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; sigmas_;</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; ECVs_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; derECVs_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void initECVs();</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : public:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   explicit ECVumbrellasFile(const ActionOptions&amp;);</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void calculateECVs(const double *) override;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   const double * getPntrToECVs(unsigned) override;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   const double * getPntrToDerECVs(unsigned) override;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;std::string&gt; getLambdas() const override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) override;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(ECVumbrellasFile,&quot;ECV_UMBRELLAS_FILE&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          5 : void ECVumbrellasFile::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : {</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          5 :   ExpansionCVs::registerKeywords(keys);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          5 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;the name of the file containing the umbrellas&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;BARRIER&quot;,&quot;a guess of the free energy barrier to be overcome (better to stay higher than lower)&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         10 :   keys.addFlag(&quot;ADD_P0&quot;,false,&quot;add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         10 :   keys.addFlag(&quot;LOWER_HALF_ONLY&quot;,false,&quot;use only the lower half of each umbrella potentials&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          5 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 : ECVumbrellasFile::ECVumbrellasFile(const ActionOptions&amp;ao):</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   Action(ao),</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :   ExpansionCVs(ao)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : {</a>
+<a name="112"><span class="lineNum">     112 </span>            : //get number of CVs</a>
+<a name="113"><span class="lineNum">     113 </span>            :   const unsigned ncv=getNumberOfArguments();</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 :   centers_.resize(ncv);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          3 :   sigmas_.resize(ncv);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : //set P0_contribution_</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          3 :   bool add_P0=false;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          3 :   parseFlag(&quot;ADD_P0&quot;,add_P0);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          3 :   if(add_P0)</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :     P0_contribution_=1;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   else</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          1 :     P0_contribution_=0;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : //set barrier_</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          3 :   barrier_=std::numeric_limits&lt;double&gt;::infinity();</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   parse(&quot;BARRIER&quot;,barrier_);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   parseFlag(&quot;LOWER_HALF_ONLY&quot;,lower_only_);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : //set umbrellas</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::string umbrellasFileName;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          3 :   parse(&quot;FILE&quot;,umbrellasFileName);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          3 :   IFile ifile;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          3 :   ifile.link(*this);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          3 :   if(ifile.FileExist(umbrellasFileName))</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          3 :     log.printf(&quot;  reading from FILE '%s'\n&quot;,umbrellasFileName.c_str());</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :     ifile.open(umbrellasFileName);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          3 :     ifile.allowIgnoredFields();</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     double time; //first field is ignored</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1332 :     while(ifile.scanField(&quot;time&quot;,time))</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1989 :       for(unsigned j=0; j&lt;ncv; j++)</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :       {</a>
+<a name="145"><span class="lineNum">     145 </span>            :         double centers_j;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1326 :         ifile.scanField(getPntrToArgument(j)-&gt;getName(),centers_j);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1326 :         centers_[j].push_back(centers_j); //this might be slow</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :       }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1989 :       for(unsigned j=0; j&lt;ncv; j++)</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :       {</a>
+<a name="151"><span class="lineNum">     151 </span>            :         double sigmas_j;</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       2652 :         ifile.scanField(&quot;sigma_&quot;+getPntrToArgument(j)-&gt;getName(),sigmas_j);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       1326 :         sigmas_[j].push_back(sigmas_j);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :       }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        663 :       ifile.scanField();</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     }</a>
+<a name="157"><span class="lineNum">     157 </span>            :   }</a>
+<a name="158"><span class="lineNum">     158 </span>            :   else</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Umbrellas FILE '&quot;+umbrellasFileName+&quot;' not found&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : //extra consistency checks</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          3 :   const unsigned sizeUmbrellas=centers_[0].size();</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          9 :   for(unsigned j=0; j&lt;ncv; j++)</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          6 :     plumed_massert(centers_[j].size()==sizeUmbrellas,&quot;mismatch in the number of centers read from file&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          6 :     plumed_massert(sigmas_[j].size()==sizeUmbrellas,&quot;mismatch in the number of sigmas read from file&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : //set ECVs stuff</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          3 :   totNumECVs_=sizeUmbrellas+P0_contribution_;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          3 :   ECVs_.resize(ncv,std::vector&lt;double&gt;(totNumECVs_));</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          3 :   derECVs_.resize(ncv,std::vector&lt;double&gt;(totNumECVs_));</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : //printing some info</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :   log.printf(&quot;  total number of umbrellas = %u\n&quot;,sizeUmbrellas);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          3 :   if(barrier_!=std::numeric_limits&lt;double&gt;::infinity())</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          1 :     log.printf(&quot;  guess for free energy BARRIER = %g\n&quot;,barrier_);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          3 :   if(P0_contribution_==1)</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :     log.printf(&quot; -- ADD_P0: the target includes also the unbiased probability itself\n&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          3 :   if(lower_only_)</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          1 :     log.printf(&quot; -- LOWER_HALF_ONLY: the ECVs are set to zero for values of the CV above the respective center\n&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          6 : }</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        131 : void ECVumbrellasFile::calculateECVs(const double * cv)</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        131 :   if(lower_only_)</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   {</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        153 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     {</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      22644 :       for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++) //if ADD_P0, the first ECVs=0</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :       {</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      22542 :         const unsigned kk=k-P0_contribution_;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      22542 :         const double dist_jk=difference(j,centers_[j][kk],cv[j])/sigmas_[j][kk]; //PBC might be present</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      22542 :         if(dist_jk&gt;=0)</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :         {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      11483 :           ECVs_[j][k]=0;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      11483 :           derECVs_[j][k]=0;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :         }</a>
+<a name="201"><span class="lineNum">     201 </span>            :         else</a>
+<a name="202"><span class="lineNum">     202 </span>            :         {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      11059 :           ECVs_[j][k]=0.5*std::pow(dist_jk,2);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      11059 :           derECVs_[j][k]=dist_jk/sigmas_[j][kk];</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :         }</a>
+<a name="206"><span class="lineNum">     206 </span>            :       }</a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span>            :   else</a>
+<a name="210"><span class="lineNum">     210 </span>            :   {</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        240 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      35520 :       for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++) //if ADD_P0, the first ECVs=0</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :       {</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      35360 :         const unsigned kk=k-P0_contribution_;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      35360 :         const double dist_jk=difference(j,centers_[j][kk],cv[j])/sigmas_[j][kk]; //PBC might be present</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      35360 :         ECVs_[j][k]=0.5*std::pow(dist_jk,2);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      35360 :         derECVs_[j][k]=dist_jk/sigmas_[j][kk];</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :       }</a>
+<a name="220"><span class="lineNum">     220 </span>            :     }</a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        131 : }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          6 : const double * ECVumbrellasFile::getPntrToECVs(unsigned j)</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : {</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          6 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          6 :   plumed_massert(j&lt;getNumberOfArguments(),getName()+&quot; has fewer CVs&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          6 :   return &amp;ECVs_[j][0];</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          6 : const double * ECVumbrellasFile::getPntrToDerECVs(unsigned j)</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : {</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          6 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          6 :   plumed_massert(j&lt;getNumberOfArguments(),getName()+&quot; has fewer CVs&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          6 :   return &amp;derECVs_[j][0];</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          3 : std::vector&lt;std::string&gt; ECVumbrellasFile::getLambdas() const</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : { //notice that sigmas are not considered!</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          3 :   std::vector&lt;std::string&gt; lambdas(totNumECVs_);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          3 :   if(P0_contribution_==1)</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   {</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          2 :     std::ostringstream subs;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          2 :     subs&lt;&lt;&quot;P0&quot;;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          4 :     for(unsigned j=1; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          2 :       subs&lt;&lt;&quot;_P0&quot;;</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          2 :     lambdas[0]=subs.str();</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          2 :   }</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        666 :   for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++)</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   {</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        663 :     const unsigned kk=k-P0_contribution_;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        663 :     std::ostringstream subs;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        663 :     subs&lt;&lt;centers_[0][kk];</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       1326 :     for(unsigned j=1; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        663 :       subs&lt;&lt;&quot;_&quot;&lt;&lt;centers_[j][kk];</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        663 :     lambdas[k]=subs.str();</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        663 :   }</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          3 :   return lambdas;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          3 : void ECVumbrellasFile::initECVs()</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          3 :   plumed_massert(!isReady_,&quot;initialization should not be called twice&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          3 :   isReady_=true;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          3 :   log.printf(&quot;  *%4u windows for %s\n&quot;,totNumECVs_,getName().c_str());</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          3 : }</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          2 : void ECVumbrellasFile::initECVs_observ(const std::vector&lt;double&gt;&amp; all_obs_cvs,const unsigned ncv,const unsigned index_j)</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : {</a>
+<a name="270"><span class="lineNum">     270 </span>            :   //this non-linear exansion never uses automatic initialization</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          2 :   initECVs();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :   calculateECVs(&amp;all_obs_cvs[index_j]); //use only first obs point</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          6 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        888 :     for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++)</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       1680 :       ECVs_[j][k]=std::min(barrier_/kbt_,ECVs_[j][k]);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          2 : }</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          1 : void ECVumbrellasFile::initECVs_restart(const std::vector&lt;std::string&gt;&amp; lambdas)</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : {</a>
+<a name="280"><span class="lineNum">     280 </span>            :   std::size_t pos=0;</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          2 :   for(unsigned j=0; j&lt;getNumberOfArguments()-1; j++)</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          1 :     pos=lambdas[0].find(&quot;_&quot;,pos+1); //checking only lambdas[0] is hopefully enough</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          1 :   plumed_massert(pos&lt;lambdas[0].length(),&quot;this should not happen, fewer '_' than expected in &quot;+getName());</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          1 :   pos=lambdas[0].find(&quot;_&quot;,pos+1);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          1 :   plumed_massert(pos&gt;lambdas[0].length(),&quot;this should not happen, more '_' than expected in &quot;+getName());</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          1 :   std::vector&lt;std::string&gt; myLambdas=getLambdas();</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          1 :   plumed_massert(myLambdas.size()==lambdas.size(),&quot;RESTART - mismatch in number of &quot;+getName());</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          1 :   plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),&quot;RESTART - mismatch in lambda values of &quot;+getName());</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          1 :   initECVs();</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          1 : }</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : }</a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVumbrellasLine.cpp.func-sort-c.html b/coverage/opes/ECVumbrellasLine.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ad5470e539
--- /dev/null
+++ b/coverage/opes/ECVumbrellasLine.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVumbrellasLine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVumbrellasLine.cpp<span style="font-size: 80%;"> (<a href="ECVumbrellasLine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntry">132</td>
+            <td class="headerCovTableEntryHi">98.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ECVumbrellasLine.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#110">_ZN4PLMD4opes16ECVumbrellasLineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#282">_ZN4PLMD4opes16ECVumbrellasLine16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#272">_ZN4PLMD4opes16ECVumbrellasLine15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#95">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasLineRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#265">_ZN4PLMD4opes16ECVumbrellasLine8initECVsEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#110">_ZN4PLMD4opes16ECVumbrellasLineC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#242">_ZNK4PLMD4opes16ECVumbrellasLine10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#228">_ZN4PLMD4opes16ECVumbrellasLine13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#235">_ZN4PLMD4opes16ECVumbrellasLine16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#97">_ZN4PLMD4opes16ECVumbrellasLine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#190">_ZN4PLMD4opes16ECVumbrellasLine13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#95">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasLineRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#95">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasLineRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVumbrellasLine.cpp.func.html b/coverage/opes/ECVumbrellasLine.cpp.func.html
new file mode 100644
index 0000000000..2ad2e3dc36
--- /dev/null
+++ b/coverage/opes/ECVumbrellasLine.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVumbrellasLine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVumbrellasLine.cpp<span style="font-size: 80%;"> (<a href="ECVumbrellasLine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntry">132</td>
+            <td class="headerCovTableEntryHi">98.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ECVumbrellasLine.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#95">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasLineRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#95">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasLineRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#95">_ZN4PLMD4opes12_GLOBAL__N_128ECVumbrellasLineRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#190">_ZN4PLMD4opes16ECVumbrellasLine13calculateECVsEPKd</a></td>
+              <td class="coverFnHi">433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#228">_ZN4PLMD4opes16ECVumbrellasLine13getPntrToECVsEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#272">_ZN4PLMD4opes16ECVumbrellasLine15initECVs_observERKSt6vectorIdSaIdEEjj</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#235">_ZN4PLMD4opes16ECVumbrellasLine16getPntrToDerECVsEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#282">_ZN4PLMD4opes16ECVumbrellasLine16initECVs_restartERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#97">_ZN4PLMD4opes16ECVumbrellasLine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#265">_ZN4PLMD4opes16ECVumbrellasLine8initECVsEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#110">_ZN4PLMD4opes16ECVumbrellasLineC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#110">_ZN4PLMD4opes16ECVumbrellasLineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ECVumbrellasLine.cpp.gcov.html#242">_ZNK4PLMD4opes16ECVumbrellasLine10getLambdasB5cxx11Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ECVumbrellasLine.cpp.gcov.html b/coverage/opes/ECVumbrellasLine.cpp.gcov.html
new file mode 100644
index 0000000000..fec6eabd95
--- /dev/null
+++ b/coverage/opes/ECVumbrellasLine.cpp.gcov.html
@@ -0,0 +1,377 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ECVumbrellasLine.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ECVumbrellasLine.cpp<span style="font-size: 80%;"> (source / <a href="ECVumbrellasLine.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">130</td>
+            <td class="headerCovTableEntry">132</td>
+            <td class="headerCovTableEntryHi">98.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : </a>
+<a name="22"><span class="lineNum">      22 </span>            : namespace PLMD {</a>
+<a name="23"><span class="lineNum">      23 </span>            : namespace opes {</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : //+PLUMEDOC OPES_EXPANSION_CV ECV_UMBRELLAS_LINE</a>
+<a name="26"><span class="lineNum">      26 </span>            : /*</a>
+<a name="27"><span class="lineNum">      27 </span>            : Target a multiumbrella ensemble, by combining systems each with a parabolic bias potential at a different location.</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : Any set of collective variables \f$\mathbf{s}\f$ can be used as ARG.</a>
+<a name="30"><span class="lineNum">      30 </span>            : \f[</a>
+<a name="31"><span class="lineNum">      31 </span>            :   \Delta u_{\mathbf{s}_i}(\mathbf{s})=\sum_j^{\text{dim}}\frac{([s]_j-[s_i]_j)^2}{2\sigma^2}\, .</a>
+<a name="32"><span class="lineNum">      32 </span>            : \f]</a>
+<a name="33"><span class="lineNum">      33 </span>            : The Gaussian umbrellas are placed along a line, from CV_MIN to CV_MAX.</a>
+<a name="34"><span class="lineNum">      34 </span>            : The umbrellas are placed at a distance SIGMA*SPACING from each other, if you need more flexibility use \ref ECV_UMBRELLAS_FILE.</a>
+<a name="35"><span class="lineNum">      35 </span>            : The unbiased fluctuations in the basin usually are a reasonable guess for the value of SIGMA.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Typically, a SPACING greater than 1 can lead to faster convergence, by reducing the total number of umbrellas.</a>
+<a name="37"><span class="lineNum">      37 </span>            : The umbrellas can be multidimensional, but the CVs dimensions should be rescaled since a single SIGMA must be used.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The keyword BARRIER can be helpful to avoid breaking your system due to a too strong initial bias.</a>
+<a name="40"><span class="lineNum">      40 </span>            : If you think the placed umbrellas will not cover the whole unbiased probability distribution you should add it explicitly to the target, with the flag ADD_P0, for more robust convergence.</a>
+<a name="41"><span class="lineNum">      41 </span>            : See also Appendix B of Ref.\cite Invernizzi2020unified for more details on these last two options.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The flag LOWER_HALF_ONLY modifies the ECVs so that they are set to zero when \f$\mathbf{s}&gt;\mathbf{s}_i\f$, as in \ref LOWER_WALLS.</a>
+<a name="44"><span class="lineNum">      44 </span>            : This can be useful e.g. when the CV used is the \ref ENERGY and one wants to sample a broad range of high energy values, similar to \ref ECV_MULTITHERMAL but with a flat energy distribution as target.</a>
+<a name="45"><span class="lineNum">      45 </span>            : By pushing only from below one can avoid too extreme forces that could crash the simulation.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \par Examples</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \plumedfile</a>
+<a name="50"><span class="lineNum">      50 </span>            : cv: DISTANCE ATOMS=1,2</a>
+<a name="51"><span class="lineNum">      51 </span>            : ecv: ECV_UMBRELLAS_LINE ARG=cv CV_MIN=1.2 CV_MAX=4.3 SIGMA=0.5 SPACING=1.5</a>
+<a name="52"><span class="lineNum">      52 </span>            : opes: OPES_EXPANDED ARG=ecv.* PACE=500</a>
+<a name="53"><span class="lineNum">      53 </span>            : \endplumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : It is also possible to combine different ECV_UMBRELLAS_LINE to build a grid of CV values that will be sampled.</a>
+<a name="56"><span class="lineNum">      56 </span>            : For example the following code will sample a whole 2D region of cv1 and cv2.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \plumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : cv1: DISTANCE ATOMS=1,2</a>
+<a name="60"><span class="lineNum">      60 </span>            : ecv2: ECV_UMBRELLAS_LINE ARG=cv1 CV_MIN=1.2 CV_MAX=4.3 SIGMA=0.5</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : cv2: DISTANCE ATOMS=3,4</a>
+<a name="63"><span class="lineNum">      63 </span>            : ecv1: ECV_UMBRELLAS_LINE ARG=cv2 CV_MIN=13.8 CV_MAX=21.4 SIGMA=4.3</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : opes: OPES_EXPANDED ARG=ecv1.*,ecv2.* PACE=500</a>
+<a name="66"><span class="lineNum">      66 </span>            : \endplumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : */</a>
+<a name="69"><span class="lineNum">      69 </span>            : //+ENDPLUMEDOC</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : class ECVumbrellasLine :</a>
+<a name="72"><span class="lineNum">      72 </span>            :   public ExpansionCVs</a>
+<a name="73"><span class="lineNum">      73 </span>            : {</a>
+<a name="74"><span class="lineNum">      74 </span>            : private:</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double barrier_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   unsigned P0_contribution_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool lower_only_;</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; centers_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double sigma_;</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; ECVs_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; derECVs_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void initECVs();</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   explicit ECVumbrellasLine(const ActionOptions&amp;);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void calculateECVs(const double *) override;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   const double * getPntrToECVs(unsigned) override;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   const double * getPntrToDerECVs(unsigned) override;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;std::string&gt; getLambdas() const override;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) override;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) override;</a>
+<a name="95"><span class="lineNum">      95 </span>            : };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(ECVumbrellasLine,&quot;ECV_UMBRELLAS_LINE&quot;)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         10 : void ECVumbrellasLine::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         10 :   ExpansionCVs::registerKeywords(keys);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         10 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;CV_MIN&quot;,&quot;the minimum of the CV range to be explored&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;CV_MAX&quot;,&quot;the maximum of the CV range to be explored&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;sigma of the umbrella Gaussians&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;SPACING&quot;,&quot;1&quot;,&quot;the distance between umbrellas, in units of SIGMA&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;,&quot;BARRIER&quot;,&quot;a guess of the free energy barrier to be overcome (better to stay higher than lower)&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         20 :   keys.addFlag(&quot;ADD_P0&quot;,false,&quot;add the unbiased Boltzmann distribution to the target distribution, to make sure to sample it&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         20 :   keys.addFlag(&quot;LOWER_HALF_ONLY&quot;,false,&quot;use only the lower half of each umbrella potentials&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         10 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 : ECVumbrellasLine::ECVumbrellasLine(const ActionOptions&amp;ao):</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   Action(ao),</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          8 :   ExpansionCVs(ao)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : {</a>
+<a name="116"><span class="lineNum">     116 </span>            : //set P0_contribution_</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          8 :   bool add_P0=false;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          8 :   parseFlag(&quot;ADD_P0&quot;,add_P0);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          8 :   if(add_P0)</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :     P0_contribution_=1;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   else</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          6 :     P0_contribution_=0;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : //set barrier_</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          8 :   barrier_=std::numeric_limits&lt;double&gt;::infinity();</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          8 :   parse(&quot;BARRIER&quot;,barrier_);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          8 :   parseFlag(&quot;LOWER_HALF_ONLY&quot;,lower_only_);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : //set umbrellas</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         16 :   parse(&quot;SIGMA&quot;,sigma_);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::vector&lt;double&gt; cv_min;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::vector&lt;double&gt; cv_max;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   parseVector(&quot;CV_MIN&quot;,cv_min);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         16 :   parseVector(&quot;CV_MAX&quot;,cv_max);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          8 :   plumed_massert(cv_min.size()==getNumberOfArguments(),&quot;wrong number of CV_MINs&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :   plumed_massert(cv_max.size()==getNumberOfArguments(),&quot;wrong number of CV_MAXs&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   double spacing;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          8 :   parse(&quot;SPACING&quot;,spacing);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   double length=0;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         18 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         10 :     length+=std::pow(cv_max[j]-cv_min[j],2);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          8 :   length=std::sqrt(length);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          8 :   unsigned sizeUmbrellas=1+std::round(length/(sigma_*spacing));</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          8 :   centers_.resize(getNumberOfArguments()); //centers_[cv][umbrellas]</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   unsigned full_period=0;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         18 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   {</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         10 :     centers_[j].resize(sizeUmbrellas);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         10 :     if(sizeUmbrellas&gt;1)</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        140 :       for(unsigned k=0; k&lt;sizeUmbrellas; k++)</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        130 :         centers_[j][k]=cv_min[j]+k*(cv_max[j]-cv_min[j])/(sizeUmbrellas-1);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :     else</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :       centers_[j][0]=(cv_min[j]+cv_max[j])/2.;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         10 :     if(getPntrToArgument(j)-&gt;isPeriodic())</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     {</a>
+<a name="156"><span class="lineNum">     156 </span>            :       double min,max;</a>
+<a name="157"><span class="lineNum">     157 </span>            :       std::string min_str,max_str;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         10 :       getPntrToArgument(j)-&gt;getDomain(min,max);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         10 :       getPntrToArgument(j)-&gt;getDomain(min_str,max_str);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         10 :       plumed_massert(cv_min[j]&gt;=min,&quot;ARG &quot;+std::to_string(j)+&quot;: CV_MIN cannot be smaller than the periodic bound &quot;+min_str);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         10 :       plumed_massert(cv_max[j]&lt;=max,&quot;ARG &quot;+std::to_string(j)+&quot;: CV_MAX cannot be greater than the periodic bound &quot;+max_str);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         10 :       if(cv_min[j]==min &amp;&amp; cv_max[j]==max)</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          6 :         full_period++;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     }</a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          8 :   if(full_period==getNumberOfArguments() &amp;&amp; sizeUmbrellas&gt;1) //first and last are the same point</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   {</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          6 :     sizeUmbrellas--;</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         12 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          6 :       centers_[j].pop_back();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : //set ECVs stuff</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          8 :   totNumECVs_=sizeUmbrellas+P0_contribution_;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          8 :   ECVs_.resize(getNumberOfArguments(),std::vector&lt;double&gt;(totNumECVs_));</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          8 :   derECVs_.resize(getNumberOfArguments(),std::vector&lt;double&gt;(totNumECVs_));</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : //printing some info</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          8 :   log.printf(&quot;  total number of umbrellas = %u\n&quot;,sizeUmbrellas);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          8 :   log.printf(&quot;    with SIGMA = %g\n&quot;,sigma_);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          8 :   log.printf(&quot;    and SPACING = %g\n&quot;,spacing);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          8 :   if(barrier_!=std::numeric_limits&lt;double&gt;::infinity())</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          2 :     log.printf(&quot;  guess for free energy BARRIER = %g\n&quot;,barrier_);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          8 :   if(P0_contribution_==1)</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          2 :     log.printf(&quot; -- ADD_P0: the target includes also the unbiased probability itself\n&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          8 :   if(lower_only_)</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          1 :     log.printf(&quot; -- LOWER_HALF_ONLY: the ECVs are set to zero for values of the CV above the respective center\n&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          8 : }</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        433 : void ECVumbrellasLine::calculateECVs(const double * cv)</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : {</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        433 :   if(lower_only_)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        153 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       2040 :       for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++) //if ADD_P0, the first ECVs=0</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :       {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1938 :         const unsigned kk=k-P0_contribution_;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1938 :         const double dist_jk=difference(j,centers_[j][kk],cv[j])/sigma_; //PBC might be present</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       1938 :         if(dist_jk&gt;=0)</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :         {</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        933 :           ECVs_[j][k]=0;</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        933 :           derECVs_[j][k]=0;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :         }</a>
+<a name="207"><span class="lineNum">     207 </span>            :         else</a>
+<a name="208"><span class="lineNum">     208 </span>            :         {</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1005 :           ECVs_[j][k]=0.5*std::pow(dist_jk,2);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       1005 :           derECVs_[j][k]=dist_jk/sigma_;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :         }</a>
+<a name="212"><span class="lineNum">     212 </span>            :       }</a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span>            :   else</a>
+<a name="216"><span class="lineNum">     216 </span>            :   {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        804 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       4678 :       for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++) //if ADD_P0, the first ECVs=0</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :       {</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       4256 :         const unsigned kk=k-P0_contribution_;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       4256 :         const double dist_jk=difference(j,centers_[j][kk],cv[j])/sigma_; //PBC might be present</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       4256 :         ECVs_[j][k]=0.5*std::pow(dist_jk,2);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       4256 :         derECVs_[j][k]=dist_jk/sigma_;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :       }</a>
+<a name="226"><span class="lineNum">     226 </span>            :     }</a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        433 : }</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         10 : const double * ECVumbrellasLine::getPntrToECVs(unsigned j)</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : {</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         10 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         10 :   plumed_massert(j&lt;getNumberOfArguments(),getName()+&quot; has fewer CVs&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         10 :   return &amp;ECVs_[j][0];</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         10 : const double * ECVumbrellasLine::getPntrToDerECVs(unsigned j)</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         10 :   plumed_massert(isReady_,&quot;cannot access ECVs before initialization&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         10 :   plumed_massert(j&lt;getNumberOfArguments(),getName()+&quot; has fewer CVs&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         10 :   return &amp;derECVs_[j][0];</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          8 : std::vector&lt;std::string&gt; ECVumbrellasLine::getLambdas() const</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : {</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          8 :   std::vector&lt;std::string&gt; lambdas(totNumECVs_);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          8 :   if(P0_contribution_==1)</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   {</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          2 :     std::ostringstream subs;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :     subs&lt;&lt;&quot;P0&quot;;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          4 :     for(unsigned j=1; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 :       subs&lt;&lt;&quot;_P0&quot;;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          2 :     lambdas[0]=subs.str();</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          2 :   }</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         94 :   for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++)</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   {</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         86 :     const unsigned kk=k-P0_contribution_;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         86 :     std::ostringstream subs;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         86 :     subs&lt;&lt;centers_[0][kk];</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        124 :     for(unsigned j=1; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         38 :       subs&lt;&lt;&quot;_&quot;&lt;&lt;centers_[j][kk];</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         86 :     lambdas[k]=subs.str();</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         86 :   }</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          8 :   return lambdas;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          8 : void ECVumbrellasLine::initECVs()</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          8 :   plumed_massert(!isReady_,&quot;initialization should not be called twice&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          8 :   isReady_=true;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          8 :   log.printf(&quot;  *%4u windows for %s\n&quot;,totNumECVs_,getName().c_str());</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          8 : }</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          5 : void ECVumbrellasLine::initECVs_observ(const std::vector&lt;double&gt;&amp; all_obs_cvs,const unsigned ncv,const unsigned index_j)</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : {</a>
+<a name="276"><span class="lineNum">     276 </span>            :   //this non-linear exansion never uses automatic initialization</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          5 :   initECVs();</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          5 :   calculateECVs(&amp;all_obs_cvs[index_j]); //use only first obs point</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         11 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         76 :     for(unsigned k=P0_contribution_; k&lt;totNumECVs_; k++)</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        123 :       ECVs_[j][k]=std::min(barrier_/kbt_,ECVs_[j][k]);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          5 : }</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          3 : void ECVumbrellasLine::initECVs_restart(const std::vector&lt;std::string&gt;&amp; lambdas)</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : {</a>
+<a name="286"><span class="lineNum">     286 </span>            :   std::size_t pos=0;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          4 :   for(unsigned j=0; j&lt;getNumberOfArguments()-1; j++)</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          1 :     pos=lambdas[0].find(&quot;_&quot;,pos+1); //checking only lambdas[0] is hopefully enough</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          3 :   plumed_massert(pos&lt;lambdas[0].length(),&quot;this should not happen, fewer '_' than expected in &quot;+getName());</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          3 :   pos=lambdas[0].find(&quot;_&quot;,pos+1);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          3 :   plumed_massert(pos&gt;lambdas[0].length(),&quot;this should not happen, more '_' than expected in &quot;+getName());</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          3 :   std::vector&lt;std::string&gt; myLambdas=getLambdas();</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          3 :   plumed_massert(myLambdas.size()==lambdas.size(),&quot;RESTART - mismatch in number of &quot;+getName());</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          3 :   plumed_massert(std::equal(myLambdas.begin(),myLambdas.end(),lambdas.begin()),&quot;RESTART - mismatch in lambda values of &quot;+getName());</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          3 :   initECVs();</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          3 : }</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : }</a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ExpansionCVs.cpp.func-sort-c.html b/coverage/opes/ExpansionCVs.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d09942282a
--- /dev/null
+++ b/coverage/opes/ExpansionCVs.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ExpansionCVs.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ExpansionCVs.cpp<span style="font-size: 80%;"> (<a href="ExpansionCVs.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExpansionCVs.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#35">_ZN4PLMD4opes12ExpansionCVsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#138">_ZNK4PLMD4opes12ExpansionCVs16estimateNumStepsEddRKSt6vectorIdSaIdEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#145">_ZZNK4PLMD4opes12ExpansionCVs16estimateNumStepsEddRKSt6vectorIdSaIdEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEENKUldS6_E_clEdS6_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#109">_ZNK4PLMD4opes12ExpansionCVs8getStepsEddjRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbd</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#98">_ZNK4PLMD4opes12ExpansionCVs10getIndex_kEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#35">_ZN4PLMD4opes12ExpansionCVsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#26">_ZN4PLMD4opes12ExpansionCVs16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#148">_ZZZNK4PLMD4opes12ExpansionCVs16estimateNumStepsEddRKSt6vectorIdSaIdEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEENKUldS6_E_clEdS6_ENKUldS6_E_clEdS6_</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#88">_ZN4PLMD4opes12ExpansionCVs5applyEv</a></td>
+              <td class="coverFnHi">1847</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#75">_ZN4PLMD4opes12ExpansionCVs9calculateEv</a></td>
+              <td class="coverFnHi">1847</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ExpansionCVs.cpp.func.html b/coverage/opes/ExpansionCVs.cpp.func.html
new file mode 100644
index 0000000000..6f2755f2ed
--- /dev/null
+++ b/coverage/opes/ExpansionCVs.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ExpansionCVs.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ExpansionCVs.cpp<span style="font-size: 80%;"> (<a href="ExpansionCVs.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExpansionCVs.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#26">_ZN4PLMD4opes12ExpansionCVs16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#88">_ZN4PLMD4opes12ExpansionCVs5applyEv</a></td>
+              <td class="coverFnHi">1847</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#75">_ZN4PLMD4opes12ExpansionCVs9calculateEv</a></td>
+              <td class="coverFnHi">1847</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#35">_ZN4PLMD4opes12ExpansionCVsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#35">_ZN4PLMD4opes12ExpansionCVsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#98">_ZNK4PLMD4opes12ExpansionCVs10getIndex_kEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#138">_ZNK4PLMD4opes12ExpansionCVs16estimateNumStepsEddRKSt6vectorIdSaIdEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#109">_ZNK4PLMD4opes12ExpansionCVs8getStepsEddjRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEbd</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#145">_ZZNK4PLMD4opes12ExpansionCVs16estimateNumStepsEddRKSt6vectorIdSaIdEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEENKUldS6_E_clEdS6_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.cpp.gcov.html#148">_ZZZNK4PLMD4opes12ExpansionCVs16estimateNumStepsEddRKSt6vectorIdSaIdEERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEENKUldS6_E_clEdS6_ENKUldS6_E_clEdS6_</a></td>
+              <td class="coverFnHi">109</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ExpansionCVs.cpp.gcov.html b/coverage/opes/ExpansionCVs.cpp.gcov.html
new file mode 100644
index 0000000000..60c219aa6a
--- /dev/null
+++ b/coverage/opes/ExpansionCVs.cpp.gcov.html
@@ -0,0 +1,309 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ExpansionCVs.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ExpansionCVs.cpp<span style="font-size: 80%;"> (source / <a href="ExpansionCVs.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : </a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace opes {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         49 : void ExpansionCVs::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="29"><span class="lineNum">      29 </span>            : {</a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         49 :   Action::registerKeywords(keys);</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         49 :   ActionWithValue::registerKeywords(keys);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         49 :   ActionWithArguments::registerKeywords(keys);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         49 :   ActionWithValue::useCustomisableComponents(keys);</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         98 :   keys.add(&quot;compulsory&quot;,&quot;TEMP&quot;,&quot;-1&quot;,&quot;temperature. If not specified tries to get it from MD engine&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         49 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         37 : ExpansionCVs::ExpansionCVs(const ActionOptions&amp;ao)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   : Action(ao)</a>
+<a name="39"><span class="lineNum">      39 </span>            :   , ActionWithValue(ao)</a>
+<a name="40"><span class="lineNum">      40 </span>            :   , ActionWithArguments(ao)</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         37 :   , isReady_(false)</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         37 :   , totNumECVs_(0)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span>            : //set kbt_</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         37 :   const double kB=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         37 :   kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         37 :   double temp=-1;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         37 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         37 :   if(temp&gt;0)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         37 :     if(kbt_&gt;0 &amp;&amp; std::abs(kbt_-kB*temp)&gt;1e-4)</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :       log.printf(&quot; +++ WARNING +++ using TEMP=%g while MD engine uses %g\n&quot;,temp,kbt_/kB);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         37 :     kbt_=kB*temp;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   }</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         37 :   plumed_massert(kbt_&gt;0,&quot;your MD engine does not pass the temperature to plumed, you must specify it using TEMP&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         37 :   log.printf(&quot;  temperature = %g, beta = %g\n&quot;,kbt_/kB,1./kbt_);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : //set components</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         37 :   plumed_massert( getNumberOfArguments()!=0, &quot;you must specify the underlying CV&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         90 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   {</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         53 :     std::string name_j=getPntrToArgument(j)-&gt;getName();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         53 :     ActionWithValue::addComponentWithDerivatives(name_j);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         53 :     getPntrToComponent(j)-&gt;resizeDerivatives(1);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         53 :     if(getPntrToArgument(j)-&gt;isPeriodic()) //it should not be necessary, but why not</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :     {</a>
+<a name="67"><span class="lineNum">      67 </span>            :       std::string min,max;</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         17 :       getPntrToArgument(j)-&gt;getDomain(min,max);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         17 :       getPntrToComponent(j)-&gt;setDomain(min,max);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :     }</a>
+<a name="71"><span class="lineNum">      71 </span>            :     else</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         36 :       getPntrToComponent(j)-&gt;setNotPeriodic();</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   }</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         37 :   plumed_massert((int)getNumberOfArguments()==getNumberOfComponents(),&quot;Expansion CVs have same number of arguments and components&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         37 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1847 : void ExpansionCVs::calculate()</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       1847 :   std::vector&lt;double&gt; args(getNumberOfArguments());</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       4470 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       2623 :     args[j]=getArgument(j);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       2623 :     getPntrToComponent(j)-&gt;set(args[j]); //components are equal to arguments</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       2623 :     getPntrToComponent(j)-&gt;addDerivative(0,1.); //the derivative of the identity is 1</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   }</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1847 :   if(isReady_)</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1417 :     calculateECVs(&amp;args[0]);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1847 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1847 : void ExpansionCVs::apply()</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : {</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       4470 :   for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       2623 :     std::vector&lt;double&gt; force_j(1);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       2623 :     if(getPntrToComponent(j)-&gt;applyForce(force_j)) //a bias is applied?</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       2623 :       getPntrToArgument(j)-&gt;addForce(force_j[0]); //just tell it to the CV!</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1847 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         26 : std::vector&lt; std::vector&lt;unsigned&gt; &gt; ExpansionCVs::getIndex_k() const</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         26 :   plumed_massert(isReady_ &amp;&amp; totNumECVs_&gt;0,&quot;cannot access getIndex_k() of ECV before initialization&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         26 :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; index_k(totNumECVs_,std::vector&lt;unsigned&gt;(getNumberOfArguments()));</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        869 :   for(unsigned k=0; k&lt;totNumECVs_; k++)</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       2391 :     for(unsigned j=0; j&lt;getNumberOfArguments(); j++)</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1548 :       index_k[k][j]=k; //each CV gives rise to the same number of ECVs</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         26 :   return index_k;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : //following methods are meant to be used only in case of linear expansions</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         24 : std::vector&lt;double&gt; ExpansionCVs::getSteps(double lambda_min,double lambda_max,const unsigned lambda_steps,const std::string&amp; msg,const bool geom_spacing, const double shift) const</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : {</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         24 :   plumed_massert(!(lambda_min==lambda_max &amp;&amp; lambda_steps&gt;1),&quot;cannot have multiple &quot;+msg+&quot;_STEPS if &quot;+msg+&quot;_MIN==&quot;+msg+&quot;_MAX&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         24 :   std::vector&lt;double&gt; lambda(lambda_steps);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         24 :   if(lambda_steps==1)</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :     lambda[0]=(lambda_min+lambda_max)/2.;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ using one single %s as target = %g\n&quot;,msg.c_str(),lambda[0]);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   }</a>
+<a name="120"><span class="lineNum">     120 </span>            :   else</a>
+<a name="121"><span class="lineNum">     121 </span>            :   {</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         24 :     if(geom_spacing) //geometric spacing</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     { //this way lambda[k]/lambda[k+1] is constant</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         14 :       lambda_min+=shift;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         14 :       lambda_max+=shift;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         14 :       plumed_massert(lambda_min&gt;0,&quot;cannot use GEOM_SPACING when %s_MIN is not greater than zero&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         14 :       plumed_massert(lambda_max&gt;0,&quot;cannot use GEOM_SPACING when %s_MAX is not greater than zero&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         14 :       const double log_lambda_min=std::log(lambda_min);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         14 :       const double log_lambda_max=std::log(lambda_max);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        196 :       for(unsigned k=0; k&lt;lambda.size(); k++)</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        182 :         lambda[k]=std::exp(log_lambda_min+k*(log_lambda_max-log_lambda_min)/(lambda_steps-1))-shift;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     }</a>
+<a name="133"><span class="lineNum">     133 </span>            :     else //linear spacing</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        108 :       for(unsigned k=0; k&lt;lambda.size(); k++)</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         98 :         lambda[k]=lambda_min+k*(lambda_max-lambda_min)/(lambda_steps-1);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         24 :   return lambda;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          6 : unsigned ExpansionCVs::estimateNumSteps(const double left_side,const double right_side,const std::vector&lt;double&gt;&amp; obs,const std::string&amp; msg) const</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : { //for linear expansions only, it uses effective sample size (Neff) to estimate the grid spacing</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          6 :   if(left_side==0 &amp;&amp; right_side==0)</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ %s_MIN and %s_MAX are equal to %s, using single step\n&quot;,msg.c_str(),msg.c_str(),msg.c_str());</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     return 1;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :   auto get_neff_HWHM=[](const double side,const std::vector&lt;double&gt;&amp; obs) //HWHM = half width at half maximum. neff is in general not symmetric</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   {</a>
+<a name="149"><span class="lineNum">     149 </span>            :     //func: Neff/N-0.5 is a function between -0.5 and 0.5</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        109 :     auto func=[](const double delta,const std::vector&lt;double&gt;&amp; obs)</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     {</a>
+<a name="152"><span class="lineNum">     152 </span>            :       double sum_w=0;</a>
+<a name="153"><span class="lineNum">     153 </span>            :       double sum_w2=0;</a>
+<a name="154"><span class="lineNum">     154 </span>            :       //we could avoid recomputing safe_shift every time, but here speed is not a concern</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        218 :       const double safe_shift=delta&lt;0?*std::max_element(obs.begin(),obs.end()):*std::min_element(obs.begin(),obs.end());</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        899 :       for(unsigned t=0; t&lt;obs.size(); t++)</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       {</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        790 :         const double w=std::exp(-delta*(obs[t]-safe_shift)); //robust to overflow</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        790 :         sum_w+=w;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        790 :         sum_w2+=w*w;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :       }</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        109 :       return sum_w*sum_w/sum_w2/obs.size()-0.5;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :     };</a>
+<a name="164"><span class="lineNum">     164 </span>            :     //here we find the root of func using the regula falsi (false position) method</a>
+<a name="165"><span class="lineNum">     165 </span>            :     //but any method would be OK, not much precision is needed. src/tools/RootFindingBase.h looked complicated</a>
+<a name="166"><span class="lineNum">     166 </span>            :     const double tolerance=1e-4; //seems to be a good default</a>
+<a name="167"><span class="lineNum">     167 </span>            :     double a=0; //default is right side case</a>
+<a name="168"><span class="lineNum">     168 </span>            :     double func_a=0.5;</a>
+<a name="169"><span class="lineNum">     169 </span>            :     double b=side;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          9 :     double func_b=func(side,obs);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          9 :     if(func_b&gt;=0)</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :       return 0.0; //no zero is present!</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 :     if(b&lt;0) //left side case</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :     {</a>
+<a name="175"><span class="lineNum">     175 </span>            :       std::swap(a,b);</a>
+<a name="176"><span class="lineNum">     176 </span>            :       std::swap(func_a,func_b);</a>
+<a name="177"><span class="lineNum">     177 </span>            :     }</a>
+<a name="178"><span class="lineNum">     178 </span>            :     double c=a;</a>
+<a name="179"><span class="lineNum">     179 </span>            :     double func_c=func_a;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        109 :     while(std::abs(func_c)&gt;tolerance)</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        100 :       if(func_a*func_c&gt;0)</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :       {</a>
+<a name="184"><span class="lineNum">     184 </span>            :         a=c;</a>
+<a name="185"><span class="lineNum">     185 </span>            :         func_a=func_c;</a>
+<a name="186"><span class="lineNum">     186 </span>            :       }</a>
+<a name="187"><span class="lineNum">     187 </span>            :       else</a>
+<a name="188"><span class="lineNum">     188 </span>            :       {</a>
+<a name="189"><span class="lineNum">     189 </span>            :         b=c;</a>
+<a name="190"><span class="lineNum">     190 </span>            :         func_b=func_c;</a>
+<a name="191"><span class="lineNum">     191 </span>            :       }</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        100 :       c=(a*func_b-b*func_a)/(func_b-func_a);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        100 :       func_c=func(c,obs); //func is evaluated only here, it might be expensive</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          9 :     return std::abs(c);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   };</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : //estimation</a>
+<a name="199"><span class="lineNum">     199 </span>            :   double left_HWHM=0;</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          6 :   if(left_side!=0)</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          4 :     left_HWHM=get_neff_HWHM(left_side,obs);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   double right_HWHM=0;</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          6 :   if(right_side!=0)</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          5 :     right_HWHM=get_neff_HWHM(right_side,obs);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          6 :   if(left_HWHM==0)</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   {</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          2 :     right_HWHM*=2;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          2 :     if(left_side==0)</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          2 :       log.printf(&quot; --- %s_MIN is equal to %s\n&quot;,msg.c_str(),msg.c_str());</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     else</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :       log.printf(&quot; +++ WARNING +++ %s_MIN is very close to %s\n&quot;,msg.c_str(),msg.c_str());</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          6 :   if(right_HWHM==0)</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   {</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          1 :     left_HWHM*=2;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          1 :     if(right_side==0)</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          1 :       log.printf(&quot; --- %s_MAX is equal to %s\n&quot;,msg.c_str(),msg.c_str());</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     else</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :       log.printf(&quot; +++ WARNING +++ %s_MAX is very close to %s\n&quot;,msg.c_str(),msg.c_str());</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          6 :   const double grid_spacing=left_HWHM+right_HWHM;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          6 :   log.printf(&quot;   estimated %s spacing = %g\n&quot;,msg.c_str(),grid_spacing);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          6 :   unsigned steps=std::ceil(std::abs(right_side-left_side)/grid_spacing);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          6 :   if(steps&lt;2 || grid_spacing==0)</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   {</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ %s range is very narrow, using %s_MIN and %s_MAX as only steps\n&quot;,msg.c_str(),msg.c_str(),msg.c_str());</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     steps=2;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   return steps;</a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ExpansionCVs.h.func-sort-c.html b/coverage/opes/ExpansionCVs.h.func-sort-c.html
new file mode 100644
index 0000000000..1ea399cf3e
--- /dev/null
+++ b/coverage/opes/ExpansionCVs.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ExpansionCVs.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ExpansionCVs.h<span style="font-size: 80%;"> (<a href="ExpansionCVs.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ExpansionCVs.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.h.gcov.html#48">_ZN4PLMD4opes12ExpansionCVsD2Ev</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.h.gcov.html#55">_ZNK4PLMD4opes12ExpansionCVs13getTotNumECVsEv</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.h.gcov.html#52">_ZN4PLMD4opes12ExpansionCVs22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">170</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ExpansionCVs.h.func.html b/coverage/opes/ExpansionCVs.h.func.html
new file mode 100644
index 0000000000..118af19f09
--- /dev/null
+++ b/coverage/opes/ExpansionCVs.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ExpansionCVs.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ExpansionCVs.h<span style="font-size: 80%;"> (<a href="ExpansionCVs.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ExpansionCVs.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.h.gcov.html#52">_ZN4PLMD4opes12ExpansionCVs22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">170</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.h.gcov.html#48">_ZN4PLMD4opes12ExpansionCVsD2Ev</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ExpansionCVs.h.gcov.html#55">_ZNK4PLMD4opes12ExpansionCVs13getTotNumECVsEv</a></td>
+              <td class="coverFnHi">50</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/ExpansionCVs.h.gcov.html b/coverage/opes/ExpansionCVs.h.gcov.html
new file mode 100644
index 0000000000..ad46d8e2ec
--- /dev/null
+++ b/coverage/opes/ExpansionCVs.h.gcov.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/ExpansionCVs.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - ExpansionCVs.h<span style="font-size: 80%;"> (source / <a href="ExpansionCVs.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #ifndef __PLUMED_opes_ExpansionCVs_h</a>
+<a name="20"><span class="lineNum">      20 </span>            : #define __PLUMED_opes_ExpansionCVs_h</a>
+<a name="21"><span class="lineNum">      21 </span>            : </a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace opes {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : /*</a>
+<a name="29"><span class="lineNum">      29 </span>            : \ingroup INHERIT</a>
+<a name="30"><span class="lineNum">      30 </span>            : This is the abstract base class to use for implementing expansion CVs (ECVs).</a>
+<a name="31"><span class="lineNum">      31 </span>            : ECVs should be used together with the OPESexpanded action.</a>
+<a name="32"><span class="lineNum">      32 </span>            : They take as argument regular CVs, and output them as components without modification.</a>
+<a name="33"><span class="lineNum">      33 </span>            : */</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class ExpansionCVs:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   public ActionWithValue,</a>
+<a name="37"><span class="lineNum">      37 </span>            :   public ActionWithArguments</a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span>            : protected:</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool isReady_; //true only after initECVs</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double kbt_;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   unsigned totNumECVs_;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //methods useful for linear expansions</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;double&gt; getSteps(double,double,const unsigned,const std::string&amp;,const bool,const double) const;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   unsigned estimateNumSteps(const double,const double,const std::vector&lt;double&gt;&amp;,const std::string&amp;) const;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : public:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   explicit ExpansionCVs(const ActionOptions&amp;);</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         37 :   virtual ~ExpansionCVs() {};</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   void apply() override;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   void calculate() override;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        170 :   inline unsigned getNumberOfDerivatives() override {return 1;};</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         67 :   inline double getKbT() const {return kbt_;};</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         50 :   inline unsigned getTotNumECVs() const {plumed_massert(isReady_,&quot;cannot ask for totNumECVs before ECV isReady&quot;); return totNumECVs_;};</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   virtual std::vector&lt; std::vector&lt;unsigned&gt; &gt; getIndex_k() const; //might need to override this</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            :   virtual void calculateECVs(const double *) = 0;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   virtual const double * getPntrToECVs(unsigned) = 0;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   virtual const double * getPntrToDerECVs(unsigned) = 0;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   virtual std::vector&lt;std::string&gt; getLambdas() const = 0;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   virtual void initECVs_observ(const std::vector&lt;double&gt;&amp;,const unsigned,const unsigned) = 0; //arg: all the observed CVs, the total numer of CVs, the first CV index referring to this ECV</a>
+<a name="65"><span class="lineNum">      65 </span>            :   virtual void initECVs_restart(const std::vector&lt;std::string&gt;&amp;) = 0; //arg: the lambdas read from DeltaF_name relative to this ECV</a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : #endif</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/OPESexpanded.cpp.func-sort-c.html b/coverage/opes/OPESexpanded.cpp.func-sort-c.html
new file mode 100644
index 0000000000..535c58e48f
--- /dev/null
+++ b/coverage/opes/OPESexpanded.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/OPESexpanded.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - OPESexpanded.cpp<span style="font-size: 80%;"> (<a href="OPESexpanded.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">431</td>
+            <td class="headerCovTableEntry">443</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OPESexpanded.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#207">_ZN4PLMD4opes12OPESexpandedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#870">_ZN4PLMD4opes12OPESexpanded15dumpStateToFileEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#784">_ZN4PLMD4opes12OPESexpanded12init_fromObsEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#724">_ZN4PLMD4opes12OPESexpanded13init_linkECVsEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#689">_ZN4PLMD4opes12OPESexpanded20init_pntrToECVsClassEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#207">_ZN4PLMD4opes12OPESexpandedC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#177">_ZN4PLMD4opes12_GLOBAL__N_125OPESexpandedRegisterMe1796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#179">_ZN4PLMD4opes12OPESexpanded16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#852">_ZN4PLMD4opes12OPESexpanded11printDeltaFEv</a></td>
+              <td class="coverFnHi">64</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#354">_ZZN4PLMD4opes12OPESexpandedC4ERKNS_13ActionOptionsEENKUlRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjjE_clESC_jj</a></td>
+              <td class="coverFnHi">525</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#908">_ZN4PLMD4opes12OPESexpanded12updateDeltaFEd</a></td>
+              <td class="coverFnHi">660</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#589">_ZN4PLMD4opes12OPESexpanded6updateEv</a></td>
+              <td class="coverFnHi">1490</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#523">_ZN4PLMD4opes12OPESexpanded9calculateEv</a></td>
+              <td class="coverFnHi">1490</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#177">_ZN4PLMD4opes12_GLOBAL__N_125OPESexpandedRegisterMe179C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#177">_ZN4PLMD4opes12_GLOBAL__N_125OPESexpandedRegisterMe179D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#933">_ZNK4PLMD4opes12OPESexpanded12getExpansionEj</a></td>
+              <td class="coverFnHi">644469</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/OPESexpanded.cpp.func.html b/coverage/opes/OPESexpanded.cpp.func.html
new file mode 100644
index 0000000000..a01378a8bd
--- /dev/null
+++ b/coverage/opes/OPESexpanded.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/OPESexpanded.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - OPESexpanded.cpp<span style="font-size: 80%;"> (<a href="OPESexpanded.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">431</td>
+            <td class="headerCovTableEntry">443</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OPESexpanded.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#852">_ZN4PLMD4opes12OPESexpanded11printDeltaFEv</a></td>
+              <td class="coverFnHi">64</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#784">_ZN4PLMD4opes12OPESexpanded12init_fromObsEv</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#908">_ZN4PLMD4opes12OPESexpanded12updateDeltaFEd</a></td>
+              <td class="coverFnHi">660</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#724">_ZN4PLMD4opes12OPESexpanded13init_linkECVsEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#870">_ZN4PLMD4opes12OPESexpanded15dumpStateToFileEv</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#179">_ZN4PLMD4opes12OPESexpanded16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#689">_ZN4PLMD4opes12OPESexpanded20init_pntrToECVsClassEv</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#589">_ZN4PLMD4opes12OPESexpanded6updateEv</a></td>
+              <td class="coverFnHi">1490</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#523">_ZN4PLMD4opes12OPESexpanded9calculateEv</a></td>
+              <td class="coverFnHi">1490</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#207">_ZN4PLMD4opes12OPESexpandedC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#207">_ZN4PLMD4opes12OPESexpandedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#177">_ZN4PLMD4opes12_GLOBAL__N_125OPESexpandedRegisterMe1796createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#177">_ZN4PLMD4opes12_GLOBAL__N_125OPESexpandedRegisterMe179C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#177">_ZN4PLMD4opes12_GLOBAL__N_125OPESexpandedRegisterMe179D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#933">_ZNK4PLMD4opes12OPESexpanded12getExpansionEj</a></td>
+              <td class="coverFnHi">644469</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESexpanded.cpp.gcov.html#354">_ZZN4PLMD4opes12OPESexpandedC4ERKNS_13ActionOptionsEENKUlRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEjjE_clESC_jj</a></td>
+              <td class="coverFnHi">525</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/OPESexpanded.cpp.gcov.html b/coverage/opes/OPESexpanded.cpp.gcov.html
new file mode 100644
index 0000000000..b33a61232c
--- /dev/null
+++ b/coverage/opes/OPESexpanded.cpp.gcov.html
@@ -0,0 +1,1020 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/OPESexpanded.cpp</title>
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - OPESexpanded.cpp<span style="font-size: 80%;"> (source / <a href="OPESexpanded.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">431</td>
+            <td class="headerCovTableEntry">443</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ExpansionCVs.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace opes {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC OPES_BIAS OPES_EXPANDED</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : On-the-fly probability enhanced sampling with expanded ensembles for the target distribution.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This method is similar to the OPES method (\ref OPES &quot;OPES&quot;) with expanded ensembles target distribution (replica-exchange-like) \cite Invernizzi2020unified.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : An expanded ensemble is obtained by summing a set of ensembles at slightly different termodynamic conditions, or with slightly different Hamiltonians.</a>
+<a name="39"><span class="lineNum">      39 </span>            : Such ensembles can be sampled via methods like replica exchange, or this \ref OPES_EXPANDED bias action.</a>
+<a name="40"><span class="lineNum">      40 </span>            : A typical example is a multicanonical simulation, in which a whole range of temperatures is sampled instead of a single one.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : In oreder to define an expanded target ensemble we use \ref EXPANSION_CV &quot;expansion collective variables&quot; (ECVs), \f$\Delta u_\lambda(\mathbf{x})\f$.</a>
+<a name="43"><span class="lineNum">      43 </span>            : The bias at step \f$n\f$ is</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f[</a>
+<a name="45"><span class="lineNum">      45 </span>            :   V_n(\mathbf{x})=-\frac{1}{\beta}\log \left(\frac{1}{N_{\{\lambda\}}}\sum_\lambda e^{-\Delta u_\lambda(\mathbf{x})+\beta\Delta F_n(\lambda)}\right)\, .</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : See Ref.\cite Invernizzi2020unified for more details on the method.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Notice that the estimates in the DELTAFS file are expressed in energy units, and should be multiplied by \f$\beta\f$ to be dimensionless as in Ref.\cite Invernizzi2020unified.</a>
+<a name="50"><span class="lineNum">      50 </span>            : The DELTAFS file also contains an estimate of \f$c(t)=\frac{1}{\beta} \log \langle e^{\beta V}\rangle\f$.</a>
+<a name="51"><span class="lineNum">      51 </span>            : Similarly to \ref OPES_METAD, it is printed only for reference, since \f$c(t)\f$ reaches a fixed value as the bias converges, and should NOT be used for reweighting.</a>
+<a name="52"><span class="lineNum">      52 </span>            : Its value is also needed for restarting a simulation.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : You can store the instantaneous \f$\Delta F_n(\lambda)\f$ estimates also in a more readable format using STATE_WFILE and STATE_WSTRIDE.</a>
+<a name="55"><span class="lineNum">      55 </span>            : Restart can be done either from a DELTAFS file or from a STATE_RFILE, it is equivalent.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : Contrary to \ref OPES_METAD, \ref OPES_EXPANDED does not use kernel density estimation.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \par Examples</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : # simulate multiple temperatures, as in parallel tempering</a>
+<a name="63"><span class="lineNum">      63 </span>            : ene: ENERGY</a>
+<a name="64"><span class="lineNum">      64 </span>            : ecv: ECV_MULTITHERMAL ARG=ene TEMP_MAX=1000</a>
+<a name="65"><span class="lineNum">      65 </span>            : opes: OPES_EXPANDED ARG=ecv.* PACE=500</a>
+<a name="66"><span class="lineNum">      66 </span>            : PRINT FILE=COLVAR STRIDE=500 ARG=ene,opes.bias</a>
+<a name="67"><span class="lineNum">      67 </span>            : \endplumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : You can easily combine multiple ECVs.</a>
+<a name="70"><span class="lineNum">      70 </span>            : The \ref OPES_EXPANDED bias will create a multidimensional target grid to sample all the combinations.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : # simulate multiple temperatures while biasing a CV</a>
+<a name="74"><span class="lineNum">      74 </span>            : ene: ENERGY</a>
+<a name="75"><span class="lineNum">      75 </span>            : dst: DISTANCE ATOMS=1,2</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : ecv1: ECV_MULTITHERMAL ARG=ene TEMP_SET_ALL=200,300,500,1000</a>
+<a name="78"><span class="lineNum">      78 </span>            : ecv2: ECV_UMBRELLAS_LINE ARG=dst CV_MIN=1.2 CV_MAX=4.3 SIGMA=0.5</a>
+<a name="79"><span class="lineNum">      79 </span>            : opes: OPES_EXPANDED ARG=ecv1.*,ecv2.* PACE=500 OBSERVATION_STEPS=1</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : PRINT FILE=COLVAR STRIDE=500 ARG=ene,dst,opes.bias</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endplumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : If an ECV is based on more than one CV you must provide all the output component, in the proper order.</a>
+<a name="85"><span class="lineNum">      85 </span>            : You can use \ref Regex for that, like in the following example.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : \plumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : # simulate multiple temperatures and pressures while biasing a two-CVs linear path</a>
+<a name="89"><span class="lineNum">      89 </span>            : ene: ENERGY</a>
+<a name="90"><span class="lineNum">      90 </span>            : vol: VOLUME</a>
+<a name="91"><span class="lineNum">      91 </span>            : ecv_mtp: ECV_MULTITHERMAL_MULTIBARIC ...</a>
+<a name="92"><span class="lineNum">      92 </span>            :   ARG=ene,vol</a>
+<a name="93"><span class="lineNum">      93 </span>            :   TEMP=300</a>
+<a name="94"><span class="lineNum">      94 </span>            :   TEMP_MIN=200</a>
+<a name="95"><span class="lineNum">      95 </span>            :   TEMP_MAX=800</a>
+<a name="96"><span class="lineNum">      96 </span>            :   PRESSURE=0.06022140857*1000 #1 kbar</a>
+<a name="97"><span class="lineNum">      97 </span>            :   PRESSURE_MIN=0</a>
+<a name="98"><span class="lineNum">      98 </span>            :   PRESSURE_MAX=0.06022140857*2000 #2 kbar</a>
+<a name="99"><span class="lineNum">      99 </span>            : ...</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : cv1: DISTANCE ATOMS=1,2</a>
+<a name="102"><span class="lineNum">     102 </span>            : cv2: DISTANCE ATOMS=3,4</a>
+<a name="103"><span class="lineNum">     103 </span>            : ecv_umb: ECV_UMBRELLAS_LINE ARG=cv1,cv2 TEMP=300 CV_MIN=0.1,0.1 CV_MAX=1.5,1.5 SIGMA=0.2 BARRIER=70</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : opes: OPES_EXPANDED ARG=(ecv_.*) PACE=500 WALKERS_MPI PRINT_STRIDE=1000</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : PRINT FILE=COLVAR STRIDE=500 ARG=ene,vol,cv1,cv2,opes.bias</a>
+<a name="108"><span class="lineNum">     108 </span>            : \endplumedfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : */</a>
+<a name="112"><span class="lineNum">     112 </span>            : //+ENDPLUMEDOC</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : class OPESexpanded : public bias::Bias {</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : private:</a>
+<a name="117"><span class="lineNum">     117 </span>            :   bool isFirstStep_;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   unsigned NumOMP_;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   unsigned NumParallel_;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   unsigned rank_;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   unsigned NumWalkers_;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   unsigned walker_rank_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   unsigned long long counter_;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::size_t ncv_;</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   std::vector&lt;const double *&gt; ECVs_;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   std::vector&lt;const double *&gt; derECVs_;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   std::vector&lt;opes::ExpansionCVs*&gt; pntrToECVsClass_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; index_k_;</a>
+<a name="130"><span class="lineNum">     130 </span>            : // A note on indexes usage:</a>
+<a name="131"><span class="lineNum">     131 </span>            : //  j -&gt; underlying CVs</a>
+<a name="132"><span class="lineNum">     132 </span>            : //  i -&gt; DeltaFs</a>
+<a name="133"><span class="lineNum">     133 </span>            : //  k -&gt; single ECVs, which might not be trivially numbered</a>
+<a name="134"><span class="lineNum">     134 </span>            : //  l -&gt; groups of ECVs, pntrToECVsClass</a>
+<a name="135"><span class="lineNum">     135 </span>            : //  h -&gt; subgroups of ECVs, arguments in ECVsClass</a>
+<a name="136"><span class="lineNum">     136 </span>            : //  w -&gt; walkers</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   double kbt_;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   unsigned stride_;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   unsigned deltaF_size_; //different from deltaF_.size() if NumParallel_&gt;1</a>
+<a name="141"><span class="lineNum">     141 </span>            :   std::vector&lt;double&gt; deltaF_;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::vector&lt;double&gt; diff_;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   double rct_;</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::vector&lt;double&gt; all_deltaF_;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   std::vector&lt;int&gt; all_size_;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;int&gt; disp_;</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   unsigned obs_steps_;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   std::vector&lt;double&gt; obs_cvs_;</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   bool calc_work_;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   double work_;</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   unsigned print_stride_;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   OFile deltaFsOfile_;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;std::string&gt; deltaF_name_;</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   OFile stateOfile_;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   int wStateStride_;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   bool storeOldStates_;</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   void init_pntrToECVsClass();</a>
+<a name="164"><span class="lineNum">     164 </span>            :   void init_linkECVs();</a>
+<a name="165"><span class="lineNum">     165 </span>            :   void init_fromObs();</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            :   void printDeltaF();</a>
+<a name="168"><span class="lineNum">     168 </span>            :   void dumpStateToFile();</a>
+<a name="169"><span class="lineNum">     169 </span>            :   void updateDeltaF(double);</a>
+<a name="170"><span class="lineNum">     170 </span>            :   double getExpansion(const unsigned) const;</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : public:</a>
+<a name="173"><span class="lineNum">     173 </span>            :   explicit OPESexpanded(const ActionOptions&amp;);</a>
+<a name="174"><span class="lineNum">     174 </span>            :   void calculate() override;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void update() override;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="177"><span class="lineNum">     177 </span>            : };</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      12564 : PLUMED_REGISTER_ACTION(OPESexpanded,&quot;OPES_EXPANDED&quot;)</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         32 : void OPESexpanded::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : {</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         32 :   Bias::registerKeywords(keys);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         32 :   keys.remove(&quot;ARG&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;ARG&quot;,&quot;the label of the ECVs that define the expansion. You can use an * to make sure all the output components of the ECVs are used, as in the examples above&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;PACE&quot;,&quot;how often the bias is updated&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;OBSERVATION_STEPS&quot;,&quot;100&quot;,&quot;number of unbiased initial PACE steps to collect statistics for initialization&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : //DeltaFs and state files</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;DELTAFS&quot;,&quot;a file with the estimate of the relative Delta F for each component of the target and of the global c(t)&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         64 :   keys.add(&quot;compulsory&quot;,&quot;PRINT_STRIDE&quot;,&quot;100&quot;,&quot;stride for printing to DELTAFS file, in units of PACE&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         64 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;specify format for DELTAFS file&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         64 :   keys.add(&quot;optional&quot;,&quot;STATE_RFILE&quot;,&quot;read from this file the Delta F estimates and all the info needed to RESTART the simulation&quot;);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         64 :   keys.add(&quot;optional&quot;,&quot;STATE_WFILE&quot;,&quot;write to this file the Delta F estimates and all the info needed to RESTART the simulation&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         64 :   keys.add(&quot;optional&quot;,&quot;STATE_WSTRIDE&quot;,&quot;number of MD steps between writing the STATE_WFILE. Default is only on CPT events (but not all MD codes set them)&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         64 :   keys.addFlag(&quot;STORE_STATES&quot;,false,&quot;append to STATE_WFILE instead of ovewriting it each time&quot;);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : //miscellaneous</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         64 :   keys.addFlag(&quot;CALC_WORK&quot;,false,&quot;calculate the total accumulated work done by the bias since last restart&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         64 :   keys.addFlag(&quot;WALKERS_MPI&quot;,false,&quot;switch on MPI version of multiple walkers&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         64 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;perform calculations in serial&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         32 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         32 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         32 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : //output components</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         32 :   componentsAreNotOptional(keys);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         64 :   keys.addOutputComponent(&quot;work&quot;,&quot;CALC_WORK&quot;,&quot;total accumulated work done by the bias&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         32 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         30 : OPESexpanded::OPESexpanded(const ActionOptions&amp;ao)</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   : PLUMED_BIAS_INIT(ao)</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         30 :   , isFirstStep_(true)</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         30 :   , counter_(0)</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         30 :   , ncv_(getNumberOfArguments())</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         30 :   , deltaF_size_(0)</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         30 :   , rct_(0)</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         30 :   , work_(0)</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : {</a>
+<a name="218"><span class="lineNum">     218 </span>            : //set pace</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         30 :   parse(&quot;PACE&quot;,stride_);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         30 :   parse(&quot;OBSERVATION_STEPS&quot;,obs_steps_);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         30 :   plumed_massert(obs_steps_!=0,&quot;minimum is OBSERVATION_STEPS=1&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         30 :   obs_cvs_.resize(obs_steps_*ncv_);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : //deltaFs file</a>
+<a name="225"><span class="lineNum">     225 </span>            :   std::string deltaFsFileName;</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         30 :   parse(&quot;FILE&quot;,deltaFsFileName);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         60 :   parse(&quot;PRINT_STRIDE&quot;,print_stride_);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   std::string fmt;</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         60 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : //output checkpoint of current state</a>
+<a name="231"><span class="lineNum">     231 </span>            :   std::string restartFileName;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         60 :   parse(&quot;STATE_RFILE&quot;,restartFileName);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   std::string stateFileName;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         30 :   parse(&quot;STATE_WFILE&quot;,stateFileName);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         30 :   wStateStride_=0;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         30 :   parse(&quot;STATE_WSTRIDE&quot;,wStateStride_);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         30 :   storeOldStates_=false;</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         30 :   parseFlag(&quot;STORE_STATES&quot;,storeOldStates_);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         30 :   if(wStateStride_!=0 || storeOldStates_)</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          5 :     plumed_massert(stateFileName.length()&gt;0,&quot;filename for storing simulation status not specified, use STATE_WFILE&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         30 :   if(wStateStride_&gt;0)</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          5 :     plumed_massert(wStateStride_&gt;=(int)stride_,&quot;STATE_WSTRIDE is in units of MD steps, thus should be a multiple of PACE&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         30 :   if(stateFileName.length()&gt;0 &amp;&amp; wStateStride_==0)</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          1 :     wStateStride_=-1;//will print only on CPT events (checkpoints set by some MD engines, like gromacs)</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : //work flag</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         30 :   parseFlag(&quot;CALC_WORK&quot;,calc_work_);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : //multiple walkers //external MW for cp2k not supported, but anyway cp2k cannot put bias on energy!</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         30 :   bool walkers_mpi=false;</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         30 :   parseFlag(&quot;WALKERS_MPI&quot;,walkers_mpi);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         30 :   if(walkers_mpi)</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   {</a>
+<a name="254"><span class="lineNum">     254 </span>            :     //If this Action is not compiled with MPI the user is informed and we exit gracefully</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          4 :     plumed_massert(Communicator::plumedHasMPI(),&quot;Invalid walkers configuration: WALKERS_MPI flag requires MPI compilation&quot;);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          4 :     plumed_massert(Communicator::initialized(),&quot;Invalid walkers configuration: WALKERS_MPI needs the communicator correctly initialized.&quot;);</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          4 :     if(comm.Get_rank()==0) //multi_sim_comm works on first rank only</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :     {</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          4 :       NumWalkers_=multi_sim_comm.Get_size();</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          4 :       walker_rank_=multi_sim_comm.Get_rank();</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :     }</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          4 :     comm.Bcast(NumWalkers_,0); //if each walker has more than one processor update them all</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          4 :     comm.Bcast(walker_rank_,0);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span>            :   else</a>
+<a name="267"><span class="lineNum">     267 </span>            :   {</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         26 :     NumWalkers_=1;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         26 :     walker_rank_=0;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            : //parallelization stuff</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         30 :   NumOMP_=OpenMP::getNumThreads();</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         30 :   NumParallel_=comm.Get_size();</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         30 :   rank_=comm.Get_rank();</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         30 :   bool serial=false;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         30 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         30 :   if(serial)</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   {</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          5 :     NumOMP_=1;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          5 :     NumParallel_=1;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          5 :     rank_=0;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :   }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         30 :   checkRead();</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : //check ECVs and link them</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         30 :   init_pntrToECVsClass();</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : //set kbt_</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         30 :   kbt_=pntrToECVsClass_[0]-&gt;getKbT();</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         67 :   for(unsigned l=0; l&lt;pntrToECVsClass_.size(); l++)</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         37 :     plumed_massert(std::abs(kbt_-pntrToECVsClass_[l]-&gt;getKbT())&lt;1e-4,&quot;must set same TEMP for each ECV&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : //restart if needed</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         30 :   if(getRestart())</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :   {</a>
+<a name="297"><span class="lineNum">     297 </span>            :     bool stateRestart=true;</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         10 :     if(restartFileName.length()==0)</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :     {</a>
+<a name="300"><span class="lineNum">     300 </span>            :       stateRestart=false;</a>
+<a name="301"><span class="lineNum">     301 </span>            :       restartFileName=deltaFsFileName;</a>
+<a name="302"><span class="lineNum">     302 </span>            :     }</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         10 :     IFile ifile;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         10 :     ifile.link(*this);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         10 :     if(ifile.FileExist(restartFileName))</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     {</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         10 :       log.printf(&quot;  RESTART - make sure all ECVs used are the same as before\n&quot;);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         10 :       log.printf(&quot;    restarting from: %s\n&quot;,restartFileName.c_str());</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         10 :       ifile.open(restartFileName);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         10 :       if(stateRestart) //get all info</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :       {</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          2 :         log.printf(&quot;    it should be a STATE file (not a DELTAFS file)\n&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :         double time; //not used</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          2 :         ifile.scanField(&quot;time&quot;,time);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          2 :         ifile.scanField(&quot;counter&quot;,counter_);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          4 :         ifile.scanField(&quot;rct&quot;,rct_);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :         std::string tmp_lambda;</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         66 :         while(ifile.scanField(getPntrToArgument(0)-&gt;getName(),tmp_lambda))</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :         {</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         64 :           std::string subs=&quot;DeltaF_&quot;+tmp_lambda;</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">        128 :           for(unsigned jj=1; jj&lt;ncv_; jj++)</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :           {</a>
+<a name="323"><span class="lineNum">     323 </span>            :             tmp_lambda.clear();</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         64 :             ifile.scanField(getPntrToArgument(jj)-&gt;getName(),tmp_lambda);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">        128 :             subs+=&quot;_&quot;+tmp_lambda;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :           }</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         64 :           deltaF_name_.push_back(subs);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :           double tmp_deltaF;</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         64 :           ifile.scanField(&quot;DeltaF&quot;,tmp_deltaF);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         64 :           deltaF_.push_back(tmp_deltaF);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         64 :           ifile.scanField();</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :           tmp_lambda.clear();</a>
+<a name="333"><span class="lineNum">     333 </span>            :         }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          2 :         log.printf(&quot;  successfully read %lu DeltaF values\n&quot;,deltaF_name_.size());</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          2 :         if(NumParallel_&gt;1)</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          2 :           all_deltaF_=deltaF_;</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :       }</a>
+<a name="338"><span class="lineNum">     338 </span>            :       else //get just deltaFs names</a>
+<a name="339"><span class="lineNum">     339 </span>            :       {</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          8 :         ifile.scanFieldList(deltaF_name_);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          8 :         plumed_massert(deltaF_name_.size()&gt;=4,&quot;RESTART - fewer than expected FIELDS found in '&quot;+deltaFsFileName+&quot;' file&quot;);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          8 :         plumed_massert(deltaF_name_[deltaF_name_.size()-1]==&quot;print_stride&quot;,&quot;RESTART - coult not find expected FIELDS in '&quot;+deltaFsFileName+&quot;' file&quot;);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          8 :         plumed_massert(deltaF_name_[0]==&quot;time&quot;,&quot;RESTART - coult not find expected FIELDS in '&quot;+deltaFsFileName+&quot;' file&quot;);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          8 :         plumed_massert(deltaF_name_[1]==&quot;rct&quot;,&quot;RESTART - coult not find expected FIELDS in '&quot;+deltaFsFileName+&quot;' file&quot;);</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :         deltaF_name_.pop_back();</a>
+<a name="346"><span class="lineNum">     346 </span>            :         deltaF_name_.erase(deltaF_name_.begin(),deltaF_name_.begin()+2);</a>
+<a name="347"><span class="lineNum">     347 </span>            :         std::size_t pos=5; //each name starts with &quot;DeltaF&quot;</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         22 :         for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         14 :           pos=deltaF_name_[0].find(&quot;_&quot;,pos+1); //checking only first one, hopefully is enough</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          8 :         plumed_massert(pos&lt;deltaF_name_[0].length(),&quot;RESTART - fewer '_' than expected in DeltaF fields: did you remove any CV?&quot;);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          8 :         pos=deltaF_name_[0].find(&quot;_&quot;,pos+1);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          8 :         plumed_massert(pos&gt;deltaF_name_[0].length(),&quot;RESTART - more '_' than expected in DeltaF fields: did you add new CV?&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :       }</a>
+<a name="354"><span class="lineNum">     354 </span>            :       //get lambdas, init ECVs and Link them</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         10 :       deltaF_size_=deltaF_name_.size();</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        525 :       auto getLambdaName=[](const std::string&amp; name,const unsigned start,const unsigned dim)</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :       {</a>
+<a name="358"><span class="lineNum">     358 </span>            :         std::size_t pos_start=5; //each name starts with &quot;DeltaF&quot;</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">       1068 :         for(unsigned j=0; j&lt;=start; j++)</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">        543 :           pos_start=name.find(&quot;_&quot;,pos_start+1);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :         std::size_t pos_end=pos_start;</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       1527 :         for(unsigned j=0; j&lt;dim; j++)</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       1002 :           pos_end=name.find(&quot;_&quot;,pos_end+1);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        525 :         pos_start++; //do not include heading &quot;_&quot;</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">        525 :         return name.substr(pos_start,pos_end-pos_start);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :       };</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         10 :       unsigned index_j=ncv_;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :       unsigned sizeSkip=1;</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         22 :       for(int l=pntrToECVsClass_.size()-1; l&gt;=0; l--)</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :       {</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         12 :         const unsigned dim_l=pntrToECVsClass_[l]-&gt;getNumberOfArguments();</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         12 :         index_j-=dim_l;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         12 :         std::vector&lt;std::string&gt; lambdas_l(1);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         12 :         lambdas_l[0]=getLambdaName(deltaF_name_[0],index_j,dim_l);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">        523 :         for(unsigned i=sizeSkip; i&lt;deltaF_size_; i+=sizeSkip)</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :         {</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        513 :           std::string tmp_lambda=getLambdaName(deltaF_name_[i],index_j,dim_l);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">        513 :           if(tmp_lambda==lambdas_l[0])</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :             break;</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">        511 :           lambdas_l.push_back(tmp_lambda);</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :         }</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         12 :         pntrToECVsClass_[l]-&gt;initECVs_restart(lambdas_l);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         12 :         sizeSkip*=lambdas_l.size();</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         12 :       }</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         10 :       plumed_massert(sizeSkip==deltaF_size_,&quot;RESTART - this should not happen&quot;);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         10 :       init_linkECVs(); //link ECVs and initializes index_k_</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         10 :       log.printf(&quot; -&gt;%4u DeltaFs in total\n&quot;,deltaF_size_);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         10 :       obs_steps_=0; //avoid initializing again</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         10 :       if(stateRestart)</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :       {</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          2 :         if(NumParallel_&gt;1)</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :         {</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          2 :           const unsigned start=(deltaF_size_/NumParallel_)*rank_+std::min(rank_,deltaF_size_%NumParallel_);</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :           unsigned iter=0;</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         34 :           for(unsigned i=start; i&lt;start+deltaF_.size(); i++)</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         32 :             deltaF_[iter++]=all_deltaF_[i];</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :         }</a>
+<a name="398"><span class="lineNum">     398 </span>            :       }</a>
+<a name="399"><span class="lineNum">     399 </span>            :       else //read each step</a>
+<a name="400"><span class="lineNum">     400 </span>            :       {</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          8 :         counter_=1;</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :         unsigned count_lines=0;</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          8 :         ifile.allowIgnoredFields(); //this allows for multiple restart, but without checking for consistency between them!</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :         double time;</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         48 :         while(ifile.scanField(&quot;time&quot;,time)) //only number of lines and last line is important</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :         {</a>
+<a name="407"><span class="lineNum">     407 </span>            :           unsigned restart_stride;</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         16 :           ifile.scanField(&quot;print_stride&quot;,restart_stride);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         16 :           ifile.scanField(&quot;rct&quot;,rct_);</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         16 :           if(NumParallel_==1)</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :           {</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">       1014 :             for(unsigned i=0; i&lt;deltaF_size_; i++)</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">        998 :               ifile.scanField(deltaF_name_[i],deltaF_[i]);</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :           }</a>
+<a name="415"><span class="lineNum">     415 </span>            :           else</a>
+<a name="416"><span class="lineNum">     416 </span>            :           {</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :             const unsigned start=(deltaF_size_/NumParallel_)*rank_+std::min(rank_,deltaF_size_%NumParallel_);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :             unsigned iter=0;</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :             for(unsigned i=start; i&lt;start+deltaF_.size(); i++)</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :               ifile.scanField(deltaF_name_[i],deltaF_[iter++]);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :           }</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         16 :           ifile.scanField();</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         16 :           if(count_lines&gt;0)</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          8 :             counter_+=restart_stride;</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         16 :           count_lines++;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :         }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          8 :         counter_*=NumWalkers_;</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          8 :         log.printf(&quot;  successfully read %u lines, up to t=%g\n&quot;,count_lines,time);</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :       }</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         10 :       ifile.reset(false);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         10 :       ifile.close();</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :     }</a>
+<a name="433"><span class="lineNum">     433 </span>            :     else //same behaviour as METAD</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;RESTART requested, but file '&quot;+restartFileName+&quot;' was not found!\n  Set RESTART=NO or provide a restart file&quot;);</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         10 :     if(NumWalkers_&gt;1) //make sure that all walkers are doing the same thing</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :     {</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          2 :       std::vector&lt;unsigned long long&gt; all_counter(NumWalkers_);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          2 :       if(comm.Get_rank()==0)</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          2 :         multi_sim_comm.Allgather(counter_,all_counter);</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          2 :       comm.Bcast(all_counter,0);</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :       bool same_number_of_steps=true;</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          4 :       for(unsigned w=1; w&lt;NumWalkers_; w++)</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          2 :         if(all_counter[0]!=all_counter[w])</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :           same_number_of_steps=false;</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          2 :       plumed_massert(same_number_of_steps,&quot;RESTART - not all walkers are reading the same file!&quot;);</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :     }</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         10 :   }</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         20 :   else if(restartFileName.length()&gt;0)</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ the provided STATE_RFILE will be ignored, since RESTART was not requested\n&quot;);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            : //sync all walkers to avoid opening files before reding is over (see also METAD)</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         30 :   comm.Barrier();</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         30 :   if(comm.Get_rank()==0 &amp;&amp; walkers_mpi)</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          4 :     multi_sim_comm.Barrier();</span></a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            : //setup DeltaFs file</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         30 :   deltaFsOfile_.link(*this);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         30 :   if(NumWalkers_&gt;1)</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :   {</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          4 :     if(walker_rank_&gt;0)</span></a>
+<a name="461"><span class="lineNum">     461 </span>            :       deltaFsFileName=&quot;/dev/null&quot;; //only first walker writes on file</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          8 :     deltaFsOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   }</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         30 :   deltaFsOfile_.open(deltaFsFileName);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         30 :   if(fmt.length()&gt;0)</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         60 :     deltaFsOfile_.fmtField(&quot; &quot;+fmt);</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :   deltaFsOfile_.setHeavyFlush(); //do I need it?</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         30 :   deltaFsOfile_.addConstantField(&quot;print_stride&quot;);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         30 :   deltaFsOfile_.printField(&quot;print_stride&quot;,print_stride_);</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            : //open file for storing state</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         30 :   if(wStateStride_!=0)</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :   {</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          6 :     stateOfile_.link(*this);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">          6 :     if(NumWalkers_&gt;1)</span></a>
+<a name="476"><span class="lineNum">     476 </span>            :     {</a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :       if(walker_rank_&gt;0)</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :         stateFileName=&quot;/dev/null&quot;; //only first walker writes on file</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineNoCov">          0 :       stateOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :     }</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          6 :     stateOfile_.open(stateFileName);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          6 :     if(fmt.length()&gt;0)</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         12 :       stateOfile_.fmtField(&quot; &quot;+fmt);</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :   }</a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span>            : //add output components</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">         30 :   if(calc_work_)</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   {</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          6 :     addComponent(&quot;work&quot;);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         12 :     componentIsNotPeriodic(&quot;work&quot;);</span></a>
+<a name="491"><span class="lineNum">     491 </span>            :   }</a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            : //printing some info</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         30 :   log.printf(&quot;  updating the bias with PACE = %u\n&quot;,stride_);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">         30 :   log.printf(&quot;  initial unbiased OBSERVATION_STEPS = %u (in units of PACE)\n&quot;,obs_steps_);</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         30 :   if(wStateStride_&gt;0)</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          5 :     log.printf(&quot;  state checkpoints are written on file %s every %d MD steps\n&quot;,stateFileName.c_str(),wStateStride_);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">         30 :   if(wStateStride_==-1)</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          1 :     log.printf(&quot;  state checkpoints are written on file '%s' only on CPT events (or never if MD code does define them!)\n&quot;,stateFileName.c_str());</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         30 :   if(walkers_mpi)</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          4 :     log.printf(&quot; -- WALKERS_MPI: if multiple replicas are present, they will share the same bias via MPI\n&quot;);</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         30 :   if(NumWalkers_&gt;1)</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   {</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          4 :     log.printf(&quot;  using multiple walkers\n&quot;);</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          4 :     log.printf(&quot;    number of walkers: %u\n&quot;,NumWalkers_);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          4 :     log.printf(&quot;    walker rank: %u\n&quot;,walker_rank_);</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :   }</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         30 :   int mw_warning=0;</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         30 :   if(!walkers_mpi &amp;&amp; comm.Get_rank()==0 &amp;&amp; multi_sim_comm.Get_size()&gt;(int)NumWalkers_)</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :     mw_warning=1;</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         30 :   comm.Bcast(mw_warning,0);</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         30 :   if(mw_warning) //log.printf messes up with comm, so never use it without Bcast!</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ multiple replicas will NOT communicate unless the flag WALKERS_MPI is used\n&quot;);</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         30 :   if(NumParallel_&gt;1)</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">          2 :     log.printf(&quot;  using multiple MPI processes per simulation: %u\n&quot;,NumParallel_);</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         30 :   if(NumOMP_&gt;1)</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         25 :     log.printf(&quot;  using multiple OpenMP threads per simulation: %u\n&quot;,NumOMP_);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         30 :   if(serial)</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          5 :     log.printf(&quot; -- SERIAL: no loop parallelization, despite %d MPI processes and %u OpenMP threads available\n&quot;,comm.Get_size(),OpenMP::getNumThreads());</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         30 :   log.printf(&quot;  Bibliography: &quot;);</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         60 :   log&lt;&lt;plumed.cite(&quot;M. Invernizzi, P.M. Piaggi, and M. Parrinello, Phys. Rev. X 10, 041034 (2020)&quot;);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         30 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         30 : }</span></a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">       1490 : void OPESexpanded::calculate()</span></a>
+<a name="526"><span class="lineNum">     526 </span>            : {</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">       1490 :   if(deltaF_size_==0) //no bias before initialization</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">        325 :     return;</span></a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : //get diffMax, to avoid over/underflow</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">       1165 :   double diffMax=-std::numeric_limits&lt;double&gt;::max();</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">       1165 :   #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   {</a>
+<a name="534"><span class="lineNum">     534 </span>            :     #pragma omp for reduction(max:diffMax)</a>
+<a name="535"><span class="lineNum">     535 </span>            :     for(unsigned i=0; i&lt;deltaF_.size(); i++)</a>
+<a name="536"><span class="lineNum">     536 </span>            :     {</a>
+<a name="537"><span class="lineNum">     537 </span>            :       diff_[i]=(-getExpansion(i)+deltaF_[i]/kbt_);</a>
+<a name="538"><span class="lineNum">     538 </span>            :       if(diff_[i]&gt;diffMax)</a>
+<a name="539"><span class="lineNum">     539 </span>            :         diffMax=diff_[i];</a>
+<a name="540"><span class="lineNum">     540 </span>            :     }</a>
+<a name="541"><span class="lineNum">     541 </span>            :   }</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">       1165 :   if(NumParallel_&gt;1)</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">        102 :     comm.Max(diffMax);</span></a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span>            : //calculate the bias and the forces</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">       1165 :   double sum=0;</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">       1165 :   std::vector&lt;double&gt; der_sum_cv(ncv_,0);</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">       1165 :   if(NumOMP_==1)</span></a>
+<a name="549"><span class="lineNum">     549 </span>            :   {</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">       2730 :     for(unsigned i=0; i&lt;deltaF_.size(); i++)</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :     {</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">       2520 :       double add_i=std::exp(diff_[i]-diffMax);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">       2520 :       sum+=add_i;</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :       //set derivatives</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">       6960 :       for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">       4440 :         der_sum_cv[j]-=derECVs_[j][index_k_[i][j]]*add_i;</span></a>
+<a name="557"><span class="lineNum">     557 </span>            :     }</a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span>            :   else</a>
+<a name="560"><span class="lineNum">     560 </span>            :   {</a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">        955 :     #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :     {</a>
+<a name="563"><span class="lineNum">     563 </span>            :       std::vector&lt;double&gt; omp_der_sum_cv(ncv_,0);</a>
+<a name="564"><span class="lineNum">     564 </span>            :       #pragma omp for reduction(+:sum) nowait</a>
+<a name="565"><span class="lineNum">     565 </span>            :       for(unsigned i=0; i&lt;deltaF_.size(); i++)</a>
+<a name="566"><span class="lineNum">     566 </span>            :       {</a>
+<a name="567"><span class="lineNum">     567 </span>            :         double add_i=std::exp(diff_[i]-diffMax);</a>
+<a name="568"><span class="lineNum">     568 </span>            :         sum+=add_i;</a>
+<a name="569"><span class="lineNum">     569 </span>            :         //set derivatives</a>
+<a name="570"><span class="lineNum">     570 </span>            :         for(unsigned j=0; j&lt;ncv_; j++)</a>
+<a name="571"><span class="lineNum">     571 </span>            :           omp_der_sum_cv[j]-=derECVs_[j][index_k_[i][j]]*add_i;</a>
+<a name="572"><span class="lineNum">     572 </span>            :       }</a>
+<a name="573"><span class="lineNum">     573 </span>            :       #pragma omp critical</a>
+<a name="574"><span class="lineNum">     574 </span>            :       for(unsigned j=0; j&lt;ncv_; j++)</a>
+<a name="575"><span class="lineNum">     575 </span>            :         der_sum_cv[j]+=omp_der_sum_cv[j];</a>
+<a name="576"><span class="lineNum">     576 </span>            :     }</a>
+<a name="577"><span class="lineNum">     577 </span>            :   }</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">       1165 :   if(NumParallel_&gt;1)</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :   { //each MPI process has part of the full deltaF_ vector, so must Sum</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">        102 :     comm.Sum(sum);</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">        102 :     comm.Sum(der_sum_cv);</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :   }</a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span>            : //set bias and forces</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">       1165 :   const double bias=-kbt_*(diffMax+std::log(sum/deltaF_size_));</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :   setBias(bias);</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">       3163 :   for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">       1998 :     setOutputForce(j,kbt_*der_sum_cv[j]/sum);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            : }</a>
+<a name="590"><span class="lineNum">     590 </span>            : </a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">       1490 : void OPESexpanded::update()</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : {</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">       1490 :   if(isFirstStep_) //skip very first step, as in METAD</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :   {</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         30 :     isFirstStep_=false;</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         30 :     if(obs_steps_!=1) //if obs_steps_==1 go on with initialization</span></a>
+<a name="597"><span class="lineNum">     597 </span>            :       return;</a>
+<a name="598"><span class="lineNum">     598 </span>            :   }</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">       1464 :   if(getStep()%stride_==0)</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :   {</a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">        739 :     if(obs_steps_&gt;0)</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :     {</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">        463 :       for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        304 :         obs_cvs_[counter_*ncv_+j]=getArgument(j);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        159 :       counter_++;</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">        159 :       if(counter_==obs_steps_)</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :       {</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">         20 :         log.printf(&quot;\nAction %s\n&quot;,getName().c_str());</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         20 :         init_fromObs();</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         20 :         log.printf(&quot;Finished initialization\n\n&quot;);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         20 :         counter_=NumWalkers_; //all preliminary observations count 1</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         20 :         obs_steps_=0; //no more observation</span></a>
+<a name="613"><span class="lineNum">     613 </span>            :       }</a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">        159 :       return;</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :     }</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            :     //update averages</a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">        580 :     const double current_bias=getOutputQuantity(0); //the first value is always the bias</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        580 :     if(NumWalkers_==1)</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">        500 :       updateDeltaF(current_bias);</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :     else</a>
+<a name="622"><span class="lineNum">     622 </span>            :     {</a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         80 :       std::vector&lt;double&gt; cvs(ncv_);</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">        240 :       for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">        160 :         cvs[j]=getArgument(j);</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         80 :       std::vector&lt;double&gt; all_bias(NumWalkers_);</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         80 :       std::vector&lt;double&gt; all_cvs(NumWalkers_*ncv_);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         80 :       if(comm.Get_rank()==0)</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :       {</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         80 :         multi_sim_comm.Allgather(current_bias,all_bias);</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         80 :         multi_sim_comm.Allgather(cvs,all_cvs);</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :       }</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">         80 :       comm.Bcast(all_bias,0);</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">         80 :       comm.Bcast(all_cvs,0);</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">        240 :       for(unsigned w=0; w&lt;NumWalkers_; w++)</span></a>
+<a name="636"><span class="lineNum">     636 </span>            :       {</a>
+<a name="637"><span class="lineNum">     637 </span>            :         //calculate ECVs</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">        160 :         unsigned index_wj=w*ncv_;</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">        380 :         for(unsigned k=0; k&lt;pntrToECVsClass_.size(); k++)</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :         {</a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">        220 :           pntrToECVsClass_[k]-&gt;calculateECVs(&amp;all_cvs[index_wj]);</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">        220 :           index_wj+=pntrToECVsClass_[k]-&gt;getNumberOfArguments();</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :         }</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">        160 :         updateDeltaF(all_bias[w]);</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :       }</a>
+<a name="646"><span class="lineNum">     646 </span>            :     }</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            :     //write DeltaFs to file</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">        580 :     if((counter_/NumWalkers_-1)%print_stride_==0)</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         44 :       printDeltaF();</span></a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :     //calculate work if requested</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">        580 :     if(calc_work_)</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :     { //some copy and paste from calculate()</a>
+<a name="655"><span class="lineNum">     655 </span>            :       //get diffMax, to avoid over/underflow</a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">        110 :       double diffMax=-std::numeric_limits&lt;double&gt;::max();</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">        110 :       #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :       {</a>
+<a name="659"><span class="lineNum">     659 </span>            :         #pragma omp for reduction(max:diffMax)</a>
+<a name="660"><span class="lineNum">     660 </span>            :         for(unsigned i=0; i&lt;deltaF_.size(); i++)</a>
+<a name="661"><span class="lineNum">     661 </span>            :         {</a>
+<a name="662"><span class="lineNum">     662 </span>            :           diff_[i]=(-getExpansion(i)+deltaF_[i]/kbt_);</a>
+<a name="663"><span class="lineNum">     663 </span>            :           if(diff_[i]&gt;diffMax)</a>
+<a name="664"><span class="lineNum">     664 </span>            :             diffMax=diff_[i];</a>
+<a name="665"><span class="lineNum">     665 </span>            :         }</a>
+<a name="666"><span class="lineNum">     666 </span>            :       }</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">        110 :       if(NumParallel_&gt;1)</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">         50 :         comm.Max(diffMax);</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :       //calculate the bias</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">        110 :       double sum=0;</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">        110 :       #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :       {</a>
+<a name="673"><span class="lineNum">     673 </span>            :         #pragma omp for reduction(+:sum) nowait</a>
+<a name="674"><span class="lineNum">     674 </span>            :         for(unsigned i=0; i&lt;deltaF_.size(); i++)</a>
+<a name="675"><span class="lineNum">     675 </span>            :           sum+=std::exp(diff_[i]-diffMax);</a>
+<a name="676"><span class="lineNum">     676 </span>            :       }</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">        110 :       if(NumParallel_&gt;1)</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         50 :         comm.Sum(sum);</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">        110 :       const double new_bias=-kbt_*(diffMax+std::log(sum/deltaF_size_));</span></a>
+<a name="680"><span class="lineNum">     680 </span>            :       //accumulate work</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">        110 :       work_+=new_bias-current_bias;</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">        220 :       getPntrToComponent(&quot;work&quot;)-&gt;set(work_);</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :     }</a>
+<a name="684"><span class="lineNum">     684 </span>            :   }</a>
+<a name="685"><span class="lineNum">     685 </span>            : </a>
+<a name="686"><span class="lineNum">     686 </span>            : //dump state if requested</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">       1305 :   if( (wStateStride_&gt;0 &amp;&amp; getStep()%wStateStride_==0) || (wStateStride_==-1 &amp;&amp; getCPT()) )</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         11 :     dumpStateToFile();</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : }</a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         30 : void OPESexpanded::init_pntrToECVsClass()</span></a>
+<a name="692"><span class="lineNum">     692 </span>            : {</a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">         30 :   std::vector&lt;opes::ExpansionCVs*&gt; all_pntrToECVsClass=plumed.getActionSet().select&lt;opes::ExpansionCVs*&gt;();</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">         30 :   plumed_massert(all_pntrToECVsClass.size()&gt;0,&quot;no Expansion CVs found&quot;);</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">         67 :   for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="696"><span class="lineNum">     696 </span>            :   {</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         74 :     std::string error_notECV(&quot;all the ARGs of &quot;+getName()+&quot; must be Expansion Collective Variables (ECV)&quot;);</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineCov">         37 :     const unsigned dot_pos=getPntrToArgument(j)-&gt;getName().find(&quot;.&quot;);</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         37 :     plumed_massert(dot_pos&lt;getPntrToArgument(j)-&gt;getName().size(),error_notECV+&quot;, thus contain a dot in the name&quot;);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         37 :     unsigned foundECV_l=all_pntrToECVsClass.size();</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">         44 :     for(unsigned l=0; l&lt;all_pntrToECVsClass.size(); l++)</span></a>
+<a name="702"><span class="lineNum">     702 </span>            :     {</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         44 :       if(getPntrToArgument(j)-&gt;getName().substr(0,dot_pos)==all_pntrToECVsClass[l]-&gt;getLabel())</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :       {</a>
+<a name="705"><span class="lineNum">     705 </span>            :         foundECV_l=l;</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">         37 :         pntrToECVsClass_.push_back(all_pntrToECVsClass[l]);</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         37 :         std::string missing_arg=&quot;some ECV component is missing from ARG&quot;;</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">         37 :         plumed_massert(j+all_pntrToECVsClass[l]-&gt;getNumberOfArguments()&lt;=getNumberOfArguments(),missing_arg);</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         90 :         for(unsigned h=0; h&lt;all_pntrToECVsClass[l]-&gt;getNumberOfArguments(); h++)</span></a>
+<a name="710"><span class="lineNum">     710 </span>            :         {</a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">         53 :           std::string argName=getPntrToArgument(j+h)-&gt;getName();</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">         53 :           std::string expectedECVname=all_pntrToECVsClass[l]-&gt;getComponentsVector()[h];</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">         53 :           plumed_massert(argName==expectedECVname,missing_arg+&quot;, or is in wrong order: given ARG=&quot;+argName+&quot; expected ARG=&quot;+expectedECVname);</span></a>
+<a name="714"><span class="lineNum">     714 </span>            :         }</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">         37 :         j+=all_pntrToECVsClass[l]-&gt;getNumberOfArguments()-1;</span></a>
+<a name="716"><span class="lineNum">     716 </span>            :         break;</a>
+<a name="717"><span class="lineNum">     717 </span>            :       }</a>
+<a name="718"><span class="lineNum">     718 </span>            :     }</a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">         37 :     plumed_massert(foundECV_l&lt;all_pntrToECVsClass.size(),error_notECV);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :   }</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">         67 :   for(unsigned l=0; l&lt;pntrToECVsClass_.size(); l++)</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">         44 :     for(unsigned ll=l+1; ll&lt;pntrToECVsClass_.size(); ll++)</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">          7 :       plumed_massert(pntrToECVsClass_[l]-&gt;getLabel()!=pntrToECVsClass_[ll]-&gt;getLabel(),&quot;cannot use same ECV twice&quot;);</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">         30 : }</span></a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">         30 : void OPESexpanded::init_linkECVs()</span></a>
+<a name="727"><span class="lineNum">     727 </span>            : {</a>
+<a name="728"><span class="lineNum">     728 </span>            :   //TODO It should be possible to make all of this more straightforward (and probably also faster):</a>
+<a name="729"><span class="lineNum">     729 </span>            :   //     - get rid of index_k_, making it trivial for each ECV</a>
+<a name="730"><span class="lineNum">     730 </span>            :   //     - store the ECVs_ and derECVs_ vectors here as a contiguous vector, and use pointers in the ECV classes</a>
+<a name="731"><span class="lineNum">     731 </span>            :   //     Some caveats:</a>
+<a name="732"><span class="lineNum">     732 </span>            :   //     - ECVmultiThermalBaric has a nontrivial index_k_ to avoid duplicates. use duplicates instead</a>
+<a name="733"><span class="lineNum">     733 </span>            :   //     - can the ECVs be MPI parallel or it's too complicated?</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">         30 :   plumed_massert(deltaF_size_&gt;0,&quot;must set deltaF_size_ before calling init_linkECVs()&quot;);</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">         30 :   if(NumParallel_==1)</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">         28 :     deltaF_.resize(deltaF_size_);</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :   else</a>
+<a name="738"><span class="lineNum">     738 </span>            :   {</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">          2 :     const unsigned extra=(rank_&lt;(deltaF_size_%NumParallel_)?1:0);</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">          2 :     deltaF_.resize(deltaF_size_/NumParallel_+extra);</span></a>
+<a name="741"><span class="lineNum">     741 </span>            :     //these are used when printing deltaF_ to file</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">          2 :     all_deltaF_.resize(deltaF_size_);</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">          2 :     all_size_.resize(NumParallel_,deltaF_size_/NumParallel_);</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">          2 :     disp_.resize(NumParallel_);</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">          4 :     for(unsigned r=0; r&lt;NumParallel_-1; r++)</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :     {</a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">          2 :       if(r&lt;deltaF_size_%NumParallel_)</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineNoCov">          0 :         all_size_[r]++;</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">          2 :       disp_[r+1]=disp_[r]+all_size_[r];</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :     }</a>
+<a name="751"><span class="lineNum">     751 </span>            :   }</a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">         30 :   diff_.resize(deltaF_.size());</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         30 :   ECVs_.resize(ncv_);</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">         30 :   derECVs_.resize(ncv_);</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">         30 :   index_k_.resize(deltaF_.size(),std::vector&lt;unsigned&gt;(ncv_));</span></a>
+<a name="756"><span class="lineNum">     756 </span>            :   unsigned index_j=0;</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">         30 :   unsigned sizeSkip=deltaF_size_;</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">         67 :   for(unsigned l=0; l&lt;pntrToECVsClass_.size(); l++)</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :   {</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">         37 :     std::vector&lt; std::vector&lt;unsigned&gt; &gt; l_index_k(pntrToECVsClass_[l]-&gt;getIndex_k());</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">         37 :     plumed_massert(deltaF_size_%l_index_k.size()==0,&quot;buggy ECV: mismatch between getTotNumECVs() and getIndex_k().size()&quot;);</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">         37 :     plumed_massert(l_index_k[0].size()==pntrToECVsClass_[l]-&gt;getNumberOfArguments(),&quot;buggy ECV: mismatch between number of ARG and underlying CVs&quot;);</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">         37 :     sizeSkip/=l_index_k.size();</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">         90 :     for(unsigned h=0; h&lt;pntrToECVsClass_[l]-&gt;getNumberOfArguments(); h++)</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :     {</a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">         53 :       ECVs_[index_j+h]=pntrToECVsClass_[l]-&gt;getPntrToECVs(h);</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">         53 :       derECVs_[index_j+h]=pntrToECVsClass_[l]-&gt;getPntrToDerECVs(h);</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">         53 :       if(NumParallel_==1)</span></a>
+<a name="769"><span class="lineNum">     769 </span>            :       {</a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">      45589 :         for(unsigned i=0; i&lt;deltaF_size_; i++)</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">      45540 :           index_k_[i][index_j+h]=l_index_k[(i/sizeSkip)%l_index_k.size()][h];</span></a>
+<a name="772"><span class="lineNum">     772 </span>            :       }</a>
+<a name="773"><span class="lineNum">     773 </span>            :       else</a>
+<a name="774"><span class="lineNum">     774 </span>            :       {</a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">          4 :         const unsigned start=(deltaF_size_/NumParallel_)*rank_+std::min(rank_,deltaF_size_%NumParallel_);</span></a>
+<a name="776"><span class="lineNum">     776 </span>            :         unsigned iter=0;</a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">         68 :         for(unsigned i=start; i&lt;start+deltaF_.size(); i++)</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">         64 :           index_k_[iter++][index_j+h]=l_index_k[(i/sizeSkip)%l_index_k.size()][h];</span></a>
+<a name="779"><span class="lineNum">     779 </span>            :       }</a>
+<a name="780"><span class="lineNum">     780 </span>            :     }</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">         37 :     index_j+=pntrToECVsClass_[l]-&gt;getNumberOfArguments();</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">         37 :   }</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">         30 :   plumed_massert(sizeSkip==1,&quot;this should not happen!&quot;);</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">         30 : }</span></a>
+<a name="785"><span class="lineNum">     785 </span>            : </a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">         20 : void OPESexpanded::init_fromObs() //This could probably be faster and/or require less memory...</span></a>
+<a name="787"><span class="lineNum">     787 </span>            : {</a>
+<a name="788"><span class="lineNum">     788 </span>            : //in case of multiple walkers gather all the statistics</a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">         20 :   if(NumWalkers_&gt;1)</span></a>
+<a name="790"><span class="lineNum">     790 </span>            :   {</a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">          2 :     std::vector&lt;double&gt; all_obs_cv(ncv_*obs_steps_*NumWalkers_);</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">          2 :     if(comm.Get_rank()==0)</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">          2 :       multi_sim_comm.Allgather(obs_cvs_,all_obs_cv);</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">          2 :     comm.Bcast(all_obs_cv,0);</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">          2 :     obs_cvs_=all_obs_cv; //could this lead to memory issues?</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">          2 :     obs_steps_*=NumWalkers_;</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :   }</a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span>            : //initialize ECVs from observations</a>
+<a name="800"><span class="lineNum">     800 </span>            :   unsigned index_j=0;</a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">         20 :   deltaF_size_=1;</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">         45 :   for(unsigned l=0; l&lt;pntrToECVsClass_.size(); l++)</span></a>
+<a name="803"><span class="lineNum">     803 </span>            :   {</a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">         25 :     pntrToECVsClass_[l]-&gt;initECVs_observ(obs_cvs_,ncv_,index_j);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">         25 :     deltaF_size_*=pntrToECVsClass_[l]-&gt;getTotNumECVs(); //ECVs from different exansions will be combined</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">         25 :     index_j+=pntrToECVsClass_[l]-&gt;getNumberOfArguments();</span></a>
+<a name="807"><span class="lineNum">     807 </span>            :   }</a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">         20 :   plumed_massert(index_j==getNumberOfArguments(),&quot;mismatch between number of linked CVs and number of ARG&quot;);</span></a>
+<a name="809"><span class="lineNum">     809 </span>            : //link ECVs and initialize index_k_, mapping each deltaF to a single ECVs set</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">         20 :   init_linkECVs();</span></a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span>            : //initialize deltaF_ from obs</a>
+<a name="813"><span class="lineNum">     813 </span>            : //for the first point, t=0, the ECVs are calculated by initECVs_observ, setting also any initial guess</a>
+<a name="814"><span class="lineNum">     814 </span>            :   index_j=0;</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">      12379 :   for(unsigned i=0; i&lt;deltaF_.size(); i++)</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">      56923 :     for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">      44564 :       deltaF_[i]+=kbt_*ECVs_[j][index_k_[i][j]];</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">        179 :   for(unsigned t=1; t&lt;obs_steps_; t++) //starts from t=1</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :   {</a>
+<a name="820"><span class="lineNum">     820 </span>            :     unsigned index_j=0;</a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">        383 :     for(unsigned l=0; l&lt;pntrToECVsClass_.size(); l++)</span></a>
+<a name="822"><span class="lineNum">     822 </span>            :     {</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">        224 :       pntrToECVsClass_[l]-&gt;calculateECVs(&amp;obs_cvs_[t*ncv_+index_j]);</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        224 :       index_j+=pntrToECVsClass_[l]-&gt;getNumberOfArguments();</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">     102677 :     for(unsigned i=0; i&lt;deltaF_.size(); i++)</span></a>
+<a name="827"><span class="lineNum">     827 </span>            :     {</a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">     102518 :       const double diff_i=(-getExpansion(i)+deltaF_[i]/kbt_-std::log(t));</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">     102518 :       if(diff_i&gt;0) //save exp from overflow</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">      16071 :         deltaF_[i]-=kbt_*(diff_i+std::log1p(std::exp(-diff_i))+std::log1p(-1./(1.+t)));</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :       else</a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">      86447 :         deltaF_[i]-=kbt_*(std::log1p(std::exp(diff_i))+std::log1p(-1./(1.+t)));</span></a>
+<a name="833"><span class="lineNum">     833 </span>            :     }</a>
+<a name="834"><span class="lineNum">     834 </span>            :   }</a>
+<a name="835"><span class="lineNum">     835 </span>            :   obs_cvs_.clear();</a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            : //set deltaF_name_</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">         20 :   deltaF_name_.resize(deltaF_size_,&quot;DeltaF&quot;);</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">         20 :   unsigned sizeSkip=deltaF_size_;</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">         45 :   for(unsigned l=0; l&lt;pntrToECVsClass_.size(); l++)</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :   {</a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">         25 :     std::vector&lt;std::string&gt; lambdas_l=pntrToECVsClass_[l]-&gt;getLambdas();</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         25 :     plumed_massert(lambdas_l.size()==pntrToECVsClass_[l]-&gt;getTotNumECVs(),&quot;buggy ECV: mismatch between getTotNumECVs() and getLambdas().size()&quot;);</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">         25 :     sizeSkip/=lambdas_l.size();</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">      22457 :     for(unsigned i=0; i&lt;deltaF_size_; i++)</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">      44864 :       deltaF_name_[i]+=&quot;_&quot;+lambdas_l[(i/sizeSkip)%lambdas_l.size()];</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">         25 :   }</span></a>
+<a name="848"><span class="lineNum">     848 </span>            : </a>
+<a name="849"><span class="lineNum">     849 </span>            : //print initialization to file</a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">         20 :   log.printf(&quot; -&gt;%4u DeltaFs in total\n&quot;,deltaF_size_);</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">         20 :   printDeltaF();</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">         20 : }</span></a>
+<a name="853"><span class="lineNum">     853 </span>            : </a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">         64 : void OPESexpanded::printDeltaF()</span></a>
+<a name="855"><span class="lineNum">     855 </span>            : {</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">         64 :   deltaFsOfile_.printField(&quot;time&quot;,getTime());</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">         64 :   deltaFsOfile_.printField(&quot;rct&quot;,rct_);</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">         64 :   if(NumParallel_==1)</span></a>
+<a name="859"><span class="lineNum">     859 </span>            :   {</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">      23988 :     for(unsigned i=0; i&lt;deltaF_.size(); i++)</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">      23926 :       deltaFsOfile_.printField(deltaF_name_[i],deltaF_[i]);</span></a>
+<a name="862"><span class="lineNum">     862 </span>            :   }</a>
+<a name="863"><span class="lineNum">     863 </span>            :   else</a>
+<a name="864"><span class="lineNum">     864 </span>            :   {</a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">          2 :     comm.Allgatherv(deltaF_,all_deltaF_,&amp;all_size_[0],&amp;disp_[0]); //can we avoid using this big vector?</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">         66 :     for(unsigned i=0; i&lt;deltaF_size_; i++)</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">         64 :       deltaFsOfile_.printField(deltaF_name_[i],all_deltaF_[i]);</span></a>
+<a name="868"><span class="lineNum">     868 </span>            :   }</a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">         64 :   deltaFsOfile_.printField();</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">         64 : }</span></a>
+<a name="871"><span class="lineNum">     871 </span>            : </a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">         11 : void OPESexpanded::dumpStateToFile()</span></a>
+<a name="873"><span class="lineNum">     873 </span>            : {</a>
+<a name="874"><span class="lineNum">     874 </span>            : //rewrite header or rewind file</a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">         11 :   if(storeOldStates_)</span></a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">          3 :     stateOfile_.clearFields();</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">          8 :   else if(walker_rank_==0)</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">          8 :     stateOfile_.rewind();</span></a>
+<a name="879"><span class="lineNum">     879 </span>            : //define fields</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">         11 :   stateOfile_.addConstantField(&quot;time&quot;);</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">         11 :   stateOfile_.addConstantField(&quot;counter&quot;);</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">         11 :   stateOfile_.addConstantField(&quot;rct&quot;);</span></a>
+<a name="883"><span class="lineNum">     883 </span>            : //print</a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         11 :   stateOfile_.printField(&quot;time&quot;,getTime());</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">         11 :   stateOfile_.printField(&quot;counter&quot;,counter_);</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">         11 :   stateOfile_.printField(&quot;rct&quot;,rct_);</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">         11 :   if(NumParallel_&gt;1)</span></a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineNoCov">          0 :     comm.Allgatherv(deltaF_,all_deltaF_,&amp;all_size_[0],&amp;disp_[0]); //can we avoid using this big vector?</span></a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">        240 :   for(unsigned i=0; i&lt;deltaF_size_; i++)</span></a>
+<a name="890"><span class="lineNum">     890 </span>            :   {</a>
+<a name="891"><span class="lineNum">     891 </span>            :     std::size_t pos_start=7; //skip &quot;DeltaF_&quot;</a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">        687 :     for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="893"><span class="lineNum">     893 </span>            :     {</a>
+<a name="894"><span class="lineNum">     894 </span>            :       plumed_dbg_massert(pos_start&gt;6,&quot;not enought _ in deltaF_name_&quot;+std::to_string(i-1)+&quot; string?&quot;);</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">        458 :       const std::size_t pos_end=deltaF_name_[i].find(&quot;_&quot;,pos_start);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">        916 :       stateOfile_.printField(getPntrToArgument(j)-&gt;getName(),&quot;  &quot;+deltaF_name_[i].substr(pos_start,pos_end-pos_start));</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">        458 :       pos_start=pos_end+1;</span></a>
+<a name="898"><span class="lineNum">     898 </span>            :     }</a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">        229 :     if(NumParallel_==1)</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">        458 :       stateOfile_.printField(&quot;DeltaF&quot;,deltaF_[i]);</span></a>
+<a name="901"><span class="lineNum">     901 </span>            :     else</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineNoCov">          0 :       stateOfile_.printField(&quot;DeltaF&quot;,all_deltaF_[i]);</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">        229 :     stateOfile_.printField();</span></a>
+<a name="904"><span class="lineNum">     904 </span>            :   }</a>
+<a name="905"><span class="lineNum">     905 </span>            : //make sure file is written even if small</a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">         11 :   if(!storeOldStates_)</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">          8 :     stateOfile_.flush();</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">         11 : }</span></a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">        660 : void OPESexpanded::updateDeltaF(double bias)</span></a>
+<a name="911"><span class="lineNum">     911 </span>            : {</a>
+<a name="912"><span class="lineNum">     912 </span>            :   plumed_dbg_massert(counter_&gt;0,&quot;deltaF_ must be initialized&quot;);</a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">        660 :   counter_++;</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">        660 :   const double arg=(bias-rct_)/kbt_-std::log(counter_-1.);</span></a>
+<a name="915"><span class="lineNum">     915 </span>            :   double increment;</a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">        660 :   if(arg&gt;0) //save exp from overflow</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">         28 :     increment=kbt_*(arg+std::log1p(std::exp(-arg)));</span></a>
+<a name="918"><span class="lineNum">     918 </span>            :   else</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">        632 :     increment=kbt_*(std::log1p(std::exp(arg)));</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">        660 :   #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :   {</a>
+<a name="922"><span class="lineNum">     922 </span>            :     #pragma omp for</a>
+<a name="923"><span class="lineNum">     923 </span>            :     for(unsigned i=0; i&lt;deltaF_.size(); i++)</a>
+<a name="924"><span class="lineNum">     924 </span>            :     {</a>
+<a name="925"><span class="lineNum">     925 </span>            :       const double diff_i=(-getExpansion(i)+(bias-rct_+deltaF_[i])/kbt_-std::log(counter_-1.));</a>
+<a name="926"><span class="lineNum">     926 </span>            :       if(diff_i&gt;0) //save exp from overflow</a>
+<a name="927"><span class="lineNum">     927 </span>            :         deltaF_[i]+=increment-kbt_*(diff_i+std::log1p(std::exp(-diff_i)));</a>
+<a name="928"><span class="lineNum">     928 </span>            :       else</a>
+<a name="929"><span class="lineNum">     929 </span>            :         deltaF_[i]+=increment-kbt_*std::log1p(std::exp(diff_i));</a>
+<a name="930"><span class="lineNum">     930 </span>            :     }</a>
+<a name="931"><span class="lineNum">     931 </span>            :   }</a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">        660 :   rct_+=increment+kbt_*std::log1p(-1./counter_);</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">        660 : }</span></a>
+<a name="934"><span class="lineNum">     934 </span>            : </a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">     644469 : double OPESexpanded::getExpansion(unsigned i) const</span></a>
+<a name="936"><span class="lineNum">     936 </span>            : {</a>
+<a name="937"><span class="lineNum">     937 </span>            :   double expansion=0;</a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">    3003062 :   for(unsigned j=0; j&lt;ncv_; j++)</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">    2358593 :     expansion+=ECVs_[j][index_k_[i][j]]; //the index_k could be trivially guessed for most ECVs, but unfourtunately not all</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">     644469 :   return expansion;</span></a>
+<a name="941"><span class="lineNum">     941 </span>            : }</a>
+<a name="942"><span class="lineNum">     942 </span>            : </a>
+<a name="943"><span class="lineNum">     943 </span>            : }</a>
+<a name="944"><span class="lineNum">     944 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/OPESmetad.cpp.func-sort-c.html b/coverage/opes/OPESmetad.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4a443657aa
--- /dev/null
+++ b/coverage/opes/OPESmetad.cpp.func-sort-c.html
@@ -0,0 +1,208 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/OPESmetad.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - OPESmetad.cpp<span style="font-size: 80%;"> (<a href="OPESmetad.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">795</td>
+            <td class="headerCovTableEntry">831</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OPESmetad.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1501">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE11updateNlistERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#298">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_eRegisterMe3006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#360">_ZN4PLMD4opes9OPESmetadINS0_11explorationEEC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1592">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE15dumpStateToFileEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#301">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1592">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE15dumpStateToFileEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#254">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_cRegisterMe2566createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#301">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1398">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE9addKernelEdRKSt6vectorIdSaIdEES8_d</a></td>
+              <td class="coverFnHi">106</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1738">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE12mergeKernelsERNS3_6kernelERKS4_</a></td>
+              <td class="coverFnHi">111</td>
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+    <tr>
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+              <td class="coverFnHi">126</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">148</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1413">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE18getMergeableKernelERKSt6vectorIdSaIdEEj</a></td>
+              <td class="coverFnHi">196</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1501">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE11updateNlistERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">250</td>
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+              <td class="coverFnHi">256</td>
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+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1738">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE12mergeKernelsERNS3_6kernelERKS4_</a></td>
+              <td class="coverFnHi">277</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1398">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE9addKernelEdRKSt6vectorIdSaIdEES8_d</a></td>
+              <td class="coverFnHi">277</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#989">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE6updateEv</a></td>
+              <td class="coverFnHi">357</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#950">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE9calculateEv</a></td>
+              <td class="coverFnHi">357</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1340">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE9addKernelEdRKSt6vectorIdSaIdEES8_</a></td>
+              <td class="coverFnHi">387</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1273">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE21getProbAndDerivativesERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnHi">387</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1721">_ZN4PLMD4opes9OPESmetadINS0_11explorationEE14evaluateKernelERKNS3_6kernelERKSt6vectorIdSaIdEERS9_SC_</a></td>
+              <td class="coverFnHi">604</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1413">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE18getMergeableKernelERKSt6vectorIdSaIdEEj</a></td>
+              <td class="coverFnHi">654</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#989">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE6updateEv</a></td>
+              <td class="coverFnHi">714</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#950">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE9calculateEv</a></td>
+              <td class="coverFnHi">714</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1273">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE21getProbAndDerivativesERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnHi">754</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#206">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE6kernelC2EdRKSt6vectorIdSaIdEES9_</a></td>
+              <td class="coverFnHi">794</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1721">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE14evaluateKernelERKNS3_6kernelERKSt6vectorIdSaIdEERS9_SC_</a></td>
+              <td class="coverFnHi">2760</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#254">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_cRegisterMe256C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#254">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_cRegisterMe256D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#298">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_eRegisterMe300C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#298">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_eRegisterMe300D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1707">_ZNK4PLMD4opes9OPESmetadINS0_11convergenceEE14evaluateKernelERKNS3_6kernelERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">5821</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/OPESmetad.cpp.func.html b/coverage/opes/OPESmetad.cpp.func.html
new file mode 100644
index 0000000000..f6b1685ca4
--- /dev/null
+++ b/coverage/opes/OPESmetad.cpp.func.html
@@ -0,0 +1,208 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/OPESmetad.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - OPESmetad.cpp<span style="font-size: 80%;"> (<a href="OPESmetad.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">795</td>
+            <td class="headerCovTableEntry">831</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OPESmetad.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#254">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_cRegisterMe2566createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#254">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_cRegisterMe256C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#254">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_cRegisterMe256D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#298">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_eRegisterMe3006createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#298">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_eRegisterMe300C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#298">_ZN4PLMD4opes12_GLOBAL__N_124OPESmetad_eRegisterMe300D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1501">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE11updateNlistERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">250</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1738">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE12mergeKernelsERNS3_6kernelERKS4_</a></td>
+              <td class="coverFnHi">277</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1721">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE14evaluateKernelERKNS3_6kernelERKSt6vectorIdSaIdEERS9_SC_</a></td>
+              <td class="coverFnHi">2760</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1592">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE15dumpStateToFileEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#301">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OPESmetad.cpp.gcov.html#1413">_ZN4PLMD4opes9OPESmetadINS0_11convergenceEE18getMergeableKernelERKSt6vectorIdSaIdEEj</a></td>
+              <td class="coverFnHi">654</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
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diff --git a/coverage/opes/OPESmetad.cpp.gcov.html b/coverage/opes/OPESmetad.cpp.gcov.html
new file mode 100644
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes/OPESmetad.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">opes</a> - OPESmetad.cpp<span style="font-size: 80%;"> (source / <a href="OPESmetad.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">795</td>
+            <td class="headerCovTableEntry">831</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryHi">97.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2020-2021 of Michele Invernizzi.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of the OPES plumed module.</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The OPES plumed module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The OPES plumed module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace opes {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC OPES_BIAS OPES_METAD</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : On-the-fly probability enhanced sampling with metadynamics-like target distribution.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This On-the-fly probability enhanced sampling (\ref OPES &quot;OPES&quot;) method with metadynamics-like target distribution is described in \cite Invernizzi2020rethinking.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This \ref OPES_METAD action samples target distributions defined via their marginal \f$p^{\text{tg}}(\mathbf{s})\f$ over some collective variables (CVs), \f$\mathbf{s}=\mathbf{s}(\mathbf{x})\f$.</a>
+<a name="37"><span class="lineNum">      37 </span>            : By default \ref OPES_METAD targets the well-tempered distribution, \f$p^{\text{WT}}(\mathbf{s})\propto [P(\mathbf{s})]^{1/\gamma}\f$, where \f$\gamma\f$ is known as BIASFACTOR.</a>
+<a name="38"><span class="lineNum">      38 </span>            : Similarly to \ref METAD, \ref OPES_METAD optimizes the bias on-the-fly, with a given PACE.</a>
+<a name="39"><span class="lineNum">      39 </span>            : It does so by reweighting via kernel density estimation the unbiased distribution in the CV space, \f$P(\mathbf{s})\f$.</a>
+<a name="40"><span class="lineNum">      40 </span>            : A compression algorithm is used to prevent the number of kernels from growing linearly with the simulation time.</a>
+<a name="41"><span class="lineNum">      41 </span>            : The bias at step \f$n\f$ is</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : V_n(\mathbf{s}) = (1-1/\gamma)\frac{1}{\beta}\log\left(\frac{P_n(\mathbf{s})}{Z_n}+\epsilon\right)\, .</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : See Ref.\cite Invernizzi2020rethinking for a complete description of the method.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : As an intuitive picture, rather than gradually filling the metastable basins, \ref OPES_METAD quickly tries to get a coarse idea of the full free energy surface (FES), and then slowly refines its details.</a>
+<a name="48"><span class="lineNum">      48 </span>            : It has a fast initial exploration phase, and then becomes extremely conservative and does not significantly change the shape of the deposited bias any more, reaching a regime of quasi-static bias.</a>
+<a name="49"><span class="lineNum">      49 </span>            : For this reason, it is possible to use standard umbrella sampling reweighting (see \ref REWEIGHT_BIAS) to analyse the trajectory.</a>
+<a name="50"><span class="lineNum">      50 </span>            : At &lt;a href=&quot;https://github.com/invemichele/opes/tree/master/postprocessing&quot;&gt;this link&lt;/a&gt; you can find some python scripts that work in a similar way to \ref sum_hills, but the preferred way to obtain a FES with OPES is via reweighting (see \ref opes-metad).</a>
+<a name="51"><span class="lineNum">      51 </span>            : The estimated \f$c(t)\f$ is printed for reference only, since it should converge to a fixed value as the bias converges.</a>
+<a name="52"><span class="lineNum">      52 </span>            : This \f$c(t)\f$ should NOT be used for reweighting.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Similarly, the \f$Z_n\f$ factor is printed only for reference, and it should converge when no new region of the CV-space is explored.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : Notice that \ref OPES_METAD is more sensitive to degenerate CVs than \ref METAD.</a>
+<a name="56"><span class="lineNum">      56 </span>            : If the employed CVs map different metastable basins onto the same CV-space region, then \ref OPES_METAD will remain stuck rather than completely reshaping the bias.</a>
+<a name="57"><span class="lineNum">      57 </span>            : This can be useful to diagnose problems with your collective variable.</a>
+<a name="58"><span class="lineNum">      58 </span>            : If it is not possible to improve the set of CVs and remove this degeneracy, then you might instead consider to use \ref OPES_METAD_EXPLORE or \ref METAD.</a>
+<a name="59"><span class="lineNum">      59 </span>            : In this way you will be able to obtain an estimate of the FES, but be aware that you most likely will not reach convergence and thus this estimate will be subjected to systematic errors (see e.g. Fig.3 in \cite Pietrucci2017review).</a>
+<a name="60"><span class="lineNum">      60 </span>            : On the contrary, if your CVs are not degenerate but only suboptimal, you should converge faster by using \ref OPES_METAD instead of \ref METAD \cite Invernizzi2020rethinking.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The parameter BARRIER should be set to be at least equal to the highest free energy barrier you wish to overcome.</a>
+<a name="63"><span class="lineNum">      63 </span>            : If it is much lower than that, you will not cross the barrier, if it is much higher, convergence might take a little longer.</a>
+<a name="64"><span class="lineNum">      64 </span>            : If the system has a basin that is clearly more stable than the others, it is better to start the simulation from there.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : By default, the kernels SIGMA is adaptive, estimated from the fluctuations over ADAPTIVE_SIGMA_STRIDE simulation steps (similar to \ref METAD ADAPTIVE=DIFF, but contrary to that, no artifacts are introduced and the bias will converge to the correct one).</a>
+<a name="67"><span class="lineNum">      67 </span>            : However, notice that depending on the system this might not be the optimal choice for SIGMA.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : You can target a uniform flat distribution by explicitly setting BIASFACTOR=inf.</a>
+<a name="70"><span class="lineNum">      70 </span>            : However, this should be useful only in very specific cases.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : It is possible to take into account also of other bias potentials besides the one of \ref OPES_METAD during the internal reweighting for \f$P(\mathbf{s})\f$ estimation.</a>
+<a name="73"><span class="lineNum">      73 </span>            : To do so, one has to add those biases with the EXTRA_BIAS keyword, as in the example below.</a>
+<a name="74"><span class="lineNum">      74 </span>            : This allows one to define a custom target distribution by adding another bias potential equal to the desired target free energy and setting BIASFACTOR=inf (see example below).</a>
+<a name="75"><span class="lineNum">      75 </span>            : Another possible usage of EXTRA_BIAS is to make sure that \ref OPES_METAD does not push against another fixed bias added to restrain the CVs range (e.g. \ref UPPER_WALLS).</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : Through the EXCLUDED_REGION keywork, it is possible to specify a region of CV space where no kernels will be deposited.</a>
+<a name="78"><span class="lineNum">      78 </span>            : This can be useful for example for making sure the bias does not modify the transition region, thus allowing for rate calculation.</a>
+<a name="79"><span class="lineNum">      79 </span>            : See below for an example of how to use this keyword.</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : Restart can be done from a KERNELS file, but it might be not perfect (due to limited precision when printing kernels to file, or if adaptive SIGMA is used).</a>
+<a name="82"><span class="lineNum">      82 </span>            : For an exact restart you must use STATE_RFILE to read a checkpoint with all the needed info.</a>
+<a name="83"><span class="lineNum">      83 </span>            : To save such checkpoints, define a STATE_WFILE and choose how often to print them with STATE_WSTRIDE.</a>
+<a name="84"><span class="lineNum">      84 </span>            : By default this file is overwritten, but you can instead append to it using the flag STORE_STATES.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : Multiple walkers are supported only with MPI communication, via the keyword WALKERS_MPI.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : \par Examples</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : Several examples can be found on the &lt;a href=&quot;https://www.plumed-nest.org/browse.html&quot;&gt;PLUMED-NEST website&lt;/a&gt;, by searching for the OPES keyword.</a>
+<a name="91"><span class="lineNum">      91 </span>            : The \ref opes-metad can also be useful to get started with the method.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : The following is a minimal working example:</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : \plumedfile</a>
+<a name="96"><span class="lineNum">      96 </span>            : cv: DISTANCE ATOMS=1,2</a>
+<a name="97"><span class="lineNum">      97 </span>            : opes: OPES_METAD ARG=cv PACE=200 BARRIER=40</a>
+<a name="98"><span class="lineNum">      98 </span>            : PRINT STRIDE=200 FILE=COLVAR ARG=*</a>
+<a name="99"><span class="lineNum">      99 </span>            : \endplumedfile</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : Another more articulated one:</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : \plumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="105"><span class="lineNum">     105 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="106"><span class="lineNum">     106 </span>            : opes: OPES_METAD ...</a>
+<a name="107"><span class="lineNum">     107 </span>            :   FILE=Kernels.data</a>
+<a name="108"><span class="lineNum">     108 </span>            :   TEMP=300</a>
+<a name="109"><span class="lineNum">     109 </span>            :   ARG=phi,psi</a>
+<a name="110"><span class="lineNum">     110 </span>            :   PACE=500</a>
+<a name="111"><span class="lineNum">     111 </span>            :   BARRIER=50</a>
+<a name="112"><span class="lineNum">     112 </span>            :   SIGMA=0.15,0.15</a>
+<a name="113"><span class="lineNum">     113 </span>            :   SIGMA_MIN=0.01,0.01</a>
+<a name="114"><span class="lineNum">     114 </span>            :   STATE_RFILE=Restart.data</a>
+<a name="115"><span class="lineNum">     115 </span>            :   STATE_WFILE=State.data</a>
+<a name="116"><span class="lineNum">     116 </span>            :   STATE_WSTRIDE=500*100</a>
+<a name="117"><span class="lineNum">     117 </span>            :   STORE_STATES</a>
+<a name="118"><span class="lineNum">     118 </span>            :   WALKERS_MPI</a>
+<a name="119"><span class="lineNum">     119 </span>            :   NLIST</a>
+<a name="120"><span class="lineNum">     120 </span>            : ...</a>
+<a name="121"><span class="lineNum">     121 </span>            : PRINT FMT=%g STRIDE=500 FILE=Colvar.data ARG=phi,psi,opes.*</a>
+<a name="122"><span class="lineNum">     122 </span>            : \endplumedfile</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : Next is an example of how to define a custom target distribution different from the well-tempered one.</a>
+<a name="125"><span class="lineNum">     125 </span>            : Here we chose to focus more on the transition state, that is around \f$\phi=0\f$.</a>
+<a name="126"><span class="lineNum">     126 </span>            : Our target distribution is a Gaussian centered there, thus the target free energy we want to sample is a parabola, \f$F^{\text{tg}}(\mathbf{s})=-\frac{1}{\beta} \log [p^{\text{tg}}(\mathbf{s})]\f$.</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : \plumedfile</a>
+<a name="129"><span class="lineNum">     129 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="130"><span class="lineNum">     130 </span>            : FtgValue: CUSTOM ARG=phi PERIODIC=NO FUNC=(x/0.4)^2</a>
+<a name="131"><span class="lineNum">     131 </span>            : Ftg: BIASVALUE ARG=FtgValue</a>
+<a name="132"><span class="lineNum">     132 </span>            : opes: OPES_METAD ...</a>
+<a name="133"><span class="lineNum">     133 </span>            :   ARG=phi</a>
+<a name="134"><span class="lineNum">     134 </span>            :   PACE=500</a>
+<a name="135"><span class="lineNum">     135 </span>            :   BARRIER=50</a>
+<a name="136"><span class="lineNum">     136 </span>            :   SIGMA=0.2</a>
+<a name="137"><span class="lineNum">     137 </span>            :   BIASFACTOR=inf</a>
+<a name="138"><span class="lineNum">     138 </span>            :   EXTRA_BIAS=Ftg.bias</a>
+<a name="139"><span class="lineNum">     139 </span>            : ...</a>
+<a name="140"><span class="lineNum">     140 </span>            : PRINT FMT=%g STRIDE=500 FILE=COLVAR ARG=phi,Ftg.bias,opes.bias</a>
+<a name="141"><span class="lineNum">     141 </span>            : \endplumedfile</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : Notice that in order to reweight for the unbiased \f$P(\mathbf{s})\f$ during postprocessing, the total bias `Ftg.bias+opes.bias` must be used.</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : Finally, an example of how to use the EXCLUDED_REGION keyword.</a>
+<a name="146"><span class="lineNum">     146 </span>            : It expects a characteristic function that is different from zero in the region to be excluded.</a>
+<a name="147"><span class="lineNum">     147 </span>            : You can use \ref CUSTOM and a combination of the step function to define it.</a>
+<a name="148"><span class="lineNum">     148 </span>            : With the following input no kernel is deposited in the transition state region of alanine dipeptide, defined by the interval \f$\phi \in [-0.6, 0.7]\f$:</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : \plumedfile</a>
+<a name="151"><span class="lineNum">     151 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="152"><span class="lineNum">     152 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="153"><span class="lineNum">     153 </span>            : xx: CUSTOM PERIODIC=NO ARG=phi FUNC=step(x+0.6)-step(x-0.7)</a>
+<a name="154"><span class="lineNum">     154 </span>            : opes: OPES_METAD ...</a>
+<a name="155"><span class="lineNum">     155 </span>            :   ARG=phi,psi</a>
+<a name="156"><span class="lineNum">     156 </span>            :   PACE=500</a>
+<a name="157"><span class="lineNum">     157 </span>            :   BARRIER=30</a>
+<a name="158"><span class="lineNum">     158 </span>            :   EXCLUDED_REGION=xx</a>
+<a name="159"><span class="lineNum">     159 </span>            :   NLIST</a>
+<a name="160"><span class="lineNum">     160 </span>            : ...</a>
+<a name="161"><span class="lineNum">     161 </span>            : PRINT FMT=%g STRIDE=500 FILE=COLVAR ARG=phi,psi,xx,opes.*</a>
+<a name="162"><span class="lineNum">     162 </span>            : \endplumedfile</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : */</a>
+<a name="165"><span class="lineNum">     165 </span>            : //+ENDPLUMEDOC</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : template &lt;class mode&gt;</a>
+<a name="168"><span class="lineNum">     168 </span>            : class OPESmetad : public bias::Bias {</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : private:</a>
+<a name="171"><span class="lineNum">     171 </span>            :   bool isFirstStep_;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   unsigned NumOMP_;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   unsigned NumParallel_;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   unsigned rank_;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   unsigned NumWalkers_;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   unsigned walker_rank_;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   unsigned long long counter_;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   std::size_t ncv_;</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :   double kbt_;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   double biasfactor_;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double bias_prefactor_;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   unsigned stride_;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   std::vector&lt;double&gt; sigma0_;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   std::vector&lt;double&gt; sigma_min_;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   unsigned adaptive_sigma_stride_;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   unsigned long long adaptive_counter_;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   std::vector&lt;double&gt; av_cv_;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::vector&lt;double&gt; av_M2_;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   bool fixed_sigma_;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   bool adaptive_sigma_;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   double epsilon_;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   double sum_weights_;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   double sum_weights2_;</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   bool no_Zed_;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   double Zed_;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   double KDEnorm_;</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            :   double threshold2_;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   bool recursive_merge_;</a>
+<a name="202"><span class="lineNum">     202 </span>            : //kernels are truncated diagonal Gaussians</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       1050 :   struct kernel</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   {</a>
+<a name="205"><span class="lineNum">     205 </span>            :     double height;</a>
+<a name="206"><span class="lineNum">     206 </span>            :     std::vector&lt;double&gt; center;</a>
+<a name="207"><span class="lineNum">     207 </span>            :     std::vector&lt;double&gt; sigma;</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       1050 :     kernel(double h, const std::vector&lt;double&gt;&amp; c,const std::vector&lt;double&gt;&amp; s):</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1050 :       height(h),center(c),sigma(s) {}</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   };</a>
+<a name="211"><span class="lineNum">     211 </span>            :   double cutoff2_;</a>
+<a name="212"><span class="lineNum">     212 </span>            :   double val_at_cutoff_;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   void mergeKernels(kernel&amp;,const kernel&amp;); //merge the second one into the first one</a>
+<a name="214"><span class="lineNum">     214 </span>            :   double evaluateKernel(const kernel&amp;,const std::vector&lt;double&gt;&amp;) const;</a>
+<a name="215"><span class="lineNum">     215 </span>            :   double evaluateKernel(const kernel&amp;,const std::vector&lt;double&gt;&amp;,std::vector&lt;double&gt;&amp;,std::vector&lt;double&gt;&amp;);</a>
+<a name="216"><span class="lineNum">     216 </span>            :   std::vector&lt;kernel&gt; kernels_; //all compressed kernels</a>
+<a name="217"><span class="lineNum">     217 </span>            :   OFile kernelsOfile_;</a>
+<a name="218"><span class="lineNum">     218 </span>            : //neighbour list stuff</a>
+<a name="219"><span class="lineNum">     219 </span>            :   bool nlist_;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   double nlist_param_[2];</a>
+<a name="221"><span class="lineNum">     221 </span>            :   std::vector&lt;unsigned&gt; nlist_index_;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   std::vector&lt;double&gt; nlist_center_;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   std::vector&lt;double&gt; nlist_dev2_;</a>
+<a name="224"><span class="lineNum">     224 </span>            :   unsigned nlist_steps_;</a>
+<a name="225"><span class="lineNum">     225 </span>            :   bool nlist_update_;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   bool nlist_pace_reset_;</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   bool calc_work_;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   double work_;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   double old_KDEnorm_;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   std::vector&lt;kernel&gt; delta_kernels_;</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            :   Value* excluded_region_;</a>
+<a name="234"><span class="lineNum">     234 </span>            :   std::vector&lt;Value*&gt; extra_biases_;</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :   OFile stateOfile_;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   int wStateStride_;</a>
+<a name="238"><span class="lineNum">     238 </span>            :   bool storeOldStates_;</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            :   double getProbAndDerivatives(const std::vector&lt;double&gt;&amp;,std::vector&lt;double&gt;&amp;);</a>
+<a name="241"><span class="lineNum">     241 </span>            :   void addKernel(const double,const std::vector&lt;double&gt;&amp;,const std::vector&lt;double&gt;&amp;);</a>
+<a name="242"><span class="lineNum">     242 </span>            :   void addKernel(const double,const std::vector&lt;double&gt;&amp;,const std::vector&lt;double&gt;&amp;,const double); //also print to file</a>
+<a name="243"><span class="lineNum">     243 </span>            :   unsigned getMergeableKernel(const std::vector&lt;double&gt;&amp;,const unsigned);</a>
+<a name="244"><span class="lineNum">     244 </span>            :   void updateNlist(const std::vector&lt;double&gt;&amp;);</a>
+<a name="245"><span class="lineNum">     245 </span>            :   void dumpStateToFile();</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : public:</a>
+<a name="248"><span class="lineNum">     248 </span>            :   explicit OPESmetad(const ActionOptions&amp;);</a>
+<a name="249"><span class="lineNum">     249 </span>            :   void calculate() override;</a>
+<a name="250"><span class="lineNum">     250 </span>            :   void update() override;</a>
+<a name="251"><span class="lineNum">     251 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="252"><span class="lineNum">     252 </span>            : };</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : struct convergence { static const bool explore=false; };</a>
+<a name="255"><span class="lineNum">     255 </span>            : typedef OPESmetad&lt;convergence&gt; OPESmetad_c;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">      12532 : PLUMED_REGISTER_ACTION(OPESmetad_c,&quot;OPES_METAD&quot;)</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : //OPES_METAD_EXPLORE is very similar from the point of view of the code,</a>
+<a name="259"><span class="lineNum">     259 </span>            : //but conceptually it is better to make it a separate BIAS action</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : //+PLUMEDOC OPES_BIAS OPES_METAD_EXPLORE</a>
+<a name="262"><span class="lineNum">     262 </span>            : /*</a>
+<a name="263"><span class="lineNum">     263 </span>            : On-the-fly probability enhanced sampling with well-tempered target distribution in exploreation mode.</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : On-the-fly probability enhanced sampling with well-tempered target distribution (\ref OPES &quot;OPES&quot;) with well-tempered target distribution, exploration mode \cite Invernizzi2022explore .</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : This \ref OPES_METAD_EXPLORE action samples the well-tempered target distribution, that is defined via its marginal \f$p^{\text{WT}}(\mathbf{s})\propto [P(\mathbf{s})]^{1/\gamma}\f$ over some collective variables (CVs), \f$\mathbf{s}=\mathbf{s}(\mathbf{x})\f$.</a>
+<a name="268"><span class="lineNum">     268 </span>            : While \ref OPES_METAD does so by estimating the unbiased distribution \f$P(\mathbf{s})\f$, \ref OPES_METAD_EXPLORE instead estimates on-the-fly the target \f$p^{\text{WT}}(\mathbf{s})\f$ and uses it to define the bias.</a>
+<a name="269"><span class="lineNum">     269 </span>            : The bias at step \f$n\f$ is</a>
+<a name="270"><span class="lineNum">     270 </span>            : \f[</a>
+<a name="271"><span class="lineNum">     271 </span>            : V_n(\mathbf{s}) = (\gamma-1)\frac{1}{\beta}\log\left(\frac{p^{\text{WT}}_n(\mathbf{s})}{Z_n}+\epsilon\right)\, .</a>
+<a name="272"><span class="lineNum">     272 </span>            : \f]</a>
+<a name="273"><span class="lineNum">     273 </span>            : See Ref.\cite Invernizzi2022explore for a complete description of the method.</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : Intuitively, while \ref OPES_METAD aims at quickly converging the reweighted free energy, \ref OPES_METAD_EXPLORE aims at quickly sampling the target well-tempered distribution.</a>
+<a name="276"><span class="lineNum">     276 </span>            : Given enough simulation time, both will converge to the same bias potential but they do so in a qualitatively different way.</a>
+<a name="277"><span class="lineNum">     277 </span>            : Compared to \ref OPES_METAD, \ref OPES_METAD_EXPLORE is more similar to \ref METAD, because it allows the bias to vary significantly, thus enhancing exploration.</a>
+<a name="278"><span class="lineNum">     278 </span>            : This goes at the expenses of a typically slower convergence of the reweight estimate.</a>
+<a name="279"><span class="lineNum">     279 </span>            : \ref OPES_METAD_EXPLORE can be useful e.g.~for simulating a new system with an unknown BARRIER, or for quickly testing the effectiveness of a new CV that might be degenerate.</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : Similarly to \ref OPES_METAD, also \ref OPES_METAD_EXPLORE uses a kernel density estimation with the same on-the-fly compression algorithm.</a>
+<a name="282"><span class="lineNum">     282 </span>            : The only difference is that the kernels are not weighted, since it estimates the sampled distribution and not the reweighted unbiased one.</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : All the options of \ref OPES_METAD are also available in \ref OPES_METAD_EXPLORE, except for those that modify the target distribution, since only a well-tempered target is allowed in this case.</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : \par Examples</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : The following is a minimal working example:</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : \plumedfile</a>
+<a name="291"><span class="lineNum">     291 </span>            : cv: DISTANCE ATOMS=1,2</a>
+<a name="292"><span class="lineNum">     292 </span>            : opes: OPES_METAD_EXPLORE ARG=cv PACE=500 BARRIER=40</a>
+<a name="293"><span class="lineNum">     293 </span>            : PRINT STRIDE=100 FILE=COLVAR ARG=cv,opes.*</a>
+<a name="294"><span class="lineNum">     294 </span>            : \endplumedfile</a>
+<a name="295"><span class="lineNum">     295 </span>            : */</a>
+<a name="296"><span class="lineNum">     296 </span>            : //+ENDPLUMEDOC</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : struct exploration { static const bool explore=true; };</a>
+<a name="299"><span class="lineNum">     299 </span>            : typedef OPESmetad&lt;exploration&gt; OPESmetad_e;</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">      12518 : PLUMED_REGISTER_ACTION(OPESmetad_e,&quot;OPES_METAD_EXPLORE&quot;)</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : template &lt;class mode&gt;</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         25 : void OPESmetad&lt;mode&gt;::registerKeywords(Keywords&amp; keys)</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         25 :   Bias::registerKeywords(keys);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         25 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         50 :   keys.add(&quot;compulsory&quot;,&quot;TEMP&quot;,&quot;-1&quot;,&quot;temperature. If not set, it is taken from MD engine, but not all MD codes provide it&quot;);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         50 :   keys.add(&quot;compulsory&quot;,&quot;PACE&quot;,&quot;the frequency for kernel deposition&quot;);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         25 :   std::string info_sigma(&quot;the initial widths of the kernels&quot;);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   if(mode::explore)</a>
+<a name="311"><span class="lineNum">     311 </span>            :     info_sigma+=&quot;, divided by the square root of gamma&quot;;</a>
+<a name="312"><span class="lineNum">     312 </span>            :   info_sigma+=&quot;. If not set, an adaptive sigma will be used with the given ADAPTIVE_SIGMA_STRIDE&quot;;</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         50 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;ADAPTIVE&quot;,info_sigma);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         50 :   keys.add(&quot;compulsory&quot;,&quot;BARRIER&quot;,&quot;the free energy barrier to be overcome. It is used to set BIASFACTOR, EPSILON, and KERNEL_CUTOFF to reasonable values&quot;);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         50 :   keys.add(&quot;compulsory&quot;,&quot;COMPRESSION_THRESHOLD&quot;,&quot;1&quot;,&quot;merge kernels if closer than this threshold, in units of sigma&quot;);</span></a>
+<a name="316"><span class="lineNum">     316 </span>            : //extra options</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;ADAPTIVE_SIGMA_STRIDE&quot;,&quot;number of steps for measuring adaptive sigma. Default is 10xPACE&quot;);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MIN&quot;,&quot;never reduce SIGMA below this value&quot;);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         25 :   std::string info_biasfactor(&quot;the gamma bias factor used for the well-tempered target distribution. &quot;);</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   if(mode::explore)</a>
+<a name="321"><span class="lineNum">     321 </span>            :     info_biasfactor+=&quot;Cannot be 'inf'&quot;;</a>
+<a name="322"><span class="lineNum">     322 </span>            :   else</a>
+<a name="323"><span class="lineNum">     323 </span>            :     info_biasfactor+=&quot;Set to 'inf' for uniform flat target&quot;;</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;BIASFACTOR&quot;,info_biasfactor);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;EPSILON&quot;,&quot;the value of the regularization constant for the probability&quot;);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;KERNEL_CUTOFF&quot;,&quot;truncate kernels at this distance, in units of sigma&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;NLIST_PARAMETERS&quot;,&quot;( default=3.0,0.5 ) the two cutoff parameters for the kernels neighbor list&quot;);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         50 :   keys.addFlag(&quot;NLIST&quot;,false,&quot;use neighbor list for kernels summation, faster but experimental&quot;);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         50 :   keys.addFlag(&quot;NLIST_PACE_RESET&quot;,false,&quot;force the reset of the neighbor list at each PACE. Can be useful with WALKERS_MPI&quot;);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         50 :   keys.addFlag(&quot;FIXED_SIGMA&quot;,false,&quot;do not decrease sigma as the simulation proceeds. Can be added in a RESTART, to keep in check the number of compressed kernels&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         50 :   keys.addFlag(&quot;RECURSIVE_MERGE_OFF&quot;,false,&quot;do not recursively attempt kernel merging when a new one is added&quot;);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         50 :   keys.addFlag(&quot;NO_ZED&quot;,false,&quot;do not normalize over the explored CV space, Z_n=1&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : //kernels and state files</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         50 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;KERNELS&quot;,&quot;a file in which the list of all deposited kernels is stored&quot;);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;specify format for KERNELS file&quot;);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;STATE_RFILE&quot;,&quot;read from this file the compressed kernels and all the info needed to RESTART the simulation&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;STATE_WFILE&quot;,&quot;write to this file the compressed kernels and all the info needed to RESTART the simulation&quot;);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;STATE_WSTRIDE&quot;,&quot;number of MD steps between writing the STATE_WFILE. Default is only on CPT events (but not all MD codes set them)&quot;);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         50 :   keys.addFlag(&quot;STORE_STATES&quot;,false,&quot;append to STATE_WFILE instead of ovewriting it each time&quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : //miscellaneous</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         50 :   keys.add(&quot;optional&quot;,&quot;EXCLUDED_REGION&quot;,&quot;kernels are not deposited when the action provided here has a nonzero value, see example above&quot;);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :   if(!mode::explore)</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         32 :     keys.add(&quot;optional&quot;,&quot;EXTRA_BIAS&quot;,&quot;consider also these other bias potentials for the internal reweighting. This can be used e.g. for sampling a custom target distribution (see example above)&quot;);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         50 :   keys.addFlag(&quot;CALC_WORK&quot;,false,&quot;calculate the total accumulated work done by the bias since last restart&quot;);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         50 :   keys.addFlag(&quot;WALKERS_MPI&quot;,false,&quot;switch on MPI version of multiple walkers&quot;);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         50 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;perform calculations in serial&quot;);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         25 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         25 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         25 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            : //output components</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;rct&quot;,&quot;default&quot;,&quot;estimate of c(t). \\f$\\frac{1}{\\beta}\\log \\langle e^{\\beta V} \\rangle\\f$, should become flat as the simulation converges. Do NOT use for reweighting&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;zed&quot;,&quot;default&quot;,&quot;estimate of Z_n. should become flat once no new CV-space region is explored&quot;);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;neff&quot;,&quot;default&quot;,&quot;effective sample size&quot;);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;nker&quot;,&quot;default&quot;,&quot;total number of compressed kernels used to represent the bias&quot;);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;work&quot;,&quot;CALC_WORK&quot;,&quot;total accumulated work done by the bias&quot;);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;nlker&quot;,&quot;NLIST&quot;,&quot;number of kernels in the neighbor list&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         50 :   keys.addOutputComponent(&quot;nlsteps&quot;,&quot;NLIST&quot;,&quot;number of steps from last neighbor list update&quot;);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         25 : }</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : template &lt;class mode&gt;</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         21 : OPESmetad&lt;mode&gt;::OPESmetad(const ActionOptions&amp; ao)</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :   : PLUMED_BIAS_INIT(ao)</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         21 :   , isFirstStep_(true)</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         21 :   , counter_(1)</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         21 :   , ncv_(getNumberOfArguments())</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         21 :   , Zed_(1)</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         21 :   , work_(0)</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         21 :   , excluded_region_(NULL)</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : {</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         42 :   std::string error_in_input1(&quot;Error in input in action &quot;+getName()+&quot; with label &quot;+getLabel()+&quot;: the keyword &quot;);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         21 :   std::string error_in_input2(&quot; could not be read correctly&quot;);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : //set kbt_</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         21 :   const double kB=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         21 :   kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         21 :   double temp=-1;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         21 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         21 :   if(temp&gt;0)</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :   {</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         21 :     if(kbt_&gt;0 &amp;&amp; std::abs(kbt_-kB*temp)&gt;1e-4)</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :       log.printf(&quot; +++ WARNING +++ using TEMP=%g while MD engine uses %g\n&quot;,temp,kbt_/kB);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         21 :     kbt_=kB*temp;</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         21 :   plumed_massert(kbt_&gt;0,&quot;your MD engine does not pass the temperature to plumed, you must specify it using TEMP&quot;);</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            : //other compulsory input</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         21 :   parse(&quot;PACE&quot;,stride_);</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         21 :   double barrier=0;</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         21 :   parse(&quot;BARRIER&quot;,barrier);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         21 :   plumed_massert(barrier&gt;=0,&quot;the BARRIER should be greater than zero&quot;);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         21 :   biasfactor_=barrier/kbt_;</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :   std::string biasfactor_str;</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         42 :   parse(&quot;BIASFACTOR&quot;,biasfactor_str);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         38 :   if(biasfactor_str==&quot;inf&quot; || biasfactor_str==&quot;INF&quot;)</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   {</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          4 :     biasfactor_=std::numeric_limits&lt;double&gt;::infinity();</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          4 :     bias_prefactor_=1;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   }</a>
+<a name="402"><span class="lineNum">     402 </span>            :   else</a>
+<a name="403"><span class="lineNum">     403 </span>            :   {</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         17 :     if(biasfactor_str.length()&gt;0)</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          3 :       plumed_massert(Tools::convertNoexcept(biasfactor_str,biasfactor_),error_in_input1+&quot;BIASFACTOR&quot;+error_in_input2);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         17 :     plumed_massert(biasfactor_&gt;1,&quot;BIASFACTOR must be greater than one (use 'inf' for uniform target)&quot;);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         17 :     bias_prefactor_=1-1./biasfactor_;</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :   }</a>
+<a name="409"><span class="lineNum">     409 </span>            :   if(mode::explore)</a>
+<a name="410"><span class="lineNum">     410 </span>            :   {</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">          7 :     plumed_massert(!std::isinf(biasfactor_),&quot;BIASFACTOR=inf is not compatible with EXPLORE mode&quot;);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">          7 :     bias_prefactor_=biasfactor_-1;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :   }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">         21 :   adaptive_sigma_=false;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         21 :   adaptive_sigma_stride_=0;</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         42 :   parse(&quot;ADAPTIVE_SIGMA_STRIDE&quot;,adaptive_sigma_stride_);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :   std::vector&lt;std::string&gt; sigma_str;</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         21 :   parseVector(&quot;SIGMA&quot;,sigma_str);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         21 :   sigma0_.resize(ncv_);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :   double dummy;</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         21 :   if(sigma_str.size()==1 &amp;&amp; !Tools::convertNoexcept(sigma_str[0],dummy))</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :   {</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         11 :     plumed_massert(sigma_str[0]==&quot;ADAPTIVE&quot; || sigma_str[0]==&quot;adaptive&quot;,error_in_input1+&quot;SIGMA&quot;+error_in_input2);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         11 :     plumed_massert(!std::isinf(biasfactor_),&quot;cannot use BIASFACTOR=inf with adaptive SIGMA&quot;);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         11 :     adaptive_counter_=0;</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         11 :     if(adaptive_sigma_stride_==0)</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          2 :       adaptive_sigma_stride_=10*stride_; //NB: this is arbitrary, chosen from few tests</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         11 :     av_cv_.resize(ncv_,0);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         11 :     av_M2_.resize(ncv_,0);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         11 :     plumed_massert(adaptive_sigma_stride_&gt;=stride_,&quot;better to chose ADAPTIVE_SIGMA_STRIDE &gt; PACE&quot;);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         11 :     adaptive_sigma_=true;</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :   }</a>
+<a name="434"><span class="lineNum">     434 </span>            :   else</a>
+<a name="435"><span class="lineNum">     435 </span>            :   {</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         10 :     plumed_massert(sigma_str.size()==ncv_,&quot;number of SIGMA parameters does not match number of arguments&quot;);</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">         10 :     plumed_massert(adaptive_sigma_stride_==0,&quot;if SIGMA is not ADAPTIVE you cannot set an ADAPTIVE_SIGMA_STRIDE&quot;);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">         29 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     {</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         19 :       plumed_massert(Tools::convertNoexcept(sigma_str[i],sigma0_[i]),error_in_input1+&quot;SIGMA&quot;+error_in_input2);</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :       if(mode::explore)</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          6 :         sigma0_[i]*=std::sqrt(biasfactor_); //the sigma of the target is broader Ftg(s)=1/gamma*F(s)</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     }</a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         42 :   parseVector(&quot;SIGMA_MIN&quot;,sigma_min_);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         21 :   plumed_massert(sigma_min_.size()==0 || sigma_min_.size()==ncv_,&quot;number of SIGMA_MIN does not match number of arguments&quot;);</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         21 :   if(sigma_min_.size()&gt;0 &amp;&amp; !adaptive_sigma_)</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :   {</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">          3 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          2 :       plumed_massert(sigma_min_[i]&lt;=sigma0_[i],&quot;SIGMA_MIN should be smaller than SIGMA&quot;);</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :   }</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         21 :   epsilon_=std::exp(-barrier/bias_prefactor_/kbt_);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">         21 :   parse(&quot;EPSILON&quot;,epsilon_);</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         21 :   plumed_massert(epsilon_&gt;0,&quot;you must choose a value for EPSILON greater than zero. Is your BARRIER too high?&quot;);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">         21 :   sum_weights_=std::pow(epsilon_,bias_prefactor_); //to avoid NANs we start with counter_=1 and w0=exp(beta*V0)</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         21 :   sum_weights2_=sum_weights_*sum_weights_;</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         21 :   double cutoff=sqrt(2.*barrier/bias_prefactor_/kbt_);</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :   if(mode::explore)</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          7 :     cutoff=sqrt(2.*barrier/kbt_); //otherwise it is too small</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         21 :   parse(&quot;KERNEL_CUTOFF&quot;,cutoff);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         21 :   plumed_massert(cutoff&gt;0,&quot;you must choose a value for KERNEL_CUTOFF greater than zero&quot;);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         21 :   cutoff2_=cutoff*cutoff;</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         21 :   val_at_cutoff_=std::exp(-0.5*cutoff2_);</span></a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         21 :   threshold2_=1;</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         21 :   parse(&quot;COMPRESSION_THRESHOLD&quot;,threshold2_);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         21 :   threshold2_*=threshold2_;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         21 :   if(threshold2_!=0)</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         21 :     plumed_massert(threshold2_&gt;0 &amp;&amp; threshold2_&lt;cutoff2_,&quot;COMPRESSION_THRESHOLD cannot be bigger than the KERNEL_CUTOFF&quot;);</span></a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            : //setup neighbor list</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         21 :   nlist_=false;</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         21 :   parseFlag(&quot;NLIST&quot;,nlist_);</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         21 :   nlist_pace_reset_=false;</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">         21 :   parseFlag(&quot;NLIST_PACE_RESET&quot;,nlist_pace_reset_);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         21 :   if(nlist_pace_reset_)</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          2 :     nlist_=true;</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :   std::vector&lt;double&gt; nlist_param;</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         42 :   parseVector(&quot;NLIST_PARAMETERS&quot;,nlist_param);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         21 :   if(nlist_param.size()==0)</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :   {</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         17 :     nlist_param_[0]=3.0;//*cutoff2_ -&gt; max distance of neighbors</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         17 :     nlist_param_[1]=0.5;//*nlist_dev2_[i] -&gt; condition for rebuilding</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :   }</a>
+<a name="487"><span class="lineNum">     487 </span>            :   else</a>
+<a name="488"><span class="lineNum">     488 </span>            :   {</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          4 :     nlist_=true;</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          4 :     plumed_massert(nlist_param.size()==2,&quot;two cutoff parameters are needed for the neighbor list&quot;);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          4 :     plumed_massert(nlist_param[0]&gt;1.0,&quot;the first of NLIST_PARAMETERS must be greater than 1. The smaller the first, the smaller should be the second as well&quot;);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          4 :     const double min_PARAM_1=(1.-1./std::sqrt(nlist_param[0]))+0.16;</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          4 :     plumed_massert(nlist_param[1]&gt;0,&quot;the second of NLIST_PARAMETERS must be greater than 0&quot;);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          4 :     plumed_massert(nlist_param[1]&lt;=min_PARAM_1,&quot;the second of NLIST_PARAMETERS must be smaller to avoid systematic errors. Largest suggested value is: 1.16-1/sqrt(PARAM_0) = &quot;+std::to_string(min_PARAM_1));</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          4 :     nlist_param_[0]=nlist_param[0];</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          4 :     nlist_param_[1]=nlist_param[1];</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :   }</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">         21 :   nlist_center_.resize(ncv_);</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         21 :   nlist_dev2_.resize(ncv_,0.);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         21 :   nlist_steps_=0;</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         21 :   nlist_update_=true;</span></a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            : //optional stuff</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         21 :   no_Zed_=false;</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         21 :   parseFlag(&quot;NO_ZED&quot;,no_Zed_);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         21 :   if(no_Zed_)</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :   { //this makes it more gentle in the initial phase</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">          6 :     sum_weights_=1;</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          6 :     sum_weights2_=1;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :   }</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         21 :   fixed_sigma_=false;</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         21 :   parseFlag(&quot;FIXED_SIGMA&quot;,fixed_sigma_);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         21 :   bool recursive_merge_off=false;</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         21 :   parseFlag(&quot;RECURSIVE_MERGE_OFF&quot;,recursive_merge_off);</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         21 :   recursive_merge_=!recursive_merge_off;</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         42 :   parseFlag(&quot;CALC_WORK&quot;,calc_work_);</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : //options involving extra arguments</a>
+<a name="519"><span class="lineNum">     519 </span>            :   std::vector&lt;Value*&gt; args;</a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         42 :   parseArgumentList(&quot;EXCLUDED_REGION&quot;,args);</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         21 :   if(args.size()&gt;0)</span></a>
+<a name="522"><span class="lineNum">     522 </span>            :   {</a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">          2 :     plumed_massert(args.size()==1,&quot;only one characteristic function should define the region to be excluded&quot;);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          2 :     requestExtraDependencies(args);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          2 :     excluded_region_=args[0];</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :   }</a>
+<a name="527"><span class="lineNum">     527 </span>            :   if(!mode::explore)</a>
+<a name="528"><span class="lineNum">     528 </span>            :   {</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         28 :     parseArgumentList(&quot;EXTRA_BIAS&quot;,extra_biases_);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         14 :     if(extra_biases_.size()&gt;0)</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">          2 :       requestExtraDependencies(extra_biases_);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :   }</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span>            : //kernels file</a>
+<a name="535"><span class="lineNum">     535 </span>            :   std::string kernelsFileName;</a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         42 :   parse(&quot;FILE&quot;,kernelsFileName);</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :   std::string fmt;</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         42 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="539"><span class="lineNum">     539 </span>            : </a>
+<a name="540"><span class="lineNum">     540 </span>            : //output checkpoint of current state</a>
+<a name="541"><span class="lineNum">     541 </span>            :   std::string restartFileName;</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         42 :   parse(&quot;STATE_RFILE&quot;,restartFileName);</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :   std::string stateFileName;</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         21 :   parse(&quot;STATE_WFILE&quot;,stateFileName);</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         21 :   wStateStride_=0;</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         21 :   parse(&quot;STATE_WSTRIDE&quot;,wStateStride_);</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         21 :   storeOldStates_=false;</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         21 :   parseFlag(&quot;STORE_STATES&quot;,storeOldStates_);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         21 :   if(wStateStride_!=0 || storeOldStates_)</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         10 :     plumed_massert(stateFileName.length()&gt;0,&quot;filename for storing simulation status not specified, use STATE_WFILE&quot;);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         21 :   if(wStateStride_&gt;0)</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         10 :     plumed_massert(wStateStride_&gt;=(int)stride_,&quot;STATE_WSTRIDE is in units of MD steps, thus it is suggested to use a multiple of PACE&quot;);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         21 :   if(stateFileName.length()&gt;0 &amp;&amp; wStateStride_==0)</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">          1 :     wStateStride_=-1;//will print only on CPT events (checkpoints set by some MD engines, like gromacs)</span></a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            : //multiple walkers //TODO implement also external mw for cp2k</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         21 :   bool walkers_mpi=false;</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         21 :   parseFlag(&quot;WALKERS_MPI&quot;,walkers_mpi);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         21 :   if(walkers_mpi)</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :   {</a>
+<a name="561"><span class="lineNum">     561 </span>            :     //If this Action is not compiled with MPI the user is informed and we exit gracefully</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         10 :     plumed_massert(Communicator::plumedHasMPI(),&quot;Invalid walkers configuration: WALKERS_MPI flag requires MPI compilation&quot;);</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         10 :     plumed_massert(Communicator::initialized(),&quot;Invalid walkers configuration: WALKERS_MPI needs the communicator correctly initialized.&quot;);</span></a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         10 :     if(comm.Get_rank()==0)//multi_sim_comm works on first rank only</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :     {</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         10 :       NumWalkers_=multi_sim_comm.Get_size();</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         10 :       walker_rank_=multi_sim_comm.Get_rank();</span></a>
+<a name="569"><span class="lineNum">     569 </span>            :     }</a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">         10 :     comm.Bcast(NumWalkers_,0); //if each walker has more than one processor update them all</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">         10 :     comm.Bcast(walker_rank_,0);</span></a>
+<a name="572"><span class="lineNum">     572 </span>            :   }</a>
+<a name="573"><span class="lineNum">     573 </span>            :   else</a>
+<a name="574"><span class="lineNum">     574 </span>            :   {</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         11 :     NumWalkers_=1;</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         11 :     walker_rank_=0;</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :   }</a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span>            : //parallelization stuff</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         21 :   NumOMP_=OpenMP::getNumThreads();</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         21 :   NumParallel_=comm.Get_size();</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         21 :   rank_=comm.Get_rank();</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         21 :   bool serial=false;</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         21 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         21 :   if(serial)</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :   {</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">          4 :     NumOMP_=1;</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">          4 :     NumParallel_=1;</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">          4 :     rank_=0;</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :   }</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">         21 :   checkRead();</span></a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span>            : //restart if needed</a>
+<a name="595"><span class="lineNum">     595 </span>            :   bool convertKernelsToState=false;</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         21 :   if(getRestart())</span></a>
+<a name="597"><span class="lineNum">     597 </span>            :   {</a>
+<a name="598"><span class="lineNum">     598 </span>            :     bool stateRestart=true;</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         11 :     if(restartFileName.length()==0)</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :     {</a>
+<a name="601"><span class="lineNum">     601 </span>            :       stateRestart=false;</a>
+<a name="602"><span class="lineNum">     602 </span>            :       restartFileName=kernelsFileName;</a>
+<a name="603"><span class="lineNum">     603 </span>            :     }</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         11 :     IFile ifile;</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">         11 :     ifile.link(*this);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">         11 :     if(ifile.FileExist(restartFileName))</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :     {</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">         11 :       bool tmp_nlist=nlist_;</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         11 :       nlist_=false; // NLIST is not needed while restarting</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         11 :       ifile.open(restartFileName);</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         11 :       log.printf(&quot;  RESTART - make sure all used options are compatible\n&quot;);</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         11 :       log.printf(&quot;    restarting from: %s\n&quot;,restartFileName.c_str());</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">         11 :       std::string action_name=getName();</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         11 :       if(stateRestart)</span></a>
+<a name="615"><span class="lineNum">     615 </span>            :       {</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">          6 :         log.printf(&quot;    it should be a STATE file (not a KERNELS file)\n&quot;);</span></a>
+<a name="617"><span class="lineNum">     617 </span>            :         action_name+=&quot;_state&quot;;</a>
+<a name="618"><span class="lineNum">     618 </span>            :       }</a>
+<a name="619"><span class="lineNum">     619 </span>            :       else</a>
+<a name="620"><span class="lineNum">     620 </span>            :       {</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">          5 :         log.printf(&quot; +++ WARNING +++ RESTART from KERNELS might be approximate, use STATE_WFILE and STATE_RFILE to restart from the exact state\n&quot;);</span></a>
+<a name="622"><span class="lineNum">     622 </span>            :         action_name+=&quot;_kernels&quot;;</a>
+<a name="623"><span class="lineNum">     623 </span>            :       }</a>
+<a name="624"><span class="lineNum">     624 </span>            :       std::string old_action_name;</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         11 :       ifile.scanField(&quot;action&quot;,old_action_name);</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         11 :       plumed_massert(action_name==old_action_name,&quot;RESTART - mismatch between old and new action name. Expected '&quot;+action_name+&quot;', but found '&quot;+old_action_name+&quot;'&quot;);</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :       std::string old_biasfactor_str;</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         22 :       ifile.scanField(&quot;biasfactor&quot;,old_biasfactor_str);</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">         21 :       if(old_biasfactor_str==&quot;inf&quot; || old_biasfactor_str==&quot;INF&quot;)</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :       {</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">          1 :         if(!std::isinf(biasfactor_))</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :           log.printf(&quot; +++ WARNING +++ previous bias factor was inf while now it is %g\n&quot;,biasfactor_);</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :       }</a>
+<a name="634"><span class="lineNum">     634 </span>            :       else</a>
+<a name="635"><span class="lineNum">     635 </span>            :       {</a>
+<a name="636"><span class="lineNum">     636 </span>            :         double old_biasfactor;</a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">         10 :         ifile.scanField(&quot;biasfactor&quot;,old_biasfactor);</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">         10 :         if(std::abs(biasfactor_-old_biasfactor)&gt;1e-6*biasfactor_)</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :           log.printf(&quot; +++ WARNING +++ previous bias factor was %g while now it is %g. diff = %g\n&quot;,old_biasfactor,biasfactor_,biasfactor_-old_biasfactor);</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :       }</a>
+<a name="641"><span class="lineNum">     641 </span>            :       double old_epsilon;</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">         11 :       ifile.scanField(&quot;epsilon&quot;,old_epsilon);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">         11 :       if(std::abs(epsilon_-old_epsilon)&gt;1e-6*epsilon_)</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">          8 :         log.printf(&quot; +++ WARNING +++ previous epsilon was %g while now it is %g. diff = %g\n&quot;,old_epsilon,epsilon_,epsilon_-old_epsilon);</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :       double old_cutoff;</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">         11 :       ifile.scanField(&quot;kernel_cutoff&quot;,old_cutoff);</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         11 :       if(std::abs(cutoff-old_cutoff)&gt;1e-6*cutoff)</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineNoCov">          0 :         log.printf(&quot; +++ WARNING +++ previous kernel_cutoff was %g while now it is %g. diff = %g\n&quot;,old_cutoff,cutoff,cutoff-old_cutoff);</span></a>
+<a name="649"><span class="lineNum">     649 </span>            :       double old_threshold;</a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">         11 :       const double threshold=sqrt(threshold2_);</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">         11 :       ifile.scanField(&quot;compression_threshold&quot;,old_threshold);</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">         11 :       if(std::abs(threshold-old_threshold)&gt;1e-6*threshold)</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineNoCov">          0 :         log.printf(&quot; +++ WARNING +++ previous compression_threshold was %g while now it is %g. diff = %g\n&quot;,old_threshold,threshold,threshold-old_threshold);</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">         11 :       if(stateRestart)</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :       {</a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">          6 :         ifile.scanField(&quot;zed&quot;,Zed_);</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">          6 :         ifile.scanField(&quot;sum_weights&quot;,sum_weights_);</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">          6 :         ifile.scanField(&quot;sum_weights2&quot;,sum_weights2_);</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">          6 :         ifile.scanField(&quot;counter&quot;,counter_);</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">          6 :         if(adaptive_sigma_)</span></a>
+<a name="661"><span class="lineNum">     661 </span>            :         {</a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">          6 :           ifile.scanField(&quot;adaptive_counter&quot;,adaptive_counter_);</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">          6 :           if(NumWalkers_==1)</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :           {</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">          6 :             for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="666"><span class="lineNum">     666 </span>            :             {</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">          8 :               ifile.scanField(&quot;sigma0_&quot;+getPntrToArgument(i)-&gt;getName(),sigma0_[i]);</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">          8 :               ifile.scanField(&quot;av_cv_&quot;+getPntrToArgument(i)-&gt;getName(),av_cv_[i]);</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">          8 :               ifile.scanField(&quot;av_M2_&quot;+getPntrToArgument(i)-&gt;getName(),av_M2_[i]);</span></a>
+<a name="670"><span class="lineNum">     670 </span>            :             }</a>
+<a name="671"><span class="lineNum">     671 </span>            :           }</a>
+<a name="672"><span class="lineNum">     672 </span>            :           else</a>
+<a name="673"><span class="lineNum">     673 </span>            :           {</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">         12 :             for(unsigned w=0; w&lt;NumWalkers_; w++)</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">         24 :               for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :               {</a>
+<a name="677"><span class="lineNum">     677 </span>            :                 double tmp0,tmp1,tmp2;</a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         32 :                 const std::string arg_iw=getPntrToArgument(i)-&gt;getName()+&quot;_&quot;+std::to_string(w);</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">         16 :                 ifile.scanField(&quot;sigma0_&quot;+arg_iw,tmp0);</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         16 :                 ifile.scanField(&quot;av_cv_&quot;+arg_iw,tmp1);</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         16 :                 ifile.scanField(&quot;av_M2_&quot;+arg_iw,tmp2);</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         16 :                 if(w==walker_rank_)</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :                 {</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">          8 :                   sigma0_[i]=tmp0;</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">          8 :                   av_cv_[i]=tmp1;</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">          8 :                   av_M2_[i]=tmp2;</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :                 }</a>
+<a name="688"><span class="lineNum">     688 </span>            :               }</a>
+<a name="689"><span class="lineNum">     689 </span>            :           }</a>
+<a name="690"><span class="lineNum">     690 </span>            :         }</a>
+<a name="691"><span class="lineNum">     691 </span>            :       }</a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         33 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :       {</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">         22 :         if(getPntrToArgument(i)-&gt;isPeriodic())</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :         {</a>
+<a name="696"><span class="lineNum">     696 </span>            :           std::string arg_min,arg_max;</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         22 :           getPntrToArgument(i)-&gt;getDomain(arg_min,arg_max);</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :           std::string file_min,file_max;</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         44 :           ifile.scanField(&quot;min_&quot;+getPntrToArgument(i)-&gt;getName(),file_min);</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         22 :           ifile.scanField(&quot;max_&quot;+getPntrToArgument(i)-&gt;getName(),file_max);</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineCov">         22 :           plumed_massert(file_min==arg_min,&quot;RESTART - mismatch between old and new ARG periodicity&quot;);</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">         22 :           plumed_massert(file_max==arg_max,&quot;RESTART - mismatch between old and new ARG periodicity&quot;);</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :         }</a>
+<a name="704"><span class="lineNum">     704 </span>            :       }</a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         11 :       if(stateRestart)</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :       {</a>
+<a name="707"><span class="lineNum">     707 </span>            :         double time;</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">         60 :         while(ifile.scanField(&quot;time&quot;,time))</span></a>
+<a name="709"><span class="lineNum">     709 </span>            :         {</a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">         24 :           std::vector&lt;double&gt; center(ncv_);</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">         24 :           std::vector&lt;double&gt; sigma(ncv_);</span></a>
+<a name="712"><span class="lineNum">     712 </span>            :           double height;</a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">         72 :           for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">         48 :             ifile.scanField(getPntrToArgument(i)-&gt;getName(),center[i]);</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">         72 :           for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">         96 :             ifile.scanField(&quot;sigma_&quot;+getPntrToArgument(i)-&gt;getName(),sigma[i]);</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">         24 :           ifile.scanField(&quot;height&quot;,height);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">         24 :           ifile.scanField();</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">         24 :           kernels_.emplace_back(height,center,sigma);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :         }</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">          6 :         log.printf(&quot;    a total of %lu kernels where read\n&quot;,kernels_.size());</span></a>
+<a name="722"><span class="lineNum">     722 </span>            :       }</a>
+<a name="723"><span class="lineNum">     723 </span>            :       else</a>
+<a name="724"><span class="lineNum">     724 </span>            :       {</a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">          5 :         ifile.allowIgnoredFields(); //this allows for multiple restart, but without checking for consistency between them!</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :         double time;</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">        270 :         while(ifile.scanField(&quot;time&quot;,time))</span></a>
+<a name="728"><span class="lineNum">     728 </span>            :         {</a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">        130 :           std::vector&lt;double&gt; center(ncv_);</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">        130 :           std::vector&lt;double&gt; sigma(ncv_);</span></a>
+<a name="731"><span class="lineNum">     731 </span>            :           double height;</a>
+<a name="732"><span class="lineNum">     732 </span>            :           double logweight;</a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">        390 :           for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">        260 :             ifile.scanField(getPntrToArgument(i)-&gt;getName(),center[i]);</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">        390 :           for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">        520 :             ifile.scanField(&quot;sigma_&quot;+getPntrToArgument(i)-&gt;getName(),sigma[i]);</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">        130 :           if(counter_==(1+walker_rank_) &amp;&amp; adaptive_sigma_)</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :             sigma0_=sigma;</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">        130 :           ifile.scanField(&quot;height&quot;,height);</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">        130 :           ifile.scanField(&quot;logweight&quot;,logweight);</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">        130 :           ifile.scanField();</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">        130 :           addKernel(height,center,sigma);</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">        130 :           const double weight=std::exp(logweight);</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">        130 :           sum_weights_+=weight; //this sum is slightly inaccurate, because when printing some precision is lost</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">        130 :           sum_weights2_+=weight*weight;</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">        130 :           counter_++;</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :         }</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">          5 :         KDEnorm_=mode::explore?counter_:sum_weights_;</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">          5 :         if(!no_Zed_)</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :         {</a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">          2 :           double sum_uprob=0;</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">         48 :           for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">       1104 :             for(unsigned kk=0; kk&lt;kernels_.size(); kk++)</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">       1058 :               sum_uprob+=evaluateKernel(kernels_[kk],kernels_[k].center);</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">          2 :           if(NumParallel_&gt;1)</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineNoCov">          0 :             comm.Sum(sum_uprob);</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">          2 :           Zed_=sum_uprob/KDEnorm_/kernels_.size();</span></a>
+<a name="758"><span class="lineNum">     758 </span>            :         }</a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">          5 :         log.printf(&quot;    a total of %llu kernels where read, and compressed to %lu\n&quot;,counter_-1,kernels_.size());</span></a>
+<a name="760"><span class="lineNum">     760 </span>            :         convertKernelsToState=true;</a>
+<a name="761"><span class="lineNum">     761 </span>            :       }</a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">         11 :       ifile.reset(false);</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">         11 :       ifile.close();</span></a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">         11 :       nlist_=tmp_nlist;</span></a>
+<a name="765"><span class="lineNum">     765 </span>            :     }</a>
+<a name="766"><span class="lineNum">     766 </span>            :     else //same behaviour as METAD</a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;RESTART requested, but file '&quot;+restartFileName+&quot;' was not found!\n  Set RESTART=NO or provide a restart file&quot;);</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">         11 :     if(NumWalkers_&gt;1) //make sure that all walkers are doing the same thing</span></a>
+<a name="769"><span class="lineNum">     769 </span>            :     {</a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">          6 :       const unsigned kernels_size=kernels_.size();</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">          6 :       std::vector&lt;unsigned&gt; all_kernels_size(NumWalkers_);</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">          6 :       if(comm.Get_rank()==0)</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">          6 :         multi_sim_comm.Allgather(kernels_size,all_kernels_size);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">          6 :       comm.Bcast(all_kernels_size,0);</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :       bool same_number_of_kernels=true;</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">         12 :       for(unsigned w=1; w&lt;NumWalkers_; w++)</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">          6 :         if(all_kernels_size[0]!=all_kernels_size[w])</span></a>
+<a name="778"><span class="lineNum">     778 </span>            :           same_number_of_kernels=false;</a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">          6 :       plumed_massert(same_number_of_kernels,&quot;RESTART - not all walkers are reading the same file!&quot;);</span></a>
+<a name="780"><span class="lineNum">     780 </span>            :     }</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">         11 :   }</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">         10 :   else if(restartFileName.length()&gt;0)</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">          4 :     log.printf(&quot; +++ WARNING +++ the provided STATE_RFILE will be ignored, since RESTART was not requested\n&quot;);</span></a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            : //sync all walkers to avoid opening files before reading is over (see also METAD)</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">         21 :   comm.Barrier();</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">         21 :   if(comm.Get_rank()==0 &amp;&amp; walkers_mpi)</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">         10 :     multi_sim_comm.Barrier();</span></a>
+<a name="789"><span class="lineNum">     789 </span>            : </a>
+<a name="790"><span class="lineNum">     790 </span>            : //setup output kernels file</a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">         21 :   kernelsOfile_.link(*this);</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">         21 :   if(NumWalkers_&gt;1)</span></a>
+<a name="793"><span class="lineNum">     793 </span>            :   {</a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">         10 :     if(walker_rank_&gt;0)</span></a>
+<a name="795"><span class="lineNum">     795 </span>            :       kernelsFileName=&quot;/dev/null&quot;; //only first walker writes on file</a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">         20 :     kernelsOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :   }</a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">         21 :   kernelsOfile_.open(kernelsFileName);</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">         21 :   if(fmt.length()&gt;0)</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">         42 :     kernelsOfile_.fmtField(&quot; &quot;+fmt);</span></a>
+<a name="801"><span class="lineNum">     801 </span>            :   kernelsOfile_.setHeavyFlush(); //do I need it?</a>
+<a name="802"><span class="lineNum">     802 </span>            :   //define and set const fields</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">         21 :   kernelsOfile_.addConstantField(&quot;action&quot;);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">         21 :   kernelsOfile_.addConstantField(&quot;biasfactor&quot;);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">         21 :   kernelsOfile_.addConstantField(&quot;epsilon&quot;);</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">         21 :   kernelsOfile_.addConstantField(&quot;kernel_cutoff&quot;);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">         21 :   kernelsOfile_.addConstantField(&quot;compression_threshold&quot;);</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">         61 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">         40 :     kernelsOfile_.setupPrintValue(getPntrToArgument(i));</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">         42 :   kernelsOfile_.printField(&quot;action&quot;,getName()+&quot;_kernels&quot;);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">         21 :   kernelsOfile_.printField(&quot;biasfactor&quot;,biasfactor_);</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         21 :   kernelsOfile_.printField(&quot;epsilon&quot;,epsilon_);</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         21 :   kernelsOfile_.printField(&quot;kernel_cutoff&quot;,sqrt(cutoff2_));</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         21 :   kernelsOfile_.printField(&quot;compression_threshold&quot;,sqrt(threshold2_));</span></a>
+<a name="815"><span class="lineNum">     815 </span>            : </a>
+<a name="816"><span class="lineNum">     816 </span>            : //open file for storing state</a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">         21 :   if(wStateStride_!=0)</span></a>
+<a name="818"><span class="lineNum">     818 </span>            :   {</a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">         11 :     stateOfile_.link(*this);</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         11 :     if(NumWalkers_&gt;1)</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :     {</a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">          8 :       if(walker_rank_&gt;0)</span></a>
+<a name="823"><span class="lineNum">     823 </span>            :         stateFileName=&quot;/dev/null&quot;; //only first walker writes on file</a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">         16 :       stateOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         11 :     stateOfile_.open(stateFileName);</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">         11 :     if(fmt.length()&gt;0)</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         22 :       stateOfile_.fmtField(&quot; &quot;+fmt);</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">         11 :     if(convertKernelsToState)</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineNoCov">          0 :       dumpStateToFile();</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :   }</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            : //set initial old values</a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">         21 :   KDEnorm_=mode::explore?counter_:sum_weights_;</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">         21 :   old_KDEnorm_=KDEnorm_;</span></a>
+<a name="836"><span class="lineNum">     836 </span>            : </a>
+<a name="837"><span class="lineNum">     837 </span>            : //add and set output components</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">         21 :   addComponent(&quot;rct&quot;);</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">         21 :   componentIsNotPeriodic(&quot;rct&quot;);</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">         21 :   getPntrToComponent(&quot;rct&quot;)-&gt;set(kbt_*std::log(sum_weights_/counter_));</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">         21 :   addComponent(&quot;zed&quot;);</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">         21 :   componentIsNotPeriodic(&quot;zed&quot;);</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">         21 :   getPntrToComponent(&quot;zed&quot;)-&gt;set(Zed_);</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">         21 :   addComponent(&quot;neff&quot;);</span></a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">         21 :   componentIsNotPeriodic(&quot;neff&quot;);</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">         21 :   getPntrToComponent(&quot;neff&quot;)-&gt;set(std::pow(1+sum_weights_,2)/(1+sum_weights2_));</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">         21 :   addComponent(&quot;nker&quot;);</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">         21 :   componentIsNotPeriodic(&quot;nker&quot;);</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">         21 :   getPntrToComponent(&quot;nker&quot;)-&gt;set(kernels_.size());</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">         21 :   if(calc_work_)</span></a>
+<a name="851"><span class="lineNum">     851 </span>            :   {</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">          7 :     addComponent(&quot;work&quot;);</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">         14 :     componentIsNotPeriodic(&quot;work&quot;);</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :   }</a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">         21 :   if(nlist_)</span></a>
+<a name="856"><span class="lineNum">     856 </span>            :   {</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">          5 :     addComponent(&quot;nlker&quot;);</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">          5 :     componentIsNotPeriodic(&quot;nlker&quot;);</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">          5 :     addComponent(&quot;nlsteps&quot;);</span></a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">         10 :     componentIsNotPeriodic(&quot;nlsteps&quot;);</span></a>
+<a name="861"><span class="lineNum">     861 </span>            :   }</a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span>            : //printing some info</a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">         21 :   log.printf(&quot;  temperature = %g\n&quot;,kbt_/kB);</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">         21 :   log.printf(&quot;  beta = %g\n&quot;,1./kbt_);</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">         21 :   log.printf(&quot;  depositing new kernels with PACE = %u\n&quot;,stride_);</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">         21 :   log.printf(&quot;  expected BARRIER is %g\n&quot;,barrier);</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">         21 :   log.printf(&quot;  using target distribution with BIASFACTOR gamma = %g\n&quot;,biasfactor_);</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">         21 :   if(std::isinf(biasfactor_))</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">          4 :     log.printf(&quot;    (thus a uniform flat target distribution, no well-tempering)\n&quot;);</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">         21 :   if(excluded_region_!=NULL)</span></a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">          2 :     log.printf(&quot; -- EXCLUDED_REGION: kernels will be deposited only when '%s' is equal to zero\n&quot;,excluded_region_-&gt;getName().c_str());</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">         21 :   if(extra_biases_.size()&gt;0)</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :   {</a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">          2 :     log.printf(&quot; -- EXTRA_BIAS: &quot;);</span></a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">          5 :     for(unsigned e=0; e&lt;extra_biases_.size(); e++)</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">          3 :       log.printf(&quot;%s &quot;,extra_biases_[e]-&gt;getName().c_str());</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">          2 :     log.printf(&quot;will be reweighted\n&quot;);</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :   }</a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">         21 :   if(adaptive_sigma_)</span></a>
+<a name="881"><span class="lineNum">     881 </span>            :   {</a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">         11 :     log.printf(&quot;  adaptive SIGMA will be used, with ADAPTIVE_SIGMA_STRIDE = %u\n&quot;,adaptive_sigma_stride_);</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">         11 :     unsigned x=std::ceil(adaptive_sigma_stride_/stride_);</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         11 :     log.printf(&quot;    thus the first x kernel depositions will be skipped, x = ADAPTIVE_SIGMA_STRIDE/PACE = %u\n&quot;,x);</span></a>
+<a name="885"><span class="lineNum">     885 </span>            :   }</a>
+<a name="886"><span class="lineNum">     886 </span>            :   else</a>
+<a name="887"><span class="lineNum">     887 </span>            :   {</a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineCov">         10 :     log.printf(&quot;  kernels have initial SIGMA = &quot;);</span></a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">         29 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">         19 :       log.printf(&quot; %g&quot;,sigma0_[i]);</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">         10 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="892"><span class="lineNum">     892 </span>            :   }</a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">         21 :   if(sigma_min_.size()&gt;0)</span></a>
+<a name="894"><span class="lineNum">     894 </span>            :   {</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">          3 :     log.printf(&quot;  kernels have a SIGMA_MIN = &quot;);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">          9 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">          6 :       log.printf(&quot; %g&quot;,sigma_min_[i]);</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">          3 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="899"><span class="lineNum">     899 </span>            :   }</a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">         21 :   if(fixed_sigma_)</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">          6 :     log.printf(&quot; -- FIXED_SIGMA: sigma will not decrease as the simulation proceeds\n&quot;);</span></a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">         21 :   log.printf(&quot;  kernels are truncated with KERNELS_CUTOFF = %g\n&quot;,cutoff);</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">         21 :   if(cutoff&lt;3.5)</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ probably kernels are truncated too much\n&quot;);</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">         21 :   log.printf(&quot;  the value at cutoff is = %g\n&quot;,val_at_cutoff_);</span></a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">         21 :   log.printf(&quot;  regularization EPSILON = %g\n&quot;,epsilon_);</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">         21 :   if(val_at_cutoff_&gt;epsilon_*(1+1e-6))</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ the KERNEL_CUTOFF might be too small for the given EPSILON\n&quot;);</span></a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">         21 :   log.printf(&quot;  kernels will be compressed when closer than COMPRESSION_THRESHOLD = %g\n&quot;,sqrt(threshold2_));</span></a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">         21 :   if(threshold2_==0)</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ kernels will never merge, expect slowdowns\n&quot;);</span></a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">         21 :   if(!recursive_merge_)</span></a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">          6 :     log.printf(&quot; -- RECURSIVE_MERGE_OFF: only one merge for each new kernel will be attempted. This is faster only if total number of kernels does not grow too much\n&quot;);</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         21 :   if(nlist_)</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">          5 :     log.printf(&quot; -- NLIST: using neighbor list for kernels, with parameters: %g,%g\n&quot;,nlist_param_[0],nlist_param_[1]);</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">         21 :   if(nlist_pace_reset_)</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">          2 :     log.printf(&quot; -- NLIST_PACE_RESET: forcing the neighbor list to update every PACE\n&quot;);</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">         21 :   if(no_Zed_)</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">          6 :     log.printf(&quot; -- NO_ZED: using fixed normalization factor = %g\n&quot;,Zed_);</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">         21 :   if(wStateStride_&gt;0)</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">         10 :     log.printf(&quot;  state checkpoints are written on file %s every %d MD steps\n&quot;,stateFileName.c_str(),wStateStride_);</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">         21 :   if(wStateStride_==-1)</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">          1 :     log.printf(&quot;  state checkpoints are written on file %s only on CPT events (or never if MD code does define them!)\n&quot;,stateFileName.c_str());</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">         21 :   if(walkers_mpi)</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">         10 :     log.printf(&quot; -- WALKERS_MPI: if multiple replicas are present, they will share the same bias via MPI\n&quot;);</span></a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">         21 :   if(NumWalkers_&gt;1)</span></a>
+<a name="927"><span class="lineNum">     927 </span>            :   {</a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">         10 :     log.printf(&quot;  using multiple walkers\n&quot;);</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">         10 :     log.printf(&quot;    number of walkers: %u\n&quot;,NumWalkers_);</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">         10 :     log.printf(&quot;    walker rank: %u\n&quot;,walker_rank_);</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :   }</a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">         21 :   int mw_warning=0;</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">         21 :   if(!walkers_mpi &amp;&amp; comm.Get_rank()==0 &amp;&amp; multi_sim_comm.Get_size()&gt;(int)NumWalkers_)</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :     mw_warning=1;</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">         21 :   comm.Bcast(mw_warning,0);</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">         21 :   if(mw_warning) //log.printf messes up with comm, so never use it without Bcast!</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ multiple replicas will NOT communicate unless the flag WALKERS_MPI is used\n&quot;);</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">         21 :   if(NumParallel_&gt;1)</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">          4 :     log.printf(&quot;  using multiple MPI processes per simulation: %u\n&quot;,NumParallel_);</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">         21 :   if(NumOMP_&gt;1)</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">         17 :     log.printf(&quot;  using multiple OpenMP threads per simulation: %u\n&quot;,NumOMP_);</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">         21 :   if(serial)</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">          4 :     log.printf(&quot; -- SERIAL: no loop parallelization, despite %d MPI processes and %u OpenMP threads available\n&quot;,comm.Get_size(),OpenMP::getNumThreads());</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">         21 :   log.printf(&quot;  Bibliography: &quot;);</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">         42 :   log&lt;&lt;plumed.cite(&quot;M. Invernizzi and M. Parrinello, J. Phys. Chem. Lett. 11, 2731-2736 (2020)&quot;);</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">         14 :   if(mode::explore || adaptive_sigma_)</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">         28 :     log&lt;&lt;plumed.cite(&quot;M. Invernizzi and M. Parrinello, J. Chem. Theory Comput. 18, 3988-3996 (2022)&quot;);</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">         21 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">         42 : }</span></a>
+<a name="950"><span class="lineNum">     950 </span>            : </a>
+<a name="951"><span class="lineNum">     951 </span>            : template &lt;class mode&gt;</a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">       1071 : void OPESmetad&lt;mode&gt;::calculate()</span></a>
+<a name="953"><span class="lineNum">     953 </span>            : {</a>
+<a name="954"><span class="lineNum">     954 </span>            : //get cv</a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">       1071 :   std::vector&lt;double&gt; cv(ncv_);</span></a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">       3111 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">       2040 :     cv[i]=getArgument(i);</span></a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span>            : //check neighbor list</a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">       1071 :   if(nlist_)</span></a>
+<a name="961"><span class="lineNum">     961 </span>            :   {</a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">        255 :     nlist_steps_++;</span></a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">        255 :     if(getExchangeStep())</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineNoCov">          0 :       nlist_update_=true;</span></a>
+<a name="965"><span class="lineNum">     965 </span>            :     else</a>
+<a name="966"><span class="lineNum">     966 </span>            :     {</a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">        275 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="968"><span class="lineNum">     968 </span>            :       {</a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">        270 :         const double diff_i=difference(i,cv[i],nlist_center_[i]);</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">        270 :         if(diff_i*diff_i&gt;nlist_param_[1]*nlist_dev2_[i])</span></a>
+<a name="971"><span class="lineNum">     971 </span>            :         {</a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">        250 :           nlist_update_=true;</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">        250 :           break;</span></a>
+<a name="974"><span class="lineNum">     974 </span>            :         }</a>
+<a name="975"><span class="lineNum">     975 </span>            :       }</a>
+<a name="976"><span class="lineNum">     976 </span>            :     }</a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">        255 :     if(nlist_update_)</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">        250 :       updateNlist(cv);</span></a>
+<a name="979"><span class="lineNum">     979 </span>            :   }</a>
+<a name="980"><span class="lineNum">     980 </span>            : </a>
+<a name="981"><span class="lineNum">     981 </span>            : //set bias and forces</a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">       1071 :   std::vector&lt;double&gt; der_prob(ncv_,0);</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">       1071 :   const double prob=getProbAndDerivatives(cv,der_prob);</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">       1071 :   const double bias=kbt_*bias_prefactor_*std::log(prob/Zed_+epsilon_);</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :   setBias(bias);</a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">       3111 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">       2040 :     setOutputForce(i,-kbt_*bias_prefactor_/(prob/Zed_+epsilon_)*der_prob[i]/Zed_);</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">       1071 : }</span></a>
+<a name="989"><span class="lineNum">     989 </span>            : </a>
+<a name="990"><span class="lineNum">     990 </span>            : template &lt;class mode&gt;</a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">       1071 : void OPESmetad&lt;mode&gt;::update()</span></a>
+<a name="992"><span class="lineNum">     992 </span>            : {</a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">       1071 :   if(isFirstStep_)//same in MetaD, useful for restarts?</span></a>
+<a name="994"><span class="lineNum">     994 </span>            :   {</a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">         21 :     isFirstStep_=false;</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">         21 :     return;</span></a>
+<a name="997"><span class="lineNum">     997 </span>            :   }</a>
+<a name="998"><span class="lineNum">     998 </span>            : </a>
+<a name="999"><span class="lineNum">     999 </span>            : //update variance if adaptive sigma</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">       1050 :   if(adaptive_sigma_)</span></a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   {</a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">        550 :     adaptive_counter_++;</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">        550 :     unsigned tau=adaptive_sigma_stride_;</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">        550 :     if(adaptive_counter_&lt;adaptive_sigma_stride_)</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">         45 :       tau=adaptive_counter_;</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">       1600 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1007"><span class="lineNum">    1007 </span>            :     { //Welford's online algorithm for standard deviation</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :       const double cv_i=getArgument(i);</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">       1050 :       const double diff_i=difference(i,av_cv_[i],cv_i);</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">       1050 :       av_cv_[i]+=diff_i/tau; //exponentially decaying average</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">       1050 :       av_M2_[i]+=diff_i*difference(i,av_cv_[i],cv_i);</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :     }</a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">        550 :     if(adaptive_counter_&lt;adaptive_sigma_stride_ &amp;&amp; counter_==1) //counter_&gt;1 if restarting</span></a>
+<a name="1014"><span class="lineNum">    1014 </span>            :       return; //do not apply bias before having measured sigma</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :   }</a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span>            : //do update</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">       1005 :   if(getStep()%stride_==0 &amp;&amp; (excluded_region_==NULL || excluded_region_-&gt;get()==0))</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            :   {</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">        257 :     old_KDEnorm_=KDEnorm_;</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">        257 :     delta_kernels_.clear();</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">        257 :     unsigned old_nker=kernels_.size();</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            : </a>
+<a name="1024"><span class="lineNum">    1024 </span>            :     //get new kernel height</a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineCov">        257 :     double log_weight=getOutputQuantity(0)/kbt_; //first value is always the current bias</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">        277 :     for(unsigned e=0; e&lt;extra_biases_.size(); e++)</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">         20 :       log_weight+=extra_biases_[e]-&gt;get()/kbt_; //extra biases contribute to the weight</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">        257 :     double height=std::exp(log_weight);</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            : </a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     //update sum_weights_ and neff</a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineCov">        257 :     double sum_heights=height;</span></a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">        257 :     double sum_heights2=height*height;</span></a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">        257 :     if(NumWalkers_&gt;1)</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :     {</a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">        126 :       if(comm.Get_rank()==0)</span></a>
+<a name="1036"><span class="lineNum">    1036 </span>            :       {</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">        126 :         multi_sim_comm.Sum(sum_heights);</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">        126 :         multi_sim_comm.Sum(sum_heights2);</span></a>
+<a name="1039"><span class="lineNum">    1039 </span>            :       }</a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">        126 :       comm.Bcast(sum_heights,0);</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">        126 :       comm.Bcast(sum_heights2,0);</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     }</a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">        257 :     counter_+=NumWalkers_;</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">        257 :     sum_weights_+=sum_heights;</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">        257 :     sum_weights2_+=sum_heights2;</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">        257 :     const double neff=std::pow(1+sum_weights_,2)/(1+sum_weights2_); //adding 1 makes it more robust at the start</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">        257 :     getPntrToComponent(&quot;rct&quot;)-&gt;set(kbt_*std::log(sum_weights_/counter_));</span></a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">        257 :     getPntrToComponent(&quot;neff&quot;)-&gt;set(neff);</span></a>
+<a name="1049"><span class="lineNum">    1049 </span>            :     if(mode::explore)</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :     {</a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">         68 :       KDEnorm_=counter_;</span></a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">         68 :       height=1; //plain KDE, bias reweight does not enter here</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            :     }</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     else</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">        189 :       KDEnorm_=sum_weights_;</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            : </a>
+<a name="1057"><span class="lineNum">    1057 </span>            :     //if needed, rescale sigma and height</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">        257 :     std::vector&lt;double&gt; sigma=sigma0_;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">        257 :     if(adaptive_sigma_)</span></a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     {</a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">         93 :       const double factor=mode::explore?1:biasfactor_;</span></a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">        131 :       if(counter_==1+NumWalkers_) //first time only</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            :       {</a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">         14 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">          9 :           av_M2_[i]*=biasfactor_; //from unbiased, thus must be adjusted</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">         14 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">          9 :           sigma0_[i]=std::sqrt(av_M2_[i]/adaptive_counter_/factor);</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">          5 :         if(sigma_min_.size()==0)</span></a>
+<a name="1069"><span class="lineNum">    1069 </span>            :         {</a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">         14 :           for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">          9 :             plumed_massert(sigma0_[i]&gt;1e-6,&quot;ADAPTIVE SIGMA is suspiciously small for CV i=&quot;+std::to_string(i)+&quot;\nManually provide SIGMA or set a safe SIGMA_MIN to avoid possible issues&quot;);</span></a>
+<a name="1072"><span class="lineNum">    1072 </span>            :         }</a>
+<a name="1073"><span class="lineNum">    1073 </span>            :         else</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :         {</a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineNoCov">          0 :           for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineNoCov">          0 :             sigma0_[i]=std::max(sigma0_[i],sigma_min_[i]);</span></a>
+<a name="1077"><span class="lineNum">    1077 </span>            :         }</a>
+<a name="1078"><span class="lineNum">    1078 </span>            :       }</a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">        388 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">        257 :         sigma[i]=std::sqrt(av_M2_[i]/adaptive_counter_/factor);</span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">        131 :       if(sigma_min_.size()==0)</span></a>
+<a name="1082"><span class="lineNum">    1082 </span>            :       {</a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">        238 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :         {</a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">        157 :           if(sigma[i]&lt;1e-6)</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            :           {</a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineNoCov">          0 :             log.printf(&quot;+++ WARNING +++ the ADAPTIVE SIGMA is suspiciously small, you should set a safe SIGMA_MIN. 1e-6 will be used here\n&quot;);</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineNoCov">          0 :             sigma[i]=1e-6;</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :             sigma_min_.resize(ncv_,1e-6);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :           }</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :         }</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :       }</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :       else</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :       {</a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">        150 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">        100 :           sigma[i]=std::max(sigma[i],sigma_min_[i]);</span></a>
+<a name="1097"><span class="lineNum">    1097 </span>            :       }</a>
+<a name="1098"><span class="lineNum">    1098 </span>            :     }</a>
+<a name="1099"><span class="lineNum">    1099 </span><span class="lineCov">        257 :     if(!fixed_sigma_)</span></a>
+<a name="1100"><span class="lineNum">    1100 </span>            :     {</a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">         38 :       const double size=mode::explore?counter_:neff; //for EXPLORE neff is not relevant</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">        197 :       const double s_rescaling=std::pow(size*(ncv_+2.)/4.,-1./(4+ncv_));</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">        576 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">        379 :         sigma[i]*=s_rescaling;</span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">        197 :       if(sigma_min_.size()&gt;0)</span></a>
+<a name="1106"><span class="lineNum">    1106 </span>            :       {</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">        150 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">        100 :           sigma[i]=std::max(sigma[i],sigma_min_[i]);</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            :       }</a>
+<a name="1110"><span class="lineNum">    1110 </span>            :     }</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :     //the height should be divided by sqrt(2*pi)*sigma0_,</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :     //but this overall factor would be canceled when dividing by Zed</a>
+<a name="1113"><span class="lineNum">    1113 </span>            :     //thus we skip it altogether, but keep any other sigma rescaling</a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">        756 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">        499 :       height*=(sigma0_[i]/sigma[i]);</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            : </a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     //get new kernel center</a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">        257 :     std::vector&lt;double&gt; center(ncv_);</span></a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">        756 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">        499 :       center[i]=getArgument(i);</span></a>
+<a name="1121"><span class="lineNum">    1121 </span>            : </a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     //add new kernel(s)</a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">        257 :     if(NumWalkers_==1)</span></a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">        131 :       addKernel(height,center,sigma,log_weight);</span></a>
+<a name="1125"><span class="lineNum">    1125 </span>            :     else</a>
+<a name="1126"><span class="lineNum">    1126 </span>            :     {</a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">        126 :       std::vector&lt;double&gt; all_height(NumWalkers_,0.0);</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">        126 :       std::vector&lt;double&gt; all_center(NumWalkers_*ncv_,0.0);</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">        126 :       std::vector&lt;double&gt; all_sigma(NumWalkers_*ncv_,0.0);</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">        126 :       std::vector&lt;double&gt; all_logweight(NumWalkers_,0.0);</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">        126 :       if(comm.Get_rank()==0)</span></a>
+<a name="1132"><span class="lineNum">    1132 </span>            :       {</a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">        126 :         multi_sim_comm.Allgather(height,all_height);</span></a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">        126 :         multi_sim_comm.Allgather(center,all_center);</span></a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">        126 :         multi_sim_comm.Allgather(sigma,all_sigma);</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">        126 :         multi_sim_comm.Allgather(log_weight,all_logweight);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span>            :       }</a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">        126 :       comm.Bcast(all_height,0);</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">        126 :       comm.Bcast(all_center,0);</span></a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineCov">        126 :       comm.Bcast(all_sigma,0);</span></a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineCov">        126 :       comm.Bcast(all_logweight,0);</span></a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">        126 :       if(nlist_)</span></a>
+<a name="1143"><span class="lineNum">    1143 </span>            :       { //gather all the nlist_index_, so merging can be done using it</a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">         50 :         std::vector&lt;int&gt; all_nlist_size(NumWalkers_);</span></a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineCov">         50 :         if(comm.Get_rank()==0)</span></a>
+<a name="1146"><span class="lineNum">    1146 </span>            :         {</a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">         50 :           all_nlist_size[walker_rank_]=nlist_index_.size();</span></a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">         50 :           multi_sim_comm.Sum(all_nlist_size);</span></a>
+<a name="1149"><span class="lineNum">    1149 </span>            :         }</a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">         50 :         comm.Bcast(all_nlist_size,0);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span>            :         unsigned tot_size=0;</a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">        150 :         for(unsigned w=0; w&lt;NumWalkers_; w++)</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineCov">        100 :           tot_size+=all_nlist_size[w];</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">         50 :         if(tot_size&gt;0)</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :         {</a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">         50 :           std::vector&lt;int&gt; disp(NumWalkers_);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">        100 :           for(unsigned w=0; w&lt;NumWalkers_-1; w++)</span></a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">         50 :             disp[w+1]=disp[w]+all_nlist_size[w];</span></a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineCov">         50 :           std::vector&lt;unsigned&gt; all_nlist_index(tot_size);</span></a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">         50 :           if(comm.Get_rank()==0)</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">         50 :             multi_sim_comm.Allgatherv(nlist_index_,all_nlist_index,&amp;all_nlist_size[0],&amp;disp[0]);</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">         50 :           comm.Bcast(all_nlist_index,0);</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">         50 :           std::set&lt;unsigned&gt; nlist_index_set(all_nlist_index.begin(),all_nlist_index.end()); //remove duplicates and sort</span></a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">         50 :           nlist_index_.assign(nlist_index_set.begin(),nlist_index_set.end());</span></a>
+<a name="1165"><span class="lineNum">    1165 </span>            :         }</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :       }</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">        378 :       for(unsigned w=0; w&lt;NumWalkers_; w++)</span></a>
+<a name="1168"><span class="lineNum">    1168 </span>            :       {</a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">        252 :         std::vector&lt;double&gt; center_w(all_center.begin()+ncv_*w,all_center.begin()+ncv_*(w+1));</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">        252 :         std::vector&lt;double&gt; sigma_w(all_sigma.begin()+ncv_*w,all_sigma.begin()+ncv_*(w+1));</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineCov">        252 :         addKernel(all_height[w],center_w,sigma_w,all_logweight[w]);</span></a>
+<a name="1172"><span class="lineNum">    1172 </span>            :       }</a>
+<a name="1173"><span class="lineNum">    1173 </span>            :     }</a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineCov">        257 :     getPntrToComponent(&quot;nker&quot;)-&gt;set(kernels_.size());</span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineCov">        257 :     if(nlist_)</span></a>
+<a name="1176"><span class="lineNum">    1176 </span>            :     {</a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">        106 :       getPntrToComponent(&quot;nlker&quot;)-&gt;set(nlist_index_.size());</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">        106 :       if(nlist_pace_reset_)</span></a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineCov">         50 :         nlist_update_=true;</span></a>
+<a name="1180"><span class="lineNum">    1180 </span>            :     }</a>
+<a name="1181"><span class="lineNum">    1181 </span>            : </a>
+<a name="1182"><span class="lineNum">    1182 </span>            :     //update Zed_</a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineCov">        257 :     if(!no_Zed_)</span></a>
+<a name="1184"><span class="lineNum">    1184 </span>            :     {</a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">        197 :       double sum_uprob=0;</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineCov">        197 :       const unsigned ks=kernels_.size();</span></a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">        197 :       const unsigned ds=delta_kernels_.size();</span></a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">        197 :       const bool few_kernels=(ks*ks&lt;(3*ks*ds+2*ds*ds*NumParallel_+100)); //this seems reasonable, but is not rigorous...</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">        197 :       if(few_kernels) //really needed? Probably is almost always false</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            :       {</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineCov">        147 :         #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1192"><span class="lineNum">    1192 </span>            :         {</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :           #pragma omp for reduction(+:sum_uprob) nowait</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :           for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</a>
+<a name="1195"><span class="lineNum">    1195 </span>            :             for(unsigned kk=0; kk&lt;kernels_.size(); kk++)</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :               sum_uprob+=evaluateKernel(kernels_[kk],kernels_[k].center);</a>
+<a name="1197"><span class="lineNum">    1197 </span>            :         }</a>
+<a name="1198"><span class="lineNum">    1198 </span><span class="lineCov">        147 :         if(NumParallel_&gt;1)</span></a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineCov">         50 :           comm.Sum(sum_uprob);</span></a>
+<a name="1200"><span class="lineNum">    1200 </span>            :       }</a>
+<a name="1201"><span class="lineNum">    1201 </span>            :       else</a>
+<a name="1202"><span class="lineNum">    1202 </span>            :       {</a>
+<a name="1203"><span class="lineNum">    1203 </span>            :         // Here instead of redoing the full summation, we add only the changes, knowing that</a>
+<a name="1204"><span class="lineNum">    1204 </span>            :         // uprob = old_uprob + delta_uprob</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :         // and we also need to consider that in the new sum there are some novel centers and some disappeared ones</a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">         50 :         double delta_sum_uprob=0;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineCov">         50 :         if(!nlist_)</span></a>
+<a name="1208"><span class="lineNum">    1208 </span>            :         {</a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineNoCov">          0 :           #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1210"><span class="lineNum">    1210 </span>            :           {</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :             #pragma omp for reduction(+:delta_sum_uprob) nowait</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :             for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</a>
+<a name="1213"><span class="lineNum">    1213 </span>            :             {</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :               for(unsigned d=0; d&lt;delta_kernels_.size(); d++)</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :               {</a>
+<a name="1216"><span class="lineNum">    1216 </span>            :                 const double sign=delta_kernels_[d].height&lt;0?-1:1; //take away contribution from kernels that are gone, and add the one from new ones</a>
+<a name="1217"><span class="lineNum">    1217 </span>            :                 delta_sum_uprob+=evaluateKernel(delta_kernels_[d],kernels_[k].center)+sign*evaluateKernel(kernels_[k],delta_kernels_[d].center);</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :               }</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :             }</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :           }</a>
+<a name="1221"><span class="lineNum">    1221 </span>            :         }</a>
+<a name="1222"><span class="lineNum">    1222 </span>            :         else</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :         {</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">         50 :           #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1225"><span class="lineNum">    1225 </span>            :           {</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :             #pragma omp for reduction(+:delta_sum_uprob) nowait</a>
+<a name="1227"><span class="lineNum">    1227 </span>            :             for(unsigned nk=rank_; nk&lt;nlist_index_.size(); nk+=NumParallel_)</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :             {</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :               const unsigned k=nlist_index_[nk];</a>
+<a name="1230"><span class="lineNum">    1230 </span>            :               for(unsigned d=0; d&lt;delta_kernels_.size(); d++)</a>
+<a name="1231"><span class="lineNum">    1231 </span>            :               {</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :                 const double sign=delta_kernels_[d].height&lt;0?-1:1; //take away contribution from kernels that are gone, and add the one from new ones</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :                 delta_sum_uprob+=evaluateKernel(delta_kernels_[d],kernels_[k].center)+sign*evaluateKernel(kernels_[k],delta_kernels_[d].center);</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :               }</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :             }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :           }</a>
+<a name="1237"><span class="lineNum">    1237 </span>            :         }</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">         50 :         if(NumParallel_&gt;1)</span></a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineNoCov">          0 :           comm.Sum(delta_sum_uprob);</span></a>
+<a name="1240"><span class="lineNum">    1240 </span><span class="lineCov">         50 :         #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1241"><span class="lineNum">    1241 </span>            :         {</a>
+<a name="1242"><span class="lineNum">    1242 </span>            :           #pragma omp for reduction(+:delta_sum_uprob)</a>
+<a name="1243"><span class="lineNum">    1243 </span>            :           for(unsigned d=0; d&lt;delta_kernels_.size(); d++)</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :           {</a>
+<a name="1245"><span class="lineNum">    1245 </span>            :             for(unsigned dd=0; dd&lt;delta_kernels_.size(); dd++)</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :             { //now subtract the delta_uprob added before, but not needed</a>
+<a name="1247"><span class="lineNum">    1247 </span>            :               const double sign=delta_kernels_[d].height&lt;0?-1:1;</a>
+<a name="1248"><span class="lineNum">    1248 </span>            :               delta_sum_uprob-=sign*evaluateKernel(delta_kernels_[dd],delta_kernels_[d].center);</a>
+<a name="1249"><span class="lineNum">    1249 </span>            :             }</a>
+<a name="1250"><span class="lineNum">    1250 </span>            :           }</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :         }</a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineCov">         50 :         sum_uprob=Zed_*old_KDEnorm_*old_nker+delta_sum_uprob;</span></a>
+<a name="1253"><span class="lineNum">    1253 </span>            :       }</a>
+<a name="1254"><span class="lineNum">    1254 </span><span class="lineCov">        197 :       Zed_=sum_uprob/KDEnorm_/kernels_.size();</span></a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineCov">        394 :       getPntrToComponent(&quot;zed&quot;)-&gt;set(Zed_);</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            :     }</a>
+<a name="1257"><span class="lineNum">    1257 </span>            : </a>
+<a name="1258"><span class="lineNum">    1258 </span>            :     //calculate work if requested</a>
+<a name="1259"><span class="lineNum">    1259 </span><span class="lineCov">        257 :     if(calc_work_)</span></a>
+<a name="1260"><span class="lineNum">    1260 </span>            :     {</a>
+<a name="1261"><span class="lineNum">    1261 </span><span class="lineCov">         70 :       std::vector&lt;double&gt; dummy(ncv_); //derivatives are not actually needed</span></a>
+<a name="1262"><span class="lineNum">    1262 </span><span class="lineCov">         70 :       const double prob=getProbAndDerivatives(center,dummy);</span></a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineCov">         70 :       const double new_bias=kbt_*bias_prefactor_*std::log(prob/Zed_+epsilon_);</span></a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineCov">         70 :       work_+=new_bias-getOutputQuantity(0);</span></a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineCov">        140 :       getPntrToComponent(&quot;work&quot;)-&gt;set(work_);</span></a>
+<a name="1266"><span class="lineNum">    1266 </span>            :     }</a>
+<a name="1267"><span class="lineNum">    1267 </span>            :   }</a>
+<a name="1268"><span class="lineNum">    1268 </span>            : </a>
+<a name="1269"><span class="lineNum">    1269 </span>            : //dump state if requested</a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineCov">       1005 :   if( (wStateStride_&gt;0 &amp;&amp; getStep()%wStateStride_==0) || (wStateStride_==-1 &amp;&amp; getCPT()) )</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineCov">         18 :     dumpStateToFile();</span></a>
+<a name="1272"><span class="lineNum">    1272 </span>            : }</a>
+<a name="1273"><span class="lineNum">    1273 </span>            : </a>
+<a name="1274"><span class="lineNum">    1274 </span>            : template &lt;class mode&gt;</a>
+<a name="1275"><span class="lineNum">    1275 </span><span class="lineCov">       1141 : double OPESmetad&lt;mode&gt;::getProbAndDerivatives(const std::vector&lt;double&gt;&amp; cv,std::vector&lt;double&gt;&amp; der_prob)</span></a>
+<a name="1276"><span class="lineNum">    1276 </span>            : {</a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineCov">       1141 :   double prob=0.0;</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineCov">       1141 :   if(!nlist_)</span></a>
+<a name="1279"><span class="lineNum">    1279 </span>            :   {</a>
+<a name="1280"><span class="lineNum">    1280 </span><span class="lineCov">        886 :     if(NumOMP_==1 || (unsigned)kernels_.size()&lt;2*NumOMP_*NumParallel_)</span></a>
+<a name="1281"><span class="lineNum">    1281 </span>            :     {</a>
+<a name="1282"><span class="lineNum">    1282 </span>            :       // for performances and thread safety</a>
+<a name="1283"><span class="lineNum">    1283 </span><span class="lineCov">        707 :       std::vector&lt;double&gt; dist(ncv_);</span></a>
+<a name="1284"><span class="lineNum">    1284 </span><span class="lineCov">       2647 :       for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</span></a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineCov">       1940 :         prob+=evaluateKernel(kernels_[k],cv,der_prob,dist);</span></a>
+<a name="1286"><span class="lineNum">    1286 </span>            :     }</a>
+<a name="1287"><span class="lineNum">    1287 </span>            :     else</a>
+<a name="1288"><span class="lineNum">    1288 </span>            :     {</a>
+<a name="1289"><span class="lineNum">    1289 </span><span class="lineCov">        179 :       #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1290"><span class="lineNum">    1290 </span>            :       {</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :         std::vector&lt;double&gt; omp_deriv(der_prob.size(),0.);</a>
+<a name="1292"><span class="lineNum">    1292 </span>            :         // for performances and thread safety</a>
+<a name="1293"><span class="lineNum">    1293 </span>            :         std::vector&lt;double&gt; dist(ncv_);</a>
+<a name="1294"><span class="lineNum">    1294 </span>            :         #pragma omp for reduction(+:prob) nowait</a>
+<a name="1295"><span class="lineNum">    1295 </span>            :         for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</a>
+<a name="1296"><span class="lineNum">    1296 </span>            :           prob+=evaluateKernel(kernels_[k],cv,omp_deriv,dist);</a>
+<a name="1297"><span class="lineNum">    1297 </span>            :         #pragma omp critical</a>
+<a name="1298"><span class="lineNum">    1298 </span>            :         for(unsigned i=0; i&lt;ncv_; i++)</a>
+<a name="1299"><span class="lineNum">    1299 </span>            :           der_prob[i]+=omp_deriv[i];</a>
+<a name="1300"><span class="lineNum">    1300 </span>            :       }</a>
+<a name="1301"><span class="lineNum">    1301 </span>            :     }</a>
+<a name="1302"><span class="lineNum">    1302 </span>            :   }</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :   else</a>
+<a name="1304"><span class="lineNum">    1304 </span>            :   {</a>
+<a name="1305"><span class="lineNum">    1305 </span><span class="lineCov">        255 :     if(NumOMP_==1 || (unsigned)nlist_index_.size()&lt;2*NumOMP_*NumParallel_)</span></a>
+<a name="1306"><span class="lineNum">    1306 </span>            :     {</a>
+<a name="1307"><span class="lineNum">    1307 </span>            :       // for performances and thread safety</a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">        230 :       std::vector&lt;double&gt; dist(ncv_);</span></a>
+<a name="1309"><span class="lineNum">    1309 </span><span class="lineCov">        660 :       for(unsigned nk=rank_; nk&lt;nlist_index_.size(); nk+=NumParallel_)</span></a>
+<a name="1310"><span class="lineNum">    1310 </span><span class="lineCov">        430 :         prob+=evaluateKernel(kernels_[nlist_index_[nk]],cv,der_prob,dist);</span></a>
+<a name="1311"><span class="lineNum">    1311 </span>            :     }</a>
+<a name="1312"><span class="lineNum">    1312 </span>            :     else</a>
+<a name="1313"><span class="lineNum">    1313 </span>            :     {</a>
+<a name="1314"><span class="lineNum">    1314 </span><span class="lineCov">         25 :       #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1315"><span class="lineNum">    1315 </span>            :       {</a>
+<a name="1316"><span class="lineNum">    1316 </span>            :         std::vector&lt;double&gt; omp_deriv(der_prob.size(),0.);</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :         // for performances and thread safety</a>
+<a name="1318"><span class="lineNum">    1318 </span>            :         std::vector&lt;double&gt; dist(ncv_);</a>
+<a name="1319"><span class="lineNum">    1319 </span>            :         #pragma omp for reduction(+:prob) nowait</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :         for(unsigned nk=rank_; nk&lt;nlist_index_.size(); nk+=NumParallel_)</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :           prob+=evaluateKernel(kernels_[nlist_index_[nk]],cv,omp_deriv,dist);</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :         #pragma omp critical</a>
+<a name="1323"><span class="lineNum">    1323 </span>            :         for(unsigned i=0; i&lt;ncv_; i++)</a>
+<a name="1324"><span class="lineNum">    1324 </span>            :           der_prob[i]+=omp_deriv[i];</a>
+<a name="1325"><span class="lineNum">    1325 </span>            :       }</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :     }</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   }</a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineCov">       1141 :   if(NumParallel_&gt;1)</span></a>
+<a name="1329"><span class="lineNum">    1329 </span>            :   {</a>
+<a name="1330"><span class="lineNum">    1330 </span><span class="lineCov">        224 :     comm.Sum(prob);</span></a>
+<a name="1331"><span class="lineNum">    1331 </span><span class="lineCov">        224 :     comm.Sum(der_prob);</span></a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   }</a>
+<a name="1333"><span class="lineNum">    1333 </span>            : //normalize the estimate</a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">       1141 :   prob/=KDEnorm_;</span></a>
+<a name="1335"><span class="lineNum">    1335 </span><span class="lineCov">       3311 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1336"><span class="lineNum">    1336 </span><span class="lineCov">       2170 :     der_prob[i]/=KDEnorm_;</span></a>
+<a name="1337"><span class="lineNum">    1337 </span>            : </a>
+<a name="1338"><span class="lineNum">    1338 </span><span class="lineCov">       1141 :   return prob;</span></a>
+<a name="1339"><span class="lineNum">    1339 </span>            : }</a>
+<a name="1340"><span class="lineNum">    1340 </span>            : </a>
+<a name="1341"><span class="lineNum">    1341 </span>            : template &lt;class mode&gt;</a>
+<a name="1342"><span class="lineNum">    1342 </span><span class="lineCov">        513 : void OPESmetad&lt;mode&gt;::addKernel(const double height,const std::vector&lt;double&gt;&amp; center,const std::vector&lt;double&gt;&amp; sigma)</span></a>
+<a name="1343"><span class="lineNum">    1343 </span>            : {</a>
+<a name="1344"><span class="lineNum">    1344 </span>            :   bool no_match=true;</a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineCov">        513 :   if(threshold2_!=0)</span></a>
+<a name="1346"><span class="lineNum">    1346 </span>            :   {</a>
+<a name="1347"><span class="lineNum">    1347 </span><span class="lineCov">        513 :     unsigned taker_k=getMergeableKernel(center,kernels_.size());</span></a>
+<a name="1348"><span class="lineNum">    1348 </span><span class="lineCov">        513 :     if(taker_k&lt;kernels_.size())</span></a>
+<a name="1349"><span class="lineNum">    1349 </span>            :     {</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :       no_match=false;</a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineCov">        388 :       delta_kernels_.emplace_back(-1*kernels_[taker_k].height,kernels_[taker_k].center,kernels_[taker_k].sigma);</span></a>
+<a name="1352"><span class="lineNum">    1352 </span><span class="lineCov">        776 :       mergeKernels(kernels_[taker_k],kernel(height,center,sigma));</span></a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineCov">        388 :       delta_kernels_.push_back(kernels_[taker_k]);</span></a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineCov">        388 :       if(recursive_merge_) //the overhead is worth it if it keeps low the total number of kernels</span></a>
+<a name="1355"><span class="lineNum">    1355 </span>            :       {</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :         unsigned giver_k=taker_k;</a>
+<a name="1357"><span class="lineNum">    1357 </span><span class="lineCov">        337 :         taker_k=getMergeableKernel(kernels_[giver_k].center,giver_k);</span></a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineCov">        337 :         while(taker_k&lt;kernels_.size())</span></a>
+<a name="1359"><span class="lineNum">    1359 </span>            :         {</a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineNoCov">          0 :           delta_kernels_.pop_back();</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineNoCov">          0 :           delta_kernels_.emplace_back(-1*kernels_[taker_k].height,kernels_[taker_k].center,kernels_[taker_k].sigma);</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineNoCov">          0 :           if(taker_k&gt;giver_k) //saves time when erasing</span></a>
+<a name="1363"><span class="lineNum">    1363 </span>            :             std::swap(taker_k,giver_k);</a>
+<a name="1364"><span class="lineNum">    1364 </span><span class="lineNoCov">          0 :           mergeKernels(kernels_[taker_k],kernels_[giver_k]);</span></a>
+<a name="1365"><span class="lineNum">    1365 </span><span class="lineNoCov">          0 :           delta_kernels_.push_back(kernels_[taker_k]);</span></a>
+<a name="1366"><span class="lineNum">    1366 </span><span class="lineNoCov">          0 :           kernels_.erase(kernels_.begin()+giver_k);</span></a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineNoCov">          0 :           if(nlist_)</span></a>
+<a name="1368"><span class="lineNum">    1368 </span>            :           {</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :             unsigned giver_nk=0;</a>
+<a name="1370"><span class="lineNum">    1370 </span>            :             bool found_giver=false;</a>
+<a name="1371"><span class="lineNum">    1371 </span><span class="lineNoCov">          0 :             for(unsigned nk=0; nk&lt;nlist_index_.size(); nk++)</span></a>
+<a name="1372"><span class="lineNum">    1372 </span>            :             {</a>
+<a name="1373"><span class="lineNum">    1373 </span><span class="lineNoCov">          0 :               if(found_giver)</span></a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineNoCov">          0 :                 nlist_index_[nk]--; //all the indexes shift due to erase</span></a>
+<a name="1375"><span class="lineNum">    1375 </span><span class="lineNoCov">          0 :               if(nlist_index_[nk]==giver_k)</span></a>
+<a name="1376"><span class="lineNum">    1376 </span>            :               {</a>
+<a name="1377"><span class="lineNum">    1377 </span>            :                 giver_nk=nk;</a>
+<a name="1378"><span class="lineNum">    1378 </span>            :                 found_giver=true;</a>
+<a name="1379"><span class="lineNum">    1379 </span>            :               }</a>
+<a name="1380"><span class="lineNum">    1380 </span>            :             }</a>
+<a name="1381"><span class="lineNum">    1381 </span>            :             plumed_dbg_massert(found_giver,&quot;problem with merging and NLIST&quot;);</a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineNoCov">          0 :             nlist_index_.erase(nlist_index_.begin()+giver_nk);</span></a>
+<a name="1383"><span class="lineNum">    1383 </span>            :           }</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :           giver_k=taker_k;</a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineNoCov">          0 :           taker_k=getMergeableKernel(kernels_[giver_k].center,giver_k);</span></a>
+<a name="1386"><span class="lineNum">    1386 </span>            :         }</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :       }</a>
+<a name="1388"><span class="lineNum">    1388 </span>            :     }</a>
+<a name="1389"><span class="lineNum">    1389 </span>            :   }</a>
+<a name="1390"><span class="lineNum">    1390 </span>            :   if(no_match)</a>
+<a name="1391"><span class="lineNum">    1391 </span>            :   {</a>
+<a name="1392"><span class="lineNum">    1392 </span><span class="lineCov">        125 :     kernels_.emplace_back(height,center,sigma);</span></a>
+<a name="1393"><span class="lineNum">    1393 </span><span class="lineCov">        125 :     delta_kernels_.emplace_back(height,center,sigma);</span></a>
+<a name="1394"><span class="lineNum">    1394 </span><span class="lineCov">        125 :     if(nlist_)</span></a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineCov">         12 :       nlist_index_.push_back(kernels_.size()-1);</span></a>
+<a name="1396"><span class="lineNum">    1396 </span>            :   }</a>
+<a name="1397"><span class="lineNum">    1397 </span><span class="lineCov">        513 : }</span></a>
+<a name="1398"><span class="lineNum">    1398 </span>            : </a>
+<a name="1399"><span class="lineNum">    1399 </span>            : template &lt;class mode&gt;</a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineCov">        383 : void OPESmetad&lt;mode&gt;::addKernel(const double height,const std::vector&lt;double&gt;&amp; center,const std::vector&lt;double&gt;&amp; sigma,const double logweight)</span></a>
+<a name="1401"><span class="lineNum">    1401 </span>            : {</a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">        383 :   addKernel(height,center,sigma);</span></a>
+<a name="1403"><span class="lineNum">    1403 </span>            : //write to file</a>
+<a name="1404"><span class="lineNum">    1404 </span><span class="lineCov">        383 :   kernelsOfile_.printField(&quot;time&quot;,getTime());</span></a>
+<a name="1405"><span class="lineNum">    1405 </span><span class="lineCov">       1134 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1406"><span class="lineNum">    1406 </span><span class="lineCov">        751 :     kernelsOfile_.printField(getPntrToArgument(i),center[i]);</span></a>
+<a name="1407"><span class="lineNum">    1407 </span><span class="lineCov">       1134 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1408"><span class="lineNum">    1408 </span><span class="lineCov">       1502 :     kernelsOfile_.printField(&quot;sigma_&quot;+getPntrToArgument(i)-&gt;getName(),sigma[i]);</span></a>
+<a name="1409"><span class="lineNum">    1409 </span><span class="lineCov">        383 :   kernelsOfile_.printField(&quot;height&quot;,height);</span></a>
+<a name="1410"><span class="lineNum">    1410 </span><span class="lineCov">        383 :   kernelsOfile_.printField(&quot;logweight&quot;,logweight);</span></a>
+<a name="1411"><span class="lineNum">    1411 </span><span class="lineCov">        383 :   kernelsOfile_.printField();</span></a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">        383 : }</span></a>
+<a name="1413"><span class="lineNum">    1413 </span>            : </a>
+<a name="1414"><span class="lineNum">    1414 </span>            : template &lt;class mode&gt;</a>
+<a name="1415"><span class="lineNum">    1415 </span><span class="lineCov">        850 : unsigned OPESmetad&lt;mode&gt;::getMergeableKernel(const std::vector&lt;double&gt;&amp; giver_center,const unsigned giver_k)</span></a>
+<a name="1416"><span class="lineNum">    1416 </span>            : { //returns kernels_.size() if no match is found</a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineCov">        850 :   unsigned min_k=kernels_.size();</span></a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineCov">        850 :   double min_norm2=threshold2_;</span></a>
+<a name="1419"><span class="lineNum">    1419 </span><span class="lineCov">        850 :   if(!nlist_)</span></a>
+<a name="1420"><span class="lineNum">    1420 </span>            :   {</a>
+<a name="1421"><span class="lineNum">    1421 </span><span class="lineCov">        550 :     #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     {</a>
+<a name="1423"><span class="lineNum">    1423 </span>            :       unsigned min_k_omp = min_k;</a>
+<a name="1424"><span class="lineNum">    1424 </span>            :       double min_norm2_omp = threshold2_;</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :       #pragma omp for nowait</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :       for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :       {</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :         if(k==giver_k) //a kernel should not be merged with itself</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :           continue;</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :         double norm2=0;</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :         for(unsigned i=0; i&lt;ncv_; i++)</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :         {</a>
+<a name="1433"><span class="lineNum">    1433 </span>            :           const double dist_i=difference(i,giver_center[i],kernels_[k].center[i])/kernels_[k].sigma[i];</a>
+<a name="1434"><span class="lineNum">    1434 </span>            :           norm2+=dist_i*dist_i;</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :           if(norm2&gt;=min_norm2_omp)</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :             break;</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :         }</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :         if(norm2&lt;min_norm2_omp)</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :         {</a>
+<a name="1440"><span class="lineNum">    1440 </span>            :           min_norm2_omp=norm2;</a>
+<a name="1441"><span class="lineNum">    1441 </span>            :           min_k_omp=k;</a>
+<a name="1442"><span class="lineNum">    1442 </span>            :         }</a>
+<a name="1443"><span class="lineNum">    1443 </span>            :       }</a>
+<a name="1444"><span class="lineNum">    1444 </span>            :       #pragma omp critical</a>
+<a name="1445"><span class="lineNum">    1445 </span>            :       {</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :         if(min_norm2_omp &lt; min_norm2)</a>
+<a name="1447"><span class="lineNum">    1447 </span>            :         {</a>
+<a name="1448"><span class="lineNum">    1448 </span>            :           min_norm2 = min_norm2_omp;</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :           min_k = min_k_omp;</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :         }</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :       }</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :     }</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :   }</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :   else</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :   {</a>
+<a name="1456"><span class="lineNum">    1456 </span><span class="lineCov">        300 :     #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1457"><span class="lineNum">    1457 </span>            :     {</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :       unsigned min_k_omp = min_k;</a>
+<a name="1459"><span class="lineNum">    1459 </span>            :       double min_norm2_omp = threshold2_;</a>
+<a name="1460"><span class="lineNum">    1460 </span>            :       #pragma omp for nowait</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :       for(unsigned nk=rank_; nk&lt;nlist_index_.size(); nk+=NumParallel_)</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :       {</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :         const unsigned k=nlist_index_[nk];</a>
+<a name="1464"><span class="lineNum">    1464 </span>            :         if(k==giver_k) //a kernel should not be merged with itself</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :           continue;</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :         double norm2=0;</a>
+<a name="1467"><span class="lineNum">    1467 </span>            :         for(unsigned i=0; i&lt;ncv_; i++)</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :         {</a>
+<a name="1469"><span class="lineNum">    1469 </span>            :           const double dist_i=difference(i,giver_center[i],kernels_[k].center[i])/kernels_[k].sigma[i];</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :           norm2+=dist_i*dist_i;</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :           if(norm2&gt;=min_norm2)</a>
+<a name="1472"><span class="lineNum">    1472 </span>            :             break;</a>
+<a name="1473"><span class="lineNum">    1473 </span>            :         }</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :         if(norm2&lt;min_norm2_omp)</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :         {</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :           min_norm2_omp=norm2;</a>
+<a name="1477"><span class="lineNum">    1477 </span>            :           min_k_omp=k;</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :         }</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :       }</a>
+<a name="1480"><span class="lineNum">    1480 </span>            :       #pragma omp critical</a>
+<a name="1481"><span class="lineNum">    1481 </span>            :       {</a>
+<a name="1482"><span class="lineNum">    1482 </span>            :         if(min_norm2_omp &lt; min_norm2)</a>
+<a name="1483"><span class="lineNum">    1483 </span>            :         {</a>
+<a name="1484"><span class="lineNum">    1484 </span>            :           min_norm2 = min_norm2_omp;</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :           min_k = min_k_omp;</a>
+<a name="1486"><span class="lineNum">    1486 </span>            :         }</a>
+<a name="1487"><span class="lineNum">    1487 </span>            :       }</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :     }</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :   }</a>
+<a name="1490"><span class="lineNum">    1490 </span><span class="lineCov">        850 :   if(NumParallel_&gt;1)</span></a>
+<a name="1491"><span class="lineNum">    1491 </span>            :   {</a>
+<a name="1492"><span class="lineNum">    1492 </span><span class="lineCov">        134 :     std::vector&lt;double&gt; all_min_norm2(NumParallel_);</span></a>
+<a name="1493"><span class="lineNum">    1493 </span><span class="lineCov">        134 :     std::vector&lt;unsigned&gt; all_min_k(NumParallel_);</span></a>
+<a name="1494"><span class="lineNum">    1494 </span><span class="lineCov">        134 :     comm.Allgather(min_norm2,all_min_norm2);</span></a>
+<a name="1495"><span class="lineNum">    1495 </span><span class="lineCov">        134 :     comm.Allgather(min_k,all_min_k);</span></a>
+<a name="1496"><span class="lineNum">    1496 </span>            :     const unsigned best=std::distance(std::begin(all_min_norm2),std::min_element(std::begin(all_min_norm2),std::end(all_min_norm2)));</a>
+<a name="1497"><span class="lineNum">    1497 </span><span class="lineCov">        134 :     min_k=all_min_k[best];</span></a>
+<a name="1498"><span class="lineNum">    1498 </span>            :   }</a>
+<a name="1499"><span class="lineNum">    1499 </span><span class="lineCov">        850 :   return min_k;</span></a>
+<a name="1500"><span class="lineNum">    1500 </span>            : }</a>
+<a name="1501"><span class="lineNum">    1501 </span>            : </a>
+<a name="1502"><span class="lineNum">    1502 </span>            : template &lt;class mode&gt;</a>
+<a name="1503"><span class="lineNum">    1503 </span><span class="lineCov">        250 : void OPESmetad&lt;mode&gt;::updateNlist(const std::vector&lt;double&gt;&amp; new_center)</span></a>
+<a name="1504"><span class="lineNum">    1504 </span>            : {</a>
+<a name="1505"><span class="lineNum">    1505 </span><span class="lineCov">        250 :   if(kernels_.size()==0) //no need to check for neighbors</span></a>
+<a name="1506"><span class="lineNum">    1506 </span><span class="lineCov">          6 :     return;</span></a>
+<a name="1507"><span class="lineNum">    1507 </span>            : </a>
+<a name="1508"><span class="lineNum">    1508 </span><span class="lineCov">        244 :   nlist_center_=new_center;</span></a>
+<a name="1509"><span class="lineNum">    1509 </span><span class="lineCov">        244 :   nlist_index_.clear();</span></a>
+<a name="1510"><span class="lineNum">    1510 </span>            :   //first we gather all the nlist_index</a>
+<a name="1511"><span class="lineNum">    1511 </span><span class="lineCov">        244 :   if(NumOMP_==1 || (unsigned)kernels_.size()&lt;2*NumOMP_*NumParallel_)</span></a>
+<a name="1512"><span class="lineNum">    1512 </span>            :   {</a>
+<a name="1513"><span class="lineNum">    1513 </span><span class="lineCov">        198 :     for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</span></a>
+<a name="1514"><span class="lineNum">    1514 </span>            :     {</a>
+<a name="1515"><span class="lineNum">    1515 </span>            :       double norm2_k=0;</a>
+<a name="1516"><span class="lineNum">    1516 </span><span class="lineCov">        444 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1517"><span class="lineNum">    1517 </span>            :       {</a>
+<a name="1518"><span class="lineNum">    1518 </span><span class="lineCov">        296 :         const double dist_ik=difference(i,nlist_center_[i],kernels_[k].center[i])/kernels_[k].sigma[i];</span></a>
+<a name="1519"><span class="lineNum">    1519 </span><span class="lineCov">        296 :         norm2_k+=dist_ik*dist_ik;</span></a>
+<a name="1520"><span class="lineNum">    1520 </span>            :       }</a>
+<a name="1521"><span class="lineNum">    1521 </span><span class="lineCov">        148 :       if(norm2_k&lt;=nlist_param_[0]*cutoff2_)</span></a>
+<a name="1522"><span class="lineNum">    1522 </span><span class="lineCov">        104 :         nlist_index_.push_back(k);</span></a>
+<a name="1523"><span class="lineNum">    1523 </span>            :     }</a>
+<a name="1524"><span class="lineNum">    1524 </span>            :   }</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :   else</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :   {</a>
+<a name="1527"><span class="lineNum">    1527 </span><span class="lineCov">        194 :     #pragma omp parallel num_threads(NumOMP_)</span></a>
+<a name="1528"><span class="lineNum">    1528 </span>            :     {</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :       std::vector&lt;unsigned&gt; private_nlist_index;</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :       #pragma omp for nowait</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :       for(unsigned k=rank_; k&lt;kernels_.size(); k+=NumParallel_)</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :       {</a>
+<a name="1533"><span class="lineNum">    1533 </span>            :         double norm2_k=0;</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :         for(unsigned i=0; i&lt;ncv_; i++)</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :         {</a>
+<a name="1536"><span class="lineNum">    1536 </span>            :           const double dist_ik=difference(i,nlist_center_[i],kernels_[k].center[i])/kernels_[k].sigma[i];</a>
+<a name="1537"><span class="lineNum">    1537 </span>            :           norm2_k+=dist_ik*dist_ik;</a>
+<a name="1538"><span class="lineNum">    1538 </span>            :         }</a>
+<a name="1539"><span class="lineNum">    1539 </span>            :         if(norm2_k&lt;=nlist_param_[0]*cutoff2_)</a>
+<a name="1540"><span class="lineNum">    1540 </span>            :           private_nlist_index.push_back(k);</a>
+<a name="1541"><span class="lineNum">    1541 </span>            :       }</a>
+<a name="1542"><span class="lineNum">    1542 </span>            :       #pragma omp critical</a>
+<a name="1543"><span class="lineNum">    1543 </span>            :       nlist_index_.insert(nlist_index_.end(),private_nlist_index.begin(),private_nlist_index.end());</a>
+<a name="1544"><span class="lineNum">    1544 </span>            :     }</a>
+<a name="1545"><span class="lineNum">    1545 </span><span class="lineCov">        194 :     if(recursive_merge_)</span></a>
+<a name="1546"><span class="lineNum">    1546 </span><span class="lineCov">        194 :       std::sort(nlist_index_.begin(),nlist_index_.end());</span></a>
+<a name="1547"><span class="lineNum">    1547 </span>            :   }</a>
+<a name="1548"><span class="lineNum">    1548 </span><span class="lineCov">        244 :   if(NumParallel_&gt;1)</span></a>
+<a name="1549"><span class="lineNum">    1549 </span>            :   {</a>
+<a name="1550"><span class="lineNum">    1550 </span><span class="lineCov">        100 :     std::vector&lt;int&gt; all_nlist_size(NumParallel_);</span></a>
+<a name="1551"><span class="lineNum">    1551 </span><span class="lineCov">        100 :     all_nlist_size[rank_]=nlist_index_.size();</span></a>
+<a name="1552"><span class="lineNum">    1552 </span><span class="lineCov">        100 :     comm.Sum(all_nlist_size);</span></a>
+<a name="1553"><span class="lineNum">    1553 </span>            :     unsigned tot_size=0;</a>
+<a name="1554"><span class="lineNum">    1554 </span><span class="lineCov">        300 :     for(unsigned r=0; r&lt;NumParallel_; r++)</span></a>
+<a name="1555"><span class="lineNum">    1555 </span><span class="lineCov">        200 :       tot_size+=all_nlist_size[r];</span></a>
+<a name="1556"><span class="lineNum">    1556 </span><span class="lineCov">        100 :     if(tot_size&gt;0)</span></a>
+<a name="1557"><span class="lineNum">    1557 </span>            :     {</a>
+<a name="1558"><span class="lineNum">    1558 </span><span class="lineCov">        100 :       std::vector&lt;int&gt; disp(NumParallel_);</span></a>
+<a name="1559"><span class="lineNum">    1559 </span><span class="lineCov">        200 :       for(unsigned r=0; r&lt;NumParallel_-1; r++)</span></a>
+<a name="1560"><span class="lineNum">    1560 </span><span class="lineCov">        100 :         disp[r+1]=disp[r]+all_nlist_size[r];</span></a>
+<a name="1561"><span class="lineNum">    1561 </span><span class="lineCov">        100 :       std::vector&lt;unsigned&gt; local_nlist_index=nlist_index_;</span></a>
+<a name="1562"><span class="lineNum">    1562 </span><span class="lineCov">        100 :       nlist_index_.resize(tot_size);</span></a>
+<a name="1563"><span class="lineNum">    1563 </span><span class="lineCov">        100 :       comm.Allgatherv(local_nlist_index,nlist_index_,&amp;all_nlist_size[0],&amp;disp[0]);</span></a>
+<a name="1564"><span class="lineNum">    1564 </span><span class="lineCov">        100 :       if(recursive_merge_)</span></a>
+<a name="1565"><span class="lineNum">    1565 </span><span class="lineCov">        100 :         std::sort(nlist_index_.begin(),nlist_index_.end());</span></a>
+<a name="1566"><span class="lineNum">    1566 </span>            :     }</a>
+<a name="1567"><span class="lineNum">    1567 </span>            :   }</a>
+<a name="1568"><span class="lineNum">    1568 </span>            :   //calculate the square deviation</a>
+<a name="1569"><span class="lineNum">    1569 </span><span class="lineCov">        244 :   std::vector&lt;double&gt; dev2(ncv_,0.);</span></a>
+<a name="1570"><span class="lineNum">    1570 </span><span class="lineCov">        773 :   for(unsigned k=rank_; k&lt;nlist_index_.size(); k+=NumParallel_)</span></a>
+<a name="1571"><span class="lineNum">    1571 </span>            :   {</a>
+<a name="1572"><span class="lineNum">    1572 </span><span class="lineCov">       1587 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1573"><span class="lineNum">    1573 </span>            :     {</a>
+<a name="1574"><span class="lineNum">    1574 </span><span class="lineCov">       1058 :       const double diff_ik=difference(i,nlist_center_[i],kernels_[nlist_index_[k]].center[i]);</span></a>
+<a name="1575"><span class="lineNum">    1575 </span><span class="lineCov">       1058 :       dev2[i]+=diff_ik*diff_ik;</span></a>
+<a name="1576"><span class="lineNum">    1576 </span>            :     }</a>
+<a name="1577"><span class="lineNum">    1577 </span>            :   }</a>
+<a name="1578"><span class="lineNum">    1578 </span><span class="lineCov">        244 :   if(NumParallel_&gt;1)</span></a>
+<a name="1579"><span class="lineNum">    1579 </span><span class="lineCov">        100 :     comm.Sum(dev2);</span></a>
+<a name="1580"><span class="lineNum">    1580 </span><span class="lineCov">        732 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1581"><span class="lineNum">    1581 </span>            :   {</a>
+<a name="1582"><span class="lineNum">    1582 </span><span class="lineCov">        488 :     if(dev2[i]==0) //e.g. if nlist_index_.size()==0</span></a>
+<a name="1583"><span class="lineNum">    1583 </span><span class="lineCov">         56 :       nlist_dev2_[i]=std::pow(kernels_.back().sigma[i],2);</span></a>
+<a name="1584"><span class="lineNum">    1584 </span>            :     else</a>
+<a name="1585"><span class="lineNum">    1585 </span><span class="lineCov">        432 :       nlist_dev2_[i]=dev2[i]/nlist_index_.size();</span></a>
+<a name="1586"><span class="lineNum">    1586 </span>            :   }</a>
+<a name="1587"><span class="lineNum">    1587 </span><span class="lineCov">        244 :   getPntrToComponent(&quot;nlker&quot;)-&gt;set(nlist_index_.size());</span></a>
+<a name="1588"><span class="lineNum">    1588 </span><span class="lineCov">        244 :   getPntrToComponent(&quot;nlsteps&quot;)-&gt;set(nlist_steps_);</span></a>
+<a name="1589"><span class="lineNum">    1589 </span><span class="lineCov">        244 :   nlist_steps_=0;</span></a>
+<a name="1590"><span class="lineNum">    1590 </span><span class="lineCov">        244 :   nlist_update_=false;</span></a>
+<a name="1591"><span class="lineNum">    1591 </span>            : }</a>
+<a name="1592"><span class="lineNum">    1592 </span>            : </a>
+<a name="1593"><span class="lineNum">    1593 </span>            : template &lt;class mode&gt;</a>
+<a name="1594"><span class="lineNum">    1594 </span><span class="lineCov">         18 : void OPESmetad&lt;mode&gt;::dumpStateToFile()</span></a>
+<a name="1595"><span class="lineNum">    1595 </span>            : {</a>
+<a name="1596"><span class="lineNum">    1596 </span>            : //gather adaptive sigma info if needed</a>
+<a name="1597"><span class="lineNum">    1597 </span>            : //doing this while writing to file can lead to misterious slowdowns</a>
+<a name="1598"><span class="lineNum">    1598 </span>            :   std::vector&lt;double&gt; all_sigma0;</a>
+<a name="1599"><span class="lineNum">    1599 </span>            :   std::vector&lt;double&gt; all_av_cv;</a>
+<a name="1600"><span class="lineNum">    1600 </span>            :   std::vector&lt;double&gt; all_av_M2;</a>
+<a name="1601"><span class="lineNum">    1601 </span><span class="lineCov">         18 :   if(adaptive_sigma_ &amp;&amp; NumWalkers_&gt;1)</span></a>
+<a name="1602"><span class="lineNum">    1602 </span>            :   {</a>
+<a name="1603"><span class="lineNum">    1603 </span><span class="lineCov">         16 :     all_sigma0.resize(NumWalkers_*ncv_);</span></a>
+<a name="1604"><span class="lineNum">    1604 </span><span class="lineCov">         16 :     all_av_cv.resize(NumWalkers_*ncv_);</span></a>
+<a name="1605"><span class="lineNum">    1605 </span><span class="lineCov">         16 :     all_av_M2.resize(NumWalkers_*ncv_);</span></a>
+<a name="1606"><span class="lineNum">    1606 </span><span class="lineCov">         16 :     if(comm.Get_rank()==0)</span></a>
+<a name="1607"><span class="lineNum">    1607 </span>            :     {</a>
+<a name="1608"><span class="lineNum">    1608 </span><span class="lineCov">         16 :       multi_sim_comm.Allgather(sigma0_,all_sigma0);</span></a>
+<a name="1609"><span class="lineNum">    1609 </span><span class="lineCov">         16 :       multi_sim_comm.Allgather(av_cv_,all_av_cv);</span></a>
+<a name="1610"><span class="lineNum">    1610 </span><span class="lineCov">         16 :       multi_sim_comm.Allgather(av_M2_,all_av_M2);</span></a>
+<a name="1611"><span class="lineNum">    1611 </span>            :     }</a>
+<a name="1612"><span class="lineNum">    1612 </span><span class="lineCov">         16 :     comm.Bcast(all_sigma0,0);</span></a>
+<a name="1613"><span class="lineNum">    1613 </span><span class="lineCov">         16 :     comm.Bcast(all_av_cv,0);</span></a>
+<a name="1614"><span class="lineNum">    1614 </span><span class="lineCov">         16 :     comm.Bcast(all_av_M2,0);</span></a>
+<a name="1615"><span class="lineNum">    1615 </span>            :   }</a>
+<a name="1616"><span class="lineNum">    1616 </span>            : </a>
+<a name="1617"><span class="lineNum">    1617 </span>            : //rewrite header or rewind file</a>
+<a name="1618"><span class="lineNum">    1618 </span><span class="lineCov">         18 :   if(storeOldStates_)</span></a>
+<a name="1619"><span class="lineNum">    1619 </span><span class="lineCov">         16 :     stateOfile_.clearFields();</span></a>
+<a name="1620"><span class="lineNum">    1620 </span><span class="lineCov">          2 :   else if(walker_rank_==0)</span></a>
+<a name="1621"><span class="lineNum">    1621 </span><span class="lineCov">          2 :     stateOfile_.rewind();</span></a>
+<a name="1622"><span class="lineNum">    1622 </span>            : //define fields</a>
+<a name="1623"><span class="lineNum">    1623 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;action&quot;);</span></a>
+<a name="1624"><span class="lineNum">    1624 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;biasfactor&quot;);</span></a>
+<a name="1625"><span class="lineNum">    1625 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;epsilon&quot;);</span></a>
+<a name="1626"><span class="lineNum">    1626 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;kernel_cutoff&quot;);</span></a>
+<a name="1627"><span class="lineNum">    1627 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;compression_threshold&quot;);</span></a>
+<a name="1628"><span class="lineNum">    1628 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;zed&quot;);</span></a>
+<a name="1629"><span class="lineNum">    1629 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;sum_weights&quot;);</span></a>
+<a name="1630"><span class="lineNum">    1630 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;sum_weights2&quot;);</span></a>
+<a name="1631"><span class="lineNum">    1631 </span><span class="lineCov">         18 :   stateOfile_.addConstantField(&quot;counter&quot;);</span></a>
+<a name="1632"><span class="lineNum">    1632 </span><span class="lineCov">         18 :   if(adaptive_sigma_)</span></a>
+<a name="1633"><span class="lineNum">    1633 </span>            :   {</a>
+<a name="1634"><span class="lineNum">    1634 </span><span class="lineCov">         18 :     stateOfile_.addConstantField(&quot;adaptive_counter&quot;);</span></a>
+<a name="1635"><span class="lineNum">    1635 </span><span class="lineCov">         18 :     if(NumWalkers_==1)</span></a>
+<a name="1636"><span class="lineNum">    1636 </span>            :     {</a>
+<a name="1637"><span class="lineNum">    1637 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1638"><span class="lineNum">    1638 </span>            :       {</a>
+<a name="1639"><span class="lineNum">    1639 </span><span class="lineCov">          8 :         stateOfile_.addConstantField(&quot;sigma0_&quot;+getPntrToArgument(i)-&gt;getName());</span></a>
+<a name="1640"><span class="lineNum">    1640 </span><span class="lineCov">          8 :         stateOfile_.addConstantField(&quot;av_cv_&quot;+getPntrToArgument(i)-&gt;getName());</span></a>
+<a name="1641"><span class="lineNum">    1641 </span><span class="lineCov">          8 :         stateOfile_.addConstantField(&quot;av_M2_&quot;+getPntrToArgument(i)-&gt;getName());</span></a>
+<a name="1642"><span class="lineNum">    1642 </span>            :       }</a>
+<a name="1643"><span class="lineNum">    1643 </span>            :     }</a>
+<a name="1644"><span class="lineNum">    1644 </span>            :     else</a>
+<a name="1645"><span class="lineNum">    1645 </span>            :     {</a>
+<a name="1646"><span class="lineNum">    1646 </span><span class="lineCov">         48 :       for(unsigned w=0; w&lt;NumWalkers_; w++)</span></a>
+<a name="1647"><span class="lineNum">    1647 </span><span class="lineCov">         96 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1648"><span class="lineNum">    1648 </span>            :         {</a>
+<a name="1649"><span class="lineNum">    1649 </span><span class="lineCov">        128 :           const std::string arg_iw=getPntrToArgument(i)-&gt;getName()+&quot;_&quot;+std::to_string(w);</span></a>
+<a name="1650"><span class="lineNum">    1650 </span><span class="lineCov">         64 :           stateOfile_.addConstantField(&quot;sigma0_&quot;+arg_iw);</span></a>
+<a name="1651"><span class="lineNum">    1651 </span><span class="lineCov">         64 :           stateOfile_.addConstantField(&quot;av_cv_&quot;+arg_iw);</span></a>
+<a name="1652"><span class="lineNum">    1652 </span><span class="lineCov">        128 :           stateOfile_.addConstantField(&quot;av_M2_&quot;+arg_iw);</span></a>
+<a name="1653"><span class="lineNum">    1653 </span>            :         }</a>
+<a name="1654"><span class="lineNum">    1654 </span>            :     }</a>
+<a name="1655"><span class="lineNum">    1655 </span>            :   }</a>
+<a name="1656"><span class="lineNum">    1656 </span>            : //print fields</a>
+<a name="1657"><span class="lineNum">    1657 </span><span class="lineCov">         54 :   for(unsigned i=0; i&lt;ncv_; i++) //periodicity of CVs</span></a>
+<a name="1658"><span class="lineNum">    1658 </span><span class="lineCov">         36 :     stateOfile_.setupPrintValue(getPntrToArgument(i));</span></a>
+<a name="1659"><span class="lineNum">    1659 </span><span class="lineCov">         36 :   stateOfile_.printField(&quot;action&quot;,getName()+&quot;_state&quot;);</span></a>
+<a name="1660"><span class="lineNum">    1660 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;biasfactor&quot;,biasfactor_);</span></a>
+<a name="1661"><span class="lineNum">    1661 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;epsilon&quot;,epsilon_);</span></a>
+<a name="1662"><span class="lineNum">    1662 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;kernel_cutoff&quot;,sqrt(cutoff2_));</span></a>
+<a name="1663"><span class="lineNum">    1663 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;compression_threshold&quot;,sqrt(threshold2_));</span></a>
+<a name="1664"><span class="lineNum">    1664 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;zed&quot;,Zed_);</span></a>
+<a name="1665"><span class="lineNum">    1665 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;sum_weights&quot;,sum_weights_);</span></a>
+<a name="1666"><span class="lineNum">    1666 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;sum_weights2&quot;,sum_weights2_);</span></a>
+<a name="1667"><span class="lineNum">    1667 </span><span class="lineCov">         18 :   stateOfile_.printField(&quot;counter&quot;,counter_);</span></a>
+<a name="1668"><span class="lineNum">    1668 </span><span class="lineCov">         18 :   if(adaptive_sigma_)</span></a>
+<a name="1669"><span class="lineNum">    1669 </span>            :   {</a>
+<a name="1670"><span class="lineNum">    1670 </span><span class="lineCov">         18 :     stateOfile_.printField(&quot;adaptive_counter&quot;,adaptive_counter_);</span></a>
+<a name="1671"><span class="lineNum">    1671 </span><span class="lineCov">         18 :     if(NumWalkers_==1)</span></a>
+<a name="1672"><span class="lineNum">    1672 </span>            :     {</a>
+<a name="1673"><span class="lineNum">    1673 </span><span class="lineCov">          6 :       for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1674"><span class="lineNum">    1674 </span>            :       {</a>
+<a name="1675"><span class="lineNum">    1675 </span><span class="lineCov">          8 :         stateOfile_.printField(&quot;sigma0_&quot;+getPntrToArgument(i)-&gt;getName(),sigma0_[i]);</span></a>
+<a name="1676"><span class="lineNum">    1676 </span><span class="lineCov">          8 :         stateOfile_.printField(&quot;av_cv_&quot;+getPntrToArgument(i)-&gt;getName(),av_cv_[i]);</span></a>
+<a name="1677"><span class="lineNum">    1677 </span><span class="lineCov">          8 :         stateOfile_.printField(&quot;av_M2_&quot;+getPntrToArgument(i)-&gt;getName(),av_M2_[i]);</span></a>
+<a name="1678"><span class="lineNum">    1678 </span>            :       }</a>
+<a name="1679"><span class="lineNum">    1679 </span>            :     }</a>
+<a name="1680"><span class="lineNum">    1680 </span>            :     else</a>
+<a name="1681"><span class="lineNum">    1681 </span>            :     {</a>
+<a name="1682"><span class="lineNum">    1682 </span><span class="lineCov">         48 :       for(unsigned w=0; w&lt;NumWalkers_; w++)</span></a>
+<a name="1683"><span class="lineNum">    1683 </span><span class="lineCov">         96 :         for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1684"><span class="lineNum">    1684 </span>            :         {</a>
+<a name="1685"><span class="lineNum">    1685 </span><span class="lineCov">        128 :           const std::string arg_iw=getPntrToArgument(i)-&gt;getName()+&quot;_&quot;+std::to_string(w);</span></a>
+<a name="1686"><span class="lineNum">    1686 </span><span class="lineCov">         64 :           stateOfile_.printField(&quot;sigma0_&quot;+arg_iw,all_sigma0[w*ncv_+i]);</span></a>
+<a name="1687"><span class="lineNum">    1687 </span><span class="lineCov">         64 :           stateOfile_.printField(&quot;av_cv_&quot;+arg_iw,all_av_cv[w*ncv_+i]);</span></a>
+<a name="1688"><span class="lineNum">    1688 </span><span class="lineCov">        128 :           stateOfile_.printField(&quot;av_M2_&quot;+arg_iw,all_av_M2[w*ncv_+i]);</span></a>
+<a name="1689"><span class="lineNum">    1689 </span>            :         }</a>
+<a name="1690"><span class="lineNum">    1690 </span>            :     }</a>
+<a name="1691"><span class="lineNum">    1691 </span>            :   }</a>
+<a name="1692"><span class="lineNum">    1692 </span>            : //print kernels</a>
+<a name="1693"><span class="lineNum">    1693 </span><span class="lineCov">         82 :   for(unsigned k=0; k&lt;kernels_.size(); k++)</span></a>
+<a name="1694"><span class="lineNum">    1694 </span>            :   {</a>
+<a name="1695"><span class="lineNum">    1695 </span><span class="lineCov">         64 :     stateOfile_.printField(&quot;time&quot;,getTime()); //this is not very usefull</span></a>
+<a name="1696"><span class="lineNum">    1696 </span><span class="lineCov">        192 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1697"><span class="lineNum">    1697 </span><span class="lineCov">        128 :       stateOfile_.printField(getPntrToArgument(i),kernels_[k].center[i]);</span></a>
+<a name="1698"><span class="lineNum">    1698 </span><span class="lineCov">        192 :     for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1699"><span class="lineNum">    1699 </span><span class="lineCov">        256 :       stateOfile_.printField(&quot;sigma_&quot;+getPntrToArgument(i)-&gt;getName(),kernels_[k].sigma[i]);</span></a>
+<a name="1700"><span class="lineNum">    1700 </span><span class="lineCov">         64 :     stateOfile_.printField(&quot;height&quot;,kernels_[k].height);</span></a>
+<a name="1701"><span class="lineNum">    1701 </span><span class="lineCov">         64 :     stateOfile_.printField();</span></a>
+<a name="1702"><span class="lineNum">    1702 </span>            :   }</a>
+<a name="1703"><span class="lineNum">    1703 </span>            : //make sure file is written even if small</a>
+<a name="1704"><span class="lineNum">    1704 </span><span class="lineCov">         18 :   if(!storeOldStates_)</span></a>
+<a name="1705"><span class="lineNum">    1705 </span><span class="lineCov">          2 :     stateOfile_.flush();</span></a>
+<a name="1706"><span class="lineNum">    1706 </span><span class="lineCov">         18 : }</span></a>
+<a name="1707"><span class="lineNum">    1707 </span>            : </a>
+<a name="1708"><span class="lineNum">    1708 </span>            : template &lt;class mode&gt;</a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineCov">       5969 : inline double OPESmetad&lt;mode&gt;::evaluateKernel(const kernel&amp; G,const std::vector&lt;double&gt;&amp; x) const</span></a>
+<a name="1710"><span class="lineNum">    1710 </span>            : { //NB: cannot be a method of kernel class, because uses external variables (for cutoff)</a>
+<a name="1711"><span class="lineNum">    1711 </span>            :   double norm2=0;</a>
+<a name="1712"><span class="lineNum">    1712 </span><span class="lineCov">      13923 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1713"><span class="lineNum">    1713 </span>            :   {</a>
+<a name="1714"><span class="lineNum">    1714 </span><span class="lineCov">      10288 :     const double dist_i=difference(i,G.center[i],x[i])/G.sigma[i];</span></a>
+<a name="1715"><span class="lineNum">    1715 </span><span class="lineCov">      10288 :     norm2+=dist_i*dist_i;</span></a>
+<a name="1716"><span class="lineNum">    1716 </span><span class="lineCov">      10288 :     if(norm2&gt;=cutoff2_)</span></a>
+<a name="1717"><span class="lineNum">    1717 </span>            :       return 0;</a>
+<a name="1718"><span class="lineNum">    1718 </span>            :   }</a>
+<a name="1719"><span class="lineNum">    1719 </span><span class="lineCov">       3635 :   return G.height*(std::exp(-0.5*norm2)-val_at_cutoff_);</span></a>
+<a name="1720"><span class="lineNum">    1720 </span>            : }</a>
+<a name="1721"><span class="lineNum">    1721 </span>            : </a>
+<a name="1722"><span class="lineNum">    1722 </span>            : template &lt;class mode&gt;</a>
+<a name="1723"><span class="lineNum">    1723 </span><span class="lineCov">       3364 : inline double OPESmetad&lt;mode&gt;::evaluateKernel(const kernel&amp; G,const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; acc_der, std::vector&lt;double&gt;&amp; dist)</span></a>
+<a name="1724"><span class="lineNum">    1724 </span>            : { //NB: cannot be a method of kernel class, because uses external variables (for cutoff)</a>
+<a name="1725"><span class="lineNum">    1725 </span>            :   double norm2=0;</a>
+<a name="1726"><span class="lineNum">    1726 </span><span class="lineCov">       7483 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1727"><span class="lineNum">    1727 </span>            :   {</a>
+<a name="1728"><span class="lineNum">    1728 </span><span class="lineCov">       5578 :     dist[i]=difference(i,G.center[i],x[i])/G.sigma[i];</span></a>
+<a name="1729"><span class="lineNum">    1729 </span><span class="lineCov">       5578 :     norm2+=dist[i]*dist[i];</span></a>
+<a name="1730"><span class="lineNum">    1730 </span><span class="lineCov">       5578 :     if(norm2&gt;=cutoff2_)</span></a>
+<a name="1731"><span class="lineNum">    1731 </span>            :       return 0;</a>
+<a name="1732"><span class="lineNum">    1732 </span>            :   }</a>
+<a name="1733"><span class="lineNum">    1733 </span><span class="lineCov">       1905 :   const double val=G.height*(std::exp(-0.5*norm2)-val_at_cutoff_);</span></a>
+<a name="1734"><span class="lineNum">    1734 </span><span class="lineCov">       5576 :   for(unsigned i=0; i&lt;ncv_; i++)</span></a>
+<a name="1735"><span class="lineNum">    1735 </span><span class="lineCov">       3671 :     acc_der[i]-=dist[i]/G.sigma[i]*val; //NB: we accumulate the derivative into der</span></a>
+<a name="1736"><span class="lineNum">    1736 </span>            :   return val;</a>
+<a name="1737"><span class="lineNum">    1737 </span>            : }</a>
+<a name="1738"><span class="lineNum">    1738 </span>            : </a>
+<a name="1739"><span class="lineNum">    1739 </span>            : template &lt;class mode&gt;</a>
+<a name="1740"><span class="lineNum">    1740 </span><span class="lineCov">        388 : inline void OPESmetad&lt;mode&gt;::mergeKernels(kernel&amp; k1,const kernel&amp; k2)</span></a>
+<a name="1741"><span class="lineNum">    1741 </span>            : {</a>
+<a name="1742"><span class="lineNum">    1742 </span><span class="lineCov">        388 :   const double h=k1.height+k2.height;</span></a>
+<a name="1743"><span class="lineNum">    1743 </span><span class="lineCov">       1159 :   for(unsigned i=0; i&lt;k1.center.size(); i++)</span></a>
+<a name="1744"><span class="lineNum">    1744 </span>            :   {</a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineCov">        771 :     const bool isPeriodic_i=getPntrToArgument(i)-&gt;isPeriodic();</span></a>
+<a name="1746"><span class="lineNum">    1746 </span><span class="lineCov">        771 :     if(isPeriodic_i)</span></a>
+<a name="1747"><span class="lineNum">    1747 </span><span class="lineCov">        771 :       k1.center[i]=k2.center[i]+difference(i,k2.center[i],k1.center[i]); //fix PBC</span></a>
+<a name="1748"><span class="lineNum">    1748 </span><span class="lineCov">        771 :     const double c_i=(k1.height*k1.center[i]+k2.height*k2.center[i])/h;</span></a>
+<a name="1749"><span class="lineNum">    1749 </span><span class="lineCov">        771 :     const double ss_k1_part=k1.height*(k1.sigma[i]*k1.sigma[i]+k1.center[i]*k1.center[i]);</span></a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineCov">        771 :     const double ss_k2_part=k2.height*(k2.sigma[i]*k2.sigma[i]+k2.center[i]*k2.center[i]);</span></a>
+<a name="1751"><span class="lineNum">    1751 </span><span class="lineCov">        771 :     const double ss_i=(ss_k1_part+ss_k2_part)/h-c_i*c_i;</span></a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineCov">        771 :     if(isPeriodic_i)</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineCov">        771 :       k1.center[i]=bringBackInPbc(i,c_i);</span></a>
+<a name="1754"><span class="lineNum">    1754 </span>            :     else</a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineNoCov">          0 :       k1.center[i]=c_i;</span></a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineCov">        771 :     k1.sigma[i]=sqrt(ss_i);</span></a>
+<a name="1757"><span class="lineNum">    1757 </span>            :   }</a>
+<a name="1758"><span class="lineNum">    1758 </span><span class="lineCov">        388 :   k1.height=h;</span></a>
+<a name="1759"><span class="lineNum">    1759 </span><span class="lineCov">        388 : }</span></a>
+<a name="1760"><span class="lineNum">    1760 </span>            : </a>
+<a name="1761"><span class="lineNum">    1761 </span>            : }</a>
+<a name="1762"><span class="lineNum">    1762 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/index-sort-f.html b/coverage/opes/index-sort-f.html
new file mode 100644
index 0000000000..08de97e823
--- /dev/null
+++ b/coverage/opes/index-sort-f.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - opes</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2161</td>
+            <td class="headerCovTableEntry">2249</td>
+            <td class="headerCovTableEntryHi">96.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpansionCVs.cpp.gcov.html">ExpansionCVs.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">102 / 111</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVumbrellasLine.cpp.gcov.html">ECVumbrellasLine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.5%"><img src="../snow.png" width=2 height=10 alt="98.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.5&nbsp;%</td>
+      <td class="coverNumHi">130 / 132</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVumbrellasFile.cpp.gcov.html">ECVumbrellasFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">119 / 121</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVmultiThermal.cpp.gcov.html">ECVmultiThermal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">108 / 113</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVlinear.cpp.gcov.html">ECVlinear.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">115 / 120</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVcustom.cpp.gcov.html">ECVcustom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.1%"><img src="../snow.png" width=8 height=10 alt="92.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.1&nbsp;%</td>
+      <td class="coverNumHi">93 / 101</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVmultiThermalBaric.cpp.gcov.html">ECVmultiThermalBaric.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">264 / 273</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OPESexpanded.cpp.gcov.html">OPESexpanded.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.3%"><img src="../snow.png" width=3 height=10 alt="97.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.3&nbsp;%</td>
+      <td class="coverNumHi">431 / 443</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OPESmetad.cpp.gcov.html">OPESmetad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">795 / 831</td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">33 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpansionCVs.h.gcov.html">ExpansionCVs.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/index-sort-l.html b/coverage/opes/index-sort-l.html
new file mode 100644
index 0000000000..771cd323c8
--- /dev/null
+++ b/coverage/opes/index-sort-l.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - opes</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2161</td>
+            <td class="headerCovTableEntry">2249</td>
+            <td class="headerCovTableEntryHi">96.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpansionCVs.cpp.gcov.html">ExpansionCVs.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">102 / 111</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVcustom.cpp.gcov.html">ECVcustom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.1%"><img src="../snow.png" width=8 height=10 alt="92.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.1&nbsp;%</td>
+      <td class="coverNumHi">93 / 101</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVmultiThermal.cpp.gcov.html">ECVmultiThermal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">108 / 113</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OPESmetad.cpp.gcov.html">OPESmetad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">795 / 831</td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">33 / 34</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVlinear.cpp.gcov.html">ECVlinear.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">115 / 120</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVmultiThermalBaric.cpp.gcov.html">ECVmultiThermalBaric.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">264 / 273</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OPESexpanded.cpp.gcov.html">OPESexpanded.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.3%"><img src="../snow.png" width=3 height=10 alt="97.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.3&nbsp;%</td>
+      <td class="coverNumHi">431 / 443</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVumbrellasFile.cpp.gcov.html">ECVumbrellasFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">119 / 121</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVumbrellasLine.cpp.gcov.html">ECVumbrellasLine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.5%"><img src="../snow.png" width=2 height=10 alt="98.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.5&nbsp;%</td>
+      <td class="coverNumHi">130 / 132</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpansionCVs.h.gcov.html">ExpansionCVs.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/opes/index.html b/coverage/opes/index.html
new file mode 100644
index 0000000000..527b6448cd
--- /dev/null
+++ b/coverage/opes/index.html
@@ -0,0 +1,183 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - opes</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - opes</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2161</td>
+            <td class="headerCovTableEntry">2249</td>
+            <td class="headerCovTableEntryHi">96.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntryHi">93.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVcustom.cpp.gcov.html">ECVcustom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.1%"><img src="../snow.png" width=8 height=10 alt="92.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.1&nbsp;%</td>
+      <td class="coverNumHi">93 / 101</td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVlinear.cpp.gcov.html">ECVlinear.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.8%"><img src="../snow.png" width=4 height=10 alt="95.8%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.8&nbsp;%</td>
+      <td class="coverNumHi">115 / 120</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVmultiThermal.cpp.gcov.html">ECVmultiThermal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.6%"><img src="../snow.png" width=4 height=10 alt="95.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.6&nbsp;%</td>
+      <td class="coverNumHi">108 / 113</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVmultiThermalBaric.cpp.gcov.html">ECVmultiThermalBaric.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">264 / 273</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVumbrellasFile.cpp.gcov.html">ECVumbrellasFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.3%"><img src="../snow.png" width=2 height=10 alt="98.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.3&nbsp;%</td>
+      <td class="coverNumHi">119 / 121</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ECVumbrellasLine.cpp.gcov.html">ECVumbrellasLine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.5%"><img src="../snow.png" width=2 height=10 alt="98.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.5&nbsp;%</td>
+      <td class="coverNumHi">130 / 132</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpansionCVs.cpp.gcov.html">ExpansionCVs.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.9%"><img src="../snow.png" width=8 height=10 alt="91.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">102 / 111</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ExpansionCVs.h.gcov.html">ExpansionCVs.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OPESexpanded.cpp.gcov.html">OPESexpanded.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.3%"><img src="../snow.png" width=3 height=10 alt="97.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.3&nbsp;%</td>
+      <td class="coverNumHi">431 / 443</td>
+      <td class="coverPerHi">93.8&nbsp;%</td>
+      <td class="coverNumHi">15 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OPESmetad.cpp.gcov.html">OPESmetad.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">795 / 831</td>
+      <td class="coverPerHi">97.1&nbsp;%</td>
+      <td class="coverNumHi">33 / 34</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammHydrogens.cpp.func-sort-c.html b/coverage/pamm/HBPammHydrogens.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b68f3b3378
--- /dev/null
+++ b/coverage/pamm/HBPammHydrogens.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammHydrogens.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammHydrogens.cpp<span style="font-size: 80%;"> (<a href="HBPammHydrogens.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryLo">70.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HBPammHydrogens.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#55">_ZN4PLMD4pamm15HBPammHydrogens10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#88">_ZN4PLMD4pamm15HBPammHydrogensC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#58">_ZN4PLMD4pamm12_GLOBAL__N_127HBPammHydrogensRegisterMe606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#88">_ZN4PLMD4pamm15HBPammHydrogensC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#60">_ZN4PLMD4pamm15HBPammHydrogens16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#166">_ZNK4PLMD4pamm15HBPammHydrogens7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">134</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#58">_ZN4PLMD4pamm12_GLOBAL__N_127HBPammHydrogensRegisterMe60C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#58">_ZN4PLMD4pamm12_GLOBAL__N_127HBPammHydrogensRegisterMe60D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammHydrogens.cpp.func.html b/coverage/pamm/HBPammHydrogens.cpp.func.html
new file mode 100644
index 0000000000..b3133af798
--- /dev/null
+++ b/coverage/pamm/HBPammHydrogens.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammHydrogens.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammHydrogens.cpp<span style="font-size: 80%;"> (<a href="HBPammHydrogens.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryLo">70.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HBPammHydrogens.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#58">_ZN4PLMD4pamm12_GLOBAL__N_127HBPammHydrogensRegisterMe606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#58">_ZN4PLMD4pamm12_GLOBAL__N_127HBPammHydrogensRegisterMe60C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#58">_ZN4PLMD4pamm12_GLOBAL__N_127HBPammHydrogensRegisterMe60D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#55">_ZN4PLMD4pamm15HBPammHydrogens10isPeriodicEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#60">_ZN4PLMD4pamm15HBPammHydrogens16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#88">_ZN4PLMD4pamm15HBPammHydrogensC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#88">_ZN4PLMD4pamm15HBPammHydrogensC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammHydrogens.cpp.gcov.html#166">_ZNK4PLMD4pamm15HBPammHydrogens7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">134</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammHydrogens.cpp.gcov.html b/coverage/pamm/HBPammHydrogens.cpp.gcov.html
new file mode 100644
index 0000000000..c5bdc03067
--- /dev/null
+++ b/coverage/pamm/HBPammHydrogens.cpp.gcov.html
@@ -0,0 +1,267 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammHydrogens.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammHydrogens.cpp<span style="font-size: 80%;"> (source / <a href="HBPammHydrogens.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">74</td>
+            <td class="headerCovTableEntryLo">70.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;HBPammObject.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : using namespace std;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace pamm {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC MCOLVAR HBPAMM_SH</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : Number of HBPAMM hydrogen bonds formed by each hydrogen atom in the system</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : */</a>
+<a name="43"><span class="lineNum">      43 </span>            : //+ENDPLUMEDOC</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : class HBPammHydrogens : public multicolvar::MultiColvarBase {</a>
+<a name="47"><span class="lineNum">      47 </span>            : private:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   double rcut2;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   unsigned block1upper,block2lower;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   Matrix&lt;HBPammObject&gt; hbpamm_obj;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit HBPammHydrogens(const ActionOptions&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span>            : // active methods:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Returns the number of coordinates of the field</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   bool isPeriodic() override { return false; }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : };</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(HBPammHydrogens,&quot;HBPAMM_SH&quot;)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          4 : void HBPammHydrogens::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          4 :   multicolvar::MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-1&quot;,&quot;HYDROGENS&quot;,&quot;The list of hydrogen atoms that can form part of a hydrogen bond.  The atoms must be specified using a comma separated list.&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-1&quot;,&quot;SITES&quot;,&quot;The list of atoms which can be part of a hydrogen bond.  When this command is used the set of atoms that can donate a &quot;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :            &quot;hydrogen bond is assumed to be the same as the set of atoms that can form hydrogen bonds.  The atoms involved must be specified &quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;DONORS&quot;,&quot;The list of atoms which can donate a hydrogen bond.  The atoms involved must be specified &quot;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="73"><span class="lineNum">      73 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="74"><span class="lineNum">      74 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="75"><span class="lineNum">      75 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;ACCEPTORS&quot;,&quot;The list of atoms which can accept a hydrogen bond.  The atoms involved must be specified &quot;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="78"><span class="lineNum">      78 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="79"><span class="lineNum">      79 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="80"><span class="lineNum">      80 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;CLUSTERS&quot;,&quot;the name of the file that contains the definitions of all the kernels for PAMM&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;REGULARISE&quot;,&quot;0.001&quot;,&quot;don't allow the denominator to be smaller then this value&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 :   keys.reset_style(&quot;CLUSTERS&quot;,&quot;compulsory&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   // Use actionWithDistributionKeywords</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         16 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MAX&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         16 :   keys.use(&quot;MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;HISTOGRAM&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         16 :   keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;); keys.use(&quot;SUM&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          4 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          2 : HBPammHydrogens::HBPammHydrogens(const ActionOptions&amp;ao):</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   Action(ao),</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 :   MultiColvarBase(ao)</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : {</a>
+<a name="94"><span class="lineNum">      94 </span>            :   // Read in the atoms</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   usespecies=true; weightHasDerivatives=false;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   // Read in hydrogen atom indicees</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          4 :   std::vector&lt;AtomNumber&gt; all_atoms; parseMultiColvarAtomList(&quot;HYDROGENS&quot;,-1,all_atoms);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :   if( atom_lab.size()==0 ) error(&quot;no hydrogens specified in input file&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   // Now create a task list - one task per hydrogen</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        136 :   unsigned nH = atom_lab.size(); for(unsigned i=0; i&lt;nH; ++i) addTaskToList(i);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   // Read in other atoms in hydrogen bond</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :   ablocks.resize(1); parseMultiColvarAtomList(&quot;SITES&quot;,-1,all_atoms);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          2 :   if( atom_lab.size()&gt;nH ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          2 :     block1upper=atom_lab.size() - nH + 1; block2lower=0; ablocks[0].resize( atom_lab.size() - nH );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         69 :     for(unsigned i=nH; i&lt;atom_lab.size(); ++i) ablocks[0][i-nH]=i;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   } else {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     parseMultiColvarAtomList(&quot;DONORS&quot;,-1,all_atoms);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     block1upper=block2lower=atom_lab.size() - nH + 1;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     for(unsigned i=nH; i&lt;atom_lab.size(); ++i) ablocks[0].push_back(i);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     parseMultiColvarAtomList(&quot;ACCEPTORS&quot;,-1,all_atoms);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     if( atom_lab.size()&gt;(block1upper+nH-1) || (block1upper-1)&gt;0 ) error(&quot;no acceptor donor pairs in input specified therefore no hydrogen bonds&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     for(unsigned i=nH+block2lower-1; i&lt;atom_lab.size(); ++i) ablocks[0].push_back(i);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          4 :   double reg; parse(&quot;REGULARISE&quot;,reg);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   unsigned nnode_t=mybasemulticolvars.size(); if( nnode_t==0 ) nnode_t=1;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   if( nnode_t==1 ) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          4 :     std::string errormsg, desc; parse(&quot;CLUSTERS&quot;,desc);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     hbpamm_obj.resize(1,1);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :     hbpamm_obj(0,0).setup(desc, reg, this, errormsg );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :     if( errormsg.length()&gt;0 ) error( errormsg );</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   } else {</a>
+<a name="124"><span class="lineNum">     124 </span>            :     unsigned nr=nnode_t, nc=nnode_t;</a>
+<a name="125"><span class="lineNum">     125 </span>            :     hbpamm_obj.resize( nr, nc );</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;nr; ++i) {</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :       // Retrieve the base number</a>
+<a name="128"><span class="lineNum">     128 </span>            :       unsigned ibase;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :       if( nc&lt;10 ) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :         ibase=(i+1)*10;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :       } else if ( nc&lt;100 ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :         ibase=(i+1)*100;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :       } else {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :         error(&quot;wow this is an error I never would have expected&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :       }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;nc; ++j) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :         std::string errormsg, desc; parseNumbered(&quot;CLUSTERS&quot;,ibase+j+1,desc);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :         if( i==j ) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :           hbpamm_obj(i,j).setup( desc, reg, this, errormsg );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :           if( errormsg.length()&gt;0 ) error( errormsg );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :         } else {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :           hbpamm_obj(i,j).setup( desc, reg, this, errormsg );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :           hbpamm_obj(j,i).setup( desc, reg, this, errormsg );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :           if( errormsg.length()&gt;0 ) error( errormsg );</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :         }</a>
+<a name="147"><span class="lineNum">     147 </span>            :       }</a>
+<a name="148"><span class="lineNum">     148 </span>            :     }</a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            :   // Set the link cell cutoff</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          2 :   double sfmax=0;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;hbpamm_obj.ncols(); ++i) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :     for(unsigned j=i; j&lt;hbpamm_obj.nrows(); ++j) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :       double rcut=hbpamm_obj(i,j).get_cutoff();</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 :       if( rcut&gt;sfmax ) { sfmax=rcut; }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     }</a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :   setLinkCellCutoff( sfmax );</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          2 :   rcut2 = sfmax*sfmax;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Setup the multicolvar base</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   setupMultiColvarBase( all_atoms );</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   // And setup the ActionWithVessel</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 : }</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        134 : double HBPammHydrogens::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   double value=0, md_da ;</a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            :   // Calculate the coordination number</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       8344 :   for(unsigned i=1; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       8210 :     if( i&gt;block1upper ) continue;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     532552 :     for(unsigned j=1; j&lt;myatoms.getNumberOfAtoms(); ++j) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     524342 :       if( i==j || j&lt;block2lower ) continue ;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :       // Get the base colvar numbers</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     516132 :       unsigned dno = atom_lab[myatoms.getIndex(i)].first;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     516132 :       unsigned ano = atom_lab[myatoms.getIndex(j)].first;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     516132 :       Vector d_da=getSeparation( myatoms.getPosition(i), myatoms.getPosition(j) );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">    1032264 :       if ( (md_da=d_da[0]*d_da[0])&lt;rcut2 &amp;&amp;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     516132 :            (md_da+=d_da[1]*d_da[1])&lt;rcut2 &amp;&amp;</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">     412196 :            (md_da+=d_da[2]*d_da[2])&lt;rcut2) value += hbpamm_obj(dno,ano).evaluate( i, j, 0, d_da, sqrt(md_da), myatoms );</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        134 :   return value;</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammMatrix.cpp.func-sort-c.html b/coverage/pamm/HBPammMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8ac558e092
--- /dev/null
+++ b/coverage/pamm/HBPammMatrix.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammMatrix.cpp<span style="font-size: 80%;"> (<a href="HBPammMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HBPammMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#87">_ZN4PLMD4pamm12HBPammMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#111">_ZN4PLMD4pamm12HBPammMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#87">_ZN4PLMD4pamm12HBPammMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#59">_ZN4PLMD4pamm12_GLOBAL__N_124HBPammMatrixRegisterMe616createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#61">_ZN4PLMD4pamm12HBPammMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#123">_ZNK4PLMD4pamm12HBPammMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">4038</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#59">_ZN4PLMD4pamm12_GLOBAL__N_124HBPammMatrixRegisterMe61C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#59">_ZN4PLMD4pamm12_GLOBAL__N_124HBPammMatrixRegisterMe61D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammMatrix.cpp.func.html b/coverage/pamm/HBPammMatrix.cpp.func.html
new file mode 100644
index 0000000000..b88b20a653
--- /dev/null
+++ b/coverage/pamm/HBPammMatrix.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammMatrix.cpp<span style="font-size: 80%;"> (<a href="HBPammMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HBPammMatrix.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#111">_ZN4PLMD4pamm12HBPammMatrix14setupConnectorERKjS3_S3_RKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#61">_ZN4PLMD4pamm12HBPammMatrix16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#87">_ZN4PLMD4pamm12HBPammMatrixC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#87">_ZN4PLMD4pamm12HBPammMatrixC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#59">_ZN4PLMD4pamm12_GLOBAL__N_124HBPammMatrixRegisterMe616createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#59">_ZN4PLMD4pamm12_GLOBAL__N_124HBPammMatrixRegisterMe61C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#59">_ZN4PLMD4pamm12_GLOBAL__N_124HBPammMatrixRegisterMe61D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammMatrix.cpp.gcov.html#123">_ZNK4PLMD4pamm12HBPammMatrix7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">4038</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammMatrix.cpp.gcov.html b/coverage/pamm/HBPammMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..8a3340cb2e
--- /dev/null
+++ b/coverage/pamm/HBPammMatrix.cpp.gcov.html
@@ -0,0 +1,224 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammMatrix.cpp<span style="font-size: 80%;"> (source / <a href="HBPammMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;adjmat/AdjacencyMatrixBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;HBPammObject.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC MATRIX HBPAMM_MATRIX</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Adjacency matrix in which two electronegative atoms are adjacent if they are hydrogen bonded</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : \par Examples</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : */</a>
+<a name="36"><span class="lineNum">      36 </span>            : //+ENDPLUMEDOC</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace pamm {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class HBPammMatrix : public adjmat::AdjacencyMatrixBase {</a>
+<a name="43"><span class="lineNum">      43 </span>            : private:</a>
+<a name="44"><span class="lineNum">      44 </span>            :   unsigned ndonor_types;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   double regulariser;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   Matrix&lt;HBPammObject&gt; myhb_objs;</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Create manual</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Constructor</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit HBPammMatrix(const ActionOptions&amp;);</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Setup the connector -- i.e. read in the clusters file</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc );</a>
+<a name="54"><span class="lineNum">      54 </span>            : ///</a>
+<a name="55"><span class="lineNum">      55 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="56"><span class="lineNum">      56 </span>            : ///</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Used to check for connections between atoms</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool checkForConnection( const std::vector&lt;double&gt;&amp; myvals ) const { return !(myvals[1]&gt;epsilon); }</a>
+<a name="59"><span class="lineNum">      59 </span>            : };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(HBPammMatrix,&quot;HBPAMM_MATRIX&quot;)</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          4 : void HBPammMatrix::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :   adjmat::AdjacencyMatrixBase::registerKeywords( keys );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-1&quot;,&quot;SITES&quot;,&quot;The list of atoms which can be part of a hydrogen bond.  When this command is used the set of atoms that can donate a &quot;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :            &quot;hydrogen bond is assumed to be the same as the set of atoms that can form hydrogen bonds.  The atoms involved must be specified &quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;DONORS&quot;,&quot;The list of atoms which can donate a hydrogen bond.  The atoms involved must be specified &quot;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="73"><span class="lineNum">      73 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="74"><span class="lineNum">      74 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="75"><span class="lineNum">      75 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          8 :   keys.add(&quot;atoms-2&quot;,&quot;ACCEPTORS&quot;,&quot;The list of atoms which can accept a hydrogen bond.  The atoms involved must be specified &quot;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :            &quot;as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions.  If you would just like to use &quot;</a>
+<a name="78"><span class="lineNum">      78 </span>            :            &quot;the atomic positions you can use a \\ref DENSITY command to specify a group of atoms.  Specifying your atomic positions using labels of &quot;</a>
+<a name="79"><span class="lineNum">      79 </span>            :            &quot;other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider &quot;</a>
+<a name="80"><span class="lineNum">      80 </span>            :            &quot;variety of functions of the contact matrix as described in \\ref contactmatrix&quot;);</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;HYDROGENS&quot;,&quot;The list of hydrogen atoms that can form part of a hydrogen bond.  The atoms must be specified using a comma separated list, &quot;</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :            &quot;an index range or by using a \\ref GROUP&quot;);</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 :   keys.add(&quot;numbered&quot;,&quot;CLUSTERS&quot;,&quot;the name of the file that contains the definitions of all the kernels for PAMM&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   keys.reset_style(&quot;CLUSTERS&quot;,&quot;compulsory&quot;); keys.use(&quot;SUM&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;REGULARISE&quot;,&quot;0.001&quot;,&quot;don't allow the denominator to be smaller then this value&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          4 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          2 : HBPammMatrix::HBPammMatrix(const ActionOptions&amp; ao):</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   Action(ao),</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 :   AdjacencyMatrixBase(ao)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          4 :   readMaxThreeSpeciesMatrix(&quot;SITES&quot;, &quot;DONORS&quot;, &quot;ACCEPTORS&quot;, &quot;HYDROGENS&quot;, false );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   // Retrieve dimensions of hbonding matrix and resize</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   unsigned nrows, ncols; retrieveTypeDimensions( nrows, ncols, ndonor_types );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   myhb_objs.resize( nrows, ncols );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   // Read in the regularisation parameter</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :   parse(&quot;REGULARISE&quot;,regulariser);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   // Read in the switching functions</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   parseConnectionDescriptions(&quot;CLUSTERS&quot;,false,ndonor_types);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   // Find cutoff for link cells</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          2 :   double sfmax=0;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          4 :   for(unsigned i=0; i&lt;myhb_objs.ncols(); ++i) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 :     for(unsigned j=i; j&lt;myhb_objs.nrows(); ++j) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :       double rcut=myhb_objs(i,j).get_cutoff();</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          2 :       if( rcut&gt;sfmax ) { sfmax=rcut; }</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :     }</a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   setLinkCellCutoff( sfmax );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 : void HBPammMatrix::setupConnector( const unsigned&amp; id, const unsigned&amp; i, const unsigned&amp; j, const std::vector&lt;std::string&gt;&amp; desc ) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :   log.printf(&quot;  reading definition of hydrogen bond between between type %u and %u from file %s \n&quot;,i,j,desc[0].c_str() );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :   plumed_assert( desc.size()==1 ); std::string errors;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          2 :   if( i==j ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :     myhb_objs( i, j ).setup( desc[0], regulariser, this, errors );</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   } else {</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :     myhb_objs( i, j ).setup( desc[0], regulariser, this, errors );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     myhb_objs( j, i ).setup( desc[0], regulariser, this, errors );</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   if( errors.length()&gt;0 ) error( errors );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       4038 : double HBPammMatrix::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       4038 :   Vector d_da = getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) ); double md_da = d_da.modulo(); // acceptor - donor</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   // Get the base colvar numbers</a>
+<a name="129"><span class="lineNum">     129 </span>            :   unsigned ano, dno = getBaseColvarNumber( myatoms.getIndex(0) );</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       4038 :   if( ndonor_types==0 ) ano = getBaseColvarNumber( myatoms.getIndex(1) );</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   else ano = getBaseColvarNumber( myatoms.getIndex(1) ) - ndonor_types;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   double value=0;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       4038 :   if( myatoms.getNumberOfAtoms()&gt;3 ) {</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :     const HBPammObject&amp; myhb=myhb_objs(dno,ano);</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     520170 :     for(unsigned i=2; i&lt;myatoms.getNumberOfAtoms(); ++i) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">     516132 :       value+=myhb.evaluate( 0, 1, i, d_da, md_da, myatoms );</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :     }</a>
+<a name="139"><span class="lineNum">     139 </span>            :   } else {</a>
+<a name="140"><span class="lineNum">     140 </span>            :     plumed_dbg_assert( myatoms.getNumberOfAtoms()==3 );</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     value=myhb_objs(dno,ano).evaluate( 0, 1, 2, d_da, md_da, myatoms );</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       4038 :   return value;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammObject.cpp.func-sort-c.html b/coverage/pamm/HBPammObject.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e6436619d3
--- /dev/null
+++ b/coverage/pamm/HBPammObject.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
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+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammObject.cpp<span style="font-size: 80%;"> (<a href="HBPammObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HBPammObject.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammObject.cpp.gcov.html#26">_ZN4PLMD4pamm12HBPammObject5setupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKdPNS_11multicolvar15MultiColvarBaseERS7_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammObject.cpp.gcov.html#33">_ZNK4PLMD4pamm12HBPammObject10get_cutoffEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammObject.cpp.gcov.html#42">_ZNK4PLMD4pamm12HBPammObject8evaluateERKjS3_S3_RKNS_13VectorGenericILj3EEERKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">787016</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
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diff --git a/coverage/pamm/HBPammObject.cpp.func.html b/coverage/pamm/HBPammObject.cpp.func.html
new file mode 100644
index 0000000000..78eb80b897
--- /dev/null
+++ b/coverage/pamm/HBPammObject.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammObject.cpp<span style="font-size: 80%;"> (<a href="HBPammObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HBPammObject.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFn"><a href="HBPammObject.cpp.gcov.html#26">_ZN4PLMD4pamm12HBPammObject5setupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKdPNS_11multicolvar15MultiColvarBaseERS7_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammObject.cpp.gcov.html#33">_ZNK4PLMD4pamm12HBPammObject10get_cutoffEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HBPammObject.cpp.gcov.html#42">_ZNK4PLMD4pamm12HBPammObject8evaluateERKjS3_S3_RKNS_13VectorGenericILj3EEERKdRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">787016</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/pamm/HBPammObject.cpp.gcov.html b/coverage/pamm/HBPammObject.cpp.gcov.html
new file mode 100644
index 0000000000..098c39077c
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+++ b/coverage/pamm/HBPammObject.cpp.gcov.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammObject.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammObject.cpp<span style="font-size: 80%;"> (source / <a href="HBPammObject.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;HBPammObject.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace pamm {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          4 : void HBPammObject::setup( const std::string&amp; filename, const double&amp; reg, multicolvar::MultiColvarBase* mybase, std::string&amp; errorstr ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          4 :   mymulti=mybase; std::vector&lt;std::string&gt; valnames(3);</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :   valnames[0]=&quot;ptc&quot;; valnames[1]=&quot;ssc&quot;; valnames[2]=&quot;adc&quot;;</a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          4 :   std::vector&lt;std::string&gt; min(3), max(3); std::vector&lt;bool&gt; pbc(3, false);</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          4 :   mypamm.setup( filename, reg, valnames, pbc, min, max, errorstr );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          4 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          4 : double HBPammObject::get_cutoff() const {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   double sfmax=0;</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         48 :   for(unsigned k=0; k&lt;mypamm.getNumberOfKernels(); ++k) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         44 :     double rcut = mypamm.getKernelCenter(k)[2] + mypamm.getKernelSupport(k)[2];</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         44 :     if( rcut&gt;sfmax ) { sfmax=rcut; }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   }</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          4 :   return sfmax;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : }</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">     787016 : double HBPammObject::evaluate( const unsigned&amp; dno, const unsigned&amp; ano, const unsigned&amp; hno,</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :                                const Vector&amp; d_da, const double&amp; md_da, multicolvar::AtomValuePack&amp; myatoms ) const {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">     787016 :   Vector d_dh = mymulti-&gt;getSeparation( myatoms.getPosition(dno), myatoms.getPosition(hno) ); double md_dh = d_dh.modulo(); // hydrogen - donor</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">     787016 :   Vector d_ah = mymulti-&gt;getSeparation( myatoms.getPosition(ano), myatoms.getPosition(hno) ); double md_ah = d_ah.modulo(); // hydrogen - acceptor</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            :   // Create some vectors locally for pamm evaluation</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">     787016 :   std::vector&lt;double&gt; invals( 3 ), outvals( mypamm.getNumberOfKernels() );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     787016 :   std::vector&lt;std:: vector&lt;double&gt; &gt; der( mypamm.getNumberOfKernels() );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">    9444192 :   for(unsigned i=0; i&lt;der.size(); ++i) der[i].resize(3);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            :   // Evaluate the pamm object</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">     787016 :   invals[0]=md_dh - md_ah; invals[1]=md_dh+md_ah; invals[2]=md_da;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     787016 :   mypamm.evaluate( invals, outvals, der );</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">     787016 :   if( !mymulti-&gt;doNotCalculateDerivatives() ) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, dno, ((-der[0][0])/md_dh)*d_dh, myatoms );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, ano, ((+der[0][0])/md_ah)*d_ah, myatoms  );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, hno, ((+der[0][0])/md_dh)*d_dh - ((+der[0][0])/md_ah)*d_ah, myatoms );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         72 :     myatoms.addBoxDerivatives( 1, ((-der[0][0])/md_dh)*Tensor(d_dh,d_dh) - ((-der[0][0])/md_ah)*Tensor(d_ah,d_ah) );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, dno, ((-der[0][1])/md_dh)*d_dh, myatoms );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, ano, ((-der[0][1])/md_ah)*d_ah, myatoms );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, hno, ((+der[0][1])/md_dh)*d_dh + ((+der[0][1])/md_ah)*d_ah, myatoms );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         72 :     myatoms.addBoxDerivatives( 1, ((-der[0][1])/md_dh)*Tensor(d_dh,d_dh) + ((-der[0][1])/md_ah)*Tensor(d_ah,d_ah) );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, dno, ((-der[0][2])/md_da)*d_da, myatoms );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         72 :     mymulti-&gt;addAtomDerivatives( 1, ano, ((+der[0][2])/md_da)*d_da, myatoms );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         72 :     myatoms.addBoxDerivatives( 1, ((-der[0][2])/md_da)*Tensor(d_da,d_da) );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   }</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     787016 :   return outvals[0];</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">     787016 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammObject.h.func-sort-c.html b/coverage/pamm/HBPammObject.h.func-sort-c.html
new file mode 100644
index 0000000000..bf425fb037
--- /dev/null
+++ b/coverage/pamm/HBPammObject.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammObject.h<span style="font-size: 80%;"> (<a href="HBPammObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HBPammObject.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammObject.h.func.html b/coverage/pamm/HBPammObject.h.func.html
new file mode 100644
index 0000000000..8de196cd9f
--- /dev/null
+++ b/coverage/pamm/HBPammObject.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammObject.h<span style="font-size: 80%;"> (<a href="HBPammObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HBPammObject.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/HBPammObject.h.gcov.html b/coverage/pamm/HBPammObject.h.gcov.html
new file mode 100644
index 0000000000..7c145e892e
--- /dev/null
+++ b/coverage/pamm/HBPammObject.h.gcov.html
@@ -0,0 +1,127 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/HBPammObject.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - HBPammObject.h<span style="font-size: 80%;"> (source / <a href="HBPammObject.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_pamm_HBPammObject_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_pamm_HBPammObject_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;PammObject.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace pamm {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          8 : class HBPammObject {</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// The Pamm object underlying this HBPamm calculation</a>
+<a name="35"><span class="lineNum">      35 </span>            :   PammObject mypamm;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Pointer to base class in multicolvar</a>
+<a name="37"><span class="lineNum">      37 </span>            :   multicolvar::MultiColvarBase* mymulti=nullptr;</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Setup the HBPamm object</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void setup( const std::string&amp; filename, const double&amp; reg, multicolvar::MultiColvarBase* mybase, std::string&amp; errorstr );</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Get the cutoff to use throughout</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double get_cutoff() const ;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Evaluate the HBPamm Object</a>
+<a name="44"><span class="lineNum">      44 </span>            :   double evaluate( const unsigned&amp; dno, const unsigned&amp; ano, const unsigned&amp; hno,</a>
+<a name="45"><span class="lineNum">      45 </span>            :                    const Vector&amp; d_da, const double&amp; md_da, multicolvar::AtomValuePack&amp; myatoms ) const ;</a>
+<a name="46"><span class="lineNum">      46 </span>            : };</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PAMM.cpp.func-sort-c.html b/coverage/pamm/PAMM.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b580252d18
--- /dev/null
+++ b/coverage/pamm/PAMM.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PAMM.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PAMM.cpp<span style="font-size: 80%;"> (<a href="PAMM.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PAMM.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#243">_ZN4PLMD4pamm4PAMM14getCentralAtomEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#189">_ZN4PLMD4pamm4PAMM15calculateWeightERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#157">_ZN4PLMD4pamm4PAMMC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#130">_ZN4PLMD4pamm12_GLOBAL__N_117PAMMRegisterMe1326createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#157">_ZN4PLMD4pamm4PAMMC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#132">_ZN4PLMD4pamm4PAMM16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#127">_ZN4PLMD4pamm4PAMM10isPeriodicEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#211">_ZNK4PLMD4pamm4PAMM7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#185">_ZNK4PLMD4pamm4PAMM21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#130">_ZN4PLMD4pamm12_GLOBAL__N_117PAMMRegisterMe132C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#130">_ZN4PLMD4pamm12_GLOBAL__N_117PAMMRegisterMe132D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PAMM.cpp.func.html b/coverage/pamm/PAMM.cpp.func.html
new file mode 100644
index 0000000000..28e639edfb
--- /dev/null
+++ b/coverage/pamm/PAMM.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PAMM.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PAMM.cpp<span style="font-size: 80%;"> (<a href="PAMM.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PAMM.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#130">_ZN4PLMD4pamm12_GLOBAL__N_117PAMMRegisterMe1326createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#130">_ZN4PLMD4pamm12_GLOBAL__N_117PAMMRegisterMe132C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#130">_ZN4PLMD4pamm12_GLOBAL__N_117PAMMRegisterMe132D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#127">_ZN4PLMD4pamm4PAMM10isPeriodicEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#243">_ZN4PLMD4pamm4PAMM14getCentralAtomEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#189">_ZN4PLMD4pamm4PAMM15calculateWeightERNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#132">_ZN4PLMD4pamm4PAMM16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#157">_ZN4PLMD4pamm4PAMMC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#157">_ZN4PLMD4pamm4PAMMC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#185">_ZNK4PLMD4pamm4PAMM21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">86</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PAMM.cpp.gcov.html#211">_ZNK4PLMD4pamm4PAMM7computeERKjRNS_11multicolvar13AtomValuePackE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PAMM.cpp.gcov.html b/coverage/pamm/PAMM.cpp.gcov.html
new file mode 100644
index 0000000000..d6b361f6c7
--- /dev/null
+++ b/coverage/pamm/PAMM.cpp.gcov.html
@@ -0,0 +1,328 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PAMM.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PAMM.cpp<span style="font-size: 80%;"> (source / <a href="PAMM.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;multicolvar/MultiColvarBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;multicolvar/AtomValuePack.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;PammObject.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC MCOLVARF PAMM</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Probabilistic analysis of molecular motifs.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Probabilistic analysis of molecular motifs (PAMM) was introduced in this paper \cite pamm.</a>
+<a name="34"><span class="lineNum">      34 </span>            : The essence of this approach involves calculating some large set of collective variables</a>
+<a name="35"><span class="lineNum">      35 </span>            : for a set of atoms in a short trajectory and fitting this data using a Gaussian Mixture Model.</a>
+<a name="36"><span class="lineNum">      36 </span>            : The idea is that modes in these distributions can be used to identify features such as hydrogen bonds or</a>
+<a name="37"><span class="lineNum">      37 </span>            : secondary structure types.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The assumption within this implementation is that the fitting of the Gaussian mixture model has been</a>
+<a name="40"><span class="lineNum">      40 </span>            : done elsewhere by a separate code.  You thus provide an input file to this action which contains the</a>
+<a name="41"><span class="lineNum">      41 </span>            : means, covariance matrices and weights for a set of Gaussian kernels, \f$\{ \phi \}\f$.  The values and</a>
+<a name="42"><span class="lineNum">      42 </span>            : derivatives for the following set of quantities is then computed:</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \f[</a>
+<a name="45"><span class="lineNum">      45 </span>            : s_k = \frac{ \phi_k}{ \sum_i \phi_i }</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : Each of the \f$\phi_k\f$ is a Gaussian function that acts on a set of quantities calculated within</a>
+<a name="49"><span class="lineNum">      49 </span>            : a \ref mcolv .  These might be \ref TORSIONS, \ref DISTANCES, \ref ANGLES or any one of the many</a>
+<a name="50"><span class="lineNum">      50 </span>            : symmetry functions that are available within \ref mcolv actions.  These quantities are then inserted into</a>
+<a name="51"><span class="lineNum">      51 </span>            : the set of \f$n\f$ kernels that are in the the input file.   This will be done for multiple sets of values</a>
+<a name="52"><span class="lineNum">      52 </span>            : for the input quantities and a final quantity will be calculated by summing the above \f$s_k\f$ values or</a>
+<a name="53"><span class="lineNum">      53 </span>            : some transformation of the above.  This sounds less complicated than it is and is best understood by</a>
+<a name="54"><span class="lineNum">      54 </span>            : looking through the example given below.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \warning Mixing \ref mcolv actions that are periodic with variables that are not periodic has not been tested</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \par Examples</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : In this example I will explain in detail what the following input is computing:</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="64"><span class="lineNum">      64 </span>            : MOLINFO MOLTYPE=protein STRUCTURE=M1d.pdb</a>
+<a name="65"><span class="lineNum">      65 </span>            : psi: TORSIONS ATOMS1=@psi-2 ATOMS2=@psi-3 ATOMS3=@psi-4</a>
+<a name="66"><span class="lineNum">      66 </span>            : phi: TORSIONS ATOMS1=@phi-2 ATOMS2=@phi-3 ATOMS3=@phi-4</a>
+<a name="67"><span class="lineNum">      67 </span>            : p: PAMM DATA=phi,psi CLUSTERS=clusters.pamm MEAN1={COMPONENT=1} MEAN2={COMPONENT=2}</a>
+<a name="68"><span class="lineNum">      68 </span>            : PRINT ARG=p.mean-1,p.mean-2 FILE=colvar</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : The best place to start our explanation is to look at the contents of the clusters.pamm file</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \auxfile{clusters.pamm}</a>
+<a name="74"><span class="lineNum">      74 </span>            : #! FIELDS height phi psi sigma_phi_phi sigma_phi_psi sigma_psi_phi sigma_psi_psi</a>
+<a name="75"><span class="lineNum">      75 </span>            : #! SET multivariate von-misses</a>
+<a name="76"><span class="lineNum">      76 </span>            : #! SET kerneltype gaussian</a>
+<a name="77"><span class="lineNum">      77 </span>            :       2.97197455E-0001     -1.91983118E+0000      2.25029540E+0000      2.45960237E-0001     -1.30615381E-0001     -1.30615381E-0001      2.40239117E-0001</a>
+<a name="78"><span class="lineNum">      78 </span>            :       2.29131448E-0002      1.39809354E+0000      9.54585380E-0002      9.61755708E-0002     -3.55657919E-0002     -3.55657919E-0002      1.06147253E-0001</a>
+<a name="79"><span class="lineNum">      79 </span>            :       5.06676398E-0001     -1.09648066E+0000     -7.17867907E-0001      1.40523052E-0001     -1.05385552E-0001     -1.05385552E-0001      1.63290557E-0001</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endauxfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : This files contains the parameters of two two-dimensional Gaussian functions.  Each of these Gaussian kernels has a weight, \f$w_k\f$,</a>
+<a name="83"><span class="lineNum">      83 </span>            : a vector that specifies the position of its center, \f$\mathbf{c}_k\f$, and a covariance matrix, \f$\Sigma_k\f$.  The \f$\phi_k\f$ functions that</a>
+<a name="84"><span class="lineNum">      84 </span>            : we use to calculate our PAMM components are thus:</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : \f[</a>
+<a name="87"><span class="lineNum">      87 </span>            : \phi_k = \frac{w_k}{N_k} \exp\left( -(\mathbf{s} - \mathbf{c}_k)^T \Sigma^{-1}_k (\mathbf{s} - \mathbf{c}_k) \right)</a>
+<a name="88"><span class="lineNum">      88 </span>            : \f]</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : In the above \f$N_k\f$ is a normalization factor that is calculated based on \f$\Sigma\f$.  The vector \f$\mathbf{s}\f$ is a vector of quantities</a>
+<a name="91"><span class="lineNum">      91 </span>            : that are calculated by the \ref TORSIONS actions.  This vector must be two dimensional and in this case each component is the value of a</a>
+<a name="92"><span class="lineNum">      92 </span>            : torsion angle.  If we look at the two \ref TORSIONS actions in the above we are calculating the \f$\phi\f$ and \f$\psi\f$ backbone torsional</a>
+<a name="93"><span class="lineNum">      93 </span>            : angles in a protein (Note the use of \ref MOLINFO to make specification of atoms straightforward).  We thus calculate the values of our</a>
+<a name="94"><span class="lineNum">      94 </span>            : 2 \f$ \{ \phi \} \f$  kernels 3 times.  The first time we use the \f$\phi\f$ and \f$\psi\f$ angles in the second residue of the protein,</a>
+<a name="95"><span class="lineNum">      95 </span>            : the second time it is the \f$\phi\f$ and \f$\psi\f$ angles of the third residue of the protein and the third time it is the \f$\phi\f$ and \f$\psi\f$ angles</a>
+<a name="96"><span class="lineNum">      96 </span>            : of the fourth residue in the protein.  The final two quantities that are output by the print command, p.mean-1 and p.mean-2, are the averages</a>
+<a name="97"><span class="lineNum">      97 </span>            : over these three residues for the quantities:</a>
+<a name="98"><span class="lineNum">      98 </span>            : \f[</a>
+<a name="99"><span class="lineNum">      99 </span>            : s_1 = \frac{ \phi_1}{ \phi_1 + \phi_2 }</a>
+<a name="100"><span class="lineNum">     100 </span>            : \f]</a>
+<a name="101"><span class="lineNum">     101 </span>            : and</a>
+<a name="102"><span class="lineNum">     102 </span>            : \f[</a>
+<a name="103"><span class="lineNum">     103 </span>            : s_2 = \frac{ \phi_2}{ \phi_1 + \phi_2 }</a>
+<a name="104"><span class="lineNum">     104 </span>            : \f]</a>
+<a name="105"><span class="lineNum">     105 </span>            : There is a great deal of flexibility in this input.  We can work with, and examine, any number of components, we can use any set of collective variables</a>
+<a name="106"><span class="lineNum">     106 </span>            : and compute these PAMM variables and we can transform the PAMM variables themselves in a large number of different ways when computing these sums.</a>
+<a name="107"><span class="lineNum">     107 </span>            : */</a>
+<a name="108"><span class="lineNum">     108 </span>            : //+ENDPLUMEDOC</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : namespace PLMD {</a>
+<a name="111"><span class="lineNum">     111 </span>            : namespace pamm {</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : class PAMM : public multicolvar::MultiColvarBase {</a>
+<a name="114"><span class="lineNum">     114 </span>            : private:</a>
+<a name="115"><span class="lineNum">     115 </span>            :   PammObject mypamm;</a>
+<a name="116"><span class="lineNum">     116 </span>            : public:</a>
+<a name="117"><span class="lineNum">     117 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="118"><span class="lineNum">     118 </span>            :   explicit PAMM(const ActionOptions&amp;);</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// We have to overwrite this here</a>
+<a name="120"><span class="lineNum">     120 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Calculate the weight of this object ( average of input weights )</a>
+<a name="122"><span class="lineNum">     122 </span>            :   using PLMD::multicolvar::MultiColvarBase::calculateWeight;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void calculateWeight( multicolvar::AtomValuePack&amp; myatoms );</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Actually do the calculation</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const override;</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// This returns the position of the central atom</a>
+<a name="127"><span class="lineNum">     127 </span>            :   Vector getCentralAtom();</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// Is the variable periodic</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         16 :   bool isPeriodic() override { return false; }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : };</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(PAMM,&quot;PAMM&quot;)</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 : void PAMM::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   MultiColvarBase::registerKeywords( keys );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;the multicolvars from which the pamm coordinates are calculated&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;CLUSTERS&quot;,&quot;the name of the file that contains the definitions of all the clusters&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;REGULARISE&quot;,&quot;0.001&quot;,&quot;don't allow the denominator to be smaller then this value&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         20 :   keys.use(&quot;MEAN&quot;); keys.use(&quot;MORE_THAN&quot;); keys.use(&quot;SUM&quot;); keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;HISTOGRAM&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         28 :   keys.use(&quot;MIN&quot;); keys.use(&quot;MAX&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;); keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;BETWEEN&quot;); keys.use(&quot;MOMENTS&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 :   keys.setComponentsIntroduction(&quot;When the label of this action is used as the input for a second you are not referring to a scalar quantity as you are in &quot;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :                                  &quot;regular collective variables.  The label is used to reference the full set of quantities calculated by &quot;</a>
+<a name="143"><span class="lineNum">     143 </span>            :                                  &quot;the action.  This is usual when using \\ref multicolvarfunction. Generally when doing this the set of PAMM variables &quot;</a>
+<a name="144"><span class="lineNum">     144 </span>            :                                  &quot;will be referenced using the DATA keyword rather than ARG.\n\n&quot;</a>
+<a name="145"><span class="lineNum">     145 </span>            :                                  &quot;This Action can be used to calculate the following scalar quantities directly from the underlying set of PAMM variables. &quot;</a>
+<a name="146"><span class="lineNum">     146 </span>            :                                  &quot;These quantities are calculated by employing the keywords listed below and they can be referenced elsewhere in the input &quot;</a>
+<a name="147"><span class="lineNum">     147 </span>            :                                  &quot;file by using this Action's label followed by a dot and the name of the quantity.  The particular PAMM variable that should &quot;</a>
+<a name="148"><span class="lineNum">     148 </span>            :                                  &quot;be averaged in a MEAN command or transformed by a switching function in a LESS_THAN command is specified using the COMPONENT &quot;</a>
+<a name="149"><span class="lineNum">     149 </span>            :                                  &quot;keyword. COMPONENT=1 refers to the PAMM variable in which the first kernel in your input file is on the numerator, COMPONENT=2 refers to &quot;</a>
+<a name="150"><span class="lineNum">     150 </span>            :                                  &quot;PAMM variable in which the second kernel in the input file is on the numerator and so on.  The same quantity can be calculated &quot;</a>
+<a name="151"><span class="lineNum">     151 </span>            :                                  &quot;multiple times for different PAMM components by a single PAMM action.  In this case the relevant keyword must appear multiple &quot;</a>
+<a name="152"><span class="lineNum">     152 </span>            :                                  &quot;times on the input line followed by a numerical identifier i.e. MEAN1, MEAN2, ...  The quantities calculated when multiple &quot;</a>
+<a name="153"><span class="lineNum">     153 </span>            :                                  &quot;MEAN commands appear on the input line can be reference elsewhere in the input file by using the name of the quantity followed &quot;</a>
+<a name="154"><span class="lineNum">     154 </span>            :                                  &quot;followed by a numerical identifier e.g. &lt;em&gt;label&lt;/em&gt;.lessthan-1, &lt;em&gt;label&lt;/em&gt;.lessthan-2 etc.  Alternatively, you can &quot;</a>
+<a name="155"><span class="lineNum">     155 </span>            :                                  &quot;customize the labels of the quantities by using the LABEL keyword in the description of the keyword.&quot;);</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :   keys.remove(&quot;ALL_INPUT_SAME_TYPE&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          4 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 : PAMM::PAMM(const ActionOptions&amp; ao):</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   Action(ao),</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          2 :   MultiColvarBase(ao)</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : {</a>
+<a name="163"><span class="lineNum">     163 </span>            :   // This builds the lists</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          2 :   buildSets();</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   // Check for reasonable input</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          5 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          3 :     if( getBaseMultiColvar(i)-&gt;getNumberOfQuantities()!=2 ) error(&quot;cannot use PAMM with &quot; + getBaseMultiColvar(i)-&gt;getName() );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :   bool mixed=getBaseMultiColvar(0)-&gt;isPeriodic();</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :   std::vector&lt;bool&gt; pbc( getNumberOfBaseMultiColvars() );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 :   std::vector&lt;std::string&gt; valnames( getNumberOfBaseMultiColvars() );</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :   std::vector&lt;std::string&gt; min( getNumberOfBaseMultiColvars() ), max( getNumberOfBaseMultiColvars() );</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          5 :   for(unsigned i=0; i&lt;getNumberOfBaseMultiColvars(); ++i) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          3 :     if( getBaseMultiColvar(i)-&gt;isPeriodic()!=mixed ) warning(&quot;mixing of periodic and aperiodic base variables in pamm is untested&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          3 :     pbc[i]=getBaseMultiColvar(i)-&gt;isPeriodic();</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          3 :     if( pbc[i] ) getBaseMultiColvar(i)-&gt;retrieveDomain( min[i], max[i] );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          3 :     valnames[i]=getBaseMultiColvar(i)-&gt;getLabel();</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          4 :   double regulariser; parse(&quot;REGULARISE&quot;,regulariser);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :   std::string errorstr, filename; parse(&quot;CLUSTERS&quot;,filename);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :   mypamm.setup( filename, regulariser, valnames, pbc, min, max, errorstr );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :   if( errorstr.length()&gt;0 ) error( errorstr );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         86 : unsigned PAMM::getNumberOfQuantities() const {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         86 :   return 1 + mypamm.getNumberOfKernels();</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 : void PAMM::calculateWeight( multicolvar::AtomValuePack&amp; myatoms ) {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   unsigned nvars = getNumberOfBaseMultiColvars();</a>
+<a name="193"><span class="lineNum">     193 </span>            :   // Weight of point is average of weights of input colvars?</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; tval(2); double ww=0;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;nvars; ++i) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     getInputData( i, false, myatoms, tval ); ww+=tval[0];</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :   myatoms.setValue( 0, ww / static_cast&lt;double&gt;( nvars ) );</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :   if(!doNotCalculateDerivatives() ) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     double pref = 1.0 / static_cast&lt;double&gt;( nvars );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     for(unsigned ivar=0; ivar&lt;nvars; ++ivar) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       // Get the values of derivatives</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :       const MultiValue&amp; myder=getInputDerivatives( ivar, false, myatoms );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;myder.getNumberActive(); ++j) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :         unsigned jder=myder.getActiveIndex(j);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :         myatoms.addDerivative( 0, jder, pref*myder.getDerivative( 0, jder ) );</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :       }</a>
+<a name="209"><span class="lineNum">     209 </span>            :     }</a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         28 : double PAMM::compute( const unsigned&amp; tindex, multicolvar::AtomValuePack&amp; myatoms ) const {</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   unsigned nvars = getNumberOfBaseMultiColvars();</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         28 :   std::vector&lt;std::vector&lt;double&gt; &gt; tderiv( mypamm.getNumberOfKernels() );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        174 :   for(unsigned i=0; i&lt;tderiv.size(); ++i) tderiv[i].resize( nvars );</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         28 :   std::vector&lt;double&gt; tval(2), invals( nvars ), vals( mypamm.getNumberOfKernels() );</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         74 :   for(unsigned i=0; i&lt;nvars; ++i) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         46 :     getInputData( i, false, myatoms, tval ); invals[i]=tval[1];</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         28 :   mypamm.evaluate( invals, vals, tderiv );</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            :   // Now set all values other than the first one</a>
+<a name="225"><span class="lineNum">     225 </span>            :   // This is because of some peverse choices in multicolvar</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        146 :   for(unsigned i=1; i&lt;vals.size(); ++i) myatoms.setValue( 1+i, vals[i] );</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         28 :   if( !doNotCalculateDerivatives() ) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         28 :     std::vector&lt;double&gt; mypref( 1 + vals.size() );</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         74 :     for(unsigned ivar=0; ivar&lt;nvars; ++ivar) {</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :       // Get the values of the derivatives</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         46 :       MultiValue&amp; myder = getInputDerivatives( ivar, false, myatoms );</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :       // And calculate the derivatives</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        318 :       for(unsigned i=0; i&lt;vals.size(); ++i) mypref[1+i] = tderiv[i][ivar];</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :       // This is basically doing the chain rule to get the final derivatives</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         46 :       splitInputDerivatives( 1, 1, 1+vals.size(), ivar, mypref, myder, myatoms );</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :       // And clear the derivatives</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         46 :       myder.clearAll();</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span>            :   }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         56 :   return vals[0];</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         28 : }</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 : Vector PAMM::getCentralAtom() {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   // Who knows how this should work</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   // return Vector(1.0,0.0,0.0);</a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PammObject.cpp.func-sort-c.html b/coverage/pamm/PammObject.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cc1725e4d2
--- /dev/null
+++ b/coverage/pamm/PammObject.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PammObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PammObject.cpp<span style="font-size: 80%;"> (<a href="PammObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryMed">82.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PammObject.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#32">_ZN4PLMD4pamm10PammObjectC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#41">_ZN4PLMD4pamm10PammObject5setupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKdRKSt6vectorIS7_SaIS7_EERKSC_IbSaIbEESG_SG_RS7_</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#27">_ZN4PLMD4pamm10PammObjectC2Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#72">_ZNK4PLMD4pamm10PammObject8evaluateERKSt6vectorIdSaIdEERS4_RS2_IS4_SaIS4_EE</a></td>
+              <td class="coverFnHi">787044</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PammObject.cpp.func.html b/coverage/pamm/PammObject.cpp.func.html
new file mode 100644
index 0000000000..e379e29dfe
--- /dev/null
+++ b/coverage/pamm/PammObject.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PammObject.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PammObject.cpp<span style="font-size: 80%;"> (<a href="PammObject.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryMed">82.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PammObject.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#41">_ZN4PLMD4pamm10PammObject5setupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKdRKSt6vectorIS7_SaIS7_EERKSC_IbSaIbEESG_SG_RS7_</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#32">_ZN4PLMD4pamm10PammObjectC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#27">_ZN4PLMD4pamm10PammObjectC2Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PammObject.cpp.gcov.html#72">_ZNK4PLMD4pamm10PammObject8evaluateERKSt6vectorIdSaIdEERS4_RS2_IS4_SaIS4_EE</a></td>
+              <td class="coverFnHi">787044</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PammObject.cpp.gcov.html b/coverage/pamm/PammObject.cpp.gcov.html
new file mode 100644
index 0000000000..cd703d4aeb
--- /dev/null
+++ b/coverage/pamm/PammObject.cpp.gcov.html
@@ -0,0 +1,179 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PammObject.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PammObject.cpp<span style="font-size: 80%;"> (source / <a href="PammObject.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryMed">82.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PammObject.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;memory&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace pamm {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          6 : PammObject::PammObject():</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">          6 :   regulariser(0.001)</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">          6 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 : PammObject::PammObject( const PammObject&amp; in ):</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 :   regulariser(in.regulariser),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 :   pbc(in.pbc),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineNoCov">          0 :   min(in.min),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   max(in.max)</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : {</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;in.kernels.size(); ++i) kernels.emplace_back( Tools::make_unique&lt;KernelFunctions&gt;( in.kernels[i].get() ) );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          6 : void PammObject::setup( const std::string&amp; filename, const double&amp; reg, const std::vector&lt;std::string&gt;&amp; valnames,</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :                         const std::vector&lt;bool&gt;&amp; pbcin, const std::vector&lt;std::string&gt;&amp; imin, const std::vector&lt;std::string&gt;&amp; imax,</a>
+<a name="45"><span class="lineNum">      45 </span>            :                         std::string&amp; errorstr ) {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          6 :   IFile ifile; regulariser=reg;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          6 :   if( !ifile.FileExist(filename) ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :     errorstr = &quot;could not find file named &quot; + filename;</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :     return;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   }</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; pos;</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          6 :   pbc.resize( valnames.size() );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          6 :   min.resize( valnames.size() );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          6 :   max.resize( valnames.size() );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         21 :   for(unsigned i=0; i&lt;valnames.size(); ++i) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         15 :     pbc[i]=pbcin[i]; min[i]=imin[i]; max[i]=imax[i];</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         15 :     pos.emplace_back( Tools::make_unique&lt;Value&gt;() );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         15 :     if( !pbc[i] ) pos[i]-&gt;setNotPeriodic();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          2 :     else pos[i]-&gt;setDomain( min[i], max[i] );</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          6 :   ifile.open(filename); ifile.allowIgnoredFields(); kernels.resize(0);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   for(unsigned k=0;; ++k) {</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         59 :     std::unique_ptr&lt;KernelFunctions&gt; kk = KernelFunctions::read( &amp;ifile, false, valnames );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         59 :     if( !kk ) break ;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         53 :     kk-&gt;normalize( Tools::unique2raw( pos ) );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         53 :     kernels.emplace_back( std::move(kk) );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         53 :     ifile.scanField();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         59 :   }</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          6 :   ifile.close();</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          6 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     787044 : void PammObject::evaluate( const std::vector&lt;double&gt;&amp; invar, std::vector&lt;double&gt;&amp; outvals, std::vector&lt;std::vector&lt;double&gt; &gt;&amp; der ) const {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; pos;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">    3148138 :   for(unsigned i=0; i&lt;pbc.size(); ++i) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">    2361094 :     pos.emplace_back( Tools::make_unique&lt;Value&gt;() );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    2361094 :     if( !pbc[i] ) pos[i]-&gt;setNotPeriodic();</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         36 :     else pos[i]-&gt;setDomain( min[i], max[i] );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     // And set the value</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">    2361094 :     pos[i]-&gt;set( invar[i] );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   // convert pointers once</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     787044 :   auto pos_ptr=Tools::unique2raw(pos);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   // Evaluate the set of kernels</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     787044 :   double denom=regulariser; std::vector&lt;double&gt; dderiv( der[0].size(), 0 );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">    9444366 :   for(unsigned i=0; i&lt;kernels.size(); ++i) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">    8657322 :     outvals[i]=kernels[i]-&gt;evaluate( pos_ptr, der[i] ); denom+=outvals[i];</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">   34629122 :     for(unsigned j=0; j&lt;der[i].size(); ++j) dderiv[j] += der[i][j];</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span>            :   // Evaluate the set of derivatives</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    9444366 :   for(unsigned i=0; i&lt;kernels.size(); ++i) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    8657322 :     outvals[i]/=denom;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">   34629122 :     for(unsigned j=0; j&lt;der[i].size(); ++j) der[i][j]=der[i][j]/denom - outvals[i]*dderiv[j]/denom;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     787044 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PammObject.h.func-sort-c.html b/coverage/pamm/PammObject.h.func-sort-c.html
new file mode 100644
index 0000000000..091f202704
--- /dev/null
+++ b/coverage/pamm/PammObject.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PammObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PammObject.h<span style="font-size: 80%;"> (<a href="PammObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PammObject.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PammObject.h.func.html b/coverage/pamm/PammObject.h.func.html
new file mode 100644
index 0000000000..8213b9180d
--- /dev/null
+++ b/coverage/pamm/PammObject.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PammObject.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PammObject.h<span style="font-size: 80%;"> (<a href="PammObject.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PammObject.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/PammObject.h.gcov.html b/coverage/pamm/PammObject.h.gcov.html
new file mode 100644
index 0000000000..9213d66fc4
--- /dev/null
+++ b/coverage/pamm/PammObject.h.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm/PammObject.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pamm</a> - PammObject.h<span style="font-size: 80%;"> (source / <a href="PammObject.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_pamm_PammObject_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_pamm_PammObject_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/KernelFunctions.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace pamm {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class PammObject {</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// Regularisation parameter to use</a>
+<a name="35"><span class="lineNum">      35 </span>            :   double regulariser;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Is the domain periodic</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;bool&gt; pbc;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// The domain of the function</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;std::string&gt; min, max;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// List of kernel functions involved</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::vector&lt;std::unique_ptr&lt;KernelFunctions&gt;&gt; kernels;</a>
+<a name="42"><span class="lineNum">      42 </span>            : public:</a>
+<a name="43"><span class="lineNum">      43 </span>            : // Explicit definitions for constructor, copy constructor and destructor</a>
+<a name="44"><span class="lineNum">      44 </span>            :   PammObject();</a>
+<a name="45"><span class="lineNum">      45 </span>            :   PammObject( const PammObject&amp; );</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// GB: I fixed this (should return PammObject&amp;, it was returning PammObject</a>
+<a name="47"><span class="lineNum">      47 </span>            : // However I am not sure the implementation makes sense.</a>
+<a name="48"><span class="lineNum">      48 </span>            :   PammObject&amp; operator=(const PammObject&amp; po) { plumed_error(); regulariser=po.regulariser; return *this; }</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Setup the Pamm object</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void setup( const std::string&amp; filename, const double&amp; reg, const std::vector&lt;std::string&gt;&amp; valnames,</a>
+<a name="51"><span class="lineNum">      51 </span>            :               const std::vector&lt;bool&gt;&amp; pbcin, const std::vector&lt;std::string&gt;&amp; imin, const std::vector&lt;std::string&gt;&amp; imax,</a>
+<a name="52"><span class="lineNum">      52 </span>            :               std::string&amp; errorstr );</a>
+<a name="53"><span class="lineNum">      53 </span>            : ///</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void evaluate( const std::vector&lt;double&gt;&amp; invar, std::vector&lt;double&gt;&amp; outvals, std::vector&lt;std::vector&lt;double&gt; &gt;&amp; der ) const ;</a>
+<a name="55"><span class="lineNum">      55 </span>            : ///</a>
+<a name="56"><span class="lineNum">      56 </span>            :   unsigned getNumberOfKernels() const ;</a>
+<a name="57"><span class="lineNum">      57 </span>            : ///</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::vector&lt;double&gt; getKernelCenter( const unsigned&amp; kno ) const ;</a>
+<a name="59"><span class="lineNum">      59 </span>            : ///</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;double&gt; getKernelSupport( const unsigned&amp; kno ) const ;</a>
+<a name="61"><span class="lineNum">      61 </span>            : };</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : inline</a>
+<a name="64"><span class="lineNum">      64 </span>            : unsigned PammObject::getNumberOfKernels() const {</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        134 :   return kernels.size();</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : inline</a>
+<a name="69"><span class="lineNum">      69 </span>            : std::vector&lt;double&gt; PammObject::getKernelCenter( const unsigned&amp; kno ) const {</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         44 :   return kernels[kno]-&gt;getCenter();</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : inline</a>
+<a name="74"><span class="lineNum">      74 </span>            : std::vector&lt;double&gt; PammObject::getKernelSupport( const unsigned&amp; kno ) const {</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         44 :   return kernels[kno]-&gt;getContinuousSupport();</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : #endif</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/index-sort-f.html b/coverage/pamm/index-sort-f.html
new file mode 100644
index 0000000000..9abfe3357d
--- /dev/null
+++ b/coverage/pamm/index-sort-f.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - pamm</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">215</td>
+            <td class="headerCovTableEntry">264</td>
+            <td class="headerCovTableEntryMed">81.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryMed">79.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PAMM.cpp.gcov.html">PAMM.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="76.9%"><img src="../snow.png" width=23 height=10 alt="76.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">50 / 65</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PammObject.cpp.gcov.html">PammObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.6%"><img src="../snow.png" width=17 height=10 alt="82.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.6&nbsp;%</td>
+      <td class="coverNumMed">38 / 46</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammHydrogens.cpp.gcov.html">HBPammHydrogens.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.3%"><img src="../snow.png" width=30 height=10 alt="70.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.3&nbsp;%</td>
+      <td class="coverNumLo">52 / 74</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammMatrix.cpp.gcov.html">HBPammMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">39 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PammObject.h.gcov.html">PammObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammObject.h.gcov.html">HBPammObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammObject.cpp.gcov.html">HBPammObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/index-sort-l.html b/coverage/pamm/index-sort-l.html
new file mode 100644
index 0000000000..b21307b740
--- /dev/null
+++ b/coverage/pamm/index-sort-l.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - pamm</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">215</td>
+            <td class="headerCovTableEntry">264</td>
+            <td class="headerCovTableEntryMed">81.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryMed">79.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammHydrogens.cpp.gcov.html">HBPammHydrogens.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.3%"><img src="../snow.png" width=30 height=10 alt="70.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.3&nbsp;%</td>
+      <td class="coverNumLo">52 / 74</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PAMM.cpp.gcov.html">PAMM.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="76.9%"><img src="../snow.png" width=23 height=10 alt="76.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">50 / 65</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PammObject.cpp.gcov.html">PammObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.6%"><img src="../snow.png" width=17 height=10 alt="82.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.6&nbsp;%</td>
+      <td class="coverNumMed">38 / 46</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammMatrix.cpp.gcov.html">HBPammMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">39 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammObject.h.gcov.html">HBPammObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PammObject.h.gcov.html">PammObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammObject.cpp.gcov.html">HBPammObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pamm/index.html b/coverage/pamm/index.html
new file mode 100644
index 0000000000..200d1be0a3
--- /dev/null
+++ b/coverage/pamm/index.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pamm</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - pamm</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">215</td>
+            <td class="headerCovTableEntry">264</td>
+            <td class="headerCovTableEntryMed">81.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntryMed">79.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammHydrogens.cpp.gcov.html">HBPammHydrogens.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.3%"><img src="../snow.png" width=30 height=10 alt="70.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.3&nbsp;%</td>
+      <td class="coverNumLo">52 / 74</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammMatrix.cpp.gcov.html">HBPammMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">39 / 43</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammObject.cpp.gcov.html">HBPammObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HBPammObject.h.gcov.html">HBPammObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PAMM.cpp.gcov.html">PAMM.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=77 height=10 alt="76.9%"><img src="../snow.png" width=23 height=10 alt="76.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">50 / 65</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PammObject.cpp.gcov.html">PammObject.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.6%"><img src="../snow.png" width=17 height=10 alt="82.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.6&nbsp;%</td>
+      <td class="coverNumMed">38 / 46</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PammObject.h.gcov.html">PammObject.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/piv/PIV.cpp.func-sort-c.html b/coverage/piv/PIV.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f00ae6d894
--- /dev/null
+++ b/coverage/piv/PIV.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - piv/PIV.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">piv</a> - PIV.cpp<span style="font-size: 80%;"> (<a href="PIV.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntry">596</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PIV.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#229">_ZN4PLMD3piv3PIV18checkFieldsAllowedEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#263">_ZN4PLMD3piv3PIVC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#232">_ZN4PLMD3piv12_GLOBAL__N_116PIVRegisterMe2346createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#263">_ZN4PLMD3piv3PIVC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#234">_ZN4PLMD3piv3PIV16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#745">_ZN4PLMD3piv3PIV9calculateEv</a></td>
+              <td class="coverFnHi">327</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#232">_ZN4PLMD3piv12_GLOBAL__N_116PIVRegisterMe234C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#232">_ZN4PLMD3piv12_GLOBAL__N_116PIVRegisterMe234D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/piv/PIV.cpp.func.html b/coverage/piv/PIV.cpp.func.html
new file mode 100644
index 0000000000..19531b6d40
--- /dev/null
+++ b/coverage/piv/PIV.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - piv/PIV.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">piv</a> - PIV.cpp<span style="font-size: 80%;"> (<a href="PIV.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntry">596</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PIV.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#232">_ZN4PLMD3piv12_GLOBAL__N_116PIVRegisterMe2346createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#232">_ZN4PLMD3piv12_GLOBAL__N_116PIVRegisterMe234C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#232">_ZN4PLMD3piv12_GLOBAL__N_116PIVRegisterMe234D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#234">_ZN4PLMD3piv3PIV16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#229">_ZN4PLMD3piv3PIV18checkFieldsAllowedEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#745">_ZN4PLMD3piv3PIV9calculateEv</a></td>
+              <td class="coverFnHi">327</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#263">_ZN4PLMD3piv3PIVC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PIV.cpp.gcov.html#263">_ZN4PLMD3piv3PIVC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/piv/PIV.cpp.gcov.html b/coverage/piv/PIV.cpp.gcov.html
new file mode 100644
index 0000000000..a91123c4ca
--- /dev/null
+++ b/coverage/piv/PIV.cpp.gcov.html
@@ -0,0 +1,1338 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - piv/PIV.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">piv</a> - PIV.cpp<span style="font-size: 80%;"> (source / <a href="PIV.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntry">596</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2017 of Pipolo Silvio and Fabio Pietrucci.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : The piv module is free software: you can redistribute it and/or modify</a>
+<a name="5"><span class="lineNum">       5 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="6"><span class="lineNum">       6 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="7"><span class="lineNum">       7 </span>            : (at your option) any later version.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : The piv module is distributed in the hope that it will be useful,</a>
+<a name="10"><span class="lineNum">      10 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="11"><span class="lineNum">      11 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="12"><span class="lineNum">      12 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="15"><span class="lineNum">      15 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="16"><span class="lineNum">      16 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="17"><span class="lineNum">      17 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="18"><span class="lineNum">      18 </span>            : #include &quot;colvar/ActionRegister.h&quot;</a>
+<a name="19"><span class="lineNum">      19 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;core/ActionWithVirtualAtom.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Stopwatch.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;iostream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : using namespace std;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD</a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace piv</a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : //+PLUMEDOC PIVMOD_COLVAR PIV</a>
+<a name="40"><span class="lineNum">      40 </span>            : /*</a>
+<a name="41"><span class="lineNum">      41 </span>            : Calculates the PIV-distance.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : PIV distance is the squared Cartesian distance between the PIV \cite gallet2013structural \cite pipolo2017navigating</a>
+<a name="44"><span class="lineNum">      44 </span>            : associated to the configuration of the system during the dynamics and a reference configuration provided</a>
+<a name="45"><span class="lineNum">      45 </span>            : as input (PDB file format).</a>
+<a name="46"><span class="lineNum">      46 </span>            : PIV can be used together with \ref FUNCPATHMSD to define a path in the PIV space.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \par Examples</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The following example calculates PIV-distances from three reference configurations in Ref1.pdb, Ref2.pdb and Ref3.pdb</a>
+<a name="51"><span class="lineNum">      51 </span>            : and prints the results in a file named colvar.</a>
+<a name="52"><span class="lineNum">      52 </span>            : Three atoms (PIVATOMS=3) with names (pdb file) A B and C are used to construct the PIV and all PIV blocks (AA, BB, CC, AB, AC, BC) are considered.</a>
+<a name="53"><span class="lineNum">      53 </span>            : SFACTOR is a scaling factor that multiplies the contribution to the PIV-distance given by the single PIV block.</a>
+<a name="54"><span class="lineNum">      54 </span>            : NLIST sets the use of neighbor lists for calculating atom-atom distances.</a>
+<a name="55"><span class="lineNum">      55 </span>            : The SWITCH keyword specifies the parameters of the switching function that transforms atom-atom distances.</a>
+<a name="56"><span class="lineNum">      56 </span>            : SORT=1 means that the PIV block elements are sorted (SORT=0 no sorting.)</a>
+<a name="57"><span class="lineNum">      57 </span>            : Values for SORT, SFACTOR and the neighbor list parameters have to be specified for each block.</a>
+<a name="58"><span class="lineNum">      58 </span>            : The order is the following: AA,BB,CC,AB,AC,BC. If ONLYDIRECT (ONLYCROSS) is used the order is AA,BB,CC (AB,AC,BC).</a>
+<a name="59"><span class="lineNum">      59 </span>            : The sorting operation within each PIV block is performed using the counting sort algorithm, PRECISION specifies the size of the counting array.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : \plumedfile</a>
+<a name="62"><span class="lineNum">      62 </span>            : PIV ...</a>
+<a name="63"><span class="lineNum">      63 </span>            : LABEL=Pivd1</a>
+<a name="64"><span class="lineNum">      64 </span>            : PRECISION=1000</a>
+<a name="65"><span class="lineNum">      65 </span>            : NLIST</a>
+<a name="66"><span class="lineNum">      66 </span>            : REF_FILE=Ref1.pdb</a>
+<a name="67"><span class="lineNum">      67 </span>            : PIVATOMS=3</a>
+<a name="68"><span class="lineNum">      68 </span>            : ATOMTYPES=A,B,C</a>
+<a name="69"><span class="lineNum">      69 </span>            : SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2</a>
+<a name="70"><span class="lineNum">      70 </span>            : SORT=1,1,1,1,1,1</a>
+<a name="71"><span class="lineNum">      71 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="72"><span class="lineNum">      72 </span>            : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="73"><span class="lineNum">      73 </span>            : SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="74"><span class="lineNum">      74 </span>            : SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="75"><span class="lineNum">      75 </span>            : SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="76"><span class="lineNum">      76 </span>            : SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="77"><span class="lineNum">      77 </span>            : NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7</a>
+<a name="78"><span class="lineNum">      78 </span>            : NL_STRIDE=10,10,10,10,10,10</a>
+<a name="79"><span class="lineNum">      79 </span>            : NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1</a>
+<a name="80"><span class="lineNum">      80 </span>            : ... PIV</a>
+<a name="81"><span class="lineNum">      81 </span>            : PIV ...</a>
+<a name="82"><span class="lineNum">      82 </span>            : LABEL=Pivd2</a>
+<a name="83"><span class="lineNum">      83 </span>            : PRECISION=1000</a>
+<a name="84"><span class="lineNum">      84 </span>            : NLIST</a>
+<a name="85"><span class="lineNum">      85 </span>            : REF_FILE=Ref2.pdb</a>
+<a name="86"><span class="lineNum">      86 </span>            : PIVATOMS=3</a>
+<a name="87"><span class="lineNum">      87 </span>            : ATOMTYPES=A,B,C</a>
+<a name="88"><span class="lineNum">      88 </span>            : SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2</a>
+<a name="89"><span class="lineNum">      89 </span>            : SORT=1,1,1,1,1,1</a>
+<a name="90"><span class="lineNum">      90 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="91"><span class="lineNum">      91 </span>            : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="92"><span class="lineNum">      92 </span>            : SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="93"><span class="lineNum">      93 </span>            : SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="94"><span class="lineNum">      94 </span>            : SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="95"><span class="lineNum">      95 </span>            : SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="96"><span class="lineNum">      96 </span>            : NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7</a>
+<a name="97"><span class="lineNum">      97 </span>            : NL_STRIDE=10,10,10,10,10,10</a>
+<a name="98"><span class="lineNum">      98 </span>            : NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1</a>
+<a name="99"><span class="lineNum">      99 </span>            : ... PIV</a>
+<a name="100"><span class="lineNum">     100 </span>            : PIV ...</a>
+<a name="101"><span class="lineNum">     101 </span>            : LABEL=Pivd3</a>
+<a name="102"><span class="lineNum">     102 </span>            : PRECISION=1000</a>
+<a name="103"><span class="lineNum">     103 </span>            : NLIST</a>
+<a name="104"><span class="lineNum">     104 </span>            : REF_FILE=Ref3.pdb</a>
+<a name="105"><span class="lineNum">     105 </span>            : PIVATOMS=3</a>
+<a name="106"><span class="lineNum">     106 </span>            : ATOMTYPES=A,B,C</a>
+<a name="107"><span class="lineNum">     107 </span>            : SFACTOR=0.3,0.5,1.0,0.2,0.2,0.2</a>
+<a name="108"><span class="lineNum">     108 </span>            : SORT=1,1,1,1,1,1</a>
+<a name="109"><span class="lineNum">     109 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="110"><span class="lineNum">     110 </span>            : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="111"><span class="lineNum">     111 </span>            : SWITCH3={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="112"><span class="lineNum">     112 </span>            : SWITCH4={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="113"><span class="lineNum">     113 </span>            : SWITCH5={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="114"><span class="lineNum">     114 </span>            : SWITCH6={RATIONAL R_0=0.5 MM=12 NN=6}</a>
+<a name="115"><span class="lineNum">     115 </span>            : NL_CUTOFF=0.8,0.6,0.6,0.7,0.7,0.7</a>
+<a name="116"><span class="lineNum">     116 </span>            : NL_STRIDE=10,10,10,10,10,10</a>
+<a name="117"><span class="lineNum">     117 </span>            : NL_SKIN=0.1,0.1,0.1,0.1,0.1,0.1</a>
+<a name="118"><span class="lineNum">     118 </span>            : ... PIV</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : PRINT ARG=Pivd1,Pivd2,Pivd3 FILE=colvar</a>
+<a name="121"><span class="lineNum">     121 </span>            : \endplumedfile</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : WARNING:</a>
+<a name="124"><span class="lineNum">     124 </span>            : Both the &quot;CRYST&quot; and &quot;ATOM&quot; lines of the PDB files must conform precisely to the official pdb format, including the width of each alphanumerical field:</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : \verbatim</a>
+<a name="127"><span class="lineNum">     127 </span>            : CRYST1   31.028   36.957   23.143  89.93  92.31  89.99 P 1           1</a>
+<a name="128"><span class="lineNum">     128 </span>            : ATOM      1  OW1 wate    1      15.630  19.750   1.520  1.00  0.00</a>
+<a name="129"><span class="lineNum">     129 </span>            : \endverbatim</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : In each pdb frame, atoms must be numbered in the same order and with the same element symbol as in the input of the MD program.</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : The following example calculates the PIV-distances from two reference configurations Ref1.pdb and Ref2.pdb</a>
+<a name="134"><span class="lineNum">     134 </span>            : and uses PIV-distances to define a Path Collective Variable (\ref FUNCPATHMSD) with only two references (Ref1.pdb and Ref2.pdb).</a>
+<a name="135"><span class="lineNum">     135 </span>            : With the VOLUME keyword one scales the atom-atom distances by the cubic root of the ratio between the specified value and the box volume of the initial step of the trajectory file.</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : \plumedfile</a>
+<a name="138"><span class="lineNum">     138 </span>            : PIV ...</a>
+<a name="139"><span class="lineNum">     139 </span>            : LABEL=c1</a>
+<a name="140"><span class="lineNum">     140 </span>            : PRECISION=1000</a>
+<a name="141"><span class="lineNum">     141 </span>            : VOLUME=12.15</a>
+<a name="142"><span class="lineNum">     142 </span>            : NLIST</a>
+<a name="143"><span class="lineNum">     143 </span>            : REF_FILE=Ref1.pdb</a>
+<a name="144"><span class="lineNum">     144 </span>            : PIVATOMS=2</a>
+<a name="145"><span class="lineNum">     145 </span>            : ATOMTYPES=A,B</a>
+<a name="146"><span class="lineNum">     146 </span>            : ONLYDIRECT</a>
+<a name="147"><span class="lineNum">     147 </span>            : SFACTOR=1.0,0.2</a>
+<a name="148"><span class="lineNum">     148 </span>            : SORT=1,1</a>
+<a name="149"><span class="lineNum">     149 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="150"><span class="lineNum">     150 </span>            : SWITCH2={RATIONAL R_0=0.5 MM=10 NN=5}</a>
+<a name="151"><span class="lineNum">     151 </span>            : NL_CUTOFF=1.2,1.2</a>
+<a name="152"><span class="lineNum">     152 </span>            : NL_STRIDE=10,10</a>
+<a name="153"><span class="lineNum">     153 </span>            : NL_SKIN=0.1,0.1</a>
+<a name="154"><span class="lineNum">     154 </span>            : ... PIV</a>
+<a name="155"><span class="lineNum">     155 </span>            : PIV ...</a>
+<a name="156"><span class="lineNum">     156 </span>            : LABEL=c2</a>
+<a name="157"><span class="lineNum">     157 </span>            : PRECISION=1000</a>
+<a name="158"><span class="lineNum">     158 </span>            : VOLUME=12.15</a>
+<a name="159"><span class="lineNum">     159 </span>            : NLIST</a>
+<a name="160"><span class="lineNum">     160 </span>            : REF_FILE=Ref2.pdb</a>
+<a name="161"><span class="lineNum">     161 </span>            : PIVATOMS=2</a>
+<a name="162"><span class="lineNum">     162 </span>            : ATOMTYPES=A,B</a>
+<a name="163"><span class="lineNum">     163 </span>            : ONLYDIRECT</a>
+<a name="164"><span class="lineNum">     164 </span>            : SFACTOR=1.0,0.2</a>
+<a name="165"><span class="lineNum">     165 </span>            : SORT=1,1</a>
+<a name="166"><span class="lineNum">     166 </span>            : SWITCH1={RATIONAL R_0=0.6 MM=12 NN=4}</a>
+<a name="167"><span class="lineNum">     167 </span>            : SWITCH2={RATIONAL R_0=0.4 MM=10 NN=5}</a>
+<a name="168"><span class="lineNum">     168 </span>            : NL_CUTOFF=1.2,1.2</a>
+<a name="169"><span class="lineNum">     169 </span>            : NL_STRIDE=10,10</a>
+<a name="170"><span class="lineNum">     170 </span>            : NL_SKIN=0.1,0.1</a>
+<a name="171"><span class="lineNum">     171 </span>            : ... PIV</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : p1: FUNCPATHMSD ARG=c1,c2 LAMBDA=0.180338</a>
+<a name="174"><span class="lineNum">     174 </span>            : METAD ARG=p1.s,p1.z SIGMA=0.01,0.2 HEIGHT=0.8 PACE=500   LABEL=res</a>
+<a name="175"><span class="lineNum">     175 </span>            : PRINT ARG=c1,c2,p1.s,p1.z,res.bias STRIDE=500  FILE=colvar FMT=%15.6f</a>
+<a name="176"><span class="lineNum">     176 </span>            : \endplumedfile</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : When using PIV please cite \cite pipolo2017navigating .</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : (See also \ref PRINT)</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : */</a>
+<a name="183"><span class="lineNum">     183 </span>            : //+ENDPLUMEDOC</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : class PIV      : public Colvar</a>
+<a name="186"><span class="lineNum">     186 </span>            : {</a>
+<a name="187"><span class="lineNum">     187 </span>            : private:</a>
+<a name="188"><span class="lineNum">     188 </span>            :   bool pbc, serial, timer;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   ForwardDecl&lt;Stopwatch&gt; stopwatch_fwd;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   Stopwatch&amp; stopwatch=*stopwatch_fwd;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   int updatePIV;</a>
+<a name="192"><span class="lineNum">     192 </span>            :   size_t Nprec;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   unsigned Natm,Nlist,NLsize;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   double Fvol,Vol0,m_PIVdistance;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   std::string ref_file;</a>
+<a name="196"><span class="lineNum">     196 </span>            :   std::unique_ptr&lt;NeighborList&gt; nlall;</a>
+<a name="197"><span class="lineNum">     197 </span>            :   std::vector&lt;SwitchingFunction&gt; sfs;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   std::vector&lt;std:: vector&lt;double&gt; &gt; rPIV;</a>
+<a name="199"><span class="lineNum">     199 </span>            :   std::vector&lt;double&gt; scaling,r00;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   std::vector&lt;double&gt; nl_skin;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   std::vector&lt;double&gt; fmass;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   std::vector&lt;bool&gt; dosort;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   std::vector&lt;Vector&gt; compos;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   std::vector&lt;string&gt; sw;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   std::vector&lt;std::unique_ptr&lt;NeighborList&gt;&gt; nl;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   std::vector&lt;std::unique_ptr&lt;NeighborList&gt;&gt; nlcom;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   std::vector&lt;Vector&gt; m_deriv;</a>
+<a name="208"><span class="lineNum">     208 </span>            :   Tensor m_virial;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   bool Svol,cross,direct,doneigh,test,CompDer,com;</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   /// Local structure, used to store data that should be</a>
+<a name="212"><span class="lineNum">     212 </span>            :   /// shared across multiple PIV instances</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          6 :   struct SharedData {</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :     int prev_stp=-1;</a>
+<a name="215"><span class="lineNum">     215 </span>            :     int init_stp=1;</a>
+<a name="216"><span class="lineNum">     216 </span>            :     std:: vector&lt;std:: vector&lt;Vector&gt; &gt; prev_pos;</a>
+<a name="217"><span class="lineNum">     217 </span>            :     std:: vector&lt;std:: vector&lt;double&gt; &gt; cPIV;</a>
+<a name="218"><span class="lineNum">     218 </span>            :     std:: vector&lt;std:: vector&lt;int&gt; &gt; Atom0;</a>
+<a name="219"><span class="lineNum">     219 </span>            :     std:: vector&lt;std:: vector&lt;int&gt; &gt; Atom1;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   };</a>
+<a name="221"><span class="lineNum">     221 </span>            :   /// Owning pointer. Will only be allocated by the first PIV instance</a>
+<a name="222"><span class="lineNum">     222 </span>            :   std::unique_ptr&lt;SharedData&gt; sharedData_unique;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   /// Raw pointer. Will have the same value for all PIV instances</a>
+<a name="224"><span class="lineNum">     224 </span>            :   SharedData* sharedData=nullptr;</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : public:</a>
+<a name="227"><span class="lineNum">     227 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="228"><span class="lineNum">     228 </span>            :   explicit PIV(const ActionOptions&amp;);</a>
+<a name="229"><span class="lineNum">     229 </span>            :   // active methods:</a>
+<a name="230"><span class="lineNum">     230 </span>            :   virtual void calculate();</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   void checkFieldsAllowed() {}</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : };</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(PIV,&quot;PIV&quot;)</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         14 : void PIV::registerKeywords( Keywords&amp; keys )</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : {</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         14 :   Colvar::registerKeywords( keys );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         28 :   keys.add(&quot;numbered&quot;,&quot;SWITCH&quot;,&quot;The switching functions parameter.&quot;</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :            &quot;You should specify a Switching function for all PIV blocks.&quot;</a>
+<a name="241"><span class="lineNum">     241 </span>            :            &quot;Details of the various switching &quot;</a>
+<a name="242"><span class="lineNum">     242 </span>            :            &quot;functions you can use are provided on \\ref switchingfunction.&quot;);</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;PRECISION&quot;,&quot;the precision for approximating reals with integers in sorting.&quot;);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;REF_FILE&quot;,&quot;PDB file name that contains the \\f$i\\f$th reference structure.&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;PIVATOMS&quot;,&quot;Number of atoms to use for PIV.&quot;);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;SORT&quot;,&quot;Whether to sort or not the PIV block.&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;ATOMTYPES&quot;,&quot;The atom types to use for PIV.&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;SFACTOR&quot;,&quot;Scale the PIV-distance by such block-specific factor&quot;);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;VOLUME&quot;,&quot;Scale atom-atom distances by the cubic root of the cell volume. The input volume is used to scale the R_0 value of the switching function. &quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;UPDATEPIV&quot;,&quot;Frequency (in steps) at which the PIV is updated.&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         28 :   keys.addFlag(&quot;TEST&quot;,false,&quot;Print the actual and reference PIV and exit&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         28 :   keys.addFlag(&quot;COM&quot;,false,&quot;Use centers of mass of groups of atoms instead of atoms as specified in the Pdb file&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         28 :   keys.addFlag(&quot;ONLYCROSS&quot;,false,&quot;Use only cross-terms (A-B, A-C, B-C, ...) in PIV&quot;);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         28 :   keys.addFlag(&quot;ONLYDIRECT&quot;,false,&quot;Use only direct-terms (A-A, B-B, C-C, ...) in PIV&quot;);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         28 :   keys.addFlag(&quot;DERIVATIVES&quot;,false,&quot;Activate the calculation of the PIV for every class (needed for numerical derivatives).&quot;);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         28 :   keys.addFlag(&quot;NLIST&quot;,false,&quot;Use a neighbor list for distance calculations.&quot;);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         28 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         28 :   keys.addFlag(&quot;TIMER&quot;,false,&quot;Perform timing analysis on heavy loops.&quot;);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;NL_CUTOFF&quot;,&quot;Neighbor lists cutoff.&quot;);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;NL_STRIDE&quot;,&quot;Update neighbor lists every NL_STRIDE steps.&quot;);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;NL_SKIN&quot;,&quot;The maximum atom displacement tolerated for the neighbor lists update.&quot;);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         28 :   keys.reset_style(&quot;SWITCH&quot;,&quot;compulsory&quot;);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         14 : }</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         12 : PIV::PIV(const ActionOptions&amp;ao):</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         12 :   pbc(true),</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         12 :   serial(false),</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         12 :   timer(false),</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         12 :   updatePIV(1),</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         12 :   Nprec(1000),</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         12 :   Natm(1),</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         12 :   Nlist(1),</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         12 :   NLsize(1),</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         12 :   Fvol(1.),</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         12 :   Vol0(0.),</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         12 :   m_PIVdistance(0.),</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         12 :   rPIV(std:: vector&lt;std:: vector&lt;double&gt; &gt;(Nlist)),</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         12 :   scaling(std:: vector&lt;double&gt;(Nlist)),</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         12 :   r00(std:: vector&lt;double&gt;(Nlist)),</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         12 :   nl_skin(std:: vector&lt;double&gt;(Nlist)),</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         12 :   fmass(std:: vector&lt;double&gt;(Nlist)),</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         12 :   dosort(std:: vector&lt;bool&gt;(Nlist)),</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         12 :   compos(std:: vector&lt;Vector&gt;(NLsize)),</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         12 :   sw(std:: vector&lt;string&gt;(Nlist)),</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         12 :   nl(Nlist),</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         12 :   nlcom(NLsize),</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         12 :   m_deriv(std:: vector&lt;Vector&gt;(1)),</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         12 :   Svol(false),</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         12 :   cross(true),</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         12 :   direct(true),</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         12 :   doneigh(false),</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         12 :   test(false),</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         12 :   CompDer(false),</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         24 :   com(false)</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : {</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;Starting PIV Constructor\n&quot;;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :   {</a>
+<a name="300"><span class="lineNum">     300 </span>            :     // look for another PIV instance previously allocated</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         12 :     auto* previous=plumed.getActionSet().selectLatest&lt;PIV*&gt;(this);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            :     // Uncommenting the following line, it is possible to force</a>
+<a name="304"><span class="lineNum">     304 </span>            :     // a separate object per instance of the PIB object.</a>
+<a name="305"><span class="lineNum">     305 </span>            :     // Results are unaffected, but performance is worse.</a>
+<a name="306"><span class="lineNum">     306 </span>            :     // I think this is the expected behavior. GB</a>
+<a name="307"><span class="lineNum">     307 </span>            :     // previous=nullptr;</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         12 :     if(!previous) {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :       // if not found, allocate the shared data struct</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         12 :       sharedData_unique=Tools::make_unique&lt;SharedData&gt;();</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :       // then set the raw pointer</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          6 :       sharedData=sharedData_unique.get();</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :     } else {</a>
+<a name="315"><span class="lineNum">     315 </span>            :       // if found, use the previous raw pointer</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          6 :       sharedData=previous-&gt;sharedData;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          6 :       log &lt;&lt; &quot;(a previous PIV action was found)\n&quot;;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            :   // Precision on the real-to-integer transformation for the sorting</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         12 :   parse(&quot;PRECISION&quot;,Nprec);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         12 :   if(Nprec&lt;2) error(&quot;Precision must be =&gt; 2&quot;);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            :   // PBC</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         12 :   bool nopbc=!pbc;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         12 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         12 :   pbc=!nopbc;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         12 :   if(pbc) {</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         12 :     log &lt;&lt; &quot;Using Periodic Boundary Conditions\n&quot;;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   } else  {</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;Isolated System (NO PBC)\n&quot;;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :   // SERIAL/PARALLEL</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         12 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         12 :   if(serial) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;Serial PIV construction\n&quot;;</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   } else     {</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         12 :     log &lt;&lt; &quot;Parallel PIV construction\n&quot;;</span></a>
+<a name="341"><span class="lineNum">     341 </span>            :   }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            :   // Derivatives</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         12 :   parseFlag(&quot;DERIVATIVES&quot;,CompDer);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         12 :   if(CompDer) log &lt;&lt; &quot;Computing Derivatives\n&quot;;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :   // Timing</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         12 :   parseFlag(&quot;TIMER&quot;,timer);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         12 :   if(timer) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          1 :     log &lt;&lt; &quot;Timing analysis\n&quot;;</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          1 :     stopwatch.start();</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          1 :     stopwatch.pause();</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :   }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :   // Test</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         12 :   parseFlag(&quot;TEST&quot;,test);</span></a>
+<a name="357"><span class="lineNum">     357 </span>            : </a>
+<a name="358"><span class="lineNum">     358 </span>            :   // UPDATEPIV</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         24 :   if(keywords.exists(&quot;UPDATEPIV&quot;)) {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         24 :     parse(&quot;UPDATEPIV&quot;,updatePIV);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            :   // Test</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         12 :   parseFlag(&quot;COM&quot;,com);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         12 :   if(com) log &lt;&lt; &quot;Building PIV using COMs\n&quot;;</span></a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            :   // Volume Scaling</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         12 :   parse(&quot;VOLUME&quot;,Vol0);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         12 :   if (Vol0&gt;0) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         12 :     Svol=true;</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :   }</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            :   // PIV direct and cross blocks</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         12 :   bool oc=false,od=false;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         12 :   parseFlag(&quot;ONLYCROSS&quot;,oc);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         12 :   parseFlag(&quot;ONLYDIRECT&quot;,od);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         12 :   if (oc&amp;&amp;od) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :     error(&quot;ONLYCROSS and ONLYDIRECT are incompatible options!&quot;);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         12 :   if(oc) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          4 :     direct=false;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          4 :     log &lt;&lt; &quot;Using only CROSS-PIV blocks\n&quot;;</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :   }</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         12 :   if(od) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">          4 :     cross=false;</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">          4 :     log &lt;&lt; &quot;Using only DIRECT-PIV blocks\n&quot;;</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :   }</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            :   // Atoms for PIV</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         12 :   parse(&quot;PIVATOMS&quot;,Natm);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         12 :   std:: vector&lt;string&gt; atype(Natm);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         12 :   parseVector(&quot;ATOMTYPES&quot;,atype);</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   //if(atype.size()!=getNumberOfArguments() &amp;&amp; atype.size()!=0) error(&quot;not enough values for ATOMTYPES&quot;);</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            :   // Reference PDB file</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         12 :   parse(&quot;REF_FILE&quot;,ref_file);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         12 :   PDB mypdb;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         12 :   FILE* fp=fopen(ref_file.c_str(),&quot;r&quot;);</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         12 :   if (fp!=NULL) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         12 :     log&lt;&lt;&quot;Opening PDB file with reference frame: &quot;&lt;&lt;ref_file.c_str()&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         24 :     mypdb.readFromFilepointer(fp,plumed.getAtoms().usingNaturalUnits(),0.1/atoms.getUnits().getLength());</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         12 :     fclose (fp);</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   } else {</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 :     error(&quot;Error in reference PDB file&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :   }</a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span>            :   // Build COM/Atom lists of AtomNumbers (this might be done in PBC.cpp)</a>
+<a name="408"><span class="lineNum">     408 </span>            :   // Atomlist or Plist used to build pair lists</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         12 :   std:: vector&lt;std:: vector&lt;AtomNumber&gt; &gt; Plist(Natm);</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   // Atomlist used to build list of atoms for each COM</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         12 :   std:: vector&lt;std:: vector&lt;AtomNumber&gt; &gt; comatm(1);</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :   // NLsize is the number of atoms in the pdb cell</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         12 :   NLsize=mypdb.getAtomNumbers().size();</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :   // In the following P stands for Point (either an Atom or a COM)</a>
+<a name="415"><span class="lineNum">     415 </span>            :   unsigned resnum=0;</a>
+<a name="416"><span class="lineNum">     416 </span>            :   // Presind (array size: number of residues) contains the contains the residue number</a>
+<a name="417"><span class="lineNum">     417 </span>            :   //   this is because the residue numbers may not always be ordered from 1 to resnum</a>
+<a name="418"><span class="lineNum">     418 </span>            :   std:: vector&lt;unsigned&gt; Presind;</a>
+<a name="419"><span class="lineNum">     419 </span>            :   // Build Presind</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      19404 :   for (unsigned i=0; i&lt;mypdb.getAtomNumbers().size(); i++) {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">      19392 :     unsigned rind=mypdb.getResidueNumber(mypdb.getAtomNumbers()[i]);</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :     bool oldres=false;</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">    7705008 :     for (unsigned j=0; j&lt;Presind.size(); j++) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">    7685616 :       if(rind==Presind[j]) {</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :         oldres=true;</a>
+<a name="426"><span class="lineNum">     426 </span>            :       }</a>
+<a name="427"><span class="lineNum">     427 </span>            :     }</a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">      19392 :     if(!oldres) {</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       4848 :       Presind.push_back(rind);</span></a>
+<a name="430"><span class="lineNum">     430 </span>            :     }</a>
+<a name="431"><span class="lineNum">     431 </span>            :   }</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         12 :   resnum=Presind.size();</span></a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span>            :   // Pind0 is the atom/COM used in Nlists (for COM Pind0 is the first atom in the pdb belonging to that COM)</a>
+<a name="435"><span class="lineNum">     435 </span>            :   unsigned Pind0size;</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         12 :   if(com) {</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :     Pind0size=resnum;</a>
+<a name="438"><span class="lineNum">     438 </span>            :   } else {</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         12 :     Pind0size=NLsize;</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   }</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         12 :   std:: vector&lt;unsigned&gt; Pind0(Pind0size);</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :   // If COM resize important arrays</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         12 :   comatm.resize(NLsize);</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         12 :   if(com) {</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :     nlcom.resize(NLsize);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :     compos.resize(NLsize);</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineNoCov">          0 :     fmass.resize(NLsize,0.);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :   }</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;Total COM/Atoms: &quot; &lt;&lt; Natm*resnum &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :   // Build lists of Atoms/COMs for NLists</a>
+<a name="451"><span class="lineNum">     451 </span>            :   //   comatm filled also for non_COM calculation for analysis purposes</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         36 :   for (unsigned j=0; j&lt;Natm; j++) {</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     unsigned oind;</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">      38808 :     for (unsigned i=0; i&lt;Pind0.size(); i++) {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">      38784 :       Pind0[i]=0;</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :     }</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">      38808 :     for (unsigned i=0; i&lt;mypdb.getAtomNumbers().size(); i++) {</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :       // Residue/Atom AtomNumber: used to build NL for COMS/Atoms pairs.</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">      38784 :       AtomNumber anum=mypdb.getAtomNumbers()[i];</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :       // ResidueName/Atomname associated to atom</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">      38784 :       string rname=mypdb.getResidueName(anum);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">      38784 :       string aname=mypdb.getAtomName(anum);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :       // Index associated to residue/atom: used to separate COM-lists</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">      38784 :       unsigned rind=mypdb.getResidueNumber(anum);</span></a>
+<a name="465"><span class="lineNum">     465 </span>            :       unsigned aind=anum.index();</a>
+<a name="466"><span class="lineNum">     466 </span>            :       // This builds lists for NL</a>
+<a name="467"><span class="lineNum">     467 </span>            :       string Pname;</a>
+<a name="468"><span class="lineNum">     468 </span>            :       unsigned Pind;</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">      38784 :       if(com) {</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :         Pname=rname;</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :         for(unsigned l=0; l&lt;resnum; l++) {</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :           if(rind==Presind[l]) {</span></a>
+<a name="473"><span class="lineNum">     473 </span>            :             Pind=l;</a>
+<a name="474"><span class="lineNum">     474 </span>            :           }</a>
+<a name="475"><span class="lineNum">     475 </span>            :         }</a>
+<a name="476"><span class="lineNum">     476 </span>            :       } else {</a>
+<a name="477"><span class="lineNum">     477 </span>            :         Pname=aname;</a>
+<a name="478"><span class="lineNum">     478 </span>            :         Pind=aind;</a>
+<a name="479"><span class="lineNum">     479 </span>            :       }</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">      38784 :       if(Pname==atype[j]) {</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">      14544 :         if(Pind0[Pind]==0) {</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :           // adding the atomnumber to the atom/COM list for pairs</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">      14544 :           Plist[j].push_back(anum);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">      14544 :           Pind0[Pind]=aind+1;</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :           oind=Pind;</a>
+<a name="486"><span class="lineNum">     486 </span>            :         }</a>
+<a name="487"><span class="lineNum">     487 </span>            :         // adding the atomnumber to list of atoms for every COM/Atoms</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">      14544 :         comatm[Pind0[Pind]-1].push_back(anum);</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :       }</a>
+<a name="490"><span class="lineNum">     490 </span>            :     }</a>
+<a name="491"><span class="lineNum">     491 </span>            :     // Output Lists</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         24 :     log &lt;&lt; &quot;  Groups of type  &quot; &lt;&lt; j &lt;&lt; &quot;: &quot; &lt;&lt; Plist[j].size() &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :     string gname;</a>
+<a name="494"><span class="lineNum">     494 </span>            :     unsigned gsize;</a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">         24 :     if(com) {</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 :       gname=mypdb.getResidueName(comatm[Pind0[oind]-1][0]);</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :       gsize=comatm[Pind0[oind]-1].size();</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :     } else {</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         48 :       gname=mypdb.getAtomName(comatm[Pind0[oind]-1][0]);</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :       gsize=1;</a>
+<a name="501"><span class="lineNum">     501 </span>            :     }</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         24 :     log.printf(&quot;    %6s %3s %13s %10i %6s\n&quot;, &quot;type  &quot;, gname.c_str(),&quot;   containing &quot;,gsize,&quot; atoms&quot;);</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   }</a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            :   // This is to build the list with all the atoms</a>
+<a name="506"><span class="lineNum">     506 </span>            :   std:: vector&lt;AtomNumber&gt; listall;</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">      19404 :   for (unsigned i=0; i&lt;mypdb.getAtomNumbers().size(); i++) {</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">      19392 :     listall.push_back(mypdb.getAtomNumbers()[i]);</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :   }</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            :   // PIV blocks and Neighbour Lists</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         12 :   Nlist=0;</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :   // Direct adds the A-A ad B-B blocks (N)</a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         12 :   if(direct) {</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">          8 :     Nlist=Nlist+unsigned(Natm);</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :   }</a>
+<a name="517"><span class="lineNum">     517 </span>            :   // Cross adds the A-B blocks (N*(N-1)/2)</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         12 :   if(cross) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          8 :     Nlist=Nlist+unsigned(double(Natm*(Natm-1))/2.);</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :   }</a>
+<a name="521"><span class="lineNum">     521 </span>            :   // Resize vectors according to Nlist</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         12 :   rPIV.resize(Nlist);</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            :   // PIV scaled option</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         12 :   scaling.resize(Nlist);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         36 :   for(unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         24 :     scaling[j]=1.;</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :   }</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         24 :   if(keywords.exists(&quot;SFACTOR&quot;)) {</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         24 :     parseVector(&quot;SFACTOR&quot;,scaling);</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :     //if(scaling.size()!=getNumberOfArguments() &amp;&amp; scaling.size()!=0) error(&quot;not enough values for SFACTOR&quot;);</a>
+<a name="532"><span class="lineNum">     532 </span>            :   }</a>
+<a name="533"><span class="lineNum">     533 </span>            :   // Neighbour Lists option</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">         12 :   parseFlag(&quot;NLIST&quot;,doneigh);</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         12 :   nl.resize(Nlist);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         12 :   nl_skin.resize(Nlist);</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">         12 :   if(doneigh) {</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         12 :     std:: vector&lt;double&gt; nl_cut(Nlist,0.);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         12 :     std:: vector&lt;int&gt; nl_st(Nlist,0);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         12 :     parseVector(&quot;NL_CUTOFF&quot;,nl_cut);</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :     //if(nl_cut.size()!=getNumberOfArguments() &amp;&amp; nl_cut.size()!=0) error(&quot;not enough values for NL_CUTOFF&quot;);</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         12 :     parseVector(&quot;NL_STRIDE&quot;,nl_st);</span></a>
+<a name="543"><span class="lineNum">     543 </span>            :     //if(nl_st.size()!=getNumberOfArguments() &amp;&amp; nl_st.size()!=0) error(&quot;not enough values for NL_STRIDE&quot;);</a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         12 :     parseVector(&quot;NL_SKIN&quot;,nl_skin);</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :     //if(nl_skin.size()!=getNumberOfArguments() &amp;&amp; nl_skin.size()!=0) error(&quot;not enough values for NL_SKIN&quot;);</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         36 :     for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         24 :       if(nl_cut[j]&lt;=0.0) error(&quot;NL_CUTOFF should be explicitly specified and positive&quot;);</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         24 :       if(nl_st[j]&lt;=0) error(&quot;NL_STRIDE should be explicitly specified and positive&quot;);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         24 :       if(nl_skin[j]&lt;=0.) error(&quot;NL_SKIN should be explicitly specified and positive&quot;);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         24 :       nl_cut[j]=nl_cut[j]+nl_skin[j];</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :     }</a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         12 :     log &lt;&lt; &quot;Creating Neighbor Lists \n&quot;;</span></a>
+<a name="553"><span class="lineNum">     553 </span>            :     // WARNING: is nl_cut meaningful here?</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         24 :     nlall= Tools::make_unique&lt;NeighborList&gt;(listall,true,pbc,getPbc(),comm,nl_cut[0],nl_st[0]);</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         12 :     if(com) {</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :       //Build lists of Atoms for every COM</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :       for (unsigned i=0; i&lt;compos.size(); i++) {</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :         // WARNING: is nl_cut meaningful here?</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :         nlcom[i] = Tools::make_unique&lt;NeighborList&gt;(comatm[i],true,pbc,getPbc(),comm,nl_cut[0],nl_st[0]);</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :       }</a>
+<a name="561"><span class="lineNum">     561 </span>            :     }</a>
+<a name="562"><span class="lineNum">     562 </span>            :     unsigned ncnt=0;</a>
+<a name="563"><span class="lineNum">     563 </span>            :     // Direct blocks AA, BB, CC, ...</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         12 :     if(direct) {</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         24 :       for (unsigned j=0; j&lt;Natm; j++) {</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         16 :         nl[ncnt]= Tools::make_unique&lt;NeighborList&gt;(Plist[j],true,pbc,getPbc(),comm,nl_cut[j],nl_st[j]);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         16 :         ncnt+=1;</span></a>
+<a name="568"><span class="lineNum">     568 </span>            :       }</a>
+<a name="569"><span class="lineNum">     569 </span>            :     }</a>
+<a name="570"><span class="lineNum">     570 </span>            :     // Cross blocks AB, AC, BC, ...</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">         12 :     if(cross) {</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         24 :       for (unsigned j=0; j&lt;Natm; j++) {</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         24 :         for (unsigned i=j+1; i&lt;Natm; i++) {</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         16 :           nl[ncnt]= Tools::make_unique&lt;NeighborList&gt;(Plist[i],Plist[j],true,false,pbc,getPbc(),comm,nl_cut[ncnt],nl_st[ncnt]);</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">          8 :           ncnt+=1;</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :         }</a>
+<a name="577"><span class="lineNum">     577 </span>            :       }</a>
+<a name="578"><span class="lineNum">     578 </span>            :     }</a>
+<a name="579"><span class="lineNum">     579 </span>            :   } else {</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;WARNING: Neighbor List not activated this has not been tested!!  \n&quot;;</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :     nlall= Tools::make_unique&lt;NeighborList&gt;(listall,true,pbc,getPbc(),comm);</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 :     for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :       nl[j]= Tools::make_unique&lt;NeighborList&gt;(Plist[j],Plist[j],true,true,pbc,getPbc(),comm);</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :     }</a>
+<a name="585"><span class="lineNum">     585 </span>            :   }</a>
+<a name="586"><span class="lineNum">     586 </span>            :   // Output Nlist</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;Total Nlists: &quot; &lt;&lt; Nlist &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         36 :   for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         24 :     log &lt;&lt; &quot;  list &quot; &lt;&lt; j+1 &lt;&lt; &quot;   size &quot; &lt;&lt; nl[j]-&gt;size() &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :   }</a>
+<a name="591"><span class="lineNum">     591 </span>            :   // Calculate COM masses once and for all from lists</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">         12 :   if(com) {</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;compos.size(); j++) {</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :       double commass=0.;</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;nlcom[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :         unsigned andx=nlcom[j]-&gt;getFullAtomList()[i].index();</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :         commass+=mypdb.getOccupancy()[andx];</span></a>
+<a name="598"><span class="lineNum">     598 </span>            :       }</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;nlcom[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :         unsigned andx=nlcom[j]-&gt;getFullAtomList()[i].index();</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :         if(commass&gt;0.) {</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :           fmass[andx]=mypdb.getOccupancy()[andx]/commass;</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :         } else {</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :           fmass[andx]=1.;</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :         }</a>
+<a name="606"><span class="lineNum">     606 </span>            :       }</a>
+<a name="607"><span class="lineNum">     607 </span>            :     }</a>
+<a name="608"><span class="lineNum">     608 </span>            :   }</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            :   // Sorting</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         12 :   dosort.resize(Nlist);</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         12 :   std:: vector&lt;int&gt; ynsort(Nlist);</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">         12 :   parseVector(&quot;SORT&quot;,ynsort);</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         36 :   for (unsigned i=0; i&lt;Nlist; i++) {</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         24 :     if(ynsort[i]==0||CompDer) {</span></a>
+<a name="616"><span class="lineNum">     616 </span>            :       dosort[i]=false;</a>
+<a name="617"><span class="lineNum">     617 </span>            :     } else {</a>
+<a name="618"><span class="lineNum">     618 </span>            :       dosort[i]=true;</a>
+<a name="619"><span class="lineNum">     619 </span>            :     }</a>
+<a name="620"><span class="lineNum">     620 </span>            :   }</a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span>            :   //build box vectors and correct for pbc</a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;Building the box from PDB data ... \n&quot;;</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">         12 :   Tensor Box=mypdb.getBoxVec();</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;  Done! A,B,C vectors in Cartesian space:  \n&quot;;</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         12 :   log.printf(&quot;  A:  %12.6f%12.6f%12.6f\n&quot;, Box[0][0],Box[0][1],Box[0][2]);</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         12 :   log.printf(&quot;  B:  %12.6f%12.6f%12.6f\n&quot;, Box[1][0],Box[1][1],Box[1][2]);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         12 :   log.printf(&quot;  C:  %12.6f%12.6f%12.6f\n&quot;, Box[2][0],Box[2][1],Box[2][2]);</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;Changing the PBC according to the new box \n&quot;;</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         12 :   Pbc mypbc;</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         12 :   mypbc.setBox(Box);</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">         12 :   log &lt;&lt; &quot;The box volume is &quot; &lt;&lt; mypbc.getBox().determinant() &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            :   //Compute scaling factor</a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">         12 :   if(Svol) {</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         12 :     Fvol=cbrt(Vol0/mypbc.getBox().determinant());</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">         12 :     log &lt;&lt; &quot;Scaling atom distances by  &quot; &lt;&lt; Fvol &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :   } else {</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;Using unscaled atom distances \n&quot;;</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :   }</a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">         12 :   r00.resize(Nlist);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">         12 :   sw.resize(Nlist);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">         36 :   for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">         48 :     if( !parseNumbered( &quot;SWITCH&quot;, j+1, sw[j] ) ) break;</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :   }</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         12 :   if(CompDer) {</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :     // Set switching function parameters here only if computing derivatives</a>
+<a name="649"><span class="lineNum">     649 </span>            :     //   now set at the beginning of the dynamics to solve the r0 issue</a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;Switching Function Parameters \n&quot;;</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">          6 :     sfs.resize(Nlist);</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :     std::string errors;</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">         18 :     for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">         12 :       if(Svol) {</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :         double r0;</a>
+<a name="656"><span class="lineNum">     656 </span>            :         std::string old_r0;</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">         12 :         vector&lt;string&gt; data=Tools::getWords(sw[j]);</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :         data.erase(data.begin());</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">         12 :         Tools::parse(data,&quot;R_0&quot;,old_r0);</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">         12 :         Tools::convert(old_r0,r0);</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         12 :         r0*=Fvol;</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         12 :         std::string new_r0; Tools::convert(r0,new_r0);</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         12 :         std::size_t pos = sw[j].find(&quot;R_0&quot;);</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">         12 :         sw[j].replace(pos+4,old_r0.size(),new_r0);</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">         12 :       }</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">         12 :       sfs[j].set(sw[j],errors);</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :       std::string num;</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">         12 :       Tools::convert(j+1, num);</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">         12 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCH&quot; + num + &quot; keyword : &quot; + errors );</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">         12 :       r00[j]=sfs[j].get_r0();</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">         12 :       log &lt;&lt; &quot;  Swf: &quot; &lt;&lt; j &lt;&lt; &quot;  r0=&quot; &lt;&lt; (sfs[j].description()).c_str() &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :     }</a>
+<a name="673"><span class="lineNum">     673 </span>            :   }</a>
+<a name="674"><span class="lineNum">     674 </span>            : </a>
+<a name="675"><span class="lineNum">     675 </span>            :   // build COMs from positions if requested</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">         12 :   if(com) {</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;compos.size(); j++) {</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :       compos[j][0]=0.;</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :       compos[j][1]=0.;</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :       compos[j][2]=0.;</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;nlcom[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :         unsigned andx=nlcom[j]-&gt;getFullAtomList()[i].index();</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :         compos[j]+=fmass[andx]*mypdb.getPositions()[andx];</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :       }</a>
+<a name="685"><span class="lineNum">     685 </span>            :     }</a>
+<a name="686"><span class="lineNum">     686 </span>            :   }</a>
+<a name="687"><span class="lineNum">     687 </span>            :   // build the rPIV distances (transformation and sorting is done afterwards)</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">         12 :   if(CompDer) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;  PIV  |  block   |     Size      |     Zeros     |     Ones      |&quot; &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :   }</a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         36 :   for(unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">   11516328 :     for(unsigned i=0; i&lt;nl[j]-&gt;size(); i++) {</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">   11516304 :       unsigned i0=(nl[j]-&gt;getClosePairAtomNumber(i).first).index();</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">   11516304 :       unsigned i1=(nl[j]-&gt;getClosePairAtomNumber(i).second).index();</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :       //calculate/get COM position of centers i0 and i1</a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">   11516304 :       Vector Pos0,Pos1;</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">   11516304 :       if(com) {</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :         //if(pbc) makeWhole();</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :         Pos0=compos[i0];</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :         Pos1=compos[i1];</span></a>
+<a name="701"><span class="lineNum">     701 </span>            :       } else {</a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">   11516304 :         Pos0=mypdb.getPositions()[i0];</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">   11516304 :         Pos1=mypdb.getPositions()[i1];</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :       }</a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">   11516304 :       Vector ddist;</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">   11516304 :       if(pbc) {</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">   11516304 :         ddist=mypbc.distance(Pos0,Pos1);</span></a>
+<a name="708"><span class="lineNum">     708 </span>            :       } else {</a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :         ddist=delta(Pos0,Pos1);</span></a>
+<a name="710"><span class="lineNum">     710 </span>            :       }</a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">   11516304 :       double df=0.;</span></a>
+<a name="712"><span class="lineNum">     712 </span>            :       // Transformation and sorting done at the first timestep to solve the r0 definition issue</a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">   11516304 :       if(CompDer) {</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">       1104 :         rPIV[j].push_back(sfs[j].calculate(ddist.modulo()*Fvol, df));</span></a>
+<a name="715"><span class="lineNum">     715 </span>            :       } else {</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">   11515200 :         rPIV[j].push_back(ddist.modulo()*Fvol);</span></a>
+<a name="717"><span class="lineNum">     717 </span>            :       }</a>
+<a name="718"><span class="lineNum">     718 </span>            :     }</a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">         24 :     if(CompDer) {</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">         12 :       if(dosort[j]) {</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineNoCov">          0 :         std::sort(rPIV[j].begin(),rPIV[j].end());</span></a>
+<a name="722"><span class="lineNum">     722 </span>            :       }</a>
+<a name="723"><span class="lineNum">     723 </span>            :       int lmt0=0;</a>
+<a name="724"><span class="lineNum">     724 </span>            :       int lmt1=0;</a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">       1116 :       for(unsigned i=0; i&lt;rPIV[j].size(); i++) {</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">       1104 :         if(int(rPIV[j][i]*double(Nprec-1))==0) {</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :           lmt0+=1;</span></a>
+<a name="728"><span class="lineNum">     728 </span>            :         }</a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">       1104 :         if(int(rPIV[j][i]*double(Nprec-1))==1) {</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineNoCov">          0 :           lmt1+=1;</span></a>
+<a name="731"><span class="lineNum">     731 </span>            :         }</a>
+<a name="732"><span class="lineNum">     732 </span>            :       }</a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">         12 :       log.printf(&quot;       |%10i|%15zu|%15i|%15i|\n&quot;, j, rPIV[j].size(), lmt0, lmt1);</span></a>
+<a name="734"><span class="lineNum">     734 </span>            :     }</a>
+<a name="735"><span class="lineNum">     735 </span>            :   }</a>
+<a name="736"><span class="lineNum">     736 </span>            : </a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">         12 :   checkRead();</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :   // From the plumed manual on how to build-up a new Colvar</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">         12 :   addValueWithDerivatives();</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">         12 :   requestAtoms(nlall-&gt;getFullAtomList());</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">         12 :   setNotPeriodic();</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :   // getValue()-&gt;setPeridodicity(false);</a>
+<a name="743"><span class="lineNum">     743 </span>            :   // set size of derivative vector</a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">         12 :   m_deriv.resize(getNumberOfAtoms());</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">         12 : }</span></a>
+<a name="746"><span class="lineNum">     746 </span>            : </a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">        327 : void PIV::calculate()</span></a>
+<a name="748"><span class="lineNum">     748 </span>            : {</a>
+<a name="749"><span class="lineNum">     749 </span>            : </a>
+<a name="750"><span class="lineNum">     750 </span>            :   // Local variables</a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineCov">        327 :   if(sharedData_unique) {</span></a>
+<a name="753"><span class="lineNum">     753 </span>            :     // This is executed by the first PIV instance.</a>
+<a name="754"><span class="lineNum">     754 </span>            :     // We initialize variables with the correct Nlist.</a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">        321 :     sharedData_unique-&gt;prev_pos.resize(Nlist);</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">        321 :     sharedData_unique-&gt;cPIV.resize(Nlist);</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">        321 :     sharedData_unique-&gt;Atom0.resize(Nlist);</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">        321 :     sharedData_unique-&gt;Atom1.resize(Nlist);</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :   }</a>
+<a name="760"><span class="lineNum">     760 </span>            : </a>
+<a name="761"><span class="lineNum">     761 </span>            :   // create references to minimize the impact of the code below</a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">        327 :   auto &amp; prev_stp(sharedData-&gt;prev_stp);</span></a>
+<a name="763"><span class="lineNum">     763 </span>            :   auto &amp; init_stp(sharedData-&gt;init_stp);</a>
+<a name="764"><span class="lineNum">     764 </span>            :   auto &amp; prev_pos(sharedData-&gt;prev_pos);</a>
+<a name="765"><span class="lineNum">     765 </span>            :   auto &amp; cPIV(sharedData-&gt;cPIV);</a>
+<a name="766"><span class="lineNum">     766 </span>            :   auto &amp; Atom0(sharedData-&gt;Atom0);</a>
+<a name="767"><span class="lineNum">     767 </span>            :   auto &amp; Atom1(sharedData-&gt;Atom1);</a>
+<a name="768"><span class="lineNum">     768 </span>            : </a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">        327 :   std:: vector&lt;std:: vector&lt;int&gt; &gt; A0(Nprec);</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">        327 :   std:: vector&lt;std:: vector&lt;int&gt; &gt; A1(Nprec);</span></a>
+<a name="771"><span class="lineNum">     771 </span>            :   size_t stride=1;</a>
+<a name="772"><span class="lineNum">     772 </span>            :   unsigned rank=0;</a>
+<a name="773"><span class="lineNum">     773 </span>            : </a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">        327 :   if(!serial) {</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">        327 :     stride=comm.Get_size();</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">        327 :     rank=comm.Get_rank();</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :   } else {</a>
+<a name="778"><span class="lineNum">     778 </span>            :     stride=1;</a>
+<a name="779"><span class="lineNum">     779 </span>            :     rank=0;</a>
+<a name="780"><span class="lineNum">     780 </span>            :   }</a>
+<a name="781"><span class="lineNum">     781 </span>            : </a>
+<a name="782"><span class="lineNum">     782 </span>            :   // Transform (and sort) the rPIV before starting the dynamics</a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">        327 :   if (((prev_stp==-1) || (init_stp==1)) &amp;&amp;!CompDer) {</span></a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">          6 :     if(prev_stp!=-1) {init_stp=0;}</span></a>
+<a name="785"><span class="lineNum">     785 </span>            :     // Calculate the volume scaling factor</a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">          6 :     if(Svol) {</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">          6 :       Fvol=cbrt(Vol0/getBox().determinant());</span></a>
+<a name="788"><span class="lineNum">     788 </span>            :     }</a>
+<a name="789"><span class="lineNum">     789 </span>            :     //Set switching function parameters</a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;REFERENCE PDB # &quot; &lt;&lt; prev_stp+2 &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="792"><span class="lineNum">     792 </span>            :     // Set switching function parameters here only if computing derivatives</a>
+<a name="793"><span class="lineNum">     793 </span>            :     //   now set at the beginning of the dynamics to solve the r0 issue</a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;Switching Function Parameters \n&quot;;</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">          6 :     sfs.resize(Nlist);</span></a>
+<a name="796"><span class="lineNum">     796 </span>            :     std::string errors;</a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">         18 :     for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">         12 :       if(Svol) {</span></a>
+<a name="799"><span class="lineNum">     799 </span>            :         double r0;</a>
+<a name="800"><span class="lineNum">     800 </span>            :         std::string old_r0;</a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">         12 :         vector&lt;string&gt; data=Tools::getWords(sw[j]);</span></a>
+<a name="802"><span class="lineNum">     802 </span>            :         data.erase(data.begin());</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">         12 :         Tools::parse(data,&quot;R_0&quot;,old_r0);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">         12 :         Tools::convert(old_r0,r0);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">         12 :         r0*=Fvol;</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">         12 :         std::string new_r0; Tools::convert(r0,new_r0);</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">         12 :         std::size_t pos = sw[j].find(&quot;R_0&quot;);</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">         12 :         sw[j].replace(pos+4,old_r0.size(),new_r0);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">         12 :       }</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">         12 :       sfs[j].set(sw[j],errors);</span></a>
+<a name="811"><span class="lineNum">     811 </span>            :       std::string num;</a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         12 :       Tools::convert(j+1, num);</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         12 :       if( errors.length()!=0 ) error(&quot;problem reading SWITCH&quot; + num + &quot; keyword : &quot; + errors );</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         12 :       r00[j]=sfs[j].get_r0();</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">         12 :       log &lt;&lt; &quot;  Swf: &quot; &lt;&lt; j &lt;&lt; &quot;  r0=&quot; &lt;&lt; (sfs[j].description()).c_str() &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="816"><span class="lineNum">     816 </span>            :     }</a>
+<a name="817"><span class="lineNum">     817 </span>            :     //Transform and sort</a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;Building Reference PIV Vector \n&quot;;</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;  PIV  |  block   |     Size      |     Zeros     |     Ones      |&quot; &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">          6 :     double df=0.;</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">         18 :     for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">   11515212 :       for (unsigned i=0; i&lt;rPIV[j].size(); i++) {</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">   11515200 :         rPIV[j][i]=sfs[j].calculate(rPIV[j][i], df);</span></a>
+<a name="824"><span class="lineNum">     824 </span>            :       }</a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">         12 :       if(dosort[j]) {</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         12 :         std::sort(rPIV[j].begin(),rPIV[j].end());</span></a>
+<a name="827"><span class="lineNum">     827 </span>            :       }</a>
+<a name="828"><span class="lineNum">     828 </span>            :       int lmt0=0;</a>
+<a name="829"><span class="lineNum">     829 </span>            :       int lmt1=0;</a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">   11515212 :       for(unsigned i=0; i&lt;rPIV[j].size(); i++) {</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">   11515200 :         if(int(rPIV[j][i]*double(Nprec-1))==0) {</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">         26 :           lmt0+=1;</span></a>
+<a name="833"><span class="lineNum">     833 </span>            :         }</a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">   11515200 :         if(int(rPIV[j][i]*double(Nprec-1))==1) {</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">      63358 :           lmt1+=1;</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :         }</a>
+<a name="837"><span class="lineNum">     837 </span>            :       }</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">         12 :       log.printf(&quot;       |%10i|%15zu|%15i|%15i|\n&quot;, j, rPIV[j].size(), lmt0, lmt1);</span></a>
+<a name="839"><span class="lineNum">     839 </span>            :     }</a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">          6 :     log &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :   }</a>
+<a name="842"><span class="lineNum">     842 </span>            :   // Do the sorting only once per timestep to avoid building the PIV N times for N rPIV PDB structures!</a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">        327 :   if ((getStep()&gt;prev_stp&amp;&amp;getStep()%updatePIV==0)||CompDer) {</span></a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">        324 :     if (CompDer) log &lt;&lt; &quot; Step &quot; &lt;&lt; getStep() &lt;&lt; &quot;  Computing Derivatives NON-SORTED PIV \n&quot;;</span></a>
+<a name="845"><span class="lineNum">     845 </span>            :     //</a>
+<a name="846"><span class="lineNum">     846 </span>            :     // build COMs from positions if requested</a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">        324 :     if(com) {</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineNoCov">          0 :       if(pbc) makeWhole();</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;compos.size(); j++) {</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineNoCov">          0 :         compos[j][0]=0.;</span></a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineNoCov">          0 :         compos[j][1]=0.;</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineNoCov">          0 :         compos[j][2]=0.;</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;nlcom[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineNoCov">          0 :           unsigned andx=nlcom[j]-&gt;getFullAtomList()[i].index();</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineNoCov">          0 :           compos[j]+=fmass[andx]*getPosition(andx);</span></a>
+<a name="856"><span class="lineNum">     856 </span>            :         }</a>
+<a name="857"><span class="lineNum">     857 </span>            :       }</a>
+<a name="858"><span class="lineNum">     858 </span>            :     }</a>
+<a name="859"><span class="lineNum">     859 </span>            :     // update neighbor lists when an atom moves out of the Neighbor list skin</a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">        324 :     if (doneigh) {</span></a>
+<a name="861"><span class="lineNum">     861 </span>            :       bool doupdate=false;</a>
+<a name="862"><span class="lineNum">     862 </span>            :       // For the first step build previous positions = actual positions</a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">        324 :       if (prev_stp==-1) {</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">          6 :         bool docom=com;</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">         18 :         for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">       9708 :           for (unsigned i=0; i&lt;nl[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">       9696 :             Vector Pos;</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">       9696 :             if(docom) {</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineNoCov">          0 :               Pos=compos[i];</span></a>
+<a name="870"><span class="lineNum">     870 </span>            :             } else {</a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">       9696 :               Pos=getPosition(nl[j]-&gt;getFullAtomList()[i].index());</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :             }</a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">       9696 :             prev_pos[j].push_back(Pos);</span></a>
+<a name="874"><span class="lineNum">     874 </span>            :           }</a>
+<a name="875"><span class="lineNum">     875 </span>            :         }</a>
+<a name="876"><span class="lineNum">     876 </span>            :         doupdate=true;</a>
+<a name="877"><span class="lineNum">     877 </span>            :       }</a>
+<a name="878"><span class="lineNum">     878 </span>            :       // Decide whether to update lists based on atom displacement, every stride</a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">        324 :       std:: vector&lt;std:: vector&lt;Vector&gt; &gt; tmp_pos(Nlist);</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">        324 :       if (getStep() % nlall-&gt;getStride() ==0) {</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">        324 :         bool docom=com;</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">        972 :         for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">      20520 :           for (unsigned i=0; i&lt;nl[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">      19872 :             Vector Pos;</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">      19872 :             if(docom) {</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineNoCov">          0 :               Pos=compos[i];</span></a>
+<a name="887"><span class="lineNum">     887 </span>            :             } else {</a>
+<a name="888"><span class="lineNum">     888 </span><span class="lineCov">      19872 :               Pos=getPosition(nl[j]-&gt;getFullAtomList()[i].index());</span></a>
+<a name="889"><span class="lineNum">     889 </span>            :             }</a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">      19872 :             tmp_pos[j].push_back(Pos);</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">      19872 :             if (pbcDistance(tmp_pos[j][i],prev_pos[j][i]).modulo()&gt;=nl_skin[j]) {</span></a>
+<a name="892"><span class="lineNum">     892 </span>            :               doupdate=true;</a>
+<a name="893"><span class="lineNum">     893 </span>            :             }</a>
+<a name="894"><span class="lineNum">     894 </span>            :           }</a>
+<a name="895"><span class="lineNum">     895 </span>            :         }</a>
+<a name="896"><span class="lineNum">     896 </span>            :       }</a>
+<a name="897"><span class="lineNum">     897 </span>            :       // Update Nlists if needed</a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">        324 :       if (doupdate==true) {</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">         18 :         for (unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineCov">       9708 :           for (unsigned i=0; i&lt;nl[j]-&gt;getFullAtomList().size(); i++) {</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineCov">       9696 :             prev_pos[j][i]=tmp_pos[j][i];</span></a>
+<a name="902"><span class="lineNum">     902 </span>            :           }</a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">         12 :           nl[j]-&gt;update(prev_pos[j]);</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">         12 :           log &lt;&lt; &quot; Step &quot; &lt;&lt; getStep() &lt;&lt; &quot;  Neighbour lists updated &quot; &lt;&lt; nl[j]-&gt;size() &lt;&lt; &quot; \n&quot;;</span></a>
+<a name="905"><span class="lineNum">     905 </span>            :         }</a>
+<a name="906"><span class="lineNum">     906 </span>            :       }</a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">        324 :     }</span></a>
+<a name="908"><span class="lineNum">     908 </span>            :     // Calculate the volume scaling factor</a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">        324 :     if(Svol) {</span></a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">        324 :       Fvol=cbrt(Vol0/getBox().determinant());</span></a>
+<a name="911"><span class="lineNum">     911 </span>            :     }</a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">        324 :     Vector ddist;</span></a>
+<a name="913"><span class="lineNum">     913 </span>            :     // Global to local variables</a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">        324 :     bool doserial=serial;</span></a>
+<a name="915"><span class="lineNum">     915 </span>            :     // Build &quot;Nlist&quot; PIV blocks</a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">        972 :     for(unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">        648 :       if(dosort[j]) {</span></a>
+<a name="918"><span class="lineNum">     918 </span>            :         // from global to local variables to speedup the for loop with if statements</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">          6 :         bool docom=com;</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">          6 :         bool dopbc=pbc;</span></a>
+<a name="921"><span class="lineNum">     921 </span>            :         // Vectors collecting occupancies: OrdVec one rank, OrdVecAll all ranks</a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">          6 :         std:: vector&lt;int&gt; OrdVec(Nprec,0);</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">          6 :         cPIV[j].resize(0);</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">          6 :         Atom0[j].resize(0);</span></a>
+<a name="925"><span class="lineNum">     925 </span><span class="lineCov">          6 :         Atom1[j].resize(0);</span></a>
+<a name="926"><span class="lineNum">     926 </span>            :         // Building distances for the PIV vector at time t</a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">          9 :         if(timer) stopwatch.start(&quot;1 Build cPIV&quot;);</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">    5757606 :         for(unsigned i=rank; i&lt;nl[j]-&gt;size(); i+=stride) {</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">    5757600 :           unsigned i0=(nl[j]-&gt;getClosePairAtomNumber(i).first).index();</span></a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">    5757600 :           unsigned i1=(nl[j]-&gt;getClosePairAtomNumber(i).second).index();</span></a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">    5757600 :           Vector Pos0,Pos1;</span></a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">    5757600 :           if(docom) {</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineNoCov">          0 :             Pos0=compos[i0];</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineNoCov">          0 :             Pos1=compos[i1];</span></a>
+<a name="935"><span class="lineNum">     935 </span>            :           } else {</a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">    5757600 :             Pos0=getPosition(i0);</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">    5757600 :             Pos1=getPosition(i1);</span></a>
+<a name="938"><span class="lineNum">     938 </span>            :           }</a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">    5757600 :           if(dopbc) {</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">    5757600 :             ddist=pbcDistance(Pos0,Pos1);</span></a>
+<a name="941"><span class="lineNum">     941 </span>            :           } else {</a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineNoCov">          0 :             ddist=delta(Pos0,Pos1);</span></a>
+<a name="943"><span class="lineNum">     943 </span>            :           }</a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">    5757600 :           double df=0.;</span></a>
+<a name="945"><span class="lineNum">     945 </span>            :           //Integer sorting ... faster!</a>
+<a name="946"><span class="lineNum">     946 </span>            :           //Transforming distances with the Switching function + real to integer transformation</a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">    5757600 :           int Vint=int(sfs[j].calculate(ddist.modulo()*Fvol, df)*double(Nprec-1)+0.5);</span></a>
+<a name="948"><span class="lineNum">     948 </span>            :           //Integer transformed distance values as index of the Ordering Vector OrdVec</a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">    5757600 :           OrdVec[Vint]+=1;</span></a>
+<a name="950"><span class="lineNum">     950 </span>            :           //Keeps track of atom indices for force and virial calculations</a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">    5757600 :           A0[Vint].push_back(i0);</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">    5757600 :           A1[Vint].push_back(i1);</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :         }</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">          9 :         if(timer) stopwatch.stop(&quot;1 Build cPIV&quot;);</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">          9 :         if(timer) stopwatch.start(&quot;2 Sort cPIV&quot;);</span></a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineCov">          6 :         if(!doserial &amp;&amp; comm.initialized()) {</span></a>
+<a name="957"><span class="lineNum">     957 </span>            :           // Vectors keeping track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.</a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineNoCov">          0 :           std:: vector&lt;int&gt; Vdim(stride,0);</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineNoCov">          0 :           std:: vector&lt;int&gt; Vpos(stride,0);</span></a>
+<a name="960"><span class="lineNum">     960 </span>            :           // Vectors collecting occupancies: OrdVec one rank, OrdVecAll all ranks</a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineNoCov">          0 :           std:: vector&lt;int&gt; OrdVecAll(stride*Nprec);</span></a>
+<a name="962"><span class="lineNum">     962 </span>            :           // Big vectors containing all Atom indexes for every occupancy (Atom0O(Nprec,n) and Atom1O(Nprec,n) matrices in one vector)</a>
+<a name="963"><span class="lineNum">     963 </span>            :           std:: vector&lt;int&gt; Atom0F;</a>
+<a name="964"><span class="lineNum">     964 </span>            :           std:: vector&lt;int&gt; Atom1F;</a>
+<a name="965"><span class="lineNum">     965 </span>            :           // Vector used to reconstruct arrays</a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineNoCov">          0 :           std:: vector&lt;unsigned&gt; k(stride,0);</span></a>
+<a name="967"><span class="lineNum">     967 </span>            :           // Zeros might be many, this slows down a lot due to MPI communication</a>
+<a name="968"><span class="lineNum">     968 </span>            :           // Avoid passing the zeros (i=1) for atom indices</a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineNoCov">          0 :           for(unsigned i=1; i&lt;Nprec; i++) {</span></a>
+<a name="970"><span class="lineNum">     970 </span>            :             // Building long vectors with all atom indexes for occupancies ordered from i=1 to i=Nprec-1</a>
+<a name="971"><span class="lineNum">     971 </span>            :             // Can this be avoided ???</a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineNoCov">          0 :             Atom0F.insert(Atom0F.end(),A0[i].begin(),A0[i].end());</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineNoCov">          0 :             Atom1F.insert(Atom1F.end(),A1[i].begin(),A1[i].end());</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineNoCov">          0 :             A0[i].resize(0);</span></a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineNoCov">          0 :             A1[i].resize(0);</span></a>
+<a name="976"><span class="lineNum">     976 </span>            :           }</a>
+<a name="977"><span class="lineNum">     977 </span>            :           // Resize partial arrays to fill up for the next PIV block</a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineNoCov">          0 :           A0[0].resize(0);</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineNoCov">          0 :           A1[0].resize(0);</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineNoCov">          0 :           A0[Nprec-1].resize(0);</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineNoCov">          0 :           A1[Nprec-1].resize(0);</span></a>
+<a name="982"><span class="lineNum">     982 </span>            :           // Avoid passing the zeros (i=1) for atom indices</a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineNoCov">          0 :           OrdVec[0]=0;</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineNoCov">          0 :           OrdVec[Nprec-1]=0;</span></a>
+<a name="985"><span class="lineNum">     985 </span>            : </a>
+<a name="986"><span class="lineNum">     986 </span>            :           // Wait for all ranks before communication of Vectors</a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineNoCov">          0 :           comm.Barrier();</span></a>
+<a name="988"><span class="lineNum">     988 </span>            : </a>
+<a name="989"><span class="lineNum">     989 </span>            :           // pass the array sizes before passing the arrays</a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineNoCov">          0 :           int dim=Atom0F.size();</span></a>
+<a name="991"><span class="lineNum">     991 </span>            :           // Vdim and Vpos keep track of the dimension and the starting-position of the rank-specific pair vector in the big pair vector.</a>
+<a name="992"><span class="lineNum">     992 </span><span class="lineNoCov">          0 :           comm.Allgather(&amp;dim,1,&amp;Vdim[0],1);</span></a>
+<a name="993"><span class="lineNum">     993 </span>            : </a>
+<a name="994"><span class="lineNum">     994 </span>            :           // TO BE IMPROVED: the following may be done by the rank 0 (now every rank does it)</a>
+<a name="995"><span class="lineNum">     995 </span>            :           int Fdim=0;</a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineNoCov">          0 :           for(unsigned i=1; i&lt;stride; i++) {</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineNoCov">          0 :             Vpos[i]=Vpos[i-1]+Vdim[i-1];</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineNoCov">          0 :             Fdim+=Vdim[i];</span></a>
+<a name="999"><span class="lineNum">     999 </span>            :           }</a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineNoCov">          0 :           Fdim+=Vdim[0];</span></a>
+<a name="1001"><span class="lineNum">    1001 </span>            :           // build big vectors for atom pairs on all ranks for all ranks</a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineNoCov">          0 :           std:: vector&lt;int&gt; Atom0FAll(Fdim);</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineNoCov">          0 :           std:: vector&lt;int&gt; Atom1FAll(Fdim);</span></a>
+<a name="1004"><span class="lineNum">    1004 </span>            :           // TO BE IMPROVED: Allgathers may be substituted by gathers by proc 0</a>
+<a name="1005"><span class="lineNum">    1005 </span>            :           //   Moreover vectors are gathered head-to-tail and assembled later-on in a serial step.</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :           // Gather the full Ordering Vector (occupancies). This is what we need to build the PIV</a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :           comm.Allgather(&amp;OrdVec[0],Nprec,&amp;OrdVecAll[0],Nprec);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span>            :           // Gather the vectors of atom pairs to keep track of the idexes for the forces</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineNoCov">          0 :           comm.Allgatherv(Atom0F.data(),Atom0F.size(),&amp;Atom0FAll[0],&amp;Vdim[0],&amp;Vpos[0]);</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineNoCov">          0 :           comm.Allgatherv(Atom1F.data(),Atom1F.size(),&amp;Atom1FAll[0],&amp;Vdim[0],&amp;Vpos[0]);</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            : </a>
+<a name="1012"><span class="lineNum">    1012 </span>            :           // Reconstruct the full vectors from collections of Allgathered parts (this is a serial step)</a>
+<a name="1013"><span class="lineNum">    1013 </span>            :           // This is the tricky serial step, to assemble together PIV and atom-pair info from head-tail big vectors</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :           // Loop before on l and then on i would be better but the allgather should be modified</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :           // Loop on blocks</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :           //for(unsigned m=0;m&lt;Nlist;m++) {</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :           // Loop on Ordering Vector size excluding zeros (i=1)</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineNoCov">          0 :           if(timer) stopwatch.stop(&quot;2 Sort cPIV&quot;);</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineNoCov">          0 :           if(timer) stopwatch.start(&quot;3 Reconstruct cPIV&quot;);</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineNoCov">          0 :           for(unsigned i=1; i&lt;Nprec; i++) {</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            :             // Loop on the ranks</a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;stride; l++) {</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            :               // Loop on the number of head-to-tail pieces</a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineNoCov">          0 :               for(unsigned m=0; m&lt;OrdVecAll[i+l*Nprec]; m++) {</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :                 // cPIV is the current PIV at time t</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineNoCov">          0 :                 cPIV[j].push_back(double(i)/double(Nprec-1));</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineNoCov">          0 :                 Atom0[j].push_back(Atom0FAll[k[l]+Vpos[l]]);</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineNoCov">          0 :                 Atom1[j].push_back(Atom1FAll[k[l]+Vpos[l]]);</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineNoCov">          0 :                 k[l]+=1;</span></a>
+<a name="1030"><span class="lineNum">    1030 </span>            :               }</a>
+<a name="1031"><span class="lineNum">    1031 </span>            :             }</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :           }</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineNoCov">          0 :           if(timer) stopwatch.stop(&quot;3 Reconstruct cPIV&quot;);</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :         } else {</a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">    6000000 :           for(unsigned i=1; i&lt;Nprec; i++) {</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">   11757594 :             for(unsigned m=0; m&lt;OrdVec[i]; m++) {</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">    5757600 :               cPIV[j].push_back(double(i)/double(Nprec-1));</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">    5757600 :               Atom0[j].push_back(A0[i][m]);</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">    5757600 :               Atom1[j].push_back(A1[i][m]);</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :             }</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :           }</a>
+<a name="1042"><span class="lineNum">    1042 </span>            :         }</a>
+<a name="1043"><span class="lineNum">    1043 </span>            :       }</a>
+<a name="1044"><span class="lineNum">    1044 </span>            :     }</a>
+<a name="1045"><span class="lineNum">    1045 </span>            :   }</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">        327 :   Vector distance;</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">        327 :   double dfunc=0.;</span></a>
+<a name="1048"><span class="lineNum">    1048 </span>            :   // Calculate volume scaling factor</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">        327 :   if(Svol) {</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">        327 :     Fvol=cbrt(Vol0/getBox().determinant());</span></a>
+<a name="1051"><span class="lineNum">    1051 </span>            :   }</a>
+<a name="1052"><span class="lineNum">    1052 </span>            : </a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   // This test may be run by specifying the TEST keyword as input, it pritnts rPIV and cPIV and quits</a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">        327 :   if(test) {</span></a>
+<a name="1055"><span class="lineNum">    1055 </span>            :     unsigned limit=0;</a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineNoCov">          0 :       if(dosort[j]) {</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineNoCov">          0 :         limit = cPIV[j].size();</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :       } else {</a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineNoCov">          0 :         limit = rPIV[j].size();</span></a>
+<a name="1061"><span class="lineNum">    1061 </span>            :       }</a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineNoCov">          0 :       log.printf(&quot;PIV Block:  %6i %12s %6i \n&quot;, j, &quot;      Size:&quot;, limit);</span></a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineNoCov">          0 :       log.printf(&quot;%6s%6s%12s%12s%36s\n&quot;,&quot;     i&quot;,&quot;     j&quot;, &quot;    c-PIV   &quot;,&quot;    r-PIV   &quot;,&quot;   i-j distance vector       &quot;);</span></a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;limit; i++) {</span></a>
+<a name="1065"><span class="lineNum">    1065 </span>            :         unsigned i0=0;</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :         unsigned i1=0;</a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineNoCov">          0 :         if(dosort[j]) {</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineNoCov">          0 :           i0=Atom0[j][i];</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineNoCov">          0 :           i1=Atom1[j][i];</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            :         } else {</a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineNoCov">          0 :           i0=(nl[j]-&gt;getClosePairAtomNumber(i).first).index();</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineNoCov">          0 :           i1=(nl[j]-&gt;getClosePairAtomNumber(i).second).index();</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :         }</a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineNoCov">          0 :         Vector Pos0,Pos1;</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineNoCov">          0 :         if(com) {</span></a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineNoCov">          0 :           Pos0=compos[i0];</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineNoCov">          0 :           Pos1=compos[i1];</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            :         } else {</a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineNoCov">          0 :           Pos0=getPosition(i0);</span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineNoCov">          0 :           Pos1=getPosition(i1);</span></a>
+<a name="1081"><span class="lineNum">    1081 </span>            :         }</a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineNoCov">          0 :         if(pbc) {</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineNoCov">          0 :           distance=pbcDistance(Pos0,Pos1);</span></a>
+<a name="1084"><span class="lineNum">    1084 </span>            :         } else {</a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineNoCov">          0 :           distance=delta(Pos0,Pos1);</span></a>
+<a name="1086"><span class="lineNum">    1086 </span>            :         }</a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineNoCov">          0 :         dfunc=0.;</span></a>
+<a name="1088"><span class="lineNum">    1088 </span>            :         double cP,rP;</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :         if(dosort[j]) {</span></a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineNoCov">          0 :           cP = cPIV[j][i];</span></a>
+<a name="1091"><span class="lineNum">    1091 </span><span class="lineNoCov">          0 :           rP = rPIV[j][rPIV[j].size()-cPIV[j].size()+i];</span></a>
+<a name="1092"><span class="lineNum">    1092 </span>            :         } else {</a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineNoCov">          0 :           double dm=distance.modulo();</span></a>
+<a name="1094"><span class="lineNum">    1094 </span><span class="lineNoCov">          0 :           cP = sfs[j].calculate(dm*Fvol, dfunc);</span></a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineNoCov">          0 :           rP = rPIV[j][i];</span></a>
+<a name="1096"><span class="lineNum">    1096 </span>            :         }</a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineNoCov">          0 :         log.printf(&quot;%6i%6i%12.6f%12.6f%12.6f%12.6f%12.6f\n&quot;,i0,i1,cP,rP,distance[0],distance[1],distance[2]);</span></a>
+<a name="1098"><span class="lineNum">    1098 </span>            :       }</a>
+<a name="1099"><span class="lineNum">    1099 </span>            :     }</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineNoCov">          0 :     log.printf(&quot;This was a test, now exit \n&quot;);</span></a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineNoCov">          0 :     exit();</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   }</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : </a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">        328 :   if(timer) stopwatch.start(&quot;4 Build For Derivatives&quot;);</span></a>
+<a name="1105"><span class="lineNum">    1105 </span>            :   // non-global variables Nder and Scalevol defined to speedup if structures in cycles</a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">        327 :   bool Nder=CompDer;</span></a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">        327 :   bool Scalevol=Svol;</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">        327 :   if(getStep()%updatePIV==0) {</span></a>
+<a name="1109"><span class="lineNum">    1109 </span>            :     // set to zero PIVdistance, derivatives and virial when they are calculated</a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">      29799 :     for(unsigned j=0; j&lt;m_deriv.size(); j++) {</span></a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">     117888 :       for(unsigned k=0; k&lt;3; k++) {m_deriv[j][k]=0.;}</span></a>
+<a name="1112"><span class="lineNum">    1112 </span>            :     }</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">       1308 :     for(unsigned j=0; j&lt;3; j++) {</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">       3924 :       for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">       2943 :         m_virial[j][k]=0.;</span></a>
+<a name="1116"><span class="lineNum">    1116 </span>            :       }</a>
+<a name="1117"><span class="lineNum">    1117 </span>            :     }</a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">        327 :     m_PIVdistance=0.;</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            :     // Re-compute atomic distances for derivatives and compute PIV-PIV distance</a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">        981 :     for(unsigned j=0; j&lt;Nlist; j++) {</span></a>
+<a name="1121"><span class="lineNum">    1121 </span>            :       unsigned limit=0;</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :       // dosorting definition is to speedup if structure in cycles with non-global variables</a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">        654 :       bool dosorting=dosort[j];</span></a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">        654 :       bool docom=com;</span></a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">        654 :       bool dopbc=pbc;</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">        654 :       if(dosorting) {</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">         12 :         limit = cPIV[j].size();</span></a>
+<a name="1128"><span class="lineNum">    1128 </span>            :       } else {</a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">        642 :         limit = rPIV[j].size();</span></a>
+<a name="1130"><span class="lineNum">    1130 </span>            :       }</a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">   11574918 :       for(unsigned i=rank; i&lt;limit; i+=stride) {</span></a>
+<a name="1132"><span class="lineNum">    1132 </span>            :         unsigned i0=0;</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :         unsigned i1=0;</a>
+<a name="1134"><span class="lineNum">    1134 </span><span class="lineCov">   11574264 :         if(dosorting) {</span></a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">   11515200 :           i0=Atom0[j][i];</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">   11515200 :           i1=Atom1[j][i];</span></a>
+<a name="1137"><span class="lineNum">    1137 </span>            :         } else {</a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">      59064 :           i0=(nl[j]-&gt;getClosePairAtomNumber(i).first).index();</span></a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">      59064 :           i1=(nl[j]-&gt;getClosePairAtomNumber(i).second).index();</span></a>
+<a name="1140"><span class="lineNum">    1140 </span>            :         }</a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineCov">   11574264 :         Vector Pos0,Pos1;</span></a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">   11574264 :         if(docom) {</span></a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineNoCov">          0 :           Pos0=compos[i0];</span></a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineNoCov">          0 :           Pos1=compos[i1];</span></a>
+<a name="1145"><span class="lineNum">    1145 </span>            :         } else {</a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">   11574264 :           Pos0=getPosition(i0);</span></a>
+<a name="1147"><span class="lineNum">    1147 </span><span class="lineCov">   11574264 :           Pos1=getPosition(i1);</span></a>
+<a name="1148"><span class="lineNum">    1148 </span>            :         }</a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">   11574264 :         if(dopbc) {</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">   11574264 :           distance=pbcDistance(Pos0,Pos1);</span></a>
+<a name="1151"><span class="lineNum">    1151 </span>            :         } else {</a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineNoCov">          0 :           distance=delta(Pos0,Pos1);</span></a>
+<a name="1153"><span class="lineNum">    1153 </span>            :         }</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">   11574264 :         dfunc=0.;</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :         // this is needed for dfunc and dervatives</a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">   11574264 :         double dm=distance.modulo();</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">   11574264 :         double tPIV = sfs[j].calculate(dm*Fvol, dfunc);</span></a>
+<a name="1158"><span class="lineNum">    1158 </span>            :         // PIV distance</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :         double coord=0.;</a>
+<a name="1160"><span class="lineNum">    1160 </span><span class="lineCov">   11574264 :         if(!dosorting||Nder) {</span></a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">      59064 :           coord = tPIV - rPIV[j][i];</span></a>
+<a name="1162"><span class="lineNum">    1162 </span>            :         } else {</a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">   11515200 :           coord = cPIV[j][i] - rPIV[j][rPIV[j].size()-cPIV[j].size()+i];</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :         }</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :         // Calculate derivatives, virial, and variable=sum_j (scaling[j] *(cPIV-rPIV)_j^2)</a>
+<a name="1166"><span class="lineNum">    1166 </span>            :         // WARNING: dfunc=dswf/(Fvol*dm)  (this may change in future Plumed versions)</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">   11574264 :         double tmp = 2.*scaling[j]*coord*Fvol*Fvol*dfunc;</span></a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineCov">   11574264 :         Vector tmpder = tmp*distance;</span></a>
+<a name="1169"><span class="lineNum">    1169 </span>            :         // 0.5*(x_i-x_k)*f_ik         (force on atom k due to atom i)</a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">   11574264 :         if(docom) {</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineNoCov">          0 :           Vector dist;</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :           for(unsigned k=0; k&lt;nlcom[i0]-&gt;getFullAtomList().size(); k++) {</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineNoCov">          0 :             unsigned x0=nlcom[i0]-&gt;getFullAtomList()[k].index();</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineNoCov">          0 :             m_deriv[x0] -= tmpder*fmass[x0];</span></a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;3; l++) {</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineNoCov">          0 :               dist[l]=0.;</span></a>
+<a name="1177"><span class="lineNum">    1177 </span>            :             }</a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineNoCov">          0 :             Vector P0=getPosition(x0);</span></a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;nlcom[i0]-&gt;getFullAtomList().size(); l++) {</span></a>
+<a name="1180"><span class="lineNum">    1180 </span><span class="lineNoCov">          0 :               unsigned x1=nlcom[i0]-&gt;getFullAtomList()[l].index();</span></a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineNoCov">          0 :               Vector P1=getPosition(x1);</span></a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineNoCov">          0 :               if(dopbc) {</span></a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineNoCov">          0 :                 dist+=pbcDistance(P0,P1);</span></a>
+<a name="1184"><span class="lineNum">    1184 </span>            :               } else {</a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineNoCov">          0 :                 dist+=delta(P0,P1);</span></a>
+<a name="1186"><span class="lineNum">    1186 </span>            :               }</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :             }</a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;nlcom[i1]-&gt;getFullAtomList().size(); l++) {</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineNoCov">          0 :               unsigned x1=nlcom[i1]-&gt;getFullAtomList()[l].index();</span></a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineNoCov">          0 :               Vector P1=getPosition(x1);</span></a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineNoCov">          0 :               if(dopbc) {</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineNoCov">          0 :                 dist+=pbcDistance(P0,P1);</span></a>
+<a name="1193"><span class="lineNum">    1193 </span>            :               } else {</a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineNoCov">          0 :                 dist+=delta(P0,P1);</span></a>
+<a name="1195"><span class="lineNum">    1195 </span>            :               }</a>
+<a name="1196"><span class="lineNum">    1196 </span>            :             }</a>
+<a name="1197"><span class="lineNum">    1197 </span><span class="lineNoCov">          0 :             m_virial    -= 0.25*fmass[x0]*Tensor(dist,tmpder);</span></a>
+<a name="1198"><span class="lineNum">    1198 </span>            :           }</a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineNoCov">          0 :           for(unsigned k=0; k&lt;nlcom[i1]-&gt;getFullAtomList().size(); k++) {</span></a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineNoCov">          0 :             unsigned x1=nlcom[i1]-&gt;getFullAtomList()[k].index();</span></a>
+<a name="1201"><span class="lineNum">    1201 </span><span class="lineNoCov">          0 :             m_deriv[x1] += tmpder*fmass[x1];</span></a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;3; l++) {</span></a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineNoCov">          0 :               dist[l]=0.;</span></a>
+<a name="1204"><span class="lineNum">    1204 </span>            :             }</a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineNoCov">          0 :             Vector P1=getPosition(x1);</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;nlcom[i1]-&gt;getFullAtomList().size(); l++) {</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineNoCov">          0 :               unsigned x0=nlcom[i1]-&gt;getFullAtomList()[l].index();</span></a>
+<a name="1208"><span class="lineNum">    1208 </span><span class="lineNoCov">          0 :               Vector P0=getPosition(x0);</span></a>
+<a name="1209"><span class="lineNum">    1209 </span><span class="lineNoCov">          0 :               if(dopbc) {</span></a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineNoCov">          0 :                 dist+=pbcDistance(P1,P0);</span></a>
+<a name="1211"><span class="lineNum">    1211 </span>            :               } else {</a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineNoCov">          0 :                 dist+=delta(P1,P0);</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            :               }</a>
+<a name="1214"><span class="lineNum">    1214 </span>            :             }</a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineNoCov">          0 :             for(unsigned l=0; l&lt;nlcom[i0]-&gt;getFullAtomList().size(); l++) {</span></a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineNoCov">          0 :               unsigned x0=nlcom[i0]-&gt;getFullAtomList()[l].index();</span></a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineNoCov">          0 :               Vector P0=getPosition(x0);</span></a>
+<a name="1218"><span class="lineNum">    1218 </span><span class="lineNoCov">          0 :               if(dopbc) {</span></a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineNoCov">          0 :                 dist+=pbcDistance(P1,P0);</span></a>
+<a name="1220"><span class="lineNum">    1220 </span>            :               } else {</a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineNoCov">          0 :                 dist+=delta(P1,P0);</span></a>
+<a name="1222"><span class="lineNum">    1222 </span>            :               }</a>
+<a name="1223"><span class="lineNum">    1223 </span>            :             }</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineNoCov">          0 :             m_virial    += 0.25*fmass[x1]*Tensor(dist,tmpder);</span></a>
+<a name="1225"><span class="lineNum">    1225 </span>            :           }</a>
+<a name="1226"><span class="lineNum">    1226 </span>            :         } else {</a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">   11574264 :           m_deriv[i0] -= tmpder;</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">   11574264 :           m_deriv[i1] += tmpder;</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">   11574264 :           m_virial    -= tmp*Tensor(distance,distance);</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :         }</a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">   11574264 :         if(Scalevol) {</span></a>
+<a name="1232"><span class="lineNum">    1232 </span><span class="lineCov">   11574264 :           m_virial+=1./3.*tmp*dm*dm*Tensor::identity();</span></a>
+<a name="1233"><span class="lineNum">    1233 </span>            :         }</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">   11574264 :         m_PIVdistance    += scaling[j]*coord*coord;</span></a>
+<a name="1235"><span class="lineNum">    1235 </span>            :       }</a>
+<a name="1236"><span class="lineNum">    1236 </span>            :     }</a>
+<a name="1237"><span class="lineNum">    1237 </span>            : </a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">        327 :     if (!serial &amp;&amp; comm.initialized()) {</span></a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineNoCov">          0 :       comm.Barrier();</span></a>
+<a name="1240"><span class="lineNum">    1240 </span><span class="lineNoCov">          0 :       comm.Sum(&amp;m_PIVdistance,1);</span></a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineNoCov">          0 :       if(!m_deriv.empty()) comm.Sum(&amp;m_deriv[0][0],3*m_deriv.size());</span></a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineNoCov">          0 :       comm.Sum(&amp;m_virial[0][0],9);</span></a>
+<a name="1243"><span class="lineNum">    1243 </span>            :     }</a>
+<a name="1244"><span class="lineNum">    1244 </span>            :   }</a>
+<a name="1245"><span class="lineNum">    1245 </span><span class="lineCov">        327 :   prev_stp=getStep();</span></a>
+<a name="1246"><span class="lineNum">    1246 </span>            : </a>
+<a name="1247"><span class="lineNum">    1247 </span>            :   //Timing</a>
+<a name="1248"><span class="lineNum">    1248 </span><span class="lineCov">        328 :   if(timer) stopwatch.stop(&quot;4 Build For Derivatives&quot;);</span></a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">        327 :   if(timer) {</span></a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">          1 :     log.printf(&quot;Timings for action %s with label %s \n&quot;, getName().c_str(), getLabel().c_str() );</span></a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineCov">          1 :     log&lt;&lt;stopwatch;</span></a>
+<a name="1252"><span class="lineNum">    1252 </span>            :   }</a>
+<a name="1253"><span class="lineNum">    1253 </span>            : </a>
+<a name="1254"><span class="lineNum">    1254 </span>            :   // Update derivatives, virial, and variable (PIV-distance^2)</a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineCov">      29799 :   for(unsigned i=0; i&lt;m_deriv.size(); ++i) setAtomsDerivatives(i,m_deriv[i]);</span></a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineCov">        327 :   setValue           (m_PIVdistance);</span></a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">        327 :   setBoxDerivatives  (m_virial);</span></a>
+<a name="1258"><span class="lineNum">    1258 </span><span class="lineCov">        327 : }</span></a>
+<a name="1259"><span class="lineNum">    1259 </span>            : //Close Namespaces at the very beginning</a>
+<a name="1260"><span class="lineNum">    1260 </span>            : }</a>
+<a name="1261"><span class="lineNum">    1261 </span>            : }</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/piv/index-sort-f.html b/coverage/piv/index-sort-f.html
new file mode 100644
index 0000000000..9ade801d39
--- /dev/null
+++ b/coverage/piv/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - piv</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - piv</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntry">596</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PIV.cpp.gcov.html">PIV.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="71.8%"><img src="../snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">428 / 596</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/piv/index-sort-l.html b/coverage/piv/index-sort-l.html
new file mode 100644
index 0000000000..6ff1c7b7ad
--- /dev/null
+++ b/coverage/piv/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - piv</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - piv</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntry">596</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PIV.cpp.gcov.html">PIV.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="71.8%"><img src="../snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">428 / 596</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/piv/index.html b/coverage/piv/index.html
new file mode 100644
index 0000000000..8cdab95126
--- /dev/null
+++ b/coverage/piv/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - piv</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - piv</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">428</td>
+            <td class="headerCovTableEntry">596</td>
+            <td class="headerCovTableEntryLo">71.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PIV.cpp.gcov.html">PIV.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=72 height=10 alt="71.8%"><img src="../snow.png" width=28 height=10 alt="71.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.8&nbsp;%</td>
+      <td class="coverNumLo">428 / 596</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pytorch/PytorchModel.cpp.func-sort-c.html b/coverage/pytorch/PytorchModel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3f6feeb4d7
--- /dev/null
+++ b/coverage/pytorch/PytorchModel.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pytorch/PytorchModel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pytorch</a> - PytorchModel.cpp<span style="font-size: 80%;"> (<a href="PytorchModel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">83.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PytorchModel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#92">_ZN4PLMD8function7pytorch12PytorchModelC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#92">_ZN4PLMD8function7pytorch12PytorchModelC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#78">_ZN4PLMD8function7pytorch12_GLOBAL__N_124PytorchModelRegisterMe806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#80">_ZN4PLMD8function7pytorch12PytorchModel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#155">_ZN4PLMD8function7pytorch12PytorchModel9calculateEv</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#88">_ZN4PLMD8function7pytorch12PytorchModel16tensor_to_vectorERKN2at6TensorE</a></td>
+              <td class="coverFnHi">103</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#78">_ZN4PLMD8function7pytorch12_GLOBAL__N_124PytorchModelRegisterMe80C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#78">_ZN4PLMD8function7pytorch12_GLOBAL__N_124PytorchModelRegisterMe80D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pytorch/PytorchModel.cpp.func.html b/coverage/pytorch/PytorchModel.cpp.func.html
new file mode 100644
index 0000000000..d160475ed0
--- /dev/null
+++ b/coverage/pytorch/PytorchModel.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pytorch/PytorchModel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pytorch</a> - PytorchModel.cpp<span style="font-size: 80%;"> (<a href="PytorchModel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">83.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PytorchModel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#80">_ZN4PLMD8function7pytorch12PytorchModel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#88">_ZN4PLMD8function7pytorch12PytorchModel16tensor_to_vectorERKN2at6TensorE</a></td>
+              <td class="coverFnHi">103</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#155">_ZN4PLMD8function7pytorch12PytorchModel9calculateEv</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#92">_ZN4PLMD8function7pytorch12PytorchModelC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#92">_ZN4PLMD8function7pytorch12PytorchModelC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#78">_ZN4PLMD8function7pytorch12_GLOBAL__N_124PytorchModelRegisterMe806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#78">_ZN4PLMD8function7pytorch12_GLOBAL__N_124PytorchModelRegisterMe80C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PytorchModel.cpp.gcov.html#78">_ZN4PLMD8function7pytorch12_GLOBAL__N_124PytorchModelRegisterMe80D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pytorch/PytorchModel.cpp.gcov.html b/coverage/pytorch/PytorchModel.cpp.gcov.html
new file mode 100644
index 0000000000..d17b6770c6
--- /dev/null
+++ b/coverage/pytorch/PytorchModel.cpp.gcov.html
@@ -0,0 +1,279 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pytorch/PytorchModel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">pytorch</a> - PytorchModel.cpp<span style="font-size: 80%;"> (source / <a href="PytorchModel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">83.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2022-2023 of Luigi Bonati.</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : The pytorch module is free software: you can redistribute it and/or modify</a>
+<a name="5"><span class="lineNum">       5 </span>            : it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="6"><span class="lineNum">       6 </span>            : the Free Software Foundation, either version 3 of the License, or</a>
+<a name="7"><span class="lineNum">       7 </span>            : (at your option) any later version.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            : The pytorch module is distributed in the hope that it will be useful,</a>
+<a name="10"><span class="lineNum">      10 </span>            : but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="11"><span class="lineNum">      11 </span>            : MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="12"><span class="lineNum">      12 </span>            : GNU Lesser General Public License for more details.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            : You should have received a copy of the GNU Lesser General Public License</a>
+<a name="15"><span class="lineNum">      15 </span>            : along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="16"><span class="lineNum">      16 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="17"><span class="lineNum">      17 </span>            : </a>
+<a name="18"><span class="lineNum">      18 </span>            : #ifdef __PLUMED_HAS_LIBTORCH</a>
+<a name="19"><span class="lineNum">      19 </span>            : // convert LibTorch version to string</a>
+<a name="20"><span class="lineNum">      20 </span>            : //#define STRINGIFY(x) #x</a>
+<a name="21"><span class="lineNum">      21 </span>            : //#define TOSTR(x) STRINGIFY(x)</a>
+<a name="22"><span class="lineNum">      22 </span>            : //#define LIBTORCH_VERSION TO_STR(TORCH_VERSION_MAJOR) &quot;.&quot; TO_STR(TORCH_VERSION_MINOR) &quot;.&quot; TO_STR(TORCH_VERSION_PATCH)</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;function/Function.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;function/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;torch/torch.h&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;torch/script.h&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;fstream&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cmath&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : using namespace std;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace function {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace pytorch {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : //+PLUMEDOC PYTORCH_FUNCTION PYTORCH_MODEL</a>
+<a name="41"><span class="lineNum">      41 </span>            : /*</a>
+<a name="42"><span class="lineNum">      42 </span>            : Load a PyTorch model compiled with TorchScript.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This can be a function defined in Python or a more complex model, such as a neural network optimized on a set of data. In both cases the derivatives of the outputs with respect to the inputs are computed using the automatic differentiation (autograd) feature of Pytorch.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : By default it is assumed that the model is saved as: `model.ptc`, unless otherwise indicated by the `FILE` keyword. The function automatically checks for the number of output dimensions and creates a component for each of them. The outputs are called node-i with i between 0 and N-1 for N outputs.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : Note that this function is active only if LibTorch is correctly linked against PLUMED. Please check the instructions in the \ref PYTORCH page.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \par Examples</a>
+<a name="51"><span class="lineNum">      51 </span>            : Load a model called `torch_model.ptc` that takes as input two dihedral angles and returns two outputs.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \plumedfile</a>
+<a name="54"><span class="lineNum">      54 </span>            : #SETTINGS AUXFILE=regtest/pytorch/rt-pytorch_model_2d/torch_model.ptc</a>
+<a name="55"><span class="lineNum">      55 </span>            : phi: TORSION ATOMS=5,7,9,15</a>
+<a name="56"><span class="lineNum">      56 </span>            : psi: TORSION ATOMS=7,9,15,17</a>
+<a name="57"><span class="lineNum">      57 </span>            : model: PYTORCH_MODEL FILE=torch_model.ptc ARG=phi,psi</a>
+<a name="58"><span class="lineNum">      58 </span>            : PRINT FILE=COLVAR ARG=model.node-0,model.node-1</a>
+<a name="59"><span class="lineNum">      59 </span>            : \endplumedfile</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : */</a>
+<a name="62"><span class="lineNum">      62 </span>            : //+ENDPLUMEDOC</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : class PytorchModel :</a>
+<a name="66"><span class="lineNum">      66 </span>            :   public Function</a>
+<a name="67"><span class="lineNum">      67 </span>            : {</a>
+<a name="68"><span class="lineNum">      68 </span>            :   unsigned _n_in;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   unsigned _n_out;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   torch::jit::script::Module _model;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   explicit PytorchModel(const ActionOptions&amp;);</a>
+<a name="74"><span class="lineNum">      74 </span>            :   void calculate();</a>
+<a name="75"><span class="lineNum">      75 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;float&gt; tensor_to_vector(const torch::Tensor&amp; x);</a>
+<a name="78"><span class="lineNum">      78 </span>            : };</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(PytorchModel,&quot;PYTORCH_MODEL&quot;)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          6 : void PytorchModel::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          6 :   Function::registerKeywords(keys);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          6 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;FILE&quot;,&quot;Filename of the PyTorch compiled model&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;node&quot;, &quot;default&quot;, &quot;Model outputs&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          6 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : // Auxiliary function to transform torch tensors in std vectors</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        103 : std::vector&lt;float&gt; PytorchModel::tensor_to_vector(const torch::Tensor&amp; x) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        206 :   return std::vector&lt;float&gt;(x.data_ptr&lt;float&gt;(), x.data_ptr&lt;float&gt;() + x.numel());</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          4 : PytorchModel::PytorchModel(const ActionOptions&amp;ao):</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   Action(ao),</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          4 :   Function(ao)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : { //print pytorch version</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   //number of inputs of the model</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          4 :   _n_in=getNumberOfArguments();</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   //parse model name</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 :   std::string fname=&quot;model.ptc&quot;;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          8 :   parse(&quot;FILE&quot;,fname);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :   //deserialize the model from file</a>
+<a name="107"><span class="lineNum">     107 </span>            :   try {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          4 :     _model = torch::jit::load(fname);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span>            :   //if an error is thrown check if the file exists or not</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   catch (const c10::Error&amp; e) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     std::ifstream infile(fname);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :     bool exist = infile.good();</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     infile.close();</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     if (exist) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :       // print libtorch version</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :       std::stringstream ss;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :       ss &lt;&lt; TORCH_VERSION_MAJOR &lt;&lt; &quot;.&quot; &lt;&lt; TORCH_VERSION_MINOR &lt;&lt; &quot;.&quot; &lt;&lt; TORCH_VERSION_PATCH;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       std::string version;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       ss &gt;&gt; version; // extract into the string.</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Cannot load FILE: '&quot;+fname+&quot;'. Please check that it is a Pytorch compiled model (exported with 'torch.jit.trace' or 'torch.jit.script') and that the Pytorch version matches the LibTorch one (&quot;+version+&quot;).&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     else {</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;The FILE: '&quot;+fname+&quot;' does not exist.&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :     }</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            :   //check the dimension of the output</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          4 :   log.printf(&quot;Checking output dimension:\n&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          4 :   std::vector&lt;float&gt; input_test (_n_in);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          4 :   torch::Tensor single_input = torch::tensor(input_test).view({1,_n_in});</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::vector&lt;torch::jit::IValue&gt; inputs;</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   inputs.push_back( single_input );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :   torch::Tensor output = _model.forward( inputs ).toTensor();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   vector&lt;float&gt; cvs = this-&gt;tensor_to_vector (output);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          4 :   _n_out=cvs.size();</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            :   //create components</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          9 :   for(unsigned j=0; j&lt;_n_out; j++) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          5 :     string name_comp = &quot;node-&quot;+std::to_string(j);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          5 :     addComponentWithDerivatives( name_comp );</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          5 :     componentIsNotPeriodic( name_comp );</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            :   //print log</a>
+<a name="148"><span class="lineNum">     148 </span>            :   //log.printf(&quot;Pytorch Model Loaded: %s \n&quot;,fname);</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          4 :   log.printf(&quot;Number of input: %d \n&quot;,_n_in);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          4 :   log.printf(&quot;Number of outputs: %d \n&quot;,_n_out);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          4 :   log.printf(&quot;  Bibliography: &quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          8 :   log&lt;&lt;plumed.cite(&quot;Bonati, Rizzi and Parrinello, J. Phys. Chem. Lett. 11, 2998-3004 (2020)&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          4 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          8 : }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         44 : void PytorchModel::calculate() {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   //retrieve arguments</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         44 :   vector&lt;float&gt; current_S(_n_in);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         99 :   for(unsigned i=0; i&lt;_n_in; i++)</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         55 :     current_S[i]=getArgument(i);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   //convert to tensor</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         44 :   torch::Tensor input_S = torch::tensor(current_S).view({1,_n_in});</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   input_S.set_requires_grad(true);</a>
+<a name="166"><span class="lineNum">     166 </span>            :   //convert to Ivalue</a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::vector&lt;torch::jit::IValue&gt; inputs;</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         44 :   inputs.push_back( input_S );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   //calculate output</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         88 :   torch::Tensor output = _model.forward( inputs ).toTensor();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   //set CV values</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         44 :   vector&lt;float&gt; cvs = this-&gt;tensor_to_vector (output);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         99 :   for(unsigned j=0; j&lt;_n_out; j++) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         55 :     string name_comp = &quot;node-&quot;+std::to_string(j);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         55 :     getPntrToComponent(name_comp)-&gt;set(cvs[j]);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span>            :   //derivatives</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         99 :   for(unsigned j=0; j&lt;_n_out; j++) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :     // expand dim to have shape (1,_n_out)</a>
+<a name="180"><span class="lineNum">     180 </span>            :     int batch_size = 1;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         55 :     auto grad_output = torch::ones({1}).expand({batch_size, 1});</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     // calculate derivatives with automatic differentiation</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        220 :     auto gradient = torch::autograd::grad({output.slice(/*dim=*/1, /*start=*/j, /*end=*/j+1)},</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     {input_S},</a>
+<a name="185"><span class="lineNum">     185 </span>            :     /*grad_outputs=*/ {grad_output},</a>
+<a name="186"><span class="lineNum">     186 </span>            :     /*retain_graph=*/true,</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        330 :     /*create_graph=*/false);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     // add dimension</a>
+<a name="189"><span class="lineNum">     189 </span>            :     auto grad = gradient[0].unsqueeze(/*dim=*/1);</a>
+<a name="190"><span class="lineNum">     190 </span>            :     //convert to vector</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         55 :     vector&lt;float&gt; der = this-&gt;tensor_to_vector ( grad );</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         55 :     string name_comp = &quot;node-&quot;+std::to_string(j);</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     //set derivatives of component j</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        132 :     for(unsigned i=0; i&lt;_n_in; i++)</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         77 :       setDerivative( getPntrToComponent(name_comp),i, der[i] );</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         55 :   }</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         88 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pytorch</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - pytorch</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">83.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PytorchModel.cpp.gcov.html">PytorchModel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.1%"><img src="../snow.png" width=17 height=10 alt="83.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.1&nbsp;%</td>
+      <td class="coverNumMed">54 / 65</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pytorch/index-sort-l.html b/coverage/pytorch/index-sort-l.html
new file mode 100644
index 0000000000..dd2bb93d31
--- /dev/null
+++ b/coverage/pytorch/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pytorch</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - pytorch</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">83.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PytorchModel.cpp.gcov.html">PytorchModel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.1%"><img src="../snow.png" width=17 height=10 alt="83.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.1&nbsp;%</td>
+      <td class="coverNumMed">54 / 65</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/pytorch/index.html b/coverage/pytorch/index.html
new file mode 100644
index 0000000000..bd49a15158
--- /dev/null
+++ b/coverage/pytorch/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - pytorch</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - pytorch</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">65</td>
+            <td class="headerCovTableEntryMed">83.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PytorchModel.cpp.gcov.html">PytorchModel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.1%"><img src="../snow.png" width=17 height=10 alt="83.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.1&nbsp;%</td>
+      <td class="coverNumMed">54 / 65</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">7 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ArgumentOnlyDistance.cpp.func-sort-c.html b/coverage/reference/ArgumentOnlyDistance.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ca6501b80a
--- /dev/null
+++ b/coverage/reference/ArgumentOnlyDistance.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ArgumentOnlyDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ArgumentOnlyDistance.cpp<span style="font-size: 80%;"> (<a href="ArgumentOnlyDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ArgumentOnlyDistance.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#25">_ZN4PLMD20ArgumentOnlyDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#35">_ZNK4PLMD20ArgumentOnlyDistance9calculateERKSt6vectorIPNS_5ValueESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#43">_ZNK4PLMD20ArgumentOnlyDistance4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">299760</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#25">_ZN4PLMD20ArgumentOnlyDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518364</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#31">_ZN4PLMD20ArgumentOnlyDistance4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">518831</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ArgumentOnlyDistance.cpp.func.html b/coverage/reference/ArgumentOnlyDistance.cpp.func.html
new file mode 100644
index 0000000000..a89a44ffe4
--- /dev/null
+++ b/coverage/reference/ArgumentOnlyDistance.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ArgumentOnlyDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ArgumentOnlyDistance.cpp<span style="font-size: 80%;"> (<a href="ArgumentOnlyDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ArgumentOnlyDistance.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#31">_ZN4PLMD20ArgumentOnlyDistance4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">518831</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#25">_ZN4PLMD20ArgumentOnlyDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#25">_ZN4PLMD20ArgumentOnlyDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518364</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#43">_ZNK4PLMD20ArgumentOnlyDistance4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">299760</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.cpp.gcov.html#35">_ZNK4PLMD20ArgumentOnlyDistance9calculateERKSt6vectorIPNS_5ValueESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ArgumentOnlyDistance.cpp.gcov.html b/coverage/reference/ArgumentOnlyDistance.cpp.gcov.html
new file mode 100644
index 0000000000..a64fa18c92
--- /dev/null
+++ b/coverage/reference/ArgumentOnlyDistance.cpp.gcov.html
@@ -0,0 +1,129 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ArgumentOnlyDistance.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ArgumentOnlyDistance.cpp<span style="font-size: 80%;"> (source / <a href="ArgumentOnlyDistance.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ArgumentOnlyDistance.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">     518364 : ArgumentOnlyDistance::ArgumentOnlyDistance( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="28"><span class="lineNum">      28 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     518364 :   ReferenceArguments(ro)</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : {</a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">     518364 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     518831 : void ArgumentOnlyDistance::read( const PDB&amp; pdb ) {</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     518831 :   readArgumentsFromPDB( pdb );</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     518831 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineNoCov">          0 : double ArgumentOnlyDistance::calculate( const std::vector&lt;Value*&gt;&amp; vals, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; tmparg( vals.size() );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;vals.size(); ++i) tmparg[i]=vals[i]-&gt;get();</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :   double d=calculateArgumentDistance( vals, tmparg, myder, squared );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :   if( !myder.updateComplete() ) myder.updateDynamicLists();</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineNoCov">          0 :   return d;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : }</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">     299760 : double ArgumentOnlyDistance::calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg,</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :                                    ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="47"><span class="lineNum">      47 </span>            :   plumed_dbg_assert( pos.size()==0 );</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">     299760 :   double d=calculateArgumentDistance( vals, arg, myder, squared );</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     299760 :   if( !myder.updateComplete() ) myder.updateDynamicLists();</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">     299760 :   return d;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ArgumentOnlyDistance.h.func-sort-c.html b/coverage/reference/ArgumentOnlyDistance.h.func-sort-c.html
new file mode 100644
index 0000000000..42147768d4
--- /dev/null
+++ b/coverage/reference/ArgumentOnlyDistance.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ArgumentOnlyDistance.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ArgumentOnlyDistance.h<span style="font-size: 80%;"> (<a href="ArgumentOnlyDistance.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ArgumentOnlyDistance.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.h.gcov.html#36">_ZN4PLMD20ArgumentOnlyDistance28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.h.gcov.html#37">_ZN4PLMD20ArgumentOnlyDistance15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">556</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ArgumentOnlyDistance.h.func.html b/coverage/reference/ArgumentOnlyDistance.h.func.html
new file mode 100644
index 0000000000..bbfff3acc3
--- /dev/null
+++ b/coverage/reference/ArgumentOnlyDistance.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ArgumentOnlyDistance.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ArgumentOnlyDistance.h<span style="font-size: 80%;"> (<a href="ArgumentOnlyDistance.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ArgumentOnlyDistance.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.h.gcov.html#37">_ZN4PLMD20ArgumentOnlyDistance15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">556</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ArgumentOnlyDistance.h.gcov.html#36">_ZN4PLMD20ArgumentOnlyDistance28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">80</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ArgumentOnlyDistance.h.gcov.html b/coverage/reference/ArgumentOnlyDistance.h.gcov.html
new file mode 100644
index 0000000000..f5cdc29411
--- /dev/null
+++ b/coverage/reference/ArgumentOnlyDistance.h.gcov.html
@@ -0,0 +1,121 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ArgumentOnlyDistance.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ArgumentOnlyDistance.h<span style="font-size: 80%;"> (source / <a href="ArgumentOnlyDistance.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_ArgumentOnlyDistance_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_ArgumentOnlyDistance_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;ReferenceArguments.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class PDB;</a>
+<a name="32"><span class="lineNum">      32 </span>            : class Pbc;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class ArgumentOnlyDistance : public ReferenceArguments {</a>
+<a name="35"><span class="lineNum">      35 </span>            : public:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   explicit ArgumentOnlyDistance( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="37"><span class="lineNum">      37 </span>            :   void read( const PDB&amp; pdb ) override;</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         80 :   bool pcaIsEnabledForThisReference() override { return true; }</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        556 :   void setupPCAStorage( ReferenceValuePack&amp; mypack ) override { mypack.switchOnPCAOption(); }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   double calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; myder, const bool&amp; squared ) const override;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double calculate( const std::vector&lt;Value*&gt;&amp; vals, ReferenceValuePack&amp; myder, const bool&amp; squared ) const ;</a>
+<a name="42"><span class="lineNum">      42 </span>            : };</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : }</a>
+<a name="45"><span class="lineNum">      45 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/DRMSD.cpp.func-sort-c.html b/coverage/reference/DRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..55af0056a0
--- /dev/null
+++ b/coverage/reference/DRMSD.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/DRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - DRMSD.cpp<span style="font-size: 80%;"> (<a href="DRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#28">_ZN4PLMD5DRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#51">_ZN4PLMD5DRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#43">_ZN4PLMD5DRMSD10readBoundsERKNS_3PDBE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#55">_ZN4PLMD5DRMSD17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#26">_ZN4PLMD12_GLOBAL__N_115DRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#60">_ZN4PLMD5DRMSD13setup_targetsEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#28">_ZN4PLMD5DRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#38">_ZN4PLMD5DRMSD20setBoundsOnDistancesEbdd</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#26">_ZN4PLMD12_GLOBAL__N_115DRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#26">_ZN4PLMD12_GLOBAL__N_115DRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#75">_ZNK4PLMD5DRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">20378</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/DRMSD.cpp.func.html b/coverage/reference/DRMSD.cpp.func.html
new file mode 100644
index 0000000000..bef1011dfd
--- /dev/null
+++ b/coverage/reference/DRMSD.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/DRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - DRMSD.cpp<span style="font-size: 80%;"> (<a href="DRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#26">_ZN4PLMD12_GLOBAL__N_115DRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#26">_ZN4PLMD12_GLOBAL__N_115DRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#26">_ZN4PLMD12_GLOBAL__N_115DRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#43">_ZN4PLMD5DRMSD10readBoundsERKNS_3PDBE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#60">_ZN4PLMD5DRMSD13setup_targetsEv</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#55">_ZN4PLMD5DRMSD17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#38">_ZN4PLMD5DRMSD20setBoundsOnDistancesEbdd</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#51">_ZN4PLMD5DRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#28">_ZN4PLMD5DRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#28">_ZN4PLMD5DRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DRMSD.cpp.gcov.html#75">_ZNK4PLMD5DRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">20378</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/DRMSD.cpp.gcov.html b/coverage/reference/DRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..2d3f0ca35e
--- /dev/null
+++ b/coverage/reference/DRMSD.cpp.gcov.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/DRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - DRMSD.cpp<span style="font-size: 80%;"> (source / <a href="DRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntryHi">93.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">      12556 : PLUMED_REGISTER_METRIC(DRMSD,&quot;DRMSD&quot;)</span></a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         28 : DRMSD::DRMSD( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="31"><span class="lineNum">      31 </span>            :   ReferenceConfiguration( ro ),</a>
+<a name="32"><span class="lineNum">      32 </span>            :   SingleDomainRMSD( ro ),</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         28 :   nopbc(true),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         28 :   bounds_were_set(false),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         28 :   lower(0),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         28 :   upper(std::numeric_limits&lt;double&gt;::max( ))</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         28 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         28 : void DRMSD::setBoundsOnDistances( bool dopbc, double lbound, double ubound ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         28 :   bounds_were_set=true; nopbc=!dopbc;</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         28 :   lower=lbound; upper=ubound;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         28 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         11 : void DRMSD::readBounds( const PDB&amp; pdb ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         11 :   if( bounds_were_set ) return;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   double tmp; nopbc=pdb.hasFlag(&quot;NOPBC&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :   if( pdb.getArgumentValue(&quot;LOWER_CUTOFF&quot;,tmp) ) lower=tmp;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 :   if( pdb.getArgumentValue(&quot;UPPER_CUTOFF&quot;,tmp) ) upper=tmp;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :   bounds_were_set=true;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          9 : void DRMSD::read( const PDB&amp; pdb ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          9 :   readAtomsFromPDB( pdb ); readBounds( pdb ); setup_targets();</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          9 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         17 : void DRMSD::setReferenceAtoms( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; align_in, const std::vector&lt;double&gt;&amp; displace_in ) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         17 :   SingleDomainRMSD::setReferenceAtoms( conf, align_in, displace_in );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         17 :   setup_targets();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         17 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         26 : void DRMSD::setup_targets() {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         26 :   plumed_massert( bounds_were_set, &quot;I am missing a call to DRMSD::setBoundsOnDistances&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         26 :   unsigned natoms = getNumberOfReferencePositions();</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        569 :   for(unsigned i=0; i&lt;natoms-1; ++i) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       7779 :     for(unsigned j=i+1; j&lt;natoms; ++j) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       7236 :       double distance = delta( getReferencePosition(i), getReferencePosition(j) ).modulo();</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       7236 :       if(distance &lt; upper &amp;&amp; distance &gt; lower ) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       6620 :         targets[std::make_pair(i,j)] = distance;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :       }</a>
+<a name="72"><span class="lineNum">      72 </span>            :     }</a>
+<a name="73"><span class="lineNum">      73 </span>            :   }</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         26 :   if( targets.empty() ) error(&quot;drmsd will compare no distances - check upper and lower bounds are sensible&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         26 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      20378 : double DRMSD::calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   plumed_dbg_assert(!targets.empty());</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      20378 :   Vector distance;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      20378 :   myder.clear();</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   double drmsd=0.;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    8126088 :   for(const auto &amp; it : targets) {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    8105710 :     const unsigned i=getAtomIndex( it.first.first );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    8105710 :     const unsigned j=getAtomIndex( it.first.second );</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    8105710 :     if(nopbc) distance=delta( pos[i], pos[j] );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">    8076310 :     else      distance=pbc.distance( pos[i], pos[j] );</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    8105710 :     const double len = distance.modulo();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    8105710 :     const double diff = len - it.second;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    8105710 :     const double der = diff / len;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    8105710 :     drmsd += diff * diff;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    8105710 :     myder.addAtomDerivatives( i, -der * distance );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    8105710 :     myder.addAtomDerivatives( j,  der * distance );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">    8105710 :     myder.addBoxDerivatives( - der * Tensor(distance,distance) );</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      20378 :   const double inpairs = 1./static_cast&lt;double&gt;(targets.size());</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   double idrmsd;</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      20378 :   if(squared) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         10 :     drmsd = drmsd * inpairs;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         10 :     idrmsd = 2.0 * inpairs;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   } else {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      20368 :     drmsd = std::sqrt( drmsd * inpairs );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      20368 :     idrmsd = inpairs / drmsd ;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      20378 :   myder.scaleAllDerivatives( idrmsd );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      20378 :   return drmsd;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/Direction.cpp.func-sort-c.html b/coverage/reference/Direction.cpp.func-sort-c.html
new file mode 100644
index 0000000000..236177eac5
--- /dev/null
+++ b/coverage/reference/Direction.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/Direction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - Direction.cpp<span style="font-size: 80%;"> (<a href="Direction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Direction.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#27">_ZN4PLMD9DirectionC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#59">_ZNK4PLMD9Direction4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#25">_ZN4PLMD12_GLOBAL__N_119DirectionRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#68">_ZNK4PLMD9Direction25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#64">_ZNK4PLMD9Direction27extractArgumentDisplacementERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERS9_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#54">_ZN4PLMD9Direction13zeroDirectionEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#35">_ZN4PLMD9Direction4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#27">_ZN4PLMD9DirectionC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#48">_ZN4PLMD9Direction12addDirectionERKdRKS0_</a></td>
+              <td class="coverFnHi">303</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#40">_ZN4PLMD9Direction12setDirectionERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#25">_ZN4PLMD12_GLOBAL__N_119DirectionRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#25">_ZN4PLMD12_GLOBAL__N_119DirectionRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/Direction.cpp.func.html b/coverage/reference/Direction.cpp.func.html
new file mode 100644
index 0000000000..316e5835ec
--- /dev/null
+++ b/coverage/reference/Direction.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/Direction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - Direction.cpp<span style="font-size: 80%;"> (<a href="Direction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Direction.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#25">_ZN4PLMD12_GLOBAL__N_119DirectionRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#25">_ZN4PLMD12_GLOBAL__N_119DirectionRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#25">_ZN4PLMD12_GLOBAL__N_119DirectionRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#48">_ZN4PLMD9Direction12addDirectionERKdRKS0_</a></td>
+              <td class="coverFnHi">303</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#40">_ZN4PLMD9Direction12setDirectionERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#54">_ZN4PLMD9Direction13zeroDirectionEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#35">_ZN4PLMD9Direction4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#27">_ZN4PLMD9DirectionC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#27">_ZN4PLMD9DirectionC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#68">_ZNK4PLMD9Direction25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#64">_ZNK4PLMD9Direction27extractArgumentDisplacementERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERS9_</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.cpp.gcov.html#59">_ZNK4PLMD9Direction4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/Direction.cpp.gcov.html b/coverage/reference/Direction.cpp.gcov.html
new file mode 100644
index 0000000000..9760669ab7
--- /dev/null
+++ b/coverage/reference/Direction.cpp.gcov.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/Direction.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - Direction.cpp<span style="font-size: 80%;"> (source / <a href="Direction.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Direction.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">      12524 : PLUMED_REGISTER_METRIC(Direction,&quot;DIRECTION&quot;)</span></a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        219 : Direction::Direction( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="31"><span class="lineNum">      31 </span>            :   ReferenceAtoms(ro),</a>
+<a name="32"><span class="lineNum">      32 </span>            :   ReferenceArguments(ro),</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        219 :   normalized(false)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        219 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        219 : void Direction::read( const PDB&amp; pdb ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        219 :   readAtomsFromPDB( pdb, true );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        219 :   readArgumentsFromPDB( pdb );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        219 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        494 : void Direction::setDirection( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; args ) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        494 :   std::vector&lt;double&gt; sigma( args.size(), 1.0 ); setReferenceArguments( args, sigma );</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        494 :   reference_atoms.resize( conf.size() ); align.resize( conf.size() );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        494 :   displace.resize( conf.size() ); atom_der_index.resize( conf.size() );</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        715 :   for(unsigned i=0; i&lt;conf.size(); ++i) { align[i]=1.0; displace[i]=1.0; atom_der_index[i]=i; reference_atoms[i]=conf[i]; }</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        494 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        303 : void Direction::addDirection( const double&amp; weight, const Direction&amp; dir ) {</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   plumed_dbg_assert( dir.getNumberOfReferenceArguments()==getNumberOfReferenceArguments() &amp;&amp; dir.reference_atoms.size()==reference_atoms.size() );</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        909 :   for(unsigned i=0; i&lt;reference_args.size(); ++i) reference_args[i] += weight*dir.reference_args[i];</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        303 :   for(unsigned i=0; i&lt;reference_atoms.size(); ++i) reference_atoms[i] += weight*reference_atoms.size()*dir.reference_atoms[i];</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        303 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         12 : void Direction::zeroDirection() {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         32 :   for(unsigned i=0; i&lt;reference_args.size(); ++i) reference_args[i] = 0.;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         38 :   for(unsigned i=0; i&lt;reference_atoms.size(); ++i) reference_atoms[i].zero();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         12 : }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 : double Direction::calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; args,</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :                         ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;You should never be calling calc for a direction&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         10 : void Direction::extractArgumentDisplacement( const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; dirout ) const {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         10 :   for(unsigned i=0; i&lt;getNumberOfReferenceArguments(); ++i) dirout[i]=getReferenceArgument(i);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         10 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         10 : void Direction::extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; dirout ) const {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         80 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) dirout[i]=getReferencePosition(i);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         10 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/Direction.h.func-sort-c.html b/coverage/reference/Direction.h.func-sort-c.html
new file mode 100644
index 0000000000..5b6438e92f
--- /dev/null
+++ b/coverage/reference/Direction.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/Direction.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - Direction.h<span style="font-size: 80%;"> (<a href="Direction.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Direction.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.h.gcov.html#40">_ZN4PLMD9Direction17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/Direction.h.func.html b/coverage/reference/Direction.h.func.html
new file mode 100644
index 0000000000..457d1fb853
--- /dev/null
+++ b/coverage/reference/Direction.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/Direction.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - Direction.h<span style="font-size: 80%;"> (<a href="Direction.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Direction.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Direction.h.gcov.html#40">_ZN4PLMD9Direction17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/Direction.h.gcov.html b/coverage/reference/Direction.h.gcov.html
new file mode 100644
index 0000000000..abba07ece7
--- /dev/null
+++ b/coverage/reference/Direction.h.gcov.html
@@ -0,0 +1,127 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/Direction.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - Direction.h<span style="font-size: 80%;"> (source / <a href="Direction.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_Direction_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_Direction_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ReferenceAtoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ReferenceArguments.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class Direction :</a>
+<a name="31"><span class="lineNum">      31 </span>            :   public ReferenceAtoms,</a>
+<a name="32"><span class="lineNum">      32 </span>            :   public ReferenceArguments</a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span>            : public:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   bool normalized;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   explicit Direction( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="37"><span class="lineNum">      37 </span>            :   void read( const PDB&amp; ) override;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   double calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; args,</a>
+<a name="39"><span class="lineNum">      39 </span>            :                ReferenceValuePack&amp; myder, const bool&amp; squared ) const override;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void setDirection( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; args );</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void addDirection( const double&amp; weight, const Direction&amp; dir );</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineNoCov">          0 :   void setReferenceAtoms( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; align_in, const std::vector&lt;double&gt;&amp; displace_in ) override { plumed_error(); }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : /// This allows us to extract the reference positions, which are the direction in this case</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void extractArgumentDisplacement( const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; dirout ) const override;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; dirout ) const override;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void zeroDirection();</a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/DotProductDistance.cpp.func-sort-c.html b/coverage/reference/DotProductDistance.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f42c76d95d
--- /dev/null
+++ b/coverage/reference/DotProductDistance.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/DotProductDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - DotProductDistance.cpp<span style="font-size: 80%;"> (<a href="DotProductDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">8.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">28.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DotProductDistance.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#34">_ZN4PLMD12_GLOBAL__N_128DotProductDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#42">_ZN4PLMD18DotProductDistance4readERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#36">_ZN4PLMD18DotProductDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#36">_ZN4PLMD18DotProductDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#46">_ZNK4PLMD18DotProductDistance25calculateArgumentDistanceERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#34">_ZN4PLMD12_GLOBAL__N_128DotProductDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#34">_ZN4PLMD12_GLOBAL__N_128DotProductDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/DotProductDistance.cpp.func.html b/coverage/reference/DotProductDistance.cpp.func.html
new file mode 100644
index 0000000000..31a22a8316
--- /dev/null
+++ b/coverage/reference/DotProductDistance.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/DotProductDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - DotProductDistance.cpp<span style="font-size: 80%;"> (<a href="DotProductDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">8.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">28.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DotProductDistance.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#34">_ZN4PLMD12_GLOBAL__N_128DotProductDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#34">_ZN4PLMD12_GLOBAL__N_128DotProductDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#34">_ZN4PLMD12_GLOBAL__N_128DotProductDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#42">_ZN4PLMD18DotProductDistance4readERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#36">_ZN4PLMD18DotProductDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#36">_ZN4PLMD18DotProductDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DotProductDistance.cpp.gcov.html#46">_ZNK4PLMD18DotProductDistance25calculateArgumentDistanceERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/DotProductDistance.cpp.gcov.html b/coverage/reference/DotProductDistance.cpp.gcov.html
new file mode 100644
index 0000000000..e99f083e67
--- /dev/null
+++ b/coverage/reference/DotProductDistance.cpp.gcov.html
@@ -0,0 +1,134 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/DotProductDistance.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - DotProductDistance.cpp<span style="font-size: 80%;"> (source / <a href="DotProductDistance.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">8.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">28.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ArgumentOnlyDistance.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;limits&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class DotProductDistance : public ArgumentOnlyDistance {</a>
+<a name="30"><span class="lineNum">      30 </span>            : public:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   explicit DotProductDistance( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="32"><span class="lineNum">      32 </span>            :   void read( const PDB&amp; ) override;</a>
+<a name="33"><span class="lineNum">      33 </span>            :   double calculateArgumentDistance( const std::vector&lt;Value*&gt; &amp; vals, const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; myder, const bool&amp; squared ) const override;</a>
+<a name="34"><span class="lineNum">      34 </span>            : };</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">      12504 : PLUMED_REGISTER_METRIC(DotProductDistance,&quot;DOTPRODUCT&quot;)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 : DotProductDistance::DotProductDistance( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :   ArgumentOnlyDistance(ro)</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : {</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 : void DotProductDistance::read( const PDB&amp; pdb ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 :   readArgumentsFromPDB( pdb );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 : double DotProductDistance::calculateArgumentDistance( const std::vector&lt;Value*&gt; &amp; vals, const std::vector&lt;double&gt;&amp; arg,</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :     ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   double dot=0.0;</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   for (std::size_t i=0; i&lt;vals.size(); ++i) dot+=getReferenceArgument(i)*arg[i];</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :   for (std::size_t i=0; i&lt;vals.size(); ++i) myder.setArgumentDerivatives( i, -getReferenceArgument(i)/dot );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   if(dot==0.0) dot=std::numeric_limits&lt;double&gt;::min();</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   return -log(dot);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/EuclideanDistance.cpp.func-sort-c.html b/coverage/reference/EuclideanDistance.cpp.func-sort-c.html
new file mode 100644
index 0000000000..73b6260c8b
--- /dev/null
+++ b/coverage/reference/EuclideanDistance.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/EuclideanDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - EuclideanDistance.cpp<span style="font-size: 80%;"> (<a href="EuclideanDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="EuclideanDistance.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#32">_ZN4PLMD17EuclideanDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_127EuclideanDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_127EuclideanDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_127EuclideanDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518364</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#32">_ZN4PLMD17EuclideanDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518364</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/EuclideanDistance.cpp.func.html b/coverage/reference/EuclideanDistance.cpp.func.html
new file mode 100644
index 0000000000..c6d189dd1b
--- /dev/null
+++ b/coverage/reference/EuclideanDistance.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/EuclideanDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - EuclideanDistance.cpp<span style="font-size: 80%;"> (<a href="EuclideanDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="EuclideanDistance.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_127EuclideanDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518364</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_127EuclideanDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_127EuclideanDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#32">_ZN4PLMD17EuclideanDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518364</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="EuclideanDistance.cpp.gcov.html#32">_ZN4PLMD17EuclideanDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/EuclideanDistance.cpp.gcov.html b/coverage/reference/EuclideanDistance.cpp.gcov.html
new file mode 100644
index 0000000000..c0e39729c6
--- /dev/null
+++ b/coverage/reference/EuclideanDistance.cpp.gcov.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/EuclideanDistance.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - EuclideanDistance.cpp<span style="font-size: 80%;"> (source / <a href="EuclideanDistance.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ArgumentOnlyDistance.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : class EuclideanDistance : public ArgumentOnlyDistance {</a>
+<a name="28"><span class="lineNum">      28 </span>            : public:</a>
+<a name="29"><span class="lineNum">      29 </span>            :   explicit EuclideanDistance( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="30"><span class="lineNum">      30 </span>            : };</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">    1049232 : PLUMED_REGISTER_METRIC(EuclideanDistance,&quot;EUCLIDEAN&quot;)</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     518364 : EuclideanDistance::EuclideanDistance( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     518364 :   ArgumentOnlyDistance(ro)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     518364 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/IntermolecularDRMSD.cpp.func-sort-c.html b/coverage/reference/IntermolecularDRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b4eee1b43a
--- /dev/null
+++ b/coverage/reference/IntermolecularDRMSD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/IntermolecularDRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - IntermolecularDRMSD.cpp<span style="font-size: 80%;"> (<a href="IntermolecularDRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="IntermolecularDRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntermolecularDRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntermolecularDRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#51">_ZN4PLMD19IntermolecularDRMSD13setup_targetsEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#44">_ZN4PLMD19IntermolecularDRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntermolecularDRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntermolecularDRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntermolecularDRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/IntermolecularDRMSD.cpp.func.html b/coverage/reference/IntermolecularDRMSD.cpp.func.html
new file mode 100644
index 0000000000..78e78a0488
--- /dev/null
+++ b/coverage/reference/IntermolecularDRMSD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <title>LCOV - plumed test coverage - reference/IntermolecularDRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - IntermolecularDRMSD.cpp<span style="font-size: 80%;"> (<a href="IntermolecularDRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="IntermolecularDRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntermolecularDRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntermolecularDRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntermolecularDRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#51">_ZN4PLMD19IntermolecularDRMSD13setup_targetsEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#44">_ZN4PLMD19IntermolecularDRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntermolecularDRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntermolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntermolecularDRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/IntermolecularDRMSD.cpp.gcov.html b/coverage/reference/IntermolecularDRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..e77d498762
--- /dev/null
+++ b/coverage/reference/IntermolecularDRMSD.cpp.gcov.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/IntermolecularDRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - IntermolecularDRMSD.cpp<span style="font-size: 80%;"> (source / <a href="IntermolecularDRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : class IntermolecularDRMSD : public DRMSD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : private:</a>
+<a name="29"><span class="lineNum">      29 </span>            :   unsigned nblocks;</a>
+<a name="30"><span class="lineNum">      30 </span>            :   std::vector&lt;unsigned&gt; blocks;</a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   explicit IntermolecularDRMSD( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   void read( const PDB&amp; pdb ) override;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   void setup_targets() override;</a>
+<a name="35"><span class="lineNum">      35 </span>            : };</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      12506 : PLUMED_REGISTER_METRIC(IntermolecularDRMSD,&quot;INTER-DRMSD&quot;)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          1 : IntermolecularDRMSD::IntermolecularDRMSD( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   ReferenceConfiguration( ro ),</a>
+<a name="41"><span class="lineNum">      41 </span>            :   DRMSD( ro ),</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          1 :   nblocks(0)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          1 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          1 : void IntermolecularDRMSD::read( const PDB&amp; pdb ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          1 :   readAtomsFromPDB( pdb, true ); nblocks = pdb.getNumberOfAtomBlocks(); blocks.resize( nblocks+1 );</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :   if( nblocks==1 ) error(&quot;Trying to compute intermolecular rmsd but found no TERs in input PDB&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          3 :   blocks[0]=0; for(unsigned i=0; i&lt;nblocks; ++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :   readBounds( pdb ); setup_targets();</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          1 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          1 : void IntermolecularDRMSD::setup_targets() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          1 :   plumed_massert( bounds_were_set, &quot;I am missing a call to DRMSD::setBoundsOnDistances&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          2 :   for(unsigned i=1; i&lt;nblocks; ++i) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          2 :     for(unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :       for(unsigned iatom=blocks[i]; iatom&lt;blocks[i+1]; ++iatom) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         15 :         for(unsigned jatom=blocks[j]; jatom&lt;blocks[j+1]; ++jatom) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         12 :           double distance = delta( getReferencePosition(iatom), getReferencePosition(jatom) ).modulo();</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         12 :           if(distance &lt; upper &amp;&amp; distance &gt; lower ) targets[std::make_pair(iatom,jatom)] = distance;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :         }</a>
+<a name="63"><span class="lineNum">      63 </span>            :       }</a>
+<a name="64"><span class="lineNum">      64 </span>            :     }</a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          1 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/IntramolecularDRMSD.cpp.func-sort-c.html b/coverage/reference/IntramolecularDRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5cb93aaf70
--- /dev/null
+++ b/coverage/reference/IntramolecularDRMSD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/IntramolecularDRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - IntramolecularDRMSD.cpp<span style="font-size: 80%;"> (<a href="IntramolecularDRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="IntramolecularDRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntramolecularDRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntramolecularDRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#51">_ZN4PLMD19IntramolecularDRMSD13setup_targetsEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#44">_ZN4PLMD19IntramolecularDRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntramolecularDRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntramolecularDRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntramolecularDRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/IntramolecularDRMSD.cpp.func.html b/coverage/reference/IntramolecularDRMSD.cpp.func.html
new file mode 100644
index 0000000000..7b13aec29c
--- /dev/null
+++ b/coverage/reference/IntramolecularDRMSD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/IntramolecularDRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - IntramolecularDRMSD.cpp<span style="font-size: 80%;"> (<a href="IntramolecularDRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="IntramolecularDRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntramolecularDRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntramolecularDRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#35">_ZN4PLMD12_GLOBAL__N_129IntramolecularDRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#51">_ZN4PLMD19IntramolecularDRMSD13setup_targetsEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#44">_ZN4PLMD19IntramolecularDRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntramolecularDRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IntramolecularDRMSD.cpp.gcov.html#37">_ZN4PLMD19IntramolecularDRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/IntramolecularDRMSD.cpp.gcov.html b/coverage/reference/IntramolecularDRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..3a2740d48f
--- /dev/null
+++ b/coverage/reference/IntramolecularDRMSD.cpp.gcov.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/IntramolecularDRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - IntramolecularDRMSD.cpp<span style="font-size: 80%;"> (source / <a href="IntramolecularDRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : class IntramolecularDRMSD : public DRMSD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : private:</a>
+<a name="29"><span class="lineNum">      29 </span>            :   unsigned nblocks;</a>
+<a name="30"><span class="lineNum">      30 </span>            :   std::vector&lt;unsigned&gt; blocks;</a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   explicit IntramolecularDRMSD( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   void read( const PDB&amp; pdb ) override;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   void setup_targets() override;</a>
+<a name="35"><span class="lineNum">      35 </span>            : };</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      12506 : PLUMED_REGISTER_METRIC(IntramolecularDRMSD,&quot;INTRA-DRMSD&quot;)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          1 : IntramolecularDRMSD::IntramolecularDRMSD( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   ReferenceConfiguration( ro ),</a>
+<a name="41"><span class="lineNum">      41 </span>            :   DRMSD( ro ),</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          1 :   nblocks(0)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          1 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          1 : void IntramolecularDRMSD::read( const PDB&amp; pdb ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          1 :   readAtomsFromPDB( pdb, true ); nblocks = pdb.getNumberOfAtomBlocks(); blocks.resize( nblocks+1 );</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :   if( nblocks==1 ) error(&quot;Trying to compute intramolecular rmsd but found no TERs in input PDB&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          3 :   blocks[0]=0; for(unsigned i=0; i&lt;nblocks; ++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :   readBounds( pdb ); setup_targets();</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          1 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          1 : void IntramolecularDRMSD::setup_targets() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          1 :   plumed_massert( bounds_were_set, &quot;I am missing a call to DRMSD::setBoundsOnDistances&quot;);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          3 :   for(unsigned i=0; i&lt;nblocks; ++i) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          7 :     for(unsigned iatom=blocks[i]+1; iatom&lt;blocks[i+1]; ++iatom) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         14 :       for(unsigned jatom=blocks[i]; jatom&lt;iatom; ++jatom) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          9 :         double distance = delta( getReferencePosition(iatom), getReferencePosition(jatom) ).modulo();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          9 :         if(distance &lt; upper &amp;&amp; distance &gt; lower ) targets[std::make_pair(iatom,jatom)] = distance;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :       }</a>
+<a name="62"><span class="lineNum">      62 </span>            :     }</a>
+<a name="63"><span class="lineNum">      63 </span>            :   }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          1 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MahalanobisDistance.cpp.func-sort-c.html b/coverage/reference/MahalanobisDistance.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0955939555
--- /dev/null
+++ b/coverage/reference/MahalanobisDistance.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MahalanobisDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MahalanobisDistance.cpp<span style="font-size: 80%;"> (<a href="MahalanobisDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MahalanobisDistance.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_129MahalanobisDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#32">_ZN4PLMD19MahalanobisDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#32">_ZN4PLMD19MahalanobisDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_129MahalanobisDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_129MahalanobisDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MahalanobisDistance.cpp.func.html b/coverage/reference/MahalanobisDistance.cpp.func.html
new file mode 100644
index 0000000000..a53f74718f
--- /dev/null
+++ b/coverage/reference/MahalanobisDistance.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MahalanobisDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MahalanobisDistance.cpp<span style="font-size: 80%;"> (<a href="MahalanobisDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MahalanobisDistance.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_129MahalanobisDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
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+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_129MahalanobisDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#32">_ZN4PLMD19MahalanobisDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MahalanobisDistance.cpp.gcov.html#32">_ZN4PLMD19MahalanobisDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MahalanobisDistance.cpp.gcov.html b/coverage/reference/MahalanobisDistance.cpp.gcov.html
new file mode 100644
index 0000000000..c780e3f73e
--- /dev/null
+++ b/coverage/reference/MahalanobisDistance.cpp.gcov.html
@@ -0,0 +1,117 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MahalanobisDistance.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MahalanobisDistance.cpp<span style="font-size: 80%;"> (source / <a href="MahalanobisDistance.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ArgumentOnlyDistance.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : class MahalanobisDistance : public ArgumentOnlyDistance {</a>
+<a name="28"><span class="lineNum">      28 </span>            : public:</a>
+<a name="29"><span class="lineNum">      29 </span>            :   explicit MahalanobisDistance( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="30"><span class="lineNum">      30 </span>            : };</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">      12504 : PLUMED_REGISTER_METRIC(MahalanobisDistance,&quot;MAHALANOBIS&quot;)</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 : MahalanobisDistance::MahalanobisDistance( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 :   ArgumentOnlyDistance(ro)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   hasmetric=true;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MetricRegister.cpp.func-sort-c.html b/coverage/reference/MetricRegister.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4643a58a16
--- /dev/null
+++ b/coverage/reference/MetricRegister.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MetricRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MetricRegister.cpp<span style="font-size: 80%;"> (<a href="MetricRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MetricRegister.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#25">_ZN4PLMD14MetricRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#46">_ZN4PLMD14MetricRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS_22ReferenceConfigurationESt14default_deleteIS8_EERKNS_29ReferenceConfigurationOptionsEE</a></td>
+              <td class="coverFnHi">45848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#38">_ZN4PLMD14MetricRegister6removeEPFSt10unique_ptrINS_22ReferenceConfigurationESt14default_deleteIS2_EERKNS_29ReferenceConfigurationOptionsEE</a></td>
+              <td class="coverFnHi">45848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#51">_ZN4PLMD14MetricRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">518879</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#33">_ZN4PLMD14metricRegisterEv</a></td>
+              <td class="coverFnHi">610575</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MetricRegister.cpp.func.html b/coverage/reference/MetricRegister.cpp.func.html
new file mode 100644
index 0000000000..9ff6e6cc0d
--- /dev/null
+++ b/coverage/reference/MetricRegister.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MetricRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MetricRegister.cpp<span style="font-size: 80%;"> (<a href="MetricRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MetricRegister.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#46">_ZN4PLMD14MetricRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS_22ReferenceConfigurationESt14default_deleteIS8_EERKNS_29ReferenceConfigurationOptionsEE</a></td>
+              <td class="coverFnHi">45848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#51">_ZN4PLMD14MetricRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">518879</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#38">_ZN4PLMD14MetricRegister6removeEPFSt10unique_ptrINS_22ReferenceConfigurationESt14default_deleteIS2_EERKNS_29ReferenceConfigurationOptionsEE</a></td>
+              <td class="coverFnHi">45848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#25">_ZN4PLMD14MetricRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.cpp.gcov.html#33">_ZN4PLMD14metricRegisterEv</a></td>
+              <td class="coverFnHi">610575</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MetricRegister.cpp.gcov.html b/coverage/reference/MetricRegister.cpp.gcov.html
new file mode 100644
index 0000000000..5866c1851c
--- /dev/null
+++ b/coverage/reference/MetricRegister.cpp.gcov.html
@@ -0,0 +1,134 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MetricRegister.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MetricRegister.cpp<span style="font-size: 80%;"> (source / <a href="MetricRegister.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;iostream&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">       4168 : MetricRegister::~MetricRegister() {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">       4168 :   if(m.size()&gt;0) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineNoCov">          0 :     std::string names=&quot;&quot;;</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineNoCov">          0 :     for(const auto &amp; p : m) names+=p.first+&quot; &quot;;</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;WARNING: ReferenceConfiguration &quot;+ names +&quot; has not been properly unregistered. This might lead to memory leak!!\n&quot;;</span></a>
+<a name="32"><span class="lineNum">      32 </span>            :   }</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       4168 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     610575 : MetricRegister&amp; metricRegister() {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     610575 :   static MetricRegister ans;</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     610575 :   return ans;</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : }</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      45848 : void MetricRegister::remove(creator_pointer f) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     266752 :   for(auto p=m.begin(); p!=m.end(); ++p) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">     266752 :     if((*p).second==f) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      45848 :       m.erase(p); break;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :     }</a>
+<a name="45"><span class="lineNum">      45 </span>            :   }</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      45848 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      45848 : void MetricRegister::add( std::string type, creator_pointer f ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 :   plumed_massert(m.count(type)==0,&quot;type has already been registered&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      45848 :   m.insert(std::pair&lt;std::string,creator_pointer&gt;(type,f));</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      45848 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     518879 : bool MetricRegister::check(const std::string &amp; type) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">     518879 :   if( m.count(type)&gt;0 ) return true;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   return false;</a>
+<a name="56"><span class="lineNum">      56 </span>            : }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MetricRegister.h.func-sort-c.html b/coverage/reference/MetricRegister.h.func-sort-c.html
new file mode 100644
index 0000000000..56bc2fddfe
--- /dev/null
+++ b/coverage/reference/MetricRegister.h.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MetricRegister.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MetricRegister.h<span style="font-size: 80%;"> (<a href="MetricRegister.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MetricRegister.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_20ArgumentOnlyDistanceEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_20ArgumentOnlyDistanceEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_15MultiDomainRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_15MultiDomainRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_5DRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_16SingleDomainRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_8RMSDBaseEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_8RMSDBaseEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_22ReferenceConfigurationEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">518743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_22ReferenceConfigurationEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnHi">518743</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MetricRegister.h.func.html b/coverage/reference/MetricRegister.h.func.html
new file mode 100644
index 0000000000..e989ad3960
--- /dev/null
+++ b/coverage/reference/MetricRegister.h.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MetricRegister.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MetricRegister.h<span style="font-size: 80%;"> (<a href="MetricRegister.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MetricRegister.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_15MultiDomainRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_15MultiDomainRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_16SingleDomainRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_20ArgumentOnlyDistanceEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_20ArgumentOnlyDistanceEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_22ReferenceConfigurationEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">518743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_22ReferenceConfigurationEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnHi">518743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_5DRMSDEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#70">_ZN4PLMD14MetricRegister6createINS_8RMSDBaseEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MetricRegister.h.gcov.html#97">_ZN4PLMD14MetricRegister6createINS_8RMSDBaseEEESt10unique_ptrIT_St14default_deleteIS4_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_3PDBE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MetricRegister.h.gcov.html b/coverage/reference/MetricRegister.h.gcov.html
new file mode 100644
index 0000000000..7d468207d4
--- /dev/null
+++ b/coverage/reference/MetricRegister.h.gcov.html
@@ -0,0 +1,189 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MetricRegister.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MetricRegister.h<span style="font-size: 80%;"> (source / <a href="MetricRegister.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">94.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_MetricRegister_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_MetricRegister_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;map&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;ReferenceConfiguration.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class PDB;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class MetricRegister {</a>
+<a name="39"><span class="lineNum">      39 </span>            : private:</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Pointer to a function which, given the type for a ReferenceConfiguration, creates it</a>
+<a name="41"><span class="lineNum">      41 </span>            :   typedef std::unique_ptr&lt;ReferenceConfiguration&gt; (*creator_pointer)(const ReferenceConfigurationOptions&amp;);</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// The set of possible distribution functions we can work with</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::map&lt;std::string,creator_pointer&gt; m;</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// The destructor</a>
+<a name="46"><span class="lineNum">      46 </span>            :   ~MetricRegister();</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Add a new metric to the register of metrics</a>
+<a name="48"><span class="lineNum">      48 </span>            :   void add( std::string type, creator_pointer );</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Remove a metric from the register of metrics</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void remove(creator_pointer f);</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Verify if a particular metric type is present in the register</a>
+<a name="52"><span class="lineNum">      52 </span>            :   bool check(const std::string &amp; type);</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Create a reference configuration and don't set a point of reference</a>
+<a name="54"><span class="lineNum">      54 </span>            :   template &lt;class T&gt;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::unique_ptr&lt;T&gt; create( const std::string&amp; type );</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Create a reference configuration and set the point of reference from the pdb</a>
+<a name="57"><span class="lineNum">      57 </span>            :   template &lt;class T&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::unique_ptr&lt;T&gt; create( const std::string&amp; type, const PDB&amp; pdb );</a>
+<a name="59"><span class="lineNum">      59 </span>            : };</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : MetricRegister&amp; metricRegister();</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : #define PLUMED_REGISTER_METRIC(classname,type) \</a>
+<a name="64"><span class="lineNum">      64 </span>            :   namespace { class classname##RegisterMe{ \</a>
+<a name="65"><span class="lineNum">      65 </span>            :     static std::unique_ptr&lt;ReferenceConfiguration&gt; create(const PLMD::ReferenceConfigurationOptions&amp;ro){return PLMD::Tools::make_unique&lt;classname&gt;(ro);} \</a>
+<a name="66"><span class="lineNum">      66 </span>            :   public: \</a>
+<a name="67"><span class="lineNum">      67 </span>            :     classname##RegisterMe(){PLMD::metricRegister().add(type,create);}; \</a>
+<a name="68"><span class="lineNum">      68 </span>            :     ~classname##RegisterMe(){PLMD::metricRegister().remove(create);}; \</a>
+<a name="69"><span class="lineNum">      69 </span>            :   } classname##RegisterMeObject; }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : template &lt;class T&gt;</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">     518879 : std::unique_ptr&lt;T&gt; MetricRegister::create( const std::string&amp; type ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::string ftype;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     518879 :   if( type.find(&quot;MULTI-&quot;)!=std::string::npos ) {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     ftype=&quot;MULTI&quot;;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   } else {</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     518874 :     std::size_t dash=type.find(&quot;-FAST&quot;); // We must remove the fast label</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    1037748 :     ftype=type.substr(0,dash);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   }</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     518879 :   plumed_massert( check(ftype), &quot;metric &quot; + ftype + &quot; does not exist&quot; );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     518879 :   ReferenceConfigurationOptions ro( type );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : // put immediately the result in a safe pointer</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     518879 :   std::unique_ptr&lt;ReferenceConfiguration&gt; conf( m[ftype]( ro ) );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : // try conversion</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        136 :   T*ptr=dynamic_cast&lt;T*&gt;( conf.get() );</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : // if this throws, the unique_ptr conf is deleted.</a>
+<a name="87"><span class="lineNum">      87 </span>            : // Notice that with the original version of the code (2.4) an error here</a>
+<a name="88"><span class="lineNum">      88 </span>            : // would have lead to a memory leak.</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     518879 :   if(!ptr ) plumed_merror( type + &quot; metric is not valid in this context&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : // release ownership in order to transfer it to returned pointer</a>
+<a name="91"><span class="lineNum">      91 </span>            :   conf.release();</a>
+<a name="92"><span class="lineNum">      92 </span>            : // notice that I should pass ptr here rather than conf.release(),</a>
+<a name="93"><span class="lineNum">      93 </span>            : // since the type is different</a>
+<a name="94"><span class="lineNum">      94 </span>            : // cppcheck-suppress returnDanglingLifetime</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     518879 :   return std::unique_ptr&lt;T&gt;(ptr);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     518879 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : template &lt;class T&gt;</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     518823 : std::unique_ptr&lt;T&gt; MetricRegister::create( const std::string&amp; type, const PDB&amp; pdb ) {</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::string rtype;</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     518823 :   if( type.length()==0 ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         20 :     rtype=pdb.getMtype();</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         10 :     plumed_massert(rtype.length()&gt;0, &quot;TYPE not specified in pdb input file&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   } else {</a>
+<a name="105"><span class="lineNum">     105 </span>            :     rtype=type;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">     518823 :   std::unique_ptr&lt;T&gt; confout( create&lt;T&gt;( rtype ) );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     518823 :   confout-&gt;read( pdb );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     518823 :   return confout;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MultiDomainRMSD.cpp.func-sort-c.html b/coverage/reference/MultiDomainRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d801a31f4b
--- /dev/null
+++ b/coverage/reference/MultiDomainRMSD.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MultiDomainRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MultiDomainRMSD.cpp<span style="font-size: 80%;"> (<a href="MultiDomainRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntryMed">87.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiDomainRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#84">_ZN4PLMD15MultiDomainRMSD17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#29">_ZN4PLMD15MultiDomainRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#161">_ZNK4PLMD15MultiDomainRMSD25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#142">_ZN4PLMD15MultiDomainRMSD15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#134">_ZN4PLMD15MultiDomainRMSD28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#27">_ZN4PLMD12_GLOBAL__N_125MultiDomainRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#36">_ZN4PLMD15MultiDomainRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#29">_ZN4PLMD15MultiDomainRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#128">_ZNK4PLMD15MultiDomainRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#88">_ZNK4PLMD15MultiDomainRMSD9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#174">_ZNK4PLMD15MultiDomainRMSD33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#27">_ZN4PLMD12_GLOBAL__N_125MultiDomainRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#27">_ZN4PLMD12_GLOBAL__N_125MultiDomainRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MultiDomainRMSD.cpp.func.html b/coverage/reference/MultiDomainRMSD.cpp.func.html
new file mode 100644
index 0000000000..cff759fbab
--- /dev/null
+++ b/coverage/reference/MultiDomainRMSD.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MultiDomainRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MultiDomainRMSD.cpp<span style="font-size: 80%;"> (<a href="MultiDomainRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntryMed">87.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiDomainRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#27">_ZN4PLMD12_GLOBAL__N_125MultiDomainRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#27">_ZN4PLMD12_GLOBAL__N_125MultiDomainRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#27">_ZN4PLMD12_GLOBAL__N_125MultiDomainRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#142">_ZN4PLMD15MultiDomainRMSD15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#84">_ZN4PLMD15MultiDomainRMSD17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#134">_ZN4PLMD15MultiDomainRMSD28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#36">_ZN4PLMD15MultiDomainRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#29">_ZN4PLMD15MultiDomainRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#29">_ZN4PLMD15MultiDomainRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#161">_ZNK4PLMD15MultiDomainRMSD25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#174">_ZNK4PLMD15MultiDomainRMSD33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#128">_ZNK4PLMD15MultiDomainRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiDomainRMSD.cpp.gcov.html#88">_ZNK4PLMD15MultiDomainRMSD9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">37</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/MultiDomainRMSD.cpp.gcov.html b/coverage/reference/MultiDomainRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..8c3316e8df
--- /dev/null
+++ b/coverage/reference/MultiDomainRMSD.cpp.gcov.html
@@ -0,0 +1,285 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/MultiDomainRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - MultiDomainRMSD.cpp<span style="font-size: 80%;"> (source / <a href="MultiDomainRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntry">103</td>
+            <td class="headerCovTableEntryMed">87.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiDomainRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;SingleDomainRMSD.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">      12514 : PLUMED_REGISTER_METRIC(MultiDomainRMSD,&quot;MULTI&quot;)</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          5 : MultiDomainRMSD::MultiDomainRMSD( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="32"><span class="lineNum">      32 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="33"><span class="lineNum">      33 </span>            :   ReferenceAtoms(ro),</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          5 :   ftype(ro.getMultiRMSDType())</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          5 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">          5 : void MultiDomainRMSD::read( const PDB&amp; pdb ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          5 :   unsigned nblocks =  pdb.getNumberOfAtomBlocks();</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          5 :   if( nblocks&lt;2 ) error(&quot;multidomain RMSD only has one block of atoms&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            :   std::vector&lt;Vector&gt; positions; std::vector&lt;double&gt; align, displace;</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          5 :   std::string num; blocks.resize( nblocks+1 ); blocks[0]=0;</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         15 :   for(unsigned i=0; i&lt;nblocks; ++i) blocks[i+1]=pdb.getAtomBlockEnds()[i];</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            :   double tmp, lower=0.0, upper=std::numeric_limits&lt;double&gt;::max( );</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         10 :   if( pdb.getArgumentValue(&quot;LOWER_CUTOFF&quot;,tmp) ) lower=tmp;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         10 :   if( pdb.getArgumentValue(&quot;UPPER_CUTOFF&quot;,tmp) ) upper=tmp;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          5 :   bool nopbc=pdb.hasFlag(&quot;NOPBC&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          5 :   domains.resize(0); weights.resize(0);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         15 :   for(unsigned i=1; i&lt;=nblocks; ++i) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         10 :     Tools::convert(i,num);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         10 :     if( ftype==&quot;RMSD&quot; ) {</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :       // parse(&quot;TYPE&quot;+num, ftype );</a>
+<a name="56"><span class="lineNum">      56 </span>            :       lower=0.0; upper=std::numeric_limits&lt;double&gt;::max( );</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :       if( pdb.getArgumentValue(&quot;LOWER_CUTOFF&quot;+num,tmp) ) lower=tmp;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :       if( pdb.getArgumentValue(&quot;UPPER_CUTOFF&quot;+num,tmp) ) upper=tmp;</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :       nopbc=pdb.hasFlag(&quot;NOPBC&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :     }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         10 :     domains.emplace_back( metricRegister().create&lt;SingleDomainRMSD&gt;( ftype ) );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         10 :     positions.resize( blocks[i] - blocks[i-1] );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         10 :     align.resize( blocks[i] - blocks[i-1] );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         10 :     displace.resize( blocks[i] - blocks[i-1] );</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :     unsigned n=0;</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         69 :     for(unsigned j=blocks[i-1]; j&lt;blocks[i]; ++j) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         59 :       positions[n]=pdb.getPositions()[j];</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         59 :       align[n]=pdb.getOccupancy()[j];</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         59 :       displace[n]=pdb.getBeta()[j];</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         59 :       n++;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :     }</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         10 :     domains[i-1]-&gt;setBoundsOnDistances( !nopbc, lower, upper );</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         10 :     domains[i-1]-&gt;setReferenceAtoms( positions, align, displace );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         10 :     domains[i-1]-&gt;setupRMSDObject();</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         10 :     double ww=0;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         20 :     if( !pdb.getArgumentValue(&quot;WEIGHT&quot;+num,ww) ) weights.push_back( 1.0 );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     else weights.push_back( ww );</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   }</a>
+<a name="80"><span class="lineNum">      80 </span>            :   // And set the atom numbers for this object</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          5 :   indices.resize(0); atom_der_index.resize(0);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         64 :   for(unsigned i=0; i&lt;pdb.size(); ++i) { indices.push_back( pdb.getAtomNumbers()[i] ); atom_der_index.push_back(i); }</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   // setAtomNumbers( pdb.getAtomNumbers() );</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          5 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 : void MultiDomainRMSD::setReferenceAtoms( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; align_in, const std::vector&lt;double&gt;&amp; displace_in ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         37 : double MultiDomainRMSD::calculate( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         37 :   double totd=0.; Tensor tvirial; std::vector&lt;Vector&gt; mypos; MultiValue tvals( 1, 3*pos.size()+9 );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         37 :   ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals ); myder.clear();</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        111 :   for(unsigned i=0; i&lt;domains.size(); ++i) {</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     // Must extract appropriate positions here</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         74 :     mypos.resize( blocks[i+1] - blocks[i] );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         74 :     if( myder.calcUsingPCAOption() ) domains[i]-&gt;setupPCAStorage( tder );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        453 :     unsigned n=0; for(unsigned j=blocks[i]; j&lt;blocks[i+1]; ++j) { tder.setAtomIndex(n,j); mypos[n]=pos[j]; n++; }</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        453 :     for(unsigned k=n; k&lt;getNumberOfAtoms(); ++k) tder.setAtomIndex(k,3*pos.size()+10);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :     // This actually does the calculation</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         74 :     totd += weights[i]*domains[i]-&gt;calculate( mypos, pbc, tder, true );</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     // Now merge the derivative</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         74 :     myder.copyScaledDerivatives( 0, weights[i], tvals );</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :     // If PCA copy PCA stuff</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         74 :     if( myder.calcUsingPCAOption() ) {</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :       unsigned n=0;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         44 :       if( tder.centeredpos.size()&gt;0 ) myder.rot[i]=tder.rot[0];</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        198 :       for(unsigned j=blocks[i]; j&lt;blocks[i+1]; ++j) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        154 :         myder.displacement[j]=weights[i]*tder.displacement[n];  // Multiplication by weights here ensures that normalisation is done correctly</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        154 :         if( tder.centeredpos.size()&gt;0 ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         77 :           myder.centeredpos[j]=tder.centeredpos[n];</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1001 :           for(unsigned p=0; p&lt;3; ++p) for(unsigned q=0; q&lt;3; ++q) myder.DRotDPos(p,q)[j]=tder.DRotDPos(p,q)[n];</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :         }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        154 :         n++;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :       }</a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span>            :     // Make sure virial status is set correctly in output derivative pack</a>
+<a name="118"><span class="lineNum">     118 </span>            :     // This is only done here so I do this by using class friendship</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         74 :     if( tder.virialWasSet() ) myder.boxWasSet=true;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         37 :   if( !myder.updateComplete() ) myder.updateDynamicLists();</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         37 :   if( !squared ) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         15 :     totd=std::sqrt(totd); double xx=0.5/totd;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         15 :     myder.scaleAllDerivatives( xx );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         37 :   return totd;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         37 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         22 : double MultiDomainRMSD::calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg,</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :                               ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="132"><span class="lineNum">     132 </span>            :   plumed_dbg_assert( vals.size()==0 &amp;&amp; pos.size()==getNumberOfAtoms() &amp;&amp; arg.size()==0 );</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         22 :   return calculate( pos, pbc, myder, squared );</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          2 : bool MultiDomainRMSD::pcaIsEnabledForThisReference() {</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   bool enabled=true;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;domains.size(); ++i) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          4 :     if( !domains[i]-&gt;pcaIsEnabledForThisReference() ) enabled=false;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :   return enabled;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          2 : void MultiDomainRMSD::setupPCAStorage( ReferenceValuePack&amp; mypack ) {</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   plumed_dbg_assert( pcaIsEnabledForThisReference() );</a>
+<a name="146"><span class="lineNum">     146 </span>            :   mypack.switchOnPCAOption();</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :   mypack.displacement.resize( getNumberOfAtoms() );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :   mypack.centeredpos.resize( getNumberOfAtoms() );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   mypack.DRotDPos.resize(3,3); mypack.rot.resize( domains.size() );</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         26 :   for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) mypack.DRotDPos(i,j).resize( getNumberOfAtoms() );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          2 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : // Vector MultiDomainRMSD::getAtomicDisplacement( const unsigned&amp; iatom ){</a>
+<a name="154"><span class="lineNum">     154 </span>            : //   for(unsigned i=0;i&lt;domains.size();++i){</a>
+<a name="155"><span class="lineNum">     155 </span>            : //       unsigned n=0;</a>
+<a name="156"><span class="lineNum">     156 </span>            : //       for(unsigned j=blocks[i];j&lt;blocks[i+1];++j){</a>
+<a name="157"><span class="lineNum">     157 </span>            : //           if( j==iatom ) return weights[i]*domains[i]-&gt;getAtomicDisplacement(n);</a>
+<a name="158"><span class="lineNum">     158 </span>            : //           n++;</a>
+<a name="159"><span class="lineNum">     159 </span>            : //       }</a>
+<a name="160"><span class="lineNum">     160 </span>            : //   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : // }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 : void MultiDomainRMSD::extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; direction ) const {</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::vector&lt;Vector&gt; mypos, mydir;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;domains.size(); ++i) {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     // Must extract appropriate positions here</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     mypos.resize( blocks[i+1] - blocks[i] ); mydir.resize( blocks[i+1] - blocks[i] );</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     unsigned n=0; for(unsigned j=blocks[i]; j&lt;blocks[i+1]; ++j) { mypos[n]=pos[j]; n++; }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     // Do the calculation</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     domains[i]-&gt;extractAtomicDisplacement( mypos, mydir );</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     // Extract the direction</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :     n=0; for(unsigned j=blocks[i]; j&lt;blocks[i+1]; ++j) { direction[j]=weights[i]*mydir[n];  n++; }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         44 : double MultiDomainRMSD::projectAtomicDisplacementOnVector( const bool&amp; normalized, const std::vector&lt;Vector&gt;&amp; vecs, ReferenceValuePack&amp; mypack ) const {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         44 :   double totd=0.; std::vector&lt;Vector&gt; tvecs; mypack.clear();</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         44 :   MultiValue tvals( 1, mypack.getNumberOfDerivatives() ); ReferenceValuePack tder( 0, getNumberOfAtoms(), tvals );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        132 :   for(unsigned i=0; i&lt;domains.size(); ++i) {</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     // Must extract appropriate positions here</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         88 :     tvecs.resize( blocks[i+1] - blocks[i] ); domains[i]-&gt;setupPCAStorage( tder );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         88 :     if( tder.centeredpos.size()&gt;0 ) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        572 :       for(unsigned p=0; p&lt;3; ++p) for(unsigned q=0; q&lt;3; ++q) tder.DRotDPos(p,q).resize( tvecs.size() );</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     }</a>
+<a name="185"><span class="lineNum">     185 </span>            :     // Extract information from storage pack and put in local pack</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         88 :     if( tder.centeredpos.size()&gt;0 ) tder.rot[0]=mypack.rot[i];</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     unsigned n=0;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        396 :     for(unsigned j=blocks[i]; j&lt;blocks[i+1]; ++j) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        308 :       tder.setAtomIndex(n,j); tvecs[n] = vecs[j]; tder.displacement[n]=mypack.displacement[j] / weights[i];</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        308 :       if( tder.centeredpos.size()&gt;0 ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        154 :         tder.centeredpos[n]=mypack.centeredpos[j];</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       2002 :         for(unsigned p=0; p&lt;3; ++p) for(unsigned q=0; q&lt;3; ++q) tder.DRotDPos(p,q)[n]=mypack.DRotDPos(p,q)[j];</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :       }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        308 :       n++;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     }</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        396 :     for(unsigned k=n; k&lt;getNumberOfAtoms(); ++k) tder.setAtomIndex(k,3*vecs.size()+10);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :     // Do the calculations</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         88 :     totd += weights[i]*domains[i]-&gt;projectAtomicDisplacementOnVector( normalized, tvecs, tder );</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            :     // And derivatives</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         88 :     mypack.copyScaledDerivatives( 0, weights[i], tvals );</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         44 :   if( !mypack.updateComplete() ) mypack.updateDynamicLists();</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         44 :   return totd;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         44 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/NormalizedEuclideanDistance.cpp.func-sort-c.html b/coverage/reference/NormalizedEuclideanDistance.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a8d399338b
--- /dev/null
+++ b/coverage/reference/NormalizedEuclideanDistance.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/NormalizedEuclideanDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - NormalizedEuclideanDistance.cpp<span style="font-size: 80%;"> (<a href="NormalizedEuclideanDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="NormalizedEuclideanDistance.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_137NormalizedEuclideanDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#32">_ZN4PLMD27NormalizedEuclideanDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#32">_ZN4PLMD27NormalizedEuclideanDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_137NormalizedEuclideanDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_137NormalizedEuclideanDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/reference/NormalizedEuclideanDistance.cpp.func.html b/coverage/reference/NormalizedEuclideanDistance.cpp.func.html
new file mode 100644
index 0000000000..9b6c1eb778
--- /dev/null
+++ b/coverage/reference/NormalizedEuclideanDistance.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/NormalizedEuclideanDistance.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - NormalizedEuclideanDistance.cpp<span style="font-size: 80%;"> (<a href="NormalizedEuclideanDistance.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_137NormalizedEuclideanDistanceRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_137NormalizedEuclideanDistanceRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#30">_ZN4PLMD12_GLOBAL__N_137NormalizedEuclideanDistanceRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#32">_ZN4PLMD27NormalizedEuclideanDistanceC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NormalizedEuclideanDistance.cpp.gcov.html#32">_ZN4PLMD27NormalizedEuclideanDistanceC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/reference/NormalizedEuclideanDistance.cpp.gcov.html b/coverage/reference/NormalizedEuclideanDistance.cpp.gcov.html
new file mode 100644
index 0000000000..0fa0c567a2
--- /dev/null
+++ b/coverage/reference/NormalizedEuclideanDistance.cpp.gcov.html
@@ -0,0 +1,117 @@
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - NormalizedEuclideanDistance.cpp<span style="font-size: 80%;"> (source / <a href="NormalizedEuclideanDistance.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">20.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">40.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ArgumentOnlyDistance.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : class NormalizedEuclideanDistance : public ArgumentOnlyDistance {</a>
+<a name="28"><span class="lineNum">      28 </span>            : public:</a>
+<a name="29"><span class="lineNum">      29 </span>            :   explicit NormalizedEuclideanDistance( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="30"><span class="lineNum">      30 </span>            : };</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">      12504 : PLUMED_REGISTER_METRIC(NormalizedEuclideanDistance,&quot;NORM-EUCLIDEAN&quot;)</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 : NormalizedEuclideanDistance::NormalizedEuclideanDistance( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 :   ArgumentOnlyDistance(ro)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   hasweights=true;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/OptimalRMSD.cpp.func-sort-c.html b/coverage/reference/OptimalRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..37946aba75
--- /dev/null
+++ b/coverage/reference/OptimalRMSD.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/OptimalRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - OptimalRMSD.cpp<span style="font-size: 80%;"> (<a href="OptimalRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OptimalRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#49">_ZN4PLMD11OptimalRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#35">_ZN4PLMD11OptimalRMSD28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#37">_ZN4PLMD11OptimalRMSD15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#56">_ZN4PLMD11OptimalRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">427</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#49">_ZN4PLMD11OptimalRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">437</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#47">_ZN4PLMD12_GLOBAL__N_121OptimalRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">437</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#36">_ZN4PLMD11OptimalRMSD15setupRMSDObjectEv</a></td>
+              <td class="coverFnHi">455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#79">_ZNK4PLMD11OptimalRMSD25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnHi">1107</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#86">_ZNK4PLMD11OptimalRMSD33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">1158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#47">_ZN4PLMD12_GLOBAL__N_121OptimalRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#47">_ZN4PLMD12_GLOBAL__N_121OptimalRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#60">_ZNK4PLMD11OptimalRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">218933</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/OptimalRMSD.cpp.func.html b/coverage/reference/OptimalRMSD.cpp.func.html
new file mode 100644
index 0000000000..a0c9054c51
--- /dev/null
+++ b/coverage/reference/OptimalRMSD.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/OptimalRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - OptimalRMSD.cpp<span style="font-size: 80%;"> (<a href="OptimalRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OptimalRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#37">_ZN4PLMD11OptimalRMSD15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">72</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#36">_ZN4PLMD11OptimalRMSD15setupRMSDObjectEv</a></td>
+              <td class="coverFnHi">455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#35">_ZN4PLMD11OptimalRMSD28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#56">_ZN4PLMD11OptimalRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">427</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#49">_ZN4PLMD11OptimalRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">437</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#49">_ZN4PLMD11OptimalRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#47">_ZN4PLMD12_GLOBAL__N_121OptimalRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">437</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#47">_ZN4PLMD12_GLOBAL__N_121OptimalRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#47">_ZN4PLMD12_GLOBAL__N_121OptimalRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#79">_ZNK4PLMD11OptimalRMSD25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnHi">1107</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#86">_ZNK4PLMD11OptimalRMSD33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">1158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OptimalRMSD.cpp.gcov.html#60">_ZNK4PLMD11OptimalRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">218933</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/OptimalRMSD.cpp.gcov.html b/coverage/reference/OptimalRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..c398838031
--- /dev/null
+++ b/coverage/reference/OptimalRMSD.cpp.gcov.html
@@ -0,0 +1,194 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/OptimalRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - OptimalRMSD.cpp<span style="font-size: 80%;"> (source / <a href="OptimalRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;RMSDBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class OptimalRMSD : public RMSDBase {</a>
+<a name="30"><span class="lineNum">      30 </span>            : private:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   bool fast;</a>
+<a name="32"><span class="lineNum">      32 </span>            :   RMSD myrmsd;</a>
+<a name="33"><span class="lineNum">      33 </span>            : public:</a>
+<a name="34"><span class="lineNum">      34 </span>            :   explicit OptimalRMSD(const ReferenceConfigurationOptions&amp; ro);</a>
+<a name="35"><span class="lineNum">      35 </span>            :   void read( const PDB&amp; ) override;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   double calc( const std::vector&lt;Vector&gt;&amp; pos, ReferenceValuePack&amp; myder, const bool&amp; squared ) const override;</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         45 :   bool pcaIsEnabledForThisReference() override { return true; }</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        910 :   void setupRMSDObject() override { myrmsd.clear(); myrmsd.set(getAlign(),getDisplace(),getReferencePositions(),&quot;OPTIMAL&quot;); }</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         72 :   void setupPCAStorage( ReferenceValuePack&amp; mypack ) override {</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :     mypack.switchOnPCAOption();</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         72 :     mypack.centeredpos.resize( getNumberOfAtoms() );</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         72 :     mypack.displacement.resize( getNumberOfAtoms() );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         72 :     mypack.DRotDPos.resize(3,3); mypack.rot.resize(1);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         72 :   }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   void extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; direction ) const override;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double projectAtomicDisplacementOnVector( const bool&amp; normalized, const std::vector&lt;Vector&gt;&amp; vecs, ReferenceValuePack&amp; mypack ) const override;</a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      13378 : PLUMED_REGISTER_METRIC(OptimalRMSD,&quot;OPTIMAL&quot;)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        437 : OptimalRMSD::OptimalRMSD(const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        437 :   RMSDBase(ro)</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        437 :   fast=ro.usingFastOption();</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        437 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        427 : void OptimalRMSD::read( const PDB&amp; pdb ) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        427 :   readReference( pdb ); setupRMSDObject();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        427 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     218933 : double OptimalRMSD::calc( const std::vector&lt;Vector&gt;&amp; pos, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   double d;</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">     218933 :   if( myder.calcUsingPCAOption() ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       2786 :     std::vector&lt;Vector&gt; centeredreference( getNumberOfAtoms () );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       2786 :     d=myrmsd.calc_PCAelements(pos,myder.getAtomVector(),myder.rot[0],myder.DRotDPos,myder.getAtomsDisplacementVector(),myder.centeredpos,centeredreference,squared);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       2786 :     unsigned nat = pos.size();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      48548 :     for(unsigned i=0; i&lt;nat; ++i) { myder.getAtomsDisplacementVector()[i] -= getReferencePosition(i); myder.getAtomsDisplacementVector()[i] *= getDisplace()[i]; }</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     216147 :   } else if( fast ) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     192640 :     if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment&lt;false,true&gt;(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 :     else d=myrmsd.optimalAlignment&lt;false,false&gt;(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   } else {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      23507 :     if( getAlign()==getDisplace() ) d=myrmsd.optimalAlignment&lt;true,true&gt;(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        111 :     else d=myrmsd.optimalAlignment&lt;true,false&gt;(getAlign(),getDisplace(),pos,getReferencePositions(),myder.getAtomVector(),squared);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">   17762561 :   myder.clear(); for(unsigned i=0; i&lt;pos.size(); ++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     218933 :   if( !myder.updateComplete() ) myder.updateDynamicLists();</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     218933 :   return d;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1107 : void OptimalRMSD::extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; direction ) const {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       1107 :   std::vector&lt;Tensor&gt; rot(1);  Matrix&lt;std::vector&lt;Vector&gt; &gt; DRotDPos( 3, 3 );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1107 :   std::vector&lt;Vector&gt; centeredreference( getNumberOfAtoms() ), centeredpos( getNumberOfAtoms() ), avector( getNumberOfAtoms() );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1107 :   myrmsd.calc_PCAelements(pos,avector,rot[0],DRotDPos,direction,centeredpos,centeredreference,true);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      15498 :   unsigned nat = pos.size(); for(unsigned i=0; i&lt;nat; ++i) direction[i] = getDisplace()[i]*( direction[i] - getReferencePosition(i) );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1107 : }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1158 : double OptimalRMSD::projectAtomicDisplacementOnVector( const bool&amp; normalized, const std::vector&lt;Vector&gt;&amp; vecs, ReferenceValuePack&amp; mypack ) const {</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   plumed_dbg_assert( mypack.calcUsingPCAOption() );</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1158 :   double proj=0.0; mypack.clear();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      15662 :   for(unsigned i=0; i&lt;vecs.size(); ++i) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      14504 :     proj += dotProduct( mypack.getAtomsDisplacementVector()[i], vecs[i] );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   }</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       4632 :   for(unsigned a=0; a&lt;3; a++) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      13896 :     for(unsigned b=0; b&lt;3; b++) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     140958 :       double tmp1=0.; for(unsigned n=0; n&lt;getNumberOfAtoms(); n++) tmp1+=mypack.centeredpos[n][b]*vecs[n][a];</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     140958 :       for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     130536 :         if( normalized ) mypack.addAtomDerivatives( iat, getDisplace()[iat]*mypack.DRotDPos[a][b][iat]*tmp1 );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     127764 :         else mypack.addAtomDerivatives( iat, mypack.DRotDPos[a][b][iat]*tmp1 );</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :       }</a>
+<a name="103"><span class="lineNum">     103 </span>            :     }</a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1158 :   Tensor trot=mypack.rot[0].transpose();</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1158 :   Vector v1; v1.zero(); double prefactor = 1. / static_cast&lt;double&gt;( getNumberOfAtoms() );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      15662 :   for(unsigned n=0; n&lt;getNumberOfAtoms(); n++) v1+=prefactor*matmul(trot,vecs[n]);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1158 :   if( normalized ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        374 :     for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) mypack.addAtomDerivatives( iat, getDisplace()[iat]*(matmul(trot,vecs[iat]) - v1) );</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   } else {</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      15288 :     for(unsigned iat=0; iat&lt;getNumberOfAtoms(); iat++) mypack.addAtomDerivatives( iat, (matmul(trot,vecs[iat]) - v1) );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1158 :   if( !mypack.updateComplete() ) mypack.updateDynamicLists();</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1158 :   return proj;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/RMSDBase.cpp.func-sort-c.html b/coverage/reference/RMSDBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9e095da53a
--- /dev/null
+++ b/coverage/reference/RMSDBase.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/RMSDBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - RMSDBase.cpp<span style="font-size: 80%;"> (<a href="RMSDBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RMSDBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#24">_ZN4PLMD8RMSDBaseC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#24">_ZN4PLMD8RMSDBaseC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">472</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#30">_ZNK4PLMD8RMSDBase9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">40496</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#35">_ZNK4PLMD8RMSDBase4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">178609</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/RMSDBase.cpp.func.html b/coverage/reference/RMSDBase.cpp.func.html
new file mode 100644
index 0000000000..b40b7d7159
--- /dev/null
+++ b/coverage/reference/RMSDBase.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/RMSDBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - RMSDBase.cpp<span style="font-size: 80%;"> (<a href="RMSDBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="RMSDBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#24">_ZN4PLMD8RMSDBaseC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#24">_ZN4PLMD8RMSDBaseC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">472</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#35">_ZNK4PLMD8RMSDBase4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">178609</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSDBase.cpp.gcov.html#30">_ZNK4PLMD8RMSDBase9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">40496</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/RMSDBase.cpp.gcov.html b/coverage/reference/RMSDBase.cpp.gcov.html
new file mode 100644
index 0000000000..a4308684a5
--- /dev/null
+++ b/coverage/reference/RMSDBase.cpp.gcov.html
@@ -0,0 +1,118 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/RMSDBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - RMSDBase.cpp<span style="font-size: 80%;"> (source / <a href="RMSDBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;RMSDBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span><span class="lineCov">        472 : RMSDBase::RMSDBase( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="27"><span class="lineNum">      27 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        472 :   SingleDomainRMSD(ro)</span></a>
+<a name="29"><span class="lineNum">      29 </span>            : {</a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        472 : }</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">      40496 : double RMSDBase::calculate( const std::vector&lt;Vector&gt;&amp; pos, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : //  clearDerivatives();</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">      40496 :   return calc( pos, myder, squared );</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : }</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     178609 : double RMSDBase::calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   plumed_dbg_assert( pos.size()==getNumberOfAtoms() );</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     178609 :   return calc( pos, myder, squared );</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : }</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceArguments.cpp.func-sort-c.html b/coverage/reference/ReferenceArguments.cpp.func-sort-c.html
new file mode 100644
index 0000000000..de585c1ccf
--- /dev/null
+++ b/coverage/reference/ReferenceArguments.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceArguments.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceArguments.cpp<span style="font-size: 80%;"> (<a href="ReferenceArguments.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntry">106</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceArguments.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#122">_ZN4PLMD18ReferenceArguments18getReferenceMetricEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#28">_ZN4PLMD18ReferenceArgumentsC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#93">_ZN4PLMD18ReferenceArguments19getArgumentRequestsERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EEb</a></td>
+              <td class="coverFnHi">187</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#71">_ZN4PLMD18ReferenceArguments21setReferenceArgumentsERKSt6vectorIdSaIdEES5_</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#88">_ZN4PLMD18ReferenceArguments22moveReferenceArgumentsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#197">_ZN4PLMD18ReferenceArguments26displaceReferenceArgumentsERKdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#173">_ZNK4PLMD18ReferenceArguments27extractArgumentDisplacementERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERS9_</a></td>
+              <td class="coverFnHi">1964</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#183">_ZNK4PLMD18ReferenceArguments30projectArgDisplacementOnVectorERKSt6vectorIdSaIdEERKS1_IPNS_5ValueESaIS7_EES5_RNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">2386</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#140">_ZNK4PLMD18ReferenceArguments25calculateArgumentDistanceERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">299760</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#28">_ZN4PLMD18ReferenceArgumentsC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518583</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#35">_ZN4PLMD18ReferenceArguments20readArgumentsFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnHi">519050</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceArguments.cpp.func.html b/coverage/reference/ReferenceArguments.cpp.func.html
new file mode 100644
index 0000000000..e998abf472
--- /dev/null
+++ b/coverage/reference/ReferenceArguments.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceArguments.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceArguments.cpp<span style="font-size: 80%;"> (<a href="ReferenceArguments.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntry">106</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceArguments.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#122">_ZN4PLMD18ReferenceArguments18getReferenceMetricEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#93">_ZN4PLMD18ReferenceArguments19getArgumentRequestsERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EEb</a></td>
+              <td class="coverFnHi">187</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#35">_ZN4PLMD18ReferenceArguments20readArgumentsFromPDBERKNS_3PDBE</a></td>
+              <td class="coverFnHi">519050</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#71">_ZN4PLMD18ReferenceArguments21setReferenceArgumentsERKSt6vectorIdSaIdEES5_</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#88">_ZN4PLMD18ReferenceArguments22moveReferenceArgumentsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#197">_ZN4PLMD18ReferenceArguments26displaceReferenceArgumentsERKdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#28">_ZN4PLMD18ReferenceArgumentsC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#28">_ZN4PLMD18ReferenceArgumentsC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">518583</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#140">_ZNK4PLMD18ReferenceArguments25calculateArgumentDistanceERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">299760</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#173">_ZNK4PLMD18ReferenceArguments27extractArgumentDisplacementERKSt6vectorIPNS_5ValueESaIS3_EERKS1_IdSaIdEERS9_</a></td>
+              <td class="coverFnHi">1964</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.cpp.gcov.html#183">_ZNK4PLMD18ReferenceArguments30projectArgDisplacementOnVectorERKSt6vectorIdSaIdEERKS1_IPNS_5ValueESaIS7_EES5_RNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">2386</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceArguments.cpp.gcov.html b/coverage/reference/ReferenceArguments.cpp.gcov.html
new file mode 100644
index 0000000000..2c28016259
--- /dev/null
+++ b/coverage/reference/ReferenceArguments.cpp.gcov.html
@@ -0,0 +1,280 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceArguments.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceArguments.cpp<span style="font-size: 80%;"> (source / <a href="ReferenceArguments.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntry">106</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReferenceArguments.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ReferenceAtoms.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">     518583 : ReferenceArguments::ReferenceArguments( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="31"><span class="lineNum">      31 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     518583 :   hasweights(false),</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     518583 :   hasmetric(false)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     518583 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     519050 : void ReferenceArguments::readArgumentsFromPDB( const PDB&amp; pdb ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     519050 :   ReferenceAtoms* aref=dynamic_cast&lt;ReferenceAtoms*&gt;( this );</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     519050 :   arg_names.resize( pdb.getArgumentNames().size() );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">    2015570 :   for(unsigned i=0; i&lt;arg_names.size(); ++i) arg_names[i]=pdb.getArgumentNames()[i];</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     519050 :   if( !aref &amp;&amp; arg_names.size()==0 ) error(&quot;no arguments in input PDB file&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">     519050 :   reference_args.resize( arg_names.size() ); arg_der_index.resize( arg_names.size() );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">    2015570 :   for(unsigned i=0; i&lt;arg_names.size(); ++i) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">    1496520 :     if( !pdb.getArgumentValue(arg_names[i], reference_args[i]) ) error(&quot;argument &quot; + arg_names[i] + &quot; was not set in pdb input&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">    1496520 :     arg_der_index[i]=i;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   }</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     519050 :   if( hasweights ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :     plumed_massert( !hasmetric, &quot;should not have weights if we are using metric&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :     weights.resize( arg_names.size() ); sqrtweight.resize( arg_names.size() );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :       if( !pdb.getArgumentValue(&quot;sigma_&quot; + arg_names[i], weights[i]) ) error(&quot;value sigma_&quot; + arg_names[i] + &quot; was not set in pdb input&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :       sqrtweight[i] = std::sqrt( weights[i] );</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     519050 :   } else if( hasmetric ) {</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :     plumed_massert( !hasweights, &quot;should not have weights if we are using metric&quot;);</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :     double thissig; metric.resize( arg_names.size(), arg_names.size() );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;reference_args.size(); ++j) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :         if( !pdb.getArgumentValue(&quot;sigma_&quot; + arg_names[i] + &quot;_&quot; + arg_names[j], thissig) ) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :           error(&quot;value sigma_&quot; + arg_names[i] + &quot;_&quot; + arg_names[j] + &quot; was not set in pdb input&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :         }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :         metric(i,j)=metric(j,i)=thissig;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :       }</a>
+<a name="66"><span class="lineNum">      66 </span>            :     }</a>
+<a name="67"><span class="lineNum">      67 </span>            :   } else {</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     519050 :     weights.resize( arg_names.size() ); sqrtweight.resize( arg_names.size() );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">    2015570 :     for(unsigned i=0; i&lt;weights.size(); ++i) sqrtweight[i]=weights[i]=1.0;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   }</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     519050 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        494 : void ReferenceArguments::setReferenceArguments( const std::vector&lt;double&gt;&amp; arg_vals, const std::vector&lt;double&gt;&amp; sigma ) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        494 :   moveReferenceArguments( arg_vals );</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        494 :   if( hasmetric ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :     unsigned k=0;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;reference_args.size(); ++j) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :         metric(i,j)=metric(j,i)=sigma[k]; k++;</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :       }</a>
+<a name="82"><span class="lineNum">      82 </span>            :     }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     plumed_assert( k==sigma.size() );</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   } else {</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        494 :     plumed_assert( reference_args.size()==sigma.size() );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1448 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) weights[i]=sigma[i];</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        494 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        494 : void ReferenceArguments::moveReferenceArguments( const std::vector&lt;double&gt;&amp; arg_vals ) {</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   plumed_dbg_assert( reference_args.size()==arg_vals.size() );</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1448 :   for(unsigned i=0; i&lt;arg_vals.size(); ++i) reference_args[i]=arg_vals[i];</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        494 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        187 : void ReferenceArguments::getArgumentRequests( std::vector&lt;std::string&gt;&amp; argout, bool disable_checks ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        187 :   arg_der_index.resize( arg_names.size() );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        187 :   if( argout.size()==0 ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         31 :     for(unsigned i=0; i&lt;arg_names.size(); ++i) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         15 :       argout.push_back( arg_names[i] );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         15 :       arg_der_index[i]=i;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :     }</a>
+<a name="103"><span class="lineNum">     103 </span>            :   } else {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        171 :     if(!disable_checks) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        171 :       if( arg_names.size()!=argout.size() ) error(&quot;mismatched numbers of arguments in pdb frames&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :     }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        762 :     for(unsigned i=0; i&lt;arg_names.size(); ++i) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        591 :       if(!disable_checks) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        591 :         if( argout[i]!=arg_names[i] ) error(&quot;found mismatched arguments in pdb frames&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        591 :         arg_der_index[i]=i;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :       } else {</a>
+<a name="112"><span class="lineNum">     112 </span>            :         bool found=false;</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;arg_names.size(); ++j) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :           if( argout[j]==arg_names[i] ) { found=true; arg_der_index[i]=j; break; }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :         }</a>
+<a name="116"><span class="lineNum">     116 </span>            :         if( !found ) {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :           arg_der_index[i]=argout.size(); argout.push_back( arg_names[i] );</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :         }</a>
+<a name="119"><span class="lineNum">     119 </span>            :       }</a>
+<a name="120"><span class="lineNum">     120 </span>            :     }</a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        187 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 : const std::vector&lt;double&gt;&amp; ReferenceArguments::getReferenceMetric() {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   if( hasmetric ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     unsigned ntot=(reference_args.size() / 2 )*(reference_args.size()+1);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     if( trig_metric.size()!=ntot ) trig_metric.resize( ntot );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     unsigned k=0;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :       for(unsigned j=i; j&lt;reference_args.size(); ++j) {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :         plumed_dbg_assert( std::fabs( metric(i,j)-metric(j,i) ) &lt; epsilon );</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :         trig_metric[k]=metric(i,j); k++;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :       }</a>
+<a name="134"><span class="lineNum">     134 </span>            :     }</a>
+<a name="135"><span class="lineNum">     135 </span>            :   } else {</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     if( trig_metric.size()!=reference_args.size() ) trig_metric.resize( reference_args.size() );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) trig_metric[i]=weights[i];</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   return trig_metric;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">     299760 : double ReferenceArguments::calculateArgumentDistance( const std::vector&lt;Value*&gt; &amp; vals, const std::vector&lt;double&gt;&amp; arg,</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">     299760 :   double r=0; std::vector&lt;double&gt; arg_ders( vals.size() );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">     299760 :   if( hasmetric ) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :       unsigned ik=arg_der_index[i]; arg_ders[ ik ]=0;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :       double dp_i=vals[ik]-&gt;difference( reference_args[i], arg[ik] );</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;reference_args.size(); ++j) {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :         double dp_j;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :         unsigned jk=arg_der_index[j];</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :         if(i==j) dp_j=dp_i;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :         else dp_j=vals[jk]-&gt;difference( reference_args[j], arg[jk] );</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :         arg_ders[ ik ]+=2.0*metric(i,j)*dp_j;    // Factor of two for off diagonal terms as you have terms from ij and ji</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :         r+=dp_i*dp_j*metric(i,j);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       }</a>
+<a name="158"><span class="lineNum">     158 </span>            :     }</a>
+<a name="159"><span class="lineNum">     159 </span>            :   } else {</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    1128420 :     for(unsigned i=0; i&lt;reference_args.size(); ++i) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     828660 :       unsigned ik=arg_der_index[i];</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     828660 :       double dp_i=vals[ik]-&gt;difference( reference_args[i], arg[ik] );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     828660 :       r+=weights[i]*dp_i*dp_i; arg_ders[ik]=2.0*weights[i]*dp_i;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     }</a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     299760 :   if(!squared) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        572 :     r=std::sqrt(r); double ir=1.0/(2.0*r);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       1716 :     for(unsigned i=0; i&lt;arg_ders.size(); ++i) myder.setArgumentDerivatives( i, arg_ders[i]*ir );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   } else {</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">    1126704 :     for(unsigned i=0; i&lt;arg_ders.size(); ++i) myder.setArgumentDerivatives( i, arg_ders[i] );</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     299760 :   return r;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1964 : void ReferenceArguments::extractArgumentDisplacement( const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; dirout ) const {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1964 :   if( hasmetric ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   } else {</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       5892 :     for(unsigned j=0; j&lt;reference_args.size(); ++j) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       3928 :       unsigned jk=arg_der_index[j]; dirout[jk]=sqrtweight[j]*vals[jk]-&gt;difference( reference_args[j], arg[jk] );</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     }</a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       1964 : }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       2386 : double ReferenceArguments::projectArgDisplacementOnVector( const std::vector&lt;double&gt;&amp; eigv, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; mypack ) const {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       2386 :   if( hasmetric ) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   } else {</a>
+<a name="189"><span class="lineNum">     189 </span>            :     double proj=0;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       7158 :     for(unsigned j=0; j&lt;reference_args.size(); ++j) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       4772 :       unsigned jk=arg_der_index[j];</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       4772 :       proj += eigv[j]*sqrtweight[j]*vals[jk]-&gt;difference( reference_args[j], arg[jk] );</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       4772 :       mypack.setArgumentDerivatives( jk, eigv[j]*sqrtweight[j] );</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       2386 :     return proj;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        500 : void ReferenceArguments::displaceReferenceArguments( const double&amp; weight, const std::vector&lt;double&gt;&amp; displace ) {</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   plumed_dbg_assert( displace.size()==getNumberOfReferenceArguments() );</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1466 :   for(unsigned i=0; i&lt;displace.size(); ++i) reference_args[i] += weight*displace[i];</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        500 : }</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceArguments.h.func-sort-c.html b/coverage/reference/ReferenceArguments.h.func-sort-c.html
new file mode 100644
index 0000000000..99ca4de9b7
--- /dev/null
+++ b/coverage/reference/ReferenceArguments.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceArguments.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceArguments.h<span style="font-size: 80%;"> (<a href="ReferenceArguments.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceArguments.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#107">_ZN4PLMD18ReferenceArguments16getArgumentNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">962</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#96">_ZNK4PLMD18ReferenceArguments20getReferenceArgumentERKj</a></td>
+              <td class="coverFnHi">1020</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#112">_ZNK4PLMD18ReferenceArguments29getNumberOfReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">39585</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#102">_ZNK4PLMD18ReferenceArguments21getReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">790964</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceArguments.h.func.html b/coverage/reference/ReferenceArguments.h.func.html
new file mode 100644
index 0000000000..cfa99cc266
--- /dev/null
+++ b/coverage/reference/ReferenceArguments.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceArguments.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceArguments.h<span style="font-size: 80%;"> (<a href="ReferenceArguments.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceArguments.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#107">_ZN4PLMD18ReferenceArguments16getArgumentNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">962</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#96">_ZNK4PLMD18ReferenceArguments20getReferenceArgumentERKj</a></td>
+              <td class="coverFnHi">1020</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#102">_ZNK4PLMD18ReferenceArguments21getReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">790964</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceArguments.h.gcov.html#112">_ZNK4PLMD18ReferenceArguments29getNumberOfReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">39585</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceArguments.h.gcov.html b/coverage/reference/ReferenceArguments.h.gcov.html
new file mode 100644
index 0000000000..0a830bc84f
--- /dev/null
+++ b/coverage/reference/ReferenceArguments.h.gcov.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceArguments.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceArguments.h<span style="font-size: 80%;"> (source / <a href="ReferenceArguments.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_ReferenceArguments_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_ReferenceArguments_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ReferenceConfiguration.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : /// \ingroup TOOLBOX</a>
+<a name="31"><span class="lineNum">      31 </span>            : /// In many applications (e.g. paths, fields, property maps) it is necessary to calculate</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// the distance between two configurations.  These distances can be calculated in a variety of</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// different ways.  For instance, one can assert that the distance between the two configuration</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// is the distance one would have to move all the atoms to transform configuration 1 into configuration</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// 2. Alternatively, one could calculate the values of a large set of collective coordinates in the two</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// configurations and then calculate the Euclidean distances between these two points in the resulting</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// high-dimensional vector space.  Lastly, one can combine these two forms of distance calculation to calculate</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// a hybrid distance.  Plumed allows one to use all these forms of distance calculations and also to implement</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// new forms of distance.  You should inherit from this class if your distance involves reference colvar values.</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// This class and \ref PLMD::ReferenceAtoms mirror the functionalities in \ref PLMD::ActionWithArguments and</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// \ref PLMD::ActionAtomistic respectively but for distances.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : class ReferenceArguments :</a>
+<a name="44"><span class="lineNum">      44 </span>            :   virtual public ReferenceConfiguration</a>
+<a name="45"><span class="lineNum">      45 </span>            : {</a>
+<a name="46"><span class="lineNum">      46 </span>            :   friend class Direction;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   friend class ReferenceConfiguration;</a>
+<a name="48"><span class="lineNum">      48 </span>            : private:</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// The weights for normed euclidean distance</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;double&gt; weights, sqrtweight;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// The N X N matrix we are using to calculate our Malanobius distance</a>
+<a name="52"><span class="lineNum">      52 </span>            :   Matrix&lt;double&gt; metric;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;double&gt; trig_metric;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// The values of the colvars in the reference configuration</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::vector&lt;double&gt; reference_args;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The names of the arguments</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;std::string&gt; arg_names;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The indices for setting derivatives</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::vector&lt;unsigned&gt; arg_der_index;</a>
+<a name="60"><span class="lineNum">      60 </span>            : protected:</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Are we reading weights from input</a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool hasweights;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Are we calculating a Malanobius distance</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool hasmetric;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Read in the atoms from the pdb file</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void readArgumentsFromPDB( const PDB&amp; pdb );</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Set the values of the colvars based on their current instantanous values (used in Analysis)</a>
+<a name="68"><span class="lineNum">      68 </span>            :   void setReferenceArguments();</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   explicit ReferenceArguments( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Get the number of reference arguments</a>
+<a name="72"><span class="lineNum">      72 </span>            :   unsigned getNumberOfReferenceArguments() const override;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Get the arguments required</a>
+<a name="74"><span class="lineNum">      74 </span>            :   void getArgumentRequests( std::vector&lt;std::string&gt;&amp;, bool disable_checks=false ) override;</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Set the positions of the reference arguments</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void setReferenceArguments( const std::vector&lt;double&gt;&amp; arg_vals, const std::vector&lt;double&gt;&amp; sigma );</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Set the positions of the reference arguments</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void moveReferenceArguments( const std::vector&lt;double&gt;&amp; arg_vals );</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// Get the value of the ith reference argument</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double getReferenceArgument( const unsigned&amp; i ) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Return all the reference arguments</a>
+<a name="82"><span class="lineNum">      82 </span>            :   const std::vector&lt;double&gt;&amp; getReferenceArguments() const override;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   const std::vector&lt;double&gt;&amp; getReferenceMetric() override;</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// Return names</a>
+<a name="85"><span class="lineNum">      85 </span>            :   const std::vector&lt;std::string&gt;&amp; getArgumentNames() override;</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Calculate the euclidean/malanobius distance the atoms have moved from the reference</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// configuration in CV space</a>
+<a name="88"><span class="lineNum">      88 </span>            :   virtual double calculateArgumentDistance( const std::vector&lt;Value*&gt; &amp; vals, const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; myder, const bool&amp; squared ) const ;</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Displace the positions of the reference atoms</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void displaceReferenceArguments( const double&amp; weight, const std::vector&lt;double&gt;&amp; displace );</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Extract the displacement from a position in a space</a>
+<a name="92"><span class="lineNum">      92 </span>            :   virtual void extractArgumentDisplacement( const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; dirout ) const ;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Project the displacement of the arguments on a vector</a>
+<a name="94"><span class="lineNum">      94 </span>            :   double projectArgDisplacementOnVector( const std::vector&lt;double&gt;&amp; eigv, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; mypack ) const ;</a>
+<a name="95"><span class="lineNum">      95 </span>            : };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : inline</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1020 : double ReferenceArguments::getReferenceArgument( const unsigned&amp; i ) const {</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   plumed_dbg_assert( i&lt;reference_args.size() );</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1040 :   return reference_args[i];</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : inline</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">     790964 : const std::vector&lt;double&gt;&amp; ReferenceArguments::getReferenceArguments() const {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">     790964 :   return reference_args;</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : inline</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        962 : const std::vector&lt;std::string&gt;&amp; ReferenceArguments::getArgumentNames() {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        962 :   return arg_names;</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : inline</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      39585 : unsigned ReferenceArguments::getNumberOfReferenceArguments() const {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      39585 :   return reference_args.size();</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : #endif</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceAtoms.cpp.func-sort-c.html b/coverage/reference/ReferenceAtoms.cpp.func-sort-c.html
new file mode 100644
index 0000000000..331324ba72
--- /dev/null
+++ b/coverage/reference/ReferenceAtoms.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceAtoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceAtoms.cpp<span style="font-size: 80%;"> (<a href="ReferenceAtoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceAtoms.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#27">_ZN4PLMD14ReferenceAtomsC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#83">_ZN4PLMD14ReferenceAtoms15getAtomRequestsERSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#87">_ZN4PLMD14ReferenceAtoms20singleDomainRequestsERSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#118">_ZN4PLMD14ReferenceAtoms22displaceReferenceAtomsERKdRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EE</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#33">_ZN4PLMD14ReferenceAtoms16readAtomsFromPDBERKNS_3PDBEb</a></td>
+              <td class="coverFnHi">688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#27">_ZN4PLMD14ReferenceAtomsC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">724</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceAtoms.cpp.func.html b/coverage/reference/ReferenceAtoms.cpp.func.html
new file mode 100644
index 0000000000..70f869016c
--- /dev/null
+++ b/coverage/reference/ReferenceAtoms.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceAtoms.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceAtoms.cpp<span style="font-size: 80%;"> (<a href="ReferenceAtoms.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceAtoms.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#83">_ZN4PLMD14ReferenceAtoms15getAtomRequestsERSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#33">_ZN4PLMD14ReferenceAtoms16readAtomsFromPDBERKNS_3PDBEb</a></td>
+              <td class="coverFnHi">688</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#87">_ZN4PLMD14ReferenceAtoms20singleDomainRequestsERSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#118">_ZN4PLMD14ReferenceAtoms22displaceReferenceAtomsERKdRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EE</a></td>
+              <td class="coverFnHi">494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#27">_ZN4PLMD14ReferenceAtomsC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.cpp.gcov.html#27">_ZN4PLMD14ReferenceAtomsC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">724</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceAtoms.cpp.gcov.html b/coverage/reference/ReferenceAtoms.cpp.gcov.html
new file mode 100644
index 0000000000..9afbaaaf9d
--- /dev/null
+++ b/coverage/reference/ReferenceAtoms.cpp.gcov.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceAtoms.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceAtoms.cpp<span style="font-size: 80%;"> (source / <a href="ReferenceAtoms.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReferenceAtoms.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        724 : ReferenceAtoms::ReferenceAtoms( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        724 :   checks_were_disabled(false)</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : {</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        724 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        688 : void ReferenceAtoms::readAtomsFromPDB( const PDB&amp; pdb, const bool allowblocks  ) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        688 :   if( !allowblocks &amp;&amp; pdb.getNumberOfAtomBlocks()!=1 ) error(&quot;found multi-atom-block pdb format but expecting only one block of atoms&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        688 :   indices.resize(0); reference_atoms.resize(0); align.resize(0); displace.resize(0); atom_der_index.resize(0);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">      10045 :   for(unsigned i=0; i&lt;pdb.size(); ++i) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       9357 :     indices.push_back( pdb.getAtomNumbers()[i] ); reference_atoms.push_back( pdb.getPositions()[i] );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       9357 :     align.push_back( pdb.getOccupancy()[i] ); displace.push_back( pdb.getBeta()[i] ); atom_der_index.push_back(i);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   }</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        688 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // void ReferenceAtoms::setAtomNumbers( const std::vector&lt;AtomNumber&gt;&amp; numbers ) {</a>
+<a name="46"><span class="lineNum">      46 </span>            : //   reference_atoms.resize( numbers.size() ); align.resize( numbers.size() );</a>
+<a name="47"><span class="lineNum">      47 </span>            : //   displace.resize( numbers.size() ); atom_der_index.resize( numbers.size() );</a>
+<a name="48"><span class="lineNum">      48 </span>            : //   indices.resize( numbers.size() );</a>
+<a name="49"><span class="lineNum">      49 </span>            : //   for(unsigned i=0; i&lt;numbers.size(); ++i) {</a>
+<a name="50"><span class="lineNum">      50 </span>            : //     indices[i]=numbers[i]; atom_der_index[i]=i;</a>
+<a name="51"><span class="lineNum">      51 </span>            : //   }</a>
+<a name="52"><span class="lineNum">      52 </span>            : // }</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : // void ReferenceAtoms::printAtoms( OFile&amp; ofile, const double&amp; lunits ) const {</a>
+<a name="55"><span class="lineNum">      55 </span>            : //   plumed_assert( indices.size()==reference_atoms.size() &amp;&amp; align.size()==reference_atoms.size() &amp;&amp; displace.size()==reference_atoms.size() );</a>
+<a name="56"><span class="lineNum">      56 </span>            : //   for(unsigned i=0; i&lt;reference_atoms.size(); ++i) {</a>
+<a name="57"><span class="lineNum">      57 </span>            : //     ofile.printf(&quot;ATOM  %5d  X   RES  %4u    %8.3f%8.3f%8.3f%6.2f%6.2f\n&quot;,</a>
+<a name="58"><span class="lineNum">      58 </span>            : //                  indices[i].serial(), i,</a>
+<a name="59"><span class="lineNum">      59 </span>            : //                  lunits*reference_atoms[i][0], lunits*reference_atoms[i][1], lunits*reference_atoms[i][2],</a>
+<a name="60"><span class="lineNum">      60 </span>            : //                  align[i], displace[i] );</a>
+<a name="61"><span class="lineNum">      61 </span>            : //   }</a>
+<a name="62"><span class="lineNum">      62 </span>            : // }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : // bool ReferenceAtoms::parseAtomList( const std::string&amp; key, std::vector&lt;unsigned&gt;&amp; numbers ) {</a>
+<a name="65"><span class="lineNum">      65 </span>            : //   plumed_assert( numbers.size()==0 );</a>
+<a name="66"><span class="lineNum">      66 </span>            : //</a>
+<a name="67"><span class="lineNum">      67 </span>            : //   std::vector&lt;std::string&gt; strings;</a>
+<a name="68"><span class="lineNum">      68 </span>            : //   if( !parseVector(key,strings,true) ) return false;</a>
+<a name="69"><span class="lineNum">      69 </span>            : //   Tools::interpretRanges(strings);</a>
+<a name="70"><span class="lineNum">      70 </span>            : //</a>
+<a name="71"><span class="lineNum">      71 </span>            : //   numbers.resize( strings.size() );</a>
+<a name="72"><span class="lineNum">      72 </span>            : //   for(unsigned i=0; i&lt;strings.size(); ++i) {</a>
+<a name="73"><span class="lineNum">      73 </span>            : //     AtomNumber atom;</a>
+<a name="74"><span class="lineNum">      74 </span>            : //     if( !Tools::convert(strings[i],atom ) ) error(&quot;could not convert &quot; + strings[i] + &quot; into atom number&quot;);</a>
+<a name="75"><span class="lineNum">      75 </span>            : //</a>
+<a name="76"><span class="lineNum">      76 </span>            : //     bool found=false;</a>
+<a name="77"><span class="lineNum">      77 </span>            : //     for(unsigned j=0; j&lt;indices.size(); ++j) {</a>
+<a name="78"><span class="lineNum">      78 </span>            : //       if( atom==indices[j] ) { found=true; numbers[i]=j; break; }</a>
+<a name="79"><span class="lineNum">      79 </span>            : //     }</a>
+<a name="80"><span class="lineNum">      80 </span>            : //     if(!found) error(&quot;atom labelled &quot; + strings[i] + &quot; is not present in pdb input file&quot;);</a>
+<a name="81"><span class="lineNum">      81 </span>            : //   }</a>
+<a name="82"><span class="lineNum">      82 </span>            : //   return true;</a>
+<a name="83"><span class="lineNum">      83 </span>            : // }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        455 : void ReferenceAtoms::getAtomRequests( std::vector&lt;AtomNumber&gt;&amp; numbers, bool disable_checks ) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        455 :   singleDomainRequests(numbers,disable_checks);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        455 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        455 : void ReferenceAtoms::singleDomainRequests( std::vector&lt;AtomNumber&gt;&amp; numbers, bool disable_checks ) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        455 :   checks_were_disabled=disable_checks;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        455 :   atom_der_index.resize( indices.size() );</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        455 :   if( numbers.size()==0 ) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       4220 :     for(unsigned i=0; i&lt;indices.size(); ++i) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       4113 :       numbers.push_back( indices[i] );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       4113 :       atom_der_index[i]=i;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :     }</a>
+<a name="98"><span class="lineNum">      98 </span>            :   } else {</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        348 :     if(!disable_checks) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        348 :       if( numbers.size()!=indices.size() ) error(&quot;mismatched numbers of atoms in pdb frames&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :     }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       4812 :     for(unsigned i=0; i&lt;indices.size(); ++i) {</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :       bool found=false;</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       4464 :       if(!disable_checks) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       4464 :         if( indices[i]!=numbers[i] ) error(&quot;found mismatched reference atoms in pdb frames&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       4464 :         atom_der_index[i]=i;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :       } else {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :         for(unsigned j=0; j&lt;numbers.size(); ++j) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :           if( indices[i]==numbers[j] ) { found=true; atom_der_index[i]=j; break; }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :         }</a>
+<a name="112"><span class="lineNum">     112 </span>            :         if( !found ) {</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :           atom_der_index[i]=numbers.size(); numbers.push_back( indices[i] );</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :         }</a>
+<a name="115"><span class="lineNum">     115 </span>            :       }</a>
+<a name="116"><span class="lineNum">     116 </span>            :     }</a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        455 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        494 : void ReferenceAtoms::displaceReferenceAtoms( const double&amp; weight, const std::vector&lt;Vector&gt;&amp; dir ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   plumed_dbg_assert( dir.size()==reference_atoms.size() );</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        715 :   for(unsigned i=0; i&lt;dir.size(); ++i) reference_atoms[i] += weight*dir.size()*dir[i];</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        494 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceAtoms.h.func-sort-c.html b/coverage/reference/ReferenceAtoms.h.func-sort-c.html
new file mode 100644
index 0000000000..22f5efa358
--- /dev/null
+++ b/coverage/reference/ReferenceAtoms.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceAtoms.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceAtoms.h<span style="font-size: 80%;"> (<a href="ReferenceAtoms.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">73.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceAtoms.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#101">_ZNK4PLMD14ReferenceAtoms25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#105">_ZNK4PLMD14ReferenceAtoms33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#154">_ZN4PLMD14ReferenceAtoms18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#125">_ZNK4PLMD14ReferenceAtoms29getNumberOfReferencePositionsEv</a></td>
+              <td class="coverFnHi">150276</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#149">_ZNK4PLMD14ReferenceAtoms21getReferencePositionsEv</a></td>
+              <td class="coverFnHi">2636058</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceAtoms.h.func.html b/coverage/reference/ReferenceAtoms.h.func.html
new file mode 100644
index 0000000000..6a9d50d357
--- /dev/null
+++ b/coverage/reference/ReferenceAtoms.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceAtoms.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceAtoms.h<span style="font-size: 80%;"> (<a href="ReferenceAtoms.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">73.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceAtoms.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#154">_ZN4PLMD14ReferenceAtoms18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#149">_ZNK4PLMD14ReferenceAtoms21getReferencePositionsEv</a></td>
+              <td class="coverFnHi">2636058</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#101">_ZNK4PLMD14ReferenceAtoms25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#125">_ZNK4PLMD14ReferenceAtoms29getNumberOfReferencePositionsEv</a></td>
+              <td class="coverFnHi">150276</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceAtoms.h.gcov.html#105">_ZNK4PLMD14ReferenceAtoms33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceAtoms.h.gcov.html b/coverage/reference/ReferenceAtoms.h.gcov.html
new file mode 100644
index 0000000000..a7727f82f6
--- /dev/null
+++ b/coverage/reference/ReferenceAtoms.h.gcov.html
@@ -0,0 +1,239 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceAtoms.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceAtoms.h<span style="font-size: 80%;"> (source / <a href="ReferenceAtoms.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryLo">73.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_ReferenceAtoms_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_ReferenceAtoms_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ReferenceConfiguration.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Pbc;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /// \ingroup TOOLBOX</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// In many applications (e.g. paths, fields, property maps) it is necessary to calculate</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// the distance between two configurations.  These distances can be calculated in a variety of</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// different ways.  For instance, one can assert that the distance between the two configuration</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// is the distance one would have to move all the atoms to transform configuration 1 into configuration</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// 2. Alternatively, one could calculate the values of a large set of collective coordinates in the two</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// configurations and then calculate the Euclidean distances between these two points in the resulting</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// high-dimensional vector space.  Lastly, one can combine these two forms of distance calculation to calculate</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// a hybrid distance.  Plumed allows one to use all these forms of distance calculations and also to implement</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// new forms of distance.  You should inherit from this class if your distance involves reference atomic positions.</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// This class and \ref PLMD::ReferenceArguments mirror the functionalities in and \ref PLMD::ActionAtomistic</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// and \ref PLMD::ActionWithArguments respectively but for distances.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class ReferenceAtoms :</a>
+<a name="45"><span class="lineNum">      45 </span>            :   virtual public ReferenceConfiguration</a>
+<a name="46"><span class="lineNum">      46 </span>            : {</a>
+<a name="47"><span class="lineNum">      47 </span>            :   friend class Direction;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   friend class SingleDomainRMSD;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   friend class MultiDomainRMSD;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   friend class ReferenceConfiguration;</a>
+<a name="51"><span class="lineNum">      51 </span>            : private:</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// This flag tells us if the user has disabled checking of the input in order to</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// do fancy paths with weird inputs</a>
+<a name="54"><span class="lineNum">      54 </span>            :   bool checks_were_disabled;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// The atoms to be used to align the instantaneous atomic positions</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// to the reference configuration</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;double&gt; align;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The atoms to be used to calculate the distance the atoms have moved</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// from the reference configuration</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;double&gt; displace;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// The positions of the atoms in the reference configuration</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;Vector&gt; reference_atoms;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// The indices of the atoms in the pdb file</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;AtomNumber&gt; indices;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// The indeces for setting derivatives</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;unsigned&gt; atom_der_index;</a>
+<a name="67"><span class="lineNum">      67 </span>            : protected:</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Read in the atoms from the pdb file</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void readAtomsFromPDB( const PDB&amp;, const bool allowblocks=false );</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Add atom indices to list</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void setAtomIndices( const std::vector&lt;AtomNumber&gt;&amp; atomnumbers );</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Read a list of atoms from the pdb input file</a>
+<a name="73"><span class="lineNum">      73 </span>            :   bool parseAtomList( const std::string&amp;, std::vector&lt;unsigned&gt;&amp; );</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Get the position of the ith atom</a>
+<a name="75"><span class="lineNum">      75 </span>            :   Vector getReferencePosition( const unsigned&amp; iatom ) const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Add derivatives to iatom th atom in list</a>
+<a name="77"><span class="lineNum">      77 </span>            : //  void addAtomicDerivatives( const unsigned&amp; , const Vector&amp; );</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Get the atomic derivatives on the ith atom in the list</a>
+<a name="79"><span class="lineNum">      79 </span>            : //  Vector retrieveAtomicDerivatives( const unsigned&amp; ) const ;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Add derivatives to the viral</a>
+<a name="81"><span class="lineNum">      81 </span>            : //  void addBoxDerivatives( const Tensor&amp; );</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// This does the checks that are always required</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void singleDomainRequests( std::vector&lt;AtomNumber&gt;&amp;, bool disable_checks );</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   explicit ReferenceAtoms( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// This returns the number of reference atom positions</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned getNumberOfReferencePositions() const override;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Get the reference positions</a>
+<a name="89"><span class="lineNum">      89 </span>            :   const std::vector&lt;Vector&gt; &amp; getReferencePositions() const override;</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// This allows us to use a single pos array with RMSD objects using different atom indexes</a>
+<a name="91"><span class="lineNum">      91 </span>            :   unsigned getAtomIndex( const unsigned&amp; ) const ;</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Get the atoms required (additional checks are required when we have multiple domains)</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void getAtomRequests( std::vector&lt;AtomNumber&gt;&amp;, bool disable_checks=false ) override;</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Set the positions of the reference atoms</a>
+<a name="95"><span class="lineNum">      95 </span>            :   virtual void setReferenceAtoms( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; align_in, const std::vector&lt;double&gt;&amp; displace_in )=0;</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// Return all atom indexes</a>
+<a name="97"><span class="lineNum">      97 </span>            :   const std::vector&lt;AtomNumber&gt;&amp; getAbsoluteIndexes() override;</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// This returns how many atoms there should be</a>
+<a name="99"><span class="lineNum">      99 </span>            :   unsigned getNumberOfAtoms() const ;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Displace the positions of the reference atoms a bit</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void displaceReferenceAtoms( const double&amp; weight, const std::vector&lt;Vector&gt;&amp; dir );</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// Extract a displacement from a position in space</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   virtual void extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; direction ) const {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Project the displacement on a vector</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   virtual double projectAtomicDisplacementOnVector( const bool&amp; normalized, const std::vector&lt;Vector&gt;&amp; eigv, ReferenceValuePack&amp; mypack ) const {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// Get the vector of alignment weights</a>
+<a name="111"><span class="lineNum">     111 </span>            :   const std::vector&lt;double&gt; &amp; getAlign() const ;</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// Get the vector of displacement weights</a>
+<a name="113"><span class="lineNum">     113 </span>            :   const std::vector&lt;double&gt; &amp; getDisplace() const ;</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : inline</a>
+<a name="117"><span class="lineNum">     117 </span>            : const std::vector&lt;double&gt; &amp; ReferenceAtoms::getAlign() const {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     216774 :   return align;</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : inline</a>
+<a name="122"><span class="lineNum">     122 </span>            : const std::vector&lt;double&gt; &amp; ReferenceAtoms::getDisplace() const {</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     216775 :   return displace;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : inline</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     150276 : unsigned ReferenceAtoms::getNumberOfReferencePositions() const {</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   plumed_dbg_assert( atom_der_index.size()==reference_atoms.size() );</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     150276 :   return reference_atoms.size();</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : }</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : inline</a>
+<a name="133"><span class="lineNum">     133 </span>            : unsigned ReferenceAtoms::getNumberOfAtoms() const {</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     314250 :   return atom_der_index.size(); // reference_atoms.size();</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : inline</a>
+<a name="138"><span class="lineNum">     138 </span>            : unsigned ReferenceAtoms::getAtomIndex( const unsigned&amp; iatom ) const {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   plumed_dbg_assert( iatom&lt;atom_der_index.size() );</a>
+<a name="140"><span class="lineNum">     140 </span>            :   plumed_dbg_assert( atom_der_index[iatom]&lt;reference_atoms.size() );</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">    9894406 :   return atom_der_index[iatom];</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : inline</a>
+<a name="145"><span class="lineNum">     145 </span>            : Vector ReferenceAtoms::getReferencePosition( const unsigned&amp; iatom ) const {</a>
+<a name="146"><span class="lineNum">     146 </span>            :   plumed_dbg_assert( iatom&lt;reference_atoms.size() );</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      67480 :   return reference_atoms[iatom];</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : inline</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">    2636058 : const std::vector&lt;Vector&gt; &amp; ReferenceAtoms::getReferencePositions() const {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">    2636058 :   return reference_atoms;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : inline</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 : const std::vector&lt;AtomNumber&gt;&amp; ReferenceAtoms::getAbsoluteIndexes() {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          4 :   return indices;</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : #endif</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceConfiguration.cpp.func-sort-c.html b/coverage/reference/ReferenceConfiguration.cpp.func-sort-c.html
new file mode 100644
index 0000000000..41756a8590
--- /dev/null
+++ b/coverage/reference/ReferenceConfiguration.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceConfiguration.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceConfiguration.cpp<span style="font-size: 80%;"> (<a href="ReferenceConfiguration.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">96.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceConfiguration.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#59">_ZN4PLMD22ReferenceConfiguration5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#51">_ZN4PLMD22ReferenceConfigurationD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#40">_ZNK4PLMD29ReferenceConfigurationOptions16getMultiRMSDTypeB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#55">_ZNK4PLMD22ReferenceConfiguration7getNameB5cxx11Ev</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#36">_ZNK4PLMD29ReferenceConfigurationOptions15usingFastOptionEv</a></td>
+              <td class="coverFnHi">437</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#70">_ZN4PLMD22ReferenceConfiguration30displaceReferenceConfigurationERKdRNS_9DirectionE</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#77">_ZNK4PLMD22ReferenceConfiguration25extractDisplacementVectorERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IPNS_5ValueESaIS9_EERKS1_IdSaIdEERKbRNS_9DirectionE</a></td>
+              <td class="coverFnHi">3081</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#102">_ZNK4PLMD22ReferenceConfiguration27projectDisplacementOnVectorERKNS_9DirectionERKSt6vectorIPNS_5ValueESaIS6_EERKS4_IdSaIdEERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">3588</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#63">_ZNK4PLMD22ReferenceConfiguration9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">175359</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#113">_ZN4PLMD8distanceERKNS_3PbcERKSt6vectorIPNS_5ValueESaIS5_EEPNS_22ReferenceConfigurationESB_RKb</a></td>
+              <td class="coverFnHi">259099</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#46">_ZN4PLMD22ReferenceConfigurationC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">519088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#31">_ZN4PLMD29ReferenceConfigurationOptionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">519088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#51">_ZN4PLMD22ReferenceConfigurationD2Ev</a></td>
+              <td class="coverFnHi">519569</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceConfiguration.cpp.func.html b/coverage/reference/ReferenceConfiguration.cpp.func.html
new file mode 100644
index 0000000000..08b1945697
--- /dev/null
+++ b/coverage/reference/ReferenceConfiguration.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceConfiguration.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceConfiguration.cpp<span style="font-size: 80%;"> (<a href="ReferenceConfiguration.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">96.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceConfiguration.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#70">_ZN4PLMD22ReferenceConfiguration30displaceReferenceConfigurationERKdRNS_9DirectionE</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#59">_ZN4PLMD22ReferenceConfiguration5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#46">_ZN4PLMD22ReferenceConfigurationC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">519088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#51">_ZN4PLMD22ReferenceConfigurationD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#51">_ZN4PLMD22ReferenceConfigurationD2Ev</a></td>
+              <td class="coverFnHi">519569</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#31">_ZN4PLMD29ReferenceConfigurationOptionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">519088</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#113">_ZN4PLMD8distanceERKNS_3PbcERKSt6vectorIPNS_5ValueESaIS5_EEPNS_22ReferenceConfigurationESB_RKb</a></td>
+              <td class="coverFnHi">259099</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#77">_ZNK4PLMD22ReferenceConfiguration25extractDisplacementVectorERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IPNS_5ValueESaIS9_EERKS1_IdSaIdEERKbRNS_9DirectionE</a></td>
+              <td class="coverFnHi">3081</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#102">_ZNK4PLMD22ReferenceConfiguration27projectDisplacementOnVectorERKNS_9DirectionERKSt6vectorIPNS_5ValueESaIS6_EERKS4_IdSaIdEERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">3588</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#55">_ZNK4PLMD22ReferenceConfiguration7getNameB5cxx11Ev</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#63">_ZNK4PLMD22ReferenceConfiguration9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">175359</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#36">_ZNK4PLMD29ReferenceConfigurationOptions15usingFastOptionEv</a></td>
+              <td class="coverFnHi">437</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.cpp.gcov.html#40">_ZNK4PLMD29ReferenceConfigurationOptions16getMultiRMSDTypeB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceConfiguration.cpp.gcov.html b/coverage/reference/ReferenceConfiguration.cpp.gcov.html
new file mode 100644
index 0000000000..a90e4308bf
--- /dev/null
+++ b/coverage/reference/ReferenceConfiguration.cpp.gcov.html
@@ -0,0 +1,207 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceConfiguration.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceConfiguration.cpp<span style="font-size: 80%;"> (source / <a href="ReferenceConfiguration.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">96.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReferenceConfiguration.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ReferenceArguments.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ReferenceAtoms.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Direction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/OFile.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     519088 : ReferenceConfigurationOptions::ReferenceConfigurationOptions( const std::string&amp; type ):</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     519088 :   tt(type)</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     519088 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        437 : bool ReferenceConfigurationOptions::usingFastOption() const {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        437 :   return (tt.find(&quot;-FAST&quot;)!=std::string::npos);</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : }</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          5 : std::string ReferenceConfigurationOptions::getMultiRMSDType() const {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          5 :   plumed_assert( tt.find(&quot;MULTI-&quot;)!=std::string::npos );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          5 :   std::size_t dot=tt.find_first_of(&quot;MULTI-&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          5 :   return tt.substr(dot+6);</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">     519088 : ReferenceConfiguration::ReferenceConfiguration( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     519088 :   name(ro.tt)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     519088 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     519569 : ReferenceConfiguration::~ReferenceConfiguration()</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">    1039138 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        284 : std::string ReferenceConfiguration::getName() const {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        284 :   return name;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 : [[noreturn]] void ReferenceConfiguration::error(const std::string&amp; msg) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;error reading reference configuration of type &quot; + name + &quot; : &quot; + msg );</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     175359 : double ReferenceConfiguration::calculate( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals,</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :     ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     175359 :   std::vector&lt;double&gt; tmparg( vals.size() );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     248599 :   for(unsigned i=0; i&lt;vals.size(); ++i) tmparg[i]=vals[i]-&gt;get();</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     350718 :   return calc( pos, pbc, vals, tmparg, myder, squared );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        500 : void ReferenceConfiguration::displaceReferenceConfiguration( const double&amp; weight, Direction&amp; dir ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        500 :   ReferenceArguments* args=dynamic_cast&lt;ReferenceArguments*&gt;(this);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        500 :   if( args ) args-&gt;displaceReferenceArguments( weight, dir.getReferenceArguments() );</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        500 :   ReferenceAtoms* atoms=dynamic_cast&lt;ReferenceAtoms*&gt;(this);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        500 :   if( atoms ) atoms-&gt;displaceReferenceAtoms( weight, dir.getReferencePositions() );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        500 : }</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       3081 : void ReferenceConfiguration::extractDisplacementVector( const std::vector&lt;Vector&gt;&amp; pos, const std::vector&lt;Value*&gt;&amp; vals,</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     const std::vector&lt;double&gt;&amp; arg, const bool&amp; nflag,</a>
+<a name="81"><span class="lineNum">      81 </span>            :     Direction&amp; mydir ) const {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       3081 :   const ReferenceAtoms* atoms=dynamic_cast&lt;const ReferenceAtoms*&gt;( this );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       3081 :   if( atoms ) atoms-&gt;extractAtomicDisplacement( pos, mydir.reference_atoms );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       3081 :   const ReferenceArguments* args=dynamic_cast&lt;const ReferenceArguments*&gt;( this );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       3081 :   if( args ) args-&gt;extractArgumentDisplacement( vals, arg, mydir.reference_args );</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            :   // Normalize direction if required</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       3081 :   if( nflag ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     // Calculate length of vector</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         10 :     double tmp, norm=0; mydir.normalized = true;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         80 :     for(unsigned i=0; i&lt;mydir.getReferencePositions().size(); ++i) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        280 :       for(unsigned k=0; k&lt;3; ++k) { tmp=mydir.getReferencePositions()[i][k]; norm+=tmp*tmp; }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :     }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         10 :     for(unsigned i=0; i&lt;mydir.getReferenceArguments().size(); ++i) { tmp=mydir.getReferenceArguments()[i]; norm+=tmp*tmp; }</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         10 :     norm = std::sqrt( norm );</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :     // And normalize</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         80 :     for(unsigned i=0; i&lt;mydir.getReferencePositions().size(); ++i) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        280 :       for(unsigned k=0; k&lt;3; ++k) { mydir.reference_atoms[i][k] /=norm; }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :     }</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         10 :     for(unsigned i=0; i&lt;mydir.getReferenceArguments().size(); ++i) { mydir.reference_args[i] /= norm; }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       3081 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       3588 : double ReferenceConfiguration::projectDisplacementOnVector( const Direction&amp; mydir,</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :     const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg,</a>
+<a name="106"><span class="lineNum">     106 </span>            :     ReferenceValuePack&amp; mypack ) const {</a>
+<a name="107"><span class="lineNum">     107 </span>            :   double proj=0;</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       3588 :   const ReferenceAtoms* atoms=dynamic_cast&lt;const ReferenceAtoms*&gt;( this );</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       3588 :   if( atoms ) proj += atoms-&gt;projectAtomicDisplacementOnVector( mydir.normalized, mydir.getReferencePositions(), mypack );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       3588 :   const ReferenceArguments* args=dynamic_cast&lt;const ReferenceArguments*&gt;( this );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       3588 :   if( args ) proj += args-&gt;projectArgDisplacementOnVector( mydir.getReferenceArguments(), vals, arg, mypack );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       3588 :   return proj;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     259099 : double distance( const Pbc&amp; pbc, const std::vector&lt;Value*&gt; &amp; vals, ReferenceConfiguration* ref1, ReferenceConfiguration* ref2, const bool&amp; squared ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   unsigned nder;</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     259099 :   if( ref1-&gt;getReferencePositions().size()&gt;0 ) nder=ref1-&gt;getReferenceArguments().size() + 3*ref1-&gt;getReferencePositions().size() + 9;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     259092 :   else nder=ref1-&gt;getReferenceArguments().size();</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     259099 :   MultiValue myvals( 1, nder ); ReferenceValuePack myder( ref1-&gt;getReferenceArguments().size(), ref1-&gt;getReferencePositions().size(), myvals );</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     259099 :   double dist1=ref1-&gt;calc( ref2-&gt;getReferencePositions(), pbc, vals, ref2-&gt;getReferenceArguments(), myder, squared );</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : #ifndef NDEBUG</a>
+<a name="123"><span class="lineNum">     123 </span>            :   // Check that A - B = B - A</a>
+<a name="124"><span class="lineNum">     124 </span>            :   double dist2=ref2-&gt;calc( ref1-&gt;getReferencePositions(), pbc, vals, ref1-&gt;getReferenceArguments(), myder, squared );</a>
+<a name="125"><span class="lineNum">     125 </span>            :   plumed_dbg_assert( std::fabs(dist1-dist2)&lt;epsilon );</a>
+<a name="126"><span class="lineNum">     126 </span>            : #endif</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     259099 :   return dist1;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">     259099 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceConfiguration.h.func-sort-c.html b/coverage/reference/ReferenceConfiguration.h.func-sort-c.html
new file mode 100644
index 0000000000..a56faacdb2
--- /dev/null
+++ b/coverage/reference/ReferenceConfiguration.h.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceConfiguration.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceConfiguration.h<span style="font-size: 80%;"> (<a href="ReferenceConfiguration.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceConfiguration.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#130">_ZN4PLMD22ReferenceConfiguration15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#146">_ZN4PLMD22ReferenceConfiguration18getReferenceMetricEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#126">_ZN4PLMD22ReferenceConfiguration28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#112">_ZNK4PLMD22ReferenceConfiguration20getReferenceArgumentERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#156">_ZN4PLMD22ReferenceConfiguration16getArgumentNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#151">_ZN4PLMD22ReferenceConfiguration18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#98">_ZN4PLMD22ReferenceConfiguration15getAtomRequestsERSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">177</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#100">_ZN4PLMD22ReferenceConfiguration19getArgumentRequestsERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EEb</a></td>
+              <td class="coverFnHi">354</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#141">_ZNK4PLMD22ReferenceConfiguration21getReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">2281</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#161">_ZNK4PLMD22ReferenceConfiguration29getNumberOfReferencePositionsEv</a></td>
+              <td class="coverFnHi">35978</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#166">_ZNK4PLMD22ReferenceConfiguration29getNumberOfReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">138192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#136">_ZNK4PLMD22ReferenceConfiguration21getReferencePositionsEv</a></td>
+              <td class="coverFnHi">781533</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceConfiguration.h.func.html b/coverage/reference/ReferenceConfiguration.h.func.html
new file mode 100644
index 0000000000..13871a80d8
--- /dev/null
+++ b/coverage/reference/ReferenceConfiguration.h.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceConfiguration.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceConfiguration.h<span style="font-size: 80%;"> (<a href="ReferenceConfiguration.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceConfiguration.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#98">_ZN4PLMD22ReferenceConfiguration15getAtomRequestsERSt6vectorINS_10AtomNumberESaIS2_EEb</a></td>
+              <td class="coverFnHi">177</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#130">_ZN4PLMD22ReferenceConfiguration15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#156">_ZN4PLMD22ReferenceConfiguration16getArgumentNamesB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#151">_ZN4PLMD22ReferenceConfiguration18getAbsoluteIndexesEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#146">_ZN4PLMD22ReferenceConfiguration18getReferenceMetricEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#100">_ZN4PLMD22ReferenceConfiguration19getArgumentRequestsERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EEb</a></td>
+              <td class="coverFnHi">354</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#126">_ZN4PLMD22ReferenceConfiguration28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#112">_ZNK4PLMD22ReferenceConfiguration20getReferenceArgumentERKj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#141">_ZNK4PLMD22ReferenceConfiguration21getReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">2281</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#136">_ZNK4PLMD22ReferenceConfiguration21getReferencePositionsEv</a></td>
+              <td class="coverFnHi">781533</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#166">_ZNK4PLMD22ReferenceConfiguration29getNumberOfReferenceArgumentsEv</a></td>
+              <td class="coverFnHi">138192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceConfiguration.h.gcov.html#161">_ZNK4PLMD22ReferenceConfiguration29getNumberOfReferencePositionsEv</a></td>
+              <td class="coverFnHi">35978</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceConfiguration.h.gcov.html b/coverage/reference/ReferenceConfiguration.h.gcov.html
new file mode 100644
index 0000000000..dd984a97d0
--- /dev/null
+++ b/coverage/reference/ReferenceConfiguration.h.gcov.html
@@ -0,0 +1,249 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceConfiguration.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceConfiguration.h<span style="font-size: 80%;"> (source / <a href="ReferenceConfiguration.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_ReferenceConfiguration_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_ReferenceConfiguration_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Tensor.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;ReferenceValuePack.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class Value;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class Pbc;</a>
+<a name="38"><span class="lineNum">      38 </span>            : class OFile;</a>
+<a name="39"><span class="lineNum">      39 </span>            : class PDB;</a>
+<a name="40"><span class="lineNum">      40 </span>            : class GenericMolInfo;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : /// \ingroup TOOLBOX</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Abstract base class for calculating the distance from a reference configuration.</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// A reference configuration can either have a particular set of atoms in a particular</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// given configuration or it can be that a particular set of colvars have a particular</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// set of values.  It could also be a combination of both.  To allow all the posible</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// permutations and in order make it easy to add new ways of calculating the distance</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// we have implemented this using polymorphism and multiple inheritance.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : class Direction;</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     519088 : class ReferenceConfigurationOptions {</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   friend class ReferenceConfiguration;</a>
+<a name="54"><span class="lineNum">      54 </span>            : private:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::string tt;</a>
+<a name="56"><span class="lineNum">      56 </span>            : public:</a>
+<a name="57"><span class="lineNum">      57 </span>            :   explicit ReferenceConfigurationOptions( const std::string&amp; type );</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool usingFastOption() const ;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::string getMultiRMSDType() const ;</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : /// \ingroup INHERIT</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Abstract base class for calculating the distance from a reference configuration.</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// A reference configuration can either have a particular set of atoms in a particular</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// given configuration or it can be that a particular set of colvars have a particular</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// set of values.  It could also be a combination of both.  To allow all the posible</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// permutations and in order make it easy to add new ways of calculating the distance</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// we have implemented this using polymorphism and multiple inheritance.  The following</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// provides \ref AddingAMetric &quot;information&quot; on how to implement a new method for</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// calculating the distance between a pair of configurations</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : class ReferenceConfiguration {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   friend class SingleDomainRMSD;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   friend double distance( const Pbc&amp; pbc, const std::vector&lt;Value*&gt; &amp; vals, ReferenceConfiguration*, ReferenceConfiguration*, const bool&amp; squared );</a>
+<a name="75"><span class="lineNum">      75 </span>            : private:</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// The name of this particular config</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::string name;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// A vector containing all the remarks from the pdb input</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;std::string&gt; line;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// These are used to do fake things when we copy frames</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;AtomNumber&gt; fake_atom_numbers;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;std::string&gt; fake_arg_names;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// These are use by the distance function above</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;Vector&gt; fake_refatoms;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;double&gt; fake_refargs;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;double&gt; fake_metric;</a>
+<a name="87"><span class="lineNum">      87 </span>            : protected:</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Crash with an error</a>
+<a name="89"><span class="lineNum">      89 </span>            :   [[noreturn]] void error(const std::string&amp; msg);</a>
+<a name="90"><span class="lineNum">      90 </span>            : public:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit ReferenceConfiguration( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Destructor</a>
+<a name="93"><span class="lineNum">      93 </span>            :   virtual ~ReferenceConfiguration();</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Return the name of this metric</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::string getName() const ;</a>
+<a name="96"><span class="lineNum">      96 </span>            : ///</a>
+<a name="97"><span class="lineNum">      97 </span>            :   virtual unsigned getNumberOfReferencePositions() const ;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   virtual unsigned getNumberOfReferenceArguments() const ;</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Retrieve the atoms that are required for this guy</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        177 :   virtual void getAtomRequests( std::vector&lt;AtomNumber&gt;&amp;, bool disable_checks=false ) {}</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Retrieve the arguments that are required for this guy</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        354 :   virtual void getArgumentRequests( std::vector&lt;std::string&gt;&amp;, bool disable_checks=false ) {}</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Do all local business for setting the configuration</a>
+<a name="104"><span class="lineNum">     104 </span>            :   virtual void read( const PDB&amp; )=0;</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Calculate the distance from the reference configuration</a>
+<a name="106"><span class="lineNum">     106 </span>            :   double calculate( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, ReferenceValuePack&amp; myder, const bool&amp; squared=false ) const ;</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// Calculate the distance from the reference configuration</a>
+<a name="108"><span class="lineNum">     108 </span>            :   virtual double calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; args,</a>
+<a name="109"><span class="lineNum">     109 </span>            :                        ReferenceValuePack&amp; myder, const bool&amp; squared ) const=0;</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// Parse something from the pdb remarks</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// Copy derivatives from one frame to this frame</a>
+<a name="112"><span class="lineNum">     112 </span>            :   void copyDerivatives( const ReferenceConfiguration* );</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Get one of the referene arguments</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   virtual double getReferenceArgument( const unsigned&amp; i ) const { plumed_error(); }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : /// These are overwritten in ReferenceArguments and ReferenceAtoms but are required here</a>
+<a name="116"><span class="lineNum">     116 </span>            : /// to make PLMD::distance work</a>
+<a name="117"><span class="lineNum">     117 </span>            :   virtual const std::vector&lt;Vector&gt;&amp; getReferencePositions() const ;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   virtual const std::vector&lt;double&gt;&amp; getReferenceArguments() const ;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   virtual const std::vector&lt;double&gt;&amp; getReferenceMetric();</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// These are overwritten in ReferenceArguments and ReferenceAtoms to make frame copying work</a>
+<a name="121"><span class="lineNum">     121 </span>            :   virtual const std::vector&lt;AtomNumber&gt;&amp; getAbsoluteIndexes();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   virtual const std::vector&lt;std::string&gt;&amp; getArgumentNames();</a>
+<a name="123"><span class="lineNum">     123 </span>            : /// Extract a Direction giving you the displacement from some position</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void extractDisplacementVector( const std::vector&lt;Vector&gt;&amp; pos, const std::vector&lt;Value*&gt;&amp; vals,</a>
+<a name="125"><span class="lineNum">     125 </span>            :                                   const std::vector&lt;double&gt;&amp; arg, const bool&amp; nflag,</a>
+<a name="126"><span class="lineNum">     126 </span>            :                                   Direction&amp; mydir ) const ;</a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Stuff for pca</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   virtual bool pcaIsEnabledForThisReference() { return false; }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   double projectDisplacementOnVector( const Direction&amp; mydir, const std::vector&lt;Value*&gt;&amp; vals,</a>
+<a name="130"><span class="lineNum">     130 </span>            :                                       const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; mypack ) const ;</a>
+<a name="131"><span class="lineNum">     131 </span>            : /// Stuff to setup pca</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   virtual void setupPCAStorage( ReferenceValuePack&amp; mypack ) { plumed_error(); }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Move the reference configuration by an amount specified using a Direction</a>
+<a name="134"><span class="lineNum">     134 </span>            :   void displaceReferenceConfiguration( const double&amp; weight, Direction&amp; dir );</a>
+<a name="135"><span class="lineNum">     135 </span>            : };</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : inline</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">     781533 : const std::vector&lt;Vector&gt;&amp; ReferenceConfiguration::getReferencePositions() const {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">     781533 :   return fake_refatoms;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : inline</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       2281 : const std::vector&lt;double&gt;&amp; ReferenceConfiguration::getReferenceArguments() const {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       2281 :   return fake_refargs;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : inline</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 : const std::vector&lt;double&gt;&amp; ReferenceConfiguration::getReferenceMetric() {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   return fake_metric;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : inline</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          8 : const std::vector&lt;AtomNumber&gt;&amp; ReferenceConfiguration::getAbsoluteIndexes() {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          8 :   return fake_atom_numbers;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : inline</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          2 : const std::vector&lt;std::string&gt;&amp; ReferenceConfiguration::getArgumentNames() {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :   return fake_arg_names;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : inline</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      35978 : unsigned ReferenceConfiguration::getNumberOfReferencePositions() const {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      35978 :   return 0;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : inline</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">     138192 : unsigned ReferenceConfiguration::getNumberOfReferenceArguments() const {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     138192 :   return 0;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceValuePack.cpp.func-sort-c.html b/coverage/reference/ReferenceValuePack.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d6c93b01cc
--- /dev/null
+++ b/coverage/reference/ReferenceValuePack.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceValuePack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceValuePack.cpp<span style="font-size: 80%;"> (<a href="ReferenceValuePack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceValuePack.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#36">_ZN4PLMD18ReferenceValuePack6resizeERKjS2_</a></td>
+              <td class="coverFnHi">104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#76">_ZN4PLMD18ReferenceValuePack21copyScaledDerivativesERKjRKdRKNS_10MultiValueE</a></td>
+              <td class="coverFnHi">162</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#84">_ZN4PLMD18ReferenceValuePack15moveDerivativesERKjS2_</a></td>
+              <td class="coverFnHi">8662</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#67">_ZN4PLMD18ReferenceValuePack19scaleAllDerivativesERKd</a></td>
+              <td class="coverFnHi">192765</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#62">_ZN4PLMD18ReferenceValuePack5clearEv</a></td>
+              <td class="coverFnHi">241460</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#41">_ZN4PLMD18ReferenceValuePack18updateDynamicListsEv</a></td>
+              <td class="coverFnHi">452950</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#24">_ZN4PLMD18ReferenceValuePackC2ERKjS2_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">471334</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceValuePack.cpp.func.html b/coverage/reference/ReferenceValuePack.cpp.func.html
new file mode 100644
index 0000000000..4dcf06dd71
--- /dev/null
+++ b/coverage/reference/ReferenceValuePack.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceValuePack.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceValuePack.cpp<span style="font-size: 80%;"> (<a href="ReferenceValuePack.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceValuePack.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#84">_ZN4PLMD18ReferenceValuePack15moveDerivativesERKjS2_</a></td>
+              <td class="coverFnHi">8662</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#41">_ZN4PLMD18ReferenceValuePack18updateDynamicListsEv</a></td>
+              <td class="coverFnHi">452950</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#67">_ZN4PLMD18ReferenceValuePack19scaleAllDerivativesERKd</a></td>
+              <td class="coverFnHi">192765</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#76">_ZN4PLMD18ReferenceValuePack21copyScaledDerivativesERKjRKdRKNS_10MultiValueE</a></td>
+              <td class="coverFnHi">162</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#62">_ZN4PLMD18ReferenceValuePack5clearEv</a></td>
+              <td class="coverFnHi">241460</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#36">_ZN4PLMD18ReferenceValuePack6resizeERKjS2_</a></td>
+              <td class="coverFnHi">104</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.cpp.gcov.html#24">_ZN4PLMD18ReferenceValuePackC2ERKjS2_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">471334</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceValuePack.cpp.gcov.html b/coverage/reference/ReferenceValuePack.cpp.gcov.html
new file mode 100644
index 0000000000..818d663c42
--- /dev/null
+++ b/coverage/reference/ReferenceValuePack.cpp.gcov.html
@@ -0,0 +1,171 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceValuePack.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceValuePack.cpp<span style="font-size: 80%;"> (source / <a href="ReferenceValuePack.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ReferenceValuePack.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span><span class="lineCov">     471334 : ReferenceValuePack::ReferenceValuePack( const unsigned&amp; nargs, const unsigned&amp; natoms, MultiValue&amp; vals ):</span></a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">     471334 :   boxWasSet(false),</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">     471334 :   numberOfArgs(nargs),</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     471334 :   oind_set(false),</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">     471334 :   myvals(vals),</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">     471334 :   atom_indices(myvals.getIndices()),</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     471334 :   pca(false)</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     471334 :   if( atom_indices.size()!=natoms ) { atom_indices.resize( natoms ); myvals.getAtomVector().resize( natoms ); }</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     471334 :   if( vals.getNumberOfValues()==1 ) { oind=0; oind_set=true; }</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     471334 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        104 : void ReferenceValuePack::resize( const unsigned&amp; nargs, const unsigned&amp; natoms ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        104 :   numberOfArgs=nargs; atom_indices.resize( natoms );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        104 :   myvals.getAtomVector().resize( natoms );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        104 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">     452950 : void ReferenceValuePack::updateDynamicLists() {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">     452950 :   myvals.emptyActiveMembers();</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">     522510 :   for(unsigned i=0; i&lt;numberOfArgs; ++i) myvals.putIndexInActiveArray( i );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">   21590009 :   for(unsigned i=0; i&lt;atom_indices.size(); ++i) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">   21137059 :     unsigned nbase = numberOfArgs + 3*atom_indices[i];</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">   21137059 :     if( atom_indices[i]&lt;myvals.getNumberOfDerivatives() &amp;&amp; myvals.isActive( nbase ) ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">   18164986 :       myvals.putIndexInActiveArray( nbase+0 ); myvals.putIndexInActiveArray( nbase+1 ); myvals.putIndexInActiveArray( nbase+2 );</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :     }</a>
+<a name="51"><span class="lineNum">      51 </span>            :   }</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     452950 :   unsigned nbase = myvals.getNumberOfDerivatives() - 9;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   // zero is added to all virial components to ensure that these are active in the dynamic list</a>
+<a name="54"><span class="lineNum">      54 </span>            :   // if this is not done there is a problem with secondary structure variables</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">     452950 :   if( atom_indices.size()&gt;0 ) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">    4181700 :     for(unsigned i=0; i&lt;9; ++i) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">    3763530 :       myvals.addDerivative( oind, nbase+i, 0.0 );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">    3763530 :       myvals.putIndexInActiveArray( nbase+i );</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :     }</a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">     452950 :   myvals.completeUpdate();</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     452950 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">     241460 : void ReferenceValuePack::clear() {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     241460 :   if( !myvals.updateComplete() ) updateDynamicLists();</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     241460 :   myvals.clearAll(); boxWasSet=false;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     241460 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     192765 : void ReferenceValuePack::scaleAllDerivatives( const double&amp; scalef ) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     192765 :   if( !myvals.updateComplete() ) updateDynamicLists();</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    8856593 :   for(unsigned i=0; i&lt;myvals.getNumberActive(); ++i) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">    8663828 :     unsigned ider=myvals.getActiveIndex(i);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    8663828 :     myvals.setDerivative( oind, ider, scalef*myvals.getDerivative( oind, ider ) );</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     192765 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        162 : void ReferenceValuePack::copyScaledDerivatives( const unsigned&amp; from, const double&amp; scalef, const MultiValue&amp; tvals ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   plumed_dbg_assert( tvals.getNumberOfDerivatives()==myvals.getNumberOfDerivatives() );</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       3681 :   for(unsigned i=0; i&lt;tvals.getNumberActive(); ++i) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       3519 :     unsigned ider=tvals.getActiveIndex(i);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       3519 :     myvals.addDerivative( oind, ider, scalef*tvals.getDerivative( from, ider ) );</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        162 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       8662 : void ReferenceValuePack::moveDerivatives( const unsigned&amp; from, const unsigned&amp; to ) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       8662 :   if( !myvals.updateComplete() ) updateDynamicLists();</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     866200 :   for(unsigned i=0; i&lt;myvals.getNumberActive(); ++i) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">     857538 :     unsigned ider=myvals.getActiveIndex(i);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     857538 :     myvals.setDerivative( to, ider, myvals.getDerivative( from, ider ) );</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       8662 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceValuePack.h.func-sort-c.html b/coverage/reference/ReferenceValuePack.h.func-sort-c.html
new file mode 100644
index 0000000000..a99129c937
--- /dev/null
+++ b/coverage/reference/ReferenceValuePack.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceValuePack.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceValuePack.h<span style="font-size: 80%;"> (<a href="ReferenceValuePack.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ReferenceValuePack.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#198">_ZNK4PLMD18ReferenceValuePack17getBoxDerivativesEv</a></td>
+              <td class="coverFnHi">600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#166">_ZN4PLMD18ReferenceValuePack17addBoxDerivativesERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">8268786</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#158">_ZN4PLMD18ReferenceValuePack18addAtomDerivativesERKjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">16356460</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#183">_ZNK4PLMD18ReferenceValuePack17getAtomDerivativeERKj</a></td>
+              <td class="coverFnHi">17175932</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#150">_ZN4PLMD18ReferenceValuePack18setAtomDerivativesERKjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">17547915</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceValuePack.h.func.html b/coverage/reference/ReferenceValuePack.h.func.html
new file mode 100644
index 0000000000..cd0dc2c45f
--- /dev/null
+++ b/coverage/reference/ReferenceValuePack.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceValuePack.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceValuePack.h<span style="font-size: 80%;"> (<a href="ReferenceValuePack.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ReferenceValuePack.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#166">_ZN4PLMD18ReferenceValuePack17addBoxDerivativesERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">8268786</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#158">_ZN4PLMD18ReferenceValuePack18addAtomDerivativesERKjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">16356460</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#150">_ZN4PLMD18ReferenceValuePack18setAtomDerivativesERKjRKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">17547915</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#183">_ZNK4PLMD18ReferenceValuePack17getAtomDerivativeERKj</a></td>
+              <td class="coverFnHi">17175932</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ReferenceValuePack.h.gcov.html#198">_ZNK4PLMD18ReferenceValuePack17getBoxDerivativesEv</a></td>
+              <td class="coverFnHi">600</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/ReferenceValuePack.h.gcov.html b/coverage/reference/ReferenceValuePack.h.gcov.html
new file mode 100644
index 0000000000..021cbfe2b6
--- /dev/null
+++ b/coverage/reference/ReferenceValuePack.h.gcov.html
@@ -0,0 +1,304 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/ReferenceValuePack.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - ReferenceValuePack.h<span style="font-size: 80%;"> (source / <a href="ReferenceValuePack.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_ReferenceValuePack_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_ReferenceValuePack_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/MultiValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class ReferenceValuePack {</a>
+<a name="30"><span class="lineNum">      30 </span>            :   friend class MultiDomainRMSD;</a>
+<a name="31"><span class="lineNum">      31 </span>            :   friend class OptimalRMSD;</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// Was the virial set</a>
+<a name="34"><span class="lineNum">      34 </span>            :   bool boxWasSet;</a>
+<a name="35"><span class="lineNum">      35 </span>            : ///</a>
+<a name="36"><span class="lineNum">      36 </span>            :   unsigned numberOfArgs;</a>
+<a name="37"><span class="lineNum">      37 </span>            : ///</a>
+<a name="38"><span class="lineNum">      38 </span>            :   bool oind_set;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   unsigned oind;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Copy of the values that we are adding to</a>
+<a name="41"><span class="lineNum">      41 </span>            :   MultiValue&amp; myvals;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Ths list of atom indices</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;unsigned&gt;&amp; atom_indices;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Are we using pca</a>
+<a name="45"><span class="lineNum">      45 </span>            :   bool pca;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// A vector of vectors to save us some overhead for vector resizes</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;Vector&gt; centeredpos;</a>
+<a name="48"><span class="lineNum">      48 </span>            : ///</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::vector&lt;Vector&gt; displacement;</a>
+<a name="50"><span class="lineNum">      50 </span>            : ///</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;Tensor&gt; rot;</a>
+<a name="52"><span class="lineNum">      52 </span>            : ///</a>
+<a name="53"><span class="lineNum">      53 </span>            :   Matrix&lt; std::vector&lt;Vector&gt; &gt;  DRotDPos;</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   ReferenceValuePack( const unsigned&amp; nargs, const unsigned&amp; natoms, MultiValue&amp; vals );</a>
+<a name="56"><span class="lineNum">      56 </span>            : ///</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void resize( const unsigned&amp; nargs, const unsigned&amp; natoms );</a>
+<a name="58"><span class="lineNum">      58 </span>            : ///</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void clear();</a>
+<a name="60"><span class="lineNum">      60 </span>            : ///</a>
+<a name="61"><span class="lineNum">      61 </span>            :   unsigned getNumberOfDerivatives() const ;</a>
+<a name="62"><span class="lineNum">      62 </span>            : ///</a>
+<a name="63"><span class="lineNum">      63 </span>            :   unsigned getNumberOfArguments() const ;</a>
+<a name="64"><span class="lineNum">      64 </span>            : ///</a>
+<a name="65"><span class="lineNum">      65 </span>            :   unsigned getNumberOfAtoms() const ;</a>
+<a name="66"><span class="lineNum">      66 </span>            : ///</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void setAtomIndex( const unsigned&amp; iatom, const unsigned&amp; jindex );</a>
+<a name="68"><span class="lineNum">      68 </span>            : ///</a>
+<a name="69"><span class="lineNum">      69 </span>            :   unsigned getAtomIndex( const unsigned&amp; iatom ) const ;</a>
+<a name="70"><span class="lineNum">      70 </span>            : ///</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void copyScaledDerivatives( const unsigned&amp; from, const double&amp; scalef, const MultiValue&amp; tvals );</a>
+<a name="72"><span class="lineNum">      72 </span>            : ///</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void addArgumentDerivatives( const unsigned&amp; iarg, const double&amp; der );</a>
+<a name="74"><span class="lineNum">      74 </span>            : ///</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void setArgumentDerivatives( const unsigned&amp; iarg, const double&amp; der );</a>
+<a name="76"><span class="lineNum">      76 </span>            : ///</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void setAtomDerivatives( const unsigned&amp; jder, const Vector&amp; der );</a>
+<a name="78"><span class="lineNum">      78 </span>            : ///</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void addAtomDerivatives( const unsigned&amp; iatom, const Vector&amp; der );</a>
+<a name="80"><span class="lineNum">      80 </span>            : ///</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void addBoxDerivatives( const Tensor&amp; vir );</a>
+<a name="82"><span class="lineNum">      82 </span>            : ///</a>
+<a name="83"><span class="lineNum">      83 </span>            :   bool updateComplete() const ;</a>
+<a name="84"><span class="lineNum">      84 </span>            : ///</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void updateDynamicLists();</a>
+<a name="86"><span class="lineNum">      86 </span>            : ///</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void scaleAllDerivatives( const double&amp; scalef );</a>
+<a name="88"><span class="lineNum">      88 </span>            : ///</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void setValIndex( const unsigned&amp; ind );</a>
+<a name="90"><span class="lineNum">      90 </span>            : ///</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void moveDerivatives( const unsigned&amp; from, const unsigned&amp; to );</a>
+<a name="92"><span class="lineNum">      92 </span>            : ///</a>
+<a name="93"><span class="lineNum">      93 </span>            :   bool virialWasSet() const ;</a>
+<a name="94"><span class="lineNum">      94 </span>            : ///</a>
+<a name="95"><span class="lineNum">      95 </span>            :   Vector getAtomDerivative( const unsigned&amp; iatom ) const ;</a>
+<a name="96"><span class="lineNum">      96 </span>            : ///</a>
+<a name="97"><span class="lineNum">      97 </span>            :   double getArgumentDerivative( const unsigned&amp; ival ) const ;</a>
+<a name="98"><span class="lineNum">      98 </span>            : ///</a>
+<a name="99"><span class="lineNum">      99 </span>            :   Tensor getBoxDerivatives() const ;</a>
+<a name="100"><span class="lineNum">     100 </span>            : ///</a>
+<a name="101"><span class="lineNum">     101 </span>            :   bool calcUsingPCAOption() const ;</a>
+<a name="102"><span class="lineNum">     102 </span>            : ///</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void switchOnPCAOption();</a>
+<a name="104"><span class="lineNum">     104 </span>            : ///</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;Vector&gt;&amp; getAtomVector();</a>
+<a name="106"><span class="lineNum">     106 </span>            : ///</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;Vector&gt;&amp; getAtomsDisplacementVector();</a>
+<a name="108"><span class="lineNum">     108 </span>            : };</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : inline</a>
+<a name="111"><span class="lineNum">     111 </span>            : unsigned ReferenceValuePack::getNumberOfDerivatives() const {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         44 :   return myvals.getNumberOfDerivatives();</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : inline</a>
+<a name="116"><span class="lineNum">     116 </span>            : unsigned ReferenceValuePack::getNumberOfArguments() const {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     172372 :   return numberOfArgs;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : }</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : inline</a>
+<a name="121"><span class="lineNum">     121 </span>            : unsigned ReferenceValuePack::getNumberOfAtoms() const {</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">    2098660 :   return atom_indices.size();</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : inline</a>
+<a name="126"><span class="lineNum">     126 </span>            : void ReferenceValuePack::setAtomIndex( const unsigned&amp; iatom, const unsigned&amp; jindex ) {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">    2967600 :   plumed_dbg_assert( iatom&lt;atom_indices.size() ); atom_indices[iatom]=jindex;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : inline</a>
+<a name="131"><span class="lineNum">     131 </span>            : unsigned ReferenceValuePack::getAtomIndex( const unsigned&amp; iatom ) const {</a>
+<a name="132"><span class="lineNum">     132 </span>            :   plumed_dbg_assert( iatom&lt;atom_indices.size() );</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">    1788696 :   return atom_indices[iatom];</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : inline</a>
+<a name="137"><span class="lineNum">     137 </span>            : void ReferenceValuePack::addArgumentDerivatives( const unsigned&amp; iarg, const double&amp; der ) {</a>
+<a name="138"><span class="lineNum">     138 </span>            :   plumed_dbg_assert( iarg&lt;numberOfArgs &amp;&amp; oind_set ); myvals.addDerivative( oind, iarg, der );</a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : inline</a>
+<a name="142"><span class="lineNum">     142 </span>            : void ReferenceValuePack::setArgumentDerivatives( const unsigned&amp; iarg, const double&amp; der ) {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">     833432 :   plumed_dbg_assert( iarg&lt;numberOfArgs &amp;&amp; oind_set ); myvals.setDerivative( oind, iarg, der );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : inline</a>
+<a name="147"><span class="lineNum">     147 </span>            : bool ReferenceValuePack::updateComplete() const {</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">     520192 :   return myvals.updateComplete();</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : inline</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">   17547915 : void ReferenceValuePack::setAtomDerivatives( const unsigned&amp; jder, const Vector&amp; der ) {</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   plumed_dbg_assert( oind_set &amp;&amp; jder&lt;atom_indices.size() );</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">   17547915 :   myvals.setDerivative( oind, numberOfArgs + 3*atom_indices[jder] + 0, der[0] );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">   17547915 :   myvals.setDerivative( oind, numberOfArgs + 3*atom_indices[jder] + 1, der[1] );</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">   17547915 :   myvals.setDerivative( oind, numberOfArgs + 3*atom_indices[jder] + 2, der[2] );</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">   17547915 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : inline</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   16356460 : void ReferenceValuePack::addAtomDerivatives( const unsigned&amp; jder, const Vector&amp; der ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   plumed_dbg_assert( oind_set &amp;&amp; jder&lt;atom_indices.size() );</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">   16356460 :   myvals.addDerivative( oind, numberOfArgs + 3*atom_indices[jder] + 0, der[0] );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">   16356460 :   myvals.addDerivative( oind, numberOfArgs + 3*atom_indices[jder] + 1, der[1] );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">   16356460 :   myvals.addDerivative( oind, numberOfArgs + 3*atom_indices[jder] + 2, der[2] );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">   16356460 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : inline</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">    8268786 : void ReferenceValuePack::addBoxDerivatives( const Tensor&amp; vir ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   plumed_dbg_assert( oind_set &amp;&amp; atom_indices.size()&gt;0 );</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">    8268786 :   boxWasSet=true; unsigned nbase = myvals.getNumberOfDerivatives() - 9;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">  107494218 :   for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) myvals.addDerivative( oind, nbase + 3*i + j, vir(i,j) );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">    8268786 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : inline</a>
+<a name="175"><span class="lineNum">     175 </span>            : void ReferenceValuePack::setValIndex( const unsigned&amp; ind ) {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     255233 :   oind=ind; oind_set=true;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : inline</a>
+<a name="180"><span class="lineNum">     180 </span>            : bool ReferenceValuePack::virialWasSet() const {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     176799 :   return boxWasSet;</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : inline</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">   17175932 : Vector ReferenceValuePack::getAtomDerivative( const unsigned&amp; iatom ) const {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">   17175932 :   Vector tmp; plumed_dbg_assert( oind_set &amp;&amp; iatom&lt;atom_indices.size() );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">   17175932 :   tmp[0]=myvals.getDerivative( oind, numberOfArgs + 3*atom_indices[iatom] + 0 );</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">   17175932 :   tmp[1]=myvals.getDerivative( oind, numberOfArgs + 3*atom_indices[iatom] + 1 );</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">   17175932 :   tmp[2]=myvals.getDerivative( oind, numberOfArgs + 3*atom_indices[iatom] + 2 );</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">   17175932 :   return tmp;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : inline</a>
+<a name="194"><span class="lineNum">     194 </span>            : double ReferenceValuePack::getArgumentDerivative( const unsigned&amp; ival ) const {</a>
+<a name="195"><span class="lineNum">     195 </span>            :   plumed_dbg_assert( oind_set &amp;&amp; ival&lt;numberOfArgs );</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      12614 :   return myvals.getDerivative( oind, ival );</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : inline</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        600 : Tensor ReferenceValuePack::getBoxDerivatives() const {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        600 :   plumed_dbg_assert( oind_set &amp;&amp; boxWasSet ); Tensor tvir; unsigned nbase = myvals.getNumberOfDerivatives() - 9;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       7800 :   for(unsigned i=0; i&lt;3; ++i) for(unsigned j=0; j&lt;3; ++j) tvir(i,j)=myvals.getDerivative( oind, nbase + 3*i + j );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        600 :   return tvir;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : inline</a>
+<a name="207"><span class="lineNum">     207 </span>            : bool ReferenceValuePack::calcUsingPCAOption() const {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     219081 :   return pca;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : inline</a>
+<a name="212"><span class="lineNum">     212 </span>            : void ReferenceValuePack::switchOnPCAOption() {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        698 :   pca=true;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : inline</a>
+<a name="217"><span class="lineNum">     217 </span>            : std::vector&lt;Vector&gt;&amp; ReferenceValuePack::getAtomVector() {</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">   17766386 :   return myvals.getAtomVector();</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : inline</a>
+<a name="222"><span class="lineNum">     222 </span>            : std::vector&lt;Vector&gt;&amp; ReferenceValuePack::getAtomsDisplacementVector() {</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       3026 :   return displacement;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SimpleRMSD.cpp.func-sort-c.html b/coverage/reference/SimpleRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d9b4708f66
--- /dev/null
+++ b/coverage/reference/SimpleRMSD.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SimpleRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SimpleRMSD.cpp<span style="font-size: 80%;"> (<a href="SimpleRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SimpleRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#43">_ZN4PLMD10SimpleRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#61">_ZNK4PLMD10SimpleRMSD25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#33">_ZN4PLMD10SimpleRMSD28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#49">_ZN4PLMD10SimpleRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#43">_ZN4PLMD10SimpleRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#41">_ZN4PLMD12_GLOBAL__N_120SimpleRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#34">_ZN4PLMD10SimpleRMSD15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#67">_ZNK4PLMD10SimpleRMSD33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#53">_ZNK4PLMD10SimpleRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">172</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#41">_ZN4PLMD12_GLOBAL__N_120SimpleRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#41">_ZN4PLMD12_GLOBAL__N_120SimpleRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SimpleRMSD.cpp.func.html b/coverage/reference/SimpleRMSD.cpp.func.html
new file mode 100644
index 0000000000..79d7400a8d
--- /dev/null
+++ b/coverage/reference/SimpleRMSD.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SimpleRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SimpleRMSD.cpp<span style="font-size: 80%;"> (<a href="SimpleRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SimpleRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#34">_ZN4PLMD10SimpleRMSD15setupPCAStorageERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#33">_ZN4PLMD10SimpleRMSD28pcaIsEnabledForThisReferenceEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#49">_ZN4PLMD10SimpleRMSD4readERKNS_3PDBE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#43">_ZN4PLMD10SimpleRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#43">_ZN4PLMD10SimpleRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#41">_ZN4PLMD12_GLOBAL__N_120SimpleRMSDRegisterMe6createERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#41">_ZN4PLMD12_GLOBAL__N_120SimpleRMSDRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#41">_ZN4PLMD12_GLOBAL__N_120SimpleRMSDRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#61">_ZNK4PLMD10SimpleRMSD25extractAtomicDisplacementERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERS5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#67">_ZNK4PLMD10SimpleRMSD33projectAtomicDisplacementOnVectorERKbRKSt6vectorINS_13VectorGenericILj3EEESaIS5_EERNS_18ReferenceValuePackE</a></td>
+              <td class="coverFnHi">88</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SimpleRMSD.cpp.gcov.html#53">_ZNK4PLMD10SimpleRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">172</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SimpleRMSD.cpp.gcov.html b/coverage/reference/SimpleRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..0a279d56d1
--- /dev/null
+++ b/coverage/reference/SimpleRMSD.cpp.gcov.html
@@ -0,0 +1,162 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SimpleRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SimpleRMSD.cpp<span style="font-size: 80%;"> (source / <a href="SimpleRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;RMSDBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;MetricRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : class SimpleRMSD : public RMSDBase {</a>
+<a name="29"><span class="lineNum">      29 </span>            : private:</a>
+<a name="30"><span class="lineNum">      30 </span>            :   RMSD myrmsd;</a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   explicit SimpleRMSD( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   void read( const PDB&amp; ) override;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   double calc( const std::vector&lt;Vector&gt;&amp; pos, ReferenceValuePack&amp; myder, const bool&amp; squared ) const override;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          4 :   bool pcaIsEnabledForThisReference() override { return true; }</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         68 :   void setupPCAStorage( ReferenceValuePack&amp; mypack ) override {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         68 :     mypack.switchOnPCAOption(); mypack.getAtomsDisplacementVector().resize( getNumberOfAtoms() );</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         68 :   }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   void extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; direction ) const override;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   double projectAtomicDisplacementOnVector( const bool&amp; normalized, const std::vector&lt;Vector&gt;&amp; vecs, ReferenceValuePack&amp; mypack ) const override;</a>
+<a name="41"><span class="lineNum">      41 </span>            : };</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      12574 : PLUMED_REGISTER_METRIC(SimpleRMSD,&quot;SIMPLE&quot;)</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         35 : SimpleRMSD::SimpleRMSD( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   ReferenceConfiguration( ro ),</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         35 :   RMSDBase( ro )</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         35 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         31 : void SimpleRMSD::read( const PDB&amp; pdb ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         31 :   readReference( pdb );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         31 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        172 : double SimpleRMSD::calc( const std::vector&lt;Vector&gt;&amp; pos, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        172 :   if( myder.getAtomsDisplacementVector().size()!=pos.size() ) myder.getAtomsDisplacementVector().resize( pos.size() );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        172 :   double d=myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), myder.getAtomVector(), myder.getAtomsDisplacementVector(), squared );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       3997 :   myder.clear(); for(unsigned i=0; i&lt;pos.size(); ++i) myder.setAtomDerivatives( i, myder.getAtomVector()[i] );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        172 :   if( !myder.updateComplete() ) myder.updateDynamicLists();</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        172 :   return d;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 : void SimpleRMSD::extractAtomicDisplacement( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; direction ) const {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   std::vector&lt;Vector&gt; tder( getNumberOfAtoms() );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   myrmsd.simpleAlignment( getAlign(), getDisplace(), pos, getReferencePositions(), tder, direction, true );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;pos.size(); ++i) direction[i] = getDisplace()[i]*direction[i];</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         88 : double SimpleRMSD::projectAtomicDisplacementOnVector( const bool&amp; normalized, const std::vector&lt;Vector&gt;&amp; vecs, ReferenceValuePack&amp; mypack ) const {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         88 :   plumed_dbg_assert( mypack.calcUsingPCAOption() ); Vector comder; comder.zero();</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        550 :   for(unsigned j=0; j&lt;vecs.size(); ++j) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       1848 :     for(unsigned k=0; k&lt;3; ++k) comder[k] += getAlign()[j]*vecs[j][k];</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         88 :   double proj=0; mypack.clear();</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        550 :   for(unsigned j=0; j&lt;vecs.size(); ++j) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1848 :     for(unsigned k=0; k&lt;3; ++k) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       1386 :       proj += vecs[j][k]*mypack.getAtomsDisplacementVector()[j][k];</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :     }</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        462 :     mypack.setAtomDerivatives( j, vecs[j] - comder );</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         88 :   if( !mypack.updateComplete() ) mypack.updateDynamicLists();</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         88 :   return proj;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SingleDomainRMSD.cpp.func-sort-c.html b/coverage/reference/SingleDomainRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7d6b1b68d3
--- /dev/null
+++ b/coverage/reference/SingleDomainRMSD.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SingleDomainRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SingleDomainRMSD.cpp<span style="font-size: 80%;"> (<a href="SingleDomainRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SingleDomainRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#26">_ZN4PLMD16SingleDomainRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#60">_ZN4PLMD16SingleDomainRMSD17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#32">_ZN4PLMD16SingleDomainRMSD13readReferenceERKNS_3PDBE</a></td>
+              <td class="coverFnHi">458</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#26">_ZN4PLMD16SingleDomainRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#90">_ZNK4PLMD16SingleDomainRMSD9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">58046</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#94">_ZNK4PLMD16SingleDomainRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">140941</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SingleDomainRMSD.cpp.func.html b/coverage/reference/SingleDomainRMSD.cpp.func.html
new file mode 100644
index 0000000000..f093ab76a6
--- /dev/null
+++ b/coverage/reference/SingleDomainRMSD.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SingleDomainRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SingleDomainRMSD.cpp<span style="font-size: 80%;"> (<a href="SingleDomainRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SingleDomainRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#32">_ZN4PLMD16SingleDomainRMSD13readReferenceERKNS_3PDBE</a></td>
+              <td class="coverFnHi">458</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#60">_ZN4PLMD16SingleDomainRMSD17setReferenceAtomsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEESB_</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#26">_ZN4PLMD16SingleDomainRMSDC1ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#26">_ZN4PLMD16SingleDomainRMSDC2ERKNS_29ReferenceConfigurationOptionsE</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#94">_ZNK4PLMD16SingleDomainRMSD4calcERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERKS1_IPNS_5ValueESaISC_EERKS1_IdSaIdEERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">140941</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.cpp.gcov.html#90">_ZNK4PLMD16SingleDomainRMSD9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERNS_18ReferenceValuePackERKb</a></td>
+              <td class="coverFnHi">58046</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SingleDomainRMSD.cpp.gcov.html b/coverage/reference/SingleDomainRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..26fc8869d9
--- /dev/null
+++ b/coverage/reference/SingleDomainRMSD.cpp.gcov.html
@@ -0,0 +1,178 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SingleDomainRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SingleDomainRMSD.cpp<span style="font-size: 80%;"> (source / <a href="SingleDomainRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SingleDomainRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;DRMSD.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        500 : SingleDomainRMSD::SingleDomainRMSD( const ReferenceConfigurationOptions&amp; ro ):</span></a>
+<a name="29"><span class="lineNum">      29 </span>            :   ReferenceConfiguration(ro),</a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        500 :   ReferenceAtoms(ro)</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : {</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        500 : }</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        458 : void SingleDomainRMSD::readReference( const PDB&amp; pdb ) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        458 :   readAtomsFromPDB( pdb );</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   double wa=0, wd=0;</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       9071 :   for(unsigned i=0; i&lt;pdb.size(); ++i) { wa+=align[i]; wd+=displace[i]; }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        458 :   if(wa&gt;epsilon) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        456 :     double w=1.0/wa;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       9039 :     for(unsigned i=0; i&lt;pdb.size(); ++i) align[i] *= w;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   } else {</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          2 :     double w=1.0/pdb.size();</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         32 :     for(unsigned i=0; i&lt;pdb.size(); ++i) align[i] = w;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   }</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        458 :   if(wd&gt;epsilon) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        456 :     double w=1.0/wd;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       9039 :     for(unsigned i=0; i&lt;pdb.size(); ++i) displace[i] *= w;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   } else {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          2 :     double w=1.0/pdb.size();</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         32 :     for(unsigned i=0; i&lt;pdb.size(); ++i) displace[i] = w;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        458 :   Vector center;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       9071 :   for(unsigned i=0; i&lt;pdb.size(); ++i) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       8613 :     center+=reference_atoms[i]*align[i];</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   }</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       9071 :   for(unsigned i=0; i&lt;pdb.size(); ++i) reference_atoms[i]-=center;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        458 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         45 : void SingleDomainRMSD::setReferenceAtoms( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; align_in, const std::vector&lt;double&gt;&amp; displace_in ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         45 :   reference_atoms.resize( conf.size() ); align.resize( conf.size() );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         45 :   displace.resize( conf.size() ); atom_der_index.resize( conf.size() );</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   double wa=0, wd=0;</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1154 :   for(unsigned i=0; i&lt;conf.size(); ++i) { wa+=align_in[i]; wd+=displace_in[i]; }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         45 :   if(wa&gt;epsilon) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         44 :     double w=1.0/wa;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       1145 :     for(unsigned i=0; i&lt;conf.size(); ++i) align[i] = align_in[i] * w;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   } else {</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          1 :     double w=1.0/conf.size();</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          9 :     for(unsigned i=0; i&lt;conf.size(); ++i) align[i] = w;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         45 :   if(wd&gt;epsilon) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         44 :     double w=1.0/wd;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       1146 :     for(unsigned i=0; i&lt;conf.size(); ++i) displace[i] = displace_in[i] * w;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   } else {</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          1 :     double w=1.0/conf.size();</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          8 :     for(unsigned i=0; i&lt;conf.size(); ++i) displace[i] = w;</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         45 :   Vector center;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1154 :   for(unsigned i=0; i&lt;conf.size(); ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1109 :     center+=conf[i]*align[i]; atom_der_index[i]=i;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1154 :   for(unsigned i=0; i&lt;conf.size(); ++i) reference_atoms[i]=conf[i]-center;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         45 :   setupRMSDObject();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         45 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      58046 : double SingleDomainRMSD::calculate( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      58046 :   return calc( pos, pbc, myder, squared );</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     140941 : double SingleDomainRMSD::calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg,</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :                                ReferenceValuePack&amp; myder, const bool&amp; squared ) const {</a>
+<a name="98"><span class="lineNum">      98 </span>            :   plumed_dbg_assert( vals.size()==0 &amp;&amp; pos.size()==getNumberOfAtoms() &amp;&amp; arg.size()==0 );</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     140941 :   return calc( pos, pbc, myder, squared );</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SingleDomainRMSD.h.func-sort-c.html b/coverage/reference/SingleDomainRMSD.h.func-sort-c.html
new file mode 100644
index 0000000000..64256b2e4d
--- /dev/null
+++ b/coverage/reference/SingleDomainRMSD.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SingleDomainRMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SingleDomainRMSD.h<span style="font-size: 80%;"> (<a href="SingleDomainRMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SingleDomainRMSD.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.h.gcov.html#44">_ZN4PLMD16SingleDomainRMSD15setupRMSDObjectEv</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.h.gcov.html#42">_ZN4PLMD16SingleDomainRMSD20setBoundsOnDistancesEbdd</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SingleDomainRMSD.h.func.html b/coverage/reference/SingleDomainRMSD.h.func.html
new file mode 100644
index 0000000000..16e81d69ec
--- /dev/null
+++ b/coverage/reference/SingleDomainRMSD.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SingleDomainRMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SingleDomainRMSD.h<span style="font-size: 80%;"> (<a href="SingleDomainRMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SingleDomainRMSD.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.h.gcov.html#44">_ZN4PLMD16SingleDomainRMSD15setupRMSDObjectEv</a></td>
+              <td class="coverFnHi">27</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SingleDomainRMSD.h.gcov.html#42">_ZN4PLMD16SingleDomainRMSD20setBoundsOnDistancesEbdd</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/SingleDomainRMSD.h.gcov.html b/coverage/reference/SingleDomainRMSD.h.gcov.html
new file mode 100644
index 0000000000..4d75babd7c
--- /dev/null
+++ b/coverage/reference/SingleDomainRMSD.h.gcov.html
@@ -0,0 +1,127 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference/SingleDomainRMSD.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">reference</a> - SingleDomainRMSD.h<span style="font-size: 80%;"> (source / <a href="SingleDomainRMSD.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_reference_SingleDomainRMSD_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_reference_SingleDomainRMSD_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ReferenceAtoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Pbc;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class SingleDomainRMSD : public ReferenceAtoms {</a>
+<a name="32"><span class="lineNum">      32 </span>            : protected:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   void readReference( const PDB&amp; pdb );</a>
+<a name="34"><span class="lineNum">      34 </span>            : public:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   explicit SingleDomainRMSD( const ReferenceConfigurationOptions&amp; ro );</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Set the reference structure</a>
+<a name="37"><span class="lineNum">      37 </span>            :   void setReferenceAtoms( const std::vector&lt;Vector&gt;&amp; conf, const std::vector&lt;double&gt;&amp; align_in, const std::vector&lt;double&gt;&amp; displace_in ) override;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Calculate</a>
+<a name="39"><span class="lineNum">      39 </span>            :   double calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, const std::vector&lt;Value*&gt;&amp; vals, const std::vector&lt;double&gt;&amp; arg, ReferenceValuePack&amp; myder, const bool&amp; squared ) const override;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   double calculate( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Calculate the distance using the input position</a>
+<a name="42"><span class="lineNum">      42 </span>            :   virtual double calc( const std::vector&lt;Vector&gt;&amp; pos, const Pbc&amp; pbc, ReferenceValuePack&amp; myder, const bool&amp; squared ) const=0;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// This sets upper and lower bounds on distances to be used in DRMSD (here it does nothing)</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         28 :   virtual void setBoundsOnDistances( bool dopbc, double lbound=0.0, double ubound=std::numeric_limits&lt;double&gt;::max( ) ) {};</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : /// This is used by MultiDomainRMSD to setup the RMSD object in Optimal RMSD type</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         27 :   virtual void setupRMSDObject() {};</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : };</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/index-sort-f.html b/coverage/reference/index-sort-f.html
new file mode 100644
index 0000000000..7ae9179858
--- /dev/null
+++ b/coverage/reference/index-sort-f.html
@@ -0,0 +1,353 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - reference</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">668</td>
+            <td class="headerCovTableEntry">776</td>
+            <td class="headerCovTableEntryMed">86.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntry">193</td>
+            <td class="headerCovTableEntryMed">79.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Direction.h.gcov.html">Direction.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DotProductDistance.cpp.gcov.html">DotProductDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=8 height=10 alt="8.3%"><img src="../snow.png" width=92 height=10 alt="8.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">8.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 12</td>
+      <td class="coverPerLo">28.6&nbsp;%</td>
+      <td class="coverNumLo">2 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NormalizedEuclideanDistance.cpp.gcov.html">NormalizedEuclideanDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=20 height=10 alt="20.0%"><img src="../snow.png" width=80 height=10 alt="20.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 5</td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MahalanobisDistance.cpp.gcov.html">MahalanobisDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=20 height=10 alt="20.0%"><img src="../snow.png" width=80 height=10 alt="20.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 5</td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceAtoms.h.gcov.html">ReferenceAtoms.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.3%"><img src="../snow.png" width=27 height=10 alt="73.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.3&nbsp;%</td>
+      <td class="coverNumLo">11 / 15</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ArgumentOnlyDistance.cpp.gcov.html">ArgumentOnlyDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=62 height=10 alt="62.5%"><img src="../snow.png" width=38 height=10 alt="62.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">10 / 16</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceConfiguration.h.gcov.html">ReferenceConfiguration.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">15 / 20</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSDBase.cpp.gcov.html">RMSDBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiDomainRMSD.cpp.gcov.html">MultiDomainRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.4%"><img src="../snow.png" width=13 height=10 alt="87.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.4&nbsp;%</td>
+      <td class="coverNumMed">90 / 103</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">10 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EuclideanDistance.cpp.gcov.html">EuclideanDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetricRegister.h.gcov.html">MetricRegister.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">18 / 19</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceArguments.cpp.gcov.html">ReferenceArguments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.2%"><img src="../snow.png" width=37 height=10 alt="63.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">67 / 106</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleRMSD.cpp.gcov.html">SimpleRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceAtoms.cpp.gcov.html">ReferenceAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">30 / 33</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SingleDomainRMSD.cpp.gcov.html">SingleDomainRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">45 / 45</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Direction.cpp.gcov.html">Direction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">28 / 30</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceConfiguration.cpp.gcov.html">ReferenceConfiguration.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.4%"><img src="../snow.png" width=4 height=10 alt="96.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.4&nbsp;%</td>
+      <td class="coverNumHi">54 / 56</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntermolecularDRMSD.cpp.gcov.html">IntermolecularDRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntramolecularDRMSD.cpp.gcov.html">IntramolecularDRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OptimalRMSD.cpp.gcov.html">OptimalRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SingleDomainRMSD.h.gcov.html">SingleDomainRMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ArgumentOnlyDistance.h.gcov.html">ArgumentOnlyDistance.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceArguments.h.gcov.html">ReferenceArguments.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceValuePack.h.gcov.html">ReferenceValuePack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 38</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetricRegister.cpp.gcov.html">MetricRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">16 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceValuePack.cpp.gcov.html">ReferenceValuePack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 49</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRMSD.cpp.gcov.html">DRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.0%"><img src="../snow.png" width=7 height=10 alt="93.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 57</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/index-sort-l.html b/coverage/reference/index-sort-l.html
new file mode 100644
index 0000000000..b530e217ce
--- /dev/null
+++ b/coverage/reference/index-sort-l.html
@@ -0,0 +1,353 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - reference</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">668</td>
+            <td class="headerCovTableEntry">776</td>
+            <td class="headerCovTableEntryMed">86.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntry">193</td>
+            <td class="headerCovTableEntryMed">79.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Direction.h.gcov.html">Direction.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DotProductDistance.cpp.gcov.html">DotProductDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=8 height=10 alt="8.3%"><img src="../snow.png" width=92 height=10 alt="8.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">8.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 12</td>
+      <td class="coverPerLo">28.6&nbsp;%</td>
+      <td class="coverNumLo">2 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NormalizedEuclideanDistance.cpp.gcov.html">NormalizedEuclideanDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=20 height=10 alt="20.0%"><img src="../snow.png" width=80 height=10 alt="20.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 5</td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MahalanobisDistance.cpp.gcov.html">MahalanobisDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=20 height=10 alt="20.0%"><img src="../snow.png" width=80 height=10 alt="20.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 5</td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ArgumentOnlyDistance.cpp.gcov.html">ArgumentOnlyDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=62 height=10 alt="62.5%"><img src="../snow.png" width=38 height=10 alt="62.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">10 / 16</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceArguments.cpp.gcov.html">ReferenceArguments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.2%"><img src="../snow.png" width=37 height=10 alt="63.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">67 / 106</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceAtoms.h.gcov.html">ReferenceAtoms.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.3%"><img src="../snow.png" width=27 height=10 alt="73.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.3&nbsp;%</td>
+      <td class="coverNumLo">11 / 15</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceConfiguration.h.gcov.html">ReferenceConfiguration.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">15 / 20</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetricRegister.cpp.gcov.html">MetricRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">16 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleRMSD.cpp.gcov.html">SimpleRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiDomainRMSD.cpp.gcov.html">MultiDomainRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.4%"><img src="../snow.png" width=13 height=10 alt="87.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.4&nbsp;%</td>
+      <td class="coverNumMed">90 / 103</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">10 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceAtoms.cpp.gcov.html">ReferenceAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">30 / 33</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRMSD.cpp.gcov.html">DRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.0%"><img src="../snow.png" width=7 height=10 alt="93.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 57</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Direction.cpp.gcov.html">Direction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">28 / 30</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetricRegister.h.gcov.html">MetricRegister.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">18 / 19</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceConfiguration.cpp.gcov.html">ReferenceConfiguration.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.4%"><img src="../snow.png" width=4 height=10 alt="96.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.4&nbsp;%</td>
+      <td class="coverNumHi">54 / 56</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SingleDomainRMSD.h.gcov.html">SingleDomainRMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ArgumentOnlyDistance.h.gcov.html">ArgumentOnlyDistance.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EuclideanDistance.cpp.gcov.html">EuclideanDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSDBase.cpp.gcov.html">RMSDBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceArguments.h.gcov.html">ReferenceArguments.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntramolecularDRMSD.cpp.gcov.html">IntramolecularDRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntermolecularDRMSD.cpp.gcov.html">IntermolecularDRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceValuePack.h.gcov.html">ReferenceValuePack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 38</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SingleDomainRMSD.cpp.gcov.html">SingleDomainRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">45 / 45</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceValuePack.cpp.gcov.html">ReferenceValuePack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 49</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OptimalRMSD.cpp.gcov.html">OptimalRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/reference/index.html b/coverage/reference/index.html
new file mode 100644
index 0000000000..d74d015e1b
--- /dev/null
+++ b/coverage/reference/index.html
@@ -0,0 +1,353 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - reference</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - reference</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">668</td>
+            <td class="headerCovTableEntry">776</td>
+            <td class="headerCovTableEntryMed">86.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntry">193</td>
+            <td class="headerCovTableEntryMed">79.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ArgumentOnlyDistance.cpp.gcov.html">ArgumentOnlyDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=62 height=10 alt="62.5%"><img src="../snow.png" width=38 height=10 alt="62.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">10 / 16</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ArgumentOnlyDistance.h.gcov.html">ArgumentOnlyDistance.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DRMSD.cpp.gcov.html">DRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.0%"><img src="../snow.png" width=7 height=10 alt="93.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 57</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Direction.cpp.gcov.html">Direction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">28 / 30</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">10 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Direction.h.gcov.html">Direction.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DotProductDistance.cpp.gcov.html">DotProductDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=8 height=10 alt="8.3%"><img src="../snow.png" width=92 height=10 alt="8.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">8.3&nbsp;%</td>
+      <td class="coverNumLo">1 / 12</td>
+      <td class="coverPerLo">28.6&nbsp;%</td>
+      <td class="coverNumLo">2 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="EuclideanDistance.cpp.gcov.html">EuclideanDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntermolecularDRMSD.cpp.gcov.html">IntermolecularDRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IntramolecularDRMSD.cpp.gcov.html">IntramolecularDRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MahalanobisDistance.cpp.gcov.html">MahalanobisDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=20 height=10 alt="20.0%"><img src="../snow.png" width=80 height=10 alt="20.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 5</td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetricRegister.cpp.gcov.html">MetricRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">16 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MetricRegister.h.gcov.html">MetricRegister.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.7%"><img src="../snow.png" width=5 height=10 alt="94.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.7&nbsp;%</td>
+      <td class="coverNumHi">18 / 19</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiDomainRMSD.cpp.gcov.html">MultiDomainRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.4%"><img src="../snow.png" width=13 height=10 alt="87.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.4&nbsp;%</td>
+      <td class="coverNumMed">90 / 103</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">10 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NormalizedEuclideanDistance.cpp.gcov.html">NormalizedEuclideanDistance.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=20 height=10 alt="20.0%"><img src="../snow.png" width=80 height=10 alt="20.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">20.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 5</td>
+      <td class="coverPerLo">40.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OptimalRMSD.cpp.gcov.html">OptimalRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">11 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSDBase.cpp.gcov.html">RMSDBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceArguments.cpp.gcov.html">ReferenceArguments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="63.2%"><img src="../snow.png" width=37 height=10 alt="63.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">67 / 106</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceArguments.h.gcov.html">ReferenceArguments.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceAtoms.cpp.gcov.html">ReferenceAtoms.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.9%"><img src="../snow.png" width=9 height=10 alt="90.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">30 / 33</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceAtoms.h.gcov.html">ReferenceAtoms.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.3%"><img src="../snow.png" width=27 height=10 alt="73.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.3&nbsp;%</td>
+      <td class="coverNumLo">11 / 15</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceConfiguration.cpp.gcov.html">ReferenceConfiguration.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.4%"><img src="../snow.png" width=4 height=10 alt="96.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.4&nbsp;%</td>
+      <td class="coverNumHi">54 / 56</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceConfiguration.h.gcov.html">ReferenceConfiguration.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.0%"><img src="../snow.png" width=25 height=10 alt="75.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">15 / 20</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">8 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceValuePack.cpp.gcov.html">ReferenceValuePack.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">49 / 49</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ReferenceValuePack.h.gcov.html">ReferenceValuePack.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">38 / 38</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SimpleRMSD.cpp.gcov.html">SimpleRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SingleDomainRMSD.cpp.gcov.html">SingleDomainRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">45 / 45</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SingleDomainRMSD.h.gcov.html">SingleDomainRMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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diff --git a/coverage/s2cm/S2ContactModel.cpp.func-sort-c.html b/coverage/s2cm/S2ContactModel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..25c10def0a
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+++ b/coverage/s2cm/S2ContactModel.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - s2cm/S2ContactModel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">s2cm</a> - S2ContactModel.cpp<span style="font-size: 80%;"> (<a href="S2ContactModel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="S2ContactModel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#99">_ZN4PLMD4s2cm14S2ContactModelC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#240">_ZN4PLMD4s2cm14S2ContactModelD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#79">_ZN4PLMD4s2cm12_GLOBAL__N_126S2ContactModelRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#99">_ZN4PLMD4s2cm14S2ContactModelC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#240">_ZN4PLMD4s2cm14S2ContactModelD0Ev</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#240">_ZN4PLMD4s2cm14S2ContactModelD1Ev</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#81">_ZN4PLMD4s2cm14S2ContactModel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#243">_ZN4PLMD4s2cm14S2ContactModel7prepareEv</a></td>
+              <td class="coverFnHi">48</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#79">_ZN4PLMD4s2cm12_GLOBAL__N_126S2ContactModelRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#79">_ZN4PLMD4s2cm12_GLOBAL__N_126S2ContactModelRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#259">_ZN4PLMD4s2cm14S2ContactModel9calculateEv</a></td>
+              <td class="coverFnHi">5952</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/s2cm/S2ContactModel.cpp.func.html b/coverage/s2cm/S2ContactModel.cpp.func.html
new file mode 100644
index 0000000000..8e254d6c33
--- /dev/null
+++ b/coverage/s2cm/S2ContactModel.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - s2cm/S2ContactModel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">s2cm</a> - S2ContactModel.cpp<span style="font-size: 80%;"> (<a href="S2ContactModel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="S2ContactModel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#79">_ZN4PLMD4s2cm12_GLOBAL__N_126S2ContactModelRegisterMe816createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#79">_ZN4PLMD4s2cm12_GLOBAL__N_126S2ContactModelRegisterMe81C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#79">_ZN4PLMD4s2cm12_GLOBAL__N_126S2ContactModelRegisterMe81D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#81">_ZN4PLMD4s2cm14S2ContactModel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#243">_ZN4PLMD4s2cm14S2ContactModel7prepareEv</a></td>
+              <td class="coverFnHi">48</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#259">_ZN4PLMD4s2cm14S2ContactModel9calculateEv</a></td>
+              <td class="coverFnHi">5952</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#99">_ZN4PLMD4s2cm14S2ContactModelC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#99">_ZN4PLMD4s2cm14S2ContactModelC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#240">_ZN4PLMD4s2cm14S2ContactModelD0Ev</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#240">_ZN4PLMD4s2cm14S2ContactModelD1Ev</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="S2ContactModel.cpp.gcov.html#240">_ZN4PLMD4s2cm14S2ContactModelD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/s2cm/S2ContactModel.cpp.gcov.html b/coverage/s2cm/S2ContactModel.cpp.gcov.html
new file mode 100644
index 0000000000..f79253e869
--- /dev/null
+++ b/coverage/s2cm/S2ContactModel.cpp.gcov.html
@@ -0,0 +1,401 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - s2cm/S2ContactModel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">s2cm</a> - S2ContactModel.cpp<span style="font-size: 80%;"> (source / <a href="S2ContactModel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2021 Omar Valsson</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            :    This file is part of S2 contact model module</a>
+<a name="5"><span class="lineNum">       5 </span>            : </a>
+<a name="6"><span class="lineNum">       6 </span>            :    The S2 contact model module is free software: you can redistribute it and/or modify</a>
+<a name="7"><span class="lineNum">       7 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="8"><span class="lineNum">       8 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="9"><span class="lineNum">       9 </span>            :    (at your option) any later version.</a>
+<a name="10"><span class="lineNum">      10 </span>            : </a>
+<a name="11"><span class="lineNum">      11 </span>            :    The S2 contact model module is distributed in the hope that it will be useful,</a>
+<a name="12"><span class="lineNum">      12 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="13"><span class="lineNum">      13 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="14"><span class="lineNum">      14 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="15"><span class="lineNum">      15 </span>            : </a>
+<a name="16"><span class="lineNum">      16 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="17"><span class="lineNum">      17 </span>            :    along with the S2 contact model module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="18"><span class="lineNum">      18 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="19"><span class="lineNum">      19 </span>            : </a>
+<a name="20"><span class="lineNum">      20 </span>            : #include &quot;colvar/Colvar.h&quot;</a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;tools/NeighborList.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace s2cm {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC S2CMMOD_COLVAR S2CM</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : S2 contact model CV.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : This CV was used in \cite Palazzesi_s2_2017, based on NH order parameter from \cite Zhang_s2_2002 and methyl order parameter from \cite Ming_s2_2004. Input parameters can be found in the relevant papers.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : \par Examples</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : */</a>
+<a name="46"><span class="lineNum">      46 </span>            : //+ENDPLUMEDOC</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : class S2ContactModel : public Colvar {</a>
+<a name="55"><span class="lineNum">      55 </span>            :   bool pbc_;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool serial_;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::unique_ptr&lt;NeighborList&gt; nl;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool invalidateList;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   bool firsttime;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   //</a>
+<a name="61"><span class="lineNum">      61 </span>            :   double r_eff_;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double inv_r_eff_;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double prefactor_a_;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double exp_b_;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double offset_c_;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double n_i_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double total_prefactor_;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double r_globalshift_;</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   enum ModelType {methyl,nh} modeltype_;</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            :   //</a>
+<a name="73"><span class="lineNum">      73 </span>            : public:</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit S2ContactModel(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ~S2ContactModel();</a>
+<a name="76"><span class="lineNum">      76 </span>            :   virtual void calculate();</a>
+<a name="77"><span class="lineNum">      77 </span>            :   virtual void prepare();</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="79"><span class="lineNum">      79 </span>            : };</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      12552 : PLUMED_REGISTER_ACTION(S2ContactModel,&quot;S2CM&quot;)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         26 : void S2ContactModel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         26 :   Colvar::registerKeywords(keys);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         52 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;Perform the calculation in serial - for debug purpose&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         52 :   keys.addFlag(&quot;NLIST&quot;,false,&quot;Use a neighbour list to speed up the calculation&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         52 :   keys.add(&quot;optional&quot;,&quot;NL_CUTOFF&quot;,&quot;The cutoff for the neighbour list&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         52 :   keys.add(&quot;optional&quot;,&quot;NL_STRIDE&quot;,&quot;The frequency with which we are updating the atoms in the neighbour list&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         52 :   keys.add(&quot;atoms&quot;,&quot;METHYL_ATOM&quot;,&quot;the methyl carbon atom of the residue (i)&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         52 :   keys.add(&quot;atoms&quot;,&quot;NH_ATOMS&quot;,&quot;the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1)&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         52 :   keys.add(&quot;atoms&quot;,&quot;HEAVY_ATOMS&quot;,&quot;the heavy atoms to be included in the calculation&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   //</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         52 :   keys.add(&quot;compulsory&quot;,&quot;R_EFF&quot;,&quot;the effective distance, r_eff in the equation, given in nm.&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         52 :   keys.add(&quot;compulsory&quot;,&quot;PREFACTOR_A&quot;,&quot;the prefactor, a in the equation&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         52 :   keys.add(&quot;compulsory&quot;,&quot;EXPONENT_B&quot;,&quot;the exponent, b in the equation&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         52 :   keys.add(&quot;compulsory&quot;,&quot;OFFSET_C&quot;,&quot;the offset, c in the equation&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         52 :   keys.add(&quot;compulsory&quot;,&quot;N_I&quot;,&quot; n_i in the equation&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         52 :   keys.add(&quot;optional&quot;,&quot;R_SHIFT&quot;,&quot;shift all distances by given amount&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         26 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         24 : S2ContactModel::S2ContactModel(const ActionOptions&amp;ao):</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         24 :   pbc_(true),</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         24 :   serial_(false),</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         24 :   invalidateList(true),</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         24 :   firsttime(true),</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         24 :   r_eff_(0.0),</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         24 :   inv_r_eff_(0.0),</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         24 :   prefactor_a_(0.0),</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         24 :   exp_b_(0.0),</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         24 :   offset_c_(0.0),</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         24 :   n_i_(0.0),</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         24 :   total_prefactor_(0.0),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         24 :   r_globalshift_(0.0),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         24 :   modeltype_(methyl)</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : {</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         48 :   parseFlag(&quot;SERIAL&quot;,serial_);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::vector&lt;AtomNumber&gt; methyl_atom;</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         48 :   parseAtomList(&quot;METHYL_ATOM&quot;,methyl_atom);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;AtomNumber&gt; nh_atoms;</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         48 :   parseAtomList(&quot;NH_ATOMS&quot;,nh_atoms);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         24 :   if(methyl_atom.size()==0 &amp;&amp; nh_atoms.size()==0) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :     error(&quot;you have to give either METHYL_ATOM or NH_ATOMS&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         24 :   if(methyl_atom.size()&gt;0 &amp;&amp; nh_atoms.size()&gt;0) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     error(&quot;you cannot give both METHYL_ATOM or NH_ATOMS&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         24 :   if(methyl_atom.size()&gt;0 &amp;&amp; methyl_atom.size()!=1) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     error(&quot;you should give one atom in METHYL_ATOM, the methyl carbon atom of the residue&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   }</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         24 :   if(nh_atoms.size()&gt;0 &amp;&amp; nh_atoms.size()!=2) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     error(&quot;you should give two atoms in NH_ATOMS, the hydrogen atom of the NH group of the residue (i) and carbonyl oxygen of the preceding residue (i-1)&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            :   std::vector&lt;AtomNumber&gt; heavy_atoms;</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         48 :   parseAtomList(&quot;HEAVY_ATOMS&quot;,heavy_atoms);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         24 :   if(heavy_atoms.size()==0) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     error(&quot;HEAVY_ATOMS is not given&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::vector&lt;AtomNumber&gt; main_atoms;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         24 :   if(methyl_atom.size()&gt;0) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     modeltype_= methyl;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :     main_atoms = methyl_atom;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         24 :   } else if(nh_atoms.size()&gt;0) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         24 :     modeltype_= nh;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         24 :     main_atoms = nh_atoms;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         24 :   bool nopbc=!pbc_;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         24 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         24 :   pbc_=!nopbc;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   // neighbor list stuff</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         24 :   bool doneigh=false;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         24 :   double nl_cut=0.0;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         24 :   int nl_st=0;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         24 :   parseFlag(&quot;NLIST&quot;,doneigh);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         24 :   if(doneigh) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         12 :     parse(&quot;NL_CUTOFF&quot;,nl_cut);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         12 :     if(nl_cut&lt;=0.0) error(&quot;NL_CUTOFF should be explicitly specified and positive&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         12 :     parse(&quot;NL_STRIDE&quot;,nl_st);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         12 :     if(nl_st&lt;=0) error(&quot;NL_STRIDE should be explicitly specified and positive&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         24 :   parse(&quot;R_EFF&quot;,r_eff_);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         24 :   inv_r_eff_ = 1.0/r_eff_;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         24 :   parse(&quot;PREFACTOR_A&quot;,prefactor_a_);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         24 :   parse(&quot;EXPONENT_B&quot;,exp_b_);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         24 :   parse(&quot;OFFSET_C&quot;,offset_c_);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   unsigned int n_i_int;</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         24 :   parse(&quot;N_I&quot;,n_i_int);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         24 :   n_i_ = static_cast&lt;double&gt;(n_i_int);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         24 :   total_prefactor_ = prefactor_a_/pow(n_i_,exp_b_);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   //</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         24 :   parse(&quot;R_SHIFT&quot;,r_globalshift_);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         24 :   checkRead();</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         24 :   addValueWithDerivatives();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         24 :   setNotPeriodic();</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         24 :   bool dopair=false;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         24 :   if(doneigh) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         24 :     nl=Tools::make_unique&lt;NeighborList&gt;(main_atoms,heavy_atoms,serial_,dopair,pbc_,getPbc(),comm,nl_cut,nl_st);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span>            :   else {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         24 :     nl=Tools::make_unique&lt;NeighborList&gt;(main_atoms,heavy_atoms,serial_,dopair,pbc_,getPbc(),comm);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         24 :   requestAtoms(nl-&gt;getFullAtomList());</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         24 :   log.printf(&quot;  NMR S2 contact model CV, please read and cite &quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         48 :   log &lt;&lt; plumed.cite(&quot;Palazzesi, Valsson, and Parrinello, J. Phys. Chem. Lett. 8, 4752 (2017) - DOI:10.1021/acs.jpclett.7b01770&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         24 :   if(modeltype_==methyl) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     log &lt;&lt; plumed.cite(&quot;Ming and Bruschweiler, J. Biomol. NMR, 29, 363 (2004) - DOI:10.1023/B:JNMR.0000032612.70767.35&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     log.printf(&quot;  calculation of methyl order parameter using atom %d \n&quot;,methyl_atom[0].serial());</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         24 :   else if(modeltype_==nh) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         48 :     log &lt;&lt; plumed.cite(&quot;Zhang and Bruschweiler, J. Am. Chem. Soc. 124, 12654 (2002) - DOI:10.1021/ja027847a&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         24 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         24 :     log.printf(&quot;  calculation of NH order parameter using atoms %d and %d\n&quot;,nh_atoms[0].serial(),nh_atoms[1].serial());</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         24 :   log.printf(&quot;  heavy atoms used in the calculation (%u in total):\n&quot;,static_cast&lt;unsigned int&gt;(heavy_atoms.size()));</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       1872 :   for(unsigned int i=0; i&lt;heavy_atoms.size(); ++i) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       1848 :     if( (i+1) % 25 == 0 ) {log.printf(&quot;  \n&quot;);}</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1848 :     log.printf(&quot;  %d&quot;, heavy_atoms[i].serial());</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         24 :   log.printf(&quot;  \n&quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         24 :   log.printf(&quot;  total number of distances: %u\n&quot;,nl-&gt;size());</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   //</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         24 :   log.printf(&quot;  using parameters&quot;);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         24 :   log.printf(&quot; r_eff=%f,&quot;,r_eff_);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         24 :   log.printf(&quot; a=%f,&quot;,prefactor_a_);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         24 :   log.printf(&quot; b=%f,&quot;,exp_b_);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         24 :   log.printf(&quot; c=%f,&quot;,offset_c_);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         24 :   log.printf(&quot; n_i=%u&quot;,n_i_int);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         24 :   if(r_globalshift_!=0.0) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :     log.printf(&quot;, r_shift=%f&quot;,r_globalshift_);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         24 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         24 :   if(pbc_) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         12 :     log.printf(&quot;  using periodic boundary conditions\n&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   } else {</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         12 :     log.printf(&quot;  without periodic boundary conditions\n&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         24 :   if(doneigh) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         12 :     log.printf(&quot;  using neighbor lists with\n&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         12 :     log.printf(&quot;  update every %d steps and cutoff %f\n&quot;,nl_st,nl_cut);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :   }</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         24 :   if(serial_) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :     log.printf(&quot;  calculation done in serial\n&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   }</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         24 : }</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         48 : S2ContactModel::~S2ContactModel() {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         48 : }</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         48 : void S2ContactModel::prepare() {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         48 :   if(nl-&gt;getStride()&gt;0) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         24 :     if(firsttime || (getStep()%nl-&gt;getStride()==0)) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         24 :       requestAtoms(nl-&gt;getFullAtomList());</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         24 :       invalidateList=true;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         24 :       firsttime=false;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     } else {</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :       requestAtoms(nl-&gt;getReducedAtomList());</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :       invalidateList=false;</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       if(getExchangeStep()) error(&quot;Neighbor lists should be updated on exchange steps - choose a NL_STRIDE which divides the exchange stride!&quot;);</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         24 :     if(getExchangeStep()) firsttime=true;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   }</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         48 : }</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            : // calculator</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       5952 : void S2ContactModel::calculate() {</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       5952 :   Tensor virial;</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       5952 :   std::vector&lt;Vector&gt; deriv(getNumberOfAtoms());</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       5952 :   if(nl-&gt;getStride()&gt;0 &amp;&amp; invalidateList) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">       2976 :     nl-&gt;update(getPositions());</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">       5952 :   unsigned int stride=comm.Get_size();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       5952 :   unsigned int rank=comm.Get_rank();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">       5952 :   if(serial_) {</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     stride=1;</a>
+<a name="274"><span class="lineNum">     274 </span>            :     rank=0;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       5952 :   double contact_sum = 0.0;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       5952 :   const unsigned int nn=nl-&gt;size();</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">     321408 :   for(unsigned int i=rank; i&lt;nn; i+=stride) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">     315456 :     Vector distance;</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">     315456 :     unsigned int i0=nl-&gt;getClosePair(i).first;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">     315456 :     unsigned int i1=nl-&gt;getClosePair(i).second;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     315456 :     if(getAbsoluteIndex(i0)==getAbsoluteIndex(i1)) {continue;}</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     315456 :     if(pbc_) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      86304 :       distance=pbcDistance(getPosition(i0),getPosition(i1));</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :     } else {</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     229152 :       distance=delta(getPosition(i0),getPosition(i1));</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :     }</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     315456 :     double exp_arg = exp(-(distance.modulo()-r_globalshift_)*inv_r_eff_);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">     315456 :     contact_sum += exp_arg;</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">     315456 :     exp_arg /= distance.modulo();</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     315456 :     Vector dd(exp_arg*distance);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">     315456 :     Tensor vv(dd,distance);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">     315456 :     deriv[i0]-=dd;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">     315456 :     deriv[i1]+=dd;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">     315456 :     virial-=vv;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       5952 :   if(!serial_) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       5952 :     comm.Sum(contact_sum);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       5952 :     if(!deriv.empty()) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       5952 :       comm.Sum(&amp;deriv[0][0],3*deriv.size());</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :     }</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       5952 :     comm.Sum(virial);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   }</a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       5952 :   double value = tanh(total_prefactor_*contact_sum);</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :   // using that d/dx[tanh(x)]= 1-[tanh(x)]^2</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       5952 :   double deriv_f = -inv_r_eff_*total_prefactor_*(1.0-value*value);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       5952 :   value -= offset_c_;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     476160 :   for(unsigned int i=0; i&lt;deriv.size(); ++i) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">     470208 :     setAtomsDerivatives(i,deriv_f*deriv[i]);</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       5952 :   setValue(value);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       5952 :   setBoxDerivatives(deriv_f*virial);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       5952 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : }</a>
+<a name="325"><span class="lineNum">     325 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/s2cm/index-sort-f.html b/coverage/s2cm/index-sort-f.html
new file mode 100644
index 0000000000..b31c2341d0
--- /dev/null
+++ b/coverage/s2cm/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - s2cm</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - s2cm</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="S2ContactModel.cpp.gcov.html">S2ContactModel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.6%"><img src="../snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
+      <td class="coverNumHi">152 / 166</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/s2cm/index-sort-l.html b/coverage/s2cm/index-sort-l.html
new file mode 100644
index 0000000000..fa41733a5a
--- /dev/null
+++ b/coverage/s2cm/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - s2cm</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - s2cm</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="S2ContactModel.cpp.gcov.html">S2ContactModel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.6%"><img src="../snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
+      <td class="coverNumHi">152 / 166</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/s2cm/index.html b/coverage/s2cm/index.html
new file mode 100644
index 0000000000..4f0b437d5e
--- /dev/null
+++ b/coverage/s2cm/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - s2cm</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - s2cm</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntry">166</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="S2ContactModel.cpp.gcov.html">S2ContactModel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.6%"><img src="../snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
+      <td class="coverNumHi">152 / 166</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">9 / 11</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/index-sort-f.html b/coverage/sasa/index-sort-f.html
new file mode 100644
index 0000000000..66ac887075
--- /dev/null
+++ b/coverage/sasa/index-sort-f.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - sasa</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">998</td>
+            <td class="headerCovTableEntry">1217</td>
+            <td class="headerCovTableEntryMed">82.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa_LCPO.cpp.gcov.html">sasa_LCPO.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.3%"><img src="../snow.png" width=18 height=10 alt="82.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.3&nbsp;%</td>
+      <td class="coverNumMed">519 / 631</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa_HASEL.cpp.gcov.html">sasa_HASEL.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.7%"><img src="../snow.png" width=18 height=10 alt="81.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.7&nbsp;%</td>
+      <td class="coverNumMed">479 / 586</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/index-sort-l.html b/coverage/sasa/index-sort-l.html
new file mode 100644
index 0000000000..e4b738ef62
--- /dev/null
+++ b/coverage/sasa/index-sort-l.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - sasa</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">998</td>
+            <td class="headerCovTableEntry">1217</td>
+            <td class="headerCovTableEntryMed">82.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa_HASEL.cpp.gcov.html">sasa_HASEL.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.7%"><img src="../snow.png" width=18 height=10 alt="81.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.7&nbsp;%</td>
+      <td class="coverNumMed">479 / 586</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa_LCPO.cpp.gcov.html">sasa_LCPO.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.3%"><img src="../snow.png" width=18 height=10 alt="82.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.3&nbsp;%</td>
+      <td class="coverNumMed">519 / 631</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/index.html b/coverage/sasa/index.html
new file mode 100644
index 0000000000..462af4f8bd
--- /dev/null
+++ b/coverage/sasa/index.html
@@ -0,0 +1,103 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - sasa</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">998</td>
+            <td class="headerCovTableEntry">1217</td>
+            <td class="headerCovTableEntryMed">82.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa_HASEL.cpp.gcov.html">sasa_HASEL.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.7%"><img src="../snow.png" width=18 height=10 alt="81.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.7&nbsp;%</td>
+      <td class="coverNumMed">479 / 586</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="sasa_LCPO.cpp.gcov.html">sasa_LCPO.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.3%"><img src="../snow.png" width=18 height=10 alt="82.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.3&nbsp;%</td>
+      <td class="coverNumMed">519 / 631</td>
+      <td class="coverPerMed">81.2&nbsp;%</td>
+      <td class="coverNumMed">13 / 16</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/sasa_HASEL.cpp.func-sort-c.html b/coverage/sasa/sasa_HASEL.cpp.func-sort-c.html
new file mode 100644
index 0000000000..73bafd553d
--- /dev/null
+++ b/coverage/sasa/sasa_HASEL.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa/sasa_HASEL.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">sasa</a> - sasa_HASEL.cpp<span style="font-size: 80%;"> (<a href="sasa_HASEL.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">479</td>
+            <td class="headerCovTableEntry">586</td>
+            <td class="headerCovTableEntryMed">81.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="sasa_HASEL.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#602">_ZN4PLMD4sasa10SASA_HASEL13computeDeltaGEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#175">_ZN4PLMD4sasa10SASA_HASELC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#561">_ZN4PLMD4sasa10SASA_HASEL10readDeltaGEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#546">_ZN4PLMD4sasa10SASA_HASEL11readMaxSurfEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#516">_ZN4PLMD4sasa10SASA_HASEL15setupMaxSurfMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#474">_ZN4PLMD4sasa10SASA_HASEL13readSASAparamEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#264">_ZN4PLMD4sasa10SASA_HASEL15setupHASELparamB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#247">_ZN4PLMD4sasa10SASA_HASEL7readPDBEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#175">_ZN4PLMD4sasa10SASA_HASELC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#163">_ZN4PLMD4sasa12_GLOBAL__N_123SASA_HASELRegisterMe1656createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#165">_ZN4PLMD4sasa10SASA_HASEL16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#759">_ZN4PLMD4sasa10SASA_HASEL9calcNlistEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#785">_ZN4PLMD4sasa10SASA_HASEL9calculateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#236">_ZN4PLMD4sasa5splitISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEEEvRKS8_RT_</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#163">_ZN4PLMD4sasa12_GLOBAL__N_123SASA_HASELRegisterMe165C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#163">_ZN4PLMD4sasa12_GLOBAL__N_123SASA_HASELRegisterMe165D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/sasa_HASEL.cpp.func.html b/coverage/sasa/sasa_HASEL.cpp.func.html
new file mode 100644
index 0000000000..3762eca2d2
--- /dev/null
+++ b/coverage/sasa/sasa_HASEL.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa/sasa_HASEL.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">sasa</a> - sasa_HASEL.cpp<span style="font-size: 80%;"> (<a href="sasa_HASEL.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">479</td>
+            <td class="headerCovTableEntry">586</td>
+            <td class="headerCovTableEntryMed">81.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="sasa_HASEL.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#561">_ZN4PLMD4sasa10SASA_HASEL10readDeltaGEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#546">_ZN4PLMD4sasa10SASA_HASEL11readMaxSurfEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#602">_ZN4PLMD4sasa10SASA_HASEL13computeDeltaGEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#474">_ZN4PLMD4sasa10SASA_HASEL13readSASAparamEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#264">_ZN4PLMD4sasa10SASA_HASEL15setupHASELparamB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#516">_ZN4PLMD4sasa10SASA_HASEL15setupMaxSurfMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#165">_ZN4PLMD4sasa10SASA_HASEL16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#247">_ZN4PLMD4sasa10SASA_HASEL7readPDBEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#759">_ZN4PLMD4sasa10SASA_HASEL9calcNlistEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#785">_ZN4PLMD4sasa10SASA_HASEL9calculateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#175">_ZN4PLMD4sasa10SASA_HASELC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#175">_ZN4PLMD4sasa10SASA_HASELC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#163">_ZN4PLMD4sasa12_GLOBAL__N_123SASA_HASELRegisterMe1656createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#163">_ZN4PLMD4sasa12_GLOBAL__N_123SASA_HASELRegisterMe165C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#163">_ZN4PLMD4sasa12_GLOBAL__N_123SASA_HASELRegisterMe165D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_HASEL.cpp.gcov.html#236">_ZN4PLMD4sasa5splitISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEEEvRKS8_RT_</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/sasa_HASEL.cpp.gcov.html b/coverage/sasa/sasa_HASEL.cpp.gcov.html
new file mode 100644
index 0000000000..40574b0e8b
--- /dev/null
+++ b/coverage/sasa/sasa_HASEL.cpp.gcov.html
@@ -0,0 +1,1088 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa/sasa_HASEL.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">sasa</a> - sasa_HASEL.cpp<span style="font-size: 80%;"> (source / <a href="sasa_HASEL.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">479</td>
+            <td class="headerCovTableEntry">586</td>
+            <td class="headerCovTableEntryMed">81.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2021, Andrea Arsiccio</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : </a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;Sasa.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdio&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;sstream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;algorithm&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;iterator&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;fstream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : using namespace std;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace sasa {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC SASAMOD_COLVAR SASA_HASEL</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The algorithm described in \cite Hasel1988 is used for the calculation. The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of SASA is updated (the default is every 10 steps).</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Different properties can be calculated and selected using the TYPE keyword:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : 1) the total SASA (TOTAL);</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : 2) the free energy of transfer for the protein according to the transfer model (TRANSFER). This keyword can be used, for instance, to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-T-SASA-2021, or to different pressures, as detailed in \cite Arsiccio-P-SASA-2021, or to different osmolyte solutions, as detailed in \cite Arsiccio-C-SASA-2022.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : When the TRANSFER keyword is used, a file with the free energy of transfer values for the sidechains and backbone atoms should be provided (using the keyword DELTAGFILE). Such file should have the following format:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \verbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : ----------------Sample DeltaG.dat file---------------------</a>
+<a name="59"><span class="lineNum">      59 </span>            : ALA     0.711019999999962</a>
+<a name="60"><span class="lineNum">      60 </span>            : ARG     -2.24832799999996</a>
+<a name="61"><span class="lineNum">      61 </span>            : ASN     -2.74838799999999</a>
+<a name="62"><span class="lineNum">      62 </span>            : ASP     -2.5626376</a>
+<a name="63"><span class="lineNum">      63 </span>            : CYS     3.89864000000006</a>
+<a name="64"><span class="lineNum">      64 </span>            : GLN     -1.76192</a>
+<a name="65"><span class="lineNum">      65 </span>            : GLU     -2.38664400000002</a>
+<a name="66"><span class="lineNum">      66 </span>            : GLY     0</a>
+<a name="67"><span class="lineNum">      67 </span>            : HIS     -3.58152799999999</a>
+<a name="68"><span class="lineNum">      68 </span>            : ILE     2.42634399999986</a>
+<a name="69"><span class="lineNum">      69 </span>            : LEU     1.77233599999988</a>
+<a name="70"><span class="lineNum">      70 </span>            : LYS     -1.92576400000002</a>
+<a name="71"><span class="lineNum">      71 </span>            : MET     -0.262827999999956</a>
+<a name="72"><span class="lineNum">      72 </span>            : PHE     1.62028800000007</a>
+<a name="73"><span class="lineNum">      73 </span>            : PRO     -2.15598800000001</a>
+<a name="74"><span class="lineNum">      74 </span>            : SER     -1.60934800000004</a>
+<a name="75"><span class="lineNum">      75 </span>            : THR     -0.591559999999987</a>
+<a name="76"><span class="lineNum">      76 </span>            : TRP     1.22936000000027</a>
+<a name="77"><span class="lineNum">      77 </span>            : TYR     0.775547999999958</a>
+<a name="78"><span class="lineNum">      78 </span>            : VAL     2.12779200000011</a>
+<a name="79"><span class="lineNum">      79 </span>            : BACKBONE        1.00066920000002</a>
+<a name="80"><span class="lineNum">      80 </span>            : -----------------------------------------------------------</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endverbatim</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : where the second column is the free energy of transfer for each sidechain/backbone, in kJ/mol.</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure (according to \cite Arsiccio-C-SASA-2022, \cite Arsiccio-T-SASA-2021 and \cite Arsiccio-P-SASA-2021) is freely available at https://github.com/andrea-arsiccio/DeltaG-calculation. The script automatically outputs a DeltaG.dat file compatible with this SASA module.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : If the DELTAGFILE is not provided, the program computes the free energy of transfer values as if they had to take into account the effect of temperature according to approaches 2 or 3 in the paper \cite Arsiccio-T-SASA-2021. Please read and cite this paper if using the transfer model for computing the effect of temperature in implicit solvent simulations. For this purpose, the keyword APPROACH should be added, and set to either 2 or 3.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : The SASA usually makes sense when atoms used for the calculation are all part of the same molecule. When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.2, by considering the ordered list of atoms and rebuilding the broken entities using a procedure that is equivalent to that done in \ref WHOLEMOLECULES. Notice that rebuilding is local to this action. This is different from \ref WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="93"><span class="lineNum">      93 </span>            : In that case you need to take care that atoms are in the correct periodic image.</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : The SASA may also be computed using the SASA_LCPO collective variable, which makes use of the LCPO algorithm \cite Weiser1999. SASA_LCPO is more accurate then SASA_HASEL, but the computation is slower.</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : \par Examples</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : The following input tells plumed to print the total SASA for atoms 10 to 20 in a protein chain.</a>
+<a name="101"><span class="lineNum">     101 </span>            : \plumedfile</a>
+<a name="102"><span class="lineNum">     102 </span>            : SASA_HASEL TYPE=TOTAL ATOMS=10-20 NL_STRIDE=10 LABEL=sasa</a>
+<a name="103"><span class="lineNum">     103 </span>            : PRINT ARG=sasa STRIDE=1 FILE=colvar</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endplumedfile</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are read from a file called DeltaG.dat.</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : \plumedfile</a>
+<a name="110"><span class="lineNum">     110 </span>            : SASA_HASEL TYPE=TRANSFER ATOMS=10-20 NL_STRIDE=10 DELTAGFILE=DeltaG.dat LABEL=sasa</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : bias: BIASVALUE ARG=sasa</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : PRINT ARG=sasa,bias.* STRIDE=1 FILE=colvar</a>
+<a name="115"><span class="lineNum">     115 </span>            : \endplumedfile</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are computed according to \cite Arsiccio-T-SASA-2021, and take into account the effect of temperature using approach 2 as described in the paper.</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : \plumedfile</a>
+<a name="120"><span class="lineNum">     120 </span>            : SASA_HASEL TYPE=TRANSFER ATOMS=10-20 NL_STRIDE=10 APPROACH=2 LABEL=sasa</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : bias: BIASVALUE ARG=sasa</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : PRINT ARG=sasa,bias.* STRIDE=1 FILE=colvar</a>
+<a name="125"><span class="lineNum">     125 </span>            : \endplumedfile</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : */</a>
+<a name="128"><span class="lineNum">     128 </span>            : //+ENDPLUMEDOC</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : class SASA_HASEL : public Colvar {</a>
+<a name="131"><span class="lineNum">     131 </span>            : private:</a>
+<a name="132"><span class="lineNum">     132 </span>            :   enum CV_TYPE {TOTAL, TRANSFER};</a>
+<a name="133"><span class="lineNum">     133 </span>            :   int sasa_type;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   bool nopbc;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   double rs;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   string DeltaGValues;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   int approach;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   unsigned stride;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   unsigned nl_update;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   int firstStepFlag;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   double Ti;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   // cppcheck-suppress duplInheritedMember</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   vector &lt; vector &lt; std::string &gt; &gt; AtomResidueName;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   vector &lt; vector &lt; double &gt; &gt; SASAparam;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   vector &lt; vector &lt; std::string &gt; &gt; CONNECTparam;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   unsigned natoms;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   vector &lt; vector &lt; double &gt; &gt; MaxSurf;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   vector &lt; vector &lt; double &gt; &gt; DeltaG;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   vector &lt; vector &lt; int &gt; &gt; Nlist;</a>
+<a name="151"><span class="lineNum">     151 </span>            : public:</a>
+<a name="152"><span class="lineNum">     152 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   explicit SASA_HASEL(const ActionOptions&amp;);</a>
+<a name="154"><span class="lineNum">     154 </span>            :   void readPDB();</a>
+<a name="155"><span class="lineNum">     155 </span>            :   map&lt;string, vector&lt;std::string&gt; &gt; setupHASELparam();</a>
+<a name="156"><span class="lineNum">     156 </span>            :   void readSASAparam();</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void calcNlist();</a>
+<a name="158"><span class="lineNum">     158 </span>            :   map&lt;string, vector&lt;double&gt; &gt; setupMaxSurfMap();</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void readMaxSurf();</a>
+<a name="160"><span class="lineNum">     160 </span>            :   void readDeltaG();</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void computeDeltaG();</a>
+<a name="162"><span class="lineNum">     162 </span>            :   virtual void calculate();</a>
+<a name="163"><span class="lineNum">     163 </span>            : };</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(SASA_HASEL,&quot;SASA_HASEL&quot;)</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          4 : void SASA_HASEL::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          4 :   Colvar::registerKeywords(keys);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the group of atoms that you are calculating the SASA for&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;TOTAL&quot;,&quot;The type of calculation you want to perform. Can be TOTAL or TRANSFER&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;, &quot;NL_STRIDE&quot;, &quot;The frequency with which the neighbor list for the calculation of SASA is updated.&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;DELTAGFILE&quot;,&quot;a file containing the free energy of transfer values for backbone and sidechains atoms. Necessary only if TYPE = TRANSFER. A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure is freely available at https://github.com/andrea-arsiccio/DeltaG-calculation. The script automatically outputs a DeltaG.dat file compatible with this SASA module. If TYPE = TRANSFER and no DELTAGFILE is provided, the free energy values are those describing the effect of temperature, and are computed using the temperature value passed by the MD engine&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;APPROACH&quot;,&quot;either approach 2 or 3. Necessary only if TYPE = TRANSFER and no DELTAGFILE is provided. If TYPE = TRANSFER and no DELTAGFILE is provided, the free energy values are those describing the effect of temperature, and the program must know if approach 2 or 3 (as described in Arsiccio and Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach, J. Phys. Chem. B, 2021) needs to be used to compute them&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          4 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 : SASA_HASEL::SASA_HASEL(const ActionOptions&amp;ao):</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :   nopbc(false),</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :   stride(10),</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :   nl_update(0),</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :   DeltaGValues(&quot;absent&quot;),</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          2 :   Ti(0),</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :   firstStepFlag(0)</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : {</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          2 :   rs = 0.14;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          2 :   parse(&quot;DELTAGFILE&quot;,DeltaGValues);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :   parse(&quot;APPROACH&quot;, approach);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          4 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          2 :   if(atoms.size()==0) error(&quot;no atoms specified&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   std::string Type;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          2 :   parse(&quot;TYPE&quot;,Type);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 :   parse(&quot;NL_STRIDE&quot;, stride);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          2 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          2 :   if(Type==&quot;TOTAL&quot;) sasa_type=TOTAL;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          1 :   else if(Type==&quot;TRANSFER&quot;) sasa_type=TRANSFER;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   else error(&quot;Unknown SASA type&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          2 :   switch(sasa_type)</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          1 :   case TOTAL:   log.printf(&quot;  TOTAL SASA;&quot;); break;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          1 :   case TRANSFER: log.printf(&quot;  TRANSFER MODEL;&quot;); break;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          2 :   log.printf(&quot;  atoms involved : &quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        240 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        240 :     log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          2 :   if(nopbc) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  PBC will be ignored\n&quot;;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   } else {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  broken molecules will be rebuilt assuming atoms are in the proper order\n&quot;;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          2 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 :   requestAtoms(atoms);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          2 :   natoms = getNumberOfAtoms();</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          2 :   AtomResidueName.resize(2);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          2 :   SASAparam.resize(natoms);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          2 :   CONNECTparam.resize(natoms);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          2 :   MaxSurf.resize(natoms);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          2 :   DeltaG.resize(natoms+1);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          2 :   Nlist.resize(natoms);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 : }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : //splits strings into tokens. Used to read into SASA parameters file and into reference pdb file</a>
+<a name="237"><span class="lineNum">     237 </span>            : template &lt;class Container&gt;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         42 : void split(const std::string&amp; str, Container&amp; cont)</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : {</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         42 :   std::istringstream iss(str);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         84 :   std::copy(std::istream_iterator&lt;std::string&gt;(iss),</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         42 :             std::istream_iterator&lt;std::string&gt;(),</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :             std::back_inserter(cont));</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         42 : }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : //reads input PDB file provided with MOLINFO, and assigns atom and residue names to each atom involved in the CV</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          2 : void SASA_HASEL::readPDB() {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 :   auto* moldat = plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          2 :   if( ! moldat ) error(&quot;Unable to find MOLINFO in input&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :   AtomResidueName[0].clear();</a>
+<a name="253"><span class="lineNum">     253 </span>            :   AtomResidueName[1].clear();</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        240 :     string Aname = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        240 :     string Rname = moldat-&gt;getResidueName(atoms[i]);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        240 :     AtomResidueName[0].push_back (Aname);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        240 :     AtomResidueName[1].push_back (Rname);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          2 : }</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : //Hasel et al. parameters database</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          2 : map&lt;string, vector&lt;std::string&gt; &gt; SASA_HASEL::setupHASELparam() {</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   map&lt;string, vector&lt;std::string&gt; &gt; haselmap;</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         16 :   haselmap[&quot;ALA_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         16 :   haselmap[&quot;ALA_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         16 :   haselmap[&quot;ALA_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         16 :   haselmap[&quot;ALA_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         16 :   haselmap[&quot;ALA_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         16 :   haselmap[&quot;ALA_CB&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_CG&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CB&quot;,  &quot;OD1&quot;,  &quot;OD2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_OD1&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         16 :   haselmap[&quot;ASP_OD2&quot;] = { &quot;1.7&quot;,  &quot;0.922&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_CG&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;CB&quot;,  &quot;OD1&quot;,  &quot;ND2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_OD1&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_ND2&quot;] = { &quot;1.6&quot;,  &quot;1.215&quot;,  &quot;CG&quot;,  &quot;1HD2&quot;,  &quot;1HD2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_1HD2&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;ND2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         16 :   haselmap[&quot;ASN_2HD2&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;ND2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_CG&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_CD&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CG&quot;,  &quot;NE&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_NE&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;CD&quot;,  &quot;HE&quot;,  &quot;CZ&quot;,  &quot;Z&quot;, };</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_NH1&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;CZ&quot;,  &quot;1HH1&quot;,  &quot;2HH1&quot;,  &quot;Z&quot;, };</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_NH2&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;CZ&quot;,  &quot;1HH2&quot;,  &quot;2HH2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_CZ&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;NE&quot;,  &quot;NH1&quot;,  &quot;NH2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_HE&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NE&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_1HH2&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NH2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_2HH2&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NH2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_2HH1&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NH1&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         16 :   haselmap[&quot;ARG_1HH1&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NH1&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;SG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_SG&quot;] = { &quot;1.8&quot;,  &quot;1.121&quot;,  &quot;CB&quot;,  &quot;HG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         16 :   haselmap[&quot;CYS_HG&quot;] = { &quot;1.2&quot;,  &quot;0.928&quot;,  &quot;SG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_CG&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_CD&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CG&quot;,  &quot;OE1&quot;,  &quot;OE2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_OE1&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         16 :   haselmap[&quot;GLU_OE2&quot;] = { &quot;1.7&quot;,  &quot;0.922&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_CG&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_CD&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CG&quot;,  &quot;OE1&quot;,  &quot;NE2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_OE1&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_NE2&quot;] = { &quot;1.6&quot;,  &quot;1.215&quot;,  &quot;CD&quot;,  &quot;2HE2&quot;,  &quot;1HE2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_2HE2&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NE2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         16 :   haselmap[&quot;GLN_1HE2&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NE2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         16 :   haselmap[&quot;GLY_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         16 :   haselmap[&quot;GLY_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         16 :   haselmap[&quot;GLY_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         16 :   haselmap[&quot;GLY_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         16 :   haselmap[&quot;GLY_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_CG&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CB&quot;,  &quot;CD2&quot;,  &quot;ND1&quot;,  &quot;Z&quot;, };</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_ND1&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;CG&quot;,  &quot;CE1&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_CE1&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;ND1&quot;,  &quot;NE2&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_NE2&quot;] = { &quot;1.55&quot;,  &quot;1.413&quot;,  &quot;CE1&quot;,  &quot;2HE&quot;,  &quot;CD2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_CD2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;NE2&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         16 :   haselmap[&quot;HIS_2HE&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NE2&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_CB&quot;] = { &quot;1.8&quot;,  &quot;1.276&quot;,  &quot;CA&quot;,  &quot;CG2&quot;,  &quot;CG1&quot;,  &quot;Z&quot;, };</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_CG2&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CB&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_CG1&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;CD1&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         16 :   haselmap[&quot;ILE_CD1&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CG1&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_CG&quot;] = { &quot;1.8&quot;,  &quot;1.276&quot;,  &quot;CB&quot;,  &quot;CD1&quot;,  &quot;CD2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_CD1&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         16 :   haselmap[&quot;LEU_CD2&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_CG&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_CD&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CG&quot;,  &quot;CE&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_CE&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CD&quot;,  &quot;NZ&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_NZ&quot;] = { &quot;1.6&quot;,  &quot;1.215&quot;,  &quot;CE&quot;,  &quot;1HZ&quot;,  &quot;2HZ&quot;,  &quot;3HZ&quot;, };</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_1HZ&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NZ&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_2HZ&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NZ&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         16 :   haselmap[&quot;LYS_3HZ&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NZ&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         16 :   haselmap[&quot;MET_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         16 :   haselmap[&quot;MET_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         16 :   haselmap[&quot;MET_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">         16 :   haselmap[&quot;MET_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         16 :   haselmap[&quot;MET_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         16 :   haselmap[&quot;MET_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         16 :   haselmap[&quot;MET_CG&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;SD&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">         16 :   haselmap[&quot;MET_SD&quot;] = { &quot;1.8&quot;,  &quot;1.121&quot;,  &quot;CG&quot;,  &quot;CE&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         16 :   haselmap[&quot;MET_CE&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;SD&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CG&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CB&quot;,  &quot;CD1&quot;,  &quot;CD2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CD1&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CG&quot;,  &quot;CE1&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CE1&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CD1&quot;,  &quot;CZ&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CZ&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CE1&quot;,  &quot;CE2&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CE2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CZ&quot;,  &quot;CD2&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         16 :   haselmap[&quot;PHE_CD2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CE2&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;CD&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_CG&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CB&quot;,  &quot;CD&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         16 :   haselmap[&quot;PRO_CD&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CG&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         16 :   haselmap[&quot;SER_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         16 :   haselmap[&quot;SER_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         16 :   haselmap[&quot;SER_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         16 :   haselmap[&quot;SER_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         16 :   haselmap[&quot;SER_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         16 :   haselmap[&quot;SER_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;OG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         16 :   haselmap[&quot;SER_OG&quot;] = { &quot;1.52&quot;,  &quot;1.08&quot;,  &quot;CB&quot;,  &quot;HG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         16 :   haselmap[&quot;SER_HG&quot;] = { &quot;1.0&quot;,  &quot;0.944&quot;,  &quot;OG&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         16 :   haselmap[&quot;THR_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         16 :   haselmap[&quot;THR_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         16 :   haselmap[&quot;THR_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         16 :   haselmap[&quot;THR_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         16 :   haselmap[&quot;THR_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         16 :   haselmap[&quot;THR_CB&quot;] = { &quot;1.8&quot;,  &quot;1.276&quot;,  &quot;CA&quot;,  &quot;CG2&quot;,  &quot;OG1&quot;,  &quot;Z&quot;, };</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         16 :   haselmap[&quot;THR_CG2&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CB&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         16 :   haselmap[&quot;THR_OG1&quot;] = { &quot;1.52&quot;,  &quot;1.08&quot;,  &quot;1HG&quot;,  &quot;CB&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         16 :   haselmap[&quot;THR_1HG&quot;] = { &quot;1.0&quot;,  &quot;0.944&quot;,  &quot;OG1&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CG&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CB&quot;,  &quot;CD2&quot;,  &quot;CD1&quot;,  &quot;Z&quot;, };</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CD1&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CG&quot;,  &quot;NE1&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_NE1&quot;] = { &quot;1.55&quot;,  &quot;1.413&quot;,  &quot;CD1&quot;,  &quot;CE2&quot;,  &quot;1HE&quot;,  &quot;Z&quot;, };</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CE2&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;NE1&quot;,  &quot;CD2&quot;,  &quot;CZ2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CZ2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CE2&quot;,  &quot;CH2&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CH2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CZ2&quot;,  &quot;CZ3&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CZ3&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CH2&quot;,  &quot;CE3&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CE3&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CZ3&quot;,  &quot;CD2&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_CD2&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CE3&quot;,  &quot;CE2&quot;,  &quot;CG&quot;,  &quot;Z&quot;, };</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">         16 :   haselmap[&quot;TRP_1HE&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;NE1&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CB&quot;] = { &quot;1.9&quot;,  &quot;1.045&quot;,  &quot;CA&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CG&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CB&quot;,  &quot;CD1&quot;,  &quot;CD2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CD1&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CG&quot;,  &quot;CE1&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CE1&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CD1&quot;,  &quot;CZ&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CZ&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CE1&quot;,  &quot;OH&quot;,  &quot;CE2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_OH&quot;] = { &quot;1.52&quot;,  &quot;1.08&quot;,  &quot;CZ&quot;,  &quot;HH&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_HH&quot;] = { &quot;1.0&quot;,  &quot;0.944&quot;,  &quot;OH&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CE2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CZ&quot;,  &quot;CD2&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         16 :   haselmap[&quot;TYR_CD2&quot;] = { &quot;1.8&quot;,  &quot;1.073&quot;,  &quot;CE2&quot;,  &quot;CG&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_N&quot;] = { &quot;1.55&quot;,  &quot;1.028&quot;,  &quot;H&quot;,  &quot;CA&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_CA&quot;] = { &quot;1.7&quot;,  &quot;2.149&quot;,  &quot;N&quot;,  &quot;C&quot;,  &quot;CB&quot;,  &quot;Z&quot;, };</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_C&quot;] = { &quot;1.72&quot;,  &quot;1.554&quot;,  &quot;CA&quot;,  &quot;O&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_O&quot;] = { &quot;1.5&quot;,  &quot;0.926&quot;,  &quot;C&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_H&quot;] = { &quot;1.1&quot;,  &quot;1.128&quot;,  &quot;N&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_CB&quot;] = { &quot;1.8&quot;,  &quot;1.276&quot;,  &quot;CA&quot;,  &quot;CG1&quot;,  &quot;CG2&quot;,  &quot;Z&quot;, };</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_CG1&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CB&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         16 :   haselmap[&quot;VAL_CG2&quot;] = { &quot;2.0&quot;,  &quot;0.88&quot;,  &quot;CB&quot;,  &quot;Z&quot;,  &quot;Z&quot;,  &quot;Z&quot;, };</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          2 :   return haselmap;</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : }</a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            : //assigns SASA parameters to each atom reading from HASEL parameter database</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          2 : void SASA_HASEL::readSASAparam() {</span></a>
+<a name="477"><span class="lineNum">     477 </span>            : </a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        240 :     SASAparam[i].clear();</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :     CONNECTparam[i].clear();</a>
+<a name="481"><span class="lineNum">     481 </span>            :   }</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            :   map&lt;string, vector&lt;std::string&gt; &gt; haselmap;</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          4 :   haselmap = setupHASELparam();</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :   vector&lt;std::string&gt; HASELparamVector;</a>
+<a name="486"><span class="lineNum">     486 </span>            :   string identifier;</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        480 :     identifier = AtomResidueName[1][i]+&quot;_&quot;+AtomResidueName[0][i];</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        240 :     if (haselmap.find(identifier)!=haselmap.end()) {</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        144 :       HASELparamVector = haselmap.at(identifier);</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        144 :       SASAparam[i].push_back (std::atof(HASELparamVector[0].c_str())+rs*10);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        144 :       SASAparam[i].push_back (std::atof(HASELparamVector[1].c_str()));</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">        288 :       CONNECTparam[i].push_back (HASELparamVector[2].c_str());</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">        288 :       CONNECTparam[i].push_back (HASELparamVector[3].c_str());</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">        288 :       CONNECTparam[i].push_back (HASELparamVector[4].c_str());</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">        288 :       CONNECTparam[i].push_back (HASELparamVector[5].c_str());</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :     }</a>
+<a name="500"><span class="lineNum">     500 </span>            :   }</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        240 :     if (SASAparam[i].size()==0 ) {</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         96 :       if ((AtomResidueName[0][i][0]=='O') || (AtomResidueName[0][i][0]=='N') || (AtomResidueName[0][i][0]=='C') || (AtomResidueName[0][i][0]=='S')) {</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :         cout &lt;&lt; &quot;Could not find SASA paramaters for atom &quot; &lt;&lt; AtomResidueName[0][i] &lt;&lt; &quot; of residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; endl;</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :         error (&quot;missing SASA parameters\n&quot;);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :       }</a>
+<a name="509"><span class="lineNum">     509 </span>            :     }</a>
+<a name="510"><span class="lineNum">     510 </span>            :   }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          4 : }</span></a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : </a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span>            : //Max Surf values, used only if TYPE=TRANSFER</a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">          1 : map&lt;string, vector&lt;double&gt; &gt; SASA_HASEL::setupMaxSurfMap() {</span></a>
+<a name="519"><span class="lineNum">     519 </span>            :   // Max Surface Area for backbone and sidechain, in nm2</a>
+<a name="520"><span class="lineNum">     520 </span>            :   map&lt;string, vector&lt;double&gt; &gt; valuemap;</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">          1 :   valuemap [&quot;ALA&quot;]= {0.56425,0.584851,};</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">          1 :   valuemap [&quot;ARG&quot;]= {0.498656,1.808093,};</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">          1 :   valuemap [&quot;ASN&quot;]= {0.473409,0.818394,};</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          1 :   valuemap [&quot;ASP&quot;]= {0.477057,0.977303,};</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          1 :   valuemap [&quot;CYS&quot;]= {0.507512,0.791483,};</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">          1 :   valuemap [&quot;GLN&quot;]= {0.485859,1.281534,};</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">          1 :   valuemap [&quot;GLU&quot;]= {0.495054,1.464718,};</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">          1 :   valuemap [&quot;GLY&quot;]= {0.658632,0,};</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">          1 :   valuemap [&quot;HIS&quot;]= {0.48194,1.118851,};</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          1 :   valuemap [&quot;ILE&quot;]= {0.461283,1.450569,};</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">          1 :   valuemap [&quot;LEU&quot;]= {0.476315,1.498843,};</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">          1 :   valuemap [&quot;LYS&quot;]= {0.493533,1.619731,};</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">          1 :   valuemap [&quot;MET&quot;]= {0.507019,1.631904,};</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">          1 :   valuemap [&quot;PHE&quot;]= {0.457462, 1.275125,};</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">          1 :   valuemap [&quot;PRO&quot;]= {0.315865,0.859456,};</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          1 :   valuemap [&quot;SER&quot;]= {0.48636,0.627233,};</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          1 :   valuemap [&quot;THR&quot;]= {0.45064,0.91088,};</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          1 :   valuemap [&quot;TRP&quot;]= {0.45762,1.366369,};</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">          1 :   valuemap [&quot;TYR&quot;]= {0.461826,1.425822,};</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">          1 :   valuemap [&quot;VAL&quot;]= {0.477054,1.149101,};</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">          1 :   return valuemap;</span></a>
+<a name="542"><span class="lineNum">     542 </span>            : }</a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span>            : //reads maximum surface values per residue type and assigns values to each atom, only used if sasa_type = TRANSFER</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">          1 : void SASA_HASEL::readMaxSurf() {</span></a>
+<a name="549"><span class="lineNum">     549 </span>            :   map&lt;string, vector&lt;double&gt; &gt; valuemap;</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">          2 :   valuemap = setupMaxSurfMap();</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :   vector&lt;double&gt; MaxSurfVector;</a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">        121 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">        120 :     MaxSurf[i].clear();</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">        120 :     MaxSurfVector = valuemap.at(AtomResidueName[1][i]);</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">        120 :     MaxSurf[i].push_back (MaxSurfVector[0]*100);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        120 :     MaxSurf[i].push_back (MaxSurfVector[1]*100);</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">          1 : }</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            : //reads file with free energy values for sidechains and for the backbone, and assigns values to each atom. Only used if sasa_type = TRANSFER</a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">          1 : void SASA_HASEL::readDeltaG() {</span></a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">        121 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">        120 :     DeltaG[i].clear();</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :   }</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span>            :   string DeltaGline;</a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">          1 :   fstream DeltaGFile;</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">          1 :   DeltaGFile.open(DeltaGValues);</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">          1 :   if (DeltaGFile) {</span></a>
+<a name="573"><span class="lineNum">     573 </span>            :     int backboneflag = 0;</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         23 :     while(getline(DeltaGFile, DeltaGline)) {</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         22 :       if(!DeltaGline.empty()) {</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :         std::vector&lt;std::string&gt; DeltaGtoken;</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         21 :         split(DeltaGline, DeltaGtoken);</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">       2541 :         for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">       2520 :           if (DeltaGtoken[0].compare(AtomResidueName[1][i])==0 ) {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">        120 :             DeltaG[i].push_back (std::atof(DeltaGtoken[1].c_str()));</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :           }</a>
+<a name="582"><span class="lineNum">     582 </span>            :         }</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         21 :         if (DeltaGtoken[0].compare(&quot;BACKBONE&quot;)==0 ) {</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :           backboneflag = 1;</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">          1 :           DeltaG[natoms].push_back (std::atof(DeltaGtoken[1].c_str()));</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :         }</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         21 :       }</span></a>
+<a name="588"><span class="lineNum">     588 </span>            :     }</a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">          1 :     if ( backboneflag == 0) error(&quot;Cannot find backbone value in Delta G parameters file\n&quot;);</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :   }</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :   else error(&quot;Cannot open DeltaG file&quot;);</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">        121 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">        120 :     if (DeltaG[i].size()==0 ) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineNoCov">          0 :       cout &lt;&lt; &quot;Delta G value for residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; &quot; not found &quot; &lt;&lt; endl;</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :       error (&quot;missing Delta G parameter\n&quot;);</span></a>
+<a name="597"><span class="lineNum">     597 </span>            :     }</a>
+<a name="598"><span class="lineNum">     598 </span>            :   }</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">          2 : }</span></a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span>            : //computes free energy values for the sidechains and for the backbone, and assigns values to each atom. Only used if sasa_type = TRANSFER, and if no DELTAGFILE is provided. In this case, the free energy values are those describing the effect of temperature, and the program must know if approach 2 or 3 (as described in Arsiccio and Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach, JPCB, 2021) needs to be used to compute them.</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 : void SASA_HASEL::computeDeltaG() {</span></a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :     DeltaG[i].clear();</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :   }</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            :   double T;</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :   T = plumed.getAtoms().getKbT()/plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineNoCov">          0 :   if (T != Ti) {</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineNoCov">          0 :       if (approach==2) {</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ALA&quot;)==0) {</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.995/1000*std::pow(T,2)+1.808*T-272.895);</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :         }</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ARG&quot;)==0) {</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.182/1000*std::pow(T,2)+1.894*T-282.032);</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :         }</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASN&quot;)==0) {</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.047/1000*std::pow(T,2)+0.6068*T-87.846);</span></a>
+<a name="624"><span class="lineNum">     624 </span>            :         }</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASP&quot;)==0) {</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-0.1794/1000*std::pow(T,2)+0.1091*T-16.526);</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :         }</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;CYS&quot;)==0) {</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.09/1000*std::pow(T,2)+1.835*T-272.26);</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :         }</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLN&quot;)==0) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.23/1000*std::pow(T,2)+1.335*T-199.707);</span></a>
+<a name="633"><span class="lineNum">     633 </span>            :         }</a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLU&quot;)==0) {</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.511/1000*std::pow(T,2)+0.8904*T-131.168);</span></a>
+<a name="636"><span class="lineNum">     636 </span>            :         }</a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLY&quot;)==0) {</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (0);</span></a>
+<a name="639"><span class="lineNum">     639 </span>            :         }</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;HIS&quot;)==0) {</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.482/1000*std::pow(T,2)+2.084*T-311.694);</span></a>
+<a name="642"><span class="lineNum">     642 </span>            :         }</a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ILE&quot;)==0) {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-6.364/1000*std::pow(T,2)+3.8*T-567.444);</span></a>
+<a name="645"><span class="lineNum">     645 </span>            :         }</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LEU&quot;)==0) {</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.466/1000*std::pow(T,2)+4.417*T-653.394);</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :         }</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LYS&quot;)==0) {</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.091/1000*std::pow(T,2)+1.2458*T-185.549);</span></a>
+<a name="651"><span class="lineNum">     651 </span>            :         }</a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;MET&quot;)==0) {</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.807/1000*std::pow(T,2)+2.272*T-339.007);</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :         }</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PHE&quot;)==0) {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.828/1000*std::pow(T,2)+4.644*T-688.874);</span></a>
+<a name="657"><span class="lineNum">     657 </span>            :         }</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PRO&quot;)==0) {</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.347/1000*std::pow(T,2)+1.411*T-212.059);</span></a>
+<a name="660"><span class="lineNum">     660 </span>            :         }</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;SER&quot;)==0) {</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (1.813/1000*std::pow(T,2)-1.05*T+151.957);</span></a>
+<a name="663"><span class="lineNum">     663 </span>            :         }</a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;THR&quot;)==0) {</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.64/1000*std::pow(T,2)+1.591*T-239.516);</span></a>
+<a name="666"><span class="lineNum">     666 </span>            :         }</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TRP&quot;)==0) {</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-11.66/1000*std::pow(T,2)+6.916*T-1025.293);</span></a>
+<a name="669"><span class="lineNum">     669 </span>            :         }</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TYR&quot;)==0) {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.513/1000*std::pow(T,2)+4.478*T-667.261);</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :         }</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;VAL&quot;)==0) {</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-4.902/1000*std::pow(T,2)+2.921*T-435.309);</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :         }</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :         DeltaG[natoms].push_back (-0.6962/1000*std::pow(T,2)+0.4426*T-70.015);</span></a>
+<a name="677"><span class="lineNum">     677 </span>            :       }</a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :       if (approach==3) {</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ALA&quot;)==0) {</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.995/1000*std::pow(T,2)+1.808*T-272.105);</span></a>
+<a name="681"><span class="lineNum">     681 </span>            :         }</a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ARG&quot;)==0) {</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.182/1000*std::pow(T,2)+1.894*T-284.086);</span></a>
+<a name="684"><span class="lineNum">     684 </span>            :         }</a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASN&quot;)==0) {</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.047/1000*std::pow(T,2)+0.6068*T-90.597);</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :         }</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASP&quot;)==0) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-0.1794/1000*std::pow(T,2)+0.1091*T-19.143);</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :         }</a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;CYS&quot;)==0) {</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.09/1000*std::pow(T,2)+1.835*T-268.527);</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :         }</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLN&quot;)==0) {</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.23/1000*std::pow(T,2)+1.335*T-201.559);</span></a>
+<a name="696"><span class="lineNum">     696 </span>            :         }</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLU&quot;)==0) {</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.511/1000*std::pow(T,2)+0.8904*T-133.543);</span></a>
+<a name="699"><span class="lineNum">     699 </span>            :         }</a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLY&quot;)==0) {</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (0);</span></a>
+<a name="702"><span class="lineNum">     702 </span>            :         }</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;HIS&quot;)==0) {</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.482/1000*std::pow(T,2)+2.084*T-315.398);</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :         }</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ILE&quot;)==0) {</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-6.364/1000*std::pow(T,2)+3.8*T-564.825);</span></a>
+<a name="708"><span class="lineNum">     708 </span>            :         }</a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LEU&quot;)==0) {</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.466/1000*std::pow(T,2)+4.417*T-651.483);</span></a>
+<a name="711"><span class="lineNum">     711 </span>            :         }</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LYS&quot;)==0) {</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.091/1000*std::pow(T,2)+1.2458*T-187.485);</span></a>
+<a name="714"><span class="lineNum">     714 </span>            :         }</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;MET&quot;)==0) {</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.807/1000*std::pow(T,2)+2.272*T-339.242);</span></a>
+<a name="717"><span class="lineNum">     717 </span>            :         }</a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PHE&quot;)==0) {</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.828/1000*std::pow(T,2)+4.644*T-687.134);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :         }</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PRO&quot;)==0) {</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.347/1000*std::pow(T,2)+1.411*T-214.211);</span></a>
+<a name="723"><span class="lineNum">     723 </span>            :         }</a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;SER&quot;)==0) {</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (1.813/1000*std::pow(T,2)-1.05*T+150.289);</span></a>
+<a name="726"><span class="lineNum">     726 </span>            :         }</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;THR&quot;)==0) {</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.64/1000*std::pow(T,2)+1.591*T-240.267);</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :         }</a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TRP&quot;)==0) {</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-11.66/1000*std::pow(T,2)+6.916*T-1024.284);</span></a>
+<a name="732"><span class="lineNum">     732 </span>            :         }</a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TYR&quot;)==0) {</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.513/1000*std::pow(T,2)+4.478*T-666.484);</span></a>
+<a name="735"><span class="lineNum">     735 </span>            :         }</a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;VAL&quot;)==0) {</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-4.902/1000*std::pow(T,2)+2.921*T-433.013);</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :         }</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :         DeltaG[natoms].push_back (-0.6927/1000*std::pow(T,2)+0.4404*T-68.724);</span></a>
+<a name="740"><span class="lineNum">     740 </span>            :       }</a>
+<a name="741"><span class="lineNum">     741 </span>            :     }</a>
+<a name="742"><span class="lineNum">     742 </span>            :   }</a>
+<a name="743"><span class="lineNum">     743 </span>            : </a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :   Ti = T;</span></a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 :   if (firstStepFlag ==0) {</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineNoCov">          0 :     if (approach!=2 &amp;&amp; approach!=3) {</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineNoCov">          0 :       cout &lt;&lt; &quot;Unknown approach &quot; &lt;&lt; approach &lt;&lt; endl;</span></a>
+<a name="749"><span class="lineNum">     749 </span>            :     }</a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineNoCov">          0 :       if (DeltaG[i].size()==0 ) {</span></a>
+<a name="752"><span class="lineNum">     752 </span><span class="lineNoCov">          0 :         cout &lt;&lt; &quot;Delta G value for residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; &quot; not found &quot; &lt;&lt; endl;</span></a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineNoCov">          0 :         error (&quot;missing Delta G parameter\n&quot;);</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :       }</a>
+<a name="755"><span class="lineNum">     755 </span>            :     }</a>
+<a name="756"><span class="lineNum">     756 </span>            :   }</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            : //calculates neighbor list</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">         24 : void SASA_HASEL::calcNlist() {</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">         24 :   if(!nopbc) makeWhole();</span></a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineCov">       2904 :   for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">       2880 :     Nlist[i].clear();</span></a>
+<a name="766"><span class="lineNum">     766 </span>            :   }</a>
+<a name="767"><span class="lineNum">     767 </span>            : </a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">       2904 :   for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">       2880 :     if (SASAparam[i].size()&gt;0) {</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">     103680 :       for (unsigned j = 0; j &lt; i; j++) {</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">     101952 :         if (SASAparam[j].size()&gt;0) {</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">      61344 :           const Vector Delta_ij_vec = delta( getPosition(i), getPosition(j) );</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">      61344 :           double Delta_ij_mod = Delta_ij_vec.modulo()*10;</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">      61344 :           double overlapD = SASAparam[i][0]+SASAparam[j][0];</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">      61344 :           if (Delta_ij_mod &lt; overlapD) {</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">      26748 :             Nlist.at(i).push_back (j);</span></a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">      26748 :             Nlist.at(j).push_back (i);</span></a>
+<a name="778"><span class="lineNum">     778 </span>            :           }</a>
+<a name="779"><span class="lineNum">     779 </span>            :         }</a>
+<a name="780"><span class="lineNum">     780 </span>            :       }</a>
+<a name="781"><span class="lineNum">     781 </span>            :     }</a>
+<a name="782"><span class="lineNum">     782 </span>            :   }</a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">         24 : }</span></a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            : </a>
+<a name="786"><span class="lineNum">     786 </span>            : //calculates SASA according to Hasel et al., Tetrahedron Computer Methodology Vol. 1, No. 2, pp. 103-116, 1988</a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">         24 : void SASA_HASEL::calculate() {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">         24 :   if(!nopbc) makeWhole();</span></a>
+<a name="789"><span class="lineNum">     789 </span>            : </a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">         24 :   if(getExchangeStep()) nl_update = 0;</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineCov">         24 :   if (firstStepFlag ==0) {</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">          2 :     readPDB();</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">          2 :     readSASAparam();</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :   }</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">         24 :   if (nl_update == 0) {</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">         24 :     calcNlist();</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :   }</a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span>            : </a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">         24 :   auto* moldat = plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">         24 :   if( ! moldat ) error(&quot;Unable to find MOLINFO in input&quot;);</span></a>
+<a name="802"><span class="lineNum">     802 </span>            :   double Si, sasai, bij;</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">         24 :   double sasa = 0;</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">         24 :   vector&lt;Vector&gt; derivatives( natoms );</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">       2904 :   for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">       2880 :     derivatives[i][0] = 0.;</span></a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">       2880 :     derivatives[i][1] = 0.;</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">       2880 :     derivatives[i][2] = 0.;</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :   }</a>
+<a name="810"><span class="lineNum">     810 </span>            : </a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">         24 :   Tensor virial;</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">         24 :   vector &lt;double&gt; ddij_di(3);</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         24 :   vector &lt;double&gt; dbij_di(3);</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         24 :   vector &lt;double&gt; dAijt_di(3);</span></a>
+<a name="815"><span class="lineNum">     815 </span>            : </a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">         24 :   if( sasa_type==TOTAL ) {</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">       1452 :     for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">       1440 :       if(SASAparam[i].size() &gt; 0) {</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">        864 :         double ri = SASAparam[i][0];</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">        864 :         Si = 4*M_PI*ri*ri;</span></a>
+<a name="821"><span class="lineNum">     821 </span>            :         sasai = 1.0;</a>
+<a name="822"><span class="lineNum">     822 </span>            : </a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">       1728 :         vector &lt;vector &lt;double&gt; &gt; derTerm( Nlist[i].size(), vector &lt;double&gt;(3));</span></a>
+<a name="824"><span class="lineNum">     824 </span>            : </a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">        864 :         dAijt_di[0] = 0;</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">        864 :         dAijt_di[1] = 0;</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">        864 :         dAijt_di[2] = 0;</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">        864 :         int NumRes_i = moldat-&gt;getResidueNumber(atoms[i]);</span></a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">      27612 :         for (unsigned j = 0; j &lt; Nlist[i].size(); j++) {</span></a>
+<a name="831"><span class="lineNum">     831 </span>            :           double pij = 0.3516;</a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">      26748 :           int NumRes_j = moldat-&gt;getResidueNumber(atoms[Nlist[i][j]]);</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">      26748 :           if (NumRes_i==NumRes_j) {</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">       4320 :             if (CONNECTparam[i][0].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][1].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][2].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][3].compare(AtomResidueName[0][Nlist[i][j]])==0) {</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :               pij = 0.8875;</a>
+<a name="837"><span class="lineNum">     837 </span>            :             }</a>
+<a name="838"><span class="lineNum">     838 </span>            :           }</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">      26748 :           if ( abs(NumRes_i-NumRes_j) == 1 ) {</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">      10380 :             if ((AtomResidueName[0][i] == &quot;N&quot;  &amp;&amp; AtomResidueName[0][Nlist[i][j]]== &quot;CA&quot;) || (AtomResidueName[0][Nlist[i][j]] == &quot;N&quot;  &amp;&amp; AtomResidueName[0][i]== &quot;CA&quot;)) {</span></a>
+<a name="841"><span class="lineNum">     841 </span>            :               pij = 0.8875;</a>
+<a name="842"><span class="lineNum">     842 </span>            :             }</a>
+<a name="843"><span class="lineNum">     843 </span>            :           }</a>
+<a name="844"><span class="lineNum">     844 </span>            : </a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">      26748 :           const Vector d_ij_vec = delta( getPosition(i), getPosition(Nlist[i][j]) );</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">      26748 :           double d_ij = d_ij_vec.modulo()*10;</span></a>
+<a name="847"><span class="lineNum">     847 </span>            : </a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">      26748 :           double rj = SASAparam[Nlist[i][j]][0];</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">      26748 :           bij = M_PI*ri*(ri+rj-d_ij)*(1+(rj-ri)/d_ij); //Angstrom2</span></a>
+<a name="850"><span class="lineNum">     850 </span>            : </a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">      26748 :           sasai = sasai*(1-SASAparam[i][1]*pij*bij/Si); //nondimensional</span></a>
+<a name="852"><span class="lineNum">     852 </span>            : </a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">      26748 :           ddij_di[0] = -10*(getPosition(Nlist[i][j])[0]-getPosition(i)[0])/d_ij; //nondimensional</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">      26748 :           ddij_di[1] = -10*(getPosition(Nlist[i][j])[1]-getPosition(i)[1])/d_ij;</span></a>
+<a name="855"><span class="lineNum">     855 </span><span class="lineCov">      26748 :           ddij_di[2] = -10*(getPosition(Nlist[i][j])[2]-getPosition(i)[2])/d_ij;</span></a>
+<a name="856"><span class="lineNum">     856 </span>            : </a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">      26748 :           dbij_di[0] = -M_PI*ri*ddij_di[0]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij)); //Angstrom</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">      26748 :           dbij_di[1] = -M_PI*ri*ddij_di[1]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">      26748 :           dbij_di[2] = -M_PI*ri*ddij_di[2]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));</span></a>
+<a name="860"><span class="lineNum">     860 </span>            : </a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">      26748 :           dAijt_di[0] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1</span></a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">      26748 :           dAijt_di[1] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">      26748 :           dAijt_di[2] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];</span></a>
+<a name="864"><span class="lineNum">     864 </span>            : </a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">      26748 :           derTerm[j][0] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1</span></a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">      26748 :           derTerm[j][1] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">      26748 :           derTerm[j][2] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];</span></a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span>            :         }</a>
+<a name="870"><span class="lineNum">     870 </span>            : </a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">        864 :         sasa += Si*sasai/100; //nm2</span></a>
+<a name="872"><span class="lineNum">     872 </span>            : </a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">        864 :         derivatives[i][0] += Si*sasai/10*dAijt_di[0]; //nm</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">        864 :         derivatives[i][1] += Si*sasai/10*dAijt_di[1];</span></a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">        864 :         derivatives[i][2] += Si*sasai/10*dAijt_di[2];</span></a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">      27612 :         for (unsigned j = 0; j &lt; Nlist[i].size(); j++) {</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">      26748 :           derivatives[Nlist[i][j]][0] += Si*sasai/10*derTerm[j][0]; //nm</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">      26748 :           derivatives[Nlist[i][j]][1] += Si*sasai/10*derTerm[j][1];</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">      26748 :           derivatives[Nlist[i][j]][2] += Si*sasai/10*derTerm[j][2];</span></a>
+<a name="881"><span class="lineNum">     881 </span>            :         }</a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">        864 :       }</span></a>
+<a name="883"><span class="lineNum">     883 </span>            :     }</a>
+<a name="884"><span class="lineNum">     884 </span>            :   }</a>
+<a name="885"><span class="lineNum">     885 </span>            : </a>
+<a name="886"><span class="lineNum">     886 </span>            : </a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineCov">         24 :   if( sasa_type==TRANSFER ) {</span></a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">         12 :     if (firstStepFlag ==0) {</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">          1 :       readMaxSurf();</span></a>
+<a name="891"><span class="lineNum">     891 </span>            :     }</a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">         12 :     if (firstStepFlag ==0 &amp;&amp; DeltaGValues != &quot;absent&quot;) {</span></a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">          1 :       readDeltaG();</span></a>
+<a name="895"><span class="lineNum">     895 </span>            :     }</a>
+<a name="896"><span class="lineNum">     896 </span>            : </a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">         12 :     if (DeltaGValues == &quot;absent&quot;) {</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineNoCov">          0 :       computeDeltaG();</span></a>
+<a name="899"><span class="lineNum">     899 </span>            :     }</a>
+<a name="900"><span class="lineNum">     900 </span>            : </a>
+<a name="901"><span class="lineNum">     901 </span>            : </a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">       1452 :     for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="903"><span class="lineNum">     903 </span>            : </a>
+<a name="904"><span class="lineNum">     904 </span>            : </a>
+<a name="905"><span class="lineNum">     905 </span>            : </a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">       1440 :       if(SASAparam[i].size() &gt; 0) {</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">        864 :         double ri = SASAparam[i][0];</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">        864 :         Si = 4*M_PI*ri*ri;</span></a>
+<a name="909"><span class="lineNum">     909 </span>            :         sasai = 1.0;</a>
+<a name="910"><span class="lineNum">     910 </span>            : </a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">       1728 :         vector &lt;vector &lt;double&gt; &gt; derTerm( Nlist[i].size(), vector &lt;double&gt;(3));</span></a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">        864 :         dAijt_di[0] = 0;</span></a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">        864 :         dAijt_di[1] = 0;</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">        864 :         dAijt_di[2] = 0;</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">        864 :         int NumRes_i = moldat-&gt;getResidueNumber(atoms[i]);</span></a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">      27612 :         for (unsigned j = 0; j &lt; Nlist[i].size(); j++) {</span></a>
+<a name="919"><span class="lineNum">     919 </span>            :           double pij = 0.3516;</a>
+<a name="920"><span class="lineNum">     920 </span>            : </a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">      26748 :           int NumRes_j = moldat-&gt;getResidueNumber(atoms[Nlist[i][j]]);</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">      26748 :           if (NumRes_i==NumRes_j) {</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">       4320 :             if (CONNECTparam[i][0].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][1].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][2].compare(AtomResidueName[0][Nlist[i][j]])==0 || CONNECTparam[i][3].compare(AtomResidueName[0][Nlist[i][j]])==0) {</span></a>
+<a name="924"><span class="lineNum">     924 </span>            :               pij = 0.8875;</a>
+<a name="925"><span class="lineNum">     925 </span>            :             }</a>
+<a name="926"><span class="lineNum">     926 </span>            :           }</a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">      26748 :           if ( abs(NumRes_i-NumRes_j) == 1 ) {</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">      10380 :             if ((AtomResidueName[0][i] == &quot;N&quot;  &amp;&amp; AtomResidueName[0][Nlist[i][j]]== &quot;CA&quot;) || (AtomResidueName[0][Nlist[i][j]] == &quot;N&quot;  &amp;&amp; AtomResidueName[0][i]== &quot;CA&quot;)) {</span></a>
+<a name="929"><span class="lineNum">     929 </span>            :               pij = 0.8875;</a>
+<a name="930"><span class="lineNum">     930 </span>            :             }</a>
+<a name="931"><span class="lineNum">     931 </span>            :           }</a>
+<a name="932"><span class="lineNum">     932 </span>            : </a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">      26748 :           const Vector d_ij_vec = delta( getPosition(i), getPosition(Nlist[i][j]) );</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">      26748 :           double d_ij = d_ij_vec.modulo()*10;</span></a>
+<a name="935"><span class="lineNum">     935 </span>            : </a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">      26748 :           double rj = SASAparam[Nlist[i][j]][0];</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">      26748 :           bij = M_PI*ri*(ri+rj-d_ij)*(1+(rj-ri)/d_ij); //Angstrom2</span></a>
+<a name="938"><span class="lineNum">     938 </span>            : </a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">      26748 :           sasai = sasai*(1-SASAparam[i][1]*pij*bij/Si); //nondimensional</span></a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">      26748 :           ddij_di[0] = -10*(getPosition(Nlist[i][j])[0]-getPosition(i)[0])/d_ij; //nondimensional</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">      26748 :           ddij_di[1] = -10*(getPosition(Nlist[i][j])[1]-getPosition(i)[1])/d_ij;</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">      26748 :           ddij_di[2] = -10*(getPosition(Nlist[i][j])[2]-getPosition(i)[2])/d_ij;</span></a>
+<a name="944"><span class="lineNum">     944 </span>            : </a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineCov">      26748 :           dbij_di[0] = -M_PI*ri*ddij_di[0]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij)); //Angstrom</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">      26748 :           dbij_di[1] = -M_PI*ri*ddij_di[1]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">      26748 :           dbij_di[2] = -M_PI*ri*ddij_di[2]*(1+(ri+rj)*(rj-ri)/(d_ij*d_ij));</span></a>
+<a name="948"><span class="lineNum">     948 </span>            : </a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineCov">      26748 :           dAijt_di[0] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">      26748 :           dAijt_di[1] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">      26748 :           dAijt_di[2] += -1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];</span></a>
+<a name="952"><span class="lineNum">     952 </span>            : </a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">      26748 :           derTerm[j][0] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[0]; //Angstrom-1</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">      26748 :           derTerm[j][1] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[1];</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">      26748 :           derTerm[j][2] = 1/(Si/(SASAparam[i][1]*pij)-bij)*dbij_di[2];</span></a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            :         }</a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">       2880 :         if (AtomResidueName[0][i] == &quot;N&quot; || AtomResidueName[0][i] == &quot;CA&quot;  || AtomResidueName[0][i] == &quot;C&quot; || AtomResidueName[0][i] == &quot;O&quot; || AtomResidueName[0][i] == &quot;H&quot;) {</span></a>
+<a name="960"><span class="lineNum">     960 </span>            : </a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">        720 :           sasa += Si*sasai/MaxSurf[i][0]*DeltaG[natoms][0]; //kJ/mol</span></a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span>            : </a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">        720 :           derivatives[i][0] += Si*sasai*dAijt_di[0]/MaxSurf[i][0]*DeltaG[natoms][0]*10; //kJ/mol/nm</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">        720 :           derivatives[i][1] += Si*sasai*dAijt_di[1]/MaxSurf[i][0]*DeltaG[natoms][0]*10;</span></a>
+<a name="966"><span class="lineNum">     966 </span><span class="lineCov">        720 :           derivatives[i][2] += Si*sasai*dAijt_di[2]/MaxSurf[i][0]*DeltaG[natoms][0]*10;</span></a>
+<a name="967"><span class="lineNum">     967 </span>            :         }</a>
+<a name="968"><span class="lineNum">     968 </span>            : </a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">       2880 :         if (AtomResidueName[0][i] != &quot;N&quot; &amp;&amp; AtomResidueName[0][i] != &quot;CA&quot;  &amp;&amp; AtomResidueName[0][i] != &quot;C&quot; &amp;&amp; AtomResidueName[0][i] != &quot;O&quot; &amp;&amp; AtomResidueName[0][i] != &quot;H&quot;) {</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">        144 :           sasa += Si*sasai/MaxSurf[i][1]*DeltaG[i][0]; //kJ/mol</span></a>
+<a name="971"><span class="lineNum">     971 </span>            : </a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">        144 :           derivatives[i][0] += Si*sasai*dAijt_di[0]/MaxSurf[i][1]*DeltaG[i][0]*10; //kJ/mol/nm</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">        144 :           derivatives[i][1] += Si*sasai*dAijt_di[1]/MaxSurf[i][1]*DeltaG[i][0]*10;</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">        144 :           derivatives[i][2] += Si*sasai*dAijt_di[2]/MaxSurf[i][1]*DeltaG[i][0]*10;</span></a>
+<a name="975"><span class="lineNum">     975 </span>            :         }</a>
+<a name="976"><span class="lineNum">     976 </span>            : </a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">      27612 :         for (unsigned j = 0; j &lt; Nlist[i].size(); j++) {</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">      86883 :           if (AtomResidueName[0][i] == &quot;N&quot; || AtomResidueName[0][i] == &quot;CA&quot;  || AtomResidueName[0][i] == &quot;C&quot; || AtomResidueName[0][i] == &quot;O&quot; || AtomResidueName[0][i] == &quot;H&quot;) {</span></a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">      22438 :             derivatives[Nlist[i][j]][0] += Si*sasai*10*derTerm[j][0]/MaxSurf[i][0]*DeltaG[natoms][0]; //kJ/mol/nm</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">      22438 :             derivatives[Nlist[i][j]][1] += Si*sasai*10*derTerm[j][1]/MaxSurf[i][0]*DeltaG[natoms][0];</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">      22438 :             derivatives[Nlist[i][j]][2] += Si*sasai*10*derTerm[j][2]/MaxSurf[i][0]*DeltaG[natoms][0];</span></a>
+<a name="983"><span class="lineNum">     983 </span>            :           }</a>
+<a name="984"><span class="lineNum">     984 </span>            : </a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">      86883 :           if (AtomResidueName[0][i] != &quot;N&quot; &amp;&amp; AtomResidueName[0][i] != &quot;CA&quot;  &amp;&amp; AtomResidueName[0][i] != &quot;C&quot; &amp;&amp; AtomResidueName[0][i] != &quot;O&quot; &amp;&amp; AtomResidueName[0][i] != &quot;H&quot;) {</span></a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">       4310 :             derivatives[Nlist[i][j]][0] += Si*sasai*10*derTerm[j][0]/MaxSurf[i][1]*DeltaG[i][0]; //kJ/mol/nm</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">       4310 :             derivatives[Nlist[i][j]][1] += Si*sasai*10*derTerm[j][1]/MaxSurf[i][1]*DeltaG[i][0];</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">       4310 :             derivatives[Nlist[i][j]][2] += Si*sasai*10*derTerm[j][2]/MaxSurf[i][1]*DeltaG[i][0];</span></a>
+<a name="989"><span class="lineNum">     989 </span>            :           }</a>
+<a name="990"><span class="lineNum">     990 </span>            :         }</a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">        864 :       }</span></a>
+<a name="992"><span class="lineNum">     992 </span>            :     }</a>
+<a name="993"><span class="lineNum">     993 </span>            :   }</a>
+<a name="994"><span class="lineNum">     994 </span>            : </a>
+<a name="995"><span class="lineNum">     995 </span>            : </a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">       2904 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">       2880 :     setAtomsDerivatives(i,derivatives[i]);</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">       2880 :     virial -= Tensor(getPosition(i),derivatives[i]);</span></a>
+<a name="999"><span class="lineNum">     999 </span>            :   }</a>
+<a name="1000"><span class="lineNum">    1000 </span>            : </a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">         24 :   setBoxDerivatives(virial);</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">         24 :   setValue(sasa);</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">         24 :   firstStepFlag = 1;</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">         24 :   ++nl_update;</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">         24 :   if (nl_update == stride) {</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">         24 :     nl_update = 0;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span>            :   }</a>
+<a name="1008"><span class="lineNum">    1008 </span>            : // setBoxDerivativesNoPbc();</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">         24 : }</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            : </a>
+<a name="1011"><span class="lineNum">    1011 </span>            : }//namespace sasa</a>
+<a name="1012"><span class="lineNum">    1012 </span>            : }//namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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index 0000000000..7a68648b76
--- /dev/null
+++ b/coverage/sasa/sasa_LCPO.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa/sasa_LCPO.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">sasa</a> - sasa_LCPO.cpp<span style="font-size: 80%;"> (<a href="sasa_LCPO.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">519</td>
+            <td class="headerCovTableEntry">631</td>
+            <td class="headerCovTableEntryMed">82.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="sasa_LCPO.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#233">_ZN4PLMD4sasa5splitISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEEEvRKS8_RT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#568">_ZN4PLMD4sasa9SASA_LCPO13computeDeltaGEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#173">_ZN4PLMD4sasa9SASA_LCPOC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#527">_ZN4PLMD4sasa9SASA_LCPO10readDeltaGEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#512">_ZN4PLMD4sasa9SASA_LCPO11readMaxSurfEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#482">_ZN4PLMD4sasa9SASA_LCPO15setupMaxSurfMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#161">_ZN4PLMD4sasa12_GLOBAL__N_122SASA_LCPORegisterMe1636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#433">_ZN4PLMD4sasa9SASA_LCPO13readLCPOparamEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#260">_ZN4PLMD4sasa9SASA_LCPO14setupLCPOparamB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#244">_ZN4PLMD4sasa9SASA_LCPO7readPDBEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#173">_ZN4PLMD4sasa9SASA_LCPOC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#163">_ZN4PLMD4sasa9SASA_LCPO16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#725">_ZN4PLMD4sasa9SASA_LCPO9calcNlistEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#751">_ZN4PLMD4sasa9SASA_LCPO9calculateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#161">_ZN4PLMD4sasa12_GLOBAL__N_122SASA_LCPORegisterMe163C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#161">_ZN4PLMD4sasa12_GLOBAL__N_122SASA_LCPORegisterMe163D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/sasa_LCPO.cpp.func.html b/coverage/sasa/sasa_LCPO.cpp.func.html
new file mode 100644
index 0000000000..81f26e3cc3
--- /dev/null
+++ b/coverage/sasa/sasa_LCPO.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa/sasa_LCPO.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">sasa</a> - sasa_LCPO.cpp<span style="font-size: 80%;"> (<a href="sasa_LCPO.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">519</td>
+            <td class="headerCovTableEntry">631</td>
+            <td class="headerCovTableEntryMed">82.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="sasa_LCPO.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#161">_ZN4PLMD4sasa12_GLOBAL__N_122SASA_LCPORegisterMe1636createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#161">_ZN4PLMD4sasa12_GLOBAL__N_122SASA_LCPORegisterMe163C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#161">_ZN4PLMD4sasa12_GLOBAL__N_122SASA_LCPORegisterMe163D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#233">_ZN4PLMD4sasa5splitISt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EEEEvRKS8_RT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#527">_ZN4PLMD4sasa9SASA_LCPO10readDeltaGEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#512">_ZN4PLMD4sasa9SASA_LCPO11readMaxSurfEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#568">_ZN4PLMD4sasa9SASA_LCPO13computeDeltaGEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#433">_ZN4PLMD4sasa9SASA_LCPO13readLCPOparamEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#260">_ZN4PLMD4sasa9SASA_LCPO14setupLCPOparamB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#482">_ZN4PLMD4sasa9SASA_LCPO15setupMaxSurfMapB5cxx11Ev</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#163">_ZN4PLMD4sasa9SASA_LCPO16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#244">_ZN4PLMD4sasa9SASA_LCPO7readPDBEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#725">_ZN4PLMD4sasa9SASA_LCPO9calcNlistEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#751">_ZN4PLMD4sasa9SASA_LCPO9calculateEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#173">_ZN4PLMD4sasa9SASA_LCPOC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="sasa_LCPO.cpp.gcov.html#173">_ZN4PLMD4sasa9SASA_LCPOC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/sasa/sasa_LCPO.cpp.gcov.html b/coverage/sasa/sasa_LCPO.cpp.gcov.html
new file mode 100644
index 0000000000..7e662a5cf2
--- /dev/null
+++ b/coverage/sasa/sasa_LCPO.cpp.gcov.html
@@ -0,0 +1,1156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - sasa/sasa_LCPO.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">sasa</a> - sasa_LCPO.cpp<span style="font-size: 80%;"> (source / <a href="sasa_LCPO.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">519</td>
+            <td class="headerCovTableEntry">631</td>
+            <td class="headerCovTableEntryMed">82.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">81.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            : Copyright (c) 2021, Andrea Arsiccio</a>
+<a name="3"><span class="lineNum">       3 </span>            : </a>
+<a name="4"><span class="lineNum">       4 </span>            : This software is provided 'as-is', without any express or implied</a>
+<a name="5"><span class="lineNum">       5 </span>            : warranty. In no event will the authors be held liable for any damages</a>
+<a name="6"><span class="lineNum">       6 </span>            : arising from the use of this software.</a>
+<a name="7"><span class="lineNum">       7 </span>            : </a>
+<a name="8"><span class="lineNum">       8 </span>            : Permission is granted to anyone to use this software for any purpose,</a>
+<a name="9"><span class="lineNum">       9 </span>            : including commercial applications, and to alter it and redistribute it</a>
+<a name="10"><span class="lineNum">      10 </span>            : freely, subject to the following restrictions:</a>
+<a name="11"><span class="lineNum">      11 </span>            : </a>
+<a name="12"><span class="lineNum">      12 </span>            : 1. The origin of this software must not be misrepresented; you must not</a>
+<a name="13"><span class="lineNum">      13 </span>            :    claim that you wrote the original software. If you use this software</a>
+<a name="14"><span class="lineNum">      14 </span>            :    in a product, an acknowledgment in the product documentation would be</a>
+<a name="15"><span class="lineNum">      15 </span>            :    appreciated but is not required.</a>
+<a name="16"><span class="lineNum">      16 </span>            : 2. Altered source versions must be plainly marked as such, and must not be</a>
+<a name="17"><span class="lineNum">      17 </span>            :    misrepresented as being the original software.</a>
+<a name="18"><span class="lineNum">      18 </span>            : 3. This notice may not be removed or altered from any source distribution.</a>
+<a name="19"><span class="lineNum">      19 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="20"><span class="lineNum">      20 </span>            : </a>
+<a name="21"><span class="lineNum">      21 </span>            : #include &quot;Sasa.h&quot;</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdio&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;sstream&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;algorithm&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;iterator&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;fstream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : using namespace std;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace sasa {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC SASAMOD_COLVAR SASA_LCPO</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Calculates the solvent accessible surface area (SASA) of a protein molecule, or other properties related to it.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The atoms for which the SASA is desired should be indicated with the keyword ATOMS, and a pdb file of the protein must be provided in input with the MOLINFO keyword. The LCPO algorithm is used for the calculation (please, read and cite \cite Weiser1999). The radius of the solvent is assumed to be 0.14 nm, which is the radius of water molecules. Using the keyword NL_STRIDE it is also possible to specify the frequency with which the neighbor list for the calculation of the SASA is updated (the default is every 10 steps).</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Different properties can be calculated and selected using the TYPE keyword:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : 1) the total SASA (TOTAL);</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : 2) the free energy of transfer for the protein according to the transfer model (TRANSFER). This keyword can be used, for instance, to compute the transfer of a protein to different temperatures, as detailed in \cite Arsiccio-T-SASA-2021, or to different pressures, as detailed in \cite Arsiccio-P-SASA-2021, or to different osmolyte solutions, as detailed in \cite Arsiccio-C-SASA-2022.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : When the TRANSFER keyword is used, a file with the free energy of transfer values for the sidechains and backbone atoms should be provided (using the keyword DELTAGFILE). Such file should have the following format:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \verbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : ----------------Sample DeltaG.dat file---------------------</a>
+<a name="58"><span class="lineNum">      58 </span>            : ALA     0.711019999999962</a>
+<a name="59"><span class="lineNum">      59 </span>            : ARG     -2.24832799999996</a>
+<a name="60"><span class="lineNum">      60 </span>            : ASN     -2.74838799999999</a>
+<a name="61"><span class="lineNum">      61 </span>            : ASP     -2.5626376</a>
+<a name="62"><span class="lineNum">      62 </span>            : CYS     3.89864000000006</a>
+<a name="63"><span class="lineNum">      63 </span>            : GLN     -1.76192</a>
+<a name="64"><span class="lineNum">      64 </span>            : GLU     -2.38664400000002</a>
+<a name="65"><span class="lineNum">      65 </span>            : GLY     0</a>
+<a name="66"><span class="lineNum">      66 </span>            : HIS     -3.58152799999999</a>
+<a name="67"><span class="lineNum">      67 </span>            : ILE     2.42634399999986</a>
+<a name="68"><span class="lineNum">      68 </span>            : LEU     1.77233599999988</a>
+<a name="69"><span class="lineNum">      69 </span>            : LYS     -1.92576400000002</a>
+<a name="70"><span class="lineNum">      70 </span>            : MET     -0.262827999999956</a>
+<a name="71"><span class="lineNum">      71 </span>            : PHE     1.62028800000007</a>
+<a name="72"><span class="lineNum">      72 </span>            : PRO     -2.15598800000001</a>
+<a name="73"><span class="lineNum">      73 </span>            : SER     -1.60934800000004</a>
+<a name="74"><span class="lineNum">      74 </span>            : THR     -0.591559999999987</a>
+<a name="75"><span class="lineNum">      75 </span>            : TRP     1.22936000000027</a>
+<a name="76"><span class="lineNum">      76 </span>            : TYR     0.775547999999958</a>
+<a name="77"><span class="lineNum">      77 </span>            : VAL     2.12779200000011</a>
+<a name="78"><span class="lineNum">      78 </span>            : BACKBONE        1.00066920000002</a>
+<a name="79"><span class="lineNum">      79 </span>            : -----------------------------------------------------------</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endverbatim</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : where the second column is the free energy of transfer for each sidechain/backbone, in kJ/mol.</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure (according to \cite Arsiccio-C-SASA-2022, \cite Arsiccio-T-SASA-2021 and \cite Arsiccio-P-SASA-2021) is freely available at https://github.com/andrea-arsiccio/DeltaG-calculation. The script automatically outputs a DeltaG.dat file compatible with this SASA module.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : If the DELTAGFILE is not provided, the program computes the free energy of transfer values as if they had to take into account the effect of temperature according to approaches 2 or 3 in the paper \cite Arsiccio-T-SASA-2021. Please read and cite this paper if using the transfer model for computing the effect of temperature in implicit solvent simulations. For this purpose, the keyword APPROACH should be added, and set to either 2 or 3.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : The SASA usually makes sense when atoms used for the calculation are all part of the same molecule. When running with periodic boundary conditions, the atoms should be in the proper periodic image. This is done automatically since PLUMED 2.2, by considering the ordered list of atoms and rebuilding the broken entities using a procedure that is equivalent to that done in \ref WHOLEMOLECULES. Notice that rebuilding is local to this action. This is different from \ref WHOLEMOLECULES which actually modifies the coordinates stored in PLUMED.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="91"><span class="lineNum">      91 </span>            : In that case you need to take care that atoms are in the correct periodic image.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : The SASA may also be computed using the SASA_HASEL collective variable, which makes use of the algorithm described in \cite Hasel1988. SASA_HASEL is less accurate then SASA_LCPO, but the computation is faster.</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : \par Examples</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : The following input tells plumed to print the total SASA for atoms 10 to 20 in a protein chain.</a>
+<a name="100"><span class="lineNum">     100 </span>            : \plumedfile</a>
+<a name="101"><span class="lineNum">     101 </span>            : SASA_LCPO TYPE=TOTAL ATOMS=10-20 NL_STRIDE=10 LABEL=sasa</a>
+<a name="102"><span class="lineNum">     102 </span>            : PRINT ARG=sasa STRIDE=1 FILE=colvar</a>
+<a name="103"><span class="lineNum">     103 </span>            : \endplumedfile</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are read from a file called DeltaG.dat.</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : \plumedfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : SASA_LCPO TYPE=TRANSFER ATOMS=10-20 NL_STRIDE=10 DELTAGFILE=DeltaG.dat LABEL=sasa</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : bias: BIASVALUE ARG=sasa</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : PRINT ARG=sasa,bias.* STRIDE=1 FILE=colvar</a>
+<a name="114"><span class="lineNum">     114 </span>            : \endplumedfile</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : The following input tells plumed to compute the transfer free energy for the protein chain containing atoms 10 to 20. Such transfer free energy is then used as a bias in the simulation (e.g., implicit solvent simulations). The free energy of transfer values are computed according to \cite Arsiccio-T-SASA-2021, and take into account the effect of temperature using approach 2 as described in the paper.</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : \plumedfile</a>
+<a name="119"><span class="lineNum">     119 </span>            : SASA_LCPO TYPE=TRANSFER ATOMS=10-20 NL_STRIDE=10 APPROACH=2 LABEL=sasa</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : bias: BIASVALUE ARG=sasa</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : PRINT ARG=sasa,bias.* STRIDE=1 FILE=colvar</a>
+<a name="124"><span class="lineNum">     124 </span>            : \endplumedfile</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : */</a>
+<a name="127"><span class="lineNum">     127 </span>            : //+ENDPLUMEDOC</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : class SASA_LCPO : public Colvar {</a>
+<a name="130"><span class="lineNum">     130 </span>            : private:</a>
+<a name="131"><span class="lineNum">     131 </span>            :   enum CV_TYPE {TOTAL, TRANSFER};</a>
+<a name="132"><span class="lineNum">     132 </span>            :   int sasa_type;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   bool nopbc;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   double rs;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   string DeltaGValues;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   int approach;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   unsigned stride;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   unsigned nl_update;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   int firstStepFlag;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   double Ti;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   // cppcheck-suppress duplInheritedMember</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   vector &lt; vector &lt; std::string &gt; &gt; AtomResidueName;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   vector &lt; vector &lt; double &gt; &gt; LCPOparam;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   unsigned natoms;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   vector &lt; vector &lt; double &gt; &gt; MaxSurf;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   vector &lt; vector &lt; double &gt; &gt; DeltaG;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   vector &lt; vector &lt; int &gt; &gt; Nlist;</a>
+<a name="149"><span class="lineNum">     149 </span>            : public:</a>
+<a name="150"><span class="lineNum">     150 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="151"><span class="lineNum">     151 </span>            :   explicit SASA_LCPO(const ActionOptions&amp;);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void readPDB();</a>
+<a name="153"><span class="lineNum">     153 </span>            :   map&lt;string, vector&lt;double&gt; &gt; setupLCPOparam();</a>
+<a name="154"><span class="lineNum">     154 </span>            :   void readLCPOparam();</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void calcNlist();</a>
+<a name="156"><span class="lineNum">     156 </span>            :   map&lt;string, vector&lt;double&gt; &gt; setupMaxSurfMap();</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void readMaxSurf();</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void readDeltaG();</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void computeDeltaG();</a>
+<a name="160"><span class="lineNum">     160 </span>            :   virtual void calculate();</a>
+<a name="161"><span class="lineNum">     161 </span>            : };</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(SASA_LCPO,&quot;SASA_LCPO&quot;)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          4 : void SASA_LCPO::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          4 :   Colvar::registerKeywords(keys);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          8 :   keys.add(&quot;atoms&quot;,&quot;ATOMS&quot;,&quot;the group of atoms that you are calculating the SASA for&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;TOTAL&quot;,&quot;The type of calculation you want to perform. Can be TOTAL or TRANSFER&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;, &quot;NL_STRIDE&quot;, &quot;The frequency with which the neighbor list is updated.&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;DELTAGFILE&quot;,&quot;a file containing the free energy values for backbone and sidechains. Necessary only if TYPE = TRANSFER. A Python script for the computation of free energy of transfer values to describe the effect of osmolyte concentration, temperature and pressure is freely available at https://github.com/andrea-arsiccio/DeltaG-calculation. The script automatically outputs a DeltaG.dat file compatible with this SASA module. If TYPE = TRANSFER and no DELTAGFILE is provided, the free energy values are those describing the effect of temperature, and are computed using the temperature value passed by the MD engine&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;APPROACH&quot;,&quot;either approach 2 or 3. Necessary only if TYPE = TRANSFER and no DELTAGFILE is provided. If TYPE = TRANSFER and no DELTAGFILE is provided, the free energy values are those describing the effect of temperature, and the program must know if approach 2 or 3 (as described in Arsiccio and Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach, J. Phys. Chem. B, 2021) needs to be used to compute them&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          2 : SASA_LCPO::SASA_LCPO(const ActionOptions&amp;ao):</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   PLUMED_COLVAR_INIT(ao),</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   nopbc(false),</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          4 :   DeltaGValues(&quot;absent&quot;),</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          2 :   Ti(0),</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :   stride(10),</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :   nl_update(0),</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :   firstStepFlag(0)</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : {</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :   rs = 0.14;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          2 :   parse(&quot;DELTAGFILE&quot;,DeltaGValues);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          2 :   parse(&quot;APPROACH&quot;, approach);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :   if(atoms.size()==0) error(&quot;no atoms specified&quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::string Type;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          2 :   parse(&quot;TYPE&quot;,Type);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          2 :   parse(&quot;NL_STRIDE&quot;, stride);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          2 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 :   if(Type==&quot;TOTAL&quot;) sasa_type=TOTAL;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          1 :   else if(Type==&quot;TRANSFER&quot;) sasa_type=TRANSFER;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   else error(&quot;Unknown SASA type&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :   switch(sasa_type)</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   {</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          1 :   case TOTAL:   log.printf(&quot;  TOTAL SASA;&quot;); break;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          1 :   case TRANSFER: log.printf(&quot;  TRANSFER MODEL;&quot;); break;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          2 :   log.printf(&quot;  atoms involved : &quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        240 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        240 :     log.printf(&quot;%d &quot;,atoms[i].serial());</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          2 :   if(nopbc) {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :     log&lt;&lt;&quot;  PBC will be ignored\n&quot;;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   } else {</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          2 :     log&lt;&lt;&quot;  broken molecules will be rebuilt assuming atoms are in the proper order\n&quot;;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          2 :   addValueWithDerivatives(); setNotPeriodic();</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">          2 :   requestAtoms(atoms);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 :   natoms = getNumberOfAtoms();</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          2 :   AtomResidueName.resize(2);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          2 :   LCPOparam.resize(natoms);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          2 :   MaxSurf.resize(natoms);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          2 :   DeltaG.resize(natoms+1);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          2 :   Nlist.resize(natoms);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          2 : }</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : //splits strings into tokens. Used to read into LCPO parameters file and into reference pdb file</a>
+<a name="234"><span class="lineNum">     234 </span>            : template &lt;class Container&gt;</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 : void split(const std::string&amp; str, Container&amp; cont)</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :   std::istringstream iss(str);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :   std::copy(std::istream_iterator&lt;std::string&gt;(iss),</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :             std::istream_iterator&lt;std::string&gt;(),</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :             std::back_inserter(cont));</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : //reads input PDB file provided with MOLINFO, and assigns atom and residue names to each atom involved in the CV</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          2 : void SASA_LCPO::readPDB() {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          2 :   auto* moldat = plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          2 :   if( ! moldat ) error(&quot;Unable to find MOLINFO in input&quot;);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :   AtomResidueName[0].clear();</a>
+<a name="250"><span class="lineNum">     250 </span>            :   AtomResidueName[1].clear();</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        240 :     string Aname = moldat-&gt;getAtomName(atoms[i]);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        240 :     string Rname = moldat-&gt;getResidueName(atoms[i]);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        240 :     AtomResidueName[0].push_back (Aname);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        240 :     AtomResidueName[1].push_back (Rname);</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   }</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          2 : }</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : //LCPO parameters database</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          2 : map&lt;string, vector&lt;double&gt; &gt; SASA_LCPO::setupLCPOparam() {</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   map&lt;string, vector&lt;double&gt; &gt; lcpomap;</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          2 :   lcpomap[&quot;ALA_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          2 :   lcpomap[&quot;ALA_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          2 :   lcpomap[&quot;ALA_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          2 :   lcpomap[&quot;ALA_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          2 :   lcpomap[&quot;ALA_CB&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_OD1&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          2 :   lcpomap[&quot;ASP_OD2&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_OD1&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          2 :   lcpomap[&quot;ASN_ND2&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_CD&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_NE&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_NH1&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_NH2&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          2 :   lcpomap[&quot;ARG_CZ&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          2 :   lcpomap[&quot;CYS_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          2 :   lcpomap[&quot;CYS_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          2 :   lcpomap[&quot;CYS_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          2 :   lcpomap[&quot;CYS_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          2 :   lcpomap[&quot;CYS_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          2 :   lcpomap[&quot;CYS_SG&quot;] = { 1.9,  0.54581,  -0.19477,  -0.0012873,  0.00029247};</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_CD&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_OE1&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          2 :   lcpomap[&quot;GLU_OE2&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_CD&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_OE1&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          2 :   lcpomap[&quot;GLN_NE2&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          2 :   lcpomap[&quot;GLY_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          2 :   lcpomap[&quot;GLY_CA&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          2 :   lcpomap[&quot;GLY_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          2 :   lcpomap[&quot;GLY_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_ND1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_NE2&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          2 :   lcpomap[&quot;HIS_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_CB&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_CG2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_CG1&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          2 :   lcpomap[&quot;ILE_CD1&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_CG&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_CD1&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          2 :   lcpomap[&quot;LEU_CD2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_CD&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_CE&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          2 :   lcpomap[&quot;LYS_NZ&quot;] = { 1.65,  0.73511,  -0.22116,  -0.00089148,  0.0002523};</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_SD&quot;] = { 1.9,  0.54581,  -0.19477,  -0.0012873,  0.00029247};</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          2 :   lcpomap[&quot;MET_CE&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CD1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CZ&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CE2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          2 :   lcpomap[&quot;PHE_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_CG&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          2 :   lcpomap[&quot;PRO_CD&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">          2 :   lcpomap[&quot;SER_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">          2 :   lcpomap[&quot;SER_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">          2 :   lcpomap[&quot;SER_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">          2 :   lcpomap[&quot;SER_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">          2 :   lcpomap[&quot;SER_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">          2 :   lcpomap[&quot;SER_OG&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_CB&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_CG2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">          2 :   lcpomap[&quot;THR_OG1&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_N&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CD1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_NE1&quot;] = { 1.65,  0.41102,  -0.12254,  -7.5448e-05,  0.00011804};</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CE2&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CZ2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CH2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CZ3&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CE3&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">          2 :   lcpomap[&quot;TRP_CD2&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_N&quot;] = { 1.65,  0.062577,  -0.017874,  -8.312e-05,  1.9849e-05};</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CB&quot;] = { 1.7,  0.56482,  -0.19608,  -0.0010219,  0.0002658};</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CG&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CD1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CE1&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CZ&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_OH&quot;] = { 1.6,  0.77914,  -0.25262,  -0.0016056,  0.00035071};</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CE2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">          2 :   lcpomap[&quot;TYR_CD2&quot;] = { 1.7,  0.51245,  -0.15966,  -0.00019781,  0.00016392};</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_N&quot;] = { 1.65,  0.062577,  -0.017874,  -8.312e-05,  1.9849e-05};</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_CA&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_C&quot;] = { 1.7,  0.070344,  -0.019015,  -2.2009e-05,  1.6875e-05};</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_O&quot;] = { 1.6,  0.68563,  -0.1868,  -0.00135573,  0.00023743};</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_CB&quot;] = { 1.7,  0.23348,  -0.072627,  -0.00020079,  7.967e-05};</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_CG1&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          2 :   lcpomap[&quot;VAL_CG2&quot;] = { 1.7,  0.77887,  -0.28063,  -0.0012968,  0.00039328};</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">          2 :   return lcpomap;</span></a>
+<a name="432"><span class="lineNum">     432 </span>            : }</a>
+<a name="433"><span class="lineNum">     433 </span>            : </a>
+<a name="434"><span class="lineNum">     434 </span>            : //assigns LCPO parameters to each atom reading from database</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          2 : void SASA_LCPO::readLCPOparam() {</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">        240 :     LCPOparam[i].clear();</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :   }</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            :   map&lt;string, vector&lt;double&gt; &gt; lcpomap;</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          4 :   lcpomap = setupLCPOparam();</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :   vector&lt;double&gt; LCPOparamVector;</a>
+<a name="444"><span class="lineNum">     444 </span>            :   string identifier;</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        240 :     if ((AtomResidueName[0][i][0]=='O') || (AtomResidueName[0][i][0]=='N') || (AtomResidueName[0][i][0]=='C') || (AtomResidueName[0][i][0]=='S')) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        240 :       identifier = AtomResidueName[1][i]+&quot;_&quot;+AtomResidueName[0][i];</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        120 :       LCPOparamVector = lcpomap.at(identifier);</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">        120 :       LCPOparam[i].push_back (LCPOparamVector[0]+rs*10);</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">        120 :       LCPOparam[i].push_back (LCPOparamVector[1]);</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        120 :       LCPOparam[i].push_back (LCPOparamVector[2]);</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">        120 :       LCPOparam[i].push_back (LCPOparamVector[3]);</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">        120 :       LCPOparam[i].push_back (LCPOparamVector[4]);</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :     }</a>
+<a name="455"><span class="lineNum">     455 </span>            :   }</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">        242 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        240 :     if (LCPOparam[i].size()==0 ) {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">        120 :       if ((AtomResidueName[0][i][0]=='O') || (AtomResidueName[0][i][0]=='N') || (AtomResidueName[0][i][0]=='C') || (AtomResidueName[0][i][0]=='S')) {</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :         cout &lt;&lt; &quot;Could not find LCPO paramaters for atom &quot; &lt;&lt; AtomResidueName[0][i] &lt;&lt; &quot; of residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; endl;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :         error (&quot;missing LCPO parameters\n&quot;);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :       }</a>
+<a name="464"><span class="lineNum">     464 </span>            :     }</a>
+<a name="465"><span class="lineNum">     465 </span>            :   }</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          2 :   if (AtomResidueName[0][0] == &quot;N&quot;) {</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          2 :     LCPOparam[0][1] = 7.3511e-01;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          2 :     LCPOparam[0][2] = -2.2116e-01;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">          2 :     LCPOparam[0][3] = -8.9148e-04;</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          2 :     LCPOparam[0][4] = 2.5230e-04;</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :   }</a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          2 :   if (AtomResidueName[0][natoms-1] == &quot;O&quot;) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">          2 :     LCPOparam[natoms-1][1] = 8.8857e-01;</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          2 :     LCPOparam[natoms-1][2] = -3.3421e-01;</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          2 :     LCPOparam[natoms-1][3] = -1.8683e-03;</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          2 :     LCPOparam[natoms-1][4] = 4.9372e-04;</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :   }</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          2 : }</span></a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            : //Max Surf values, used only if TYPE=TRANSFER</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          1 : map&lt;string, vector&lt;double&gt; &gt; SASA_LCPO::setupMaxSurfMap() {</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :   // Max Surface Area for backbone and sidechain, in nm2</a>
+<a name="486"><span class="lineNum">     486 </span>            :   map&lt;string, vector&lt;double&gt; &gt; valuemap;</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          1 :   valuemap [&quot;ALA&quot;]= {0.671446,0.420263,};</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          1 :   valuemap [&quot;ARG&quot;]= {0.578582,1.95454,};</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">          1 :   valuemap [&quot;ASN&quot;]= {0.559411,1.07102,};</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          1 :   valuemap [&quot;ASP&quot;]= {0.558363,1.03971,};</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          1 :   valuemap [&quot;CYS&quot;]= {0.609271,0.657612,};</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          1 :   valuemap [&quot;GLN&quot;]= {0.565651,1.433031,};</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          1 :   valuemap [&quot;GLU&quot;]= {0.572399,1.41848,};</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          1 :   valuemap [&quot;GLY&quot;]= {0.861439,0,};</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          1 :   valuemap [&quot;HIS&quot;]= {0.559929,1.143827,};</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          1 :   valuemap [&quot;ILE&quot;]= {0.553491,1.25334,};</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          1 :   valuemap [&quot;LEU&quot;]= {0.570103,1.260459,};</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          1 :   valuemap [&quot;LYS&quot;]= {0.580304,1.687487,};</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          1 :   valuemap [&quot;MET&quot;]= {0.5856,1.498954,};</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          1 :   valuemap [&quot;PHE&quot;]= {0.54155,1.394861,};</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          1 :   valuemap [&quot;PRO&quot;]= {0.456048,0.849461,};</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          1 :   valuemap [&quot;SER&quot;]= {0.59074,0.714538,};</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          1 :   valuemap [&quot;THR&quot;]= {0.559116,0.951644,};</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          1 :   valuemap [&quot;TRP&quot;]= {0.55536,1.59324,};</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          1 :   valuemap [&quot;TYR&quot;]= {0.451171,1.566918,};</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          1 :   valuemap [&quot;VAL&quot;]= {0.454809,0.928685,};</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          1 :   return valuemap;</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            : //reads maximum surface values per residue type and assigns values to each atom, only used if sasa_type = TRANSFER</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          1 : void SASA_LCPO::readMaxSurf() {</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :   map&lt;string, vector&lt;double&gt; &gt; valuemap;</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">          2 :   valuemap = setupMaxSurfMap();</span></a>
+<a name="517"><span class="lineNum">     517 </span>            :   vector&lt;double&gt; MaxSurfVector;</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">        121 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">        120 :     MaxSurf[i].clear();</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">        120 :     MaxSurfVector = valuemap.at(AtomResidueName[1][i]);</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        120 :     MaxSurf[i].push_back (MaxSurfVector[0]*100);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">        120 :     MaxSurf[i].push_back (MaxSurfVector[1]*100);</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :   }</a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          1 : }</span></a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            : //reads file with free energy values for sidechains and for the backbone, and assigns values to each atom. Only used if sasa_type = TRANSFER</a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">          1 : void SASA_LCPO::readDeltaG() {</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">        121 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        120 :     DeltaG[i].clear();</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   }</a>
+<a name="534"><span class="lineNum">     534 </span>            : </a>
+<a name="535"><span class="lineNum">     535 </span>            :   string DeltaGline;</a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          1 :   fstream DeltaGFile;</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">          1 :   DeltaGFile.open(DeltaGValues);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          1 :   if (DeltaGFile) {</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :     int backboneflag = 0;</a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         23 :     while(getline(DeltaGFile, DeltaGline)) {</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">         22 :       if(!DeltaGline.empty()) {</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :         std::vector&lt;std::string&gt; DeltaGtoken;</a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         21 :         split(DeltaGline, DeltaGtoken);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">       2541 :         for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">       2520 :           if (DeltaGtoken[0].compare(AtomResidueName[1][i])==0 ) {</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">        120 :             DeltaG[i].push_back (std::atof(DeltaGtoken[1].c_str()));</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :           }</a>
+<a name="548"><span class="lineNum">     548 </span>            :         }</a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         21 :         if (DeltaGtoken[0].compare(&quot;BACKBONE&quot;)==0 ) {</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :           backboneflag = 1;</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          1 :           DeltaG[natoms].push_back (std::atof(DeltaGtoken[1].c_str()));</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :         }</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         21 :       }</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :     }</a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">          1 :     if ( backboneflag == 0) error(&quot;Cannot find backbone value in Delta G parameters file\n&quot;);</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :   }</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineNoCov">          0 :   else error(&quot;Cannot open DeltaG file&quot;);</span></a>
+<a name="558"><span class="lineNum">     558 </span>            : </a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">        121 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">        120 :     if (DeltaG[i].size()==0 ) {</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineNoCov">          0 :       cout &lt;&lt; &quot;Delta G value for residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; &quot; not found &quot; &lt;&lt; endl;</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 :       error (&quot;missing Delta G parameter\n&quot;);</span></a>
+<a name="563"><span class="lineNum">     563 </span>            :     }</a>
+<a name="564"><span class="lineNum">     564 </span>            :   }</a>
+<a name="565"><span class="lineNum">     565 </span>            : </a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">          2 : }</span></a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span>            : //computes free energy values for the sidechains and for the backbone, and assigns values to each atom. Only used if sasa_type = TRANSFER, and if no DELTAGFILE is provided. In this case, the free energy values are those describing the effect of temperature, and the program must know if approach 2 or 3 (as described in Arsiccio and Shea, Protein Cold Denaturation in Implicit Solvent Simulations: A Transfer Free Energy Approach, JPCB, 2021) needs to be used to compute them.</a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 : void SASA_LCPO::computeDeltaG() {</span></a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :     DeltaG[i].clear();</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :   }</a>
+<a name="575"><span class="lineNum">     575 </span>            : </a>
+<a name="576"><span class="lineNum">     576 </span>            :   double T;</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :   T = plumed.getAtoms().getKbT()/plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineNoCov">          0 :   if (T != Ti) {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 :       if (approach==2) {</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ALA&quot;)==0) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.995/1000*std::pow(T,2)+1.808*T-272.895);</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :         }</a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ARG&quot;)==0) {</span></a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.182/1000*std::pow(T,2)+1.894*T-282.032);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :         }</a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASN&quot;)==0) {</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.047/1000*std::pow(T,2)+0.6068*T-87.846);</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :         }</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASP&quot;)==0) {</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-0.1794/1000*std::pow(T,2)+0.1091*T-16.526);</span></a>
+<a name="593"><span class="lineNum">     593 </span>            :         }</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;CYS&quot;)==0) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.09/1000*std::pow(T,2)+1.835*T-272.26);</span></a>
+<a name="596"><span class="lineNum">     596 </span>            :         }</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLN&quot;)==0) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.23/1000*std::pow(T,2)+1.335*T-199.707);</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :         }</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLU&quot;)==0) {</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.511/1000*std::pow(T,2)+0.8904*T-131.168);</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :         }</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLY&quot;)==0) {</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (0);</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :         }</a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;HIS&quot;)==0) {</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.482/1000*std::pow(T,2)+2.084*T-311.694);</span></a>
+<a name="608"><span class="lineNum">     608 </span>            :         }</a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ILE&quot;)==0) {</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-6.364/1000*std::pow(T,2)+3.8*T-567.444);</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :         }</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LEU&quot;)==0) {</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.466/1000*std::pow(T,2)+4.417*T-653.394);</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :         }</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LYS&quot;)==0) {</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.091/1000*std::pow(T,2)+1.2458*T-185.549);</span></a>
+<a name="617"><span class="lineNum">     617 </span>            :         }</a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;MET&quot;)==0) {</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.807/1000*std::pow(T,2)+2.272*T-339.007);</span></a>
+<a name="620"><span class="lineNum">     620 </span>            :         }</a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PHE&quot;)==0) {</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.828/1000*std::pow(T,2)+4.644*T-688.874);</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :         }</a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PRO&quot;)==0) {</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.347/1000*std::pow(T,2)+1.411*T-212.059);</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :         }</a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;SER&quot;)==0) {</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (1.813/1000*std::pow(T,2)-1.05*T+151.957);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :         }</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;THR&quot;)==0) {</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.64/1000*std::pow(T,2)+1.591*T-239.516);</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :         }</a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TRP&quot;)==0) {</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-11.66/1000*std::pow(T,2)+6.916*T-1025.293);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :         }</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TYR&quot;)==0) {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.513/1000*std::pow(T,2)+4.478*T-667.261);</span></a>
+<a name="638"><span class="lineNum">     638 </span>            :         }</a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;VAL&quot;)==0) {</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-4.902/1000*std::pow(T,2)+2.921*T-435.309);</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :         }</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :         DeltaG[natoms].push_back (-0.6962/1000*std::pow(T,2)+0.4426*T-70.015);</span></a>
+<a name="643"><span class="lineNum">     643 </span>            :       }</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :       if (approach==3) {</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ALA&quot;)==0) {</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.995/1000*std::pow(T,2)+1.808*T-272.105);</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :         }</a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ARG&quot;)==0) {</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.182/1000*std::pow(T,2)+1.894*T-284.086);</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :         }</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASN&quot;)==0) {</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.047/1000*std::pow(T,2)+0.6068*T-90.597);</span></a>
+<a name="653"><span class="lineNum">     653 </span>            :         }</a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ASP&quot;)==0) {</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-0.1794/1000*std::pow(T,2)+0.1091*T-19.143);</span></a>
+<a name="656"><span class="lineNum">     656 </span>            :         }</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;CYS&quot;)==0) {</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.09/1000*std::pow(T,2)+1.835*T-268.527);</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :         }</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLN&quot;)==0) {</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.23/1000*std::pow(T,2)+1.335*T-201.559);</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :         }</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLU&quot;)==0) {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-1.511/1000*std::pow(T,2)+0.8904*T-133.543);</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :         }</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;GLY&quot;)==0) {</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (0);</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :         }</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;HIS&quot;)==0) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.482/1000*std::pow(T,2)+2.084*T-315.398);</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :         }</a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;ILE&quot;)==0) {</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-6.364/1000*std::pow(T,2)+3.8*T-564.825);</span></a>
+<a name="674"><span class="lineNum">     674 </span>            :         }</a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LEU&quot;)==0) {</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.466/1000*std::pow(T,2)+4.417*T-651.483);</span></a>
+<a name="677"><span class="lineNum">     677 </span>            :         }</a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;LYS&quot;)==0) {</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.091/1000*std::pow(T,2)+1.2458*T-187.485);</span></a>
+<a name="680"><span class="lineNum">     680 </span>            :         }</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;MET&quot;)==0) {</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-3.807/1000*std::pow(T,2)+2.272*T-339.242);</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :         }</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PHE&quot;)==0) {</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.828/1000*std::pow(T,2)+4.644*T-687.134);</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :         }</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;PRO&quot;)==0) {</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.347/1000*std::pow(T,2)+1.411*T-214.211);</span></a>
+<a name="689"><span class="lineNum">     689 </span>            :         }</a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;SER&quot;)==0) {</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (1.813/1000*std::pow(T,2)-1.05*T+150.289);</span></a>
+<a name="692"><span class="lineNum">     692 </span>            :         }</a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;THR&quot;)==0) {</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-2.64/1000*std::pow(T,2)+1.591*T-240.267);</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :         }</a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TRP&quot;)==0) {</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-11.66/1000*std::pow(T,2)+6.916*T-1024.284);</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :         }</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;TYR&quot;)==0) {</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-7.513/1000*std::pow(T,2)+4.478*T-666.484);</span></a>
+<a name="701"><span class="lineNum">     701 </span>            :         }</a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineNoCov">          0 :         if (AtomResidueName[1][i].compare(&quot;VAL&quot;)==0) {</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :           DeltaG[i].push_back (-4.902/1000*std::pow(T,2)+2.921*T-433.013);</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :         }</a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineNoCov">          0 :         DeltaG[natoms].push_back (-0.6927/1000*std::pow(T,2)+0.4404*T-68.724);</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :       }</a>
+<a name="707"><span class="lineNum">     707 </span>            :     }</a>
+<a name="708"><span class="lineNum">     708 </span>            :   }</a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :   Ti = T;</span></a>
+<a name="711"><span class="lineNum">     711 </span>            : </a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :   if (firstStepFlag ==0) {</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :     if (approach!=2 &amp;&amp; approach!=3) {</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :       cout &lt;&lt; &quot;Unknown approach &quot; &lt;&lt; approach &lt;&lt; endl;</span></a>
+<a name="715"><span class="lineNum">     715 </span>            :     }</a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;natoms; i++) {</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :       if (DeltaG[i].size()==0 ) {</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineNoCov">          0 :         cout &lt;&lt; &quot;Delta G value for residue &quot; &lt;&lt; AtomResidueName[1][i] &lt;&lt; &quot; not found &quot; &lt;&lt; endl;</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :         error (&quot;missing Delta G parameter\n&quot;);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :       }</a>
+<a name="721"><span class="lineNum">     721 </span>            :     }</a>
+<a name="722"><span class="lineNum">     722 </span>            :   }</a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="724"><span class="lineNum">     724 </span>            : </a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            : //calculates neighbor list</a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">         24 : void SASA_LCPO::calcNlist() {</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">         24 :   if(!nopbc) makeWhole();</span></a>
+<a name="729"><span class="lineNum">     729 </span>            : </a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">       2904 :   for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">       2880 :     Nlist[i].clear();</span></a>
+<a name="732"><span class="lineNum">     732 </span>            :   }</a>
+<a name="733"><span class="lineNum">     733 </span>            : </a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">       2904 :   for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">       2880 :     if (LCPOparam[i].size()&gt;0) {</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">      87264 :       for (unsigned j = 0; j &lt; i; j++) {</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">      85824 :         if (LCPOparam[j].size()&gt;0) {</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">      42480 :           const Vector Delta_ij_vec = delta( getPosition(i), getPosition(j) );</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">      42480 :           double Delta_ij_mod = Delta_ij_vec.modulo()*10;</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">      42480 :           double overlapD = LCPOparam[i][0]+LCPOparam[j][0];</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineCov">      42480 :           if (Delta_ij_mod &lt; overlapD) {</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">      19030 :             Nlist.at(i).push_back (j);</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">      19030 :             Nlist.at(j).push_back (i);</span></a>
+<a name="744"><span class="lineNum">     744 </span>            :           }</a>
+<a name="745"><span class="lineNum">     745 </span>            :         }</a>
+<a name="746"><span class="lineNum">     746 </span>            :       }</a>
+<a name="747"><span class="lineNum">     747 </span>            :     }</a>
+<a name="748"><span class="lineNum">     748 </span>            :   }</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">         24 : }</span></a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span>            : //calculates SASA according to LCPO algorithm</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">         24 : void SASA_LCPO::calculate() {</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">         24 :   if(!nopbc) makeWhole();</span></a>
+<a name="755"><span class="lineNum">     755 </span>            : </a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">         24 :   if(getExchangeStep()) nl_update = 0;</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">         24 :   if (firstStepFlag ==0) {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">          2 :     readPDB();</span></a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">          2 :     readLCPOparam();</span></a>
+<a name="760"><span class="lineNum">     760 </span>            :   }</a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">         24 :   if (nl_update == 0) {</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">         24 :     calcNlist();</span></a>
+<a name="763"><span class="lineNum">     763 </span>            :   }</a>
+<a name="764"><span class="lineNum">     764 </span>            : </a>
+<a name="765"><span class="lineNum">     765 </span>            : </a>
+<a name="766"><span class="lineNum">     766 </span>            : </a>
+<a name="767"><span class="lineNum">     767 </span>            :   double S1, Aij, Ajk, Aijk, Aijt, Ajkt, Aikt;</a>
+<a name="768"><span class="lineNum">     768 </span>            :   double dAdd;</a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">         24 :   double sasa = 0;</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">         24 :   vector&lt;Vector&gt; derivatives( natoms );</span></a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineCov">         24 :   Tensor virial;</span></a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">         24 :   vector &lt;double&gt; dAijdc_2t(3);</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">         24 :   vector &lt;double&gt; dSASA_2_neigh_dc(3);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">         24 :   vector &lt;double&gt; ddij_di(3);</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">         24 :   vector &lt;double&gt; ddik_di(3);</span></a>
+<a name="776"><span class="lineNum">     776 </span>            : </a>
+<a name="777"><span class="lineNum">     777 </span><span class="lineCov">         24 :   if( sasa_type==TOTAL ) {</span></a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">       1452 :     for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">       1440 :       derivatives[i][0] = 0.;</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">       1440 :       derivatives[i][1] = 0.;</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">       1440 :       derivatives[i][2] = 0.;</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">       1440 :       if ( LCPOparam[i].size()&gt;1) {</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">        720 :         if (LCPOparam[i][1]&gt;0.0) {</span></a>
+<a name="784"><span class="lineNum">     784 </span>            :           Aij = 0.0;</a>
+<a name="785"><span class="lineNum">     785 </span>            :           Aijk = 0.0;</a>
+<a name="786"><span class="lineNum">     786 </span>            :           Ajk = 0.0;</a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">        720 :           double ri = LCPOparam[i][0];</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">        720 :           S1 = 4*M_PI*ri*ri;</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">        720 :           vector &lt;double&gt; dAijdc_2(3, 0);</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">        720 :           vector &lt;double&gt; dAijdc_4(3, 0);</span></a>
+<a name="791"><span class="lineNum">     791 </span>            : </a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">      19750 :           for (unsigned j = 0; j &lt; Nlist[i].size(); j++) {</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">      19030 :             const Vector d_ij_vec = delta( getPosition(i), getPosition(Nlist[i][j]) );</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">      19030 :             double d_ij = d_ij_vec.modulo()*10;</span></a>
+<a name="796"><span class="lineNum">     796 </span>            : </a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">      19030 :             double rj = LCPOparam[Nlist[i][j]][0];</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">      19030 :             Aijt = (2*M_PI*ri*(ri-d_ij/2-((ri*ri-rj*rj)/(2*d_ij))));</span></a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">      19030 :             double sji = (2*M_PI*rj*(rj-d_ij/2+((ri*ri-rj*rj)/(2*d_ij))));</span></a>
+<a name="800"><span class="lineNum">     800 </span>            : </a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">      19030 :             dAdd = M_PI*rj*(-(ri*ri-rj*rj)/(d_ij*d_ij)-1);</span></a>
+<a name="802"><span class="lineNum">     802 </span>            : </a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">      19030 :             ddij_di[0] = -10*(getPosition(Nlist[i][j])[0]-getPosition(i)[0])/d_ij;</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">      19030 :             ddij_di[1] = -10*(getPosition(Nlist[i][j])[1]-getPosition(i)[1])/d_ij;</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">      19030 :             ddij_di[2] = -10*(getPosition(Nlist[i][j])[2]-getPosition(i)[2])/d_ij;</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span>            :             Ajkt = 0.0;</a>
+<a name="808"><span class="lineNum">     808 </span>            :             Aikt = 0.0;</a>
+<a name="809"><span class="lineNum">     809 </span>            : </a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_3_neigh_dc(3, 0.0);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_4_neigh_dc(3, 0.0);</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_3_neigh_dc2(3, 0.0);</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_4_neigh_dc2(3, 0.0);</span></a>
+<a name="814"><span class="lineNum">     814 </span>            : </a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">      19030 :             dSASA_2_neigh_dc[0] = dAdd * ddij_di[0];</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">      19030 :             dSASA_2_neigh_dc[1] = dAdd * ddij_di[1];</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">      19030 :             dSASA_2_neigh_dc[2] = dAdd * ddij_di[2];</span></a>
+<a name="818"><span class="lineNum">     818 </span>            : </a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">      19030 :             dAdd = M_PI*ri*((ri*ri-rj*rj)/(d_ij*d_ij)-1);</span></a>
+<a name="820"><span class="lineNum">     820 </span>            : </a>
+<a name="821"><span class="lineNum">     821 </span>            : </a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineCov">      19030 :             dAijdc_2t[0] = dAdd * ddij_di[0];</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">      19030 :             dAijdc_2t[1] = dAdd * ddij_di[1];</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">      19030 :             dAijdc_2t[2] = dAdd * ddij_di[2];</span></a>
+<a name="825"><span class="lineNum">     825 </span>            : </a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">     560038 :             for (unsigned k = 0; k &lt; Nlist[Nlist[i][j]].size(); k++) {</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">     541008 :               if (std::find (Nlist[i].begin(), Nlist[i].end(), Nlist[Nlist[i][j]][k]) !=  Nlist[i].end()) {</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">     370872 :                 const Vector d_jk_vec = delta( getPosition(Nlist[i][j]), getPosition(Nlist[Nlist[i][j]][k]) );</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">     370872 :                 const Vector d_ik_vec = delta( getPosition(i), getPosition(Nlist[Nlist[i][j]][k]) );</span></a>
+<a name="830"><span class="lineNum">     830 </span>            : </a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">     370872 :                 double d_jk = d_jk_vec.modulo()*10;</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">     370872 :                 double d_ik = d_ik_vec.modulo()*10;</span></a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">     370872 :                 double rk = LCPOparam[Nlist[Nlist[i][j]][k]][0];</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">     370872 :                 double sjk =  (2*M_PI*rj*(rj-d_jk/2-((rj*rj-rk*rk)/(2*d_jk))));</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">     370872 :                 Ajkt += sjk;</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">     370872 :                 Aikt += (2*M_PI*ri*(ri-d_ik/2-((ri*ri-rk*rk)/(2*d_ik))));</span></a>
+<a name="838"><span class="lineNum">     838 </span>            : </a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">     370872 :                 dAdd = M_PI*ri*((ri*ri-rk*rk)/(d_ik*d_ik)-1);</span></a>
+<a name="840"><span class="lineNum">     840 </span>            : </a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">     370872 :                 ddik_di[0] = -10*(getPosition(Nlist[Nlist[i][j]][k])[0]-getPosition(i)[0])/d_ik;</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">     370872 :                 ddik_di[1] = -10*(getPosition(Nlist[Nlist[i][j]][k])[1]-getPosition(i)[1])/d_ik;</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">     370872 :                 ddik_di[2] = -10*(getPosition(Nlist[Nlist[i][j]][k])[2]-getPosition(i)[2])/d_ik;</span></a>
+<a name="844"><span class="lineNum">     844 </span>            : </a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc[0] += dAdd*ddik_di[0];</span></a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc[1] += dAdd*ddik_di[1];</span></a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc[2] += dAdd*ddik_di[2];</span></a>
+<a name="849"><span class="lineNum">     849 </span>            : </a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">     370872 :                 dAdd = M_PI*rk*(-(ri*ri-rk*rk)/(d_ik*d_ik)-1);</span></a>
+<a name="851"><span class="lineNum">     851 </span>            : </a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc2[0] += dAdd*ddik_di[0];</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc2[1] += dAdd*ddik_di[1];</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc2[2] += dAdd*ddik_di[2];</span></a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">     370872 :                 dSASA_4_neigh_dc2[0] += sjk*dAdd*ddik_di[0];</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">     370872 :                 dSASA_4_neigh_dc2[1] += sjk*dAdd*ddik_di[1];</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">     370872 :                 dSASA_4_neigh_dc2[2] += sjk*dAdd*ddik_di[2];</span></a>
+<a name="859"><span class="lineNum">     859 </span>            : </a>
+<a name="860"><span class="lineNum">     860 </span>            :               }</a>
+<a name="861"><span class="lineNum">     861 </span>            :             }</a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[0] = sji*dSASA_3_neigh_dc[0] + dSASA_4_neigh_dc2[0];</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[1] = sji*dSASA_3_neigh_dc[1] + dSASA_4_neigh_dc2[1];</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[2] = sji*dSASA_3_neigh_dc[2] + dSASA_4_neigh_dc2[2];</span></a>
+<a name="865"><span class="lineNum">     865 </span>            : </a>
+<a name="866"><span class="lineNum">     866 </span><span class="lineCov">      19030 :             dSASA_3_neigh_dc[0] += dSASA_3_neigh_dc2[0];</span></a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">      19030 :             dSASA_3_neigh_dc[1] += dSASA_3_neigh_dc2[1];</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">      19030 :             dSASA_3_neigh_dc[2] += dSASA_3_neigh_dc2[2];</span></a>
+<a name="869"><span class="lineNum">     869 </span>            : </a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[0] += dSASA_2_neigh_dc[0] * Aikt;</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[1] += dSASA_2_neigh_dc[1] * Aikt;</span></a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[2] += dSASA_2_neigh_dc[2] * Aikt;</span></a>
+<a name="873"><span class="lineNum">     873 </span>            : </a>
+<a name="874"><span class="lineNum">     874 </span>            : </a>
+<a name="875"><span class="lineNum">     875 </span><span class="lineCov">      19030 :             derivatives[i][0] += (dSASA_2_neigh_dc[0]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[0]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[0]*LCPOparam[Nlist[i][j]][4])/10;</span></a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">      19030 :             derivatives[i][1] += (dSASA_2_neigh_dc[1]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[1]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[1]*LCPOparam[Nlist[i][j]][4])/10;</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">      19030 :             derivatives[i][2] += (dSASA_2_neigh_dc[2]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[2]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[2]*LCPOparam[Nlist[i][j]][4])/10;</span></a>
+<a name="878"><span class="lineNum">     878 </span>            : </a>
+<a name="879"><span class="lineNum">     879 </span>            : </a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">      19030 :             Aijk += (Aijt * Ajkt);</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">      19030 :             Aij += Aijt;</span></a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">      19030 :             Ajk += Ajkt;</span></a>
+<a name="883"><span class="lineNum">     883 </span>            : </a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">      19030 :             dAijdc_2[0] += dAijdc_2t[0];</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">      19030 :             dAijdc_2[1] += dAijdc_2t[1];</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">      19030 :             dAijdc_2[2] += dAijdc_2t[2];</span></a>
+<a name="887"><span class="lineNum">     887 </span>            : </a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">      19030 :             dAijdc_4[0] += Ajkt*dAijdc_2t[0];</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">      19030 :             dAijdc_4[1] += Ajkt*dAijdc_2t[1];</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">      19030 :             dAijdc_4[2] += Ajkt*dAijdc_2t[2];</span></a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            : </a>
+<a name="894"><span class="lineNum">     894 </span>            :           }</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">        720 :           double sasai = (LCPOparam[i][1]*S1+LCPOparam[i][2]*Aij+LCPOparam[i][3]*Ajk+LCPOparam[i][4]*Aijk);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">        720 :           if (sasai &gt; 0 ) sasa += sasai/100;</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">        720 :           derivatives[i][0] += (dAijdc_2[0]*LCPOparam[i][2]+dAijdc_4[0]*LCPOparam[i][4])/10;</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">        720 :           derivatives[i][1] += (dAijdc_2[1]*LCPOparam[i][2]+dAijdc_4[1]*LCPOparam[i][4])/10;</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">        720 :           derivatives[i][2] += (dAijdc_2[2]*LCPOparam[i][2]+dAijdc_4[2]*LCPOparam[i][4])/10;</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :         }</a>
+<a name="901"><span class="lineNum">     901 </span>            :       }</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">       1440 :       virial -= Tensor(getPosition(i),derivatives[i]);</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :     }</a>
+<a name="904"><span class="lineNum">     904 </span>            :   }</a>
+<a name="905"><span class="lineNum">     905 </span>            : </a>
+<a name="906"><span class="lineNum">     906 </span>            : </a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">         24 :   if( sasa_type==TRANSFER ) {</span></a>
+<a name="909"><span class="lineNum">     909 </span>            : </a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">         12 :     if (firstStepFlag ==0) {</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineCov">          1 :       readMaxSurf();</span></a>
+<a name="912"><span class="lineNum">     912 </span>            :     }</a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         12 :     if (firstStepFlag ==0 &amp;&amp; DeltaGValues != &quot;absent&quot;) {</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">          1 :       readDeltaG();</span></a>
+<a name="916"><span class="lineNum">     916 </span>            :     }</a>
+<a name="917"><span class="lineNum">     917 </span>            : </a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">         12 :     if (DeltaGValues == &quot;absent&quot;) {</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :       computeDeltaG();</span></a>
+<a name="920"><span class="lineNum">     920 </span>            :     }</a>
+<a name="921"><span class="lineNum">     921 </span>            : </a>
+<a name="922"><span class="lineNum">     922 </span>            : </a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">       1452 :     for(unsigned i = 0; i &lt; natoms; i++) {</span></a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span>            : </a>
+<a name="926"><span class="lineNum">     926 </span>            : </a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">       1440 :       derivatives[i][0] = 0.;</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">       1440 :       derivatives[i][1] = 0.;</span></a>
+<a name="929"><span class="lineNum">     929 </span><span class="lineCov">       1440 :       derivatives[i][2] = 0.;</span></a>
+<a name="930"><span class="lineNum">     930 </span>            : </a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineCov">       1440 :       if ( LCPOparam[i].size()&gt;1) {</span></a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">        720 :         if (LCPOparam[i][1]&gt;0.0) {</span></a>
+<a name="933"><span class="lineNum">     933 </span>            :           Aij = 0.0;</a>
+<a name="934"><span class="lineNum">     934 </span>            :           Aijk = 0.0;</a>
+<a name="935"><span class="lineNum">     935 </span>            :           Ajk = 0.0;</a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">        720 :           double ri = LCPOparam[i][0];</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">        720 :           S1 = 4*M_PI*ri*ri;</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">        720 :           vector &lt;double&gt; dAijdc_2(3, 0);</span></a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">        720 :           vector &lt;double&gt; dAijdc_4(3, 0);</span></a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span>            : </a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">      19750 :           for (unsigned j = 0; j &lt; Nlist[i].size(); j++) {</span></a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineCov">      19030 :             const Vector d_ij_vec = delta( getPosition(i), getPosition(Nlist[i][j]) );</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">      19030 :             double d_ij = d_ij_vec.modulo()*10;</span></a>
+<a name="945"><span class="lineNum">     945 </span>            : </a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">      19030 :             double rj = LCPOparam[Nlist[i][j]][0];</span></a>
+<a name="947"><span class="lineNum">     947 </span><span class="lineCov">      19030 :             Aijt = (2*M_PI*ri*(ri-d_ij/2-((ri*ri-rj*rj)/(2*d_ij))));</span></a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">      19030 :             double sji = (2*M_PI*rj*(rj-d_ij/2+((ri*ri-rj*rj)/(2*d_ij))));</span></a>
+<a name="949"><span class="lineNum">     949 </span>            : </a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">      19030 :             dAdd = M_PI*rj*(-(ri*ri-rj*rj)/(d_ij*d_ij)-1);</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineCov">      19030 :             ddij_di[0] = -10*(getPosition(Nlist[i][j])[0]-getPosition(i)[0])/d_ij;</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">      19030 :             ddij_di[1] = -10*(getPosition(Nlist[i][j])[1]-getPosition(i)[1])/d_ij;</span></a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">      19030 :             ddij_di[2] = -10*(getPosition(Nlist[i][j])[2]-getPosition(i)[2])/d_ij;</span></a>
+<a name="954"><span class="lineNum">     954 </span>            : </a>
+<a name="955"><span class="lineNum">     955 </span>            :             Ajkt = 0.0;</a>
+<a name="956"><span class="lineNum">     956 </span>            :             Aikt = 0.0;</a>
+<a name="957"><span class="lineNum">     957 </span>            : </a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_3_neigh_dc(3, 0.0);</span></a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_4_neigh_dc(3, 0.0);</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_3_neigh_dc2(3, 0.0);</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineCov">      19030 :             vector &lt;double&gt; dSASA_4_neigh_dc2(3, 0.0);</span></a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">      19030 :             dSASA_2_neigh_dc[0] = dAdd * ddij_di[0];</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineCov">      19030 :             dSASA_2_neigh_dc[1] = dAdd * ddij_di[1];</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineCov">      19030 :             dSASA_2_neigh_dc[2] = dAdd * ddij_di[2];</span></a>
+<a name="966"><span class="lineNum">     966 </span>            : </a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineCov">      19030 :             dAdd = M_PI*ri*((ri*ri-rj*rj)/(d_ij*d_ij)-1);</span></a>
+<a name="968"><span class="lineNum">     968 </span>            : </a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineCov">      19030 :             dAijdc_2t[0] = dAdd * ddij_di[0];</span></a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">      19030 :             dAijdc_2t[1] = dAdd * ddij_di[1];</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">      19030 :             dAijdc_2t[2] = dAdd * ddij_di[2];</span></a>
+<a name="972"><span class="lineNum">     972 </span>            : </a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">     560038 :             for (unsigned k = 0; k &lt; Nlist[Nlist[i][j]].size(); k++) {</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">     541008 :               if (std::find (Nlist[i].begin(), Nlist[i].end(), Nlist[Nlist[i][j]][k]) !=  Nlist[i].end()) {</span></a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineCov">     370872 :                 const Vector d_jk_vec = delta( getPosition(Nlist[i][j]), getPosition(Nlist[Nlist[i][j]][k]) );</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineCov">     370872 :                 const Vector d_ik_vec = delta( getPosition(i), getPosition(Nlist[Nlist[i][j]][k]) );</span></a>
+<a name="977"><span class="lineNum">     977 </span>            : </a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">     370872 :                 double d_jk = d_jk_vec.modulo()*10;</span></a>
+<a name="979"><span class="lineNum">     979 </span><span class="lineCov">     370872 :                 double d_ik = d_ik_vec.modulo()*10;</span></a>
+<a name="980"><span class="lineNum">     980 </span>            : </a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">     370872 :                 double rk = LCPOparam[Nlist[Nlist[i][j]][k]][0];</span></a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">     370872 :                 double sjk =  (2*M_PI*rj*(rj-d_jk/2-((rj*rj-rk*rk)/(2*d_jk))));</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">     370872 :                 Ajkt += sjk;</span></a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">     370872 :                 Aikt += (2*M_PI*ri*(ri-d_ik/2-((ri*ri-rk*rk)/(2*d_ik))));</span></a>
+<a name="985"><span class="lineNum">     985 </span>            : </a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">     370872 :                 dAdd = M_PI*ri*((ri*ri-rk*rk)/(d_ik*d_ik)-1);</span></a>
+<a name="987"><span class="lineNum">     987 </span>            : </a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">     370872 :                 ddik_di[0] = -10*(getPosition(Nlist[Nlist[i][j]][k])[0]-getPosition(i)[0])/d_ik;</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">     370872 :                 ddik_di[1] = -10*(getPosition(Nlist[Nlist[i][j]][k])[1]-getPosition(i)[1])/d_ik;</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">     370872 :                 ddik_di[2] = -10*(getPosition(Nlist[Nlist[i][j]][k])[2]-getPosition(i)[2])/d_ik;</span></a>
+<a name="991"><span class="lineNum">     991 </span>            : </a>
+<a name="992"><span class="lineNum">     992 </span>            : </a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc[0] += dAdd*ddik_di[0];</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc[1] += dAdd*ddik_di[1];</span></a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc[2] += dAdd*ddik_di[2];</span></a>
+<a name="996"><span class="lineNum">     996 </span>            : </a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">     370872 :                 dAdd = M_PI*rk*(-(ri*ri-rk*rk)/(d_ik*d_ik)-1);</span></a>
+<a name="998"><span class="lineNum">     998 </span>            : </a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc2[0] += dAdd*ddik_di[0];</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc2[1] += dAdd*ddik_di[1];</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">     370872 :                 dSASA_3_neigh_dc2[2] += dAdd*ddik_di[2];</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            : </a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">     370872 :                 dSASA_4_neigh_dc2[0] += sjk*dAdd*ddik_di[0];</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">     370872 :                 dSASA_4_neigh_dc2[1] += sjk*dAdd*ddik_di[1];</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">     370872 :                 dSASA_4_neigh_dc2[2] += sjk*dAdd*ddik_di[2];</span></a>
+<a name="1006"><span class="lineNum">    1006 </span>            : </a>
+<a name="1007"><span class="lineNum">    1007 </span>            :               }</a>
+<a name="1008"><span class="lineNum">    1008 </span>            :             }</a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[0] = sji*dSASA_3_neigh_dc[0] + dSASA_4_neigh_dc2[0];</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[1] = sji*dSASA_3_neigh_dc[1] + dSASA_4_neigh_dc2[1];</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[2] = sji*dSASA_3_neigh_dc[2] + dSASA_4_neigh_dc2[2];</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            : </a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">      19030 :             dSASA_3_neigh_dc[0] += dSASA_3_neigh_dc2[0];</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">      19030 :             dSASA_3_neigh_dc[1] += dSASA_3_neigh_dc2[1];</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">      19030 :             dSASA_3_neigh_dc[2] += dSASA_3_neigh_dc2[2];</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[0] += dSASA_2_neigh_dc[0] * Aikt;</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[1] += dSASA_2_neigh_dc[1] * Aikt;</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">      19030 :             dSASA_4_neigh_dc[2] += dSASA_2_neigh_dc[2] * Aikt;</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            : </a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">      19030 :             if (AtomResidueName[0][Nlist[i][j]] == &quot;N&quot; || AtomResidueName[0][Nlist[i][j]] == &quot;CA&quot;  || AtomResidueName[0][Nlist[i][j]] == &quot;C&quot; || AtomResidueName[0][Nlist[i][j]] == &quot;O&quot;) {</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">      15720 :               derivatives[i][0] += ((dSASA_2_neigh_dc[0]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[0]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[0]*LCPOparam[Nlist[i][j]][4])/MaxSurf[Nlist[i][j]][0]*DeltaG[natoms][0])*10;</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">      15720 :               derivatives[i][1] += ((dSASA_2_neigh_dc[1]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[1]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[1]*LCPOparam[Nlist[i][j]][4])/MaxSurf[Nlist[i][j]][0]*DeltaG[natoms][0])*10;</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">      15720 :               derivatives[i][2] += ((dSASA_2_neigh_dc[2]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[2]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[2]*LCPOparam[Nlist[i][j]][4])/MaxSurf[Nlist[i][j]][0]*DeltaG[natoms][0])*10;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :             }</a>
+<a name="1026"><span class="lineNum">    1026 </span>            : </a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">      19030 :             if (AtomResidueName[0][Nlist[i][j]] != &quot;N&quot; &amp;&amp; AtomResidueName[0][Nlist[i][j]] != &quot;CA&quot;  &amp;&amp; AtomResidueName[0][Nlist[i][j]] != &quot;C&quot; &amp;&amp; AtomResidueName[0][Nlist[i][j]] != &quot;O&quot;) {</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">       3310 :               derivatives[i][0] += ((dSASA_2_neigh_dc[0]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[0]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[0]*LCPOparam[Nlist[i][j]][4])/MaxSurf[Nlist[i][j]][1]*DeltaG[Nlist[i][j]][0])*10;</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">       3310 :               derivatives[i][1] += ((dSASA_2_neigh_dc[1]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[1]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[1]*LCPOparam[Nlist[i][j]][4])/MaxSurf[Nlist[i][j]][1]*DeltaG[Nlist[i][j]][0])*10;</span></a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">       3310 :               derivatives[i][2] += ((dSASA_2_neigh_dc[2]*LCPOparam[Nlist[i][j]][2] + dSASA_3_neigh_dc[2]*LCPOparam[Nlist[i][j]][3]+dSASA_4_neigh_dc[2]*LCPOparam[Nlist[i][j]][4])/MaxSurf[Nlist[i][j]][1]*DeltaG[Nlist[i][j]][0])*10;</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :             }</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : </a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">      19030 :             Aijk += (Aijt * Ajkt);</span></a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">      19030 :             Aij += Aijt;</span></a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineCov">      19030 :             Ajk += Ajkt;</span></a>
+<a name="1036"><span class="lineNum">    1036 </span>            : </a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">      19030 :             dAijdc_2[0] += dAijdc_2t[0];</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">      19030 :             dAijdc_2[1] += dAijdc_2t[1];</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">      19030 :             dAijdc_2[2] += dAijdc_2t[2];</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            : </a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">      19030 :             dAijdc_4[0] += Ajkt*dAijdc_2t[0];</span></a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineCov">      19030 :             dAijdc_4[1] += Ajkt*dAijdc_2t[1];</span></a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">      19030 :             dAijdc_4[2] += Ajkt*dAijdc_2t[2];</span></a>
+<a name="1044"><span class="lineNum">    1044 </span>            : </a>
+<a name="1045"><span class="lineNum">    1045 </span>            :           }</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :           double sasai = (LCPOparam[i][1]*S1+LCPOparam[i][2]*Aij+LCPOparam[i][3]*Ajk+LCPOparam[i][4]*Aijk);</a>
+<a name="1047"><span class="lineNum">    1047 </span>            : </a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">       2016 :           if (AtomResidueName[0][i] == &quot;N&quot; || AtomResidueName[0][i] == &quot;CA&quot;  || AtomResidueName[0][i] == &quot;C&quot; || AtomResidueName[0][i] == &quot;O&quot;) {</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">        576 :             if (sasai &gt; 0 ) sasa += (sasai/MaxSurf[i][0]*DeltaG[natoms][0]);</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">        576 :             derivatives[i][0] += ((dAijdc_2[0]*LCPOparam[i][2]+dAijdc_4[0]*LCPOparam[i][4])/MaxSurf[i][0]*DeltaG[natoms][0])*10;</span></a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">        576 :             derivatives[i][1] += ((dAijdc_2[1]*LCPOparam[i][2]+dAijdc_4[1]*LCPOparam[i][4])/MaxSurf[i][0]*DeltaG[natoms][0])*10;</span></a>
+<a name="1052"><span class="lineNum">    1052 </span><span class="lineCov">        576 :             derivatives[i][2] += ((dAijdc_2[2]*LCPOparam[i][2]+dAijdc_4[2]*LCPOparam[i][4])/MaxSurf[i][0]*DeltaG[natoms][0])*10;</span></a>
+<a name="1053"><span class="lineNum">    1053 </span>            :           }</a>
+<a name="1054"><span class="lineNum">    1054 </span>            : </a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">       2016 :           if (AtomResidueName[0][i] != &quot;N&quot; &amp;&amp; AtomResidueName[0][i] != &quot;CA&quot;  &amp;&amp; AtomResidueName[0][i] != &quot;C&quot; &amp;&amp; AtomResidueName[0][i] != &quot;O&quot;) {</span></a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">        144 :             if (sasai &gt; 0. ) sasa += (sasai/MaxSurf[i][1]*DeltaG[i][0]);</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineCov">        144 :             derivatives[i][0] += ((dAijdc_2[0]*LCPOparam[i][2]+dAijdc_4[0]*LCPOparam[i][4])/MaxSurf[i][1]*DeltaG[i][0])*10;</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">        144 :             derivatives[i][1] += ((dAijdc_2[1]*LCPOparam[i][2]+dAijdc_4[1]*LCPOparam[i][4])/MaxSurf[i][1]*DeltaG[i][0])*10;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">        144 :             derivatives[i][2] += ((dAijdc_2[2]*LCPOparam[i][2]+dAijdc_4[2]*LCPOparam[i][4])/MaxSurf[i][1]*DeltaG[i][0])*10;</span></a>
+<a name="1060"><span class="lineNum">    1060 </span>            :           }</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :         }</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :       }</a>
+<a name="1063"><span class="lineNum">    1063 </span><span class="lineCov">       1440 :       virial -= Tensor(getPosition(i),derivatives[i]);</span></a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     }</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   }</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : </a>
+<a name="1067"><span class="lineNum">    1067 </span>            : </a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">       2904 :   for(unsigned i=0; i&lt;natoms; i++) { setAtomsDerivatives(i,derivatives[i]);}</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">         24 :   setBoxDerivatives(virial);</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">         24 :   setValue(sasa);</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         24 :   firstStepFlag = 1;</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         24 :   ++nl_update;</span></a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">         24 :   if (nl_update == stride) {</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">         24 :     nl_update = 0;</span></a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   }</a>
+<a name="1076"><span class="lineNum">    1076 </span>            : // setBoxDerivativesNoPbc();</a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">         24 : }</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            : </a>
+<a name="1079"><span class="lineNum">    1079 </span>            : }//namespace sasa</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : }//namespace PLMD</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/AlphaRMSD.cpp.func-sort-c.html b/coverage/secondarystructure/AlphaRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..dfc2b1672d
--- /dev/null
+++ b/coverage/secondarystructure/AlphaRMSD.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/AlphaRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - AlphaRMSD.cpp<span style="font-size: 80%;"> (<a href="AlphaRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AlphaRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#98">_ZN4PLMD18secondarystructure9AlphaRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#92">_ZN4PLMD18secondarystructure12_GLOBAL__N_121AlphaRMSDRegisterMe946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#98">_ZN4PLMD18secondarystructure9AlphaRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure9AlphaRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#92">_ZN4PLMD18secondarystructure12_GLOBAL__N_121AlphaRMSDRegisterMe94C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#92">_ZN4PLMD18secondarystructure12_GLOBAL__N_121AlphaRMSDRegisterMe94D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/AlphaRMSD.cpp.func.html b/coverage/secondarystructure/AlphaRMSD.cpp.func.html
new file mode 100644
index 0000000000..a36e90734e
--- /dev/null
+++ b/coverage/secondarystructure/AlphaRMSD.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/AlphaRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - AlphaRMSD.cpp<span style="font-size: 80%;"> (<a href="AlphaRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AlphaRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#92">_ZN4PLMD18secondarystructure12_GLOBAL__N_121AlphaRMSDRegisterMe946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#92">_ZN4PLMD18secondarystructure12_GLOBAL__N_121AlphaRMSDRegisterMe94C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#92">_ZN4PLMD18secondarystructure12_GLOBAL__N_121AlphaRMSDRegisterMe94D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure9AlphaRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#98">_ZN4PLMD18secondarystructure9AlphaRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AlphaRMSD.cpp.gcov.html#98">_ZN4PLMD18secondarystructure9AlphaRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/AlphaRMSD.cpp.gcov.html b/coverage/secondarystructure/AlphaRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..ead0a2bef5
--- /dev/null
+++ b/coverage/secondarystructure/AlphaRMSD.cpp.gcov.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/AlphaRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - AlphaRMSD.cpp<span style="font-size: 80%;"> (source / <a href="AlphaRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntry">50</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SecondaryStructureRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace secondarystructure {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR ALPHARMSD</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Probe the alpha helical content of a protein structure.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Any chain of six contiguous residues in a protein chain can form an alpha helix. This</a>
+<a name="34"><span class="lineNum">      34 </span>            : colvar thus generates the set of all possible six residue sections and calculates</a>
+<a name="35"><span class="lineNum">      35 </span>            : the RMSD distance between the configuration in which the residues find themselves</a>
+<a name="36"><span class="lineNum">      36 </span>            : and an idealized alpha helical structure. These distances can be calculated by either</a>
+<a name="37"><span class="lineNum">      37 </span>            : aligning the instantaneous structure with the reference structure and measuring each</a>
+<a name="38"><span class="lineNum">      38 </span>            : atomic displacement or by calculating differences between the set of inter-atomic</a>
+<a name="39"><span class="lineNum">      39 </span>            : distances in the reference and instantaneous structures.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : This colvar is based on the following reference \cite pietrucci09jctc.  The authors of</a>
+<a name="42"><span class="lineNum">      42 </span>            : this paper use the set of distances from the alpha helix configurations to measure</a>
+<a name="43"><span class="lineNum">      43 </span>            : the number of segments that have an alpha helical configuration. This is done by calculating</a>
+<a name="44"><span class="lineNum">      44 </span>            : the following sum of functions of the rmsd distances:</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            : s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m }</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : where the sum runs over all possible segments of alpha helix.  By default the</a>
+<a name="51"><span class="lineNum">      51 </span>            : NN, MM and D_0 parameters are set equal to those used in \cite pietrucci09jctc.  The R_0</a>
+<a name="52"><span class="lineNum">      52 </span>            : parameter must be set by the user - the value used in \cite pietrucci09jctc was 0.08 nm.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : If you change the function in the above sum you can calculate quantities such as the average</a>
+<a name="55"><span class="lineNum">      55 </span>            : distance from a purely the alpha helical configuration or the distance between the set of</a>
+<a name="56"><span class="lineNum">      56 </span>            : residues that is closest to an alpha helix and the reference configuration. To do these sorts of</a>
+<a name="57"><span class="lineNum">      57 </span>            : calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN</a>
+<a name="58"><span class="lineNum">      58 </span>            : keyword if you would like to change the form of the switching function. If you use any of these</a>
+<a name="59"><span class="lineNum">      59 </span>            : options you no longer need to specify NN, R_0, MM and D_0.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : Please be aware that for codes like gromacs you must ensure that plumed</a>
+<a name="62"><span class="lineNum">      62 </span>            : reconstructs the chains involved in your CV when you calculate this CV using</a>
+<a name="63"><span class="lineNum">      63 </span>            : anything other than TYPE=DRMSD.  For more details as to how to do this see \ref WHOLEMOLECULES.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \par Examples</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : The following input calculates the number of six residue segments of</a>
+<a name="68"><span class="lineNum">      68 </span>            : protein that are in an alpha helical configuration.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \plumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="72"><span class="lineNum">      72 </span>            : MOLINFO STRUCTURE=helix.pdb</a>
+<a name="73"><span class="lineNum">      73 </span>            : alpha: ALPHARMSD RESIDUES=all</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : Here the same is done use RMSD instead of DRMSD</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="80"><span class="lineNum">      80 </span>            : MOLINFO STRUCTURE=helix.pdb</a>
+<a name="81"><span class="lineNum">      81 </span>            : WHOLEMOLECULES ENTITY0=1-100</a>
+<a name="82"><span class="lineNum">      82 </span>            : alpha: ALPHARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1</a>
+<a name="83"><span class="lineNum">      83 </span>            : \endplumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : */</a>
+<a name="86"><span class="lineNum">      86 </span>            : //+ENDPLUMEDOC</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : class AlphaRMSD : public SecondaryStructureRMSD {</a>
+<a name="89"><span class="lineNum">      89 </span>            : public:</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit AlphaRMSD(const ActionOptions&amp;);</a>
+<a name="92"><span class="lineNum">      92 </span>            : };</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(AlphaRMSD,&quot;ALPHARMSD&quot;)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          5 : void AlphaRMSD::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          5 :   SecondaryStructureRMSD::registerKeywords( keys );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          5 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          3 : AlphaRMSD::AlphaRMSD(const ActionOptions&amp;ao):</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   Action(ao),</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          3 :   SecondaryStructureRMSD(ao)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span>            :   // read in the backbone atoms</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          3 :   std::vector&lt;unsigned&gt; chains; readBackboneAtoms( &quot;protein&quot;, chains);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            :   // This constructs all conceivable sections of alpha helix in the backbone of the chains</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 :   unsigned nprevious=0; std::vector&lt;unsigned&gt; nlist(30);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          6 :   for(unsigned i=0; i&lt;chains.size(); ++i) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :     if( chains[i]&lt;30 ) error(&quot;segment of backbone defined is not long enough to form an alpha helix. Each backbone fragment must contain a minimum of 6 residues&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          3 :     unsigned nres=chains[i]/5;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 :     if( chains[i]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         12 :     for(unsigned ires=0; ires&lt;nres-5; ires++) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          9 :       unsigned accum=nprevious + 5*ires;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        279 :       for(unsigned k=0; k&lt;30; ++k) nlist[k] = accum+k;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          9 :       addColvar( nlist );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          3 :     nprevious+=chains[i];</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   // Build the reference structure ( in angstroms )</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 :   std::vector&lt;Vector&gt; reference(30);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          3 :   reference[0] = Vector( 0.733,  0.519,  5.298 ); // N    i</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 :   reference[1] = Vector( 1.763,  0.810,  4.301 ); // CA</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   reference[2] = Vector( 3.166,  0.543,  4.881 ); // CB</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          3 :   reference[3] = Vector( 1.527, -0.045,  3.053 ); // C</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   reference[4] = Vector( 1.646,  0.436,  1.928 ); // O</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          3 :   reference[5] = Vector( 1.180, -1.312,  3.254 ); // N    i+1</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :   reference[6] = Vector( 0.924, -2.203,  2.126 ); // CA</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          3 :   reference[7] = Vector( 0.650, -3.626,  2.626 ); // CB</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          3 :   reference[8] = Vector(-0.239, -1.711,  1.261 ); // C</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          3 :   reference[9] = Vector(-0.190, -1.815,  0.032 ); // O</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          3 :   reference[10] = Vector(-1.280, -1.172,  1.891 ); // N    i+2</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          3 :   reference[11] = Vector(-2.416, -0.661,  1.127 ); // CA</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          3 :   reference[12] = Vector(-3.548, -0.217,  2.056 ); // CB</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 :   reference[13] = Vector(-1.964,  0.529,  0.276 ); // C</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          3 :   reference[14] = Vector(-2.364,  0.659, -0.880 ); // O</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :   reference[15] = Vector(-1.130,  1.391,  0.856 ); // N    i+3</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          3 :   reference[16] = Vector(-0.620,  2.565,  0.148 ); // CA</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          3 :   reference[17] = Vector( 0.228,  3.439,  1.077 ); // CB</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          3 :   reference[18] = Vector( 0.231,  2.129, -1.032 ); // C</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          3 :   reference[19] = Vector( 0.179,  2.733, -2.099 ); // O</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 :   reference[20] = Vector( 1.028,  1.084, -0.833 ); // N    i+4</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          3 :   reference[21] = Vector( 1.872,  0.593, -1.919 ); // CA</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 :   reference[22] = Vector( 2.850, -0.462, -1.397 ); // CB</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          3 :   reference[23] = Vector( 1.020,  0.020, -3.049 ); // C</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          3 :   reference[24] = Vector( 1.317,  0.227, -4.224 ); // O</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 :   reference[25] = Vector(-0.051, -0.684, -2.696 ); // N    i+5</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          3 :   reference[26] = Vector(-0.927, -1.261, -3.713 ); // CA</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :   reference[27] = Vector(-1.933, -2.219, -3.074 ); // CB</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :   reference[28] = Vector(-1.663, -0.171, -4.475 ); // C</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          3 :   reference[29] = Vector(-1.916, -0.296, -5.673 ); // O</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   // Store the secondary structure ( last number makes sure we convert to internal units nm )</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          3 :   setSecondaryStructure( reference, 0.17/atoms.getUnits().getLength(), 0.1/atoms.getUnits().getLength() );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          3 : }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/AntibetaRMSD.cpp.func-sort-c.html b/coverage/secondarystructure/AntibetaRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cbf13cf676
--- /dev/null
+++ b/coverage/secondarystructure/AntibetaRMSD.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/AntibetaRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - AntibetaRMSD.cpp<span style="font-size: 80%;"> (<a href="AntibetaRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AntibetaRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#104">_ZN4PLMD18secondarystructure12AntibetaRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#104">_ZN4PLMD18secondarystructure12AntibetaRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#93">_ZN4PLMD18secondarystructure12_GLOBAL__N_124AntibetaRMSDRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#95">_ZN4PLMD18secondarystructure12AntibetaRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#93">_ZN4PLMD18secondarystructure12_GLOBAL__N_124AntibetaRMSDRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#93">_ZN4PLMD18secondarystructure12_GLOBAL__N_124AntibetaRMSDRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/AntibetaRMSD.cpp.func.html b/coverage/secondarystructure/AntibetaRMSD.cpp.func.html
new file mode 100644
index 0000000000..c2f5ece148
--- /dev/null
+++ b/coverage/secondarystructure/AntibetaRMSD.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/AntibetaRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - AntibetaRMSD.cpp<span style="font-size: 80%;"> (<a href="AntibetaRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AntibetaRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#95">_ZN4PLMD18secondarystructure12AntibetaRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#104">_ZN4PLMD18secondarystructure12AntibetaRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#104">_ZN4PLMD18secondarystructure12AntibetaRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#93">_ZN4PLMD18secondarystructure12_GLOBAL__N_124AntibetaRMSDRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#93">_ZN4PLMD18secondarystructure12_GLOBAL__N_124AntibetaRMSDRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AntibetaRMSD.cpp.gcov.html#93">_ZN4PLMD18secondarystructure12_GLOBAL__N_124AntibetaRMSDRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/secondarystructure/AntibetaRMSD.cpp.gcov.html b/coverage/secondarystructure/AntibetaRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..c4331d6400
--- /dev/null
+++ b/coverage/secondarystructure/AntibetaRMSD.cpp.gcov.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/AntibetaRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - AntibetaRMSD.cpp<span style="font-size: 80%;"> (source / <a href="AntibetaRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SecondaryStructureRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace secondarystructure {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR ANTIBETARMSD</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Probe the antiparallel beta sheet content of your protein structure.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Two protein segments containing three contiguous residues can form an antiparallel beta sheet.</a>
+<a name="34"><span class="lineNum">      34 </span>            : Although if the two segments are part of the same protein chain they must be separated by</a>
+<a name="35"><span class="lineNum">      35 </span>            : a minimum of 2 residues to make room for the turn. This colvar thus generates the set of</a>
+<a name="36"><span class="lineNum">      36 </span>            : all possible six residue sections that could conceivably form an antiparallel beta sheet</a>
+<a name="37"><span class="lineNum">      37 </span>            : and calculates the RMSD distance between the configuration in which the residues find themselves</a>
+<a name="38"><span class="lineNum">      38 </span>            : and an idealized antiparallel beta sheet structure. These distances can be calculated by either</a>
+<a name="39"><span class="lineNum">      39 </span>            : aligning the instantaneous structure with the reference structure and measuring each</a>
+<a name="40"><span class="lineNum">      40 </span>            : atomic displacement or by calculating differences between the set of inter-atomic</a>
+<a name="41"><span class="lineNum">      41 </span>            : distances in the reference and instantaneous structures.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : This colvar is based on the following reference \cite pietrucci09jctc.  The authors of</a>
+<a name="44"><span class="lineNum">      44 </span>            : this paper use the set of distances from the anti parallel beta sheet configurations to measure</a>
+<a name="45"><span class="lineNum">      45 </span>            : the number of segments that have an configuration that resembles an anti parallel beta sheet. This is done by calculating</a>
+<a name="46"><span class="lineNum">      46 </span>            : the following sum of functions of the rmsd distances:</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m }</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : where the sum runs over all possible segments of antiparallel beta sheet.  By default the</a>
+<a name="53"><span class="lineNum">      53 </span>            : NN, MM and D_0 parameters are set equal to those used in \cite pietrucci09jctc.  The R_0</a>
+<a name="54"><span class="lineNum">      54 </span>            : parameter must be set by the user - the value used in \cite pietrucci09jctc was 0.08 nm.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : If you change the function in the above sum you can calculate quantities such as the average</a>
+<a name="57"><span class="lineNum">      57 </span>            : distance from a purely configuration composed of pure anti-parallel beta sheets or the distance between the set of</a>
+<a name="58"><span class="lineNum">      58 </span>            : residues that is closest to an anti-parallel beta sheet and the reference configuration. To do these sorts of</a>
+<a name="59"><span class="lineNum">      59 </span>            : calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN</a>
+<a name="60"><span class="lineNum">      60 </span>            : keyword if you would like to change the form of the switching function. If you use any of these</a>
+<a name="61"><span class="lineNum">      61 </span>            : options you no longer need to specify NN, R_0, MM and D_0.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : Please be aware that for codes like gromacs you must ensure that plumed</a>
+<a name="64"><span class="lineNum">      64 </span>            : reconstructs the chains involved in your CV when you calculate this CV using</a>
+<a name="65"><span class="lineNum">      65 </span>            : anything other than TYPE=DRMSD.  For more details as to how to do this see \ref WHOLEMOLECULES.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \par Examples</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : The following input calculates the number of six residue segments of</a>
+<a name="70"><span class="lineNum">      70 </span>            : protein that are in an antiparallel beta sheet configuration.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="74"><span class="lineNum">      74 </span>            : MOLINFO STRUCTURE=beta.pdb</a>
+<a name="75"><span class="lineNum">      75 </span>            : ab: ANTIBETARMSD RESIDUES=all STRANDS_CUTOFF=1</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : Here the same is done use RMSD instead of DRMSD</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="82"><span class="lineNum">      82 </span>            : MOLINFO STRUCTURE=helix.pdb</a>
+<a name="83"><span class="lineNum">      83 </span>            : WHOLEMOLECULES ENTITY0=1-100</a>
+<a name="84"><span class="lineNum">      84 </span>            : hh: ANTIBETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1  STRANDS_CUTOFF=1</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endplumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : */</a>
+<a name="87"><span class="lineNum">      87 </span>            : //+ENDPLUMEDOC</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : class AntibetaRMSD : public SecondaryStructureRMSD {</a>
+<a name="90"><span class="lineNum">      90 </span>            : public:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="92"><span class="lineNum">      92 </span>            :   explicit AntibetaRMSD(const ActionOptions&amp;);</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      12528 : PLUMED_REGISTER_ACTION(AntibetaRMSD,&quot;ANTIBETARMSD&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         14 : void AntibetaRMSD::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         14 :   SecondaryStructureRMSD::registerKeywords( keys );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;STYLE&quot;,&quot;all&quot;,&quot;Antiparallel beta sheets can either form in a single chain or from a pair of chains. If STYLE=all all &quot;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :            &quot;chain configuration with the appropriate geometry are counted.  If STYLE=inter &quot;</a>
+<a name="101"><span class="lineNum">     101 </span>            :            &quot;only sheet-like configurations involving two chains are counted, while if STYLE=intra &quot;</a>
+<a name="102"><span class="lineNum">     102 </span>            :            &quot;only sheet-like configurations involving a single chain are counted&quot;);</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         14 :   keys.use(&quot;STRANDS_CUTOFF&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         14 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 : AntibetaRMSD::AntibetaRMSD(const ActionOptions&amp;ao):</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   Action(ao),</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   SecondaryStructureRMSD(ao)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : {</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // read in the backbone atoms</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         24 :   std::vector&lt;unsigned&gt; chains; readBackboneAtoms( &quot;protein&quot;, chains );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            :   bool intra_chain(false), inter_chain(false);</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         24 :   std::string style; parse(&quot;STYLE&quot;,style);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         12 :   if( style==&quot;all&quot; ) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     intra_chain=true; inter_chain=true;</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   } else if( style==&quot;inter&quot;) {</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :     intra_chain=false; inter_chain=true;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   } else if( style==&quot;intra&quot;) {</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     intra_chain=true; inter_chain=false;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   } else {</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     error( style + &quot; is not a valid directive for the STYLE keyword&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   // Align the atoms based on the positions of these two atoms</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         12 :   setAtomsFromStrands( 6, 21 );</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            :   // This constructs all conceivable sections of antibeta sheet in the backbone of the chains</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         12 :   if( intra_chain ) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         10 :     unsigned nprevious=0; std::vector&lt;unsigned&gt; nlist(30);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        173 :     for(unsigned i=0; i&lt;chains.size(); ++i) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        163 :       if( chains[i]&lt;40 ) error(&quot;segment of backbone is not long enough to form an antiparallel beta hairpin. Each backbone fragment must contain a minimum of 8 residues&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :       // Loop over all possible triples in each 8 residue segment of protein</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        163 :       unsigned nres=chains[i]/5;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        163 :       if( chains[i]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        330 :       for(unsigned ires=0; ires&lt;nres-7; ires++) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        344 :         for(unsigned jres=ires+7; jres&lt;nres; jres++) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       2832 :           for(unsigned k=0; k&lt;15; ++k) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       2655 :             nlist[k]=nprevious + ires*5+k;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       2655 :             nlist[k+15]=nprevious + (jres-2)*5+k;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :           }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        177 :           addColvar( nlist );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :         }</a>
+<a name="144"><span class="lineNum">     144 </span>            :       }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        163 :       nprevious+=chains[i];</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     }</a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         12 :   if( inter_chain ) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         13 :     if( chains.size()==1 &amp;&amp; style!=&quot;all&quot; ) error(&quot;there is only one chain defined so cannot use inter_chain option&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         12 :     std::vector&lt;unsigned&gt; nlist(30);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        167 :     for(unsigned ichain=1; ichain&lt;chains.size(); ++ichain) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1534 :       unsigned iprev=0; for(unsigned i=0; i&lt;ichain; ++i) iprev+=chains[i];</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        155 :       unsigned inres=chains[ichain]/5;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        155 :       if( chains[ichain]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       1075 :       for(unsigned ires=0; ires&lt;inres-2; ++ires) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       9184 :         for(unsigned jchain=0; jchain&lt;ichain; ++jchain) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      52328 :           unsigned jprev=0; for(unsigned i=0; i&lt;jchain; ++i) jprev+=chains[i];</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       8264 :           unsigned jnres=chains[jchain]/5;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       8264 :           if( chains[jchain]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      57838 :           for(unsigned jres=0; jres&lt;jnres-2; ++jres) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     793184 :             for(unsigned k=0; k&lt;15; ++k) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     743610 :               nlist[k]=iprev+ ires*5+k;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     743610 :               nlist[k+15]=jprev+ jres*5+k;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :             }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      49574 :             addColvar( nlist );</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :           }</a>
+<a name="167"><span class="lineNum">     167 </span>            :         }</a>
+<a name="168"><span class="lineNum">     168 </span>            :       }</a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :   // Build the reference structure ( in angstroms )</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         12 :   std::vector&lt;Vector&gt; reference(30);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         12 :   reference[0]=Vector( 2.263, -3.795,  1.722); // N    i</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         12 :   reference[1]=Vector( 2.493, -2.426,  2.263); // CA</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         12 :   reference[2]=Vector( 3.847, -1.838,  1.761); // CB</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         12 :   reference[3]=Vector( 1.301, -1.517,  1.921); // C</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         12 :   reference[4]=Vector( 0.852, -1.504,  0.739); // O</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         12 :   reference[5]=Vector( 0.818, -0.738,  2.917); // N    i+1</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         12 :   reference[6]=Vector(-0.299,  0.243,  2.748); // CA</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         12 :   reference[7]=Vector(-1.421, -0.076,  3.757); // CB</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         12 :   reference[8]=Vector( 0.273,  1.680,  2.854); // C</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         12 :   reference[9]=Vector( 0.902,  1.993,  3.888); // O</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         12 :   reference[10]=Vector( 0.119,  2.532,  1.813); // N    i+2</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         12 :   reference[11]=Vector( 0.683,  3.916,  1.680); // CA</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         12 :   reference[12]=Vector( 1.580,  3.940,  0.395); // CB</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         12 :   reference[13]=Vector(-0.394,  5.011,  1.630); // C</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         12 :   reference[14]=Vector(-1.459,  4.814,  0.982); // O</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         12 :   reference[15]=Vector(-2.962,  3.559, -1.359); // N    j-2</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         12 :   reference[16]=Vector(-2.439,  2.526, -2.287); // CA</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         12 :   reference[17]=Vector(-1.189,  3.006, -3.087); // CB</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         12 :   reference[18]=Vector(-2.081,  1.231, -1.520); // C</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         12 :   reference[19]=Vector(-1.524,  1.324, -0.409); // O</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         12 :   reference[20]=Vector(-2.326,  0.037, -2.095); // N    j-1</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         12 :   reference[21]=Vector(-1.858, -1.269, -1.554); // CA</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         12 :   reference[22]=Vector(-3.053, -2.199, -1.291); // CB</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         12 :   reference[23]=Vector(-0.869, -1.949, -2.512); // C</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         12 :   reference[24]=Vector(-1.255, -2.070, -3.710); // O</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         12 :   reference[25]=Vector( 0.326, -2.363, -2.072); // N    j</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         12 :   reference[26]=Vector( 1.405, -2.992, -2.872); // CA</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         12 :   reference[27]=Vector( 2.699, -2.129, -2.917); // CB</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         12 :   reference[28]=Vector( 1.745, -4.399, -2.330); // C</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         12 :   reference[29]=Vector( 1.899, -4.545, -1.102); // O</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            :   // Store the secondary structure ( last number makes sure we convert to internal units nm )</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         12 :   setSecondaryStructure( reference, 0.17/atoms.getUnits().getLength(), 0.1/atoms.getUnits().getLength() );</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         12 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/ParabetaRMSD.cpp.func-sort-c.html b/coverage/secondarystructure/ParabetaRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..de36c9326f
--- /dev/null
+++ b/coverage/secondarystructure/ParabetaRMSD.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/ParabetaRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - ParabetaRMSD.cpp<span style="font-size: 80%;"> (<a href="ParabetaRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">106</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ParabetaRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#105">_ZN4PLMD18secondarystructure12ParabetaRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#105">_ZN4PLMD18secondarystructure12ParabetaRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure12_GLOBAL__N_124ParabetaRMSDRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure12ParabetaRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure12_GLOBAL__N_124ParabetaRMSDRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure12_GLOBAL__N_124ParabetaRMSDRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/ParabetaRMSD.cpp.func.html b/coverage/secondarystructure/ParabetaRMSD.cpp.func.html
new file mode 100644
index 0000000000..a6c1398c1b
--- /dev/null
+++ b/coverage/secondarystructure/ParabetaRMSD.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/ParabetaRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - ParabetaRMSD.cpp<span style="font-size: 80%;"> (<a href="ParabetaRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">106</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ParabetaRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure12ParabetaRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#105">_ZN4PLMD18secondarystructure12ParabetaRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#105">_ZN4PLMD18secondarystructure12ParabetaRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure12_GLOBAL__N_124ParabetaRMSDRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure12_GLOBAL__N_124ParabetaRMSDRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ParabetaRMSD.cpp.gcov.html#94">_ZN4PLMD18secondarystructure12_GLOBAL__N_124ParabetaRMSDRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/ParabetaRMSD.cpp.gcov.html b/coverage/secondarystructure/ParabetaRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..74997a54d1
--- /dev/null
+++ b/coverage/secondarystructure/ParabetaRMSD.cpp.gcov.html
@@ -0,0 +1,320 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/ParabetaRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - ParabetaRMSD.cpp<span style="font-size: 80%;"> (source / <a href="ParabetaRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">106</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SecondaryStructureRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace secondarystructure {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC COLVAR PARABETARMSD</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Probe the parallel beta sheet content of your protein structure.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Two protein segments containing three contiguous residues can form a parallel beta sheet.</a>
+<a name="34"><span class="lineNum">      34 </span>            : Although if the two segments are part of the same protein chain they must be separated by</a>
+<a name="35"><span class="lineNum">      35 </span>            : a minimum of 3 residues to make room for the turn. This colvar thus generates the set of</a>
+<a name="36"><span class="lineNum">      36 </span>            : all possible six residue sections that could conceivably form a parallel beta sheet</a>
+<a name="37"><span class="lineNum">      37 </span>            : and calculates the RMSD distance between the configuration in which the residues find themselves</a>
+<a name="38"><span class="lineNum">      38 </span>            : and an idealized parallel beta sheet structure. These distances can be calculated by either</a>
+<a name="39"><span class="lineNum">      39 </span>            : aligning the instantaneous structure with the reference structure and measuring each</a>
+<a name="40"><span class="lineNum">      40 </span>            : atomic displacement or by calculating differences between the set of inter-atomic</a>
+<a name="41"><span class="lineNum">      41 </span>            : distances in the reference and instantaneous structures.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : This colvar is based on the following reference \cite pietrucci09jctc.  The authors of</a>
+<a name="44"><span class="lineNum">      44 </span>            : this paper use the set of distances from the parallel beta sheet configurations to measure</a>
+<a name="45"><span class="lineNum">      45 </span>            : the number of segments whose configuration resembles a parallel beta sheet. This is done by calculating</a>
+<a name="46"><span class="lineNum">      46 </span>            : the following sum of functions of the rmsd distances:</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : s = \sum_i \frac{ 1 - \left(\frac{r_i-d_0}{r_0}\right)^n } { 1 - \left(\frac{r_i-d_0}{r_0}\right)^m }</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : where the sum runs over all possible segments of parallel beta sheet.  By default the</a>
+<a name="53"><span class="lineNum">      53 </span>            : NN, MM and D_0 parameters are set equal to those used in \cite pietrucci09jctc.  The R_0</a>
+<a name="54"><span class="lineNum">      54 </span>            : parameter must be set by the user - the value used in \cite pietrucci09jctc was 0.08 nm.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : If you change the function in the above sum you can calculate quantities such as the average</a>
+<a name="57"><span class="lineNum">      57 </span>            : distance from a structure composed of only parallel beta sheets or the distance between the set of</a>
+<a name="58"><span class="lineNum">      58 </span>            : residues that is closest to a parallel beta sheet and the reference configuration. To do these sorts of</a>
+<a name="59"><span class="lineNum">      59 </span>            : calculations you can use the AVERAGE and MIN keywords. In addition you can use the LESS_THAN</a>
+<a name="60"><span class="lineNum">      60 </span>            : keyword if you would like to change the form of the switching function. If you use any of these</a>
+<a name="61"><span class="lineNum">      61 </span>            : options you no longer need to specify NN, R_0, MM and D_0.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : Please be aware that for codes like gromacs you must ensure that plumed</a>
+<a name="64"><span class="lineNum">      64 </span>            : reconstructs the chains involved in your CV when you calculate this CV using</a>
+<a name="65"><span class="lineNum">      65 </span>            : anything other than TYPE=DRMSD.  For more details as to how to do this see \ref WHOLEMOLECULES.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \par Examples</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : The following input calculates the number of six residue segments of</a>
+<a name="70"><span class="lineNum">      70 </span>            : protein that are in an parallel beta sheet configuration.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="74"><span class="lineNum">      74 </span>            : MOLINFO STRUCTURE=beta.pdb</a>
+<a name="75"><span class="lineNum">      75 </span>            : pb: PARABETARMSD RESIDUES=all STRANDS_CUTOFF=1</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : Here the same is done use RMSD instead of DRMSD</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : #SETTINGS MOLFILE=regtest/basic/rt32/helix.pdb</a>
+<a name="82"><span class="lineNum">      82 </span>            : MOLINFO STRUCTURE=helix.pdb</a>
+<a name="83"><span class="lineNum">      83 </span>            : WHOLEMOLECULES ENTITY0=1-100</a>
+<a name="84"><span class="lineNum">      84 </span>            : hh: PARABETARMSD RESIDUES=all TYPE=OPTIMAL R_0=0.1  STRANDS_CUTOFF=1</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endplumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : */</a>
+<a name="88"><span class="lineNum">      88 </span>            : //+ENDPLUMEDOC</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : class ParabetaRMSD : public SecondaryStructureRMSD {</a>
+<a name="91"><span class="lineNum">      91 </span>            : public:</a>
+<a name="92"><span class="lineNum">      92 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit ParabetaRMSD(const ActionOptions&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            : };</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12524 : PLUMED_REGISTER_ACTION(ParabetaRMSD,&quot;PARABETARMSD&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         12 : void ParabetaRMSD::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         12 :   SecondaryStructureRMSD::registerKeywords( keys );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         24 :   keys.add(&quot;compulsory&quot;,&quot;STYLE&quot;,&quot;all&quot;,&quot;Parallel beta sheets can either form in a single chain or from a pair of chains. If STYLE=all all &quot;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :            &quot;chain configuration with the appropriate geometry are counted.  If STYLE=inter &quot;</a>
+<a name="102"><span class="lineNum">     102 </span>            :            &quot;only sheet-like configurations involving two chains are counted, while if STYLE=intra &quot;</a>
+<a name="103"><span class="lineNum">     103 </span>            :            &quot;only sheet-like configurations involving a single chain are counted&quot;);</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         12 :   keys.use(&quot;STRANDS_CUTOFF&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         12 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         10 : ParabetaRMSD::ParabetaRMSD(const ActionOptions&amp;ao):</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   Action(ao),</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         10 :   SecondaryStructureRMSD(ao)</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : {</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // read in the backbone atoms</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         20 :   std::vector&lt;unsigned&gt; chains; readBackboneAtoms( &quot;protein&quot;, chains );</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   bool intra_chain(false), inter_chain(false);</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         20 :   std::string style; parse(&quot;STYLE&quot;,style);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         10 :   if( style==&quot;all&quot; ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     intra_chain=true; inter_chain=true;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :   } else if( style==&quot;inter&quot;) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :     intra_chain=false; inter_chain=true;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   } else if( style==&quot;intra&quot;) {</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     intra_chain=true; inter_chain=false;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   } else {</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :     error( style + &quot; is not a valid directive for the STYLE keyword&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :   // Align the atoms based on the positions of these two atoms</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         10 :   setAtomsFromStrands( 6, 21 );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            :   // This constructs all conceivable sections of antibeta sheet in the backbone of the chains</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         10 :   if( intra_chain ) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         10 :     unsigned nprevious=0; std::vector&lt;unsigned&gt; nlist(30);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        173 :     for(unsigned i=0; i&lt;chains.size(); ++i) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        163 :       if( chains[i]&lt;40 ) error(&quot;segment of backbone is not long enough to form an antiparallel beta hairpin. Each backbone fragment must contain a minimum of 8 residues&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :       // Loop over all possible triples in each 8 residue segment of protein</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        163 :       unsigned nres=chains[i]/5;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        163 :       if( chains[i]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        167 :       for(unsigned ires=0; ires&lt;nres-8; ires++) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         14 :         for(unsigned jres=ires+6; jres&lt;nres-2; jres++) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        160 :           for(unsigned k=0; k&lt;15; ++k) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        150 :             nlist[k]=nprevious + ires*5+k;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        150 :             nlist[k+15]=nprevious + jres*5+k;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :           }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         10 :           addColvar( nlist );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :         }</a>
+<a name="145"><span class="lineNum">     145 </span>            :       }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        163 :       nprevious+=chains[i];</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span>            :   // This constructs all conceivable sections of antibeta sheet that form between chains</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         10 :   if( inter_chain ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         11 :     if( chains.size()==1 &amp;&amp; style!=&quot;all&quot; ) error(&quot;there is only one chain defined so cannot use inter_chain option&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         10 :     std::vector&lt;unsigned&gt; nlist(30);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        163 :     for(unsigned ichain=1; ichain&lt;chains.size(); ++ichain) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1530 :       unsigned iprev=0; for(unsigned i=0; i&lt;ichain; ++i) iprev+=chains[i];</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        153 :       unsigned inres=chains[ichain]/5;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        153 :       if( chains[ichain]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1071 :       for(unsigned ires=0; ires&lt;inres-2; ++ires) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       9180 :         for(unsigned jchain=0; jchain&lt;ichain; ++jchain) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      52326 :           unsigned jprev=0; for(unsigned i=0; i&lt;jchain; ++i) jprev+=chains[i];</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       8262 :           unsigned jnres=chains[jchain]/5;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       8262 :           if( chains[jchain]%5!=0 ) error(&quot;backbone segment received does not contain a multiple of five residues&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">      57834 :           for(unsigned jres=0; jres&lt;jnres-2; ++jres) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     793152 :             for(unsigned k=0; k&lt;15; ++k) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     743580 :               nlist[k]=iprev + ires*5+k;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">     743580 :               nlist[k+15]=jprev + jres*5+k;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :             }</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      49572 :             addColvar( nlist );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :           }</a>
+<a name="169"><span class="lineNum">     169 </span>            :         }</a>
+<a name="170"><span class="lineNum">     170 </span>            :       }</a>
+<a name="171"><span class="lineNum">     171 </span>            :     }</a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // Build the reference structure ( in angstroms )</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         10 :   std::vector&lt;Vector&gt; reference(30);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         10 :   reference[0]=Vector( 1.244, -4.620, -2.127); // N    i</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         10 :   reference[1]=Vector(-0.016, -4.500, -1.395); // CA</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         10 :   reference[2]=Vector( 0.105, -5.089,  0.024); // CB</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         10 :   reference[3]=Vector(-0.287, -3.000, -1.301); // C</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         10 :   reference[4]=Vector( 0.550, -2.245, -0.822); // O</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         10 :   reference[5]=Vector(-1.445, -2.551, -1.779); // N    i+1</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         10 :   reference[6]=Vector(-1.752, -1.130, -1.677); // CA</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         10 :   reference[7]=Vector(-2.113, -0.550, -3.059); // CB</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         10 :   reference[8]=Vector(-2.906, -0.961, -0.689); // C</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         10 :   reference[9]=Vector(-3.867, -1.738, -0.695); // O</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         10 :   reference[10]=Vector(-2.774,  0.034,  0.190); // N    i+2</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         10 :   reference[11]=Vector(-3.788,  0.331,  1.201); // CA</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         10 :   reference[12]=Vector(-3.188,  0.300,  2.624); // CB</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         10 :   reference[13]=Vector(-4.294,  1.743,  0.937); // C</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         10 :   reference[14]=Vector(-3.503,  2.671,  0.821); // O</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         10 :   reference[15]=Vector( 4.746, -2.363,  0.188); // N    j</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         10 :   reference[16]=Vector( 3.427, -1.839,  0.545); // CA</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         10 :   reference[17]=Vector( 3.135, -1.958,  2.074); // CB</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         10 :   reference[18]=Vector( 3.346, -0.365,  0.181); // C</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         10 :   reference[19]=Vector( 4.237,  0.412,  0.521); // O</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         10 :   reference[20]=Vector( 2.261,  0.013, -0.487); // N    j+1</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         10 :   reference[21]=Vector( 2.024,  1.401, -0.875); // CA</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         10 :   reference[22]=Vector( 1.489,  1.514, -2.313); // CB</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         10 :   reference[23]=Vector( 0.914,  1.902,  0.044); // C</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         10 :   reference[24]=Vector(-0.173,  1.330,  0.052); // O</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         10 :   reference[25]=Vector( 1.202,  2.940,  0.828); // N    j+2</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         10 :   reference[26]=Vector( 0.190,  3.507,  1.718); // CA</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         10 :   reference[27]=Vector( 0.772,  3.801,  3.104); // CB</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         10 :   reference[28]=Vector(-0.229,  4.791,  1.038); // C</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         10 :   reference[29]=Vector( 0.523,  5.771,  0.996); // O</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   // Store the secondary structure ( last number makes sure we convert to internal units nm )</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         10 :   setSecondaryStructure( reference, 0.17/atoms.getUnits().getLength(), 0.1/atoms.getUnits().getLength() );</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         10 :   reference[0]=Vector(-1.439, -5.122, -1.144); // N    i</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         10 :   reference[1]=Vector(-0.816, -3.803, -1.013); // CA</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         10 :   reference[2]=Vector( 0.099, -3.509, -2.206); // CB</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         10 :   reference[3]=Vector(-1.928, -2.770, -0.952); // C</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         10 :   reference[4]=Vector(-2.991, -2.970, -1.551); // O</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         10 :   reference[5]=Vector(-1.698, -1.687, -0.215); // N    i+1</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         10 :   reference[6]=Vector(-2.681, -0.613, -0.143); // CA</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         10 :   reference[7]=Vector(-3.323, -0.477,  1.267); // CB</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         10 :   reference[8]=Vector(-1.984,  0.681, -0.574); // C</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         10 :   reference[9]=Vector(-0.807,  0.921, -0.273); // O</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         10 :   reference[10]=Vector(-2.716,  1.492, -1.329); // N    i+2</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         10 :   reference[11]=Vector(-2.196,  2.731, -1.883); // CA</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         10 :   reference[12]=Vector(-2.263,  2.692, -3.418); // CB</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         10 :   reference[13]=Vector(-2.989,  3.949, -1.433); // C</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         10 :   reference[14]=Vector(-4.214,  3.989, -1.583); // O</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         10 :   reference[15]=Vector( 2.464, -4.352,  2.149); // N    j</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         10 :   reference[16]=Vector( 3.078, -3.170,  1.541); // CA</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         10 :   reference[17]=Vector( 3.398, -3.415,  0.060); // CB</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         10 :   reference[18]=Vector( 2.080, -2.021,  1.639); // C</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         10 :   reference[19]=Vector( 0.938, -2.178,  1.225); // O</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         10 :   reference[20]=Vector( 2.525, -0.886,  2.183); // N    j+1</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         10 :   reference[21]=Vector( 1.692,  0.303,  2.346); // CA</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         10 :   reference[22]=Vector( 1.541,  0.665,  3.842); // CB</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         10 :   reference[23]=Vector( 2.420,  1.410,  1.608); // C</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         10 :   reference[24]=Vector( 3.567,  1.733,  1.937); // O</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         10 :   reference[25]=Vector( 1.758,  1.976,  0.600); // N    j+2</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         10 :   reference[26]=Vector( 2.373,  2.987, -0.238); // CA</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         10 :   reference[27]=Vector( 2.367,  2.527, -1.720); // CB</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         10 :   reference[28]=Vector( 1.684,  4.331, -0.148); // C</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         10 :   reference[29]=Vector( 0.486,  4.430, -0.415); // O</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   // Store the secondary structure ( last number makes sure we convert to internal units nm )</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         10 :   setSecondaryStructure( reference, 0.17/atoms.getUnits().getLength(), 0.1/atoms.getUnits().getLength() );</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         10 : }</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/SecondaryStructureRMSD.cpp.func-sort-c.html b/coverage/secondarystructure/SecondaryStructureRMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cb231afa3c
--- /dev/null
+++ b/coverage/secondarystructure/SecondaryStructureRMSD.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/SecondaryStructureRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - SecondaryStructureRMSD.cpp<span style="font-size: 80%;"> (<a href="SecondaryStructureRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryHi">94.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SecondaryStructureRMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#71">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#105">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD19setAtomsFromStrandsERKjS3_</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#109">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD17readBackboneAtomsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#71">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDD2Ev</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#32">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#147">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD21setSecondaryStructureERSt6vectorINS_13VectorGenericILj3EEESaIS4_EEdd</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#100">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#261">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD5applyEv</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#185">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD9calculateEv</a></td>
+              <td class="coverFnHi">2568</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#136">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD9addColvarERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">99342</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#189">_ZNK4PLMD18secondarystructure22SecondaryStructureRMSD11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">400032</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/SecondaryStructureRMSD.cpp.func.html b/coverage/secondarystructure/SecondaryStructureRMSD.cpp.func.html
new file mode 100644
index 0000000000..8f40463922
--- /dev/null
+++ b/coverage/secondarystructure/SecondaryStructureRMSD.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/SecondaryStructureRMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - SecondaryStructureRMSD.cpp<span style="font-size: 80%;"> (<a href="SecondaryStructureRMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryHi">94.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SecondaryStructureRMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#32">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#109">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD17readBackboneAtomsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#100">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD17turnOnDerivativesEv</a></td>
+              <td class="coverFnHi">62</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#105">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD19setAtomsFromStrandsERKjS3_</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#147">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD21setSecondaryStructureERSt6vectorINS_13VectorGenericILj3EEESaIS4_EEdd</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#261">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD5applyEv</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#136">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD9addColvarERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">99342</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#185">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD9calculateEv</a></td>
+              <td class="coverFnHi">2568</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#71">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#71">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSDD2Ev</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.cpp.gcov.html#189">_ZNK4PLMD18secondarystructure22SecondaryStructureRMSD11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">400032</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/SecondaryStructureRMSD.cpp.gcov.html b/coverage/secondarystructure/SecondaryStructureRMSD.cpp.gcov.html
new file mode 100644
index 0000000000..2b1e4db3a6
--- /dev/null
+++ b/coverage/secondarystructure/SecondaryStructureRMSD.cpp.gcov.html
@@ -0,0 +1,344 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/SecondaryStructureRMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - SecondaryStructureRMSD.cpp<span style="font-size: 80%;"> (source / <a href="SecondaryStructureRMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">138</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntryHi">94.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SecondaryStructureRMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;vesselbase/Vessel.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;reference/MetricRegister.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;reference/SingleDomainRMSD.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace secondarystructure {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         31 : void SecondaryStructureRMSD::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         31 :   Action::registerKeywords( keys );</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         31 :   ActionWithValue::registerKeywords( keys );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         31 :   ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         62 :   keys.add(&quot;residues&quot;,&quot;RESIDUES&quot;,&quot;this command is used to specify the set of residues that could conceivably form part of the secondary structure. &quot;</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :            &quot;It is possible to use residues numbers as the various chains and residues should have been identified else using an instance of the &quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :            &quot;\\ref MOLINFO action. If you wish to use all the residues from all the chains in your system you can do so by &quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            :            &quot;specifying all. Alternatively, if you wish to use a subset of the residues you can specify the particular residues &quot;</a>
+<a name="42"><span class="lineNum">      42 </span>            :            &quot;you are interested in as a list of numbers. Please be aware that to form secondary structure elements your chain &quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            :            &quot;must contain at least N residues, where N is dependent on the particular secondary structure you are interested in. &quot;</a>
+<a name="44"><span class="lineNum">      44 </span>            :            &quot;As such if you define portions of the chain with fewer than N residues the code will crash.&quot;);</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         62 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;DRMSD&quot;,&quot;the manner in which RMSD alignment is performed. Should be OPTIMAL, SIMPLE or DRMSD. &quot;</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :            &quot;For more details on the OPTIMAL and SIMPLE methods see \\ref RMSD. For more details on the &quot;</a>
+<a name="47"><span class="lineNum">      47 </span>            :            &quot;DRMSD method see \\ref DRMSD.&quot;);</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         62 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         62 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;0.08&quot;,&quot;The r_0 parameter of the switching function.&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         62 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;The d_0 parameter of the switching function&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         62 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;8&quot;,&quot;The n parameter of the switching function&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         62 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;12&quot;,&quot;The m parameter of the switching function&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         62 :   keys.reserve(&quot;optional&quot;,&quot;STRANDS_CUTOFF&quot;,&quot;If in a segment of protein the two strands are further apart then the calculation &quot;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :                &quot;of the actual RMSD is skipped as the structure is very far from being beta-sheet like. &quot;</a>
+<a name="55"><span class="lineNum">      55 </span>            :                &quot;This keyword speeds up the calculation enormously when you are using the LESS_THAN option. &quot;</a>
+<a name="56"><span class="lineNum">      56 </span>            :                &quot;However, if you are using some other option, then this cannot be used&quot;);</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         62 :   keys.addFlag(&quot;VERBOSE&quot;,false,&quot;write a more detailed output&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         62 :   keys.add(&quot;hidden&quot;,&quot;NL_STRIDE&quot;,&quot;the frequency with which the neighbor list should be updated. Between neighbour list update steps all quantities &quot;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :            &quot;that contributed less than TOL at the previous neighbor list update step are ignored.&quot;);</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         31 :   ActionWithVessel::registerKeywords( keys );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        155 :   keys.use(&quot;LESS_THAN&quot;); keys.use(&quot;MIN&quot;); keys.use(&quot;ALT_MIN&quot;); keys.use(&quot;LOWEST&quot;); keys.use(&quot;HIGHEST&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         31 :   keys.setComponentsIntroduction(&quot;By default this Action calculates the number of structural units that are within a certain &quot;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :                                  &quot;distance of a idealized secondary structure element. This quantity can then be referenced &quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            :                                  &quot;elsewhere in the input by using the label of the action. However, this Action can also be used to &quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            :                                  &quot;calculate the following quantities by using the keywords as described below.  The quantities then &quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            :                                  &quot;calculated can be referenced using the label of the action followed by a dot and then the name &quot;</a>
+<a name="67"><span class="lineNum">      67 </span>            :                                  &quot;from the table below.  Please note that you can use the LESS_THAN keyword more than once.  The resulting &quot;</a>
+<a name="68"><span class="lineNum">      68 </span>            :                                  &quot;components will be labelled &lt;em&gt;label&lt;/em&gt;.lessthan-1, &lt;em&gt;label&lt;/em&gt;.lessthan-2 and so on unless you &quot;</a>
+<a name="69"><span class="lineNum">      69 </span>            :                                  &quot;exploit the fact that these labels can be given custom labels by using the LABEL keyword in the &quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :                                  &quot;description of you LESS_THAN function that you are computing&quot;);</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         31 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         25 : SecondaryStructureRMSD::SecondaryStructureRMSD(const ActionOptions&amp;ao):</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   Action(ao),</a>
+<a name="75"><span class="lineNum">      75 </span>            :   ActionAtomistic(ao),</a>
+<a name="76"><span class="lineNum">      76 </span>            :   ActionWithValue(ao),</a>
+<a name="77"><span class="lineNum">      77 </span>            :   ActionWithVessel(ao),</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         25 :   nopbc(false),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         25 :   align_strands(false),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         25 :   s_cutoff2(0),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         25 :   align_atom_1(0),</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         25 :   align_atom_2(0)</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         50 :   parse(&quot;TYPE&quot;,alignType); parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         25 :   log.printf(&quot;  distances from secondary structure elements are calculated using %s algorithm\n&quot;,alignType.c_str() );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         50 :   log&lt;&lt;&quot;  Bibliography &quot;&lt;&lt;plumed.cite(&quot;Pietrucci and Laio, J. Chem. Theory Comput. 5, 2197 (2009)&quot;); log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         25 :   parseFlag(&quot;VERBOSE&quot;,verbose_output);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         50 :   if( keywords.exists(&quot;STRANDS_CUTOFF&quot;) ) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         22 :     double s_cutoff = 0;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         22 :     parse(&quot;STRANDS_CUTOFF&quot;,s_cutoff); align_strands=true;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         22 :     if( s_cutoff&gt;0) log.printf(&quot;  ignoring contributions from strands that are more than %f apart\n&quot;,s_cutoff);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         22 :     s_cutoff2=s_cutoff*s_cutoff;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         25 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         25 : SecondaryStructureRMSD::~SecondaryStructureRMSD() {</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : // destructor needed to delete forward declarated objects</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         50 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         62 : void SecondaryStructureRMSD::turnOnDerivatives() {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         62 :   ActionWithValue::turnOnDerivatives();</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         62 :   needsDerivatives();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         62 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         22 : void SecondaryStructureRMSD::setAtomsFromStrands( const unsigned&amp; atom1, const unsigned&amp; atom2 ) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         22 :   align_atom_1=atom1; align_atom_2=atom2;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         22 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         25 : void SecondaryStructureRMSD::readBackboneAtoms( const std::string&amp; moltype, std::vector&lt;unsigned&gt;&amp; chain_lengths ) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         25 :   auto* moldat=plumed.getActionSet().selectLatest&lt;GenericMolInfo*&gt;(this);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         25 :   if( ! moldat ) error(&quot;Unable to find MOLINFO in input&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         25 :   std::vector&lt;std::string&gt; resstrings; parseVector( &quot;RESIDUES&quot;, resstrings );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         25 :   if( !verbose_output ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         25 :     if(resstrings.size()==0) error(&quot;residues are not defined, check the keyword RESIDUES&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         25 :     else if(resstrings[0]==&quot;all&quot;) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         21 :       log.printf(&quot;  examining all possible secondary structure combinations\n&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     } else {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          4 :       log.printf(&quot;  examining secondary structure in residue positions : %s \n&quot;,resstrings[0].c_str() );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          6 :       for(unsigned i=1; i&lt;resstrings.size(); ++i) log.printf(&quot;, %s&quot;,resstrings[i].c_str() );</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :     }</a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            :   std::vector&lt; std::vector&lt;AtomNumber&gt; &gt; backatoms;</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         25 :   moldat-&gt;getBackbone( resstrings, moltype, backatoms );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         25 :   chain_lengths.resize( backatoms.size() );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        358 :   for(unsigned i=0; i&lt;backatoms.size(); ++i) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        333 :     chain_lengths[i]=backatoms[i].size();</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      13593 :     for(unsigned j=0; j&lt;backatoms[i].size(); ++j) all_atoms.push_back( backatoms[i][j] );</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   }</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         25 :   ActionAtomistic::requestAtoms( all_atoms );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         25 :   forcesToApply.resize( getNumberOfDerivatives() );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         25 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      99342 : void SecondaryStructureRMSD::addColvar( const std::vector&lt;unsigned&gt;&amp; newatoms ) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      99342 :   if( colvar_atoms.size()&gt;0 ) plumed_assert( colvar_atoms[0].size()==newatoms.size() );</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      99342 :   if( verbose_output ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     log.printf(&quot;  Secondary structure segment %u contains atoms : &quot;, static_cast&lt;unsigned&gt;(colvar_atoms.size()+1));</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;newatoms.size(); ++i) log.printf(&quot;%d &quot;,all_atoms[newatoms[i]].serial() );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      99342 :   addTaskToList( colvar_atoms.size() );</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      99342 :   colvar_atoms.push_back( newatoms );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      99342 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         35 : void SecondaryStructureRMSD::setSecondaryStructure( std::vector&lt;Vector&gt;&amp; structure, double bondlength, double units ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   // If we are in natural units get conversion factor from nm into natural length units</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         35 :   if( plumed.getAtoms().usingNaturalUnits() ) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :     error(&quot;cannot use this collective variable when using natural units&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         35 :   plumed_massert( !(align_strands &amp;&amp; align_atom_1==0 &amp;&amp; align_atom_2==0), &quot;you must use setAtomsFromStrands with strands cutoff&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Convert into correct units</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       1085 :   for(unsigned i=0; i&lt;structure.size(); ++i) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1050 :     structure[i][0]*=units; structure[i][1]*=units; structure[i][2]*=units;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         35 :   if( references.size()==0 ) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         25 :     readVesselKeywords();</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         25 :     if( getNumberOfVessels()==0 ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          4 :       double r0; parse(&quot;R_0&quot;,r0); double d0; parse(&quot;D_0&quot;,d0);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          4 :       int nn; parse(&quot;NN&quot;,nn); int mm; parse(&quot;MM&quot;,mm);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 :       std::ostringstream ostr;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :       ostr&lt;&lt;&quot;RATIONAL R_0=&quot;&lt;&lt;r0&lt;&lt;&quot; D_0=&quot;&lt;&lt;d0&lt;&lt;&quot; NN=&quot;&lt;&lt;nn&lt;&lt;&quot; MM=&quot;&lt;&lt;mm;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          2 :       std::string input=ostr.str(); addVessel( &quot;LESS_THAN&quot;, input, -1 ); // -1 here means that this value will be named getLabel()</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          2 :       readVesselKeywords();  // This makes sure resizing is done</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          2 :     }</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :   // Set the reference structure</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         35 :   references.emplace_back( metricRegister().create&lt;SingleDomainRMSD&gt;( alignType ) );</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         35 :   unsigned nn=references.size()-1;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         35 :   std::vector&lt;double&gt; align( structure.size(), 1.0 ), displace( structure.size(), 1.0 );</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         35 :   references[nn]-&gt;setBoundsOnDistances( true, bondlength );   // We always use pbc</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         35 :   references[nn]-&gt;setReferenceAtoms( structure, align, displace );</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : //  references[nn]-&gt;setNumberOfAtoms( structure.size() );</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   // And prepare the task list</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         35 :   deactivateAllTasks();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">     148959 :   for(unsigned i=0; i&lt;getFullNumberOfTasks(); ++i) taskFlags[i]=1;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         35 :   lockContributors();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         35 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       2568 : void SecondaryStructureRMSD::calculate() {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       2568 :   runAllTasks();</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       2568 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     400032 : void SecondaryStructureRMSD::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   // Retrieve the positions</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">     400032 :   std::vector&lt;Vector&gt; pos( references[0]-&gt;getNumberOfAtoms() );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     400032 :   const unsigned n=pos.size();</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">   12400992 :   for(unsigned i=0; i&lt;n; ++i) pos[i]=ActionAtomistic::getPosition( getAtomIndex(current,i) );</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            :   // This does strands cutoff</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">     400032 :   Vector distance;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     400032 :   if( nopbc ) distance=delta( pos[align_atom_1],pos[align_atom_2] );</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">     400032 :   else distance=pbcDistance( pos[align_atom_1],pos[align_atom_2] );</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     400032 :   if( s_cutoff2&gt;0 ) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     397524 :     if( distance.modulo2()&gt;s_cutoff2 ) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       myvals.setValue( 0, 0.0 );</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     360914 :       return;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   // This aligns the two strands if this is required</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      39118 :   if( alignType!=&quot;DRMSD&quot; &amp;&amp; align_strands &amp;&amp; !nopbc ) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     382260 :     for(unsigned i=0; i&lt;14; ++i) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">     356776 :       const Vector &amp; first (pos[i]);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     356776 :       Vector &amp; second (pos[i+1]);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">     356776 :       second=first+pbcDistance(first,second);</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :     }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">     356776 :     for(unsigned i=16; i&lt;n-1; ++i) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     331292 :       const Vector &amp; first (pos[i]);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     331292 :       Vector &amp; second (pos[i+1]);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     331292 :       second=first+pbcDistance(first,second);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :     }</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      25484 :     Vector origin_old, origin_new; origin_old=pos[align_atom_2];</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      25484 :     origin_new=pos[align_atom_1]+distance;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">     407744 :     for(unsigned i=15; i&lt;30; ++i) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     382260 :       pos[i]+=( origin_new - origin_old );</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :     }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      13634 :   } else if( alignType!=&quot;DRMSD&quot; &amp;&amp; !nopbc ) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;n-1; ++i) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       const Vector &amp; first (pos[i]);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :       Vector &amp; second (pos[i+1]);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       second=first+pbcDistance(first,second);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :     }</a>
+<a name="231"><span class="lineNum">     231 </span>            :   }</a>
+<a name="232"><span class="lineNum">     232 </span>            :   // Create a holder for the derivatives</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      39118 :   ReferenceValuePack mypack( 0, pos.size(), myvals ); mypack.setValIndex( 1 );</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">    1212658 :   for(unsigned i=0; i&lt;n; ++i) mypack.setAtomIndex( i, getAtomIndex(current,i) );</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            :   // And now calculate the RMSD</a>
+<a name="237"><span class="lineNum">     237 </span>            :   const Pbc&amp; pbc=getPbc();</a>
+<a name="238"><span class="lineNum">     238 </span>            :   unsigned closest=0;</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      39118 :   double r = references[0]-&gt;calculate( pos, pbc, mypack, false );</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      39118 :   const unsigned rs = references.size();</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">      57377 :   for(unsigned i=1; i&lt;rs; ++i) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">      18259 :     mypack.setValIndex( i+1 );</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      18259 :     double nr=references[i]-&gt;calculate( pos, pbc, mypack, false );</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">      18259 :     if( nr&lt;r ) { closest=i; r=nr; }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            :   // Transfer everything to the value</a>
+<a name="248"><span class="lineNum">     248 </span>            :   myvals.setValue( 0, 1.0 ); myvals.setValue( 1, r );</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      39118 :   if( closest&gt;0 ) mypack.moveDerivatives( closest+1, 1 );</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">      39118 :   if( !mypack.virialWasSet() ) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">      25484 :     Tensor vir;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      25484 :     const unsigned cacs = colvar_atoms[current].size();</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">     790004 :     for(unsigned i=0; i&lt;cacs; ++i) {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">     764520 :       vir+=(-1.0*Tensor( pos[i], mypack.getAtomDerivative(i) ));</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :     }</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">      25484 :     mypack.setValIndex(1); mypack.addBoxDerivatives( vir );</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            :   return;</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">      39118 : }</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        192 : void SecondaryStructureRMSD::apply() {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        192 :   if( getForcesFromVessels( forcesToApply ) ) setForcesOnAtoms( forcesToApply );</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        192 : }</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+<a name="268"><span class="lineNum">     268 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/SecondaryStructureRMSD.h.func-sort-c.html b/coverage/secondarystructure/SecondaryStructureRMSD.h.func-sort-c.html
new file mode 100644
index 0000000000..c9d8edd878
--- /dev/null
+++ b/coverage/secondarystructure/SecondaryStructureRMSD.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/SecondaryStructureRMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - SecondaryStructureRMSD.h<span style="font-size: 80%;"> (<a href="SecondaryStructureRMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SecondaryStructureRMSD.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.h.gcov.html#81">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD10isPeriodicEv</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.h.gcov.html#85">_ZNK4PLMD18secondarystructure22SecondaryStructureRMSD21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">5424</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.h.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">5607</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/SecondaryStructureRMSD.h.func.html b/coverage/secondarystructure/SecondaryStructureRMSD.h.func.html
new file mode 100644
index 0000000000..0a840cb3a0
--- /dev/null
+++ b/coverage/secondarystructure/SecondaryStructureRMSD.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/SecondaryStructureRMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - SecondaryStructureRMSD.h<span style="font-size: 80%;"> (<a href="SecondaryStructureRMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SecondaryStructureRMSD.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.h.gcov.html#81">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD10isPeriodicEv</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.h.gcov.html#96">_ZN4PLMD18secondarystructure22SecondaryStructureRMSD22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">5607</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SecondaryStructureRMSD.h.gcov.html#85">_ZNK4PLMD18secondarystructure22SecondaryStructureRMSD21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">5424</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/SecondaryStructureRMSD.h.gcov.html b/coverage/secondarystructure/SecondaryStructureRMSD.h.gcov.html
new file mode 100644
index 0000000000..a623471f28
--- /dev/null
+++ b/coverage/secondarystructure/SecondaryStructureRMSD.h.gcov.html
@@ -0,0 +1,186 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure/SecondaryStructureRMSD.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">secondarystructure</a> - SecondaryStructureRMSD.h<span style="font-size: 80%;"> (source / <a href="SecondaryStructureRMSD.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_secondarystructure_SecondaryStructureRMSD_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_secondarystructure_SecondaryStructureRMSD_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;vesselbase/ActionWithVessel.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class SingleDomainRMSD;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace secondarystructure {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Base action for calculating things like AlphRMSD, AntibetaRMSD, etc</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class SecondaryStructureRMSD :</a>
+<a name="39"><span class="lineNum">      39 </span>            :   public ActionAtomistic,</a>
+<a name="40"><span class="lineNum">      40 </span>            :   public ActionWithValue,</a>
+<a name="41"><span class="lineNum">      41 </span>            :   public vesselbase::ActionWithVessel</a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span>            : private:</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Are we operating without periodic boundary conditions</a>
+<a name="45"><span class="lineNum">      45 </span>            :   bool nopbc;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// The type of rmsd we are calculating</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::string alignType;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// List of all the atoms we require</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::vector&lt;AtomNumber&gt; all_atoms;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// The atoms involved in each of the secondary structure segments</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt; std::vector&lt;unsigned&gt; &gt; colvar_atoms;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// The list of reference configurations</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;std::unique_ptr&lt;SingleDomainRMSD&gt;&gt; references;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Variables for strands cutoff</a>
+<a name="55"><span class="lineNum">      55 </span>            :   bool align_strands;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   double s_cutoff2;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   unsigned align_atom_1, align_atom_2;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool verbose_output;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Tempory variables for getting positions of atoms and applying forces</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::vector&lt;double&gt; forcesToApply;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Get the index of an atom</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned getAtomIndex( const unsigned&amp; current, const unsigned&amp; iatom ) const ;</a>
+<a name="63"><span class="lineNum">      63 </span>            : protected:</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Get the atoms in the backbone</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void readBackboneAtoms( const std::string&amp; backnames, std::vector&lt;unsigned&gt;&amp; chain_lengths );</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Add a set of atoms to calculat ethe rmsd from</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void addColvar( const std::vector&lt;unsigned&gt;&amp; newatoms );</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Set a reference configuration</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void setSecondaryStructure( std::vector&lt;Vector&gt;&amp; structure, double bondlength, double units );</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Setup a pair of atoms to use for strands cutoff</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void setAtomsFromStrands( const unsigned&amp; atom1, const unsigned&amp; atom2 );</a>
+<a name="72"><span class="lineNum">      72 </span>            : public:</a>
+<a name="73"><span class="lineNum">      73 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="74"><span class="lineNum">      74 </span>            :   explicit SecondaryStructureRMSD(const ActionOptions&amp;);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   virtual ~SecondaryStructureRMSD();</a>
+<a name="76"><span class="lineNum">      76 </span>            :   unsigned getNumberOfFunctionsInAction();</a>
+<a name="77"><span class="lineNum">      77 </span>            :   unsigned getNumberOfDerivatives() override;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void turnOnDerivatives() override;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void calculate() override;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void apply() override;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         25 :   bool isPeriodic() override { return false; }</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : };</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : inline</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       5424 : unsigned SecondaryStructureRMSD::getNumberOfQuantities() const {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       5424 :   return 1 + references.size();</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : inline</a>
+<a name="93"><span class="lineNum">      93 </span>            : unsigned SecondaryStructureRMSD::getNumberOfFunctionsInAction() {</a>
+<a name="94"><span class="lineNum">      94 </span>            :   return colvar_atoms.size();</a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : inline</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       5607 : unsigned SecondaryStructureRMSD::getNumberOfDerivatives() {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       5607 :   return 3*getNumberOfAtoms()+9;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : inline</a>
+<a name="103"><span class="lineNum">     103 </span>            : unsigned SecondaryStructureRMSD::getAtomIndex( const unsigned&amp; current, const unsigned&amp; iatom ) const {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">   13174500 :   return colvar_atoms[current][iatom];</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/index-sort-f.html b/coverage/secondarystructure/index-sort-f.html
new file mode 100644
index 0000000000..f6527fd20a
--- /dev/null
+++ b/coverage/secondarystructure/index-sort-f.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - secondarystructure</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">376</td>
+            <td class="headerCovTableEntry">389</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">82.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SecondaryStructureRMSD.cpp.gcov.html">SecondaryStructureRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.5%"><img src="../snow.png" width=5 height=10 alt="94.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.5&nbsp;%</td>
+      <td class="coverNumHi">138 / 146</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParabetaRMSD.cpp.gcov.html">ParabetaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">106 / 109</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlphaRMSD.cpp.gcov.html">AlphaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 50</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AntibetaRMSD.cpp.gcov.html">AntibetaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">76 / 78</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SecondaryStructureRMSD.h.gcov.html">SecondaryStructureRMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/index-sort-l.html b/coverage/secondarystructure/index-sort-l.html
new file mode 100644
index 0000000000..0af2166965
--- /dev/null
+++ b/coverage/secondarystructure/index-sort-l.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - secondarystructure</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">376</td>
+            <td class="headerCovTableEntry">389</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">82.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SecondaryStructureRMSD.cpp.gcov.html">SecondaryStructureRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.5%"><img src="../snow.png" width=5 height=10 alt="94.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.5&nbsp;%</td>
+      <td class="coverNumHi">138 / 146</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParabetaRMSD.cpp.gcov.html">ParabetaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">106 / 109</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AntibetaRMSD.cpp.gcov.html">AntibetaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">76 / 78</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SecondaryStructureRMSD.h.gcov.html">SecondaryStructureRMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlphaRMSD.cpp.gcov.html">AlphaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 50</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/secondarystructure/index.html b/coverage/secondarystructure/index.html
new file mode 100644
index 0000000000..2c868e1452
--- /dev/null
+++ b/coverage/secondarystructure/index.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - secondarystructure</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - secondarystructure</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">376</td>
+            <td class="headerCovTableEntry">389</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">82.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AlphaRMSD.cpp.gcov.html">AlphaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">50 / 50</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AntibetaRMSD.cpp.gcov.html">AntibetaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">76 / 78</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ParabetaRMSD.cpp.gcov.html">ParabetaRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">106 / 109</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SecondaryStructureRMSD.cpp.gcov.html">SecondaryStructureRMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.5%"><img src="../snow.png" width=5 height=10 alt="94.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.5&nbsp;%</td>
+      <td class="coverNumHi">138 / 146</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="SecondaryStructureRMSD.h.gcov.html">SecondaryStructureRMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Load.cpp.func-sort-c.html b/coverage/setup/Load.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f7100f05dc
--- /dev/null
+++ b/coverage/setup/Load.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Load.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Load.cpp<span style="font-size: 80%;"> (<a href="Load.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Load.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#109">_ZN4PLMD5setup4LoadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#102">_ZN4PLMD5setup12_GLOBAL__N_117LoadRegisterMe1046createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#109">_ZN4PLMD5setup4LoadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#104">_ZN4PLMD5setup4Load16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#102">_ZN4PLMD5setup12_GLOBAL__N_117LoadRegisterMe104C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#102">_ZN4PLMD5setup12_GLOBAL__N_117LoadRegisterMe104D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Load.cpp.func.html b/coverage/setup/Load.cpp.func.html
new file mode 100644
index 0000000000..8619549171
--- /dev/null
+++ b/coverage/setup/Load.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Load.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Load.cpp<span style="font-size: 80%;"> (<a href="Load.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Load.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#102">_ZN4PLMD5setup12_GLOBAL__N_117LoadRegisterMe1046createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#102">_ZN4PLMD5setup12_GLOBAL__N_117LoadRegisterMe104C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#102">_ZN4PLMD5setup12_GLOBAL__N_117LoadRegisterMe104D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#104">_ZN4PLMD5setup4Load16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#109">_ZN4PLMD5setup4LoadC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Load.cpp.gcov.html#109">_ZN4PLMD5setup4LoadC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Load.cpp.gcov.html b/coverage/setup/Load.cpp.gcov.html
new file mode 100644
index 0000000000..41cd6ea239
--- /dev/null
+++ b/coverage/setup/Load.cpp.gcov.html
@@ -0,0 +1,199 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Load.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Load.cpp<span style="font-size: 80%;"> (source / <a href="Load.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionSetup.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace setup {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC GENERIC LOAD</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Loads a library, possibly defining new actions.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : It is available only</a>
+<a name="35"><span class="lineNum">      35 </span>            : on systems allowing for dynamic loading. It can also be fed with a cpp file,</a>
+<a name="36"><span class="lineNum">      36 </span>            : in which case the file is compiled first.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : If you have a shared object named extensions.so and want to</a>
+<a name="41"><span class="lineNum">      41 </span>            : use the functions implemented within it within PLUMED you can</a>
+<a name="42"><span class="lineNum">      42 </span>            : load it with the following syntax</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : LOAD FILE=extensions.so</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : As a more practical example, imagine that you want to make a</a>
+<a name="49"><span class="lineNum">      49 </span>            : small change to one collective variable that is already implemented</a>
+<a name="50"><span class="lineNum">      50 </span>            : in PLUMED, say \ref DISTANCE . Copy the file `src/colvar/Distance.cpp`</a>
+<a name="51"><span class="lineNum">      51 </span>            : into your work directory, rename it as `Distance2.cpp`</a>
+<a name="52"><span class="lineNum">      52 </span>            : and  edit it as you wish. It might be better</a>
+<a name="53"><span class="lineNum">      53 </span>            : to also replace any occurrence of the string DISTANCE within the file</a>
+<a name="54"><span class="lineNum">      54 </span>            : with DISTANCE2, so that both old and new implementation will be available</a>
+<a name="55"><span class="lineNum">      55 </span>            : with different names. Then you can compile it into a shared object using</a>
+<a name="56"><span class="lineNum">      56 </span>            : \verbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : &gt; plumed mklib Distance2.cpp</a>
+<a name="58"><span class="lineNum">      58 </span>            : \endverbatim</a>
+<a name="59"><span class="lineNum">      59 </span>            : This will generate a file `Distance2.so` (or `Distance2.dylib` on a mac)</a>
+<a name="60"><span class="lineNum">      60 </span>            : that can be loaded.</a>
+<a name="61"><span class="lineNum">      61 </span>            : Now you can use your new implementation with the following input</a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : # load the new library</a>
+<a name="64"><span class="lineNum">      64 </span>            : LOAD FILE=Distance2.so</a>
+<a name="65"><span class="lineNum">      65 </span>            : # compute standard distance</a>
+<a name="66"><span class="lineNum">      66 </span>            : d: DISTANCE ATOMS=1,10</a>
+<a name="67"><span class="lineNum">      67 </span>            : # compute modified distance</a>
+<a name="68"><span class="lineNum">      68 </span>            : d2: DISTANCE2 ATOMS=1,10</a>
+<a name="69"><span class="lineNum">      69 </span>            : # print them on a file</a>
+<a name="70"><span class="lineNum">      70 </span>            : PRINT ARG=d,d2 FILE=compare-them</a>
+<a name="71"><span class="lineNum">      71 </span>            : \endplumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : You can even skip the initial step and directly feed PLUMED</a>
+<a name="74"><span class="lineNum">      74 </span>            : with the `Distance2.cpp` file: it will be compiled on the fly.</a>
+<a name="75"><span class="lineNum">      75 </span>            : \plumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : # load the new definition</a>
+<a name="77"><span class="lineNum">      77 </span>            : # this is a cpp file so it will be compiled</a>
+<a name="78"><span class="lineNum">      78 </span>            : LOAD FILE=Distance2.cpp</a>
+<a name="79"><span class="lineNum">      79 </span>            : # compute standard distance</a>
+<a name="80"><span class="lineNum">      80 </span>            : d: DISTANCE ATOMS=1,10</a>
+<a name="81"><span class="lineNum">      81 </span>            : # compute modified distance</a>
+<a name="82"><span class="lineNum">      82 </span>            : d2: DISTANCE2 ATOMS=1,10</a>
+<a name="83"><span class="lineNum">      83 </span>            : # print them on a file</a>
+<a name="84"><span class="lineNum">      84 </span>            : PRINT ARG=d,d2 FILE=compare-them</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endplumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : This will allow to make quick tests while developing your own</a>
+<a name="88"><span class="lineNum">      88 </span>            : variables. Of course, after your implementation is ready you might</a>
+<a name="89"><span class="lineNum">      89 </span>            : want to add it to the PLUMED source tree and recompile</a>
+<a name="90"><span class="lineNum">      90 </span>            : the whole PLUMED.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : */</a>
+<a name="94"><span class="lineNum">      94 </span>            : //+ENDPLUMEDOC</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : class Load :</a>
+<a name="97"><span class="lineNum">      97 </span>            :   public virtual ActionSetup</a>
+<a name="98"><span class="lineNum">      98 </span>            : {</a>
+<a name="99"><span class="lineNum">      99 </span>            : public:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit Load(const ActionOptions&amp;ao);</a>
+<a name="102"><span class="lineNum">     102 </span>            : };</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      12507 : PLUMED_REGISTER_ACTION(Load,&quot;LOAD&quot;)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 : void Load::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          4 :   ActionSetup::registerKeywords(keys);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;file to be loaded&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 : Load::Load(const ActionOptions&amp;ao):</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   Action(ao),</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   ActionSetup(ao)</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : {</a>
+<a name="115"><span class="lineNum">     115 </span>            :   std::string f;</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          3 :   parse(&quot;FILE&quot;,f);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          2 :   plumed.load(f);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Restart.cpp.func-sort-c.html b/coverage/setup/Restart.cpp.func-sort-c.html
new file mode 100644
index 0000000000..68d9708fb8
--- /dev/null
+++ b/coverage/setup/Restart.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Restart.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Restart.cpp<span style="font-size: 80%;"> (<a href="Restart.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Restart.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#103">_ZN4PLMD5setup7RestartC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_119RestartRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#103">_ZN4PLMD5setup7RestartC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#98">_ZN4PLMD5setup7Restart16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_119RestartRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_119RestartRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Restart.cpp.func.html b/coverage/setup/Restart.cpp.func.html
new file mode 100644
index 0000000000..31f1343c8e
--- /dev/null
+++ b/coverage/setup/Restart.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Restart.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Restart.cpp<span style="font-size: 80%;"> (<a href="Restart.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Restart.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_119RestartRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_119RestartRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_119RestartRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#98">_ZN4PLMD5setup7Restart16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#103">_ZN4PLMD5setup7RestartC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Restart.cpp.gcov.html#103">_ZN4PLMD5setup7RestartC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Restart.cpp.gcov.html b/coverage/setup/Restart.cpp.gcov.html
new file mode 100644
index 0000000000..f80a58ea48
--- /dev/null
+++ b/coverage/setup/Restart.cpp.gcov.html
@@ -0,0 +1,201 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Restart.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Restart.cpp<span style="font-size: 80%;"> (source / <a href="Restart.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionSetup.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace setup {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC GENERIC RESTART</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Activate restart.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This is a Setup directive and, as such, should appear</a>
+<a name="35"><span class="lineNum">      35 </span>            : at the beginning of the input file. It influences the way</a>
+<a name="36"><span class="lineNum">      36 </span>            : PLUMED treat files open for writing (see also \ref Files).</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Notice that it is also possible to enable or disable restart on a per-action</a>
+<a name="39"><span class="lineNum">      39 </span>            : basis using the RESTART keyword on a single action. In this case,</a>
+<a name="40"><span class="lineNum">      40 </span>            : the keyword should be assigned a value. RESTART=AUTO means that global</a>
+<a name="41"><span class="lineNum">      41 </span>            : settings are used, RESTART=YES or RESTART=NO respectively enable</a>
+<a name="42"><span class="lineNum">      42 </span>            : and disable restart for that single action.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \attention</a>
+<a name="45"><span class="lineNum">      45 </span>            : This directive can have also other side effects, e.g. on \ref METAD</a>
+<a name="46"><span class="lineNum">      46 </span>            : and \ref PBMETAD and on some analysis action.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \par Examples</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : Using the following input:</a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : d: DISTANCE ATOMS=1,2</a>
+<a name="53"><span class="lineNum">      53 </span>            : PRINT ARG=d FILE=out</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endplumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : a new 'out' file will be created. If an old one is on the way, it will be automatically backed up.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : On the other hand, using the following input:</a>
+<a name="58"><span class="lineNum">      58 </span>            : \plumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : RESTART</a>
+<a name="60"><span class="lineNum">      60 </span>            : d: DISTANCE ATOMS=1,2</a>
+<a name="61"><span class="lineNum">      61 </span>            : PRINT ARG=d FILE=out</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : the file 'out' will be appended.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : In the following case, file out1 will be backed up and file out2 will be concatenated</a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : RESTART</a>
+<a name="68"><span class="lineNum">      68 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="69"><span class="lineNum">      69 </span>            : d2: DISTANCE ATOMS=1,2</a>
+<a name="70"><span class="lineNum">      70 </span>            : PRINT ARG=d1 FILE=out1 RESTART=NO</a>
+<a name="71"><span class="lineNum">      71 </span>            : PRINT ARG=d2 FILE=out2</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endplumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : In the following case, file out will backed up even if the MD code thinks that we</a>
+<a name="75"><span class="lineNum">      75 </span>            : are restarting. Notice that not all the MD code send to PLUMED information about restarts.</a>
+<a name="76"><span class="lineNum">      76 </span>            : If you are not sure, always put `RESTART` when you are restarting and nothing when you aren't</a>
+<a name="77"><span class="lineNum">      77 </span>            : \plumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : RESTART NO</a>
+<a name="79"><span class="lineNum">      79 </span>            : d1: DISTANCE ATOMS=1,2</a>
+<a name="80"><span class="lineNum">      80 </span>            : PRINT ARG=d1 FILE=out1</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endplumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : */</a>
+<a name="88"><span class="lineNum">      88 </span>            : //+ENDPLUMEDOC</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : class Restart :</a>
+<a name="91"><span class="lineNum">      91 </span>            :   public virtual ActionSetup</a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span>            : public:</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="95"><span class="lineNum">      95 </span>            :   explicit Restart(const ActionOptions&amp;ao);</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      12616 : PLUMED_REGISTER_ACTION(Restart,&quot;RESTART&quot;)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         58 : void Restart::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         58 :   ActionSetup::registerKeywords(keys);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        116 :   keys.addFlag(&quot;NO&quot;,false,&quot;switch off restart - can be used to override the behavior of the MD engine&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         58 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         56 : Restart::Restart(const ActionOptions&amp;ao):</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   Action(ao),</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         56 :   ActionSetup(ao)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         56 :   bool no=false;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         56 :   parseFlag(&quot;NO&quot;,no);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         56 :   bool md=plumed.getRestart();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        111 :   log&lt;&lt;&quot;  MD code &quot;&lt;&lt;(md?&quot;did&quot;:&quot;didn't&quot;)&lt;&lt;&quot; require restart\n&quot;;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         56 :   if(no) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :     if(md) log&lt;&lt;&quot;  Switching off restart\n&quot;;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          1 :     plumed.setRestart(false);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          1 :     log&lt;&lt;&quot;  Not restarting simulation: files will be backed up\n&quot;;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   } else {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         55 :     if(!md) log&lt;&lt;&quot;  Switching on restart\n&quot;;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         55 :     plumed.setRestart(true);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         55 :     log&lt;&lt;&quot;  Restarting simulation: files will be appended\n&quot;;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         56 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Units.cpp.func-sort-c.html b/coverage/setup/Units.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cb9d336b3a
--- /dev/null
+++ b/coverage/setup/Units.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Units.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Units.cpp<span style="font-size: 80%;"> (<a href="Units.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Units.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#108">_ZN4PLMD5setup5UnitsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_117UnitsRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#108">_ZN4PLMD5setup5UnitsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#98">_ZN4PLMD5setup5Units16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_117UnitsRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_117UnitsRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Units.cpp.func.html b/coverage/setup/Units.cpp.func.html
new file mode 100644
index 0000000000..efc121f75a
--- /dev/null
+++ b/coverage/setup/Units.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Units.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Units.cpp<span style="font-size: 80%;"> (<a href="Units.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Units.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_117UnitsRegisterMe986createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_117UnitsRegisterMe98C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#96">_ZN4PLMD5setup12_GLOBAL__N_117UnitsRegisterMe98D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#98">_ZN4PLMD5setup5Units16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#108">_ZN4PLMD5setup5UnitsC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#108">_ZN4PLMD5setup5UnitsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/Units.cpp.gcov.html b/coverage/setup/Units.cpp.gcov.html
new file mode 100644
index 0000000000..571e30f221
--- /dev/null
+++ b/coverage/setup/Units.cpp.gcov.html
@@ -0,0 +1,277 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup/Units.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">setup</a> - Units.cpp<span style="font-size: 80%;"> (source / <a href="Units.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">57</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;core/ActionSetup.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace setup {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC GENERIC UNITS</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : This command sets the internal units for the code.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : A new unit can be set by either</a>
+<a name="36"><span class="lineNum">      36 </span>            : specifying a conversion factor from the plumed default unit or by using a string</a>
+<a name="37"><span class="lineNum">      37 </span>            : corresponding to one of the defined units given below.  This directive MUST</a>
+<a name="38"><span class="lineNum">      38 </span>            : appear at the BEGINNING of the plumed.dat file.  The same units must be used</a>
+<a name="39"><span class="lineNum">      39 </span>            : throughout the plumed.dat file.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : Notice that all input/output will then be made using the specified units.</a>
+<a name="42"><span class="lineNum">      42 </span>            : That is: all the input parameters, all the output files, etc. The only</a>
+<a name="43"><span class="lineNum">      43 </span>            : exceptions are file formats for which there is a specific convention concerning</a>
+<a name="44"><span class="lineNum">      44 </span>            : the units. For example, trajectories written in .gro format (with \ref DUMPATOMS)</a>
+<a name="45"><span class="lineNum">      45 </span>            : are going to be always in nm.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The following strings can be used to specify units. Note that the strings are</a>
+<a name="48"><span class="lineNum">      48 </span>            : case sensitive.</a>
+<a name="49"><span class="lineNum">      49 </span>            : - LENGTH: nm (default), A (for Angstrom), um (for micrometer), Bohr (0.052917721067 nm)</a>
+<a name="50"><span class="lineNum">      50 </span>            : - ENERGY: kj/mol (default), j/mol, kcal/mol (4.184 kj/mol), eV (96.48530749925792 kj/mol), Ha (for Hartree, 2625.499638 kj/mol)</a>
+<a name="51"><span class="lineNum">      51 </span>            : - TIME: ps (default), fs, ns, atomic (2.418884326509e-5 ps)</a>
+<a name="52"><span class="lineNum">      52 </span>            : - MASS: amu (default)</a>
+<a name="53"><span class="lineNum">      53 </span>            : - CHARGE: e (default)</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \par Examples</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : \plumedfile</a>
+<a name="59"><span class="lineNum">      59 </span>            : # this is using Angstrom - kj/mol - fs</a>
+<a name="60"><span class="lineNum">      60 </span>            : UNITS LENGTH=A TIME=fs</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : # compute distance between atoms 1 and 4</a>
+<a name="63"><span class="lineNum">      63 </span>            : d: DISTANCE ATOMS=1,4</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : # print time and distance on a COLVAR file</a>
+<a name="66"><span class="lineNum">      66 </span>            : PRINT ARG=d FILE=COLVAR</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : # dump atoms 1 to 100 on a 'out.gro' file</a>
+<a name="69"><span class="lineNum">      69 </span>            : DUMPATOMS FILE=out.gro STRIDE=10 ATOMS=1-100</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : # dump atoms 1 to 100 on a 'out.xyz' file</a>
+<a name="72"><span class="lineNum">      72 </span>            : DUMPATOMS FILE=out.xyz STRIDE=10 ATOMS=1-100</a>
+<a name="73"><span class="lineNum">      73 </span>            : \endplumedfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : In the `COLVAR` file, time and distance will appear in fs and A respectively, *irrespective* of which units</a>
+<a name="76"><span class="lineNum">      76 </span>            : you are using in the host MD code. The coordinates in the `out.gro` file will be expressed in nm,</a>
+<a name="77"><span class="lineNum">      77 </span>            : since `gro` files are by convention written in nm. The coordinates in the `out.xyz` file</a>
+<a name="78"><span class="lineNum">      78 </span>            : will be written in Angstrom *since we used the UNITS command setting Angstrom units*.</a>
+<a name="79"><span class="lineNum">      79 </span>            : Indeed, within PLUMED xyz files are using internal PLUMED units and not necessarily Angstrom!</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : If a number, x, is found instead of a string, the new unit is equal to x times the default units.</a>
+<a name="82"><span class="lineNum">      82 </span>            : Using the following command as first line of the previous example would have lead to an identical result:</a>
+<a name="83"><span class="lineNum">      83 </span>            : \plumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : UNITS LENGTH=0.1 TIME=0.001</a>
+<a name="85"><span class="lineNum">      85 </span>            : \endplumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : */</a>
+<a name="88"><span class="lineNum">      88 </span>            : //+ENDPLUMEDOC</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : class Units :</a>
+<a name="91"><span class="lineNum">      91 </span>            :   public virtual ActionSetup</a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span>            : public:</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="95"><span class="lineNum">      95 </span>            :   explicit Units(const ActionOptions&amp;ao);</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      12544 : PLUMED_REGISTER_ACTION(Units,&quot;UNITS&quot;)</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         22 : void Units::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         22 :   ActionSetup::registerKeywords(keys);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;LENGTH&quot;,&quot;the units of lengths.  Either specify a conversion factor from the default, nm, or use one of the defined units, A (for angstroms), um (for micrometer), and Bohr.&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;ENERGY&quot;,&quot;the units of energy.  Either specify a conversion factor from the default, kj/mol, or use one of the defined units, j/mol, kcal/mol and Ha (for Hartree)&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;TIME&quot;,&quot;the units of time.  Either specify a conversion factor from the default, ps, or use one of the defined units, ns, fs, and atomic&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;MASS&quot;,&quot;the units of masses.  Specify a conversion factor from the default, amu&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         44 :   keys.add(&quot;optional&quot;,&quot;CHARGE&quot;,&quot;the units of charges.  Specify a conversion factor from the default, e&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         44 :   keys.addFlag(&quot;NATURAL&quot;,false,&quot;use natural units&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         22 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         20 : Units::Units(const ActionOptions&amp;ao):</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   Action(ao),</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         20 :   ActionSetup(ao)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         20 :   PLMD::Units u;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::string s;</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   s=&quot;&quot;;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         40 :   parse(&quot;LENGTH&quot;,s);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         20 :   if(s.length()&gt;0) u.setLength(s);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         38 :   if(u.getLengthString().length()&gt;0 &amp;&amp; u.getLengthString()==&quot;nm&quot;) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          8 :     log.printf(&quot;  length: %s\n&quot;,u.getLengthString().c_str());</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         22 :   else if(u.getLengthString().length()&gt;0 &amp;&amp; u.getLengthString()!=&quot;nm&quot;) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         10 :     log.printf(&quot;  length: %s = %g nm\n&quot;,u.getLengthString().c_str(),u.getLength());</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span>            :   else {</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          2 :     log.printf(&quot;  length: %g nm\n&quot;,u.getLength());</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            :   s=&quot;&quot;;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         40 :   parse(&quot;ENERGY&quot;,s);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         20 :   if(s.length()&gt;0) u.setEnergy(s);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         38 :   if(u.getEnergyString().length()&gt;0 &amp;&amp; u.getEnergyString()==&quot;kj/mol&quot;) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         13 :     log.printf(&quot;  energy: %s\n&quot;,u.getEnergyString().c_str());</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         12 :   else if(u.getEnergyString().length()&gt;0 &amp;&amp; u.getEnergyString()!=&quot;kj/mol&quot;) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          5 :     log.printf(&quot;  energy: %s = %g kj/mol\n&quot;,u.getEnergyString().c_str(),u.getEnergy());</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   else {</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          2 :     log.printf(&quot;  energy: %g kj/mol\n&quot;,u.getEnergy());</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            :   s=&quot;&quot;;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         40 :   parse(&quot;TIME&quot;,s);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         20 :   if(s.length()&gt;0) u.setTime(s);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         38 :   if(u.getTimeString().length()&gt;0 &amp;&amp; u.getTimeString()==&quot;ps&quot;) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         15 :     log.printf(&quot;  time: %s\n&quot;,u.getTimeString().c_str());</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          8 :   else if(u.getTimeString().length()&gt;0 &amp;&amp; u.getTimeString()!=&quot;ps&quot;) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :     log.printf(&quot;  time: %s = %g ps\n&quot;,u.getTimeString().c_str(),u.getTime());</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            :   else {</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          2 :     log.printf(&quot;  time: %g ps\n&quot;,u.getTime());</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   s=&quot;&quot;;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         40 :   parse(&quot;CHARGE&quot;,s);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         20 :   if(s.length()&gt;0) u.setCharge(s);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         38 :   if(u.getChargeString().length()&gt;0 &amp;&amp; u.getChargeString()==&quot;e&quot;) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         18 :     log.printf(&quot;  charge: %s\n&quot;,u.getChargeString().c_str());</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          2 :   else if(u.getChargeString().length()&gt;0 &amp;&amp; u.getChargeString()!=&quot;e&quot;) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :     log.printf(&quot;  charge: %s = %g e\n&quot;,u.getChargeString().c_str(),u.getCharge());</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span>            :   else {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          2 :     log.printf(&quot;  charge: %g e\n&quot;,u.getCharge());</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            :   s=&quot;&quot;;</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         40 :   parse(&quot;MASS&quot;,s);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         20 :   if(s.length()&gt;0) u.setMass(s);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         39 :   if(u.getMassString().length()&gt;0 &amp;&amp; u.getMassString()==&quot;amu&quot;) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         19 :     log.printf(&quot;  mass: %s\n&quot;,u.getMassString().c_str());</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          1 :   else if(u.getMassString().length()&gt;0 &amp;&amp; u.getMassString()!=&quot;amu&quot;) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     log.printf(&quot;  mass: %s = %g amu\n&quot;,u.getMassString().c_str(),u.getMass());</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            :   else {</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          1 :     log.printf(&quot;  mass: %g amu\n&quot;,u.getMass());</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         20 :   bool natural=false;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         20 :   parseFlag(&quot;NATURAL&quot;,natural);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         20 :   plumed.getAtoms().setNaturalUnits(natural);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         20 :   checkRead();</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         20 :   plumed.getAtoms().setUnits(u);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         20 :   if(natural) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          6 :     log.printf(&quot;  using natural units\n&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   } else {</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         14 :     log.printf(&quot;  using physical units\n&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         20 :   log.printf(&quot;  inside PLUMED, Boltzmann constant is %g\n&quot;,plumed.getAtoms().getKBoltzmann());</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         20 :   plumed.getAtoms().updateUnits();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         20 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/index-sort-f.html b/coverage/setup/index-sort-f.html
new file mode 100644
index 0000000000..9249c7593a
--- /dev/null
+++ b/coverage/setup/index-sort-f.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - setup</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryHi">97.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Restart.cpp.gcov.html">Restart.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Units.cpp.gcov.html">Units.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">57 / 59</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Load.cpp.gcov.html">Load.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/index-sort-l.html b/coverage/setup/index-sort-l.html
new file mode 100644
index 0000000000..fa11770c21
--- /dev/null
+++ b/coverage/setup/index-sort-l.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - setup</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryHi">97.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Units.cpp.gcov.html">Units.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">57 / 59</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Load.cpp.gcov.html">Load.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Restart.cpp.gcov.html">Restart.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/setup/index.html b/coverage/setup/index.html
new file mode 100644
index 0000000000..8f05f1692d
--- /dev/null
+++ b/coverage/setup/index.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - setup</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - setup</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">87</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryHi">97.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Load.cpp.gcov.html">Load.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Restart.cpp.gcov.html">Restart.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">19 / 19</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Units.cpp.gcov.html">Units.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">57 / 59</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">5 / 6</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/snow.png b/coverage/snow.png
new file mode 100644
index 0000000000000000000000000000000000000000..2cdae107fceec6e7f02ac7acb4a34a82a540caa5
GIT binary patch
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diff --git a/coverage/tools/Angle.cpp.func-sort-c.html b/coverage/tools/Angle.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b6696b8442
--- /dev/null
+++ b/coverage/tools/Angle.cpp.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Angle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Angle.cpp<span style="font-size: 80%;"> (<a href="Angle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Angle.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#26">_ZNK4PLMD5Angle7computeERKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#30">_ZNK4PLMD5Angle7computeERKNS_13VectorGenericILj3EEES4_RS2_S5_</a></td>
+              <td class="coverFnHi">543453</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Angle.cpp.func.html b/coverage/tools/Angle.cpp.func.html
new file mode 100644
index 0000000000..514cc66d2c
--- /dev/null
+++ b/coverage/tools/Angle.cpp.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Angle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Angle.cpp<span style="font-size: 80%;"> (<a href="Angle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Angle.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#26">_ZNK4PLMD5Angle7computeERKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Angle.cpp.gcov.html#30">_ZNK4PLMD5Angle7computeERKNS_13VectorGenericILj3EEES4_RS2_S5_</a></td>
+              <td class="coverFnHi">543453</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Angle.cpp.gcov.html b/coverage/tools/Angle.cpp.gcov.html
new file mode 100644
index 0000000000..d44558435b
--- /dev/null
+++ b/coverage/tools/Angle.cpp.gcov.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Angle.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Angle.cpp<span style="font-size: 80%;"> (source / <a href="Angle.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Angle.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cmath&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">          2 : double Angle::compute(const Vector&amp; v1,const Vector&amp; v2)const {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          2 :   return std::acos(dotProduct(v1,v2)/(v1.modulo()*v2.modulo()));</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : }</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     543453 : double Angle::compute(const Vector&amp; v1,const Vector&amp; v2,Vector&amp; d1,Vector&amp; d2)const {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     543453 :   const double dp(dotProduct(v1,v2));</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   const Vector&amp; dp_dv1(v2);</a>
+<a name="35"><span class="lineNum">      35 </span>            :   const Vector&amp; dp_dv2(v1);</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     543453 :   const double sv1(v1.modulo2());</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     543453 :   const double sv2(v2.modulo2());</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     543453 :   const Vector dsv1_dv1(2*v1);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     543453 :   const Vector dsv2_dv2(2*v2);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     543453 :   const double nn(1.0/std::sqrt(sv1*sv2));</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     543453 :   const Vector dnn_dv1(-0.5*nn/sv1*dsv1_dv1);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">     543453 :   const Vector dnn_dv2(-0.5*nn/sv2*dsv2_dv2);</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">     543453 :   const double dpnn(dp*nn);</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">     543453 :   if(dpnn&gt;=1.0-epsilon) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          1 :     d1=Vector(0.0,0.0,0.0);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :     d2=Vector(0.0,0.0,0.0);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :     return 0.0;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   }</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     543452 :   if(dpnn&lt;=-1.0+epsilon) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          1 :     d1=Vector(0.0,0.0,0.0);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          1 :     d2=Vector(0.0,0.0,0.0);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          1 :     return pi;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     543451 :   const Vector ddpnn_dv1(dp*dnn_dv1+dp_dv1*nn);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">     543451 :   const Vector ddpnn_dv2(dp*dnn_dv2+dp_dv2*nn);</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">     543451 :   const double x(-1.0/std::sqrt(1-dpnn*dpnn));</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">     543451 :   d1=x*ddpnn_dv1;</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     543451 :   d2=x*ddpnn_dv2;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     543451 :   return std::acos(dpnn);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/AtomNumber.h.func-sort-c.html b/coverage/tools/AtomNumber.h.func-sort-c.html
new file mode 100644
index 0000000000..69ce3d699c
--- /dev/null
+++ b/coverage/tools/AtomNumber.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/AtomNumber.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - AtomNumber.h<span style="font-size: 80%;"> (<a href="AtomNumber.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AtomNumber.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomNumber.h.gcov.html#106">_ZN4PLMD10AtomNumber6serialEj</a></td>
+              <td class="coverFnHi">696</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomNumber.h.gcov.html#92">_ZN4PLMD10AtomNumber9setSerialEj</a></td>
+              <td class="coverFnHi">713333</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/AtomNumber.h.func.html b/coverage/tools/AtomNumber.h.func.html
new file mode 100644
index 0000000000..8b2278aed0
--- /dev/null
+++ b/coverage/tools/AtomNumber.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/AtomNumber.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - AtomNumber.h<span style="font-size: 80%;"> (<a href="AtomNumber.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AtomNumber.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomNumber.h.gcov.html#106">_ZN4PLMD10AtomNumber6serialEj</a></td>
+              <td class="coverFnHi">696</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AtomNumber.h.gcov.html#92">_ZN4PLMD10AtomNumber9setSerialEj</a></td>
+              <td class="coverFnHi">713333</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/AtomNumber.h.gcov.html b/coverage/tools/AtomNumber.h.gcov.html
new file mode 100644
index 0000000000..49bd412112
--- /dev/null
+++ b/coverage/tools/AtomNumber.h.gcov.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/AtomNumber.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - AtomNumber.h<span style="font-size: 80%;"> (source / <a href="AtomNumber.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_AtomNumber_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_AtomNumber_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;limits&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : /**</a>
+<a name="31"><span class="lineNum">      31 </span>            : \ingroup TOOLBOX</a>
+<a name="32"><span class="lineNum">      32 </span>            :  Simple class to store the index of an atom.</a>
+<a name="33"><span class="lineNum">      33 </span>            :  It is just an unsigned, with all the methods inlined for better efficiency.</a>
+<a name="34"><span class="lineNum">      34 </span>            :  Its special thing is that it is only accessed through serial(), index(),</a>
+<a name="35"><span class="lineNum">      35 </span>            :  setSerial() and setIndex() methods, so that there</a>
+<a name="36"><span class="lineNum">      36 </span>            :  no ambiguity about using the &quot;from 0&quot; (index) or</a>
+<a name="37"><span class="lineNum">      37 </span>            :  &quot;from 1&quot; (serial) numbering (names as in VMD convention).</a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : class AtomNumber {</a>
+<a name="40"><span class="lineNum">      40 </span>            :   unsigned index_;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Construct with a given index.</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// This constructor is kept private to avoid implicit cast.</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit AtomNumber(unsigned);</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Initialize to index=0 (serial=1)</a>
+<a name="46"><span class="lineNum">      46 </span>            :   AtomNumber();</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Returns the serial number</a>
+<a name="48"><span class="lineNum">      48 </span>            :   unsigned serial()const;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Returns the index number</a>
+<a name="50"><span class="lineNum">      50 </span>            :   unsigned index()const;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Sets the atom number by serial, returning a reference to the AtomNumber itself.</a>
+<a name="52"><span class="lineNum">      52 </span>            :   AtomNumber &amp; setSerial(unsigned);</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Sets the atom number by index, returning a reference to the AtomNumber itself.</a>
+<a name="54"><span class="lineNum">      54 </span>            :   AtomNumber &amp; setIndex(unsigned);</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Returns an AtomNumber with a specified serial.</a>
+<a name="56"><span class="lineNum">      56 </span>            :   static AtomNumber serial(unsigned);</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Returns an AtomNumber with a specified index.</a>
+<a name="58"><span class="lineNum">      58 </span>            :   static AtomNumber index(unsigned);</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Comparison operators</a>
+<a name="60"><span class="lineNum">      60 </span>            :   friend bool operator&lt;(const AtomNumber&amp;,const AtomNumber&amp;);</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Comparison operators</a>
+<a name="62"><span class="lineNum">      62 </span>            :   friend bool operator&gt;(const AtomNumber&amp;,const AtomNumber&amp;);</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Comparison operators</a>
+<a name="64"><span class="lineNum">      64 </span>            :   friend bool operator&lt;=(const AtomNumber&amp;,const AtomNumber&amp;);</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Comparison operators</a>
+<a name="66"><span class="lineNum">      66 </span>            :   friend bool operator&gt;=(const AtomNumber&amp;,const AtomNumber&amp;);</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Comparison operators</a>
+<a name="68"><span class="lineNum">      68 </span>            :   friend bool operator==(const AtomNumber&amp;,const AtomNumber&amp;);</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Comparison operators</a>
+<a name="70"><span class="lineNum">      70 </span>            :   friend bool operator!=(const AtomNumber&amp;,const AtomNumber&amp;);</a>
+<a name="71"><span class="lineNum">      71 </span>            : };</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : inline</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    1581971 : AtomNumber::AtomNumber() {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">    1581923 :   index_=0;</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : inline</a>
+<a name="79"><span class="lineNum">      79 </span>            : AtomNumber::AtomNumber(unsigned i) {</a>
+<a name="80"><span class="lineNum">      80 </span>            :   index_=i;</a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : inline</a>
+<a name="84"><span class="lineNum">      84 </span>            : unsigned AtomNumber::serial()const {</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     411757 :   return index_+1;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : inline</a>
+<a name="89"><span class="lineNum">      89 </span>            : unsigned AtomNumber::index()const {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">   38158570 :   return index_;</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : inline</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     713333 : AtomNumber &amp; AtomNumber::setSerial(unsigned i) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     713333 :   plumed_massert(i&gt;0,&quot;serial of an atom cannot be zero&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     713333 :   plumed_massert(i&lt;std::numeric_limits&lt;unsigned&gt;::max()/2,&quot;serial cannot be negative&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     713333 :   index_=i-1;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     713333 :   return *this;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : inline</a>
+<a name="102"><span class="lineNum">     102 </span>            : AtomNumber &amp; AtomNumber::setIndex(unsigned i) {</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         56 :   index_=i;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   return *this;</a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : inline</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        696 : AtomNumber AtomNumber::serial(unsigned i) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        696 :   plumed_massert(i&gt;0,&quot;serial of an atom cannot be zero&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        696 :   plumed_massert(i&lt;std::numeric_limits&lt;unsigned&gt;::max()/2,&quot;serial cannot be negative&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        696 :   return AtomNumber(i-1);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : inline</a>
+<a name="115"><span class="lineNum">     115 </span>            : AtomNumber AtomNumber::index(unsigned i) {</a>
+<a name="116"><span class="lineNum">     116 </span>            :   return AtomNumber(i);</a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : inline</a>
+<a name="120"><span class="lineNum">     120 </span>            : bool operator&lt;(const AtomNumber&amp;a,const AtomNumber&amp;b) {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">  376001907 :   return a.index_&lt;b.index_;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : inline</a>
+<a name="125"><span class="lineNum">     125 </span>            : bool operator&gt;(const AtomNumber&amp;a,const AtomNumber&amp;b) {</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">     692645 :   return a.index_&gt;b.index_;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : }</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : inline</a>
+<a name="130"><span class="lineNum">     130 </span>            : bool operator&lt;=(const AtomNumber&amp;a,const AtomNumber&amp;b) {</a>
+<a name="131"><span class="lineNum">     131 </span>            :   return a.index_&lt;=b.index_;</a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : inline</a>
+<a name="135"><span class="lineNum">     135 </span>            : bool operator&gt;=(const AtomNumber&amp;a,const AtomNumber&amp;b) {</a>
+<a name="136"><span class="lineNum">     136 </span>            :   return a.index_&gt;=b.index_;</a>
+<a name="137"><span class="lineNum">     137 </span>            : }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : inline</a>
+<a name="140"><span class="lineNum">     140 </span>            : bool operator==(const AtomNumber&amp;a,const AtomNumber&amp;b) {</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">  172343719 :   return a.index_==b.index_;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : inline</a>
+<a name="145"><span class="lineNum">     145 </span>            : bool operator!=(const AtomNumber&amp;a,const AtomNumber&amp;b) {</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">  117933074 :   return a.index_!=b.index_;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : #endif</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/BiasRepresentation.cpp.func-sort-c.html b/coverage/tools/BiasRepresentation.cpp.func-sort-c.html
new file mode 100644
index 0000000000..efefc03be0
--- /dev/null
+++ b/coverage/tools/BiasRepresentation.cpp.func-sort-c.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/BiasRepresentation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - BiasRepresentation.cpp<span style="font-size: 80%;"> (<a href="BiasRepresentation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">129</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntryMed">75.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BiasRepresentation.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#128">_ZN4PLMD18BiasRepresentation13getPtrToValueEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#124">_ZN4PLMD18BiasRepresentation14getPtrToValuesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#108">_ZN4PLMD18BiasRepresentation16isRescaledToBiasEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#112">_ZN4PLMD18BiasRepresentation21getNumberOfDimensionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#276">_ZN4PLMD18BiasRepresentation5clearEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#120">_ZN4PLMD18BiasRepresentation7getNameB5cxx11Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#116">_ZN4PLMD18BiasRepresentation8getNamesB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#103">_ZN4PLMD18BiasRepresentation17setRescaledToBiasEb</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#74">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorERKS1_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISF_EESJ_RKS1_IjSaIjEERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#43">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#31">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#241">_ZN4PLMD18BiasRepresentation12getMinMaxBinERSt6vectorIdSaIdEES4_RS1_IjSaIjEE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#57">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorERKS1_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISF_EESJ_RKS1_IjSaIjEEbdd</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#90">_ZN4PLMD18BiasRepresentation7addGridERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESB_RKS1_IjSaIjEE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#236">_ZN4PLMD18BiasRepresentation10getGridPtrEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#132">_ZN4PLMD18BiasRepresentation13readFromPointEPNS_5IFileE</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#141">_ZN4PLMD18BiasRepresentation10pushKernelEPNS_5IFileE</a></td>
+              <td class="coverFnHi">5563</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#99">_ZN4PLMD18BiasRepresentation15hasSigmaInInputEv</a></td>
+              <td class="coverFnHi">5563</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#232">_ZN4PLMD18BiasRepresentation18getNumberOfKernelsEv</a></td>
+              <td class="coverFnHi">5578</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/BiasRepresentation.cpp.func.html b/coverage/tools/BiasRepresentation.cpp.func.html
new file mode 100644
index 0000000000..81b44a8798
--- /dev/null
+++ b/coverage/tools/BiasRepresentation.cpp.func.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/BiasRepresentation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - BiasRepresentation.cpp<span style="font-size: 80%;"> (<a href="BiasRepresentation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">129</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntryMed">75.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BiasRepresentation.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#236">_ZN4PLMD18BiasRepresentation10getGridPtrEv</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#141">_ZN4PLMD18BiasRepresentation10pushKernelEPNS_5IFileE</a></td>
+              <td class="coverFnHi">5563</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#241">_ZN4PLMD18BiasRepresentation12getMinMaxBinERSt6vectorIdSaIdEES4_RS1_IjSaIjEE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#128">_ZN4PLMD18BiasRepresentation13getPtrToValueEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#132">_ZN4PLMD18BiasRepresentation13readFromPointEPNS_5IFileE</a></td>
+              <td class="coverFnHi">1092</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#124">_ZN4PLMD18BiasRepresentation14getPtrToValuesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#99">_ZN4PLMD18BiasRepresentation15hasSigmaInInputEv</a></td>
+              <td class="coverFnHi">5563</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#108">_ZN4PLMD18BiasRepresentation16isRescaledToBiasEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#103">_ZN4PLMD18BiasRepresentation17setRescaledToBiasEb</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#232">_ZN4PLMD18BiasRepresentation18getNumberOfKernelsEv</a></td>
+              <td class="coverFnHi">5578</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#112">_ZN4PLMD18BiasRepresentation21getNumberOfDimensionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#276">_ZN4PLMD18BiasRepresentation5clearEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#90">_ZN4PLMD18BiasRepresentation7addGridERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESB_RKS1_IjSaIjEE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#120">_ZN4PLMD18BiasRepresentation7getNameB5cxx11Ej</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#116">_ZN4PLMD18BiasRepresentation8getNamesB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#31">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#74">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorERKS1_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISF_EESJ_RKS1_IjSaIjEERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#57">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorERKS1_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISF_EESJ_RKS1_IjSaIjEEbdd</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BiasRepresentation.cpp.gcov.html#43">_ZN4PLMD18BiasRepresentationC2ERKSt6vectorIPNS_5ValueESaIS3_EERNS_12CommunicatorERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/BiasRepresentation.cpp.gcov.html b/coverage/tools/BiasRepresentation.cpp.gcov.html
new file mode 100644
index 0000000000..c2a11bdbbb
--- /dev/null
+++ b/coverage/tools/BiasRepresentation.cpp.gcov.html
@@ -0,0 +1,363 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/BiasRepresentation.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - BiasRepresentation.cpp<span style="font-size: 80%;"> (source / <a href="BiasRepresentation.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">129</td>
+            <td class="headerCovTableEntry">170</td>
+            <td class="headerCovTableEntryMed">75.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">19</td>
+            <td class="headerCovTableEntryLo">63.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;BiasRepresentation.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;iostream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;KernelFunctions.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;File.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Grid.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /// the constructor here</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          4 : BiasRepresentation::BiasRepresentation(const std::vector&lt;Value*&gt; &amp; tmpvalues, Communicator &amp;cc ):hasgrid(false),rescaledToBias(false),mycomm(cc) {</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          4 :   lowI_=0.0;</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          4 :   uppI_=0.0;</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          4 :   doInt_=false;</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          4 :   ndim=tmpvalues.size();</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         12 :   for(int i=0; i&lt;ndim; i++) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          8 :     values.push_back(tmpvalues[i]);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          8 :     names.push_back(values[i]-&gt;getName());</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   }</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          4 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : /// overload the constructor: add the sigma  at constructor time</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          1 : BiasRepresentation::BiasRepresentation(const std::vector&lt;Value*&gt; &amp; tmpvalues, Communicator &amp;cc, const std::vector&lt;double&gt; &amp; sigma ):</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          1 :   hasgrid(false), rescaledToBias(false), histosigma(sigma),mycomm(cc)</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : {</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :   lowI_=0.0;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :   uppI_=0.0;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :   doInt_=false;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          1 :   ndim=tmpvalues.size();</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          3 :   for(int i=0; i&lt;ndim; i++) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          2 :     values.push_back(tmpvalues[i]);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          2 :     names.push_back(values[i]-&gt;getName());</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          1 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : /// overload the constructor: add the grid at constructor time</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          8 : BiasRepresentation::BiasRepresentation(const std::vector&lt;Value*&gt; &amp; tmpvalues, Communicator &amp;cc, const std::vector&lt;std::string&gt; &amp; gmin, const std::vector&lt;std::string&gt; &amp; gmax,</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          8 :                                        const std::vector&lt;unsigned&gt; &amp; nbin, bool doInt, double lowI, double uppI):</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          8 :   hasgrid(false), rescaledToBias(false), mycomm(cc)</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : {</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          8 :   ndim=tmpvalues.size();</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         23 :   for(int i=0; i&lt;ndim; i++) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         15 :     values.push_back(tmpvalues[i]);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         15 :     names.push_back(values[i]-&gt;getName());</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   }</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          8 :   doInt_=doInt;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          8 :   lowI_=lowI;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          8 :   uppI_=uppI;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   // initialize the grid</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          8 :   addGrid(gmin,gmax,nbin);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          8 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : /// overload the constructor with some external sigmas: needed for histogram</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          1 : BiasRepresentation::BiasRepresentation(const std::vector&lt;Value*&gt; &amp; tmpvalues, Communicator &amp;cc, const std::vector&lt;std::string&gt; &amp; gmin, const std::vector&lt;std::string&gt; &amp; gmax,</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          1 :                                        const std::vector&lt;unsigned&gt; &amp; nbin, const std::vector&lt;double&gt; &amp; sigma):</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :   hasgrid(false), rescaledToBias(false),histosigma(sigma),mycomm(cc)</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : {</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          1 :   lowI_=0.0;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          1 :   uppI_=0.0;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 :   doInt_=false;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          1 :   ndim=tmpvalues.size();</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          3 :   for(int  i=0; i&lt;ndim; i++) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          2 :     values.push_back(tmpvalues[i]);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :     names.push_back(values[i]-&gt;getName());</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span>            :   // initialize the grid</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          1 :   addGrid(gmin,gmax,nbin);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          1 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          9 : void BiasRepresentation::addGrid(const std::vector&lt;std::string&gt; &amp; gmin, const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin ) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          9 :   plumed_massert(hills.size()==0,&quot;you can set the grid before loading the hills&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          9 :   plumed_massert(hasgrid==false,&quot;to build the grid you should not having the grid in this bias representation&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::string ss; ss=&quot;file.free&quot;;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         26 :   std::vector&lt;Value*&gt; vv; for(unsigned i=0; i&lt;values.size(); i++) vv.push_back(values[i]);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         18 :   BiasGrid_=Tools::make_unique&lt;Grid&gt;(ss,vv,gmin,gmax,nbin,false,true);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          9 :   hasgrid=true;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          9 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       5563 : bool BiasRepresentation::hasSigmaInInput() {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       5563 :   if(histosigma.size()==0) {return false;} else {return true;}</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          1 : void BiasRepresentation::setRescaledToBias(bool rescaled) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :   plumed_massert(hills.size()==0,&quot;you can set the rescaling function only before loading hills&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   rescaledToBias=rescaled;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          1 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 : const bool &amp; BiasRepresentation::isRescaledToBias() {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   return rescaledToBias;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 : unsigned BiasRepresentation::getNumberOfDimensions() {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   return values.size();</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 : std::vector&lt;std::string&gt; BiasRepresentation::getNames() {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   return names;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 : const std::string &amp; BiasRepresentation::getName(unsigned i) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :   return names[i];</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 : const std::vector&lt;Value*&gt;&amp; BiasRepresentation::getPtrToValues() {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :   return values;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 : Value*  BiasRepresentation::getPtrToValue(unsigned i) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   return values[i];</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1092 : std::unique_ptr&lt;KernelFunctions&gt; BiasRepresentation::readFromPoint(IFile *ifile) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1092 :   std::vector&lt;double&gt; cc( names.size() );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       3276 :   for(unsigned i=0; i&lt;names.size(); ++i) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       2184 :     ifile-&gt;scanField(names[i],cc[i]);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       1092 :   double h=1.0;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       2184 :   return Tools::make_unique&lt;KernelFunctions&gt;(cc,histosigma,&quot;stretched-gaussian&quot;,&quot;DIAGONAL&quot;,h);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       5563 : void BiasRepresentation::pushKernel( IFile *ifile ) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       5563 :   std::unique_ptr&lt;KernelFunctions&gt; kk;</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   // here below the reading of the kernel is completely hidden</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       5563 :   if(histosigma.size()==0) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       4471 :     ifile-&gt;allowIgnoredFields();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       8942 :     kk=KernelFunctions::read(ifile,true,names);</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   } else {</a>
+<a name="150"><span class="lineNum">     150 </span>            :     // when doing histogram assume gaussian with a given diagonal sigma</a>
+<a name="151"><span class="lineNum">     151 </span>            :     // and neglect all the rest</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       2184 :     kk=readFromPoint(ifile);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span>            :   // the bias factor is not something about the kernels but</a>
+<a name="155"><span class="lineNum">     155 </span>            :   // must be stored to keep the  bias/free energy duality</a>
+<a name="156"><span class="lineNum">     156 </span>            :   std::string dummy; double dummyd;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      11126 :   if(ifile-&gt;FieldExist(&quot;biasf&quot;)) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       5563 :     ifile-&gt;scanField(&quot;biasf&quot;,dummy);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       5563 :     Tools::convert(dummy,dummyd);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :   } else {dummyd=1.0;}</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       5563 :   biasf.push_back(dummyd);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   // the domain does not pertain to the kernel but to the values here defined</a>
+<a name="163"><span class="lineNum">     163 </span>            :   std::string mins,maxs,minv,maxv,mini,maxi; mins=&quot;min_&quot;; maxs=&quot;max_&quot;;</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      16688 :   for(int i=0 ; i&lt;ndim; i++) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      11125 :     if(values[i]-&gt;isPeriodic()) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      22216 :       ifile-&gt;scanField(mins+names[i],minv);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      22216 :       ifile-&gt;scanField(maxs+names[i],maxv);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :       // verify that the domain is correct</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      11108 :       values[i]-&gt;getDomain(mini,maxi);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      11108 :       plumed_massert(mini==minv,&quot;the input periodicity in hills and in value definition does not match&quot;  );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      11108 :       plumed_massert(maxi==maxv,&quot;the input periodicity in hills and in value definition does not match&quot;  );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     }</a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span>            :   // if grid is defined then it should be added on the grid</a>
+<a name="175"><span class="lineNum">     175 </span>            :   //cerr&lt;&lt;&quot;now with &quot;&lt;&lt;hills.size()&lt;&lt;endl;</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       5563 :   if(hasgrid) {</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :     std::vector&lt;unsigned&gt; nneighb;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       3375 :     if(doInt_&amp;&amp;(kk-&gt;getCenter()[0]+kk-&gt;getContinuousSupport()[0] &gt; uppI_ || kk-&gt;getCenter()[0]-kk-&gt;getContinuousSupport()[0] &lt; lowI_ )) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :       nneighb=BiasGrid_-&gt;getNbin();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       6750 :     } else nneighb=kk-&gt;getSupport(BiasGrid_-&gt;getDx());</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       3375 :     std::vector&lt;Grid::index_t&gt; neighbors=BiasGrid_-&gt;getNeighbors(kk-&gt;getCenter(),nneighb);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       3375 :     std::vector&lt;double&gt; der(ndim);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       3375 :     std::vector&lt;double&gt; xx(ndim);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       3375 :     if(mycomm.Get_size()==1) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">    1027680 :       for(unsigned i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">    1024305 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">    3072823 :         for(int j=0; j&lt;ndim; ++j) {der[j]=0.0;}</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">    1024305 :         BiasGrid_-&gt;getPoint(ineigh,xx);</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :         // assign xx to a new vector of values</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">    3072823 :         for(int j=0; j&lt;ndim; ++j) {values[j]-&gt;set(xx[j]);}</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :         double bias;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">    1024305 :         if(doInt_) bias=kk-&gt;evaluate(values,der,true,doInt_,lowI_,uppI_);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">    1024305 :         else bias=kk-&gt;evaluate(values,der,true);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">    1024305 :         if(rescaledToBias) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      45234 :           double f=(biasf.back()-1.)/(biasf.back());</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      45234 :           bias*=f;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">     135702 :           for(int j=0; j&lt;ndim; ++j) {der[j]*=f;}</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :         }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">    1024305 :         BiasGrid_-&gt;addValueAndDerivatives(ineigh,bias,der);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :       }</a>
+<a name="201"><span class="lineNum">     201 </span>            :     } else {</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :       unsigned stride=mycomm.Get_size();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :       unsigned rank=mycomm.Get_rank();</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :       std::vector&lt;double&gt; allder(ndim*neighbors.size(),0.0);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :       std::vector&lt;double&gt; allbias(neighbors.size(),0.0);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       std::vector&lt;double&gt; tmpder(ndim);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :       for(unsigned i=rank; i&lt;neighbors.size(); i+=stride) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :         BiasGrid_-&gt;getPoint(ineigh,xx);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :         for(int j=0; j&lt;ndim; ++j) {values[j]-&gt;set(xx[j]);}</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :         if(doInt_) allbias[i]=kk-&gt;evaluate(values,der,true,doInt_,lowI_,uppI_);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :         else allbias[i]=kk-&gt;evaluate(values,der,true);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :         if(rescaledToBias) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :           double f=(biasf.back()-1.)/(biasf.back());</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :           allbias[i]*=f;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :           for(int j=0; j&lt;ndim; ++j) {tmpder[j]*=f;}</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :         }</a>
+<a name="218"><span class="lineNum">     218 </span>            :         // this solution with the temporary vector is rather bad, probably better to take</a>
+<a name="219"><span class="lineNum">     219 </span>            :         // a pointer of double as it was in old gaussian</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :         for(int j=0; j&lt;ndim; ++j) { allder[ndim*i+j]=tmpder[j]; tmpder[j]=0.;}</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :       }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :       mycomm.Sum(allbias);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :       mycomm.Sum(allder);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :         Grid::index_t ineigh=neighbors[i];</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :         for(int j=0; j&lt;ndim; ++j) {der[j]=allder[ndim*i+j];}</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :         BiasGrid_-&gt;addValueAndDerivatives(ineigh,allbias[i],der);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :       }</a>
+<a name="229"><span class="lineNum">     229 </span>            :     }</a>
+<a name="230"><span class="lineNum">     230 </span>            :   }</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       5563 :   hills.emplace_back(std::move(kk));</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       5563 : }</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       5578 : int BiasRepresentation::getNumberOfKernels() {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       5578 :   return hills.size();</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         10 : Grid* BiasRepresentation::getGridPtr() {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         10 :   plumed_massert(hasgrid,&quot;if you want the grid pointer then you should have defined a grid before&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         10 :   return BiasGrid_.get();</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          5 : void BiasRepresentation::getMinMaxBin(std::vector&lt;double&gt; &amp;vmin, std::vector&lt;double&gt; &amp;vmax, std::vector&lt;unsigned&gt; &amp;vbin) {</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   std::vector&lt;double&gt; ss,cc,binsize;</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          5 :   vmin.clear(); vmin.resize(ndim,10.e20);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          5 :   vmax.clear(); vmax.resize(ndim,-10.e20);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          5 :   vbin.clear(); vbin.resize(ndim);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          5 :   binsize.clear(); binsize.resize(ndim,10.e20);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :   int ndiv=10; // adjustable parameter: division per support</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       2193 :   for(unsigned i=0; i&lt;hills.size(); i++) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       2188 :     if(histosigma.size()!=0) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        546 :       ss=histosigma;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     } else {</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       3284 :       ss=hills[i]-&gt;getContinuousSupport();</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       2188 :     cc=hills[i]-&gt;getCenter();</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       6564 :     for(int j=0; j&lt;ndim; j++) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       4376 :       double dmin=cc[j]-ss[j];</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       4376 :       double dmax=cc[j]+ss[j];</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       4376 :       double ddiv=ss[j]/double(ndiv);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       4376 :       if(dmin&lt;vmin[j])vmin[j]=dmin;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       4376 :       if(dmax&gt;vmax[j])vmax[j]=dmax;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">       4376 :       if(ddiv&lt;binsize[j])binsize[j]=ddiv;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :     }</a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         15 :   for(int j=0; j&lt;ndim; j++) {</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :     // reset to periodicity</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         10 :     if(values[j]-&gt;isPeriodic()) {</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :       double minv,maxv;</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          8 :       values[j]-&gt;getDomain(minv,maxv);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          8 :       if(minv&gt;vmin[j])vmin[j]=minv;</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          8 :       if(maxv&lt;vmax[j])vmax[j]=maxv;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         10 :     vbin[j]=static_cast&lt;unsigned&gt;(std::ceil((vmax[j]-vmin[j])/binsize[j]) );</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :   }</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          5 : }</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 : void BiasRepresentation::clear() {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   hills.clear();</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   // clear the grid</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :   if(hasgrid) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :     BiasGrid_-&gt;clear();</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :   }</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Brent1DRootSearch.h.func-sort-c.html b/coverage/tools/Brent1DRootSearch.h.func-sort-c.html
new file mode 100644
index 0000000000..908d29a1ae
--- /dev/null
+++ b/coverage/tools/Brent1DRootSearch.h.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Brent1DRootSearch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Brent1DRootSearch.h<span style="font-size: 80%;"> (<a href="Brent1DRootSearch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Brent1DRootSearch.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#81">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_4GridEEEE6searchEMS3_FdRKdE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#74">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_4GridEEEE7bracketERKdS6_MS3_FdS6_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#61">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_4GridEEEEC2ERKS3_RKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#81">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_11multicolvar19DistanceFromContourEEEE6searchEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#74">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_11multicolvar19DistanceFromContourEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#61">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_11multicolvar19DistanceFromContourEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#81">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_9gridtools18ContourFindingBaseEEEE6searchEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#74">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_9gridtools18ContourFindingBaseEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#61">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_9gridtools18ContourFindingBaseEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Brent1DRootSearch.h.func.html b/coverage/tools/Brent1DRootSearch.h.func.html
new file mode 100644
index 0000000000..eab4770aae
--- /dev/null
+++ b/coverage/tools/Brent1DRootSearch.h.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Brent1DRootSearch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Brent1DRootSearch.h<span style="font-size: 80%;"> (<a href="Brent1DRootSearch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Brent1DRootSearch.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#81">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_11multicolvar19DistanceFromContourEEEE6searchEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#74">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_11multicolvar19DistanceFromContourEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#61">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_11multicolvar19DistanceFromContourEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#81">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_4GridEEEE6searchEMS3_FdRKdE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#74">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_4GridEEEE7bracketERKdS6_MS3_FdS6_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#61">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_4GridEEEEC2ERKS3_RKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#81">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_9gridtools18ContourFindingBaseEEEE6searchEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#74">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_9gridtools18ContourFindingBaseEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Brent1DRootSearch.h.gcov.html#61">_ZN4PLMD17Brent1DRootSearchINS_5F1dimINS_9gridtools18ContourFindingBaseEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Brent1DRootSearch.h.gcov.html b/coverage/tools/Brent1DRootSearch.h.gcov.html
new file mode 100644
index 0000000000..533466b9bd
--- /dev/null
+++ b/coverage/tools/Brent1DRootSearch.h.gcov.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Brent1DRootSearch.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Brent1DRootSearch.h<span style="font-size: 80%;"> (source / <a href="Brent1DRootSearch.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Brent1DRootSearch_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Brent1DRootSearch_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /// A class for doing parabolic interpolation and minimisation of</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// 1D functions using Brent's method.</a>
+<a name="34"><span class="lineNum">      34 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       1516 : class Brent1DRootSearch {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : private:</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Has the minimum been bracketed</a>
+<a name="38"><span class="lineNum">      38 </span>            :   bool bracketed;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// The tolerance for the line minimiser</a>
+<a name="40"><span class="lineNum">      40 </span>            :   double tol;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Maximum number of interactions in line minimiser</a>
+<a name="42"><span class="lineNum">      42 </span>            :   const unsigned ITMAX;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// A small number that protects against trying to achieve fractional</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// accuracy for a minimum that happens to be exactly zero</a>
+<a name="45"><span class="lineNum">      45 </span>            :   const double EPS;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// The factor by which to expand the range when bracketing</a>
+<a name="47"><span class="lineNum">      47 </span>            :   const double EXPAND;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// This is the type specifier for the function to minimise</a>
+<a name="49"><span class="lineNum">      49 </span>            :   typedef double(FCLASS::*eng_pointer)( const double&amp; val );</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Three points bracketting the minimum and the corresponding function values</a>
+<a name="51"><span class="lineNum">      51 </span>            :   double ax,bx,fa,fb;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// The class containing the function we are trying to minimise</a>
+<a name="53"><span class="lineNum">      53 </span>            :   FCLASS myclass_func;</a>
+<a name="54"><span class="lineNum">      54 </span>            : public:</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1516 :   explicit Brent1DRootSearch( const FCLASS&amp; pf,  const double&amp; t=3.0E-8 );</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Bracket the minium</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void bracket( const double&amp; ax, const double&amp; xx, eng_pointer eng );</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Find the minimum between two brackets</a>
+<a name="59"><span class="lineNum">      59 </span>            :   double search( eng_pointer eng );</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       1516 : Brent1DRootSearch&lt;FCLASS&gt;::Brent1DRootSearch( const FCLASS&amp; pf, const double&amp; t ):</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       1516 :   bracketed(false),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1516 :   tol(t),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1516 :   ITMAX(100),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       1516 :   EPS(3.0E-8),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       1516 :   EXPAND(1.6),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1516 :   ax(0), bx(0),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       1516 :   fa(0), fb(0),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1516 :   myclass_func(pf)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       1516 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       1516 : void Brent1DRootSearch&lt;FCLASS&gt;::bracket( const double&amp; a, const double&amp; b, eng_pointer eng ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1516 :   plumed_assert( a!=b ); ax=a; bx=b; fa=(myclass_func.*eng)(a); fb=(myclass_func.*eng)(b);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       1516 :   if ((fa &gt; 0.0 &amp;&amp; fb &gt; 0.0) || (fa &lt; 0.0 &amp;&amp; fb &lt; 0.0)) plumed_merror(&quot;input points do not bracket root&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       1516 :   bracketed=true;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       1516 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1516 : double Brent1DRootSearch&lt;FCLASS&gt;::search( eng_pointer eng ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   plumed_dbg_assert( bracketed );</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1516 :   double cx=bx, d, e, min1, min2, fc=fb, p, q, r, s, tol1, xm;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       8929 :   for(unsigned iter=0; iter&lt;ITMAX; iter++) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       8929 :     if ( (fb&gt;0.0 &amp;&amp; fc&gt;0.0) || (fb&lt;0.0 &amp;&amp; fc&lt;0.0) ) { cx=ax; fc=fa; e=d=bx-ax; }</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       8929 :     if( std::fabs(fc) &lt; std::fabs(fb) ) { ax=bx; bx=cx; cx=ax; fa=fb; fb=fc; fc=fa; }</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       8929 :     tol1=2*EPS*std::fabs(bx)+0.5*tol; xm=0.5*(cx-bx);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       8929 :     if( std::fabs(xm) &lt;= tol1 || fb == 0.0 ) return bx;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       7413 :     if( std::fabs(e) &gt;= tol1 &amp;&amp; std::fabs(fa) &gt; std::fabs(fb) ) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       7349 :       s=fb/fa;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       7349 :       if( ax==cx ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       5193 :         p=2.0*xm*s; q=1.0-s;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :       } else {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       2156 :         q=fa/fc; r=fb/fc; p=s*(2.0*xm*q*(q-r)-(bx-ax)*(r-1.0)); q=(q-1.0)*(r-1.0)*(s-1.0);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :       }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       7349 :       if (p &gt; 0.0) q = -q;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       7349 :       p=std::fabs(p); min1=3.0*xm*q-std::fabs(tol1*q); min2=std::fabs(e*q);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      14274 :       if (2.0*p &lt; (min1 &lt; min2 ? min1 : min2)) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       7090 :         e=d; d=p/q;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :       } else {</a>
+<a name="104"><span class="lineNum">     104 </span>            :         d=xm; e=d;</a>
+<a name="105"><span class="lineNum">     105 </span>            :       }</a>
+<a name="106"><span class="lineNum">     106 </span>            :     } else {</a>
+<a name="107"><span class="lineNum">     107 </span>            :       d=xm; e=d;</a>
+<a name="108"><span class="lineNum">     108 </span>            :     }</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       7413 :     ax=bx; fa=fb;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       7413 :     if( std::fabs(d) &gt; tol1 ) bx+=d;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1426 :     else if(xm&lt;0 ) bx -= std::fabs(tol1); // SIGN(tol1,xm);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        699 :     else bx += tol1;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       7413 :     fb = (myclass_func.*eng)(bx);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;Too many interactions in zbrent&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Citations.cpp.func-sort-c.html b/coverage/tools/Citations.cpp.func-sort-c.html
new file mode 100644
index 0000000000..acc6885844
--- /dev/null
+++ b/coverage/tools/Citations.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Citations.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Citations.cpp<span style="font-size: 80%;"> (<a href="Citations.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Citations.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#48">_ZNK4PLMD9Citations5emptyEv</a></td>
+              <td class="coverFnHi">318</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#44">_ZN4PLMD9Citations5clearEv</a></td>
+              <td class="coverFnHi">358</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#38">_ZN4PLMDlsERSoRKNS_9CitationsE</a></td>
+              <td class="coverFnHi">1009</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#27">_ZN4PLMD9Citations4citeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3798</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Citations.cpp.func.html b/coverage/tools/Citations.cpp.func.html
new file mode 100644
index 0000000000..d8b9d79dc7
--- /dev/null
+++ b/coverage/tools/Citations.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Citations.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Citations.cpp<span style="font-size: 80%;"> (<a href="Citations.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Citations.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#27">_ZN4PLMD9Citations4citeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3798</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#44">_ZN4PLMD9Citations5clearEv</a></td>
+              <td class="coverFnHi">358</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#38">_ZN4PLMDlsERSoRKNS_9CitationsE</a></td>
+              <td class="coverFnHi">1009</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Citations.cpp.gcov.html#48">_ZNK4PLMD9Citations5emptyEv</a></td>
+              <td class="coverFnHi">318</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Citations.cpp.gcov.html b/coverage/tools/Citations.cpp.gcov.html
new file mode 100644
index 0000000000..9338a3cd2d
--- /dev/null
+++ b/coverage/tools/Citations.cpp.gcov.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Citations.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Citations.cpp<span style="font-size: 80%;"> (source / <a href="Citations.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Citations.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;iostream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       3798 : std::string Citations::cite(const std::string &amp; item) {</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :   unsigned i;</a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">      10462 :   for(i=0; i&lt;items.size(); ++i) if(items[i]==item) break;</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">       3798 :   if(i==items.size()) items.push_back(item);</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       3798 :   plumed_assert(i&lt;items.size());</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   std::string ret;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       3798 :   Tools::convert(i+1,ret);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       7596 :   ret=&quot;[&quot;+ret+&quot;]&quot;;</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       3798 :   return ret;</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : }</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       1009 : std::ostream &amp; operator&lt;&lt;(std::ostream &amp;log,const Citations&amp;cit) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       4135 :   for(unsigned i=0; i&lt;cit.items.size(); ++i)</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       6252 :     log&lt;&lt;&quot;  [&quot;&lt;&lt;i+1&lt;&lt;&quot;] &quot;&lt;&lt;cit.items[i]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       1009 :   return log;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : }</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        358 : void Citations::clear() {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        358 :   items.clear();</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        358 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        318 : bool Citations::empty()const {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        318 :   return items.empty();</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : }</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : }</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Citations.h.func-sort-c.html b/coverage/tools/Citations.h.func-sort-c.html
new file mode 100644
index 0000000000..c6b61823d3
--- /dev/null
+++ b/coverage/tools/Citations.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Citations.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Citations.h<span style="font-size: 80%;"> (<a href="Citations.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Citations.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Citations.h.func.html b/coverage/tools/Citations.h.func.html
new file mode 100644
index 0000000000..e0905c09bf
--- /dev/null
+++ b/coverage/tools/Citations.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Citations.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Citations.h<span style="font-size: 80%;"> (<a href="Citations.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Citations.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Citations.h.gcov.html b/coverage/tools/Citations.h.gcov.html
new file mode 100644
index 0000000000..466430857d
--- /dev/null
+++ b/coverage/tools/Citations.h.gcov.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Citations.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Citations.h<span style="font-size: 80%;"> (source / <a href="Citations.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Citations_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Citations_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iosfwd&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /**</a>
+<a name="32"><span class="lineNum">      32 </span>            : \ingroup TOOLBOX</a>
+<a name="33"><span class="lineNum">      33 </span>            : Class taking care of bibliography.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This class contains a vector of citations. To add a new citations, use cite(). To print</a>
+<a name="36"><span class="lineNum">      36 </span>            : the entire bibliography, just dump on a ostream. Everytime cite is used, a string</a>
+<a name="37"><span class="lineNum">      37 </span>            : containing the number of the citation is returned. If the same citation is added twice,</a>
+<a name="38"><span class="lineNum">      38 </span>            : the same string is returned, so that this example will produce only two bibliographic items:</a>
+<a name="39"><span class="lineNum">      39 </span>            : \verbatim</a>
+<a name="40"><span class="lineNum">      40 </span>            : #include &quot;Citations.h&quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &lt;iostream&gt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : int main(int argc,char**argv){</a>
+<a name="43"><span class="lineNum">      43 </span>            :   PLMD::Citations citations;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::cout &lt;&lt; citations.cite(&quot;Pinco e Pallino, Il Piccolo 33, 444 (2012)&quot;) &lt;&lt; &quot;\n&quot;;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::cout &lt;&lt; citations.cite(&quot;Other cite&quot;) &lt;&lt; &quot;\n&quot;;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::cout &lt;&lt; citations.cite(&quot;Pinco e Pallino, Il Piccolo 33, 444 (2012)&quot;) &lt;&lt; &quot;\n&quot;;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::cout &lt;&lt; &quot;Bibliography\n&quot;&lt;&lt; citations;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   return 0;</a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : \endverbatim</a>
+<a name="52"><span class="lineNum">      52 </span>            : */</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">     805268 : class Citations {</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::vector&lt;std::string&gt; items;</a>
+<a name="56"><span class="lineNum">      56 </span>            : public:</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Add a citation.</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// It returns a string containing the reference number, something like &quot;[10]&quot;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::string cite(const std::string &amp;);</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Dumps the bibliography.</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// It writes on the ostream the list of all the bibliographic items</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// prefixed with their reference number</a>
+<a name="63"><span class="lineNum">      63 </span>            :   friend std::ostream &amp;operator&lt;&lt;(std::ostream &amp;,const Citations&amp;);</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Delete all references</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void clear();</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Check if bibliography is empty</a>
+<a name="67"><span class="lineNum">      67 </span>            :   bool empty()const;</a>
+<a name="68"><span class="lineNum">      68 </span>            : };</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : std::ostream &amp; operator&lt;&lt;(std::ostream &amp;,const Citations&amp;);</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Communicator.cpp.func-sort-c.html b/coverage/tools/Communicator.cpp.func-sort-c.html
new file mode 100644
index 0000000000..802df7d8c4
--- /dev/null
+++ b/coverage/tools/Communicator.cpp.func-sort-c.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Communicator.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Communicator.cpp<span style="font-size: 80%;"> (<a href="Communicator.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryMed">83.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Communicator.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Communicator.cpp.gcov.html#279">_ZN4PLMD12Communicator10getMPITypeIeEEP15ompi_datatype_tv</a></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
+
+</body>
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diff --git a/coverage/tools/Communicator.cpp.func.html b/coverage/tools/Communicator.cpp.func.html
new file mode 100644
index 0000000000..54d7f54024
--- /dev/null
+++ b/coverage/tools/Communicator.cpp.func.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Communicator.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Communicator.cpp<span style="font-size: 80%;"> (<a href="Communicator.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryMed">83.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Communicator.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
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diff --git a/coverage/tools/Communicator.cpp.gcov.html b/coverage/tools/Communicator.cpp.gcov.html
new file mode 100644
index 0000000000..72f4739272
--- /dev/null
+++ b/coverage/tools/Communicator.cpp.gcov.html
@@ -0,0 +1,394 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Communicator.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Communicator.cpp<span style="font-size: 80%;"> (source / <a href="Communicator.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryMed">83.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         54 : bool Communicator::plumedHasMPI() {</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         54 :   return true;</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : #else</a>
+<a name="35"><span class="lineNum">      35 </span>            :   return false;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #endif</a>
+<a name="37"><span class="lineNum">      37 </span>            : }</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">    2422194 : Communicator::Communicator()</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">    2422194 :   : communicator(MPI_COMM_SELF)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : #endif</a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">    2422194 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 : Communicator::Communicator(const Communicator&amp;pc) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   Set_comm(pc.communicator);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : Communicator::Status Communicator::StatusIgnore;</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 : Communicator&amp; Communicator::operator=(const Communicator&amp;pc) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   if (this != &amp;pc) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :     Set_comm(pc.communicator);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">    6784149 : int Communicator::Get_rank()const {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">    6784149 :   int r=0;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">    6784149 :   if(initialized()) MPI_Comm_rank(communicator,&amp;r);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : #endif</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">    6784149 :   return r;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">    2584342 : int Communicator::Get_size()const {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    2584342 :   int s=1;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    2584342 :   if(initialized()) MPI_Comm_size(communicator,&amp;s);</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : #endif</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    2584342 :   return s;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
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+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       1673 :     if(communicator!=MPI_COMM_SELF &amp;&amp; communicator!=MPI_COMM_WORLD) MPI_Comm_free(&amp;communicator);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       1673 :     if(c!=MPI_COMM_SELF) MPI_Comm_dup(c,&amp;communicator);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span>            : #else</a>
+<a name="82"><span class="lineNum">      82 </span>            :   (void) c;</a>
+<a name="83"><span class="lineNum">      83 </span>            : #endif</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       2172 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    4037355 : Communicator::~Communicator() {</span></a>
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+<a name="97"><span class="lineNum">      97 </span>            :   (void) val;</a>
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+<a name="101"><span class="lineNum">     101 </span>            : </a>
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+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :   std::abort();</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">    4893288 : void Communicator::Bcast(Data data,int root) {</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">    4893288 :   if(initialized()) MPI_Bcast(data.pointer,data.size,data.type,root,communicator);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : #else</a>
+<a name="129"><span class="lineNum">     129 </span>            :   (void) data;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   (void) root;</a>
+<a name="131"><span class="lineNum">     131 </span>            : #endif</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    4893288 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">    4283901 : void Communicator::Sum(Data data) {</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">    4283901 :   if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_SUM,communicator);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : #else</a>
+<a name="138"><span class="lineNum">     138 </span>            :   (void) data;</a>
+<a name="139"><span class="lineNum">     139 </span>            : #endif</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">    4283901 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          3 : void Communicator::Prod(Data data) {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          3 :   if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_PROD,communicator);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : #else</a>
+<a name="146"><span class="lineNum">     146 </span>            :   (void) data;</a>
+<a name="147"><span class="lineNum">     147 </span>            : #endif</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        155 : void Communicator::Max(Data data) {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        155 :   if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_MAX,communicator);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : #else</a>
+<a name="154"><span class="lineNum">     154 </span>            :   (void) data;</a>
+<a name="155"><span class="lineNum">     155 </span>            : #endif</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        155 : }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 : void Communicator::Min(Data data) {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          3 :   if(initialized()) MPI_Allreduce(MPI_IN_PLACE,data.pointer,data.size,data.type,MPI_MIN,communicator);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : #else</a>
+<a name="162"><span class="lineNum">     162 </span>            :   (void) data;</a>
+<a name="163"><span class="lineNum">     163 </span>            : #endif</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          3 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      15302 : Communicator::Request Communicator::Isend(ConstData data,int source,int tag) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   Request req;</a>
+<a name="168"><span class="lineNum">     168 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      15302 :   plumed_massert(initialized(),&quot;you are trying to use an MPI function, but MPI is not initialized&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      15302 :   void*s=const_cast&lt;void*&gt;((const void*)data.pointer);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      15302 :   MPI_Isend(s,data.size,data.type,source,tag,communicator,&amp;req.r);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : #else</a>
+<a name="173"><span class="lineNum">     173 </span>            :   (void) data;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   (void) source;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   (void) tag;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   plumed_merror(&quot;you are trying to use an MPI function, but PLUMED has been compiled without MPI support&quot;);</a>
+<a name="177"><span class="lineNum">     177 </span>            : #endif</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">      15302 :   return req;</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      19063 : void Communicator::Allgatherv(ConstData in,Data out,const int*recvcounts,const int*displs) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      19063 :   void*s=const_cast&lt;void*&gt;((const void*)in.pointer);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      19063 :   void*r=const_cast&lt;void*&gt;((const void*)out.pointer);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   int*rc=const_cast&lt;int*&gt;(recvcounts);</a>
+<a name="185"><span class="lineNum">     185 </span>            :   int*di=const_cast&lt;int*&gt;(displs);</a>
+<a name="186"><span class="lineNum">     186 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      19063 :   if(initialized()) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      19062 :     if(s==NULL)s=MPI_IN_PLACE;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      19062 :     MPI_Allgatherv(s,in.size,in.type,r,rc,di,out.type,communicator);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   } else {</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          1 :     plumed_assert(in.nbytes==out.nbytes);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          1 :     plumed_assert(in.size==out.size);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          1 :     plumed_assert(rc);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          1 :     plumed_assert(rc[0]==in.size);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          1 :     plumed_assert(di);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          1 :     if(s) std::memcpy(static_cast&lt;char*&gt;(r)+displs[0]*in.nbytes,s,size_t(in.size)*in.nbytes);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span>            : #else</a>
+<a name="199"><span class="lineNum">     199 </span>            :   plumed_assert(in.nbytes==out.nbytes);</a>
+<a name="200"><span class="lineNum">     200 </span>            :   plumed_assert(in.size==out.size);</a>
+<a name="201"><span class="lineNum">     201 </span>            :   plumed_assert(rc);</a>
+<a name="202"><span class="lineNum">     202 </span>            :   plumed_assert(rc[0]==in.size);</a>
+<a name="203"><span class="lineNum">     203 </span>            :   plumed_assert(di);</a>
+<a name="204"><span class="lineNum">     204 </span>            :   if(s) std::memcpy(static_cast&lt;char*&gt;(r)+displs[0]*in.nbytes,s,size_t(in.size)*in.nbytes);</a>
+<a name="205"><span class="lineNum">     205 </span>            : #endif</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      19063 : }</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       5838 : void Communicator::Allgather(ConstData in,Data out) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       5838 :   void*s=const_cast&lt;void*&gt;((const void*)in.pointer);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       5838 :   void*r=const_cast&lt;void*&gt;((const void*)out.pointer);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       5838 :   if(initialized()) {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       5837 :     if(s==NULL)s=MPI_IN_PLACE;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       5837 :     MPI_Allgather(s,in.size,in.type,r,out.size/Get_size(),out.type,communicator);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   } else {</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          1 :     plumed_assert(in.nbytes==out.nbytes);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          1 :     plumed_assert(in.size==out.size);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 :     if(s) std::memcpy(r,s,size_t(in.size)*in.nbytes);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :   }</a>
+<a name="220"><span class="lineNum">     220 </span>            : #else</a>
+<a name="221"><span class="lineNum">     221 </span>            :   plumed_assert(in.nbytes==out.nbytes);</a>
+<a name="222"><span class="lineNum">     222 </span>            :   plumed_assert(in.size==out.size);</a>
+<a name="223"><span class="lineNum">     223 </span>            :   if(s) std::memcpy(r,s,size_t(in.size)*in.nbytes);</a>
+<a name="224"><span class="lineNum">     224 </span>            : #endif</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       5838 : }</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      15302 : void Communicator::Recv(Data data,int source,int tag,Status&amp;status) {</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      15302 :   plumed_massert(initialized(),&quot;you are trying to use an MPI function, but MPI is not initialized&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      15302 :   if(&amp;status==&amp;StatusIgnore) MPI_Recv(data.pointer,data.size,data.type,source,tag,communicator,MPI_STATUS_IGNORE);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       7589 :   else                       MPI_Recv(data.pointer,data.size,data.type,source,tag,communicator,&amp;status.s);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : #else</a>
+<a name="233"><span class="lineNum">     233 </span>            :   (void) data;</a>
+<a name="234"><span class="lineNum">     234 </span>            :   (void) source;</a>
+<a name="235"><span class="lineNum">     235 </span>            :   (void) tag;</a>
+<a name="236"><span class="lineNum">     236 </span>            :   (void) status;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   plumed_merror(&quot;you are trying to use an MPI function, but PLUMED has been compiled without MPI support&quot;);</a>
+<a name="238"><span class="lineNum">     238 </span>            : #endif</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      15302 : }</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">    4608891 : void Communicator::Barrier()const {</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">    4608891 :   if(initialized()) MPI_Barrier(communicator);</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : #endif</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    4608891 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       1674 : MPI_Comm &amp; Communicator::Get_comm() {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       1674 :   return communicator;</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">   25663216 : bool Communicator::initialized() {</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : #if defined(__PLUMED_HAS_MPI)</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">   25663216 :   int flag=0;</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">   25663216 :   MPI_Initialized(&amp;flag);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">   25663216 :   if(flag) return true;</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">   16411613 :   else return false;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : #endif</a>
+<a name="258"><span class="lineNum">     258 </span>            :   return false;</a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">      14902 : void Communicator::Request::wait(Status&amp;s) {</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">      14902 :   plumed_massert(initialized(),&quot;you are trying to use an MPI function, but MPI is not initialized&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">      14902 :   if(&amp;s==&amp;StatusIgnore) MPI_Wait(&amp;r,MPI_STATUS_IGNORE);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          1 :   else MPI_Wait(&amp;r,&amp;s.s);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : #else</a>
+<a name="267"><span class="lineNum">     267 </span>            :   (void) s;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   plumed_merror(&quot;you are trying to use an MPI function, but PLUMED has been compiled without MPI support&quot;);</a>
+<a name="269"><span class="lineNum">     269 </span>            : #endif</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">      14902 : }</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;float&gt;() { return MPI_FLOAT;}</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">    4558765 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;double&gt;() { return MPI_DOUBLE;}</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      59667 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;int&gt;()   { return MPI_INT;}</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        295 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;char&gt;()   { return MPI_CHAR;}</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">      43101 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;unsigned&gt;()   { return MPI_UNSIGNED;}</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         24 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;AtomNumber&gt;()   { return MPI_UNSIGNED;}</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    4603487 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;long unsigned&gt;()   { return MPI_UNSIGNED_LONG;}</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          6 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;long long unsigned&gt;() { return MPI_UNSIGNED_LONG_LONG;}</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;long double&gt;()   { return MPI_LONG_DOUBLE;}</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : #else</a>
+<a name="283"><span class="lineNum">     283 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;float&gt;() { return MPI_Datatype();}</a>
+<a name="284"><span class="lineNum">     284 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;double&gt;() { return MPI_Datatype();}</a>
+<a name="285"><span class="lineNum">     285 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;int&gt;() { return MPI_Datatype();}</a>
+<a name="286"><span class="lineNum">     286 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;char&gt;() { return MPI_Datatype();}</a>
+<a name="287"><span class="lineNum">     287 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;unsigned&gt;() { return MPI_Datatype();}</a>
+<a name="288"><span class="lineNum">     288 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;AtomNumber&gt;()   { return MPI_Datatype();}</a>
+<a name="289"><span class="lineNum">     289 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;long unsigned&gt;() { return MPI_Datatype();}</a>
+<a name="290"><span class="lineNum">     290 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;long long unsigned&gt;() { return MPI_Datatype();}</a>
+<a name="291"><span class="lineNum">     291 </span>            : template&lt;&gt; MPI_Datatype Communicator::getMPIType&lt;long double&gt;() { return MPI_Datatype();}</a>
+<a name="292"><span class="lineNum">     292 </span>            : #endif</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        406 : void Communicator::Split(int color,int key,Communicator&amp;pc)const {</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        406 :   MPI_Comm_split(communicator,color,key,&amp;pc.communicator);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : #else</a>
+<a name="298"><span class="lineNum">     298 </span>            :   (void) color;</a>
+<a name="299"><span class="lineNum">     299 </span>            :   (void) key;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   (void) pc;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   plumed_merror(&quot;you are trying to use an MPI function, but PLUMED has been compiled without MPI support&quot;);</a>
+<a name="302"><span class="lineNum">     302 </span>            : #endif</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        406 : }</span></a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       7589 : int Communicator::Status::Get_count(MPI_Datatype type)const {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   int i;</a>
+<a name="307"><span class="lineNum">     307 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       7589 :   plumed_massert(initialized(),&quot;you are trying to use an MPI function, but MPI is not initialized&quot;);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       7589 :   MPI_Get_count(const_cast&lt;MPI_Status*&gt;(&amp;s),type,&amp;i);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            : #else</a>
+<a name="311"><span class="lineNum">     311 </span>            :   i=0;</a>
+<a name="312"><span class="lineNum">     312 </span>            :   plumed_merror(&quot;you are trying to use an MPI function, but PLUMED has been compiled without MPI support&quot;);</a>
+<a name="313"><span class="lineNum">     313 </span>            : #endif</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       7589 :   return i;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : }</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Communicator.h.func-sort-c.html b/coverage/tools/Communicator.h.func-sort-c.html
new file mode 100644
index 0000000000..9fcf043524
--- /dev/null
+++ b/coverage/tools/Communicator.h.func-sort-c.html
@@ -0,0 +1,320 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Communicator.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Communicator.h<span style="font-size: 80%;"> (<a href="Communicator.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">91.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Communicator.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Communicator.h.gcov.html#199">_ZN4PLMD12Communicator3MinIdEEvRT_</a></td>
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+              <td class="coverFnHi">250957</td>
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+    <tr>
+              <td class="coverFn"><a href="Communicator.h.gcov.html#181">_ZN4PLMD12Communicator3SumIdEEvRT_</a></td>
+              <td class="coverFnHi">2033708</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Communicator.h.gcov.html#181">_ZN4PLMD12Communicator3SumISt6vectorIdSaIdEEEEvRT_</a></td>
+              <td class="coverFnHi">2125775</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Communicator.h.gcov.html#82">_ZN4PLMD12Communicator4DataC2IdEERSt6vectorIT_SaIS4_EE</a></td>
+              <td class="coverFnHi">2382091</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Communicator.h.gcov.html#206">_ZN4PLMD12Communicator5BcastImEEvRT_i</a></td>
+              <td class="coverFnHi">4603487</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Communicator.h.func.html b/coverage/tools/Communicator.h.func.html
new file mode 100644
index 0000000000..d990b3c4c1
--- /dev/null
+++ b/coverage/tools/Communicator.h.func.html
@@ -0,0 +1,320 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Communicator.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Communicator.h<span style="font-size: 80%;"> (<a href="Communicator.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">91.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Communicator.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Communicator.h.gcov.html b/coverage/tools/Communicator.h.gcov.html
new file mode 100644
index 0000000000..c8e85b160c
--- /dev/null
+++ b/coverage/tools/Communicator.h.gcov.html
@@ -0,0 +1,328 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Communicator.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Communicator.h<span style="font-size: 80%;"> (source / <a href="Communicator.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">91.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Communicator_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Communicator_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;mpi.h&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #endif</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;TypesafePtr.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;string&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;Matrix.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : #ifndef  __PLUMED_HAS_MPI</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Surrogate of MPI_Comm when MPI library is not available</a>
+<a name="40"><span class="lineNum">      40 </span>            : class MPI_Comm {};</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Surrogate of MPI_Datatype when MPI library is not available</a>
+<a name="42"><span class="lineNum">      42 </span>            : class MPI_Datatype {};</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Surrogate of MPI_Status when MPI library is not available</a>
+<a name="44"><span class="lineNum">      44 </span>            : class MPI_Status {};</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Surrogate of MPI_Request when MPI library is not available</a>
+<a name="46"><span class="lineNum">      46 </span>            : class MPI_Request {};</a>
+<a name="47"><span class="lineNum">      47 </span>            : #endif</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /// \ingroup TOOLBOX</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Class containing wrappers to MPI.</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// All the MPI related stuff is relegated here.</a>
+<a name="52"><span class="lineNum">      52 </span>            : class Communicator {</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Communicator</a>
+<a name="54"><span class="lineNum">      54 </span>            :   MPI_Comm communicator;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Function returning the MPI type.</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// You can use it to access to the MPI type of a C++ type, e.g.</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// `MPI_Datatype type=getMPIType&lt;double&gt;();`</a>
+<a name="58"><span class="lineNum">      58 </span>            :   template &lt;class T&gt;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   static MPI_Datatype getMPIType();</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Structure defining a buffer for MPI.</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// It contains info on the pointed data and its type and size. It is useful to</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// allow wrapper of MPI functions where the triplet (buffer,type,size)</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// is grouped into a single object. It can be built starting from</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// different kinds of data. To implement compatibility of MPI wrappers</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// with e.g. vectors, add constructors here.</a>
+<a name="66"><span class="lineNum">      66 </span>            :   struct Data {</a>
+<a name="67"><span class="lineNum">      67 </span>            :     void*pointer;</a>
+<a name="68"><span class="lineNum">      68 </span>            :     int size;</a>
+<a name="69"><span class="lineNum">      69 </span>            :     int nbytes=0;</a>
+<a name="70"><span class="lineNum">      70 </span>            :     MPI_Datatype type;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Init from pointer and size</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    2623992 :     template &lt;typename T&gt; Data(T*p,int s): pointer(p), size(s), nbytes(sizeof(T)), type(getMPIType&lt;T&gt;()) {}</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : /// Init from reference</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">   13309906 :     template &lt;typename T&gt; explicit Data(T&amp;p): pointer(&amp;p), size(1), nbytes(sizeof(T)), type(getMPIType&lt;T&gt;()) {}</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Init from pointer to VectorGeneric</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      11179 :     template &lt;unsigned n&gt; explicit Data(VectorGeneric&lt;n&gt; *p,int s): pointer(p), size(n*s), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Init from reference to VectorGeneric</a>
+<a name="78"><span class="lineNum">      78 </span>            :     template &lt;unsigned n&gt; explicit Data(VectorGeneric&lt;n&gt; &amp;p): pointer(&amp;p), size(n), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// Init from pointer to TensorGeneric</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         16 :     template &lt;unsigned n,unsigned m&gt; explicit Data(TensorGeneric&lt;n,m&gt; *p,int s): pointer(p), size(n*m*s), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Init from reference to TensorGeneric</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      83442 :     template &lt;unsigned n,unsigned m&gt; explicit Data(TensorGeneric&lt;n,m&gt; &amp;p): pointer(&amp;p), size(n*m), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Init from reference to std::vector</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    2398011 :     template &lt;typename T&gt; explicit Data(std::vector&lt;T&gt;&amp;v) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    2398182 :       Data d(v.data(),v.size()); pointer=d.pointer; size=d.size; type=d.type;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    2398011 :     }</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Init from reference to PLMD::Matrix</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         17 :     template &lt;typename T&gt; explicit Data(Matrix&lt;T&gt;&amp;m ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         17 :       if(m.nrows()*m.ncols()&gt;0) { Data d(&amp;m(0,0),m.nrows()*m.ncols()); pointer=d.pointer; size=d.size; type=d.type; }</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :       else { pointer=NULL; size=0; }</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         17 :     }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Init from reference to std::string</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         61 :     explicit Data(std::string&amp;s) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         61 :       if(s.size()&gt;0) { Data d(&amp;s[0],s.size()); pointer=d.pointer; size=d.size; type=d.type; }</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :       else { pointer=NULL; size=0; }</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         61 :     }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   };</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Const version of Communicator::Data</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// See Communicator::Data documentation</a>
+<a name="100"><span class="lineNum">     100 </span>            :   struct ConstData {</a>
+<a name="101"><span class="lineNum">     101 </span>            :     const void*pointer;</a>
+<a name="102"><span class="lineNum">     102 </span>            :     int size;</a>
+<a name="103"><span class="lineNum">     103 </span>            :     int nbytes=0;</a>
+<a name="104"><span class="lineNum">     104 </span>            :     MPI_Datatype type;</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      19900 :     template &lt;typename T&gt; explicit ConstData(const T*p,int s): pointer(p), size(s), nbytes(sizeof(T)), type(getMPIType&lt;T&gt;()) {}</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       5164 :     template &lt;typename T&gt; explicit ConstData(const T&amp;p): pointer(&amp;p), size(1), nbytes(sizeof(T)), type(getMPIType&lt;T&gt;()) {}</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     template &lt;unsigned n&gt; explicit ConstData(const VectorGeneric&lt;n&gt; *p,int s): pointer(p), size(n*s), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</a>
+<a name="108"><span class="lineNum">     108 </span>            :     template &lt;unsigned n&gt; explicit ConstData(const VectorGeneric&lt;n&gt; &amp;p): pointer(&amp;p), size(n), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</a>
+<a name="109"><span class="lineNum">     109 </span>            :     template &lt;unsigned n,unsigned m&gt; explicit ConstData(const TensorGeneric&lt;n,m&gt; *p,int s): pointer(p), size(n*m*s), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</a>
+<a name="110"><span class="lineNum">     110 </span>            :     template &lt;unsigned n,unsigned m&gt; explicit ConstData(const TensorGeneric&lt;n,m&gt; &amp;p): pointer(&amp;p), size(n*m), nbytes(sizeof(double)), type(getMPIType&lt;double&gt;()) {}</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        732 :     template &lt;typename T&gt; explicit ConstData(const std::vector&lt;T&gt;&amp;v) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        732 :       ConstData d(v.data(),v.size()); pointer=d.pointer; size=d.size; type=d.type;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        732 :     }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     template &lt;typename T&gt; explicit ConstData(const Matrix&lt;T&gt;&amp;m ) {</a>
+<a name="115"><span class="lineNum">     115 </span>            :       if(m.nrows()*m.ncols()&gt;0) { ConstData d(&amp;m(0,0),m.nrows()*m.ncols()); pointer=d.pointer; size=d.size; type=d.type; }</a>
+<a name="116"><span class="lineNum">     116 </span>            :       else { pointer=NULL; size=0; }</a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         57 :     explicit ConstData(const std::string&amp;s) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         57 :       if(s.size()&gt;0) { ConstData d(&amp;s[0],s.size()); pointer=d.pointer; size=d.size; type=d.type; }</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       else { pointer=NULL; size=0; }</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         57 :     }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   };</a>
+<a name="123"><span class="lineNum">     123 </span>            : public:</a>
+<a name="124"><span class="lineNum">     124 </span>            :   ///Runtime acces to the __PLUMED_HAS_MPI definition</a>
+<a name="125"><span class="lineNum">     125 </span>            :   static bool plumedHasMPI();</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Wrapper class for MPI_Status</a>
+<a name="128"><span class="lineNum">     128 </span>            :   class Status {</a>
+<a name="129"><span class="lineNum">     129 </span>            :     int Get_count(MPI_Datatype)const;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   public:</a>
+<a name="131"><span class="lineNum">     131 </span>            :     MPI_Status s;</a>
+<a name="132"><span class="lineNum">     132 </span>            :     template &lt;class T&gt;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       7588 :     int Get_count()const {return Get_count(getMPIType&lt;T&gt;());}</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   };</a>
+<a name="135"><span class="lineNum">     135 </span>            : /// Special status used when status should be ignored.</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// E.g. `Recv(a,0,1,Communicator::StatusIgnore);`</a>
+<a name="137"><span class="lineNum">     137 </span>            : /// Notice that this is the default for Recv, so this is equivalent to</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// `Recv(a,0,1);`</a>
+<a name="139"><span class="lineNum">     139 </span>            :   static Status StatusIgnore;</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Wrapper class for MPI_Request</a>
+<a name="141"><span class="lineNum">     141 </span>            :   class Request {</a>
+<a name="142"><span class="lineNum">     142 </span>            :   public:</a>
+<a name="143"><span class="lineNum">     143 </span>            :     MPI_Request r;</a>
+<a name="144"><span class="lineNum">     144 </span>            :     void wait(Status&amp;s=StatusIgnore);</a>
+<a name="145"><span class="lineNum">     145 </span>            :   };</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Default constructor</a>
+<a name="147"><span class="lineNum">     147 </span>            :   Communicator();</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// Copy constructor.</a>
+<a name="149"><span class="lineNum">     149 </span>            : /// It effectively &quot;clones&quot; the communicator, providing a new one acting on the same group</a>
+<a name="150"><span class="lineNum">     150 </span>            :   Communicator(const Communicator&amp;);</a>
+<a name="151"><span class="lineNum">     151 </span>            : /// Assignment operator.</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// It effectively &quot;clones&quot; the communicator, providing a new one acting on the same group</a>
+<a name="153"><span class="lineNum">     153 </span>            :   Communicator&amp; operator=(const Communicator&amp;);</a>
+<a name="154"><span class="lineNum">     154 </span>            : /// Destructor</a>
+<a name="155"><span class="lineNum">     155 </span>            :   virtual ~Communicator();</a>
+<a name="156"><span class="lineNum">     156 </span>            : /// Obtain the rank of the present process</a>
+<a name="157"><span class="lineNum">     157 </span>            :   int Get_rank()const;</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// Obtain the number of processes</a>
+<a name="159"><span class="lineNum">     159 </span>            :   int Get_size()const;</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Set from a real MPI communicator.</a>
+<a name="161"><span class="lineNum">     161 </span>            : /// \param comm MPI communicator</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void Set_comm(MPI_Comm comm);</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// Reference to MPI communicator</a>
+<a name="164"><span class="lineNum">     164 </span>            :   MPI_Comm &amp; Get_comm();</a>
+<a name="165"><span class="lineNum">     165 </span>            : /// Set from a pointer to a real MPI communicator (C).</a>
+<a name="166"><span class="lineNum">     166 </span>            : /// \param comm Pointer to a C MPI communicator</a>
+<a name="167"><span class="lineNum">     167 </span>            :   void Set_comm(const TypesafePtr &amp; comm);</a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Set from a pointer to a real MPI communicator (FORTRAN).</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// \param comm Pointer to a FORTRAN MPI communicator (INTEGER)</a>
+<a name="170"><span class="lineNum">     170 </span>            :   void Set_fcomm(const TypesafePtr &amp; comm);</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// Wrapper to MPI_Abort.</a>
+<a name="172"><span class="lineNum">     172 </span>            : /// \param code Error code</a>
+<a name="173"><span class="lineNum">     173 </span>            :   void Abort(int code);</a>
+<a name="174"><span class="lineNum">     174 </span>            : /// Wrapper to MPI_Barrier</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void Barrier()const;</a>
+<a name="176"><span class="lineNum">     176 </span>            : /// Tests if MPI library is initialized</a>
+<a name="177"><span class="lineNum">     177 </span>            :   static bool initialized();</a>
+<a name="178"><span class="lineNum">     178 </span>            : /// Wrapper for MPI_Allreduce with MPI_SUM (data struct)</a>
+<a name="179"><span class="lineNum">     179 </span>            :   void Sum(Data);</a>
+<a name="180"><span class="lineNum">     180 </span>            : /// Wrapper for MPI_Allreduce with MPI_SUM (pointer)</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      88290 :   template &lt;class T&gt; void Sum(T*buf,int count) {Sum(Data(buf,count));}</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : /// Wrapper for MPI_Allreduce with MPI_SUM (reference)</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">    4195607 :   template &lt;class T&gt; void Sum(T&amp;buf) {Sum(Data(buf));}</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : /// Wrapper for MPI_Allreduce with MPI_PROD (data struct)</a>
+<a name="185"><span class="lineNum">     185 </span>            :   void Prod(Data);</a>
+<a name="186"><span class="lineNum">     186 </span>            : /// Wrapper for MPI_Allreduce with MPI_PROD (pointer)</a>
+<a name="187"><span class="lineNum">     187 </span>            :   template &lt;class T&gt; void Prod(T*buf,int count) {Prod(Data(buf,count));}</a>
+<a name="188"><span class="lineNum">     188 </span>            : /// Wrapper for MPI_Allreduce with MPI_PROD (reference)</a>
+<a name="189"><span class="lineNum">     189 </span>            :   template &lt;class T&gt; void Prod(T&amp;buf) {Prod(Data(buf));}</a>
+<a name="190"><span class="lineNum">     190 </span>            : /// Wrapper for MPI_Allreduce with MPI_MAX (data struct)</a>
+<a name="191"><span class="lineNum">     191 </span>            :   void Max(Data);</a>
+<a name="192"><span class="lineNum">     192 </span>            : /// Wrapper for MPI_Allreduce with MPI_MAX (pointer)</a>
+<a name="193"><span class="lineNum">     193 </span>            :   template &lt;class T&gt; void Max(T*buf,int count) {Max(Data(buf,count));}</a>
+<a name="194"><span class="lineNum">     194 </span>            : /// Wrapper for MPI_Allreduce with MPI_MAX (reference)</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        152 :   template &lt;class T&gt; void Max(T&amp;buf) {Max(Data(buf));}</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : /// Wrapper for MPI_Allreduce with MPI_MIN (data struct)</a>
+<a name="197"><span class="lineNum">     197 </span>            :   void Min(Data);</a>
+<a name="198"><span class="lineNum">     198 </span>            : /// Wrapper for MPI_Allreduce with MPI_MIN (pointer)</a>
+<a name="199"><span class="lineNum">     199 </span>            :   template &lt;class T&gt; void Min(T*buf,int count) {Min(Data(buf,count));}</a>
+<a name="200"><span class="lineNum">     200 </span>            : /// Wrapper for MPI_Allreduce with MPI_MIN (reference)</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   template &lt;class T&gt; void Min(T&amp;buf) {Min(Data(buf));}</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : /// Wrapper for MPI_Bcast (data struct)</a>
+<a name="204"><span class="lineNum">     204 </span>            :   void Bcast(Data,int);</a>
+<a name="205"><span class="lineNum">     205 </span>            : /// Wrapper for MPI_Bcast (pointer)</a>
+<a name="206"><span class="lineNum">     206 </span>            :   template &lt;class T&gt; void Bcast(T*buf,int count,int root) {Bcast(Data(buf,count),root);}</a>
+<a name="207"><span class="lineNum">     207 </span>            : /// Wrapper for MPI_Bcast (reference)</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">    4893279 :   template &lt;class T&gt; void Bcast(T&amp;buf,int root) {Bcast(Data(buf),root);}</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : /// Wrapper for MPI_Isend (data struct)</a>
+<a name="211"><span class="lineNum">     211 </span>            :   Request Isend(ConstData,int,int);</a>
+<a name="212"><span class="lineNum">     212 </span>            : /// Wrapper for MPI_Isend (pointer)</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      15176 :   template &lt;class T&gt; Request Isend(const T*buf,int count,int source,int tag) {return Isend(ConstData(buf,count),source,tag);}</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : /// Wrapper for MPI_Isend (reference)</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        114 :   template &lt;class T&gt; Request Isend(const T&amp;buf,int source,int tag) {return Isend(ConstData(buf),source,tag);}</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : /// Wrapper for MPI_Allgatherv (data struct)</a>
+<a name="218"><span class="lineNum">     218 </span>            :   void Allgatherv(ConstData in,Data out,const int*,const int*);</a>
+<a name="219"><span class="lineNum">     219 </span>            : /// Wrapper for MPI_Allgatherv (pointer)</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      18907 :   template &lt;class T,class S&gt; void Allgatherv(const T*sendbuf,int sendcount,S*recvbuf,const int*recvcounts,const int*displs) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      18907 :     Allgatherv(ConstData(sendbuf,sendcount),Data(recvbuf,0),recvcounts,displs);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      18907 :   }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : /// Wrapper for MPI_Allgatherv (reference)</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        152 :   template &lt;class T,class S&gt; void Allgatherv(const T&amp;sendbuf,S&amp;recvbuf,const int*recvcounts,const int*displs) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        152 :     Allgatherv(ConstData(sendbuf),Data(recvbuf),recvcounts,displs);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        152 :   }</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : /// Wrapper for MPI_Allgather (data struct)</a>
+<a name="229"><span class="lineNum">     229 </span>            :   void Allgather(ConstData in,Data out);</a>
+<a name="230"><span class="lineNum">     230 </span>            : /// Wrapper for MPI_Allgatherv (pointer)</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        204 :   template &lt;class T,class S&gt; void Allgather(const T*sendbuf,int sendcount,S*recvbuf,int recvcount) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        408 :     Allgather(ConstData(sendbuf,sendcount),Data(recvbuf,recvcount*Get_size()));</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        204 :   }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : /// Wrapper for MPI_Allgatherv (reference)</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       5630 :   template &lt;class T,class S&gt; void Allgather(const T&amp;sendbuf,S&amp;recvbuf) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      10680 :     Allgather(ConstData(sendbuf),Data(recvbuf));</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       5630 :   }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : /// Wrapper for MPI_Recv (data struct)</a>
+<a name="240"><span class="lineNum">     240 </span>            :   void Recv(Data,int,int,Status&amp;s=StatusIgnore);</a>
+<a name="241"><span class="lineNum">     241 </span>            : /// Wrapper for MPI_Recv (pointer)</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">      15176 :   template &lt;class T&gt; void Recv(T*buf,int count,int source,int tag,Status&amp;s=StatusIgnore) {Recv(Data(buf,count),source,tag,s);}</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : /// Wrapper for MPI_Recv (reference)</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        114 :   template &lt;class T&gt; void Recv(T&amp;buf,int source,int tag,Status&amp;s=StatusIgnore) {Recv(Data(buf),source,tag,s);}</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : /// Wrapper to MPI_Comm_split</a>
+<a name="247"><span class="lineNum">     247 </span>            :   void Split(int,int,Communicator&amp;)const;</a>
+<a name="248"><span class="lineNum">     248 </span>            : };</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : }</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ConjugateGradient.h.func-sort-c.html b/coverage/tools/ConjugateGradient.h.func-sort-c.html
new file mode 100644
index 0000000000..84130831ef
--- /dev/null
+++ b/coverage/tools/ConjugateGradient.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ConjugateGradient.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ConjugateGradient.h<span style="font-size: 80%;"> (<a href="ConjugateGradient.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ConjugateGradient.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ConjugateGradient.h.gcov.html#41">_ZN4PLMD17ConjugateGradientINS_6dimred17SketchMapConjGradEE8minimiseERKdRSt6vectorIdSaIdEEMS2_FdRKS8_S9_E</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConjugateGradient.h.gcov.html#41">_ZN4PLMD17ConjugateGradientINS_6dimred18SketchMapPointwiseEE8minimiseERKdRSt6vectorIdSaIdEEMS2_FdRKS8_S9_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConjugateGradient.h.gcov.html#41">_ZN4PLMD17ConjugateGradientINS_6dimred24ProjectNonLandmarkPointsEE8minimiseERKdRSt6vectorIdSaIdEEMS2_FdRKS8_S9_E</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ConjugateGradient.h.func.html b/coverage/tools/ConjugateGradient.h.func.html
new file mode 100644
index 0000000000..3c6c516f1b
--- /dev/null
+++ b/coverage/tools/ConjugateGradient.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ConjugateGradient.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ConjugateGradient.h<span style="font-size: 80%;"> (<a href="ConjugateGradient.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ConjugateGradient.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ConjugateGradient.h.gcov.html#41">_ZN4PLMD17ConjugateGradientINS_6dimred17SketchMapConjGradEE8minimiseERKdRSt6vectorIdSaIdEEMS2_FdRKS8_S9_E</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConjugateGradient.h.gcov.html#41">_ZN4PLMD17ConjugateGradientINS_6dimred18SketchMapPointwiseEE8minimiseERKdRSt6vectorIdSaIdEEMS2_FdRKS8_S9_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ConjugateGradient.h.gcov.html#41">_ZN4PLMD17ConjugateGradientINS_6dimred24ProjectNonLandmarkPointsEE8minimiseERKdRSt6vectorIdSaIdEEMS2_FdRKS8_S9_E</a></td>
+              <td class="coverFnHi">500</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ConjugateGradient.h.gcov.html b/coverage/tools/ConjugateGradient.h.gcov.html
new file mode 100644
index 0000000000..c12ed60bb2
--- /dev/null
+++ b/coverage/tools/ConjugateGradient.h.gcov.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ConjugateGradient.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ConjugateGradient.h<span style="font-size: 80%;"> (source / <a href="ConjugateGradient.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_ConjugateGradient_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_ConjugateGradient_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;MinimiseBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : class ConjugateGradient : public MinimiseBase&lt;FCLASS&gt; {</a>
+<a name="31"><span class="lineNum">      31 </span>            : private:</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// This is the pointer to the member function in the energy</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// calculating class that calculates the energy</a>
+<a name="34"><span class="lineNum">      34 </span>            :   typedef double(FCLASS::*engf_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der );</a>
+<a name="35"><span class="lineNum">      35 </span>            :   const unsigned ITMAX;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   const double EPS;</a>
+<a name="37"><span class="lineNum">      37 </span>            : public:</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        505 :   explicit ConjugateGradient( FCLASS* funcc ) : MinimiseBase&lt;FCLASS&gt;(funcc), ITMAX(200), EPS(1E-10) {}</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   void minimise( const double&amp; ftol, std::vector&lt;double&gt;&amp; p, engf_pointer myfunc );</a>
+<a name="40"><span class="lineNum">      40 </span>            : };</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        526 : void ConjugateGradient&lt;FCLASS&gt;::minimise( const double&amp; ftol, std::vector&lt;double&gt;&amp; p, engf_pointer myfunc ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        526 :   std::vector&lt;double&gt; xi( p.size() ), g( p.size() ), h( p.size() );</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        526 :   double fp = this-&gt;calcDerivatives( p, xi, myfunc );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       6826 :   for(unsigned j=0; j&lt;p.size(); ++j) { g[j] = -xi[j]; xi[j]=h[j]=g[j]; }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        897 :   for(unsigned its=0; its&lt;ITMAX; ++its) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        897 :     double fret=this-&gt;linemin( xi, p, myfunc );</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :     // The exit condition</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        897 :     if( 2.0*std::fabs(fret-fp) &lt;= ftol*(std::fabs(fret)+std::fabs(fp)+EPS)) { return; }</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        371 :     fp = fret; this-&gt;calcDerivatives( p, xi, myfunc );</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :     double ddg=0., gg=0.;</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      12899 :     for(unsigned j=0; j&lt;p.size(); ++j) { gg += g[j]*g[j]; ddg += (xi[j]+g[j])*xi[j]; }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        371 :     if( gg==0.0 ) return;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        371 :     double gam=ddg/gg;</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      12899 :     for(unsigned j=0; j&lt;p.size(); ++j) { g[j] = -xi[j]; xi[j]=h[j]=g[j]+gam*h[j]; }</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;Too many interactions in conjugate gradient&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/DLLoader.cpp.func-sort-c.html b/coverage/tools/DLLoader.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e2b6ccf1f6
--- /dev/null
+++ b/coverage/tools/DLLoader.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/DLLoader.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - DLLoader.cpp<span style="font-size: 80%;"> (<a href="DLLoader.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DLLoader.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#53">_ZN4PLMD8DLLoader5errorB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#38">_ZN4PLMD8DLLoader4loadERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#29">_ZN4PLMD8DLLoader9installedEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#72">_ZN4PLMD8DLLoaderC2Ev</a></td>
+              <td class="coverFnHi">809485</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#57">_ZN4PLMD8DLLoaderD2Ev</a></td>
+              <td class="coverFnHi">809485</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/DLLoader.cpp.func.html b/coverage/tools/DLLoader.cpp.func.html
new file mode 100644
index 0000000000..2e2d35f555
--- /dev/null
+++ b/coverage/tools/DLLoader.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/DLLoader.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - DLLoader.cpp<span style="font-size: 80%;"> (<a href="DLLoader.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DLLoader.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#38">_ZN4PLMD8DLLoader4loadERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#53">_ZN4PLMD8DLLoader5errorB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#29">_ZN4PLMD8DLLoader9installedEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#72">_ZN4PLMD8DLLoaderC2Ev</a></td>
+              <td class="coverFnHi">809485</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DLLoader.cpp.gcov.html#57">_ZN4PLMD8DLLoaderD2Ev</a></td>
+              <td class="coverFnHi">809485</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/DLLoader.cpp.gcov.html b/coverage/tools/DLLoader.cpp.gcov.html
new file mode 100644
index 0000000000..283c6fb9ce
--- /dev/null
+++ b/coverage/tools/DLLoader.cpp.gcov.html
@@ -0,0 +1,155 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/DLLoader.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - DLLoader.cpp<span style="font-size: 80%;"> (source / <a href="DLLoader.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;DLLoader.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;dlfcn.h&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #endif</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          2 : bool DLLoader::installed() {</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          2 :   return true;</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : #else</a>
+<a name="35"><span class="lineNum">      35 </span>            :   return false;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #endif</a>
+<a name="37"><span class="lineNum">      37 </span>            : }</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          1 : void* DLLoader::load(const std::string&amp;s) {</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          1 :   void* p=dlopen(s.c_str(),RTLD_NOW|RTLD_LOCAL);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          1 :   if(!p) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :     lastError=dlerror();</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   } else {</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          1 :     lastError=&quot;&quot;;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :     handles.push(p);</a>
+<a name="48"><span class="lineNum">      48 </span>            :   }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :   return p;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : #else</a>
+<a name="51"><span class="lineNum">      51 </span>            :   return NULL;</a>
+<a name="52"><span class="lineNum">      52 </span>            : #endif</a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 : const std::string &amp; DLLoader::error() {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   return lastError;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : }</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">     809485 : DLLoader::~DLLoader() {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">     809485 :   auto debug=std::getenv(&quot;PLUMED_LOAD_DEBUG&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">     809485 :   if(debug) std::fprintf(stderr,&quot;delete dlloader\n&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">     809486 :   while(!handles.empty()) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          1 :     int ret=dlclose(handles.top());</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          1 :     if(ret) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :       std::fprintf(stderr,&quot;+++ error reported by dlclose: %s\n&quot;,dlerror());</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     }</a>
+<a name="68"><span class="lineNum">      68 </span>            :     handles.pop();</a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     809485 :   if(debug) std::fprintf(stderr,&quot;end delete dlloader\n&quot;);</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : #endif</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">     809485 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">     809485 : DLLoader::DLLoader() {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   // do nothing</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     809485 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/DynamicList.h.func-sort-c.html b/coverage/tools/DynamicList.h.func-sort-c.html
new file mode 100644
index 0000000000..7edf84e186
--- /dev/null
+++ b/coverage/tools/DynamicList.h.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/DynamicList.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - DynamicList.h<span style="font-size: 80%;"> (<a href="DynamicList.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="DynamicList.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#237">_ZN4PLMD11DynamicListIjE14addIndexToListERKj</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#216">_ZN4PLMD11DynamicListIjE5clearEv</a></td>
+              <td class="coverFnHi">41860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#334">_ZN4PLMD11DynamicListIjE14sortActiveListEv</a></td>
+              <td class="coverFnHi">56305</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#305">_ZN4PLMD11DynamicListIjE19updateActiveMembersEv</a></td>
+              <td class="coverFnHi">62072</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#242">_ZN4PLMD11DynamicListIjE25createIndexListFromVectorERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">402101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#328">_ZN4PLMD11DynamicListIjE14completeUpdateEv</a></td>
+              <td class="coverFnHi">876595</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#315">_ZN4PLMD11DynamicListIjE18emptyActiveMembersEv</a></td>
+              <td class="coverFnHi">932900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#272">_ZN4PLMD11DynamicListIjE13deactivateAllEv</a></td>
+              <td class="coverFnHi">2099234</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#341">_ZNK4PLMD11DynamicListIjE14updateCompleteEv</a></td>
+              <td class="coverFnHi">4878695</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#232">_ZNK4PLMD11DynamicListIjE15getNumberActiveEv</a></td>
+              <td class="coverFnHi">54365506</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#321">_ZN4PLMD11DynamicListIjE21putIndexInActiveArrayERKj</a></td>
+              <td class="coverFnHi">77411726</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#222">_ZNK4PLMD11DynamicListIjE8isActiveERKj</a></td>
+              <td class="coverFnHi">424180368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#282">_ZN4PLMD11DynamicListIjE8activateEj</a></td>
+              <td class="coverFnHi">1544110399</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/DynamicList.h.func.html b/coverage/tools/DynamicList.h.func.html
new file mode 100644
index 0000000000..6e5d4ae981
--- /dev/null
+++ b/coverage/tools/DynamicList.h.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/DynamicList.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - DynamicList.h<span style="font-size: 80%;"> (<a href="DynamicList.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="DynamicList.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#272">_ZN4PLMD11DynamicListIjE13deactivateAllEv</a></td>
+              <td class="coverFnHi">2099234</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#237">_ZN4PLMD11DynamicListIjE14addIndexToListERKj</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#328">_ZN4PLMD11DynamicListIjE14completeUpdateEv</a></td>
+              <td class="coverFnHi">876595</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#334">_ZN4PLMD11DynamicListIjE14sortActiveListEv</a></td>
+              <td class="coverFnHi">56305</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#315">_ZN4PLMD11DynamicListIjE18emptyActiveMembersEv</a></td>
+              <td class="coverFnHi">932900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#305">_ZN4PLMD11DynamicListIjE19updateActiveMembersEv</a></td>
+              <td class="coverFnHi">62072</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#321">_ZN4PLMD11DynamicListIjE21putIndexInActiveArrayERKj</a></td>
+              <td class="coverFnHi">77411726</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#242">_ZN4PLMD11DynamicListIjE25createIndexListFromVectorERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">402101</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#216">_ZN4PLMD11DynamicListIjE5clearEv</a></td>
+              <td class="coverFnHi">41860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#282">_ZN4PLMD11DynamicListIjE8activateEj</a></td>
+              <td class="coverFnHi">1544110399</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#341">_ZNK4PLMD11DynamicListIjE14updateCompleteEv</a></td>
+              <td class="coverFnHi">4878695</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#232">_ZNK4PLMD11DynamicListIjE15getNumberActiveEv</a></td>
+              <td class="coverFnHi">54365506</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="DynamicList.h.gcov.html#222">_ZNK4PLMD11DynamicListIjE8isActiveERKj</a></td>
+              <td class="coverFnHi">424180368</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/DynamicList.h.gcov.html b/coverage/tools/DynamicList.h.gcov.html
new file mode 100644
index 0000000000..4cd0233d66
--- /dev/null
+++ b/coverage/tools/DynamicList.h.gcov.html
@@ -0,0 +1,455 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/DynamicList.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - DynamicList.h<span style="font-size: 80%;"> (source / <a href="DynamicList.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntry">47</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_DynamicList_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_DynamicList_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : /**</a>
+<a name="31"><span class="lineNum">      31 </span>            : \ingroup TOOLBOX</a>
+<a name="32"><span class="lineNum">      32 </span>            : A class for storing a list that changes which members are active as a function of time.  It also</a>
+<a name="33"><span class="lineNum">      33 </span>            : contains friends method that allows you to link two dynamic lists so that you can request</a>
+<a name="34"><span class="lineNum">      34 </span>            : stuff from list2 in list1</a>
+<a name="35"><span class="lineNum">      35 </span>            : A PLMD::DynamicList can be used to change what elements in a list should be looped over at any given</a>
+<a name="36"><span class="lineNum">      36 </span>            : time. This class is, for the most part, used in tandem with PLMD::NeighbourList.  For complex reasons</a>
+<a name="37"><span class="lineNum">      37 </span>            : related to the PLMD::MultiColvar object the dynamic list class is separate from PLMD::NeighbourList.</a>
+<a name="38"><span class="lineNum">      38 </span>            : This is no bad thing though as there may be occasions where one needs to change the elements currently</a>
+<a name="39"><span class="lineNum">      39 </span>            : involved in a calculation using some non neighbour list based method.  To be clear though PLMD::NeighbourList</a>
+<a name="40"><span class="lineNum">      40 </span>            : will look after everything connected with PLMD::DynamicList other than the initial setup of PLMD::DynamicList</a>
+<a name="41"><span class="lineNum">      41 </span>            : and the loops over the active elements of the list.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The essence of a dynamic list is as follows.  Consider the following loop:</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \verbatim</a>
+<a name="46"><span class="lineNum">      46 </span>            : std::vector&lt;something&gt; aa;</a>
+<a name="47"><span class="lineNum">      47 </span>            : for(unsigned i=0;i&lt;aa.size();++i){ aa[i].doSomething(); }</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endverbatim</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : This takes all the members in aa and does something or other to them - simple.  Now it may well</a>
+<a name="51"><span class="lineNum">      51 </span>            : be that the precise set of things from aa that you want to do in any given time or place is not</a>
+<a name="52"><span class="lineNum">      52 </span>            : always the same.  We can thus use dynamic lists to control what particular things are done are done</a>
+<a name="53"><span class="lineNum">      53 </span>            : at a given time.  That is to say we can use PLMD::DynamicList to specify a subset of things from</a>
+<a name="54"><span class="lineNum">      54 </span>            : aa to do at a given time.  This is done by:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \verbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : DynamicList list; std::vector&lt;something&gt; aa; unsigned kk;</a>
+<a name="58"><span class="lineNum">      58 </span>            : for(unsigned i=0;i&lt;list.getNumberActive();++i){ kk=list[i]; aa[kk].doSomething(); }</a>
+<a name="59"><span class="lineNum">      59 </span>            : \endverbatim</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : where we somewhere set up the list and make some decisions (in PLMD::NeighbourList for example) as to what elements</a>
+<a name="62"><span class="lineNum">      62 </span>            : from aa are currently active.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \section Setup</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : Setting up a dynamic list is a matter of declaring it and passing a set of indices to it.  For the example</a>
+<a name="67"><span class="lineNum">      67 </span>            : above with aa one can do this using:</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \verbatim</a>
+<a name="70"><span class="lineNum">      70 </span>            : DynamicList list;</a>
+<a name="71"><span class="lineNum">      71 </span>            : for(unsigned i=0;i&lt;aa.size();++i) list.addIndexToList( i );</a>
+<a name="72"><span class="lineNum">      72 </span>            : \endverbatim</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : Doing this creates the list of all members.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \section arse1 Cycling over the full set of members</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : To cycle over the full set of members in the list one should do:</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \verbatim</a>
+<a name="81"><span class="lineNum">      81 </span>            : for(unsigned i=0;i&lt;list.fullSize();++i){ kk=list(i); aa[kk].doSomething(); }</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endverbatim</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : If the DynamicList was set up as per the example above then this code is equivalent to:</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : \verbatim</a>
+<a name="87"><span class="lineNum">      87 </span>            : for(unsigned i=0;i&lt;aa.size();++i){ aa[i].doSomething(); }</a>
+<a name="88"><span class="lineNum">      88 </span>            : \endverbatim</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \section arse2 Activating and deactivating members</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : The important business comes when we start activating and deactivating members.  When we create</a>
+<a name="93"><span class="lineNum">      93 </span>            : a dynamic list none of the members are active for business.  Hence, getNumberActive() returns 0.</a>
+<a name="94"><span class="lineNum">      94 </span>            : There are four routines that we can use to change this situation.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : &lt;table align=&quot;center&quot; frame=&quot;void&quot; width=&quot;95%&quot; cellpadding=&quot;5%&quot;&gt;</a>
+<a name="97"><span class="lineNum">      97 </span>            : &lt;tr&gt;</a>
+<a name="98"><span class="lineNum">      98 </span>            : &lt;td width=&quot;5%&quot;&gt; activateAll() &lt;/td&gt; &lt;td&gt; make all members active &lt;/td&gt;</a>
+<a name="99"><span class="lineNum">      99 </span>            : &lt;/tr&gt;&lt;tr&gt;</a>
+<a name="100"><span class="lineNum">     100 </span>            : &lt;td&gt; activate(i) &lt;/td&gt; &lt;td&gt; make the ith element of the list active (in the example above this mean we doSomething() for element i of aa) &lt;/td&gt;</a>
+<a name="101"><span class="lineNum">     101 </span>            : &lt;/tr&gt;&lt;tr&gt;</a>
+<a name="102"><span class="lineNum">     102 </span>            : &lt;td&gt; deactivateAll() &lt;/td&gt; &lt;td&gt; make all members inactive &lt;/td&gt;</a>
+<a name="103"><span class="lineNum">     103 </span>            : &lt;/tr&gt;&lt;tr&gt;</a>
+<a name="104"><span class="lineNum">     104 </span>            : &lt;td&gt; deactivate(i) &lt;/td&gt; &lt;td&gt; make th ith element of the list active (in the example above this mean we dont doSomething() for element i of aa) &lt;/td&gt;</a>
+<a name="105"><span class="lineNum">     105 </span>            : &lt;/tr&gt;</a>
+<a name="106"><span class="lineNum">     106 </span>            : &lt;/table&gt;</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : Once you have activated and deactivated members to your hearts content you can then update the dynamic list using</a>
+<a name="109"><span class="lineNum">     109 </span>            : PLMD::DynamicList::updateActiveMembers().  Once this is done you can loop over only the members you have specifically</a>
+<a name="110"><span class="lineNum">     110 </span>            : made active using:</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : \verbatim</a>
+<a name="113"><span class="lineNum">     113 </span>            : DynamicList list;</a>
+<a name="114"><span class="lineNum">     114 </span>            : for(unsigned i=0;i&lt;list.getNumberActive();++i){ kk=list[i]; aa[kk].doSomething(); }</a>
+<a name="115"><span class="lineNum">     115 </span>            : \endverbatim</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : as was described above.</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : \section arse3 Using MPI</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : If your loop is distributed over processesors you can still use dynamic lists to activate and deactivate members.</a>
+<a name="122"><span class="lineNum">     122 </span>            : When running with mpi however you must call PLMD::DynamicList::setupMPICommunication during initialization.  To</a>
+<a name="123"><span class="lineNum">     123 </span>            : gather the members that have been activated/deactivated during the running of all the processes on all the nodes</a>
+<a name="124"><span class="lineNum">     124 </span>            : you must call PLMD::DynamicList::mpi_gatherActiveMembers in place of PLMD::DynamicList::updateActiveMembers.</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : \section arse4 A final note</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : When using dynamic_lists we strongly recommend that you first compile without the -DNDEBUG flag.  When this</a>
+<a name="129"><span class="lineNum">     129 </span>            : flag is not present many checks are performed inside the dynamic list class, which will help you ensure that</a>
+<a name="130"><span class="lineNum">     130 </span>            : the dynamic list is used correctly.</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : */</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : template &lt;typename T&gt;</a>
+<a name="135"><span class="lineNum">     135 </span>            : class DynamicList {</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// This gathers data split across nodes list of Dynamic lists</a>
+<a name="137"><span class="lineNum">     137 </span>            :   template &lt;typename U&gt;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   friend void mpi_gatherActiveMembers(Communicator&amp;, std::vector&lt; DynamicList&lt;U&gt; &gt;&amp; );</a>
+<a name="139"><span class="lineNum">     139 </span>            : private:</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// This is the list of all the relevant members</a>
+<a name="141"><span class="lineNum">     141 </span>            :   std::vector&lt;T&gt; all;</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// This tells us what members of all are on/off at any given time</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::vector&lt;unsigned&gt; onoff;</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// The current number of active members</a>
+<a name="145"><span class="lineNum">     145 </span>            :   unsigned nactive;</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// This is the list of active members</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::vector&lt;unsigned&gt; active;</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// the number of processors the jobs in the Dynamic list are distributed across</a>
+<a name="149"><span class="lineNum">     149 </span>            :   unsigned nprocessors;</a>
+<a name="150"><span class="lineNum">     150 </span>            : /// The rank of the node we are on</a>
+<a name="151"><span class="lineNum">     151 </span>            :   unsigned rank;</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// These are flags that are used internally to ensure that dynamic lists are being used properly</a>
+<a name="153"><span class="lineNum">     153 </span>            :   bool allWereActivated, allWereDeactivated;</a>
+<a name="154"><span class="lineNum">     154 </span>            : public:</a>
+<a name="155"><span class="lineNum">     155 </span>            : /// Constructor</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     360242 :   DynamicList():nactive(0),nprocessors(1),rank(0),allWereActivated(false),allWereDeactivated(false) {}</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : /// An operator that returns the element from the current active list</a>
+<a name="158"><span class="lineNum">     158 </span>            :   inline T operator [] (const unsigned&amp; i) const {</a>
+<a name="159"><span class="lineNum">     159 </span>            :     plumed_dbg_assert( i&lt;nactive );</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">  642999946 :     return all[ active[i] ];</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// An operator that returns the element from the full list (used in neighbour lists)</a>
+<a name="163"><span class="lineNum">     163 </span>            :   inline T operator () (const unsigned&amp; i) const {</a>
+<a name="164"><span class="lineNum">     164 </span>            :     plumed_dbg_assert( i&lt;all.size() );</a>
+<a name="165"><span class="lineNum">     165 </span>            :     return all[i];</a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// Clear the list</a>
+<a name="168"><span class="lineNum">     168 </span>            :   void clear();</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// Return the total number of elements in the list</a>
+<a name="170"><span class="lineNum">     170 </span>            :   unsigned fullSize() const;</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// Return the number of elements that are currently active</a>
+<a name="172"><span class="lineNum">     172 </span>            :   unsigned getNumberActive() const;</a>
+<a name="173"><span class="lineNum">     173 </span>            : /// Find out if a member is active</a>
+<a name="174"><span class="lineNum">     174 </span>            :   bool isActive(const unsigned&amp; ) const;</a>
+<a name="175"><span class="lineNum">     175 </span>            : /// Setup MPI communication if things are activated/deactivated on different nodes</a>
+<a name="176"><span class="lineNum">     176 </span>            :   void setupMPICommunication( Communicator&amp; comm );</a>
+<a name="177"><span class="lineNum">     177 </span>            : /// Add something to the active list</a>
+<a name="178"><span class="lineNum">     178 </span>            :   void addIndexToList( const T &amp; ii );</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// Create the list from a vector</a>
+<a name="180"><span class="lineNum">     180 </span>            :   void createIndexListFromVector( const std::vector&lt;T&gt;&amp; myind );</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// Find the index of in the list which has value t</a>
+<a name="182"><span class="lineNum">     182 </span>            :   int getIndexOfElement( const T&amp; t ) const ;</a>
+<a name="183"><span class="lineNum">     183 </span>            : /// Make a particular element inactive</a>
+<a name="184"><span class="lineNum">     184 </span>            :   void deactivate( const T&amp; t );</a>
+<a name="185"><span class="lineNum">     185 </span>            : /// Make everything in the list inactive</a>
+<a name="186"><span class="lineNum">     186 </span>            :   void deactivateAll();</a>
+<a name="187"><span class="lineNum">     187 </span>            : /// Make something active</a>
+<a name="188"><span class="lineNum">     188 </span>            :   void activate( const unsigned ii );</a>
+<a name="189"><span class="lineNum">     189 </span>            : /// Make everything in the list active</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void activateAll();</a>
+<a name="191"><span class="lineNum">     191 </span>            : /// Do updateActiveMembers for a loop that has been distributed over multiple nodes</a>
+<a name="192"><span class="lineNum">     192 </span>            :   void mpi_gatherActiveMembers(Communicator&amp; comm);</a>
+<a name="193"><span class="lineNum">     193 </span>            : /// Get the list of active members</a>
+<a name="194"><span class="lineNum">     194 </span>            :   void updateActiveMembers();</a>
+<a name="195"><span class="lineNum">     195 </span>            : /// Empty the list of active members</a>
+<a name="196"><span class="lineNum">     196 </span>            :   void emptyActiveMembers();</a>
+<a name="197"><span class="lineNum">     197 </span>            : /// This can be used for a fast version of updateActiveMembers in which only a subset of the</a>
+<a name="198"><span class="lineNum">     198 </span>            : /// indexes are checked</a>
+<a name="199"><span class="lineNum">     199 </span>            :   void putIndexInActiveArray( const unsigned&amp; ii );</a>
+<a name="200"><span class="lineNum">     200 </span>            : /// This can be called on once update is complete</a>
+<a name="201"><span class="lineNum">     201 </span>            :   void completeUpdate();</a>
+<a name="202"><span class="lineNum">     202 </span>            : /// This tells one if an update has been completed</a>
+<a name="203"><span class="lineNum">     203 </span>            :   bool updateComplete() const ;</a>
+<a name="204"><span class="lineNum">     204 </span>            : /// This sorts the elements in the active list</a>
+<a name="205"><span class="lineNum">     205 </span>            :   void sortActiveList();</a>
+<a name="206"><span class="lineNum">     206 </span>            : /// Retriee the list of active objects</a>
+<a name="207"><span class="lineNum">     207 </span>            :   std::vector&lt;T&gt; retrieveActiveList();</a>
+<a name="208"><span class="lineNum">     208 </span>            : };</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : template &lt;typename T&gt;</a>
+<a name="211"><span class="lineNum">     211 </span>            : std::vector&lt;T&gt; DynamicList&lt;T&gt;::retrieveActiveList() {</a>
+<a name="212"><span class="lineNum">     212 </span>            :   std::vector&lt;T&gt; this_active(nactive);</a>
+<a name="213"><span class="lineNum">     213 </span>            :   for(unsigned k=0; k&lt;nactive; ++k) this_active[k]=all[ active[k] ];</a>
+<a name="214"><span class="lineNum">     214 </span>            :   return this_active;</a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : template &lt;typename T&gt;</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      41860 : void DynamicList&lt;T&gt;::clear() {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      41860 :   all.resize(0);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      41860 :   onoff.resize(0); active.resize(0);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      41860 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : template &lt;typename T&gt;</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">  424180368 : bool DynamicList&lt;T&gt;::isActive( const unsigned&amp; i ) const {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">  424180368 :   return (onoff[i]&gt;0 &amp;&amp; onoff[i]%nprocessors==0);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : template &lt;typename T&gt;</a>
+<a name="229"><span class="lineNum">     229 </span>            : unsigned DynamicList&lt;T&gt;::fullSize() const {</a>
+<a name="230"><span class="lineNum">     230 </span>            :   return all.size();</a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : template &lt;typename T&gt;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">   54365506 : unsigned DynamicList&lt;T&gt;::getNumberActive() const {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">   54365506 :   return nactive;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : template &lt;typename T&gt;</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         91 : void DynamicList&lt;T&gt;::addIndexToList( const T &amp; ii ) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         91 :   all.push_back(ii); active.resize( all.size() ); onoff.push_back(0);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         91 : }</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : template &lt;typename T&gt;</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">     402101 : void DynamicList&lt;T&gt;::createIndexListFromVector( const std::vector&lt;T&gt;&amp; myind ) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">     402101 :   plumed_dbg_assert( all.size()==0 ); onoff.resize( myind.size(), 0 );</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">     402101 :   active.resize( myind.size() );</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">     402101 :   all.insert( all.end(), myind.begin(), myind.end() );</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">     402101 : }</span></a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : template &lt;typename T&gt;</a>
+<a name="251"><span class="lineNum">     251 </span>            : void DynamicList&lt;T&gt;::setupMPICommunication( Communicator&amp; comm ) {</a>
+<a name="252"><span class="lineNum">     252 </span>            :   nprocessors=comm.Get_size(); rank=comm.Get_rank();</a>
+<a name="253"><span class="lineNum">     253 </span>            : }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            : template &lt;typename T&gt;</a>
+<a name="256"><span class="lineNum">     256 </span>            : int DynamicList&lt;T&gt;::getIndexOfElement( const T&amp; t ) const {</a>
+<a name="257"><span class="lineNum">     257 </span>            :   for(unsigned i=0; i&lt;all.size(); ++i) {</a>
+<a name="258"><span class="lineNum">     258 </span>            :     if( t==all[i] ) {return i; }</a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span>            :   plumed_merror(&quot;Could not find an element in the dynamic list&quot;);</a>
+<a name="261"><span class="lineNum">     261 </span>            : }</a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : template &lt;typename T&gt;</a>
+<a name="264"><span class="lineNum">     264 </span>            : void DynamicList&lt;T&gt;::deactivate( const T&amp; t ) {</a>
+<a name="265"><span class="lineNum">     265 </span>            :   plumed_dbg_assert( allWereActivated );</a>
+<a name="266"><span class="lineNum">     266 </span>            :   unsigned ii=getIndexOfElement( t );</a>
+<a name="267"><span class="lineNum">     267 </span>            :   if( onoff[ii]==0 || onoff[ii]%nprocessors!=0 ) return;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   // Deactivates the component</a>
+<a name="269"><span class="lineNum">     269 </span>            :   if( rank==0 ) onoff[ii]=nprocessors-1;</a>
+<a name="270"><span class="lineNum">     270 </span>            :   else onoff[ii]=nprocessors-rank;</a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : template &lt;typename T&gt;</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">    2099234 : void DynamicList&lt;T&gt;::deactivateAll() {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">    2099234 :   allWereDeactivated=true; allWereActivated=false;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">   82076346 :   for(unsigned i=0; i&lt;nactive; ++i) onoff[ active[i] ]= 0;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    2099234 :   nactive=0;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : #ifndef NDEBUG</a>
+<a name="279"><span class="lineNum">     279 </span>            :   for(unsigned i=0; i&lt;onoff.size(); ++i) plumed_dbg_assert( onoff[i]==0 );</a>
+<a name="280"><span class="lineNum">     280 </span>            : #endif</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">    2099234 : }</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : template &lt;typename T&gt;</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov"> 1544110399 : void DynamicList&lt;T&gt;::activate( const unsigned ii ) {</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   plumed_dbg_massert(ii&lt;all.size(),&quot;ii is out of bounds&quot;);</a>
+<a name="286"><span class="lineNum">     286 </span>            :   plumed_dbg_assert( !allWereActivated );</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov"> 1544110399 :   onoff[ii]=nprocessors;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov"> 1544110399 : }</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : template &lt;typename T&gt;</a>
+<a name="291"><span class="lineNum">     291 </span>            : void DynamicList&lt;T&gt;::activateAll() {</a>
+<a name="292"><span class="lineNum">     292 </span>            :   for(unsigned i=0; i&lt;onoff.size(); ++i) onoff[i]=nprocessors;</a>
+<a name="293"><span class="lineNum">     293 </span>            :   allWereActivated=true; updateActiveMembers(); allWereActivated=true;</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span>            : template &lt;typename T&gt;</a>
+<a name="298"><span class="lineNum">     298 </span>            : void DynamicList&lt;T&gt;::mpi_gatherActiveMembers(Communicator&amp; comm) {</a>
+<a name="299"><span class="lineNum">     299 </span>            :   plumed_massert( comm.Get_size()==nprocessors, &quot;error missing a call to DynamicList::setupMPICommunication&quot;);</a>
+<a name="300"><span class="lineNum">     300 </span>            :   comm.Sum(&amp;onoff[0],onoff.size());</a>
+<a name="301"><span class="lineNum">     301 </span>            :   // When we mpi gather onoff to be on it should be active on ALL nodes</a>
+<a name="302"><span class="lineNum">     302 </span>            :   for(unsigned i=0; i&lt;all.size(); ++i) if( onoff[i]&gt;0 &amp;&amp; onoff[i]%nprocessors==0 ) { onoff[i]=nprocessors; }</a>
+<a name="303"><span class="lineNum">     303 </span>            :   updateActiveMembers();</a>
+<a name="304"><span class="lineNum">     304 </span>            : }</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            : template &lt;typename T&gt;</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">      62072 : void DynamicList&lt;T&gt;::updateActiveMembers() {</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :   plumed_dbg_assert( allWereActivated || allWereDeactivated );</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">      62072 :   unsigned kk=0; allWereActivated=allWereDeactivated=false;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">   19025522 :   for(unsigned i=0; i&lt;all.size(); ++i) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">   18963450 :     if( onoff[i]&gt;0 &amp;&amp; onoff[i]%nprocessors==0 ) { active[kk]=i; kk++; }</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   }</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">      62072 :   nactive=kk;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">      62072 : }</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : template &lt;typename T&gt;</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     932900 : void DynamicList&lt;T&gt;::emptyActiveMembers() {</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :   plumed_dbg_assert( allWereActivated || allWereDeactivated );</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">     932900 :   nactive=0;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">     932900 : }</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : template &lt;typename T&gt;</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">   77411726 : void DynamicList&lt;T&gt;::putIndexInActiveArray( const unsigned&amp; ii ) {</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   plumed_dbg_assert( allWereActivated || allWereDeactivated );</a>
+<a name="325"><span class="lineNum">     325 </span>            :   plumed_dbg_assert( onoff[ii]&gt;0 &amp;&amp; onoff[ii]%nprocessors==0 );</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">   77411726 :   active[nactive]=ii; nactive++;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">   77411726 : }</span></a>
+<a name="328"><span class="lineNum">     328 </span>            : </a>
+<a name="329"><span class="lineNum">     329 </span>            : template &lt;typename T&gt;</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">     876595 : void DynamicList&lt;T&gt;::completeUpdate() {</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   plumed_dbg_assert( allWereActivated || allWereDeactivated );</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">     876595 :   allWereActivated=allWereDeactivated=false;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">     876595 : }</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            : template &lt;typename T&gt;</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">      56305 : void DynamicList&lt;T&gt;::sortActiveList() {</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   plumed_dbg_assert( allWereActivated || allWereDeactivated );</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      56305 :   allWereActivated=allWereDeactivated=false;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      56305 :   std::sort( active.begin(), active.begin()+nactive );</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      56305 : }</span></a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            : template &lt;typename T&gt;</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">    4878695 : bool DynamicList&lt;T&gt;::updateComplete() const {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">    4878695 :   if( !allWereActivated &amp;&amp; !allWereDeactivated ) return true;</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   return false;</a>
+<a name="346"><span class="lineNum">     346 </span>            : }</a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            : template &lt;typename U&gt;</a>
+<a name="349"><span class="lineNum">     349 </span>            : void mpi_gatherActiveMembers(Communicator&amp; comm, std::vector&lt; DynamicList&lt;U&gt; &gt;&amp; ll ) {</a>
+<a name="350"><span class="lineNum">     350 </span>            :   // Setup an array to hold all data</a>
+<a name="351"><span class="lineNum">     351 </span>            :   unsigned bufsize=0; unsigned size=comm.Get_size();</a>
+<a name="352"><span class="lineNum">     352 </span>            :   for(unsigned i=0; i&lt;ll.size(); ++i) {</a>
+<a name="353"><span class="lineNum">     353 </span>            :     plumed_dbg_massert( ll[i].nprocessors==size, &quot;missing a call to DynamicList::setupMPICommunication&quot; );</a>
+<a name="354"><span class="lineNum">     354 </span>            :     bufsize+=ll[i].onoff.size();</a>
+<a name="355"><span class="lineNum">     355 </span>            :   }</a>
+<a name="356"><span class="lineNum">     356 </span>            :   std::vector&lt;unsigned&gt; buffer( bufsize );</a>
+<a name="357"><span class="lineNum">     357 </span>            :   // Gather all onoff data into a single array</a>
+<a name="358"><span class="lineNum">     358 </span>            :   bufsize=0;</a>
+<a name="359"><span class="lineNum">     359 </span>            :   for(unsigned i=0; i&lt;ll.size(); ++i) {</a>
+<a name="360"><span class="lineNum">     360 </span>            :     for(unsigned j=0; j&lt;ll[i].onoff.size(); ++j) { buffer[bufsize]=ll[i].onoff[j]; bufsize++; }</a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span>            :   // GATHER from all nodes</a>
+<a name="363"><span class="lineNum">     363 </span>            :   comm.Sum(&amp;buffer[0],buffer.size());</a>
+<a name="364"><span class="lineNum">     364 </span>            :   // distribute back to original lists</a>
+<a name="365"><span class="lineNum">     365 </span>            :   bufsize=0;</a>
+<a name="366"><span class="lineNum">     366 </span>            :   for(unsigned i=0; i&lt;ll.size(); ++i) {</a>
+<a name="367"><span class="lineNum">     367 </span>            :     for(unsigned j=0; j&lt;ll[i].onoff.size(); ++j) {</a>
+<a name="368"><span class="lineNum">     368 </span>            :       if( buffer[bufsize]&gt;0 &amp;&amp; buffer[bufsize]%size==0 ) ll[i].onoff[j]=size;</a>
+<a name="369"><span class="lineNum">     369 </span>            :       else ll[i].onoff[j]=size-1;</a>
+<a name="370"><span class="lineNum">     370 </span>            :       bufsize++;</a>
+<a name="371"><span class="lineNum">     371 </span>            :     }</a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span>            :   for(unsigned i=0; i&lt;ll.size(); ++i) ll[i].updateActiveMembers();</a>
+<a name="374"><span class="lineNum">     374 </span>            : }</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : #endif</a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ERMSD.cpp.func-sort-c.html b/coverage/tools/ERMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..b6818fe891
--- /dev/null
+++ b/coverage/tools/ERMSD.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ERMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ERMSD.cpp<span style="font-size: 80%;"> (<a href="ERMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ERMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#38">_ZN4PLMD5ERMSD5clearEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#44">_ZN4PLMD5ERMSD12setReferenceERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IjSaIjEEd</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#259">_ZN4PLMD5ERMSD9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERS5_RNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">222</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#76">_ZN4PLMD5ERMSD7calcMatERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERS1_INS2_ILj4EEESaISB_EERS1_INS_13TensorGenericILj4ELj3EEESaISG_EE</a></td>
+              <td class="coverFnHi">226</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#66">_ZN4PLMD5ERMSD6inPairEjj</a></td>
+              <td class="coverFnHi">1139266</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ERMSD.cpp.func.html b/coverage/tools/ERMSD.cpp.func.html
new file mode 100644
index 0000000000..0d31d4e56f
--- /dev/null
+++ b/coverage/tools/ERMSD.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ERMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ERMSD.cpp<span style="font-size: 80%;"> (<a href="ERMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ERMSD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#44">_ZN4PLMD5ERMSD12setReferenceERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IjSaIjEEd</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#38">_ZN4PLMD5ERMSD5clearEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#66">_ZN4PLMD5ERMSD6inPairEjj</a></td>
+              <td class="coverFnHi">1139266</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#76">_ZN4PLMD5ERMSD7calcMatERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERS1_INS2_ILj4EEESaISB_EERS1_INS_13TensorGenericILj4ELj3EEESaISG_EE</a></td>
+              <td class="coverFnHi">226</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ERMSD.cpp.gcov.html#259">_ZN4PLMD5ERMSD9calculateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKNS_3PbcERS5_RNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">222</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ERMSD.cpp.gcov.html b/coverage/tools/ERMSD.cpp.gcov.html
new file mode 100644
index 0000000000..3e1d381506
--- /dev/null
+++ b/coverage/tools/ERMSD.cpp.gcov.html
@@ -0,0 +1,379 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ERMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ERMSD.cpp<span style="font-size: 80%;"> (source / <a href="ERMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : /*</a>
+<a name="24"><span class="lineNum">      24 </span>            :  This vast majority of the source code in this file was writting by</a>
+<a name="25"><span class="lineNum">      25 </span>            :  Sandro Bottaro with some help from Giovanni Bussi</a>
+<a name="26"><span class="lineNum">      26 </span>            : */</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ERMSD.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;PDB.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Matrix.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;Pbc.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;cmath&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;iostream&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 : void ERMSD::clear() {</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   reference_mat.clear();</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : //void ERMSD::calcLcs(const vector&lt;Vector&gt; &amp; positions, vector&lt;Vector&gt; &amp;)</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          4 : void ERMSD::setReference(const std::vector&lt;Vector&gt; &amp; reference, const std::vector&lt;unsigned&gt; &amp; pairs_vec, double mycutoff) {</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          4 :   natoms = reference.size();</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          4 :   nresidues = natoms/3;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          4 :   unsigned npairs = pairs_vec.size()/2;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          4 :   pairs.resize(npairs);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         16 :   for(unsigned i=0; i&lt;npairs; ++i) {</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         12 :     pairs[i].first = pairs_vec[2*i];</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         12 :     pairs[i].second = pairs_vec[2*i+1];</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          4 :   cutoff = mycutoff;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::vector&lt;TensorGeneric&lt;4,3&gt; &gt; deri;</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          4 :   deri.resize(natoms*natoms);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          4 :   reference_mat.resize(nresidues*nresidues);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          4 :   Pbc fake_pbc;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :   calcMat(reference,fake_pbc,reference_mat,deri);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          4 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    1139266 : bool ERMSD::inPair(unsigned i, unsigned j) {</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    1139266 :   if(pairs.size()==0) return true;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    3982685 :   for(unsigned idx=0; idx&lt;pairs.size(); idx++) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    3414408 :     if(pairs[idx].first == i &amp;&amp; pairs[idx].second == j) return true;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">    3413730 :     if(pairs[idx].second == i &amp;&amp; pairs[idx].first == j) return true;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span>            :   return false;</a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        226 : void ERMSD::calcMat(const std::vector&lt;Vector&gt; &amp; positions,const Pbc&amp; pbc, std::vector&lt;Vector4d&gt; &amp;mat, std::vector&lt;TensorGeneric&lt;4,3&gt; &gt; &amp;Gderi) {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;Vector3d&gt; pos;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        226 :   pos.resize(3*nresidues);</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;Tensor3d&gt; deri;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        226 :   deri.resize(nresidues*9);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;Vector&gt; centers;</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        226 :   centers.resize(nresidues);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            :   unsigned idx_deri = 0;</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        226 :   Tensor da_dxa = (2./3.)*Tensor::identity();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        226 :   Tensor da_dxb = -(1./3.)*Tensor::identity();</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        226 :   Tensor da_dxc = -(1./3.)*Tensor::identity();</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        226 :   Tensor db_dxa = -(1./3.)*Tensor::identity();</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        226 :   Tensor db_dxb = (2./3.)*Tensor::identity();</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        226 :   Tensor db_dxc = -(1./3.)*Tensor::identity();</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   // Form factors - should this be somewhere else?</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   double w = 1./3.;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        226 :   Vector form_factor = Vector(2.0,2.0,1.0/0.3);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      16272 :   for(unsigned res_idx=0; res_idx&lt;natoms/3; res_idx++) {</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      16046 :     const unsigned at_idx = 3*res_idx;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :     //center</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      64184 :     for (unsigned j=0; j&lt;3; j++) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      48138 :       centers[res_idx] += w*positions[at_idx+j];</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     }</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      16046 :     Vector3d a = delta(centers[res_idx],positions[at_idx]);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      16046 :     Vector3d b = delta(centers[res_idx],positions[at_idx+1]);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      16046 :     Vector3d d = crossProduct(a,b);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      16046 :     double ianorm = 1./a.modulo();</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      16046 :     double idnorm = 1./d.modulo();</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :     // X vector: COM-C2</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      16046 :     pos[at_idx] = a*ianorm;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     // Z versor: C2 x (COM-C4/C6)</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      16046 :     pos[at_idx+2] = d*idnorm;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     // Y versor: Z x Y</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      16046 :     pos[at_idx+1] = crossProduct(pos[at_idx+2],pos[at_idx]);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            :     // Derivatives ////////</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      16046 :     Tensor3d t1 = ianorm*(Tensor::identity()-extProduct(pos[at_idx],pos[at_idx]));</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     // dv1/dxa</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      16046 :     deri[idx_deri] = (2./3. )*t1;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :     // dv1/dxb</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      16046 :     deri[idx_deri+3] = -(1./3.)*t1;</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     // dv1/dxc</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      16046 :     deri[idx_deri+6] = -(1./3.)*t1;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      16046 :     Tensor dd_dxa =  VcrossTensor(a,db_dxa) -VcrossTensor(b,da_dxa);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      16046 :     Tensor dd_dxb =  VcrossTensor(a,db_dxb)-VcrossTensor(b,da_dxb);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      16046 :     Tensor dd_dxc =  VcrossTensor(a,db_dxc)-VcrossTensor(b,da_dxc);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :     // dv3/dxa</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      16046 :     deri[idx_deri+2] = deriNorm(d,dd_dxa);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     // dv3/dxb</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      16046 :     deri[idx_deri+5] = deriNorm(d,dd_dxb);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     // dv3/dxc</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      16046 :     deri[idx_deri+8] = deriNorm(d,dd_dxc);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :     // dv2/dxa = dv3/dxa cross v1 + v3 cross dv1/dxa</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      16046 :     deri[idx_deri+1] =  (VcrossTensor(deri[idx_deri+2],pos[at_idx]) + \</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      32092 :                          VcrossTensor(pos[at_idx+2],deri[idx_deri]));</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     // dv2/dxb</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      16046 :     deri[idx_deri+4] =  (VcrossTensor(deri[idx_deri+5],pos[at_idx]) + \</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      32092 :                          VcrossTensor(pos[at_idx+2],deri[idx_deri+3]));</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :     // dv2/dxc</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      16046 :     deri[idx_deri+7] =  (VcrossTensor(deri[idx_deri+8],pos[at_idx]) + \</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      32092 :                          VcrossTensor(pos[at_idx+2],deri[idx_deri+6]));</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      16046 :     idx_deri += 9;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     // End derivatives ///////</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Initialization (unnecessary?)</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">    1139492 :   for (unsigned i1=0; i1&lt;nresidues*nresidues; i1++) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">    5696330 :     for (unsigned i2=0; i2&lt;4; i2++) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">    4557064 :       mat[i1][i2] = 0.0;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     }</a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        226 :   double maxdist = cutoff/form_factor[0];</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        226 :   double gamma = pi/cutoff;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   unsigned idx;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   unsigned idx1 = 0;</a>
+<a name="173"><span class="lineNum">     173 </span>            :   // Calculate mat</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      16272 :   for (unsigned i=0; i&lt;nresidues; i++) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">    1155312 :     for (unsigned j=0; j&lt;nresidues; j++) {</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            :       // skip i==j</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    1139266 :       if(inPair(i,j) and i != j) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :         //if(i!=j){</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :         // Calculate normal distance first</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">     562966 :         Vector diff = delta(centers[i],centers[j]);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     562966 :         double d1 = diff.modulo();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">     562966 :         if(d1&lt;maxdist) {</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :           // calculate r_tilde_ij</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      85382 :           Vector3d rtilde;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">     341528 :           for (unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">    1024584 :             for (unsigned l=0; l&lt;3; l++) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     768438 :               rtilde[l] += pos[3*i+l][k]*diff[k]*form_factor[l];</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :             }</a>
+<a name="193"><span class="lineNum">     193 </span>            :           }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      85382 :           double rtilde_norm = rtilde.modulo();</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      85382 :           double irnorm = 1./rtilde_norm;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :           // ellipsoidal cutoff</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      85382 :           if(rtilde_norm &lt; cutoff) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">      53822 :             idx = i*nresidues + j;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :             // fill 4d matrix</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      53822 :             double dummy = std::sin(gamma*rtilde_norm)/(rtilde_norm*gamma);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      53822 :             mat[idx][0] = dummy*rtilde[0];</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      53822 :             mat[idx][1] = dummy*rtilde[1];</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      53822 :             mat[idx][2] = dummy*rtilde[2];</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">      53822 :             mat[idx][3] = (1.+ std::cos(gamma*rtilde_norm))/gamma;</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            :             // Derivative (drtilde_dx)</a>
+<a name="211"><span class="lineNum">     211 </span>            :             std::vector&lt;Tensor3d&gt; drtilde_dx;</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      53822 :             drtilde_dx.resize(6);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      53822 :             unsigned pos_idx = 3*i;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      53822 :             unsigned deri_idx = 9*i;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">     215288 :             for (unsigned at=0; at&lt;3; at++) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     645864 :               for (unsigned l=0; l&lt;3; l++) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     484398 :                 Vector3d rvec = form_factor[l]*((pos[pos_idx+l])/3.);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     484398 :                 Vector3d vvec = form_factor[l]*(matmul(deri[deri_idx+3*at+l],diff));</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">     484398 :                 drtilde_dx[at].setRow(l,vvec-rvec);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     484398 :                 drtilde_dx[at+3].setRow(l,rvec);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :               }</a>
+<a name="222"><span class="lineNum">     222 </span>            :             }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      53822 :             double dummy1 = (std::cos(gamma*rtilde_norm) - dummy);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      53822 :             idx1 = i*nresidues*6 + j*6;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">     376754 :             for (unsigned l=0; l&lt;6; l++) {</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :               //std::cout &lt;&lt; i &lt;&lt; &quot; &quot; &lt;&lt; j &lt;&lt; &quot; &quot; &lt;&lt; idx1 &lt;&lt; &quot; &quot; &lt;&lt; idx1+l &lt;&lt; &quot;\n&quot;;</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            :               // components 1,2,3</a>
+<a name="232"><span class="lineNum">     232 </span>            :               // std::sin(gamma*|rtilde|)/gamma*|rtilde|*d_rtilde +</a>
+<a name="233"><span class="lineNum">     233 </span>            :               // + ((d_rtilde*r_tilde/r_tilde^2) out r_tilde)*</a>
+<a name="234"><span class="lineNum">     234 </span>            :               // (std::cos(gamma*|rtilde| - std::sin(gamma*|rtilde|)/gamma*|rtilde|))</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     322932 :               Vector3d rdr = matmul(rtilde,drtilde_dx[l]);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">     322932 :               Tensor tt = dummy*drtilde_dx[l] + (dummy1*irnorm*irnorm)*Tensor(rtilde,rdr);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">    1291728 :               for (unsigned m=0; m&lt;3; m++) {</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :                 // Transpose here</a>
+<a name="239"><span class="lineNum">     239 </span>            :                 //dG_dx[l].setRow(m,tt.getRow(m));</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">     968796 :                 Gderi[idx1+l].setRow(m,tt.getRow(m));</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :               }</a>
+<a name="242"><span class="lineNum">     242 </span>            :               // component 4</a>
+<a name="243"><span class="lineNum">     243 </span>            :               // - std::sin(gamma*|rtilde|)/|rtilde|*(r_tilde*d_rtilde)</a>
+<a name="244"><span class="lineNum">     244 </span>            :               //dG_dx[l].setRow(3,-dummy*gamma*rdr);</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">     322932 :               Gderi[idx1+l].setRow(3,-dummy*gamma*rdr);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :             }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :           }</a>
+<a name="252"><span class="lineNum">     252 </span>            :         }</a>
+<a name="253"><span class="lineNum">     253 </span>            :       }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        226 : }</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        222 : double ERMSD::calculate(const std::vector&lt;Vector&gt; &amp; positions,const Pbc&amp; pbc,\</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :                         std::vector&lt;Vector&gt; &amp;derivatives, Tensor&amp; virial) {</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   double ermsd=0.;</a>
+<a name="266"><span class="lineNum">     266 </span>            :   std::vector&lt;Vector4d&gt; mat;</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        222 :   mat.resize(nresidues*nresidues);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :   std::vector&lt;TensorGeneric&lt;4,3&gt; &gt; Gderi;</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        222 :   Gderi.resize(natoms*natoms);</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        222 :   calcMat(positions,pbc,mat,Gderi);</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   unsigned idx1 = 0;</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      15984 :   for(unsigned i=0; i&lt;nresidues; i++) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">    1134864 :     for(unsigned j=0; j&lt;nresidues; j++) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    1119102 :       unsigned ii = i*nresidues + j;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    1119102 :       Vector4d dd = delta(reference_mat[ii],mat[ii]);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">    1119102 :       double val = dd.modulo2();</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">    1119102 :       if(val&gt;0.0 &amp;&amp; i!=j) {</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">     256596 :         for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     192447 :           idx1 = i*nresidues*6 + j*6 + k;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     192447 :           derivatives[3*i+k] += matmul(dd,Gderi[idx1]);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     192447 :           derivatives[3*j+k] += matmul(dd,Gderi[idx1+3]);</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :         }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">      64149 :         ermsd += val;</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :       }</a>
+<a name="292"><span class="lineNum">     292 </span>            :     }</a>
+<a name="293"><span class="lineNum">     293 </span>            :   }</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        222 :   ermsd = std::sqrt(ermsd/nresidues);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        222 :   double iermsd = 1.0/(ermsd*nresidues);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">      47508 :   for(unsigned i=0; i&lt;natoms; ++i) {derivatives[i] *= iermsd;}</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        222 :   return ermsd;</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : }</a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ERMSD.h.func-sort-c.html b/coverage/tools/ERMSD.h.func-sort-c.html
new file mode 100644
index 0000000000..8fbad8c95f
--- /dev/null
+++ b/coverage/tools/ERMSD.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ERMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ERMSD.h<span style="font-size: 80%;"> (<a href="ERMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ERMSD.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ERMSD.h.func.html b/coverage/tools/ERMSD.h.func.html
new file mode 100644
index 0000000000..3dfc8504e9
--- /dev/null
+++ b/coverage/tools/ERMSD.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ERMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ERMSD.h<span style="font-size: 80%;"> (<a href="ERMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ERMSD.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ERMSD.h.gcov.html b/coverage/tools/ERMSD.h.gcov.html
new file mode 100644
index 0000000000..ab2cc49004
--- /dev/null
+++ b/coverage/tools/ERMSD.h.gcov.html
@@ -0,0 +1,149 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ERMSD.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ERMSD.h<span style="font-size: 80%;"> (source / <a href="ERMSD.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_ERMSD_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_ERMSD_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;limits&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;string&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;map&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;utility&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cstddef&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class PDB;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class Pbc;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : /// A class that implements ERMSD calculations</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 : class ERMSD {</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   //std::map&lt; std::pair &lt;unsigned,unsigned&gt; , double&gt; targets;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   //unsigned natoms;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;Vector4d&gt; reference_mat;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::size_t natoms;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::size_t nresidues;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::vector&lt;std::pair &lt;unsigned,unsigned&gt; &gt; pairs;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   double cutoff;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : public:</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Constructor</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          4 :   ERMSD(): natoms(0),nresidues(0), cutoff(0.0) {}</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : /// clear the structure</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void clear();</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool inPair(unsigned i, unsigned j);</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : /// set reference coordinates</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void setReference(const std::vector&lt;Vector&gt; &amp; reference, const std::vector&lt;unsigned&gt; &amp; pairs_vec,double mycutoff=0.24);</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            :   void calcMat(const std::vector&lt;Vector&gt; &amp; positions, const Pbc&amp; pbc,std::vector&lt;Vector4d&gt; &amp;mat,std::vector&lt;TensorGeneric&lt;4,3&gt; &gt; &amp; Gderivatives);</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Compute ermsd ( no pbc )</a>
+<a name="64"><span class="lineNum">      64 </span>            : //  double calculate(const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="65"><span class="lineNum">      65 </span>            : //                   std::vector&lt;Vector&gt; &amp;derivatives, Tensor&amp; virial) const ;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Compute ermsd ( with pbc )</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double calculate(const std::vector&lt;Vector&gt;&amp; positions, const Pbc&amp; pbc,std::vector&lt;Vector&gt; &amp;derivatives, Tensor&amp; virial);</a>
+<a name="68"><span class="lineNum">      68 </span>            : };</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : #endif</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Exception.cpp.func-sort-c.html b/coverage/tools/Exception.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4c299e3831
--- /dev/null
+++ b/coverage/tools/Exception.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Exception.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Exception.cpp<span style="font-size: 80%;"> (<a href="Exception.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntryHi">94.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Exception.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#141">_ZNK4PLMD9Exception5stackEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#131">_ZN4PLMD9ExceptionlsERKNS0_9AssertionE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#38">_ZN4PLMD12_GLOBAL__N_18simplifyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#107">_ZN4PLMD9ExceptionlsERKNS0_8LocationE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#83">_ZN4PLMD9ExceptionC2Ev</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#97">_ZN4PLMD9ExceptionlsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">130</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Exception.cpp.func.html b/coverage/tools/Exception.cpp.func.html
new file mode 100644
index 0000000000..422b4b0f1d
--- /dev/null
+++ b/coverage/tools/Exception.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Exception.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Exception.cpp<span style="font-size: 80%;"> (<a href="Exception.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntryHi">94.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Exception.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#38">_ZN4PLMD12_GLOBAL__N_18simplifyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#83">_ZN4PLMD9ExceptionC2Ev</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#107">_ZN4PLMD9ExceptionlsERKNS0_8LocationE</a></td>
+              <td class="coverFnHi">56</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#131">_ZN4PLMD9ExceptionlsERKNS0_9AssertionE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#97">_ZN4PLMD9ExceptionlsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">130</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.cpp.gcov.html#141">_ZNK4PLMD9Exception5stackEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Exception.cpp.gcov.html b/coverage/tools/Exception.cpp.gcov.html
new file mode 100644
index 0000000000..6883436334
--- /dev/null
+++ b/coverage/tools/Exception.cpp.gcov.html
@@ -0,0 +1,232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Exception.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Exception.cpp<span style="font-size: 80%;"> (source / <a href="Exception.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">48</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntryHi">94.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : #if defined(__PLUMED_HAS_EXECINFO)</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;execinfo.h&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #endif</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstdio&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstring&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;vector&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace {</a>
+<a name="36"><span class="lineNum">      36 </span>            : // see https://www.geeksforgeeks.org/simplify-directory-path-unix-like/</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : // function to simplify a Unix - styled</a>
+<a name="39"><span class="lineNum">      39 </span>            : // absolute path</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         56 : std::string simplify(const std::string &amp; path)</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : {</a>
+<a name="42"><span class="lineNum">      42 </span>            :   // using vector in place of stack</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;std::string&gt; v;</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         56 :   int n = path.length();</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::string ans;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        186 :   for (int i = 0; i &lt; n; i++) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        130 :     std::string dir = &quot;&quot;;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :     // forming the current directory.</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       1095 :     while (i &lt; n &amp;&amp; path[i] != '/') {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        965 :       dir += path[i];</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        965 :       i++;</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :     }</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            :     // if &quot;..&quot; , we pop.</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        130 :     if (dir == &quot;..&quot;) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          6 :       if (!v.empty())</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :         v.pop_back();</a>
+<a name="58"><span class="lineNum">      58 </span>            :     }</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        248 :     else if (dir == &quot;.&quot; || dir == &quot;&quot;) {</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :       // do nothing (added for better understanding.)</a>
+<a name="61"><span class="lineNum">      61 </span>            :     }</a>
+<a name="62"><span class="lineNum">      62 </span>            :     else {</a>
+<a name="63"><span class="lineNum">      63 </span>            :       // push the current directory into the vector.</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        123 :       v.push_back(dir);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :     }</a>
+<a name="66"><span class="lineNum">      66 </span>            :   }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   // forming the ans</a>
+<a name="69"><span class="lineNum">      69 </span>            :   bool first=true;</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        173 :   for (auto i : v) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        117 :     if(!first) ans += &quot;/&quot;;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :     first=false;</a>
+<a name="73"><span class="lineNum">      73 </span>            :     ans += i;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            :   // vector is empty</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         56 :   if (ans == &quot;&quot;)</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     return &quot;/&quot;;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   return ans;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         56 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         95 : Exception::Exception()</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : {</a>
+<a name="87"><span class="lineNum">      87 </span>            :   callstack.fill(nullptr);</a>
+<a name="88"><span class="lineNum">      88 </span>            : #ifdef __PLUMED_HAS_EXECINFO</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         95 :   callstack_n = backtrace(&amp;callstack[0], callstack.size()-1);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         95 :   const char* env=std::getenv(&quot;PLUMED_STACK_TRACE&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         95 :   if(env &amp;&amp; !std::strcmp(env,&quot;yes&quot;)) {</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :     msg+=&quot;\n\n********** STACK DUMP **********\n&quot;;</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          3 :     msg+=stack();</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :     msg+=&quot;\n********** END STACK DUMP **********\n&quot;;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span>            : #endif</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         95 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        130 : Exception&amp; Exception::operator&lt;&lt;(const std::string&amp;msg)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        130 :   if(msg.length()&gt;0) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        130 :     if(note) this-&gt;msg +=&quot;\n&quot;;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        130 :     this-&gt;msg +=msg;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        130 :     note=false;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        130 :   return *this;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         56 : Exception&amp; Exception::operator&lt;&lt;(const Location&amp;loc)</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : {</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         56 :   if(loc.file) {</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :     const std::size_t clinelen=1000;</a>
+<a name="113"><span class="lineNum">     113 </span>            :     char cline[clinelen];</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         56 :     std::snprintf(cline,clinelen,&quot;%u&quot;,loc.line);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         56 :     this-&gt;msg += &quot;\n(&quot;;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :     try {</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        112 :       this-&gt;msg += simplify(loc.file);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :     } catch(...) {</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       // ignore</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     this-&gt;msg += &quot;:&quot;;</a>
+<a name="122"><span class="lineNum">     122 </span>            :     this-&gt;msg += cline;</a>
+<a name="123"><span class="lineNum">     123 </span>            :     this-&gt;msg += &quot;)&quot;;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         56 :     if(loc.pretty &amp;&amp; loc.pretty[0]) {</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :       this-&gt;msg += &quot; &quot;;</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         56 :       this-&gt;msg += loc.pretty;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :     }</a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         56 :   note=true;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         56 :   return *this;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         11 : Exception&amp; Exception::operator&lt;&lt;(const Assertion&amp;as)</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : {</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         11 :   if(as.assertion) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         11 :     this-&gt;msg += &quot;\n+++ assertion failed: &quot;;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         11 :     this-&gt;msg += as.assertion;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         11 :   note=true;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         11 :   return *this;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 : const char* Exception::stack() const {</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : #ifdef __PLUMED_HAS_EXECINFO</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 :   if(stackTrace.length()==0) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          3 :     char** strs = backtrace_symbols(&amp;callstack[0], callstack_n);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         30 :     for (int i = 0; i &lt; callstack_n; ++i) {stackTrace+=strs[i]; stackTrace+=&quot;\n&quot;;}</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 :     free(strs);</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span>            : #endif</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :   return stackTrace.c_str();</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Exception.h.func-sort-c.html b/coverage/tools/Exception.h.func-sort-c.html
new file mode 100644
index 0000000000..d9c986977a
--- /dev/null
+++ b/coverage/tools/Exception.h.func-sort-c.html
@@ -0,0 +1,612 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Exception.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Exception.h<span style="font-size: 80%;"> (<a href="Exception.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryLo">17.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Exception.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Exception.h.gcov.html#205">_ZN4PLMD9Exception5ThrowlSIRNS_14ExceptionErrorEEEvOT_</a></td>
+              <td class="coverFnLo">0</td>
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+            </tr>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Exception.h.gcov.html b/coverage/tools/Exception.h.gcov.html
new file mode 100644
index 0000000000..944a3f7a5f
--- /dev/null
+++ b/coverage/tools/Exception.h.gcov.html
@@ -0,0 +1,478 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Exception.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Exception.h<span style="font-size: 80%;"> (source / <a href="Exception.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">135</td>
+            <td class="headerCovTableEntryLo">17.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Exception_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Exception_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;exception&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;stdexcept&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;sstream&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;array&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /**</a>
+<a name="34"><span class="lineNum">      34 </span>            : \ingroup TOOLBOX</a>
+<a name="35"><span class="lineNum">      35 </span>            : Class to deal with Plumed runtime errors.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This class and the related macros can be used to detect programming</a>
+<a name="38"><span class="lineNum">      38 </span>            : errors. Typical cases are internal inconsistencies or errors in the plumed&lt;-&gt;MD</a>
+<a name="39"><span class="lineNum">      39 </span>            : interface. Mistakes made by final users (i.e. in the `plumed.dat` file)</a>
+<a name="40"><span class="lineNum">      40 </span>            : should probably be documented in some better way (e.g. printing parts of the manual in the output).</a>
+<a name="41"><span class="lineNum">      41 </span>            : However, also this class allows for significant information to be attached.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Let's try to make error messages as informative as possible!</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \note This class has been rewritten in PLUMED 2.5. It works in a backward compatible manner,</a>
+<a name="45"><span class="lineNum">      45 </span>            : but is much more flexible. The main novelty is that we can use insertion operators to</a>
+<a name="46"><span class="lineNum">      46 </span>            : add arbitrary messages, as in `plumed_error()&lt;&lt;&quot;check this vector &quot;&lt;&lt;v;`</a>
+<a name="47"><span class="lineNum">      47 </span>            : See below for more details.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : To throw an error, just throw a c++ exception</a>
+<a name="50"><span class="lineNum">      50 </span>            : \verbatim</a>
+<a name="51"><span class="lineNum">      51 </span>            :   if(something_bad) throw Exception();</a>
+<a name="52"><span class="lineNum">      52 </span>            : \endverbatim</a>
+<a name="53"><span class="lineNum">      53 </span>            : or better add an error message to that</a>
+<a name="54"><span class="lineNum">      54 </span>            : \verbatim</a>
+<a name="55"><span class="lineNum">      55 </span>            :   if(something_bad) throw Exception(&quot;describe the error here&quot;);</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endverbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : As of PLUMED 2.5 you can add multiple messages, they will just be concatenated,</a>
+<a name="59"><span class="lineNum">      59 </span>            : but to do se you should use the insertion operator. Notice that anything that</a>
+<a name="60"><span class="lineNum">      60 </span>            : can be formatted with an insertion operator can go to the exception, even a \ref Vector</a>
+<a name="61"><span class="lineNum">      61 </span>            : \verbatim</a>
+<a name="62"><span class="lineNum">      62 </span>            :   Vector v;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   if(something_bad) throw Exception()&lt;&lt;&quot;problem with this &quot;&lt;&lt;v;</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endverbatim</a>
+<a name="65"><span class="lineNum">      65 </span>            : In principle you can mix the two syntax (add a message as an argument and insert others with `&lt;&lt;`),</a>
+<a name="66"><span class="lineNum">      66 </span>            : however it is not very clear and should be avoided.</a>
+<a name="67"><span class="lineNum">      67 </span>            : We only allow using arguments in parenthesis in order to keep backward compatibility.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : \par Using macros</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : In order to provide more context, especially for debugging, it might be useful to know where the exception</a>
+<a name="72"><span class="lineNum">      72 </span>            : originated from. The macros below add information about the exact location of the error in the file (filename, line</a>
+<a name="73"><span class="lineNum">      73 </span>            : and, when available, function name). Macros ending in &quot;error&quot; unconditionally throw</a>
+<a name="74"><span class="lineNum">      74 </span>            : the exception, whereas macros ending in &quot;assert&quot; first perform a conditional check</a>
+<a name="75"><span class="lineNum">      75 </span>            : (similarly to standard assert()).</a>
+<a name="76"><span class="lineNum">      76 </span>            : An extra `m` in the name (e.g. `plumed_merror`) indicates a macro that provides a message as its argument.</a>
+<a name="77"><span class="lineNum">      77 </span>            : However, as of PLUMED 2.5 we should prefer adding messages using insertion operators.</a>
+<a name="78"><span class="lineNum">      78 </span>            : \verbatim</a>
+<a name="79"><span class="lineNum">      79 </span>            : // this is correct but not recommended. add a message please!</a>
+<a name="80"><span class="lineNum">      80 </span>            :   plumed_assert(a&gt;0);</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : // this is the old syntax (with argument).</a>
+<a name="83"><span class="lineNum">      83 </span>            : // this syntax is basically available for backward compatibility.</a>
+<a name="84"><span class="lineNum">      84 </span>            :   plumed_massert(a&gt;0,&quot;a should be larger than zero);</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : // this is the recommended syntax, with insertion operators.</a>
+<a name="87"><span class="lineNum">      87 </span>            : // it allows to easily insert multiple objects</a>
+<a name="88"><span class="lineNum">      88 </span>            :   plumed_assert(a&gt;0)&lt;&lt;&quot;a should be larger than zero. a=&quot;&lt;&lt;a;</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : // same as above, but the test is made explicitly:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   if(a&lt;=0) plumed_error();</a>
+<a name="92"><span class="lineNum">      92 </span>            :   if(a&lt;=0) plumed_error(&quot;a should be larger than zero);</a>
+<a name="93"><span class="lineNum">      93 </span>            :   if(a&lt;=0) plumed_error()&lt;&lt;&quot;a should be larger than zero. a=&quot;&lt;&lt;a;</a>
+<a name="94"><span class="lineNum">      94 </span>            : \endverbatim</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : The additional macros</a>
+<a name="97"><span class="lineNum">      97 </span>            : plumed_dbg_assert() and plumed_dbg_massert() are similar</a>
+<a name="98"><span class="lineNum">      98 </span>            : to plumed_assert() and plumed_massert() respectively, but the corresponding</a>
+<a name="99"><span class="lineNum">      99 </span>            : check is only performed when NDEBUG macro is not defined. They should</a>
+<a name="100"><span class="lineNum">     100 </span>            : be used when the check is expensive and should be skipped in production</a>
+<a name="101"><span class="lineNum">     101 </span>            : code. So, for instance, in the following case:</a>
+<a name="102"><span class="lineNum">     102 </span>            : \verbatim</a>
+<a name="103"><span class="lineNum">     103 </span>            :   plumed_dbg_assert(expensive_function(i)&gt;0)&lt;&lt;&quot;message&quot;;</a>
+<a name="104"><span class="lineNum">     104 </span>            : \endverbatim</a>
+<a name="105"><span class="lineNum">     105 </span>            : `expensive_function()` is not called in the production code.</a>
+<a name="106"><span class="lineNum">     106 </span>            : Notice that the compiler should be able to completely optimize away the</a>
+<a name="107"><span class="lineNum">     107 </span>            : whole statement including functions used to produce the message as in this example:</a>
+<a name="108"><span class="lineNum">     108 </span>            : \verbatim</a>
+<a name="109"><span class="lineNum">     109 </span>            :   plumed_dbg_assert(expensive_function(i)&gt;0)&lt;&lt;&quot;I did this check &quot;&lt;&lt;other_expensive_function(i);</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endverbatim</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : Finally, notice that there is another macro available, \ref plumed_here.</a>
+<a name="113"><span class="lineNum">     113 </span>            : In can be used in order to create an exception with information about the</a>
+<a name="114"><span class="lineNum">     114 </span>            : line/file coordinates without trowing it. That is, the two following syntaxes</a>
+<a name="115"><span class="lineNum">     115 </span>            : are equivalent</a>
+<a name="116"><span class="lineNum">     116 </span>            : \verbatim</a>
+<a name="117"><span class="lineNum">     117 </span>            : // First way, all at once</a>
+<a name="118"><span class="lineNum">     118 </span>            : plumed_error()&lt;&lt;&quot;some message&quot;;</a>
+<a name="119"><span class="lineNum">     119 </span>            : /////////////////////////////////</a>
+<a name="120"><span class="lineNum">     120 </span>            : // Second way, one step at a time</a>
+<a name="121"><span class="lineNum">     121 </span>            : // Create exception</a>
+<a name="122"><span class="lineNum">     122 </span>            : Exception e;</a>
+<a name="123"><span class="lineNum">     123 </span>            : // Append information about line and file</a>
+<a name="124"><span class="lineNum">     124 </span>            : e&lt;&lt;plumed_here;</a>
+<a name="125"><span class="lineNum">     125 </span>            : // Append some other message</a>
+<a name="126"><span class="lineNum">     126 </span>            : e&lt;&lt;&quot;some message&quot;;</a>
+<a name="127"><span class="lineNum">     127 </span>            : // Throw the resulting exception</a>
+<a name="128"><span class="lineNum">     128 </span>            : throw e;</a>
+<a name="129"><span class="lineNum">     129 </span>            : \endverbatim</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : Exceptions can be caught within plumed or outside of it.</a>
+<a name="132"><span class="lineNum">     132 </span>            : E.g., in an external c++ code using PLUMED as a library, one can type</a>
+<a name="133"><span class="lineNum">     133 </span>            : \verbatim</a>
+<a name="134"><span class="lineNum">     134 </span>            :   try{</a>
+<a name="135"><span class="lineNum">     135 </span>            :     plumed.cmd(&quot;setPrecision&quot;,n);</a>
+<a name="136"><span class="lineNum">     136 </span>            :   } catch (const std::exception &amp; e) {</a>
+<a name="137"><span class="lineNum">     137 </span>            :     std::printf(&quot;ee %s&quot;,e.what());</a>
+<a name="138"><span class="lineNum">     138 </span>            :     exit(1);</a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            : \endverbatim</a>
+<a name="141"><span class="lineNum">     141 </span>            : This can be useful if an external code wants to exit in a controlled manner</a>
+<a name="142"><span class="lineNum">     142 </span>            : (e.g. flushing files, printing the error message in a specific file, etc.)</a>
+<a name="143"><span class="lineNum">     143 </span>            : but is anyway limited to c++ codes. Moreover,</a>
+<a name="144"><span class="lineNum">     144 </span>            : since these errors are expected to be unrecoverable, the MD code will</a>
+<a name="145"><span class="lineNum">     145 </span>            : usually not be able to do something more clever than exiting.</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : \note</a>
+<a name="148"><span class="lineNum">     148 </span>            : We store message and stack trace in growing strings. This is in</a>
+<a name="149"><span class="lineNum">     149 </span>            : principle not recommended, since copying the exception might fail if</a>
+<a name="150"><span class="lineNum">     150 </span>            : copying the string throw another exception. However, this has been like</a>
+<a name="151"><span class="lineNum">     151 </span>            : this in all previous PLUMED versions. In case it is necessary, we can replace</a>
+<a name="152"><span class="lineNum">     152 </span>            : it later with a fixed size array placed on the stack.</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : */</a>
+<a name="155"><span class="lineNum">     155 </span>            : class Exception : public std::exception</a>
+<a name="156"><span class="lineNum">     156 </span>            : {</a>
+<a name="157"><span class="lineNum">     157 </span>            : /// Reported message. Can be updated.</a>
+<a name="158"><span class="lineNum">     158 </span>            :   std::string msg;</a>
+<a name="159"><span class="lineNum">     159 </span>            : /// Flag to remember if we have to write the `+++ message follows +++` string.</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Needed so that the string appears only at the beginning of the message.</a>
+<a name="161"><span class="lineNum">     161 </span>            :   bool note=true;</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// Stream used to insert objects.</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// It is not copied when the Exception is copied.</a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::stringstream stream;</a>
+<a name="165"><span class="lineNum">     165 </span>            : /// Stack trace, computed at construction</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::array&lt;void*,128&gt; callstack;</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// Number of frames in stack, computed at construction</a>
+<a name="168"><span class="lineNum">     168 </span>            :   int callstack_n=0;</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// Parsed stack trace. Built at first use, thus mutable.</a>
+<a name="170"><span class="lineNum">     170 </span>            :   mutable std::string stackTrace;</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : public:</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : /// Auxiliary containing the location of the exception in the file.</a>
+<a name="175"><span class="lineNum">     175 </span>            : /// Typically used from the macros below.</a>
+<a name="176"><span class="lineNum">     176 </span>            :   class Location {</a>
+<a name="177"><span class="lineNum">     177 </span>            :   public:</a>
+<a name="178"><span class="lineNum">     178 </span>            :     const char*file;</a>
+<a name="179"><span class="lineNum">     179 </span>            :     const unsigned line;</a>
+<a name="180"><span class="lineNum">     180 </span>            :     const char* pretty;</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         55 :     explicit Location(const char*file,unsigned line,const char* pretty=nullptr):</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         55 :       file(file),</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         55 :       line(line),</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         55 :       pretty(pretty)</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     {}</a>
+<a name="186"><span class="lineNum">     186 </span>            :   };</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : /// Auxiliary containing the failed assertion.</a>
+<a name="189"><span class="lineNum">     189 </span>            : /// Typically used from the macros below.</a>
+<a name="190"><span class="lineNum">     190 </span>            :   class Assertion {</a>
+<a name="191"><span class="lineNum">     191 </span>            :   public:</a>
+<a name="192"><span class="lineNum">     192 </span>            :     const char*assertion;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         10 :     explicit Assertion(const char*assertion=nullptr):</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         10 :       assertion(assertion)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     {}</a>
+<a name="196"><span class="lineNum">     196 </span>            :   };</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : /// Auxiliary class used to throw exceptions.</a>
+<a name="199"><span class="lineNum">     199 </span>            : /// It just defines &lt;&lt;= operator so that:</a>
+<a name="200"><span class="lineNum">     200 </span>            : /// - exceptions can be thrown calling std::throw_with_nested</a>
+<a name="201"><span class="lineNum">     201 </span>            : ///   with a &quot;throw like&quot; syntax</a>
+<a name="202"><span class="lineNum">     202 </span>            : /// - precedence is the same as the throw operator</a>
+<a name="203"><span class="lineNum">     203 </span>            : /// (see https://en.cppreference.com/w/cpp/language/operator_precedence)</a>
+<a name="204"><span class="lineNum">     204 </span>            :   class Throw {</a>
+<a name="205"><span class="lineNum">     205 </span>            :   public:</a>
+<a name="206"><span class="lineNum">     206 </span>            :     template &lt;typename E&gt;</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :     [[noreturn]] void operator &lt;&lt;=(E&amp;&amp;e) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :       if(std::current_exception()) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :         std::throw_with_nested(e);</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :       } else {</a>
+<a name="211"><span class="lineNum">     211 </span>            :         // if not nested, avoid modifying the exception type</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :         throw e;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :       }</a>
+<a name="214"><span class="lineNum">     214 </span>            :     }</a>
+<a name="215"><span class="lineNum">     215 </span>            :   };</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : /// Default constructor with no message.</a>
+<a name="218"><span class="lineNum">     218 </span>            : /// Only records the stack trace.</a>
+<a name="219"><span class="lineNum">     219 </span>            :   Exception();</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : /// Constructor compatible with PLUMED &lt;=2.4.</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         31 :   explicit Exception(const std::string &amp; msg):</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         31 :     Exception()</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         31 :     *this &lt;&lt; msg;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         31 :   }</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : /// Copy constructor.</a>
+<a name="229"><span class="lineNum">     229 </span>            : /// Needed to make sure stream is not copied</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         25 :   Exception(const Exception &amp; e):</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         25 :     msg(e.msg),</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         25 :     note(e.note),</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         25 :     callstack(e.callstack),</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         25 :     callstack_n(e.callstack_n),</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         25 :     stackTrace(e.stackTrace)</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :   {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         25 :   }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : /// Assignment.</a>
+<a name="240"><span class="lineNum">     240 </span>            : /// Needed to make sure stream is not copied</a>
+<a name="241"><span class="lineNum">     241 </span>            :   Exception &amp; operator=(const Exception &amp; e) {</a>
+<a name="242"><span class="lineNum">     242 </span>            :     msg=e.msg;</a>
+<a name="243"><span class="lineNum">     243 </span>            :     note=e.note;</a>
+<a name="244"><span class="lineNum">     244 </span>            :     callstack=e.callstack;</a>
+<a name="245"><span class="lineNum">     245 </span>            :     callstack_n=e.callstack_n;</a>
+<a name="246"><span class="lineNum">     246 </span>            :     stackTrace=e.stackTrace;</a>
+<a name="247"><span class="lineNum">     247 </span>            :     stream.str(&quot;&quot;);</a>
+<a name="248"><span class="lineNum">     248 </span>            :     return *this;</a>
+<a name="249"><span class="lineNum">     249 </span>            :   }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : /// Returns the error message.</a>
+<a name="252"><span class="lineNum">     252 </span>            : /// In case the environment variable PLUMED_STACK_TRACE was defined</a>
+<a name="253"><span class="lineNum">     253 </span>            : /// and equal to `yes` when the exception was raised,</a>
+<a name="254"><span class="lineNum">     254 </span>            : /// the error message will contain the stack trace as well.</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         37 :   const char* what() const noexcept override {return msg.c_str();}</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : /// Returns the stack trace as a string.</a>
+<a name="258"><span class="lineNum">     258 </span>            : /// This function is slow as it requires building a parsed string.</a>
+<a name="259"><span class="lineNum">     259 </span>            : /// If storing the stack for later usage, you might prefer to use trace().</a>
+<a name="260"><span class="lineNum">     260 </span>            :   const char* stack() const;</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : /// Returns the callstack.</a>
+<a name="263"><span class="lineNum">     263 </span>            :   const std::array&lt;void*,128&gt; &amp; trace() const noexcept {return callstack;}</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : /// Returns the number of elements in the trace array</a>
+<a name="266"><span class="lineNum">     266 </span>            :   int trace_n() const noexcept {return callstack_n;}</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : /// Destructor should be defined and should not throw other exceptions</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         54 :   ~Exception() noexcept override {}</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : /// Insert location.</a>
+<a name="272"><span class="lineNum">     272 </span>            : /// Format the location properly.</a>
+<a name="273"><span class="lineNum">     273 </span>            :   Exception&amp; operator&lt;&lt;(const Location&amp;);</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : /// Insert assertion.</a>
+<a name="276"><span class="lineNum">     276 </span>            : /// Format the assertion properly</a>
+<a name="277"><span class="lineNum">     277 </span>            :   Exception&amp; operator&lt;&lt;(const Assertion&amp;);</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : /// Insert string.</a>
+<a name="280"><span class="lineNum">     280 </span>            : /// Append this string to the message.</a>
+<a name="281"><span class="lineNum">     281 </span>            :   Exception&amp; operator&lt;&lt;(const std::string&amp;);</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : /// Insert anything else.</a>
+<a name="284"><span class="lineNum">     284 </span>            : /// This allows to dump also other types (e.g. double, or even Vector).</a>
+<a name="285"><span class="lineNum">     285 </span>            : /// Anything that can be written on a stream can go here.</a>
+<a name="286"><span class="lineNum">     286 </span>            :   template&lt;typename T&gt;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         37 :   Exception&amp; operator&lt;&lt;(const T &amp; x) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         37 :     stream&lt;&lt;x;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         37 :     (*this)&lt;&lt;stream.str();</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         37 :     stream.str(&quot;&quot;);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         37 :     return *this;</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :   }</a>
+<a name="293"><span class="lineNum">     293 </span>            : };</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : /// Class representing a generic error</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        151 : class ExceptionError :</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :   public Exception {</a>
+<a name="298"><span class="lineNum">     298 </span>            : public:</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          1 :   using Exception::Exception;</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :   template&lt;typename T&gt;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   ExceptionError&amp; operator&lt;&lt;(const T &amp; x) {</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         96 :     *static_cast&lt;Exception*&gt;(this) &lt;&lt;x;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     return *this;</a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span>            : };</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : /// Class representing a debug error (can only be thrown when using debug options)</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 : class ExceptionDebug :</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   public Exception {</a>
+<a name="310"><span class="lineNum">     310 </span>            : public:</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          1 :   using Exception::Exception;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   template&lt;typename T&gt;</a>
+<a name="313"><span class="lineNum">     313 </span>            :   ExceptionDebug&amp; operator&lt;&lt;(const T &amp; x) {</a>
+<a name="314"><span class="lineNum">     314 </span>            :     *static_cast&lt;Exception*&gt;(this) &lt;&lt;x;</a>
+<a name="315"><span class="lineNum">     315 </span>            :     return *this;</a>
+<a name="316"><span class="lineNum">     316 </span>            :   }</a>
+<a name="317"><span class="lineNum">     317 </span>            : };</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            : /// Class representing a type error in the PLMD::Plumed interface</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         21 : class ExceptionTypeError :</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :   public Exception {</a>
+<a name="322"><span class="lineNum">     322 </span>            : public:</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :   using Exception::Exception;</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   template&lt;typename T&gt;</a>
+<a name="325"><span class="lineNum">     325 </span>            :   ExceptionTypeError&amp; operator&lt;&lt;(const T &amp; x) {</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         21 :     *static_cast&lt;Exception*&gt;(this) &lt;&lt;x;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     return *this;</a>
+<a name="328"><span class="lineNum">     328 </span>            :   }</a>
+<a name="329"><span class="lineNum">     329 </span>            : };</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            : #ifdef __GNUG__</a>
+<a name="332"><span class="lineNum">     332 </span>            : // With GNU compiler, we can use __PRETTY_FUNCTION__ to get the function name</a>
+<a name="333"><span class="lineNum">     333 </span>            : #define __PLUMED_FUNCNAME __PRETTY_FUNCTION__</a>
+<a name="334"><span class="lineNum">     334 </span>            : #else</a>
+<a name="335"><span class="lineNum">     335 </span>            : // Otherwise, we use the standard C++11 variable</a>
+<a name="336"><span class="lineNum">     336 </span>            : #define __PLUMED_FUNCNAME __func__</a>
+<a name="337"><span class="lineNum">     337 </span>            : #endif</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : #ifndef PLUMED_MODULE_DIR</a>
+<a name="340"><span class="lineNum">     340 </span>            : #define PLUMED_MODULE_DIR &quot;&quot;</a>
+<a name="341"><span class="lineNum">     341 </span>            : #endif</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            : /// \relates PLMD::Exception</a>
+<a name="344"><span class="lineNum">     344 </span>            : /// Auxiliary macro that generates a PLMD::Exception::Location object.</a>
+<a name="345"><span class="lineNum">     345 </span>            : /// Might be useful if we want to use derived exceptions that could</a>
+<a name="346"><span class="lineNum">     346 </span>            : /// be thrown using `throw DerivedException()&lt;&lt;plumed_here&lt;&lt;&quot; &quot;&lt;&lt;other stuff&quot;`.</a>
+<a name="347"><span class="lineNum">     347 </span>            : /// It is used in the macros below to throw PLMD::Exception.</a>
+<a name="348"><span class="lineNum">     348 </span>            : #define plumed_here PLMD::Exception::Location(PLUMED_MODULE_DIR __FILE__,__LINE__,__PLUMED_FUNCNAME)</a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : /// \relates PLMD::Exception</a>
+<a name="351"><span class="lineNum">     351 </span>            : /// Throw an exception with information about the position in the file.</a>
+<a name="352"><span class="lineNum">     352 </span>            : /// Messages can be inserted with `plumed_error()&lt;&lt;&quot;message&quot;`.</a>
+<a name="353"><span class="lineNum">     353 </span>            : #define plumed_error() throw PLMD::ExceptionError() &lt;&lt; plumed_here</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : /// \relates PLMD::Exception</a>
+<a name="356"><span class="lineNum">     356 </span>            : /// Throw a nested exception with information about the position in the file.</a>
+<a name="357"><span class="lineNum">     357 </span>            : /// It preliminary checks if we are in a catch block. If so, the caught exception</a>
+<a name="358"><span class="lineNum">     358 </span>            : /// is rethrown as nested. If not, it throws a normal ExceptionError.</a>
+<a name="359"><span class="lineNum">     359 </span>            : /// NB in theory we could have just redefined plumed_error to this, but</a>
+<a name="360"><span class="lineNum">     360 </span>            : /// for some reason cppcheck does not understand that the &lt;&lt;= operator used here is</a>
+<a name="361"><span class="lineNum">     361 </span>            : /// [[noreturn]] and thus gives many false warnings</a>
+<a name="362"><span class="lineNum">     362 </span>            : #define plumed_error_nested() PLMD::Exception::Throw() &lt;&lt;= PLMD::ExceptionError() &lt;&lt; plumed_here</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            : /// \relates PLMD::Exception</a>
+<a name="365"><span class="lineNum">     365 </span>            : /// Throw an exception with information about the position in the file</a>
+<a name="366"><span class="lineNum">     366 </span>            : /// and a message. Mostly available for backward compatibility</a>
+<a name="367"><span class="lineNum">     367 </span>            : #define plumed_merror(msg) plumed_error() &lt;&lt; msg</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : /// \relates PLMD::Exception</a>
+<a name="370"><span class="lineNum">     370 </span>            : /// Launches plumed_merror only if test evaluates to false.</a>
+<a name="371"><span class="lineNum">     371 </span>            : /// The string describing the test is also reported.</a>
+<a name="372"><span class="lineNum">     372 </span>            : /// Further messages can be inserted with `&lt;&lt;`.</a>
+<a name="373"><span class="lineNum">     373 </span>            : #define plumed_assert(test) if(!(test)) plumed_error() &lt;&lt; PLMD::Exception::Assertion(#test)</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            : /// \relates PLMD::Exception</a>
+<a name="376"><span class="lineNum">     376 </span>            : /// Launches plumed_merror only if test evaluates to false.</a>
+<a name="377"><span class="lineNum">     377 </span>            : /// The string describing the test is also reported, in addition to</a>
+<a name="378"><span class="lineNum">     378 </span>            : /// messages reported in the extra argument. Mostly available for backward compatibility.</a>
+<a name="379"><span class="lineNum">     379 </span>            : #define plumed_massert(test,msg) plumed_assert(test) &lt;&lt; msg</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            : #ifdef NDEBUG</a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            : // These are the versions used when compiling with NDEBUG flag.</a>
+<a name="384"><span class="lineNum">     384 </span>            : // The condition is always true, so that the rest of the statement</a>
+<a name="385"><span class="lineNum">     385 </span>            : // should be optimized away.</a>
+<a name="386"><span class="lineNum">     386 </span>            : #define plumed_dbg_assert(test) plumed_assert(true)</a>
+<a name="387"><span class="lineNum">     387 </span>            : #define plumed_dbg_massert(test,msg) plumed_massert(true,msg)</a>
+<a name="388"><span class="lineNum">     388 </span>            : </a>
+<a name="389"><span class="lineNum">     389 </span>            : #else</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            : /// \relates PLMD::Exception</a>
+<a name="392"><span class="lineNum">     392 </span>            : /// Same as \ref plumed_assert, but only evaluates the condition if NDEBUG is not defined.</a>
+<a name="393"><span class="lineNum">     393 </span>            : #define plumed_dbg_assert(test) if(!(test)) PLMD::Exception::Throw() &lt;&lt;= PLMD::ExceptionDebug() &lt;&lt; plumed_here &lt;&lt; PLMD::Exception::Assertion(#test) &lt;&lt; &quot;(this check is enabled only in debug builds)\n&quot;</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            : /// \relates PLMD::Exception</a>
+<a name="396"><span class="lineNum">     396 </span>            : /// Same as \ref plumed_massert, but only evaluates the condition if NDEBUG is not defined.</a>
+<a name="397"><span class="lineNum">     397 </span>            : #define plumed_dbg_massert(test,msg) plumed_dbg_assert(test) &lt;&lt; msg</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : #endif</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            : }</a>
+<a name="402"><span class="lineNum">     402 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/FileBase.cpp.func-sort-c.html b/coverage/tools/FileBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a6de05eba9
--- /dev/null
+++ b/coverage/tools/FileBase.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/FileBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - FileBase.cpp<span style="font-size: 80%;"> (<a href="FileBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FileBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#125">_ZN4PLMD8FileBaseD0Ev</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#161">_ZN4PLMD8FileBase13enforceSuffixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">258</td>
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+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#99">_ZN4PLMD8FileBase5closeEv</a></td>
+              <td class="coverFnHi">982</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#72">_ZN4PLMD8FileBase9FileExistERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1893</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#65">_ZN4PLMD8FileBase4linkERNS_6ActionE</a></td>
+              <td class="coverFnHi">3949</td>
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+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#58">_ZN4PLMD8FileBase4linkERNS_10PlumedMainE</a></td>
+              <td class="coverFnHi">4833</td>
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+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#47">_ZN4PLMD8FileBase5flushEv</a></td>
+              <td class="coverFnHi">5028</td>
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+              <td class="coverFnHi">6734</td>
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+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#40">_ZN4PLMD8FileBase4linkEP8_IO_FILE</a></td>
+              <td class="coverFnHi">20959</td>
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+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#52">_ZN4PLMD8FileBase4linkERNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">810316</td>
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+    <tr>
+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#93">_ZN4PLMD8FileBase6isOpenEv</a></td>
+              <td class="coverFnHi">812522</td>
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+              <td class="coverFn"><a href="FileBase.cpp.gcov.html#111">_ZN4PLMD8FileBaseC2Ev</a></td>
+              <td class="coverFnHi">831502</td>
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+              <td class="coverFnHi">831502</td>
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+              <td class="coverFnHi">29221912</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/FileBase.cpp.func.html b/coverage/tools/FileBase.cpp.func.html
new file mode 100644
index 0000000000..b065423771
--- /dev/null
+++ b/coverage/tools/FileBase.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/FileBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - FileBase.cpp<span style="font-size: 80%;"> (<a href="FileBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FileBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+  <br>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/FileBase.cpp.gcov.html b/coverage/tools/FileBase.cpp.gcov.html
new file mode 100644
index 0000000000..309633eeaa
--- /dev/null
+++ b/coverage/tools/FileBase.cpp.gcov.html
@@ -0,0 +1,251 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/FileBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - FileBase.cpp<span style="font-size: 80%;"> (source / <a href="FileBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;FileBase.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdarg&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstring&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;iostream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;string&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;zlib.h&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #endif</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      20959 : FileBase&amp; FileBase::link(FILE*fp) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      20959 :   plumed_massert(!this-&gt;fp,&quot;cannot link an already open file&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      20959 :   this-&gt;fp=fp;</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      20959 :   cloned=true;</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      20959 :   return *this;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       5028 : FileBase&amp; FileBase::flush() {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       5028 :   if(fp) fflush(fp);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       5028 :   return *this;</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : }</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">     810316 : FileBase&amp; FileBase::link(Communicator&amp;comm) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">     810316 :   plumed_massert(!fp,&quot;cannot link an already open file&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     810316 :   this-&gt;comm=&amp;comm;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">     810316 :   return *this;</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : }</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       4833 : FileBase&amp; FileBase::link(PlumedMain&amp;plumed) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       4833 :   plumed_massert(!fp,&quot;cannot link an already open file&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       4833 :   this-&gt;plumed=&amp;plumed;</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       4833 :   link(plumed.comm);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4833 :   return *this;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       3949 : FileBase&amp; FileBase::link(Action&amp;action) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       3949 :   plumed_massert(!fp,&quot;cannot link an already open file&quot;);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       3949 :   this-&gt;action=&amp;action;</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       3949 :   link(action.plumed);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       3949 :   return *this;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       1893 : bool FileBase::FileExist(const std::string&amp; path) {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool do_exist=false;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       3786 :   this-&gt;path=appendSuffix(path,getSuffix());</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       1893 :   mode=&quot;r&quot;;</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   // first try with suffix</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       1893 :   FILE *ff=std::fopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;r&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : // call fclose when ff goes out of scope</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1321 :   auto deleter=[](FILE* f) { if(f) std::fclose(f); };</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(ff,deleter);</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1893 :   if(!ff) {</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :     this-&gt;path=path;</a>
+<a name="86"><span class="lineNum">      86 </span>            :     // then try without suffic</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        572 :     ff=std::fopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;r&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :     mode=&quot;r&quot;;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1893 :   if(ff) do_exist=true;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1893 :   if(comm) comm-&gt;Barrier();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1893 :   return do_exist;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     812522 : bool FileBase::isOpen() {</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   bool isopen=false;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     812522 :   if(fp) isopen=true;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     812522 :   return isopen;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        982 : void        FileBase::close() {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        982 :   plumed_assert(!cloned);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        982 :   eof=false;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        982 :   err=false;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        982 :   if(fp)   std::fclose(fp);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        982 :   if(gzfp) gzclose(gzFile(gzfp));</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : #endif</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        982 :   fp=NULL;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        982 :   gzfp=NULL;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        982 : }</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">     831502 : FileBase::FileBase():</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     831502 :   fp(NULL),</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     831502 :   gzfp(NULL),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     831502 :   comm(NULL),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     831502 :   plumed(NULL),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     831502 :   action(NULL),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     831502 :   cloned(false),</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     831502 :   eof(false),</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     831502 :   err(false),</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     831502 :   heavyFlush(false),</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     831502 :   enforcedSuffix_(false)</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">     831502 : }</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     831502 : FileBase::~FileBase()</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">     831502 :   if(plumed) plumed-&gt;eraseFile(*this);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     831502 :   if(!cloned &amp;&amp; fp)   std::fclose(fp);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     831502 :   if(!cloned &amp;&amp; gzfp) gzclose(gzFile(gzfp));</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : #endif</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     831502 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">   29221912 : FileBase::operator bool()const {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">   29221912 :   return !eof;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       6734 : std::string FileBase::appendSuffix(const std::string&amp;path,const std::string&amp;suffix) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       6734 :   if(path==&quot;/dev/null&quot;) return path; // do not append a suffix to /dev/null</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       6559 :   std::string ret=path;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       6559 :   std::string ext=Tools::extension(path);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : // These are the recognized extensions so far:</a>
+<a name="146"><span class="lineNum">     146 </span>            : // gz xtc trr</a>
+<a name="147"><span class="lineNum">     147 </span>            : // If a file name ends with one of these extensions, the suffix is added *before*</a>
+<a name="148"><span class="lineNum">     148 </span>            : // the extension. This is useful when extensions are conventionally used</a>
+<a name="149"><span class="lineNum">     149 </span>            : // to detect file type, so as to allow easier file manipulation.</a>
+<a name="150"><span class="lineNum">     150 </span>            : // Removing this line, any extension recognized by Tools::extension() would be considered</a>
+<a name="151"><span class="lineNum">     151 </span>            : //  if(ext!=&quot;gz&quot; &amp;&amp; ext!=&quot;xtc&quot; &amp;&amp; ext!=&quot;trr&quot;) ext=&quot;&quot;;</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       6559 :   if(ext.length()&gt;0) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       4780 :     int l=path.length()-(ext.length()+1);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       4780 :     plumed_assert(l&gt;=0);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       4780 :     ret.resize(l);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   }</a>
+<a name="158"><span class="lineNum">     158 </span>            :   ret+=suffix;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      11339 :   if(ext.length()&gt;0)ret+=&quot;.&quot;+ext;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   return ret;</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        258 : FileBase&amp; FileBase::enforceSuffix(const std::string&amp;suffix) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        258 :   enforcedSuffix_=true;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        258 :   enforcedSuffix=suffix;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        258 :   return *this;</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       5539 : std::string FileBase::getSuffix()const {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       5539 :   if(enforcedSuffix_) return enforcedSuffix;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       5275 :   if(plumed) return plumed-&gt;getSuffix();</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        503 :   return &quot;&quot;;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/FileBase.h.func-sort-c.html b/coverage/tools/FileBase.h.func-sort-c.html
new file mode 100644
index 0000000000..8dd6b36f1c
--- /dev/null
+++ b/coverage/tools/FileBase.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/FileBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - FileBase.h<span style="font-size: 80%;"> (<a href="FileBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FileBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/FileBase.h.func.html b/coverage/tools/FileBase.h.func.html
new file mode 100644
index 0000000000..692e042d7c
--- /dev/null
+++ b/coverage/tools/FileBase.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/FileBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - FileBase.h<span style="font-size: 80%;"> (<a href="FileBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FileBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/FileBase.h.gcov.html b/coverage/tools/FileBase.h.gcov.html
new file mode 100644
index 0000000000..0fffb0744b
--- /dev/null
+++ b/coverage/tools/FileBase.h.gcov.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/FileBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - FileBase.h<span style="font-size: 80%;"> (source / <a href="FileBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_FileBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_FileBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Communicator;</a>
+<a name="30"><span class="lineNum">      30 </span>            : class PlumedMain;</a>
+<a name="31"><span class="lineNum">      31 </span>            : class Action;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /**</a>
+<a name="34"><span class="lineNum">      34 </span>            : Base class for dealing with files.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This class just provides things which are common among OFile and IFile</a>
+<a name="37"><span class="lineNum">      37 </span>            : */</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class FileBase {</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Copy constructor is disabled</a>
+<a name="41"><span class="lineNum">      41 </span>            :   FileBase(const FileBase&amp;) = delete;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Assignment operator is disabled</a>
+<a name="43"><span class="lineNum">      43 </span>            :   FileBase&amp; operator=(const FileBase&amp;) = delete;</a>
+<a name="44"><span class="lineNum">      44 </span>            : protected:</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Internal tool.</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Base for IFile::Field and OFile::Field</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">   16816705 :   class FieldBase {</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : // everything is public to simplify usage</a>
+<a name="49"><span class="lineNum">      49 </span>            :   public:</a>
+<a name="50"><span class="lineNum">      50 </span>            :     std::string name;</a>
+<a name="51"><span class="lineNum">      51 </span>            :     std::string value;</a>
+<a name="52"><span class="lineNum">      52 </span>            :     bool constant;</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">   16682324 :     FieldBase(): constant(false) {}</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : /// file pointer</a>
+<a name="57"><span class="lineNum">      57 </span>            :   FILE* fp;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// zip file pointer.</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void* gzfp;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// communicator. NULL if not set</a>
+<a name="61"><span class="lineNum">      61 </span>            :   Communicator* comm;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// pointer to main plumed object. NULL if not linked</a>
+<a name="63"><span class="lineNum">      63 </span>            :   PlumedMain* plumed;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// pointer to corresponding action. NULL if not linked</a>
+<a name="65"><span class="lineNum">      65 </span>            :   Action* action;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Control closing on destructor.</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// If true, file will not be closed in destructor</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool cloned;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Private constructor.</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// In this manner one cannot instantiate a FileBase object</a>
+<a name="71"><span class="lineNum">      71 </span>            :   FileBase();</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Set to true when end of file is encountered</a>
+<a name="73"><span class="lineNum">      73 </span>            :   bool eof;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Set to true when error is encountered</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool err;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// path of the opened file</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::string path;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// mode of the opened file</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::string mode;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Set to true if you want flush to be heavy (close/reopen)</a>
+<a name="81"><span class="lineNum">      81 </span>            :   bool heavyFlush;</a>
+<a name="82"><span class="lineNum">      82 </span>            : public:</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Append suffix.</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// It appends the desired suffix to the string. Notice that</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// it conserves some suffix (e.g. gz/xtc/trr).</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static std::string appendSuffix(const std::string&amp;path,const std::string&amp;suffix);</a>
+<a name="87"><span class="lineNum">      87 </span>            : private:</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Enforced suffix:</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::string enforcedSuffix;</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// If true, use enforcedSuffix, else get it from PlumedMain</a>
+<a name="91"><span class="lineNum">      91 </span>            :   bool enforcedSuffix_;</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Link to an already open filed</a>
+<a name="94"><span class="lineNum">      94 </span>            :   FileBase&amp; link(FILE*);</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Link to a PlumedMain object</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// Automatically links also the corresponding Communicator.</a>
+<a name="97"><span class="lineNum">      97 </span>            :   FileBase&amp; link(PlumedMain&amp;);</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Link to a Communicator object</a>
+<a name="99"><span class="lineNum">      99 </span>            :   FileBase&amp; link(Communicator&amp;);</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Link to an Action object.</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Automatically links also the corresponding PlumedMain and Communicator.</a>
+<a name="102"><span class="lineNum">     102 </span>            :   FileBase&amp; link(Action&amp;);</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Enforce suffix.</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// Overrides the one set in PlumedMain&amp;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   FileBase&amp; enforceSuffix(const std::string&amp;suffix);</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Flushes the file to disk</a>
+<a name="107"><span class="lineNum">     107 </span>            :   virtual FileBase&amp; flush();</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Closes the file</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Should be used only for explicitely opened files.</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void        close();</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// Virtual destructor (allows inheritance)</a>
+<a name="112"><span class="lineNum">     112 </span>            :   virtual ~FileBase();</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Check for error/eof.</a>
+<a name="114"><span class="lineNum">     114 </span>            :   operator bool () const;</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Set heavyFlush flag</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        634 :   void setHeavyFlush() { heavyFlush=true;}</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Opens the file</a>
+<a name="118"><span class="lineNum">     118 </span>            :   virtual FileBase&amp; open(const std::string&amp;name)=0;</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Check if the file exists</a>
+<a name="120"><span class="lineNum">     120 </span>            :   bool FileExist(const std::string&amp; path);</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Check if a file is open</a>
+<a name="122"><span class="lineNum">     122 </span>            :   bool isOpen();</a>
+<a name="123"><span class="lineNum">     123 </span>            : /// Retrieve the path</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::string getPath()const;</a>
+<a name="125"><span class="lineNum">     125 </span>            : /// Retrieve the mode</a>
+<a name="126"><span class="lineNum">     126 </span>            :   std::string getMode()const;</a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Get the file suffix</a>
+<a name="128"><span class="lineNum">     128 </span>            :   std::string getSuffix()const;</a>
+<a name="129"><span class="lineNum">     129 </span>            : /// Get the underlying file pointer.</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// It might be null even if the file is open, e.g. when the file</a>
+<a name="131"><span class="lineNum">     131 </span>            : /// was open as a gzipped file.</a>
+<a name="132"><span class="lineNum">     132 </span>            :   FILE* getFILE()const;</a>
+<a name="133"><span class="lineNum">     133 </span>            : };</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : inline</a>
+<a name="136"><span class="lineNum">     136 </span>            : std::string FileBase::getPath()const {</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        824 :   return path;</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : inline</a>
+<a name="141"><span class="lineNum">     141 </span>            : std::string FileBase::getMode()const {</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        173 :   return mode;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : inline</a>
+<a name="146"><span class="lineNum">     146 </span>            : FILE* FileBase::getFILE()const {</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         18 :   return fp;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ForwardDecl.h.func-sort-c.html b/coverage/tools/ForwardDecl.h.func-sort-c.html
new file mode 100644
index 0000000000..66567e555f
--- /dev/null
+++ b/coverage/tools/ForwardDecl.h.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ForwardDecl.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ForwardDecl.h<span style="font-size: 80%;"> (<a href="ForwardDecl.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ForwardDecl.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_3PDBEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9StopwatchEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">582</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_11TypesafePtrEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_16ExchangePatternsEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_3LogEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_5AtomsEEC2IJRNS_10PlumedMainEEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_6RandomEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_8DLLoaderEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9ActionSetEEC2IJRNS_10PlumedMainEEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9CitationsEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9StopwatchEEC2IJRNS_3LogEEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_3PbcEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">815523</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_12CommunicatorEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">1615161</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ForwardDecl.h.func.html b/coverage/tools/ForwardDecl.h.func.html
new file mode 100644
index 0000000000..4df248a2e5
--- /dev/null
+++ b/coverage/tools/ForwardDecl.h.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ForwardDecl.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ForwardDecl.h<span style="font-size: 80%;"> (<a href="ForwardDecl.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ForwardDecl.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_11TypesafePtrEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_12CommunicatorEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">1615161</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_16ExchangePatternsEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_3LogEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_3PDBEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_3PbcEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">815523</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_5AtomsEEC2IJRNS_10PlumedMainEEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_6RandomEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_8DLLoaderEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9ActionSetEEC2IJRNS_10PlumedMainEEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9CitationsEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9StopwatchEEC2IJEEEDpOT_</a></td>
+              <td class="coverFnHi">582</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ForwardDecl.h.gcov.html#46">_ZN4PLMD11ForwardDeclINS_9StopwatchEEC2IJRNS_3LogEEEEDpOT_</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/ForwardDecl.h.gcov.html b/coverage/tools/ForwardDecl.h.gcov.html
new file mode 100644
index 0000000000..b0dfbf0549
--- /dev/null
+++ b/coverage/tools/ForwardDecl.h.gcov.html
@@ -0,0 +1,131 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/ForwardDecl.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - ForwardDecl.h<span style="font-size: 80%;"> (source / <a href="ForwardDecl.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2017-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_ForwardDecl_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_ForwardDecl_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;memory&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;utility&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : /**</a>
+<a name="31"><span class="lineNum">      31 </span>            :   Utility class for forward declaration of references.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : */</a>
+<a name="34"><span class="lineNum">      34 </span>            : template &lt;class T&gt;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">    4846941 : class ForwardDecl:</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::unique_ptr&lt;T&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            : // Construction with arbitrary argument.</a>
+<a name="40"><span class="lineNum">      40 </span>            :   template&lt;typename ...Args&gt;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   explicit ForwardDecl(Args &amp;&amp;...args);</a>
+<a name="42"><span class="lineNum">      42 </span>            : // Dereference operator is inherited from std::unique_ptr&lt;T&gt;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   using std::unique_ptr&lt;T&gt;::operator *;</a>
+<a name="44"><span class="lineNum">      44 </span>            : };</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : template &lt;class T&gt;</a>
+<a name="47"><span class="lineNum">      47 </span>            : template&lt;typename ...Args&gt;</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">    9678765 : ForwardDecl&lt;T&gt;::ForwardDecl(Args &amp;&amp;...args):</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">    9678765 :   std::unique_ptr&lt;T&gt;(new T(std::forward&lt;Args&gt;(args)...))</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    9678765 : {}</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : #endif</a>
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Grid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Grid.cpp<span style="font-size: 80%;"> (<a href="Grid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">440</td>
+            <td class="headerCovTableEntry">619</td>
+            <td class="headerCovTableEntryLo">71.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">77</td>
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diff --git a/coverage/tools/Grid.cpp.gcov.html b/coverage/tools/Grid.cpp.gcov.html
new file mode 100644
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Grid.cpp<span style="font-size: 80%;"> (source / <a href="Grid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">440</td>
+            <td class="headerCovTableEntry">619</td>
+            <td class="headerCovTableEntryLo">71.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Grid.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;KernelFunctions.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;RootFindingBase.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;vector&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;cmath&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;iostream&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;sstream&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;cstdio&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;cfloat&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;array&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : constexpr std::size_t GridBase::maxdim;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       1327 : GridBase::GridBase(const std::string&amp; funcl, const std::vector&lt;Value*&gt; &amp; args, const std::vector&lt;std::string&gt; &amp; gmin,</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1327 :                    const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline, bool usederiv) {</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : // various checks</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1327 :   plumed_assert(args.size()&lt;=maxdim) &lt;&lt; &quot;grid dim cannot exceed &quot;&lt;&lt;maxdim;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1327 :   plumed_massert(args.size()==gmin.size(),&quot;grid min dimensions in input do not match number of arguments&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       1327 :   plumed_massert(args.size()==nbin.size(),&quot;number of bins on input do not match number of arguments&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1327 :   plumed_massert(args.size()==gmax.size(),&quot;grid max dimensions in input do not match number of arguments&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1327 :   unsigned dim=gmax.size();</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;std::string&gt; names;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;bool&gt; isperiodic;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;std::string&gt; pmin,pmax;</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1327 :   names.resize( dim );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       1327 :   isperiodic.resize( dim );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1327 :   pmin.resize( dim );</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       1327 :   pmax.resize( dim );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       2933 :   for(unsigned int i=0; i&lt;dim; ++i) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       1606 :     names[i]=args[i]-&gt;getName();</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1606 :     if( args[i]-&gt;isPeriodic() ) {</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :       isperiodic[i]=true;</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        502 :       args[i]-&gt;getDomain( pmin[i], pmax[i] );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :     } else {</a>
+<a name="65"><span class="lineNum">      65 </span>            :       isperiodic[i]=false;</a>
+<a name="66"><span class="lineNum">      66 </span>            :       pmin[i]=&quot;0.&quot;;</a>
+<a name="67"><span class="lineNum">      67 </span>            :       pmax[i]=&quot;0.&quot;;</a>
+<a name="68"><span class="lineNum">      68 </span>            :     }</a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span>            : // this is a value-independent initializator</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1327 :   Init(funcl,names,gmin,gmax,nbin,dospline,usederiv,isperiodic,pmin,pmax);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       2654 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        128 : GridBase::GridBase(const std::string&amp; funcl, const std::vector&lt;std::string&gt; &amp;names, const std::vector&lt;std::string&gt; &amp; gmin,</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :                    const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline, bool usederiv,</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        128 :                    const std::vector&lt;bool&gt; &amp;isperiodic, const std::vector&lt;std::string&gt; &amp;pmin, const std::vector&lt;std::string&gt; &amp;pmax ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : // this calls the initializator</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        128 :   Init(funcl,names,gmin,gmax,nbin,dospline,usederiv,isperiodic,pmin,pmax);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        128 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1455 : void GridBase::Init(const std::string&amp; funcl, const std::vector&lt;std::string&gt; &amp;names, const std::vector&lt;std::string&gt; &amp; gmin,</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :                     const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline, bool usederiv,</a>
+<a name="83"><span class="lineNum">      83 </span>            :                     const std::vector&lt;bool&gt; &amp;isperiodic, const std::vector&lt;std::string&gt; &amp;pmin, const std::vector&lt;std::string&gt; &amp;pmax ) {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1455 :   fmt_=&quot;%14.9f&quot;;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : // various checks</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1455 :   plumed_assert(names.size()&lt;=maxdim) &lt;&lt; &quot;grid size cannot exceed &quot;&lt;&lt;maxdim;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1455 :   plumed_massert(names.size()==gmin.size(),&quot;grid dimensions in input do not match number of arguments&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1455 :   plumed_massert(names.size()==nbin.size(),&quot;grid dimensions in input do not match number of arguments&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1455 :   plumed_massert(names.size()==gmax.size(),&quot;grid dimensions in input do not match number of arguments&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1455 :   dimension_=gmax.size();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       1455 :   str_min_=gmin; str_max_=gmax;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       1455 :   argnames.resize( dimension_ );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       1455 :   min_.resize( dimension_ );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1455 :   max_.resize( dimension_ );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1455 :   pbc_.resize( dimension_ );</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       3189 :   for(unsigned int i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1734 :     argnames[i]=names[i];</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1734 :     if( isperiodic[i] ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :       pbc_[i]=true;</a>
+<a name="100"><span class="lineNum">     100 </span>            :       str_min_[i]=pmin[i];</a>
+<a name="101"><span class="lineNum">     101 </span>            :       str_max_[i]=pmax[i];</a>
+<a name="102"><span class="lineNum">     102 </span>            :     } else {</a>
+<a name="103"><span class="lineNum">     103 </span>            :       pbc_[i]=false;</a>
+<a name="104"><span class="lineNum">     104 </span>            :     }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1734 :     Tools::convert(str_min_[i],min_[i]);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1734 :     Tools::convert(str_max_[i],max_[i]);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1734 :     funcname=funcl;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1734 :     plumed_massert(max_[i]&gt;min_[i],&quot;maximum in grid must be larger than minimum&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1734 :     plumed_massert(nbin[i]&gt;0,&quot;number of grid points must be greater than zero&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1455 :   nbin_=nbin;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1455 :   dospline_=dospline;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1455 :   usederiv_=usederiv;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1455 :   if(dospline_) plumed_assert(dospline_==usederiv_);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1455 :   maxsize_=1;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       3189 :   for(unsigned int i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       1734 :     dx_.push_back( (max_[i]-min_[i])/static_cast&lt;double&gt;( nbin_[i] ) );</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1734 :     if( !pbc_[i] ) { max_[i] += dx_[i]; nbin_[i] += 1; }</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1734 :     maxsize_*=nbin_[i];</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       1455 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">    1360394 : std::vector&lt;std::string&gt; GridBase::getMin() const {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">    1360394 :   return str_min_;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        343 : std::vector&lt;std::string&gt; GridBase::getMax() const {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        343 :   return str_max_;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">    1319573 : std::vector&lt;double&gt; GridBase::getDx() const {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    1319573 :   return dx_;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      11890 : double GridBase::getDx(index_t j) const {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      11890 :   return dx_[j];</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         37 : double GridBase::getBinVolume() const {</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   double vol=1.;</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        102 :   for(unsigned i=0; i&lt;dx_.size(); ++i) vol*=dx_[i];</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         37 :   return vol;</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       2240 : std::vector&lt;bool&gt; GridBase::getIsPeriodic() const {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       2240 :   return pbc_;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">    1012510 : std::vector&lt;unsigned&gt; GridBase::getNbin() const {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">    1012510 :   return nbin_;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       9436 : std::vector&lt;std::string&gt; GridBase::getArgNames() const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       9436 :   return argnames;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">   18321217 : unsigned GridBase::getDimension() const {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">   18321217 :   return dimension_;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : // we are flattening arrays using a column-major order</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">    7145799 : GridBase::index_t GridBase::getIndex(const std::vector&lt;unsigned&gt; &amp; indices) const {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   plumed_dbg_assert(indices.size()==dimension_);</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">   19319332 :   for(unsigned int i=0; i&lt;dimension_; i++)</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">   12173533 :     if(indices[i]&gt;=nbin_[i]) {</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :       std::string is;</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       Tools::convert(i,is);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :       plumed_error() &lt;&lt; &quot;Looking for a value outside the grid along the &quot; &lt;&lt; is &lt;&lt; &quot; dimension (arg name: &quot;&lt;&lt;getArgNames()[i]&lt;&lt;&quot;)&quot;;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">    7145799 :   index_t index=indices[dimension_-1];</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">   12173533 :   for(unsigned int i=dimension_-1; i&gt;0; --i) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">    5027734 :     index=index*nbin_[i-1]+indices[i-1];</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">    7145799 :   return index;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : }</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">    1100069 : GridBase::index_t GridBase::getIndex(const std::vector&lt;double&gt; &amp; x) const {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   plumed_dbg_assert(x.size()==dimension_);</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">    2200138 :   return getIndex(getIndices(x));</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : // we are flattening arrays using a column-major order</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">   37829485 : std::vector&lt;unsigned&gt; GridBase::getIndices(index_t index) const {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">   37829485 :   std::vector&lt;unsigned&gt; indices(dimension_);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   index_t kk=index;</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">   37829485 :   indices[0]=(index%nbin_[0]);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">   54778194 :   for(unsigned int i=1; i&lt;dimension_-1; ++i) {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">   16948709 :     kk=(kk-indices[i-1])/nbin_[i-1];</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">   16948709 :     indices[i]=(kk%nbin_[i]);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">   37829485 :   if(dimension_&gt;=2) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">   36999987 :     indices[dimension_-1]=((kk-indices[dimension_-2])/nbin_[dimension_-2]);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">   37829485 :   return indices;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       8910 : void GridBase::getIndices(index_t index, std::vector&lt;unsigned&gt;&amp; indices) const {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       8910 :   if (indices.size()!=dimension_) indices.resize(dimension_);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   index_t kk=index;</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       8910 :   indices[0]=(index%nbin_[0]);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       8910 :   for(unsigned int i=1; i&lt;dimension_-1; ++i) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     kk=(kk-indices[i-1])/nbin_[i-1];</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     indices[i]=(kk%nbin_[i]);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       8910 :   if(dimension_&gt;=2) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       2980 :     indices[dimension_-1]=((kk-indices[dimension_-2])/nbin_[dimension_-2]);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       8910 : }</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">    1104281 : std::vector&lt;unsigned&gt; GridBase::getIndices(const std::vector&lt;double&gt; &amp; x) const {</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   plumed_dbg_assert(x.size()==dimension_);</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">    1104281 :   std::vector&lt;unsigned&gt; indices(dimension_);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">    3308069 :   for(unsigned int i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">    2203788 :     indices[i] = unsigned(std::floor((x[i]-min_[i])/dx_[i]));</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">    1104281 :   return indices;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       3711 : void GridBase::getIndices(const std::vector&lt;double&gt; &amp; x, std::vector&lt;unsigned&gt;&amp; indices) const {</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   plumed_dbg_assert(x.size()==dimension_);</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       3711 :   if (indices.size()!=dimension_) indices.resize(dimension_);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       8167 :   for(unsigned int i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       4456 :     indices[i] = unsigned(std::floor((x[i]-min_[i])/dx_[i]));</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       3711 : }</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">   31542440 : std::vector&lt;double&gt; GridBase::getPoint(const std::vector&lt;unsigned&gt; &amp; indices) const {</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   plumed_dbg_assert(indices.size()==dimension_);</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">   31542440 :   std::vector&lt;double&gt; x(dimension_);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">  108460905 :   for(unsigned int i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">   76918465 :     x[i]=min_[i]+(double)(indices[i])*dx_[i];</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">   31542440 :   return x;</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">   28822338 : std::vector&lt;double&gt; GridBase::getPoint(index_t index) const {</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   plumed_dbg_assert(index&lt;maxsize_);</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">   57644676 :   return getPoint(getIndices(index));</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : }</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 : std::vector&lt;double&gt; GridBase::getPoint(const std::vector&lt;double&gt; &amp; x) const {</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   plumed_dbg_assert(x.size()==dimension_);</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   return getPoint(getIndices(x));</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">    1110281 : void GridBase::getPoint(index_t index,std::vector&lt;double&gt; &amp; point) const {</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   plumed_dbg_assert(index&lt;maxsize_);</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">    1110281 :   getPoint(getIndices(index),point);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">    1110281 : }</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">    1113992 : void GridBase::getPoint(const std::vector&lt;unsigned&gt; &amp; indices,std::vector&lt;double&gt; &amp; point) const {</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :   plumed_dbg_assert(indices.size()==dimension_);</a>
+<a name="253"><span class="lineNum">     253 </span>            :   plumed_dbg_assert(point.size()==dimension_);</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">    3329356 :   for(unsigned int i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">    2215364 :     point[i]=min_[i]+(double)(indices[i])*dx_[i];</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">    1113992 : }</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 : void GridBase::getPoint(const std::vector&lt;double&gt; &amp; x,std::vector&lt;double&gt; &amp; point) const {</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   plumed_dbg_assert(x.size()==dimension_);</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   getPoint(getIndices(x),point);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">      23364 : std::vector&lt;GridBase::index_t&gt; GridBase::getNeighbors(const std::vector&lt;unsigned&gt; &amp;indices,const std::vector&lt;unsigned&gt; &amp;nneigh)const {</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   plumed_dbg_assert(indices.size()==dimension_ &amp;&amp; nneigh.size()==dimension_);</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            :   std::vector&lt;index_t&gt; neighbors;</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">      23364 :   std::vector&lt;unsigned&gt; small_bin(dimension_);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            :   unsigned small_nbin=1;</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      69592 :   for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">      46228 :     small_bin[j]=(2*nneigh[j]+1);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">      46228 :     small_nbin*=small_bin[j];</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :   }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      23364 :   std::vector&lt;unsigned&gt; small_indices(dimension_);</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   std::vector&lt;unsigned&gt; tmp_indices;</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">    1291958 :   for(unsigned index=0; index&lt;small_nbin; ++index) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    1268594 :     tmp_indices.resize(dimension_);</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :     unsigned kk=index;</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">    1268594 :     small_indices[0]=(index%small_bin[0]);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">    1268594 :     for(unsigned i=1; i&lt;dimension_-1; ++i) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :       kk=(kk-small_indices[i-1])/small_bin[i-1];</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :       small_indices[i]=(kk%small_bin[i]);</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">    1268594 :     if(dimension_&gt;=2) {</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">    1255566 :       small_indices[dimension_-1]=((kk-small_indices[dimension_-2])/small_bin[dimension_-2]);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span>            :     unsigned ll=0;</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">    3792754 :     for(unsigned i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">    2524160 :       int i0=small_indices[i]-nneigh[i]+indices[i];</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">    2524160 :       if(!pbc_[i] &amp;&amp; i0&lt;0)         continue;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">    2504438 :       if(!pbc_[i] &amp;&amp; i0&gt;=static_cast&lt;int&gt;(nbin_[i])) continue;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">    2483466 :       if( pbc_[i] &amp;&amp; i0&lt;0)         i0=nbin_[i]-(-i0)%nbin_[i];</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">    2483466 :       if( pbc_[i] &amp;&amp; i0&gt;=static_cast&lt;int&gt;(nbin_[i])) i0%=nbin_[i];</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">    2483466 :       tmp_indices[ll]=static_cast&lt;unsigned&gt;(i0);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">    2483466 :       ll++;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     }</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">    1268594 :     tmp_indices.resize(ll);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">    1268594 :     if(tmp_indices.size()==dimension_) {neighbors.push_back(getIndex(tmp_indices));}</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">      23364 :   return neighbors;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : }</a>
+<a name="304"><span class="lineNum">     304 </span>            : </a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       4211 : std::vector&lt;GridBase::index_t&gt; GridBase::getNeighbors(const std::vector&lt;double&gt; &amp; x,const std::vector&lt;unsigned&gt; &amp; nneigh)const {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   plumed_dbg_assert(x.size()==dimension_ &amp;&amp; nneigh.size()==dimension_);</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       8422 :   return getNeighbors(getIndices(x),nneigh);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : }</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      19153 : std::vector&lt;GridBase::index_t&gt; GridBase::getNeighbors(index_t index,const std::vector&lt;unsigned&gt; &amp; nneigh)const {</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   plumed_dbg_assert(index&lt;maxsize_ &amp;&amp; nneigh.size()==dimension_);</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">      38306 :   return getNeighbors(getIndices(index),nneigh);</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : }</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       3711 : void GridBase::getSplineNeighbors(const std::vector&lt;unsigned&gt; &amp; indices, std::vector&lt;GridBase::index_t&gt;&amp; neighbors, unsigned&amp; nneighbors)const {</span></a>
+<a name="316"><span class="lineNum">     316 </span>            :   plumed_dbg_assert(indices.size()==dimension_);</a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       3711 :   unsigned nneigh=unsigned(std::pow(2.0,int(dimension_)));</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       3711 :   if (neighbors.size()!=nneigh) neighbors.resize(nneigh);</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">       3711 :   std::vector&lt;unsigned&gt; nindices(dimension_);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       3711 :   unsigned inind; nneighbors = 0;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      12623 :   for(unsigned int i=0; i&lt;nneigh; ++i) {</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :     unsigned tmp=i; inind=0;</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      20804 :     for(unsigned int j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      11892 :       unsigned i0=tmp%2+indices[j];</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">      11892 :       tmp/=2;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      11892 :       if(!pbc_[j] &amp;&amp; i0==nbin_[j]) continue;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">      11890 :       if( pbc_[j] &amp;&amp; i0==nbin_[j]) i0=0;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">      11890 :       nindices[inind++]=i0;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       8912 :     if(inind==dimension_) neighbors[nneighbors++]=getIndex(nindices);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :   }</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       3711 : }</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">       9577 : std::vector&lt;GridBase::index_t&gt; GridBase::getNearestNeighbors(const index_t index) const {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">       9577 :   std::vector&lt;index_t&gt; nearest_neighs = std::vector&lt;index_t&gt;();</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      28730 :   for (unsigned i = 0; i &lt; dimension_; i++) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      19153 :     std::vector&lt;unsigned&gt; neighsneeded = std::vector&lt;unsigned&gt;(dimension_, 0);</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      19153 :     neighsneeded[i] = 1;</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      19153 :     std::vector&lt;index_t&gt; singledim_nearest_neighs = getNeighbors(index, neighsneeded);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      74978 :     for (unsigned j = 0; j &lt; singledim_nearest_neighs.size(); j++) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">      55825 :       index_t neigh = singledim_nearest_neighs[j];</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">      55825 :       if (neigh != index) {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">      36672 :         nearest_neighs.push_back(neigh);</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :       }</a>
+<a name="346"><span class="lineNum">     346 </span>            :     }</a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       9577 :   return nearest_neighs;</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : }</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 : std::vector&lt;GridBase::index_t&gt; GridBase::getNearestNeighbors(const std::vector&lt;unsigned&gt; &amp;indices) const {</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   plumed_dbg_assert(indices.size() == dimension_);</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :   return getNearestNeighbors(getIndex(indices));</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 : void GridBase::addKernel( const KernelFunctions&amp; kernel ) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   plumed_dbg_assert( kernel.ndim()==dimension_ );</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; nneighb=kernel.getSupport( dx_ );</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :   std::vector&lt;index_t&gt; neighbors=getNeighbors( kernel.getCenter(), nneighb );</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; xx( dimension_ );</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; vv( dimension_ );</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :   std::string str_min, str_max;</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :     vv[i]=Tools::make_unique&lt;Value&gt;();</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :     if( pbc_[i] ) {</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :       Tools::convert(min_[i],str_min);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :       Tools::convert(max_[i],str_max);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :       vv[i]-&gt;setDomain( str_min, str_max );</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :     } else {</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :       vv[i]-&gt;setNotPeriodic();</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :     }</a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : // vv_ptr contains plain pointers obtained from vv.</a>
+<a name="375"><span class="lineNum">     375 </span>            : // this is the simplest way to replace a unique_ptr here.</a>
+<a name="376"><span class="lineNum">     376 </span>            : // perhaps the interface of kernel.evaluate() should be changed</a>
+<a name="377"><span class="lineNum">     377 </span>            : // in order to accept a std::vector&lt;std::unique_ptr&lt;Value&gt;&gt;</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :   auto vv_ptr=Tools::unique2raw(vv);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; der( dimension_ );</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;neighbors.size(); ++i) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :     index_t ineigh=neighbors[i];</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :     getPoint( ineigh, xx );</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;dimension_; ++j) vv[j]-&gt;set(xx[j]);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :     double newval = kernel.evaluate( vv_ptr, der, usederiv_ );</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :     if( usederiv_ ) addValueAndDerivatives( ineigh, newval, der );</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :     else addValue( ineigh, newval );</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :   }</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">    1193613 : double GridBase::getValue(const std::vector&lt;unsigned&gt; &amp; indices) const {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">    1193613 :   return getValue(getIndex(indices));</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : }</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">        345 : double GridBase::getValue(const std::vector&lt;double&gt; &amp; x) const {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        345 :   if(!dospline_) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         18 :     return getValue(getIndex(x));</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :   } else {</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">        327 :     std::vector&lt;double&gt; der(dimension_);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        327 :     return getValueAndDerivatives(x,der);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :   }</a>
+<a name="402"><span class="lineNum">     402 </span>            : }</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">    2527708 : double GridBase::getValueAndDerivatives(const std::vector&lt;unsigned&gt; &amp; indices, std::vector&lt;double&gt;&amp; der) const {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">    2527708 :   return getValueAndDerivatives(getIndex(indices),der);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">       3711 : double GridBase::getValueAndDerivatives(const std::vector&lt;double&gt; &amp; x, std::vector&lt;double&gt;&amp; der) const {</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :   plumed_dbg_assert(der.size()==dimension_ &amp;&amp; usederiv_);</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       3711 :   if(dospline_) {</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :     double X,X2,X3,value;</a>
+<a name="413"><span class="lineNum">     413 </span>            :     std::array&lt;double,maxdim&gt; fd, C, D;</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">       3711 :     std::vector&lt;double&gt; dder(dimension_);</span></a>
+<a name="415"><span class="lineNum">     415 </span>            : // reset</a>
+<a name="416"><span class="lineNum">     416 </span>            :     value=0.0;</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">       8167 :     for(unsigned int i=0; i&lt;dimension_; ++i) der[i]=0.0;</span></a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">       3711 :     std::vector&lt;unsigned&gt; indices(dimension_);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">       3711 :     getIndices(x, indices);</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">       3711 :     std::vector&lt;double&gt; xfloor(dimension_);</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">       3711 :     getPoint(indices, xfloor);</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">       3711 :     std::vector&lt;index_t&gt; neigh; unsigned nneigh; getSplineNeighbors(indices, neigh, nneigh);</span></a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            : // loop over neighbors</a>
+<a name="426"><span class="lineNum">     426 </span>            :     std::vector&lt;unsigned&gt; nindices;</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">      12621 :     for(unsigned int ipoint=0; ipoint&lt;nneigh; ++ipoint) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">       8910 :       double grid=getValueAndDerivatives(neigh[ipoint],dder);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       8910 :       getIndices(neigh[ipoint], nindices);</span></a>
+<a name="430"><span class="lineNum">     430 </span>            :       double ff=1.0;</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">      20800 :       for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :         int x0=1;</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">      11890 :         if(nindices[j]==indices[j]) x0=0;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">      11890 :         double dx=getDx(j);</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">      11890 :         X=std::abs((x[j]-xfloor[j])/dx-(double)x0);</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">      11890 :         X2=X*X;</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">      11890 :         X3=X2*X;</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :         double yy;</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">      11890 :         if(std::abs(grid)&lt;0.0000001) yy=0.0;</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">       8996 :         else yy=-dder[j]/grid;</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">      11890 :         C[j]=(1.0-3.0*X2+2.0*X3) - (x0?-1.0:1.0)*yy*(X-2.0*X2+X3)*dx;</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">      11890 :         D[j]=( -6.0*X +6.0*X2) - (x0?-1.0:1.0)*yy*(1.0-4.0*X +3.0*X2)*dx;</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">      11890 :         D[j]*=(x0?-1.0:1.0)/dx;</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">      11890 :         ff*=C[j];</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :       }</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">      20800 :       for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">      11890 :         fd[j]=D[j];</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">      29740 :         for(unsigned i=0; i&lt;dimension_; ++i) if(i!=j) fd[j]*=C[i];</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :       }</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">       8910 :       value+=grid*ff;</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">      20800 :       for(unsigned j=0; j&lt;dimension_; ++j) der[j]+=grid*fd[j];</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     }</a>
+<a name="454"><span class="lineNum">     454 </span>            :     return value;</a>
+<a name="455"><span class="lineNum">     455 </span>            :   } else {</a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :     return getValueAndDerivatives(getIndex(x),der);</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :   }</a>
+<a name="458"><span class="lineNum">     458 </span>            : }</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 : void GridBase::setValue(const std::vector&lt;unsigned&gt; &amp; indices, double value) {</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :   setValue(getIndex(indices),value);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineNoCov">          0 : void GridBase::setValueAndDerivatives(const std::vector&lt;unsigned&gt; &amp; indices, double value, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 :   setValueAndDerivatives(getIndex(indices),value,der);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 : void GridBase::addValue(const std::vector&lt;unsigned&gt; &amp; indices, double value) {</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :   addValue(getIndex(indices),value);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 : void GridBase::addValueAndDerivatives(const std::vector&lt;unsigned&gt; &amp; indices, double value, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :   addValueAndDerivatives(getIndex(indices),value,der);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">       1147 : void GridBase::writeHeader(OFile&amp; ofile) {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">       2611 :   for(unsigned i=0; i&lt;dimension_; ++i) {</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">       2928 :     ofile.addConstantField(&quot;min_&quot; + argnames[i]);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">       2928 :     ofile.addConstantField(&quot;max_&quot; + argnames[i]);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">       2928 :     ofile.addConstantField(&quot;nbins_&quot; + argnames[i]);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">       2928 :     ofile.addConstantField(&quot;periodic_&quot; + argnames[i]);</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   }</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">       1147 : }</span></a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          1 : void Grid::clear() {</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          1 :   grid_.assign(maxsize_,0.0);</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          1 :   if(usederiv_) der_.assign(maxsize_*dimension_,0.0);</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          1 : }</span></a>
+<a name="489"><span class="lineNum">     489 </span>            : </a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">       1147 : void Grid::writeToFile(OFile&amp; ofile) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">       1147 :   std::vector&lt;double&gt; xx(dimension_);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">       1147 :   std::vector&lt;double&gt; der(dimension_);</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :   double f;</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">       1147 :   writeHeader(ofile);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">    2533412 :   for(index_t i=0; i&lt;getSize(); ++i) {</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">    2532265 :     xx=getPoint(i);</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">    2532265 :     if(usederiv_) {f=getValueAndDerivatives(i,der);}</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">    1989707 :     else {f=getValue(i);}</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">    4914902 :     if(i&gt;0 &amp;&amp; dimension_&gt;1 &amp;&amp; getIndices(i)[dimension_-2]==0) ofile.printf(&quot;\n&quot;);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">    7484524 :     for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">    9904518 :       ofile.printField(&quot;min_&quot; + argnames[j], str_min_[j] );</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">    9904518 :       ofile.printField(&quot;max_&quot; + argnames[j], str_max_[j] );</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">    9904518 :       ofile.printField(&quot;nbins_&quot; + argnames[j], static_cast&lt;int&gt;(nbin_[j]) );</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">    6986607 :       if( pbc_[j] ) ofile.printField(&quot;periodic_&quot; + argnames[j], &quot;true&quot; );</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">    5835822 :       else          ofile.printField(&quot;periodic_&quot; + argnames[j], &quot;false&quot; );</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     }</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">    7484524 :     for(unsigned j=0; j&lt;dimension_; ++j) { ofile.fmtField(&quot; &quot;+fmt_); ofile.printField(argnames[j],xx[j]); }</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">    5064530 :     ofile.fmtField(&quot; &quot;+fmt_); ofile.printField(funcname,f);</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">    5194297 :     if(usederiv_) for(unsigned j=0; j&lt;dimension_; ++j) { ofile.fmtField(&quot; &quot;+fmt_); ofile.printField(&quot;der_&quot; + argnames[j],der[j]); }</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">    2532265 :     ofile.printField();</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   }</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">       1147 : }</span></a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 : void GridBase::writeCubeFile(OFile&amp; ofile, const double&amp; lunit) {</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :   plumed_assert( dimension_==3 );</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;PLUMED CUBE FILE\n&quot;);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;OUTER LOOP: X, MIDDLE LOOP: Y, INNER LOOP: Z\n&quot;);</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :   // Number of atoms followed by position of origin (origin set so that center of grid is in center of cell)</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;%d %f %f %f\n&quot;,1,-0.5*lunit*(max_[0]-min_[0]),-0.5*lunit*(max_[1]-min_[1]),-0.5*lunit*(max_[2]-min_[2]));</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;%u %f %f %f\n&quot;,nbin_[0],lunit*dx_[0],0.0,0.0);  // Number of bins in each direction followed by</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;%u %f %f %f\n&quot;,nbin_[1],0.0,lunit*dx_[1],0.0);  // shape of voxel</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;%u %f %f %f\n&quot;,nbin_[2],0.0,0.0,lunit*dx_[2]);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;%d %f %f %f\n&quot;,1,0.0,0.0,0.0); // Fake atom otherwise VMD doesn't work</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; pp(3);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :   for(pp[0]=0; pp[0]&lt;nbin_[0]; ++pp[0]) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :     for(pp[1]=0; pp[1]&lt;nbin_[1]; ++pp[1]) {</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :       for(pp[2]=0; pp[2]&lt;nbin_[2]; ++pp[2]) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 :         ofile.printf(&quot;%f &quot;,getValue(pp) );</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :         if(pp[2]%6==5) ofile.printf(&quot;\n&quot;);</span></a>
+<a name="530"><span class="lineNum">     530 </span>            :       }</a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :       ofile.printf(&quot;\n&quot;);</span></a>
+<a name="532"><span class="lineNum">     532 </span>            :     }</a>
+<a name="533"><span class="lineNum">     533 </span>            :   }</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         20 : std::unique_ptr&lt;GridBase&gt; GridBase::create(const std::string&amp; funcl, const std::vector&lt;Value*&gt; &amp; args, IFile&amp; ifile,</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :     const std::vector&lt;std::string&gt; &amp; gmin,const std::vector&lt;std::string&gt; &amp; gmax,</a>
+<a name="538"><span class="lineNum">     538 </span>            :     const std::vector&lt;unsigned&gt; &amp; nbin,bool dosparse, bool dospline, bool doder) {</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         20 :   std::unique_ptr&lt;GridBase&gt; grid=GridBase::create(funcl,args,ifile,dosparse,dospline,doder);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         20 :   std::vector&lt;unsigned&gt; cbin( grid-&gt;getNbin() );</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">         20 :   std::vector&lt;std::string&gt; cmin( grid-&gt;getMin() ), cmax( grid-&gt;getMax() );</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         49 :   for(unsigned i=0; i&lt;args.size(); ++i) {</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         29 :     plumed_massert( cmin[i]==gmin[i], &quot;mismatched grid min&quot; );</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         29 :     plumed_massert( cmax[i]==gmax[i], &quot;mismatched grid max&quot; );</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">         29 :     if( args[i]-&gt;isPeriodic() ) {</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">          8 :       plumed_massert( cbin[i]==nbin[i], &quot;mismatched grid nbins&quot; );</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :     } else {</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         21 :       plumed_massert( (cbin[i]-1)==nbin[i], &quot;mismatched grid nbins&quot;);</span></a>
+<a name="549"><span class="lineNum">     549 </span>            :     }</a>
+<a name="550"><span class="lineNum">     550 </span>            :   }</a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         20 :   return grid;</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         20 : }</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         70 : std::unique_ptr&lt;GridBase&gt; GridBase::create(const std::string&amp; funcl, const std::vector&lt;Value*&gt; &amp; args, IFile&amp; ifile, bool dosparse, bool dospline, bool doder)</span></a>
+<a name="555"><span class="lineNum">     555 </span>            : {</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">         70 :   std::unique_ptr&lt;GridBase&gt; grid;</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         70 :   unsigned nvar=args.size(); bool hasder=false; std::string pstring;</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         70 :   std::vector&lt;int&gt; gbin1(nvar); std::vector&lt;unsigned&gt; gbin(nvar);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         70 :   std::vector&lt;std::string&gt; labels(nvar),gmin(nvar),gmax(nvar);</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         70 :   std::vector&lt;std::string&gt; fieldnames; ifile.scanFieldList( fieldnames );</span></a>
+<a name="561"><span class="lineNum">     561 </span>            : // Retrieve names for fields</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">        158 :   for(unsigned i=0; i&lt;args.size(); ++i) labels[i]=args[i]-&gt;getName();</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : // And read the stuff from the header</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         70 :   plumed_massert( ifile.FieldExist( funcl ), &quot;no column labelled &quot; + funcl + &quot; in in grid input&quot;);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">        158 :   for(unsigned i=0; i&lt;args.size(); ++i) {</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">        176 :     ifile.scanField( &quot;min_&quot; + labels[i], gmin[i]);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">        176 :     ifile.scanField( &quot;max_&quot; + labels[i], gmax[i]);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">        176 :     ifile.scanField( &quot;periodic_&quot; + labels[i], pstring );</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">        176 :     ifile.scanField( &quot;nbins_&quot; + labels[i], gbin1[i]);</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">         88 :     plumed_assert( gbin1[i]&gt;0 );</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">         88 :     if( args[i]-&gt;isPeriodic() ) {</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         26 :       plumed_massert( pstring==&quot;true&quot;, &quot;input value is periodic but grid is not&quot;);</span></a>
+<a name="573"><span class="lineNum">     573 </span>            :       std::string pmin, pmax;</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         26 :       args[i]-&gt;getDomain( pmin, pmax ); gbin[i]=gbin1[i];</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         26 :       if( pmin!=gmin[i] || pmax!=gmax[i] ) plumed_merror(&quot;mismatch between grid boundaries and periods of values&quot;);</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :     } else {</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         62 :       gbin[i]=gbin1[i]-1;  // Note header in grid file indicates one more bin that there should be when data is not periodic</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         62 :       plumed_massert( pstring==&quot;false&quot;, &quot;input value is not periodic but grid is&quot;);</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :     }</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         88 :     hasder=ifile.FieldExist( &quot;der_&quot; + args[i]-&gt;getName() );</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         88 :     if( doder &amp;&amp; !hasder ) plumed_merror(&quot;missing derivatives from grid file&quot;);</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">        106 :     for(unsigned j=0; j&lt;fieldnames.size(); ++j) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">        124 :       for(unsigned k=i+1; k&lt;args.size(); ++k) {</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         18 :         if( fieldnames[j]==labels[k] ) plumed_merror(&quot;arguments in input are not in same order as in grid file&quot;);</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :       }</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">        106 :       if( fieldnames[j]==labels[i] ) break;</span></a>
+<a name="587"><span class="lineNum">     587 </span>            :     }</a>
+<a name="588"><span class="lineNum">     588 </span>            :   }</a>
+<a name="589"><span class="lineNum">     589 </span>            : </a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         70 :   if(!dosparse) {grid=Tools::make_unique&lt;Grid&gt;(funcl,args,gmin,gmax,gbin,dospline,doder);}</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineNoCov">          0 :   else {grid=Tools::make_unique&lt;SparseGrid&gt;(funcl,args,gmin,gmax,gbin,dospline,doder);}</span></a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         70 :   std::vector&lt;double&gt; xx(nvar),dder(nvar);</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         70 :   std::vector&lt;double&gt; dx=grid-&gt;getDx();</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :   double f,x;</a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">    1099575 :   while( ifile.scanField(funcl,f) ) {</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">    3294553 :     for(unsigned i=0; i&lt;nvar; ++i) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">    2195048 :       ifile.scanField(labels[i],x); xx[i]=x+dx[i]/2.0;</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">    4390096 :       ifile.scanField( &quot;min_&quot; + labels[i], gmin[i]);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">    4390096 :       ifile.scanField( &quot;max_&quot; + labels[i], gmax[i]);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">    4390096 :       ifile.scanField( &quot;nbins_&quot; + labels[i], gbin1[i]);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">    4390096 :       ifile.scanField( &quot;periodic_&quot; + labels[i], pstring );</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :     }</a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">    3211140 :     if(hasder) { for(unsigned i=0; i&lt;nvar; ++i) { ifile.scanField( &quot;der_&quot; + args[i]-&gt;getName(), dder[i] ); } }</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">    1099505 :     index_t index=grid-&gt;getIndex(xx);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">    1099505 :     if(doder) {grid-&gt;setValueAndDerivatives(index,f,dder);}</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">      42717 :     else {grid-&gt;setValue(index,f);}</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">    1099505 :     ifile.scanField();</span></a>
+<a name="609"><span class="lineNum">     609 </span>            :   }</a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         70 :   return grid;</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">         70 : }</span></a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">        861 : double Grid::getMinValue() const {</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :   double minval;</a>
+<a name="615"><span class="lineNum">     615 </span>            :   minval=DBL_MAX;</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">    2258311 :   for(index_t i=0; i&lt;grid_.size(); ++i) {</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">    2257450 :     if(grid_[i]&lt;minval)minval=grid_[i];</span></a>
+<a name="618"><span class="lineNum">     618 </span>            :   }</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        861 :   return minval;</span></a>
+<a name="620"><span class="lineNum">     620 </span>            : }</a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        629 : double Grid::getMaxValue() const {</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :   double maxval;</a>
+<a name="624"><span class="lineNum">     624 </span>            :   maxval=DBL_MIN;</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">    3755246 :   for(index_t i=0; i&lt;grid_.size(); ++i) {</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">    3754617 :     if(grid_[i]&gt;maxval)maxval=grid_[i];</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :   }</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">        629 :   return maxval;</span></a>
+<a name="629"><span class="lineNum">     629 </span>            : }</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">        594 : void Grid::scaleAllValuesAndDerivatives( const double&amp; scalef ) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">        594 :   if(usederiv_) {</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">      21474 :     for(index_t i=0; i&lt;grid_.size(); ++i) {</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">      21463 :       grid_[i]*=scalef;</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">      63888 :       for(unsigned j=0; j&lt;dimension_; ++j) der_[i*dimension_+j]*=scalef;</span></a>
+<a name="636"><span class="lineNum">     636 </span>            :     }</a>
+<a name="637"><span class="lineNum">     637 </span>            :   } else {</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">    1572834 :     for(index_t i=0; i&lt;grid_.size(); ++i) grid_[i]*=scalef;</span></a>
+<a name="639"><span class="lineNum">     639 </span>            :   }</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">        594 : }</span></a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 : void Grid::logAllValuesAndDerivatives( const double&amp; scalef ) {</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :   if(usederiv_) {</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :     for(index_t i=0; i&lt;grid_.size(); ++i) {</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :       grid_[i] = scalef*std::log(grid_[i]);</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;dimension_; ++j) der_[i*dimension_+j] = scalef/der_[i*dimension_+j];</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :     }</a>
+<a name="648"><span class="lineNum">     648 </span>            :   } else {</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :     for(index_t i=0; i&lt;grid_.size(); ++i) grid_[i] = scalef*std::log(grid_[i]);</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :   }</a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">       1329 : void Grid::setMinToZero() {</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">       1329 :   double min=grid_[0];</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">    3518541 :   for(index_t i=1; i&lt;grid_.size(); ++i) if(grid_[i]&lt;min) min=grid_[i];</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">    3519870 :   for(index_t i=0; i&lt;grid_.size(); ++i) grid_[i] -= min;</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">       1329 : }</span></a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">          1 : void Grid::applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) ) {</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">          1 :   if(usederiv_) {</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">        901 :     for(index_t i=0; i&lt;grid_.size(); ++i) {</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">        900 :       grid_[i]=func(grid_[i]);</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">       2700 :       for(unsigned j=0; j&lt;dimension_; ++j) der_[i*dimension_+j]=funcder(der_[i*dimension_+j]);</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :     }</a>
+<a name="665"><span class="lineNum">     665 </span>            :   } else {</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :     for(index_t i=0; i&lt;grid_.size(); ++i) grid_[i]=func(grid_[i]);</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :   }</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">          1 : }</span></a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 : double Grid::getDifferenceFromContour( const std::vector&lt;double&gt;&amp; x, std::vector&lt;double&gt;&amp; der ) const {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :   return getValueAndDerivatives( x, der ) - contour_location;</span></a>
+<a name="672"><span class="lineNum">     672 </span>            : }</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 : void Grid::findSetOfPointsOnContour(const double&amp; target, const std::vector&lt;bool&gt;&amp; nosearch,</span></a>
+<a name="675"><span class="lineNum">     675 </span>            :                                     unsigned&amp; npoints, std::vector&lt;std::vector&lt;double&gt; &gt;&amp; points ) {</a>
+<a name="676"><span class="lineNum">     676 </span>            : // Set contour location for function</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :   contour_location=target;</span></a>
+<a name="678"><span class="lineNum">     678 </span>            : // Resize points to maximum possible value</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :   points.resize( dimension_*maxsize_ );</span></a>
+<a name="680"><span class="lineNum">     680 </span>            : </a>
+<a name="681"><span class="lineNum">     681 </span>            : // Two points for search</a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; ind(dimension_);</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; direction( dimension_, 0 );</span></a>
+<a name="684"><span class="lineNum">     684 </span>            : </a>
+<a name="685"><span class="lineNum">     685 </span>            : // Run over whole grid</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :   npoints=0; RootFindingBase&lt;Grid&gt; mymin( this );</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;maxsize_; ++i) {</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;dimension_; ++j) ind[j]=getIndices(i)[j];</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : </a>
+<a name="690"><span class="lineNum">     690 </span>            :     // Get the value of a point on the grid</a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :     double val1=getValue(i) - target;</span></a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            :     // Now search for contour in each direction</a>
+<a name="694"><span class="lineNum">     694 </span>            :     bool edge=false;</a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :       if( nosearch[j] ) continue ;</span></a>
+<a name="697"><span class="lineNum">     697 </span>            :       // Make sure we don't search at the edge of the grid</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :       if( !pbc_[j] &amp;&amp; (ind[j]+1)==nbin_[j] ) continue;</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :       else if( (ind[j]+1)==nbin_[j] ) { edge=true; ind[j]=0; }</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :       else ind[j]+=1;</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :       double val2=getValue(ind) - target;</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineNoCov">          0 :       if( val1*val2&lt;0 ) {</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :         // Use initial point location as first guess for search</a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineNoCov">          0 :         points[npoints].resize(dimension_); for(unsigned k=0; k&lt;dimension_; ++k) points[npoints][k]=getPoint(i)[k];</span></a>
+<a name="705"><span class="lineNum">     705 </span>            :         // Setup direction vector</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineNoCov">          0 :         direction[j]=0.999999999*dx_[j];</span></a>
+<a name="707"><span class="lineNum">     707 </span>            :         // And do proper search for contour point</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :         mymin.linesearch( direction, points[npoints], &amp;Grid::getDifferenceFromContour );</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :         direction[j]=0.0; npoints++;</span></a>
+<a name="710"><span class="lineNum">     710 </span>            :       }</a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineNoCov">          0 :       if( pbc_[j] &amp;&amp; edge ) { edge=false; ind[j]=nbin_[j]-1; }</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :       else ind[j]-=1;</span></a>
+<a name="713"><span class="lineNum">     713 </span>            :     }</a>
+<a name="714"><span class="lineNum">     714 </span>            :   }</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="716"><span class="lineNum">     716 </span>            : </a>
+<a name="717"><span class="lineNum">     717 </span>            : /// OVERRIDES ARE BELOW</a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">   28865222 : Grid::index_t Grid::getSize() const {</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineCov">   28865222 :   return maxsize_;</span></a>
+<a name="721"><span class="lineNum">     721 </span>            : }</a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">   27284983 : double Grid::getValue(index_t index) const {</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :   plumed_dbg_assert(index&lt;maxsize_);</a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">   27284983 :   return grid_[index];</span></a>
+<a name="726"><span class="lineNum">     726 </span>            : }</a>
+<a name="727"><span class="lineNum">     727 </span>            : </a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">    3079776 : double Grid::getValueAndDerivatives(index_t index, std::vector&lt;double&gt;&amp; der) const {</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :   plumed_dbg_assert(index&lt;maxsize_ &amp;&amp; usederiv_ &amp;&amp; der.size()==dimension_);</a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">    3079776 :   der.resize(dimension_);</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">    6679531 :   for(unsigned i=0; i&lt;dimension_; i++) der[i]=der_[dimension_*index+i];</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">    3079776 :   return grid_[index];</span></a>
+<a name="733"><span class="lineNum">     733 </span>            : }</a>
+<a name="734"><span class="lineNum">     734 </span>            : </a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">    6444104 : void Grid::setValue(index_t index, double value) {</span></a>
+<a name="736"><span class="lineNum">     736 </span>            :   plumed_dbg_assert(index&lt;maxsize_ &amp;&amp; !usederiv_);</a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">    6444104 :   grid_[index]=value;</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineCov">    6444104 : }</span></a>
+<a name="739"><span class="lineNum">     739 </span>            : </a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineCov">    2552369 : void Grid::setValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="741"><span class="lineNum">     741 </span>            :   plumed_dbg_assert(index&lt;maxsize_ &amp;&amp; usederiv_ &amp;&amp; der.size()==dimension_);</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">    2552369 :   grid_[index]=value;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">    7609163 :   for(unsigned i=0; i&lt;dimension_; i++) der_[dimension_*index+i]=der[i];</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">    2552369 : }</span></a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">          1 : void Grid::addValue(index_t index, double value) {</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :   plumed_dbg_assert(index&lt;maxsize_ &amp;&amp; !usederiv_);</a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineCov">          1 :   grid_[index]+=value;</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">          1 : }</span></a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">    1171742 : void Grid::addValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="752"><span class="lineNum">     752 </span>            :   plumed_dbg_assert(index&lt;maxsize_ &amp;&amp; usederiv_ &amp;&amp; der.size()==dimension_);</a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">    1171742 :   grid_[index]+=value;</span></a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">    3500479 :   for(unsigned int i=0; i&lt;dimension_; ++i) der_[index*dimension_+i]+=der[i];</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">    1171742 : }</span></a>
+<a name="756"><span class="lineNum">     756 </span>            : </a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 : Grid::index_t SparseGrid::getSize() const {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineNoCov">          0 :   return map_.size();</span></a>
+<a name="759"><span class="lineNum">     759 </span>            : }</a>
+<a name="760"><span class="lineNum">     760 </span>            : </a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineNoCov">          0 : Grid::index_t SparseGrid::getMaxSize() const {</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :   return maxsize_;</span></a>
+<a name="763"><span class="lineNum">     763 </span>            : }</a>
+<a name="764"><span class="lineNum">     764 </span>            : </a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineNoCov">          0 : double SparseGrid::getValue(index_t index)const {</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineNoCov">          0 :   plumed_assert(index&lt;maxsize_);</span></a>
+<a name="767"><span class="lineNum">     767 </span>            :   double value=0.0;</a>
+<a name="768"><span class="lineNum">     768 </span>            :   const auto it=map_.find(index);</a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :   if(it!=map_.end()) value=it-&gt;second;</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineNoCov">          0 :   return value;</span></a>
+<a name="771"><span class="lineNum">     771 </span>            : }</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">        200 : double SparseGrid::getValueAndDerivatives(index_t index, std::vector&lt;double&gt;&amp; der)const {</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">        200 :   plumed_assert(index&lt;maxsize_ &amp;&amp; usederiv_ &amp;&amp; der.size()==dimension_);</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :   double value=0.0;</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">        580 :   for(unsigned int i=0; i&lt;dimension_; ++i) der[i]=0.0;</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :   const auto it=map_.find(index);</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">        200 :   if(it!=map_.end()) value=it-&gt;second;</span></a>
+<a name="779"><span class="lineNum">     779 </span>            :   const auto itder=der_.find(index);</a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">        200 :   if(itder!=der_.end()) der=itder-&gt;second;</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">        200 :   return value;</span></a>
+<a name="782"><span class="lineNum">     782 </span>            : }</a>
+<a name="783"><span class="lineNum">     783 </span>            : </a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineNoCov">          0 : void SparseGrid::setValue(index_t index, double value) {</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineNoCov">          0 :   plumed_assert(index&lt;maxsize_ &amp;&amp; !usederiv_);</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineNoCov">          0 :   map_[index]=value;</span></a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="788"><span class="lineNum">     788 </span>            : </a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineNoCov">          0 : void SparseGrid::setValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineNoCov">          0 :   plumed_assert(index&lt;maxsize_ &amp;&amp; usederiv_ &amp;&amp; der.size()==dimension_);</span></a>
+<a name="791"><span class="lineNum">     791 </span><span class="lineNoCov">          0 :   map_[index]=value;</span></a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineNoCov">          0 :   der_[index]=der;</span></a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="794"><span class="lineNum">     794 </span>            : </a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineNoCov">          0 : void SparseGrid::addValue(index_t index, double value) {</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineNoCov">          0 :   plumed_assert(index&lt;maxsize_ &amp;&amp; !usederiv_);</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineNoCov">          0 :   map_[index]+=value;</span></a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="799"><span class="lineNum">     799 </span>            : </a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">      19999 : void SparseGrid::addValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">      19999 :   plumed_assert(index&lt;maxsize_ &amp;&amp; usederiv_ &amp;&amp; der.size()==dimension_);</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">      19999 :   map_[index]+=value;</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">      19999 :   der_[index].resize(dimension_);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">      59682 :   for(unsigned int i=0; i&lt;dimension_; ++i) der_[index][i]+=der[i];</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">      19999 : }</span></a>
+<a name="806"><span class="lineNum">     806 </span>            : </a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineNoCov">          0 : void SparseGrid::writeToFile(OFile&amp; ofile) {</span></a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; xx(dimension_);</span></a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; der(dimension_);</span></a>
+<a name="810"><span class="lineNum">     810 </span>            :   double f;</a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineNoCov">          0 :   writeHeader(ofile);</span></a>
+<a name="812"><span class="lineNum">     812 </span><span class="lineNoCov">          0 :   ofile.fmtField(&quot; &quot;+fmt_);</span></a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineNoCov">          0 :   for(const auto &amp; it : map_) {</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineNoCov">          0 :     index_t i=it.first;</span></a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineNoCov">          0 :     xx=getPoint(i);</span></a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineNoCov">          0 :     if(usederiv_) {f=getValueAndDerivatives(i,der);}</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineNoCov">          0 :     else {f=getValue(i);}</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineNoCov">          0 :     if(i&gt;0 &amp;&amp; dimension_&gt;1 &amp;&amp; getIndices(i)[dimension_-2]==0) ofile.printf(&quot;\n&quot;);</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineNoCov">          0 :       ofile.printField(&quot;min_&quot; + argnames[j], str_min_[j] );</span></a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineNoCov">          0 :       ofile.printField(&quot;max_&quot; + argnames[j], str_max_[j] );</span></a>
+<a name="822"><span class="lineNum">     822 </span><span class="lineNoCov">          0 :       ofile.printField(&quot;nbins_&quot; + argnames[j], static_cast&lt;int&gt;(nbin_[j]) );</span></a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineNoCov">          0 :       if( pbc_[j] ) ofile.printField(&quot;periodic_&quot; + argnames[j], &quot;true&quot; );</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineNoCov">          0 :       else          ofile.printField(&quot;periodic_&quot; + argnames[j], &quot;false&quot; );</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :     }</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;dimension_; ++j) ofile.printField(argnames[j],xx[j]);</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineNoCov">          0 :     ofile.printField(funcname, f);</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineNoCov">          0 :     if(usederiv_) { for(unsigned j=0; j&lt;dimension_; ++j) ofile.printField(&quot;der_&quot; + argnames[j],der[j]); }</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineNoCov">          0 :     ofile.printField();</span></a>
+<a name="830"><span class="lineNum">     830 </span>            :   }</a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineNoCov">          0 : double SparseGrid::getMinValue() const {</span></a>
+<a name="834"><span class="lineNum">     834 </span>            :   double minval;</a>
+<a name="835"><span class="lineNum">     835 </span>            :   minval=0.0;</a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineNoCov">          0 :   for(auto const &amp; i : map_) {</span></a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineNoCov">          0 :     if(i.second&lt;minval) minval=i.second;</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :   }</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineNoCov">          0 :   return minval;</span></a>
+<a name="840"><span class="lineNum">     840 </span>            : }</a>
+<a name="841"><span class="lineNum">     841 </span>            : </a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">          9 : double SparseGrid::getMaxValue() const {</span></a>
+<a name="843"><span class="lineNum">     843 </span>            :   double maxval;</a>
+<a name="844"><span class="lineNum">     844 </span>            :   maxval=0.0;</a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">        590 :   for(auto const &amp; i : map_) {</span></a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">        581 :     if(i.second&gt;maxval) maxval=i.second;</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :   }</a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">          9 :   return maxval;</span></a>
+<a name="849"><span class="lineNum">     849 </span>            : }</a>
+<a name="850"><span class="lineNum">     850 </span>            : </a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">    1010062 : void Grid::projectOnLowDimension(double &amp;val, std::vector&lt;int&gt; &amp;vHigh, WeightBase * ptr2obj ) {</span></a>
+<a name="852"><span class="lineNum">     852 </span>            :   unsigned i=0;</a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">    3016945 :   for(i=0; i&lt;vHigh.size(); i++) {</span></a>
+<a name="854"><span class="lineNum">     854 </span><span class="lineCov">    2015726 :     if(vHigh[i]&lt;0) { // this bin needs to be integrated out</span></a>
+<a name="855"><span class="lineNum">     855 </span>            :       // parallelize here???</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">    1010062 :       for(unsigned j=0; j&lt;(getNbin())[i]; j++) {</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">    1001219 :         vHigh[i]=int(j);</span></a>
+<a name="858"><span class="lineNum">     858 </span><span class="lineCov">    1001219 :         projectOnLowDimension(val,vHigh,ptr2obj); // recursive function: this is the core of the mechanism</span></a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">    1001219 :         vHigh[i]=-1;</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :       }</a>
+<a name="861"><span class="lineNum">     861 </span>            :       return; //</a>
+<a name="862"><span class="lineNum">     862 </span>            :     }</a>
+<a name="863"><span class="lineNum">     863 </span>            :   }</a>
+<a name="864"><span class="lineNum">     864 </span>            :   // when there are no more bin to dig in then retrieve the value</a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">    1001219 :   if(i==vHigh.size()) {</span></a>
+<a name="866"><span class="lineNum">     866 </span>            :     //std::cerr&lt;&lt;&quot;POINT: &quot;;</a>
+<a name="867"><span class="lineNum">     867 </span>            :     //for(unsigned j=0;j&lt;vHigh.size();j++){</a>
+<a name="868"><span class="lineNum">     868 </span>            :     //   std::cerr&lt;&lt;vHigh[j]&lt;&lt;&quot; &quot;;</a>
+<a name="869"><span class="lineNum">     869 </span>            :     //}</a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">    1001219 :     std::vector&lt;unsigned&gt; vv(vHigh.size());</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineCov">    3003657 :     for(unsigned j=0; j&lt;vHigh.size(); j++)vv[j]=unsigned(vHigh[j]);</span></a>
+<a name="872"><span class="lineNum">     872 </span>            :     //</a>
+<a name="873"><span class="lineNum">     873 </span>            :     // this is the real assignment !!!!! (hack this to have bias or other stuff)</a>
+<a name="874"><span class="lineNum">     874 </span>            :     //</a>
+<a name="875"><span class="lineNum">     875 </span>            : </a>
+<a name="876"><span class="lineNum">     876 </span>            :     // this case: produce fes</a>
+<a name="877"><span class="lineNum">     877 </span>            :     //val+=exp(beta*getValue(vv)) ;</a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">    1001219 :     double myv=getValue(vv);</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">    1001219 :     val=ptr2obj-&gt;projectInnerLoop(val,myv) ;</span></a>
+<a name="880"><span class="lineNum">     880 </span>            :     // to be added: bias (same as before without negative sign)</a>
+<a name="881"><span class="lineNum">     881 </span>            :     //std::cerr&lt;&lt;&quot; VAL: &quot;&lt;&lt;val &lt;&lt;endl;</a>
+<a name="882"><span class="lineNum">     882 </span>            :   }</a>
+<a name="883"><span class="lineNum">     883 </span>            : }</a>
+<a name="884"><span class="lineNum">     884 </span>            : </a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">         81 : Grid Grid::project(const std::vector&lt;std::string&gt; &amp; proj, WeightBase *ptr2obj ) {</span></a>
+<a name="886"><span class="lineNum">     886 </span>            :   // find extrema only for the projection</a>
+<a name="887"><span class="lineNum">     887 </span>            :   std::vector&lt;std::string&gt;   smallMin,smallMax;</a>
+<a name="888"><span class="lineNum">     888 </span>            :   std::vector&lt;unsigned&gt; smallBin;</a>
+<a name="889"><span class="lineNum">     889 </span>            :   std::vector&lt;unsigned&gt; dimMapping;</a>
+<a name="890"><span class="lineNum">     890 </span>            :   std::vector&lt;bool&gt; smallIsPeriodic;</a>
+<a name="891"><span class="lineNum">     891 </span>            :   std::vector&lt;std::string&gt; smallName;</a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            :   // check if the two key methods are there</a>
+<a name="894"><span class="lineNum">     894 </span>            :   WeightBase* pp = dynamic_cast&lt;WeightBase*&gt;(ptr2obj);</a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">         81 :   if (!pp)plumed_merror(&quot;This WeightBase is not complete: you need a projectInnerLoop and projectOuterLoop &quot;);</span></a>
+<a name="896"><span class="lineNum">     896 </span>            : </a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">        162 :   for(unsigned j=0; j&lt;proj.size(); j++) {</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">        120 :     for(unsigned i=0; i&lt;getArgNames().size(); i++) {</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">        120 :       if(proj[j]==getArgNames()[i]) {</span></a>
+<a name="900"><span class="lineNum">     900 </span>            :         unsigned offset;</a>
+<a name="901"><span class="lineNum">     901 </span>            :         // note that at sizetime the non periodic dimension get a bin more</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">        162 :         if(getIsPeriodic()[i]) {offset=0;} else {offset=1;}</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">         81 :         smallMax.push_back(getMax()[i]);</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">         81 :         smallMin.push_back(getMin()[i]);</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">         81 :         smallBin.push_back(getNbin()[i]-offset);</span></a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">        162 :         smallIsPeriodic.push_back(getIsPeriodic()[i]);</span></a>
+<a name="907"><span class="lineNum">     907 </span><span class="lineCov">         81 :         dimMapping.push_back(i);</span></a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">         81 :         smallName.push_back(getArgNames()[i]);</span></a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineCov">         81 :         break;</span></a>
+<a name="910"><span class="lineNum">     910 </span>            :       }</a>
+<a name="911"><span class="lineNum">     911 </span>            :     }</a>
+<a name="912"><span class="lineNum">     912 </span>            :   }</a>
+<a name="913"><span class="lineNum">     913 </span><span class="lineCov">         81 :   Grid smallgrid(&quot;projection&quot;,smallName,smallMin,smallMax,smallBin,false,false,smallIsPeriodic,smallMin,smallMax);</span></a>
+<a name="914"><span class="lineNum">     914 </span>            :   // check that the two grids are commensurate</a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">        162 :   for(unsigned i=0; i&lt;dimMapping.size(); i++) {</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">         81 :     plumed_massert(  (smallgrid.getMax())[i] == (getMax())[dimMapping[i]],  &quot;the two input grids are not compatible in max&quot;   );</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">         81 :     plumed_massert(  (smallgrid.getMin())[i] == (getMin())[dimMapping[i]],  &quot;the two input grids are not compatible in min&quot;   );</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">         81 :     plumed_massert(  (smallgrid.getNbin())[i]== (getNbin())[dimMapping[i]], &quot;the two input grids are not compatible in bin&quot;   );</span></a>
+<a name="919"><span class="lineNum">     919 </span>            :   }</a>
+<a name="920"><span class="lineNum">     920 </span>            :   std::vector&lt;unsigned&gt; toBeIntegrated;</a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">        243 :   for(unsigned i=0; i&lt;getArgNames().size(); i++) {</span></a>
+<a name="922"><span class="lineNum">     922 </span>            :     bool doappend=true;</a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">        243 :     for(unsigned j=0; j&lt;dimMapping.size(); j++) {</span></a>
+<a name="924"><span class="lineNum">     924 </span><span class="lineCov">        162 :       if(dimMapping[j]==i) {doappend=false; break;}</span></a>
+<a name="925"><span class="lineNum">     925 </span>            :     }</a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">        162 :     if(doappend)toBeIntegrated.push_back(i);</span></a>
+<a name="927"><span class="lineNum">     927 </span>            :   }</a>
+<a name="928"><span class="lineNum">     928 </span>            : </a>
+<a name="929"><span class="lineNum">     929 </span>            :   // loop over all the points in the Grid, find the corresponding fixed index, rotate over all the other ones</a>
+<a name="930"><span class="lineNum">     930 </span><span class="lineCov">       8924 :   for(unsigned i=0; i&lt;smallgrid.getSize(); i++) {</span></a>
+<a name="931"><span class="lineNum">     931 </span>            :     std::vector&lt;unsigned&gt; v;</a>
+<a name="932"><span class="lineNum">     932 </span><span class="lineCov">       8843 :     v=smallgrid.getIndices(i);</span></a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">       8843 :     std::vector&lt;int&gt; vHigh((getArgNames()).size(),-1);</span></a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">      17686 :     for(unsigned j=0; j&lt;dimMapping.size(); j++)vHigh[dimMapping[j]]=int(v[j]);</span></a>
+<a name="935"><span class="lineNum">     935 </span>            :     // the vector vhigh now contains at the beginning the index of the low dimension and -1 for the values that need to be integrated</a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">       8843 :     double initval=0.;</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">       8843 :     projectOnLowDimension(initval,vHigh, ptr2obj);</span></a>
+<a name="938"><span class="lineNum">     938 </span><span class="lineCov">       8843 :     smallgrid.setValue(i,ptr2obj-&gt;projectOuterLoop(initval));</span></a>
+<a name="939"><span class="lineNum">     939 </span>            :   }</a>
+<a name="940"><span class="lineNum">     940 </span>            : </a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">         81 :   return smallgrid;</span></a>
+<a name="942"><span class="lineNum">     942 </span><span class="lineCov">        162 : }</span></a>
+<a name="943"><span class="lineNum">     943 </span>            : </a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 : double Grid::integrate( std::vector&lt;unsigned&gt;&amp; npoints ) {</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineNoCov">          0 :   plumed_dbg_assert( npoints.size()==dimension_ ); plumed_assert( dospline_ );</span></a>
+<a name="946"><span class="lineNum">     946 </span>            : </a>
+<a name="947"><span class="lineNum">     947 </span>            :   unsigned ntotgrid=1; double box_vol=1.0;</a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; ispacing( npoints.size() );</span></a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineNoCov">          0 :   for(unsigned j=0; j&lt;dimension_; ++j) {</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineNoCov">          0 :     if( !pbc_[j] ) {</span></a>
+<a name="951"><span class="lineNum">     951 </span><span class="lineNoCov">          0 :       ispacing[j] = ( max_[j] - dx_[j] - min_[j] ) / static_cast&lt;double&gt;( npoints[j] );</span></a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineNoCov">          0 :       npoints[j]+=1;</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :     } else {</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineNoCov">          0 :       ispacing[j] = ( max_[j] - min_[j] ) / static_cast&lt;double&gt;( npoints[j] );</span></a>
+<a name="955"><span class="lineNum">     955 </span>            :     }</a>
+<a name="956"><span class="lineNum">     956 </span><span class="lineNoCov">          0 :     ntotgrid*=npoints[j]; box_vol*=ispacing[j];</span></a>
+<a name="957"><span class="lineNum">     957 </span>            :   }</a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; vals( dimension_ );</span></a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned&gt; t_index( dimension_ ); double integral=0.0;</span></a>
+<a name="961"><span class="lineNum">     961 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;ntotgrid; ++i) {</span></a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineNoCov">          0 :     t_index[0]=(i%npoints[0]);</span></a>
+<a name="963"><span class="lineNum">     963 </span>            :     unsigned kk=i;</a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineNoCov">          0 :     for(unsigned j=1; j&lt;dimension_-1; ++j) { kk=(kk-t_index[j-1])/npoints[j-1]; t_index[j]=(kk%npoints[j]); }</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineNoCov">          0 :     if( dimension_&gt;=2 ) t_index[dimension_-1]=((kk-t_index[dimension_-2])/npoints[dimension_-2]);</span></a>
+<a name="966"><span class="lineNum">     966 </span>            : </a>
+<a name="967"><span class="lineNum">     967 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;dimension_; ++j) vals[j]=min_[j] + t_index[j]*ispacing[j];</span></a>
+<a name="968"><span class="lineNum">     968 </span>            : </a>
+<a name="969"><span class="lineNum">     969 </span><span class="lineNoCov">          0 :     integral += getValue( vals );</span></a>
+<a name="970"><span class="lineNum">     970 </span>            :   }</a>
+<a name="971"><span class="lineNum">     971 </span>            : </a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineNoCov">          0 :   return box_vol*integral;</span></a>
+<a name="973"><span class="lineNum">     973 </span>            : }</a>
+<a name="974"><span class="lineNum">     974 </span>            : </a>
+<a name="975"><span class="lineNum">     975 </span><span class="lineNoCov">          0 : void Grid::mpiSumValuesAndDerivatives( Communicator&amp; comm ) {</span></a>
+<a name="976"><span class="lineNum">     976 </span><span class="lineNoCov">          0 :   comm.Sum( grid_ ); for(unsigned i=0; i&lt;der_.size(); ++i) comm.Sum( der_[i] );</span></a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="978"><span class="lineNum">     978 </span>            : </a>
+<a name="979"><span class="lineNum">     979 </span>            : </a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">      59573 : bool indexed_lt(std::pair&lt;Grid::index_t, double&gt; const &amp;x, std::pair&lt;Grid::index_t, double&gt; const   &amp;y) {</span></a>
+<a name="981"><span class="lineNum">     981 </span><span class="lineCov">      59573 :   return x.second &lt; y.second;</span></a>
+<a name="982"><span class="lineNum">     982 </span>            : }</a>
+<a name="983"><span class="lineNum">     983 </span>            : </a>
+<a name="984"><span class="lineNum">     984 </span><span class="lineCov">        273 : double GridBase::findMaximalPathMinimum(const std::vector&lt;double&gt; &amp;source, const std::vector&lt;double&gt; &amp;sink) {</span></a>
+<a name="985"><span class="lineNum">     985 </span>            :   plumed_dbg_assert(source.size() == dimension_);</a>
+<a name="986"><span class="lineNum">     986 </span>            :   plumed_dbg_assert(sink.size() == dimension_);</a>
+<a name="987"><span class="lineNum">     987 </span>            :   // Start and end indices</a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">        273 :   index_t source_idx = getIndex(source);</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">        273 :   index_t sink_idx = getIndex(sink);</span></a>
+<a name="990"><span class="lineNum">     990 </span>            :   // Path cost</a>
+<a name="991"><span class="lineNum">     991 </span>            :   double maximal_minimum = 0;</a>
+<a name="992"><span class="lineNum">     992 </span>            :   // In one dimension, path searching is very easy--either go one way if it's not periodic,</a>
+<a name="993"><span class="lineNum">     993 </span>            :   // or go both ways if it is periodic. There's no reason to pay the cost of Dijkstra.</a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">        273 :   if (dimension_ == 1) {</span></a>
+<a name="995"><span class="lineNum">     995 </span>            :     // Do a search from the grid source to grid sink that does not</a>
+<a name="996"><span class="lineNum">     996 </span>            :     // cross the grid boundary.</a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">        147 :     double curr_min_bias = getValue(source_idx);</span></a>
+<a name="998"><span class="lineNum">     998 </span>            :     // Either search from a high source to a low sink.</a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">        147 :     if (source_idx &gt; sink_idx) {</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">        735 :       for (index_t i = source_idx; i &gt;= sink_idx; i--) {</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">        588 :         if (curr_min_bias == 0.0) {</span></a>
+<a name="1002"><span class="lineNum">    1002 </span>            :           break;</a>
+<a name="1003"><span class="lineNum">    1003 </span>            :         }</a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">        588 :         curr_min_bias = fmin(curr_min_bias, getValue(i));</span></a>
+<a name="1005"><span class="lineNum">    1005 </span>            :       }</a>
+<a name="1006"><span class="lineNum">    1006 </span>            :       // Or search from a low source to a high sink.</a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :     } else if (source_idx &lt; sink_idx) {</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineNoCov">          0 :       for (index_t i = source_idx; i &lt;= sink_idx; i++) {</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineNoCov">          0 :         if (curr_min_bias == 0.0) {</span></a>
+<a name="1010"><span class="lineNum">    1010 </span>            :           break;</a>
+<a name="1011"><span class="lineNum">    1011 </span>            :         }</a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineNoCov">          0 :         curr_min_bias = fmin(curr_min_bias, getValue(i));</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :       }</a>
+<a name="1014"><span class="lineNum">    1014 </span>            :     }</a>
+<a name="1015"><span class="lineNum">    1015 </span>            :     maximal_minimum = curr_min_bias;</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :     // If the grid is periodic, also do the search that crosses</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :     // the grid boundary.</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">        147 :     if (pbc_[0]) {</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">         42 :       double curr_min_bias = getValue(source_idx);</span></a>
+<a name="1020"><span class="lineNum">    1020 </span>            :       // Either go from a high source to the upper boundary and</a>
+<a name="1021"><span class="lineNum">    1021 </span>            :       // then from the bottom boundary to the sink</a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">         42 :       if (source_idx &gt; sink_idx) {</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">        210 :         for (index_t i = source_idx; i &lt; maxsize_; i++) {</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">        168 :           if (curr_min_bias == 0.0) {</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :             break;</a>
+<a name="1026"><span class="lineNum">    1026 </span>            :           }</a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">        168 :           curr_min_bias = fmin(curr_min_bias, getValue(i));</span></a>
+<a name="1028"><span class="lineNum">    1028 </span>            :         }</a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">        210 :         for (index_t i = 0; i &lt;= sink_idx; i++) {</span></a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">        168 :           if (curr_min_bias == 0.0) {</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :             break;</a>
+<a name="1032"><span class="lineNum">    1032 </span>            :           }</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">        168 :           curr_min_bias = fmin(curr_min_bias, getValue(i));</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :         }</a>
+<a name="1035"><span class="lineNum">    1035 </span>            :         // Or go from a low source to the bottom boundary and</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :         // then from the high boundary to the sink</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineNoCov">          0 :       } else if (source_idx &lt; sink_idx) {</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineNoCov">          0 :         for (index_t i = source_idx; i &gt; 0; i--) {</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineNoCov">          0 :           if (curr_min_bias == 0.0) {</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :             break;</a>
+<a name="1041"><span class="lineNum">    1041 </span>            :           }</a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineNoCov">          0 :           curr_min_bias = fmin(curr_min_bias, getValue(i));</span></a>
+<a name="1043"><span class="lineNum">    1043 </span>            :         }</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineNoCov">          0 :         curr_min_bias = fmin(curr_min_bias, getValue(0));</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineNoCov">          0 :         for (index_t i = maxsize_ - 1; i &lt;= sink_idx; i--) {</span></a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineNoCov">          0 :           if (curr_min_bias == 0.0) {</span></a>
+<a name="1047"><span class="lineNum">    1047 </span>            :             break;</a>
+<a name="1048"><span class="lineNum">    1048 </span>            :           }</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineNoCov">          0 :           curr_min_bias = fmin(curr_min_bias, getValue(i));</span></a>
+<a name="1050"><span class="lineNum">    1050 </span>            :         }</a>
+<a name="1051"><span class="lineNum">    1051 </span>            :       }</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :       // If the boundary crossing paths was more biased, it's</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :       // minimal bias replaces the non-boundary-crossing path's</a>
+<a name="1054"><span class="lineNum">    1054 </span>            :       // minimum.</a>
+<a name="1055"><span class="lineNum">    1055 </span><span class="lineCov">         42 :       maximal_minimum = fmax(maximal_minimum, curr_min_bias);</span></a>
+<a name="1056"><span class="lineNum">    1056 </span>            :     }</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :     // The one dimensional path search is complete.</a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineCov">        147 :     return maximal_minimum;</span></a>
+<a name="1059"><span class="lineNum">    1059 </span>            :     // In two or more dimensions, path searching isn't trivial and we really</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     // do need to use a path search algorithm. Dijkstra is the simplest decent</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :     // one. Using it we've never found the path search to be performance</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     // limiting in any solvated biomolecule test system, but faster options are</a>
+<a name="1063"><span class="lineNum">    1063 </span>            :     // easy to imagine if they become necessary. NB-In this case, we're actually</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :     // using a greedy variant of Dijkstra's algorithm where the first possible</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :     // path to a point always controls the path cost to that point. The structure</a>
+<a name="1066"><span class="lineNum">    1066 </span>            :     // of the cost function in this case guarantees that the calculated costs will</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :     // be correct using this variant even though fine details of the paths may not</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     // match a normal Dijkstra search.</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">        126 :   } else if (dimension_ &gt; 1) {</span></a>
+<a name="1070"><span class="lineNum">    1070 </span>            :     // Prepare calculation temporaries for Dijkstra's algorithm.</a>
+<a name="1071"><span class="lineNum">    1071 </span>            :     // Minimal path costs from source to a given grid point</a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">        126 :     std::vector&lt;double&gt; mins_from_source = std::vector&lt;double&gt;(maxsize_, -1.0);</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :     // Heap for tracking available steps, steps are recorded as std::pairs of</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :     // an index and a value.</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :     std::vector&lt; std::pair&lt;index_t, double&gt; &gt; next_steps;</a>
+<a name="1076"><span class="lineNum">    1076 </span>            :     std::pair&lt;index_t, double&gt; curr_indexed_val;</a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">        126 :     std::make_heap(next_steps.begin(), next_steps.end(), indexed_lt);</span></a>
+<a name="1078"><span class="lineNum">    1078 </span>            :     // The search begins at the source index.</a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">        252 :     next_steps.push_back(std::pair&lt;index_t, double&gt;(source_idx, getValue(source_idx)));</span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">        126 :     std::push_heap(next_steps.begin(), next_steps.end(), indexed_lt);</span></a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     // At first no points have been examined and the optimal path has not been found.</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     index_t n_examined = 0;</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :     bool path_not_found = true;</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :     // Until a path is found,</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     while (path_not_found) {</a>
+<a name="1086"><span class="lineNum">    1086 </span>            :       // Examine the grid point currently most accessible from</a>
+<a name="1087"><span class="lineNum">    1087 </span>            :       // the set of all previously explored grid points by popping</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :       // it from the top of the heap.</a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineCov">       9702 :       std::pop_heap(next_steps.begin(), next_steps.end(), indexed_lt);</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :       curr_indexed_val = next_steps.back();</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :       next_steps.pop_back();</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :       n_examined++;</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :       // Check if this point is the sink point, and if so</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :       // finish the loop.</a>
+<a name="1095"><span class="lineNum">    1095 </span><span class="lineCov">       9702 :       if (curr_indexed_val.first == sink_idx) {</span></a>
+<a name="1096"><span class="lineNum">    1096 </span>            :         path_not_found = false;</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :         maximal_minimum = curr_indexed_val.second;</a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">        126 :         break;</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            :         // Check if this point has reached the worst possible</a>
+<a name="1100"><span class="lineNum">    1100 </span>            :         // value, and if so stop looking for paths.</a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">       9576 :       } else if (curr_indexed_val.second == 0.0) {</span></a>
+<a name="1102"><span class="lineNum">    1102 </span>            :         maximal_minimum = 0.0;</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :         break;</a>
+<a name="1104"><span class="lineNum">    1104 </span>            :       }</a>
+<a name="1105"><span class="lineNum">    1105 </span>            :       // If the search is not over, add this grid point's neighbors to the</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :       // possible next points to search for the sink.</a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">       9576 :       std::vector&lt;index_t&gt; neighs = getNearestNeighbors(curr_indexed_val.first);</span></a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">      46246 :       for (unsigned k = 0; k &lt; neighs.size(); k++) {</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineCov">      36670 :         index_t i = neighs[k];</span></a>
+<a name="1110"><span class="lineNum">    1110 </span>            :         // If the neighbor has not already been added to the list of possible next steps,</a>
+<a name="1111"><span class="lineNum">    1111 </span><span class="lineCov">      36670 :         if (mins_from_source[i] == -1.0) {</span></a>
+<a name="1112"><span class="lineNum">    1112 </span>            :           // Set the cost to reach it via a path through the current point being examined.</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">      12284 :           mins_from_source[i] = fmin(curr_indexed_val.second, getValue(i));</span></a>
+<a name="1114"><span class="lineNum">    1114 </span>            :           // Add the neighboring point to the heap of potential next steps.</a>
+<a name="1115"><span class="lineNum">    1115 </span><span class="lineCov">      12284 :           next_steps.push_back(std::pair&lt;index_t, double&gt;(i, mins_from_source[i]));</span></a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">      12284 :           std::push_heap(next_steps.begin(), next_steps.end(), indexed_lt);</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            :         }</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :       }</a>
+<a name="1119"><span class="lineNum">    1119 </span>            :       // Move on to the next best looking step along any of the paths</a>
+<a name="1120"><span class="lineNum">    1120 </span>            :       // growing from the source.</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :     }</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :     // The multidimensional path search is now complete.</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :     return maximal_minimum;</a>
+<a name="1124"><span class="lineNum">    1124 </span>            :   }</a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   return 0.0;</a>
+<a name="1126"><span class="lineNum">    1126 </span>            : }</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : </a>
+<a name="1128"><span class="lineNum">    1128 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Grid.h.func-sort-c.html b/coverage/tools/Grid.h.func-sort-c.html
new file mode 100644
index 0000000000..3419843d67
--- /dev/null
+++ b/coverage/tools/Grid.h.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Grid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Grid.h<span style="font-size: 80%;"> (<a href="Grid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Grid.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#216">_ZN4PLMD8GridBaseD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#312">_ZN4PLMD10SparseGridC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIPNS_5ValueESaISB_EERKS9_IS6_SaIS6_EESJ_RKS9_IjSaIjEEbb</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#349">_ZN4PLMD10SparseGridD0Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#349">_ZN4PLMD10SparseGridD2Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#243">_ZN4PLMD4GridC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIS6_SaIS6_EESD_SD_RKS9_IjSaIjEEbbRKS9_IbSaIbEESD_SD_</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#59">_ZN4PLMD10BiasWeight16projectOuterLoopERd</a></td>
+              <td class="coverFnHi">187</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#234">_ZN4PLMD4GridC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIPNS_5ValueESaISB_EERKS9_IS6_SaIS6_EESJ_RKS9_IjSaIjEEbb</a></td>
+              <td class="coverFnHi">1321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#216">_ZN4PLMD8GridBaseD2Ev</a></td>
+              <td class="coverFnHi">1504</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#49">_ZN4PLMD10BiasWeight16projectInnerLoopERdS1_</a></td>
+              <td class="coverFnHi">13603</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Grid.h.func.html b/coverage/tools/Grid.h.func.html
new file mode 100644
index 0000000000..7b7a2d9e06
--- /dev/null
+++ b/coverage/tools/Grid.h.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Grid.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Grid.h<span style="font-size: 80%;"> (<a href="Grid.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Grid.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#49">_ZN4PLMD10BiasWeight16projectInnerLoopERdS1_</a></td>
+              <td class="coverFnHi">13603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#59">_ZN4PLMD10BiasWeight16projectOuterLoopERd</a></td>
+              <td class="coverFnHi">187</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#312">_ZN4PLMD10SparseGridC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIPNS_5ValueESaISB_EERKS9_IS6_SaIS6_EESJ_RKS9_IjSaIjEEbb</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#349">_ZN4PLMD10SparseGridD0Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#349">_ZN4PLMD10SparseGridD2Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#234">_ZN4PLMD4GridC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIPNS_5ValueESaISB_EERKS9_IS6_SaIS6_EESJ_RKS9_IjSaIjEEbb</a></td>
+              <td class="coverFnHi">1321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#243">_ZN4PLMD4GridC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKSt6vectorIS6_SaIS6_EESD_SD_RKS9_IjSaIjEEbbRKS9_IbSaIbEESD_SD_</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#216">_ZN4PLMD8GridBaseD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Grid.h.gcov.html#216">_ZN4PLMD8GridBaseD2Ev</a></td>
+              <td class="coverFnHi">1504</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Grid.h.gcov.html b/coverage/tools/Grid.h.gcov.html
new file mode 100644
index 0000000000..17948a3e3c
--- /dev/null
+++ b/coverage/tools/Grid.h.gcov.html
@@ -0,0 +1,431 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Grid.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Grid.h<span style="font-size: 80%;"> (source / <a href="Grid.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Grid_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Grid_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;map&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;memory&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstddef&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : // simple function to enable various weighting</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class WeightBase {</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   virtual double projectInnerLoop(double &amp;input, double &amp;v)=0;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   virtual double projectOuterLoop(double &amp;v)=0;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   virtual ~WeightBase() {}</a>
+<a name="42"><span class="lineNum">      42 </span>            : };</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          3 : class BiasWeight:public WeightBase {</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double beta,invbeta;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   double shift=0.0;</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          3 :   explicit BiasWeight(double v) {beta=v; invbeta=1./beta;}</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   //double projectInnerLoop(double &amp;input, double &amp;v) override {return  input+exp(beta*v);}</a>
+<a name="50"><span class="lineNum">      50 </span>            :   //double projectOuterLoop(double &amp;v) override {return -invbeta*std::log(v);}</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      13603 :   double projectInnerLoop(double &amp;input, double &amp;v) override {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      13603 :     auto betav=beta*v;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      13603 :     auto x=betav-shift;</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      13603 :     if(x&gt;0) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1187 :       shift=betav;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       1187 :       return input*std::exp(-x)+1;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :     } else {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      12416 :       return input+std::exp(x);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :     }</a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        187 :   double projectOuterLoop(double &amp;v) override {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        187 :     auto res=-invbeta*(std::log(v)+shift);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        187 :     shift=0.0;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        187 :     return res;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : class ProbWeight:public WeightBase {</a>
+<a name="69"><span class="lineNum">      69 </span>            : public:</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double beta,invbeta;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   explicit ProbWeight(double v) {beta=v; invbeta=1./beta;}</a>
+<a name="72"><span class="lineNum">      72 </span>            :   double projectInnerLoop(double &amp;input, double &amp;v) override {return  input+v;}</a>
+<a name="73"><span class="lineNum">      73 </span>            :   double projectOuterLoop(double &amp;v) override {return -invbeta*std::log(v);}</a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class Value;</a>
+<a name="82"><span class="lineNum">      82 </span>            : class IFile;</a>
+<a name="83"><span class="lineNum">      83 </span>            : class OFile;</a>
+<a name="84"><span class="lineNum">      84 </span>            : class KernelFunctions;</a>
+<a name="85"><span class="lineNum">      85 </span>            : class Communicator;</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : /// \ingroup TOOLBOX</a>
+<a name="88"><span class="lineNum">      88 </span>            : class GridBase</a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            : public:</a>
+<a name="91"><span class="lineNum">      91 </span>            : // we use a size_t here</a>
+<a name="92"><span class="lineNum">      92 </span>            : // should be 8 bytes on all 64-bit machines</a>
+<a name="93"><span class="lineNum">      93 </span>            : // and more portable than &quot;unsigned long long&quot;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   typedef std::size_t index_t;</a>
+<a name="95"><span class="lineNum">      95 </span>            : // to restore old implementation (unsigned) use the following instead:</a>
+<a name="96"><span class="lineNum">      96 </span>            : // typedef unsigned index_t;</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Maximum dimension (exaggerated value).</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Can be used to replace local std::vectors with std::arrays (allocated on stack).</a>
+<a name="99"><span class="lineNum">      99 </span>            :   static constexpr std::size_t maxdim=64;</a>
+<a name="100"><span class="lineNum">     100 </span>            : protected:</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::string funcname;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;std::string&gt; argnames;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;std::string&gt; str_min_, str_max_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;double&gt; min_,max_,dx_;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;unsigned&gt; nbin_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;bool&gt; pbc_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   index_t maxsize_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   unsigned dimension_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   bool dospline_, usederiv_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   std::string fmt_; // format for output</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// get &quot;neighbors&quot; for spline</a>
+<a name="112"><span class="lineNum">     112 </span>            :   void getSplineNeighbors(const std::vector&lt;unsigned&gt; &amp; indices, std::vector&lt;index_t&gt;&amp; neigh, unsigned&amp; nneigh )const;</a>
+<a name="113"><span class="lineNum">     113 </span>            : // std::vector&lt;index_t&gt; getSplineNeighbors(const std::vector&lt;unsigned&gt; &amp; indices)const;</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : public:</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// this constructor here is Value-aware</a>
+<a name="118"><span class="lineNum">     118 </span>            :   GridBase(const std::string&amp; funcl, const std::vector&lt;Value*&gt; &amp; args, const std::vector&lt;std::string&gt; &amp; gmin,</a>
+<a name="119"><span class="lineNum">     119 </span>            :            const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline,</a>
+<a name="120"><span class="lineNum">     120 </span>            :            bool usederiv);</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// this constructor here is not Value-aware</a>
+<a name="122"><span class="lineNum">     122 </span>            :   GridBase(const std::string&amp; funcl, const std::vector&lt;std::string&gt; &amp;names, const std::vector&lt;std::string&gt; &amp; gmin,</a>
+<a name="123"><span class="lineNum">     123 </span>            :            const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline,</a>
+<a name="124"><span class="lineNum">     124 </span>            :            bool usederiv, const std::vector&lt;bool&gt; &amp;isperiodic, const std::vector&lt;std::string&gt; &amp;pmin,</a>
+<a name="125"><span class="lineNum">     125 </span>            :            const std::vector&lt;std::string&gt; &amp;pmax );</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// this is the real initializator</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void Init(const std::string &amp; funcl, const std::vector&lt;std::string&gt; &amp;names, const std::vector&lt;std::string&gt; &amp; gmin,</a>
+<a name="128"><span class="lineNum">     128 </span>            :             const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline, bool usederiv,</a>
+<a name="129"><span class="lineNum">     129 </span>            :             const std::vector&lt;bool&gt; &amp;isperiodic, const std::vector&lt;std::string&gt; &amp;pmin, const std::vector&lt;std::string&gt; &amp;pmax);</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// get lower boundary</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::vector&lt;std::string&gt; getMin() const;</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// get upper boundary</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::vector&lt;std::string&gt; getMax() const;</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// get bin size</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::vector&lt;double&gt; getDx() const;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   double getDx(index_t j) const ;</a>
+<a name="137"><span class="lineNum">     137 </span>            : /// get bin volume</a>
+<a name="138"><span class="lineNum">     138 </span>            :   double getBinVolume() const;</a>
+<a name="139"><span class="lineNum">     139 </span>            : /// get number of bins</a>
+<a name="140"><span class="lineNum">     140 </span>            :   std::vector&lt;unsigned&gt; getNbin() const;</a>
+<a name="141"><span class="lineNum">     141 </span>            : /// get if periodic</a>
+<a name="142"><span class="lineNum">     142 </span>            :   std::vector&lt;bool&gt; getIsPeriodic() const;</a>
+<a name="143"><span class="lineNum">     143 </span>            : /// get grid dimension</a>
+<a name="144"><span class="lineNum">     144 </span>            :   unsigned getDimension() const;</a>
+<a name="145"><span class="lineNum">     145 </span>            : /// get argument names  of this grid</a>
+<a name="146"><span class="lineNum">     146 </span>            :   std::vector&lt;std::string&gt; getArgNames() const;</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// get if the grid has derivatives</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">    1986398 :   bool hasDerivatives() const {return usederiv_;}</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : /// methods to handle grid indices</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void getIndices(index_t index, std::vector&lt;unsigned&gt;&amp; rindex) const;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void getIndices(const std::vector&lt;double&gt; &amp; x, std::vector&lt;unsigned&gt;&amp; rindex) const;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   std::vector&lt;unsigned&gt; getIndices(index_t index) const;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::vector&lt;unsigned&gt; getIndices(const std::vector&lt;double&gt; &amp; x) const;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   index_t getIndex(const std::vector&lt;unsigned&gt; &amp; indices) const;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   index_t getIndex(const std::vector&lt;double&gt; &amp; x) const;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;double&gt; getPoint(index_t index) const;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   std::vector&lt;double&gt; getPoint(const std::vector&lt;unsigned&gt; &amp; indices) const;</a>
+<a name="159"><span class="lineNum">     159 </span>            :   std::vector&lt;double&gt; getPoint(const std::vector&lt;double&gt; &amp; x) const;</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// faster versions relying on preallocated vectors</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void getPoint(index_t index,std::vector&lt;double&gt; &amp; point) const;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void getPoint(const std::vector&lt;unsigned&gt; &amp; indices,std::vector&lt;double&gt; &amp; point) const;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   void getPoint(const std::vector&lt;double&gt; &amp; x,std::vector&lt;double&gt; &amp; point) const;</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : /// get neighbors</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::vector&lt;index_t&gt; getNeighbors(index_t index,const std::vector&lt;unsigned&gt; &amp; neigh) const;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::vector&lt;index_t&gt; getNeighbors(const std::vector&lt;unsigned&gt; &amp; indices,const std::vector&lt;unsigned&gt; &amp; neigh) const;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   std::vector&lt;index_t&gt; getNeighbors(const std::vector&lt;double&gt; &amp; x,const std::vector&lt;unsigned&gt; &amp; neigh) const;</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// get nearest neighbors (those separated by exactly one lattice unit)</a>
+<a name="170"><span class="lineNum">     170 </span>            :   std::vector&lt;index_t&gt; getNearestNeighbors(const index_t index) const;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::vector&lt;index_t&gt; getNearestNeighbors(const std::vector&lt;unsigned&gt; &amp;indices) const;</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : /// write header for grid file</a>
+<a name="174"><span class="lineNum">     174 </span>            :   void writeHeader(OFile&amp; file);</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : /// read grid from file</a>
+<a name="177"><span class="lineNum">     177 </span>            :   static std::unique_ptr&lt;GridBase&gt; create(const std::string&amp;,const std::vector&lt;Value*&gt;&amp;,IFile&amp;,bool,bool,bool);</a>
+<a name="178"><span class="lineNum">     178 </span>            : /// read grid from file and check boundaries are what is expected from input</a>
+<a name="179"><span class="lineNum">     179 </span>            :   static std::unique_ptr&lt;GridBase&gt; create(const std::string&amp;,const std::vector&lt;Value*&gt;&amp;, IFile&amp;,</a>
+<a name="180"><span class="lineNum">     180 </span>            :                                           const std::vector&lt;std::string&gt;&amp;,const std::vector&lt;std::string&gt;&amp;,</a>
+<a name="181"><span class="lineNum">     181 </span>            :                                           const std::vector&lt;unsigned&gt;&amp;,bool,bool,bool);</a>
+<a name="182"><span class="lineNum">     182 </span>            : /// get grid size</a>
+<a name="183"><span class="lineNum">     183 </span>            :   virtual index_t getSize() const=0;</a>
+<a name="184"><span class="lineNum">     184 </span>            : /// get grid value</a>
+<a name="185"><span class="lineNum">     185 </span>            :   virtual double getValue(index_t index) const=0;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   double getValue(const std::vector&lt;unsigned&gt; &amp; indices) const;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   double getValue(const std::vector&lt;double&gt; &amp; x) const;</a>
+<a name="188"><span class="lineNum">     188 </span>            : /// get grid value and derivatives</a>
+<a name="189"><span class="lineNum">     189 </span>            :   virtual double getValueAndDerivatives(index_t index, std::vector&lt;double&gt;&amp; der) const=0;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   double getValueAndDerivatives(const std::vector&lt;unsigned&gt; &amp; indices, std::vector&lt;double&gt;&amp; der) const;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   double getValueAndDerivatives(const std::vector&lt;double&gt; &amp; x, std::vector&lt;double&gt;&amp; der) const;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : /// set grid value</a>
+<a name="194"><span class="lineNum">     194 </span>            :   virtual void setValue(index_t index, double value)=0;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   void setValue(const std::vector&lt;unsigned&gt; &amp; indices, double value);</a>
+<a name="196"><span class="lineNum">     196 </span>            : /// set grid value and derivatives</a>
+<a name="197"><span class="lineNum">     197 </span>            :   virtual void setValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der)=0;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   void setValueAndDerivatives(const std::vector&lt;unsigned&gt; &amp; indices, double value, std::vector&lt;double&gt;&amp; der);</a>
+<a name="199"><span class="lineNum">     199 </span>            : /// add to grid value</a>
+<a name="200"><span class="lineNum">     200 </span>            :   virtual void addValue(index_t index, double value)=0;</a>
+<a name="201"><span class="lineNum">     201 </span>            :   void addValue(const std::vector&lt;unsigned&gt; &amp; indices, double value);</a>
+<a name="202"><span class="lineNum">     202 </span>            : /// add to grid value and derivatives</a>
+<a name="203"><span class="lineNum">     203 </span>            :   virtual void addValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der)=0;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   void addValueAndDerivatives(const std::vector&lt;unsigned&gt; &amp; indices, double value, std::vector&lt;double&gt;&amp; der);</a>
+<a name="205"><span class="lineNum">     205 </span>            : /// add a kernel function to the grid</a>
+<a name="206"><span class="lineNum">     206 </span>            :   void addKernel( const KernelFunctions&amp; kernel );</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            : /// get minimum value</a>
+<a name="209"><span class="lineNum">     209 </span>            :   virtual double getMinValue() const = 0;</a>
+<a name="210"><span class="lineNum">     210 </span>            : /// get maximum value</a>
+<a name="211"><span class="lineNum">     211 </span>            :   virtual double getMaxValue() const = 0;</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : /// dump grid on file</a>
+<a name="214"><span class="lineNum">     214 </span>            :   virtual void writeToFile(OFile&amp;)=0;</a>
+<a name="215"><span class="lineNum">     215 </span>            : /// dump grid to gaussian cube file</a>
+<a name="216"><span class="lineNum">     216 </span>            :   void writeCubeFile(OFile&amp;, const double&amp; lunit);</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       3008 :   virtual ~GridBase() {}</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : /// set output format</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        197 :   void setOutputFmt(const std::string &amp; ss) {fmt_=ss;}</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : /// reset output format to the default %14.9f format</a>
+<a name="223"><span class="lineNum">     223 </span>            :   void resetToDefaultOutputFmt() {fmt_=&quot;%14.9f&quot;;}</a>
+<a name="224"><span class="lineNum">     224 </span>            : ///</a>
+<a name="225"><span class="lineNum">     225 </span>            : /// Find the maximum over paths of the minimum value of the gridded function along the paths</a>
+<a name="226"><span class="lineNum">     226 </span>            : /// for all paths of neighboring grid lattice points from a source point to a sink point.</a>
+<a name="227"><span class="lineNum">     227 </span>            :   double findMaximalPathMinimum(const std::vector&lt;double&gt; &amp;source, const std::vector&lt;double&gt; &amp;sink);</a>
+<a name="228"><span class="lineNum">     228 </span>            : };</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : class Grid : public GridBase</a>
+<a name="231"><span class="lineNum">     231 </span>            : {</a>
+<a name="232"><span class="lineNum">     232 </span>            :   std::vector&lt;double&gt; grid_;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   std::vector&lt;double&gt; der_;</a>
+<a name="234"><span class="lineNum">     234 </span>            :   double contour_location=0.0;</a>
+<a name="235"><span class="lineNum">     235 </span>            : public:</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       1321 :   Grid(const std::string&amp; funcl, const std::vector&lt;Value*&gt; &amp; args, const std::vector&lt;std::string&gt; &amp; gmin,</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :        const std::vector&lt;std::string&gt; &amp; gmax,</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       1321 :        const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline, bool usederiv):</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       1321 :     GridBase(funcl,args,gmin,gmax,nbin,dospline,usederiv)</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   {</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       1321 :     grid_.assign(maxsize_,0.0);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">       1321 :     if(usederiv_) der_.assign(maxsize_*dimension_,0.0);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       1321 :   }</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : /// this constructor here is not Value-aware</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        128 :   Grid(const std::string&amp; funcl, const std::vector&lt;std::string&gt; &amp;names, const std::vector&lt;std::string&gt; &amp; gmin,</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :        const std::vector&lt;std::string&gt; &amp; gmax, const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline,</a>
+<a name="247"><span class="lineNum">     247 </span>            :        bool usederiv, const std::vector&lt;bool&gt; &amp;isperiodic, const std::vector&lt;std::string&gt; &amp;pmin,</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        128 :        const std::vector&lt;std::string&gt; &amp;pmax ):</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        128 :     GridBase(funcl,names,gmin,gmax,nbin,dospline,usederiv,isperiodic,pmin,pmax)</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   {</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        128 :     grid_.assign(maxsize_,0.0);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        128 :     if(usederiv_) der_.assign(maxsize_*dimension_,0.0);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        128 :   }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   index_t getSize() const override;</a>
+<a name="255"><span class="lineNum">     255 </span>            : /// this is to access to Grid:: version of these methods (allowing overloading of virtual methods)</a>
+<a name="256"><span class="lineNum">     256 </span>            :   using GridBase::getValue;</a>
+<a name="257"><span class="lineNum">     257 </span>            :   using GridBase::getValueAndDerivatives;</a>
+<a name="258"><span class="lineNum">     258 </span>            :   using GridBase::setValue;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   using GridBase::setValueAndDerivatives;</a>
+<a name="260"><span class="lineNum">     260 </span>            :   using GridBase::addValue;</a>
+<a name="261"><span class="lineNum">     261 </span>            :   using GridBase::addValueAndDerivatives;</a>
+<a name="262"><span class="lineNum">     262 </span>            : /// get grid value</a>
+<a name="263"><span class="lineNum">     263 </span>            :   double getValue(index_t index) const override;</a>
+<a name="264"><span class="lineNum">     264 </span>            : /// get grid value and derivatives</a>
+<a name="265"><span class="lineNum">     265 </span>            :   double getValueAndDerivatives(index_t index, std::vector&lt;double&gt;&amp; der) const override;</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : /// set grid value</a>
+<a name="268"><span class="lineNum">     268 </span>            :   void setValue(index_t index, double value) override;</a>
+<a name="269"><span class="lineNum">     269 </span>            : /// set grid value and derivatives</a>
+<a name="270"><span class="lineNum">     270 </span>            :   void setValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) override;</a>
+<a name="271"><span class="lineNum">     271 </span>            : /// add to grid value</a>
+<a name="272"><span class="lineNum">     272 </span>            :   void addValue(index_t index, double value) override;</a>
+<a name="273"><span class="lineNum">     273 </span>            : /// add to grid value and derivatives</a>
+<a name="274"><span class="lineNum">     274 </span>            :   void addValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) override;</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : /// get minimum value</a>
+<a name="277"><span class="lineNum">     277 </span>            :   double getMinValue() const override;</a>
+<a name="278"><span class="lineNum">     278 </span>            : /// get maximum value</a>
+<a name="279"><span class="lineNum">     279 </span>            :   double getMaxValue() const override;</a>
+<a name="280"><span class="lineNum">     280 </span>            : /// Scale all grid values and derivatives by a constant factor</a>
+<a name="281"><span class="lineNum">     281 </span>            :   void scaleAllValuesAndDerivatives( const double&amp; scalef );</a>
+<a name="282"><span class="lineNum">     282 </span>            : /// Takes the scalef times the logarithm of all grid values and derivatives</a>
+<a name="283"><span class="lineNum">     283 </span>            :   void logAllValuesAndDerivatives( const double&amp; scalef );</a>
+<a name="284"><span class="lineNum">     284 </span>            : /// dump grid on file</a>
+<a name="285"><span class="lineNum">     285 </span>            :   void writeToFile(OFile&amp;) override;</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : /// Set the minimum value of the grid to zero and translates accordingly</a>
+<a name="288"><span class="lineNum">     288 </span>            :   void setMinToZero();</a>
+<a name="289"><span class="lineNum">     289 </span>            : /// apply function: takes  pointer to  function that accepts a double and apply</a>
+<a name="290"><span class="lineNum">     290 </span>            :   void applyFunctionAllValuesAndDerivatives( double (*func)(double val), double (*funcder)(double valder) );</a>
+<a name="291"><span class="lineNum">     291 </span>            : /// Get the difference from the contour</a>
+<a name="292"><span class="lineNum">     292 </span>            :   double getDifferenceFromContour(const std::vector&lt;double&gt; &amp; x, std::vector&lt;double&gt;&amp; der) const ;</a>
+<a name="293"><span class="lineNum">     293 </span>            : /// Find a set of points on a contour in the function</a>
+<a name="294"><span class="lineNum">     294 </span>            :   void findSetOfPointsOnContour(const double&amp; target, const std::vector&lt;bool&gt;&amp; nosearch, unsigned&amp; npoints, std::vector&lt;std::vector&lt;double&gt; &gt;&amp; points );</a>
+<a name="295"><span class="lineNum">     295 </span>            : /// Since this method returns a concrete Grid, it should be here and not in GridBase - GB</a>
+<a name="296"><span class="lineNum">     296 </span>            : /// project a high dimensional grid onto a low dimensional one: this should be changed at some time</a>
+<a name="297"><span class="lineNum">     297 </span>            : /// to enable many types of weighting</a>
+<a name="298"><span class="lineNum">     298 </span>            :   Grid project( const std::vector&lt;std::string&gt; &amp; proj, WeightBase *ptr2obj  );</a>
+<a name="299"><span class="lineNum">     299 </span>            :   void projectOnLowDimension(double &amp;val, std::vector&lt;int&gt; &amp;varHigh, WeightBase* ptr2obj );</a>
+<a name="300"><span class="lineNum">     300 </span>            :   void mpiSumValuesAndDerivatives( Communicator&amp; comm );</a>
+<a name="301"><span class="lineNum">     301 </span>            : /// Integrate the function calculated on the grid</a>
+<a name="302"><span class="lineNum">     302 </span>            :   double integrate( std::vector&lt;unsigned&gt;&amp; npoints );</a>
+<a name="303"><span class="lineNum">     303 </span>            :   void clear();</a>
+<a name="304"><span class="lineNum">     304 </span>            : };</a>
+<a name="305"><span class="lineNum">     305 </span>            : </a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : class SparseGrid : public GridBase</a>
+<a name="308"><span class="lineNum">     308 </span>            : {</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            :   std::map&lt;index_t,double&gt; map_;</a>
+<a name="311"><span class="lineNum">     311 </span>            :   std::map&lt; index_t,std::vector&lt;double&gt; &gt; der_;</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : public:</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          6 :   SparseGrid(const std::string&amp; funcl, const std::vector&lt;Value*&gt; &amp; args, const std::vector&lt;std::string&gt; &amp; gmin,</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :              const std::vector&lt;std::string&gt; &amp; gmax,</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          6 :              const std::vector&lt;unsigned&gt; &amp; nbin, bool dospline, bool usederiv):</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          6 :     GridBase(funcl,args,gmin,gmax,nbin,dospline,usederiv) {}</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :   index_t getSize() const override;</a>
+<a name="320"><span class="lineNum">     320 </span>            :   index_t getMaxSize() const;</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : /// this is to access to Grid:: version of these methods (allowing overloading of virtual methods)</a>
+<a name="323"><span class="lineNum">     323 </span>            :   using GridBase::getValue;</a>
+<a name="324"><span class="lineNum">     324 </span>            :   using GridBase::getValueAndDerivatives;</a>
+<a name="325"><span class="lineNum">     325 </span>            :   using GridBase::setValue;</a>
+<a name="326"><span class="lineNum">     326 </span>            :   using GridBase::setValueAndDerivatives;</a>
+<a name="327"><span class="lineNum">     327 </span>            :   using GridBase::addValue;</a>
+<a name="328"><span class="lineNum">     328 </span>            :   using GridBase::addValueAndDerivatives;</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            : /// get grid value</a>
+<a name="331"><span class="lineNum">     331 </span>            :   double getValue(index_t index) const override;</a>
+<a name="332"><span class="lineNum">     332 </span>            : /// get grid value and derivatives</a>
+<a name="333"><span class="lineNum">     333 </span>            :   double getValueAndDerivatives(index_t index, std::vector&lt;double&gt;&amp; der) const override;</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            : /// set grid value</a>
+<a name="336"><span class="lineNum">     336 </span>            :   void setValue(index_t index, double value) override;</a>
+<a name="337"><span class="lineNum">     337 </span>            : /// set grid value and derivatives</a>
+<a name="338"><span class="lineNum">     338 </span>            :   void setValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) override;</a>
+<a name="339"><span class="lineNum">     339 </span>            : /// add to grid value</a>
+<a name="340"><span class="lineNum">     340 </span>            :   void addValue(index_t index, double value) override;</a>
+<a name="341"><span class="lineNum">     341 </span>            : /// add to grid value and derivatives</a>
+<a name="342"><span class="lineNum">     342 </span>            :   void addValueAndDerivatives(index_t index, double value, std::vector&lt;double&gt;&amp; der) override;</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            : /// get minimum value</a>
+<a name="345"><span class="lineNum">     345 </span>            :   double getMinValue() const override;</a>
+<a name="346"><span class="lineNum">     346 </span>            : /// get maximum value</a>
+<a name="347"><span class="lineNum">     347 </span>            :   double getMaxValue() const override;</a>
+<a name="348"><span class="lineNum">     348 </span>            : /// dump grid on file</a>
+<a name="349"><span class="lineNum">     349 </span>            :   void writeToFile(OFile&amp;) override;</a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         18 :   virtual ~SparseGrid() {}</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : };</a>
+<a name="353"><span class="lineNum">     353 </span>            : }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/HistogramBead.cpp.func-sort-c.html b/coverage/tools/HistogramBead.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3b0e217c6a
--- /dev/null
+++ b/coverage/tools/HistogramBead.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/HistogramBead.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - HistogramBead.cpp<span style="font-size: 80%;"> (<a href="HistogramBead.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">118</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HistogramBead.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#112">_ZN4PLMD13HistogramBead12generateBinsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIS6_SaIS6_EE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#138">_ZN4PLMD13HistogramBead3setERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#106">_ZNK4PLMD13HistogramBead11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#85">_ZN4PLMD13HistogramBead16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">76</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#232">_ZNK4PLMD13HistogramBead16lboundDerivativeERKd</a></td>
+              <td class="coverFnHi">4860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#247">_ZNK4PLMD13HistogramBead16uboundDerivativeERKd</a></td>
+              <td class="coverFnHi">4860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#169">_ZN4PLMD13HistogramBead13setKernelTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">79236</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#91">_ZN4PLMD13HistogramBeadC2Ev</a></td>
+              <td class="coverFnHi">79304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#203">_ZNK4PLMD13HistogramBead19calculateWithCutoffEdRd</a></td>
+              <td class="coverFnHi">132418</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#175">_ZNK4PLMD13HistogramBead9calculateEdRd</a></td>
+              <td class="coverFnHi">160612</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#161">_ZN4PLMD13HistogramBead3setEddd</a></td>
+              <td class="coverFnHi">573574</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/HistogramBead.cpp.func.html b/coverage/tools/HistogramBead.cpp.func.html
new file mode 100644
index 0000000000..c18d2d9d3c
--- /dev/null
+++ b/coverage/tools/HistogramBead.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/HistogramBead.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - HistogramBead.cpp<span style="font-size: 80%;"> (<a href="HistogramBead.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">118</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HistogramBead.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#112">_ZN4PLMD13HistogramBead12generateBinsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIS6_SaIS6_EE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#169">_ZN4PLMD13HistogramBead13setKernelTypeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">79236</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#85">_ZN4PLMD13HistogramBead16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">76</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#138">_ZN4PLMD13HistogramBead3setERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#161">_ZN4PLMD13HistogramBead3setEddd</a></td>
+              <td class="coverFnHi">573574</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#91">_ZN4PLMD13HistogramBeadC2Ev</a></td>
+              <td class="coverFnHi">79304</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#106">_ZNK4PLMD13HistogramBead11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#232">_ZNK4PLMD13HistogramBead16lboundDerivativeERKd</a></td>
+              <td class="coverFnHi">4860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#247">_ZNK4PLMD13HistogramBead16uboundDerivativeERKd</a></td>
+              <td class="coverFnHi">4860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#203">_ZNK4PLMD13HistogramBead19calculateWithCutoffEdRd</a></td>
+              <td class="coverFnHi">132418</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.cpp.gcov.html#175">_ZNK4PLMD13HistogramBead9calculateEdRd</a></td>
+              <td class="coverFnHi">160612</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/HistogramBead.cpp.gcov.html b/coverage/tools/HistogramBead.cpp.gcov.html
new file mode 100644
index 0000000000..2f5ea32579
--- /dev/null
+++ b/coverage/tools/HistogramBead.cpp.gcov.html
@@ -0,0 +1,341 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/HistogramBead.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - HistogramBead.cpp<span style="font-size: 80%;"> (source / <a href="HistogramBead.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">93</td>
+            <td class="headerCovTableEntry">118</td>
+            <td class="headerCovTableEntryMed">78.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;HistogramBead.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;vector&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;limits&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Keywords.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC INTERNAL histogrambead</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : A function that can be used to calculate whether quantities are between fixed upper and lower bounds.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : If we have multiple instances of a variable we can estimate the probability density function</a>
+<a name="35"><span class="lineNum">      35 </span>            : for that variable using a process called kernel density estimation:</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : P(s) = \sum_i K\left( \frac{s - s_i}{w} \right)</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : In this equation \f$K\f$ is a symmetric function that must integrate to one that is often</a>
+<a name="42"><span class="lineNum">      42 </span>            : called a kernel function and \f$w\f$ is a smearing parameter.  From a probability density function calculated using</a>
+<a name="43"><span class="lineNum">      43 </span>            : kernel density estimation we can calculate the number/fraction of values between an upper and lower</a>
+<a name="44"><span class="lineNum">      44 </span>            : bound using:</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \f[</a>
+<a name="47"><span class="lineNum">      47 </span>            : w(s) = \int_a^b \sum_i K\left( \frac{s - s_i}{w} \right)</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : All the input to calculate a quantity like \f$w(s)\f$ is generally provided through a single</a>
+<a name="51"><span class="lineNum">      51 </span>            : keyword that will have the following form:</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : KEYWORD={TYPE UPPER=\f$a\f$ LOWER=\f$b\f$ SMEAR=\f$\frac{w}{b-a}\f$}</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : This will calculate the number of values between \f$a\f$ and \f$b\f$.  To calculate</a>
+<a name="56"><span class="lineNum">      56 </span>            : the fraction of values you add the word NORM to the input specification.  If the</a>
+<a name="57"><span class="lineNum">      57 </span>            : function keyword SMEAR is not present \f$w\f$ is set equal to \f$0.5(b-a)\f$. Finally,</a>
+<a name="58"><span class="lineNum">      58 </span>            : type should specify one of the kernel types that is present in plumed. These are listed</a>
+<a name="59"><span class="lineNum">      59 </span>            : in the table below:</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : &lt;table align=center frame=void width=95%% cellpadding=5%%&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : &lt;tr&gt;</a>
+<a name="63"><span class="lineNum">      63 </span>            : &lt;td&gt; TYPE &lt;/td&gt; &lt;td&gt; FUNCTION &lt;/td&gt;</a>
+<a name="64"><span class="lineNum">      64 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="65"><span class="lineNum">      65 </span>            : &lt;td&gt; GAUSSIAN &lt;/td&gt; &lt;td&gt; \f$\frac{1}{\sqrt{2\pi}w} \exp\left( -\frac{(s-s_i)^2}{2w^2} \right)\f$ &lt;/td&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            : &lt;td&gt; TRIANGULAR &lt;/td&gt; &lt;td&gt; \f$ \frac{1}{2w} \left( 1. - \left| \frac{s-s_i}{w} \right| \right) \quad \frac{s-s_i}{w}&lt;1 \f$ &lt;/td&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : &lt;/tr&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            : &lt;/table&gt;</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : Some keywords can also be used to calculate a discrete version of the histogram.  That</a>
+<a name="72"><span class="lineNum">      72 </span>            : is to say the number of values between \f$a\f$ and \f$b\f$, the number of values between</a>
+<a name="73"><span class="lineNum">      73 </span>            : \f$b\f$ and \f$c\f$ and so on.  A keyword that specifies this sort of calculation would look</a>
+<a name="74"><span class="lineNum">      74 </span>            : something like</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : KEYWORD={TYPE UPPER=\f$a\f$ LOWER=\f$b\f$ NBINS=\f$n\f$ SMEAR=\f$\frac{w}{n(b-a)}\f$}</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : This specification would calculate the following vector of quantities:</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \f[</a>
+<a name="81"><span class="lineNum">      81 </span>            : w_j(s) = \int_{a + \frac{j-1}{n}(b-a)}^{a + \frac{j}{n}(b-a)} \sum_i K\left( \frac{s - s_i}{w} \right)</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f]</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : */</a>
+<a name="85"><span class="lineNum">      85 </span>            : //+ENDPLUMEDOC</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         76 : void HistogramBead::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        152 :   keys.add(&quot;compulsory&quot;,&quot;LOWER&quot;,&quot;the lower boundary for this particular bin&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        152 :   keys.add(&quot;compulsory&quot;,&quot;UPPER&quot;,&quot;the upper boundary for this particular bin&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        152 :   keys.add(&quot;compulsory&quot;,&quot;SMEAR&quot;,&quot;0.5&quot;,&quot;the amount to smear the Gaussian for each value in the distribution&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         76 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      79304 : HistogramBead::HistogramBead():</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      79304 :   init(false),</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      79304 :   lowb(0.0),</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      79304 :   highb(0.0),</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      79304 :   width(0.0),</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      79304 :   cutoff(std::numeric_limits&lt;double&gt;::max()),</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      79304 :   type(gaussian),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      79304 :   periodicity(unset),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      79304 :   min(0.0),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">      79304 :   max(0.0),</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      79304 :   max_minus_min(0.0),</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      79304 :   inv_max_minus_min(0.0)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      79304 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         68 : std::string HistogramBead::description() const {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         68 :   std::ostringstream ostr;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         68 :   ostr&lt;&lt;&quot;between &quot;&lt;&lt;lowb&lt;&lt;&quot; and &quot;&lt;&lt;highb&lt;&lt;&quot; width of gaussian window equals &quot;&lt;&lt;width;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         68 :   return ostr.str();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         68 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         11 : void HistogramBead::generateBins( const std::string&amp; params, std::vector&lt;std::string&gt;&amp; bins ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         11 :   std::vector&lt;std::string&gt; data=Tools::getWords(params);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         11 :   plumed_massert(data.size()&gt;=1,&quot;There is no input for this keyword&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         11 :   std::string name=data[0];</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         11 :   unsigned nbins; std::vector&lt;double&gt; range(2); std::string smear;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         11 :   bool found_nb=Tools::parse(data,&quot;NBINS&quot;,nbins);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         11 :   plumed_massert(found_nb,&quot;Number of bins in histogram not found&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         11 :   bool found_r=Tools::parse(data,&quot;LOWER&quot;,range[0]);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         11 :   plumed_massert(found_r,&quot;Lower bound for histogram not specified&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         11 :   found_r=Tools::parse(data,&quot;UPPER&quot;,range[1]);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         11 :   plumed_massert(found_r,&quot;Upper bound for histogram not specified&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         11 :   plumed_massert(range[0]&lt;range[1],&quot;Range specification is dubious&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         11 :   bool found_b=Tools::parse(data,&quot;SMEAR&quot;,smear);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         11 :   if(!found_b) { Tools::convert(0.5,smear); }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         11 :   std::string lb,ub; double delr = ( range[1]-range[0] ) / static_cast&lt;double&gt;( nbins );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         43 :   for(unsigned i=0; i&lt;nbins; ++i) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         32 :     Tools::convert( range[0]+i*delr, lb );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         32 :     Tools::convert( range[0]+(i+1)*delr, ub );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         64 :     bins.push_back( name + &quot; &quot; +  &quot;LOWER=&quot; + lb + &quot; &quot; + &quot;UPPER=&quot; + ub + &quot; &quot; + &quot;SMEAR=&quot; + smear );</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         11 :   plumed_assert(bins.size()==nbins);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         11 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         68 : void HistogramBead::set( const std::string&amp; params, std::string&amp; errormsg ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         68 :   std::vector&lt;std::string&gt; data=Tools::getWords(params);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         68 :   if(data.size()&lt;1) {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     errormsg=&quot;No input has been specified&quot;;</a>
+<a name="144"><span class="lineNum">     144 </span>            :     return;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         68 :   std::string name=data[0]; const double DP2CUTOFF=6.25;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         68 :   if(name==&quot;GAUSSIAN&quot;) { type=gaussian; cutoff=std::sqrt(2.0*DP2CUTOFF); }</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   else if(name==&quot;TRIANGULAR&quot;) { type=triangular; cutoff=1.; }</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   else plumed_merror(&quot;cannot understand kernel type &quot; + name );</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   double smear;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         68 :   bool found_r=Tools::parse(data,&quot;LOWER&quot;,lowb);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         68 :   if( !found_r ) errormsg=&quot;Lower bound has not been specified use LOWER&quot;;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         68 :   found_r=Tools::parse(data,&quot;UPPER&quot;,highb);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         68 :   if( !found_r ) errormsg=&quot;Upper bound has not been specified use UPPER&quot;;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         68 :   if( lowb&gt;=highb ) errormsg=&quot;Lower bound is higher than upper bound&quot;;</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         68 :   smear=0.5; Tools::parse(data,&quot;SMEAR&quot;,smear);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         68 :   width=smear*(highb-lowb); init=true;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         68 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     573574 : void HistogramBead::set( double l, double h, double w) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     573574 :   init=true; lowb=l; highb=h; width=w;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   const double DP2CUTOFF=6.25;</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     573574 :   if( type==gaussian ) cutoff=std::sqrt(2.0*DP2CUTOFF);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">     425920 :   else if( type==triangular ) cutoff=1.;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :   else plumed_error();</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     573574 : }</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      79236 : void HistogramBead::setKernelType( const std::string&amp; ktype ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      79236 :   if(ktype==&quot;gaussian&quot;) type=gaussian;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       9622 :   else if(ktype==&quot;triangular&quot;) type=triangular;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :   else plumed_merror(&quot;cannot understand kernel type &quot; + ktype );</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      79236 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     160612 : double HistogramBead::calculate( double x, double&amp; df ) const {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   plumed_dbg_assert(init &amp;&amp; periodicity!=unset );</a>
+<a name="179"><span class="lineNum">     179 </span>            :   double lowB, upperB, f;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     160612 :   if( type==gaussian ) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     160612 :     lowB = difference( x, lowb ) / ( std::sqrt(2.0) * width );</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">     160612 :     upperB = difference( x, highb ) / ( std::sqrt(2.0) * width );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">     160612 :     df = ( exp( -lowB*lowB ) - exp( -upperB*upperB ) ) / ( std::sqrt(2*pi)*width );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     160612 :     f = 0.5*( erf( upperB ) - erf( lowB ) );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   } else if( type==triangular ) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :     lowB = ( difference( x, lowb ) / width );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     upperB = ( difference( x, highb ) / width );</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :     df=0;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     if( std::fabs(lowB)&lt;1. ) df = (1 - std::fabs(lowB)) / width;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :     if( std::fabs(upperB)&lt;1. ) df -= (1 - std::fabs(upperB)) / width;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     if (upperB&lt;=-1. || lowB &gt;=1.) {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :       f=0.;</a>
+<a name="193"><span class="lineNum">     193 </span>            :     } else {</a>
+<a name="194"><span class="lineNum">     194 </span>            :       double ia, ib;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :       if( lowB&gt;-1.0 ) { ia=lowB; } else { ia=-1.0; }</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       if( upperB&lt;1.0 ) { ib=upperB; } else { ib=1.0; }</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :       f = (ib*(2.-std::fabs(ib))-ia*(2.-std::fabs(ia)))*0.5;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     }</a>
+<a name="199"><span class="lineNum">     199 </span>            :   } else {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;function type does not exist&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     160612 :   return f;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     132418 : double HistogramBead::calculateWithCutoff( double x, double&amp; df ) const {</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   plumed_dbg_assert(init &amp;&amp; periodicity!=unset );</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   double lowB, upperB, f;</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     132418 :   lowB = difference( x, lowb ) / width ; upperB = difference( x, highb ) / width;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     132418 :   if( upperB&lt;=-cutoff || lowB&gt;=cutoff ) { df=0; return 0; }</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     132418 :   if( type==gaussian ) {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :     lowB /= std::sqrt(2.0); upperB /= std::sqrt(2.0);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     df = ( exp( -lowB*lowB ) - exp( -upperB*upperB ) ) / ( std::sqrt(2*pi)*width );</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     f = 0.5*( erf( upperB ) - erf( lowB ) );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     132418 :   } else if( type==triangular ) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     132418 :     df=0;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     132418 :     if( std::fabs(lowB)&lt;1. ) df = (1 - std::fabs(lowB)) / width;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">     132418 :     if( std::fabs(upperB)&lt;1. ) df -= (1 - std::fabs(upperB)) / width;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">     132418 :     if (upperB&lt;=-1. || lowB &gt;=1.) {</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :       f=0.;</a>
+<a name="222"><span class="lineNum">     222 </span>            :     } else {</a>
+<a name="223"><span class="lineNum">     223 </span>            :       double ia, ib;</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     132418 :       if( lowB&gt;-1.0 ) { ia=lowB; } else { ia=-1.0; }</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     132418 :       if( upperB&lt;1.0 ) { ib=upperB; } else { ib=1.0; }</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">     132418 :       f = (ib*(2.-std::fabs(ib))-ia*(2.-std::fabs(ia)))*0.5;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span>            :   } else {</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;function type does not exist&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   }</a>
+<a name="231"><span class="lineNum">     231 </span>            :   return f;</a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       4860 : double HistogramBead::lboundDerivative( const double&amp; x ) const {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       4860 :   if( type==gaussian ) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       4860 :     double lowB = difference( x, lowb ) / ( std::sqrt(2.0) * width );</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       4860 :     return exp( -lowB*lowB ) / ( std::sqrt(2*pi)*width );</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :   } else if ( type==triangular ) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : //      lowB = fabs( difference( x, lowb ) / width );</a>
+<a name="241"><span class="lineNum">     241 </span>            : //      if( lowB&lt;1 ) return ( 1 - (lowB) ) / 2*width;</a>
+<a name="242"><span class="lineNum">     242 </span>            : //      else return 0;</a>
+<a name="243"><span class="lineNum">     243 </span>            :   } else {</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;function type does not exist&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span>            :   return 0;</a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       4860 : double HistogramBead::uboundDerivative( const double&amp; x ) const {</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   plumed_dbg_assert(init &amp;&amp; periodicity!=unset );</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       4860 :   if( type==gaussian ) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">       4860 :     double upperB = difference( x, highb ) / ( std::sqrt(2.0) * width );</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       4860 :     return exp( -upperB*upperB ) / ( std::sqrt(2*pi)*width );</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   } else if ( type==triangular ) {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : //      upperB = fabs( difference( x, highb ) / width );</a>
+<a name="257"><span class="lineNum">     257 </span>            : //      if( upperB&lt;1 ) return ( 1 - (upperB) ) / 2*width;</a>
+<a name="258"><span class="lineNum">     258 </span>            : //      else return 0;</a>
+<a name="259"><span class="lineNum">     259 </span>            :   } else {</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;function type does not exist&quot;);</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            :   return 0;</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/HistogramBead.h.func-sort-c.html b/coverage/tools/HistogramBead.h.func-sort-c.html
new file mode 100644
index 0000000000..014b7b4dda
--- /dev/null
+++ b/coverage/tools/HistogramBead.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/HistogramBead.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
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+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - HistogramBead.h<span style="font-size: 80%;"> (<a href="HistogramBead.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="HistogramBead.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.h.gcov.html#80">_ZN4PLMD13HistogramBead10isPeriodicERKdS2_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.h.gcov.html#97">_ZNK4PLMD13HistogramBead10differenceERKdS2_</a></td>
+              <td class="coverFnHi">595780</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/HistogramBead.h.func.html b/coverage/tools/HistogramBead.h.func.html
new file mode 100644
index 0000000000..0159b8dca6
--- /dev/null
+++ b/coverage/tools/HistogramBead.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/HistogramBead.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - HistogramBead.h<span style="font-size: 80%;"> (<a href="HistogramBead.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="HistogramBead.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.h.gcov.html#80">_ZN4PLMD13HistogramBead10isPeriodicERKdS2_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="HistogramBead.h.gcov.html#97">_ZNK4PLMD13HistogramBead10differenceERKdS2_</a></td>
+              <td class="coverFnHi">595780</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/HistogramBead.h.gcov.html b/coverage/tools/HistogramBead.h.gcov.html
new file mode 100644
index 0000000000..03cb0e2698
--- /dev/null
+++ b/coverage/tools/HistogramBead.h.gcov.html
@@ -0,0 +1,190 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/HistogramBead.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - HistogramBead.h<span style="font-size: 80%;"> (source / <a href="HistogramBead.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_HistogramBead_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_HistogramBead_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class Keywords;</a>
+<a name="33"><span class="lineNum">      33 </span>            : class Log;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : /**</a>
+<a name="36"><span class="lineNum">      36 </span>            : \ingroup TOOLBOX</a>
+<a name="37"><span class="lineNum">      37 </span>            : A class for calculating whether or not values are within a given range using : \f$ \sum_i \int_a^b G( s_i, \sigma*(b-a) ) \f$</a>
+<a name="38"><span class="lineNum">      38 </span>            : */</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class HistogramBead {</a>
+<a name="41"><span class="lineNum">      41 </span>            : private:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   bool init;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double lowb;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   double highb;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   double width;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double cutoff;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   enum {gaussian,triangular} type;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   enum {unset,periodic,notperiodic} periodicity;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double min, max, max_minus_min, inv_max_minus_min;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   double difference( const double&amp; d1, const double&amp; d2 ) const ;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="53"><span class="lineNum">      53 </span>            :   static void generateBins( const std::string&amp; params, std::vector&lt;std::string&gt;&amp; bins );</a>
+<a name="54"><span class="lineNum">      54 </span>            :   HistogramBead();</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::string description() const ;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool hasBeenSet() const;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void isNotPeriodic();</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void isPeriodic( const double&amp; mlow, const double&amp; mhigh );</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void setKernelType( const std::string&amp; ktype );</a>
+<a name="60"><span class="lineNum">      60 </span>            :   void set(const std::string&amp; params, std::string&amp; errormsg);</a>
+<a name="61"><span class="lineNum">      61 </span>            :   void set(double l, double h, double w);</a>
+<a name="62"><span class="lineNum">      62 </span>            :   double calculate(double x, double&amp;df) const;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   double calculateWithCutoff( double x, double&amp; df ) const;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double lboundDerivative( const double&amp; x ) const;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double uboundDerivative( const double&amp; x ) const;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   double getlowb() const ;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double getbigb() const ;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   double getCutoff() const ;</a>
+<a name="69"><span class="lineNum">      69 </span>            : };</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : inline</a>
+<a name="72"><span class="lineNum">      72 </span>            : bool HistogramBead::hasBeenSet() const {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   return init;</a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : inline</a>
+<a name="77"><span class="lineNum">      77 </span>            : void HistogramBead::isNotPeriodic() {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      79303 :   periodicity=notperiodic;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         67 : }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : inline</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          1 : void HistogramBead::isPeriodic( const double&amp; mlow, const double&amp; mhigh ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          1 :   periodicity=periodic; min=mlow; max=mhigh;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          1 :   max_minus_min=max-min;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          1 :   plumed_massert(max_minus_min&gt;0, &quot;your function has a very strange domain?&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          1 :   inv_max_minus_min=1.0/max_minus_min;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          1 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : inline</a>
+<a name="90"><span class="lineNum">      90 </span>            : double HistogramBead::getlowb() const { return lowb; }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : inline</a>
+<a name="93"><span class="lineNum">      93 </span>            : double HistogramBead::getbigb() const { return highb; }</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : inline</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">   82228271 : double HistogramBead::getCutoff() const { return cutoff*width; }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : inline</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     595780 : double HistogramBead::difference( const double&amp; d1, const double&amp; d2 ) const {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     595780 :   if(periodicity==notperiodic) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     595760 :     return d2-d1;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         20 :   } else if(periodicity==periodic) {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :     // Make sure the point is in the target range</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         20 :     double newx=d1*inv_max_minus_min;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         20 :     newx=Tools::pbc(newx);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         20 :     newx*=max_minus_min;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         20 :     return d2-newx;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :   } else plumed_merror(&quot;periodicty was not set&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   return 0;</a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/IFile.cpp.func-sort-c.html b/coverage/tools/IFile.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e51bab8a61
--- /dev/null
+++ b/coverage/tools/IFile.cpp.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/IFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - IFile.cpp<span style="font-size: 80%;"> (<a href="IFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="IFile.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
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+    <tr>
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+              <td class="coverFnHi">17</td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#233">_ZN4PLMD5IFileD0Ev</a></td>
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+              <td class="coverFnHi">1320</td>
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+    <tr>
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+              <td class="coverFnHi">5778</td>
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+              <td class="coverFn"><a href="IFile.cpp.gcov.html#275">_ZN4PLMD5IFile5resetEb</a></td>
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+              <td class="coverFnHi">11584</td>
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+              <td class="coverFn"><a href="IFile.cpp.gcov.html#233">_ZN4PLMD5IFileD1Ev</a></td>
+              <td class="coverFnHi">11584</td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#201">_ZN4PLMD5IFile9scanFieldEPNS_5ValueE</a></td>
+              <td class="coverFnHi">1101706</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#134">_ZN4PLMD5IFile10FieldExistERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1138015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#124">_ZN4PLMD5IFile13scanFieldListERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE</a></td>
+              <td class="coverFnHi">1138112</td>
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+              <td class="coverFn"><a href="IFile.cpp.gcov.html#216">_ZN4PLMD5IFile9scanFieldEv</a></td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#59">_ZN4PLMD5IFile12advanceFieldEv</a></td>
+              <td class="coverFnHi">1325668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#237">_ZN4PLMD5IFile7getlineERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1470682</td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#159">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERi</a></td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#152">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERd</a></td>
+              <td class="coverFnHi">7009037</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#266">_ZNK4PLMD5IFile9findFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">15849069</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#142">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_</a></td>
+              <td class="coverFnHi">15855403</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#39">_ZN4PLMD5IFile6llreadEPcm</a></td>
+              <td class="coverFnHi">99982988</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/IFile.cpp.func.html b/coverage/tools/IFile.cpp.func.html
new file mode 100644
index 0000000000..10168ed650
--- /dev/null
+++ b/coverage/tools/IFile.cpp.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/IFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - IFile.cpp<span style="font-size: 80%;"> (<a href="IFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="IFile.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#134">_ZN4PLMD5IFile10FieldExistERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1138015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#289">_ZN4PLMD5IFile10allowNoEOLEv</a></td>
+              <td class="coverFnHi">884</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#59">_ZN4PLMD5IFile12advanceFieldEv</a></td>
+              <td class="coverFnHi">1325668</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#124">_ZN4PLMD5IFile13scanFieldListERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EE</a></td>
+              <td class="coverFnHi">1138112</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#285">_ZN4PLMD5IFile18allowIgnoredFieldsEv</a></td>
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+              <td class="coverFnHi">1320</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#275">_ZN4PLMD5IFile5resetEb</a></td>
+              <td class="coverFnHi">6135</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#39">_ZN4PLMD5IFile6llreadEPcm</a></td>
+              <td class="coverFnHi">99982988</td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#237">_ZN4PLMD5IFile7getlineERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1470682</td>
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+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#201">_ZN4PLMD5IFile9scanFieldEPNS_5ValueE</a></td>
+              <td class="coverFnHi">1101706</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#142">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_</a></td>
+              <td class="coverFnHi">15855403</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#152">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERd</a></td>
+              <td class="coverFnHi">7009037</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#159">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERi</a></td>
+              <td class="coverFnHi">2213283</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#180">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERj</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#166">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERl</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#187">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERm</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#173">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERx</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#194">_ZN4PLMD5IFile9scanFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERy</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#216">_ZN4PLMD5IFile9scanFieldEv</a></td>
+              <td class="coverFnHi">1319261</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#226">_ZN4PLMD5IFileC1Ev</a></td>
+              <td class="coverFnHi">11584</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#226">_ZN4PLMD5IFileC2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#233">_ZN4PLMD5IFileD0Ev</a></td>
+              <td class="coverFnHi">348</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#233">_ZN4PLMD5IFileD1Ev</a></td>
+              <td class="coverFnHi">11584</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#233">_ZN4PLMD5IFileD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="IFile.cpp.gcov.html#266">_ZNK4PLMD5IFile9findFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">15849069</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/IFile.cpp.gcov.html b/coverage/tools/IFile.cpp.gcov.html
new file mode 100644
index 0000000000..d991620f6f
--- /dev/null
+++ b/coverage/tools/IFile.cpp.gcov.html
@@ -0,0 +1,371 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/IFile.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - IFile.cpp<span style="font-size: 80%;"> (source / <a href="IFile.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryMed">88.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;IFile.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdarg&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstring&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cmath&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;iostream&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;string&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;zlib.h&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #endif</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">   99982988 : size_t IFile::llread(char*ptr,size_t s) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">   99982988 :   plumed_assert(fp);</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   size_t r;</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">   99982988 :   if(gzfp) {</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       3522 :     int rr=gzread(gzFile(gzfp),ptr,s);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       3522 :     if(rr==0)   eof=true;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       3522 :     if(rr&lt;0)    err=true;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       3522 :     r=rr;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : #else</a>
+<a name="51"><span class="lineNum">      51 </span>            :     plumed_merror(&quot;file &quot; + getPath() + &quot;: trying to use a gz file without zlib being linked&quot;);</a>
+<a name="52"><span class="lineNum">      52 </span>            : #endif</a>
+<a name="53"><span class="lineNum">      53 </span>            :   } else {</a>
+<a name="54"><span class="lineNum">      54 </span>            :     r=std::fread(ptr,1,s,fp);</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">   99979466 :     if(std::feof(fp))   eof=true;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">   99979466 :     if(std::ferror(fp)) err=true;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">   99982988 :   return r;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">    1325668 : IFile&amp; IFile::advanceField() {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">    1325668 :   plumed_assert(!inMiddleOfField);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   std::string line;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool done=false;</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">    2653144 :   while(!done) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">    1333886 :     getline(line);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : // using explicit conversion not to confuse cppcheck 1.86</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    1333886 :     if(!bool(*this)) {return *this;}</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">    1327476 :     std::vector&lt;std::string&gt; words=Tools::getWords(line);</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    2654707 :     if(words.size()&gt;=2 &amp;&amp; words[0]==&quot;#!&quot; &amp;&amp; words[1]==&quot;FIELDS&quot;) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        711 :       fields.clear();</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       4712 :       for(unsigned i=2; i&lt;words.size(); i++) {</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :         Field field;</a>
+<a name="74"><span class="lineNum">      74 </span>            :         field.name=words[i];</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       4001 :         fields.push_back(field);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :       }</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">    1348441 :     } else if(words.size()==4 &amp;&amp; words[0]==&quot;#!&quot; &amp;&amp; words[1]==&quot;SET&quot;) {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :       Field field;</a>
+<a name="79"><span class="lineNum">      79 </span>            :       field.name=words[2];</a>
+<a name="80"><span class="lineNum">      80 </span>            :       field.value=words[3];</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       3252 :       field.constant=true;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       3252 :       fields.push_back(field);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :     } else {</a>
+<a name="84"><span class="lineNum">      84 </span>            :       unsigned nf=0;</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">   17100274 :       for(unsigned i=0; i&lt;fields.size(); i++) if(!fields[i].constant) nf++;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">    1323513 :       Tools::trimComments(line);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    2647026 :       words=Tools::getWords(line);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    1323513 :       if( words.size()==nf ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :         unsigned j=0;</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">   17045662 :         for(unsigned i=0; i&lt;fields.size(); i++) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">   15726404 :           if(fields[i].constant) continue;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    6859861 :           fields[i].value=words[j];</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    6859861 :           fields[i].read=false;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    6859861 :           j++;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :         }</a>
+<a name="96"><span class="lineNum">      96 </span>            :         done=true;</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       4255 :       } else if( !words.empty() ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;file &quot; + getPath() + &quot;: mismatch between number of fields in file and expected number\n this is the faulty line:\n&quot;+line);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :       }</a>
+<a name="100"><span class="lineNum">     100 </span>            :     }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">    1327476 :   }</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">    1319258 :   inMiddleOfField=true;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">    1319258 :   return *this;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1320 : IFile&amp; IFile::open(const std::string&amp;path) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">       1320 :   plumed_massert(!cloned,&quot;file &quot;+path+&quot; appears to be cloned&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       1320 :   eof=false;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1320 :   err=false;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">       1320 :   fp=NULL;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       1320 :   gzfp=NULL;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1320 :   bool do_exist=FileExist(path);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1322 :   plumed_massert(do_exist,&quot;file &quot; + path + &quot; cannot be found&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1319 :   fp=std::fopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;r&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       2638 :   if(Tools::extension(this-&gt;path)==&quot;gz&quot;) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          6 :     gzfp=(void*)gzopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;r&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : #else</a>
+<a name="119"><span class="lineNum">     119 </span>            :     plumed_merror(&quot;file &quot; + getPath() + &quot;: trying to use a gz file without zlib being linked&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span>            : #endif</a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       1319 :   if(plumed) plumed-&gt;insertFile(*this);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       1319 :   return *this;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">    1138112 : IFile&amp; IFile::scanFieldList(std::vector&lt;std::string&gt;&amp;s) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">    1138112 :   if(!inMiddleOfField) advanceField();</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : // using explicit conversion not to confuse cppcheck 1.86</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">    1138112 :   if(!bool(*this)) return *this;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   s.clear();</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">    9188413 :   for(unsigned i=0; i&lt;fields.size(); i++)</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    8050377 :     s.push_back(fields[i].name);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   return *this;</a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">    1138015 : bool IFile::FieldExist(const std::string&amp; s) {</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   std::vector&lt;std::string&gt; slist;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">    1138015 :   scanFieldList(slist);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">    1138015 :   int mycount = (int) std::count(slist.begin(), slist.end(), s);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">    1138015 :   if(mycount&gt;0) return true;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">    1114745 :   else return false;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">    1138015 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">   15855403 : IFile&amp; IFile::scanField(const std::string&amp;name,std::string&amp;str) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">   15855403 :   if(!inMiddleOfField) advanceField();</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : // using explicit conversion not to confuse cppcheck 1.86</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">   15855403 :   if(!bool(*this)) return *this;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">   15849069 :   unsigned i=findField(name);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">   15849069 :   str=fields[i].value;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">   15849069 :   fields[i].read=true;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">   15849069 :   return *this;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    7009037 : IFile&amp; IFile::scanField(const std::string&amp;name,double &amp;x) {</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   std::string str;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">    7009037 :   scanField(name,str);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">    7009037 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">    7009037 :   return *this;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    2213283 : IFile&amp; IFile::scanField(const std::string&amp;name,int &amp;x) {</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   std::string str;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">    2213283 :   scanField(name,str);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">    2213283 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">    2213283 :   return *this;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 : IFile&amp; IFile::scanField(const std::string&amp;name,long int &amp;x) {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   std::string str;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 :   scanField(name,str);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          1 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          1 :   return *this;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 : IFile&amp; IFile::scanField(const std::string&amp;name,long long int &amp;x) {</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   std::string str;</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   scanField(name,str);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         17 : IFile&amp; IFile::scanField(const std::string&amp;name,unsigned &amp;x) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   std::string str;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         17 :   scanField(name,str);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         17 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         17 :   return *this;</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          1 : IFile&amp; IFile::scanField(const std::string&amp;name,long unsigned &amp;x) {</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   std::string str;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          1 :   scanField(name,str);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          1 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          1 :   return *this;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         14 : IFile&amp; IFile::scanField(const std::string&amp;name,long long unsigned &amp;x) {</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   std::string str;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         14 :   scanField(name,str);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         14 :   if(*this) Tools::convert(str,x);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         14 :   return *this;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">    1101706 : IFile&amp; IFile::scanField(Value* val) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">    1101706 :   double ff=std::numeric_limits&lt;double&gt;::quiet_NaN(); // this is to be sure a NaN value is replaced upon failure</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">    1101706 :   scanField(  val-&gt;getName(), ff );</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">    1101706 :   val-&gt;set( ff );</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">    2203412 :   if( FieldExist(&quot;min_&quot; + val-&gt;getName() ) ) {</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :     std::string min, max;</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       3309 :     scanField(&quot;min_&quot; + val-&gt;getName(), min );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       3309 :     scanField(&quot;max_&quot; + val-&gt;getName(), max );</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       3309 :     val-&gt;setDomain( min, max );</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   } else {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">    1098397 :     val-&gt;setNotPeriodic();</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">    1101706 :   return *this;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">    1319261 : IFile&amp; IFile::scanField() {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">    1319261 :   if(!ignoreFields) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">   15343306 :     for(unsigned i=0; i&lt;fields.size(); i++) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">   14238618 :       plumed_massert(fields[i].read,&quot;field &quot;+fields[i].name+&quot; was not read: all the fields need to be read otherwise you could miss important infos&quot; );</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     }</a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">    1319261 :   inMiddleOfField=false;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">    1319261 :   return *this;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      11584 : IFile::IFile():</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      11584 :   inMiddleOfField(false),</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      11584 :   ignoreFields(false),</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      11584 :   noEOL(false)</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : {</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      11584 : }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      11932 : IFile::~IFile() {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">      11584 :   if(inMiddleOfField) std::cerr&lt;&lt;&quot;WARNING: IFile closed in the middle of reading. seems strange!\n&quot;;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      11932 : }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">    1470682 : IFile&amp; IFile::getline(std::string &amp;str) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">    1470682 :   char tmp=0;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   str=&quot;&quot;;</a>
+<a name="242"><span class="lineNum">     242 </span>            :   fpos_t pos;</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">    1470682 :   fgetpos(fp,&amp;pos);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">   99982935 :   while(llread(&amp;tmp,1)==1 &amp;&amp; tmp &amp;&amp; tmp!='\n' &amp;&amp; tmp!='\r' &amp;&amp; !eof &amp;&amp; !err) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">   98512253 :     str+=tmp;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">    1470682 :   if(tmp=='\r') {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         53 :     llread(&amp;tmp,1);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         53 :     plumed_massert(tmp=='\n',&quot;plumed only accepts \\n (unix) or \\r\\n (dos) new lines&quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   }</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">    1470682 :   if(eof &amp;&amp; noEOL) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        869 :     if(str.length()&gt;0) eof=false;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">    1469813 :   } else if(eof || err || tmp!='\n') {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">       6437 :     eof = true;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     str=&quot;&quot;;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">       6437 :     if(!err) fsetpos(fp,&amp;pos);</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : // there was a fsetpos here that apparently is not necessary</a>
+<a name="258"><span class="lineNum">     258 </span>            : //  fsetpos(fp,&amp;pos);</a>
+<a name="259"><span class="lineNum">     259 </span>            : // I think it was necessary to have rewind working correctly</a>
+<a name="260"><span class="lineNum">     260 </span>            : // after end of file. Since rewind is not used now anywhere,</a>
+<a name="261"><span class="lineNum">     261 </span>            : // it should be ok not to reset position.</a>
+<a name="262"><span class="lineNum">     262 </span>            : // This is necessary so that eof works properly for emacs files</a>
+<a name="263"><span class="lineNum">     263 </span>            : // with no endline at end of file.</a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">    1470682 :   return *this;</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">   15849069 : unsigned IFile::findField(const std::string&amp;name)const {</span></a>
+<a name="269"><span class="lineNum">     269 </span>            :   unsigned i;</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">  105136661 :   for(i=0; i&lt;fields.size(); i++) if(fields[i].name==name) break;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">   15849069 :   if(i&gt;=fields.size()) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;file &quot; + getPath() + &quot;: field &quot; + name + &quot; cannot be found&quot;);</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :   }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">   15849069 :   return i;</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       6135 : void IFile::reset(bool reset) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       6135 :   eof = reset;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">       6135 :   err = reset;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">       6135 :   if(!reset &amp;&amp; fp) clearerr(fp);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">       6135 :   if(!reset &amp;&amp; gzfp) gzclearerr(gzFile(gzfp));</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : #endif</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       6135 :   return;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : }</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       5778 : void IFile::allowIgnoredFields() {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       5778 :   ignoreFields=true;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       5778 : }</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        884 : void IFile::allowNoEOL() {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        884 :   noEOL=true;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        884 : }</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/IFile.h.func-sort-c.html b/coverage/tools/IFile.h.func-sort-c.html
new file mode 100644
index 0000000000..ed8cb360d0
--- /dev/null
+++ b/coverage/tools/IFile.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/IFile.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - IFile.h<span style="font-size: 80%;"> (<a href="IFile.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="IFile.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/IFile.h.func.html b/coverage/tools/IFile.h.func.html
new file mode 100644
index 0000000000..a22ddf87f1
--- /dev/null
+++ b/coverage/tools/IFile.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/IFile.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - IFile.h<span style="font-size: 80%;"> (<a href="IFile.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="IFile.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/IFile.h.gcov.html b/coverage/tools/IFile.h.gcov.html
new file mode 100644
index 0000000000..d1b2f8b5c0
--- /dev/null
+++ b/coverage/tools/IFile.h.gcov.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/IFile.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - IFile.h<span style="font-size: 80%;"> (source / <a href="IFile.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_IFile_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_IFile_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;FileBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstddef&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class Value;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /**</a>
+<a name="34"><span class="lineNum">      34 </span>            : \ingroup TOOLBOX</a>
+<a name="35"><span class="lineNum">      35 </span>            : Class for input files</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : This class provides features similar to those in the standard C &quot;FILE*&quot; type,</a>
+<a name="38"><span class="lineNum">      38 </span>            : but only for sequential input. See OFile for sequential output.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : */</a>
+<a name="41"><span class="lineNum">      41 </span>            : class IFile:</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Class identifying a single field for fielded output</a>
+<a name="43"><span class="lineNum">      43 </span>            :   public virtual FileBase {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      18804 :   class Field:</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :     public FieldBase {</a>
+<a name="46"><span class="lineNum">      46 </span>            :   public:</a>
+<a name="47"><span class="lineNum">      47 </span>            :     bool read;</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       7253 :     Field(): read(false) {}</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   };</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Low-level read.</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Note: in parallel, all processes read</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::size_t llread(char*,std::size_t);</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// All the defined fields</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;Field&gt; fields;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Flag set in the middle of a field reading</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool inMiddleOfField;</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Set to true if you want to allow fields to be ignored in the read in file</a>
+<a name="58"><span class="lineNum">      58 </span>            :   bool ignoreFields;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Set to true to allow files without end-of-line at the end</a>
+<a name="60"><span class="lineNum">      60 </span>            :   bool noEOL;</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Advance to next field (= read one line)</a>
+<a name="62"><span class="lineNum">      62 </span>            :   IFile&amp; advanceField();</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Find field index by name</a>
+<a name="64"><span class="lineNum">      64 </span>            :   unsigned findField(const std::string&amp;name)const;</a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Constructor</a>
+<a name="67"><span class="lineNum">      67 </span>            :   IFile();</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Destructor</a>
+<a name="69"><span class="lineNum">      69 </span>            :   ~IFile();</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Opens the file</a>
+<a name="71"><span class="lineNum">      71 </span>            :   IFile&amp; open(const std::string&amp;name) override;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Gets the list of all fields</a>
+<a name="73"><span class="lineNum">      73 </span>            :   IFile&amp; scanFieldList(std::vector&lt;std::string&gt;&amp;);</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Read a double field</a>
+<a name="75"><span class="lineNum">      75 </span>            :   IFile&amp; scanField(const std::string&amp;,double&amp;);</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Read a int field</a>
+<a name="77"><span class="lineNum">      77 </span>            :   IFile&amp; scanField(const std::string&amp;,int&amp;);</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Read a long int field</a>
+<a name="79"><span class="lineNum">      79 </span>            :   IFile&amp; scanField(const std::string&amp;,long int&amp;);</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Read a long long int field</a>
+<a name="81"><span class="lineNum">      81 </span>            :   IFile&amp; scanField(const std::string&amp;,long long int&amp;);</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Read a unsigned field</a>
+<a name="83"><span class="lineNum">      83 </span>            :   IFile&amp; scanField(const std::string&amp;,unsigned&amp;);</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// Read a long unsigned field</a>
+<a name="85"><span class="lineNum">      85 </span>            :   IFile&amp; scanField(const std::string&amp;,long unsigned&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Read a long long unsigned field</a>
+<a name="87"><span class="lineNum">      87 </span>            :   IFile&amp; scanField(const std::string&amp;,long long unsigned&amp;);</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Read a string field</a>
+<a name="89"><span class="lineNum">      89 </span>            :   IFile&amp; scanField(const std::string&amp;,std::string&amp;);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   /**</a>
+<a name="91"><span class="lineNum">      91 </span>            :    Ends a field-formatted line.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   Typically used as</a>
+<a name="94"><span class="lineNum">      94 </span>            :   \verbatim</a>
+<a name="95"><span class="lineNum">      95 </span>            :     if.scanField(&quot;a&quot;,a).scanField(&quot;b&quot;,b).scanField();</a>
+<a name="96"><span class="lineNum">      96 </span>            :   \endverbatim</a>
+<a name="97"><span class="lineNum">      97 </span>            :   */</a>
+<a name="98"><span class="lineNum">      98 </span>            :   IFile&amp; scanField();</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Get a full line as a string</a>
+<a name="100"><span class="lineNum">     100 </span>            :   IFile&amp; getline(std::string&amp;);</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Reset end of file</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void reset(bool);</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Check if a field exist</a>
+<a name="104"><span class="lineNum">     104 </span>            :   bool FieldExist(const std::string&amp; s);</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Read in a value</a>
+<a name="106"><span class="lineNum">     106 </span>            :   IFile&amp; scanField(Value* val);</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// Allow some of the fields in the input to be ignored</a>
+<a name="108"><span class="lineNum">     108 </span>            :   void allowIgnoredFields();</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Allow files without EOL at the end.</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// This in practice should be only used when opening</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// plumed input files</a>
+<a name="112"><span class="lineNum">     112 </span>            :   void allowNoEOL();</a>
+<a name="113"><span class="lineNum">     113 </span>            : };</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/KernelFunctions.cpp.func-sort-c.html b/coverage/tools/KernelFunctions.cpp.func-sort-c.html
new file mode 100644
index 0000000000..57b96a49e6
--- /dev/null
+++ b/coverage/tools/KernelFunctions.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/KernelFunctions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - KernelFunctions.cpp<span style="font-size: 80%;"> (<a href="KernelFunctions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">189</td>
+            <td class="headerCovTableEntry">224</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="KernelFunctions.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#138">_ZN4PLMD15KernelFunctionsC2EPKS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#93">_ZN4PLMD15KernelFunctionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#308">_ZNK4PLMD15KernelFunctions10getSupportERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">3415</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#412">_ZN4PLMD15KernelFunctions4readEPNS_5IFileERKbRKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE</a></td>
+              <td class="coverFnHi">4530</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#283">_ZNK4PLMD15KernelFunctions20getContinuousSupportEv</a></td>
+              <td class="coverFnHi">5141</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#274">_ZNK4PLMD15KernelFunctions9getCutoffERKd</a></td>
+              <td class="coverFnHi">10294</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#177">_ZN4PLMD15KernelFunctions9normalizeERKSt6vectorIPNS_5ValueESaIS3_EE</a></td>
+              <td class="coverFnHi">24625</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#128">_ZN4PLMD15KernelFunctionsC2ERKSt6vectorIdSaIdEES5_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESD_RKd</a></td>
+              <td class="coverFnHi">30229</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#151">_ZN4PLMD15KernelFunctions7setDataERKSt6vectorIdSaIdEES5_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESD_RKd</a></td>
+              <td class="coverFnHi">30241</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#316">_ZNK4PLMD15KernelFunctions8evaluateERKSt6vectorIPNS_5ValueESaIS3_EERS1_IdSaIdEEbbdd</a></td>
+              <td class="coverFnHi">23606894</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/KernelFunctions.cpp.func.html b/coverage/tools/KernelFunctions.cpp.func.html
new file mode 100644
index 0000000000..ae90ab49d8
--- /dev/null
+++ b/coverage/tools/KernelFunctions.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/KernelFunctions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - KernelFunctions.cpp<span style="font-size: 80%;"> (<a href="KernelFunctions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">189</td>
+            <td class="headerCovTableEntry">224</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="KernelFunctions.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#412">_ZN4PLMD15KernelFunctions4readEPNS_5IFileERKbRKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISB_EE</a></td>
+              <td class="coverFnHi">4530</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#151">_ZN4PLMD15KernelFunctions7setDataERKSt6vectorIdSaIdEES5_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESD_RKd</a></td>
+              <td class="coverFnHi">30241</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#177">_ZN4PLMD15KernelFunctions9normalizeERKSt6vectorIPNS_5ValueESaIS3_EE</a></td>
+              <td class="coverFnHi">24625</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#138">_ZN4PLMD15KernelFunctionsC2EPKS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#93">_ZN4PLMD15KernelFunctionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#128">_ZN4PLMD15KernelFunctionsC2ERKSt6vectorIdSaIdEES5_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESD_RKd</a></td>
+              <td class="coverFnHi">30229</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#308">_ZNK4PLMD15KernelFunctions10getSupportERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">3415</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#283">_ZNK4PLMD15KernelFunctions20getContinuousSupportEv</a></td>
+              <td class="coverFnHi">5141</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#316">_ZNK4PLMD15KernelFunctions8evaluateERKSt6vectorIPNS_5ValueESaIS3_EERS1_IdSaIdEEbbdd</a></td>
+              <td class="coverFnHi">23606894</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.cpp.gcov.html#274">_ZNK4PLMD15KernelFunctions9getCutoffERKd</a></td>
+              <td class="coverFnHi">10294</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/KernelFunctions.cpp.gcov.html b/coverage/tools/KernelFunctions.cpp.gcov.html
new file mode 100644
index 0000000000..7aace69f05
--- /dev/null
+++ b/coverage/tools/KernelFunctions.cpp.gcov.html
@@ -0,0 +1,531 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/KernelFunctions.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - KernelFunctions.cpp<span style="font-size: 80%;"> (source / <a href="KernelFunctions.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">189</td>
+            <td class="headerCovTableEntry">224</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;KernelFunctions.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;IFile.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;iostream&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cmath&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : //+PLUMEDOC INTERNAL kernelfunctions</a>
+<a name="30"><span class="lineNum">      30 </span>            : /*</a>
+<a name="31"><span class="lineNum">      31 </span>            : Functions that are used to construct histograms</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : Constructing histograms is something you learned to do relatively early in life. You perform an experiment a number of times,</a>
+<a name="34"><span class="lineNum">      34 </span>            : count the number of times each result comes up and then draw a bar graph that describes how often each of the results came up.</a>
+<a name="35"><span class="lineNum">      35 </span>            : This only works when there are a finite number of possible results.  If the result a number between 0 and 1 the bar chart is</a>
+<a name="36"><span class="lineNum">      36 </span>            : less easy to draw as there are as many possible results as there are numbers between zero and one - an infinite number.</a>
+<a name="37"><span class="lineNum">      37 </span>            : To resolve this problem we replace probability, \f$P\f$ with probability density, \f$\pi\f$, and write the probability of getting</a>
+<a name="38"><span class="lineNum">      38 </span>            : a number between \f$a\f$ and \f$b\f$ as:</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            : P = \int_{a}^b \textrm{d}x \pi(x)</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f]</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : To calculate probability densities from a set of results we use a process called kernel density estimation.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Histograms are accumulated by adding up kernel functions, \f$K\f$, with finite spatial extent, that integrate to one.</a>
+<a name="46"><span class="lineNum">      46 </span>            : These functions are centered on each of the \f$n\f$-dimensional data points, \f$\mathbf{x}_i\f$. The overall effect of this</a>
+<a name="47"><span class="lineNum">      47 </span>            : is that each result we obtain in our experiments contributes to the probability density in a finite sized region of the space.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Expressing all this mathematically in kernel density estimation we write the probability density as:</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \f[</a>
+<a name="52"><span class="lineNum">      52 </span>            : \pi(\mathbf{x}) =  \sum_i K\left[ (\mathbf{x} - \mathbf{x}_i)^T \Sigma (\mathbf{x} - \mathbf{x}_i) \right]</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f]</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : where \f$\Sigma\f$ is an \f$n \times n\f$ matrix called the bandwidth that controls the spatial extent of</a>
+<a name="56"><span class="lineNum">      56 </span>            : the kernel. Whenever we accumulate a histogram (e.g. in \ref HISTOGRAM or in \ref METAD) we use this</a>
+<a name="57"><span class="lineNum">      57 </span>            : technique.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : There is thus some flexibility in the particular function we use for \f$K[\mathbf{r}]\f$ in the above.</a>
+<a name="60"><span class="lineNum">      60 </span>            : The following variants are available.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : &lt;table align=center frame=void width=95%% cellpadding=5%%&gt;</a>
+<a name="63"><span class="lineNum">      63 </span>            : &lt;tr&gt;</a>
+<a name="64"><span class="lineNum">      64 </span>            : &lt;td&gt; TYPE &lt;/td&gt; &lt;td&gt; FUNCTION &lt;/td&gt;</a>
+<a name="65"><span class="lineNum">      65 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            : &lt;td&gt; gaussian &lt;/td&gt; &lt;td&gt; \f$f(r) = \frac{1}{(2 \pi)^{n} \sqrt{|\Sigma^{-1}|}} \exp\left(-0.5 r^2 \right)\f$ &lt;/td&gt;</a>
+<a name="67"><span class="lineNum">      67 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="68"><span class="lineNum">      68 </span>            : &lt;td&gt; truncated-gaussian &lt;/td&gt; &lt;td&gt; \f$f(r) = \frac{1}{(2 \pi)^{n} \sqrt{|\Sigma^{-1}|} \left(\frac{\mathrm{erf}(-6.25/sqrt{2}) - \mathrm{erf}(-6.25/sqrt{2})}{2}\right)^n} \exp\left(-0.5 r^2 \right)\f$ &lt;/td&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="70"><span class="lineNum">      70 </span>            : &lt;td&gt; triangular &lt;/td&gt; &lt;td&gt; \f$f(r) = \frac{3}{V} ( 1 - | r | )H(1-|r|) \f$ &lt;/td&gt;</a>
+<a name="71"><span class="lineNum">      71 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : &lt;td&gt; uniform &lt;/td&gt; &lt;td&gt; \f$f(r) = \frac{1}{V}H(1-|r|)\f$ &lt;/td&gt;</a>
+<a name="73"><span class="lineNum">      73 </span>            : &lt;/tr&gt;</a>
+<a name="74"><span class="lineNum">      74 </span>            : &lt;/table&gt;</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : In the above \f$H(y)\f$ is a function that is equal to one when \f$y&gt;0\f$ and zero when \f$y \le 0\f$. \f$n\f$ is</a>
+<a name="77"><span class="lineNum">      77 </span>            : the dimensionality of the vector \f$\mathbf{x}\f$ and \f$V\f$ is the volume of an ellipse in an \f$n\f$ dimensional</a>
+<a name="78"><span class="lineNum">      78 </span>            : space which is given by:</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \f{eqnarray*}{</a>
+<a name="81"><span class="lineNum">      81 </span>            : V &amp;=&amp; | \Sigma^{-1} | \frac{ \pi^{\frac{n}{2}} }{\left( \frac{n}{2} \right)! } \qquad \textrm{for even} \quad n \\</a>
+<a name="82"><span class="lineNum">      82 </span>            : V &amp;=&amp; | \Sigma^{-1} | \frac{ 2^{\frac{n+1}{2}} \pi^{\frac{n-1}{2}} }{ n!! }</a>
+<a name="83"><span class="lineNum">      83 </span>            : \f}</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : In \ref METAD the normalization constants are ignored so that the value of the function at \f$r=0\f$ is equal</a>
+<a name="86"><span class="lineNum">      86 </span>            : to one.  In addition in \ref METAD we must be able to differentiate the bias in order to get forces.  This limits</a>
+<a name="87"><span class="lineNum">      87 </span>            : the kernels we can use in this method.  Notice also that Gaussian kernels should have infinite support.  When used</a>
+<a name="88"><span class="lineNum">      88 </span>            : with grids, however, they are assumed to only be non-zero over a finite range.  The difference between the</a>
+<a name="89"><span class="lineNum">      89 </span>            : truncated-gaussian and regular gaussian is that the truncated gaussian is scaled so that its integral over the grid</a>
+<a name="90"><span class="lineNum">      90 </span>            : is equal to one when it is normalized.  The integral of a regular gaussian when it is evaluated on a grid will be</a>
+<a name="91"><span class="lineNum">      91 </span>            : slightly less that one because of the truncation of a function that should have infinite support.</a>
+<a name="92"><span class="lineNum">      92 </span>            : */</a>
+<a name="93"><span class="lineNum">      93 </span>            : //+ENDPLUMEDOC</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         12 : KernelFunctions::KernelFunctions( const std::string&amp; input ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         12 :   if(!dp2cutoffNoStretch()) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         12 :     stretchA=dp2cutoffA;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         12 :     stretchB=dp2cutoffB;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         12 :   std::vector&lt;std::string&gt; data=Tools::getWords(input);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         12 :   std::string name=data[0];</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   data.erase(data.begin());</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;double&gt; at;</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         12 :   bool foundc = Tools::parseVector(data,&quot;CENTER&quot;,at);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         12 :   if(!foundc) plumed_merror(&quot;failed to find center keyword in definition of kernel&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;double&gt; sig;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         12 :   bool founds = Tools::parseVector(data,&quot;SIGMA&quot;,sig);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         12 :   if(!founds) plumed_merror(&quot;failed to find sigma keyword in definition of kernel&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         12 :   bool multi=false; Tools::parseFlag(data,&quot;MULTIVARIATE&quot;,multi);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         24 :   bool vonmises=false; Tools::parseFlag(data,&quot;VON-MISSES&quot;,vonmises);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         12 :   if( center.size()==1 &amp;&amp; multi ) plumed_merror(&quot;one dimensional kernel cannot be multivariate&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         12 :   if( center.size()==1 &amp;&amp; vonmises ) plumed_merror(&quot;one dimensional kernal cannot be von-misses&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         12 :   if( center.size()==1 &amp;&amp; sig.size()!=1 ) plumed_merror(&quot;size mismatch between center size and sigma size&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         12 :   if( multi &amp;&amp; center.size()&gt;1 &amp;&amp; sig.size()!=0.5*center.size()*(center.size()-1) ) plumed_merror(&quot;size mismatch between center size and sigma size&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         12 :   if( !multi &amp;&amp; center.size()&gt;1 &amp;&amp; sig.size()!=center.size() ) plumed_merror(&quot;size mismatch between center size and sigma size&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            :   double h;</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         12 :   bool foundh = Tools::parse(data,&quot;HEIGHT&quot;,h);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         12 :   if( !foundh) h=1.0;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         12 :   if( multi ) setData( at, sig, name, &quot;MULTIVARIATE&quot;, h );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         12 :   else if( vonmises ) setData( at, sig, name, &quot;VON-MISSES&quot;, h );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         24 :   else setData( at, sig, name, &quot;DIAGONAL&quot;, h );</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         12 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      30229 : KernelFunctions::KernelFunctions( const std::vector&lt;double&gt;&amp; at, const std::vector&lt;double&gt;&amp; sig, const std::string&amp; type, const std::string&amp; mtype, const double&amp; w ) {</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      30229 :   if(!dp2cutoffNoStretch()) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      30229 :     stretchA=dp2cutoffA;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      30229 :     stretchB=dp2cutoffB;</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      30229 :   setData( at, sig, type, mtype, w );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      30229 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 : KernelFunctions::KernelFunctions( const KernelFunctions* in ):</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   dtype(in-&gt;dtype),</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   ktype(in-&gt;ktype),</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   center(in-&gt;center),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   width(in-&gt;width),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   height(in-&gt;height)</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : {</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   if(!dp2cutoffNoStretch()) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :     stretchA=dp2cutoffA;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     stretchB=dp2cutoffB;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      30241 : void KernelFunctions::setData( const std::vector&lt;double&gt;&amp; at, const std::vector&lt;double&gt;&amp; sig, const std::string&amp; type, const std::string&amp; mtype, const double&amp; w ) {</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      30241 :   height=w;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     114820 :   center.resize( at.size() ); for(unsigned i=0; i&lt;at.size(); ++i) center[i]=at[i];</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">     119327 :   width.resize( sig.size() ); for(unsigned i=0; i&lt;sig.size(); ++i) width[i]=sig[i];</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      30241 :   if( mtype==&quot;MULTIVARIATE&quot; ) dtype=multi;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      25829 :   else if( mtype==&quot;VON-MISSES&quot; ) dtype=vonmises;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      25820 :   else if( mtype==&quot;DIAGONAL&quot; ) dtype=diagonal;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   else plumed_merror(mtype + &quot; is not a valid metric type&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            :   // Setup the kernel type</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      60474 :   if(type==&quot;GAUSSIAN&quot; || type==&quot;gaussian&quot; ) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      24674 :     ktype=gaussian;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">      11134 :   } else if(type==&quot;STRETCHED-GAUSSIAN&quot; || type==&quot;stretched-gaussian&quot; ) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       5563 :     ktype=stretchedgaussian;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          8 :   } else if(type==&quot;TRUNCATED-GAUSSIAN&quot; || type==&quot;truncated-gaussian&quot; ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     ktype=truncatedgaussian;</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          8 :   } else if(type==&quot;UNIFORM&quot; || type==&quot;uniform&quot;) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :     ktype=uniform;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 :   } else if(type==&quot;TRIANGULAR&quot; || type==&quot;triangular&quot;) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 :     ktype=triangular;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   } else {</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     plumed_merror(type+&quot; is an invalid kernel type\n&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      30241 : }</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      24625 : void KernelFunctions::normalize( const std::vector&lt;Value*&gt;&amp; myvals ) {</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   double det=1.;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   unsigned ncv=ndim();</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      24625 :   if(dtype==diagonal) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      97800 :     for(unsigned i=0; i&lt;width.size(); ++i) det*=width[i]*width[i];</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         53 :   } else if(dtype==multi) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         44 :     Matrix&lt;double&gt; mymatrix( getMatrix() ), myinv( ncv, ncv );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         44 :     Invert(mymatrix,myinv); double logd;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         44 :     logdet( myinv, logd );</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         44 :     det=std::exp(logd);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      24625 :   if( dtype==diagonal || dtype==multi ) {</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     double volume;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      24616 :     if( ktype==gaussian || ktype==stretchedgaussian ) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      24616 :       volume=pow( 2*pi, 0.5*ncv ) * pow( det, 0.5 );</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     } else if( ktype==truncatedgaussian ) {</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :       // This makes it so the gaussian integrates to one over the range over which it has support</a>
+<a name="197"><span class="lineNum">     197 </span>            :       const double DP2CUTOFF=std::sqrt(6.25);</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :       volume=pow( 2*pi, 0.5*ncv ) * pow( det, 0.5 ) * pow( 0.5 * ( erf(DP2CUTOFF) - erf(-DP2CUTOFF) ), ncv);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :     } else if( ktype==uniform || ktype==triangular ) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :       if( ncv%2==1 ) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :         double dfact=1;</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :         for(unsigned i=1; i&lt;ncv; i+=2) dfact*=static_cast&lt;double&gt;(i);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :         volume=( pow( pi, (ncv-1)/2 ) ) * ( pow( 2., (ncv+1)/2 ) ) / dfact;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       } else {</a>
+<a name="205"><span class="lineNum">     205 </span>            :         double fact=1.;</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :         for(unsigned i=1; i&lt;ncv/2; ++i) fact*=static_cast&lt;double&gt;(i);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :         volume=pow( pi,ncv/2 ) / fact;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :       }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :       if(ktype==uniform) volume*=det;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :       else if(ktype==triangular) volume*=det / 3.;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     } else {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;not a valid kernel type&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      24616 :     height /= volume;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      24616 :     return;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   }</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          9 :   plumed_assert( dtype==vonmises &amp;&amp; ktype==gaussian );</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   // Now calculate determinant for aperiodic variables</a>
+<a name="219"><span class="lineNum">     219 </span>            :   unsigned naper=0;</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         16 :     if( !myvals[i]-&gt;isPeriodic() ) naper++;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span>            :   // Now construct sub matrix</a>
+<a name="224"><span class="lineNum">     224 </span>            :   double volume=1;</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          9 :   if( naper&gt;0 ) {</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :     unsigned isub=0;</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          2 :     Matrix&lt;double&gt; mymatrix( getMatrix() ), mysub( naper, naper );</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          4 :     for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          2 :       if( myvals[i]-&gt;isPeriodic() ) continue;</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       unsigned jsub=0;</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          4 :       for(unsigned j=0; j&lt;ncv; ++j) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          2 :         if( myvals[j]-&gt;isPeriodic() ) continue;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 :         mysub( isub, jsub ) = mymatrix( i, j ); jsub++;</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :       }</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          2 :       isub++;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :     }</a>
+<a name="237"><span class="lineNum">     237 </span>            :     Matrix&lt;double&gt; myisub( naper, naper ); double logd;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          2 :     Invert( mysub, myisub ); logdet( myisub, logd );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :     det=std::exp(logd);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          2 :     volume=pow( 2*pi, 0.5*ncv ) * pow( det, 0.5 );</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            :   // Calculate volume of periodic variables</a>
+<a name="244"><span class="lineNum">     244 </span>            :   unsigned nper=0;</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         25 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         16 :     if( myvals[i]-&gt;isPeriodic() ) nper++;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :   // Now construct sub matrix</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          9 :   if( nper&gt;0 ) {</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     unsigned isub=0;</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          7 :     Matrix&lt;double&gt; mymatrix( getMatrix() ),  mysub( nper, nper );</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         21 :     for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         14 :       if( !myvals[i]-&gt;isPeriodic() ) continue;</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :       unsigned jsub=0;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         42 :       for(unsigned j=0; j&lt;ncv; ++j) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         28 :         if( !myvals[j]-&gt;isPeriodic() ) continue;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         28 :         mysub( isub, jsub ) = mymatrix( i, j ); jsub++;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :       }</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         14 :       isub++;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     }</a>
+<a name="262"><span class="lineNum">     262 </span>            :     Matrix&lt;double&gt;  eigvec( nper, nper );</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          7 :     std::vector&lt;double&gt; eigval( nper );</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          7 :     diagMat( mysub, eigval, eigvec );</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     unsigned iper=0; volume=1;</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         21 :     for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         14 :       if( myvals[i]-&gt;isPeriodic() ) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         14 :         volume *= myvals[i]-&gt;getMaxMinusMin()*Tools::bessel0(eigval[iper])*std::exp(-eigval[iper]);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         14 :         iper++;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :       }</a>
+<a name="271"><span class="lineNum">     271 </span>            :     }</a>
+<a name="272"><span class="lineNum">     272 </span>            :   }</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          9 :   height /= volume;</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      10294 : double KernelFunctions::getCutoff( const double&amp; width ) const {</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   const double DP2CUTOFF=6.25;</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      10294 :   if( ktype==gaussian || ktype==truncatedgaussian || ktype==stretchedgaussian ) return std::sqrt(2.0*DP2CUTOFF)*width;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   else if(ktype==triangular ) return width;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :   else if(ktype==uniform) return width;</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :   else plumed_merror(&quot;No valid kernel type&quot;);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :   return 0.0;</a>
+<a name="283"><span class="lineNum">     283 </span>            : }</a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       5141 : std::vector&lt;double&gt; KernelFunctions::getContinuousSupport( ) const {</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   unsigned ncv=ndim();</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">       5141 :   std::vector&lt;double&gt; support( ncv );</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">       5141 :   if(dtype==diagonal) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">       2152 :     for(unsigned i=0; i&lt;ncv; ++i) support[i]=getCutoff(width[i]);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       4412 :   } else if(dtype==multi) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">       4412 :     Matrix&lt;double&gt; mymatrix( getMatrix() ), myinv( ncv,ncv );</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">       4412 :     Invert(mymatrix,myinv);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       4412 :     Matrix&lt;double&gt; myautovec(ncv,ncv); std::vector&lt;double&gt; myautoval(ncv);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       4412 :     diagMat(myinv,myautoval,myautovec);</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :     double maxautoval=0.;</a>
+<a name="296"><span class="lineNum">     296 </span>            :     unsigned ind_maxautoval=0;</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">      13280 :     for (unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       8868 :       if(myautoval[i]&gt;maxautoval) {maxautoval=myautoval[i]; ind_maxautoval=i;}</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :     }</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">      13280 :     for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       8868 :       double extent=std::fabs(std::sqrt(maxautoval)*myautovec(i,ind_maxautoval));</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       8868 :       support[i]=getCutoff( extent );</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     }</a>
+<a name="304"><span class="lineNum">     304 </span>            :   } else {</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;cannot find support if metric is not multi or diagonal type&quot;);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   }</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       5141 :   return support;</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : }</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">       3415 : std::vector&lt;unsigned&gt; KernelFunctions::getSupport( const std::vector&lt;double&gt;&amp; dx ) const {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">       3415 :   plumed_assert( ndim()==dx.size() );</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">       3415 :   std::vector&lt;unsigned&gt; support( dx.size() );</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       3415 :   std::vector&lt;double&gt; vv=getContinuousSupport( );</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">      10227 :   for(unsigned i=0; i&lt;dx.size(); ++i) support[i]=static_cast&lt;unsigned&gt;(ceil( vv[i]/dx[i] ));</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       3415 :   return support;</span></a>
+<a name="316"><span class="lineNum">     316 </span>            : }</a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">   23606894 : double KernelFunctions::evaluate( const std::vector&lt;Value*&gt;&amp; pos, std::vector&lt;double&gt;&amp; derivatives, bool usederiv, bool doInt, double lowI_, double uppI_) const {</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :   plumed_dbg_assert( pos.size()==ndim() &amp;&amp; derivatives.size()==ndim() );</a>
+<a name="320"><span class="lineNum">     320 </span>            : #ifndef NDEBUG</a>
+<a name="321"><span class="lineNum">     321 </span>            :   if( usederiv ) plumed_massert( ktype!=uniform, &quot;step function can not be differentiated&quot; );</a>
+<a name="322"><span class="lineNum">     322 </span>            : #endif</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">   23606894 :   if(doInt) {</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :     plumed_dbg_assert(center.size()==1);</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :     if(pos[0]-&gt;get()&lt;lowI_) pos[0]-&gt;set(lowI_);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :     if(pos[0]-&gt;get()&gt;uppI_) pos[0]-&gt;set(uppI_);</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :   }</a>
+<a name="328"><span class="lineNum">     328 </span>            :   double r2=0;</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">   23606894 :   if(dtype==diagonal) {</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">   51709439 :     for(unsigned i=0; i&lt;ndim(); ++i) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">   37730371 :       derivatives[i]=-pos[i]-&gt;difference( center[i] ) / width[i];</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">   37730371 :       r2+=derivatives[i]*derivatives[i];</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">   37730371 :       derivatives[i] /= width[i];</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :     }</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">    9627826 :   } else if(dtype==multi) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">    9627680 :     Matrix&lt;double&gt; mymatrix( getMatrix() );</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">   37540216 :     for(unsigned i=0; i&lt;mymatrix.nrows(); ++i) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">   27912536 :       double dp_i, dp_j; derivatives[i]=0;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">   27912536 :       dp_i=-pos[i]-&gt;difference( center[i] );</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">  109709136 :       for(unsigned j=0; j&lt;mymatrix.ncols(); ++j) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">   81796600 :         if(i==j) dp_j=dp_i;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">   53884064 :         else dp_j=-pos[j]-&gt;difference( center[j] );</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">   81796600 :         derivatives[i]+=mymatrix(i,j)*dp_j;</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">   81796600 :         r2+=dp_i*dp_j*mymatrix(i,j);</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :       }</a>
+<a name="347"><span class="lineNum">     347 </span>            :     }</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        146 :   } else if(dtype==vonmises) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        146 :     std::vector&lt;double&gt; costmp( ndim() ), sintmp( ndim() ), sinout( ndim(), 0.0 );</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        418 :     for(unsigned i=0; i&lt;ndim(); ++i) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        272 :       if( pos[i]-&gt;isPeriodic() ) {</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        252 :         sintmp[i]=std::sin( 2.*pi*(pos[i]-&gt;get() - center[i])/pos[i]-&gt;getMaxMinusMin() );</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        252 :         costmp[i]=std::cos( 2.*pi*(pos[i]-&gt;get() - center[i])/pos[i]-&gt;getMaxMinusMin() );</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :       } else {</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         20 :         sintmp[i]=pos[i]-&gt;get() - center[i];</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         20 :         costmp[i]=1.0;</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :       }</a>
+<a name="358"><span class="lineNum">     358 </span>            :     }</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">        146 :     Matrix&lt;double&gt; mymatrix( getMatrix() );</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        418 :     for(unsigned i=0; i&lt;mymatrix.nrows(); ++i) {</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        272 :       derivatives[i]=0;</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">        272 :       if( pos[i]-&gt;isPeriodic() ) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        252 :         r2+=2*( 1 - costmp[i] )*mymatrix(i,i);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :       } else {</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         20 :         r2+=sintmp[i]*sintmp[i]*mymatrix(i,i);</span></a>
+<a name="367"><span class="lineNum">     367 </span>            :       }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        796 :       for(unsigned j=0; j&lt;mymatrix.ncols(); ++j) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        524 :         if( i!=j ) sinout[i]+=mymatrix(i,j)*sintmp[j];</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :       }</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        272 :       derivatives[i] = mymatrix(i,i)*sintmp[i] + sinout[i]*costmp[i];</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        272 :       if( pos[i]-&gt;isPeriodic() ) derivatives[i] *= (2*pi/pos[i]-&gt;getMaxMinusMin());</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :     }</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        418 :     for(unsigned i=0; i&lt;sinout.size(); ++i) r2+=sintmp[i]*sinout[i];</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :   }</a>
+<a name="376"><span class="lineNum">     376 </span>            :   double kderiv, kval;</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">   23606894 :   if(ktype==gaussian || ktype==truncatedgaussian) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">   22547753 :     kval=height*std::exp(-0.5*r2); kderiv=-kval;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">    1059141 :   } else if(ktype==stretchedgaussian) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">    1024305 :     auto dp=0.5*r2;</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">    1024305 :     if(dp&lt;dp2cutoff) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">     630478 :       auto ee=std::exp(-0.5*r2);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">     630478 :       kval=height*(stretchA*ee+stretchB);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">     630478 :       kderiv=-height*stretchA*ee;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :     } else {</a>
+<a name="386"><span class="lineNum">     386 </span>            :       kval=0.0;</a>
+<a name="387"><span class="lineNum">     387 </span>            :       kderiv=0.0;</a>
+<a name="388"><span class="lineNum">     388 </span>            :     }</a>
+<a name="389"><span class="lineNum">     389 </span>            :   } else {</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      34836 :     double r=std::sqrt(r2);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">      34836 :     if(ktype==triangular) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">      34836 :       if( r&lt;1.0 ) {</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :         if(r==0) kderiv=0;</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       9753 :         kderiv=-1; kval=height*( 1. - std::fabs(r) );</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :       } else {</a>
+<a name="396"><span class="lineNum">     396 </span>            :         kval=0.; kderiv=0.;</a>
+<a name="397"><span class="lineNum">     397 </span>            :       }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :     } else if(ktype==uniform) {</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :       kderiv=0.;</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :       if(r&lt;1.0) kval=height;</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :       else kval=0;</a>
+<a name="402"><span class="lineNum">     402 </span>            :     } else {</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Not a valid kernel type&quot;);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :     }</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">      34836 :     kderiv*=height / r ;</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :   }</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">   89250073 :   for(unsigned i=0; i&lt;ndim(); ++i) derivatives[i]*=kderiv;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">   23606894 :   if(doInt) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :     if((pos[0]-&gt;get() &lt;= lowI_ || pos[0]-&gt;get() &gt;= uppI_) &amp;&amp; usederiv ) for(unsigned i=0; i&lt;ndim(); ++i)derivatives[i]=0;</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">   23606894 :   return kval;</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">       4530 : std::unique_ptr&lt;KernelFunctions&gt; KernelFunctions::read( IFile* ifile, const bool&amp; cholesky, const std::vector&lt;std::string&gt;&amp; valnames ) {</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   double h;</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       9060 :   if( !ifile-&gt;scanField(&quot;height&quot;,h) ) return NULL;;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">       4524 :   std::string sss; ifile-&gt;scanField(&quot;multivariate&quot;,sss);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      12480 :   std::string ktype=&quot;stretched-gaussian&quot;; if( ifile-&gt;FieldExist(&quot;kerneltype&quot;) ) ifile-&gt;scanField(&quot;kerneltype&quot;,ktype);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">       8954 :   plumed_massert( sss==&quot;false&quot; || sss==&quot;true&quot; || sss==&quot;von-misses&quot;, &quot;multivariate flag must be either false, true or von-misses&quot;);</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            :   // Read the position of the center</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">       4524 :   std::vector&lt;double&gt; cc( valnames.size() );</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">      13613 :   for(unsigned i=0; i&lt;valnames.size(); ++i) ifile-&gt;scanField(valnames[i],cc[i]);</span></a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            :   std::vector&lt;double&gt; sig;</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">       4524 :   if( sss==&quot;false&quot; ) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">        103 :     sig.resize( valnames.size() );</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">        308 :     for(unsigned i=0; i&lt;valnames.size(); ++i) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        205 :       ifile-&gt;scanField(&quot;sigma_&quot;+valnames[i],sig[i]);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        205 :       if( !cholesky ) sig[i]=std::sqrt(sig[i]);</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :     }</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        103 :     return Tools::make_unique&lt;KernelFunctions&gt;(cc, sig, ktype, &quot;DIAGONAL&quot;, h);</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :   }</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">       4421 :   unsigned ncv=valnames.size();</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">       4421 :   sig.resize( (ncv*(ncv+1))/2 );</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :   Matrix&lt;double&gt; upper(ncv,ncv), lower(ncv,ncv), mymult( ncv, ncv ), invmatrix(ncv,ncv);</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">      13305 :   for(unsigned i=0; i&lt;ncv; ++i) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">      22275 :     for(unsigned j=0; j&lt;ncv-i; j++) {</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">      26782 :       ifile-&gt;scanField(&quot;sigma_&quot; +valnames[j+i] + &quot;_&quot; + valnames[j], lower(j+i,j) );</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">      13391 :       upper(j,j+i)=lower(j+i,j); mymult(j+i,j)=mymult(j,j+i)=lower(j+i,j);</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :     }</a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">       4421 :   if( cholesky ) mult(lower,upper,mymult);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">       4421 :   Invert( mymult, invmatrix );</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   unsigned k=0;</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">      13305 :   for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">      22275 :     for(unsigned j=i; j&lt;ncv; j++) { sig[k]=invmatrix(i,j); k++; }</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">       4421 :   if( sss==&quot;true&quot; ) return Tools::make_unique&lt;KernelFunctions&gt;(cc, sig, ktype, &quot;MULTIVARIATE&quot;, h);</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">          9 :   return Tools::make_unique&lt;KernelFunctions&gt;( cc, sig, ktype, &quot;VON-MISSES&quot;, h );</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/KernelFunctions.h.func-sort-c.html b/coverage/tools/KernelFunctions.h.func-sort-c.html
new file mode 100644
index 0000000000..bc4180b141
--- /dev/null
+++ b/coverage/tools/KernelFunctions.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/KernelFunctions.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - KernelFunctions.h<span style="font-size: 80%;"> (<a href="KernelFunctions.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="KernelFunctions.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.h.gcov.html#73">_ZNK4PLMD15KernelFunctions9getMatrixEv</a></td>
+              <td class="coverFnHi">9632291</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/KernelFunctions.h.func.html b/coverage/tools/KernelFunctions.h.func.html
new file mode 100644
index 0000000000..b8457a5494
--- /dev/null
+++ b/coverage/tools/KernelFunctions.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/KernelFunctions.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - KernelFunctions.h<span style="font-size: 80%;"> (<a href="KernelFunctions.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="KernelFunctions.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="KernelFunctions.h.gcov.html#73">_ZNK4PLMD15KernelFunctions9getMatrixEv</a></td>
+              <td class="coverFnHi">9632291</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/KernelFunctions.h.gcov.html b/coverage/tools/KernelFunctions.h.gcov.html
new file mode 100644
index 0000000000..b5b7629ec4
--- /dev/null
+++ b/coverage/tools/KernelFunctions.h.gcov.html
@@ -0,0 +1,173 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/KernelFunctions.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - KernelFunctions.h<span style="font-size: 80%;"> (source / <a href="KernelFunctions.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_KernelFunctions_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_KernelFunctions_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Matrix.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;memory&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">      30253 : class KernelFunctions {</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// Is the metric matrix diagonal</a>
+<a name="35"><span class="lineNum">      35 </span>            :   enum {diagonal,multi,vonmises} dtype;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// What type of kernel are we using</a>
+<a name="37"><span class="lineNum">      37 </span>            :   enum {gaussian,truncatedgaussian,stretchedgaussian,uniform,triangular} ktype;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// The center of the kernel function</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;double&gt; center;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// The width of the kernel</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::vector&lt;double&gt; width;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// The height of the kernel</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double height;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            :   double stretchA=1.0;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double stretchB=0.0;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Used to set all the data in the kernel during construction - avoids double coding as this has two constructors</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void setData( const std::vector&lt;double&gt;&amp; at, const std::vector&lt;double&gt;&amp; sig, const std::string&amp; type, const std::string&amp; mtype, const double&amp; w );</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Convert the width into matrix form</a>
+<a name="51"><span class="lineNum">      51 </span>            :   Matrix&lt;double&gt; getMatrix() const;</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit KernelFunctions( const std::string&amp; input );</a>
+<a name="54"><span class="lineNum">      54 </span>            :   KernelFunctions( const std::vector&lt;double&gt;&amp; at, const std::vector&lt;double&gt;&amp; sig, const std::string&amp; type, const std::string&amp; mtype, const double&amp; w );</a>
+<a name="55"><span class="lineNum">      55 </span>            :   explicit KernelFunctions( const KernelFunctions* in );</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Normalise the function and scale the height accordingly</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void normalize( const std::vector&lt;Value*&gt;&amp; myvals );</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Get the dimensionality of the kernel</a>
+<a name="59"><span class="lineNum">      59 </span>            :   unsigned ndim() const;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Get the cutoff for a kernel</a>
+<a name="61"><span class="lineNum">      61 </span>            :   double getCutoff( const double&amp; width ) const ;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Get the position of the center</a>
+<a name="63"><span class="lineNum">      63 </span>            :   std::vector&lt;double&gt; getCenter() const;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Get the support</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;unsigned&gt; getSupport( const std::vector&lt;double&gt;&amp; dx ) const;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// get it in continuous form</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;double&gt; getContinuousSupport( ) const;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Evaluate the kernel function with constant intervals</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double evaluate( const std::vector&lt;Value*&gt;&amp; pos, std::vector&lt;double&gt;&amp; derivatives, bool usederiv=true, bool doInt=false, double lowI_=-1, double uppI_=-1 ) const;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Read a kernel function from a file</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static std::unique_ptr&lt;KernelFunctions&gt; read( IFile* ifile, const bool&amp; cholesky, const std::vector&lt;std::string&gt;&amp; valnames );</a>
+<a name="72"><span class="lineNum">      72 </span>            : };</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : inline</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">    9632291 : Matrix&lt;double&gt; KernelFunctions::getMatrix() const {</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   unsigned k=0, ncv=ndim(); Matrix&lt;double&gt; mymatrix(ncv,ncv);</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">   37554115 :   for(unsigned i=0; i&lt;ncv; i++) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">   82790445 :     for(unsigned j=i; j&lt;ncv; j++) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">   54868621 :       mymatrix(i,j)=mymatrix(j,i)=width[k]; // recompose the full inverse matrix</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">   54868621 :       k++;</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :     }</a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    9632291 :   return mymatrix;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            : }</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : inline</a>
+<a name="87"><span class="lineNum">      87 </span>            : unsigned KernelFunctions::ndim() const {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">  150621987 :   return center.size();</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : }</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : inline</a>
+<a name="92"><span class="lineNum">      92 </span>            : std::vector&lt;double&gt; KernelFunctions::getCenter() const {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      27064 :   return center;</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : }</a>
+<a name="97"><span class="lineNum">      97 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Keywords.cpp.func-sort-c.html b/coverage/tools/Keywords.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a76e144953
--- /dev/null
+++ b/coverage/tools/Keywords.cpp.func-sort-c.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Keywords.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Keywords.cpp<span style="font-size: 80%;"> (<a href="Keywords.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">240</td>
+            <td class="headerCovTableEntry">395</td>
+            <td class="headerCovTableEntryLo">60.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Keywords.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#579">_ZN4PLMD8Keywords11destroyDataEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#637">_ZN4PLMD8Keywords15removeComponentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#526">_ZNK4PLMD8Keywords10getTooltipERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#324">_ZNK4PLMD8Keywords10print_htmlEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#452">_ZNK4PLMD8Keywords14print_spellingEv</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#270">_ZNK4PLMD8Keywords14print_templateERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEb</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#547">_ZNK4PLMD8Keywords15print_html_itemERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#518">_ZNK4PLMD8Keywords5printERNS_3LogE</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFnHi">222</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#312">_ZNK4PLMD8Keywords9print_vimEv</a></td>
+              <td class="coverFnHi">292</td>
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+    <tr>
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+              <td class="coverFnHi">796</td>
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+              <td class="coverFnHi">2398</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#657">_ZNK4PLMD8Keywords21getKeywordDescriptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">4486</td>
+            </tr>
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+              <td class="coverFnHi">4679</td>
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+              <td class="coverFnHi">4679</td>
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+            </tr>
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+              <td class="coverFnHi">219537</td>
+            </tr>
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+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#197">_ZN4PLMD8Keywords3addERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_S8_</a></td>
+              <td class="coverFnHi">230553</td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#554">_ZNK4PLMD8Keywords3getB5cxx11Ej</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#179">_ZN4PLMD8Keywords3addERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_</a></td>
+              <td class="coverFnHi">533817</td>
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+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#242">_ZNK4PLMD8Keywords5styleERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">827901</td>
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+              <td class="coverFnHi">1113354</td>
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+              <td class="coverFnHi">1392419</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Keywords.cpp.func.html b/coverage/tools/Keywords.cpp.func.html
new file mode 100644
index 0000000000..b01228ae4f
--- /dev/null
+++ b/coverage/tools/Keywords.cpp.func.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Keywords.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Keywords.cpp<span style="font-size: 80%;"> (<a href="Keywords.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">240</td>
+            <td class="headerCovTableEntry">395</td>
+            <td class="headerCovTableEntryLo">60.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Keywords.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#579">_ZN4PLMD8Keywords11destroyDataEv</a></td>
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+              <td class="coverFnHi">2118</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#172">_ZN4PLMD8Keywords11reset_styleERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">4679</td>
+            </tr>
+    <tr>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFnHi">85623</td>
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+              <td class="coverFnHi">6758</td>
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+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#179">_ZN4PLMD8Keywords3addERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_S8_</a></td>
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+              <td class="coverFnHi">230553</td>
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+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#69">_ZN4PLMD8Keywords3addERKS0_</a></td>
+              <td class="coverFnHi">796</td>
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+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#165">_ZN4PLMD8Keywords3useERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
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+              <td class="coverFnHi">119433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#622">_ZNK4PLMD8Keywords22getOutputComponentFlagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">4523</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#626">_ZNK4PLMD8Keywords29getOutputComponentDescriptionERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2398</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#554">_ZNK4PLMD8Keywords3getB5cxx11Ej</a></td>
+              <td class="coverFnHi">419194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#247">_ZNK4PLMD8Keywords4sizeEv</a></td>
+              <td class="coverFnHi">916902</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#522">_ZNK4PLMD8Keywords5printEP8_IO_FILE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#518">_ZNK4PLMD8Keywords5printERNS_3LogE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#242">_ZNK4PLMD8Keywords5styleERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">827901</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#256">_ZNK4PLMD8Keywords6existsERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1392419</td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#73">_ZNK4PLMD8Keywords8copyDataERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS7_EESA_RSt3mapIS7_NS0_7KeyTypeESt4lessIS7_ESaISt4pairIKS7_SC_EEERSB_IS7_bSE_SaISF_ISG_bEEERSB_IS7_S7_SE_SaISF_ISG_S7_EEESO_SS_SS_SA_SS_SS_</a></td>
+              <td class="coverFnHi">796</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#64">_ZNK4PLMD8Keywords8getStyleERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">832387</td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#236">_ZNK4PLMD8Keywords8numberedERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#263">_ZNK4PLMD8Keywords8reservedERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1133339</td>
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+    <tr>
+              <td class="coverFn"><a href="Keywords.cpp.gcov.html#312">_ZNK4PLMD8Keywords9print_vimEv</a></td>
+              <td class="coverFnHi">292</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Keywords.cpp.gcov.html b/coverage/tools/Keywords.cpp.gcov.html
new file mode 100644
index 0000000000..9da953b4f1
--- /dev/null
+++ b/coverage/tools/Keywords.cpp.gcov.html
@@ -0,0 +1,739 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Keywords.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Keywords.cpp<span style="font-size: 80%;"> (source / <a href="Keywords.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">240</td>
+            <td class="headerCovTableEntry">395</td>
+            <td class="headerCovTableEntryLo">60.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryMed">78.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Keywords.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Log.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;iostream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iomanip&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">    1113354 : Keywords::KeyType::KeyType( const std::string&amp; type ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">    1113354 :   if( type==&quot;compulsory&quot; ) {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     297210 :     style=compulsory;</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">     816144 :   } else if( type==&quot;flag&quot; ) {</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     221655 :     style=flag;</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     594489 :   } else if( type==&quot;optional&quot; ) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     313638 :     style=optional;</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     280851 :   } else if( type.find(&quot;atoms&quot;)!=std::string::npos || type.find(&quot;residues&quot;)!=std::string::npos ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     143376 :     style=atoms;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     137475 :   } else if( type==&quot;hidden&quot; ) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      66619 :     style=hidden;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      70856 :   } else if( type==&quot;vessel&quot; ) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      70856 :     style=vessel;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   } else {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :     plumed_massert(false,&quot;invalid keyword specifier &quot; + type);</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :   }</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">    1113354 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       4679 : void Keywords::KeyType::setStyle( const std::string&amp; type ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       4679 :   if( type==&quot;compulsory&quot; ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         93 :     style=compulsory;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       4586 :   } else if( type==&quot;flag&quot; ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :     style=flag;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       4586 :   } else if( type==&quot;optional&quot; ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         30 :     style=optional;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       4556 :   } else if( type.find(&quot;atoms&quot;)!=std::string::npos || type.find(&quot;residues&quot;)!=std::string::npos ) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        239 :     style=atoms;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       4317 :   } else if( type==&quot;hidden&quot; ) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        149 :     style=hidden;</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       4168 :   } else if( type==&quot;vessel&quot; ) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       4168 :     style=vessel;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   } else {</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :     plumed_massert(false,&quot;invalid keyword specifier &quot; + type);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       4679 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     832387 : std::string Keywords::getStyle( const std::string &amp; k ) const {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   plumed_massert( types.count(k), &quot;Did not find keyword &quot; + k );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     832387 :   return (types.find(k)-&gt;second).toString();</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        796 : void Keywords::add( const Keywords&amp; newkeys ) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        796 :   newkeys.copyData( keys, reserved_keys, types, allowmultiple, documentation, booldefs, numdefs, atomtags, cnames, ckey, cdocs  );</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        796 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        796 : void Keywords::copyData( std::vector&lt;std::string&gt;&amp; kk, std::vector&lt;std::string&gt;&amp; rk, std::map&lt;std::string,KeyType&gt;&amp; tt, std::map&lt;std::string,bool&gt;&amp; am,</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :                          std::map&lt;std::string,std::string&gt;&amp; docs, std::map&lt;std::string,bool&gt;&amp; bools, std::map&lt;std::string,std::string&gt;&amp; nums,</a>
+<a name="77"><span class="lineNum">      77 </span>            :                          std::map&lt;std::string,std::string&gt;&amp; atags, std::vector&lt;std::string&gt;&amp; cnam, std::map&lt;std::string,std::string&gt;&amp; ck,</a>
+<a name="78"><span class="lineNum">      78 </span>            :                          std::map&lt;std::string,std::string&gt;&amp; cd ) const {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        796 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :     std::string thiskey=keys[i];</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;kk.size(); ++j) plumed_massert( thiskey!=kk[j], &quot;keyword &quot; + thiskey + &quot; is in twice&quot; );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;rk.size(); ++j) plumed_massert( thiskey!=rk[j], &quot;keyword &quot; + thiskey + &quot; is in twice&quot; );</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     kk.push_back( thiskey );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :     plumed_massert( types.count( thiskey ), &quot;no type data on keyword &quot; + thiskey + &quot; to copy&quot; );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :     tt.insert( std::pair&lt;std::string,KeyType&gt;( thiskey,types.find(thiskey)-&gt;second) );</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :     if( (types.find(thiskey)-&gt;second).isAtomList() ) atags.insert( std::pair&lt;std::string,std::string&gt;( thiskey,atomtags.find(thiskey)-&gt;second) );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :     plumed_massert( allowmultiple.count( thiskey ), &quot;no numbered data on keyword &quot; + thiskey + &quot; to copy&quot; );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     am.insert( std::pair&lt;std::string,bool&gt;(thiskey,allowmultiple.find(thiskey)-&gt;second) );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :     plumed_massert( documentation.count( thiskey ), &quot;no documentation for keyword &quot; + thiskey + &quot; to copy&quot; );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :     docs.insert( std::pair&lt;std::string,std::string&gt;(thiskey,documentation.find(thiskey)-&gt;second) );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :     if( booldefs.count( thiskey ) ) bools.insert( std::pair&lt;std::string,bool&gt;( thiskey,booldefs.find(thiskey)-&gt;second) );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     if( numdefs.count( thiskey ) ) nums.insert( std::pair&lt;std::string,std::string&gt;( thiskey,numdefs.find(thiskey)-&gt;second) );</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      15124 :   for(unsigned i=0; i&lt;reserved_keys.size(); ++i) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      14328 :     std::string thiskey=reserved_keys[i];</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     140310 :     for(unsigned j=0; j&lt;kk.size(); ++j) plumed_massert( thiskey!=kk[j], &quot;keyword &quot; + thiskey + &quot; is in twice&quot; );</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     198630 :     for(unsigned j=0; j&lt;rk.size(); ++j) plumed_massert( thiskey!=rk[j], &quot;keyword &quot; + thiskey + &quot; is in twice&quot; );</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      14328 :     rk.push_back( thiskey );</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     plumed_massert( types.count( thiskey ), &quot;no type data on keyword &quot; + thiskey + &quot; to copy&quot; );</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      14328 :     tt.insert( std::pair&lt;std::string,KeyType&gt;( thiskey,types.find(thiskey)-&gt;second) );</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">      14328 :     if( (types.find(thiskey)-&gt;second).isAtomList() ) atags.insert( std::pair&lt;std::string,std::string&gt;( thiskey,atomtags.find(thiskey)-&gt;second) );</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :     plumed_massert( allowmultiple.count( thiskey ), &quot;no numbered data on keyword &quot; + thiskey + &quot; to copy&quot; );</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      14328 :     am.insert( std::pair&lt;std::string,bool&gt;(thiskey,allowmultiple.find(thiskey)-&gt;second) );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     plumed_massert( documentation.count( thiskey ), &quot;no documentation for keyword &quot; + thiskey + &quot; to copy&quot; );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      28656 :     docs.insert( std::pair&lt;std::string,std::string&gt;(thiskey,documentation.find(thiskey)-&gt;second) );</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :     if( booldefs.count( thiskey ) ) bools.insert( std::pair&lt;std::string,bool&gt;( thiskey,booldefs.find(thiskey)-&gt;second) );</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :     if( numdefs.count( thiskey ) ) nums.insert( std::pair&lt;std::string,std::string&gt;( thiskey,numdefs.find(thiskey)-&gt;second) );</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      15124 :   for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      14328 :     std::string thisnam=cnames[i];</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">     136116 :     for(unsigned j=0; j&lt;cnam.size(); ++j) plumed_massert( thisnam!=cnam[j], &quot;component &quot; + thisnam + &quot; is in twice&quot; );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      14328 :     cnam.push_back( thisnam );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :     plumed_massert( ckey.count( thisnam ), &quot;no keyword data on component &quot; + thisnam + &quot; to copy&quot; );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      28656 :     ck.insert( std::pair&lt;std::string,std::string&gt;( thisnam, ckey.find(thisnam)-&gt;second) );</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     plumed_massert( cdocs.count( thisnam ), &quot;no documentation on component &quot; + thisnam + &quot; to copy&quot; );</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      28656 :     cd.insert( std::pair&lt;std::string,std::string&gt;( thisnam, cdocs.find(thisnam)-&gt;second) );</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        796 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     127329 : void Keywords::reserve( const std::string &amp; t, const std::string &amp; k, const std::string &amp; d ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     127329 :   plumed_assert( !exists(k) &amp;&amp; !reserved(k) );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     127329 :   std::string fd, lowkey=k;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   // Convert to lower case</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">    1078677 :   std::transform(lowkey.begin(),lowkey.end(),lowkey.begin(),[](unsigned char c) { return std::tolower(c); });</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : // Remove any underscore characters</a>
+<a name="126"><span class="lineNum">     126 </span>            :   for(unsigned i=0;; ++i) {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     172466 :     std::size_t num=lowkey.find_first_of(&quot;_&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">     172466 :     if( num==std::string::npos ) break;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      45137 :     lowkey.erase( lowkey.begin() + num, lowkey.begin() + num + 1 );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      45137 :   }</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     127329 :   if( t==&quot;vessel&quot; ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     141712 :     fd = d + &quot; The final value can be referenced using &lt;em&gt;label&lt;/em&gt;.&quot; + lowkey;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">     133376 :     if(d.find(&quot;flag&quot;)==std::string::npos) fd += &quot;.  You can use multiple instances of this keyword i.e. &quot; +</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     125040 :           k +&quot;1, &quot; + k + &quot;2, &quot; + k + &quot;3...  The corresponding values are then &quot;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">     125040 :           &quot;referenced using &lt;em&gt;label&lt;/em&gt;.&quot;+ lowkey +&quot;-1,  &lt;em&gt;label&lt;/em&gt;.&quot; + lowkey +</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     125040 :           &quot;-2,  &lt;em&gt;label&lt;/em&gt;.&quot; + lowkey + &quot;-3...&quot;;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      70856 :     allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,true) );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">     141712 :     types.insert( std::pair&lt;std::string,KeyType&gt;(k,KeyType(&quot;vessel&quot;)) );</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      56473 :   } else if( t==&quot;numbered&quot; ) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       6318 :     fd = d + &quot;. You can use multiple instances of this keyword i.e. &quot; + k +&quot;1, &quot; + k + &quot;2, &quot; + k + &quot;3...&quot;;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       3159 :     allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,true) );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       6318 :     types.insert( std::pair&lt;std::string,KeyType&gt;(k,KeyType(&quot;optional&quot;)) );</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   } else {</a>
+<a name="144"><span class="lineNum">     144 </span>            :     fd = d;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      53314 :     if( t==&quot;atoms&quot; &amp;&amp; isaction ) fd = d + &quot;.  For more information on how to specify lists of atoms see \\ref Group&quot;;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      53314 :     allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,false) );</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">     106628 :     types.insert( std::pair&lt;std::string,KeyType&gt;(k,KeyType(t)) );</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      54817 :     if( (types.find(k)-&gt;second).isAtomList() ) atomtags.insert( std::pair&lt;std::string,std::string&gt;(k,t) );</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">     127329 :   documentation.insert( std::pair&lt;std::string,std::string&gt;(k,fd) );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">     127329 :   reserved_keys.push_back(k);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     127329 : }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       2118 : void Keywords::reserveFlag( const std::string &amp; k, const bool def, const std::string &amp; d ) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       2118 :   plumed_assert( !exists(k) &amp;&amp; !reserved(k) );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   std::string defstr;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       2118 :   if( def ) { defstr=&quot;( default=on ) &quot;; } else { defstr=&quot;( default=off ) &quot;; }</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       4236 :   types.insert( std::pair&lt;std::string,KeyType&gt;(k,KeyType(&quot;flag&quot;)) );</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      25931 :   std::string fd,lowkey=k; std::transform(lowkey.begin(),lowkey.end(),lowkey.begin(),[](unsigned char c) { return std::tolower(c); });</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       2118 :   fd=defstr + d;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       4236 :   documentation.insert( std::pair&lt;std::string,std::string&gt;(k,fd) );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       2118 :   allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,false) );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   booldefs.insert( std::pair&lt;std::string,bool&gt;(k,def) );</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       2118 :   reserved_keys.push_back(k);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       2118 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      15681 : void Keywords::use( const std::string &amp; k ) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      15681 :   plumed_massert( reserved(k), &quot;the &quot; + k + &quot; keyword is not reserved&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     199333 :   for(unsigned i=0; i&lt;reserved_keys.size(); ++i) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     183652 :     if(reserved_keys[i]==k) keys.push_back( reserved_keys[i] );</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      15681 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       4679 : void Keywords::reset_style( const std::string &amp; k, const std::string &amp; style ) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       4679 :   plumed_massert( exists(k) || reserved(k), &quot;no &quot; + k + &quot; keyword&quot; );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       4679 :   (types.find(k)-&gt;second).setStyle(style);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       4679 :   if( (types.find(k)-&gt;second).isVessel() ) allowmultiple[k]=true;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       4918 :   if( (types.find(k)-&gt;second).isAtomList() ) atomtags.insert( std::pair&lt;std::string,std::string&gt;(k,style) );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       4679 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     533817 : void Keywords::add( const std::string &amp; t, const std::string &amp; k, const std::string &amp; d ) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    1601451 :   plumed_massert( !exists(k) &amp;&amp; t!=&quot;flag&quot; &amp;&amp; !reserved(k) &amp;&amp; t!=&quot;vessel&quot;, &quot;keyword &quot; + k + &quot; has already been registered&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   std::string fd;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     533817 :   if( t==&quot;numbered&quot; ) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       3106 :     fd=d + &quot;. You can use multiple instances of this keyword i.e. &quot; + k +&quot;1, &quot; + k + &quot;2, &quot; + k + &quot;3...&quot;;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       1553 :     allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,true) );</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       3106 :     types.insert( std::pair&lt;std::string,KeyType&gt;(k, KeyType(&quot;optional&quot;)) );</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   } else {</a>
+<a name="189"><span class="lineNum">     189 </span>            :     fd=d;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">     532264 :     allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,false) );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">    1064528 :     types.insert( std::pair&lt;std::string,KeyType&gt;(k,KeyType(t)) );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">     674137 :     if( (types.find(k)-&gt;second).isAtomList() ) atomtags.insert( std::pair&lt;std::string,std::string&gt;(k,t) );</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     551511 :   if( t==&quot;atoms&quot; &amp;&amp; isaction ) fd = d + &quot;.  For more information on how to specify lists of atoms see \\ref Group&quot;;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     533817 :   documentation.insert( std::pair&lt;std::string,std::string&gt;(k,fd) );</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     533817 :   keys.push_back(k);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">     533817 : }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">     230553 : void Keywords::add( const std::string &amp; t, const std::string &amp; k, const std::string &amp;  def, const std::string &amp; d ) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">     461106 :   plumed_assert( !exists(k) &amp;&amp; !reserved(k) &amp;&amp;  (t==&quot;compulsory&quot; || t==&quot;hidden&quot; )); // An optional keyword can't have a default</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     230553 :   types.insert(  std::pair&lt;std::string,KeyType&gt;(k, KeyType(t)) );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     461106 :   documentation.insert( std::pair&lt;std::string,std::string&gt;(k,&quot;( default=&quot; + def + &quot; ) &quot; + d) );</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     230553 :   allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,false) );</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     230553 :   numdefs.insert( std::pair&lt;std::string,std::string&gt;(k,def) );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     230553 :   keys.push_back(k);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">     230553 : }</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     219537 : void Keywords::addFlag( const std::string &amp; k, const bool def, const std::string &amp; d ) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     219537 :   plumed_massert( !exists(k) &amp;&amp; !reserved(k), &quot;keyword &quot; + k + &quot; has already been registered&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     219537 :   std::string defstr; plumed_massert( !def, &quot;the second argument to addFlag must be false &quot; + k );</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   defstr=&quot;( default=off ) &quot;;</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     439074 :   types.insert( std::pair&lt;std::string,KeyType&gt;(k,KeyType(&quot;flag&quot;)) );</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">     439074 :   documentation.insert( std::pair&lt;std::string,std::string&gt;(k,defstr + d) );</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">     219537 :   allowmultiple.insert( std::pair&lt;std::string,bool&gt;(k,false) );</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :   booldefs.insert( std::pair&lt;std::string,bool&gt;(k,def) );</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     219537 :   keys.push_back(k);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     219537 : }</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1585 : void Keywords::remove( const std::string &amp; k ) {</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   bool found=false; unsigned j=0, n=0;</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            :   while(true) {</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      17980 :     for(j=0; j&lt;keys.size(); j++) if(keys[j]==k)break;</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      37620 :     for(n=0; n&lt;reserved_keys.size(); n++) if(reserved_keys[n]==k)break;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       3170 :     if(j&lt;keys.size()) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">       1491 :       keys.erase(keys.begin()+j);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :       found=true;</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       1679 :     } else if(n&lt;reserved_keys.size()) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         94 :       reserved_keys.erase(reserved_keys.begin()+n);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       found=true;</a>
+<a name="231"><span class="lineNum">     231 </span>            :     } else break;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span>            :   // Delete documentation, type and so on from the description</a>
+<a name="234"><span class="lineNum">     234 </span>            :   types.erase(k); documentation.erase(k); allowmultiple.erase(k); booldefs.erase(k); numdefs.erase(k);</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       1585 :   plumed_massert(found,&quot;You are trying to forbid &quot; + k + &quot; a keyword that isn't there&quot;); // You have tried to forbid a keyword that isn't there</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       1585 : }</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      12781 : bool Keywords::numbered( const std::string &amp; k ) const {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      25562 :   if( style( k,&quot;atoms&quot;) ) return true;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :   plumed_massert( allowmultiple.count(k), &quot;Did not find keyword &quot; + k );</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">      10526 :   return allowmultiple.find(k)-&gt;second;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">     827901 : bool Keywords::style( const std::string &amp; k, const std::string &amp; t ) const {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">     827901 :   if( getStyle(k)==t ) return true;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   return false;</a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">     916902 : unsigned Keywords::size() const {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">     916902 :   return keys.size();</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      27663 : std::string Keywords::getKeyword( const unsigned i ) const {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">      27663 :   plumed_assert( i&lt;size() );</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">      27663 :   return keys[i];</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : }</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">    1392419 : bool Keywords::exists( const std::string &amp; k ) const {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">   14982399 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">   13822984 :     if( keys[i]==k ) return true;</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span>            :   return false;</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">    1133339 : bool Keywords::reserved( const std::string &amp; k ) const {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">    2588147 :   for(unsigned i=0; i&lt;reserved_keys.size(); ++i) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">    1474793 :     if( reserved_keys[i]==k ) return true;</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span>            :   return false;</a>
+<a name="270"><span class="lineNum">     270 </span>            : }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 : void Keywords::print_template(const std::string&amp; actionname, bool include_optional) const {</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :   unsigned nkeys=0;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   std::printf(&quot;%s&quot;,actionname.c_str());</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     if ( (types.find(keys[i])-&gt;second).isAtomList() ) nkeys++;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   }</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   if( nkeys&gt;0 ) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :     std::string prevtag=&quot;start&quot;;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :       if( (types.find(keys[i])-&gt;second).isAtomList() ) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :         plumed_massert( atomtags.count(keys[i]), &quot;keyword &quot; + keys[i] + &quot; allegedly specifies atoms but no tag has been specified. Please email Gareth Tribello&quot;);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :         if( prevtag!=&quot;start&quot; &amp;&amp; prevtag!=atomtags.find(keys[i])-&gt;second ) break;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :         if( (atomtags.find(keys[i])-&gt;second).find(&quot;residues&quot;)!=std::string::npos) std::printf(&quot; %s=&lt;residue selection&gt;&quot;, keys[i].c_str() );</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :         else std::printf(&quot; %s=&lt;atom selection&gt;&quot;, keys[i].c_str() );</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :         prevtag=atomtags.find(keys[i])-&gt;second;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :       }</a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span>            :   nkeys=0;</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :     if ( include_optional || \</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :          (types.find(keys[i])-&gt;second).isCompulsory() ) nkeys++;</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   }</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :   if( nkeys&gt;0 ) {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :       if ( (types.find(keys[i])-&gt;second).isCompulsory() ) {</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :         std::string def;</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :         if( getDefaultValue( keys[i], def) ) {</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :           std::printf(&quot; %s=%s &quot;, keys[i].c_str(), def.c_str() );</a>
+<a name="301"><span class="lineNum">     301 </span>            :         } else {</a>
+<a name="302"><span class="lineNum">     302 </span>            :           std::printf(&quot; %s=    &quot;, keys[i].c_str() );</a>
+<a name="303"><span class="lineNum">     303 </span>            :         }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :       } else if (include_optional) {</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :         // TG no defaults for optional keywords?</a>
+<a name="306"><span class="lineNum">     306 </span>            :         std::printf(&quot; [%s]&quot;, keys[i].c_str() );</a>
+<a name="307"><span class="lineNum">     307 </span>            :       }</a>
+<a name="308"><span class="lineNum">     308 </span>            :     }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   }</a>
+<a name="310"><span class="lineNum">     310 </span>            :   std::printf(&quot;\n&quot;);</a>
+<a name="311"><span class="lineNum">     311 </span>            :   std::flush(std::cout);</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">        292 : void Keywords::print_vim() const {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       4778 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">       4486 :     if( (types.find(keys[i])-&gt;second).isFlag() ) {</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :       std::printf( &quot;,flag:%s&quot;, keys[i].c_str() );</a>
+<a name="318"><span class="lineNum">     318 </span>            :     } else {</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       3535 :       if( allowmultiple.find(keys[i])-&gt;second ) std::printf(&quot;,numbered:%s&quot;,keys[i].c_str() );</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :       else std::printf(&quot;,option:%s&quot;,keys[i].c_str() );</a>
+<a name="321"><span class="lineNum">     321 </span>            :     }</a>
+<a name="322"><span class="lineNum">     322 </span>            :   }</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        292 :   std::fprintf(stdout, &quot;\n%s&quot;, getHelpString().c_str() );</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        292 : }</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 : void Keywords::print_html() const {</span></a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            : // This is the part that outputs the details of the components</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :   if( cnames.size()&gt;0 ) {</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     unsigned ndef=0;</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :       if(ckey.find(cnames[i])-&gt;second==&quot;default&quot;) ndef++;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :     if( ndef&gt;0 ) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 :       std::cout&lt;&lt;&quot;\\par Description of components\n\n&quot;;</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :       std::cout&lt;&lt;cstring&lt;&lt;&quot;\n\n&quot;;</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :       std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :       std::printf(&quot;&lt;tr&gt; &lt;td width=5%%&gt; &lt;b&gt; Quantity &lt;/b&gt; &lt;/td&gt; &lt;td&gt; &lt;b&gt; Description &lt;/b&gt; &lt;/td&gt; &lt;/tr&gt;\n&quot;);</a>
+<a name="340"><span class="lineNum">     340 </span>            :       unsigned nndef=0;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :         //plumed_assert( ckey.find(cnames[i])-&gt;second==&quot;default&quot; );</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :         if( ckey.find(cnames[i])-&gt;second!=&quot;default&quot; ) { nndef++; continue; }</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :         std::printf(&quot;&lt;tr&gt;\n&quot;);</a>
+<a name="345"><span class="lineNum">     345 </span>            :         std::printf(&quot;&lt;td width=15%%&gt; &lt;b&gt; %s &lt;/b&gt;&lt;/td&gt;\n&quot;,cnames[i].c_str() );</a>
+<a name="346"><span class="lineNum">     346 </span>            :         std::printf(&quot;&lt;td&gt; %s &lt;/td&gt;\n&quot;,(cdocs.find(cnames[i])-&gt;second).c_str() );</a>
+<a name="347"><span class="lineNum">     347 </span>            :         std::printf(&quot;&lt;/tr&gt;\n&quot;);</a>
+<a name="348"><span class="lineNum">     348 </span>            :       }</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :       std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :       if( nndef&gt;0 ) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot;In addition the following quantities can be calculated by employing the keywords listed below&quot;&lt;&lt;std::endl;</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot;\n\n&quot;;</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :         std::printf(&quot;&lt;tr&gt; &lt;td width=5%%&gt; &lt;b&gt; Quantity &lt;/b&gt; &lt;/td&gt; &lt;td&gt; &lt;b&gt; Keyword &lt;/b&gt; &lt;/td&gt; &lt;td&gt; &lt;b&gt; Description &lt;/b&gt; &lt;/td&gt; &lt;/tr&gt;\n&quot;);</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :           if( ckey.find(cnames[i])-&gt;second!=&quot;default&quot;) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :             std::printf(&quot;&lt;tr&gt;\n&quot;);</a>
+<a name="358"><span class="lineNum">     358 </span>            :             std::printf(&quot;&lt;td width=5%%&gt; &lt;b&gt; %s &lt;/b&gt;&lt;/td&gt; &lt;td width=10%%&gt; &lt;b&gt; %s &lt;/b&gt; &lt;/td&gt; \n&quot;,</a>
+<a name="359"><span class="lineNum">     359 </span>            :                         cnames[i].c_str(),(ckey.find(cnames[i])-&gt;second).c_str() );</a>
+<a name="360"><span class="lineNum">     360 </span>            :             std::printf(&quot;&lt;td&gt; %s &lt;/td&gt;\n&quot;,(cdocs.find(cnames[i])-&gt;second).c_str() );</a>
+<a name="361"><span class="lineNum">     361 </span>            :             std::printf(&quot;&lt;/tr&gt;\n&quot;);</a>
+<a name="362"><span class="lineNum">     362 </span>            :           }</a>
+<a name="363"><span class="lineNum">     363 </span>            :         }</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :       }</a>
+<a name="366"><span class="lineNum">     366 </span>            :     } else {</a>
+<a name="367"><span class="lineNum">     367 </span>            :       unsigned nregs=0;</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :         if( exists(ckey.find(cnames[i])-&gt;second) ) nregs++;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :       }</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :       if( nregs&gt;0 ) {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot;\\par Description of components\n\n&quot;;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;cstring&lt;&lt;&quot;\n\n&quot;;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :         std::printf(&quot;&lt;tr&gt; &lt;td width=5%%&gt; &lt;b&gt; Quantity &lt;/b&gt; &lt;/td&gt; &lt;td&gt; &lt;b&gt; Keyword &lt;/b&gt; &lt;/td&gt; &lt;td&gt; &lt;b&gt; Description &lt;/b&gt; &lt;/td&gt; &lt;/tr&gt;\n&quot;);</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :           if( exists(ckey.find(cnames[i])-&gt;second) ) {</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :             std::printf(&quot;&lt;tr&gt;\n&quot;);</a>
+<a name="379"><span class="lineNum">     379 </span>            :             std::printf(&quot;&lt;td width=5%%&gt; &lt;b&gt; %s &lt;/b&gt;&lt;/td&gt; &lt;td width=10%%&gt; &lt;b&gt; %s &lt;/b&gt; &lt;/td&gt; \n&quot;,</a>
+<a name="380"><span class="lineNum">     380 </span>            :                         cnames[i].c_str(),(ckey.find(cnames[i])-&gt;second).c_str() );</a>
+<a name="381"><span class="lineNum">     381 </span>            :             std::printf(&quot;&lt;td&gt; %s &lt;/td&gt;\n&quot;,(cdocs.find(cnames[i])-&gt;second).c_str() );</a>
+<a name="382"><span class="lineNum">     382 </span>            :             std::printf(&quot;&lt;/tr&gt;\n&quot;);</a>
+<a name="383"><span class="lineNum">     383 </span>            :           }</a>
+<a name="384"><span class="lineNum">     384 </span>            :         }</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :         std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :       }</a>
+<a name="387"><span class="lineNum">     387 </span>            :     }</a>
+<a name="388"><span class="lineNum">     388 </span>            :   }</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span>            :   unsigned nkeys=0;</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 :     if ( (types.find(keys[i])-&gt;second).isAtomList() ) nkeys++;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :   }</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :   if( nkeys&gt;0 ) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :     if(isaction &amp;&amp; isatoms) std::cout&lt;&lt;&quot;\\par The atoms involved can be specified using\n\n&quot;;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :     else if(isaction) std::cout&lt;&lt;&quot;\\par The data to analyze can be the output from another analysis algorithm\n\n&quot;;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :     else std::cout&lt;&lt;&quot;\\par The input trajectory is specified using one of the following\n\n&quot;;</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :     std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 :     std::string prevtag=&quot;start&quot;; unsigned counter=0;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :       if ( (types.find(keys[i])-&gt;second).isAtomList() ) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :         plumed_massert( atomtags.count(keys[i]), &quot;keyword &quot; + keys[i] + &quot; allegedly specifies atoms but no tag has been specified. Please email Gareth Tribello&quot;);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :         if( prevtag!=&quot;start&quot; &amp;&amp; prevtag!=atomtags.find(keys[i])-&gt;second &amp;&amp; isaction ) {</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 :           std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :           if( isatoms ) std::cout&lt;&lt;&quot;\\par Or alternatively by using\n\n&quot;;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineNoCov">          0 :           else if( counter==0 ) { std::cout&lt;&lt;&quot;\\par Alternatively data can be collected from the trajectory using \n\n&quot;; counter++; }</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 :           else std::cout&lt;&lt;&quot;\\par Lastly data collected in a previous analysis action can be reanalyzed by using the keyword \n\n&quot;;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :           std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :         }</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :         print_html_item( keys[i] );</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineNoCov">          0 :         prevtag=atomtags.find(keys[i])-&gt;second;</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :       }</a>
+<a name="413"><span class="lineNum">     413 </span>            :     }</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineNoCov">          0 :     std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   }</a>
+<a name="416"><span class="lineNum">     416 </span>            :   nkeys=0;</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :     if ( (types.find(keys[i])-&gt;second).isCompulsory() ) nkeys++;</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :   }</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineNoCov">          0 :   if( nkeys&gt;0 ) {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineNoCov">          0 :     if(isaction) std::cout&lt;&lt; &quot;\\par Compulsory keywords\n\n&quot;;</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 :     else std::cout&lt;&lt;&quot;\\par The following must be present\n\n&quot;;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :     std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :       if ( (types.find(keys[i])-&gt;second).isCompulsory() ) print_html_item( keys[i] );</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :     }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 :     std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :   }</a>
+<a name="429"><span class="lineNum">     429 </span>            :   nkeys=0;</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :     if ( (types.find(keys[i])-&gt;second).isFlag() || (types.find(keys[i])-&gt;second).isOptional() || (types.find(keys[i])-&gt;second).isVessel() ) nkeys++;</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :   }</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :   if( nkeys&gt;0 ) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     if(isaction) std::cout&lt;&lt;&quot;\\par Options\n\n&quot;;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :     else std::cout&lt;&lt;&quot;\\par The following options are available\n\n&quot;;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineNoCov">          0 :     std::cout&lt;&lt;&quot; &lt;table align=center frame=void width=95%% cellpadding=5%%&gt; \n&quot;;</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :       if ( (types.find(keys[i])-&gt;second).isFlag() ) print_html_item( keys[i] );</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     }</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :     std::cout&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   }</a>
+<a name="442"><span class="lineNum">     442 </span>            :   nkeys=0;</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 :     if ( (types.find(keys[i])-&gt;second).isOptional() || (types.find(keys[i])-&gt;second).isVessel() ) nkeys++;</span></a>
+<a name="445"><span class="lineNum">     445 </span>            :   }</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineNoCov">          0 :   if( nkeys&gt;0 ) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :       if ( (types.find(keys[i])-&gt;second).isOptional() || (types.find(keys[i])-&gt;second).isVessel() ) print_html_item( keys[i] );</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :     }</a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :   std::cout&lt;&lt;&quot;&lt;/table&gt;\n\n&quot;;</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 : void Keywords::print_spelling() const {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;keys.size(); ++i) std::printf(&quot;%s\n&quot;, keys[i].c_str() );</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;cnames.size(); ++i) std::printf(&quot;%s\n&quot;,cnames[i].c_str() );</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">       7064 : std::string Keywords::getKeywordDocs( const std::string&amp; key ) const {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">       7064 :   bool killdot=( (documentation.find(key)-&gt;second).find(&quot;\\f$&quot;)!=std::string::npos ); // Check for latex</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">       7064 :   std::vector&lt;std::string&gt; w=Tools::getWords( documentation.find(key)-&gt;second );</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">      14128 :   std::stringstream sstr; sstr&lt;&lt;std::setw(23)&lt;&lt;key&lt;&lt;&quot; - &quot;;</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">       7064 :   unsigned nl=0; std::string blank=&quot; &quot;;</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">     149960 :   for(unsigned i=0; i&lt;w.size(); ++i) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">     143434 :     nl+=w[i].length() + 1;</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">     143434 :     if( nl&gt;60 ) {</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">      33114 :       sstr&lt;&lt;&quot;\n&quot;&lt;&lt;std::setw(23)&lt;&lt;blank&lt;&lt;&quot;   &quot;&lt;&lt;w[i]&lt;&lt;&quot; &quot;; nl=0;</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">     132396 :     } else sstr&lt;&lt;w[i]&lt;&lt;&quot; &quot;;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">     143434 :     if( killdot &amp;&amp; w[i].find(&quot;.&quot;)!=std::string::npos ) break; // If there is latex only write up to first dot</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :   }</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">      14128 :   sstr&lt;&lt;&quot;\n&quot;; return sstr.str();</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">       7064 : }</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        584 : std::string Keywords::getHelpString() const {</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :   std::string helpstr; unsigned nkeys=0;</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">       9556 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">       8972 :     if ( (types.find(keys[i])-&gt;second).isAtomList() ) nkeys++;</span></a>
+<a name="478"><span class="lineNum">     478 </span>            :   }</a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        584 :   if( nkeys&gt;0 ) {</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :     helpstr += &quot;The input trajectory can be in any of the following formats: \n\n&quot;;</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">       5254 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">       5534 :       if ( (types.find(keys[i])-&gt;second).isAtomList() ) helpstr += getKeywordDocs( keys[i] );</span></a>
+<a name="483"><span class="lineNum">     483 </span>            :     }</a>
+<a name="484"><span class="lineNum">     484 </span>            :   }</a>
+<a name="485"><span class="lineNum">     485 </span>            :   nkeys=0;</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">       9556 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">       8972 :     if ( (types.find(keys[i])-&gt;second).isCompulsory() ) nkeys++;</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   }</a>
+<a name="489"><span class="lineNum">     489 </span>            :   unsigned ncompulsory=nkeys;</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        584 :   if( nkeys&gt;0 ) {</span></a>
+<a name="491"><span class="lineNum">     491 </span>            :     helpstr += &quot;\nThe following arguments are compulsory: \n\n&quot;;</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">       7824 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">       9118 :       if ( (types.find(keys[i])-&gt;second).isCompulsory() ) helpstr += getKeywordDocs( keys[i] );</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :     }</a>
+<a name="495"><span class="lineNum">     495 </span>            :   }</a>
+<a name="496"><span class="lineNum">     496 </span>            :   nkeys=0;</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">       9556 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">       8972 :     if ( (types.find(keys[i])-&gt;second).isFlag() ) nkeys++;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :   }</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        584 :   if( nkeys&gt;0 ) {</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        518 :     if(ncompulsory&gt;0) helpstr += &quot;\nIn addition you may use the following options: \n\n&quot;;</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :     else helpstr += &quot;\nThe following options are available\n\n&quot;;</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">       9126 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">      10510 :       if ( (types.find(keys[i])-&gt;second).isFlag() ) helpstr += getKeywordDocs( keys[i] ).c_str();</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     }</a>
+<a name="506"><span class="lineNum">     506 </span>            :   }</a>
+<a name="507"><span class="lineNum">     507 </span>            :   nkeys=0;</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">       9556 :   for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">      16134 :     if ( (types.find(keys[i])-&gt;second).isOptional() || (types.find(keys[i])-&gt;second).isVessel() ) nkeys++;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            :   }</a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">        584 :   if( nkeys&gt;0 ) {</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">       8318 :     for(unsigned i=0; i&lt;keys.size(); ++i) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">      16802 :       if ( (types.find(keys[i])-&gt;second).isOptional() || (types.find(keys[i])-&gt;second).isVessel() ) helpstr += getKeywordDocs( keys[i] );</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :     }</a>
+<a name="515"><span class="lineNum">     515 </span>            :     helpstr += &quot;\n&quot;;</a>
+<a name="516"><span class="lineNum">     516 </span>            :   }</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">        584 :   return helpstr;</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : }</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 : void Keywords::print( Log&amp; log ) const {</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :   log.printf(&quot;%s&quot;, getHelpString().c_str() );</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 : void Keywords::print( FILE* out ) const {</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :   fprintf( out,&quot;%s&quot;, getHelpString().c_str() );</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 : std::string Keywords::getTooltip( const std::string&amp; name ) const {</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :   std::size_t dd=name.find_first_of(&quot;0123456789&quot;); std::string kname=name.substr(0,dd);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :   if( !exists(kname) ) return &quot;&lt;b&gt; could not find this keyword &lt;/b&gt;&quot;;</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 :   std::string mystring, docstr = documentation.find(kname)-&gt;second;</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :   if( types.find(kname)-&gt;second.isCompulsory() ) {</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :     mystring += &quot;&lt;b&gt;compulsory keyword &quot;;</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :     if( docstr.find(&quot;default&quot;)!=std::string::npos ) {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :       std::size_t bra = docstr.find_first_of(&quot;)&quot;); mystring += docstr.substr(0,bra+1); docstr = docstr.substr(bra+1);</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :     }</a>
+<a name="537"><span class="lineNum">     537 </span>            :     mystring += &quot;&lt;/b&gt;\n&quot;;</a>
+<a name="538"><span class="lineNum">     538 </span>            :   }</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :   std::vector&lt;std::string&gt; w=Tools::getWords( docstr ); unsigned nl=0;</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;w.size(); ++i) {</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :     nl+=w[i].length() + 1;</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :     if( nl&gt;80 ) { mystring += w[i] + &quot;\n&quot;; nl=0; }</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     else { mystring += w[i] + &quot; &quot;; }</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :     if( w[i].find(&quot;.&quot;)!=std::string::npos ) break; // Only write up the the first dot</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :   }</a>
+<a name="546"><span class="lineNum">     546 </span>            :   return mystring;</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineNoCov">          0 : void Keywords::print_html_item( const std::string&amp; key ) const {</span></a>
+<a name="550"><span class="lineNum">     550 </span>            :   std::printf(&quot;&lt;tr&gt;\n&quot;);</a>
+<a name="551"><span class="lineNum">     551 </span>            :   std::printf(&quot;&lt;td width=15%%&gt; &lt;b&gt; %s &lt;/b&gt;&lt;/td&gt;\n&quot;,key.c_str() );</a>
+<a name="552"><span class="lineNum">     552 </span>            :   std::printf(&quot;&lt;td&gt; %s &lt;/td&gt;\n&quot;,(documentation.find(key)-&gt;second).c_str() );</a>
+<a name="553"><span class="lineNum">     553 </span>            :   std::printf(&quot;&lt;/tr&gt;\n&quot;);</a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">     419194 : std::string Keywords::get( const unsigned k ) const {</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">     419194 :   plumed_assert( k&lt;size() );</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">     419194 :   return keys[k];</span></a>
+<a name="559"><span class="lineNum">     559 </span>            : }</a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">      36898 : bool Keywords::getLogicalDefault(const std::string &amp; key, bool&amp; def ) const {</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">      36898 :   if( booldefs.find(key)!=booldefs.end() ) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">      36898 :     def=booldefs.find(key)-&gt;second;</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">      36898 :     return true;</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :   } else {</a>
+<a name="566"><span class="lineNum">     566 </span>            :     return false;</a>
+<a name="567"><span class="lineNum">     567 </span>            :   }</a>
+<a name="568"><span class="lineNum">     568 </span>            : }</a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">      11123 : bool Keywords::getDefaultValue(const std::string &amp; key, std::string&amp; def ) const {</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">      21893 :   plumed_assert( style(key,&quot;compulsory&quot;) || style(key,&quot;hidden&quot;) );</span></a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">      11123 :   if( numdefs.find(key)!=numdefs.end() ) {</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">       5738 :     def=numdefs.find(key)-&gt;second;</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">       5738 :     return true;</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :   } else {</a>
+<a name="577"><span class="lineNum">     577 </span>            :     return false;</a>
+<a name="578"><span class="lineNum">     578 </span>            :   }</a>
+<a name="579"><span class="lineNum">     579 </span>            : }</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineNoCov">          0 : void Keywords::destroyData() {</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 :   keys.clear(); reserved_keys.clear(); types.clear();</span></a>
+<a name="583"><span class="lineNum">     583 </span>            :   allowmultiple.clear(); documentation.clear();</a>
+<a name="584"><span class="lineNum">     584 </span>            :   booldefs.clear(); numdefs.clear(); atomtags.clear();</a>
+<a name="585"><span class="lineNum">     585 </span>            :   ckey.clear(); cdocs.clear(); ckey.clear();</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">       6758 : void Keywords::setComponentsIntroduction( const std::string&amp; instr ) {</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">       6758 :   cstring = instr;</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">       6758 : }</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">      85623 : void Keywords::addOutputComponent( const std::string&amp; name, const std::string&amp; key, const std::string&amp; descr ) {</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">      85623 :   plumed_assert( !outputComponentExists( name, false ) );</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">      85623 :   plumed_massert( name.find(&quot;-&quot;)==std::string::npos,&quot;dash is reseved character in component names&quot; );</span></a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">      85623 :   std::size_t num2=name.find_first_of(&quot;_&quot;);</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">      85623 :   if( num2!=std::string::npos ) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">        318 :     char uu = '_'; plumed_massert( std::count(name.begin(),name.end(), uu)==1, &quot;underscore is reserved character in component names and there should only be one&quot;);</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">        318 :     plumed_massert( num2==0, &quot;underscore is reserved character in component names that has special meaning&quot;);</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :   }</a>
+<a name="601"><span class="lineNum">     601 </span>            : </a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">      85623 :   ckey.insert( std::pair&lt;std::string,std::string&gt;(name,key) );</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">      85623 :   cdocs.insert( std::pair&lt;std::string,std::string&gt;(name,descr) );</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">      85623 :   cnames.push_back(name);</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">      85623 : }</span></a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">     119433 : bool Keywords::outputComponentExists( const std::string&amp; name, const bool&amp; custom ) const {</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">     119433 :   if( custom &amp;&amp; cstring.find(&quot;customize&quot;)!=std::string::npos ) return true;</span></a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span>            :   std::string sname;</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">     115972 :   std::size_t num=name.find_first_of(&quot;-&quot;);</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">     115972 :   std::size_t num2=name.find_last_of(&quot;_&quot;);</span></a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">     117910 :   if( num2!=std::string::npos ) sname=name.substr(num2);</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">     139969 :   else if( num!=std::string::npos ) sname=name.substr(0,num);</span></a>
+<a name="616"><span class="lineNum">     616 </span>            :   else sname=name;</a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">    1101134 :   for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">    1015511 :     if( sname==cnames[i] ) return true;</span></a>
+<a name="620"><span class="lineNum">     620 </span>            :   }</a>
+<a name="621"><span class="lineNum">     621 </span>            :   return false;</a>
+<a name="622"><span class="lineNum">     622 </span>            : }</a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">       4523 : std::string Keywords::getOutputComponentFlag( const std::string&amp; name ) const {</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">       4523 :   return ckey.find(name)-&gt;second;</span></a>
+<a name="626"><span class="lineNum">     626 </span>            : }</a>
+<a name="627"><span class="lineNum">     627 </span>            : </a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">       2398 : std::string Keywords::getOutputComponentDescription( const std::string&amp; name ) const {</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">       2398 :   if( cstring.find(&quot;customized&quot;)!=std::string::npos ) return &quot;the label of this action is set by user in the input. See documentation above.&quot;;</span></a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            :   bool found=false;</a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">      42138 :   for(unsigned i=0; i&lt;cnames.size(); ++i) {</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">      39796 :     if( name==cnames[i] ) found=true;</span></a>
+<a name="634"><span class="lineNum">     634 </span>            :   }</a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">       2342 :   if( !found ) plumed_merror(&quot;could not find output component named &quot; + name );</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       2342 :   return cdocs.find(name)-&gt;second;</span></a>
+<a name="637"><span class="lineNum">     637 </span>            : }</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 : void Keywords::removeComponent( const std::string&amp; name ) {</span></a>
+<a name="640"><span class="lineNum">     640 </span>            :   bool found=false;</a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span>            :   while(true) {</a>
+<a name="643"><span class="lineNum">     643 </span>            :     unsigned j;</a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :     for(j=0; j&lt;cnames.size(); j++) if(cnames[j]==name)break;</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 :     if(j&lt;cnames.size()) {</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 :       cnames.erase(cnames.begin()+j);</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :       found=true;</a>
+<a name="648"><span class="lineNum">     648 </span>            :     } else break;</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :   // Delete documentation, type and so on from the description</a>
+<a name="651"><span class="lineNum">     651 </span>            :   cdocs.erase(name); ckey.erase(name);</a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineNoCov">          0 :   plumed_massert(found,&quot;You are trying to remove &quot; + name + &quot; a component that isn't there&quot;);</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">        222 : std::vector&lt;std::string&gt; Keywords::getOutputComponents() const {</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">        222 :   return cnames;</span></a>
+<a name="657"><span class="lineNum">     657 </span>            : }</a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       4486 : std::string Keywords::getKeywordDescription( const std::string&amp; key ) const {</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">       8972 :   plumed_assert( exists( key ) ); return documentation.find(key)-&gt;second;</span></a>
+<a name="661"><span class="lineNum">     661 </span>            : }</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Keywords.h.func-sort-c.html b/coverage/tools/Keywords.h.func-sort-c.html
new file mode 100644
index 0000000000..e6a78db496
--- /dev/null
+++ b/coverage/tools/Keywords.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Keywords.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Keywords.h<span style="font-size: 80%;"> (<a href="Keywords.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Keywords.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.h.gcov.html#91">_ZN4PLMD8KeywordsC2Ev</a></td>
+              <td class="coverFnHi">98697</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.h.gcov.html#46">_ZNK4PLMD8Keywords7KeyType8toStringB5cxx11Ev</a></td>
+              <td class="coverFnHi">832387</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Keywords.h.func.html b/coverage/tools/Keywords.h.func.html
new file mode 100644
index 0000000000..2d060c952b
--- /dev/null
+++ b/coverage/tools/Keywords.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Keywords.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Keywords.h<span style="font-size: 80%;"> (<a href="Keywords.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Keywords.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.h.gcov.html#91">_ZN4PLMD8KeywordsC2Ev</a></td>
+              <td class="coverFnHi">98697</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Keywords.h.gcov.html#46">_ZNK4PLMD8Keywords7KeyType8toStringB5cxx11Ev</a></td>
+              <td class="coverFnHi">832387</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Keywords.h.gcov.html b/coverage/tools/Keywords.h.gcov.html
new file mode 100644
index 0000000000..0f79395757
--- /dev/null
+++ b/coverage/tools/Keywords.h.gcov.html
@@ -0,0 +1,260 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Keywords.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Keywords.h<span style="font-size: 80%;"> (source / <a href="Keywords.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryMed">88.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Keywords_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Keywords_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;vector&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;set&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;map&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class Log;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : /// This class holds the keywords and their documentation</a>
+<a name="36"><span class="lineNum">      36 </span>            : class Keywords {</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// This class lets me pass keyword types easily</a>
+<a name="38"><span class="lineNum">      38 </span>            :   class KeyType {</a>
+<a name="39"><span class="lineNum">      39 </span>            :   public:</a>
+<a name="40"><span class="lineNum">      40 </span>            :     enum {hidden,compulsory,flag,optional,atoms,vessel} style;</a>
+<a name="41"><span class="lineNum">      41 </span>            :     explicit KeyType( const std::string&amp; type );</a>
+<a name="42"><span class="lineNum">      42 </span>            :     void setStyle( const std::string&amp; type );</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      16332 :     bool isCompulsory() const { return (style==compulsory); }</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      22066 :     bool isFlag() const { return (style==flag); }</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      16846 :     bool isOptional() const { return (style==optional); }</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">     618551 :     bool isAtomList() const { return (style==atoms); }</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      17905 :     bool isVessel() const { return (style==vessel); }</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">     832387 :     std::string toString() const {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     832387 :       if(style==compulsory) return &quot;compulsory&quot;;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">     199530 :       else if(style==optional) return &quot;optional&quot;;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     159101 :       else if(style==atoms) return &quot;atoms&quot;;</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     319669 :       else if(style==flag) return &quot;flag&quot;;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      74060 :       else if(style==hidden) return &quot;hidden&quot;;</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      22570 :       else if(style==vessel) return &quot;vessel&quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :       else plumed_assert(0);</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :       return &quot;&quot;;</a>
+<a name="57"><span class="lineNum">      57 </span>            :     }</a>
+<a name="58"><span class="lineNum">      58 </span>            :   };</a>
+<a name="59"><span class="lineNum">      59 </span>            :   friend class Action;</a>
+<a name="60"><span class="lineNum">      60 </span>            : private:</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Is this an action or driver (this bool affects what style==atoms does in print)</a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool isaction;</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// This allows us to overwrite the behavior of the atoms type in analysis actions</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool isatoms;</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// The names of the allowed keywords</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;std::string&gt; keys;</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// The names of the reserved keywords</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;std::string&gt; reserved_keys;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Whether the keyword is compulsory, optional...</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::map&lt;std::string,KeyType&gt; types;</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Do we allow stuff like key1, key2 etc</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::map&lt;std::string,bool&gt; allowmultiple;</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// The documentation for the keywords</a>
+<a name="74"><span class="lineNum">      74 </span>            :   std::map&lt;std::string,std::string&gt; documentation;</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// The default values for the flags (are they on or of)</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::map&lt;std::string,bool&gt; booldefs;</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// The default values (if there are default values) for compulsory keywords</a>
+<a name="78"><span class="lineNum">      78 </span>            :   std::map&lt;std::string,std::string&gt; numdefs;</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// The tags for atoms - we use this so the manual can differentiate between different ways of specifying atoms</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::map&lt;std::string,std::string&gt; atomtags;</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// The string that should be printed out to describe how the components work for this particular action</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::string cstring;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// The names of all the possible components for an action</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;std::string&gt; cnames;</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// The keyword that turns on a particular component</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::map&lt;std::string,std::string&gt; ckey;</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// The documentation for a particular component</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::map&lt;std::string,std::string&gt; cdocs;</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Print the documentation for the jth keyword in html</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void print_html_item( const std::string&amp; ) const;</a>
+<a name="91"><span class="lineNum">      91 </span>            : public:</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// Constructor</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      98697 :   Keywords() : isaction(true), isatoms(true) {}</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : ///</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       8336 :   void isDriver() { isaction=false; }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : ///</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        149 :   void isAnalysis() { isatoms=false; }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : /// find out whether flag key is on or off by default.</a>
+<a name="99"><span class="lineNum">      99 </span>            :   bool getLogicalDefault(const std::string &amp; key, bool&amp; def ) const ;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Get the value of the default for the keyword named key</a>
+<a name="101"><span class="lineNum">     101 </span>            :   bool getDefaultValue(const std::string &amp; key, std::string&amp; def ) const ;</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// Return the number of defined keywords</a>
+<a name="103"><span class="lineNum">     103 </span>            :   unsigned size() const;</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// Check if numbered keywords are allowed for this action</a>
+<a name="105"><span class="lineNum">     105 </span>            :   bool numbered( const std::string &amp; k ) const ;</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Return the ith keyword</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::string getKeyword( const unsigned i ) const ;</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Get the documentation for a particular keyword</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::string getKeywordDocs( const std::string&amp; key ) const ;</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// Print the documentation to the log file (used by PLMD::Action::error)</a>
+<a name="111"><span class="lineNum">     111 </span>            :   void print( Log&amp; log ) const ;</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// Print the documentation to a file (use by PLUMED::CLTool::readCommandLineArgs)</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void print( FILE* out ) const ;</a>
+<a name="114"><span class="lineNum">     114 </span>            : /// Get the help string</a>
+<a name="115"><span class="lineNum">     115 </span>            :   std::string getHelpString() const ;</a>
+<a name="116"><span class="lineNum">     116 </span>            : /// Print a file containing the list of keywords for a particular action (used for spell checking)</a>
+<a name="117"><span class="lineNum">     117 </span>            :   void print_spelling() const ;</a>
+<a name="118"><span class="lineNum">     118 </span>            : /// Reserve a keyword</a>
+<a name="119"><span class="lineNum">     119 </span>            :   void reserve( const std::string &amp; t, const std::string &amp; k, const std::string &amp; d );</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// Reserve a flag</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void reserveFlag( const std::string &amp; k, const bool def, const std::string &amp; d );</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// Use one of the reserved keywords</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void use( const std::string  &amp; k );</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Get the ith keyword</a>
+<a name="125"><span class="lineNum">     125 </span>            :   std::string get( const unsigned k ) const ;</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// Add a new keyword of type t with name k and description d</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void add( const std::string &amp; t, const std::string &amp; k, const std::string &amp; d );</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// Add a new compulsory keyword (t must equal compulsory) with name k, default value def and description d</a>
+<a name="129"><span class="lineNum">     129 </span>            :   void add( const std::string &amp; t, const std::string &amp; k, const std::string &amp; def, const std::string &amp; d );</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// Add a falg with name k that is by default on if def is true and off if def is false.  d should provide a description of the flag</a>
+<a name="131"><span class="lineNum">     131 </span>            :   void addFlag( const std::string &amp; k, const bool def, const std::string &amp; d );</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Remove the keyword with name k</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void remove( const std::string &amp; k );</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Check if there is a keyword with name k</a>
+<a name="135"><span class="lineNum">     135 </span>            :   bool exists( const std::string &amp; k ) const ;</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Check the keyword k has been reserved</a>
+<a name="137"><span class="lineNum">     137 </span>            :   bool reserved( const std::string &amp; k ) const ;</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Get the type for the keyword with string k</a>
+<a name="139"><span class="lineNum">     139 </span>            :   std::string getStyle( const std::string &amp; k ) const ;</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Check if the keyword with name k has style t</a>
+<a name="141"><span class="lineNum">     141 </span>            :   bool style( const std::string &amp; k, const std::string &amp; t ) const ;</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// Print an html version of the documentation</a>
+<a name="143"><span class="lineNum">     143 </span>            :   void print_html() const ;</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// Print keywords in form readable by vim</a>
+<a name="145"><span class="lineNum">     145 </span>            :   void print_vim() const ;</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Print the template version for the documentation</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void print_template( const std::string&amp; actionname, bool include_optional) const ;</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// Change the style of a keyword</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void reset_style( const std::string &amp; k, const std::string &amp; style );</a>
+<a name="150"><span class="lineNum">     150 </span>            : /// Add keywords from one keyword object to another</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void add( const Keywords&amp; keys );</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Copy the keywords data</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void copyData( std::vector&lt;std::string&gt;&amp; kk, std::vector&lt;std::string&gt;&amp; rk, std::map&lt;std::string,KeyType&gt;&amp; tt, std::map&lt;std::string,bool&gt;&amp; am,</a>
+<a name="154"><span class="lineNum">     154 </span>            :                  std::map&lt;std::string,std::string&gt;&amp; docs, std::map&lt;std::string,bool&gt;&amp; bools, std::map&lt;std::string,std::string&gt;&amp; nums,</a>
+<a name="155"><span class="lineNum">     155 </span>            :                  std::map&lt;std::string,std::string&gt;&amp; atags, std::vector&lt;std::string&gt;&amp; cnam, std::map&lt;std::string,std::string&gt;&amp; ck,</a>
+<a name="156"><span class="lineNum">     156 </span>            :                  std::map&lt;std::string,std::string&gt;&amp; cd ) const ;</a>
+<a name="157"><span class="lineNum">     157 </span>            : /// Clear everything from the keywords object.</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// Not actually needed if your Keywords object is going out of scope.</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void destroyData();</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Set the text that introduces how the components for this action are introduced</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void setComponentsIntroduction( const std::string&amp; instr );</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// Add a potential component which can be output by this particular action</a>
+<a name="163"><span class="lineNum">     163 </span>            :   void addOutputComponent( const std::string&amp; name, const std::string&amp; key, const std::string&amp; descr );</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// Has a component with this name been added?</a>
+<a name="165"><span class="lineNum">     165 </span>            :   bool outputComponentExists( const std::string&amp; name, const bool&amp; custom ) const ;</a>
+<a name="166"><span class="lineNum">     166 </span>            : /// Get the flag that forces this component to be calculated</a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::string getOutputComponentFlag( const std::string&amp; name ) const ;</a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Get the description of this component</a>
+<a name="169"><span class="lineNum">     169 </span>            :   std::string getOutputComponentDescription( const std::string&amp; name ) const ;</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// Get the full list of output components</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::vector&lt;std::string&gt; getOutputComponents() const ;</a>
+<a name="172"><span class="lineNum">     172 </span>            : /// Get the description of a particular keyword</a>
+<a name="173"><span class="lineNum">     173 </span>            :   std::string getKeywordDescription( const std::string&amp; name ) const ;</a>
+<a name="174"><span class="lineNum">     174 </span>            : /// Remove a component with a particular name from the keywords</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void removeComponent( const std::string&amp; name );</a>
+<a name="176"><span class="lineNum">     176 </span>            : /// Reference to keys</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   std::vector&lt;std::string&gt; getKeys() const { return keys; }</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : /// Get the description of a particular keyword</a>
+<a name="179"><span class="lineNum">     179 </span>            :   std::string getTooltip( const std::string&amp; name ) const ;</a>
+<a name="180"><span class="lineNum">     180 </span>            : };</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LatticeReduction.cpp.func-sort-c.html b/coverage/tools/LatticeReduction.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f0bd38c6cb
--- /dev/null
+++ b/coverage/tools/LatticeReduction.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LatticeReduction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LatticeReduction.cpp<span style="font-size: 80%;"> (<a href="LatticeReduction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntryMed">82.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LatticeReduction.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#189">_ZN4PLMD16LatticeReduction10isReduced2ERKNS_13VectorGenericILj3EEES4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#99">_ZN4PLMD16LatticeReduction7reduce2ERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#160">_ZN4PLMD16LatticeReduction10reduceSlowERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#67">_ZN4PLMD16LatticeReduction7reduce2ERNS_13VectorGenericILj3EEES3_S3_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#193">_ZN4PLMD16LatticeReduction9isReducedERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#91">_ZN4PLMD16LatticeReduction9isReducedERKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#109">_ZN4PLMD16LatticeReduction6reduceERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">20632</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#113">_ZN4PLMD16LatticeReduction10reduceFastERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">20633</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#43">_ZN4PLMD16LatticeReduction6reduceERNS_13VectorGenericILj3EEES3_</a></td>
+              <td class="coverFnHi">27311</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#29">_ZN4PLMD16LatticeReduction4sortEPNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">47938</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/tools/LatticeReduction.cpp.func.html b/coverage/tools/LatticeReduction.cpp.func.html
new file mode 100644
index 0000000000..5f60c5c6b4
--- /dev/null
+++ b/coverage/tools/LatticeReduction.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LatticeReduction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LatticeReduction.cpp<span style="font-size: 80%;"> (<a href="LatticeReduction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntryMed">82.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LatticeReduction.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#189">_ZN4PLMD16LatticeReduction10isReduced2ERKNS_13VectorGenericILj3EEES4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#113">_ZN4PLMD16LatticeReduction10reduceFastERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">20633</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#160">_ZN4PLMD16LatticeReduction10reduceSlowERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#29">_ZN4PLMD16LatticeReduction4sortEPNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">47938</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#109">_ZN4PLMD16LatticeReduction6reduceERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">20632</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#43">_ZN4PLMD16LatticeReduction6reduceERNS_13VectorGenericILj3EEES3_</a></td>
+              <td class="coverFnHi">27311</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#99">_ZN4PLMD16LatticeReduction7reduce2ERNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#67">_ZN4PLMD16LatticeReduction7reduce2ERNS_13VectorGenericILj3EEES3_S3_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#193">_ZN4PLMD16LatticeReduction9isReducedERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LatticeReduction.cpp.gcov.html#91">_ZN4PLMD16LatticeReduction9isReducedERKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/tools/LatticeReduction.cpp.gcov.html b/coverage/tools/LatticeReduction.cpp.gcov.html
new file mode 100644
index 0000000000..fc3571f022
--- /dev/null
+++ b/coverage/tools/LatticeReduction.cpp.gcov.html
@@ -0,0 +1,291 @@
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+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LatticeReduction.cpp<span style="font-size: 80%;"> (source / <a href="LatticeReduction.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">123</td>
+            <td class="headerCovTableEntryMed">82.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LatticeReduction.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cstdio&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cmath&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : const double epsilon=1e-14;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">      47938 : void LatticeReduction::sort(Vector v[3]) {</span></a>
+<a name="32"><span class="lineNum">      32 </span>            :   const double onePlusEpsilon=(1.0+epsilon);</a>
+<a name="33"><span class="lineNum">      33 </span>            :   double m[3];</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">      47938 :   m[0]=modulo2(v[0]);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">      47938 :   m[1]=modulo2(v[1]);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">      47938 :   m[2]=modulo2(v[2]);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     335566 :   for(int i=0; i&lt;3; i++) for(int j=i+1; j&lt;3; j++) if(m[i]&gt;m[j]) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      11780 :         std::swap(v[i],v[j]);</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :         std::swap(m[i],m[j]);</a>
+<a name="40"><span class="lineNum">      40 </span>            :       }</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      47938 :   plumed_assert(m[0]&lt;=m[1]*onePlusEpsilon);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      47938 :   plumed_assert(m[1]&lt;=m[2]*onePlusEpsilon);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      47938 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      27311 : void LatticeReduction::reduce(Vector&amp;a,Vector&amp;b) {</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   const double onePlusEpsilon=(1.0+epsilon);</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      27311 :   double ma=modulo2(a);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      27311 :   double mb=modulo2(b);</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   unsigned counter=0;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   while(true) {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      27877 :     if(mb&gt;ma) {</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :       std::swap(a,b);</a>
+<a name="53"><span class="lineNum">      53 </span>            :       std::swap(ma,mb);</a>
+<a name="54"><span class="lineNum">      54 </span>            :     }</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      27877 :     a-=b*floor(dotProduct(a,b)/mb+0.5);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      27877 :     ma=modulo2(a);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      27877 :     if(mb&lt;=ma*onePlusEpsilon) break;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        566 :     counter++;</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        566 :     if(counter%100==0) { // only test rarely since this might be expensive</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :       plumed_assert(!std::isnan(ma));</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :       plumed_assert(!std::isnan(mb));</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :     }</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        566 :     if(counter%10000==0) std::fprintf(stderr,&quot;WARNING: LatticeReduction::reduce stuck after %u iterations\n&quot;,counter);</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::swap(a,b);</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">      27311 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          1 : void LatticeReduction::reduce2(Vector&amp;a,Vector&amp;b,Vector&amp;c) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          4 :   Vector v[3];</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 :   v[0]=a; v[1]=b; v[2]=c;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   int iter=0;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   int ok=0;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         12 :   while(ok&lt;3) {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     int i,j;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         11 :     if(iter%3==0) {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :       i=0; j=1;</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          7 :     } else if(iter%3==1) {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :       i=0; j=2;</a>
+<a name="80"><span class="lineNum">      80 </span>            :     } else {</a>
+<a name="81"><span class="lineNum">      81 </span>            :       i=1; j=2;</a>
+<a name="82"><span class="lineNum">      82 </span>            :     }</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         11 :     if(isReduced(v[i],v[j])) ok++;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :     else {</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          7 :       reduce(v[i],v[j]);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :       ok=1;</a>
+<a name="87"><span class="lineNum">      87 </span>            :     }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         11 :     iter++;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          1 :   a=v[0]; b=v[1]; c=v[2];</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          1 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         11 : bool LatticeReduction::isReduced(const Vector&amp;a,const Vector&amp;b) {</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   const int cut=5;</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         84 :   for(int i=-cut; i&lt;=cut; i++) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         79 :     if(modulo2(b+i*a)&lt;modulo2(b)) return false;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          5 :   return modulo2(a)&lt;=modulo2(b) &amp;&amp; 2.0*dotProduct(a,b)&lt;=modulo2(a);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 : void LatticeReduction::reduce2(Tensor&amp;t) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   Vector a=t.getRow(0);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   Vector b=t.getRow(1);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   Vector c=t.getRow(2);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   reduce2(a,b,c);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   t.setRow(0,a);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   t.setRow(1,b);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :   t.setRow(2,c);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      20632 : void LatticeReduction::reduce(Tensor&amp;t) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      20632 :   reduceFast(t);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      20632 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      20633 : void LatticeReduction::reduceFast(Tensor&amp;t) {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   const double onePlusEpsilon=(1.0+epsilon);</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      82532 :   Vector v[3];</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      20633 :   v[0]=t.getRow(0);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      20633 :   v[1]=t.getRow(1);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      20633 :   v[2]=t.getRow(2);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   unsigned counter=0;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   while(true) {</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      27304 :     sort(v);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      27304 :     reduce(v[0],v[1]);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      27304 :     double b11=modulo2(v[0]);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      27304 :     double b22=modulo2(v[1]);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      27304 :     double b12=dotProduct(v[0],v[1]);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      27304 :     double b13=dotProduct(v[0],v[2]);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      27304 :     double b23=dotProduct(v[1],v[2]);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">      27304 :     double z=b11*b22-b12*b12;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      27304 :     double y2=-(b11*b23-b12*b13)/z;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">      27304 :     double y1=-(b22*b13-b12*b23)/z;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      27304 :     int x1min=floor(y1);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      27304 :     int x1max=x1min+1;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">      27304 :     int x2min=floor(y2);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      27304 :     int x2max=x2min+1;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     bool first=true;</a>
+<a name="138"><span class="lineNum">     138 </span>            :     double mbest,mtrial;</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      27304 :     Vector trial,best;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      81912 :     for(int x1=x1min; x1&lt;=x1max; x1++)</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">     163824 :       for(int x2=x2min; x2&lt;=x2max; x2++) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">     109216 :         trial=v[2]+x2*v[1]+x1*v[0];</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">     109216 :         mtrial=modulo2(trial);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">     109216 :         if(first || mtrial&lt;mbest) {</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :           mbest=mtrial;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      34848 :           best=trial;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :           first=false;</a>
+<a name="148"><span class="lineNum">     148 </span>            :         }</a>
+<a name="149"><span class="lineNum">     149 </span>            :       }</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      27304 :     if(modulo2(best)*onePlusEpsilon&gt;=modulo2(v[2])) break;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       6671 :     counter++;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       6671 :     if(counter%10000==0) std::fprintf(stderr,&quot;WARNING: LatticeReduction::reduceFast stuck after %u iterations\n&quot;,counter);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       6671 :     v[2]=best;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       6671 :   }</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      20633 :   sort(v);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      20633 :   t.setRow(0,v[0]);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      20633 :   t.setRow(1,v[1]);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      20633 :   t.setRow(2,v[2]);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      20633 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 : void LatticeReduction::reduceSlow(Tensor&amp;t) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          4 :   Vector v[3];</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          1 :   v[0]=t.getRow(0);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          1 :   v[1]=t.getRow(1);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          1 :   v[2]=t.getRow(2);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          1 :   reduce2(v[0],v[1],v[2]);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          1 :   double e01=dotProduct(v[0],v[1]);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          1 :   double e02=dotProduct(v[0],v[2]);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 :   double e12=dotProduct(v[1],v[2]);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          1 :   if(e01*e02*e12&lt;0) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :     int eps01=0; if(e01&gt;0.0) eps01=1; else if(e01&lt;0.0) eps01=-1;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :     int eps02=0; if(e02&gt;0.0) eps02=1; else if(e02&lt;0.0) eps02=-1;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :     Vector n=v[0]-eps01*v[1]-eps02*v[2];</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :     int i=0; double mx=modulo2(v[i]);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :     for(int j=1; j&lt;3; j++) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :       double f=modulo2(v[j]);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :       if(f&gt;mx) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :         i=j;</a>
+<a name="180"><span class="lineNum">     180 </span>            :         mx=f;</a>
+<a name="181"><span class="lineNum">     181 </span>            :       }</a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     if(modulo2(n)&lt;mx) v[i]=n;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          1 :   sort(v);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          1 :   t.setRow(0,v[0]);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          1 :   t.setRow(1,v[1]);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          1 :   t.setRow(2,v[2]);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          1 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 : bool LatticeReduction::isReduced2(const Vector&amp;a,const Vector&amp;b,const Vector &amp;c) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :   return isReduced(a,b) &amp;&amp; isReduced(a,b) &amp;&amp; isReduced(b,c);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 : bool LatticeReduction::isReduced(const Tensor&amp;t) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          8 :   Vector v[3];</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   double m[3];</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          2 :   v[0]=t.getRow(0);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :   v[1]=t.getRow(1);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          2 :   v[2]=t.getRow(2);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          8 :   for(int i=0; i&lt;3; i++) m[i]=modulo2(v[i]);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :   if(!((m[0]&lt;=m[1]) &amp;&amp; m[1]&lt;=m[2])) return false;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   const int cut=5;</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         13 :   for(int i=-cut; i&lt;=cut; i++) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         12 :     double mm=modulo2(v[1]+i*v[0]);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         12 :     if(mm&lt;m[1]) return false;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        142 :     for(int j=-cut; j&lt;=cut; j++) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        131 :       double mx=modulo2(v[2]+i*v[1]+j*v[0]);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        131 :       if(mx&lt;m[2])return false;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     }</a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span>            :   return true;</a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LinkCells.cpp.func-sort-c.html b/coverage/tools/LinkCells.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0f0a38b67a
--- /dev/null
+++ b/coverage/tools/LinkCells.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LinkCells.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LinkCells.cpp<span style="font-size: 80%;"> (<a href="LinkCells.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntryHi">98.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LinkCells.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#39">_ZNK4PLMD9LinkCells9getCutoffEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#35">_ZN4PLMD9LinkCells9setCutoffERKd</a></td>
+              <td class="coverFnHi">385</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#26">_ZN4PLMD9LinkCellsC2ERNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">703</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#43">_ZN4PLMD9LinkCells14buildCellListsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IjSaIjEERKNS_3PbcE</a></td>
+              <td class="coverFnHi">1295</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#131">_ZNK4PLMD9LinkCells24retrieveNeighboringAtomsERKNS_13VectorGenericILj3EEERSt6vectorIjSaIjEERjS8_</a></td>
+              <td class="coverFnHi">6576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#107">_ZNK4PLMD9LinkCells16addRequiredCellsERKSt5arrayIjLm3EERjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">227239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#138">_ZNK4PLMD9LinkCells20retrieveAtomsInCellsERKjRKSt6vectorIjSaIjEERjRS5_</a></td>
+              <td class="coverFnHi">227239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#164">_ZNK4PLMD9LinkCells21convertIndicesToIndexERKjS2_S2_</a></td>
+              <td class="coverFnHi">409838</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#168">_ZNK4PLMD9LinkCells8findCellERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">409838</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#154">_ZNK4PLMD9LinkCells10findMyCellERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">637077</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LinkCells.cpp.func.html b/coverage/tools/LinkCells.cpp.func.html
new file mode 100644
index 0000000000..cdaa23f1b1
--- /dev/null
+++ b/coverage/tools/LinkCells.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LinkCells.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LinkCells.cpp<span style="font-size: 80%;"> (<a href="LinkCells.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntryHi">98.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LinkCells.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#43">_ZN4PLMD9LinkCells14buildCellListsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IjSaIjEERKNS_3PbcE</a></td>
+              <td class="coverFnHi">1295</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#35">_ZN4PLMD9LinkCells9setCutoffERKd</a></td>
+              <td class="coverFnHi">385</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#26">_ZN4PLMD9LinkCellsC2ERNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">703</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#154">_ZNK4PLMD9LinkCells10findMyCellERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">637077</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#107">_ZNK4PLMD9LinkCells16addRequiredCellsERKSt5arrayIjLm3EERjRSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">227239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#138">_ZNK4PLMD9LinkCells20retrieveAtomsInCellsERKjRKSt6vectorIjSaIjEERjRS5_</a></td>
+              <td class="coverFnHi">227239</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#164">_ZNK4PLMD9LinkCells21convertIndicesToIndexERKjS2_S2_</a></td>
+              <td class="coverFnHi">409838</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#131">_ZNK4PLMD9LinkCells24retrieveNeighboringAtomsERKNS_13VectorGenericILj3EEERSt6vectorIjSaIjEERjS8_</a></td>
+              <td class="coverFnHi">6576</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#168">_ZNK4PLMD9LinkCells8findCellERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">409838</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinkCells.cpp.gcov.html#39">_ZNK4PLMD9LinkCells9getCutoffEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LinkCells.cpp.gcov.html b/coverage/tools/LinkCells.cpp.gcov.html
new file mode 100644
index 0000000000..e8ec937501
--- /dev/null
+++ b/coverage/tools/LinkCells.cpp.gcov.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LinkCells.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LinkCells.cpp<span style="font-size: 80%;"> (source / <a href="LinkCells.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntryHi">98.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LinkCells.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        703 : LinkCells::LinkCells( Communicator&amp; cc ) :</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        703 :   comm(cc),</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        703 :   cutoffwasset(false),</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        703 :   link_cutoff(0.0),</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        703 :   ncells(3),</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       1406 :   nstride(3)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        703 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        385 : void LinkCells::setCutoff( const double&amp; lcut ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        385 :   cutoffwasset=true; link_cutoff=lcut;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        385 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          8 : double LinkCells::getCutoff() const {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          8 :   plumed_assert( cutoffwasset ); return link_cutoff;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : }</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1295 : void LinkCells::buildCellLists( const std::vector&lt;Vector&gt;&amp; pos, const std::vector&lt;unsigned&gt;&amp; indices, const Pbc&amp; pbc ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1295 :   plumed_assert( cutoffwasset &amp;&amp; pos.size()==indices.size() );</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            :   // Must be able to check that pbcs are not nonsensical in some way?? -- GAT</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            :   // Setup the pbc object by copying it from action</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1295 :   mypbc.setBox( pbc.getBox() );</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            :   // Setup the lists</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1295 :   if( pos.size()!=allcells.size() ) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        313 :     allcells.resize( pos.size() ); lcell_lists.resize( pos.size() );</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   {</a>
+<a name="59"><span class="lineNum">      59 </span>            : // This is the reciprocal lattice</a>
+<a name="60"><span class="lineNum">      60 </span>            : // notice that reciprocal.getRow(0) is a vector that is orthogonal to b and c</a>
+<a name="61"><span class="lineNum">      61 </span>            : // This allows to use linked cells in non orthorhomic boxes</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       1295 :     Tensor reciprocal(transpose(mypbc.getInvBox()));</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       1295 :     ncells[0] = std::floor( 1.0/ reciprocal.getRow(0).modulo() / link_cutoff );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       1295 :     if( ncells[0]==0 ) ncells[0]=1;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1295 :     ncells[1] = std::floor( 1.0/ reciprocal.getRow(1).modulo() / link_cutoff );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1295 :     if( ncells[1]==0 ) ncells[1]=1;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       1295 :     ncells[2] = std::floor( 1.0/ reciprocal.getRow(2).modulo() / link_cutoff );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       1295 :     if( ncells[2]==0 ) ncells[2]=1;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Setup the strides</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1295 :   nstride[0]=1; nstride[1]=ncells[0]; nstride[2]=ncells[0]*ncells[1];</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   // Setup the storage for link cells</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       1295 :   unsigned ncellstot=ncells[0]*ncells[1]*ncells[2];</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       1295 :   if( lcell_tots.size()!=ncellstot ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        303 :     lcell_tots.resize( ncellstot ); lcell_starts.resize( ncellstot );</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   }</a>
+<a name="78"><span class="lineNum">      78 </span>            :   // Clear nlcells</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     299535 :   for(unsigned i=0; i&lt;ncellstot; ++i) lcell_tots[i]=0;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   // Clear allcells</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1295 :   allcells.assign( allcells.size(), 0 );</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            :   // Find out what cell everyone is in</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1295 :   unsigned rank=comm.Get_rank(), size=comm.Get_size();</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     411133 :   for(unsigned i=rank; i&lt;pos.size(); i+=size) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     409838 :     allcells[i]=findCell( pos[i] );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     409838 :     lcell_tots[allcells[i]]++;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   }</a>
+<a name="89"><span class="lineNum">      89 </span>            :   // And gather all this information on every node</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1295 :   comm.Sum( allcells ); comm.Sum( lcell_tots );</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   // Now prepare the link cell lists</a>
+<a name="93"><span class="lineNum">      93 </span>            :   unsigned tot=0;</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     299535 :   for(unsigned i=0; i&lt;lcell_tots.size(); ++i) { lcell_starts[i]=tot; tot+=lcell_tots[i]; lcell_tots[i]=0; }</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1295 :   plumed_assert( tot==pos.size() );</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :   // And setup the link cells properly</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     456412 :   for(unsigned j=0; j&lt;pos.size(); ++j) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     455117 :     unsigned myind = lcell_starts[ allcells[j] ] + lcell_tots[ allcells[j] ];</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     455117 :     lcell_lists[ myind ] = indices[j];</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     455117 :     lcell_tots[allcells[j]]++;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       1295 : }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : #define LINKC_MIN(n) ((n&lt;2)? 0 : -1)</a>
+<a name="106"><span class="lineNum">     106 </span>            : #define LINKC_MAX(n) ((n&lt;3)? 1 : 2)</a>
+<a name="107"><span class="lineNum">     107 </span>            : #define LINKC_PBC(n,num) ((n&lt;0)? num-1 : n%num )</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     227239 : void LinkCells::addRequiredCells( const std::array&lt;unsigned,3&gt;&amp; celn, unsigned&amp; ncells_required,</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :                                   std::vector&lt;unsigned&gt;&amp; cells_required ) const {</a>
+<a name="111"><span class="lineNum">     111 </span>            :   unsigned nnew_cells=0;</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">    1298325 :   for(int nx=LINKC_MIN(ncells[0]); nx&lt;LINKC_MAX(ncells[0]); ++nx) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">     433287 :     int xval = celn[0] + nx;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     433287 :     xval=LINKC_PBC(xval,ncells[0])*nstride[0];</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">    3144327 :     for(int ny=LINKC_MIN(ncells[1]); ny&lt;LINKC_MAX(ncells[1]); ++ny) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">    1049433 :       int yval = celn[1] + ny;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">    1049433 :       yval=LINKC_PBC(yval,ncells[1])*nstride[1];</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">    8649248 :       for(int nz=LINKC_MIN(ncells[2]); nz&lt;LINKC_MAX(ncells[2]); ++nz) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">    2886542 :         int zval = celn[2] + nz;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">    2886542 :         zval=LINKC_PBC(zval,ncells[2])*nstride[2];</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">    2886542 :         unsigned mybox=xval+yval+zval; bool added=false;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">    2886542 :         for(unsigned k=0; k&lt;ncells_required; ++k) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :           if( mybox==cells_required[k] ) { added=true; break; }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :         }</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">    2886542 :         if( !added ) { cells_required[ncells_required+nnew_cells]=mybox; nnew_cells++; }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :       }</a>
+<a name="128"><span class="lineNum">     128 </span>            :     }</a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">     227239 :   ncells_required += nnew_cells;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     227239 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       6576 : void LinkCells::retrieveNeighboringAtoms( const Vector&amp; pos, std::vector&lt;unsigned&gt;&amp; cell_list,</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :     unsigned&amp; natomsper, std::vector&lt;unsigned&gt;&amp; atoms ) const {</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       6576 :   if( cell_list.size()!=getNumberOfCells() ) cell_list.resize( getNumberOfCells() );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       6576 :   unsigned ncellt=0; addRequiredCells( findMyCell( pos ), ncellt, cell_list );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       6576 :   retrieveAtomsInCells( ncellt, cell_list, natomsper, atoms );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       6576 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">     227239 : void LinkCells::retrieveAtomsInCells( const unsigned&amp; ncells_required,</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :                                       const std::vector&lt;unsigned&gt;&amp; cells_required,</a>
+<a name="142"><span class="lineNum">     142 </span>            :                                       unsigned&amp; natomsper, std::vector&lt;unsigned&gt;&amp; atoms ) const {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">     227239 :   plumed_assert( natomsper==1 || natomsper==2 );  // This is really a bug. If you are trying to reuse this ask GAT for help</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">    3113781 :   for(unsigned i=0; i&lt;ncells_required; ++i) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">    2886542 :     unsigned mybox=cells_required[i];</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">  407341248 :     for(unsigned k=0; k&lt;lcell_tots[mybox]; ++k) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">  404454706 :       unsigned myatom = lcell_lists[lcell_starts[mybox]+k];</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">  404454706 :       if( myatom!=atoms[0] ) { // Ideally would provide an option to not do this</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">  404273206 :         atoms[natomsper]=myatom;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">  404273206 :         natomsper++;</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :       }</a>
+<a name="152"><span class="lineNum">     152 </span>            :     }</a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     227239 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     637077 : std::array&lt;unsigned,3&gt; LinkCells::findMyCell( const Vector&amp; pos ) const {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">     637077 :   Vector fpos=mypbc.realToScaled( pos );</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   std::array&lt;unsigned,3&gt; celn;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    2548308 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    1911231 :     celn[j] = std::floor( ( Tools::pbc(fpos[j]) + 0.5 ) * ncells[j] );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    1911231 :     plumed_assert( celn[j]&gt;=0 &amp;&amp; celn[j]&lt;ncells[j] ); // Check that atom is in box</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     637077 :   return celn;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     409838 : unsigned LinkCells::convertIndicesToIndex( const unsigned&amp; nx, const unsigned&amp; ny, const unsigned&amp; nz ) const {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">     409838 :   return nx*nstride[0] + ny*nstride[1] + nz*nstride[2];</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">     409838 : unsigned LinkCells::findCell( const Vector&amp; pos ) const {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     409838 :   std::array&lt;unsigned,3&gt; celn( findMyCell(pos ) );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     409838 :   return convertIndicesToIndex( celn[0], celn[1], celn[2] );</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LinkCells.h.func-sort-c.html b/coverage/tools/LinkCells.h.func-sort-c.html
new file mode 100644
index 0000000000..278bcc5f9e
--- /dev/null
+++ b/coverage/tools/LinkCells.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LinkCells.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LinkCells.h<span style="font-size: 80%;"> (<a href="LinkCells.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LinkCells.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LinkCells.h.func.html b/coverage/tools/LinkCells.h.func.html
new file mode 100644
index 0000000000..6b72148ba5
--- /dev/null
+++ b/coverage/tools/LinkCells.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LinkCells.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LinkCells.h<span style="font-size: 80%;"> (<a href="LinkCells.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LinkCells.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LinkCells.h.gcov.html b/coverage/tools/LinkCells.h.gcov.html
new file mode 100644
index 0000000000..61582cdaf0
--- /dev/null
+++ b/coverage/tools/LinkCells.h.gcov.html
@@ -0,0 +1,175 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LinkCells.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LinkCells.h<span style="font-size: 80%;"> (source / <a href="LinkCells.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_LinkCells_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_LinkCells_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Pbc.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class Communicator;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /// \ingroup TOOLBOX</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// A class for doing link cells</a>
+<a name="35"><span class="lineNum">      35 </span>            : class LinkCells {</a>
+<a name="36"><span class="lineNum">      36 </span>            : private:</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Symbolic link to plumed communicator</a>
+<a name="38"><span class="lineNum">      38 </span>            :   Communicator &amp; comm;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Check that the link cells were set up correctly</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool cutoffwasset;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// The cutoff to use for the sizes of the cells</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double link_cutoff;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// The pbc we are using for link cells</a>
+<a name="44"><span class="lineNum">      44 </span>            :   Pbc mypbc;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// The number of cells in each direction</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::vector&lt;unsigned&gt; ncells;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// The number of cells to stride through to get the link cells</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::vector&lt;unsigned&gt; nstride;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// The list of cells each atom is inside</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;unsigned&gt; allcells;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// The start of each block corresponding to each link cell</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;unsigned&gt; lcell_starts;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// The number of atoms in each link cell</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;unsigned&gt; lcell_tots;</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// The atoms ordered by link cells</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::vector&lt;unsigned&gt; lcell_lists;</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            : ///</a>
+<a name="59"><span class="lineNum">      59 </span>            :   explicit LinkCells( Communicator&amp; comm );</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Have the link cells been enabled</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool enabled() const ;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Set the value of the cutoff</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void setCutoff( const double&amp; lcut );</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Get the value of the cutoff</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double getCutoff() const ;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Get the total number of link cells</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned getNumberOfCells() const ;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Build the link cell lists</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void buildCellLists( const std::vector&lt;Vector&gt;&amp; pos, const std::vector&lt;unsigned&gt;&amp; indices, const Pbc&amp; pbc );</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Take three indices and return the index of the corresponding cell</a>
+<a name="71"><span class="lineNum">      71 </span>            :   unsigned convertIndicesToIndex( const unsigned&amp; nx, const unsigned&amp; ny, const unsigned&amp; nz ) const ;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Find the cell index in which this position is contained</a>
+<a name="73"><span class="lineNum">      73 </span>            :   unsigned findCell( const Vector&amp; pos ) const ;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Find the cell in which this position is contained</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::array&lt;unsigned,3&gt; findMyCell( const Vector&amp; pos ) const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Get the list of cells we need to surround the a particular cell</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void addRequiredCells( const std::array&lt;unsigned,3&gt;&amp; celn, unsigned&amp; ncells_required,</a>
+<a name="78"><span class="lineNum">      78 </span>            :                          std::vector&lt;unsigned&gt;&amp; cells_required ) const ;</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// Retrieve the atoms in a list of cells</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void retrieveAtomsInCells( const unsigned&amp; ncells_required,</a>
+<a name="81"><span class="lineNum">      81 </span>            :                              const std::vector&lt;unsigned&gt;&amp; cells_required,</a>
+<a name="82"><span class="lineNum">      82 </span>            :                              unsigned&amp; natomsper, std::vector&lt;unsigned&gt;&amp; atoms ) const ;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Retrieve the atoms we need to consider</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void retrieveNeighboringAtoms( const Vector&amp; pos, std::vector&lt;unsigned&gt;&amp; cell_list, unsigned&amp; natomsper, std::vector&lt;unsigned&gt;&amp; atoms ) const ;</a>
+<a name="85"><span class="lineNum">      85 </span>            : };</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : inline</a>
+<a name="88"><span class="lineNum">      88 </span>            : bool LinkCells::enabled() const {</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1940 :   return cutoffwasset;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : inline</a>
+<a name="93"><span class="lineNum">      93 </span>            : unsigned LinkCells::getNumberOfCells() const {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     227239 :   return ncells[0]*ncells[1]*ncells[2];</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LoopUnroller.h.func-sort-c.html b/coverage/tools/LoopUnroller.h.func-sort-c.html
new file mode 100644
index 0000000000..3bff31d880
--- /dev/null
+++ b/coverage/tools/LoopUnroller.h.func-sort-c.html
@@ -0,0 +1,280 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LoopUnroller.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LoopUnroller.h<span style="font-size: 80%;"> (<a href="LoopUnroller.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LoopUnroller.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj4EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj5EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj6EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj7EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj8EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj9EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj13EE5_zeroEPd</a></td>
+              <td class="coverFnHi">608260</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj14EE5_zeroEPd</a></td>
+              <td class="coverFnHi">608260</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj15EE5_zeroEPd</a></td>
+              <td class="coverFnHi">608260</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj16EE5_zeroEPd</a></td>
+              <td class="coverFnHi">608260</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#135">_ZN4PLMD12LoopUnrollerILj4EE5_sum2EPKd</a></td>
+              <td class="coverFnHi">1119102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj10EE5_zeroEPd</a></td>
+              <td class="coverFnHi">10861654</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj11EE5_zeroEPd</a></td>
+              <td class="coverFnHi">10861654</td>
+            </tr>
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diff --git a/coverage/tools/LoopUnroller.h.func.html b/coverage/tools/LoopUnroller.h.func.html
new file mode 100644
index 0000000000..9dffe407b8
--- /dev/null
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+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#87">_ZN4PLMD12LoopUnrollerILj9EE4_addEPdPKd</a></td>
+              <td class="coverFnHi">42880312</td>
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+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#111">_ZN4PLMD12LoopUnrollerILj9EE4_mulEPdd</a></td>
+              <td class="coverFnHi">154207316</td>
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+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#123">_ZN4PLMD12LoopUnrollerILj9EE4_negEPdPKd</a></td>
+              <td class="coverFnHi">63425</td>
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+    <tr>
+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#99">_ZN4PLMD12LoopUnrollerILj9EE4_subEPdPKd</a></td>
+              <td class="coverFnHi">47075253</td>
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+              <td class="coverFn"><a href="LoopUnroller.h.gcov.html#75">_ZN4PLMD12LoopUnrollerILj9EE5_zeroEPd</a></td>
+              <td class="coverFnHi">59077181</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/LoopUnroller.h.gcov.html b/coverage/tools/LoopUnroller.h.gcov.html
new file mode 100644
index 0000000000..7aa561245d
--- /dev/null
+++ b/coverage/tools/LoopUnroller.h.gcov.html
@@ -0,0 +1,236 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/LoopUnroller.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - LoopUnroller.h<span style="font-size: 80%;"> (source / <a href="LoopUnroller.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntry">31</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntry">52</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_LoopUnroller_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_LoopUnroller_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : /**</a>
+<a name="28"><span class="lineNum">      28 </span>            : \ingroup TOOLBOX</a>
+<a name="29"><span class="lineNum">      29 </span>            : Utiliy class for loop unrolling.</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : Many c++ compilers do not unroll small loops such as those</a>
+<a name="32"><span class="lineNum">      32 </span>            : used in the PLMD::Vector and PLMD::Tensor classes.</a>
+<a name="33"><span class="lineNum">      33 </span>            : This class provides methods to perform basic vector</a>
+<a name="34"><span class="lineNum">      34 </span>            : operations with unrolled loops. The methods work on double*</a>
+<a name="35"><span class="lineNum">      35 </span>            : so that they can be used in principles in other places of the code,</a>
+<a name="36"><span class="lineNum">      36 </span>            : but they are designed to be used in PLMD::Vector and PLMD::Tensor .</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : In case in the future we see that some compiler better optimize explicit loops,</a>
+<a name="39"><span class="lineNum">      39 </span>            : it should be easy to replace the methods here with loops. Alternatively,</a>
+<a name="40"><span class="lineNum">      40 </span>            : we could provide two paths using a cpp macro (e.g. __PLUMED_UNROLL_LOOPS or so).</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : All the methods for class LoopUnroller&lt;n&gt; act on n elements.</a>
+<a name="43"><span class="lineNum">      43 </span>            : Implementation is made using template metaprogramming, that is:</a>
+<a name="44"><span class="lineNum">      44 </span>            : - LoopUnroller&lt;1&gt;::xxx acts on the element [0] of the array.</a>
+<a name="45"><span class="lineNum">      45 </span>            : - LoopUnroller&lt;n&gt;::xxx calls LoopUnroller&lt;n-1&gt;::xxx then acts on element [n-1] of the array.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Here xxx is any of the methods of the class.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : */</a>
+<a name="50"><span class="lineNum">      50 </span>            : template&lt;unsigned n&gt;</a>
+<a name="51"><span class="lineNum">      51 </span>            : class LoopUnroller {</a>
+<a name="52"><span class="lineNum">      52 </span>            : public:</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Set to zero.</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Same as `for(unsigned i=0;i&lt;n;i++) d[i]=0.0;`</a>
+<a name="55"><span class="lineNum">      55 </span>            :   static void _zero(double*d);</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Add v to d.</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// Same as `for(unsigned i=0;i&lt;n;i++) d[i]+=v[i];`</a>
+<a name="58"><span class="lineNum">      58 </span>            :   static void _add(double*d,const double*v);</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Subtract v from d.</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Same as `for(unsigned i=0;i&lt;n;i++) d[i]-=v[i];`</a>
+<a name="61"><span class="lineNum">      61 </span>            :   static void _sub(double*d,const double*v);</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Multiply d by s.</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// Same as `for(unsigned i=0;i&lt;n;i++) d[i]*=s;`</a>
+<a name="64"><span class="lineNum">      64 </span>            :   static void _mul(double*d,const double s);</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Set d to -v.</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Same as `for(unsigned i=0;i&lt;n;i++) d[i]=-v[i];`</a>
+<a name="67"><span class="lineNum">      67 </span>            :   static void _neg(double*d,const double*v);</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Squared modulo of d;</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Same as `r=0.0; for(unsigned i=0;i&lt;n;i++) r+=d[i]*d[i]; return r;`</a>
+<a name="70"><span class="lineNum">      70 </span>            :   static double _sum2(const double*d);</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Dot product of d and v</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Same as `r=0.0; for(unsigned i=0;i&lt;n;i++) r+=d[i]*v[i]; return r;`</a>
+<a name="73"><span class="lineNum">      73 </span>            :   static double _dot(const double*d,const double*v);</a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : template&lt;unsigned n&gt;</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov"> 1501036708 : void LoopUnroller&lt;n&gt;::_zero(double*d) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">  946413127 :   LoopUnroller&lt;n-1&gt;::_zero(d);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov"> 1501036708 :   d[n-1]=0.0;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov"> 1501036708 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : template&lt;&gt;</a>
+<a name="83"><span class="lineNum">      83 </span>            : inline</a>
+<a name="84"><span class="lineNum">      84 </span>            : void LoopUnroller&lt;1&gt;::_zero(double*d) {</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">  555172501 :   d[0]=0.0;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : }</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : template&lt;unsigned n&gt;</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov"> 3838386978 : void LoopUnroller&lt;n&gt;::_add(double*d,const double*a) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov"> 2047834425 :   LoopUnroller&lt;n-1&gt;::_add(d,a);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov"> 3838386978 :   d[n-1]+=a[n-1];</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov"> 3838386978 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : template&lt;&gt;</a>
+<a name="95"><span class="lineNum">      95 </span>            : inline</a>
+<a name="96"><span class="lineNum">      96 </span>            : void LoopUnroller&lt;1&gt;::_add(double*d,const double*a) {</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov"> 1790552553 :   d[0]+=a[0];</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : template&lt;unsigned n&gt;</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov"> 2817704050 : void LoopUnroller&lt;n&gt;::_sub(double*d,const double*a) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov"> 1550637335 :   LoopUnroller&lt;n-1&gt;::_sub(d,a);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov"> 2817704050 :   d[n-1]-=a[n-1];</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov"> 2817704050 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : template&lt;&gt;</a>
+<a name="107"><span class="lineNum">     107 </span>            : inline</a>
+<a name="108"><span class="lineNum">     108 </span>            : void LoopUnroller&lt;1&gt;::_sub(double*d,const double*a) {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov"> 1267066715 :   d[0]-=a[0];</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : template&lt;unsigned n&gt;</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov"> 4884138288 : void LoopUnroller&lt;n&gt;::_mul(double*d,const double s) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov"> 2904691092 :   LoopUnroller&lt;n-1&gt;::_mul(d,s);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov"> 4884138288 :   d[n-1]*=s;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov"> 4884138288 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : template&lt;&gt;</a>
+<a name="119"><span class="lineNum">     119 </span>            : inline</a>
+<a name="120"><span class="lineNum">     120 </span>            : void LoopUnroller&lt;1&gt;::_mul(double*d,const double s) {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov"> 1979447196 :   d[0]*=s;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : }</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : template&lt;unsigned n&gt;</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">  212691790 : void LoopUnroller&lt;n&gt;::_neg(double*d,const double*a ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">  106536170 :   LoopUnroller&lt;n-1&gt;::_neg(d,a);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">  212691790 :   d[n-1]=-a[n-1];</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">  212691790 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : template&lt;&gt;</a>
+<a name="131"><span class="lineNum">     131 </span>            : inline</a>
+<a name="132"><span class="lineNum">     132 </span>            : void LoopUnroller&lt;1&gt;::_neg(double*d,const double*a) {</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">  106155620 :   d[0]=-a[0];</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : template&lt;unsigned n&gt;</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov"> 1572461500 : double LoopUnroller&lt;n&gt;::_sum2(const double*d) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov"> 1572461500 :   return LoopUnroller&lt;n-1&gt;::_sum2(d)+d[n-1]*d[n-1];</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : template&lt;&gt;</a>
+<a name="142"><span class="lineNum">     142 </span>            : inline</a>
+<a name="143"><span class="lineNum">     143 </span>            : double LoopUnroller&lt;1&gt;::_sum2(const double*d) {</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">  785671199 :   return d[0]*d[0];</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : template&lt;unsigned n&gt;</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">  332983464 : double LoopUnroller&lt;n&gt;::_dot(const double*d,const double*v) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">  332983464 :   return LoopUnroller&lt;n-1&gt;::_dot(d,v)+d[n-1]*v[n-1];</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : template&lt;&gt;</a>
+<a name="153"><span class="lineNum">     153 </span>            : inline</a>
+<a name="154"><span class="lineNum">     154 </span>            : double LoopUnroller&lt;1&gt;::_dot(const double*d,const double*v) {</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">  166491732 :   return d[0]*v[0];</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Matrix.h.func-sort-c.html b/coverage/tools/Matrix.h.func-sort-c.html
new file mode 100644
index 0000000000..0edda4f9dc
--- /dev/null
+++ b/coverage/tools/Matrix.h.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Matrix.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Matrix.h<span style="font-size: 80%;"> (<a href="Matrix.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Matrix.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#258">_ZN4PLMD12pseudoInvertIdEEiRKNS_6MatrixIT_EERNS1_IdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#99">_ZN4PLMD6MatrixIdE13setFromVectorERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#160">_ZN4PLMDmlIdEENS_6MatrixIT_EERS2_RKS3_</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#373">_ZN4PLMD6logdetIdEEiRKNS_6MatrixIT_EERd</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#129">_ZN4PLMD6MatrixIdEmLERKd</a></td>
+              <td class="coverFnHi">112</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#341">_ZN4PLMD8choleskyIdEEvRKNS_6MatrixIT_EERS3_</a></td>
+              <td class="coverFnHi">446</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#172">_ZN4PLMD4multIdEEvRKNS_6MatrixIT_EERKSt6vectorIS2_SaIS2_EERS8_</a></td>
+              <td class="coverFnHi">2141</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#305">_ZN4PLMD6InvertIdEEiRKNS_6MatrixIT_EERNS1_IdEE</a></td>
+              <td class="coverFnHi">9383</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#166">_ZN4PLMD4multIdEEvRKNS_6MatrixIT_EES5_RS3_</a></td>
+              <td class="coverFnHi">13725</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#204">_ZN4PLMD7diagMatIdEEiRKNS_6MatrixIT_EERSt6vectorIdSaIdEERNS1_IdEE</a></td>
+              <td class="coverFnHi">14151</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#151">_ZNK4PLMD6MatrixIdE11isSymmetricEv</a></td>
+              <td class="coverFnHi">23980</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Matrix.h.func.html b/coverage/tools/Matrix.h.func.html
new file mode 100644
index 0000000000..6979113929
--- /dev/null
+++ b/coverage/tools/Matrix.h.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Matrix.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Matrix.h<span style="font-size: 80%;"> (<a href="Matrix.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Matrix.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#258">_ZN4PLMD12pseudoInvertIdEEiRKNS_6MatrixIT_EERNS1_IdEE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#172">_ZN4PLMD4multIdEEvRKNS_6MatrixIT_EERKSt6vectorIS2_SaIS2_EERS8_</a></td>
+              <td class="coverFnHi">2141</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#166">_ZN4PLMD4multIdEEvRKNS_6MatrixIT_EES5_RS3_</a></td>
+              <td class="coverFnHi">13725</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#305">_ZN4PLMD6InvertIdEEiRKNS_6MatrixIT_EERNS1_IdEE</a></td>
+              <td class="coverFnHi">9383</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#99">_ZN4PLMD6MatrixIdE13setFromVectorERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#129">_ZN4PLMD6MatrixIdEmLERKd</a></td>
+              <td class="coverFnHi">112</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#373">_ZN4PLMD6logdetIdEEiRKNS_6MatrixIT_EERd</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#204">_ZN4PLMD7diagMatIdEEiRKNS_6MatrixIT_EERSt6vectorIdSaIdEERNS1_IdEE</a></td>
+              <td class="coverFnHi">14151</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#341">_ZN4PLMD8choleskyIdEEvRKNS_6MatrixIT_EERS3_</a></td>
+              <td class="coverFnHi">446</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#160">_ZN4PLMDmlIdEENS_6MatrixIT_EERS2_RKS3_</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Matrix.h.gcov.html#151">_ZNK4PLMD6MatrixIdE11isSymmetricEv</a></td>
+              <td class="coverFnHi">23980</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Matrix.h.gcov.html b/coverage/tools/Matrix.h.gcov.html
new file mode 100644
index 0000000000..7f722d684e
--- /dev/null
+++ b/coverage/tools/Matrix.h.gcov.html
@@ -0,0 +1,490 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Matrix.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Matrix.h<span style="font-size: 80%;"> (source / <a href="Matrix.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Matrix_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Matrix_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;vector&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;set&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cmath&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;MatrixSquareBracketsAccess.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;Log.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;lapack/lapack.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Calculate the dot product between two vectors</a>
+<a name="37"><span class="lineNum">      37 </span>            : template &lt;typename T&gt; T dotProduct( const std::vector&lt;T&gt;&amp; A, const std::vector&lt;T&gt;&amp; B ) {</a>
+<a name="38"><span class="lineNum">      38 </span>            :   plumed_assert( A.size()==B.size() );</a>
+<a name="39"><span class="lineNum">      39 </span>            :   T val; for(unsigned i=0; i&lt;A.size(); ++i) { val+=A[i]*B[i]; }</a>
+<a name="40"><span class="lineNum">      40 </span>            :   return val;</a>
+<a name="41"><span class="lineNum">      41 </span>            : }</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Calculate the dot product between a vector and itself</a>
+<a name="44"><span class="lineNum">      44 </span>            : template &lt;typename T&gt; T norm( const std::vector&lt;T&gt;&amp; A ) {</a>
+<a name="45"><span class="lineNum">      45 </span>            :   T val; for(unsigned i=0; i&lt;A.size(); ++i) { val+=A[i]*A[i]; }</a>
+<a name="46"><span class="lineNum">      46 </span>            :   return val;</a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /// This class stores a full matrix and allows one to do some simple matrix operations</a>
+<a name="50"><span class="lineNum">      50 </span>            : template &lt;typename T&gt;</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">    9736586 : class Matrix:</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   public MatrixSquareBracketsAccess&lt;Matrix&lt;T&gt;,T&gt;</a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   /// Multiply matrix by scalar</a>
+<a name="55"><span class="lineNum">      55 </span>            :   template &lt;typename U&gt; friend Matrix&lt;U&gt; operator*(U&amp;, const Matrix&lt;U&gt;&amp; );</a>
+<a name="56"><span class="lineNum">      56 </span>            :   /// Matrix matrix multiply</a>
+<a name="57"><span class="lineNum">      57 </span>            :   template &lt;typename U&gt; friend void mult( const Matrix&lt;U&gt;&amp;, const Matrix&lt;U&gt;&amp;, Matrix&lt;U&gt;&amp; );</a>
+<a name="58"><span class="lineNum">      58 </span>            :   /// Matrix times a std::vector</a>
+<a name="59"><span class="lineNum">      59 </span>            :   template &lt;typename U&gt; friend void mult( const Matrix&lt;U&gt;&amp;, const std::vector&lt;U&gt;&amp;, std::vector&lt;U&gt;&amp; );</a>
+<a name="60"><span class="lineNum">      60 </span>            :   /// std::vector times a Matrix</a>
+<a name="61"><span class="lineNum">      61 </span>            :   template &lt;typename U&gt; friend void mult( const std::vector&lt;U&gt;&amp;, const Matrix&lt;U&gt;&amp;, std::vector&lt;U&gt;&amp; );</a>
+<a name="62"><span class="lineNum">      62 </span>            :   /// Matrix transpose</a>
+<a name="63"><span class="lineNum">      63 </span>            :   template &lt;typename U&gt; friend void transpose( const Matrix&lt;U&gt;&amp;, Matrix&lt;U&gt;&amp; );</a>
+<a name="64"><span class="lineNum">      64 </span>            :   /// Output the entire matrix on a single line</a>
+<a name="65"><span class="lineNum">      65 </span>            :   template &lt;typename U&gt; friend Log&amp; operator&lt;&lt;(Log&amp;, const Matrix&lt;U&gt;&amp; );</a>
+<a name="66"><span class="lineNum">      66 </span>            :   /// Output the Matrix in matrix form</a>
+<a name="67"><span class="lineNum">      67 </span>            :   template &lt;typename U&gt; friend void matrixOut( Log&amp;, const Matrix&lt;U&gt;&amp; );</a>
+<a name="68"><span class="lineNum">      68 </span>            :   /// Diagonalize a symmetric matrix - returns zero if diagonalization worked</a>
+<a name="69"><span class="lineNum">      69 </span>            :   template &lt;typename U&gt; friend int diagMat( const Matrix&lt;U&gt;&amp;, std::vector&lt;double&gt;&amp;, Matrix&lt;double&gt;&amp; );</a>
+<a name="70"><span class="lineNum">      70 </span>            :   /// Calculate the Moore-Penrose Pseudoinverse of a matrix</a>
+<a name="71"><span class="lineNum">      71 </span>            :   template &lt;typename U&gt; friend int pseudoInvert( const Matrix&lt;U&gt;&amp;, Matrix&lt;double&gt;&amp; );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   /// Calculate the logarithm of the determinant of a symmetric matrix - returns zero if succesfull</a>
+<a name="73"><span class="lineNum">      73 </span>            :   template &lt;typename U&gt; friend int logdet( const Matrix&lt;U&gt;&amp;, double&amp; );</a>
+<a name="74"><span class="lineNum">      74 </span>            :   /// Invert a matrix (works for both symmetric and asymmetric matrices) - returns zero if sucesfull</a>
+<a name="75"><span class="lineNum">      75 </span>            :   template &lt;typename U&gt; friend int Invert( const Matrix&lt;U&gt;&amp;, Matrix&lt;double&gt;&amp; );</a>
+<a name="76"><span class="lineNum">      76 </span>            :   /// Do a cholesky decomposition of a matrix</a>
+<a name="77"><span class="lineNum">      77 </span>            :   template &lt;typename U&gt; friend void cholesky( const Matrix&lt;U&gt;&amp;, Matrix&lt;U&gt;&amp; );</a>
+<a name="78"><span class="lineNum">      78 </span>            :   /// Solve a system of equations using the cholesky decomposition</a>
+<a name="79"><span class="lineNum">      79 </span>            :   template &lt;typename U&gt; friend void chol_elsolve( const Matrix&lt;U&gt;&amp;, const std::vector&lt;U&gt;&amp;, std::vector&lt;U&gt;&amp; );</a>
+<a name="80"><span class="lineNum">      80 </span>            : private:</a>
+<a name="81"><span class="lineNum">      81 </span>            :   /// Number of elements in matrix (nrows*ncols)</a>
+<a name="82"><span class="lineNum">      82 </span>            :   unsigned sz;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   /// Number of rows in matrix</a>
+<a name="84"><span class="lineNum">      84 </span>            :   unsigned rw;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   /// Number of columns in matrix</a>
+<a name="86"><span class="lineNum">      86 </span>            :   unsigned cl;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   /// The data in the matrix</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;T&gt; data;</a>
+<a name="89"><span class="lineNum">      89 </span>            : public:</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">   10723152 :   explicit Matrix(const unsigned nr=0, const unsigned nc=0 )  : sz(nr*nc), rw(nr), cl(nc), data(nr*nc) {}</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        259 :   Matrix(const Matrix&lt;T&gt;&amp; t) : sz(t.sz), rw(t.rw), cl(t.cl), data(t.data) {}</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   /// Resize the matrix</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        331 :   void resize( const unsigned nr, const unsigned nc ) { rw=nr; cl=nc; sz=nr*nc; data.resize(sz); }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   /// Return the number of rows</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">   37740101 :   inline unsigned nrows() const { return rw; }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   /// Return the number of columns</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">  116551156 :   inline unsigned ncols() const { return cl; }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   /// Return the contents of the matrix as a vector of length rw*cl</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         26 :   inline std::vector&lt;T&gt;&amp; getVector() { return data; }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   /// Set the matrix from a vector input</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        908 :   inline void setFromVector( const std::vector&lt;T&gt;&amp; vecin ) { plumed_assert( vecin.size()==sz ); for(unsigned i=0; i&lt;sz; ++i) data[i]=vecin[i]; }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   /// Return element i,j of the matrix</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov"> 2267477073 :   inline const T&amp; operator () (const unsigned&amp; i, const unsigned&amp; j) const { return data[j+i*cl]; }</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   /// Return a referenre to element i,j of the matrix</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">  231234617 :   inline T&amp; operator () (const unsigned&amp; i, const unsigned&amp; j)      { return data[j+i*cl]; }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   /// Set all elements of the matrix equal to the value of v</a>
+<a name="107"><span class="lineNum">     107 </span>            :   Matrix&lt;T&gt;&amp; operator=(const T&amp; v) {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">    6748667 :     for(unsigned i=0; i&lt;sz; ++i) { data[i]=v; }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     return *this;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            :   /// Set the Matrix equal to another Matrix</a>
+<a name="112"><span class="lineNum">     112 </span>            :   Matrix&lt;T&gt;&amp; operator=(const Matrix&lt;T&gt;&amp; m) {</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       5208 :     sz=m.sz;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       5208 :     rw=m.rw;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       5208 :     cl=m.cl;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       5208 :     data=m.data;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       5208 :     return *this;</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   }</a>
+<a name="119"><span class="lineNum">     119 </span>            :   /// Set the Matrix equal to the value of a standard vector - used for readin</a>
+<a name="120"><span class="lineNum">     120 </span>            :   Matrix&lt;T&gt;&amp; operator=(const std::vector&lt;T&gt;&amp; v) {</a>
+<a name="121"><span class="lineNum">     121 </span>            :     plumed_dbg_assert( v.size()==sz );</a>
+<a name="122"><span class="lineNum">     122 </span>            :     for(unsigned i=0; i&lt;sz; ++i) { data[i]=v[i]; }</a>
+<a name="123"><span class="lineNum">     123 </span>            :     return *this;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   }</a>
+<a name="125"><span class="lineNum">     125 </span>            :   /// Add v to all elements of the Matrix</a>
+<a name="126"><span class="lineNum">     126 </span>            :   Matrix&lt;T&gt; operator+=(const T&amp; v) {</a>
+<a name="127"><span class="lineNum">     127 </span>            :     for(unsigned i=0; i&lt;sz; ++i) { data[i]+=v; }</a>
+<a name="128"><span class="lineNum">     128 </span>            :     return *this;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span>            :   /// Multiply all elements by v</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        112 :   Matrix&lt;T&gt; operator*=(const T&amp; v) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     440804 :     for(unsigned i=0; i&lt;sz; ++i) { data[i]*=v; }</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        112 :     return *this;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   }</a>
+<a name="135"><span class="lineNum">     135 </span>            :   /// Matrix addition</a>
+<a name="136"><span class="lineNum">     136 </span>            :   Matrix&lt;T&gt;&amp; operator+=(const Matrix&lt;T&gt;&amp; m) {</a>
+<a name="137"><span class="lineNum">     137 </span>            :     plumed_dbg_assert( m.rw==rw &amp;&amp; m.cl==cl );</a>
+<a name="138"><span class="lineNum">     138 </span>            :     data+=m.data;</a>
+<a name="139"><span class="lineNum">     139 </span>            :     return *this;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span>            :   /// Subtract v from all elements of the Matrix</a>
+<a name="142"><span class="lineNum">     142 </span>            :   Matrix&lt;T&gt; operator-=(const T&amp; v) {</a>
+<a name="143"><span class="lineNum">     143 </span>            :     for(unsigned i=0; i&lt;sz; ++i) { data-=v; }</a>
+<a name="144"><span class="lineNum">     144 </span>            :     return *this;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span>            :   /// Matrix subtraction</a>
+<a name="147"><span class="lineNum">     147 </span>            :   Matrix&lt;T&gt;&amp; operator-=(const Matrix&lt;T&gt;&amp; m) {</a>
+<a name="148"><span class="lineNum">     148 </span>            :     plumed_dbg_assert( m.rw==rw &amp;&amp; m.cl==cl );</a>
+<a name="149"><span class="lineNum">     149 </span>            :     data-=m.data;</a>
+<a name="150"><span class="lineNum">     150 </span>            :     return *this;</a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span>            :   /// Test if the matrix is symmetric or not</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      23980 :   unsigned isSymmetric() const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      23980 :     if (rw!=cl) { return 0; }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     unsigned sym=1;</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     268903 :     for(unsigned i=1; i&lt;rw; ++i) for(unsigned j=0; j&lt;i; ++j) if( std::fabs(data[i+j*cl]-data[j+i*cl])&gt;1.e-10 ) { sym=0; break; }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     return sym;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span>            : };</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : /// Multiply matrix by scalar</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         12 : template &lt;typename T&gt; Matrix&lt;T&gt; operator*(T&amp; v, const Matrix&lt;T&gt;&amp; m ) {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   Matrix&lt;T&gt; new_m(m);</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         12 :   new_m*=v;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         12 :   return new_m;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      13725 : template &lt;typename T&gt; void mult( const Matrix&lt;T&gt;&amp; A, const Matrix&lt;T&gt;&amp; B, Matrix&lt;T&gt;&amp; C ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      13725 :   plumed_assert(A.cl==B.rw);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      13725 :   if( A.rw !=C.rw  || B.cl !=C.cl ) { C.resize( A.rw, B.cl ); } C=static_cast&lt;T&gt;( 0 );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov"> 2011234560 :   for(unsigned i=0; i&lt;A.rw; ++i) for(unsigned j=0; j&lt;B.cl; ++j) for (unsigned k=0; k&lt;A.cl; ++k) C(i,j)+=A(i,k)*B(k,j);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">      13725 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       2141 : template &lt;typename T&gt; void mult( const Matrix&lt;T&gt;&amp; A, const std::vector&lt;T&gt;&amp; B, std::vector&lt;T&gt;&amp; C) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       2141 :   plumed_assert( A.cl==B.size() );</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       2141 :   if( C.size()!=A.rw  ) { C.resize(A.rw); }</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      37323 :   for(unsigned i=0; i&lt;A.rw; ++i) { C[i]= static_cast&lt;T&gt;( 0 ); }</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     681459 :   for(unsigned i=0; i&lt;A.rw; ++i) for(unsigned k=0; k&lt;A.cl; ++k) C[i]+=A(i,k)*B[k] ;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       2141 : }</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : template &lt;typename T&gt; void mult( const std::vector&lt;T&gt;&amp; A, const Matrix&lt;T&gt;&amp; B, std::vector&lt;T&gt;&amp; C) {</a>
+<a name="182"><span class="lineNum">     182 </span>            :   plumed_assert( B.rw==A.size() );</a>
+<a name="183"><span class="lineNum">     183 </span>            :   if( C.size()!=B.cl ) {C.resize( B.cl );}</a>
+<a name="184"><span class="lineNum">     184 </span>            :   for(unsigned i=0; i&lt;B.cl; ++i) { C[i]=static_cast&lt;T&gt;( 0 ); }</a>
+<a name="185"><span class="lineNum">     185 </span>            :   for(unsigned i=0; i&lt;B.cl; ++i) for(unsigned k=0; k&lt;B.rw; ++k) C[i]+=A[k]*B(k,i);</a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : template &lt;typename T&gt; void transpose( const Matrix&lt;T&gt;&amp; A, Matrix&lt;T&gt;&amp; AT ) {</a>
+<a name="189"><span class="lineNum">     189 </span>            :   if( A.rw!=AT.cl || A.cl!=AT.rw ) AT.resize( A.cl, A.rw );</a>
+<a name="190"><span class="lineNum">     190 </span>            :   for(unsigned i=0; i&lt;A.cl; ++i) for(unsigned j=0; j&lt;A.rw; ++j) AT(i,j)=A(j,i);</a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : template &lt;typename T&gt; Log&amp; operator&lt;&lt;(Log&amp; ostr, const Matrix&lt;T&gt;&amp; mat) {</a>
+<a name="194"><span class="lineNum">     194 </span>            :   for(unsigned i=0; i&lt;mat.sz; ++i) ostr&lt;&lt;mat.data[i]&lt;&lt;&quot; &quot;;</a>
+<a name="195"><span class="lineNum">     195 </span>            :   return ostr;</a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : template &lt;typename T&gt; void matrixOut( Log&amp; ostr, const Matrix&lt;T&gt;&amp; mat) {</a>
+<a name="199"><span class="lineNum">     199 </span>            :   for(unsigned i=0; i&lt;mat.rw; ++i) {</a>
+<a name="200"><span class="lineNum">     200 </span>            :     for(unsigned j=0; j&lt;mat.cl; ++j) { ostr&lt;&lt;mat(i,j)&lt;&lt;&quot; &quot;; }</a>
+<a name="201"><span class="lineNum">     201 </span>            :     ostr&lt;&lt;&quot;\n&quot;;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   }</a>
+<a name="203"><span class="lineNum">     203 </span>            :   return;</a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      14151 : template &lt;typename T&gt; int diagMat( const Matrix&lt;T&gt;&amp; A, std::vector&lt;double&gt;&amp; eigenvals, Matrix&lt;double&gt;&amp; eigenvecs ) {</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            :   // Check matrix is square and symmetric</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      14151 :   plumed_assert( A.rw==A.cl ); plumed_assert( A.isSymmetric()==1 );</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      14151 :   std::vector&lt;double&gt; da(A.sz);</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   unsigned k=0;</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      14151 :   std::vector&lt;double&gt; evals(A.cl);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   // Transfer the matrix to the local array</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">     494643 :   for (unsigned i=0; i&lt;A.cl; ++i) for (unsigned j=0; j&lt;A.rw; ++j) da[k++]=static_cast&lt;double&gt;( A(j,i) );</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      14151 :   int n=A.cl; int lwork=-1, liwork=-1, m, info, one=1;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      14151 :   std::vector&lt;double&gt; work(A.cl);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      14151 :   std::vector&lt;int&gt; iwork(A.cl);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      14151 :   double vl, vu, abstol=0.0;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      14151 :   std::vector&lt;int&gt; isup(2*A.cl);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      14151 :   std::vector&lt;double&gt; evecs(A.sz);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      14151 :   plumed_lapack_dsyevr(&quot;V&quot;, &quot;I&quot;, &quot;U&quot;, &amp;n, da.data(), &amp;n, &amp;vl, &amp;vu, &amp;one, &amp;n,</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :                        &amp;abstol, &amp;m, evals.data(), evecs.data(), &amp;n,</a>
+<a name="225"><span class="lineNum">     225 </span>            :                        isup.data(), work.data(), &amp;lwork, iwork.data(), &amp;liwork, &amp;info);</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      14151 :   if (info!=0) return info;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   // Retrieve correct sizes for work and iwork then reallocate</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      14151 :   liwork=iwork[0]; iwork.resize(liwork);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      14151 :   lwork=static_cast&lt;int&gt;( work[0] ); work.resize(lwork);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      14151 :   plumed_lapack_dsyevr(&quot;V&quot;, &quot;I&quot;, &quot;U&quot;, &amp;n, da.data(), &amp;n, &amp;vl, &amp;vu, &amp;one, &amp;n,</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :                        &amp;abstol, &amp;m, evals.data(), evecs.data(), &amp;n,</a>
+<a name="234"><span class="lineNum">     234 </span>            :                        isup.data(), work.data(), &amp;lwork, iwork.data(), &amp;liwork, &amp;info);</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      14151 :   if (info!=0) return info;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">      14151 :   if( eigenvals.size()!=A.cl ) { eigenvals.resize( A.cl ); }</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      14151 :   if( eigenvecs.rw!=A.rw || eigenvecs.cl!=A.cl ) { eigenvecs.resize( A.rw, A.cl ); }</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   k=0;</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      43840 :   for(unsigned i=0; i&lt;A.cl; ++i) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">      29689 :     eigenvals[i]=evals[i];</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     // N.B. For ease of producing projectors we store the eigenvectors</a>
+<a name="243"><span class="lineNum">     243 </span>            :     // ROW-WISE in the eigenvectors matrix.  The first index is the</a>
+<a name="244"><span class="lineNum">     244 </span>            :     // eigenvector number and the second the component</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">     480492 :     for(unsigned j=0; j&lt;A.rw; ++j) { eigenvecs(i,j)=evecs[k++]; }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   // This changes eigenvectors so that the first non-null element</a>
+<a name="249"><span class="lineNum">     249 </span>            :   // of each of them is positive</a>
+<a name="250"><span class="lineNum">     250 </span>            :   // We can do it because the phase is arbitrary, and helps making</a>
+<a name="251"><span class="lineNum">     251 </span>            :   // the result reproducible</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">      43840 :   for(int i=0; i&lt;n; ++i) {</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     int j;</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">      29689 :     for(j=0; j&lt;n; j++) if(eigenvecs(i,j)*eigenvecs(i,j)&gt;1e-14) break;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">     232782 :     if(j&lt;n) if(eigenvecs(i,j)&lt;0.0) for(j=0; j&lt;n; j++) eigenvecs(i,j)*=-1;</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span>            :   return 0;</a>
+<a name="258"><span class="lineNum">     258 </span>            : }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 : template &lt;typename T&gt; int pseudoInvert( const Matrix&lt;T&gt;&amp; A, Matrix&lt;double&gt;&amp; pseudoinverse ) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; da(A.sz);</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   unsigned k=0;</a>
+<a name="263"><span class="lineNum">     263 </span>            :   // Transfer the matrix to the local array</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">     250501 :   for (unsigned i=0; i&lt;A.cl; ++i) for (unsigned j=0; j&lt;A.rw; ++j) da[k++]=static_cast&lt;double&gt;( A(j,i) );</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          1 :   int nsv, info, nrows=A.rw, ncols=A.cl;</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          1 :   if(A.rw&gt;A.cl) {nsv=A.cl;} else {nsv=A.rw;}</span></a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            :   // Create some containers for stuff from single value decomposition</a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; S(nsv);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; U(nrows*nrows);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; VT(ncols*ncols);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          1 :   std::vector&lt;int&gt; iwork(8*nsv);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :   // This optimizes the size of the work array used in lapack singular value decomposition</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          1 :   int lwork=-1;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          1 :   std::vector&lt;double&gt; work(1);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          1 :   plumed_lapack_dgesdd( &quot;A&quot;, &amp;nrows, &amp;ncols, da.data(), &amp;nrows, S.data(), U.data(), &amp;nrows, VT.data(), &amp;ncols, work.data(), &amp;lwork, iwork.data(), &amp;info );</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          1 :   if(info!=0) return info;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            :   // Retrieve correct sizes for work and rellocate</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          1 :   lwork=(int) work[0]; work.resize(lwork);</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   // This does the singular value decomposition</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          1 :   plumed_lapack_dgesdd( &quot;A&quot;, &amp;nrows, &amp;ncols, da.data(), &amp;nrows, S.data(), U.data(), &amp;nrows, VT.data(), &amp;ncols, work.data(), &amp;lwork, iwork.data(), &amp;info );</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          1 :   if(info!=0) return info;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :   // Compute the tolerance on the singular values ( machine epsilon * number of singular values * maximum singular value )</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        500 :   double tol; tol=S[0]; for(int i=1; i&lt;nsv; ++i) { if( S[i]&gt;tol ) { tol=S[i]; } } tol*=nsv*epsilon;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            :   // Get the inverses of the singlular values</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          1 :   Matrix&lt;double&gt; Si( ncols, nrows ); Si=0.0;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        501 :   for(int i=0; i&lt;nsv; ++i) { if( S[i]&gt;tol ) { Si(i,i)=1./S[i]; } else { Si(i,i)=0.0; } }</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            :   // Now extract matrices for pseudoinverse</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          1 :   Matrix&lt;double&gt; V( ncols, ncols ), UT( nrows, nrows ), tmp( ncols, nrows );</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     250501 :   k=0; for(int i=0; i&lt;nrows; ++i) { for(int j=0; j&lt;nrows; ++j) { UT(i,j)=U[k++]; } }</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">     250501 :   k=0; for(int i=0; i&lt;ncols; ++i) { for(int j=0; j&lt;ncols; ++j) { V(i,j)=VT[k++]; } }</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            :   // And do matrix algebra to construct the pseudoinverse</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          1 :   if( pseudoinverse.rw!=ncols || pseudoinverse.cl!=nrows ) pseudoinverse.resize( ncols, nrows );</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          1 :   mult( V, Si, tmp ); mult( tmp, UT, pseudoinverse );</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            :   return 0;</a>
+<a name="305"><span class="lineNum">     305 </span>            : }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">       9383 : template &lt;typename T&gt; int Invert( const Matrix&lt;T&gt;&amp; A, Matrix&lt;double&gt;&amp; inverse ) {</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       9383 :   if( A.isSymmetric()==1 ) {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     // GAT -- I only ever use symmetric matrices so I can invert them like this.</a>
+<a name="311"><span class="lineNum">     311 </span>            :     // I choose to do this as I have had problems with the more general way of doing this that</a>
+<a name="312"><span class="lineNum">     312 </span>            :     // is implemented below.</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       9326 :     std::vector&lt;double&gt; eval(A.rw); Matrix&lt;double&gt; evec(A.rw,A.cl), tevec(A.rw,A.cl);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       9326 :     int err; err=diagMat( A, eval, evec );</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       9326 :     if(err!=0) return err;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      64900 :     for (unsigned i=0; i&lt;A.rw; ++i) for (unsigned j=0; j&lt;A.cl; ++j) tevec(i,j)=evec(j,i)/eval[j];</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">       9326 :     mult(tevec,evec,inverse);</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :   } else {</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         57 :     std::vector&lt;double&gt; da(A.sz);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         57 :     std::vector&lt;int&gt; ipiv(A.cl);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         57 :     unsigned k=0; int n=A.rw, info;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        399 :     for(unsigned i=0; i&lt;A.cl; ++i) for(unsigned j=0; j&lt;A.rw; ++j) da[k++]=static_cast&lt;double&gt;( A(j,i) );</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         57 :     plumed_lapack_dgetrf(&amp;n,&amp;n,da.data(),&amp;n,ipiv.data(),&amp;info);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         57 :     if(info!=0) return info;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         57 :     int lwork=-1;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         57 :     std::vector&lt;double&gt; work(A.cl);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         57 :     plumed_lapack_dgetri(&amp;n,da.data(),&amp;n,ipiv.data(),work.data(),&amp;lwork,&amp;info);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         57 :     if(info!=0) return info;</span></a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         57 :     lwork=static_cast&lt;int&gt;( work[0] ); work.resize(lwork);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         57 :     plumed_lapack_dgetri(&amp;n,da.data(),&amp;n,ipiv.data(),work.data(),&amp;lwork,&amp;info);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         57 :     if(info!=0) return info;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         57 :     if( inverse.cl!=A.cl || inverse.rw!=A.rw ) { inverse.resize(A.rw,A.cl); }</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        399 :     k=0; for(unsigned i=0; i&lt;A.rw; ++i) for(unsigned j=0; j&lt;A.cl; ++j) inverse(j,i)=da[k++];</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   }</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            :   return 0;</a>
+<a name="341"><span class="lineNum">     341 </span>            : }</a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">        446 : template &lt;typename T&gt; void cholesky( const Matrix&lt;T&gt;&amp; A, Matrix&lt;T&gt;&amp; B ) {</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        446 :   plumed_assert( A.rw==A.cl &amp;&amp; A.isSymmetric() );</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :   Matrix&lt;T&gt; L(A.rw,A.cl); L=0.;</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">        446 :   std::vector&lt;T&gt; D(A.rw,0.);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       1047 :   for(unsigned i=0; i&lt;A.rw; ++i) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        601 :     L(i,i)=static_cast&lt;T&gt;( 1 );</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        756 :     for (unsigned j=0; j&lt;i; ++j) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        155 :       L(i,j)=A(i,j);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        155 :       for (unsigned k=0; k&lt;j; ++k) L(i,j)-=L(i,k)*L(j,k)*D[k];</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        155 :       if (D[j]!=0.) L(i,j)/=D[j]; else L(i,j)=static_cast&lt;T&gt;( 0 );</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :     }</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">        601 :     D[i]=A(i,i);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        756 :     for (unsigned k=0; k&lt;i; ++k) D[i]-=L(i,k)*L(i,k)*D[k];</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   }</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">       1047 :   for(unsigned i=0; i&lt;A.rw; ++i) D[i]=(D[i]&gt;0.?std::sqrt(D[i]):0.);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">        446 :   if( B.rw!=A.rw || B.cl!=A.cl ) { B.resize( A.rw, A.cl); }</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">       1803 :   B=0.; for(unsigned i=0; i&lt;A.rw; ++i) for(unsigned j=0; j&lt;=i; ++j) B(i,j)+=L(i,j)*D[j];</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        446 : }</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span>            : template &lt;typename T&gt; void chol_elsolve( const Matrix&lt;T&gt;&amp; M, const std::vector&lt;T&gt;&amp; b, std::vector&lt;T&gt;&amp; y ) {</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            :   plumed_assert( M.rw==M.cl &amp;&amp; M(0,1)==0.0 &amp;&amp; b.size()==M.rw );</a>
+<a name="367"><span class="lineNum">     367 </span>            :   if( y.size()!=M.rw ) { y.resize( M.rw ); }</a>
+<a name="368"><span class="lineNum">     368 </span>            :   for(unsigned i=0; i&lt;M.rw; ++i) {</a>
+<a name="369"><span class="lineNum">     369 </span>            :     y[i]=b[i];</a>
+<a name="370"><span class="lineNum">     370 </span>            :     for(unsigned j=0; j&lt;i; ++j) y[i]-=M(i,j)*y[j];</a>
+<a name="371"><span class="lineNum">     371 </span>            :     y[i]*=1.0/M(i,i);</a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span>            : }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         46 : template &lt;typename T&gt; int logdet( const Matrix&lt;T&gt;&amp; M, double&amp; ldet ) {</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   // Check matrix is square and symmetric</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         46 :   plumed_assert( M.rw==M.cl || M.isSymmetric() );</span></a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         46 :   std::vector&lt;double&gt; da(M.sz);</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :   unsigned k=0;</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         46 :   std::vector&lt;double&gt; evals(M.cl);</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   // Transfer the matrix to the local array</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        578 :   for (unsigned i=0; i&lt;M.rw; ++i) for (unsigned j=0; j&lt;M.cl; ++j) da[k++]=static_cast&lt;double&gt;( M(j,i) );</span></a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         46 :   int n=M.cl; int lwork=-1, liwork=-1, info, m, one=1;</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         46 :   std::vector&lt;double&gt; work(M.rw);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         46 :   std::vector&lt;int&gt; iwork(M.rw);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         46 :   double vl, vu, abstol=0.0;</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         46 :   std::vector&lt;int&gt; isup(2*M.rw);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         46 :   std::vector&lt;double&gt; evecs(M.sz);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         46 :   plumed_lapack_dsyevr(&quot;N&quot;, &quot;I&quot;, &quot;U&quot;, &amp;n, da.data(), &amp;n, &amp;vl, &amp;vu, &amp;one, &amp;n,</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :                        &amp;abstol, &amp;m, evals.data(), evecs.data(), &amp;n,</a>
+<a name="393"><span class="lineNum">     393 </span>            :                        isup.data(), work.data(), &amp;lwork, iwork.data(), &amp;liwork, &amp;info);</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">         46 :   if (info!=0) return info;</span></a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            :   // Retrieve correct sizes for work and iwork then reallocate</a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">         46 :   lwork=static_cast&lt;int&gt;( work[0] ); work.resize(lwork);</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         46 :   liwork=iwork[0]; iwork.resize(liwork);</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">         46 :   plumed_lapack_dsyevr(&quot;N&quot;, &quot;I&quot;, &quot;U&quot;, &amp;n, da.data(), &amp;n, &amp;vl, &amp;vu, &amp;one, &amp;n,</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :                        &amp;abstol, &amp;m, evals.data(), evecs.data(), &amp;n,</a>
+<a name="402"><span class="lineNum">     402 </span>            :                        isup.data(), work.data(), &amp;lwork, iwork.data(), &amp;liwork, &amp;info);</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         46 :   if (info!=0) return info;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            :   // Transfer the eigenvalues and eigenvectors to the output</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">        180 :   ldet=0; for(unsigned i=0; i&lt;M.cl; i++) { ldet+=log(evals[i]); }</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            :   return 0;</a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span>            : }</a>
+<a name="414"><span class="lineNum">     414 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MatrixSquareBracketsAccess.h.func-sort-c.html b/coverage/tools/MatrixSquareBracketsAccess.h.func-sort-c.html
new file mode 100644
index 0000000000..b72f651c71
--- /dev/null
+++ b/coverage/tools/MatrixSquareBracketsAccess.h.func-sort-c.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MatrixSquareBracketsAccess.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MatrixSquareBracketsAccess.h<span style="font-size: 80%;"> (<a href="MatrixSquareBracketsAccess.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MatrixSquareBracketsAccess.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#98">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE9Const_rowC2ERKS3_j</a></td>
+              <td class="coverFnHi">5433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#106">_ZNK4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE9Const_rowixEj</a></td>
+              <td class="coverFnHi">5433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#127">_ZNK4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjEixEj</a></td>
+              <td class="coverFnHi">5433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixIdEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">30474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixIdEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">30474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixIdEEdjjEixEj</a></td>
+              <td class="coverFnHi">30474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj1ELj4EEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">2744600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj1ELj4EEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">2744600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj1ELj4EEEdjjEixEj</a></td>
+              <td class="coverFnHi">2744600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj4ELj4EEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">16897856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj4ELj4EEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">16897856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj4ELj4EEEdjjEixEj</a></td>
+              <td class="coverFnHi">16897856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">27681477</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">27681477</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjEixEj</a></td>
+              <td class="coverFnHi">27681477</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEES6_jjE3RowC2ERS8_j</a></td>
+              <td class="coverFnHi">35212356</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEES6_jjE3RowixEj</a></td>
+              <td class="coverFnHi">35212356</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEES6_jjEixEj</a></td>
+              <td class="coverFnHi">35212356</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MatrixSquareBracketsAccess.h.func.html b/coverage/tools/MatrixSquareBracketsAccess.h.func.html
new file mode 100644
index 0000000000..f40740bf1b
--- /dev/null
+++ b/coverage/tools/MatrixSquareBracketsAccess.h.func.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MatrixSquareBracketsAccess.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MatrixSquareBracketsAccess.h<span style="font-size: 80%;"> (<a href="MatrixSquareBracketsAccess.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MatrixSquareBracketsAccess.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj1ELj4EEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">2744600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj1ELj4EEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">2744600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj1ELj4EEEdjjEixEj</a></td>
+              <td class="coverFnHi">2744600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">27681477</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">27681477</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#98">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE9Const_rowC2ERKS3_j</a></td>
+              <td class="coverFnHi">5433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjEixEj</a></td>
+              <td class="coverFnHi">27681477</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj4ELj4EEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">16897856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj4ELj4EEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">16897856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj4ELj4EEEdjjEixEj</a></td>
+              <td class="coverFnHi">16897856</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEES6_jjE3RowC2ERS8_j</a></td>
+              <td class="coverFnHi">35212356</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEES6_jjE3RowixEj</a></td>
+              <td class="coverFnHi">35212356</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEES6_jjEixEj</a></td>
+              <td class="coverFnHi">35212356</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#102">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixIdEEdjjE3RowC2ERS3_j</a></td>
+              <td class="coverFnHi">30474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#114">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixIdEEdjjE3RowixEj</a></td>
+              <td class="coverFnHi">30474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#122">_ZN4PLMD26MatrixSquareBracketsAccessINS_6MatrixIdEEdjjEixEj</a></td>
+              <td class="coverFnHi">30474</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#106">_ZNK4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjE9Const_rowixEj</a></td>
+              <td class="coverFnHi">5433</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MatrixSquareBracketsAccess.h.gcov.html#127">_ZNK4PLMD26MatrixSquareBracketsAccessINS_13TensorGenericILj3ELj3EEEdjjEixEj</a></td>
+              <td class="coverFnHi">5433</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MatrixSquareBracketsAccess.h.gcov.html b/coverage/tools/MatrixSquareBracketsAccess.h.gcov.html
new file mode 100644
index 0000000000..fefc3896cf
--- /dev/null
+++ b/coverage/tools/MatrixSquareBracketsAccess.h.gcov.html
@@ -0,0 +1,214 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MatrixSquareBracketsAccess.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MatrixSquareBracketsAccess.h<span style="font-size: 80%;"> (source / <a href="MatrixSquareBracketsAccess.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_MatrixSquareBracketsAccess_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_MatrixSquareBracketsAccess_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : /**</a>
+<a name="28"><span class="lineNum">      28 </span>            : Utility class to add [][] access</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : \tparam T The type of the matrix class.</a>
+<a name="31"><span class="lineNum">      31 </span>            : \tparam C The type of the returned value.</a>
+<a name="32"><span class="lineNum">      32 </span>            : \tparam I The type of the first index (default unsigned).</a>
+<a name="33"><span class="lineNum">      33 </span>            : \tparam J The type of the second index (default unsigned).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : It implements the trick described in C++ FAQ 13.12 to allow [][] access</a>
+<a name="36"><span class="lineNum">      36 </span>            : to matrix-like classes, based on the (,) syntax, thus translating</a>
+<a name="37"><span class="lineNum">      37 </span>            : [i][j] into (i,j).  In practice, one only needs to implement the (,) syntax and to inherit from</a>
+<a name="38"><span class="lineNum">      38 </span>            : MatrixSquareBracketsAccess.</a>
+<a name="39"><span class="lineNum">      39 </span>            : The first template parameter (T) should be the</a>
+<a name="40"><span class="lineNum">      40 </span>            : class itself, the second (C) is the type of the returned value,</a>
+<a name="41"><span class="lineNum">      41 </span>            : and the third (I) and fourth (J) are the types of the two indexes (unsigned by default).</a>
+<a name="42"><span class="lineNum">      42 </span>            : As everything is inlined, no overhead is expected.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : \verbatim</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : class MyMatrixClass:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   public MatrixSquareBracketsAccess&lt;MyMatrixClass,double&gt;</a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double data[16];</a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   double &amp; operator ()(unsigned i,unsigned j){</a>
+<a name="52"><span class="lineNum">      52 </span>            :     return data[4*i+j];</a>
+<a name="53"><span class="lineNum">      53 </span>            :   }</a>
+<a name="54"><span class="lineNum">      54 </span>            :   const double &amp; operator ()(unsigned i,unsigned j)const{</a>
+<a name="55"><span class="lineNum">      55 </span>            :     return data[4*i+j];</a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span>            : };</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : int main(){</a>
+<a name="60"><span class="lineNum">      60 </span>            :   MyMatrixClass m;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   m[0][1]=3.0;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   return 0;</a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : \endverbatim</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : template&lt;class T,class C,class I=unsigned,class J=unsigned&gt;</a>
+<a name="69"><span class="lineNum">      69 </span>            : class MatrixSquareBracketsAccess {</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Small utility class which just contains a pointer to the T and the row number</a>
+<a name="71"><span class="lineNum">      71 </span>            :   class Const_row {</a>
+<a name="72"><span class="lineNum">      72 </span>            :     friend class MatrixSquareBracketsAccess; // this so as to allow only T to instantiate Const_row</a>
+<a name="73"><span class="lineNum">      73 </span>            :     // the user should not manipulate it directly</a>
+<a name="74"><span class="lineNum">      74 </span>            :     const MatrixSquareBracketsAccess&amp; t;</a>
+<a name="75"><span class="lineNum">      75 </span>            :     const I i;</a>
+<a name="76"><span class="lineNum">      76 </span>            :     Const_row(const MatrixSquareBracketsAccess&amp;t,I i); // constructor is private and cannot be manipulated by the user</a>
+<a name="77"><span class="lineNum">      77 </span>            :   public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :     /// access element</a>
+<a name="79"><span class="lineNum">      79 </span>            :     const C &amp; operator[] (J j)const;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   };</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Small utility class which just contains a pointer to the T and the row number</a>
+<a name="82"><span class="lineNum">      82 </span>            :   class Row {</a>
+<a name="83"><span class="lineNum">      83 </span>            :     friend class MatrixSquareBracketsAccess; // this so as to allow only T to instantiate Const_row</a>
+<a name="84"><span class="lineNum">      84 </span>            :     // the user should not manipulate it directly</a>
+<a name="85"><span class="lineNum">      85 </span>            :     MatrixSquareBracketsAccess&amp; t;</a>
+<a name="86"><span class="lineNum">      86 </span>            :     const I i;</a>
+<a name="87"><span class="lineNum">      87 </span>            :     Row(MatrixSquareBracketsAccess&amp;t,I i); // constructor is private and cannot be manipulated by the user</a>
+<a name="88"><span class="lineNum">      88 </span>            :   public:</a>
+<a name="89"><span class="lineNum">      89 </span>            :     /// access element</a>
+<a name="90"><span class="lineNum">      90 </span>            :     C &amp; operator[] (J j);</a>
+<a name="91"><span class="lineNum">      91 </span>            :   };</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// access element (with [][] syntax)</a>
+<a name="94"><span class="lineNum">      94 </span>            :   Row operator[] (I i);</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// access element (with [][] syntax)</a>
+<a name="96"><span class="lineNum">      96 </span>            :   Const_row operator[] (I i)const;</a>
+<a name="97"><span class="lineNum">      97 </span>            : };</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : template&lt;class T,class C,class I,class J&gt;</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       5433 : MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::Const_row::Const_row(const MatrixSquareBracketsAccess&amp;t,I i):</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       5433 :   t(t),i(i) {}</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : template&lt;class T,class C,class I,class J&gt;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">   82566763 : MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::Row::Row(MatrixSquareBracketsAccess&amp;t,I i):</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">   82566763 :   t(t),i(i) {}</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : template&lt;class T,class C,class I,class J&gt;</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">       5433 : const C &amp; MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::Const_row::operator[] (J j)const {</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : // This appears as a reference to a temporary object</a>
+<a name="110"><span class="lineNum">     110 </span>            : // however, in reality we know it is a reference to an object that is stored in the</a>
+<a name="111"><span class="lineNum">     111 </span>            : // t object. We thus suppress the warning raised by cppcheck</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       5433 :   return (*static_cast&lt;const T*&gt;(&amp;t))(i,j);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : template&lt;class T,class C,class I,class J&gt;</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">   82566763 : C &amp; MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::Row::operator[] (J j) {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : // This appears as a reference to a temporary object</a>
+<a name="118"><span class="lineNum">     118 </span>            : // however, in reality we know it is a reference to an object that is stored in the</a>
+<a name="119"><span class="lineNum">     119 </span>            : // t object. We thus suppress the warning raised by cppcheck</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">   82566763 :   return (*static_cast&lt;T*&gt;(&amp;t))(i,j);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : template&lt;class T,class C,class I,class J&gt;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">   82566763 : typename MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::Row MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::operator[] (I i) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">   82566763 :   return Row(*this,i);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : template&lt;class T,class C,class I,class J&gt;</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       5433 : typename MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::Const_row MatrixSquareBracketsAccess&lt;T,C,I,J&gt;::operator[] (I i)const {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       5433 :   return Const_row(*this,i);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : #endif</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Minimise1DBrent.h.func-sort-c.html b/coverage/tools/Minimise1DBrent.h.func-sort-c.html
new file mode 100644
index 0000000000..64f396f2be
--- /dev/null
+++ b/coverage/tools/Minimise1DBrent.h.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Minimise1DBrent.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Minimise1DBrent.h<span style="font-size: 80%;"> (<a href="Minimise1DBrent.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Minimise1DBrent.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#89">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#132">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEE8minimiseEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#71">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#187">_ZNK4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEE15getMinimumValueEv</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#89">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#132">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEE8minimiseEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#71">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#187">_ZNK4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEE15getMinimumValueEv</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#89">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#132">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEE8minimiseEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#71">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#187">_ZNK4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEE15getMinimumValueEv</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Minimise1DBrent.h.func.html b/coverage/tools/Minimise1DBrent.h.func.html
new file mode 100644
index 0000000000..4de0584ad4
--- /dev/null
+++ b/coverage/tools/Minimise1DBrent.h.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Minimise1DBrent.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Minimise1DBrent.h<span style="font-size: 80%;"> (<a href="Minimise1DBrent.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Minimise1DBrent.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#89">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#132">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEE8minimiseEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#71">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#89">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#132">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEE8minimiseEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#71">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#89">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEE7bracketERKdS7_MS4_FdS7_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#132">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEE8minimiseEMS4_FdRKdE</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#71">_ZN4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEEC2ERKS4_RKd</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#187">_ZNK4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred17SketchMapConjGradEEEE15getMinimumValueEv</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#187">_ZNK4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred18SketchMapPointwiseEEEE15getMinimumValueEv</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Minimise1DBrent.h.gcov.html#187">_ZNK4PLMD15Minimise1DBrentINS_5F1dimINS_6dimred24ProjectNonLandmarkPointsEEEE15getMinimumValueEv</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Minimise1DBrent.h.gcov.html b/coverage/tools/Minimise1DBrent.h.gcov.html
new file mode 100644
index 0000000000..db9d4fa994
--- /dev/null
+++ b/coverage/tools/Minimise1DBrent.h.gcov.html
@@ -0,0 +1,271 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Minimise1DBrent.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Minimise1DBrent.h<span style="font-size: 80%;"> (source / <a href="Minimise1DBrent.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">81</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntryHi">97.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Minimise1DBrent_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Minimise1DBrent_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /// A class for doing parabolic interpolation and minimisation of</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// 1D functions using Brent's method.</a>
+<a name="34"><span class="lineNum">      34 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        897 : class Minimise1DBrent {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : private:</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// Has the minimum been bracketed</a>
+<a name="38"><span class="lineNum">      38 </span>            :   bool bracketed;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Has the function been minimised</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool minimised;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// The tolerance for the line minimiser</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double tol;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// The default ration by which successive intervals are magnified</a>
+<a name="44"><span class="lineNum">      44 </span>            :   const double GOLD;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// The maximum magnification allowed for a parabolic fit step</a>
+<a name="46"><span class="lineNum">      46 </span>            :   const double GLIMIT;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Use to prevent any possible division by zero</a>
+<a name="48"><span class="lineNum">      48 </span>            :   const double TINY;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Maximum number of interactions in line minimiser</a>
+<a name="50"><span class="lineNum">      50 </span>            :   const unsigned ITMAX;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// The value of the golden ratio</a>
+<a name="52"><span class="lineNum">      52 </span>            :   const double CGOLD;</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// A small number that protects against trying to achieve fractional</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// accuracy for a minimum that happens to be exactly zero</a>
+<a name="55"><span class="lineNum">      55 </span>            :   const double ZEPS;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// This is the type specifier for the function to minimise</a>
+<a name="57"><span class="lineNum">      57 </span>            :   typedef double(FCLASS::*eng_pointer)( const double&amp; val );</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Three points bracketting the minimum and the corresponding function values</a>
+<a name="59"><span class="lineNum">      59 </span>            :   double ax,bx,cx,fa,fb,fc,fmin;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// The class containing the function we are trying to minimise</a>
+<a name="61"><span class="lineNum">      61 </span>            :   FCLASS myclass_func;</a>
+<a name="62"><span class="lineNum">      62 </span>            : public:</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        897 :   explicit Minimise1DBrent( const FCLASS&amp; pf,  const double&amp; t=3.0E-8 );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Bracket the minium</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void bracket( const double&amp; ax, const double&amp; xx, eng_pointer eng );</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Find the minimum between two brackets</a>
+<a name="67"><span class="lineNum">      67 </span>            :   double minimise( eng_pointer eng );</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Return the value of the function at the minimum</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double getMinimumValue() const ;</a>
+<a name="70"><span class="lineNum">      70 </span>            : };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        897 : Minimise1DBrent&lt;FCLASS&gt;::Minimise1DBrent( const FCLASS&amp; pf, const double&amp; t ):</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        897 :   bracketed(false),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        897 :   minimised(false),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        897 :   tol(t),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        897 :   GOLD(1.618034),</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        897 :   GLIMIT(100.0),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        897 :   TINY(1.0E-20),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        897 :   ITMAX(100),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        897 :   CGOLD(0.3819660),</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        897 :   ZEPS(epsilon*1.0E-3),</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        897 :   ax(0),bx(0),cx(0),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        897 :   fa(0),fb(0),fc(0),</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        897 :   fmin(0),</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        897 :   myclass_func(pf)</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        897 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        897 : void Minimise1DBrent&lt;FCLASS&gt;::bracket( const double&amp; a, const double&amp; b, eng_pointer eng ) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        897 :   ax=a; bx=b; double fu;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        897 :   fa=(myclass_func.*eng)(ax); fb=(myclass_func.*eng)(bx);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        897 :   if( fb&gt;fa ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     double tmp;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        809 :     tmp=ax; ax=bx; bx=tmp;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        809 :     tmp=fa; fa=fb; fb=tmp;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        897 :   cx=bx+GOLD*(bx-ax);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        897 :   fc=(myclass_func.*eng)(cx);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1113 :   while ( fb &gt; fc ) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        220 :     double r=(bx-ax)*(fb-fc);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        220 :     double q=(bx-cx)*(fb-fa);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        220 :     double u=bx-((bx-cx)*q-(bx-ax)*r)/(2.0*(std::fabs(q-r)&gt;TINY?std::fabs(q-r):TINY)*(q-r&gt;=0?1:-1));</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        220 :     double ulim=bx+GLIMIT*(cx-bx);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        220 :     if((bx-u)*(u-cx) &gt; 0.0 ) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          5 :       fu=(myclass_func.*eng)(u);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          5 :       if( fu &lt; fc ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :         ax=bx; bx=u; fa=fb; fb=fu; bracketed=true; return;</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          1 :       } else if( fu &gt; fb ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :         cx=u; fc=fu; bracketed=true; return;</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :       }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 :       u=cx+GOLD*(cx-bx); fu=(myclass_func.*eng)(u);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        215 :     } else if((cx-u)*(u-ulim) &gt; 0.0 ) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         81 :       fu=(myclass_func.*eng)(u);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         81 :       if( fu&lt;fc ) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         80 :         bx=cx; cx=u; u+=GOLD*(u-bx);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         80 :         fb=fc; fc=fu; fu=(myclass_func.*eng)(u);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       }</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        134 :     } else if( (u-ulim)*(ulim-cx) &gt;= 0.0 ) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        124 :       u=ulim;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        124 :       fu=(myclass_func.*eng)(u);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     } else {</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         10 :       u=cx+GOLD*(cx-bx);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         10 :       fu=(myclass_func.*eng)(u);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        216 :     ax=bx; bx=cx; cx=u;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        216 :     fa=fb; fb=fc; fc=fu;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        893 :   bracketed=true;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        897 : double Minimise1DBrent&lt;FCLASS&gt;::minimise( eng_pointer eng ) {</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   plumed_dbg_assert( bracketed );</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            :   double a,b,d=0.0,etemp,fu,fv,fw,fx;</a>
+<a name="138"><span class="lineNum">     138 </span>            :   double p,q,r,tol1,tol2,u,v,w,x,xm;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   double e=0.0;</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        897 :   a=(ax &lt; cx ? ax : cx );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        897 :   b=(ax &gt;= cx ? ax : cx );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        897 :   x=w=v=bx;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        897 :   fw=fv=fx=(myclass_func.*eng)(x);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      14768 :   for(unsigned iter=0; iter&lt;ITMAX; ++iter) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      14768 :     xm=0.5*(a+b);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      14768 :     tol2=2.0*(tol1=tol*std::fabs(x)+ZEPS);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      14768 :     if( std::fabs(x-xm) &lt;= (tol2-0.5*(b-a))) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        897 :       fmin=fx; minimised=true; return x;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      13871 :     if( std::fabs(e) &gt; tol1 ) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">      12810 :       r=(x-w)*(fx-fv);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      12810 :       q=(x-v)*(fx-fw);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      12810 :       p=(x-v)*q-(x-w)*r;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      12810 :       q=2.0*(q-r);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      12810 :       if( q &gt; 0.0 ) p = -p;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      12810 :       q=std::fabs(q);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :       etemp=e;</a>
+<a name="159"><span class="lineNum">     159 </span>            :       e=d;</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      12810 :       if( std::fabs(p) &gt;= std::fabs(0.5*q*etemp) || p &lt;= q*(a-x) || p &gt;= q*(b-x) ) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       5079 :         d = CGOLD*(e=(x &gt;= xm ? a-x : b-x ));</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :       } else {</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       7731 :         d=p/q; u=x+d;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       7731 :         if(u-a &lt; tol2 || b-u &lt; tol2 ) d=(xm-x&gt;=0?std::fabs(tol1):-std::fabs(tol1));</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :       }</a>
+<a name="166"><span class="lineNum">     166 </span>            :     } else {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1061 :       d=CGOLD*(e=( x &gt;= xm ? a-x : b-x ));</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      13871 :     if( std::fabs(d)&gt;=tol1) u=x+d; else u=x+(d&gt;=0?std::fabs(tol1):-std::fabs(tol1));</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      13871 :     fu=(myclass_func.*eng)(u);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      13871 :     if( fu &lt;= fx ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       5411 :       if( u &gt;= x ) a=x; else b=x;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :       v=w; fv=fw;</a>
+<a name="174"><span class="lineNum">     174 </span>            :       w=x; fw=fx;</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       5411 :       x=u; fx=fu;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :     } else {</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       8460 :       if( u &lt; x ) a=u; else b=u;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       8460 :       if( fu &lt;=fw || w==x ) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :         v=w; w=u; fv=fw; fw=fu;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">       5096 :       } else if( fu &lt;= fv || v==x || v==w ) {</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :         v=u; fv=fu;</a>
+<a name="182"><span class="lineNum">     182 </span>            :       }</a>
+<a name="183"><span class="lineNum">     183 </span>            :     }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;Too many interactions in brent&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        897 : double Minimise1DBrent&lt;FCLASS&gt;::getMinimumValue() const {</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   plumed_dbg_assert( minimised );</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        897 :   return fmin;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+<a name="195"><span class="lineNum">     195 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MinimiseBase.h.func-sort-c.html b/coverage/tools/MinimiseBase.h.func-sort-c.html
new file mode 100644
index 0000000000..b1738bb456
--- /dev/null
+++ b/coverage/tools/MinimiseBase.h.func-sort-c.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MinimiseBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MinimiseBase.h<span style="font-size: 80%;"> (<a href="MinimiseBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MinimiseBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_4GridEE6getEngERKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_4GridEEC2ERKSt6vectorIdSaIdEES7_PS1_MS1_KFdS7_RS5_EMS1_FdS7_S9_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#108">_ZN4PLMD12MinimiseBaseINS_6dimred18SketchMapPointwiseEE15calcDerivativesERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#92">_ZN4PLMD12MinimiseBaseINS_6dimred18SketchMapPointwiseEE7lineminERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_6dimred18SketchMapPointwiseEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#108">_ZN4PLMD12MinimiseBaseINS_6dimred17SketchMapConjGradEE15calcDerivativesERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#92">_ZN4PLMD12MinimiseBaseINS_6dimred17SketchMapConjGradEE7lineminERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_6dimred17SketchMapConjGradEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_11multicolvar19DistanceFromContourEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_6dimred18SketchMapPointwiseEE6getEngERKd</a></td>
+              <td class="coverFnHi">478</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#108">_ZN4PLMD12MinimiseBaseINS_6dimred24ProjectNonLandmarkPointsEE15calcDerivativesERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#92">_ZN4PLMD12MinimiseBaseINS_6dimred24ProjectNonLandmarkPointsEE7lineminERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_6dimred24ProjectNonLandmarkPointsEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_9gridtools18ContourFindingBaseEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_6dimred17SketchMapConjGradEE6getEngERKd</a></td>
+              <td class="coverFnHi">1352</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_11multicolvar19DistanceFromContourEE6getEngERKd</a></td>
+              <td class="coverFnHi">2200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_9gridtools18ContourFindingBaseEE6getEngERKd</a></td>
+              <td class="coverFnHi">8245</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_6dimred24ProjectNonLandmarkPointsEE6getEngERKd</a></td>
+              <td class="coverFnHi">15930</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MinimiseBase.h.func.html b/coverage/tools/MinimiseBase.h.func.html
new file mode 100644
index 0000000000..9570cbb720
--- /dev/null
+++ b/coverage/tools/MinimiseBase.h.func.html
@@ -0,0 +1,144 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MinimiseBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MinimiseBase.h<span style="font-size: 80%;"> (<a href="MinimiseBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MinimiseBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#108">_ZN4PLMD12MinimiseBaseINS_6dimred17SketchMapConjGradEE15calcDerivativesERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#92">_ZN4PLMD12MinimiseBaseINS_6dimred17SketchMapConjGradEE7lineminERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#108">_ZN4PLMD12MinimiseBaseINS_6dimred18SketchMapPointwiseEE15calcDerivativesERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#92">_ZN4PLMD12MinimiseBaseINS_6dimred18SketchMapPointwiseEE7lineminERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#108">_ZN4PLMD12MinimiseBaseINS_6dimred24ProjectNonLandmarkPointsEE15calcDerivativesERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#92">_ZN4PLMD12MinimiseBaseINS_6dimred24ProjectNonLandmarkPointsEE7lineminERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_11multicolvar19DistanceFromContourEE6getEngERKd</a></td>
+              <td class="coverFnHi">2200</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_11multicolvar19DistanceFromContourEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_4GridEE6getEngERKd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_4GridEEC2ERKSt6vectorIdSaIdEES7_PS1_MS1_KFdS7_RS5_EMS1_FdS7_S9_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_6dimred17SketchMapConjGradEE6getEngERKd</a></td>
+              <td class="coverFnHi">1352</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_6dimred17SketchMapConjGradEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_6dimred18SketchMapPointwiseEE6getEngERKd</a></td>
+              <td class="coverFnHi">478</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_6dimred18SketchMapPointwiseEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_6dimred24ProjectNonLandmarkPointsEE6getEngERKd</a></td>
+              <td class="coverFnHi">15930</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_6dimred24ProjectNonLandmarkPointsEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">814</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#68">_ZN4PLMD5F1dimINS_9gridtools18ContourFindingBaseEE6getEngERKd</a></td>
+              <td class="coverFnHi">8245</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MinimiseBase.h.gcov.html#55">_ZN4PLMD5F1dimINS_9gridtools18ContourFindingBaseEEC2ERKSt6vectorIdSaIdEES8_PS2_MS2_KFdS8_RS6_EMS2_FdS8_SA_E</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MinimiseBase.h.gcov.html b/coverage/tools/MinimiseBase.h.gcov.html
new file mode 100644
index 0000000000..fc07bf984a
--- /dev/null
+++ b/coverage/tools/MinimiseBase.h.gcov.html
@@ -0,0 +1,191 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MinimiseBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MinimiseBase.h<span style="font-size: 80%;"> (source / <a href="MinimiseBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_MinimiseBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_MinimiseBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Minimise1DBrent.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">       2413 : class F1dim {</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : private:</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// This is the pointer to the member function in the energy</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// calculating class that calculates the energy</a>
+<a name="34"><span class="lineNum">      34 </span>            :   typedef double(FCLASS::*engf_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der ) const ;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   typedef double(FCLASS::*engfnc_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der ) ;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Pointer to the vector containing an initial position on the vector</a>
+<a name="37"><span class="lineNum">      37 </span>            :   const std::vector&lt;double&gt;&amp; p;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// The direction of the vector we are minimising along</a>
+<a name="39"><span class="lineNum">      39 </span>            :   const std::vector&lt;double&gt;&amp; dir;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Tempory vector that holds a point at which we want to calculate the energy</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::vector&lt;double&gt; pt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Vector that holds the derivatives at the point at which we calculate the energy (these are not used)</a>
+<a name="43"><span class="lineNum">      43 </span>            :   std::vector&lt;double&gt; fake_der;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Class containging the function in the class</a>
+<a name="45"><span class="lineNum">      45 </span>            :   FCLASS* func;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Member of class that calculates the energy we are trying to mnimise</a>
+<a name="47"><span class="lineNum">      47 </span>            :   engf_pointer calc;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Member of class that calcualtes the energy we are trying to minimise</a>
+<a name="49"><span class="lineNum">      49 </span>            :   engfnc_pointer calc2;</a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit F1dim( const std::vector&lt;double&gt;&amp; pp, const std::vector&lt;double&gt;&amp; dd, FCLASS* ff, engf_pointer cc, engfnc_pointer cc2 );</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Calculate the energy at \f$\mathbf{p} + xt*\mathbf{dir}\f$</a>
+<a name="53"><span class="lineNum">      53 </span>            :   double getEng( const double&amp; xt );</a>
+<a name="54"><span class="lineNum">      54 </span>            : };</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       2413 : F1dim&lt;FCLASS&gt;::F1dim( const std::vector&lt;double&gt;&amp; pp, const std::vector&lt;double&gt;&amp; dd, FCLASS* ff, engf_pointer cc, engfnc_pointer cc2 ):</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       2413 :   p(pp),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       2413 :   dir(dd),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       2413 :   pt(pp.size()),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       2413 :   fake_der(pp.size()),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       2413 :   func(ff),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       2413 :   calc(cc),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       2413 :   calc2(cc2)</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : {</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       2413 :   plumed_assert( calc || calc2 );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       2413 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">      28205 : double F1dim&lt;FCLASS&gt;::getEng( const double&amp; xt ) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     465500 :   for(unsigned j=0; j&lt;pt.size(); ++j) pt[j] = p[j] + xt*dir[j];</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      28205 :   if( calc ) return (func-&gt;*calc)(pt,fake_der);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">      19960 :   return (func-&gt;*calc2)(pt,fake_der);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="77"><span class="lineNum">      77 </span>            : class MinimiseBase {</a>
+<a name="78"><span class="lineNum">      78 </span>            : private:</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// This is the pointer to the member function in the energy</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// calculating class that calculates the energy</a>
+<a name="81"><span class="lineNum">      81 </span>            :   typedef double(FCLASS::*engf_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der );</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// The class that calculates the energy given a position</a>
+<a name="83"><span class="lineNum">      83 </span>            :   FCLASS* myclass_func;</a>
+<a name="84"><span class="lineNum">      84 </span>            : protected:</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// This calculates the derivatives at a point</a>
+<a name="86"><span class="lineNum">      86 </span>            :   double calcDerivatives( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der, engf_pointer myfunc );</a>
+<a name="87"><span class="lineNum">      87 </span>            : public:</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        505 :   explicit MinimiseBase( FCLASS* funcc ) : myclass_func(funcc) {}</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : /// This is the line minimiser</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double linemin( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, engf_pointer myfunc );</a>
+<a name="91"><span class="lineNum">      91 </span>            : };</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        897 : double MinimiseBase&lt;FCLASS&gt;::linemin( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, engf_pointer myfunc ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   // Construct the object that turns points on a line into vectors</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        897 :   F1dim&lt;FCLASS&gt; f1dim( p, dir, myclass_func, NULL, myfunc );</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            :   // Construct an object that will do the line search for the minimum</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        897 :   Minimise1DBrent&lt;F1dim&lt;FCLASS&gt; &gt; bb(f1dim);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   // This does the actual line minimisation</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        897 :   double ax=0.0, xx=1.0;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        897 :   bb.bracket( ax, xx, &amp;F1dim&lt;FCLASS&gt;::getEng );</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        897 :   double xmin=bb.minimise( &amp;F1dim&lt;FCLASS&gt;::getEng );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      19725 :   for(unsigned i=0; i&lt;p.size(); ++i) p[i] += xmin*dir[i];</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       1794 :   return bb.getMinimumValue();</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        897 : double MinimiseBase&lt;FCLASS&gt;::calcDerivatives( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der, engf_pointer myfunc ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        897 :   return (myclass_func-&gt;*myfunc)( p, der );</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MolDataClass.cpp.func-sort-c.html b/coverage/tools/MolDataClass.cpp.func-sort-c.html
new file mode 100644
index 0000000000..71ee4ef471
--- /dev/null
+++ b/coverage/tools/MolDataClass.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MolDataClass.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MolDataClass.cpp<span style="font-size: 80%;"> (<a href="MolDataClass.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">406</td>
+            <td class="headerCovTableEntry">477</td>
+            <td class="headerCovTableEntryMed">85.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MolDataClass.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#27">_ZN4PLMD12MolDataClass33numberOfAtomsPerResidueInBackboneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#212">_ZN4PLMD12MolDataClass13specialSymbolERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_RKNS_3PDBERSt6vectorINS_10AtomNumberESaISD_EE</a></td>
+              <td class="coverFnHi">593</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#161">_ZN4PLMD12MolDataClass21getBackboneForResidueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKjRKNS_3PDBERSt6vectorINS_10AtomNumberESaISF_EE</a></td>
+              <td class="coverFnHi">2652</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#200">_ZN4PLMD12MolDataClass15isTerminalGroupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">3417</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#34">_ZN4PLMD12MolDataClass14allowedResidueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">8129</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MolDataClass.cpp.func.html b/coverage/tools/MolDataClass.cpp.func.html
new file mode 100644
index 0000000000..5a7a7facd2
--- /dev/null
+++ b/coverage/tools/MolDataClass.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MolDataClass.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MolDataClass.cpp<span style="font-size: 80%;"> (<a href="MolDataClass.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">406</td>
+            <td class="headerCovTableEntry">477</td>
+            <td class="headerCovTableEntryMed">85.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MolDataClass.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#212">_ZN4PLMD12MolDataClass13specialSymbolERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_RKNS_3PDBERSt6vectorINS_10AtomNumberESaISD_EE</a></td>
+              <td class="coverFnHi">593</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#34">_ZN4PLMD12MolDataClass14allowedResidueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">8129</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#200">_ZN4PLMD12MolDataClass15isTerminalGroupERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">3417</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#161">_ZN4PLMD12MolDataClass21getBackboneForResidueERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKjRKNS_3PDBERSt6vectorINS_10AtomNumberESaISF_EE</a></td>
+              <td class="coverFnHi">2652</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MolDataClass.cpp.gcov.html#27">_ZN4PLMD12MolDataClass33numberOfAtomsPerResidueInBackboneERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">25</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MolDataClass.cpp.gcov.html b/coverage/tools/MolDataClass.cpp.gcov.html
new file mode 100644
index 0000000000..024dc1e3ad
--- /dev/null
+++ b/coverage/tools/MolDataClass.cpp.gcov.html
@@ -0,0 +1,663 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MolDataClass.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MolDataClass.cpp<span style="font-size: 80%;"> (source / <a href="MolDataClass.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">406</td>
+            <td class="headerCovTableEntry">477</td>
+            <td class="headerCovTableEntryMed">85.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MolDataClass.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;PDB.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         25 : unsigned MolDataClass::numberOfAtomsPerResidueInBackbone( const std::string&amp; type ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         25 :   if( type==&quot;protein&quot; ) return 5;</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineNoCov">          0 :   else if( type==&quot;dna&quot; ) return 6;</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineNoCov">          0 :   else if( type==&quot;rna&quot; ) return 6;</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :   else return 0;</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : }</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       8129 : bool MolDataClass::allowedResidue( const std::string&amp; type, const std::string&amp; residuename ) {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       8129 :   if( type==&quot;protein&quot; ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       6022 :     if(residuename==&quot;ALA&quot;) return true;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       5756 :     else if(residuename==&quot;ARG&quot;) return true;</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       5756 :     else if(residuename==&quot;ASN&quot;) return true;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       5756 :     else if(residuename==&quot;ASP&quot;) return true;</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       5748 :     else if(residuename==&quot;CYS&quot;) return true;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       5748 :     else if(residuename==&quot;GLN&quot;) return true;</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       5748 :     else if(residuename==&quot;GLU&quot;) return true;</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       5740 :     else if(residuename==&quot;GLY&quot;) return true;</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       5732 :     else if(residuename==&quot;HIS&quot;) return true;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       5732 :     else if(residuename==&quot;ILE&quot;) return true;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       5730 :     else if(residuename==&quot;LEU&quot;) return true;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       5730 :     else if(residuename==&quot;LYS&quot;) return true;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       5726 :     else if(residuename==&quot;MET&quot;) return true;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       5726 :     else if(residuename==&quot;PHE&quot;) return true;</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       5722 :     else if(residuename==&quot;PRO&quot;) return true;</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       5715 :     else if(residuename==&quot;SER&quot;) return true;</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       5711 :     else if(residuename==&quot;THR&quot;) return true;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       5691 :     else if(residuename==&quot;TRP&quot;) return true;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       5681 :     else if(residuename==&quot;TYR&quot;) return true;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       5677 :     else if(residuename==&quot;VAL&quot;) return true;</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : // Terminal groups</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        489 :     else if(residuename==&quot;ACE&quot;) return true;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        483 :     else if(residuename==&quot;NME&quot;) return true;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        477 :     else if(residuename==&quot;NH2&quot;) return true;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : // Alternative residue names in common force fields</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        477 :     else if(residuename==&quot;GLH&quot;) return true; // neutral GLU</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        477 :     else if(residuename==&quot;ASH&quot;) return true; // neutral ASP</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        477 :     else if(residuename==&quot;HID&quot;) return true; // HIS-D amber</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        477 :     else if(residuename==&quot;HSD&quot;) return true; // HIS-D charmm</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        477 :     else if(residuename==&quot;HIE&quot;) return true; // HIS-E amber</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        477 :     else if(residuename==&quot;HSE&quot;) return true; // HIS-E charmm</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        477 :     else if(residuename==&quot;HIP&quot;) return true; // HIS-P amber</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        477 :     else if(residuename==&quot;HSP&quot;) return true; // HIS-P charmm</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : // Weird amino acids</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        477 :     else if(residuename==&quot;NLE&quot;) return true;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        475 :     else if(residuename==&quot;SFO&quot;) return true;</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        475 :     else return false;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       2107 :   } else if( type==&quot;dna&quot; ) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        462 :     if(residuename==&quot;A&quot;) return true;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        397 :     else if(residuename==&quot;A5&quot;) return true;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        397 :     else if(residuename==&quot;A3&quot;) return true;</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        397 :     else if(residuename==&quot;AN&quot;) return true;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        397 :     else if(residuename==&quot;G&quot;) return true;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        397 :     else if(residuename==&quot;G5&quot;) return true;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        397 :     else if(residuename==&quot;G3&quot;) return true;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        397 :     else if(residuename==&quot;GN&quot;) return true;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        397 :     else if(residuename==&quot;T&quot;) return true;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        393 :     else if(residuename==&quot;T5&quot;) return true;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        393 :     else if(residuename==&quot;T3&quot;) return true;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        393 :     else if(residuename==&quot;TN&quot;) return true;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        393 :     else if(residuename==&quot;C&quot;) return true;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        393 :     else if(residuename==&quot;C5&quot;) return true;</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        393 :     else if(residuename==&quot;C3&quot;) return true;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        393 :     else if(residuename==&quot;CN&quot;) return true;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        393 :     else if(residuename==&quot;DA&quot;) return true;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        393 :     else if(residuename==&quot;DA5&quot;) return true;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        393 :     else if(residuename==&quot;DA3&quot;) return true;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        393 :     else if(residuename==&quot;DAN&quot;) return true;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        393 :     else if(residuename==&quot;DG&quot;) return true;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        392 :     else if(residuename==&quot;DG5&quot;) return true;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        392 :     else if(residuename==&quot;DG3&quot;) return true;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        392 :     else if(residuename==&quot;DGN&quot;) return true;</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        392 :     else if(residuename==&quot;DT&quot;) return true;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        392 :     else if(residuename==&quot;DT5&quot;) return true;</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        392 :     else if(residuename==&quot;DT3&quot;) return true;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        392 :     else if(residuename==&quot;DTN&quot;) return true;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        392 :     else if(residuename==&quot;DC&quot;) return true;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        391 :     else if(residuename==&quot;DC5&quot;) return true;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        391 :     else if(residuename==&quot;DC3&quot;) return true;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        391 :     else if(residuename==&quot;DCN&quot;) return true;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        391 :     else return false;</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">       1645 :   } else if( type==&quot;rna&quot; ) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        865 :     if(residuename==&quot;A&quot;) return true;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        808 :     else if(residuename==&quot;A5&quot;) return true;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        808 :     else if(residuename==&quot;A3&quot;) return true;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        808 :     else if(residuename==&quot;AN&quot;) return true;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        808 :     else if(residuename==&quot;G&quot;) return true;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        786 :     else if(residuename==&quot;G5&quot;) return true;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        782 :     else if(residuename==&quot;G3&quot;) return true;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        782 :     else if(residuename==&quot;GN&quot;) return true;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        782 :     else if(residuename==&quot;U&quot;) return true;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        759 :     else if(residuename==&quot;U5&quot;) return true;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        759 :     else if(residuename==&quot;U3&quot;) return true;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        759 :     else if(residuename==&quot;UN&quot;) return true;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        759 :     else if(residuename==&quot;C&quot;) return true;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        744 :     else if(residuename==&quot;C5&quot;) return true;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        744 :     else if(residuename==&quot;C3&quot;) return true;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        740 :     else if(residuename==&quot;CN&quot;) return true;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        740 :     else if(residuename==&quot;RA&quot;) return true;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        632 :     else if(residuename==&quot;RA5&quot;) return true;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        601 :     else if(residuename==&quot;RA3&quot;) return true;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        601 :     else if(residuename==&quot;RAN&quot;) return true;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        601 :     else if(residuename==&quot;RG&quot;) return true;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        481 :     else if(residuename==&quot;RG5&quot;) return true;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        481 :     else if(residuename==&quot;RG3&quot;) return true;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        442 :     else if(residuename==&quot;RGN&quot;) return true;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        442 :     else if(residuename==&quot;RU&quot;) return true;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        342 :     else if(residuename==&quot;RU5&quot;) return true;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        342 :     else if(residuename==&quot;RU3&quot;) return true;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        311 :     else if(residuename==&quot;RUN&quot;) return true;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        311 :     else if(residuename==&quot;RC&quot;) return true;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        177 :     else if(residuename==&quot;RC5&quot;) return true;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        144 :     else if(residuename==&quot;RC3&quot;) return true;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        144 :     else if(residuename==&quot;RCN&quot;) return true;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        141 :     else return false;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        780 :   } else if( type==&quot;water&quot; ) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        390 :     if(residuename==&quot;SOL&quot;) return true;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        274 :     if(residuename==&quot;WAT&quot;) return true;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        274 :     return false;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        390 :   } else if( type==&quot;ion&quot; ) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        390 :     if(residuename==&quot;IB+&quot;) return true;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        390 :     if(residuename==&quot;CA&quot;) return true;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        390 :     if(residuename==&quot;CL&quot;) return true;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        384 :     if(residuename==&quot;NA&quot;) return true;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        372 :     if(residuename==&quot;MG&quot;) return true;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        372 :     if(residuename==&quot;K&quot;) return true;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        372 :     if(residuename==&quot;RB&quot;) return true;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        372 :     if(residuename==&quot;CS&quot;) return true;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        372 :     if(residuename==&quot;LI&quot;) return true;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        372 :     if(residuename==&quot;ZN&quot;) return true;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        372 :     return false;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   return false;</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       2652 : void MolDataClass::getBackboneForResidue( const std::string&amp; type, const unsigned&amp; residuenum, const PDB&amp; mypdb, std::vector&lt;AtomNumber&gt;&amp; atoms ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       2652 :   std::string residuename=mypdb.getResidueName( residuenum );</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       2652 :   plumed_massert( MolDataClass::allowedResidue( type, residuename ), &quot;residue &quot; + residuename + &quot; unrecognized for molecule type &quot; + type );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       2652 :   if( type==&quot;protein&quot; ) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       2652 :     if( residuename==&quot;GLY&quot;) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :       atoms.resize(5);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       atoms[0]=mypdb.getNamedAtomFromResidue(&quot;N&quot;,residuenum);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :       atoms[1]=mypdb.getNamedAtomFromResidue(&quot;CA&quot;,residuenum);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :       atoms[2]=mypdb.getNamedAtomFromResidue(&quot;HA2&quot;,residuenum);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :       atoms[3]=mypdb.getNamedAtomFromResidue(&quot;C&quot;,residuenum);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :       atoms[4]=mypdb.getNamedAtomFromResidue(&quot;O&quot;,residuenum);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       2652 :     } else if( residuename==&quot;ACE&quot;) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 :       atoms.resize(1);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :       atoms[0]=mypdb.getNamedAtomFromResidue(&quot;C&quot;,residuenum);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       5304 :     } else if( residuename==&quot;NME&quot;||residuename==&quot;NH2&quot;) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :       atoms.resize(1);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :       atoms[0]=mypdb.getNamedAtomFromResidue(&quot;N&quot;,residuenum);</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     } else {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       2652 :       atoms.resize(5);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       2652 :       atoms[0]=mypdb.getNamedAtomFromResidue(&quot;N&quot;,residuenum);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       2652 :       atoms[1]=mypdb.getNamedAtomFromResidue(&quot;CA&quot;,residuenum);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       2652 :       atoms[2]=mypdb.getNamedAtomFromResidue(&quot;CB&quot;,residuenum);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       2652 :       atoms[3]=mypdb.getNamedAtomFromResidue(&quot;C&quot;,residuenum);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       5304 :       atoms[4]=mypdb.getNamedAtomFromResidue(&quot;O&quot;,residuenum);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   } else if( type==&quot;dna&quot; || type==&quot;rna&quot; ) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     atoms.resize(6);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :     atoms[0]=mypdb.getNamedAtomFromResidue(&quot;P&quot;,residuenum);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     atoms[1]=mypdb.getNamedAtomFromResidue(&quot;O5\'&quot;,residuenum);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     atoms[2]=mypdb.getNamedAtomFromResidue(&quot;C5\'&quot;,residuenum);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     atoms[3]=mypdb.getNamedAtomFromResidue(&quot;C4\'&quot;,residuenum);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     atoms[4]=mypdb.getNamedAtomFromResidue(&quot;C3\'&quot;,residuenum);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     atoms[5]=mypdb.getNamedAtomFromResidue(&quot;O3\'&quot;,residuenum);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span>            :   else {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :     plumed_merror(type + &quot; is not a valid molecule type&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       2652 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       3417 : bool MolDataClass::isTerminalGroup( const std::string&amp; type, const std::string&amp; residuename ) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">       3417 :   if( type==&quot;protein&quot; ) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       3417 :     if( residuename==&quot;ACE&quot; ) return true;</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       3090 :     else if( residuename==&quot;NME&quot; ) return true;</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       2763 :     else if( residuename==&quot;NH2&quot; ) return true;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       2763 :     else return false;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   } else {</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :     plumed_merror(type + &quot; is not a valid molecule type&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span>            :   return false;</a>
+<a name="212"><span class="lineNum">     212 </span>            : }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        593 : void MolDataClass::specialSymbol( const std::string&amp; type, const std::string&amp; symbol, const PDB&amp; mypdb, std::vector&lt;AtomNumber&gt;&amp; numbers ) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        823 :   if(type==&quot;protein&quot; || type==&quot;rna&quot; || type==&quot;dna&quot;) {</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : // symbol should be something like</a>
+<a name="217"><span class="lineNum">     217 </span>            : // phi-123 i.e. phi torsion of residue 123 of first chain</a>
+<a name="218"><span class="lineNum">     218 </span>            : // psi-A321 i.e. psi torsion of residue 321 of chain A</a>
+<a name="219"><span class="lineNum">     219 </span>            : // psi-4_321 is psi torsion of residue 321 of chain 4</a>
+<a name="220"><span class="lineNum">     220 </span>            : // psi-A_321 is equivalent to psi-A321</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        593 :     numbers.resize(0);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : // special cases:</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        593 :     if(symbol==&quot;protein&quot;) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          1 :       const auto &amp; all = mypdb.getAtomNumbers();</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        133 :       for(auto a : all) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        132 :         auto resname=mypdb.getResidueName(a);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        132 :         Tools::stripLeadingAndTrailingBlanks(resname);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        264 :         if(allowedResidue(&quot;protein&quot;,resname)) numbers.push_back(a);</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :       }</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          7 :       return;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        592 :     if(symbol==&quot;nucleic&quot;) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          2 :       const auto &amp; all = mypdb.getAtomNumbers();</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        457 :       for(auto a : all) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        455 :         auto resname=mypdb.getResidueName(a);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        455 :         Tools::stripLeadingAndTrailingBlanks(resname);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       1101 :         if(allowedResidue(&quot;dna&quot;,resname) || allowedResidue(&quot;rna&quot;,resname)) numbers.push_back(a);</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :       }</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          2 :       return;</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        590 :     if(symbol==&quot;ions&quot;) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          1 :       const auto &amp; all = mypdb.getAtomNumbers();</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        391 :       for(auto a : all) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        390 :         auto resname=mypdb.getResidueName(a);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        390 :         Tools::stripLeadingAndTrailingBlanks(resname);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        780 :         if(allowedResidue(&quot;ion&quot;,resname)) numbers.push_back(a);</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :       }</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          1 :       return;</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        589 :     if(symbol==&quot;water&quot;) {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          1 :       const auto &amp; all = mypdb.getAtomNumbers();</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        391 :       for(auto a : all) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        390 :         auto resname=mypdb.getResidueName(a);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        390 :         Tools::stripLeadingAndTrailingBlanks(resname);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        780 :         if(allowedResidue(&quot;water&quot;,resname)) numbers.push_back(a);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :       }</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          1 :       return;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :     }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        588 :     if(symbol==&quot;hydrogens&quot;) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          1 :       const auto &amp; all = mypdb.getAtomNumbers();</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        391 :       for(auto a : all) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        390 :         auto atomname=mypdb.getAtomName(a);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        390 :         Tools::stripLeadingAndTrailingBlanks(atomname);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        390 :         auto notnumber=atomname.find_first_not_of(&quot;0123456789&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        390 :         if(notnumber!=std::string::npos &amp;&amp; atomname[notnumber]=='H') numbers.push_back(a);</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :       }</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          1 :       return;</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        587 :     if(symbol==&quot;nonhydrogens&quot;) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          1 :       const auto &amp; all = mypdb.getAtomNumbers();</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        391 :       for(auto a : all) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        390 :         auto atomname=mypdb.getAtomName(a);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        390 :         Tools::stripLeadingAndTrailingBlanks(atomname);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        390 :         auto notnumber=atomname.find_first_not_of(&quot;0123456789&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        390 :         if(!(notnumber!=std::string::npos &amp;&amp; atomname[notnumber]=='H')) numbers.push_back(a);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :       }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          1 :       return;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :     }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            :     std::size_t dash=symbol.find_first_of('-');</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        586 :     if(dash==std::string::npos) plumed_error() &lt;&lt; &quot;Unrecognized symbol &quot;&lt;&lt;symbol;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        586 :     std::size_t firstunderscore=symbol.find_first_of('_',dash+1);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        586 :     std::size_t firstnum=symbol.find_first_of(&quot;0123456789&quot;,dash+1);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        586 :     std::string name=symbol.substr(0,dash);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :     unsigned resnum;</a>
+<a name="294"><span class="lineNum">     294 </span>            :     std::string resname;</a>
+<a name="295"><span class="lineNum">     295 </span>            :     std::string chainid;</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        586 :     if(firstunderscore != std::string::npos) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          6 :       Tools::convert( symbol.substr(firstunderscore+1), resnum );</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         12 :       chainid=symbol.substr(dash+1,firstunderscore-(dash+1));</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        580 :     } else if(firstnum==dash+1) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1140 :       Tools::convert( symbol.substr(dash+1), resnum );</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :       chainid=&quot;*&quot;; // this is going to match the first chain</a>
+<a name="302"><span class="lineNum">     302 </span>            :     } else {</a>
+<a name="303"><span class="lineNum">     303 </span>            :       // if chain id is provided:</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         10 :       Tools::convert( symbol.substr(firstnum), resnum );</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         20 :       chainid=symbol.substr(dash+1,firstnum-(dash+1)); // this is going to match the proper chain</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     }</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">        586 :     resname= mypdb.getResidueName(resnum,chainid);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">        586 :     Tools::stripLeadingAndTrailingBlanks(resname);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1172 :     if(allowedResidue(&quot;protein&quot;,resname)) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        151 :       if( name==&quot;phi&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         80 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C&quot;,resnum-1,chainid));</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         80 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N&quot;,resnum,chainid));</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         80 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CA&quot;,resnum,chainid));</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         80 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C&quot;,resnum,chainid));</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        137 :       } else if( name==&quot;psi&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        132 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N&quot;,resnum,chainid));</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        132 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CA&quot;,resnum,chainid));</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        132 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C&quot;,resnum,chainid));</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        132 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N&quot;,resnum+1,chainid));</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          6 :       } else if( name==&quot;omega&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CA&quot;,resnum-1,chainid));</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C&quot;,resnum-1,chainid));</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N&quot;,resnum,chainid));</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CA&quot;,resnum,chainid));</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          5 :       } else if( name==&quot;chi1&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          3 :         if ( resname==&quot;GLY&quot; || resname==&quot;ALA&quot; || resname==&quot;SFO&quot; ) plumed_merror(&quot;chi-1 is not defined for ALA, GLY and SFO&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N&quot;,resnum,chainid));</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CA&quot;,resnum,chainid));</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CB&quot;,resnum,chainid));</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          2 :         if(resname==&quot;ILE&quot;||resname==&quot;VAL&quot;) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CG1&quot;,resnum,chainid));</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          1 :         } else if(resname==&quot;CYS&quot;) {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;SG&quot;,resnum,chainid));</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          1 :         } else if(resname==&quot;THR&quot;) {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;OG1&quot;,resnum,chainid));</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          1 :         } else if(resname==&quot;SER&quot;) {</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;OG&quot;,resnum,chainid));</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :         } else {</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          2 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CG&quot;,resnum,chainid));</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :         }</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          4 :       } else if( name==&quot;chi2&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          5 :         if ( resname==&quot;GLY&quot; || resname==&quot;ALA&quot; || resname==&quot;SFO&quot; || resname==&quot;CYS&quot; || resname==&quot;SER&quot; ||</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          2 :              resname==&quot;THR&quot; || resname==&quot;VAL&quot; ) plumed_merror(&quot;chi-2 is not defined for ALA, GLY, CYS, SER, THR, VAL and SFO&quot;);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CA&quot;,resnum,chainid));</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CB&quot;,resnum,chainid));</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          1 :         if(resname==&quot;ILE&quot;) {</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CG1&quot;,resnum,chainid));</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :         } else {</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          2 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CG&quot;,resnum,chainid));</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :         }</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          2 :         if(resname==&quot;ASN&quot; || resname==&quot;ASP&quot;) {</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;OD1&quot;,resnum,chainid));</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          1 :         } else if(resname==&quot;HIS&quot;) {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;ND1&quot;,resnum,chainid));</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          4 :         } else if(resname==&quot;LEU&quot; || resname==&quot;PHE&quot; || resname==&quot;TRP&quot; || resname==&quot;TYR&quot;) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CD1&quot;,resnum,chainid));</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          1 :         } else if(resname==&quot;MET&quot;) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;SD&quot;,resnum,chainid));</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :         } else {</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          2 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CD&quot;,resnum,chainid));</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :         }</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          2 :       } else if( name==&quot;chi3&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :         if (!( resname==&quot;ARG&quot; || resname==&quot;GLN&quot; || resname==&quot;GLU&quot; || resname==&quot;LYS&quot; ||</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :                resname==&quot;MET&quot; )) plumed_merror(&quot;chi-3 is defined only for ARG, GLN, GLU, LYS and MET&quot;);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CB&quot;,resnum,chainid));</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CG&quot;,resnum,chainid));</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :         if(resname==&quot;MET&quot;) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;SD&quot;,resnum,chainid));</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :         } else {</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CD&quot;,resnum,chainid));</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :         }</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :         if(resname==&quot;GLN&quot; || resname==&quot;GLU&quot;) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;OE1&quot;,resnum,chainid));</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :         } else if(resname==&quot;LYS&quot; || resname==&quot;MET&quot;) {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CE&quot;,resnum,chainid));</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :         } else {</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;NE&quot;,resnum,chainid));</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :         }</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          2 :       } else if( name==&quot;chi4&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :         if (!( resname==&quot;ARG&quot; || resname==&quot;LYS&quot; )) plumed_merror(&quot;chi-4 is defined only for ARG and LYS&quot;);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CG&quot;,resnum,chainid));</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CD&quot;,resnum,chainid));</span></a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :         if(resname==&quot;ARG&quot;) {</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;NE&quot;,resnum,chainid));</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CZ&quot;,resnum,chainid));</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :         } else {</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CE&quot;,resnum,chainid));</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;NZ&quot;,resnum,chainid));</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :         }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          2 :       } else if( name==&quot;chi5&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :         if (!( resname==&quot;ARG&quot; )) plumed_merror(&quot;chi-5 is defined only for ARG&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CD&quot;,resnum,chainid));</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;NE&quot;,resnum,chainid));</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;CZ&quot;,resnum,chainid));</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineNoCov">          0 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;NH1&quot;,resnum,chainid));</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          3 :       } else if( name==&quot;sidechain&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          1 :         if(resname==&quot;GLY&quot;) plumed_merror(&quot;sidechain is not defined for GLY&quot;);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          1 :         std::vector&lt;AtomNumber&gt; tmpnum1(mypdb.getAtomsInResidue(resnum,chainid));</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         15 :         for(unsigned i=0; i&lt;tmpnum1.size(); i++) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         66 :           if(mypdb.getAtomName(tmpnum1[i])!=&quot;N&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;CA&quot;&amp;&amp;</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         70 :               mypdb.getAtomName(tmpnum1[i])!=&quot;C&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;O&quot;&amp;&amp;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         61 :               mypdb.getAtomName(tmpnum1[i])!=&quot;HA&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;H&quot;&amp;&amp;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])!=&quot;HN&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;H1&quot;&amp;&amp;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])!=&quot;H2&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;H3&quot;&amp;&amp;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])!=&quot;OXT&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;OT1&quot;&amp;&amp;</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         73 :               mypdb.getAtomName(tmpnum1[i])!=&quot;OT2&quot;&amp;&amp;mypdb.getAtomName(tmpnum1[i])!=&quot;OC1&quot;&amp;&amp;</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         32 :               mypdb.getAtomName(tmpnum1[i])!=&quot;OC2&quot;) {</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">          9 :             numbers.push_back( tmpnum1[i] );</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :           }</a>
+<a name="413"><span class="lineNum">     413 </span>            :         }</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          2 :       } else if( name==&quot;back&quot; &amp;&amp; !isTerminalGroup(&quot;protein&quot;,resname) ) {</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">          1 :         std::vector&lt;AtomNumber&gt; tmpnum1(mypdb.getAtomsInResidue(resnum,chainid));</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         15 :         for(unsigned i=0; i&lt;tmpnum1.size(); i++) {</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         66 :           if(mypdb.getAtomName(tmpnum1[i])==&quot;N&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;CA&quot;||</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         70 :               mypdb.getAtomName(tmpnum1[i])==&quot;C&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;O&quot;||</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         61 :               mypdb.getAtomName(tmpnum1[i])==&quot;HA&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;H&quot;||</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])==&quot;HN&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;H1&quot;||</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])==&quot;H2&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;H3&quot;||</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])==&quot;OXT&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;OT1&quot;||</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])==&quot;OT2&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;OC1&quot;||</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         59 :               mypdb.getAtomName(tmpnum1[i])==&quot;OC2&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;HA1&quot;||</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         63 :               mypdb.getAtomName(tmpnum1[i])==&quot;HA2&quot;||mypdb.getAtomName(tmpnum1[i])==&quot;HA3&quot;) {</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          5 :             numbers.push_back( tmpnum1[i] );</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :           }</a>
+<a name="428"><span class="lineNum">     428 </span>            :         }</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :       } else numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(name,resnum,chainid));</span></a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        488 :     } else if( allowedResidue(&quot;rna&quot;,resname) || allowedResidue(&quot;dna&quot;,resname)) {</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :       std::string basetype;</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        474 :       if(resname.find_first_of(&quot;A&quot;)!=std::string::npos) basetype+=&quot;A&quot;;</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        474 :       if(resname.find_first_of(&quot;U&quot;)!=std::string::npos) basetype+=&quot;U&quot;;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">        474 :       if(resname.find_first_of(&quot;T&quot;)!=std::string::npos) basetype+=&quot;T&quot;;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">        474 :       if(resname.find_first_of(&quot;C&quot;)!=std::string::npos) basetype+=&quot;C&quot;;</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">        474 :       if(resname.find_first_of(&quot;G&quot;)!=std::string::npos) basetype+=&quot;G&quot;;</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">        474 :       plumed_massert(basetype.length()==1,&quot;cannot find type of rna/dna residue &quot;+resname+&quot; &quot;+basetype);</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">        474 :       if( name==&quot;chi&quot; ) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         68 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4\'&quot;,resnum,chainid));</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         68 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C1\'&quot;,resnum,chainid));</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">         99 :         if(basetype==&quot;T&quot; || basetype==&quot;U&quot; || basetype==&quot;C&quot;) {</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N1&quot;,resnum,chainid));</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         47 :         } else if(basetype==&quot;G&quot; || basetype==&quot;A&quot;) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         50 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N9&quot;,resnum,chainid));</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         50 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineNoCov">          0 :         } else plumed_error();</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">        440 :       } else if( name==&quot;alpha&quot; ) {</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O3\'&quot;,resnum-1,chainid));</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;P&quot;,resnum,chainid));</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O5\'&quot;,resnum,chainid));</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5\'&quot;,resnum,chainid));</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">        433 :       } else if( name==&quot;beta&quot; ) {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;P&quot;,resnum,chainid));</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O5\'&quot;,resnum,chainid));</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5\'&quot;,resnum,chainid));</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        426 :       } else if( name==&quot;gamma&quot; ) {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         54 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O5\'&quot;,resnum,chainid));</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         54 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5\'&quot;,resnum,chainid));</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         54 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         54 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        399 :       } else if( name==&quot;delta&quot; ) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5\'&quot;,resnum,chainid));</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O3\'&quot;,resnum,chainid));</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        398 :       } else if( name==&quot;epsilon&quot; ) {</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         16 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         16 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         16 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O3\'&quot;,resnum,chainid));</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         16 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;P&quot;,resnum+1,chainid));</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        390 :       } else if( name==&quot;zeta&quot; ) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O3\'&quot;,resnum,chainid));</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;P&quot;,resnum+1,chainid));</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         14 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O5\'&quot;,resnum+1,chainid));</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        383 :       } else if( name==&quot;v0&quot; ) {</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4\'&quot;,resnum,chainid));</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C1\'&quot;,resnum,chainid));</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2\'&quot;,resnum,chainid));</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        380 :       } else if( name==&quot;v1&quot; ) {</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4\'&quot;,resnum,chainid));</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C1\'&quot;,resnum,chainid));</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2\'&quot;,resnum,chainid));</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">        377 :       } else if( name==&quot;v2&quot; ) {</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C1\'&quot;,resnum,chainid));</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2\'&quot;,resnum,chainid));</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        374 :       } else if( name==&quot;v3&quot; ) {</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2\'&quot;,resnum,chainid));</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4\'&quot;,resnum,chainid));</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        371 :       } else if( name==&quot;v4&quot; ) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4\'&quot;,resnum,chainid));</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">          6 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C1\'&quot;,resnum,chainid));</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        368 :       } else if( name==&quot;back&quot; ) {</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;P&quot;,resnum,chainid));</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O5\'&quot;,resnum,chainid));</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5\'&quot;,resnum,chainid));</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">          2 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O3\'&quot;,resnum,chainid));</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">        367 :       } else if( name==&quot;sugar&quot; ) {</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">        104 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4\'&quot;,resnum,chainid));</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">        104 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4\'&quot;,resnum,chainid));</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">        104 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C1\'&quot;,resnum,chainid));</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        104 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2\'&quot;,resnum,chainid));</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        104 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C3\'&quot;,resnum,chainid));</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">        315 :       } else if( name==&quot;base&quot; ) {</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         25 :         if(basetype==&quot;C&quot;) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N1&quot;,resnum,chainid));</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O2&quot;,resnum,chainid));</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N3&quot;,resnum,chainid));</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N4&quot;,resnum,chainid));</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5&quot;,resnum,chainid));</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         18 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         16 :         } else if(basetype==&quot;U&quot;) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N1&quot;,resnum,chainid));</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O2&quot;,resnum,chainid));</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N3&quot;,resnum,chainid));</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4&quot;,resnum,chainid));</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5&quot;,resnum,chainid));</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">          4 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         14 :         } else if(basetype==&quot;T&quot;) {</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N1&quot;,resnum,chainid));</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O2&quot;,resnum,chainid));</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N3&quot;,resnum,chainid));</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O4&quot;,resnum,chainid));</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5&quot;,resnum,chainid));</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C7&quot;,resnum,chainid));</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         14 :         } else if(basetype==&quot;G&quot;) {</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N9&quot;,resnum,chainid));</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N3&quot;,resnum,chainid));</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N2&quot;,resnum,chainid));</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N1&quot;,resnum,chainid));</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;O6&quot;,resnum,chainid));</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5&quot;,resnum,chainid));</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N7&quot;,resnum,chainid));</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">          6 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C8&quot;,resnum,chainid));</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         11 :         } else if(basetype==&quot;A&quot;) {</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N9&quot;,resnum,chainid));</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N1&quot;,resnum,chainid));</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N3&quot;,resnum,chainid));</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N6&quot;,resnum,chainid));</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C5&quot;,resnum,chainid));</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;N7&quot;,resnum,chainid));</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         22 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C8&quot;,resnum,chainid));</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :         } else plumed_error();</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">        290 :       } else if( name==&quot;lcs&quot; ) {</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">        568 :         numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C2&quot;,resnum,chainid));</span></a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">        752 :         if(basetype==&quot;T&quot; || basetype==&quot;U&quot; || basetype==&quot;C&quot;) {</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        296 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        296 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        216 :         } else if(basetype==&quot;G&quot; || basetype==&quot;A&quot;) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">        272 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C6&quot;,resnum,chainid));</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">        272 :           numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(&quot;C4&quot;,resnum,chainid));</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :         } else plumed_error();</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         12 :       } else numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(name,resnum,chainid));</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">          2 :     } else numbers.push_back(mypdb.getNamedAtomFromResidueAndChain(name,resnum,chainid));</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :   }</a>
+<a name="582"><span class="lineNum">     582 </span>            :   else {</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :     plumed_merror(type + &quot; is not a valid molecule type&quot;);</span></a>
+<a name="584"><span class="lineNum">     584 </span>            :   }</a>
+<a name="585"><span class="lineNum">     585 </span>            : }</a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MultiValue.cpp.func-sort-c.html b/coverage/tools/MultiValue.cpp.func-sort-c.html
new file mode 100644
index 0000000000..204ff304cf
--- /dev/null
+++ b/coverage/tools/MultiValue.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MultiValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MultiValue.cpp<span style="font-size: 80%;"> (<a href="MultiValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiValue.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#37">_ZN4PLMD10MultiValue6resizeERKmS2_</a></td>
+              <td class="coverFnHi">41860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#81">_ZN4PLMD10MultiValue15copyDerivativesERS0_</a></td>
+              <td class="coverFnHi">50656</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#75">_ZNK4PLMD10MultiValue10copyValuesERS0_</a></td>
+              <td class="coverFnHi">57565</td>
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+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#24">_ZN4PLMD10MultiValueC2ERKmS2_</a></td>
+              <td class="coverFnHi">360241</td>
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+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#62">_ZN4PLMD10MultiValue9chainRuleERKjS2_S2_S2_RKdS2_RSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">502652</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#100">_ZN4PLMD10MultiValue12quotientRuleERKjS2_</a></td>
+              <td class="coverFnHi">1869892</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#57">_ZN4PLMD10MultiValue23clearTemporyDerivativesEv</a></td>
+              <td class="coverFnHi">2099217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#45">_ZN4PLMD10MultiValue8clearAllEv</a></td>
+              <td class="coverFnHi">2099217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#51">_ZN4PLMD10MultiValue5clearERKj</a></td>
+              <td class="coverFnHi">8343013</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MultiValue.cpp.func.html b/coverage/tools/MultiValue.cpp.func.html
new file mode 100644
index 0000000000..aca62fc189
--- /dev/null
+++ b/coverage/tools/MultiValue.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MultiValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MultiValue.cpp<span style="font-size: 80%;"> (<a href="MultiValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiValue.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#100">_ZN4PLMD10MultiValue12quotientRuleERKjS2_</a></td>
+              <td class="coverFnHi">1869892</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#81">_ZN4PLMD10MultiValue15copyDerivativesERS0_</a></td>
+              <td class="coverFnHi">50656</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#57">_ZN4PLMD10MultiValue23clearTemporyDerivativesEv</a></td>
+              <td class="coverFnHi">2099217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#51">_ZN4PLMD10MultiValue5clearERKj</a></td>
+              <td class="coverFnHi">8343013</td>
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+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#37">_ZN4PLMD10MultiValue6resizeERKmS2_</a></td>
+              <td class="coverFnHi">41860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#45">_ZN4PLMD10MultiValue8clearAllEv</a></td>
+              <td class="coverFnHi">2099217</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#62">_ZN4PLMD10MultiValue9chainRuleERKjS2_S2_S2_RKdS2_RSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">502652</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#24">_ZN4PLMD10MultiValueC2ERKmS2_</a></td>
+              <td class="coverFnHi">360241</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.cpp.gcov.html#75">_ZNK4PLMD10MultiValue10copyValuesERS0_</a></td>
+              <td class="coverFnHi">57565</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MultiValue.cpp.gcov.html b/coverage/tools/MultiValue.cpp.gcov.html
new file mode 100644
index 0000000000..5f6a5ba61b
--- /dev/null
+++ b/coverage/tools/MultiValue.cpp.gcov.html
@@ -0,0 +1,196 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MultiValue.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MultiValue.cpp<span style="font-size: 80%;"> (source / <a href="MultiValue.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntry">62</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;MultiValue.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span><span class="lineCov">     360241 : MultiValue::MultiValue( const size_t&amp; nvals, const size_t&amp; nder ):</span></a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">     360241 :   values(nvals),</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">     360241 :   nderivatives(nder),</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     360241 :   derivatives(nvals*nder),</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">     360241 :   tmpval(0),</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">     360241 :   tmpder(nder),</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     720482 :   atLeastOneSet(false)</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : {</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     360241 :   std::vector&lt;unsigned&gt; myind( nder );</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">   10704348 :   for(unsigned i=0; i&lt;nder; ++i) myind[i]=i;</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     360241 :   hasDerivatives.createIndexListFromVector( myind );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     360241 : }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">      41860 : void MultiValue::resize( const size_t&amp; nvals, const size_t&amp; nder ) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      41860 :   values.resize(nvals); nderivatives=nder; derivatives.resize( nvals*nder );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      41860 :   tmpder.resize( nder ); hasDerivatives.clear(); std::vector&lt;unsigned&gt; myind( nder );</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">   10858510 :   for(unsigned i=0; i&lt;nder; ++i) myind[i]=i;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      41860 :   hasDerivatives.createIndexListFromVector( myind );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">      41860 :   atLeastOneSet=false;</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      41860 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">    2099217 : void MultiValue::clearAll() {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">    2099217 :   if( atLeastOneSet &amp;&amp; !hasDerivatives.updateComplete() ) hasDerivatives.updateActiveMembers();</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">   10442230 :   for(unsigned i=0; i&lt;values.size(); ++i) clear(i);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    2099217 :   clearTemporyDerivatives(); hasDerivatives.deactivateAll(); atLeastOneSet=false;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">    2099217 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">    8343013 : void MultiValue::clear( const unsigned&amp; ival ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">    8343013 :   values[ival]=0;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">    8343013 :   unsigned base=ival*nderivatives, ndert=hasDerivatives.getNumberActive();</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">  311771833 :   for(unsigned i=0; i&lt;ndert; ++i) derivatives[ base+hasDerivatives[i] ]=0.;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">    8343013 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">    2099217 : void MultiValue::clearTemporyDerivatives() {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">    2099217 :   unsigned ndert=hasDerivatives.getNumberActive(); tmpval=0.;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">   82074873 :   for(unsigned i=0; i&lt;ndert; ++i) tmpder[ hasDerivatives[i] ]=0.;</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">    2099217 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">     502652 : void MultiValue::chainRule( const unsigned&amp; ival, const unsigned&amp; iout, const unsigned&amp; stride, const unsigned&amp; off,</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :                             const double&amp; df, const unsigned&amp; bufstart, std::vector&lt;double&gt;&amp; buffer ) {</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     502652 :   if( !hasDerivatives.updateComplete() ) hasDerivatives.updateActiveMembers();</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            :   plumed_dbg_assert( off&lt;stride );</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">     502652 :   unsigned base=nderivatives*ival, ndert=hasDerivatives.getNumberActive();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     502652 :   unsigned start=bufstart+stride*(nderivatives+1)*iout + stride;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">   29225155 :   for(unsigned i=0; i&lt;ndert; ++i) {</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :     unsigned jder=hasDerivatives[i];</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">   28722503 :     buffer[start+jder*stride] += df*derivatives[base+jder];</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     502652 : }</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      57565 : void MultiValue::copyValues( MultiValue&amp; outvals ) const {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   plumed_dbg_assert( values.size()&lt;=outvals.getNumberOfValues() );</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     183225 :   for(unsigned i=0; i&lt;values.size(); ++i) outvals.setValue( i, values[i] );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      57565 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      50656 : void MultiValue::copyDerivatives( MultiValue&amp; outvals ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   plumed_dbg_assert( values.size()&lt;=outvals.getNumberOfValues() &amp;&amp; nderivatives&lt;=outvals.getNumberOfDerivatives() );</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      50656 :   if( !hasDerivatives.updateComplete() ) hasDerivatives.updateActiveMembers();</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      50656 :   outvals.atLeastOneSet=true; unsigned ndert=hasDerivatives.getNumberActive();</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    3766585 :   for(unsigned j=0; j&lt;ndert; ++j) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">    3715929 :     unsigned jder=hasDerivatives[j]; outvals.hasDerivatives.activate(jder);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   unsigned base=0, obase=0;</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     162498 :   for(unsigned i=0; i&lt;values.size(); ++i) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    8330096 :     for(unsigned j=0; j&lt;ndert; ++j) {</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :       unsigned jder=hasDerivatives[j];</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    8218254 :       outvals.derivatives[obase+jder] += derivatives[base+jder];</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :     }</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     111842 :     obase+=outvals.nderivatives; base+=nderivatives;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">      50656 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">    1869892 : void MultiValue::quotientRule( const unsigned&amp; nder, const unsigned&amp; oder ) {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   plumed_dbg_assert( nder&lt;values.size() &amp;&amp; oder&lt;values.size() );</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">    1869892 :   if( !hasDerivatives.updateComplete() ) hasDerivatives.updateActiveMembers();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">    1869892 :   unsigned ndert=hasDerivatives.getNumberActive(); double wpref;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    1869892 :   unsigned obase=oder*nderivatives, nbase=nder*nderivatives;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">    1869892 :   if( std::fabs(tmpval)&gt;epsilon ) { wpref=1.0/tmpval; }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   else { wpref=1.0; }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">    1869892 :   double pref = values[nder]*wpref*wpref;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">  179899336 :   for(unsigned j=0; j&lt;ndert; ++j) {</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :     unsigned jder=hasDerivatives[j];</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">  178029444 :     derivatives[obase+jder] = wpref*derivatives[nbase+jder]  - pref*tmpder[jder];</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">    1869892 :   values[oder] = wpref*values[nder];</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">    1869892 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MultiValue.h.func-sort-c.html b/coverage/tools/MultiValue.h.func-sort-c.html
new file mode 100644
index 0000000000..4cfdad0b6b
--- /dev/null
+++ b/coverage/tools/MultiValue.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MultiValue.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MultiValue.h<span style="font-size: 80%;"> (<a href="MultiValue.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MultiValue.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#188">_ZN4PLMD10MultiValue11updateIndexERKj</a></td>
+              <td class="coverFnHi">222000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#147">_ZN4PLMD10MultiValue20addTemporyDerivativeERKjRKd</a></td>
+              <td class="coverFnHi">35718834</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#154">_ZN4PLMD10MultiValue13setDerivativeERKjS2_RKd</a></td>
+              <td class="coverFnHi">145616121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#136">_ZN4PLMD10MultiValue13addDerivativeERKjS2_RKd</a></td>
+              <td class="coverFnHi">1359057968</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MultiValue.h.func.html b/coverage/tools/MultiValue.h.func.html
new file mode 100644
index 0000000000..63972e23ba
--- /dev/null
+++ b/coverage/tools/MultiValue.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MultiValue.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MultiValue.h<span style="font-size: 80%;"> (<a href="MultiValue.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MultiValue.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#188">_ZN4PLMD10MultiValue11updateIndexERKj</a></td>
+              <td class="coverFnHi">222000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#136">_ZN4PLMD10MultiValue13addDerivativeERKjS2_RKd</a></td>
+              <td class="coverFnHi">1359057968</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#154">_ZN4PLMD10MultiValue13setDerivativeERKjS2_RKd</a></td>
+              <td class="coverFnHi">145616121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MultiValue.h.gcov.html#147">_ZN4PLMD10MultiValue20addTemporyDerivativeERKjRKd</a></td>
+              <td class="coverFnHi">35718834</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/MultiValue.h.gcov.html b/coverage/tools/MultiValue.h.gcov.html
new file mode 100644
index 0000000000..4c1d0800e4
--- /dev/null
+++ b/coverage/tools/MultiValue.h.gcov.html
@@ -0,0 +1,317 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/MultiValue.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - MultiValue.h<span style="font-size: 80%;"> (source / <a href="MultiValue.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_MultiValue_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_MultiValue_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;DynamicList.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstddef&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class MultiValue {</a>
+<a name="33"><span class="lineNum">      33 </span>            : private:</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// Used to ensure rapid accumulation of derivatives</a>
+<a name="35"><span class="lineNum">      35 </span>            :   DynamicList&lt;unsigned&gt; hasDerivatives;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Values of quantities</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;double&gt; values;</a>
+<a name="38"><span class="lineNum">      38 </span>            : /// Number of derivatives per value</a>
+<a name="39"><span class="lineNum">      39 </span>            :   unsigned nderivatives;</a>
+<a name="40"><span class="lineNum">      40 </span>            : /// Derivatives</a>
+<a name="41"><span class="lineNum">      41 </span>            :   std::vector&lt;double&gt; derivatives;</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Tempory value</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double tmpval;</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// Tempory vector of derivatives (used for calculating quotients</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;double&gt; tmpder;</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Logical to check if any derivatives were set</a>
+<a name="47"><span class="lineNum">      47 </span>            :   bool atLeastOneSet;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// This is a fudge to save on vector resizing in MultiColvar</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::vector&lt;unsigned&gt; indices, sort_indices;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;Vector&gt; tmp_atoms;</a>
+<a name="51"><span class="lineNum">      51 </span>            : public:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   MultiValue( const std::size_t&amp;, const std::size_t&amp; );</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void resize( const std::size_t&amp;, const std::size_t&amp; );</a>
+<a name="54"><span class="lineNum">      54 </span>            : ///</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::vector&lt;unsigned&gt;&amp; getIndices();</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::vector&lt;unsigned&gt;&amp; getSortIndices();</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;Vector&gt;&amp; getAtomVector();</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Get the number of values in the stash</a>
+<a name="59"><span class="lineNum">      59 </span>            :   unsigned getNumberOfValues() const ;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Get the number of derivatives in the stash</a>
+<a name="61"><span class="lineNum">      61 </span>            :   unsigned getNumberOfDerivatives() const ;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Set value numbered</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void setValue( const unsigned&amp;,  const double&amp; );</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Add value numbered</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void addValue( const unsigned&amp;,  const double&amp; );</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Add derivative</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void addDerivative( const unsigned&amp;, const unsigned&amp;, const double&amp; );</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Add to the tempory value</a>
+<a name="69"><span class="lineNum">      69 </span>            :   void addTemporyValue( const double&amp; val );</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Add tempory derivatives - this is used for calculating quotients</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void addTemporyDerivative( const unsigned&amp; jder, const double&amp; der );</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Set the value of the derivative</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void setDerivative( const unsigned&amp; ival, const unsigned&amp; jder, const double&amp; der);</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Return the ith value</a>
+<a name="75"><span class="lineNum">      75 </span>            :   double get( const unsigned&amp; ) const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Return a derivative value</a>
+<a name="77"><span class="lineNum">      77 </span>            :   double getDerivative( const unsigned&amp;, const unsigned&amp; ) const ;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Get one of the tempory derivatives</a>
+<a name="79"><span class="lineNum">      79 </span>            :   double getTemporyDerivative( const unsigned&amp; jder ) const ;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Clear all values</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void clearAll();</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Clear the tempory derivatives</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void clearTemporyDerivatives();</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// Clear a value</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void clear( const unsigned&amp; );</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Functions for accessing active list</a>
+<a name="87"><span class="lineNum">      87 </span>            :   bool updateComplete();</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void emptyActiveMembers();</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void putIndexInActiveArray( const unsigned &amp; );</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void updateIndex( const unsigned&amp; );</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void sortActiveList();</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void completeUpdate();</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void updateDynamicList();</a>
+<a name="94"><span class="lineNum">      94 </span>            :   bool isActive( const unsigned&amp; ind ) const ;</a>
+<a name="95"><span class="lineNum">      95 </span>            : ///</a>
+<a name="96"><span class="lineNum">      96 </span>            :   unsigned getNumberActive() const ;</a>
+<a name="97"><span class="lineNum">      97 </span>            : ///</a>
+<a name="98"><span class="lineNum">      98 </span>            :   unsigned getActiveIndex( const unsigned&amp; ) const ;</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Transfer derivatives to buffer</a>
+<a name="100"><span class="lineNum">     100 </span>            :   void chainRule( const unsigned&amp;, const unsigned&amp;, const unsigned&amp;, const unsigned&amp;, const double&amp;, const unsigned&amp;, std::vector&lt;double&gt;&amp; buffer );</a>
+<a name="101"><span class="lineNum">     101 </span>            : ///</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void copyValues( MultiValue&amp; ) const ;</a>
+<a name="103"><span class="lineNum">     103 </span>            : ///</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void copyDerivatives( MultiValue&amp; );</a>
+<a name="105"><span class="lineNum">     105 </span>            : ///</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void quotientRule( const unsigned&amp; nder, const unsigned&amp; oder );</a>
+<a name="107"><span class="lineNum">     107 </span>            : };</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : inline</a>
+<a name="110"><span class="lineNum">     110 </span>            : unsigned MultiValue::getNumberOfValues() const {</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">  172403995 :   return values.size();</span></a>
+<a name="112"><span class="lineNum">     112 </span>            : }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : inline</a>
+<a name="115"><span class="lineNum">     115 </span>            : unsigned MultiValue::getNumberOfDerivatives() const {</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">   30913737 :   return nderivatives; //derivatives.ncols();</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : inline</a>
+<a name="120"><span class="lineNum">     120 </span>            : double MultiValue::get( const unsigned&amp; ival ) const {</a>
+<a name="121"><span class="lineNum">     121 </span>            :   plumed_dbg_assert( ival&lt;=values.size() );</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">  173450831 :   return values[ival];</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : }</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : inline</a>
+<a name="126"><span class="lineNum">     126 </span>            : void MultiValue::setValue( const unsigned&amp; ival,  const double&amp; val) {</a>
+<a name="127"><span class="lineNum">     127 </span>            :   plumed_dbg_assert( ival&lt;=values.size() );</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">    1829663 :   values[ival]=val;</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : inline</a>
+<a name="132"><span class="lineNum">     132 </span>            : void MultiValue::addValue( const unsigned&amp; ival,  const double&amp; val) {</a>
+<a name="133"><span class="lineNum">     133 </span>            :   plumed_dbg_assert( ival&lt;=values.size() );</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">   62235725 :   values[ival]+=val;</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : inline</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov"> 1359057968 : void MultiValue::addDerivative( const unsigned&amp; ival, const unsigned&amp; jder, const double&amp; der) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov"> 1359057968 :   plumed_dbg_assert( ival&lt;=values.size() &amp;&amp; jder&lt;nderivatives ); atLeastOneSet=true;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov"> 1359057968 :   hasDerivatives.activate(jder); derivatives[nderivatives*ival+jder] += der;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov"> 1359057968 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : inline</a>
+<a name="144"><span class="lineNum">     144 </span>            : void MultiValue::addTemporyValue( const double&amp; val ) {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">    2752543 :   tmpval += val;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : inline</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">   35718834 : void MultiValue::addTemporyDerivative( const unsigned&amp; jder, const double&amp; der ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">   35718834 :   plumed_dbg_assert( jder&lt;nderivatives ); atLeastOneSet=true;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">   35718834 :   hasDerivatives.activate(jder); tmpder[jder] += der;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">   35718834 : }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : inline</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">  145616121 : void MultiValue::setDerivative( const unsigned&amp; ival, const unsigned&amp; jder, const double&amp; der) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">  145616121 :   plumed_dbg_assert( ival&lt;=values.size() &amp;&amp; jder&lt;nderivatives ); atLeastOneSet=true;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">  145616121 :   hasDerivatives.activate(jder); derivatives[nderivatives*ival+jder]=der;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">  145616121 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : inline</a>
+<a name="163"><span class="lineNum">     163 </span>            : double MultiValue::getDerivative( const unsigned&amp; ival, const unsigned&amp; jder ) const {</a>
+<a name="164"><span class="lineNum">     164 </span>            :   plumed_dbg_assert( jder&lt;nderivatives &amp;&amp; hasDerivatives.isActive(jder) );</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">  535798761 :   return derivatives[nderivatives*ival+jder];</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : inline</a>
+<a name="169"><span class="lineNum">     169 </span>            : double MultiValue::getTemporyDerivative( const unsigned&amp; jder ) const {</a>
+<a name="170"><span class="lineNum">     170 </span>            :   plumed_dbg_assert( jder&lt;nderivatives &amp;&amp; hasDerivatives.isActive(jder) );</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">      49704 :   return tmpder[jder];</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : inline</a>
+<a name="175"><span class="lineNum">     175 </span>            : bool MultiValue::updateComplete() {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">    1621315 :   return hasDerivatives.updateComplete();</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : inline</a>
+<a name="180"><span class="lineNum">     180 </span>            : void MultiValue::emptyActiveMembers() {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     932900 :   hasDerivatives.emptyActiveMembers();</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : inline</a>
+<a name="185"><span class="lineNum">     185 </span>            : void MultiValue::putIndexInActiveArray( const unsigned&amp; ind ) {</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">   32661660 :   hasDerivatives.putIndexInActiveArray( ind );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : }</a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : inline</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">     222000 : void MultiValue::updateIndex( const unsigned&amp; ind ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">     222000 :   if( hasDerivatives.isActive(ind) ) hasDerivatives.putIndexInActiveArray( ind );</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">     222000 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : inline</a>
+<a name="195"><span class="lineNum">     195 </span>            : void MultiValue::sortActiveList() {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      56305 :   hasDerivatives.sortActiveList();</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      56305 : }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : inline</a>
+<a name="200"><span class="lineNum">     200 </span>            : void MultiValue::completeUpdate() {</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     876595 :   hasDerivatives.completeUpdate();</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      94076 : }</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : inline</a>
+<a name="205"><span class="lineNum">     205 </span>            : unsigned MultiValue::getNumberActive() const {</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">   41498512 :   return hasDerivatives.getNumberActive();</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : inline</a>
+<a name="210"><span class="lineNum">     210 </span>            : unsigned MultiValue::getActiveIndex( const unsigned&amp; ind ) const {</a>
+<a name="211"><span class="lineNum">     211 </span>            :   plumed_dbg_assert( ind&lt;hasDerivatives.getNumberActive() );</a>
+<a name="212"><span class="lineNum">     212 </span>            :   return hasDerivatives[ind];</a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : inline</a>
+<a name="216"><span class="lineNum">     216 </span>            : void MultiValue::updateDynamicList() {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     140764 :   if( atLeastOneSet ) hasDerivatives.updateActiveMembers();</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : inline</a>
+<a name="221"><span class="lineNum">     221 </span>            : std::vector&lt;unsigned&gt;&amp; MultiValue::getIndices() {</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">     919465 :   return indices;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : inline</a>
+<a name="226"><span class="lineNum">     226 </span>            : std::vector&lt;unsigned&gt;&amp; MultiValue::getSortIndices() {</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">     448077 :   return sort_indices;</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : inline</a>
+<a name="231"><span class="lineNum">     231 </span>            : std::vector&lt;Vector&gt;&amp; MultiValue::getAtomVector() {</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     678824 :   return tmp_atoms;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : inline</a>
+<a name="236"><span class="lineNum">     236 </span>            : bool MultiValue::isActive( const unsigned&amp; ind ) const {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">  423958368 :   return hasDerivatives.isActive( ind );</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : }</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/NeighborList.cpp.func-sort-c.html b/coverage/tools/NeighborList.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1f41aeba3d
--- /dev/null
+++ b/coverage/tools/NeighborList.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/NeighborList.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - NeighborList.cpp<span style="font-size: 80%;"> (<a href="NeighborList.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryMed">89.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="NeighborList.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#214">_ZN4PLMD12NeighborList12getNeighborsEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#196">_ZN4PLMD12NeighborList13setLastUpdateEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#192">_ZNK4PLMD12NeighborList13getLastUpdateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#56">_ZN4PLMD12NeighborListC2ERKSt6vectorINS_10AtomNumberESaIS2_EERKbS8_RKNS_3PbcERNS_12CommunicatorERKdRKj</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#174">_ZN4PLMD12NeighborList18getReducedAtomListEv</a></td>
+              <td class="coverFnHi">240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#33">_ZN4PLMD12NeighborListC2ERKSt6vectorINS_10AtomNumberESaIS2_EES6_RKbS8_S8_RKNS_3PbcERNS_12CommunicatorERKdRKj</a></td>
+              <td class="coverFnHi">245</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#69">_ZN4PLMD12NeighborList10initializeEv</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#164">_ZN4PLMD12NeighborList14setRequestListEv</a></td>
+              <td class="coverFnHi">3138</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#95">_ZN4PLMD12NeighborList6updateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EE</a></td>
+              <td class="coverFnHi">3138</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#188">_ZNK4PLMD12NeighborList9getStrideEv</a></td>
+              <td class="coverFnHi">13616</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#76">_ZN4PLMD12NeighborList15getFullAtomListEv</a></td>
+              <td class="coverFnHi">69974</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#200">_ZNK4PLMD12NeighborList4sizeEv</a></td>
+              <td class="coverFnHi">23715961</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#208">_ZNK4PLMD12NeighborList22getClosePairAtomNumberEj</a></td>
+              <td class="coverFnHi">34665936</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#80">_ZN4PLMD12NeighborList12getIndexPairEj</a></td>
+              <td class="coverFnHi">49191551</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#204">_ZNK4PLMD12NeighborList12getClosePairEj</a></td>
+              <td class="coverFnHi">77870860</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/NeighborList.cpp.func.html b/coverage/tools/NeighborList.cpp.func.html
new file mode 100644
index 0000000000..14a0e3eda0
--- /dev/null
+++ b/coverage/tools/NeighborList.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/NeighborList.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - NeighborList.cpp<span style="font-size: 80%;"> (<a href="NeighborList.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryMed">89.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="NeighborList.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#69">_ZN4PLMD12NeighborList10initializeEv</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#80">_ZN4PLMD12NeighborList12getIndexPairEj</a></td>
+              <td class="coverFnHi">49191551</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#214">_ZN4PLMD12NeighborList12getNeighborsEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#196">_ZN4PLMD12NeighborList13setLastUpdateEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#164">_ZN4PLMD12NeighborList14setRequestListEv</a></td>
+              <td class="coverFnHi">3138</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#76">_ZN4PLMD12NeighborList15getFullAtomListEv</a></td>
+              <td class="coverFnHi">69974</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#174">_ZN4PLMD12NeighborList18getReducedAtomListEv</a></td>
+              <td class="coverFnHi">240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#95">_ZN4PLMD12NeighborList6updateERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EE</a></td>
+              <td class="coverFnHi">3138</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#56">_ZN4PLMD12NeighborListC2ERKSt6vectorINS_10AtomNumberESaIS2_EERKbS8_RKNS_3PbcERNS_12CommunicatorERKdRKj</a></td>
+              <td class="coverFnHi">39</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#33">_ZN4PLMD12NeighborListC2ERKSt6vectorINS_10AtomNumberESaIS2_EES6_RKbS8_S8_RKNS_3PbcERNS_12CommunicatorERKdRKj</a></td>
+              <td class="coverFnHi">245</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#204">_ZNK4PLMD12NeighborList12getClosePairEj</a></td>
+              <td class="coverFnHi">77870860</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#192">_ZNK4PLMD12NeighborList13getLastUpdateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#208">_ZNK4PLMD12NeighborList22getClosePairAtomNumberEj</a></td>
+              <td class="coverFnHi">34665936</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#200">_ZNK4PLMD12NeighborList4sizeEv</a></td>
+              <td class="coverFnHi">23715961</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.cpp.gcov.html#188">_ZNK4PLMD12NeighborList9getStrideEv</a></td>
+              <td class="coverFnHi">13616</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/NeighborList.cpp.gcov.html b/coverage/tools/NeighborList.cpp.gcov.html
new file mode 100644
index 0000000000..fbf0b4acc4
--- /dev/null
+++ b/coverage/tools/NeighborList.cpp.gcov.html
@@ -0,0 +1,301 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/NeighborList.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - NeighborList.cpp<span style="font-size: 80%;"> (source / <a href="NeighborList.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryMed">89.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;NeighborList.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Pbc.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;OpenMP.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;vector&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;algorithm&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;numeric&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        245 : NeighborList::NeighborList(const std::vector&lt;AtomNumber&gt;&amp; list0, const std::vector&lt;AtomNumber&gt;&amp; list1,</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :                            const bool&amp; serial, const bool&amp; do_pair, const bool&amp; do_pbc, const Pbc&amp; pbc, Communicator&amp; cm,</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        245 :                            const double&amp; distance, const unsigned&amp; stride): reduced(false),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        245 :   serial_(serial), do_pair_(do_pair), do_pbc_(do_pbc), pbc_(&amp;pbc), comm(cm),</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        245 :   distance_(distance), stride_(stride)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span>            : // store full list of atoms needed</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        245 :   fullatomlist_=list0;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        245 :   fullatomlist_.insert(fullatomlist_.end(),list1.begin(),list1.end());</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        245 :   nlist0_=list0.size();</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        245 :   nlist1_=list1.size();</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        245 :   twolists_=true;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        245 :   if(!do_pair) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        220 :     nallpairs_=nlist0_*nlist1_;</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   } else {</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         25 :     plumed_assert(nlist0_==nlist1_) &lt;&lt; &quot;when using PAIR option, the two groups should have the same number of elements\n&quot;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :                                     &lt;&lt; &quot;the groups you specified have size &quot;&lt;&lt;nlist0_&lt;&lt;&quot; and &quot;&lt;&lt;nlist1_;</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         25 :     nallpairs_=nlist0_;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   }</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        245 :   initialize();</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        245 :   lastupdate_=0;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        245 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         39 : NeighborList::NeighborList(const std::vector&lt;AtomNumber&gt;&amp; list0, const bool&amp; serial, const bool&amp; do_pbc,</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :                            const Pbc&amp; pbc, Communicator&amp; cm, const double&amp; distance,</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         39 :                            const unsigned&amp; stride): reduced(false),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         39 :   serial_(serial), do_pbc_(do_pbc), pbc_(&amp;pbc), comm(cm),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         39 :   distance_(distance), stride_(stride) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         39 :   fullatomlist_=list0;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         39 :   nlist0_=list0.size();</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         39 :   twolists_=false;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         39 :   nallpairs_=nlist0_*(nlist0_-1)/2;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         39 :   initialize();</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         39 :   lastupdate_=0;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         39 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        284 : void NeighborList::initialize() {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        284 :   neighbors_.clear();</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">   42954115 :   for(unsigned int i=0; i&lt;nallpairs_; ++i) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">   85907662 :     neighbors_.push_back(getIndexPair(i));</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        284 : }</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      69974 : std::vector&lt;AtomNumber&gt;&amp; NeighborList::getFullAtomList() {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      69974 :   return fullatomlist_;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">   49191551 : std::pair&lt;unsigned,unsigned&gt; NeighborList::getIndexPair(unsigned ipair) {</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::pair&lt;unsigned,unsigned&gt; index;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">   49191551 :   if(twolists_ &amp;&amp; do_pair_) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        636 :     index=std::pair&lt;unsigned,unsigned&gt;(ipair,ipair+nlist0_);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">   49190915 :   } else if (twolists_ &amp;&amp; !do_pair_) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    8866469 :     index=std::pair&lt;unsigned,unsigned&gt;(ipair/nlist1_,ipair%nlist1_+nlist0_);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">   40324446 :   } else if (!twolists_) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">   40324446 :     unsigned ii = nallpairs_-1-ipair;</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">   40324446 :     unsigned  K = unsigned(std::floor((std::sqrt(double(8*ii+1))+1)/2));</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">   40324446 :     unsigned jj = ii-K*(K-1)/2;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">   40324446 :     index=std::pair&lt;unsigned,unsigned&gt;(nlist0_-1-K,nlist0_-1-jj);</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">   49191551 :   return index;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       3138 : void NeighborList::update(const std::vector&lt;Vector&gt;&amp; positions) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       3138 :   neighbors_.clear();</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">       3138 :   const double d2=distance_*distance_;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   // check if positions array has the correct length</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       3138 :   plumed_assert(positions.size()==fullatomlist_.size());</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       3138 :   unsigned stride=comm.Get_size();</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">       3138 :   unsigned rank=comm.Get_rank();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       3138 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">       3138 :   if(serial_) {</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :     stride=1;</a>
+<a name="108"><span class="lineNum">     108 </span>            :     rank=0;</a>
+<a name="109"><span class="lineNum">     109 </span>            :     nt=1;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;unsigned&gt; local_flat_nl;</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       3138 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   {</a>
+<a name="115"><span class="lineNum">     115 </span>            :     std::vector&lt;unsigned&gt; private_flat_nl;</a>
+<a name="116"><span class="lineNum">     116 </span>            :     #pragma omp for nowait</a>
+<a name="117"><span class="lineNum">     117 </span>            :     for(unsigned int i=rank; i&lt;nallpairs_; i+=stride) {</a>
+<a name="118"><span class="lineNum">     118 </span>            :       std::pair&lt;unsigned,unsigned&gt; index=getIndexPair(i);</a>
+<a name="119"><span class="lineNum">     119 </span>            :       unsigned index0=index.first;</a>
+<a name="120"><span class="lineNum">     120 </span>            :       unsigned index1=index.second;</a>
+<a name="121"><span class="lineNum">     121 </span>            :       Vector distance;</a>
+<a name="122"><span class="lineNum">     122 </span>            :       if(do_pbc_) {</a>
+<a name="123"><span class="lineNum">     123 </span>            :         distance=pbc_-&gt;distance(positions[index0],positions[index1]);</a>
+<a name="124"><span class="lineNum">     124 </span>            :       } else {</a>
+<a name="125"><span class="lineNum">     125 </span>            :         distance=delta(positions[index0],positions[index1]);</a>
+<a name="126"><span class="lineNum">     126 </span>            :       }</a>
+<a name="127"><span class="lineNum">     127 </span>            :       double value=modulo2(distance);</a>
+<a name="128"><span class="lineNum">     128 </span>            :       if(value&lt;=d2) {</a>
+<a name="129"><span class="lineNum">     129 </span>            :         private_flat_nl.push_back(index0);</a>
+<a name="130"><span class="lineNum">     130 </span>            :         private_flat_nl.push_back(index1);</a>
+<a name="131"><span class="lineNum">     131 </span>            :       }</a>
+<a name="132"><span class="lineNum">     132 </span>            :     }</a>
+<a name="133"><span class="lineNum">     133 </span>            :     #pragma omp critical</a>
+<a name="134"><span class="lineNum">     134 </span>            :     local_flat_nl.insert(local_flat_nl.end(), private_flat_nl.begin(), private_flat_nl.end());</a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            :   // find total dimension of neighborlist</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       3138 :   std::vector &lt;int&gt; local_nl_size(stride, 0);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       3138 :   local_nl_size[rank] = local_flat_nl.size();</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       3138 :   if(!serial_) comm.Sum(&amp;local_nl_size[0], stride);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   int tot_size = std::accumulate(local_nl_size.begin(), local_nl_size.end(), 0);</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       3138 :   if(tot_size==0) {setRequestList(); return;}</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   // merge</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       3120 :   std::vector&lt;unsigned&gt; merge_nl(tot_size, 0);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   // calculate vector of displacement</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       3120 :   std::vector&lt;int&gt; disp(stride);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       3120 :   disp[0] = 0;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   int rank_size = 0;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       9216 :   for(unsigned i=0; i&lt;stride-1; ++i) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       6096 :     rank_size += local_nl_size[i];</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       6096 :     disp[i+1] = rank_size;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            :   // Allgather neighbor list</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       5197 :   if(comm.initialized()&amp;&amp;!serial_) comm.Allgatherv((!local_flat_nl.empty()?&amp;local_flat_nl[0]:NULL), local_nl_size[rank], &amp;merge_nl[0], &amp;local_nl_size[0], &amp;disp[0]);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       1016 :   else merge_nl = local_flat_nl;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   // resize neighbor stuff</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       3120 :   neighbors_.resize(tot_size/2);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">    6114036 :   for(unsigned i=0; i&lt;tot_size/2; i++) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    6110916 :     unsigned j=2*i;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    6110916 :     neighbors_[i] = std::make_pair(merge_nl[j],merge_nl[j+1]);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       3120 :   setRequestList();</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       3138 : void NeighborList::setRequestList() {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       3138 :   requestlist_.clear();</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">    6114054 :   for(unsigned int i=0; i&lt;size(); ++i) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">    6110916 :     requestlist_.push_back(fullatomlist_[neighbors_[i].first]);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">    6110916 :     requestlist_.push_back(fullatomlist_[neighbors_[i].second]);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       3138 :   Tools::removeDuplicates(requestlist_);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       3138 :   reduced=false;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       3138 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        240 : std::vector&lt;AtomNumber&gt;&amp; NeighborList::getReducedAtomList() {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     168359 :   if(!reduced)for(unsigned int i=0; i&lt;size(); ++i) {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :       unsigned newindex0=0,newindex1=0;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     168119 :       AtomNumber index0=fullatomlist_[neighbors_[i].first];</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     168119 :       AtomNumber index1=fullatomlist_[neighbors_[i].second];</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : // I exploit the fact that requestlist_ is an ordered vector</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">     168119 :       auto p = std::find(requestlist_.begin(), requestlist_.end(), index0); plumed_dbg_assert(p!=requestlist_.end()); newindex0=p-requestlist_.begin();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">     168119 :       p = std::find(requestlist_.begin(), requestlist_.end(), index1); plumed_dbg_assert(p!=requestlist_.end()); newindex1=p-requestlist_.begin();</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :       neighbors_[i]=std::pair&lt;unsigned,unsigned&gt;(newindex0,newindex1);</a>
+<a name="185"><span class="lineNum">     185 </span>            :     }</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        240 :   reduced=true;</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        240 :   return requestlist_;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      13616 : unsigned NeighborList::getStride() const {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">      13616 :   return stride_;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 : unsigned NeighborList::getLastUpdate() const {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   return lastupdate_;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 : void NeighborList::setLastUpdate(unsigned step) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   lastupdate_=step;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">   23715961 : unsigned NeighborList::size() const {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">   23715961 :   return neighbors_.size();</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">   77870860 : std::pair&lt;unsigned,unsigned&gt; NeighborList::getClosePair(unsigned i) const {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">   77870860 :   return neighbors_[i];</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">   34665936 : std::pair&lt;AtomNumber,AtomNumber&gt; NeighborList::getClosePairAtomNumber(unsigned i) const {</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   std::pair&lt;AtomNumber,AtomNumber&gt; Aneigh;</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">   34665936 :   Aneigh=std::pair&lt;AtomNumber,AtomNumber&gt;(fullatomlist_[neighbors_[i].first],fullatomlist_[neighbors_[i].second]);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">   34665936 :   return Aneigh;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 : std::vector&lt;unsigned&gt; NeighborList::getNeighbors(unsigned index) {</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   std::vector&lt;unsigned&gt; neighbors;</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;size(); ++i) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :     if(neighbors_[i].first==index)  neighbors.push_back(neighbors_[i].second);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :     if(neighbors_[i].second==index) neighbors.push_back(neighbors_[i].first);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :   return neighbors;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/NeighborList.h.func-sort-c.html b/coverage/tools/NeighborList.h.func-sort-c.html
new file mode 100644
index 0000000000..fe2a0a51e3
--- /dev/null
+++ b/coverage/tools/NeighborList.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/NeighborList.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - NeighborList.h<span style="font-size: 80%;"> (<a href="NeighborList.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="NeighborList.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.h.gcov.html#85">_ZN4PLMD12NeighborListD2Ev</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/NeighborList.h.func.html b/coverage/tools/NeighborList.h.func.html
new file mode 100644
index 0000000000..c3805e8cde
--- /dev/null
+++ b/coverage/tools/NeighborList.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/NeighborList.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - NeighborList.h<span style="font-size: 80%;"> (<a href="NeighborList.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="NeighborList.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="NeighborList.h.gcov.html#85">_ZN4PLMD12NeighborListD2Ev</a></td>
+              <td class="coverFnHi">284</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/NeighborList.h.gcov.html b/coverage/tools/NeighborList.h.gcov.html
new file mode 100644
index 0000000000..c82c48ebba
--- /dev/null
+++ b/coverage/tools/NeighborList.h.gcov.html
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/NeighborList.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - NeighborList.h<span style="font-size: 80%;"> (source / <a href="NeighborList.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_NeighborList_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_NeighborList_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class Pbc;</a>
+<a name="33"><span class="lineNum">      33 </span>            : class Communicator;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : /// \ingroup TOOLBOX</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// A class that implements neighbor lists from two lists or a single list of atoms</a>
+<a name="37"><span class="lineNum">      37 </span>            : class NeighborList</a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span>            :   bool reduced;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool serial_;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   bool do_pair_,do_pbc_,twolists_;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   const PLMD::Pbc* pbc_;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   Communicator&amp; comm;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::vector&lt;PLMD::AtomNumber&gt; fullatomlist_,requestlist_;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;std::pair&lt;unsigned,unsigned&gt; &gt; neighbors_;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double distance_;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   unsigned stride_,nlist0_,nlist1_,nallpairs_,lastupdate_;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Initialize the neighbor list with all possible pairs</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void initialize();</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Return the pair of indexes in the positions array</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// of the two atoms forming the i-th pair among all possible pairs</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::pair&lt;unsigned,unsigned&gt; getIndexPair(unsigned i);</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// Extract the list of atoms from the current list of close pairs</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void setRequestList();</a>
+<a name="55"><span class="lineNum">      55 </span>            : public:</a>
+<a name="56"><span class="lineNum">      56 </span>            :   NeighborList(const std::vector&lt;PLMD::AtomNumber&gt;&amp; list0,</a>
+<a name="57"><span class="lineNum">      57 </span>            :                const std::vector&lt;PLMD::AtomNumber&gt;&amp; list1,</a>
+<a name="58"><span class="lineNum">      58 </span>            :                const bool&amp; serial,</a>
+<a name="59"><span class="lineNum">      59 </span>            :                const bool&amp; do_pair, const bool&amp; do_pbc, const PLMD::Pbc&amp; pbc, Communicator &amp;cm,</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        388 :                const double&amp; distance=1.0e+30, const unsigned&amp; stride=0);</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   NeighborList(const std::vector&lt;PLMD::AtomNumber&gt;&amp; list0,</a>
+<a name="62"><span class="lineNum">      62 </span>            :                const bool&amp; serial,</a>
+<a name="63"><span class="lineNum">      63 </span>            :                const bool&amp; do_pbc,</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         22 :                const PLMD::Pbc&amp; pbc, Communicator &amp;cm, const double&amp; distance=1.0e+30,</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         22 :                const unsigned&amp; stride=0);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Return the list of all atoms. These are needed to rebuild the neighbor list.</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;PLMD::AtomNumber&gt;&amp; getFullAtomList();</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Update the indexes in the neighbor list to match the</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// ordering in the new positions array</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// and return the new list of atoms that must be requested to the main code</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;PLMD::AtomNumber&gt;&amp; getReducedAtomList();</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Update the neighbor list and prepare the new</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// list of atoms that will be requested to the main code</a>
+<a name="74"><span class="lineNum">      74 </span>            :   void update(const std::vector&lt;PLMD::Vector&gt;&amp; positions);</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Get the update stride of the neighbor list</a>
+<a name="76"><span class="lineNum">      76 </span>            :   unsigned getStride() const;</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Get the last step in which the neighbor list was updated</a>
+<a name="78"><span class="lineNum">      78 </span>            :   unsigned getLastUpdate() const;</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// Set the step of the last update</a>
+<a name="80"><span class="lineNum">      80 </span>            :   void setLastUpdate(unsigned step);</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Get the size of the neighbor list</a>
+<a name="82"><span class="lineNum">      82 </span>            :   unsigned size() const;</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Get the i-th pair of the neighbor list</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::pair&lt;unsigned,unsigned&gt; getClosePair(unsigned i) const;</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Get the list of neighbors of the i-th atom</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;unsigned&gt; getNeighbors(unsigned i);</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        284 :   ~NeighborList() {}</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Get the i-th pair of AtomNumbers from the neighbor list</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::pair&lt;AtomNumber,AtomNumber&gt; getClosePairAtomNumber(unsigned i) const;</a>
+<a name="90"><span class="lineNum">      90 </span>            : };</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OFile.cpp.func-sort-c.html b/coverage/tools/OFile.cpp.func-sort-c.html
new file mode 100644
index 0000000000..dc5e28a092
--- /dev/null
+++ b/coverage/tools/OFile.cpp.func-sort-c.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OFile.cpp<span style="font-size: 80%;"> (<a href="OFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">220</td>
+            <td class="headerCovTableEntry">227</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OFile.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#186">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEx</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#180">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEl</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#198">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#421">_ZN4PLMD5OFile14enforceRestartEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#90">_ZN4PLMD5OFile4linkERS0_</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#192">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj</a></td>
+              <td class="coverFnHi">31</td>
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+              <td class="coverFn"><a href="OFile.cpp.gcov.html#275">_ZN4PLMD5OFile14backupAllFilesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">121</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#355">_ZN4PLMD5OFile6rewindEv</a></td>
+              <td class="coverFnHi">135</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#427">_ZN4PLMD5OFile13enforceBackupEv</a></td>
+              <td class="coverFnHi">1144</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#147">_ZN4PLMD5OFile11clearFieldsEv</a></td>
+              <td class="coverFnHi">3202</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#291">_ZN4PLMD5OFile10backupFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">3327</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#320">_ZN4PLMD5OFile4openERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3610</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#413">_ZNK4PLMD5OFile12checkRestartEv</a></td>
+              <td class="coverFnHi">3646</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#225">_ZN4PLMD5OFile15setupPrintValueEPNS_5ValueE</a></td>
+              <td class="coverFnHi">5905</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#388">_ZN4PLMD5OFile5flushEv</a></td>
+              <td class="coverFnHi">8753</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#73">_ZN4PLMD5OFileC1Ev</a></td>
+              <td class="coverFnHi">14650</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#139">_ZN4PLMD5OFile16addConstantFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">27848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#233">_ZN4PLMD5OFile10printFieldEPNS_5ValueERKd</a></td>
+              <td class="coverFnHi">538348</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#97">_ZN4PLMD5OFile13setLinePrefixERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#73">_ZN4PLMD5OFileC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#159">_ZN4PLMD5OFile8fmtFieldEv</a></td>
+              <td class="coverFnHi">825789</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#243">_ZN4PLMD5OFile10printFieldEv</a></td>
+              <td class="coverFnHi">3929842</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#44">_ZN4PLMD5OFile7llwriteEPKcm</a></td>
+              <td class="coverFnHi">5460515</td>
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+              <td class="coverFnHi">14601947</td>
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+    <tr>
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+              <td class="coverFnHi">15531588</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#102">_ZN4PLMD5OFile6printfEPKcz</a></td>
+              <td class="coverFnHi">23588117</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#210">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">37423941</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OFile.cpp.func.html b/coverage/tools/OFile.cpp.func.html
new file mode 100644
index 0000000000..8b9589cfdb
--- /dev/null
+++ b/coverage/tools/OFile.cpp.func.html
@@ -0,0 +1,192 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OFile.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OFile.cpp<span style="font-size: 80%;"> (<a href="OFile.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">220</td>
+            <td class="headerCovTableEntry">227</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OFile.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#291">_ZN4PLMD5OFile10backupFileERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">3327</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#233">_ZN4PLMD5OFile10printFieldEPNS_5ValueERKd</a></td>
+              <td class="coverFnHi">538348</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#210">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnHi">37423941</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#164">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEd</a></td>
+              <td class="coverFnHi">15531588</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#174">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEi</a></td>
+              <td class="coverFnHi">6074528</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#192">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#180">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEl</a></td>
+              <td class="coverFnHi">1</td>
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+              <td class="coverFn"><a href="OFile.cpp.gcov.html#198">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEm</a></td>
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+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#204">_ZN4PLMD5OFile10printFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEy</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#243">_ZN4PLMD5OFile10printFieldEv</a></td>
+              <td class="coverFnHi">3929842</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#147">_ZN4PLMD5OFile11clearFieldsEv</a></td>
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+              <td class="coverFnHi">805268</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#275">_ZN4PLMD5OFile14backupAllFilesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#421">_ZN4PLMD5OFile14enforceRestartEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#271">_ZN4PLMD5OFile15setBackupStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">121</td>
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+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#225">_ZN4PLMD5OFile15setupPrintValueEPNS_5ValueE</a></td>
+              <td class="coverFnHi">5905</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#139">_ZN4PLMD5OFile16addConstantFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">27848</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#90">_ZN4PLMD5OFile4linkERS0_</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#320">_ZN4PLMD5OFile4openERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3610</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#388">_ZN4PLMD5OFile5flushEv</a></td>
+              <td class="coverFnHi">8753</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#102">_ZN4PLMD5OFile6printfEPKcz</a></td>
+              <td class="coverFnHi">23588117</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#355">_ZN4PLMD5OFile6rewindEv</a></td>
+              <td class="coverFnHi">135</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#44">_ZN4PLMD5OFile7llwriteEPKcm</a></td>
+              <td class="coverFnHi">5460515</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#154">_ZN4PLMD5OFile8fmtFieldERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">14601947</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#159">_ZN4PLMD5OFile8fmtFieldEv</a></td>
+              <td class="coverFnHi">825789</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#73">_ZN4PLMD5OFileC1Ev</a></td>
+              <td class="coverFnHi">14650</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#73">_ZN4PLMD5OFileC2Ev</a></td>
+              <td class="coverFnHi">805268</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.cpp.gcov.html#413">_ZNK4PLMD5OFile12checkRestartEv</a></td>
+              <td class="coverFnHi">3646</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OFile.cpp.gcov.html b/coverage/tools/OFile.cpp.gcov.html
new file mode 100644
index 0000000000..50e3213c5b
--- /dev/null
+++ b/coverage/tools/OFile.cpp.gcov.html
@@ -0,0 +1,512 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OFile.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OFile.cpp<span style="font-size: 80%;"> (source / <a href="OFile.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">220</td>
+            <td class="headerCovTableEntry">227</td>
+            <td class="headerCovTableEntryHi">96.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OFile.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Communicator.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstdarg&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cstring&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;iostream&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;string&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;cerrno&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;memory&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;utility&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &lt;zlib.h&gt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #endif</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace PLMD {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">    5460515 : size_t OFile::llwrite(const char*ptr,size_t s) {</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   size_t r;</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">    5460515 :   if(linked) return linked-&gt;llwrite(ptr,s);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">    5460463 :   if(! (comm &amp;&amp; comm-&gt;Get_rank()&gt;0)) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    4636247 :     if(!fp) plumed_merror(&quot;writing on uninitialized File&quot;);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">    4636247 :     if(gzfp) {</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       1263 :       r=gzwrite(gzFile(gzfp),ptr,s);</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : #else</a>
+<a name="55"><span class="lineNum">      55 </span>            :       plumed_merror(&quot;file &quot; + getPath() + &quot;: trying to use a gz file without zlib being linked&quot;);</a>
+<a name="56"><span class="lineNum">      56 </span>            : #endif</a>
+<a name="57"><span class="lineNum">      57 </span>            :     } else {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">    4634984 :       r=std::fwrite(ptr,1,s,fp);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :     }</a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">    5460463 :   if(comm) {</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : //  This barrier is apparently useless since it comes</a>
+<a name="63"><span class="lineNum">      63 </span>            : //  just before a Bcast.</a>
+<a name="64"><span class="lineNum">      64 </span>            : //</a>
+<a name="65"><span class="lineNum">      65 </span>            : //  Anyway, it looks like it is solving an issue that appeared on</a>
+<a name="66"><span class="lineNum">      66 </span>            : //  TRAVIS (at least on my laptop) so I add it here.</a>
+<a name="67"><span class="lineNum">      67 </span>            : //  GB</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    4603429 :     comm-&gt;Barrier();</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">    4603429 :     comm-&gt;Bcast(r,0);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    5460463 :   return r;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">     819918 : OFile::OFile():</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     819918 :   linked(NULL),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     819918 :   fieldChanged(false),</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     819918 :   backstring(&quot;bck&quot;),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     819918 :   enforceRestart_(false),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">     819918 :   enforceBackup_(false)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     819918 :   fmtField();</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">     819918 :   buflen=1;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">     819918 :   actual_buffer_length=0;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     819918 :   buffer.resize(buflen);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : // these are set to zero to avoid valgrind errors</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">    1639836 :   for(int i=0; i&lt;buflen; ++i) buffer[i]=0;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : // these are set to zero to avoid valgrind errors</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">     819918 :   buffer_string.resize(1000,0);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">     819918 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         11 : OFile&amp; OFile::link(OFile&amp;l) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         11 :   fp=NULL;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         11 :   gzfp=NULL;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         11 :   linked=&amp;l;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         11 :   return *this;</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     805268 : OFile&amp; OFile::setLinePrefix(const std::string&amp;l) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     805268 :   linePrefix=l;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     805268 :   return *this;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">   23588117 : int OFile::printf(const char*fmt,...) {</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   va_list arg;</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">   23588117 :   va_start(arg, fmt);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">   23588117 :   int r=std::vsnprintf(&amp;buffer[actual_buffer_length],buflen-actual_buffer_length,fmt,arg);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">   23588117 :   va_end(arg);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">   23588117 :   if(r&gt;=buflen-actual_buffer_length) {</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     int newlen=buflen;</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      47782 :     while(newlen&lt;=r+actual_buffer_length) newlen*=2;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      16019 :     std::vector&lt;char&gt; newbuf(newlen);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      16019 :     std::memmove(newbuf.data(),buffer.data(),buflen);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">    3288347 :     for(int k=buflen; k&lt;newlen; k++) newbuf[k]=0;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     std::swap(buffer,newbuf);</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      16019 :     buflen=newlen;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     va_list arg;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">      16019 :     va_start(arg, fmt);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      16019 :     r=std::vsnprintf(&amp;buffer[actual_buffer_length],buflen-actual_buffer_length,fmt,arg);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      16019 :     va_end(arg);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">   23588117 :   plumed_massert(r&gt;-1 &amp;&amp; r&lt;buflen-actual_buffer_length,&quot;error using fmt string &quot; + std::string(fmt));</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : // Line is buffered until newline, then written with a PLUMED: prefix</a>
+<a name="125"><span class="lineNum">     125 </span>            :   char*p1=buffer.data();</a>
+<a name="126"><span class="lineNum">     126 </span>            :   char*p2;</a>
+<a name="127"><span class="lineNum">     127 </span>            : // newline is only searched in the just added portion:</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">   23588117 :   char*psearch=p1+actual_buffer_length;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">   23588117 :   actual_buffer_length+=r;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">   28811925 :   while((p2=std::strchr(psearch,'\n'))) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">    5223808 :     if(linePrefix.length()&gt;0) llwrite(linePrefix.c_str(),linePrefix.length());</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    5223808 :     llwrite(p1,p2-p1+1);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">    5223808 :     actual_buffer_length-=(p2-p1)+1;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">    5223808 :     p1=p2+1;</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :     psearch=p1;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   };</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">   23588117 :   if(buffer.data()!=p1) std::memmove(buffer.data(),p1,actual_buffer_length);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">   23588117 :   return r;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">      27848 : OFile&amp; OFile::addConstantField(const std::string&amp;name) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   Field f;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   f.name=name;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      27848 :   const_fields.push_back(f);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      27848 :   return *this;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       3202 : OFile&amp; OFile::clearFields() {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       3202 :   fields.clear();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       3202 :   const_fields.clear();</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       3202 :   previous_fields.clear();</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       3202 :   return *this;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">   14601947 : OFile&amp; OFile::fmtField(const std::string&amp;fmt) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">   14601947 :   this-&gt;fieldFmt=fmt;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">   14601947 :   return *this;</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     825789 : OFile&amp; OFile::fmtField() {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     825789 :   this-&gt;fieldFmt=&quot;%23.16lg&quot;;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     825789 :   return *this;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">   15531588 : OFile&amp; OFile::printField(const std::string&amp;name,double v) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : // When one tries to print -nan we print nan instead.</a>
+<a name="168"><span class="lineNum">     168 </span>            : // The distinction between +nan and -nan is not well defined</a>
+<a name="169"><span class="lineNum">     169 </span>            : // Always printing nan simplifies some regtest (special functions computed our of range).</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">   15531588 :   if(std::isnan(v)) v=std::numeric_limits&lt;double&gt;::quiet_NaN();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),fieldFmt.c_str(),v);</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">   15531588 :   printField(name,buffer_string.data());</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">   15531588 :   return *this;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">    6074528 : OFile&amp; OFile::printField(const std::string&amp;name,int v) {</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),&quot; %d&quot;,v);</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    6074528 :   printField(name,buffer_string.data());</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">    6074528 :   return *this;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          1 : OFile&amp; OFile::printField(const std::string&amp;name,long int v) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),&quot; %ld&quot;,v);</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          1 :   printField(name,buffer_string.data());</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          1 :   return *this;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 : OFile&amp; OFile::printField(const std::string&amp;name,long long int v) {</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),&quot; %lld&quot;,v);</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   printField(name,buffer_string.data());</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         31 : OFile&amp; OFile::printField(const std::string&amp;name,unsigned v) {</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),&quot; %u&quot;,v);</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         31 :   printField(name,buffer_string.data());</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         31 :   return *this;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          1 : OFile&amp; OFile::printField(const std::string&amp;name,long unsigned v) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),&quot; %lu&quot;,v);</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          1 :   printField(name,buffer_string.data());</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          1 :   return *this;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         47 : OFile&amp; OFile::printField(const std::string&amp;name,long long unsigned v) {</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   std::snprintf(buffer_string.data(),buffer_string.size(),&quot; %llu&quot;,v);</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         47 :   printField(name,buffer_string.data());</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         47 :   return *this;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : }</a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">   37423941 : OFile&amp; OFile::printField(const std::string&amp;name,const std::string &amp; v) {</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   unsigned i;</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">  190174315 :   for(i=0; i&lt;const_fields.size(); i++) if(const_fields[i].name==name) break;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">   37423941 :   if(i&gt;=const_fields.size()) {</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :     Field field;</a>
+<a name="217"><span class="lineNum">     217 </span>            :     field.name=name;</a>
+<a name="218"><span class="lineNum">     218 </span>            :     field.value=v;</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">   16647223 :     fields.push_back(field);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   } else {</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">   20776718 :     if(const_fields[i].value!=v) fieldChanged=true;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     const_fields[i].value=v;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">   37423941 :   return *this;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       5905 : OFile&amp; OFile::setupPrintValue( Value *val ) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">       5905 :   if( val-&gt;isPeriodic() ) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        480 :     addConstantField(&quot;min_&quot; + val-&gt;getName() );</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        960 :     addConstantField(&quot;max_&quot; + val-&gt;getName() );</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   }</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       5905 :   return *this;</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">     538348 : OFile&amp; OFile::printField( Value* val, const double&amp; v ) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">     538348 :   printField( val-&gt;getName(), v );</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">     538348 :   if( val-&gt;isPeriodic() ) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      12973 :     std::string min, max; val-&gt;getDomain( min, max );</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      12973 :     printField( &quot;min_&quot; + val-&gt;getName(), min );</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      25946 :     printField(&quot;max_&quot; + val-&gt;getName(), max );</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">     538348 :   return *this;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    3929842 : OFile&amp; OFile::printField() {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   bool reprint=false;</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">    3929842 :   if(fieldChanged || fields.size()!=previous_fields.size()) {</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :     reprint=true;</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">   20512897 :   } else for(unsigned i=0; i&lt;fields.size(); i++) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">   16589024 :       if( previous_fields[i].name!=fields[i].name ||</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">   16589022 :           (fields[i].constant &amp;&amp; fields[i].value!=previous_fields[i].value) ) {</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :         reprint=true;</a>
+<a name="253"><span class="lineNum">     253 </span>            :         break;</a>
+<a name="254"><span class="lineNum">     254 </span>            :       }</a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">    3929842 :   if(reprint) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       5969 :     printf(&quot;#! FIELDS&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">      64172 :     for(unsigned i=0; i&lt;fields.size(); i++) printf(&quot; %s&quot;,fields[i].name.c_str());</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       5969 :     printf(&quot;\n&quot;);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">      33753 :     for(unsigned i=0; i&lt;const_fields.size(); i++) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">      27784 :       printf(&quot;#! SET %s %s&quot;,const_fields[i].name.c_str(),const_fields[i].value.c_str());</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      27784 :       printf(&quot;\n&quot;);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :     }</a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">   20577065 :   for(unsigned i=0; i&lt;fields.size(); i++) printf(&quot;%s&quot;,fields[i].value.c_str());</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">    3929842 :   printf(&quot;\n&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">    3929842 :   previous_fields=fields;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">    3929842 :   fields.clear();</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">    3929842 :   fieldChanged=false;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">    3929842 :   return *this;</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        121 : void OFile::setBackupString( const std::string&amp; str ) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        121 :   backstring=str;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        121 : }</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         36 : void OFile::backupAllFiles( const std::string&amp; str ) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         36 :   if(str==&quot;/dev/null&quot;) return;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         36 :   plumed_assert( backstring!=&quot;bck&quot; &amp;&amp; !checkRestart());</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         36 :   size_t found=str.find_last_of(&quot;/\\&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         36 :   std::string filename = appendSuffix(str,getSuffix());</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         36 :   std::string directory=filename.substr(0,found+1);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         36 :   std::string file=filename.substr(found+1);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         36 :   if( FileExist(filename) ) backupFile(&quot;bck&quot;, filename);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         36 :   for(int i=0;; i++) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         36 :     std::string num; Tools::convert(i,num);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         72 :     std::string filestr = directory + backstring + &quot;.&quot; + num + &quot;.&quot; + file;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         36 :     if( !FileExist(filestr) ) break;</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :     backupFile( &quot;bck&quot;, filestr);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : }</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       3327 : void OFile::backupFile( const std::string&amp; bstring, const std::string&amp; fname ) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       3327 :   if(fname==&quot;/dev/null&quot;) return;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       3173 :   int maxbackup=100;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       3173 :   if(std::getenv(&quot;PLUMED_MAXBACKUP&quot;)) Tools::convert(std::getenv(&quot;PLUMED_MAXBACKUP&quot;),maxbackup);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       3173 :   if(maxbackup&gt;0 &amp;&amp; (!comm || comm-&gt;Get_rank()==0)) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       2701 :     FILE* ff=std::fopen(const_cast&lt;char*&gt;(fname.c_str()),&quot;r&quot;);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       2701 :     if(ff) {</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :       // no exception here</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         65 :       std::fclose(ff);</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :       std::string backup;</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         65 :       size_t found=fname.find_last_of(&quot;/\\&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         65 :       std::string directory=fname.substr(0,found+1);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         65 :       std::string file=fname.substr(found+1);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         65 :       for(int i=0;; i++) {</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :         std::string num;</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         65 :         Tools::convert(i,num);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         65 :         if(i&gt;maxbackup) plumed_merror(&quot;cannot backup file &quot;+file+&quot; maximum number of backup is &quot;+num+&quot;\n&quot;);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        130 :         backup=directory+bstring +&quot;.&quot;+num+&quot;.&quot;+file;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         65 :         FILE* fff=std::fopen(backup.c_str(),&quot;r&quot;);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :         // no exception here</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         65 :         if(!fff) break;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :         else std::fclose(fff);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         65 :       int check=rename(fname.c_str(),backup.c_str());</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         65 :       plumed_massert(check==0,&quot;renaming &quot;+fname+&quot; into &quot;+backup+&quot; failed for reason: &quot;+std::strerror(errno));</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            :   }</a>
+<a name="320"><span class="lineNum">     320 </span>            : }</a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       3610 : OFile&amp; OFile::open(const std::string&amp;path) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       3610 :   plumed_assert(!cloned);</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">       3610 :   eof=false;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       3610 :   err=false;</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       3610 :   fp=NULL;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">       3610 :   gzfp=NULL;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       3610 :   this-&gt;path=path;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       7220 :   this-&gt;path=appendSuffix(path,getSuffix());</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       3610 :   if(checkRestart()) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        283 :     fp=std::fopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;a&quot;);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        283 :     mode=&quot;a&quot;;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        566 :     if(Tools::extension(this-&gt;path)==&quot;gz&quot;) {</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         12 :       gzfp=(void*)gzopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;a9&quot;);</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : #else</a>
+<a name="337"><span class="lineNum">     337 </span>            :       plumed_merror(&quot;file &quot; + getPath() + &quot;: trying to use a gz file without zlib being linked&quot;);</a>
+<a name="338"><span class="lineNum">     338 </span>            : #endif</a>
+<a name="339"><span class="lineNum">     339 </span>            :     }</a>
+<a name="340"><span class="lineNum">     340 </span>            :   } else {</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       3327 :     backupFile( backstring, this-&gt;path );</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       3327 :     if(comm)comm-&gt;Barrier();</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">       3327 :     fp=std::fopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;w&quot;);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">       3327 :     mode=&quot;w&quot;;</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">       6654 :     if(Tools::extension(this-&gt;path)==&quot;gz&quot;) {</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         13 :       gzfp=(void*)gzopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;w9&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : #else</a>
+<a name="349"><span class="lineNum">     349 </span>            :       plumed_merror(&quot;file &quot; + getPath() + &quot;: trying to use a gz file without zlib being linked&quot;);</a>
+<a name="350"><span class="lineNum">     350 </span>            : #endif</a>
+<a name="351"><span class="lineNum">     351 </span>            :     }</a>
+<a name="352"><span class="lineNum">     352 </span>            :   }</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">       3610 :   if(plumed) plumed-&gt;insertFile(*this);</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">       3610 :   return *this;</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : }</a>
+<a name="356"><span class="lineNum">     356 </span>            : </a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        135 : OFile&amp; OFile::rewind() {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : // we use here &quot;hard&quot; rewind, which means close/reopen</a>
+<a name="359"><span class="lineNum">     359 </span>            : // the reason is that normal rewind does not work when in append mode</a>
+<a name="360"><span class="lineNum">     360 </span>            : // moreover, we can take a backup of the file</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">        135 :   plumed_assert(fp);</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        135 :   clearFields();</span></a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        135 :   if(!comm || comm-&gt;Get_rank()==0) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">        104 :     std::string fname=this-&gt;path;</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        104 :     size_t found=fname.find_last_of(&quot;/\\&quot;);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        104 :     std::string directory=fname.substr(0,found+1);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        104 :     std::string file=fname.substr(found+1);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">        208 :     std::string backup=directory+backstring +&quot;.last.&quot;+file;</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        104 :     int check=rename(fname.c_str(),backup.c_str());</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        104 :     plumed_massert(check==0,&quot;renaming &quot;+fname+&quot; into &quot;+backup+&quot; failed for reason: &quot;+std::strerror(errno));</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   }</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        135 :   if(comm) comm-&gt;Barrier();</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        135 :   if(gzfp) {</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         15 :     gzclose((gzFile)gzfp);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :     // no exception here</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         15 :     gzfp=(void*)gzopen(const_cast&lt;char*&gt;(this-&gt;path.c_str()),&quot;w9&quot;);</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : #endif</a>
+<a name="382"><span class="lineNum">     382 </span>            :   } else {</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">        120 :     std::fclose(fp);</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :     // no exception here</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        120 :     fp=std::fopen(const_cast&lt;char*&gt;(path.c_str()),&quot;w&quot;);</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :   }</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        135 :   return *this;</span></a>
+<a name="388"><span class="lineNum">     388 </span>            : }</a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">       8753 : FileBase&amp; OFile::flush() {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">       8753 :   if(heavyFlush) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       3909 :     if(gzfp) {</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          9 :       gzclose(gzFile(gzfp));</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :       // no exception here</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          9 :       gzfp=(void*)gzopen(const_cast&lt;char*&gt;(path.c_str()),&quot;a&quot;);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            : #endif</a>
+<a name="398"><span class="lineNum">     398 </span>            :     } else {</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       3900 :       std::fclose(fp);</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :       // no exception here</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       3900 :       fp=std::fopen(const_cast&lt;char*&gt;(path.c_str()),&quot;a&quot;);</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :     }</a>
+<a name="403"><span class="lineNum">     403 </span>            :   } else {</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       4844 :     FileBase::flush();</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :     // if(gzfp) gzflush(gzFile(gzfp),Z_FINISH);</a>
+<a name="406"><span class="lineNum">     406 </span>            :     // for some reason flushing with Z_FINISH has problems on linux</a>
+<a name="407"><span class="lineNum">     407 </span>            :     // I thus use this (incomplete) flush</a>
+<a name="408"><span class="lineNum">     408 </span>            : #ifdef __PLUMED_HAS_ZLIB</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">       4844 :     if(gzfp) gzflush(gzFile(gzfp),Z_FULL_FLUSH);</span></a>
+<a name="410"><span class="lineNum">     410 </span>            : #endif</a>
+<a name="411"><span class="lineNum">     411 </span>            :   }</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">       8753 :   return *this;</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">       3646 : bool OFile::checkRestart()const {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">       3646 :   if(enforceRestart_) return true;</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">       3645 :   else if(enforceBackup_) return false;</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">       2501 :   else if(action) return action-&gt;getRestart();</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        219 :   else if(plumed) return plumed-&gt;getRestart();</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   else return false;</a>
+<a name="421"><span class="lineNum">     421 </span>            : }</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">          1 : OFile&amp; OFile::enforceRestart() {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">          1 :   enforceRestart_=true;</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          1 :   enforceBackup_=false;</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          1 :   return *this;</span></a>
+<a name="427"><span class="lineNum">     427 </span>            : }</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">       1144 : OFile&amp; OFile::enforceBackup() {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">       1144 :   enforceBackup_=true;</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">       1144 :   enforceRestart_=false;</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">       1144 :   return *this;</span></a>
+<a name="433"><span class="lineNum">     433 </span>            : }</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OFile.h.func-sort-c.html b/coverage/tools/OFile.h.func-sort-c.html
new file mode 100644
index 0000000000..dcea216f69
--- /dev/null
+++ b/coverage/tools/OFile.h.func-sort-c.html
@@ -0,0 +1,500 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OFile.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OFile.h<span style="font-size: 80%;"> (<a href="OFile.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryMed">89.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OFile.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA1000_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA103_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA110_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA120_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA129_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA47_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA52_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA67_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA72_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA88_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA90_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA50_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA54_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA63_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA65_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA81_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsINS_14ActionRegisterEEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA34_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA48_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA58_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA62_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA42_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA56_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA61_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIA59_cEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">10</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OFile.h.func.html b/coverage/tools/OFile.h.func.html
new file mode 100644
index 0000000000..d959f0a821
--- /dev/null
+++ b/coverage/tools/OFile.h.func.html
@@ -0,0 +1,500 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OFile.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OFile.h<span style="font-size: 80%;"> (<a href="OFile.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryMed">89.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+              <td class="coverFnHi">213020</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIPKcEERNS_5OFileES4_RKT_</a></td>
+              <td class="coverFnHi">169</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIPcEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">100109</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsISt13_SetprecisionEERNS_5OFileES3_RKT_</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIcEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">510</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIdEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">91744</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIfEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">45192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIiEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">176</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIjEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">283938</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsImEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">1452</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OFile.h.gcov.html#274">_ZN4PLMDlsIxEERNS_5OFileES2_RKT_</a></td>
+              <td class="coverFnHi">45554</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OFile.h.gcov.html b/coverage/tools/OFile.h.gcov.html
new file mode 100644
index 0000000000..c9d5bd2160
--- /dev/null
+++ b/coverage/tools/OFile.h.gcov.html
@@ -0,0 +1,362 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OFile.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OFile.h<span style="font-size: 80%;"> (source / <a href="OFile.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryMed">89.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_OFile_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_OFile_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;FileBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;sstream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;memory&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cstddef&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : class Value;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : /**</a>
+<a name="36"><span class="lineNum">      36 </span>            : \ingroup TOOLBOX</a>
+<a name="37"><span class="lineNum">      37 </span>            : Class for output files</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : This class provides features similar to those in the standard C &quot;FILE*&quot; type,</a>
+<a name="40"><span class="lineNum">      40 </span>            : but only for sequential output. See IFile for sequential input.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : See the example here for a possible use:</a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;File.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : int main(){</a>
+<a name="47"><span class="lineNum">      47 </span>            :   PLMD::OFile pof;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   pof.open(&quot;ciao&quot;);</a>
+<a name="49"><span class="lineNum">      49 </span>            :   pof.printf(&quot;%s\n&quot;,&quot;test1&quot;);</a>
+<a name="50"><span class="lineNum">      50 </span>            :   pof.setLinePrefix(&quot;plumed: &quot;);</a>
+<a name="51"><span class="lineNum">      51 </span>            :   pof.printf(&quot;%s\n&quot;,&quot;test2&quot;);</a>
+<a name="52"><span class="lineNum">      52 </span>            :   pof.setLinePrefix(&quot;&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span>            :   pof.addConstantField(&quot;x2&quot;).printField(&quot;x2&quot;,67.0);</a>
+<a name="54"><span class="lineNum">      54 </span>            :   pof.printField(&quot;x1&quot;,10.0).printField(&quot;x3&quot;,20.12345678901234567890).printField();</a>
+<a name="55"><span class="lineNum">      55 </span>            :   pof.printField(&quot;x1&quot;,10.0).printField(&quot;x3&quot;,-1e70*20.12345678901234567890).printField();</a>
+<a name="56"><span class="lineNum">      56 </span>            :   pof.printField(&quot;x3&quot;,10.0).printField(&quot;x2&quot;,777.0).printField(&quot;x1&quot;,-1e70*20.12345678901234567890).printField();</a>
+<a name="57"><span class="lineNum">      57 </span>            :   pof.printField(&quot;x3&quot;,67.0).printField(&quot;x1&quot;,18.0).printField();</a>
+<a name="58"><span class="lineNum">      58 </span>            :   return 0;</a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endverbatim</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : This program is expected to produce a file &quot;ciao&quot; which reads</a>
+<a name="63"><span class="lineNum">      63 </span>            : \verbatim</a>
+<a name="64"><span class="lineNum">      64 </span>            : test1</a>
+<a name="65"><span class="lineNum">      65 </span>            : plumed: test2</a>
+<a name="66"><span class="lineNum">      66 </span>            : #! FIELDS x1 x3</a>
+<a name="67"><span class="lineNum">      67 </span>            : #! SET x2                      67</a>
+<a name="68"><span class="lineNum">      68 </span>            :                      10      20.12345678901234</a>
+<a name="69"><span class="lineNum">      69 </span>            :                      10 -2.012345678901235e+71</a>
+<a name="70"><span class="lineNum">      70 </span>            : #! FIELDS x1 x3</a>
+<a name="71"><span class="lineNum">      71 </span>            : #! SET x2                     777</a>
+<a name="72"><span class="lineNum">      72 </span>            :  -2.012345678901235e+71                     10</a>
+<a name="73"><span class="lineNum">      73 </span>            :                      18                     67</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endverbatim</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : Notes</a>
+<a name="77"><span class="lineNum">      77 </span>            : - &quot;x2&quot; is declared as &quot;constant&quot;, which means that it is written using the &quot;SET&quot;</a>
+<a name="78"><span class="lineNum">      78 </span>            : keyword. Thus, everytime it is modified, all the headers are repeated in the output file.</a>
+<a name="79"><span class="lineNum">      79 </span>            : - printField() without arguments is used as a &quot;newline&quot;.</a>
+<a name="80"><span class="lineNum">      80 </span>            : - most methods return a reference to the OFile itself, to allow chaining many calls on the same line</a>
+<a name="81"><span class="lineNum">      81 </span>            : (this is similar to &lt;&lt; operator in std::ostream)</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \section using-correctly-ofile Using correctly OFile in PLUMED</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : When a OFile object is used in PLUMED it can be convenient to link() it</a>
+<a name="86"><span class="lineNum">      86 </span>            : to the Action object where it is defined, or to the PlumedMain object.</a>
+<a name="87"><span class="lineNum">      87 </span>            : This will save in the OFile a pointer to the linked object and will</a>
+<a name="88"><span class="lineNum">      88 </span>            : allow to have some extra information. E.g., if PLUMED is restarting,</a>
+<a name="89"><span class="lineNum">      89 </span>            : files will be appended. Notice that one can enforce this behavior using</a>
+<a name="90"><span class="lineNum">      90 </span>            : the enforceRestart() method before opening a file.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : To have all files managed consistently, it is important to use OFile in the proper way.</a>
+<a name="93"><span class="lineNum">      93 </span>            : This should allow multi-replica plumed, restart and backups to work in</a>
+<a name="94"><span class="lineNum">      94 </span>            : the expected way. For this reason all the operations in OFile and IFile</a>
+<a name="95"><span class="lineNum">      95 </span>            : are synchronizing all the processors of the group, so call to OFile functions</a>
+<a name="96"><span class="lineNum">      96 </span>            : should always be performed by all processes; for this reason is also not useful</a>
+<a name="97"><span class="lineNum">      97 </span>            : to use Log for debugging because only master threads will actually write.</a>
+<a name="98"><span class="lineNum">      98 </span>            : For debugging is better to use the standard stderr.</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : \verbatim</a>
+<a name="101"><span class="lineNum">     101 </span>            : int main(){</a>
+<a name="102"><span class="lineNum">     102 </span>            : // this is a growing file, containing a full history</a>
+<a name="103"><span class="lineNum">     103 </span>            : // (frames are appended, as in traditional HILLS and COLVAR)</a>
+<a name="104"><span class="lineNum">     104 </span>            :   OFile grw;</a>
+<a name="105"><span class="lineNum">     105 </span>            : // this is a single-snapshopt file used e.g. for checkpointing</a>
+<a name="106"><span class="lineNum">     106 </span>            : // (rewritten every time)</a>
+<a name="107"><span class="lineNum">     107 </span>            :   OFile snp;</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : // open both files at the beginning</a>
+<a name="110"><span class="lineNum">     110 </span>            : // (will go in \ref Action constructor)</a>
+<a name="111"><span class="lineNum">     111 </span>            :   grw.open(&quot;growing&quot;);</a>
+<a name="112"><span class="lineNum">     112 </span>            :   snp.open(&quot;snapshot&quot;);</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : // trajectory loop</a>
+<a name="115"><span class="lineNum">     115 </span>            :   for(int i=0;i&lt;nsteps;i++){</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : // files should be written in the update() method of an \ref Action</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : // write on growing file</a>
+<a name="120"><span class="lineNum">     120 </span>            :     grw&lt;&lt;&quot;data at step &quot;&lt;&lt;i&lt;&lt;\n&quot;;</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : // flushing</a>
+<a name="123"><span class="lineNum">     123 </span>            : // it takes time, so do it only if data is critical</a>
+<a name="124"><span class="lineNum">     124 </span>            : // better to leave this choice to the user with the FLUSH keyword</a>
+<a name="125"><span class="lineNum">     125 </span>            : //    grw.flush();</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : // write on snapshot file</a>
+<a name="128"><span class="lineNum">     128 </span>            :     snp.rewind();</a>
+<a name="129"><span class="lineNum">     129 </span>            :     snp&lt;&lt;&quot;snapshot at step &quot;&lt;&lt;i&lt;&lt;&quot;\n&quot;;</a>
+<a name="130"><span class="lineNum">     130 </span>            :     snp.flush();</a>
+<a name="131"><span class="lineNum">     131 </span>            : // the only difference is that snp is rewound</a>
+<a name="132"><span class="lineNum">     132 </span>            : // notice that it should be rewound just before writing</a>
+<a name="133"><span class="lineNum">     133 </span>            : // because rewind is going to move the file out of the way</a>
+<a name="134"><span class="lineNum">     134 </span>            : // to have a safe copy of the file (&quot;bck.last.filename&quot;)</a>
+<a name="135"><span class="lineNum">     135 </span>            : // Also notice that snapshots should be flushed</a>
+<a name="136"><span class="lineNum">     136 </span>            : // for this reason, it is better to write them only</a>
+<a name="137"><span class="lineNum">     137 </span>            : // rarely to avoid excessive slow down</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : \notice</a>
+<a name="143"><span class="lineNum">     143 </span>            : Notice that it is not necessary to explicitely close files, since they are closed implicitly</a>
+<a name="144"><span class="lineNum">     144 </span>            : when the object goes out of scope. In case you need to explicitly close the file before it is</a>
+<a name="145"><span class="lineNum">     145 </span>            : destroyed, please check it the procedure is exception safe and, if necessary, add some `try/catch`</a>
+<a name="146"><span class="lineNum">     146 </span>            : statement.</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : \endverbatim</a>
+<a name="149"><span class="lineNum">     149 </span>            : */</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : class OFile:</a>
+<a name="152"><span class="lineNum">     152 </span>            :   public virtual FileBase {</a>
+<a name="153"><span class="lineNum">     153 </span>            : /// Pointer to a linked OFile.</a>
+<a name="154"><span class="lineNum">     154 </span>            : /// see link(OFile&amp;)</a>
+<a name="155"><span class="lineNum">     155 </span>            :   OFile* linked;</a>
+<a name="156"><span class="lineNum">     156 </span>            : /// Internal buffer for printf</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;char&gt; buffer_string;</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// Internal buffer (generic use)</a>
+<a name="159"><span class="lineNum">     159 </span>            :   std::vector&lt;char&gt; buffer;</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// Internal buffer length</a>
+<a name="161"><span class="lineNum">     161 </span>            :   int buflen;</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// This variables stores the actual buffer length</a>
+<a name="163"><span class="lineNum">     163 </span>            :   int actual_buffer_length;</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// Class identifying a single field for fielded output</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">   50127448 :   class Field:</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     public FieldBase {</a>
+<a name="167"><span class="lineNum">     167 </span>            :   };</a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Low-level write</a>
+<a name="169"><span class="lineNum">     169 </span>            :   std::size_t llwrite(const char*,std::size_t);</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// True if fields has changed.</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// This could be due to a change in the list of fields or a reset</a>
+<a name="172"><span class="lineNum">     172 </span>            : /// of a nominally constant field</a>
+<a name="173"><span class="lineNum">     173 </span>            :   bool fieldChanged;</a>
+<a name="174"><span class="lineNum">     174 </span>            : /// Format for fields writing</a>
+<a name="175"><span class="lineNum">     175 </span>            :   std::string fieldFmt;</a>
+<a name="176"><span class="lineNum">     176 </span>            : /// All the previously defined variable fields</a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::vector&lt;Field&gt; previous_fields;</a>
+<a name="178"><span class="lineNum">     178 </span>            : /// All the defined variable fields</a>
+<a name="179"><span class="lineNum">     179 </span>            :   std::vector&lt;Field&gt; fields;</a>
+<a name="180"><span class="lineNum">     180 </span>            : /// All the defined constant fields</a>
+<a name="181"><span class="lineNum">     181 </span>            :   std::vector&lt;Field&gt; const_fields;</a>
+<a name="182"><span class="lineNum">     182 </span>            : /// Prefix for line (e.g. &quot;PLUMED: &quot;)</a>
+<a name="183"><span class="lineNum">     183 </span>            :   std::string linePrefix;</a>
+<a name="184"><span class="lineNum">     184 </span>            : /// Temporary ostringstream for &lt;&lt; output</a>
+<a name="185"><span class="lineNum">     185 </span>            :   std::ostringstream oss;</a>
+<a name="186"><span class="lineNum">     186 </span>            : /// The string used for backing up files</a>
+<a name="187"><span class="lineNum">     187 </span>            :   std::string backstring;</a>
+<a name="188"><span class="lineNum">     188 </span>            : /// Find field index given name</a>
+<a name="189"><span class="lineNum">     189 </span>            :   unsigned findField(const std::string&amp;name)const;</a>
+<a name="190"><span class="lineNum">     190 </span>            : /// check if we are restarting</a>
+<a name="191"><span class="lineNum">     191 </span>            :   bool checkRestart()const;</a>
+<a name="192"><span class="lineNum">     192 </span>            : /// True if restart behavior should be forced</a>
+<a name="193"><span class="lineNum">     193 </span>            :   bool enforceRestart_;</a>
+<a name="194"><span class="lineNum">     194 </span>            : /// True if backup behavior (i.e. non restart) should be forced</a>
+<a name="195"><span class="lineNum">     195 </span>            :   bool enforceBackup_;</a>
+<a name="196"><span class="lineNum">     196 </span>            : public:</a>
+<a name="197"><span class="lineNum">     197 </span>            : /// Constructor</a>
+<a name="198"><span class="lineNum">     198 </span>            :   OFile();</a>
+<a name="199"><span class="lineNum">     199 </span>            : /// Allows overloading of link</a>
+<a name="200"><span class="lineNum">     200 </span>            :   using FileBase::link;</a>
+<a name="201"><span class="lineNum">     201 </span>            : /// Allows overloading of open</a>
+<a name="202"><span class="lineNum">     202 </span>            :   using FileBase::open;</a>
+<a name="203"><span class="lineNum">     203 </span>            : /// Allows linking this OFile to another one.</a>
+<a name="204"><span class="lineNum">     204 </span>            : /// In this way, everything written to this OFile will be immediately</a>
+<a name="205"><span class="lineNum">     205 </span>            : /// written on the linked OFile. Notice that a OFile should</a>
+<a name="206"><span class="lineNum">     206 </span>            : /// be either opened explicitly, linked to a FILE or linked to a OFile</a>
+<a name="207"><span class="lineNum">     207 </span>            :   OFile&amp; link(OFile&amp;);</a>
+<a name="208"><span class="lineNum">     208 </span>            : /// Set the string name to be used for automatic backup</a>
+<a name="209"><span class="lineNum">     209 </span>            :   void setBackupString( const std::string&amp; );</a>
+<a name="210"><span class="lineNum">     210 </span>            : /// Backup a file by giving it a different name</a>
+<a name="211"><span class="lineNum">     211 </span>            :   void backupFile( const std::string&amp; bstring, const std::string&amp; fname );</a>
+<a name="212"><span class="lineNum">     212 </span>            : /// This backs up all the files that would have been created with the</a>
+<a name="213"><span class="lineNum">     213 </span>            : /// name str.  It is used in analysis when you are not restarting.  Analysis</a>
+<a name="214"><span class="lineNum">     214 </span>            : /// output files at different times, which are names analysis.0.&lt;filename&gt;,</a>
+<a name="215"><span class="lineNum">     215 </span>            : /// analysis.1.&lt;filename&gt; and &lt;filename&gt;, are backed up to bck.0.analysis.0.&lt;filename&gt;,</a>
+<a name="216"><span class="lineNum">     216 </span>            : /// bck.0.analysis.1.&lt;filename&gt; and bck.0.&lt;filename&gt;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   void backupAllFiles( const std::string&amp; str );</a>
+<a name="218"><span class="lineNum">     218 </span>            : /// Opens the file using automatic append/backup</a>
+<a name="219"><span class="lineNum">     219 </span>            :   OFile&amp; open(const std::string&amp;name) override;</a>
+<a name="220"><span class="lineNum">     220 </span>            : /// Set the prefix for output.</a>
+<a name="221"><span class="lineNum">     221 </span>            : /// Typically &quot;PLUMED: &quot;. Notice that lines with a prefix cannot</a>
+<a name="222"><span class="lineNum">     222 </span>            : /// be parsed using fields in a IFile.</a>
+<a name="223"><span class="lineNum">     223 </span>            :   OFile&amp; setLinePrefix(const std::string&amp;);</a>
+<a name="224"><span class="lineNum">     224 </span>            : /// Set the format for writing double precision fields</a>
+<a name="225"><span class="lineNum">     225 </span>            :   OFile&amp; fmtField(const std::string&amp;);</a>
+<a name="226"><span class="lineNum">     226 </span>            : /// Reset the format for writing double precision fields to its default</a>
+<a name="227"><span class="lineNum">     227 </span>            :   OFile&amp; fmtField();</a>
+<a name="228"><span class="lineNum">     228 </span>            : /// Set the value of a double precision field</a>
+<a name="229"><span class="lineNum">     229 </span>            :   OFile&amp; printField(const std::string&amp;,double);</a>
+<a name="230"><span class="lineNum">     230 </span>            : /// Set the value of a int type field</a>
+<a name="231"><span class="lineNum">     231 </span>            :   OFile&amp; printField(const std::string&amp;,int);</a>
+<a name="232"><span class="lineNum">     232 </span>            :   OFile&amp; printField(const std::string&amp;,long int);</a>
+<a name="233"><span class="lineNum">     233 </span>            :   OFile&amp; printField(const std::string&amp;,long long int);</a>
+<a name="234"><span class="lineNum">     234 </span>            :   OFile&amp; printField(const std::string&amp;,unsigned);</a>
+<a name="235"><span class="lineNum">     235 </span>            :   OFile&amp; printField(const std::string&amp;,long unsigned);</a>
+<a name="236"><span class="lineNum">     236 </span>            :   OFile&amp; printField(const std::string&amp;,long long unsigned);</a>
+<a name="237"><span class="lineNum">     237 </span>            : /// Set the value of a string field</a>
+<a name="238"><span class="lineNum">     238 </span>            :   OFile&amp; printField(const std::string&amp;,const std::string&amp;);</a>
+<a name="239"><span class="lineNum">     239 </span>            : ///</a>
+<a name="240"><span class="lineNum">     240 </span>            :   OFile&amp; addConstantField(const std::string&amp;);</a>
+<a name="241"><span class="lineNum">     241 </span>            : /// Used to setup printing of values</a>
+<a name="242"><span class="lineNum">     242 </span>            :   OFile&amp; setupPrintValue( Value *val );</a>
+<a name="243"><span class="lineNum">     243 </span>            : /// Print a value</a>
+<a name="244"><span class="lineNum">     244 </span>            :   OFile&amp; printField( Value* val, const double&amp; v );</a>
+<a name="245"><span class="lineNum">     245 </span>            :   /** Close a line.</a>
+<a name="246"><span class="lineNum">     246 </span>            :   Typically used as</a>
+<a name="247"><span class="lineNum">     247 </span>            :   \verbatim</a>
+<a name="248"><span class="lineNum">     248 </span>            :     of.printField(&quot;a&quot;,a).printField(&quot;b&quot;,b).printField();</a>
+<a name="249"><span class="lineNum">     249 </span>            :   \endverbatim</a>
+<a name="250"><span class="lineNum">     250 </span>            :   */</a>
+<a name="251"><span class="lineNum">     251 </span>            :   OFile&amp; printField();</a>
+<a name="252"><span class="lineNum">     252 </span>            :   /**</a>
+<a name="253"><span class="lineNum">     253 </span>            :   Resets the list of fields.</a>
+<a name="254"><span class="lineNum">     254 </span>            :   As it is only possible to add new constant fields (addConstantField()),</a>
+<a name="255"><span class="lineNum">     255 </span>            :   this method can be used to clean the field list.</a>
+<a name="256"><span class="lineNum">     256 </span>            :   */</a>
+<a name="257"><span class="lineNum">     257 </span>            :   OFile&amp; clearFields();</a>
+<a name="258"><span class="lineNum">     258 </span>            : /// Formatted output with explicit format - a la printf</a>
+<a name="259"><span class="lineNum">     259 </span>            :   int printf(const char*fmt,...);</a>
+<a name="260"><span class="lineNum">     260 </span>            : /// Formatted output with &lt;&lt; operator</a>
+<a name="261"><span class="lineNum">     261 </span>            :   template &lt;class T&gt;</a>
+<a name="262"><span class="lineNum">     262 </span>            :   friend OFile&amp; operator&lt;&lt;(OFile&amp;,const T &amp;);</a>
+<a name="263"><span class="lineNum">     263 </span>            : /// Rewind a file</a>
+<a name="264"><span class="lineNum">     264 </span>            :   OFile&amp;rewind();</a>
+<a name="265"><span class="lineNum">     265 </span>            : /// Flush a file</a>
+<a name="266"><span class="lineNum">     266 </span>            :   FileBase&amp;flush() override;</a>
+<a name="267"><span class="lineNum">     267 </span>            : /// Enforce restart, also if the attached plumed object is not restarting.</a>
+<a name="268"><span class="lineNum">     268 </span>            : /// Useful for tests</a>
+<a name="269"><span class="lineNum">     269 </span>            :   OFile&amp;enforceRestart();</a>
+<a name="270"><span class="lineNum">     270 </span>            : /// Enforce backup, even if the attached plumed object is restarting.</a>
+<a name="271"><span class="lineNum">     271 </span>            :   OFile&amp;enforceBackup();</a>
+<a name="272"><span class="lineNum">     272 </span>            : };</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : /// Write using &lt;&lt; syntax</a>
+<a name="275"><span class="lineNum">     275 </span>            : template &lt;class T&gt;</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">    1480978 : OFile&amp; operator&lt;&lt;(OFile&amp;of,const T &amp;t) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    1480978 :   of.oss&lt;&lt;t;</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">    1480978 :   of.printf(&quot;%s&quot;,of.oss.str().c_str());</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    1480978 :   of.oss.str(&quot;&quot;);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">    1480978 :   return of;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : }</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OpenMP.cpp.func-sort-c.html b/coverage/tools/OpenMP.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ed003f4bcc
--- /dev/null
+++ b/coverage/tools/OpenMP.cpp.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OpenMP.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OpenMP.cpp<span style="font-size: 80%;"> (<a href="OpenMP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OpenMP.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#43">_ZN4PLMD6OpenMP13setNumThreadsEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#47">_ZN4PLMD6OpenMP16getCachelineSizeEv</a></td>
+              <td class="coverFnHi">55762</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#55">_ZN4PLMD6OpenMP13getNumThreadsEv</a></td>
+              <td class="coverFnHi">1840372</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#38">_ZN4PLMDL13getOpenMPVarsEv</a></td>
+              <td class="coverFnHi">1896134</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#63">_ZN4PLMD6OpenMP12getThreadNumEv</a></td>
+              <td class="coverFnHi">6263516</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OpenMP.cpp.func.html b/coverage/tools/OpenMP.cpp.func.html
new file mode 100644
index 0000000000..bf48be6489
--- /dev/null
+++ b/coverage/tools/OpenMP.cpp.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OpenMP.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OpenMP.cpp<span style="font-size: 80%;"> (<a href="OpenMP.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OpenMP.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#63">_ZN4PLMD6OpenMP12getThreadNumEv</a></td>
+              <td class="coverFnHi">6263516</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#55">_ZN4PLMD6OpenMP13getNumThreadsEv</a></td>
+              <td class="coverFnHi">1840372</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#43">_ZN4PLMD6OpenMP13setNumThreadsEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#47">_ZN4PLMD6OpenMP16getCachelineSizeEv</a></td>
+              <td class="coverFnHi">55762</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.cpp.gcov.html#38">_ZN4PLMDL13getOpenMPVarsEv</a></td>
+              <td class="coverFnHi">1896134</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OpenMP.cpp.gcov.html b/coverage/tools/OpenMP.cpp.gcov.html
new file mode 100644
index 0000000000..19779c1d13
--- /dev/null
+++ b/coverage/tools/OpenMP.cpp.gcov.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OpenMP.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OpenMP.cpp<span style="font-size: 80%;"> (source / <a href="OpenMP.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;OpenMP.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #if defined(_OPENMP)</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;omp.h&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #endif</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : struct OpenMPVars {</a>
+<a name="34"><span class="lineNum">      34 </span>            :   unsigned cacheline_size=512;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   bool cache_set=false;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   unsigned num_threads=1;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   bool nt_env_set=false;</a>
+<a name="38"><span class="lineNum">      38 </span>            : };</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">    1896134 : static OpenMPVars &amp; getOpenMPVars() {</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :   static OpenMPVars vars;</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">    1896134 :   return vars;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : }</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 : void OpenMP::setNumThreads(const unsigned nt) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 :   getOpenMPVars().num_threads=nt;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      55762 : unsigned OpenMP::getCachelineSize() {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      55762 :   if(!getOpenMPVars().cache_set) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        800 :     if(std::getenv(&quot;PLUMED_CACHELINE_SIZE&quot;)) Tools::convert(std::getenv(&quot;PLUMED_CACHELINE_SIZE&quot;),getOpenMPVars().cacheline_size);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        800 :     getOpenMPVars().cache_set = true;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   }</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      55762 :   return getOpenMPVars().cacheline_size;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">    1840372 : unsigned OpenMP::getNumThreads() {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">    1840372 :   if(!getOpenMPVars().nt_env_set) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        800 :     if(std::getenv(&quot;PLUMED_NUM_THREADS&quot;)) Tools::convert(std::getenv(&quot;PLUMED_NUM_THREADS&quot;),getOpenMPVars().num_threads);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        800 :     getOpenMPVars().nt_env_set = true;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :   }</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">    1840372 :   return getOpenMPVars().num_threads;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">    6263516 : unsigned OpenMP::getThreadNum() {</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : #if defined(_OPENMP)</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">    6263516 :   return omp_get_thread_num();</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : #else</a>
+<a name="69"><span class="lineNum">      69 </span>            :   return 0;</a>
+<a name="70"><span class="lineNum">      70 </span>            : #endif</a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OpenMP.h.func-sort-c.html b/coverage/tools/OpenMP.h.func-sort-c.html
new file mode 100644
index 0000000000..580a6b1f0d
--- /dev/null
+++ b/coverage/tools/OpenMP.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OpenMP.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OpenMP.h<span style="font-size: 80%;"> (<a href="OpenMP.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OpenMP.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#54">_ZN4PLMD6OpenMP17getGoodNumThreadsIfEEjPKT_j</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#68">_ZN4PLMD6OpenMP17getGoodNumThreadsINS_13VectorGenericILj3EEEEEjRKSt6vectorIT_SaIS5_EE</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#54">_ZN4PLMD6OpenMP17getGoodNumThreadsIdEEjPKT_j</a></td>
+              <td class="coverFnHi">27208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#54">_ZN4PLMD6OpenMP17getGoodNumThreadsINS_13VectorGenericILj3EEEEEjPKT_j</a></td>
+              <td class="coverFnHi">27547</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OpenMP.h.func.html b/coverage/tools/OpenMP.h.func.html
new file mode 100644
index 0000000000..640df1ba41
--- /dev/null
+++ b/coverage/tools/OpenMP.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OpenMP.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OpenMP.h<span style="font-size: 80%;"> (<a href="OpenMP.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OpenMP.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#54">_ZN4PLMD6OpenMP17getGoodNumThreadsINS_13VectorGenericILj3EEEEEjPKT_j</a></td>
+              <td class="coverFnHi">27547</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#68">_ZN4PLMD6OpenMP17getGoodNumThreadsINS_13VectorGenericILj3EEEEEjRKSt6vectorIT_SaIS5_EE</a></td>
+              <td class="coverFnHi">450</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#54">_ZN4PLMD6OpenMP17getGoodNumThreadsIdEEjPKT_j</a></td>
+              <td class="coverFnHi">27208</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OpenMP.h.gcov.html#54">_ZN4PLMD6OpenMP17getGoodNumThreadsIfEEjPKT_j</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/OpenMP.h.gcov.html b/coverage/tools/OpenMP.h.gcov.html
new file mode 100644
index 0000000000..ebc84f3e2d
--- /dev/null
+++ b/coverage/tools/OpenMP.h.gcov.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/OpenMP.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - OpenMP.h<span style="font-size: 80%;"> (source / <a href="OpenMP.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_OpenMP_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_OpenMP_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class OpenMP {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /// Set number of threads that can be used by openMP</a>
+<a name="34"><span class="lineNum">      34 </span>            :   static void setNumThreads(const unsigned nt);</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /// Get number of threads that can be used by openMP</a>
+<a name="37"><span class="lineNum">      37 </span>            :   static unsigned getNumThreads();</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Returns a unique thread identification number within the current team</a>
+<a name="40"><span class="lineNum">      40 </span>            :   static unsigned getThreadNum();</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : /// get cacheline size</a>
+<a name="43"><span class="lineNum">      43 </span>            :   static unsigned getCachelineSize();</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Get a reasonable number of threads so as to access to an array of size s located at x</a>
+<a name="46"><span class="lineNum">      46 </span>            :   template&lt;typename T&gt;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   static unsigned getGoodNumThreads(const T*x,unsigned s);</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Get a reasonable number of threads so as to access to vector v;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   template&lt;typename T&gt;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   static unsigned getGoodNumThreads(const std::vector&lt;T&gt; &amp; v);</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : };</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : template&lt;typename T&gt;</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      54755 : unsigned OpenMP::getGoodNumThreads(const T*x,unsigned n) {</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   unsigned long long p=(unsigned long long) x;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   (void) p; // this is not to have warnings. notice that the pointer location is not used actually.</a>
+<a name="59"><span class="lineNum">      59 </span>            : // a factor two is necessary since there is no guarantee that x is aligned</a>
+<a name="60"><span class="lineNum">      60 </span>            : // to cache line boundary</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      54755 :   unsigned m=n*sizeof(T)/(2*getCachelineSize());</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      54755 :   unsigned numThreads=getNumThreads();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      54755 :   if(m&gt;=numThreads) m=numThreads;</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   else m=1;</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      54755 :   return m;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : template&lt;typename T&gt;</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        450 : unsigned OpenMP::getGoodNumThreads(const std::vector&lt;T&gt; &amp; v) {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        450 :   if(v.size()==0) return 1;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        438 :   else return getGoodNumThreads(&amp;v[0],v.size());</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/PDB.cpp.func-sort-c.html b/coverage/tools/PDB.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c4a1ac5afe
--- /dev/null
+++ b/coverage/tools/PDB.cpp.func-sort-c.html
@@ -0,0 +1,248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/PDB.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - PDB.cpp<span style="font-size: 80%;"> (<a href="PDB.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">275</td>
+            <td class="headerCovTableEntry">412</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PDB.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PDB.cpp.gcov.html#198">_ZN4PLMD3PDB12setPositionsERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EE</a></td>
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/PDB.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - PDB.cpp<span style="font-size: 80%;"> (<a href="PDB.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">275</td>
+            <td class="headerCovTableEntry">412</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
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+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PDB.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">474</td>
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+              <td class="coverFn"><a href="PDB.cpp.gcov.html#556">_ZNK4PLMD3PDB8getMtypeB5cxx11Ev</a></td>
+              <td class="coverFnHi">10</td>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="PDB.cpp.gcov.html#247">_ZNK4PLMD3PDB9getBoxVecEv</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/PDB.cpp.gcov.html b/coverage/tools/PDB.cpp.gcov.html
new file mode 100644
index 0000000000..c4149815d6
--- /dev/null
+++ b/coverage/tools/PDB.cpp.gcov.html
@@ -0,0 +1,827 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/PDB.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - PDB.cpp<span style="font-size: 80%;"> (source / <a href="PDB.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">275</td>
+            <td class="headerCovTableEntry">412</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PDB.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Log.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;h36.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstdio&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC INTERNAL pdbreader</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : PLUMED can use the PDB format in several places</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : - To read molecular structure (\ref MOLINFO).</a>
+<a name="36"><span class="lineNum">      36 </span>            : - To read reference conformations (\ref RMSD, but also many other methods in \ref dists, \ref FIT_TO_TEMPLATE, etc).</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : The implemented PDB reader expects a file formatted correctly according to the</a>
+<a name="39"><span class="lineNum">      39 </span>            : [PDB standard](http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html).</a>
+<a name="40"><span class="lineNum">      40 </span>            : In particular, the following columns are read from ATOM records</a>
+<a name="41"><span class="lineNum">      41 </span>            : \verbatim</a>
+<a name="42"><span class="lineNum">      42 </span>            : columns | content</a>
+<a name="43"><span class="lineNum">      43 </span>            : 1-6     | record name (ATOM or HETATM)</a>
+<a name="44"><span class="lineNum">      44 </span>            : 7-11    | serial number of the atom (starting from 1)</a>
+<a name="45"><span class="lineNum">      45 </span>            : 13-16   | atom name</a>
+<a name="46"><span class="lineNum">      46 </span>            : 18-20   | residue name</a>
+<a name="47"><span class="lineNum">      47 </span>            : 22      | chain id</a>
+<a name="48"><span class="lineNum">      48 </span>            : 23-26   | residue number</a>
+<a name="49"><span class="lineNum">      49 </span>            : 31-38   | x coordinate</a>
+<a name="50"><span class="lineNum">      50 </span>            : 39-46   | y coordinate</a>
+<a name="51"><span class="lineNum">      51 </span>            : 47-54   | z coordinate</a>
+<a name="52"><span class="lineNum">      52 </span>            : 55-60   | occupancy</a>
+<a name="53"><span class="lineNum">      53 </span>            : 61-66   | beta factor</a>
+<a name="54"><span class="lineNum">      54 </span>            : \endverbatim</a>
+<a name="55"><span class="lineNum">      55 </span>            : PLUMED parser is slightly more permissive than the official PDB format</a>
+<a name="56"><span class="lineNum">      56 </span>            : in the fact that the format of real numbers is not fixed. In other words,</a>
+<a name="57"><span class="lineNum">      57 </span>            : any real number that can be parsed is OK and the dot can be placed anywhere. However,</a>
+<a name="58"><span class="lineNum">      58 </span>            : __columns are interpret strictly__. A sample PDB should look like the following</a>
+<a name="59"><span class="lineNum">      59 </span>            : \verbatim</a>
+<a name="60"><span class="lineNum">      60 </span>            : ATOM      2  CH3 ACE     1      12.932 -14.718  -6.016  1.00  1.00</a>
+<a name="61"><span class="lineNum">      61 </span>            : ATOM      5  C   ACE     1      21.312  -9.928  -5.946  1.00  1.00</a>
+<a name="62"><span class="lineNum">      62 </span>            : ATOM      9  CA  ALA     2      19.462 -11.088  -8.986  1.00  1.00</a>
+<a name="63"><span class="lineNum">      63 </span>            : \endverbatim</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : Notice that serial numbers need not to be consecutive. In the three-line example above,</a>
+<a name="66"><span class="lineNum">      66 </span>            : only the coordinates of three atoms are provided. This is perfectly legal and indicates PLUMED</a>
+<a name="67"><span class="lineNum">      67 </span>            : that information about these atoms only is available. This could be both for structural</a>
+<a name="68"><span class="lineNum">      68 </span>            : information in \ref MOLINFO, where the other atoms would have no name assigned, and for</a>
+<a name="69"><span class="lineNum">      69 </span>            : reference structures used in \ref RMSD, where only the provided atoms would be used to compute RMSD.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \par Occupancy and beta factors</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : PLUMED reads also occupancy and beta factors that however are given a very special meaning.</a>
+<a name="74"><span class="lineNum">      74 </span>            : In cases where the PDB structure is used as a reference for an alignment (that's the case</a>
+<a name="75"><span class="lineNum">      75 </span>            : for instance in \ref RMSD and in \ref FIT_TO_TEMPLATE), the occupancy column is used</a>
+<a name="76"><span class="lineNum">      76 </span>            : to provide the weight of each atom in the alignment. In cases where, perhaps after alignment,</a>
+<a name="77"><span class="lineNum">      77 </span>            : the displacement between running coordinates and the provided PDB is computed, the beta factors</a>
+<a name="78"><span class="lineNum">      78 </span>            : are used as weight for the displacement.</a>
+<a name="79"><span class="lineNum">      79 </span>            : Since setting the weights to zero is the same as __not__ including an atom in the alignment or</a>
+<a name="80"><span class="lineNum">      80 </span>            : displacement calculation, the two following reference files would be equivalent when used in an \ref RMSD</a>
+<a name="81"><span class="lineNum">      81 </span>            : calculation. First file:</a>
+<a name="82"><span class="lineNum">      82 </span>            : \verbatim</a>
+<a name="83"><span class="lineNum">      83 </span>            : ATOM      2  CH3 ACE     1      12.932 -14.718  -6.016  1.00  1.00</a>
+<a name="84"><span class="lineNum">      84 </span>            : ATOM      5  C   ACE     1      21.312  -9.928  -5.946  1.00  1.00</a>
+<a name="85"><span class="lineNum">      85 </span>            : ATOM      9  CA  ALA     2      19.462 -11.088  -8.986  0.00  0.00</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endverbatim</a>
+<a name="87"><span class="lineNum">      87 </span>            : Second file:</a>
+<a name="88"><span class="lineNum">      88 </span>            : \verbatim</a>
+<a name="89"><span class="lineNum">      89 </span>            : ATOM      2  CH3 ACE     1      12.932 -14.718  -6.016  1.00  1.00</a>
+<a name="90"><span class="lineNum">      90 </span>            : ATOM      5  C   ACE     1      21.312  -9.928  -5.946  1.00  1.00</a>
+<a name="91"><span class="lineNum">      91 </span>            : \endverbatim</a>
+<a name="92"><span class="lineNum">      92 </span>            : However notice that many extra atoms with zero weight might slow down the calculation, so</a>
+<a name="93"><span class="lineNum">      93 </span>            : removing lines is better than setting their weights to zero.</a>
+<a name="94"><span class="lineNum">      94 </span>            : In addition, weights for alignment need not to be equivalent to weights for displacement.</a>
+<a name="95"><span class="lineNum">      95 </span>            : Starting with PLUMED 2.7, if all the weights are set to zero they will be normalized to be equal to the</a>
+<a name="96"><span class="lineNum">      96 </span>            : inverse of the number of involved atoms. This means that it will be possible to use files with</a>
+<a name="97"><span class="lineNum">      97 </span>            : the weight columns set to zero obtaining a meaningful result. In previous PLUMED versions,</a>
+<a name="98"><span class="lineNum">      98 </span>            : setting all weights to zero was resulting in an error instead.</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : \par Systems with more than 100k atoms</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : Notice that it very likely does not make any sense to compute the \ref RMSD or any other structural</a>
+<a name="104"><span class="lineNum">     104 </span>            : deviation __using__ so many atoms. However, if the protein for which you want to compute \ref RMSD</a>
+<a name="105"><span class="lineNum">     105 </span>            : has atoms with large serial numbers (e.g. because it is located __after__ solvent in the sorted list of atoms)</a>
+<a name="106"><span class="lineNum">     106 </span>            : you might end up with troubles with the limitations of the PDB format. Indeed, since there are 5</a>
+<a name="107"><span class="lineNum">     107 </span>            : columns available for atom serial number, this number cannot be larger than 99999.</a>
+<a name="108"><span class="lineNum">     108 </span>            : In addition, providing \ref MOLINFO with names associated to atoms with a serial larger than 99999 would be impossible.</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : Since PLUMED 2.4 we allow [hybrid 36](http://cci.lbl.gov/hybrid_36/) format to be used to specify atom numbers.</a>
+<a name="111"><span class="lineNum">     111 </span>            : This format is not particularly widespread, but has the nice feature that it provides a one-to-one mapping</a>
+<a name="112"><span class="lineNum">     112 </span>            : between numbers up to approximately 80 millions and strings with 5 characters, plus it is backward compatible</a>
+<a name="113"><span class="lineNum">     113 </span>            : for numbers smaller than 100000. This is not true for notations like the hex notation exported by VMD.</a>
+<a name="114"><span class="lineNum">     114 </span>            : Using the hybrid 36 format, the ATOM records for atom ranging from 99997 to 100002 would read like these:</a>
+<a name="115"><span class="lineNum">     115 </span>            : \verbatim</a>
+<a name="116"><span class="lineNum">     116 </span>            : ATOM  99997  Ar      X   1      45.349  38.631  15.116  1.00  1.00</a>
+<a name="117"><span class="lineNum">     117 </span>            : ATOM  99998  Ar      X   1      46.189  38.631  15.956  1.00  1.00</a>
+<a name="118"><span class="lineNum">     118 </span>            : ATOM  99999  Ar      X   1      46.189  39.471  15.116  1.00  1.00</a>
+<a name="119"><span class="lineNum">     119 </span>            : ATOM  A0000  Ar      X   1      45.349  39.471  15.956  1.00  1.00</a>
+<a name="120"><span class="lineNum">     120 </span>            : ATOM  A0000  Ar      X   1      45.349  38.631  16.796  1.00  1.00</a>
+<a name="121"><span class="lineNum">     121 </span>            : ATOM  A0001  Ar      X   1      46.189  38.631  17.636  1.00  1.00</a>
+<a name="122"><span class="lineNum">     122 </span>            : \endverbatim</a>
+<a name="123"><span class="lineNum">     123 </span>            : There are tools that can be found to translate from integers to strings and back using hybrid 36 format</a>
+<a name="124"><span class="lineNum">     124 </span>            : (a simple python script can be found [here](https://sourceforge.net/p/cctbx/code/HEAD/tree/trunk/iotbx/pdb/hybrid_36.py)).</a>
+<a name="125"><span class="lineNum">     125 </span>            : In addition, as of PLUMED 2.5, we provide a \ref pdbrenumber &quot;command line tool&quot; that can be used to renumber atoms in a PDB file.</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : */</a>
+<a name="128"><span class="lineNum">     128 </span>            : //+ENDPLUMEDOC</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : namespace PLMD {</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         27 : void PDB::setAtomNumbers( const std::vector&lt;AtomNumber&gt;&amp; atoms ) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         27 :   positions.resize( atoms.size() ); occupancy.resize( atoms.size() );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         27 :   beta.resize( atoms.size() ); numbers.resize( atoms.size() );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        210 :   for(unsigned i=0; i&lt;atoms.size(); ++i) { numbers[i]=atoms[i]; beta[i]=1.0; occupancy[i]=1.0; }</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         27 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         34 : void PDB::setArgumentNames( const std::vector&lt;std::string&gt;&amp; argument_names ) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         34 :   argnames.resize( argument_names.size() );</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         98 :   for(unsigned i=0; i&lt;argument_names.size(); ++i) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     argnames[i]=argument_names[i];</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         64 :     arg_data.insert( std::pair&lt;std::string,double&gt;( argnames[i], 0.0 ) );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         34 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">    1504260 : bool PDB::getArgumentValue( const std::string&amp; name, double&amp; value ) const {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   std::map&lt;std::string,double&gt;::const_iterator it = arg_data.find(name);</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">    1504260 :   if( it!=arg_data.end() ) { value = it-&gt;second; return true; }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   return false;</a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">     493287 : void PDB::setAtomPositions( const std::vector&lt;Vector&gt;&amp; pos ) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     493287 :   plumed_assert( pos.size()==positions.size() );</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">     519464 :   for(unsigned i=0; i&lt;positions.size(); ++i) positions[i]=pos[i];</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     493287 : }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">    1502798 : void PDB::setArgumentValue( const std::string&amp; argname, const double&amp; val ) {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   // First set the value of the value of the argument in the map</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    1502798 :   arg_data.find(argname)-&gt;second = val;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">    1502798 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : // bool PDB::hasRequiredProperties( const std::vector&lt;std::string&gt;&amp; inproperties ){</a>
+<a name="164"><span class="lineNum">     164 </span>            : //   bool hasprop=false;</a>
+<a name="165"><span class="lineNum">     165 </span>            : //   for(unsigned i=0;i&lt;remark.size();++i){</a>
+<a name="166"><span class="lineNum">     166 </span>            : //       if( remark[i].find(&quot;PROPERTIES=&quot;)!=std::string::npos){ hasprop=true; break; }</a>
+<a name="167"><span class="lineNum">     167 </span>            : //   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : //   if( !hasprop ){</a>
+<a name="169"><span class="lineNum">     169 </span>            : //       std::string mypropstr=&quot;PROPERTIES=&quot; + inproperties[0];</a>
+<a name="170"><span class="lineNum">     170 </span>            : //       for(unsigned i=1;i&lt;inproperties.size();++i) mypropstr += &quot;,&quot; + inproperties[i];</a>
+<a name="171"><span class="lineNum">     171 </span>            : //       remark.push_back( mypropstr );</a>
+<a name="172"><span class="lineNum">     172 </span>            : //   }</a>
+<a name="173"><span class="lineNum">     173 </span>            : //   // Now check that all required properties are there</a>
+<a name="174"><span class="lineNum">     174 </span>            : //   for(unsigned i=0;i&lt;inproperties.size();++i){</a>
+<a name="175"><span class="lineNum">     175 </span>            : //       hasprop=false;</a>
+<a name="176"><span class="lineNum">     176 </span>            : //       for(unsigned j=0;j&lt;remark.size();++j){</a>
+<a name="177"><span class="lineNum">     177 </span>            : //           if( remark[j].find(inproperties[i]+&quot;=&quot;)!=std::string::npos){ hasprop=true; break; }</a>
+<a name="178"><span class="lineNum">     178 </span>            : //       }</a>
+<a name="179"><span class="lineNum">     179 </span>            : //       if( !hasprop ) return false;</a>
+<a name="180"><span class="lineNum">     180 </span>            : //   }</a>
+<a name="181"><span class="lineNum">     181 </span>            : //   return true;</a>
+<a name="182"><span class="lineNum">     182 </span>            : // }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         17 : void PDB::addBlockEnd( const unsigned&amp; end ) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         17 :   block_ends.push_back( end );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         17 : }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        474 : unsigned PDB::getNumberOfAtomBlocks()const {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        474 :   return block_ends.size();</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         14 : const std::vector&lt;unsigned&gt; &amp; PDB::getAtomBlockEnds()const {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         14 :   return block_ends;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">   23534547 : const std::vector&lt;Vector&gt; &amp; PDB::getPositions()const {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">   23534547 :   return positions;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 : void PDB::setPositions(const std::vector&lt;Vector&gt; &amp;v ) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   plumed_assert( v.size()==positions.size() );</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   positions=v;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      38558 : const std::vector&lt;double&gt; &amp; PDB::getOccupancy()const {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      38558 :   return occupancy;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      38558 : const std::vector&lt;double&gt; &amp; PDB::getBeta()const {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      38558 :   return beta;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1337 : void PDB::addRemark( std::vector&lt;std::string&gt;&amp; v1 ) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1337 :   Tools::parse(v1,&quot;TYPE&quot;,mtype);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1337 :   Tools::parseVector(v1,&quot;ARG&quot;,argnames);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       3747 :   for(unsigned i=0; i&lt;v1.size(); ++i) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       2410 :     if( v1[i].find(&quot;=&quot;)!=std::string::npos ) {</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :       std::size_t eq=v1[i].find_first_of('=');</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       1864 :       std::string name=v1[i].substr(0,eq);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       1864 :       std::string sval=v1[i].substr(eq+1);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       1864 :       double val; Tools::convert( sval, val );</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       1864 :       arg_data.insert( std::pair&lt;std::string,double&gt;( name, val ) );</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :     } else {</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        546 :       flags.push_back(v1[i]);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       1337 : }</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          8 : bool PDB::hasFlag( const std::string&amp; fname ) const {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;flags.size(); ++i) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     if( flags[i]==fname ) return true;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span>            :   return false;</a>
+<a name="234"><span class="lineNum">     234 </span>            : }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">     722721 : const std::vector&lt;AtomNumber&gt; &amp; PDB::getAtomNumbers()const {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">     722721 :   return numbers;</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : }</a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 : const Vector &amp; PDB::getBoxAxs()const {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :   return BoxXYZ;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 : const Vector &amp; PDB::getBoxAng()const {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   return BoxABG;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         12 : const Tensor &amp; PDB::getBoxVec()const {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         12 :   return Box;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">    6870274 : std::string PDB::getAtomName(AtomNumber a)const {</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   const auto p=number2index.find(a);</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">    6870274 :   if(p==number2index.end()) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert( a.serial(), num );</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Name of atom &quot; + num + &quot; not found&quot; );</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">    6870274 :   } else return atomsymb[p-&gt;second];</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">     166259 : unsigned PDB::getResidueNumber(AtomNumber a)const {</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   const auto p=number2index.find(a);</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">     166259 :   if(p==number2index.end()) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert( a.serial(), num );</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Residue for atom &quot; + num + &quot; not found&quot; );</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">     166259 :   } else return residue[p-&gt;second];</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">     151942 : std::string PDB::getResidueName(AtomNumber a) const {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   const auto p=number2index.find(a);</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">     151942 :   if(p==number2index.end()) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert( a.serial(), num );</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Residue for atom &quot; + num + &quot; not found&quot; );</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">     151942 :   } else return residuenames[p-&gt;second];</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">  216516274 : unsigned PDB::size()const {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">  216516274 :   return positions.size();</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       2069 : bool PDB::readFromFilepointer(FILE *fp,bool naturalUnits,double scale) {</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :   //cerr&lt;&lt;file&lt;&lt;endl;</a>
+<a name="283"><span class="lineNum">     283 </span>            :   bool file_is_alive=false;</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">       2069 :   if(naturalUnits) scale=1.0;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   std::string line;</a>
+<a name="286"><span class="lineNum">     286 </span>            :   fpos_t pos; bool between_ters=true;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">     275284 :   while(Tools::getline(fp,line)) {</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     //cerr&lt;&lt;line&lt;&lt;&quot;\n&quot;;</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     275066 :     fgetpos (fp,&amp;pos);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">    1969071 :     while(line.length()&lt;80) line.push_back(' ');</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     275066 :     std::string record=line.substr(0,6);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">     275066 :     std::string serial=line.substr(6,5);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     275066 :     std::string atomname=line.substr(12,4);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">     275066 :     std::string residuename=line.substr(17,3);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">     275066 :     std::string chainID=line.substr(21,1);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">     275066 :     std::string resnum=line.substr(22,4);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     275066 :     std::string x=line.substr(30,8);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">     275066 :     std::string y=line.substr(38,8);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">     275066 :     std::string z=line.substr(46,8);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">     275066 :     std::string occ=line.substr(54,6);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">     275066 :     std::string bet=line.substr(60,6);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">     275066 :     std::string BoxX=line.substr(6,9);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">     275066 :     std::string BoxY=line.substr(15,9);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     275066 :     std::string BoxZ=line.substr(24,9);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">     275066 :     std::string BoxA=line.substr(33,7);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">     275066 :     std::string BoxB=line.substr(40,7);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">     275066 :     std::string BoxG=line.substr(47,7);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">     275066 :     Tools::trim(record);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">     275066 :     if(record==&quot;TER&quot;) { between_ters=false; block_ends.push_back( positions.size() ); }</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">     275066 :     if(record==&quot;END&quot;) { file_is_alive=true;  break;}</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">     273352 :     if(record==&quot;ENDMDL&quot;) { file_is_alive=true;  break;}</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">     273215 :     if(record==&quot;REMARK&quot;) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">       2674 :       std::vector&lt;std::string&gt; v1;  v1=Tools::getWords(line.substr(6));</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       1337 :       addRemark( v1 );</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">       1337 :     }</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">     273215 :     if(record==&quot;CRYST1&quot;) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         68 :       Tools::convert(BoxX,BoxXYZ[0]);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         68 :       Tools::convert(BoxY,BoxXYZ[1]);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         68 :       Tools::convert(BoxZ,BoxXYZ[2]);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         68 :       Tools::convert(BoxA,BoxABG[0]);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         68 :       Tools::convert(BoxB,BoxABG[1]);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         68 :       Tools::convert(BoxG,BoxABG[2]);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         68 :       BoxXYZ*=scale;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         68 :       double cosA=std::cos(BoxABG[0]*pi/180.);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         68 :       double cosB=std::cos(BoxABG[1]*pi/180.);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         68 :       double cosG=std::cos(BoxABG[2]*pi/180.);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         68 :       double sinG=std::sin(BoxABG[2]*pi/180.);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        272 :       for (unsigned i=0; i&lt;3; i++) {Box[i][0]=0.; Box[i][1]=0.; Box[i][2]=0.;}</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         68 :       Box[0][0]=BoxXYZ[0];</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         68 :       Box[1][0]=BoxXYZ[1]*cosG;</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         68 :       Box[1][1]=BoxXYZ[1]*sinG;</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         68 :       Box[2][0]=BoxXYZ[2]*cosB;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         68 :       Box[2][1]=(BoxXYZ[2]*BoxXYZ[1]*cosA-Box[2][0]*Box[1][0])/Box[1][1];</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         68 :       Box[2][2]=std::sqrt(BoxXYZ[2]*BoxXYZ[2]-Box[2][0]*Box[2][0]-Box[2][1]*Box[2][1]);</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :     }</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">     275261 :     if(record==&quot;ATOM&quot; || record==&quot;HETATM&quot;) {</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :       between_ters=true;</a>
+<a name="338"><span class="lineNum">     338 </span>            :       AtomNumber a;</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">     271169 :       unsigned resno=0; // GB: when resnum string is not present, we set res number to zero</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :       double o,b;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">     271169 :       Vector p;</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :       {</a>
+<a name="343"><span class="lineNum">     343 </span>            :         int result;</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">     271169 :         auto trimmed=serial;</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">     271169 :         Tools::trim(trimmed);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">     271231 :         while(trimmed.length()&lt;5) trimmed = std::string(&quot; &quot;) + trimmed;</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">     271169 :         const char* errmsg = h36::hy36decode(5, trimmed.c_str(),trimmed.length(), &amp;result);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">     271169 :         if(errmsg) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :           std::string msg(errmsg);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :           plumed_merror(msg);</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :         }</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">     271169 :         a.setSerial(result);</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :       }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            :       // allow skipping residue number</a>
+<a name="356"><span class="lineNum">     356 </span>            :       {</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">     271169 :         auto trimmed=resnum;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">     271169 :         Tools::trim(trimmed);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">     271169 :         if(trimmed.length()&gt;0) {</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :           int result;</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">     271169 :           while(trimmed.length()&lt;4) trimmed = std::string(&quot; &quot;) + trimmed;</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">     271169 :           const char* errmsg = h36::hy36decode(4, trimmed.c_str(),trimmed.length(), &amp;result);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">     271169 :           if(errmsg) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :             std::string msg(errmsg);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :             plumed_merror(msg);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :           }</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">     271169 :           resno=result;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :         }</a>
+<a name="369"><span class="lineNum">     369 </span>            :       }</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">     271169 :       Tools::convert(occ,o);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">     271169 :       Tools::convert(bet,b);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">     271169 :       Tools::convert(x,p[0]);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">     271169 :       Tools::convert(y,p[1]);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">     271169 :       Tools::convert(z,p[2]);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :       // scale into nm</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">     271169 :       p*=scale;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">     271169 :       numbers.push_back(a);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">     271169 :       number2index[a]=positions.size();</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">     271169 :       std::size_t startpos=atomname.find_first_not_of(&quot; \t&quot;);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">     271169 :       std::size_t endpos=atomname.find_last_not_of(&quot; \t&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">     271169 :       atomsymb.push_back( atomname.substr(startpos, endpos-startpos+1) );</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">     271169 :       residue.push_back(resno);</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">     271169 :       chain.push_back(chainID);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">     271169 :       occupancy.push_back(o);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">     271169 :       beta.push_back(b);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">     271169 :       positions.push_back(p);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">     271169 :       residuenames.push_back(residuename);</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :     }</a>
+<a name="390"><span class="lineNum">     390 </span>            :   }</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">       2069 :   if( between_ters ) block_ends.push_back( positions.size() );</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       2069 :   return file_is_alive;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : }</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">        323 : bool PDB::read(const std::string&amp;file,bool naturalUnits,double scale) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">        323 :   FILE* fp=std::fopen(file.c_str(),&quot;r&quot;);</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">        323 :   if(!fp) return false;</span></a>
+<a name="398"><span class="lineNum">     398 </span>            : // call fclose when exiting this function</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">        321 :   auto deleter=[](FILE* f) { std::fclose(f); };</span></a>
+<a name="400"><span class="lineNum">     400 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">        321 :   readFromFilepointer(fp,naturalUnits,scale);</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :   return true;</a>
+<a name="403"><span class="lineNum">     403 </span>            : }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">        244 : void PDB::getChainNames( std::vector&lt;std::string&gt;&amp; chains ) const {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">        244 :   chains.resize(0);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">        244 :   chains.push_back( chain[0] );</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">     500977 :   for(unsigned i=1; i&lt;size(); ++i) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">     500733 :     if( chains[chains.size()-1]!=chain[i] ) chains.push_back( chain[i] );</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        244 : }</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">      11608 : void PDB::getResidueRange( const std::string&amp; chainname, unsigned&amp; res_start, unsigned&amp; res_end, std::string&amp; errmsg ) const {</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :   bool inres=false, foundchain=false;</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">   30321511 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">   30309903 :     if( chain[i]==chainname ) {</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">   26640541 :       if(!inres) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">      11608 :         if(foundchain) errmsg=&quot;found second start of chain named &quot; + chainname;</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      11608 :         res_start=residue[i];</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :       }</a>
+<a name="421"><span class="lineNum">     421 </span>            :       inres=true; foundchain=true;</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">    3669362 :     } else if( inres &amp;&amp; chain[i]!=chainname ) {</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :       inres=false;</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">      11094 :       res_end=residue[i-1];</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :     }</a>
+<a name="426"><span class="lineNum">     426 </span>            :   }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">      11608 :   if(inres) res_end=residue[size()-1];</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">      11608 : }</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        161 : void PDB::getAtomRange( const std::string&amp; chainname, AtomNumber&amp; a_start, AtomNumber&amp; a_end, std::string&amp; errmsg ) const {</span></a>
+<a name="431"><span class="lineNum">     431 </span>            :   bool inres=false, foundchain=false;</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">     434018 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">     433857 :     if( chain[i]==chainname ) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">      90643 :       if(!inres) {</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">        161 :         if(foundchain) errmsg=&quot;found second start of chain named &quot; + chainname;</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">        161 :         a_start=numbers[i];</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :       }</a>
+<a name="438"><span class="lineNum">     438 </span>            :       inres=true; foundchain=true;</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">     343214 :     } else if( inres &amp;&amp; chain[i]!=chainname ) {</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :       inres=false;</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         74 :       a_end=numbers[i-1];</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :     }</a>
+<a name="443"><span class="lineNum">     443 </span>            :   }</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">        161 :   if(inres) a_end=numbers[size()-1];</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">        161 : }</span></a>
+<a name="446"><span class="lineNum">     446 </span>            : </a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">       5958 : std::string PDB::getResidueName( const unsigned&amp; resnum ) const {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">    7317600 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">    7317600 :     if( residue[i]==resnum ) return residuenames[i];</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineNoCov">          0 :   std::string num; Tools::convert( resnum, num );</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;residue &quot; + num + &quot; not found&quot; );</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">      48690 : std::string PDB::getResidueName(const unsigned&amp; resnum,const std::string&amp; chainid ) const {</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">   62791939 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">   62840809 :     if( residue[i]==resnum &amp;&amp; ( chainid==&quot;*&quot; || chain[i]==chainid) ) return residuenames[i];</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :   }</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineNoCov">          0 :   std::string num; Tools::convert( resnum, num );</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;residue &quot; + num + &quot; not found in chain &quot; + chainid );</span></a>
+<a name="461"><span class="lineNum">     461 </span>            : }</a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">      13260 : AtomNumber PDB::getNamedAtomFromResidue( const std::string&amp; aname, const unsigned&amp; resnum ) const {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">   16347180 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">   16347180 :     if( residue[i]==resnum &amp;&amp; atomsymb[i]==aname ) return numbers[i];</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :   }</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :   std::string num; Tools::convert( resnum, num );</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;residue &quot; + num + &quot; does not contain an atom named &quot; + aname );</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : }</a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">       2216 : AtomNumber PDB::getNamedAtomFromResidueAndChain( const std::string&amp; aname, const unsigned&amp; resnum, const std::string&amp; chainid ) const {</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">    1070584 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">    1072800 :     if( residue[i]==resnum &amp;&amp; atomsymb[i]==aname &amp;&amp; ( chainid==&quot;*&quot; || chain[i]==chainid) ) return numbers[i];</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :   }</a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :   std::string num; Tools::convert( resnum, num );</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;residue &quot; + num + &quot; from chain &quot; + chainid + &quot; does not contain an atom named &quot; + aname );</span></a>
+<a name="478"><span class="lineNum">     478 </span>            : }</a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">      34246 : std::vector&lt;AtomNumber&gt; PDB::getAtomsInResidue(const unsigned&amp; resnum,const std::string&amp; chainid)const {</span></a>
+<a name="481"><span class="lineNum">     481 </span>            :   std::vector&lt;AtomNumber&gt; tmp;</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">   91444766 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">   91931870 :     if( residue[i]==resnum &amp;&amp; ( chainid==&quot;*&quot; || chain[i]==chainid) ) tmp.push_back(numbers[i]);</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :   }</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">      34246 :   if(tmp.size()==0) {</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert( resnum, num );</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Cannot find residue &quot; + num + &quot; from chain &quot; + chainid  );</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   }</a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">      34246 :   return tmp;</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : }</a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 : std::vector&lt;AtomNumber&gt; PDB::getAtomsInChain(const std::string&amp; chainid)const {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :   std::vector&lt;AtomNumber&gt; tmp;</a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineNoCov">          0 :     if( chainid==&quot;*&quot; || chain[i]==chainid ) tmp.push_back(numbers[i]);</span></a>
+<a name="496"><span class="lineNum">     496 </span>            :   }</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :   if(tmp.size()==0) {</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Cannot find atoms from chain &quot; + chainid  );</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :   }</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :   return tmp;</span></a>
+<a name="501"><span class="lineNum">     501 </span>            : }</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">       4638 : std::string PDB::getChainID(const unsigned&amp; resnumber) const {</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">    5689172 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">    5689172 :     if(resnumber==residue[i]) return chain[i];</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :   }</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;Not enough residues in pdb input file&quot;);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            : }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 : std::string PDB::getChainID(AtomNumber a) const {</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   const auto p=number2index.find(a);</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :   if(p==number2index.end()) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :     std::string num; Tools::convert( a.serial(), num );</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Chain for atom &quot; + num + &quot; not found&quot; );</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :   }</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :   return chain[p-&gt;second];</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : }</a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 : bool PDB::checkForResidue( const std::string&amp; name ) const {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineNoCov">          0 :     if( residuenames[i]==name ) return true;</span></a>
+<a name="522"><span class="lineNum">     522 </span>            :   }</a>
+<a name="523"><span class="lineNum">     523 </span>            :   return false;</a>
+<a name="524"><span class="lineNum">     524 </span>            : }</a>
+<a name="525"><span class="lineNum">     525 </span>            : </a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 : bool PDB::checkForAtom( const std::string&amp; name ) const {</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;size(); ++i) {</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 :     if( atomsymb[i]==name ) return true;</span></a>
+<a name="529"><span class="lineNum">     529 </span>            :   }</a>
+<a name="530"><span class="lineNum">     530 </span>            :   return false;</a>
+<a name="531"><span class="lineNum">     531 </span>            : }</a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        249 : bool PDB::checkForAtom( AtomNumber a ) const {</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :   const auto p=number2index.find(a);</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">        249 :   return (p!=number2index.end());</span></a>
+<a name="536"><span class="lineNum">     536 </span>            : }</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 : Log&amp; operator&lt;&lt;(Log&amp; ostr, const PDB&amp;  pdb) {</span></a>
+<a name="539"><span class="lineNum">     539 </span>            :   const std::size_t bufferlen=1000;</a>
+<a name="540"><span class="lineNum">     540 </span>            :   char buffer[bufferlen];</a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;pdb.positions.size(); i++) {</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :     std::snprintf(buffer,bufferlen,&quot;ATOM %3u %8.3f %8.3f %8.3f\n&quot;,pdb.numbers[i].serial(),pdb.positions[i][0],pdb.positions[i][1],pdb.positions[i][2]);</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     ostr&lt;&lt;buffer;</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :   }</a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :   return ostr;</span></a>
+<a name="546"><span class="lineNum">     546 </span>            : }</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">      38554 : Vector PDB::getPosition(AtomNumber a)const {</span></a>
+<a name="549"><span class="lineNum">     549 </span>            :   const auto p=number2index.find(a);</a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">      38554 :   if(p==number2index.end()) plumed_merror(&quot;atom not available&quot;);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">      38554 :   else return positions[p-&gt;second];</span></a>
+<a name="552"><span class="lineNum">     552 </span>            : }</a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">    2539432 : std::vector&lt;std::string&gt; PDB::getArgumentNames()const {</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">    2539432 :   return argnames;</span></a>
+<a name="556"><span class="lineNum">     556 </span>            : }</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         10 : std::string PDB::getMtype() const {</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         10 :   return mtype;</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : }</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">        497 : void PDB::print( const double&amp; lunits, GenericMolInfo* mymoldat, OFile&amp; ofile, const std::string&amp; fmt ) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">        497 :   if( argnames.size()&gt;0 ) {</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">        476 :     ofile.printf(&quot;REMARK ARG=%s&quot;, argnames[0].c_str() );</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">       1744 :     for(unsigned i=1; i&lt;argnames.size(); ++i) ofile.printf(&quot;,%s&quot;,argnames[i].c_str() );</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">        476 :     ofile.printf(&quot;\n&quot;); ofile.printf(&quot;REMARK &quot;);</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :   }</a>
+<a name="568"><span class="lineNum">     568 </span>            :   std::string descr2;</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">        497 :   if(fmt.find(&quot;-&quot;)!=std::string::npos) {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :     descr2=&quot;%s=&quot; + fmt + &quot; &quot;;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :   } else {</a>
+<a name="572"><span class="lineNum">     572 </span>            :     // This ensures numbers are left justified (i.e. next to the equals sign</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">        497 :     std::size_t psign=fmt.find(&quot;%&quot;);</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        497 :     plumed_assert( psign!=std::string::npos );</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        994 :     descr2=&quot;%s=%-&quot; + fmt.substr(psign+1) + &quot; &quot;;</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :   }</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">       2241 :   for(std::map&lt;std::string,double&gt;::iterator it=arg_data.begin(); it!=arg_data.end(); ++it) ofile.printf( descr2.c_str(),it-&gt;first.c_str(), it-&gt;second );</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">        497 :   if( argnames.size()&gt;0 ) ofile.printf(&quot;\n&quot;);</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">        497 :   if( !mymoldat ) {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">       2263 :     for(unsigned i=0; i&lt;positions.size(); ++i) {</span></a>
+<a name="581"><span class="lineNum">     581 </span>            :       std::array&lt;char,6&gt; at;</a>
+<a name="582"><span class="lineNum">     582 </span>            :       {</a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">       1769 :         const char* msg = h36::hy36encode(5,numbers[i].serial(),&amp;at[0]);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">       1769 :         plumed_assert(msg==nullptr) &lt;&lt; msg;</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">       1769 :         at[5]=0;</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :       }</a>
+<a name="587"><span class="lineNum">     587 </span>            :       std::array&lt;char,5&gt; res;</a>
+<a name="588"><span class="lineNum">     588 </span>            :       {</a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">       1769 :         const char* msg = h36::hy36encode(4,i,&amp;res[0]);</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">       1769 :         plumed_assert(msg==nullptr) &lt;&lt; msg;</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">       1769 :         res[4]=0;</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :       }</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">       1769 :       ofile.printf(&quot;ATOM  %s  X   RES  %s    %8.3f%8.3f%8.3f%6.2f%6.2f\n&quot;,</span></a>
+<a name="594"><span class="lineNum">     594 </span>            :                    &amp;at[0], &amp;res[0],</a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">       1769 :                    lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],</span></a>
+<a name="596"><span class="lineNum">     596 </span>            :                    occupancy[i], beta[i] );</a>
+<a name="597"><span class="lineNum">     597 </span>            :     }</a>
+<a name="598"><span class="lineNum">     598 </span>            :   } else {</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         69 :     for(unsigned i=0; i&lt;positions.size(); ++i) {</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :       std::array&lt;char,6&gt; at;</a>
+<a name="601"><span class="lineNum">     601 </span>            :       {</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         66 :         const char* msg = h36::hy36encode(5,numbers[i].serial(),&amp;at[0]);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         66 :         plumed_assert(msg==nullptr) &lt;&lt; msg;</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         66 :         at[5]=0;</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :       }</a>
+<a name="606"><span class="lineNum">     606 </span>            :       std::array&lt;char,5&gt; res;</a>
+<a name="607"><span class="lineNum">     607 </span>            :       {</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">         66 :         const char* msg = h36::hy36encode(4,mymoldat-&gt;getResidueNumber(numbers[i]),&amp;res[0]);</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">         66 :         plumed_assert(msg==nullptr) &lt;&lt; msg;</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">         66 :         res[4]=0;</span></a>
+<a name="611"><span class="lineNum">     611 </span>            :       }</a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">         66 :       ofile.printf(&quot;ATOM  %s %-4s %3s  %s    %8.3f%8.3f%8.3f%6.2f%6.2f\n&quot;,</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">        132 :                    &amp;at[0], mymoldat-&gt;getAtomName(numbers[i]).c_str(),</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         66 :                    mymoldat-&gt;getResidueName(numbers[i]).c_str(), &amp;res[0],</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         66 :                    lunits*positions[i][0], lunits*positions[i][1], lunits*positions[i][2],</span></a>
+<a name="616"><span class="lineNum">     616 </span>            :                    occupancy[i], beta[i] );</a>
+<a name="617"><span class="lineNum">     617 </span>            :     }</a>
+<a name="618"><span class="lineNum">     618 </span>            :   }</a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        497 :   ofile.printf(&quot;END\n&quot;);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">        497 : }</span></a>
+<a name="621"><span class="lineNum">     621 </span>            : </a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">      37562 : bool PDB::allowedResidue( const std::string&amp; type, const std::string&amp; residuename ) const {</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">      37562 :   if( type==&quot;protein&quot; ) {</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">      37562 :     if(residuename==&quot;ALA&quot;) return true;</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">      35552 :     else if(residuename==&quot;ARG&quot;) return true;</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">      33312 :     else if(residuename==&quot;ASN&quot;) return true;</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">      31392 :     else if(residuename==&quot;ASP&quot;) return true;</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">      29712 :     else if(residuename==&quot;CYS&quot;) return true;</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">      29582 :     else if(residuename==&quot;GLN&quot;) return true;</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">      26782 :     else if(residuename==&quot;GLU&quot;) return true;</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">      25522 :     else if(residuename==&quot;GLY&quot;) return true;</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">      23702 :     else if(residuename==&quot;HIS&quot;) return true;</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">      23702 :     else if(residuename==&quot;ILE&quot;) return true;</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">      21452 :     else if(residuename==&quot;LEU&quot;) return true;</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">      17462 :     else if(residuename==&quot;LYS&quot;) return true;</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">      14762 :     else if(residuename==&quot;MET&quot;) return true;</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">      13162 :     else if(residuename==&quot;PHE&quot;) return true;</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">      10522 :     else if(residuename==&quot;PRO&quot;) return true;</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">       8542 :     else if(residuename==&quot;SER&quot;) return true;</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">       7112 :     else if(residuename==&quot;THR&quot;) return true;</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">       5762 :     else if(residuename==&quot;TRP&quot;) return true;</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">       5762 :     else if(residuename==&quot;TYR&quot;) return true;</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">       4382 :     else if(residuename==&quot;VAL&quot;) return true;</span></a>
+<a name="644"><span class="lineNum">     644 </span>            : // Terminal groups</a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">       1492 :     else if(residuename==&quot;ACE&quot;) return true;</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">       1492 :     else if(residuename==&quot;NME&quot;) return true;</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">       1492 :     else if(residuename==&quot;NH2&quot;) return true;</span></a>
+<a name="648"><span class="lineNum">     648 </span>            : // Alternative residue names in common force fields</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">       1492 :     else if(residuename==&quot;GLH&quot;) return true; // neutral GLU</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">       1492 :     else if(residuename==&quot;ASH&quot;) return true; // neutral ASP</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">       1492 :     else if(residuename==&quot;HID&quot;) return true; // HIS-D amber</span></a>
+<a name="652"><span class="lineNum">     652 </span><span class="lineCov">       1492 :     else if(residuename==&quot;HSD&quot;) return true; // HIS-D charmm</span></a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">       1492 :     else if(residuename==&quot;HIE&quot;) return true; // HIS-E amber</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">       1112 :     else if(residuename==&quot;HSE&quot;) return true; // HIS-E charmm</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">       1112 :     else if(residuename==&quot;HIP&quot;) return true; // HIS-P amber</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">       1112 :     else if(residuename==&quot;HSP&quot;) return true; // HIS-P charmm</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">       1112 :     else if(residuename==&quot;CYX&quot;) return true; // disulfide bridge CYS</span></a>
+<a name="658"><span class="lineNum">     658 </span>            : // Weird amino acids</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       1112 :     else if(residuename==&quot;NLE&quot;) return true;</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">       1112 :     else if(residuename==&quot;SFO&quot;) return true;</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">       1112 :     else return false;</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineNoCov">          0 :   } else if( type==&quot;dna&quot; ) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineNoCov">          0 :     if(residuename==&quot;A&quot;) return true;</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;A5&quot;) return true;</span></a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;A3&quot;) return true;</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;AN&quot;) return true;</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;G&quot;) return true;</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;G5&quot;) return true;</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;G3&quot;) return true;</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;GN&quot;) return true;</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;T&quot;) return true;</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;T5&quot;) return true;</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;T3&quot;) return true;</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;TN&quot;) return true;</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;C&quot;) return true;</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;C5&quot;) return true;</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;C3&quot;) return true;</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;CN&quot;) return true;</span></a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DA&quot;) return true;</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DA5&quot;) return true;</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DA3&quot;) return true;</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DAN&quot;) return true;</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DG&quot;) return true;</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DG5&quot;) return true;</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DG3&quot;) return true;</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DGN&quot;) return true;</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DT&quot;) return true;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DT5&quot;) return true;</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DT3&quot;) return true;</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DTN&quot;) return true;</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DC&quot;) return true;</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DC5&quot;) return true;</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DC3&quot;) return true;</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;DCN&quot;) return true;</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :     else return false;</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :   } else if( type==&quot;rna&quot; ) {</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :     if(residuename==&quot;A&quot;) return true;</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;A5&quot;) return true;</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;A3&quot;) return true;</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;AN&quot;) return true;</span></a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;G&quot;) return true;</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;G5&quot;) return true;</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;G3&quot;) return true;</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;GN&quot;) return true;</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;U&quot;) return true;</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;U5&quot;) return true;</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;U3&quot;) return true;</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;UN&quot;) return true;</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;C&quot;) return true;</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;C5&quot;) return true;</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;C3&quot;) return true;</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;CN&quot;) return true;</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RA&quot;) return true;</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RA5&quot;) return true;</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RA3&quot;) return true;</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RAN&quot;) return true;</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RG&quot;) return true;</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RG5&quot;) return true;</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RG3&quot;) return true;</span></a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RGN&quot;) return true;</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RU&quot;) return true;</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RU5&quot;) return true;</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RU3&quot;) return true;</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RUN&quot;) return true;</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RC&quot;) return true;</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RC5&quot;) return true;</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RC3&quot;) return true;</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :     else if(residuename==&quot;RCN&quot;) return true;</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineNoCov">          0 :     else return false;</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineNoCov">          0 :   } else if( type==&quot;water&quot; ) {</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :     if(residuename==&quot;SOL&quot;) return true;</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineNoCov">          0 :     if(residuename==&quot;WAT&quot;) return true;</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineNoCov">          0 :     return false;</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineNoCov">          0 :   } else if( type==&quot;ion&quot; ) {</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineNoCov">          0 :     if(residuename==&quot;IB+&quot;) return true;</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :     if(residuename==&quot;CA&quot;) return true;</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineNoCov">          0 :     if(residuename==&quot;CL&quot;) return true;</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :     if(residuename==&quot;NA&quot;) return true;</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :     if(residuename==&quot;MG&quot;) return true;</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :     if(residuename==&quot;K&quot;) return true;</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 :     if(residuename==&quot;RB&quot;) return true;</span></a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineNoCov">          0 :     if(residuename==&quot;CS&quot;) return true;</span></a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineNoCov">          0 :     if(residuename==&quot;LI&quot;) return true;</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :     if(residuename==&quot;ZN&quot;) return true;</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :     return false;</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :   }</a>
+<a name="747"><span class="lineNum">     747 </span>            :   return false;</a>
+<a name="748"><span class="lineNum">     748 </span>            : }</a>
+<a name="749"><span class="lineNum">     749 </span>            : </a>
+<a name="750"><span class="lineNum">     750 </span>            : }</a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Pbc.cpp.func-sort-c.html b/coverage/tools/Pbc.cpp.func-sort-c.html
new file mode 100644
index 0000000000..514e0e8e82
--- /dev/null
+++ b/coverage/tools/Pbc.cpp.func-sort-c.html
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+  <title>LCOV - plumed test coverage - tools/Pbc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Pbc.cpp<span style="font-size: 80%;"> (<a href="Pbc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Pbc.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#151">_ZNK4PLMD3Pbc8distanceEbRKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#241">_ZNK4PLMD3Pbc9getInvBoxEv</a></td>
+              <td class="coverFnHi">2174</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#233">_ZNK4PLMD3Pbc13isOrthorombicEv</a></td>
+              <td class="coverFnHi">8526</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#37">_ZNK4PLMD3Pbc11buildShiftsEPA2_A2_St6vectorINS_13VectorGenericILj3EEESaIS3_EE</a></td>
+              <td class="coverFnHi">20630</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#237">_ZNK4PLMD3Pbc6getBoxEv</a></td>
+              <td class="coverFnHi">42335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#113">_ZN4PLMD3Pbc6setBoxERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">71263</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#156">_ZNK4PLMD3Pbc5applyERSt6vectorINS_13VectorGenericILj3EEESaIS3_EEj</a></td>
+              <td class="coverFnHi">220663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#229">_ZNK4PLMD3Pbc12scaledToRealERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">223368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#91">_ZNK4PLMD3Pbc10fullSearchERNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">600000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#30">_ZN4PLMD3PbcC2Ev</a></td>
+              <td class="coverFnHi">822494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#225">_ZNK4PLMD3Pbc12realToScaledERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">1219963</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#178">_ZNK4PLMD3Pbc8distanceERKNS_13VectorGenericILj3EEES4_Pi</a></td>
+              <td class="coverFnHi">209084305</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Pbc.cpp.func.html b/coverage/tools/Pbc.cpp.func.html
new file mode 100644
index 0000000000..96fa3a8f4e
--- /dev/null
+++ b/coverage/tools/Pbc.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Pbc.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Pbc.cpp<span style="font-size: 80%;"> (<a href="Pbc.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Pbc.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#113">_ZN4PLMD3Pbc6setBoxERKNS_13TensorGenericILj3ELj3EEE</a></td>
+              <td class="coverFnHi">71263</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#30">_ZN4PLMD3PbcC2Ev</a></td>
+              <td class="coverFnHi">822494</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#91">_ZNK4PLMD3Pbc10fullSearchERNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">600000</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#37">_ZNK4PLMD3Pbc11buildShiftsEPA2_A2_St6vectorINS_13VectorGenericILj3EEESaIS3_EE</a></td>
+              <td class="coverFnHi">20630</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#225">_ZNK4PLMD3Pbc12realToScaledERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">1219963</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#229">_ZNK4PLMD3Pbc12scaledToRealERKNS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">223368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#233">_ZNK4PLMD3Pbc13isOrthorombicEv</a></td>
+              <td class="coverFnHi">8526</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#156">_ZNK4PLMD3Pbc5applyERSt6vectorINS_13VectorGenericILj3EEESaIS3_EEj</a></td>
+              <td class="coverFnHi">220663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#237">_ZNK4PLMD3Pbc6getBoxEv</a></td>
+              <td class="coverFnHi">42335</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#178">_ZNK4PLMD3Pbc8distanceERKNS_13VectorGenericILj3EEES4_Pi</a></td>
+              <td class="coverFnHi">209084305</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#151">_ZNK4PLMD3Pbc8distanceEbRKNS_13VectorGenericILj3EEES4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Pbc.cpp.gcov.html#241">_ZNK4PLMD3Pbc9getInvBoxEv</a></td>
+              <td class="coverFnHi">2174</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Pbc.cpp.gcov.html b/coverage/tools/Pbc.cpp.gcov.html
new file mode 100644
index 0000000000..9f4ab5bd54
--- /dev/null
+++ b/coverage/tools/Pbc.cpp.gcov.html
@@ -0,0 +1,323 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Pbc.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Pbc.cpp<span style="font-size: 80%;"> (source / <a href="Pbc.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">102</td>
+            <td class="headerCovTableEntry">107</td>
+            <td class="headerCovTableEntryHi">95.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Pbc.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;LatticeReduction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iostream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Random.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cmath&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     822494 : Pbc::Pbc():</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">   12337410 :   type(unset)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     822494 :   box.zero();</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     822494 :   invBox.zero();</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     822494 : }</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">      20630 : void Pbc::buildShifts(std::vector&lt;Vector&gt; shifts[2][2][2])const {</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   const double small=1e-28;</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : // clear all shifts</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">     309450 :   for(int i=0; i&lt;2; i++) for(int j=0; j&lt;2; j++) for(int k=0; k&lt;2; k++) shifts[i][j][k].clear();</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : // enumerate all possible shifts</a>
+<a name="46"><span class="lineNum">      46 </span>            : // since box is reduced, only 27 shifts have to be attempted</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">     825200 :   for(int l=-1; l&lt;=1; l++) for(int m=-1; m&lt;=1; m++) for(int n=-1; n&lt;=1; n++) {</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : // int/double shift vectors</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">     557010 :         const int ishift[3]= {l,m,n};</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     557010 :         Vector dshift(l,m,n);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : // count how many components are != 0</a>
+<a name="54"><span class="lineNum">      54 </span>            :         unsigned count=0;</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">    2228040 :         for(int s=0; s&lt;3; s++) if(ishift[s]!=0) count++;</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : // skips trivial (0,0,0) and cases with three shifts</a>
+<a name="58"><span class="lineNum">      58 </span>            : // only 18 shifts survive past this point</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">     647898 :         if(count==0 || count==3) continue;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : // check if that Wigner-Seitz face is perpendicular to the axis.</a>
+<a name="62"><span class="lineNum">      62 </span>            : // this allows to eliminate shifts in symmetric cells.</a>
+<a name="63"><span class="lineNum">      63 </span>            : // e.g., if one lactice vector is orthogonal to the plane spanned</a>
+<a name="64"><span class="lineNum">      64 </span>            : // by the other two vectors, that shift should never be tried</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     371340 :         Vector cosdir=matmul(reduced,transpose(reduced),dshift);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     371340 :         double dp=dotProduct(dshift,cosdir);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     371340 :         double ref=modulo2(dshift)*modulo2(cosdir);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     371340 :         if(std::fabs(ref-dp*dp)&lt;small) continue;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : // here we start pruning depending on the sign of the scaled coordinate</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    4206780 :         for(int i=0; i&lt;2; i++) for(int j=0; j&lt;2; j++) for(int k=0; k&lt;2; k++) {</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">    2243616 :               const int block[3]= {2*i-1,2*j-1,2*k-1};</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : // skip cases where shift would bring too far from origin</a>
+<a name="76"><span class="lineNum">      76 </span>            :               bool skip=false;</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">    8974464 :               for(int s=0; s&lt;3; s++) if(ishift[s]*block[s]&gt;0) skip=true;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">    2534702 :               if(skip) continue;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :               skip=true;</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">    3066608 :               for(int s=0; s&lt;3; s++) {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : // check that the components of cosdir along the non-shifted directions</a>
+<a name="82"><span class="lineNum">      82 </span>            : // have the proper sign</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    2299956 :                 if(((1-ishift[s]*ishift[s])*block[s])*cosdir[s]&lt;-small) skip=false;</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :               }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     766652 :               if(skip)continue;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : // if we arrive to this point, shift is eligible and is added to the list</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">     951132 :               shifts[i][j][k].push_back(matmul(transpose(reduced),dshift));</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :             }</a>
+<a name="90"><span class="lineNum">      90 </span>            :       }</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      20630 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     600000 : void Pbc::fullSearch(Vector&amp;d)const {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">     600000 :   if(type==unset) return;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     528100 :   Vector s=matmul(invReduced.transpose(),d);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    2112400 :   for(int i=0; i&lt;3; i++) s[i]=Tools::pbc(s[i]);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">     528100 :   d=matmul(reduced.transpose(),s);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   const int smax=4;</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">     528100 :   Vector a0(reduced.getRow(0));</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     528100 :   Vector a1(reduced.getRow(1));</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">     528100 :   Vector a2(reduced.getRow(2));</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     528100 :   Vector best(d);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">     528100 :   double lbest=d.modulo2();</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">  433042000 :   for(int i=-smax; i&lt;=smax; i++) for(int j=-smax; j&lt;=smax; j++) for(int k=-smax; k&lt;=smax; k++) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">  384984900 :         Vector trial=d+i*a0+j*a1+k*a2;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">  384984900 :         double ltrial=trial.modulo2();</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">  384984900 :         if(ltrial&lt;lbest) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      29897 :           best=trial;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :           lbest=ltrial;</a>
+<a name="110"><span class="lineNum">     110 </span>            :         }</a>
+<a name="111"><span class="lineNum">     111 </span>            :       }</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     528100 :   d=best;</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">      71263 : void Pbc::setBox(const Tensor&amp;b) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      71263 :   box=b;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : // detect type:</a>
+<a name="118"><span class="lineNum">     118 </span>            :   const double epsilon=1e-28;</a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">      71263 :   type=unset;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">      71263 :   double det=box.determinant();</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      71263 :   if(det*det&lt;epsilon) return;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            :   bool cxy=false;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   bool cxz=false;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   bool cyz=false;</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      65176 :   if(box(0,1)*box(0,1)&lt;epsilon &amp;&amp; box(1,0)*box(1,0)&lt;epsilon) cxy=true;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      65176 :   if(box(0,2)*box(0,2)&lt;epsilon &amp;&amp; box(2,0)*box(2,0)&lt;epsilon) cxz=true;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      65176 :   if(box(1,2)*box(1,2)&lt;epsilon &amp;&amp; box(2,1)*box(2,1)&lt;epsilon) cyz=true;</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      65176 :   invBox=box.inverse();</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">      65176 :   if(cxy &amp;&amp; cxz &amp;&amp; cyz) type=orthorombic;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      20630 :   else type=generic;</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      65176 :   if(type==orthorombic) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      44546 :     reduced=box;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      44546 :     invReduced=inverse(reduced);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">     178184 :     for(unsigned i=0; i&lt;3; i++) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">     133638 :       diag[i]=box[i][i];</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">     133638 :       hdiag[i]=0.5*box[i][i];</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">     133638 :       mdiag[i]=-0.5*box[i][i];</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            :   } else {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      20630 :     reduced=box;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      20630 :     LatticeReduction::reduce(reduced);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      20630 :     invReduced=inverse(reduced);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      20630 :     buildShifts(shifts);</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 : double Pbc::distance( const bool pbc, const Vector&amp; v1, const Vector&amp; v2 ) const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :   if(pbc) { return ( distance(v1,v2) ).modulo(); }</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :   else { return ( delta(v1,v2) ).modulo(); }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">     220663 : void Pbc::apply(std::vector&lt;Vector&gt;&amp; dlist, unsigned max_index) const {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">     220663 :   if (max_index==0) max_index=dlist.size();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">     220663 :   if(type==unset) {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :     // do nothing</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     214239 :   } else if(type==orthorombic) {</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : #ifdef __PLUMED_PBC_WHILE</a>
+<a name="164"><span class="lineNum">     164 </span>            :     for(unsigned k=0; k&lt;max_index; ++k) {</a>
+<a name="165"><span class="lineNum">     165 </span>            :       while(dlist[k][0]&gt;hdiag[0])   dlist[k][0]-=diag[0];</a>
+<a name="166"><span class="lineNum">     166 </span>            :       while(dlist[k][0]&lt;=mdiag[0])  dlist[k][0]+=diag[0];</a>
+<a name="167"><span class="lineNum">     167 </span>            :       while(dlist[k][1]&gt;hdiag[1])   dlist[k][1]-=diag[1];</a>
+<a name="168"><span class="lineNum">     168 </span>            :       while(dlist[k][1]&lt;=mdiag[1])  dlist[k][1]+=diag[1];</a>
+<a name="169"><span class="lineNum">     169 </span>            :       while(dlist[k][2]&gt;hdiag[2])   dlist[k][2]-=diag[2];</a>
+<a name="170"><span class="lineNum">     170 </span>            :       while(dlist[k][2]&lt;=mdiag[2])  dlist[k][2]+=diag[2];</a>
+<a name="171"><span class="lineNum">     171 </span>            :     }</a>
+<a name="172"><span class="lineNum">     172 </span>            : #else</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov"> 1603605381 :     for(unsigned k=0; k&lt;max_index; ++k) for(int i=0; i&lt;3; i++) dlist[k][i]=Tools::pbc(dlist[k][i]*invBox(i,i))*box(i,i);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : #endif</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1810 :   } else if(type==generic) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      67768 :     for(unsigned k=0; k&lt;max_index; ++k) dlist[k]=distance(Vector(0.0,0.0,0.0),dlist[k]);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :   } else plumed_merror(&quot;unknown pbc type&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     220663 : }</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">  209084305 : Vector Pbc::distance(const Vector&amp;v1,const Vector&amp;v2,int*nshifts)const {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">  209084305 :   Vector d=delta(v1,v2);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">  209084305 :   if(type==unset) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     // do nothing</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">  184840816 :   } else if(type==orthorombic) {</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : #ifdef __PLUMED_PBC_WHILE</a>
+<a name="186"><span class="lineNum">     186 </span>            :     for(unsigned i=0; i&lt;3; i++) {</a>
+<a name="187"><span class="lineNum">     187 </span>            :       while(d[i]&gt;hdiag[i]) d[i]-=diag[i];</a>
+<a name="188"><span class="lineNum">     188 </span>            :       while(d[i]&lt;=mdiag[i]) d[i]+=diag[i];</a>
+<a name="189"><span class="lineNum">     189 </span>            :     }</a>
+<a name="190"><span class="lineNum">     190 </span>            : #else</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">  546059116 :     for(int i=0; i&lt;3; i++) d[i]=Tools::pbc(d[i]*invBox(i,i))*box(i,i);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : #endif</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">   48326037 :   } else if(type==generic) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">   48326037 :     Vector s=matmul(d,invReduced);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : // check if images have to be computed:</a>
+<a name="196"><span class="lineNum">     196 </span>            : //    if((std::fabs(s[0])+std::fabs(s[1])+std::fabs(s[2])&gt;0.5)){</a>
+<a name="197"><span class="lineNum">     197 </span>            : // NOTICE: the check in the previous line, albeit correct, is breaking many regtest</a>
+<a name="198"><span class="lineNum">     198 </span>            : //         since it does not apply Tools::pbc in many cases. Moreover, it does not</a>
+<a name="199"><span class="lineNum">     199 </span>            : //         introduce a significant gain. I thus leave it out for the moment.</a>
+<a name="200"><span class="lineNum">     200 </span>            :     if(true) {</a>
+<a name="201"><span class="lineNum">     201 </span>            : // bring to -0.5,+0.5 region in scaled coordinates:</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">  193304148 :       for(int i=0; i&lt;3; i++) s[i]=Tools::pbc(s[i]);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">   48326037 :       d=matmul(s,reduced);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : // check if shifts have to be attempted:</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">   48326037 :       if((std::fabs(s[0])+std::fabs(s[1])+std::fabs(s[2])&gt;0.5)) {</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : // list of shifts is specific for that &quot;octant&quot; (depends on signs of s[i]):</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">   78765012 :         const std::vector&lt;Vector&gt; &amp; myshifts(shifts[(s[0]&gt;0?1:0)][(s[1]&gt;0?1:0)][(s[2]&gt;0?1:0)]);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">   39867229 :         Vector best(d);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">   39867229 :         double lbest(modulo2(best));</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : // loop over possible shifts:</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">   39867229 :         if(nshifts) *nshifts+=myshifts.size();</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">  179420109 :         for(unsigned i=0; i&lt;myshifts.size(); i++) {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">  139552880 :           Vector trial=d+myshifts[i];</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">  139552880 :           double ltrial=modulo2(trial);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">  139552880 :           if(ltrial&lt;lbest) {</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :             lbest=ltrial;</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">    3759325 :             best=trial;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :           }</a>
+<a name="219"><span class="lineNum">     219 </span>            :         }</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">   39867229 :         d=best;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :       }</a>
+<a name="222"><span class="lineNum">     222 </span>            :     }</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :   } else plumed_merror(&quot;unknown pbc type&quot;);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">  209084305 :   return d;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">    1219963 : Vector Pbc::realToScaled(const Vector&amp;d)const {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">    1219963 :   return matmul(invBox.transpose(),d);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">     223368 : Vector Pbc::scaledToReal(const Vector&amp;d)const {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">     223368 :   return matmul(box.transpose(),d);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : }</a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       8526 : bool Pbc::isOrthorombic()const {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       8526 :   return type==orthorombic;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      42335 : const Tensor&amp; Pbc::getBox()const {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">      42335 :   return box;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       2174 : const Tensor&amp; Pbc::getInvBox()const {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">       2174 :   return invBox;</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Pbc.h.func-sort-c.html b/coverage/tools/Pbc.h.func-sort-c.html
new file mode 100644
index 0000000000..e148cb55d3
--- /dev/null
+++ b/coverage/tools/Pbc.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Pbc.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Pbc.h<span style="font-size: 80%;"> (<a href="Pbc.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Pbc.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Pbc.h.func.html b/coverage/tools/Pbc.h.func.html
new file mode 100644
index 0000000000..cfbf2e3b6f
--- /dev/null
+++ b/coverage/tools/Pbc.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Pbc.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Pbc.h<span style="font-size: 80%;"> (<a href="Pbc.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Pbc.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Pbc.h.gcov.html b/coverage/tools/Pbc.h.gcov.html
new file mode 100644
index 0000000000..a724d07337
--- /dev/null
+++ b/coverage/tools/Pbc.h.gcov.html
@@ -0,0 +1,188 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Pbc.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Pbc.h<span style="font-size: 80%;"> (source / <a href="Pbc.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Pbc_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Pbc_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstddef&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Tool to deal with periodic boundary conditions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : This class is useful to apply periodic boundary conditions on interatomic</a>
+<a name="36"><span class="lineNum">      36 </span>            : distances. It stores privately information about reduced lattice vectors</a>
+<a name="37"><span class="lineNum">      37 </span>            : */</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       2403 : class Pbc {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Type of box</a>
+<a name="40"><span class="lineNum">      40 </span>            :   enum {unset,orthorombic,generic} type;</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Box</a>
+<a name="42"><span class="lineNum">      42 </span>            :   Tensor box;</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Inverse box</a>
+<a name="44"><span class="lineNum">      44 </span>            :   Tensor invBox;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Reduced box.</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// This is a set of lattice vectors generating the same lattice</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// but &quot;minimally skewed&quot;. Useful to optimize image search.</a>
+<a name="48"><span class="lineNum">      48 </span>            :   Tensor reduced;</a>
+<a name="49"><span class="lineNum">      49 </span>            : /// Inverse of the reduced box</a>
+<a name="50"><span class="lineNum">      50 </span>            :   Tensor invReduced;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// List of shifts that should be attempted.</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Depending on the sign of the scaled coordinates representing</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// a distance vector, a different set of shifts must be tried.</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;Vector&gt; shifts[2][2][2];</a>
+<a name="55"><span class="lineNum">      55 </span>            : /// Alternative representation for orthorombic cells.</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Not really used, but could be used to optimize search in</a>
+<a name="57"><span class="lineNum">      57 </span>            : /// orthorombic cells.</a>
+<a name="58"><span class="lineNum">      58 </span>            :   Vector diag,hdiag,mdiag;</a>
+<a name="59"><span class="lineNum">      59 </span>            : /// Build list of shifts.</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// This is expensive, and must be called only when box is</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// reset. It allows building a minimal set of shifts</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// depending on the sign of the scaled coordinates representing</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// a distance vector.</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void buildShifts(std::vector&lt;Vector&gt; shifts[2][2][2])const;</a>
+<a name="65"><span class="lineNum">      65 </span>            : public:</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Constructor</a>
+<a name="67"><span class="lineNum">      67 </span>            :   Pbc();</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Compute modulo of (v2-v1), using or not pbc depending on bool pbc.</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double distance( const bool pbc, const Vector&amp; v1, const Vector&amp; v2 ) const;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Computes v2-v1, using minimal image convention</a>
+<a name="71"><span class="lineNum">      71 </span>            :   Vector distance(const Vector&amp; v1,const Vector&amp; v2)const;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// version of distance which also returns the number</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// of attempted shifts</a>
+<a name="74"><span class="lineNum">      74 </span>            :   Vector distance(const Vector&amp;,const Vector&amp;,int*nshifts)const;</a>
+<a name="75"><span class="lineNum">      75 </span>            : /// Apply PBC to a set of positions or distance vectors</a>
+<a name="76"><span class="lineNum">      76 </span>            :   void apply(std::vector&lt;Vector&gt;&amp;dlist, unsigned max_index=0) const;</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Set the lattice vectors.</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// b[i][j] is the j-th component of the i-th vector</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void setBox(const Tensor&amp;b);</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Returns the box</a>
+<a name="81"><span class="lineNum">      81 </span>            :   const Tensor&amp; getBox()const;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Returns the inverse matrix of box.</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Thus: pbc.getInvBox() == inverse(pbc.getBox()).</a>
+<a name="84"><span class="lineNum">      84 </span>            :   const Tensor&amp; getInvBox()const;</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Transform a vector in real space to a vector in scaled coordinates.</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Thus:pbc.realToScaled(v) == matmul(transpose(inverse(pbc.getBox(),v)));</a>
+<a name="87"><span class="lineNum">      87 </span>            :   Vector realToScaled(const Vector&amp;)const;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Transform a vector in scaled coordinates to a vector in real space.</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Thus:pbc.scaledToRead(v) == matmul(transpose(pbc.getBox()),v);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   Vector scaledToReal(const Vector&amp;)const;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Returns true if the box vectors are orthogonal</a>
+<a name="92"><span class="lineNum">      92 </span>            :   bool isOrthorombic()const;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Full search (for testing).</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// Perform a full search on vector</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void fullSearch(Vector&amp;)const;</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// Returns true if box is set and non zero</a>
+<a name="97"><span class="lineNum">      97 </span>            :   bool isSet()const;</a>
+<a name="98"><span class="lineNum">      98 </span>            : };</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : inline</a>
+<a name="101"><span class="lineNum">     101 </span>            : Vector Pbc::distance(const Vector&amp; v1,const Vector&amp; v2)const {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">  202246585 :   return distance(v1,v2,NULL);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : inline</a>
+<a name="106"><span class="lineNum">     106 </span>            : bool Pbc::isSet()const {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      14258 :   return type!=unset;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/PlumedHandle.cpp.func-sort-c.html b/coverage/tools/PlumedHandle.cpp.func-sort-c.html
new file mode 100644
index 0000000000..47b2287f52
--- /dev/null
+++ b/coverage/tools/PlumedHandle.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/PlumedHandle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - PlumedHandle.cpp<span style="font-size: 80%;"> (<a href="PlumedHandle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryLo">62.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="PlumedHandle.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#87">_ZN4PLMD12PlumedHandleC2EOS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#65">_ZN4PLMD12PlumedHandleD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#94">_ZN4PLMD12PlumedHandleaSEOS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#69">_ZN4PLMD12PlumedHandle6dlopenEPKc</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#48">_ZN4PLMD12PlumedHandleC2EPKc</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#43">_ZN4PLMD12PlumedHandleC2Ev</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#65">_ZN4PLMD12PlumedHandleD2Ev</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#73">_ZN4PLMD12PlumedHandle3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">1476</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/PlumedHandle.cpp.func.html b/coverage/tools/PlumedHandle.cpp.func.html
new file mode 100644
index 0000000000..60a238a24f
--- /dev/null
+++ b/coverage/tools/PlumedHandle.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/PlumedHandle.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - PlumedHandle.cpp<span style="font-size: 80%;"> (<a href="PlumedHandle.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryLo">62.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="PlumedHandle.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#73">_ZN4PLMD12PlumedHandle3cmdERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_11TypesafePtrE</a></td>
+              <td class="coverFnHi">1476</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#69">_ZN4PLMD12PlumedHandle6dlopenEPKc</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#87">_ZN4PLMD12PlumedHandleC2EOS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#48">_ZN4PLMD12PlumedHandleC2EPKc</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#43">_ZN4PLMD12PlumedHandleC2Ev</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#65">_ZN4PLMD12PlumedHandleD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#65">_ZN4PLMD12PlumedHandleD2Ev</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="PlumedHandle.cpp.gcov.html#94">_ZN4PLMD12PlumedHandleaSEOS0_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/PlumedHandle.cpp.gcov.html b/coverage/tools/PlumedHandle.cpp.gcov.html
new file mode 100644
index 0000000000..59583a20f9
--- /dev/null
+++ b/coverage/tools/PlumedHandle.cpp.gcov.html
@@ -0,0 +1,182 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/PlumedHandle.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - PlumedHandle.cpp<span style="font-size: 80%;"> (source / <a href="PlumedHandle.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryLo">62.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;PlumedHandle.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;lepton/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;dlfcn.h&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #endif</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : // Including Plumed.h in this manner allows to create a local</a>
+<a name="32"><span class="lineNum">      32 </span>            : // implementation of the wrapper in an anonymous namespace.</a>
+<a name="33"><span class="lineNum">      33 </span>            : // This allows to avoid recoding all the Plumed.h stuff here</a>
+<a name="34"><span class="lineNum">      34 </span>            : // and at the same time avoids possible conflicts.</a>
+<a name="35"><span class="lineNum">      35 </span>            : #define __PLUMED_WRAPPER_IMPLEMENTATION 1</a>
+<a name="36"><span class="lineNum">      36 </span>            : #define __PLUMED_WRAPPER_EXTERN 0</a>
+<a name="37"><span class="lineNum">      37 </span>            : #define __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE 1</a>
+<a name="38"><span class="lineNum">      38 </span>            : #define __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS 1</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;../wrapper/Plumed.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD</a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         11 : PlumedHandle::PlumedHandle():</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         11 :   local(Tools::make_unique&lt;PlumedMain&gt;())</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : {</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         11 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 : PlumedHandle::PlumedHandle(const char* kernel)</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="52"><span class="lineNum">      52 </span>            :   :</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          1 :   loaded(plumed_c2v(plumed_create_dlopen(kernel)))</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span>            :   if(!plumed_valid(plumed_v2c(loaded))) {</a>
+<a name="56"><span class="lineNum">      56 </span>            :     // this is necessary to make sure loaded is properly destroyed</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :     plumed_finalize(plumed_v2c(loaded));</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :     plumed_error() &lt;&lt; &quot;You are trying to dynamically load a kernel, but the path &quot; &lt;&lt; kernel &lt;&lt;&quot; could not be opened&quot;;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   }</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          1 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : #else</a>
+<a name="62"><span class="lineNum">      62 </span>            : {</a>
+<a name="63"><span class="lineNum">      63 </span>            :   plumed_error() &lt;&lt; &quot;You are trying to dynamically load a kernel, but PLUMED was compiled without dlopen&quot;;</a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : #endif</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         12 : PlumedHandle::~PlumedHandle() {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         12 :   if(loaded) plumed_finalize(plumed_v2c(loaded));</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         12 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 : PlumedHandle PlumedHandle::dlopen(const char* path) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          1 :   return PlumedHandle(path);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">       1476 : void PlumedHandle::cmd(const std::string &amp; key,const TypesafePtr &amp; ptr) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       1476 :   if(local) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       2508 :     local-&gt;cmd(key.c_str(),ptr);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        222 :   } else if(loaded) {</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :     plumed_safeptr safe;</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        222 :     safe.ptr=ptr.getRaw();</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        222 :     safe.nelem=ptr.getNelem();</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        222 :     safe.shape=const_cast&lt;std::size_t*&gt;(ptr.getShape());</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        222 :     safe.flags=ptr.getFlags();</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        222 :     safe.opt=nullptr;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        222 :     plumed_cmd(plumed_v2c(loaded),key.c_str(),safe);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   } else plumed_error() &lt;&lt; &quot;should never arrive here (either one or the other should work)&quot;;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       1476 : }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 : PlumedHandle::PlumedHandle(PlumedHandle &amp;&amp; other) noexcept:</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   local(std::move(other.local)),</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   loaded(other.loaded)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :   other.loaded=nullptr;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 : PlumedHandle &amp; PlumedHandle::operator=(PlumedHandle &amp;&amp; other) noexcept {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   if(this!=&amp;other) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     if(loaded) plumed_finalize(plumed_v2c(loaded));</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :     local=std::move(other.local);</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     loaded=other.loaded;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :     other.loaded=nullptr;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RMSD.cpp.func-sort-c.html b/coverage/tools/RMSD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a64026e8bf
--- /dev/null
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@@ -0,0 +1,392 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RMSD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RMSD.cpp<span style="font-size: 80%;"> (<a href="RMSD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">540</td>
+            <td class="headerCovTableEntry">735</td>
+            <td class="headerCovTableEntryLo">73.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryLo">52.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RMSD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
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+<head>
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+          <tr>
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+            <td class="headerCovTableEntry">735</td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RMSD.cpp.gcov.html b/coverage/tools/RMSD.cpp.gcov.html
new file mode 100644
index 0000000000..ac2ff09e61
--- /dev/null
+++ b/coverage/tools/RMSD.cpp.gcov.html
@@ -0,0 +1,1548 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RMSD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RMSD.cpp<span style="font-size: 80%;"> (source / <a href="RMSD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">540</td>
+            <td class="headerCovTableEntry">735</td>
+            <td class="headerCovTableEntryLo">73.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">42</td>
+            <td class="headerCovTableEntry">80</td>
+            <td class="headerCovTableEntryLo">52.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;RMSD.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;PDB.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Log.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iostream&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">      46809 : RMSD::RMSD() : alignmentMethod(SIMPLE),reference_center_is_calculated(false),reference_center_is_removed(false),positions_center_is_calculated(false),positions_center_is_removed(false) {}</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : ///</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// general method to set all the rmsd property at once by using a pdb where occupancy column sets the weights for the atoms involved in the</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// alignment and beta sets the weight that are used for calculating the displacement.</a>
+<a name="37"><span class="lineNum">      37 </span>            : ///</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       1108 : void RMSD::set(const PDB&amp;pdb, const std::string &amp; mytype, bool remove_center, bool normalize_weights ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       1108 :   set(pdb.getOccupancy(),pdb.getBeta(),pdb.getPositions(),mytype,remove_center,normalize_weights);</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       1108 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       1575 : void RMSD::set(const std::vector&lt;double&gt; &amp; align, const std::vector&lt;double&gt; &amp; displace, const std::vector&lt;Vector&gt; &amp; reference, const std::string &amp; mytype, bool remove_center, bool normalize_weights ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1575 :   setReference(reference); // this by default remove the com and assumes uniform weights</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1575 :   setAlign(align, normalize_weights, remove_center); // this recalculates the com with weights. If remove_center=false then it restore the center back</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1575 :   setDisplace(displace, normalize_weights);  // this is does not affect any calculation of the weights</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1575 :   setType(mytype);</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1575 : }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      46767 : void RMSD::setType(const std::string &amp; mytype) {</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      46767 :   alignmentMethod=SIMPLE; // initialize with the simplest case: no rotation</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      46767 :   if (mytype==&quot;SIMPLE&quot;) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :     alignmentMethod=SIMPLE;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      46767 :   else if (mytype==&quot;OPTIMAL&quot;) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      46767 :     alignmentMethod=OPTIMAL;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   else if (mytype==&quot;OPTIMAL-FAST&quot;) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :     alignmentMethod=OPTIMAL_FAST;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   else plumed_merror(&quot;unknown RMSD type&quot; + mytype);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      46767 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        471 : void RMSD::clear() {</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   reference.clear();</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        471 :   reference_center.zero();</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        471 :   reference_center_is_calculated=false;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        471 :   reference_center_is_removed=false;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   align.clear();</a>
+<a name="74"><span class="lineNum">      74 </span>            :   displace.clear();</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        471 :   positions_center.zero();</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        471 :   positions_center_is_calculated=false;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        471 :   positions_center_is_removed=false;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        471 : }</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          5 : std::string RMSD::getMethod() {</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::string mystring;</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          5 :   switch(alignmentMethod) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   case SIMPLE: mystring.assign(&quot;SIMPLE&quot;); break;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          5 :   case OPTIMAL: mystring.assign(&quot;OPTIMAL&quot;); break;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST: mystring.assign(&quot;OPTIMAL-FAST&quot;); break;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          5 :   return mystring;</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : ///</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// this calculates the center of mass for the reference and removes it from the reference itself</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// considering uniform weights for alignment</a>
+<a name="92"><span class="lineNum">      92 </span>            : ///</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      46783 : void RMSD::setReference(const std::vector&lt;Vector&gt; &amp; reference) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      46783 :   unsigned n=reference.size();</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      46783 :   this-&gt;reference=reference;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      46783 :   plumed_massert(align.empty(),&quot;you should first clear() an RMSD object, then set a new reference&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      46783 :   plumed_massert(displace.empty(),&quot;you should first clear() an RMSD object, then set a new reference&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      46783 :   align.resize(n,1.0/n);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      46783 :   displace.resize(n,1.0/n);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">     673845 :   for(unsigned i=0; i&lt;n; i++) reference_center+=this-&gt;reference[i]*align[i];</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   #pragma omp simd</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     627062 :   for(unsigned i=0; i&lt;n; i++) this-&gt;reference[i]-=reference_center;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      46783 :   reference_center_is_calculated=true;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      46783 :   reference_center_is_removed=true;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      46783 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      45192 : std::vector&lt;Vector&gt; RMSD::getReference() {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      45192 :   return reference;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+<a name="109"><span class="lineNum">     109 </span>            : ///</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// the alignment weights are here normalized to 1 and  the center of the reference is removed accordingly</a>
+<a name="111"><span class="lineNum">     111 </span>            : ///</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1575 : void RMSD::setAlign(const std::vector&lt;double&gt; &amp; align, bool normalize_weights, bool remove_center) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1575 :   unsigned n=reference.size();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">       1575 :   plumed_massert(this-&gt;align.size()==align.size(),&quot;mismatch in dimension of align/displace arrays&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1575 :   this-&gt;align=align;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       1575 :   if(normalize_weights) {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     double w=0.0;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       3140 :     #pragma omp simd reduction(+:w)</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      39333 :     for(unsigned i=0; i&lt;n; i++) w+=this-&gt;align[i];</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1570 :     if(w&gt;epsilon) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       1570 :       double inv=1.0/w;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :       #pragma omp simd</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      39333 :       for(unsigned i=0; i&lt;n; i++) this-&gt;align[i]*=inv;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :     } else {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :       double inv=1.0/n;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :       #pragma omp simd</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;n; i++) this-&gt;align[i]=inv;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     }</a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span>            :   // recalculate the center anyway</a>
+<a name="131"><span class="lineNum">     131 </span>            :   // just remove the center if that is asked</a>
+<a name="132"><span class="lineNum">     132 </span>            :   // if the center was removed before, then add it and store the new one</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       1575 :   if(reference_center_is_removed) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1575 :     plumed_massert(reference_center_is_calculated,&quot; seems that the reference center has been removed but not calculated and stored!&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1575 :     addCenter(reference,reference_center);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">       1575 :   reference_center=calculateCenter(reference,this-&gt;align);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">       1575 :   reference_center_is_calculated=true;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       1575 :   if(remove_center) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1570 :     removeCenter(reference,reference_center);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1570 :     reference_center_is_removed=true;</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   } else {</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          5 :     reference_center_is_removed=false;</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   }</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1575 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 : std::vector&lt;double&gt; RMSD::getAlign() {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   return align;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : ///</a>
+<a name="150"><span class="lineNum">     150 </span>            : /// here the weigth for normalized weighths are normalized and set</a>
+<a name="151"><span class="lineNum">     151 </span>            : ///</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1575 : void RMSD::setDisplace(const std::vector&lt;double&gt; &amp; displace, bool normalize_weights) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       1575 :   unsigned n=reference.size();</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1575 :   plumed_massert(this-&gt;displace.size()==displace.size(),&quot;mismatch in dimension of align/displace arrays&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       1575 :   this-&gt;displace=displace;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       1575 :   if(normalize_weights) {</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     double w=0.0;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       3140 :     #pragma omp simd reduction(+:w)</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      39333 :     for(unsigned i=0; i&lt;n; i++) w+=this-&gt;displace[i];</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       1570 :     if(w&gt;epsilon) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1570 :       double inv=1.0/w;</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :       #pragma omp simd</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">      39333 :       for(unsigned i=0; i&lt;n; i++) this-&gt;displace[i]*=inv;</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :     } else {</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :       double inv=1.0/n;</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :       #pragma omp simd</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       for(unsigned i=0; i&lt;n; i++) this-&gt;displace[i]=inv;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span>            :   }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       1575 : }</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 : std::vector&lt;double&gt; RMSD::getDisplace() {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   return displace;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : }</a>
+<a name="174"><span class="lineNum">     174 </span>            : ///</a>
+<a name="175"><span class="lineNum">     175 </span>            : /// This is the main workhorse for rmsd that decides to use specific optimal alignment versions</a>
+<a name="176"><span class="lineNum">     176 </span>            : ///</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     332887 : double RMSD::calculate(const std::vector&lt;Vector&gt; &amp; positions,std::vector&lt;Vector&gt; &amp;derivatives, bool squared)const {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            :   double ret=0.;</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     332887 :   switch(alignmentMethod) {</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   case SIMPLE : {</a>
+<a name="183"><span class="lineNum">     183 </span>            :     //  do a simple alignment without rotation</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :     std::vector&lt;Vector&gt; displacement( derivatives.size() );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :     ret=simpleAlignment(align,displace,positions,reference,derivatives,displacement,squared);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     break;</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   } case OPTIMAL_FAST : {</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     // this is calling the fastest option:</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment&lt;false,true&gt;(align,displace,positions,reference,derivatives,squared);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment&lt;false,false&gt;(align,displace,positions,reference,derivatives,squared);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     break;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">     332887 :   } case OPTIMAL : {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     // this is the fast routine but in the &quot;safe&quot; mode, which gives less numerical error:</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     332887 :     if(align==displace) ret=optimalAlignment&lt;true,true&gt;(align,displace,positions,reference,derivatives,squared);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          1 :     else ret=optimalAlignment&lt;true,false&gt;(align,displace,positions,reference,derivatives,squared);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     break;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            :   }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">     332887 :   return ret;</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : /// convenience method for calculating the standard derivatives and the derivative of the rmsd respect to the reference position</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          1 : double RMSD::calc_DDistDRef( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;derivatives, std::vector&lt;Vector&gt;&amp; DDistDRef, const bool squared  ) {</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   double ret=0.;</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          1 :   switch(alignmentMethod) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     break;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_DDistDRef&lt;false,true&gt;(align,displace,positions,reference,derivatives,DDistDRef, squared);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_DDistDRef&lt;false,false&gt;(align,displace,positions,reference,derivatives,DDistDRef,squared);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :     break;</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          1 :   case OPTIMAL:</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 :     if(align==displace) ret=optimalAlignment_DDistDRef&lt;true,true&gt;(align,displace,positions,reference,derivatives,DDistDRef,squared);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          1 :     else                ret=optimalAlignment_DDistDRef&lt;true,false&gt;(align,displace,positions,reference,derivatives,DDistDRef,squared);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :     break;</a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          1 :   return ret;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : /// convenience method for calculating the standard derivatives and the derivative of the rmsd respect to the reference position without the matrix contribution</a>
+<a name="227"><span class="lineNum">     227 </span>            : /// as required by SOMA</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 : double RMSD::calc_SOMA( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;derivatives, std::vector&lt;Vector&gt;&amp; DDistDRef, const bool squared  ) {</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   double ret=0.;</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :   switch(alignmentMethod) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :     break;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_SOMA&lt;false,true&gt;(align,displace,positions,reference,derivatives,DDistDRef, squared);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_SOMA&lt;false,false&gt;(align,displace,positions,reference,derivatives,DDistDRef,squared);</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     break;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 :   case OPTIMAL:</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_SOMA&lt;true,true&gt;(align,displace,positions,reference,derivatives,DDistDRef,squared);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_SOMA&lt;true,false&gt;(align,displace,positions,reference,derivatives,DDistDRef,squared);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :     break;</a>
+<a name="242"><span class="lineNum">     242 </span>            :   }</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   return ret;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 : double RMSD::calc_DDistDRef_Rot_DRotDPos( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;derivatives, std::vector&lt;Vector&gt;&amp; DDistDRef, Tensor &amp; Rot, Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos, const bool squared  ) {</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   double ret=0.;</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   switch(alignmentMethod) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span>            :     break;</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_DDistDRef_Rot_DRotDPos&lt;false,true&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos,  squared);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_DDistDRef_Rot_DRotDPos&lt;false,false&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, squared);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :     break;</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 :   case OPTIMAL:</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_DDistDRef_Rot_DRotDPos&lt;true,true&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, squared);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_DDistDRef_Rot_DRotDPos&lt;true,false&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, squared);</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :     break;</a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :   return ret;</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 : double RMSD::calc_DDistDRef_Rot_DRotDPos_DRotDRef( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;derivatives, std::vector&lt;Vector&gt;&amp; DDistDRef, Tensor &amp; Rot, Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos,  Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDRef, const bool squared  ) {</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :   double ret=0.;</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :   switch(alignmentMethod) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     break;</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef&lt;false,true&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, DRotDRef,   squared);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef&lt;false,false&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, DRotDRef,  squared);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :     break;</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :   case OPTIMAL:</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef&lt;true,true&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, DRotDRef, squared);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef&lt;true,false&gt;(align,displace,positions,reference,derivatives,DDistDRef, Rot, DRotDPos, DRotDRef, squared);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     break;</a>
+<a name="279"><span class="lineNum">     279 </span>            :   }</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :   return ret;</span></a>
+<a name="281"><span class="lineNum">     281 </span>            : }</a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">       1092 : double RMSD::calc_Rot_DRotDRr01( const std::vector&lt;Vector&gt;&amp; positions, Tensor &amp; Rotation, std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; DRotDRr01, const bool squared) {</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   double ret=0.;</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">       1092 :   switch(alignmentMethod) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :     break;</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_Rot_DRotDRr01&lt;false,true&gt;(align,displace,positions,reference, Rotation, DRotDRr01,   squared);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_Rot_DRotDRr01&lt;false,false&gt;(align,displace,positions,reference, Rotation, DRotDRr01,  squared);</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :     break;</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       1092 :   case OPTIMAL:</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">       1092 :     if(align==displace) ret=optimalAlignment_Rot_DRotDRr01&lt;true,true&gt;(align,displace,positions,reference, Rotation, DRotDRr01, squared);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_Rot_DRotDRr01&lt;true,false&gt;(align,displace,positions,reference, Rotation, DRotDRr01, squared);</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :     break;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   }</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1092 :   return ret;</span></a>
+<a name="299"><span class="lineNum">     299 </span>            : }</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        672 : double RMSD::calc_Rot( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;derivatives, Tensor &amp; Rotation, const bool squared) {</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :   double ret=0.;</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        672 :   switch(alignmentMethod) {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     break;</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_Rot&lt;false,true&gt;(align,displace,positions,reference,derivatives, Rotation, squared);</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_Rot&lt;false,false&gt;(align,displace,positions,reference,derivatives, Rotation, squared);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     break;</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        672 :   case OPTIMAL:</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        672 :     if(align==displace) ret=optimalAlignment_Rot&lt;true,true&gt;(align,displace,positions,reference,derivatives, Rotation, squared);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_Rot&lt;true,false&gt;(align,displace,positions,reference,derivatives, Rotation, squared);</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :     break;</a>
+<a name="315"><span class="lineNum">     315 </span>            :   }</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        672 :   return ret;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : }</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">      45192 : double RMSD::calculateWithCloseStructure( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;derivatives, const Tensor &amp; rotationPosClose, const Tensor &amp; rotationRefClose, std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01, const bool squared) {</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   double ret=0.;</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">      45192 :   switch(alignmentMethod) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :     break;</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignmentWithCloseStructure&lt;false,true&gt;(align,displace,positions,reference,derivatives, rotationPosClose, rotationRefClose, drotationPosCloseDrr01, squared);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignmentWithCloseStructure&lt;false,false&gt;(align,displace,positions,reference,derivatives, rotationPosClose, rotationRefClose, drotationPosCloseDrr01, squared);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :     break;</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">      45192 :   case OPTIMAL:</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">      45192 :     if(align==displace) ret=optimalAlignmentWithCloseStructure&lt;true,true&gt;(align,displace,positions,reference,derivatives, rotationPosClose, rotationRefClose, drotationPosCloseDrr01, squared);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignmentWithCloseStructure&lt;true,false&gt;(align,displace,positions,reference,derivatives, rotationPosClose, rotationRefClose, drotationPosCloseDrr01, squared);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :     break;</a>
+<a name="333"><span class="lineNum">     333 </span>            :   }</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      45192 :   return ret;</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : }</a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">       4985 : double RMSD::calc_PCAelements( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, Tensor &amp; Rotation, Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,std::vector&lt;Vector&gt;  &amp; alignedpositions, std::vector&lt;Vector&gt; &amp; centeredpositions, std::vector&lt;Vector&gt; &amp;centeredreference, const bool&amp; squared  ) const {</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   double ret=0.;</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       4985 :   switch(alignmentMethod) {</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :     break;</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :     if(align==displace) ret=optimalAlignment_PCA&lt;false,true&gt;(align,displace,positions,reference, alignedpositions, centeredpositions,centeredreference,Rotation,DDistDPos,DRotDPos,squared);</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_PCA&lt;false,false&gt;(align,displace,positions,reference, alignedpositions, centeredpositions,centeredreference,Rotation,DDistDPos,DRotDPos,squared);</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :     break;</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">       4985 :   case OPTIMAL:</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">       4985 :     if(align==displace) ret=optimalAlignment_PCA&lt;true,true&gt;(align,displace,positions,reference, alignedpositions, centeredpositions,centeredreference,Rotation,DDistDPos,DRotDPos,squared);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :     else                ret=optimalAlignment_PCA&lt;true,false&gt;(align,displace,positions,reference, alignedpositions, centeredpositions,centeredreference,Rotation,DDistDPos,DRotDPos,squared);</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :     break;</a>
+<a name="351"><span class="lineNum">     351 </span>            :   }</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       4985 :   return ret;</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        210 : double RMSD::calc_FitElements( const std::vector&lt;Vector&gt;&amp; positions, Tensor &amp; Rotation, Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos, std::vector&lt;Vector&gt; &amp; centeredpositions, Vector &amp;center_positions, const bool&amp; squared  ) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   double ret=0.;</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        210 :   switch(alignmentMethod) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :   case SIMPLE:</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;derivative of the refreence frame not implemented for SIMPLE alignmentMethod \n&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :     break;</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 :   case OPTIMAL_FAST:</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :     if(align==displace)ret=optimalAlignment_Fit&lt;false,true&gt;(align,displace,positions,reference, Rotation,DRotDPos,centeredpositions,center_positions,squared);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :     else               ret=optimalAlignment_Fit&lt;false,false&gt;(align,displace,positions,reference, Rotation,DRotDPos,centeredpositions,center_positions,squared);</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :     break;</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">        210 :   case OPTIMAL:</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        210 :     if(align==displace)ret=optimalAlignment_Fit&lt;true,true&gt;(align,displace,positions,reference,Rotation,DRotDPos,centeredpositions,center_positions,squared);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         60 :     else               ret=optimalAlignment_Fit&lt;true,false&gt;(align,displace,positions,reference,Rotation,DRotDPos,centeredpositions,center_positions,squared);</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :     break;</a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        210 :   return ret;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : }</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        172 : double RMSD::simpleAlignment(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :                              const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="381"><span class="lineNum">     381 </span>            :                              const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="382"><span class="lineNum">     382 </span>            :                              const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="383"><span class="lineNum">     383 </span>            :                              std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="384"><span class="lineNum">     384 </span>            :                              std::vector&lt;Vector&gt;  &amp; displacement,</a>
+<a name="385"><span class="lineNum">     385 </span>            :                              bool squared)const {</a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            :   double dist(0);</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">        172 :   unsigned n=reference.size();</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : </a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        172 :   Vector apositions;</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">        172 :   Vector areference;</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">        172 :   Vector dpositions;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">        172 :   Vector dreference;</span></a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       3997 :   for(unsigned i=0; i&lt;n; i++) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       3825 :     double aw=align[i];</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">       3825 :     double dw=displace[i];</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       3825 :     apositions+=positions[i]*aw;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">       3825 :     areference+=reference[i]*aw;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       3825 :     dpositions+=positions[i]*dw;</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">       3825 :     dreference+=reference[i]*dw;</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :   }</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">        172 :   Vector shift=((apositions-areference)-(dpositions-dreference));</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       3997 :   for(unsigned i=0; i&lt;n; i++) {</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">       3825 :     displacement[i]=(positions[i]-apositions)-(reference[i]-areference);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">       3825 :     dist+=displace[i]*displacement[i].modulo2();</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">       3825 :     derivatives[i]=2*(displace[i]*displacement[i]+align[i]*shift);</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :   }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">        172 :   if(!squared) {</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :     // sqrt</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">        118 :     dist=std::sqrt(dist);</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :     ///// sqrt on derivatives</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">       3637 :     for(unsigned i=0; i&lt;n; i++) {derivatives[i]*=(0.5/dist);}</span></a>
+<a name="416"><span class="lineNum">     416 </span>            :   }</a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">        172 :   return dist;</span></a>
+<a name="418"><span class="lineNum">     418 </span>            : }</a>
+<a name="419"><span class="lineNum">     419 </span>            : </a>
+<a name="420"><span class="lineNum">     420 </span>            : // this below enable the standard case for rmsd where the rmsd is calculated and the derivative of rmsd respect to positions is retrieved</a>
+<a name="421"><span class="lineNum">     421 </span>            : // additionally this assumes that the com of the reference is already subtracted.</a>
+<a name="422"><span class="lineNum">     422 </span>            : #define OLDRMSD</a>
+<a name="423"><span class="lineNum">     423 </span>            : #ifdef OLDRMSD</a>
+<a name="424"><span class="lineNum">     424 </span>            : // notice that in the current implementation the safe argument only makes sense for</a>
+<a name="425"><span class="lineNum">     425 </span>            : // align==displace</a>
+<a name="426"><span class="lineNum">     426 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">     549034 : double RMSD::optimalAlignment(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :                               const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="429"><span class="lineNum">     429 </span>            :                               const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="430"><span class="lineNum">     430 </span>            :                               const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="431"><span class="lineNum">     431 </span>            :                               std::vector&lt;Vector&gt;  &amp; derivatives, bool squared)const {</a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">     549034 :   const unsigned n=reference.size();</span></a>
+<a name="433"><span class="lineNum">     433 </span>            : // This is the trace of positions*positions + reference*reference</a>
+<a name="434"><span class="lineNum">     434 </span>            :   double rr00(0);</a>
+<a name="435"><span class="lineNum">     435 </span>            :   double rr11(0);</a>
+<a name="436"><span class="lineNum">     436 </span>            : // This is positions*reference</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">     549034 :   Tensor rr01;</span></a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">     549034 :   derivatives.resize(n);</span></a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">     549034 :   Vector cpositions;</span></a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            : // first expensive loop: compute centers</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">   22365073 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">   21816039 :     double w=align[iat];</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">   21816039 :     cpositions+=positions[iat]*w;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   }</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            : // second expensive loop: compute second moments wrt centers</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">   22365073 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">   21816039 :     double w=align[iat];</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">   21816039 :     rr00+=dotProduct(positions[iat]-cpositions,positions[iat]-cpositions)*w;</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">   21813863 :     rr11+=dotProduct(reference[iat],reference[iat])*w;</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">   21816039 :     rr01+=Tensor(positions[iat]-cpositions,reference[iat])*w;</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :   }</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">     549034 :   Tensor4d m;</span></a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">     549034 :   m[0][0]=2.0*(-rr01[0][0]-rr01[1][1]-rr01[2][2]);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">     549034 :   m[1][1]=2.0*(-rr01[0][0]+rr01[1][1]+rr01[2][2]);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">     549034 :   m[2][2]=2.0*(+rr01[0][0]-rr01[1][1]+rr01[2][2]);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">     549034 :   m[3][3]=2.0*(+rr01[0][0]+rr01[1][1]-rr01[2][2]);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">     549034 :   m[0][1]=2.0*(-rr01[1][2]+rr01[2][1]);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">     549034 :   m[0][2]=2.0*(+rr01[0][2]-rr01[2][0]);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">     549034 :   m[0][3]=2.0*(-rr01[0][1]+rr01[1][0]);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">     549034 :   m[1][2]=2.0*(-rr01[0][1]-rr01[1][0]);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">     549034 :   m[1][3]=2.0*(-rr01[0][2]-rr01[2][0]);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">     549034 :   m[2][3]=2.0*(-rr01[1][2]-rr01[2][1]);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">     549034 :   m[1][0] = m[0][1];</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">     549034 :   m[2][0] = m[0][2];</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">     549034 :   m[2][1] = m[1][2];</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">     549034 :   m[3][0] = m[0][3];</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">     549034 :   m[3][1] = m[1][3];</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">     549034 :   m[3][2] = m[2][3];</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">   11529714 :   Tensor dm_drr01[4][4];</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :   if(!alEqDis) {</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        114 :     dm_drr01[0][0] = 2.0*Tensor(-1.0, 0.0, 0.0,  0.0,-1.0, 0.0,  0.0, 0.0,-1.0);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        114 :     dm_drr01[1][1] = 2.0*Tensor(-1.0, 0.0, 0.0,  0.0,+1.0, 0.0,  0.0, 0.0,+1.0);</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">        114 :     dm_drr01[2][2] = 2.0*Tensor(+1.0, 0.0, 0.0,  0.0,-1.0, 0.0,  0.0, 0.0,+1.0);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">        114 :     dm_drr01[3][3] = 2.0*Tensor(+1.0, 0.0, 0.0,  0.0,+1.0, 0.0,  0.0, 0.0,-1.0);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">        114 :     dm_drr01[0][1] = 2.0*Tensor( 0.0, 0.0, 0.0,  0.0, 0.0,-1.0,  0.0,+1.0, 0.0);</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">        114 :     dm_drr01[0][2] = 2.0*Tensor( 0.0, 0.0,+1.0,  0.0, 0.0, 0.0, -1.0, 0.0, 0.0);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        114 :     dm_drr01[0][3] = 2.0*Tensor( 0.0,-1.0, 0.0, +1.0, 0.0, 0.0,  0.0, 0.0, 0.0);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">        114 :     dm_drr01[1][2] = 2.0*Tensor( 0.0,-1.0, 0.0, -1.0, 0.0, 0.0,  0.0, 0.0, 0.0);</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">        114 :     dm_drr01[1][3] = 2.0*Tensor( 0.0, 0.0,-1.0,  0.0, 0.0, 0.0, -1.0, 0.0, 0.0);</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        114 :     dm_drr01[2][3] = 2.0*Tensor( 0.0, 0.0, 0.0,  0.0, 0.0,-1.0,  0.0,-1.0, 0.0);</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">        114 :     dm_drr01[1][0] = dm_drr01[0][1];</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">        114 :     dm_drr01[2][0] = dm_drr01[0][2];</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        114 :     dm_drr01[2][1] = dm_drr01[1][2];</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        114 :     dm_drr01[3][0] = dm_drr01[0][3];</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        114 :     dm_drr01[3][1] = dm_drr01[1][3];</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        114 :     dm_drr01[3][2] = dm_drr01[2][3];</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :   }</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            :   double dist=0.0;</a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">     549034 :   Vector4d q;</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">    2745170 :   Tensor dq_drr01[4];</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :   if(!alEqDis) {</a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        114 :     Vector4d eigenvals;</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        114 :     Tensor4d eigenvecs;</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">        114 :     diagMatSym(m, eigenvals, eigenvecs );</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :     dist=eigenvals[0]+rr00+rr11;</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">        114 :     q=Vector4d(eigenvecs[0][0],eigenvecs[0][1],eigenvecs[0][2],eigenvecs[0][3]);</span></a>
+<a name="506"><span class="lineNum">     506 </span>            :     double dq_dm[4][4][4];</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">       9690 :     for(unsigned i=0; i&lt;4; i++) for(unsigned j=0; j&lt;4; j++) for(unsigned k=0; k&lt;4; k++) {</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :           double tmp=0.0;</a>
+<a name="509"><span class="lineNum">     509 </span>            : // perturbation theory for matrix m</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">      29184 :           for(unsigned l=1; l&lt;4; l++) tmp+=eigenvecs[l][j]*eigenvecs[l][i]/(eigenvals[0]-eigenvals[l])*eigenvecs[0][k];</span></a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">       7296 :           dq_dm[i][j][k]=tmp;</span></a>
+<a name="512"><span class="lineNum">     512 </span>            :         }</a>
+<a name="513"><span class="lineNum">     513 </span>            : // propagation to _drr01</a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">        570 :     for(unsigned i=0; i&lt;4; i++) {</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">        456 :       Tensor tmp;</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">       9576 :       for(unsigned j=0; j&lt;4; j++) for(unsigned k=0; k&lt;4; k++) {</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">       7296 :           tmp+=dq_dm[i][j][k]*dm_drr01[j][k];</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :         }</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">        456 :       dq_drr01[i]=tmp;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :     }</a>
+<a name="521"><span class="lineNum">     521 </span>            :   } else {</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">     548920 :     VectorGeneric&lt;1&gt; eigenvals;</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">     548920 :     TensorGeneric&lt;1,4&gt; eigenvecs;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">     548920 :     diagMatSym(m, eigenvals, eigenvecs );</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">     548920 :     dist=eigenvals[0]+rr00+rr11;</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">     548920 :     q=Vector4d(eigenvecs[0][0],eigenvecs[0][1],eigenvecs[0][2],eigenvecs[0][3]);</span></a>
+<a name="527"><span class="lineNum">     527 </span>            :   }</a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : // This is the rotation matrix that brings reference to positions</a>
+<a name="531"><span class="lineNum">     531 </span>            : // i.e. matmul(rotation,reference[iat])+shift is fitted to positions[iat]</a>
+<a name="532"><span class="lineNum">     532 </span>            : </a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">     549034 :   Tensor rotation;</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">     549034 :   rotation[0][0]=q[0]*q[0]+q[1]*q[1]-q[2]*q[2]-q[3]*q[3];</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">     549034 :   rotation[1][1]=q[0]*q[0]-q[1]*q[1]+q[2]*q[2]-q[3]*q[3];</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">     549034 :   rotation[2][2]=q[0]*q[0]-q[1]*q[1]-q[2]*q[2]+q[3]*q[3];</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">     549034 :   rotation[0][1]=2*(+q[0]*q[3]+q[1]*q[2]);</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">     549034 :   rotation[0][2]=2*(-q[0]*q[2]+q[1]*q[3]);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">     549034 :   rotation[1][2]=2*(+q[0]*q[1]+q[2]*q[3]);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">     549034 :   rotation[1][0]=2*(-q[0]*q[3]+q[1]*q[2]);</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">     549034 :   rotation[2][0]=2*(+q[0]*q[2]+q[1]*q[3]);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">     549034 :   rotation[2][1]=2*(-q[0]*q[1]+q[2]*q[3]);</span></a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span>            : </a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">     549034 :   std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; drotation_drr01;</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :   if(!alEqDis) {</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">        114 :     drotation_drr01[0][0]=2*q[0]*dq_drr01[0]+2*q[1]*dq_drr01[1]-2*q[2]*dq_drr01[2]-2*q[3]*dq_drr01[3];</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        114 :     drotation_drr01[1][1]=2*q[0]*dq_drr01[0]-2*q[1]*dq_drr01[1]+2*q[2]*dq_drr01[2]-2*q[3]*dq_drr01[3];</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">        114 :     drotation_drr01[2][2]=2*q[0]*dq_drr01[0]-2*q[1]*dq_drr01[1]-2*q[2]*dq_drr01[2]+2*q[3]*dq_drr01[3];</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        114 :     drotation_drr01[0][1]=2*(+(q[0]*dq_drr01[3]+dq_drr01[0]*q[3])+(q[1]*dq_drr01[2]+dq_drr01[1]*q[2]));</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">        114 :     drotation_drr01[0][2]=2*(-(q[0]*dq_drr01[2]+dq_drr01[0]*q[2])+(q[1]*dq_drr01[3]+dq_drr01[1]*q[3]));</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">        114 :     drotation_drr01[1][2]=2*(+(q[0]*dq_drr01[1]+dq_drr01[0]*q[1])+(q[2]*dq_drr01[3]+dq_drr01[2]*q[3]));</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">        114 :     drotation_drr01[1][0]=2*(-(q[0]*dq_drr01[3]+dq_drr01[0]*q[3])+(q[1]*dq_drr01[2]+dq_drr01[1]*q[2]));</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">        114 :     drotation_drr01[2][0]=2*(+(q[0]*dq_drr01[2]+dq_drr01[0]*q[2])+(q[1]*dq_drr01[3]+dq_drr01[1]*q[3]));</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">        114 :     drotation_drr01[2][1]=2*(-(q[0]*dq_drr01[1]+dq_drr01[0]*q[1])+(q[2]*dq_drr01[3]+dq_drr01[2]*q[3]));</span></a>
+<a name="556"><span class="lineNum">     556 </span>            :   }</a>
+<a name="557"><span class="lineNum">     557 </span>            : </a>
+<a name="558"><span class="lineNum">     558 </span>            :   double prefactor=2.0;</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">     548920 :   if(!squared &amp;&amp; alEqDis) prefactor*=0.5/std::sqrt(dist);</span></a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span>            : // if &quot;safe&quot;, recompute dist here to a better accuracy</a>
+<a name="563"><span class="lineNum">     563 </span>            :   if(safe || !alEqDis) dist=0.0;</a>
+<a name="564"><span class="lineNum">     564 </span>            : </a>
+<a name="565"><span class="lineNum">     565 </span>            : // If safe is set to &quot;false&quot;, MSD is taken from the eigenvalue of the M matrix</a>
+<a name="566"><span class="lineNum">     566 </span>            : // If safe is set to &quot;true&quot;, MSD is recomputed from the rotational matrix</a>
+<a name="567"><span class="lineNum">     567 </span>            : // For some reason, this last approach leads to less numerical noise but adds an overhead</a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">     549034 :   Tensor ddist_drotation;</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">     549034 :   Vector ddist_dcpositions;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span>            : // third expensive loop: derivatives</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">   22365073 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">   21816039 :     Vector d(positions[iat]-cpositions - matmul(rotation,reference[iat]));</span></a>
+<a name="575"><span class="lineNum">     575 </span>            :     if(alEqDis) {</a>
+<a name="576"><span class="lineNum">     576 </span>            : // there is no need for derivatives of rotation and shift here as it is by construction zero</a>
+<a name="577"><span class="lineNum">     577 </span>            : // (similar to Hellman-Feynman forces)</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">   21813863 :       derivatives[iat]= prefactor*align[iat]*d;</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">    4952157 :       if(safe) dist+=align[iat]*modulo2(d);</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :     } else {</a>
+<a name="581"><span class="lineNum">     581 </span>            : // the case for align != displace is different, sob:</a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">       2176 :       dist+=displace[iat]*modulo2(d);</span></a>
+<a name="583"><span class="lineNum">     583 </span>            : // these are the derivatives assuming the roto-translation as frozen</a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">       2176 :       derivatives[iat]=2*displace[iat]*d;</span></a>
+<a name="585"><span class="lineNum">     585 </span>            : // here I accumulate derivatives wrt rotation matrix ..</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineCov">       2176 :       ddist_drotation+=-2*displace[iat]*extProduct(d,reference[iat]);</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : // .. and cpositions</a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">       2176 :       ddist_dcpositions+=-2*displace[iat]*d;</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :     }</a>
+<a name="590"><span class="lineNum">     590 </span>            :   }</a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            :   if(!alEqDis) {</a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">        114 :     Tensor ddist_drr01;</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">       1482 :     for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++) ddist_drr01+=ddist_drotation[i][j]*drotation_drr01[i][j];</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">       2290 :     for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="596"><span class="lineNum">     596 </span>            : // this is propagating to positions.</a>
+<a name="597"><span class="lineNum">     597 </span>            : // I am implicitly using the derivative of rr01 wrt positions here</a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">       2176 :       derivatives[iat]+=matmul(ddist_drr01,reference[iat])*align[iat];</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">       2176 :       derivatives[iat]+=ddist_dcpositions*align[iat];</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :     }</a>
+<a name="601"><span class="lineNum">     601 </span>            :   }</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">     549034 :   if(!squared) {</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">      74171 :     dist=std::sqrt(dist);</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :     if(!alEqDis) {</a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        114 :       double xx=0.5/dist;</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">       2290 :       for(unsigned iat=0; iat&lt;n; iat++) derivatives[iat]*=xx;</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :     }</a>
+<a name="608"><span class="lineNum">     608 </span>            :   }</a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">     549034 :   return dist;</span></a>
+<a name="611"><span class="lineNum">     611 </span>            : }</a>
+<a name="612"><span class="lineNum">     612 </span>            : #else</a>
+<a name="613"><span class="lineNum">     613 </span>            : /// note that this method is intended to be repeatedly invoked</a>
+<a name="614"><span class="lineNum">     614 </span>            : /// when the reference does already have the center subtracted</a>
+<a name="615"><span class="lineNum">     615 </span>            : /// but the position has not calculated center and not subtracted</a>
+<a name="616"><span class="lineNum">     616 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="617"><span class="lineNum">     617 </span>            : double RMSD::optimalAlignment(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="618"><span class="lineNum">     618 </span>            :                               const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="619"><span class="lineNum">     619 </span>            :                               const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="620"><span class="lineNum">     620 </span>            :                               const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="621"><span class="lineNum">     621 </span>            :                               std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="622"><span class="lineNum">     622 </span>            :                               bool squared) const {</a>
+<a name="623"><span class="lineNum">     623 </span>            :   //std::cerr&lt;&lt;&quot;setting up the core data \n&quot;;</a>
+<a name="624"><span class="lineNum">     624 </span>            :   RMSDCoreData cd(align,displace,positions,reference);</a>
+<a name="625"><span class="lineNum">     625 </span>            : </a>
+<a name="626"><span class="lineNum">     626 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="627"><span class="lineNum">     627 </span>            :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</a>
+<a name="628"><span class="lineNum">     628 </span>            :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</a>
+<a name="629"><span class="lineNum">     629 </span>            :   else {cd.calcPositionsCenter();};</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</a>
+<a name="632"><span class="lineNum">     632 </span>            :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</a>
+<a name="633"><span class="lineNum">     633 </span>            :   else {cd.setReferenceCenter(reference_center);}</a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="636"><span class="lineNum">     636 </span>            :   cd.doCoreCalc(safe,alEqDis);</a>
+<a name="637"><span class="lineNum">     637 </span>            :   // make the core calc distance</a>
+<a name="638"><span class="lineNum">     638 </span>            :   double dist=cd.getDistance(squared);</a>
+<a name="639"><span class="lineNum">     639 </span>            : //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="640"><span class="lineNum">     640 </span>            :   derivatives=cd.getDDistanceDPositions();</a>
+<a name="641"><span class="lineNum">     641 </span>            :   return dist;</a>
+<a name="642"><span class="lineNum">     642 </span>            : }</a>
+<a name="643"><span class="lineNum">     643 </span>            : #endif</a>
+<a name="644"><span class="lineNum">     644 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">          1 : double RMSD::optimalAlignment_DDistDRef(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="646"><span class="lineNum">     646 </span>            :                                         const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="647"><span class="lineNum">     647 </span>            :                                         const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="648"><span class="lineNum">     648 </span>            :                                         const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="649"><span class="lineNum">     649 </span>            :                                         std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="650"><span class="lineNum">     650 </span>            :                                         std::vector&lt;Vector&gt; &amp; ddistdref,</a>
+<a name="651"><span class="lineNum">     651 </span>            :                                         bool squared) const {</a>
+<a name="652"><span class="lineNum">     652 </span>            :   //initialize the data into the structure</a>
+<a name="653"><span class="lineNum">     653 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">          1 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="656"><span class="lineNum">     656 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">          1 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">          1 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">          1 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">          1 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">          1 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">          1 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="664"><span class="lineNum">     664 </span>            : </a>
+<a name="665"><span class="lineNum">     665 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">          1 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :   // make the core calc distance</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">          1 :   double dist=cd.getDistance(squared);</span></a>
+<a name="669"><span class="lineNum">     669 </span>            : //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">          1 :   derivatives=cd.getDDistanceDPositions();</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">          2 :   ddistdref=cd.getDDistanceDReference();</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">          1 :   return dist;</span></a>
+<a name="673"><span class="lineNum">     673 </span>            : }</a>
+<a name="674"><span class="lineNum">     674 </span>            : </a>
+<a name="675"><span class="lineNum">     675 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineNoCov">          0 : double RMSD::optimalAlignment_SOMA(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="677"><span class="lineNum">     677 </span>            :                                    const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="678"><span class="lineNum">     678 </span>            :                                    const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="679"><span class="lineNum">     679 </span>            :                                    const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="680"><span class="lineNum">     680 </span>            :                                    std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="681"><span class="lineNum">     681 </span>            :                                    std::vector&lt;Vector&gt; &amp; ddistdref,</a>
+<a name="682"><span class="lineNum">     682 </span>            :                                    bool squared) const {</a>
+<a name="683"><span class="lineNum">     683 </span>            :   //initialize the data into the structure</a>
+<a name="684"><span class="lineNum">     684 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="687"><span class="lineNum">     687 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="691"><span class="lineNum">     691 </span>            : </a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="695"><span class="lineNum">     695 </span>            : </a>
+<a name="696"><span class="lineNum">     696 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :   // make the core calc distance</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :   double dist=cd.getDistance(squared);</span></a>
+<a name="700"><span class="lineNum">     700 </span>            : //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :   derivatives=cd.getDDistanceDPositions();</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineNoCov">          0 :   ddistdref=cd.getDDistanceDReferenceSOMA();</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :   return dist;</span></a>
+<a name="704"><span class="lineNum">     704 </span>            : }</a>
+<a name="705"><span class="lineNum">     705 </span>            : </a>
+<a name="706"><span class="lineNum">     706 </span>            : </a>
+<a name="707"><span class="lineNum">     707 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 : double RMSD::optimalAlignment_DDistDRef_Rot_DRotDPos(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="709"><span class="lineNum">     709 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="710"><span class="lineNum">     710 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="711"><span class="lineNum">     711 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="712"><span class="lineNum">     712 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="713"><span class="lineNum">     713 </span>            :     std::vector&lt;Vector&gt; &amp; ddistdref,</a>
+<a name="714"><span class="lineNum">     714 </span>            :     Tensor &amp; Rotation,</a>
+<a name="715"><span class="lineNum">     715 </span>            :     Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos,</a>
+<a name="716"><span class="lineNum">     716 </span>            :     bool squared) const {</a>
+<a name="717"><span class="lineNum">     717 </span>            :   //initialize the data into the structure</a>
+<a name="718"><span class="lineNum">     718 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineNoCov">          0 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="721"><span class="lineNum">     721 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineNoCov">          0 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineNoCov">          0 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineNoCov">          0 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="729"><span class="lineNum">     729 </span>            : </a>
+<a name="730"><span class="lineNum">     730 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="732"><span class="lineNum">     732 </span>            :   // make the core calc distance</a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineNoCov">          0 :   double dist=cd.getDistance(squared);</span></a>
+<a name="734"><span class="lineNum">     734 </span>            : //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineNoCov">          0 :   derivatives=cd.getDDistanceDPositions();</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :   ddistdref=cd.getDDistanceDReference();</span></a>
+<a name="737"><span class="lineNum">     737 </span>            :   // get the rotation matrix</a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :   Rotation=cd.getRotationMatrixReferenceToPositions();</span></a>
+<a name="739"><span class="lineNum">     739 </span>            :   // get its derivative</a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :   DRotDPos=cd.getDRotationDPositions();</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 :   return dist;</span></a>
+<a name="742"><span class="lineNum">     742 </span>            : }</a>
+<a name="743"><span class="lineNum">     743 </span>            : </a>
+<a name="744"><span class="lineNum">     744 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 : double RMSD::optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="746"><span class="lineNum">     746 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="747"><span class="lineNum">     747 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="748"><span class="lineNum">     748 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="749"><span class="lineNum">     749 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="750"><span class="lineNum">     750 </span>            :     std::vector&lt;Vector&gt; &amp; ddistdref,</a>
+<a name="751"><span class="lineNum">     751 </span>            :     Tensor &amp; Rotation,</a>
+<a name="752"><span class="lineNum">     752 </span>            :     Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos,</a>
+<a name="753"><span class="lineNum">     753 </span>            :     Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDRef,</a>
+<a name="754"><span class="lineNum">     754 </span>            :     bool squared) const {</a>
+<a name="755"><span class="lineNum">     755 </span>            :   //initialize the data into the structure</a>
+<a name="756"><span class="lineNum">     756 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineNoCov">          0 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="758"><span class="lineNum">     758 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="759"><span class="lineNum">     759 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineNoCov">          0 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineNoCov">          0 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineNoCov">          0 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="763"><span class="lineNum">     763 </span>            : </a>
+<a name="764"><span class="lineNum">     764 </span><span class="lineNoCov">          0 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineNoCov">          0 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineNoCov">          0 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="767"><span class="lineNum">     767 </span>            : </a>
+<a name="768"><span class="lineNum">     768 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineNoCov">          0 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :   // make the core calc distance</a>
+<a name="771"><span class="lineNum">     771 </span><span class="lineNoCov">          0 :   double dist=cd.getDistance(squared);</span></a>
+<a name="772"><span class="lineNum">     772 </span>            : //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineNoCov">          0 :   derivatives=cd.getDDistanceDPositions();</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineNoCov">          0 :   ddistdref=cd.getDDistanceDReference();</span></a>
+<a name="775"><span class="lineNum">     775 </span>            :   // get the rotation matrix</a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineNoCov">          0 :   Rotation=cd.getRotationMatrixReferenceToPositions();</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :   // get its derivative</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineNoCov">          0 :   DRotDPos=cd.getDRotationDPositions();</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineNoCov">          0 :   DRotDRef=cd.getDRotationDReference();</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineNoCov">          0 :   return dist;</span></a>
+<a name="781"><span class="lineNum">     781 </span>            : }</a>
+<a name="782"><span class="lineNum">     782 </span>            : </a>
+<a name="783"><span class="lineNum">     783 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">       1092 : double RMSD::optimalAlignment_Rot_DRotDRr01(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="785"><span class="lineNum">     785 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="786"><span class="lineNum">     786 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="787"><span class="lineNum">     787 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="788"><span class="lineNum">     788 </span>            :     Tensor &amp; Rotation,</a>
+<a name="789"><span class="lineNum">     789 </span>            :     std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; DRotDRr01,</a>
+<a name="790"><span class="lineNum">     790 </span>            :     bool squared) const {</a>
+<a name="791"><span class="lineNum">     791 </span>            :   //initialize the data into the structure</a>
+<a name="792"><span class="lineNum">     792 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">       1092 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="794"><span class="lineNum">     794 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">       1092 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">       1092 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">       1092 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span><span class="lineCov">       1092 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">       1092 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">       1092 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="802"><span class="lineNum">     802 </span>            : </a>
+<a name="803"><span class="lineNum">     803 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">       1092 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="805"><span class="lineNum">     805 </span>            :   // make the core calc distance</a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">       1092 :   double dist=cd.getDistance(squared);</span></a>
+<a name="807"><span class="lineNum">     807 </span>            :   // get the rotation matrix</a>
+<a name="808"><span class="lineNum">     808 </span><span class="lineCov">       1092 :   Rotation=cd.getRotationMatrixReferenceToPositions();</span></a>
+<a name="809"><span class="lineNum">     809 </span>            :   //get detivative w.r.t. rr01</a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">       1092 :   DRotDRr01=cd.getDRotationDRr01();</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">       1092 :   return dist;</span></a>
+<a name="812"><span class="lineNum">     812 </span>            : }</a>
+<a name="813"><span class="lineNum">     813 </span>            : </a>
+<a name="814"><span class="lineNum">     814 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="815"><span class="lineNum">     815 </span><span class="lineCov">        672 : double RMSD::optimalAlignment_Rot(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="816"><span class="lineNum">     816 </span>            :                                   const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="817"><span class="lineNum">     817 </span>            :                                   const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="818"><span class="lineNum">     818 </span>            :                                   const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="819"><span class="lineNum">     819 </span>            :                                   std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="820"><span class="lineNum">     820 </span>            :                                   Tensor &amp; Rotation,</a>
+<a name="821"><span class="lineNum">     821 </span>            :                                   bool squared) const {</a>
+<a name="822"><span class="lineNum">     822 </span>            :   //initialize the data into the structure</a>
+<a name="823"><span class="lineNum">     823 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        672 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">        672 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">        672 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">        672 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="829"><span class="lineNum">     829 </span>            : </a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">        672 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">        672 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="832"><span class="lineNum">     832 </span><span class="lineCov">        672 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">        672 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :   // make the core calc distance</a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">        672 :   double dist=cd.getDistance(squared);</span></a>
+<a name="838"><span class="lineNum">     838 </span>            :   //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">        672 :   derivatives=cd.getDDistanceDPositions();</span></a>
+<a name="840"><span class="lineNum">     840 </span>            :   // get the rotation matrix</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">        672 :   Rotation=cd.getRotationMatrixReferenceToPositions();</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">        672 :   return dist;</span></a>
+<a name="843"><span class="lineNum">     843 </span>            : }</a>
+<a name="844"><span class="lineNum">     844 </span>            : </a>
+<a name="845"><span class="lineNum">     845 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">      45192 : double RMSD::optimalAlignmentWithCloseStructure(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="848"><span class="lineNum">     848 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="849"><span class="lineNum">     849 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="850"><span class="lineNum">     850 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="851"><span class="lineNum">     851 </span>            :     const Tensor &amp; rotationPosClose,</a>
+<a name="852"><span class="lineNum">     852 </span>            :     const Tensor &amp; rotationRefClose,</a>
+<a name="853"><span class="lineNum">     853 </span>            :     std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01,</a>
+<a name="854"><span class="lineNum">     854 </span>            :     bool squared) const {</a>
+<a name="855"><span class="lineNum">     855 </span>            :   //initialize the data into the structure</a>
+<a name="856"><span class="lineNum">     856 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">      45192 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="858"><span class="lineNum">     858 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">      45192 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="860"><span class="lineNum">     860 </span><span class="lineCov">      45192 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">      45192 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="862"><span class="lineNum">     862 </span>            : </a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">      45192 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">      45192 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">      45192 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span>            :   // instead of diagonalization, approximate with saved rotation matrix</a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">      45192 :   cd.doCoreCalcWithCloseStructure(safe,alEqDis, rotationPosClose, rotationRefClose, drotationPosCloseDrr01);</span></a>
+<a name="869"><span class="lineNum">     869 </span>            :   // make the core calc distance</a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineCov">      45192 :   double dist=cd.getDistance(squared);</span></a>
+<a name="871"><span class="lineNum">     871 </span>            :   //  make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">      90384 :   derivatives=cd.getDDistanceDPositions();</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">      45192 :   return dist;</span></a>
+<a name="874"><span class="lineNum">     874 </span>            : }</a>
+<a name="875"><span class="lineNum">     875 </span>            : </a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">       4985 : double RMSD::optimalAlignment_PCA(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="879"><span class="lineNum">     879 </span>            :                                   const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="880"><span class="lineNum">     880 </span>            :                                   const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="881"><span class="lineNum">     881 </span>            :                                   const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="882"><span class="lineNum">     882 </span>            :                                   std::vector&lt;Vector&gt; &amp; alignedpositions,</a>
+<a name="883"><span class="lineNum">     883 </span>            :                                   std::vector&lt;Vector&gt; &amp; centeredpositions,</a>
+<a name="884"><span class="lineNum">     884 </span>            :                                   std::vector&lt;Vector&gt; &amp; centeredreference,</a>
+<a name="885"><span class="lineNum">     885 </span>            :                                   Tensor &amp; Rotation,</a>
+<a name="886"><span class="lineNum">     886 </span>            :                                   std::vector&lt;Vector&gt; &amp; DDistDPos,</a>
+<a name="887"><span class="lineNum">     887 </span>            :                                   Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,</a>
+<a name="888"><span class="lineNum">     888 </span>            :                                   bool squared) const {</a>
+<a name="889"><span class="lineNum">     889 </span>            :   //initialize the data into the structure</a>
+<a name="890"><span class="lineNum">     890 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">       4985 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="892"><span class="lineNum">     892 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">       4985 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">       4985 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">       4985 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="896"><span class="lineNum">     896 </span>            : </a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">       4985 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">       4985 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">       4985 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="900"><span class="lineNum">     900 </span>            : </a>
+<a name="901"><span class="lineNum">     901 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">       4985 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="903"><span class="lineNum">     903 </span>            :   // make the core calc distance</a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">       4985 :   double dist=cd.getDistance(squared);</span></a>
+<a name="905"><span class="lineNum">     905 </span>            :   // make the derivatives by using pieces calculated in coreCalc (probably the best is just to copy the vector...)</a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">       4985 :   DDistDPos=cd.getDDistanceDPositions();</span></a>
+<a name="907"><span class="lineNum">     907 </span>            :   // get the rotation matrix</a>
+<a name="908"><span class="lineNum">     908 </span><span class="lineCov">       4985 :   Rotation=cd.getRotationMatrixPositionsToReference();</span></a>
+<a name="909"><span class="lineNum">     909 </span>            :   // get its derivative</a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineCov">       4985 :   DRotDPos=cd.getDRotationDPositions(true); // this gives back the inverse</span></a>
+<a name="911"><span class="lineNum">     911 </span>            :   // get aligned positions</a>
+<a name="912"><span class="lineNum">     912 </span><span class="lineCov">       4985 :   alignedpositions=cd.getAlignedPositionsToReference();</span></a>
+<a name="913"><span class="lineNum">     913 </span>            :   // get centered positions</a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">       4985 :   centeredpositions=cd.getCenteredPositions();</span></a>
+<a name="915"><span class="lineNum">     915 </span>            :   // get centered reference</a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">       9970 :   centeredreference=cd.getCenteredReference();</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">       4985 :   return dist;</span></a>
+<a name="918"><span class="lineNum">     918 </span>            : }</a>
+<a name="919"><span class="lineNum">     919 </span>            : </a>
+<a name="920"><span class="lineNum">     920 </span>            : </a>
+<a name="921"><span class="lineNum">     921 </span>            : template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">        210 : double RMSD::optimalAlignment_Fit(const  std::vector&lt;double&gt;  &amp; align,</span></a>
+<a name="923"><span class="lineNum">     923 </span>            :                                   const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="924"><span class="lineNum">     924 </span>            :                                   const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="925"><span class="lineNum">     925 </span>            :                                   const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="926"><span class="lineNum">     926 </span>            :                                   Tensor &amp; Rotation,</a>
+<a name="927"><span class="lineNum">     927 </span>            :                                   Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,</a>
+<a name="928"><span class="lineNum">     928 </span>            :                                   std::vector&lt;Vector&gt; &amp; centeredpositions,</a>
+<a name="929"><span class="lineNum">     929 </span>            :                                   Vector &amp; center_positions,</a>
+<a name="930"><span class="lineNum">     930 </span>            :                                   bool squared) {</a>
+<a name="931"><span class="lineNum">     931 </span>            :   //initialize the data into the structure</a>
+<a name="932"><span class="lineNum">     932 </span>            :   // typically the positions do not have the com neither calculated nor subtracted. This layer takes care of this business</a>
+<a name="933"><span class="lineNum">     933 </span><span class="lineCov">        210 :   RMSDCoreData cd(align,displace,positions,reference);</span></a>
+<a name="934"><span class="lineNum">     934 </span>            :   // transfer the settings for the center to let the CoreCalc deal with it</a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">        210 :   cd.setPositionsCenterIsRemoved(positions_center_is_removed);</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">        210 :   if(positions_center_is_calculated) {cd.setPositionsCenter(positions_center);}</span></a>
+<a name="937"><span class="lineNum">     937 </span><span class="lineCov">        210 :   else {cd.calcPositionsCenter();};</span></a>
+<a name="938"><span class="lineNum">     938 </span>            : </a>
+<a name="939"><span class="lineNum">     939 </span><span class="lineCov">        210 :   cd.setReferenceCenterIsRemoved(reference_center_is_removed);</span></a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">        210 :   if(!reference_center_is_calculated) {cd.calcReferenceCenter();}</span></a>
+<a name="941"><span class="lineNum">     941 </span><span class="lineCov">        210 :   else {cd.setReferenceCenter(reference_center);}</span></a>
+<a name="942"><span class="lineNum">     942 </span>            : </a>
+<a name="943"><span class="lineNum">     943 </span>            :   // Perform the diagonalization and all the needed stuff</a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineCov">        210 :   cd.doCoreCalc(safe,alEqDis);</span></a>
+<a name="945"><span class="lineNum">     945 </span>            :   // make the core calc distance</a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineCov">        210 :   double dist=cd.getDistance(squared);</span></a>
+<a name="947"><span class="lineNum">     947 </span>            :   // get the rotation matrix</a>
+<a name="948"><span class="lineNum">     948 </span><span class="lineCov">        210 :   Rotation=cd.getRotationMatrixPositionsToReference();</span></a>
+<a name="949"><span class="lineNum">     949 </span>            :   // get its derivative</a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineCov">        210 :   DRotDPos=cd.getDRotationDPositions(true); // this gives back the inverse</span></a>
+<a name="951"><span class="lineNum">     951 </span>            :   // get centered positions</a>
+<a name="952"><span class="lineNum">     952 </span><span class="lineCov">        210 :   centeredpositions=cd.getCenteredPositions();</span></a>
+<a name="953"><span class="lineNum">     953 </span>            :   // get center</a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">        210 :   center_positions=cd.getPositionsCenter();</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">        210 :   return dist;</span></a>
+<a name="956"><span class="lineNum">     956 </span>            : }</a>
+<a name="957"><span class="lineNum">     957 </span>            : </a>
+<a name="958"><span class="lineNum">     958 </span>            : </a>
+<a name="959"><span class="lineNum">     959 </span>            : </a>
+<a name="960"><span class="lineNum">     960 </span>            : </a>
+<a name="961"><span class="lineNum">     961 </span>            : </a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span>            : /// This calculates the elements needed by the quaternion to calculate everything that is needed</a>
+<a name="964"><span class="lineNum">     964 </span>            : /// additional calls retrieve different components</a>
+<a name="965"><span class="lineNum">     965 </span>            : /// note that this considers that the centers of both reference and positions are already setted</a>
+<a name="966"><span class="lineNum">     966 </span>            : /// but automatically should properly account for non removed components: if not removed then it</a>
+<a name="967"><span class="lineNum">     967 </span>            : /// removes prior to calculation of the alignment</a>
+<a name="968"><span class="lineNum">     968 </span><span class="lineCov">       6960 : void RMSDCoreData::doCoreCalc(bool safe,bool alEqDis, bool only_rotation) {</span></a>
+<a name="969"><span class="lineNum">     969 </span>            : </a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">       6960 :   retrieve_only_rotation=only_rotation;</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">       6960 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="972"><span class="lineNum">     972 </span>            : </a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">       6960 :   plumed_massert(creference_is_calculated,&quot;the center of the reference frame must be already provided at this stage&quot;);</span></a>
+<a name="974"><span class="lineNum">     974 </span><span class="lineCov">       6960 :   plumed_massert(cpositions_is_calculated,&quot;the center of the positions frame must be already provided at this stage&quot;);</span></a>
+<a name="975"><span class="lineNum">     975 </span>            : </a>
+<a name="976"><span class="lineNum">     976 </span>            : // This is the trace of positions*positions + reference*reference</a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">       6960 :   rr00=0.;</span></a>
+<a name="978"><span class="lineNum">     978 </span><span class="lineCov">       6960 :   rr11=0.;</span></a>
+<a name="979"><span class="lineNum">     979 </span>            : // This is positions*reference</a>
+<a name="980"><span class="lineNum">     980 </span><span class="lineCov">       6960 :   Tensor rr01;</span></a>
+<a name="981"><span class="lineNum">     981 </span>            : // center of mass managing: must subtract the center from the position or not?</a>
+<a name="982"><span class="lineNum">     982 </span><span class="lineCov">       6960 :   Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;</span></a>
+<a name="983"><span class="lineNum">     983 </span><span class="lineCov">       6960 :   Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;</span></a>
+<a name="984"><span class="lineNum">     984 </span>            : // second expensive loop: compute second moments wrt centers</a>
+<a name="985"><span class="lineNum">     985 </span><span class="lineCov">     588912 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="986"><span class="lineNum">     986 </span><span class="lineCov">     581952 :     double w=align[iat];</span></a>
+<a name="987"><span class="lineNum">     987 </span><span class="lineCov">     581952 :     rr00+=dotProduct(positions[iat]-cp,positions[iat]-cp)*w;</span></a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">     581952 :     rr11+=dotProduct(reference[iat]-cr,reference[iat]-cr)*w;</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">     581952 :     rr01+=Tensor(positions[iat]-cp,reference[iat]-cr)*w;</span></a>
+<a name="990"><span class="lineNum">     990 </span>            :   }</a>
+<a name="991"><span class="lineNum">     991 </span>            : </a>
+<a name="992"><span class="lineNum">     992 </span>            : // the quaternion matrix: this is internal</a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">       6960 :   Tensor4d m;</span></a>
+<a name="994"><span class="lineNum">     994 </span>            : </a>
+<a name="995"><span class="lineNum">     995 </span><span class="lineCov">       6960 :   m[0][0]=2.0*(-rr01[0][0]-rr01[1][1]-rr01[2][2]);</span></a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">       6960 :   m[1][1]=2.0*(-rr01[0][0]+rr01[1][1]+rr01[2][2]);</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">       6960 :   m[2][2]=2.0*(+rr01[0][0]-rr01[1][1]+rr01[2][2]);</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">       6960 :   m[3][3]=2.0*(+rr01[0][0]+rr01[1][1]-rr01[2][2]);</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">       6960 :   m[0][1]=2.0*(-rr01[1][2]+rr01[2][1]);</span></a>
+<a name="1000"><span class="lineNum">    1000 </span><span class="lineCov">       6960 :   m[0][2]=2.0*(+rr01[0][2]-rr01[2][0]);</span></a>
+<a name="1001"><span class="lineNum">    1001 </span><span class="lineCov">       6960 :   m[0][3]=2.0*(-rr01[0][1]+rr01[1][0]);</span></a>
+<a name="1002"><span class="lineNum">    1002 </span><span class="lineCov">       6960 :   m[1][2]=2.0*(-rr01[0][1]-rr01[1][0]);</span></a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">       6960 :   m[1][3]=2.0*(-rr01[0][2]-rr01[2][0]);</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">       6960 :   m[2][3]=2.0*(-rr01[1][2]-rr01[2][1]);</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">       6960 :   m[1][0] = m[0][1];</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineCov">       6960 :   m[2][0] = m[0][2];</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">       6960 :   m[2][1] = m[1][2];</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineCov">       6960 :   m[3][0] = m[0][3];</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">       6960 :   m[3][1] = m[1][3];</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">       6960 :   m[3][2] = m[2][3];</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            : </a>
+<a name="1012"><span class="lineNum">    1012 </span>            : </a>
+<a name="1013"><span class="lineNum">    1013 </span><span class="lineCov">     146160 :   Tensor dm_drr01[4][4];</span></a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">       6960 :   if(!alEqDis or !retrieve_only_rotation) {</span></a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineCov">       6960 :     dm_drr01[0][0] = 2.0*Tensor(-1.0, 0.0, 0.0,  0.0,-1.0, 0.0,  0.0, 0.0,-1.0);</span></a>
+<a name="1016"><span class="lineNum">    1016 </span><span class="lineCov">       6960 :     dm_drr01[1][1] = 2.0*Tensor(-1.0, 0.0, 0.0,  0.0,+1.0, 0.0,  0.0, 0.0,+1.0);</span></a>
+<a name="1017"><span class="lineNum">    1017 </span><span class="lineCov">       6960 :     dm_drr01[2][2] = 2.0*Tensor(+1.0, 0.0, 0.0,  0.0,-1.0, 0.0,  0.0, 0.0,+1.0);</span></a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineCov">       6960 :     dm_drr01[3][3] = 2.0*Tensor(+1.0, 0.0, 0.0,  0.0,+1.0, 0.0,  0.0, 0.0,-1.0);</span></a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">       6960 :     dm_drr01[0][1] = 2.0*Tensor( 0.0, 0.0, 0.0,  0.0, 0.0,-1.0,  0.0,+1.0, 0.0);</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">       6960 :     dm_drr01[0][2] = 2.0*Tensor( 0.0, 0.0,+1.0,  0.0, 0.0, 0.0, -1.0, 0.0, 0.0);</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">       6960 :     dm_drr01[0][3] = 2.0*Tensor( 0.0,-1.0, 0.0, +1.0, 0.0, 0.0,  0.0, 0.0, 0.0);</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">       6960 :     dm_drr01[1][2] = 2.0*Tensor( 0.0,-1.0, 0.0, -1.0, 0.0, 0.0,  0.0, 0.0, 0.0);</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineCov">       6960 :     dm_drr01[1][3] = 2.0*Tensor( 0.0, 0.0,-1.0,  0.0, 0.0, 0.0, -1.0, 0.0, 0.0);</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineCov">       6960 :     dm_drr01[2][3] = 2.0*Tensor( 0.0, 0.0, 0.0,  0.0, 0.0,-1.0,  0.0,-1.0, 0.0);</span></a>
+<a name="1025"><span class="lineNum">    1025 </span><span class="lineCov">       6960 :     dm_drr01[1][0] = dm_drr01[0][1];</span></a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">       6960 :     dm_drr01[2][0] = dm_drr01[0][2];</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineCov">       6960 :     dm_drr01[2][1] = dm_drr01[1][2];</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineCov">       6960 :     dm_drr01[3][0] = dm_drr01[0][3];</span></a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineCov">       6960 :     dm_drr01[3][1] = dm_drr01[1][3];</span></a>
+<a name="1030"><span class="lineNum">    1030 </span><span class="lineCov">       6960 :     dm_drr01[3][2] = dm_drr01[2][3];</span></a>
+<a name="1031"><span class="lineNum">    1031 </span>            :   }</a>
+<a name="1032"><span class="lineNum">    1032 </span>            : </a>
+<a name="1033"><span class="lineNum">    1033 </span>            : </a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">       6960 :   Vector4d q;</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            : </a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineCov">      34800 :   Tensor dq_drr01[4];</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">       6960 :   if(!alEqDis or !only_rotation) {</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">       6960 :     diagMatSym(m, eigenvals, eigenvecs );</span></a>
+<a name="1039"><span class="lineNum">    1039 </span><span class="lineCov">       6960 :     q=Vector4d(eigenvecs[0][0],eigenvecs[0][1],eigenvecs[0][2],eigenvecs[0][3]);</span></a>
+<a name="1040"><span class="lineNum">    1040 </span>            :     double dq_dm[4][4][4];</a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">     591600 :     for(unsigned i=0; i&lt;4; i++) for(unsigned j=0; j&lt;4; j++) for(unsigned k=0; k&lt;4; k++) {</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            :           double tmp=0.0;</a>
+<a name="1043"><span class="lineNum">    1043 </span>            : // perturbation theory for matrix m</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">    1781760 :           for(unsigned l=1; l&lt;4; l++) tmp+=eigenvecs[l][j]*eigenvecs[l][i]/(eigenvals[0]-eigenvals[l])*eigenvecs[0][k];</span></a>
+<a name="1045"><span class="lineNum">    1045 </span><span class="lineCov">     445440 :           dq_dm[i][j][k]=tmp;</span></a>
+<a name="1046"><span class="lineNum">    1046 </span>            :         }</a>
+<a name="1047"><span class="lineNum">    1047 </span>            : // propagation to _drr01</a>
+<a name="1048"><span class="lineNum">    1048 </span><span class="lineCov">      34800 :     for(unsigned i=0; i&lt;4; i++) {</span></a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">      27840 :       Tensor tmp;</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">     584640 :       for(unsigned j=0; j&lt;4; j++) for(unsigned k=0; k&lt;4; k++) {</span></a>
+<a name="1051"><span class="lineNum">    1051 </span><span class="lineCov">     445440 :           tmp+=dq_dm[i][j][k]*dm_drr01[j][k];</span></a>
+<a name="1052"><span class="lineNum">    1052 </span>            :         }</a>
+<a name="1053"><span class="lineNum">    1053 </span><span class="lineCov">      27840 :       dq_drr01[i]=tmp;</span></a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     }</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   } else {</a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineNoCov">          0 :     TensorGeneric&lt;1,4&gt; here_eigenvecs;</span></a>
+<a name="1057"><span class="lineNum">    1057 </span><span class="lineNoCov">          0 :     VectorGeneric&lt;1&gt; here_eigenvals;</span></a>
+<a name="1058"><span class="lineNum">    1058 </span><span class="lineNoCov">          0 :     diagMatSym(m, here_eigenvals, here_eigenvecs );</span></a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;4; i++) eigenvecs[0][i]=here_eigenvecs[0][i];</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineNoCov">          0 :     eigenvals[0]=here_eigenvals[0];</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineNoCov">          0 :     q=Vector4d(eigenvecs[0][0],eigenvecs[0][1],eigenvecs[0][2],eigenvecs[0][3]);</span></a>
+<a name="1062"><span class="lineNum">    1062 </span>            :   }</a>
+<a name="1063"><span class="lineNum">    1063 </span>            : </a>
+<a name="1064"><span class="lineNum">    1064 </span>            : // This is the rotation matrix that brings reference to positions</a>
+<a name="1065"><span class="lineNum">    1065 </span>            : // i.e. matmul(rotation,reference[iat])+shift is fitted to positions[iat]</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : </a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">       6960 :   rotation[0][0]=q[0]*q[0]+q[1]*q[1]-q[2]*q[2]-q[3]*q[3];</span></a>
+<a name="1068"><span class="lineNum">    1068 </span><span class="lineCov">       6960 :   rotation[1][1]=q[0]*q[0]-q[1]*q[1]+q[2]*q[2]-q[3]*q[3];</span></a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">       6960 :   rotation[2][2]=q[0]*q[0]-q[1]*q[1]-q[2]*q[2]+q[3]*q[3];</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">       6960 :   rotation[0][1]=2*(+q[0]*q[3]+q[1]*q[2]);</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">       6960 :   rotation[0][2]=2*(-q[0]*q[2]+q[1]*q[3]);</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">       6960 :   rotation[1][2]=2*(+q[0]*q[1]+q[2]*q[3]);</span></a>
+<a name="1073"><span class="lineNum">    1073 </span><span class="lineCov">       6960 :   rotation[1][0]=2*(-q[0]*q[3]+q[1]*q[2]);</span></a>
+<a name="1074"><span class="lineNum">    1074 </span><span class="lineCov">       6960 :   rotation[2][0]=2*(+q[0]*q[2]+q[1]*q[3]);</span></a>
+<a name="1075"><span class="lineNum">    1075 </span><span class="lineCov">       6960 :   rotation[2][1]=2*(-q[0]*q[1]+q[2]*q[3]);</span></a>
+<a name="1076"><span class="lineNum">    1076 </span>            : </a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">       6960 :   if(!alEqDis or !only_rotation) {</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineCov">       6960 :     drotation_drr01[0][0]=2*q[0]*dq_drr01[0]+2*q[1]*dq_drr01[1]-2*q[2]*dq_drr01[2]-2*q[3]*dq_drr01[3];</span></a>
+<a name="1080"><span class="lineNum">    1080 </span><span class="lineCov">       6960 :     drotation_drr01[1][1]=2*q[0]*dq_drr01[0]-2*q[1]*dq_drr01[1]+2*q[2]*dq_drr01[2]-2*q[3]*dq_drr01[3];</span></a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">       6960 :     drotation_drr01[2][2]=2*q[0]*dq_drr01[0]-2*q[1]*dq_drr01[1]-2*q[2]*dq_drr01[2]+2*q[3]*dq_drr01[3];</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">       6960 :     drotation_drr01[0][1]=2*(+(q[0]*dq_drr01[3]+dq_drr01[0]*q[3])+(q[1]*dq_drr01[2]+dq_drr01[1]*q[2]));</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">       6960 :     drotation_drr01[0][2]=2*(-(q[0]*dq_drr01[2]+dq_drr01[0]*q[2])+(q[1]*dq_drr01[3]+dq_drr01[1]*q[3]));</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">       6960 :     drotation_drr01[1][2]=2*(+(q[0]*dq_drr01[1]+dq_drr01[0]*q[1])+(q[2]*dq_drr01[3]+dq_drr01[2]*q[3]));</span></a>
+<a name="1085"><span class="lineNum">    1085 </span><span class="lineCov">       6960 :     drotation_drr01[1][0]=2*(-(q[0]*dq_drr01[3]+dq_drr01[0]*q[3])+(q[1]*dq_drr01[2]+dq_drr01[1]*q[2]));</span></a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">       6960 :     drotation_drr01[2][0]=2*(+(q[0]*dq_drr01[2]+dq_drr01[0]*q[2])+(q[1]*dq_drr01[3]+dq_drr01[1]*q[3]));</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineCov">       6960 :     drotation_drr01[2][1]=2*(-(q[0]*dq_drr01[1]+dq_drr01[0]*q[1])+(q[2]*dq_drr01[3]+dq_drr01[2]*q[3]));</span></a>
+<a name="1088"><span class="lineNum">    1088 </span>            :   }</a>
+<a name="1089"><span class="lineNum">    1089 </span>            : </a>
+<a name="1090"><span class="lineNum">    1090 </span><span class="lineCov">       6960 :   d.resize(n);</span></a>
+<a name="1091"><span class="lineNum">    1091 </span>            : </a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   // calculate rotation matrix derivatives and components distances needed for components only when align!=displacement</a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">       6960 :   if(!alEqDis)ddist_drotation.zero();</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            :   // This pragma leads to incorrect results with INTEL compiler.</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   // Failures are seen in rt65-rmsd2, rt-close-structure, rt64-pca, and others.</a>
+<a name="1096"><span class="lineNum">    1096 </span>            :   // Not really clear why. GB</a>
+<a name="1097"><span class="lineNum">    1097 </span>            :   // #pragma omp simd</a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">     588912 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            :     // components differences: this is useful externally</a>
+<a name="1100"><span class="lineNum">    1100 </span><span class="lineCov">     581952 :     d[iat]=positions[iat]-cp - matmul(rotation,reference[iat]-cr);</span></a>
+<a name="1101"><span class="lineNum">    1101 </span>            :     //cerr&lt;&lt;&quot;D &quot;&lt;&lt;iat&lt;&lt;&quot; &quot;&lt;&lt;d[iat][0]&lt;&lt;&quot; &quot;&lt;&lt;d[iat][1]&lt;&lt;&quot; &quot;&lt;&lt;d[iat][2]&lt;&lt;&quot;\n&quot;;</a>
+<a name="1102"><span class="lineNum">    1102 </span>            :   }</a>
+<a name="1103"><span class="lineNum">    1103 </span>            :   // ddist_drotation if needed</a>
+<a name="1104"><span class="lineNum">    1104 </span><span class="lineCov">       6960 :   if(!alEqDis or !only_rotation) {</span></a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">     588912 :     for (unsigned iat=0; iat&lt;n; iat++)</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">     581952 :       ddist_drotation+=-2*displace[iat]*extProduct(d[iat],reference[iat]-cr);</span></a>
+<a name="1107"><span class="lineNum">    1107 </span>            : </a>
+<a name="1108"><span class="lineNum">    1108 </span><span class="lineCov">       6960 :     ddist_drr01.zero();</span></a>
+<a name="1109"><span class="lineNum">    1109 </span><span class="lineCov">      90480 :     for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++) ddist_drr01+=ddist_drotation[i][j]*drotation_drr01[i][j];</span></a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   }</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   // transfer this bools to the cd so that this settings will be reflected in the other calls</a>
+<a name="1112"><span class="lineNum">    1112 </span><span class="lineCov">       6960 :   this-&gt;alEqDis=alEqDis;</span></a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">       6960 :   this-&gt;safe=safe;</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">       6960 :   isInitialized=true;</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            : </a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">       6960 : }</span></a>
+<a name="1117"><span class="lineNum">    1117 </span>            : /// just retrieve the distance already calculated</a>
+<a name="1118"><span class="lineNum">    1118 </span><span class="lineCov">      52152 : double RMSDCoreData::getDistance( bool squared) {</span></a>
+<a name="1119"><span class="lineNum">    1119 </span>            : </a>
+<a name="1120"><span class="lineNum">    1120 </span><span class="lineCov">      52152 :   if(!isInitialized)plumed_merror(&quot;getDistance cannot calculate the distance without being initialized first by doCoreCalc &quot;);</span></a>
+<a name="1121"><span class="lineNum">    1121 </span>            : </a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   double localDist=0.0;</a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">      52152 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">      52152 :   if(safe || !alEqDis) localDist=0.0;</span></a>
+<a name="1125"><span class="lineNum">    1125 </span>            :   else</a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineNoCov">          0 :     localDist=eigenvals[0]+rr00+rr11;</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">     104304 :   #pragma omp simd reduction(+:localDist)</span></a>
+<a name="1128"><span class="lineNum">    1128 </span>            :   for(unsigned iat=0; iat&lt;n; iat++) {</a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">    1169448 :     if(alEqDis) {</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">    1168293 :       if(safe) localDist+=align[iat]*modulo2(d[iat]);</span></a>
+<a name="1131"><span class="lineNum">    1131 </span>            :     } else {</a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">       1155 :       localDist+=displace[iat]*modulo2(d[iat]);</span></a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     }</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :   }</a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">      52152 :   if(!squared) {</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">         85 :     dist=std::sqrt(localDist);</span></a>
+<a name="1137"><span class="lineNum">    1137 </span><span class="lineCov">         85 :     distanceIsMSD=false;</span></a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   } else {</a>
+<a name="1139"><span class="lineNum">    1139 </span><span class="lineCov">      52067 :     dist=localDist;</span></a>
+<a name="1140"><span class="lineNum">    1140 </span><span class="lineCov">      52067 :     distanceIsMSD=true;</span></a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   }</a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">      52152 :   hasDistance=true;</span></a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">      52152 :   return dist;</span></a>
+<a name="1144"><span class="lineNum">    1144 </span>            : }</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : </a>
+<a name="1146"><span class="lineNum">    1146 </span><span class="lineCov">      45192 : void RMSDCoreData::doCoreCalcWithCloseStructure(bool safe,bool alEqDis, const Tensor &amp; rotationPosClose, const Tensor &amp; rotationRefClose, std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01) {</span></a>
+<a name="1147"><span class="lineNum">    1147 </span>            : </a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">      45192 :   unsigned natoms = reference.size();</span></a>
+<a name="1149"><span class="lineNum">    1149 </span><span class="lineCov">      45192 :   Tensor ddist_drxy;</span></a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">      45192 :   ddist_drr01.zero();</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">      45192 :   d.resize(natoms);</span></a>
+<a name="1152"><span class="lineNum">    1152 </span>            : </a>
+<a name="1153"><span class="lineNum">    1153 </span>            :   // center of mass managing: must subtract the center from the position or not?</a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">      45192 :   Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;</span></a>
+<a name="1155"><span class="lineNum">    1155 </span><span class="lineCov">      45192 :   Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;</span></a>
+<a name="1156"><span class="lineNum">    1156 </span>            :   //distance = \sum_{n=0}^{N} w_n(x_n-cpos-R_{XY} R_{AY} a_n)^2</a>
+<a name="1157"><span class="lineNum">    1157 </span>            : </a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineCov">      45192 :   Tensor rotation = matmul(rotationPosClose, rotationRefClose);</span></a>
+<a name="1159"><span class="lineNum">    1159 </span>            : </a>
+<a name="1160"><span class="lineNum">    1160 </span>            :   // This pragma leads to incorrect results with INTEL compiler.</a>
+<a name="1161"><span class="lineNum">    1161 </span>            :   // Failures are seen in rt65-rmsd2, rt-close-structure, rt64-pca, and others.</a>
+<a name="1162"><span class="lineNum">    1162 </span>            :   // Not really clear why. GB</a>
+<a name="1163"><span class="lineNum">    1163 </span>            :   // #pragma omp simd</a>
+<a name="1164"><span class="lineNum">    1164 </span><span class="lineCov">     632688 :   for (unsigned iat=0; iat&lt;natoms; iat++) {</span></a>
+<a name="1165"><span class="lineNum">    1165 </span><span class="lineCov">     587496 :     d[iat] = positions[iat] - cp - matmul(rotation, reference[iat]-cr);</span></a>
+<a name="1166"><span class="lineNum">    1166 </span>            :   }</a>
+<a name="1167"><span class="lineNum">    1167 </span><span class="lineCov">      45192 :   if (!alEqDis) {</span></a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineNoCov">          0 :     for (unsigned iat=0; iat&lt;natoms; iat++) {</span></a>
+<a name="1169"><span class="lineNum">    1169 </span>            :       //dist = \sum w_i(x_i - cpos - R_xy * R_ay * a_i)</a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineNoCov">          0 :       ddist_drxy += -2*displace[iat]*extProduct(matmul(d[iat], rotationRefClose), reference[iat]-cr);</span></a>
+<a name="1171"><span class="lineNum">    1171 </span>            :     }</a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;3; i++)</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;3; j++)</span></a>
+<a name="1174"><span class="lineNum">    1174 </span><span class="lineNoCov">          0 :         ddist_drr01+=ddist_drxy[i][j]*drotationPosCloseDrr01[i][j];</span></a>
+<a name="1175"><span class="lineNum">    1175 </span>            :   }</a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">      45192 :   this-&gt;alEqDis=alEqDis;</span></a>
+<a name="1177"><span class="lineNum">    1177 </span><span class="lineCov">      45192 :   this-&gt;safe=safe;</span></a>
+<a name="1178"><span class="lineNum">    1178 </span><span class="lineCov">      45192 :   isInitialized=true;</span></a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineCov">      45192 : }</span></a>
+<a name="1180"><span class="lineNum">    1180 </span>            : </a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineCov">      50850 : std::vector&lt;Vector&gt; RMSDCoreData::getDDistanceDPositions() {</span></a>
+<a name="1182"><span class="lineNum">    1182 </span>            :   std::vector&lt;Vector&gt;  derivatives;</a>
+<a name="1183"><span class="lineNum">    1183 </span><span class="lineCov">      50850 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1184"><span class="lineNum">    1184 </span><span class="lineCov">      50850 :   Vector ddist_dcpositions;</span></a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">      50850 :   derivatives.resize(n);</span></a>
+<a name="1186"><span class="lineNum">    1186 </span>            :   double prefactor=1.0;</a>
+<a name="1187"><span class="lineNum">    1187 </span><span class="lineCov">      50850 :   if(!distanceIsMSD) prefactor*=0.5/dist;</span></a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">      50850 :   plumed_massert(!retrieve_only_rotation,&quot;You used  only_rotation=true in doCoreCalc therefore you cannot retrieve this information now&quot;);</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineCov">      50850 :   if(!hasDistance)plumed_merror(&quot;getDPositionsDerivatives needs to calculate the distance via getDistance first !&quot;);</span></a>
+<a name="1190"><span class="lineNum">    1190 </span><span class="lineCov">      50850 :   if(!isInitialized)plumed_merror(&quot;getDPositionsDerivatives needs to initialize the coreData first!&quot;);</span></a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineCov">      50850 :   Vector csum;</span></a>
+<a name="1192"><span class="lineNum">    1192 </span><span class="lineCov">     720102 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineCov">     669252 :     if(alEqDis) {</span></a>
+<a name="1194"><span class="lineNum">    1194 </span>            : // there is no need for derivatives of rotation and shift here as it is by construction zero</a>
+<a name="1195"><span class="lineNum">    1195 </span>            : // (similar to Hellman-Feynman forces)</a>
+<a name="1196"><span class="lineNum">    1196 </span><span class="lineCov">     668397 :       derivatives[iat]= 2*prefactor*align[iat]*d[iat];</span></a>
+<a name="1197"><span class="lineNum">    1197 </span>            :     } else {</a>
+<a name="1198"><span class="lineNum">    1198 </span>            : // these are the derivatives assuming the roto-translation as frozen</a>
+<a name="1199"><span class="lineNum">    1199 </span><span class="lineCov">        855 :       Vector tmp1=2*displace[iat]*d[iat];</span></a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineCov">        855 :       derivatives[iat]=tmp1;</span></a>
+<a name="1201"><span class="lineNum">    1201 </span>            : // derivative of cpositions</a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineCov">        855 :       ddist_dcpositions+=-tmp1;</span></a>
+<a name="1203"><span class="lineNum">    1203 </span>            :       // these needed for com corrections</a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineCov">        855 :       Vector tmp2=matmul(ddist_drr01,reference[iat]-creference)*align[iat];</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">        855 :       derivatives[iat]+=tmp2;</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">        855 :       csum+=tmp2;</span></a>
+<a name="1207"><span class="lineNum">    1207 </span>            :     }</a>
+<a name="1208"><span class="lineNum">    1208 </span>            :   }</a>
+<a name="1209"><span class="lineNum">    1209 </span>            : </a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">      50850 :   if(!alEqDis)</span></a>
+<a name="1211"><span class="lineNum">    1211 </span>            :     #pragma omp simd</a>
+<a name="1212"><span class="lineNum">    1212 </span><span class="lineCov">        855 :     for(unsigned iat=0; iat&lt;n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcpositions-csum)*align[iat]); }</span></a>
+<a name="1213"><span class="lineNum">    1213 </span>            : </a>
+<a name="1214"><span class="lineNum">    1214 </span><span class="lineCov">      50850 :   return derivatives;</span></a>
+<a name="1215"><span class="lineNum">    1215 </span>            : }</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span><span class="lineCov">          1 : std::vector&lt;Vector&gt;  RMSDCoreData::getDDistanceDReference() {</span></a>
+<a name="1218"><span class="lineNum">    1218 </span>            :   std::vector&lt;Vector&gt;  derivatives;</a>
+<a name="1219"><span class="lineNum">    1219 </span><span class="lineCov">          1 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">          1 :   Vector ddist_dcreference;</span></a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineCov">          1 :   derivatives.resize(n);</span></a>
+<a name="1222"><span class="lineNum">    1222 </span>            :   double prefactor=1.0;</a>
+<a name="1223"><span class="lineNum">    1223 </span><span class="lineCov">          1 :   if(!distanceIsMSD) prefactor*=0.5/dist;</span></a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">          1 :   Vector csum;</span></a>
+<a name="1225"><span class="lineNum">    1225 </span>            : </a>
+<a name="1226"><span class="lineNum">    1226 </span><span class="lineCov">          1 :   plumed_massert(!retrieve_only_rotation,&quot;You used  only_rotation=true in doCoreCalc therefore you cannot retrieve this information now&quot;);</span></a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">          1 :   if(!hasDistance)plumed_merror(&quot;getDDistanceDReference needs to calculate the distance via getDistance first !&quot;);</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">          1 :   if(!isInitialized)plumed_merror(&quot;getDDistanceDReference to initialize the coreData first!&quot;);</span></a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   // get the transpose rotation</a>
+<a name="1230"><span class="lineNum">    1230 </span><span class="lineCov">          1 :   Tensor t_rotation=rotation.transpose();</span></a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">          1 :   Tensor t_ddist_drr01=ddist_drr01.transpose();</span></a>
+<a name="1232"><span class="lineNum">    1232 </span>            : </a>
+<a name="1233"><span class="lineNum">    1233 </span>            : // third expensive loop: derivatives</a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">        856 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineCov">        855 :     if(alEqDis) {</span></a>
+<a name="1236"><span class="lineNum">    1236 </span>            : // there is no need for derivatives of rotation and shift here as it is by construction zero</a>
+<a name="1237"><span class="lineNum">    1237 </span>            : // (similar to Hellman-Feynman forces)</a>
+<a name="1238"><span class="lineNum">    1238 </span>            :       //TODO: check this derivative down here</a>
+<a name="1239"><span class="lineNum">    1239 </span><span class="lineNoCov">          0 :       derivatives[iat]= -2*prefactor*align[iat]*matmul(t_rotation,d[iat]);</span></a>
+<a name="1240"><span class="lineNum">    1240 </span>            :     } else {</a>
+<a name="1241"><span class="lineNum">    1241 </span>            : // these are the derivatives assuming the roto-translation as frozen</a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineCov">        855 :       Vector tmp1=2*displace[iat]*matmul(t_rotation,d[iat]);</span></a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">        855 :       derivatives[iat]= -tmp1;</span></a>
+<a name="1244"><span class="lineNum">    1244 </span>            : // derivative of cpositions</a>
+<a name="1245"><span class="lineNum">    1245 </span><span class="lineCov">        855 :       ddist_dcreference+=tmp1;</span></a>
+<a name="1246"><span class="lineNum">    1246 </span>            :       // these below are needed for com correction</a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">        855 :       Vector tmp2=matmul(t_ddist_drr01,positions[iat]-cpositions)*align[iat];</span></a>
+<a name="1248"><span class="lineNum">    1248 </span><span class="lineCov">        855 :       derivatives[iat]+=tmp2;</span></a>
+<a name="1249"><span class="lineNum">    1249 </span><span class="lineCov">        855 :       csum+=tmp2;</span></a>
+<a name="1250"><span class="lineNum">    1250 </span>            :     }</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :   }</a>
+<a name="1252"><span class="lineNum">    1252 </span>            : </a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineCov">          1 :   if(!alEqDis)</span></a>
+<a name="1254"><span class="lineNum">    1254 </span>            :     #pragma omp simd</a>
+<a name="1255"><span class="lineNum">    1255 </span><span class="lineCov">        855 :     for(unsigned iat=0; iat&lt;n; iat++) {derivatives[iat]= prefactor*(derivatives[iat]+(ddist_dcreference-csum)*align[iat]);}</span></a>
+<a name="1256"><span class="lineNum">    1256 </span>            : </a>
+<a name="1257"><span class="lineNum">    1257 </span><span class="lineCov">          1 :   return derivatives;</span></a>
+<a name="1258"><span class="lineNum">    1258 </span>            : }</a>
+<a name="1259"><span class="lineNum">    1259 </span>            : </a>
+<a name="1260"><span class="lineNum">    1260 </span>            : /// this version does not calculate the derivative of rotation matrix as needed for SOMA</a>
+<a name="1261"><span class="lineNum">    1261 </span><span class="lineNoCov">          0 : std::vector&lt;Vector&gt;  RMSDCoreData::getDDistanceDReferenceSOMA() {</span></a>
+<a name="1262"><span class="lineNum">    1262 </span>            :   std::vector&lt;Vector&gt;  derivatives;</a>
+<a name="1263"><span class="lineNum">    1263 </span><span class="lineNoCov">          0 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1264"><span class="lineNum">    1264 </span><span class="lineNoCov">          0 :   Vector ddist_dcreference;</span></a>
+<a name="1265"><span class="lineNum">    1265 </span><span class="lineNoCov">          0 :   derivatives.resize(n);</span></a>
+<a name="1266"><span class="lineNum">    1266 </span>            :   double prefactor=1.0;</a>
+<a name="1267"><span class="lineNum">    1267 </span><span class="lineNoCov">          0 :   if(!distanceIsMSD) prefactor*=0.5/dist;</span></a>
+<a name="1268"><span class="lineNum">    1268 </span><span class="lineNoCov">          0 :   Vector csum,tmp1,tmp2;</span></a>
+<a name="1269"><span class="lineNum">    1269 </span>            : </a>
+<a name="1270"><span class="lineNum">    1270 </span><span class="lineNoCov">          0 :   plumed_massert(!retrieve_only_rotation,&quot;You used  only_rotation=true in doCoreCalc therefore you cannot retrieve this information now&quot;);</span></a>
+<a name="1271"><span class="lineNum">    1271 </span><span class="lineNoCov">          0 :   if(!hasDistance)plumed_merror(&quot;getDDistanceDReference needs to calculate the distance via getDistance first !&quot;);</span></a>
+<a name="1272"><span class="lineNum">    1272 </span><span class="lineNoCov">          0 :   if(!isInitialized)plumed_merror(&quot;getDDistanceDReference to initialize the coreData first!&quot;);</span></a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   // get the transpose rotation</a>
+<a name="1274"><span class="lineNum">    1274 </span><span class="lineNoCov">          0 :   Tensor t_rotation=rotation.transpose();</span></a>
+<a name="1275"><span class="lineNum">    1275 </span>            : </a>
+<a name="1276"><span class="lineNum">    1276 </span>            : // third expensive loop: derivatives</a>
+<a name="1277"><span class="lineNum">    1277 </span><span class="lineNoCov">          0 :   for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1278"><span class="lineNum">    1278 </span><span class="lineNoCov">          0 :     if(alEqDis) {</span></a>
+<a name="1279"><span class="lineNum">    1279 </span>            : // there is no need for derivatives of rotation and shift here as it is by construction zero</a>
+<a name="1280"><span class="lineNum">    1280 </span>            : // (similar to Hellman-Feynman forces)</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :       //TODO: check this derivative down here</a>
+<a name="1282"><span class="lineNum">    1282 </span><span class="lineNoCov">          0 :       derivatives[iat]= -2*prefactor*align[iat]*matmul(t_rotation,d[iat]);</span></a>
+<a name="1283"><span class="lineNum">    1283 </span>            :     } else {</a>
+<a name="1284"><span class="lineNum">    1284 </span>            : // these are the derivatives assuming the roto-translation as frozen</a>
+<a name="1285"><span class="lineNum">    1285 </span><span class="lineNoCov">          0 :       tmp1=2*displace[iat]*matmul(t_rotation,d[iat]);</span></a>
+<a name="1286"><span class="lineNum">    1286 </span><span class="lineNoCov">          0 :       derivatives[iat]= -tmp1;</span></a>
+<a name="1287"><span class="lineNum">    1287 </span>            : // derivative of cpositions</a>
+<a name="1288"><span class="lineNum">    1288 </span><span class="lineNoCov">          0 :       ddist_dcreference+=tmp1;</span></a>
+<a name="1289"><span class="lineNum">    1289 </span>            :     }</a>
+<a name="1290"><span class="lineNum">    1290 </span>            :   }</a>
+<a name="1291"><span class="lineNum">    1291 </span>            : </a>
+<a name="1292"><span class="lineNum">    1292 </span><span class="lineNoCov">          0 :   if(!alEqDis) for(unsigned iat=0; iat&lt;n; iat++)derivatives[iat]=prefactor*(derivatives[iat]+ddist_dcreference*align[iat]);</span></a>
+<a name="1293"><span class="lineNum">    1293 </span>            : </a>
+<a name="1294"><span class="lineNum">    1294 </span><span class="lineNoCov">          0 :   return derivatives;</span></a>
+<a name="1295"><span class="lineNum">    1295 </span>            : }</a>
+<a name="1296"><span class="lineNum">    1296 </span>            : </a>
+<a name="1297"><span class="lineNum">    1297 </span>            : </a>
+<a name="1298"><span class="lineNum">    1298 </span>            : </a>
+<a name="1299"><span class="lineNum">    1299 </span>            : /*</a>
+<a name="1300"><span class="lineNum">    1300 </span>            : This below is the derivative of the rotation matrix that aligns the reference onto the positions</a>
+<a name="1301"><span class="lineNum">    1301 </span>            : respect to positions</a>
+<a name="1302"><span class="lineNum">    1302 </span>            : note that the this transformation overlap the  reference onto position</a>
+<a name="1303"><span class="lineNum">    1303 </span>            : if inverseTransform=true then aligns the positions onto reference</a>
+<a name="1304"><span class="lineNum">    1304 </span>            : */</a>
+<a name="1305"><span class="lineNum">    1305 </span><span class="lineCov">       5195 : Matrix&lt;std::vector&lt;Vector&gt; &gt;  RMSDCoreData::getDRotationDPositions( bool inverseTransform ) {</span></a>
+<a name="1306"><span class="lineNum">    1306 </span><span class="lineCov">       5195 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1307"><span class="lineNum">    1307 </span><span class="lineCov">       5195 :   plumed_massert(!retrieve_only_rotation,&quot;You used  only_rotation=true in doCoreCalc therefore you cannot retrieve this information now&quot;);</span></a>
+<a name="1308"><span class="lineNum">    1308 </span><span class="lineCov">       5195 :   if(!isInitialized)plumed_merror(&quot;getDRotationDPosition to initialize the coreData first!&quot;);</span></a>
+<a name="1309"><span class="lineNum">    1309 </span>            :   Matrix&lt;std::vector&lt;Vector&gt; &gt; DRotDPos=Matrix&lt;std::vector&lt;Vector&gt; &gt;(3,3);</a>
+<a name="1310"><span class="lineNum">    1310 </span>            :   // remember drotation_drr01 is Tensor drotation_drr01[3][3]</a>
+<a name="1311"><span class="lineNum">    1311 </span>            :   //           (3x3 rot) (3x3 components of rr01)</a>
+<a name="1312"><span class="lineNum">    1312 </span><span class="lineCov">       5195 :   std::vector&lt;Vector&gt; v(n);</span></a>
+<a name="1313"><span class="lineNum">    1313 </span><span class="lineCov">       5195 :   Vector csum;</span></a>
+<a name="1314"><span class="lineNum">    1314 </span>            :   // these below could probably be calculated in the main routine</a>
+<a name="1315"><span class="lineNum">    1315 </span><span class="lineCov">       5195 :   Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;</span></a>
+<a name="1316"><span class="lineNum">    1316 </span><span class="lineCov">       5195 :   Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;</span></a>
+<a name="1317"><span class="lineNum">    1317 </span><span class="lineCov">     563360 :   for(unsigned iat=0; iat&lt;n; iat++) csum+=(reference[iat]-cr)*align[iat];</span></a>
+<a name="1318"><span class="lineNum">    1318 </span><span class="lineCov">     563360 :   for(unsigned iat=0; iat&lt;n; iat++) v[iat]=(reference[iat]-cr-csum)*align[iat];</span></a>
+<a name="1319"><span class="lineNum">    1319 </span><span class="lineCov">      20780 :   for(unsigned a=0; a&lt;3; a++) {</span></a>
+<a name="1320"><span class="lineNum">    1320 </span><span class="lineCov">      62340 :     for(unsigned b=0; b&lt;3; b++) {</span></a>
+<a name="1321"><span class="lineNum">    1321 </span><span class="lineCov">      46755 :       if(inverseTransform) {</span></a>
+<a name="1322"><span class="lineNum">    1322 </span><span class="lineCov">      46755 :         DRotDPos[b][a].resize(n);</span></a>
+<a name="1323"><span class="lineNum">    1323 </span><span class="lineCov">    5070240 :         for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1324"><span class="lineNum">    1324 </span><span class="lineCov">    5023485 :           DRotDPos[b][a][iat]=matmul(drotation_drr01[a][b],v[iat]);</span></a>
+<a name="1325"><span class="lineNum">    1325 </span>            :         }</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :       } else {</a>
+<a name="1327"><span class="lineNum">    1327 </span><span class="lineNoCov">          0 :         DRotDPos[a][b].resize(n);</span></a>
+<a name="1328"><span class="lineNum">    1328 </span><span class="lineNoCov">          0 :         for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1329"><span class="lineNum">    1329 </span><span class="lineNoCov">          0 :           DRotDPos[a][b][iat]=matmul(drotation_drr01[a][b],v[iat]);</span></a>
+<a name="1330"><span class="lineNum">    1330 </span>            :         }</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :       }</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :     }</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :   }</a>
+<a name="1334"><span class="lineNum">    1334 </span><span class="lineCov">       5195 :   return DRotDPos;</span></a>
+<a name="1335"><span class="lineNum">    1335 </span>            : }</a>
+<a name="1336"><span class="lineNum">    1336 </span>            : </a>
+<a name="1337"><span class="lineNum">    1337 </span>            : /*</a>
+<a name="1338"><span class="lineNum">    1338 </span>            : This below is the derivative of the rotation matrix that aligns the reference onto the positions</a>
+<a name="1339"><span class="lineNum">    1339 </span>            : respect to reference</a>
+<a name="1340"><span class="lineNum">    1340 </span>            : note that the this transformation overlap the  reference onto position</a>
+<a name="1341"><span class="lineNum">    1341 </span>            : if inverseTransform=true then aligns the positions onto reference</a>
+<a name="1342"><span class="lineNum">    1342 </span>            : */</a>
+<a name="1343"><span class="lineNum">    1343 </span><span class="lineNoCov">          0 : Matrix&lt;std::vector&lt;Vector&gt; &gt;  RMSDCoreData::getDRotationDReference( bool inverseTransform ) {</span></a>
+<a name="1344"><span class="lineNum">    1344 </span><span class="lineNoCov">          0 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1345"><span class="lineNum">    1345 </span><span class="lineNoCov">          0 :   plumed_massert(!retrieve_only_rotation,&quot;You used  only_rotation=true in doCoreCalc therefore you cannot retrieve this information now&quot;);</span></a>
+<a name="1346"><span class="lineNum">    1346 </span><span class="lineNoCov">          0 :   if(!isInitialized)plumed_merror(&quot;getDRotationDPositions to initialize the coreData first!&quot;);</span></a>
+<a name="1347"><span class="lineNum">    1347 </span>            :   Matrix&lt;std::vector&lt;Vector&gt; &gt; DRotDRef=Matrix&lt;std::vector&lt;Vector&gt; &gt;(3,3);</a>
+<a name="1348"><span class="lineNum">    1348 </span>            :   // remember drotation_drr01 is Tensor drotation_drr01[3][3]</a>
+<a name="1349"><span class="lineNum">    1349 </span>            :   //           (3x3 rot) (3x3 components of rr01)</a>
+<a name="1350"><span class="lineNum">    1350 </span><span class="lineNoCov">          0 :   std::vector&lt;Vector&gt; v(n);</span></a>
+<a name="1351"><span class="lineNum">    1351 </span><span class="lineNoCov">          0 :   Vector csum;</span></a>
+<a name="1352"><span class="lineNum">    1352 </span>            :   // these below could probably be calculated in the main routine</a>
+<a name="1353"><span class="lineNum">    1353 </span><span class="lineNoCov">          0 :   Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;</span></a>
+<a name="1354"><span class="lineNum">    1354 </span><span class="lineNoCov">          0 :   Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;</span></a>
+<a name="1355"><span class="lineNum">    1355 </span><span class="lineNoCov">          0 :   for(unsigned iat=0; iat&lt;n; iat++) csum+=(positions[iat]-cp)*align[iat];</span></a>
+<a name="1356"><span class="lineNum">    1356 </span><span class="lineNoCov">          0 :   for(unsigned iat=0; iat&lt;n; iat++) v[iat]=(positions[iat]-cp-csum)*align[iat];</span></a>
+<a name="1357"><span class="lineNum">    1357 </span>            : </a>
+<a name="1358"><span class="lineNum">    1358 </span><span class="lineNoCov">          0 :   for(unsigned a=0; a&lt;3; a++) {</span></a>
+<a name="1359"><span class="lineNum">    1359 </span><span class="lineNoCov">          0 :     for(unsigned b=0; b&lt;3; b++) {</span></a>
+<a name="1360"><span class="lineNum">    1360 </span><span class="lineNoCov">          0 :       Tensor t_drotation_drr01=drotation_drr01[a][b].transpose();</span></a>
+<a name="1361"><span class="lineNum">    1361 </span><span class="lineNoCov">          0 :       if(inverseTransform) {</span></a>
+<a name="1362"><span class="lineNum">    1362 </span><span class="lineNoCov">          0 :         DRotDRef[b][a].resize(n);</span></a>
+<a name="1363"><span class="lineNum">    1363 </span><span class="lineNoCov">          0 :         for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1364"><span class="lineNum">    1364 </span><span class="lineNoCov">          0 :           DRotDRef[b][a][iat]=matmul(t_drotation_drr01,v[iat]);</span></a>
+<a name="1365"><span class="lineNum">    1365 </span>            :         }</a>
+<a name="1366"><span class="lineNum">    1366 </span>            :       } else {</a>
+<a name="1367"><span class="lineNum">    1367 </span><span class="lineNoCov">          0 :         DRotDRef[a][b].resize(n);</span></a>
+<a name="1368"><span class="lineNum">    1368 </span><span class="lineNoCov">          0 :         for(unsigned iat=0; iat&lt;n; iat++) {</span></a>
+<a name="1369"><span class="lineNum">    1369 </span><span class="lineNoCov">          0 :           DRotDRef[a][b][iat]=matmul(t_drotation_drr01,v[iat]);</span></a>
+<a name="1370"><span class="lineNum">    1370 </span>            :         }</a>
+<a name="1371"><span class="lineNum">    1371 </span>            :       }</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :     }</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :   }</a>
+<a name="1374"><span class="lineNum">    1374 </span><span class="lineNoCov">          0 :   return DRotDRef;</span></a>
+<a name="1375"><span class="lineNum">    1375 </span>            : }</a>
+<a name="1376"><span class="lineNum">    1376 </span>            : </a>
+<a name="1377"><span class="lineNum">    1377 </span>            : </a>
+<a name="1378"><span class="lineNum">    1378 </span><span class="lineNoCov">          0 : std::vector&lt;Vector&gt; RMSDCoreData::getAlignedReferenceToPositions() {</span></a>
+<a name="1379"><span class="lineNum">    1379 </span>            :   std::vector&lt;Vector&gt; alignedref;</a>
+<a name="1380"><span class="lineNum">    1380 </span><span class="lineNoCov">          0 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1381"><span class="lineNum">    1381 </span><span class="lineNoCov">          0 :   alignedref.resize(n);</span></a>
+<a name="1382"><span class="lineNum">    1382 </span><span class="lineNoCov">          0 :   if(!isInitialized)plumed_merror(&quot;getAlignedReferenceToPostions needs to initialize the coreData first!&quot;);</span></a>
+<a name="1383"><span class="lineNum">    1383 </span>            :   // avoid to calculate matrix element but use the sum of what you have</a>
+<a name="1384"><span class="lineNum">    1384 </span><span class="lineNoCov">          0 :   Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;</span></a>
+<a name="1385"><span class="lineNum">    1385 </span><span class="lineNoCov">          0 :   for(unsigned iat=0; iat&lt;n; iat++)alignedref[iat]=-d[iat]+positions[iat]-cp;</span></a>
+<a name="1386"><span class="lineNum">    1386 </span><span class="lineNoCov">          0 :   return alignedref;</span></a>
+<a name="1387"><span class="lineNum">    1387 </span>            : }</a>
+<a name="1388"><span class="lineNum">    1388 </span><span class="lineCov">       4985 : std::vector&lt;Vector&gt; RMSDCoreData::getAlignedPositionsToReference() {</span></a>
+<a name="1389"><span class="lineNum">    1389 </span>            :   std::vector&lt;Vector&gt; alignedpos;</a>
+<a name="1390"><span class="lineNum">    1390 </span><span class="lineCov">       4985 :   if(!isInitialized)plumed_merror(&quot;getAlignedPostionsToReference needs to initialize the coreData first!&quot;);</span></a>
+<a name="1391"><span class="lineNum">    1391 </span><span class="lineCov">       4985 :   const unsigned n=static_cast&lt;unsigned int&gt;(positions.size());</span></a>
+<a name="1392"><span class="lineNum">    1392 </span><span class="lineCov">       4985 :   alignedpos.resize(n);</span></a>
+<a name="1393"><span class="lineNum">    1393 </span><span class="lineCov">       4985 :   Vector cp; cp.zero(); if(!cpositions_is_removed)cp=cpositions;</span></a>
+<a name="1394"><span class="lineNum">    1394 </span>            :   // avoid to calculate matrix element but use the sum of what you have</a>
+<a name="1395"><span class="lineNum">    1395 </span><span class="lineCov">      77150 :   for(unsigned iat=0; iat&lt;n; iat++)alignedpos[iat]=matmul(rotation.transpose(),positions[iat]-cp);</span></a>
+<a name="1396"><span class="lineNum">    1396 </span><span class="lineCov">       4985 :   return alignedpos;</span></a>
+<a name="1397"><span class="lineNum">    1397 </span>            : }</a>
+<a name="1398"><span class="lineNum">    1398 </span>            : </a>
+<a name="1399"><span class="lineNum">    1399 </span>            : </a>
+<a name="1400"><span class="lineNum">    1400 </span><span class="lineCov">       5195 : std::vector&lt;Vector&gt; RMSDCoreData::getCenteredPositions() {</span></a>
+<a name="1401"><span class="lineNum">    1401 </span>            :   std::vector&lt;Vector&gt; centeredpos;</a>
+<a name="1402"><span class="lineNum">    1402 </span><span class="lineCov">       5195 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1403"><span class="lineNum">    1403 </span><span class="lineCov">       5195 :   centeredpos.resize(n);</span></a>
+<a name="1404"><span class="lineNum">    1404 </span><span class="lineCov">       5195 :   if(!isInitialized)plumed_merror(&quot;getCenteredPositions needs to initialize the coreData first!&quot;);</span></a>
+<a name="1405"><span class="lineNum">    1405 </span>            :   // avoid to calculate matrix element but use the sum of what you have</a>
+<a name="1406"><span class="lineNum">    1406 </span><span class="lineCov">     563360 :   for(unsigned iat=0; iat&lt;n; iat++)centeredpos[iat]=positions[iat]-cpositions;</span></a>
+<a name="1407"><span class="lineNum">    1407 </span><span class="lineCov">       5195 :   return centeredpos;</span></a>
+<a name="1408"><span class="lineNum">    1408 </span>            : }</a>
+<a name="1409"><span class="lineNum">    1409 </span>            : </a>
+<a name="1410"><span class="lineNum">    1410 </span><span class="lineCov">       4985 : std::vector&lt;Vector&gt; RMSDCoreData::getCenteredReference() {</span></a>
+<a name="1411"><span class="lineNum">    1411 </span>            :   std::vector&lt;Vector&gt; centeredref;</a>
+<a name="1412"><span class="lineNum">    1412 </span><span class="lineCov">       4985 :   const unsigned n=static_cast&lt;unsigned int&gt;(reference.size());</span></a>
+<a name="1413"><span class="lineNum">    1413 </span><span class="lineCov">       4985 :   centeredref.resize(n);</span></a>
+<a name="1414"><span class="lineNum">    1414 </span><span class="lineCov">       4985 :   if(!isInitialized)plumed_merror(&quot;getCenteredReference needs to initialize the coreData first!&quot;);</span></a>
+<a name="1415"><span class="lineNum">    1415 </span>            :   // avoid to calculate matrix element but use the sum of what you have</a>
+<a name="1416"><span class="lineNum">    1416 </span><span class="lineCov">       4985 :   Vector cr; cr.zero(); if(!creference_is_removed)cr=creference;</span></a>
+<a name="1417"><span class="lineNum">    1417 </span><span class="lineCov">      77150 :   for(unsigned iat=0; iat&lt;n; iat++)centeredref[iat]=reference[iat]-cr;</span></a>
+<a name="1418"><span class="lineNum">    1418 </span><span class="lineCov">       4985 :   return centeredref;</span></a>
+<a name="1419"><span class="lineNum">    1419 </span>            : }</a>
+<a name="1420"><span class="lineNum">    1420 </span>            : </a>
+<a name="1421"><span class="lineNum">    1421 </span>            : </a>
+<a name="1422"><span class="lineNum">    1422 </span><span class="lineCov">        210 : Vector RMSDCoreData::getPositionsCenter() {</span></a>
+<a name="1423"><span class="lineNum">    1423 </span><span class="lineCov">        210 :   if(!isInitialized)plumed_merror(&quot;getCenteredPositions needs to initialize the coreData first!&quot;);</span></a>
+<a name="1424"><span class="lineNum">    1424 </span><span class="lineCov">        210 :   return cpositions;</span></a>
+<a name="1425"><span class="lineNum">    1425 </span>            : }</a>
+<a name="1426"><span class="lineNum">    1426 </span>            : </a>
+<a name="1427"><span class="lineNum">    1427 </span><span class="lineNoCov">          0 : Vector RMSDCoreData::getReferenceCenter() {</span></a>
+<a name="1428"><span class="lineNum">    1428 </span><span class="lineNoCov">          0 :   if(!isInitialized)plumed_merror(&quot;getCenteredPositions needs to initialize the coreData first!&quot;);</span></a>
+<a name="1429"><span class="lineNum">    1429 </span><span class="lineNoCov">          0 :   return creference;</span></a>
+<a name="1430"><span class="lineNum">    1430 </span>            : }</a>
+<a name="1431"><span class="lineNum">    1431 </span>            : </a>
+<a name="1432"><span class="lineNum">    1432 </span><span class="lineCov">       1764 : Tensor RMSDCoreData::getRotationMatrixReferenceToPositions() {</span></a>
+<a name="1433"><span class="lineNum">    1433 </span><span class="lineCov">       1764 :   if(!isInitialized)plumed_merror(&quot;getRotationMatrixReferenceToPositions needs to initialize the coreData first!&quot;);</span></a>
+<a name="1434"><span class="lineNum">    1434 </span><span class="lineCov">       1764 :   return rotation;</span></a>
+<a name="1435"><span class="lineNum">    1435 </span>            : }</a>
+<a name="1436"><span class="lineNum">    1436 </span>            : </a>
+<a name="1437"><span class="lineNum">    1437 </span><span class="lineCov">       5195 : Tensor RMSDCoreData::getRotationMatrixPositionsToReference() {</span></a>
+<a name="1438"><span class="lineNum">    1438 </span><span class="lineCov">       5195 :   if(!isInitialized)plumed_merror(&quot;getRotationMatrixReferenceToPositions needs to initialize the coreData first!&quot;);</span></a>
+<a name="1439"><span class="lineNum">    1439 </span><span class="lineCov">       5195 :   return rotation.transpose();</span></a>
+<a name="1440"><span class="lineNum">    1440 </span>            : }</a>
+<a name="1441"><span class="lineNum">    1441 </span>            : </a>
+<a name="1442"><span class="lineNum">    1442 </span><span class="lineCov">       1092 : const std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp;  RMSDCoreData::getDRotationDRr01() const {</span></a>
+<a name="1443"><span class="lineNum">    1443 </span><span class="lineCov">       1092 :   if(!isInitialized)plumed_merror(&quot;getDRotationDRr01 needs to initialize the coreData first!&quot;);</span></a>
+<a name="1444"><span class="lineNum">    1444 </span><span class="lineCov">       1092 :   return drotation_drr01;</span></a>
+<a name="1445"><span class="lineNum">    1445 </span>            : }</a>
+<a name="1446"><span class="lineNum">    1446 </span>            : </a>
+<a name="1447"><span class="lineNum">    1447 </span>            : </a>
+<a name="1448"><span class="lineNum">    1448 </span>            : </a>
+<a name="1449"><span class="lineNum">    1449 </span>            : template double RMSD::optimalAlignment&lt;true,true&gt;(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives, bool squared)const;</a>
+<a name="1454"><span class="lineNum">    1454 </span>            : template double RMSD::optimalAlignment&lt;true,false&gt;(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="1456"><span class="lineNum">    1456 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives, bool squared)const;</a>
+<a name="1459"><span class="lineNum">    1459 </span>            : template double RMSD::optimalAlignment&lt;false,true&gt;(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="1460"><span class="lineNum">    1460 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives, bool squared)const;</a>
+<a name="1464"><span class="lineNum">    1464 </span>            : template double RMSD::optimalAlignment&lt;false,false&gt;(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="1467"><span class="lineNum">    1467 </span>            :     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :     std::vector&lt;Vector&gt;  &amp; derivatives, bool squared)const;</a>
+<a name="1469"><span class="lineNum">    1469 </span>            : </a>
+<a name="1470"><span class="lineNum">    1470 </span>            : </a>
+<a name="1471"><span class="lineNum">    1471 </span>            : </a>
+<a name="1472"><span class="lineNum">    1472 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RMSD.h.func-sort-c.html b/coverage/tools/RMSD.h.func-sort-c.html
new file mode 100644
index 0000000000..f1cc9614bb
--- /dev/null
+++ b/coverage/tools/RMSD.h.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RMSD.h<span style="font-size: 80%;"> (<a href="RMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RMSD.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#322">_ZN4PLMD12RMSDCoreData18setPositionsCenterENS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#317">_ZN4PLMD12RMSDCoreData19calcReferenceCenterEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#249">_ZN4PLMD4RMSD17getMatrixFromDRotERKNS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEERKjSB_</a></td>
+              <td class="coverFnHi">900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#81">_ZN4PLMD4RMSD15calculateCenterERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">1575</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#94">_ZN4PLMD4RMSD9addCenterERSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS3_</a></td>
+              <td class="coverFnHi">1575</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#89">_ZN4PLMD4RMSD12removeCenterERSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS3_</a></td>
+              <td class="coverFnHi">3145</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#323">_ZN4PLMD12RMSDCoreData18setReferenceCenterENS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">52152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#313">_ZN4PLMD12RMSDCoreData19calcPositionsCenterEv</a></td>
+              <td class="coverFnHi">52152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#306">_ZN4PLMD12RMSDCoreDataC2ERKSt6vectorIdSaIdEES5_RKS1_INS_13VectorGenericILj3EEESaIS7_EESB_</a></td>
+              <td class="coverFnHi">52152</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RMSD.h.func.html b/coverage/tools/RMSD.h.func.html
new file mode 100644
index 0000000000..c6b520e4a4
--- /dev/null
+++ b/coverage/tools/RMSD.h.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RMSD.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RMSD.h<span style="font-size: 80%;"> (<a href="RMSD.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="RMSD.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#322">_ZN4PLMD12RMSDCoreData18setPositionsCenterENS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#323">_ZN4PLMD12RMSDCoreData18setReferenceCenterENS_13VectorGenericILj3EEE</a></td>
+              <td class="coverFnHi">52152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#313">_ZN4PLMD12RMSDCoreData19calcPositionsCenterEv</a></td>
+              <td class="coverFnHi">52152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#317">_ZN4PLMD12RMSDCoreData19calcReferenceCenterEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#306">_ZN4PLMD12RMSDCoreDataC2ERKSt6vectorIdSaIdEES5_RKS1_INS_13VectorGenericILj3EEESaIS7_EESB_</a></td>
+              <td class="coverFnHi">52152</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#89">_ZN4PLMD4RMSD12removeCenterERSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS3_</a></td>
+              <td class="coverFnHi">3145</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#81">_ZN4PLMD4RMSD15calculateCenterERKSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS1_IdSaIdEE</a></td>
+              <td class="coverFnHi">1575</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#249">_ZN4PLMD4RMSD17getMatrixFromDRotERKNS_6MatrixISt6vectorINS_13VectorGenericILj3EEESaIS4_EEEERKjSB_</a></td>
+              <td class="coverFnHi">900</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RMSD.h.gcov.html#94">_ZN4PLMD4RMSD9addCenterERSt6vectorINS_13VectorGenericILj3EEESaIS3_EERKS3_</a></td>
+              <td class="coverFnHi">1575</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RMSD.h.gcov.html b/coverage/tools/RMSD.h.gcov.html
new file mode 100644
index 0000000000..23c8c193f4
--- /dev/null
+++ b/coverage/tools/RMSD.h.gcov.html
@@ -0,0 +1,450 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RMSD.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RMSD.h<span style="font-size: 80%;"> (source / <a href="RMSD.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_RMSD_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_RMSD_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Matrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;string&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;array&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class Log;</a>
+<a name="35"><span class="lineNum">      35 </span>            : class PDB;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : /** \ingroup TOOLBOX</a>
+<a name="38"><span class="lineNum">      38 </span>            : A class that implements RMSD calculations</a>
+<a name="39"><span class="lineNum">      39 </span>            : This is a class that implements the various infrastructure to calculate the</a>
+<a name="40"><span class="lineNum">      40 </span>            : RMSD or MSD respect a given frame. It can be done through an optimal alignment scheme</a>
+<a name="41"><span class="lineNum">      41 </span>            : as Kearsley or, more simply, by resetting the center of mass.</a>
+<a name="42"><span class="lineNum">      42 </span>            : This is the class that decides this. A very simple use is</a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &quot;tools/PDB.h&quot;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &quot;tools/RMSD.h&quot;</a>
+<a name="46"><span class="lineNum">      46 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="47"><span class="lineNum">      47 </span>            : using namespace PLMD;</a>
+<a name="48"><span class="lineNum">      48 </span>            : RMSD rmsd;</a>
+<a name="49"><span class="lineNum">      49 </span>            : PDB pdb;</a>
+<a name="50"><span class="lineNum">      50 </span>            : // get the pdb (see PDB documentation)</a>
+<a name="51"><span class="lineNum">      51 </span>            : pdb.read(&quot;file.pdb&quot;,true,1.0);</a>
+<a name="52"><span class="lineNum">      52 </span>            : string type;</a>
+<a name="53"><span class="lineNum">      53 </span>            : type.assign(&quot;OPTIMAL&quot;);</a>
+<a name="54"><span class="lineNum">      54 </span>            : // set the reference and the type</a>
+<a name="55"><span class="lineNum">      55 </span>            : rmsd.set(pdb,type);</a>
+<a name="56"><span class="lineNum">      56 </span>            : // this calculates the rmsd and the derivatives</a>
+<a name="57"><span class="lineNum">      57 </span>            : vector&lt;Vector&gt; derivs;</a>
+<a name="58"><span class="lineNum">      58 </span>            : double val;</a>
+<a name="59"><span class="lineNum">      59 </span>            : val=rmsd.calculate(getPositions(),derivs,true);</a>
+<a name="60"><span class="lineNum">      60 </span>            : \endverbatim</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : **/</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : class RMSD</a>
+<a name="65"><span class="lineNum">      65 </span>            : {</a>
+<a name="66"><span class="lineNum">      66 </span>            :   enum AlignmentMethod {SIMPLE, OPTIMAL, OPTIMAL_FAST};</a>
+<a name="67"><span class="lineNum">      67 </span>            :   AlignmentMethod alignmentMethod;</a>
+<a name="68"><span class="lineNum">      68 </span>            : // Reference coordinates</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;Vector&gt; reference;</a>
+<a name="70"><span class="lineNum">      70 </span>            : // Weights for alignment</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;double&gt; align;</a>
+<a name="72"><span class="lineNum">      72 </span>            : // Weights for deviation</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;double&gt; displace;</a>
+<a name="74"><span class="lineNum">      74 </span>            : // Center for reference and flag for its calculation</a>
+<a name="75"><span class="lineNum">      75 </span>            :   Vector reference_center;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   bool reference_center_is_calculated;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool reference_center_is_removed;</a>
+<a name="78"><span class="lineNum">      78 </span>            : // Center for running position (not used in principle but here to reflect reference/positio symmetry</a>
+<a name="79"><span class="lineNum">      79 </span>            :   Vector positions_center;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool positions_center_is_calculated;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   bool positions_center_is_removed;</a>
+<a name="82"><span class="lineNum">      82 </span>            : // calculates the center from the position provided</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1575 :   Vector calculateCenter(const std::vector&lt;Vector&gt; &amp;p,const std::vector&lt;double&gt; &amp;w) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       1575 :     plumed_massert(p.size()==w.size(),&quot;mismatch in dimension of position/align arrays while calculating the center&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       1575 :     unsigned n; n=p.size();</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       1575 :     Vector c; c.zero();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">      40933 :     for(unsigned i=0; i&lt;n; i++)c+=p[i]*w[i];</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1575 :     return c;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   };</a>
+<a name="90"><span class="lineNum">      90 </span>            : // removes the center for the position provided</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">       3145 :   void removeCenter(std::vector&lt;Vector&gt; &amp;p, const Vector &amp;c) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       3145 :     unsigned n; n=p.size();</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      81836 :     for(unsigned i=0; i&lt;n; i++)p[i]-=c;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       3145 :   };</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : // add center</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       1575 :   void addCenter(std::vector&lt;Vector&gt; &amp;p, const Vector &amp;c) {Vector cc=c*-1.; removeCenter(p,cc);};</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : public:</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Constructor</a>
+<a name="100"><span class="lineNum">     100 </span>            :   RMSD();</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// clear the structure</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void clear();</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// set reference, align and displace from input pdb structure: evtl remove com from the initial structure and normalize the input weights from the pdb</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void set(const PDB&amp;,const std::string &amp; mytype, bool remove_center=true, bool normalize_weights=true);</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// set align displace reference and type from input vectors</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void set(const std::vector&lt;double&gt; &amp; align, const std::vector&lt;double&gt; &amp; displace, const std::vector&lt;Vector&gt; &amp; reference,const std::string &amp; mytype, bool remove_center=true, bool normalize_weights=true );</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// set the type of alignment we are doing</a>
+<a name="108"><span class="lineNum">     108 </span>            :   void setType(const std::string &amp; mytype);</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// set reference coordinates, remove the com by using uniform weights</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void setReference(const std::vector&lt;Vector&gt; &amp; reference);</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;Vector&gt; getReference();</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// set weights and remove the center from reference with normalized weights. If the com has been removed, it resets to the new value</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void setAlign(const std::vector&lt;double&gt; &amp; align, bool normalize_weights=true, bool remove_center=true);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;double&gt; getAlign();</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// set align</a>
+<a name="116"><span class="lineNum">     116 </span>            :   void setDisplace(const std::vector&lt;double&gt; &amp; displace, bool normalize_weights=true);</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;double&gt; getDisplace();</a>
+<a name="118"><span class="lineNum">     118 </span>            : ///</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::string getMethod();</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// workhorses</a>
+<a name="121"><span class="lineNum">     121 </span>            :   double simpleAlignment(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="122"><span class="lineNum">     122 </span>            :                          const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="123"><span class="lineNum">     123 </span>            :                          const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="124"><span class="lineNum">     124 </span>            :                          const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="125"><span class="lineNum">     125 </span>            :                          std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="126"><span class="lineNum">     126 </span>            :                          std::vector&lt;Vector&gt;  &amp; displacement,</a>
+<a name="127"><span class="lineNum">     127 </span>            :                          bool squared=false)const;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   double optimalAlignment(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="130"><span class="lineNum">     130 </span>            :                           const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="131"><span class="lineNum">     131 </span>            :                           const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="132"><span class="lineNum">     132 </span>            :                           const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="133"><span class="lineNum">     133 </span>            :                           std::vector&lt;Vector&gt;  &amp; DDistDPos, bool squared=false)const;</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   template &lt;bool safe, bool alEqDis&gt;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   double optimalAlignmentWithCloseStructure(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="137"><span class="lineNum">     137 </span>            :       const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="138"><span class="lineNum">     138 </span>            :       const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="139"><span class="lineNum">     139 </span>            :       const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="140"><span class="lineNum">     140 </span>            :       std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="141"><span class="lineNum">     141 </span>            :       const Tensor &amp; rotationPosClose,</a>
+<a name="142"><span class="lineNum">     142 </span>            :       const Tensor &amp; rotationRefClose,</a>
+<a name="143"><span class="lineNum">     143 </span>            :       std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01,</a>
+<a name="144"><span class="lineNum">     144 </span>            :       bool squared=false)const;</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   template &lt;bool safe, bool alEqDis&gt;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   double optimalAlignment_Rot_DRotDRr01(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="148"><span class="lineNum">     148 </span>            :                                         const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="149"><span class="lineNum">     149 </span>            :                                         const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="150"><span class="lineNum">     150 </span>            :                                         const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="151"><span class="lineNum">     151 </span>            :                                         Tensor &amp; Rotation,</a>
+<a name="152"><span class="lineNum">     152 </span>            :                                         std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01,</a>
+<a name="153"><span class="lineNum">     153 </span>            :                                         bool squared=false)const;</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   template &lt;bool safe, bool alEqDis&gt;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   double optimalAlignment_Rot(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="157"><span class="lineNum">     157 </span>            :                               const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="158"><span class="lineNum">     158 </span>            :                               const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="159"><span class="lineNum">     159 </span>            :                               const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="160"><span class="lineNum">     160 </span>            :                               std::vector&lt;Vector&gt;  &amp; derivatives,</a>
+<a name="161"><span class="lineNum">     161 </span>            :                               Tensor &amp; Rotation,</a>
+<a name="162"><span class="lineNum">     162 </span>            :                               bool squared=false)const;</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   double optimalAlignment_DDistDRef(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="166"><span class="lineNum">     166 </span>            :                                     const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="167"><span class="lineNum">     167 </span>            :                                     const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="168"><span class="lineNum">     168 </span>            :                                     const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="169"><span class="lineNum">     169 </span>            :                                     std::vector&lt;Vector&gt;  &amp; DDistDPos,</a>
+<a name="170"><span class="lineNum">     170 </span>            :                                     std::vector&lt;Vector&gt; &amp;  DDistDRef,</a>
+<a name="171"><span class="lineNum">     171 </span>            :                                     bool squared=false) const;</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="174"><span class="lineNum">     174 </span>            :   double optimalAlignment_SOMA(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="175"><span class="lineNum">     175 </span>            :                                const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="176"><span class="lineNum">     176 </span>            :                                const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="177"><span class="lineNum">     177 </span>            :                                const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="178"><span class="lineNum">     178 </span>            :                                std::vector&lt;Vector&gt;  &amp; DDistDPos,</a>
+<a name="179"><span class="lineNum">     179 </span>            :                                std::vector&lt;Vector&gt; &amp;  DDistDRef,</a>
+<a name="180"><span class="lineNum">     180 </span>            :                                bool squared=false) const;</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   double optimalAlignment_DDistDRef_Rot_DRotDPos(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="184"><span class="lineNum">     184 </span>            :       const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="185"><span class="lineNum">     185 </span>            :       const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="186"><span class="lineNum">     186 </span>            :       const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="187"><span class="lineNum">     187 </span>            :       std::vector&lt;Vector&gt;  &amp; DDistDPos,</a>
+<a name="188"><span class="lineNum">     188 </span>            :       std::vector&lt;Vector&gt; &amp;  DDistDRef,</a>
+<a name="189"><span class="lineNum">     189 </span>            :       Tensor &amp; Rotation,</a>
+<a name="190"><span class="lineNum">     190 </span>            :       Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos,</a>
+<a name="191"><span class="lineNum">     191 </span>            :       bool squared=false) const;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   double optimalAlignment_DDistDRef_Rot_DRotDPos_DRotDRef(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="195"><span class="lineNum">     195 </span>            :       const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="196"><span class="lineNum">     196 </span>            :       const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="197"><span class="lineNum">     197 </span>            :       const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="198"><span class="lineNum">     198 </span>            :       std::vector&lt;Vector&gt;  &amp; DDistDPos,</a>
+<a name="199"><span class="lineNum">     199 </span>            :       std::vector&lt;Vector&gt; &amp;  DDistDRef,</a>
+<a name="200"><span class="lineNum">     200 </span>            :       Tensor &amp; Rotation,</a>
+<a name="201"><span class="lineNum">     201 </span>            :       Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos,</a>
+<a name="202"><span class="lineNum">     202 </span>            :       Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDRef,</a>
+<a name="203"><span class="lineNum">     203 </span>            :       bool squared=false) const;</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   double optimalAlignment_PCA(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="207"><span class="lineNum">     207 </span>            :                               const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="208"><span class="lineNum">     208 </span>            :                               const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="209"><span class="lineNum">     209 </span>            :                               const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="210"><span class="lineNum">     210 </span>            :                               std::vector&lt;Vector&gt; &amp; alignedpositions,</a>
+<a name="211"><span class="lineNum">     211 </span>            :                               std::vector&lt;Vector&gt; &amp; centeredpositions,</a>
+<a name="212"><span class="lineNum">     212 </span>            :                               std::vector&lt;Vector&gt; &amp; centeredreference,</a>
+<a name="213"><span class="lineNum">     213 </span>            :                               Tensor &amp; Rotation,</a>
+<a name="214"><span class="lineNum">     214 </span>            :                               std::vector&lt;Vector&gt; &amp; DDistDPos,</a>
+<a name="215"><span class="lineNum">     215 </span>            :                               Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,</a>
+<a name="216"><span class="lineNum">     216 </span>            :                               bool squared=false) const ;</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   template &lt;bool safe,bool alEqDis&gt;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   double optimalAlignment_Fit(const  std::vector&lt;double&gt;  &amp; align,</a>
+<a name="220"><span class="lineNum">     220 </span>            :                               const  std::vector&lt;double&gt;  &amp; displace,</a>
+<a name="221"><span class="lineNum">     221 </span>            :                               const std::vector&lt;Vector&gt; &amp; positions,</a>
+<a name="222"><span class="lineNum">     222 </span>            :                               const std::vector&lt;Vector&gt; &amp; reference,</a>
+<a name="223"><span class="lineNum">     223 </span>            :                               Tensor &amp; Rotation,</a>
+<a name="224"><span class="lineNum">     224 </span>            :                               Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,</a>
+<a name="225"><span class="lineNum">     225 </span>            :                               std::vector&lt;Vector&gt; &amp; centeredpositions,</a>
+<a name="226"><span class="lineNum">     226 </span>            :                               Vector &amp; center_positions,</a>
+<a name="227"><span class="lineNum">     227 </span>            :                               bool squared=false);</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : /// Compute rmsd: note that this is an intermediate layer which is kept in order to evtl expand with more alignment types/user options to be called while keeping the workhorses separated</a>
+<a name="231"><span class="lineNum">     231 </span>            :   double calculate(const std::vector&lt;Vector&gt; &amp; positions,std::vector&lt;Vector&gt; &amp;derivatives, bool squared=false)const;</a>
+<a name="232"><span class="lineNum">     232 </span>            : /// Other convenience methods:</a>
+<a name="233"><span class="lineNum">     233 </span>            : /// calculate the derivative of distance respect to position(DDistDPos) and reference (DDistDPos)</a>
+<a name="234"><span class="lineNum">     234 </span>            :   double calc_DDistDRef( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, std::vector&lt;Vector&gt;&amp; DDistDRef, const bool squared=false   );</a>
+<a name="235"><span class="lineNum">     235 </span>            : /// calculate the derivative for SOMA (i.e. derivative respect to reference frame without the matrix derivative)</a>
+<a name="236"><span class="lineNum">     236 </span>            :   double calc_SOMA( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, std::vector&lt;Vector&gt;&amp; DDistDRef, const bool squared=false   );</a>
+<a name="237"><span class="lineNum">     237 </span>            : ///</a>
+<a name="238"><span class="lineNum">     238 </span>            :   double calc_DDistDRef_Rot_DRotDPos( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, std::vector&lt;Vector&gt;&amp; DDistDRef, Tensor &amp; Rotation,Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos, const bool squared=false   );</a>
+<a name="239"><span class="lineNum">     239 </span>            :   double calc_DDistDRef_Rot_DRotDPos_DRotDRef( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, std::vector&lt;Vector&gt;&amp; DDistDRef, Tensor &amp; Rotation,Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDPos,Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp;DRotDRef, const bool squared=false   );</a>
+<a name="240"><span class="lineNum">     240 </span>            : /// convenience method to retrieve all the bits and pieces for PCA</a>
+<a name="241"><span class="lineNum">     241 </span>            :   double calc_PCAelements( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt; &amp;DDistDPos, Tensor &amp; Rotation, Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,std::vector&lt;Vector&gt;  &amp; alignedpositions, std::vector&lt;Vector&gt; &amp; centeredpositions, std::vector&lt;Vector&gt; &amp;centeredreference, const bool&amp; squared=false) const ;</a>
+<a name="242"><span class="lineNum">     242 </span>            : /// convenience method to retrieve all the bits and pieces needed by FitToTemplate</a>
+<a name="243"><span class="lineNum">     243 </span>            :   double calc_FitElements( const std::vector&lt;Vector&gt;&amp; pos, Tensor &amp; Rotation, Matrix&lt;std::vector&lt;Vector&gt; &gt; &amp; DRotDPos,std::vector&lt;Vector&gt; &amp; centeredpositions,Vector &amp; center_positions, const bool&amp; squared=false );</a>
+<a name="244"><span class="lineNum">     244 </span>            : ///calculate rotation matrix, derivative of rotation matrix w.r.t. positions, derivative of rotation matrix w.r.t. rr01</a>
+<a name="245"><span class="lineNum">     245 </span>            :   double calc_Rot_DRotDRr01( const std::vector&lt;Vector&gt;&amp; positions, Tensor &amp; Rotation, std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; DRotDRr01, const bool squared=false   );</a>
+<a name="246"><span class="lineNum">     246 </span>            : ///calculate rotation matrix, derivative of rotation matrix w.r.t. positions</a>
+<a name="247"><span class="lineNum">     247 </span>            :   double calc_Rot( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, Tensor &amp; Rotation, const bool squared=false   );</a>
+<a name="248"><span class="lineNum">     248 </span>            : ///calculate with close structure, i.e. approximate the RMSD without expensive computation of rotation matrix by reusing saved rotation matrices from previous iterations</a>
+<a name="249"><span class="lineNum">     249 </span>            :   double calculateWithCloseStructure( const std::vector&lt;Vector&gt;&amp; positions, std::vector&lt;Vector&gt; &amp;DDistDPos, const Tensor &amp; rotationPosClose, const Tensor &amp; rotationRefClose, std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01, const bool squared=false   );</a>
+<a name="250"><span class="lineNum">     250 </span>            : /// static convenience method to get the matrix i,a from drotdpos (which is a bit tricky)</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        900 :   static  Tensor getMatrixFromDRot(const Matrix&lt; std::vector&lt;Vector&gt; &gt; &amp;drotdpos, const unsigned &amp;i, const unsigned &amp;a) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        900 :     Tensor t;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        900 :     t[0][0]=drotdpos(0,0)[i][a]; t[0][1]=drotdpos(0,1)[i][a]; t[0][2]=drotdpos(0,2)[i][a];</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        900 :     t[1][0]=drotdpos(1,0)[i][a]; t[1][1]=drotdpos(1,1)[i][a]; t[1][2]=drotdpos(1,2)[i][a];</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        900 :     t[2][0]=drotdpos(2,0)[i][a]; t[2][1]=drotdpos(2,1)[i][a]; t[2][2]=drotdpos(2,2)[i][a];</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        900 :     return t;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   };</a>
+<a name="258"><span class="lineNum">     258 </span>            : };</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            : /// this is a class which is needed to share information across the various non-threadsafe routines</a>
+<a name="261"><span class="lineNum">     261 </span>            : /// so that the public function of rmsd are threadsafe while the inner core can safely share information</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      52152 : class RMSDCoreData</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : {</a>
+<a name="264"><span class="lineNum">     264 </span>            : private:</a>
+<a name="265"><span class="lineNum">     265 </span>            :   bool alEqDis;</a>
+<a name="266"><span class="lineNum">     266 </span>            :   bool distanceIsMSD; // default is RMSD but can deliver the MSD</a>
+<a name="267"><span class="lineNum">     267 </span>            :   bool hasDistance;  // distance is already calculated</a>
+<a name="268"><span class="lineNum">     268 </span>            :   bool isInitialized;</a>
+<a name="269"><span class="lineNum">     269 </span>            :   bool safe;</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :   // this need to be copied and they are small, should not affect the performance</a>
+<a name="272"><span class="lineNum">     272 </span>            :   Vector creference;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   bool creference_is_calculated;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   bool creference_is_removed;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   Vector cpositions;</a>
+<a name="276"><span class="lineNum">     276 </span>            :   bool cpositions_is_calculated;</a>
+<a name="277"><span class="lineNum">     277 </span>            :   bool cpositions_is_removed;</a>
+<a name="278"><span class="lineNum">     278 </span>            :   bool retrieve_only_rotation;</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :   // use reference assignment to speed up instead of copying</a>
+<a name="281"><span class="lineNum">     281 </span>            :   const std::vector&lt;Vector&gt; &amp;positions;</a>
+<a name="282"><span class="lineNum">     282 </span>            :   const std::vector&lt;Vector&gt; &amp;reference;</a>
+<a name="283"><span class="lineNum">     283 </span>            :   const std::vector&lt;double&gt; &amp;align;</a>
+<a name="284"><span class="lineNum">     284 </span>            :   const std::vector&lt;double&gt; &amp;displace;</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            :   // the needed stuff for distance and more (one could use eigenvecs components and eigenvals for some reason)</a>
+<a name="287"><span class="lineNum">     287 </span>            :   double dist;</a>
+<a name="288"><span class="lineNum">     288 </span>            :   Vector4d eigenvals;</a>
+<a name="289"><span class="lineNum">     289 </span>            :   Tensor4d eigenvecs;</a>
+<a name="290"><span class="lineNum">     290 </span>            :   double rr00; //  sum of positions squared (needed for dist calc)</a>
+<a name="291"><span class="lineNum">     291 </span>            :   double rr11; //  sum of reference squared (needed for dist calc)</a>
+<a name="292"><span class="lineNum">     292 </span>            :   Tensor rotation; // rotation derived from the eigenvector having the smallest eigenvalue</a>
+<a name="293"><span class="lineNum">     293 </span>            :   std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; drotation_drr01; // derivative of the rotation only available when align!=displace</a>
+<a name="294"><span class="lineNum">     294 </span>            :   Tensor ddist_drr01;</a>
+<a name="295"><span class="lineNum">     295 </span>            :   Tensor ddist_drotation;</a>
+<a name="296"><span class="lineNum">     296 </span>            :   std::vector&lt;Vector&gt; d; // difference of components</a>
+<a name="297"><span class="lineNum">     297 </span>            : public:</a>
+<a name="298"><span class="lineNum">     298 </span>            :   /// the constructor (note: only references are passed, therefore is rather fast)</a>
+<a name="299"><span class="lineNum">     299 </span>            :   /// note: this aligns the reference onto the positions</a>
+<a name="300"><span class="lineNum">     300 </span>            :   ///</a>
+<a name="301"><span class="lineNum">     301 </span>            :   /// this method assumes that the centers are already calculated and subtracted</a>
+<a name="302"><span class="lineNum">     302 </span>            :   RMSDCoreData(const std::vector&lt;double&gt; &amp;a,const std::vector&lt;double&gt; &amp;d,const std::vector&lt;Vector&gt; &amp;p, const std::vector&lt;Vector&gt; &amp;r, Vector &amp;cp, Vector &amp;cr ):</a>
+<a name="303"><span class="lineNum">     303 </span>            :     alEqDis(false),distanceIsMSD(false),hasDistance(false),isInitialized(false),safe(false),</a>
+<a name="304"><span class="lineNum">     304 </span>            :     creference(cr),creference_is_calculated(true),creference_is_removed(true),</a>
+<a name="305"><span class="lineNum">     305 </span>            :     cpositions(cp),cpositions_is_calculated(true),cpositions_is_removed(true),retrieve_only_rotation(false),positions(p),reference(r),align(a),displace(d),dist(0.0),rr00(0.0),rr11(0.0) {};</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   // this constructor does not assume that the positions and reference have the center subtracted</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">      52152 :   RMSDCoreData(const std::vector&lt;double&gt; &amp;a,const std::vector&lt;double&gt; &amp;d,const std::vector&lt;Vector&gt; &amp;p, const std::vector&lt;Vector&gt; &amp;r):</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">      52152 :     alEqDis(false),distanceIsMSD(false),hasDistance(false),isInitialized(false),safe(false),</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      52152 :     creference_is_calculated(false),creference_is_removed(false),</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      52152 :     cpositions_is_calculated(false),cpositions_is_removed(false),retrieve_only_rotation(false),positions(p),reference(r),align(a),displace(d),dist(0.0),rr00(0.0),rr11(0.0)</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">      52152 :   {cpositions.zero(); creference.zero();};</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            :   // set the center on the fly without subtracting</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      52152 :   void calcPositionsCenter() {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      52152 :     plumed_massert(!cpositions_is_calculated,&quot;the center was already calculated&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">    1221600 :     cpositions.zero(); for(unsigned i=0; i&lt;positions.size(); i++) {cpositions+=positions[i]*align[i];} cpositions_is_calculated=true;</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">      52152 :   }</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :   void calcReferenceCenter() {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :     plumed_massert(!creference_is_calculated,&quot;the center was already calculated&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :     creference.zero(); for(unsigned i=0; i&lt;reference.size(); i++) {creference+=reference[i]*align[i];} creference_is_calculated=true;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :   };</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   // assume the center is given externally</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :   void setPositionsCenter(Vector v) {plumed_massert(!cpositions_is_calculated,&quot;You are setting the center two times!&quot;); cpositions=v; cpositions_is_calculated=true;};</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      52152 :   void setReferenceCenter(Vector v) {plumed_massert(!creference_is_calculated,&quot;You are setting the center two times!&quot;); creference=v; creference_is_calculated=true;};</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :   // the center is already removed</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      52152 :   void setPositionsCenterIsRemoved(bool t) {cpositions_is_removed=t;};</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">      52152 :   void setReferenceCenterIsRemoved(bool t) {creference_is_removed=t;};</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   bool getPositionsCenterIsRemoved() {return cpositions_is_removed;};</a>
+<a name="330"><span class="lineNum">     330 </span>            :   bool getReferenceCenterIsRemoved() {return creference_is_removed;};</a>
+<a name="331"><span class="lineNum">     331 </span>            :   //  does the core calc : first thing to call after the constructor:</a>
+<a name="332"><span class="lineNum">     332 </span>            :   // only_rotation=true does not retrieve the derivatives, just retrieve the optimal rotation (the same calc cannot be exploit further)</a>
+<a name="333"><span class="lineNum">     333 </span>            :   void doCoreCalc(bool safe,bool alEqDis, bool only_rotation=false);</a>
+<a name="334"><span class="lineNum">     334 </span>            :   // do calculation with close structure data structures</a>
+<a name="335"><span class="lineNum">     335 </span>            :   void doCoreCalcWithCloseStructure(bool safe,bool alEqDis, const Tensor &amp; rotationPosClose, const Tensor &amp; rotationRefClose, std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; drotationPosCloseDrr01);</a>
+<a name="336"><span class="lineNum">     336 </span>            :   // retrieve the distance if required after doCoreCalc</a>
+<a name="337"><span class="lineNum">     337 </span>            :   double getDistance(bool squared);</a>
+<a name="338"><span class="lineNum">     338 </span>            :   // retrieve the derivative of the distance respect to the position</a>
+<a name="339"><span class="lineNum">     339 </span>            :   std::vector&lt;Vector&gt; getDDistanceDPositions();</a>
+<a name="340"><span class="lineNum">     340 </span>            :   // retrieve the derivative of the distance respect to the reference</a>
+<a name="341"><span class="lineNum">     341 </span>            :   std::vector&lt;Vector&gt; getDDistanceDReference();</a>
+<a name="342"><span class="lineNum">     342 </span>            :   // specific version for SOMA calculation (i.e. does not need derivative respect to rotation matrix)</a>
+<a name="343"><span class="lineNum">     343 </span>            :   std::vector&lt;Vector&gt; getDDistanceDReferenceSOMA();</a>
+<a name="344"><span class="lineNum">     344 </span>            :   // get aligned reference onto position</a>
+<a name="345"><span class="lineNum">     345 </span>            :   std::vector&lt;Vector&gt; getAlignedReferenceToPositions();</a>
+<a name="346"><span class="lineNum">     346 </span>            :   // get aligned position onto reference</a>
+<a name="347"><span class="lineNum">     347 </span>            :   std::vector&lt;Vector&gt; getAlignedPositionsToReference();</a>
+<a name="348"><span class="lineNum">     348 </span>            :   // get centered positions</a>
+<a name="349"><span class="lineNum">     349 </span>            :   std::vector&lt;Vector&gt; getCenteredPositions();</a>
+<a name="350"><span class="lineNum">     350 </span>            :   // get centered reference</a>
+<a name="351"><span class="lineNum">     351 </span>            :   std::vector&lt;Vector&gt; getCenteredReference();</a>
+<a name="352"><span class="lineNum">     352 </span>            :   // get center of positions</a>
+<a name="353"><span class="lineNum">     353 </span>            :   Vector getPositionsCenter();</a>
+<a name="354"><span class="lineNum">     354 </span>            :   // get center of reference</a>
+<a name="355"><span class="lineNum">     355 </span>            :   Vector getReferenceCenter();</a>
+<a name="356"><span class="lineNum">     356 </span>            :   // get rotation matrix (reference -&gt;positions)</a>
+<a name="357"><span class="lineNum">     357 </span>            :   Tensor getRotationMatrixReferenceToPositions();</a>
+<a name="358"><span class="lineNum">     358 </span>            :   // get rotation matrix (positions -&gt; reference)</a>
+<a name="359"><span class="lineNum">     359 </span>            :   Tensor getRotationMatrixPositionsToReference();</a>
+<a name="360"><span class="lineNum">     360 </span>            :   // get the derivative of the rotation matrix respect to positions</a>
+<a name="361"><span class="lineNum">     361 </span>            :   // note that the this transformation overlap the  reference onto position</a>
+<a name="362"><span class="lineNum">     362 </span>            :   // if inverseTransform=true then aligns the positions onto reference</a>
+<a name="363"><span class="lineNum">     363 </span>            :   Matrix&lt;std::vector&lt;Vector&gt; &gt; getDRotationDPositions( bool inverseTransform=false );</a>
+<a name="364"><span class="lineNum">     364 </span>            :   // get the derivative of the rotation matrix respect to reference</a>
+<a name="365"><span class="lineNum">     365 </span>            :   // note that the this transformation overlap the  reference onto position</a>
+<a name="366"><span class="lineNum">     366 </span>            :   // if inverseTransform=true then aligns the positions onto reference</a>
+<a name="367"><span class="lineNum">     367 </span>            :   Matrix&lt;std::vector&lt;Vector&gt; &gt;  getDRotationDReference(bool inverseTransform=false );</a>
+<a name="368"><span class="lineNum">     368 </span>            :   const std::array&lt;std::array&lt;Tensor,3&gt;,3&gt; &amp; getDRotationDRr01() const;</a>
+<a name="369"><span class="lineNum">     369 </span>            : };</a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span>            : }</a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span>            : #endif</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Random.cpp.func-sort-c.html b/coverage/tools/Random.cpp.func-sort-c.html
new file mode 100644
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+++ b/coverage/tools/Random.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Random.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Random.cpp<span style="font-size: 80%;"> (<a href="Random.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Random.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#109">_ZN4PLMD6Random13ReadStateFullERSi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#98">_ZNK4PLMD6Random14WriteStateFullERSo</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#126">_ZN4PLMD6Random10fromStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#66">_ZN4PLMD6Random4U01dEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#158">_ZN4PLMD6Random7ShuffleERSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#117">_ZNK4PLMD6Random8toStringERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#36">_ZN4PLMD6RandomC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">807031</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#51">_ZN4PLMD6Random7setSeedEi</a></td>
+              <td class="coverFnHi">807870</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#140">_ZN4PLMD6Random8GaussianEv</a></td>
+              <td class="coverFnHi">1242377</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#57">_ZN4PLMD6Random7RandU01Ev</a></td>
+              <td class="coverFnHi">1582605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#74">_ZN4PLMD6Random3U01Ev</a></td>
+              <td class="coverFnHi">5583575</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Random.cpp.func.html b/coverage/tools/Random.cpp.func.html
new file mode 100644
index 0000000000..4b7da0ec27
--- /dev/null
+++ b/coverage/tools/Random.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Random.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Random.cpp<span style="font-size: 80%;"> (<a href="Random.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Random.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#126">_ZN4PLMD6Random10fromStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#109">_ZN4PLMD6Random13ReadStateFullERSi</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#74">_ZN4PLMD6Random3U01Ev</a></td>
+              <td class="coverFnHi">5583575</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#66">_ZN4PLMD6Random4U01dEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#57">_ZN4PLMD6Random7RandU01Ev</a></td>
+              <td class="coverFnHi">1582605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#158">_ZN4PLMD6Random7ShuffleERSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#51">_ZN4PLMD6Random7setSeedEi</a></td>
+              <td class="coverFnHi">807870</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#140">_ZN4PLMD6Random8GaussianEv</a></td>
+              <td class="coverFnHi">1242377</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#36">_ZN4PLMD6RandomC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">807031</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#98">_ZNK4PLMD6Random14WriteStateFullERSo</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Random.cpp.gcov.html#117">_ZNK4PLMD6Random8toStringERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Random.cpp.gcov.html b/coverage/tools/Random.cpp.gcov.html
new file mode 100644
index 0000000000..91ebe59e10
--- /dev/null
+++ b/coverage/tools/Random.cpp.gcov.html
@@ -0,0 +1,245 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Random.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Random.cpp<span style="font-size: 80%;"> (source / <a href="Random.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">83</td>
+            <td class="headerCovTableEntryHi">91.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Random.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;cmath&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;cstdlib&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;sstream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iostream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iterator&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;functional&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : const double Random::fact=5.9604644775390625e-8;     /* 1 / 2^24  */</a>
+<a name="33"><span class="lineNum">      33 </span>            : const double Random::EPS=3.0e-16;</a>
+<a name="34"><span class="lineNum">      34 </span>            : const double Random::AM=1.0/IM;</a>
+<a name="35"><span class="lineNum">      35 </span>            : const double Random::RNMX=(1.0-EPS); // 1.0-EPS;</a>
+<a name="36"><span class="lineNum">      36 </span>            : const std::string Random::noname=&quot;noname&quot;;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     807031 : Random::Random(const std::string &amp; name):</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     807031 :   switchGaussian(false),</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     807031 :   saveGaussian(0.0),</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : // this is required because if a Random object is created during</a>
+<a name="42"><span class="lineNum">      42 </span>            : // initialization than Random::noname could still be initialized.</a>
+<a name="43"><span class="lineNum">      43 </span>            : // In practice: without this it is not possible to declare</a>
+<a name="44"><span class="lineNum">      44 </span>            : // a static Random object without enforcing the order of the</a>
+<a name="45"><span class="lineNum">      45 </span>            : // static constructors.</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">     807031 :   name(&amp;name!=&amp;noname?name:&quot;noname&quot;)</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : {</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">     807031 :   iy=0;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">   26632023 :   for(unsigned i=0; i&lt;NTAB; i++) iv[i]=0;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">     807031 :   setSeed(0);</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">     807031 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     807870 : void Random::setSeed(int idum_) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">     807870 :   if(idum_&gt;0) idum_=-idum_;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">     807870 :   idum=idum_;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">     807870 :   incPrec=false;</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">     807870 : }</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">    1582605 : double Random::RandU01 ()</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">    1582605 :   if (incPrec)</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :     return U01d();</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   else</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">    1582604 :     return U01();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          2 : double Random::U01d ()</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : {</a>
+<a name="70"><span class="lineNum">      70 </span>            :   double u;</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          2 :   u = U01();</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          2 :   u += U01() * fact;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 :   return (u &lt; 1.0) ? u : (u - 1.0);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">    5583575 : double Random::U01() {</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   int j,k;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   double temp;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">    5583575 :   if (idum &lt;= 0 || !iy) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">       1376 :     if (-idum &lt; 1) idum=1;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        626 :     else idum = -idum;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      56416 :     for (j=NTAB+7; j&gt;=0; j--) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      55040 :       k=idum/IQ;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      55040 :       idum=IA*(idum-k*IQ)-IR*k;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      55040 :       if (idum &lt; 0) idum += IM;</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      55040 :       if (j &lt; NTAB) iv[j] = idum;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :     }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1376 :     iy=iv[0];</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">    5583575 :   k=idum/IQ;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">    5583575 :   idum=IA*(idum-k*IQ)-IR*k;</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">    5583575 :   if (idum &lt; 0) idum += IM;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">    5583575 :   j=iy/NDIV;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    5583575 :   iy=iv[j];</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    5583575 :   iv[j] = idum;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">    5583575 :   if ((temp=AM*iy) &gt; RNMX) return RNMX;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">    5583575 :   else return temp;</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : }</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          1 : void Random::WriteStateFull(std::ostream &amp; out)const {</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   out&lt;&lt;name&lt;&lt;std::endl;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 :   out&lt;&lt;idum&lt;&lt;&quot; &quot;&lt;&lt;iy;</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         33 :   for(int i=0; i&lt;NTAB; i++) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         32 :     out&lt;&lt;&quot; &quot;&lt;&lt;iv[i];</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   };</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :   out&lt;&lt;&quot; &quot;&lt;&lt;switchGaussian;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :   out&lt;&lt;&quot; &quot;&lt;&lt;saveGaussian;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   out&lt;&lt;std::endl;</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          1 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 : void Random::ReadStateFull (std::istream &amp; in) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   getline(in,name);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   in&gt;&gt;idum&gt;&gt;iy;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   for (int i = 0; i &lt; NTAB; i++) in&gt;&gt;iv[i];</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   in&gt;&gt;switchGaussian;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :   in&gt;&gt;saveGaussian;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 : void Random::toString(std::string &amp; str)const {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   std::ostringstream ostr;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   ostr&lt;&lt;idum&lt;&lt;&quot;|&quot;&lt;&lt;iy;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         66 :   for(int i=0; i&lt;NTAB; i++) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         64 :     ostr&lt;&lt;&quot;|&quot;&lt;&lt;iv[i];</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   };</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   str=ostr.str();</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          2 : void Random::fromString(const std::string &amp; str) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :   std::string s=str;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        425 :   for(unsigned i=0; i&lt;s.length(); i++) if(s[i]=='|') s[i]=' ';</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          2 :   std::istringstream istr(s.c_str());</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          2 :   istr&gt;&gt;idum&gt;&gt;iy;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         66 :   for (int i = 0; i &lt; NTAB; i++) istr&gt;&gt;iv[i];</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : // This allows to have the same stream of random numbers</a>
+<a name="137"><span class="lineNum">     137 </span>            : // with different compilers:</a>
+<a name="138"><span class="lineNum">     138 </span>            : #ifdef __INTEL_COMPILER</a>
+<a name="139"><span class="lineNum">     139 </span>            : #pragma intel optimization_level 0</a>
+<a name="140"><span class="lineNum">     140 </span>            : #endif</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">    1242377 : double Random::Gaussian() {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :   double v1,v2,rsq;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">    1242377 :   if(switchGaussian) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">     621162 :     switchGaussian=false;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">     621162 :     return saveGaussian;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span>            :   while(true) {</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">     790796 :     v1=2.0*RandU01()-1.0;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">     790796 :     v2=2.0*RandU01()-1.0;</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">     790796 :     rsq=v1*v1+v2*v2;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     790796 :     if(rsq&lt;1.0 &amp;&amp; rsq&gt;0.0) break;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     621215 :   double fac=std::sqrt(-2.*std::log(rsq)/rsq);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">     621215 :   saveGaussian=v1*fac;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     621215 :   switchGaussian=true;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">     621215 :   return v2*fac;</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          2 : void Random::Shuffle(std::vector&lt;unsigned&gt;&amp; vec) {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   std::iterator_traits&lt;std::vector&lt;unsigned&gt;::iterator &gt;::difference_type i, n;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   n = vec.end() - vec.begin();</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          6 :   for(i=n-1; i&gt;0; --i) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          4 :     std::swap(vec[i], vec[(int)round(RandU01() * IM) % i]);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   }</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          2 : }</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Random.h.func-sort-c.html b/coverage/tools/Random.h.func-sort-c.html
new file mode 100644
index 0000000000..034553de80
--- /dev/null
+++ b/coverage/tools/Random.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Random.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Random.h<span style="font-size: 80%;"> (<a href="Random.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Random.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Random.h.func.html b/coverage/tools/Random.h.func.html
new file mode 100644
index 0000000000..77b695841f
--- /dev/null
+++ b/coverage/tools/Random.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Random.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Random.h<span style="font-size: 80%;"> (<a href="Random.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Random.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Random.h.gcov.html b/coverage/tools/Random.h.gcov.html
new file mode 100644
index 0000000000..2bd46c9f2f
--- /dev/null
+++ b/coverage/tools/Random.h.gcov.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Random.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Random.h<span style="font-size: 80%;"> (source / <a href="Random.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Random_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Random_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iosfwd&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : /// \ingroup TOOLBOX</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">     806981 : class Random {</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :   static const int IA=16807,IM=2147483647,IQ=127773,IR=2836,NTAB=32;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   static const int NDIV=(1+(IM-1)/NTAB);</a>
+<a name="35"><span class="lineNum">      35 </span>            :   static const double EPS;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   static const double AM;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   static const double RNMX;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   static const double fact;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static const std::string noname;</a>
+<a name="40"><span class="lineNum">      40 </span>            :   bool incPrec;</a>
+<a name="41"><span class="lineNum">      41 </span>            :   bool switchGaussian;</a>
+<a name="42"><span class="lineNum">      42 </span>            :   double saveGaussian;</a>
+<a name="43"><span class="lineNum">      43 </span>            :   int iy;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   int iv[NTAB];</a>
+<a name="45"><span class="lineNum">      45 </span>            :   int idum;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::string name;</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   explicit Random(const std::string &amp; name=noname);</a>
+<a name="49"><span class="lineNum">      49 </span>            :   void setSeed(int idum);</a>
+<a name="50"><span class="lineNum">      50 </span>            :   double RandU01();</a>
+<a name="51"><span class="lineNum">      51 </span>            :   double U01();</a>
+<a name="52"><span class="lineNum">      52 </span>            :   double U01d();</a>
+<a name="53"><span class="lineNum">      53 </span>            :   int RandInt(int i);</a>
+<a name="54"><span class="lineNum">      54 </span>            :   void Shuffle(std::vector&lt;unsigned&gt;&amp; vec);</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void WriteStateFull(std::ostream &amp;)const;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   void ReadStateFull (std::istream &amp;);</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void fromString(const std::string &amp; str);</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void toString(std::string &amp; str)const;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   friend std::ostream &amp; operator&lt;&lt;(std::ostream &amp; out,const Random &amp; rng) {</a>
+<a name="60"><span class="lineNum">      60 </span>            :     rng.WriteStateFull(out); return out;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   }</a>
+<a name="62"><span class="lineNum">      62 </span>            :   friend std::istream &amp; operator&gt;&gt;(std::istream &amp; in,Random &amp; rng) {</a>
+<a name="63"><span class="lineNum">      63 </span>            :     rng.ReadStateFull(in); return in;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span>            :   double Gaussian();</a>
+<a name="66"><span class="lineNum">      66 </span>            :   void IncreasedPrecis(bool i) {incPrec=i;}</a>
+<a name="67"><span class="lineNum">      67 </span>            : };</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : #endif</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RootFindingBase.h.func-sort-c.html b/coverage/tools/RootFindingBase.h.func-sort-c.html
new file mode 100644
index 0000000000..2be4b98a6b
--- /dev/null
+++ b/coverage/tools/RootFindingBase.h.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RootFindingBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RootFindingBase.h<span style="font-size: 80%;"> (<a href="RootFindingBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="RootFindingBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#59">_ZNK4PLMD15RootFindingBaseINS_4GridEE10linesearchERKSt6vectorIdSaIdEERS5_MS1_KFdS7_S8_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#47">_ZNK4PLMD15RootFindingBaseINS_4GridEE8doSearchERKSt6vectorIdSaIdEERS5_RNS_5F1dimIS1_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#67">_ZNK4PLMD15RootFindingBaseINS_11multicolvar19DistanceFromContourEE7lsearchERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#47">_ZNK4PLMD15RootFindingBaseINS_11multicolvar19DistanceFromContourEE8doSearchERKSt6vectorIdSaIdEERS6_RNS_5F1dimIS2_EE</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#59">_ZNK4PLMD15RootFindingBaseINS_9gridtools18ContourFindingBaseEE10linesearchERKSt6vectorIdSaIdEERS6_MS2_KFdS8_S9_E</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#47">_ZNK4PLMD15RootFindingBaseINS_9gridtools18ContourFindingBaseEE8doSearchERKSt6vectorIdSaIdEERS6_RNS_5F1dimIS2_EE</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RootFindingBase.h.func.html b/coverage/tools/RootFindingBase.h.func.html
new file mode 100644
index 0000000000..1b77086d4c
--- /dev/null
+++ b/coverage/tools/RootFindingBase.h.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RootFindingBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RootFindingBase.h<span style="font-size: 80%;"> (<a href="RootFindingBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="RootFindingBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#67">_ZNK4PLMD15RootFindingBaseINS_11multicolvar19DistanceFromContourEE7lsearchERKSt6vectorIdSaIdEERS6_MS2_FdS8_S9_E</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#47">_ZNK4PLMD15RootFindingBaseINS_11multicolvar19DistanceFromContourEE8doSearchERKSt6vectorIdSaIdEERS6_RNS_5F1dimIS2_EE</a></td>
+              <td class="coverFnHi">274</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#59">_ZNK4PLMD15RootFindingBaseINS_4GridEE10linesearchERKSt6vectorIdSaIdEERS5_MS1_KFdS7_S8_E</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#47">_ZNK4PLMD15RootFindingBaseINS_4GridEE8doSearchERKSt6vectorIdSaIdEERS5_RNS_5F1dimIS1_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#59">_ZNK4PLMD15RootFindingBaseINS_9gridtools18ContourFindingBaseEE10linesearchERKSt6vectorIdSaIdEERS6_MS2_KFdS8_S9_E</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="RootFindingBase.h.gcov.html#47">_ZNK4PLMD15RootFindingBaseINS_9gridtools18ContourFindingBaseEE8doSearchERKSt6vectorIdSaIdEERS6_RNS_5F1dimIS2_EE</a></td>
+              <td class="coverFnHi">1242</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/RootFindingBase.h.gcov.html b/coverage/tools/RootFindingBase.h.gcov.html
new file mode 100644
index 0000000000..9ba6e53d02
--- /dev/null
+++ b/coverage/tools/RootFindingBase.h.gcov.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/RootFindingBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - RootFindingBase.h<span style="font-size: 80%;"> (source / <a href="RootFindingBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_RootFindingBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_RootFindingBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;MinimiseBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Brent1DRootSearch.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : class RootFindingBase {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            : /// This is the pointer to the member function in the energy</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// calculating class that calculates the energy</a>
+<a name="35"><span class="lineNum">      35 </span>            :   typedef double(FCLASS::*engf_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der ) const ;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   typedef double(FCLASS::*engfnc_pointer)( const std::vector&lt;double&gt;&amp; p, std::vector&lt;double&gt;&amp; der ) ;</a>
+<a name="37"><span class="lineNum">      37 </span>            : /// The class that calculates the energy given a position</a>
+<a name="38"><span class="lineNum">      38 </span>            :   FCLASS* myclass_func;</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// This actually does the search for a root</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void doSearch( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, F1dim&lt;FCLASS&gt;&amp; f1dim  ) const ;</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          4 :   explicit RootFindingBase( FCLASS* funcc ) : myclass_func(funcc) {}</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : /// This is the line minimiser</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void linesearch( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, engf_pointer myfunc ) const ;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void lsearch( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, engfnc_pointer myfunc ) const ;</a>
+<a name="46"><span class="lineNum">      46 </span>            : };</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       1516 : void RootFindingBase&lt;FCLASS&gt;::doSearch( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, F1dim&lt;FCLASS&gt;&amp; f1dim ) const {</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   // Construct an object that will do the line search for the minimum</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1516 :   Brent1DRootSearch&lt;F1dim&lt;FCLASS&gt; &gt; bb(f1dim);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            :   // This does the actual search for the root</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1516 :   double ax=0.0, xx=1.0;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       1516 :   bb.bracket( ax, xx, &amp;F1dim&lt;FCLASS&gt;::getEng );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       1516 :   double xmin=bb.search( &amp;F1dim&lt;FCLASS&gt;::getEng );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       6064 :   for(unsigned i=0; i&lt;p.size(); ++i) p[i] += xmin*dir[i];</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       1516 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1242 : void RootFindingBase&lt;FCLASS&gt;::linesearch( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, engf_pointer myfunc ) const {</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   // Construct the object that turns points on a line into vectors</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">       1242 :   F1dim&lt;FCLASS&gt; f1dim( p, dir, myclass_func, myfunc, NULL );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   // Actually do the search</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1242 :   doSearch( dir, p, f1dim );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">       1242 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : template &lt;class FCLASS&gt;</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        274 : void RootFindingBase&lt;FCLASS&gt;::lsearch( const std::vector&lt;double&gt;&amp; dir, std::vector&lt;double&gt;&amp; p, engfnc_pointer myfunc ) const {</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Construct the object that turns points on a line into vectors</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        274 :   F1dim&lt;FCLASS&gt; f1dim( p, dir, myclass_func, NULL, myfunc );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :   // Actually do the search</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        274 :   doSearch( dir, p, f1dim );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        274 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Stopwatch.cpp.func-sort-c.html b/coverage/tools/Stopwatch.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d8d92ab83a
--- /dev/null
+++ b/coverage/tools/Stopwatch.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Stopwatch.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Stopwatch.cpp<span style="font-size: 80%;"> (<a href="Stopwatch.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Stopwatch.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.cpp.gcov.html#33">_ZN4PLMDlsERSoRKNS_9StopwatchE</a></td>
+              <td class="coverFnHi">1019</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.cpp.gcov.html#49">_ZNK4PLMD9Stopwatch3logERSo</a></td>
+              <td class="coverFnHi">1019</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.cpp.gcov.html#37">_ZN4PLMD9StopwatchD2Ev</a></td>
+              <td class="coverFnHi">805862</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Stopwatch.cpp.func.html b/coverage/tools/Stopwatch.cpp.func.html
new file mode 100644
index 0000000000..9f4630bfd4
--- /dev/null
+++ b/coverage/tools/Stopwatch.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Stopwatch.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Stopwatch.cpp<span style="font-size: 80%;"> (<a href="Stopwatch.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Stopwatch.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.cpp.gcov.html#37">_ZN4PLMD9StopwatchD2Ev</a></td>
+              <td class="coverFnHi">805862</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.cpp.gcov.html#33">_ZN4PLMDlsERSoRKNS_9StopwatchE</a></td>
+              <td class="coverFnHi">1019</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.cpp.gcov.html#49">_ZNK4PLMD9Stopwatch3logERSo</a></td>
+              <td class="coverFnHi">1019</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Stopwatch.cpp.gcov.html b/coverage/tools/Stopwatch.cpp.gcov.html
new file mode 100644
index 0000000000..b04d453bb6
--- /dev/null
+++ b/coverage/tools/Stopwatch.cpp.gcov.html
@@ -0,0 +1,154 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Stopwatch.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Stopwatch.cpp<span style="font-size: 80%;"> (source / <a href="Stopwatch.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Stopwatch.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Log.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstdio&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;iostream&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;vector&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;algorithm&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : // this is needed for friend operators</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       1019 : std::ostream&amp; operator&lt;&lt;(std::ostream&amp;os,const Stopwatch&amp;sw) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       1019 :   return sw.log(os);</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : }</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     805862 : Stopwatch::~Stopwatch() {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     805862 :   if(mylog &amp;&amp; mylog-&gt;isOpen()) {</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : // Make sure paused watches are stopped.</a>
+<a name="42"><span class="lineNum">      42 </span>            : // this is necessary e.g. to make sure the main watch present in PlumedMain</a>
+<a name="43"><span class="lineNum">      43 </span>            : // is stopped correctly.</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       7673 :     for(auto &amp; w : watches) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       6657 :       if(w.second.state==Watch::State::paused) w.second.start().stop();</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :     }</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1016 :     *mylog &lt;&lt; *this;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   }</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">     805862 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">       1019 : std::ostream&amp; Stopwatch::log(std::ostream&amp;os)const {</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   const std::size_t bufferlen=1000;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   char buffer[bufferlen];</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       1019 :   buffer[0]=0;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      41779 :   for(unsigned i=0; i&lt;40; i++) os&lt;&lt;&quot; &quot;;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       1019 :   os&lt;&lt;&quot;      Cycles        Total      Average      Minimum      Maximum\n&quot;;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::vector&lt;std::string&gt; names;</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       7682 :   for(const auto &amp; it : watches) names.push_back(it.first);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       1019 :   std::sort(names.begin(),names.end());</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            :   const double frac=1.0/1000000000.0;</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       7682 :   for(const auto &amp; name : names) {</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :     const Watch&amp;t(watches.find(name)-&gt;second);</a>
+<a name="66"><span class="lineNum">      66 </span>            :     os&lt;&lt;name;</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     164528 :     for(unsigned i=name.length(); i&lt;40; i++) os&lt;&lt;&quot; &quot;;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       6663 :     std::snprintf(buffer,bufferlen,&quot;%12u %12.6f %12.6f %12.6f %12.6f\n&quot;, t.cycles, frac*t.total, frac*t.total/t.cycles, frac*t.min,frac*t.max);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       6663 :     os&lt;&lt;buffer;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   }</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       1019 :   return os;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       1019 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Stopwatch.h.func-sort-c.html b/coverage/tools/Stopwatch.h.func-sort-c.html
new file mode 100644
index 0000000000..48385b8f42
--- /dev/null
+++ b/coverage/tools/Stopwatch.h.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Stopwatch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Stopwatch.h<span style="font-size: 80%;"> (<a href="Stopwatch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Stopwatch.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#314">_ZN4PLMD9Stopwatch5pauseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">571</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#308">_ZN4PLMD9Stopwatch4stopERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">574</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#302">_ZN4PLMD9Stopwatch5startERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1148</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#338">_ZN4PLMD9Stopwatch7HandleraSEOS1_</a></td>
+              <td class="coverFnHi">3493</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#325">_ZN4PLMD9Stopwatch10startPauseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1118951</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#169">_ZN4PLMDL20StopwatchEmptyStringEv</a></td>
+              <td class="coverFnHi">1121233</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#320">_ZN4PLMD9Stopwatch9startStopERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1530756</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#366">_ZN4PLMD9Stopwatch5Watch4stopEv</a></td>
+              <td class="coverFnHi">1532337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#378">_ZN4PLMD9Stopwatch5Watch5pauseEv</a></td>
+              <td class="coverFnHi">2651728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#294">_ZN4PLMD9Stopwatch7HandlerD2Ev</a></td>
+              <td class="coverFnHi">6203636</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Stopwatch.h.func.html b/coverage/tools/Stopwatch.h.func.html
new file mode 100644
index 0000000000..1aef6a23ea
--- /dev/null
+++ b/coverage/tools/Stopwatch.h.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Stopwatch.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Stopwatch.h<span style="font-size: 80%;"> (<a href="Stopwatch.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Stopwatch.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#325">_ZN4PLMD9Stopwatch10startPauseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1118951</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#308">_ZN4PLMD9Stopwatch4stopERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">574</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#366">_ZN4PLMD9Stopwatch5Watch4stopEv</a></td>
+              <td class="coverFnHi">1532337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#378">_ZN4PLMD9Stopwatch5Watch5pauseEv</a></td>
+              <td class="coverFnHi">2651728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#314">_ZN4PLMD9Stopwatch5pauseERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">571</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#302">_ZN4PLMD9Stopwatch5startERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1148</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#294">_ZN4PLMD9Stopwatch7HandlerD2Ev</a></td>
+              <td class="coverFnHi">6203636</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#338">_ZN4PLMD9Stopwatch7HandleraSEOS1_</a></td>
+              <td class="coverFnHi">3493</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#320">_ZN4PLMD9Stopwatch9startStopERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">1530756</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Stopwatch.h.gcov.html#169">_ZN4PLMDL20StopwatchEmptyStringEv</a></td>
+              <td class="coverFnHi">1121233</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Stopwatch.h.gcov.html b/coverage/tools/Stopwatch.h.gcov.html
new file mode 100644
index 0000000000..98a930b4db
--- /dev/null
+++ b/coverage/tools/Stopwatch.h.gcov.html
@@ -0,0 +1,485 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Stopwatch.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Stopwatch.h<span style="font-size: 80%;"> (source / <a href="Stopwatch.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Stopwatch_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Stopwatch_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;unordered_map&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;iosfwd&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;chrono&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /**</a>
+<a name="34"><span class="lineNum">      34 </span>            : \ingroup TOOLBOX</a>
+<a name="35"><span class="lineNum">      35 </span>            : Class implementing stopwatch to time execution.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : Each instance of this class is a container which</a>
+<a name="38"><span class="lineNum">      38 </span>            : can keep track of several named stopwatches at</a>
+<a name="39"><span class="lineNum">      39 </span>            : the same time. Access to the stopwatches</a>
+<a name="40"><span class="lineNum">      40 </span>            : is obtained using start(), stop(), pause() methods,</a>
+<a name="41"><span class="lineNum">      41 </span>            : giving as a parameter the name of the specific stopwatch.</a>
+<a name="42"><span class="lineNum">      42 </span>            : Also an empty string can be used (un-named stopwatch).</a>
+<a name="43"><span class="lineNum">      43 </span>            : Finally, all the times can be logged using &lt;&lt; operator</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : \verbatim</a>
+<a name="46"><span class="lineNum">      46 </span>            : #include &quot;Stopwatch.h&quot;</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : int main(){</a>
+<a name="49"><span class="lineNum">      49 </span>            :   Stopwatch sw;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   sw.start();</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   sw.start(&quot;initialization&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span>            : // do initialization ...</a>
+<a name="54"><span class="lineNum">      54 </span>            :   sw.stop(&quot;initialization&quot;);</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   for(int i=0;i&lt;100;i++){</a>
+<a name="57"><span class="lineNum">      57 </span>            :     sw.start(&quot;loop&quot;);</a>
+<a name="58"><span class="lineNum">      58 </span>            : // do calculation</a>
+<a name="59"><span class="lineNum">      59 </span>            :     sw.stop(&quot;loop&quot;);</a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            :   sw.stop();</a>
+<a name="63"><span class="lineNum">      63 </span>            :   return 0;</a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : \endverbatim</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : Using pause a stopwatch can be put on hold until</a>
+<a name="69"><span class="lineNum">      69 </span>            : the next start:</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \verbatim</a>
+<a name="72"><span class="lineNum">      72 </span>            : #include &quot;Stopwatch.h&quot;</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : int main(){</a>
+<a name="75"><span class="lineNum">      75 </span>            :   Stopwatch sw;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   sw.start();</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            :   sw.start(&quot;initialization&quot;);</a>
+<a name="79"><span class="lineNum">      79 </span>            : // do initialization ...</a>
+<a name="80"><span class="lineNum">      80 </span>            :   sw.stop(&quot;initialization&quot;);</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            :   for(int i=0;i&lt;100;i++){</a>
+<a name="83"><span class="lineNum">      83 </span>            :     sw.start(&quot;loop&quot;);</a>
+<a name="84"><span class="lineNum">      84 </span>            : // do calculation</a>
+<a name="85"><span class="lineNum">      85 </span>            :     sw.pause(&quot;loop&quot;);</a>
+<a name="86"><span class="lineNum">      86 </span>            : // here goes something that we do not want to include</a>
+<a name="87"><span class="lineNum">      87 </span>            :     sw.start(&quot;loop&quot;);</a>
+<a name="88"><span class="lineNum">      88 </span>            : // do calculation</a>
+<a name="89"><span class="lineNum">      89 </span>            :     sw.stop(&quot;loop&quot;);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :   sw.stop();</a>
+<a name="93"><span class="lineNum">      93 </span>            :   return 0;</a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \endverbatim</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : Notice that as of PLUMED 2.5 it is possible to use a slightly modified</a>
+<a name="99"><span class="lineNum">      99 </span>            : interface that allow for exception safety. In practice,</a>
+<a name="100"><span class="lineNum">     100 </span>            : one can replace a pair of calls to Stopwatch::start() and Stopwatch::stop()</a>
+<a name="101"><span class="lineNum">     101 </span>            : with a single call to Stopwatch::startStop(). This call will return an object</a>
+<a name="102"><span class="lineNum">     102 </span>            : that, when goes out of scope, will stop the timer.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : \notice The exception safety interace is highly recommended since it allows</a>
+<a name="105"><span class="lineNum">     105 </span>            : to make sure that stopwatches are started and stopped consistently.</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : For instance the following</a>
+<a name="108"><span class="lineNum">     108 </span>            : code</a>
+<a name="109"><span class="lineNum">     109 </span>            : \verbatim</a>
+<a name="110"><span class="lineNum">     110 </span>            :   {</a>
+<a name="111"><span class="lineNum">     111 </span>            :     sw.start(&quot;A&quot;);</a>
+<a name="112"><span class="lineNum">     112 </span>            :   // any code</a>
+<a name="113"><span class="lineNum">     113 </span>            :     sw.stop(&quot;A&quot;);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span>            : \endverbatim</a>
+<a name="116"><span class="lineNum">     116 </span>            : can be replaced with</a>
+<a name="117"><span class="lineNum">     117 </span>            : \verbatim</a>
+<a name="118"><span class="lineNum">     118 </span>            :   {</a>
+<a name="119"><span class="lineNum">     119 </span>            :     auto sww=sw.startStop(&quot;A&quot;);</a>
+<a name="120"><span class="lineNum">     120 </span>            :   // any code</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            :   // stopwatch is stopped when sww goes out of scope</a>
+<a name="123"><span class="lineNum">     123 </span>            :   }</a>
+<a name="124"><span class="lineNum">     124 </span>            : \endverbatim</a>
+<a name="125"><span class="lineNum">     125 </span>            : Similarly, Stopwatch::startPause() can be used to replace a pair of</a>
+<a name="126"><span class="lineNum">     126 </span>            : Stopwatch::start() and Stopwatch::pause().</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : The older syntax (explicitly calling `Stopwatch::start()` and `Stopwatch::pause()`) is still</a>
+<a name="129"><span class="lineNum">     129 </span>            : allowed for backward compatibility.</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : Notice that the returned object is of type `Stopwatch::Handler`.</a>
+<a name="132"><span class="lineNum">     132 </span>            : You might be willing to explicitly declare a `Stopwatch::Handler` (instead of using `auto`)</a>
+<a name="133"><span class="lineNum">     133 </span>            : when you want to conditionally start the stopwatch. For instance:</a>
+<a name="134"><span class="lineNum">     134 </span>            : \verbatim</a>
+<a name="135"><span class="lineNum">     135 </span>            :   {</a>
+<a name="136"><span class="lineNum">     136 </span>            :     Stopwatch::Handler handler;</a>
+<a name="137"><span class="lineNum">     137 </span>            :     if(you_want_to_time_this) handler=sw.startStop();</a>
+<a name="138"><span class="lineNum">     138 </span>            :     ... do something ...</a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            :   // in case it was started, the stopwatch will stop here, at the end of the block</a>
+<a name="141"><span class="lineNum">     141 </span>            :   // in case it was not started, nothing will happen</a>
+<a name="142"><span class="lineNum">     142 </span>            : \endverbatim</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : A `Stopwatch::Handler` can not be copied but it can be moved (it behaves like a unique_ptr).</a>
+<a name="145"><span class="lineNum">     145 </span>            : Moving it explicitly allows one to transfer it to another `Stopwatch::Handler` with a different scope.</a>
+<a name="146"><span class="lineNum">     146 </span>            : For instance, in case you want to conditionally stop the stopwatch you might use something like this:</a>
+<a name="147"><span class="lineNum">     147 </span>            : \verbatim</a>
+<a name="148"><span class="lineNum">     148 </span>            :   {</a>
+<a name="149"><span class="lineNum">     149 </span>            :     Stopwatch::Handler handler;</a>
+<a name="150"><span class="lineNum">     150 </span>            :     if(you_want_to_time_this) handler=sw.startStop();</a>
+<a name="151"><span class="lineNum">     151 </span>            :     ... do something ...</a>
+<a name="152"><span class="lineNum">     152 </span>            :     if(you_want_to_stop_here) auto h2=std::move(handler);</a>
+<a name="153"><span class="lineNum">     153 </span>            :     // the previous instruction moves handler to h2 that is then destroyed, stopping the watch</a>
+<a name="154"><span class="lineNum">     154 </span>            :     // notice that if the stop was not started it will not stop.</a>
+<a name="155"><span class="lineNum">     155 </span>            :     ... do something else ...</a>
+<a name="156"><span class="lineNum">     156 </span>            :   }</a>
+<a name="157"><span class="lineNum">     157 </span>            :   // in case it is running, the stopwatch will stop here, at the end of the block</a>
+<a name="158"><span class="lineNum">     158 </span>            : \endverbatim</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : Finally, notice that in order to write the timers on an output file when the</a>
+<a name="161"><span class="lineNum">     161 </span>            : Stopwatch is destroyed, one can store a reference to a PLMD::Log by passing it</a>
+<a name="162"><span class="lineNum">     162 </span>            : to the Stopwatch constructor.</a>
+<a name="163"><span class="lineNum">     163 </span>            : This will make sure timers are written also in case of a premature end.</a>
+<a name="164"><span class="lineNum">     164 </span>            : */</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : class Log;</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Return an empty string.</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// Inline static so that it can store a static variable (for quicker access)</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// without adding a unique global symbol to a library including this header file.</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">    1121233 : inline static const std::string &amp; StopwatchEmptyString() noexcept {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">    1121233 :   const static std::string s;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">    1121233 :   return s;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : class Stopwatch {</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : public:</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// Forward declaration</a>
+<a name="180"><span class="lineNum">     180 </span>            :   class Watch;</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// Auxiliary class for handling exception-safe start/pause and start/stop.</a>
+<a name="182"><span class="lineNum">     182 </span>            :   class Handler {</a>
+<a name="183"><span class="lineNum">     183 </span>            :     Watch* watch=nullptr;</a>
+<a name="184"><span class="lineNum">     184 </span>            :     /// stop (true) or pause (false).</a>
+<a name="185"><span class="lineNum">     185 </span>            :     /// might be changed to an enum if clearer.</a>
+<a name="186"><span class="lineNum">     186 </span>            :     bool stop=false;</a>
+<a name="187"><span class="lineNum">     187 </span>            :     /// Private constructor.</a>
+<a name="188"><span class="lineNum">     188 </span>            :     /// This is kept private to avoid misuse. Handler objects should</a>
+<a name="189"><span class="lineNum">     189 </span>            :     /// only be created using startPause() or startStop().</a>
+<a name="190"><span class="lineNum">     190 </span>            :     /// stop is required to know if the destructor should stop or pause the watch.</a>
+<a name="191"><span class="lineNum">     191 </span>            :     Handler(Watch* watch,bool stop);</a>
+<a name="192"><span class="lineNum">     192 </span>            :     /// Allows usage of private constructor</a>
+<a name="193"><span class="lineNum">     193 </span>            :     friend class Stopwatch;</a>
+<a name="194"><span class="lineNum">     194 </span>            :   public:</a>
+<a name="195"><span class="lineNum">     195 </span>            :     /// Default constructor</a>
+<a name="196"><span class="lineNum">     196 </span>            :     Handler() = default;</a>
+<a name="197"><span class="lineNum">     197 </span>            :     /// Default copy constructor is deleted (not copyable)</a>
+<a name="198"><span class="lineNum">     198 </span>            :     Handler(const Handler &amp; handler) = delete;</a>
+<a name="199"><span class="lineNum">     199 </span>            :     /// Default copy assignment is deleted (not copyable)</a>
+<a name="200"><span class="lineNum">     200 </span>            :     Handler &amp; operator=(const Handler &amp; handler) = delete;</a>
+<a name="201"><span class="lineNum">     201 </span>            :     /// Move constructor.</a>
+<a name="202"><span class="lineNum">     202 </span>            :     Handler(Handler &amp;&amp; handler) noexcept;</a>
+<a name="203"><span class="lineNum">     203 </span>            :     /// Move assignment.</a>
+<a name="204"><span class="lineNum">     204 </span>            :     Handler &amp; operator=(Handler &amp;&amp; handler) noexcept;</a>
+<a name="205"><span class="lineNum">     205 </span>            :     /// Destructor either stops or pauses the watch</a>
+<a name="206"><span class="lineNum">     206 </span>            :     ~Handler();</a>
+<a name="207"><span class="lineNum">     207 </span>            :   };</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : /// Class to store a single stopwatch.</a>
+<a name="210"><span class="lineNum">     210 </span>            : /// Class Stopwatch contains a collection of them</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">      11467 :   class Watch {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : /// Instant in time when Watch was started last time</a>
+<a name="213"><span class="lineNum">     213 </span>            :     std::chrono::time_point&lt;std::chrono::high_resolution_clock&gt; lastStart;</a>
+<a name="214"><span class="lineNum">     214 </span>            : /// Total accumulated time, in nanoseconds</a>
+<a name="215"><span class="lineNum">     215 </span>            :     long long int total = 0;</a>
+<a name="216"><span class="lineNum">     216 </span>            : /// Accumulated time for this lap, in nanoseconds</a>
+<a name="217"><span class="lineNum">     217 </span>            :     long long int lap = 0;</a>
+<a name="218"><span class="lineNum">     218 </span>            : /// Slowest lap so far, in nanoseconds</a>
+<a name="219"><span class="lineNum">     219 </span>            :     long long int max = 0;</a>
+<a name="220"><span class="lineNum">     220 </span>            : /// Fastest lap so far, in nanoseconds</a>
+<a name="221"><span class="lineNum">     221 </span>            :     long long int min = 0;</a>
+<a name="222"><span class="lineNum">     222 </span>            : /// Total number of cycles</a>
+<a name="223"><span class="lineNum">     223 </span>            :     unsigned cycles = 0;</a>
+<a name="224"><span class="lineNum">     224 </span>            : /// count how many times Watch was started (+1) or stopped/paused (-1).</a>
+<a name="225"><span class="lineNum">     225 </span>            :     unsigned running = 0;</a>
+<a name="226"><span class="lineNum">     226 </span>            :     enum class State {started, stopped, paused};</a>
+<a name="227"><span class="lineNum">     227 </span>            : /// keep track of state</a>
+<a name="228"><span class="lineNum">     228 </span>            :     State state = State::stopped;</a>
+<a name="229"><span class="lineNum">     229 </span>            : /// Allows access to internal data</a>
+<a name="230"><span class="lineNum">     230 </span>            :     friend class Stopwatch;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   public:</a>
+<a name="232"><span class="lineNum">     232 </span>            : /// start the watch</a>
+<a name="233"><span class="lineNum">     233 </span>            :     Watch &amp; start();</a>
+<a name="234"><span class="lineNum">     234 </span>            : /// stop the watch</a>
+<a name="235"><span class="lineNum">     235 </span>            :     Watch &amp; stop();</a>
+<a name="236"><span class="lineNum">     236 </span>            : /// pause the watch</a>
+<a name="237"><span class="lineNum">     237 </span>            :     Watch &amp; pause();</a>
+<a name="238"><span class="lineNum">     238 </span>            : /// returns a start-stop handler</a>
+<a name="239"><span class="lineNum">     239 </span>            :     Handler startStop();</a>
+<a name="240"><span class="lineNum">     240 </span>            : /// returns a start-pause handler</a>
+<a name="241"><span class="lineNum">     241 </span>            :     Handler startPause();</a>
+<a name="242"><span class="lineNum">     242 </span>            :   };</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : private:</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : /// Pointer to a log file.</a>
+<a name="247"><span class="lineNum">     247 </span>            : /// If set, the stopwatch is logged in its destructor.</a>
+<a name="248"><span class="lineNum">     248 </span>            :   Log*mylog=nullptr;</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : /// List of watches.</a>
+<a name="251"><span class="lineNum">     251 </span>            : /// Each watch is labeled with a string.</a>
+<a name="252"><span class="lineNum">     252 </span>            :   std::unordered_map&lt;std::string,Watch&gt; watches;</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : /// Log over stream os.</a>
+<a name="255"><span class="lineNum">     255 </span>            :   std::ostream&amp; log(std::ostream&amp; os)const;</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : public:</a>
+<a name="258"><span class="lineNum">     258 </span>            : // Constructor.</a>
+<a name="259"><span class="lineNum">     259 </span>            :   explicit Stopwatch() = default;</a>
+<a name="260"><span class="lineNum">     260 </span>            : // Constructor.</a>
+<a name="261"><span class="lineNum">     261 </span>            : // When destructing, stopwatch is logged.</a>
+<a name="262"><span class="lineNum">     262 </span>            : // Make sure that log survives stopwatch. Typically, it should be declared earlier, in order</a>
+<a name="263"><span class="lineNum">     263 </span>            : // to be destroyed later.</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">     805277 :   explicit Stopwatch(Log&amp;log): mylog(&amp;log) {}</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : // Destructor.</a>
+<a name="266"><span class="lineNum">     266 </span>            :   ~Stopwatch();</a>
+<a name="267"><span class="lineNum">     267 </span>            : /// Start timer named &quot;name&quot;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   Stopwatch&amp; start(const std::string&amp;name=StopwatchEmptyString());</a>
+<a name="269"><span class="lineNum">     269 </span>            : /// Stop timer named &quot;name&quot;</a>
+<a name="270"><span class="lineNum">     270 </span>            :   Stopwatch&amp; stop(const std::string&amp;name=StopwatchEmptyString());</a>
+<a name="271"><span class="lineNum">     271 </span>            : /// Pause timer named &quot;name&quot;</a>
+<a name="272"><span class="lineNum">     272 </span>            :   Stopwatch&amp; pause(const std::string&amp;name=StopwatchEmptyString());</a>
+<a name="273"><span class="lineNum">     273 </span>            : /// Dump all timers on an ostream</a>
+<a name="274"><span class="lineNum">     274 </span>            :   friend std::ostream&amp; operator&lt;&lt;(std::ostream&amp;,const Stopwatch&amp;);</a>
+<a name="275"><span class="lineNum">     275 </span>            : /// Start with exception safety, then stop.</a>
+<a name="276"><span class="lineNum">     276 </span>            : /// Starts the Stopwatch and returns an object that, when goes out of scope,</a>
+<a name="277"><span class="lineNum">     277 </span>            : /// stops the watch. This allows Stopwatch to be started and stopped in</a>
+<a name="278"><span class="lineNum">     278 </span>            : /// an exception safe manner.</a>
+<a name="279"><span class="lineNum">     279 </span>            :   Handler startStop(const std::string&amp;name=StopwatchEmptyString());</a>
+<a name="280"><span class="lineNum">     280 </span>            : /// Start with exception safety, then pause.</a>
+<a name="281"><span class="lineNum">     281 </span>            : /// Starts the Stopwatch and returns an object that, when goes out of scope,</a>
+<a name="282"><span class="lineNum">     282 </span>            : /// pauses the watch. This allows Stopwatch to be started and paused in</a>
+<a name="283"><span class="lineNum">     283 </span>            : /// an exception safe manner.</a>
+<a name="284"><span class="lineNum">     284 </span>            :   Handler startPause(const std::string&amp;name=StopwatchEmptyString());</a>
+<a name="285"><span class="lineNum">     285 </span>            : };</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : inline</a>
+<a name="288"><span class="lineNum">     288 </span>            : Stopwatch::Handler::Handler(Watch* watch,bool stop) :</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">    2649707 :   watch(watch),</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">    2649707 :   stop(stop)</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : {</a>
+<a name="292"><span class="lineNum">     292 </span>            :   watch-&gt;start();</a>
+<a name="293"><span class="lineNum">     293 </span>            : }</a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : inline</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">    6203636 : Stopwatch::Handler::~Handler() {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">    6203636 :   if(watch) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">    2649707 :     if(stop) watch-&gt;stop();</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">    1118951 :     else watch-&gt;pause();</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :   }</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">    6203636 : }</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : inline</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       1148 : Stopwatch&amp; Stopwatch::start(const std::string &amp; name) {</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :   watches[name].start();</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       1148 :   return *this;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : inline</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        574 : Stopwatch&amp; Stopwatch::stop(const std::string &amp; name) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        574 :   watches[name].stop();</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        574 :   return *this;</span></a>
+<a name="313"><span class="lineNum">     313 </span>            : }</a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span>            : inline</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        571 : Stopwatch&amp; Stopwatch::pause(const std::string &amp; name) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">        571 :   watches[name].pause();</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">        571 :   return *this;</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : inline</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">    1530756 : Stopwatch::Handler Stopwatch::startStop(const std::string&amp;name) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">    1530756 :   return watches[name].startStop();</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : inline</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">    1118951 : Stopwatch::Handler Stopwatch::startPause(const std::string&amp;name) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">    1118951 :   return watches[name].startPause();</span></a>
+<a name="329"><span class="lineNum">     329 </span>            : }</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            : inline</a>
+<a name="332"><span class="lineNum">     332 </span>            : Stopwatch::Handler::Handler(Handler &amp;&amp; handler) noexcept :</a>
+<a name="333"><span class="lineNum">     333 </span>            :   watch(handler.watch),</a>
+<a name="334"><span class="lineNum">     334 </span>            :   stop(handler.stop)</a>
+<a name="335"><span class="lineNum">     335 </span>            : {</a>
+<a name="336"><span class="lineNum">     336 </span>            :   handler.watch=nullptr;</a>
+<a name="337"><span class="lineNum">     337 </span>            : }</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : inline</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">       3493 : Stopwatch::Handler &amp; Stopwatch::Handler::operator=(Handler &amp;&amp; handler) noexcept {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       3493 :   if(this!=&amp;handler) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       3493 :     if(watch) {</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :       try {</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :         if(stop) watch-&gt;stop();</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :         else watch-&gt;pause();</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :       } catch(...) {</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : // this is to avoid problems with cppcheck, given than this method is declared as</a>
+<a name="348"><span class="lineNum">     348 </span>            : // noexcept and stop and pause might throw in case of an internal bug</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :         std::terminate();</span></a>
+<a name="350"><span class="lineNum">     350 </span>            :       }</a>
+<a name="351"><span class="lineNum">     351 </span>            :     }</a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       3493 :     watch=handler.watch;</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">       3493 :     stop=handler.stop;</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">       3493 :     handler.watch=nullptr;</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :   }</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       3493 :   return *this;</span></a>
+<a name="357"><span class="lineNum">     357 </span>            : }</a>
+<a name="358"><span class="lineNum">     358 </span>            : </a>
+<a name="359"><span class="lineNum">     359 </span>            : inline</a>
+<a name="360"><span class="lineNum">     360 </span>            : Stopwatch::Watch &amp; Stopwatch::Watch::start() {</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">    2651862 :   state=State::started;</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">    2651862 :   running++;</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">    2651862 :   lastStart=std::chrono::high_resolution_clock::now();</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   return *this;</a>
+<a name="365"><span class="lineNum">     365 </span>            : }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            : inline</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">    1532337 : Stopwatch::Watch &amp; Stopwatch::Watch::stop() {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">    1532337 :   pause();</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">    1532337 :   state=State::stopped;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">    1532337 :   cycles++;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">    1532337 :   total+=lap;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">    1532337 :   if(lap&gt;max)max=lap;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">    1532337 :   if(min&gt;lap || cycles==1)min=lap;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">    1532337 :   lap=0;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">    1532337 :   return *this;</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : }</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            : inline</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">    2651728 : Stopwatch::Watch &amp; Stopwatch::Watch::pause() {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">    2651728 :   state=State::paused;</span></a>
+<a name="382"><span class="lineNum">     382 </span>            : // In case of an internal bug (non matching start stop within the startStop or startPause interface)</a>
+<a name="383"><span class="lineNum">     383 </span>            : // this assertion could fail in a destructor.</a>
+<a name="384"><span class="lineNum">     384 </span>            : // If this happens, the program should crash immediately</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">    2651728 :   plumed_assert(running&gt;0) &lt;&lt; &quot;Non matching start/pause or start/stop commands in a Stopwatch&quot;;</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">    2651728 :   running--;</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : // notice: with exception safety the following might be converted to a plain error.</a>
+<a name="388"><span class="lineNum">     388 </span>            : // I leave it like this for now:</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">    2651728 :   if(running!=0) return *this;</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">    2651677 :   auto t=std::chrono::duration_cast&lt;std::chrono::nanoseconds&gt;(std::chrono::high_resolution_clock::now()-lastStart);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">    2651677 :   lap+=t.count();</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">    2651677 :   return *this;</span></a>
+<a name="393"><span class="lineNum">     393 </span>            : }</a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            : inline</a>
+<a name="396"><span class="lineNum">     396 </span>            : Stopwatch::Handler Stopwatch::Watch::startStop() {</a>
+<a name="397"><span class="lineNum">     397 </span>            :   return Handler( this,true );</a>
+<a name="398"><span class="lineNum">     398 </span>            : }</a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            : inline</a>
+<a name="401"><span class="lineNum">     401 </span>            : Stopwatch::Handler Stopwatch::Watch::startPause() {</a>
+<a name="402"><span class="lineNum">     402 </span>            :   return Handler( this,false );</a>
+<a name="403"><span class="lineNum">     403 </span>            : }</a>
+<a name="404"><span class="lineNum">     404 </span>            : </a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            : }</a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Subprocess.cpp.func-sort-c.html b/coverage/tools/Subprocess.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9c117e376d
--- /dev/null
+++ b/coverage/tools/Subprocess.cpp.func-sort-c.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Subprocess.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Subprocess.cpp<span style="font-size: 80%;"> (<a href="Subprocess.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryMed">75.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Subprocess.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#171">_ZN4PLMD10Subprocess7HandlerC2EOS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#177">_ZN4PLMD10Subprocess7HandleraSEOS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#145">_ZN4PLMD10Subprocess4contEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#151">_ZN4PLMD10Subprocess5flushEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#161">_ZN4PLMD10Subprocess7HandlerC2EPS0_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#167">_ZN4PLMD10Subprocess7HandlerD2Ev</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#155">_ZN4PLMD10Subprocess7getlineERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#54">_ZN4PLMD13SubprocessPid4contEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#139">_ZN4PLMD10Subprocess4stopEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#49">_ZN4PLMD13SubprocessPid4stopEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#34">_ZN4PLMDL26SubprocessPidGetenvSignalsEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#131">_ZN4PLMD10Subprocess9availableEv</a></td>
+              <td class="coverFnHi">85</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#70">_ZN4PLMD10SubprocessC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#117">_ZN4PLMD10SubprocessD2Ev</a></td>
+              <td class="coverFnHi">10002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#44">_ZN4PLMD13SubprocessPidC2Ei</a></td>
+              <td class="coverFnHi">10002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#59">_ZN4PLMD13SubprocessPidD2Ev</a></td>
+              <td class="coverFnHi">10002</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Subprocess.cpp.func.html b/coverage/tools/Subprocess.cpp.func.html
new file mode 100644
index 0000000000..5f268653fb
--- /dev/null
+++ b/coverage/tools/Subprocess.cpp.func.html
@@ -0,0 +1,136 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Subprocess.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Subprocess.cpp<span style="font-size: 80%;"> (<a href="Subprocess.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryMed">75.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Subprocess.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#145">_ZN4PLMD10Subprocess4contEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#139">_ZN4PLMD10Subprocess4stopEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#151">_ZN4PLMD10Subprocess5flushEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#171">_ZN4PLMD10Subprocess7HandlerC2EOS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#161">_ZN4PLMD10Subprocess7HandlerC2EPS0_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#167">_ZN4PLMD10Subprocess7HandlerD2Ev</a></td>
+              <td class="coverFnHi">16</td>
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+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#177">_ZN4PLMD10Subprocess7HandleraSEOS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#155">_ZN4PLMD10Subprocess7getlineERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#131">_ZN4PLMD10Subprocess9availableEv</a></td>
+              <td class="coverFnHi">85</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#70">_ZN4PLMD10SubprocessC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
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+              <td class="coverFnHi">10002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#54">_ZN4PLMD13SubprocessPid4contEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#49">_ZN4PLMD13SubprocessPid4stopEv</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#44">_ZN4PLMD13SubprocessPidC2Ei</a></td>
+              <td class="coverFnHi">10002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#59">_ZN4PLMD13SubprocessPidD2Ev</a></td>
+              <td class="coverFnHi">10002</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.cpp.gcov.html#34">_ZN4PLMDL26SubprocessPidGetenvSignalsEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Subprocess.cpp.gcov.html b/coverage/tools/Subprocess.cpp.gcov.html
new file mode 100644
index 0000000000..3683b322ee
--- /dev/null
+++ b/coverage/tools/Subprocess.cpp.gcov.html
@@ -0,0 +1,265 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Subprocess.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Subprocess.cpp<span style="font-size: 80%;"> (source / <a href="Subprocess.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryMed">75.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">16</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Subprocess.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;unistd.h&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;csignal&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;sys/wait.h&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #endif</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /// Retrieve PLUMED_ENABLE_SIGNALS.</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// Inline static so that it can store a static variable (for quicker access)</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// without adding a unique global symbol to a library including this header file.</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         34 : inline static bool SubprocessPidGetenvSignals() noexcept {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         34 :   static const bool res=std::getenv(&quot;PLUMED_ENABLE_SIGNALS&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         34 :   return res;</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : }</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Small utility class, used to avoid inclusion of unistd.h&gt; in a header file.</a>
+<a name="42"><span class="lineNum">      42 </span>            : class SubprocessPid {</a>
+<a name="43"><span class="lineNum">      43 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   pid_t pid;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">      10002 :   explicit SubprocessPid(pid_t pid):</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">      10002 :     pid(pid)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   {</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">      10002 :     plumed_assert(pid!=0 &amp;&amp; pid!=-1);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      10002 :   }</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         18 :   void stop() noexcept {</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :     // Signals give problems with MPI on Travis.</a>
+<a name="53"><span class="lineNum">      53 </span>            :     // I disable them for now.</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         18 :     if(SubprocessPidGetenvSignals()) if(pid!=0 &amp;&amp; pid!=-1) kill(pid,SIGSTOP);</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         18 :   }</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         16 :   void cont() noexcept {</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :     // Signals give problems with MPI on Travis.</a>
+<a name="58"><span class="lineNum">      58 </span>            :     // I disable them for now.</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         16 :     if(SubprocessPidGetenvSignals()) if(pid!=0 &amp;&amp; pid!=-1) kill(pid,SIGCONT);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         16 :   }</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      10002 :   ~SubprocessPid() {</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :     // this is apparently working also with MPI on Travis.</a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      10002 :     if(pid!=0 &amp;&amp; pid!=-1) {</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :       int status;</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      10002 :       kill(pid,SIGINT);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      10002 :       waitpid(pid, &amp;status, 0); // Wait for the child process to terminate</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     }</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      10002 :   }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : #endif</a>
+<a name="70"><span class="lineNum">      70 </span>            : };</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      10002 : Subprocess::Subprocess(const std::string &amp; cmd) {</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">      10002 :   char* arr [] = {</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     // const_cast are necessary here due to the declaration of execv</a>
+<a name="76"><span class="lineNum">      76 </span>            :     const_cast&lt;char*&gt;(&quot;/bin/sh&quot;),</a>
+<a name="77"><span class="lineNum">      77 </span>            :     const_cast&lt;char*&gt;(&quot;-c&quot;),</a>
+<a name="78"><span class="lineNum">      78 </span>            :     const_cast&lt;char*&gt;(cmd.c_str()),</a>
+<a name="79"><span class="lineNum">      79 </span>            :     nullptr</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      10002 :   };</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   int cp[2];</a>
+<a name="82"><span class="lineNum">      82 </span>            :   int pc[2];</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      10002 :   if(pipe(pc)&lt;0) plumed_error()&lt;&lt;&quot;error creating parent to child pipe&quot;;</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      10002 :   if(pipe(cp)&lt;0) plumed_error()&lt;&lt;&quot;error creating child to parent pipe&quot;;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      10002 :   pid_t pid=fork();</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      10002 :   switch(pid) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   case -1:</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     plumed_error()&lt;&lt;&quot;error forking&quot;;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     break;</a>
+<a name="90"><span class="lineNum">      90 </span>            : // CHILD:</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   case 0:</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineNoCov">          0 :     if(close(1)&lt;0) plumed_error()&lt;&lt;&quot;error closing file&quot;;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     if(dup(cp[1])&lt;0) plumed_error()&lt;&lt;&quot;error duplicating file&quot;;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     if(close(0)&lt;0) plumed_error()&lt;&lt;&quot;error closing file&quot;;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     if(dup(pc[0])&lt;0) plumed_error()&lt;&lt;&quot;error duplicating file&quot;;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :     if(close(pc[1])&lt;0) plumed_error()&lt;&lt;&quot;error closing file&quot;;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     if(close(cp[0])&lt;0) plumed_error()&lt;&lt;&quot;error closing file&quot;;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     execv(arr[0],arr);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :     plumed_error()&lt;&lt;&quot;error in script file&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span>            : // PARENT::</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      10002 :   default:</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">      20004 :     this-&gt;pid=Tools::make_unique&lt;SubprocessPid&gt;(pid);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">      10002 :     if(close(pc[0])&lt;0) plumed_error()&lt;&lt;&quot;error closing file&quot;;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      10002 :     if(close(cp[1])&lt;0) plumed_error()&lt;&lt;&quot;error closing file&quot;;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">      10002 :     fpc=pc[1];</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">      10002 :     fcp=cp[0];</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">      10002 :     fppc=fdopen(fpc,&quot;w&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      10002 :     parent_to_child.link(fppc);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      10002 :     fpcp=fdopen(fcp,&quot;r&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      10002 :     child_to_parent.link(fpcp);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span>            : #else</a>
+<a name="115"><span class="lineNum">     115 </span>            :   plumed_error()&lt;&lt;&quot;Subprocess not supported&quot;;</a>
+<a name="116"><span class="lineNum">     116 </span>            : #endif</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      10002 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      10002 : Subprocess::~Subprocess() {</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="121"><span class="lineNum">     121 </span>            : // close files:</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">      10002 :   fclose(fppc);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      10002 :   fclose(fpcp);</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : // fclose also closes the underlying descriptors,</a>
+<a name="125"><span class="lineNum">     125 </span>            : // so this is not needed:</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      10002 :   close(fpc);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      10002 :   close(fcp);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : // after closing the communication, the subprocess is killed</a>
+<a name="129"><span class="lineNum">     129 </span>            : // in pid's destructor</a>
+<a name="130"><span class="lineNum">     130 </span>            : #endif</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">      10002 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         85 : bool Subprocess::available() noexcept {</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         85 :   return true;</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : #else</a>
+<a name="137"><span class="lineNum">     137 </span>            :   return false;</a>
+<a name="138"><span class="lineNum">     138 </span>            : #endif</a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         18 : void Subprocess::stop() noexcept {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         18 :   pid-&gt;stop();</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : #endif</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         18 : }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         16 : void Subprocess::cont() noexcept {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : #ifdef __PLUMED_HAS_SUBPROCESS</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         16 :   pid-&gt;cont();</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : #endif</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         16 : }</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         16 : void Subprocess::flush() {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         16 :   parent_to_child.flush();</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         16 : }</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         16 : Subprocess &amp; Subprocess::getline(std::string &amp; line) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         16 :   child_to_parent.getline(line);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         16 :   if(!child_to_parent) plumed_error() &lt;&lt;&quot;error reading subprocess&quot;;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         16 :   return (*this);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         16 : Subprocess::Handler::Handler(Subprocess *sp) noexcept:</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         16 :   sp(sp)</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : {</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         16 :   sp-&gt;cont();</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         16 : }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         16 : Subprocess::Handler::~Handler() {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         16 :   if(sp) sp-&gt;stop();</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         16 : }</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 : Subprocess::Handler::Handler(Handler &amp;&amp; handler) noexcept :</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :   sp(handler.sp)</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : {</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :   handler.sp=nullptr;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 : Subprocess::Handler &amp; Subprocess::Handler::operator=(Handler &amp;&amp; handler) noexcept {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   if(this!=&amp;handler) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :     if(sp) sp-&gt;stop();</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 :     sp=handler.sp;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :     handler.sp=nullptr;</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Subprocess.h.func-sort-c.html b/coverage/tools/Subprocess.h.func-sort-c.html
new file mode 100644
index 0000000000..542dedf2c9
--- /dev/null
+++ b/coverage/tools/Subprocess.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Subprocess.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Subprocess.h<span style="font-size: 80%;"> (<a href="Subprocess.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Subprocess.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.h.gcov.html#132">_ZN4PLMDlsIA2_cEERNS_10SubprocessES3_RKT_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.h.gcov.html#132">_ZN4PLMDlsINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEERNS_10SubprocessES8_RKT_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Subprocess.h.func.html b/coverage/tools/Subprocess.h.func.html
new file mode 100644
index 0000000000..179b47c26d
--- /dev/null
+++ b/coverage/tools/Subprocess.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Subprocess.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Subprocess.h<span style="font-size: 80%;"> (<a href="Subprocess.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Subprocess.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.h.gcov.html#132">_ZN4PLMDlsIA2_cEERNS_10SubprocessES3_RKT_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Subprocess.h.gcov.html#132">_ZN4PLMDlsINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEERNS_10SubprocessES8_RKT_</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Subprocess.h.gcov.html b/coverage/tools/Subprocess.h.gcov.html
new file mode 100644
index 0000000000..9e9c02aaa5
--- /dev/null
+++ b/coverage/tools/Subprocess.h.gcov.html
@@ -0,0 +1,218 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Subprocess.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Subprocess.h<span style="font-size: 80%;"> (source / <a href="Subprocess.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2019-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Subprocess_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Subprocess_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;OFile.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;IFile.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;string&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstdio&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;memory&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /// Small class to avoid including unistd.h here</a>
+<a name="34"><span class="lineNum">      34 </span>            : class SubprocessPid;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /**</a>
+<a name="37"><span class="lineNum">      37 </span>            : Class managing a subprocess.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The subprocess is launched and one can interact with it through a pipe.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : In order not to consume resources, it might be possible to use this syntax:</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : \verbatim</a>
+<a name="44"><span class="lineNum">      44 </span>            : // at construction:</a>
+<a name="45"><span class="lineNum">      45 </span>            : Subprocess sp;</a>
+<a name="46"><span class="lineNum">      46 </span>            : sp.stop();</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : // when needed</a>
+<a name="49"><span class="lineNum">      49 </span>            : {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   auto h=sp.contStop();</a>
+<a name="51"><span class="lineNum">      51 </span>            :   sp&lt;&lt;&quot;command\n&quot;;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   sp.flush();</a>
+<a name="53"><span class="lineNum">      53 </span>            :   sp.getline(answer);</a>
+<a name="54"><span class="lineNum">      54 </span>            : }</a>
+<a name="55"><span class="lineNum">      55 </span>            : // when h goes out of scope, subprocess is stopped again.</a>
+<a name="56"><span class="lineNum">      56 </span>            : // If an exception is raised in the block, the subprocess is stopped as well.</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endverbatim</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : \warning</a>
+<a name="60"><span class="lineNum">      60 </span>            : Currently `stop` and `cont` are giving problems with some MPI implementation,</a>
+<a name="61"><span class="lineNum">      61 </span>            : In addition, notice that the stop signal is only sent to the child process and</a>
+<a name="62"><span class="lineNum">      62 </span>            : not to the subsequently spawn processes, so it might not work as intended.</a>
+<a name="63"><span class="lineNum">      63 </span>            : This feature is left here but is probably no a good idea to use it.</a>
+<a name="64"><span class="lineNum">      64 </span>            : It can be enabled with `export PLUMED_ENABLE_SIGNALS=1`.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : */</a>
+<a name="67"><span class="lineNum">      67 </span>            : class Subprocess {</a>
+<a name="68"><span class="lineNum">      68 </span>            :   /// Process ID.</a>
+<a name="69"><span class="lineNum">      69 </span>            :   /// We store this rather than pid_t to avoid including &lt;unistd.h&gt; in this header file.</a>
+<a name="70"><span class="lineNum">      70 </span>            :   /// This remains nullptr in the child process.</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::unique_ptr&lt;SubprocessPid&gt; pid;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   /// File descriptor, parent to child</a>
+<a name="73"><span class="lineNum">      73 </span>            :   int fpc=0;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   /// File descriptor, child to parent</a>
+<a name="75"><span class="lineNum">      75 </span>            :   int fcp=0;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   /// File pointer, parent to child</a>
+<a name="77"><span class="lineNum">      77 </span>            :   FILE* fppc=NULL;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   /// File pointer, child to parent</a>
+<a name="79"><span class="lineNum">      79 </span>            :   FILE* fpcp=NULL;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   /// PLUMED file object, parent to child.</a>
+<a name="81"><span class="lineNum">      81 </span>            :   /// Used to simplify formatting</a>
+<a name="82"><span class="lineNum">      82 </span>            :   OFile parent_to_child;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   /// PLUMED file object, child to parent.</a>
+<a name="84"><span class="lineNum">      84 </span>            :   /// Used to simplify formatting</a>
+<a name="85"><span class="lineNum">      85 </span>            :   IFile child_to_parent;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   /// Class used to cont/stop a Subprocess in an exception safe manner.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   class Handler {</a>
+<a name="89"><span class="lineNum">      89 </span>            :     Subprocess* sp=nullptr;</a>
+<a name="90"><span class="lineNum">      90 </span>            :     /// Private constructor.</a>
+<a name="91"><span class="lineNum">      91 </span>            :     /// Only to be called by Subprocess::contStop()</a>
+<a name="92"><span class="lineNum">      92 </span>            :     explicit Handler(Subprocess* sp) noexcept;</a>
+<a name="93"><span class="lineNum">      93 </span>            :     friend class Subprocess;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   public:</a>
+<a name="95"><span class="lineNum">      95 </span>            :     /// Default constructor</a>
+<a name="96"><span class="lineNum">      96 </span>            :     Handler() = default;</a>
+<a name="97"><span class="lineNum">      97 </span>            :     /// Destructor stops the subprocess.</a>
+<a name="98"><span class="lineNum">      98 </span>            :     ~Handler();</a>
+<a name="99"><span class="lineNum">      99 </span>            :     /// Default copy constructor is deleted (not copyable)</a>
+<a name="100"><span class="lineNum">     100 </span>            :     Handler(const Handler &amp;) = delete;</a>
+<a name="101"><span class="lineNum">     101 </span>            :     /// Default copy assignment is deleted (not copyable)</a>
+<a name="102"><span class="lineNum">     102 </span>            :     Handler &amp; operator=(const Handler &amp; handler) = delete;</a>
+<a name="103"><span class="lineNum">     103 </span>            :     /// Move constructor.</a>
+<a name="104"><span class="lineNum">     104 </span>            :     Handler(Handler &amp;&amp;) noexcept;</a>
+<a name="105"><span class="lineNum">     105 </span>            :     /// Move assignment.</a>
+<a name="106"><span class="lineNum">     106 </span>            :     Handler &amp; operator=(Handler &amp;&amp; handler) noexcept;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   };</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Constructor with a command line.</a>
+<a name="109"><span class="lineNum">     109 </span>            :   explicit Subprocess(const std::string &amp; cmd);</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// Destructor</a>
+<a name="111"><span class="lineNum">     111 </span>            :   ~Subprocess();</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// Flush communication to process.</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void flush();</a>
+<a name="114"><span class="lineNum">     114 </span>            : /// Check if subprocess facilities are available.</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// If it returns false, any call to Subprocess constructor will raise an exception.</a>
+<a name="116"><span class="lineNum">     116 </span>            :   static bool available() noexcept;</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Get a line from the subprocess.</a>
+<a name="118"><span class="lineNum">     118 </span>            :   Subprocess &amp; getline(std::string &amp;);</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Write something to the subprocess.</a>
+<a name="120"><span class="lineNum">     120 </span>            :   template &lt;class T&gt; friend Subprocess&amp; operator&lt;&lt;(Subprocess&amp; ep,const T &amp;t);</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Send a SIGCONT to the subprocess.</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// Better used through contStop() method.</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void cont() noexcept;</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Send a SIGSTOP to the subprocess.</a>
+<a name="125"><span class="lineNum">     125 </span>            : /// Better used through contStop() method.</a>
+<a name="126"><span class="lineNum">     126 </span>            :   void stop() noexcept;</a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Returns a handler to temporarily resume the process.</a>
+<a name="128"><span class="lineNum">     128 </span>            :   Handler contStop() noexcept {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         16 :     return Handler(this);</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   }</a>
+<a name="131"><span class="lineNum">     131 </span>            : };</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : template &lt;class T&gt;</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         32 : Subprocess&amp; operator&lt;&lt;(Subprocess&amp; ep,const T &amp;t) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         32 :   ep.parent_to_child&lt;&lt;t;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         32 :   return ep;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : }</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : #endif</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/SwitchingFunction.cpp.func-sort-c.html b/coverage/tools/SwitchingFunction.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cac4ffe090
--- /dev/null
+++ b/coverage/tools/SwitchingFunction.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/SwitchingFunction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - SwitchingFunction.cpp<span style="font-size: 80%;"> (<a href="SwitchingFunction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">256</td>
+            <td class="headerCovTableEntry">263</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="SwitchingFunction.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#536">_ZNK4PLMD17SwitchingFunction6get_d0Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#532">_ZNK4PLMD17SwitchingFunction6get_r0Ev</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#511">_ZN4PLMD17SwitchingFunction3setEiidd</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#174">_ZN4PLMD17SwitchingFunction16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#184">_ZN4PLMD17SwitchingFunction3setERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_</a></td>
+              <td class="coverFnHi">1019</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#323">_ZNK4PLMD17SwitchingFunction11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">1069</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#391">_ZNK4PLMD17SwitchingFunction12calculateSqrEdRd</a></td>
+              <td class="coverFnHi">19721455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#544">_ZNK4PLMD17SwitchingFunction9get_dmax2Ev</a></td>
+              <td class="coverFnHi">23893569</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#363">_ZNK4PLMD17SwitchingFunction11do_rationalEdRdii</a></td>
+              <td class="coverFnHi">41286095</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#429">_ZNK4PLMD17SwitchingFunction9calculateEdRd</a></td>
+              <td class="coverFnHi">88945983</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#540">_ZNK4PLMD17SwitchingFunction8get_dmaxEv</a></td>
+              <td class="coverFnHi">117918073</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/SwitchingFunction.cpp.func.html b/coverage/tools/SwitchingFunction.cpp.func.html
new file mode 100644
index 0000000000..b95a3816d0
--- /dev/null
+++ b/coverage/tools/SwitchingFunction.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/SwitchingFunction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - SwitchingFunction.cpp<span style="font-size: 80%;"> (<a href="SwitchingFunction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">256</td>
+            <td class="headerCovTableEntry">263</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="SwitchingFunction.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#174">_ZN4PLMD17SwitchingFunction16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">91</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#184">_ZN4PLMD17SwitchingFunction3setERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS6_</a></td>
+              <td class="coverFnHi">1019</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#511">_ZN4PLMD17SwitchingFunction3setEiidd</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#323">_ZNK4PLMD17SwitchingFunction11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">1069</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#363">_ZNK4PLMD17SwitchingFunction11do_rationalEdRdii</a></td>
+              <td class="coverFnHi">41286095</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#391">_ZNK4PLMD17SwitchingFunction12calculateSqrEdRd</a></td>
+              <td class="coverFnHi">19721455</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#536">_ZNK4PLMD17SwitchingFunction6get_d0Ev</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#532">_ZNK4PLMD17SwitchingFunction6get_r0Ev</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#540">_ZNK4PLMD17SwitchingFunction8get_dmaxEv</a></td>
+              <td class="coverFnHi">117918073</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#429">_ZNK4PLMD17SwitchingFunction9calculateEdRd</a></td>
+              <td class="coverFnHi">88945983</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="SwitchingFunction.cpp.gcov.html#544">_ZNK4PLMD17SwitchingFunction9get_dmax2Ev</a></td>
+              <td class="coverFnHi">23893569</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/SwitchingFunction.cpp.gcov.html b/coverage/tools/SwitchingFunction.cpp.gcov.html
new file mode 100644
index 0000000000..d17dc4d3ea
--- /dev/null
+++ b/coverage/tools/SwitchingFunction.cpp.gcov.html
@@ -0,0 +1,629 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/SwitchingFunction.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - SwitchingFunction.cpp<span style="font-size: 80%;"> (source / <a href="SwitchingFunction.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">256</td>
+            <td class="headerCovTableEntry">263</td>
+            <td class="headerCovTableEntryHi">97.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;SwitchingFunction.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Keywords.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;OpenMP.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;vector&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;limits&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;algorithm&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #define PI 3.14159265358979323846</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC INTERNAL switchingfunction</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Functions that measure whether values are less than a certain quantity.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Switching functions \f$s(r)\f$ take a minimum of one input parameter \f$r_0\f$.</a>
+<a name="39"><span class="lineNum">      39 </span>            : For \f$r \le d_0 \quad s(r)=1.0\f$ while for \f$r &gt; d_0\f$ the function decays smoothly to 0.</a>
+<a name="40"><span class="lineNum">      40 </span>            : The various switching functions available in PLUMED differ in terms of how this decay is performed.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Where there is an accepted convention in the literature (e.g. \ref COORDINATION) on the form of the</a>
+<a name="43"><span class="lineNum">      43 </span>            : switching function we use the convention as the default.  However, the flexibility to use different</a>
+<a name="44"><span class="lineNum">      44 </span>            : switching functions is always present generally through a single keyword. This keyword generally</a>
+<a name="45"><span class="lineNum">      45 </span>            : takes an input with the following form:</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : \verbatim</a>
+<a name="48"><span class="lineNum">      48 </span>            : KEYWORD={TYPE &lt;list of parameters&gt;}</a>
+<a name="49"><span class="lineNum">      49 </span>            : \endverbatim</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The following table contains a list of the various switching functions that are available in PLUMED 2</a>
+<a name="52"><span class="lineNum">      52 </span>            : together with an example input.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : &lt;table align=center frame=void width=95%% cellpadding=5%%&gt;</a>
+<a name="55"><span class="lineNum">      55 </span>            : &lt;tr&gt;</a>
+<a name="56"><span class="lineNum">      56 </span>            : &lt;td&gt; TYPE &lt;/td&gt; &lt;td&gt; FUNCTION &lt;/td&gt; &lt;td&gt; EXAMPLE INPUT &lt;/td&gt; &lt;td&gt; DEFAULT PARAMETERS &lt;/td&gt;</a>
+<a name="57"><span class="lineNum">      57 </span>            : &lt;/tr&gt; &lt;tr&gt; &lt;td&gt;RATIONAL &lt;/td&gt; &lt;td&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f$</a>
+<a name="59"><span class="lineNum">      59 </span>            : s(r)=\frac{ 1 - \left(\frac{ r - d_0 }{ r_0 }\right)^{n} }{ 1 - \left(\frac{ r - d_0 }{ r_0 }\right)^{m} }</a>
+<a name="60"><span class="lineNum">      60 </span>            : \f$</a>
+<a name="61"><span class="lineNum">      61 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="62"><span class="lineNum">      62 </span>            : {RATIONAL R_0=\f$r_0\f$ D_0=\f$d_0\f$ NN=\f$n\f$ MM=\f$m\f$}</a>
+<a name="63"><span class="lineNum">      63 </span>            : &lt;/td&gt; &lt;td&gt; \f$d_0=0.0\f$, \f$n=6\f$, \f$m=2n\f$ &lt;/td&gt;</a>
+<a name="64"><span class="lineNum">      64 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="65"><span class="lineNum">      65 </span>            : &lt;td&gt; EXP &lt;/td&gt; &lt;td&gt;</a>
+<a name="66"><span class="lineNum">      66 </span>            : \f$</a>
+<a name="67"><span class="lineNum">      67 </span>            : s(r)=\exp\left(-\frac{ r - d_0 }{ r_0 }\right)</a>
+<a name="68"><span class="lineNum">      68 </span>            : \f$</a>
+<a name="69"><span class="lineNum">      69 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="70"><span class="lineNum">      70 </span>            : {EXP  R_0=\f$r_0\f$ D_0=\f$d_0\f$}</a>
+<a name="71"><span class="lineNum">      71 </span>            : &lt;/td&gt; &lt;td&gt; \f$d_0=0.0\f$ &lt;/td&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="73"><span class="lineNum">      73 </span>            : &lt;td&gt; GAUSSIAN &lt;/td&gt; &lt;td&gt;</a>
+<a name="74"><span class="lineNum">      74 </span>            : \f$</a>
+<a name="75"><span class="lineNum">      75 </span>            : s(r)=\exp\left(-\frac{ (r - d_0)^2 }{ 2r_0^2 }\right)</a>
+<a name="76"><span class="lineNum">      76 </span>            : \f$</a>
+<a name="77"><span class="lineNum">      77 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="78"><span class="lineNum">      78 </span>            : {GAUSSIAN R_0=\f$r_0\f$ D_0=\f$d_0\f$}</a>
+<a name="79"><span class="lineNum">      79 </span>            : &lt;/td&gt; &lt;td&gt; \f$d_0=0.0\f$ &lt;/td&gt;</a>
+<a name="80"><span class="lineNum">      80 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="81"><span class="lineNum">      81 </span>            : &lt;td&gt; SMAP &lt;/td&gt; &lt;td&gt;</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f$</a>
+<a name="83"><span class="lineNum">      83 </span>            : s(r) = \left[ 1 + ( 2^{a/b} -1 )\left( \frac{r-d_0}{r_0} \right)^a \right]^{-b/a}</a>
+<a name="84"><span class="lineNum">      84 </span>            : \f$</a>
+<a name="85"><span class="lineNum">      85 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="86"><span class="lineNum">      86 </span>            : {SMAP R_0=\f$r_0\f$ D_0=\f$d_0\f$ A=\f$a\f$ B=\f$b\f$}</a>
+<a name="87"><span class="lineNum">      87 </span>            : &lt;/td&gt; &lt;td&gt; \f$d_0=0.0\f$ &lt;/td&gt;</a>
+<a name="88"><span class="lineNum">      88 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="89"><span class="lineNum">      89 </span>            : &lt;td&gt; Q &lt;/td&gt; &lt;td&gt;</a>
+<a name="90"><span class="lineNum">      90 </span>            : \f$</a>
+<a name="91"><span class="lineNum">      91 </span>            : s(r) = \frac{1}{1 + \exp(\beta(r_{ij} - \lambda r_{ij}^0))}</a>
+<a name="92"><span class="lineNum">      92 </span>            : \f$</a>
+<a name="93"><span class="lineNum">      93 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="94"><span class="lineNum">      94 </span>            : {Q REF=\f$r_{ij}^0\f$ BETA=\f$\beta\f$ LAMBDA=\f$\lambda\f$ }</a>
+<a name="95"><span class="lineNum">      95 </span>            : &lt;/td&gt; &lt;td&gt; \f$\lambda=1.8\f$,  \f$\beta=50 nm^-1\f$ (all-atom)&lt;br/&gt;\f$\lambda=1.5\f$,  \f$\beta=50 nm^-1\f$ (coarse-grained)  &lt;/td&gt;</a>
+<a name="96"><span class="lineNum">      96 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="97"><span class="lineNum">      97 </span>            : &lt;td&gt; CUBIC &lt;/td&gt; &lt;td&gt;</a>
+<a name="98"><span class="lineNum">      98 </span>            : \f$</a>
+<a name="99"><span class="lineNum">      99 </span>            : s(r) = (y-1)^2(1+2y) \qquad \textrm{where} \quad y = \frac{r - r_1}{r_0-r_1}</a>
+<a name="100"><span class="lineNum">     100 </span>            : \f$</a>
+<a name="101"><span class="lineNum">     101 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="102"><span class="lineNum">     102 </span>            : {CUBIC D_0=\f$r_1\f$ D_MAX=\f$r_0\f$}</a>
+<a name="103"><span class="lineNum">     103 </span>            : &lt;/td&gt; &lt;td&gt; &lt;/td&gt;</a>
+<a name="104"><span class="lineNum">     104 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="105"><span class="lineNum">     105 </span>            : &lt;td&gt; TANH &lt;/td&gt; &lt;td&gt;</a>
+<a name="106"><span class="lineNum">     106 </span>            : \f$</a>
+<a name="107"><span class="lineNum">     107 </span>            : s(r) = 1 - \tanh\left( \frac{ r - d_0 }{ r_0 } \right)</a>
+<a name="108"><span class="lineNum">     108 </span>            : \f$</a>
+<a name="109"><span class="lineNum">     109 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="110"><span class="lineNum">     110 </span>            : {TANH R_0=\f$r_0\f$ D_0=\f$d_0\f$}</a>
+<a name="111"><span class="lineNum">     111 </span>            : &lt;/td&gt; &lt;td&gt; &lt;/td&gt;</a>
+<a name="112"><span class="lineNum">     112 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="113"><span class="lineNum">     113 </span>            : &lt;td&gt; COSINUS &lt;/td&gt; &lt;td&gt;</a>
+<a name="114"><span class="lineNum">     114 </span>            : \f$s(r) =\left\{\begin{array}{ll}</a>
+<a name="115"><span class="lineNum">     115 </span>            :    1                                                           &amp; \mathrm{if } r \leq d_0 \\</a>
+<a name="116"><span class="lineNum">     116 </span>            :    0.5 \left( \cos ( \frac{ r - d_0 }{ r_0 } \pi ) + 1 \right) &amp; \mathrm{if } d_0 &lt; r\leq d_0 + r_0 \\</a>
+<a name="117"><span class="lineNum">     117 </span>            :    0                                                           &amp; \mathrm{if } r &lt; d_0 + r_0</a>
+<a name="118"><span class="lineNum">     118 </span>            :   \end{array}\right.</a>
+<a name="119"><span class="lineNum">     119 </span>            : \f$</a>
+<a name="120"><span class="lineNum">     120 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="121"><span class="lineNum">     121 </span>            : {COSINUS R_0=\f$r_0\f$ D_0=\f$d_0\f$}</a>
+<a name="122"><span class="lineNum">     122 </span>            : &lt;/td&gt; &lt;td&gt; &lt;/td&gt;</a>
+<a name="123"><span class="lineNum">     123 </span>            : &lt;/tr&gt; &lt;tr&gt;</a>
+<a name="124"><span class="lineNum">     124 </span>            : &lt;td&gt; CUSTOM &lt;/td&gt; &lt;td&gt;</a>
+<a name="125"><span class="lineNum">     125 </span>            : \f$</a>
+<a name="126"><span class="lineNum">     126 </span>            : s(r) = FUNC</a>
+<a name="127"><span class="lineNum">     127 </span>            : \f$</a>
+<a name="128"><span class="lineNum">     128 </span>            : &lt;/td&gt; &lt;td&gt;</a>
+<a name="129"><span class="lineNum">     129 </span>            : {CUSTOM FUNC=1/(1+x^6) R_0=\f$r_0\f$ D_0=\f$d_0\f$}</a>
+<a name="130"><span class="lineNum">     130 </span>            : &lt;/td&gt; &lt;td&gt; &lt;/td&gt;</a>
+<a name="131"><span class="lineNum">     131 </span>            : &lt;/tr&gt;</a>
+<a name="132"><span class="lineNum">     132 </span>            : &lt;/table&gt;</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : Notice that for backward compatibility we allow using `MATHEVAL` instead of `CUSTOM`.</a>
+<a name="135"><span class="lineNum">     135 </span>            : Also notice that if the a `CUSTOM` switching function only depends on even powers of `x` it can be</a>
+<a name="136"><span class="lineNum">     136 </span>            : made faster by using `x2` as a variable. For instance</a>
+<a name="137"><span class="lineNum">     137 </span>            : \verbatim</a>
+<a name="138"><span class="lineNum">     138 </span>            : {CUSTOM FUNC=1/(1+x2^3) R_0=0.3}</a>
+<a name="139"><span class="lineNum">     139 </span>            : \endverbatim</a>
+<a name="140"><span class="lineNum">     140 </span>            : is equivalent to</a>
+<a name="141"><span class="lineNum">     141 </span>            : \verbatim</a>
+<a name="142"><span class="lineNum">     142 </span>            : {CUSTOM FUNC=1/(1+x^6) R_0=0.3}</a>
+<a name="143"><span class="lineNum">     143 </span>            : \endverbatim</a>
+<a name="144"><span class="lineNum">     144 </span>            : but runs faster. The reason is that there is an expensive square root calculation that can be optimized out.</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : \attention</a>
+<a name="148"><span class="lineNum">     148 </span>            : With the default implementation CUSTOM is slower than other functions</a>
+<a name="149"><span class="lineNum">     149 </span>            : (e.g., it is slower than an equivalent RATIONAL function by approximately a factor 2).</a>
+<a name="150"><span class="lineNum">     150 </span>            : Checkout page \ref Lepton to see how to improve its performance.</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : For all the switching functions in the above table one can also specify a further (optional) parameter using the parameter</a>
+<a name="153"><span class="lineNum">     153 </span>            : keyword D_MAX to assert that for \f$r&gt;d_{\textrm{max}}\f$ the switching function can be assumed equal to zero.</a>
+<a name="154"><span class="lineNum">     154 </span>            : In this case the function is brought smoothly to zero by stretching and shifting it.</a>
+<a name="155"><span class="lineNum">     155 </span>            : \verbatim</a>
+<a name="156"><span class="lineNum">     156 </span>            : KEYWORD={RATIONAL R_0=1 D_MAX=3}</a>
+<a name="157"><span class="lineNum">     157 </span>            : \endverbatim</a>
+<a name="158"><span class="lineNum">     158 </span>            : the resulting switching function will be</a>
+<a name="159"><span class="lineNum">     159 </span>            : \f$</a>
+<a name="160"><span class="lineNum">     160 </span>            : s(r) = \frac{s'(r)-s'(d_{max})}{s'(0)-s'(d_{max})}</a>
+<a name="161"><span class="lineNum">     161 </span>            : \f$</a>
+<a name="162"><span class="lineNum">     162 </span>            : where</a>
+<a name="163"><span class="lineNum">     163 </span>            : \f$</a>
+<a name="164"><span class="lineNum">     164 </span>            : s'(r)=\frac{1-r^6}{1-r^{12}}</a>
+<a name="165"><span class="lineNum">     165 </span>            : \f$</a>
+<a name="166"><span class="lineNum">     166 </span>            : Since PLUMED 2.2 this is the default. The old behavior (no stretching) can be obtained with the</a>
+<a name="167"><span class="lineNum">     167 </span>            : NOSTRETCH flag. The NOSTRETCH keyword is only provided for backward compatibility and might be</a>
+<a name="168"><span class="lineNum">     168 </span>            : removed in the future. Similarly, the STRETCH keyword is still allowed but has no effect.</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : Notice that switching functions defined with the simplified syntax are never stretched</a>
+<a name="171"><span class="lineNum">     171 </span>            : for backward compatibility. This might change in the future.</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : */</a>
+<a name="174"><span class="lineNum">     174 </span>            : //+ENDPLUMEDOC</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         91 : void SwitchingFunction::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        182 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;the value of R_0 in the switching function&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        182 :   keys.add(&quot;compulsory&quot;,&quot;D_0&quot;,&quot;0.0&quot;,&quot;the value of D_0 in the switching function&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        182 :   keys.add(&quot;optional&quot;,&quot;D_MAX&quot;,&quot;the value at which the switching function can be assumed equal to zero&quot;);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        182 :   keys.add(&quot;compulsory&quot;,&quot;NN&quot;,&quot;6&quot;,&quot;the value of n in the switching function (only needed for TYPE=RATIONAL)&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        182 :   keys.add(&quot;compulsory&quot;,&quot;MM&quot;,&quot;0&quot;,&quot;the value of m in the switching function (only needed for TYPE=RATIONAL); 0 implies 2*NN&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        182 :   keys.add(&quot;compulsory&quot;,&quot;A&quot;,&quot;the value of a in the switching function (only needed for TYPE=SMAP)&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        182 :   keys.add(&quot;compulsory&quot;,&quot;B&quot;,&quot;the value of b in the switching function (only needed for TYPE=SMAP)&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         91 : }</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       1019 : void SwitchingFunction::set(const std::string &amp; definition,std::string&amp; errormsg) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       1019 :   std::vector&lt;std::string&gt; data=Tools::getWords(definition);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       1019 :   if( data.size()&lt;1 ) {</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     errormsg=&quot;missing all input for switching function&quot;;</a>
+<a name="190"><span class="lineNum">     190 </span>            :     return;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   }</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1019 :   std::string name=data[0];</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   data.erase(data.begin());</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       1019 :   invr0=0.0;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1019 :   invr0_2=0.0;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       1019 :   d0=0.0;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       1019 :   dmax=std::numeric_limits&lt;double&gt;::max();</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       1019 :   dmax_2=std::numeric_limits&lt;double&gt;::max();</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       1019 :   stretch=1.0;</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">       1019 :   shift=0.0;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">       1019 :   init=true;</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   bool present;</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       1019 :   present=Tools::findKeyword(data,&quot;D_0&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       1313 :   if(present &amp;&amp; !Tools::parse(data,&quot;D_0&quot;,d0)) errormsg=&quot;could not parse D_0&quot;;</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       1019 :   present=Tools::findKeyword(data,&quot;D_MAX&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       1247 :   if(present &amp;&amp; !Tools::parse(data,&quot;D_MAX&quot;,dmax)) errormsg=&quot;could not parse D_MAX&quot;;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       1019 :   if(dmax&lt;std::sqrt(std::numeric_limits&lt;double&gt;::max())) dmax_2=dmax*dmax;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       1019 :   bool dostretch=false;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       1019 :   Tools::parseFlag(data,&quot;STRETCH&quot;,dostretch); // this is ignored now</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       1019 :   dostretch=true;</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">       1019 :   bool dontstretch=false;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       1019 :   Tools::parseFlag(data,&quot;NOSTRETCH&quot;,dontstretch); // this is ignored now</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1019 :   if(dontstretch) dostretch=false;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   double r0;</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       1019 :   if(name==&quot;CUBIC&quot;) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         18 :     r0 = dmax - d0;</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   } else {</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       1001 :     bool found_r0=Tools::parse(data,&quot;R_0&quot;,r0);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       1001 :     if(!found_r0) errormsg=&quot;R_0 is required&quot;;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">       1019 :   invr0=1.0/r0;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">       1019 :   invr0_2=invr0*invr0;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">       1019 :   if(name==&quot;RATIONAL&quot;) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        291 :     type=rational;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">        291 :     nn=6;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        291 :     mm=0;</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        291 :     present=Tools::findKeyword(data,&quot;NN&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        441 :     if(present &amp;&amp; !Tools::parse(data,&quot;NN&quot;,nn)) errormsg=&quot;could not parse NN&quot;;</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        291 :     present=Tools::findKeyword(data,&quot;MM&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        441 :     if(present &amp;&amp; !Tools::parse(data,&quot;MM&quot;,mm)) errormsg=&quot;could not parse MM&quot;;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        291 :     if(mm==0) mm=2*nn;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        357 :     fastrational=(nn%2==0 &amp;&amp; mm%2==0 &amp;&amp; d0==0.0);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        728 :   } else if(name==&quot;SMAP&quot;) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         10 :     type=smap;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         10 :     present=Tools::findKeyword(data,&quot;A&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         30 :     if(present &amp;&amp; !Tools::parse(data,&quot;A&quot;,a)) errormsg=&quot;could not parse A&quot;;</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         10 :     present=Tools::findKeyword(data,&quot;B&quot;);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         30 :     if(present &amp;&amp; !Tools::parse(data,&quot;B&quot;,b)) errormsg=&quot;could not parse B&quot;;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         10 :     c=std::pow(2., static_cast&lt;double&gt;(a)/static_cast&lt;double&gt;(b) ) - 1;</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         10 :     d = -static_cast&lt;double&gt;(b) / static_cast&lt;double&gt;(a);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        718 :   else if(name==&quot;Q&quot;) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        570 :     type=nativeq;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        570 :     beta = 50.0;  // nm-1</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        570 :     lambda = 1.8; // unitless</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        570 :     present=Tools::findKeyword(data,&quot;BETA&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">       1710 :     if(present &amp;&amp; !Tools::parse(data, &quot;BETA&quot;, beta)) errormsg=&quot;could not parse BETA&quot;;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        570 :     present=Tools::findKeyword(data,&quot;LAMBDA&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">       1710 :     if(present &amp;&amp; !Tools::parse(data, &quot;LAMBDA&quot;, lambda)) errormsg=&quot;could not parse LAMBDA&quot;;</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        570 :     bool found_ref=Tools::parse(data,&quot;REF&quot;,ref); // nm</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        570 :     if(!found_ref) errormsg=&quot;REF (reference disatance) is required for native Q&quot;;</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :   }</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        148 :   else if(name==&quot;EXP&quot;) type=exponential;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         83 :   else if(name==&quot;GAUSSIAN&quot;) type=gaussian;</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         35 :   else if(name==&quot;CUBIC&quot;) type=cubic;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         17 :   else if(name==&quot;TANH&quot;) type=tanh;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         15 :   else if(name==&quot;COSINUS&quot;) type=cosinus;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         25 :   else if((name==&quot;MATHEVAL&quot; || name==&quot;CUSTOM&quot;)) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         13 :     type=leptontype;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :     std::string func;</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         13 :     Tools::parse(data,&quot;FUNC&quot;,func);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         15 :     lepton::ParsedExpression pe=lepton::Parser::parse(func).optimize(lepton::Constants());</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         13 :     lepton_func=func;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         13 :     expression.resize(OpenMP::getNumThreads());</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         39 :     for(auto &amp; e : expression) e=pe.createCompiledExpression();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         13 :     lepton_ref.resize(expression.size());</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         35 :     for(unsigned t=0; t&lt;lepton_ref.size(); t++) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         24 :       auto vars=expression[t].getVariables();</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         24 :       bool found_x=std::find(vars.begin(),vars.end(),&quot;x&quot;)!=vars.end();</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         24 :       bool found_x2=std::find(vars.begin(),vars.end(),&quot;x2&quot;)!=vars.end();</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         24 :       if (vars.size()==0) {</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : // this is necessary since in some cases lepton thinks a variable is not present even though it is present</a>
+<a name="278"><span class="lineNum">     278 </span>            : // e.g. func=0*x</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :         lepton_ref[t]=nullptr;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         24 :       } else if(vars.size()==1 &amp;&amp; found_x) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         16 :         lepton_ref[t]=&amp;const_cast&lt;lepton::CompiledExpression*&gt;(&amp;expression[t])-&gt;getVariableReference(&quot;x&quot;);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          8 :       } else if(vars.size()==1 &amp;&amp; found_x2) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          8 :         lepton_ref[t]=&amp;const_cast&lt;lepton::CompiledExpression*&gt;(&amp;expression[t])-&gt;getVariableReference(&quot;x2&quot;);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          6 :         leptonx2=true;</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          2 :       } else if(vars.size()==2 &amp;&amp; found_x &amp;&amp; found_x2) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          2 :         plumed_error() &lt;&lt; &quot;Cannot use simultaneously x and x2 argument in switching function: &quot;&lt;&lt;func;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :       } else {</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          2 :         plumed_error() &lt;&lt; &quot;Something wrong in the arguments for switching function: &quot;&lt;&lt;func;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :       }</a>
+<a name="290"><span class="lineNum">     290 </span>            :     }</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         13 :     std::string arg=&quot;x&quot;;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         11 :     if(leptonx2) arg=&quot;x2&quot;;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         22 :     lepton::ParsedExpression ped=lepton::Parser::parse(func).differentiate(arg).optimize(lepton::Constants());</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         11 :     expression_deriv.resize(OpenMP::getNumThreads());</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         33 :     for(auto &amp; e : expression_deriv) e=ped.createCompiledExpression();</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">         11 :     lepton_ref_deriv.resize(expression_deriv.size());</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">         33 :     for(unsigned t=0; t&lt;lepton_ref_deriv.size(); t++) {</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :       try {</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         22 :         lepton_ref_deriv[t]=&amp;const_cast&lt;lepton::CompiledExpression*&gt;(&amp;expression_deriv[t])-&gt;getVariableReference(arg);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :       } catch(const PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : // this is necessary since in some cases lepton things a variable is not present even though it is present</a>
+<a name="302"><span class="lineNum">     302 </span>            : // e.g. func=3*x</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :         lepton_ref_deriv[t]=nullptr;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineNoCov">          0 :       }</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :     }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">          2 :   else errormsg=&quot;cannot understand switching function type '&quot;+name+&quot;'&quot;;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">       1017 :   if( !data.empty() ) {</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     errormsg=&quot;found the following rogue keywords in switching function input : &quot;;</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          2 :     for(unsigned i=0; i&lt;data.size(); ++i) errormsg = errormsg + data[i] + &quot; &quot;;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   }</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">       1017 :   if(dostretch &amp;&amp; dmax!=std::numeric_limits&lt;double&gt;::max()) {</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :     double dummy;</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         95 :     double s0=calculate(0.0,dummy);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         95 :     double sd=calculate(dmax,dummy);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         95 :     stretch=1.0/(s0-sd);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         95 :     shift=-sd*stretch;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :   }</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       1017 :   plumed_assert(!(leptonx2 &amp;&amp; d0!=0.0)) &lt;&lt; &quot;You cannot use lepton x2 optimization with d0!=0.0 (d0=&quot; &lt;&lt; d0 &lt;&lt;&quot;)\n&quot;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :                                         &lt;&lt; &quot;Please rewrite your function using x as a variable&quot;;</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">       1019 : }</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">       1069 : std::string SwitchingFunction::description() const {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       1069 :   std::ostringstream ostr;</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">       1069 :   ostr&lt;&lt;1./invr0&lt;&lt;&quot;.  Using &quot;;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       1069 :   if(type==rational) {</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        348 :     ostr&lt;&lt;&quot;rational&quot;;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :   } else if(type==exponential) {</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         61 :     ostr&lt;&lt;&quot;exponential&quot;;</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :   } else if(type==nativeq) {</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        570 :     ostr&lt;&lt;&quot;nativeq&quot;;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :   } else if(type==gaussian) {</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         48 :     ostr&lt;&lt;&quot;gaussian&quot;;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   } else if(type==smap) {</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         10 :     ostr&lt;&lt;&quot;smap&quot;;</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :   } else if(type==cubic) {</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         18 :     ostr&lt;&lt;&quot;cubic&quot;;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :   } else if(type==tanh) {</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          2 :     ostr&lt;&lt;&quot;tanh&quot;;</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :   } else if(type==cosinus) {</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          1 :     ostr&lt;&lt;&quot;cosinus&quot;;</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :   } else if(type==leptontype) {</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         11 :     ostr&lt;&lt;&quot;lepton&quot;;</span></a>
+<a name="346"><span class="lineNum">     346 </span>            :   } else {</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Unknown switching function type&quot;);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :   }</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">       1069 :   ostr&lt;&lt;&quot; switching function with parameters d0=&quot;&lt;&lt;d0;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">       1069 :   if(type==rational) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        348 :     ostr&lt;&lt;&quot; nn=&quot;&lt;&lt;nn&lt;&lt;&quot; mm=&quot;&lt;&lt;mm;</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        721 :   } else if(type==nativeq) {</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        570 :     ostr&lt;&lt;&quot; beta=&quot;&lt;&lt;beta&lt;&lt;&quot; lambda=&quot;&lt;&lt;lambda&lt;&lt;&quot; ref=&quot;&lt;&lt;ref;</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        151 :   } else if(type==smap) {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         10 :     ostr&lt;&lt;&quot; a=&quot;&lt;&lt;a&lt;&lt;&quot; b=&quot;&lt;&lt;b;</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        141 :   } else if(type==cubic) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         18 :     ostr&lt;&lt;&quot; dmax=&quot;&lt;&lt;dmax;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        123 :   } else if(type==leptontype) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         11 :     ostr&lt;&lt;&quot; func=&quot;&lt;&lt;lepton_func;</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">       1069 :   return ostr.str();</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       1069 : }</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">   41286095 : double SwitchingFunction::do_rational(double rdist,double&amp;dfunc,int nn,int mm)const {</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   double result;</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">   41286095 :   if(2*nn==mm) {</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : // if 2*N==M, then (1.0-rdist^N)/(1.0-rdist^M) = 1.0/(1.0+rdist^N)</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">   25190757 :     double rNdist=Tools::fastpow(rdist,nn-1);</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">   25190757 :     double iden=1.0/(1+rNdist*rdist);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">   25190757 :     dfunc = -nn*rNdist*iden*iden;</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :     result = iden;</a>
+<a name="373"><span class="lineNum">     373 </span>            :   } else {</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">   16095338 :     if(rdist&gt;(1.-5.0e10*epsilon) &amp;&amp; rdist&lt;(1+5.0e10*epsilon)) {</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         10 :       const double secDev = ((nn * (mm * mm - 3.0* mm * (-1 + nn ) + nn *(-3 + 2* nn )))/(6.0* mm ));</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         10 :       const double x =(rdist-1.0);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         10 :       dfunc=0.5*nn*double(nn-mm)/mm;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         10 :       result = double(nn)/mm+ x * ( dfunc + 0.5 * x * secDev);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         10 :       dfunc  = dfunc + x * secDev;</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         10 :     } else {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">   16095328 :       double rNdist=Tools::fastpow(rdist,nn-1);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">   16095328 :       double rMdist=Tools::fastpow(rdist,mm-1);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">   16095328 :       double num = 1.-rNdist*rdist;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">   16095328 :       double iden = 1./(1.-rMdist*rdist);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">   16095328 :       double func = num*iden;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :       result = func;</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">   16095328 :       dfunc = ((-nn*rNdist*iden)+(func*(iden*mm)*rMdist));</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :     }</a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">   41286095 :   return result;</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : }</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">   19721455 : double SwitchingFunction::calculateSqr(double distance2,double&amp;dfunc)const {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">   19721455 :   if(fastrational) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">    7657979 :     if(distance2&gt;dmax_2) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">     144482 :       dfunc=0.0;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">     144482 :       return 0.0;</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :     }</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">    7513497 :     const double rdist_2 = distance2*invr0_2;</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">    7513497 :     double result=do_rational(rdist_2,dfunc,nn/2,mm/2);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : // chain rule:</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">    7513497 :     dfunc*=2*invr0_2;</span></a>
+<a name="403"><span class="lineNum">     403 </span>            : // stretch:</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">    7513497 :     result=result*stretch+shift;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">    7513497 :     dfunc*=stretch;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">    7513497 :     return result;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">   12063476 :   } else if(leptonx2) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">    1248110 :     if(distance2&gt;dmax_2) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">          8 :       dfunc=0.0;</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">          8 :       return 0.0;</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :     }</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">    1248102 :     const unsigned t=OpenMP::getThreadNum();</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">    1248102 :     const double rdist_2 = distance2*invr0_2;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">    1248102 :     plumed_assert(t&lt;expression.size());</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">    1248102 :     if(lepton_ref[t]) *lepton_ref[t]=rdist_2;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">    1248102 :     if(lepton_ref_deriv[t]) *lepton_ref_deriv[t]=rdist_2;</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">    1248102 :     double result=expression[t].evaluate();</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">    1248102 :     dfunc=expression_deriv[t].evaluate();</span></a>
+<a name="419"><span class="lineNum">     419 </span>            : // chain rule:</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">    1248102 :     dfunc*=2*invr0_2;</span></a>
+<a name="421"><span class="lineNum">     421 </span>            : // stretch:</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">    1248102 :     result=result*stretch+shift;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">    1248102 :     dfunc*=stretch;</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">    1248102 :     return result;</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :   } else {</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">   10815366 :     double distance=std::sqrt(distance2);</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">   10815366 :     return calculate(distance,dfunc);</span></a>
+<a name="428"><span class="lineNum">     428 </span>            :   }</a>
+<a name="429"><span class="lineNum">     429 </span>            : }</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">   88945983 : double SwitchingFunction::calculate(double distance,double&amp;dfunc)const {</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">   88945983 :   plumed_massert(init,&quot;you are trying to use an unset SwitchingFunction&quot;);</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">   88945983 :   if(distance&gt;dmax) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">     450541 :     dfunc=0.0;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">     450541 :     return 0.0;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :   }</a>
+<a name="437"><span class="lineNum">     437 </span>            : // in this case, the lepton object stores only the calculateSqr function</a>
+<a name="438"><span class="lineNum">     438 </span>            : // so we have to implement calculate in terms of calculateSqr</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">   88495442 :   if(leptonx2) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          2 :     return calculateSqr(distance*distance,dfunc);</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   }</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">   88495440 :   const double rdist = (distance-d0)*invr0;</span></a>
+<a name="443"><span class="lineNum">     443 </span>            :   double result;</a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">   88495440 :   if(rdist&lt;=0.) {</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :     result=1.;</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">   24431541 :     dfunc=0.0;</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :   } else {</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">   64063899 :     if(type==smap) {</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">   21789971 :       double sx=c*Tools::fastpow( rdist, a );</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">   21789971 :       result=std::pow( 1.0 + sx, d );</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">   21789971 :       dfunc=-b*sx/rdist*result/(1.0+sx);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :     } else if(type==rational) {</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">   33772598 :       result=do_rational(rdist,dfunc,nn,mm);</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :     } else if(type==exponential) {</a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">    2486478 :       result=std::exp(-rdist);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">    2486478 :       dfunc=-result;</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :     } else if(type==nativeq) {</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">     146570 :       double rdist2 = beta*(distance - lambda * ref);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">     146570 :       double exprdist=std::exp(rdist2);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">     146570 :       double exprmdist=1.0/exprdist;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">     146570 :       result=1./(1.+exprdist);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">     146570 :       dfunc=-beta/(exprmdist+1.0)/(1.+exprdist)/invr0;</span></a>
+<a name="464"><span class="lineNum">     464 </span>            :     } else if(type==gaussian) {</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">     195683 :       result=std::exp(-0.5*rdist*rdist);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">     195683 :       dfunc=-rdist*result;</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :     } else if(type==cubic) {</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">     127132 :       double tmp1=rdist-1, tmp2=(1+2*rdist);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">     127132 :       result=tmp1*tmp1*tmp2;</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">     127132 :       dfunc=2*tmp1*tmp2 + 2*tmp1*tmp1;</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :     } else if(type==tanh) {</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">       8000 :       double tmp1=std::tanh(rdist);</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">       8000 :       result = 1.0 - tmp1;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">       8000 :       dfunc=-(1-tmp1*tmp1);</span></a>
+<a name="475"><span class="lineNum">     475 </span>            :     } else if(type==cosinus) {</a>
+<a name="476"><span class="lineNum">     476 </span>            :       if(rdist&lt;=0.0) {</a>
+<a name="477"><span class="lineNum">     477 </span>            : // rdist = (r-r1)/(r2-r1) ; rdist&lt;=0.0 if r &lt;=r1</a>
+<a name="478"><span class="lineNum">     478 </span>            :         result=1.;</a>
+<a name="479"><span class="lineNum">     479 </span>            :         dfunc=0.0;</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">     522053 :       } else if(rdist&lt;=1.0) {</span></a>
+<a name="481"><span class="lineNum">     481 </span>            : // rdist = (r-r1)/(r2-r1) ; 0.0&lt;=rdist&lt;=1.0 if r1 &lt;= r &lt;=r2; (r2-r1)/(r2-r1)=1</a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">     226962 :         double tmpcos = std::cos ( rdist * PI );</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">     226962 :         double tmpsin = std::sin ( rdist * PI );</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">     226962 :         result = 0.5 * (tmpcos + 1.0);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">     226962 :         dfunc=-0.5 * PI * tmpsin * invr0;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :       } else {</a>
+<a name="487"><span class="lineNum">     487 </span>            :         result=0.;</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">     295091 :         dfunc=0.0;</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :       }</a>
+<a name="490"><span class="lineNum">     490 </span>            :     } else if(type==leptontype) {</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">    5015414 :       const unsigned t=OpenMP::getThreadNum();</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">    5015414 :       plumed_assert(t&lt;expression.size());</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">    5015414 :       if(lepton_ref[t]) *lepton_ref[t]=rdist;</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">    5015414 :       if(lepton_ref_deriv[t]) *lepton_ref_deriv[t]=rdist;</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">    5015414 :       result=expression[t].evaluate();</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">    5015414 :       dfunc=expression_deriv[t].evaluate();</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 :     } else plumed_merror(&quot;Unknown switching function type&quot;);</span></a>
+<a name="498"><span class="lineNum">     498 </span>            : // this is for the chain rule (derivative of rdist):</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">   64063899 :     dfunc*=invr0;</span></a>
+<a name="500"><span class="lineNum">     500 </span>            : // for any future switching functions, be aware that multiplying invr0 is only correct for functions of rdist = (r-d0)/r0.</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            : // this is because calculate() sets dfunc to the derivative divided times the distance.</a>
+<a name="503"><span class="lineNum">     503 </span>            : // (I think this is misleading and I would like to modify it - GB)</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">   64063899 :     dfunc/=distance;</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :   }</a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">   88495440 :   result=result*stretch+shift;</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">   88495440 :   dfunc*=stretch;</span></a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">   88495440 :   return result;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            : }</a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         61 : void SwitchingFunction::set(int nn,int mm,double r0,double d0) {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">         61 :   init=true;</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         61 :   type=rational;</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         61 :   if(mm==0) mm=2*nn;</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         61 :   this-&gt;nn=nn;</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         61 :   this-&gt;mm=mm;</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         61 :   this-&gt;invr0=1.0/r0;</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         61 :   this-&gt;invr0_2=this-&gt;invr0*this-&gt;invr0;</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         61 :   this-&gt;d0=d0;</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         61 :   this-&gt;dmax=d0+r0*std::pow(0.00001,1./(nn-mm));</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         61 :   this-&gt;dmax_2=this-&gt;dmax*this-&gt;dmax;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         61 :   this-&gt;leptonx2=false;</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         61 :   this-&gt;fastrational=(nn%2==0 &amp;&amp; mm%2==0 &amp;&amp; d0==0.0);</span></a>
+<a name="526"><span class="lineNum">     526 </span>            : </a>
+<a name="527"><span class="lineNum">     527 </span>            :   double dummy;</a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         61 :   double s0=calculate(0.0,dummy);</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">         61 :   double sd=calculate(dmax,dummy);</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         61 :   stretch=1.0/(s0-sd);</span></a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">         61 :   shift=-sd*stretch;</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">         61 : }</span></a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">         30 : double SwitchingFunction::get_r0() const {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         30 :   return 1./invr0;</span></a>
+<a name="536"><span class="lineNum">     536 </span>            : }</a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">          6 : double SwitchingFunction::get_d0() const {</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">          6 :   return d0;</span></a>
+<a name="540"><span class="lineNum">     540 </span>            : }</a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">  117918073 : double SwitchingFunction::get_dmax() const {</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">  117918073 :   return dmax;</span></a>
+<a name="544"><span class="lineNum">     544 </span>            : }</a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">   23893569 : double SwitchingFunction::get_dmax2() const {</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">   23893569 :   return dmax_2;</span></a>
+<a name="548"><span class="lineNum">     548 </span>            : }</a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            : }</a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span>            : </a>
+<a name="553"><span class="lineNum">     553 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tensor.cpp.func-sort-c.html b/coverage/tools/Tensor.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a483d5a5fd
--- /dev/null
+++ b/coverage/tools/Tensor.cpp.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tensor.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tensor.cpp<span style="font-size: 80%;"> (<a href="Tensor.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
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+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
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+          <tr>
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+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
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+            <td class="headerCovTableEntryHi">100.0 %</td>
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+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Tensor.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tensor.cpp.gcov.html#27">_ZN4PLMD16TensorGenericAux12local_dsyevrEPKcS2_S2_PiPdS3_S4_S4_S3_S3_S4_S3_S4_S4_S3_S3_S4_S3_S3_S3_S3_</a></td>
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+  <br>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tensor.cpp.func.html b/coverage/tools/Tensor.cpp.func.html
new file mode 100644
index 0000000000..c043ca71ac
--- /dev/null
+++ b/coverage/tools/Tensor.cpp.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tensor.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tensor.cpp<span style="font-size: 80%;"> (<a href="Tensor.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
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+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Tensor.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tensor.cpp.gcov.html#27">_ZN4PLMD16TensorGenericAux12local_dsyevrEPKcS2_S2_PiPdS3_S4_S4_S3_S3_S4_S3_S4_S4_S3_S3_S4_S3_S3_S3_S3_</a></td>
+              <td class="coverFnHi">556397</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tensor.cpp.gcov.html b/coverage/tools/Tensor.cpp.gcov.html
new file mode 100644
index 0000000000..5e92eabeda
--- /dev/null
+++ b/coverage/tools/Tensor.cpp.gcov.html
@@ -0,0 +1,115 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tensor.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tensor.cpp<span style="font-size: 80%;"> (source / <a href="Tensor.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;lapack/lapack.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">     556397 : void TensorGenericAux::local_dsyevr(const char *jobz, const char *range, const char *uplo, int *n,</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :                                     double *a, int *lda, double *vl, double *vu, int *</a>
+<a name="31"><span class="lineNum">      31 </span>            :                                     il, int *iu, double *abstol, int *m, double *w,</a>
+<a name="32"><span class="lineNum">      32 </span>            :                                     double *z__, int *ldz, int *isuppz, double *work,</a>
+<a name="33"><span class="lineNum">      33 </span>            :                                     int *lwork, int *iwork, int *liwork, int *info) {</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     556397 :   plumed_lapack_dsyevr(jobz,range,uplo,n,a,lda,vl,vu,il,iu,abstol,m,w,z__,ldz,isuppz,work,lwork,iwork,liwork,info);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     556397 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : }</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+  <br>
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new file mode 100644
index 0000000000..03e162f85e
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tensor.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
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+            <td width="15%"></td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tensor.h.gcov.html b/coverage/tools/Tensor.h.gcov.html
new file mode 100644
index 0000000000..d2de773fac
--- /dev/null
+++ b/coverage/tools/Tensor.h.gcov.html
@@ -0,0 +1,650 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tensor.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tensor.h<span style="font-size: 80%;"> (source / <a href="Tensor.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">146</td>
+            <td class="headerCovTableEntry">151</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Tensor_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Tensor_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;MatrixSquareBracketsAccess.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;LoopUnroller.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;array&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /// Small class to contain local utilities.</a>
+<a name="35"><span class="lineNum">      35 </span>            : /// Should not be used outside of the TensorGeneric class.</a>
+<a name="36"><span class="lineNum">      36 </span>            : class TensorGenericAux {</a>
+<a name="37"><span class="lineNum">      37 </span>            : public:</a>
+<a name="38"><span class="lineNum">      38 </span>            : // local redefinition, just to avoid including lapack.h here</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void local_dsyevr(const char *jobz, const char *range, const char *uplo, int *n,</a>
+<a name="40"><span class="lineNum">      40 </span>            :                            double *a, int *lda, double *vl, double *vu, int *</a>
+<a name="41"><span class="lineNum">      41 </span>            :                            il, int *iu, double *abstol, int *m, double *w,</a>
+<a name="42"><span class="lineNum">      42 </span>            :                            double *z__, int *ldz, int *isuppz, double *work,</a>
+<a name="43"><span class="lineNum">      43 </span>            :                            int *lwork, int *iwork, int *liwork, int *info);</a>
+<a name="44"><span class="lineNum">      44 </span>            : };</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : /**</a>
+<a name="47"><span class="lineNum">      47 </span>            : \ingroup TOOLBOX</a>
+<a name="48"><span class="lineNum">      48 </span>            : Class implementing fixed size matrices of doubles</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : \tparam n The number rows</a>
+<a name="51"><span class="lineNum">      51 </span>            : \tparam m The number columns</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : This class implements a matrix of doubles with size fixed at</a>
+<a name="54"><span class="lineNum">      54 </span>            : compile time. It is useful for small fixed size objects (e.g.</a>
+<a name="55"><span class="lineNum">      55 </span>            : 3x3 tensors) as it does not waste space to store the vector size.</a>
+<a name="56"><span class="lineNum">      56 </span>            : Moreover, as the compiler knows the size, it can be completely</a>
+<a name="57"><span class="lineNum">      57 </span>            : opimized inline.</a>
+<a name="58"><span class="lineNum">      58 </span>            : Most of the loops are explicitly unrolled using PLMD::LoopUnroller class</a>
+<a name="59"><span class="lineNum">      59 </span>            : Matrix elements are initialized to zero by default. Notice that</a>
+<a name="60"><span class="lineNum">      60 </span>            : this means that constructor is a bit slow. This point might change</a>
+<a name="61"><span class="lineNum">      61 </span>            : in future if we find performance issues.</a>
+<a name="62"><span class="lineNum">      62 </span>            : It takes advantage of MatrixSquareBracketsAccess to provide both</a>
+<a name="63"><span class="lineNum">      63 </span>            : () and [] syntax for access.</a>
+<a name="64"><span class="lineNum">      64 </span>            : Several functions are declared as friends even if not necessary so as to</a>
+<a name="65"><span class="lineNum">      65 </span>            : properly appear in Doxygen documentation.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : Aliases are defined to simplify common declarations (Tensor, Tensor2d, Tensor3d, Tensor4d).</a>
+<a name="68"><span class="lineNum">      68 </span>            : Also notice that some operations are only available for 3x3 tensors.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : Example of usage</a>
+<a name="71"><span class="lineNum">      71 </span>            : \verbatim</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : using namespace PLMD;</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : int main(){</a>
+<a name="78"><span class="lineNum">      78 </span>            :   Tensor a;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   TensorGeneric&lt;3,2&gt; b;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   TensorGeneric&lt;3,2&gt; c=matmul(a,b);</a>
+<a name="81"><span class="lineNum">      81 </span>            :   return 0;</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : \endverbatim</a>
+<a name="85"><span class="lineNum">      85 </span>            : */</a>
+<a name="86"><span class="lineNum">      86 </span>            : template &lt;unsigned n,unsigned m&gt;</a>
+<a name="87"><span class="lineNum">      87 </span>            : class TensorGeneric:</a>
+<a name="88"><span class="lineNum">      88 </span>            :   public MatrixSquareBracketsAccess&lt;TensorGeneric&lt;n,m&gt;,double&gt;</a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::array&lt;double,n*m&gt; d;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Auxiliary private function for constructor</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void auxiliaryConstructor();</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Auxiliary private function for constructor</a>
+<a name="94"><span class="lineNum">      94 </span>            :   template&lt;typename... Args&gt;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void auxiliaryConstructor(double first,Args... arg);</a>
+<a name="96"><span class="lineNum">      96 </span>            : public:</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Constructor accepting n*m double parameters.</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// Can be used as Tensor&lt;2,2&gt;(1.0,2.0,3.0,4.0)</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// In case a wrong number of parameters is given, a static assertion will fail.</a>
+<a name="100"><span class="lineNum">     100 </span>            :   template&lt;typename... Args&gt;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   TensorGeneric(double first,Args... arg);</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// initialize the tensor to zero</a>
+<a name="103"><span class="lineNum">     103 </span>            :   TensorGeneric();</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// initialize a tensor as an external product of two Vector</a>
+<a name="105"><span class="lineNum">     105 </span>            :   TensorGeneric(const VectorGeneric&lt;n&gt;&amp;v1,const VectorGeneric&lt;m&gt;&amp;v2);</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// set it to zero</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void zero();</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// access element</a>
+<a name="109"><span class="lineNum">     109 </span>            :   double &amp; operator() (unsigned i,unsigned j);</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// access element</a>
+<a name="111"><span class="lineNum">     111 </span>            :   const double &amp; operator() (unsigned i,unsigned j)const;</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// increment</a>
+<a name="113"><span class="lineNum">     113 </span>            :   TensorGeneric&amp; operator +=(const TensorGeneric&lt;n,m&gt;&amp; b);</a>
+<a name="114"><span class="lineNum">     114 </span>            : /// decrement</a>
+<a name="115"><span class="lineNum">     115 </span>            :   TensorGeneric&amp; operator -=(const TensorGeneric&lt;n,m&gt;&amp; b);</a>
+<a name="116"><span class="lineNum">     116 </span>            : /// multiply</a>
+<a name="117"><span class="lineNum">     117 </span>            :   TensorGeneric&amp; operator *=(double);</a>
+<a name="118"><span class="lineNum">     118 </span>            : /// divide</a>
+<a name="119"><span class="lineNum">     119 </span>            :   TensorGeneric&amp; operator /=(double);</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// return +t</a>
+<a name="121"><span class="lineNum">     121 </span>            :   TensorGeneric operator +()const;</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// return -t</a>
+<a name="123"><span class="lineNum">     123 </span>            :   TensorGeneric operator -()const;</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// set j-th column</a>
+<a name="125"><span class="lineNum">     125 </span>            :   TensorGeneric&amp; setCol(unsigned j,const VectorGeneric&lt;n&gt; &amp; c);</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// set i-th row</a>
+<a name="127"><span class="lineNum">     127 </span>            :   TensorGeneric&amp; setRow(unsigned i,const VectorGeneric&lt;m&gt; &amp; r);</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// get j-th column</a>
+<a name="129"><span class="lineNum">     129 </span>            :   VectorGeneric&lt;n&gt; getCol(unsigned j)const;</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// get i-th row</a>
+<a name="131"><span class="lineNum">     131 </span>            :   VectorGeneric&lt;m&gt; getRow(unsigned i)const;</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// return t1+t2</a>
+<a name="133"><span class="lineNum">     133 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   friend TensorGeneric&lt;n_,m_&gt; operator+(const TensorGeneric&lt;n_,m_&gt;&amp;,const TensorGeneric&lt;n_,m_&gt;&amp;);</a>
+<a name="135"><span class="lineNum">     135 </span>            : /// return t1+t2</a>
+<a name="136"><span class="lineNum">     136 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   friend TensorGeneric&lt;n_,m_&gt; operator-(const TensorGeneric&lt;n_,m_&gt;&amp;,const TensorGeneric&lt;n_,m_&gt;&amp;);</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// scale the tensor by a factor s</a>
+<a name="139"><span class="lineNum">     139 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   friend TensorGeneric&lt;n_,m_&gt; operator*(double,const TensorGeneric&lt;n_,m_&gt;&amp;);</a>
+<a name="141"><span class="lineNum">     141 </span>            : /// scale the tensor by a factor s</a>
+<a name="142"><span class="lineNum">     142 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   friend TensorGeneric&lt;n_,m_&gt; operator*(const TensorGeneric&lt;n_,m_&gt;&amp;,double s);</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// scale the tensor by a factor 1/s</a>
+<a name="145"><span class="lineNum">     145 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   friend TensorGeneric&lt;n_,m_&gt; operator/(const TensorGeneric&lt;n_,m_&gt;&amp;,double s);</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// returns the determinant</a>
+<a name="148"><span class="lineNum">     148 </span>            :   double determinant()const;</a>
+<a name="149"><span class="lineNum">     149 </span>            : /// return an identity tensor</a>
+<a name="150"><span class="lineNum">     150 </span>            :   static TensorGeneric&lt;n,n&gt; identity();</a>
+<a name="151"><span class="lineNum">     151 </span>            : /// return the matrix inverse</a>
+<a name="152"><span class="lineNum">     152 </span>            :   TensorGeneric inverse()const;</a>
+<a name="153"><span class="lineNum">     153 </span>            : /// return the transpose matrix</a>
+<a name="154"><span class="lineNum">     154 </span>            :   TensorGeneric&lt;m,n&gt; transpose()const;</a>
+<a name="155"><span class="lineNum">     155 </span>            : /// matrix-matrix multiplication</a>
+<a name="156"><span class="lineNum">     156 </span>            :   template&lt;unsigned n_,unsigned m_,unsigned l_&gt;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   friend TensorGeneric&lt;n_,l_&gt; matmul(const TensorGeneric&lt;n_,m_&gt;&amp;,const TensorGeneric&lt;m_,l_&gt;&amp;);</a>
+<a name="158"><span class="lineNum">     158 </span>            : /// matrix-vector multiplication</a>
+<a name="159"><span class="lineNum">     159 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   friend VectorGeneric&lt;n_&gt; matmul(const TensorGeneric&lt;n_,m_&gt;&amp;,const VectorGeneric&lt;m_&gt;&amp;);</a>
+<a name="161"><span class="lineNum">     161 </span>            : /// vector-matrix multiplication</a>
+<a name="162"><span class="lineNum">     162 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   friend VectorGeneric&lt;n_&gt; matmul(const VectorGeneric&lt;m_&gt;&amp;,const TensorGeneric&lt;m_,n_&gt;&amp;);</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// vector-vector multiplication (maps to dotProduct)</a>
+<a name="165"><span class="lineNum">     165 </span>            :   template&lt;unsigned n_&gt;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   friend double matmul(const VectorGeneric&lt;n_&gt;&amp;,const VectorGeneric&lt;n_&gt;&amp;);</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// matrix-matrix-matrix multiplication</a>
+<a name="168"><span class="lineNum">     168 </span>            :   template&lt;unsigned n_,unsigned m_,unsigned l_,unsigned i_&gt;</a>
+<a name="169"><span class="lineNum">     169 </span>            :   friend TensorGeneric&lt;n_,i_&gt; matmul(const TensorGeneric&lt;n_,m_&gt;&amp;,const TensorGeneric&lt;m_,l_&gt;&amp;,const TensorGeneric&lt;l_,i_&gt;&amp;);</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// matrix-matrix-vector multiplication</a>
+<a name="171"><span class="lineNum">     171 </span>            :   template&lt;unsigned n_,unsigned m_,unsigned l_&gt;</a>
+<a name="172"><span class="lineNum">     172 </span>            :   friend VectorGeneric&lt;n_&gt; matmul(const TensorGeneric&lt;n_,m_&gt;&amp;,const TensorGeneric&lt;m_,l_&gt;&amp;,const VectorGeneric&lt;l_&gt;&amp;);</a>
+<a name="173"><span class="lineNum">     173 </span>            : /// vector-matrix-matrix multiplication</a>
+<a name="174"><span class="lineNum">     174 </span>            :   template&lt;unsigned n_,unsigned m_,unsigned l_&gt;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   friend VectorGeneric&lt;l_&gt; matmul(const VectorGeneric&lt;n_&gt;&amp;,const TensorGeneric&lt;n_,m_&gt;&amp;,const TensorGeneric&lt;m_,l_&gt;&amp;);</a>
+<a name="176"><span class="lineNum">     176 </span>            : /// vector-matrix-vector multiplication</a>
+<a name="177"><span class="lineNum">     177 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   friend double matmul(const VectorGeneric&lt;n_&gt;&amp;,const TensorGeneric&lt;n_,m_&gt;&amp;,const VectorGeneric&lt;m_&gt;&amp;);</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// returns the determinant of a tensor</a>
+<a name="180"><span class="lineNum">     180 </span>            :   friend double determinant(const TensorGeneric&lt;3,3&gt;&amp;);</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// returns the inverse of a tensor (same as inverse())</a>
+<a name="182"><span class="lineNum">     182 </span>            :   friend TensorGeneric&lt;3,3&gt; inverse(const TensorGeneric&lt;3,3&gt;&amp;);</a>
+<a name="183"><span class="lineNum">     183 </span>            : /// returns the transpose of a tensor (same as transpose())</a>
+<a name="184"><span class="lineNum">     184 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   friend TensorGeneric&lt;n_,m_&gt; transpose(const TensorGeneric&lt;m_,n_&gt;&amp;);</a>
+<a name="186"><span class="lineNum">     186 </span>            : /// returns the transpose of a tensor (same as TensorGeneric(const VectorGeneric&amp;,const VectorGeneric&amp;))</a>
+<a name="187"><span class="lineNum">     187 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   friend TensorGeneric&lt;n_,m_&gt; extProduct(const VectorGeneric&lt;n&gt;&amp;,const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   friend TensorGeneric&lt;3,3&gt; dcrossDv1(const VectorGeneric&lt;3&gt;&amp;,const VectorGeneric&lt;3&gt;&amp;);</a>
+<a name="190"><span class="lineNum">     190 </span>            :   friend TensorGeneric&lt;3,3&gt; dcrossDv2(const VectorGeneric&lt;3&gt;&amp;,const VectorGeneric&lt;3&gt;&amp;);</a>
+<a name="191"><span class="lineNum">     191 </span>            :   friend TensorGeneric&lt;3,3&gt; VcrossTensor(const VectorGeneric&lt;3&gt;&amp;,const TensorGeneric&lt;3,3&gt;&amp;);</a>
+<a name="192"><span class="lineNum">     192 </span>            :   friend TensorGeneric&lt;3,3&gt; VcrossTensor(const TensorGeneric&lt;3,3&gt;&amp;,const VectorGeneric&lt;3&gt;&amp;);</a>
+<a name="193"><span class="lineNum">     193 </span>            : /// Derivative of a normalized vector</a>
+<a name="194"><span class="lineNum">     194 </span>            :   friend TensorGeneric&lt;3,3&gt; deriNorm(const VectorGeneric&lt;3&gt;&amp;,const TensorGeneric&lt;3,3&gt;&amp;);</a>
+<a name="195"><span class="lineNum">     195 </span>            : /// &lt;&lt; operator.</a>
+<a name="196"><span class="lineNum">     196 </span>            : /// Allows printing tensor `t` with `std::cout&lt;&lt;t;`</a>
+<a name="197"><span class="lineNum">     197 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   friend std::ostream &amp; operator&lt;&lt;(std::ostream &amp;os, const TensorGeneric&lt;n_,m_&gt;&amp;);</a>
+<a name="199"><span class="lineNum">     199 </span>            : /// Diagonalize tensor.</a>
+<a name="200"><span class="lineNum">     200 </span>            : /// Syntax is the same as Matrix::diagMat.</a>
+<a name="201"><span class="lineNum">     201 </span>            : /// In addition, it is possible to call if with m_ smaller than n_. In this case,</a>
+<a name="202"><span class="lineNum">     202 </span>            : /// only the first (smaller) m_ eigenvalues and eigenvectors are retrieved.</a>
+<a name="203"><span class="lineNum">     203 </span>            : /// If case lapack fails (info!=0) it throws an exception.</a>
+<a name="204"><span class="lineNum">     204 </span>            : /// Notice that tensor is assumed to be symmetric!!!</a>
+<a name="205"><span class="lineNum">     205 </span>            :   template&lt;unsigned n_,unsigned m_&gt;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   friend void diagMatSym(const TensorGeneric&lt;n_,n_&gt;&amp;,VectorGeneric&lt;m_&gt;&amp;evals,TensorGeneric&lt;m_,n_&gt;&amp;evec);</a>
+<a name="207"><span class="lineNum">     207 </span>            : };</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : template &lt;unsigned n,unsigned m&gt;</a>
+<a name="210"><span class="lineNum">     210 </span>            : void TensorGeneric&lt;n,m&gt;::auxiliaryConstructor()</a>
+<a name="211"><span class="lineNum">     211 </span>            : {}</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : template &lt;unsigned n,unsigned m&gt;</a>
+<a name="214"><span class="lineNum">     214 </span>            : template&lt;typename... Args&gt;</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">   83937843 : void TensorGeneric&lt;n,m&gt;::auxiliaryConstructor(double first,Args... arg)</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : {</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">   83937843 :   d[n*m-(sizeof...(Args))-1]=first;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">   74611416 :   auxiliaryConstructor(arg...);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">   83937843 : }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : template &lt;unsigned n,unsigned m&gt;</a>
+<a name="222"><span class="lineNum">     222 </span>            : template&lt;typename... Args&gt;</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">    9326427 : TensorGeneric&lt;n,m&gt;::TensorGeneric(double first,Args... arg)</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : {</a>
+<a name="225"><span class="lineNum">     225 </span>            :   static_assert((sizeof...(Args))+1==n*m,&quot;you are trying to initialize a Tensor with the wrong number of arguments&quot;);</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">    9326427 :   auxiliaryConstructor(first,arg...);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">    9326427 : }</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">   58879995 : TensorGeneric&lt;n,m&gt;::TensorGeneric() {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">   58879995 :   LoopUnroller&lt;n*m&gt;::_zero(d.data());</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">   58879995 : }</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">  148935080 : TensorGeneric&lt;n,m&gt;::TensorGeneric(const VectorGeneric&lt;n&gt;&amp;v1,const VectorGeneric&lt;m&gt;&amp;v2) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov"> 1936156040 :   for(unsigned i=0; i&lt;n; i++)for(unsigned j=0; j&lt;m; j++)d[i*m+j]=v1[i]*v2[j];</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">  148935080 : }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">    2093614 : void TensorGeneric&lt;n,m&gt;::zero() {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">    2093614 :   LoopUnroller&lt;n*m&gt;::_zero(d.data());</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">    2093614 : }</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">  260754920 : double &amp; TensorGeneric&lt;n,m&gt;::operator() (unsigned i,unsigned j) {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : #ifdef _GLIBCXX_DEBUG</a>
+<a name="247"><span class="lineNum">     247 </span>            : // index i is implicitly checked by the std::array class</a>
+<a name="248"><span class="lineNum">     248 </span>            :   plumed_assert(j&lt;m);</a>
+<a name="249"><span class="lineNum">     249 </span>            : #endif</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">  260754920 :   return d[m*i+j];</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov"> 5399914846 : const double &amp; TensorGeneric&lt;n,m&gt;::operator() (unsigned i,unsigned j)const {</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : #ifdef _GLIBCXX_DEBUG</a>
+<a name="256"><span class="lineNum">     256 </span>            : // index i is implicitly checked by the std::array class</a>
+<a name="257"><span class="lineNum">     257 </span>            :   plumed_assert(j&lt;m);</a>
+<a name="258"><span class="lineNum">     258 </span>            : #endif</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov"> 5399914846 :   return d[m*i+j];</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">   42880312 : TensorGeneric&lt;n,m&gt;&amp; TensorGeneric&lt;n,m&gt;::operator +=(const TensorGeneric&lt;n,m&gt;&amp; b) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">   42880312 :   LoopUnroller&lt;n*m&gt;::_add(d.data(),b.d.data());</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">   42880312 :   return *this;</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">   47075253 : TensorGeneric&lt;n,m&gt;&amp; TensorGeneric&lt;n,m&gt;::operator -=(const TensorGeneric&lt;n,m&gt;&amp; b) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">   47075253 :   LoopUnroller&lt;n*m&gt;::_sub(d.data(),b.d.data());</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">   47075253 :   return *this;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">  154207316 : TensorGeneric&lt;n,m&gt;&amp; TensorGeneric&lt;n,m&gt;::operator *=(double s) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">  154207316 :   LoopUnroller&lt;n*m&gt;::_mul(d.data(),s);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">  154207316 :   return *this;</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : }</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="281"><span class="lineNum">     281 </span>            : TensorGeneric&lt;n,m&gt;&amp; TensorGeneric&lt;n,m&gt;::operator /=(double s) {</a>
+<a name="282"><span class="lineNum">     282 </span>            :   LoopUnroller&lt;n*m&gt;::_mul(d.data(),1.0/s);</a>
+<a name="283"><span class="lineNum">     283 </span>            :   return *this;</a>
+<a name="284"><span class="lineNum">     284 </span>            : }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">      21229 : TensorGeneric&lt;n,m&gt; TensorGeneric&lt;n,m&gt;::operator+()const {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      21229 :   return *this;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : }</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">      63425 : TensorGeneric&lt;n,m&gt; TensorGeneric&lt;n,m&gt;::operator-()const {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">      63425 :   TensorGeneric&lt;n,m&gt; r;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      63425 :   LoopUnroller&lt;n*m&gt;::_neg(r.d.data(),d.data());</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">      63425 :   return r;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : }</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      29160 : TensorGeneric&lt;n,m&gt;&amp; TensorGeneric&lt;n,m&gt;::setCol(unsigned j,const VectorGeneric&lt;n&gt; &amp; c) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">     116640 :   for(unsigned i=0; i&lt;n; ++i) (*this)(i,j)=c(i);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">      29160 :   return *this;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">    2888253 : TensorGeneric&lt;n,m&gt;&amp; TensorGeneric&lt;n,m&gt;::setRow(unsigned i,const VectorGeneric&lt;m&gt; &amp; r) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">   11553012 :   for(unsigned j=0; j&lt;m; ++j) (*this)(i,j)=r(j);</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">    2888253 :   return *this;</span></a>
+<a name="308"><span class="lineNum">     308 </span>            : }</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      24300 : VectorGeneric&lt;n&gt; TensorGeneric&lt;n,m&gt;::getCol(unsigned j)const {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">      24300 :   VectorGeneric&lt;n&gt; v;</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">      97200 :   for(unsigned i=0; i&lt;n; ++i) v(i)=(*this)(i,j);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">      24300 :   return v;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">    3202134 : VectorGeneric&lt;m&gt; TensorGeneric&lt;n,m&gt;::getRow(unsigned i)const {</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">    3202134 :   VectorGeneric&lt;m&gt; v;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">   12808536 :   for(unsigned j=0; j&lt;m; ++j) v(j)=(*this)(i,j);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">    3202134 :   return v;</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : }</a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">    1730074 : TensorGeneric&lt;n,m&gt; operator+(const TensorGeneric&lt;n,m&gt;&amp;t1,const TensorGeneric&lt;n,m&gt;&amp;t2) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">    1730074 :   TensorGeneric&lt;n,m&gt; t(t1);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">    1730074 :   t+=t2;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">    1730074 :   return t;</span></a>
+<a name="329"><span class="lineNum">     329 </span>            : }</a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">    1261656 : TensorGeneric&lt;n,m&gt; operator-(const TensorGeneric&lt;n,m&gt;&amp;t1,const TensorGeneric&lt;n,m&gt;&amp;t2) {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">    1261656 :   TensorGeneric&lt;n,m&gt; t(t1);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">    1261656 :   t-=t2;</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">    1261656 :   return t;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">  154202291 : TensorGeneric&lt;n,m&gt; operator*(const TensorGeneric&lt;n,m&gt;&amp;t1,double s) {</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">  154202291 :   TensorGeneric&lt;n,m&gt; t(t1);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">  154202291 :   t*=s;</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">  154202291 :   return t;</span></a>
+<a name="343"><span class="lineNum">     343 </span>            : }</a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">  130591419 : TensorGeneric&lt;n,m&gt; operator*(double s,const TensorGeneric&lt;n,m&gt;&amp;t1) {</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">  130591419 :   return t1*s;</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : }</a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        254 : TensorGeneric&lt;n,m&gt; operator/(const TensorGeneric&lt;n,m&gt;&amp;t1,double s) {</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        254 :   return t1*(1.0/s);</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : }</a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : template&lt;&gt;</a>
+<a name="356"><span class="lineNum">     356 </span>            : inline</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">     204967 : double TensorGeneric&lt;3,3&gt;::determinant()const {</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   return</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">     204967 :     d[0]*d[4]*d[8]</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">     204967 :     + d[1]*d[5]*d[6]</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">     204967 :     + d[2]*d[3]*d[7]</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">     204967 :     - d[0]*d[5]*d[7]</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">     204967 :     - d[1]*d[3]*d[8]</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">     204967 :     - d[2]*d[4]*d[6];</span></a>
+<a name="365"><span class="lineNum">     365 </span>            : }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="368"><span class="lineNum">     368 </span>            : inline</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">   13395760 : TensorGeneric&lt;n,n&gt; TensorGeneric&lt;n,m&gt;::identity() {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">   13395760 :   TensorGeneric&lt;n,n&gt; t;</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">   53583040 :   for(unsigned i=0; i&lt;n; i++) t(i,i)=1.0;</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">   13395760 :   return t;</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">    3439149 : TensorGeneric&lt;m,n&gt; TensorGeneric&lt;n,m&gt;::transpose()const {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">    3439149 :   TensorGeneric&lt;m,n&gt; t;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">   44708937 :   for(unsigned i=0; i&lt;m; i++)for(unsigned j=0; j&lt;n; j++) t(i,j)=(*this)(j,i);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">    3439149 :   return t;</span></a>
+<a name="380"><span class="lineNum">     380 </span>            : }</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            : template&lt;&gt;</a>
+<a name="383"><span class="lineNum">     383 </span>            : inline</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">     130819 : TensorGeneric&lt;3,3&gt; TensorGeneric&lt;3,3&gt;::inverse()const {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">     130819 :   TensorGeneric t;</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">     130819 :   double invdet=1.0/determinant();</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">    1700647 :   for(unsigned i=0; i&lt;3; i++) for(unsigned j=0; j&lt;3; j++)</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">    1177371 :       t(j,i)=invdet*(   (*this)((i+1)%3,(j+1)%3)*(*this)((i+2)%3,(j+2)%3)</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">    1177371 :                         -(*this)((i+1)%3,(j+2)%3)*(*this)((i+2)%3,(j+1)%3));</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">     130819 :   return t;</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : }</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span>            : template&lt;unsigned n,unsigned m,unsigned l&gt;</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">    4758860 : TensorGeneric&lt;n,l&gt; matmul(const TensorGeneric&lt;n,m&gt;&amp;a,const TensorGeneric&lt;m,l&gt;&amp;b) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">    4758860 :   TensorGeneric&lt;n,l&gt; t;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">  190354400 :   for(unsigned i=0; i&lt;n; i++) for(unsigned j=0; j&lt;l; j++) for(unsigned k=0; k&lt;m; k++) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">  128489220 :         t(i,j)+=a(i,k)*b(k,j);</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :       }</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">    4758860 :   return t;</span></a>
+<a name="400"><span class="lineNum">     400 </span>            : }</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">   33529052 : VectorGeneric&lt;n&gt; matmul(const TensorGeneric&lt;n,m&gt;&amp;a,const VectorGeneric&lt;m&gt;&amp;b) {</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">   33529052 :   VectorGeneric&lt;n&gt; t;</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">  435877676 :   for(unsigned i=0; i&lt;n; i++) for(unsigned j=0; j&lt;m; j++) t(i)+=a(i,j)*b(j);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">   33529052 :   return t;</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : }</a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">  106109282 : VectorGeneric&lt;n&gt; matmul(const VectorGeneric&lt;m&gt;&amp;a,const TensorGeneric&lt;m,n&gt;&amp;b) {</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">  106109282 :   VectorGeneric&lt;n&gt; t;</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov"> 1380575348 :   for(unsigned i=0; i&lt;n; i++) for(unsigned j=0; j&lt;m; j++) t(i)+=a(j)*b(j,i);</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">  106109282 :   return t;</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : }</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            : template&lt;unsigned n_&gt;</a>
+<a name="417"><span class="lineNum">     417 </span>            : double matmul(const VectorGeneric&lt;n_&gt;&amp;a,const VectorGeneric&lt;n_&gt;&amp;b) {</a>
+<a name="418"><span class="lineNum">     418 </span>            :   return dotProduct(a,b);</a>
+<a name="419"><span class="lineNum">     419 </span>            : }</a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            : template&lt;unsigned n,unsigned m,unsigned l,unsigned i&gt;</a>
+<a name="422"><span class="lineNum">     422 </span>            : TensorGeneric&lt;n,i&gt; matmul(const TensorGeneric&lt;n,m&gt;&amp;a,const TensorGeneric&lt;m,l&gt;&amp;b,const TensorGeneric&lt;l,i&gt;&amp;c) {</a>
+<a name="423"><span class="lineNum">     423 </span>            :   return matmul(matmul(a,b),c);</a>
+<a name="424"><span class="lineNum">     424 </span>            : }</a>
+<a name="425"><span class="lineNum">     425 </span>            : </a>
+<a name="426"><span class="lineNum">     426 </span>            : template&lt;unsigned n,unsigned m,unsigned l&gt;</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">     371340 : VectorGeneric&lt;n&gt; matmul(const TensorGeneric&lt;n,m&gt;&amp;a,const TensorGeneric&lt;m,l&gt;&amp;b,const VectorGeneric&lt;l&gt;&amp;c) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">     371340 :   return matmul(matmul(a,b),c);</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : }</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            : template&lt;unsigned n,unsigned m,unsigned l&gt;</a>
+<a name="432"><span class="lineNum">     432 </span>            : VectorGeneric&lt;l&gt; matmul(const VectorGeneric&lt;n&gt;&amp;a,const TensorGeneric&lt;n,m&gt;&amp;b,const TensorGeneric&lt;m,l&gt;&amp;c) {</a>
+<a name="433"><span class="lineNum">     433 </span>            :   return matmul(matmul(a,b),c);</a>
+<a name="434"><span class="lineNum">     434 </span>            : }</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="437"><span class="lineNum">     437 </span>            : double matmul(const VectorGeneric&lt;n&gt;&amp;a,const TensorGeneric&lt;n,m&gt;&amp;b,const VectorGeneric&lt;m&gt;&amp;c) {</a>
+<a name="438"><span class="lineNum">     438 </span>            :   return matmul(matmul(a,b),c);</a>
+<a name="439"><span class="lineNum">     439 </span>            : }</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            : inline</a>
+<a name="442"><span class="lineNum">     442 </span>            : double determinant(const TensorGeneric&lt;3,3&gt;&amp;t) {</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">        417 :   return t.determinant();</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : }</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            : inline</a>
+<a name="447"><span class="lineNum">     447 </span>            : TensorGeneric&lt;3,3&gt; inverse(const TensorGeneric&lt;3,3&gt;&amp;t) {</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">      65643 :   return t.inverse();</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : }</a>
+<a name="450"><span class="lineNum">     450 </span>            : </a>
+<a name="451"><span class="lineNum">     451 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">     859175 : TensorGeneric&lt;n,m&gt; transpose(const TensorGeneric&lt;m,n&gt;&amp;t) {</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">     859175 :   return t.transpose();</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">    1747545 : TensorGeneric&lt;n,m&gt; extProduct(const VectorGeneric&lt;n&gt;&amp;v1,const VectorGeneric&lt;m&gt;&amp;v2) {</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">    1747545 :   return TensorGeneric&lt;n,m&gt;(v1,v2);</span></a>
+<a name="459"><span class="lineNum">     459 </span>            : }</a>
+<a name="460"><span class="lineNum">     460 </span>            : </a>
+<a name="461"><span class="lineNum">     461 </span>            : inline</a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">    4339003 : TensorGeneric&lt;3,3&gt; dcrossDv1(const VectorGeneric&lt;3&gt;&amp;v1,const VectorGeneric&lt;3&gt;&amp;v2) {</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   (void) v1; // this is to avoid warnings. still the syntax of this function is a bit dummy...</a>
+<a name="464"><span class="lineNum">     464 </span>            :   return TensorGeneric&lt;3,3&gt;(</a>
+<a name="465"><span class="lineNum">     465 </span>            :            0.0, v2[2],-v2[1],</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">    4339003 :            -v2[2],   0.0, v2[0],</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">    4339003 :            v2[1],-v2[0],   0.0);</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : }</a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            : inline</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">    4916659 : TensorGeneric&lt;3,3&gt; dcrossDv2(const VectorGeneric&lt;3&gt;&amp;v1,const VectorGeneric&lt;3&gt;&amp;v2) {</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :   (void) v2; // this is to avoid warnings. still the syntax of this function is a bit dummy...</a>
+<a name="473"><span class="lineNum">     473 </span>            :   return TensorGeneric&lt;3,3&gt;(</a>
+<a name="474"><span class="lineNum">     474 </span>            :            0.0,-v1[2],v1[1],</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">    4916659 :            v1[2],0.0,-v1[0],</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">    4916659 :            -v1[1],v1[0],0.0);</span></a>
+<a name="477"><span class="lineNum">     477 </span>            : }</a>
+<a name="478"><span class="lineNum">     478 </span>            : </a>
+<a name="479"><span class="lineNum">     479 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineNoCov">          0 : std::ostream &amp; operator&lt;&lt;(std::ostream &amp;os, const TensorGeneric&lt;n,m&gt;&amp; t) {</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;n; i++)for(unsigned j=0; j&lt;m; j++) {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :       if(i!=(n-1) || j!=(m-1)) os&lt;&lt;t(i,j)&lt;&lt;&quot; &quot;;</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineNoCov">          0 :       else os&lt;&lt;t(i,j);</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :     }</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineNoCov">          0 :   return os;</span></a>
+<a name="486"><span class="lineNum">     486 </span>            : }</a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            : /// \ingroup TOOLBOX</a>
+<a name="489"><span class="lineNum">     489 </span>            : typedef TensorGeneric&lt;1,1&gt; Tensor1d;</a>
+<a name="490"><span class="lineNum">     490 </span>            : /// \ingroup TOOLBOX</a>
+<a name="491"><span class="lineNum">     491 </span>            : typedef TensorGeneric&lt;2,2&gt; Tensor2d;</a>
+<a name="492"><span class="lineNum">     492 </span>            : /// \ingroup TOOLBOX</a>
+<a name="493"><span class="lineNum">     493 </span>            : typedef TensorGeneric&lt;3,3&gt; Tensor3d;</a>
+<a name="494"><span class="lineNum">     494 </span>            : /// \ingroup TOOLBOX</a>
+<a name="495"><span class="lineNum">     495 </span>            : typedef TensorGeneric&lt;4,4&gt; Tensor4d;</a>
+<a name="496"><span class="lineNum">     496 </span>            : /// \ingroup TOOLBOX</a>
+<a name="497"><span class="lineNum">     497 </span>            : typedef TensorGeneric&lt;5,5&gt; Tensor5d;</a>
+<a name="498"><span class="lineNum">     498 </span>            : /// \ingroup TOOLBOX</a>
+<a name="499"><span class="lineNum">     499 </span>            : typedef Tensor3d Tensor;</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            : inline</a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">     144414 : TensorGeneric&lt;3,3&gt; VcrossTensor(const VectorGeneric&lt;3&gt;&amp;v1,const TensorGeneric&lt;3,3&gt;&amp;v2) {</span></a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">     144414 :   TensorGeneric&lt;3,3&gt; t;</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">     577656 :   for(unsigned i=0; i&lt;3; i++) {</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">     433242 :     t.setRow(i,matmul(dcrossDv2(v1,v1),v2.getRow(i)));</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :   }</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">     144414 :   return t;</span></a>
+<a name="509"><span class="lineNum">     509 </span>            : }</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            : inline</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">      48138 : TensorGeneric&lt;3,3&gt; VcrossTensor(const TensorGeneric&lt;3,3&gt;&amp;v2,const VectorGeneric&lt;3&gt;&amp;v1) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">      48138 :   TensorGeneric&lt;3,3&gt; t;</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">     192552 :   for(unsigned i=0; i&lt;3; i++) {</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">     144414 :     t.setRow(i,-matmul(dcrossDv2(v1,v1),v2.getRow(i)));</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :   }</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">      48138 :   return t;</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : }</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            : inline</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">      48138 : TensorGeneric&lt;3,3&gt; deriNorm(const VectorGeneric&lt;3&gt;&amp;v1,const TensorGeneric&lt;3,3&gt;&amp;v2) {</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :   // delta(v) = delta(v1/v1.norm) = 1/v1.norm*(delta(v1) - (v.delta(v1))cross v;</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">      48138 :   double over_norm = 1./v1.modulo();</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">      48138 :   return over_norm*(v2 - over_norm*over_norm*(extProduct(matmul(v2,v1),v1)));</span></a>
+<a name="526"><span class="lineNum">     526 </span>            : }</a>
+<a name="527"><span class="lineNum">     527 </span>            : </a>
+<a name="528"><span class="lineNum">     528 </span>            : template&lt;unsigned n,unsigned m&gt;</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">     556394 : void diagMatSym(const TensorGeneric&lt;n,n&gt;&amp;mat,VectorGeneric&lt;m&gt;&amp;evals,TensorGeneric&lt;m,n&gt;&amp;evec) {</span></a>
+<a name="530"><span class="lineNum">     530 </span>            :   // some guess number to make sure work is large enough.</a>
+<a name="531"><span class="lineNum">     531 </span>            :   // for correctness it should be &gt;=20. However, it is recommended to be the block size.</a>
+<a name="532"><span class="lineNum">     532 </span>            :   // I put some likely exaggerated number</a>
+<a name="533"><span class="lineNum">     533 </span>            :   constexpr int bs=100;</a>
+<a name="534"><span class="lineNum">     534 </span>            :   // temporary data, on stack so as to avoid allocations</a>
+<a name="535"><span class="lineNum">     535 </span>            :   std::array&lt;int,10*n&gt; iwork;</a>
+<a name="536"><span class="lineNum">     536 </span>            :   std::array&lt;double,(6+bs)*n&gt; work;</a>
+<a name="537"><span class="lineNum">     537 </span>            :   std::array&lt;int,2*m&gt; isup;</a>
+<a name="538"><span class="lineNum">     538 </span>            :   // documentation says that &quot;matrix is destroyed&quot; !!!</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">     556394 :   auto mat_copy=mat;</span></a>
+<a name="540"><span class="lineNum">     540 </span>            :   // documentation says this is size n (even if m&lt;n)</a>
+<a name="541"><span class="lineNum">     541 </span>            :   std::array&lt;double,n&gt; evals_tmp;</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">     556394 :   int nn=n;              // dimension of matrix</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">     556394 :   double vl=0.0, vu=1.0; // ranges - not used</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">     556394 :   int one=1,mm=m;        // minimum and maximum index</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">     556394 :   double abstol=0.0;     // tolerance</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">     556394 :   int mout=0;            // number of eigenvalues found (same as mm)</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">     556394 :   int info=0;            // result</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">     556394 :   int liwork=iwork.size();</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">     556394 :   int lwork=work.size();</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">     556394 :   TensorGenericAux::local_dsyevr(&quot;V&quot;, (n==m?&quot;A&quot;:&quot;I&quot;), &quot;U&quot;, &amp;nn, const_cast&lt;double*&gt;(&amp;mat_copy[0][0]), &amp;nn, &amp;vl, &amp;vu, &amp;one, &amp;mm,</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">     556394 :                                  &amp;abstol, &amp;mout, &amp;evals_tmp[0], &amp;evec[0][0], &amp;nn,</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :                                  isup.data(), work.data(), &amp;lwork, iwork.data(), &amp;liwork, &amp;info);</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">     556394 :   if(info!=0) plumed_error()&lt;&lt;&quot;Error diagonalizing matrix\n&quot;</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :                               &lt;&lt;&quot;Matrix:\n&quot;&lt;&lt;mat&lt;&lt;&quot;\n&quot;</a>
+<a name="555"><span class="lineNum">     555 </span>            :                               &lt;&lt;&quot;Info: &quot;&lt;&lt;info&lt;&lt;&quot;\n&quot;;</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">     556394 :   plumed_assert(mout==m);</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">    1134810 :   for(unsigned i=0; i&lt;m; i++) evals[i]=evals_tmp[i];</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   // This changes eigenvectors so that the first non-null element</a>
+<a name="559"><span class="lineNum">     559 </span>            :   // of each of them is positive</a>
+<a name="560"><span class="lineNum">     560 </span>            :   // We can do it because the phase is arbitrary, and helps making</a>
+<a name="561"><span class="lineNum">     561 </span>            :   // the result reproducible</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">    1134810 :   for(unsigned i=0; i&lt;m; ++i) {</span></a>
+<a name="563"><span class="lineNum">     563 </span>            :     unsigned j=0;</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">     578516 :     for(j=0; j&lt;n; j++) if(evec(i,j)*evec(i,j)&gt;1e-14) break;</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">     946879 :     if(j&lt;n) if(evec(i,j)&lt;0.0) for(j=0; j&lt;n; j++) evec(i,j)*=-1;</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :   }</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">     556394 : }</span></a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span>            : static_assert(sizeof(Tensor)==9*sizeof(double), &quot;code cannot work if this is not satisfied&quot;);</a>
+<a name="570"><span class="lineNum">     570 </span>            : </a>
+<a name="571"><span class="lineNum">     571 </span>            : }</a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span>            : #endif</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tools.cpp.func-sort-c.html b/coverage/tools/Tools.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4d0dbe94ff
--- /dev/null
+++ b/coverage/tools/Tools.cpp.func-sort-c.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tools.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tools.cpp<span style="font-size: 80%;"> (<a href="Tools.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">255</td>
+            <td class="headerCovTableEntry">278</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <center>
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+    <tr>
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tools.cpp.gcov.html b/coverage/tools/Tools.cpp.gcov.html
new file mode 100644
index 0000000000..2a7a600981
--- /dev/null
+++ b/coverage/tools/Tools.cpp.gcov.html
@@ -0,0 +1,596 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tools.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tools.cpp<span style="font-size: 80%;"> (source / <a href="Tools.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">255</td>
+            <td class="headerCovTableEntry">278</td>
+            <td class="headerCovTableEntryHi">91.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryHi">92.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;IFile.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;lepton/Lepton.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;cstring&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;dirent.h&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;map&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #if defined(__PLUMED_HAS_CHDIR) || defined(__PLUMED_HAS_GETCWD)</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;unistd.h&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #endif</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;iomanip&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : template&lt;class T&gt;</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">   16905001 : bool Tools::convertToAny(const std::string &amp; str,T &amp; t) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">   31584409 :   std::istringstream istr(str.c_str());</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">   16905001 :   bool ok=static_cast&lt;bool&gt;(istr&gt;&gt;t);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">   16905001 :   if(!ok) return false;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::string remaining;</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">   14801582 :   istr&gt;&gt;remaining;</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">   14801582 :   return remaining.length()==0;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">   16905001 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">    2222876 : bool Tools::convertNoexcept(const std::string &amp; str,int &amp; t) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    2222876 :   return convertToInt(str,t);</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          3 : bool Tools::convertNoexcept(const std::string &amp; str,long int &amp; t) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 :   return convertToInt(str,t);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         85 : bool Tools::convertNoexcept(const std::string &amp; str,long long int &amp; t) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         85 :   return convertToInt(str,t);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       4985 : bool Tools::convertNoexcept(const std::string &amp; str,unsigned &amp; t) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">       4985 :   return convertToInt(str,t);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         97 : bool Tools::convertNoexcept(const std::string &amp; str,long unsigned &amp; t) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         97 :   return convertToInt(str,t);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         54 : bool Tools::convertNoexcept(const std::string &amp; str,long long unsigned &amp; t) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         54 :   return convertToInt(str,t);</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">     450408 : bool Tools::convertNoexcept(const std::string &amp; str,AtomNumber &amp;a) {</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   // Note: AtomNumber's are NOT converted as int, so as to</a>
+<a name="75"><span class="lineNum">      75 </span>            :   // avoid using lepton conversions.</a>
+<a name="76"><span class="lineNum">      76 </span>            :   unsigned i;</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     450408 :   bool r=convertToAny(str,i);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     450408 :   if(r) a.setSerial(i);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     450408 :   return r;</span></a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : template&lt;class T&gt;</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    2228100 : bool Tools::convertToInt(const std::string &amp; str,T &amp; t) {</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   // First try standard conversion</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">    2228100 :   if(convertToAny(str,t)) return true;</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   // Then use lepton</a>
+<a name="87"><span class="lineNum">      87 </span>            :   try {</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">    2008031 :     double r=lepton::Parser::parse(str).evaluate(lepton::Constants());</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :     // now sanity checks on the resulting number</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            :     // it should not overflow the requested int type:</a>
+<a name="93"><span class="lineNum">      93 </span>            :     // (see https://stackoverflow.com/a/526092)</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    2008031 :     if(r&gt;std::nextafter(std::numeric_limits&lt;T&gt;::max(), 0)) return false;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">    2008031 :     if(r&lt;std::nextafter(std::numeric_limits&lt;T&gt;::min(), 0)) return false;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            :     // do the actual conversion</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">    2008031 :     auto tmp=static_cast&lt;T&gt;(std::round(r));</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            :     // it should be *very close* to itself if converted back to double</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">    2008031 :     double diff= r-static_cast&lt;double&gt;(tmp);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">    2008031 :     if(diff*diff &gt; 1e-20) return false;</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :     // this is to accomodate small numerical errors and allow e.g. exp(log(7)) to be integer</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            :     // it should be change if incremented or decremented by one (see https://stackoverflow.com/a/43656140)</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">    2008027 :     if(r == static_cast&lt;double&gt;(tmp-1)) return false;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    2008026 :     if(r == static_cast&lt;double&gt;(tmp+1)) return false;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :     // everything is fine, then store in t</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">    2008026 :     t=tmp;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">    2008026 :     return true;</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   } catch(const PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   return false;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : template&lt;class T&gt;</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">   14223776 : bool Tools::convertToReal(const std::string &amp; str,T &amp; t) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">   14223776 :   if(convertToAny(str,t)) return true;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    8378094 :   if(str==&quot;PI&quot; || str==&quot;+PI&quot; || str==&quot;+pi&quot; || str==&quot;pi&quot;) {</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">    1047301 :     t=pi; return true;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">    2094570 :   } else if(str==&quot;-PI&quot; || str==&quot;-pi&quot;) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">    1047220 :     t=-pi; return true;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            :   try {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         65 :     t=lepton::Parser::parse(str).evaluate(lepton::Constants());</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         24 :     return true;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         41 :   } catch(const PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   }</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         41 :   if( str.find(&quot;PI&quot;)!=std::string::npos ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     std::size_t pi_start=str.find_first_of(&quot;PI&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     if(str.substr(pi_start)!=&quot;PI&quot;) return false;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :     std::istringstream nstr(str.substr(0,pi_start));</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :     T ff=0.0; bool ok=static_cast&lt;bool&gt;(nstr&gt;&gt;ff);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :     if(!ok) return false;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :     t=ff*pi;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     std::string remains; nstr&gt;&gt;remains;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     return remains.length()==0;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         41 :   } else if( str.find(&quot;pi&quot;)!=std::string::npos ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         15 :     std::size_t pi_start=str.find_first_of(&quot;pi&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         30 :     if(str.substr(pi_start)!=&quot;pi&quot;) return false;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         15 :     std::istringstream nstr(str.substr(0,pi_start));</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         15 :     T ff=0.0; bool ok=static_cast&lt;bool&gt;(nstr&gt;&gt;ff);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         15 :     if(!ok) return false;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         15 :     t=ff*pi;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         15 :     std::string remains; nstr&gt;&gt;remains;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         15 :     return remains.length()==0;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         41 :   } else if(str==&quot;NAN&quot;) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :     t=std::numeric_limits&lt;double&gt;::quiet_NaN();</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :     return true;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            :   return false;</a>
+<a name="154"><span class="lineNum">     154 </span>            : }</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 : bool Tools::convertNoexcept(const std::string &amp; str,float &amp; t) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   return convertToReal(str,t);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   14223648 : bool Tools::convertNoexcept(const std::string &amp; str,double &amp; t) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">   14223648 :   return convertToReal(str,t);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        128 : bool Tools::convertNoexcept(const std::string &amp; str,long double &amp; t) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        128 :   return convertToReal(str,t);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : }</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      78989 : bool Tools::convertNoexcept(const std::string &amp; str,std::string &amp; t) {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   t=str;</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      78989 :   return true;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">    3875992 : std::vector&lt;std::string&gt; Tools::getWords(const std::string &amp; line,const char* separators,int * parlevel,const char* parenthesis, const bool&amp; delete_parenthesis) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">    3875992 :   plumed_massert(std::strlen(parenthesis)==1,&quot;multiple parenthesis type not available&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">    3875992 :   plumed_massert(parenthesis[0]=='(' || parenthesis[0]=='[' || parenthesis[0]=='{',</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :                  &quot;only ( [ { allowed as parenthesis&quot;);</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">    3875992 :   if(!separators) separators=&quot; \t\n&quot;;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    3875992 :   const std::string sep(separators);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">    3875992 :   char openpar=parenthesis[0];</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   char closepar;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   if(openpar=='(') closepar=')';</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    3875992 :   if(openpar=='[') closepar=']';</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">    3875992 :   if(openpar=='{') closepar='}';</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   std::vector&lt;std::string&gt; words;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   std::string word;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   int parenthesisLevel=0;</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">    3875992 :   if(parlevel) parenthesisLevel=*parlevel;</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">  199253205 :   for(unsigned i=0; i&lt;line.length(); i++) {</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     bool found=false;</a>
+<a name="190"><span class="lineNum">     190 </span>            :     bool onParenthesis=false;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">  195377213 :     if( (line[i]==openpar || line[i]==closepar) &amp;&amp; delete_parenthesis ) onParenthesis=true;</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">  195377213 :     if(line[i]==closepar) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       2767 :       parenthesisLevel--;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       2767 :       plumed_massert(parenthesisLevel&gt;=0,&quot;Extra closed parenthesis in '&quot; + line + &quot;'&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     }</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">  781725929 :     if(parenthesisLevel==0) for(unsigned j=0; j&lt;sep.length(); j++) if(line[i]==sep[j]) found=true;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : // If at parenthesis level zero (outer)</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">  195377213 :     if(!(parenthesisLevel==0 &amp;&amp; (found||onParenthesis))) word.push_back(line[i]);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     //if(onParenthesis) word.push_back(' ');</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">  195377213 :     if(line[i]==openpar) parenthesisLevel++;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">  195377213 :     if(found &amp;&amp; word.length()&gt;0) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">   11607876 :       if(!parlevel) plumed_massert(parenthesisLevel==0,&quot;Unmatching parenthesis in '&quot; + line + &quot;'&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">   11607876 :       words.push_back(word);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       word.clear();</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">    3875992 :   if(word.length()&gt;0) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">    3758560 :     if(!parlevel) plumed_massert(parenthesisLevel==0,&quot;Unmatching parenthesis in '&quot; + line + &quot;'&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">    3758560 :     words.push_back(word);</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">    3875992 :   if(parlevel) *parlevel=parenthesisLevel;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">    3875992 :   return words;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      15000 : bool Tools::getParsedLine(IFile&amp; ifile,std::vector&lt;std::string&gt; &amp; words, bool trimcomments) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      15000 :   std::string line(&quot;&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   words.clear();</a>
+<a name="218"><span class="lineNum">     218 </span>            :   bool stat;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   bool inside=false;</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      15000 :   int parlevel=0;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   bool mergenext=false;</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">      32510 :   while((stat=ifile.getline(line))) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      31640 :     if(trimcomments) trimComments(line);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">      31640 :     trim(line);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      31640 :     if(line.length()==0) continue;</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      25728 :     std::vector&lt;std::string&gt; w=getWords(line,NULL,&amp;parlevel,&quot;{&quot;,trimcomments);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      25728 :     if(!w.empty()) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      36992 :       if(inside &amp;&amp; *(w.begin())==&quot;...&quot;) {</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :         inside=false;</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       1221 :         if(w.size()==2) plumed_massert(w[1]==words[0],&quot;second word in terminating \&quot;...\&quot; &quot;+w[1]+&quot; line, if present, should be equal to first word of directive: &quot;+words[0]);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       1221 :         plumed_massert(w.size()&lt;=2,&quot;terminating \&quot;...\&quot; lines cannot consist of more than two words&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       1221 :         w.clear(); if(!trimcomments) words.push_back(&quot;...&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      24262 :       } else if(*(w.end()-1)==&quot;...&quot;) {</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :         inside=true;</a>
+<a name="235"><span class="lineNum">     235 </span>            :         w.erase(w.end()-1);</a>
+<a name="236"><span class="lineNum">     236 </span>            :       };</a>
+<a name="237"><span class="lineNum">     237 </span>            :       int i0=0;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">      25483 :       if(mergenext &amp;&amp; words.size()&gt;0 &amp;&amp; w.size()&gt;0) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">        128 :         words[words.size()-1]+=&quot; &quot;+w[0];</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :         i0=1;</a>
+<a name="241"><span class="lineNum">     241 </span>            :       }</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">      91109 :       for(unsigned i=i0; i&lt;w.size(); ++i) words.push_back(w[i]);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :     }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">      25728 :     mergenext=(parlevel&gt;0);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      25728 :     if(!inside)break;</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">      11598 :     if(!trimcomments &amp;&amp; parlevel==0) words.push_back(&quot;@newline&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      11598 :     else if(!trimcomments) words[words.size()-1] += &quot; @newline&quot;;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">      25728 :   }</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      15000 :   plumed_massert(parlevel==0,&quot;non matching parenthesis&quot;);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      15000 :   if(words.size()&gt;0) return true;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   return stat;</a>
+<a name="252"><span class="lineNum">     252 </span>            : }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">    2739484 : bool Tools::getline(FILE* fp,std::string &amp; line) {</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   line=&quot;&quot;;</a>
+<a name="257"><span class="lineNum">     257 </span>            :   const int bufferlength=1024;</a>
+<a name="258"><span class="lineNum">     258 </span>            :   char buffer[bufferlength];</a>
+<a name="259"><span class="lineNum">     259 </span>            :   bool ret;</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov"> 2807971100 :   for(int i=0; i&lt;bufferlength; i++) buffer[i]='\0';</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">    2739484 :   while((ret=fgets(buffer,bufferlength,fp))) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">    2738744 :     line.append(buffer);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">    2738744 :     unsigned ss=std::strlen(buffer);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">    2738744 :     if(ss&gt;0) if(buffer[ss-1]=='\n') break;</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   };</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">    2739484 :   if(line.length()&gt;0) if(*(line.end()-1)=='\n') line.erase(line.end()-1);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">    2739484 :   if(line.length()&gt;0) if(*(line.end()-1)=='\r') line.erase(line.end()-1);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">    2739484 :   return ret;</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">     949153 : void Tools::trim(std::string &amp; s) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">     949153 :   auto n=s.find_last_not_of(&quot; \t&quot;);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">     949153 :   if(n!=std::string::npos) s.resize(n+1);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">     949153 : }</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">    1355153 : void Tools::trimComments(std::string &amp; s) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    1355153 :   auto n=s.find_first_of(&quot;#&quot;);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">    1355153 :   if(n!=std::string::npos) s.resize(n);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    1355153 : }</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">     332007 : bool Tools::caseInSensStringCompare(const std::string &amp; str1, const std::string &amp;str2)</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : {</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">     332007 :   return ((str1.size() == str2.size()) &amp;&amp; std::equal(str1.begin(), str1.end(), str2.begin(), [](char c1, char c2) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">     644164 :     return (c1 == c2 || std::toupper(c1) == std::toupper(c2));</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     332007 :   }));</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     107190 : bool Tools::getKey(std::vector&lt;std::string&gt;&amp; line,const std::string &amp; key,std::string &amp; s,int rep) {</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   s.clear();</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     384422 :   for(auto p=line.begin(); p!=line.end(); ++p) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     332007 :     if((*p).length()==0) continue;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">     332007 :     std::string x=(*p).substr(0,key.length());</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     332007 :     if(caseInSensStringCompare(x,key)) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      54775 :       if((*p).length()==key.length())return false;</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">      54774 :       std::string tmp=(*p).substr(key.length(),(*p).length());</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :       line.erase(p);</a>
+<a name="297"><span class="lineNum">     297 </span>            :       s=tmp;</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">      54774 :       const std::string multi(&quot;@replicas:&quot;);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      54774 :       if(rep&gt;=0 &amp;&amp; startWith(s,multi)) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         24 :         s=s.substr(multi.length(),s.length());</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         24 :         std::vector&lt;std::string&gt; words=getWords(s,&quot;\t\n ,&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         24 :         plumed_massert(rep&lt;static_cast&lt;int&gt;(words.size()),&quot;Number of fields in &quot; + s + &quot; not consistent with number of replicas&quot;);</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         24 :         s=words[rep];</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         24 :       }</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :       return true;</a>
+<a name="306"><span class="lineNum">     306 </span>            :     }</a>
+<a name="307"><span class="lineNum">     307 </span>            :   };</a>
+<a name="308"><span class="lineNum">     308 </span>            :   return false;</a>
+<a name="309"><span class="lineNum">     309 </span>            : }</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      11454 : void Tools::interpretRanges(std::vector&lt;std::string&gt;&amp;s) {</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   std::vector&lt;std::string&gt; news;</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">      57296 :   for(const auto &amp; p :s) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">      45842 :     news.push_back(p);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      45842 :     size_t dash=p.find(&quot;-&quot;);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      46453 :     if(dash==std::string::npos) continue;</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     int first;</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">       3292 :     if(!Tools::convertToAny(p.substr(0,dash),first)) continue;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">       1035 :     int stride=1;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :     int second;</a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">       1035 :     size_t colon=p.substr(dash+1).find(&quot;:&quot;);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">       1035 :     if(colon!=std::string::npos) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        108 :       if(!Tools::convertToAny(p.substr(dash+1).substr(0,colon),second) ||</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">        144 :           !Tools::convertToAny(p.substr(dash+1).substr(colon+1),stride)) continue;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :     } else {</a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">       1998 :       if(!Tools::convertToAny(p.substr(dash+1),second)) continue;</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :     }</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">       1035 :     news.resize(news.size()-1);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">       1035 :     if(first&lt;=second) {</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">       1034 :       plumed_massert(stride&gt;0,&quot;interpreting ranges &quot;+ p + &quot;, stride should be positive&quot;);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">     403537 :       for(int i=first; i&lt;=second; i+=stride) {</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :         std::string ss;</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">     402503 :         convert(i,ss);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">     402503 :         news.push_back(ss);</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :       }</a>
+<a name="336"><span class="lineNum">     336 </span>            :     } else {</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          1 :       plumed_massert(stride&lt;0,&quot;interpreting ranges &quot;+ p + &quot;, stride should be positive&quot;);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          3 :       for(int i=first; i&gt;=second; i+=stride) {</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :         std::string ss;</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">          2 :         convert(i,ss);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          2 :         news.push_back(ss);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :       }</a>
+<a name="343"><span class="lineNum">     343 </span>            :     }</a>
+<a name="344"><span class="lineNum">     344 </span>            :   }</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">      11454 :   s=news;</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">      11454 : }</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      14304 : void Tools::interpretLabel(std::vector&lt;std::string&gt;&amp;s) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">      14304 :   if(s.size()&lt;2)return;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">      13984 :   std::string s0=s[0];</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">      13984 :   unsigned l=s0.length();</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">      13984 :   if(l&lt;1) return;</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">      13984 :   if(s0[l-1]==':') {</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :     s[0]=s[1];</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      21596 :     s[1]=&quot;LABEL=&quot;+s0.substr(0,l-1);</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :   }</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">      13984 :   std::transform(s[0].begin(), s[0].end(), s[0].begin(), ::toupper);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            : }</a>
+<a name="359"><span class="lineNum">     359 </span>            : </a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">       7162 : std::vector&lt;std::string&gt; Tools::ls(const std::string&amp;d) {</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :   DIR*dir;</a>
+<a name="362"><span class="lineNum">     362 </span>            :   std::vector&lt;std::string&gt; result;</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">       7162 :   if ((dir=opendir(d.c_str()))) {</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : #if defined(__PLUMED_HAS_READDIR_R)</a>
+<a name="365"><span class="lineNum">     365 </span>            :     struct dirent ent;</a>
+<a name="366"><span class="lineNum">     366 </span>            : #endif</a>
+<a name="367"><span class="lineNum">     367 </span>            :     while(true) {</a>
+<a name="368"><span class="lineNum">     368 </span>            :       struct dirent *res;</a>
+<a name="369"><span class="lineNum">     369 </span>            : #if defined(__PLUMED_HAS_READDIR_R)</a>
+<a name="370"><span class="lineNum">     370 </span>            :       readdir_r(dir,&amp;ent,&amp;res);</a>
+<a name="371"><span class="lineNum">     371 </span>            : #else</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">     113564 :       res=readdir(dir);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : #endif</a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">     113564 :       if(!res) break;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">     510524 :       if(std::string(res-&gt;d_name)!=&quot;.&quot; &amp;&amp; std::string(res-&gt;d_name)!=&quot;..&quot;) result.push_back(res-&gt;d_name);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     }</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">       7162 :     closedir (dir);</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :   }</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">       7162 :   return result;</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       4320 : void Tools::stripLeadingAndTrailingBlanks( std::string&amp; str ) {</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       4320 :   std::size_t first=str.find_first_not_of(' ');</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       4320 :   std::size_t last=str.find_last_not_of(' ');</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       8603 :   if( first&lt;=last &amp;&amp; first!=std::string::npos) str=str.substr(first,last+1);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       4320 : }</span></a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">      11684 : std::string Tools::extension(const std::string&amp;s) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      11684 :   size_t n=s.find_last_of(&quot;.&quot;);</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :   std::string ext;</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">      11684 :   if(n!=std::string::npos &amp;&amp; n+1&lt;s.length() &amp;&amp; n+5&gt;=s.length()) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       8620 :     ext=s.substr(n+1);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       8620 :     if(ext.find(&quot;/&quot;)!=std::string::npos) ext=&quot;&quot;;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       8620 :     std::string base=s.substr(0,n);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       8620 :     if(base.length()==0) ext=&quot;&quot;;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       8620 :     if(base.length()&gt;0 &amp;&amp; base[base.length()-1]=='/') ext=&quot;&quot;;</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">      11684 :   return ext;</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : }</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">         14 : double Tools::bessel0( const double&amp; val ) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         14 :   if (std::abs(val)&lt;3.75) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          2 :     double y = Tools::fastpow( val/3.75, 2 );</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          2 :     return 1 + y*(3.5156229 +y*(3.0899424 + y*(1.2067492+y*(0.2659732+y*(0.0360768+y*0.0045813)))));</span></a>
+<a name="405"><span class="lineNum">     405 </span>            :   }</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         12 :   double ax=std::abs(val), y=3.75/ax, bx=std::exp(ax)/std::sqrt(ax);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         12 :   ax=0.39894228+y*(0.01328592+y*(0.00225319+y*(-0.00157565+y*(0.00916281+y*(-0.02057706+y*(0.02635537+y*(-0.01647633+y*0.00392377)))))));</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         12 :   return ax*bx;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">     907035 : bool Tools::startWith(const std::string &amp; full,const std::string &amp;start) {</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">     907035 :   return (full.substr(0,start.length())==start);</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">      98872 : bool Tools::findKeyword(const std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">      98872 :   const std::string search(key+&quot;=&quot;);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">     583189 :   for(const auto &amp; p : line) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">     532145 :     if(startWith(p,search)) return true;</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :   }</a>
+<a name="420"><span class="lineNum">     420 </span>            :   return false;</a>
+<a name="421"><span class="lineNum">     421 </span>            : }</a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        521 : Tools::DirectoryChanger::DirectoryChanger(const char*path) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        521 :   if(!path) return;</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">        521 :   if(std::strlen(path)==0) return;</span></a>
+<a name="426"><span class="lineNum">     426 </span>            : #ifdef __PLUMED_HAS_GETCWD</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">          2 :   char* ret=getcwd(cwd,buffersize);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">          2 :   plumed_assert(ret)&lt;&lt;&quot;Name of current directory too long, increase buffer size&quot;;</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : #else</a>
+<a name="430"><span class="lineNum">     430 </span>            :   plumed_error()&lt;&lt;&quot;You are trying to use DirectoryChanger but your system does not support getcwd&quot;;</a>
+<a name="431"><span class="lineNum">     431 </span>            : #endif</a>
+<a name="432"><span class="lineNum">     432 </span>            : #ifdef __PLUMED_HAS_CHDIR</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">          2 :   int r=chdir(path);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          3 :   plumed_assert(r==0) &lt;&lt;&quot;Cannot chdir to directory &quot;&lt;&lt;path&lt;&lt;&quot;. The directory must exist!&quot;;</span></a>
+<a name="435"><span class="lineNum">     435 </span>            : #else</a>
+<a name="436"><span class="lineNum">     436 </span>            :   plumed_error()&lt;&lt;&quot;You are trying to use DirectoryChanger but your system does not support chdir&quot;;</a>
+<a name="437"><span class="lineNum">     437 </span>            : #endif</a>
+<a name="438"><span class="lineNum">     438 </span>            : }</a>
+<a name="439"><span class="lineNum">     439 </span>            : </a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        521 : Tools::DirectoryChanger::~DirectoryChanger() {</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : #ifdef __PLUMED_HAS_CHDIR</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">        520 :   if(std::strlen(cwd)==0) return;</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          1 :   int ret=chdir(cwd);</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : // we cannot put an assertion here (in a destructor) otherwise cppcheck complains</a>
+<a name="445"><span class="lineNum">     445 </span>            : // we thus just report the problem</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          1 :   if(ret!=0) std::fprintf(stderr,&quot;+++ WARNING: cannot cd back to directory %s\n&quot;,cwd);</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : #endif</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        520 : }</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">      18842 : std::unique_ptr&lt;std::lock_guard&lt;std::mutex&gt;&gt; Tools::molfile_lock() {</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :   static std::mutex mtx;</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">      18842 :   return Tools::make_unique&lt;std::lock_guard&lt;std::mutex&gt;&gt;(mtx);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : }</a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            : /// Internal tool, I am keeping it private for now</a>
+<a name="456"><span class="lineNum">     456 </span>            : namespace {</a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span>            : class process_one_exception {</a>
+<a name="459"><span class="lineNum">     459 </span>            :   std::string &amp; msg;</a>
+<a name="460"><span class="lineNum">     460 </span>            :   bool first=true;</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">        134 :   void update() {</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">        134 :     if(!first) msg+=&quot;\n\nThe above exception was the direct cause of the following exception:\n&quot;;</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">        134 :     first=false;</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        134 :   }</span></a>
+<a name="465"><span class="lineNum">     465 </span>            : public:</a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">        120 :   process_one_exception(std::string &amp; msg):</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">        120 :     msg(msg)</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :   {}</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        133 :   void operator()(const std::exception &amp; e) {</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">        133 :     update();</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">        133 :     msg+=e.what();</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">        133 :   }</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineNoCov">          0 :   void operator()(const std::string &amp; e) {</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineNoCov">          0 :     update();</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineNoCov">          0 :     msg+=e;</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          1 :   void operator()(const char* e) {</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          1 :     update();</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          1 :     msg+=e;</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          1 :   }</span></a>
+<a name="481"><span class="lineNum">     481 </span>            : };</a>
+<a name="482"><span class="lineNum">     482 </span>            : </a>
+<a name="483"><span class="lineNum">     483 </span>            : template&lt;class T&gt;</a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">        134 : static void process_all_exceptions(T&amp;&amp; f) {</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :   try {</a>
+<a name="486"><span class="lineNum">     486 </span>            :     // First throw the current exception</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        134 :     throw;</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">        148 :   } catch(const std::nested_exception &amp; e) {</span></a>
+<a name="489"><span class="lineNum">     489 </span>            :     // If nested, we go recursive</a>
+<a name="490"><span class="lineNum">     490 </span>            :     // notice that we apply function f only if exception is also a std::exception</a>
+<a name="491"><span class="lineNum">     491 </span>            :     try {</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">         14 :       e.rethrow_nested();</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         28 :     } catch(...) {</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         14 :       process_all_exceptions(f);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     }</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         14 :     auto d=dynamic_cast&lt;const std::exception*&gt;(&amp;e);</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         14 :     if(d) f(*d);</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">        238 :   } catch(const std::exception &amp;e) {</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :     // If not nested, we end recursion</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        119 :     f(e);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineNoCov">          0 :   } catch(const std::string &amp;e) {</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :     // If not nested, we end recursion</a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :     f(e);</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          2 :   } catch(const char* e) {</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     // If not nested, we end recursion</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          1 :     f(e);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :   } catch(...) {</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :     // If not nested and of unknown type, we stop the chain</a>
+<a name="509"><span class="lineNum">     509 </span>            :   }</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">        134 : }</span></a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            : }</a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">        120 : std::string Tools::concatenateExceptionMessages() {</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :   std::string msg;</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        120 :   process_all_exceptions(process_one_exception(msg));</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">        120 :   return msg;</span></a>
+<a name="518"><span class="lineNum">     518 </span>            : }</a>
+<a name="519"><span class="lineNum">     519 </span>            : </a>
+<a name="520"><span class="lineNum">     520 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tools.h.func-sort-c.html b/coverage/tools/Tools.h.func-sort-c.html
new file mode 100644
index 0000000000..59ab50bb6b
--- /dev/null
+++ b/coverage/tools/Tools.h.func-sort-c.html
@@ -0,0 +1,1808 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tools.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tools.h<span style="font-size: 80%;"> (<a href="Tools.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">82.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">399</td>
+            <td class="headerCovTableEntry">434</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Tools.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/tools/Tools.h.func.html b/coverage/tools/Tools.h.func.html
new file mode 100644
index 0000000000..3d258a2452
--- /dev/null
+++ b/coverage/tools/Tools.h.func.html
@@ -0,0 +1,1808 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tools.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tools.h<span style="font-size: 80%;"> (<a href="Tools.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">82.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">399</td>
+            <td class="headerCovTableEntry">434</td>
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+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+      </td>
+    </tr>
+
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
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+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Tools.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tools.h.gcov.html b/coverage/tools/Tools.h.gcov.html
new file mode 100644
index 0000000000..683459d3be
--- /dev/null
+++ b/coverage/tools/Tools.h.gcov.html
@@ -0,0 +1,542 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tools.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tools.h<span style="font-size: 80%;"> (source / <a href="Tools.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">82.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">399</td>
+            <td class="headerCovTableEntry">434</td>
+            <td class="headerCovTableEntryHi">91.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Tools_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Tools_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;string&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;cctype&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;cstdio&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cmath&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;limits&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;algorithm&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;sstream&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;memory&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;cstddef&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;queue&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;mutex&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : class IFile;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : /// \ingroup TOOLBOX</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// Very small non-zero number</a>
+<a name="47"><span class="lineNum">      47 </span>            : const double epsilon(std::numeric_limits&lt;double&gt;::epsilon());</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /// \ingroup TOOLBOX</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// Boltzman constant in kj/K</a>
+<a name="51"><span class="lineNum">      51 </span>            : const double kBoltzmann(0.0083144621);</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : /// \ingroup TOOLBOX</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// PI</a>
+<a name="55"><span class="lineNum">      55 </span>            : const double pi(3.141592653589793238462643383279502884197169399375105820974944592307);</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : const double dp2cutoff(6.25);</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : const double dp2cutoffA=1.00193418799744762399; // 1.0/(1-std::exp(-dp2cutoff));</a>
+<a name="60"><span class="lineNum">      60 </span>            : const double dp2cutoffB=-.00193418799744762399; // -std::exp(-dp2cutoff)/(1-std::exp(-dp2cutoff));</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      30397 : inline static bool dp2cutoffNoStretch() {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      30397 :   static const auto* res=std::getenv(&quot;PLUMED_DP2CUTOFF_NOSTRETCH&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      30397 :   return res;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : /// \ingroup TOOLBOX</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Empty class which just contains several (static) tools</a>
+<a name="69"><span class="lineNum">      69 </span>            : class Tools {</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// class to convert a string to a generic type T</a>
+<a name="71"><span class="lineNum">      71 </span>            :   template&lt;class T&gt;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   static bool convertToAny(const std::string &amp; str,T &amp;t);</a>
+<a name="73"><span class="lineNum">      73 </span>            : /// class to convert a string to a real type T.</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// T should be either float, double, or long double</a>
+<a name="75"><span class="lineNum">      75 </span>            :   template&lt;class T&gt;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   static bool convertToReal(const std::string &amp; str,T &amp;t);</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// class to convert a string to a int type T</a>
+<a name="78"><span class="lineNum">      78 </span>            :   template&lt;class T&gt;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   static bool convertToInt(const std::string &amp; str,T &amp;t);</a>
+<a name="80"><span class="lineNum">      80 </span>            : public:</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Split the line in words using separators.</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// It also take into account parenthesis. Outer parenthesis found are removed from</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// output, and the text between them is considered as a single word. Only the</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// outer parenthesis are processed, to allow nesting them.</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// parlevel, if not NULL, is increased or decreased according to the number of opened/closed parenthesis</a>
+<a name="86"><span class="lineNum">      86 </span>            :   static std::vector&lt;std::string&gt; getWords(const std::string &amp; line,const char* sep=NULL,int* parlevel=NULL,const char* parenthesis=&quot;{&quot;, const bool&amp; delete_parenthesis=true);</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Get a line from the file pointer ifile</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static bool getline(FILE*,std::string &amp; line);</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Get a parsed line from the file pointer ifile</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// This function already takes care of joining continued lines and splitting the</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// resulting line into an array of words</a>
+<a name="92"><span class="lineNum">      92 </span>            :   static bool getParsedLine(IFile&amp;ifile,std::vector&lt;std::string&gt; &amp; line, const bool trimcomments=true);</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// compare two string in a case insensitive manner</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static bool caseInSensStringCompare(const std::string &amp; str1, const std::string &amp;str2);</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Convert a string to a double, reading it</a>
+<a name="96"><span class="lineNum">      96 </span>            :   static bool convertNoexcept(const std::string &amp; str,double &amp; t);</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Convert a string to a long double, reading it</a>
+<a name="98"><span class="lineNum">      98 </span>            :   static bool convertNoexcept(const std::string &amp; str,long double &amp; t);</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Convert a string to a float, reading it</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static bool convertNoexcept(const std::string &amp; str,float &amp; t);</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Convert a string to a int, reading it</a>
+<a name="102"><span class="lineNum">     102 </span>            :   static bool convertNoexcept(const std::string &amp; str,int &amp; t);</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Convert a string to a long int, reading it</a>
+<a name="104"><span class="lineNum">     104 </span>            :   static bool convertNoexcept(const std::string &amp; str,long int &amp; t);</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Convert a string to a long long int, reading it</a>
+<a name="106"><span class="lineNum">     106 </span>            :   static bool convertNoexcept(const std::string &amp; str,long long int &amp; t);</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// Convert a string to an unsigned int, reading it</a>
+<a name="108"><span class="lineNum">     108 </span>            :   static bool convertNoexcept(const std::string &amp; str,unsigned &amp; t);</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Convert a string to a long unsigned int, reading it</a>
+<a name="110"><span class="lineNum">     110 </span>            :   static bool convertNoexcept(const std::string &amp; str,long unsigned &amp; t);</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// Convert a string to a long long unsigned int, reading it</a>
+<a name="112"><span class="lineNum">     112 </span>            :   static bool convertNoexcept(const std::string &amp; str,long long unsigned &amp; t);</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Convert a string to a atom number, reading it</a>
+<a name="114"><span class="lineNum">     114 </span>            :   static bool convertNoexcept(const std::string &amp; str,AtomNumber &amp; t);</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Convert a string to a string (i.e. copy)</a>
+<a name="116"><span class="lineNum">     116 </span>            :   static bool convertNoexcept(const std::string &amp; str,std::string &amp; t);</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Convert anything into a string</a>
+<a name="118"><span class="lineNum">     118 </span>            :   template&lt;typename T&gt;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   static bool convertNoexcept(T i,std::string &amp; str);</a>
+<a name="120"><span class="lineNum">     120 </span>            : /// Convert anything into anything, throwing an exception in case there is an error</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Remove trailing blanks</a>
+<a name="122"><span class="lineNum">     122 </span>            :   static void trim(std::string &amp; s);</a>
+<a name="123"><span class="lineNum">     123 </span>            : /// Remove trailing comments</a>
+<a name="124"><span class="lineNum">     124 </span>            :   static void trimComments(std::string &amp; s);</a>
+<a name="125"><span class="lineNum">     125 </span>            : /// Apply pbc for a unitary cell</a>
+<a name="126"><span class="lineNum">     126 </span>            :   static double pbc(double);</a>
+<a name="127"><span class="lineNum">     127 </span>            : /// Retrieve a key from a vector of options.</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// It finds a key starting with &quot;key=&quot; or equal to &quot;key&quot; and copy the</a>
+<a name="129"><span class="lineNum">     129 </span>            : /// part after the = on s. E.g.:</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// line.push_back(&quot;aa=xx&quot;);</a>
+<a name="131"><span class="lineNum">     131 </span>            : /// getKey(line,&quot;aa&quot;,s);</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// will set s=&quot;xx&quot;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   static bool getKey(std::vector&lt;std::string&gt;&amp; line,const std::string &amp; key,std::string &amp; s,int rep=-1);</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Find a keyword on the input line, eventually deleting it, and saving its value to val</a>
+<a name="135"><span class="lineNum">     135 </span>            :   template &lt;typename T,typename U&gt;</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">   14638235 :   static void convert(const T &amp; t,U &amp; u) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">   14639036 :     plumed_assert(convertNoexcept(t,u)) &lt;&lt;&quot;Error converting  &quot;&lt;&lt;t;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">   14638234 :   }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   template &lt;typename T&gt;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   static bool parse(std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key,T&amp;val,int rep=-1);</a>
+<a name="141"><span class="lineNum">     141 </span>            : /// Find a keyword on the input line, eventually deleting it, and saving its value to a vector</a>
+<a name="142"><span class="lineNum">     142 </span>            :   template &lt;class T&gt;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   static bool parseVector(std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key,std::vector&lt;T&gt;&amp;val,int rep=-1);</a>
+<a name="144"><span class="lineNum">     144 </span>            : /// Find a keyword without arguments on the input line</a>
+<a name="145"><span class="lineNum">     145 </span>            :   static bool parseFlag(std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key,bool&amp;val);</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Find a keyword on the input line, just reporting if it exists or not</a>
+<a name="147"><span class="lineNum">     147 </span>            :   static bool findKeyword(const std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key);</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// Interpret atom ranges</a>
+<a name="149"><span class="lineNum">     149 </span>            :   static void interpretRanges(std::vector&lt;std::string&gt;&amp;);</a>
+<a name="150"><span class="lineNum">     150 </span>            : /// Remove duplicates from a vector of type T</a>
+<a name="151"><span class="lineNum">     151 </span>            :   template &lt;typename T&gt;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   static void removeDuplicates(std::vector&lt;T&gt;&amp; vec);</a>
+<a name="153"><span class="lineNum">     153 </span>            : /// interpret &quot;:&quot; syntax for labels</a>
+<a name="154"><span class="lineNum">     154 </span>            :   static void interpretLabel(std::vector&lt;std::string&gt;&amp;s);</a>
+<a name="155"><span class="lineNum">     155 </span>            : /// list files in a directory</a>
+<a name="156"><span class="lineNum">     156 </span>            :   static std::vector&lt;std::string&gt; ls(const std::string&amp;);</a>
+<a name="157"><span class="lineNum">     157 </span>            : /// removes leading and trailing blanks from a string</a>
+<a name="158"><span class="lineNum">     158 </span>            :   static void stripLeadingAndTrailingBlanks( std::string&amp; str );</a>
+<a name="159"><span class="lineNum">     159 </span>            : /// Extract the extensions from a file name.</a>
+<a name="160"><span class="lineNum">     160 </span>            : /// E.g.: extension(&quot;pippo.xyz&quot;)=&quot;xyz&quot;.</a>
+<a name="161"><span class="lineNum">     161 </span>            : /// It only returns extensions with a length between 1 and 4</a>
+<a name="162"><span class="lineNum">     162 </span>            : /// E.g.: extension(&quot;pippo.12345&quot;)=&quot;&quot; whereas extenion(&quot;pippo.1234&quot;)=&quot;1234&quot;;</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// It is also smart enough to detect &quot;/&quot;, so that</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// extension(&quot;pippo/.t&quot;)=&quot;&quot; whereas extension(&quot;pippo/a.t&quot;)=&quot;t&quot;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   static std::string extension(const std::string&amp;);</a>
+<a name="166"><span class="lineNum">     166 </span>            : /// Fast int power</a>
+<a name="167"><span class="lineNum">     167 </span>            :   static double fastpow(double base,int exp);</a>
+<a name="168"><span class="lineNum">     168 </span>            : /// Modified 0th-order Bessel function of the first kind</a>
+<a name="169"><span class="lineNum">     169 </span>            :   static double bessel0(const double&amp; val);</a>
+<a name="170"><span class="lineNum">     170 </span>            : /// Check if a string full starts with string start.</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// Same as full.find(start)==0</a>
+<a name="172"><span class="lineNum">     172 </span>            :   static bool startWith(const std::string &amp; full,const std::string &amp;start);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   /**</a>
+<a name="174"><span class="lineNum">     174 </span>            :     Tool to create a vector of raw pointers from a vector of unique_pointers (const version).</a>
+<a name="175"><span class="lineNum">     175 </span>            :   Returning a vector is fast in C++11. It can be used in order to feed a vector&lt;unique_ptr&lt;T&gt;&gt;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   to a function that takes a vector&lt;T*&gt;.</a>
+<a name="177"><span class="lineNum">     177 </span>            :   \verbatim</a>
+<a name="178"><span class="lineNum">     178 </span>            :   // some function that takes a vec</a>
+<a name="179"><span class="lineNum">     179 </span>            :   void func(std::vector&lt;Data*&gt; &amp; vec);</a>
+<a name="180"><span class="lineNum">     180 </span>            :   std::vector&lt;std::unique_ptr&lt;Data&gt;&gt; vec;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   // func(vec); // does not compile</a>
+<a name="182"><span class="lineNum">     182 </span>            :   func(Tools::unique2raw(vec)); // compiles</a>
+<a name="183"><span class="lineNum">     183 </span>            :   \endverbatim</a>
+<a name="184"><span class="lineNum">     184 </span>            :   Notice that the conversion is fast but takes</a>
+<a name="185"><span class="lineNum">     185 </span>            :   some time to allocate the new vector and copy the pointers. In case the function</a>
+<a name="186"><span class="lineNum">     186 </span>            :   acting on the vector&lt;T*&gt; is very fast and we do not want to add significant overhead,</a>
+<a name="187"><span class="lineNum">     187 </span>            :   it might be convenient to store a separate set of raw pointers.</a>
+<a name="188"><span class="lineNum">     188 </span>            :   \verbatim</a>
+<a name="189"><span class="lineNum">     189 </span>            :   // some function that takes a vec</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void func(std::vector&lt;Data*&gt; &amp; vec);</a>
+<a name="191"><span class="lineNum">     191 </span>            :   std::vector&lt;std::unique_ptr&lt;Data&gt;&gt; vec;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            :   // conversion done only once:</a>
+<a name="194"><span class="lineNum">     194 </span>            :   auto vec_ptr=Tools::unique2raw(vec);</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            :   for(int i=0;i&lt;1000;i++){</a>
+<a name="197"><span class="lineNum">     197 </span>            :     func(vec_ptr);</a>
+<a name="198"><span class="lineNum">     198 </span>            :   }</a>
+<a name="199"><span class="lineNum">     199 </span>            :   \endverbatim</a>
+<a name="200"><span class="lineNum">     200 </span>            :   */</a>
+<a name="201"><span class="lineNum">     201 </span>            :   template &lt;typename T&gt;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   static std::vector&lt;T*&gt; unique2raw(const std::vector&lt;std::unique_ptr&lt;T&gt;&gt;&amp;);</a>
+<a name="203"><span class="lineNum">     203 </span>            : /// Tool to create a vector of raw pointers from a vector of unique_pointers.</a>
+<a name="204"><span class="lineNum">     204 </span>            : /// See the non const version.</a>
+<a name="205"><span class="lineNum">     205 </span>            :   template &lt;typename T&gt;</a>
+<a name="206"><span class="lineNum">     206 </span>            :   static std::vector&lt;const T*&gt; unique2raw(const std::vector&lt;std::unique_ptr&lt;const T&gt;&gt;&amp;);</a>
+<a name="207"><span class="lineNum">     207 </span>            : /// Tiny class that changes directory and comes back when going out of scope.</a>
+<a name="208"><span class="lineNum">     208 </span>            : /// In case system calls to change dir are not available it throws an exception.</a>
+<a name="209"><span class="lineNum">     209 </span>            : /// \warning By construction, changing directory breaks thread safety! Use with care.</a>
+<a name="210"><span class="lineNum">     210 </span>            :   class DirectoryChanger {</a>
+<a name="211"><span class="lineNum">     211 </span>            :     static const std::size_t buffersize=4096;</a>
+<a name="212"><span class="lineNum">     212 </span>            :     char cwd[buffersize]= {0};</a>
+<a name="213"><span class="lineNum">     213 </span>            :   public:</a>
+<a name="214"><span class="lineNum">     214 </span>            :     explicit DirectoryChanger(const char*path);</a>
+<a name="215"><span class="lineNum">     215 </span>            :     ~DirectoryChanger();</a>
+<a name="216"><span class="lineNum">     216 </span>            :   };</a>
+<a name="217"><span class="lineNum">     217 </span>            : /// Mimic C++14 std::make_unique</a>
+<a name="218"><span class="lineNum">     218 </span>            :   template&lt;class T&gt; struct _Unique_if {</a>
+<a name="219"><span class="lineNum">     219 </span>            :     typedef std::unique_ptr&lt;T&gt; _Single_object;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   };</a>
+<a name="221"><span class="lineNum">     221 </span>            :   template&lt;class T&gt; struct _Unique_if&lt;T[]&gt; {</a>
+<a name="222"><span class="lineNum">     222 </span>            :     typedef std::unique_ptr&lt;T[]&gt; _Unknown_bound;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   };</a>
+<a name="224"><span class="lineNum">     224 </span>            :   template&lt;class T, std::size_t N&gt; struct _Unique_if&lt;T[N]&gt; {</a>
+<a name="225"><span class="lineNum">     225 </span>            :     typedef void _Known_bound;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   };</a>
+<a name="227"><span class="lineNum">     227 </span>            :   template&lt;class T, class... Args&gt;</a>
+<a name="228"><span class="lineNum">     228 </span>            :   static typename _Unique_if&lt;T&gt;::_Single_object</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">    5810122 :   make_unique(Args&amp;&amp;... args) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">    9423218 :     return std::unique_ptr&lt;T&gt;(new T(std::forward&lt;Args&gt;(args)...));</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   }</a>
+<a name="232"><span class="lineNum">     232 </span>            :   template&lt;class T&gt;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   static typename _Unique_if&lt;T&gt;::_Unknown_bound</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">        189 :   make_unique(std::size_t n) {</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     typedef typename std::remove_extent&lt;T&gt;::type U;</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       9473 :     return std::unique_ptr&lt;T&gt;(new U[n]());</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span>            :   template&lt;class T, class... Args&gt;</a>
+<a name="239"><span class="lineNum">     239 </span>            :   static typename _Unique_if&lt;T&gt;::_Known_bound</a>
+<a name="240"><span class="lineNum">     240 </span>            :   make_unique(Args&amp;&amp;...) = delete;</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :   static void set_to_zero(double*ptr,unsigned n) {</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">   22309121 :     for(unsigned i=0; i&lt;n; i++) ptr[i]=0.0;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   }</a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            :   template&lt;unsigned n&gt;</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">     218589 :   static void set_to_zero(std::vector&lt;VectorGeneric&lt;n&gt;&gt; &amp; vec) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">     218589 :     unsigned s=vec.size();</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">     218589 :     if(s==0) return;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">     196256 :     set_to_zero(&amp;vec[0][0],s*n);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            :   template&lt;unsigned n,unsigned m&gt;</a>
+<a name="254"><span class="lineNum">     254 </span>            :   static void set_to_zero(std::vector&lt;TensorGeneric&lt;n,m&gt;&gt; &amp; vec) {</a>
+<a name="255"><span class="lineNum">     255 </span>            :     unsigned s=vec.size();</a>
+<a name="256"><span class="lineNum">     256 </span>            :     if(s==0) return;</a>
+<a name="257"><span class="lineNum">     257 </span>            :     set_to_zero(&amp;vec[0](0,0),s*n*m);</a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            :   /// Merge sorted vectors.</a>
+<a name="264"><span class="lineNum">     264 </span>            :   /// Takes a vector of pointers to containers and merge them.</a>
+<a name="265"><span class="lineNum">     265 </span>            :   /// Containers should be already sorted.</a>
+<a name="266"><span class="lineNum">     266 </span>            :   /// The content is appended to the result vector.</a>
+<a name="267"><span class="lineNum">     267 </span>            :   /// Optionally, uses a priority_queue implementation.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   template&lt;class C&gt;</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">      27123 :   static void mergeSortedVectors(const std::vector&lt;C*&gt; &amp; vecs, std::vector&lt;typename C::value_type&gt; &amp; result,bool priority_queue=false) {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            :     /// local class storing the range of remaining objects to be pushed</a>
+<a name="272"><span class="lineNum">     272 </span>            :     struct Entry</a>
+<a name="273"><span class="lineNum">     273 </span>            :     {</a>
+<a name="274"><span class="lineNum">     274 </span>            :       typename C::const_iterator fwdIt,endIt;</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      52989 :       explicit Entry(C const&amp; v) : fwdIt(v.begin()), endIt(v.end()) {}</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :       /// check if this vector still contains something to be pushed</a>
+<a name="278"><span class="lineNum">     278 </span>            :       explicit operator bool () const { return fwdIt != endIt; }</a>
+<a name="279"><span class="lineNum">     279 </span>            :       /// to allow using a priority_queu, which selects the highest element.</a>
+<a name="280"><span class="lineNum">     280 </span>            :       /// we here (counterintuitively) define &lt; as &gt;</a>
+<a name="281"><span class="lineNum">     281 </span>            :       bool operator&lt; (Entry const&amp; rhs) const { return *fwdIt &gt; *rhs.fwdIt; }</a>
+<a name="282"><span class="lineNum">     282 </span>            :     };</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">      27123 :     if(priority_queue) {</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :       std::priority_queue&lt;Entry&gt; queue;</a>
+<a name="286"><span class="lineNum">     286 </span>            :       // note: queue does not have reserve() method</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            :       // add vectors to the queue</a>
+<a name="289"><span class="lineNum">     289 </span>            :       {</a>
+<a name="290"><span class="lineNum">     290 </span>            :         std::size_t maxsize=0;</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;vecs.size(); i++) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :           if(vecs[i]-&gt;size()&gt;maxsize) maxsize=vecs[i]-&gt;size();</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :           if(!vecs[i]-&gt;empty())queue.push(Entry(*vecs[i]));</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :         }</a>
+<a name="295"><span class="lineNum">     295 </span>            :         // this is just to save multiple reallocations on push_back</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :         result.reserve(maxsize);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :       }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :       // first iteration (to avoid a if in the main loop)</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :       if(queue.empty()) return;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 :       auto tmp=queue.top();</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :       queue.pop();</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :       result.push_back(*tmp.fwdIt);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :       tmp.fwdIt++;</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :       if(tmp) queue.push(tmp);</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :       // main loop</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :       while(!queue.empty()) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :         auto tmp=queue.top();</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :         queue.pop();</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :         if(result.back() &lt; *tmp.fwdIt) result.push_back(*tmp.fwdIt);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :         tmp.fwdIt++;</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :         if(tmp) queue.push(tmp);</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :       }</a>
+<a name="315"><span class="lineNum">     315 </span>            :     } else {</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            :       std::vector&lt;Entry&gt; entries;</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">      27123 :       entries.reserve(vecs.size());</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            :       {</a>
+<a name="321"><span class="lineNum">     321 </span>            :         std::size_t maxsize=0;</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      82853 :         for(int i=0; i&lt;vecs.size(); i++) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">      55730 :           if(vecs[i]-&gt;size()&gt;maxsize) maxsize=vecs[i]-&gt;size();</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">     108719 :           if(!vecs[i]-&gt;empty())entries.push_back(Entry(*vecs[i]));</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :         }</a>
+<a name="326"><span class="lineNum">     326 </span>            :         // this is just to save multiple reallocations on push_back</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      27123 :         result.reserve(maxsize);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :       }</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">     401812 :       while(!entries.empty()) {</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :         // find smallest pending element</a>
+<a name="332"><span class="lineNum">     332 </span>            :         // we use max_element instead of min_element because we are defining &lt; as &gt; (see above)</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">     374689 :         const auto minval=*std::max_element(entries.begin(),entries.end())-&gt;fwdIt;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :         // push it</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">     374689 :         result.push_back(minval);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            :         // fast forward vectors with elements equal to minval (to avoid duplicates)</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">    2150654 :         for(auto &amp; e : entries) while(e &amp;&amp; *e.fwdIt==minval) ++e.fwdIt;</span></a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :         // remove from the entries vector all exhausted vectors</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">     374689 :         auto erase=std::remove_if(entries.begin(),entries.end(),[](const Entry &amp; e) {return !e;});</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :         entries.erase(erase,entries.end());</a>
+<a name="344"><span class="lineNum">     344 </span>            :       }</a>
+<a name="345"><span class="lineNum">     345 </span>            :     }</a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span>            :   static std::unique_ptr&lt;std::lock_guard&lt;std::mutex&gt;&gt; molfile_lock();</a>
+<a name="349"><span class="lineNum">     349 </span>            :   /// Build a concatenated exception message.</a>
+<a name="350"><span class="lineNum">     350 </span>            :   /// Should be called with an in-flight exception.</a>
+<a name="351"><span class="lineNum">     351 </span>            :   static std::string concatenateExceptionMessages();</a>
+<a name="352"><span class="lineNum">     352 </span>            : };</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : template &lt;class T&gt;</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      71710 : bool Tools::parse(std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key,T&amp;val,int rep) {</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :   std::string s;</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">     143420 :   if(!getKey(line,key+&quot;=&quot;,s,rep)) return false;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">      28567 :   if(s.length()&gt;0 &amp;&amp; !convertNoexcept(s,val))return false;</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :   return true;</a>
+<a name="360"><span class="lineNum">     360 </span>            : }</a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            : template &lt;class T&gt;</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">      35447 : bool Tools::parseVector(std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key,std::vector&lt;T&gt;&amp;val,int rep) {</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   std::string s;</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">      70894 :   if(!getKey(line,key+&quot;=&quot;,s,rep)) return false;</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   val.clear();</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">      26174 :   std::vector&lt;std::string&gt; words=getWords(s,&quot;\t\n ,&quot;);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">     113682 :   for(unsigned i=0; i&lt;words.size(); ++i) {</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :     T v;</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      87508 :     std::string s=words[i];</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      87508 :     const std::string multi(&quot;@replicas:&quot;);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">      87508 :     if(rep&gt;=0 &amp;&amp; startWith(s,multi)) {</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          6 :       s=s.substr(multi.length(),s.length());</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          6 :       std::vector&lt;std::string&gt; words=getWords(s,&quot;\t\n ,&quot;);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          6 :       plumed_assert(rep&lt;static_cast&lt;int&gt;(words.size()));</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          6 :       s=words[rep];</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          6 :     }</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">      87508 :     if(!convertNoexcept(s,v))return false;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">      87508 :     val.push_back(v);</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :   }</a>
+<a name="381"><span class="lineNum">     381 </span>            :   return true;</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">      26174 : }</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            : template&lt;typename T&gt;</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      13462 : void Tools::removeDuplicates(std::vector&lt;T&gt;&amp; vec)</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : {</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">      13462 :   std::sort(vec.begin(), vec.end());</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">      13462 :   vec.erase(std::unique(vec.begin(), vec.end()), vec.end());</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      13462 : }</span></a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            : inline</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">      43084 : bool Tools::parseFlag(std::vector&lt;std::string&gt;&amp;line,const std::string&amp;key,bool&amp;val) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">     106891 :   for(auto p=line.begin(); p!=line.end(); ++p) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">      65332 :     if(key==*p) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       1525 :       val=true;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :       line.erase(p);</a>
+<a name="397"><span class="lineNum">     397 </span>            :       return true;</a>
+<a name="398"><span class="lineNum">     398 </span>            :     }</a>
+<a name="399"><span class="lineNum">     399 </span>            :   }</a>
+<a name="400"><span class="lineNum">     400 </span>            :   return false;</a>
+<a name="401"><span class="lineNum">     401 </span>            : }</a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            : /// beware: this brings any number into a pbc that ranges from -0.5 to 0.5</a>
+<a name="404"><span class="lineNum">     404 </span>            : inline</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov"> 1826108571 : double Tools::pbc(double x) {</span></a>
+<a name="406"><span class="lineNum">     406 </span>            : #ifdef __PLUMED_PBC_WHILE</a>
+<a name="407"><span class="lineNum">     407 </span>            :   while (x&gt;0.5) x-=1.0;</a>
+<a name="408"><span class="lineNum">     408 </span>            :   while (x&lt;-0.5) x+=1.0;</a>
+<a name="409"><span class="lineNum">     409 </span>            :   return x;</a>
+<a name="410"><span class="lineNum">     410 </span>            : #else</a>
+<a name="411"><span class="lineNum">     411 </span>            :   if(std::numeric_limits&lt;int&gt;::round_style == std::round_toward_zero) {</a>
+<a name="412"><span class="lineNum">     412 </span>            :     const double offset=100.0;</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov"> 1826108571 :     const double y=x+offset;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov"> 1826108571 :     if(y&gt;=0) return y-int(y+0.5);</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">       4577 :     else     return y-int(y-0.5);</span></a>
+<a name="416"><span class="lineNum">     416 </span>            :   } else if(std::numeric_limits&lt;int&gt;::round_style == std::round_to_nearest) {</a>
+<a name="417"><span class="lineNum">     417 </span>            :     return x-int(x);</a>
+<a name="418"><span class="lineNum">     418 </span>            :   } else return x-floor(x+0.5);</a>
+<a name="419"><span class="lineNum">     419 </span>            : #endif</a>
+<a name="420"><span class="lineNum">     420 </span>            : }</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            : template&lt;typename T&gt;</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">     530103 : bool Tools::convertNoexcept(T i,std::string &amp; str) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">     530103 :   std::ostringstream ostr;</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">     416075 :   ostr&lt;&lt;i;</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">     530103 :   str=ostr.str();</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">     530103 :   return true;</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">     530103 : }</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span>            : inline</a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">   79175830 : double Tools::fastpow(double base, int exp)</span></a>
+<a name="432"><span class="lineNum">     432 </span>            : {</a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">   79175830 :   if(exp&lt;0) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :     exp=-exp;</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :     base=1.0/base;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            :   }</a>
+<a name="437"><span class="lineNum">     437 </span>            :   double result = 1.0;</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">  375015129 :   while (exp)</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :   {</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">  262239105 :     if (exp &amp; 1)</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">  181137476 :       result *= base;</span></a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">  262239105 :     exp &gt;&gt;= 1;</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">  262239105 :     base *= base;</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">   79175830 :   return result;</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : }</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            : template&lt;typename T&gt;</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">   13703470 : std::vector&lt;T*&gt; Tools::unique2raw(const std::vector&lt;std::unique_ptr&lt;T&gt;&gt; &amp; x) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">   13703470 :   std::vector&lt;T*&gt; v(x.size());</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">   52721172 :   for(unsigned i=0; i&lt;x.size(); i++) v[i]=x[i].get();</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">   13703470 :   return v;</span></a>
+<a name="454"><span class="lineNum">     454 </span>            : }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            : template&lt;typename T&gt;</a>
+<a name="457"><span class="lineNum">     457 </span>            : std::vector&lt;const T*&gt; Tools::unique2raw(const std::vector&lt;std::unique_ptr&lt;const T&gt;&gt; &amp; x) {</a>
+<a name="458"><span class="lineNum">     458 </span>            :   std::vector&lt;const T*&gt; v(x.size());</a>
+<a name="459"><span class="lineNum">     459 </span>            :   for(unsigned i=0; i&lt;x.size(); i++) v[i]=x[i].get();</a>
+<a name="460"><span class="lineNum">     460 </span>            :   return v;</a>
+<a name="461"><span class="lineNum">     461 </span>            : }</a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span>            : }</a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span>            : #endif</a>
+<a name="466"><span class="lineNum">     466 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Torsion.cpp.func-sort-c.html b/coverage/tools/Torsion.cpp.func-sort-c.html
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index 0000000000..029ac01005
--- /dev/null
+++ b/coverage/tools/Torsion.cpp.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Torsion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Torsion.cpp<span style="font-size: 80%;"> (<a href="Torsion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Torsion.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#28">_ZNK4PLMD7Torsion7computeERKNS_13VectorGenericILj3EEES4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#37">_ZNK4PLMD7Torsion7computeERKNS_13VectorGenericILj3EEES4_S4_RS2_S5_S5_</a></td>
+              <td class="coverFnHi">1084725</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Torsion.cpp.func.html b/coverage/tools/Torsion.cpp.func.html
new file mode 100644
index 0000000000..2e8fd6cdee
--- /dev/null
+++ b/coverage/tools/Torsion.cpp.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Torsion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Torsion.cpp<span style="font-size: 80%;"> (<a href="Torsion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Torsion.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#28">_ZNK4PLMD7Torsion7computeERKNS_13VectorGenericILj3EEES4_S4_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Torsion.cpp.gcov.html#37">_ZNK4PLMD7Torsion7computeERKNS_13VectorGenericILj3EEES4_S4_RS2_S5_S5_</a></td>
+              <td class="coverFnHi">1084725</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Torsion.cpp.gcov.html b/coverage/tools/Torsion.cpp.gcov.html
new file mode 100644
index 0000000000..bcbf90dcba
--- /dev/null
+++ b/coverage/tools/Torsion.cpp.gcov.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Torsion.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Torsion.cpp<span style="font-size: 80%;"> (source / <a href="Torsion.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntryMed">80.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Torsion.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tensor.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cmath&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iostream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineNoCov">          0 : double Torsion::compute(const Vector&amp; v1,const Vector&amp; v2,const Vector&amp; v3)const {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineNoCov">          0 :   const Vector nv2(v2*(1.0/v2.modulo()));</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineNoCov">          0 :   const Vector a(crossProduct(nv2,v1));</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :   const Vector b(crossProduct(v3,nv2));</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 :   const double cosangle=dotProduct(a,b);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineNoCov">          0 :   const double sinangle=dotProduct(crossProduct(a,b),nv2);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 :   return std::atan2(-sinangle,cosangle);</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : }</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">    1084725 : double Torsion::compute(const Vector&amp; v1,const Vector&amp; v2,const Vector&amp; v3,Vector&amp; d1,Vector&amp; d2,Vector&amp; d3)const {</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">    1084725 :   const double modv2(1./v2.modulo());</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">    1084725 :   const Vector nv2(v2*modv2);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">    1084725 :   const Tensor dnv2_v2((Tensor::identity()-extProduct(nv2,nv2))*modv2);</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">    1084725 :   const Vector a(crossProduct(v2,v1));</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">    1084725 :   const Tensor da_dv2(dcrossDv1(v2,v1));</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">    1084725 :   const Tensor da_dv1(dcrossDv2(v2,v1));</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">    1084725 :   const Vector b(crossProduct(v3,v2));</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">    1084725 :   const Tensor db_dv3(dcrossDv1(v3,v2));</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    1084725 :   const Tensor db_dv2(dcrossDv2(v3,v2));</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">    1084725 :   const double cosangle=dotProduct(a,b);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">    1084725 :   const Vector dcosangle_dv1=matmul(b,da_dv1);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">    1084725 :   const Vector dcosangle_dv2=matmul(b,da_dv2) + matmul(a,db_dv2);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">    1084725 :   const Vector dcosangle_dv3=matmul(a,db_dv3);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">    1084725 :   const Vector cab(crossProduct(a,b));</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">    1084725 :   const Tensor dcab_dv1(matmul(dcrossDv1(a,b),da_dv1));</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">    1084725 :   const Tensor dcab_dv2(matmul(dcrossDv1(a,b),da_dv2) + matmul(dcrossDv2(a,b),db_dv2));</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">    1084725 :   const Tensor dcab_dv3(matmul(dcrossDv2(a,b),db_dv3));</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">    1084725 :   const double sinangle=dotProduct(cab,nv2);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">    1084725 :   const Vector dsinangle_dv1=matmul(nv2,dcab_dv1);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">    1084725 :   const Vector dsinangle_dv2=matmul(nv2,dcab_dv2)+matmul(cab,dnv2_v2);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">    1084725 :   const Vector dsinangle_dv3=matmul(nv2,dcab_dv3);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">    1084725 :   const double torsion=std::atan2(-sinangle,cosangle);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : // this is required since v1 and v3 are not normalized:</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">    1084725 :   const double invR2=1.0/(cosangle*cosangle+sinangle*sinangle);</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    1084725 :   d1= ( -dsinangle_dv1*cosangle + sinangle * dcosangle_dv1 ) *invR2;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    1084725 :   d2= ( -dsinangle_dv2*cosangle + sinangle * dcosangle_dv2 ) *invR2;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">    1084725 :   d3= ( -dsinangle_dv3*cosangle + sinangle * dcosangle_dv3 ) *invR2;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">    1084725 :   return torsion;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tree.cpp.func-sort-c.html b/coverage/tools/Tree.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1d54c5e30d
--- /dev/null
+++ b/coverage/tools/Tree.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tree.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tree.cpp<span style="font-size: 80%;"> (<a href="Tree.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Tree.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tree.cpp.gcov.html#40">_ZN4PLMD4Tree7getTreeESt6vectorINS_10AtomNumberESaIS2_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tree.cpp.gcov.html#31">_ZN4PLMD4TreeC2EPNS_14GenericMolInfoE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tree.cpp.gcov.html#110">_ZNK4PLMD4Tree7getRootEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tree.cpp.func.html b/coverage/tools/Tree.cpp.func.html
new file mode 100644
index 0000000000..23ed0e41a4
--- /dev/null
+++ b/coverage/tools/Tree.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tree.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tree.cpp<span style="font-size: 80%;"> (<a href="Tree.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Tree.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Tree.cpp.gcov.html#40">_ZN4PLMD4Tree7getTreeESt6vectorINS_10AtomNumberESaIS2_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tree.cpp.gcov.html#31">_ZN4PLMD4TreeC2EPNS_14GenericMolInfoE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Tree.cpp.gcov.html#110">_ZNK4PLMD4Tree7getRootEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tree.cpp.gcov.html b/coverage/tools/Tree.cpp.gcov.html
new file mode 100644
index 0000000000..61a89f469e
--- /dev/null
+++ b/coverage/tools/Tree.cpp.gcov.html
@@ -0,0 +1,193 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tree.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tree.cpp<span style="font-size: 80%;"> (source / <a href="Tree.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2021-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tree.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;limits&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          2 : Tree::Tree(GenericMolInfo* moldat) {</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : // initialize class</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">          2 :   moldat_ = moldat;</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : // check if molinfo present</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          2 :   if(!moldat_) plumed_merror(&quot;MOLINFO DATA not found&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : // check if reference structure is whole</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          2 :   if(!moldat_-&gt;isWhole()) plumed_merror(&quot;Check that reference structure in PDB file is not broken by pbc and set WHOLE in MOLINFO line&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          2 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          2 : std::vector&lt;AtomNumber&gt; Tree::getTree(std::vector&lt;AtomNumber&gt; atoms)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span>            :   // Implementation inspired from:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   // https://mayanknatani.wordpress.com/2013/05/31/euclidean-minimummaximum-spanning-tree-emst/</a>
+<a name="46"><span class="lineNum">      46 </span>            :   //</a>
+<a name="47"><span class="lineNum">      47 </span>            :   // list of AtomNumbers ordered by proximity in PDB file</a>
+<a name="48"><span class="lineNum">      48 </span>            :   std::vector&lt;AtomNumber&gt; tree;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   // clear root_ vector</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          2 :   root_.clear();</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   // remove atoms not in PDB file</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::vector&lt;AtomNumber&gt; addtotree, addtoroot;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;AtomNumber&gt; newatoms;</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          2 :   newatoms.reserve(atoms.size());</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          2 :   if(!moldat_-&gt;checkForAtom(atoms[0])) plumed_merror(&quot;The first atom in the list should be present in the PDB file&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   // store first atom</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          2 :   newatoms.push_back(atoms[0]);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        245 :   for(unsigned i=1; i&lt;atoms.size(); ++i) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        243 :     if(!moldat_-&gt;checkForAtom(atoms[i])) {</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :       // store this atom for later</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         61 :       addtotree.push_back(atoms[i]);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :       // along with its root (the previous atom)</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         61 :       addtoroot.push_back(atoms[i-1]);</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :     } else {</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        182 :       newatoms.push_back(atoms[i]);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :     }</a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // reassign atoms</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">          2 :   atoms=newatoms;</span></a>
+<a name="71"><span class="lineNum">      71 </span>            :   // start EMST</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          2 :   std::vector&lt;bool&gt; intree(atoms.size(), false);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          2 :   std::vector&lt;double&gt; mindist(atoms.size(), std::numeric_limits&lt;double&gt;::max());</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   // initialize tree with first atom</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          2 :   mindist[0] = 0.0;</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   // loops</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        186 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :     int selected_vertex = -1;</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      19034 :     for(unsigned j=0; j&lt;atoms.size(); ++j) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      18850 :       if( !intree[j] &amp;&amp; (selected_vertex==-1 || mindist[j] &lt; mindist[selected_vertex]) )</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">       1078 :         selected_vertex = j;</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :     }</a>
+<a name="83"><span class="lineNum">      83 </span>            :     // add to tree</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        184 :     plumed_assert(selected_vertex&gt;=0);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        184 :     tree.push_back(atoms[selected_vertex]);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     intree[selected_vertex] = true;</a>
+<a name="87"><span class="lineNum">      87 </span>            :     // update distances</a>
+<a name="88"><span class="lineNum">      88 </span>            :     double minroot = std::numeric_limits&lt;double&gt;::max();</a>
+<a name="89"><span class="lineNum">      89 </span>            :     int iroot = -1;</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      19034 :     for(unsigned j=0; j&lt;atoms.size(); ++j) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      18850 :       double dist = delta(moldat_-&gt;getPosition(atoms[selected_vertex]), moldat_-&gt;getPosition(atoms[j])).modulo2();</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      18850 :       if(dist &lt; mindist[j]) mindist[j] = dist;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      22401 :       if(dist &lt; minroot &amp;&amp; intree[j] &amp;&amp; dist&gt;0.0) {</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :         minroot = dist;</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       2822 :         iroot = j;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :       }</a>
+<a name="97"><span class="lineNum">      97 </span>            :     }</a>
+<a name="98"><span class="lineNum">      98 </span>            :     // add to root vector</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        184 :     if(iroot&gt;=0) root_.push_back(atoms[iroot]);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            :   // now re-add atoms not present in the PDB</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         63 :   for(unsigned i=0; i&lt;addtotree.size(); ++i) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         61 :     tree.push_back(addtotree[i]);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         61 :     root_.push_back(addtoroot[i]);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // return</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          2 :   return tree;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 : std::vector&lt;AtomNumber&gt; Tree::getRoot() const</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :   return root_;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : }</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tree.h.func-sort-c.html b/coverage/tools/Tree.h.func-sort-c.html
new file mode 100644
index 0000000000..7980b6efac
--- /dev/null
+++ b/coverage/tools/Tree.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tree.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tree.h<span style="font-size: 80%;"> (<a href="Tree.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Tree.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tree.h.func.html b/coverage/tools/Tree.h.func.html
new file mode 100644
index 0000000000..ce6d811d04
--- /dev/null
+++ b/coverage/tools/Tree.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tree.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tree.h<span style="font-size: 80%;"> (<a href="Tree.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Tree.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Tree.h.gcov.html b/coverage/tools/Tree.h.gcov.html
new file mode 100644
index 0000000000..aec63ec290
--- /dev/null
+++ b/coverage/tools/Tree.h.gcov.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Tree.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Tree.h<span style="font-size: 80%;"> (source / <a href="Tree.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2021-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Tree_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Tree_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/GenericMolInfo.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;AtomNumber.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /// \ingroup TOOLBOX</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          2 : class Tree</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : private:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   GenericMolInfo* moldat_;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;AtomNumber&gt; root_;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// constructor</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit Tree(GenericMolInfo* moldat);</a>
+<a name="44"><span class="lineNum">      44 </span>            : /// build a tree</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;AtomNumber&gt; getTree(std::vector&lt;AtomNumber&gt; atoms);</a>
+<a name="46"><span class="lineNum">      46 </span>            : /// get root</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::vector&lt;AtomNumber&gt; getRoot() const;</a>
+<a name="48"><span class="lineNum">      48 </span>            : };</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/TypesafePtr.cpp.func-sort-c.html b/coverage/tools/TypesafePtr.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ba07ef5aa6
--- /dev/null
+++ b/coverage/tools/TypesafePtr.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/TypesafePtr.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - TypesafePtr.cpp<span style="font-size: 80%;"> (<a href="TypesafePtr.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TypesafePtr.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.cpp.gcov.html#45">_ZN4PLMD11TypesafePtr9extra_msgB5cxx11Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.cpp.gcov.html#27">_ZN4PLMD11TypesafePtr11fromSafePtrEPv</a></td>
+              <td class="coverFnHi">14881</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.cpp.gcov.html#32">_ZNK4PLMD11TypesafePtr4copyEv</a></td>
+              <td class="coverFnHi">564903</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/TypesafePtr.cpp.func.html b/coverage/tools/TypesafePtr.cpp.func.html
new file mode 100644
index 0000000000..9556ce5b9d
--- /dev/null
+++ b/coverage/tools/TypesafePtr.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/TypesafePtr.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - TypesafePtr.cpp<span style="font-size: 80%;"> (<a href="TypesafePtr.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TypesafePtr.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.cpp.gcov.html#27">_ZN4PLMD11TypesafePtr11fromSafePtrEPv</a></td>
+              <td class="coverFnHi">14881</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.cpp.gcov.html#45">_ZN4PLMD11TypesafePtr9extra_msgB5cxx11Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.cpp.gcov.html#32">_ZNK4PLMD11TypesafePtr4copyEv</a></td>
+              <td class="coverFnHi">564903</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/TypesafePtr.cpp.gcov.html b/coverage/tools/TypesafePtr.cpp.gcov.html
new file mode 100644
index 0000000000..c728f77db6
--- /dev/null
+++ b/coverage/tools/TypesafePtr.cpp.gcov.html
@@ -0,0 +1,133 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/TypesafePtr.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - TypesafePtr.cpp<span style="font-size: 80%;"> (source / <a href="TypesafePtr.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;TypesafePtr.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/PlumedMainInitializer.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;iostream&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">      14881 : TypesafePtr TypesafePtr::fromSafePtr(void* safe) {</span></a>
+<a name="30"><span class="lineNum">      30 </span>            :   auto s=(plumed_safeptr_x*)safe;</a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">      14881 :   return TypesafePtr(const_cast&lt;void*&gt;(s-&gt;ptr), s-&gt;nelem, s-&gt;shape, s-&gt;flags);</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : }</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">     564903 : TypesafePtr TypesafePtr::copy() const {</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     564903 :   auto passbyvalue=((flags&gt;&gt;25)&amp;0x7)==1;</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">     564903 :   if(passbyvalue) throw ExceptionTypeError()&lt;&lt;&quot;PLUMED is trying to copy the pointer of an object passed by value&quot;;</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     564903 :   auto forbidstore=flags&amp;0x10000000;</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     564903 :   if(forbidstore) throw ExceptionTypeError()&lt;&lt;&quot;PLUMED is trying to copy the pointer of an object for which this was forbidden&quot;;</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   TypesafePtr ret;</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">     564903 :   ret.ptr=ptr;</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">     564903 :   ret.flags=flags;</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">     564903 :   ret.nelem=nelem;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">     564903 :   ret.shape=shape;</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">     564903 :   return ret;</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : }</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          8 : std::string TypesafePtr::extra_msg() {</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   const char *text = &quot;\n&quot;</a>
+<a name="49"><span class="lineNum">      49 </span>            :                      &quot;If you are sure your code is correct you can disable this check with export PLUMED_TYPESAFE_IGNORE=yes\n&quot;</a>
+<a name="50"><span class="lineNum">      50 </span>            :                      &quot;In case this is necessary, please report an issue to developers of PLUMED and of the MD code\n&quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :                      &quot;See also https://github.com/plumed/plumed2/pull/653&quot;;</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          8 :   return std::string(text);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : }</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/TypesafePtr.h.func-sort-c.html b/coverage/tools/TypesafePtr.h.func-sort-c.html
new file mode 100644
index 0000000000..5cf467064f
--- /dev/null
+++ b/coverage/tools/TypesafePtr.h.func-sort-c.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/TypesafePtr.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - TypesafePtr.h<span style="font-size: 80%;"> (<a href="TypesafePtr.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">131</td>
+            <td class="headerCovTableEntryMed">87.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TypesafePtr.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.h.gcov.html#178">_ZN4PLMD11TypesafePtrC2EfmPKm</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TypesafePtr.h.gcov.html#45">_ZN4PLMD17typesafePtrSizeofI8_IO_FILEEEmv</a></td>
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+              <td class="coverFnLo">0</td>
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+    <tr>
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+  <br>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/tools/TypesafePtr.h.func.html b/coverage/tools/TypesafePtr.h.func.html
new file mode 100644
index 0000000000..4c01e45d87
--- /dev/null
+++ b/coverage/tools/TypesafePtr.h.func.html
@@ -0,0 +1,292 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/TypesafePtr.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
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+            <td width="5%"></td>
+            <td width="15%"></td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">131</td>
+            <td class="headerCovTableEntryMed">87.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
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+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+  <center>
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+    <tr><td><br></td></tr>
+    <tr>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
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+</body>
+</html>
diff --git a/coverage/tools/TypesafePtr.h.gcov.html b/coverage/tools/TypesafePtr.h.gcov.html
new file mode 100644
index 0000000000..b601c3f940
--- /dev/null
+++ b/coverage/tools/TypesafePtr.h.gcov.html
@@ -0,0 +1,475 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/TypesafePtr.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - TypesafePtr.h<span style="font-size: 80%;"> (source / <a href="TypesafePtr.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">115</td>
+            <td class="headerCovTableEntry">131</td>
+            <td class="headerCovTableEntryMed">87.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">40</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntryLo">72.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_TypesafePtr_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_TypesafePtr_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;memory&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;iosfwd&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;map&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;utility&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;mutex&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cstdio&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;array&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;cstring&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;type_traits&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;climits&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;initializer_list&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">    1115406 : static inline bool typesafePtrSkipCheck() {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">    1115406 :   static const bool ret=std::getenv(&quot;PLUMED_TYPESAFE_IGNORE&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">    1115406 :   return ret;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : }</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : template&lt;class T&gt;</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">    1108194 : std::size_t typesafePtrSizeof() {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">    1108194 :   return sizeof(T);</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : }</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : template&lt;&gt;</a>
+<a name="52"><span class="lineNum">      52 </span>            : inline</a>
+<a name="53"><span class="lineNum">      53 </span>            : std::size_t typesafePtrSizeof&lt;void&gt;() {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   return 0;</a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : template&lt;&gt;</a>
+<a name="58"><span class="lineNum">      58 </span>            : inline</a>
+<a name="59"><span class="lineNum">      59 </span>            : std::size_t typesafePtrSizeof&lt;const void&gt;() {</a>
+<a name="60"><span class="lineNum">      60 </span>            :   return 0;</a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : /**</a>
+<a name="64"><span class="lineNum">      64 </span>            : \ingroup TOOLBOX</a>
+<a name="65"><span class="lineNum">      65 </span>            : Class to deal with propoagation of typesafe pointers.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : */</a>
+<a name="68"><span class="lineNum">      68 </span>            : class TypesafePtr {</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">    1135275 :   inline void init_shape(const std::size_t* shape) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">    1135275 :     this-&gt;shape[0]=0;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">    1135275 :     if(shape &amp;&amp; *shape&gt;0) {</span></a>
+<a name="72"><span class="lineNum">      72 </span>            :       std::size_t nelem_=1;</a>
+<a name="73"><span class="lineNum">      73 </span>            :       unsigned i=0;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        820 :       for(i=0; i&lt;this-&gt;shape.size(); i++) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        820 :         this-&gt;shape[i]=*shape;</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        820 :         if(*shape==0) break;</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        468 :         nelem_*=*shape;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        468 :         shape++;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :       }</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        352 :       plumed_assert(i&lt;this-&gt;shape.size()); // check that last element is actually zero</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        352 :       if(nelem==0) nelem=nelem_;</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        352 :       plumed_assert(nelem==nelem_) &lt;&lt; &quot;Inconsistent shape/nelem&quot;;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :     }</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    1135275 :   }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            :   static std::string extra_msg();</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : public:</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            :   TypesafePtr(void* ptr, std::size_t nelem, const std::size_t* shape, std::size_t flags):</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     291328 :     ptr(ptr),</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">     291328 :     nelem(nelem),</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">     291328 :     flags(flags)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   {</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">     291328 :     buffer[0]='\0';</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     291328 :     init_shape(shape);</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            :   static const unsigned maxrank=4;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static TypesafePtr fromSafePtr(void* safe);</a>
+<a name="101"><span class="lineNum">     101 </span>            :   static TypesafePtr setNelemAndShape(const TypesafePtr &amp;other, std::size_t nelem, const std::size_t* shape) {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     276090 :     return TypesafePtr(other.ptr,nelem,shape,other.flags);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   }</a>
+<a name="104"><span class="lineNum">     104 </span>            :   static TypesafePtr unchecked(const void* ptr) {</a>
+<a name="105"><span class="lineNum">     105 </span>            :     return TypesafePtr(const_cast&lt;void*&gt;(ptr),0,nullptr,0);</a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span>            :   static constexpr unsigned short is_integral=3;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   static constexpr unsigned short is_floating_point=4;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   static constexpr unsigned short is_file=5;</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">    1704911 :   TypesafePtr() {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">    1704911 :     shape[0]=0;</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">    1481759 :     buffer[0]='\0';</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            :   TypesafePtr(std::nullptr_t)</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">     260571 :   {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     260571 :     shape[0]=0;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     259455 :     buffer[0]='\0';</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : /// Macro that generate a constructor with given type and flags</a>
+<a name="123"><span class="lineNum">     123 </span>            : #define __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type,type_,flags_) \</a>
+<a name="124"><span class="lineNum">     124 </span>            :   TypesafePtr(type_*ptr, std::size_t nelem=0, const std::size_t* shape=nullptr) : \</a>
+<a name="125"><span class="lineNum">     125 </span>            :     ptr((void*)const_cast&lt;type*&gt;(ptr)), \</a>
+<a name="126"><span class="lineNum">     126 </span>            :     nelem(nelem), \</a>
+<a name="127"><span class="lineNum">     127 </span>            :     flags(flags_) \</a>
+<a name="128"><span class="lineNum">     128 </span>            :   { \</a>
+<a name="129"><span class="lineNum">     129 </span>            :     init_shape(shape); \</a>
+<a name="130"><span class="lineNum">     130 </span>            :     buffer[0]='\0'; \</a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Macro that uses __PLUMED_WRAPPER_TYPESAFEPTR_INNER to generate constructors with</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// all possible pointer-const combinations</a>
+<a name="135"><span class="lineNum">     135 </span>            : #define __PLUMED_WRAPPER_TYPESAFEPTR(type, code,size) \</a>
+<a name="136"><span class="lineNum">     136 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type, type,             size | (0x10000*(code)) | (0x2000000*2)) \</a>
+<a name="137"><span class="lineNum">     137 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type, type const,       size | (0x10000*(code)) | (0x2000000*3)) \</a>
+<a name="138"><span class="lineNum">     138 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type*,type*,            size | (0x10000*(code)) | (0x2000000*4)) \</a>
+<a name="139"><span class="lineNum">     139 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type*,type*const,       size | (0x10000*(code)) | (0x2000000*5)) \</a>
+<a name="140"><span class="lineNum">     140 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type*,type const*,      size | (0x10000*(code)) | (0x2000000*6)) \</a>
+<a name="141"><span class="lineNum">     141 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_INNER(type*,type const*const, size | (0x10000*(code)) | (0x2000000*7))</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : /// Macro that generates the constructors from empy types (those of which sizeof cannot be computed)</a>
+<a name="144"><span class="lineNum">     144 </span>            : #define __PLUMED_WRAPPER_TYPESAFEPTR_EMPTY(type,code) __PLUMED_WRAPPER_TYPESAFEPTR(type,code,0)</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Macro that generates the constructors from sized types (those of which sizeof can be computed).</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// In addition to generating constructors with all pointer types, it generates a constructor to</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// allow pass-by-value</a>
+<a name="149"><span class="lineNum">     149 </span>            : #define __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(type,code) \</a>
+<a name="150"><span class="lineNum">     150 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR(type,code,sizeof(type)) \</a>
+<a name="151"><span class="lineNum">     151 </span>            :   TypesafePtr(type val, std::size_t nelem=0, const std::size_t* shape=nullptr): \</a>
+<a name="152"><span class="lineNum">     152 </span>            :       nelem(1), \</a>
+<a name="153"><span class="lineNum">     153 </span>            :       flags(sizeof(type) | (0x10000*(code)) | (0x2000000*1)) \</a>
+<a name="154"><span class="lineNum">     154 </span>            :     { \</a>
+<a name="155"><span class="lineNum">     155 </span>            :     plumed_assert(sizeof(type)&lt;=32); \</a>
+<a name="156"><span class="lineNum">     156 </span>            :     ptr=&amp;buffer[0]; \</a>
+<a name="157"><span class="lineNum">     157 </span>            :     flags=sizeof(type) | (0x10000*(code)) | (0x2000000*1); \</a>
+<a name="158"><span class="lineNum">     158 </span>            :     std::memcpy(&amp;buffer[0],&amp;val,sizeof(type)); \</a>
+<a name="159"><span class="lineNum">     159 </span>            :     init_shape(shape); \</a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : /// Here we create all the required instances</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// 1: void</a>
+<a name="164"><span class="lineNum">     164 </span>            : /// 3: integral</a>
+<a name="165"><span class="lineNum">     165 </span>            : /// 4: floating</a>
+<a name="166"><span class="lineNum">     166 </span>            : /// 5: FILE</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// 0x100: unsigned</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       1217 :   __PLUMED_WRAPPER_TYPESAFEPTR_EMPTY(void,1)</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1761 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(char,(CHAR_MIN==0)*0x100+3)</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(signed char,3)</a>
+<a name="171"><span class="lineNum">     171 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(unsigned char,0x100+3)</a>
+<a name="172"><span class="lineNum">     172 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(short,3)</a>
+<a name="173"><span class="lineNum">     173 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(unsigned short,0x100+3)</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     264252 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(int,3)</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         98 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(unsigned int,0x100+3)</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(long,3)</a>
+<a name="177"><span class="lineNum">     177 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(unsigned long,0x100+3)</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     246118 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(long long,3)</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">       3939 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(unsigned long long,0x100+3)</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(float,4)</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     325712 :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(double,4)</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   __PLUMED_WRAPPER_TYPESAFEPTR_SIZED(long double,4)</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        850 :   __PLUMED_WRAPPER_TYPESAFEPTR_EMPTY(FILE,5)</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            :   ~TypesafePtr() {</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">    2290733 :   }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            :   TypesafePtr(const TypesafePtr&amp;other) = delete;</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   TypesafePtr &amp; operator=(const TypesafePtr &amp; other) = delete;</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         64 :   TypesafePtr(TypesafePtr&amp;&amp;other):</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         64 :     buffer(other.buffer),</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         64 :     ptr(other.ptr==&amp;other.buffer[0] ? &amp;buffer[0] : other.ptr),</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         64 :     nelem(other.nelem),</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         64 :     shape(other.shape),</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         64 :     flags(other.flags)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         64 :     other.ptr=nullptr;</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         64 :   }</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            :   TypesafePtr copy() const;</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     899637 :   TypesafePtr &amp; operator=(TypesafePtr &amp;&amp; other) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">     899637 :     ptr=(other.ptr==&amp;other.buffer[0] ? &amp;buffer[0] : other.ptr);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">     899637 :     flags=other.flags;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">     899637 :     nelem=other.nelem;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     899637 :     shape=other.shape;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     899637 :     buffer=other.buffer;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">     899637 :     other.ptr=nullptr;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     899637 :     return *this;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          5 :   std::string type_str() const {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">          5 :     auto type=(flags&gt;&gt;16)&amp;0xff;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          5 :     if(type==0) return &quot;wildcard&quot;;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">          1 :     if(type==1) return &quot;void&quot;;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :     if(type==2) return &quot;integral&quot;;</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :     if(type==3) return &quot;integral&quot;;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          4 :     if(type==4) return &quot;floating point&quot;;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :     if(type==5) return &quot;FILE&quot;;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :     return &quot;unknown&quot;;</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : private:</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            :   template&lt;typename T&gt;</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">    1115406 :   T* get_priv(std::size_t nelem, const std::size_t* shape, bool byvalue) const {</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">    1115406 :     if(typesafePtrSkipCheck()) return (T*) ptr;</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     typedef typename std::remove_pointer&lt;T&gt;::type T_noptr;</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">    1115406 :     if(flags==0) return (T*) ptr; // no check</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">    1109051 :     auto size=flags&amp;0xffff;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">    1109051 :     auto type=(flags&gt;&gt;16)&amp;0xff;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :     // auto unsi=(flags&gt;&gt;24)&amp;0x1; // ignored</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">    1110766 :     auto cons=(flags&gt;&gt;25)&amp;0x7;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            :     // type=0: ignore check</a>
+<a name="240"><span class="lineNum">     240 </span>            :     // type&gt;5: undefined yet</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">    1109051 :     if(type!=0 &amp;&amp; type&lt;=5) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">     530236 :       if(std::is_integral&lt;T_noptr&gt;::value &amp;&amp; (type!=is_integral)) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         20 :         throw ExceptionTypeError() &lt;&lt;&quot;This command expects an integer type. Received a &quot; &lt;&lt; type_str() &lt;&lt; &quot; instead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :       }</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">     577963 :       if(std::is_floating_point&lt;T_noptr&gt;::value &amp;&amp; (type!=is_floating_point)) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :         throw ExceptionTypeError() &lt;&lt;&quot;This command expects a floating point type. Received a &quot; &lt;&lt; type_str() &lt;&lt; &quot; instead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :       }</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        851 :       if(std::is_same&lt;FILE,typename std::remove_const&lt;T_noptr&gt;::type&gt;::value &amp;&amp; (type!=is_file)) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :         throw ExceptionTypeError() &lt;&lt;&quot;This command expects a FILE. Received a &quot; &lt;&lt; type_str() &lt;&lt; &quot; instead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :       }</a>
+<a name="251"><span class="lineNum">     251 </span>            :     }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">    1109046 :     if(size&gt;0 &amp;&amp; typesafePtrSizeof&lt;T_noptr&gt;() &gt;0 &amp;&amp; typesafePtrSizeof&lt;T_noptr&gt;()!=size) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :       throw ExceptionTypeError() &lt;&lt; &quot;This command expects a type with size &quot; &lt;&lt; typesafePtrSizeof&lt;T_noptr&gt;() &lt;&lt; &quot;. Received type has size &quot; &lt;&lt; size &lt;&lt; &quot; instead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">    1110761 :     if(!byvalue) if(cons==1) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          3 :         throw ExceptionTypeError() &lt;&lt; &quot;This command is trying to take the address of an argument that was passed by value&quot;&lt;&lt;extra_msg();</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :       }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            :     // cons==1 (by value) is here treated as cons==3 (const type*)</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">    1106627 :     if(cons&gt;0) {</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :       if(!std::is_pointer&lt;T&gt;::value) {</a>
+<a name="264"><span class="lineNum">     264 </span>            :         if(std::is_void&lt;T&gt;::value) {</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       1715 :           if(cons==1) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :             throw ExceptionTypeError() &lt;&lt; &quot;This command expects a void pointer. It received a value instead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :           }</a>
+<a name="268"><span class="lineNum">     268 </span>            :         } else {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">    1104796 :           if(cons!=1 &amp;&amp; cons!=2 &amp;&amp; cons!=3) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineNoCov">          0 :             throw ExceptionTypeError() &lt;&lt; &quot;This command expects a pointer or a value. It received a pointer-to-pointer instead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="271"><span class="lineNum">     271 </span>            :           }</a>
+<a name="272"><span class="lineNum">     272 </span>            :         }</a>
+<a name="273"><span class="lineNum">     273 </span>            :         if(!std::is_const&lt;T&gt;::value) {</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">     458062 :           if(cons==3) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :             throw ExceptionTypeError() &lt;&lt; &quot;This command expects a modifiable pointer (T*). It received a non modifiable pointer instead (const T*)&quot;&lt;&lt;extra_msg();</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">     458062 :           } else if(cons==1) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 :             throw ExceptionTypeError() &lt;&lt; &quot;This command expects a modifiable pointer (T*). It received a value instead (T)&quot;&lt;&lt;extra_msg();</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :           }</a>
+<a name="279"><span class="lineNum">     279 </span>            :         }</a>
+<a name="280"><span class="lineNum">     280 </span>            :       } else {</a>
+<a name="281"><span class="lineNum">     281 </span>            :         if(!std::is_const&lt;T&gt;::value) {</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        116 :           if(cons==1) throw ExceptionTypeError() &lt;&lt; &quot;This command expects a pointer-to-pointer. It received a value intead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        116 :           if(cons==2 || cons==3) throw ExceptionTypeError() &lt;&lt; &quot;This command expects a pointer-to-pointer. It received a pointer intead&quot;&lt;&lt;extra_msg();</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :           if(!std::is_const&lt;T_noptr&gt;::value) {</a>
+<a name="285"><span class="lineNum">     285 </span>            :             if(cons!=4) throw ExceptionTypeError() &lt;&lt; &quot;This command expects a modifiable pointer-to-pointer (T**)&quot;&lt;&lt;extra_msg();</a>
+<a name="286"><span class="lineNum">     286 </span>            :           } else {</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        116 :             if(cons!=6) throw ExceptionTypeError() &lt;&lt; &quot;This command expects a modifiable pointer to unmodifiable pointer (const T**)&quot;&lt;&lt;extra_msg();</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :           }</a>
+<a name="289"><span class="lineNum">     289 </span>            :         } else {</a>
+<a name="290"><span class="lineNum">     290 </span>            :           if(!std::is_const&lt;T_noptr&gt;::value) {</a>
+<a name="291"><span class="lineNum">     291 </span>            :             if(cons!=4 &amp;&amp; cons!=5) throw ExceptionTypeError() &lt;&lt; &quot;This command expects T*const* pointer, and can only receive T**  or T*const* pointers&quot;&lt;&lt;extra_msg();</a>
+<a name="292"><span class="lineNum">     292 </span>            :           }</a>
+<a name="293"><span class="lineNum">     293 </span>            :         }</a>
+<a name="294"><span class="lineNum">     294 </span>            :       }</a>
+<a name="295"><span class="lineNum">     295 </span>            :     }</a>
+<a name="296"><span class="lineNum">     296 </span>            :     // check full shape, if possible</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">    1110760 :     if(shape &amp;&amp; shape[0] &amp;&amp; this-&gt;shape[0]) {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">        510 :       for(unsigned i=0; i&lt;this-&gt;shape.size(); i++) {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        510 :         if(shape[i]==0 &amp;&amp; this-&gt;shape[i]!=0) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :           throw ExceptionTypeError() &lt;&lt; &quot;Incorrect number of axis (passed greater than requested)&quot;&lt;&lt;extra_msg();</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :         }</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        510 :         if(shape[i]!=0 &amp;&amp; this-&gt;shape[i]==0) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineNoCov">          0 :           throw ExceptionTypeError() &lt;&lt; &quot;Incorrect number of axis (requested greater than passed)&quot;&lt;&lt;extra_msg();</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :         }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        510 :         if(shape[i]==0) break;</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        340 :         if((shape[i]&gt;this-&gt;shape[i])) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineNoCov">          0 :           throw ExceptionTypeError() &lt;&lt; &quot;This command wants &quot; &lt;&lt; shape[i] &lt;&lt; &quot; elements on axis &quot; &lt;&lt; i &lt;&lt;&quot; of this pointer, but &quot; &lt;&lt; this-&gt;shape[i] &lt;&lt; &quot; have been passed&quot;&lt;&lt;extra_msg();</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :         }</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        340 :         if(i&gt;0 &amp;&amp; (shape[i]&lt;this-&gt;shape[i])) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :           throw ExceptionTypeError() &lt;&lt; &quot;This command wants &quot; &lt;&lt; shape[i] &lt;&lt; &quot; elements on axis &quot; &lt;&lt; i &lt;&lt;&quot; of this pointer, but &quot; &lt;&lt; this-&gt;shape[i] &lt;&lt; &quot; have been passed&quot;&lt;&lt;extra_msg();</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :         }</a>
+<a name="312"><span class="lineNum">     312 </span>            :       }</a>
+<a name="313"><span class="lineNum">     313 </span>            :     }</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">    1110760 :     if(nelem==0 &amp;&amp; shape &amp;&amp; shape[0]&gt;0) {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">     293774 :       nelem=1;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">     881322 :       for(unsigned i=0; i&lt;this-&gt;shape.size(); i++) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">     881322 :         if(shape[i]==0) break;</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">     587548 :         nelem*=shape[i];</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :       }</a>
+<a name="320"><span class="lineNum">     320 </span>            :     }</a>
+<a name="321"><span class="lineNum">     321 </span>            :     // check number of elements</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">    1110760 :     if(nelem&gt;0 &amp;&amp; this-&gt;nelem&gt;0) if(!(nelem&lt;=this-&gt;nelem)) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          8 :         throw ExceptionTypeError() &lt;&lt; &quot;This command wants to access &quot; &lt;&lt; nelem &lt;&lt; &quot; from this pointer, but only &quot; &lt;&lt; this-&gt;nelem &lt;&lt; &quot; have been passed&quot;&lt;&lt;extra_msg();</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :       }</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">    1110758 :     return (T*) ptr;</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span>            : public:</a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            :   template&lt;typename T&gt;</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">       7642 :   void set(T val) const {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">       7642 :     *get_priv&lt;T&gt;(0,nullptr,false)=val;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">       7642 :   }</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :   template&lt;typename T&gt;</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">     467240 :   typename std::enable_if&lt;std::is_pointer&lt;T&gt;::value,T&gt;::type get() const {</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     typedef typename std::remove_pointer&lt;T&gt;::type T_noptr;</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">     472212 :     return get_priv&lt;T_noptr&gt;(0,nullptr,false);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   template&lt;typename T&gt;</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">     277704 :   typename std::enable_if&lt;!std::is_pointer&lt;T&gt;::value,T&gt;::type get() const {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">     277704 :     return *get_priv&lt;const T&gt;(1,nullptr,true);</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :   }</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            :   template&lt;typename T&gt;</a>
+<a name="347"><span class="lineNum">     347 </span>            :   T get(std::size_t nelem) const {</a>
+<a name="348"><span class="lineNum">     348 </span>            :     static_assert(std::is_pointer&lt;T&gt;::value,&quot;only pointer types allowed here&quot;);</a>
+<a name="349"><span class="lineNum">     349 </span>            :     typedef typename std::remove_pointer&lt;T&gt;::type T_noptr;</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">       6875 :     return get_priv&lt;T_noptr&gt;(nelem,nullptr,false);</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :   }</a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            :   template&lt;typename T&gt;</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">     350969 :   T get(std::initializer_list&lt;std::size_t&gt; shape) const {</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :     static_assert(std::is_pointer&lt;T&gt;::value,&quot;only pointer types allowed here&quot;);</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">     350969 :     plumed_assert(shape.size()&lt;=maxrank);</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :     std::array&lt;std::size_t,maxrank+1&gt; shape_;</a>
+<a name="358"><span class="lineNum">     358 </span>            :     typedef typename std::remove_pointer&lt;T&gt;::type T_noptr;</a>
+<a name="359"><span class="lineNum">     359 </span>            :     unsigned j=0;</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">    1052907 :     for(auto i : shape) {</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">     701938 :       shape_[j]=i;</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">     701938 :       j++;</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :     }</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">     350969 :     shape_[j]=0;</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">     350969 :     return get_priv&lt;T_noptr&gt;(0,&amp;shape_[0],false);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   }</a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span>            :   operator bool() const noexcept {</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">     964835 :     return ptr;</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span>            : </a>
+<a name="372"><span class="lineNum">     372 </span>            :   void* getRaw() const noexcept {</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        222 :     return ptr;</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :   }</a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            :   std::size_t getNelem() const noexcept {</a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">        222 :     return nelem;</span></a>
+<a name="378"><span class="lineNum">     378 </span>            :   }</a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span>            :   const std::size_t* getShape() const noexcept {</a>
+<a name="381"><span class="lineNum">     381 </span>            :     return shape.data();</a>
+<a name="382"><span class="lineNum">     382 </span>            :   }</a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            :   std::size_t getFlags() const noexcept {</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        222 :     return flags;</span></a>
+<a name="386"><span class="lineNum">     386 </span>            :   }</a>
+<a name="387"><span class="lineNum">     387 </span>            : </a>
+<a name="388"><span class="lineNum">     388 </span>            : private:</a>
+<a name="389"><span class="lineNum">     389 </span>            :   std::array&lt;char,32&gt; buffer;</a>
+<a name="390"><span class="lineNum">     390 </span>            :   void* ptr=nullptr;</a>
+<a name="391"><span class="lineNum">     391 </span>            :   std::size_t nelem=0;</a>
+<a name="392"><span class="lineNum">     392 </span>            :   std::array&lt;std::size_t,maxrank+1&gt; shape; // make sure to initialize this!</a>
+<a name="393"><span class="lineNum">     393 </span>            :   std::size_t flags=0;</a>
+<a name="394"><span class="lineNum">     394 </span>            : };</a>
+<a name="395"><span class="lineNum">     395 </span>            : </a>
+<a name="396"><span class="lineNum">     396 </span>            : }</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Units.cpp.func-sort-c.html b/coverage/tools/Units.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8aafae7a02
--- /dev/null
+++ b/coverage/tools/Units.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Units.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Units.cpp<span style="font-size: 80%;"> (<a href="Units.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">88</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Units.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#115">_ZN4PLMD5Units7setMassERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#101">_ZN4PLMD5Units9setChargeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#139">_ZN4PLMD5Units7setTimeEd</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#81">_ZN4PLMD5Units7setTimeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#39">_ZN4PLMD5Units9setEnergyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#61">_ZN4PLMD5Units9setLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#129">_ZN4PLMD5Units9setEnergyEd</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#149">_ZN4PLMD5Units7setMassEd</a></td>
+              <td class="coverFnHi">810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#144">_ZN4PLMD5Units9setChargeEd</a></td>
+              <td class="coverFnHi">810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#134">_ZN4PLMD5Units9setLengthEd</a></td>
+              <td class="coverFnHi">810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#25">_ZN4PLMD5UnitsC2Ev</a></td>
+              <td class="coverFnHi">1611377</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Units.cpp.func.html b/coverage/tools/Units.cpp.func.html
new file mode 100644
index 0000000000..f2a42b6cd6
--- /dev/null
+++ b/coverage/tools/Units.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Units.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Units.cpp<span style="font-size: 80%;"> (<a href="Units.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">88</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Units.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#115">_ZN4PLMD5Units7setMassERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#149">_ZN4PLMD5Units7setMassEd</a></td>
+              <td class="coverFnHi">810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#81">_ZN4PLMD5Units7setTimeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#139">_ZN4PLMD5Units7setTimeEd</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#101">_ZN4PLMD5Units9setChargeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#144">_ZN4PLMD5Units9setChargeEd</a></td>
+              <td class="coverFnHi">810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#39">_ZN4PLMD5Units9setEnergyERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#129">_ZN4PLMD5Units9setEnergyEd</a></td>
+              <td class="coverFnHi">45</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#61">_ZN4PLMD5Units9setLengthERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">35</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#134">_ZN4PLMD5Units9setLengthEd</a></td>
+              <td class="coverFnHi">810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Units.cpp.gcov.html#25">_ZN4PLMD5UnitsC2Ev</a></td>
+              <td class="coverFnHi">1611377</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Units.cpp.gcov.html b/coverage/tools/Units.cpp.gcov.html
new file mode 100644
index 0000000000..f154c8c1df
--- /dev/null
+++ b/coverage/tools/Units.cpp.gcov.html
@@ -0,0 +1,234 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Units.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Units.cpp<span style="font-size: 80%;"> (source / <a href="Units.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">88</td>
+            <td class="headerCovTableEntry">97</td>
+            <td class="headerCovTableEntryHi">90.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Units.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Tools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">    1611377 : Units::Units():</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">    1611377 :   energy(1.0),</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">    1611377 :   energyString(&quot;kj/mol&quot;),</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">    1611377 :   length(1.0),</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">    1611377 :   lengthString(&quot;nm&quot;),</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">    1611377 :   time(1.0),</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">    1611377 :   timeString(&quot;ps&quot;),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">    1611377 :   charge(1.0),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">    1611377 :   chargeString(&quot;e&quot;),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">    1611377 :   mass(1.0),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">    1611377 :   massString(&quot;amu&quot;)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : {</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">    1611377 : }</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         13 : void Units::setEnergy(const std::string &amp;s) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         13 :   energyString=s;</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         13 :   if(s==&quot;kj/mol&quot;) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          5 :     energy=1.0;</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          8 :   } else if(s==&quot;kcal/mol&quot;) {</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          5 :     energy=4.184;</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          3 :   } else if(s==&quot;j/mol&quot;) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :     energy=0.001;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          3 :   } else if(s==&quot;eV&quot;) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :     energy=96.48530749925792;</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          3 :   } else if(s ==&quot;Ha&quot;) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          1 :     energy=2625.499638;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :   } else {</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          2 :     energy=-1.0;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     energyString=&quot;&quot;;</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          2 :     if(!Tools::convertNoexcept(s,energy)) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;problem with setting the energy unit, either use give an numerical value or use one of the defined units: kj/mol, kcal/mol, j/mol, eV, Ha (case sensitive)&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :     }</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          2 :     plumed_massert(energy&gt;0.0,&quot;energy unit should be positive&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   }</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         13 : }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         35 : void Units::setLength(const std::string &amp;s) {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         35 :   lengthString=s;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         35 :   if(s==&quot;nm&quot;) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          2 :     length=1.0;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         33 :   } else if(s==&quot;A&quot;) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         26 :     length=0.1;</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          7 :   } else if(s==&quot;um&quot;) {</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 :     length=1000.0;</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          7 :   } else if(s==&quot;Bohr&quot;) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          1 :     length=0.052917721067;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   } else {</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 :     length=-1.0;</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     lengthString=&quot;&quot;;</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 :     if(!Tools::convertNoexcept(s,length)) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;problem with setting the length unit, either use a numerical value or use one of the defined units: nm, A, um, Bohr (case sensitive)&quot;);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :     }</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          6 :     plumed_massert(length&gt;0.0,&quot;length unit should be positive&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         35 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          7 : void Units::setTime(const std::string &amp;s) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          7 :   timeString=s;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          7 :   if(s==&quot;ps&quot;) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          2 :     time=1.0;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          5 :   } else if(s==&quot;ns&quot;) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :     time=1000.0;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          5 :   } else if(s==&quot;fs&quot;) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          2 :     time=0.001;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          3 :   } else if(s==&quot;atomic&quot;) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          1 :     time=2.418884326509e-5;</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   } else {</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :     time=-1.0;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :     timeString=&quot;&quot;;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :     if(!Tools::convertNoexcept(s,time)) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;problem with setting the time unit, either use a numerical value or use one of the defined units: ps, fs, atomic (case sensitive)&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :     }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :     plumed_massert(time&gt;0.0,&quot;time unit should be positive&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          7 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 : void Units::setCharge(const std::string &amp;s) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          4 :   chargeString=s;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 :   if(s==&quot;e&quot;) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :     charge=1.0;</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   } else {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          3 :     charge=-1.0;</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     chargeString=&quot;&quot;;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          3 :     if(!Tools::convertNoexcept(s,charge)) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;problem with setting the charge unit, either use a numerical value or use one of the defined units: e (case sensitive)&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :     }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          3 :     plumed_massert(charge&gt;0.0,&quot;charge unit should be positive&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          4 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          3 : void Units::setMass(const std::string &amp;s) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          3 :   massString=s;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          3 :   if(s==&quot;amu&quot;) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          1 :     mass=1.0;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   } else {</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :     mass=-1.0;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :     massString=&quot;&quot;;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :     if(!Tools::convertNoexcept(s,mass)) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;problem with setting the mass unit, either use a numerical value or use one of the defined units: amu (case sensitive)&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     }</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          2 :     plumed_massert(mass&gt;0.0,&quot;mass unit should be positive&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 : }</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         45 : void Units::setEnergy(const double s) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         45 :   energyString=&quot;&quot;;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         45 :   energy=s;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         45 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        810 : void Units::setLength(const double s) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        810 :   lengthString=&quot;&quot;;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        810 :   length=s;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        810 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          6 : void Units::setTime(const double s) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          6 :   timeString=&quot;&quot;;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          6 :   time=s;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          6 : }</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        810 : void Units::setCharge(const double s) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        810 :   chargeString=&quot;&quot;;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        810 :   charge=s;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        810 : }</span></a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        810 : void Units::setMass(const double s) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        810 :   massString=&quot;&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        810 :   mass=s;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        810 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Units.h.func-sort-c.html b/coverage/tools/Units.h.func-sort-c.html
new file mode 100644
index 0000000000..92f4dd9ed4
--- /dev/null
+++ b/coverage/tools/Units.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Units.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Units.h<span style="font-size: 80%;"> (<a href="Units.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Units.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Units.h.func.html b/coverage/tools/Units.h.func.html
new file mode 100644
index 0000000000..d361456672
--- /dev/null
+++ b/coverage/tools/Units.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Units.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Units.h<span style="font-size: 80%;"> (<a href="Units.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Units.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Units.h.gcov.html b/coverage/tools/Units.h.gcov.html
new file mode 100644
index 0000000000..95714cfd52
--- /dev/null
+++ b/coverage/tools/Units.h.gcov.html
@@ -0,0 +1,243 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Units.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Units.h<span style="font-size: 80%;"> (source / <a href="Units.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Units_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Units_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : /**</a>
+<a name="30"><span class="lineNum">      30 </span>            : \ingroup TOOLBOX</a>
+<a name="31"><span class="lineNum">      31 </span>            : Small utility class that contains information about units.</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : This class can be used to contain in a single place all the</a>
+<a name="34"><span class="lineNum">      34 </span>            : information about units. Units are expressed in terms of</a>
+<a name="35"><span class="lineNum">      35 </span>            : standard PLUMED units, i.e. kj/mol, nm, and ps.</a>
+<a name="36"><span class="lineNum">      36 </span>            : Units can be set as double or as string. In the latter case,</a>
+<a name="37"><span class="lineNum">      37 </span>            : one can also use strings such as kcal/mol.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : */</a>
+<a name="41"><span class="lineNum">      41 </span>            : class Units {</a>
+<a name="42"><span class="lineNum">      42 </span>            : /// Units for energy, expressed in kj/mol (e.g. 4.184 means kcal/mol)</a>
+<a name="43"><span class="lineNum">      43 </span>            :   double energy;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::string energyString;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Units for length, expressed in nm (e.g. 0.1 means A)</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double length;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   std::string lengthString;</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Units for time, expressed in ps (e.g. 0.001 means fs)</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double time;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string timeString;</a>
+<a name="51"><span class="lineNum">      51 </span>            : /// Units for charges, expressed in proton charge (e.g. 1./18.2223 are sqrt(kcal/mol*A), as used in Amber)</a>
+<a name="52"><span class="lineNum">      52 </span>            :   double charge;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::string chargeString;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Units for masses, expressed in amu</a>
+<a name="55"><span class="lineNum">      55 </span>            :   double mass;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::string massString;</a>
+<a name="57"><span class="lineNum">      57 </span>            : public:</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Constructor, setting default values (1.0)</a>
+<a name="59"><span class="lineNum">      59 </span>            :   Units();</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Set energy units from string.</a>
+<a name="61"><span class="lineNum">      61 </span>            : /// Also understands the following strings:</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// kj/mol, kcal/mol, j/mol, eV, and Ha.</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void setEnergy(const std::string &amp;);</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Set time units from string.</a>
+<a name="65"><span class="lineNum">      65 </span>            : /// Also understands the following strings:</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// ps, ns, fs, and atomic.</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void setTime(const std::string &amp;);</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// Set length units from string.</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Also understands the following strings:</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// nm, A, um, and Bohr.</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void setLength(const std::string &amp;);</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Set charge units from string.</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void setCharge(const std::string &amp;);</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Set mass units from string.</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void setMass(const std::string &amp;);</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Set energy units from double.</a>
+<a name="77"><span class="lineNum">      77 </span>            : /// Should be specified in units of kj/mol (e.g. 4.184 means kcal/mol)</a>
+<a name="78"><span class="lineNum">      78 </span>            :   void setEnergy(double);</a>
+<a name="79"><span class="lineNum">      79 </span>            : /// Set time units from double.</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Should be specified in units of ps (e.g. 0.001 means fs)</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void setTime(double);</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Set length units from double.</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Should be specified in units of nm (e.g. 0.1 means A)</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void setLength(double);</a>
+<a name="85"><span class="lineNum">      85 </span>            : /// Set charge units from double.</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// Should be specified in units of proton charge.</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void setCharge(double);</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Set mass units from double.</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Should be specified in units of amu.</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void setMass(double);</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Get energy units as double.</a>
+<a name="92"><span class="lineNum">      92 </span>            :   const double &amp; getEnergy()const;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Get length units as double.</a>
+<a name="94"><span class="lineNum">      94 </span>            :   const double &amp; getLength()const;</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Get time units as double.</a>
+<a name="96"><span class="lineNum">      96 </span>            :   const double &amp; getTime()const;</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Get charge units as double.</a>
+<a name="98"><span class="lineNum">      98 </span>            :   const double &amp; getCharge()const;</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Get mass units as double.</a>
+<a name="100"><span class="lineNum">     100 </span>            :   const double &amp; getMass()const;</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Get energy units as string.</a>
+<a name="102"><span class="lineNum">     102 </span>            :   const std::string &amp; getEnergyString()const;</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Get length units as string.</a>
+<a name="104"><span class="lineNum">     104 </span>            :   const std::string &amp; getLengthString()const;</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Get time units as string.</a>
+<a name="106"><span class="lineNum">     106 </span>            :   const std::string &amp; getTimeString()const;</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// Get charge units as string.</a>
+<a name="108"><span class="lineNum">     108 </span>            :   const std::string &amp; getChargeString()const;</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Get mass units as string.</a>
+<a name="110"><span class="lineNum">     110 </span>            :   const std::string &amp; getMassString()const;</a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : inline</a>
+<a name="114"><span class="lineNum">     114 </span>            : const double &amp; Units::getEnergy()const {</a>
+<a name="115"><span class="lineNum">     115 </span>            :   return energy;</a>
+<a name="116"><span class="lineNum">     116 </span>            : }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : inline</a>
+<a name="119"><span class="lineNum">     119 </span>            : const double &amp; Units::getLength()const {</a>
+<a name="120"><span class="lineNum">     120 </span>            :   return length;</a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : inline</a>
+<a name="124"><span class="lineNum">     124 </span>            : const double &amp; Units::getTime()const {</a>
+<a name="125"><span class="lineNum">     125 </span>            :   return time;</a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : inline</a>
+<a name="129"><span class="lineNum">     129 </span>            : const double &amp; Units::getCharge()const {</a>
+<a name="130"><span class="lineNum">     130 </span>            :   return charge;</a>
+<a name="131"><span class="lineNum">     131 </span>            : }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : inline</a>
+<a name="134"><span class="lineNum">     134 </span>            : const double &amp; Units::getMass()const {</a>
+<a name="135"><span class="lineNum">     135 </span>            :   return mass;</a>
+<a name="136"><span class="lineNum">     136 </span>            : }</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : inline</a>
+<a name="139"><span class="lineNum">     139 </span>            : const std::string &amp; Units::getEnergyString()const {</a>
+<a name="140"><span class="lineNum">     140 </span>            :   return energyString;</a>
+<a name="141"><span class="lineNum">     141 </span>            : }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : inline</a>
+<a name="144"><span class="lineNum">     144 </span>            : const std::string &amp; Units::getLengthString()const {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">   15290970 :   return lengthString;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : inline</a>
+<a name="149"><span class="lineNum">     149 </span>            : const std::string &amp; Units::getTimeString()const {</a>
+<a name="150"><span class="lineNum">     150 </span>            :   return timeString;</a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : inline</a>
+<a name="154"><span class="lineNum">     154 </span>            : const std::string &amp; Units::getChargeString()const {</a>
+<a name="155"><span class="lineNum">     155 </span>            :   return chargeString;</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : inline</a>
+<a name="159"><span class="lineNum">     159 </span>            : const std::string &amp; Units::getMassString()const {</a>
+<a name="160"><span class="lineNum">     160 </span>            :   return massString;</a>
+<a name="161"><span class="lineNum">     161 </span>            : }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Vector.h.func-sort-c.html b/coverage/tools/Vector.h.func-sort-c.html
new file mode 100644
index 0000000000..ca76797259
--- /dev/null
+++ b/coverage/tools/Vector.h.func-sort-c.html
@@ -0,0 +1,288 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Vector.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Vector.h<span style="font-size: 80%;"> (<a href="Vector.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Vector.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#161">_ZN4PLMD13VectorGenericILj3EE20auxiliaryConstructorIJfEEEvdDpT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#161">_ZN4PLMD13VectorGenericILj3EE20auxiliaryConstructorIJffEEEvdDpT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#169">_ZN4PLMD13VectorGenericILj3EEC2IJffEEEdDpT_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#181">_ZN4PLMD13VectorGenericILj6EEC2Ev</a></td>
+              <td class="coverFnHi">4004</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#224">_ZN4PLMD13VectorGenericILj3EEdVEd</a></td>
+              <td class="coverFnHi">43767</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">103260</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#161">_ZN4PLMD13VectorGenericILj3EE20auxiliaryConstructorIJidEEEvdDpT_</a></td>
+              <td class="coverFnHi">103260</td>
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+    <tr>
+              <td class="coverFn"><a href="Vector.h.gcov.html#169">_ZN4PLMD13VectorGenericILj3EEC2IJdiEEEdDpT_</a></td>
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diff --git a/coverage/tools/Vector.h.func.html b/coverage/tools/Vector.h.func.html
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/Vector.h.gcov.html b/coverage/tools/Vector.h.gcov.html
new file mode 100644
index 0000000000..5184c9907d
--- /dev/null
+++ b/coverage/tools/Vector.h.gcov.html
@@ -0,0 +1,419 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/Vector.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - Vector.h<span style="font-size: 80%;"> (source / <a href="Vector.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">51</td>
+            <td class="headerCovTableEntry">54</td>
+            <td class="headerCovTableEntryHi">94.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_tools_Vector_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_tools_Vector_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;cmath&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;iosfwd&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;array&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;LoopUnroller.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /**</a>
+<a name="33"><span class="lineNum">      33 </span>            : \ingroup TOOLBOX</a>
+<a name="34"><span class="lineNum">      34 </span>            : Class implementing fixed size vectors of doubles</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \tparam n The number of elements of the vector.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : This class implements a vector of doubles with size fixed at</a>
+<a name="39"><span class="lineNum">      39 </span>            : compile time. It is useful for small fixed size objects (e.g.</a>
+<a name="40"><span class="lineNum">      40 </span>            : 3d vectors) as it does not waste space to store the vector size.</a>
+<a name="41"><span class="lineNum">      41 </span>            : Moreover, as the compiler knows the size, it can be completely</a>
+<a name="42"><span class="lineNum">      42 </span>            : opimized inline.</a>
+<a name="43"><span class="lineNum">      43 </span>            : All the methods are inlined for better optimization and</a>
+<a name="44"><span class="lineNum">      44 </span>            : all the loops are explicitly unrolled using PLMD::LoopUnroller class.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Vector elements are initialized to zero by default. Notice that</a>
+<a name="46"><span class="lineNum">      46 </span>            : this means that constructor is a bit slow. This point might change</a>
+<a name="47"><span class="lineNum">      47 </span>            : in future if we find performance issues.</a>
+<a name="48"><span class="lineNum">      48 </span>            : Accepts both [] and () syntax for access.</a>
+<a name="49"><span class="lineNum">      49 </span>            : Several functions are declared as friends even if not necessary so as to</a>
+<a name="50"><span class="lineNum">      50 </span>            : properly appear in Doxygen documentation.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : Aliases are defined to simplify common declarations (Vector, Vector2d, Vector3d, Vector4d).</a>
+<a name="53"><span class="lineNum">      53 </span>            : Also notice that some operations are only available for 3 dimensional vectors.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : Example of usage</a>
+<a name="56"><span class="lineNum">      56 </span>            : \verbatim</a>
+<a name="57"><span class="lineNum">      57 </span>            : #include &quot;Vector.h&quot;</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : using namespace PLMD;</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : int main(){</a>
+<a name="62"><span class="lineNum">      62 </span>            :   VectorGeneric&lt;3&gt; v1;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   v1[0]=3.0;</a>
+<a name="64"><span class="lineNum">      64 </span>            : // use equivalently () and [] syntax:</a>
+<a name="65"><span class="lineNum">      65 </span>            :   v1(1)=5.0;</a>
+<a name="66"><span class="lineNum">      66 </span>            : // initialize with components</a>
+<a name="67"><span class="lineNum">      67 </span>            :   VectorGeneric&lt;3&gt; v2=VectorGeneric&lt;3&gt;(1.0,2.0,3.0);</a>
+<a name="68"><span class="lineNum">      68 </span>            :   VectorGeneric&lt;3&gt; v3=crossProduct(v1,v2);</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double d=dotProduct(v1,v2);</a>
+<a name="70"><span class="lineNum">      70 </span>            :   v3+=v1;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   v2=v1+2.0*v3;</a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : \endverbatim</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : */</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : template &lt;unsigned n&gt;</a>
+<a name="79"><span class="lineNum">      79 </span>            : class VectorGeneric {</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::array&lt;double,n&gt; d;</a>
+<a name="81"><span class="lineNum">      81 </span>            : /// Auxiliary private function for constructor</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void auxiliaryConstructor();</a>
+<a name="83"><span class="lineNum">      83 </span>            : /// Auxiliary private function for constructor</a>
+<a name="84"><span class="lineNum">      84 </span>            :   template&lt;typename... Args&gt;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void auxiliaryConstructor(double first,Args... arg);</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Constructor accepting n double parameters.</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Can be used as Vector&lt;3&gt;(1.0,2.0,3.0) or Vector&lt;2&gt;(2.0,3.0).</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// In case a wrong number of parameters is given, a static assertion will fail.</a>
+<a name="90"><span class="lineNum">      90 </span>            :   template&lt;typename... Args&gt;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   VectorGeneric(double first,Args... arg);</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// create it null</a>
+<a name="93"><span class="lineNum">      93 </span>            :   VectorGeneric();</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// set it to zero</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void zero();</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// array-like access [i]</a>
+<a name="97"><span class="lineNum">      97 </span>            :   double &amp; operator[](unsigned i);</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// array-like access [i]</a>
+<a name="99"><span class="lineNum">      99 </span>            :   const double &amp; operator[](unsigned i)const;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// parenthesis access (i)</a>
+<a name="101"><span class="lineNum">     101 </span>            :   double &amp; operator()(unsigned i);</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// parenthesis access (i)</a>
+<a name="103"><span class="lineNum">     103 </span>            :   const double &amp; operator()(unsigned i)const;</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// increment</a>
+<a name="105"><span class="lineNum">     105 </span>            :   VectorGeneric&amp; operator +=(const VectorGeneric&amp; b);</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// decrement</a>
+<a name="107"><span class="lineNum">     107 </span>            :   VectorGeneric&amp; operator -=(const VectorGeneric&amp; b);</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// multiply</a>
+<a name="109"><span class="lineNum">     109 </span>            :   VectorGeneric&amp; operator *=(double s);</a>
+<a name="110"><span class="lineNum">     110 </span>            : /// divide</a>
+<a name="111"><span class="lineNum">     111 </span>            :   VectorGeneric&amp; operator /=(double s);</a>
+<a name="112"><span class="lineNum">     112 </span>            : /// sign +</a>
+<a name="113"><span class="lineNum">     113 </span>            :   VectorGeneric operator +()const;</a>
+<a name="114"><span class="lineNum">     114 </span>            : /// sign -</a>
+<a name="115"><span class="lineNum">     115 </span>            :   VectorGeneric operator -()const;</a>
+<a name="116"><span class="lineNum">     116 </span>            : /// return v1+v2</a>
+<a name="117"><span class="lineNum">     117 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   friend VectorGeneric&lt;m&gt; operator+(const VectorGeneric&lt;m&gt;&amp;,const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// return v1-v2</a>
+<a name="120"><span class="lineNum">     120 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   friend VectorGeneric&lt;m&gt; operator-(const VectorGeneric&lt;m&gt;&amp;,const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="122"><span class="lineNum">     122 </span>            : /// return s*v</a>
+<a name="123"><span class="lineNum">     123 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   friend VectorGeneric&lt;m&gt; operator*(double,const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="125"><span class="lineNum">     125 </span>            : /// return v*s</a>
+<a name="126"><span class="lineNum">     126 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   friend VectorGeneric&lt;m&gt; operator*(const VectorGeneric&lt;m&gt;&amp;,double);</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// return v/s</a>
+<a name="129"><span class="lineNum">     129 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   friend VectorGeneric&lt;m&gt; operator/(const VectorGeneric&lt;m&gt;&amp;,double);</a>
+<a name="131"><span class="lineNum">     131 </span>            : /// return v2-v1</a>
+<a name="132"><span class="lineNum">     132 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   friend VectorGeneric&lt;m&gt; delta(const VectorGeneric&lt;m&gt;&amp;v1,const VectorGeneric&lt;m&gt;&amp;v2);</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// return v1 .scalar. v2</a>
+<a name="135"><span class="lineNum">     135 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   friend double dotProduct(const VectorGeneric&lt;m&gt;&amp;,const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="137"><span class="lineNum">     137 </span>            : /// return v1 .vector. v2</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Only available for size 3</a>
+<a name="139"><span class="lineNum">     139 </span>            :   friend VectorGeneric&lt;3&gt; crossProduct(const VectorGeneric&lt;3&gt;&amp;,const VectorGeneric&lt;3&gt;&amp;);</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// compute the squared modulo</a>
+<a name="141"><span class="lineNum">     141 </span>            :   double modulo2()const;</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// Compute the modulo.</a>
+<a name="143"><span class="lineNum">     143 </span>            : /// Shortcut for sqrt(v.modulo2())</a>
+<a name="144"><span class="lineNum">     144 </span>            :   double modulo()const;</a>
+<a name="145"><span class="lineNum">     145 </span>            : /// friend version of modulo2 (to simplify some syntax)</a>
+<a name="146"><span class="lineNum">     146 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   friend double modulo2(const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// friend version of modulo (to simplify some syntax)</a>
+<a name="149"><span class="lineNum">     149 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   friend double modulo(const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="151"><span class="lineNum">     151 </span>            : /// &lt;&lt; operator.</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Allows printing vector `v` with `std::cout&lt;&lt;v;`</a>
+<a name="153"><span class="lineNum">     153 </span>            :   template&lt;unsigned m&gt;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   friend std::ostream &amp; operator&lt;&lt;(std::ostream &amp;os, const VectorGeneric&lt;m&gt;&amp;);</a>
+<a name="155"><span class="lineNum">     155 </span>            : };</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : template &lt;unsigned n&gt;</a>
+<a name="158"><span class="lineNum">     158 </span>            : void VectorGeneric&lt;n&gt;::auxiliaryConstructor()</a>
+<a name="159"><span class="lineNum">     159 </span>            : {}</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : template &lt;unsigned n&gt;</a>
+<a name="162"><span class="lineNum">     162 </span>            : template&lt;typename... Args&gt;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">  130542469 : void VectorGeneric&lt;n&gt;::auxiliaryConstructor(double first,Args... arg)</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : {</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">  130542469 :   d[n-(sizeof...(Args))-1]=first;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">   87213644 :   auxiliaryConstructor(arg...);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">  130542469 : }</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : template &lt;unsigned n&gt;</a>
+<a name="170"><span class="lineNum">     170 </span>            : template&lt;typename... Args&gt;</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">   43328825 : VectorGeneric&lt;n&gt;::VectorGeneric(double first,Args... arg)</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : {</a>
+<a name="173"><span class="lineNum">     173 </span>            :   static_assert((sizeof...(Args))+1==n,&quot;you are trying to initialize a Vector with the wrong number of arguments&quot;);</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">   43328825 :   auxiliaryConstructor(first,arg...);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">   43328825 : }</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : template &lt;unsigned n&gt;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">    4597856 : void VectorGeneric&lt;n&gt;::zero() {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">    4597856 :   LoopUnroller&lt;n&gt;::_zero(d.data());</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">    4597856 : }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : template &lt;unsigned n&gt;</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">  490948560 : VectorGeneric&lt;n&gt;::VectorGeneric() {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">  490399640 :   LoopUnroller&lt;n&gt;::_zero(d.data());</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">  490948560 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : template &lt;unsigned n&gt;</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov"> 2744771880 : double &amp; VectorGeneric&lt;n&gt;::operator[](unsigned i) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov"> 2744771880 :   return d[i];</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : template &lt;unsigned n&gt;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov"> 3739426547 : const double &amp; VectorGeneric&lt;n&gt;::operator[](unsigned i)const {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov"> 3739426547 :   return d[i];</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : template &lt;unsigned n&gt;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov"> 1267578990 : double &amp; VectorGeneric&lt;n&gt;::operator()(unsigned i) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov"> 1267578990 :   return d[i];</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : template &lt;unsigned n&gt;</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov"> 1266916071 : const double &amp; VectorGeneric&lt;n&gt;::operator()(unsigned i)const {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov"> 1266916071 :   return d[i];</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : template &lt;unsigned n&gt;</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov"> 1747672241 : VectorGeneric&lt;n&gt;&amp; VectorGeneric&lt;n&gt;::operator +=(const VectorGeneric&lt;n&gt;&amp; b) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov"> 1747672241 :   LoopUnroller&lt;n&gt;::_add(d.data(),b.d.data());</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov"> 1747672241 :   return *this;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : template &lt;unsigned n&gt;</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov"> 1219991462 : VectorGeneric&lt;n&gt;&amp; VectorGeneric&lt;n&gt;::operator -=(const VectorGeneric&lt;n&gt;&amp; b) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov"> 1219991462 :   LoopUnroller&lt;n&gt;::_sub(d.data(),b.d.data());</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov"> 1219991462 :   return *this;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            : template &lt;unsigned n&gt;</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov"> 1825196113 : VectorGeneric&lt;n&gt;&amp; VectorGeneric&lt;n&gt;::operator *=(double s) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov"> 1825196113 :   LoopUnroller&lt;n&gt;::_mul(d.data(),s);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov"> 1825196113 :   return *this;</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : template &lt;unsigned n&gt;</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      43767 : VectorGeneric&lt;n&gt;&amp; VectorGeneric&lt;n&gt;::operator /=(double s) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">      43767 :   LoopUnroller&lt;n&gt;::_mul(d.data(),1.0/s);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      43767 :   return *this;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : template &lt;unsigned n&gt;</a>
+<a name="232"><span class="lineNum">     232 </span>            : VectorGeneric&lt;n&gt;  VectorGeneric&lt;n&gt;::operator +()const {</a>
+<a name="233"><span class="lineNum">     233 </span>            :   return *this;</a>
+<a name="234"><span class="lineNum">     234 </span>            : }</a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : template &lt;unsigned n&gt;</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">  106092195 : VectorGeneric&lt;n&gt; VectorGeneric&lt;n&gt;::operator -()const {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">  106092195 :   VectorGeneric&lt;n&gt; r;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">  106092195 :   LoopUnroller&lt;n&gt;::_neg(r.d.data(),d.data());</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">  106092195 :   return r;</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : template &lt;unsigned n&gt;</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov"> 1368655774 : VectorGeneric&lt;n&gt; operator+(const VectorGeneric&lt;n&gt;&amp;v1,const VectorGeneric&lt;n&gt;&amp;v2) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov"> 1368655774 :   VectorGeneric&lt;n&gt; v(v1);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov"> 1368655774 :   return v+=v2;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : }</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : template &lt;unsigned n&gt;</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">  901857607 : VectorGeneric&lt;n&gt; operator-(const VectorGeneric&lt;n&gt;&amp;v1,const VectorGeneric&lt;n&gt;&amp;v2) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">  901857607 :   VectorGeneric&lt;n&gt; v(v1);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">  901857607 :   return v-=v2;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            : template &lt;unsigned n&gt;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov"> 1824810154 : VectorGeneric&lt;n&gt; operator*(double s,const VectorGeneric&lt;n&gt;&amp;v) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov"> 1824810154 :   VectorGeneric&lt;n&gt; vv(v);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov"> 1824810154 :   return vv*=s;</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : template &lt;unsigned n&gt;</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">  441991235 : VectorGeneric&lt;n&gt; operator*(const VectorGeneric&lt;n&gt;&amp;v,double s) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">  441991235 :   return s*v;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            : template &lt;unsigned n&gt;</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">   72569397 : VectorGeneric&lt;n&gt; operator/(const VectorGeneric&lt;n&gt;&amp;v,double s) {</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">   72569397 :   return v*(1.0/s);</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : }</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : template &lt;unsigned n&gt;</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">  355492930 : VectorGeneric&lt;n&gt; delta(const VectorGeneric&lt;n&gt;&amp;v1,const VectorGeneric&lt;n&gt;&amp;v2) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">  355492930 :   return v2-v1;</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : template &lt;unsigned n&gt;</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">  785671199 : double VectorGeneric&lt;n&gt;::modulo2()const {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">  785671199 :   return LoopUnroller&lt;n&gt;::_sum2(d.data());</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : template &lt;unsigned n&gt;</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">  166491732 : double dotProduct(const VectorGeneric&lt;n&gt;&amp; v1,const VectorGeneric&lt;n&gt;&amp; v2) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">  166491732 :   return LoopUnroller&lt;n&gt;::_dot(v1.d.data(),v2.d.data());</span></a>
+<a name="284"><span class="lineNum">     284 </span>            : }</a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : inline</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">    4881282 : VectorGeneric&lt;3&gt; crossProduct(const VectorGeneric&lt;3&gt;&amp; v1,const VectorGeneric&lt;3&gt;&amp; v2) {</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   return VectorGeneric&lt;3&gt;(</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">    4881282 :            v1[1]*v2[2]-v1[2]*v2[1],</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">    4881282 :            v1[2]*v2[0]-v1[0]*v2[2],</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">    4881282 :            v1[0]*v2[1]-v1[1]*v2[0]);</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : }</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : template&lt;unsigned n&gt;</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">  119462618 : double VectorGeneric&lt;n&gt;::modulo()const {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">  119462618 :   return sqrt(modulo2());</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : template&lt;unsigned n&gt;</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">  202717593 : double modulo2(const VectorGeneric&lt;n&gt;&amp;v) {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">  202717593 :   return v.modulo2();</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : }</a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : template&lt;unsigned n&gt;</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">   22918220 : double modulo(const VectorGeneric&lt;n&gt;&amp;v) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">   22918220 :   return v.modulo();</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : template&lt;unsigned n&gt;</a>
+<a name="310"><span class="lineNum">     310 </span>            : std::ostream &amp; operator&lt;&lt;(std::ostream &amp;os, const VectorGeneric&lt;n&gt;&amp; v) {</a>
+<a name="311"><span class="lineNum">     311 </span>            :   for(unsigned i=0; i&lt;n-1; i++) os&lt;&lt;v(i)&lt;&lt;&quot; &quot;;</a>
+<a name="312"><span class="lineNum">     312 </span>            :   os&lt;&lt;v(n-1);</a>
+<a name="313"><span class="lineNum">     313 </span>            :   return os;</a>
+<a name="314"><span class="lineNum">     314 </span>            : }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : /// \ingroup TOOLBOX</a>
+<a name="318"><span class="lineNum">     318 </span>            : /// Alias for one dimensional vectors</a>
+<a name="319"><span class="lineNum">     319 </span>            : typedef VectorGeneric&lt;1&gt; Vector1d;</a>
+<a name="320"><span class="lineNum">     320 </span>            : /// \ingroup TOOLBOX</a>
+<a name="321"><span class="lineNum">     321 </span>            : /// Alias for two dimensional vectors</a>
+<a name="322"><span class="lineNum">     322 </span>            : typedef VectorGeneric&lt;2&gt; Vector2d;</a>
+<a name="323"><span class="lineNum">     323 </span>            : /// \ingroup TOOLBOX</a>
+<a name="324"><span class="lineNum">     324 </span>            : /// Alias for three dimensional vectors</a>
+<a name="325"><span class="lineNum">     325 </span>            : typedef VectorGeneric&lt;3&gt; Vector3d;</a>
+<a name="326"><span class="lineNum">     326 </span>            : /// \ingroup TOOLBOX</a>
+<a name="327"><span class="lineNum">     327 </span>            : /// Alias for four dimensional vectors</a>
+<a name="328"><span class="lineNum">     328 </span>            : typedef VectorGeneric&lt;4&gt; Vector4d;</a>
+<a name="329"><span class="lineNum">     329 </span>            : /// \ingroup TOOLBOX</a>
+<a name="330"><span class="lineNum">     330 </span>            : /// Alias for five dimensional vectors</a>
+<a name="331"><span class="lineNum">     331 </span>            : typedef VectorGeneric&lt;5&gt; Vector5d;</a>
+<a name="332"><span class="lineNum">     332 </span>            : /// \ingroup TOOLBOX</a>
+<a name="333"><span class="lineNum">     333 </span>            : /// Alias for three dimensional vectors</a>
+<a name="334"><span class="lineNum">     334 </span>            : typedef Vector3d Vector;</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            : static_assert(sizeof(VectorGeneric&lt;2&gt;)==2*sizeof(double), &quot;code cannot work if this is not satisfied&quot;);</a>
+<a name="337"><span class="lineNum">     337 </span>            : static_assert(sizeof(VectorGeneric&lt;3&gt;)==3*sizeof(double), &quot;code cannot work if this is not satisfied&quot;);</a>
+<a name="338"><span class="lineNum">     338 </span>            : static_assert(sizeof(VectorGeneric&lt;4&gt;)==4*sizeof(double), &quot;code cannot work if this is not satisfied&quot;);</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            : }</a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span>            : #endif</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/h36.cpp.func-sort-c.html b/coverage/tools/h36.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fda2e274c6
--- /dev/null
+++ b/coverage/tools/h36.cpp.func-sort-c.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/h36.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - h36.cpp<span style="font-size: 80%;"> (<a href="h36.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntryLo">70.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="h36.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#77">_ZN4PLMD3h36L15fill_with_starsEjPc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#73">_ZN4PLMD3h36L17unsupported_widthEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#67">_ZN4PLMD3h36L18value_out_of_rangeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#70">_ZN4PLMD3h36L22invalid_number_literalEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#272">_ZZN4PLMD3h3610hy36decodeEjPKcjPiENKUlvE0_clEv</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#260">_ZZN4PLMD3h3610hy36decodeEjPKcjPiENKUlvE_clEv</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#63">_ZN4PLMD3h36L12digits_lowerEv</a></td>
+              <td class="coverFnHi">7885</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#184">_ZN4PLMD3h3610hy36encodeEjiPc</a></td>
+              <td class="coverFnHi">103780</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#88">_ZN4PLMD3h36L11encode_pureEPKcjjiPc</a></td>
+              <td class="coverFnHi">103780</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#59">_ZN4PLMD3h36L12digits_upperEv</a></td>
+              <td class="coverFnHi">111663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#258">_ZN4PLMD3h3610hy36decodeEjPKcjPi</a></td>
+              <td class="coverFnHi">542340</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#118">_ZN4PLMD3h36L11decode_pureEPKijPKcjPi</a></td>
+              <td class="coverFnHi">542340</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/h36.cpp.func.html b/coverage/tools/h36.cpp.func.html
new file mode 100644
index 0000000000..8d5c3bf0b0
--- /dev/null
+++ b/coverage/tools/h36.cpp.func.html
@@ -0,0 +1,120 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/h36.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - h36.cpp<span style="font-size: 80%;"> (<a href="h36.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntryLo">70.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="h36.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#258">_ZN4PLMD3h3610hy36decodeEjPKcjPi</a></td>
+              <td class="coverFnHi">542340</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#184">_ZN4PLMD3h3610hy36encodeEjiPc</a></td>
+              <td class="coverFnHi">103780</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#118">_ZN4PLMD3h36L11decode_pureEPKijPKcjPi</a></td>
+              <td class="coverFnHi">542340</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#88">_ZN4PLMD3h36L11encode_pureEPKcjjiPc</a></td>
+              <td class="coverFnHi">103780</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#63">_ZN4PLMD3h36L12digits_lowerEv</a></td>
+              <td class="coverFnHi">7885</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#59">_ZN4PLMD3h36L12digits_upperEv</a></td>
+              <td class="coverFnHi">111663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#77">_ZN4PLMD3h36L15fill_with_starsEjPc</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#73">_ZN4PLMD3h36L17unsupported_widthEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#67">_ZN4PLMD3h36L18value_out_of_rangeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#70">_ZN4PLMD3h36L22invalid_number_literalEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#272">_ZZN4PLMD3h3610hy36decodeEjPKcjPiENKUlvE0_clEv</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="h36.cpp.gcov.html#260">_ZZN4PLMD3h3610hy36decodeEjPKcjPiENKUlvE_clEv</a></td>
+              <td class="coverFnHi">219</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/h36.cpp.gcov.html b/coverage/tools/h36.cpp.gcov.html
new file mode 100644
index 0000000000..00d9228295
--- /dev/null
+++ b/coverage/tools/h36.cpp.gcov.html
@@ -0,0 +1,411 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools/h36.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">tools</a> - h36.cpp<span style="font-size: 80%;"> (source / <a href="h36.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntryLo">70.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2018-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;h36.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &lt;vector&gt;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : /// Tiny namespace for hybrid36 format.</a>
+<a name="29"><span class="lineNum">      29 </span>            : /// This namespace includes freely available tools for h36 format.</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace h36 {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : /*! C port of the hy36encode() and hy36decode() functions in the</a>
+<a name="34"><span class="lineNum">      34 </span>            :     hybrid_36.py Python prototype/reference implementation.</a>
+<a name="35"><span class="lineNum">      35 </span>            :     See the Python script for more information.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            :     This file has no external dependencies, NOT even standard C headers.</a>
+<a name="38"><span class="lineNum">      38 </span>            :     Optionally, use hybrid_36_c.h, or simply copy the declarations</a>
+<a name="39"><span class="lineNum">      39 </span>            :     into your code.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            :     This file is unrestricted Open Source (cctbx.sf.net).</a>
+<a name="42"><span class="lineNum">      42 </span>            :     Please send corrections and enhancements to cctbx@cci.lbl.gov .</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            :     See also: http://cci.lbl.gov/hybrid_36/</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            :     Ralf W. Grosse-Kunstleve, Feb 2007.</a>
+<a name="47"><span class="lineNum">      47 </span>            :  */</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : /* The following #include may be commented out.</a>
+<a name="50"><span class="lineNum">      50 </span>            :    It is here only to enforce consistency of the declarations</a>
+<a name="51"><span class="lineNum">      51 </span>            :    and the definitions.</a>
+<a name="52"><span class="lineNum">      52 </span>            :  */</a>
+<a name="53"><span class="lineNum">      53 </span>            : // #include &lt;iotbx/pdb/hybrid_36_c.h&gt;</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : /* All static functions below are implementation details</a>
+<a name="56"><span class="lineNum">      56 </span>            :    (and not accessible from other translation units).</a>
+<a name="57"><span class="lineNum">      57 </span>            :  */</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : static</a>
+<a name="60"><span class="lineNum">      60 </span>            : const char*</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">     111663 : digits_upper() { return &quot;0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ&quot;; }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : static</a>
+<a name="64"><span class="lineNum">      64 </span>            : const char*</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       7885 : digits_lower() { return &quot;0123456789abcdefghijklmnopqrstuvwxyz&quot;; }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : static</a>
+<a name="68"><span class="lineNum">      68 </span>            : const char*</a>
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+<a name="70"><span class="lineNum">      70 </span>            : </a>
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+<a name="73"><span class="lineNum">      73 </span>            : </a>
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+<a name="76"><span class="lineNum">      76 </span>            : </a>
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+<a name="78"><span class="lineNum">      78 </span>            : void</a>
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+<a name="89"><span class="lineNum">      89 </span>            : void</a>
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+<a name="91"><span class="lineNum">      91 </span>            :   const char* digits,</a>
+<a name="92"><span class="lineNum">      92 </span>            :   unsigned digits_size,</a>
+<a name="93"><span class="lineNum">      93 </span>            :   unsigned width,</a>
+<a name="94"><span class="lineNum">      94 </span>            :   int value,</a>
+<a name="95"><span class="lineNum">      95 </span>            :   char* result)</a>
+<a name="96"><span class="lineNum">      96 </span>            : {</a>
+<a name="97"><span class="lineNum">      97 </span>            :   char buf[16];</a>
+<a name="98"><span class="lineNum">      98 </span>            :   int rest;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   unsigned i, j;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   i = 0;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   j = 0;</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">     103780 :   if (value &lt; 0) {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :     j = 1;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :     value = -value;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span>            :   while (1) {</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">     493492 :     rest = value / digits_size;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     493492 :     buf[i++] = digits[value - rest * digits_size];</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">     493492 :     if (rest == 0) break;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     value = rest;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     103780 :   if (j) buf[i++] = '-';</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">     127352 :   for(j=i; j&lt;width; j++) *result++ = ' ';</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">     597272 :   while (i != 0) *result++ = buf[--i];</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">     103780 :   *result = '\0';</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     103780 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : static</a>
+<a name="119"><span class="lineNum">     119 </span>            : const char*</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     542340 : decode_pure(</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   const int* digits_values,</a>
+<a name="122"><span class="lineNum">     122 </span>            :   unsigned digits_size,</a>
+<a name="123"><span class="lineNum">     123 </span>            :   const char* s,</a>
+<a name="124"><span class="lineNum">     124 </span>            :   unsigned s_size,</a>
+<a name="125"><span class="lineNum">     125 </span>            :   int* result)</a>
+<a name="126"><span class="lineNum">     126 </span>            : {</a>
+<a name="127"><span class="lineNum">     127 </span>            :   int si, dv;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   int have_minus = 0;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   int have_non_blank = 0;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   int value = 0;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   unsigned i = 0;</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    2982869 :   for(; i&lt;s_size; i++) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">    2440530 :     si = s[i];</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">    2440530 :     if (si &lt; 0 || si &gt; 127) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :       *result = 0;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :       return invalid_number_literal();</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     }</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">    2440530 :     if (si == ' ') {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">     908622 :       if (!have_non_blank) continue;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :       value *= digits_size;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">    1531908 :     else if (si == '-') {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :       if (have_non_blank) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :         *result = 0;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :         return invalid_number_literal();</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :       }</a>
+<a name="147"><span class="lineNum">     147 </span>            :       have_non_blank = 1;</a>
+<a name="148"><span class="lineNum">     148 </span>            :       have_minus = 1;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :       continue;</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :     }</a>
+<a name="151"><span class="lineNum">     151 </span>            :     else {</a>
+<a name="152"><span class="lineNum">     152 </span>            :       have_non_blank = 1;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">    1531908 :       dv = digits_values[si];</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    1531908 :       if (dv &lt; 0 || dv &gt;= digits_size) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          1 :         *result = 0;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          1 :         return invalid_number_literal();</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :       }</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">    1531907 :       value *= digits_size;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    1531907 :       value += dv;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     542339 :   if (have_minus) value = -value;</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">     542339 :   *result = value;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">     542339 :   return 0;</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : /*! hybrid-36 encoder: converts integer value to string result</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :       width: must be 4 (e.g. for residue sequence numbers)</a>
+<a name="170"><span class="lineNum">     170 </span>            :                   or 5 (e.g. for atom serial numbers)</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            :       value: integer value to be converted</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :       result: pointer to char array of size width+1 or greater</a>
+<a name="175"><span class="lineNum">     175 </span>            :               on return result is null-terminated</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            :       return value: pointer to error message, if any,</a>
+<a name="178"><span class="lineNum">     178 </span>            :                     or 0 on success</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            :     Example usage (from C++):</a>
+<a name="181"><span class="lineNum">     181 </span>            :       char result[4+1];</a>
+<a name="182"><span class="lineNum">     182 </span>            :       const char* errmsg = hy36encode(4, 12345, result);</a>
+<a name="183"><span class="lineNum">     183 </span>            :       if (errmsg) throw std::runtime_error(errmsg);</a>
+<a name="184"><span class="lineNum">     184 </span>            :  */</a>
+<a name="185"><span class="lineNum">     185 </span>            : const char*</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     103780 : hy36encode(unsigned width, int value, char* result)</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : {</a>
+<a name="188"><span class="lineNum">     188 </span>            :   int i = value;</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">     103780 :   if (width == 4U) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       1836 :     if (i &gt;= -999) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1836 :       if (i &lt; 10000) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1835 :         encode_pure(digits_upper(), 10U, 4U, i, result);</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       1835 :         return 0;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :       }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          1 :       i -= 10000;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          1 :       if (i &lt; 1213056 /* 26*36**3 */) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          1 :         i += 466560 /* 10*36**3 */;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          1 :         encode_pure(digits_upper(), 36U, 0U, i, result);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          1 :         return 0;</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :       }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :       i -= 1213056;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :       if (i &lt; 1213056) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :         i += 466560;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :         encode_pure(digits_lower(), 36U, 0U, i, result);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :         return 0;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :       }</a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">     101944 :   else if (width == 5U) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">     101944 :     if (i &gt;= -9999) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">     101944 :       if (i &lt; 100000) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">     101835 :         encode_pure(digits_upper(), 10U, 5U, i, result);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">     101835 :         return 0;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :       }</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        109 :       i -= 100000;</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        109 :       if (i &lt; 43670016 /* 26*36**4 */) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        108 :         i += 16796160 /* 10*36**4 */;</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        108 :         encode_pure(digits_upper(), 36U, 0U, i, result);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        108 :         return 0;</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :       }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          1 :       i -= 43670016;</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          1 :       if (i &lt; 43670016) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          1 :         i += 16796160;</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          1 :         encode_pure(digits_lower(), 36U, 0U, i, result);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          1 :         return 0;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :       }</a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   else {</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :     fill_with_stars(width, result);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     return unsupported_width();</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :   fill_with_stars(width, result);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :   return value_out_of_range();</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : /*! hybrid-36 decoder: converts string s to integer result</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            :       width: must be 4 (e.g. for residue sequence numbers)</a>
+<a name="240"><span class="lineNum">     240 </span>            :                   or 5 (e.g. for atom serial numbers)</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            :       s: string to be converted</a>
+<a name="243"><span class="lineNum">     243 </span>            :          does not have to be null-terminated</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :       s_size: size of s</a>
+<a name="246"><span class="lineNum">     246 </span>            :               must be equal to width, or an error message is</a>
+<a name="247"><span class="lineNum">     247 </span>            :               returned otherwise</a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            :       result: integer holding the conversion result</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            :       return value: pointer to error message, if any,</a>
+<a name="252"><span class="lineNum">     252 </span>            :                     or 0 on success</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            :     Example usage (from C++):</a>
+<a name="255"><span class="lineNum">     255 </span>            :       int result;</a>
+<a name="256"><span class="lineNum">     256 </span>            :       const char* errmsg = hy36decode(width, &quot;A1T5&quot;, 4, &amp;result);</a>
+<a name="257"><span class="lineNum">     257 </span>            :       if (errmsg) throw std::runtime_error(errmsg);</a>
+<a name="258"><span class="lineNum">     258 </span>            :  */</a>
+<a name="259"><span class="lineNum">     259 </span>            : const char*</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">     542340 : hy36decode(unsigned width, const char* s, unsigned s_size, int* result)</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : {</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        219 :   static const std::vector&lt;int&gt; digits_values_upper_vector([]() {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        219 :     std::vector&lt;int&gt; ret(128U,-1);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">       8103 :     for(unsigned i=0; i&lt;36U; i++) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">       7884 :       int di = digits_upper()[i];</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">       7884 :       if (di &lt; 0 || di &gt; 127) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :         plumed_error()&lt;&lt;&quot;internal error hy36decode: integer value out of range&quot;;</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :       }</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">       7884 :       ret[di] = i;</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        219 :     return ret;</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">     542340 :   }());</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">     542340 :   static const int* digits_values_upper=digits_values_upper_vector.data();</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        219 :   static const std::vector&lt;int&gt; digits_values_lower_vector([]() {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        219 :     std::vector&lt;int&gt; ret(128U,-1);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">       8103 :     for(unsigned i=0; i&lt;36U; i++) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">       7884 :       int di = digits_lower()[i];</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">       7884 :       if (di &lt; 0 || di &gt; 127) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :         plumed_error()&lt;&lt;&quot;internal error hy36decode: integer value out of range&quot;;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :       }</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">       7884 :       ret[di] = i;</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :     }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        219 :     return ret;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">     542340 :   }());</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     542340 :   static const int* digits_values_lower=digits_values_lower_vector.data();</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   int di;</a>
+<a name="287"><span class="lineNum">     287 </span>            :   const char* errmsg;</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">     542340 :   if (s_size == width) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     542340 :     di = s[0];</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">     542340 :     if (di &gt;= 0 &amp;&amp; di &lt;= 127) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     542340 :       if (digits_values_upper[di] &gt;= 10) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">          6 :         errmsg = decode_pure(digits_values_upper, 36U, s, s_size, result);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          6 :         if (errmsg == 0) {</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :           /* result - 10*36**(width-1) + 10**width */</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          5 :           if      (width == 4U) (*result) -= 456560;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          2 :           else if (width == 5U) (*result) -= 16696160;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :           else {</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :             *result = 0;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 :             return unsupported_width();</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :           }</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          5 :           return 0;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :         }</a>
+<a name="303"><span class="lineNum">     303 </span>            :       }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">     542334 :       else if (digits_values_lower[di] &gt;= 10) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :         errmsg = decode_pure(digits_values_lower, 36U, s, s_size, result);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineNoCov">          0 :         if (errmsg == 0) {</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :           /* result + 16*36**(width-1) + 10**width */</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineNoCov">          0 :           if      (width == 4U) (*result) += 756496;</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 :           else if (width == 5U) (*result) += 26973856;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :           else {</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineNoCov">          0 :             *result = 0;</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 :             return unsupported_width();</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :           }</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :           return 0;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :         }</a>
+<a name="316"><span class="lineNum">     316 </span>            :       }</a>
+<a name="317"><span class="lineNum">     317 </span>            :       else {</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">     542334 :         errmsg = decode_pure(digits_values_upper, 10U, s, s_size, result);</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">     542334 :         if (errmsg) return errmsg;</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">     542334 :         if (!(width == 4U || width == 5U)) {</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :           *result = 0;</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :           return unsupported_width();</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :         }</a>
+<a name="324"><span class="lineNum">     324 </span>            :         return 0;</a>
+<a name="325"><span class="lineNum">     325 </span>            :       }</a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span>            :   }</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          1 :   *result = 0;</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          1 :   return invalid_number_literal();</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            : }</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            : }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/index-sort-f.html b/coverage/tools/index-sort-f.html
new file mode 100644
index 0000000000..cdffebdadc
--- /dev/null
+++ b/coverage/tools/index-sort-f.html
@@ -0,0 +1,803 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - tools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5629</td>
+            <td class="headerCovTableEntry">6739</td>
+            <td class="headerCovTableEntryMed">83.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1406</td>
+            <td class="headerCovTableEntry">1728</td>
+            <td class="headerCovTableEntryMed">81.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.h.gcov.html">Exception.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+      <td class="coverPerLo">17.0&nbsp;%</td>
+      <td class="coverNumLo">23 / 135</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsion.cpp.gcov.html">Torsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">28 / 35</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.cpp.gcov.html">RMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.5%"><img src="../snow.png" width=27 height=10 alt="73.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.5&nbsp;%</td>
+      <td class="coverNumLo">540 / 735</td>
+      <td class="coverPerLo">52.5&nbsp;%</td>
+      <td class="coverNumLo">42 / 80</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedHandle.cpp.gcov.html">PlumedHandle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="62.9%"><img src="../snow.png" width=37 height=10 alt="62.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.9&nbsp;%</td>
+      <td class="coverNumLo">22 / 35</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BiasRepresentation.cpp.gcov.html">BiasRepresentation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.9%"><img src="../snow.png" width=24 height=10 alt="75.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.9&nbsp;%</td>
+      <td class="coverNumMed">129 / 170</td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RootFindingBase.h.gcov.html">RootFindingBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">16 / 16</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Brent1DRootSearch.h.gcov.html">Brent1DRootSearch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">38 / 39</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Grid.cpp.gcov.html">Grid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="71.1%"><img src="../snow.png" width=29 height=10 alt="71.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.1&nbsp;%</td>
+      <td class="coverNumLo">440 / 619</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">55 / 77</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TypesafePtr.h.gcov.html">TypesafePtr.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.8%"><img src="../snow.png" width=12 height=10 alt="87.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 131</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">40 / 55</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OpenMP.h.gcov.html">OpenMP.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">3 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="h36.cpp.gcov.html">h36.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.1%"><img src="../snow.png" width=30 height=10 alt="70.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.1&nbsp;%</td>
+      <td class="coverNumLo">89 / 127</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.h.gcov.html">RMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">30 / 35</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Keywords.cpp.gcov.html">Keywords.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=61 height=10 alt="60.8%"><img src="../snow.png" width=39 height=10 alt="60.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">60.8&nbsp;%</td>
+      <td class="coverNumLo">240 / 395</td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">32 / 41</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OpenMP.cpp.gcov.html">OpenMP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.4%"><img src="../snow.png" width=18 height=10 alt="82.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">14 / 17</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DLLoader.cpp.gcov.html">DLLoader.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.0%"><img src="../snow.png" width=19 height=10 alt="81.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 21</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.cpp.gcov.html">ERMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">120 / 122</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LatticeReduction.cpp.gcov.html">LatticeReduction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.9%"><img src="../snow.png" width=17 height=10 alt="82.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.9&nbsp;%</td>
+      <td class="coverNumMed">102 / 123</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NeighborList.cpp.gcov.html">NeighborList.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.7%"><img src="../snow.png" width=10 height=10 alt="89.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.7&nbsp;%</td>
+      <td class="coverNumMed">96 / 107</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PDB.cpp.gcov.html">PDB.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">275 / 412</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">36 / 44</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tensor.h.gcov.html">Tensor.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">146 / 151</td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">56 / 68</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Communicator.cpp.gcov.html">Communicator.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="83.6%"><img src="../snow.png" width=16 height=10 alt="83.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.6&nbsp;%</td>
+      <td class="coverNumMed">102 / 122</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Subprocess.cpp.gcov.html">Subprocess.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.3%"><img src="../snow.png" width=25 height=10 alt="75.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.3&nbsp;%</td>
+      <td class="coverNumMed">64 / 85</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IFile.cpp.gcov.html">IFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">145 / 151</td>
+      <td class="coverPerMed">88.0&nbsp;%</td>
+      <td class="coverNumMed">22 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Grid.h.gcov.html">Grid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MinimiseBase.h.gcov.html">MinimiseBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">16 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OFile.h.gcov.html">OFile.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerMed">89.7&nbsp;%</td>
+      <td class="coverNumMed">96 / 107</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="KernelFunctions.cpp.gcov.html">KernelFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.4%"><img src="../snow.png" width=16 height=10 alt="84.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">189 / 224</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Random.cpp.gcov.html">Random.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.6%"><img src="../snow.png" width=8 height=10 alt="91.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.6&nbsp;%</td>
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+      <td class="coverFile"><a href="HistogramBead.cpp.gcov.html">HistogramBead.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">93 / 118</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Minimise1DBrent.h.gcov.html">Minimise1DBrent.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="97.6%"><img src="../snow.png" width=2 height=10 alt="97.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.6&nbsp;%</td>
+      <td class="coverNumHi">81 / 83</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DynamicList.h.gcov.html">DynamicList.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ForwardDecl.h.gcov.html">ForwardDecl.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MatrixSquareBracketsAccess.h.gcov.html">MatrixSquareBracketsAccess.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LoopUnroller.h.gcov.html">LoopUnroller.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">52 / 52</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/index-sort-l.html b/coverage/tools/index-sort-l.html
new file mode 100644
index 0000000000..fd969cba6d
--- /dev/null
+++ b/coverage/tools/index-sort-l.html
@@ -0,0 +1,803 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - tools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5629</td>
+            <td class="headerCovTableEntry">6739</td>
+            <td class="headerCovTableEntryMed">83.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1406</td>
+            <td class="headerCovTableEntry">1728</td>
+            <td class="headerCovTableEntryMed">81.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.h.gcov.html">ERMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Keywords.cpp.gcov.html">Keywords.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=61 height=10 alt="60.8%"><img src="../snow.png" width=39 height=10 alt="60.8%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">60.8&nbsp;%</td>
+      <td class="coverNumLo">240 / 395</td>
+      <td class="coverPerMed">78.0&nbsp;%</td>
+      <td class="coverNumMed">32 / 41</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PlumedHandle.cpp.gcov.html">PlumedHandle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=63 height=10 alt="62.9%"><img src="../snow.png" width=37 height=10 alt="62.9%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">62.9&nbsp;%</td>
+      <td class="coverNumLo">22 / 35</td>
+      <td class="coverPerLo">62.5&nbsp;%</td>
+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="PDB.cpp.gcov.html">PDB.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">275 / 412</td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">36 / 44</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="h36.cpp.gcov.html">h36.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.1%"><img src="../snow.png" width=30 height=10 alt="70.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">70.1&nbsp;%</td>
+      <td class="coverNumLo">89 / 127</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Grid.cpp.gcov.html">Grid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="71.1%"><img src="../snow.png" width=29 height=10 alt="71.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.1&nbsp;%</td>
+      <td class="coverNumLo">440 / 619</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">55 / 77</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.cpp.gcov.html">RMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=73 height=10 alt="73.5%"><img src="../snow.png" width=27 height=10 alt="73.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.5&nbsp;%</td>
+      <td class="coverNumLo">540 / 735</td>
+      <td class="coverPerLo">52.5&nbsp;%</td>
+      <td class="coverNumLo">42 / 80</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Subprocess.cpp.gcov.html">Subprocess.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=75 height=10 alt="75.3%"><img src="../snow.png" width=25 height=10 alt="75.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.3&nbsp;%</td>
+      <td class="coverNumMed">64 / 85</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">14 / 16</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BiasRepresentation.cpp.gcov.html">BiasRepresentation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.9%"><img src="../snow.png" width=24 height=10 alt="75.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.9&nbsp;%</td>
+      <td class="coverNumMed">129 / 170</td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramBead.cpp.gcov.html">HistogramBead.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">93 / 118</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsion.cpp.gcov.html">Torsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">28 / 35</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DLLoader.cpp.gcov.html">DLLoader.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.0%"><img src="../snow.png" width=19 height=10 alt="81.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 21</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OpenMP.cpp.gcov.html">OpenMP.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.4%"><img src="../snow.png" width=18 height=10 alt="82.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">14 / 17</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tools.h.gcov.html">Tools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.6%"><img src="../snow.png" width=17 height=10 alt="82.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.6&nbsp;%</td>
+      <td class="coverNumMed">76 / 92</td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">399 / 434</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LatticeReduction.cpp.gcov.html">LatticeReduction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.9%"><img src="../snow.png" width=17 height=10 alt="82.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.9&nbsp;%</td>
+      <td class="coverNumMed">102 / 123</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">8 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.h.gcov.html">Exception.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+      <td class="coverPerLo">17.0&nbsp;%</td>
+      <td class="coverNumLo">23 / 135</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Communicator.cpp.gcov.html">Communicator.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="83.6%"><img src="../snow.png" width=16 height=10 alt="83.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.6&nbsp;%</td>
+      <td class="coverNumMed">102 / 122</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="KernelFunctions.cpp.gcov.html">KernelFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="84.4%"><img src="../snow.png" width=16 height=10 alt="84.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">189 / 224</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MolDataClass.cpp.gcov.html">MolDataClass.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="85.1%"><img src="../snow.png" width=15 height=10 alt="85.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.1&nbsp;%</td>
+      <td class="coverNumMed">406 / 477</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="RMSD.h.gcov.html">RMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="85.7%"><img src="../snow.png" width=14 height=10 alt="85.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">30 / 35</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TypesafePtr.h.gcov.html">TypesafePtr.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.8%"><img src="../snow.png" width=12 height=10 alt="87.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 131</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">40 / 55</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Keywords.h.gcov.html">Keywords.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.2%"><img src="../snow.png" width=12 height=10 alt="88.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">88.2&nbsp;%</td>
+      <td class="coverNumMed">15 / 17</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="NeighborList.cpp.gcov.html">NeighborList.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.7%"><img src="../snow.png" width=10 height=10 alt="89.7%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.7&nbsp;%</td>
+      <td class="coverNumMed">96 / 107</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">12 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Units.cpp.gcov.html">Units.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">88 / 97</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Communicator.h.gcov.html">Communicator.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.5%"><img src="../snow.png" width=9 height=10 alt="91.5%"></td></tr></table>
+      </td>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LoopUnroller.h.gcov.html">LoopUnroller.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">31 / 31</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">52 / 52</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Grid.h.gcov.html">Grid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiValue.h.gcov.html">MultiValue.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tree.cpp.gcov.html">Tree.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DynamicList.h.gcov.html">DynamicList.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MultiValue.cpp.gcov.html">MultiValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">62 / 62</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vector.h.gcov.html">Vector.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">66 / 66</td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">51 / 54</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FileBase.cpp.gcov.html">FileBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">80 / 80</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Matrix.h.gcov.html">Matrix.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">140 / 140</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/tools/index.html b/coverage/tools/index.html
new file mode 100644
index 0000000000..707805a29e
--- /dev/null
+++ b/coverage/tools/index.html
@@ -0,0 +1,803 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - tools</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - tools</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5629</td>
+            <td class="headerCovTableEntry">6739</td>
+            <td class="headerCovTableEntryMed">83.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1406</td>
+            <td class="headerCovTableEntry">1728</td>
+            <td class="headerCovTableEntryMed">81.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Angle.cpp.gcov.html">Angle.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">26 / 26</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AtomNumber.h.gcov.html">AtomNumber.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">18 / 18</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BiasRepresentation.cpp.gcov.html">BiasRepresentation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.9%"><img src="../snow.png" width=24 height=10 alt="75.9%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">75.9&nbsp;%</td>
+      <td class="coverNumMed">129 / 170</td>
+      <td class="coverPerLo">63.2&nbsp;%</td>
+      <td class="coverNumLo">12 / 19</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Brent1DRootSearch.h.gcov.html">Brent1DRootSearch.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">38 / 39</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">6 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Citations.cpp.gcov.html">Citations.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">16 / 16</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Citations.h.gcov.html">Citations.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Communicator.cpp.gcov.html">Communicator.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=84 height=10 alt="83.6%"><img src="../snow.png" width=16 height=10 alt="83.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.6&nbsp;%</td>
+      <td class="coverNumMed">102 / 122</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Communicator.h.gcov.html">Communicator.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.5%"><img src="../snow.png" width=9 height=10 alt="91.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.5&nbsp;%</td>
+      <td class="coverNumHi">43 / 47</td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">58 / 62</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ConjugateGradient.h.gcov.html">ConjugateGradient.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="92.9%"><img src="../snow.png" width=7 height=10 alt="92.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.9&nbsp;%</td>
+      <td class="coverNumHi">13 / 14</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DLLoader.cpp.gcov.html">DLLoader.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="81.0%"><img src="../snow.png" width=19 height=10 alt="81.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 21</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="DynamicList.h.gcov.html">DynamicList.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">47 / 47</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.cpp.gcov.html">ERMSD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">120 / 122</td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">4 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ERMSD.h.gcov.html">ERMSD.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.cpp.gcov.html">Exception.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.1%"><img src="../snow.png" width=6 height=10 alt="94.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.1&nbsp;%</td>
+      <td class="coverNumHi">48 / 51</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Exception.h.gcov.html">Exception.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+      <td class="coverPerLo">17.0&nbsp;%</td>
+      <td class="coverNumLo">23 / 135</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FileBase.cpp.gcov.html">FileBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">80 / 80</td>
+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">14 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FileBase.h.gcov.html">FileBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ForwardDecl.h.gcov.html">ForwardDecl.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">13 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Grid.cpp.gcov.html">Grid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=71 height=10 alt="71.1%"><img src="../snow.png" width=29 height=10 alt="71.1%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">71.1&nbsp;%</td>
+      <td class="coverNumLo">440 / 619</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">55 / 77</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Grid.h.gcov.html">Grid.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramBead.cpp.gcov.html">HistogramBead.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=79 height=10 alt="78.8%"><img src="../snow.png" width=21 height=10 alt="78.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">78.8&nbsp;%</td>
+      <td class="coverNumMed">93 / 118</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="HistogramBead.h.gcov.html">HistogramBead.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="94.4%"><img src="../snow.png" width=6 height=10 alt="94.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">17 / 18</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="IFile.cpp.gcov.html">IFile.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.0&nbsp;%</td>
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+      <td class="coverNumHi">10 / 10</td>
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+      <td class="coverNumMed">14 / 16</td>
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+      <td class="coverFile"><a href="Subprocess.h.gcov.html">Subprocess.h</a></td>
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+      <td class="coverNumHi">11 / 11</td>
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+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">146 / 151</td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">56 / 68</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tools.cpp.gcov.html">Tools.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="91.7%"><img src="../snow.png" width=8 height=10 alt="91.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">91.7&nbsp;%</td>
+      <td class="coverNumHi">255 / 278</td>
+      <td class="coverPerHi">92.7&nbsp;%</td>
+      <td class="coverNumHi">51 / 55</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tools.h.gcov.html">Tools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="82.6%"><img src="../snow.png" width=17 height=10 alt="82.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.6&nbsp;%</td>
+      <td class="coverNumMed">76 / 92</td>
+      <td class="coverPerHi">91.9&nbsp;%</td>
+      <td class="coverNumHi">399 / 434</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Torsion.cpp.gcov.html">Torsion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=80 height=10 alt="80.0%"><img src="../snow.png" width=20 height=10 alt="80.0%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.0&nbsp;%</td>
+      <td class="coverNumMed">28 / 35</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tree.cpp.gcov.html">Tree.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">37 / 37</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Tree.h.gcov.html">Tree.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TypesafePtr.cpp.gcov.html">TypesafePtr.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">14 / 14</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TypesafePtr.h.gcov.html">TypesafePtr.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="87.8%"><img src="../snow.png" width=12 height=10 alt="87.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.8&nbsp;%</td>
+      <td class="coverNumMed">115 / 131</td>
+      <td class="coverPerLo">72.7&nbsp;%</td>
+      <td class="coverNumLo">40 / 55</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Units.cpp.gcov.html">Units.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.7%"><img src="../snow.png" width=9 height=10 alt="90.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.7&nbsp;%</td>
+      <td class="coverNumHi">88 / 97</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Units.h.gcov.html">Units.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vector.h.gcov.html">Vector.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">66 / 66</td>
+      <td class="coverPerHi">94.4&nbsp;%</td>
+      <td class="coverNumHi">51 / 54</td>
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+    <tr>
+      <td class="coverFile"><a href="h36.cpp.gcov.html">h36.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=70 height=10 alt="70.1%"><img src="../snow.png" width=30 height=10 alt="70.1%"></td></tr></table>
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+      <td class="coverNumLo">89 / 127</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">9 / 12</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/vatom/Center.cpp.func-sort-c.html b/coverage/vatom/Center.cpp.func-sort-c.html
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+++ b/coverage/vatom/Center.cpp.func-sort-c.html
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/Center.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
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+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - Center.cpp<span style="font-size: 80%;"> (<a href="Center.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
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+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Center.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#150">_ZN4PLMD5vatom6CenterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#138">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe1406createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#137">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe139C2Ev</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#137">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#138">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe140C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#138">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe140D2Ev</a></td>
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+              <td class="coverFn"><a href="Center.cpp.gcov.html#137">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe1396createERKNS_13ActionOptionsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#150">_ZN4PLMD5vatom6CenterC1ERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFn"><a href="Center.cpp.gcov.html#140">_ZN4PLMD5vatom6Center16registerKeywordsERNS_8KeywordsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#210">_ZN4PLMD5vatom6Center9calculateEv</a></td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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new file mode 100644
index 0000000000..9f4ebf4489
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@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/Center.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - Center.cpp<span style="font-size: 80%;"> (<a href="Center.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Center.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#137">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe1396createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7089</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#137">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe139C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#137">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe139D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#138">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe1406createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">74</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#138">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe140C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#138">_ZN4PLMD5vatom12_GLOBAL__N_119CenterRegisterMe140D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#140">_ZN4PLMD5vatom6Center16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7167</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#210">_ZN4PLMD5vatom6Center9calculateEv</a></td>
+              <td class="coverFnHi">13808</td>
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+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#150">_ZN4PLMD5vatom6CenterC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">7163</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Center.cpp.gcov.html#150">_ZN4PLMD5vatom6CenterC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/Center.cpp.gcov.html b/coverage/vatom/Center.cpp.gcov.html
new file mode 100644
index 0000000000..e802d84a70
--- /dev/null
+++ b/coverage/vatom/Center.cpp.gcov.html
@@ -0,0 +1,398 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/Center.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - Center.cpp<span style="font-size: 80%;"> (source / <a href="Center.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntry">122</td>
+            <td class="headerCovTableEntryHi">98.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace vatom {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VATOM CENTER</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Calculate the center for a group of atoms, with arbitrary weights.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : The computed</a>
+<a name="36"><span class="lineNum">      36 </span>            : center is stored as a virtual atom that can be accessed in</a>
+<a name="37"><span class="lineNum">      37 </span>            : an atom list through the label for the CENTER action that creates it.</a>
+<a name="38"><span class="lineNum">      38 </span>            : Notice that the generated virtual atom has charge equal to the sum of the</a>
+<a name="39"><span class="lineNum">      39 </span>            : charges and mass equal to the sum of the masses. If used with the MASS flag,</a>
+<a name="40"><span class="lineNum">      40 </span>            : then it provides a result identical to \ref COM.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="43"><span class="lineNum">      43 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.2,</a>
+<a name="44"><span class="lineNum">      44 </span>            : by considering the ordered list of atoms and rebuilding the molecule using a procedure</a>
+<a name="45"><span class="lineNum">      45 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="46"><span class="lineNum">      46 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="47"><span class="lineNum">      47 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="50"><span class="lineNum">      50 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="51"><span class="lineNum">      51 </span>            : periodic image.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : \note As an experimental feature, CENTER also supports a keyword PHASES.</a>
+<a name="54"><span class="lineNum">      54 </span>            : This keyword finds the center of mass for sets of atoms that have been split by the period boundaries by computing scaled coordinates and average</a>
+<a name="55"><span class="lineNum">      55 </span>            : trigonometric functions, similarly to \ref CENTER_OF_MULTICOLVAR.</a>
+<a name="56"><span class="lineNum">      56 </span>            : Notice that by construction this center position is</a>
+<a name="57"><span class="lineNum">      57 </span>            : not invariant with respect to rotations of the atoms at fixed cell lattice.</a>
+<a name="58"><span class="lineNum">      58 </span>            : In addition, for symmetric Bravais lattices, it is not invariant with respect</a>
+<a name="59"><span class="lineNum">      59 </span>            : to special symmetries. E.g., if you have an hexagonal cell, the center will</a>
+<a name="60"><span class="lineNum">      60 </span>            : not be invariant with respect to rotations of 120 degrees.</a>
+<a name="61"><span class="lineNum">      61 </span>            : On the other hand, it might make the treatment of PBC easier in difficult cases.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \par Examples</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \plumedfile</a>
+<a name="66"><span class="lineNum">      66 </span>            : # a point which is on the line connecting atoms 1 and 10, so that its distance</a>
+<a name="67"><span class="lineNum">      67 </span>            : # from 10 is twice its distance from 1:</a>
+<a name="68"><span class="lineNum">      68 </span>            : c1: CENTER ATOMS=1,1,10</a>
+<a name="69"><span class="lineNum">      69 </span>            : # this is another way of stating the same:</a>
+<a name="70"><span class="lineNum">      70 </span>            : c1bis: CENTER ATOMS=1,10 WEIGHTS=2,1</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : # center of mass among these atoms:</a>
+<a name="73"><span class="lineNum">      73 </span>            : c2: CENTER ATOMS=2,3,4,5 MASS</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : d1: DISTANCE ATOMS=c1,c2</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : PRINT ARG=d1</a>
+<a name="78"><span class="lineNum">      78 </span>            : \endplumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : */</a>
+<a name="81"><span class="lineNum">      81 </span>            : //+ENDPLUMEDOC</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : //+PLUMEDOC VATOM COM</a>
+<a name="84"><span class="lineNum">      84 </span>            : /*</a>
+<a name="85"><span class="lineNum">      85 </span>            : Calculate the center of mass for a group of atoms.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : The computed</a>
+<a name="88"><span class="lineNum">      88 </span>            : center of mass is stored as a virtual atom that can be accessed in</a>
+<a name="89"><span class="lineNum">      89 </span>            : an atom list through the label for the COM action that creates it.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : For arbitrary weights (e.g. geometric center) see \ref CENTER.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : When running with periodic boundary conditions, the atoms should be</a>
+<a name="94"><span class="lineNum">      94 </span>            : in the proper periodic image. This is done automatically since PLUMED 2.2,</a>
+<a name="95"><span class="lineNum">      95 </span>            : by considering the ordered list of atoms and rebuilding the molecule using a procedure</a>
+<a name="96"><span class="lineNum">      96 </span>            : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that</a>
+<a name="97"><span class="lineNum">      97 </span>            : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES</a>
+<a name="98"><span class="lineNum">      98 </span>            : which actually modifies the coordinates stored in PLUMED.</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : In case you want to recover the old behavior you should use the NOPBC flag.</a>
+<a name="101"><span class="lineNum">     101 </span>            : In that case you need to take care that atoms are in the correct</a>
+<a name="102"><span class="lineNum">     102 </span>            : periodic image.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : \par Examples</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : The following input instructs plumed to print the distance between the</a>
+<a name="107"><span class="lineNum">     107 </span>            : center of mass for atoms 1,2,3,4,5,6,7 and that for atoms 15,20:</a>
+<a name="108"><span class="lineNum">     108 </span>            : \plumedfile</a>
+<a name="109"><span class="lineNum">     109 </span>            : c1: COM ATOMS=1-7</a>
+<a name="110"><span class="lineNum">     110 </span>            : c2: COM ATOMS=15,20</a>
+<a name="111"><span class="lineNum">     111 </span>            : d1: DISTANCE ATOMS=c1,c2</a>
+<a name="112"><span class="lineNum">     112 </span>            : PRINT ARG=d1</a>
+<a name="113"><span class="lineNum">     113 </span>            : \endplumedfile</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : */</a>
+<a name="116"><span class="lineNum">     116 </span>            : //+ENDPLUMEDOC</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : class Center:</a>
+<a name="120"><span class="lineNum">     120 </span>            :   public ActionWithVirtualAtom</a>
+<a name="121"><span class="lineNum">     121 </span>            : {</a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;double&gt; weights;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::vector&lt;Tensor&gt; dcenter_sin;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   std::vector&lt;Tensor&gt; dcenter_cos;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double charge_;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   double mass_;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   bool isChargeSet_;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   bool isMassSet_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   bool weight_mass;</a>
+<a name="130"><span class="lineNum">     130 </span>            :   bool nopbc;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool first;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   bool phases;</a>
+<a name="133"><span class="lineNum">     133 </span>            : public:</a>
+<a name="134"><span class="lineNum">     134 </span>            :   explicit Center(const ActionOptions&amp;ao);</a>
+<a name="135"><span class="lineNum">     135 </span>            :   void calculate() override;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="137"><span class="lineNum">     137 </span>            : };</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      26680 : PLUMED_REGISTER_ACTION(Center,&quot;CENTER&quot;)</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      12652 : PLUMED_REGISTER_ACTION(Center,&quot;COM&quot;)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       7167 : void Center::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       7167 :   ActionWithVirtualAtom::registerKeywords(keys);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">      14334 :   keys.add(&quot;optional&quot;,&quot;WEIGHTS&quot;,&quot;Center is computed as a weighted average.&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">      14334 :   keys.add(&quot;optional&quot;,&quot;SET_CHARGE&quot;,&quot;Set the charge of the virtual atom to a given value.&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      14334 :   keys.add(&quot;optional&quot;,&quot;SET_MASS&quot;,&quot;Set the mass of the virtual atom to a given value.&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">      14334 :   keys.addFlag(&quot;NOPBC&quot;,false,&quot;ignore the periodic boundary conditions when calculating distances&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">      14334 :   keys.addFlag(&quot;MASS&quot;,false,&quot;If set center is mass weighted&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">      14334 :   keys.addFlag(&quot;PHASES&quot;,false,&quot;Compute center using trigonometric phases&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       7167 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       7163 : Center::Center(const ActionOptions&amp;ao):</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   Action(ao),</a>
+<a name="154"><span class="lineNum">     154 </span>            :   ActionWithVirtualAtom(ao),</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       7163 :   charge_(nan(&quot;&quot;)),</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       7163 :   mass_(-1),</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       7163 :   isChargeSet_(false),</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       7163 :   isMassSet_(false),</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       7163 :   weight_mass(false),</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       7163 :   nopbc(false),</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       7163 :   first(true),</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       7163 :   phases(false)</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : {</a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">      14326 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       7163 :   if(atoms.size()==0) error(&quot;at least one atom should be specified&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       7163 :   parseVector(&quot;WEIGHTS&quot;,weights);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       7163 :   parseFlag(&quot;MASS&quot;,weight_mass);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       7163 :   parseFlag(&quot;NOPBC&quot;,nopbc);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       7163 :   parseFlag(&quot;PHASES&quot;,phases);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       7163 :   parse(&quot;SET_CHARGE&quot;,charge_);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       7163 :   if(!std::isnan(charge_)) isChargeSet_=true;</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       7163 :   parse(&quot;SET_MASS&quot;,mass_);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       7163 :   if(mass_&gt;0.) isMassSet_=true;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       7163 :   if(mass_==0.) error(&quot;SETMASS must be greater than 0&quot;);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       7163 :   if( getName()==&quot;COM&quot;) weight_mass=true;</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       7163 :   checkRead();</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       7163 :   log.printf(&quot;  of atoms:&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">      37425 :   for(unsigned i=0; i&lt;atoms.size(); ++i) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      30262 :     if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      30262 :     log.printf(&quot; %d&quot;,atoms[i].serial());</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       7163 :   log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       7163 :   if(weight_mass) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         77 :     log&lt;&lt;&quot;  mass weighted\n&quot;;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         77 :     if(weights.size()!=0) error(&quot;WEIGHTS and MASS keywords cannot not be used simultaneously&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   } else {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       7086 :     if( weights.size()==0) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        109 :       log&lt;&lt;&quot; using the geometric center\n&quot;;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        109 :       weights.resize( atoms.size() );</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">       1330 :       for(unsigned i=0; i&lt;atoms.size(); i++) weights[i] = 1.;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     } else {</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       6977 :       log&lt;&lt;&quot; with weights:&quot;;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       6979 :       if( weights.size()!=atoms.size() ) error(&quot;number of elements in weight vector does not match the number of atoms&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      35074 :       for(unsigned i=0; i&lt;weights.size(); ++i) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">      28098 :         if(i%25==0) log&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      28098 :         log.printf(&quot; %f&quot;,weights[i]);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :       }</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">       6976 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       7161 :   if(phases) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          3 :     log&lt;&lt;&quot;  Phases will be used to take into account PBC\n&quot;;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">       7158 :   } else if(nopbc) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         45 :     log&lt;&lt;&quot;  PBC will be ignored\n&quot;;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   } else {</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">       7113 :     log&lt;&lt;&quot;  broken molecules will be rebuilt assuming atoms are in the proper order\n&quot;;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       7161 :   requestAtoms(atoms);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       7165 : }</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">      13808 : void Center::calculate() {</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      13808 :   Vector pos;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   double mass(0.0);</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      13808 :   const bool dophases=(getPbc().isSet() ? phases : false);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">      13808 :   if(!nopbc &amp;&amp; !dophases) makeWhole();</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">      13808 :   if( first &amp;&amp; weight_mass) {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        725 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        659 :       if(std::isnan(getMass(i))) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :         error(</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :           &quot;You are trying to compute a CENTER or COM but masses are not known.\n&quot;</a>
+<a name="224"><span class="lineNum">     224 </span>            :           &quot;        If you are using plumed driver, please use the --mc option&quot;</a>
+<a name="225"><span class="lineNum">     225 </span>            :         );</a>
+<a name="226"><span class="lineNum">     226 </span>            :       }</a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         66 :     first=false;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      13808 :   std::vector&lt;Tensor&gt; deriv(getNumberOfAtoms());</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      93301 :   for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) mass+=getMass(i);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      13808 :   if( plumed.getAtoms().chargesWereSet() &amp;&amp; !isChargeSet_) {</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     double charge(0.0);</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">      60621 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) charge+=getCharge(i);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :     setCharge(charge);</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">       4066 :   } else if(isChargeSet_) {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         10 :     setCharge(charge_);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   } else {</a>
+<a name="240"><span class="lineNum">     240 </span>            :     setCharge(0.0);</a>
+<a name="241"><span class="lineNum">     241 </span>            :   }</a>
+<a name="242"><span class="lineNum">     242 </span>            :   double wtot=0.0;</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      57967 :   for(unsigned i=0; i&lt;weights.size(); i++) wtot+=weights[i];</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      13808 :   if(dophases) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        240 :     dcenter_sin.resize(getNumberOfAtoms());</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        240 :     dcenter_cos.resize(getNumberOfAtoms());</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        240 :     Vector center_sin;</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        240 :     Vector center_cos;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        240 :     Tensor invbox2pi=2*pi*getPbc().getInvBox();</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        240 :     Tensor box2pi=getPbc().getBox() / (2*pi);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        960 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :       double w=0;</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        720 :       if(weight_mass) w=getMass(i)/mass;</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        720 :       else w=weights[i]/wtot;</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            :       // real to scaled</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        720 :       const Vector scaled=matmul(getPosition(i),invbox2pi);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :       const Vector ccos(</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        720 :         w*std::cos(scaled[0]),</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        720 :         w*std::cos(scaled[1]),</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        720 :         w*std::cos(scaled[2])</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        720 :       );</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :       const Vector csin(</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">        720 :         w*std::sin(scaled[0]),</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        720 :         w*std::sin(scaled[1]),</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        720 :         w*std::sin(scaled[2])</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        720 :       );</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        720 :       center_cos+=ccos;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        720 :       center_sin+=csin;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">       9360 :       for(unsigned l=0; l&lt;3; l++) for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :           // k over real coordinates</a>
+<a name="273"><span class="lineNum">     273 </span>            :           // l over scaled coordinates</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">       6480 :           dcenter_sin[i][l][k]=ccos[l]*invbox2pi[k][l];</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       6480 :           dcenter_cos[i][l][k]=-csin[l]*invbox2pi[k][l];</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :         }</a>
+<a name="277"><span class="lineNum">     277 </span>            :     }</a>
+<a name="278"><span class="lineNum">     278 </span>            :     const Vector c(</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        240 :       std::atan2(center_sin[0],center_cos[0]),</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        240 :       std::atan2(center_sin[1],center_cos[1]),</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        240 :       std::atan2(center_sin[2],center_cos[2])</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        240 :     );</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :     // normalization is convenient for doing derivatives later</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        960 :     for(unsigned l=0; l&lt;3; l++) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">        720 :       double norm=1.0/(center_sin[l]*center_sin[l]+center_cos[l]*center_cos[l]);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        720 :       center_sin[l]*=norm;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        720 :       center_cos[l]*=norm;</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :     }</a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        960 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); ++i) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        720 :       Tensor dd;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       9360 :       for(unsigned l=0; l&lt;3; l++) for(unsigned k=0; k&lt;3; k++) {</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :           // k over real coordinates</a>
+<a name="295"><span class="lineNum">     295 </span>            :           // l over scaled coordinates</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       6480 :           dd[l][k]= (center_cos[l]*dcenter_sin[i][l][k] - center_sin[l]*dcenter_cos[i][l][k]);</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :         }</a>
+<a name="298"><span class="lineNum">     298 </span>            :       // scaled to real</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        720 :       deriv[i]=matmul(dd,box2pi);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     }</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        240 :     if(!isMassSet_) setMass(mass);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineNoCov">          0 :     else setMass(mass_);</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     setAtomsDerivatives(deriv);</a>
+<a name="304"><span class="lineNum">     304 </span>            :     // scaled to real</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        240 :     setPosition(matmul(c,box2pi));</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :   } else {</a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">      92341 :     for(unsigned i=0; i&lt;getNumberOfAtoms(); i++) {</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :       double w=0;</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">      78773 :       if(weight_mass) w=getMass(i)/mass;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">      43439 :       else w=weights[i]/wtot;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      78773 :       pos+=w*getPosition(i);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">      78773 :       deriv[i]=w*Tensor::identity();</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :     }</a>
+<a name="314"><span class="lineNum">     314 </span>            :     setPosition(pos);</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      13568 :     if(!isMassSet_) setMass(mass);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         10 :     else setMass(mass_);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     setAtomsDerivatives(deriv);</a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">      13808 : }</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : }</a>
+<a name="322"><span class="lineNum">     322 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/FixedAtom.cpp.func-sort-c.html b/coverage/vatom/FixedAtom.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6cf1c1ddda
--- /dev/null
+++ b/coverage/vatom/FixedAtom.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/FixedAtom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - FixedAtom.cpp<span style="font-size: 80%;"> (<a href="FixedAtom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FixedAtom.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#105">_ZN4PLMD5vatom9FixedAtomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#95">_ZN4PLMD5vatom12_GLOBAL__N_121FixedAtomRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#105">_ZN4PLMD5vatom9FixedAtomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#97">_ZN4PLMD5vatom9FixedAtom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#131">_ZN4PLMD5vatom9FixedAtom9calculateEv</a></td>
+              <td class="coverFnHi">603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#95">_ZN4PLMD5vatom12_GLOBAL__N_121FixedAtomRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#95">_ZN4PLMD5vatom12_GLOBAL__N_121FixedAtomRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/FixedAtom.cpp.func.html b/coverage/vatom/FixedAtom.cpp.func.html
new file mode 100644
index 0000000000..360f1a2bb2
--- /dev/null
+++ b/coverage/vatom/FixedAtom.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/FixedAtom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - FixedAtom.cpp<span style="font-size: 80%;"> (<a href="FixedAtom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FixedAtom.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#95">_ZN4PLMD5vatom12_GLOBAL__N_121FixedAtomRegisterMe976createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#95">_ZN4PLMD5vatom12_GLOBAL__N_121FixedAtomRegisterMe97C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#95">_ZN4PLMD5vatom12_GLOBAL__N_121FixedAtomRegisterMe97D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#97">_ZN4PLMD5vatom9FixedAtom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#131">_ZN4PLMD5vatom9FixedAtom9calculateEv</a></td>
+              <td class="coverFnHi">603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#105">_ZN4PLMD5vatom9FixedAtomC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FixedAtom.cpp.gcov.html#105">_ZN4PLMD5vatom9FixedAtomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/FixedAtom.cpp.gcov.html b/coverage/vatom/FixedAtom.cpp.gcov.html
new file mode 100644
index 0000000000..cfc5a425b3
--- /dev/null
+++ b/coverage/vatom/FixedAtom.cpp.gcov.html
@@ -0,0 +1,225 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/FixedAtom.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - FixedAtom.cpp<span style="font-size: 80%;"> (source / <a href="FixedAtom.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace vatom {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC VATOM FIXEDATOM</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Add a virtual atom in a fixed position.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : This action creates a virtual atom at a fixed position.</a>
+<a name="35"><span class="lineNum">      35 </span>            : The coordinates can be specified in Cartesian components (by default)</a>
+<a name="36"><span class="lineNum">      36 </span>            : or in scaled coordinates (SCALED_COMPONENTS).</a>
+<a name="37"><span class="lineNum">      37 </span>            : It is also possible to assign a predefined charge or mass to the atom.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \attention</a>
+<a name="40"><span class="lineNum">      40 </span>            : Similar to \ref POSITION this variable is not invariant for translation</a>
+<a name="41"><span class="lineNum">      41 </span>            : of the system. Adding a force on it can create serious troubles.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : Notice that the distance between two atoms created</a>
+<a name="44"><span class="lineNum">      44 </span>            : using FIXEDATOM is invariant for translation.</a>
+<a name="45"><span class="lineNum">      45 </span>            : Additionally, if one first align atoms to a reference using \ref FIT_TO_TEMPLATE,</a>
+<a name="46"><span class="lineNum">      46 </span>            : then it is safe to add further fixed atoms without breaking translational invariance.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : \par Examples</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The following input instructs plumed to compute the angle between</a>
+<a name="51"><span class="lineNum">      51 </span>            : distance of atoms 15 and 20 and the z axis and keeping it close to zero.</a>
+<a name="52"><span class="lineNum">      52 </span>            : \plumedfile</a>
+<a name="53"><span class="lineNum">      53 </span>            : a: FIXEDATOM AT=0,0,0</a>
+<a name="54"><span class="lineNum">      54 </span>            : b: FIXEDATOM AT=0,0,1</a>
+<a name="55"><span class="lineNum">      55 </span>            : an: ANGLE ATOMS=a,b,15,20</a>
+<a name="56"><span class="lineNum">      56 </span>            : RESTRAINT ARG=an AT=0.0 KAPPA=100.0</a>
+<a name="57"><span class="lineNum">      57 </span>            : \endplumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The following input instructs plumed to align a protein to a template</a>
+<a name="60"><span class="lineNum">      60 </span>            : and to then compute the distance between one of the atoms in the protein and the point</a>
+<a name="61"><span class="lineNum">      61 </span>            : (10,20,30).</a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : FIT_TO_TEMPLATE STRIDE=1 REFERENCE=ref.pdb TYPE=SIMPLE</a>
+<a name="64"><span class="lineNum">      64 </span>            : a: FIXEDATOM AT=10,20,30</a>
+<a name="65"><span class="lineNum">      65 </span>            : d: DISTANCE ATOMS=a,20</a>
+<a name="66"><span class="lineNum">      66 </span>            : PRINT ARG=d FILE=colvar</a>
+<a name="67"><span class="lineNum">      67 </span>            : \endplumedfile</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : The reference structure to align to is provided in a pdb file called ref.pdb as shown below:</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \auxfile{ref.pdb}</a>
+<a name="72"><span class="lineNum">      72 </span>            : ATOM      8  HT3 ALA     2      -1.480  -1.560   1.212  1.00  1.00      DIA  H</a>
+<a name="73"><span class="lineNum">      73 </span>            : ATOM      9  CAY ALA     2      -0.096   2.144  -0.669  1.00  1.00      DIA  C</a>
+<a name="74"><span class="lineNum">      74 </span>            : ATOM     10  HY1 ALA     2       0.871   2.385  -0.588  1.00  1.00      DIA  H</a>
+<a name="75"><span class="lineNum">      75 </span>            : ATOM     12  HY3 ALA     2      -0.520   2.679  -1.400  1.00  1.00      DIA  H</a>
+<a name="76"><span class="lineNum">      76 </span>            : ATOM     14  OY  ALA     2      -1.139   0.931  -0.973  1.00  1.00      DIA  O</a>
+<a name="77"><span class="lineNum">      77 </span>            : END</a>
+<a name="78"><span class="lineNum">      78 </span>            : \endauxfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : */</a>
+<a name="82"><span class="lineNum">      82 </span>            : //+ENDPLUMEDOC</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : class FixedAtom:</a>
+<a name="86"><span class="lineNum">      86 </span>            :   public ActionWithVirtualAtom</a>
+<a name="87"><span class="lineNum">      87 </span>            : {</a>
+<a name="88"><span class="lineNum">      88 </span>            :   Vector coord;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   double mass,charge;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   bool scaled_components;</a>
+<a name="91"><span class="lineNum">      91 </span>            : public:</a>
+<a name="92"><span class="lineNum">      92 </span>            :   explicit FixedAtom(const ActionOptions&amp;ao);</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void calculate() override;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="95"><span class="lineNum">      95 </span>            : };</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">      12522 : PLUMED_REGISTER_ACTION(FixedAtom,&quot;FIXEDATOM&quot;)</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         11 : void FixedAtom::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         11 :   ActionWithVirtualAtom::registerKeywords(keys);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;AT&quot;,&quot;coordinates of the virtual atom&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;SET_MASS&quot;,&quot;1&quot;,&quot;mass of the virtual atom&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;SET_CHARGE&quot;,&quot;0&quot;,&quot;charge of the virtual atom&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         22 :   keys.addFlag(&quot;SCALED_COMPONENTS&quot;,false,&quot;use scaled components&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         11 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          9 : FixedAtom::FixedAtom(const ActionOptions&amp;ao):</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   Action(ao),</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          9 :   ActionWithVirtualAtom(ao)</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : {</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         18 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          9 :   if(atoms.size()!=0) error(&quot;ATOMS should be empty&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         18 :   parseFlag(&quot;SCALED_COMPONENTS&quot;,scaled_components);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::vector&lt;double&gt; at;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         18 :   parseVector(&quot;AT&quot;,at);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          9 :   if(at.size()!=3) error(&quot;AT should be a list of three real numbers&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          9 :   parse(&quot;SET_MASS&quot;,mass);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         18 :   parse(&quot;SET_CHARGE&quot;,charge);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          9 :   coord[0]=at[0];</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          9 :   coord[1]=at[1];</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          9 :   coord[2]=at[2];</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          9 :   log&lt;&lt;&quot;  AT position &quot;&lt;&lt;coord[0]&lt;&lt;&quot; &quot;&lt;&lt;coord[1]&lt;&lt;&quot; &quot;&lt;&lt;coord[2]&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          9 :   if(scaled_components) log&lt;&lt;&quot;  position is in scaled components\n&quot;;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          9 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        603 : void FixedAtom::calculate() {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        603 :   std::vector&lt;Tensor&gt; deriv(getNumberOfAtoms());</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        603 :   if(scaled_components) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          5 :     setPosition(getPbc().scaledToReal(coord));</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   } else {</a>
+<a name="138"><span class="lineNum">     138 </span>            :     setPosition(coord);</a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        603 :   setMass(mass);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        603 :   setCharge(charge);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   setAtomsDerivatives(deriv);</a>
+<a name="143"><span class="lineNum">     143 </span>            : // Virial contribution</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        603 :   if(!scaled_components) setBoxDerivativesNoPbc();</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : // notice that with scaled components there is no additional virial contribution</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        603 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/Ghost.cpp.func-sort-c.html b/coverage/vatom/Ghost.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3e976a4e50
--- /dev/null
+++ b/coverage/vatom/Ghost.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/Ghost.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - Ghost.cpp<span style="font-size: 80%;"> (<a href="Ghost.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Ghost.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#67">_ZN4PLMD5vatom5GhostC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#60">_ZN4PLMD5vatom12_GLOBAL__N_117GhostRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#67">_ZN4PLMD5vatom5GhostC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#62">_ZN4PLMD5vatom5Ghost16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#85">_ZN4PLMD5vatom5Ghost9calculateEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#60">_ZN4PLMD5vatom12_GLOBAL__N_117GhostRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#60">_ZN4PLMD5vatom12_GLOBAL__N_117GhostRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/Ghost.cpp.func.html b/coverage/vatom/Ghost.cpp.func.html
new file mode 100644
index 0000000000..3307ec6915
--- /dev/null
+++ b/coverage/vatom/Ghost.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/Ghost.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - Ghost.cpp<span style="font-size: 80%;"> (<a href="Ghost.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Ghost.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#60">_ZN4PLMD5vatom12_GLOBAL__N_117GhostRegisterMe626createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#60">_ZN4PLMD5vatom12_GLOBAL__N_117GhostRegisterMe62C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#60">_ZN4PLMD5vatom12_GLOBAL__N_117GhostRegisterMe62D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#62">_ZN4PLMD5vatom5Ghost16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#85">_ZN4PLMD5vatom5Ghost9calculateEv</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#67">_ZN4PLMD5vatom5GhostC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Ghost.cpp.gcov.html#67">_ZN4PLMD5vatom5GhostC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/Ghost.cpp.gcov.html b/coverage/vatom/Ghost.cpp.gcov.html
new file mode 100644
index 0000000000..e053a1646c
--- /dev/null
+++ b/coverage/vatom/Ghost.cpp.gcov.html
@@ -0,0 +1,260 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom/Ghost.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vatom</a> - Ghost.cpp<span style="font-size: 80%;"> (source / <a href="Ghost.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithVirtualAtom.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace vatom {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : //+PLUMEDOC VATOM GHOST</a>
+<a name="31"><span class="lineNum">      31 </span>            : /*</a>
+<a name="32"><span class="lineNum">      32 </span>            : Calculate the absolute position of a ghost atom with fixed coordinates in the local reference frame formed by three atoms.</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : The computed ghost atom is stored as a virtual atom that can be accessed in</a>
+<a name="35"><span class="lineNum">      35 </span>            :  an atom list through the the label for the GHOST action that creates it.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \par Examples</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : The following input instructs plumed to print the distance between the</a>
+<a name="40"><span class="lineNum">      40 </span>            : ghost atom and the center of mass for atoms 15,20:</a>
+<a name="41"><span class="lineNum">      41 </span>            : \plumedfile</a>
+<a name="42"><span class="lineNum">      42 </span>            : c1: GHOST ATOMS=1,5,10 COORDINATES=10.0,10.0,10.0</a>
+<a name="43"><span class="lineNum">      43 </span>            : c2: COM ATOMS=15,20</a>
+<a name="44"><span class="lineNum">      44 </span>            : d1: DISTANCE ATOMS=c1,c2</a>
+<a name="45"><span class="lineNum">      45 </span>            : PRINT ARG=d1</a>
+<a name="46"><span class="lineNum">      46 </span>            : \endplumedfile</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : */</a>
+<a name="49"><span class="lineNum">      49 </span>            : //+ENDPLUMEDOC</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : class Ghost:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   public ActionWithVirtualAtom</a>
+<a name="54"><span class="lineNum">      54 </span>            : {</a>
+<a name="55"><span class="lineNum">      55 </span>            :   std::vector&lt;double&gt; coord;</a>
+<a name="56"><span class="lineNum">      56 </span>            : public:</a>
+<a name="57"><span class="lineNum">      57 </span>            :   explicit Ghost(const ActionOptions&amp;ao);</a>
+<a name="58"><span class="lineNum">      58 </span>            :   void calculate() override;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(Ghost,&quot;GHOST&quot;)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          5 : void Ghost::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          5 :   ActionWithVirtualAtom::registerKeywords(keys);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         10 :   keys.add(&quot;atoms&quot;,&quot;COORDINATES&quot;,&quot;coordinates of the ghost atom in the local reference frame&quot;);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          5 : }</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          3 : Ghost::Ghost(const ActionOptions&amp;ao):</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   Action(ao),</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          3 :   ActionWithVirtualAtom(ao)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;AtomNumber&gt; atoms;</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          6 :   parseAtomList(&quot;ATOMS&quot;,atoms);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          3 :   if(atoms.size()!=3) error(&quot;ATOMS should contain a list of three atoms&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          6 :   parseVector(&quot;COORDINATES&quot;,coord);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          3 :   if(coord.size()!=3) error(&quot;COORDINATES should be a list of three real numbers&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          3 :   log.printf(&quot;  of atoms&quot;);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         12 :   for(unsigned i=0; i&lt;atoms.size(); ++i) log.printf(&quot; %d&quot;,atoms[i].serial());</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          3 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          3 :   requestAtoms(atoms);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          3 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          7 : void Ghost::calculate() {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          7 :   Vector pos;</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          7 :   std::vector&lt;Tensor&gt; deriv(getNumberOfAtoms());</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;Vector&gt; n;</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : // first versor</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          7 :   Vector n01 = delta(getPosition(0), getPosition(1));</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         14 :   n.push_back(n01/n01.modulo());</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : // auxiliary vector</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          7 :   Vector n02 = delta(getPosition(0), getPosition(2));</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : // second versor</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          7 :   Vector n03 = crossProduct(n[0],n02);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          7 :   double n03_norm = n03.modulo();</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         14 :   n.push_back(n03/n03_norm);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : // third versor</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         14 :   n.push_back(crossProduct(n[0],n[1]));</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : // origin of the reference system</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          7 :   pos = getPosition(0);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         28 :   for(unsigned i=0; i&lt;3; ++i) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         21 :     pos += coord[i] * n[i];</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   setPosition(pos);</a>
+<a name="115"><span class="lineNum">     115 </span>            :   setMass(1.0);</a>
+<a name="116"><span class="lineNum">     116 </span>            :   setCharge(0.0);</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : // some useful tensors for derivatives</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          7 :   Tensor dn0d0  = (-Tensor::identity()+Tensor(n[0],n[0]))/n01.modulo();</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          7 :   Tensor dn0d1  = (+Tensor::identity()-Tensor(n[0],n[0]))/n01.modulo();</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          7 :   Tensor dn02d0 = -Tensor::identity();</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          7 :   Tensor dn02d2 =  Tensor::identity();</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : // derivative of n1 = n0 x n02</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          7 :   Tensor dn1d0, dn1d1, dn1d2;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          7 :   Vector aux0, aux1, aux2;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         28 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : // derivative of n0 x n02 with respect to point 0, coordinate j</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         21 :     Vector tmp00  = Vector( dn0d0(j,0),  dn0d0(j,1),  dn0d0(j,2));</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         21 :     Vector tmp020 = Vector(dn02d0(j,0), dn02d0(j,1), dn02d0(j,2));</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         21 :     Vector tmp0   = crossProduct(tmp00,n02) + crossProduct(n[0],tmp020);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         21 :     aux0[j]       = dotProduct(tmp0,n[1]);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : // derivative of n0 x n02 with respect to point 1, coordinate j</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         21 :     Vector tmp01  = Vector( dn0d1(j,0),  dn0d1(j,1),  dn0d1(j,2));</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         21 :     Vector tmp1   = crossProduct(tmp01,n02);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         21 :     aux1[j]       = dotProduct(tmp1,n[1]);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : // derivative of n0 x n02 with respect to point 2, coordinate j</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         21 :     Vector tmp022 = Vector(dn02d2(j,0), dn02d2(j,1), dn02d2(j,2));</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         21 :     Vector tmp2   = crossProduct(n[0],tmp022);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         21 :     aux2[j]       = dotProduct(tmp2,n[1]);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : // derivative of n1 = (n0 x n02) / || (n0 x n02) ||</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         84 :     for(unsigned i=0; i&lt;3; ++i) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         63 :       dn1d0(j,i) = ( tmp0[i] - aux0[j] * n[1][i] ) / n03_norm;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         63 :       dn1d1(j,i) = ( tmp1[i] - aux1[j] * n[1][i] ) / n03_norm;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         63 :       dn1d2(j,i) = ( tmp2[i] - aux2[j] * n[1][i] ) / n03_norm;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : // Derivative of the last versor n2 = n0 x n1 =  ( n0( n0 n02 ) - n02 ) / || n0 x n02 ||</a>
+<a name="151"><span class="lineNum">     151 </span>            : // Scalar product and derivatives</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          7 :   double n0_n02 = dotProduct(n[0],n02);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          7 :   Vector dn0_n02d0, dn0_n02d1, dn0_n02d2;</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         28 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         84 :     for(unsigned i=0; i&lt;3; ++i) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         63 :       dn0_n02d0[j] += dn0d0(j,i)*n02[i] + n[0][i]*dn02d0(j,i);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         63 :       dn0_n02d1[j] += dn0d1(j,i)*n02[i];</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         63 :       dn0_n02d2[j] +=                     n[0][i]*dn02d2(j,i);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          7 :   Tensor dn2d0, dn2d1, dn2d2;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         28 :   for(unsigned j=0; j&lt;3; ++j) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         84 :     for(unsigned i=0; i&lt;3; ++i) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         63 :       dn2d0(j,i) = ( dn0d0(j,i) * n0_n02 + n[0][i] * dn0_n02d0[j] - dn02d0(j,i) - ( n[0][i] * n0_n02 - n02[i] ) * aux0[j] / n03_norm ) / n03_norm;</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         63 :       dn2d1(j,i) = ( dn0d1(j,i) * n0_n02 + n[0][i] * dn0_n02d1[j]               - ( n[0][i] * n0_n02 - n02[i] ) * aux1[j] / n03_norm ) / n03_norm;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         63 :       dn2d2(j,i) = (                       n[0][i] * dn0_n02d2[j] - dn02d2(j,i) - ( n[0][i] * n0_n02 - n02[i] ) * aux2[j] / n03_norm ) / n03_norm;</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : // Finally, the derivative tensor</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          7 :   deriv[0] = Tensor::identity() + coord[0]*dn0d0 + coord[1]*dn1d0 + coord[2]*dn2d0;</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          7 :   deriv[1] =                      coord[0]*dn0d1 + coord[1]*dn1d1 + coord[2]*dn2d1;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          7 :   deriv[2] =                                       coord[1]*dn1d2 + coord[2]*dn2d2;</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            :   setAtomsDerivatives(deriv);</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : // Virial contribution</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          7 :   setBoxDerivativesNoPbc();</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          7 : }</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : }</a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/index-sort-f.html b/coverage/vatom/index-sort-f.html
new file mode 100644
index 0000000000..b42412aa10
--- /dev/null
+++ b/coverage/vatom/index-sort-f.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - vatom</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">221</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryHi">99.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Ghost.cpp.gcov.html">Ghost.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">69 / 69</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FixedAtom.cpp.gcov.html">FixedAtom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Center.cpp.gcov.html">Center.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">120 / 122</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/index-sort-l.html b/coverage/vatom/index-sort-l.html
new file mode 100644
index 0000000000..3925ab71be
--- /dev/null
+++ b/coverage/vatom/index-sort-l.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - vatom</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">221</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryHi">99.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Center.cpp.gcov.html">Center.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">120 / 122</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FixedAtom.cpp.gcov.html">FixedAtom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Ghost.cpp.gcov.html">Ghost.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">69 / 69</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vatom/index.html b/coverage/vatom/index.html
new file mode 100644
index 0000000000..1d571c1a65
--- /dev/null
+++ b/coverage/vatom/index.html
@@ -0,0 +1,113 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vatom</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - vatom</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">221</td>
+            <td class="headerCovTableEntry">223</td>
+            <td class="headerCovTableEntryHi">99.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Center.cpp.gcov.html">Center.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.4%"><img src="../snow.png" width=2 height=10 alt="98.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.4&nbsp;%</td>
+      <td class="coverNumHi">120 / 122</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FixedAtom.cpp.gcov.html">FixedAtom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Ghost.cpp.gcov.html">Ghost.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">69 / 69</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Chebyshev.cpp.func-sort-c.html b/coverage/ves/BF_Chebyshev.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3c80aeb297
--- /dev/null
+++ b/coverage/ves/BF_Chebyshev.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Chebyshev.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Chebyshev.cpp<span style="font-size: 80%;"> (<a href="BF_Chebyshev.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Chebyshev.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#141">_ZN4PLMD3ves12BF_Chebyshev21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#104">_ZN4PLMD3ves12BF_ChebyshevC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_124BF_ChebyshevRegisterMe996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#100">_ZN4PLMD3ves12BF_Chebyshev16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_124BF_ChebyshevRegisterMe99C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_124BF_ChebyshevRegisterMe99D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#119">_ZNK4PLMD3ves12BF_Chebyshev12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">7882</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Chebyshev.cpp.func.html b/coverage/ves/BF_Chebyshev.cpp.func.html
new file mode 100644
index 0000000000..1b543ec328
--- /dev/null
+++ b/coverage/ves/BF_Chebyshev.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Chebyshev.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Chebyshev.cpp<span style="font-size: 80%;"> (<a href="BF_Chebyshev.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Chebyshev.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#100">_ZN4PLMD3ves12BF_Chebyshev16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#141">_ZN4PLMD3ves12BF_Chebyshev21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#104">_ZN4PLMD3ves12BF_ChebyshevC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_124BF_ChebyshevRegisterMe996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_124BF_ChebyshevRegisterMe99C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_124BF_ChebyshevRegisterMe99D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Chebyshev.cpp.gcov.html#119">_ZNK4PLMD3ves12BF_Chebyshev12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">7882</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Chebyshev.cpp.gcov.html b/coverage/ves/BF_Chebyshev.cpp.gcov.html
new file mode 100644
index 0000000000..e98ba0014f
--- /dev/null
+++ b/coverage/ves/BF_Chebyshev.cpp.gcov.html
@@ -0,0 +1,232 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Chebyshev.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Chebyshev.cpp<span style="font-size: 80%;"> (source / <a href="BF_Chebyshev.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_CHEBYSHEV</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Chebyshev polynomial basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Use as basis functions [Chebyshev polynomials](https://en.wikipedia.org/wiki/Chebyshev_polynomials)</a>
+<a name="36"><span class="lineNum">      36 </span>            : of the first kind \f$T_{n}(x)\f$ defined on a bounded interval.</a>
+<a name="37"><span class="lineNum">      37 </span>            : You need to provide the interval \f$[a,b]\f$</a>
+<a name="38"><span class="lineNum">      38 </span>            : on which the basis functions are to be used, and the order of the</a>
+<a name="39"><span class="lineNum">      39 </span>            : expansion \f$N\f$ (i.e. the highest order polynomial used).</a>
+<a name="40"><span class="lineNum">      40 </span>            : The total number of basis functions is \f$N+1\f$ as the constant \f$T_{0}(x)=1\f$</a>
+<a name="41"><span class="lineNum">      41 </span>            : is also included.</a>
+<a name="42"><span class="lineNum">      42 </span>            : These basis functions should not be used for periodic CVs.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : Intrinsically the Chebyshev polynomials are defined on the interval \f$[-1,1]\f$.</a>
+<a name="45"><span class="lineNum">      45 </span>            : A variable \f$t\f$ in the interval \f$[a,b]\f$ is transformed to a variable \f$x\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : in the intrinsic interval \f$[-1,1]\f$ by using the transform function</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            : x(t) = \frac{t-(a+b)/2}</a>
+<a name="49"><span class="lineNum">      49 </span>            : {(b-a)/2}</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The Chebyshev polynomials are given by the recurrence relation</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f{align}{</a>
+<a name="54"><span class="lineNum">      54 </span>            : T_{0}(x)    &amp;= 1 \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : T_{1}(x)    &amp;= x \\</a>
+<a name="56"><span class="lineNum">      56 </span>            : T_{n+1}(x)  &amp;= 2 \, x \, T_{n}(x) - T_{n-1}(x)</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f}</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The first 6 polynomials are shown below</a>
+<a name="60"><span class="lineNum">      60 </span>            : \image html ves_basisf-chebyshev.png</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The Chebyshev polynomial are orthogonal over the interval \f$[-1,1]\f$</a>
+<a name="63"><span class="lineNum">      63 </span>            : with respect to the weight \f$\frac{1}{\sqrt{1-x^2}}\f$</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f[</a>
+<a name="65"><span class="lineNum">      65 </span>            : \int_{-1}^{1} dx \, T_{n}(x)\, T_{m}(x) \, \frac{1}{\sqrt{1-x^2}} =</a>
+<a name="66"><span class="lineNum">      66 </span>            : \begin{cases}</a>
+<a name="67"><span class="lineNum">      67 </span>            : 0 &amp; n \neq m \\</a>
+<a name="68"><span class="lineNum">      68 </span>            : \pi &amp; n = m = 0 \\</a>
+<a name="69"><span class="lineNum">      69 </span>            : \pi/2 &amp; n = m \neq 0</a>
+<a name="70"><span class="lineNum">      70 </span>            : \end{cases}</a>
+<a name="71"><span class="lineNum">      71 </span>            : \f]</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : For further mathematical properties of the Chebyshev polynomials see for example</a>
+<a name="74"><span class="lineNum">      74 </span>            : the [Wikipedia page](https://en.wikipedia.org/wiki/Chebyshev_polynomials).</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \par Examples</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : Here we employ a Chebyshev expansion of order 20 over the interval 0.0 to 10.0.</a>
+<a name="79"><span class="lineNum">      79 </span>            : This results in a total number of 21 basis functions.</a>
+<a name="80"><span class="lineNum">      80 </span>            : The label used to identify  the basis function action can then be</a>
+<a name="81"><span class="lineNum">      81 </span>            : referenced later on in the input file.</a>
+<a name="82"><span class="lineNum">      82 </span>            : \plumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : bfC: BF_CHEBYSHEV MINIMUM=0.0 MAXIMUM=10.0 ORDER=20</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endplumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : */</a>
+<a name="87"><span class="lineNum">      87 </span>            : //+ENDPLUMEDOC</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : class BF_Chebyshev : public BasisFunctions {</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void setupUniformIntegrals() override;</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            :   explicit BF_Chebyshev(const ActionOptions&amp;);</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(BF_Chebyshev,&quot;BF_CHEBYSHEV&quot;)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          6 : void BF_Chebyshev::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          6 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          6 : }</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          4 : BF_Chebyshev::BF_Chebyshev(const ActionOptions&amp;ao):</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          4 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : {</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   setNumberOfBasisFunctions(getOrder()+1);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          8 :   setIntrinsicInterval(&quot;-1.0&quot;,&quot;+1.0&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   setNonPeriodic();</a>
+<a name="112"><span class="lineNum">     112 </span>            :   setIntervalBounded();</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 :   setType(&quot;chebyshev-1st-kind&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          4 :   setDescription(&quot;Chebyshev polynomials of the first kind&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          4 :   setLabelPrefix(&quot;T&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          4 :   setupBF();</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          4 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       7882 : void BF_Chebyshev::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   // plumed_assert(values.size()==numberOfBasisFunctions());</a>
+<a name="123"><span class="lineNum">     123 </span>            :   // plumed_assert(derivs.size()==numberOfBasisFunctions());</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">       7882 :   inside_range=true;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">       7882 :   argT=translateArgument(arg, inside_range);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">       7882 :   std::vector&lt;double&gt; derivsT(derivs.size());</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   //</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">       7882 :   values[0]=1.0;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       7882 :   derivsT[0]=0.0;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       7882 :   derivs[0]=0.0;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">       7882 :   values[1]=argT;</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       7882 :   derivsT[1]=1.0;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       7882 :   derivs[1]=intervalDerivf();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     135100 :   for(unsigned int i=1; i &lt; getOrder(); i++) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">     127218 :     values[i+1]  = 2.0*argT*values[i]-values[i-1];</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     127218 :     derivsT[i+1] = 2.0*values[i]+2.0*argT*derivsT[i]-derivsT[i-1];</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">     127218 :     derivs[i+1]  = intervalDerivf()*derivsT[i+1];</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">       9906 :   if(!inside_range) {for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}}</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       7882 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 : void BF_Chebyshev::setupUniformIntegrals() {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         56 :   for(unsigned int i=0; i&lt;numberOfBasisFunctions(); i++) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         53 :     double io = i;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :     double value = 0.0;</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         53 :     if(i % 2 == 0) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         28 :       value = -2.0/( pow(io,2.0)-1.0)*0.5;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :     }</a>
+<a name="150"><span class="lineNum">     150 </span>            :     setUniformIntegral(i,value);</a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          3 : }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+</body>
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diff --git a/coverage/ves/BF_Combined.cpp.func-sort-c.html b/coverage/ves/BF_Combined.cpp.func-sort-c.html
new file mode 100644
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@@ -0,0 +1,104 @@
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Combined.cpp<span style="font-size: 80%;"> (<a href="BF_Combined.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Combined.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#174">_ZN4PLMD3ves11BF_Combined11setupLabelsEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#186">_ZN4PLMD3ves11BF_Combined21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#89">_ZN4PLMD3ves11BF_CombinedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#75">_ZN4PLMD3ves12_GLOBAL__N_123BF_CombinedRegisterMe776createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#78">_ZN4PLMD3ves11BF_Combined16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#148">_ZNK4PLMD3ves11BF_Combined12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">3616</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#75">_ZN4PLMD3ves12_GLOBAL__N_123BF_CombinedRegisterMe77C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#75">_ZN4PLMD3ves12_GLOBAL__N_123BF_CombinedRegisterMe77D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/ves/BF_Combined.cpp.func.html b/coverage/ves/BF_Combined.cpp.func.html
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+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
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+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
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+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
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+
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+
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#78">_ZN4PLMD3ves11BF_Combined16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
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+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#186">_ZN4PLMD3ves11BF_Combined21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#89">_ZN4PLMD3ves11BF_CombinedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#75">_ZN4PLMD3ves12_GLOBAL__N_123BF_CombinedRegisterMe776createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#75">_ZN4PLMD3ves12_GLOBAL__N_123BF_CombinedRegisterMe77C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#75">_ZN4PLMD3ves12_GLOBAL__N_123BF_CombinedRegisterMe77D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Combined.cpp.gcov.html#148">_ZNK4PLMD3ves11BF_Combined12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">3616</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <title>LCOV - plumed test coverage - ves/BF_Combined.cpp</title>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Combined.cpp<span style="font-size: 80%;"> (source / <a href="BF_Combined.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace ves {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC VES_BASISF BF_COMBINED</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Combining other basis functions types</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : \par Examples</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : Here we define both Fourier cosine and sine expansions of order 10,</a>
+<a name="41"><span class="lineNum">      41 </span>            : each with 11 basis functions, which are combined. This results</a>
+<a name="42"><span class="lineNum">      42 </span>            : in a total number of 21 basis functions as only the constant from</a>
+<a name="43"><span class="lineNum">      43 </span>            : is bf_cos is used.</a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : bf_cos: BF_COSINE MINIMUM=-pi MAXIMUM=+pi ORDER=10</a>
+<a name="46"><span class="lineNum">      46 </span>            : bf_sin: BF_SINE   MINIMUM=-pi MAXIMUM=+pi ORDER=10</a>
+<a name="47"><span class="lineNum">      47 </span>            : bf_comb: BF_COMBINED BASIS_FUNCTIONS=bf_cos,bf_sin</a>
+<a name="48"><span class="lineNum">      48 </span>            : \endplumedfile</a>
+<a name="49"><span class="lineNum">      49 </span>            : In principle this is the same as using BF_FOURIER with</a>
+<a name="50"><span class="lineNum">      50 </span>            : ORDER=10 but with different ordering of the basis functions.</a>
+<a name="51"><span class="lineNum">      51 </span>            : Note that the order used in BASIS_FUNCTIONS matters for the ordering</a>
+<a name="52"><span class="lineNum">      52 </span>            : of the basis functions, using BASIS_FUNCTIONS=bf_sin,bf_cos would</a>
+<a name="53"><span class="lineNum">      53 </span>            : results in a different order of the basis functions.</a>
+<a name="54"><span class="lineNum">      54 </span>            : This should be kept in mind when restarting from previous</a>
+<a name="55"><span class="lineNum">      55 </span>            : coefficients.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : */</a>
+<a name="63"><span class="lineNum">      63 </span>            : //+ENDPLUMEDOC</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : class BF_Combined : public BasisFunctions {</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;BasisFunctions*&gt; basisf_pntrs_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void setupLabels() override;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   void setupUniformIntegrals() override;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // void getBFandValueIndices(const unsigned int, unsigned int&amp;, unsigned int&amp;) const;</a>
+<a name="70"><span class="lineNum">      70 </span>            : public:</a>
+<a name="71"><span class="lineNum">      71 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="72"><span class="lineNum">      72 </span>            :   explicit BF_Combined(const ActionOptions&amp;);</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="74"><span class="lineNum">      74 </span>            : };</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(BF_Combined,&quot;BF_COMBINED&quot;)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          4 : void BF_Combined::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   keys.remove(&quot;ORDER&quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   keys.remove(&quot;MAXIMUM&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          4 :   keys.remove(&quot;MINIMUM&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          4 :   keys.remove(&quot;NUMERICAL_INTEGRALS&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          4 :   keys.remove(&quot;NGRID_POINTS&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;BASIS_FUNCTIONS&quot;,&quot;Labels of the basis functions that should be combined. Note that the order used matters for the ordering of the basis functions. This needs to be kept in mind when restarting from previous coefficients.&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          4 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          2 : BF_Combined::BF_Combined(const ActionOptions&amp;ao):</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   PLUMED_VES_BASISFUNCTIONS_INIT(ao),</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          2 :   basisf_pntrs_(0)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : {</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::vector&lt;std::string&gt; basisf_labels;</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 :   parseVector(&quot;BASIS_FUNCTIONS&quot;,basisf_labels); addKeywordToList(&quot;BASIS_FUNCTIONS&quot;,basisf_labels);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   if(basisf_labels.size()==1) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;using only one basis function in BF_COMBINED does not make sense&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 :   basisf_pntrs_ = VesTools::getPointersFromLabels&lt;BasisFunctions*&gt;(basisf_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          2 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword BASIS_FUNCTIONS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   unsigned int nbasisf_total_ = 1;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   bool periodic = true;</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          7 :   for(unsigned int i=0; i&lt;basisf_pntrs_.size(); i++) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          5 :     nbasisf_total_ += basisf_pntrs_[i]-&gt;getNumberOfBasisFunctions() - 1;</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         15 :     if(basisf_pntrs_[i]-&gt;intervalMinStr()!=basisf_pntrs_[0]-&gt;intervalMinStr() || basisf_pntrs_[i]-&gt;intervalMaxStr()!=basisf_pntrs_[0]-&gt;intervalMaxStr()) {</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;all the basis functions to be combined should have same MINIMUM and MAXIMUM&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     }</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          5 :     if(!basisf_pntrs_[i]-&gt;arePeriodic()) {periodic=false;}</span></a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :   setOrder(nbasisf_total_-1);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          2 :   setNumberOfBasisFunctions(nbasisf_total_);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          4 :   setInterval(basisf_pntrs_[0]-&gt;intervalMinStr(),basisf_pntrs_[0]-&gt;intervalMaxStr());</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          4 :   setIntrinsicInterval(&quot;-1.0&quot;,&quot;+1.0&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          2 :   if(periodic) {setPeriodic();}</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   else {setNonPeriodic();}</a>
+<a name="119"><span class="lineNum">     119 </span>            :   setIntervalBounded();</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   setType(&quot;combined&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   setDescription(&quot;Combined&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   setupBF();</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : // void BF_Combined::getBFandValueIndices(const unsigned int n, unsigned int&amp; bf_index, unsigned int&amp; value_index) const {</a>
+<a name="128"><span class="lineNum">     128 </span>            : //   bf_index = 0; value_index = 0;</a>
+<a name="129"><span class="lineNum">     129 </span>            : //   if(n==0){</a>
+<a name="130"><span class="lineNum">     130 </span>            : //     bf_index = 0;</a>
+<a name="131"><span class="lineNum">     131 </span>            : //     value_index = 0;</a>
+<a name="132"><span class="lineNum">     132 </span>            : //     return;</a>
+<a name="133"><span class="lineNum">     133 </span>            : //   }</a>
+<a name="134"><span class="lineNum">     134 </span>            : //   else{</a>
+<a name="135"><span class="lineNum">     135 </span>            : //     unsigned int r=1;</a>
+<a name="136"><span class="lineNum">     136 </span>            : //     for(unsigned int i=0; i&lt;basisf_pntrs_.size(); i++){</a>
+<a name="137"><span class="lineNum">     137 </span>            : //       for(unsigned int l=1; l&lt;basisf_pntrs_[i]-&gt;numberOfBasisFunctions(); l++){</a>
+<a name="138"><span class="lineNum">     138 </span>            : //         if(r==n){</a>
+<a name="139"><span class="lineNum">     139 </span>            : //           bf_index = i;</a>
+<a name="140"><span class="lineNum">     140 </span>            : //           value_index = l;</a>
+<a name="141"><span class="lineNum">     141 </span>            : //           return;</a>
+<a name="142"><span class="lineNum">     142 </span>            : //         }</a>
+<a name="143"><span class="lineNum">     143 </span>            : //         r++;</a>
+<a name="144"><span class="lineNum">     144 </span>            : //       }</a>
+<a name="145"><span class="lineNum">     145 </span>            : //     }</a>
+<a name="146"><span class="lineNum">     146 </span>            : //   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : // }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       3616 : void BF_Combined::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   // first BF, constant, argT, and inside_range taken from here</a>
+<a name="152"><span class="lineNum">     152 </span>            :   unsigned int r=0;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       3616 :   std::vector&lt;double&gt; values_tmp(basisf_pntrs_[0]-&gt;numberOfBasisFunctions(),0.0);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       3616 :   std::vector&lt;double&gt; derivs_tmp(basisf_pntrs_[0]-&gt;numberOfBasisFunctions(),0.0);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       3616 :   basisf_pntrs_[0]-&gt;getAllValues(arg,argT,inside_range,values_tmp,derivs_tmp);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">      43392 :   for(unsigned int l=0; l&lt;basisf_pntrs_[0]-&gt;numberOfBasisFunctions(); l++) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      39776 :     values[r] = values_tmp[l];</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      39776 :     derivs[r] = derivs_tmp[l];</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      39776 :     r++;</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            :   // other BF</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       9043 :   for(unsigned int i=1; i&lt;basisf_pntrs_.size(); i++) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       5427 :     values_tmp.assign(basisf_pntrs_[i]-&gt;numberOfBasisFunctions(),0.0);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       5427 :     derivs_tmp.assign(basisf_pntrs_[i]-&gt;numberOfBasisFunctions(),0.0);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       5427 :     double dummy_dbl; bool dummy_bool=true;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       5427 :     basisf_pntrs_[i]-&gt;getAllValues(arg,dummy_dbl,dummy_bool,values_tmp,derivs_tmp);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">      59697 :     for(unsigned int l=1; l&lt;basisf_pntrs_[i]-&gt;numberOfBasisFunctions(); l++) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      54270 :       values[r] = values_tmp[l];</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      54270 :       derivs[r] = derivs_tmp[l];</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      54270 :       r++;</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     }</a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       3616 : }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 : void BF_Combined::setupLabels() {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   setLabel(0,basisf_pntrs_[0]-&gt;getBasisFunctionLabel(0));</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   unsigned int r=1;</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          7 :   for(unsigned int i=0; i&lt;basisf_pntrs_.size(); i++) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         55 :     for(unsigned int l=1; l&lt;basisf_pntrs_[i]-&gt;numberOfBasisFunctions(); l++) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         50 :       setLabel(r,basisf_pntrs_[i]-&gt;getBasisFunctionLabel(l));</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         50 :       r++;</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :     }</a>
+<a name="184"><span class="lineNum">     184 </span>            :   }</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          2 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 : void BF_Combined::setupUniformIntegrals() {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          2 :   setUniformIntegral(0,basisf_pntrs_[0]-&gt;getUniformIntegrals()[0]);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :   unsigned int r=1;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          7 :   for(unsigned int i=0; i&lt;basisf_pntrs_.size(); i++) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          5 :     std::vector&lt;double&gt; uniform_tmp = basisf_pntrs_[i]-&gt;getUniformIntegrals();</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         55 :     for(unsigned int l=1; l&lt;basisf_pntrs_[i]-&gt;numberOfBasisFunctions(); l++) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         50 :       setUniformIntegral(r,uniform_tmp[l]);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         50 :       r++;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :     }</a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          2 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Cosine.cpp.func-sort-c.html b/coverage/ves/BF_Cosine.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4fabddd6c6
--- /dev/null
+++ b/coverage/ves/BF_Cosine.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Cosine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Cosine.cpp<span style="font-size: 80%;"> (<a href="BF_Cosine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Cosine.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#143">_ZN4PLMD3ves9BF_Cosine21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#92">_ZN4PLMD3ves12_GLOBAL__N_121BF_CosineRegisterMe946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#134">_ZN4PLMD3ves9BF_Cosine11setupLabelsEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#100">_ZN4PLMD3ves9BF_CosineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#95">_ZN4PLMD3ves9BF_Cosine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#92">_ZN4PLMD3ves12_GLOBAL__N_121BF_CosineRegisterMe94C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#92">_ZN4PLMD3ves12_GLOBAL__N_121BF_CosineRegisterMe94D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#114">_ZNK4PLMD3ves9BF_Cosine12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9229</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Cosine.cpp.func.html b/coverage/ves/BF_Cosine.cpp.func.html
new file mode 100644
index 0000000000..b35ef25225
--- /dev/null
+++ b/coverage/ves/BF_Cosine.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Cosine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Cosine.cpp<span style="font-size: 80%;"> (<a href="BF_Cosine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Cosine.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#92">_ZN4PLMD3ves12_GLOBAL__N_121BF_CosineRegisterMe946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#92">_ZN4PLMD3ves12_GLOBAL__N_121BF_CosineRegisterMe94C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#92">_ZN4PLMD3ves12_GLOBAL__N_121BF_CosineRegisterMe94D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#134">_ZN4PLMD3ves9BF_Cosine11setupLabelsEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#95">_ZN4PLMD3ves9BF_Cosine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#143">_ZN4PLMD3ves9BF_Cosine21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#100">_ZN4PLMD3ves9BF_CosineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Cosine.cpp.gcov.html#114">_ZNK4PLMD3ves9BF_Cosine12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9229</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Cosine.cpp.gcov.html b/coverage/ves/BF_Cosine.cpp.gcov.html
new file mode 100644
index 0000000000..88d686b87c
--- /dev/null
+++ b/coverage/ves/BF_Cosine.cpp.gcov.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Cosine.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Cosine.cpp<span style="font-size: 80%;"> (source / <a href="BF_Cosine.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_COSINE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Fourier cosine basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Use as basis functions Fourier cosine series defined on a periodic interval.</a>
+<a name="36"><span class="lineNum">      36 </span>            : You need to provide the periodic interval \f$[a,b]\f$</a>
+<a name="37"><span class="lineNum">      37 </span>            : on which the basis functions are to be used, and the order of the</a>
+<a name="38"><span class="lineNum">      38 </span>            : expansion \f$N\f$ (i.e. the highest Fourier cosine mode used).</a>
+<a name="39"><span class="lineNum">      39 </span>            : The total number of basis functions is \f$N+1\f$ as</a>
+<a name="40"><span class="lineNum">      40 </span>            : the constant \f$f_{0}(x)=1\f$ is also included.</a>
+<a name="41"><span class="lineNum">      41 </span>            : These basis functions should only be used for periodic CVs.</a>
+<a name="42"><span class="lineNum">      42 </span>            : They can be useful if the periodic function being expanded is an</a>
+<a name="43"><span class="lineNum">      43 </span>            : even function, i.e. \f$F(-x)=F(x)\f$.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The Fourier cosine basis functions are given by</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f{align}{</a>
+<a name="47"><span class="lineNum">      47 </span>            : f_{0}(x)    &amp;= 1 \\</a>
+<a name="48"><span class="lineNum">      48 </span>            : f_{1}(x)    &amp;= cos(\frac{2\pi }{P} x) \\</a>
+<a name="49"><span class="lineNum">      49 </span>            : f_{2}(x)    &amp;= cos(2 \cdot \frac{2\pi}{P} x) \\</a>
+<a name="50"><span class="lineNum">      50 </span>            : f_{3}(x)    &amp;= cos(3 \cdot \frac{2\pi}{P} x) \\</a>
+<a name="51"><span class="lineNum">      51 </span>            : &amp; \vdots \\</a>
+<a name="52"><span class="lineNum">      52 </span>            : f_{n}(x) &amp;= cos(n \cdot \frac{2\pi}{P} x) \\</a>
+<a name="53"><span class="lineNum">      53 </span>            : &amp; \vdots \\</a>
+<a name="54"><span class="lineNum">      54 </span>            : f_{N}(x)   &amp;= cos(N \cdot \frac{2\pi}{P} x) \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f}</a>
+<a name="56"><span class="lineNum">      56 </span>            : where \f$P=(b-a)\f$ is the periodicity of the interval.</a>
+<a name="57"><span class="lineNum">      57 </span>            : They are orthogonal over the interval \f$[a,b]\f$</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f[</a>
+<a name="59"><span class="lineNum">      59 </span>            : \int_{a}^{b} dx \, f_{n}(x)\, f_{m}(x)  =</a>
+<a name="60"><span class="lineNum">      60 </span>            : \begin{cases}</a>
+<a name="61"><span class="lineNum">      61 </span>            : 0 &amp; n \neq m \\</a>
+<a name="62"><span class="lineNum">      62 </span>            : (b-a) &amp; n = m = 0 \\</a>
+<a name="63"><span class="lineNum">      63 </span>            : (b-a)/2 &amp; n = m \neq 0</a>
+<a name="64"><span class="lineNum">      64 </span>            : \end{cases}.</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f]</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \par Examples</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : Here we employ a Fourier cosine expansion of order 10 over the periodic interval</a>
+<a name="70"><span class="lineNum">      70 </span>            : \f$-\pi\f$ to \f$+\pi\f$.</a>
+<a name="71"><span class="lineNum">      71 </span>            : This results in a total number of 11 basis functions.</a>
+<a name="72"><span class="lineNum">      72 </span>            : The label used to identify  the basis function action can then be</a>
+<a name="73"><span class="lineNum">      73 </span>            : referenced later on in the input file.</a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : BF_COSINE MINIMUM=-pi MAXIMUM=+pi ORDER=10 LABEL=bf1</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : */</a>
+<a name="81"><span class="lineNum">      81 </span>            : //+ENDPLUMEDOC</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : class BF_Cosine : public BasisFunctions {</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void setupLabels() override;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void setupUniformIntegrals() override;</a>
+<a name="87"><span class="lineNum">      87 </span>            : public:</a>
+<a name="88"><span class="lineNum">      88 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   explicit BF_Cosine(const ActionOptions&amp;);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="91"><span class="lineNum">      91 </span>            : };</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(BF_Cosine,&quot;BF_COSINE&quot;)</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 : void BF_Cosine::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          6 : }</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 : BF_Cosine::BF_Cosine(const ActionOptions&amp;ao):</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          4 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : {</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          4 :   setNumberOfBasisFunctions(getOrder()+1);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          8 :   setIntrinsicInterval(&quot;-pi&quot;,&quot;+pi&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            :   setPeriodic();</a>
+<a name="108"><span class="lineNum">     108 </span>            :   setIntervalBounded();</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   setType(&quot;trigonometric_cos&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          4 :   setDescription(&quot;Cosine&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          4 :   setupBF();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       9229 : void BF_Cosine::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   // plumed_assert(values.size()==numberOfBasisFunctions());</a>
+<a name="118"><span class="lineNum">     118 </span>            :   // plumed_assert(derivs.size()==numberOfBasisFunctions());</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       9229 :   inside_range=true;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       9229 :   argT=translateArgument(arg, inside_range);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       9229 :   values[0]=1.0;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">       9229 :   derivs[0]=0.0;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     101519 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      92290 :     double io = i;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      92290 :     double cos_tmp = cos(io*argT);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      92290 :     double sin_tmp = sin(io*argT);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      92290 :     values[i] = cos_tmp;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">      92290 :     derivs[i] = -io*sin_tmp*intervalDerivf();</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">       9229 :   if(!inside_range) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        960 :     for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   }</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">       9229 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 : void BF_Cosine::setupLabels() {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   setLabel(0,&quot;1&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         44 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         40 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         80 :     setLabel(i,&quot;cos(&quot;+is+&quot;*s)&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          4 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 : void BF_Cosine::setupUniformIntegrals() {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          3 :   setAllUniformIntegralsToZero();</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   setUniformIntegral(0,1.0);</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_CubicBsplines.cpp.func-sort-c.html b/coverage/ves/BF_CubicBsplines.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e1141a725f
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+  <title>LCOV - plumed test coverage - ves/BF_CubicBsplines.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_CubicBsplines.cpp<span style="font-size: 80%;"> (<a href="BF_CubicBsplines.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_CubicBsplines.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_128BF_CubicBsplinesRegisterMe996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#109">_ZN4PLMD3ves16BF_CubicBsplinesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#102">_ZN4PLMD3ves16BF_CubicBsplines16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_128BF_CubicBsplinesRegisterMe99C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_128BF_CubicBsplinesRegisterMe99D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#143">_ZNK4PLMD3ves16BF_CubicBsplines12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9236</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#166">_ZNK4PLMD3ves16BF_CubicBsplines6splineEdRd</a></td>
+              <td class="coverFnHi">202807</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/ves/BF_CubicBsplines.cpp.func.html b/coverage/ves/BF_CubicBsplines.cpp.func.html
new file mode 100644
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_CubicBsplines.cpp<span style="font-size: 80%;"> (<a href="BF_CubicBsplines.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
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+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_128BF_CubicBsplinesRegisterMe996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_128BF_CubicBsplinesRegisterMe99C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#97">_ZN4PLMD3ves12_GLOBAL__N_128BF_CubicBsplinesRegisterMe99D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#102">_ZN4PLMD3ves16BF_CubicBsplines16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#109">_ZN4PLMD3ves16BF_CubicBsplinesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#143">_ZNK4PLMD3ves16BF_CubicBsplines12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9236</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_CubicBsplines.cpp.gcov.html#166">_ZNK4PLMD3ves16BF_CubicBsplines6splineEdRd</a></td>
+              <td class="coverFnHi">202807</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/ves/BF_CubicBsplines.cpp.gcov.html b/coverage/ves/BF_CubicBsplines.cpp.gcov.html
new file mode 100644
index 0000000000..18d62c957d
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_CubicBsplines.cpp<span style="font-size: 80%;"> (source / <a href="BF_CubicBsplines.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
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+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace ves {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC VES_BASISF BF_CUBIC_B_SPLINES</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Cubic B spline basis functions.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \attention</a>
+<a name="37"><span class="lineNum">      37 </span>            : __These basis functions do not form orthogonal bases. We recommend using wavelets (\ref BF_WAVELETS) instead that do for orthogonal bases__.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : A basis using cubic B spline functions according to \cite habermann_multidimensional_2007. See \cite ValssonPampel_Wavelets_2022 for full details.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : The mathematical expression of the individual splines is given by</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f{align*}{</a>
+<a name="43"><span class="lineNum">      43 </span>            :   h\left(x\right) =</a>
+<a name="44"><span class="lineNum">      44 </span>            :   \begin{cases}</a>
+<a name="45"><span class="lineNum">      45 </span>            :     \left(2 - \lvert x \rvert\right)^3, &amp; 1 \leq \lvert x \rvert \leq 2\\</a>
+<a name="46"><span class="lineNum">      46 </span>            :     4 - 6\lvert x \rvert^2 + 3 \lvert x \rvert^3,\qquad &amp; \lvert x \rvert \leq 1\\</a>
+<a name="47"><span class="lineNum">      47 </span>            :     0, &amp; \text{elsewhere}.</a>
+<a name="48"><span class="lineNum">      48 </span>            :   \end{cases}</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f}</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The full basis consists of equidistant splines at positions \f$\mu_i\f$ which are optimized in their height:</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f{align*}{</a>
+<a name="53"><span class="lineNum">      53 </span>            :   f_i\left(x\right) = h\left(\frac{x-\mu_i}{\sigma}\right)</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f}</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : Note that the distance between individual splines cannot be chosen freely but is equal to the width: \f$\mu_{i+1} = \mu_{i} + \sigma\f$.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The ORDER keyword of the basis set determines the number of equally sized sub-intervalls to be used.</a>
+<a name="60"><span class="lineNum">      60 </span>            : On the borders of each of these sub-intervalls the mean \f$\mu_i\f$ of a spline function is placed.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The total number of basis functions is \f$\text{ORDER}+4\f$ as the constant \f$f_{0}(x)=1\f$, as well as the two splines with means just outside the interval are also included.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : As an example two adjacent basis functions can be seen below.</a>
+<a name="65"><span class="lineNum">      65 </span>            : The full basis consists of shifted splines in the full specified interval.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \image html ves_basisf-splines.png</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : When the splines are used for a periodic CV (with the PERIODIC keyword),</a>
+<a name="70"><span class="lineNum">      70 </span>            : the sub-intervals are chosen in the same way, but only \f$\text{ORDER}+1\f$ functions</a>
+<a name="71"><span class="lineNum">      71 </span>            : are required to fill it (the ones at the boundary coincide and the ones outside</a>
+<a name="72"><span class="lineNum">      72 </span>            : can be omitted).</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : To avoid 'blind' optimization of the basis functions outside the currently sampled area, it is often beneficial to use the OPTIMIZATION_THRESHOLD keyword of the VES_LINEAR_EXPANSION (set it to a small value, e.g. 1e-6)</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \par Examples</a>
+<a name="77"><span class="lineNum">      77 </span>            : The bias is expanded with cubic B splines in the intervall from 0.0 to 10.0 specifying an order of 20.</a>
+<a name="78"><span class="lineNum">      78 </span>            : This results in 24 basis functions.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : \plumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : bf: BF_CUBIC_B_SPLINES MINIMUM=0.0 MAXIMUM=10.0 ORDER=20</a>
+<a name="82"><span class="lineNum">      82 </span>            : \endplumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : */</a>
+<a name="85"><span class="lineNum">      85 </span>            : //+ENDPLUMEDOC</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : class BF_CubicBsplines : public BasisFunctions {</a>
+<a name="88"><span class="lineNum">      88 </span>            :   double spacing_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   double inv_spacing_;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double inv_normfactor_;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   double spline(const double, double&amp;) const;</a>
+<a name="92"><span class="lineNum">      92 </span>            : public:</a>
+<a name="93"><span class="lineNum">      93 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="94"><span class="lineNum">      94 </span>            :   explicit BF_CubicBsplines(const ActionOptions&amp;);</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const;</a>
+<a name="96"><span class="lineNum">      96 </span>            : };</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      12507 : PLUMED_REGISTER_ACTION(BF_CubicBsplines,&quot;BF_CUBIC_B_SPLINES&quot;)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : // See DOI 10.1007/s10614-007-9092-4 for more information;</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          5 : void BF_CubicBsplines::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          5 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;NORMALIZATION&quot;,&quot;the normalization factor that is used to normalize the basis functions by dividing the values. By default it is 2.&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         10 :   keys.addFlag(&quot;PERIODIC&quot;, false, &quot;Use periodic version of basis set.&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          5 :   keys.remove(&quot;NUMERICAL_INTEGRALS&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          5 : }</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          3 : BF_CubicBsplines::BF_CubicBsplines(const ActionOptions&amp;ao):</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          3 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : {</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          3 :   log.printf(&quot;  Cubic B spline basis functions, see and cite &quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          6 :   log &lt;&lt; plumed.cite(&quot;Pampel and Valsson, J. Chem. Theory Comput. 18, 4127-4141 (2022) - DOI:10.1021/acs.jctc.2c00197&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          3 :   setIntrinsicInterval(intervalMin(),intervalMax());</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          3 :   spacing_=(intervalMax()-intervalMin())/static_cast&lt;double&gt;(getOrder());</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          3 :   inv_spacing_ = 1.0/spacing_;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          3 :   bool periodic = false;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          3 :   parseFlag(&quot;PERIODIC&quot;,periodic);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          4 :   if (periodic) {addKeywordToList(&quot;PERIODIC&quot;,periodic);}</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            :   // 1 constant, getOrder() on interval, 1 (left) + 2 (right) at boundaries if not periodic</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          3 :   unsigned int num_BFs = periodic ? getOrder()+1U : getOrder()+4U;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   setNumberOfBasisFunctions(num_BFs);</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :   double normfactor_=2.0;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          3 :   parse(&quot;NORMALIZATION&quot;,normfactor_);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          3 :   if(normfactor_!=2.0) {addKeywordToList(&quot;NORMALIZATION&quot;,normfactor_);}</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          3 :   inv_normfactor_=1.0/normfactor_;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          3 :   periodic ? setPeriodic() : setNonPeriodic();</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   setIntervalBounded();</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 :   setType(&quot;splines_2nd-order&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          3 :   setDescription(&quot;Cubic B-splines (2nd order splines)&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :   setLabelPrefix(&quot;S&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          3 :   setupBF();</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          3 :   log.printf(&quot;   normalization factor: %f\n&quot;,normfactor_);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          3 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       9236 : void BF_CubicBsplines::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   // plumed_assert(values.size()==numberOfBasisFunctions());</a>
+<a name="147"><span class="lineNum">     147 </span>            :   // plumed_assert(derivs.size()==numberOfBasisFunctions());</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       9236 :   inside_range=true;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       9236 :   argT=checkIfArgumentInsideInterval(arg,inside_range);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   //</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       9236 :   values[0]=1.0;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       9236 :   derivs[0]=0.0;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   //</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">     212043 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">     202807 :     double argx = ((argT-intervalMin())*inv_spacing_) - (static_cast&lt;double&gt;(i) - 2.0);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     202807 :     if(arePeriodic()) { // periodic range of argx is [-intervalRange/spacing,+intervalRange/spacing]</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      64140 :       argx /= intervalRange()*inv_spacing_;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">      64140 :       argx = Tools::pbc(argx);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      64140 :       argx *= (intervalRange()*inv_spacing_);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">     202807 :     values[i] = spline(argx, derivs[i]);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">     202807 :     derivs[i] *= inv_spacing_;</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">      11156 :   if(!inside_range) {for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}}</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       9236 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">     202807 : double BF_CubicBsplines::spline(const double arg, double&amp; deriv) const {</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   double value=0.0;</a>
+<a name="170"><span class="lineNum">     170 </span>            :   double x=arg;</a>
+<a name="171"><span class="lineNum">     171 </span>            :   // derivative of abs(x);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   double dx = 1.0;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     202807 :   if(x &lt; 0) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     101208 :     x=-x;</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     dx = -1.0;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span>            :   //</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     202807 :   if(x &gt; 2) {</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :     value=0.0;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     165556 :     deriv=0.0;</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">      37251 :   else if(x &gt;= 1) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      18896 :     value = ((2.0-x)*(2.0-x)*(2.0-x));</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">      18896 :     deriv = dx*(-3.0*(2.0-x)*(2.0-x));</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     // value=((2.0-x)*(2.0-x)*(2.0-x))/6.0;</a>
+<a name="186"><span class="lineNum">     186 </span>            :     // deriv=-x*x*(2.0-x)*(2.0-x);</a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span>            :   else {</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">      18355 :     value = 4.0-6.0*x*x+3.0*x*x*x;</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      18355 :     deriv = dx*(-12.0*x+9.0*x*x);</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     // value=x*x*x*0.5-x*x+2.0/3.0;</a>
+<a name="192"><span class="lineNum">     192 </span>            :     // deriv=(3.0/2.0)*x*x-2.0*x;</a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     202807 :   value *= inv_normfactor_;</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">     202807 :   deriv *= inv_normfactor_;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">     202807 :   return value;</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : }</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Custom.cpp.func-sort-c.html b/coverage/ves/BF_Custom.cpp.func-sort-c.html
new file mode 100644
index 0000000000..392df4b731
--- /dev/null
+++ b/coverage/ves/BF_Custom.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Custom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Custom.cpp<span style="font-size: 80%;"> (<a href="BF_Custom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">126</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Custom.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#124">_ZN4PLMD3ves12_GLOBAL__N_122BF_CustomRegisterMe1266createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#137">_ZN4PLMD3ves9BF_CustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#120">_ZN4PLMD3ves9BF_CustomD0Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#120">_ZN4PLMD3ves9BF_CustomD2Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#126">_ZN4PLMD3ves9BF_Custom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#124">_ZN4PLMD3ves12_GLOBAL__N_122BF_CustomRegisterMe126C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#124">_ZN4PLMD3ves12_GLOBAL__N_122BF_CustomRegisterMe126D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#312">_ZNK4PLMD3ves9BF_Custom12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">24204</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Custom.cpp.func.html b/coverage/ves/BF_Custom.cpp.func.html
new file mode 100644
index 0000000000..81b5eed8f6
--- /dev/null
+++ b/coverage/ves/BF_Custom.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Custom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Custom.cpp<span style="font-size: 80%;"> (<a href="BF_Custom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">126</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Custom.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#124">_ZN4PLMD3ves12_GLOBAL__N_122BF_CustomRegisterMe1266createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#124">_ZN4PLMD3ves12_GLOBAL__N_122BF_CustomRegisterMe126C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#124">_ZN4PLMD3ves12_GLOBAL__N_122BF_CustomRegisterMe126D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#126">_ZN4PLMD3ves9BF_Custom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#137">_ZN4PLMD3ves9BF_CustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#120">_ZN4PLMD3ves9BF_CustomD0Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#120">_ZN4PLMD3ves9BF_CustomD2Ev</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Custom.cpp.gcov.html#312">_ZNK4PLMD3ves9BF_Custom12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">24204</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Custom.cpp.gcov.html b/coverage/ves/BF_Custom.cpp.gcov.html
new file mode 100644
index 0000000000..5d64aecc4b
--- /dev/null
+++ b/coverage/ves/BF_Custom.cpp.gcov.html
@@ -0,0 +1,445 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Custom.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Custom.cpp<span style="font-size: 80%;"> (source / <a href="BF_Custom.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">126</td>
+            <td class="headerCovTableEntry">153</td>
+            <td class="headerCovTableEntryMed">82.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;lepton/Lepton.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace ves {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC VES_BASISF BF_CUSTOM</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Basis functions given by arbitrary mathematical expressions.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This allows you to define basis functions using arbitrary mathematical expressions</a>
+<a name="37"><span class="lineNum">      37 </span>            : that are parsed using the lepton library.</a>
+<a name="38"><span class="lineNum">      38 </span>            : The basis functions</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f$f_{i}(x)\f$ are given in mathematical expressions with _x_ as a variable using</a>
+<a name="40"><span class="lineNum">      40 </span>            : the numbered FUNC keywords that start from</a>
+<a name="41"><span class="lineNum">      41 </span>            : FUNC1. Consistent with other basis functions is \f$f_{0}(x)=1\f$ defined as</a>
+<a name="42"><span class="lineNum">      42 </span>            : the constant. The interval on which the basis functions are defined is</a>
+<a name="43"><span class="lineNum">      43 </span>            : given using the MINIMUM and MAXIMUM keywords.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Using the TRANSFORM keyword it is possible to define a function \f$x(t)\f$ that</a>
+<a name="46"><span class="lineNum">      46 </span>            : is used to transform the argument before calculating the basis functions</a>
+<a name="47"><span class="lineNum">      47 </span>            : values. The variables _min_ and _max_ can be used to indicate the minimum</a>
+<a name="48"><span class="lineNum">      48 </span>            : and the maximum of the interval. By default the arguments are not transformed,</a>
+<a name="49"><span class="lineNum">      49 </span>            : i.e. \f$x(t)=t\f$.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : For periodic basis functions you should use the PERIODIC flag to indicate</a>
+<a name="52"><span class="lineNum">      52 </span>            : that they are periodic.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The basis functions \f$f_{i}(x)\f$ and the transform function \f$x(t)\f$ need</a>
+<a name="55"><span class="lineNum">      55 </span>            : to be well behaved in the interval on which the basis functions are defined,</a>
+<a name="56"><span class="lineNum">      56 </span>            : e.g. not result in a not a number (nan) or infinity (inf).</a>
+<a name="57"><span class="lineNum">      57 </span>            : The code will not perform checks to make sure that this is the case unless the</a>
+<a name="58"><span class="lineNum">      58 </span>            : flag CHECK_NAN_INF is enabled.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : \par Examples</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : Defining Legendre polynomial basis functions of order 6 using BF_CUSTOM</a>
+<a name="63"><span class="lineNum">      63 </span>            : where the appropriate transform function is given by the TRANSFORM keyword.</a>
+<a name="64"><span class="lineNum">      64 </span>            : This is just an example of what can be done, in practice you should use</a>
+<a name="65"><span class="lineNum">      65 </span>            : \ref BF_LEGENDRE for Legendre polynomial basis functions.</a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : BF_CUSTOM ...</a>
+<a name="68"><span class="lineNum">      68 </span>            :  TRANSFORM=(t-(min+max)/2)/((max-min)/2)</a>
+<a name="69"><span class="lineNum">      69 </span>            :  FUNC1=x</a>
+<a name="70"><span class="lineNum">      70 </span>            :  FUNC2=(1/2)*(3*x^2-1)</a>
+<a name="71"><span class="lineNum">      71 </span>            :  FUNC3=(1/2)*(5*x^3-3*x)</a>
+<a name="72"><span class="lineNum">      72 </span>            :  FUNC4=(1/8)*(35*x^4-30*x^2+3)</a>
+<a name="73"><span class="lineNum">      73 </span>            :  FUNC5=(1/8)*(63*x^5-70*x^3+15*x)</a>
+<a name="74"><span class="lineNum">      74 </span>            :  FUNC6=(1/16)*(231*x^6-315*x^4+105*x^2-5)</a>
+<a name="75"><span class="lineNum">      75 </span>            :  MINIMUM=-4.0</a>
+<a name="76"><span class="lineNum">      76 </span>            :  MAXIMUM=4.0</a>
+<a name="77"><span class="lineNum">      77 </span>            :  LABEL=bf1</a>
+<a name="78"><span class="lineNum">      78 </span>            : ... BF_CUSTOM</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : Defining Fourier basis functions of order 3 using BF_CUSTOM where the</a>
+<a name="83"><span class="lineNum">      83 </span>            : periodicity is indicated using the PERIODIC flag. This is just an example</a>
+<a name="84"><span class="lineNum">      84 </span>            : of what can be done, in practice you should use \ref BF_FOURIER</a>
+<a name="85"><span class="lineNum">      85 </span>            : for Fourier basis functions.</a>
+<a name="86"><span class="lineNum">      86 </span>            : \plumedfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : BF_CUSTOM ...</a>
+<a name="88"><span class="lineNum">      88 </span>            :  FUNC1=cos(x)</a>
+<a name="89"><span class="lineNum">      89 </span>            :  FUNC2=sin(x)</a>
+<a name="90"><span class="lineNum">      90 </span>            :  FUNC3=cos(2*x)</a>
+<a name="91"><span class="lineNum">      91 </span>            :  FUNC4=sin(2*x)</a>
+<a name="92"><span class="lineNum">      92 </span>            :  FUNC5=cos(3*x)</a>
+<a name="93"><span class="lineNum">      93 </span>            :  FUNC6=sin(3*x)</a>
+<a name="94"><span class="lineNum">      94 </span>            :  MINIMUM=-pi</a>
+<a name="95"><span class="lineNum">      95 </span>            :  MAXIMUM=+pi</a>
+<a name="96"><span class="lineNum">      96 </span>            :  LABEL=bf1</a>
+<a name="97"><span class="lineNum">      97 </span>            :  PERIODIC</a>
+<a name="98"><span class="lineNum">      98 </span>            : ... BF_CUSTOM</a>
+<a name="99"><span class="lineNum">      99 </span>            : \endplumedfile</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : */</a>
+<a name="103"><span class="lineNum">     103 </span>            : //+ENDPLUMEDOC</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : class BF_Custom : public BasisFunctions {</a>
+<a name="106"><span class="lineNum">     106 </span>            : private:</a>
+<a name="107"><span class="lineNum">     107 </span>            :   lepton::CompiledExpression transf_value_expression_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   lepton::CompiledExpression transf_deriv_expression_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   double* transf_value_lepton_ref_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double* transf_deriv_lepton_ref_;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;lepton::CompiledExpression&gt; bf_values_expressions_;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;lepton::CompiledExpression&gt; bf_derivs_expressions_;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::vector&lt;double*&gt; bf_values_lepton_ref_;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   std::vector&lt;double*&gt; bf_derivs_lepton_ref_;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   std::string variable_str_;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   std::string transf_variable_str_;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   bool do_transf_;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   bool check_nan_inf_;</a>
+<a name="119"><span class="lineNum">     119 </span>            : public:</a>
+<a name="120"><span class="lineNum">     120 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="121"><span class="lineNum">     121 </span>            :   explicit BF_Custom(const ActionOptions&amp;);</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         30 :   ~BF_Custom() {};</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="124"><span class="lineNum">     124 </span>            : };</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      12514 : PLUMED_REGISTER_ACTION(BF_Custom,&quot;BF_CUSTOM&quot;)</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         12 : void BF_Custom::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         12 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         12 :   keys.remove(&quot;ORDER&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         24 :   keys.add(&quot;numbered&quot;,&quot;FUNC&quot;,&quot;The basis functions f_i(x) given in mathematical expressions using _x_ as a variable.&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         24 :   keys.add(&quot;optional&quot;,&quot;TRANSFORM&quot;,&quot;An optional function that can be used to transform the argument before calculating the basis function values. You should use _t_ as a variable. You can use the variables _min_ and _max_ to give the minimum and the maximum of the interval.&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         24 :   keys.addFlag(&quot;PERIODIC&quot;,false,&quot;Indicate that the basis functions are periodic.&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         24 :   keys.addFlag(&quot;CHECK_NAN_INF&quot;,false,&quot;Check that the basis functions do not result in a not a number (nan) or infinity (inf).&quot;);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         12 :   keys.remove(&quot;NUMERICAL_INTEGRALS&quot;);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         12 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         10 : BF_Custom::BF_Custom(const ActionOptions&amp;ao):</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   PLUMED_VES_BASISFUNCTIONS_INIT(ao),</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         10 :   transf_value_lepton_ref_(nullptr),</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         10 :   transf_deriv_lepton_ref_(nullptr),</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         10 :   bf_values_expressions_(0),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         10 :   bf_derivs_expressions_(0),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         10 :   bf_values_lepton_ref_(0,nullptr),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         10 :   bf_derivs_lepton_ref_(0,nullptr),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         10 :   variable_str_(&quot;x&quot;),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         10 :   transf_variable_str_(&quot;t&quot;),</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         10 :   do_transf_(false),</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         20 :   check_nan_inf_(false)</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : {</a>
+<a name="152"><span class="lineNum">     152 </span>            :   std::vector&lt;std::string&gt; bf_str;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         10 :   std::string str_t1=&quot;1&quot;;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         10 :   bf_str.push_back(str_t1);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         10 :   for(int i=1;; i++) {</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     std::string str_t2;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        112 :     if(!parseNumbered(&quot;FUNC&quot;,i,str_t2)) {break;}</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         46 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         92 :     addKeywordToList(&quot;FUNC&quot;+is,str_t2);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         46 :     bf_str.push_back(str_t2);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         46 :   }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   //</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         10 :   if(bf_str.size()==1) {plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: No FUNC keywords given&quot;);}</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         10 :   setOrder(bf_str.size()-1);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         10 :   setNumberOfBasisFunctions(getOrder()+1);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         10 :   setIntrinsicInterval(intervalMin(),intervalMax());</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         10 :   bool periodic = false;</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         20 :   parseFlag(&quot;PERIODIC&quot;,periodic); addKeywordToList(&quot;PERIODIC&quot;,periodic);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         10 :   if(periodic) {setPeriodic();}</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   else {setNonPeriodic();}</a>
+<a name="172"><span class="lineNum">     172 </span>            :   setIntervalBounded();</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         10 :   setType(&quot;custom_functions&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         20 :   setDescription(&quot;Custom Functions&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   //</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         10 :   std::vector&lt;std::string&gt; bf_values_parsed(getNumberOfBasisFunctions());</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         10 :   std::vector&lt;std::string&gt; bf_derivs_parsed(getNumberOfBasisFunctions());</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   bf_values_parsed[0] = &quot;1&quot;;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   bf_derivs_parsed[0] = &quot;0&quot;;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   //</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         10 :   bf_values_expressions_.resize(getNumberOfBasisFunctions());</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         10 :   bf_derivs_expressions_.resize(getNumberOfBasisFunctions());</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         10 :   bf_values_lepton_ref_.resize(getNumberOfBasisFunctions());</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         10 :   bf_derivs_lepton_ref_.resize(getNumberOfBasisFunctions());</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   //</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         56 :   for(unsigned int i=1; i&lt;getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         46 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     try {</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         46 :       lepton::ParsedExpression pe_value = lepton::Parser::parse(bf_str[i]).optimize(lepton::Constants());</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         46 :       std::ostringstream tmp_stream; tmp_stream &lt;&lt; pe_value;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         46 :       bf_values_parsed[i] = tmp_stream.str();</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         46 :       bf_values_expressions_[i] = pe_value.createCompiledExpression();</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         46 :     }</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     catch(PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;There was some problem in parsing the function &quot;+bf_str[i]+&quot; given in FUNC&quot;+is + &quot; with lepton&quot;);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :     std::vector&lt;std::string&gt; var_str;</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         92 :     for(auto &amp;p: bf_values_expressions_[i].getVariables()) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         46 :       var_str.push_back(p);</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :     }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         46 :     if(var_str.size()!=1) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Problem with function &quot;+bf_str[i]+&quot; given in FUNC&quot;+is+&quot;: there should only be one variable&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :     }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         46 :     if(var_str[0]!=variable_str_) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Problem with function &quot;+bf_str[i]+&quot; given in FUNC&quot;+is+&quot;: you should use &quot;+variable_str_+&quot; as a variable&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :     }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            :     try {</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         92 :       lepton::ParsedExpression pe_deriv = lepton::Parser::parse(bf_str[i]).differentiate(variable_str_).optimize(lepton::Constants());</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         46 :       std::ostringstream tmp_stream2; tmp_stream2 &lt;&lt; pe_deriv;</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         46 :       bf_derivs_parsed[i] = tmp_stream2.str();</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         46 :       bf_derivs_expressions_[i] = pe_deriv.createCompiledExpression();</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         46 :     }</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     catch(PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;There was some problem in parsing the derivative of the function &quot;+bf_str[i]+&quot; given in FUNC&quot;+is + &quot; with lepton&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :     try {</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         46 :       bf_values_lepton_ref_[i] = &amp;bf_values_expressions_[i].getVariableReference(variable_str_);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :     try {</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         46 :       bf_derivs_lepton_ref_[i] = &amp;bf_derivs_expressions_[i].getVariableReference(variable_str_);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          8 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         46 :   }</span></a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            :   std::string transf_value_parsed;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   std::string transf_deriv_parsed;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   std::string transf_str;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         20 :   parse(&quot;TRANSFORM&quot;,transf_str);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         10 :   if(transf_str.size()&gt;0) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          6 :     do_transf_ = true;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         12 :     addKeywordToList(&quot;TRANSFORM&quot;,transf_str);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :     for(unsigned int k=0;; k++) {</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         14 :       if(transf_str.find(&quot;min&quot;)!=std::string::npos) {transf_str.replace(transf_str.find(&quot;min&quot;), std::string(&quot;min&quot;).length(),intervalMinStr());}</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :       else {break;}</a>
+<a name="239"><span class="lineNum">     239 </span>            :     }</a>
+<a name="240"><span class="lineNum">     240 </span>            :     for(unsigned int k=0;; k++) {</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         14 :       if(transf_str.find(&quot;max&quot;)!=std::string::npos) {transf_str.replace(transf_str.find(&quot;max&quot;), std::string(&quot;max&quot;).length(),intervalMaxStr());}</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :       else {break;}</a>
+<a name="243"><span class="lineNum">     243 </span>            :     }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            :     try {</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          6 :       lepton::ParsedExpression pe_value = lepton::Parser::parse(transf_str).optimize(lepton::Constants());;</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          6 :       std::ostringstream tmp_stream; tmp_stream &lt;&lt; pe_value;</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          6 :       transf_value_parsed = tmp_stream.str();</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          6 :       transf_value_expression_ = pe_value.createCompiledExpression();</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          6 :     }</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :     catch(PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;There was some problem in parsing the function &quot;+transf_str+&quot; given in TRANSFORM with lepton&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            :     std::vector&lt;std::string&gt; var_str;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         12 :     for(auto &amp;p: transf_value_expression_.getVariables()) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          6 :       var_str.push_back(p);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :     }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          6 :     if(var_str.size()!=1) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Problem with function &quot;+transf_str+&quot; given in TRANSFORM: there should only be one variable&quot;);</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     }</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          6 :     if(var_str[0]!=transf_variable_str_) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Problem with function &quot;+transf_str+&quot; given in TRANSFORM: you should use &quot;+transf_variable_str_+&quot; as a variable&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :     }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            :     try {</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         12 :       lepton::ParsedExpression pe_deriv = lepton::Parser::parse(transf_str).differentiate(transf_variable_str_).optimize(lepton::Constants());;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          6 :       std::ostringstream tmp_stream2; tmp_stream2 &lt;&lt; pe_deriv;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          6 :       transf_deriv_parsed = tmp_stream2.str();</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          6 :       transf_deriv_expression_ = pe_deriv.createCompiledExpression();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          6 :     }</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineNoCov">          0 :     catch(PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;There was some problem in parsing the derivative of the function &quot;+transf_str+&quot; given in TRANSFORM with lepton&quot;);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            :     try {</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          6 :       transf_value_lepton_ref_ = &amp;transf_value_expression_.getVariableReference(transf_variable_str_);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :     try {</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          6 :       transf_deriv_lepton_ref_ = &amp;transf_deriv_expression_.getVariableReference(transf_variable_str_);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          3 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          6 :   }</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   //</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         10 :   log.printf(&quot;  Using the following functions [lepton parsed function and derivative]:\n&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         66 :   for(unsigned int i=0; i&lt;getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         56 :     log.printf(&quot;   %u:  %s   [   %s   |   %s   ] \n&quot;,i,bf_str[i].c_str(),bf_values_parsed[i].c_str(),bf_derivs_parsed[i].c_str());</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            :   }</a>
+<a name="291"><span class="lineNum">     291 </span>            :   //</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         10 :   if(do_transf_) {</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          6 :     log.printf(&quot;  Arguments are transformed using the following function [lepton parsed function and derivative]:\n&quot;);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          6 :     log.printf(&quot;   %s   [   %s   |   %s   ] \n&quot;,transf_str.c_str(),transf_value_parsed.c_str(),transf_deriv_parsed.c_str());</span></a>
+<a name="295"><span class="lineNum">     295 </span>            :   }</a>
+<a name="296"><span class="lineNum">     296 </span>            :   else {</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          4 :     log.printf(&quot;  Arguments are not transformed\n&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :   }</a>
+<a name="299"><span class="lineNum">     299 </span>            :   //</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         20 :   parseFlag(&quot;CHECK_NAN_INF&quot;,check_nan_inf_); addKeywordToList(&quot;CHECK_NAN_INF&quot;,check_nan_inf_);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         10 :   if(check_nan_inf_) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          6 :     log.printf(&quot;  The code will check that values given are numercially stable, e.g. do not result in a not a number (nan) or infinity (inf).\n&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span>            :   else {</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          4 :     log.printf(&quot;  The code will NOT check that values given are numercially stable, e.g. do not result in a not a number (nan) or infinity (inf).\n&quot;);</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         10 :   setupBF();</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         10 :   checkRead();</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         20 : }</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">      24204 : void BF_Custom::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      24204 :   inside_range=true;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      24204 :   argT=checkIfArgumentInsideInterval(arg,inside_range);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">      24204 :   double transf_derivf=1.0;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            :   //</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">      24204 :   if(do_transf_) {</span></a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">      14062 :     if(transf_value_lepton_ref_) {*transf_value_lepton_ref_ = argT;}</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      14062 :     if(transf_deriv_lepton_ref_) {*transf_deriv_lepton_ref_ = argT;}</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      14062 :     argT = transf_value_expression_.evaluate();</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      14062 :     transf_derivf = transf_deriv_expression_.evaluate();</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">      14062 :     if(check_nan_inf_ &amp;&amp; (std::isnan(argT) || std::isinf(argT)) ) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :       std::string vs; Tools::convert(argT,vs);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: problem with the transform function, it gives &quot; + vs);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      14062 :     if(check_nan_inf_ &amp;&amp; (std::isnan(transf_derivf) || std::isinf(transf_derivf)) ) {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 :       std::string vs; Tools::convert(transf_derivf,vs);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: problem with the transform function, its derivative gives &quot; + vs);</span></a>
+<a name="335"><span class="lineNum">     335 </span>            :     }</a>
+<a name="336"><span class="lineNum">     336 </span>            :   }</a>
+<a name="337"><span class="lineNum">     337 </span>            :   //</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      24204 :   values[0]=1.0;</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      24204 :   derivs[0]=0.0;</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">     137488 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">     113284 :     if(bf_values_lepton_ref_[i]) {*bf_values_lepton_ref_[i] = argT;}</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">     113284 :     if(bf_derivs_lepton_ref_[i]) {*bf_derivs_lepton_ref_[i] = argT;}</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">     113284 :     values[i] = bf_values_expressions_[i].evaluate();</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">     113284 :     derivs[i] = bf_derivs_expressions_[i].evaluate();</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">     113284 :     if(do_transf_) {derivs[i]*=transf_derivf;}</span></a>
+<a name="349"><span class="lineNum">     349 </span>            :     // NaN checks</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">     113284 :     if(check_nan_inf_ &amp;&amp; (std::isnan(values[i]) || std::isinf(values[i])) ) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :       std::string vs; Tools::convert(values[i],vs);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :       std::string is; Tools::convert(i,is);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: problem with the basis function given in FUNC&quot;+is+&quot;, it gives &quot;+vs);</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :     }</a>
+<a name="355"><span class="lineNum">     355 </span>            :     //</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">     113284 :     if(check_nan_inf_ &amp;&amp; (std::isnan(derivs[i])|| std::isinf(derivs[i])) ) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :       std::string vs; Tools::convert(derivs[i],vs);</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :       std::string is; Tools::convert(i,is);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: problem with derivative of the basis function given in FUNC&quot;+is+&quot;, it gives &quot;+vs);</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :     }</a>
+<a name="361"><span class="lineNum">     361 </span>            :   }</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">      26218 :   if(!inside_range) {for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}}</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">      24204 : }</span></a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span>            : }</a>
+<a name="369"><span class="lineNum">     369 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Fourier.cpp.func-sort-c.html b/coverage/ves/BF_Fourier.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c5184d211a
--- /dev/null
+++ b/coverage/ves/BF_Fourier.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Fourier.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Fourier.cpp<span style="font-size: 80%;"> (<a href="BF_Fourier.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Fourier.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#147">_ZN4PLMD3ves10BF_Fourier21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">94</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#137">_ZN4PLMD3ves10BF_Fourier11setupLabelsEv</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#101">_ZN4PLMD3ves10BF_FourierC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#93">_ZN4PLMD3ves12_GLOBAL__N_122BF_FourierRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#96">_ZN4PLMD3ves10BF_Fourier16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">97</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#93">_ZN4PLMD3ves12_GLOBAL__N_122BF_FourierRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#93">_ZN4PLMD3ves12_GLOBAL__N_122BF_FourierRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#115">_ZNK4PLMD3ves10BF_Fourier12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">3244265</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Fourier.cpp.func.html b/coverage/ves/BF_Fourier.cpp.func.html
new file mode 100644
index 0000000000..37fbe5b6d0
--- /dev/null
+++ b/coverage/ves/BF_Fourier.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Fourier.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Fourier.cpp<span style="font-size: 80%;"> (<a href="BF_Fourier.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Fourier.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#137">_ZN4PLMD3ves10BF_Fourier11setupLabelsEv</a></td>
+              <td class="coverFnHi">95</td>
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+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#96">_ZN4PLMD3ves10BF_Fourier16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">97</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#147">_ZN4PLMD3ves10BF_Fourier21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">94</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#101">_ZN4PLMD3ves10BF_FourierC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">95</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#93">_ZN4PLMD3ves12_GLOBAL__N_122BF_FourierRegisterMe956createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">95</td>
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+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#93">_ZN4PLMD3ves12_GLOBAL__N_122BF_FourierRegisterMe95C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#93">_ZN4PLMD3ves12_GLOBAL__N_122BF_FourierRegisterMe95D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Fourier.cpp.gcov.html#115">_ZNK4PLMD3ves10BF_Fourier12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">3244265</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</html>
diff --git a/coverage/ves/BF_Fourier.cpp.gcov.html b/coverage/ves/BF_Fourier.cpp.gcov.html
new file mode 100644
index 0000000000..08c9e4dc5c
--- /dev/null
+++ b/coverage/ves/BF_Fourier.cpp.gcov.html
@@ -0,0 +1,232 @@
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+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Fourier.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Fourier.cpp<span style="font-size: 80%;"> (source / <a href="BF_Fourier.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_FOURIER</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Fourier basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Use as basis functions Fourier series defined on a periodic interval.</a>
+<a name="36"><span class="lineNum">      36 </span>            : You need to provide the periodic interval \f$[a,b]\f$</a>
+<a name="37"><span class="lineNum">      37 </span>            : on which the basis functions are to be used, and the order of the</a>
+<a name="38"><span class="lineNum">      38 </span>            : expansion \f$N\f$ (i.e. the highest Fourier mode used).</a>
+<a name="39"><span class="lineNum">      39 </span>            : The total number of basis functions is \f$2N+1\f$ as for each Fourier</a>
+<a name="40"><span class="lineNum">      40 </span>            : mode there is both the cosine and sine term,</a>
+<a name="41"><span class="lineNum">      41 </span>            : and the constant \f$f_{0}(x)=1\f$ is also included.</a>
+<a name="42"><span class="lineNum">      42 </span>            : These basis functions should only be used for periodic CVs.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : The Fourier series basis functions are given by</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f{align}{</a>
+<a name="46"><span class="lineNum">      46 </span>            : f_{0}(x)    &amp;= 1 \\</a>
+<a name="47"><span class="lineNum">      47 </span>            : f_{1}(x)    &amp;= cos(\frac{2\pi }{P} x) \\</a>
+<a name="48"><span class="lineNum">      48 </span>            : f_{2}(x)    &amp;= sin(\frac{2\pi }{P} x) \\</a>
+<a name="49"><span class="lineNum">      49 </span>            : f_{3}(x)    &amp;= cos(2 \cdot \frac{2\pi}{P} x) \\</a>
+<a name="50"><span class="lineNum">      50 </span>            : f_{4}(x)    &amp;= sin(2 \cdot \frac{2\pi}{P} x) \\</a>
+<a name="51"><span class="lineNum">      51 </span>            : &amp; \vdots \\</a>
+<a name="52"><span class="lineNum">      52 </span>            : f_{2k-1}(x) &amp;= cos(k \cdot \frac{2\pi}{P} x) \\</a>
+<a name="53"><span class="lineNum">      53 </span>            : f_{2k}(x)   &amp;= sin(k \cdot \frac{2\pi}{P} x) \\</a>
+<a name="54"><span class="lineNum">      54 </span>            : &amp; \vdots \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : f_{2N-1}(x) &amp;= cos(N \cdot \frac{2\pi}{P} x) \\</a>
+<a name="56"><span class="lineNum">      56 </span>            : f_{2N}(x)   &amp;= sin(N \cdot \frac{2\pi}{P} x) \\</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f}</a>
+<a name="58"><span class="lineNum">      58 </span>            : where \f$P=(b-a)\f$ is the periodicity of the interval.</a>
+<a name="59"><span class="lineNum">      59 </span>            : They are orthogonal over the interval \f$[a,b]\f$</a>
+<a name="60"><span class="lineNum">      60 </span>            : \f[</a>
+<a name="61"><span class="lineNum">      61 </span>            : \int_{a}^{b} dx \, f_{n}(x)\, f_{m}(x)  =</a>
+<a name="62"><span class="lineNum">      62 </span>            : \begin{cases}</a>
+<a name="63"><span class="lineNum">      63 </span>            : 0 &amp; n \neq m \\</a>
+<a name="64"><span class="lineNum">      64 </span>            : (b-a) &amp; n = m = 0 \\</a>
+<a name="65"><span class="lineNum">      65 </span>            : (b-a)/2 &amp; n = m \neq 0</a>
+<a name="66"><span class="lineNum">      66 </span>            : \end{cases}.</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f]</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : Here we employ a Fourier expansion of order 10 over the periodic interval</a>
+<a name="73"><span class="lineNum">      73 </span>            : \f$-\pi\f$ to \f$+\pi\f$.</a>
+<a name="74"><span class="lineNum">      74 </span>            : This results in a total number of 21 basis functions.</a>
+<a name="75"><span class="lineNum">      75 </span>            : The label used to identify  the basis function action can then be</a>
+<a name="76"><span class="lineNum">      76 </span>            : referenced later on in the input file.</a>
+<a name="77"><span class="lineNum">      77 </span>            : \plumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : BF_FOURIER MINIMUM=-pi MAXIMUM=+pi ORDER=10 LABEL=bf_fourier</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : */</a>
+<a name="83"><span class="lineNum">      83 </span>            : //+ENDPLUMEDOC</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : class BF_Fourier : public BasisFunctions {</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void setupLabels() override;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   void setupUniformIntegrals() override;</a>
+<a name="88"><span class="lineNum">      88 </span>            : public:</a>
+<a name="89"><span class="lineNum">      89 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   explicit BF_Fourier(const ActionOptions&amp;);</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="92"><span class="lineNum">      92 </span>            : };</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      12599 : PLUMED_REGISTER_ACTION(BF_Fourier,&quot;BF_FOURIER&quot;)</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         97 : void BF_Fourier::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         97 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         97 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         95 : BF_Fourier::BF_Fourier(const ActionOptions&amp;ao):</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         95 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         95 :   setNumberOfBasisFunctions(2*getOrder()+1);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        190 :   setIntrinsicInterval(&quot;-pi&quot;,&quot;+pi&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   setPeriodic();</a>
+<a name="109"><span class="lineNum">     109 </span>            :   setIntervalBounded();</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         95 :   setType(&quot;trigonometric_cos-sin&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         95 :   setDescription(&quot;Trigonometric (cos/sin)&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         95 :   setupBF();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         95 :   checkRead();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         95 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">    3244265 : void BF_Fourier::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   // plumed_assert(values.size()==numberOfBasisFunctions());</a>
+<a name="119"><span class="lineNum">     119 </span>            :   // plumed_assert(derivs.size()==numberOfBasisFunctions());</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">    3244265 :   inside_range=true;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    3244265 :   argT=translateArgument(arg, inside_range);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">    3244265 :   values[0]=1.0;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">    3244265 :   derivs[0]=0.0;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">   17806383 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">   14562118 :     double io = i;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">   14562118 :     double cos_tmp = cos(io*argT);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">   14562118 :     double sin_tmp = sin(io*argT);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">   14562118 :     values[2*i-1] = cos_tmp;</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">   14562118 :     derivs[2*i-1] = -io*sin_tmp*intervalDerivf();</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">   14562118 :     values[2*i] = sin_tmp;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">   14562118 :     derivs[2*i] = io*cos_tmp*intervalDerivf();</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   }</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">    3244265 :   if(!inside_range) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">      23980 :     for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">    3244265 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         95 : void BF_Fourier::setupLabels() {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         95 :   setLabel(0,&quot;1&quot;);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        568 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        473 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        946 :     setLabel(2*i-1,&quot;cos(&quot;+is+&quot;*s)&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        946 :     setLabel(2*i,&quot;sin(&quot;+is+&quot;*s)&quot;);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         95 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         94 : void BF_Fourier::setupUniformIntegrals() {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         94 :   setAllUniformIntegralsToZero();</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   setUniformIntegral(0,1.0);</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         94 : }</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : }</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Gaussians.cpp.func-sort-c.html b/coverage/ves/BF_Gaussians.cpp.func-sort-c.html
new file mode 100644
index 0000000000..f5da80cd56
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@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <title>LCOV - plumed test coverage - ves/BF_Gaussians.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
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+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Gaussians.cpp<span style="font-size: 80%;"> (<a href="BF_Gaussians.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Gaussians.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#178">_ZN4PLMD3ves12BF_Gaussians11setupLabelsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#122">_ZN4PLMD3ves12BF_GaussiansC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_125BF_GaussiansRegisterMe1146createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#115">_ZN4PLMD3ves12BF_Gaussians16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_125BF_GaussiansRegisterMe114C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_125BF_GaussiansRegisterMe114D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#158">_ZNK4PLMD3ves12BF_Gaussians12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9236</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
+</html>
diff --git a/coverage/ves/BF_Gaussians.cpp.func.html b/coverage/ves/BF_Gaussians.cpp.func.html
new file mode 100644
index 0000000000..6d8149c2b4
--- /dev/null
+++ b/coverage/ves/BF_Gaussians.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Gaussians.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Gaussians.cpp<span style="font-size: 80%;"> (<a href="BF_Gaussians.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Gaussians.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#178">_ZN4PLMD3ves12BF_Gaussians11setupLabelsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#115">_ZN4PLMD3ves12BF_Gaussians16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#122">_ZN4PLMD3ves12BF_GaussiansC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_125BF_GaussiansRegisterMe1146createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_125BF_GaussiansRegisterMe114C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_125BF_GaussiansRegisterMe114D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Gaussians.cpp.gcov.html#158">_ZNK4PLMD3ves12BF_Gaussians12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9236</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/ves/BF_Gaussians.cpp.gcov.html b/coverage/ves/BF_Gaussians.cpp.gcov.html
new file mode 100644
index 0000000000..be8327c8d3
--- /dev/null
+++ b/coverage/ves/BF_Gaussians.cpp.gcov.html
@@ -0,0 +1,265 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Gaussians.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Gaussians.cpp<span style="font-size: 80%;"> (source / <a href="BF_Gaussians.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_GAUSSIANS</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Gaussian basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \attention</a>
+<a name="36"><span class="lineNum">      36 </span>            : __These basis functions do not form orthogonal bases. We recommend using wavelets (\ref BF_WAVELETS) instead that do form orthogonal bases__.</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Basis functions given by Gaussian distributions with shifted centers defined on a</a>
+<a name="39"><span class="lineNum">      39 </span>            : bounded interval. See \cite ValssonPampel_Wavelets_2022 for full details.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : You need to provide the interval \f$[a,b]\f$ on which the bias is to be</a>
+<a name="42"><span class="lineNum">      42 </span>            : expanded.</a>
+<a name="43"><span class="lineNum">      43 </span>            : The ORDER keyword of the basis set \f$N\f$ determines the number of equally sized</a>
+<a name="44"><span class="lineNum">      44 </span>            : sub-intervalls to be used.</a>
+<a name="45"><span class="lineNum">      45 </span>            : On the borders of each of these sub-intervalls the mean \f$\mu\f$ of a Gaussian</a>
+<a name="46"><span class="lineNum">      46 </span>            : basis function is placed:</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f{align}{</a>
+<a name="48"><span class="lineNum">      48 </span>            :   \mu_i = a + (i-1) \frac{b-a}{N}</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f}</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The total number of basis functions is \f$N+4\f$ as the constant</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f$f_{0}(x)=1\f$, as well as two additional Gaussians at the Boundaries are also included.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The basis functions are given by</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f{align}{</a>
+<a name="56"><span class="lineNum">      56 </span>            :   f_0(x) &amp;= 1 \\</a>
+<a name="57"><span class="lineNum">      57 </span>            :   f_i(x) &amp;= \exp\left(-\frac{{\left(x-\mu_i\right)}^2}{2\sigma^2}\right)</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f}</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : When the Gaussians are used for a periodic CV (with the PERIODIC keyword),</a>
+<a name="61"><span class="lineNum">      61 </span>            : the sub-intervals are chosen in the same way, but only \f$N+1\f$ functions</a>
+<a name="62"><span class="lineNum">      62 </span>            : are required to fill it (the ones at the boundary coincide and the ones outside</a>
+<a name="63"><span class="lineNum">      63 </span>            : can be omitted).</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : It is possible to specify the width \f$\sigma\f$ (i.e. the standard deviation)</a>
+<a name="66"><span class="lineNum">      66 </span>            : of the Gaussians using the WIDTH keyword.</a>
+<a name="67"><span class="lineNum">      67 </span>            : By default it is set to the sub-intervall length.</a>
+<a name="68"><span class="lineNum">      68 </span>            : It was found that performance can be typically improved with a smaller value (around 75 % of the sub-interval length), although a too small overlap will prevent the basis set from working correctly at all.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : The optimization procedure then adjusts the heigths of the individual Gaussians.</a>
+<a name="71"><span class="lineNum">      71 </span>            : To avoid 'blind' optimization of the basis functions outside the currently sampled area, it is often beneficial to use the OPTIMIZATION_THRESHOLD keyword of the VES_LINEAR_EXPANSION (set it to a small value, e.g. 1e-6)</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : As an example two adjacent basis functions (with the mentioned width choice of 75% of the sub-interval length) can be seen below.</a>
+<a name="74"><span class="lineNum">      74 </span>            : The full basis consists of shifted Gaussians in the full specified interval.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \image html ves_basisf-gaussians.png</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : \par Examples</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : The bias is expanded with Gaussian functions in the intervall from 0.0 to</a>
+<a name="82"><span class="lineNum">      82 </span>            : 10.0 using order 20.</a>
+<a name="83"><span class="lineNum">      83 </span>            : This results in 24 basis functions.</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : \plumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : bfG: BF_GAUSSIANS MINIMUM=0.0 MAXIMUM=10.0 ORDER=20</a>
+<a name="87"><span class="lineNum">      87 </span>            : \endplumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : Because it was not specified, the width of the Gaussians is by default</a>
+<a name="90"><span class="lineNum">      90 </span>            : set to the sub-intervall length, i.e.\ \f$\sigma=0.5\f$.</a>
+<a name="91"><span class="lineNum">      91 </span>            : To e.g. enhance the overlap between neighbouring basis functions, it can be</a>
+<a name="92"><span class="lineNum">      92 </span>            : specified explicitely:</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : \plumedfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : bfG: BF_GAUSSIANS MINIMUM=0.0 MAXIMUM=10.0 ORDER=20 WIDTH=0.7</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endplumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : */</a>
+<a name="99"><span class="lineNum">      99 </span>            : //+ENDPLUMEDOC</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : class BF_Gaussians : public BasisFunctions {</a>
+<a name="102"><span class="lineNum">     102 </span>            :   /// one over width of the Gaussians</a>
+<a name="103"><span class="lineNum">     103 </span>            :   double inv_sigma_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   /// positions of the centers</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;double&gt; centers_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void setupLabels() override;</a>
+<a name="107"><span class="lineNum">     107 </span>            : public:</a>
+<a name="108"><span class="lineNum">     108 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="109"><span class="lineNum">     109 </span>            :   explicit BF_Gaussians(const ActionOptions&amp;);</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      12507 : PLUMED_REGISTER_ACTION(BF_Gaussians,&quot;BF_GAUSSIANS&quot;)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">          5 : void BF_Gaussians::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          5 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;WIDTH&quot;,&quot;The width (i.e. standart deviation) of the Gaussian functions. By default it is equal to the sub-intervall size.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         10 :   keys.addFlag(&quot;PERIODIC&quot;, false, &quot;Use periodic version of basis set.&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          5 :   keys.remove(&quot;NUMERICAL_INTEGRALS&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          5 : }</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 : BF_Gaussians::BF_Gaussians(const ActionOptions&amp;ao):</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          3 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          3 :   log.printf(&quot;  Gaussian basis functions, see and cite &quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   log &lt;&lt; plumed.cite(&quot;Pampel and Valsson, J. Chem. Theory Comput. 18, 4127-4141 (2022) - DOI:10.1021/acs.jctc.2c00197&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          3 :   setIntrinsicInterval(intervalMin(),intervalMax());</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          3 :   double width = (intervalMax()-intervalMin()) / getOrder();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          3 :   parse(&quot;WIDTH&quot;,width);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          3 :   if(width &lt;= 0.0) {plumed_merror(&quot;WIDTH should be larger than 0&quot;);}</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :   if(width != (intervalMax()-intervalMin())/getOrder()) {addKeywordToList(&quot;WIDTH&quot;,width);}</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 :   inv_sigma_ = 1/(width);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :   bool periodic = false;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          3 :   parseFlag(&quot;PERIODIC&quot;,periodic);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          4 :   if (periodic) {addKeywordToList(&quot;PERIODIC&quot;,periodic);}</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   // 1 constant, getOrder() on interval, 1 (left) + 2 (right) at boundaries if not periodic</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          3 :   unsigned int num_BFs = periodic ? getOrder()+1U : getOrder()+4U;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          3 :   setNumberOfBasisFunctions(num_BFs);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          3 :   centers_.push_back(0.0); // constant one</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         69 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         66 :     centers_.push_back(intervalMin()+(static_cast&lt;int&gt;(i) - 1 - static_cast&lt;int&gt;(!periodic))*(intervalMax()-intervalMin())/getOrder());</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :   periodic ? setPeriodic() : setNonPeriodic();</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   setIntervalBounded();</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          3 :   setType(&quot;gaussian_functions&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 :   setDescription(&quot;Gaussian functions with shifted centers that are being optimized in their height&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          3 :   setupBF();</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          3 :   log.printf(&quot;   width: %f\n&quot;,width);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       9236 : void BF_Gaussians::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       9236 :   inside_range=true;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       9236 :   argT=checkIfArgumentInsideInterval(arg,inside_range);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       9236 :   values[0]=1.0;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       9236 :   derivs[0]=0.0;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">     212043 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     202807 :     double dist = argT - centers_[i];</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">     202807 :     if(arePeriodic()) { // wrap around similar to MetaD</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      64140 :       dist /= intervalRange();</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      64140 :       dist = Tools::pbc(dist);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      64140 :       dist *= intervalRange();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     202807 :     values[i] = exp(-0.5*pow(dist*inv_sigma_,2.0));</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     202807 :     derivs[i] = -values[i] * (dist)*pow(inv_sigma_,2.0);</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      11156 :   if(!inside_range) {for (auto&amp; d: derivs) {d=0.0;}}</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       9236 : }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : // label according to position of mean</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          3 : void BF_Gaussians::setupLabels() {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          3 :   setLabel(0,&quot;const&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         69 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         66 :     std::string is; Tools::convert(centers_[i],is);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        132 :     setLabel(i,&quot;m=&quot;+is);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          3 : }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Legendre.cpp.func-sort-c.html b/coverage/ves/BF_Legendre.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4d19bbb492
--- /dev/null
+++ b/coverage/ves/BF_Legendre.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Legendre.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Legendre.cpp<span style="font-size: 80%;"> (<a href="BF_Legendre.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Legendre.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#161">_ZN4PLMD3ves11BF_Legendre21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#112">_ZN4PLMD3ves11BF_LegendreC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#104">_ZN4PLMD3ves12_GLOBAL__N_124BF_LegendreRegisterMe1066createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">61</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#107">_ZN4PLMD3ves11BF_Legendre16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#104">_ZN4PLMD3ves12_GLOBAL__N_124BF_LegendreRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#104">_ZN4PLMD3ves12_GLOBAL__N_124BF_LegendreRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#129">_ZNK4PLMD3ves11BF_Legendre12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">1625057</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Legendre.cpp.func.html b/coverage/ves/BF_Legendre.cpp.func.html
new file mode 100644
index 0000000000..8c21ff39d1
--- /dev/null
+++ b/coverage/ves/BF_Legendre.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Legendre.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Legendre.cpp<span style="font-size: 80%;"> (<a href="BF_Legendre.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Legendre.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
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+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#107">_ZN4PLMD3ves11BF_Legendre16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">63</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#161">_ZN4PLMD3ves11BF_Legendre21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">61</td>
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+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#104">_ZN4PLMD3ves12_GLOBAL__N_124BF_LegendreRegisterMe106C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#104">_ZN4PLMD3ves12_GLOBAL__N_124BF_LegendreRegisterMe106D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Legendre.cpp.gcov.html#129">_ZNK4PLMD3ves11BF_Legendre12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">1625057</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Legendre.cpp.gcov.html b/coverage/ves/BF_Legendre.cpp.gcov.html
new file mode 100644
index 0000000000..8af2c7d39a
--- /dev/null
+++ b/coverage/ves/BF_Legendre.cpp.gcov.html
@@ -0,0 +1,248 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Legendre.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Legendre.cpp<span style="font-size: 80%;"> (source / <a href="BF_Legendre.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntry">43</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_LEGENDRE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Legendre polynomials basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Use as basis functions [Legendre polynomials](https://en.wikipedia.org/wiki/Legendre_polynomials)</a>
+<a name="36"><span class="lineNum">      36 </span>            : \f$P_{n}(x)\f$ defined on a bounded interval.</a>
+<a name="37"><span class="lineNum">      37 </span>            : You need to provide the interval \f$[a,b]\f$</a>
+<a name="38"><span class="lineNum">      38 </span>            : on which the basis functions are to be used, and the order of the</a>
+<a name="39"><span class="lineNum">      39 </span>            : expansion \f$N\f$ (i.e. the highest order polynomial used).</a>
+<a name="40"><span class="lineNum">      40 </span>            : The total number of basis functions is \f$N+1\f$ as the constant \f$P_{0}(x)=1\f$</a>
+<a name="41"><span class="lineNum">      41 </span>            : is also included.</a>
+<a name="42"><span class="lineNum">      42 </span>            : These basis functions should not be used for periodic CVs.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : Intrinsically the Legendre polynomials are defined on the interval \f$[-1,1]\f$.</a>
+<a name="45"><span class="lineNum">      45 </span>            : A variable \f$t\f$ in the interval \f$[a,b]\f$ is transformed to a variable \f$x\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : in the intrinsic interval \f$[-1,1]\f$ by using the transform function</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            : x(t) = \frac{t-(a+b)/2}</a>
+<a name="49"><span class="lineNum">      49 </span>            : {(b-a)/2}</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The Legendre polynomials are given by the recurrence relation</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f{align}{</a>
+<a name="54"><span class="lineNum">      54 </span>            : P_{0}(x)    &amp;= 1 \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : P_{1}(x)    &amp;= x \\</a>
+<a name="56"><span class="lineNum">      56 </span>            : P_{n+1}(x)  &amp;= \frac{2n+1}{n+1} \, x \, P_{n}(x) -  \frac{n}{n+1} \, P_{n-1}(x)</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f}</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The first 6 polynomials are shown below</a>
+<a name="60"><span class="lineNum">      60 </span>            : \image html ves_basisf-legendre.png</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The Legendre polynomial are orthogonal over the interval \f$[-1,1]\f$</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f[</a>
+<a name="64"><span class="lineNum">      64 </span>            : \int_{-1}^{1} dx \, P_{n}(x)\, P_{m}(x)  =  \frac{2}{2n+1} \delta_{n,m}</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f]</a>
+<a name="66"><span class="lineNum">      66 </span>            : By using the SCALED keyword the polynomials are scaled by a factor of</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f$ \sqrt{\frac{2n+1}{2}}\f$ such that they are orthonormal to 1.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : From the above equation it follows that integral of the basis functions</a>
+<a name="71"><span class="lineNum">      71 </span>            : over the uniform target distribution \f$p_{\mathrm{u}}(x)\f$ are given by</a>
+<a name="72"><span class="lineNum">      72 </span>            : \f[</a>
+<a name="73"><span class="lineNum">      73 </span>            : \int_{-1}^{1} dx \, P_{n}(x) p_{\mathrm{u}}(x) =  \delta_{n,0},</a>
+<a name="74"><span class="lineNum">      74 </span>            : \f]</a>
+<a name="75"><span class="lineNum">      75 </span>            : and thus always zero except for the constant \f$P_{0}(x)=1\f$.</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : For further mathematical properties of the Legendre polynomials see for example</a>
+<a name="79"><span class="lineNum">      79 </span>            : the [Wikipedia page](https://en.wikipedia.org/wiki/Legendre_polynomials).</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : \par Examples</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : Here we employ a Legendre expansion of order 20 over the interval -4.0 to 8.0.</a>
+<a name="84"><span class="lineNum">      84 </span>            : This results in a total number of 21 basis functions.</a>
+<a name="85"><span class="lineNum">      85 </span>            : The label used to identify  the basis function action can then be</a>
+<a name="86"><span class="lineNum">      86 </span>            : referenced later on in the input file.</a>
+<a name="87"><span class="lineNum">      87 </span>            : \plumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : bf_leg: BF_LEGENDRE MINIMUM=-4.0 MAXIMUM=8.0 ORDER=20</a>
+<a name="89"><span class="lineNum">      89 </span>            : \endplumedfile</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \par Examples</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : */</a>
+<a name="94"><span class="lineNum">      94 </span>            : //+ENDPLUMEDOC</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : class BF_Legendre : public BasisFunctions {</a>
+<a name="97"><span class="lineNum">      97 </span>            :   bool scaled_;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void setupUniformIntegrals() override;</a>
+<a name="99"><span class="lineNum">      99 </span>            : public:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit BF_Legendre(const ActionOptions&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="103"><span class="lineNum">     103 </span>            : };</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">      12565 : PLUMED_REGISTER_ACTION(BF_Legendre,&quot;BF_LEGENDRE&quot;)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         63 : void BF_Legendre::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         63 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        126 :   keys.addFlag(&quot;SCALED&quot;,false,&quot;Scale the polynomials such that they are orthonormal to 1.&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         63 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         61 : BF_Legendre::BF_Legendre(const ActionOptions&amp;ao):</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   PLUMED_VES_BASISFUNCTIONS_INIT(ao),</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         61 :   scaled_(false)</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : {</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        183 :   parseFlag(&quot;SCALED&quot;,scaled_); addKeywordToList(&quot;SCALED&quot;,scaled_);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         61 :   setNumberOfBasisFunctions(getOrder()+1);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        122 :   setIntrinsicInterval(&quot;-1.0&quot;,&quot;+1.0&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   setNonPeriodic();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   setIntervalBounded();</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         61 :   setType(&quot;Legendre&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         61 :   setDescription(&quot;Legendre polynomials&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         61 :   setLabelPrefix(&quot;L&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         61 :   setupBF();</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         61 :   checkRead();</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         61 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">    1625057 : void BF_Legendre::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   // plumed_assert(values.size()==numberOfBasisFunctions());</a>
+<a name="133"><span class="lineNum">     133 </span>            :   // plumed_assert(derivs.size()==numberOfBasisFunctions());</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">    1625057 :   inside_range=true;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">    1625057 :   argT=translateArgument(arg, inside_range);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">    1625057 :   std::vector&lt;double&gt; derivsT(derivs.size());</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   //</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">    1625057 :   values[0]=1.0;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">    1625057 :   derivsT[0]=0.0;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">    1625057 :   derivs[0]=0.0;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">    1625057 :   values[1]=argT;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">    1625057 :   derivsT[1]=1.0;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">    1625057 :   derivs[1]=intervalDerivf();</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">   15470320 :   for(unsigned int i=1; i &lt; getOrder(); i++) {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">   13845263 :     double io = static_cast&lt;double&gt;(i);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">   13845263 :     values[i+1]  = ((2.0*io+1.0)/(io+1.0))*argT*values[i] - (io/(io+1.0))*values[i-1];</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">   13845263 :     derivsT[i+1] = ((2.0*io+1.0)/(io+1.0))*(values[i]+argT*derivsT[i])-(io/(io+1.0))*derivsT[i-1];</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">   13845263 :     derivs[i+1]  = intervalDerivf()*derivsT[i+1];</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   }</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">    1625057 :   if(scaled_) {</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :     // L0 is also scaled!</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">    5088852 :     for(unsigned int i=0; i&lt;values.size(); i++) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">    4632062 :       double io = static_cast&lt;double&gt;(i);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    4632062 :       double sf = sqrt(io+0.5);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">    4632062 :       values[i] *= sf;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">    4632062 :       derivs[i] *= sf;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :     }</a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">    1756541 :   if(!inside_range) {for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}}</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    1625057 : }</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         59 : void BF_Legendre::setupUniformIntegrals() {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         59 :   setAllUniformIntegralsToZero();</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   double L0_int = 1.0;</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         59 :   if(scaled_) {L0_int = sqrt(0.5);}</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   setUniformIntegral(0,L0_int);</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         59 : }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : }</a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Powers.cpp.func-sort-c.html b/coverage/ves/BF_Powers.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5e92892ec9
--- /dev/null
+++ b/coverage/ves/BF_Powers.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Powers.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Powers.cpp<span style="font-size: 80%;"> (<a href="BF_Powers.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Powers.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#88">_ZN4PLMD3ves12_GLOBAL__N_121BF_PowersRegisterMe906createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#134">_ZN4PLMD3ves9BF_Powers11setupLabelsEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#97">_ZN4PLMD3ves9BF_PowersC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#91">_ZN4PLMD3ves9BF_Powers16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#88">_ZN4PLMD3ves12_GLOBAL__N_121BF_PowersRegisterMe90C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#88">_ZN4PLMD3ves12_GLOBAL__N_121BF_PowersRegisterMe90D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#116">_ZNK4PLMD3ves9BF_Powers12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">842119</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Powers.cpp.func.html b/coverage/ves/BF_Powers.cpp.func.html
new file mode 100644
index 0000000000..a294c2109e
--- /dev/null
+++ b/coverage/ves/BF_Powers.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Powers.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Powers.cpp<span style="font-size: 80%;"> (<a href="BF_Powers.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Powers.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#88">_ZN4PLMD3ves12_GLOBAL__N_121BF_PowersRegisterMe906createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#88">_ZN4PLMD3ves12_GLOBAL__N_121BF_PowersRegisterMe90C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#88">_ZN4PLMD3ves12_GLOBAL__N_121BF_PowersRegisterMe90D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#134">_ZN4PLMD3ves9BF_Powers11setupLabelsEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#91">_ZN4PLMD3ves9BF_Powers16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#97">_ZN4PLMD3ves9BF_PowersC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Powers.cpp.gcov.html#116">_ZNK4PLMD3ves9BF_Powers12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">842119</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Powers.cpp.gcov.html b/coverage/ves/BF_Powers.cpp.gcov.html
new file mode 100644
index 0000000000..c22ae14574
--- /dev/null
+++ b/coverage/ves/BF_Powers.cpp.gcov.html
@@ -0,0 +1,221 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Powers.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Powers.cpp<span style="font-size: 80%;"> (source / <a href="BF_Powers.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_POWERS</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Polynomial power basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : \attention</a>
+<a name="36"><span class="lineNum">      36 </span>            : __These basis functions should not be used in conventional biasing simulations__.</a>
+<a name="37"><span class="lineNum">      37 </span>            : Instead you should use orthogonal basis functions like Legendre or</a>
+<a name="38"><span class="lineNum">      38 </span>            : Chebyshev polynomials. They are only included for usage in \ref ves_md_linearexpansion</a>
+<a name="39"><span class="lineNum">      39 </span>            : and some special cases.</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : Basis functions given by polynomial powers defined on a bounded interval.</a>
+<a name="42"><span class="lineNum">      42 </span>            : You need to provide the interval \f$[a,b]\f$</a>
+<a name="43"><span class="lineNum">      43 </span>            : on which the basis functions are to be used, and the order of the</a>
+<a name="44"><span class="lineNum">      44 </span>            : expansion \f$N\f$ (i.e. the highest power used).</a>
+<a name="45"><span class="lineNum">      45 </span>            : The total number of basis functions is \f$N+1\f$ as the constant \f$f_{0}(x)=1\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : is also included.</a>
+<a name="47"><span class="lineNum">      47 </span>            : These basis functions should not be used for periodic CVs.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : The basis functions are given by</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f{align}{</a>
+<a name="51"><span class="lineNum">      51 </span>            : f_{0}(x)    &amp;= 1 \\</a>
+<a name="52"><span class="lineNum">      52 </span>            : f_{1}(x)    &amp;= x \\</a>
+<a name="53"><span class="lineNum">      53 </span>            : f_{2}(x)    &amp;= x^2 \\</a>
+<a name="54"><span class="lineNum">      54 </span>            : &amp; \vdots \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : f_{n}(x)    &amp;= x^n \\</a>
+<a name="56"><span class="lineNum">      56 </span>            : &amp; \vdots \\</a>
+<a name="57"><span class="lineNum">      57 </span>            : f_{N}(x)    &amp;= x^N \\</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f}</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : Note that these basis functions are __not__ orthogonal. In fact the integral</a>
+<a name="61"><span class="lineNum">      61 </span>            : over the uniform target distribution blows up as the interval is increased.</a>
+<a name="62"><span class="lineNum">      62 </span>            : Therefore they should not be used in conventional biasing simulations.</a>
+<a name="63"><span class="lineNum">      63 </span>            : However, they can be useful for usage with \ref ves_md_linearexpansion.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \par Examples</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : Here we employ a polynomial power expansion of order 5</a>
+<a name="68"><span class="lineNum">      68 </span>            : over the interval -2.0 to 2.0.</a>
+<a name="69"><span class="lineNum">      69 </span>            : This results in a total number of 6 basis functions.</a>
+<a name="70"><span class="lineNum">      70 </span>            : The label used to identify  the basis function action can then be</a>
+<a name="71"><span class="lineNum">      71 </span>            : referenced later on in the input file.</a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : BF_POWERS MINIMUM=-2.0 MAXIMUM=2.0 ORDER=5 LABEL=bf_pow</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : class BF_Powers : public BasisFunctions {</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double inv_normfactor_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void setupLabels() override;</a>
+<a name="83"><span class="lineNum">      83 </span>            : public:</a>
+<a name="84"><span class="lineNum">      84 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="85"><span class="lineNum">      85 </span>            :   explicit BF_Powers(const ActionOptions&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="87"><span class="lineNum">      87 </span>            : };</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(BF_Powers,&quot;BF_POWERS&quot;)</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         18 : void BF_Powers::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         18 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         36 :   keys.add(&quot;optional&quot;,&quot;NORMALIZATION&quot;,&quot;The normalization factor that is used to normalize the basis functions. By default it is 1.0.&quot;);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         18 :   keys.remove(&quot;NUMERICAL_INTEGRALS&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         18 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         16 : BF_Powers::BF_Powers(const ActionOptions&amp;ao):</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         16 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         16 :   setNumberOfBasisFunctions(getOrder()+1);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         16 :   setIntrinsicInterval(intervalMin(),intervalMax());</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         16 :   double normfactor_=1.0;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         16 :   parse(&quot;NORMALIZATION&quot;,normfactor_);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         16 :   if(normfactor_!=1.0) {addKeywordToList(&quot;NORMALIZATION&quot;,normfactor_);}</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         16 :   inv_normfactor_=1.0/normfactor_;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   setNonPeriodic();</a>
+<a name="109"><span class="lineNum">     109 </span>            :   setIntervalBounded();</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         16 :   setType(&quot;polynom_powers&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         16 :   setDescription(&quot;Polynomial Powers&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         16 :   setupBF();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         16 :   log.printf(&quot;   normalization factor: %f\n&quot;,normfactor_);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         16 :   checkRead();</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         16 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     842119 : void BF_Powers::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">     842119 :   inside_range=true;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">     842119 :   argT=checkIfArgumentInsideInterval(arg,inside_range);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   //</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     842119 :   values[0]=1.0;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">     842119 :   derivs[0]=0.0;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            :   //</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">    4210595 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :     // double io = static_cast&lt;double&gt;(i);</a>
+<a name="127"><span class="lineNum">     127 </span>            :     // values[i] = pow(argT,io);</a>
+<a name="128"><span class="lineNum">     128 </span>            :     // derivs[i] = io*pow(argT,io-1.0);</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">    3368476 :     values[i] = argT*values[i-1];</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">    3368476 :     derivs[i]=values[i-1]+argT*derivs[i-1];</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     842599 :   if(!inside_range) {for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}}</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">     842119 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         16 : void BF_Powers::setupLabels() {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         16 :   setLabel(0,&quot;1&quot;);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         80 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         64 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        128 :     setLabel(i,&quot;s^&quot;+is);</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         16 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : }</a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Sine.cpp.func-sort-c.html b/coverage/ves/BF_Sine.cpp.func-sort-c.html
new file mode 100644
index 0000000000..dc1bb75140
--- /dev/null
+++ b/coverage/ves/BF_Sine.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Sine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Sine.cpp<span style="font-size: 80%;"> (<a href="BF_Sine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Sine.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#142">_ZN4PLMD3ves7BF_Sine21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#91">_ZN4PLMD3ves12_GLOBAL__N_119BF_SineRegisterMe936createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#133">_ZN4PLMD3ves7BF_Sine11setupLabelsEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#99">_ZN4PLMD3ves7BF_SineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#94">_ZN4PLMD3ves7BF_Sine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#91">_ZN4PLMD3ves12_GLOBAL__N_119BF_SineRegisterMe93C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#91">_ZN4PLMD3ves12_GLOBAL__N_119BF_SineRegisterMe93D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#113">_ZNK4PLMD3ves7BF_Sine12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9229</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Sine.cpp.func.html b/coverage/ves/BF_Sine.cpp.func.html
new file mode 100644
index 0000000000..7b72738ca0
--- /dev/null
+++ b/coverage/ves/BF_Sine.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Sine.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Sine.cpp<span style="font-size: 80%;"> (<a href="BF_Sine.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BF_Sine.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#91">_ZN4PLMD3ves12_GLOBAL__N_119BF_SineRegisterMe936createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#91">_ZN4PLMD3ves12_GLOBAL__N_119BF_SineRegisterMe93C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#91">_ZN4PLMD3ves12_GLOBAL__N_119BF_SineRegisterMe93D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#133">_ZN4PLMD3ves7BF_Sine11setupLabelsEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#94">_ZN4PLMD3ves7BF_Sine16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#142">_ZN4PLMD3ves7BF_Sine21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#99">_ZN4PLMD3ves7BF_SineC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Sine.cpp.gcov.html#113">_ZNK4PLMD3ves7BF_Sine12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">9229</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Sine.cpp.gcov.html b/coverage/ves/BF_Sine.cpp.gcov.html
new file mode 100644
index 0000000000..8b24c54226
--- /dev/null
+++ b/coverage/ves/BF_Sine.cpp.gcov.html
@@ -0,0 +1,227 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Sine.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Sine.cpp<span style="font-size: 80%;"> (source / <a href="BF_Sine.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_BASISF BF_SINE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Fourier sine basis functions.</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Use as basis functions Fourier sine series defined on a periodic interval.</a>
+<a name="36"><span class="lineNum">      36 </span>            : You need to provide the periodic interval \f$[a,b]\f$</a>
+<a name="37"><span class="lineNum">      37 </span>            : on which the basis functions are to be used, and the order of the</a>
+<a name="38"><span class="lineNum">      38 </span>            : expansion \f$N\f$ (i.e. the highest Fourier sine mode used).</a>
+<a name="39"><span class="lineNum">      39 </span>            : The total number of basis functions is \f$N+1\f$ as</a>
+<a name="40"><span class="lineNum">      40 </span>            : the constant \f$f_{0}(x)=1\f$ is also included.</a>
+<a name="41"><span class="lineNum">      41 </span>            : These basis functions should only be used for periodic CVs.</a>
+<a name="42"><span class="lineNum">      42 </span>            : They can be useful if the periodic function being expanded is an</a>
+<a name="43"><span class="lineNum">      43 </span>            : odd function, i.e. \f$F(-x)=-F(x)\f$.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The Fourier sine basis functions are given by</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f{align}{</a>
+<a name="47"><span class="lineNum">      47 </span>            : f_{0}(x)    &amp;= 1 \\</a>
+<a name="48"><span class="lineNum">      48 </span>            : f_{1}(x)    &amp;= sin(\frac{2\pi }{P} x) \\</a>
+<a name="49"><span class="lineNum">      49 </span>            : f_{2}(x)    &amp;= sin(2 \cdot \frac{2\pi}{P} x) \\</a>
+<a name="50"><span class="lineNum">      50 </span>            : f_{3}(x)    &amp;= sin(3 \cdot \frac{2\pi}{P} x) \\</a>
+<a name="51"><span class="lineNum">      51 </span>            : &amp; \vdots \\</a>
+<a name="52"><span class="lineNum">      52 </span>            : f_{n}(x) &amp;= sin(n \cdot \frac{2\pi}{P} x) \\</a>
+<a name="53"><span class="lineNum">      53 </span>            : &amp; \vdots \\</a>
+<a name="54"><span class="lineNum">      54 </span>            : f_{N}(x)   &amp;= sin(N \cdot \frac{2\pi}{P} x) \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f}</a>
+<a name="56"><span class="lineNum">      56 </span>            : where \f$P=(b-a)\f$ is the periodicity of the interval.</a>
+<a name="57"><span class="lineNum">      57 </span>            : They are orthogonal over the interval \f$[a,b]\f$</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f[</a>
+<a name="59"><span class="lineNum">      59 </span>            : \int_{a}^{b} dx \, f_{n}(x)\, f_{m}(x)  =</a>
+<a name="60"><span class="lineNum">      60 </span>            : \begin{cases}</a>
+<a name="61"><span class="lineNum">      61 </span>            : 0 &amp; n \neq m \\</a>
+<a name="62"><span class="lineNum">      62 </span>            : (b-a) &amp; n = m = 0 \\</a>
+<a name="63"><span class="lineNum">      63 </span>            : (b-a)/2 &amp; n = m \neq 0</a>
+<a name="64"><span class="lineNum">      64 </span>            : \end{cases}.</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f]</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \par Examples</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : Here we employ a Fourier sine expansion of order 10 over the periodic interval</a>
+<a name="70"><span class="lineNum">      70 </span>            : \f$-\pi\f$ to \f$+\pi\f$.</a>
+<a name="71"><span class="lineNum">      71 </span>            : This results in a total number of 11 basis functions.</a>
+<a name="72"><span class="lineNum">      72 </span>            : The label used to identify  the basis function action can then be</a>
+<a name="73"><span class="lineNum">      73 </span>            : referenced later on in the input file.</a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : BF_SINE MINIMUM=-pi MAXIMUM=+pi ORDER=10 LABEL=bfS</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \par Examples</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : */</a>
+<a name="81"><span class="lineNum">      81 </span>            : //+ENDPLUMEDOC</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : class BF_Sine : public BasisFunctions {</a>
+<a name="84"><span class="lineNum">      84 </span>            :   void setupLabels() override;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   void setupUniformIntegrals() override;</a>
+<a name="86"><span class="lineNum">      86 </span>            : public:</a>
+<a name="87"><span class="lineNum">      87 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit BF_Sine(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="90"><span class="lineNum">      90 </span>            : };</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(BF_Sine,&quot;BF_SINE&quot;)</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          6 : void BF_Sine::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          6 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          6 : }</span></a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          4 : BF_Sine::BF_Sine(const ActionOptions&amp;ao):</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          4 :   PLUMED_VES_BASISFUNCTIONS_INIT(ao)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          4 :   setNumberOfBasisFunctions(getOrder()+1);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          8 :   setIntrinsicInterval(&quot;-pi&quot;,&quot;+pi&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   setPeriodic();</a>
+<a name="107"><span class="lineNum">     107 </span>            :   setIntervalBounded();</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          4 :   setType(&quot;trigonometric_sin&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :   setDescription(&quot;Sine&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          4 :   setupBF();</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          4 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       9229 : void BF_Sine::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   // plumed_assert(values.size()==numberOfBasisFunctions());</a>
+<a name="117"><span class="lineNum">     117 </span>            :   // plumed_assert(derivs.size()==numberOfBasisFunctions());</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       9229 :   inside_range=true;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       9229 :   argT=translateArgument(arg, inside_range);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       9229 :   values[0]=1.0;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       9229 :   derivs[0]=0.0;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">     101519 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">      92290 :     double io = i;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">      92290 :     double cos_tmp = cos(io*argT);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">      92290 :     double sin_tmp = sin(io*argT);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">      92290 :     values[i] = sin_tmp;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">      92290 :     derivs[i] = io*cos_tmp*intervalDerivf();</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">       9229 :   if(!inside_range) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        960 :     for(unsigned int i=0; i&lt;derivs.size(); i++) {derivs[i]=0.0;}</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">       9229 : }</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 : void BF_Sine::setupLabels() {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 :   setLabel(0,&quot;1&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         44 :   for(unsigned int i=1; i &lt; getOrder()+1; i++) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         40 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         80 :     setLabel(i,&quot;sin(&quot;+is+&quot;*s)&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          4 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          3 : void BF_Sine::setupUniformIntegrals() {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 :   setAllUniformIntegralsToZero();</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   setUniformIntegral(0,1.0);</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          3 : }</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Wavelets.cpp.func-sort-c.html b/coverage/ves/BF_Wavelets.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c5077e3b10
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@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Wavelets.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Wavelets.cpp<span style="font-size: 80%;"> (<a href="BF_Wavelets.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BF_Wavelets.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#379">_ZN4PLMD3ves11BF_Wavelets15getCutoffPointsERKd</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#402">_ZN4PLMD3ves11BF_Wavelets11setupLabelsEv</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#234">_ZN4PLMD3ves11BF_WaveletsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#216">_ZN4PLMD3ves12_GLOBAL__N_124BF_WaveletsRegisterMe2186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#219">_ZN4PLMD3ves11BF_Wavelets16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#216">_ZN4PLMD3ves12_GLOBAL__N_124BF_WaveletsRegisterMe218C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#216">_ZN4PLMD3ves12_GLOBAL__N_124BF_WaveletsRegisterMe218D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#352">_ZNK4PLMD3ves11BF_Wavelets12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">62249</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BF_Wavelets.cpp.func.html b/coverage/ves/BF_Wavelets.cpp.func.html
new file mode 100644
index 0000000000..81b73518d8
--- /dev/null
+++ b/coverage/ves/BF_Wavelets.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Wavelets.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Wavelets.cpp<span style="font-size: 80%;"> (<a href="BF_Wavelets.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+      </td>
+    </tr>
+
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+    </tr>
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+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#402">_ZN4PLMD3ves11BF_Wavelets11setupLabelsEv</a></td>
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+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#379">_ZN4PLMD3ves11BF_Wavelets15getCutoffPointsERKd</a></td>
+              <td class="coverFnHi">2</td>
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+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#219">_ZN4PLMD3ves11BF_Wavelets16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">49</td>
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+    <tr>
+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#234">_ZN4PLMD3ves11BF_WaveletsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">47</td>
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+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#216">_ZN4PLMD3ves12_GLOBAL__N_124BF_WaveletsRegisterMe2186createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">47</td>
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+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#216">_ZN4PLMD3ves12_GLOBAL__N_124BF_WaveletsRegisterMe218C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#216">_ZN4PLMD3ves12_GLOBAL__N_124BF_WaveletsRegisterMe218D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+              <td class="coverFn"><a href="BF_Wavelets.cpp.gcov.html#352">_ZNK4PLMD3ves11BF_Wavelets12getAllValuesEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnHi">62249</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/ves/BF_Wavelets.cpp.gcov.html b/coverage/ves/BF_Wavelets.cpp.gcov.html
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BF_Wavelets.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BF_Wavelets.cpp<span style="font-size: 80%;"> (source / <a href="BF_Wavelets.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntry">119</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;GridLinearInterpolation.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;WaveletGrid.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace ves {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC VES_BASISF BF_WAVELETS</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Daubechies Wavelets basis functions.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Note: at the moment only bases with a single level of scaling functions are usable, as multiscale optimization is not yet implemented.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This basis set uses Daubechies Wavelets \cite daubechies_ten_1992 to construct a complete and orthogonal basis. See \cite ValssonPampel_Wavelets_2022 for full details.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : The basis set is based on using a pair of functions, the scaling function (or father wavelet) \f$\phi\f$ and the wavelet function (or mother wavelet) \f$\psi\f$.</a>
+<a name="47"><span class="lineNum">      47 </span>            : They are defined via the two-scale relations for scale \f$j\f$ and shift \f$k\f$:</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \f{align*}{</a>
+<a name="50"><span class="lineNum">      50 </span>            :   \phi_k^j \left(x\right) = 2^{-j/2} \phi \left( 2^{-j} x - k\right)\\</a>
+<a name="51"><span class="lineNum">      51 </span>            :   \psi_k^j \left(x\right) = 2^{-j/2} \psi \left( 2^{-j} x - k\right)</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f}</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : The exact properties are set by choosing filter coefficients, e.g. choosing \f$h_k\f$ for the father wavelet:</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : \f[</a>
+<a name="57"><span class="lineNum">      57 </span>            :   \phi\left(x\right) = \sqrt{2} \sum_k h_k\, \phi \left( 2 x - k\right)</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f]</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : The filter coefficients by Daubechies result in an orthonormal basis of all integer shifted functions:</a>
+<a name="61"><span class="lineNum">      61 </span>            : \f[</a>
+<a name="62"><span class="lineNum">      62 </span>            :   \int \phi(x+i) \phi(x+j) \mathop{}\!\mathrm{d}x = \delta_{ij} \quad \text{for} \quad i,j \in \mathbb{Z}</a>
+<a name="63"><span class="lineNum">      63 </span>            : \f]</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : Because no analytic formula for these wavelets exist, they are instead constructed iteratively on a grid.</a>
+<a name="66"><span class="lineNum">      66 </span>            : The method of construction is close to the &quot;Vector cascade algorithm&quot; described in \cite strang_wavelets_1997 .</a>
+<a name="67"><span class="lineNum">      67 </span>            : The needed filter coefficients of the scaling function are hardcoded, and were previously generated via a python script.</a>
+<a name="68"><span class="lineNum">      68 </span>            : Currently the &quot;maximum phase&quot; type (Db) and the &quot;least asymmetric&quot; (Sym) type are implemented.</a>
+<a name="69"><span class="lineNum">      69 </span>            : We recommend to use Symlets.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : As an example two adjacent basis functions of both Sym8 (ORDER=8, TYPE=SYMLET) and Db8 (ORDER=8, TYPE=DAUBECHIES) is shown in the figure.</a>
+<a name="72"><span class="lineNum">      72 </span>            : The full basis consists of shifted wavelets in the full specified interval.</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : \image html ves_basisf-wavelets.png</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : \par Specify the wavelet type</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : The TYPE keyword sets the type of Wavelet, at the moment &quot;DAUBECHIES&quot; and &quot;SYMLETS&quot; are available.</a>
+<a name="80"><span class="lineNum">      80 </span>            : The specified ORDER of the basis corresponds to the number of vanishing moments of the wavelet, i.e. if TYPE was specified as &quot;DAUBECHIES&quot; an order of 8 results in Db8 wavelets.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : \par Specify the number of functions</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The resulting basis set consists of integer shifts of the wavelet with some scaling \f$j\f$,</a>
+<a name="86"><span class="lineNum">      86 </span>            : \f[</a>
+<a name="87"><span class="lineNum">      87 </span>            :   V(x) = \sum_i \alpha_i * \phi_i (x) = \sum_i \alpha_i * \phi(\frac{x+i}{j})</a>
+<a name="88"><span class="lineNum">      88 </span>            : \f]</a>
+<a name="89"><span class="lineNum">      89 </span>            : with the variational parameters \f$ \alpha \f$.</a>
+<a name="90"><span class="lineNum">      90 </span>            : Additionally a constant basis function is included.</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : There are two different ways to specify the number of used basis functions implemented.</a>
+<a name="93"><span class="lineNum">      93 </span>            : You can either specify the scale or alternatively a fixed number of basis function.</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : Coming from the multiresolution aspect of wavelets, you can set the scale of the father wavelets, i.e. the largest scale used for approximation.</a>
+<a name="96"><span class="lineNum">      96 </span>            : This can be done with the FUNCTION_LENGTH keyword.</a>
+<a name="97"><span class="lineNum">      97 </span>            : It should be given in the same units as the used CV and specifies the length (of the domain interval) of the individual father wavelet functions.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : Alternatively a fixed number of basis functions for the bias expansion can be specified with the NUM_BF keyword, which will set the scale automatically to match the desired number of functions.</a>
+<a name="100"><span class="lineNum">     100 </span>            : Note that this also includes the constant function.</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : If you do not specify anything, it is assumed that the range of the bias should match the scale of the wavelet functions.</a>
+<a name="103"><span class="lineNum">     103 </span>            : More precise, the basis functions are scaled to match the specified size of the CV space (MINIMUM and MAXIMUM keywords).</a>
+<a name="104"><span class="lineNum">     104 </span>            : This has so far been a good initial choice.</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : If the wavelets are scaled to match the CV range exactly there would be \f$4*\text{ORDER} -3\f$ basis functions whose domain is at least partially in this region.</a>
+<a name="107"><span class="lineNum">     107 </span>            : This number is adjusted if FUNCTION_LENGTH or NUM_BF is specified.</a>
+<a name="108"><span class="lineNum">     108 </span>            : Additionally, some of the shifted basis functions will not have significant contributions because of their function values being close to zero over the full range of the bias.</a>
+<a name="109"><span class="lineNum">     109 </span>            : These 'tail wavelets' can be omitted by using the TAILS_THRESHOLD keyword.</a>
+<a name="110"><span class="lineNum">     110 </span>            : This omits all shifted functions that have only function values smaller than a fraction of their maximum value inside the bias range.</a>
+<a name="111"><span class="lineNum">     111 </span>            : Using a value of e.g. 0.01 will already reduce the number of basis functions significantly.</a>
+<a name="112"><span class="lineNum">     112 </span>            : The default setting will not omit any tail wavelets (i.e. TAILS_THRESHOLD=0).</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : The number of basis functions is then not easily determinable a priori but will be given in the logfile.</a>
+<a name="115"><span class="lineNum">     115 </span>            : Additionally the starting point (leftmost defined point) of the individual basis functions is printed.</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : With the PERIODIC keyword the basis set can also be used to bias periodic CVs.</a>
+<a name="119"><span class="lineNum">     119 </span>            : Then the shift between the functions will be chosen such that the function at the left border and right border coincide.</a>
+<a name="120"><span class="lineNum">     120 </span>            : If the FUNCTION_LENGTH keyword is used together with PERIODIC, a smaller length might be chosen to satisfy this requirement.</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : \par Grid</a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : The values of the wavelet function are generated on a grid.</a>
+<a name="126"><span class="lineNum">     126 </span>            : Using the cascade algorithm results in doubling the grid values for each iteration.</a>
+<a name="127"><span class="lineNum">     127 </span>            : This means that the grid size will always be a power of two multiplied by the number of coefficients (\f$ 2*\text{ORDER} -1\f$) for the specified wavelet.</a>
+<a name="128"><span class="lineNum">     128 </span>            : Using the MIN_GRID_SIZE keyword a lower bound for the number of grid points can be specified.</a>
+<a name="129"><span class="lineNum">     129 </span>            : By default at least 1,000 grid points are used.</a>
+<a name="130"><span class="lineNum">     130 </span>            : Function values in between grid points are calculated by linear interpolation.</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : \par Optimization notes</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : To avoid 'blind' optimization of the basis functions outside the currently sampled area, it is often beneficial to use the OPTIMIZATION_THRESHOLD keyword of the \ref VES_LINEAR_EXPANSION (set it to a small value, e.g. 1e-6)</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \par Examples</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : First a very simple example that relies on the default values.</a>
+<a name="140"><span class="lineNum">     140 </span>            : We want to bias some CV in the range of 0 to 4.</a>
+<a name="141"><span class="lineNum">     141 </span>            : The wavelets will therefore be scaled to match that range.</a>
+<a name="142"><span class="lineNum">     142 </span>            : Using Db8 wavelets this results in 30 basis functions (including the constant one), with their starting points given by \f$ -14*\frac{4}{15}, -13*\frac{4}{15}, \cdots , 0 , \cdots, 13*\frac{4}{15}, 14*\frac{4}{15} \f$.</a>
+<a name="143"><span class="lineNum">     143 </span>            : \plumedfile</a>
+<a name="144"><span class="lineNum">     144 </span>            : BF_WAVELETS ...</a>
+<a name="145"><span class="lineNum">     145 </span>            :  ORDER=8</a>
+<a name="146"><span class="lineNum">     146 </span>            :  TYPE=DAUBECHIES</a>
+<a name="147"><span class="lineNum">     147 </span>            :  MINIMUM=0.0</a>
+<a name="148"><span class="lineNum">     148 </span>            :  MAXIMUM=4.0</a>
+<a name="149"><span class="lineNum">     149 </span>            :  LABEL=bf</a>
+<a name="150"><span class="lineNum">     150 </span>            : ... BF_WAVELETS</a>
+<a name="151"><span class="lineNum">     151 </span>            : \endplumedfile</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : By omitting wavelets with only insignificant parts, we can reduce the number of basis functions. Using a threshold of 0.01 will in this example remove the 8 leftmost shifts, which we can check in the logfile.</a>
+<a name="155"><span class="lineNum">     155 </span>            : \plumedfile</a>
+<a name="156"><span class="lineNum">     156 </span>            : BF_WAVELETS ...</a>
+<a name="157"><span class="lineNum">     157 </span>            :  ORDER=8</a>
+<a name="158"><span class="lineNum">     158 </span>            :  TYPE=DAUBECHIES</a>
+<a name="159"><span class="lineNum">     159 </span>            :  MINIMUM=0.0</a>
+<a name="160"><span class="lineNum">     160 </span>            :  MAXIMUM=4.0</a>
+<a name="161"><span class="lineNum">     161 </span>            :  TAILS_THRESHOLD=0.01</a>
+<a name="162"><span class="lineNum">     162 </span>            :  LABEL=bf</a>
+<a name="163"><span class="lineNum">     163 </span>            : ... BF_WAVELETS</a>
+<a name="164"><span class="lineNum">     164 </span>            : \endplumedfile</a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : The length of the individual basis functions can also be adjusted to fit the specific problem.</a>
+<a name="168"><span class="lineNum">     168 </span>            : If for example the wavelets are instead scaled to length 3, there will be 35 basis functions, with leftmost points at \f$ -14*\frac{3}{15}, -13*\frac{3}{15}, \cdots, 0, \cdots, 18*\frac{3}{15}, 19*\frac{3}{15} \f$.</a>
+<a name="169"><span class="lineNum">     169 </span>            : \plumedfile</a>
+<a name="170"><span class="lineNum">     170 </span>            : BF_WAVELETS ...</a>
+<a name="171"><span class="lineNum">     171 </span>            :  ORDER=8</a>
+<a name="172"><span class="lineNum">     172 </span>            :  TYPE=DAUBECHIES</a>
+<a name="173"><span class="lineNum">     173 </span>            :  MINIMUM=0.0</a>
+<a name="174"><span class="lineNum">     174 </span>            :  MAXIMUM=4.0</a>
+<a name="175"><span class="lineNum">     175 </span>            :  FUNCTION_LENGTH=3</a>
+<a name="176"><span class="lineNum">     176 </span>            :  LABEL=bf</a>
+<a name="177"><span class="lineNum">     177 </span>            : ... BF_WAVELETS</a>
+<a name="178"><span class="lineNum">     178 </span>            : \endplumedfile</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : Alternatively you can also specify the number of basis functions. Here we specify the usage of 40 Sym10 wavelet functions. We also used a custom minimum size for the grid and want it to be printed to a file with a specific numerical format.</a>
+<a name="182"><span class="lineNum">     182 </span>            : \plumedfile</a>
+<a name="183"><span class="lineNum">     183 </span>            : BF_WAVELETS ...</a>
+<a name="184"><span class="lineNum">     184 </span>            :  ORDER=10</a>
+<a name="185"><span class="lineNum">     185 </span>            :  TYPE=SYMLETS</a>
+<a name="186"><span class="lineNum">     186 </span>            :  MINIMUM=0.0</a>
+<a name="187"><span class="lineNum">     187 </span>            :  MAXIMUM=4.0</a>
+<a name="188"><span class="lineNum">     188 </span>            :  NUM_BF=40</a>
+<a name="189"><span class="lineNum">     189 </span>            :  MIN_GRID_SIZE=500</a>
+<a name="190"><span class="lineNum">     190 </span>            :  DUMP_WAVELET_GRID</a>
+<a name="191"><span class="lineNum">     191 </span>            :  WAVELET_FILE_FMT=%11.4f</a>
+<a name="192"><span class="lineNum">     192 </span>            :  LABEL=bf</a>
+<a name="193"><span class="lineNum">     193 </span>            : ... BF_WAVELETS</a>
+<a name="194"><span class="lineNum">     194 </span>            : \endplumedfile</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : */</a>
+<a name="197"><span class="lineNum">     197 </span>            : //+ENDPLUMEDOC</a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : class BF_Wavelets : public BasisFunctions {</a>
+<a name="201"><span class="lineNum">     201 </span>            : private:</a>
+<a name="202"><span class="lineNum">     202 </span>            :   void setupLabels() override;</a>
+<a name="203"><span class="lineNum">     203 </span>            :   /// ptr to Grid that holds the Wavelet values and its derivative</a>
+<a name="204"><span class="lineNum">     204 </span>            :   std::unique_ptr&lt;Grid&gt; waveletGrid_;</a>
+<a name="205"><span class="lineNum">     205 </span>            :   /// calculate threshold for omitted tail wavelets</a>
+<a name="206"><span class="lineNum">     206 </span>            :   std::vector&lt;double&gt; getCutoffPoints(const double&amp; threshold);</a>
+<a name="207"><span class="lineNum">     207 </span>            :   /// scale factor of the individual BFs to match specified length</a>
+<a name="208"><span class="lineNum">     208 </span>            :   double scale_;</a>
+<a name="209"><span class="lineNum">     209 </span>            :   /// shift of the individual BFs</a>
+<a name="210"><span class="lineNum">     210 </span>            :   std::vector&lt;double&gt; shifts_;</a>
+<a name="211"><span class="lineNum">     211 </span>            : public:</a>
+<a name="212"><span class="lineNum">     212 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="213"><span class="lineNum">     213 </span>            :   explicit BF_Wavelets(const ActionOptions&amp;);</a>
+<a name="214"><span class="lineNum">     214 </span>            :   void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="215"><span class="lineNum">     215 </span>            : };</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      12551 : PLUMED_REGISTER_ACTION(BF_Wavelets,&quot;BF_WAVELETS&quot;)</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         49 : void BF_Wavelets::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         49 :   BasisFunctions::registerKeywords(keys);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         98 :   keys.add(&quot;compulsory&quot;,&quot;TYPE&quot;,&quot;Specify the wavelet type. Currently available are DAUBECHIES Wavelets with minimum phase and the more symmetric SYMLETS&quot;);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         98 :   keys.add(&quot;optional&quot;,&quot;FUNCTION_LENGTH&quot;,&quot;The domain size of the individual basis functions. (length) This is used to alter the scaling of the basis functions. By default it is set to the total size of the interval. This also influences the number of actually used basis functions, as all shifted functions that are partially supported in the CV space are used.&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         98 :   keys.add(&quot;optional&quot;,&quot;NUM_BF&quot;,&quot;The number of basis functions that should be used. Includes the constant one and N-1 shifted wavelets within the specified range. Cannot be used together with FUNCTION_LENGTH.&quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         98 :   keys.add(&quot;optional&quot;,&quot;TAILS_THRESHOLD&quot;,&quot;The threshold for cutting off tail wavelets as a fraction of the maximum value. All shifted wavelet functions that only have values smaller than the threshold in the bias range will be excluded from the basis set. Defaults to 0 (include all).&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         98 :   keys.addFlag(&quot;MOTHER_WAVELET&quot;, false, &quot;If this flag is set mother wavelets will be used instead of the scaling function (father wavelet). Makes only sense for multiresolution, which is at the moment not usable.&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         98 :   keys.add(&quot;optional&quot;,&quot;MIN_GRID_SIZE&quot;,&quot;The minimal number of grid bins of the Wavelet function. The true number depends also on the used wavelet type and will probably be larger. Defaults to 1000.&quot;);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         98 :   keys.addFlag(&quot;DUMP_WAVELET_GRID&quot;, false, &quot;If this flag is set the grid with the wavelet values will be written to a file.  This file is called wavelet_grid.data.&quot;);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         98 :   keys.add(&quot;optional&quot;,&quot;WAVELET_FILE_FMT&quot;,&quot;The number format of the wavelet grid values and derivatives written to file. By default it is %15.8f.\n&quot;);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         98 :   keys.addFlag(&quot;PERIODIC&quot;, false, &quot;Use periodic version of basis set.&quot;);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         49 :   keys.remove(&quot;NUMERICAL_INTEGRALS&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         49 : }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         47 : BF_Wavelets::BF_Wavelets(const ActionOptions&amp; ao):</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   PLUMED_VES_BASISFUNCTIONS_INIT(ao),</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         47 :   waveletGrid_(nullptr),</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         47 :   scale_(0.0)</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : {</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         47 :   log.printf(&quot;  Wavelet basis functions, see and cite &quot;);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         94 :   log &lt;&lt; plumed.cite(&quot;Pampel and Valsson, J. Chem. Theory Comput. 18, 4127-4141 (2022) - DOI:10.1021/acs.jctc.2c00197&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            :   // parse properties for waveletGrid and set it up</a>
+<a name="245"><span class="lineNum">     245 </span>            :   bool use_mother_wavelet;</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         94 :   parseFlag(&quot;MOTHER_WAVELET&quot;, use_mother_wavelet);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            :   std::string wavelet_type_str;</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         47 :   parse(&quot;TYPE&quot;, wavelet_type_str);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         94 :   addKeywordToList(&quot;TYPE&quot;, wavelet_type_str);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         47 :   unsigned min_grid_size = 1000;</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         47 :   parse(&quot;MIN_GRID_SIZE&quot;, min_grid_size);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         83 :   if(min_grid_size != 1000) {addKeywordToList(&quot;MIN_GRID_SIZE&quot;,min_grid_size);}</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         94 :   waveletGrid_ = WaveletGrid::setupGrid(getOrder(), min_grid_size, use_mother_wavelet, WaveletGrid::stringToType(wavelet_type_str));</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         47 :   bool dump_wavelet_grid=false;</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         47 :   parseFlag(&quot;DUMP_WAVELET_GRID&quot;, dump_wavelet_grid);</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         47 :   if (dump_wavelet_grid) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         36 :     OFile wavelet_gridfile;</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         36 :     std::string fmt = &quot;%13.6f&quot;;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         72 :     parse(&quot;WAVELET_FILE_FMT&quot;,fmt);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :     waveletGrid_-&gt;setOutputFmt(fmt); // property of grid not OFile determines fmt</a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">         36 :     wavelet_gridfile.link(*this);</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">         36 :     wavelet_gridfile.enforceBackup();</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         72 :     wavelet_gridfile.open(getLabel()+&quot;.wavelet_grid.data&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         36 :     waveletGrid_-&gt;writeToFile(wavelet_gridfile);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         36 :   }</span></a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         47 :   bool periodic = false;</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         47 :   parseFlag(&quot;PERIODIC&quot;,periodic);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         51 :   if (periodic) {addKeywordToList(&quot;PERIODIC&quot;,periodic);}</span></a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            :   // now set up properties of basis set</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         47 :   unsigned intrinsic_length = 2*getOrder() - 1; // length of unscaled wavelet</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         47 :   double bias_length = intervalMax() - intervalMin(); // intervalRange() is not yet set</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            :   // parse threshold for tail wavelets and get respective cutoff points</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         47 :   double threshold = 0.0;</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         47 :   std::vector&lt;double&gt; cutoffpoints (2);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         47 :   parse(&quot;TAILS_THRESHOLD&quot;,threshold);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         47 :   plumed_massert(threshold &lt; 1, &quot;TAILS_THRESHOLD should be significantly smaller than 1.&quot;);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         47 :   if(threshold == 0.0) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         45 :     cutoffpoints = {0.0, static_cast&lt;double&gt;(intrinsic_length)};</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span>            :   else {</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          2 :     plumed_massert(!periodic, &quot;TAILS_THRESHOLD can't be used with the periodic wavelet variant&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          2 :     addKeywordToList(&quot;TAILS_THRESHOLD&quot;,threshold);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          4 :     cutoffpoints = getCutoffPoints(threshold);</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   };</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         47 :   double function_length = bias_length;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         47 :   parse(&quot;FUNCTION_LENGTH&quot;,function_length);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         47 :   if(function_length != bias_length) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          4 :     if (periodic) {  // shifted functions need to fit into interval exactly -&gt; reduce size if not</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          2 :       unsigned num_shifts = ceil(bias_length * intrinsic_length / function_length);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          2 :       function_length = bias_length * intrinsic_length / num_shifts;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            :     }</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          8 :     addKeywordToList(&quot;FUNCTION_LENGTH&quot;,function_length);</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :   }</a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            :   // determine number of BFs and needed scaling</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         47 :   unsigned num_BFs = 0;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         47 :   parse(&quot;NUM_BF&quot;,num_BFs);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         47 :   if(num_BFs == 0) { // get from function length</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">         43 :     scale_ = intrinsic_length / function_length;</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">         43 :     if (periodic) {</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :       // this is the same value as num_shifts above + constant</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">          2 :       num_BFs = static_cast&lt;unsigned&gt;(bias_length * scale_) + 1;</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :     }</a>
+<a name="311"><span class="lineNum">     311 </span>            :     else {</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         41 :       num_BFs = 1; // constant one</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :       // left shifts (w/o left cutoff) + right shifts - right cutoff - 1</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         41 :       num_BFs += static_cast&lt;unsigned&gt;(ceil(cutoffpoints[1] + (bias_length)*scale_ - cutoffpoints[0]) - 1);</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :     }</a>
+<a name="316"><span class="lineNum">     316 </span>            :   }</a>
+<a name="317"><span class="lineNum">     317 </span>            :   else {</a>
+<a name="318"><span class="lineNum">     318 </span>            :     plumed_massert(num_BFs &gt; 0, &quot;The number of basis functions has to be positive (NUM_BF &gt; 0)&quot;);</a>
+<a name="319"><span class="lineNum">     319 </span>            :     // check does not work if function length was given as intrinsic length, but can't check for keyword use directly</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :     plumed_massert(function_length==bias_length,&quot;The keywords \&quot;NUM_BF\&quot; and \&quot;FUNCTION_LENGTH\&quot; cannot be used at the same time&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          4 :     addKeywordToList(&quot;NUM_BF&quot;,num_BFs);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">          4 :     if (periodic) {  // inverted num_BFs calculation from where FUNCTION_LENGTH is specified</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          2 :       scale_ = (num_BFs  - 1) / bias_length ;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            :     }</a>
+<a name="326"><span class="lineNum">     326 </span>            :     else {</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          2 :       double cutoff_length = cutoffpoints[1] - cutoffpoints [0];</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          2 :       double intrinsic_bias_length = num_BFs - cutoff_length + 1; // length of bias in intrinsic scale of wavelets</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          2 :       scale_ = intrinsic_bias_length / bias_length;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span>            :   }</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         47 :   setNumberOfBasisFunctions(num_BFs);</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            :   // now set up the starting points of the basis functions</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         47 :   shifts_.push_back(0.0); // constant BF – never used, just for clearer notation</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">       1908 :   for(unsigned int i = 1; i &lt; getNumberOfBasisFunctions(); ++i) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">       1861 :     shifts_.push_back(-intervalMin()*scale_ + cutoffpoints[1] - i);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span>            :   // set some properties</a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         47 :   setIntrinsicInterval(0.0,intrinsic_length);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         47 :   periodic ? setPeriodic() : setNonPeriodic();</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :   setIntervalBounded();</a>
+<a name="345"><span class="lineNum">     345 </span>            :   setType(wavelet_type_str);</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         47 :   setDescription(&quot;Wavelets as localized basis functions&quot;);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         47 :   setupBF();</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         47 :   checkRead();</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         47 :   log.printf(&quot;  Each basisfunction spans %f in CV space\n&quot;, intrinsic_length/scale_);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         47 : }</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : </a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">      62249 : void BF_Wavelets::getAllValues(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">      62249 :   argT=checkIfArgumentInsideInterval(arg,inside_range);</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :   //</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">      62249 :   values[0]=1.0;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">      62249 :   derivs[0]=0.0;</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">    2315762 :   for(unsigned int i = 1; i &lt; getNumberOfBasisFunctions(); ++i) {</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :     // scale and shift argument to match current wavelet</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">    2253513 :     double x = shifts_[i] + argT*scale_;</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">    2253513 :     if (arePeriodic()) { // periodic interval [0,intervalRange*scale]</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">     171766 :       x = x - floor(x/(intervalRange()*scale_))*intervalRange()*scale_;</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :     }</a>
+<a name="365"><span class="lineNum">     365 </span>            : </a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">    2253513 :     if (x &lt; 0 || x &gt;= intrinsicIntervalMax()) { // Wavelets are 0 outside the defined range</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">     989659 :       values[i] = 0.0; derivs[i] = 0.0;</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :     }</a>
+<a name="369"><span class="lineNum">     369 </span>            :     else {</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">    1263854 :       std::vector&lt;double&gt; temp_deriv (1);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">    1263854 :       values[i] = GridLinearInterpolation::getGridValueAndDerivativesWithLinearInterpolation(waveletGrid_.get(), {x}, temp_deriv);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">    1263854 :       derivs[i] = temp_deriv[0] * scale_; // scale derivative</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :     }</a>
+<a name="374"><span class="lineNum">     374 </span>            :   }</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      67885 :   if(!inside_range) {for(auto&amp; deriv : derivs) {deriv=0.0;}}</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      62249 : }</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            : // returns left and right cutoff point of Wavelet</a>
+<a name="380"><span class="lineNum">     380 </span>            : // threshold is a percent value of maximum</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          2 : std::vector&lt;double&gt; BF_Wavelets::getCutoffPoints(const double&amp; threshold) {</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          2 :   double threshold_value = threshold * waveletGrid_-&gt;getMaxValue();</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :   std::vector&lt;double&gt; cutoffpoints;</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        475 :   for (size_t i = 0; i &lt; waveletGrid_-&gt;getSize(); ++i) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        475 :     if (fabs(waveletGrid_-&gt;getValue(i)) &gt;= threshold_value) {</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">          2 :       cutoffpoints.push_back(waveletGrid_-&gt;getPoint(i)[0]);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">          2 :       break;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :     }</a>
+<a name="390"><span class="lineNum">     390 </span>            :   }</a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       1073 :   for (int i = waveletGrid_-&gt;getSize() - 1; i &gt;= 0; --i) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       1073 :     if (fabs(waveletGrid_-&gt;getValue(i)) &gt;= threshold_value) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          2 :       cutoffpoints.push_back(waveletGrid_-&gt;getPoint(i)[0]);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          2 :       break;</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :     }</a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          2 :   return cutoffpoints;</span></a>
+<a name="400"><span class="lineNum">     400 </span>            : }</a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            : // labels according to minimum position in CV space</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         47 : void BF_Wavelets::setupLabels() {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         47 :   setLabel(0,&quot;const&quot;);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">       1908 :   for(unsigned int i=1; i &lt; getNumberOfBasisFunctions(); i++) {</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">       1861 :     double pos = -shifts_[i]/scale_;</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">       1861 :     if (arePeriodic()) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         88 :       pos = pos - floor((pos-intervalMin())/intervalRange())*intervalRange();</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :     }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       1861 :     std::string is; Tools::convert(pos, is);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">       3722 :     setLabel(i,&quot;i=&quot;+is);</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :   }</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         47 : }</span></a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            : }</a>
+<a name="418"><span class="lineNum">     418 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BasisFunctions.cpp.func-sort-c.html b/coverage/ves/BasisFunctions.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d44c106b9f
--- /dev/null
+++ b/coverage/ves/BasisFunctions.cpp.func-sort-c.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BasisFunctions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BasisFunctions.cpp<span style="font-size: 80%;"> (<a href="BasisFunctions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntry">253</td>
+            <td class="headerCovTableEntryMed">87.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BasisFunctions.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#232">_ZN4PLMD3ves14BasisFunctions10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#226">_ZN4PLMD3ves14BasisFunctions11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#135">_ZN4PLMD3ves14BasisFunctions11setIntervalEdd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#308">_ZNK4PLMD3ves14BasisFunctions27getAllValuesNumericalDerivsEdRdRbRSt6vectorIdSaIdEES7_</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
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+              <td class="coverFnHi">2</td>
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+              <td class="coverFnHi">78</td>
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+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#113">_ZN4PLMD3ves14BasisFunctions20setIntrinsicIntervalEdd</a></td>
+              <td class="coverFnHi">79</td>
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+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#175">_ZN4PLMD3ves14BasisFunctions21setupUniformIntegralsEv</a></td>
+              <td class="coverFnHi">79</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#237">_ZN4PLMD3ves14BasisFunctions25numericalUniformIntegralsEv</a></td>
+              <td class="coverFnHi">85</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#291">_ZNK4PLMD3ves14BasisFunctions16getKeywordStringB5cxx11Ev</a></td>
+              <td class="coverFnHi">142</td>
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+              <td class="coverFnHi">170</td>
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+              <td class="coverFnHi">249</td>
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+              <td class="coverFnHi">249</td>
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+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#254">_ZNK4PLMD3ves14BasisFunctions44numericalTargetDistributionIntegralsFromGridEPKNS_4GridE</a></td>
+              <td class="coverFnHi">261</td>
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+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#298">_ZNK4PLMD3ves14BasisFunctions8getValueEdjRdRb</a></td>
+              <td class="coverFnHi">261</td>
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+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#34">_ZN4PLMD3ves14BasisFunctions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">271</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+</body>
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diff --git a/coverage/ves/BasisFunctions.cpp.func.html b/coverage/ves/BasisFunctions.cpp.func.html
new file mode 100644
index 0000000000..e29212763d
--- /dev/null
+++ b/coverage/ves/BasisFunctions.cpp.func.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BasisFunctions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BasisFunctions.cpp<span style="font-size: 80%;"> (<a href="BasisFunctions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntry">253</td>
+            <td class="headerCovTableEntryMed">87.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BasisFunctions.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#232">_ZN4PLMD3ves14BasisFunctions10linkActionEPNS_6ActionE</a></td>
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+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.cpp.gcov.html#135">_ZN4PLMD3ves14BasisFunctions11setIntervalEdd</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFnHi">78</td>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+
+</body>
+</html>
diff --git a/coverage/ves/BasisFunctions.cpp.gcov.html b/coverage/ves/BasisFunctions.cpp.gcov.html
new file mode 100644
index 0000000000..0b860f9f31
--- /dev/null
+++ b/coverage/ves/BasisFunctions.cpp.gcov.html
@@ -0,0 +1,481 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BasisFunctions.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BasisFunctions.cpp<span style="font-size: 80%;"> (source / <a href="BasisFunctions.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">222</td>
+            <td class="headerCovTableEntry">253</td>
+            <td class="headerCovTableEntryMed">87.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryMed">81.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace ves {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        271 : void BasisFunctions::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        271 :   Action::registerKeywords(keys);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        542 :   keys.add(&quot;compulsory&quot;,&quot;ORDER&quot;,&quot;The order of the basis function expansion.&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        542 :   keys.add(&quot;compulsory&quot;,&quot;MINIMUM&quot;,&quot;The minimum of the interval on which the basis functions are defined.&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        542 :   keys.add(&quot;compulsory&quot;,&quot;MAXIMUM&quot;,&quot;The maximum of the interval on which the basis functions are defined.&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        542 :   keys.add(&quot;hidden&quot;,&quot;NGRID_POINTS&quot;,&quot;The number of grid points used for numerical integrals&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        542 :   keys.addFlag(&quot;DEBUG_INFO&quot;,false,&quot;Print out more detailed information about the basis set. Useful for debugging.&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        542 :   keys.addFlag(&quot;NUMERICAL_INTEGRALS&quot;,false,&quot;Calculate basis function integral for the uniform distribution numerically. Useful for debugging.&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        271 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        249 : BasisFunctions::BasisFunctions(const ActionOptions&amp;ao):</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   Action(ao),</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        249 :   print_debug_info_(false),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        249 :   has_been_set(false),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        498 :   description_(&quot;Undefined&quot;),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        249 :   type_(&quot;Undefined&quot;),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        249 :   norder_(0),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        249 :   nbasis_(1),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        249 :   bf_label_prefix_(&quot;f&quot;),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        249 :   bf_labels_(nbasis_,&quot;f0&quot;),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        249 :   periodic_(false),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        249 :   interval_bounded_(true),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        249 :   interval_intrinsic_min_str_(&quot;1.0&quot;),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        249 :   interval_intrinsic_max_str_(&quot;-1.0&quot;),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        249 :   interval_intrinsic_min_(1.0),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        249 :   interval_intrinsic_max_(-1.0),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        249 :   interval_intrinsic_range_(0.0),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        249 :   interval_intrinsic_mean_(0.0),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        249 :   interval_min_str_(&quot;&quot;),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        249 :   interval_max_str_(&quot;&quot;),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        249 :   interval_min_(0.0),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        249 :   interval_max_(0.0),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        249 :   interval_range_(0.0),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        249 :   interval_mean_(0.0),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        249 :   argT_derivf_(1.0),</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        249 :   numerical_uniform_integrals_(false),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        249 :   nbins_(1001),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        249 :   uniform_integrals_(nbasis_,0.0),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        249 :   vesbias_pntr_(NULL),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        747 :   action_pntr_(NULL)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        249 :   bf_keywords_.push_back(getName());</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        498 :   if(keywords.exists(&quot;ORDER&quot;)) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        711 :     parse(&quot;ORDER&quot;,norder_); addKeywordToList(&quot;ORDER&quot;,norder_);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        249 :   nbasis_=norder_+1;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   //</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::string str_imin; std::string str_imax;</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        496 :   if(keywords.exists(&quot;MINIMUM&quot;) &amp;&amp; keywords.exists(&quot;MAXIMUM&quot;)) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        741 :     parse(&quot;MINIMUM&quot;,str_imin); addKeywordToList(&quot;MINIMUM&quot;,str_imin);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        741 :     parse(&quot;MAXIMUM&quot;,str_imax); addKeywordToList(&quot;MAXIMUM&quot;,str_imax);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   }</a>
+<a name="89"><span class="lineNum">      89 </span>            :   else {</a>
+<a name="90"><span class="lineNum">      90 </span>            :     str_imin = &quot;-1.0&quot;;</a>
+<a name="91"><span class="lineNum">      91 </span>            :     str_imax = &quot;1.0&quot;;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span>            :   interval_min_str_ = str_imin;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   interval_max_str_ = str_imax;</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        249 :   if(!Tools::convertNoexcept(str_imin,interval_min_)) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: cannot convert the value given in MINIMUM to a double&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   }</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        249 :   if(!Tools::convertNoexcept(str_imax,interval_max_)) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: cannot convert the value given in MAXIMUM to a double&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        249 :   if(interval_min_&gt;interval_max_) {plumed_merror(getName()+&quot;: MINIMUM and MAXIMUM are not correctly defined&quot;);}</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   //</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        249 :   parseFlag(&quot;DEBUG_INFO&quot;,print_debug_info_);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        498 :   if(keywords.exists(&quot;NUMERICAL_INTEGRALS&quot;)) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        336 :     parseFlag(&quot;NUMERICAL_INTEGRALS&quot;,numerical_uniform_integrals_);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        498 :   if(keywords.exists(&quot;NGRID_POINTS&quot;)) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        494 :     parse(&quot;NGRID_POINTS&quot;,nbins_);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   }</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // log.printf(&quot; %s \n&quot;,getKeywordString().c_str());</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        249 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         79 : void BasisFunctions::setIntrinsicInterval(const double interval_intrinsic_min_in, const double interval_intrinsic_max_in) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         79 :   interval_intrinsic_min_ = interval_intrinsic_min_in;</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         79 :   interval_intrinsic_max_ = interval_intrinsic_max_in;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         79 :   VesTools::convertDbl2Str(interval_intrinsic_min_,interval_intrinsic_min_str_);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         79 :   VesTools::convertDbl2Str(interval_intrinsic_max_,interval_intrinsic_max_str_);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         79 :   plumed_massert(interval_intrinsic_min_&lt;interval_intrinsic_max_,&quot;setIntrinsicInterval: intrinsic intervals are not defined correctly&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         79 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        170 : void BasisFunctions::setIntrinsicInterval(const std::string&amp; interval_intrinsic_min_str_in, const std::string&amp; interval_intrinsic_max_str_in) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        170 :   interval_intrinsic_min_str_ = interval_intrinsic_min_str_in;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        170 :   interval_intrinsic_max_str_ = interval_intrinsic_max_str_in;</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        170 :   if(!Tools::convertNoexcept(interval_intrinsic_min_str_,interval_intrinsic_min_)) {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;setIntrinsicInterval: cannot convert string value given for the minimum of the intrinsic interval to a double&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        170 :   if(!Tools::convertNoexcept(interval_intrinsic_max_str_,interval_intrinsic_max_)) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;setIntrinsicInterval: cannot convert string value given for the maximum of the intrinsic interval to a double&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   }</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        170 :   plumed_massert(interval_intrinsic_min_&lt;interval_intrinsic_max_,&quot;setIntrinsicInterval: intrinsic intervals are not defined correctly&quot;);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        170 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 : void BasisFunctions::setInterval(const double interval_min_in, const double interval_max_in) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   interval_min_ = interval_min_in;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   interval_max_ = interval_max_in;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   VesTools::convertDbl2Str(interval_min_,interval_min_str_);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   VesTools::convertDbl2Str(interval_max_,interval_max_str_);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   plumed_massert(interval_min_&lt;interval_max_,&quot;setInterval: intervals are not defined correctly&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          2 : void BasisFunctions::setInterval(const std::string&amp; interval_min_str_in, const std::string&amp; interval_max_str_in) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          2 :   interval_min_str_ = interval_min_str_in;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          2 :   interval_max_str_ = interval_max_str_in;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   if(!Tools::convertNoexcept(interval_min_str_,interval_min_)) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;setInterval: cannot convert string value given for the minimum of the interval to a double&quot;);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            :   }</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          2 :   if(!Tools::convertNoexcept(interval_max_str_,interval_max_)) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;setInterval: cannot convert string value given for the maximum of the interval to a double&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          2 :   plumed_massert(interval_min_&lt;interval_max_,&quot;setInterval: intervals are not defined correctly&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          2 : }</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        249 : void BasisFunctions::setupInterval() {</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   // if(!intervalBounded()){plumed_merror(&quot;setupInterval() only works for bounded interval&quot;);}</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        249 :   interval_intrinsic_range_ = interval_intrinsic_max_-interval_intrinsic_min_;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        249 :   interval_intrinsic_mean_  = 0.5*(interval_intrinsic_max_+interval_intrinsic_min_);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        249 :   interval_range_ = interval_max_-interval_min_;</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        249 :   interval_mean_  = 0.5*(interval_max_+interval_min_);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        249 :   argT_derivf_ = interval_intrinsic_range_/interval_range_;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        249 : }</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         78 : void BasisFunctions::setupLabels() {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        884 :   for(unsigned int i=0; i &lt; nbasis_; i++) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        806 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       1612 :     bf_labels_[i]=bf_label_prefix_+is+&quot;(s)&quot;;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   }</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         78 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         79 : void BasisFunctions::setupUniformIntegrals() {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         79 :   numerical_uniform_integrals_=true;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         79 :   numericalUniformIntegrals();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         79 : }</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        249 : void BasisFunctions::setupBF() {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        249 :   if(interval_intrinsic_min_&gt;interval_intrinsic_max_) {plumed_merror(&quot;setupBF: default intervals are not correctly set&quot;);}</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        249 :   setupInterval();</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        249 :   setupLabels();</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        249 :   if(bf_labels_.size()==1) {plumed_merror(&quot;setupBF: the labels of the basis functions are not correct.&quot;);}</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        249 :   if(!numerical_uniform_integrals_) {setupUniformIntegrals();}</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          6 :   else {numericalUniformIntegrals();}</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        249 :   if(uniform_integrals_.size()==1) {plumed_merror(&quot;setupBF: the integrals of the basis functions is not correct.&quot;);}</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        249 :   if(type_==&quot;Undefined&quot;) {plumed_merror(&quot;setupBF: the type of the basis function is not defined.&quot;);}</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        249 :   if(description_==&quot;Undefined&quot;) {plumed_merror(&quot;setupBF: the description of the basis function is not defined.&quot;);}</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        249 :   has_been_set=true;</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        249 :   printInfo();</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        249 : }</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        249 : void BasisFunctions::printInfo() const {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        249 :   if(!has_been_set) {plumed_merror(&quot;the basis set has not be setup correctly&quot;);}</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        249 :   log.printf(&quot;  One-dimensional basis set\n&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        249 :   log.printf(&quot;   Description: %s\n&quot;,description_.c_str());</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        249 :   log.printf(&quot;   Type: %s\n&quot;,type_.c_str());</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        249 :   if(periodic_) {log.printf(&quot;   The basis functions are periodic\n&quot;);}</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        249 :   log.printf(&quot;   Order of basis set: %u\n&quot;,norder_);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        249 :   log.printf(&quot;   Number of basis functions: %u\n&quot;,nbasis_);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   // log.printf(&quot;   Interval of basis set: %f to %f\n&quot;,interval_min_,interval_max_);</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        249 :   log.printf(&quot;   Interval of basis set: %s to %s\n&quot;,interval_min_str_.c_str(),interval_max_str_.c_str());</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        249 :   log.printf(&quot;   Description of basis functions:\n&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">       4293 :   for(unsigned int i=0; i &lt; nbasis_; i++) {log.printf(&quot;    %2u       %10s\n&quot;,i,bf_labels_[i].c_str());}</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   //</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        249 :   if(print_debug_info_) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         38 :     log.printf(&quot;  Debug information:\n&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     // log.printf(&quot;   Default interval of basis set: [%f,%f]\n&quot;,interval_intrinsic_min_,interval_intrinsic_max_);</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         38 :     log.printf(&quot;   Intrinsic interval of basis set: [%s,%s]\n&quot;,interval_intrinsic_min_str_.c_str(),interval_intrinsic_max_str_.c_str());</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         38 :     log.printf(&quot;   Intrinsic interval of basis set: range=%f,  mean=%f\n&quot;,interval_intrinsic_range_,interval_intrinsic_mean_);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :     // log.printf(&quot;   Defined interval of basis set: [%f,%f]\n&quot;,interval_min_,interval_max_);</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         38 :     log.printf(&quot;   Defined interval of basis set: [%s,%s]\n&quot;,interval_min_str_.c_str(),interval_max_str_.c_str());</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         38 :     log.printf(&quot;   Defined interval of basis set: range=%f,  mean=%f\n&quot;,interval_range_,interval_mean_);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         38 :     log.printf(&quot;   Derivative factor due to interval translation: %f\n&quot;,argT_derivf_);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         38 :     log.printf(&quot;   Integral of basis functions over the interval:\n&quot;);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         38 :     if(numerical_uniform_integrals_) {log.printf(&quot;   Note: calculated numerically\n&quot;);}</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        558 :     for(unsigned int i=0; i &lt; nbasis_; i++) {log.printf(&quot;    %2u       %16.10f\n&quot;,i,uniform_integrals_[i]);}</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         38 :     log.printf(&quot;   --------------------------\n&quot;);</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :   }</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        249 : }</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 : void BasisFunctions::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :   vesbias_pntr_ = vesbias_pntr_in;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :   action_pntr_ = static_cast&lt;Action*&gt;(vesbias_pntr_in);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 : void BasisFunctions::linkAction(Action* action_pntr_in) {</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   action_pntr_ = action_pntr_in;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         85 : void BasisFunctions::numericalUniformIntegrals() {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         85 :   std::vector&lt;std::string&gt; grid_min(1); grid_min[0]=intervalMinStr();</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         85 :   std::vector&lt;std::string&gt; grid_max(1); grid_max[0]=intervalMaxStr();</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         85 :   std::vector&lt;unsigned int&gt; grid_bins(1); grid_bins[0]=nbins_;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        170 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; arguments(1); arguments[0]= Tools::make_unique&lt;Value&gt;(nullptr,&quot;arg&quot;,false);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        105 :   if(arePeriodic()) {arguments[0]-&gt;setDomain(intervalMinStr(),intervalMaxStr());}</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         75 :   else {arguments[0]-&gt;setNotPeriodic();}</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">        170 :   auto uniform_grid = Tools::make_unique&lt;Grid&gt;(&quot;uniform&quot;,Tools::unique2raw(arguments),grid_min,grid_max,grid_bins,false,false);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   //</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         85 :   double inverse_normalization = 1.0/(intervalMax()-intervalMin());</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      85245 :   for(Grid::index_t l=0; l&lt;uniform_grid-&gt;getSize(); l++) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      85160 :     uniform_grid-&gt;setValue(l,inverse_normalization);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         85 :   uniform_integrals_ = numericalTargetDistributionIntegralsFromGrid(uniform_grid.get());</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        170 : }</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        261 : std::vector&lt;double&gt; BasisFunctions::numericalTargetDistributionIntegralsFromGrid(const Grid* grid_pntr) const {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">        261 :   plumed_massert(grid_pntr!=NULL,&quot;the grid is not defined&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        261 :   plumed_massert(grid_pntr-&gt;getDimension()==1,&quot;the target distribution grid should be one dimensional&quot;);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   //</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        261 :   std::vector&lt;double&gt; targetdist_integrals(nbasis_,0.0);</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        522 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(grid_pntr);</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">     138336 :   for(Grid::index_t k=0; k &lt; grid_pntr-&gt;getSize(); k++) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">     138075 :     double arg = grid_pntr-&gt;getPoint(k)[0];</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">     138075 :     std::vector&lt;double&gt; bf_values(nbasis_);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">     138075 :     std::vector&lt;double&gt; bf_derivs(nbasis_);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">     138075 :     bool inside=true;</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">     138075 :     double argT=0.0;</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">     138075 :     getAllValues(arg,argT,inside,bf_values,bf_derivs);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">    3336092 :     for(unsigned int i=0; i &lt; nbasis_; i++) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">    3198017 :       targetdist_integrals[i] += (integration_weights[k] * grid_pntr-&gt;getValue(k)) * bf_values[i];</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :     }</a>
+<a name="273"><span class="lineNum">     273 </span>            :   }</a>
+<a name="274"><span class="lineNum">     274 </span>            :   // assume that the first function is the constant</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        261 :   bool inside=true;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">        261 :   double argT=0.0;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        261 :   targetdist_integrals[0] = getValue(0.0,0,argT,inside);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        261 :   return targetdist_integrals;</span></a>
+<a name="279"><span class="lineNum">     279 </span>            : }</a>
+<a name="280"><span class="lineNum">     280 </span>            : </a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        247 : std::vector&lt;double&gt; BasisFunctions::getTargetDistributionIntegrals(const TargetDistribution* targetdist_pntr) const {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        247 :   if(targetdist_pntr==NULL) {</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :     return getUniformIntegrals();</a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span>            :   else {</a>
+<a name="287"><span class="lineNum">     287 </span>            :     Grid* targetdist_grid = targetdist_pntr-&gt;getTargetDistGridPntr();</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        176 :     return numericalTargetDistributionIntegralsFromGrid(targetdist_grid);</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span>            : }</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">        142 : std::string BasisFunctions::getKeywordString() const {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        142 :   std::string str_keywords=bf_keywords_[0];</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        762 :   for(unsigned int i=1; i&lt;bf_keywords_.size(); i++) {str_keywords+=&quot; &quot;+bf_keywords_[i];}</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">        142 :   return str_keywords;</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">        261 : double BasisFunctions::getValue(const double arg, const unsigned int n, double&amp; argT, bool&amp; inside_range) const {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">        261 :   plumed_massert(n&lt;numberOfBasisFunctions(),&quot;getValue: n is outside range of the defined order of the basis set&quot;);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        261 :   inside_range=true;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        261 :   std::vector&lt;double&gt; tmp_values(numberOfBasisFunctions());</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        261 :   std::vector&lt;double&gt; tmp_derivs(numberOfBasisFunctions());</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        261 :   getAllValues(arg, argT, inside_range, tmp_values, tmp_derivs);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        522 :   return tmp_values[n];</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 : void BasisFunctions::getAllValuesNumericalDerivs(const double arg, double&amp; argT, bool&amp; inside_range, std::vector&lt;double&gt;&amp; values, std::vector&lt;double&gt;&amp; derivs) const {</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   // use forward difference, unless very close to the boundary</a>
+<a name="312"><span class="lineNum">     312 </span>            :   double delta = sqrt(epsilon);</a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :   if((arg+delta)&gt;intervalMax()) {</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :     delta *= -1.0;</a>
+<a name="315"><span class="lineNum">     315 </span>            :   }</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :   inside_range=true;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; values_delta(numberOfBasisFunctions());</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; derivs_dummy(numberOfBasisFunctions());</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 :   getAllValues(arg+delta, argT, inside_range, values_delta, derivs_dummy);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :   getAllValues(arg, argT, inside_range, values, derivs_dummy);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;numberOfBasisFunctions(); i++) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 :     derivs[i] = (values_delta[i]-values[i])/delta;</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   }</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         71 : void BasisFunctions::getMultipleValue(const std::vector&lt;double&gt;&amp; args, std::vector&lt;double&gt;&amp; argsT, std::vector&lt;std::vector&lt;double&gt; &gt;&amp; values, std::vector&lt;std::vector&lt;double&gt; &gt;&amp; derivs, const bool numerical_deriv) const {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         71 :   argsT.resize(args.size());</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   values.clear();</a>
+<a name="330"><span class="lineNum">     330 </span>            :   derivs.clear();</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">      23019 :   for(unsigned int i=0; i&lt;args.size(); i++) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">      22948 :     std::vector&lt;double&gt; tmp_values(getNumberOfBasisFunctions());</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">      22948 :     std::vector&lt;double&gt; tmp_derivs(getNumberOfBasisFunctions());</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      22948 :     bool inside_interval=true;</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      22948 :     if(!numerical_deriv) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">      22948 :       getAllValues(args[i],argsT[i],inside_interval,tmp_values,tmp_derivs);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     } else {</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineNoCov">          0 :       getAllValuesNumericalDerivs(args[i],argsT[i],inside_interval,tmp_values,tmp_derivs);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :     }</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      22948 :     values.push_back(tmp_values);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">      22948 :     derivs.push_back(tmp_derivs);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :   }</a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         71 : }</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         71 : void BasisFunctions::writeBasisFunctionsToFile(OFile&amp; ofile_values, OFile&amp; ofile_derivs, const std::string&amp; min_in, const std::string&amp; max_in, unsigned int nbins_in, const bool ignore_periodicity, const std::string&amp; output_fmt_values, const std::string&amp; output_fmt_derivs, const bool numerical_deriv) const {</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         71 :   std::vector&lt;std::string&gt; min(1); min[0]=min_in;</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         71 :   std::vector&lt;std::string&gt; max(1); max[0]=max_in;</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         71 :   std::vector&lt;unsigned int&gt; nbins(1); nbins[0]=nbins_in;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         71 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; value_pntr(1);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        142 :   value_pntr[0]= Tools::make_unique&lt;Value&gt;(nullptr,&quot;arg&quot;,false);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">        117 :   if(arePeriodic() &amp;&amp; !ignore_periodicity) {value_pntr[0]-&gt;setDomain(intervalMinStr(),intervalMaxStr());}</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         48 :   else {value_pntr[0]-&gt;setNotPeriodic();}</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">        142 :   Grid args_grid = Grid(&quot;grid&quot;,Tools::unique2raw(value_pntr),min,max,nbins,false,false);</span></a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         71 :   std::vector&lt;double&gt; args(args_grid.getSize(),0.0);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">      23019 :   for(unsigned int i=0; i&lt;args.size(); i++) {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">      22948 :     args[i] = args_grid.getPoint(i)[0];</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :   }</a>
+<a name="360"><span class="lineNum">     360 </span>            :   std::vector&lt;double&gt; argsT;</a>
+<a name="361"><span class="lineNum">     361 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; values;</a>
+<a name="362"><span class="lineNum">     362 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; derivs;</a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">        142 :   ofile_values.addConstantField(&quot;bf_keywords&quot;).printField(&quot;bf_keywords&quot;,&quot;{&quot;+getKeywordString()+&quot;}&quot;);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">        142 :   ofile_derivs.addConstantField(&quot;bf_keywords&quot;).printField(&quot;bf_keywords&quot;,&quot;{&quot;+getKeywordString()+&quot;}&quot;);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">        213 :   ofile_values.addConstantField(&quot;min&quot;).printField(&quot;min&quot;,intervalMinStr());</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">        213 :   ofile_values.addConstantField(&quot;max&quot;).printField(&quot;max&quot;,intervalMaxStr());</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">        213 :   ofile_derivs.addConstantField(&quot;min&quot;).printField(&quot;min&quot;,intervalMinStr());</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">        213 :   ofile_derivs.addConstantField(&quot;max&quot;).printField(&quot;max&quot;,intervalMaxStr());</span></a>
+<a name="372"><span class="lineNum">     372 </span>            : </a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">        142 :   ofile_values.addConstantField(&quot;nbins&quot;).printField(&quot;nbins&quot;,static_cast&lt;int&gt;(args_grid.getNbin()[0]));</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">        142 :   ofile_derivs.addConstantField(&quot;nbins&quot;).printField(&quot;nbins&quot;,static_cast&lt;int&gt;(args_grid.getNbin()[0]));</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         71 :   if(arePeriodic()) {</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">         52 :     ofile_values.addConstantField(&quot;periodic&quot;).printField(&quot;periodic&quot;,&quot;true&quot;);</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         52 :     ofile_derivs.addConstantField(&quot;periodic&quot;).printField(&quot;periodic&quot;,&quot;true&quot;);</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span>            :   else {</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         90 :     ofile_values.addConstantField(&quot;periodic&quot;).printField(&quot;periodic&quot;,&quot;false&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         90 :     ofile_derivs.addConstantField(&quot;periodic&quot;).printField(&quot;periodic&quot;,&quot;false&quot;);</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :   }</a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         71 :   getMultipleValue(args,argsT,values,derivs,numerical_deriv);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         71 :   ofile_values.fmtField(output_fmt_values);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         71 :   ofile_derivs.fmtField(output_fmt_derivs);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">      23019 :   for(unsigned int i=0; i&lt;args.size(); i++) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">      45896 :     ofile_values.printField(&quot;arg&quot;,args[i]);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      22948 :     ofile_derivs.printField(&quot;arg&quot;,args[i]);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">     410060 :     for(unsigned int k=0; k&lt;getNumberOfBasisFunctions(); k++) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">     774224 :       ofile_values.printField(getBasisFunctionLabel(k),values[i][k]);</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">     774224 :       ofile_derivs.printField(&quot;d_&quot;+getBasisFunctionLabel(k),derivs[i][k]);</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :     }</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">      22948 :     ofile_values.printField();</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">      22948 :     ofile_derivs.printField();</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         71 :   ofile_values.fmtField();</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         71 :   ofile_derivs.fmtField();</span></a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">        213 : }</span></a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span>            : }</a>
+<a name="405"><span class="lineNum">     405 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BasisFunctions.h.func-sort-c.html b/coverage/ves/BasisFunctions.h.func-sort-c.html
new file mode 100644
index 0000000000..097cf8e249
--- /dev/null
+++ b/coverage/ves/BasisFunctions.h.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BasisFunctions.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BasisFunctions.h<span style="font-size: 80%;"> (<a href="BasisFunctions.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BasisFunctions.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#178">_ZN4PLMD3ves14BasisFunctions5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#179">_ZN4PLMD3ves14BasisFunctions9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#293">_ZN4PLMD3ves14BasisFunctions16addKeywordToListINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_RKSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#285">_ZN4PLMD3ves14BasisFunctions16addKeywordToListIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#228">_ZN4PLMD3ves14BasisFunctions28setAllUniformIntegralsToZeroEv</a></td>
+              <td class="coverFnHi">159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#193">_ZN4PLMD3ves14BasisFunctions25setNumberOfBasisFunctionsEj</a></td>
+              <td class="coverFnHi">249</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#285">_ZN4PLMD3ves14BasisFunctions16addKeywordToListIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_</a></td>
+              <td class="coverFnHi">277</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#285">_ZN4PLMD3ves14BasisFunctions16addKeywordToListINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_T_</a></td>
+              <td class="coverFnHi">593</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BasisFunctions.h.func.html b/coverage/ves/BasisFunctions.h.func.html
new file mode 100644
index 0000000000..eff7118822
--- /dev/null
+++ b/coverage/ves/BasisFunctions.h.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BasisFunctions.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BasisFunctions.h<span style="font-size: 80%;"> (<a href="BasisFunctions.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BasisFunctions.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#293">_ZN4PLMD3ves14BasisFunctions16addKeywordToListINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_RKSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#285">_ZN4PLMD3ves14BasisFunctions16addKeywordToListINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_T_</a></td>
+              <td class="coverFnHi">593</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#285">_ZN4PLMD3ves14BasisFunctions16addKeywordToListIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#285">_ZN4PLMD3ves14BasisFunctions16addKeywordToListIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEET_</a></td>
+              <td class="coverFnHi">277</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#193">_ZN4PLMD3ves14BasisFunctions25setNumberOfBasisFunctionsEj</a></td>
+              <td class="coverFnHi">249</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#228">_ZN4PLMD3ves14BasisFunctions28setAllUniformIntegralsToZeroEv</a></td>
+              <td class="coverFnHi">159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#178">_ZN4PLMD3ves14BasisFunctions5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BasisFunctions.h.gcov.html#179">_ZN4PLMD3ves14BasisFunctions9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/BasisFunctions.h.gcov.html b/coverage/ves/BasisFunctions.h.gcov.html
new file mode 100644
index 0000000000..08fd39de5f
--- /dev/null
+++ b/coverage/ves/BasisFunctions.h.gcov.html
@@ -0,0 +1,393 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/BasisFunctions.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - BasisFunctions.h<span style="font-size: 80%;"> (source / <a href="BasisFunctions.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryMed">75.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_BasisFunctions_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_BasisFunctions_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #define PLUMED_VES_BASISFUNCTIONS_INIT(ao) BasisFunctions(ao)</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /**</a>
+<a name="37"><span class="lineNum">      37 </span>            : \ingroup INHERIT</a>
+<a name="38"><span class="lineNum">      38 </span>            : Abstract base class for implenting new 1D basis sets.</a>
+<a name="39"><span class="lineNum">      39 </span>            : */</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class Action;</a>
+<a name="42"><span class="lineNum">      42 </span>            : class Grid;</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : namespace ves {</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : class VesBias;</a>
+<a name="47"><span class="lineNum">      47 </span>            : class TargetDistribution;</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : class BasisFunctions :</a>
+<a name="50"><span class="lineNum">      50 </span>            :   public Action</a>
+<a name="51"><span class="lineNum">      51 </span>            : {</a>
+<a name="52"><span class="lineNum">      52 </span>            : private:</a>
+<a name="53"><span class="lineNum">      53 </span>            :   // print extra info about the basis set</a>
+<a name="54"><span class="lineNum">      54 </span>            :   bool print_debug_info_;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // to check if the basis set has been defined</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool has_been_set;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   // description of the basis set</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::string description_;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   // the type of the basis set</a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::string type_;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   // the maximum order of the basis functions</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned int norder_;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   // the total number of basis functions</a>
+<a name="64"><span class="lineNum">      64 </span>            :   unsigned int nbasis_;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   // the keywords used to invoke the basis set</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;std::string&gt; bf_keywords_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   // prefix for the basis function labels</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::string bf_label_prefix_;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   // label of each basis function</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt;std::string&gt; bf_labels_;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   // if the basis functions are periodic or not</a>
+<a name="72"><span class="lineNum">      72 </span>            :   bool periodic_;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   // if the basis functions are defined on a bounded interval or not</a>
+<a name="74"><span class="lineNum">      74 </span>            :   bool interval_bounded_;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   // the intrinsic interval of the basis functions</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::string interval_intrinsic_min_str_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::string interval_intrinsic_max_str_;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   double interval_intrinsic_min_;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   double interval_intrinsic_max_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double interval_intrinsic_range_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double interval_intrinsic_mean_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   // the defined (translated) interval of the basis functions</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::string interval_min_str_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::string interval_max_str_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   double interval_min_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   double interval_max_;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   double interval_range_;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   double interval_mean_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   // the derivative term in the chain rule coming from the translation of the interval</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double argT_derivf_;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // calculate numerically the integrals of the basis functions over the intervals</a>
+<a name="92"><span class="lineNum">      92 </span>            :   bool numerical_uniform_integrals_;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   unsigned int nbins_;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   // the integrals of the basis functions over the interval on which they are defined</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::vector &lt;double&gt; uniform_integrals_;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   //</a>
+<a name="97"><span class="lineNum">      97 </span>            :   VesBias* vesbias_pntr_;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   Action* action_pntr_;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   //</a>
+<a name="100"><span class="lineNum">     100 </span>            :   void getAllValuesNumericalDerivs(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const;</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : protected:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   // setup various stuff</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void setupBF();</a>
+<a name="105"><span class="lineNum">     105 </span>            :   void setupInterval();</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void setNumericalIntegrationBins(const unsigned int nbins) {nbins_=nbins;}</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void numericalUniformIntegrals();</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt;double&gt; numericalTargetDistributionIntegralsFromGrid(const Grid*) const ;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   virtual void setupLabels();</a>
+<a name="110"><span class="lineNum">     110 </span>            :   virtual void setupUniformIntegrals();</a>
+<a name="111"><span class="lineNum">     111 </span>            :   template&lt;typename T&gt;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   void addKeywordToList(const std::string&amp;, const T);</a>
+<a name="113"><span class="lineNum">     113 </span>            :   template&lt;typename T&gt;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   void addKeywordToList(const std::string&amp;, const std::vector&lt;T&gt;&amp;);</a>
+<a name="115"><span class="lineNum">     115 </span>            :   void addKeywordToList(const std::string&amp;, const bool);</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        111 :   void setPeriodic() {periodic_=true;}</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        138 :   void setNonPeriodic() {periodic_=false;}</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        249 :   void setIntervalBounded() {interval_bounded_=true;}</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :   void setIntervalNonBounded() {interval_bounded_=false;}</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        249 :   void setType(const std::string&amp; type_in) {type_=type_in;}</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        249 :   void setDescription(const std::string&amp; description_in) {description_=description_in;}</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   //</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void setNumberOfBasisFunctions(const unsigned int);</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         12 :   void setOrder(const unsigned int norder_in) {norder_=norder_in;}</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   void setIntrinsicInterval(const double, const double);</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void setIntrinsicInterval(const std::string&amp;, const std::string&amp;);</a>
+<a name="128"><span class="lineNum">     128 </span>            :   void setInterval(const double, const double);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   void setInterval(const std::string&amp;, const std::string&amp;);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   //</a>
+<a name="131"><span class="lineNum">     131 </span>            :   double intrinsicIntervalMin() const {return interval_intrinsic_min_;}</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    1752567 :   double intrinsicIntervalMax() const {return interval_intrinsic_max_;}</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::string intrinsicIntervalMinStr() const {return interval_intrinsic_min_str_;}</a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::string intrinsicIntervalMaxStr() const {return interval_intrinsic_max_str_;}</a>
+<a name="135"><span class="lineNum">     135 </span>            :   //</a>
+<a name="136"><span class="lineNum">     136 </span>            :   void setUniformIntegral(const unsigned int, const double);</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void setUniformIntegrals(const std::vector&lt;double&gt;&amp;);</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void setAllUniformIntegralsToZero();</a>
+<a name="139"><span class="lineNum">     139 </span>            :   //</a>
+<a name="140"><span class="lineNum">     140 </span>            :   void setLabelPrefix(const std::string&amp;);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void setLabel(const unsigned int, const std::string&amp;);</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void setLabels(const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : public:</a>
+<a name="145"><span class="lineNum">     145 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="146"><span class="lineNum">     146 </span>            :   explicit BasisFunctions(const ActionOptions&amp;ao);</a>
+<a name="147"><span class="lineNum">     147 </span>            :   bool hasBeenSet() const {return has_been_set;}</a>
+<a name="148"><span class="lineNum">     148 </span>            :   std::string getType() const {return type_;}</a>
+<a name="149"><span class="lineNum">     149 </span>            :   std::string getDescription() const {return description_;}</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">   33615870 :   unsigned int getOrder() const {return norder_;}</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">   13201612 :   unsigned int getNumberOfBasisFunctions() const {return nbasis_;}</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     112559 :   unsigned int numberOfBasisFunctions() const {return nbasis_;}</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   unsigned int getSize() const {return nbasis_;}</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    2661456 :   bool arePeriodic() const {return periodic_;}</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   bool intervalBounded() const {return interval_bounded_;}</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">     204981 :   double intervalMin() const {return interval_min_;}</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        281 :   double intervalMax() const {return interval_max_;}</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">     300134 :   double intervalRange() const {return interval_range_;}</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   double intervalMean() const {return interval_mean_;}</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   30352118 :   double intervalDerivf() const {return argT_derivf_;}</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        601 :   std::string intervalMinStr() const {return interval_min_str_;}</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        601 :   std::string intervalMaxStr() const {return interval_max_str_;}</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        133 :   std::vector&lt;double&gt; getUniformIntegrals() const {return uniform_integrals_;}</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::vector&lt;double&gt; getTargetDistributionIntegrals(const TargetDistribution*) const;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   //</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::vector&lt;std::string&gt; getKeywordList() const {return bf_keywords_;}</a>
+<a name="167"><span class="lineNum">     167 </span>            :   std::string getKeywordString() const;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   //</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">     787685 :   std::string getBasisFunctionLabel(const unsigned int index) const {return bf_labels_[index];}</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   std::vector&lt;std::string&gt; getBasisFunctionLabels() const {return bf_labels_;}</a>
+<a name="171"><span class="lineNum">     171 </span>            :   //</a>
+<a name="172"><span class="lineNum">     172 </span>            :   void linkVesBias(VesBias*);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   void linkAction(Action*);</a>
+<a name="174"><span class="lineNum">     174 </span>            :   VesBias* getPntrToVesBias() const;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   Action* getPntrToAction() const;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   //</a>
+<a name="177"><span class="lineNum">     177 </span>            :   double translateArgument(const double, bool&amp;) const;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   double checkIfArgumentInsideInterval(const double, bool&amp;) const;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   //</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   void apply() override {};</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :   void calculate() override {};</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   // calculate the value for the n-th basis function</a>
+<a name="183"><span class="lineNum">     183 </span>            :   double getValue(const double, const unsigned int, double&amp;, bool&amp;) const;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   // calculate the values for all basis functions</a>
+<a name="185"><span class="lineNum">     185 </span>            :   virtual void getAllValues(const double, double&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const = 0;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   //virtual void get2ndDerivatives(const double, std::vector&lt;double&gt;&amp;)=0;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   void printInfo() const;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   //</a>
+<a name="189"><span class="lineNum">     189 </span>            :   void getMultipleValue(const std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;std::vector&lt;double&gt; &gt;&amp;, std::vector&lt;std::vector&lt;double&gt; &gt;&amp;, const bool numerical_deriv=false) const;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void writeBasisFunctionsToFile(OFile&amp;, OFile&amp;, const std::string&amp; min_in, const std::string&amp; max_in, unsigned int nbins=1000, const bool ignore_periodicity=false, const std::string&amp; output_fmt_values=&quot;%15.8f&quot;, const std::string&amp; output_fmt_derivs=&quot;%15.8f&quot;, const bool numerical_deriv=false) const;</a>
+<a name="191"><span class="lineNum">     191 </span>            : };</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : inline</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        249 : void BasisFunctions::setNumberOfBasisFunctions(const unsigned int nbasis_in) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        249 :   nbasis_=nbasis_in;</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        249 :   bf_labels_.assign(nbasis_,&quot;&quot;);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        249 :   uniform_integrals_.assign(nbasis_,0.0);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        249 : }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : inline</a>
+<a name="203"><span class="lineNum">     203 </span>            : VesBias* BasisFunctions::getPntrToVesBias() const {</a>
+<a name="204"><span class="lineNum">     204 </span>            :   plumed_massert(vesbias_pntr_!=NULL,&quot;the VES bias has not been linked&quot;);</a>
+<a name="205"><span class="lineNum">     205 </span>            :   return vesbias_pntr_;</a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : inline</a>
+<a name="210"><span class="lineNum">     210 </span>            : Action* BasisFunctions::getPntrToAction() const {</a>
+<a name="211"><span class="lineNum">     211 </span>            :   plumed_massert(action_pntr_!=NULL,&quot;the action has not been linked&quot;);</a>
+<a name="212"><span class="lineNum">     212 </span>            :   return action_pntr_;</a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : inline</a>
+<a name="217"><span class="lineNum">     217 </span>            : void BasisFunctions::setUniformIntegral(const unsigned index, const double value) {</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        264 :   uniform_integrals_[index] = value;</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : inline</a>
+<a name="223"><span class="lineNum">     223 </span>            : void BasisFunctions::setUniformIntegrals(const std::vector&lt;double&gt;&amp; uniform_integrals_in) {</a>
+<a name="224"><span class="lineNum">     224 </span>            :   plumed_assert(uniform_integrals_in.size()==nbasis_);</a>
+<a name="225"><span class="lineNum">     225 </span>            :   uniform_integrals_ = uniform_integrals_in;</a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : inline</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">        159 : void BasisFunctions::setAllUniformIntegralsToZero() {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        159 :   uniform_integrals_.assign(nbasis_,0.0);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">        159 : }</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : inline</a>
+<a name="235"><span class="lineNum">     235 </span>            : void BasisFunctions::setLabelPrefix(const std::string&amp; bf_label_prefix_in) {</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         68 :   bf_label_prefix_ = bf_label_prefix_in;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         68 : }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : inline</a>
+<a name="241"><span class="lineNum">     241 </span>            : void BasisFunctions::setLabel(const unsigned int index, const std::string&amp; label) {</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">       1140 :   bf_labels_[index] = label;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">       3238 : }</span></a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : inline</a>
+<a name="247"><span class="lineNum">     247 </span>            : void BasisFunctions::setLabels(const std::vector&lt;std::string&gt;&amp; bf_labels_in) {</a>
+<a name="248"><span class="lineNum">     248 </span>            :   bf_labels_ = bf_labels_in;</a>
+<a name="249"><span class="lineNum">     249 </span>            : }</a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : inline</a>
+<a name="253"><span class="lineNum">     253 </span>            : double BasisFunctions::translateArgument(const double arg, bool&amp; inside_interval) const {</a>
+<a name="254"><span class="lineNum">     254 </span>            :   // NOTE: only works for symmetric intrinsic intervals</a>
+<a name="255"><span class="lineNum">     255 </span>            :   inside_interval=true;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">    4895662 :   double argT = (arg-interval_mean_)*argT_derivf_;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">    4895662 :   if(argT &lt; interval_intrinsic_min_) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">        433 :     inside_interval=false;</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        433 :     argT=interval_intrinsic_min_;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   }</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">    4895229 :   else if(argT &gt; interval_intrinsic_max_) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      13665 :     inside_interval=false;</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">      13665 :     argT=interval_intrinsic_max_;</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span>            :   return argT;</a>
+<a name="266"><span class="lineNum">     266 </span>            : }</a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            : inline</a>
+<a name="270"><span class="lineNum">     270 </span>            : double BasisFunctions::checkIfArgumentInsideInterval(const double arg, bool&amp; inside_interval) const {</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      62249 :   inside_interval=true;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :   double argT = arg;</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">     947044 :   if(arg &lt; interval_min_) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        362 :     inside_interval=false;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">        362 :     argT=interval_min_;</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :   }</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">     946682 :   else if(arg &gt; interval_max_) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">        369 :     inside_interval=false;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        369 :     argT=interval_max_;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   }</a>
+<a name="281"><span class="lineNum">     281 </span>            :   return argT;</a>
+<a name="282"><span class="lineNum">     282 </span>            : }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span>            : </a>
+<a name="286"><span class="lineNum">     286 </span>            : template&lt;typename T&gt;</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        877 : void BasisFunctions::addKeywordToList(const std::string&amp; keyword, const T value) {</span></a>
+<a name="288"><span class="lineNum">     288 </span>            :   std::string str_value;</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        877 :   Tools::convert(value,str_value);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">       1754 :   bf_keywords_.push_back(keyword+&quot;=&quot;+str_value);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        877 : }</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : template&lt;typename T&gt;</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          2 : void BasisFunctions::addKeywordToList(const std::string&amp; keyword, const std::vector&lt;T&gt;&amp; values) {</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :   std::string str_value;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   std::string str_keywordvalues;</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          2 :   Tools::convert(values[0],str_value);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          4 :   str_keywordvalues = keyword + &quot;=&quot; + str_value;</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">          5 :   for(unsigned int i=1; i&lt;values.size(); i++) {</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          3 :     Tools::convert(values[i],str_value);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          6 :     str_keywordvalues += &quot;,&quot; + str_value;</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :   }</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          2 :   bf_keywords_.push_back(str_keywordvalues);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          2 : }</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : inline</a>
+<a name="309"><span class="lineNum">     309 </span>            : void BasisFunctions::addKeywordToList(const std::string&amp; keyword, const bool value) {</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         87 :   if(value) {bf_keywords_.push_back(keyword);}</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : }</a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : }</a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsBase.cpp.func-sort-c.html b/coverage/ves/CoeffsBase.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2bb587f5c7
--- /dev/null
+++ b/coverage/ves/CoeffsBase.cpp.func-sort-c.html
@@ -0,0 +1,200 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsBase.cpp<span style="font-size: 80%;"> (<a href="CoeffsBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntry">301</td>
+            <td class="headerCovTableEntryLo">42.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryLo">46.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoeffsBase.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#321">_ZN4PLMD3ves10CoeffsBase10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#278">_ZN4PLMD3ves10CoeffsBase12setDataLabelERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#238">_ZN4PLMD3ves10CoeffsBase13resizeIndicesERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#245">_ZN4PLMD3ves10CoeffsBase13resizeIndicesERSt6vectorIPNS0_14BasisFunctionsESaIS4_EE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#369">_ZN4PLMD3ves10CoeffsBase17setDimensionLabelEjRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#191">_ZN4PLMD3ves10CoeffsBase19reinitializeIndicesERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/ves/CoeffsBase.cpp.func.html b/coverage/ves/CoeffsBase.cpp.func.html
new file mode 100644
index 0000000000..20e2cf51c0
--- /dev/null
+++ b/coverage/ves/CoeffsBase.cpp.func.html
@@ -0,0 +1,200 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsBase.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsBase.cpp<span style="font-size: 80%;"> (<a href="CoeffsBase.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntry">301</td>
+            <td class="headerCovTableEntryLo">42.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryLo">46.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CoeffsBase.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+    <tr>
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+    <tr>
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+              <td class="coverFnHi">2721</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.cpp.gcov.html#257">_ZNK4PLMD3ves10CoeffsBase9sameShapeERKS1_</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsBase.cpp.gcov.html b/coverage/ves/CoeffsBase.cpp.gcov.html
new file mode 100644
index 0000000000..4945ceef6e
--- /dev/null
+++ b/coverage/ves/CoeffsBase.cpp.gcov.html
@@ -0,0 +1,593 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsBase.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsBase.cpp<span style="font-size: 80%;"> (source / <a href="CoeffsBase.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">127</td>
+            <td class="headerCovTableEntry">301</td>
+            <td class="headerCovTableEntryLo">42.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryLo">46.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CoeffsBase.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;vector&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;string&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace ves {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 : CoeffsBase::CoeffsBase(</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   const std::string&amp; label,</a>
+<a name="41"><span class="lineNum">      41 </span>            :   const std::vector&lt;std::string&gt;&amp; dimension_labels,</a>
+<a name="42"><span class="lineNum">      42 </span>            :   const std::vector&lt;unsigned int&gt;&amp; indices_shape,</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :   const bool use_iteration_counter):</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :   label_(label),</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 :   data_label_(label),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineNoCov">          0 :   coeffs_type_(Generic),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineNoCov">          0 :   iteration_and_time_active_(use_iteration_counter),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineNoCov">          0 :   iteration_opt(0),</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineNoCov">          0 :   time_md(-1.0),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :   active(true),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   action_pntr_(NULL),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :   vesbias_pntr_(NULL),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   ndimensions_(0),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   indices_shape_(0),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :   ncoeffs_(0),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   coeffs_descriptions_(0),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   dimension_labels_(0),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :   args_(0),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   basisf_(0),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :   multicoeffs_(false),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :   multicoeffs_args_(0),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   multicoeffs_basisf_(0),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :   field_type_(&quot;type&quot;),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :   field_ndimensions_(&quot;ndimensions&quot;),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   field_ncoeffs_total_(&quot;ncoeffs_total&quot;),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :   field_shape_prefix_(&quot;shape_&quot;),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   field_time_(&quot;time&quot;),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :   field_iteration_(&quot;iteration&quot;),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   output_fmt_(&quot;%30.16e&quot;)</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : {</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   initializeIndices(indices_shape,dimension_labels);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   setAllCoeffsDescriptions();</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        377 : CoeffsBase::CoeffsBase(</span></a>
+<a name="77"><span class="lineNum">      77 </span>            :   const std::string&amp; label,</a>
+<a name="78"><span class="lineNum">      78 </span>            :   const std::vector&lt;Value*&gt;&amp; args,</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;BasisFunctions*&gt;&amp; basisf,</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        377 :   const bool use_iteration_counter):</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        377 :   label_(label),</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        377 :   data_label_(label),</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        377 :   coeffs_type_(LinearBasisSet),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        377 :   iteration_and_time_active_(use_iteration_counter),</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        377 :   iteration_opt(0),</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        377 :   time_md(-1.0),</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        377 :   active(true),</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        377 :   action_pntr_(NULL),</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        377 :   vesbias_pntr_(NULL),</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        377 :   ndimensions_(0),</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        377 :   indices_shape_(0),</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        377 :   ncoeffs_(0),</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        377 :   coeffs_descriptions_(0),</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        377 :   dimension_labels_(0),</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        377 :   args_(args),</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        377 :   basisf_(basisf),</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        377 :   multicoeffs_(false),</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        377 :   multicoeffs_args_(0),</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        377 :   multicoeffs_basisf_(0),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        377 :   field_type_(&quot;type&quot;),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        377 :   field_ndimensions_(&quot;ndimensions&quot;),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        377 :   field_ncoeffs_total_(&quot;ncoeffs_total&quot;),</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        377 :   field_shape_prefix_(&quot;shape_&quot;),</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        377 :   field_time_(&quot;time&quot;),</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        377 :   field_iteration_(&quot;iteration&quot;),</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        377 :   output_fmt_(&quot;%30.16e&quot;)</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : {</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        377 :   plumed_massert(args_.size()==basisf_.size(),&quot;CoeffsBase: number of arguments do not match number of basis functions&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        377 :   std::vector&lt;std::string&gt; dimension_labels(args_.size());</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        377 :   std::vector&lt;unsigned int&gt; indices_shape(args_.size());</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        789 :   for(unsigned int i=0; i&lt;args_.size(); i++) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        412 :     dimension_labels[i]=args_[i]-&gt;getName();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        412 :     indices_shape[i]=basisf_[i]-&gt;getNumberOfBasisFunctions();</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        377 :   initializeIndices(indices_shape,dimension_labels);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        377 :   setupBasisFunctionsInfo();</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        377 : }</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 : CoeffsBase::CoeffsBase(</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   const std::string&amp; label,</a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;std::vector&lt;Value*&gt; &gt;&amp; multicoeffs_args,</a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;&amp; multicoeffs_basisf,</a>
+<a name="124"><span class="lineNum">     124 </span>            :   const bool use_iteration_counter,</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   const std::string&amp; multicoeffs_label):</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 :   label_(label),</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :   data_label_(label),</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :   coeffs_type_(MultiCoeffs_LinearBasisSet),</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :   iteration_and_time_active_(use_iteration_counter),</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :   iteration_opt(0),</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   time_md(-1.0),</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   active(true),</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :   action_pntr_(NULL),</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :   vesbias_pntr_(NULL),</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :   ndimensions_(0),</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :   indices_shape_(0),</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :   ncoeffs_(0),</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :   coeffs_descriptions_(0),</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :   dimension_labels_(0),</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   args_(0),</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   basisf_(0),</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   multicoeffs_(true),</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   multicoeffs_args_(multicoeffs_args),</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   multicoeffs_basisf_(multicoeffs_basisf),</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   field_type_(&quot;type&quot;),</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :   field_ndimensions_(&quot;ndimensions&quot;),</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   field_ncoeffs_total_(&quot;ncoeffs_total&quot;),</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineNoCov">          0 :   field_shape_prefix_(&quot;shape_&quot;),</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   field_time_(&quot;time&quot;),</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   field_iteration_(&quot;iteration&quot;),</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   output_fmt_(&quot;%30.16e&quot;)</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : {</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   plumed_massert(multicoeffs_args.size()==multicoeffs_basisf.size(),&quot;Multi Coeffs: number of arguments vectors does not match number of basis functions vectors&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 :   unsigned int num_args = multicoeffs_args[0].size();</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 :   unsigned int dim = num_args+1;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   std::vector&lt;std::string&gt; dimension_labels(dim);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned int&gt; indices_shape(dim);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;num_args; i++) {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     std::string ip;</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     Tools::convert(i+1,ip);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     dimension_labels[i] = &quot;bf&quot; + ip;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     indices_shape[i] = multicoeffs_basisf[0][i]-&gt;getNumberOfBasisFunctions();</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   indices_shape[dim-1] = multicoeffs_args.size();</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   dimension_labels[dim-1] = multicoeffs_label;</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   for(unsigned int k=0; k&lt;multicoeffs_args.size(); k++) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :     plumed_massert(multicoeffs_args[k].size()==num_args &amp;&amp; multicoeffs_basisf[k].size()==num_args,&quot;Multi Coeffs: arguments and basis functions vectors for each bias should be of the same size&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :     for(unsigned int i=0; i&lt;num_args; i++) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       plumed_massert(indices_shape[i]==multicoeffs_basisf[k][i]-&gt;getNumberOfBasisFunctions(),&quot;Multi Coeffs: the coeffs shape for each bias should be identical&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineNoCov">          0 :   initializeIndices(indices_shape,dimension_labels);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   setupBasisFunctionsInfo();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">    1026402 : CoeffsBase::~CoeffsBase() {}</span></a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        377 : void CoeffsBase::initializeIndices(const std::vector&lt;unsigned int&gt;&amp; indices_shape, const std::vector&lt;std::string&gt;&amp; dimension_labels) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        377 :   plumed_massert(indices_shape.size()==dimension_labels.size(),&quot;indices shape and dimension labels must be of the same size&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        377 :   ndimensions_=indices_shape.size();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        377 :   indices_shape_=indices_shape;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        377 :   dimension_labels_=dimension_labels;</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        377 :   ncoeffs_=1;</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        789 :   for(unsigned int i=0; i&lt;ndimensions_; i++) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        412 :     ncoeffs_*=indices_shape_[i];</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        377 :   coeffs_descriptions_.resize(ncoeffs_);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        377 : }</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 : void CoeffsBase::reinitializeIndices(const std::vector&lt;unsigned int&gt;&amp; indices_shape_new) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   plumed_massert(indices_shape_.size()&gt;0,&quot;indices must have been previously initialized before using this function&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   plumed_massert(dimension_labels_.size()&gt;0,&quot;indices must have been previously initialized before using this function&quot;);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   plumed_massert(indices_shape_new.size()==numberOfDimensions(),&quot;when resizeing Coeffs the dimension must be constant&quot;);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   indices_shape_=indices_shape_new;</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineNoCov">          0 :   ncoeffs_=1;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndimensions_; i++) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :     ncoeffs_*=indices_shape_[i];</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   coeffs_descriptions_.clear();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :   coeffs_descriptions_.resize(ncoeffs_);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        377 : void CoeffsBase::setupBasisFunctionsInfo() {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        377 :   plumed_massert(indices_shape_.size()&gt;0,&quot;indices must be initialized before running this function&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        377 :   if(coeffs_type_==LinearBasisSet) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">       9305 :     for(unsigned int i=0; i&lt;numberOfCoeffs(); i++) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       8928 :       std::vector&lt;unsigned int&gt; indices=getIndices(i);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :       std::string desc;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">       8928 :       desc=basisf_[0]-&gt;getBasisFunctionLabel(indices[0]);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      13409 :       for(unsigned int k=1; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       8962 :         desc+=&quot;*&quot;+basisf_[k]-&gt;getBasisFunctionLabel(indices[k]);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :       }</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       8928 :       setCoeffDescription(i,desc);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     }</a>
+<a name="219"><span class="lineNum">     219 </span>            :   }</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :   else if(coeffs_type_==MultiCoeffs_LinearBasisSet) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     for(unsigned int i=0; i&lt;numberOfCoeffs(); i++) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :       std::vector&lt;unsigned int&gt; indices=getIndices(i);</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :       unsigned int mc_id = indices[ndimensions_-1];</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :       std::string mc_idstr;</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :       Tools::convert(mc_id,mc_idstr);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :       // std::string mc_label = getDimensionLabel(ndimensions_-1);</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       std::string postfix = &quot;:&quot; + mc_idstr;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :       std::string desc =&quot;&quot;;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 :       desc+=multicoeffs_basisf_[mc_id][0]-&gt;getBasisFunctionLabel(indices[0]);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 :       for(unsigned int k=1; k&lt;(numberOfDimensions()-1); k++) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :         desc+=&quot;*&quot;+multicoeffs_basisf_[mc_id][k]-&gt;getBasisFunctionLabel(indices[k]);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :       }</a>
+<a name="233"><span class="lineNum">     233 </span>            :       desc+=postfix;</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :       setCoeffDescription(i,desc);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     }</a>
+<a name="236"><span class="lineNum">     236 </span>            :   }</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">        377 : }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 : void CoeffsBase::resizeIndices(const std::vector&lt;unsigned int&gt;&amp; indices_shape_new) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   plumed_massert(coeffs_type_==Generic,&quot;Coeffs type must be Generic when resizeing based on a new indices shape vector&quot;);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :   reinitializeIndices(indices_shape_new);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineNoCov">          0 :   setAllCoeffsDescriptions();</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 : void CoeffsBase::resizeIndices(std::vector&lt;BasisFunctions*&gt;&amp; basisf_new) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   plumed_massert(coeffs_type_==LinearBasisSet,&quot;Coeffs type must be LinearBasisSet when resizeing based on a new basis function set&quot;);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   basisf_=basisf_new;</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned int&gt; indices_shape_new(basisf_new.size());</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;basisf_new.size(); i++) {</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :     indices_shape_new[i]=basisf_new[i]-&gt;getNumberOfBasisFunctions();</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   reinitializeIndices(indices_shape_new);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :   setupBasisFunctionsInfo();</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          6 : bool CoeffsBase::sameShape(const CoeffsBase&amp; coeffsbase_in) const {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          6 :   if(numberOfDimensions()!=coeffsbase_in.numberOfDimensions()) {</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     return false;</a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          6 :   if(numberOfCoeffs()!=coeffsbase_in.numberOfCoeffs()) {</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :     return false;</a>
+<a name="265"><span class="lineNum">     265 </span>            :   }</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         12 :   for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          6 :     if(shapeOfIndices(k)!=coeffsbase_in.shapeOfIndices(k)) {</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :       return false;</a>
+<a name="269"><span class="lineNum">     269 </span>            :     }</a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span>            :   return true;</a>
+<a name="272"><span class="lineNum">     272 </span>            : }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 : void CoeffsBase::setLabel(const std::string&amp; label) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineNoCov">          0 :   label_=label;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 : void CoeffsBase::setDataLabel(const std::string&amp; data_label) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineNoCov">          0 :   data_label_=data_label;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">        754 : void CoeffsBase::setLabels(const std::string&amp; label) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">        754 :   label_=label;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">        754 :   data_label_=label;</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        754 : }</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 : void CoeffsBase::setLabels(const std::string&amp; label, const std::string&amp; data_label) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   label_=label;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineNoCov">          0 :   data_label_=data_label;</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span>            : </a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       3376 : std::string CoeffsBase::getTypeStr() const {</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       3376 :   std::string type_str=&quot;&quot;;</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       3376 :   if(coeffs_type_==Generic) {</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     type_str = &quot;Generic&quot;;</a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       3376 :   else if(coeffs_type_==LinearBasisSet) {</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     type_str = &quot;LinearBasisSet&quot;;</a>
+<a name="304"><span class="lineNum">     304 </span>            :   }</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineNoCov">          0 :   else if(coeffs_type_==MultiCoeffs_LinearBasisSet) {</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     type_str = &quot;MultiCoeffs_LinearBasisSet&quot;;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">       3376 :   return type_str;</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : }</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineNoCov">          0 : void CoeffsBase::setType(const CoeffsType coeffs_type) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 :   coeffs_type_=coeffs_type;</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         90 : void CoeffsBase::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         90 :   vesbias_pntr_ = vesbias_pntr_in;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         90 :   action_pntr_ = static_cast&lt;Action*&gt;(vesbias_pntr_in);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         90 : }</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 : void CoeffsBase::linkAction(Action* action_pntr_in) {</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineNoCov">          0 :   action_pntr_ = action_pntr_in;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            : </a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 : bool CoeffsBase::indicesExist(const std::vector&lt;unsigned int&gt;&amp; indices) const {</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   plumed_dbg_assert(indices.size()==ndimensions_);</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :   for(unsigned int k=0; k&lt;ndimensions_; k++) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 :     if(indices[k]&gt;=indices_shape_[k]) {</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :       return false;</a>
+<a name="333"><span class="lineNum">     333 </span>            :     }</a>
+<a name="334"><span class="lineNum">     334 </span>            :   }</a>
+<a name="335"><span class="lineNum">     335 </span>            :   return true;</a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">       8928 : void CoeffsBase::setCoeffDescription(const size_t index, const std::string&amp; description) {</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :   coeffs_descriptions_[index]=description;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       8928 : }</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 : void CoeffsBase::setCoeffDescription(const std::vector&lt;unsigned int&gt;&amp; indices, const std::string&amp; description) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 :   setCoeffDescription(getIndex(indices), description);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 : void CoeffsBase::setAllCoeffsDescriptions(const std::string&amp; description_prefix) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;numberOfCoeffs(); i++) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :     std::vector&lt;unsigned int&gt; indices=getIndices(i);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :     std::string is; Tools::convert(indices[0],is);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineNoCov">          0 :     std::string desc=description_prefix+&quot;(&quot;+is;</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineNoCov">          0 :     for(unsigned int k=1; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 :       Tools::convert(indices[k],is); desc+=&quot;,&quot;+is;</span></a>
+<a name="356"><span class="lineNum">     356 </span>            :     }</a>
+<a name="357"><span class="lineNum">     357 </span>            :     desc+=&quot;)&quot;;</a>
+<a name="358"><span class="lineNum">     358 </span>            :     coeffs_descriptions_[i]=desc;</a>
+<a name="359"><span class="lineNum">     359 </span>            :   }</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 : void CoeffsBase::setAllCoeffsDescriptions(const std::vector&lt;std::string&gt;&amp; coeffs_descriptions) {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :   plumed_massert(coeffs_descriptions.size()==numberOfCoeffs(),&quot;The coeffs description vector doesn't match the number of coeffs&quot;);</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;numberOfCoeffs(); i++) {</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :     coeffs_descriptions_[i]=coeffs_descriptions[i];</a>
+<a name="367"><span class="lineNum">     367 </span>            :   }</a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 : void CoeffsBase::setDimensionLabel(const unsigned int dim_index, const std::string&amp; label) {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :   plumed_massert(dim_index&lt;numberOfDimensions(),&quot;Trying to set the label of a dimension outside the number of dimensions&quot;);</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :   dimension_labels_[dim_index]=label;</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 : void CoeffsBase::setAllDimensionLabels(const std::string&amp; label_prefix) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;numberOfDimensions(); i++) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     dimension_labels_[i]=label_prefix + is;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :   }</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 : void CoeffsBase::setAllDimensionLabels(const std::vector&lt;std::string&gt;&amp; labels) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;numberOfDimensions(); i++) {</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :     dimension_labels_[i]=labels[i];</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :   }</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">       3008 : void CoeffsBase::writeCoeffsInfoToFile(OFile&amp; ofile) const {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">       3008 :   ofile.addConstantField(field_type_).printField(field_type_,getTypeStr());</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       3008 :   ofile.addConstantField(field_ndimensions_).printField(field_ndimensions_,(int) numberOfDimensions());</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">       3008 :   ofile.addConstantField(field_ncoeffs_total_).printField(field_ncoeffs_total_,(int) numberOfCoeffs());</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">       6780 :   for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">       7544 :     ofile.addConstantField(field_shape_prefix_+getDimensionLabel(k));</span></a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">       7544 :     ofile.printField(field_shape_prefix_+getDimensionLabel(k),(int) shapeOfIndices(k));</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :   }</a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">       3008 : }</span></a>
+<a name="401"><span class="lineNum">     401 </span>            : </a>
+<a name="402"><span class="lineNum">     402 </span>            : </a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">        368 : void CoeffsBase::getCoeffsInfoFromFile(IFile&amp; ifile, const bool ignore_coeffs_info) {</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :   int int_tmp;</a>
+<a name="405"><span class="lineNum">     405 </span>            :   // label</a>
+<a name="406"><span class="lineNum">     406 </span>            :   std::string coeffs_type_f;</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">        368 :   if(ifile.scanField(field_type_,coeffs_type_f)) {</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :     // empty for now</a>
+<a name="409"><span class="lineNum">     409 </span>            :   }</a>
+<a name="410"><span class="lineNum">     410 </span>            :   else {</a>
+<a name="411"><span class="lineNum">     411 </span>            :     return;</a>
+<a name="412"><span class="lineNum">     412 </span>            :   }</a>
+<a name="413"><span class="lineNum">     413 </span>            :   // number of dimensions</a>
+<a name="414"><span class="lineNum">     414 </span>            :   unsigned int ndimensions_f = 0;</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        368 :   if(ifile.scanField(field_ndimensions_,int_tmp)) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        368 :     ndimensions_f=(unsigned int) int_tmp;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :   }</a>
+<a name="418"><span class="lineNum">     418 </span>            :   else {</a>
+<a name="419"><span class="lineNum">     419 </span>            :     return;</a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span>            :   // total number of coeffs</a>
+<a name="422"><span class="lineNum">     422 </span>            :   size_t ncoeffs_total_f = 0;</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        368 :   if(ifile.scanField(field_ncoeffs_total_,int_tmp)) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        368 :     ncoeffs_total_f=(size_t) int_tmp;</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :   }</a>
+<a name="426"><span class="lineNum">     426 </span>            :   else {</a>
+<a name="427"><span class="lineNum">     427 </span>            :     return;</a>
+<a name="428"><span class="lineNum">     428 </span>            :   }</a>
+<a name="429"><span class="lineNum">     429 </span>            :   // shape of indices</a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">        368 :   std::vector&lt;unsigned int&gt; indices_shape_f(numberOfDimensions());</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        747 :   for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        758 :     if(ifile.scanField(field_shape_prefix_+getDimensionLabel(k),int_tmp)) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        379 :       indices_shape_f[k]=(unsigned int) int_tmp;</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :     }</a>
+<a name="435"><span class="lineNum">     435 </span>            :     else {</a>
+<a name="436"><span class="lineNum">     436 </span>            :       return;</a>
+<a name="437"><span class="lineNum">     437 </span>            :     }</a>
+<a name="438"><span class="lineNum">     438 </span>            :   }</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">        368 :   if(!ignore_coeffs_info) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">        736 :     std::string msg_header=&quot;Error when reading in coeffs from file &quot; + ifile.getPath() + &quot;: &quot;;</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">        368 :     checkCoeffsInfo(msg_header, coeffs_type_f, ndimensions_f, ncoeffs_total_f, indices_shape_f);</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :   }</a>
+<a name="443"><span class="lineNum">     443 </span>            : }</a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        368 : void CoeffsBase::checkCoeffsInfo(const std::string&amp; msg_header, const std::string&amp; coeffs_type_f, const unsigned int ndimensions_f, const size_t ncoeffs_total_f, const std::vector&lt;unsigned int&gt;&amp; indices_shape_f) {</span></a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        736 :   if(coeffs_type_f != getTypeStr()) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 :     std::string msg = msg_header + &quot; coeffs type &quot; + coeffs_type_f + &quot; from file doesn't match the defined value &quot; + getTypeStr();</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :     plumed_merror(msg);</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :   }</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">        368 :   if(ndimensions_f != numberOfDimensions() ) {</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineNoCov">          0 :     std::string s1; Tools::convert(ndimensions_f,s1);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 :     std::string s2; Tools::convert(numberOfDimensions(),s2);</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :     std::string msg = msg_header + &quot; the number of dimensions &quot; + s1 + &quot; in file doesn't match the defined value &quot; + s2;</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :     plumed_merror(msg);</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :   }</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">        368 :   if(ncoeffs_total_f != numberOfCoeffs() ) {</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineNoCov">          0 :     std::string s1; Tools::convert(ncoeffs_total_f,s1);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 :     std::string s2; Tools::convert(numberOfCoeffs(),s2);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :     std::string msg = msg_header + &quot; the number of coeffs &quot; + s1 + &quot; in file doesn't match the defined value &quot; + s2;</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineNoCov">          0 :     plumed_merror(msg);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   }</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        747 :   for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">        379 :     if(indices_shape_f[k] != shapeOfIndices(k) ) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :       std::string s1; Tools::convert(indices_shape_f[k],s1);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineNoCov">          0 :       std::string s2; Tools::convert(shapeOfIndices(k),s2);</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineNoCov">          0 :       std::string msg = msg_header + &quot; for dimension labeled &quot; + getDimensionLabel(k) + &quot; the shape of indices &quot; + s1 + &quot; in file doesn't match defined value &quot; + s2;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineNoCov">          0 :       plumed_merror(msg);</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :     }</a>
+<a name="471"><span class="lineNum">     471 </span>            :   }</a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">        368 : }</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">       2721 : void CoeffsBase::writeIterationCounterAndTimeToFile(OFile&amp; ofile) const {</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">       2721 :   if(time_md&gt;=0.0) {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">       2721 :     ofile.fmtField(&quot;%f&quot;);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">       2721 :     ofile.addConstantField(field_time_).printField(field_time_,time_md);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">       2721 :     ofile.fmtField();</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :   }</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">       2721 :   ofile.addConstantField(field_iteration_).printField(field_iteration_,(int) iteration_opt);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">       2721 : }</span></a>
+<a name="483"><span class="lineNum">     483 </span>            : </a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">        406 : bool CoeffsBase::getIterationCounterAndTimeFromFile(IFile&amp; ifile) {</span></a>
+<a name="486"><span class="lineNum">     486 </span>            :   bool field_found=false;</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        406 :   if(ifile.FieldExist(field_time_)) {</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :     field_found=true;</a>
+<a name="489"><span class="lineNum">     489 </span>            :     double time_tmp;</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        368 :     ifile.scanField(field_time_,time_tmp);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        368 :     time_md=time_tmp;</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :   }</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">        406 :   if(ifile.FieldExist(field_iteration_)) {</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :     field_found=true;</a>
+<a name="495"><span class="lineNum">     495 </span>            :     int iter_tmp;</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">        368 :     ifile.scanField(field_iteration_,iter_tmp);</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">        368 :     iteration_opt=(unsigned int) iter_tmp;</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :   }</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        406 :   return field_found;</span></a>
+<a name="500"><span class="lineNum">     500 </span>            : }</a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span>            : // replace string in Label, if old string was not found simply add the new string to the label</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">          5 : void CoeffsBase::replaceLabelString(const std::string&amp; oldstring, const std::string&amp; newstring) {</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :   std::string label = getLabel();</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          5 :   if(label.find(oldstring)!=std::string::npos) {</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">          8 :     label.replace(label.find(oldstring), std::string(oldstring).length(), newstring);</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   }</a>
+<a name="509"><span class="lineNum">     509 </span>            :   else {</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">          2 :     label += &quot;_&quot; + newstring;</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   }</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">          5 :   setLabels(label);</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          5 : }</span></a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            : </a>
+<a name="516"><span class="lineNum">     516 </span>            : }</a>
+<a name="517"><span class="lineNum">     517 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsBase.h.func-sort-c.html b/coverage/ves/CoeffsBase.h.func-sort-c.html
new file mode 100644
index 0000000000..4b3595d3ff
--- /dev/null
+++ b/coverage/ves/CoeffsBase.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsBase.h<span style="font-size: 80%;"> (<a href="CoeffsBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoeffsBase.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.h.gcov.html#218">_ZNK4PLMD3ves10CoeffsBase8getIndexERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">10870</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.h.gcov.html#237">_ZNK4PLMD3ves10CoeffsBase10getIndicesEm</a></td>
+              <td class="coverFnHi">237974265</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsBase.h.func.html b/coverage/ves/CoeffsBase.h.func.html
new file mode 100644
index 0000000000..cc45eee909
--- /dev/null
+++ b/coverage/ves/CoeffsBase.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsBase.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsBase.h<span style="font-size: 80%;"> (<a href="CoeffsBase.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CoeffsBase.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.h.gcov.html#237">_ZNK4PLMD3ves10CoeffsBase10getIndicesEm</a></td>
+              <td class="coverFnHi">237974265</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="CoeffsBase.h.gcov.html#218">_ZNK4PLMD3ves10CoeffsBase8getIndexERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">10870</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsBase.h.gcov.html b/coverage/ves/CoeffsBase.h.gcov.html
new file mode 100644
index 0000000000..3275e162e3
--- /dev/null
+++ b/coverage/ves/CoeffsBase.h.gcov.html
@@ -0,0 +1,335 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsBase.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsBase.h<span style="font-size: 80%;"> (source / <a href="CoeffsBase.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_CoeffsBase_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_CoeffsBase_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class Action;</a>
+<a name="32"><span class="lineNum">      32 </span>            : class Value;</a>
+<a name="33"><span class="lineNum">      33 </span>            : class IFile;</a>
+<a name="34"><span class="lineNum">      34 </span>            : class OFile;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace ves {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : class BasisFunctions;</a>
+<a name="39"><span class="lineNum">      39 </span>            : class VesBias;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : /// \ingroup TOOLBOX</a>
+<a name="42"><span class="lineNum">      42 </span>            : class CoeffsBase</a>
+<a name="43"><span class="lineNum">      43 </span>            : {</a>
+<a name="44"><span class="lineNum">      44 </span>            : public:</a>
+<a name="45"><span class="lineNum">      45 </span>            :   // the type of 1D index</a>
+<a name="46"><span class="lineNum">      46 </span>            :   // typedef size_t index_t;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   // typedef unsigned int index_t;</a>
+<a name="48"><span class="lineNum">      48 </span>            : private:</a>
+<a name="49"><span class="lineNum">      49 </span>            :   std::string label_;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string data_label_;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   enum CoeffsType {</a>
+<a name="52"><span class="lineNum">      52 </span>            :     Generic,</a>
+<a name="53"><span class="lineNum">      53 </span>            :     LinearBasisSet,</a>
+<a name="54"><span class="lineNum">      54 </span>            :     MultiCoeffs_LinearBasisSet</a>
+<a name="55"><span class="lineNum">      55 </span>            :   } coeffs_type_;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   //</a>
+<a name="57"><span class="lineNum">      57 </span>            :   bool iteration_and_time_active_;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   unsigned int iteration_opt;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   double time_md;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   //</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool active;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   //</a>
+<a name="63"><span class="lineNum">      63 </span>            :   Action* action_pntr_;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   VesBias* vesbias_pntr_;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   //</a>
+<a name="66"><span class="lineNum">      66 </span>            :   unsigned int ndimensions_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;unsigned int&gt; indices_shape_;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   size_t ncoeffs_;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;std::string&gt; coeffs_descriptions_;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt;std::string&gt; dimension_labels_;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   //</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;Value*&gt; args_;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;BasisFunctions*&gt; basisf_;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   //</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool multicoeffs_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::vector&lt;std::vector&lt;Value*&gt; &gt; multicoeffs_args_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;multicoeffs_basisf_;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   // Labels for fields in output/input files</a>
+<a name="79"><span class="lineNum">      79 </span>            :   const std::string field_type_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   const std::string field_ndimensions_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   const std::string field_ncoeffs_total_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   const std::string field_shape_prefix_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   const std::string field_time_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   const std::string field_iteration_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   //</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::string output_fmt_;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void initializeIndices(const std::vector&lt;unsigned int&gt;&amp;, const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   void reinitializeIndices(const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="90"><span class="lineNum">      90 </span>            : public:</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit CoeffsBase();</a>
+<a name="92"><span class="lineNum">      92 </span>            :   //</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit CoeffsBase(</a>
+<a name="94"><span class="lineNum">      94 </span>            :     const std::string&amp;,</a>
+<a name="95"><span class="lineNum">      95 </span>            :     const std::vector&lt;std::string&gt;&amp;,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     const std::vector&lt;unsigned int&gt;&amp;,</a>
+<a name="97"><span class="lineNum">      97 </span>            :     const bool use_iteration_counter=false);</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //</a>
+<a name="99"><span class="lineNum">      99 </span>            :   explicit CoeffsBase(</a>
+<a name="100"><span class="lineNum">     100 </span>            :     const std::string&amp;,</a>
+<a name="101"><span class="lineNum">     101 </span>            :     const std::vector&lt;Value*&gt;&amp;,</a>
+<a name="102"><span class="lineNum">     102 </span>            :     std::vector&lt;BasisFunctions*&gt;&amp;,</a>
+<a name="103"><span class="lineNum">     103 </span>            :     const bool use_iteration_counter=false);</a>
+<a name="104"><span class="lineNum">     104 </span>            :   //</a>
+<a name="105"><span class="lineNum">     105 </span>            :   explicit CoeffsBase(</a>
+<a name="106"><span class="lineNum">     106 </span>            :     const std::string&amp;,</a>
+<a name="107"><span class="lineNum">     107 </span>            :     std::vector&lt;std::vector&lt;Value*&gt; &gt;&amp;,</a>
+<a name="108"><span class="lineNum">     108 </span>            :     std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;&amp;,</a>
+<a name="109"><span class="lineNum">     109 </span>            :     const bool use_iteration_counter=false,</a>
+<a name="110"><span class="lineNum">     110 </span>            :     const std::string&amp; multicoeffs_label=&quot;bias&quot;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   );</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //</a>
+<a name="113"><span class="lineNum">     113 </span>            :   ~CoeffsBase();</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        228 :   std::string getLabel() const {return label_;}</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   void setLabel(const std::string&amp;);</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">       4366 :   std::string getDataLabel() const {return data_label_;};</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   void setDataLabel(const std::string&amp;);</a>
+<a name="119"><span class="lineNum">     119 </span>            :   void setLabels(const std::string&amp;);</a>
+<a name="120"><span class="lineNum">     120 </span>            :   void setLabels(const std::string&amp;, const std::string&amp;);</a>
+<a name="121"><span class="lineNum">     121 </span>            :   //</a>
+<a name="122"><span class="lineNum">     122 </span>            :   CoeffsType getType() const {return coeffs_type_;}</a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::string getTypeStr() const;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void setType(const CoeffsType coeffs_type);</a>
+<a name="125"><span class="lineNum">     125 </span>            :   void linkVesBias(VesBias*);</a>
+<a name="126"><span class="lineNum">     126 </span>            :   void linkAction(Action*);</a>
+<a name="127"><span class="lineNum">     127 </span>            :   VesBias* getPntrToVesBias() const {return vesbias_pntr_;}</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          9 :   Action* getPntrToAction() const {return action_pntr_;}</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   bool isGenericCoeffs() const {return coeffs_type_==Generic;}</a>
+<a name="130"><span class="lineNum">     130 </span>            :   bool isLinearBasisSetCoeffs() const {return coeffs_type_==LinearBasisSet;}</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool isMultiLinearBasisSetCoeffs() const {return coeffs_type_==MultiCoeffs_LinearBasisSet;}</a>
+<a name="132"><span class="lineNum">     132 </span>            :   //</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::vector&lt;unsigned int&gt; shapeOfIndices() const {return indices_shape_;}</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       4157 :   unsigned int shapeOfIndices(const unsigned int dim_index) const {return indices_shape_[dim_index];}</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">  243037069 :   size_t numberOfCoeffs() const {return ncoeffs_;}</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">    2992522 :   unsigned int numberOfDimensions() const {return ndimensions_;}</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   //</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      22810 :   bool isActive() const {return active;}</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      22810 :   void activate() {active=true;}</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         95 :   void deactivate() {active=false;}</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   //</a>
+<a name="142"><span class="lineNum">     142 </span>            :   size_t getIndex(const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::vector&lt;unsigned int&gt; getIndices(const size_t) const;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   bool indicesExist(const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   //</a>
+<a name="146"><span class="lineNum">     146 </span>            :   std::string getCoeffDescription(const size_t index) const {return coeffs_descriptions_[index];}</a>
+<a name="147"><span class="lineNum">     147 </span>            :   std::string getCoeffDescription(const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       2348 :   std::vector&lt;std::string&gt; getAllCoeffsDescriptions() const {return coeffs_descriptions_;}</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   void setCoeffDescription(const size_t, const std::string&amp;);</a>
+<a name="150"><span class="lineNum">     150 </span>            :   void setCoeffDescription(const std::vector&lt;unsigned int&gt;&amp;, const std::string&amp;);</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void setAllCoeffsDescriptions(const std::string&amp; description_prefix=&quot;C&quot;);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void setAllCoeffsDescriptions(const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   //</a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::string getDimensionLabel(const unsigned int) const;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   std::vector&lt;std::string&gt; getAllDimensionLabels() const {return dimension_labels_;}</a>
+<a name="156"><span class="lineNum">     156 </span>            :   void setDimensionLabel(const unsigned int, const std::string&amp;);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void setAllDimensionLabels(const std::string&amp;);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void setAllDimensionLabels(const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void writeCoeffsInfoToFile(OFile&amp;) const;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   void writeTimeInfoToFile(OFile&amp;, const double) const;</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void getCoeffsInfoFromFile(IFile&amp;, const bool ignore_coeffs_info=false);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void checkCoeffsInfo(const std::string&amp;, const std::string&amp;, const unsigned int, const size_t, const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        167 :   void turnOnIterationCounter() {iteration_and_time_active_=true;}</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   void turnOffIterationCounter() {iteration_and_time_active_=false;}</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       3414 :   bool isIterationCounterActive() const {return iteration_and_time_active_;}</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   void setIterationCounter(const unsigned int);</a>
+<a name="168"><span class="lineNum">     168 </span>            :   void setTime(const double);</a>
+<a name="169"><span class="lineNum">     169 </span>            :   void setIterationCounterAndTime(const unsigned int, const double);</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        161 :   unsigned int getIterationCounter() const {return iteration_opt;}</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   double getTimeValue() const {return time_md;}</a>
+<a name="172"><span class="lineNum">     172 </span>            :   //</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        679 :   void setOutputFmt(const std::string&amp; ss) { output_fmt_=ss; }</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   void resetOutputFmt() {output_fmt_=&quot;%30.16e&quot;;}</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      29978 :   std::string getOutputFmt() const {return output_fmt_;}</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   //</a>
+<a name="177"><span class="lineNum">     177 </span>            :   void replaceLabelString(const std::string&amp;, const std::string&amp;);</a>
+<a name="178"><span class="lineNum">     178 </span>            : protected:</a>
+<a name="179"><span class="lineNum">     179 </span>            :   void setupBasisFunctionsInfo();</a>
+<a name="180"><span class="lineNum">     180 </span>            :   void resizeIndices(const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="181"><span class="lineNum">     181 </span>            :   void resizeIndices(std::vector&lt;BasisFunctions*&gt;&amp;);</a>
+<a name="182"><span class="lineNum">     182 </span>            :   bool sameShape(const CoeffsBase&amp;) const;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //</a>
+<a name="184"><span class="lineNum">     184 </span>            :   void writeIterationCounterAndTimeToFile(OFile&amp;) const;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   bool getIterationCounterAndTimeFromFile(IFile&amp;);</a>
+<a name="186"><span class="lineNum">     186 </span>            :   //</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : };</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : inline</a>
+<a name="191"><span class="lineNum">     191 </span>            : void CoeffsBase::setIterationCounter(const unsigned int iteration_opt_in) {</a>
+<a name="192"><span class="lineNum">     192 </span>            :   iteration_opt=iteration_opt_in;</a>
+<a name="193"><span class="lineNum">     193 </span>            : }</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : inline</a>
+<a name="196"><span class="lineNum">     196 </span>            : void CoeffsBase::setTime(const double time_md_in) {</a>
+<a name="197"><span class="lineNum">     197 </span>            :   time_md=time_md_in;</a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : inline</a>
+<a name="201"><span class="lineNum">     201 </span>            : void CoeffsBase::setIterationCounterAndTime(const unsigned int iteration_opt_in, const double time_md_in) {</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      46613 :   iteration_opt=iteration_opt_in;</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      23077 :   time_md=time_md_in;</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      22780 : }</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : inline</a>
+<a name="207"><span class="lineNum">     207 </span>            : std::string CoeffsBase::getCoeffDescription(const std::vector&lt;unsigned int&gt;&amp; indices) const {</a>
+<a name="208"><span class="lineNum">     208 </span>            :   return getCoeffDescription(getIndex(indices));</a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : inline</a>
+<a name="212"><span class="lineNum">     212 </span>            : std::string CoeffsBase::getDimensionLabel(const unsigned int dim_index) const {</a>
+<a name="213"><span class="lineNum">     213 </span>            :   // plumed_massert(dim_index&lt;numberOfDimensions(),&quot;Trying to get the label of a dimension outside the number of dimensions&quot;);</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      12156 :   return dimension_labels_[dim_index];</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : // we are flattening arrays using a column-major order</a>
+<a name="219"><span class="lineNum">     219 </span>            : inline</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      10870 : size_t CoeffsBase::getIndex(const std::vector&lt;unsigned int&gt;&amp; indices) const {</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   // plumed_dbg_assert(indices.size()==ndimensions_);</a>
+<a name="222"><span class="lineNum">     222 </span>            :   // for(unsigned int i=0; i&lt;ndimensions_; i++){</a>
+<a name="223"><span class="lineNum">     223 </span>            :   //   if(indices[i]&gt;=indices_shape_[i]){</a>
+<a name="224"><span class="lineNum">     224 </span>            :   //     std::string is;</a>
+<a name="225"><span class="lineNum">     225 </span>            :   //     Tools::convert(i,is);</a>
+<a name="226"><span class="lineNum">     226 </span>            :   //     std::string msg=&quot;ERROR: the system is looking for a value outside the indices along the &quot; + is + &quot;dimension!&quot;;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   //     plumed_merror(msg);</a>
+<a name="228"><span class="lineNum">     228 </span>            :   //   }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   // }</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      10870 :   size_t index=indices[ndimensions_-1];</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      13392 :   for(unsigned int i=ndimensions_-1; i&gt;0; --i) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">       2522 :     index=index*indices_shape_[i-1]+indices[i-1];</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      10870 :   return index;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : // we are flattening arrays using a column-major order</a>
+<a name="238"><span class="lineNum">     238 </span>            : inline</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">  237974265 : std::vector&lt;unsigned int&gt; CoeffsBase::getIndices(const size_t index) const {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">  237974265 :   std::vector&lt;unsigned int&gt; indices(ndimensions_);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   size_t kk=index;</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">  237974265 :   indices[0]=(index%indices_shape_[0]);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">  258960719 :   for(unsigned int i=1; i&lt;ndimensions_-1; ++i) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">   20986454 :     kk=(kk-indices[i-1])/indices_shape_[i-1];</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">   20986454 :     indices[i]=(kk%indices_shape_[i]);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">  237974265 :   if(ndimensions_&gt;=2) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">  236955949 :     indices[ndimensions_-1]=((kk-indices[ndimensions_-2])/indices_shape_[ndimensions_-2]);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :   }</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">  237974265 :   return indices;</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : }</a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span>            : }</a>
+<a name="257"><span class="lineNum">     257 </span>            : }</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsMatrix.cpp.func-sort-c.html b/coverage/ves/CoeffsMatrix.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c3ffd2605e
--- /dev/null
+++ b/coverage/ves/CoeffsMatrix.cpp.func-sort-c.html
@@ -0,0 +1,388 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsMatrix.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsMatrix.cpp<span style="font-size: 80%;"> (<a href="CoeffsMatrix.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntry">356</td>
+            <td class="headerCovTableEntryLo">29.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryLo">25.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoeffsMatrix.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
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+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/ves/CoeffsMatrix.cpp.gcov.html b/coverage/ves/CoeffsMatrix.cpp.gcov.html
new file mode 100644
index 0000000000..110f7c11a0
--- /dev/null
+++ b/coverage/ves/CoeffsMatrix.cpp.gcov.html
@@ -0,0 +1,791 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsMatrix.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsMatrix.cpp<span style="font-size: 80%;"> (source / <a href="CoeffsMatrix.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntry">356</td>
+            <td class="headerCovTableEntryLo">29.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">79</td>
+            <td class="headerCovTableEntryLo">25.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;vector&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;cmath&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;iostream&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;sstream&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;cstdio&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;cfloat&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace ves {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 : CoeffsMatrix::CoeffsMatrix(</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   const std::string&amp; label,</a>
+<a name="47"><span class="lineNum">      47 </span>            :   const std::vector&lt;std::string&gt;&amp; dimension_labels,</a>
+<a name="48"><span class="lineNum">      48 </span>            :   const std::vector&lt;unsigned int&gt;&amp; indices_shape,</a>
+<a name="49"><span class="lineNum">      49 </span>            :   Communicator&amp; cc,</a>
+<a name="50"><span class="lineNum">      50 </span>            :   const bool diagonal,</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   const bool use_iteration_counter):</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   CoeffsBase(label,dimension_labels,indices_shape,use_iteration_counter),</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   data(0),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   size_(0),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :   nrows_(0),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineNoCov">          0 :   ncolumns_(0),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   diagonal_(diagonal),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 :   averaging_counter(0),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   averaging_exp_decay_(0),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :   mycomm(cc)</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : {</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :   setupMatrix();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 : CoeffsMatrix::CoeffsMatrix(</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   const std::string&amp; label,</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;Value*&gt;&amp; args,</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;BasisFunctions*&gt;&amp; basisf,</a>
+<a name="70"><span class="lineNum">      70 </span>            :   Communicator&amp; cc,</a>
+<a name="71"><span class="lineNum">      71 </span>            :   const bool diagonal,</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   const bool use_iteration_counter):</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   CoeffsBase(label,args,basisf,use_iteration_counter),</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :   data(0),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   size_(0),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 :   nrows_(0),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :   ncolumns_(0),</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :   diagonal_(diagonal),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :   averaging_counter(0),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   averaging_exp_decay_(0),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 :   mycomm(cc)</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : {</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   setupMatrix();</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 : CoeffsMatrix::CoeffsMatrix(</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   const std::string&amp; label,</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;std::vector&lt;Value*&gt; &gt;&amp; argsv,</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;&amp; basisfv,</a>
+<a name="91"><span class="lineNum">      91 </span>            :   Communicator&amp; cc,</a>
+<a name="92"><span class="lineNum">      92 </span>            :   const bool diagonal,</a>
+<a name="93"><span class="lineNum">      93 </span>            :   const bool use_iteration_counter,</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :   const std::string&amp; multicoeffs_label):</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   CoeffsBase(label,argsv,basisfv,use_iteration_counter,multicoeffs_label),</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineNoCov">          0 :   data(0),</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   size_(0),</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 :   nrows_(0),</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   ncolumns_(0),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   diagonal_(diagonal),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   averaging_counter(0),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   averaging_exp_decay_(0),</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineNoCov">          0 :   mycomm(cc)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : {</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   setupMatrix();</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        172 : CoeffsMatrix::CoeffsMatrix(</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   const std::string&amp; label,</a>
+<a name="111"><span class="lineNum">     111 </span>            :   CoeffsVector* coeffsVec,</a>
+<a name="112"><span class="lineNum">     112 </span>            :   Communicator&amp; cc,</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        172 :   const bool diagonal):</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   CoeffsBase( *(static_cast&lt;CoeffsBase*&gt;(coeffsVec)) ),</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        172 :   data(0),</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        172 :   size_(0),</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        172 :   nrows_(0),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        172 :   ncolumns_(0),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        172 :   diagonal_(diagonal),</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        172 :   averaging_counter(0),</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        172 :   averaging_exp_decay_(0),</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        172 :   mycomm(cc)</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : {</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        172 :   setLabels(label);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        172 :   setupMatrix();</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        172 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        172 : CoeffsMatrix::~CoeffsMatrix() {}</span></a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        172 : void CoeffsMatrix::setupMatrix() {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        172 :   nrows_=numberOfCoeffs();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        172 :   ncolumns_=nrows_;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        172 :   if(diagonal_) {</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        172 :     size_=nrows_;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   }</a>
+<a name="138"><span class="lineNum">     138 </span>            :   else {</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     size_=(nrows_*nrows_-nrows_)/2+nrows_;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        172 :   clear();</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        172 : }</span></a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        439 : size_t CoeffsMatrix::getSize() const {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        439 :   return size_;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      23395 : bool CoeffsMatrix::isDiagonal() const {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      23395 :   return diagonal_;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineNoCov">          0 : bool CoeffsMatrix::sameShape(CoeffsVector&amp; coeffsvector_in) const {</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   return CoeffsBase::sameShape( *(static_cast&lt;CoeffsBase*&gt;(&amp;coeffsvector_in)) );</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 : bool CoeffsMatrix::sameShape(CoeffsMatrix&amp; coeffsmat_in) const {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   return CoeffsBase::sameShape( *(static_cast&lt;CoeffsBase*&gt;(&amp;coeffsmat_in)) );</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : bool CoeffsMatrix::sameShape(CoeffsMatrix&amp; coeffsmat0, CoeffsMatrix&amp; coeffsmat1) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :   return coeffsmat0.sameShape(coeffsmat1);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 : bool CoeffsMatrix::sameShape(CoeffsVector&amp; coeffsvec, CoeffsMatrix&amp; coeffsmat) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :   return coeffsmat.sameShape(coeffsvec);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineNoCov">          0 : bool CoeffsMatrix::sameShape(CoeffsMatrix&amp; coeffsmat, CoeffsVector&amp; coeffsvec) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineNoCov">          0 :   return coeffsmat.sameShape(coeffsvec);</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 : void CoeffsMatrix::sumCommMPI() {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :   mycomm.Sum(data);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 : void CoeffsMatrix::sumCommMPI(Communicator&amp; cc) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   cc.Sum(data);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 : void CoeffsMatrix::sumMultiSimCommMPI(Communicator&amp; multi_sim_cc) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :   if(mycomm.Get_rank()==0) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     double nwalkers = static_cast&lt;double&gt;(multi_sim_cc.Get_size());</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     multi_sim_cc.Sum(data);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     scaleAllValues(1.0/nwalkers);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   }</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   mycomm.Bcast(data,0);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">    5425906 : size_t CoeffsMatrix::getMatrixIndex(const size_t index1, const size_t index2) const {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   size_t matrix_idx;</a>
+<a name="202"><span class="lineNum">     202 </span>            :   plumed_dbg_assert(index1&lt;nrows_);</a>
+<a name="203"><span class="lineNum">     203 </span>            :   plumed_dbg_assert(index2&lt;ncolumns_);</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">    5425906 :   if(diagonal_) {</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     // plumed_massert(index1==index2,&quot;CoeffsMatrix: you trying to access a off-diagonal element of a diagonal coeffs matrix&quot;);</a>
+<a name="206"><span class="lineNum">     206 </span>            :     matrix_idx=index1;</a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :   else if (index1&lt;=index2) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :     matrix_idx=index2+index1*(nrows_-1)-index1*(index1-1)/2;</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span>            :   else {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :     matrix_idx=index1+index2*(nrows_-1)-index2*(index2-1)/2;</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">    5425906 :   return matrix_idx;</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        267 : void CoeffsMatrix::clear() {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        267 :   data.resize(getSize());</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">      19388 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      19121 :     data[i]=0.0;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        267 : }</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 : void CoeffsMatrix::setAllValuesToZero() {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :     data[i]=0.0;</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      27630 : double CoeffsMatrix::getValue(const size_t index1, const size_t index2) const {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">      27630 :   return data[getMatrixIndex(index1,index2)];</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 : double CoeffsMatrix::getValue(const std::vector&lt;unsigned int&gt;&amp; indices1, const std::vector&lt;unsigned int&gt;&amp; indices2) const {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   return getValue(getIndex(indices1),getIndex(indices2));</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        219 : void CoeffsMatrix::setValue(const size_t index1, const size_t index2, const double value) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">        219 :   data[getMatrixIndex(index1,index2)]=value;</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        219 : }</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 : void CoeffsMatrix::setValue(const std::vector&lt;unsigned int&gt;&amp; indices1, const std::vector&lt;unsigned int&gt;&amp; indices2, const double value) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   setValue(getIndex(indices1),getIndex(indices2),value);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 : double&amp; CoeffsMatrix::operator()(const size_t index1, const size_t index2) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   return data[getMatrixIndex(index1,index2)];</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : }</a>
+<a name="256"><span class="lineNum">     256 </span>            : </a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">    1790345 : const double&amp; CoeffsMatrix::operator()(const size_t index1, const size_t index2) const {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">    1790345 :   return data[getMatrixIndex(index1,index2)];</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 : double&amp; CoeffsMatrix::operator()(const std::vector&lt;unsigned int&gt;&amp; indices1, const std::vector&lt;unsigned int&gt;&amp; indices2) {</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :   return data[getMatrixIndex(getIndex(indices1),getIndex(indices2))];</span></a>
+<a name="265"><span class="lineNum">     265 </span>            : }</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineNoCov">          0 : const double&amp; CoeffsMatrix::operator()(const std::vector&lt;unsigned int&gt;&amp; indices1, const std::vector&lt;unsigned int&gt;&amp; indices2) const {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :   return data[getMatrixIndex(getIndex(indices1),getIndex(indices2))];</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : }</a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">      22735 : CoeffsVector operator*(const CoeffsMatrix&amp; coeffs_matrix, const CoeffsVector&amp; coeffs_vector) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      22735 :   CoeffsVector new_coeffs_vector(coeffs_vector);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      22735 :   new_coeffs_vector.clear();</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      22735 :   plumed_massert(coeffs_vector.numberOfCoeffs()==coeffs_matrix.numberOfCoeffs(),&quot;CoeffsMatrix and CoeffsVector are of the wrong size&quot;);</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   size_t numcoeffs = coeffs_vector.numberOfCoeffs();</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      22735 :   if(coeffs_matrix.isDiagonal()) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    1813080 :     for(size_t i=0; i&lt;numcoeffs; i++) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">    1790345 :       new_coeffs_vector(i) = coeffs_matrix(i,i)*coeffs_vector(i);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     }</a>
+<a name="282"><span class="lineNum">     282 </span>            :   }</a>
+<a name="283"><span class="lineNum">     283 </span>            :   else {</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :     for(size_t i=0; i&lt;numcoeffs; i++) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 :       for(size_t j=0; j&lt;numcoeffs; j++) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :         new_coeffs_vector(i) += coeffs_matrix(i,j)*coeffs_vector(j);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :       }</a>
+<a name="288"><span class="lineNum">     288 </span>            :     }</a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">      22735 :   return new_coeffs_vector;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineNoCov">          0 : void CoeffsMatrix::addToValue(const size_t index1, const size_t index2, const double value) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :   data[getMatrixIndex(index1,index2)]+=value;</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 : void CoeffsMatrix::addToValue(const std::vector&lt;unsigned int&gt;&amp; indices1, const std::vector&lt;unsigned int&gt;&amp; indices2, const double value) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   addToValue(getIndex(indices1),getIndex(indices2),value);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">      22810 : void CoeffsMatrix::scaleAllValues(const double scalef) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">    1823850 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">    1801040 :     data[i]*=scalef;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">      22810 : }</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      22810 : CoeffsMatrix&amp; CoeffsMatrix::operator*=(const double scalef) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">      22810 :   scaleAllValues(scalef);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">      22810 :   return *this;</span></a>
+<a name="314"><span class="lineNum">     314 </span>            : }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineNoCov">          0 : CoeffsMatrix operator*(const double scalef, const CoeffsMatrix&amp; coeffsmatrix) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(coeffsmatrix)*=scalef;</span></a>
+<a name="319"><span class="lineNum">     319 </span>            : }</a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 : CoeffsMatrix operator*(const CoeffsMatrix&amp; coeffsmatrix, const double scalef) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineNoCov">          0 :   return scalef*coeffsmatrix;</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator*=(const CoeffsMatrix&amp; other_coeffsmatrix) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :   plumed_massert(data.size()==other_coeffsmatrix.getSize(),&quot;Coeffs matrices do not have the same size&quot;);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineNoCov">          0 :     data[i]*=other_coeffsmatrix.data[i];</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :   }</a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="333"><span class="lineNum">     333 </span>            : }</a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineNoCov">          0 : CoeffsMatrix CoeffsMatrix::operator*(const CoeffsMatrix&amp; other_coeffsmatrix) const {</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(*this)*=other_coeffsmatrix;</span></a>
+<a name="338"><span class="lineNum">     338 </span>            : }</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 : void CoeffsMatrix::setValues(const double value) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :     data[i]=value;</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :   }</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">      22810 : void CoeffsMatrix::setValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">      22810 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">    1823850 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">    1801040 :     data[i]=values[i];</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   }</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">      22810 : }</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 : void CoeffsMatrix::setValues(const CoeffsMatrix&amp; other_coeffsmatrix) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==other_coeffsmatrix.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 :     data[i]=other_coeffsmatrix.data[i];</span></a>
+<a name="360"><span class="lineNum">     360 </span>            :   }</a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span>            : </a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator=(const double value) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :   setValues(value);</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="367"><span class="lineNum">     367 </span>            : }</a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      22810 : CoeffsMatrix&amp; CoeffsMatrix::operator=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      22810 :   setValues(values);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">      22810 :   return *this;</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : }</a>
+<a name="374"><span class="lineNum">     374 </span>            : </a>
+<a name="375"><span class="lineNum">     375 </span>            : </a>
+<a name="376"><span class="lineNum">     376 </span>            : // CoeffsMatrix&amp; CoeffsMatrix::operator=(const CoeffsMatrix&amp; other_coeffsmatrix) {</a>
+<a name="377"><span class="lineNum">     377 </span>            : //   setValues(other_coeffsmatrix);</a>
+<a name="378"><span class="lineNum">     378 </span>            : //   return *this;</a>
+<a name="379"><span class="lineNum">     379 </span>            : // }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 : CoeffsMatrix CoeffsMatrix::operator+() const {</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="384"><span class="lineNum">     384 </span>            : }</a>
+<a name="385"><span class="lineNum">     385 </span>            : </a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 : CoeffsMatrix CoeffsMatrix::operator-() const {</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(*this)*=-1.0;</span></a>
+<a name="389"><span class="lineNum">     389 </span>            : }</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineNoCov">          0 : void CoeffsMatrix::addToValues(const double value) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineNoCov">          0 :     data[i]+=value;</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :   }</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            : </a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineNoCov">          0 : void CoeffsMatrix::addToValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :     data[i]+=values[i];</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :   }</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 : void CoeffsMatrix::addToValues(const CoeffsMatrix&amp; other_coeffsmatrix) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==other_coeffsmatrix.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :     data[i]+=other_coeffsmatrix.data[i];</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :   }</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineNoCov">          0 : void CoeffsMatrix::subtractFromValues(const double value) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 :     data[i]-=value;</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :   }</a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="420"><span class="lineNum">     420 </span>            : </a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineNoCov">          0 : void CoeffsMatrix::subtractFromValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineNoCov">          0 :     data[i]-=values[i];</span></a>
+<a name="426"><span class="lineNum">     426 </span>            :   }</a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineNoCov">          0 : void CoeffsMatrix::subtractFromValues(const CoeffsMatrix&amp; other_coeffsmatrix) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==other_coeffsmatrix.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 :     data[i]-=other_coeffsmatrix.data[i];</span></a>
+<a name="434"><span class="lineNum">     434 </span>            :   }</a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator+=(const double value) {</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :   addToValues(value);</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : }</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 : CoeffsMatrix operator+(const double value, const CoeffsMatrix&amp; coeffsmatrix) {</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :   return coeffsmatrix+value;</span></a>
+<a name="446"><span class="lineNum">     446 </span>            : }</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineNoCov">          0 : CoeffsMatrix operator+(const CoeffsMatrix&amp; coeffsmatrix, const double value) {</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(coeffsmatrix)+=value;</span></a>
+<a name="451"><span class="lineNum">     451 </span>            : }</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator+=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 :   addToValues(values);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="457"><span class="lineNum">     457 </span>            : }</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineNoCov">          0 : CoeffsMatrix operator+(const std::vector&lt;double&gt;&amp; values, const CoeffsMatrix&amp; coeffsmatrix) {</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineNoCov">          0 :   return coeffsmatrix+values;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : }</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineNoCov">          0 : CoeffsMatrix operator+(const CoeffsMatrix&amp; coeffsmatrix, const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(coeffsmatrix)+=values;</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : }</a>
+<a name="468"><span class="lineNum">     468 </span>            : </a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator-=(const double value) {</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineNoCov">          0 :   subtractFromValues(value);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : }</a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineNoCov">          0 : CoeffsMatrix operator-(const double value, const CoeffsMatrix&amp; coeffsmatrix) {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineNoCov">          0 :   return -1.0*coeffsmatrix+value;</span></a>
+<a name="478"><span class="lineNum">     478 </span>            : }</a>
+<a name="479"><span class="lineNum">     479 </span>            : </a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineNoCov">          0 : CoeffsMatrix operator-(const CoeffsMatrix&amp; coeffsmatrix, const double value) {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(coeffsmatrix)-=value;</span></a>
+<a name="483"><span class="lineNum">     483 </span>            : }</a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator-=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 :   subtractFromValues(values);</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="489"><span class="lineNum">     489 </span>            : }</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 : CoeffsMatrix operator-(const std::vector&lt;double&gt;&amp; values, const CoeffsMatrix&amp; coeffsmatrix) {</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :   return -1.0*coeffsmatrix+values;</span></a>
+<a name="494"><span class="lineNum">     494 </span>            : }</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineNoCov">          0 : CoeffsMatrix operator-(const CoeffsMatrix&amp; coeffsmatrix, const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(coeffsmatrix)-=values;</span></a>
+<a name="499"><span class="lineNum">     499 </span>            : }</a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator+=(const CoeffsMatrix&amp; other_coeffsmatrix) {</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineNoCov">          0 :   addToValues(other_coeffsmatrix);</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="505"><span class="lineNum">     505 </span>            : }</a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span>            : </a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineNoCov">          0 : CoeffsMatrix CoeffsMatrix::operator+(const CoeffsMatrix&amp; other_coeffsmatrix) const {</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(*this)+=other_coeffsmatrix;</span></a>
+<a name="510"><span class="lineNum">     510 </span>            : }</a>
+<a name="511"><span class="lineNum">     511 </span>            : </a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 : CoeffsMatrix&amp; CoeffsMatrix::operator-=(const CoeffsMatrix&amp; other_coeffsmatrix) {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :   subtractFromValues(other_coeffsmatrix);</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="516"><span class="lineNum">     516 </span>            : }</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : </a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 : CoeffsMatrix CoeffsMatrix::operator-(const CoeffsMatrix&amp; other_coeffsmatrix) const {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineNoCov">          0 :   return CoeffsMatrix(*this)-=other_coeffsmatrix;</span></a>
+<a name="521"><span class="lineNum">     521 </span>            : }</a>
+<a name="522"><span class="lineNum">     522 </span>            : </a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineNoCov">          0 : void CoeffsMatrix::averageMatrices(CoeffsMatrix&amp; coeffsmat0, CoeffsMatrix&amp; coeffsmat1) {</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 :   plumed_massert(sameShape(coeffsmat0,coeffsmat1),&quot;both CoeffsMatrix objects need to have the same shape&quot;);</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;coeffsmat0.getSize(); i++) {</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :     coeffsmat0.data[i] = coeffsmat1.data[i] = 0.5 * (coeffsmat0.data[i]+coeffsmat1.data[i]);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :   }</a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 : void CoeffsMatrix::averageMatrices(const std::vector&lt;CoeffsMatrix*&gt;&amp; coeffsmatSet) {</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineNoCov">          0 :   double norm_factor = 1.0/static_cast&lt;double&gt;(coeffsmatSet.size());</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :   for(unsigned int k=1; k&lt;coeffsmatSet.size(); k++) {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :     plumed_massert(coeffsmatSet[0]-&gt;sameShape(*coeffsmatSet[k]),&quot;All CoeffsMatrix objects need to have the same shape&quot;);</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :   }</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;coeffsmatSet[0]-&gt;getSize(); i++) {</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :     double value = 0.0;</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :     for(unsigned int k=0; k&lt;coeffsmatSet.size(); k++) {</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 :       value += coeffsmatSet[k]-&gt;data[i];</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :     }</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineNoCov">          0 :     value *= norm_factor;</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineNoCov">          0 :     for(unsigned int k=0; k&lt;coeffsmatSet.size(); k++) {</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 :       coeffsmatSet[k]-&gt;data[i] = value;</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :     }</a>
+<a name="546"><span class="lineNum">     546 </span>            :   }</a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 : double CoeffsMatrix::getMinValue() const {</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   double min_value=DBL_MAX;</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :     if(data[i]&lt;min_value) {</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :       min_value=data[i];</a>
+<a name="556"><span class="lineNum">     556 </span>            :     }</a>
+<a name="557"><span class="lineNum">     557 </span>            :   }</a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineNoCov">          0 :   return min_value;</span></a>
+<a name="559"><span class="lineNum">     559 </span>            : }</a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineNoCov">          0 : double CoeffsMatrix::getMaxValue() const {</span></a>
+<a name="563"><span class="lineNum">     563 </span>            :   double max_value=DBL_MIN;</a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :     if(data[i]&gt;max_value) {</span></a>
+<a name="566"><span class="lineNum">     566 </span>            :       max_value=data[i];</a>
+<a name="567"><span class="lineNum">     567 </span>            :     }</a>
+<a name="568"><span class="lineNum">     568 </span>            :   }</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :   return max_value;</span></a>
+<a name="570"><span class="lineNum">     570 </span>            : }</a>
+<a name="571"><span class="lineNum">     571 </span>            : </a>
+<a name="572"><span class="lineNum">     572 </span>            : </a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 : void CoeffsMatrix::randomizeValuesGaussian(int randomSeed) {</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineNoCov">          0 :   Random rnd;</span></a>
+<a name="575"><span class="lineNum">     575 </span>            :   if (randomSeed&lt;0) {randomSeed = -randomSeed;}</a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineNoCov">          0 :   rnd.setSeed(-randomSeed);</span></a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :     data[i]=rnd.Gaussian();</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :   }</a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 : void CoeffsMatrix::resetAveraging() {</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :   resetAveragingCounter();</a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 : void CoeffsMatrix::addToAverage(const CoeffsMatrix&amp; coeffsmat) {</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==coeffsmat.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :   //</a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineNoCov">          0 :   double aver_decay = 1.0 / ( static_cast&lt;double&gt;(averaging_counter) + 1.0 );</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 :   if(averaging_exp_decay_&gt;0 &amp;&amp;  (averaging_counter+1 &gt; averaging_exp_decay_) ) {</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 :     aver_decay = 1.0 / static_cast&lt;double&gt;(averaging_exp_decay_);</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :   }</a>
+<a name="596"><span class="lineNum">     596 </span>            :   //</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :     data[i]+=(coeffsmat.data[i]-data[i])*aver_decay;</span></a>
+<a name="599"><span class="lineNum">     599 </span>            :   }</a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :   averaging_counter++;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="602"><span class="lineNum">     602 </span>            : </a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">        660 : void CoeffsMatrix::writeToFile(OFile&amp; ofile) {</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">        660 :   writeHeaderToFile(ofile);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">        660 :   writeDataToFile(ofile);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">        660 : }</span></a>
+<a name="608"><span class="lineNum">     608 </span>            : </a>
+<a name="609"><span class="lineNum">     609 </span>            : </a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineNoCov">          0 : void CoeffsMatrix::writeToFile(const std::string&amp; filepath, const bool append_file, Action* action_pntr) {</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :   OFile file;</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :   if(action_pntr!=NULL) {</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineNoCov">          0 :     file.link(*action_pntr);</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :   }</a>
+<a name="615"><span class="lineNum">     615 </span>            :   else {</a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineNoCov">          0 :     file.link(mycomm);</span></a>
+<a name="617"><span class="lineNum">     617 </span>            :   }</a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineNoCov">          0 :   if(append_file) { file.enforceRestart(); }</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineNoCov">          0 :   file.open(filepath);</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineNoCov">          0 :   writeToFile(file);</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineNoCov">          0 :   file.close();</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">        660 : void CoeffsMatrix::writeMatrixInfoToFile(OFile&amp; ofile) {</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">        660 :   std::string field_diagonal = &quot;diagonal_matrix&quot;;</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">        660 :   ofile.addConstantField(field_diagonal).printField(field_diagonal,isDiagonal());</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">        660 : }</span></a>
+<a name="629"><span class="lineNum">     629 </span>            : </a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">        660 : void CoeffsMatrix::writeHeaderToFile(OFile&amp; ofile) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">        660 :   ofile.clearFields();</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">        660 :   if(isIterationCounterActive()) {</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">        660 :     writeIterationCounterAndTimeToFile(ofile);</span></a>
+<a name="635"><span class="lineNum">     635 </span>            :   }</a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">        660 :   writeCoeffsInfoToFile(ofile);</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineCov">        660 :   writeMatrixInfoToFile(ofile);</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">        660 : }</span></a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span>            : </a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">        660 : void CoeffsMatrix::writeDataToFile(OFile&amp; ofile) {</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">        660 :   if(diagonal_) {</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">        660 :     writeDataDiagonalToFile(ofile);</span></a>
+<a name="644"><span class="lineNum">     644 </span>            :   }</a>
+<a name="645"><span class="lineNum">     645 </span>            :   else {</a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 :     writeDataFullToFile(ofile);</span></a>
+<a name="647"><span class="lineNum">     647 </span>            :   }</a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">        660 : }</span></a>
+<a name="649"><span class="lineNum">     649 </span>            : </a>
+<a name="650"><span class="lineNum">     650 </span>            : </a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineCov">        660 : void CoeffsMatrix::writeDataDiagonalToFile(OFile&amp; ofile) {</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :   //</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">        660 :   std::string field_indices_prefix = &quot;idx_&quot;;</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :   std::string field_coeffs = getDataLabel();</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">        660 :   std::string field_index = &quot;index&quot;;</span></a>
+<a name="656"><span class="lineNum">     656 </span>            :   //</a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">        660 :   std::string int_fmt = &quot;%8d&quot;;</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">        660 :   std::string str_separate = &quot;#!-------------------&quot;;</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :   //</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">        660 :   std::vector&lt;char&gt; s1(20);</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">        660 :   std::vector&lt;unsigned int&gt; indices(numberOfDimensions());</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">        660 :   std::vector&lt;std::string&gt; ilabels(numberOfDimensions());</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">       1520 :   for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineCov">       1720 :     ilabels[k]=field_indices_prefix+getDimensionLabel(k);</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :   }</a>
+<a name="666"><span class="lineNum">     666 </span>            :   //</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">      28290 :   for(size_t i=0; i&lt;numberOfCoeffs(); i++) {</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">      27630 :     indices=getIndices(i);</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">      77540 :     for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">      49910 :       std::snprintf(s1.data(),s1.size(),int_fmt.c_str(),indices[k]);</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">      99820 :       ofile.printField(ilabels[k],s1.data());</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :     }</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">      55260 :     ofile.fmtField(&quot; &quot;+getOutputFmt()).printField(field_coeffs,getValue(i,i));</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">      27630 :     std::snprintf(s1.data(),s1.size(),int_fmt.c_str(),i); ofile.printField(field_index,s1.data());</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">      27630 :     ofile.printField();</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :   }</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">        660 :   ofile.fmtField();</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :   // blank line between iterations to allow proper plotting with gnuplot</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">        660 :   ofile.printf(&quot;%s\n&quot;,str_separate.c_str());</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">        660 :   ofile.printf(&quot;\n&quot;);</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">        660 :   ofile.printf(&quot;\n&quot;);</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">       1320 : }</span></a>
+<a name="683"><span class="lineNum">     683 </span>            : </a>
+<a name="684"><span class="lineNum">     684 </span>            : </a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineNoCov">          0 : void CoeffsMatrix::writeDataFullToFile(OFile&amp; ofile) {</span></a>
+<a name="686"><span class="lineNum">     686 </span>            :   //</a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineNoCov">          0 :   std::string field_index_row = &quot;idx_row&quot;;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 :   std::string field_index_column = &quot;idx_column&quot;;</span></a>
+<a name="689"><span class="lineNum">     689 </span>            :   std::string field_coeffs = getDataLabel();</a>
+<a name="690"><span class="lineNum">     690 </span>            :   //</a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :   std::string int_fmt = &quot;%8d&quot;;</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 :   std::string str_separate = &quot;#!-------------------&quot;;</span></a>
+<a name="693"><span class="lineNum">     693 </span>            :   //</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :   std::vector&lt;char&gt; s1(20);</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :   //</a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;nrows_; i++) {</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :     for(size_t j=0; j&lt;ncolumns_; j++) {</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :       std::snprintf(s1.data(),s1.size(),int_fmt.c_str(),i);</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :       ofile.printField(field_index_row,s1.data());</span></a>
+<a name="700"><span class="lineNum">     700 </span>            :       std::snprintf(s1.data(),s1.size(),int_fmt.c_str(),j);</a>
+<a name="701"><span class="lineNum">     701 </span><span class="lineNoCov">          0 :       ofile.printField(field_index_column,s1.data());</span></a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineNoCov">          0 :       ofile.fmtField(&quot; &quot;+getOutputFmt()).printField(field_coeffs,getValue(i,j));</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineNoCov">          0 :       ofile.printField();</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :     }</a>
+<a name="705"><span class="lineNum">     705 </span>            :   }</a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineNoCov">          0 :   ofile.fmtField();</span></a>
+<a name="707"><span class="lineNum">     707 </span>            :   // blank line between iterations to allow proper plotting with gnuplot</a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;%s\n&quot;,str_separate.c_str());</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;\n&quot;);</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineNoCov">          0 :   ofile.printf(&quot;\n&quot;);</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="712"><span class="lineNum">     712 </span>            : </a>
+<a name="713"><span class="lineNum">     713 </span>            : </a>
+<a name="714"><span class="lineNum">     714 </span>            : }</a>
+<a name="715"><span class="lineNum">     715 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsMatrix.h.func-sort-c.html b/coverage/ves/CoeffsMatrix.h.func-sort-c.html
new file mode 100644
index 0000000000..ae50ee70f9
--- /dev/null
+++ b/coverage/ves/CoeffsMatrix.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsMatrix.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsMatrix.h<span style="font-size: 80%;"> (<a href="CoeffsMatrix.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoeffsMatrix.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsMatrix.h.func.html b/coverage/ves/CoeffsMatrix.h.func.html
new file mode 100644
index 0000000000..471a9b36be
--- /dev/null
+++ b/coverage/ves/CoeffsMatrix.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsMatrix.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsMatrix.h<span style="font-size: 80%;"> (<a href="CoeffsMatrix.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="CoeffsMatrix.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsMatrix.h.gcov.html b/coverage/ves/CoeffsMatrix.h.gcov.html
new file mode 100644
index 0000000000..d944e750fe
--- /dev/null
+++ b/coverage/ves/CoeffsMatrix.h.gcov.html
@@ -0,0 +1,287 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsMatrix.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsMatrix.h<span style="font-size: 80%;"> (source / <a href="CoeffsMatrix.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_CoeffsMatrix_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_CoeffsMatrix_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : class Action;</a>
+<a name="35"><span class="lineNum">      35 </span>            : class Value;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class IFile;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class OFile;</a>
+<a name="38"><span class="lineNum">      38 </span>            : class Communicator;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace ves {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class BasisFunctions;</a>
+<a name="43"><span class="lineNum">      43 </span>            : class CoeffsVector;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : class CoeffsMatrix:</a>
+<a name="47"><span class="lineNum">      47 </span>            :   public CoeffsBase</a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span>            : public:</a>
+<a name="50"><span class="lineNum">      50 </span>            : private:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::vector&lt;double&gt; data;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   //</a>
+<a name="53"><span class="lineNum">      53 </span>            :   size_t size_;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   size_t nrows_;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   size_t ncolumns_;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   //</a>
+<a name="57"><span class="lineNum">      57 </span>            :   bool diagonal_;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   //</a>
+<a name="59"><span class="lineNum">      59 </span>            :   unsigned int averaging_counter;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   unsigned int averaging_exp_decay_;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   //</a>
+<a name="62"><span class="lineNum">      62 </span>            :   Communicator&amp; mycomm;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   //</a>
+<a name="64"><span class="lineNum">      64 </span>            :   void setupMatrix();</a>
+<a name="65"><span class="lineNum">      65 </span>            :   //</a>
+<a name="66"><span class="lineNum">      66 </span>            :   CoeffsMatrix&amp; operator=(const CoeffsMatrix&amp;);</a>
+<a name="67"><span class="lineNum">      67 </span>            : public:</a>
+<a name="68"><span class="lineNum">      68 </span>            :   explicit CoeffsMatrix(</a>
+<a name="69"><span class="lineNum">      69 </span>            :     const std::string&amp;,</a>
+<a name="70"><span class="lineNum">      70 </span>            :     const std::vector&lt;std::string&gt;&amp;,</a>
+<a name="71"><span class="lineNum">      71 </span>            :     const std::vector&lt;unsigned int&gt;&amp;,</a>
+<a name="72"><span class="lineNum">      72 </span>            :     Communicator&amp; cc,</a>
+<a name="73"><span class="lineNum">      73 </span>            :     const bool diagonal=true,</a>
+<a name="74"><span class="lineNum">      74 </span>            :     const bool use_iteration_counter=false);</a>
+<a name="75"><span class="lineNum">      75 </span>            :   //</a>
+<a name="76"><span class="lineNum">      76 </span>            :   explicit CoeffsMatrix(</a>
+<a name="77"><span class="lineNum">      77 </span>            :     const std::string&amp;,</a>
+<a name="78"><span class="lineNum">      78 </span>            :     std::vector&lt;Value*&gt;&amp;,</a>
+<a name="79"><span class="lineNum">      79 </span>            :     std::vector&lt;BasisFunctions*&gt;&amp;,</a>
+<a name="80"><span class="lineNum">      80 </span>            :     Communicator&amp; cc,</a>
+<a name="81"><span class="lineNum">      81 </span>            :     const bool diagonal=true,</a>
+<a name="82"><span class="lineNum">      82 </span>            :     const bool use_iteration_counter=false);</a>
+<a name="83"><span class="lineNum">      83 </span>            :   //</a>
+<a name="84"><span class="lineNum">      84 </span>            :   explicit CoeffsMatrix(</a>
+<a name="85"><span class="lineNum">      85 </span>            :     const std::string&amp;,</a>
+<a name="86"><span class="lineNum">      86 </span>            :     std::vector&lt;std::vector&lt;Value*&gt; &gt;&amp; argsv,</a>
+<a name="87"><span class="lineNum">      87 </span>            :     std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;&amp; basisfv,</a>
+<a name="88"><span class="lineNum">      88 </span>            :     Communicator&amp; cc,</a>
+<a name="89"><span class="lineNum">      89 </span>            :     const bool diagonal=true,</a>
+<a name="90"><span class="lineNum">      90 </span>            :     const bool use_iteration_counter=false,</a>
+<a name="91"><span class="lineNum">      91 </span>            :     const std::string&amp; multicoeffs_label=&quot;bias&quot;);</a>
+<a name="92"><span class="lineNum">      92 </span>            :   //</a>
+<a name="93"><span class="lineNum">      93 </span>            :   explicit CoeffsMatrix(</a>
+<a name="94"><span class="lineNum">      94 </span>            :     const std::string&amp;,</a>
+<a name="95"><span class="lineNum">      95 </span>            :     CoeffsVector*,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     Communicator&amp; cc,</a>
+<a name="97"><span class="lineNum">      97 </span>            :     const bool diagonal=true);</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //</a>
+<a name="99"><span class="lineNum">      99 </span>            :   ~CoeffsMatrix();</a>
+<a name="100"><span class="lineNum">     100 </span>            :   //</a>
+<a name="101"><span class="lineNum">     101 </span>            :   size_t getSize() const;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   //</a>
+<a name="103"><span class="lineNum">     103 </span>            :   bool isSymmetric() const;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   bool isDiagonal() const;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   //</a>
+<a name="106"><span class="lineNum">     106 </span>            :   bool sameShape(CoeffsVector&amp;) const;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   bool sameShape(CoeffsMatrix&amp;) const;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   static bool sameShape(CoeffsMatrix&amp;, CoeffsMatrix&amp;);</a>
+<a name="109"><span class="lineNum">     109 </span>            :   static bool sameShape(CoeffsVector&amp;, CoeffsMatrix&amp;);</a>
+<a name="110"><span class="lineNum">     110 </span>            :   static bool sameShape(CoeffsMatrix&amp;, CoeffsVector&amp;);</a>
+<a name="111"><span class="lineNum">     111 </span>            :   //</a>
+<a name="112"><span class="lineNum">     112 </span>            :   void sumCommMPI();</a>
+<a name="113"><span class="lineNum">     113 </span>            :   void sumCommMPI(Communicator&amp;);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //</a>
+<a name="115"><span class="lineNum">     115 </span>            :   void sumMultiSimCommMPI(Communicator&amp;);</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //</a>
+<a name="117"><span class="lineNum">     117 </span>            :   size_t getMatrixIndex(const size_t, const size_t) const;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   //</a>
+<a name="119"><span class="lineNum">     119 </span>            :   // clear coeffs</a>
+<a name="120"><span class="lineNum">     120 </span>            :   void clear();</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void setAllValuesToZero();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   //</a>
+<a name="123"><span class="lineNum">     123 </span>            :   std::vector&lt;double&gt; getDataAsVector() const {return data;}</a>
+<a name="124"><span class="lineNum">     124 </span>            :   // get value</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double getValue(const size_t, const size_t) const;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   double getValue(const std::vector&lt;unsigned int&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   // set value</a>
+<a name="128"><span class="lineNum">     128 </span>            :   void setValue(const size_t, const size_t, const double);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   void setValue(const std::vector&lt;unsigned int&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;, const double);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   double&amp; operator()(const size_t, const size_t);</a>
+<a name="131"><span class="lineNum">     131 </span>            :   const double&amp; operator()(const size_t, const size_t) const;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   double&amp; operator()(const std::vector&lt;unsigned int&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="133"><span class="lineNum">     133 </span>            :   const double&amp; operator()(const std::vector&lt;unsigned int&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   //</a>
+<a name="135"><span class="lineNum">     135 </span>            :   friend CoeffsVector operator*(const CoeffsMatrix&amp;, const CoeffsVector&amp;);</a>
+<a name="136"><span class="lineNum">     136 </span>            :   // add to value</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void addToValue(const size_t, const size_t, const double);</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void addToValue(const std::vector&lt;unsigned int&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;, const double);</a>
+<a name="139"><span class="lineNum">     139 </span>            :   // scale all values</a>
+<a name="140"><span class="lineNum">     140 </span>            :   void scaleAllValues(const double);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   CoeffsMatrix&amp; operator*=(const double);</a>
+<a name="142"><span class="lineNum">     142 </span>            :   friend CoeffsMatrix operator*(const double, const CoeffsMatrix&amp;);</a>
+<a name="143"><span class="lineNum">     143 </span>            :   friend CoeffsMatrix operator*(const CoeffsMatrix&amp;, const double);</a>
+<a name="144"><span class="lineNum">     144 </span>            :   CoeffsMatrix&amp; operator*=(const CoeffsMatrix&amp;);</a>
+<a name="145"><span class="lineNum">     145 </span>            :   CoeffsMatrix operator*(const CoeffsMatrix&amp;) const;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   // set all values</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void setValues(const double);</a>
+<a name="148"><span class="lineNum">     148 </span>            :   void setValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void setValues(const CoeffsMatrix&amp;);</a>
+<a name="150"><span class="lineNum">     150 </span>            :   CoeffsMatrix&amp; operator=(const double);</a>
+<a name="151"><span class="lineNum">     151 </span>            :   CoeffsMatrix&amp; operator=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   // CoeffsMatrix&amp; operator=(const CoeffsMatrix&amp;);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   // add to all values</a>
+<a name="154"><span class="lineNum">     154 </span>            :   CoeffsMatrix operator+() const;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   CoeffsMatrix operator-() const;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   void addToValues(const double);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void addToValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void addToValues(const CoeffsMatrix&amp;);</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void subtractFromValues(const double);</a>
+<a name="160"><span class="lineNum">     160 </span>            :   void subtractFromValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void subtractFromValues(const CoeffsMatrix&amp;);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   CoeffsMatrix&amp; operator+=(const double);</a>
+<a name="163"><span class="lineNum">     163 </span>            :   friend CoeffsMatrix operator+(const double, const CoeffsMatrix&amp;);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   friend CoeffsMatrix operator+(const CoeffsMatrix&amp;, const double);</a>
+<a name="165"><span class="lineNum">     165 </span>            :   CoeffsMatrix&amp; operator+=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="166"><span class="lineNum">     166 </span>            :   friend CoeffsMatrix operator+(const std::vector&lt;double&gt;&amp;, const CoeffsMatrix&amp;);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   friend CoeffsMatrix operator+(const CoeffsMatrix&amp;, const std::vector&lt;double&gt;&amp;);</a>
+<a name="168"><span class="lineNum">     168 </span>            :   CoeffsMatrix&amp; operator-=(const double);</a>
+<a name="169"><span class="lineNum">     169 </span>            :   friend CoeffsMatrix operator-(const double, const CoeffsMatrix&amp;);</a>
+<a name="170"><span class="lineNum">     170 </span>            :   friend CoeffsMatrix operator-(const CoeffsMatrix&amp;, const double);</a>
+<a name="171"><span class="lineNum">     171 </span>            :   CoeffsMatrix&amp; operator-=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   friend CoeffsMatrix operator-(const std::vector&lt;double&gt;&amp;, const CoeffsMatrix&amp;);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   friend CoeffsMatrix operator-(const CoeffsMatrix&amp;, const std::vector&lt;double&gt;&amp;);</a>
+<a name="174"><span class="lineNum">     174 </span>            :   CoeffsMatrix&amp; operator+=(const CoeffsMatrix&amp;);</a>
+<a name="175"><span class="lineNum">     175 </span>            :   CoeffsMatrix operator+(const CoeffsMatrix&amp;) const;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   CoeffsMatrix&amp; operator-=(const CoeffsMatrix&amp;);</a>
+<a name="177"><span class="lineNum">     177 </span>            :   CoeffsMatrix operator-(const CoeffsMatrix&amp;) const;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   //</a>
+<a name="179"><span class="lineNum">     179 </span>            :   static void averageMatrices(CoeffsMatrix&amp;, CoeffsMatrix&amp;);</a>
+<a name="180"><span class="lineNum">     180 </span>            :   static void averageMatrices(const std::vector&lt;CoeffsMatrix*&gt;&amp;);</a>
+<a name="181"><span class="lineNum">     181 </span>            :   //</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double getMinValue() const;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   double getMaxValue() const;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   //</a>
+<a name="185"><span class="lineNum">     185 </span>            :   void randomizeValuesGaussian(int);</a>
+<a name="186"><span class="lineNum">     186 </span>            :   //</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   void resetAveragingCounter() {averaging_counter=0;}</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   void setupExponentiallyDecayingAveraging(const unsigned int averaging_exp_decay_in) {averaging_exp_decay_=averaging_exp_decay_in;}</a>
+<a name="189"><span class="lineNum">     189 </span>            :   void turnOffExponentiallyDecayingAveraging() { averaging_exp_decay_=0;}</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void resetAveraging();</a>
+<a name="191"><span class="lineNum">     191 </span>            :   void addToAverage(const CoeffsMatrix&amp;);</a>
+<a name="192"><span class="lineNum">     192 </span>            :   void addToAverage(const CoeffsMatrix&amp;, const unsigned int);</a>
+<a name="193"><span class="lineNum">     193 </span>            :   //</a>
+<a name="194"><span class="lineNum">     194 </span>            :   // file input/output stuff</a>
+<a name="195"><span class="lineNum">     195 </span>            :   void writeToFile(OFile&amp;);</a>
+<a name="196"><span class="lineNum">     196 </span>            :   void writeToFile(const std::string&amp;, const bool append_file=false, Action* action_pntr=NULL);</a>
+<a name="197"><span class="lineNum">     197 </span>            : private:</a>
+<a name="198"><span class="lineNum">     198 </span>            :   void writeDataToFile(OFile&amp;);</a>
+<a name="199"><span class="lineNum">     199 </span>            :   void writeMatrixInfoToFile(OFile&amp;);</a>
+<a name="200"><span class="lineNum">     200 </span>            :   void writeHeaderToFile(OFile&amp;);</a>
+<a name="201"><span class="lineNum">     201 </span>            :   void writeDataDiagonalToFile(OFile&amp;);</a>
+<a name="202"><span class="lineNum">     202 </span>            :   void writeDataFullToFile(OFile&amp;);</a>
+<a name="203"><span class="lineNum">     203 </span>            : public:</a>
+<a name="204"><span class="lineNum">     204 </span>            :   Communicator&amp; getCommunicator() const {return mycomm;}</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : };</a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsVector.cpp.func-sort-c.html b/coverage/ves/CoeffsVector.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3a5506d28a
--- /dev/null
+++ b/coverage/ves/CoeffsVector.cpp.func-sort-c.html
@@ -0,0 +1,468 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsVector.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsVector.cpp<span style="font-size: 80%;"> (<a href="CoeffsVector.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">232</td>
+            <td class="headerCovTableEntry">458</td>
+            <td class="headerCovTableEntryLo">50.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryLo">45.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoeffsVector.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
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diff --git a/coverage/ves/CoeffsVector.cpp.func.html b/coverage/ves/CoeffsVector.cpp.func.html
new file mode 100644
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+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsVector.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsVector.cpp<span style="font-size: 80%;"> (<a href="CoeffsVector.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
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+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
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+            <td class="headerCovTableEntry">232</td>
+            <td class="headerCovTableEntry">458</td>
+            <td class="headerCovTableEntryLo">50.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsVector.cpp.gcov.html b/coverage/ves/CoeffsVector.cpp.gcov.html
new file mode 100644
index 0000000000..5416735202
--- /dev/null
+++ b/coverage/ves/CoeffsVector.cpp.gcov.html
@@ -0,0 +1,971 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsVector.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsVector.cpp<span style="font-size: 80%;"> (source / <a href="CoeffsVector.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">232</td>
+            <td class="headerCovTableEntry">458</td>
+            <td class="headerCovTableEntryLo">50.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryLo">45.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;vector&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;cmath&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;iostream&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &lt;sstream&gt;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;cstdio&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &lt;cfloat&gt;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : namespace PLMD {</a>
+<a name="43"><span class="lineNum">      43 </span>            : namespace ves {</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineNoCov">          0 : CoeffsVector::CoeffsVector(</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   const std::string&amp; label,</a>
+<a name="47"><span class="lineNum">      47 </span>            :   const std::vector&lt;std::string&gt;&amp; dimension_labels,</a>
+<a name="48"><span class="lineNum">      48 </span>            :   const std::vector&lt;unsigned int&gt;&amp; indices_shape,</a>
+<a name="49"><span class="lineNum">      49 </span>            :   Communicator&amp; cc,</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineNoCov">          0 :   const bool use_iteration_counter):</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   CoeffsBase(label,dimension_labels,indices_shape,use_iteration_counter),</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :   data(0),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineNoCov">          0 :   averaging_counter(0),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineNoCov">          0 :   averaging_exp_decay_(0),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineNoCov">          0 :   mycomm(cc)</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        377 : CoeffsVector::CoeffsVector(</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   const std::string&amp; label,</a>
+<a name="63"><span class="lineNum">      63 </span>            :   const std::vector&lt;Value*&gt;&amp; args,</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;BasisFunctions*&gt;&amp; basisf,</a>
+<a name="65"><span class="lineNum">      65 </span>            :   Communicator&amp; cc,</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        377 :   const bool use_iteration_counter):</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   CoeffsBase(label,args,basisf,use_iteration_counter),</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        377 :   data(0),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        377 :   averaging_counter(0),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        377 :   averaging_exp_decay_(0),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        377 :   mycomm(cc)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        377 :   clear();</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        377 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 : CoeffsVector::CoeffsVector(</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   const std::string&amp; label,</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::vector&lt;std::vector&lt;Value*&gt; &gt;&amp; argsv,</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;&amp; basisfv,</a>
+<a name="81"><span class="lineNum">      81 </span>            :   Communicator&amp; cc,</a>
+<a name="82"><span class="lineNum">      82 </span>            :   const bool use_iteration_counter,</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :   const std::string&amp; multicoeffs_label):</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   CoeffsBase(label,argsv,basisfv,use_iteration_counter,multicoeffs_label),</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 :   data(0),</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   averaging_counter(0),</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   averaging_exp_decay_(0),</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineNoCov">          0 :   mycomm(cc)</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : {</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 : CoeffsVector::CoeffsVector(</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   const std::string&amp; label,</a>
+<a name="96"><span class="lineNum">      96 </span>            :   CoeffsMatrix* coeffsMat,</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineNoCov">          0 :   Communicator&amp; cc):</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   CoeffsBase( *(static_cast&lt;CoeffsBase*&gt;(coeffsMat)) ),</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   data(0),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   averaging_counter(0),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   averaging_exp_decay_(0),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   mycomm(cc)</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : {</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">     341962 : CoeffsVector::~CoeffsVector() {}</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">      23209 : void CoeffsVector::clear() {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      23209 :   data.resize(getSize());</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">    1833419 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">    1810210 :     data[i]=0.0;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   }</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">      23209 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 : void CoeffsVector::setAllValuesToZero() {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         24 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         22 :     data[i]=0.0;</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          2 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          6 : bool CoeffsVector::sameShape(CoeffsVector&amp; coeffsvector_in) const {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          6 :   return CoeffsBase::sameShape( *(static_cast&lt;CoeffsBase*&gt;(&amp;coeffsvector_in)) );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 : bool CoeffsVector::sameShape(CoeffsMatrix&amp; coeffsmat_in) const {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :   return CoeffsBase::sameShape( *(static_cast&lt;CoeffsBase*&gt;(&amp;coeffsmat_in)) );</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : }</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 : bool CoeffsVector::sameShape(CoeffsVector&amp; coeffsvec0, CoeffsVector&amp; coeffsvec1) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineNoCov">          0 :   return coeffsvec0.sameShape(coeffsvec1);</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 : void CoeffsVector::resizeCoeffs(const std::vector&lt;unsigned int&gt;&amp; indices_shape_new) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :   CoeffsVector coeffsVecOld(*this);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   resizeIndices(indices_shape_new);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   setValuesFromDifferentShape(coeffsVecOld);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 : void CoeffsVector::resizeCoeffs(std::vector&lt;BasisFunctions*&gt;&amp; basisf_new) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineNoCov">          0 :   CoeffsVector coeffsVecOld(*this);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   resizeIndices(basisf_new);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   setValuesFromDifferentShape(coeffsVecOld);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 : void CoeffsVector::sumCommMPI() {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :   mycomm.Sum(data);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 : void CoeffsVector::sumCommMPI(Communicator&amp; cc) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :   cc.Sum(data);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 : void CoeffsVector::sumMultiSimCommMPI(Communicator&amp; multi_sim_cc) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineNoCov">          0 :   if(mycomm.Get_rank()==0) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     double nwalkers = static_cast&lt;double&gt;(multi_sim_cc.Get_size());</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     multi_sim_cc.Sum(data);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineNoCov">          0 :     scaleAllValues(1.0/nwalkers);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineNoCov">          0 :   mycomm.Bcast(data,0);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        178 : double&amp; CoeffsVector::operator[](const size_t index) {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   plumed_dbg_assert(index&lt;data.size());</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        178 :   return data[index];</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : }</a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 : const double&amp; CoeffsVector::operator[](const size_t index) const {</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :   plumed_dbg_assert(index&lt;data.size());</a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   return data[index];</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            : </a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 : double&amp; CoeffsVector::operator[](const std::vector&lt;unsigned int&gt;&amp; indices) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :   return data[getIndex(indices)];</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 : const double&amp; CoeffsVector::operator[](const std::vector&lt;unsigned int&gt;&amp; indices) const {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   return data[getIndex(indices)];</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">    1790345 : double&amp; CoeffsVector::operator()(const size_t index) {</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   plumed_dbg_assert(index&lt;data.size());</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">    1790345 :   return data[index];</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : }</a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">    1790345 : const double&amp; CoeffsVector::operator()(const size_t index) const {</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   plumed_dbg_assert(index&lt;data.size());</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">    1790345 :   return data[index];</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 : double&amp; CoeffsVector::operator()(const std::vector&lt;unsigned int&gt;&amp; indices) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   return data[getIndex(indices)];</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 : const double&amp; CoeffsVector::operator()(const std::vector&lt;unsigned int&gt;&amp; indices) const {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   return data[getIndex(indices)];</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        219 : void CoeffsVector::setValue(const size_t index, const double value) {</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   plumed_dbg_assert(index&lt;data.size());</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        219 :   data[index]=value;</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        219 : }</span></a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : </a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 : void CoeffsVector::setValue(const std::vector&lt;unsigned int&gt;&amp; indices, const double value) {</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   setValue(getIndex(indices),value);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 : void CoeffsVector::addToValue(const size_t index, const double value) {</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   plumed_dbg_assert(index&lt;data.size());</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :   data[index]+=value;</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineNoCov">          0 : void CoeffsVector::addToValue(const std::vector&lt;unsigned int&gt;&amp; indices, const double value) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 :   addToValue(getIndex(indices),value);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">      45477 : void CoeffsVector::scaleAllValues(const double scalef) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">    3626338 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">    3580861 :     data[i]*=scalef;</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   }</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      45477 : }</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      45470 : CoeffsVector&amp; CoeffsVector::operator*=(const double scalef) {</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">      45470 :   scaleAllValues(scalef);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">      45470 :   return *this;</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : }</a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">      45430 : CoeffsVector operator*(const double scalef, const CoeffsVector&amp; coeffsvector) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">      45430 :   return CoeffsVector(coeffsvector)*=scalef;</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : }</a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 : CoeffsVector operator*(const CoeffsVector&amp; coeffsvector, const double scalef) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :   return scalef*coeffsvector;</span></a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         20 : void CoeffsVector::multiplyWithValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">         20 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        240 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        220 :     data[i]*=values[i];</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   }</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         20 : }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      22765 : CoeffsVector&amp; CoeffsVector::operator*=(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      22765 :   plumed_massert(data.size()==other_coeffsvector.getSize(),&quot;Coeffs vectors do not have the same size&quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">    1813440 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    1790675 :     data[i]*=other_coeffsvector.data[i];</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :   }</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">      22765 :   return *this;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            : }</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">      22765 : CoeffsVector CoeffsVector::operator*(const CoeffsVector&amp; other_coeffsvector) const {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">      22765 :   return CoeffsVector(*this)*=other_coeffsvector;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            : }</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 : CoeffsVector operator*(const std::vector&lt;double&gt;&amp; values, const CoeffsVector&amp; coeffsvector) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineNoCov">          0 :   return coeffsvector*values;</span></a>
+<a name="290"><span class="lineNum">     290 </span>            : }</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         20 : CoeffsVector&amp; CoeffsVector::operator*=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         20 :   multiplyWithValues(values);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         20 :   return *this;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            : }</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">         20 : CoeffsVector operator*(const CoeffsVector&amp; coeffsvector, const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         20 :   return CoeffsVector(coeffsvector)*=values;</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        174 : void CoeffsVector::setValues(const double value) {</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">       8402 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">       8228 :     data[i]=value;</span></a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">        174 : }</span></a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        700 : void CoeffsVector::setValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        700 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">      23133 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">      22433 :     data[i]=values[i];</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :   }</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">        700 : }</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">      23410 : void CoeffsVector::setValues(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">      23410 :   plumed_massert( data.size()==other_coeffsvector.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">    1847404 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">    1823994 :     data[i]=other_coeffsvector.data[i];</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   }</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      23410 : }</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 : CoeffsVector&amp; CoeffsVector::operator=(const double value) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineNoCov">          0 :   setValues(value);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        453 : CoeffsVector&amp; CoeffsVector::operator=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">        453 :   setValues(values);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        453 :   return *this;</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : }</a>
+<a name="337"><span class="lineNum">     337 </span>            : </a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : // CoeffsVector&amp; CoeffsVector::operator=(const CoeffsVector&amp; other_coeffsvector) {</a>
+<a name="340"><span class="lineNum">     340 </span>            : //   setValues(other_coeffsvector);</a>
+<a name="341"><span class="lineNum">     341 </span>            : //   return *this;</a>
+<a name="342"><span class="lineNum">     342 </span>            : // }</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            : </a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineNoCov">          0 : CoeffsVector CoeffsVector::operator+() const {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : }</a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 : CoeffsVector CoeffsVector::operator-() const {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :   return CoeffsVector(*this)*=-1.0;</span></a>
+<a name="352"><span class="lineNum">     352 </span>            : }</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineNoCov">          0 : void CoeffsVector::addToValues(const double value) {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :     data[i]+=value;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   }</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineNoCov">          0 : void CoeffsVector::addToValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineNoCov">          0 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineNoCov">          0 :     data[i]+=values[i];</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   }</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : </a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      68145 : void CoeffsVector::addToValues(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      68145 :   plumed_massert( data.size()==other_coeffsvector.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">    5438520 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">    5370375 :     data[i]+=other_coeffsvector.data[i];</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :   }</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      68145 : }</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : </a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 : void CoeffsVector::subtractFromValues(const double value) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineNoCov">          0 :     data[i]-=value;</span></a>
+<a name="381"><span class="lineNum">     381 </span>            :   }</a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="383"><span class="lineNum">     383 </span>            : </a>
+<a name="384"><span class="lineNum">     384 </span>            : </a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">      22810 : void CoeffsVector::subtractFromValues(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">      22810 :   plumed_massert( data.size()==values.size(), &quot;Incorrect size&quot;);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">    1823850 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">    1801040 :     data[i]-=values[i];</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">      22810 : }</span></a>
+<a name="391"><span class="lineNum">     391 </span>            : </a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">      45440 : void CoeffsVector::subtractFromValues(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">      45440 :   plumed_massert( data.size()==other_coeffsvector.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">    3625800 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">    3580360 :     data[i]-=other_coeffsvector.data[i];</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">      45440 : }</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : </a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 : CoeffsVector&amp; CoeffsVector::operator+=(const double value) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineNoCov">          0 :   addToValues(value);</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            : }</a>
+<a name="405"><span class="lineNum">     405 </span>            : </a>
+<a name="406"><span class="lineNum">     406 </span>            : </a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineNoCov">          0 : CoeffsVector operator+(const double value, const CoeffsVector&amp; coeffsvector) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineNoCov">          0 :   return coeffsvector+value;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineNoCov">          0 : CoeffsVector operator+(const CoeffsVector&amp; coeffsvector, const double value) {</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineNoCov">          0 :   return CoeffsVector(coeffsvector)+=value;</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : }</a>
+<a name="415"><span class="lineNum">     415 </span>            : </a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineNoCov">          0 : CoeffsVector&amp; CoeffsVector::operator+=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineNoCov">          0 :   addToValues(values);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="420"><span class="lineNum">     420 </span>            : }</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineNoCov">          0 : CoeffsVector operator+(const std::vector&lt;double&gt;&amp; values, const CoeffsVector&amp; coeffsvector) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineNoCov">          0 :   return coeffsvector+values;</span></a>
+<a name="425"><span class="lineNum">     425 </span>            : }</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            : </a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineNoCov">          0 : CoeffsVector operator+(const CoeffsVector&amp; coeffsvector, const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineNoCov">          0 :   return CoeffsVector(coeffsvector)+=values;</span></a>
+<a name="430"><span class="lineNum">     430 </span>            : }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span>            : </a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineNoCov">          0 : CoeffsVector&amp; CoeffsVector::operator-=(const double value) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :   subtractFromValues(value);</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineNoCov">          0 :   return *this;</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : }</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 : CoeffsVector operator-(const double value, const CoeffsVector&amp; coeffsvector) {</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineNoCov">          0 :   return -1.0*coeffsvector+value;</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : }</a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineNoCov">          0 : CoeffsVector operator-(const CoeffsVector&amp; coeffsvector, const double value) {</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :   return CoeffsVector(coeffsvector)-=value;</span></a>
+<a name="446"><span class="lineNum">     446 </span>            : }</a>
+<a name="447"><span class="lineNum">     447 </span>            : </a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">      22810 : CoeffsVector&amp; CoeffsVector::operator-=(const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">      22810 :   subtractFromValues(values);</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">      22810 :   return *this;</span></a>
+<a name="452"><span class="lineNum">     452 </span>            : }</a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineNoCov">          0 : CoeffsVector operator-(const std::vector&lt;double&gt;&amp; values, const CoeffsVector&amp; coeffsvector) {</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineNoCov">          0 :   return -1.0*coeffsvector+values;</span></a>
+<a name="457"><span class="lineNum">     457 </span>            : }</a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">      22810 : CoeffsVector operator-(const CoeffsVector&amp; coeffsvector, const std::vector&lt;double&gt;&amp; values) {</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">      22810 :   return CoeffsVector(coeffsvector)-=values;</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : }</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">      68145 : CoeffsVector&amp; CoeffsVector::operator+=(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">      68145 :   addToValues(other_coeffsvector);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">      68145 :   return *this;</span></a>
+<a name="468"><span class="lineNum">     468 </span>            : }</a>
+<a name="469"><span class="lineNum">     469 </span>            : </a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">      22735 : CoeffsVector CoeffsVector::operator+(const CoeffsVector&amp; other_coeffsvector) const {</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">      22735 :   return CoeffsVector(*this)+=other_coeffsvector;</span></a>
+<a name="473"><span class="lineNum">     473 </span>            : }</a>
+<a name="474"><span class="lineNum">     474 </span>            : </a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">      45440 : CoeffsVector&amp; CoeffsVector::operator-=(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">      45440 :   subtractFromValues(other_coeffsvector);</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">      45440 :   return *this;</span></a>
+<a name="479"><span class="lineNum">     479 </span>            : }</a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">      45420 : CoeffsVector CoeffsVector::operator-(const CoeffsVector&amp; other_coeffsvector) const {</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">      45420 :   return CoeffsVector(*this)-=other_coeffsvector;</span></a>
+<a name="484"><span class="lineNum">     484 </span>            : }</a>
+<a name="485"><span class="lineNum">     485 </span>            : </a>
+<a name="486"><span class="lineNum">     486 </span>            : </a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineNoCov">          0 : void CoeffsVector::setValuesFromDifferentShape(const CoeffsVector&amp; other_coeffsvector) {</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineNoCov">          0 :   plumed_massert(numberOfDimensions()==other_coeffsvector.numberOfDimensions(),&quot;both coeffs vector need to have the same dimension&quot;);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineNoCov">          0 :     std::vector&lt;unsigned int&gt; indices=getIndices(i);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineNoCov">          0 :     if(other_coeffsvector.indicesExist(indices)) {</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineNoCov">          0 :       size_t oidx = other_coeffsvector.getIndex(indices);</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineNoCov">          0 :       data[i] = other_coeffsvector.data[oidx];</span></a>
+<a name="494"><span class="lineNum">     494 </span>            :     }</a>
+<a name="495"><span class="lineNum">     495 </span>            :   }</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 : void CoeffsVector::averageVectors(CoeffsVector&amp; coeffsvec0, CoeffsVector&amp; coeffsvec1) {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineNoCov">          0 :   plumed_massert(sameShape(coeffsvec0,coeffsvec1),&quot;both CoeffsVector objects need to have the same shape&quot;);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;coeffsvec0.getSize(); i++) {</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineNoCov">          0 :     coeffsvec0.data[i] = coeffsvec1.data[i] = 0.5 * (coeffsvec0.data[i]+coeffsvec1.data[i]);</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   }</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 : void CoeffsVector::averageVectors(const std::vector&lt;CoeffsVector*&gt;&amp; coeffsvecSet) {</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineNoCov">          0 :   const double norm_factor = 1.0/static_cast&lt;double&gt;(coeffsvecSet.size());</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :   for(unsigned int k=1; k&lt;coeffsvecSet.size(); k++) {</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :     plumed_massert(coeffsvecSet[0]-&gt;sameShape(*coeffsvecSet[k]),&quot;All CoeffsVector objects need to have the same shape&quot;);</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   }</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;coeffsvecSet[0]-&gt;getSize(); i++) {</span></a>
+<a name="513"><span class="lineNum">     513 </span>            :     double value = 0.0;</a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :     for(unsigned int k=0; k&lt;coeffsvecSet.size(); k++) {</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :       value += coeffsvecSet[k]-&gt;data[i];</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :     }</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineNoCov">          0 :     value *= norm_factor;</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineNoCov">          0 :     for(unsigned int k=0; k&lt;coeffsvecSet.size(); k++) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineNoCov">          0 :       coeffsvecSet[k]-&gt;data[i] = value;</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :     }</a>
+<a name="521"><span class="lineNum">     521 </span>            :   }</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 : double CoeffsVector::getMinValue() const {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   size_t min_index=0;</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :   return getMinValue(min_index);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            : }</a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineNoCov">          0 : double CoeffsVector::getMinValue(size_t&amp; min_index) const {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineNoCov">          0 :   min_index=0;</span></a>
+<a name="533"><span class="lineNum">     533 </span>            :   double min_value=DBL_MAX;</a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineNoCov">          0 :     if(data[i]&lt;min_value) {</span></a>
+<a name="536"><span class="lineNum">     536 </span>            :       min_value=data[i];</a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 :       min_index=i;</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :     }</a>
+<a name="539"><span class="lineNum">     539 </span>            :   }</a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 :   return min_value;</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : }</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineNoCov">          0 : double CoeffsVector::getMinAbsValue() const {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :   size_t min_index=0;</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :   return getMinAbsValue(min_index);</span></a>
+<a name="547"><span class="lineNum">     547 </span>            : }</a>
+<a name="548"><span class="lineNum">     548 </span>            : </a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineNoCov">          0 : double CoeffsVector::getMinAbsValue(size_t&amp; min_index) const {</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 :   min_index=0;</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   double min_value=DBL_MAX;</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineNoCov">          0 :     if(std::abs(data[i])&lt;min_value) {</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :       min_value=std::abs(data[i]);</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineNoCov">          0 :       min_index=i;</span></a>
+<a name="557"><span class="lineNum">     557 </span>            :     }</a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineNoCov">          0 :   return min_value;</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : }</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineNoCov">          0 : double CoeffsVector::getMaxValue() const {</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineNoCov">          0 :   size_t max_index=0;</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineNoCov">          0 :   return getMaxValue(max_index);</span></a>
+<a name="566"><span class="lineNum">     566 </span>            : }</a>
+<a name="567"><span class="lineNum">     567 </span>            : </a>
+<a name="568"><span class="lineNum">     568 </span>            : </a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 : double CoeffsVector::getMaxValue(size_t&amp; max_index) const {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :   max_index=0;</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :   double max_value=DBL_MIN;</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineNoCov">          0 :     if(data[i]&gt;max_value) {</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :       max_value=data[i];</a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineNoCov">          0 :       max_index=i;</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :     }</a>
+<a name="577"><span class="lineNum">     577 </span>            :   }</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineNoCov">          0 :   return max_value;</span></a>
+<a name="579"><span class="lineNum">     579 </span>            : }</a>
+<a name="580"><span class="lineNum">     580 </span>            : </a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineNoCov">          0 : double CoeffsVector::getMaxAbsValue() const {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineNoCov">          0 :   size_t max_index=0;</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineNoCov">          0 :   return getMaxAbsValue(max_index);</span></a>
+<a name="585"><span class="lineNum">     585 </span>            : }</a>
+<a name="586"><span class="lineNum">     586 </span>            : </a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         80 : double CoeffsVector::getMaxAbsValue(size_t&amp; max_index) const {</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineCov">         80 :   max_index=0;</span></a>
+<a name="590"><span class="lineNum">     590 </span>            :   double max_value=0.0;</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">        960 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">        880 :     if(std::abs(data[i])&gt;max_value) {</span></a>
+<a name="593"><span class="lineNum">     593 </span>            :       max_value=std::abs(data[i]);</a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">        180 :       max_index=i;</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :     }</a>
+<a name="596"><span class="lineNum">     596 </span>            :   }</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">         80 :   return max_value;</span></a>
+<a name="598"><span class="lineNum">     598 </span>            : }</a>
+<a name="599"><span class="lineNum">     599 </span>            : </a>
+<a name="600"><span class="lineNum">     600 </span>            : </a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">         80 : double CoeffsVector::getNorm() const {</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         80 :   return getL2Norm();</span></a>
+<a name="603"><span class="lineNum">     603 </span>            : }</a>
+<a name="604"><span class="lineNum">     604 </span>            : </a>
+<a name="605"><span class="lineNum">     605 </span>            : </a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 : double CoeffsVector::getL1Norm() const {</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :   double norm=0.0;</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :     norm+=std::abs(data[i]);</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :   }</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineNoCov">          0 :   return norm;</span></a>
+<a name="612"><span class="lineNum">     612 </span>            : }</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         80 : double CoeffsVector::getL2Norm() const {</span></a>
+<a name="616"><span class="lineNum">     616 </span>            :   double norm=0.0;</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">        960 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">        880 :     norm+=data[i]*data[i];</span></a>
+<a name="619"><span class="lineNum">     619 </span>            :   }</a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         80 :   norm=sqrt(norm);</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">         80 :   return norm;</span></a>
+<a name="622"><span class="lineNum">     622 </span>            : }</a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            : </a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineNoCov">          0 : double CoeffsVector::getLpNorm(const double p) const {</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :   double norm=0.0;</a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineNoCov">          0 :     norm+=pow(data[i],p);</span></a>
+<a name="629"><span class="lineNum">     629 </span>            :   }</a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineNoCov">          0 :   norm=pow(norm,(1.0/p));</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineNoCov">          0 :   return norm;</span></a>
+<a name="632"><span class="lineNum">     632 </span>            : }</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">         80 : double CoeffsVector::getRMS() const {</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         80 :   return getNorm()/sqrt(numberOfCoeffs());</span></a>
+<a name="637"><span class="lineNum">     637 </span>            : }</a>
+<a name="638"><span class="lineNum">     638 </span>            : </a>
+<a name="639"><span class="lineNum">     639 </span>            : </a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineNoCov">          0 : void CoeffsVector::normalizeCoeffs() {</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineNoCov">          0 :   double norm=getNorm();</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 :   scaleAllValues(norm);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span>            : </a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineNoCov">          0 : void CoeffsVector::randomizeValuesGaussian(int randomSeed) {</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineNoCov">          0 :   Random rnd;</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :   if (randomSeed&lt;0) {randomSeed = -randomSeed;}</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :   rnd.setSeed(-randomSeed);</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineNoCov">          0 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 :     data[i]=rnd.Gaussian();</span></a>
+<a name="652"><span class="lineNum">     652 </span>            :   }</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="654"><span class="lineNum">     654 </span>            : </a>
+<a name="655"><span class="lineNum">     655 </span>            : </a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineNoCov">          0 : void CoeffsVector::resetAveraging() {</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 :   clear();</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :   resetAveragingCounter();</a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="660"><span class="lineNum">     660 </span>            : </a>
+<a name="661"><span class="lineNum">     661 </span>            : </a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         20 : void CoeffsVector::addToAverage(const CoeffsVector&amp; coeffsvec) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         20 :   plumed_massert( data.size()==coeffsvec.getSize(), &quot;Incorrect size&quot;);</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :   //</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">         20 :   double aver_decay = 1.0 / ( static_cast&lt;double&gt;(averaging_counter) + 1.0 );</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">         20 :   if(averaging_exp_decay_&gt;0 &amp;&amp;  (averaging_counter+1 &gt; averaging_exp_decay_) ) {</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">          9 :     aver_decay = 1.0 / static_cast&lt;double&gt;(averaging_exp_decay_);</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :   }</a>
+<a name="669"><span class="lineNum">     669 </span>            :   //</a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">        240 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">        220 :     data[i]+=(coeffsvec.data[i]-data[i])*aver_decay;</span></a>
+<a name="672"><span class="lineNum">     672 </span>            :   }</a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">         20 :   averaging_counter++;</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">         20 : }</span></a>
+<a name="675"><span class="lineNum">     675 </span>            : </a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">          1 : size_t CoeffsVector::countValues(const double value) const {</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :   size_t numvalues=0;</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">         12 :   for(size_t i=0; i&lt;data.size(); i++) {</span></a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">         11 :     if(data[i]==value) {</span></a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">          2 :       numvalues++;</span></a>
+<a name="682"><span class="lineNum">     682 </span>            :     }</a>
+<a name="683"><span class="lineNum">     683 </span>            :   }</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">          1 :   return numvalues;</span></a>
+<a name="685"><span class="lineNum">     685 </span>            : }</a>
+<a name="686"><span class="lineNum">     686 </span>            : </a>
+<a name="687"><span class="lineNum">     687 </span>            : </a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineNoCov">          0 : void CoeffsVector::writeToFile(const std::string&amp; filepath, const bool print_coeffs_descriptions, const bool append_file, Action* action_pntr) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :   OFile file;</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineNoCov">          0 :   if(action_pntr!=NULL) {</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineNoCov">          0 :     file.link(*action_pntr);</span></a>
+<a name="692"><span class="lineNum">     692 </span>            :   }</a>
+<a name="693"><span class="lineNum">     693 </span>            :   else {</a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :     file.link(mycomm);</span></a>
+<a name="695"><span class="lineNum">     695 </span>            :   }</a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :   if(append_file) { file.enforceRestart(); }</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineNoCov">          0 :   file.open(filepath);</span></a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :   writeToFile(file,print_coeffs_descriptions);</span></a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineNoCov">          0 :   file.close();</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span>            : </a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">       1467 : void CoeffsVector::writeToFile(OFile&amp; ofile, const bool print_coeffs_descriptions) {</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :   std::vector&lt;CoeffsVector*&gt; CoeffsSetTmp;</a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">       1467 :   CoeffsSetTmp.push_back(this);</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">       1467 :   writeHeaderToFile(ofile);</span></a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">       1467 :   writeDataToFile(ofile,CoeffsSetTmp,print_coeffs_descriptions);</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">       1467 : }</span></a>
+<a name="709"><span class="lineNum">     709 </span>            : </a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">        881 : void CoeffsVector::writeToFile(OFile&amp; ofile, CoeffsVector* aux_coeffsvector, const bool print_coeffs_descriptions) {</span></a>
+<a name="712"><span class="lineNum">     712 </span>            :   std::vector&lt;CoeffsVector*&gt; CoeffsSetTmp;</a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">        881 :   CoeffsSetTmp.push_back(this);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">        881 :   CoeffsSetTmp.push_back(aux_coeffsvector);</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">        881 :   writeHeaderToFile(ofile);</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">        881 :   writeDataToFile(ofile,CoeffsSetTmp,print_coeffs_descriptions);</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">        881 : }</span></a>
+<a name="718"><span class="lineNum">     718 </span>            : </a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span><span class="lineNoCov">          0 : void CoeffsVector::writeToFile(const std::string&amp; filepath, const std::vector&lt;CoeffsVector*&gt;&amp; coeffsvecSet, const bool print_coeffs_descriptions, const bool append_file, Action* action_pntr) {</span></a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineNoCov">          0 :   OFile file;</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineNoCov">          0 :   if(action_pntr!=NULL) {</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineNoCov">          0 :     file.link(*action_pntr);</span></a>
+<a name="724"><span class="lineNum">     724 </span>            :   }</a>
+<a name="725"><span class="lineNum">     725 </span>            :   else {</a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineNoCov">          0 :     file.link(coeffsvecSet[0]-&gt;getCommunicator());</span></a>
+<a name="727"><span class="lineNum">     727 </span>            :   }</a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineNoCov">          0 :   if(append_file) { file.enforceRestart(); }</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineNoCov">          0 :   file.open(filepath);</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineNoCov">          0 :   writeToFile(file,coeffsvecSet,print_coeffs_descriptions);</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineNoCov">          0 :   file.close();</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="733"><span class="lineNum">     733 </span>            : </a>
+<a name="734"><span class="lineNum">     734 </span>            : </a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineNoCov">          0 : void CoeffsVector::writeToFile(OFile&amp; ofile, const std::vector&lt;CoeffsVector*&gt;&amp; coeffsvecSet, const bool print_coeffs_descriptions) {</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineNoCov">          0 :   for(unsigned int k=1; k&lt;coeffsvecSet.size(); k++) {</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineNoCov">          0 :     plumed_massert(coeffsvecSet[k]-&gt;sameShape(*coeffsvecSet[0]),&quot;Error in writing a set of coeffs to file: The coeffs do not have the same shape and size&quot;);</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :   }</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :   coeffsvecSet[0]-&gt;writeHeaderToFile(ofile);</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :   writeDataToFile(ofile,coeffsvecSet, print_coeffs_descriptions);</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="742"><span class="lineNum">     742 </span>            : </a>
+<a name="743"><span class="lineNum">     743 </span>            : </a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineCov">       2348 : void CoeffsVector::writeHeaderToFile(OFile&amp; ofile) const {</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineCov">       2348 :   ofile.clearFields();</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineCov">       2348 :   if(isIterationCounterActive()) {</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineCov">       2061 :     writeIterationCounterAndTimeToFile(ofile);</span></a>
+<a name="748"><span class="lineNum">     748 </span>            :   }</a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineCov">       2348 :   writeCoeffsInfoToFile(ofile);</span></a>
+<a name="750"><span class="lineNum">     750 </span><span class="lineCov">       2348 : }</span></a>
+<a name="751"><span class="lineNum">     751 </span>            : </a>
+<a name="752"><span class="lineNum">     752 </span>            : </a>
+<a name="753"><span class="lineNum">     753 </span><span class="lineCov">       2348 : void CoeffsVector::writeDataToFile(OFile&amp; ofile, const std::vector&lt;CoeffsVector*&gt;&amp; coeffsvecSet, const bool print_coeffs_descriptions) {</span></a>
+<a name="754"><span class="lineNum">     754 </span>            :   //</a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineCov">       2348 :   std::string field_indices_prefix = &quot;idx_&quot;;</span></a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">       2348 :   std::string field_index = &quot;index&quot;;</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">       2348 :   std::string field_description = &quot;description&quot;;</span></a>
+<a name="758"><span class="lineNum">     758 </span>            :   //</a>
+<a name="759"><span class="lineNum">     759 </span><span class="lineCov">       2348 :   std::string int_fmt = &quot;%8d&quot;;</span></a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">       2348 :   std::string str_separate = &quot;#!-------------------&quot;;</span></a>
+<a name="761"><span class="lineNum">     761 </span>            :   //</a>
+<a name="762"><span class="lineNum">     762 </span><span class="lineCov">       2348 :   unsigned int numvec = coeffsvecSet.size();</span></a>
+<a name="763"><span class="lineNum">     763 </span><span class="lineCov">       2348 :   unsigned int numdim = coeffsvecSet[0]-&gt;numberOfDimensions();</span></a>
+<a name="764"><span class="lineNum">     764 </span>            :   unsigned int numcoeffs = coeffsvecSet[0]-&gt;getSize();</a>
+<a name="765"><span class="lineNum">     765 </span>            :   std::vector&lt;std::string&gt; coeffs_descriptions = coeffsvecSet[0]-&gt;getAllCoeffsDescriptions();</a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">       2348 :   std::string output_fmt = coeffsvecSet[0]-&gt;getOutputFmt();</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">       2348 :   std::vector&lt;std::string&gt; coeffs_datalabels(numvec);</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">       5577 :   for(unsigned int k=0; k&lt;numvec; k++) {</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">       6458 :     coeffs_datalabels[k] = coeffsvecSet[k]-&gt;getDataLabel();</span></a>
+<a name="770"><span class="lineNum">     770 </span>            :   }</a>
+<a name="771"><span class="lineNum">     771 </span>            :   //</a>
+<a name="772"><span class="lineNum">     772 </span><span class="lineCov">       2348 :   std::vector&lt;char&gt; s1(20);</span></a>
+<a name="773"><span class="lineNum">     773 </span><span class="lineCov">       2348 :   std::vector&lt;unsigned int&gt; indices(numdim);</span></a>
+<a name="774"><span class="lineNum">     774 </span><span class="lineCov">       2348 :   std::vector&lt;std::string&gt; ilabels(numdim);</span></a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">       5260 :   for(unsigned int k=0; k&lt;numdim; k++) {</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">       5824 :     ilabels[k]=field_indices_prefix+coeffsvecSet[0]-&gt;getDimensionLabel(k);</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :   }</a>
+<a name="778"><span class="lineNum">     778 </span>            :   //</a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">      86666 :   for(size_t i=0; i&lt;numcoeffs; i++) {</span></a>
+<a name="780"><span class="lineNum">     780 </span><span class="lineCov">      84318 :     indices=coeffsvecSet[0]-&gt;getIndices(i);</span></a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">     233206 :     for(unsigned int k=0; k&lt;numdim; k++) {</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">     148888 :       std::snprintf(s1.data(),s1.size(),int_fmt.c_str(),indices[k]);</span></a>
+<a name="783"><span class="lineNum">     783 </span><span class="lineCov">     297776 :       ofile.printField(ilabels[k],s1.data());</span></a>
+<a name="784"><span class="lineNum">     784 </span>            :     }</a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">     203216 :     for(unsigned int l=0; l&lt;numvec; l++) {</span></a>
+<a name="786"><span class="lineNum">     786 </span><span class="lineCov">     237796 :       ofile.fmtField(&quot; &quot;+output_fmt).printField(coeffs_datalabels[l],coeffsvecSet[l]-&gt;getValue(i));</span></a>
+<a name="787"><span class="lineNum">     787 </span>            :     }</a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">      84318 :     std::snprintf(s1.data(),s1.size(),int_fmt.c_str(),i); ofile.printField(field_index,s1.data());</span></a>
+<a name="789"><span class="lineNum">     789 </span><span class="lineCov">      89064 :     if(print_coeffs_descriptions) { ofile.printField(field_description,&quot;  &quot;+coeffs_descriptions[i]);}</span></a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">      84318 :     ofile.printField();</span></a>
+<a name="791"><span class="lineNum">     791 </span>            :   }</a>
+<a name="792"><span class="lineNum">     792 </span><span class="lineCov">       2348 :   ofile.fmtField();</span></a>
+<a name="793"><span class="lineNum">     793 </span>            :   // blank line between iterations to allow proper plotting with gnuplot</a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">       2348 :   ofile.printf(&quot;%s\n&quot;,str_separate.c_str());</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">       2348 :   ofile.printf(&quot;\n&quot;);</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">       2348 :   ofile.printf(&quot;\n&quot;);</span></a>
+<a name="797"><span class="lineNum">     797 </span><span class="lineCov">       9392 : }</span></a>
+<a name="798"><span class="lineNum">     798 </span>            : </a>
+<a name="799"><span class="lineNum">     799 </span>            : </a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">         75 : size_t CoeffsVector::readFromFile(IFile&amp; ifile, const bool ignore_missing_coeffs, const bool ignore_header) {</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">         75 :   ifile.allowIgnoredFields();</span></a>
+<a name="802"><span class="lineNum">     802 </span>            :   size_t ncoeffs_read=0;</a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">        594 :   while(ifile) {</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">        444 :     if(!ignore_header) {readHeaderFromFile(ifile);}</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">        444 :     if(ifile) {</span></a>
+<a name="806"><span class="lineNum">     806 </span><span class="lineCov">        409 :       ncoeffs_read=readDataFromFile(ifile,ignore_missing_coeffs);</span></a>
+<a name="807"><span class="lineNum">     807 </span>            :     }</a>
+<a name="808"><span class="lineNum">     808 </span>            :   }</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">         75 :   return ncoeffs_read;</span></a>
+<a name="810"><span class="lineNum">     810 </span>            : }</a>
+<a name="811"><span class="lineNum">     811 </span>            : </a>
+<a name="812"><span class="lineNum">     812 </span>            : </a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">         36 : size_t CoeffsVector::readOneSetFromFile(IFile&amp; ifile, const bool ignore_header) {</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">         36 :   ifile.allowIgnoredFields();</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :   size_t ncoeffs_read=0;</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">         36 :   if(ifile) {</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">         36 :     if(!ignore_header) {readHeaderFromFile(ifile);}</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">         36 :     if(ifile) {ncoeffs_read=readDataFromFile(ifile,false);}</span></a>
+<a name="819"><span class="lineNum">     819 </span>            :   }</a>
+<a name="820"><span class="lineNum">     820 </span><span class="lineCov">         36 :   return ncoeffs_read;</span></a>
+<a name="821"><span class="lineNum">     821 </span>            : }</a>
+<a name="822"><span class="lineNum">     822 </span>            : </a>
+<a name="823"><span class="lineNum">     823 </span>            : </a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">         40 : size_t CoeffsVector::readFromFile(const std::string&amp; filepath, const bool ignore_missing_coeffs, const bool ignore_header) {</span></a>
+<a name="825"><span class="lineNum">     825 </span><span class="lineCov">         40 :   IFile file;</span></a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">         40 :   file.link(mycomm);</span></a>
+<a name="827"><span class="lineNum">     827 </span><span class="lineCov">         40 :   file.open(filepath);</span></a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">         40 :   size_t ncoeffs_read=readFromFile(file,ignore_missing_coeffs, ignore_header);</span></a>
+<a name="829"><span class="lineNum">     829 </span><span class="lineCov">         40 :   file.close();</span></a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">         40 :   return ncoeffs_read;</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">         40 : }</span></a>
+<a name="832"><span class="lineNum">     832 </span>            : </a>
+<a name="833"><span class="lineNum">     833 </span>            : </a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">        406 : void CoeffsVector::readHeaderFromFile(IFile&amp; ifile, const bool ignore_coeffs_info) {</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">        406 :   if(ifile &amp;&amp; isIterationCounterActive()) {</span></a>
+<a name="836"><span class="lineNum">     836 </span><span class="lineCov">        406 :     getIterationCounterAndTimeFromFile(ifile);</span></a>
+<a name="837"><span class="lineNum">     837 </span>            :   }</a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">        406 :   if(ifile) {</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">        368 :     getCoeffsInfoFromFile(ifile,ignore_coeffs_info);</span></a>
+<a name="840"><span class="lineNum">     840 </span>            :   }</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">        406 : }</span></a>
+<a name="842"><span class="lineNum">     842 </span>            : </a>
+<a name="843"><span class="lineNum">     843 </span>            : </a>
+<a name="844"><span class="lineNum">     844 </span><span class="lineCov">        442 : size_t CoeffsVector::readDataFromFile(IFile&amp; ifile, const bool ignore_missing_coeffs) {</span></a>
+<a name="845"><span class="lineNum">     845 </span>            :   //</a>
+<a name="846"><span class="lineNum">     846 </span><span class="lineCov">        442 :   std::string field_indices_prefix = &quot;idx_&quot;;</span></a>
+<a name="847"><span class="lineNum">     847 </span>            :   std::string field_coeffs = getDataLabel();</a>
+<a name="848"><span class="lineNum">     848 </span><span class="lineCov">        442 :   std::string field_index = &quot;index&quot;;</span></a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">        442 :   std::string field_description = &quot;description&quot;;</span></a>
+<a name="850"><span class="lineNum">     850 </span>            :   //</a>
+<a name="851"><span class="lineNum">     851 </span><span class="lineCov">        442 :   std::vector&lt;std::string&gt; ilabels(numberOfDimensions());</span></a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">        903 :   for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">        922 :     ilabels[k]=field_indices_prefix+getDimensionLabel(k);</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :   }</a>
+<a name="855"><span class="lineNum">     855 </span>            :   //</a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">        442 :   std::vector&lt;unsigned int&gt; indices(numberOfDimensions());</span></a>
+<a name="857"><span class="lineNum">     857 </span><span class="lineCov">        442 :   double coeff_tmp=0.0;</span></a>
+<a name="858"><span class="lineNum">     858 </span>            :   std::string str_tmp;</a>
+<a name="859"><span class="lineNum">     859 </span>            :   size_t ncoeffs_read=0;</a>
+<a name="860"><span class="lineNum">     860 </span>            :   //</a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">       5475 :   while(ifile.scanField(field_coeffs,coeff_tmp)) {</span></a>
+<a name="862"><span class="lineNum">     862 </span>            :     int idx_tmp;</a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">      12131 :     for(unsigned int k=0; k&lt;numberOfDimensions(); k++) {</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">       6696 :       ifile.scanField(ilabels[k],idx_tmp);</span></a>
+<a name="865"><span class="lineNum">     865 </span><span class="lineCov">       6696 :       indices[k] = static_cast&lt;unsigned int&gt;(idx_tmp);</span></a>
+<a name="866"><span class="lineNum">     866 </span>            :     }</a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">       5435 :     data[getIndex(indices)] = coeff_tmp;</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">       5435 :     ifile.scanField(field_index,idx_tmp);</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">       5435 :     if(getIndex(indices)!=static_cast&lt;unsigned int&gt;(idx_tmp)) {</span></a>
+<a name="870"><span class="lineNum">     870 </span><span class="lineNoCov">          0 :       std::string is1; Tools::convert(idx_tmp,is1);</span></a>
+<a name="871"><span class="lineNum">     871 </span><span class="lineNoCov">          0 :       std::string msg=&quot;ERROR: problem with indices at index &quot; + is1 + &quot; when reading coefficients from file&quot;;</span></a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineNoCov">          0 :       plumed_merror(msg);</span></a>
+<a name="873"><span class="lineNum">     873 </span>            :     }</a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">       5435 :     if(ifile.FieldExist(field_description)) { ifile.scanField(field_description,str_tmp); }</span></a>
+<a name="875"><span class="lineNum">     875 </span>            :     //</a>
+<a name="876"><span class="lineNum">     876 </span><span class="lineCov">       5435 :     ifile.scanField();</span></a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">       5435 :     ncoeffs_read++;</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">       5435 :     if(ncoeffs_read==numberOfCoeffs()) {</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">        402 :       if((static_cast&lt;unsigned int&gt;(idx_tmp)+1)!=numberOfCoeffs()) {</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;something strange about the coefficient file that is being read in, perhaps multiple entries or missing values&quot;);</span></a>
+<a name="881"><span class="lineNum">     881 </span>            :       }</a>
+<a name="882"><span class="lineNum">     882 </span><span class="lineCov">        402 :       break;</span></a>
+<a name="883"><span class="lineNum">     883 </span>            :     }</a>
+<a name="884"><span class="lineNum">     884 </span>            :   }</a>
+<a name="885"><span class="lineNum">     885 </span>            :   // checks on the coeffs read</a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">        442 :   if(ncoeffs_read&gt;0 &amp;&amp;!ignore_missing_coeffs &amp;&amp; ncoeffs_read &lt; numberOfCoeffs()) {</span></a>
+<a name="887"><span class="lineNum">     887 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;ERROR: missing coefficients when reading from file&quot;);</span></a>
+<a name="888"><span class="lineNum">     888 </span>            :   }</a>
+<a name="889"><span class="lineNum">     889 </span>            :   //</a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">        442 :   return ncoeffs_read;</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">        442 : }</span></a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            : </a>
+<a name="894"><span class="lineNum">     894 </span>            : }</a>
+<a name="895"><span class="lineNum">     895 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsVector.h.func-sort-c.html b/coverage/ves/CoeffsVector.h.func-sort-c.html
new file mode 100644
index 0000000000..56d31a4b96
--- /dev/null
+++ b/coverage/ves/CoeffsVector.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsVector.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsVector.h<span style="font-size: 80%;"> (<a href="CoeffsVector.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="CoeffsVector.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/CoeffsVector.h.func.html b/coverage/ves/CoeffsVector.h.func.html
new file mode 100644
index 0000000000..ee3b8eab77
--- /dev/null
+++ b/coverage/ves/CoeffsVector.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/CoeffsVector.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsVector.h<span style="font-size: 80%;"> (<a href="CoeffsVector.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/ves/CoeffsVector.h.gcov.html b/coverage/ves/CoeffsVector.h.gcov.html
new file mode 100644
index 0000000000..53f22145c1
--- /dev/null
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+  <title>LCOV - plumed test coverage - ves/CoeffsVector.h</title>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - CoeffsVector.h<span style="font-size: 80%;"> (source / <a href="CoeffsVector.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_CoeffsVector_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_CoeffsVector_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsBase.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;memory&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class Action;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class Value;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class IFile;</a>
+<a name="38"><span class="lineNum">      38 </span>            : class OFile;</a>
+<a name="39"><span class="lineNum">      39 </span>            : class Communicator;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace ves {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : class BasisFunctions;</a>
+<a name="44"><span class="lineNum">      44 </span>            : class CoeffsMatrix;</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : class CoeffsVector:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   public CoeffsBase</a>
+<a name="49"><span class="lineNum">      49 </span>            : {</a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            : private:</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;double&gt; data;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   //</a>
+<a name="54"><span class="lineNum">      54 </span>            :   unsigned int averaging_counter;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   unsigned int averaging_exp_decay_;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   //</a>
+<a name="57"><span class="lineNum">      57 </span>            :   Communicator&amp; mycomm;</a>
+<a name="58"><span class="lineNum">      58 </span>            :   //</a>
+<a name="59"><span class="lineNum">      59 </span>            :   CoeffsVector&amp; operator=(const CoeffsVector&amp;);</a>
+<a name="60"><span class="lineNum">      60 </span>            : public:</a>
+<a name="61"><span class="lineNum">      61 </span>            :   explicit CoeffsVector(</a>
+<a name="62"><span class="lineNum">      62 </span>            :     const std::string&amp;,</a>
+<a name="63"><span class="lineNum">      63 </span>            :     const std::vector&lt;std::string&gt;&amp;,</a>
+<a name="64"><span class="lineNum">      64 </span>            :     const std::vector&lt;unsigned int&gt;&amp;,</a>
+<a name="65"><span class="lineNum">      65 </span>            :     Communicator&amp;,</a>
+<a name="66"><span class="lineNum">      66 </span>            :     const bool use_counter=false);</a>
+<a name="67"><span class="lineNum">      67 </span>            :   //</a>
+<a name="68"><span class="lineNum">      68 </span>            :   explicit CoeffsVector(</a>
+<a name="69"><span class="lineNum">      69 </span>            :     const std::string&amp;,</a>
+<a name="70"><span class="lineNum">      70 </span>            :     const std::vector&lt;Value*&gt;&amp;,</a>
+<a name="71"><span class="lineNum">      71 </span>            :     std::vector&lt;BasisFunctions*&gt;&amp;,</a>
+<a name="72"><span class="lineNum">      72 </span>            :     Communicator&amp;,</a>
+<a name="73"><span class="lineNum">      73 </span>            :     const bool use_counter=false);</a>
+<a name="74"><span class="lineNum">      74 </span>            :   //</a>
+<a name="75"><span class="lineNum">      75 </span>            :   explicit CoeffsVector(</a>
+<a name="76"><span class="lineNum">      76 </span>            :     const std::string&amp;,</a>
+<a name="77"><span class="lineNum">      77 </span>            :     std::vector&lt;std::vector&lt;Value*&gt; &gt;&amp;,</a>
+<a name="78"><span class="lineNum">      78 </span>            :     std::vector&lt;std::vector&lt;BasisFunctions*&gt; &gt;&amp;,</a>
+<a name="79"><span class="lineNum">      79 </span>            :     Communicator&amp;,</a>
+<a name="80"><span class="lineNum">      80 </span>            :     const bool use_counter=false,</a>
+<a name="81"><span class="lineNum">      81 </span>            :     const std::string&amp; multicoeffs_label=&quot;bias&quot;);</a>
+<a name="82"><span class="lineNum">      82 </span>            :   //</a>
+<a name="83"><span class="lineNum">      83 </span>            :   explicit CoeffsVector(</a>
+<a name="84"><span class="lineNum">      84 </span>            :     const std::string&amp;,</a>
+<a name="85"><span class="lineNum">      85 </span>            :     CoeffsMatrix*,</a>
+<a name="86"><span class="lineNum">      86 </span>            :     Communicator&amp;);</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //</a>
+<a name="88"><span class="lineNum">      88 </span>            :   ~CoeffsVector();</a>
+<a name="89"><span class="lineNum">      89 </span>            :   //</a>
+<a name="90"><span class="lineNum">      90 </span>            :   size_t getSize() const {return numberOfCoeffs();}</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // clear coeffs</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void clear();</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void setAllValuesToZero();</a>
+<a name="94"><span class="lineNum">      94 </span>            :   //</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::vector&lt;double&gt; getDataAsVector() const {return data;}</a>
+<a name="96"><span class="lineNum">      96 </span>            :   //</a>
+<a name="97"><span class="lineNum">      97 </span>            :   bool sameShape(CoeffsVector&amp;) const;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   bool sameShape(CoeffsMatrix&amp;) const;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   static bool sameShape(CoeffsVector&amp;, CoeffsVector&amp;);</a>
+<a name="100"><span class="lineNum">     100 </span>            :   //</a>
+<a name="101"><span class="lineNum">     101 </span>            :   void resizeCoeffs(const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void resizeCoeffs(std::vector&lt;BasisFunctions*&gt;&amp;);</a>
+<a name="103"><span class="lineNum">     103 </span>            :   //</a>
+<a name="104"><span class="lineNum">     104 </span>            :   void sumCommMPI();</a>
+<a name="105"><span class="lineNum">     105 </span>            :   void sumCommMPI(Communicator&amp; cc);</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void sumMultiSimCommMPI(Communicator&amp;);</a>
+<a name="108"><span class="lineNum">     108 </span>            :   // get value</a>
+<a name="109"><span class="lineNum">     109 </span>            :   double getValue(const size_t) const;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double getValue(const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   double&amp; operator[](const size_t index);</a>
+<a name="112"><span class="lineNum">     112 </span>            :   const double&amp; operator[](const size_t index) const;</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double&amp; operator[](const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   const double&amp; operator[](const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   double&amp; operator()(const size_t index);</a>
+<a name="116"><span class="lineNum">     116 </span>            :   const double&amp; operator()(const size_t index) const;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   double&amp; operator()(const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="118"><span class="lineNum">     118 </span>            :   const double&amp; operator()(const std::vector&lt;unsigned int&gt;&amp;) const;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   // set value</a>
+<a name="120"><span class="lineNum">     120 </span>            :   void setValue(const size_t, const double);</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void setValue(const std::vector&lt;unsigned int&gt;&amp;, const double);</a>
+<a name="122"><span class="lineNum">     122 </span>            :   // add to value</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void addToValue(const size_t, const double);</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void addToValue(const std::vector&lt;unsigned int&gt;&amp;, const double);</a>
+<a name="125"><span class="lineNum">     125 </span>            :   // scale all values</a>
+<a name="126"><span class="lineNum">     126 </span>            :   void scaleAllValues(const double);</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void multiplyWithValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="128"><span class="lineNum">     128 </span>            :   CoeffsVector&amp; operator*=(const double);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   friend CoeffsVector operator*(const double, const CoeffsVector&amp;);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   friend CoeffsVector operator*(const CoeffsVector&amp;, const double);</a>
+<a name="131"><span class="lineNum">     131 </span>            :   CoeffsVector&amp; operator*=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="132"><span class="lineNum">     132 </span>            :   friend CoeffsVector operator*(const std::vector&lt;double&gt;&amp;, const CoeffsVector&amp;);</a>
+<a name="133"><span class="lineNum">     133 </span>            :   friend CoeffsVector operator*(const CoeffsVector&amp;, const std::vector&lt;double&gt;&amp;);</a>
+<a name="134"><span class="lineNum">     134 </span>            :   CoeffsVector&amp; operator*=(const CoeffsVector&amp;);</a>
+<a name="135"><span class="lineNum">     135 </span>            :   CoeffsVector operator*(const CoeffsVector&amp;) const;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   // set all values</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void setValues(const double);</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void setValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void setValues(const CoeffsVector&amp;);</a>
+<a name="140"><span class="lineNum">     140 </span>            :   CoeffsVector&amp; operator=(const double);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   CoeffsVector&amp; operator=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="142"><span class="lineNum">     142 </span>            :   // CoeffsVector&amp; operator=(const CoeffsVector&amp;);</a>
+<a name="143"><span class="lineNum">     143 </span>            :   // add to all values</a>
+<a name="144"><span class="lineNum">     144 </span>            :   CoeffsVector operator+() const;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   CoeffsVector operator-() const;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void addToValues(const double);</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void addToValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="148"><span class="lineNum">     148 </span>            :   void addToValues(const CoeffsVector&amp;);</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void subtractFromValues(const double);</a>
+<a name="150"><span class="lineNum">     150 </span>            :   void subtractFromValues(const std::vector&lt;double&gt;&amp;);</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void subtractFromValues(const CoeffsVector&amp;);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   CoeffsVector&amp; operator+=(const double);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   friend CoeffsVector operator+(const double, const CoeffsVector&amp;);</a>
+<a name="154"><span class="lineNum">     154 </span>            :   friend CoeffsVector operator+(const CoeffsVector&amp;, const double);</a>
+<a name="155"><span class="lineNum">     155 </span>            :   CoeffsVector&amp; operator+=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   friend CoeffsVector operator+(const std::vector&lt;double&gt;&amp;, const CoeffsVector&amp;);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   friend CoeffsVector operator+(const CoeffsVector&amp;, const std::vector&lt;double&gt;&amp;);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   CoeffsVector&amp; operator-=(const double);</a>
+<a name="159"><span class="lineNum">     159 </span>            :   friend CoeffsVector operator-(const double, const CoeffsVector&amp;);</a>
+<a name="160"><span class="lineNum">     160 </span>            :   friend CoeffsVector operator-(const CoeffsVector&amp;, const double);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   CoeffsVector&amp; operator-=(const std::vector&lt;double&gt;&amp;);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   friend CoeffsVector operator-(const std::vector&lt;double&gt;&amp;, const CoeffsVector&amp;);</a>
+<a name="163"><span class="lineNum">     163 </span>            :   friend CoeffsVector operator-(const CoeffsVector&amp;, const std::vector&lt;double&gt;&amp;);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   CoeffsVector&amp; operator+=(const CoeffsVector&amp;);</a>
+<a name="165"><span class="lineNum">     165 </span>            :   CoeffsVector operator+(const CoeffsVector&amp;) const;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   CoeffsVector&amp; operator-=(const CoeffsVector&amp;);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   CoeffsVector operator-(const CoeffsVector&amp;) const;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   //</a>
+<a name="169"><span class="lineNum">     169 </span>            :   void setValuesFromDifferentShape(const CoeffsVector&amp;);</a>
+<a name="170"><span class="lineNum">     170 </span>            :   //</a>
+<a name="171"><span class="lineNum">     171 </span>            :   static void averageVectors(CoeffsVector&amp;, CoeffsVector&amp;);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   static void averageVectors(const std::vector&lt;CoeffsVector*&gt;&amp;);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   //</a>
+<a name="174"><span class="lineNum">     174 </span>            :   double getMinValue() const;</a>
+<a name="175"><span class="lineNum">     175 </span>            :   double getMinValue(size_t&amp;) const;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   double getMinAbsValue() const;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   double getMinAbsValue(size_t&amp;) const;</a>
+<a name="178"><span class="lineNum">     178 </span>            :   //</a>
+<a name="179"><span class="lineNum">     179 </span>            :   double getMaxValue() const;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   double getMaxValue(size_t&amp;) const;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   double getMaxAbsValue() const;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double getMaxAbsValue(size_t&amp;) const;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //</a>
+<a name="184"><span class="lineNum">     184 </span>            :   double getNorm() const;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   double getL1Norm() const;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   double getL2Norm() const;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   double getLpNorm(const double) const;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   double getRMS() const;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void normalizeCoeffs();</a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Random values</a>
+<a name="192"><span class="lineNum">     192 </span>            :   void randomizeValuesGaussian(int);</a>
+<a name="193"><span class="lineNum">     193 </span>            :   //</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   void resetAveragingCounter() {averaging_counter=0;}</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          1 :   void setupExponentiallyDecayingAveraging(const unsigned int averaging_exp_decay_in) {averaging_exp_decay_=averaging_exp_decay_in;}</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   void turnOffExponentiallyDecayingAveraging() {averaging_exp_decay_=0;}</a>
+<a name="197"><span class="lineNum">     197 </span>            :   void resetAveraging();</a>
+<a name="198"><span class="lineNum">     198 </span>            :   void addToAverage(const CoeffsVector&amp;);</a>
+<a name="199"><span class="lineNum">     199 </span>            :   //</a>
+<a name="200"><span class="lineNum">     200 </span>            :   size_t countValues(const double) const;</a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            :   // file input/output stuff</a>
+<a name="203"><span class="lineNum">     203 </span>            :   void writeToFile(const std::string&amp;, const bool print_description=false, const bool append_file=false, Action* action_pntr=NULL);</a>
+<a name="204"><span class="lineNum">     204 </span>            :   void writeToFile(OFile&amp;, const bool print_description=false);</a>
+<a name="205"><span class="lineNum">     205 </span>            :   void writeToFile(OFile&amp; ofile, CoeffsVector*, const bool print_coeffs_descriptions=false);</a>
+<a name="206"><span class="lineNum">     206 </span>            :   static void writeToFile(const std::string&amp;, const std::vector&lt;CoeffsVector*&gt;&amp;, const bool print_description=false, const bool append_file=false, Action* action_pntr=NULL);</a>
+<a name="207"><span class="lineNum">     207 </span>            :   static void writeToFile(OFile&amp;, const std::vector&lt;CoeffsVector*&gt;&amp;, const bool print_description=false);</a>
+<a name="208"><span class="lineNum">     208 </span>            : private:</a>
+<a name="209"><span class="lineNum">     209 </span>            :   void writeHeaderToFile(OFile&amp;) const;</a>
+<a name="210"><span class="lineNum">     210 </span>            :   static void writeDataToFile(OFile&amp;, const std::vector&lt;CoeffsVector*&gt;&amp;, const bool print_description=false);</a>
+<a name="211"><span class="lineNum">     211 </span>            : public:</a>
+<a name="212"><span class="lineNum">     212 </span>            :   size_t readFromFile(IFile&amp;, const bool ignore_missing_coeffs=false, const bool ignore_header=false);</a>
+<a name="213"><span class="lineNum">     213 </span>            :   size_t readFromFile(const std::string&amp;, const bool ignore_missing_coeffs=false, const bool ignore_header=false);</a>
+<a name="214"><span class="lineNum">     214 </span>            :   size_t readOneSetFromFile(IFile&amp; ifile, const bool ignore_header=false);</a>
+<a name="215"><span class="lineNum">     215 </span>            : private:</a>
+<a name="216"><span class="lineNum">     216 </span>            :   void readHeaderFromFile(IFile&amp;, const bool ignore_coeffs_info=false);</a>
+<a name="217"><span class="lineNum">     217 </span>            :   size_t readDataFromFile(IFile&amp;, const bool ignore_missing_coeffs=false);</a>
+<a name="218"><span class="lineNum">     218 </span>            : public:</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :   Communicator&amp; getCommunicator() const {return mycomm;}</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : };</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : inline</a>
+<a name="224"><span class="lineNum">     224 </span>            : double CoeffsVector::getValue(const size_t index) const {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">  142877485 :   return data[index];</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : inline</a>
+<a name="230"><span class="lineNum">     230 </span>            : double CoeffsVector::getValue(const std::vector&lt;unsigned int&gt;&amp; indices) const {</a>
+<a name="231"><span class="lineNum">     231 </span>            :   return data[getIndex(indices)];</a>
+<a name="232"><span class="lineNum">     232 </span>            : }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/FermiSwitchingFunction.cpp.func-sort-c.html b/coverage/ves/FermiSwitchingFunction.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ae817bdf45
--- /dev/null
+++ b/coverage/ves/FermiSwitchingFunction.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/FermiSwitchingFunction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - FermiSwitchingFunction.cpp<span style="font-size: 80%;"> (<a href="FermiSwitchingFunction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntryLo">49.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">44.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FermiSwitchingFunction.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#34">_ZN4PLMD3ves22FermiSwitchingFunction16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#116">_ZN4PLMD3ves22FermiSwitchingFunction3setEddd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#106">_ZN4PLMD3ves22FermiSwitchingFunctionC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#68">_ZNK4PLMD3ves22FermiSwitchingFunction11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#130">_ZNK4PLMD3ves22FermiSwitchingFunction6get_r0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#40">_ZN4PLMD3ves22FermiSwitchingFunction3setERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS7_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#96">_ZN4PLMD3ves22FermiSwitchingFunctionC2Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#135">_ZN4PLMD3ves22FermiSwitchingFunctionD2Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#82">_ZNK4PLMD3ves22FermiSwitchingFunction9calculateEdRd</a></td>
+              <td class="coverFnHi">3263</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/FermiSwitchingFunction.cpp.func.html b/coverage/ves/FermiSwitchingFunction.cpp.func.html
new file mode 100644
index 0000000000..53726c8313
--- /dev/null
+++ b/coverage/ves/FermiSwitchingFunction.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/FermiSwitchingFunction.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - FermiSwitchingFunction.cpp<span style="font-size: 80%;"> (<a href="FermiSwitchingFunction.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntryLo">49.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">44.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FermiSwitchingFunction.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#34">_ZN4PLMD3ves22FermiSwitchingFunction16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#40">_ZN4PLMD3ves22FermiSwitchingFunction3setERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS7_</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#116">_ZN4PLMD3ves22FermiSwitchingFunction3setEddd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#106">_ZN4PLMD3ves22FermiSwitchingFunctionC2ERKS1_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#96">_ZN4PLMD3ves22FermiSwitchingFunctionC2Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#135">_ZN4PLMD3ves22FermiSwitchingFunctionD2Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#68">_ZNK4PLMD3ves22FermiSwitchingFunction11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#130">_ZNK4PLMD3ves22FermiSwitchingFunction6get_r0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FermiSwitchingFunction.cpp.gcov.html#82">_ZNK4PLMD3ves22FermiSwitchingFunction9calculateEdRd</a></td>
+              <td class="coverFnHi">3263</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/FermiSwitchingFunction.cpp.gcov.html b/coverage/ves/FermiSwitchingFunction.cpp.gcov.html
new file mode 100644
index 0000000000..6eb84cad64
--- /dev/null
+++ b/coverage/ves/FermiSwitchingFunction.cpp.gcov.html
@@ -0,0 +1,218 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/FermiSwitchingFunction.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - FermiSwitchingFunction.cpp<span style="font-size: 80%;"> (source / <a href="FermiSwitchingFunction.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntry">67</td>
+            <td class="headerCovTableEntryLo">49.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">44.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;FermiSwitchingFunction.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Keywords.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;vector&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;limits&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineNoCov">          0 : void FermiSwitchingFunction::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineNoCov">          0 :   keys.add(&quot;compulsory&quot;,&quot;R_0&quot;,&quot;the value of R_0 in the switching function&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineNoCov">          0 :   keys.add(&quot;compulsory&quot;,&quot;FERMI_LAMBDA&quot;,&quot;the value of lambda in the Fermi-type switching function (only needed for TYPE=FERMI).&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :   keys.add(&quot;optional&quot;,&quot;FERMI_EXP_MAX&quot;,&quot;only needed for TYPE=FERMI&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          3 : void FermiSwitchingFunction::set(const std::string&amp; definition,std::string&amp; errormsg) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          3 :   std::vector&lt;std::string&gt; data=Tools::getWords(definition);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          3 :   if( data.size()&lt;1 ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :     errormsg=&quot;missing all input for switching function&quot;;</a>
+<a name="46"><span class="lineNum">      46 </span>            :     return;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   }</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          3 :   std::string name=data[0];</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   data.erase(data.begin());</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          3 :   if(name!=&quot;FERMI&quot;) {errormsg=&quot;only FERMI is supported&quot;;}</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          3 :   type=fermi;</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   //</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          3 :   bool found_r0=Tools::parse(data,&quot;R_0&quot;,r0_);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 :   if(!found_r0) {errormsg=&quot;R_0 is required&quot;;}</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   //</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          3 :   fermi_exp_max_=std::numeric_limits&lt;double&gt;::max();</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 :   Tools::parse(data,&quot;FERMI_EXP_MAX&quot;,fermi_exp_max_);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            :   //</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          3 :   bool found_lambda=Tools::parse(data,&quot;FERMI_LAMBDA&quot;,fermi_lambda_);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          3 :   if(!found_lambda) {errormsg=&quot;FERMI_LAMBDA is required for FERMI&quot;;}</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          3 :   if( !data.empty() ) {</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     errormsg=&quot;found the following rogue keywords in switching function input : &quot;;</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;data.size(); ++i) errormsg = errormsg + data[i] + &quot; &quot;;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          3 :   init=true;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          3 :   if(errormsg.size()&gt;0) {init=false;}</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          3 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineNoCov">          0 : std::string FermiSwitchingFunction::description() const {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :   std::ostringstream ostr;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :   ostr&lt;&lt;1./invr0_&lt;&lt;&quot;.  Using &quot;;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 :   if(type==fermi) {</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineNoCov">          0 :     ostr&lt;&lt; &quot;fermi switching function with parameter&quot;;</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :     ostr&lt;&lt; &quot; lambda=&quot;&lt;&lt;fermi_lambda_;</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span>            :   else {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Unknown switching function type&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   }</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :   return ostr.str();</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       3263 : double FermiSwitchingFunction::calculate(double distance, double&amp; dfunc) const {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">       3263 :   plumed_massert(init,&quot;you are trying to use an unset FermiSwitchingFunction&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">       3263 :   double rdist=fermi_lambda_*(distance-r0_);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">       3263 :   if(rdist &gt;= fermi_exp_max_) {rdist = fermi_exp_max_;}</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       3263 :   double result = 1.0/(1.0+exp(rdist));</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       3263 :   dfunc=-fermi_lambda_*exp(rdist)*result*result;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   // this is because calculate() sets dfunc to the derivative divided times the distance.</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // (I think this is misleading and I would like to modify it - GB)</a>
+<a name="92"><span class="lineNum">      92 </span>            :   // dfunc/=distance;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   //</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       3263 :   return result;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          3 : FermiSwitchingFunction::FermiSwitchingFunction():</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          3 :   init(false),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          3 :   type(fermi),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          3 :   r0_(0.0),</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          3 :   invr0_(0.0),</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          3 :   fermi_lambda_(1.0),</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          3 :   fermi_exp_max_(100.0)</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : {</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          3 : }</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 : FermiSwitchingFunction::FermiSwitchingFunction(const FermiSwitchingFunction&amp;sf):</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :   init(sf.init),</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   type(sf.type),</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :   r0_(sf.r0_),</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :   invr0_(sf.invr0_),</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   fermi_lambda_(sf.fermi_lambda_),</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :   fermi_exp_max_(sf.fermi_exp_max_)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : {</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 : void FermiSwitchingFunction::set(const double r0, const double fermi_lambda, const double fermi_exp_max) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   init=true;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :   type=fermi;</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :   r0_=r0;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :   fermi_lambda_=fermi_lambda;</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineNoCov">          0 :   if(fermi_exp_max&gt;0.0) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :     fermi_exp_max_=fermi_exp_max;</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            :   else {</a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     fermi_exp_max_=100.0;</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 : double FermiSwitchingFunction::get_r0() const {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :   return r0_;</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          3 : FermiSwitchingFunction::~FermiSwitchingFunction() {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : }</a>
+<a name="142"><span class="lineNum">     142 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridIntegrationWeights.cpp.func-sort-c.html b/coverage/ves/GridIntegrationWeights.cpp.func-sort-c.html
new file mode 100644
index 0000000000..301f096f40
--- /dev/null
+++ b/coverage/ves/GridIntegrationWeights.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridIntegrationWeights.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridIntegrationWeights.cpp<span style="font-size: 80%;"> (<a href="GridIntegrationWeights.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryMed">75.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridIntegrationWeights.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridIntegrationWeights.cpp.gcov.html#73">_ZN4PLMD3ves22GridIntegrationWeights44getOneDimensionalIntegrationPointsAndWeightsERSt6vectorIdSaIdEES5_jddRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridIntegrationWeights.cpp.gcov.html#31">_ZN4PLMD3ves22GridIntegrationWeights21getIntegrationWeightsEPKNS_4GridERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESC_</a></td>
+              <td class="coverFnHi">2036</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridIntegrationWeights.cpp.gcov.html#86">_ZN4PLMD3ves22GridIntegrationWeights35getOneDimensionalTrapezoidalWeightsEjdb</a></td>
+              <td class="coverFnHi">2563</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridIntegrationWeights.cpp.func.html b/coverage/ves/GridIntegrationWeights.cpp.func.html
new file mode 100644
index 0000000000..0f8ff976f2
--- /dev/null
+++ b/coverage/ves/GridIntegrationWeights.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridIntegrationWeights.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridIntegrationWeights.cpp<span style="font-size: 80%;"> (<a href="GridIntegrationWeights.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryMed">75.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridIntegrationWeights.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridIntegrationWeights.cpp.gcov.html#31">_ZN4PLMD3ves22GridIntegrationWeights21getIntegrationWeightsEPKNS_4GridERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESC_</a></td>
+              <td class="coverFnHi">2036</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridIntegrationWeights.cpp.gcov.html#86">_ZN4PLMD3ves22GridIntegrationWeights35getOneDimensionalTrapezoidalWeightsEjdb</a></td>
+              <td class="coverFnHi">2563</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridIntegrationWeights.cpp.gcov.html#73">_ZN4PLMD3ves22GridIntegrationWeights44getOneDimensionalIntegrationPointsAndWeightsERSt6vectorIdSaIdEES5_jddRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridIntegrationWeights.cpp.gcov.html b/coverage/ves/GridIntegrationWeights.cpp.gcov.html
new file mode 100644
index 0000000000..d89b17b2c1
--- /dev/null
+++ b/coverage/ves/GridIntegrationWeights.cpp.gcov.html
@@ -0,0 +1,184 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridIntegrationWeights.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridIntegrationWeights.cpp<span style="font-size: 80%;"> (source / <a href="GridIntegrationWeights.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">34</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryMed">75.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace ves {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">       2036 : std::vector&lt;double&gt; GridIntegrationWeights::getIntegrationWeights(const Grid* grid_pntr, const std::string&amp; fname_weights_grid, const std::string&amp; weights_type) {</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       2036 :   std::vector&lt;double&gt; dx = grid_pntr-&gt;getDx();</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       2036 :   std::vector&lt;bool&gt; isPeriodic = grid_pntr-&gt;getIsPeriodic();</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       2036 :   std::vector&lt;unsigned int&gt; nbins = grid_pntr-&gt;getNbin();</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; weights_perdim;</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       4580 :   for(unsigned int k=0; k&lt;grid_pntr-&gt;getDimension(); k++) {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :     std::vector&lt;double&gt; weights_tmp;</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       2544 :     if(weights_type==&quot;trapezoidal&quot;) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       2544 :       weights_tmp = getOneDimensionalTrapezoidalWeights(nbins[k],dx[k],isPeriodic[k]);</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :     }</a>
+<a name="43"><span class="lineNum">      43 </span>            :     else {</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;getIntegrationWeights: unknown weight type, the available type is trapezoidal&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span>            :     }</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       2544 :     weights_perdim.push_back(weights_tmp);</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   }</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       2036 :   std::vector&lt;double&gt; weights_vector(grid_pntr-&gt;getSize(),0.0);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">    5323391 :   for(Grid::index_t l=0; l&lt;grid_pntr-&gt;getSize(); l++) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">    5321355 :     std::vector&lt;unsigned int&gt; ind = grid_pntr-&gt;getIndices(l);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :     double value = 1.0;</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">   15690443 :     for(unsigned int k=0; k&lt;grid_pntr-&gt;getDimension(); k++) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">   10369088 :       value *= weights_perdim[k][ind[k]];</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :     }</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">    5321355 :     weights_vector[l] = value;</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       2036 :   if(fname_weights_grid.size()&gt;0) {</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineNoCov">          0 :     Grid weights_grid = Grid(*grid_pntr);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineNoCov">          0 :     for(Grid::index_t l=0; l&lt;weights_grid.getSize(); l++) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineNoCov">          0 :       weights_grid.setValue(l,weights_vector[l]);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     }</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :     OFile ofile;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :     ofile.enforceBackup();</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 :     ofile.open(fname_weights_grid);</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :     weights_grid.writeToFile(ofile);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :     ofile.close();</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   //</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       2036 :   return weights_vector;</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       2036 : }</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         19 : void GridIntegrationWeights::getOneDimensionalIntegrationPointsAndWeights(std::vector&lt;double&gt;&amp; points, std::vector&lt;double&gt;&amp; weights, const unsigned int nbins, const double min, const double max, const std::string&amp; weights_type) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         19 :   double dx = (max-min)/(static_cast&lt;double&gt;(nbins)-1.0);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         19 :   points.resize(nbins);</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      19038 :   for(unsigned int i=0; i&lt;nbins; i++) {points[i] = min + i*dx;}</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         19 :   if(weights_type==&quot;trapezoidal&quot;) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         19 :     weights = getOneDimensionalTrapezoidalWeights(nbins,dx,false);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span>            :   else {</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;getOneDimensionalIntegrationWeights: unknown weight type, the available type is trapezoidal&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span>            :   }</a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         19 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       2563 : std::vector&lt;double&gt; GridIntegrationWeights::getOneDimensionalTrapezoidalWeights(const unsigned int nbins, const double dx, const bool periodic) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       2563 :   std::vector&lt;double&gt; weights_1d(nbins);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">     444294 :   for(unsigned int i=1; i&lt;(nbins-1); i++) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     441731 :     weights_1d[i] = dx;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       2563 :   if(!periodic) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1202 :     weights_1d[0]= 0.5*dx;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1202 :     weights_1d[(nbins-1)]= 0.5*dx;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span>            :   else {</a>
+<a name="98"><span class="lineNum">      98 </span>            :     // as for periodic arguments the first point should be counted twice as the</a>
+<a name="99"><span class="lineNum">      99 </span>            :     // grid doesn't include its periodic copy</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       1361 :     weights_1d[0]= dx;</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1361 :     weights_1d[(nbins-1)]= dx;</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">       2563 :   return weights_1d;</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : }</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : }</a>
+<a name="108"><span class="lineNum">     108 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridLinearInterpolation.cpp.func-sort-c.html b/coverage/ves/GridLinearInterpolation.cpp.func-sort-c.html
new file mode 100644
index 0000000000..240680fb42
--- /dev/null
+++ b/coverage/ves/GridLinearInterpolation.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridLinearInterpolation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridLinearInterpolation.cpp<span style="font-size: 80%;"> (<a href="GridLinearInterpolation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryLo">55.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridLinearInterpolation.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#208">_ZN4PLMD3ves23GridLinearInterpolation17getAdjacentPointsEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#190">_ZN4PLMD3ves23GridLinearInterpolation18getAdjacentIndicesEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#96">_ZN4PLMD3ves23GridLinearInterpolation38getGridValueWithLinearInterpolation_NDEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#141">_ZN4PLMD3ves23GridLinearInterpolation52getGridValueAndDerivativesWithLinearInterpolation_NDEPNS_8GridBaseERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#32">_ZN4PLMD3ves23GridLinearInterpolation38getGridValueWithLinearInterpolation_1DEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1869</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#52">_ZN4PLMD3ves23GridLinearInterpolation38getGridValueWithLinearInterpolation_2DEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">47164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#166">_ZN4PLMD3ves23GridLinearInterpolation35getGridValueWithLinearInterpolationEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">49033</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#180">_ZN4PLMD3ves23GridLinearInterpolation49getGridValueAndDerivativesWithLinearInterpolationEPNS_8GridBaseERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnHi">1263854</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#117">_ZN4PLMD3ves23GridLinearInterpolation52getGridValueAndDerivativesWithLinearInterpolation_1DEPNS_8GridBaseERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnHi">1263854</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridLinearInterpolation.cpp.func.html b/coverage/ves/GridLinearInterpolation.cpp.func.html
new file mode 100644
index 0000000000..33da162dd4
--- /dev/null
+++ b/coverage/ves/GridLinearInterpolation.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridLinearInterpolation.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridLinearInterpolation.cpp<span style="font-size: 80%;"> (<a href="GridLinearInterpolation.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryLo">55.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridLinearInterpolation.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#208">_ZN4PLMD3ves23GridLinearInterpolation17getAdjacentPointsEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#190">_ZN4PLMD3ves23GridLinearInterpolation18getAdjacentIndicesEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#166">_ZN4PLMD3ves23GridLinearInterpolation35getGridValueWithLinearInterpolationEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">49033</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#32">_ZN4PLMD3ves23GridLinearInterpolation38getGridValueWithLinearInterpolation_1DEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1869</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#52">_ZN4PLMD3ves23GridLinearInterpolation38getGridValueWithLinearInterpolation_2DEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">47164</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#96">_ZN4PLMD3ves23GridLinearInterpolation38getGridValueWithLinearInterpolation_NDEPNS_8GridBaseERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#180">_ZN4PLMD3ves23GridLinearInterpolation49getGridValueAndDerivativesWithLinearInterpolationEPNS_8GridBaseERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnHi">1263854</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#117">_ZN4PLMD3ves23GridLinearInterpolation52getGridValueAndDerivativesWithLinearInterpolation_1DEPNS_8GridBaseERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnHi">1263854</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.cpp.gcov.html#141">_ZN4PLMD3ves23GridLinearInterpolation52getGridValueAndDerivativesWithLinearInterpolation_NDEPNS_8GridBaseERKSt6vectorIdSaIdEERS6_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridLinearInterpolation.cpp.gcov.html b/coverage/ves/GridLinearInterpolation.cpp.gcov.html
new file mode 100644
index 0000000000..a6512141ce
--- /dev/null
+++ b/coverage/ves/GridLinearInterpolation.cpp.gcov.html
@@ -0,0 +1,311 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridLinearInterpolation.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridLinearInterpolation.cpp<span style="font-size: 80%;"> (source / <a href="GridLinearInterpolation.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">120</td>
+            <td class="headerCovTableEntryLo">55.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">55.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;GridLinearInterpolation.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace ves {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">       1869 : double GridLinearInterpolation::getGridValueWithLinearInterpolation_1D(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg) {</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       1869 :   plumed_massert(grid_pntr-&gt;getDimension()==1,&quot;The grid is of the wrong dimension, should be one-dimensional&quot;);</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       1869 :   plumed_massert(arg.size()==1,&quot;input value is of the wrong size&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       1869 :   double x = arg[0];</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">       1869 :   double grid_dx = grid_pntr-&gt;getDx()[0];</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       1869 :   double grid_min; Tools::convert( grid_pntr-&gt;getMin()[0], grid_min);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       1869 :   std::vector&lt;unsigned int&gt; i0(1); i0[0] = unsigned( std::floor( (x-grid_min)/grid_dx ) );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       1869 :   std::vector&lt;unsigned int&gt; i1(1); i1[0] = unsigned( std::ceil(  (x-grid_min)/grid_dx ) );</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   //</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1869 :   double x0 = grid_pntr-&gt;getPoint(i0)[0];</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1869 :   double x1 = grid_pntr-&gt;getPoint(i1)[0];</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1869 :   double y0 = grid_pntr-&gt;getValue(i0);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1869 :   double y1 = grid_pntr-&gt;getValue(i1);</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   //</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       1869 :   return linearInterpolation(x,x0,x1,y0,y1);</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      47164 : double GridLinearInterpolation::getGridValueWithLinearInterpolation_2D(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">      47164 :   plumed_massert(grid_pntr-&gt;getDimension()==2,&quot;The grid is of the wrong dimension, should be two-dimensional&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">      47164 :   plumed_massert(arg.size()==2,&quot;input value is of the wrong size&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      47164 :   std::vector&lt;double&gt; grid_delta = grid_pntr-&gt;getDx();</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">      47164 :   std::vector&lt;double&gt; grid_min(2);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      47164 :   Tools::convert( grid_pntr-&gt;getMin()[0], grid_min[0]);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      47164 :   Tools::convert( grid_pntr-&gt;getMin()[1], grid_min[1]);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      47164 :   std::vector&lt;unsigned int&gt; i00(2);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      47164 :   std::vector&lt;unsigned int&gt; i01(2);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">      47164 :   std::vector&lt;unsigned int&gt; i10(2);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">      47164 :   std::vector&lt;unsigned int&gt; i11(2);</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      47164 :   i00[0] = i01[0] = unsigned( std::floor( (arg[0]-grid_min[0])/grid_delta[0] ) );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">      47164 :   i10[0] = i11[0] = unsigned( std::ceil(  (arg[0]-grid_min[0])/grid_delta[0] ) );</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      47164 :   i00[1] = i10[1] = unsigned( std::floor( (arg[1]-grid_min[1])/grid_delta[1] ) );</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      47164 :   i01[1] = i11[1] = unsigned( std::ceil(  (arg[1]-grid_min[1])/grid_delta[1] ) );</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            :   // https://en.wikipedia.org/wiki/Bilinear_interpolation</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      47164 :   double x = arg[0];</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">      47164 :   double y = arg[1];</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">      47164 :   double x0 = grid_pntr-&gt;getPoint(i00)[0];</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">      47164 :   double x1 = grid_pntr-&gt;getPoint(i10)[0];</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      47164 :   double y0 = grid_pntr-&gt;getPoint(i00)[1];</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      47164 :   double y1 = grid_pntr-&gt;getPoint(i11)[1];</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">      47164 :   double f00 = grid_pntr-&gt;getValue(i00);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      47164 :   double f01 = grid_pntr-&gt;getValue(i01);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      47164 :   double f10 = grid_pntr-&gt;getValue(i10);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">      47164 :   double f11 = grid_pntr-&gt;getValue(i11);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            :   // linear interpolation in x-direction</a>
+<a name="89"><span class="lineNum">      89 </span>            :   double fx0 = linearInterpolation(x,x0,x1,f00,f10);</a>
+<a name="90"><span class="lineNum">      90 </span>            :   double fx1 = linearInterpolation(x,x0,x1,f01,f11);</a>
+<a name="91"><span class="lineNum">      91 </span>            :   // linear interpolation in y-direction</a>
+<a name="92"><span class="lineNum">      92 </span>            :   double fxy = linearInterpolation(y,y0,y1,fx0,fx1);</a>
+<a name="93"><span class="lineNum">      93 </span>            :   //</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      47164 :   return fxy;</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineNoCov">          0 : double GridLinearInterpolation::getGridValueWithLinearInterpolation_ND(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :   unsigned int dimension = grid_pntr-&gt;getDimension();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   plumed_massert(dimension==arg.size(),&quot;The grid dimensions do not match the the given arguments.&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   // get points first</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;unsigned&gt;&gt; point_indices = GridLinearInterpolation::getAdjacentPoints(grid_pntr, arg);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   unsigned npoints = point_indices.size();</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   // reserve space for the point vectors and values</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;double&gt;&gt; points(npoints, std::vector&lt;double&gt;(dimension));</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; values(npoints);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            :   // fill point and value vectors for all the grid points</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   for (unsigned i = 0; i &lt; npoints; ++i) {</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineNoCov">          0 :     points[i] = grid_pntr-&gt;getPoint(point_indices[i]);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineNoCov">          0 :     values[i] = grid_pntr-&gt;getValue(point_indices[i]);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :   return multiLinearInterpolation(arg, points, values, dimension);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">    1263854 : double GridLinearInterpolation::getGridValueAndDerivativesWithLinearInterpolation_1D(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">    1263854 :   plumed_massert(grid_pntr-&gt;getDimension()==1,&quot;The grid is of the wrong dimension, should be one-dimensional&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">    1263854 :   plumed_massert(arg.size()==1,&quot;input value is of the wrong size&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">    1263854 :   double x = arg[0];</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">    1263854 :   double grid_dx = grid_pntr-&gt;getDx()[0];</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">    1263854 :   double grid_min; Tools::convert( grid_pntr-&gt;getMin()[0], grid_min);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">    1263854 :   double xtoindex = (x-grid_min)/grid_dx;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">    1263854 :   std::vector&lt;unsigned int&gt; i0(1); i0[0] = unsigned(std::floor(xtoindex));</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">    1263854 :   std::vector&lt;unsigned int&gt; i1(1); i1[0] = unsigned(std::ceil(xtoindex));</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   //</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">    1263854 :   std::vector&lt;double&gt; d0 (1), d1 (1);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">    1263854 :   double x0 = grid_pntr-&gt;getPoint(i0)[0];</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">    1263854 :   double x1 = grid_pntr-&gt;getPoint(i1)[0];</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">    1263854 :   double y0 = grid_pntr-&gt;getValueAndDerivatives(i0, d0);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">    1263854 :   double y1 = grid_pntr-&gt;getValueAndDerivatives(i1, d1);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   //</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">    1263854 :   der.resize(1);</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">    2500429 :   der[0] = linearInterpolation(arg[0],x0,x1,d0[0],d1[0]);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">    2527708 :   return linearInterpolation(arg[0],x0,x1,y0,y1);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 : double GridLinearInterpolation::getGridValueAndDerivativesWithLinearInterpolation_ND(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineNoCov">          0 :   unsigned int dimension = grid_pntr-&gt;getDimension();</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :   plumed_massert(dimension==arg.size(),&quot;The grid dimensions do not match the given arguments&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   // get points first</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;unsigned&gt;&gt; point_indices = getAdjacentPoints(grid_pntr, arg);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :   unsigned npoints = point_indices.size();</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   // allocate space for the point vectors and values</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;double&gt;&gt; points(npoints, std::vector&lt;double&gt;(dimension));</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; values(npoints);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;double&gt;&gt; derivs(npoints, std::vector&lt;double&gt;(dimension));</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            :   // fill point, value and deriv vectors for all the grid points</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineNoCov">          0 :   for (unsigned i = 0; i &lt; npoints; ++i) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     points[i] = grid_pntr-&gt;getPoint(point_indices[i]);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineNoCov">          0 :     values[i] = grid_pntr-&gt;getValueAndDerivatives(point_indices[i], derivs[i]);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :   for (size_t i = 0; i &lt; derivs.size(); ++i) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineNoCov">          0 :     der[i] = multiLinearInterpolation(arg, points, derivs[i], dimension);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineNoCov">          0 :   return multiLinearInterpolation(arg, points, values, dimension);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">      49033 : double GridLinearInterpolation::getGridValueWithLinearInterpolation(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      49033 :   unsigned int dim = grid_pntr-&gt;getDimension();</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">      49033 :   if(dim==1) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1869 :     return getGridValueWithLinearInterpolation_1D(grid_pntr,arg);</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">      47164 :   else if(dim==2) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      47164 :     return getGridValueWithLinearInterpolation_2D(grid_pntr,arg);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   }</a>
+<a name="176"><span class="lineNum">     176 </span>            :   else {</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :     return getGridValueWithLinearInterpolation_ND(grid_pntr,arg);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   }</a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    1263854 : double GridLinearInterpolation::getGridValueAndDerivativesWithLinearInterpolation(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; der) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">    1263854 :   unsigned int dim = grid_pntr-&gt;getDimension();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">    1263854 :   if(dim==1) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">    1263854 :     return getGridValueAndDerivativesWithLinearInterpolation_1D(grid_pntr,arg,der);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :   return getGridValueAndDerivativesWithLinearInterpolation_ND(grid_pntr,arg,der);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : // returns the adjacent Grid indices of all double arg as vector of vectors</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 : std::vector&lt;std::vector&lt;unsigned&gt;&gt; GridLinearInterpolation::getAdjacentIndices(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :   unsigned int dimension = grid_pntr-&gt;getDimension();</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;unsigned&gt;&gt; indices(dimension, std::vector&lt;unsigned&gt;(2));</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   for (unsigned i=0; i&lt;dimension; ++i) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :     std::vector&lt;unsigned&gt; temp_indices(2);</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :     //</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineNoCov">          0 :     double grid_dx = grid_pntr-&gt;getDx()[i];</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 :     double grid_min; Tools::convert( grid_pntr-&gt;getMin()[i], grid_min);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :     double xtoindex = (arg[i]-grid_min)/grid_dx;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :     temp_indices[0] = static_cast&lt;unsigned&gt;(std::floor(xtoindex));</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     temp_indices[1] = static_cast&lt;unsigned&gt;(std::ceil(xtoindex));</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :     indices[i] = temp_indices;</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :   }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :   return indices;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 : std::vector&lt;std::vector&lt;unsigned&gt;&gt; GridLinearInterpolation::getAdjacentPoints(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg) {</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   // upper and lower grid indices as vectors for each dimension</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;unsigned&gt;&gt; grid_indices = getAdjacentIndices(grid_pntr, arg);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 :   unsigned npoints = 1U &lt;&lt; grid_pntr-&gt;getDimension();</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            :   // generate combination of grid indices if multidimensional to match the actual points</a>
+<a name="216"><span class="lineNum">     216 </span>            :   // the retrieved combinations will be in column-major order</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   std::vector&lt;std::vector&lt;unsigned&gt;&gt; point_indices(npoints);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :   for (unsigned i = 0; i &lt; npoints; ++i) {</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :     unsigned temp = i;</a>
+<a name="220"><span class="lineNum">     220 </span>            :     std::vector&lt;unsigned&gt; current_indices;</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 :     for (const auto&amp; vec: grid_indices) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineNoCov">          0 :       unsigned j = temp % 2;</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineNoCov">          0 :       current_indices.push_back(vec[j]);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :       temp /= 2;</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     point_indices[i] = current_indices;</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineNoCov">          0 :   return point_indices;</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : }</a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridLinearInterpolation.h.func-sort-c.html b/coverage/ves/GridLinearInterpolation.h.func-sort-c.html
new file mode 100644
index 0000000000..992c37700d
--- /dev/null
+++ b/coverage/ves/GridLinearInterpolation.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridLinearInterpolation.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridLinearInterpolation.h<span style="font-size: 80%;"> (<a href="GridLinearInterpolation.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridLinearInterpolation.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.h.gcov.html#64">_ZN4PLMD3ves23GridLinearInterpolation24multiLinearInterpolationERKSt6vectorIdSaIdEERKS2_IS4_SaIS4_EERS4_d</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridLinearInterpolation.h.func.html b/coverage/ves/GridLinearInterpolation.h.func.html
new file mode 100644
index 0000000000..36e17bfa32
--- /dev/null
+++ b/coverage/ves/GridLinearInterpolation.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridLinearInterpolation.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridLinearInterpolation.h<span style="font-size: 80%;"> (<a href="GridLinearInterpolation.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridLinearInterpolation.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridLinearInterpolation.h.gcov.html#64">_ZN4PLMD3ves23GridLinearInterpolation24multiLinearInterpolationERKSt6vectorIdSaIdEERKS2_IS4_SaIS4_EERS4_d</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridLinearInterpolation.h.gcov.html b/coverage/ves/GridLinearInterpolation.h.gcov.html
new file mode 100644
index 0000000000..8eb46d822e
--- /dev/null
+++ b/coverage/ves/GridLinearInterpolation.h.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridLinearInterpolation.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridLinearInterpolation.h<span style="font-size: 80%;"> (source / <a href="GridLinearInterpolation.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryLo">22.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_GridLinearInterpolation_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_GridLinearInterpolation_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class GridBase;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace ves {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class GridLinearInterpolation {</a>
+<a name="37"><span class="lineNum">      37 </span>            : private:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   static double getGridValueWithLinearInterpolation_1D(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg);</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static double getGridValueWithLinearInterpolation_2D(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg);</a>
+<a name="40"><span class="lineNum">      40 </span>            :   static double getGridValueWithLinearInterpolation_ND(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg);</a>
+<a name="41"><span class="lineNum">      41 </span>            :   static double getGridValueAndDerivativesWithLinearInterpolation_1D(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; der);</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static double getGridValueAndDerivativesWithLinearInterpolation_ND(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; der);</a>
+<a name="43"><span class="lineNum">      43 </span>            :   static double linearInterpolation(const double x, const double x0, const double x1, const double y0, const double y1);</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static double multiLinearInterpolation(const std::vector&lt;double&gt;&amp; x, const std::vector&lt;std::vector&lt;double&gt;&gt;&amp; points, std::vector&lt;double&gt;&amp; values, const double dim);</a>
+<a name="45"><span class="lineNum">      45 </span>            : public:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static double getGridValueWithLinearInterpolation(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg);</a>
+<a name="47"><span class="lineNum">      47 </span>            :   static double getGridValueAndDerivativesWithLinearInterpolation(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg, std::vector&lt;double&gt;&amp; der);</a>
+<a name="48"><span class="lineNum">      48 </span>            :   static std::vector&lt;std::vector&lt;unsigned&gt;&gt; getAdjacentIndices(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg);</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static std::vector&lt;std::vector&lt;unsigned&gt;&gt; getAdjacentPoints(GridBase* grid_pntr, const std::vector&lt;double&gt;&amp; arg);</a>
+<a name="50"><span class="lineNum">      50 </span>            : };</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : inline</a>
+<a name="54"><span class="lineNum">      54 </span>            : double GridLinearInterpolation::linearInterpolation(const double x, const double x0, const double x1, const double y0, const double y1) {</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // https://en.wikipedia.org/wiki/Linear_interpolation</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">    2624038 :   if(x1!=x0) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">    2586242 :     return y0 + (x-x0) * ((y1-y0)/(x1-x0));</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   }</a>
+<a name="59"><span class="lineNum">      59 </span>            :   else {</a>
+<a name="60"><span class="lineNum">      60 </span>            :     return y0;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : inline</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineNoCov">          0 : double GridLinearInterpolation::multiLinearInterpolation(const std::vector&lt;double&gt;&amp; x, const std::vector&lt;std::vector&lt;double&gt;&gt;&amp; points, std::vector&lt;double&gt;&amp; values, const double dim) {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :   for (unsigned direction = 0; direction &lt; dim; ++direction) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineNoCov">          0 :     unsigned shift = 1&lt;&lt;(direction+1); // shift by 2, then 4, then 8 etc</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :     for (unsigned i = 0; i &lt; points.size(); i += shift) {</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :       // replace every second value with interpolated ones</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineNoCov">          0 :       values[i] = linearInterpolation(</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineNoCov">          0 :                     x[direction], points[i][direction], points[i+shift/2][direction], values[i], values[i+shift/2]);</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :     }</a>
+<a name="74"><span class="lineNum">      74 </span>            :   }</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :   return values[0];</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridProjWeights.h.func-sort-c.html b/coverage/ves/GridProjWeights.h.func-sort-c.html
new file mode 100644
index 0000000000..57797c8ce7
--- /dev/null
+++ b/coverage/ves/GridProjWeights.h.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridProjWeights.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridProjWeights.h<span style="font-size: 80%;"> (<a href="GridProjWeights.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="GridProjWeights.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#34">_ZN4PLMD3ves14MarginalWeight16projectOuterLoopERd</a></td>
+              <td class="coverFnHi">2822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#42">_ZN4PLMD3ves9FesWeight16projectOuterLoopERd</a></td>
+              <td class="coverFnHi">5834</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#33">_ZN4PLMD3ves14MarginalWeight16projectInnerLoopERdS2_</a></td>
+              <td class="coverFnHi">284402</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#41">_ZN4PLMD3ves9FesWeight16projectInnerLoopERdS2_</a></td>
+              <td class="coverFnHi">703214</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridProjWeights.h.func.html b/coverage/ves/GridProjWeights.h.func.html
new file mode 100644
index 0000000000..469c67c694
--- /dev/null
+++ b/coverage/ves/GridProjWeights.h.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridProjWeights.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridProjWeights.h<span style="font-size: 80%;"> (<a href="GridProjWeights.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="GridProjWeights.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#33">_ZN4PLMD3ves14MarginalWeight16projectInnerLoopERdS2_</a></td>
+              <td class="coverFnHi">284402</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#34">_ZN4PLMD3ves14MarginalWeight16projectOuterLoopERd</a></td>
+              <td class="coverFnHi">2822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#41">_ZN4PLMD3ves9FesWeight16projectInnerLoopERdS2_</a></td>
+              <td class="coverFnHi">703214</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="GridProjWeights.h.gcov.html#42">_ZN4PLMD3ves9FesWeight16projectOuterLoopERd</a></td>
+              <td class="coverFnHi">5834</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/GridProjWeights.h.gcov.html b/coverage/ves/GridProjWeights.h.gcov.html
new file mode 100644
index 0000000000..81f6f5606e
--- /dev/null
+++ b/coverage/ves/GridProjWeights.h.gcov.html
@@ -0,0 +1,126 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/GridProjWeights.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - GridProjWeights.h<span style="font-size: 80%;"> (source / <a href="GridProjWeights.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_GridProjWeights_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_GridProjWeights_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class MarginalWeight:public WeightBase {</a>
+<a name="33"><span class="lineNum">      33 </span>            : public:</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         28 :   explicit MarginalWeight() {}</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">     284402 :   double projectInnerLoop(double &amp;input, double &amp;v) {return  input+v;}</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       2822 :   double projectOuterLoop(double &amp;v) {return v;}</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : };</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class FesWeight:public WeightBase {</a>
+<a name="40"><span class="lineNum">      40 </span>            : public:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   double beta,invbeta;</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         50 :   explicit FesWeight(double v) {beta=v; invbeta=1./beta;}</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">     703214 :   double projectInnerLoop(double &amp;input, double &amp;v) {return  input+exp(-beta*v);}</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       5834 :   double projectOuterLoop(double &amp;v) {return -invbeta*std::log(v);}</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/LinearBasisSetExpansion.cpp.func-sort-c.html b/coverage/ves/LinearBasisSetExpansion.cpp.func-sort-c.html
new file mode 100644
index 0000000000..880bdf8468
--- /dev/null
+++ b/coverage/ves/LinearBasisSetExpansion.cpp.func-sort-c.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/LinearBasisSetExpansion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - LinearBasisSetExpansion.cpp<span style="font-size: 80%;"> (<a href="LinearBasisSetExpansion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">313</td>
+            <td class="headerCovTableEntry">353</td>
+            <td class="headerCovTableEntryMed">88.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
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+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
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+    <tr>
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+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.cpp.gcov.html#122">_ZN4PLMD3ves23LinearBasisSetExpansion10linkActionEPNS_6ActionE</a></td>
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+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
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+</html>
diff --git a/coverage/ves/LinearBasisSetExpansion.cpp.func.html b/coverage/ves/LinearBasisSetExpansion.cpp.func.html
new file mode 100644
index 0000000000..95fc681bb4
--- /dev/null
+++ b/coverage/ves/LinearBasisSetExpansion.cpp.func.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/LinearBasisSetExpansion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - LinearBasisSetExpansion.cpp<span style="font-size: 80%;"> (<a href="LinearBasisSetExpansion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">313</td>
+            <td class="headerCovTableEntry">353</td>
+            <td class="headerCovTableEntryMed">88.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
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+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LinearBasisSetExpansion.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+              <td class="coverFnHi">130</td>
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+              <td class="coverFnHi">169</td>
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+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.cpp.gcov.html#286">_ZNK4PLMD3ves23LinearBasisSetExpansion19writeBiasGridToFileERNS_5OFileEb</a></td>
+              <td class="coverFnHi">212</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.cpp.gcov.html#307">_ZNK4PLMD3ves23LinearBasisSetExpansion22writeFesProjGridToFileERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERNS_5OFileEb</a></td>
+              <td class="coverFnHi">36</td>
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+              <td class="coverFnHi">82</td>
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+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.cpp.gcov.html#324">_ZNK4PLMD3ves23LinearBasisSetExpansion28writeLogTargetDistGridToFileERNS_5OFileEb</a></td>
+              <td class="coverFnHi">82</td>
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+              <td class="coverFnHi">20</td>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFn"><a href="LinearBasisSetExpansion.cpp.gcov.html#293">_ZNK4PLMD3ves23LinearBasisSetExpansion32writeBiasWithoutCutoffGridToFileERNS_5OFileEb</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.cpp.gcov.html#106">_ZNK4PLMD3ves23LinearBasisSetExpansion34isStaticTargetDistFileOutputActiveEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/LinearBasisSetExpansion.cpp.gcov.html b/coverage/ves/LinearBasisSetExpansion.cpp.gcov.html
new file mode 100644
index 0000000000..2642bed164
--- /dev/null
+++ b/coverage/ves/LinearBasisSetExpansion.cpp.gcov.html
@@ -0,0 +1,693 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/LinearBasisSetExpansion.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - LinearBasisSetExpansion.cpp<span style="font-size: 80%;"> (source / <a href="LinearBasisSetExpansion.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">313</td>
+            <td class="headerCovTableEntry">353</td>
+            <td class="headerCovTableEntryMed">88.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;LinearBasisSetExpansion.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Keywords.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;GridProjWeights.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &lt;limits&gt;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace PLMD {</a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace ves {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 : void LinearBasisSetExpansion::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        130 : LinearBasisSetExpansion::LinearBasisSetExpansion(</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   const std::string&amp; label,</a>
+<a name="49"><span class="lineNum">      49 </span>            :   const double beta_in,</a>
+<a name="50"><span class="lineNum">      50 </span>            :   Communicator&amp; cc,</a>
+<a name="51"><span class="lineNum">      51 </span>            :   const std::vector&lt;Value*&gt;&amp; args_pntrs_in,</a>
+<a name="52"><span class="lineNum">      52 </span>            :   std::vector&lt;BasisFunctions*&gt;&amp; basisf_pntrs_in,</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        130 :   CoeffsVector* bias_coeffs_pntr_in):</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        130 :   label_(label),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        130 :   action_pntr_(NULL),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        130 :   vesbias_pntr_(NULL),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        130 :   mycomm_(cc),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        130 :   serial_(false),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        130 :   beta_(beta_in),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        130 :   kbt_(1.0/beta_),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        130 :   args_pntrs_(args_pntrs_in),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        130 :   nargs_(args_pntrs_.size()),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        130 :   basisf_pntrs_(basisf_pntrs_in),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        130 :   nbasisf_(basisf_pntrs_.size()),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        130 :   bias_coeffs_pntr_(bias_coeffs_pntr_in),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        130 :   ncoeffs_(0),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        130 :   grid_min_(nargs_),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        130 :   grid_max_(nargs_),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        130 :   grid_bins_(nargs_,100),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        130 :   targetdist_grid_label_(&quot;targetdist&quot;),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        130 :   step_of_last_biasgrid_update(-1000),</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        130 :   step_of_last_biaswithoutcutoffgrid_update(-1000),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        130 :   step_of_last_fesgrid_update(-1000),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        130 :   log_targetdist_grid_pntr_(NULL),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        130 :   targetdist_grid_pntr_(NULL),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        260 :   targetdist_pntr_(NULL)</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : {</a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        130 :   plumed_massert(args_pntrs_.size()==basisf_pntrs_.size(),&quot;number of arguments and basis functions do not match&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        295 :   for(unsigned int k=0; k&lt;nargs_; k++) {nbasisf_[k]=basisf_pntrs_[k]-&gt;getNumberOfBasisFunctions();}</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   //</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">        130 :   if(bias_coeffs_pntr_==NULL) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineNoCov">          0 :     bias_coeffs_pntr_ = new CoeffsVector(label_+&quot;.coeffs&quot;,args_pntrs_,basisf_pntrs_,mycomm_,true);</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :   }</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        130 :   plumed_massert(bias_coeffs_pntr_-&gt;numberOfDimensions()==basisf_pntrs_.size(),&quot;dimension of coeffs does not match with number of basis functions &quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   //</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        130 :   ncoeffs_ = bias_coeffs_pntr_-&gt;numberOfCoeffs();</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        260 :   targetdist_averages_pntr_ = Tools::make_unique&lt;CoeffsVector&gt;(*bias_coeffs_pntr_);</span></a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        130 :   std::string targetdist_averages_label = bias_coeffs_pntr_-&gt;getLabel();</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">        130 :   if(targetdist_averages_label.find(&quot;coeffs&quot;)!=std::string::npos) {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        260 :     targetdist_averages_label.replace(targetdist_averages_label.find(&quot;coeffs&quot;), std::string(&quot;coeffs&quot;).length(), &quot;targetdist_averages&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span>            :   else {</a>
+<a name="94"><span class="lineNum">      94 </span>            :     targetdist_averages_label += &quot;_targetdist_averages&quot;;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        130 :   targetdist_averages_pntr_-&gt;setLabels(targetdist_averages_label);</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   //</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        295 :   for(unsigned int k=0; k&lt;nargs_; k++) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        330 :     grid_min_[k] = basisf_pntrs_[k]-&gt;intervalMinStr();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        330 :     grid_max_[k] = basisf_pntrs_[k]-&gt;intervalMaxStr();</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        130 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        130 : LinearBasisSetExpansion::~LinearBasisSetExpansion() {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        390 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 : bool LinearBasisSetExpansion::isStaticTargetDistFileOutputActive() const {</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   bool output_static_targetdist_files=true;</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :   if(vesbias_pntr_!=NULL) {</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :     output_static_targetdist_files = vesbias_pntr_-&gt;isStaticTargetDistFileOutputActive();</a>
+<a name="112"><span class="lineNum">     112 </span>            :   }</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :   return output_static_targetdist_files;</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         90 : void LinearBasisSetExpansion::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         90 :   vesbias_pntr_ = vesbias_pntr_in;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         90 :   action_pntr_ = static_cast&lt;Action*&gt;(vesbias_pntr_in);</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         90 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 : void LinearBasisSetExpansion::linkAction(Action* action_pntr_in) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   action_pntr_ = action_pntr_in;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        129 : void LinearBasisSetExpansion::setGridBins(const std::vector&lt;unsigned int&gt;&amp; grid_bins_in) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        129 :   plumed_massert(grid_bins_in.size()==nargs_,&quot;the number of grid bins given doesn't match the number of arguments&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        129 :   plumed_massert(!bias_grid_pntr_,&quot;setGridBins should be used before setting up the grids, otherwise it doesn't work&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        129 :   plumed_massert(!fes_grid_pntr_,&quot;setGridBins should be used before setting up the grids, otherwise it doesn't work&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        129 :   grid_bins_=grid_bins_in;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        129 : }</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         39 : void LinearBasisSetExpansion::setGridBins(const unsigned int nbins) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         39 :   std::vector&lt;unsigned int&gt; grid_bins_in(nargs_,nbins);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         39 :   setGridBins(grid_bins_in);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         39 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        220 : std::unique_ptr&lt;Grid&gt; LinearBasisSetExpansion::setupGeneralGrid(const std::string&amp; label_suffix, const bool usederiv) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        220 :   bool use_spline = false;</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">        440 :   auto grid_pntr = Tools::make_unique&lt;Grid&gt;(label_+&quot;.&quot;+label_suffix,args_pntrs_,grid_min_,grid_max_,grid_bins_,use_spline,usederiv);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        220 :   return grid_pntr;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        166 : void LinearBasisSetExpansion::setupBiasGrid(const bool usederiv) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        166 :   if(bias_grid_pntr_) {return;}</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        258 :   bias_grid_pntr_ = setupGeneralGrid(&quot;bias&quot;,usederiv);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        129 :   if(biasCutoffActive()) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          6 :     bias_withoutcutoff_grid_pntr_ = setupGeneralGrid(&quot;bias_withoutcutoff&quot;,usederiv);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        120 : void LinearBasisSetExpansion::setupFesGrid() {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        120 :   if(fes_grid_pntr_) {return;}</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         88 :   if(!bias_grid_pntr_) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         37 :     setupBiasGrid(true);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        176 :   fes_grid_pntr_ = setupGeneralGrid(&quot;fes&quot;,false);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : }</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          8 : void LinearBasisSetExpansion::setupFesProjGrid() {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :   if(!fes_grid_pntr_) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          1 :     setupFesGrid();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          8 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        829 : void LinearBasisSetExpansion::updateBiasGrid() {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        829 :   plumed_massert(bias_grid_pntr_,&quot;the bias grid is not defined&quot;);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        829 :   if(action_pntr_!=NULL &amp;&amp;  getStepOfLastBiasGridUpdate()==action_pntr_-&gt;getStep()) {</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     return;</a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">    1982290 :   for(Grid::index_t l=0; l&lt;bias_grid_pntr_-&gt;getSize(); l++) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">    1981698 :     std::vector&lt;double&gt; forces(nargs_);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">    1981698 :     std::vector&lt;double&gt; args = bias_grid_pntr_-&gt;getPoint(l);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">    1981698 :     bool all_inside=true;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">    1981698 :     double bias=getBiasAndForces(args,all_inside,forces);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     //</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">    1981698 :     if(biasCutoffActive()) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        600 :       vesbias_pntr_-&gt;applyBiasCutoff(bias,forces);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :     }</a>
+<a name="189"><span class="lineNum">     189 </span>            :     //</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">    1981698 :     if(bias_grid_pntr_-&gt;hasDerivatives()) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">    1473981 :       bias_grid_pntr_-&gt;setValueAndDerivatives(l,bias,forces);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     }</a>
+<a name="193"><span class="lineNum">     193 </span>            :     else {</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     507717 :       bias_grid_pntr_-&gt;setValue(l,bias);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     }</a>
+<a name="196"><span class="lineNum">     196 </span>            :     //</a>
+<a name="197"><span class="lineNum">     197 </span>            :   }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        592 :   if(vesbias_pntr_!=NULL) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        475 :     vesbias_pntr_-&gt;setCurrentBiasMaxValue(bias_grid_pntr_-&gt;getMaxValue());</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        592 :   if(action_pntr_!=NULL) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        475 :     setStepOfLastBiasGridUpdate(action_pntr_-&gt;getStep());</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         27 : void LinearBasisSetExpansion::updateBiasWithoutCutoffGrid() {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         27 :   plumed_massert(bias_withoutcutoff_grid_pntr_,&quot;the bias without cutoff grid is not defined&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         27 :   plumed_massert(biasCutoffActive(),&quot;the bias cutoff has to be active&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         27 :   plumed_massert(vesbias_pntr_!=NULL,&quot;has to be linked to a VesBias to work&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         27 :   if(action_pntr_!=NULL &amp;&amp;  getStepOfLastBiasWithoutCutoffGridUpdate()==action_pntr_-&gt;getStep()) {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :     return;</a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span>            :   //</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">       2423 :   for(Grid::index_t l=0; l&lt;bias_withoutcutoff_grid_pntr_-&gt;getSize(); l++) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       2400 :     std::vector&lt;double&gt; forces(nargs_);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">       2400 :     std::vector&lt;double&gt; args = bias_withoutcutoff_grid_pntr_-&gt;getPoint(l);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       2400 :     bool all_inside=true;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       2400 :     double bias=getBiasAndForces(args,all_inside,forces);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       2400 :     if(bias_withoutcutoff_grid_pntr_-&gt;hasDerivatives()) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">       2400 :       bias_withoutcutoff_grid_pntr_-&gt;setValueAndDerivatives(l,bias,forces);</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     }</a>
+<a name="223"><span class="lineNum">     223 </span>            :     else {</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :       bias_withoutcutoff_grid_pntr_-&gt;setValue(l,bias);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span>            :   //</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         23 :   double bias_max = bias_withoutcutoff_grid_pntr_-&gt;getMaxValue();</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         23 :   double bias_min = bias_withoutcutoff_grid_pntr_-&gt;getMinValue();</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   double shift = 0.0;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   bool bias_shifted=false;</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         23 :   if(bias_min &lt; 0.0) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         22 :     shift += -bias_min;</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     bias_shifted=true;</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         22 :     BiasCoeffs()[0] -= bias_min;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         22 :     bias_max -= bias_min;</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         23 :   if(bias_max &gt; vesbias_pntr_-&gt;getBiasCutoffValue()) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         22 :     shift += -(bias_max-vesbias_pntr_-&gt;getBiasCutoffValue());</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :     bias_shifted=true;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         22 :     BiasCoeffs()[0] -= (bias_max-vesbias_pntr_-&gt;getBiasCutoffValue());</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         22 :     bias_max -= (bias_max-vesbias_pntr_-&gt;getBiasCutoffValue());</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         23 :   if(bias_shifted) {</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :     // this should be done inside a grid function really,</a>
+<a name="246"><span class="lineNum">     246 </span>            :     // need to define my grid class for that</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">       2322 :     for(Grid::index_t l=0; l&lt;bias_withoutcutoff_grid_pntr_-&gt;getSize(); l++) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">       2300 :       if(bias_withoutcutoff_grid_pntr_-&gt;hasDerivatives()) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">       2300 :         std::vector&lt;double&gt; zeros(nargs_,0.0);</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">       2300 :         bias_withoutcutoff_grid_pntr_-&gt;addValueAndDerivatives(l,shift,zeros);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :       }</a>
+<a name="252"><span class="lineNum">     252 </span>            :       else {</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :         bias_withoutcutoff_grid_pntr_-&gt;addValue(l,shift);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :       }</a>
+<a name="255"><span class="lineNum">     255 </span>            :     }</a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         23 :   if(vesbias_pntr_!=NULL) {</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :     vesbias_pntr_-&gt;setCurrentBiasMaxValue(bias_max);</a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         23 :   if(action_pntr_!=NULL) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         23 :     setStepOfLastBiasWithoutCutoffGridUpdate(action_pntr_-&gt;getStep());</span></a>
+<a name="262"><span class="lineNum">     262 </span>            :   }</a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        539 : void LinearBasisSetExpansion::updateFesGrid() {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        539 :   plumed_massert(fes_grid_pntr_,&quot;the FES grid is not defined&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        539 :   updateBiasGrid();</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        539 :   if(action_pntr_!=NULL &amp;&amp; getStepOfLastFesGridUpdate() == action_pntr_-&gt;getStep()) {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     return;</a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span>            :   //</a>
+<a name="273"><span class="lineNum">     273 </span>            :   double bias2fes_scalingf = -1.0;</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">    1474154 :   for(Grid::index_t l=0; l&lt;fes_grid_pntr_-&gt;getSize(); l++) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">    1473681 :     double fes_value = bias2fes_scalingf*bias_grid_pntr_-&gt;getValue(l);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">    1473681 :     if(log_targetdist_grid_pntr_!=NULL) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">    1224051 :       fes_value += kBT()*log_targetdist_grid_pntr_-&gt;getValue(l);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     }</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">    1473681 :     fes_grid_pntr_-&gt;setValue(l,fes_value);</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   }</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        473 :   fes_grid_pntr_-&gt;setMinToZero();</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">        473 :   if(action_pntr_!=NULL) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">        473 :     setStepOfLastFesGridUpdate(action_pntr_-&gt;getStep());</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   }</a>
+<a name="285"><span class="lineNum">     285 </span>            : }</a>
+<a name="286"><span class="lineNum">     286 </span>            : </a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">        212 : void LinearBasisSetExpansion::writeBiasGridToFile(OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">        212 :   plumed_massert(bias_grid_pntr_,&quot;the bias grid is not defined&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">        212 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">        212 :   bias_grid_pntr_-&gt;writeToFile(ofile);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        212 : }</span></a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          5 : void LinearBasisSetExpansion::writeBiasWithoutCutoffGridToFile(OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          5 :   plumed_massert(bias_withoutcutoff_grid_pntr_,&quot;the bias without cutoff grid is not defined&quot;);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          5 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          5 :   bias_withoutcutoff_grid_pntr_-&gt;writeToFile(ofile);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          5 : }</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">        169 : void LinearBasisSetExpansion::writeFesGridToFile(OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">        169 :   plumed_massert(fes_grid_pntr_!=NULL,&quot;the FES grid is not defined&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">        169 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">        169 :   fes_grid_pntr_-&gt;writeToFile(ofile);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">        169 : }</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         36 : void LinearBasisSetExpansion::writeFesProjGridToFile(const std::vector&lt;std::string&gt;&amp; proj_arg, OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         36 :   plumed_massert(fes_grid_pntr_,&quot;the FES grid is not defined&quot;);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         36 :   auto Fw = Tools::make_unique&lt;FesWeight&gt;(beta_);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         36 :   Grid proj_grid = fes_grid_pntr_-&gt;project(proj_arg,Fw.get());</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         36 :   proj_grid.setMinToZero();</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         36 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         36 :   proj_grid.writeToFile(ofile);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         36 : }</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         82 : void LinearBasisSetExpansion::writeTargetDistGridToFile(OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         82 :   if(targetdist_grid_pntr_==NULL) {return;}</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         82 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         82 :   targetdist_grid_pntr_-&gt;writeToFile(ofile);</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : }</a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         82 : void LinearBasisSetExpansion::writeLogTargetDistGridToFile(OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         82 :   if(log_targetdist_grid_pntr_==NULL) {return;}</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         82 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         82 :   log_targetdist_grid_pntr_-&gt;writeToFile(ofile);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         20 : void LinearBasisSetExpansion::writeTargetDistProjGridToFile(const std::vector&lt;std::string&gt;&amp; proj_arg, OFile&amp; ofile, const bool append_file) const {</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         20 :   if(targetdist_grid_pntr_==NULL) {return;}</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         20 :   if(append_file) {ofile.enforceRestart();}</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         20 :   Grid proj_grid = TargetDistribution::getMarginalDistributionGrid(targetdist_grid_pntr_,proj_arg);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         20 :   proj_grid.writeToFile(ofile);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         20 : }</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 : void LinearBasisSetExpansion::writeTargetDistributionToFile(const std::string&amp; filename) const {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :   OFile of1; OFile of2;</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :   if(action_pntr_!=NULL) {</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineNoCov">          0 :     of1.link(*action_pntr_); of2.link(*action_pntr_);</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineNoCov">          0 :   of1.enforceBackup(); of2.enforceBackup();</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :   of1.open(filename);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineNoCov">          0 :   of2.open(FileBase::appendSuffix(filename,&quot;.log&quot;));</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineNoCov">          0 :   writeTargetDistGridToFile(of1);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineNoCov">          0 :   writeLogTargetDistGridToFile(of2);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :   of1.close(); of2.close();</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : </a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">    2011787 : double LinearBasisSetExpansion::getBiasAndForces(const std::vector&lt;double&gt;&amp; args_values, bool&amp; all_inside, std::vector&lt;double&gt;&amp; forces, std::vector&lt;double&gt;&amp; coeffsderivs_values, std::vector&lt;BasisFunctions*&gt;&amp; basisf_pntrs_in, CoeffsVector* coeffs_pntr_in, Communicator* comm_in) {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">    2011787 :   unsigned int nargs = args_values.size();</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">    2011787 :   plumed_assert(coeffs_pntr_in-&gt;numberOfDimensions()==nargs);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">    2011787 :   plumed_assert(basisf_pntrs_in.size()==nargs);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">    2011787 :   plumed_assert(forces.size()==nargs);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">    2011787 :   plumed_assert(coeffsderivs_values.size()==coeffs_pntr_in-&gt;numberOfCoeffs());</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">    2011787 :   std::vector&lt;double&gt; args_values_trsfrm(nargs);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :   // std::vector&lt;bool&gt;   inside_interval(nargs,true);</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">    2011787 :   all_inside = true;</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :   //</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">    2011787 :   std::vector&lt; std::vector &lt;double&gt; &gt; bf_values(nargs);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">    2011787 :   std::vector&lt; std::vector &lt;double&gt; &gt; bf_derivs(nargs);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   //</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">    5966255 :   for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">    3954468 :     bf_values[k].assign(basisf_pntrs_in[k]-&gt;getNumberOfBasisFunctions(),0.0);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">    3954468 :     bf_derivs[k].assign(basisf_pntrs_in[k]-&gt;getNumberOfBasisFunctions(),0.0);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">    3954468 :     bool curr_inside=true;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">    3954468 :     basisf_pntrs_in[k]-&gt;getAllValues(args_values[k],args_values_trsfrm[k],curr_inside,bf_values[k],bf_derivs[k]);</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :     // inside_interval[k]=curr_inside;</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">    3954468 :     if(!curr_inside) {all_inside=false;}</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">    3954468 :     forces[k]=0.0;</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :   }</a>
+<a name="378"><span class="lineNum">     378 </span>            :   //</a>
+<a name="379"><span class="lineNum">     379 </span>            :   size_t stride=1;</a>
+<a name="380"><span class="lineNum">     380 </span>            :   size_t rank=0;</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">    2011787 :   if(comm_in!=NULL)</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   {</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">    2011787 :     stride=comm_in-&gt;Get_size();</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">    2011787 :     rank=comm_in-&gt;Get_rank();</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :   }</a>
+<a name="386"><span class="lineNum">     386 </span>            :   // loop over coeffs</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">    2011787 :   double bias=0.0;</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">  144769949 :   for(size_t i=rank; i&lt;coeffs_pntr_in-&gt;numberOfCoeffs(); i+=stride) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">  142758162 :     std::vector&lt;unsigned int&gt; indices=coeffs_pntr_in-&gt;getIndices(i);</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :     double coeff = coeffs_pntr_in-&gt;getValue(i);</a>
+<a name="391"><span class="lineNum">     391 </span>            :     double bf_curr=1.0;</a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">  435044808 :     for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">  292286646 :       bf_curr*=bf_values[k][indices[k]];</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :     }</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">  142758162 :     bias+=coeff*bf_curr;</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">  142758162 :     coeffsderivs_values[i] = bf_curr;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineCov">  435044808 :     for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :       double der = 1.0;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">  898592256 :       for(unsigned int l=0; l&lt;nargs; l++) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">  606305610 :         if(l!=k) {der*=bf_values[l][indices[l]];}</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">  292286646 :         else {der*=bf_derivs[l][indices[l]];}</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :       }</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">  292286646 :       forces[k]-=coeff*der;</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :       // maybe faster but dangerous</a>
+<a name="405"><span class="lineNum">     405 </span>            :       // forces[k]-=coeff*bf_curr*(bf_derivs[k][indices[k]]/bf_values[k][indices[k]]);</a>
+<a name="406"><span class="lineNum">     406 </span>            :     }</a>
+<a name="407"><span class="lineNum">     407 </span>            :   }</a>
+<a name="408"><span class="lineNum">     408 </span>            :   //</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">    2011787 :   if(comm_in!=NULL) {</span></a>
+<a name="410"><span class="lineNum">     410 </span>            :     // coeffsderivs_values is not summed as the mpi Sum is done later on for the averages</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">    2011787 :     comm_in-&gt;Sum(bias);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">    2011787 :     comm_in-&gt;Sum(forces);</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :   }</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">    2011787 :   return bias;</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">    2011787 : }</span></a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">     862315 : void LinearBasisSetExpansion::getBasisSetValues(const std::vector&lt;double&gt;&amp; args_values, std::vector&lt;double&gt;&amp; basisset_values, std::vector&lt;BasisFunctions*&gt;&amp; basisf_pntrs_in, CoeffsVector* coeffs_pntr_in, Communicator* comm_in) {</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">     862315 :   unsigned int nargs = args_values.size();</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">     862315 :   plumed_assert(coeffs_pntr_in-&gt;numberOfDimensions()==nargs);</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">     862315 :   plumed_assert(basisf_pntrs_in.size()==nargs);</span></a>
+<a name="422"><span class="lineNum">     422 </span>            : </a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">     862315 :   std::vector&lt;double&gt; args_values_trsfrm(nargs);</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :   std::vector&lt; std::vector &lt;double&gt; &gt; bf_values;</a>
+<a name="425"><span class="lineNum">     425 </span>            :   //</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">    2583312 :   for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">    1720997 :     std::vector&lt;double&gt; tmp_val(basisf_pntrs_in[k]-&gt;getNumberOfBasisFunctions());</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">    1720997 :     std::vector&lt;double&gt; tmp_der(tmp_val.size());</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">    1720997 :     bool inside=true;</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">    1720997 :     basisf_pntrs_in[k]-&gt;getAllValues(args_values[k],args_values_trsfrm[k],inside,tmp_val,tmp_der);</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">    1720997 :     bf_values.push_back(tmp_val);</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :   }</a>
+<a name="433"><span class="lineNum">     433 </span>            :   //</a>
+<a name="434"><span class="lineNum">     434 </span>            :   size_t stride=1;</a>
+<a name="435"><span class="lineNum">     435 </span>            :   size_t rank=0;</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">     862315 :   if(comm_in!=NULL)</span></a>
+<a name="437"><span class="lineNum">     437 </span>            :   {</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineNoCov">          0 :     stride=comm_in-&gt;Get_size();</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineNoCov">          0 :     rank=comm_in-&gt;Get_rank();</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   }</a>
+<a name="441"><span class="lineNum">     441 </span>            :   // loop over basis set</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">   95955507 :   for(size_t i=rank; i&lt;coeffs_pntr_in-&gt;numberOfCoeffs(); i+=stride) {</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">   95093192 :     std::vector&lt;unsigned int&gt; indices=coeffs_pntr_in-&gt;getIndices(i);</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :     double bf_curr=1.0;</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">  298507612 :     for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">  203414420 :       bf_curr*=bf_values[k][indices[k]];</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :     }</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">   95093192 :     basisset_values[i] = bf_curr;</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   }</a>
+<a name="450"><span class="lineNum">     450 </span>            :   //</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">     862315 :   if(comm_in!=NULL) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineNoCov">          0 :     comm_in-&gt;Sum(basisset_values);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :   }</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">    1724630 : }</span></a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">        408 : double LinearBasisSetExpansion::getBasisSetValue(const std::vector&lt;double&gt;&amp; args_values, const size_t index, std::vector&lt;BasisFunctions*&gt;&amp; basisf_pntrs_in, CoeffsVector* coeffs_pntr_in) {</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">        408 :   unsigned int nargs = args_values.size();</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        408 :   plumed_assert(coeffs_pntr_in-&gt;numberOfDimensions()==nargs);</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">        408 :   plumed_assert(basisf_pntrs_in.size()==nargs);</span></a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">        408 :   std::vector&lt;double&gt; args_values_trsfrm(nargs);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   std::vector&lt; std::vector &lt;double&gt; &gt; bf_values;</a>
+<a name="464"><span class="lineNum">     464 </span>            :   //</a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">        938 :   for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">        530 :     std::vector&lt;double&gt; tmp_val(basisf_pntrs_in[k]-&gt;getNumberOfBasisFunctions());</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">        530 :     std::vector&lt;double&gt; tmp_der(tmp_val.size());</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">        530 :     bool inside=true;</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">        530 :     basisf_pntrs_in[k]-&gt;getAllValues(args_values[k],args_values_trsfrm[k],inside,tmp_val,tmp_der);</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">        530 :     bf_values.push_back(tmp_val);</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :   }</a>
+<a name="472"><span class="lineNum">     472 </span>            :   //</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">        408 :   std::vector&lt;unsigned int&gt; indices=coeffs_pntr_in-&gt;getIndices(index);</span></a>
+<a name="474"><span class="lineNum">     474 </span>            :   double bf_value=1.0;</a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">        938 :   for(unsigned int k=0; k&lt;nargs; k++) {</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">        530 :     bf_value*=bf_values[k][indices[k]];</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :   }</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        408 :   return bf_value;</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        408 : }</span></a>
+<a name="480"><span class="lineNum">     480 </span>            : </a>
+<a name="481"><span class="lineNum">     481 </span>            : </a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         45 : void LinearBasisSetExpansion::setupUniformTargetDistribution() {</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         45 :   std::vector&lt; std::vector &lt;double&gt; &gt; bf_integrals(0);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">         45 :   std::vector&lt;double&gt; targetdist_averages(ncoeffs_,0.0);</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :   //</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">        100 :   for(unsigned int k=0; k&lt;nargs_; k++) {</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        110 :     bf_integrals.push_back(basisf_pntrs_[k]-&gt;getUniformIntegrals());</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :   }</a>
+<a name="489"><span class="lineNum">     489 </span>            :   //</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">       1672 :   for(size_t i=0; i&lt;ncoeffs_; i++) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">       1627 :     std::vector&lt;unsigned int&gt; indices=bias_coeffs_pntr_-&gt;getIndices(i);</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :     double value = 1.0;</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">       4492 :     for(unsigned int k=0; k&lt;nargs_; k++) {</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">       2865 :       value*=bf_integrals[k][indices[k]];</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     }</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">       1627 :     targetdist_averages[i]=value;</span></a>
+<a name="497"><span class="lineNum">     497 </span>            :   }</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">         45 :   TargetDistAverages() = targetdist_averages;</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         45 : }</span></a>
+<a name="500"><span class="lineNum">     500 </span>            : </a>
+<a name="501"><span class="lineNum">     501 </span>            : </a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">         45 : void LinearBasisSetExpansion::setupTargetDistribution(TargetDistribution* targetdist_pntr_in) {</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         45 :   targetdist_pntr_ = targetdist_pntr_in;</span></a>
+<a name="504"><span class="lineNum">     504 </span>            :   //</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">         45 :   targetdist_pntr_-&gt;setupGrids(args_pntrs_,grid_min_,grid_max_,grid_bins_);</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         45 :   targetdist_grid_pntr_      = targetdist_pntr_-&gt;getTargetDistGridPntr();</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         45 :   log_targetdist_grid_pntr_  = targetdist_pntr_-&gt;getLogTargetDistGridPntr();</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   //</a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">         45 :   if(targetdist_pntr_-&gt;isDynamic()) {</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">         39 :     vesbias_pntr_-&gt;enableDynamicTargetDistribution();</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   }</a>
+<a name="512"><span class="lineNum">     512 </span>            :   //</a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">         45 :   if(targetdist_pntr_-&gt;biasGridNeeded()) {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :     setupBiasGrid(true);</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineNoCov">          0 :     targetdist_pntr_-&gt;linkBiasGrid(bias_grid_pntr_.get());</span></a>
+<a name="516"><span class="lineNum">     516 </span>            :   }</a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         45 :   if(targetdist_pntr_-&gt;biasWithoutCutoffGridNeeded()) {</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">          3 :     setupBiasGrid(true);</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          3 :     targetdist_pntr_-&gt;linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_.get());</span></a>
+<a name="520"><span class="lineNum">     520 </span>            :   }</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         45 :   if(targetdist_pntr_-&gt;fesGridNeeded()) {</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         36 :     setupFesGrid();</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         36 :     targetdist_pntr_-&gt;linkFesGrid(fes_grid_pntr_.get());</span></a>
+<a name="524"><span class="lineNum">     524 </span>            :   }</a>
+<a name="525"><span class="lineNum">     525 </span>            :   //</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         45 :   targetdist_pntr_-&gt;updateTargetDist();</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         45 :   calculateTargetDistAveragesFromGrid(targetdist_grid_pntr_);</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         45 : }</span></a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">        355 : void LinearBasisSetExpansion::updateTargetDistribution() {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        355 :   plumed_massert(targetdist_pntr_!=NULL,&quot;the target distribution hasn't been setup!&quot;);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        355 :   plumed_massert(targetdist_pntr_-&gt;isDynamic(),&quot;this should only be used for dynamically updated target distributions!&quot;);</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">        355 :   if(targetdist_pntr_-&gt;biasGridNeeded()) {updateBiasGrid();}</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">        355 :   if(biasCutoffActive()) {updateBiasWithoutCutoffGrid();}</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">        355 :   if(targetdist_pntr_-&gt;fesGridNeeded()) {updateFesGrid();}</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">        355 :   targetdist_pntr_-&gt;updateTargetDist();</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">        355 :   calculateTargetDistAveragesFromGrid(targetdist_grid_pntr_);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">        355 : }</span></a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">          8 : void LinearBasisSetExpansion::readInRestartTargetDistribution(const std::string&amp; grid_fname) {</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">          8 :   targetdist_pntr_-&gt;readInRestartTargetDistGrid(grid_fname);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">          8 :   if(biasCutoffActive()) {targetdist_pntr_-&gt;clearLogTargetDistGrid();}</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">          8 : }</span></a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">          8 : void LinearBasisSetExpansion::restartTargetDistribution() {</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">          8 :   plumed_massert(targetdist_pntr_!=NULL,&quot;the target distribution hasn't been setup!&quot;);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">          8 :   plumed_massert(targetdist_pntr_-&gt;isDynamic(),&quot;this should only be used for dynamically updated target distributions!&quot;);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">          8 :   if(biasCutoffActive()) {updateBiasWithoutCutoffGrid();}</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">          8 :   calculateTargetDistAveragesFromGrid(targetdist_grid_pntr_);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">          8 : }</span></a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">        408 : void LinearBasisSetExpansion::calculateTargetDistAveragesFromGrid(const Grid* targetdist_grid_pntr) {</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        408 :   plumed_assert(targetdist_grid_pntr!=NULL);</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">        408 :   std::vector&lt;double&gt; targetdist_averages(ncoeffs_,0.0);</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">        816 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(targetdist_grid_pntr);</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">        408 :   Grid::index_t stride=mycomm_.Get_size();</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">        408 :   Grid::index_t rank=mycomm_.Get_rank();</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">     862723 :   for(Grid::index_t l=rank; l&lt;targetdist_grid_pntr-&gt;getSize(); l+=stride) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">     862315 :     std::vector&lt;double&gt; args_values = targetdist_grid_pntr-&gt;getPoint(l);</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">     862315 :     std::vector&lt;double&gt; basisset_values(ncoeffs_);</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :     // parallelization done over the grid -&gt; should NOT use parallel in getBasisSetValues!!</a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">     862315 :     getBasisSetValues(args_values,basisset_values,false);</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">     862315 :     double weight = integration_weights[l]*targetdist_grid_pntr-&gt;getValue(l);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">   95955507 :     for(unsigned int i=0; i&lt;ncoeffs_; i++) {</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">   95093192 :       targetdist_averages[i] += weight*basisset_values[i];</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :     }</a>
+<a name="571"><span class="lineNum">     571 </span>            :   }</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">        408 :   mycomm_.Sum(targetdist_averages);</span></a>
+<a name="573"><span class="lineNum">     573 </span>            :   // the overall constant;</a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">        408 :   targetdist_averages[0] = getBasisSetConstant();</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        408 :   TargetDistAverages() = targetdist_averages;</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">        408 : }</span></a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         39 : void LinearBasisSetExpansion::setBiasMinimumToZero() {</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         39 :   plumed_massert(bias_grid_pntr_,&quot;setBiasMinimumToZero can only be used if the bias grid is defined&quot;);</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         39 :   updateBiasGrid();</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         39 :   BiasCoeffs()[0]-=bias_grid_pntr_-&gt;getMinValue();</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         39 : }</span></a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span>            : </a>
+<a name="586"><span class="lineNum">     586 </span><span class="lineNoCov">          0 : void LinearBasisSetExpansion::setBiasMaximumToZero() {</span></a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineNoCov">          0 :   plumed_massert(bias_grid_pntr_,&quot;setBiasMaximumToZero can only be used if the bias grid is defined&quot;);</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :   updateBiasGrid();</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :   BiasCoeffs()[0]-=bias_grid_pntr_-&gt;getMaxValue();</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">    1982225 : bool LinearBasisSetExpansion::biasCutoffActive() const {</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">    1982225 :   if(vesbias_pntr_!=NULL) {return vesbias_pntr_-&gt;biasCutoffActive();}</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :   else {return false;}</a>
+<a name="596"><span class="lineNum">     596 </span>            : }</a>
+<a name="597"><span class="lineNum">     597 </span>            : </a>
+<a name="598"><span class="lineNum">     598 </span>            : </a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 : double LinearBasisSetExpansion::calculateReweightFactor() const {</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineNoCov">          0 :   plumed_massert(targetdist_grid_pntr_!=NULL,&quot;calculateReweightFactor only be used if the target distribution grid is defined&quot;);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineNoCov">          0 :   plumed_massert(bias_grid_pntr_,&quot;calculateReweightFactor only be used if the bias grid is defined&quot;);</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :   double sum = 0.0;</a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(targetdist_grid_pntr_);</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :   //</a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 :   for(Grid::index_t l=0; l&lt;targetdist_grid_pntr_-&gt;getSize(); l++) {</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineNoCov">          0 :     sum += integration_weights[l] * targetdist_grid_pntr_-&gt;getValue(l) * exp(+beta_*bias_grid_pntr_-&gt;getValue(l));</span></a>
+<a name="607"><span class="lineNum">     607 </span>            :   }</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineNoCov">          0 :   if(sum==0.0) sum=std::numeric_limits&lt;double&gt;::min();</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineNoCov">          0 :   return (1.0/beta_)*std::log(sum);</span></a>
+<a name="610"><span class="lineNum">     610 </span>            : }</a>
+<a name="611"><span class="lineNum">     611 </span>            : </a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            : </a>
+<a name="615"><span class="lineNum">     615 </span>            : }</a>
+<a name="616"><span class="lineNum">     616 </span>            : </a>
+<a name="617"><span class="lineNum">     617 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/LinearBasisSetExpansion.h.func-sort-c.html b/coverage/ves/LinearBasisSetExpansion.h.func-sort-c.html
new file mode 100644
index 0000000000..106776a630
--- /dev/null
+++ b/coverage/ves/LinearBasisSetExpansion.h.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/LinearBasisSetExpansion.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - LinearBasisSetExpansion.h<span style="font-size: 80%;"> (<a href="LinearBasisSetExpansion.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LinearBasisSetExpansion.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.h.gcov.html#238">_ZN4PLMD3ves23LinearBasisSetExpansion19getBasisSetConstantEv</a></td>
+              <td class="coverFnHi">408</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.h.gcov.html#221">_ZN4PLMD3ves23LinearBasisSetExpansion17getBasisSetValuesERKSt6vectorIdSaIdEERS4_b</a></td>
+              <td class="coverFnHi">862315</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.h.gcov.html#201">_ZN4PLMD3ves23LinearBasisSetExpansion16getBiasAndForcesERKSt6vectorIdSaIdEERbRS4_</a></td>
+              <td class="coverFnHi">1988037</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/LinearBasisSetExpansion.h.func.html b/coverage/ves/LinearBasisSetExpansion.h.func.html
new file mode 100644
index 0000000000..fac7025234
--- /dev/null
+++ b/coverage/ves/LinearBasisSetExpansion.h.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/LinearBasisSetExpansion.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - LinearBasisSetExpansion.h<span style="font-size: 80%;"> (<a href="LinearBasisSetExpansion.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LinearBasisSetExpansion.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.h.gcov.html#201">_ZN4PLMD3ves23LinearBasisSetExpansion16getBiasAndForcesERKSt6vectorIdSaIdEERbRS4_</a></td>
+              <td class="coverFnHi">1988037</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.h.gcov.html#221">_ZN4PLMD3ves23LinearBasisSetExpansion17getBasisSetValuesERKSt6vectorIdSaIdEERS4_b</a></td>
+              <td class="coverFnHi">862315</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LinearBasisSetExpansion.h.gcov.html#238">_ZN4PLMD3ves23LinearBasisSetExpansion19getBasisSetConstantEv</a></td>
+              <td class="coverFnHi">408</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/LinearBasisSetExpansion.h.gcov.html b/coverage/ves/LinearBasisSetExpansion.h.gcov.html
new file mode 100644
index 0000000000..3543668d48
--- /dev/null
+++ b/coverage/ves/LinearBasisSetExpansion.h.gcov.html
@@ -0,0 +1,326 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/LinearBasisSetExpansion.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - LinearBasisSetExpansion.h<span style="font-size: 80%;"> (source / <a href="LinearBasisSetExpansion.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_LinearBasisSetExpansion_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_LinearBasisSetExpansion_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;string&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;memory&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : class Action;</a>
+<a name="33"><span class="lineNum">      33 </span>            : class Keywords;</a>
+<a name="34"><span class="lineNum">      34 </span>            : class Value;</a>
+<a name="35"><span class="lineNum">      35 </span>            : class Communicator;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class Grid;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class OFile;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace ves {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class CoeffsVector;</a>
+<a name="43"><span class="lineNum">      43 </span>            : class BasisFunctions;</a>
+<a name="44"><span class="lineNum">      44 </span>            : class TargetDistribution;</a>
+<a name="45"><span class="lineNum">      45 </span>            : class VesBias;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : class LinearBasisSetExpansion {</a>
+<a name="49"><span class="lineNum">      49 </span>            :   LinearBasisSetExpansion&amp; operator=(const LinearBasisSetExpansion&amp;) = delete;</a>
+<a name="50"><span class="lineNum">      50 </span>            : private:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::string label_;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   //</a>
+<a name="53"><span class="lineNum">      53 </span>            :   Action* action_pntr_;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   VesBias* vesbias_pntr_;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   Communicator&amp; mycomm_;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   bool serial_;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   //</a>
+<a name="58"><span class="lineNum">      58 </span>            :   double beta_;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   double kbt_;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   //</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::vector&lt;Value*&gt; args_pntrs_;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   unsigned int nargs_;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   //</a>
+<a name="64"><span class="lineNum">      64 </span>            :   std::vector&lt;BasisFunctions*&gt; basisf_pntrs_;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;unsigned int&gt; nbasisf_;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   //</a>
+<a name="67"><span class="lineNum">      67 </span>            :   CoeffsVector* bias_coeffs_pntr_;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   size_t ncoeffs_;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::unique_ptr&lt;CoeffsVector&gt; targetdist_averages_pntr_;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   //</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::vector&lt;std::string&gt; grid_min_;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   std::vector&lt;std::string&gt; grid_max_;</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;unsigned int&gt; grid_bins_;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   //</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::string targetdist_grid_label_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   //</a>
+<a name="77"><span class="lineNum">      77 </span>            :   long long int step_of_last_biasgrid_update;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   long long int step_of_last_biaswithoutcutoffgrid_update;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   long long int step_of_last_fesgrid_update;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   //</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::unique_ptr&lt;Grid&gt; bias_grid_pntr_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::unique_ptr&lt;Grid&gt; bias_withoutcutoff_grid_pntr_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::unique_ptr&lt;Grid&gt; fes_grid_pntr_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   Grid* log_targetdist_grid_pntr_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   Grid* targetdist_grid_pntr_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //</a>
+<a name="87"><span class="lineNum">      87 </span>            :   TargetDistribution* targetdist_pntr_;</a>
+<a name="88"><span class="lineNum">      88 </span>            : public:</a>
+<a name="89"><span class="lineNum">      89 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="90"><span class="lineNum">      90 </span>            :   // Constructor</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit LinearBasisSetExpansion(</a>
+<a name="92"><span class="lineNum">      92 </span>            :     const std::string&amp;,</a>
+<a name="93"><span class="lineNum">      93 </span>            :     const double,</a>
+<a name="94"><span class="lineNum">      94 </span>            :     Communicator&amp;,</a>
+<a name="95"><span class="lineNum">      95 </span>            :     const std::vector&lt;Value*&gt;&amp;,</a>
+<a name="96"><span class="lineNum">      96 </span>            :     std::vector&lt;BasisFunctions*&gt;&amp;,</a>
+<a name="97"><span class="lineNum">      97 </span>            :     CoeffsVector* bias_coeffs_pntr_in=NULL);</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //</a>
+<a name="99"><span class="lineNum">      99 </span>            : private:</a>
+<a name="100"><span class="lineNum">     100 </span>            :   // copy constructor is disabled (private and unimplemented)</a>
+<a name="101"><span class="lineNum">     101 </span>            :   explicit LinearBasisSetExpansion(const LinearBasisSetExpansion&amp;);</a>
+<a name="102"><span class="lineNum">     102 </span>            : public:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   ~LinearBasisSetExpansion();</a>
+<a name="104"><span class="lineNum">     104 </span>            :   //</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;Value*&gt; getPntrsToArguments() const {return args_pntrs_;}</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;BasisFunctions*&gt; getPntrsToBasisFunctions() const {return basisf_pntrs_;}</a>
+<a name="107"><span class="lineNum">     107 </span>            :   CoeffsVector* getPntrToBiasCoeffs() const {return bias_coeffs_pntr_;}</a>
+<a name="108"><span class="lineNum">     108 </span>            :   Grid* getPntrToBiasGrid() const {return bias_grid_pntr_.get();};</a>
+<a name="109"><span class="lineNum">     109 </span>            :   //</a>
+<a name="110"><span class="lineNum">     110 </span>            :   unsigned int getNumberOfArguments() const {return nargs_;};</a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::vector&lt;unsigned int&gt; getNumberOfBasisFunctions() const {return nbasisf_;};</a>
+<a name="112"><span class="lineNum">     112 </span>            :   size_t getNumberOfCoeffs() const {return ncoeffs_;};</a>
+<a name="113"><span class="lineNum">     113 </span>            :   //</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         83 :   CoeffsVector&amp; BiasCoeffs() const {return *bias_coeffs_pntr_;};</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :   CoeffsVector&amp; TargetDistAverages() const {return *targetdist_averages_pntr_;};</a>
+<a name="116"><span class="lineNum">     116 </span>            :   //</a>
+<a name="117"><span class="lineNum">     117 </span>            :   void setSerial() {serial_=true;}</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void setParallel() {serial_=false;}</a>
+<a name="119"><span class="lineNum">     119 </span>            :   //</a>
+<a name="120"><span class="lineNum">     120 </span>            :   void linkVesBias(VesBias*);</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void linkAction(Action*);</a>
+<a name="122"><span class="lineNum">     122 </span>            :   // calculate bias and derivatives</a>
+<a name="123"><span class="lineNum">     123 </span>            :   static double getBiasAndForces(const std::vector&lt;double&gt;&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;BasisFunctions*&gt;&amp;, CoeffsVector*, Communicator* comm_in=NULL);</a>
+<a name="124"><span class="lineNum">     124 </span>            :   double getBiasAndForces(const std::vector&lt;double&gt;&amp;, bool&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;);</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double getBiasAndForces(const std::vector&lt;double&gt;&amp;, bool&amp;, std::vector&lt;double&gt;&amp;);</a>
+<a name="126"><span class="lineNum">     126 </span>            :   double getBias(const std::vector&lt;double&gt;&amp;, bool&amp;, const bool parallel=true);</a>
+<a name="127"><span class="lineNum">     127 </span>            :   //</a>
+<a name="128"><span class="lineNum">     128 </span>            :   static void getBasisSetValues(const std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;BasisFunctions*&gt;&amp;, CoeffsVector*, Communicator* comm_in=NULL);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   void getBasisSetValues(const std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;, const bool parallel=true);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   //</a>
+<a name="131"><span class="lineNum">     131 </span>            :   static double getBasisSetValue(const std::vector&lt;double&gt;&amp;, const size_t, std::vector&lt;BasisFunctions*&gt;&amp;, CoeffsVector*);</a>
+<a name="132"><span class="lineNum">     132 </span>            :   double getBasisSetValue(const std::vector&lt;double&gt;&amp;, const size_t);</a>
+<a name="133"><span class="lineNum">     133 </span>            :   double getBasisSetConstant();</a>
+<a name="134"><span class="lineNum">     134 </span>            :   // Bias grid and output stuff</a>
+<a name="135"><span class="lineNum">     135 </span>            :   void setupBiasGrid(const bool usederiv=false);</a>
+<a name="136"><span class="lineNum">     136 </span>            :   void updateBiasGrid();</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         36 :   void resetStepOfLastBiasGridUpdate() {step_of_last_biasgrid_update = -1000;}</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        475 :   void setStepOfLastBiasGridUpdate(long long int step) {step_of_last_biasgrid_update = step;}</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">        712 :   long long int getStepOfLastBiasGridUpdate() const {return step_of_last_biasgrid_update;}</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   void writeBiasGridToFile(OFile&amp;, const bool append=false) const;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   //</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void updateBiasWithoutCutoffGrid();</a>
+<a name="143"><span class="lineNum">     143 </span>            :   void resetStepOfLastBiasWithoutCutoffGridUpdate() {step_of_last_biaswithoutcutoffgrid_update = -1000;}</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         23 :   void setStepOfLastBiasWithoutCutoffGridUpdate(long long int step) {step_of_last_biaswithoutcutoffgrid_update = step;}</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         27 :   long long int getStepOfLastBiasWithoutCutoffGridUpdate() const {return step_of_last_biaswithoutcutoffgrid_update;}</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   void writeBiasWithoutCutoffGridToFile(OFile&amp;, const bool append=false) const;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //</a>
+<a name="148"><span class="lineNum">     148 </span>            :   void setBiasMinimumToZero();</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void setBiasMaximumToZero();</a>
+<a name="150"><span class="lineNum">     150 </span>            :   //</a>
+<a name="151"><span class="lineNum">     151 </span>            :   void setupFesGrid();</a>
+<a name="152"><span class="lineNum">     152 </span>            :   void updateFesGrid();</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         36 :   void resetStepOfLastFesGridUpdate() {step_of_last_fesgrid_update = -1000;}</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        473 :   void setStepOfLastFesGridUpdate(long long int step) {step_of_last_fesgrid_update = step;}</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">        539 :   long long int getStepOfLastFesGridUpdate() const {return step_of_last_fesgrid_update;}</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   void writeFesGridToFile(OFile&amp;, const bool append=false) const;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   //</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void setupFesProjGrid();</a>
+<a name="159"><span class="lineNum">     159 </span>            :   void writeFesProjGridToFile(const std::vector&lt;std::string&gt;&amp;, OFile&amp;, const bool append=false) const;</a>
+<a name="160"><span class="lineNum">     160 </span>            :   //</a>
+<a name="161"><span class="lineNum">     161 </span>            :   void writeTargetDistGridToFile(OFile&amp;, const bool append=false) const;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void writeLogTargetDistGridToFile(OFile&amp;, const bool append=false) const;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   void writeTargetDistProjGridToFile(const std::vector&lt;std::string&gt;&amp;, OFile&amp;, const bool append=false) const;</a>
+<a name="164"><span class="lineNum">     164 </span>            :   void writeTargetDistributionToFile(const std::string&amp;) const;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   //</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::vector&lt;unsigned int&gt; getGridBins() const {return grid_bins_;}</a>
+<a name="167"><span class="lineNum">     167 </span>            :   void setGridBins(const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="168"><span class="lineNum">     168 </span>            :   void setGridBins(const unsigned int);</a>
+<a name="169"><span class="lineNum">     169 </span>            :   //</a>
+<a name="170"><span class="lineNum">     170 </span>            :   double getBeta() const {return beta_;}</a>
+<a name="171"><span class="lineNum">     171 </span>            :   double getKbT() const {return kbt_;}</a>
+<a name="172"><span class="lineNum">     172 </span>            :   double beta() const {return beta_;}</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">    1224051 :   double kBT() const {return kbt_;}</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   //</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void setupUniformTargetDistribution();</a>
+<a name="176"><span class="lineNum">     176 </span>            :   void setupTargetDistribution(TargetDistribution*);</a>
+<a name="177"><span class="lineNum">     177 </span>            :   void updateTargetDistribution();</a>
+<a name="178"><span class="lineNum">     178 </span>            :   //</a>
+<a name="179"><span class="lineNum">     179 </span>            :   void readInRestartTargetDistribution(const std::string&amp;);</a>
+<a name="180"><span class="lineNum">     180 </span>            :   void restartTargetDistribution();</a>
+<a name="181"><span class="lineNum">     181 </span>            :   //</a>
+<a name="182"><span class="lineNum">     182 </span>            :   bool biasCutoffActive() const;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //</a>
+<a name="184"><span class="lineNum">     184 </span>            :   double calculateReweightFactor() const;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   //</a>
+<a name="186"><span class="lineNum">     186 </span>            : private:</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //</a>
+<a name="188"><span class="lineNum">     188 </span>            :   std::unique_ptr&lt;Grid&gt; setupGeneralGrid(const std::string&amp;, const bool usederiv=false);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void calculateTargetDistAveragesFromGrid(const Grid*);</a>
+<a name="191"><span class="lineNum">     191 </span>            :   //</a>
+<a name="192"><span class="lineNum">     192 </span>            :   bool isStaticTargetDistFileOutputActive() const;</a>
+<a name="193"><span class="lineNum">     193 </span>            : };</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : inline</a>
+<a name="197"><span class="lineNum">     197 </span>            : double LinearBasisSetExpansion::getBiasAndForces(const std::vector&lt;double&gt;&amp; args_values, bool&amp; all_inside, std::vector&lt;double&gt;&amp; forces, std::vector&lt;double&gt;&amp; coeffsderivs_values) {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">      23750 :   return getBiasAndForces(args_values,all_inside,forces,coeffsderivs_values,basisf_pntrs_, bias_coeffs_pntr_, &amp;mycomm_);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span>            : inline</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">    1988037 : double LinearBasisSetExpansion::getBiasAndForces(const std::vector&lt;double&gt;&amp; args_values, bool&amp; all_inside, std::vector&lt;double&gt;&amp; forces) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">    1988037 :   std::vector&lt;double&gt; coeffsderivs_values_dummy(ncoeffs_);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">    3976074 :   return getBiasAndForces(args_values,all_inside,forces,coeffsderivs_values_dummy,basisf_pntrs_, bias_coeffs_pntr_, &amp;mycomm_);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : inline</a>
+<a name="210"><span class="lineNum">     210 </span>            : double LinearBasisSetExpansion::getBias(const std::vector&lt;double&gt;&amp; args_values, bool&amp; all_inside, const bool parallel) {</a>
+<a name="211"><span class="lineNum">     211 </span>            :   std::vector&lt;double&gt; forces_dummy(nargs_);</a>
+<a name="212"><span class="lineNum">     212 </span>            :   std::vector&lt;double&gt; coeffsderivs_values_dummy(ncoeffs_);</a>
+<a name="213"><span class="lineNum">     213 </span>            :   if(parallel) {</a>
+<a name="214"><span class="lineNum">     214 </span>            :     return getBiasAndForces(args_values,all_inside,forces_dummy,coeffsderivs_values_dummy,basisf_pntrs_, bias_coeffs_pntr_, &amp;mycomm_);</a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            :   else {</a>
+<a name="217"><span class="lineNum">     217 </span>            :     return getBiasAndForces(args_values,all_inside,forces_dummy,coeffsderivs_values_dummy,basisf_pntrs_, bias_coeffs_pntr_, NULL);</a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span>            : }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : inline</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     862315 : void LinearBasisSetExpansion::getBasisSetValues(const std::vector&lt;double&gt;&amp; args_values, std::vector&lt;double&gt;&amp; basisset_values, const bool parallel) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">     862315 :   if(parallel) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :     getBasisSetValues(args_values,basisset_values,basisf_pntrs_, bias_coeffs_pntr_, &amp;mycomm_);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   }</a>
+<a name="227"><span class="lineNum">     227 </span>            :   else {</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">     862315 :     getBasisSetValues(args_values,basisset_values,basisf_pntrs_, bias_coeffs_pntr_, NULL);</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">     862315 : }</span></a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : inline</a>
+<a name="234"><span class="lineNum">     234 </span>            : double LinearBasisSetExpansion::getBasisSetValue(const std::vector&lt;double&gt;&amp; args_values, const size_t basisset_index) {</a>
+<a name="235"><span class="lineNum">     235 </span>            :   return getBasisSetValue(args_values,basisset_index,basisf_pntrs_, bias_coeffs_pntr_);</a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : inline</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        408 : double LinearBasisSetExpansion::getBasisSetConstant() {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        408 :   std::vector&lt;double&gt; args_dummy(nargs_,0.0);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        816 :   return getBasisSetValue(args_dummy,0,basisf_pntrs_, bias_coeffs_pntr_);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : }</a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/MD_LinearExpansionPES.cpp.func-sort-c.html b/coverage/ves/MD_LinearExpansionPES.cpp.func-sort-c.html
new file mode 100644
index 0000000000..40cf64097f
--- /dev/null
+++ b/coverage/ves/MD_LinearExpansionPES.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/MD_LinearExpansionPES.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - MD_LinearExpansionPES.cpp<span style="font-size: 80%;"> (<a href="MD_LinearExpansionPES.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">336</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MD_LinearExpansionPES.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#135">_ZNK4PLMD3ves21MD_LinearExpansionPES11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#209">_ZN4PLMD3ves21MD_LinearExpansionPES4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#148">_ZN4PLMD3ves12_GLOBAL__N_131MD_LinearExpansionPESRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#175">_ZN4PLMD3ves21MD_LinearExpansionPESC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#184">_ZN4PLMD3ves21MD_LinearExpansionPES11calc_energyERKSt6vectorINS_13VectorGenericILj3EEESaIS4_EERS6_</a></td>
+              <td class="coverFnHi">3939</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#200">_ZN4PLMD3ves21MD_LinearExpansionPES9calc_tempERKSt6vectorINS_13VectorGenericILj3EEESaIS4_EE</a></td>
+              <td class="coverFnHi">3939</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#148">_ZN4PLMD3ves12_GLOBAL__N_131MD_LinearExpansionPESRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#148">_ZN4PLMD3ves12_GLOBAL__N_131MD_LinearExpansionPESRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#150">_ZN4PLMD3ves21MD_LinearExpansionPES16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/MD_LinearExpansionPES.cpp.func.html b/coverage/ves/MD_LinearExpansionPES.cpp.func.html
new file mode 100644
index 0000000000..3d291a231c
--- /dev/null
+++ b/coverage/ves/MD_LinearExpansionPES.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/MD_LinearExpansionPES.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - MD_LinearExpansionPES.cpp<span style="font-size: 80%;"> (<a href="MD_LinearExpansionPES.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">336</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MD_LinearExpansionPES.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#148">_ZN4PLMD3ves12_GLOBAL__N_131MD_LinearExpansionPESRegisterMe6createERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#148">_ZN4PLMD3ves12_GLOBAL__N_131MD_LinearExpansionPESRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#148">_ZN4PLMD3ves12_GLOBAL__N_131MD_LinearExpansionPESRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#184">_ZN4PLMD3ves21MD_LinearExpansionPES11calc_energyERKSt6vectorINS_13VectorGenericILj3EEESaIS4_EERS6_</a></td>
+              <td class="coverFnHi">3939</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#150">_ZN4PLMD3ves21MD_LinearExpansionPES16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#209">_ZN4PLMD3ves21MD_LinearExpansionPES4mainEP8_IO_FILES3_RNS_12CommunicatorE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#200">_ZN4PLMD3ves21MD_LinearExpansionPES9calc_tempERKSt6vectorINS_13VectorGenericILj3EEESaIS4_EE</a></td>
+              <td class="coverFnHi">3939</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#175">_ZN4PLMD3ves21MD_LinearExpansionPESC2ERKNS_13CLToolOptionsE</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MD_LinearExpansionPES.cpp.gcov.html#135">_ZNK4PLMD3ves21MD_LinearExpansionPES11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/MD_LinearExpansionPES.cpp.gcov.html b/coverage/ves/MD_LinearExpansionPES.cpp.gcov.html
new file mode 100644
index 0000000000..1fba1b9ef7
--- /dev/null
+++ b/coverage/ves/MD_LinearExpansionPES.cpp.gcov.html
@@ -0,0 +1,757 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/MD_LinearExpansionPES.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - MD_LinearExpansionPES.cpp<span style="font-size: 80%;"> (source / <a href="MD_LinearExpansionPES.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">326</td>
+            <td class="headerCovTableEntry">336</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;LinearBasisSetExpansion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;GridProjWeights.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;cltools/CLTool.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;cltools/CLToolRegister.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Vector.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Random.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;tools/FileBase.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="39"><span class="lineNum">      39 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : #include &lt;string&gt;</a>
+<a name="42"><span class="lineNum">      42 </span>            : #include &lt;cstdio&gt;</a>
+<a name="43"><span class="lineNum">      43 </span>            : #include &lt;cmath&gt;</a>
+<a name="44"><span class="lineNum">      44 </span>            : #include &lt;vector&gt;</a>
+<a name="45"><span class="lineNum">      45 </span>            : #include &lt;iostream&gt;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : #ifdef __PLUMED_HAS_MPI</a>
+<a name="48"><span class="lineNum">      48 </span>            : #include &lt;mpi.h&gt;</a>
+<a name="49"><span class="lineNum">      49 </span>            : #endif</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : namespace PLMD {</a>
+<a name="53"><span class="lineNum">      53 </span>            : namespace ves {</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : //+PLUMEDOC VES_TOOLS ves_md_linearexpansion</a>
+<a name="56"><span class="lineNum">      56 </span>            : /*</a>
+<a name="57"><span class="lineNum">      57 </span>            : Simple MD code for dynamics on a potential energy surface given by a linear basis set expansion.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : This is simple MD code that allows running dynamics of a single particle on a</a>
+<a name="60"><span class="lineNum">      60 </span>            : potential energy surface given by some linear basis set expansion in one to three</a>
+<a name="61"><span class="lineNum">      61 </span>            : dimensions.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : It is possible to run more than one replica of the system in parallel.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \par Examples</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : In the following example we perform dynamics on the</a>
+<a name="68"><span class="lineNum">      68 </span>            : Wolfe-Quapp potential that is defined as</a>
+<a name="69"><span class="lineNum">      69 </span>            : \f[</a>
+<a name="70"><span class="lineNum">      70 </span>            : U(x,y) = x^4 + y^4 - 2 x^2 - 4 y^2 + xy + 0.3 x + 0.1 y</a>
+<a name="71"><span class="lineNum">      71 </span>            : \f]</a>
+<a name="72"><span class="lineNum">      72 </span>            : To define the potential we employ polynomial power basis</a>
+<a name="73"><span class="lineNum">      73 </span>            : functions (\ref BF_POWERS). The input file is given as</a>
+<a name="74"><span class="lineNum">      74 </span>            : \verbatim</a>
+<a name="75"><span class="lineNum">      75 </span>            : nstep             10000</a>
+<a name="76"><span class="lineNum">      76 </span>            : tstep             0.005</a>
+<a name="77"><span class="lineNum">      77 </span>            : temperature       1.0</a>
+<a name="78"><span class="lineNum">      78 </span>            : friction          10.0</a>
+<a name="79"><span class="lineNum">      79 </span>            : random_seed       4525</a>
+<a name="80"><span class="lineNum">      80 </span>            : plumed_input      plumed.dat</a>
+<a name="81"><span class="lineNum">      81 </span>            : dimension         2</a>
+<a name="82"><span class="lineNum">      82 </span>            : replicas          1</a>
+<a name="83"><span class="lineNum">      83 </span>            : basis_functions_1 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0</a>
+<a name="84"><span class="lineNum">      84 </span>            : basis_functions_2 BF_POWERS ORDER=4 MINIMUM=-3.0 MAXIMUM=+3.0</a>
+<a name="85"><span class="lineNum">      85 </span>            : input_coeffs       pot_coeffs_input.data</a>
+<a name="86"><span class="lineNum">      86 </span>            : initial_position   -1.174,+1.477</a>
+<a name="87"><span class="lineNum">      87 </span>            : output_potential        potential.data</a>
+<a name="88"><span class="lineNum">      88 </span>            : output_potential_grid   150</a>
+<a name="89"><span class="lineNum">      89 </span>            : output_histogram        histogram.data</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : # Wolfe-Quapp potential given by the equation</a>
+<a name="92"><span class="lineNum">      92 </span>            : # U(x,y) = x**4 + y**4 - 2.0*x**2 - 4.0*y**2 + x*y + 0.3*x + 0.1*y</a>
+<a name="93"><span class="lineNum">      93 </span>            : # Minima around (-1.174,1.477); (-0.831,-1.366); (1.124,-1.486)</a>
+<a name="94"><span class="lineNum">      94 </span>            : # Maxima around (0.100,0.050)</a>
+<a name="95"><span class="lineNum">      95 </span>            : # Saddle points around (-1.013,-0.036); (0.093,0.174); (-0.208,-1.407)</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endverbatim</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : This input is then run by using the following command.</a>
+<a name="99"><span class="lineNum">      99 </span>            : \verbatim</a>
+<a name="100"><span class="lineNum">     100 </span>            : plumed ves_md_linearexpansion input</a>
+<a name="101"><span class="lineNum">     101 </span>            : \endverbatim</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : The corresponding pot_coeffs_input.data file is</a>
+<a name="104"><span class="lineNum">     104 </span>            : \verbatim</a>
+<a name="105"><span class="lineNum">     105 </span>            : #! FIELDS idx_dim1 idx_dim2 pot.coeffs index description</a>
+<a name="106"><span class="lineNum">     106 </span>            : #! SET type LinearBasisSet</a>
+<a name="107"><span class="lineNum">     107 </span>            : #! SET ndimensions  2</a>
+<a name="108"><span class="lineNum">     108 </span>            : #! SET ncoeffs_total  25</a>
+<a name="109"><span class="lineNum">     109 </span>            : #! SET shape_dim1  5</a>
+<a name="110"><span class="lineNum">     110 </span>            : #! SET shape_dim2  5</a>
+<a name="111"><span class="lineNum">     111 </span>            :        0       0         0.0000000000000000e+00       0  1*1</a>
+<a name="112"><span class="lineNum">     112 </span>            :        1       0         0.3000000000000000e+00       1  s^1*1</a>
+<a name="113"><span class="lineNum">     113 </span>            :        2       0        -2.0000000000000000e+00       2  s^2*1</a>
+<a name="114"><span class="lineNum">     114 </span>            :        4       0         1.0000000000000000e+00       4  s^4*1</a>
+<a name="115"><span class="lineNum">     115 </span>            :        0       1         0.1000000000000000e+00       5  1*s^1</a>
+<a name="116"><span class="lineNum">     116 </span>            :        1       1        +1.0000000000000000e+00       6  s^1*s^1</a>
+<a name="117"><span class="lineNum">     117 </span>            :        0       2        -4.0000000000000000e+00      10  1*s^2</a>
+<a name="118"><span class="lineNum">     118 </span>            :        0       4         1.0000000000000000e+00      20  1*s^4</a>
+<a name="119"><span class="lineNum">     119 </span>            : #!-------------------</a>
+<a name="120"><span class="lineNum">     120 </span>            : \endverbatim</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : One then uses the (x,y) position of the particle as CVs by using the \ref POSITION</a>
+<a name="123"><span class="lineNum">     123 </span>            : action as shown in the following PLUMED input</a>
+<a name="124"><span class="lineNum">     124 </span>            : \plumedfile</a>
+<a name="125"><span class="lineNum">     125 </span>            : p: POSITION ATOM=1</a>
+<a name="126"><span class="lineNum">     126 </span>            : ene: ENERGY</a>
+<a name="127"><span class="lineNum">     127 </span>            : PRINT ARG=p.x,p.y,ene FILE=colvar.data FMT=%8.4f</a>
+<a name="128"><span class="lineNum">     128 </span>            : \endplumedfile</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : */</a>
+<a name="133"><span class="lineNum">     133 </span>            : //+ENDPLUMEDOC</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : class MD_LinearExpansionPES : public PLMD::CLTool {</a>
+<a name="136"><span class="lineNum">     136 </span>            : public:</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          4 :   std::string description() const override {return &quot;MD of a one particle on a linear expansion PES&quot;;}</span></a>
+<a name="138"><span class="lineNum">     138 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="139"><span class="lineNum">     139 </span>            :   explicit MD_LinearExpansionPES( const CLToolOptions&amp; co );</a>
+<a name="140"><span class="lineNum">     140 </span>            :   int main( FILE* in, FILE* out, PLMD::Communicator&amp; pc) override;</a>
+<a name="141"><span class="lineNum">     141 </span>            : private:</a>
+<a name="142"><span class="lineNum">     142 </span>            :   size_t dim;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::string dim_string_prefix;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::unique_ptr&lt;LinearBasisSetExpansion&gt; potential_expansion_pntr;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   //</a>
+<a name="146"><span class="lineNum">     146 </span>            :   double calc_energy( const std::vector&lt;Vector&gt;&amp;, std::vector&lt;Vector&gt;&amp; );</a>
+<a name="147"><span class="lineNum">     147 </span>            :   double calc_temp( const std::vector&lt;Vector&gt;&amp; );</a>
+<a name="148"><span class="lineNum">     148 </span>            : };</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">      12548 : PLUMED_REGISTER_CLTOOL(MD_LinearExpansionPES,&quot;ves_md_linearexpansion&quot;)</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       4168 : void MD_LinearExpansionPES::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">       4168 :   CLTool::registerKeywords( keys );</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;nstep&quot;,&quot;10&quot;,&quot;The number of steps of dynamics you want to run.&quot;);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;tstep&quot;,&quot;0.005&quot;,&quot;The integration timestep.&quot;);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;temperature&quot;,&quot;1.0&quot;,&quot;The temperature to perform the simulation at. For multiple replica you can give a separate value for each replica.&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;friction&quot;,&quot;10.&quot;,&quot;The friction of the Langevin thermostat. For multiple replica you can give a separate value for each replica.&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;random_seed&quot;,&quot;5293818&quot;,&quot;Value of random number seed.&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;plumed_input&quot;,&quot;plumed.dat&quot;,&quot;The name of the plumed input file(s). For multiple replica you can give a separate value for each replica.&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;dimension&quot;,&quot;1&quot;,&quot;Number of dimensions, supports 1 to 3.&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;initial_position&quot;,&quot;Initial position of the particle. For multiple replica you can give a separate value for each replica.&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;replicas&quot;,&quot;1&quot;,&quot;Number of replicas.&quot;);</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;basis_functions_1&quot;,&quot;Basis functions for dimension 1.&quot;);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;basis_functions_2&quot;,&quot;Basis functions for dimension 2 if needed.&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;basis_functions_3&quot;,&quot;Basis functions for dimension 3 if needed.&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;input_coeffs&quot;,&quot;potential-coeffs.in.data&quot;,&quot;Filename of the input coefficient file for the potential. For multiple replica you can give a separate value for each replica.&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;output_coeffs&quot;,&quot;potential-coeffs.out.data&quot;,&quot;Filename of the output coefficient file for the potential.&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;output_coeffs_fmt&quot;,&quot;%30.16e&quot;,&quot;Format of the output coefficient file for the potential. Useful for regtests.&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;coeffs_prefactor&quot;,&quot;prefactor for multiplying the coefficients with. For multiple replica you can give a separate value for each replica.&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       8336 :   keys.add(&quot;optional&quot;,&quot;template_coeffs_file&quot;,&quot;only generate a template coefficient file with the filename given and exit.&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;output_potential_grid&quot;,&quot;100&quot;,&quot;The number of grid points used for the potential and histogram output files.&quot;);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;output_potential&quot;,&quot;potential.data&quot;,&quot;Filename of the potential output file.&quot;);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       8336 :   keys.add(&quot;compulsory&quot;,&quot;output_histogram&quot;,&quot;histogram.data&quot;,&quot;Filename of the histogram output file.&quot;);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       4168 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         44 : MD_LinearExpansionPES::MD_LinearExpansionPES( const CLToolOptions&amp; co ):</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   CLTool(co),</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         44 :   dim(0),</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         44 :   dim_string_prefix(&quot;dim&quot;)</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         44 :   inputdata=ifile; //commandline;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         44 : }</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : inline</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       3939 : double MD_LinearExpansionPES::calc_energy( const std::vector&lt;Vector&gt;&amp; pos, std::vector&lt;Vector&gt;&amp; forces) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">       3939 :   std::vector&lt;double&gt; pos_tmp(dim);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">       3939 :   std::vector&lt;double&gt; forces_tmp(dim,0.0);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">       8585 :   for(unsigned int j=0; j&lt;dim; ++j) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">       4646 :     pos_tmp[j]=pos[0][j];</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   }</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       3939 :   bool all_inside = true;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       3939 :   double potential = potential_expansion_pntr-&gt;getBiasAndForces(pos_tmp,all_inside,forces_tmp);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">       8585 :   for(unsigned int j=0; j&lt;dim; ++j) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       4646 :     forces[0][j] = forces_tmp[j];</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       3939 :   return potential;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : inline</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       3939 : double MD_LinearExpansionPES::calc_temp( const std::vector&lt;Vector&gt;&amp; vel) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   double total_KE=0.0;</a>
+<a name="204"><span class="lineNum">     204 </span>            :   //! Double the total kinetic energy of the system</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       8585 :   for(unsigned int j=0; j&lt;dim; ++j) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">       4646 :     total_KE+=vel[0][j]*vel[0][j];</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">       3939 :   return total_KE / (double) dim; // total_KE is actually 2*KE</span></a>
+<a name="209"><span class="lineNum">     209 </span>            : }</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         40 : int MD_LinearExpansionPES::main( FILE* in, FILE* out, PLMD::Communicator&amp; pc) {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   int plumedWantsToStop;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         40 :   Random random;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   unsigned int stepWrite=1000;</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         40 :   std::unique_ptr&lt;PLMD::PlumedMain&gt; plumed;</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :   size_t replicas;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   unsigned int coresPerReplica;</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         40 :   parse(&quot;replicas&quot;,replicas);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         40 :   if(replicas==1) {</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          9 :     coresPerReplica = pc.Get_size();</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   } else {</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         31 :     if(pc.Get_size()%replicas!=0) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 :       error(&quot;the number of MPI processes is not a multiple of the number of replicas.&quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :     }</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         31 :     coresPerReplica = pc.Get_size()/replicas;</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   // create intra and inter communicators</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         40 :   Communicator intra, inter;</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         40 :   if(Communicator::initialized()) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         33 :     int iworld=(pc.Get_rank() / coresPerReplica);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         33 :     pc.Split(iworld,0,intra);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         33 :     pc.Split(intra.Get_rank(),0,inter);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            :   long long unsigned int nsteps;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         40 :   parse(&quot;nstep&quot;,nsteps);</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   double tstep;</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         40 :   parse(&quot;tstep&quot;,tstep);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :   // initialize to solve a cppcheck 1.86 warning</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         40 :   double temp=0.0;</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         40 :   std::vector&lt;double&gt; temps_vec(0);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         80 :   parseVector(&quot;temperature&quot;,temps_vec);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         40 :   if(temps_vec.size()==1) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         36 :     temp = temps_vec[0];</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   }</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">          4 :   else if(replicas &gt; 1 &amp;&amp; temps_vec.size()==replicas) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">          4 :     temp = temps_vec[inter.Get_rank()];</span></a>
+<a name="250"><span class="lineNum">     250 </span>            :   }</a>
+<a name="251"><span class="lineNum">     251 </span>            :   else {</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 :     error(&quot;problem with temperature keyword, you need to give either one value or a value for each replica.&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   }</a>
+<a name="254"><span class="lineNum">     254 </span>            :   //</a>
+<a name="255"><span class="lineNum">     255 </span>            :   double friction;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         40 :   std::vector&lt;double&gt; frictions_vec(0);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         80 :   parseVector(&quot;friction&quot;,frictions_vec);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         40 :   if(frictions_vec.size()==1) {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         36 :     friction = frictions_vec[0];</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :   }</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          4 :   else if(frictions_vec.size()==replicas) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          4 :     friction = frictions_vec[inter.Get_rank()];</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   }</a>
+<a name="264"><span class="lineNum">     264 </span>            :   else {</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :     error(&quot;problem with friction keyword, you need to give either one value or a value for each replica.&quot;);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :   }</a>
+<a name="267"><span class="lineNum">     267 </span>            :   //</a>
+<a name="268"><span class="lineNum">     268 </span>            :   int seed;</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         40 :   std::vector&lt;int&gt; seeds_vec(0);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         40 :   parseVector(&quot;random_seed&quot;,seeds_vec);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         92 :   for(unsigned int i=0; i&lt;seeds_vec.size(); i++) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         52 :     if(seeds_vec[i]&gt;0) {seeds_vec[i] = -seeds_vec[i];}</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :   }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         40 :   if(replicas==1) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">          9 :     if(seeds_vec.size()&gt;1) {error(&quot;problem with random_seed keyword, for a single replica you should only give one value&quot;);}</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          9 :     seed = seeds_vec[0];</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   }</a>
+<a name="278"><span class="lineNum">     278 </span>            :   else {</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         31 :     if(seeds_vec.size()!=1 &amp;&amp; seeds_vec.size()!=replicas) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :       error(&quot;problem with random_seed keyword, for multiple replicas you should give either one value or a separate value for each replica&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :     }</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         31 :     if(seeds_vec.size()==1) {</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         27 :       seeds_vec.resize(replicas);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">        109 :       for(unsigned int i=1; i&lt;seeds_vec.size(); i++) {seeds_vec[i] = seeds_vec[0] + i;}</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :     }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         31 :     seed = seeds_vec[inter.Get_rank()];</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :   }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            :   //</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         80 :   parse(&quot;dimension&quot;,dim);</span></a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            :   std::vector&lt;std::string&gt; plumed_inputfiles;</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         80 :   parseVector(&quot;plumed_input&quot;,plumed_inputfiles);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">         40 :   if(plumed_inputfiles.size()!=1 &amp;&amp; plumed_inputfiles.size()!=replicas) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :     error(&quot;in plumed_input you should either give one file or separate files for each replica.&quot;);</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :   }</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">         40 :   std::vector&lt;Vector&gt; initPos(replicas);</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :   std::vector&lt;double&gt; initPosTmp;</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">         80 :   parseVector(&quot;initial_position&quot;,initPosTmp);</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">         40 :   if(initPosTmp.size()==dim) {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         48 :     for(unsigned int i=0; i&lt;replicas; i++) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         72 :       for(unsigned int k=0; k&lt;dim; k++) {</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         38 :         initPos[i][k]=initPosTmp[k];</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :       }</a>
+<a name="306"><span class="lineNum">     306 </span>            :     }</a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         26 :   else if(initPosTmp.size()==dim*replicas) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        126 :     for(unsigned int i=0; i&lt;replicas; i++) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        216 :       for(unsigned int k=0; k&lt;dim; k++) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        116 :         initPos[i][k]=initPosTmp[i*dim+k];</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :       }</a>
+<a name="313"><span class="lineNum">     313 </span>            :     }</a>
+<a name="314"><span class="lineNum">     314 </span>            :   }</a>
+<a name="315"><span class="lineNum">     315 </span>            :   else {</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :     error(&quot;problem with initial_position keyword, you need to give either one value or a value for each replica.&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :   }</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         79 :   auto deleter=[](FILE* f) { fclose(f); };</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">         40 :   FILE* file_dummy = fopen(&quot;/dev/null&quot;,&quot;w+&quot;);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">         40 :   plumed_assert(file_dummy);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   // call fclose when file_dummy_deleter goes out of scope</a>
+<a name="323"><span class="lineNum">     323 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; file_dummy_deleter(file_dummy,deleter);</a>
+<a name="324"><span class="lineNum">     324 </span>            :   // Note: this should be declared before plumed_bf to make sure the file is closed after plumed_bf has been destroyed</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         40 :   auto plumed_bf = Tools::make_unique&lt;PLMD::PlumedMain&gt;();</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         40 :   unsigned int nn=1;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         80 :   plumed_bf-&gt;cmd(&quot;setNatoms&quot;,&amp;nn);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         80 :   plumed_bf-&gt;cmd(&quot;setLog&quot;,file_dummy);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         80 :   plumed_bf-&gt;cmd(&quot;init&quot;,&amp;nn);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         40 :   std::vector&lt;BasisFunctions*&gt; basisf_pntrs(dim);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         40 :   std::vector&lt;std::string&gt; basisf_keywords(dim);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         40 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; args(dim);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         40 :   std::vector&lt;bool&gt; periodic(dim);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">         40 :   std::vector&lt;double&gt; interval_min(dim);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         40 :   std::vector&lt;double&gt; interval_max(dim);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         40 :   std::vector&lt;double&gt; interval_range(dim);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         88 :   for(unsigned int i=0; i&lt;dim; i++) {</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :     std::string bf_keyword;</a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         48 :     std::string is; Tools::convert(i+1,is);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         96 :     parse(&quot;basis_functions_&quot;+is,bf_keyword);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         48 :     if(bf_keyword.size()==0) {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :       error(&quot;basis_functions_&quot;+is+&quot; is needed&quot;);</span></a>
+<a name="344"><span class="lineNum">     344 </span>            :     }</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         48 :     if(bf_keyword.at(0)=='{' &amp;&amp; bf_keyword.at(bf_keyword.size()-1)=='}') {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          4 :       bf_keyword = bf_keyword.substr(1,bf_keyword.size()-2);</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :     }</a>
+<a name="348"><span class="lineNum">     348 </span>            :     basisf_keywords[i] = bf_keyword;</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         96 :     plumed_bf-&gt;readInputLine(bf_keyword+&quot; LABEL=&quot;+dim_string_prefix+is);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         48 :     basisf_pntrs[i] = plumed_bf-&gt;getActionSet().selectWithLabel&lt;BasisFunctions*&gt;(dim_string_prefix+is);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         96 :     args[i] = Tools::make_unique&lt;Value&gt;(nullptr,dim_string_prefix+is,false);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         48 :     args[i]-&gt;setNotPeriodic();</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         48 :     periodic[i] = basisf_pntrs[i]-&gt;arePeriodic();</span></a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         48 :     interval_min[i] = basisf_pntrs[i]-&gt;intervalMin();</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         48 :     interval_max[i] = basisf_pntrs[i]-&gt;intervalMax();</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         48 :     interval_range[i] = basisf_pntrs[i]-&gt;intervalMax()-basisf_pntrs[i]-&gt;intervalMin();</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   }</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         40 :   Communicator comm_dummy;</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">         80 :   auto coeffs_pntr = Tools::make_unique&lt;CoeffsVector&gt;(&quot;pot.coeffs&quot;,Tools::unique2raw(args),basisf_pntrs,comm_dummy,false);</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         80 :   potential_expansion_pntr = Tools::make_unique&lt;LinearBasisSetExpansion&gt;(&quot;potential&quot;,1.0/temp,comm_dummy,Tools::unique2raw(args),basisf_pntrs,coeffs_pntr.get());</span></a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">         40 :   std::string template_coeffs_fname=&quot;&quot;;</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         80 :   parse(&quot;template_coeffs_file&quot;,template_coeffs_fname);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         40 :   if(template_coeffs_fname.size()&gt;0) {</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          1 :     OFile ofile_coeffstmpl;</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          1 :     ofile_coeffstmpl.link(pc);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          1 :     ofile_coeffstmpl.open(template_coeffs_fname);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          1 :     coeffs_pntr-&gt;writeToFile(ofile_coeffstmpl,true);</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          1 :     ofile_coeffstmpl.close();</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :     std::printf(&quot;Only generating a template coefficient file - Should stop now.&quot;);</a>
+<a name="371"><span class="lineNum">     371 </span>            :     return 0;</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          1 :   }</span></a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         39 :   std::vector&lt;std::string&gt; input_coeffs_fnames(0);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         78 :   parseVector(&quot;input_coeffs&quot;,input_coeffs_fnames);</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :   std::string input_coeffs_fname;</a>
+<a name="377"><span class="lineNum">     377 </span>            :   bool diff_input_coeffs = false;</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         39 :   if(input_coeffs_fnames.size()==1) {</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :     input_coeffs_fname = input_coeffs_fnames[0];</a>
+<a name="380"><span class="lineNum">     380 </span>            :   }</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          9 :   else if(replicas &gt; 1 &amp;&amp; input_coeffs_fnames.size()==replicas) {</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :     diff_input_coeffs = true;</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          9 :     input_coeffs_fname = input_coeffs_fnames[inter.Get_rank()];</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span>            :   else {</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :     error(&quot;problem with coeffs_file keyword, you need to give either one value or a value for each replica.&quot;);</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :   }</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         39 :   coeffs_pntr-&gt;readFromFile(input_coeffs_fname,true,true);</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">         39 :   std::vector&lt;double&gt; coeffs_prefactors(0);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         78 :   parseVector(&quot;coeffs_prefactor&quot;,coeffs_prefactors);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">         39 :   if(coeffs_prefactors.size()&gt;0) {</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :     double coeffs_prefactor = 1.0;</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          7 :     if(coeffs_prefactors.size()==1) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          3 :       coeffs_prefactor = coeffs_prefactors[0];</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :     }</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          4 :     else if(replicas &gt; 1 &amp;&amp; coeffs_prefactors.size()==replicas) {</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :       diff_input_coeffs = true;</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          4 :       coeffs_prefactor = coeffs_prefactors[inter.Get_rank()];</span></a>
+<a name="399"><span class="lineNum">     399 </span>            :     }</a>
+<a name="400"><span class="lineNum">     400 </span>            :     else {</a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineNoCov">          0 :       error(&quot;problem with coeffs_prefactor keyword, you need to give either one value or a value for each replica.&quot;);</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :     }</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          7 :     coeffs_pntr-&gt;scaleAllValues(coeffs_prefactor);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :   }</a>
+<a name="405"><span class="lineNum">     405 </span>            :   unsigned int pot_grid_bins;</a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         78 :   parse(&quot;output_potential_grid&quot;,pot_grid_bins);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">         39 :   potential_expansion_pntr-&gt;setGridBins(pot_grid_bins);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         39 :   potential_expansion_pntr-&gt;setupBiasGrid(false);</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">         39 :   potential_expansion_pntr-&gt;updateBiasGrid();</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         39 :   potential_expansion_pntr-&gt;setBiasMinimumToZero();</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         39 :   potential_expansion_pntr-&gt;updateBiasGrid();</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">         39 :   OFile ofile_potential;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">         39 :   ofile_potential.link(pc);</span></a>
+<a name="415"><span class="lineNum">     415 </span>            :   std::string output_potential_fname;</a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         39 :   parse(&quot;output_potential&quot;,output_potential_fname);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         39 :   if(diff_input_coeffs) {</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         13 :     ofile_potential.link(intra);</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :     std::string suffix;</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">         13 :     Tools::convert(inter.Get_rank(),suffix);</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         26 :     output_potential_fname = FileBase::appendSuffix(output_potential_fname,&quot;.&quot;+suffix);</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :   }</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">         39 :   ofile_potential.open(output_potential_fname);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         39 :   potential_expansion_pntr-&gt;writeBiasGridToFile(ofile_potential);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         39 :   ofile_potential.close();</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         39 :   if(dim&gt;1) {</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">         21 :     for(unsigned int i=0; i&lt;dim; i++) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         14 :       std::string is; Tools::convert(i+1,is);</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">         14 :       std::vector&lt;std::string&gt; proj_arg(1);</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">         14 :       proj_arg[0] = dim_string_prefix+is;</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">         14 :       auto Fw = Tools::make_unique&lt;FesWeight&gt;(1/temp);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         14 :       Grid proj_grid = (potential_expansion_pntr-&gt;getPntrToBiasGrid())-&gt;project(proj_arg,Fw.get());</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         14 :       proj_grid.setMinToZero();</span></a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">         28 :       std::string output_potential_proj_fname = FileBase::appendSuffix(output_potential_fname,&quot;.&quot;+dim_string_prefix+is);</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">         14 :       OFile ofile_potential_proj;</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">         14 :       ofile_potential_proj.link(pc);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">         14 :       ofile_potential_proj.open(output_potential_proj_fname);</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         14 :       proj_grid.writeToFile(ofile_potential_proj);</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">         14 :       ofile_potential_proj.close();</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">         28 :     }</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :   }</a>
+<a name="443"><span class="lineNum">     443 </span>            : </a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">         39 :   Grid histo_grid(*potential_expansion_pntr-&gt;getPntrToBiasGrid());</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">         78 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(&amp;histo_grid);</span></a>
+<a name="447"><span class="lineNum">     447 </span>            :   double norm=0.0;</a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">     169278 :   for(Grid::index_t i=0; i&lt;histo_grid.getSize(); i++) {</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">     169239 :     double value = integration_weights[i]*exp(-histo_grid.getValue(i)/temp);</span></a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">     169239 :     norm += value;</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">     169239 :     histo_grid.setValue(i,value);</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :   }</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         39 :   histo_grid.scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">         39 :   OFile ofile_histogram;</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         39 :   ofile_histogram.link(pc);</span></a>
+<a name="456"><span class="lineNum">     456 </span>            :   std::string output_histogram_fname;</a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         39 :   parse(&quot;output_histogram&quot;,output_histogram_fname);</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">         39 :   if(diff_input_coeffs || temps_vec.size()&gt;1) {</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         17 :     ofile_histogram.link(intra);</span></a>
+<a name="460"><span class="lineNum">     460 </span>            :     std::string suffix;</a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">         17 :     Tools::convert(inter.Get_rank(),suffix);</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">         34 :     output_histogram_fname = FileBase::appendSuffix(output_histogram_fname,&quot;.&quot;+suffix);</span></a>
+<a name="463"><span class="lineNum">     463 </span>            :   }</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         39 :   ofile_histogram.open(output_histogram_fname);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">         39 :   histo_grid.writeToFile(ofile_histogram);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         39 :   ofile_histogram.close();</span></a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   std::string output_coeffs_fname;</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">         78 :   parse(&quot;output_coeffs&quot;,output_coeffs_fname);</span></a>
+<a name="470"><span class="lineNum">     470 </span>            :   std::string output_coeffs_fmt;</a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">         78 :   parse(&quot;output_coeffs_fmt&quot;,output_coeffs_fmt);</span></a>
+<a name="472"><span class="lineNum">     472 </span>            :   coeffs_pntr-&gt;setOutputFmt(output_coeffs_fmt);</a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         39 :   OFile ofile_coeffsout;</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         39 :   ofile_coeffsout.link(pc);</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">         39 :   if(diff_input_coeffs) {</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">         13 :     ofile_coeffsout.link(intra);</span></a>
+<a name="477"><span class="lineNum">     477 </span>            :     std::string suffix;</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">         13 :     Tools::convert(inter.Get_rank(),suffix);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">         26 :     output_coeffs_fname = FileBase::appendSuffix(output_coeffs_fname,&quot;.&quot;+suffix);</span></a>
+<a name="480"><span class="lineNum">     480 </span>            :   }</a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         39 :   ofile_coeffsout.open(output_coeffs_fname);</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">         39 :   coeffs_pntr-&gt;writeToFile(ofile_coeffsout,true);</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         39 :   ofile_coeffsout.close();</span></a>
+<a name="484"><span class="lineNum">     484 </span>            : </a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         39 :   if(pc.Get_rank() == 0) {</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Replicas                              %zu\n&quot;,replicas);</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     std::fprintf(out,&quot;Cores per replica                     %u\n&quot;,coresPerReplica);</a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Number of steps                       %llu\n&quot;,nsteps);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Timestep                              %f\n&quot;,tstep);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Temperature                           %f&quot;,temps_vec[0]);</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">         18 :     for(unsigned int i=1; i&lt;temps_vec.size(); i++) {std::fprintf(out,&quot;,%f&quot;,temps_vec[i]);}</span></a>
+<a name="492"><span class="lineNum">     492 </span>            :     std::fprintf(out,&quot;\n&quot;);</a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Friction                              %f&quot;,frictions_vec[0]);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         18 :     for(unsigned int i=1; i&lt;frictions_vec.size(); i++) {std::fprintf(out,&quot;,%f&quot;,frictions_vec[i]);}</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     std::fprintf(out,&quot;\n&quot;);</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Random seed                           %d&quot;,seeds_vec[0]);</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         38 :     for(unsigned int i=1; i&lt;seeds_vec.size(); i++) {std::fprintf(out,&quot;,%d&quot;,seeds_vec[i]);}</span></a>
+<a name="498"><span class="lineNum">     498 </span>            :     std::fprintf(out,&quot;\n&quot;);</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">         15 :     std::fprintf(out,&quot;Dimensions                            %zu\n&quot;,dim);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">         34 :     for(unsigned int i=0; i&lt;dim; i++) {</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">         19 :       std::fprintf(out,&quot;Basis Function %u                      %s\n&quot;,i+1,basisf_keywords[i].c_str());</span></a>
+<a name="502"><span class="lineNum">     502 </span>            :     }</a>
+<a name="503"><span class="lineNum">     503 </span>            :     std::fprintf(out,&quot;PLUMED input                          %s&quot;,plumed_inputfiles[0].c_str());</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         16 :     for(unsigned int i=1; i&lt;plumed_inputfiles.size(); i++) {std::fprintf(out,&quot;,%s&quot;,plumed_inputfiles[i].c_str());}</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     std::fprintf(out,&quot;\n&quot;);</a>
+<a name="506"><span class="lineNum">     506 </span>            :     std::fprintf(out,&quot;kBoltzmann taken as 1, use NATURAL_UNITS in the plumed input\n&quot;);</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">         15 :     if(diff_input_coeffs) {std::fprintf(out,&quot;using different coefficients for each replica\n&quot;);}</span></a>
+<a name="508"><span class="lineNum">     508 </span>            :   }</a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         78 :   plumed=Tools::make_unique&lt;PLMD::PlumedMain&gt;();</span></a>
+<a name="512"><span class="lineNum">     512 </span>            : </a>
+<a name="513"><span class="lineNum">     513 </span>            : </a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         39 :   if(plumed) {</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         39 :     int s=sizeof(double);</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setRealPrecision&quot;,&amp;s);</span></a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         39 :     if(replicas&gt;1) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         31 :       if (Communicator::initialized()) {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         93 :         plumed-&gt;cmd(&quot;GREX setMPIIntracomm&quot;,&amp;intra.Get_comm());</span></a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">         31 :         if (intra.Get_rank()==0) {</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         93 :           plumed-&gt;cmd(&quot;GREX setMPIIntercomm&quot;,&amp;inter.Get_comm());</span></a>
+<a name="523"><span class="lineNum">     523 </span>            :         }</a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         62 :         plumed-&gt;cmd(&quot;GREX init&quot;);</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">         93 :         plumed-&gt;cmd(&quot;setMPIComm&quot;,&amp;intra.Get_comm());</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :       } else {</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :         error(&quot;More than 1 replica but no MPI&quot;);</span></a>
+<a name="528"><span class="lineNum">     528 </span>            :       }</a>
+<a name="529"><span class="lineNum">     529 </span>            :     } else {</a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">         12 :       if(Communicator::initialized()) plumed-&gt;cmd(&quot;setMPIComm&quot;,&amp;pc.Get_comm());</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :     }</a>
+<a name="532"><span class="lineNum">     532 </span>            :   }</a>
+<a name="533"><span class="lineNum">     533 </span>            : </a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">         39 :   std::string plumed_logfile = &quot;plumed.log&quot;;</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         39 :   std::string stats_filename = &quot;stats.out&quot;;</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         39 :   std::string plumed_input = plumed_inputfiles[0];</span></a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineCov">         39 :   if(inter.Get_size()&gt;1) {</span></a>
+<a name="538"><span class="lineNum">     538 </span>            :     std::string suffix;</a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         31 :     Tools::convert(inter.Get_rank(),suffix);</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         62 :     plumed_logfile = FileBase::appendSuffix(plumed_logfile,&quot;.&quot;+suffix);</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">         62 :     stats_filename = FileBase::appendSuffix(stats_filename,&quot;.&quot;+suffix);</span></a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         31 :     if(plumed_inputfiles.size()&gt;1) {</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">          2 :       plumed_input = plumed_inputfiles[inter.Get_rank()];</span></a>
+<a name="544"><span class="lineNum">     544 </span>            :     }</a>
+<a name="545"><span class="lineNum">     545 </span>            :   }</a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         39 :   if(plumed) {</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setNoVirial&quot;);</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">         39 :     int natoms=1;</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setNatoms&quot;,&amp;natoms);</span></a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setMDEngine&quot;,&quot;mdrunner_linearexpansion&quot;);</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setTimestep&quot;,&amp;tstep);</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setPlumedDat&quot;,plumed_input.c_str());</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setLogFile&quot;,plumed_logfile.c_str());</span></a>
+<a name="555"><span class="lineNum">     555 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setKbT&quot;,&amp;temp);</span></a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">         39 :     double energyunits=1.0;</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setMDEnergyUnits&quot;,&amp;energyunits);</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;init&quot;);</span></a>
+<a name="559"><span class="lineNum">     559 </span>            :   }</a>
+<a name="560"><span class="lineNum">     560 </span>            : </a>
+<a name="561"><span class="lineNum">     561 </span>            :   // Setup random number generator</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         39 :   random.setSeed(seed);</span></a>
+<a name="563"><span class="lineNum">     563 </span>            : </a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         39 :   double potential, therm_eng=0; std::vector&lt;double&gt; masses(1,1);</span></a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         39 :   std::vector&lt;Vector&gt; positions(1), velocities(1), forces(1);</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         85 :   for(unsigned int k=0; k&lt;dim; k++) {</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         46 :     positions[0][k] = initPos[inter.Get_rank()][k];</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">         46 :     if(periodic[k]) {</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">          4 :       positions[0][k] = positions[0][k] - floor((positions[0][k]-interval_min[k])/interval_range[k])*interval_range[k];</span></a>
+<a name="570"><span class="lineNum">     570 </span>            :     }</a>
+<a name="571"><span class="lineNum">     571 </span>            :     else {</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         42 :       if(positions[0][k]&gt;interval_max[k]) {positions[0][k]=interval_max[k];}</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         42 :       if(positions[0][k]&lt;interval_min[k]) {positions[0][k]=interval_min[k];}</span></a>
+<a name="574"><span class="lineNum">     574 </span>            :     }</a>
+<a name="575"><span class="lineNum">     575 </span>            :   }</a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         85 :   for(unsigned k=0; k&lt;dim; ++k) {</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         46 :     velocities[0][k]=random.Gaussian() * sqrt( temp );</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :   }</a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">         39 :   potential=calc_energy(positions,forces); double ttt=calc_temp(velocities);</span></a>
+<a name="583"><span class="lineNum">     583 </span>            : </a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         39 :   FILE* fp=fopen(stats_filename.c_str(),&quot;w+&quot;);</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :   // call fclose when fp_deleter goes out of scope</a>
+<a name="586"><span class="lineNum">     586 </span>            :   std::unique_ptr&lt;FILE,decltype(deleter)&gt; fp_deleter(fp,deleter);</a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         39 :   double conserved = potential+1.5*ttt+therm_eng;</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :   //std::fprintf(fp,&quot;%d %f %f %f %f %f %f %f %f \n&quot;, 0, 0., positions[0][0], positions[0][1], positions[0][2], conserved, ttt, potential, therm_eng );</a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         39 :   if( intra.Get_rank()==0 ) {</span></a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         38 :     std::fprintf(fp,&quot;%d %f %f %f %f %f %f %f %f \n&quot;, 0, 0., positions[0][0], positions[0][1], positions[0][2], conserved, ttt, potential, therm_eng );</span></a>
+<a name="592"><span class="lineNum">     592 </span>            :   }</a>
+<a name="593"><span class="lineNum">     593 </span>            : </a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         39 :   if(plumed) {</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineCov">         39 :     long long unsigned int step_tmp = 0;</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setStepLongLong&quot;,&amp;step_tmp);</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setMasses&quot;,&amp;masses[0]);</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setForces&quot;,&amp;forces[0][0]);</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setEnergy&quot;,&amp;potential);</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;setPositions&quot;,&amp;positions[0][0]);</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">         78 :     plumed-&gt;cmd(&quot;calc&quot;);</span></a>
+<a name="602"><span class="lineNum">     602 </span>            :   }</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">       3939 :   for(long long unsigned int istep=0; istep&lt;nsteps; ++istep) {</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :     //if( istep%20==0 &amp;&amp; pc.Get_rank()==0 ) printf(&quot;Doing step %llu\n&quot;,istep);</a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span>            :     // Langevin thermostat</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">       3900 :     double lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">       3900 :     double lrand=sqrt((1.-lscale*lscale)*temp);</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">       8500 :     for(unsigned k=0; k&lt;dim; ++k) {</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">       4600 :       therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">       4600 :       velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       4600 :       therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :     }</a>
+<a name="615"><span class="lineNum">     615 </span>            : </a>
+<a name="616"><span class="lineNum">     616 </span>            :     // First step of velocity verlet</a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">       8500 :     for(unsigned k=0; k&lt;dim; ++k) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">       4600 :       velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">       4600 :       positions[0][k] = positions[0][k] + tstep*velocities[0][k];</span></a>
+<a name="620"><span class="lineNum">     620 </span>            : </a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">       4600 :       if(periodic[k]) {</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        400 :         positions[0][k] = positions[0][k] - floor((positions[0][k]-interval_min[k])/interval_range[k])*interval_range[k];</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :       }</a>
+<a name="624"><span class="lineNum">     624 </span>            :       else {</a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">       4200 :         if(positions[0][k]&gt;interval_max[k]) {</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">          7 :           positions[0][k]=interval_max[k];</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">          7 :           velocities[0][k]=-std::abs(velocities[0][k]);</span></a>
+<a name="628"><span class="lineNum">     628 </span>            :         }</a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">       4200 :         if(positions[0][k]&lt;interval_min[k]) {</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">          2 :           positions[0][k]=interval_min[k];</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">          2 :           velocities[0][k]=-std::abs(velocities[0][k]);</span></a>
+<a name="632"><span class="lineNum">     632 </span>            :         }</a>
+<a name="633"><span class="lineNum">     633 </span>            :       }</a>
+<a name="634"><span class="lineNum">     634 </span>            :     }</a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">       3900 :     potential=calc_energy(positions,forces);</span></a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">       3900 :     if(plumed) {</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineCov">       3900 :       long long unsigned int istepplusone=istep+1;</span></a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">       3900 :       plumedWantsToStop=0;</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;setStepLongLong&quot;,&amp;istepplusone);</span></a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;setMasses&quot;,&amp;masses[0]);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;setForces&quot;,&amp;forces[0][0]);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;setEnergy&quot;,&amp;potential);</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;setPositions&quot;,&amp;positions[0][0]);</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;setStopFlag&quot;,&amp;plumedWantsToStop);</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">       7800 :       plumed-&gt;cmd(&quot;calc&quot;);</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :       //if(istep%2000==0) plumed-&gt;cmd(&quot;writeCheckPointFile&quot;);</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">       3900 :       if(plumedWantsToStop) nsteps=istep;</span></a>
+<a name="650"><span class="lineNum">     650 </span>            :     }</a>
+<a name="651"><span class="lineNum">     651 </span>            : </a>
+<a name="652"><span class="lineNum">     652 </span>            :     // Second step of velocity verlet</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">       8500 :     for(unsigned k=0; k&lt;dim; ++k) {</span></a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">       4600 :       velocities[0][k] = velocities[0][k] + 0.5*tstep*forces[0][k];</span></a>
+<a name="655"><span class="lineNum">     655 </span>            :     }</a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            :     // Langevin thermostat</a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineCov">       3900 :     lscale=exp(-0.5*tstep*friction); //exp(-0.5*tstep/friction);</span></a>
+<a name="659"><span class="lineNum">     659 </span><span class="lineCov">       3900 :     lrand=sqrt((1.-lscale*lscale)*temp);</span></a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">       8500 :     for(unsigned k=0; k&lt;dim; ++k) {</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">       4600 :       therm_eng=therm_eng+0.5*velocities[0][k]*velocities[0][k];</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">       4600 :       velocities[0][k]=lscale*velocities[0][k]+lrand*random.Gaussian();</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">       4600 :       therm_eng=therm_eng-0.5*velocities[0][k]*velocities[0][k];</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :     }</a>
+<a name="665"><span class="lineNum">     665 </span>            : </a>
+<a name="666"><span class="lineNum">     666 </span>            :     // Print everything</a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">       3900 :     ttt = calc_temp( velocities );</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">       3900 :     conserved = potential+1.5*ttt+therm_eng;</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">       3900 :     if( (intra.Get_rank()==0) &amp;&amp; ((istep % stepWrite)==0) ) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">         38 :       std::fprintf(fp,&quot;%llu %f %f %f %f %f %f %f %f \n&quot;, istep, istep*tstep, positions[0][0], positions[0][1], positions[0][2], conserved, ttt, potential, therm_eng );</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :     }</a>
+<a name="672"><span class="lineNum">     672 </span>            :   }</a>
+<a name="673"><span class="lineNum">     673 </span>            : </a>
+<a name="674"><span class="lineNum">     674 </span>            :   //printf(&quot;Rank: %d, Size: %d \n&quot;, pc.Get_rank(), pc.Get_size() );</a>
+<a name="675"><span class="lineNum">     675 </span>            :   //printf(&quot;Rank: %d, Size: %d, MultiSimCommRank: %d, MultiSimCommSize: %d \n&quot;, pc.Get_rank(), pc.Get_size(), multi_sim_comm.Get_rank(), multi_sim_comm.Get_size() );</a>
+<a name="676"><span class="lineNum">     676 </span>            : </a>
+<a name="677"><span class="lineNum">     677 </span>            :   return 0;</a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">        395 : }</span></a>
+<a name="679"><span class="lineNum">     679 </span>            : </a>
+<a name="680"><span class="lineNum">     680 </span>            : }</a>
+<a name="681"><span class="lineNum">     681 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_Adam.cpp.func-sort-c.html b/coverage/ves/Opt_Adam.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cee39428eb
--- /dev/null
+++ b/coverage/ves/Opt_Adam.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_Adam.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_Adam.cpp<span style="font-size: 80%;"> (<a href="Opt_Adam.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">93.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Opt_Adam.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#90">_ZN4PLMD3ves8Opt_AdamC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#73">_ZN4PLMD3ves12_GLOBAL__N_120Opt_AdamRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#90">_ZN4PLMD3ves8Opt_AdamC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#76">_ZN4PLMD3ves8Opt_Adam16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#151">_ZN4PLMD3ves8Opt_Adam12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#73">_ZN4PLMD3ves12_GLOBAL__N_120Opt_AdamRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#73">_ZN4PLMD3ves12_GLOBAL__N_120Opt_AdamRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_Adam.cpp.func.html b/coverage/ves/Opt_Adam.cpp.func.html
new file mode 100644
index 0000000000..22b7dfcf3c
--- /dev/null
+++ b/coverage/ves/Opt_Adam.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_Adam.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_Adam.cpp<span style="font-size: 80%;"> (<a href="Opt_Adam.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">93.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Opt_Adam.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#73">_ZN4PLMD3ves12_GLOBAL__N_120Opt_AdamRegisterMe756createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#73">_ZN4PLMD3ves12_GLOBAL__N_120Opt_AdamRegisterMe75C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#73">_ZN4PLMD3ves12_GLOBAL__N_120Opt_AdamRegisterMe75D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#151">_ZN4PLMD3ves8Opt_Adam12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">20</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#76">_ZN4PLMD3ves8Opt_Adam16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#90">_ZN4PLMD3ves8Opt_AdamC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Adam.cpp.gcov.html#90">_ZN4PLMD3ves8Opt_AdamC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_Adam.cpp.gcov.html b/coverage/ves/Opt_Adam.cpp.gcov.html
new file mode 100644
index 0000000000..1c671f13d5
--- /dev/null
+++ b/coverage/ves/Opt_Adam.cpp.gcov.html
@@ -0,0 +1,272 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_Adam.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_Adam.cpp<span style="font-size: 80%;"> (source / <a href="Opt_Adam.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">68</td>
+            <td class="headerCovTableEntry">73</td>
+            <td class="headerCovTableEntryHi">93.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace ves {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : //+PLUMEDOC VES_OPTIMIZER OPT_ADAM</a>
+<a name="34"><span class="lineNum">      34 </span>            : /*</a>
+<a name="35"><span class="lineNum">      35 </span>            : Adaptive moment estimation (ADAM) optimizer.</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : \attention</a>
+<a name="38"><span class="lineNum">      38 </span>            : __This optimizer is still experimental and not fully documented. The syntax might change. Restarting does not work. We recommend to use the averaged stochastic gradient decent optimizer (\ref OPT_AVERAGED_SGD) for now__.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \par Examples</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : */</a>
+<a name="44"><span class="lineNum">      44 </span>            : //+ENDPLUMEDOC</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : class Opt_Adam: public Optimizer {</a>
+<a name="47"><span class="lineNum">      47 </span>            : private:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   unsigned int time_;</a>
+<a name="49"><span class="lineNum">      49 </span>            :   double beta_1_;</a>
+<a name="50"><span class="lineNum">      50 </span>            :   double beta_2_;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   double epsilon_;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   double one_minus_weight_decay_;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   bool amsgrad_;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   bool adamw_;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // 1st gradient moment uses the &quot;AuxCoeffs&quot;, so only 2nd moment needs new CoeffVectors</a>
+<a name="56"><span class="lineNum">      56 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; var_coeffs_pntrs_;</a>
+<a name="57"><span class="lineNum">      57 </span>            :   // used only for AMSGrad variant</a>
+<a name="58"><span class="lineNum">      58 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; varmax_coeffs_pntrs_;</a>
+<a name="59"><span class="lineNum">      59 </span>            : protected:</a>
+<a name="60"><span class="lineNum">      60 </span>            :   CoeffsVector&amp; VarCoeffs(const unsigned int coeffs_id = 0) const;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   CoeffsVector&amp; VarmaxCoeffs(const unsigned int coeffs_id = 0) const;</a>
+<a name="62"><span class="lineNum">      62 </span>            : public:</a>
+<a name="63"><span class="lineNum">      63 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="64"><span class="lineNum">      64 </span>            :   explicit Opt_Adam(const ActionOptions&amp;);</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void coeffsUpdate(const unsigned int c_id = 0) override;</a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : inline</a>
+<a name="69"><span class="lineNum">      69 </span>            : CoeffsVector&amp; Opt_Adam::VarCoeffs(const unsigned int coeffs_id) const {return *var_coeffs_pntrs_[coeffs_id];}</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : inline</a>
+<a name="72"><span class="lineNum">      72 </span>            : CoeffsVector&amp; Opt_Adam::VarmaxCoeffs(const unsigned int coeffs_id) const {return *varmax_coeffs_pntrs_[coeffs_id];}</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(Opt_Adam,&quot;OPT_ADAM&quot;)</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          4 : void Opt_Adam::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          4 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          4 :   Optimizer::useFixedStepSizeKeywords(keys);</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          4 :   Optimizer::useMultipleWalkersKeywords(keys);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          4 :   Optimizer::useMaskKeywords(keys);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          4 :   Optimizer::useDynamicTargetDistributionKeywords(keys);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;BETA_1&quot;,&quot;Parameter for the first moment estimate. Defaults to 0.9&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;BETA_2&quot;,&quot;Parameter for the second moment estimate. Defaults to 0.999&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;EPSILON&quot;,&quot;Small parameter to avoid division by zero. Defaults to 1e-8&quot;);</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;ADAMW_WEIGHT_DECAY&quot;,&quot;Weight decay parameter for the AdamW variant. Defaults to 0&quot;);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          8 :   keys.addFlag(&quot;AMSGRAD&quot;, false, &quot;Use the AMSGrad variant&quot;);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          4 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          2 : Opt_Adam::Opt_Adam(const ActionOptions&amp;ao):</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   PLUMED_VES_OPTIMIZER_INIT(ao),</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          2 :   time_(0),</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :   beta_1_(0.9),</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          2 :   beta_2_(0.999),</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          2 :   epsilon_(0.00000001),</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          2 :   one_minus_weight_decay_(1.0),</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          2 :   amsgrad_(false),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          2 :   adamw_(false),</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          2 :   var_coeffs_pntrs_(0)</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : {</a>
+<a name="103"><span class="lineNum">     103 </span>            :   // add citation and print it to log</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          2 :   log &lt;&lt; &quot;  Adam type stochastic gradient decent\n&quot;;</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          2 :   parseFlag(&quot;AMSGRAD&quot;,amsgrad_);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          2 :   if (amsgrad_) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :     log &lt;&lt; &quot;  Using the AMSGrad variant of the Adam algorithm, see and cite\n&quot;;</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          2 :   double tmp_weight_decay = 0.0;</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          2 :   parse(&quot;ADAMW_WEIGHT_DECAY&quot;,tmp_weight_decay);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :   if (tmp_weight_decay != 0.0) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :     adamw_ = true;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;  Using the AdamW variant (Adam with weight decay), see and cite\n&quot;;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineNoCov">          0 :     one_minus_weight_decay_ = 1 - tmp_weight_decay;</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     log &lt;&lt; &quot;    weight decay parameter: &quot; &lt;&lt; tmp_weight_decay &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          2 :   log &lt;&lt; &quot;  Adam parameters:\n&quot;;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          2 :   parse(&quot;BETA_1&quot;,beta_1_);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          2 :   plumed_massert(beta_1_ &gt; 0 &amp;&amp; beta_1_ &lt;= 1, &quot;BETA_1 must be between 0 and 1&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          2 :   log &lt;&lt; &quot;    beta_1: &quot; &lt;&lt; beta_1_ &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          2 :   parse(&quot;BETA_2&quot;,beta_2_);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          2 :   plumed_massert(beta_2_ &gt; 0 &amp;&amp; beta_2_ &lt;= 1, &quot;BETA_2 must be between 0 and 1&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          2 :   log &lt;&lt; &quot;    beta_2: &quot; &lt;&lt; beta_2_ &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          2 :   parse(&quot;EPSILON&quot;,epsilon_);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          2 :   plumed_massert(epsilon_ &gt; 0 &amp;&amp; epsilon_ &lt;= 1, &quot;EPSILON must be between 0 and 1&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          2 :   log &lt;&lt; &quot;    epsilon: &quot; &lt;&lt; epsilon_ &lt;&lt; &quot;\n&quot;;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            :   // set up the coeff vector for the 2nd moment of the gradient (variance)</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          4 :   for (unsigned i = 0; i &lt; numberOfCoeffsSets(); ++i) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          2 :     var_coeffs_pntrs_.emplace_back(std::unique_ptr&lt;CoeffsVector&gt;(new CoeffsVector(Coeffs(i))));</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          4 :     VarCoeffs(i).replaceLabelString(&quot;coeffs&quot;,&quot;grad_var&quot;);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          2 :     VarCoeffs(i).setAllValuesToZero(); // can Coeffs(i) even be non-zero at this point?</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            :     // add second set of coefficients to store the maximum values of the 2nd moment</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          2 :     if (amsgrad_) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :       varmax_coeffs_pntrs_.emplace_back(std::unique_ptr&lt;CoeffsVector&gt;(new CoeffsVector(VarCoeffs(i))));</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          2 :       VarmaxCoeffs(i).replaceLabelString(&quot;coeffs&quot;,&quot;grad_varmax&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :     // also rename the Coeffs used for the mean of the gradient</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          4 :     AuxCoeffs(i).replaceLabelString(&quot;coeffs&quot;,&quot;grad_mean&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 : }</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         20 : void Opt_Adam::coeffsUpdate(const unsigned int c_id) {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         20 :   time_++;</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :   // AuxCoeffs is used for first moment (mean)</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         20 :   AuxCoeffs(c_id) *= beta_1_;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         20 :   AuxCoeffs(c_id) += (1 - beta_1_ ) * Gradient(c_id) * CoeffsMask(c_id);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         20 :   VarCoeffs(c_id) *= beta_2_;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         20 :   VarCoeffs(c_id) += (1 - beta_2_ ) * Gradient(c_id) * Gradient(c_id) * CoeffsMask(c_id);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         20 :   if (amsgrad_) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        120 :     for (size_t i = 0; i&lt; VarCoeffs(c_id).getSize(); ++i) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        110 :       if (VarCoeffs(c_id).getValue(i) &gt; VarmaxCoeffs(c_id).getValue(i)) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         95 :         VarmaxCoeffs(c_id)[i] = VarCoeffs(c_id).getValue(i);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :       }</a>
+<a name="166"><span class="lineNum">     166 </span>            :     }</a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   // store sqrt of VarCoeffs in vector, easier than writing a CoeffsVector::sqrt() function</a>
+<a name="170"><span class="lineNum">     170 </span>            :   // also directly add epsilon and invert to multiply with the Coeffs in last step</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::vector&lt;double&gt; var_coeffs_sqrt;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         20 :   if (!amsgrad_) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        120 :     for (size_t i = 0; i&lt; VarCoeffs(c_id).getSize(); ++i) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        110 :       var_coeffs_sqrt.push_back(1 / (sqrt(VarCoeffs(c_id).getValue(i)) + epsilon));</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span>            :   else { // use VarmaxCoffs instead of VarCoeffs</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        120 :     for (size_t i = 0; i&lt; VarmaxCoeffs(c_id).getSize(); ++i) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        110 :       var_coeffs_sqrt.push_back(1 / (sqrt(VarmaxCoeffs(c_id).getValue(i)) + epsilon));</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span>            :   }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            :   // bias correction</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         20 :   double scalefactor = StepSize(c_id) * sqrt(1 - pow(beta_2_, time_)) / (1 - pow(beta_1_, time_));</span></a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         20 :   if (adamw_) { // check is not necessary but probably faster than always multiplying by 1</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     Coeffs(c_id) *= one_minus_weight_decay_ * CoeffsMask(c_id);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   // coeff update</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         20 :   Coeffs(c_id) -= scalefactor * AuxCoeffs(c_id) * var_coeffs_sqrt * CoeffsMask(c_id);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         20 : }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_BachAveragedSGD.cpp.func-sort-c.html b/coverage/ves/Opt_BachAveragedSGD.cpp.func-sort-c.html
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+++ b/coverage/ves/Opt_BachAveragedSGD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_BachAveragedSGD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_BachAveragedSGD.cpp<span style="font-size: 80%;"> (<a href="Opt_BachAveragedSGD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Opt_BachAveragedSGD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#217">_ZN4PLMD3ves19Opt_BachAveragedSGDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#197">_ZN4PLMD3ves12_GLOBAL__N_132Opt_BachAveragedSGDRegisterMe1996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#217">_ZN4PLMD3ves19Opt_BachAveragedSGDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#200">_ZN4PLMD3ves19Opt_BachAveragedSGD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#197">_ZN4PLMD3ves12_GLOBAL__N_132Opt_BachAveragedSGDRegisterMe199C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#197">_ZN4PLMD3ves12_GLOBAL__N_132Opt_BachAveragedSGDRegisterMe199D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#274">_ZN4PLMD3ves19Opt_BachAveragedSGD12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">22675</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/ves/Opt_BachAveragedSGD.cpp.func.html b/coverage/ves/Opt_BachAveragedSGD.cpp.func.html
new file mode 100644
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_BachAveragedSGD.cpp<span style="font-size: 80%;"> (<a href="Opt_BachAveragedSGD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
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+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#197">_ZN4PLMD3ves12_GLOBAL__N_132Opt_BachAveragedSGDRegisterMe1996createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#197">_ZN4PLMD3ves12_GLOBAL__N_132Opt_BachAveragedSGDRegisterMe199C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#197">_ZN4PLMD3ves12_GLOBAL__N_132Opt_BachAveragedSGDRegisterMe199D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#274">_ZN4PLMD3ves19Opt_BachAveragedSGD12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">22675</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#200">_ZN4PLMD3ves19Opt_BachAveragedSGD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">77</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#217">_ZN4PLMD3ves19Opt_BachAveragedSGDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_BachAveragedSGD.cpp.gcov.html#217">_ZN4PLMD3ves19Opt_BachAveragedSGDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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diff --git a/coverage/ves/Opt_BachAveragedSGD.cpp.gcov.html b/coverage/ves/Opt_BachAveragedSGD.cpp.gcov.html
new file mode 100644
index 0000000000..d1b2b2df4d
--- /dev/null
+++ b/coverage/ves/Opt_BachAveragedSGD.cpp.gcov.html
@@ -0,0 +1,378 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_BachAveragedSGD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
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+
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+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_BachAveragedSGD.cpp<span style="font-size: 80%;"> (source / <a href="Opt_BachAveragedSGD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">60</td>
+            <td class="headerCovTableEntry">63</td>
+            <td class="headerCovTableEntryHi">95.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC VES_OPTIMIZER OPT_AVERAGED_SGD</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Averaged stochastic gradient decent with fixed step size.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Algorithm</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : This optimizer updates the coefficients according to the averaged stochastic gradient decent algorithm described in ref \cite Bach-NIPS-2013. This algorithm considers two sets of coefficients, the so-called instantaneous coefficients that are updated according to the recursion formula given by</a>
+<a name="42"><span class="lineNum">      42 </span>            : \f[</a>
+<a name="43"><span class="lineNum">      43 </span>            : \boldsymbol{\alpha}^{(n+1)} = \boldsymbol{\alpha}^{(n)} -</a>
+<a name="44"><span class="lineNum">      44 </span>            : \mu \left[</a>
+<a name="45"><span class="lineNum">      45 </span>            : \nabla \Omega(\bar{\boldsymbol{\alpha}}^{(n)}) +</a>
+<a name="46"><span class="lineNum">      46 </span>            : \mathbf{H}(\bar{\boldsymbol{\alpha}}^{(n)})</a>
+<a name="47"><span class="lineNum">      47 </span>            : [\boldsymbol{\alpha}^{(n)}-\bar{\boldsymbol{\alpha}}^{(n)}]</a>
+<a name="48"><span class="lineNum">      48 </span>            : \right],</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f]</a>
+<a name="50"><span class="lineNum">      50 </span>            : where \f$\mu\f$ is a fixed step size and the gradient \f$ \nabla\Omega(\bar{\boldsymbol{\alpha}}^{(n)})\f$ and the Hessian \f$\mathbf{H}(\bar{\boldsymbol{\alpha}}^{(n)})\f$ depend on the averaged coefficients defined as</a>
+<a name="51"><span class="lineNum">      51 </span>            : \f[</a>
+<a name="52"><span class="lineNum">      52 </span>            : \bar{\boldsymbol{\alpha}}^{(n)} = \frac{1}{n+1} \sum_{k=0}^{n} \boldsymbol{\alpha}^{(k)}.</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f]</a>
+<a name="54"><span class="lineNum">      54 </span>            : This means that the bias acting on the system depends on the averaged coefficients \f$\bar{\boldsymbol{\alpha}}^{(n)}\f$ which leads to a smooth convergence of the bias and the estimated free energy surface. Furthermore, this allows for a rather short sampling time for each iteration, for classical MD simulations typical sampling times are on the order of few ps (around 1000-4000 MD steps).</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : Currently it is only supported to employ the diagonal part of the Hessian which is generally sufficient. Support for employing the full Hessian will be added later on.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The VES bias that is to be optimized should be specified using the</a>
+<a name="59"><span class="lineNum">      59 </span>            : BIAS keyword.</a>
+<a name="60"><span class="lineNum">      60 </span>            : The fixed step size \f$\mu\f$ is given using the STEPSIZE keyword.</a>
+<a name="61"><span class="lineNum">      61 </span>            : The frequency of updating the coefficients is given using the</a>
+<a name="62"><span class="lineNum">      62 </span>            : STRIDE keyword where the value is given in the number of MD steps.</a>
+<a name="63"><span class="lineNum">      63 </span>            : For example, if the MD time step is 0.02 ps and STRIDE=2000 will the</a>
+<a name="64"><span class="lineNum">      64 </span>            : coefficients be updated every 4 ps.</a>
+<a name="65"><span class="lineNum">      65 </span>            : The coefficients will be outputted to the file given by the</a>
+<a name="66"><span class="lineNum">      66 </span>            : COEFFS_FILE keyword. How often the coefficients are written</a>
+<a name="67"><span class="lineNum">      67 </span>            : to this file is controlled by the COEFFS_OUTPUT keyword.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : If the VES bias employs a dynamic target distribution that needs to be</a>
+<a name="70"><span class="lineNum">      70 </span>            : iteratively updated (e.g. \ref TD_WELLTEMPERED) \cite Valsson-JCTC-2015, you will need to specify</a>
+<a name="71"><span class="lineNum">      71 </span>            : the stride for updating the target distribution by using</a>
+<a name="72"><span class="lineNum">      72 </span>            : the TARGETDIST_STRIDE keyword where the stride</a>
+<a name="73"><span class="lineNum">      73 </span>            : is given in terms coefficient iterations. For example if the</a>
+<a name="74"><span class="lineNum">      74 </span>            : MD time step is 0.02 ps and STRIDE=1000, such that the coefficients</a>
+<a name="75"><span class="lineNum">      75 </span>            : are updated every 2 ps, will TARGETDIST_STRIDE=500 mean that the</a>
+<a name="76"><span class="lineNum">      76 </span>            : target distribution will be updated every 1000 ps.</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : The output of the free energy surfaces and biases is controlled by the FES_OUTPUT and the BIAS_OUTPUT</a>
+<a name="79"><span class="lineNum">      79 </span>            : keywords. It is also possible to output one-dimensional projections of the free energy surfaces</a>
+<a name="80"><span class="lineNum">      80 </span>            : by using the FES_PROJ_OUTPUT keyword but for that to work you will need to select</a>
+<a name="81"><span class="lineNum">      81 </span>            : for which argument to do the projections by using the numbered PROJ_ARG keyword in</a>
+<a name="82"><span class="lineNum">      82 </span>            : the VES bias that is optimized.</a>
+<a name="83"><span class="lineNum">      83 </span>            : You can also output dynamic target distributions by using the</a>
+<a name="84"><span class="lineNum">      84 </span>            : TARGETDIST_OUTPUT and TARGETDIST_PROJ_OUTPUT keywords.</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : It is possible to start the optimization from some initial set of</a>
+<a name="87"><span class="lineNum">      87 </span>            : coefficients that have been previously obtained by using the INITIAL_COEFFS</a>
+<a name="88"><span class="lineNum">      88 </span>            : keyword.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : When restarting simulations it should be sufficient to put the \ref RESTART action</a>
+<a name="91"><span class="lineNum">      91 </span>            : in the beginning of the input files (or some MD codes the PLUMED should automatically</a>
+<a name="92"><span class="lineNum">      92 </span>            : detect if it is a restart run) and keep the same input as before The restarting of</a>
+<a name="93"><span class="lineNum">      93 </span>            : the optimization should be automatic as the optimizer will then read in the</a>
+<a name="94"><span class="lineNum">      94 </span>            : coefficients from the file given in COEFFS_FILE. For dynamic target</a>
+<a name="95"><span class="lineNum">      95 </span>            : distribution the code will also read in the final target distribution from the</a>
+<a name="96"><span class="lineNum">      96 </span>            : previous run (which is always outputted even if the TARGETDIST_OUTPUT keyword</a>
+<a name="97"><span class="lineNum">      97 </span>            : is not used).</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : This optimizer supports the usage of multiple walkers where different copies of the system share the same bias potential (i.e. coefficients) and cooperatively sample the averages needed for the gradient and Hessian. This can significantly help with convergence in difficult cases. It is of course best to start the different copies from different positions in CV space. To activate this option you just need to add the MULTIPLE_WALKERS flag. Note that this is only supported if the MD code support running multiple replicas connected via MPI.</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : The optimizer supports the usage of a so-called mask file that can be used to employ different step sizes for different coefficients and/or deactivate the optimization of certain coefficients (by putting values of 0.0). The mask file is read in by using the MASK_FILE keyword and should be in the same format as the coefficient file. It is possible to generate a template mask file by using the OUTPUT_MASK_FILE keyword.</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : \par Examples</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : In the following input we employ an averaged stochastic gradient decent with a</a>
+<a name="106"><span class="lineNum">     106 </span>            : fixed step size of 1.0 and update the coefficient every 1000 MD steps</a>
+<a name="107"><span class="lineNum">     107 </span>            : (e.g. every 2 ps if the MD time step is 0.02 ps). The coefficient are outputted</a>
+<a name="108"><span class="lineNum">     108 </span>            : to the coefficients.data every 50 iterations while the FES and bias is outputted</a>
+<a name="109"><span class="lineNum">     109 </span>            : to files every 500 iterations (e.g. every 1000 ps).</a>
+<a name="110"><span class="lineNum">     110 </span>            : \plumedfile</a>
+<a name="111"><span class="lineNum">     111 </span>            : phi:   TORSION ATOMS=5,7,9,15</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="116"><span class="lineNum">     116 </span>            :  ARG=phi</a>
+<a name="117"><span class="lineNum">     117 </span>            :  BASIS_FUNCTIONS=bf1</a>
+<a name="118"><span class="lineNum">     118 </span>            :  LABEL=ves1</a>
+<a name="119"><span class="lineNum">     119 </span>            :  TEMP=300.0</a>
+<a name="120"><span class="lineNum">     120 </span>            :  GRID_BINS=100</a>
+<a name="121"><span class="lineNum">     121 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="124"><span class="lineNum">     124 </span>            :   BIAS=ves1</a>
+<a name="125"><span class="lineNum">     125 </span>            :   STRIDE=1000</a>
+<a name="126"><span class="lineNum">     126 </span>            :   LABEL=o1</a>
+<a name="127"><span class="lineNum">     127 </span>            :   STEPSIZE=1.0</a>
+<a name="128"><span class="lineNum">     128 </span>            :   COEFFS_FILE=coefficients.data</a>
+<a name="129"><span class="lineNum">     129 </span>            :   COEFFS_OUTPUT=50</a>
+<a name="130"><span class="lineNum">     130 </span>            :   FES_OUTPUT=500</a>
+<a name="131"><span class="lineNum">     131 </span>            :   BIAS_OUTPUT=500</a>
+<a name="132"><span class="lineNum">     132 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="133"><span class="lineNum">     133 </span>            : \endplumedfile</a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : In the following example we employ a well-tempered target distribution that</a>
+<a name="137"><span class="lineNum">     137 </span>            : is updated every 500 iterations (e.g. every 1000 ps). The target distribution is</a>
+<a name="138"><span class="lineNum">     138 </span>            : also output to a file every 2000 iterations (the TARGETDIST_OUTPUT keyword).</a>
+<a name="139"><span class="lineNum">     139 </span>            : Here we also employ MULTIPLE_WALKERS flag to enable the usage of</a>
+<a name="140"><span class="lineNum">     140 </span>            : multiple walkers.</a>
+<a name="141"><span class="lineNum">     141 </span>            : \plumedfile</a>
+<a name="142"><span class="lineNum">     142 </span>            : #SETTINGS NREPLICAS=2</a>
+<a name="143"><span class="lineNum">     143 </span>            : phi:   TORSION ATOMS=5,7,9,15</a>
+<a name="144"><span class="lineNum">     144 </span>            : psi:   TORSION ATOMS=7,9,15,17</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            : bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi</a>
+<a name="147"><span class="lineNum">     147 </span>            : bf2: BF_FOURIER ORDER=4 MINIMUM=-pi MAXIMUM=pi</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : td1: TD_WELLTEMPERED BIASFACTOR=10</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="152"><span class="lineNum">     152 </span>            :  ARG=phi,psi</a>
+<a name="153"><span class="lineNum">     153 </span>            :  BASIS_FUNCTIONS=bf1,bf2</a>
+<a name="154"><span class="lineNum">     154 </span>            :  LABEL=ves1</a>
+<a name="155"><span class="lineNum">     155 </span>            :  TEMP=300.0</a>
+<a name="156"><span class="lineNum">     156 </span>            :  GRID_BINS=100,100</a>
+<a name="157"><span class="lineNum">     157 </span>            :  TARGET_DISTRIBUTION=td1</a>
+<a name="158"><span class="lineNum">     158 </span>            :  PROJ_ARG1=phi</a>
+<a name="159"><span class="lineNum">     159 </span>            :  PROJ_ARG2=psi</a>
+<a name="160"><span class="lineNum">     160 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="163"><span class="lineNum">     163 </span>            :   BIAS=ves1</a>
+<a name="164"><span class="lineNum">     164 </span>            :   STRIDE=1000</a>
+<a name="165"><span class="lineNum">     165 </span>            :   LABEL=o1</a>
+<a name="166"><span class="lineNum">     166 </span>            :   STEPSIZE=1.0</a>
+<a name="167"><span class="lineNum">     167 </span>            :   MULTIPLE_WALKERS</a>
+<a name="168"><span class="lineNum">     168 </span>            :   COEFFS_FILE=coefficients.data</a>
+<a name="169"><span class="lineNum">     169 </span>            :   COEFFS_OUTPUT=50</a>
+<a name="170"><span class="lineNum">     170 </span>            :   FES_OUTPUT=500</a>
+<a name="171"><span class="lineNum">     171 </span>            :   FES_PROJ_OUTPUT=500</a>
+<a name="172"><span class="lineNum">     172 </span>            :   BIAS_OUTPUT=500</a>
+<a name="173"><span class="lineNum">     173 </span>            :   TARGETDIST_STRIDE=500</a>
+<a name="174"><span class="lineNum">     174 </span>            :   TARGETDIST_OUTPUT=2000</a>
+<a name="175"><span class="lineNum">     175 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="176"><span class="lineNum">     176 </span>            : \endplumedfile</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : */</a>
+<a name="181"><span class="lineNum">     181 </span>            : //+ENDPLUMEDOC</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : class Opt_BachAveragedSGD : public Optimizer {</a>
+<a name="184"><span class="lineNum">     184 </span>            : private:</a>
+<a name="185"><span class="lineNum">     185 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; combinedgradient_pntrs_;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   unsigned int combinedgradient_wstride_;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; combinedgradientOFiles_;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   double decaying_aver_tau_;</a>
+<a name="189"><span class="lineNum">     189 </span>            : private:</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         60 :   CoeffsVector&amp; CombinedGradient(const unsigned int c_id) const {return *combinedgradient_pntrs_[c_id];}</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :   double getAverDecay() const;</a>
+<a name="192"><span class="lineNum">     192 </span>            : public:</a>
+<a name="193"><span class="lineNum">     193 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="194"><span class="lineNum">     194 </span>            :   explicit Opt_BachAveragedSGD(const ActionOptions&amp;);</a>
+<a name="195"><span class="lineNum">     195 </span>            :   void coeffsUpdate(const unsigned int c_id = 0) override;</a>
+<a name="196"><span class="lineNum">     196 </span>            : };</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      12654 : PLUMED_REGISTER_ACTION(Opt_BachAveragedSGD,&quot;OPT_AVERAGED_SGD&quot;)</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         77 : void Opt_BachAveragedSGD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         77 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         77 :   Optimizer::useFixedStepSizeKeywords(keys);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         77 :   Optimizer::useMultipleWalkersKeywords(keys);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         77 :   Optimizer::useHessianKeywords(keys);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         77 :   Optimizer::useMaskKeywords(keys);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         77 :   Optimizer::useRestartKeywords(keys);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         77 :   Optimizer::useMonitorAverageGradientKeywords(keys);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         77 :   Optimizer::useDynamicTargetDistributionKeywords(keys);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        154 :   keys.add(&quot;hidden&quot;,&quot;COMBINED_GRADIENT_FILE&quot;,&quot;the name of output file for the combined gradient (gradient + Hessian term)&quot;);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        154 :   keys.add(&quot;hidden&quot;,&quot;COMBINED_GRADIENT_OUTPUT&quot;,&quot;how often the combined gradient should be written to file. This parameter is given as the number of bias iterations. It is by default 100 if COMBINED_GRADIENT_FILE is specficed&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        154 :   keys.add(&quot;hidden&quot;,&quot;COMBINED_GRADIENT_FMT&quot;,&quot;specify format for combined gradient file(s) (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        154 :   keys.add(&quot;optional&quot;,&quot;EXP_DECAYING_AVER&quot;,&quot;calculate the averaged coefficients using exponentially decaying averaging using the decaying constant given here in the number of iterations&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         77 : }</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         75 : Opt_BachAveragedSGD::Opt_BachAveragedSGD(const ActionOptions&amp;ao):</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   PLUMED_VES_OPTIMIZER_INIT(ao),</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         75 :   combinedgradient_wstride_(100),</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         75 :   decaying_aver_tau_(0.0)</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : {</a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         75 :   log.printf(&quot;  Averaged stochastic gradient decent, see and cite &quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        150 :   log &lt;&lt; plumed.cite(&quot;Bach and Moulines, NIPS 26, 773-781 (2013)&quot;);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         75 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         75 :   unsigned int decaying_aver_tau_int=0;</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         75 :   parse(&quot;EXP_DECAYING_AVER&quot;,decaying_aver_tau_int);</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         75 :   if(decaying_aver_tau_int&gt;0) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          2 :     decaying_aver_tau_ = static_cast&lt;double&gt;(decaying_aver_tau_int);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          2 :     log.printf(&quot;  Coefficients calculated using an exponentially decaying average with a decaying constant of %u iterations, see and cite &quot;,decaying_aver_tau_int);</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          4 :     log &lt;&lt; plumed.cite(&quot;Invernizzi, Valsson, and Parrinello, Proc. Natl. Acad. Sci. USA 114, 3370-3374 (2017)&quot;);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span>            :   //</a>
+<a name="236"><span class="lineNum">     236 </span>            :   std::vector&lt;std::string&gt; combinedgradient_fnames;</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         75 :   parseFilenames(&quot;COMBINED_GRADIENT_FILE&quot;,combinedgradient_fnames);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        150 :   parse(&quot;COMBINED_GRADIENT_OUTPUT&quot;,combinedgradient_wstride_);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         75 :   setupOFiles(combinedgradient_fnames,combinedgradientOFiles_,useMultipleWalkers());</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         75 :   std::string combinedgradient_fmt=&quot;&quot;;</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">        150 :   parse(&quot;COMBINED_GRADIENT_FMT&quot;,combinedgradient_fmt);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         75 :   if(combinedgradient_fnames.size()&gt;0) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         12 :     for(unsigned int i=0; i&lt;numberOfCoeffsSets(); i++) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         12 :       auto combinedgradient_tmp = Tools::make_unique&lt;CoeffsVector&gt;(*getGradientPntrs()[i]);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          6 :       std::string label = getGradientPntrs()[i]-&gt;getLabel();</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          6 :       if(label.find(&quot;gradient&quot;)!=std::string::npos) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         12 :         label.replace(label.find(&quot;gradient&quot;), std::string(&quot;gradient&quot;).length(), &quot;combined_gradient&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :       }</a>
+<a name="249"><span class="lineNum">     249 </span>            :       else {</a>
+<a name="250"><span class="lineNum">     250 </span>            :         label += &quot;_combined&quot;;</a>
+<a name="251"><span class="lineNum">     251 </span>            :       }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          6 :       combinedgradient_tmp-&gt;setLabels(label);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          6 :       if(combinedgradient_fmt.size()&gt;0) {</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :         combinedgradient_tmp-&gt;setOutputFmt(combinedgradient_fmt);</a>
+<a name="255"><span class="lineNum">     255 </span>            :       }</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          6 :       combinedgradient_pntrs_.emplace_back(std::move(combinedgradient_tmp));</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          6 :     }</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :     //</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          6 :     if(numberOfCoeffsSets()==1) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         12 :       log.printf(&quot;  Combined gradient (gradient + Hessian term) will be written out to file %s every %u iterations\n&quot;,combinedgradientOFiles_[0]-&gt;getPath().c_str(),combinedgradient_wstride_);</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     }</a>
+<a name="262"><span class="lineNum">     262 </span>            :     else {</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :       log.printf(&quot;  Combined gradient (gradient + Hessian term) will be written out to the following files every %u iterations:\n&quot;,combinedgradient_wstride_);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineNoCov">          0 :       for(unsigned int i=0; i&lt;combinedgradientOFiles_.size(); i++) {</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :         log.printf(&quot;   coefficient set %u: %s\n&quot;,i,combinedgradientOFiles_[i]-&gt;getPath().c_str());</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :       }</a>
+<a name="267"><span class="lineNum">     267 </span>            :     }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   }</a>
+<a name="269"><span class="lineNum">     269 </span>            :   //</a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         75 :   turnOnHessian();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         75 :   checkRead();</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         75 : }</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      22675 : void Opt_BachAveragedSGD::coeffsUpdate(const unsigned int c_id) {</span></a>
+<a name="277"><span class="lineNum">     277 </span>            :   //</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      22675 :   if(combinedgradientOFiles_.size()&gt;0 &amp;&amp; (getIterationCounter()+1)%combinedgradient_wstride_==0) {</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         60 :     CombinedGradient(c_id).setValues( ( Gradient(c_id) + Hessian(c_id)*(AuxCoeffs(c_id)-Coeffs(c_id)) ) );</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         60 :     combinedgradient_pntrs_[c_id]-&gt;setIterationCounterAndTime(getIterationCounter()+1,getTime());</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         60 :     combinedgradient_pntrs_[c_id]-&gt;writeToFile(*combinedgradientOFiles_[c_id]);</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :   }</a>
+<a name="283"><span class="lineNum">     283 </span>            :   //</a>
+<a name="284"><span class="lineNum">     284 </span>            :   double aver_decay = getAverDecay();</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">      22675 :   AuxCoeffs(c_id) += - StepSize(c_id)*CoeffsMask(c_id) * ( Gradient(c_id) + Hessian(c_id)*(AuxCoeffs(c_id)-Coeffs(c_id)) );</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   //AuxCoeffs() = AuxCoeffs() - StepSize() * ( Gradient() + Hessian()*(AuxCoeffs()-Coeffs()) );</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">      22675 :   Coeffs(c_id) += aver_decay * ( AuxCoeffs(c_id)-Coeffs(c_id) );</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">      22675 : }</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span>            : inline</a>
+<a name="292"><span class="lineNum">     292 </span>            : double Opt_BachAveragedSGD::getAverDecay() const {</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">      22675 :   double aver_decay = 1.0 / ( getIterationCounterDbl() + 1.0 );</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">      22675 :   if(decaying_aver_tau_ &gt; 0.0 &amp;&amp; (getIterationCounterDbl() + 1.0) &gt; decaying_aver_tau_) {</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">         14 :     aver_decay = 1.0 / decaying_aver_tau_;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :   }</a>
+<a name="297"><span class="lineNum">     297 </span>            :   return aver_decay;</a>
+<a name="298"><span class="lineNum">     298 </span>            : }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : }</a>
+<a name="302"><span class="lineNum">     302 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_Dummy.cpp.func-sort-c.html b/coverage/ves/Opt_Dummy.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a50b918ef1
--- /dev/null
+++ b/coverage/ves/Opt_Dummy.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_Dummy.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_Dummy.cpp<span style="font-size: 80%;"> (<a href="Opt_Dummy.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Opt_Dummy.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#96">_ZN4PLMD3ves9Opt_DummyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#83">_ZN4PLMD3ves12_GLOBAL__N_121Opt_DummyRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#96">_ZN4PLMD3ves9Opt_DummyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#86">_ZN4PLMD3ves9Opt_Dummy16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#115">_ZN4PLMD3ves9Opt_Dummy12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#83">_ZN4PLMD3ves12_GLOBAL__N_121Opt_DummyRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#83">_ZN4PLMD3ves12_GLOBAL__N_121Opt_DummyRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_Dummy.cpp.func.html b/coverage/ves/Opt_Dummy.cpp.func.html
new file mode 100644
index 0000000000..c5b1301ca3
--- /dev/null
+++ b/coverage/ves/Opt_Dummy.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_Dummy.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_Dummy.cpp<span style="font-size: 80%;"> (<a href="Opt_Dummy.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Opt_Dummy.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#83">_ZN4PLMD3ves12_GLOBAL__N_121Opt_DummyRegisterMe856createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#83">_ZN4PLMD3ves12_GLOBAL__N_121Opt_DummyRegisterMe85C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#83">_ZN4PLMD3ves12_GLOBAL__N_121Opt_DummyRegisterMe85D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#115">_ZN4PLMD3ves9Opt_Dummy12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#86">_ZN4PLMD3ves9Opt_Dummy16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#96">_ZN4PLMD3ves9Opt_DummyC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_Dummy.cpp.gcov.html#96">_ZN4PLMD3ves9Opt_DummyC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_Dummy.cpp.gcov.html b/coverage/ves/Opt_Dummy.cpp.gcov.html
new file mode 100644
index 0000000000..d22c4193e8
--- /dev/null
+++ b/coverage/ves/Opt_Dummy.cpp.gcov.html
@@ -0,0 +1,197 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_Dummy.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_Dummy.cpp<span style="font-size: 80%;"> (source / <a href="Opt_Dummy.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">95.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace ves {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC VES_OPTIMIZER OPT_DUMMY</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Dummy optimizer for debugging.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : This is dummy optimizer that can be used for debugging. It will not update the</a>
+<a name="37"><span class="lineNum">      37 </span>            : coefficients but can be used to monitor the gradient and Hessian for a given</a>
+<a name="38"><span class="lineNum">      38 </span>            : VES bias.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : \par Examples</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : In the following input we use the OPT_DUMMY to monitor the gradient and</a>
+<a name="43"><span class="lineNum">      43 </span>            : Hessian for a given VES bias every 1 iteration.</a>
+<a name="44"><span class="lineNum">      44 </span>            : \plumedfile</a>
+<a name="45"><span class="lineNum">      45 </span>            : phi:   TORSION ATOMS=5,7,9,15</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="50"><span class="lineNum">      50 </span>            :  ARG=phi</a>
+<a name="51"><span class="lineNum">      51 </span>            :  BASIS_FUNCTIONS=bf1</a>
+<a name="52"><span class="lineNum">      52 </span>            :  LABEL=ves1</a>
+<a name="53"><span class="lineNum">      53 </span>            :  TEMP=300.0</a>
+<a name="54"><span class="lineNum">      54 </span>            :  GRID_BINS=100</a>
+<a name="55"><span class="lineNum">      55 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : OPT_DUMMY ...</a>
+<a name="58"><span class="lineNum">      58 </span>            :   BIAS=ves1</a>
+<a name="59"><span class="lineNum">      59 </span>            :   STRIDE=1000</a>
+<a name="60"><span class="lineNum">      60 </span>            :   LABEL=o1</a>
+<a name="61"><span class="lineNum">      61 </span>            :   MONITOR_HESSIAN</a>
+<a name="62"><span class="lineNum">      62 </span>            :   GRADIENT_FILE=gradient.data</a>
+<a name="63"><span class="lineNum">      63 </span>            :   GRADIENT_OUTPUT=1</a>
+<a name="64"><span class="lineNum">      64 </span>            :   GRADIENT_FMT=%12.6f</a>
+<a name="65"><span class="lineNum">      65 </span>            :   HESSIAN_FILE=hessian.data</a>
+<a name="66"><span class="lineNum">      66 </span>            :   HESSIAN_OUTPUT=1</a>
+<a name="67"><span class="lineNum">      67 </span>            :   HESSIAN_FMT=%12.6f</a>
+<a name="68"><span class="lineNum">      68 </span>            : ... OPT_DUMMY</a>
+<a name="69"><span class="lineNum">      69 </span>            : \endplumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : */</a>
+<a name="72"><span class="lineNum">      72 </span>            : //+ENDPLUMEDOC</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : class Opt_Dummy : public Optimizer {</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="80"><span class="lineNum">      80 </span>            :   explicit Opt_Dummy(const ActionOptions&amp;);</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void coeffsUpdate(const unsigned int c_id = 0) override;</a>
+<a name="82"><span class="lineNum">      82 </span>            : };</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Opt_Dummy,&quot;OPT_DUMMY&quot;)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          3 : void Opt_Dummy::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          3 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   //</a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">          3 :   Optimizer::useMultipleWalkersKeywords(keys);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">          3 :   Optimizer::useHessianKeywords(keys);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          3 :   Optimizer::useMonitorAverageGradientKeywords(keys);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          6 :   keys.addFlag(&quot;MONITOR_HESSIAN&quot;,false,&quot;also monitor the Hessian&quot;);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          3 : }</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">          1 : Opt_Dummy::Opt_Dummy(const ActionOptions&amp;ao):</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">          1 :   PLUMED_VES_OPTIMIZER_INIT(ao)</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : {</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">          1 :   log.printf(&quot;  fake optimizer that does not update coefficients\n&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          1 :   log.printf(&quot;  can be used to monitor gradient and Hessian for debugging purposes\n&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          1 :   bool monitor_hessian = false;</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          1 :   parseFlag(&quot;MONITOR_HESSIAN&quot;,monitor_hessian);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          1 :   if(monitor_hessian) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">          1 :     turnOnHessian();</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          1 :     log.printf(&quot;  the Hessian will also be monitored\n&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   }</a>
+<a name="109"><span class="lineNum">     109 </span>            :   else {</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineNoCov">          0 :     turnOffHessian();</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   }</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          1 :   turnOffCoeffsOutputFiles();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         10 : void Opt_Dummy::coeffsUpdate(const unsigned int c_id) {}</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_RobbinsMonroSGD.cpp.func-sort-c.html b/coverage/ves/Opt_RobbinsMonroSGD.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6fd5010dcb
--- /dev/null
+++ b/coverage/ves/Opt_RobbinsMonroSGD.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_RobbinsMonroSGD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_RobbinsMonroSGD.cpp<span style="font-size: 80%;"> (<a href="Opt_RobbinsMonroSGD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Opt_RobbinsMonroSGD.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#67">_ZN4PLMD3ves19Opt_RobbinsMonroSGDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#52">_ZN4PLMD3ves12_GLOBAL__N_131Opt_RobbinsMonroSGDRegisterMe546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#67">_ZN4PLMD3ves19Opt_RobbinsMonroSGDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#55">_ZN4PLMD3ves19Opt_RobbinsMonroSGD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#82">_ZN4PLMD3ves19Opt_RobbinsMonroSGD12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#52">_ZN4PLMD3ves12_GLOBAL__N_131Opt_RobbinsMonroSGDRegisterMe54C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#52">_ZN4PLMD3ves12_GLOBAL__N_131Opt_RobbinsMonroSGDRegisterMe54D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_RobbinsMonroSGD.cpp.func.html b/coverage/ves/Opt_RobbinsMonroSGD.cpp.func.html
new file mode 100644
index 0000000000..00d86d7101
--- /dev/null
+++ b/coverage/ves/Opt_RobbinsMonroSGD.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_RobbinsMonroSGD.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_RobbinsMonroSGD.cpp<span style="font-size: 80%;"> (<a href="Opt_RobbinsMonroSGD.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Opt_RobbinsMonroSGD.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#52">_ZN4PLMD3ves12_GLOBAL__N_131Opt_RobbinsMonroSGDRegisterMe546createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#52">_ZN4PLMD3ves12_GLOBAL__N_131Opt_RobbinsMonroSGDRegisterMe54C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#52">_ZN4PLMD3ves12_GLOBAL__N_131Opt_RobbinsMonroSGDRegisterMe54D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#82">_ZN4PLMD3ves19Opt_RobbinsMonroSGD12coeffsUpdateEj</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#55">_ZN4PLMD3ves19Opt_RobbinsMonroSGD16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#67">_ZN4PLMD3ves19Opt_RobbinsMonroSGDC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html#67">_ZN4PLMD3ves19Opt_RobbinsMonroSGDC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Opt_RobbinsMonroSGD.cpp.gcov.html b/coverage/ves/Opt_RobbinsMonroSGD.cpp.gcov.html
new file mode 100644
index 0000000000..41c684289d
--- /dev/null
+++ b/coverage/ves/Opt_RobbinsMonroSGD.cpp.gcov.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Opt_RobbinsMonroSGD.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Opt_RobbinsMonroSGD.cpp<span style="font-size: 80%;"> (source / <a href="Opt_RobbinsMonroSGD.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryHi">96.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace ves {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : //+PLUMEDOC VES_OPTIMIZER OPT_ROBBINS_MONRO_SGD</a>
+<a name="33"><span class="lineNum">      33 </span>            : /*</a>
+<a name="34"><span class="lineNum">      34 </span>            : Robbins-Monro stochastic gradient decent.</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : \attention</a>
+<a name="37"><span class="lineNum">      37 </span>            : __This optimizer is only included for reference. We recommend to use the averaged stochastic gradient decent optimizer (\ref OPT_AVERAGED_SGD)__.</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \par Examples</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : */</a>
+<a name="42"><span class="lineNum">      42 </span>            : //+ENDPLUMEDOC</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : class Opt_RobbinsMonroSGD : public Optimizer {</a>
+<a name="45"><span class="lineNum">      45 </span>            : private:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double decay_constant_;</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="49"><span class="lineNum">      49 </span>            :   explicit Opt_RobbinsMonroSGD(const ActionOptions&amp;);</a>
+<a name="50"><span class="lineNum">      50 </span>            :   void coeffsUpdate(const unsigned int c_id = 0);</a>
+<a name="51"><span class="lineNum">      51 </span>            : };</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(Opt_RobbinsMonroSGD,&quot;OPT_ROBBINS_MONRO_SGD&quot;)</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          3 : void Opt_RobbinsMonroSGD::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 :   Optimizer::registerKeywords(keys);</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          3 :   Optimizer::useDynamicStepSizeKeywords(keys);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          3 :   Optimizer::useMultipleWalkersKeywords(keys);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          3 :   Optimizer::useMaskKeywords(keys);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          3 :   Optimizer::useRestartKeywords(keys);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :   // Optimizer::useMonitorAveragesKeywords(keys);</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          3 :   Optimizer::useDynamicTargetDistributionKeywords(keys);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          6 :   keys.add(&quot;optional&quot;,&quot;DECAY_CONSTANT&quot;,&quot;the decay constant used for the step size.&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          3 : }</span></a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          1 : Opt_RobbinsMonroSGD::Opt_RobbinsMonroSGD(const ActionOptions&amp;ao):</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :   PLUMED_VES_OPTIMIZER_INIT(ao),</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          1 :   decay_constant_(1.0)</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : {</a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          1 :   parse(&quot;DECAY_CONSTANT&quot;,decay_constant_);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          1 :   if(decay_constant_&lt;1.0) {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;the value given in DECAY_CONSTANT doesn't make sense, it should be larger than 1.0&quot;);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          1 :   if(decay_constant_&gt;1.0) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :     log.printf(&quot;  using a decay constant of %f\n&quot;,decay_constant_);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            :   }</a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          1 :   checkRead();</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          1 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         10 : void Opt_RobbinsMonroSGD::coeffsUpdate(const unsigned int c_id) {</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   // getIterationCounterDbl() gives n-1 as it is updated afterwards.</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         10 :   double current_stepsize =  StepSize(c_id) /(1.0 + getIterationCounterDbl()/decay_constant_);</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   setCurrentStepSize(current_stepsize,c_id);</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         10 :   Coeffs(c_id) += - current_stepsize * CoeffsMask(c_id) * Gradient(c_id);</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :   //</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         10 :   double aver_decay = 1.0 / ( getIterationCounterDbl() + 1.0 );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         10 :   AuxCoeffs(c_id) += aver_decay * ( Coeffs(c_id)-AuxCoeffs(c_id) );</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         10 : }</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : }</a>
+<a name="96"><span class="lineNum">      96 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Optimizer.cpp.func-sort-c.html b/coverage/ves/Optimizer.cpp.func-sort-c.html
new file mode 100644
index 0000000000..95326b4b71
--- /dev/null
+++ b/coverage/ves/Optimizer.cpp.func-sort-c.html
@@ -0,0 +1,200 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Optimizer.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Optimizer.cpp<span style="font-size: 80%;"> (<a href="Optimizer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">682</td>
+            <td class="headerCovTableEntry">762</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Optimizer.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
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+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#941">_ZN4PLMD3ves9Optimizer14turnOffHessianEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#907">_ZN4PLMD3ves9Optimizer25useReweightFactorKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
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+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#37">_ZN4PLMD3ves9OptimizerC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#752">_ZN4PLMD3ves9OptimizerD0Ev</a></td>
+              <td class="coverFnLo">0</td>
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+              <td class="coverFnHi">1</td>
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+              <td class="coverFnHi">3</td>
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+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#1248">_ZNK4PLMD3ves9Optimizer30writeTargetDistProjOutputFilesEv</a></td>
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+              <td class="coverFnHi">80</td>
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+              <td class="coverFnHi">81</td>
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+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#951">_ZN4PLMD3ves9Optimizer13enableHessianEPNS0_7VesBiasEb</a></td>
+              <td class="coverFnHi">82</td>
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+    <tr>
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+              <td class="coverFnHi">84</td>
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+    <tr>
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+              <td class="coverFnHi">84</td>
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+              <td class="coverFnHi">85</td>
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+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#1198">_ZN4PLMD3ves9Optimizer32setAllCoeffsSetIterationCountersEv</a></td>
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+              <td class="coverFnHi">388</td>
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+              <td class="coverFnHi">22750</td>
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+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#1099">_ZN4PLMD3ves9Optimizer16writeOutputFilesEj</a></td>
+              <td class="coverFnHi">22810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#986">_ZN4PLMD3ves9Optimizer6updateEv</a></td>
+              <td class="coverFnHi">22879</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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+</body>
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diff --git a/coverage/ves/Optimizer.cpp.func.html b/coverage/ves/Optimizer.cpp.func.html
new file mode 100644
index 0000000000..1bfceca417
--- /dev/null
+++ b/coverage/ves/Optimizer.cpp.func.html
@@ -0,0 +1,200 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Optimizer.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Optimizer.cpp<span style="font-size: 80%;"> (<a href="Optimizer.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">682</td>
+            <td class="headerCovTableEntry">762</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Optimizer.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFn"><a href="Optimizer.cpp.gcov.html#1120">_ZN4PLMD3ves9Optimizer11setupOFilesERSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EERS2_ISt10unique_ptrINS_5OFileESt14default_deleteISD_EESaISG_EEb</a></td>
+              <td class="coverFnHi">388</td>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Optimizer.cpp.gcov.html b/coverage/ves/Optimizer.cpp.gcov.html
new file mode 100644
index 0000000000..5db9a63681
--- /dev/null
+++ b/coverage/ves/Optimizer.cpp.gcov.html
@@ -0,0 +1,1337 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Optimizer.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Optimizer.cpp<span style="font-size: 80%;"> (source / <a href="Optimizer.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">682</td>
+            <td class="headerCovTableEntry">762</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryMed">84.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/FileBase.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace PLMD {</a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace ves {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         79 : Optimizer::Optimizer(const ActionOptions&amp;ao):</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   Action(ao),</a>
+<a name="41"><span class="lineNum">      41 </span>            :   ActionPilot(ao),</a>
+<a name="42"><span class="lineNum">      42 </span>            :   ActionWithValue(ao),</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        158 :   description_(&quot;Undefined&quot;),</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         79 :   type_(&quot;Undefined&quot;),</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         79 :   stepsizes_(0),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         79 :   current_stepsizes(0),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         79 :   fixed_stepsize_(true),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         79 :   iter_counter(0),</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         79 :   use_hessian_(false),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         79 :   diagonal_hessian_(true),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         79 :   monitor_instantaneous_gradient_(false),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         79 :   use_mwalkers_mpi_(false),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         79 :   mwalkers_mpi_single_files_(true),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         79 :   dynamic_targetdists_(0),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         79 :   ustride_targetdist_(0),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         79 :   ustride_reweightfactor_(0),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         79 :   coeffssetid_prefix_(&quot;&quot;),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         79 :   coeffs_wstride_(100),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         79 :   coeffs_output_fmt_(&quot;&quot;),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         79 :   gradient_wstride_(100),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         79 :   gradient_output_fmt_(&quot;&quot;),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         79 :   hessian_wstride_(100),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         79 :   hessianOFiles_(0),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         79 :   hessian_output_fmt_(&quot;&quot;),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         79 :   targetdist_averages_wstride_(0),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         79 :   targetdist_averages_output_fmt_(&quot;&quot;),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         79 :   nbiases_(0),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         79 :   bias_pntrs_(0),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         79 :   ncoeffssets_(0),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         79 :   coeffs_pntrs_(0),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         79 :   gradient_pntrs_(0),</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         79 :   hessian_pntrs_(0),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         79 :   targetdist_averages_pntrs_(0),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         79 :   identical_coeffs_shape_(true),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         79 :   bias_output_active_(false),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         79 :   bias_output_stride_(0),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         79 :   fes_output_active_(false),</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         79 :   fes_output_stride_(0),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         79 :   fesproj_output_active_(false),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         79 :   fesproj_output_stride_(0),</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         79 :   targetdist_output_active_(false),</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         79 :   targetdist_output_stride_(0),</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         79 :   targetdist_proj_output_active_(false),</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         79 :   targetdist_proj_output_stride_(0),</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        316 :   isFirstStep(true)</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : {</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         79 :   std::vector&lt;std::string&gt; bias_labels(0);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        158 :   parseVector(&quot;BIAS&quot;,bias_labels);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         79 :   plumed_massert(bias_labels.size()&gt;0,&quot;problem with BIAS keyword&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         79 :   nbiases_ = bias_labels.size();</span></a>
+<a name="91"><span class="lineNum">      91 </span>            :   //</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         79 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        158 :   bias_pntrs_ = VesTools::getPointersFromLabels&lt;VesBias*&gt;(bias_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         79 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword BIAS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        164 :   for(unsigned int i=0; i&lt;bias_pntrs_.size(); i++) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         85 :     bias_pntrs_[i]-&gt;linkOptimizer(this);</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :     //</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         85 :     std::vector&lt;CoeffsVector*&gt; pntrs_coeffs = bias_pntrs_[i]-&gt;getCoeffsPntrs();</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         85 :     std::vector&lt;CoeffsVector*&gt; pntrs_gradient = bias_pntrs_[i]-&gt;getGradientPntrs();</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         85 :     std::vector&lt;CoeffsVector*&gt; pntrs_targetdist_averages = bias_pntrs_[i]-&gt;getTargetDistAveragesPntrs();</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         85 :     plumed_massert(pntrs_coeffs.size()==pntrs_gradient.size(),&quot;something wrong in the coefficients and gradient passed from VES bias&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         85 :     plumed_massert(pntrs_coeffs.size()==pntrs_targetdist_averages.size(),&quot;something wrong in the coefficients and target distribution averages passed from VES bias&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        170 :     for(unsigned int k=0; k&lt;pntrs_coeffs.size(); k++) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">         85 :       plumed_massert(pntrs_coeffs[k] != NULL,&quot;some coefficient is not linked correctly&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         85 :       plumed_massert(pntrs_gradient[k] != NULL,&quot;some gradient is not linked correctly&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         85 :       plumed_massert(pntrs_targetdist_averages[k] != NULL,&quot;some target distribution average is not linked correctly&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :       pntrs_coeffs[k]-&gt;turnOnIterationCounter();</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         85 :       coeffs_pntrs_.push_back(pntrs_coeffs[k]);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         85 :       pntrs_gradient[k]-&gt;turnOnIterationCounter();</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         85 :       gradient_pntrs_.push_back(pntrs_gradient[k]);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         85 :       pntrs_targetdist_averages[k]-&gt;turnOnIterationCounter();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         85 :       targetdist_averages_pntrs_.push_back(pntrs_targetdist_averages[k]);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :       //</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         85 :       auto aux_coeffs_tmp = Tools::make_unique&lt;CoeffsVector&gt;(*pntrs_coeffs[k]);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         85 :       std::string aux_label = pntrs_coeffs[k]-&gt;getLabel();</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         85 :       if(aux_label.find(&quot;coeffs&quot;)!=std::string::npos) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        170 :         aux_label.replace(aux_label.find(&quot;coeffs&quot;), std::string(&quot;coeffs&quot;).length(), &quot;aux_coeffs&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :       }</a>
+<a name="120"><span class="lineNum">     120 </span>            :       else {</a>
+<a name="121"><span class="lineNum">     121 </span>            :         aux_label += &quot;_aux&quot;;</a>
+<a name="122"><span class="lineNum">     122 </span>            :       }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         85 :       aux_coeffs_tmp-&gt;setLabels(aux_label);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         85 :       aux_coeffs_pntrs_.emplace_back(std::move(aux_coeffs_tmp));</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         85 :       AuxCoeffs(i).setValues( Coeffs(i) );</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         85 :     }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   }</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         79 :   ncoeffssets_ = coeffs_pntrs_.size();</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         79 :   plumed_massert(aux_coeffs_pntrs_.size()==ncoeffssets_,&quot;problems in linking aux coefficients&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         79 :   plumed_massert(gradient_pntrs_.size()==ncoeffssets_,&quot;problems in linking gradients&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         79 :   setAllCoeffsSetIterationCounters();</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            :   //</a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         79 :   identical_coeffs_shape_ = true;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         85 :   for(unsigned int i=1; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :     if(!coeffs_pntrs_[0]-&gt;sameShape(*coeffs_pntrs_[i])) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :       identical_coeffs_shape_ = false;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            :   //</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;STEPSIZE&quot;)) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        154 :     plumed_assert(!keywords.exists(&quot;INITIAL_STEPSIZE&quot;));</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         77 :     fixed_stepsize_=true;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         77 :     parseMultipleValues(&quot;STEPSIZE&quot;,stepsizes_);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         77 :     setCurrentStepSizes(stepsizes_);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;INITIAL_STEPSIZE&quot;)) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          2 :     plumed_assert(!keywords.exists(&quot;STEPSIZE&quot;));</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          1 :     fixed_stepsize_=false;</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          1 :     parseMultipleValues(&quot;INITIAL_STEPSIZE&quot;,stepsizes_);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          1 :     setCurrentStepSizes(stepsizes_);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span>            :   //</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         79 :   if(ncoeffssets_==1) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         76 :     log.printf(&quot;  optimizing VES bias %s with label %s: \n&quot;,bias_pntrs_[0]-&gt;getName().c_str(),bias_pntrs_[0]-&gt;getLabel().c_str());</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         76 :     log.printf(&quot;   KbT: %f\n&quot;,bias_pntrs_[0]-&gt;getKbT());</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         76 :     log.printf(&quot;  number of coefficients: %zu\n&quot;,coeffs_pntrs_[0]-&gt;numberOfCoeffs());</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         76 :     if(stepsizes_.size()&gt;0) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         75 :       if(fixed_stepsize_) {log.printf(&quot;  using a constant step size of %f\n&quot;,stepsizes_[0]);}</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          1 :       else {log.printf(&quot;  using an initial step size of %f\n&quot;,stepsizes_[0]);}</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :     }</a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span>            :   else {</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          3 :     log.printf(&quot;  optimizing %u coefficient sets from following %u VES biases:\n&quot;,ncoeffssets_,nbiases_);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         12 :     for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          9 :       log.printf(&quot;   %s of type %s (KbT: %f) \n&quot;,bias_pntrs_[i]-&gt;getLabel().c_str(),bias_pntrs_[i]-&gt;getName().c_str(),bias_pntrs_[i]-&gt;getKbT());</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :     }</a>
+<a name="170"><span class="lineNum">     170 </span>            :     size_t tot_ncoeffs = 0;</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         12 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          9 :       log.printf(&quot;  coefficient set %u: \n&quot;,i);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 :       log.printf(&quot;   used in bias %s (type %s)\n&quot;,coeffs_pntrs_[i]-&gt;getPntrToAction()-&gt;getLabel().c_str(),coeffs_pntrs_[i]-&gt;getPntrToAction()-&gt;getName().c_str());</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          9 :       log.printf(&quot;   number of coefficients: %zu\n&quot;,coeffs_pntrs_[i]-&gt;numberOfCoeffs());</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          9 :       if(stepsizes_.size()&gt;0) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          9 :         if(fixed_stepsize_) {log.printf(&quot;   using a constant step size of %f\n&quot;,stepsizes_[i]);}</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :         else {log.printf(&quot;   using an initial step size of %f\n&quot;,stepsizes_[i]);}</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :       }</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          9 :       tot_ncoeffs += coeffs_pntrs_[i]-&gt;numberOfCoeffs();</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :     }</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          3 :     log.printf(&quot;  total number of coefficients: %zu\n&quot;,tot_ncoeffs);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          3 :     if(identical_coeffs_shape_) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :       log.printf(&quot;  the indices shape is identical for all coefficient sets\n&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     }</a>
+<a name="185"><span class="lineNum">     185 </span>            :     else {</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :       log.printf(&quot;  the indices shape differs between coefficient sets\n&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :     }</a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            :   //</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;FULL_HESSIAN&quot;)) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     bool full_hessian=false;</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     parseFlag(&quot;FULL_HESSIAN&quot;,full_hessian);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :     diagonal_hessian_ = !full_hessian;</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :   }</a>
+<a name="196"><span class="lineNum">     196 </span>            :   //</a>
+<a name="197"><span class="lineNum">     197 </span>            :   bool mw_single_files = false;</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;MULTIPLE_WALKERS&quot;)) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         79 :     parseFlag(&quot;MULTIPLE_WALKERS&quot;,use_mwalkers_mpi_);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         79 :     if(use_mwalkers_mpi_) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :       mw_single_files=true;</a>
+<a name="202"><span class="lineNum">     202 </span>            :     }</a>
+<a name="203"><span class="lineNum">     203 </span>            :   }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         79 :   int numwalkers=1;</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         79 :   int walker_rank=0;</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         79 :   if(comm.Get_rank()==0) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         70 :     numwalkers = multi_sim_comm.Get_size();</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         70 :     walker_rank = multi_sim_comm.Get_rank();</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         79 :   comm.Bcast(numwalkers,0);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         79 :   comm.Bcast(walker_rank,0);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         79 :   if(use_mwalkers_mpi_ &amp;&amp; numwalkers==1) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;using the MULTIPLE_WALKERS keyword does not make sense if running the MD code with a single replica&quot;);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         79 :   if(use_mwalkers_mpi_) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         12 :     log.printf(&quot;  optimization performed using multiple walkers connected via MPI:\n&quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         12 :     log.printf(&quot;   number of walkers: %d\n&quot;,numwalkers);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         12 :     log.printf(&quot;   walker number: %d\n&quot;,walker_rank);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         12 :     log.printf(&quot;   please see and cite &quot;);</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         24 :     log &lt;&lt; plumed.cite(&quot;Raiteri, Laio, Gervasio, Micheletti, and Parrinello, J. Phys. Chem. B 110, 3533 (2006)&quot;);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         12 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   }</a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         79 :   dynamic_targetdists_.resize(nbiases_,false);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;TARGETDIST_STRIDE&quot;)) {</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     bool need_stride = false;</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">        162 :     for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         84 :       dynamic_targetdists_[i] = bias_pntrs_[i]-&gt;dynamicTargetDistribution();</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         84 :       if(dynamic_targetdists_[i]) {need_stride = true;}</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     }</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         78 :     parse(&quot;TARGETDIST_STRIDE&quot;,ustride_targetdist_);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         78 :     if(need_stride &amp;&amp; ustride_targetdist_==0) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;one of the biases has a dynamic target distribution so you need to give stride for updating it by using the TARGETDIST_STRIDE keyword&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         78 :     if(!need_stride &amp;&amp; ustride_targetdist_!=0) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;using the TARGETDIST_STRIDE keyword doesn't make sense as there is no dynamic target distribution to update&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :     }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         78 :     if(ustride_targetdist_&gt;0) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">         38 :       if(nbiases_==1) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         38 :         log.printf(&quot;  the target distribution will be updated very %u coefficient iterations\n&quot;,ustride_targetdist_);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :       }</a>
+<a name="243"><span class="lineNum">     243 </span>            :       else {</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :         log.printf(&quot;  the target distribution will be updated very %u coefficient iterations for the following biases\n   &quot;,ustride_targetdist_);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :         for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :           log.printf(&quot;%s &quot;,bias_pntrs_[i]-&gt;getLabel().c_str());</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :         }</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :         log.printf(&quot;\n&quot;);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :       }</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         38 :       log.printf(&quot;  See and cite &quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         76 :       log &lt;&lt; plumed.cite(&quot;Valsson and Parrinello, J. Chem. Theory Comput. 11, 1996-2002 (2015)&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         38 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :     }</a>
+<a name="254"><span class="lineNum">     254 </span>            :   }</a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;REWEIGHT_FACTOR_STRIDE&quot;)) {</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :     bool reweightfactor_calculated = false;</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineNoCov">          0 :     for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineNoCov">          0 :       reweightfactor_calculated = bias_pntrs_[i]-&gt;isReweightFactorCalculated();</span></a>
+<a name="260"><span class="lineNum">     260 </span>            :     }</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :     parse(&quot;REWEIGHT_FACTOR_STRIDE&quot;,ustride_reweightfactor_);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :     if(ustride_reweightfactor_==0 &amp;&amp; reweightfactor_calculated) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;the calculation of the reweight factor is enabled, You need to use the REWEIGHT_FACTOR_STRIDE keyword to specfiy how often it should be updated.&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :     }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 :     if(ustride_reweightfactor_&gt;0) {</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineNoCov">          0 :       if(!reweightfactor_calculated) {</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;In order to use the REWEIGHT_FACTOR_STRIDE keyword you need to enable the calculation of the reweight factor in the VES bias by using the CALC_REWEIGHT_FACTOR flag.&quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :       }</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineNoCov">          0 :       log.printf(&quot;  the reweight factor c(t) will be updated very %u coefficient iterations\n&quot;,ustride_reweightfactor_);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     }</a>
+<a name="271"><span class="lineNum">     271 </span>            :   }</a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;MONITOR_INSTANTANEOUS_GRADIENT&quot;)) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">        158 :     parseFlag(&quot;MONITOR_INSTANTANEOUS_GRADIENT&quot;,monitor_instantaneous_gradient_);</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :   }</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;MONITOR_AVERAGE_GRADIENT&quot;)) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         76 :     bool monitor_aver_gradient = false;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         76 :     parseFlag(&quot;MONITOR_AVERAGE_GRADIENT&quot;,monitor_aver_gradient);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">         76 :     if(monitor_aver_gradient) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          2 :       unsigned int averaging_exp_decay=0;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          4 :       parse(&quot;MONITOR_AVERAGES_GRADIENT_EXP_DECAY&quot;,averaging_exp_decay);</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :       aver_gradient_pntrs_.clear();</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          4 :       for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          2 :         auto aver_gradient_tmp = Tools::make_unique&lt;CoeffsVector&gt;(*gradient_pntrs_[i]);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          2 :         aver_gradient_tmp-&gt;clear();</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :         std::string aver_grad_label = aver_gradient_tmp-&gt;getLabel();</a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          2 :         if(aver_grad_label.find(&quot;gradient&quot;)!=std::string::npos) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          4 :           aver_grad_label.replace(aver_grad_label.find(&quot;gradient&quot;), std::string(&quot;gradient&quot;).length(), &quot;aver_gradient&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :         }</a>
+<a name="291"><span class="lineNum">     291 </span>            :         else {</a>
+<a name="292"><span class="lineNum">     292 </span>            :           aver_grad_label += &quot;_aver&quot;;</a>
+<a name="293"><span class="lineNum">     293 </span>            :         }</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          2 :         aver_gradient_tmp-&gt;setLabels(aver_grad_label);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          2 :         if(averaging_exp_decay&gt;0) {</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :           aver_gradient_tmp-&gt;setupExponentiallyDecayingAveraging(averaging_exp_decay);</a>
+<a name="297"><span class="lineNum">     297 </span>            :         }</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          2 :         aver_gradient_pntrs_.emplace_back(std::move(aver_gradient_tmp));</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          2 :       }</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     }</a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         79 :   if(ncoeffssets_&gt;1) {</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :     coeffssetid_prefix_=&quot;c-&quot;;</a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          6 :     if(keywords.exists(&quot;COEFFS_SET_ID_PREFIX&quot;)) {</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">          6 :       parse(&quot;COEFFS_SET_ID_PREFIX&quot;,coeffssetid_prefix_);</span></a>
+<a name="308"><span class="lineNum">     308 </span>            :     }</a>
+<a name="309"><span class="lineNum">     309 </span>            :   }</a>
+<a name="310"><span class="lineNum">     310 </span>            :   else {</a>
+<a name="311"><span class="lineNum">     311 </span>            :     coeffssetid_prefix_=&quot;&quot;;</a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">        152 :     if(keywords.exists(&quot;COEFFS_SET_ID_PREFIX&quot;)) {</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">        152 :       parse(&quot;COEFFS_SET_ID_PREFIX&quot;,coeffssetid_prefix_);</span></a>
+<a name="314"><span class="lineNum">     314 </span>            :     }</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         76 :     if(coeffssetid_prefix_.size()&gt;0) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;COEFFS_SET_ID_PREFIX should only be given if optimizing multiple coefficient sets&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     }</a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;INITIAL_COEFFS&quot;)) {</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :     std::vector&lt;std::string&gt; initial_coeffs_fnames;</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">        158 :     parseFilenames(&quot;INITIAL_COEFFS&quot;,initial_coeffs_fnames);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         79 :     if(initial_coeffs_fnames.size()&gt;0) {</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          1 :       readCoeffsFromFiles(initial_coeffs_fnames,false);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          1 :       comm.Barrier();</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">          1 :       if(comm.Get_rank()==0 &amp;&amp; use_mwalkers_mpi_) {</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineNoCov">          0 :         multi_sim_comm.Barrier();</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :       }</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          1 :       setAllCoeffsSetIterationCounters();</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :     }</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         79 :   }</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :   //</a>
+<a name="333"><span class="lineNum">     333 </span>            : </a>
+<a name="334"><span class="lineNum">     334 </span>            :   std::vector&lt;std::string&gt; coeffs_fnames;</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;COEFFS_FILE&quot;)) {</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">        158 :     parseFilenames(&quot;COEFFS_FILE&quot;,coeffs_fnames,&quot;coeffs.data&quot;);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         79 :     bool start_opt_afresh=false;</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        158 :     if(keywords.exists(&quot;START_OPTIMIZATION_AFRESH&quot;)) {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         76 :       parseFlag(&quot;START_OPTIMIZATION_AFRESH&quot;,start_opt_afresh);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         76 :       if(start_opt_afresh &amp;&amp; !getRestart()) {</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;the START_OPTIMIZATION_AFRESH keyword should only be used when a restart has been triggered by the RESTART keyword or the MD code&quot;);</span></a>
+<a name="342"><span class="lineNum">     342 </span>            :       }</a>
+<a name="343"><span class="lineNum">     343 </span>            :     }</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">         79 :     if(getRestart()) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">         28 :       for(unsigned int i=0; i&lt;coeffs_fnames.size(); i++) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         15 :         IFile ifile;</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         15 :         ifile.link(*this);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         19 :         if(use_mwalkers_mpi_) {ifile.enforceSuffix(&quot;&quot;);}</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         15 :         bool file_exist = ifile.FileExist(coeffs_fnames[i]);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">         15 :         if(!file_exist) {</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :           std::string fname = FileBase::appendSuffix(coeffs_fnames[i],ifile.getSuffix());</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :           plumed_merror(&quot;Cannot find coefficient file &quot; + fname + &quot; when trying to restart an optimzation. If you don't want to restart the optimzation please remove the RESTART keyword or use the RESTART=NO within the &quot;+getName()+&quot; action to locally disable the restart.&quot;);</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :         }</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         15 :       }</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         13 :       readCoeffsFromFiles(coeffs_fnames,true);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">         13 :       comm.Barrier();</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         13 :       if(comm.Get_rank()==0 &amp;&amp; use_mwalkers_mpi_) {</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">          4 :         multi_sim_comm.Barrier();</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :       }</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         13 :       unsigned int iter_opt_tmp = coeffs_pntrs_[0]-&gt;getIterationCounter();</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         15 :       for(unsigned int i=1; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          2 :         plumed_massert(coeffs_pntrs_[i]-&gt;getIterationCounter()==iter_opt_tmp,&quot;the iteraton counter should be the same for all files when restarting from previous coefficient files\n&quot;);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :       }</a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">         13 :       if(start_opt_afresh) {</span></a>
+<a name="365"><span class="lineNum">     365 </span>            :         setIterationCounter(0);</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          1 :         log.printf(&quot;  Optimization started afresh at iteration %u\n&quot;,getIterationCounter());</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          2 :         for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          1 :           AuxCoeffs(i).setValues( Coeffs(i) );</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :         }</a>
+<a name="370"><span class="lineNum">     370 </span>            :       }</a>
+<a name="371"><span class="lineNum">     371 </span>            :       else {</a>
+<a name="372"><span class="lineNum">     372 </span>            :         setIterationCounter(coeffs_pntrs_[0]-&gt;getIterationCounter());</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         12 :         log.printf(&quot;  Optimization restarted at iteration %u\n&quot;,getIterationCounter());</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :       }</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         13 :       setAllCoeffsSetIterationCounters();</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :     }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">         79 :     std::string coeffs_wstride_tmpstr=&quot;&quot;;</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">        158 :     parse(&quot;COEFFS_OUTPUT&quot;,coeffs_wstride_tmpstr);</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         79 :     if(coeffs_wstride_tmpstr!=&quot;OFF&quot; &amp;&amp; coeffs_wstride_tmpstr.size()&gt;0) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         79 :       Tools::convert(coeffs_wstride_tmpstr,coeffs_wstride_);</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :     }</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         79 :     if(coeffs_wstride_tmpstr==&quot;OFF&quot;) {</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :       coeffs_fnames.clear();</a>
+<a name="385"><span class="lineNum">     385 </span>            :     }</a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         79 :     setupOFiles(coeffs_fnames,coeffsOFiles_,mw_single_files);</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">        158 :     parse(&quot;COEFFS_FMT&quot;,coeffs_output_fmt_);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         79 :     if(coeffs_output_fmt_.size()&gt;0) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        162 :       for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">         84 :         coeffs_pntrs_[i]-&gt;setOutputFmt(coeffs_output_fmt_);</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :       }</a>
+<a name="392"><span class="lineNum">     392 </span>            :     }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         79 :     if(!getRestart()) {</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        136 :       for(unsigned int i=0; i&lt;coeffsOFiles_.size(); i++) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         70 :         coeffs_pntrs_[i]-&gt;writeToFile(*coeffsOFiles_[i],aux_coeffs_pntrs_[i].get(),false);</span></a>
+<a name="396"><span class="lineNum">     396 </span>            :       }</a>
+<a name="397"><span class="lineNum">     397 </span>            :     }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">         79 :     if(coeffs_fnames.size()&gt;0) {</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         79 :       if(ncoeffssets_==1) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">        152 :         log.printf(&quot;  Coefficients will be written out to file %s every %u iterations\n&quot;,coeffsOFiles_[0]-&gt;getPath().c_str(),coeffs_wstride_);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :       }</a>
+<a name="402"><span class="lineNum">     402 </span>            :       else {</a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">          3 :         log.printf(&quot;  Coefficients will be written out to the following files every %u iterations:\n&quot;,coeffs_wstride_);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         12 :         for(unsigned int i=0; i&lt;coeffs_fnames.size(); i++) {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         18 :           log.printf(&quot;   coefficient set %u: %s\n&quot;,i,coeffsOFiles_[i]-&gt;getPath().c_str());</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :         }</a>
+<a name="407"><span class="lineNum">     407 </span>            :       }</a>
+<a name="408"><span class="lineNum">     408 </span>            :     }</a>
+<a name="409"><span class="lineNum">     409 </span>            :     else {</a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineNoCov">          0 :       log.printf(&quot;  Output of coefficients to file has been disabled\n&quot;);</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :     }</a>
+<a name="412"><span class="lineNum">     412 </span>            :   }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            :   std::vector&lt;std::string&gt; gradient_fnames;</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;GRADIENT_FILE&quot;)) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         79 :     parseFilenames(&quot;GRADIENT_FILE&quot;,gradient_fnames);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">        158 :     parse(&quot;GRADIENT_OUTPUT&quot;,gradient_wstride_);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            : </a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">         79 :     if(coeffs_fnames.size()&gt;0) {</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">        151 :       for(unsigned int i=0; i&lt;gradient_fnames.size(); i++) {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">         72 :         plumed_massert(gradient_fnames[i]!=coeffs_fnames[i],&quot;COEFFS_FILE and GRADIENT_FILE cannot be the same&quot;);</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :       }</a>
+<a name="423"><span class="lineNum">     423 </span>            :     }</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">         79 :     setupOFiles(gradient_fnames,gradientOFiles_,mw_single_files);</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">        158 :     parse(&quot;GRADIENT_FMT&quot;,gradient_output_fmt_);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         79 :     if(gradient_output_fmt_.size()&gt;0) {</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">        138 :       for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">         72 :         gradient_pntrs_[i]-&gt;setOutputFmt(gradient_output_fmt_);</span></a>
+<a name="429"><span class="lineNum">     429 </span>            :       }</a>
+<a name="430"><span class="lineNum">     430 </span>            :     }</a>
+<a name="431"><span class="lineNum">     431 </span>            : </a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">         79 :     if(gradient_fnames.size()&gt;0) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">         66 :       if(ncoeffssets_==1) {</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        126 :         log.printf(&quot;  Gradient will be written out to file %s every %u iterations\n&quot;,gradientOFiles_[0]-&gt;getPath().c_str(),gradient_wstride_);</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :       }</a>
+<a name="436"><span class="lineNum">     436 </span>            :       else {</a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">          3 :         log.printf(&quot;  Gradient will be written out to the following files every %u iterations:\n&quot;,gradient_wstride_);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">         12 :         for(unsigned int i=0; i&lt;gradient_fnames.size(); i++) {</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">         18 :           log.printf(&quot;   coefficient set %u: %s\n&quot;,i,gradientOFiles_[i]-&gt;getPath().c_str());</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :         }</a>
+<a name="441"><span class="lineNum">     441 </span>            :       }</a>
+<a name="442"><span class="lineNum">     442 </span>            :     }</a>
+<a name="443"><span class="lineNum">     443 </span>            :   }</a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span>            :   std::vector&lt;std::string&gt; hessian_fnames;</a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;HESSIAN_FILE&quot;)) {</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">         76 :     parseFilenames(&quot;HESSIAN_FILE&quot;,hessian_fnames);</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">        152 :     parse(&quot;HESSIAN_OUTPUT&quot;,hessian_wstride_);</span></a>
+<a name="449"><span class="lineNum">     449 </span>            : </a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">         76 :     if(coeffs_fnames.size()&gt;0) {</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">        142 :       for(unsigned int i=0; i&lt;hessian_fnames.size(); i++) {</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">         66 :         plumed_massert(hessian_fnames[i]!=coeffs_fnames[i],&quot;COEFFS_FILE and HESSIAN_FILE cannot be the same&quot;);</span></a>
+<a name="453"><span class="lineNum">     453 </span>            :       }</a>
+<a name="454"><span class="lineNum">     454 </span>            :     }</a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">         76 :     if(gradient_fnames.size()&gt;0) {</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">        131 :       for(unsigned int i=0; i&lt;hessian_fnames.size(); i++) {</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         66 :         plumed_massert(hessian_fnames[i]!=gradient_fnames[i],&quot;GRADIENT_FILE and HESSIAN_FILE cannot be the same&quot;);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :       }</a>
+<a name="459"><span class="lineNum">     459 </span>            :     }</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         76 :     setupOFiles(hessian_fnames,hessianOFiles_,mw_single_files);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">        152 :     parse(&quot;HESSIAN_FMT&quot;,hessian_output_fmt_);</span></a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">         76 :     if(hessian_fnames.size()&gt;0) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">         62 :       if(ncoeffssets_==1) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">        120 :         log.printf(&quot;  Hessian will be written out to file %s every %u iterations\n&quot;,hessianOFiles_[0]-&gt;getPath().c_str(),hessian_wstride_);</span></a>
+<a name="466"><span class="lineNum">     466 </span>            :       }</a>
+<a name="467"><span class="lineNum">     467 </span>            :       else {</a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          2 :         log.printf(&quot;  Hessian will be written out to the following files every %u iterations:\n&quot;,hessian_wstride_);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          8 :         for(unsigned int i=0; i&lt;hessian_fnames.size(); i++) {</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">         12 :           log.printf(&quot;   coefficient set %u: %s\n&quot;,i,hessianOFiles_[i]-&gt;getPath().c_str());</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :         }</a>
+<a name="472"><span class="lineNum">     472 </span>            :       }</a>
+<a name="473"><span class="lineNum">     473 </span>            :     }</a>
+<a name="474"><span class="lineNum">     474 </span>            :   }</a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span>            :   //</a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;MASK_FILE&quot;)) {</span></a>
+<a name="479"><span class="lineNum">     479 </span>            :     std::vector&lt;std::string&gt; mask_fnames_in;</a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">        156 :     parseVector(&quot;MASK_FILE&quot;,mask_fnames_in);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">         78 :     if(mask_fnames_in.size()==1 &amp;&amp; ncoeffssets_&gt;1) {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineNoCov">          0 :       if(identical_coeffs_shape_) {mask_fnames_in.resize(ncoeffssets_,mask_fnames_in[0]);}</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineNoCov">          0 :       else {plumed_merror(&quot;the coefficients indices shape differs between biases so you need to give a separate file for each coefficient set\n&quot;);}</span></a>
+<a name="484"><span class="lineNum">     484 </span>            :     }</a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">         78 :     if(mask_fnames_in.size()&gt;0 &amp;&amp; mask_fnames_in.size()!=ncoeffssets_) {</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Error in MASK_FILE keyword: either give one value for all biases or a separate value for each coefficient set&quot;);</span></a>
+<a name="487"><span class="lineNum">     487 </span>            :     }</a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         78 :     coeffs_mask_pntrs_.resize(ncoeffssets_);</span></a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineCov">        162 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">        168 :       coeffs_mask_pntrs_[i] = Tools::make_unique&lt;CoeffsVector&gt;(*coeffs_pntrs_[i]);</span></a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">        168 :       coeffs_mask_pntrs_[i]-&gt;setLabels(&quot;mask&quot;);</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">         84 :       coeffs_mask_pntrs_[i]-&gt;setValues(1.0);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">        168 :       coeffs_mask_pntrs_[i]-&gt;setOutputFmt(&quot;%f&quot;);</span></a>
+<a name="495"><span class="lineNum">     495 </span>            :     }</a>
+<a name="496"><span class="lineNum">     496 </span>            : </a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">         78 :     if(mask_fnames_in.size()&gt;0) {</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">          1 :       if(ncoeffssets_==1) {</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          1 :         size_t nread = coeffs_mask_pntrs_[0]-&gt;readFromFile(mask_fnames_in[0],true,true);</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          1 :         log.printf(&quot;  read %zu values from mask file %s\n&quot;,nread,mask_fnames_in[0].c_str());</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          1 :         size_t ndeactived = coeffs_mask_pntrs_[0]-&gt;countValues(0.0);</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          1 :         log.printf(&quot;  deactived optimization of %zu coefficients\n&quot;,ndeactived);</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :       }</a>
+<a name="504"><span class="lineNum">     504 </span>            :       else {</a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineNoCov">          0 :         for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineNoCov">          0 :           size_t nread = coeffs_mask_pntrs_[i]-&gt;readFromFile(mask_fnames_in[i],true,true);</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineNoCov">          0 :           log.printf(&quot;  mask for coefficient set %u:\n&quot;,i);</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineNoCov">          0 :           log.printf(&quot;   read %zu values from file %s\n&quot;,nread,mask_fnames_in[i].c_str());</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineNoCov">          0 :           size_t ndeactived = coeffs_mask_pntrs_[0]-&gt;countValues(0.0);</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineNoCov">          0 :           log.printf(&quot;   deactived optimization of %zu coefficients\n&quot;,ndeactived);</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :         }</a>
+<a name="512"><span class="lineNum">     512 </span>            :       }</a>
+<a name="513"><span class="lineNum">     513 </span>            :     }</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :     std::vector&lt;std::string&gt; mask_fnames_out;</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">         78 :     parseFilenames(&quot;OUTPUT_MASK_FILE&quot;,mask_fnames_out);</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         79 :     for(unsigned int i=0; i&lt;mask_fnames_out.size(); i++) {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">          1 :       if(mask_fnames_in.size()&gt;0) {</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">          1 :         plumed_massert(mask_fnames_out[i]!=mask_fnames_in[i],&quot;MASK_FILE and OUTPUT_MASK_FILE cannot be the same&quot;);</span></a>
+<a name="521"><span class="lineNum">     521 </span>            :       }</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">          1 :       OFile maskOFile;</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">          1 :       maskOFile.link(*this);</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">          1 :       maskOFile.enforceBackup();</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">          1 :       if(use_mwalkers_mpi_ &amp;&amp; mwalkers_mpi_single_files_) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :         unsigned int r=0;</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :         if(comm.Get_rank()==0) {r=multi_sim_comm.Get_rank();}</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 :         comm.Bcast(r,0);</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineNoCov">          0 :         if(r&gt;0) {mask_fnames_out[i]=&quot;/dev/null&quot;;}</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineNoCov">          0 :         maskOFile.enforceSuffix(&quot;&quot;);</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :       }</a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">          1 :       maskOFile.open(mask_fnames_out[i]);</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">          1 :       coeffs_mask_pntrs_[i]-&gt;writeToFile(maskOFile,true);</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">          1 :       maskOFile.close();</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">          1 :     }</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         78 :   }</span></a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">         79 :   if(getRestart() &amp;&amp; ustride_targetdist_&gt;0) {</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         16 :     for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">          8 :       if(dynamic_targetdists_[i]) {</span></a>
+<a name="541"><span class="lineNum">     541 </span><span class="lineCov">          8 :         bias_pntrs_[i]-&gt;restartTargetDistributions();</span></a>
+<a name="542"><span class="lineNum">     542 </span>            :       }</a>
+<a name="543"><span class="lineNum">     543 </span>            :     }</a>
+<a name="544"><span class="lineNum">     544 </span>            :   }</a>
+<a name="545"><span class="lineNum">     545 </span>            : </a>
+<a name="546"><span class="lineNum">     546 </span>            : </a>
+<a name="547"><span class="lineNum">     547 </span>            :   std::vector&lt;std::string&gt; targetdist_averages_fnames;</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;TARGETDIST_AVERAGES_FILE&quot;)) {</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">        158 :     parseFilenames(&quot;TARGETDIST_AVERAGES_FILE&quot;,targetdist_averages_fnames,&quot;targetdist-averages.data&quot;);</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        158 :     parse(&quot;TARGETDIST_AVERAGES_OUTPUT&quot;,targetdist_averages_wstride_);</span></a>
+<a name="551"><span class="lineNum">     551 </span>            : </a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineCov">         79 :     if(coeffs_fnames.size()&gt;0) {</span></a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">        164 :       for(unsigned int i=0; i&lt;targetdist_averages_fnames.size(); i++) {</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">         85 :         plumed_massert(targetdist_averages_fnames[i]!=coeffs_fnames[i],&quot;COEFFS_FILE and TARGETDIST_AVERAGES_FILE cannot be the same&quot;);</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :       }</a>
+<a name="556"><span class="lineNum">     556 </span>            :     }</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">         79 :     if(gradient_fnames.size()&gt;0) {</span></a>
+<a name="558"><span class="lineNum">     558 </span><span class="lineCov">        138 :       for(unsigned int i=0; i&lt;targetdist_averages_fnames.size(); i++) {</span></a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">         72 :         plumed_massert(targetdist_averages_fnames[i]!=gradient_fnames[i],&quot;GRADIENT_FILE and TARGETDIST_AVERAGES_FILE cannot be the same&quot;);</span></a>
+<a name="560"><span class="lineNum">     560 </span>            :       }</a>
+<a name="561"><span class="lineNum">     561 </span>            :     }</a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">         79 :     if(hessian_fnames.size()&gt;0) {</span></a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">        128 :       for(unsigned int i=0; i&lt;targetdist_averages_fnames.size(); i++) {</span></a>
+<a name="564"><span class="lineNum">     564 </span><span class="lineCov">         66 :         plumed_massert(targetdist_averages_fnames[i]!=hessian_fnames[i],&quot;HESSIAN_FILE and TARGETDIST_AVERAGES_FILE cannot be the same&quot;);</span></a>
+<a name="565"><span class="lineNum">     565 </span>            :       }</a>
+<a name="566"><span class="lineNum">     566 </span>            :     }</a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">         79 :     setupOFiles(targetdist_averages_fnames,targetdist_averagesOFiles_,mw_single_files);</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">        158 :     parse(&quot;TARGETDIST_AVERAGES_FMT&quot;,targetdist_averages_output_fmt_);</span></a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineCov">         79 :     if(targetdist_averages_output_fmt_.size()&gt;0) {</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineCov">        156 :       for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">         81 :         targetdist_averages_pntrs_[i]-&gt;setOutputFmt(targetdist_averages_output_fmt_);</span></a>
+<a name="572"><span class="lineNum">     572 </span>            :       }</a>
+<a name="573"><span class="lineNum">     573 </span>            :     }</a>
+<a name="574"><span class="lineNum">     574 </span>            : </a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">        164 :     for(unsigned int i=0; i&lt;targetdist_averagesOFiles_.size(); i++) {</span></a>
+<a name="576"><span class="lineNum">     576 </span><span class="lineCov">         85 :       targetdist_averages_pntrs_[i]-&gt;writeToFile(*targetdist_averagesOFiles_[i]);</span></a>
+<a name="577"><span class="lineNum">     577 </span>            :     }</a>
+<a name="578"><span class="lineNum">     578 </span>            : </a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         79 :     if(targetdist_averages_wstride_==0) {</span></a>
+<a name="580"><span class="lineNum">     580 </span>            :       targetdist_averagesOFiles_.clear();</a>
+<a name="581"><span class="lineNum">     581 </span>            :     }</a>
+<a name="582"><span class="lineNum">     582 </span>            : </a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         79 :     if(targetdist_averages_fnames.size()&gt;0 &amp;&amp; targetdist_averages_wstride_ &gt; 0) {</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">         34 :       if(ncoeffssets_==1) {</span></a>
+<a name="585"><span class="lineNum">     585 </span><span class="lineCov">         68 :         log.printf(&quot;  Target distribution averages will be written out to file %s every %u iterations\n&quot;,targetdist_averagesOFiles_[0]-&gt;getPath().c_str(),targetdist_averages_wstride_);</span></a>
+<a name="586"><span class="lineNum">     586 </span>            :       }</a>
+<a name="587"><span class="lineNum">     587 </span>            :       else {</a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineNoCov">          0 :         log.printf(&quot;  Target distribution averages will be written out to the following files every %u iterations:\n&quot;,targetdist_averages_wstride_);</span></a>
+<a name="589"><span class="lineNum">     589 </span><span class="lineNoCov">          0 :         for(unsigned int i=0; i&lt;targetdist_averages_fnames.size(); i++) {</span></a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineNoCov">          0 :           log.printf(&quot;   coefficient set %u: %s\n&quot;,i,targetdist_averagesOFiles_[i]-&gt;getPath().c_str());</span></a>
+<a name="591"><span class="lineNum">     591 </span>            :         }</a>
+<a name="592"><span class="lineNum">     592 </span>            :       }</a>
+<a name="593"><span class="lineNum">     593 </span>            :     }</a>
+<a name="594"><span class="lineNum">     594 </span>            :   }</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            : </a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;BIAS_OUTPUT&quot;)) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineCov">         79 :     parse(&quot;BIAS_OUTPUT&quot;,bias_output_stride_);</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">         79 :     if(bias_output_stride_&gt;0) {</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">         74 :       bias_output_active_=true;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">        154 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         80 :         bias_pntrs_[i]-&gt;enableBiasFileOutput();</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">         80 :         bias_pntrs_[i]-&gt;setupBiasFileOutput();</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">         80 :         bias_pntrs_[i]-&gt;writeBiasToFile();</span></a>
+<a name="605"><span class="lineNum">     605 </span>            :       }</a>
+<a name="606"><span class="lineNum">     606 </span>            :     }</a>
+<a name="607"><span class="lineNum">     607 </span>            :     else {</a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">          5 :       bias_output_active_=false;</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">          5 :       bias_output_stride_=1000;</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :     }</a>
+<a name="611"><span class="lineNum">     611 </span>            :   }</a>
+<a name="612"><span class="lineNum">     612 </span>            : </a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;FES_OUTPUT&quot;)) {</span></a>
+<a name="614"><span class="lineNum">     614 </span><span class="lineCov">         79 :     parse(&quot;FES_OUTPUT&quot;,fes_output_stride_);</span></a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">         79 :     if(fes_output_stride_&gt;0) {</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">         74 :       fes_output_active_=true;</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">        154 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">         80 :         bias_pntrs_[i]-&gt;enableFesFileOutput();</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">         80 :         bias_pntrs_[i]-&gt;setupFesFileOutput();</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">         80 :         bias_pntrs_[i]-&gt;writeFesToFile();</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :       }</a>
+<a name="622"><span class="lineNum">     622 </span>            :     }</a>
+<a name="623"><span class="lineNum">     623 </span>            :     else {</a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">          5 :       fes_output_active_=false;</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">          5 :       fes_output_stride_=1000;</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :     }</a>
+<a name="627"><span class="lineNum">     627 </span>            :   }</a>
+<a name="628"><span class="lineNum">     628 </span>            : </a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;FES_PROJ_OUTPUT&quot;)) {</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         79 :     parse(&quot;FES_PROJ_OUTPUT&quot;,fesproj_output_stride_);</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         79 :     if(fesproj_output_stride_&gt;0) {</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">         16 :       fesproj_output_active_=true;</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">         32 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="634"><span class="lineNum">     634 </span><span class="lineCov">         16 :         bias_pntrs_[i]-&gt;enableFesProjFileOutput();</span></a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">         16 :         bias_pntrs_[i]-&gt;setupFesProjFileOutput();</span></a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineCov">         16 :         bias_pntrs_[i]-&gt;writeFesProjToFile();</span></a>
+<a name="637"><span class="lineNum">     637 </span>            :       }</a>
+<a name="638"><span class="lineNum">     638 </span>            :     }</a>
+<a name="639"><span class="lineNum">     639 </span>            :     else {</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">         63 :       fesproj_output_active_=false;</span></a>
+<a name="641"><span class="lineNum">     641 </span><span class="lineCov">         63 :       fesproj_output_stride_=1000;</span></a>
+<a name="642"><span class="lineNum">     642 </span>            :     }</a>
+<a name="643"><span class="lineNum">     643 </span>            :   }</a>
+<a name="644"><span class="lineNum">     644 </span>            : </a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">        164 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">         85 :     if(!dynamic_targetdists_[i] &amp;&amp; bias_pntrs_[i]-&gt;isStaticTargetDistFileOutputActive()) {</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          4 :       bias_pntrs_[i]-&gt;setupTargetDistFileOutput();</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">          4 :       bias_pntrs_[i]-&gt;writeTargetDistToFile();</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          4 :       bias_pntrs_[i]-&gt;setupTargetDistProjFileOutput();</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          4 :       bias_pntrs_[i]-&gt;writeTargetDistProjToFile();</span></a>
+<a name="651"><span class="lineNum">     651 </span>            :     }</a>
+<a name="652"><span class="lineNum">     652 </span>            :   }</a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;TARGETDIST_OUTPUT&quot;)) {</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineCov">         78 :     parse(&quot;TARGETDIST_OUTPUT&quot;,targetdist_output_stride_);</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineCov">         78 :     if(targetdist_output_stride_&gt;0) {</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineCov">         37 :       if(ustride_targetdist_==0) {</span></a>
+<a name="658"><span class="lineNum">     658 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;it doesn't make sense to use the TARGETDIST_OUTPUT keyword if you don't have a target distribution that needs to be updated&quot;);</span></a>
+<a name="659"><span class="lineNum">     659 </span>            :       }</a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">         37 :       if(targetdist_output_stride_%ustride_targetdist_!=0) {</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;the value given in TARGETDIST_OUTPUT doesn't make sense, it should be multiple of TARGETDIST_STRIDE&quot;);</span></a>
+<a name="662"><span class="lineNum">     662 </span>            :       }</a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         37 :       if(targetdist_output_stride_%coeffs_wstride_!=0) {</span></a>
+<a name="664"><span class="lineNum">     664 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;the value given in TARGETDIST_OUTPUT doesn't make sense, it should be multiple of COEFFS_OUTPUT&quot;);</span></a>
+<a name="665"><span class="lineNum">     665 </span>            :       }</a>
+<a name="666"><span class="lineNum">     666 </span>            : </a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         37 :       targetdist_output_active_=true;</span></a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">         74 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">         37 :         if(dynamic_targetdists_[i]) {</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">         37 :           bias_pntrs_[i]-&gt;enableDynamicTargetDistFileOutput();</span></a>
+<a name="671"><span class="lineNum">     671 </span><span class="lineCov">         37 :           bias_pntrs_[i]-&gt;setupTargetDistFileOutput();</span></a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">         37 :           bias_pntrs_[i]-&gt;writeTargetDistToFile();</span></a>
+<a name="673"><span class="lineNum">     673 </span>            :         }</a>
+<a name="674"><span class="lineNum">     674 </span>            :       }</a>
+<a name="675"><span class="lineNum">     675 </span>            :     }</a>
+<a name="676"><span class="lineNum">     676 </span>            :     else {</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         41 :       targetdist_output_active_=false;</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">         41 :       targetdist_output_stride_=1000;</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :     }</a>
+<a name="680"><span class="lineNum">     680 </span>            :   }</a>
+<a name="681"><span class="lineNum">     681 </span>            : </a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">        158 :   if(keywords.exists(&quot;TARGETDIST_PROJ_OUTPUT&quot;)) {</span></a>
+<a name="683"><span class="lineNum">     683 </span><span class="lineCov">         78 :     parse(&quot;TARGETDIST_PROJ_OUTPUT&quot;,targetdist_proj_output_stride_);</span></a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         78 :     if(targetdist_proj_output_stride_&gt;0) {</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">          3 :       if(ustride_targetdist_==0) {</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;it doesn't make sense to use the TARGETDIST_PROJ_OUTPUT keyword if you don't have a target distribution that needs to be updated&quot;);</span></a>
+<a name="687"><span class="lineNum">     687 </span>            :       }</a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">          3 :       if(targetdist_proj_output_stride_%ustride_targetdist_!=0) {</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;the value given in TARGETDIST_PROJ_OUTPUT doesn't make sense, it should be multiple of TARGETDIST_STRIDE&quot;);</span></a>
+<a name="690"><span class="lineNum">     690 </span>            :       }</a>
+<a name="691"><span class="lineNum">     691 </span>            : </a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">          3 :       targetdist_proj_output_active_=true;</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">          6 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineCov">          3 :         if(dynamic_targetdists_[i]) {</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineCov">          3 :           bias_pntrs_[i]-&gt;enableDynamicTargetDistFileOutput();</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineCov">          3 :           bias_pntrs_[i]-&gt;setupTargetDistProjFileOutput();</span></a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">          3 :           bias_pntrs_[i]-&gt;writeTargetDistProjToFile();</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :         }</a>
+<a name="699"><span class="lineNum">     699 </span>            :       }</a>
+<a name="700"><span class="lineNum">     700 </span>            :     }</a>
+<a name="701"><span class="lineNum">     701 </span>            :     else {</a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">         75 :       targetdist_proj_output_active_=false;</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         75 :       targetdist_proj_output_stride_=1000;</span></a>
+<a name="704"><span class="lineNum">     704 </span>            :     }</a>
+<a name="705"><span class="lineNum">     705 </span>            :   }</a>
+<a name="706"><span class="lineNum">     706 </span>            : </a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         79 :   if(ncoeffssets_==1) {</span></a>
+<a name="708"><span class="lineNum">     708 </span><span class="lineCov">         76 :     log.printf(&quot;  Output Components:\n&quot;);</span></a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         76 :     log.printf(&quot; &quot;);</span></a>
+<a name="710"><span class="lineNum">     710 </span><span class="lineCov">         76 :     if(monitor_instantaneous_gradient_) {</span></a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">          6 :       addComponent(&quot;gradrms&quot;); componentIsNotPeriodic(&quot;gradrms&quot;);</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">          3 :       log.printf(&quot; &quot;);</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">          9 :       addComponent(&quot;gradmax&quot;); componentIsNotPeriodic(&quot;gradmax&quot;);</span></a>
+<a name="714"><span class="lineNum">     714 </span>            :     }</a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">         76 :     if(aver_gradient_pntrs_.size()&gt;0) {</span></a>
+<a name="716"><span class="lineNum">     716 </span><span class="lineCov">          2 :       log.printf(&quot; &quot;);</span></a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineCov">          4 :       addComponent(&quot;avergradrms&quot;); componentIsNotPeriodic(&quot;avergradrms&quot;);</span></a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">          2 :       log.printf(&quot; &quot;);</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">          6 :       addComponent(&quot;avergradmax&quot;); componentIsNotPeriodic(&quot;avergradmax&quot;);</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :     }</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">         76 :     if(!fixed_stepsize_) {</span></a>
+<a name="722"><span class="lineNum">     722 </span><span class="lineCov">          1 :       log.printf(&quot; &quot;);</span></a>
+<a name="723"><span class="lineNum">     723 </span><span class="lineCov">          2 :       addComponent(&quot;stepsize&quot;); componentIsNotPeriodic(&quot;stepsize&quot;);</span></a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">          2 :       getPntrToComponent(&quot;stepsize&quot;)-&gt;set( getCurrentStepSize(0) );</span></a>
+<a name="725"><span class="lineNum">     725 </span>            :     }</a>
+<a name="726"><span class="lineNum">     726 </span>            :   }</a>
+<a name="727"><span class="lineNum">     727 </span>            :   else {</a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">         12 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="729"><span class="lineNum">     729 </span><span class="lineCov">          9 :       log.printf(&quot;  Output Components for coefficient set %u:\n&quot;,i);</span></a>
+<a name="730"><span class="lineNum">     730 </span><span class="lineCov">         18 :       std::string is=&quot;&quot;; Tools::convert(i,is); is = &quot;-&quot; + coeffssetid_prefix_ + is;</span></a>
+<a name="731"><span class="lineNum">     731 </span><span class="lineCov">          9 :       log.printf(&quot; &quot;);</span></a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">          9 :       if(monitor_instantaneous_gradient_) {</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">          6 :         addComponent(&quot;gradrms&quot;+is); componentIsNotPeriodic(&quot;gradrms&quot;+is);</span></a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">          3 :         log.printf(&quot; &quot;);</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">          9 :         addComponent(&quot;gradmax&quot;+is); componentIsNotPeriodic(&quot;gradmax&quot;+is);</span></a>
+<a name="736"><span class="lineNum">     736 </span>            :       }</a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">          9 :       if(aver_gradient_pntrs_.size()&gt;0) {</span></a>
+<a name="738"><span class="lineNum">     738 </span><span class="lineNoCov">          0 :         log.printf(&quot; &quot;);</span></a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineNoCov">          0 :         addComponent(&quot;avergradrms&quot;+is); componentIsNotPeriodic(&quot;avergradrms&quot;+is);</span></a>
+<a name="740"><span class="lineNum">     740 </span><span class="lineNoCov">          0 :         log.printf(&quot; &quot;);</span></a>
+<a name="741"><span class="lineNum">     741 </span><span class="lineNoCov">          0 :         addComponent(&quot;avergradmax&quot;+is); componentIsNotPeriodic(&quot;avergradmax&quot;+is);</span></a>
+<a name="742"><span class="lineNum">     742 </span>            :       }</a>
+<a name="743"><span class="lineNum">     743 </span><span class="lineCov">          9 :       if(!fixed_stepsize_) {</span></a>
+<a name="744"><span class="lineNum">     744 </span><span class="lineNoCov">          0 :         log.printf(&quot; &quot;);</span></a>
+<a name="745"><span class="lineNum">     745 </span><span class="lineNoCov">          0 :         addComponent(&quot;stepsize&quot;+is); componentIsNotPeriodic(&quot;stepsize&quot;+is);</span></a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 :         getPntrToComponent(&quot;stepsize&quot;+is)-&gt;set( getCurrentStepSize(i) );</span></a>
+<a name="747"><span class="lineNum">     747 </span>            :       }</a>
+<a name="748"><span class="lineNum">     748 </span>            :     }</a>
+<a name="749"><span class="lineNum">     749 </span>            :   }</a>
+<a name="750"><span class="lineNum">     750 </span>            : </a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineCov">        158 : }</span></a>
+<a name="752"><span class="lineNum">     752 </span>            : </a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineCov">         79 : Optimizer::~Optimizer() {</span></a>
+<a name="755"><span class="lineNum">     755 </span>            :   //</a>
+<a name="756"><span class="lineNum">     756 </span><span class="lineCov">        164 :   for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="757"><span class="lineNum">     757 </span><span class="lineCov">         85 :     if(coeffsOFiles_.size()&gt;0 &amp;&amp; getIterationCounter()%coeffs_wstride_!=0) {</span></a>
+<a name="758"><span class="lineNum">     758 </span><span class="lineCov">          2 :       coeffs_pntrs_[i]-&gt;writeToFile(*coeffsOFiles_[i],aux_coeffs_pntrs_[i].get(),false);</span></a>
+<a name="759"><span class="lineNum">     759 </span>            :     }</a>
+<a name="760"><span class="lineNum">     760 </span><span class="lineCov">         85 :     if(targetdist_averagesOFiles_.size()&gt;0 &amp;&amp; iter_counter%targetdist_averages_wstride_!=0) {</span></a>
+<a name="761"><span class="lineNum">     761 </span><span class="lineCov">          1 :       targetdist_averages_pntrs_[i]-&gt;writeToFile(*targetdist_averagesOFiles_[i]);</span></a>
+<a name="762"><span class="lineNum">     762 </span>            :     }</a>
+<a name="763"><span class="lineNum">     763 </span>            :   }</a>
+<a name="764"><span class="lineNum">     764 </span>            :   //</a>
+<a name="765"><span class="lineNum">     765 </span><span class="lineCov">         79 :   if(!isTargetDistOutputActive()) {</span></a>
+<a name="766"><span class="lineNum">     766 </span><span class="lineCov">         90 :     for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">         48 :       if(dynamic_targetdists_[i]) {</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">          1 :         bias_pntrs_[i]-&gt;enableDynamicTargetDistFileOutput();</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">          1 :         bias_pntrs_[i]-&gt;setupTargetDistFileOutput();</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">          1 :         bias_pntrs_[i]-&gt;writeTargetDistToFile();</span></a>
+<a name="771"><span class="lineNum">     771 </span>            :       }</a>
+<a name="772"><span class="lineNum">     772 </span>            :     }</a>
+<a name="773"><span class="lineNum">     773 </span>            :   }</a>
+<a name="774"><span class="lineNum">     774 </span>            :   //</a>
+<a name="775"><span class="lineNum">     775 </span><span class="lineCov">         79 :   if(isBiasOutputActive() &amp;&amp; getIterationCounter()%getBiasOutputStride()!=0) {</span></a>
+<a name="776"><span class="lineNum">     776 </span><span class="lineCov">          1 :     writeBiasOutputFiles();</span></a>
+<a name="777"><span class="lineNum">     777 </span>            :   }</a>
+<a name="778"><span class="lineNum">     778 </span><span class="lineCov">         79 :   if(isFesOutputActive() &amp;&amp; getIterationCounter()%getFesOutputStride()!=0) {</span></a>
+<a name="779"><span class="lineNum">     779 </span><span class="lineCov">          1 :     writeFesOutputFiles();</span></a>
+<a name="780"><span class="lineNum">     780 </span>            :   }</a>
+<a name="781"><span class="lineNum">     781 </span><span class="lineCov">         79 :   if(isFesProjOutputActive() &amp;&amp; getIterationCounter()%getFesProjOutputStride()!=0) {</span></a>
+<a name="782"><span class="lineNum">     782 </span><span class="lineCov">          1 :     writeFesProjOutputFiles();</span></a>
+<a name="783"><span class="lineNum">     783 </span>            :   }</a>
+<a name="784"><span class="lineNum">     784 </span><span class="lineCov">         79 :   if(isTargetDistOutputActive() &amp;&amp; getIterationCounter()%getTargetDistOutputStride()!=0) {</span></a>
+<a name="785"><span class="lineNum">     785 </span><span class="lineCov">          2 :     writeTargetDistOutputFiles();</span></a>
+<a name="786"><span class="lineNum">     786 </span>            :   }</a>
+<a name="787"><span class="lineNum">     787 </span><span class="lineCov">         79 :   if(isTargetDistProjOutputActive() &amp;&amp; getIterationCounter()%getTargetDistProjOutputStride()!=0) {</span></a>
+<a name="788"><span class="lineNum">     788 </span><span class="lineCov">          1 :     writeTargetDistProjOutputFiles();</span></a>
+<a name="789"><span class="lineNum">     789 </span>            :   }</a>
+<a name="790"><span class="lineNum">     790 </span><span class="lineCov">        395 : }</span></a>
+<a name="791"><span class="lineNum">     791 </span>            : </a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span><span class="lineCov">         87 : void Optimizer::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="794"><span class="lineNum">     794 </span><span class="lineCov">         87 :   Action::registerKeywords(keys);</span></a>
+<a name="795"><span class="lineNum">     795 </span><span class="lineCov">         87 :   ActionPilot::registerKeywords(keys);</span></a>
+<a name="796"><span class="lineNum">     796 </span><span class="lineCov">         87 :   ActionWithValue::registerKeywords(keys);</span></a>
+<a name="797"><span class="lineNum">     797 </span>            :   //</a>
+<a name="798"><span class="lineNum">     798 </span><span class="lineCov">         87 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="799"><span class="lineNum">     799 </span>            :   // Default always active keywords</a>
+<a name="800"><span class="lineNum">     800 </span><span class="lineCov">        174 :   keys.add(&quot;compulsory&quot;,&quot;BIAS&quot;,&quot;the label of the VES bias to be optimized&quot;);</span></a>
+<a name="801"><span class="lineNum">     801 </span><span class="lineCov">        174 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;the frequency of updating the coefficients given in the number of MD steps.&quot;);</span></a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">        174 :   keys.add(&quot;compulsory&quot;,&quot;COEFFS_FILE&quot;,&quot;coeffs.data&quot;,&quot;the name of output file for the coefficients&quot;);</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">        174 :   keys.add(&quot;compulsory&quot;,&quot;COEFFS_OUTPUT&quot;,&quot;100&quot;,&quot;how often the coefficients should be written to file. This parameter is given as the number of iterations.&quot;);</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;COEFFS_FMT&quot;,&quot;specify format for coefficient file(s) (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;COEFFS_SET_ID_PREFIX&quot;,&quot;suffix to add to the filename given in FILE to identify the bias, should only be given if a single filename is given in FILE when optimizing multiple biases.&quot;);</span></a>
+<a name="806"><span class="lineNum">     806 </span>            :   //</a>
+<a name="807"><span class="lineNum">     807 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;INITIAL_COEFFS&quot;,&quot;the name(s) of file(s) with the initial coefficients&quot;);</span></a>
+<a name="808"><span class="lineNum">     808 </span>            :   // Hidden keywords to output the gradient to a file.</a>
+<a name="809"><span class="lineNum">     809 </span><span class="lineCov">        174 :   keys.add(&quot;hidden&quot;,&quot;GRADIENT_FILE&quot;,&quot;the name of output file for the gradient&quot;);</span></a>
+<a name="810"><span class="lineNum">     810 </span><span class="lineCov">        174 :   keys.add(&quot;hidden&quot;,&quot;GRADIENT_OUTPUT&quot;,&quot;how often the gradient should be written to file. This parameter is given as the number of bias iterations. It is by default 100 if GRADIENT_FILE is specficed&quot;);</span></a>
+<a name="811"><span class="lineNum">     811 </span><span class="lineCov">        174 :   keys.add(&quot;hidden&quot;,&quot;GRADIENT_FMT&quot;,&quot;specify format for gradient file(s) (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="812"><span class="lineNum">     812 </span>            :   // Either use a fixed stepsize (useFixedStepSizeKeywords) or changing stepsize (useDynamicsStepSizeKeywords)</a>
+<a name="813"><span class="lineNum">     813 </span><span class="lineCov">        174 :   keys.reserve(&quot;compulsory&quot;,&quot;STEPSIZE&quot;,&quot;the step size used for the optimization&quot;);</span></a>
+<a name="814"><span class="lineNum">     814 </span><span class="lineCov">        174 :   keys.reserve(&quot;compulsory&quot;,&quot;INITIAL_STEPSIZE&quot;,&quot;the initial step size used for the optimization&quot;);</span></a>
+<a name="815"><span class="lineNum">     815 </span>            :   // Keywords related to the Hessian, actived with the useHessianKeywords function</a>
+<a name="816"><span class="lineNum">     816 </span><span class="lineCov">        174 :   keys.reserveFlag(&quot;FULL_HESSIAN&quot;,false,&quot;if the full Hessian matrix should be used for the optimization, otherwise only the diagonal part of the Hessian is used&quot;);</span></a>
+<a name="817"><span class="lineNum">     817 </span><span class="lineCov">        174 :   keys.reserve(&quot;hidden&quot;,&quot;HESSIAN_FILE&quot;,&quot;the name of output file for the Hessian&quot;);</span></a>
+<a name="818"><span class="lineNum">     818 </span><span class="lineCov">        174 :   keys.reserve(&quot;hidden&quot;,&quot;HESSIAN_OUTPUT&quot;,&quot;how often the Hessian should be written to file. This parameter is given as the number of bias iterations. It is by default 100 if HESSIAN_FILE is specficed&quot;);</span></a>
+<a name="819"><span class="lineNum">     819 </span><span class="lineCov">        174 :   keys.reserve(&quot;hidden&quot;,&quot;HESSIAN_FMT&quot;,&quot;specify format for hessian file(s) (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="820"><span class="lineNum">     820 </span>            :   // Keywords related to the multiple walkers, actived with the useMultipleWalkersKeywords function</a>
+<a name="821"><span class="lineNum">     821 </span><span class="lineCov">        174 :   keys.reserveFlag(&quot;MULTIPLE_WALKERS&quot;,false,&quot;if optimization is to be performed using multiple walkers connected via MPI&quot;);</span></a>
+<a name="822"><span class="lineNum">     822 </span>            :   // Keywords related to the mask file, actived with the useMaskKeywords function</a>
+<a name="823"><span class="lineNum">     823 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;MASK_FILE&quot;,&quot;read in a mask file which allows one to employ different step sizes for different coefficients and/or deactivate the optimization of certain coefficients (by putting values of 0.0). One can write out the resulting mask by using the OUTPUT_MASK_FILE keyword.&quot;);</span></a>
+<a name="824"><span class="lineNum">     824 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;OUTPUT_MASK_FILE&quot;,&quot;Name of the file to write out the mask resulting from using the MASK_FILE keyword. Can also be used to generate a template mask file.&quot;);</span></a>
+<a name="825"><span class="lineNum">     825 </span>            :   //</a>
+<a name="826"><span class="lineNum">     826 </span><span class="lineCov">        174 :   keys.reserveFlag(&quot;START_OPTIMIZATION_AFRESH&quot;,false,&quot;if the iterations should be started afresh when a restart has been triggered by the RESTART keyword or the MD code.&quot;);</span></a>
+<a name="827"><span class="lineNum">     827 </span>            :   //</a>
+<a name="828"><span class="lineNum">     828 </span><span class="lineCov">        174 :   keys.addFlag(&quot;MONITOR_INSTANTANEOUS_GRADIENT&quot;,false,&quot;if quantities related to the instantaneous gradient should be outputted.&quot;);</span></a>
+<a name="829"><span class="lineNum">     829 </span>            :   //</a>
+<a name="830"><span class="lineNum">     830 </span><span class="lineCov">        174 :   keys.reserveFlag(&quot;MONITOR_AVERAGE_GRADIENT&quot;,false,&quot;if the averaged gradient should be monitored and quantities related to it should be outputted.&quot;);</span></a>
+<a name="831"><span class="lineNum">     831 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;MONITOR_AVERAGES_GRADIENT_EXP_DECAY&quot;,&quot;use an exponentially decaying averaging with a given time constant when monitoring the averaged gradient&quot;);</span></a>
+<a name="832"><span class="lineNum">     832 </span>            :   //</a>
+<a name="833"><span class="lineNum">     833 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;TARGETDIST_STRIDE&quot;,&quot;stride for updating a target distribution that is iteratively updated during the optimization. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="834"><span class="lineNum">     834 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;TARGETDIST_OUTPUT&quot;,&quot;how often the dynamic target distribution(s) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="835"><span class="lineNum">     835 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;TARGETDIST_PROJ_OUTPUT&quot;,&quot;how often the projections of the dynamic target distribution(s) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="836"><span class="lineNum">     836 </span>            :   //</a>
+<a name="837"><span class="lineNum">     837 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;TARGETDIST_AVERAGES_FILE&quot;,&quot;the name of output file for the target distribution averages. By default it is targetdist-averages.data.&quot;);</span></a>
+<a name="838"><span class="lineNum">     838 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;TARGETDIST_AVERAGES_OUTPUT&quot;,&quot;how often the target distribution averages should be written out to file. Note that the value is given in terms of coefficient iterations. If no value is given are the averages only written at the beginning of the optimization&quot;);</span></a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">        174 :   keys.add(&quot;hidden&quot;,&quot;TARGETDIST_AVERAGES_FMT&quot;,&quot;specify format for target distribution averages file(s) (useful for decrease the number of digits in regtests)&quot;);</span></a>
+<a name="840"><span class="lineNum">     840 </span>            :   //</a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;BIAS_OUTPUT&quot;,&quot;how often the bias(es) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;FES_OUTPUT&quot;,&quot;how often the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="843"><span class="lineNum">     843 </span><span class="lineCov">        174 :   keys.add(&quot;optional&quot;,&quot;FES_PROJ_OUTPUT&quot;,&quot;how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="844"><span class="lineNum">     844 </span>            :   //</a>
+<a name="845"><span class="lineNum">     845 </span><span class="lineCov">        174 :   keys.reserve(&quot;optional&quot;,&quot;REWEIGHT_FACTOR_STRIDE&quot;,&quot;stride for updating the reweighting factor c(t). Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="846"><span class="lineNum">     846 </span>            :   //</a>
+<a name="847"><span class="lineNum">     847 </span><span class="lineCov">         87 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="848"><span class="lineNum">     848 </span>            :   //</a>
+<a name="849"><span class="lineNum">     849 </span><span class="lineCov">         87 :   keys.use(&quot;UPDATE_FROM&quot;);</span></a>
+<a name="850"><span class="lineNum">     850 </span><span class="lineCov">         87 :   keys.use(&quot;UPDATE_UNTIL&quot;);</span></a>
+<a name="851"><span class="lineNum">     851 </span>            :   // Components that are always active</a>
+<a name="852"><span class="lineNum">     852 </span><span class="lineCov">        174 :   keys.addOutputComponent(&quot;gradrms&quot;,&quot;MONITOR_INSTANTANEOUS_GRADIENT&quot;,&quot;the root mean square value of the coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.&quot;);</span></a>
+<a name="853"><span class="lineNum">     853 </span><span class="lineCov">        174 :   keys.addOutputComponent(&quot;gradmax&quot;,&quot;MONITOR_INSTANTANEOUS_GRADIENT&quot;,&quot;the largest absolute value of the coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.&quot;);</span></a>
+<a name="854"><span class="lineNum">     854 </span>            :   // keys.addOutputComponent(&quot;gradmaxidx&quot;,&quot;default&quot;,&quot;the index of the maximum absolute value of the gradient&quot;);</a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span><span class="lineCov">         87 : }</span></a>
+<a name="857"><span class="lineNum">     857 </span>            : </a>
+<a name="858"><span class="lineNum">     858 </span>            : </a>
+<a name="859"><span class="lineNum">     859 </span><span class="lineCov">         80 : void Optimizer::useHessianKeywords(Keywords&amp; keys) {</span></a>
+<a name="860"><span class="lineNum">     860 </span>            :   // keys.use(&quot;FULL_HESSIAN&quot;);</a>
+<a name="861"><span class="lineNum">     861 </span><span class="lineCov">         80 :   keys.use(&quot;HESSIAN_FILE&quot;);</span></a>
+<a name="862"><span class="lineNum">     862 </span><span class="lineCov">         80 :   keys.use(&quot;HESSIAN_OUTPUT&quot;);</span></a>
+<a name="863"><span class="lineNum">     863 </span><span class="lineCov">         80 :   keys.use(&quot;HESSIAN_FMT&quot;);</span></a>
+<a name="864"><span class="lineNum">     864 </span><span class="lineCov">         80 : }</span></a>
+<a name="865"><span class="lineNum">     865 </span>            : </a>
+<a name="866"><span class="lineNum">     866 </span>            : </a>
+<a name="867"><span class="lineNum">     867 </span><span class="lineCov">         87 : void Optimizer::useMultipleWalkersKeywords(Keywords&amp; keys) {</span></a>
+<a name="868"><span class="lineNum">     868 </span><span class="lineCov">         87 :   keys.use(&quot;MULTIPLE_WALKERS&quot;);</span></a>
+<a name="869"><span class="lineNum">     869 </span><span class="lineCov">         87 : }</span></a>
+<a name="870"><span class="lineNum">     870 </span>            : </a>
+<a name="871"><span class="lineNum">     871 </span>            : </a>
+<a name="872"><span class="lineNum">     872 </span><span class="lineCov">         81 : void Optimizer::useFixedStepSizeKeywords(Keywords&amp; keys) {</span></a>
+<a name="873"><span class="lineNum">     873 </span><span class="lineCov">         81 :   keys.use(&quot;STEPSIZE&quot;);</span></a>
+<a name="874"><span class="lineNum">     874 </span><span class="lineCov">         81 : }</span></a>
+<a name="875"><span class="lineNum">     875 </span>            : </a>
+<a name="876"><span class="lineNum">     876 </span>            : </a>
+<a name="877"><span class="lineNum">     877 </span><span class="lineCov">          3 : void Optimizer::useDynamicStepSizeKeywords(Keywords&amp; keys) {</span></a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">          3 :   keys.use(&quot;INITIAL_STEPSIZE&quot;);</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">          6 :   keys.addOutputComponent(&quot;stepsize&quot;,&quot;default&quot;,&quot;the current value of step size used to update the coefficients. For multiple biases this component is labeled using the number of the bias as stepsize-#.&quot;);</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">          3 : }</span></a>
+<a name="881"><span class="lineNum">     881 </span>            : </a>
+<a name="882"><span class="lineNum">     882 </span>            : </a>
+<a name="883"><span class="lineNum">     883 </span><span class="lineCov">         84 : void Optimizer::useMaskKeywords(Keywords&amp; keys) {</span></a>
+<a name="884"><span class="lineNum">     884 </span><span class="lineCov">         84 :   keys.use(&quot;MASK_FILE&quot;);</span></a>
+<a name="885"><span class="lineNum">     885 </span><span class="lineCov">         84 :   keys.use(&quot;OUTPUT_MASK_FILE&quot;);</span></a>
+<a name="886"><span class="lineNum">     886 </span><span class="lineCov">         84 : }</span></a>
+<a name="887"><span class="lineNum">     887 </span>            : </a>
+<a name="888"><span class="lineNum">     888 </span>            : </a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">         80 : void Optimizer::useRestartKeywords(Keywords&amp; keys) {</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">         80 :   keys.use(&quot;START_OPTIMIZATION_AFRESH&quot;);</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">         80 : }</span></a>
+<a name="892"><span class="lineNum">     892 </span>            : </a>
+<a name="893"><span class="lineNum">     893 </span>            : </a>
+<a name="894"><span class="lineNum">     894 </span><span class="lineCov">         80 : void Optimizer::useMonitorAverageGradientKeywords(Keywords&amp; keys) {</span></a>
+<a name="895"><span class="lineNum">     895 </span><span class="lineCov">         80 :   keys.use(&quot;MONITOR_AVERAGE_GRADIENT&quot;);</span></a>
+<a name="896"><span class="lineNum">     896 </span><span class="lineCov">         80 :   keys.use(&quot;MONITOR_AVERAGES_GRADIENT_EXP_DECAY&quot;);</span></a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineCov">        160 :   keys.addOutputComponent(&quot;avergradrms&quot;,&quot;MONITOR_AVERAGE_GRADIENT&quot;,&quot;the root mean square value of the averaged coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradrms-#.&quot;);</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineCov">        160 :   keys.addOutputComponent(&quot;avergradmax&quot;,&quot;MONITOR_AVERAGE_GRADIENT&quot;,&quot;the largest absolute value of the averaged coefficient gradient. For multiple biases this component is labeled using the number of the bias as gradmax-#.&quot;);</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineCov">         80 : }</span></a>
+<a name="900"><span class="lineNum">     900 </span>            : </a>
+<a name="901"><span class="lineNum">     901 </span>            : </a>
+<a name="902"><span class="lineNum">     902 </span><span class="lineCov">         84 : void Optimizer::useDynamicTargetDistributionKeywords(Keywords&amp; keys) {</span></a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineCov">         84 :   keys.use(&quot;TARGETDIST_STRIDE&quot;);</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineCov">         84 :   keys.use(&quot;TARGETDIST_OUTPUT&quot;);</span></a>
+<a name="905"><span class="lineNum">     905 </span><span class="lineCov">         84 :   keys.use(&quot;TARGETDIST_PROJ_OUTPUT&quot;);</span></a>
+<a name="906"><span class="lineNum">     906 </span><span class="lineCov">         84 : }</span></a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span>            : </a>
+<a name="909"><span class="lineNum">     909 </span><span class="lineNoCov">          0 : void Optimizer::useReweightFactorKeywords(Keywords&amp; keys) {</span></a>
+<a name="910"><span class="lineNum">     910 </span><span class="lineNoCov">          0 :   keys.use(&quot;REWEIGHT_FACTOR_STRIDE&quot;);</span></a>
+<a name="911"><span class="lineNum">     911 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span>            : </a>
+<a name="914"><span class="lineNum">     914 </span><span class="lineCov">         76 : void Optimizer::turnOnHessian() {</span></a>
+<a name="915"><span class="lineNum">     915 </span><span class="lineCov">         76 :   plumed_massert(hessian_pntrs_.size()==0,&quot;turnOnHessian() should only be run during initialization&quot;);</span></a>
+<a name="916"><span class="lineNum">     916 </span><span class="lineCov">         76 :   use_hessian_=true;</span></a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineCov">         76 :   hessian_pntrs_.clear();</span></a>
+<a name="918"><span class="lineNum">     918 </span><span class="lineCov">        158 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">         82 :     std::vector&lt;CoeffsMatrix*&gt; pntrs_hessian = enableHessian(bias_pntrs_[i],diagonal_hessian_);</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">        164 :     for(unsigned int k=0; k&lt;pntrs_hessian.size(); k++) {</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">         82 :       pntrs_hessian[k]-&gt;turnOnIterationCounter();</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineCov">         82 :       pntrs_hessian[k]-&gt;setIterationCounterAndTime(getIterationCounter(),getTime());</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineCov">         82 :       hessian_pntrs_.push_back(pntrs_hessian[k]);</span></a>
+<a name="924"><span class="lineNum">     924 </span>            :     }</a>
+<a name="925"><span class="lineNum">     925 </span>            :   }</a>
+<a name="926"><span class="lineNum">     926 </span><span class="lineCov">         76 :   plumed_massert(hessian_pntrs_.size()==ncoeffssets_,&quot;problems in linking Hessians&quot;);</span></a>
+<a name="927"><span class="lineNum">     927 </span><span class="lineCov">         76 :   if(diagonal_hessian_) {</span></a>
+<a name="928"><span class="lineNum">     928 </span><span class="lineCov">         76 :     log.printf(&quot;  Optimization performed using diagonal Hessian matrix\n&quot;);</span></a>
+<a name="929"><span class="lineNum">     929 </span>            :   }</a>
+<a name="930"><span class="lineNum">     930 </span>            :   else {</a>
+<a name="931"><span class="lineNum">     931 </span><span class="lineNoCov">          0 :     log.printf(&quot;  Optimization performed using full Hessian matrix\n&quot;);</span></a>
+<a name="932"><span class="lineNum">     932 </span>            :   }</a>
+<a name="933"><span class="lineNum">     933 </span>            :   //</a>
+<a name="934"><span class="lineNum">     934 </span><span class="lineCov">         76 :   if(hessian_output_fmt_.size()&gt;0) {</span></a>
+<a name="935"><span class="lineNum">     935 </span><span class="lineCov">        128 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="936"><span class="lineNum">     936 </span><span class="lineCov">         66 :       hessian_pntrs_[i]-&gt;setOutputFmt(hessian_output_fmt_);</span></a>
+<a name="937"><span class="lineNum">     937 </span>            :     }</a>
+<a name="938"><span class="lineNum">     938 </span>            :   }</a>
+<a name="939"><span class="lineNum">     939 </span>            : </a>
+<a name="940"><span class="lineNum">     940 </span><span class="lineCov">         76 : }</span></a>
+<a name="941"><span class="lineNum">     941 </span>            : </a>
+<a name="942"><span class="lineNum">     942 </span>            : </a>
+<a name="943"><span class="lineNum">     943 </span><span class="lineNoCov">          0 : void Optimizer::turnOffHessian() {</span></a>
+<a name="944"><span class="lineNum">     944 </span><span class="lineNoCov">          0 :   use_hessian_=false;</span></a>
+<a name="945"><span class="lineNum">     945 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="946"><span class="lineNum">     946 </span><span class="lineNoCov">          0 :     bias_pntrs_[i]-&gt;disableHessian();</span></a>
+<a name="947"><span class="lineNum">     947 </span>            :   }</a>
+<a name="948"><span class="lineNum">     948 </span>            :   hessian_pntrs_.clear();</a>
+<a name="949"><span class="lineNum">     949 </span><span class="lineNoCov">          0 :   hessianOFiles_.clear();</span></a>
+<a name="950"><span class="lineNum">     950 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="951"><span class="lineNum">     951 </span>            : </a>
+<a name="952"><span class="lineNum">     952 </span>            : </a>
+<a name="953"><span class="lineNum">     953 </span><span class="lineCov">         82 : std::vector&lt;CoeffsMatrix*&gt; Optimizer::enableHessian(VesBias* bias_pntr_in, const bool diagonal_hessian) {</span></a>
+<a name="954"><span class="lineNum">     954 </span><span class="lineCov">         82 :   plumed_massert(use_hessian_,&quot;the Hessian should not be used&quot;);</span></a>
+<a name="955"><span class="lineNum">     955 </span><span class="lineCov">         82 :   bias_pntr_in-&gt;enableHessian(diagonal_hessian);</span></a>
+<a name="956"><span class="lineNum">     956 </span>            :   std::vector&lt;CoeffsMatrix*&gt; hessian_pntrs_out = bias_pntr_in-&gt;getHessianPntrs();</a>
+<a name="957"><span class="lineNum">     957 </span><span class="lineCov">        164 :   for(unsigned int k=0; k&lt;hessian_pntrs_out.size(); k++) {</span></a>
+<a name="958"><span class="lineNum">     958 </span><span class="lineCov">         82 :     plumed_massert(hessian_pntrs_out[k] != NULL,&quot;Hessian is needed but not linked correctly&quot;);</span></a>
+<a name="959"><span class="lineNum">     959 </span>            :   }</a>
+<a name="960"><span class="lineNum">     960 </span><span class="lineCov">         82 :   return hessian_pntrs_out;</span></a>
+<a name="961"><span class="lineNum">     961 </span>            : }</a>
+<a name="962"><span class="lineNum">     962 </span>            : </a>
+<a name="963"><span class="lineNum">     963 </span>            : </a>
+<a name="964"><span class="lineNum">     964 </span>            : // CoeffsMatrix* Optimizer::switchToDiagonalHessian(VesBias* bias_pntr_in) {</a>
+<a name="965"><span class="lineNum">     965 </span>            : //   plumed_massert(use_hessian_,&quot;it does not make sense to switch to diagonal Hessian if it Hessian is not used&quot;);</a>
+<a name="966"><span class="lineNum">     966 </span>            : //   diagonal_hessian_=true;</a>
+<a name="967"><span class="lineNum">     967 </span>            : //   bias_pntr_in-&gt;enableHessian(diagonal_hessian_);</a>
+<a name="968"><span class="lineNum">     968 </span>            : //   CoeffsMatrix* hessian_pntr_out = bias_pntr_in-&gt;getHessianPntr();</a>
+<a name="969"><span class="lineNum">     969 </span>            : //   plumed_massert(hessian_pntr_out != NULL,&quot;Hessian is needed but not linked correctly&quot;);</a>
+<a name="970"><span class="lineNum">     970 </span>            : //   //</a>
+<a name="971"><span class="lineNum">     971 </span>            : //   log.printf(&quot;  %s (with label %s): switching to a diagonal Hessian for VES bias %s (with label %s) at time  %f\n&quot;,getName().c_str(),getLabel().c_str(),bias_pntr_in-&gt;getName().c_str(),bias_pntr_in-&gt;getLabel().c_str(),getTime());</a>
+<a name="972"><span class="lineNum">     972 </span>            : //   return hessian_pntr_out;</a>
+<a name="973"><span class="lineNum">     973 </span>            : // }</a>
+<a name="974"><span class="lineNum">     974 </span>            : </a>
+<a name="975"><span class="lineNum">     975 </span>            : </a>
+<a name="976"><span class="lineNum">     976 </span>            : // CoeffsMatrix* Optimizer::switchToFullHessian(VesBias* bias_pntr_in) {</a>
+<a name="977"><span class="lineNum">     977 </span>            : //   plumed_massert(use_hessian_,&quot;it does not make sense to switch to diagonal Hessian if it Hessian is not used&quot;);</a>
+<a name="978"><span class="lineNum">     978 </span>            : //   diagonal_hessian_=false;</a>
+<a name="979"><span class="lineNum">     979 </span>            : //   bias_pntr_in-&gt;enableHessian(diagonal_hessian_);</a>
+<a name="980"><span class="lineNum">     980 </span>            : //   CoeffsMatrix* hessian_pntr_out = bias_pntr_in-&gt;getHessianPntr();</a>
+<a name="981"><span class="lineNum">     981 </span>            : //   plumed_massert(hessian_pntr_out != NULL,&quot;Hessian is needed but not linked correctly&quot;);</a>
+<a name="982"><span class="lineNum">     982 </span>            : //   //</a>
+<a name="983"><span class="lineNum">     983 </span>            : //   log.printf(&quot;  %s (with label %s): switching to a diagonal Hessian for VES bias %s (with label %s) at time  %f\n&quot;,getName().c_str(),getLabel().c_str(),bias_pntr_in-&gt;getName().c_str(),bias_pntr_in-&gt;getLabel().c_str(),getTime());</a>
+<a name="984"><span class="lineNum">     984 </span>            : //   return hessian_pntr_out;</a>
+<a name="985"><span class="lineNum">     985 </span>            : // }</a>
+<a name="986"><span class="lineNum">     986 </span>            : </a>
+<a name="987"><span class="lineNum">     987 </span>            : </a>
+<a name="988"><span class="lineNum">     988 </span><span class="lineCov">      22879 : void Optimizer::update() {</span></a>
+<a name="989"><span class="lineNum">     989 </span><span class="lineCov">      22879 :   if(onStep() &amp;&amp; !isFirstStep) {</span></a>
+<a name="990"><span class="lineNum">     990 </span><span class="lineCov">      45560 :     for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="991"><span class="lineNum">     991 </span><span class="lineCov">      22810 :       bias_pntrs_[i]-&gt;updateGradientAndHessian(use_mwalkers_mpi_);</span></a>
+<a name="992"><span class="lineNum">     992 </span>            :     }</a>
+<a name="993"><span class="lineNum">     993 </span><span class="lineCov">      45560 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="994"><span class="lineNum">     994 </span><span class="lineCov">      22810 :       if(gradient_pntrs_[i]-&gt;isActive()) {coeffsUpdate(i);}</span></a>
+<a name="995"><span class="lineNum">     995 </span>            :       else {</a>
+<a name="996"><span class="lineNum">     996 </span><span class="lineCov">        190 :         std::string msg = &quot;iteration &quot; + getIterationCounterStr(+1) +</span></a>
+<a name="997"><span class="lineNum">     997 </span><span class="lineCov">        285 :                           &quot; for &quot; + bias_pntrs_[i]-&gt;getLabel() +</span></a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineCov">         95 :                           &quot; - the coefficients are not updated as CV values are outside the bias intervals&quot;;</span></a>
+<a name="999"><span class="lineNum">     999 </span><span class="lineCov">         95 :         warning(msg);</span></a>
+<a name="1000"><span class="lineNum">    1000 </span>            :       }</a>
+<a name="1001"><span class="lineNum">    1001 </span>            : </a>
+<a name="1002"><span class="lineNum">    1002 </span>            :       // +1 as this is done before increaseIterationCounter() is used</a>
+<a name="1003"><span class="lineNum">    1003 </span><span class="lineCov">      22810 :       unsigned int curr_iter = getIterationCounter()+1;</span></a>
+<a name="1004"><span class="lineNum">    1004 </span><span class="lineCov">      22810 :       double curr_time = getTime();</span></a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineCov">      22810 :       coeffs_pntrs_[i]-&gt;setIterationCounterAndTime(curr_iter,curr_time);</span></a>
+<a name="1006"><span class="lineNum">    1006 </span>            :       aux_coeffs_pntrs_[i]-&gt;setIterationCounterAndTime(curr_iter,curr_time);</a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineCov">      22810 :       gradient_pntrs_[i]-&gt;setIterationCounterAndTime(curr_iter,curr_time);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineCov">      22810 :       targetdist_averages_pntrs_[i]-&gt;setIterationCounterAndTime(curr_iter,curr_time);</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineCov">      22810 :       if(use_hessian_) {</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineCov">      22780 :         hessian_pntrs_[i]-&gt;setIterationCounterAndTime(curr_iter,curr_time);</span></a>
+<a name="1011"><span class="lineNum">    1011 </span>            :       }</a>
+<a name="1012"><span class="lineNum">    1012 </span><span class="lineCov">      22810 :       if(aver_gradient_pntrs_.size()&gt;0) {</span></a>
+<a name="1013"><span class="lineNum">    1013 </span>            :         aver_gradient_pntrs_[i]-&gt;setIterationCounterAndTime(curr_iter,curr_time);</a>
+<a name="1014"><span class="lineNum">    1014 </span><span class="lineCov">         20 :         aver_gradient_pntrs_[i]-&gt;addToAverage(*gradient_pntrs_[i]);</span></a>
+<a name="1015"><span class="lineNum">    1015 </span>            :       }</a>
+<a name="1016"><span class="lineNum">    1016 </span>            :     }</a>
+<a name="1017"><span class="lineNum">    1017 </span>            :     increaseIterationCounter();</a>
+<a name="1018"><span class="lineNum">    1018 </span>            : </a>
+<a name="1019"><span class="lineNum">    1019 </span><span class="lineCov">      22750 :     if(ustride_targetdist_&gt;0 &amp;&amp; getIterationCounter()%ustride_targetdist_==0) {</span></a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineCov">        708 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1021"><span class="lineNum">    1021 </span><span class="lineCov">        354 :         if(dynamic_targetdists_[i]) {</span></a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineCov">        354 :           bias_pntrs_[i]-&gt;updateTargetDistributions();</span></a>
+<a name="1023"><span class="lineNum">    1023 </span>            :         }</a>
+<a name="1024"><span class="lineNum">    1024 </span>            :       }</a>
+<a name="1025"><span class="lineNum">    1025 </span>            :     }</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineCov">      22750 :     if(ustride_reweightfactor_&gt;0 &amp;&amp; getIterationCounter()%ustride_reweightfactor_==0) {</span></a>
+<a name="1027"><span class="lineNum">    1027 </span><span class="lineNoCov">          0 :       for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1028"><span class="lineNum">    1028 </span><span class="lineNoCov">          0 :         bias_pntrs_[i]-&gt;updateReweightFactor();</span></a>
+<a name="1029"><span class="lineNum">    1029 </span>            :       }</a>
+<a name="1030"><span class="lineNum">    1030 </span>            :     }</a>
+<a name="1031"><span class="lineNum">    1031 </span>            : </a>
+<a name="1032"><span class="lineNum">    1032 </span><span class="lineCov">      22750 :     updateOutputComponents();</span></a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineCov">      45560 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="1034"><span class="lineNum">    1034 </span><span class="lineCov">      22810 :       writeOutputFiles(i);</span></a>
+<a name="1035"><span class="lineNum">    1035 </span>            :     }</a>
+<a name="1036"><span class="lineNum">    1036 </span>            :     //</a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineCov">      22750 :     if(isBiasOutputActive() &amp;&amp; getIterationCounter()%getBiasOutputStride()==0) {</span></a>
+<a name="1038"><span class="lineNum">    1038 </span><span class="lineCov">         74 :       writeBiasOutputFiles();</span></a>
+<a name="1039"><span class="lineNum">    1039 </span>            :     }</a>
+<a name="1040"><span class="lineNum">    1040 </span><span class="lineCov">      22750 :     if(isFesOutputActive() &amp;&amp; getIterationCounter()%getFesOutputStride()==0) {</span></a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineCov">         74 :       writeFesOutputFiles();</span></a>
+<a name="1042"><span class="lineNum">    1042 </span>            :     }</a>
+<a name="1043"><span class="lineNum">    1043 </span><span class="lineCov">      22750 :     if(isFesProjOutputActive() &amp;&amp; getIterationCounter()%getFesProjOutputStride()==0) {</span></a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineCov">         16 :       writeFesProjOutputFiles();</span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     }</a>
+<a name="1046"><span class="lineNum">    1046 </span><span class="lineCov">      22750 :     if(isTargetDistOutputActive() &amp;&amp; getIterationCounter()%getTargetDistOutputStride()==0) {</span></a>
+<a name="1047"><span class="lineNum">    1047 </span><span class="lineCov">         36 :       writeTargetDistOutputFiles();</span></a>
+<a name="1048"><span class="lineNum">    1048 </span>            :     }</a>
+<a name="1049"><span class="lineNum">    1049 </span><span class="lineCov">      22750 :     if(isTargetDistProjOutputActive() &amp;&amp; getIterationCounter()%getTargetDistProjOutputStride()==0) {</span></a>
+<a name="1050"><span class="lineNum">    1050 </span><span class="lineCov">          3 :       writeTargetDistProjOutputFiles();</span></a>
+<a name="1051"><span class="lineNum">    1051 </span>            :     }</a>
+<a name="1052"><span class="lineNum">    1052 </span>            :   }</a>
+<a name="1053"><span class="lineNum">    1053 </span>            :   else {</a>
+<a name="1054"><span class="lineNum">    1054 </span><span class="lineCov">        129 :     isFirstStep=false;</span></a>
+<a name="1055"><span class="lineNum">    1055 </span>            :   }</a>
+<a name="1056"><span class="lineNum">    1056 </span><span class="lineCov">      22879 : }</span></a>
+<a name="1057"><span class="lineNum">    1057 </span>            : </a>
+<a name="1058"><span class="lineNum">    1058 </span>            : </a>
+<a name="1059"><span class="lineNum">    1059 </span><span class="lineCov">      22750 : void Optimizer::updateOutputComponents() {</span></a>
+<a name="1060"><span class="lineNum">    1060 </span><span class="lineCov">      22750 :   if(ncoeffssets_==1) {</span></a>
+<a name="1061"><span class="lineNum">    1061 </span><span class="lineCov">      22720 :     if(!fixed_stepsize_) {</span></a>
+<a name="1062"><span class="lineNum">    1062 </span><span class="lineCov">         20 :       getPntrToComponent(&quot;stepsize&quot;)-&gt;set( getCurrentStepSize(0) );</span></a>
+<a name="1063"><span class="lineNum">    1063 </span>            :     }</a>
+<a name="1064"><span class="lineNum">    1064 </span><span class="lineCov">      22720 :     if(monitor_instantaneous_gradient_) {</span></a>
+<a name="1065"><span class="lineNum">    1065 </span><span class="lineCov">         30 :       getPntrToComponent(&quot;gradrms&quot;)-&gt;set( gradient_pntrs_[0]-&gt;getRMS() );</span></a>
+<a name="1066"><span class="lineNum">    1066 </span><span class="lineCov">         30 :       size_t gradient_maxabs_idx=0;</span></a>
+<a name="1067"><span class="lineNum">    1067 </span><span class="lineCov">         60 :       getPntrToComponent(&quot;gradmax&quot;)-&gt;set( gradient_pntrs_[0]-&gt;getMaxAbsValue(gradient_maxabs_idx) );</span></a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     }</a>
+<a name="1069"><span class="lineNum">    1069 </span><span class="lineCov">      22720 :     if(aver_gradient_pntrs_.size()&gt;0) {</span></a>
+<a name="1070"><span class="lineNum">    1070 </span><span class="lineCov">         20 :       getPntrToComponent(&quot;avergradrms&quot;)-&gt;set( aver_gradient_pntrs_[0]-&gt;getRMS() );</span></a>
+<a name="1071"><span class="lineNum">    1071 </span><span class="lineCov">         20 :       size_t avergradient_maxabs_idx=0;</span></a>
+<a name="1072"><span class="lineNum">    1072 </span><span class="lineCov">         40 :       getPntrToComponent(&quot;avergradmax&quot;)-&gt;set( aver_gradient_pntrs_[0]-&gt;getMaxAbsValue(avergradient_maxabs_idx) );</span></a>
+<a name="1073"><span class="lineNum">    1073 </span>            :     }</a>
+<a name="1074"><span class="lineNum">    1074 </span>            :   }</a>
+<a name="1075"><span class="lineNum">    1075 </span>            :   else {</a>
+<a name="1076"><span class="lineNum">    1076 </span><span class="lineCov">        120 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="1077"><span class="lineNum">    1077 </span><span class="lineCov">        180 :       std::string is=&quot;&quot;; Tools::convert(i,is); is = &quot;-&quot; + coeffssetid_prefix_ + is;</span></a>
+<a name="1078"><span class="lineNum">    1078 </span><span class="lineCov">         90 :       if(!fixed_stepsize_) {</span></a>
+<a name="1079"><span class="lineNum">    1079 </span><span class="lineNoCov">          0 :         getPntrToComponent(&quot;stepsize&quot;+is)-&gt;set( getCurrentStepSize(i) );</span></a>
+<a name="1080"><span class="lineNum">    1080 </span>            :       }</a>
+<a name="1081"><span class="lineNum">    1081 </span><span class="lineCov">         90 :       if(monitor_instantaneous_gradient_) {</span></a>
+<a name="1082"><span class="lineNum">    1082 </span><span class="lineCov">         30 :         getPntrToComponent(&quot;gradrms&quot;+is)-&gt;set( gradient_pntrs_[i]-&gt;getRMS() );</span></a>
+<a name="1083"><span class="lineNum">    1083 </span><span class="lineCov">         30 :         size_t gradient_maxabs_idx=0;</span></a>
+<a name="1084"><span class="lineNum">    1084 </span><span class="lineCov">         60 :         getPntrToComponent(&quot;gradmax&quot;+is)-&gt;set( gradient_pntrs_[i]-&gt;getMaxAbsValue(gradient_maxabs_idx) );</span></a>
+<a name="1085"><span class="lineNum">    1085 </span>            :       }</a>
+<a name="1086"><span class="lineNum">    1086 </span><span class="lineCov">         90 :       if(aver_gradient_pntrs_.size()&gt;0) {</span></a>
+<a name="1087"><span class="lineNum">    1087 </span><span class="lineNoCov">          0 :         getPntrToComponent(&quot;avergradrms&quot;+is)-&gt;set( aver_gradient_pntrs_[0]-&gt;getRMS() );</span></a>
+<a name="1088"><span class="lineNum">    1088 </span><span class="lineNoCov">          0 :         size_t avergradient_maxabs_idx=0;</span></a>
+<a name="1089"><span class="lineNum">    1089 </span><span class="lineNoCov">          0 :         getPntrToComponent(&quot;avergradmax&quot;+is)-&gt;set( aver_gradient_pntrs_[0]-&gt;getMaxAbsValue(avergradient_maxabs_idx) );</span></a>
+<a name="1090"><span class="lineNum">    1090 </span>            :       }</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :     }</a>
+<a name="1092"><span class="lineNum">    1092 </span>            :   }</a>
+<a name="1093"><span class="lineNum">    1093 </span><span class="lineCov">      22750 : }</span></a>
+<a name="1094"><span class="lineNum">    1094 </span>            : </a>
+<a name="1095"><span class="lineNum">    1095 </span>            : </a>
+<a name="1096"><span class="lineNum">    1096 </span><span class="lineCov">          1 : void Optimizer::turnOffCoeffsOutputFiles() {</span></a>
+<a name="1097"><span class="lineNum">    1097 </span><span class="lineCov">          1 :   coeffsOFiles_.clear();</span></a>
+<a name="1098"><span class="lineNum">    1098 </span><span class="lineCov">          1 : }</span></a>
+<a name="1099"><span class="lineNum">    1099 </span>            : </a>
+<a name="1100"><span class="lineNum">    1100 </span>            : </a>
+<a name="1101"><span class="lineNum">    1101 </span><span class="lineCov">      22810 : void Optimizer::writeOutputFiles(const unsigned int coeffs_id) {</span></a>
+<a name="1102"><span class="lineNum">    1102 </span><span class="lineCov">      22810 :   if(coeffsOFiles_.size()&gt;0 &amp;&amp; iter_counter%coeffs_wstride_==0) {</span></a>
+<a name="1103"><span class="lineNum">    1103 </span><span class="lineCov">        789 :     coeffs_pntrs_[coeffs_id]-&gt;writeToFile(*coeffsOFiles_[coeffs_id],aux_coeffs_pntrs_[coeffs_id].get(),false);</span></a>
+<a name="1104"><span class="lineNum">    1104 </span>            :   }</a>
+<a name="1105"><span class="lineNum">    1105 </span><span class="lineCov">      22810 :   if(gradientOFiles_.size()&gt;0 &amp;&amp; iter_counter%gradient_wstride_==0) {</span></a>
+<a name="1106"><span class="lineNum">    1106 </span><span class="lineCov">        720 :     if(aver_gradient_pntrs_.size()==0) {</span></a>
+<a name="1107"><span class="lineNum">    1107 </span><span class="lineCov">        700 :       gradient_pntrs_[coeffs_id]-&gt;writeToFile(*gradientOFiles_[coeffs_id],false);</span></a>
+<a name="1108"><span class="lineNum">    1108 </span>            :     }</a>
+<a name="1109"><span class="lineNum">    1109 </span>            :     else {</a>
+<a name="1110"><span class="lineNum">    1110 </span><span class="lineCov">         20 :       gradient_pntrs_[coeffs_id]-&gt;writeToFile(*gradientOFiles_[coeffs_id],aver_gradient_pntrs_[coeffs_id].get(),false);</span></a>
+<a name="1111"><span class="lineNum">    1111 </span>            :     }</a>
+<a name="1112"><span class="lineNum">    1112 </span>            :   }</a>
+<a name="1113"><span class="lineNum">    1113 </span><span class="lineCov">      22810 :   if(hessianOFiles_.size()&gt;0 &amp;&amp; iter_counter%hessian_wstride_==0) {</span></a>
+<a name="1114"><span class="lineNum">    1114 </span><span class="lineCov">        660 :     hessian_pntrs_[coeffs_id]-&gt;writeToFile(*hessianOFiles_[coeffs_id]);</span></a>
+<a name="1115"><span class="lineNum">    1115 </span>            :   }</a>
+<a name="1116"><span class="lineNum">    1116 </span><span class="lineCov">      22810 :   if(targetdist_averagesOFiles_.size()&gt;0 &amp;&amp; iter_counter%targetdist_averages_wstride_==0) {</span></a>
+<a name="1117"><span class="lineNum">    1117 </span><span class="lineCov">        333 :     targetdist_averages_pntrs_[coeffs_id]-&gt;writeToFile(*targetdist_averagesOFiles_[coeffs_id]);</span></a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   }</a>
+<a name="1119"><span class="lineNum">    1119 </span><span class="lineCov">      22810 : }</span></a>
+<a name="1120"><span class="lineNum">    1120 </span>            : </a>
+<a name="1121"><span class="lineNum">    1121 </span>            : </a>
+<a name="1122"><span class="lineNum">    1122 </span><span class="lineCov">        388 : void Optimizer::setupOFiles(std::vector&lt;std::string&gt;&amp; fnames, std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt;&amp; OFiles, const bool multi_sim_single_files) {</span></a>
+<a name="1123"><span class="lineNum">    1123 </span><span class="lineCov">        388 :   plumed_assert(ncoeffssets_&gt;0);</span></a>
+<a name="1124"><span class="lineNum">    1124 </span><span class="lineCov">        388 :   OFiles.resize(fnames.size());</span></a>
+<a name="1125"><span class="lineNum">    1125 </span><span class="lineCov">        702 :   for(unsigned int i=0; i&lt;fnames.size(); i++) {</span></a>
+<a name="1126"><span class="lineNum">    1126 </span><span class="lineCov">        628 :     OFiles[i] = Tools::make_unique&lt;OFile&gt;();</span></a>
+<a name="1127"><span class="lineNum">    1127 </span><span class="lineCov">        314 :     OFiles[i]-&gt;link(*this);</span></a>
+<a name="1128"><span class="lineNum">    1128 </span><span class="lineCov">        314 :     if(multi_sim_single_files) {</span></a>
+<a name="1129"><span class="lineNum">    1129 </span><span class="lineCov">         48 :       unsigned int r=0;</span></a>
+<a name="1130"><span class="lineNum">    1130 </span><span class="lineCov">         48 :       if(comm.Get_rank()==0) {r=multi_sim_comm.Get_rank();}</span></a>
+<a name="1131"><span class="lineNum">    1131 </span><span class="lineCov">         48 :       comm.Bcast(r,0);</span></a>
+<a name="1132"><span class="lineNum">    1132 </span><span class="lineCov">         48 :       if(r&gt;0) {fnames[i]=&quot;/dev/null&quot;;}</span></a>
+<a name="1133"><span class="lineNum">    1133 </span><span class="lineCov">         96 :       OFiles[i]-&gt;enforceSuffix(&quot;&quot;);</span></a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     }</a>
+<a name="1135"><span class="lineNum">    1135 </span><span class="lineCov">        314 :     OFiles[i]-&gt;open(fnames[i]);</span></a>
+<a name="1136"><span class="lineNum">    1136 </span><span class="lineCov">        314 :     OFiles[i]-&gt;setHeavyFlush();</span></a>
+<a name="1137"><span class="lineNum">    1137 </span>            :   }</a>
+<a name="1138"><span class="lineNum">    1138 </span><span class="lineCov">        388 : }</span></a>
+<a name="1139"><span class="lineNum">    1139 </span>            : </a>
+<a name="1140"><span class="lineNum">    1140 </span>            : </a>
+<a name="1141"><span class="lineNum">    1141 </span><span class="lineCov">         14 : void Optimizer::readCoeffsFromFiles(const std::vector&lt;std::string&gt;&amp; fnames, const bool read_aux_coeffs) {</span></a>
+<a name="1142"><span class="lineNum">    1142 </span><span class="lineCov">         14 :   plumed_assert(ncoeffssets_&gt;0);</span></a>
+<a name="1143"><span class="lineNum">    1143 </span><span class="lineCov">         14 :   plumed_assert(fnames.size()==ncoeffssets_);</span></a>
+<a name="1144"><span class="lineNum">    1144 </span><span class="lineCov">         14 :   if(ncoeffssets_==1) {</span></a>
+<a name="1145"><span class="lineNum">    1145 </span><span class="lineCov">         13 :     log.printf(&quot;  Read in coefficients from file &quot;);</span></a>
+<a name="1146"><span class="lineNum">    1146 </span>            :   }</a>
+<a name="1147"><span class="lineNum">    1147 </span>            :   else {</a>
+<a name="1148"><span class="lineNum">    1148 </span><span class="lineCov">          1 :     log.printf(&quot;  Read in coefficients from files:\n&quot;);</span></a>
+<a name="1149"><span class="lineNum">    1149 </span>            :   }</a>
+<a name="1150"><span class="lineNum">    1150 </span><span class="lineCov">         30 :   for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="1151"><span class="lineNum">    1151 </span><span class="lineCov">         16 :     IFile ifile;</span></a>
+<a name="1152"><span class="lineNum">    1152 </span><span class="lineCov">         16 :     ifile.link(*this);</span></a>
+<a name="1153"><span class="lineNum">    1153 </span><span class="lineCov">         16 :     if(use_mwalkers_mpi_ &amp;&amp; mwalkers_mpi_single_files_) {</span></a>
+<a name="1154"><span class="lineNum">    1154 </span><span class="lineCov">          8 :       ifile.enforceSuffix(&quot;&quot;);</span></a>
+<a name="1155"><span class="lineNum">    1155 </span>            :     }</a>
+<a name="1156"><span class="lineNum">    1156 </span><span class="lineCov">         16 :     ifile.open(fnames[i]);</span></a>
+<a name="1157"><span class="lineNum">    1157 </span><span class="lineCov">         32 :     if(!ifile.FieldExist(coeffs_pntrs_[i]-&gt;getDataLabel())) {</span></a>
+<a name="1158"><span class="lineNum">    1158 </span><span class="lineNoCov">          0 :       std::string error_msg = &quot;Problem with reading coefficients from file &quot; + ifile.getPath() + &quot;: no field with name &quot; + coeffs_pntrs_[i]-&gt;getDataLabel() + &quot;\n&quot;;</span></a>
+<a name="1159"><span class="lineNum">    1159 </span><span class="lineNoCov">          0 :       plumed_merror(error_msg);</span></a>
+<a name="1160"><span class="lineNum">    1160 </span>            :     }</a>
+<a name="1161"><span class="lineNum">    1161 </span><span class="lineCov">         16 :     size_t ncoeffs_read = coeffs_pntrs_[i]-&gt;readFromFile(ifile,false,false);</span></a>
+<a name="1162"><span class="lineNum">    1162 </span><span class="lineCov">         16 :     if(ncoeffssets_==1) {</span></a>
+<a name="1163"><span class="lineNum">    1163 </span><span class="lineCov">         26 :       log.printf(&quot;%s (read %zu of %zu values)\n&quot;, ifile.getPath().c_str(),ncoeffs_read,coeffs_pntrs_[i]-&gt;numberOfCoeffs());</span></a>
+<a name="1164"><span class="lineNum">    1164 </span>            :     }</a>
+<a name="1165"><span class="lineNum">    1165 </span>            :     else {</a>
+<a name="1166"><span class="lineNum">    1166 </span><span class="lineCov">          6 :       log.printf(&quot;   coefficient set %u: %s (read %zu of %zu values)\n&quot;,i,ifile.getPath().c_str(),ncoeffs_read,coeffs_pntrs_[i]-&gt;numberOfCoeffs());</span></a>
+<a name="1167"><span class="lineNum">    1167 </span>            :     }</a>
+<a name="1168"><span class="lineNum">    1168 </span><span class="lineCov">         16 :     ifile.close();</span></a>
+<a name="1169"><span class="lineNum">    1169 </span><span class="lineCov">         16 :     if(read_aux_coeffs) {</span></a>
+<a name="1170"><span class="lineNum">    1170 </span><span class="lineCov">         15 :       ifile.open(fnames[i]);</span></a>
+<a name="1171"><span class="lineNum">    1171 </span><span class="lineCov">         30 :       if(!ifile.FieldExist(aux_coeffs_pntrs_[i]-&gt;getDataLabel())) {</span></a>
+<a name="1172"><span class="lineNum">    1172 </span><span class="lineNoCov">          0 :         std::string error_msg = &quot;Problem with reading coefficients from file &quot; + ifile.getPath() + &quot;: no field with name &quot; + aux_coeffs_pntrs_[i]-&gt;getDataLabel() + &quot;\n&quot;;</span></a>
+<a name="1173"><span class="lineNum">    1173 </span><span class="lineNoCov">          0 :         plumed_merror(error_msg);</span></a>
+<a name="1174"><span class="lineNum">    1174 </span>            :       }</a>
+<a name="1175"><span class="lineNum">    1175 </span><span class="lineCov">         15 :       aux_coeffs_pntrs_[i]-&gt;readFromFile(ifile,false,false);</span></a>
+<a name="1176"><span class="lineNum">    1176 </span><span class="lineCov">         15 :       ifile.close();</span></a>
+<a name="1177"><span class="lineNum">    1177 </span>            :     }</a>
+<a name="1178"><span class="lineNum">    1178 </span>            :     else {</a>
+<a name="1179"><span class="lineNum">    1179 </span><span class="lineCov">          1 :       AuxCoeffs(i).setValues( Coeffs(i) );</span></a>
+<a name="1180"><span class="lineNum">    1180 </span>            :     }</a>
+<a name="1181"><span class="lineNum">    1181 </span><span class="lineCov">         16 :   }</span></a>
+<a name="1182"><span class="lineNum">    1182 </span><span class="lineCov">         14 : }</span></a>
+<a name="1183"><span class="lineNum">    1183 </span>            : </a>
+<a name="1184"><span class="lineNum">    1184 </span>            : </a>
+<a name="1185"><span class="lineNum">    1185 </span><span class="lineCov">         85 : void Optimizer::addCoeffsSetIDsToFilenames(std::vector&lt;std::string&gt;&amp; fnames, std::string&amp; coeffssetid_prefix) {</span></a>
+<a name="1186"><span class="lineNum">    1186 </span><span class="lineCov">         85 :   if(ncoeffssets_==1) {return;}</span></a>
+<a name="1187"><span class="lineNum">    1187 </span>            :   //</a>
+<a name="1188"><span class="lineNum">    1188 </span><span class="lineCov">          9 :   if(fnames.size()==1) {</span></a>
+<a name="1189"><span class="lineNum">    1189 </span><span class="lineNoCov">          0 :     fnames.resize(ncoeffssets_,fnames[0]);</span></a>
+<a name="1190"><span class="lineNum">    1190 </span>            :   }</a>
+<a name="1191"><span class="lineNum">    1191 </span><span class="lineCov">          9 :   plumed_assert(fnames.size()==ncoeffssets_);</span></a>
+<a name="1192"><span class="lineNum">    1192 </span>            :   //</a>
+<a name="1193"><span class="lineNum">    1193 </span><span class="lineCov">         36 :   for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="1194"><span class="lineNum">    1194 </span><span class="lineCov">         27 :     std::string is=&quot;&quot;; Tools::convert(i,is);</span></a>
+<a name="1195"><span class="lineNum">    1195 </span><span class="lineCov">         54 :     fnames[i] = FileBase::appendSuffix(fnames[i],&quot;.&quot;+coeffssetid_prefix_+is);</span></a>
+<a name="1196"><span class="lineNum">    1196 </span>            :   }</a>
+<a name="1197"><span class="lineNum">    1197 </span>            : }</a>
+<a name="1198"><span class="lineNum">    1198 </span>            : </a>
+<a name="1199"><span class="lineNum">    1199 </span>            : </a>
+<a name="1200"><span class="lineNum">    1200 </span><span class="lineCov">         93 : void Optimizer::setAllCoeffsSetIterationCounters() {</span></a>
+<a name="1201"><span class="lineNum">    1201 </span><span class="lineCov">        194 :   for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="1202"><span class="lineNum">    1202 </span><span class="lineCov">        101 :     coeffs_pntrs_[i]-&gt;setIterationCounterAndTime(getIterationCounter(),getTime());</span></a>
+<a name="1203"><span class="lineNum">    1203 </span><span class="lineCov">        101 :     aux_coeffs_pntrs_[i]-&gt;setIterationCounterAndTime(getIterationCounter(),getTime());</span></a>
+<a name="1204"><span class="lineNum">    1204 </span><span class="lineCov">        101 :     gradient_pntrs_[i]-&gt;setIterationCounterAndTime(getIterationCounter(),getTime());</span></a>
+<a name="1205"><span class="lineNum">    1205 </span><span class="lineCov">        101 :     targetdist_averages_pntrs_[i]-&gt;setIterationCounterAndTime(getIterationCounter(),getTime());</span></a>
+<a name="1206"><span class="lineNum">    1206 </span><span class="lineCov">        101 :     if(use_hessian_) {</span></a>
+<a name="1207"><span class="lineNum">    1207 </span><span class="lineNoCov">          0 :       hessian_pntrs_[i]-&gt;setIterationCounterAndTime(getIterationCounter(),getTime());</span></a>
+<a name="1208"><span class="lineNum">    1208 </span>            :     }</a>
+<a name="1209"><span class="lineNum">    1209 </span>            :   }</a>
+<a name="1210"><span class="lineNum">    1210 </span><span class="lineCov">         93 : }</span></a>
+<a name="1211"><span class="lineNum">    1211 </span>            : </a>
+<a name="1212"><span class="lineNum">    1212 </span>            : </a>
+<a name="1213"><span class="lineNum">    1213 </span><span class="lineCov">         95 : std::string Optimizer::getIterationCounterStr(const int offset) const {</span></a>
+<a name="1214"><span class="lineNum">    1214 </span>            :   std::string s;</a>
+<a name="1215"><span class="lineNum">    1215 </span><span class="lineCov">         95 :   Tools::convert(getIterationCounter()+offset,s);</span></a>
+<a name="1216"><span class="lineNum">    1216 </span><span class="lineCov">         95 :   return s;</span></a>
+<a name="1217"><span class="lineNum">    1217 </span>            : }</a>
+<a name="1218"><span class="lineNum">    1218 </span>            : </a>
+<a name="1219"><span class="lineNum">    1219 </span>            : </a>
+<a name="1220"><span class="lineNum">    1220 </span><span class="lineCov">         75 : void Optimizer::writeBiasOutputFiles() const {</span></a>
+<a name="1221"><span class="lineNum">    1221 </span><span class="lineCov">        156 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1222"><span class="lineNum">    1222 </span><span class="lineCov">         81 :     bias_pntrs_[i]-&gt;writeBiasToFile();</span></a>
+<a name="1223"><span class="lineNum">    1223 </span>            :   }</a>
+<a name="1224"><span class="lineNum">    1224 </span><span class="lineCov">         75 : }</span></a>
+<a name="1225"><span class="lineNum">    1225 </span>            : </a>
+<a name="1226"><span class="lineNum">    1226 </span>            : </a>
+<a name="1227"><span class="lineNum">    1227 </span><span class="lineCov">         75 : void Optimizer::writeFesOutputFiles() const {</span></a>
+<a name="1228"><span class="lineNum">    1228 </span><span class="lineCov">        156 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1229"><span class="lineNum">    1229 </span><span class="lineCov">         81 :     bias_pntrs_[i]-&gt;writeFesToFile();</span></a>
+<a name="1230"><span class="lineNum">    1230 </span>            :   }</a>
+<a name="1231"><span class="lineNum">    1231 </span><span class="lineCov">         75 : }</span></a>
+<a name="1232"><span class="lineNum">    1232 </span>            : </a>
+<a name="1233"><span class="lineNum">    1233 </span>            : </a>
+<a name="1234"><span class="lineNum">    1234 </span><span class="lineCov">         17 : void Optimizer::writeFesProjOutputFiles() const {</span></a>
+<a name="1235"><span class="lineNum">    1235 </span><span class="lineCov">         34 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1236"><span class="lineNum">    1236 </span><span class="lineCov">         17 :     bias_pntrs_[i]-&gt;writeFesProjToFile();</span></a>
+<a name="1237"><span class="lineNum">    1237 </span>            :   }</a>
+<a name="1238"><span class="lineNum">    1238 </span><span class="lineCov">         17 : }</span></a>
+<a name="1239"><span class="lineNum">    1239 </span>            : </a>
+<a name="1240"><span class="lineNum">    1240 </span>            : </a>
+<a name="1241"><span class="lineNum">    1241 </span><span class="lineCov">         38 : void Optimizer::writeTargetDistOutputFiles() const {</span></a>
+<a name="1242"><span class="lineNum">    1242 </span><span class="lineCov">         76 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1243"><span class="lineNum">    1243 </span><span class="lineCov">         38 :     if(dynamic_targetdists_[i]) {</span></a>
+<a name="1244"><span class="lineNum">    1244 </span><span class="lineCov">         38 :       bias_pntrs_[i]-&gt;writeTargetDistToFile();</span></a>
+<a name="1245"><span class="lineNum">    1245 </span>            :     }</a>
+<a name="1246"><span class="lineNum">    1246 </span>            :   }</a>
+<a name="1247"><span class="lineNum">    1247 </span><span class="lineCov">         38 : }</span></a>
+<a name="1248"><span class="lineNum">    1248 </span>            : </a>
+<a name="1249"><span class="lineNum">    1249 </span>            : </a>
+<a name="1250"><span class="lineNum">    1250 </span><span class="lineCov">          4 : void Optimizer::writeTargetDistProjOutputFiles() const {</span></a>
+<a name="1251"><span class="lineNum">    1251 </span><span class="lineCov">          8 :   for(unsigned int i=0; i&lt;nbiases_; i++) {</span></a>
+<a name="1252"><span class="lineNum">    1252 </span><span class="lineCov">          4 :     if(dynamic_targetdists_[i]) {</span></a>
+<a name="1253"><span class="lineNum">    1253 </span><span class="lineCov">          4 :       bias_pntrs_[i]-&gt;writeTargetDistProjToFile();</span></a>
+<a name="1254"><span class="lineNum">    1254 </span>            :     }</a>
+<a name="1255"><span class="lineNum">    1255 </span>            :   }</a>
+<a name="1256"><span class="lineNum">    1256 </span><span class="lineCov">          4 : }</span></a>
+<a name="1257"><span class="lineNum">    1257 </span>            : </a>
+<a name="1258"><span class="lineNum">    1258 </span>            : </a>
+<a name="1259"><span class="lineNum">    1259 </span>            : </a>
+<a name="1260"><span class="lineNum">    1260 </span>            : }</a>
+<a name="1261"><span class="lineNum">    1261 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Optimizer.h.func-sort-c.html b/coverage/ves/Optimizer.h.func-sort-c.html
new file mode 100644
index 0000000000..69d001b1c2
--- /dev/null
+++ b/coverage/ves/Optimizer.h.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Optimizer.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Optimizer.h<span style="font-size: 80%;"> (<a href="Optimizer.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Optimizer.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#193">_ZN4PLMD3ves9Optimizer22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#307">_ZN4PLMD3ves9Optimizer19parseMultipleValuesIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#288">_ZN4PLMD3ves9Optimizer19setCurrentStepSizesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#335">_ZN4PLMD3ves9Optimizer14parseFilenamesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIS7_SaIS7_EES9_</a></td>
+              <td class="coverFnHi">158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#325">_ZN4PLMD3ves9Optimizer19parseMultipleValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS8_RSt6vectorIT_SaISC_EERKSC_</a></td>
+              <td class="coverFnHi">158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#342">_ZN4PLMD3ves9Optimizer14parseFilenamesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIS7_SaIS7_EE</a></td>
+              <td class="coverFnHi">387</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#307">_ZN4PLMD3ves9Optimizer19parseMultipleValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS8_RSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">545</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#251">_ZNK4PLMD3ves9Optimizer7HessianEj</a></td>
+              <td class="coverFnHi">22735</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#190">_ZN4PLMD3ves9Optimizer5applyEv</a></td>
+              <td class="coverFnHi">22879</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#191">_ZN4PLMD3ves9Optimizer9calculateEv</a></td>
+              <td class="coverFnHi">22879</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Optimizer.h.func.html b/coverage/ves/Optimizer.h.func.html
new file mode 100644
index 0000000000..8ae8034d14
--- /dev/null
+++ b/coverage/ves/Optimizer.h.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Optimizer.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Optimizer.h<span style="font-size: 80%;"> (<a href="Optimizer.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Optimizer.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#342">_ZN4PLMD3ves9Optimizer14parseFilenamesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIS7_SaIS7_EE</a></td>
+              <td class="coverFnHi">387</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#335">_ZN4PLMD3ves9Optimizer14parseFilenamesERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIS7_SaIS7_EES9_</a></td>
+              <td class="coverFnHi">158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#307">_ZN4PLMD3ves9Optimizer19parseMultipleValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS8_RSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">545</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#325">_ZN4PLMD3ves9Optimizer19parseMultipleValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS8_RSt6vectorIT_SaISC_EERKSC_</a></td>
+              <td class="coverFnHi">158</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#307">_ZN4PLMD3ves9Optimizer19parseMultipleValuesIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#288">_ZN4PLMD3ves9Optimizer19setCurrentStepSizesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">78</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#193">_ZN4PLMD3ves9Optimizer22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#190">_ZN4PLMD3ves9Optimizer5applyEv</a></td>
+              <td class="coverFnHi">22879</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#191">_ZN4PLMD3ves9Optimizer9calculateEv</a></td>
+              <td class="coverFnHi">22879</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Optimizer.h.gcov.html#251">_ZNK4PLMD3ves9Optimizer7HessianEj</a></td>
+              <td class="coverFnHi">22735</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/Optimizer.h.gcov.html b/coverage/ves/Optimizer.h.gcov.html
new file mode 100644
index 0000000000..e2fa8db282
--- /dev/null
+++ b/coverage/ves/Optimizer.h.gcov.html
@@ -0,0 +1,430 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/Optimizer.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - Optimizer.h<span style="font-size: 80%;"> (source / <a href="Optimizer.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">53</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">94.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_Optimizer_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_Optimizer_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;string&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &lt;cmath&gt;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;memory&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : #define PLUMED_VES_OPTIMIZER_INIT(ao) Action(ao),Optimizer(ao)</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : /**</a>
+<a name="41"><span class="lineNum">      41 </span>            : \ingroup INHERIT</a>
+<a name="42"><span class="lineNum">      42 </span>            : Abstract base class for implenting new optimization methods</a>
+<a name="43"><span class="lineNum">      43 </span>            : */</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : class OFile;</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : namespace ves {</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : class CoeffsVector;</a>
+<a name="50"><span class="lineNum">      50 </span>            : class VesBias;</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : class Optimizer :</a>
+<a name="54"><span class="lineNum">      54 </span>            :   public ActionPilot,</a>
+<a name="55"><span class="lineNum">      55 </span>            :   public ActionWithValue</a>
+<a name="56"><span class="lineNum">      56 </span>            : {</a>
+<a name="57"><span class="lineNum">      57 </span>            : private:</a>
+<a name="58"><span class="lineNum">      58 </span>            :   const std::string description_;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   const std::string type_;</a>
+<a name="60"><span class="lineNum">      60 </span>            :   //</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::vector&lt;double&gt; stepsizes_;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   std::vector&lt;double&gt; current_stepsizes;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   bool fixed_stepsize_;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   //</a>
+<a name="65"><span class="lineNum">      65 </span>            :   unsigned int iter_counter;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   //</a>
+<a name="67"><span class="lineNum">      67 </span>            :   bool use_hessian_;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool diagonal_hessian_;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   bool hessian_covariance_from_averages_;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   //</a>
+<a name="71"><span class="lineNum">      71 </span>            :   bool monitor_instantaneous_gradient_;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   //</a>
+<a name="73"><span class="lineNum">      73 </span>            :   bool use_mwalkers_mpi_;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   bool mwalkers_mpi_single_files_;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   //</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::vector&lt;bool&gt; dynamic_targetdists_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   unsigned int ustride_targetdist_;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   //</a>
+<a name="79"><span class="lineNum">      79 </span>            :   unsigned int ustride_reweightfactor_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   //</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::string coeffssetid_prefix_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   //</a>
+<a name="83"><span class="lineNum">      83 </span>            :   unsigned int coeffs_wstride_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; coeffsOFiles_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::string coeffs_output_fmt_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned int gradient_wstride_;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; gradientOFiles_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::string gradient_output_fmt_;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   //</a>
+<a name="91"><span class="lineNum">      91 </span>            :   unsigned int hessian_wstride_;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; hessianOFiles_;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   std::string hessian_output_fmt_;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   //</a>
+<a name="95"><span class="lineNum">      95 </span>            :   unsigned int targetdist_averages_wstride_;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt; targetdist_averagesOFiles_;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::string targetdist_averages_output_fmt_;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   //</a>
+<a name="99"><span class="lineNum">      99 </span>            :   unsigned int nbiases_;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;VesBias*&gt; bias_pntrs_;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   //</a>
+<a name="102"><span class="lineNum">     102 </span>            :   unsigned int ncoeffssets_;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;CoeffsVector*&gt; coeffs_pntrs_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; aux_coeffs_pntrs_;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;CoeffsVector*&gt; gradient_pntrs_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; aver_gradient_pntrs_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;CoeffsMatrix*&gt; hessian_pntrs_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; coeffs_mask_pntrs_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;CoeffsVector*&gt; targetdist_averages_pntrs_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   //</a>
+<a name="111"><span class="lineNum">     111 </span>            :   bool identical_coeffs_shape_;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //</a>
+<a name="113"><span class="lineNum">     113 </span>            :   bool bias_output_active_;</a>
+<a name="114"><span class="lineNum">     114 </span>            :   unsigned int bias_output_stride_;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   bool fes_output_active_;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   unsigned int fes_output_stride_;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   bool fesproj_output_active_;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   unsigned int fesproj_output_stride_;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   bool targetdist_output_active_;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   unsigned int targetdist_output_stride_;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   bool targetdist_proj_output_active_;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   unsigned int targetdist_proj_output_stride_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   //</a>
+<a name="124"><span class="lineNum">     124 </span>            :   bool isFirstStep;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   //</a>
+<a name="126"><span class="lineNum">     126 </span>            : private:</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void updateOutputComponents();</a>
+<a name="128"><span class="lineNum">     128 </span>            :   void writeOutputFiles(const unsigned int coeffs_id = 0);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   void readCoeffsFromFiles(const std::vector&lt;std::string&gt;&amp;, const bool);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   void setAllCoeffsSetIterationCounters();</a>
+<a name="131"><span class="lineNum">     131 </span>            : protected:</a>
+<a name="132"><span class="lineNum">     132 </span>            :   void turnOnHessian();</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void turnOffHessian();</a>
+<a name="134"><span class="lineNum">     134 </span>            :   std::vector&lt;CoeffsMatrix*&gt; enableHessian(VesBias*, const bool diagonal_hessian=false);</a>
+<a name="135"><span class="lineNum">     135 </span>            :   // CoeffsMatrix* switchToDiagonalHessian(VesBias*);</a>
+<a name="136"><span class="lineNum">     136 </span>            :   // CoeffsMatrix* switchToFullHessian(VesBias*);</a>
+<a name="137"><span class="lineNum">     137 </span>            :   //</a>
+<a name="138"><span class="lineNum">     138 </span>            :   CoeffsVector&amp; Coeffs(const unsigned int coeffs_id = 0) const;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   CoeffsVector&amp; AuxCoeffs(const unsigned int coeffs_id = 0) const;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   CoeffsVector&amp; Gradient(const unsigned int coeffs_id = 0) const;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   CoeffsMatrix&amp; Hessian(const unsigned int coeffs_id = 0) const;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   CoeffsVector&amp; CoeffsMask(const unsigned int coeffs_id = 0) const;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   CoeffsVector&amp; TargetDistAverages(const unsigned int coeffs_id = 0) const;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   double StepSize(const unsigned int coeffs_id = 0) const;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   virtual void coeffsUpdate(const unsigned int coeffs_id = 0) = 0;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void setCurrentStepSize(const double,const unsigned int i = 0);</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void setCurrentStepSizes(const std::vector&lt;double&gt;&amp;);</a>
+<a name="148"><span class="lineNum">     148 </span>            :   //</a>
+<a name="149"><span class="lineNum">     149 </span>            :   void turnOffCoeffsOutputFiles();</a>
+<a name="150"><span class="lineNum">     150 </span>            :   //</a>
+<a name="151"><span class="lineNum">     151 </span>            :   template&lt;class T&gt;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   bool parseMultipleValues(const std::string&amp;, std::vector&lt;T&gt;&amp;);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   template&lt;class T&gt;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   bool parseMultipleValues(const std::string&amp;, std::vector&lt;T&gt;&amp;, const T&amp;);</a>
+<a name="155"><span class="lineNum">     155 </span>            :   void parseFilenames(const std::string&amp;, std::vector&lt;std::string&gt;&amp;, const std::string&amp;);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   void parseFilenames(const std::string&amp;, std::vector&lt;std::string&gt;&amp;);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void addCoeffsSetIDsToFilenames(std::vector&lt;std::string&gt;&amp;, std::string&amp;);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   void setupOFiles(std::vector&lt;std::string&gt;&amp;, std::vector&lt;std::unique_ptr&lt;OFile&gt;&gt;&amp;, const bool multi_sim_single_files=false);</a>
+<a name="159"><span class="lineNum">     159 </span>            : public:</a>
+<a name="160"><span class="lineNum">     160 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   static void useMultipleWalkersKeywords(Keywords&amp;);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   static void useHessianKeywords(Keywords&amp;);</a>
+<a name="163"><span class="lineNum">     163 </span>            :   static void useFixedStepSizeKeywords(Keywords&amp;);</a>
+<a name="164"><span class="lineNum">     164 </span>            :   static void useDynamicStepSizeKeywords(Keywords&amp;);</a>
+<a name="165"><span class="lineNum">     165 </span>            :   static void useMaskKeywords(Keywords&amp;);</a>
+<a name="166"><span class="lineNum">     166 </span>            :   static void useRestartKeywords(Keywords&amp;);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   static void useMonitorAverageGradientKeywords(Keywords&amp;);</a>
+<a name="168"><span class="lineNum">     168 </span>            :   static void useDynamicTargetDistributionKeywords(Keywords&amp;);</a>
+<a name="169"><span class="lineNum">     169 </span>            :   static void useReweightFactorKeywords(Keywords&amp;);</a>
+<a name="170"><span class="lineNum">     170 </span>            :   //</a>
+<a name="171"><span class="lineNum">     171 </span>            :   explicit Optimizer(const ActionOptions&amp;ao);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   ~Optimizer();</a>
+<a name="173"><span class="lineNum">     173 </span>            :   std::string getType() const {return type_;}</a>
+<a name="174"><span class="lineNum">     174 </span>            :   std::string getDescription() const {return description_;}</a>
+<a name="175"><span class="lineNum">     175 </span>            :   //</a>
+<a name="176"><span class="lineNum">     176 </span>            :   unsigned int numberOfBiases() const {return nbiases_;}</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         16 :   unsigned int numberOfCoeffsSets() const {return ncoeffssets_;}</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   //</a>
+<a name="179"><span class="lineNum">     179 </span>            :   std::vector&lt;double&gt; getStepSizes() const;</a>
+<a name="180"><span class="lineNum">     180 </span>            :   std::vector&lt;double&gt; getCurrentStepSizes() const;</a>
+<a name="181"><span class="lineNum">     181 </span>            :   double getStepSize(const unsigned int coeffs_id = 0) const;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   double getCurrentStepSize(const unsigned int coeffs_id = 0) const;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   void setStepSizes(const std::vector&lt;double&gt;&amp;);</a>
+<a name="184"><span class="lineNum">     184 </span>            :   void setStepSize(const double, const unsigned int coeffs_id = 0);</a>
+<a name="185"><span class="lineNum">     185 </span>            :   //</a>
+<a name="186"><span class="lineNum">     186 </span>            :   unsigned int getIterationCounter() const;</a>
+<a name="187"><span class="lineNum">     187 </span>            :   double getIterationCounterDbl() const;</a>
+<a name="188"><span class="lineNum">     188 </span>            :   std::string getIterationCounterStr(const int offset=0) const;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   void setIterationCounter(const unsigned int);</a>
+<a name="190"><span class="lineNum">     190 </span>            :   void increaseIterationCounter();</a>
+<a name="191"><span class="lineNum">     191 </span>            :   //</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      22879 :   void apply() override {};</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">      22879 :   void calculate() override {};</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   void update() override;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :   unsigned int getNumberOfDerivatives() override {return 0;}</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   //</a>
+<a name="197"><span class="lineNum">     197 </span>            :   bool fixedStepSize() const {return fixed_stepsize_;}</a>
+<a name="198"><span class="lineNum">     198 </span>            :   bool dynamicStepSize() const {return !fixed_stepsize_;}</a>
+<a name="199"><span class="lineNum">     199 </span>            :   //</a>
+<a name="200"><span class="lineNum">     200 </span>            :   bool useHessian() const {return use_hessian_;}</a>
+<a name="201"><span class="lineNum">     201 </span>            :   bool diagonalHessian() const {return diagonal_hessian_;}</a>
+<a name="202"><span class="lineNum">     202 </span>            :   //</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        609 :   bool useMultipleWalkers() const {return use_mwalkers_mpi_;}</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   //</a>
+<a name="205"><span class="lineNum">     205 </span>            :   std::vector&lt;VesBias*&gt; getBiasPntrs() const {return bias_pntrs_;}</a>
+<a name="206"><span class="lineNum">     206 </span>            :   std::vector&lt;CoeffsVector*&gt; getCoeffsPntrs() const {return coeffs_pntrs_;}</a>
+<a name="207"><span class="lineNum">     207 </span>            :   std::vector&lt;CoeffsVector*&gt; getAuxCoeffsPntrs() const {return Tools::unique2raw(aux_coeffs_pntrs_);}</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         12 :   std::vector&lt;CoeffsVector*&gt; getGradientPntrs()const {return gradient_pntrs_;}</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   std::vector&lt;CoeffsMatrix*&gt; getHessianPntrs() const {return hessian_pntrs_;}</a>
+<a name="210"><span class="lineNum">     210 </span>            :   std::vector&lt;CoeffsVector*&gt; getCoeffsMaskPntrs() const {return Tools::unique2raw(coeffs_mask_pntrs_);}</a>
+<a name="211"><span class="lineNum">     211 </span>            :   std::vector&lt;CoeffsVector*&gt; getTargetDistAveragesPntrs() const {return targetdist_averages_pntrs_;}</a>
+<a name="212"><span class="lineNum">     212 </span>            :   //</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      22829 :   bool isBiasOutputActive() const {return bias_output_active_;}</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        814 :   unsigned int getBiasOutputStride() const {return bias_output_stride_;}</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   void setBiasOutputStride(unsigned int stride) {bias_output_stride_=stride;}</a>
+<a name="216"><span class="lineNum">     216 </span>            :   void writeBiasOutputFiles() const;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   //</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      22829 :   bool isFesOutputActive() const {return fes_output_active_;}</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        814 :   unsigned int getFesOutputStride() const {return fes_output_stride_;}</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   void setFesOutputStride(unsigned int stride) {fes_output_stride_=stride;}</a>
+<a name="221"><span class="lineNum">     221 </span>            :   void writeFesOutputFiles() const;</a>
+<a name="222"><span class="lineNum">     222 </span>            :   //</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      22829 :   bool isFesProjOutputActive() const {return fesproj_output_active_;}</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        176 :   unsigned int getFesProjOutputStride() const {return fesproj_output_stride_;}</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :   void setFesProjOutputStride(unsigned int stride) {fesproj_output_stride_=stride;}</a>
+<a name="226"><span class="lineNum">     226 </span>            :   void writeFesProjOutputFiles() const;</a>
+<a name="227"><span class="lineNum">     227 </span>            :   //</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">      22908 :   bool isTargetDistOutputActive() const {return targetdist_output_active_;}</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">      22367 :   unsigned int getTargetDistOutputStride() const {return targetdist_output_stride_;}</span></a>
+<a name="230"><span class="lineNum">     230 </span>            :   void setTargetDistOutputStride(unsigned int stride) {targetdist_output_stride_=stride;}</a>
+<a name="231"><span class="lineNum">     231 </span>            :   void writeTargetDistOutputFiles() const;</a>
+<a name="232"><span class="lineNum">     232 </span>            :   //</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">      22829 :   bool isTargetDistProjOutputActive() const {return targetdist_proj_output_active_;}</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         33 :   unsigned int getTargetDistProjOutputStride() const {return targetdist_proj_output_stride_;}</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   void setTargetDistProjOutputStride(unsigned int stride) {targetdist_proj_output_stride_=stride;}</a>
+<a name="236"><span class="lineNum">     236 </span>            :   void writeTargetDistProjOutputFiles() const;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   //</a>
+<a name="238"><span class="lineNum">     238 </span>            : };</a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : inline</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">      22705 : double Optimizer::StepSize(const unsigned int coeffs_id) const {return stepsizes_[coeffs_id];}</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : inline</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">      68214 : CoeffsVector&amp; Optimizer::Coeffs(const unsigned int coeffs_id) const {return *coeffs_pntrs_[coeffs_id];}</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : inline</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         21 : CoeffsVector&amp; Optimizer::AuxCoeffs(const unsigned int coeffs_id) const {return *aux_coeffs_pntrs_[coeffs_id];}</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : inline</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      22785 : CoeffsVector&amp; Optimizer::Gradient(const unsigned int coeffs_id) const {return *gradient_pntrs_[coeffs_id];}</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : inline</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      22735 : CoeffsMatrix&amp; Optimizer::Hessian(const unsigned int coeffs_id) const {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">      22735 :   plumed_massert(use_hessian_,&quot;You cannot use the Hessian without asking for before&quot;);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">      22735 :   return *hessian_pntrs_[coeffs_id];</span></a>
+<a name="256"><span class="lineNum">     256 </span>            : }</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : inline</a>
+<a name="259"><span class="lineNum">     259 </span>            : CoeffsVector&amp; Optimizer::CoeffsMask(const unsigned int coeffs_id) const {return *coeffs_mask_pntrs_[coeffs_id];}</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span>            : inline</a>
+<a name="262"><span class="lineNum">     262 </span>            : std::vector&lt;double&gt; Optimizer::getStepSizes() const {return stepsizes_;}</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : inline</a>
+<a name="265"><span class="lineNum">     265 </span>            : std::vector&lt;double&gt; Optimizer::getCurrentStepSizes() const {return current_stepsizes;}</a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : inline</a>
+<a name="268"><span class="lineNum">     268 </span>            : double Optimizer::getStepSize(const unsigned int coeffs_id) const {return stepsizes_[coeffs_id];}</a>
+<a name="269"><span class="lineNum">     269 </span>            : </a>
+<a name="270"><span class="lineNum">     270 </span>            : inline</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         11 : double Optimizer::getCurrentStepSize(const unsigned int coeffs_id) const {return current_stepsizes[coeffs_id];}</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : inline</a>
+<a name="274"><span class="lineNum">     274 </span>            : void Optimizer::setStepSizes(const std::vector&lt;double&gt;&amp; stepsizes_in) {</a>
+<a name="275"><span class="lineNum">     275 </span>            :   plumed_assert(stepsizes_in.size()==ncoeffssets_);</a>
+<a name="276"><span class="lineNum">     276 </span>            :   stepsizes_ = stepsizes_in;</a>
+<a name="277"><span class="lineNum">     277 </span>            : }</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : inline</a>
+<a name="280"><span class="lineNum">     280 </span>            : void Optimizer::setStepSize(const double stepsize_in, const unsigned int coeffs_id) {</a>
+<a name="281"><span class="lineNum">     281 </span>            :   stepsizes_[coeffs_id] = stepsize_in;</a>
+<a name="282"><span class="lineNum">     282 </span>            : }</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : inline</a>
+<a name="285"><span class="lineNum">     285 </span>            : void Optimizer::setCurrentStepSize(const double current_stepsize_in, const unsigned int coeffs_id) {</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         10 :   current_stepsizes[coeffs_id] = current_stepsize_in;</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : inline</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         78 : void Optimizer::setCurrentStepSizes(const std::vector&lt;double&gt;&amp; current_stepsizes_in) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         78 :   plumed_assert(current_stepsizes_in.size()==ncoeffssets_);</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         78 :   current_stepsizes = current_stepsizes_in;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         78 : }</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : inline</a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">      48388 : unsigned int Optimizer::getIterationCounter() const {return iter_counter;}</span></a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            : inline</a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">      22695 : double Optimizer::getIterationCounterDbl() const {return static_cast&lt;double&gt;(iter_counter);}</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : inline</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">      22750 : void Optimizer::increaseIterationCounter() {iter_counter++;}</span></a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : inline</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         13 : void Optimizer::setIterationCounter(const unsigned int iter_counter_in) {iter_counter = iter_counter_in;}</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : template&lt;class T&gt;</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">        623 : bool Optimizer::parseMultipleValues(const std::string&amp; keyword, std::vector&lt;T&gt;&amp; values) {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">        623 :   plumed_assert(ncoeffssets_&gt;0);</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">        623 :   plumed_assert(values.size()==0);</span></a>
+<a name="312"><span class="lineNum">     312 </span>            :   bool identical_values=false;</a>
+<a name="313"><span class="lineNum">     313 </span>            :   //</a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">        623 :   parseVector(keyword,values);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">        623 :   if(values.size()==1 &amp;&amp; ncoeffssets_&gt;1) {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          9 :     values.resize(ncoeffssets_,values[0]);</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :     identical_values=true;</a>
+<a name="318"><span class="lineNum">     318 </span>            :   }</a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">        623 :   if(values.size()&gt;0 &amp;&amp; values.size()!=ncoeffssets_) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :     std::string s1; Tools::convert(ncoeffssets_,s1);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Error in &quot; + keyword + &quot; keyword: either give 1 common value for all coefficient sets or &quot; + s1 + &quot; separate value for each set&quot;);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            :   }</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        623 :   return identical_values;</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : template&lt;class T&gt;</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">        158 : bool Optimizer::parseMultipleValues(const std::string&amp; keyword, std::vector&lt;T&gt;&amp; values, const T&amp; default_value) {</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">        158 :   bool identical_values = parseMultipleValues(keyword,values);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        158 :   if(values.size()==0) {</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         79 :     values.resize(ncoeffssets_,default_value);</span></a>
+<a name="331"><span class="lineNum">     331 </span>            :     identical_values=true;</a>
+<a name="332"><span class="lineNum">     332 </span>            :   }</a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        158 :   return identical_values;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : }</a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span>            : inline</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">        158 : void Optimizer::parseFilenames(const std::string&amp; keyword, std::vector&lt;std::string&gt;&amp; fnames, const std::string&amp; default_fname) {</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">        158 :   if(parseMultipleValues&lt;std::string&gt;(keyword,fnames,default_fname)) {</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         81 :     addCoeffsSetIDsToFilenames(fnames,coeffssetid_prefix_);</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :   }</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        158 : }</span></a>
+<a name="342"><span class="lineNum">     342 </span>            : </a>
+<a name="343"><span class="lineNum">     343 </span>            : inline</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        387 : void Optimizer::parseFilenames(const std::string&amp; keyword, std::vector&lt;std::string&gt;&amp; fnames) {</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        387 :   if(parseMultipleValues&lt;std::string&gt;(keyword,fnames)) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">          4 :     addCoeffsSetIDsToFilenames(fnames,coeffssetid_prefix_);</span></a>
+<a name="347"><span class="lineNum">     347 </span>            :   }</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        387 : }</span></a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : </a>
+<a name="351"><span class="lineNum">     351 </span>            : }</a>
+<a name="352"><span class="lineNum">     352 </span>            : }</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputBasisFunctions.cpp.func-sort-c.html b/coverage/ves/OutputBasisFunctions.cpp.func-sort-c.html
new file mode 100644
index 0000000000..6cd04de090
--- /dev/null
+++ b/coverage/ves/OutputBasisFunctions.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputBasisFunctions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputBasisFunctions.cpp<span style="font-size: 80%;"> (<a href="OutputBasisFunctions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntryHi">98.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputBasisFunctions.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#89">_ZN4PLMD3ves20OutputBasisFunctions5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#88">_ZN4PLMD3ves20OutputBasisFunctions9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#94">_ZN4PLMD3ves12_GLOBAL__N_132OutputBasisFunctionsRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#115">_ZN4PLMD3ves20OutputBasisFunctionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#96">_ZN4PLMD3ves20OutputBasisFunctions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#94">_ZN4PLMD3ves12_GLOBAL__N_132OutputBasisFunctionsRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#94">_ZN4PLMD3ves12_GLOBAL__N_132OutputBasisFunctionsRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputBasisFunctions.cpp.func.html b/coverage/ves/OutputBasisFunctions.cpp.func.html
new file mode 100644
index 0000000000..ca4afefc70
--- /dev/null
+++ b/coverage/ves/OutputBasisFunctions.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputBasisFunctions.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputBasisFunctions.cpp<span style="font-size: 80%;"> (<a href="OutputBasisFunctions.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntryHi">98.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputBasisFunctions.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#94">_ZN4PLMD3ves12_GLOBAL__N_132OutputBasisFunctionsRegisterMe966createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#94">_ZN4PLMD3ves12_GLOBAL__N_132OutputBasisFunctionsRegisterMe96C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#94">_ZN4PLMD3ves12_GLOBAL__N_132OutputBasisFunctionsRegisterMe96D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#96">_ZN4PLMD3ves20OutputBasisFunctions16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#89">_ZN4PLMD3ves20OutputBasisFunctions5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#88">_ZN4PLMD3ves20OutputBasisFunctions9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputBasisFunctions.cpp.gcov.html#115">_ZN4PLMD3ves20OutputBasisFunctionsC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">71</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputBasisFunctions.cpp.gcov.html b/coverage/ves/OutputBasisFunctions.cpp.gcov.html
new file mode 100644
index 0000000000..dd6037159d
--- /dev/null
+++ b/coverage/ves/OutputBasisFunctions.cpp.gcov.html
@@ -0,0 +1,312 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputBasisFunctions.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputBasisFunctions.cpp<span style="font-size: 80%;"> (source / <a href="OutputBasisFunctions.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntry">111</td>
+            <td class="headerCovTableEntryHi">98.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace ves {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : //+PLUMEDOC VES_UTILS VES_OUTPUT_BASISFUNCTIONS</a>
+<a name="41"><span class="lineNum">      41 </span>            : /*</a>
+<a name="42"><span class="lineNum">      42 </span>            : Output basis functions to file.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : This action can be used to write out to a grid file the values and derivatives of</a>
+<a name="45"><span class="lineNum">      45 </span>            : given basis functions. This is normally used for debugging when programming new</a>
+<a name="46"><span class="lineNum">      46 </span>            : types of basis functions. For example, it is possible to calculate the</a>
+<a name="47"><span class="lineNum">      47 </span>            : derivatives numerically and compare to the analytically calculated</a>
+<a name="48"><span class="lineNum">      48 </span>            : derivatives.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : This action is normally used through the \ref driver.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : \par Examples</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : In the following input we define a Legendre polynomials basis functions</a>
+<a name="55"><span class="lineNum">      55 </span>            : of order 14 over the interval -4.0 to 4.0 and output their values</a>
+<a name="56"><span class="lineNum">      56 </span>            : and derivatives to files called bfL.values.data and bfL.derivs.data.</a>
+<a name="57"><span class="lineNum">      57 </span>            : \plumedfile</a>
+<a name="58"><span class="lineNum">      58 </span>            : BF_LEGENDRE ...</a>
+<a name="59"><span class="lineNum">      59 </span>            :  ORDER=14</a>
+<a name="60"><span class="lineNum">      60 </span>            :  MINIMUM=-4.0</a>
+<a name="61"><span class="lineNum">      61 </span>            :  MAXIMUM=4.0</a>
+<a name="62"><span class="lineNum">      62 </span>            :  LABEL=bfL</a>
+<a name="63"><span class="lineNum">      63 </span>            : ... BF_LEGENDRE</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : VES_OUTPUT_BASISFUNCTIONS ...</a>
+<a name="66"><span class="lineNum">      66 </span>            :  BASIS_FUNCTIONS=bfL</a>
+<a name="67"><span class="lineNum">      67 </span>            :  GRID_BINS=200</a>
+<a name="68"><span class="lineNum">      68 </span>            :  FORMAT_VALUES_DERIVS=%13.6f</a>
+<a name="69"><span class="lineNum">      69 </span>            : ... VES_OUTPUT_BASISFUNCTIONS</a>
+<a name="70"><span class="lineNum">      70 </span>            : \endplumedfile</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : This input should be run through the driver by using a command similar to the</a>
+<a name="73"><span class="lineNum">      73 </span>            : following one where the trajectory/configuration file configuration.gro is needed to</a>
+<a name="74"><span class="lineNum">      74 </span>            : trick the code to exit correctly.</a>
+<a name="75"><span class="lineNum">      75 </span>            : \verbatim</a>
+<a name="76"><span class="lineNum">      76 </span>            : plumed driver --plumed plumed.dat --igro configuration.gro</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endverbatim</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : */</a>
+<a name="80"><span class="lineNum">      80 </span>            : //+ENDPLUMEDOC</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : class OutputBasisFunctions :</a>
+<a name="84"><span class="lineNum">      84 </span>            :   public Action</a>
+<a name="85"><span class="lineNum">      85 </span>            : {</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;BasisFunctions*&gt; bf_pntrs;</a>
+<a name="87"><span class="lineNum">      87 </span>            : public:</a>
+<a name="88"><span class="lineNum">      88 </span>            :   explicit OutputBasisFunctions(const ActionOptions&amp;);</a>
+<a name="89"><span class="lineNum">      89 </span>            :   TargetDistribution* setupTargetDistPntr(std::string keyword) const;</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="93"><span class="lineNum">      93 </span>            : };</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      12575 : PLUMED_REGISTER_ACTION(OutputBasisFunctions,&quot;VES_OUTPUT_BASISFUNCTIONS&quot;)</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         73 : void OutputBasisFunctions::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         73 :   Action::registerKeywords(keys);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        146 :   keys.add(&quot;compulsory&quot;,&quot;BASIS_FUNCTIONS&quot;,&quot;the label of the basis functions that you want to use&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;GRID_BINS&quot;,&quot;the number of bins used for the grid for writing the basis function values and derivatives. The default value is 1000.&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;GRID_MIN&quot;,&quot;the minimum of the grid for writing the basis function values and derivatives. By default it is the minimum of the interval on which the basis functions are defined.&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;GRID_MAX&quot;,&quot;the maximum of the grid for writing the basis function values and derivatives. By default it is the maximum of the interval on which the basis functions are defined.&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FILE_VALUES&quot;,&quot;filename of the file on which the basis function values are written. By default it is BF_LABEL.values.data.&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FILE_DERIVS&quot;,&quot;filename of the file on which the basis function derivatives are written. By default it is BF_LABEL.derivs.data.&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FORMAT_VALUES_DERIVS&quot;,&quot;the numerical format of the basis function values and derivatives written to file. By default it is %15.8f.\n. You can also use FORMAT_VALUES and FORMAT_DERIVS to give the numerical formats separately.&quot;);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FORMAT_VALUES&quot;,&quot;the numerical format of the basis function derivatives written to file. By default it is %15.8f.\n&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FORMAT_DERIVS&quot;,&quot;the numerical format of the basis function values written to file. By default it is %15.8f.\n&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FILE_TARGETDIST_AVERAGES&quot;,&quot;filename of the file on which the averages over the target distributions are written. By default it is BF_LABEL.targetdist-averages.data.&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FORMAT_TARGETDIST_AVERAGES&quot;,&quot;the numerical format of the target distribution averages written to file. By default it is %15.8f.\n&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        146 :   keys.add(&quot;optional&quot;,&quot;FILE_TARGETDIST&quot;,&quot;filename of the files on which the target distributions are written. By default it is BF_LABEL.targetdist-#.data.&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        146 :   keys.add(&quot;numbered&quot;,&quot;TARGET_DISTRIBUTION&quot;,&quot;the target distribution to be used.&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        146 :   keys.addFlag(&quot;IGNORE_PERIODICITY&quot;,false,&quot;if the periodicity of the basis functions should be ignored.&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        146 :   keys.addFlag(&quot;NUMERICAL_DERIVATIVES&quot;,false,&quot;if the derivatives of the basis functions should be calculated numerically.&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         73 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         71 : OutputBasisFunctions::OutputBasisFunctions(const ActionOptions&amp;ao):</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   Action(ao),</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         71 :   bf_pntrs(0)</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : {</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         71 :   std::vector&lt;std::string&gt; basisset_labels(0);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        142 :   parseVector(&quot;BASIS_FUNCTIONS&quot;,basisset_labels);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         71 :   if(basisset_labels.size()&gt;1) {plumed_merror(&quot;Only one basis set label allowed in keyword BASIS_FUNCTIONS of &quot;+getName());}</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         71 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        142 :   bf_pntrs = VesTools::getPointersFromLabels&lt;BasisFunctions*&gt;(basisset_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         71 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword BASIS_FUNCTIONS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         71 :   unsigned int nbins = 1000;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        142 :   parse(&quot;GRID_BINS&quot;,nbins);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         71 :   std::string min_str = bf_pntrs[0]-&gt;intervalMinStr();</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         71 :   std::string max_str = bf_pntrs[0]-&gt;intervalMaxStr();</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         71 :   parse(&quot;GRID_MIN&quot;,min_str);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        142 :   parse(&quot;GRID_MAX&quot;,max_str);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         71 :   std::string fname_values = bf_pntrs[0]-&gt;getLabel()+&quot;.values.data&quot;;</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        142 :   parse(&quot;FILE_VALUES&quot;,fname_values);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         71 :   std::string fname_derives = bf_pntrs[0]-&gt;getLabel()+&quot;.derivs.data&quot;;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        142 :   parse(&quot;FILE_DERIVS&quot;,fname_derives);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         71 :   std::string fname_targetdist_aver = bf_pntrs[0]-&gt;getLabel()+&quot;.targetdist-averages.data&quot;;</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        142 :   parse(&quot;FILE_TARGETDIST_AVERAGES&quot;,fname_targetdist_aver);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         71 :   std::string fname_targetdist = bf_pntrs[0]-&gt;getLabel()+&quot;.targetdist-.data&quot;;</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         71 :   parse(&quot;FILE_TARGETDIST&quot;,fname_targetdist);</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         71 :   std::string fmt_values_derivs = &quot;%15.8f&quot;;</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         71 :   parse(&quot;FORMAT_VALUES_DERIVS&quot;,fmt_values_derivs);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         71 :   std::string fmt_values = fmt_values_derivs;</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         71 :   std::string fmt_derivs = fmt_values_derivs;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         71 :   parse(&quot;FORMAT_VALUES&quot;,fmt_values);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         71 :   parse(&quot;FORMAT_DERIVS&quot;,fmt_derivs);</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         71 :   std::string fmt_targetdist_aver = &quot;%15.8f&quot;;</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         71 :   parse(&quot;FORMAT_TARGETDIST_AVERAGES&quot;,fmt_targetdist_aver);</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         71 :   bool ignore_periodicity = false;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         71 :   parseFlag(&quot;IGNORE_PERIODICITY&quot;,ignore_periodicity);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         71 :   bool numerical_deriv = false;</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        142 :   parseFlag(&quot;NUMERICAL_DERIVATIVES&quot;,numerical_deriv);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   std::vector&lt;TargetDistribution*&gt; targetdist_pntrs;</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         71 :   targetdist_pntrs.push_back(NULL);</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         71 :   std::string targetdist_label=&quot;&quot;;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        176 :   for(int i=1;; i++) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        494 :     if(!parseNumbered(&quot;TARGET_DISTRIBUTION&quot;,i,targetdist_label)) {break;}</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        176 :     std::string error_msg = &quot;&quot;;</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        176 :     TargetDistribution* pntr_tmp = VesTools::getPointerFromLabel&lt;TargetDistribution*&gt;(targetdist_label,plumed.getActionSet(),error_msg);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        176 :     if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword TARGET_DISTRIBUTION of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        176 :     targetdist_pntrs.push_back(pntr_tmp);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        176 :   }</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         71 :   checkRead();</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   //</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         71 :   OFile ofile_values;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         71 :   ofile_values.link(*this);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         71 :   ofile_values.enforceBackup();</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         71 :   ofile_values.open(fname_values);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         71 :   OFile ofile_derivs;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         71 :   ofile_derivs.link(*this);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         71 :   ofile_derivs.enforceBackup();</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         71 :   ofile_derivs.open(fname_derives);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         71 :   bf_pntrs[0]-&gt;writeBasisFunctionsToFile(ofile_values,ofile_derivs,min_str,max_str,nbins,ignore_periodicity,fmt_values,fmt_derivs,numerical_deriv);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         71 :   ofile_values.close();</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         71 :   ofile_derivs.close();</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   //</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         71 :   std::vector&lt;std::string&gt; grid_min(1); grid_min[0]=bf_pntrs[0]-&gt;intervalMinStr();</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         71 :   std::vector&lt;std::string&gt; grid_max(1); grid_max[0]=bf_pntrs[0]-&gt;intervalMaxStr();</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         71 :   std::vector&lt;unsigned int&gt; grid_bins(1); grid_bins[0]=nbins;</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         71 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; arguments(1);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        142 :   arguments[0]= Tools::make_unique&lt;Value&gt;(nullptr,&quot;arg&quot;,false);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         71 :   if(bf_pntrs[0]-&gt;arePeriodic() &amp;&amp; !ignore_periodicity) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         46 :     arguments[0]-&gt;setDomain(bf_pntrs[0]-&gt;intervalMinStr(),bf_pntrs[0]-&gt;intervalMaxStr());</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span>            :   else {</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         48 :     arguments[0]-&gt;setNotPeriodic();</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         71 :   OFile ofile_targetdist_aver;</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         71 :   ofile_targetdist_aver.link(*this);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         71 :   ofile_targetdist_aver.enforceBackup();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         71 :   ofile_targetdist_aver.open(fname_targetdist_aver);</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        318 :   for(unsigned int i=0; i&lt;targetdist_pntrs.size(); i++) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        247 :     std::string is; Tools::convert(i,is);</span></a>
+<a name="205"><span class="lineNum">     205 </span>            :     //</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        247 :     if(targetdist_pntrs[i]!=NULL) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        352 :       targetdist_pntrs[i]-&gt;setupGrids(Tools::unique2raw(arguments),grid_min,grid_max,grid_bins);</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        176 :       plumed_massert(targetdist_pntrs[i]-&gt;getDimension()==1,&quot;the target distribution must be one dimensional&quot;);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        176 :       targetdist_pntrs[i]-&gt;updateTargetDist();</span></a>
+<a name="210"><span class="lineNum">     210 </span>            :     }</a>
+<a name="211"><span class="lineNum">     211 </span>            :     //</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">        247 :     std::vector&lt;double&gt; bf_integrals = bf_pntrs[0]-&gt;getTargetDistributionIntegrals(targetdist_pntrs[i]);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">        494 :     CoeffsVector targetdist_averages = CoeffsVector(&quot;aver.targetdist-&quot;+is,Tools::unique2raw(arguments),bf_pntrs,comm,false);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">        247 :     targetdist_averages.setValues(bf_integrals);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        247 :     if(fmt_targetdist_aver.size()&gt;0) {targetdist_averages.setOutputFmt(fmt_targetdist_aver);}</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        247 :     targetdist_averages.writeToFile(ofile_targetdist_aver,true);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        247 :     if(targetdist_pntrs[i]!=NULL) {</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :       Grid* targetdist_grid_pntr = targetdist_pntrs[i]-&gt;getTargetDistGridPntr();</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        176 :       std::string fname = FileBase::appendSuffix(fname_targetdist,is);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        176 :       OFile ofile;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">        176 :       ofile.link(*this);</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        176 :       ofile.enforceBackup();</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        176 :       ofile.open(fname);</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        176 :       targetdist_grid_pntr-&gt;writeToFile(ofile);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        176 :       ofile.close();</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        176 :     }</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">        247 :   }</span></a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         71 :   ofile_targetdist_aver.close();</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        213 : }</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputFesBias.cpp.func-sort-c.html b/coverage/ves/OutputFesBias.cpp.func-sort-c.html
new file mode 100644
index 0000000000..2ccc80d751
--- /dev/null
+++ b/coverage/ves/OutputFesBias.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputFesBias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputFesBias.cpp<span style="font-size: 80%;"> (<a href="OutputFesBias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryMed">88.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputFesBias.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#104">_ZN4PLMD3ves13OutputFesBias5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#102">_ZN4PLMD3ves13OutputFesBias6updateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#103">_ZN4PLMD3ves13OutputFesBias9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#108">_ZN4PLMD3ves12_GLOBAL__N_126OutputFesBiasRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#121">_ZN4PLMD3ves13OutputFesBiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#111">_ZN4PLMD3ves13OutputFesBias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#108">_ZN4PLMD3ves12_GLOBAL__N_126OutputFesBiasRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#108">_ZN4PLMD3ves12_GLOBAL__N_126OutputFesBiasRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputFesBias.cpp.func.html b/coverage/ves/OutputFesBias.cpp.func.html
new file mode 100644
index 0000000000..6ff10fa008
--- /dev/null
+++ b/coverage/ves/OutputFesBias.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputFesBias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputFesBias.cpp<span style="font-size: 80%;"> (<a href="OutputFesBias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryMed">88.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputFesBias.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#108">_ZN4PLMD3ves12_GLOBAL__N_126OutputFesBiasRegisterMe1106createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#108">_ZN4PLMD3ves12_GLOBAL__N_126OutputFesBiasRegisterMe110C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#108">_ZN4PLMD3ves12_GLOBAL__N_126OutputFesBiasRegisterMe110D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#111">_ZN4PLMD3ves13OutputFesBias16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#104">_ZN4PLMD3ves13OutputFesBias5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#102">_ZN4PLMD3ves13OutputFesBias6updateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#103">_ZN4PLMD3ves13OutputFesBias9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputFesBias.cpp.gcov.html#121">_ZN4PLMD3ves13OutputFesBiasC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputFesBias.cpp.gcov.html b/coverage/ves/OutputFesBias.cpp.gcov.html
new file mode 100644
index 0000000000..2446a58f86
--- /dev/null
+++ b/coverage/ves/OutputFesBias.cpp.gcov.html
@@ -0,0 +1,306 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputFesBias.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputFesBias.cpp<span style="font-size: 80%;"> (source / <a href="OutputFesBias.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">61</td>
+            <td class="headerCovTableEntry">69</td>
+            <td class="headerCovTableEntryMed">88.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryLo">62.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace ves {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC VES_UTILS VES_OUTPUT_FES</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : Tool to output biases and free energy surfaces for VES biases from previously obtained coefficients.</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : This action can be used to output to file biases and free energy surfaces for VES biases from</a>
+<a name="41"><span class="lineNum">      41 </span>            : previously obtained coefficients. It should be used through the \ref driver and</a>
+<a name="42"><span class="lineNum">      42 </span>            : can only be used in post processing. The VES bias needs to be defined in the</a>
+<a name="43"><span class="lineNum">      43 </span>            : exact same way as during the simulation. At the current moment this action does</a>
+<a name="44"><span class="lineNum">      44 </span>            : not support dynamic target distributions (e.g. well-tempered).</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : \par Examples</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : In the following input we define a VES bias and then read in the coefficient</a>
+<a name="49"><span class="lineNum">      49 </span>            : file coeffs.input.data and output the FES and bias every 500 iterations.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \plumedfile</a>
+<a name="52"><span class="lineNum">      52 </span>            : phi:   TORSION ATOMS=5,7,9,15</a>
+<a name="53"><span class="lineNum">      53 </span>            : psi:   TORSION ATOMS=7,9,15,17</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : bf1: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi</a>
+<a name="56"><span class="lineNum">      56 </span>            : bf2: BF_FOURIER ORDER=5 MINIMUM=-pi MAXIMUM=pi</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="59"><span class="lineNum">      59 </span>            :  ARG=phi,psi</a>
+<a name="60"><span class="lineNum">      60 </span>            :  BASIS_FUNCTIONS=bf1,bf2</a>
+<a name="61"><span class="lineNum">      61 </span>            :  LABEL=ves1</a>
+<a name="62"><span class="lineNum">      62 </span>            :  GRID_BINS=100,100</a>
+<a name="63"><span class="lineNum">      63 </span>            :  PROJ_ARG1=phi</a>
+<a name="64"><span class="lineNum">      64 </span>            :  PROJ_ARG2=psi</a>
+<a name="65"><span class="lineNum">      65 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : VES_OUTPUT_FES ...</a>
+<a name="68"><span class="lineNum">      68 </span>            :   BIAS=ves1</a>
+<a name="69"><span class="lineNum">      69 </span>            :   FES_OUTPUT=500</a>
+<a name="70"><span class="lineNum">      70 </span>            :   FES_PROJ_OUTPUT=500</a>
+<a name="71"><span class="lineNum">      71 </span>            :   BIAS_OUTPUT=500</a>
+<a name="72"><span class="lineNum">      72 </span>            :   COEFFS_INPUT=coeffs.input.data</a>
+<a name="73"><span class="lineNum">      73 </span>            : ... VES_OUTPUT_FES</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : The header of coeffs.input.data should look like the following:</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : \auxfile{coeffs.input.data}</a>
+<a name="79"><span class="lineNum">      79 </span>            : #! FIELDS idx_phi idx_psi ves1.coeffs ves1.aux_coeffs index</a>
+<a name="80"><span class="lineNum">      80 </span>            : #! SET time 100.000000</a>
+<a name="81"><span class="lineNum">      81 </span>            : #! SET iteration  10</a>
+<a name="82"><span class="lineNum">      82 </span>            : #! SET type LinearBasisSet</a>
+<a name="83"><span class="lineNum">      83 </span>            : #! SET ndimensions  2</a>
+<a name="84"><span class="lineNum">      84 </span>            : #! SET ncoeffs_total  121</a>
+<a name="85"><span class="lineNum">      85 </span>            : #! SET shape_phi  11</a>
+<a name="86"><span class="lineNum">      86 </span>            : #! SET shape_psi  11</a>
+<a name="87"><span class="lineNum">      87 </span>            : \endauxfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : This input should be run through the driver by using a command similar to the</a>
+<a name="90"><span class="lineNum">      90 </span>            : following one where the trajectory/configuration file configuration.gro is needed to</a>
+<a name="91"><span class="lineNum">      91 </span>            : correctly define the CVs</a>
+<a name="92"><span class="lineNum">      92 </span>            : \verbatim</a>
+<a name="93"><span class="lineNum">      93 </span>            : plumed driver --plumed plumed.dat --igro configuration.gro</a>
+<a name="94"><span class="lineNum">      94 </span>            : \endverbatim</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : */</a>
+<a name="97"><span class="lineNum">      97 </span>            : //+ENDPLUMEDOC</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : class OutputFesBias : public Action {</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : public:</a>
+<a name="102"><span class="lineNum">     102 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="103"><span class="lineNum">     103 </span>            :   explicit OutputFesBias(const ActionOptions&amp;);</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineNoCov">          0 :   void update() override {}</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : };</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">      12507 : PLUMED_REGISTER_ACTION(OutputFesBias,&quot;VES_OUTPUT_FES&quot;)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          5 : void OutputFesBias::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;BIAS&quot;,&quot;the label of the VES bias for to output the free energy surfaces and the bias files&quot;);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         10 :   keys.add(&quot;compulsory&quot;,&quot;COEFFS_INPUT&quot;,&quot;the name of input coefficient file&quot;);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;BIAS_OUTPUT&quot;,&quot;how often the bias(es) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;FES_OUTPUT&quot;,&quot;how often the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         10 :   keys.add(&quot;optional&quot;,&quot;FES_PROJ_OUTPUT&quot;,&quot;how often the projections of the FES(s) should be written out to file. Note that the value is given in terms of coefficient iterations.&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            :   //</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          5 : }</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          3 : OutputFesBias::OutputFesBias(const ActionOptions&amp;ao):</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          3 :   Action(ao)</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : {</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   std::vector&lt;std::string&gt; bias_labels;</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          6 :   parseVector(&quot;BIAS&quot;,bias_labels);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          3 :   if(bias_labels.size()&gt;1) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot; only support one VES bias&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          3 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          3 :   std::vector&lt;VesBias*&gt; bias_pntrs = VesTools::getPointersFromLabels&lt;VesBias*&gt;(bias_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          3 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword BIAS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :   for(unsigned int i=0; i&lt;bias_pntrs.size(); i++) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          3 :     if(bias_pntrs[i]-&gt;numberOfCoeffsSets()&gt;1) {</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; at the moment supports only VES biases with a single coefficient set&quot;);</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     }</a>
+<a name="141"><span class="lineNum">     141 </span>            :   }</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::vector&lt;std::string&gt; coeffs_fnames;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          6 :   parseVector(&quot;COEFFS_INPUT&quot;,coeffs_fnames);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 :   if(coeffs_fnames.size()!=bias_pntrs.size()) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there have to be as many coefficient file given in COEFFS_INPUT as VES biases given in BIAS&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">          3 :   unsigned int bias_output_stride = 0;</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          3 :   parse(&quot;BIAS_OUTPUT&quot;,bias_output_stride);</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          3 :   unsigned int fes_output_stride = 0;</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          3 :   parse(&quot;FES_OUTPUT&quot;,fes_output_stride);</span></a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          3 :   unsigned int fesproj_output_stride = 0;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          3 :   parse(&quot;FES_PROJ_OUTPUT&quot;,fesproj_output_stride);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 :   if(bias_output_stride == 0 &amp;&amp; fes_output_stride == 0 &amp;&amp; fesproj_output_stride == 0) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: you are not telling the action to do anything, you need to use one of the keywords BIAS_OUTPUT, FES_OUTPUT, or FES_PROJ_OUTPUT&quot;);</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :   }</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          3 :   checkRead();</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          6 :   for(unsigned int i=0; i&lt;bias_pntrs.size(); i++) {</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          3 :     if(bias_pntrs[i]-&gt;dynamicTargetDistribution()) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; does not support dynamic target distributions at the moment&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          3 :     if(bias_pntrs[i]-&gt;isStaticTargetDistFileOutputActive()) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          2 :       bias_pntrs[i]-&gt;setupTargetDistFileOutput();</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          2 :       bias_pntrs[i]-&gt;writeTargetDistToFile();</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          2 :       bias_pntrs[i]-&gt;setupTargetDistProjFileOutput();</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 :       bias_pntrs[i]-&gt;writeTargetDistProjToFile();</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          3 :     if(bias_output_stride&gt;0) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :       bias_pntrs[i]-&gt;enableBiasFileOutput();</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          3 :       bias_pntrs[i]-&gt;setupBiasFileOutput();</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     }</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :     if(fes_output_stride&gt;0) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          3 :       bias_pntrs[i]-&gt;enableFesFileOutput();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          3 :       bias_pntrs[i]-&gt;setupFesFileOutput();</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          3 :     if(fesproj_output_stride&gt;0) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          1 :       bias_pntrs[i]-&gt;enableFesProjFileOutput();</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          1 :       bias_pntrs[i]-&gt;setupFesProjFileOutput();</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          3 :     bias_pntrs[i]-&gt;enableIterationNumberInFilenames();</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          3 :     IFile ifile;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          3 :     ifile.open(coeffs_fnames[i]);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         39 :     while(ifile) {</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         36 :       bias_pntrs[i]-&gt;resetBiasFileOutput();</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         36 :       bias_pntrs[i]-&gt;resetFesFileOutput();</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         72 :       if(bias_pntrs[i]-&gt;getCoeffsPntrs()[0]-&gt;readOneSetFromFile(ifile)&gt;0) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         33 :         unsigned int iteration = bias_pntrs[i]-&gt;getCoeffsPntrs()[0]-&gt;getIterationCounter();</span></a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         33 :         if(bias_output_stride&gt;0 &amp;&amp; iteration%bias_output_stride==0) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          8 :           bias_pntrs[i]-&gt;writeBiasToFile();</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :         }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         33 :         if(fes_output_stride&gt;0 &amp;&amp; iteration%fes_output_stride==0) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          8 :           bias_pntrs[i]-&gt;writeFesToFile();</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :         }</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         33 :         if(fesproj_output_stride&gt;0 &amp;&amp; iteration%fesproj_output_stride==0) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          3 :           bias_pntrs[i]-&gt;writeFesProjToFile();</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :         }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            :       }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            :     }</a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          3 :   }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          3 :   log.printf(&quot;Stopping&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          3 :   plumed.stop();</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          6 : }</span></a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+<a name="230"><span class="lineNum">     230 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputTargetDistribution.cpp.func-sort-c.html b/coverage/ves/OutputTargetDistribution.cpp.func-sort-c.html
new file mode 100644
index 0000000000..102ac86b0b
--- /dev/null
+++ b/coverage/ves/OutputTargetDistribution.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputTargetDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputTargetDistribution.cpp<span style="font-size: 80%;"> (<a href="OutputTargetDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OutputTargetDistribution.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#85">_ZN4PLMD3ves24OutputTargetDistribution5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#84">_ZN4PLMD3ves24OutputTargetDistribution9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#90">_ZN4PLMD3ves12_GLOBAL__N_136OutputTargetDistributionRegisterMe926createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#105">_ZN4PLMD3ves24OutputTargetDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#92">_ZN4PLMD3ves24OutputTargetDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">122</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#90">_ZN4PLMD3ves12_GLOBAL__N_136OutputTargetDistributionRegisterMe92C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#90">_ZN4PLMD3ves12_GLOBAL__N_136OutputTargetDistributionRegisterMe92D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputTargetDistribution.cpp.func.html b/coverage/ves/OutputTargetDistribution.cpp.func.html
new file mode 100644
index 0000000000..677cee95ac
--- /dev/null
+++ b/coverage/ves/OutputTargetDistribution.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputTargetDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputTargetDistribution.cpp<span style="font-size: 80%;"> (<a href="OutputTargetDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OutputTargetDistribution.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#90">_ZN4PLMD3ves12_GLOBAL__N_136OutputTargetDistributionRegisterMe926createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#90">_ZN4PLMD3ves12_GLOBAL__N_136OutputTargetDistributionRegisterMe92C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#90">_ZN4PLMD3ves12_GLOBAL__N_136OutputTargetDistributionRegisterMe92D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#92">_ZN4PLMD3ves24OutputTargetDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">122</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#85">_ZN4PLMD3ves24OutputTargetDistribution5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#84">_ZN4PLMD3ves24OutputTargetDistribution9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OutputTargetDistribution.cpp.gcov.html#105">_ZN4PLMD3ves24OutputTargetDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">120</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/OutputTargetDistribution.cpp.gcov.html b/coverage/ves/OutputTargetDistribution.cpp.gcov.html
new file mode 100644
index 0000000000..c20a2de8b7
--- /dev/null
+++ b/coverage/ves/OutputTargetDistribution.cpp.gcov.html
@@ -0,0 +1,302 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/OutputTargetDistribution.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - OutputTargetDistribution.cpp<span style="font-size: 80%;"> (source / <a href="OutputTargetDistribution.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">84</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryHi">93.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryLo">71.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace ves {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC VES_UTILS VES_OUTPUT_TARGET_DISTRIBUTION</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Output target distribution to file.</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : This action can be used to output target distributions to a grid file,</a>
+<a name="43"><span class="lineNum">      43 </span>            : for example to see how they look like before using them in a VES bias.</a>
+<a name="44"><span class="lineNum">      44 </span>            : This action only support static target distributions.</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : This action is normally used through the \ref driver.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : \par Examples</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : In the following input we define a target distribution that is uniform for</a>
+<a name="52"><span class="lineNum">      52 </span>            : argument 1 and a Gaussian for argument 2 and then output it to a file</a>
+<a name="53"><span class="lineNum">      53 </span>            : called targetdist-1.data.</a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : t1_1: TD_UNIFORM  MINIMA=-4.0  MAXIMA=+4.0</a>
+<a name="56"><span class="lineNum">      56 </span>            : t1_2: TD_GAUSSIAN  CENTER1=-2.0  SIGMA1=0.5</a>
+<a name="57"><span class="lineNum">      57 </span>            : t1: TD_PRODUCT_DISTRIBUTION  DISTRIBUTIONS=t1_1,t1_2</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : VES_OUTPUT_TARGET_DISTRIBUTION ...</a>
+<a name="60"><span class="lineNum">      60 </span>            :  GRID_MIN=-4.0,-4.0</a>
+<a name="61"><span class="lineNum">      61 </span>            :  GRID_MAX=+4.0,+4.0</a>
+<a name="62"><span class="lineNum">      62 </span>            :  GRID_BINS=100,100</a>
+<a name="63"><span class="lineNum">      63 </span>            :  TARGET_DISTRIBUTION=t1</a>
+<a name="64"><span class="lineNum">      64 </span>            :  TARGETDIST_FILE=targetdist-1.data</a>
+<a name="65"><span class="lineNum">      65 </span>            :  LOG_TARGETDIST_FILE=targetdist-1.log.data</a>
+<a name="66"><span class="lineNum">      66 </span>            :  FMT_GRIDS=%11.6f</a>
+<a name="67"><span class="lineNum">      67 </span>            : ... VES_OUTPUT_TARGET_DISTRIBUTION</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : This input should be run through the driver by using a command similar to the</a>
+<a name="71"><span class="lineNum">      71 </span>            : following one where the trajectory/configuration file configuration.gro is needed to</a>
+<a name="72"><span class="lineNum">      72 </span>            : trick the code to exit correctly.</a>
+<a name="73"><span class="lineNum">      73 </span>            : \verbatim</a>
+<a name="74"><span class="lineNum">      74 </span>            : plumed driver --plumed plumed.dat --igro configuration.gro</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endverbatim</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : */</a>
+<a name="78"><span class="lineNum">      78 </span>            : //+ENDPLUMEDOC</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : class OutputTargetDistribution :</a>
+<a name="82"><span class="lineNum">      82 </span>            :   public Action</a>
+<a name="83"><span class="lineNum">      83 </span>            : {</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   explicit OutputTargetDistribution(const ActionOptions&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :   void calculate() override {}</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :   void apply() override {}</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="89"><span class="lineNum">      89 </span>            : };</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      12624 : PLUMED_REGISTER_ACTION(OutputTargetDistribution,&quot;VES_OUTPUT_TARGET_DISTRIBUTION&quot;)</span></a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        122 : void OutputTargetDistribution::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        122 :   Action::registerKeywords(keys);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        244 :   keys.add(&quot;compulsory&quot;,&quot;GRID_MIN&quot;,&quot;the lower bounds for the grid&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        244 :   keys.add(&quot;compulsory&quot;,&quot;GRID_MAX&quot;,&quot;the upper bounds for the grid&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        244 :   keys.add(&quot;compulsory&quot;,&quot;GRID_BINS&quot;,&quot;the number of bins used for the grid.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        244 :   keys.add(&quot;optional&quot;,&quot;GRID_PERIODICITY&quot;,&quot;specify if the individual arguments should be made periodic (YES) or not (NO). By default all arguments are taken as not periodic.&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        244 :   keys.add(&quot;compulsory&quot;,&quot;TARGETDIST_FILE&quot;,&quot;filename of the file for writing the target distribution&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        244 :   keys.add(&quot;optional&quot;,&quot;LOG_TARGETDIST_FILE&quot;,&quot;filename of the file for writing the log of the target distribution&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        244 :   keys.add(&quot;compulsory&quot;,&quot;TARGET_DISTRIBUTION&quot;,&quot;the target distribution to be used.&quot;);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        244 :   keys.add(&quot;optional&quot;,&quot;FMT_GRIDS&quot;,&quot;the numerical format of the target distribution grids written to file. By default it is %14.9f&quot;);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        244 :   keys.addFlag(&quot;DO_1D_PROJECTIONS&quot;,false,&quot;Also output the one-dimensional marginal distributions for multi-dimensional target distribution.&quot;);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        122 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        120 : OutputTargetDistribution::OutputTargetDistribution(const ActionOptions&amp;ao):</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        120 :   Action(ao)</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : {</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   std::string targetdist_fname;</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        240 :   parse(&quot;TARGETDIST_FILE&quot;,targetdist_fname);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   std::string log_targetdist_fname;</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        120 :   parse(&quot;LOG_TARGETDIST_FILE&quot;,log_targetdist_fname);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        120 :   if(targetdist_fname==log_targetdist_fname) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;error in &quot; + getName() + &quot;:TARGETDIST_FILE and LOG_TARGETDIST_FILE cannot be the same&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::vector&lt;unsigned int&gt; grid_bins;</a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        240 :   parseVector(&quot;GRID_BINS&quot;,grid_bins);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        120 :   unsigned int nargs = grid_bins.size();</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        120 :   std::vector&lt;std::string&gt; grid_min(nargs);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        120 :   parseVector(&quot;GRID_MIN&quot;,grid_min);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        120 :   std::vector&lt;std::string&gt; grid_max(nargs);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        120 :   parseVector(&quot;GRID_MAX&quot;,grid_max);</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        120 :   std::vector&lt;std::string&gt; grid_periodicity(nargs);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        240 :   parseVector(&quot;GRID_PERIODICITY&quot;,grid_periodicity);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        232 :   if(grid_periodicity.size()==0) {grid_periodicity.assign(nargs,&quot;NO&quot;);}</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        120 :   std::string fmt_grids=&quot;%14.9f&quot;;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        120 :   parse(&quot;FMT_GRIDS&quot;,fmt_grids);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        120 :   bool do_1d_proj = false;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        120 :   parseFlag(&quot;DO_1D_PROJECTIONS&quot;,do_1d_proj);</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        120 :   if(do_1d_proj &amp;&amp; nargs==1) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;doesn't make sense to use the DO_1D_PROJECTIONS keyword for a one-dimensional distribution&quot;);</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :   }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        120 :   plumed_massert(grid_min.size()==nargs,&quot;mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        120 :   plumed_massert(grid_max.size()==nargs,&quot;mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        120 :   plumed_massert(grid_periodicity.size()==nargs,&quot;mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::string targetdist_label;</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        120 :   parse(&quot;TARGET_DISTRIBUTION&quot;,targetdist_label);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        120 :   checkRead();</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :   //</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        120 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; arguments(nargs);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        287 :   for(unsigned int i=0; i &lt; nargs; i++) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        167 :     std::string is; Tools::convert(i+1,is);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        167 :     if(nargs==1) {is=&quot;&quot;;}</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">        167 :     arguments[i]= Tools::make_unique&lt;Value&gt;(nullptr,&quot;arg&quot;+is,false);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        167 :     if(grid_periodicity[i]==&quot;YES&quot;) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         11 :       arguments[i]-&gt;setDomain(grid_min[i],grid_max[i]);</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     }</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        156 :     else if(grid_periodicity[i]==&quot;NO&quot;) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        156 :       arguments[i]-&gt;setNotPeriodic();</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span>            :     else {</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;wrong value given in GRID_PERIODICITY, either specify YES or NO&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     }</a>
+<a name="163"><span class="lineNum">     163 </span>            :   }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        120 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        120 :   TargetDistribution* targetdist_pntr = VesTools::getPointerFromLabel&lt;TargetDistribution*&gt;(targetdist_label,plumed.getActionSet(),error_msg);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        120 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword TARGET_DISTRIBUTION of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   //</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        120 :   if(targetdist_pntr-&gt;isDynamic()) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineNoCov">          0 :     plumed_merror(getName() + &quot; only works for static target distributions&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :   }</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        120 :   targetdist_pntr-&gt;setupGrids(Tools::unique2raw(arguments),grid_min,grid_max,grid_bins);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        120 :   targetdist_pntr-&gt;updateTargetDist();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   Grid* targetdist_grid_pntr = targetdist_pntr-&gt;getTargetDistGridPntr();</a>
+<a name="175"><span class="lineNum">     175 </span>            :   Grid* log_targetdist_grid_pntr = targetdist_pntr-&gt;getLogTargetDistGridPntr();</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        120 :   double sum_grid = TargetDistribution::integrateGrid(targetdist_grid_pntr);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        120 :   log.printf(&quot;  target distribution integrated over the grid: %16.12f\n&quot;,sum_grid);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        120 :   log.printf(&quot;                                                (%30.16e)\n&quot;,sum_grid);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   //</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        120 :   OFile ofile;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        120 :   ofile.link(*this);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        120 :   ofile.enforceBackup();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        120 :   ofile.open(targetdist_fname);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   targetdist_grid_pntr-&gt;setOutputFmt(fmt_grids);</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        120 :   targetdist_grid_pntr-&gt;writeToFile(ofile);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        120 :   ofile.close();</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        120 :   if(log_targetdist_fname.size()&gt;0) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         23 :     OFile ofile2;</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         23 :     ofile2.link(*this);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         23 :     ofile2.enforceBackup();</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         23 :     ofile2.open(log_targetdist_fname);</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :     log_targetdist_grid_pntr-&gt;setOutputFmt(fmt_grids);</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         23 :     log_targetdist_grid_pntr-&gt;writeToFile(ofile2);</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         23 :     ofile2.close();</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         23 :   }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        120 :   if(do_1d_proj) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         12 :     for(unsigned int i=0; i&lt;nargs; i++) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          8 :       std::vector&lt;std::string&gt; arg1d(1);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          8 :       arg1d[0] = arguments[i]-&gt;getName();</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          8 :       Grid marginal_grid = targetdist_pntr-&gt;getMarginal(arg1d);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       //</a>
+<a name="205"><span class="lineNum">     205 </span>            :       std::string suffix;</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          8 :       Tools::convert(i+1,suffix);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">          8 :       suffix = &quot;proj-&quot; + suffix;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          8 :       std::string marginal_fname = FileBase::appendSuffix(targetdist_fname,&quot;.&quot;+suffix);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :       //</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          8 :       OFile ofile3;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          8 :       ofile3.link(*this);</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">          8 :       ofile3.enforceBackup();</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          8 :       ofile3.open(marginal_fname);</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :       marginal_grid.setOutputFmt(fmt_grids);</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">          8 :       marginal_grid.writeToFile(ofile3);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         16 :     }</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   }</a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        480 : }</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Chi.cpp.func-sort-c.html b/coverage/ves/TD_Chi.cpp.func-sort-c.html
new file mode 100644
index 0000000000..7dca1657cd
--- /dev/null
+++ b/coverage/ves/TD_Chi.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Chi.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Chi.cpp<span style="font-size: 80%;"> (<a href="TD_Chi.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Chi.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_118TD_ChiRegisterMe916createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#103">_ZN4PLMD3ves6TD_ChiC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#92">_ZN4PLMD3ves6TD_Chi16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#139">_ZNK4PLMD3ves6TD_Chi8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1509</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_118TD_ChiRegisterMe91C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_118TD_ChiRegisterMe91D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Chi.cpp.func.html b/coverage/ves/TD_Chi.cpp.func.html
new file mode 100644
index 0000000000..ef2627e283
--- /dev/null
+++ b/coverage/ves/TD_Chi.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Chi.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Chi.cpp<span style="font-size: 80%;"> (<a href="TD_Chi.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Chi.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_118TD_ChiRegisterMe916createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_118TD_ChiRegisterMe91C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_118TD_ChiRegisterMe91D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#92">_ZN4PLMD3ves6TD_Chi16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#103">_ZN4PLMD3ves6TD_ChiC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Chi.cpp.gcov.html#139">_ZNK4PLMD3ves6TD_Chi8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1509</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Chi.cpp.gcov.html b/coverage/ves/TD_Chi.cpp.gcov.html
new file mode 100644
index 0000000000..10f948b901
--- /dev/null
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Chi.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
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+<body>
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Chi.cpp<span style="font-size: 80%;"> (source / <a href="TD_Chi.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_CHI</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Chi distribution (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution given by a</a>
+<a name="36"><span class="lineNum">      36 </span>            : [chi distribution](https://en.wikipedia.org/wiki/Chi_distribution)</a>
+<a name="37"><span class="lineNum">      37 </span>            : that is defined as</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : p(s) =</a>
+<a name="40"><span class="lineNum">      40 </span>            : \frac</a>
+<a name="41"><span class="lineNum">      41 </span>            : {2^{1-\frac{k}{2}}}</a>
+<a name="42"><span class="lineNum">      42 </span>            : {\sigma \, \Gamma\left(\frac{k}{2}\right) }</a>
+<a name="43"><span class="lineNum">      43 </span>            : \, \left(\frac{s-a}{\sigma}\right)^{k-1} \, \exp\left(- \frac{1}{2} \left(\frac{s-a}{\sigma}\right)^2\right),</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : where \f$a\f$ is the minimum of the distribution that is defined on the interval \f$[a,\infty)\f$,</a>
+<a name="46"><span class="lineNum">      46 </span>            : the parameter \f$k\f$ (given as a positive integer larger than 1) determines how far</a>
+<a name="47"><span class="lineNum">      47 </span>            : the peak of the distribution is from the minimum (known as the &quot;degrees of freedom&quot;),</a>
+<a name="48"><span class="lineNum">      48 </span>            : and the parameter \f$\sigma&gt;0\f$ determines the broadness of the distribution.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The minimum \f$a\f$ is given using the MINIMUM keyword, the parameter \f$k\f$ is given</a>
+<a name="51"><span class="lineNum">      51 </span>            : using the KAPPA keyword, and the parameter \f$\sigma\f$ is given using the SIGMA keyword.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : This target distribution action is only defined for one dimension, for multiple dimensions</a>
+<a name="54"><span class="lineNum">      54 </span>            : it should be used in combination with the \ref TD_PRODUCT_DISTRIBUTION action.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \par Examples</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : Chi distribution with \f$a=10.0\f$, \f$\sigma=2.0\f$, and \f$k=2\f$</a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : td: TD_CHI  MINIMUM=10.0  SIGMA=2.0  KAPPA=2</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The Chi distribution is only defined for one dimension so for multiple</a>
+<a name="65"><span class="lineNum">      65 </span>            : dimensions we have to use it in combination with the \ref TD_PRODUCT_DISTRIBUTION action as shown in</a>
+<a name="66"><span class="lineNum">      66 </span>            : the following example where we have a uniform distribution for argument 1 and</a>
+<a name="67"><span class="lineNum">      67 </span>            : a Chi distribution for argument 1</a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : td_uni: TD_UNIFORM</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : td_chi: TD_CHI  MINIMUM=-10.0  SIGMA=2.0  KAPPA=2</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : td_pd: TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS=td_uni,td_chi</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : */</a>
+<a name="77"><span class="lineNum">      77 </span>            : //+ENDPLUMEDOC</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : class TD_Chi: public TargetDistribution {</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;double&gt; minima_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;double&gt; kappa_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;double&gt; normalization_;</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span>            :   explicit TD_Chi(const ActionOptions&amp; ao);</a>
+<a name="87"><span class="lineNum">      87 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="88"><span class="lineNum">      88 </span>            : };</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      12513 : PLUMED_REGISTER_ACTION(TD_Chi,&quot;TD_CHI&quot;)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         11 : void TD_Chi::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         11 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;MINIMUM&quot;,&quot;The minimum of the chi distribution.&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;The sigma parameter of the chi distribution given as a positive number.&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;The k parameter of the chi distribution given as positive integer larger than 1.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         11 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         11 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         11 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         11 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          9 : TD_Chi::TD_Chi(const ActionOptions&amp; ao):</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         18 :   minima_(0),</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          9 :   sigma_(0),</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          9 :   kappa_(0),</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         18 :   normalization_(0)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          9 :   parseVector(&quot;MINIMUM&quot;,minima_);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          9 :   parseVector(&quot;SIGMA&quot;,sigma_);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         18 :   for(unsigned int k=0; k&lt;sigma_.size(); k++) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          9 :     if(sigma_[k] &lt; 0.0) {plumed_merror(getName()+&quot;: the value given in SIGMA should be positive.&quot;);}</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          9 :   std::vector&lt;unsigned int&gt; kappa_int(0);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         18 :   parseVector(&quot;KAPPA&quot;,kappa_int);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          9 :   if(kappa_int.size()==0) {plumed_merror(getName()+&quot;: some problem with KAPPA keyword, should given as positive integer larger than 1&quot;);}</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          9 :   kappa_.resize(kappa_int.size());</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         18 :   for(unsigned int k=0; k&lt;kappa_int.size(); k++) {</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          9 :     if(kappa_int[k] &lt; 1) {plumed_merror(getName()+&quot;: KAPPA should be an integer 1 or higher&quot;);}</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">          9 :     kappa_[k] = static_cast&lt;double&gt;(kappa_int[k]);</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :   }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          9 :   setDimension(minima_.size());</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          9 :   if(getDimension()&gt;1) {plumed_merror(getName()+&quot;: only defined for one dimension, for multiple dimensions it should be used in combination with the TD_PRODUCT_DISTRIBUTION action.&quot;);}</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          9 :   if(sigma_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the SIGMA keyword does not match the given dimension in MINIMUM&quot;);}</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          9 :   if(kappa_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the KAPPA keyword does not match the given dimension in MINIMUM&quot;);}</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          9 :   normalization_.resize(getDimension());</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         18 :   for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          9 :     normalization_[k] = pow(2.0,(1.0-0.5*kappa_[k]))/(tgamma(0.5*kappa_[k])*sigma_[k]);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            :   }</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          9 : }</span></a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       1509 : double TD_Chi::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   double value = 1.0;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       3018 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       1509 :     double arg=(argument[k]-minima_[k])/sigma_[k];</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1509 :     if(arg&lt;0.0) {plumed_merror(getName()+&quot;: the chi distribution is not defined for values less that ones given in MINIMUM&quot;);}</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">       1509 :     value *= normalization_[k] * pow(arg,kappa_[k]-1.0) * exp(-0.5*arg*arg);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       1509 :   return value;</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ChiSquared.cpp.func-sort-c.html b/coverage/ves/TD_ChiSquared.cpp.func-sort-c.html
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index 0000000000..3610a95e4b
--- /dev/null
+++ b/coverage/ves/TD_ChiSquared.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ChiSquared.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ChiSquared.cpp<span style="font-size: 80%;"> (<a href="TD_ChiSquared.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_ChiSquared.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_125TD_ChiSquaredRegisterMe916createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#103">_ZN4PLMD3ves13TD_ChiSquaredC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#92">_ZN4PLMD3ves13TD_ChiSquared16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#138">_ZNK4PLMD3ves13TD_ChiSquared8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1509</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_125TD_ChiSquaredRegisterMe91C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_125TD_ChiSquaredRegisterMe91D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ChiSquared.cpp.func.html b/coverage/ves/TD_ChiSquared.cpp.func.html
new file mode 100644
index 0000000000..982b26a3f1
--- /dev/null
+++ b/coverage/ves/TD_ChiSquared.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ChiSquared.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ChiSquared.cpp<span style="font-size: 80%;"> (<a href="TD_ChiSquared.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_ChiSquared.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_125TD_ChiSquaredRegisterMe916createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_125TD_ChiSquaredRegisterMe91C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#89">_ZN4PLMD3ves12_GLOBAL__N_125TD_ChiSquaredRegisterMe91D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#92">_ZN4PLMD3ves13TD_ChiSquared16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#103">_ZN4PLMD3ves13TD_ChiSquaredC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ChiSquared.cpp.gcov.html#138">_ZNK4PLMD3ves13TD_ChiSquared8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1509</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ChiSquared.cpp.gcov.html b/coverage/ves/TD_ChiSquared.cpp.gcov.html
new file mode 100644
index 0000000000..7cdf6ba8fe
--- /dev/null
+++ b/coverage/ves/TD_ChiSquared.cpp.gcov.html
@@ -0,0 +1,228 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ChiSquared.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ChiSquared.cpp<span style="font-size: 80%;"> (source / <a href="TD_ChiSquared.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntry">41</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_CHISQUARED</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Chi-squared distribution (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution given by a</a>
+<a name="36"><span class="lineNum">      36 </span>            : [chi-squared distribution](https://en.wikipedia.org/wiki/Chi-squared_distribution)</a>
+<a name="37"><span class="lineNum">      37 </span>            : that is defined as</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : p(s) =</a>
+<a name="40"><span class="lineNum">      40 </span>            : \frac</a>
+<a name="41"><span class="lineNum">      41 </span>            : {1}</a>
+<a name="42"><span class="lineNum">      42 </span>            : {\sigma \, 2^{\frac{k}{2}}  \,  \Gamma\left(\frac{k}{2}\right) }</a>
+<a name="43"><span class="lineNum">      43 </span>            : \, \left(\frac{s-a}{\sigma}\right)^{\frac{k}{2}-1} \, \exp\left(- \frac{1}{2}</a>
+<a name="44"><span class="lineNum">      44 </span>            : \left(\frac{s-a}{\sigma}\right) \right),</a>
+<a name="45"><span class="lineNum">      45 </span>            : \f]</a>
+<a name="46"><span class="lineNum">      46 </span>            : where \f$a\f$ is the minimum of the distribution that is defined on the interval \f$[a,\infty)\f$,</a>
+<a name="47"><span class="lineNum">      47 </span>            : the parameter \f$k\f$ (given as a positive integer larger than 2) determines how far</a>
+<a name="48"><span class="lineNum">      48 </span>            : the peak of the distribution is from the minimum (known as the &quot;degrees of freedom&quot;),</a>
+<a name="49"><span class="lineNum">      49 </span>            : and the parameter \f$\sigma&gt;0\f$ determines the broadness of the distribution.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The minimum \f$a\f$ is given using the MINIMUM keyword, the parameter \f$k\f$ is given</a>
+<a name="52"><span class="lineNum">      52 </span>            : using the KAPPA keyword, and the parameter \f$\sigma\f$ is given using the SIGMA keyword.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : This target distribution action is only defined for one dimension, for multiple dimensions</a>
+<a name="55"><span class="lineNum">      55 </span>            : it should be used in combination with the \ref TD_PRODUCT_DISTRIBUTION action.</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : \par Examples</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : Chi-squared distribution with \f$a=-10.0\f$, \f$\sigma=2.0\f$, and \f$k=2\f$</a>
+<a name="60"><span class="lineNum">      60 </span>            : \plumedfile</a>
+<a name="61"><span class="lineNum">      61 </span>            : td: TD_CHISQUARED  MINIMUM=-10.0  SIGMA=2.0  KAPPA=2</a>
+<a name="62"><span class="lineNum">      62 </span>            : \endplumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The Chi-squared distribution is only defined for one dimension so for multiple</a>
+<a name="65"><span class="lineNum">      65 </span>            : dimensions we have to use it in combination with the \ref TD_PRODUCT_DISTRIBUTION action as shown in</a>
+<a name="66"><span class="lineNum">      66 </span>            : the following example where we have a Chi-squared distribution for argument 1</a>
+<a name="67"><span class="lineNum">      67 </span>            : and uniform distribution for argument 2</a>
+<a name="68"><span class="lineNum">      68 </span>            : \plumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : td_chisq: TD_CHISQUARED  MINIMUM=10.0  SIGMA=2.0  KAPPA=2</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : td_uni: TD_UNIFORM</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : td_pd: TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS=td_chisq,td_uni</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : */</a>
+<a name="77"><span class="lineNum">      77 </span>            : //+ENDPLUMEDOC</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : class TD_ChiSquared: public TargetDistribution {</a>
+<a name="80"><span class="lineNum">      80 </span>            :   std::vector&lt;double&gt; minima_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;double&gt; kappa_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;double&gt; normalization_;</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="86"><span class="lineNum">      86 </span>            :   explicit TD_ChiSquared(const ActionOptions&amp; ao);</a>
+<a name="87"><span class="lineNum">      87 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="88"><span class="lineNum">      88 </span>            : };</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      12513 : PLUMED_REGISTER_ACTION(TD_ChiSquared,&quot;TD_CHISQUARED&quot;)</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         11 : void TD_ChiSquared::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         11 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;MINIMUM&quot;,&quot;The minimum of the chi-squared distribution.&quot;);</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;SIGMA&quot;,&quot;The sigma parameter of the chi-squared distribution given as a positive number.&quot;);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;KAPPA&quot;,&quot;The k parameter of the chi-squared distribution given as positive integer larger than 2.&quot;);</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         11 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         11 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         11 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">         11 : }</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          9 : TD_ChiSquared::TD_ChiSquared(const ActionOptions&amp; ao):</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         18 :   minima_(0),</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          9 :   sigma_(0),</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          9 :   kappa_(0),</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         18 :   normalization_(0)</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          9 :   parseVector(&quot;MINIMUM&quot;,minima_);</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          9 :   parseVector(&quot;SIGMA&quot;,sigma_);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         18 :   for(unsigned int k=0; k&lt;sigma_.size(); k++) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          9 :     if(sigma_[k] &lt; 0.0) {plumed_merror(getName()+&quot;: the value given in SIGMA should be positive.&quot;);}</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   }</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">          9 :   std::vector&lt;unsigned int&gt; kappa_int(0);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         18 :   parseVector(&quot;KAPPA&quot;,kappa_int);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          9 :   if(kappa_int.size()==0) {plumed_merror(getName()+&quot;: some problem with KAPPA keyword, should given as positive integer larger than 2&quot;);}</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          9 :   kappa_.resize(kappa_int.size());</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         18 :   for(unsigned int k=0; k&lt;kappa_int.size(); k++) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          9 :     if(kappa_int[k] &lt; 2) {plumed_merror(getName()+&quot;: KAPPA should be an integer 2 or higher&quot;);}</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">          9 :     kappa_[k] = static_cast&lt;double&gt;(kappa_int[k]);</span></a>
+<a name="125"><span class="lineNum">     125 </span>            :   }</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          9 :   setDimension(minima_.size());</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          9 :   if(getDimension()&gt;1) {plumed_merror(getName()+&quot;: only defined for one dimension, for multiple dimensions it should be used in combination with the TD_PRODUCT_DISTRIBUTION action.&quot;);}</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          9 :   if(sigma_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the SIGMA keyword does not match the given dimension in MINIMUM&quot;);}</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          9 :   if(kappa_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the KAPPA keyword does not match the given dimension in MINIMUM&quot;);}</span></a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          9 :   normalization_.resize(getDimension());</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         18 :   for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          9 :     normalization_[k] = 1.0/(pow(2.0,0.5*kappa_[k])*tgamma(0.5*kappa_[k])*sigma_[k]);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          9 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">       1509 : double TD_ChiSquared::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   double value = 1.0;</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       3018 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1509 :     double arg=(argument[k]-minima_[k])/sigma_[k];</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       1509 :     if(arg&lt;0.0) {plumed_merror(getName()+&quot;: the chi-squared istribution is not defined for values less that ones given in MINIMUM&quot;);}</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">       1509 :     value *= normalization_[k] * pow(arg,0.5*kappa_[k]-1.0) * exp(-0.5*arg);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1509 :   return value;</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : }</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : }</a>
+<a name="152"><span class="lineNum">     152 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Custom.cpp.func-sort-c.html b/coverage/ves/TD_Custom.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ec4faa5ff7
--- /dev/null
+++ b/coverage/ves/TD_Custom.cpp.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Custom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Custom.cpp<span style="font-size: 80%;"> (<a href="TD_Custom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Custom.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#247">_ZNK4PLMD3ves9TD_Custom8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#144">_ZN4PLMD3ves12_GLOBAL__N_122TD_CustomRegisterMe1466createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#240">_ZN4PLMD3ves9TD_Custom20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#155">_ZN4PLMD3ves9TD_CustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#141">_ZN4PLMD3ves9TD_CustomD0Ev</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#141">_ZN4PLMD3ves9TD_CustomD2Ev</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#147">_ZN4PLMD3ves9TD_Custom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#253">_ZN4PLMD3ves9TD_Custom10updateGridEv</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#144">_ZN4PLMD3ves12_GLOBAL__N_122TD_CustomRegisterMe146C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#144">_ZN4PLMD3ves12_GLOBAL__N_122TD_CustomRegisterMe146D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Custom.cpp.func.html b/coverage/ves/TD_Custom.cpp.func.html
new file mode 100644
index 0000000000..e22e2141b3
--- /dev/null
+++ b/coverage/ves/TD_Custom.cpp.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Custom.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Custom.cpp<span style="font-size: 80%;"> (<a href="TD_Custom.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Custom.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#144">_ZN4PLMD3ves12_GLOBAL__N_122TD_CustomRegisterMe1466createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#144">_ZN4PLMD3ves12_GLOBAL__N_122TD_CustomRegisterMe146C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#144">_ZN4PLMD3ves12_GLOBAL__N_122TD_CustomRegisterMe146D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#253">_ZN4PLMD3ves9TD_Custom10updateGridEv</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#147">_ZN4PLMD3ves9TD_Custom16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">18</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#240">_ZN4PLMD3ves9TD_Custom20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#155">_ZN4PLMD3ves9TD_CustomC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#141">_ZN4PLMD3ves9TD_CustomD0Ev</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#141">_ZN4PLMD3ves9TD_CustomD2Ev</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Custom.cpp.gcov.html#247">_ZNK4PLMD3ves9TD_Custom8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Custom.cpp.gcov.html b/coverage/ves/TD_Custom.cpp.gcov.html
new file mode 100644
index 0000000000..d52ee42669
--- /dev/null
+++ b/coverage/ves/TD_Custom.cpp.gcov.html
@@ -0,0 +1,371 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Custom.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Custom.cpp<span style="font-size: 80%;"> (source / <a href="TD_Custom.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntry">90</td>
+            <td class="headerCovTableEntryMed">86.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;lepton/Lepton.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC VES_TARGETDIST TD_CUSTOM</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Target distribution given by an arbitrary mathematical expression (static or dynamic).</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Use as a target distribution the distribution defined by</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            : p(\mathbf{s}) =</a>
+<a name="42"><span class="lineNum">      42 </span>            : \frac{f(\mathbf{s})}{\int d\mathbf{s} \, f(\mathbf{s})}</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : where \f$f(\mathbf{s})\f$ is some arbitrary mathematical function that</a>
+<a name="45"><span class="lineNum">      45 </span>            : is parsed by the lepton library.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : The function \f$f(\mathbf{s})\f$ is given by the FUNCTION keywords by</a>
+<a name="48"><span class="lineNum">      48 </span>            : using _s1_,_s2_,..., as variables for the arguments</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f$\mathbf{s}=(s_1,s_2,\ldots,s_d)\f$.</a>
+<a name="50"><span class="lineNum">      50 </span>            : If one variable is not given the target distribution will be</a>
+<a name="51"><span class="lineNum">      51 </span>            : taken as uniform in that argument.</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : It is also possible to include the free energy surface \f$F(\mathbf{s})\f$</a>
+<a name="54"><span class="lineNum">      54 </span>            : in the target distribution by using the _FE_ variable. In this case the</a>
+<a name="55"><span class="lineNum">      55 </span>            : target distribution is dynamic and needs to be updated with current</a>
+<a name="56"><span class="lineNum">      56 </span>            : best estimate of \f$F(\mathbf{s})\f$, similarly as for the</a>
+<a name="57"><span class="lineNum">      57 </span>            : \ref TD_WELLTEMPERED &quot;well-tempered target distribution&quot;.</a>
+<a name="58"><span class="lineNum">      58 </span>            : Furthermore, the inverse temperature \f$\beta = (k_{\mathrm{B}}T)^{-1}\f$ and</a>
+<a name="59"><span class="lineNum">      59 </span>            : the thermal energy \f$k_{\mathrm{B}}T\f$ can be included</a>
+<a name="60"><span class="lineNum">      60 </span>            : by using the _beta_ and \f$k_B T\f$ variables.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The target distribution will be automatically normalized over the region on</a>
+<a name="63"><span class="lineNum">      63 </span>            : which it is defined on. Therefore, the function given in</a>
+<a name="64"><span class="lineNum">      64 </span>            : FUNCTION needs to be non-negative and it must be possible to normalize the function. The</a>
+<a name="65"><span class="lineNum">      65 </span>            : code will perform checks to make sure that this is indeed the case.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : \par Examples</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : Here we use as shifted [Maxwell-Boltzmann distribution](https://en.wikipedia.org/wiki/Maxwell%E2%80%93Boltzmann_distribution)</a>
+<a name="71"><span class="lineNum">      71 </span>            : as a target distribution in one-dimension.</a>
+<a name="72"><span class="lineNum">      72 </span>            : Note that it is not need to include the normalization factor as the distribution will be</a>
+<a name="73"><span class="lineNum">      73 </span>            : automatically normalized.</a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : TD_CUSTOM ...</a>
+<a name="76"><span class="lineNum">      76 </span>            :  FUNCTION=(s1+20)^2*exp(-(s1+20)^2/(2*10.0^2))</a>
+<a name="77"><span class="lineNum">      77 </span>            :  LABEL=td</a>
+<a name="78"><span class="lineNum">      78 </span>            : ... TD_CUSTOM</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : Here we have a two dimensional target distribution where we</a>
+<a name="82"><span class="lineNum">      82 </span>            : use a [generalized normal distribution](https://en.wikipedia.org/wiki/Generalized_normal_distribution)</a>
+<a name="83"><span class="lineNum">      83 </span>            : for argument \f$s_2\f$ while the distribution for \f$s_1\f$ is taken as</a>
+<a name="84"><span class="lineNum">      84 </span>            : uniform as the variable _s1_ is not included in the function.</a>
+<a name="85"><span class="lineNum">      85 </span>            : \plumedfile</a>
+<a name="86"><span class="lineNum">      86 </span>            : TD_CUSTOM ...</a>
+<a name="87"><span class="lineNum">      87 </span>            :  FUNCTION=exp(-(abs(s2-20.0)/5.0)^4.0)</a>
+<a name="88"><span class="lineNum">      88 </span>            :  LABEL=td</a>
+<a name="89"><span class="lineNum">      89 </span>            : ... TD_CUSTOM</a>
+<a name="90"><span class="lineNum">      90 </span>            : \endplumedfile</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : By using the _FE_ variable the target distribution can depend on</a>
+<a name="93"><span class="lineNum">      93 </span>            : the free energy surface \f$F(\mathbf{s})\f$. For example,</a>
+<a name="94"><span class="lineNum">      94 </span>            : the following input is identical to using \ref TD_WELLTEMPERED with</a>
+<a name="95"><span class="lineNum">      95 </span>            : a bias factor of 10.</a>
+<a name="96"><span class="lineNum">      96 </span>            : \plumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : TD_CUSTOM ...</a>
+<a name="98"><span class="lineNum">      98 </span>            :  FUNCTION=exp(-(beta/10.0)*FE)</a>
+<a name="99"><span class="lineNum">      99 </span>            :  LABEL=td</a>
+<a name="100"><span class="lineNum">     100 </span>            : ... TD_CUSTOM</a>
+<a name="101"><span class="lineNum">     101 </span>            : \endplumedfile</a>
+<a name="102"><span class="lineNum">     102 </span>            : Here the inverse temperature is automatically obtained by using the _beta_</a>
+<a name="103"><span class="lineNum">     103 </span>            : variable. It is also possible to use the \f$k_B T\f$ variable. The following</a>
+<a name="104"><span class="lineNum">     104 </span>            : syntax will give the exact same results as the syntax above</a>
+<a name="105"><span class="lineNum">     105 </span>            : \plumedfile</a>
+<a name="106"><span class="lineNum">     106 </span>            : TD_CUSTOM ...</a>
+<a name="107"><span class="lineNum">     107 </span>            :  FUNCTION=exp(-(1.0/(kBT*10.0))*FE)</a>
+<a name="108"><span class="lineNum">     108 </span>            :  LABEL=td</a>
+<a name="109"><span class="lineNum">     109 </span>            : ... TD_CUSTOM</a>
+<a name="110"><span class="lineNum">     110 </span>            : \endplumedfile</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : */</a>
+<a name="114"><span class="lineNum">     114 </span>            : //+ENDPLUMEDOC</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : class TD_Custom : public TargetDistribution {</a>
+<a name="117"><span class="lineNum">     117 </span>            : private:</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) override;</a>
+<a name="119"><span class="lineNum">     119 </span>            :   //</a>
+<a name="120"><span class="lineNum">     120 </span>            :   lepton::CompiledExpression expression;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   //</a>
+<a name="122"><span class="lineNum">     122 </span>            :   std::vector&lt;double*&gt; cv_var_lepton_refs_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   double* kbt_var_lepton_ref_;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   double* beta_var_lepton_ref_;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   double* fes_var_lepton_ref_;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   //</a>
+<a name="127"><span class="lineNum">     127 </span>            :   std::vector&lt;unsigned int&gt; cv_var_idx_;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   std::vector&lt;std::string&gt; cv_var_str_;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   //</a>
+<a name="130"><span class="lineNum">     130 </span>            :   std::string cv_var_prefix_str_;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::string fes_var_str_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::string kbt_var_str_;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::string beta_var_str_;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   //</a>
+<a name="135"><span class="lineNum">     135 </span>            :   bool use_fes_;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   bool use_kbt_;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   bool use_beta_;</a>
+<a name="138"><span class="lineNum">     138 </span>            : public:</a>
+<a name="139"><span class="lineNum">     139 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="140"><span class="lineNum">     140 </span>            :   explicit TD_Custom(const ActionOptions&amp; ao);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void updateGrid() override;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         48 :   ~TD_Custom() {};</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : };</a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">      12520 : PLUMED_REGISTER_ACTION(TD_Custom,&quot;TD_CUSTOM&quot;)</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         18 : void TD_Custom::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         18 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         36 :   keys.add(&quot;compulsory&quot;,&quot;FUNCTION&quot;,&quot;The function you wish to use for the target distribution where you should use the variables _s1_,_s2_,... for the arguments. You can also use the current estimate of the FES by using the variable _FE_ and the temperature by using the \\f$k_B T\\f$ and _beta_ variables.&quot;);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         18 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         18 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         18 : }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         16 : TD_Custom::TD_Custom(const ActionOptions&amp; ao):</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="159"><span class="lineNum">     159 </span>            : //</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         16 :   cv_var_lepton_refs_(0,nullptr),</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         16 :   kbt_var_lepton_ref_(nullptr),</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         16 :   beta_var_lepton_ref_(nullptr),</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         16 :   fes_var_lepton_ref_(nullptr),</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : //</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         16 :   cv_var_idx_(0),</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         16 :   cv_var_str_(0),</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : //</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         16 :   cv_var_prefix_str_(&quot;s&quot;),</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         16 :   fes_var_str_(&quot;FE&quot;),</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">         16 :   kbt_var_str_(&quot;kBT&quot;),</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         16 :   beta_var_str_(&quot;beta&quot;),</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : //</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         16 :   use_fes_(false),</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         16 :   use_kbt_(false),</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         32 :   use_beta_(false)</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : {</a>
+<a name="177"><span class="lineNum">     177 </span>            :   std::string func_str;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         16 :   parse(&quot;FUNCTION&quot;,func_str);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         16 :   checkRead();</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   //</a>
+<a name="181"><span class="lineNum">     181 </span>            :   try {</a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         16 :     lepton::ParsedExpression pe=lepton::Parser::parse(func_str).optimize(lepton::Constants());</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         16 :     log&lt;&lt;&quot;  function as parsed by lepton: &quot;&lt;&lt;pe&lt;&lt;&quot;\n&quot;;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         16 :     expression=pe.createCompiledExpression();</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   catch(PLMD::lepton::Exception&amp; exc) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;There was some problem in parsing the function &quot;+func_str+&quot; given in FUNCTION with lepton&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineNoCov">          0 :   }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         39 :   for(auto &amp;p: expression.getVariables()) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         23 :     std::string curr_var = p;</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :     unsigned int cv_idx;</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         39 :     if(curr_var.substr(0,cv_var_prefix_str_.size())==cv_var_prefix_str_ &amp;&amp; Tools::convertNoexcept(curr_var.substr(cv_var_prefix_str_.size()),cv_idx) &amp;&amp; cv_idx&gt;0) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">         16 :       cv_var_idx_.push_back(cv_idx-1);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :     }</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">          7 :     else if(curr_var==fes_var_str_) {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          3 :       use_fes_=true;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :       setDynamic();</a>
+<a name="199"><span class="lineNum">     199 </span>            :       setFesGridNeeded();</a>
+<a name="200"><span class="lineNum">     200 </span>            :     }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          4 :     else if(curr_var==kbt_var_str_) {</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :       use_kbt_=true;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     }</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          2 :     else if(curr_var==beta_var_str_) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          2 :       use_beta_=true;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     }</a>
+<a name="207"><span class="lineNum">     207 </span>            :     else {</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: problem with parsing formula with lepton, cannot recognise the variable &quot;+curr_var);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :     }</a>
+<a name="210"><span class="lineNum">     210 </span>            :   }</a>
+<a name="211"><span class="lineNum">     211 </span>            :   //</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         16 :   std::sort(cv_var_idx_.begin(),cv_var_idx_.end());</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         16 :   cv_var_str_.resize(cv_var_idx_.size());</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         16 :   cv_var_lepton_refs_.resize(cv_var_str_.size());</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         32 :   for(unsigned int j=0; j&lt;cv_var_idx_.size(); j++) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         16 :     std::string str1; Tools::convert(cv_var_idx_[j]+1,str1);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         32 :     cv_var_str_[j] = cv_var_prefix_str_+str1;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :     try {</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         16 :       cv_var_lepton_refs_[j] = &amp;expression.getVariableReference(cv_var_str_[j]);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         16 :   if(use_kbt_) {</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :     try {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          2 :       kbt_var_lepton_ref_ = &amp;expression.getVariableReference(kbt_var_str_);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">         16 :   if(use_beta_) {</span></a>
+<a name="229"><span class="lineNum">     229 </span>            :     try {</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          2 :       beta_var_lepton_ref_ = &amp;expression.getVariableReference(beta_var_str_);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         16 :   if(use_fes_) {</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     try {</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          3 :       fes_var_lepton_ref_ = &amp;expression.getVariableReference(fes_var_str_);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 :     } catch(PLMD::lepton::Exception&amp; exc) {}</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :   }</a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         16 : }</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         16 : void TD_Custom::setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp; arguments, const std::vector&lt;std::string&gt;&amp; min, const std::vector&lt;std::string&gt;&amp; max, const std::vector&lt;unsigned int&gt;&amp; nbins) {</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         16 :   if(cv_var_idx_.size()&gt;0 &amp;&amp; cv_var_idx_[cv_var_idx_.size()-1]&gt;getDimension()) {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: mismatch between CVs given in FUNC and the dimension of the target distribution&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            :   }</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         16 : }</span></a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 : double TD_Custom::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_Custom&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   return 0.0;</a>
+<a name="252"><span class="lineNum">     252 </span>            : }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">         46 : void TD_Custom::updateGrid() {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         46 :   if(use_fes_) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         33 :     plumed_massert(getFesGridPntr()!=NULL,&quot;the FES grid has to be linked to the free energy in the target distribution&quot;);</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         46 :   if(use_kbt_) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         22 :     if(kbt_var_lepton_ref_) {*kbt_var_lepton_ref_= 1.0/getBeta();}</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   }</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         46 :   if(use_beta_) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         22 :     if(beta_var_lepton_ref_) {*beta_var_lepton_ref_= getBeta();}</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span>            :   //</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         92 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   double norm = 0.0;</a>
+<a name="268"><span class="lineNum">     268 </span>            :   //</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">      40909 :   for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">      40863 :     std::vector&lt;double&gt; point = targetDistGrid().getPoint(l);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      99928 :     for(unsigned int k=0; k&lt;cv_var_str_.size() ; k++) {</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">      59065 :       if(cv_var_lepton_refs_[k]) {*cv_var_lepton_refs_[k] = point[cv_var_idx_[k]];}</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     }</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      40863 :     if(use_fes_) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">       3300 :       if(fes_var_lepton_ref_) {*fes_var_lepton_ref_ = getFesGridPntr()-&gt;getValue(l);}</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     }</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">      40863 :     double value = expression.evaluate();</span></a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">      40863 :     if(value&lt;0.0 &amp;&amp; !isTargetDistGridShiftedToZero()) {plumed_merror(getName()+&quot;: The target distribution function gives negative values. You should change the definition of the function used for the target distribution to avoid this. You can also use the SHIFT_TO_ZERO keyword to avoid this problem.&quot;);}</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      40863 :     targetDistGrid().setValue(l,value);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">      40863 :     norm += integration_weights[l]*value;</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">      40863 :     logTargetDistGrid().setValue(l,-std::log(value));</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :   }</a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         46 :   if(norm&gt;0.0) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         45 :     targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   }</a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          1 :   else if(!isTargetDistGridShiftedToZero()) {</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: The target distribution function cannot be normalized proberly. You should change the definition of the function used for the target distribution to avoid this. You can also use the SHIFT_TO_ZERO keyword to avoid this problem.&quot;);</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   }</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         46 :   logTargetDistGrid().setMinToZero();</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         46 : }</span></a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            : }</a>
+<a name="295"><span class="lineNum">     295 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Exponential.cpp.func-sort-c.html b/coverage/ves/TD_Exponential.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fec6256389
--- /dev/null
+++ b/coverage/ves/TD_Exponential.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Exponential.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Exponential.cpp<span style="font-size: 80%;"> (<a href="TD_Exponential.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Exponential.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#82">_ZN4PLMD3ves12_GLOBAL__N_126TD_ExponentialRegisterMe846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#95">_ZN4PLMD3ves14TD_ExponentialC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#85">_ZN4PLMD3ves14TD_Exponential16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#114">_ZNK4PLMD3ves14TD_Exponential8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1308</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#82">_ZN4PLMD3ves12_GLOBAL__N_126TD_ExponentialRegisterMe84C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#82">_ZN4PLMD3ves12_GLOBAL__N_126TD_ExponentialRegisterMe84D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Exponential.cpp.func.html b/coverage/ves/TD_Exponential.cpp.func.html
new file mode 100644
index 0000000000..64177d1064
--- /dev/null
+++ b/coverage/ves/TD_Exponential.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Exponential.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Exponential.cpp<span style="font-size: 80%;"> (<a href="TD_Exponential.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Exponential.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#82">_ZN4PLMD3ves12_GLOBAL__N_126TD_ExponentialRegisterMe846createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#82">_ZN4PLMD3ves12_GLOBAL__N_126TD_ExponentialRegisterMe84C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#82">_ZN4PLMD3ves12_GLOBAL__N_126TD_ExponentialRegisterMe84D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#85">_ZN4PLMD3ves14TD_Exponential16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#95">_ZN4PLMD3ves14TD_ExponentialC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Exponential.cpp.gcov.html#114">_ZNK4PLMD3ves14TD_Exponential8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1308</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Exponential.cpp.gcov.html b/coverage/ves/TD_Exponential.cpp.gcov.html
new file mode 100644
index 0000000000..656c0376f0
--- /dev/null
+++ b/coverage/ves/TD_Exponential.cpp.gcov.html
@@ -0,0 +1,205 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Exponential.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Exponential.cpp<span style="font-size: 80%;"> (source / <a href="TD_Exponential.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_EXPONENTIAL</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Exponential distribution (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution given by an</a>
+<a name="36"><span class="lineNum">      36 </span>            : [exponential distribution](https://en.wikipedia.org/wiki/Exponential_distribution)</a>
+<a name="37"><span class="lineNum">      37 </span>            : that is defined as</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : p(s) =</a>
+<a name="40"><span class="lineNum">      40 </span>            : \lambda e^{-\lambda(s-a)}</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : where \f$a\f$ is the minimum of the distribution that is defined on the interval \f$[a,\infty)\f$,</a>
+<a name="43"><span class="lineNum">      43 </span>            : and \f$\lambda&gt;0\f$ is the so-called rate parameter.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The minimum \f$a\f$ is given using the MINIMUM keyword, and the rate parameter \f$\lambda\f$ is given</a>
+<a name="46"><span class="lineNum">      46 </span>            : using the LAMBDA keyword.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : This target distribution action is only defined for one dimension, for multiple dimensions</a>
+<a name="49"><span class="lineNum">      49 </span>            : it should be used in combination with \ref TD_PRODUCT_DISTRIBUTION action.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : \par Examples</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : Exponential distribution with \f$a=10.0\f$ and \f$\lambda=0.5\f$</a>
+<a name="54"><span class="lineNum">      54 </span>            : \plumedfile</a>
+<a name="55"><span class="lineNum">      55 </span>            : td: TD_EXPONENTIAL  MINIMUM=-10.0  LAMBDA=0.5</a>
+<a name="56"><span class="lineNum">      56 </span>            : \endplumedfile</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : The exponential distribution is only defined for one dimension so for multiple</a>
+<a name="59"><span class="lineNum">      59 </span>            : dimensions we have to use it in combination with the \ref TD_PRODUCT_DISTRIBUTION action as shown in</a>
+<a name="60"><span class="lineNum">      60 </span>            : the following example where we have a uniform distribution for argument 1 and</a>
+<a name="61"><span class="lineNum">      61 </span>            : and an exponential distribution for argument 2</a>
+<a name="62"><span class="lineNum">      62 </span>            : \plumedfile</a>
+<a name="63"><span class="lineNum">      63 </span>            : td_uni: TD_UNIFORM</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : td_exp: TD_EXPONENTIAL  MINIMUM=-10.0  LAMBDA=0.5</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : td_pd: TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS=td_uni,td_exp</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : */</a>
+<a name="72"><span class="lineNum">      72 </span>            : //+ENDPLUMEDOC</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : class TD_Exponential: public TargetDistribution {</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::vector&lt;double&gt; minima_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   std::vector&lt;double&gt; lambda_;</a>
+<a name="77"><span class="lineNum">      77 </span>            : public:</a>
+<a name="78"><span class="lineNum">      78 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="79"><span class="lineNum">      79 </span>            :   explicit TD_Exponential(const ActionOptions&amp; ao);</a>
+<a name="80"><span class="lineNum">      80 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="81"><span class="lineNum">      81 </span>            : };</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(TD_Exponential,&quot;TD_EXPONENTIAL&quot;)</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         10 : void TD_Exponential::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         10 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;MINIMUM&quot;,&quot;The minimum of the exponential distribution.&quot;);</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         20 :   keys.add(&quot;compulsory&quot;,&quot;LAMBDA&quot;,&quot;The lambda parameter of the exponential distribution given as positive number.&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         10 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         10 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         10 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         10 : }</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">          8 : TD_Exponential::TD_Exponential(const ActionOptions&amp; ao):</span></a>
+<a name="98"><span class="lineNum">      98 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">         16 :   minima_(0),</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">          8 :   lambda_(0)</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          8 :   parseVector(&quot;MINIMUM&quot;,minima_);</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">          8 :   parseVector(&quot;LAMBDA&quot;,lambda_);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         16 :   for(unsigned int k=0; k&lt;lambda_.size(); k++) {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          8 :     if(lambda_[k] &lt; 0.0) {plumed_merror(getName()+&quot;: the value given in LAMBDA should be positive.&quot;);}</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          8 :   setDimension(minima_.size());</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">          8 :   if(getDimension()&gt;1) {plumed_merror(getName()+&quot;: only defined for one dimension, for multiple dimensions it should be used in combination with the TD_PRODUCT_DISTRIBUTION action.&quot;);}</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">          8 :   if(lambda_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the LAMBDA keyword does not match the given dimension in MINIMUM&quot;);}</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          8 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       1308 : double TD_Exponential::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   double value = 1.0;</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       2616 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">       1308 :     double arg = (argument[k]-minima_[k])*lambda_[k];</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1308 :     if(arg&lt;0.0) {plumed_merror(getName()+&quot;: the exponential distribution is not defined for values less that ones given in MINIMUM&quot;);}</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">       1308 :     value *= lambda_[k]*exp(-arg);</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       1308 :   return value;</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : }</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.func-sort-c.html b/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.func-sort-c.html
new file mode 100644
index 0000000000..46624021ec
--- /dev/null
+++ b/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ExponentiallyModifiedGaussian.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ExponentiallyModifiedGaussian.cpp<span style="font-size: 80%;"> (<a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_ExponentiallyModifiedGaussian.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#117">_ZN4PLMD3ves12_GLOBAL__N_145TD_ExponentiallyModifiedGaussianRegisterMe1196createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#132">_ZN4PLMD3ves32TD_ExponentiallyModifiedGaussianC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#120">_ZN4PLMD3ves32TD_ExponentiallyModifiedGaussian16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#117">_ZN4PLMD3ves12_GLOBAL__N_145TD_ExponentiallyModifiedGaussianRegisterMe119C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#117">_ZN4PLMD3ves12_GLOBAL__N_145TD_ExponentiallyModifiedGaussianRegisterMe119D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#200">_ZNK4PLMD3ves32TD_ExponentiallyModifiedGaussian8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">11206</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#209">_ZNK4PLMD3ves32TD_ExponentiallyModifiedGaussian37ExponentiallyModifiedGaussianDiagonalERKSt6vectorIdSaIdEES6_S6_S6_</a></td>
+              <td class="coverFnHi">21809</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.func.html b/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.func.html
new file mode 100644
index 0000000000..48fa988df4
--- /dev/null
+++ b/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ExponentiallyModifiedGaussian.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ExponentiallyModifiedGaussian.cpp<span style="font-size: 80%;"> (<a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_ExponentiallyModifiedGaussian.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#117">_ZN4PLMD3ves12_GLOBAL__N_145TD_ExponentiallyModifiedGaussianRegisterMe1196createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#117">_ZN4PLMD3ves12_GLOBAL__N_145TD_ExponentiallyModifiedGaussianRegisterMe119C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#117">_ZN4PLMD3ves12_GLOBAL__N_145TD_ExponentiallyModifiedGaussianRegisterMe119D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#120">_ZN4PLMD3ves32TD_ExponentiallyModifiedGaussian16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#132">_ZN4PLMD3ves32TD_ExponentiallyModifiedGaussianC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#209">_ZNK4PLMD3ves32TD_ExponentiallyModifiedGaussian37ExponentiallyModifiedGaussianDiagonalERKSt6vectorIdSaIdEES6_S6_S6_</a></td>
+              <td class="coverFnHi">21809</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html#200">_ZNK4PLMD3ves32TD_ExponentiallyModifiedGaussian8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">11206</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.gcov.html b/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.gcov.html
new file mode 100644
index 0000000000..51c93e7977
--- /dev/null
+++ b/coverage/ves/TD_ExponentiallyModifiedGaussian.cpp.gcov.html
@@ -0,0 +1,300 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ExponentiallyModifiedGaussian.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ExponentiallyModifiedGaussian.cpp<span style="font-size: 80%;"> (source / <a href="TD_ExponentiallyModifiedGaussian.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">58</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_EXPONENTIALLY_MODIFIED_GAUSSIAN</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Target distribution given by a sum of exponentially modified Gaussian distributions (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution that is given by a sum where each</a>
+<a name="36"><span class="lineNum">      36 </span>            : term is a product of one-dimensional</a>
+<a name="37"><span class="lineNum">      37 </span>            : [exponentially modified Gaussian distributions](http://en.wikipedia.org/wiki/Exponentially_modified_Gaussian_distribution),</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : p(\mathbf{s}) = \sum_{i} \, w_{i}</a>
+<a name="40"><span class="lineNum">      40 </span>            : \prod_{k}^{d}</a>
+<a name="41"><span class="lineNum">      41 </span>            : \frac{\lambda_{k,i}}{2}</a>
+<a name="42"><span class="lineNum">      42 </span>            : \,</a>
+<a name="43"><span class="lineNum">      43 </span>            : \exp\left[</a>
+<a name="44"><span class="lineNum">      44 </span>            : \frac{\lambda_{k,i}}{2}</a>
+<a name="45"><span class="lineNum">      45 </span>            : (2 \mu_{k,i} + \lambda_{k,i} \sigma_{k,i}^2 -2 s_{k})</a>
+<a name="46"><span class="lineNum">      46 </span>            : \right]</a>
+<a name="47"><span class="lineNum">      47 </span>            : \,</a>
+<a name="48"><span class="lineNum">      48 </span>            : \mathrm{erfc}\left[</a>
+<a name="49"><span class="lineNum">      49 </span>            : \frac{\mu_{k,i} + \lambda_{k,i} \sigma_{k,i}^2 - s_{k})}{\sqrt{2} \sigma_{k,i}}</a>
+<a name="50"><span class="lineNum">      50 </span>            : \right]</a>
+<a name="51"><span class="lineNum">      51 </span>            : \f]</a>
+<a name="52"><span class="lineNum">      52 </span>            : where \f$(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$</a>
+<a name="53"><span class="lineNum">      53 </span>            : are the centers of the Gaussian component,</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f$(\sigma_{1,i},\sigma_{2,i},\ldots,\sigma_{d,i})\f$ are the</a>
+<a name="55"><span class="lineNum">      55 </span>            : standard deviations of the Gaussian component,</a>
+<a name="56"><span class="lineNum">      56 </span>            : \f$(\lambda_{1,i},\lambda_{2,i},\ldots,\lambda_{d,i})\f$ are the</a>
+<a name="57"><span class="lineNum">      57 </span>            : rate parameters of the exponential component, and</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f$\mathrm{erfc}(x)=1-\mathrm{erf}(x)\f$ is the</a>
+<a name="59"><span class="lineNum">      59 </span>            : complementary error function.</a>
+<a name="60"><span class="lineNum">      60 </span>            : The weights \f$w_{i}\f$ are normalized to 1, \f$\sum_{i}w_{i}=1\f$.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The centers \f$(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$ are</a>
+<a name="63"><span class="lineNum">      63 </span>            : given using the numbered CENTER keywords, the standard deviations</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f$(\sigma_{1,i},\sigma_{2,i},\ldots,\sigma_{d,i})\f$ using the</a>
+<a name="65"><span class="lineNum">      65 </span>            : the numbered SIGMA keywords, and the rate parameters</a>
+<a name="66"><span class="lineNum">      66 </span>            : \f$(\lambda_{1,i},\lambda_{2,i},\ldots,\lambda_{d,i})\f$ using the</a>
+<a name="67"><span class="lineNum">      67 </span>            : numbered LAMBDA keywords.</a>
+<a name="68"><span class="lineNum">      68 </span>            : The weights are given using the WEIGHTS keywords, if no weights are</a>
+<a name="69"><span class="lineNum">      69 </span>            : given are all terms weighted equally.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \par Examples</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : An exponentially modified Gaussian distribution in one-dimension</a>
+<a name="74"><span class="lineNum">      74 </span>            : \plumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : td1: TD_EXPONENTIALLY_MODIFIED_GAUSSIAN CENTER1=-10.0 SIGMA1=1.0 LAMBDA1=0.25</a>
+<a name="76"><span class="lineNum">      76 </span>            : \endplumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : A sum of two one-dimensional exponentially modified Gaussian distributions</a>
+<a name="79"><span class="lineNum">      79 </span>            : \plumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : TD_EXPONENTIALLY_MODIFIED_GAUSSIAN ...</a>
+<a name="81"><span class="lineNum">      81 </span>            :  CENTER1=-10.0 SIGMA1=1.0 LAMBDA1=0.5</a>
+<a name="82"><span class="lineNum">      82 </span>            :  CENTER2=+10.0 SIGMA2=1.0 LAMBDA2=1.0</a>
+<a name="83"><span class="lineNum">      83 </span>            :  WEIGHTS=2.0,1.0</a>
+<a name="84"><span class="lineNum">      84 </span>            :  LABEL=td1</a>
+<a name="85"><span class="lineNum">      85 </span>            : ... TD_EXPONENTIALLY_MODIFIED_GAUSSIAN</a>
+<a name="86"><span class="lineNum">      86 </span>            : \endplumedfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : A sum of two two-dimensional exponentially modified Gaussian distributions</a>
+<a name="89"><span class="lineNum">      89 </span>            : \plumedfile</a>
+<a name="90"><span class="lineNum">      90 </span>            : TD_EXPONENTIALLY_MODIFIED_GAUSSIAN ...</a>
+<a name="91"><span class="lineNum">      91 </span>            :  CENTER1=-5.0,+5.0 SIGMA1=1.0,1.0 LAMBDA1=0.5,0.5</a>
+<a name="92"><span class="lineNum">      92 </span>            :  CENTER2=+5.0,+5.0 SIGMA2=1.0,1.0 LAMBDA2=1.0,1.0</a>
+<a name="93"><span class="lineNum">      93 </span>            :  WEIGHTS=1.0,1.0</a>
+<a name="94"><span class="lineNum">      94 </span>            :  LABEL=td1</a>
+<a name="95"><span class="lineNum">      95 </span>            : ... TD_EXPONENTIALLY_MODIFIED_GAUSSIAN</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endplumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : */</a>
+<a name="103"><span class="lineNum">     103 </span>            : //+ENDPLUMEDOC</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : class TD_ExponentiallyModifiedGaussian: public TargetDistribution {</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; centers_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; sigmas_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; lambdas_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   std::vector&lt;double&gt; weights_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   unsigned int ncenters_;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   double ExponentiallyModifiedGaussianDiagonal(const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;) const;</a>
+<a name="112"><span class="lineNum">     112 </span>            : public:</a>
+<a name="113"><span class="lineNum">     113 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="114"><span class="lineNum">     114 </span>            :   explicit TD_ExponentiallyModifiedGaussian(const ActionOptions&amp; ao);</a>
+<a name="115"><span class="lineNum">     115 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="116"><span class="lineNum">     116 </span>            : };</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">      12510 : PLUMED_REGISTER_ACTION(TD_ExponentiallyModifiedGaussian,&quot;TD_EXPONENTIALLY_MODIFIED_GAUSSIAN&quot;)</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          8 : void TD_ExponentiallyModifiedGaussian::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          8 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;CENTER&quot;,&quot;The center of each exponentially modified Gaussian distributions.&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;SIGMA&quot;,&quot;The sigma parameters for each exponentially modified Gaussian distributions.&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         16 :   keys.add(&quot;numbered&quot;,&quot;LAMBDA&quot;,&quot;The lambda parameters for each exponentially modified Gaussian distributions&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;WEIGHTS&quot;,&quot;The weights of the distributions. By default all are weighted equally.&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">          8 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          8 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          8 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          8 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          6 : TD_ExponentiallyModifiedGaussian::TD_ExponentiallyModifiedGaussian(const ActionOptions&amp; ao):</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         12 :   centers_(0),</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          6 :   sigmas_(0),</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          6 :   lambdas_(0),</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          6 :   weights_(0),</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         12 :   ncenters_(0)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : {</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          9 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     std::vector&lt;double&gt; tmp_center;</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         30 :     if(!parseNumberedVector(&quot;CENTER&quot;,i,tmp_center) ) {break;}</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          9 :     centers_.push_back(tmp_center);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          9 :   }</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     std::vector&lt;double&gt; tmp_sigma;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         30 :     if(!parseNumberedVector(&quot;SIGMA&quot;,i,tmp_sigma) ) {break;}</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         20 :     for(unsigned int k=0; k&lt;tmp_sigma.size(); k++) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         11 :       if(tmp_sigma[k]&lt;=0.0) {plumed_merror(getName()+&quot;: the values given in SIGMA should be positive&quot;);}</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :     }</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          9 :     sigmas_.push_back(tmp_sigma);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          9 :   }</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          9 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     std::vector&lt;double&gt; tmp_lambda;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         30 :     if(!parseNumberedVector(&quot;LAMBDA&quot;,i,tmp_lambda) ) {break;}</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         20 :     for(unsigned int k=0; k&lt;tmp_lambda.size(); k++) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         11 :       if(tmp_lambda[k]&lt;=0.0) {plumed_merror(getName()+&quot;: the values given in LAMBDA should be positive&quot;);}</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     }</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          9 :     lambdas_.push_back(tmp_lambda);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          9 :   }</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   //</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          6 :   if(centers_.size()==0) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: CENTER keywords seem to be missing. Note that numbered keywords start at CENTER1.&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span>            :   //</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          6 :   if(centers_.size()!=sigmas_.size() || centers_.size()!=lambdas_.size() ) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there has to be an equal amount of CENTER, SIGMA, and LAMBDA keywords&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            :   //</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          6 :   setDimension(centers_[0].size());</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          6 :   ncenters_ = centers_.size();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   //</a>
+<a name="175"><span class="lineNum">     175 </span>            :   // check centers and sigmas</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         15 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          9 :     if(centers_[i].size()!=getDimension()) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the CENTER keyword does not match the given dimension&quot;);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :     }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          9 :     if(sigmas_[i].size()!=getDimension()) {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the SIGMA keyword does not match the given dimension&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :     }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          9 :     if(lambdas_[i].size()!=getDimension()) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the LAMBDA keyword does not match the given dimension&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     }</a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">         12 :   parseVector(&quot;WEIGHTS&quot;,weights_);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          6 :   if(weights_.size()==0) {weights_.assign(centers_.size(),1.0);}</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          6 :   if(centers_.size()!=weights_.size()) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there has to be as many weights given in WEIGHTS as numbered CENTER keywords&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span>            :   //</a>
+<a name="194"><span class="lineNum">     194 </span>            :   double sum_weights=0.0;</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         15 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {sum_weights+=weights_[i];}</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         15 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {weights_[i]/=sum_weights;}</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   //</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          6 :   checkRead();</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          6 : }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      11206 : double TD_ExponentiallyModifiedGaussian::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :   double value=0.0;</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      33015 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      21809 :     value+=weights_[i]*ExponentiallyModifiedGaussianDiagonal(argument,centers_[i],sigmas_[i],lambdas_[i]);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      11206 :   return value;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">      21809 : double TD_ExponentiallyModifiedGaussian::ExponentiallyModifiedGaussianDiagonal(const std::vector&lt;double&gt;&amp; argument, const std::vector&lt;double&gt;&amp; center, const std::vector&lt;double&gt;&amp; sigma, const std::vector&lt;double&gt;&amp; lambda) const {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   double value = 1.0;</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      64020 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      42211 :     double arg1 = 0.5*lambda[k]*(2.0*center[k]+lambda[k]*sigma[k]*sigma[k]-2.0*argument[k]);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">      42211 :     double arg2 = (center[k]+lambda[k]*sigma[k]*sigma[k]-argument[k])/(sqrt(2.0)*sigma[k]);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">      42211 :     value *= 0.5*lambda[k]*exp(arg1)*erfc(arg2);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   }</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">      21809 :   return value;</span></a>
+<a name="219"><span class="lineNum">     219 </span>            : }</a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : }</a>
+<a name="224"><span class="lineNum">     224 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Gaussian.cpp.func-sort-c.html b/coverage/ves/TD_Gaussian.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d03d7fcb02
--- /dev/null
+++ b/coverage/ves/TD_Gaussian.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Gaussian.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Gaussian.cpp<span style="font-size: 80%;"> (<a href="TD_Gaussian.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Gaussian.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#189">_ZN4PLMD3ves11TD_GaussianC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">191</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#174">_ZN4PLMD3ves12_GLOBAL__N_124TD_GaussianRegisterMe1766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">191</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#177">_ZN4PLMD3ves11TD_Gaussian16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#174">_ZN4PLMD3ves12_GLOBAL__N_124TD_GaussianRegisterMe176C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#174">_ZN4PLMD3ves12_GLOBAL__N_124TD_GaussianRegisterMe176D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#299">_ZNK4PLMD3ves11TD_Gaussian10Gaussian2DERKSt6vectorIdSaIdEES6_S6_S6_b</a></td>
+              <td class="coverFnHi">40804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#271">_ZNK4PLMD3ves11TD_Gaussian8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">229739</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#287">_ZNK4PLMD3ves11TD_Gaussian16GaussianDiagonalERKSt6vectorIdSaIdEES6_S6_b</a></td>
+              <td class="coverFnHi">292252</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Gaussian.cpp.func.html b/coverage/ves/TD_Gaussian.cpp.func.html
new file mode 100644
index 0000000000..758963dbaf
--- /dev/null
+++ b/coverage/ves/TD_Gaussian.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Gaussian.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Gaussian.cpp<span style="font-size: 80%;"> (<a href="TD_Gaussian.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Gaussian.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#177">_ZN4PLMD3ves11TD_Gaussian16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">193</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#189">_ZN4PLMD3ves11TD_GaussianC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">191</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#174">_ZN4PLMD3ves12_GLOBAL__N_124TD_GaussianRegisterMe1766createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">191</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#174">_ZN4PLMD3ves12_GLOBAL__N_124TD_GaussianRegisterMe176C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#174">_ZN4PLMD3ves12_GLOBAL__N_124TD_GaussianRegisterMe176D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#299">_ZNK4PLMD3ves11TD_Gaussian10Gaussian2DERKSt6vectorIdSaIdEES6_S6_S6_b</a></td>
+              <td class="coverFnHi">40804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#287">_ZNK4PLMD3ves11TD_Gaussian16GaussianDiagonalERKSt6vectorIdSaIdEES6_S6_b</a></td>
+              <td class="coverFnHi">292252</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Gaussian.cpp.gcov.html#271">_ZNK4PLMD3ves11TD_Gaussian8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">229739</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Gaussian.cpp.gcov.html b/coverage/ves/TD_Gaussian.cpp.gcov.html
new file mode 100644
index 0000000000..021a691a65
--- /dev/null
+++ b/coverage/ves/TD_Gaussian.cpp.gcov.html
@@ -0,0 +1,391 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Gaussian.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Gaussian.cpp<span style="font-size: 80%;"> (source / <a href="TD_Gaussian.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntry">85</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_GAUSSIAN</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Target distribution given by a sum of Gaussian kernels (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution that is given by a sum of multivariate Gaussian (or normal)</a>
+<a name="36"><span class="lineNum">      36 </span>            : distributions, defined as</a>
+<a name="37"><span class="lineNum">      37 </span>            : \f[</a>
+<a name="38"><span class="lineNum">      38 </span>            : p(\mathbf{s}) = \sum_{i} \, w_{i} \, N(\mathbf{s};\mathbf{\mu}_{i},\mathbf{\Sigma}_{i})</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f]</a>
+<a name="40"><span class="lineNum">      40 </span>            : where \f$\mathbf{\mu}_{i}=(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$</a>
+<a name="41"><span class="lineNum">      41 </span>            : and \f$\mathbf{\Sigma}_{i}\f$ are</a>
+<a name="42"><span class="lineNum">      42 </span>            : the center and the covariance matrix for the \f$i\f$-th Gaussian.</a>
+<a name="43"><span class="lineNum">      43 </span>            : The weights \f$w_{i}\f$ are normalized to 1, \f$\sum_{i}w_{i}=1\f$.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : By default the Gaussian distributions are considered as separable into</a>
+<a name="46"><span class="lineNum">      46 </span>            : independent one-dimensional Gaussian distributions. In other words,</a>
+<a name="47"><span class="lineNum">      47 </span>            : the covariance matrix is taken as diagonal</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f$\mathbf{\Sigma}_{i}=(\sigma^2_{1,i},\sigma^2_{2,i},\ldots,\sigma^{2}_{d,i})\f$.</a>
+<a name="49"><span class="lineNum">      49 </span>            : The Gaussian distribution is then written as</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f[</a>
+<a name="51"><span class="lineNum">      51 </span>            : N(\mathbf{s};\mathbf{\mu}_{i},\mathbf{\sigma}_{i}) =</a>
+<a name="52"><span class="lineNum">      52 </span>            : \prod^{d}_{k} \, \frac{1}{\sqrt{2\pi\sigma^2_{d,i}}} \,</a>
+<a name="53"><span class="lineNum">      53 </span>            : \exp\left(</a>
+<a name="54"><span class="lineNum">      54 </span>            : -\frac{(s_{d}-\mu_{d,i})^2}{2\sigma^2_{d,i}}</a>
+<a name="55"><span class="lineNum">      55 </span>            : \right)</a>
+<a name="56"><span class="lineNum">      56 </span>            : \f]</a>
+<a name="57"><span class="lineNum">      57 </span>            : where</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f$\mathbf{\sigma}_{i}=(\sigma_{1,i},\sigma_{2,i},\ldots,\sigma_{d,i})\f$</a>
+<a name="59"><span class="lineNum">      59 </span>            : is the standard deviation.</a>
+<a name="60"><span class="lineNum">      60 </span>            : In this case you need to specify the centers \f$\mathbf{\mu}_{i}\f$ using the</a>
+<a name="61"><span class="lineNum">      61 </span>            : numbered CENTER keywords and the standard deviations \f$\mathbf{\sigma}_{i}\f$</a>
+<a name="62"><span class="lineNum">      62 </span>            : using the numbered SIGMA keywords.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : For two arguments it is possible to employ</a>
+<a name="65"><span class="lineNum">      65 </span>            : [bivariate Gaussian kernels](https://en.wikipedia.org/wiki/Multivariate_normal_distribution)</a>
+<a name="66"><span class="lineNum">      66 </span>            : with correlation between arguments, defined as</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f[</a>
+<a name="68"><span class="lineNum">      68 </span>            : N(\mathbf{s};\mathbf{\mu}_{i},\mathbf{\sigma}_{i},\rho_i) =</a>
+<a name="69"><span class="lineNum">      69 </span>            : \frac{1}{2 \pi \sigma_{1,i} \sigma_{2,i} \sqrt{1-\rho_i^2}}</a>
+<a name="70"><span class="lineNum">      70 </span>            : \,</a>
+<a name="71"><span class="lineNum">      71 </span>            : \exp\left(</a>
+<a name="72"><span class="lineNum">      72 </span>            : -\frac{1}{2(1-\rho_i^2)}</a>
+<a name="73"><span class="lineNum">      73 </span>            : \left[</a>
+<a name="74"><span class="lineNum">      74 </span>            : \frac{(s_{1}-\mu_{1,i})^2}{\sigma_{1,i}^2}+</a>
+<a name="75"><span class="lineNum">      75 </span>            : \frac{(s_{2}-\mu_{2,i})^2}{\sigma_{2,i}^2}-</a>
+<a name="76"><span class="lineNum">      76 </span>            : \frac{2 \rho_i (s_{1}-\mu_{1,i})(s_{2}-\mu_{2,i})}{\sigma_{1,i}\sigma_{2,i}}</a>
+<a name="77"><span class="lineNum">      77 </span>            : \right]</a>
+<a name="78"><span class="lineNum">      78 </span>            : \right)</a>
+<a name="79"><span class="lineNum">      79 </span>            : \f]</a>
+<a name="80"><span class="lineNum">      80 </span>            : where \f$\rho_i\f$ is the correlation between \f$s_{1}\f$ and \f$s_{2}\f$</a>
+<a name="81"><span class="lineNum">      81 </span>            : that goes from -1 to 1. In this case the covariance matrix is given as</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f[</a>
+<a name="83"><span class="lineNum">      83 </span>            : \mathbf{\Sigma}=</a>
+<a name="84"><span class="lineNum">      84 </span>            : \left[</a>
+<a name="85"><span class="lineNum">      85 </span>            : \begin{array}{cc}</a>
+<a name="86"><span class="lineNum">      86 </span>            : \sigma^2_{1,i} &amp; \rho_i \sigma_{1,i} \sigma_{2,i} \\</a>
+<a name="87"><span class="lineNum">      87 </span>            : \rho_i \sigma_{1,i} \sigma_{2,i} &amp; \sigma^2_{2,i}</a>
+<a name="88"><span class="lineNum">      88 </span>            : \end{array}</a>
+<a name="89"><span class="lineNum">      89 </span>            : \right]</a>
+<a name="90"><span class="lineNum">      90 </span>            : \f]</a>
+<a name="91"><span class="lineNum">      91 </span>            : The correlation \f$\rho\f$ is given using</a>
+<a name="92"><span class="lineNum">      92 </span>            : the numbered CORRELATION keywords. A value of \f$\rho=0\f$ means</a>
+<a name="93"><span class="lineNum">      93 </span>            : that the arguments are considered as</a>
+<a name="94"><span class="lineNum">      94 </span>            : un-correlated, which is the default behavior.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : The Gaussian distributions are always defined with the conventional</a>
+<a name="97"><span class="lineNum">      97 </span>            : normalization factor such that they are normalized to 1 over an unbounded</a>
+<a name="98"><span class="lineNum">      98 </span>            : region. However, in calculation within VES we normally consider bounded</a>
+<a name="99"><span class="lineNum">      99 </span>            : region on which the target distribution is defined. Thus, if the center of</a>
+<a name="100"><span class="lineNum">     100 </span>            : a Gaussian is close to the boundary of the region it can happen that the</a>
+<a name="101"><span class="lineNum">     101 </span>            : tails go outside the region. In that case it might be needed to use the</a>
+<a name="102"><span class="lineNum">     102 </span>            : NORMALIZE keyword to make sure that the target distribution is properly</a>
+<a name="103"><span class="lineNum">     103 </span>            : normalized to 1 over the bounded region. The code will issue a warning</a>
+<a name="104"><span class="lineNum">     104 </span>            : if that is needed.</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : For periodic CVs it is generally better to use \ref TD_VONMISES &quot;Von Mises&quot;</a>
+<a name="107"><span class="lineNum">     107 </span>            : distributions instead of Gaussian kernels as these distributions properly</a>
+<a name="108"><span class="lineNum">     108 </span>            : account for the periodicity of the CVs.</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : \par Examples</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : One single Gaussian kernel in one-dimension.</a>
+<a name="114"><span class="lineNum">     114 </span>            : \plumedfile</a>
+<a name="115"><span class="lineNum">     115 </span>            : td: TD_GAUSSIAN CENTER1=-1.5 SIGMA1=0.8</a>
+<a name="116"><span class="lineNum">     116 </span>            : \endplumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : Sum of three Gaussian kernels in two-dimensions with equal weights as</a>
+<a name="119"><span class="lineNum">     119 </span>            : no weights are given.</a>
+<a name="120"><span class="lineNum">     120 </span>            : \plumedfile</a>
+<a name="121"><span class="lineNum">     121 </span>            : TD_GAUSSIAN ...</a>
+<a name="122"><span class="lineNum">     122 </span>            :  CENTER1=-1.5,+1.5 SIGMA1=0.8,0.3</a>
+<a name="123"><span class="lineNum">     123 </span>            :  CENTER2=+1.5,-1.5 SIGMA2=0.3,0.8</a>
+<a name="124"><span class="lineNum">     124 </span>            :  CENTER3=+1.5,+1.5 SIGMA3=0.4,0.4</a>
+<a name="125"><span class="lineNum">     125 </span>            :  LABEL=td</a>
+<a name="126"><span class="lineNum">     126 </span>            : ... TD_GAUSSIAN</a>
+<a name="127"><span class="lineNum">     127 </span>            : \endplumedfile</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : Sum of three Gaussian kernels in two-dimensions which</a>
+<a name="130"><span class="lineNum">     130 </span>            : are weighted unequally. Note that weights are automatically</a>
+<a name="131"><span class="lineNum">     131 </span>            : normalized to 1 so that WEIGHTS=1.0,2.0,1.0 is equal to</a>
+<a name="132"><span class="lineNum">     132 </span>            : specifying WEIGHTS=0.25,0.50,0.25.</a>
+<a name="133"><span class="lineNum">     133 </span>            : \plumedfile</a>
+<a name="134"><span class="lineNum">     134 </span>            : TD_GAUSSIAN ...</a>
+<a name="135"><span class="lineNum">     135 </span>            :  CENTER1=-1.5,+1.5 SIGMA1=0.8,0.3</a>
+<a name="136"><span class="lineNum">     136 </span>            :  CENTER2=+1.5,-1.5 SIGMA2=0.3,0.8</a>
+<a name="137"><span class="lineNum">     137 </span>            :  CENTER3=+1.5,+1.5 SIGMA3=0.4,0.4</a>
+<a name="138"><span class="lineNum">     138 </span>            :  WEIGHTS=1.0,2.0,1.0</a>
+<a name="139"><span class="lineNum">     139 </span>            :  LABEL=td</a>
+<a name="140"><span class="lineNum">     140 </span>            : ... TD_GAUSSIAN</a>
+<a name="141"><span class="lineNum">     141 </span>            : \endplumedfile</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : Sum of two bivariate Gaussian kernels where there is correlation of</a>
+<a name="144"><span class="lineNum">     144 </span>            : \f$\rho_{2}=0.75\f$ between the two arguments for the second Gaussian.</a>
+<a name="145"><span class="lineNum">     145 </span>            : \plumedfile</a>
+<a name="146"><span class="lineNum">     146 </span>            : TD_GAUSSIAN ...</a>
+<a name="147"><span class="lineNum">     147 </span>            :  CENTER1=-1.5,+1.5 SIGMA1=0.8,0.3</a>
+<a name="148"><span class="lineNum">     148 </span>            :  CENTER2=+1.5,-1.5 SIGMA2=0.3,0.8 CORRELATION2=0.75</a>
+<a name="149"><span class="lineNum">     149 </span>            :  LABEL=td</a>
+<a name="150"><span class="lineNum">     150 </span>            : ... TD_GAUSSIAN</a>
+<a name="151"><span class="lineNum">     151 </span>            : \endplumedfile</a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            : */</a>
+<a name="158"><span class="lineNum">     158 </span>            : //+ENDPLUMEDOC</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : class TD_Gaussian: public TargetDistribution {</a>
+<a name="161"><span class="lineNum">     161 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; centers_;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; sigmas_;</a>
+<a name="163"><span class="lineNum">     163 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; correlation_;</a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::vector&lt;double&gt; weights_;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   bool diagonal_;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   unsigned int ncenters_;</a>
+<a name="167"><span class="lineNum">     167 </span>            :   double GaussianDiagonal(const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const bool normalize=true) const;</a>
+<a name="168"><span class="lineNum">     168 </span>            :   double Gaussian2D(const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const bool normalize=true) const;</a>
+<a name="169"><span class="lineNum">     169 </span>            : public:</a>
+<a name="170"><span class="lineNum">     170 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="171"><span class="lineNum">     171 </span>            :   explicit TD_Gaussian(const ActionOptions&amp; ao);</a>
+<a name="172"><span class="lineNum">     172 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="173"><span class="lineNum">     173 </span>            : };</a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">      12695 : PLUMED_REGISTER_ACTION(TD_Gaussian,&quot;TD_GAUSSIAN&quot;)</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        193 : void TD_Gaussian::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        193 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        386 :   keys.add(&quot;numbered&quot;,&quot;CENTER&quot;,&quot;The centers of the Gaussian distributions.&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        386 :   keys.add(&quot;numbered&quot;,&quot;SIGMA&quot;,&quot;The standard deviations of the Gaussian distributions.&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        386 :   keys.add(&quot;numbered&quot;,&quot;CORRELATION&quot;,&quot;The correlation for two-dimensional bivariate Gaussian distributions. Only works for two arguments. The value should be between -1 and 1. If no value is given the Gaussian kernels is considered as un-correlated (i.e. value of 0.0).&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        386 :   keys.add(&quot;optional&quot;,&quot;WEIGHTS&quot;,&quot;The weights of the Gaussian distributions. Have to be as many as the number of centers given with the numbered CENTER keywords. If no weights are given the distributions are weighted equally. The weights are automatically normalized to 1.&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        193 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">        193 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        193 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        193 : }</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        191 : TD_Gaussian::TD_Gaussian(const ActionOptions&amp; ao):</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        382 :   centers_(0),</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        191 :   sigmas_(0),</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">        191 :   correlation_(0),</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">        191 :   weights_(0),</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">        191 :   diagonal_(true),</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        382 :   ncenters_(0)</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : {</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        211 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :     std::vector&lt;double&gt; tmp_center;</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        804 :     if(!parseNumberedVector(&quot;CENTER&quot;,i,tmp_center) ) {break;}</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        211 :     centers_.push_back(tmp_center);</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">        211 :   }</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        211 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     std::vector&lt;double&gt; tmp_sigma;</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        804 :     if(!parseNumberedVector(&quot;SIGMA&quot;,i,tmp_sigma) ) {break;}</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        211 :     sigmas_.push_back(tmp_sigma);</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        211 :   }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        191 :   if(centers_.size()==0) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: CENTER keywords seem to be missing. Note that numbered keywords start at CENTER1.&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :   }</a>
+<a name="214"><span class="lineNum">     214 </span>            :   //</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        191 :   if(centers_.size()!=sigmas_.size()) {</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there has to be an equal amount of CENTER and SIGMA keywords&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :   }</a>
+<a name="218"><span class="lineNum">     218 </span>            :   //</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">        191 :   setDimension(centers_[0].size());</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">        191 :   ncenters_ = centers_.size();</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   // check centers and sigmas</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">        402 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">        211 :     if(centers_[i].size()!=getDimension()) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the CENTER keyword does not match the given dimension&quot;);</span></a>
+<a name="225"><span class="lineNum">     225 </span>            :     }</a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">        211 :     if(sigmas_[i].size()!=getDimension()) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the SIGMA keyword does not match the given dimension&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     }</a>
+<a name="229"><span class="lineNum">     229 </span>            :   }</a>
+<a name="230"><span class="lineNum">     230 </span>            :   //</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">        191 :   correlation_.resize(ncenters_);</span></a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        402 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :     std::vector&lt;double&gt; corr;</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">        422 :     parseNumberedVector(&quot;CORRELATION&quot;,(i+1),corr);</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">        211 :     if(corr.size()&gt;0) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          3 :       diagonal_ = false;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :     }</a>
+<a name="239"><span class="lineNum">     239 </span>            :     else {</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">        208 :       corr.assign(1,0.0);</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :     }</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">        211 :     correlation_[i] = corr;</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        191 :   if(!diagonal_ &amp;&amp; getDimension()!=2) {</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: CORRELATION is only defined for two-dimensional Gaussians for now.&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :   }</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        402 :   for(unsigned int i=0; i&lt;correlation_.size(); i++) {</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        211 :     if(correlation_[i].size()!=1) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: only one value should be given in CORRELATION&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :     }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        422 :     for(unsigned int k=0; k&lt;correlation_[i].size(); k++) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        211 :       if(correlation_[i][k] &lt;= -1.0 ||  correlation_[i][k] &gt;= 1.0) {</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :         plumed_merror(getName()+&quot;: values given in CORRELATION should be between -1.0 and 1.0&quot; );</span></a>
+<a name="255"><span class="lineNum">     255 </span>            :       }</a>
+<a name="256"><span class="lineNum">     256 </span>            :     }</a>
+<a name="257"><span class="lineNum">     257 </span>            :   }</a>
+<a name="258"><span class="lineNum">     258 </span>            :   //</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        382 :   parseVector(&quot;WEIGHTS&quot;,weights_);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        191 :   if(weights_.size()==0) {weights_.assign(centers_.size(),1.0);}</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">        191 :   if(centers_.size()!=weights_.size()) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there has to be as many weights given in WEIGHTS as numbered CENTER keywords&quot;);</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :   }</a>
+<a name="264"><span class="lineNum">     264 </span>            :   //</a>
+<a name="265"><span class="lineNum">     265 </span>            :   double sum_weights=0.0;</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        402 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {sum_weights+=weights_[i];}</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">        402 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {weights_[i]/=sum_weights;}</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   //</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        191 :   checkRead();</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">        191 : }</span></a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">     229739 : double TD_Gaussian::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :   double value=0.0;</a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">     229739 :   if(diagonal_) {</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">     501589 :     for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">     292252 :       value+=weights_[i]*GaussianDiagonal(argument, centers_[i], sigmas_[i]);</span></a>
+<a name="278"><span class="lineNum">     278 </span>            :     }</a>
+<a name="279"><span class="lineNum">     279 </span>            :   }</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      20402 :   else if(!diagonal_ &amp;&amp; getDimension()==2) {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">      61206 :     for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">      40804 :       value+=weights_[i]*Gaussian2D(argument, centers_[i], sigmas_[i],correlation_[i]);</span></a>
+<a name="283"><span class="lineNum">     283 </span>            :     }</a>
+<a name="284"><span class="lineNum">     284 </span>            :   }</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     229739 :   return value;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">     292252 : double TD_Gaussian::GaussianDiagonal(const std::vector&lt;double&gt;&amp; argument, const std::vector&lt;double&gt;&amp; center, const std::vector&lt;double&gt;&amp; sigma, bool normalize) const {</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   double value = 1.0;</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">     828323 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">     536071 :     double arg=(argument[k]-center[k])/sigma[k];</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">     536071 :     double tmp_exp = exp(-0.5*arg*arg);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">     536071 :     if(normalize) {tmp_exp/=(sigma[k]*sqrt(2.0*pi));}</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">     536071 :     value*=tmp_exp;</span></a>
+<a name="296"><span class="lineNum">     296 </span>            :   }</a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">     292252 :   return value;</span></a>
+<a name="298"><span class="lineNum">     298 </span>            : }</a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">      40804 : double TD_Gaussian::Gaussian2D(const std::vector&lt;double&gt;&amp; argument, const std::vector&lt;double&gt;&amp; center, const std::vector&lt;double&gt;&amp; sigma, const std::vector&lt;double&gt;&amp; correlation, bool normalize) const {</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">      40804 :   double arg1 = (argument[0]-center[0])/sigma[0];</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">      40804 :   double arg2 = (argument[1]-center[1])/sigma[1];</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">      40804 :   double corr = correlation[0];</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">      40804 :   double value = (arg1*arg1 + arg2*arg2 - 2.0*corr*arg1*arg2);</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">      40804 :   value *= -1.0 / ( 2.0*(1.0-corr*corr) );</span></a>
+<a name="307"><span class="lineNum">     307 </span><span class="lineCov">      40804 :   value = exp(value);</span></a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">      40804 :   if(normalize) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">      40804 :     value /=  2*pi*sigma[0]*sigma[1]*sqrt(1.0-corr*corr);</span></a>
+<a name="310"><span class="lineNum">     310 </span>            :   }</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">      40804 :   return value;</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : }</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : }</a>
+<a name="315"><span class="lineNum">     315 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_GeneralizedExtremeValue.cpp.func-sort-c.html b/coverage/ves/TD_GeneralizedExtremeValue.cpp.func-sort-c.html
new file mode 100644
index 0000000000..192578b09d
--- /dev/null
+++ b/coverage/ves/TD_GeneralizedExtremeValue.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_GeneralizedExtremeValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_GeneralizedExtremeValue.cpp<span style="font-size: 80%;"> (<a href="TD_GeneralizedExtremeValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_GeneralizedExtremeValue.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_139TD_GeneralizedExtremeValueRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#124">_ZN4PLMD3ves26TD_GeneralizedExtremeValueC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#113">_ZN4PLMD3ves26TD_GeneralizedExtremeValue16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">7</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#154">_ZNK4PLMD3ves26TD_GeneralizedExtremeValue11GEVdiagonalERKSt6vectorIdSaIdEES6_S6_S6_S6_</a></td>
+              <td class="coverFnHi">1605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#149">_ZNK4PLMD3ves26TD_GeneralizedExtremeValue8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1605</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_139TD_GeneralizedExtremeValueRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_139TD_GeneralizedExtremeValueRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_GeneralizedExtremeValue.cpp.func.html b/coverage/ves/TD_GeneralizedExtremeValue.cpp.func.html
new file mode 100644
index 0000000000..dc5e041eeb
--- /dev/null
+++ b/coverage/ves/TD_GeneralizedExtremeValue.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_GeneralizedExtremeValue.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_GeneralizedExtremeValue.cpp<span style="font-size: 80%;"> (<a href="TD_GeneralizedExtremeValue.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_GeneralizedExtremeValue.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_139TD_GeneralizedExtremeValueRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_GeneralizedExtremeValue.cpp.gcov.html b/coverage/ves/TD_GeneralizedExtremeValue.cpp.gcov.html
new file mode 100644
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+  <title>LCOV - plumed test coverage - ves/TD_GeneralizedExtremeValue.cpp</title>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_GeneralizedExtremeValue.cpp<span style="font-size: 80%;"> (source / <a href="TD_GeneralizedExtremeValue.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntry">39</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_GENERALIZED_EXTREME_VALUE</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Generalized extreme value distribution (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution given by a</a>
+<a name="36"><span class="lineNum">      36 </span>            : [generalized extreme value distribution](https://en.wikipedia.org/wiki/Generalized_extreme_value_distribution)</a>
+<a name="37"><span class="lineNum">      37 </span>            : that is defined as</a>
+<a name="38"><span class="lineNum">      38 </span>            : \f[</a>
+<a name="39"><span class="lineNum">      39 </span>            : p(s) =</a>
+<a name="40"><span class="lineNum">      40 </span>            : \frac{1}{\sigma} \, t(s)^{\xi+1} \, e^{-t(s)},</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f]</a>
+<a name="42"><span class="lineNum">      42 </span>            : where</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : t(s) =</a>
+<a name="45"><span class="lineNum">      45 </span>            : \begin{cases}</a>
+<a name="46"><span class="lineNum">      46 </span>            : \left( 1 + \xi \left( \frac{s-\mu}{\sigma} \right) \right)^{-1/\xi} &amp; \mathrm{if\ }\xi \neq 0 \\</a>
+<a name="47"><span class="lineNum">      47 </span>            : \exp\left(- \frac{s-\mu}{\sigma} \right) &amp; \mathrm{if\ } \xi = 0</a>
+<a name="48"><span class="lineNum">      48 </span>            : \end{cases},</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f]</a>
+<a name="50"><span class="lineNum">      50 </span>            : and \f$\mu\f$ is the location parameter which approximately determines the location of the</a>
+<a name="51"><span class="lineNum">      51 </span>            : maximum of the distribution, \f$\sigma&gt;0\f$ is the scale parameter that determines the</a>
+<a name="52"><span class="lineNum">      52 </span>            : broadness of the distribution, and \f$\xi\f$ is the shape parameter that determines</a>
+<a name="53"><span class="lineNum">      53 </span>            : the tail behavior of the distribution. For \f$\xi=0\f$, \f$\xi&gt;0\f$, and \f$\xi&lt;0\f$</a>
+<a name="54"><span class="lineNum">      54 </span>            : the Gumbel, Frechet, and Weibull families of distributions are obtained, respectively.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The location parameter \f$\mu\f$ is given using the LOCATION keyword, the scale parameter \f$\sigma\f$</a>
+<a name="57"><span class="lineNum">      57 </span>            : using the SCALE keyword, and the shape parameter \f$\xi\f$ using the SHAPE</a>
+<a name="58"><span class="lineNum">      58 </span>            : keyword.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : This target distribution action is only defined for one dimension, for multiple dimensions</a>
+<a name="61"><span class="lineNum">      61 </span>            : it should be used in combination with \ref TD_PRODUCT_DISTRIBUTION action.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : \par Examples</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : Generalized extreme value distribution with \f$\mu=0.0\f$, \f$\sigma=2.0\f$, and \f$\xi=0.0\f$ (Gumbel distribution)</a>
+<a name="66"><span class="lineNum">      66 </span>            : \plumedfile</a>
+<a name="67"><span class="lineNum">      67 </span>            : td: TD_GENERALIZED_EXTREME_VALUE  LOCATION=0.0  SCALE=2.0 SHAPE=0.0</a>
+<a name="68"><span class="lineNum">      68 </span>            : \endplumedfile</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : Generalized extreme value distribution with \f$\mu=-5.0\f$, \f$\sigma=1.0\f$, and \f$\xi=0.5\f$ (Frechet distribution)</a>
+<a name="72"><span class="lineNum">      72 </span>            : \plumedfile</a>
+<a name="73"><span class="lineNum">      73 </span>            : td: TD_GENERALIZED_EXTREME_VALUE  LOCATION=-5.0  SCALE=1.0 SHAPE=0.5</a>
+<a name="74"><span class="lineNum">      74 </span>            : \endplumedfile</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : Generalized extreme value distribution with \f$\mu=5.0\f$, \f$\sigma=2.0\f$, and \f$\xi=-0.5\f$ (Weibull distribution)</a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : td: TD_GENERALIZED_EXTREME_VALUE  LOCATION=5.0  SCALE=1.0 SHAPE=-0.5</a>
+<a name="80"><span class="lineNum">      80 </span>            : \endplumedfile</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : The generalized extreme value distribution is only defined for one dimension so for multiple</a>
+<a name="84"><span class="lineNum">      84 </span>            : dimensions we have to use it in combination with the \ref TD_PRODUCT_DISTRIBUTION action as shown in</a>
+<a name="85"><span class="lineNum">      85 </span>            : the following example where we have a Generalized extreme value distribution for argument 1</a>
+<a name="86"><span class="lineNum">      86 </span>            : and uniform distribution for argument 2</a>
+<a name="87"><span class="lineNum">      87 </span>            : \plumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : td_gev: TD_GENERALIZED_EXTREME_VALUE  LOCATION=-5.0  SCALE=1.0 SHAPE=0.5</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : td_uni: TD_UNIFORM</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : td_pd: TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS=td_gev,td_uni</a>
+<a name="93"><span class="lineNum">      93 </span>            : \endplumedfile</a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : */</a>
+<a name="97"><span class="lineNum">      97 </span>            : //+ENDPLUMEDOC</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : class TD_GeneralizedExtremeValue: public TargetDistribution {</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;double&gt; center_;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;double&gt; scale_;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt;double&gt; shape_;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt;double&gt; normalization_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   double GEVdiagonal(const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;) const;</a>
+<a name="105"><span class="lineNum">     105 </span>            : public:</a>
+<a name="106"><span class="lineNum">     106 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="107"><span class="lineNum">     107 </span>            :   explicit TD_GeneralizedExtremeValue(const ActionOptions&amp; ao);</a>
+<a name="108"><span class="lineNum">     108 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="109"><span class="lineNum">     109 </span>            : };</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      12509 : PLUMED_REGISTER_ACTION(TD_GeneralizedExtremeValue,&quot;TD_GENERALIZED_EXTREME_VALUE&quot;)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          7 : void TD_GeneralizedExtremeValue::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          7 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;LOCATION&quot;,&quot;The mu parameter of the generalized extreme value distribution.&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;SCALE&quot;,&quot;The sigma parameter for the generalized extreme value distribution given as a positive number.&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         14 :   keys.add(&quot;compulsory&quot;,&quot;SHAPE&quot;,&quot;The xi parameter for the generalized extreme value distribution.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">          7 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">          7 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">          7 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">          7 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">          5 : TD_GeneralizedExtremeValue::TD_GeneralizedExtremeValue(const ActionOptions&amp; ao):</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         10 :   center_(0),</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          5 :   scale_(0),</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          5 :   shape_(0),</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         10 :   normalization_(0)</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : {</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          5 :   parseVector(&quot;LOCATION&quot;,center_);</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          5 :   parseVector(&quot;SCALE&quot;,scale_);</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         10 :   parseVector(&quot;SHAPE&quot;,shape_);</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          5 :   setDimension(center_.size());</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          5 :   if(getDimension()&gt;1) {plumed_merror(getName()+&quot;: only defined for one dimension, for multiple dimensions it should be used in combination with the TD_PRODUCT_DISTRIBUTION action.&quot;);}</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          5 :   if(scale_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the SCALE keyword does not match the given dimension in MINIMA&quot;);}</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          5 :   if(shape_.size()!=getDimension()) {plumed_merror(getName()+&quot;: the SHAPE keyword does not match the given dimension in MINIMA&quot;);}</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">          5 :   normalization_.resize(getDimension());</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         10 :   for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          5 :     if(scale_[k]&lt;0.0) {plumed_merror(getName()+&quot;: the value given for the scale parameter in SCALE should be larger than 0.0&quot;);}</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          5 :     normalization_[k] = 1.0/scale_[k];</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          5 :   checkRead();</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          5 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       1605 : double TD_GeneralizedExtremeValue::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       1605 :   return GEVdiagonal(argument,center_,scale_,shape_,normalization_);</span></a>
+<a name="153"><span class="lineNum">     153 </span>            : }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">       1605 : double TD_GeneralizedExtremeValue::GEVdiagonal(const std::vector&lt;double&gt;&amp; argument, const std::vector&lt;double&gt;&amp; center, const std::vector&lt;double&gt;&amp; scale, const std::vector&lt;double&gt;&amp; shape, const std::vector&lt;double&gt;&amp; normalization) const {</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   double value = 1.0;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       2940 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">       1605 :     double arg=(argument[k]-center[k])/scale[k];</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :     double tx;</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       1605 :     if(shape_[k]!=0.0) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       1404 :       if( shape_[k]&gt;0 &amp;&amp; argument[k] &lt;= (center[k]-scale[k]/shape[k]) ) {return 0.0;}</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       1214 :       if( shape_[k]&lt;0 &amp;&amp; argument[k] &gt; (center[k]-scale[k]/shape[k]) ) {return 0.0;}</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       1134 :       tx = pow( (1.0+arg*shape[k]), -1.0/shape[k] );</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     }</a>
+<a name="166"><span class="lineNum">     166 </span>            :     else {</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        201 :       tx = exp(-arg);</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :     }</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1335 :     value *= normalization[k] * pow(tx,shape[k]+1.0) * exp(-tx);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span>            :   return value;</a>
+<a name="172"><span class="lineNum">     172 </span>            : }</a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            : </a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_GeneralizedNormal.cpp.func-sort-c.html b/coverage/ves/TD_GeneralizedNormal.cpp.func-sort-c.html
new file mode 100644
index 0000000000..298851ef00
--- /dev/null
+++ b/coverage/ves/TD_GeneralizedNormal.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_GeneralizedNormal.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_GeneralizedNormal.cpp<span style="font-size: 80%;"> (<a href="TD_GeneralizedNormal.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_GeneralizedNormal.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_133TD_GeneralizedNormalRegisterMe1146createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#127">_ZN4PLMD3ves20TD_GeneralizedNormalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#115">_ZN4PLMD3ves20TD_GeneralizedNormal16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_133TD_GeneralizedNormalRegisterMe114C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_133TD_GeneralizedNormalRegisterMe114D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#203">_ZNK4PLMD3ves20TD_GeneralizedNormal8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">21608</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#212">_ZNK4PLMD3ves20TD_GeneralizedNormal24ExponentialPowerDiagonalERKSt6vectorIdSaIdEES6_S6_S6_S6_</a></td>
+              <td class="coverFnHi">53015</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_GeneralizedNormal.cpp.func.html b/coverage/ves/TD_GeneralizedNormal.cpp.func.html
new file mode 100644
index 0000000000..11332a4d96
--- /dev/null
+++ b/coverage/ves/TD_GeneralizedNormal.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_GeneralizedNormal.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_GeneralizedNormal.cpp<span style="font-size: 80%;"> (<a href="TD_GeneralizedNormal.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_GeneralizedNormal.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_133TD_GeneralizedNormalRegisterMe1146createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_133TD_GeneralizedNormalRegisterMe114C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#112">_ZN4PLMD3ves12_GLOBAL__N_133TD_GeneralizedNormalRegisterMe114D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#115">_ZN4PLMD3ves20TD_GeneralizedNormal16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#127">_ZN4PLMD3ves20TD_GeneralizedNormalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#212">_ZNK4PLMD3ves20TD_GeneralizedNormal24ExponentialPowerDiagonalERKSt6vectorIdSaIdEES6_S6_S6_S6_</a></td>
+              <td class="coverFnHi">53015</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_GeneralizedNormal.cpp.gcov.html#203">_ZNK4PLMD3ves20TD_GeneralizedNormal8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">21608</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_GeneralizedNormal.cpp.gcov.html b/coverage/ves/TD_GeneralizedNormal.cpp.gcov.html
new file mode 100644
index 0000000000..294a90df33
--- /dev/null
+++ b/coverage/ves/TD_GeneralizedNormal.cpp.gcov.html
@@ -0,0 +1,303 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_GeneralizedNormal.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_GeneralizedNormal.cpp<span style="font-size: 80%;"> (source / <a href="TD_GeneralizedNormal.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">70</td>
+            <td class="headerCovTableEntryHi">91.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_GENERALIZED_NORMAL</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Target distribution given by a sum of generalized normal distributions (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Employ a target distribution that is given by a sum where each</a>
+<a name="36"><span class="lineNum">      36 </span>            : term is a product of one-dimensional</a>
+<a name="37"><span class="lineNum">      37 </span>            : [generalized normal distributions](https://en.wikipedia.org/wiki/Generalized_normal_distribution)</a>
+<a name="38"><span class="lineNum">      38 </span>            : (version 1, also know as an exponential power distribution), defined as</a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : p(\mathbf{s}) = \sum_{i} \, w_{i}</a>
+<a name="41"><span class="lineNum">      41 </span>            : \prod_{k}^{d}</a>
+<a name="42"><span class="lineNum">      42 </span>            : \frac{\beta_{k,i}}{2 \, \alpha_{k,i} \, \Gamma(1/\beta_{k,i})}</a>
+<a name="43"><span class="lineNum">      43 </span>            : \exp\left( -\left\vert \frac{s_{k}-\mu_{k,i}}{\alpha_{k,i}} \right\vert^{\beta_{k,i}} \right)</a>
+<a name="44"><span class="lineNum">      44 </span>            : \f]</a>
+<a name="45"><span class="lineNum">      45 </span>            : where \f$(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$</a>
+<a name="46"><span class="lineNum">      46 </span>            : are the centers of the distributions,</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f$(\alpha_{1,i},\alpha_{2,i},\ldots,\alpha_{d,i})\f$ are the scale</a>
+<a name="48"><span class="lineNum">      48 </span>            : parameters of the distributions,</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f$(\beta_{1,i},\beta_{2,i},\ldots,\beta_{d,i})\f$ are the shape</a>
+<a name="50"><span class="lineNum">      50 </span>            : parameters of the distributions, and \f$\Gamma(x)\f$ is the</a>
+<a name="51"><span class="lineNum">      51 </span>            : gamma function.</a>
+<a name="52"><span class="lineNum">      52 </span>            : The weights \f$w_{i}\f$ are normalized to 1, \f$\sum_{i}w_{i}=1\f$.</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : Employing \f$\beta=2\f$ results in a</a>
+<a name="55"><span class="lineNum">      55 </span>            : Gaussian (normal) distributions with mean</a>
+<a name="56"><span class="lineNum">      56 </span>            : \f$\mu\f$ and variance \f$\alpha^2/2\f$,</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f$\beta=1\f$ gives the Laplace distribution, and</a>
+<a name="58"><span class="lineNum">      58 </span>            : the limit \f$\beta \to \infty\f$ results in a</a>
+<a name="59"><span class="lineNum">      59 </span>            : uniform  distribution on the interval \f$[\mu-\alpha,\mu+\alpha]\f$.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The centers \f$(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$</a>
+<a name="62"><span class="lineNum">      62 </span>            : are given using the numbered CENTER keywords, the scale</a>
+<a name="63"><span class="lineNum">      63 </span>            : parameters \f$(\alpha_{1,i},\alpha_{2,i},\ldots,\alpha_{d,i})\f$</a>
+<a name="64"><span class="lineNum">      64 </span>            : using the numbered SCALE keywords, and the shape parameters</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f$(\beta_{1,i},\beta_{2,i},\ldots,\beta_{d,i})\f$ using the</a>
+<a name="66"><span class="lineNum">      66 </span>            : numbered SHAPE keywords.</a>
+<a name="67"><span class="lineNum">      67 </span>            : The weights are given using the WEIGHTS keywords, if no weights are</a>
+<a name="68"><span class="lineNum">      68 </span>            : given are all terms weighted equally.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : \par Examples</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : A generalized normal distribution in one-dimensional</a>
+<a name="73"><span class="lineNum">      73 </span>            : \plumedfile</a>
+<a name="74"><span class="lineNum">      74 </span>            : td1: TD_GENERALIZED_NORMAL CENTER1=+20.0  ALPHA1=5.0  BETA1=4.0</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : A sum of two one-dimensional generalized normal distributions</a>
+<a name="78"><span class="lineNum">      78 </span>            : \plumedfile</a>
+<a name="79"><span class="lineNum">      79 </span>            : TD_GENERALIZED_NORMAL ...</a>
+<a name="80"><span class="lineNum">      80 </span>            :  CENTER1=+20.0  ALPHA1=5.0  BETA1=4.0</a>
+<a name="81"><span class="lineNum">      81 </span>            :  CENTER2=-20.0  ALPHA2=5.0  BETA2=3.0</a>
+<a name="82"><span class="lineNum">      82 </span>            :  LABEL=td1</a>
+<a name="83"><span class="lineNum">      83 </span>            : ... TD_GENERALIZED_NORMAL</a>
+<a name="84"><span class="lineNum">      84 </span>            : \endplumedfile</a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span>            : A sum of two two-dimensional generalized normal distributions</a>
+<a name="87"><span class="lineNum">      87 </span>            : \plumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : TD_GENERALIZED_NORMAL ...</a>
+<a name="89"><span class="lineNum">      89 </span>            :  CENTER1=-20.0,-20.0 ALPHA1=5.0,3.0 BETA1=2.0,4.0</a>
+<a name="90"><span class="lineNum">      90 </span>            :  CENTER2=-20.0,+20.0 ALPHA2=3.0,5.0 BETA2=4.0,2.0</a>
+<a name="91"><span class="lineNum">      91 </span>            :  WEIGHTS=2.0,1.0</a>
+<a name="92"><span class="lineNum">      92 </span>            :  LABEL=td1</a>
+<a name="93"><span class="lineNum">      93 </span>            : ... TD_GENERALIZED_NORMAL</a>
+<a name="94"><span class="lineNum">      94 </span>            : \endplumedfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : */</a>
+<a name="97"><span class="lineNum">      97 </span>            : //+ENDPLUMEDOC</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : class TD_GeneralizedNormal: public TargetDistribution {</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; centers_;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; alphas_;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; betas_;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; normalization_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::vector&lt;double&gt; weights_;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   unsigned int ncenters_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   double ExponentialPowerDiagonal(const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;) const;</a>
+<a name="107"><span class="lineNum">     107 </span>            : public:</a>
+<a name="108"><span class="lineNum">     108 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="109"><span class="lineNum">     109 </span>            :   explicit TD_GeneralizedNormal(const ActionOptions&amp; ao);</a>
+<a name="110"><span class="lineNum">     110 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="111"><span class="lineNum">     111 </span>            : };</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(TD_GeneralizedNormal,&quot;TD_GENERALIZED_NORMAL&quot;)</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         10 : void TD_GeneralizedNormal::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         10 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;CENTER&quot;,&quot;The center of each generalized normal distribution.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;ALPHA&quot;,&quot;The alpha parameters for each generalized normal distribution.&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         20 :   keys.add(&quot;numbered&quot;,&quot;BETA&quot;,&quot;The beta parameters for each generalized normal distribution.&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         20 :   keys.add(&quot;optional&quot;,&quot;WEIGHTS&quot;,&quot;The weights of the generalized normal distribution. By default all are weighted equally.&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         10 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         10 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         10 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         10 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">          8 : TD_GeneralizedNormal::TD_GeneralizedNormal(const ActionOptions&amp; ao):</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         16 :   centers_(0),</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          8 :   alphas_(0),</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          8 :   betas_(0),</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          8 :   normalization_(0),</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          8 :   weights_(0),</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         16 :   ncenters_(0)</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : {</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         15 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     std::vector&lt;double&gt; tmp_center;</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         46 :     if(!parseNumberedVector(&quot;CENTER&quot;,i,tmp_center) ) {break;}</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         15 :     centers_.push_back(tmp_center);</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         15 :   }</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         15 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     std::vector&lt;double&gt; tmp_alpha;</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         46 :     if(!parseNumberedVector(&quot;ALPHA&quot;,i,tmp_alpha) ) {break;}</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">         35 :     for(unsigned int k=0; k&lt;tmp_alpha.size(); k++) {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         20 :       if(tmp_alpha[k]&lt;=0.0) {plumed_merror(getName()+&quot;: the values given in ALPHA should be positive&quot;);}</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         15 :     alphas_.push_back(tmp_alpha);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         15 :   }</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         15 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :     std::vector&lt;double&gt; tmp_beta;</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         46 :     if(!parseNumberedVector(&quot;BETA&quot;,i,tmp_beta) ) {break;}</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         35 :     for(unsigned int k=0; k&lt;tmp_beta.size(); k++) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         20 :       if(tmp_beta[k]&lt;=0.0) {plumed_merror(getName()+&quot;: the values given in BETA should be positive&quot;);}</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :     }</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         15 :     betas_.push_back(tmp_beta);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         15 :   }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   //</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          8 :   if(centers_.size()==0) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: CENTER keywords seem to be missing. Note that numbered keywords start at CENTER1.&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          8 :   if(centers_.size()!=alphas_.size() || centers_.size()!=betas_.size() ) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there has to be an equal amount of CENTER, ALPHA, and BETA keywords&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   }</a>
+<a name="167"><span class="lineNum">     167 </span>            :   //</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          8 :   setDimension(centers_[0].size());</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :   ncenters_ = centers_.size();</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   //</a>
+<a name="171"><span class="lineNum">     171 </span>            :   // check centers and sigmas</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         23 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         15 :     if(centers_[i].size()!=getDimension()) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the CENTER keyword does not match the given dimension&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         15 :     if(alphas_[i].size()!=getDimension()) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the ALPHA keyword does not match the given dimension&quot;);</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :     }</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         15 :     if(betas_[i].size()!=getDimension()) {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: one of the BETA keyword does not match the given dimension&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :     }</a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span>            :   //</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         16 :   parseVector(&quot;WEIGHTS&quot;,weights_);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          8 :   if(weights_.size()==0) {weights_.assign(centers_.size(),1.0);}</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          8 :   if(centers_.size()!=weights_.size()) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: there has to be as many weights given in WEIGHTS as numbered CENTER keywords&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span>            :   //</a>
+<a name="190"><span class="lineNum">     190 </span>            :   double sum_weights=0.0;</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         23 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {sum_weights+=weights_[i];}</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         23 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {weights_[i]/=sum_weights;}</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   //</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">          8 :   normalization_.resize(ncenters_);</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         23 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         15 :     normalization_[i].resize(getDimension());</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         35 :     for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         20 :       normalization_[i][k] = 0.5*betas_[i][k]/(alphas_[i][k]*tgamma(1.0/betas_[i][k]));</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :     }</a>
+<a name="200"><span class="lineNum">     200 </span>            :   }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          8 :   checkRead();</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          8 : }</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      21608 : double TD_GeneralizedNormal::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   double value=0.0;</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      74623 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">      53015 :     value+=weights_[i]*ExponentialPowerDiagonal(argument,centers_[i],alphas_[i],betas_[i],normalization_[i]);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :   }</a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      21608 :   return value;</span></a>
+<a name="211"><span class="lineNum">     211 </span>            : }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">      53015 : double TD_GeneralizedNormal::ExponentialPowerDiagonal(const std::vector&lt;double&gt;&amp; argument, const std::vector&lt;double&gt;&amp; center, const std::vector&lt;double&gt;&amp; alpha, const std::vector&lt;double&gt;&amp; beta, const std::vector&lt;double&gt;&amp; normalization) const {</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   double value = 1.0;</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     157035 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     104020 :     double arg=(std::abs(argument[k]-center[k]))/alpha[k];</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">     104020 :     arg = pow(arg,beta[k]);</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">     104020 :     value*=normalization[k]*exp(-arg);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">      53015 :   return value;</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Grid.cpp.func-sort-c.html b/coverage/ves/TD_Grid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0917638918
--- /dev/null
+++ b/coverage/ves/TD_Grid.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Grid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Grid.cpp<span style="font-size: 80%;"> (<a href="TD_Grid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Grid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#115">_ZN4PLMD3ves12_GLOBAL__N_120TD_GridRegisterMe1176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#128">_ZN4PLMD3ves7TD_GridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#118">_ZN4PLMD3ves7TD_Grid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#115">_ZN4PLMD3ves12_GLOBAL__N_120TD_GridRegisterMe117C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#115">_ZN4PLMD3ves12_GLOBAL__N_120TD_GridRegisterMe117D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#197">_ZNK4PLMD3ves7TD_Grid8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">49369</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Grid.cpp.func.html b/coverage/ves/TD_Grid.cpp.func.html
new file mode 100644
index 0000000000..001faf4733
--- /dev/null
+++ b/coverage/ves/TD_Grid.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Grid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Grid.cpp<span style="font-size: 80%;"> (<a href="TD_Grid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Grid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#115">_ZN4PLMD3ves12_GLOBAL__N_120TD_GridRegisterMe1176createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#115">_ZN4PLMD3ves12_GLOBAL__N_120TD_GridRegisterMe117C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#115">_ZN4PLMD3ves12_GLOBAL__N_120TD_GridRegisterMe117D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#118">_ZN4PLMD3ves7TD_Grid16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#128">_ZN4PLMD3ves7TD_GridC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Grid.cpp.gcov.html#197">_ZNK4PLMD3ves7TD_Grid8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">49369</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Grid.cpp.gcov.html b/coverage/ves/TD_Grid.cpp.gcov.html
new file mode 100644
index 0000000000..9dd619db2b
--- /dev/null
+++ b/coverage/ves/TD_Grid.cpp.gcov.html
@@ -0,0 +1,294 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Grid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Grid.cpp<span style="font-size: 80%;"> (source / <a href="TD_Grid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntryHi">94.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;GridLinearInterpolation.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace ves {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : //+PLUMEDOC VES_TARGETDIST TD_GRID</a>
+<a name="39"><span class="lineNum">      39 </span>            : /*</a>
+<a name="40"><span class="lineNum">      40 </span>            : Target distribution from an external grid file (static).</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : Using this keyword you can use a target distribution that is read from an</a>
+<a name="43"><span class="lineNum">      43 </span>            : external grid file that is in the proper PLUMED file format. You do not to</a>
+<a name="44"><span class="lineNum">      44 </span>            : give any information about the external grid file as all relevant information</a>
+<a name="45"><span class="lineNum">      45 </span>            : should be automatically detected. It is assumed that the distribution read in</a>
+<a name="46"><span class="lineNum">      46 </span>            : from the grid is a proper probability distribution, i.e. always non-negative</a>
+<a name="47"><span class="lineNum">      47 </span>            : and can be normalized.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : By default the target distribution from the external grid is always normalized</a>
+<a name="50"><span class="lineNum">      50 </span>            : inside the code. You can disable this normalization by using DO_NOT_NORMALIZE</a>
+<a name="51"><span class="lineNum">      51 </span>            : keyword. However, be warned that this will generally lead to the wrong</a>
+<a name="52"><span class="lineNum">      52 </span>            : behavior if the distribution from the external grid is not properly</a>
+<a name="53"><span class="lineNum">      53 </span>            : normalized to 1.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : If the distribution from the external grid file has for some reason</a>
+<a name="56"><span class="lineNum">      56 </span>            : negative values can you use the SHIFT keyword to shift the distribution</a>
+<a name="57"><span class="lineNum">      57 </span>            : by a given value. Another option is to use</a>
+<a name="58"><span class="lineNum">      58 </span>            : the SHIFT_TO_ZERO keyword to shift the minimum of the distribution to zero.</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : Note that the number of grid bins used in the external grid file do not have</a>
+<a name="61"><span class="lineNum">      61 </span>            : to be the same as used in the bias or action where the target distribution is</a>
+<a name="62"><span class="lineNum">      62 </span>            : employed as the code will employ a linear (or bilinear for two dimensions)</a>
+<a name="63"><span class="lineNum">      63 </span>            : interpolation to calculate values. Currently only one or two dimensional grids</a>
+<a name="64"><span class="lineNum">      64 </span>            : are supported.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : It can happen that the intervals on which the target distribution is defined is</a>
+<a name="67"><span class="lineNum">      67 </span>            : larger than the intervals covered by the external grid file. In this case the</a>
+<a name="68"><span class="lineNum">      68 </span>            : default option is to consider the target distribution as continuous such that</a>
+<a name="69"><span class="lineNum">      69 </span>            : values outside the boundary of the external grid file are the same as at</a>
+<a name="70"><span class="lineNum">      70 </span>            : the boundary. This can be changed by using the ZERO_OUTSIDE keyword which</a>
+<a name="71"><span class="lineNum">      71 </span>            : will make values outside to be taken as zero.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \par Examples</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : Generally you only need to provide the the filename of the external grid</a>
+<a name="76"><span class="lineNum">      76 </span>            : file.</a>
+<a name="77"><span class="lineNum">      77 </span>            : \plumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : td: TD_GRID FILE=input-grid.data</a>
+<a name="79"><span class="lineNum">      79 </span>            : \endplumedfile</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : The input grid is then specified using the usual format employed by PLUMED an example of which</a>
+<a name="82"><span class="lineNum">      82 </span>            : is shown below:</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            : \auxfile{input-grid.data}</a>
+<a name="85"><span class="lineNum">      85 </span>            : #! FIELDS d1 external.bias der_d1</a>
+<a name="86"><span class="lineNum">      86 </span>            : #! SET min_d1 1.14</a>
+<a name="87"><span class="lineNum">      87 </span>            : #! SET max_d1 1.32</a>
+<a name="88"><span class="lineNum">      88 </span>            : #! SET nbins_d1 6</a>
+<a name="89"><span class="lineNum">      89 </span>            : #! SET periodic_d1 false</a>
+<a name="90"><span class="lineNum">      90 </span>            :    1.1400   0.0031   0.1101</a>
+<a name="91"><span class="lineNum">      91 </span>            :    1.1700   0.0086   0.2842</a>
+<a name="92"><span class="lineNum">      92 </span>            :    1.2000   0.0222   0.6648</a>
+<a name="93"><span class="lineNum">      93 </span>            :    1.2300   0.0521   1.4068</a>
+<a name="94"><span class="lineNum">      94 </span>            :    1.2600   0.1120   2.6873</a>
+<a name="95"><span class="lineNum">      95 </span>            :    1.2900   0.2199   4.6183</a>
+<a name="96"><span class="lineNum">      96 </span>            :    1.3200   0.3948   7.1055</a>
+<a name="97"><span class="lineNum">      97 </span>            : \endauxfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : */</a>
+<a name="100"><span class="lineNum">     100 </span>            : //+ENDPLUMEDOC</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : class TD_Grid : public TargetDistribution {</a>
+<a name="104"><span class="lineNum">     104 </span>            :   std::unique_ptr&lt;GridBase&gt; distGrid_;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   std::vector&lt;double&gt; minima_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   std::vector&lt;double&gt; maxima_;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;bool&gt; periodic_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   bool zero_outside_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   double shift_;</a>
+<a name="110"><span class="lineNum">     110 </span>            : public:</a>
+<a name="111"><span class="lineNum">     111 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="112"><span class="lineNum">     112 </span>            :   explicit TD_Grid(const ActionOptions&amp; ao);</a>
+<a name="113"><span class="lineNum">     113 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="114"><span class="lineNum">     114 </span>            : };</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">      12513 : PLUMED_REGISTER_ACTION(TD_Grid,&quot;TD_GRID&quot;)</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         11 : void TD_Grid::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         11 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;FILE&quot;,&quot;The name of the external grid file to be used as a target distribution.&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;SHIFT&quot;,&quot;Shift the grid read in by some constant value. Due to normalization the final shift in the target distribution will generally not be the same as the value given here&quot;);</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         22 :   keys.addFlag(&quot;ZERO_OUTSIDE&quot;,false,&quot;By default the target distribution is continuous such that values outside the boundary of the external grid file are the same as at the boundary. This can be changed by using this flag which will make values outside to be taken as zero.&quot;);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         22 :   keys.addFlag(&quot;DO_NOT_NORMALIZE&quot;,false,&quot;By default the target distribution from the external grid is always normalized inside the code. You can use this flag to disable this normalization. However, be warned that this will generally lead to the wrong behavior if the distribution from the external grid is not properly normalized to 1.&quot;);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         11 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         11 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         11 : }</span></a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          9 : TD_Grid::TD_Grid(const ActionOptions&amp; ao):</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          9 :   minima_(0),</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          9 :   maxima_(0),</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          9 :   zero_outside_(false),</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         18 :   shift_(0.0)</span></a>
+<a name="136"><span class="lineNum">     136 </span>            : {</a>
+<a name="137"><span class="lineNum">     137 </span>            :   std::string filename;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          9 :   parse(&quot;FILE&quot;,filename);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          9 :   parse(&quot;SHIFT&quot;,shift_);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">          9 :   if(shift_!=0.0) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">          1 :     if(isTargetDistGridShiftedToZero()) {plumed_merror(getName() + &quot;: using both SHIFT and SHIFT_TO_ZERO is not allowed.&quot;);}</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          9 :   parseFlag(&quot;ZERO_OUTSIDE&quot;,zero_outside_);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          9 :   bool do_not_normalize=false;</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          9 :   parseFlag(&quot;DO_NOT_NORMALIZE&quot;,do_not_normalize);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :   if(do_not_normalize &amp;&amp; shift_!=0.0) {plumed_merror(getName() + &quot;: using both SHIFT and DO_NOT_NORMALIZE is not allowed.&quot;);}</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          9 :   if(!do_not_normalize) {setForcedNormalization();}</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   std::string gridlabel;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   std::vector&lt;std::string&gt; arglabels;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   std::vector&lt;std::string&gt; argmin;</a>
+<a name="155"><span class="lineNum">     155 </span>            :   std::vector&lt;std::string&gt; argmax;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   std::vector&lt;bool&gt; argperiodic;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;unsigned int&gt; argnbins;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          9 :   bool has_deriv = false;</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          9 :   unsigned int nargs = VesTools::getGridFileInfo(filename,gridlabel,arglabels,argmin,argmax,argperiodic,argnbins,has_deriv);</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          9 :   if(nargs==0) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :     plumed_merror(getName() + &quot;: problem in parsing information from grid file&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          9 :   setDimension(arglabels.size());</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          9 :   std::vector&lt;std::unique_ptr&lt;Value&gt;&gt; arguments(arglabels.size());</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         22 :   for(unsigned int i=0; i &lt; arglabels.size(); i++) {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         26 :     arguments[i]= Tools::make_unique&lt;Value&gt;(nullptr,arglabels[i],false);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         13 :     if(argperiodic[i]) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineNoCov">          0 :       arguments[i]-&gt;setDomain(argmin[i],argmax[i]);</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :     }</a>
+<a name="171"><span class="lineNum">     171 </span>            :     else {</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         13 :       arguments[i]-&gt;setNotPeriodic();</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     }</a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          9 :   IFile gridfile; gridfile.open(filename);</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          9 :   if(has_deriv) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :     distGrid_=GridBase::create(gridlabel,Tools::unique2raw(arguments),gridfile,false,true,true);</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span>            :   else {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         18 :     distGrid_=GridBase::create(gridlabel,Tools::unique2raw(arguments),gridfile,false,false,false);</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          9 :   gridfile.close();</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          9 :   minima_.resize(getDimension());</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          9 :   maxima_.resize(getDimension());</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          9 :   periodic_.resize(getDimension());</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         22 :   for (unsigned int i=0; i &lt; getDimension(); i++) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         13 :     Tools::convert(distGrid_-&gt;getMin()[i],minima_[i]);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         13 :     Tools::convert(distGrid_-&gt;getMax()[i],maxima_[i]);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">         13 :     periodic_[i] = argperiodic[i];</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         13 :     if(periodic_[i]) {maxima_[i]-=distGrid_-&gt;getDx()[i];}</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         27 : }</span></a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">      49369 : double TD_Grid::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   double outside = 0.0;</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      49369 :   std::vector&lt;double&gt; arg = argument;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     145566 :   for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">      96533 :     if(zero_outside_ &amp;&amp; (argument[k] &lt; minima_[k] || argument[k] &gt; maxima_[k])) {</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :       return outside;</a>
+<a name="205"><span class="lineNum">     205 </span>            :     }</a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">      96197 :     else if(argument[k] &lt; minima_[k]) {</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        168 :       arg[k] = minima_[k];</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :     }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      96029 :     else if(argument[k] &gt; maxima_[k]) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">        168 :       arg[k] =maxima_[k];</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :     }</a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">      49033 :   return GridLinearInterpolation::getGridValueWithLinearInterpolation(distGrid_.get(),arg)+shift_;</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : }</a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            : }</a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_LinearCombination.cpp.func-sort-c.html b/coverage/ves/TD_LinearCombination.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a3d3e02c96
--- /dev/null
+++ b/coverage/ves/TD_LinearCombination.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_LinearCombination.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_LinearCombination.cpp<span style="font-size: 80%;"> (<a href="TD_LinearCombination.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryMed">75.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_LinearCombination.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#242">_ZN4PLMD3ves20TD_LinearCombination10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#250">_ZN4PLMD3ves20TD_LinearCombination12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#258">_ZN4PLMD3ves20TD_LinearCombination25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#200">_ZNK4PLMD3ves20TD_LinearCombination8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#266">_ZN4PLMD3ves20TD_LinearCombination11linkFesGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#234">_ZN4PLMD3ves20TD_LinearCombination11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#149">_ZN4PLMD3ves12_GLOBAL__N_133TD_LinearCombinationRegisterMe1516createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#206">_ZN4PLMD3ves20TD_LinearCombination20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#162">_ZN4PLMD3ves20TD_LinearCombinationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#152">_ZN4PLMD3ves20TD_LinearCombination16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#217">_ZN4PLMD3ves20TD_LinearCombination10updateGridEv</a></td>
+              <td class="coverFnHi">22</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#149">_ZN4PLMD3ves12_GLOBAL__N_133TD_LinearCombinationRegisterMe151C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#149">_ZN4PLMD3ves12_GLOBAL__N_133TD_LinearCombinationRegisterMe151D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_LinearCombination.cpp.func.html b/coverage/ves/TD_LinearCombination.cpp.func.html
new file mode 100644
index 0000000000..f8c85b39df
--- /dev/null
+++ b/coverage/ves/TD_LinearCombination.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_LinearCombination.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_LinearCombination.cpp<span style="font-size: 80%;"> (<a href="TD_LinearCombination.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryMed">75.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_LinearCombination.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_LinearCombination.cpp.gcov.html#149">_ZN4PLMD3ves12_GLOBAL__N_133TD_LinearCombinationRegisterMe1516createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">12</td>
+            </tr>
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+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
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+
+</body>
+</html>
diff --git a/coverage/ves/TD_LinearCombination.cpp.gcov.html b/coverage/ves/TD_LinearCombination.cpp.gcov.html
new file mode 100644
index 0000000000..e8a04d642a
--- /dev/null
+++ b/coverage/ves/TD_LinearCombination.cpp.gcov.html
@@ -0,0 +1,353 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_LinearCombination.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_LinearCombination.cpp<span style="font-size: 80%;"> (source / <a href="TD_LinearCombination.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">59</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryMed">75.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &lt;limits&gt;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // class Grid;</a>
+<a name="37"><span class="lineNum">      37 </span>            : class Action;</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace ves {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC VES_TARGETDIST TD_LINEAR_COMBINATION</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Target distribution given by linear combination of distributions (static or dynamic).</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : Employ a target distribution that is a linear combination of the other</a>
+<a name="46"><span class="lineNum">      46 </span>            : distributions, defined as</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f[</a>
+<a name="48"><span class="lineNum">      48 </span>            : p(\mathbf{s}) = \sum_{i} w_{i} \, p_{i}(\mathbf{s})</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f]</a>
+<a name="50"><span class="lineNum">      50 </span>            : where the weights \f$w_{i}\f$ are normalized to 1, \f$\sum_{i}w_{i}=1\f$.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The labels of the distributions \f$p_{i}(\mathbf{s})\f$ to be used in the</a>
+<a name="53"><span class="lineNum">      53 </span>            : linear combination are given in the DISTRIBUTIONS keyword.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : The weights \f$w_{i}\f$ can be given using</a>
+<a name="56"><span class="lineNum">      56 </span>            : the WEIGHTS keyword. The distributions are weighted equally if no weights are given.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : It is assumed that all the distributions \f$p_{i}(\mathbf{s})\f$ are normalized.</a>
+<a name="59"><span class="lineNum">      59 </span>            : If that is not the case for some reason should you</a>
+<a name="60"><span class="lineNum">      60 </span>            : normalize each distribution separately by using the NORMALIZE</a>
+<a name="61"><span class="lineNum">      61 </span>            : keyword when defining them in the input file (i.e. before the</a>
+<a name="62"><span class="lineNum">      62 </span>            : TD_LINEAR_COMBINATION action).</a>
+<a name="63"><span class="lineNum">      63 </span>            : Note that normalizing the overall</a>
+<a name="64"><span class="lineNum">      64 </span>            : linear combination will generally lead to different results than normalizing</a>
+<a name="65"><span class="lineNum">      65 </span>            : each distribution separately.</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : The linear combination will be a dynamic target distribution if one or more</a>
+<a name="68"><span class="lineNum">      68 </span>            : of the distributions used is a dynamic distribution, otherwise it will be a</a>
+<a name="69"><span class="lineNum">      69 </span>            : static distribution.</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : \par Examples</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : Here we employ a linear combination of a uniform and a Gaussian distribution.</a>
+<a name="74"><span class="lineNum">      74 </span>            : No weights are given so the two distributions will be weighted equally.</a>
+<a name="75"><span class="lineNum">      75 </span>            : \plumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : td_uni: TD_UNIFORM</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : td_gauss: TD_GAUSSIAN CENTER1=-2.0 SIGMA1=0.5</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : td_comb: TD_LINEAR_COMBINATION DISTRIBUTIONS=td_uni,td_gauss</a>
+<a name="81"><span class="lineNum">      81 </span>            : \endplumedfile</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : Here we employ a linear combination of a uniform and two Gaussian distribution.</a>
+<a name="84"><span class="lineNum">      84 </span>            : The weights are automatically normalized to 1 such that giving</a>
+<a name="85"><span class="lineNum">      85 </span>            : WEIGHTS=1.0,1.0,2.0 as we do here is equal to giving WEIGHTS=0.25,0.25,0.50.</a>
+<a name="86"><span class="lineNum">      86 </span>            : \plumedfile</a>
+<a name="87"><span class="lineNum">      87 </span>            : td_uni: TD_UNIFORM</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : td_gauss1: TD_GAUSSIAN CENTER1=-2.0,-2.0 SIGMA1=0.5,0.3</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : td_gauss2: TD_GAUSSIAN CENTER1=+2.0,+2.0 SIGMA1=0.3,0.5</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : TD_LINEAR_COMBINATION ...</a>
+<a name="94"><span class="lineNum">      94 </span>            :  DISTRIBUTIONS=td_uni,td_gauss1,td_gauss2</a>
+<a name="95"><span class="lineNum">      95 </span>            :  WEIGHTS=1.0,1.0,2.0</a>
+<a name="96"><span class="lineNum">      96 </span>            :  LABEL=td_comb</a>
+<a name="97"><span class="lineNum">      97 </span>            : ... TD_LINEAR_COMBINATION</a>
+<a name="98"><span class="lineNum">      98 </span>            : \endplumedfile</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : In the above example the two Gaussian kernels are given using two separate</a>
+<a name="101"><span class="lineNum">     101 </span>            : DISTRIBUTION keywords. As the \ref TD_GAUSSIAN target distribution allows multiple</a>
+<a name="102"><span class="lineNum">     102 </span>            : centers is it also possible to use just one DISTRIBUTION keyword for the two</a>
+<a name="103"><span class="lineNum">     103 </span>            : Gaussian kernels. This is shown in the following example which will give the</a>
+<a name="104"><span class="lineNum">     104 </span>            : exact same result as the one above as the weights have been appropriately</a>
+<a name="105"><span class="lineNum">     105 </span>            : adjusted</a>
+<a name="106"><span class="lineNum">     106 </span>            : \plumedfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : td_uni: TD_UNIFORM</a>
+<a name="108"><span class="lineNum">     108 </span>            : </a>
+<a name="109"><span class="lineNum">     109 </span>            : TD_GAUSSIAN ...</a>
+<a name="110"><span class="lineNum">     110 </span>            :  CENTER1=-2.0,-2.0  SIGMA1=0.5,0.3</a>
+<a name="111"><span class="lineNum">     111 </span>            :  CENTER2=+2.0,+2.0  SIGMA2=0.3,0.5</a>
+<a name="112"><span class="lineNum">     112 </span>            :  WEIGHTS=1.0,2.0</a>
+<a name="113"><span class="lineNum">     113 </span>            :  LABEL=td_gauss</a>
+<a name="114"><span class="lineNum">     114 </span>            : ... TD_GAUSSIAN</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : TD_LINEAR_COMBINATION ...</a>
+<a name="117"><span class="lineNum">     117 </span>            :  DISTRIBUTIONS=td_uni,td_gauss</a>
+<a name="118"><span class="lineNum">     118 </span>            :  WEIGHTS=0.25,0.75</a>
+<a name="119"><span class="lineNum">     119 </span>            :  LABEL=td_comb</a>
+<a name="120"><span class="lineNum">     120 </span>            : ... TD_LINEAR_COMBINATION</a>
+<a name="121"><span class="lineNum">     121 </span>            : \endplumedfile</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : */</a>
+<a name="124"><span class="lineNum">     124 </span>            : //+ENDPLUMEDOC</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : class VesBias;</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : class TD_LinearCombination: public TargetDistribution {</a>
+<a name="129"><span class="lineNum">     129 </span>            : private:</a>
+<a name="130"><span class="lineNum">     130 </span>            :   std::vector&lt;TargetDistribution*&gt; distribution_pntrs_;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::vector&lt;Grid*&gt; grid_pntrs_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::vector&lt;double&gt; weights_;</a>
+<a name="133"><span class="lineNum">     133 </span>            :   unsigned int ndist_;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   void setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) override;</a>
+<a name="135"><span class="lineNum">     135 </span>            : public:</a>
+<a name="136"><span class="lineNum">     136 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="137"><span class="lineNum">     137 </span>            :   explicit TD_LinearCombination(const ActionOptions&amp; ao);</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void updateGrid() override;</a>
+<a name="139"><span class="lineNum">     139 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   //</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void linkVesBias(VesBias*) override;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void linkAction(Action*) override;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   //</a>
+<a name="144"><span class="lineNum">     144 </span>            :   void linkBiasGrid(Grid*) override;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   void linkBiasWithoutCutoffGrid(Grid*) override;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void linkFesGrid(Grid*) override;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   //</a>
+<a name="148"><span class="lineNum">     148 </span>            : };</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">      12516 : PLUMED_REGISTER_ACTION(TD_LinearCombination,&quot;TD_LINEAR_COMBINATION&quot;)</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            : </a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         14 : void TD_LinearCombination::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">         14 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         28 :   keys.add(&quot;compulsory&quot;,&quot;DISTRIBUTIONS&quot;,&quot;The labels of the target distribution actions to be used in the linear combination.&quot;);</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         28 :   keys.add(&quot;optional&quot;,&quot;WEIGHTS&quot;,&quot;The weights of target distributions. Have to be as many as the number of target distribution labels given in DISTRIBUTIONS. If no weights are given the distributions are weighted equally. The weights are automatically normalized to 1.&quot;);</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         14 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   //keys.use(&quot;SHIFT_TO_ZERO&quot;);</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         14 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">         14 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         12 : TD_LinearCombination::TD_LinearCombination(const ActionOptions&amp; ao):</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         24 :   distribution_pntrs_(0),</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         12 :   grid_pntrs_(0),</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         12 :   weights_(0),</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         24 :   ndist_(0)</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : {</a>
+<a name="171"><span class="lineNum">     171 </span>            :   std::vector&lt;std::string&gt; targetdist_labels;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         12 :   parseVector(&quot;DISTRIBUTIONS&quot;,targetdist_labels);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         12 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         24 :   distribution_pntrs_ = VesTools::getPointersFromLabels&lt;TargetDistribution*&gt;(targetdist_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">         12 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword DISTRIBUTIONS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         40 :   for(unsigned int i=0; i&lt;distribution_pntrs_.size(); i++) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         28 :     if(distribution_pntrs_[i]-&gt;isDynamic()) {setDynamic();}</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         28 :     if(distribution_pntrs_[i]-&gt;fesGridNeeded()) {setFesGridNeeded();}</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         28 :     if(distribution_pntrs_[i]-&gt;biasGridNeeded()) {setBiasGridNeeded();}</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         12 :   ndist_ = distribution_pntrs_.size();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         12 :   grid_pntrs_.assign(ndist_,NULL);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         12 :   if(ndist_==0) {plumed_merror(getName()+ &quot;: no distributions are given.&quot;);}</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         12 :   if(ndist_==1) {plumed_merror(getName()+ &quot;: giving only one distribution does not make sense.&quot;);}</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   //</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         24 :   parseVector(&quot;WEIGHTS&quot;,weights_);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         12 :   if(weights_.size()==0) {weights_.assign(distribution_pntrs_.size(),1.0);}</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         12 :   if(distribution_pntrs_.size()!=weights_.size()) {</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+ &quot;: there has to be as many weights given in WEIGHTS as the number of target distribution labels given in DISTRIBUTIONS&quot;);</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   }</a>
+<a name="194"><span class="lineNum">     194 </span>            :   //</a>
+<a name="195"><span class="lineNum">     195 </span>            :   double sum_weights=0.0;</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         40 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {sum_weights+=weights_[i];}</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         40 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {weights_[i]/=sum_weights;}</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         12 :   checkRead();</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         12 : }</span></a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : </a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 : double TD_LinearCombination::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_LinearCombination&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   return 0.0;</a>
+<a name="205"><span class="lineNum">     205 </span>            : }</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">         12 : void TD_LinearCombination::setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp; arguments, const std::vector&lt;std::string&gt;&amp; min, const std::vector&lt;std::string&gt;&amp; max, const std::vector&lt;unsigned int&gt;&amp; nbins) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         40 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         28 :     distribution_pntrs_[i]-&gt;setupGrids(arguments,min,max,nbins);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         28 :     if(distribution_pntrs_[i]-&gt;getDimension()!=this-&gt;getDimension()) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineNoCov">          0 :       plumed_merror(getName() + &quot;: all target distribution must have the same dimension&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span>            :     }</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         28 :     grid_pntrs_[i]=distribution_pntrs_[i]-&gt;getTargetDistGridPntr();</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         12 : }</span></a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         22 : void TD_LinearCombination::updateGrid() {</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         70 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         48 :     distribution_pntrs_[i]-&gt;updateTargetDist();</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">     162033 :   for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :     double value = 0.0;</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     506837 :     for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">     344826 :       value += weights_[i]*grid_pntrs_[i]-&gt;getValue(l);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">     162011 :     if(value==0.0) value=std::numeric_limits&lt;double&gt;::denorm_min();</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">     162011 :     targetDistGrid().setValue(l,value);</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">     162011 :     logTargetDistGrid().setValue(l,-std::log(value));</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :   }</a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         22 :   logTargetDistGrid().setMinToZero();</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">         22 : }</span></a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          1 : void TD_LinearCombination::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          1 :   TargetDistribution::linkVesBias(vesbias_pntr_in);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          3 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          2 :     distribution_pntrs_[i]-&gt;linkVesBias(vesbias_pntr_in);</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   }</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          1 : }</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 : void TD_LinearCombination::linkAction(Action* action_pntr_in) {</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineNoCov">          0 :   TargetDistribution::linkAction(action_pntr_in);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkAction(action_pntr_in);</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : </a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 : void TD_LinearCombination::linkBiasGrid(Grid* bias_grid_pntr_in) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineNoCov">          0 :   TargetDistribution::linkBiasGrid(bias_grid_pntr_in);</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkBiasGrid(bias_grid_pntr_in);</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :   }</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : </a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineNoCov">          0 : void TD_LinearCombination::linkBiasWithoutCutoffGrid(Grid* bias_withoutcutoff_grid_pntr_in) {</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineNoCov">          0 :   TargetDistribution::linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_in);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_in);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="266"><span class="lineNum">     266 </span>            : </a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          1 : void TD_LinearCombination::linkFesGrid(Grid* fes_grid_pntr_in) {</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          1 :   TargetDistribution::linkFesGrid(fes_grid_pntr_in);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          3 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          2 :     distribution_pntrs_[i]-&gt;linkFesGrid(fes_grid_pntr_in);</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :   }</a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          1 : }</span></a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span>            : }</a>
+<a name="277"><span class="lineNum">     277 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Multicanonical.cpp.func-sort-c.html b/coverage/ves/TD_Multicanonical.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d6f3982e0f
--- /dev/null
+++ b/coverage/ves/TD_Multicanonical.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Multicanonical.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Multicanonical.cpp<span style="font-size: 80%;"> (<a href="TD_Multicanonical.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">198</td>
+            <td class="headerCovTableEntry">205</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Multicanonical.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#223">_ZNK4PLMD3ves17TD_Multicanonical8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#158">_ZN4PLMD3ves12_GLOBAL__N_130TD_MulticanonicalRegisterMe1606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#172">_ZN4PLMD3ves17TD_MulticanonicalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#153">_ZN4PLMD3ves17TD_MulticanonicalD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#153">_ZN4PLMD3ves17TD_MulticanonicalD2Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#161">_ZN4PLMD3ves17TD_Multicanonical16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#229">_ZN4PLMD3ves17TD_Multicanonical10updateGridEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#158">_ZN4PLMD3ves12_GLOBAL__N_130TD_MulticanonicalRegisterMe160C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#158">_ZN4PLMD3ves12_GLOBAL__N_130TD_MulticanonicalRegisterMe160D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Multicanonical.cpp.func.html b/coverage/ves/TD_Multicanonical.cpp.func.html
new file mode 100644
index 0000000000..79981a756f
--- /dev/null
+++ b/coverage/ves/TD_Multicanonical.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Multicanonical.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Multicanonical.cpp<span style="font-size: 80%;"> (<a href="TD_Multicanonical.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">198</td>
+            <td class="headerCovTableEntry">205</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Multicanonical.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#158">_ZN4PLMD3ves12_GLOBAL__N_130TD_MulticanonicalRegisterMe1606createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#158">_ZN4PLMD3ves12_GLOBAL__N_130TD_MulticanonicalRegisterMe160C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#158">_ZN4PLMD3ves12_GLOBAL__N_130TD_MulticanonicalRegisterMe160D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#229">_ZN4PLMD3ves17TD_Multicanonical10updateGridEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#161">_ZN4PLMD3ves17TD_Multicanonical16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#172">_ZN4PLMD3ves17TD_MulticanonicalC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#153">_ZN4PLMD3ves17TD_MulticanonicalD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#153">_ZN4PLMD3ves17TD_MulticanonicalD2Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Multicanonical.cpp.gcov.html#223">_ZNK4PLMD3ves17TD_Multicanonical8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/ves/TD_Multicanonical.cpp.gcov.html b/coverage/ves/TD_Multicanonical.cpp.gcov.html
new file mode 100644
index 0000000000..880c1451dc
--- /dev/null
+++ b/coverage/ves/TD_Multicanonical.cpp.gcov.html
@@ -0,0 +1,551 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Multicanonical.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Multicanonical.cpp<span style="font-size: 80%;"> (source / <a href="TD_Multicanonical.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">198</td>
+            <td class="headerCovTableEntry">205</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cfloat&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC VES_TARGETDIST TD_MULTICANONICAL</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Multicanonical target distribution (dynamic).</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Use the target distribution to sample the multicanonical ensemble \cite Berg-PRL-1992 \cite Piaggi-PRL-2019.</a>
+<a name="40"><span class="lineNum">      40 </span>            : In this way, in a single molecular dynamics simulation one can obtain information about the system in a range of temperatures.</a>
+<a name="41"><span class="lineNum">      41 </span>            : This range is determined through the keywords MIN_TEMP and MAX_TEMP.</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : The collective variables (CVs) used to construct the bias potential must be:</a>
+<a name="44"><span class="lineNum">      44 </span>            :  1. the energy or,</a>
+<a name="45"><span class="lineNum">      45 </span>            :  2. the energy and an order parameter.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Other choices of CVs or a different order of the above mentioned CVs are nonsensical.</a>
+<a name="48"><span class="lineNum">      48 </span>            : The second CV, the order parameter, must be used when one aims at studying a first order phase transition in the chosen temperature interval \cite Piaggi-JCP-2019.</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : The algorithm will explore the free energy at each temperature up to a predefined free</a>
+<a name="51"><span class="lineNum">      51 </span>            :  energy threshold \f$\epsilon\f$ specified through the keyword THRESHOLD (in kT units).</a>
+<a name="52"><span class="lineNum">      52 </span>            : If only the energy is biased, i.e. no phase transition is considered, then THRESHOLD can be set to around 5.</a>
+<a name="53"><span class="lineNum">      53 </span>            : If also an order parameter is used then the THRESHOLD should be greater than the barrier for the transformation in kT.</a>
+<a name="54"><span class="lineNum">      54 </span>            : For small systems undergoing a freezing transition THRESHOLD is typically between 20 and 50.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : When only the potential energy is used as CV the method is equivalent to the Wang-Landau algorithm \cite wanglandau.</a>
+<a name="57"><span class="lineNum">      57 </span>            : The advantage with respect to Wang-Landau is that instead of sampling the potential energy indiscriminately, an interval is chosen on the fly based on the minimum and maximum targeted temperatures.</a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span>            : The algorithm works as follows.</a>
+<a name="60"><span class="lineNum">      60 </span>            : The target distribution for the potential energy is chosen to be:</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : \f[</a>
+<a name="63"><span class="lineNum">      63 </span>            : p(E)= \left\{\begin{array}{ll}</a>
+<a name="64"><span class="lineNum">      64 </span>            :          \frac{1}{E_2-E_1} &amp; \mathrm{if} \quad E_1&lt;E&lt;E_2 \\</a>
+<a name="65"><span class="lineNum">      65 </span>            :          0 &amp; \mathrm{otherwise}</a>
+<a name="66"><span class="lineNum">      66 </span>            :       \end{array}\right.</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f]</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : where the energy limits \f$E_1\f$ and \f$E_2\f$ are yet to be determined.</a>
+<a name="70"><span class="lineNum">      70 </span>            : Clearly the interval \f$E_1–E_2\f$ chosen is related to the interval of temperatures \f$T_1-T_2\f$.</a>
+<a name="71"><span class="lineNum">      71 </span>            : To link these two intervals we make use of the following relation:</a>
+<a name="72"><span class="lineNum">      72 </span>            : \f[</a>
+<a name="73"><span class="lineNum">      73 </span>            : \beta' F_{\beta'}(E) = \beta F_{\beta}(E) + (\beta' - \beta) E + C,</a>
+<a name="74"><span class="lineNum">      74 </span>            : \f]</a>
+<a name="75"><span class="lineNum">      75 </span>            : where \f$F_{\beta}(E)\f$ is determined during the optimization and we shall choose \f$C\f$ such that \f$F_{\beta'}(E_{m})=0\f$ with \f$E_{m}\f$ the position of the free energy minimum.</a>
+<a name="76"><span class="lineNum">      76 </span>            : Using this relation we employ an iterative procedure to find the energy interval.</a>
+<a name="77"><span class="lineNum">      77 </span>            : At iteration \f$k\f$ we have the estimates \f$E_1^k\f$ and \f$E_2^k\f$ for \f$E_1\f$ and \f$E_2\f$, and the target distribution is:</a>
+<a name="78"><span class="lineNum">      78 </span>            : \f[</a>
+<a name="79"><span class="lineNum">      79 </span>            : p^k(E)=\frac{1}{E_2^k-E_1^k} \quad \mathrm{for} \quad E_1^k&lt;E&lt;E_2^k.</a>
+<a name="80"><span class="lineNum">      80 </span>            : \f]</a>
+<a name="81"><span class="lineNum">      81 </span>            : \f$E_1^k\f$ and \f$E_2^k\f$ are obtained from the leftmost solution of \f$\beta_2 F_{\beta_2}^{k-1}(E_1^k)=\epsilon\f$ and the rightmost solution of \f$\beta_1 F_{\beta_1}^{k-1}(E_2^k)=\epsilon\f$.</a>
+<a name="82"><span class="lineNum">      82 </span>            : The procedure is repeated until convergence.</a>
+<a name="83"><span class="lineNum">      83 </span>            : This iterative approach is similar to that in \ref TD_WELLTEMPERED.</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span>            : The version of this algorithm in which the energy and an order parameter are biased is similar to the one described in \ref TD_MULTITHERMAL_MULTIBARIC.</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : The output of these simulations can be reweighted in order to obtain information at all temperatures in the targeted temperature interval.</a>
+<a name="88"><span class="lineNum">      88 </span>            : The reweighting can be performed using the action \ref REWEIGHT_TEMP_PRESS.</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : \par Examples</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : The following input can be used to run a simulation in the multicanonical ensemble.</a>
+<a name="93"><span class="lineNum">      93 </span>            : The temperature interval to be explored is 400-600 K.</a>
+<a name="94"><span class="lineNum">      94 </span>            : The energy is used as collective variable.</a>
+<a name="95"><span class="lineNum">      95 </span>            : Legendre polynomials are used to construct the bias potential.</a>
+<a name="96"><span class="lineNum">      96 </span>            : The averaged stochastic gradient descent algorithm is chosen to optimize the VES functional.</a>
+<a name="97"><span class="lineNum">      97 </span>            : The target distribution is updated every 100 optimization steps (200 ps here) using the last estimation of the free energy.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : \plumedfile</a>
+<a name="100"><span class="lineNum">     100 </span>            : # Use energy and volume as CVs</a>
+<a name="101"><span class="lineNum">     101 </span>            : energy: ENERGY</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : # Basis functions</a>
+<a name="104"><span class="lineNum">     104 </span>            : bf1: BF_LEGENDRE ORDER=20 MINIMUM=-25000 MAXIMUM=-23500</a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span>            : # Target distributions</a>
+<a name="107"><span class="lineNum">     107 </span>            : TD_MULTICANONICAL ...</a>
+<a name="108"><span class="lineNum">     108 </span>            :  LABEL=td_multi</a>
+<a name="109"><span class="lineNum">     109 </span>            :  MIN_TEMP=400</a>
+<a name="110"><span class="lineNum">     110 </span>            :  MAX_TEMP=600</a>
+<a name="111"><span class="lineNum">     111 </span>            : ... TD_MULTICANONICAL</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : # Expansion</a>
+<a name="114"><span class="lineNum">     114 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="115"><span class="lineNum">     115 </span>            :  ARG=energy</a>
+<a name="116"><span class="lineNum">     116 </span>            :  BASIS_FUNCTIONS=bf1</a>
+<a name="117"><span class="lineNum">     117 </span>            :  TEMP=500.0</a>
+<a name="118"><span class="lineNum">     118 </span>            :  GRID_BINS=1000</a>
+<a name="119"><span class="lineNum">     119 </span>            :  TARGET_DISTRIBUTION=td_multi</a>
+<a name="120"><span class="lineNum">     120 </span>            :  LABEL=b1</a>
+<a name="121"><span class="lineNum">     121 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : # Optimization algorithm</a>
+<a name="124"><span class="lineNum">     124 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="125"><span class="lineNum">     125 </span>            :   BIAS=b1</a>
+<a name="126"><span class="lineNum">     126 </span>            :   STRIDE=500</a>
+<a name="127"><span class="lineNum">     127 </span>            :   LABEL=o1</a>
+<a name="128"><span class="lineNum">     128 </span>            :   STEPSIZE=1.0</a>
+<a name="129"><span class="lineNum">     129 </span>            :   FES_OUTPUT=500</a>
+<a name="130"><span class="lineNum">     130 </span>            :   BIAS_OUTPUT=500</a>
+<a name="131"><span class="lineNum">     131 </span>            :   TARGETDIST_OUTPUT=500</a>
+<a name="132"><span class="lineNum">     132 </span>            :   COEFFS_OUTPUT=10</a>
+<a name="133"><span class="lineNum">     133 </span>            :   TARGETDIST_STRIDE=100</a>
+<a name="134"><span class="lineNum">     134 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : \endplumedfile</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : The multicanonical target distribution can also be used to explore a temperature interval in which a first order phase transitions is observed.</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : */</a>
+<a name="141"><span class="lineNum">     141 </span>            : //+ENDPLUMEDOC</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : class TD_Multicanonical: public TargetDistribution {</a>
+<a name="144"><span class="lineNum">     144 </span>            : private:</a>
+<a name="145"><span class="lineNum">     145 </span>            :   double threshold_, min_temp_, max_temp_;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   unsigned steps_temp_;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   double epsilon_;</a>
+<a name="149"><span class="lineNum">     149 </span>            :   bool smoothening_;</a>
+<a name="150"><span class="lineNum">     150 </span>            : public:</a>
+<a name="151"><span class="lineNum">     151 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   explicit TD_Multicanonical(const ActionOptions&amp; ao);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   void updateGrid() override;</a>
+<a name="154"><span class="lineNum">     154 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          4 :   ~TD_Multicanonical() {}</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   double GaussianSwitchingFunc(const double, const double, const double) const;</a>
+<a name="157"><span class="lineNum">     157 </span>            : };</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(TD_Multicanonical,&quot;TD_MULTICANONICAL&quot;)</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">          4 : void TD_Multicanonical::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">          4 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;THRESHOLD&quot;,&quot;5&quot;,&quot;Maximum exploration free energy in kT.&quot;);</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;EPSILON&quot;,&quot;10&quot;,&quot;The zeros of the target distribution are changed to e^-EPSILON.&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MIN_TEMP&quot;,&quot;Minimum temperature.&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MAX_TEMP&quot;,&quot;Maximum temperature.&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;STEPS_TEMP&quot;,&quot;Number of temperature steps. Only for the 2D version, i.e. energy and order parameter.&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;SIGMA&quot;,&quot;The standard deviation parameters of the Gaussian kernels used for smoothing the target distribution. One value must be specified for each argument, i.e. one value per CV. A value of 0.0 means that no smoothing is performed, this is the default behavior.&quot;);</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 : }</span></a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">          2 : TD_Multicanonical::TD_Multicanonical(const ActionOptions&amp; ao):</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          2 :   threshold_(5.0),</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">          2 :   min_temp_(0.0),</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          2 :   max_temp_(1000.0),</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          4 :   sigma_(0.0),</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          2 :   steps_temp_(20),</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          2 :   epsilon_(10.0),</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          2 :   smoothening_(true)</span></a>
+<a name="183"><span class="lineNum">     183 </span>            : {</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          2 :   log.printf(&quot;  Multicanonical target distribution&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">          2 :   log.printf(&quot;  Please read and cite &quot;);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          4 :   log &lt;&lt; plumed.cite(&quot;Piaggi and Parrinello, Phys. Rev. Lett. 122 (5), 050601 (2019)&quot;);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          2 :   log.printf(&quot; and &quot;);</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          4 :   log &lt;&lt; plumed.cite(&quot;Piaggi and Parrinello, J. Chem. Phys. 150 (24), 244119 (2019)&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          2 :   parse(&quot;THRESHOLD&quot;,threshold_);</span></a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">          2 :   if(threshold_&lt;=0.0) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: the value of the threshold should be positive.&quot;);</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :   }</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">          2 :   log.printf(&quot;  exploring free energy up to %f kT for each temperature \n&quot;,threshold_);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">          2 :   parse(&quot;MIN_TEMP&quot;,min_temp_);</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">          2 :   parse(&quot;MAX_TEMP&quot;,max_temp_);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          2 :   log.printf(&quot;  temperatures between %f and %f will be explored \n&quot;,min_temp_,max_temp_);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">          4 :   parseVector(&quot;SIGMA&quot;,sigma_);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">          2 :   if(sigma_.size()==0) smoothening_=false;</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">          2 :   if(smoothening_ &amp;&amp; (sigma_.size()&lt;1 || sigma_.size()&gt;2) ) plumed_merror(getName()+&quot;: SIGMA takes 1 or 2 values as input.&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">          2 :   if (smoothening_) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">          2 :     log.printf(&quot;  the target distribution will be smoothed using sigma values&quot;);</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">          5 :     for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,sigma_[i]);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">          2 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   }</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          2 :   parse(&quot;STEPS_TEMP&quot;,steps_temp_); // Only used in the 2D version</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          2 :   steps_temp_ += 1;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 :   log.printf(&quot;  %d steps in temperatures will be employed (if TD is two-dimensional) \n&quot;,steps_temp_);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">          2 :   parse(&quot;EPSILON&quot;,epsilon_);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          2 :   if(epsilon_&lt;=1.0) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: the value of epsilon should be greater than 1.&quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   }</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          2 :   log.printf(&quot;  the non relevant regions of the target distribution are set to e^-%f \n&quot;,epsilon_);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span>            :   setDynamic();</a>
+<a name="220"><span class="lineNum">     220 </span>            :   setFesGridNeeded();</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          2 : }</span></a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : </a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineNoCov">          0 : double TD_Multicanonical::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_Multicanonical&quot;);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   return 0.0;</a>
+<a name="228"><span class="lineNum">     228 </span>            : }</a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         14 : void TD_Multicanonical::updateGrid() {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         14 :   if (getStep() == 0) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          2 :     if(targetDistGrid().getDimension()&gt;2 || targetDistGrid().getDimension()&lt;1) plumed_merror(getName()+&quot; works only with 1 or 2 arguments, i.e. energy, or energy and CV&quot;);</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">          2 :     if(smoothening_ &amp;&amp; sigma_.size()!=targetDistGrid().getDimension()) plumed_merror(getName()+&quot;: mismatch between SIGMA dimension and number of arguments&quot;);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :     // Use uniform TD</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          4 :     std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="237"><span class="lineNum">     237 </span>            :     double norm = 0.0;</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       2704 :     for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :       double value = 1.0;</a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       2702 :       norm += integration_weights[l]*value;</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       2702 :       targetDistGrid().setValue(l,value);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :     }</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          2 :     targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   } else {</a>
+<a name="245"><span class="lineNum">     245 </span>            :     // Two variants: 1D and 2D</a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         12 :     if(targetDistGrid().getDimension()==1) {</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :       // 1D variant: Multicanonical without order parameter</a>
+<a name="248"><span class="lineNum">     248 </span>            :       // In this variant we find the minimum and maximum relevant potential energies.</a>
+<a name="249"><span class="lineNum">     249 </span>            :       // Using this information we construct a uniform target distribution in between these two.</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         10 :       double beta = getBeta();</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         10 :       double beta_prime_min = 1./(plumed.getAtoms().getKBoltzmann()*min_temp_);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         10 :       double beta_prime_max = 1./(plumed.getAtoms().getKBoltzmann()*max_temp_);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">         10 :       plumed_massert(getFesGridPntr()!=NULL,&quot;the FES grid has to be linked to use TD_Multicanonical!&quot;);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :       // Find minimum of F(U) at temperature min</a>
+<a name="255"><span class="lineNum">     255 </span>            :       double minval=DBL_MAX;</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         10 :       Grid::index_t minindex = (targetDistGrid().getSize())/2;</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         10 :       double minpos = targetDistGrid().getPoint(minindex)[0];</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">       1020 :       for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">       1010 :         double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">       1010 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">       1010 :         value = beta*value + (beta_prime_min-beta)*argument;</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">       1010 :         if(value&lt;minval) {</span></a>
+<a name="263"><span class="lineNum">     263 </span>            :           minval=value;</a>
+<a name="264"><span class="lineNum">     264 </span>            :           minpos=argument;</a>
+<a name="265"><span class="lineNum">     265 </span>            :           minindex=l;</a>
+<a name="266"><span class="lineNum">     266 </span>            :         }</a>
+<a name="267"><span class="lineNum">     267 </span>            :       }</a>
+<a name="268"><span class="lineNum">     268 </span>            :       // Find minimum energy at low temperature</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">         10 :       double minimum_low = minpos;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">         11 :       for(Grid::index_t l=minindex; l&gt;1; l-=1) {</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         11 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">         11 :         double argument_next = targetDistGrid().getPoint(l-1)[0];</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">         11 :         double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         11 :         double value_next = getFesGridPntr()-&gt;getValue(l-1);</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         11 :         value = beta*value + (beta_prime_min-beta)*argument - minval;</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         11 :         value_next = beta*value_next + (beta_prime_min-beta)*argument_next - minval;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">         11 :         if (value&lt;threshold_ &amp;&amp; value_next&gt;threshold_) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">         10 :           minimum_low = argument_next;</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         10 :           break;</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :         }</a>
+<a name="281"><span class="lineNum">     281 </span>            :       }</a>
+<a name="282"><span class="lineNum">     282 </span>            :       // Find maximum energy at low temperature</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">         10 :       double maximum_low = minpos;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         12 :       for(Grid::index_t l=minindex; l&lt;(targetDistGrid().getSize()-1); l++) {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         12 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         12 :         double argument_next = targetDistGrid().getPoint(l+1)[0];</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">         12 :         double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">         12 :         double value_next = getFesGridPntr()-&gt;getValue(l+1);</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         12 :         value = beta*value + (beta_prime_min-beta)*argument - minval;</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         12 :         value_next = beta*value_next + (beta_prime_min-beta)*argument_next - minval;</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         12 :         if (value&lt;threshold_ &amp;&amp; value_next&gt;threshold_) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         10 :           maximum_low = argument_next;</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         10 :           break;</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :         }</a>
+<a name="295"><span class="lineNum">     295 </span>            :       }</a>
+<a name="296"><span class="lineNum">     296 </span>            :       // Find minimum of F(U) at temperature max</a>
+<a name="297"><span class="lineNum">     297 </span>            :       minval=DBL_MAX;</a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       1020 :       for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">       1010 :         double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       1010 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       1010 :         value = beta*value + (beta_prime_max-beta)*argument;</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">       1010 :         if(value&lt;minval) {</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :           minval=value;</a>
+<a name="304"><span class="lineNum">     304 </span>            :           minpos=argument;</a>
+<a name="305"><span class="lineNum">     305 </span>            :           minindex=l;</a>
+<a name="306"><span class="lineNum">     306 </span>            :         }</a>
+<a name="307"><span class="lineNum">     307 </span>            :       }</a>
+<a name="308"><span class="lineNum">     308 </span>            :       // Find minimum energy at high temperature</a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         10 :       double minimum_high = minpos;</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         13 :       for(Grid::index_t l=minindex; l&gt;1; l-=1) {</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">         13 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">         13 :         double argument_next = targetDistGrid().getPoint(l-1)[0];</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">         13 :         double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">         13 :         double value_next = getFesGridPntr()-&gt;getValue(l-1);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">         13 :         value = beta*value + (beta_prime_max-beta)*argument - minval;</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         13 :         value_next = beta*value_next + (beta_prime_max-beta)*argument_next - minval;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">         13 :         if (value&lt;threshold_ &amp;&amp; value_next&gt;threshold_) {</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">         10 :           minimum_high = argument_next;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">         10 :           break;</span></a>
+<a name="320"><span class="lineNum">     320 </span>            :         }</a>
+<a name="321"><span class="lineNum">     321 </span>            :       }</a>
+<a name="322"><span class="lineNum">     322 </span>            :       // Find maximum energy at high temperature</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         10 :       double maximum_high = minpos;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">         11 :       for(Grid::index_t l=minindex; l&lt;(targetDistGrid().getSize()-1); l++) {</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         11 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         11 :         double argument_next = targetDistGrid().getPoint(l+1)[0];</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         11 :         double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         11 :         double value_next = getFesGridPntr()-&gt;getValue(l+1);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         11 :         value = beta*value + (beta_prime_max-beta)*argument - minval;</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">         11 :         value_next = beta*value_next + (beta_prime_max-beta)*argument_next - minval;</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         11 :         if (value&lt;threshold_ &amp;&amp; value_next&gt;threshold_) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         10 :           maximum_high = argument_next;</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">         10 :           break;</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :         }</a>
+<a name="335"><span class="lineNum">     335 </span>            :       }</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         10 :       double minimum = std::min(minimum_low,minimum_high);</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         10 :       double maximum = std::max(maximum_low,maximum_high);</span></a>
+<a name="338"><span class="lineNum">     338 </span>            :       // Construct uniform TD in the interval between minimum and maximum</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         20 :       std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :       double norm = 0.0;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">       1020 :       for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">       1010 :         double argument = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :         double value = 1.0;</a>
+<a name="344"><span class="lineNum">     344 </span>            :         double tmp;</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">       1010 :         if(argument &lt; minimum) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">        217 :           if (smoothening_) tmp = GaussianSwitchingFunc(argument,minimum,sigma_[0]);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineNoCov">          0 :           else tmp = exp(-1.0*epsilon_);</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :         }</a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        793 :         else if(argument &gt; maximum) {</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        199 :           if (smoothening_) tmp = GaussianSwitchingFunc(argument,maximum,sigma_[0]);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineNoCov">          0 :           else tmp = exp(-1.0*epsilon_);</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :         }</a>
+<a name="353"><span class="lineNum">     353 </span>            :         else {</a>
+<a name="354"><span class="lineNum">     354 </span>            :           tmp = 1.0;</a>
+<a name="355"><span class="lineNum">     355 </span>            :         }</a>
+<a name="356"><span class="lineNum">     356 </span>            :         value *= tmp;</a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">       1010 :         norm += integration_weights[l]*value;</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">       1010 :         targetDistGrid().setValue(l,value);</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :       }</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">         10 :       targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          2 :     } else if(targetDistGrid().getDimension()==2) {</span></a>
+<a name="362"><span class="lineNum">     362 </span>            :       // 2D variant: Multicanonical with order parameter</a>
+<a name="363"><span class="lineNum">     363 </span>            :       // In this variant we find for each temperature the relevant region of potential energy and order parameter.</a>
+<a name="364"><span class="lineNum">     364 </span>            :       // The target distribution will be the union of the relevant regions at all temperatures in the temperature interval.</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          2 :       double beta = getBeta();</span></a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">          2 :       double beta_prime_min = 1./(plumed.getAtoms().getKBoltzmann()*min_temp_);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          2 :       double beta_prime_max = 1./(plumed.getAtoms().getKBoltzmann()*max_temp_);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          2 :       plumed_massert(getFesGridPntr()!=NULL,&quot;the FES grid has to be linked to use TD_Multicanonical!&quot;);</span></a>
+<a name="369"><span class="lineNum">     369 </span>            :       // Set all to zero</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">       5204 :       for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">       5202 :         double value = exp(-1.0*epsilon_);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">       5202 :         targetDistGrid().setValue(l,value);</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :       }</a>
+<a name="374"><span class="lineNum">     374 </span>            :       // Loop over temperatures</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         44 :       for(unsigned i=0; i&lt;steps_temp_; i++) {</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         42 :         double beta_prime=beta_prime_min + (beta_prime_max-beta_prime_min)*i/(steps_temp_-1);</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :         // Find minimum for this temperature</a>
+<a name="378"><span class="lineNum">     378 </span>            :         double minval=DBL_MAX;</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">     109284 :         for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">     109242 :           double energy = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">     109242 :           double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">     109242 :           value = beta*value + (beta_prime-beta)*energy;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">     109242 :           if(value&lt;minval) {</span></a>
+<a name="384"><span class="lineNum">     384 </span>            :             minval=value;</a>
+<a name="385"><span class="lineNum">     385 </span>            :           }</a>
+<a name="386"><span class="lineNum">     386 </span>            :         }</a>
+<a name="387"><span class="lineNum">     387 </span>            :         // Now check which energies and volumes are below X kt</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">     109284 :         for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">     109242 :           double energy = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">     109242 :           double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">     109242 :           value = beta*value + (beta_prime-beta)*energy - minval;</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">     109242 :           if (value&lt;threshold_) {</span></a>
+<a name="393"><span class="lineNum">     393 </span>            :             double value = 1.0;</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">       7076 :             targetDistGrid().setValue(l,value);</span></a>
+<a name="395"><span class="lineNum">     395 </span>            :           }</a>
+<a name="396"><span class="lineNum">     396 </span>            :         }</a>
+<a name="397"><span class="lineNum">     397 </span>            :       }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          2 :       if (smoothening_) {</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          2 :         std::vector&lt;unsigned&gt; nbin=targetDistGrid().getNbin();</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          2 :         std::vector&lt;double&gt; dx=targetDistGrid().getDx();</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :         // Smoothening</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">        104 :         for(unsigned i=0; i&lt;nbin[0]; i++) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       5304 :           for(unsigned j=0; j&lt;nbin[1]; j++) {</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">       5202 :             std::vector&lt;unsigned&gt; indices(2);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">       5202 :             indices[0]=i;</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">       5202 :             indices[1]=j;</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">       5202 :             Grid::index_t index = targetDistGrid().getIndex(indices);</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">       5202 :             double energy = targetDistGrid().getPoint(index)[0];</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">       5202 :             double volume = targetDistGrid().getPoint(index)[1];</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">       5202 :             double value = targetDistGrid().getValue(index);</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">       5202 :             if (value&gt;(1-1.e-5)) { // Apply only if this grid point was 1.</span></a>
+<a name="412"><span class="lineNum">     412 </span>            :               // Apply gaussians around</a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">        773 :               std::vector&lt;int&gt; minBin(2), maxBin(2), deltaBin(2); // These cannot be unsigned</span></a>
+<a name="414"><span class="lineNum">     414 </span>            :               // Only consider contributions less than n*sigma bins apart from the actual distance</a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">        773 :               deltaBin[0]=std::floor(6*sigma_[0]/dx[0]);;</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">        773 :               deltaBin[1]=std::floor(6*sigma_[1]/dx[1]);;</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :               // For energy</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">        773 :               minBin[0]=i - deltaBin[0];</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">        773 :               if (minBin[0] &lt; 0) minBin[0]=0;</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">        773 :               if (minBin[0] &gt; (nbin[0]-1)) minBin[0]=nbin[0]-1;</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">        773 :               maxBin[0]=i +  deltaBin[0];</span></a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        773 :               if (maxBin[0] &gt; (nbin[0]-1)) maxBin[0]=nbin[0]-1;</span></a>
+<a name="423"><span class="lineNum">     423 </span>            :               // For volume</a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">        773 :               minBin[1]=j - deltaBin[1];</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">        773 :               if (minBin[1] &lt; 0) minBin[1]=0;</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">        773 :               if (minBin[1] &gt; (nbin[1]-1)) minBin[1]=nbin[1]-1;</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">        773 :               maxBin[1]=j +  deltaBin[1];</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">        773 :               if (maxBin[1] &gt; (nbin[1]-1)) maxBin[1]=nbin[1]-1;</span></a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">      31273 :               for(unsigned l=minBin[0]; l&lt;maxBin[0]+1; l++) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">     549973 :                 for(unsigned m=minBin[1]; m&lt;maxBin[1]+1; m++) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">     519473 :                   std::vector&lt;unsigned&gt; indices_prime(2);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">     519473 :                   indices_prime[0]=l;</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">     519473 :                   indices_prime[1]=m;</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">     519473 :                   Grid::index_t index_prime = targetDistGrid().getIndex(indices_prime);</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">     519473 :                   double energy_prime = targetDistGrid().getPoint(index_prime)[0];</span></a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">     519473 :                   double volume_prime = targetDistGrid().getPoint(index_prime)[1];</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">     519473 :                   double value_prime = targetDistGrid().getValue(index_prime);</span></a>
+<a name="438"><span class="lineNum">     438 </span>            :                   // Apply gaussian</a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">    1558419 :                   double gaussian_value = GaussianSwitchingFunc(energy_prime,energy,sigma_[0])*GaussianSwitchingFunc(volume_prime,volume,sigma_[1]);</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">     519473 :                   if (value_prime&lt;gaussian_value) {</span></a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">      19817 :                     targetDistGrid().setValue(index_prime,gaussian_value);</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :                   }</a>
+<a name="443"><span class="lineNum">     443 </span>            :                 }</a>
+<a name="444"><span class="lineNum">     444 </span>            :               }</a>
+<a name="445"><span class="lineNum">     445 </span>            :             }</a>
+<a name="446"><span class="lineNum">     446 </span>            :           }</a>
+<a name="447"><span class="lineNum">     447 </span>            :         }</a>
+<a name="448"><span class="lineNum">     448 </span>            :       }</a>
+<a name="449"><span class="lineNum">     449 </span>            :       // Normalize</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          4 :       std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="451"><span class="lineNum">     451 </span>            :       double norm = 0.0;</a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">       5204 :       for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">       5202 :         double value = targetDistGrid().getValue(l);</span></a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">       5202 :         norm += integration_weights[l]*value;</span></a>
+<a name="455"><span class="lineNum">     455 </span>            :       }</a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          2 :       targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineNoCov">          0 :     } else plumed_merror(getName()+&quot;: Number of arguments for this target distribution must be 1 or 2&quot;);</span></a>
+<a name="458"><span class="lineNum">     458 </span>            :   }</a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">         14 :   updateLogTargetDistGrid();</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">         14 : }</span></a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            : inline</a>
+<a name="463"><span class="lineNum">     463 </span>            : double TD_Multicanonical::GaussianSwitchingFunc(const double argument, const double center, const double sigma) const {</a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">    1039362 :   if(sigma&gt;0.0) {</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">    1039362 :     double arg=(argument-center)/sigma;</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">    1039362 :     return exp(-0.5*arg*arg);</span></a>
+<a name="467"><span class="lineNum">     467 </span>            :   }</a>
+<a name="468"><span class="lineNum">     468 </span>            :   else {</a>
+<a name="469"><span class="lineNum">     469 </span>            :     return 0.0;</a>
+<a name="470"><span class="lineNum">     470 </span>            :   }</a>
+<a name="471"><span class="lineNum">     471 </span>            : }</a>
+<a name="472"><span class="lineNum">     472 </span>            : </a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span>            : }</a>
+<a name="475"><span class="lineNum">     475 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_MultithermalMultibaric.cpp.func-sort-c.html b/coverage/ves/TD_MultithermalMultibaric.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4a769ffab1
--- /dev/null
+++ b/coverage/ves/TD_MultithermalMultibaric.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_MultithermalMultibaric.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_MultithermalMultibaric.cpp<span style="font-size: 80%;"> (<a href="TD_MultithermalMultibaric.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">148</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_MultithermalMultibaric.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#307">_ZNK4PLMD3ves25TD_MultithermalMultibaric8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#230">_ZN4PLMD3ves12_GLOBAL__N_138TD_MultithermalMultibaricRegisterMe2326createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#248">_ZN4PLMD3ves25TD_MultithermalMultibaricC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#225">_ZN4PLMD3ves25TD_MultithermalMultibaricD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#225">_ZN4PLMD3ves25TD_MultithermalMultibaricD2Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#313">_ZN4PLMD3ves25TD_MultithermalMultibaric10updateGridEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
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+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_MultithermalMultibaric.cpp<span style="font-size: 80%;"> (<a href="TD_MultithermalMultibaric.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
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+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">148</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
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+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
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+              <td class="coverFnHi">2</td>
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+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#230">_ZN4PLMD3ves12_GLOBAL__N_138TD_MultithermalMultibaricRegisterMe232C2Ev</a></td>
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+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#230">_ZN4PLMD3ves12_GLOBAL__N_138TD_MultithermalMultibaricRegisterMe232D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#313">_ZN4PLMD3ves25TD_MultithermalMultibaric10updateGridEv</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#233">_ZN4PLMD3ves25TD_MultithermalMultibaric16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#248">_ZN4PLMD3ves25TD_MultithermalMultibaricC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#225">_ZN4PLMD3ves25TD_MultithermalMultibaricD0Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#225">_ZN4PLMD3ves25TD_MultithermalMultibaricD2Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_MultithermalMultibaric.cpp.gcov.html#307">_ZNK4PLMD3ves25TD_MultithermalMultibaric8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_MultithermalMultibaric.cpp<span style="font-size: 80%;"> (source / <a href="TD_MultithermalMultibaric.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">148</td>
+            <td class="headerCovTableEntry">152</td>
+            <td class="headerCovTableEntryHi">97.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">88.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
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+
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+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cfloat&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC VES_TARGETDIST TD_MULTITHERMAL_MULTIBARIC</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Multithermal-multibaric target distribution (dynamic).</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Use the target distribution to sample the multithermal-multibaric ensemble \cite Piaggi-PRL-2019 \cite Okumura-CPL-2004.</a>
+<a name="40"><span class="lineNum">      40 </span>            : In this way, in a single molecular dynamics simulation one can obtain information</a>
+<a name="41"><span class="lineNum">      41 </span>            : about the simulated system in a range of temperatures and pressures.</a>
+<a name="42"><span class="lineNum">      42 </span>            : This range is determined through the keywords MIN_TEMP, MAX_TEMP, MIN_PRESSURE, and MAX_PRESSURE.</a>
+<a name="43"><span class="lineNum">      43 </span>            : One should also specified the target pressure of the barostat with the keyword PRESSURE.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : The collective variables (CVs) used to construct the bias potential must be:</a>
+<a name="46"><span class="lineNum">      46 </span>            :   1. the potential energy and the volume or,</a>
+<a name="47"><span class="lineNum">      47 </span>            :   2. the potential energy, the volume, and an order parameter.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : Other choices of CVs or a different order of the above mentioned CVs are nonsensical.</a>
+<a name="50"><span class="lineNum">      50 </span>            : The third CV, the order parameter, must be used when the region of the phase diagram under study is crossed by a first order phase transition \cite Piaggi-JCP-2019 .</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : The algorithm will explore the free energy at each temperature and pressure up to a predefined free</a>
+<a name="53"><span class="lineNum">      53 </span>            :  energy threshold \f$\epsilon\f$ specified through the keyword THRESHOLD (in kT units).</a>
+<a name="54"><span class="lineNum">      54 </span>            : If only the energy and the volume are being biased, i.e. no phase transition is considered, then THRESHOLD can be set to around 5.</a>
+<a name="55"><span class="lineNum">      55 </span>            : If also an order parameter is used then the THRESHOLD should be greater than the barrier for the transformation in kT.</a>
+<a name="56"><span class="lineNum">      56 </span>            : For small systems undergoing a freezing transition THRESHOLD is typically between 20 and 50.</a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span>            : It is also important to specify the number of intermediate temperatures and pressures to consider.</a>
+<a name="59"><span class="lineNum">      59 </span>            : This is done through the keywords STEPS_TEMP and STEPS_PRESSURE.</a>
+<a name="60"><span class="lineNum">      60 </span>            : If the number of intermediate temperature and pressures is too small, then holes might appear in the target distribution.</a>
+<a name="61"><span class="lineNum">      61 </span>            : If it is too large, the performance will deteriorate with no additional advantage.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : We now describe the algorithm more rigorously.</a>
+<a name="64"><span class="lineNum">      64 </span>            : The target distribution is given by</a>
+<a name="65"><span class="lineNum">      65 </span>            : \f[</a>
+<a name="66"><span class="lineNum">      66 </span>            : p(E,\mathcal{V},s)=</a>
+<a name="67"><span class="lineNum">      67 </span>            :   \begin{cases}</a>
+<a name="68"><span class="lineNum">      68 </span>            :     1/\Omega_{E,\mathcal{V},s} &amp; \text{if there is at least one } \beta',P' \text{ such} \\</a>
+<a name="69"><span class="lineNum">      69 </span>            :              &amp; \text{that } \beta' F_{\beta',P'}(E,\mathcal{V},s)&lt;\epsilon \text{ with}  \\</a>
+<a name="70"><span class="lineNum">      70 </span>            :              &amp; \beta_1&gt;\beta'&gt;\beta_2 \text{ and } P_1&lt;P'&lt;P_2 \\</a>
+<a name="71"><span class="lineNum">      71 </span>            :     0 &amp; \text{otherwise}</a>
+<a name="72"><span class="lineNum">      72 </span>            :   \end{cases}</a>
+<a name="73"><span class="lineNum">      73 </span>            : \f]</a>
+<a name="74"><span class="lineNum">      74 </span>            : with \f$F_{\beta',P'}(E,\mathcal{V},s)\f$ the free energy as a function of energy \f$E\f$ and volume \f$\mathcal{V}\f$ (and optionally the order parameter \f$s\f$) at temperature \f$\beta'\f$ and pressure \f$P'\f$, \f$\Omega_{E,\mathcal{V},s}\f$ is a normalization constant, and \f$\epsilon\f$ is the THRESHOLD.</a>
+<a name="75"><span class="lineNum">      75 </span>            : In practice the condition \f$\beta' F_{\beta',P'}(E,\mathcal{V},s)&lt;\epsilon\f$  is checked in equally spaced points in each dimension \f$\beta'\f$ and \f$P'\f$.</a>
+<a name="76"><span class="lineNum">      76 </span>            : The number of points is determined with the keywords STEPS_TEMP and STEPS_PRESSURE.</a>
+<a name="77"><span class="lineNum">      77 </span>            : In practice the target distribution is never set to zero but rather to a small value controlled by the keyword EPSILON.</a>
+<a name="78"><span class="lineNum">      78 </span>            : The small value is e^-EPSILON.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : Much like in the Wang-Landau algorithm \cite wanglandau or in the multicanonical ensemble \cite Berg-PRL-1992 , a flat histogram is targeted.</a>
+<a name="81"><span class="lineNum">      81 </span>            : The idea behind this choice of target distribution is that all regions of potential energy and volume (and optionally order parameter) that are relevant at all temperatures \f$\beta_1&lt;\beta'&lt;\beta_2\f$ and pressure \f$P_1&lt;P'&lt;P_2\f$ are included in the distribution.</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : The free energy at temperature \f$\beta'\f$ and pressure \f$P'\f$ is calculated from the free energy at \f$\beta\f$ and \f$P\f$ using:</a>
+<a name="84"><span class="lineNum">      84 </span>            : \f[</a>
+<a name="85"><span class="lineNum">      85 </span>            : \beta' F_{\beta',P'}(E,\mathcal{V},s) = \beta F_{\beta,P}(E,\mathcal{V},s) + (\beta' - \beta) E + (\beta' P' - \beta P ) \mathcal{V} + C</a>
+<a name="86"><span class="lineNum">      86 </span>            : \f]</a>
+<a name="87"><span class="lineNum">      87 </span>            : with \f$C\f$ such that \f$F_{\beta',P'}(E_m,\mathcal{V}_m,s_m)=0\f$ with \f$E_{m},\mathcal{V}_m,s_m\f$ the position of the free energy minimum.</a>
+<a name="88"><span class="lineNum">      88 </span>            : \f$ \beta F_{\beta,P}(E,\mathcal{V},s) \f$ is not know from the start and is instead found during the simulation.</a>
+<a name="89"><span class="lineNum">      89 </span>            : Therefore \f$ p(E,\mathcal{V},s) \f$ is determined iteratively as done in the well tempered target distribution \cite Valsson-JCTC-2015.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : The output of these simulations can be reweighted in order to obtain information at all temperatures and pressures in the targeted region of Temperature-Pressure plane.</a>
+<a name="92"><span class="lineNum">      92 </span>            : The reweighting can be performed using the action \ref REWEIGHT_TEMP_PRESS.</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : The multicanonical ensemble (fixed volume) can be targeted using \ref TD_MULTICANONICAL.</a>
+<a name="95"><span class="lineNum">      95 </span>            : </a>
+<a name="96"><span class="lineNum">      96 </span>            : \par Examples</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : The following input can be used to run a simulation in the multithermal-multibaric ensemble.</a>
+<a name="99"><span class="lineNum">      99 </span>            : The region of the temperature-pressure plane that will be explored is 260-350 K and 1 bar- 300 MPa.</a>
+<a name="100"><span class="lineNum">     100 </span>            : The energy and the volume are used as collective variables.</a>
+<a name="101"><span class="lineNum">     101 </span>            : Legendre polynomials are used to construct the two dimensional bias potential.</a>
+<a name="102"><span class="lineNum">     102 </span>            : The averaged stochastic gradient descent algorithm is chosen to optimize the VES functional.</a>
+<a name="103"><span class="lineNum">     103 </span>            : The target distribution is updated every 100 optimization steps (200 ps here) using the last estimation of the free energy.</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : \plumedfile</a>
+<a name="106"><span class="lineNum">     106 </span>            : # Use energy and volume as CVs</a>
+<a name="107"><span class="lineNum">     107 </span>            : energy: ENERGY</a>
+<a name="108"><span class="lineNum">     108 </span>            : vol: VOLUME</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : # Basis functions</a>
+<a name="111"><span class="lineNum">     111 </span>            : bf1: BF_LEGENDRE ORDER=10 MINIMUM=-14750 MAXIMUM=-12250</a>
+<a name="112"><span class="lineNum">     112 </span>            : bf2: BF_LEGENDRE ORDER=10 MINIMUM=6.5 MAXIMUM=8.25</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : # Target distribution - 1 bar = 0.06022140857 and 300 MPa = 180.66422571</a>
+<a name="115"><span class="lineNum">     115 </span>            : TD_MULTITHERMAL_MULTIBARIC ...</a>
+<a name="116"><span class="lineNum">     116 </span>            :  MIN_TEMP=260</a>
+<a name="117"><span class="lineNum">     117 </span>            :  MAX_TEMP=350</a>
+<a name="118"><span class="lineNum">     118 </span>            :  MAX_PRESSURE=180.66422571</a>
+<a name="119"><span class="lineNum">     119 </span>            :  MIN_PRESSURE=0.06022140857</a>
+<a name="120"><span class="lineNum">     120 </span>            :  PRESSURE=0.06022140857</a>
+<a name="121"><span class="lineNum">     121 </span>            :  LABEL=td_multi</a>
+<a name="122"><span class="lineNum">     122 </span>            : ... TD_MULTITHERMAL_MULTIBARIC</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : # Bias expansion</a>
+<a name="125"><span class="lineNum">     125 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="126"><span class="lineNum">     126 </span>            :  ARG=energy,vol</a>
+<a name="127"><span class="lineNum">     127 </span>            :  BASIS_FUNCTIONS=bf1,bf2</a>
+<a name="128"><span class="lineNum">     128 </span>            :  TEMP=300.0</a>
+<a name="129"><span class="lineNum">     129 </span>            :  GRID_BINS=200,200</a>
+<a name="130"><span class="lineNum">     130 </span>            :  TARGET_DISTRIBUTION=td_multi</a>
+<a name="131"><span class="lineNum">     131 </span>            :  LABEL=b1</a>
+<a name="132"><span class="lineNum">     132 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : # Optimization algorithm</a>
+<a name="135"><span class="lineNum">     135 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="136"><span class="lineNum">     136 </span>            :   BIAS=b1</a>
+<a name="137"><span class="lineNum">     137 </span>            :   STRIDE=500</a>
+<a name="138"><span class="lineNum">     138 </span>            :   LABEL=o1</a>
+<a name="139"><span class="lineNum">     139 </span>            :   STEPSIZE=1.0</a>
+<a name="140"><span class="lineNum">     140 </span>            :   FES_OUTPUT=500</a>
+<a name="141"><span class="lineNum">     141 </span>            :   BIAS_OUTPUT=500</a>
+<a name="142"><span class="lineNum">     142 </span>            :   TARGETDIST_OUTPUT=500</a>
+<a name="143"><span class="lineNum">     143 </span>            :   COEFFS_OUTPUT=100</a>
+<a name="144"><span class="lineNum">     144 </span>            :   TARGETDIST_STRIDE=100</a>
+<a name="145"><span class="lineNum">     145 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : \endplumedfile</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : The multithermal-multibaric target distribution can also be used to explore regions of the phase diagram crossed by first order phase transitions.</a>
+<a name="151"><span class="lineNum">     151 </span>            : Consider a system of 250 atoms that crystallizes in the FCC crystal structure.</a>
+<a name="152"><span class="lineNum">     152 </span>            : The region of the temperature-pressure plane that will be explored is 350-450 K and 1bar-1GPa.</a>
+<a name="153"><span class="lineNum">     153 </span>            : We assume that inside this region we can find the liquid-FCC coexistence line that we would like to obtain.</a>
+<a name="154"><span class="lineNum">     154 </span>            : In this case in addition to the energy and volume, an order parameter must also be biased.</a>
+<a name="155"><span class="lineNum">     155 </span>            : The energy, volume, and an order parameter are used as collective variables to construct the bias potential.</a>
+<a name="156"><span class="lineNum">     156 </span>            : We choose as order parameter the \ref FCCUBIC.</a>
+<a name="157"><span class="lineNum">     157 </span>            : Legendre polynomials are used to construct the three dimensional bias potential.</a>
+<a name="158"><span class="lineNum">     158 </span>            : The averaged stochastic gradient descent algorithm is chosen to optimize the VES functional.</a>
+<a name="159"><span class="lineNum">     159 </span>            : The target distribution is updated every 100 optimization steps (200 ps here) using the last estimation of the free energy.</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : \plumedfile</a>
+<a name="162"><span class="lineNum">     162 </span>            : # Use energy, volume and FCCUBIC as CVs</a>
+<a name="163"><span class="lineNum">     163 </span>            : energy: ENERGY</a>
+<a name="164"><span class="lineNum">     164 </span>            : vol: VOLUME</a>
+<a name="165"><span class="lineNum">     165 </span>            : fcc: FCCUBIC SPECIES=1-256 SWITCH={CUBIC D_0=0.4 D_MAX=0.5} MORE_THAN={RATIONAL R_0=0.45 NN=12 MM=24}</a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span>            : # Basis functions</a>
+<a name="168"><span class="lineNum">     168 </span>            : bf1: BF_LEGENDRE ORDER=8 MINIMUM=-26500 MAXIMUM=-23500</a>
+<a name="169"><span class="lineNum">     169 </span>            : bf2: BF_LEGENDRE ORDER=8 MINIMUM=8.0 MAXIMUM=11.5</a>
+<a name="170"><span class="lineNum">     170 </span>            : bf3: BF_LEGENDRE ORDER=8 MINIMUM=0.0 MAXIMUM=256.0</a>
+<a name="171"><span class="lineNum">     171 </span>            : </a>
+<a name="172"><span class="lineNum">     172 </span>            : # Target distribution</a>
+<a name="173"><span class="lineNum">     173 </span>            : TD_MULTITHERMAL_MULTIBARIC ...</a>
+<a name="174"><span class="lineNum">     174 </span>            :  LABEL=td_multitp</a>
+<a name="175"><span class="lineNum">     175 </span>            :  MIN_TEMP=350.0</a>
+<a name="176"><span class="lineNum">     176 </span>            :  MAX_TEMP=450.0</a>
+<a name="177"><span class="lineNum">     177 </span>            :  MIN_PRESSURE=0.06022140857</a>
+<a name="178"><span class="lineNum">     178 </span>            :  MAX_PRESSURE=602.2140857</a>
+<a name="179"><span class="lineNum">     179 </span>            :  PRESSURE=301.10704285</a>
+<a name="180"><span class="lineNum">     180 </span>            :  SIGMA=250.0,0.1,10.0</a>
+<a name="181"><span class="lineNum">     181 </span>            :  THRESHOLD=15</a>
+<a name="182"><span class="lineNum">     182 </span>            :  STEPS_TEMP=20</a>
+<a name="183"><span class="lineNum">     183 </span>            :  STEPS_PRESSURE=20</a>
+<a name="184"><span class="lineNum">     184 </span>            : ... TD_MULTITHERMAL_MULTIBARIC</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : # Expansion</a>
+<a name="187"><span class="lineNum">     187 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="188"><span class="lineNum">     188 </span>            :  ARG=energy,vol,fcc.morethan</a>
+<a name="189"><span class="lineNum">     189 </span>            :  BASIS_FUNCTIONS=bf1,bf2,bf3</a>
+<a name="190"><span class="lineNum">     190 </span>            :  TEMP=400.0</a>
+<a name="191"><span class="lineNum">     191 </span>            :  GRID_BINS=40,40,40</a>
+<a name="192"><span class="lineNum">     192 </span>            :  TARGET_DISTRIBUTION=td_multitp</a>
+<a name="193"><span class="lineNum">     193 </span>            :  LABEL=b1</a>
+<a name="194"><span class="lineNum">     194 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : # Optimization algorithm</a>
+<a name="197"><span class="lineNum">     197 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="198"><span class="lineNum">     198 </span>            :   BIAS=b1</a>
+<a name="199"><span class="lineNum">     199 </span>            :   STRIDE=500</a>
+<a name="200"><span class="lineNum">     200 </span>            :   LABEL=o1</a>
+<a name="201"><span class="lineNum">     201 </span>            :   STEPSIZE=1.0</a>
+<a name="202"><span class="lineNum">     202 </span>            :   FES_OUTPUT=500</a>
+<a name="203"><span class="lineNum">     203 </span>            :   BIAS_OUTPUT=500</a>
+<a name="204"><span class="lineNum">     204 </span>            :   TARGETDIST_OUTPUT=500</a>
+<a name="205"><span class="lineNum">     205 </span>            :   COEFFS_OUTPUT=100</a>
+<a name="206"><span class="lineNum">     206 </span>            :   TARGETDIST_STRIDE=500</a>
+<a name="207"><span class="lineNum">     207 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : \endplumedfile</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : */</a>
+<a name="212"><span class="lineNum">     212 </span>            : //+ENDPLUMEDOC</a>
+<a name="213"><span class="lineNum">     213 </span>            : </a>
+<a name="214"><span class="lineNum">     214 </span>            : class TD_MultithermalMultibaric: public TargetDistribution {</a>
+<a name="215"><span class="lineNum">     215 </span>            : private:</a>
+<a name="216"><span class="lineNum">     216 </span>            :   double threshold_, min_temp_, max_temp_;</a>
+<a name="217"><span class="lineNum">     217 </span>            :   double min_press_, max_press_, press_;</a>
+<a name="218"><span class="lineNum">     218 </span>            :   double epsilon_;</a>
+<a name="219"><span class="lineNum">     219 </span>            :   bool smoothening_;</a>
+<a name="220"><span class="lineNum">     220 </span>            :   std::vector&lt;double&gt; sigma_;</a>
+<a name="221"><span class="lineNum">     221 </span>            :   unsigned steps_temp_, steps_pressure_;</a>
+<a name="222"><span class="lineNum">     222 </span>            : public:</a>
+<a name="223"><span class="lineNum">     223 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="224"><span class="lineNum">     224 </span>            :   explicit TD_MultithermalMultibaric(const ActionOptions&amp; ao);</a>
+<a name="225"><span class="lineNum">     225 </span>            :   void updateGrid() override;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">          4 :   ~TD_MultithermalMultibaric() {}</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   double GaussianSwitchingFunc(const double, const double, const double) const;</a>
+<a name="229"><span class="lineNum">     229 </span>            : };</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      12506 : PLUMED_REGISTER_ACTION(TD_MultithermalMultibaric,&quot;TD_MULTITHERMAL_MULTIBARIC&quot;)</span></a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : </a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">          4 : void TD_MultithermalMultibaric::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">          4 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;THRESHOLD&quot;,&quot;5&quot;,&quot;Maximum exploration free energy in kT.&quot;);</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;EPSILON&quot;,&quot;10&quot;,&quot;The zeros of the target distribution are changed to e^-EPSILON.&quot;);</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MIN_TEMP&quot;,&quot;Minimum energy.&quot;);</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MAX_TEMP&quot;,&quot;Maximum energy.&quot;);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MIN_PRESSURE&quot;,&quot;Minimum pressure.&quot;);</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;MAX_PRESSURE&quot;,&quot;Maximum pressure.&quot;);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;PRESSURE&quot;,&quot;Target pressure of the barostat used in the MD engine.&quot;);</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;STEPS_TEMP&quot;,&quot;20&quot;,&quot;Number of temperature steps.&quot;);</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          8 :   keys.add(&quot;compulsory&quot;,&quot;STEPS_PRESSURE&quot;,&quot;20&quot;,&quot;Number of pressure steps.&quot;);</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">          8 :   keys.add(&quot;optional&quot;,&quot;SIGMA&quot;,&quot;The standard deviation parameters of the Gaussian kernels used for smoothing the target distribution. One value must be specified for each argument, i.e. one value per CV. A value of 0.0 means that no smoothing is performed, this is the default behavior.&quot;);</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">          4 : }</span></a>
+<a name="248"><span class="lineNum">     248 </span>            : </a>
+<a name="249"><span class="lineNum">     249 </span>            : </a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          2 : TD_MultithermalMultibaric::TD_MultithermalMultibaric(const ActionOptions&amp; ao):</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          2 :   threshold_(5.0),</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          2 :   min_temp_(0.0),</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">          2 :   max_temp_(1000.0),</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          2 :   min_press_(0.0),</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          2 :   max_press_(1000.0),</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          2 :   epsilon_(10.0),</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          2 :   smoothening_(true),</span></a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">          2 :   steps_temp_(20),</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          2 :   steps_pressure_(20)</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : {</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">          2 :   log.printf(&quot;  Multithermal-multibaric target distribution&quot;);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          2 :   log.printf(&quot;  Please read and cite &quot;);</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">          4 :   log &lt;&lt; plumed.cite(&quot;Piaggi and Parrinello, Phys. Rev. Lett. 122 (5), 050601 (2019)&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          2 :   log.printf(&quot; and &quot;);</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          4 :   log &lt;&lt; plumed.cite(&quot;Piaggi and Parrinello, J. Chem. Phys. 150 (24), 244119 (2019)&quot;);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          2 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span>            : </a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          2 :   parse(&quot;THRESHOLD&quot;,threshold_);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          2 :   if(threshold_&lt;=0.0) {</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: the value of the threshold should be positive.&quot;);</span></a>
+<a name="275"><span class="lineNum">     275 </span>            :   }</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          2 :   log.printf(&quot;  exploring free energy up to %f kT for each temperature and pressure\n&quot;,threshold_);</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          2 :   parse(&quot;MIN_TEMP&quot;,min_temp_);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          2 :   parse(&quot;MAX_TEMP&quot;,max_temp_);</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">          2 :   log.printf(&quot;  temperatures between %f and %f will be explored \n&quot;,min_temp_,max_temp_);</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          2 :   parse(&quot;MIN_PRESSURE&quot;,min_press_);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          2 :   parse(&quot;MAX_PRESSURE&quot;,max_press_);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">          2 :   log.printf(&quot;  pressures between %f and %f will be explored \n&quot;,min_press_,max_press_);</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          2 :   parse(&quot;PRESSURE&quot;,press_);</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          2 :   log.printf(&quot;  pressure of the barostat should have been set to %f. Please check this in the MD engine \n&quot;,press_);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          4 :   parseVector(&quot;SIGMA&quot;,sigma_);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          2 :   if(sigma_.size()==0) smoothening_=false;</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineCov">          2 :   if(smoothening_ &amp;&amp; (sigma_.size()&lt;2 || sigma_.size()&gt;3) ) plumed_merror(getName()+&quot;: SIGMA takes 2 or 3 values as input.&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineCov">          2 :   if (smoothening_) {</span></a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">          2 :     log.printf(&quot;  the target distribution will be smoothed using sigma values&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">          7 :     for(unsigned i=0; i&lt;sigma_.size(); ++i) log.printf(&quot; %f&quot;,sigma_[i]);</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">          2 :     log.printf(&quot;\n&quot;);</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :   }</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">          2 :   parse(&quot;STEPS_TEMP&quot;,steps_temp_);</span></a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          2 :   parse(&quot;STEPS_PRESSURE&quot;,steps_pressure_);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">          2 :   log.printf(&quot;  %d steps in temperatures and %d steps in pressure will be employed \n&quot;,steps_temp_,steps_pressure_);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">          2 :   steps_temp_ += 1;</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">          2 :   steps_pressure_ += 1;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">          2 :   parse(&quot;EPSILON&quot;,epsilon_);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">          2 :   if(epsilon_&lt;=1.0) {</span></a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: the value of epsilon should be greater than 1.&quot;);</span></a>
+<a name="301"><span class="lineNum">     301 </span>            :   }</a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          2 :   log.printf(&quot;  the non relevant regions of the target distribution are set to e^-%f \n&quot;,epsilon_);</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :   setDynamic();</a>
+<a name="304"><span class="lineNum">     304 </span>            :   setFesGridNeeded();</a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          2 :   checkRead();</span></a>
+<a name="306"><span class="lineNum">     306 </span><span class="lineCov">          2 : }</span></a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineNoCov">          0 : double TD_MultithermalMultibaric::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_MultithermalMultibaric&quot;);</span></a>
+<a name="311"><span class="lineNum">     311 </span>            :   return 0.0;</a>
+<a name="312"><span class="lineNum">     312 </span>            : }</a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : </a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">          4 : void TD_MultithermalMultibaric::updateGrid() {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          4 :   if (getStep() == 0) {</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          2 :     if(targetDistGrid().getDimension()&gt;3 || targetDistGrid().getDimension()&lt;2) plumed_merror(getName()+&quot; works only with 2 or 3 arguments, i.e. energy and volume, or energy, volume, and CV&quot;);</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          2 :     if(smoothening_ &amp;&amp; sigma_.size()!=targetDistGrid().getDimension()) plumed_merror(getName()+&quot;: mismatch between SIGMA dimension and number of arguments&quot;);</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :     // Use uniform TD</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :     std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="321"><span class="lineNum">     321 </span>            :     double norm = 0.0;</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      11864 :     for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :       double value = 1.0;</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      11862 :       norm += integration_weights[l]*value;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      11862 :       targetDistGrid().setValue(l,value);</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :     }</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          2 :     targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="328"><span class="lineNum">     328 </span>            :   } else {</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          2 :     double beta = getBeta();</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          2 :     double beta_prime_min = 1./(plumed.getAtoms().getKBoltzmann()*min_temp_);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          2 :     double beta_prime_max = 1./(plumed.getAtoms().getKBoltzmann()*max_temp_);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">          2 :     plumed_massert(getFesGridPntr()!=NULL,&quot;the FES grid has to be linked to use TD_MultithermalMultibaric!&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span>            :     // Set all to current epsilon value</a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">      11864 :     for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      11862 :       double value = exp(-1.0*epsilon_);</span></a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">      11862 :       targetDistGrid().setValue(l,value);</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :     }</a>
+<a name="338"><span class="lineNum">     338 </span>            :     // Loop over pressures and temperatures</a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         44 :     for(unsigned i=0; i&lt;steps_temp_; i++) {</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         42 :       double beta_prime=beta_prime_min + (beta_prime_max-beta_prime_min)*i/(steps_temp_-1);</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        924 :       for(unsigned j=0; j&lt;steps_pressure_; j++) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">        882 :         double pressure_prime=min_press_ + (max_press_-min_press_)*j/(steps_pressure_-1);</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :         // Find minimum for this pressure and temperature</a>
+<a name="344"><span class="lineNum">     344 </span>            :         double minval=DBL_MAX;</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">    5232024 :         for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">    5231142 :           double energy = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">    5231142 :           double volume = targetDistGrid().getPoint(l)[1];</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">    5231142 :           double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">    5231142 :           value = beta*value + (beta_prime-beta)*energy + (beta_prime*pressure_prime-beta*press_)*volume;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">    5231142 :           if(value&lt;minval) {</span></a>
+<a name="351"><span class="lineNum">     351 </span>            :             minval=value;</a>
+<a name="352"><span class="lineNum">     352 </span>            :           }</a>
+<a name="353"><span class="lineNum">     353 </span>            :         }</a>
+<a name="354"><span class="lineNum">     354 </span>            :         // Now check which energies and volumes are below X kt</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">    5232024 :         for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">    5231142 :           double energy = targetDistGrid().getPoint(l)[0];</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">    5231142 :           double volume = targetDistGrid().getPoint(l)[1];</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">    5231142 :           double value = getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">    5231142 :           value = beta*value + (beta_prime-beta)*energy + (beta_prime*pressure_prime-beta*press_)*volume - minval;</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">    5231142 :           if (value&lt;threshold_) {</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :             double value = 1.0;</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">      65261 :             targetDistGrid().setValue(l,value);</span></a>
+<a name="363"><span class="lineNum">     363 </span>            :           }</a>
+<a name="364"><span class="lineNum">     364 </span>            :         }</a>
+<a name="365"><span class="lineNum">     365 </span>            :       }</a>
+<a name="366"><span class="lineNum">     366 </span>            :     }</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          2 :     if (smoothening_) {</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">          2 :       std::vector&lt;unsigned&gt; nbin=targetDistGrid().getNbin();</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">          2 :       std::vector&lt;double&gt; dx=targetDistGrid().getDx();</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          2 :       unsigned dim=targetDistGrid().getDimension();</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :       // Smoothening</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">      11864 :       for(Grid::index_t index=0; index&lt;targetDistGrid().getSize(); index++) {</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">      11862 :         std::vector&lt;unsigned&gt; indices = targetDistGrid().getIndices(index);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">      11862 :         std::vector&lt;double&gt; point = targetDistGrid().getPoint(index);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">      11862 :         double value = targetDistGrid().getValue(index);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">      11862 :         if (value&gt;(1-1.e-5)) { // Apply only if this grid point was 1.</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :           // Apply gaussians around</a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">       1242 :           std::vector&lt;int&gt; minBin(dim), maxBin(dim); // These cannot be unsigned</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :           // Only consider contributions less than n*sigma bins apart from the actual distance</a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">       4384 :           for(unsigned k=0; k&lt;dim; k++) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">       3142 :             int deltaBin=std::floor(6*sigma_[k]/dx[k]);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">       3142 :             minBin[k]=indices[k] - deltaBin;</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">       3142 :             if (minBin[k] &lt; 0) minBin[k]=0;</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">       3142 :             if (minBin[k] &gt; (nbin[k]-1)) minBin[k]=nbin[k]-1;</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">       3142 :             maxBin[k]=indices[k] + deltaBin;</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">       3142 :             if (maxBin[k] &gt; (nbin[k]-1)) maxBin[k]=nbin[k]-1;</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :           }</a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">       1242 :           if (dim==2) {</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">       7008 :             for(unsigned l=minBin[0]; l&lt;maxBin[0]+1; l++) {</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">     115632 :               for(unsigned m=minBin[1]; m&lt;maxBin[1]+1; m++) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">     109208 :                 std::vector&lt;unsigned&gt; indices_prime(dim);</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">     109208 :                 indices_prime[0]=l;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">     109208 :                 indices_prime[1]=m;</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">     109208 :                 Grid::index_t index_prime = targetDistGrid().getIndex(indices_prime);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">     109208 :                 std::vector&lt;double&gt; point_prime = targetDistGrid().getPoint(index_prime);</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">     109208 :                 double value_prime = targetDistGrid().getValue(index_prime);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :                 // Apply gaussian</a>
+<a name="398"><span class="lineNum">     398 </span>            :                 double gaussian_value = 1;</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">     327624 :                 for(unsigned k=0; k&lt;dim; k++) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">     436832 :                   gaussian_value *= GaussianSwitchingFunc(point_prime[k],point[k],sigma_[k]);</span></a>
+<a name="401"><span class="lineNum">     401 </span>            :                 }</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">     109208 :                 if (value_prime&lt;gaussian_value) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">       2761 :                   targetDistGrid().setValue(index_prime,gaussian_value);</span></a>
+<a name="404"><span class="lineNum">     404 </span>            :                 }</a>
+<a name="405"><span class="lineNum">     405 </span>            :               }</a>
+<a name="406"><span class="lineNum">     406 </span>            :             }</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">        658 :           } else if (dim==3) {</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">      12352 :             for(unsigned l=minBin[0]; l&lt;maxBin[0]+1; l++) {</span></a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">      84952 :               for(unsigned m=minBin[1]; m&lt;maxBin[1]+1; m++) {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">     509608 :                 for(unsigned n=minBin[2]; n&lt;maxBin[2]+1; n++) {</span></a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">     436350 :                   std::vector&lt;unsigned&gt; indices_prime(dim);</span></a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">     436350 :                   indices_prime[0]=l;</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">     436350 :                   indices_prime[1]=m;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">     436350 :                   indices_prime[2]=n;</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">     436350 :                   Grid::index_t index_prime = targetDistGrid().getIndex(indices_prime);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">     436350 :                   std::vector&lt;double&gt; point_prime = targetDistGrid().getPoint(index_prime);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">     436350 :                   double value_prime = targetDistGrid().getValue(index_prime);</span></a>
+<a name="418"><span class="lineNum">     418 </span>            :                   // Apply gaussian</a>
+<a name="419"><span class="lineNum">     419 </span>            :                   double gaussian_value = 1;</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">    1745400 :                   for(unsigned k=0; k&lt;dim; k++) {</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">    2618100 :                     gaussian_value *= GaussianSwitchingFunc(point_prime[k],point[k],sigma_[k]);</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :                   }</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">     436350 :                   if (value_prime&lt;gaussian_value) {</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">      13789 :                     targetDistGrid().setValue(index_prime,gaussian_value);</span></a>
+<a name="425"><span class="lineNum">     425 </span>            :                   }</a>
+<a name="426"><span class="lineNum">     426 </span>            :                 }</a>
+<a name="427"><span class="lineNum">     427 </span>            :               }</a>
+<a name="428"><span class="lineNum">     428 </span>            :             }</a>
+<a name="429"><span class="lineNum">     429 </span>            :           }</a>
+<a name="430"><span class="lineNum">     430 </span>            :         }</a>
+<a name="431"><span class="lineNum">     431 </span>            :       }</a>
+<a name="432"><span class="lineNum">     432 </span>            :     }</a>
+<a name="433"><span class="lineNum">     433 </span>            :     // Normalize</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">          4 :     std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :     double norm = 0.0;</a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">      11864 :     for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">      11862 :       double value = targetDistGrid().getValue(l);</span></a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">      11862 :       norm += integration_weights[l]*value;</span></a>
+<a name="439"><span class="lineNum">     439 </span>            :     }</a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">          2 :     targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="441"><span class="lineNum">     441 </span>            :   }</a>
+<a name="442"><span class="lineNum">     442 </span><span class="lineCov">          4 :   updateLogTargetDistGrid();</span></a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          4 : }</span></a>
+<a name="444"><span class="lineNum">     444 </span>            : </a>
+<a name="445"><span class="lineNum">     445 </span>            : inline</a>
+<a name="446"><span class="lineNum">     446 </span>            : double TD_MultithermalMultibaric::GaussianSwitchingFunc(const double argument, const double center, const double sigma) const {</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">    1527466 :   if(sigma&gt;0.0) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">    1527466 :     double arg=(argument-center)/sigma;</span></a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">    1527466 :     return exp(-0.5*arg*arg);</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :   }</a>
+<a name="451"><span class="lineNum">     451 </span>            :   else {</a>
+<a name="452"><span class="lineNum">     452 </span>            :     return 0.0;</a>
+<a name="453"><span class="lineNum">     453 </span>            :   }</a>
+<a name="454"><span class="lineNum">     454 </span>            : }</a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            : }</a>
+<a name="458"><span class="lineNum">     458 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ProductCombination.cpp.func-sort-c.html b/coverage/ves/TD_ProductCombination.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ce6ffa78a9
--- /dev/null
+++ b/coverage/ves/TD_ProductCombination.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ProductCombination.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ProductCombination.cpp<span style="font-size: 80%;"> (<a href="TD_ProductCombination.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntryLo">73.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_ProductCombination.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#229">_ZN4PLMD3ves21TD_ProductCombination10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#237">_ZN4PLMD3ves21TD_ProductCombination12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#245">_ZN4PLMD3ves21TD_ProductCombination25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#177">_ZNK4PLMD3ves21TD_ProductCombination8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#253">_ZN4PLMD3ves21TD_ProductCombination11linkFesGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#221">_ZN4PLMD3ves21TD_ProductCombination11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#138">_ZN4PLMD3ves12_GLOBAL__N_134TD_ProductCombinationRegisterMe1406createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#183">_ZN4PLMD3ves21TD_ProductCombination20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#149">_ZN4PLMD3ves21TD_ProductCombinationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#141">_ZN4PLMD3ves21TD_ProductCombination16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#194">_ZN4PLMD3ves21TD_ProductCombination10updateGridEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#138">_ZN4PLMD3ves12_GLOBAL__N_134TD_ProductCombinationRegisterMe140C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#138">_ZN4PLMD3ves12_GLOBAL__N_134TD_ProductCombinationRegisterMe140D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ProductCombination.cpp.func.html b/coverage/ves/TD_ProductCombination.cpp.func.html
new file mode 100644
index 0000000000..5a76d6a560
--- /dev/null
+++ b/coverage/ves/TD_ProductCombination.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ProductCombination.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ProductCombination.cpp<span style="font-size: 80%;"> (<a href="TD_ProductCombination.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntryLo">73.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_ProductCombination.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#138">_ZN4PLMD3ves12_GLOBAL__N_134TD_ProductCombinationRegisterMe1406createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#138">_ZN4PLMD3ves12_GLOBAL__N_134TD_ProductCombinationRegisterMe140C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#138">_ZN4PLMD3ves12_GLOBAL__N_134TD_ProductCombinationRegisterMe140D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#229">_ZN4PLMD3ves21TD_ProductCombination10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#194">_ZN4PLMD3ves21TD_ProductCombination10updateGridEv</a></td>
+              <td class="coverFnHi">14</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#253">_ZN4PLMD3ves21TD_ProductCombination11linkFesGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#221">_ZN4PLMD3ves21TD_ProductCombination11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#237">_ZN4PLMD3ves21TD_ProductCombination12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#141">_ZN4PLMD3ves21TD_ProductCombination16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#183">_ZN4PLMD3ves21TD_ProductCombination20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#245">_ZN4PLMD3ves21TD_ProductCombination25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#149">_ZN4PLMD3ves21TD_ProductCombinationC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductCombination.cpp.gcov.html#177">_ZNK4PLMD3ves21TD_ProductCombination8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ProductCombination.cpp.gcov.html b/coverage/ves/TD_ProductCombination.cpp.gcov.html
new file mode 100644
index 0000000000..3fec13cc34
--- /dev/null
+++ b/coverage/ves/TD_ProductCombination.cpp.gcov.html
@@ -0,0 +1,340 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ProductCombination.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ProductCombination.cpp<span style="font-size: 80%;"> (source / <a href="TD_ProductCombination.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntryLo">73.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">69.2 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : // class Grid;</a>
+<a name="38"><span class="lineNum">      38 </span>            : class Action;</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace ves {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : //+PLUMEDOC VES_TARGETDIST TD_PRODUCT_COMBINATION</a>
+<a name="43"><span class="lineNum">      43 </span>            : /*</a>
+<a name="44"><span class="lineNum">      44 </span>            : Target distribution given by product combination of distributions (static or dynamic).</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : Employ a target distribution that is a product combination of the other</a>
+<a name="47"><span class="lineNum">      47 </span>            : distributions, defined as</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : p(\mathbf{s}) =</a>
+<a name="50"><span class="lineNum">      50 </span>            : \frac{\prod_{i} p_{i}(\mathbf{s})}</a>
+<a name="51"><span class="lineNum">      51 </span>            : {\int d \mathbf{s} \prod_{i} p_{i}(\mathbf{s})}</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f]</a>
+<a name="53"><span class="lineNum">      53 </span>            : where the distributions \f$p_{i}(\mathbf{s})\f$ are in full dimensional space</a>
+<a name="54"><span class="lineNum">      54 </span>            : of the arguments used.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : Note the difference between this target distribution and the one defined in</a>
+<a name="57"><span class="lineNum">      57 </span>            : \ref TD_PRODUCT_DISTRIBUTION. Here we have a non-separable distribution given</a>
+<a name="58"><span class="lineNum">      58 </span>            : as a product of distribution \f$p_{i}(\mathbf{s})\f$ which are in full dimensional</a>
+<a name="59"><span class="lineNum">      59 </span>            : space of the arguments used.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The labels of the distributions \f$p_{i}(\mathbf{s})\f$ to be used in the</a>
+<a name="62"><span class="lineNum">      62 </span>            : product combination are given in the DISTRIBUTIONS keyword.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : The target distribution resulting from the product combination will be</a>
+<a name="65"><span class="lineNum">      65 </span>            : automatically normalized. Therefore, the product combination needs to</a>
+<a name="66"><span class="lineNum">      66 </span>            : be a proper distribution that is non-negative and that can be normalized. The</a>
+<a name="67"><span class="lineNum">      67 </span>            : code will perform checks to make sure that this is indeed the case.</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : The product combination will be a dynamic target distribution if one or more</a>
+<a name="70"><span class="lineNum">      70 </span>            : of the distributions used is a dynamic distribution. Otherwise it will be a</a>
+<a name="71"><span class="lineNum">      71 </span>            : static distribution.</a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            : \par Examples</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : In the following example the overall interval on which the</a>
+<a name="76"><span class="lineNum">      76 </span>            : target distribution is defined is from 0.23 to 0.8.</a>
+<a name="77"><span class="lineNum">      77 </span>            : We employ a product combination of a well-tempered</a>
+<a name="78"><span class="lineNum">      78 </span>            : distribution and a uniform distribution that decays to</a>
+<a name="79"><span class="lineNum">      79 </span>            : zero at 0.6. This results in a target distribution that</a>
+<a name="80"><span class="lineNum">      80 </span>            : is well-tempered from 0.23 to 0.6 and then decays to zero.</a>
+<a name="81"><span class="lineNum">      81 </span>            : In other words, we cut off the tail of the well-tempered</a>
+<a name="82"><span class="lineNum">      82 </span>            : distribution at 0.6</a>
+<a name="83"><span class="lineNum">      83 </span>            : \plumedfile</a>
+<a name="84"><span class="lineNum">      84 </span>            : td_welltemp: TD_WELLTEMPERED BIASFACTOR=5</a>
+<a name="85"><span class="lineNum">      85 </span>            : td_uniform: TD_UNIFORM MINIMA=0.23 MAXIMA=0.6 SIGMA_MAXIMA=0.05</a>
+<a name="86"><span class="lineNum">      86 </span>            : td_combination: TD_PRODUCT_COMBINATION DISTRIBUTIONS=td_uniform,td_welltemp</a>
+<a name="87"><span class="lineNum">      87 </span>            : \endplumedfile</a>
+<a name="88"><span class="lineNum">      88 </span>            : </a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : In the following example the overall interval on which the</a>
+<a name="91"><span class="lineNum">      91 </span>            : target distribution is defined is from -4 to 4.</a>
+<a name="92"><span class="lineNum">      92 </span>            : We employ a product of a Gaussian distribution with two centers</a>
+<a name="93"><span class="lineNum">      93 </span>            : and distribution that is uniform on the interval -3 to 3 and</a>
+<a name="94"><span class="lineNum">      94 </span>            : then smoothly decays to zero outside that interval.</a>
+<a name="95"><span class="lineNum">      95 </span>            : The overall effect will then be to cut off the tails of the</a>
+<a name="96"><span class="lineNum">      96 </span>            : Gaussian distribution</a>
+<a name="97"><span class="lineNum">      97 </span>            : \plumedfile</a>
+<a name="98"><span class="lineNum">      98 </span>            : TD_GAUSSIAN ...</a>
+<a name="99"><span class="lineNum">      99 </span>            :  CENTER1=-2.9 SIGMA1=1.0</a>
+<a name="100"><span class="lineNum">     100 </span>            :  CENTER2=+2.9 SIGMA2=0.4</a>
+<a name="101"><span class="lineNum">     101 </span>            :  LABEL=td_gauss</a>
+<a name="102"><span class="lineNum">     102 </span>            : ... TD_GAUSSIAN</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : TD_UNIFORM ...</a>
+<a name="105"><span class="lineNum">     105 </span>            :  MINIMA=-3.0 SIGMA_MINIMA=0.20</a>
+<a name="106"><span class="lineNum">     106 </span>            :  MAXIMA=+3.0 SIGMA_MAXIMA=0.15</a>
+<a name="107"><span class="lineNum">     107 </span>            :  LABEL=td_uni</a>
+<a name="108"><span class="lineNum">     108 </span>            : ... TD_UNIFORM</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : td_pc: TD_PRODUCT_COMBINATION DISTRIBUTIONS=td_gauss,td_uni</a>
+<a name="111"><span class="lineNum">     111 </span>            : \endplumedfile</a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span>            : */</a>
+<a name="114"><span class="lineNum">     114 </span>            : //+ENDPLUMEDOC</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : class VesBias;</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            : class TD_ProductCombination: public TargetDistribution {</a>
+<a name="119"><span class="lineNum">     119 </span>            : private:</a>
+<a name="120"><span class="lineNum">     120 </span>            :   std::vector&lt;TargetDistribution*&gt; distribution_pntrs_;</a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::vector&lt;Grid*&gt; grid_pntrs_;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   unsigned int ndist_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) override;</a>
+<a name="124"><span class="lineNum">     124 </span>            : public:</a>
+<a name="125"><span class="lineNum">     125 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="126"><span class="lineNum">     126 </span>            :   explicit TD_ProductCombination(const ActionOptions&amp; ao);</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void updateGrid() override;</a>
+<a name="128"><span class="lineNum">     128 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="129"><span class="lineNum">     129 </span>            :   //</a>
+<a name="130"><span class="lineNum">     130 </span>            :   void linkVesBias(VesBias*) override;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   void linkAction(Action*) override;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   //</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void linkBiasGrid(Grid*) override;</a>
+<a name="134"><span class="lineNum">     134 </span>            :   void linkBiasWithoutCutoffGrid(Grid*) override;</a>
+<a name="135"><span class="lineNum">     135 </span>            :   void linkFesGrid(Grid*) override;</a>
+<a name="136"><span class="lineNum">     136 </span>            :   //</a>
+<a name="137"><span class="lineNum">     137 </span>            : };</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">      12508 : PLUMED_REGISTER_ACTION(TD_ProductCombination,&quot;TD_PRODUCT_COMBINATION&quot;)</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">          6 : void TD_ProductCombination::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          6 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;DISTRIBUTIONS&quot;,&quot;The labels of the target distribution actions to be used in the product combination.&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">          6 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          6 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          6 : }</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          4 : TD_ProductCombination::TD_ProductCombination(const ActionOptions&amp; ao):</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          8 :   distribution_pntrs_(0),</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">          4 :   grid_pntrs_(0),</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">          8 :   ndist_(0)</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : {</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;std::string&gt; targetdist_labels;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          4 :   parseVector(&quot;DISTRIBUTIONS&quot;,targetdist_labels);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          4 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          8 :   distribution_pntrs_ = VesTools::getPointersFromLabels&lt;TargetDistribution*&gt;(targetdist_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">          4 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword DISTRIBUTIONS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         12 :   for(unsigned int i=0; i&lt;distribution_pntrs_.size(); i++) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">          8 :     if(distribution_pntrs_[i]-&gt;isDynamic()) {setDynamic();}</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">          8 :     if(distribution_pntrs_[i]-&gt;fesGridNeeded()) {setFesGridNeeded();}</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">          8 :     if(distribution_pntrs_[i]-&gt;biasGridNeeded()) {setBiasGridNeeded();}</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          4 :   ndist_ = distribution_pntrs_.size();</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          4 :   grid_pntrs_.assign(ndist_,NULL);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">          4 :   if(ndist_==0) {plumed_merror(getName()+ &quot;: no distributions are given.&quot;);}</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          4 :   if(ndist_==1) {plumed_merror(getName()+ &quot;: giving only one distribution does not make sense.&quot;);}</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   //</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">          4 : }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : </a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 : double TD_ProductCombination::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_ProductCombination&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   return 0.0;</a>
+<a name="182"><span class="lineNum">     182 </span>            : }</a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">          4 : void TD_ProductCombination::setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp; arguments, const std::vector&lt;std::string&gt;&amp; min, const std::vector&lt;std::string&gt;&amp; max, const std::vector&lt;unsigned int&gt;&amp; nbins) {</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         12 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">          8 :     distribution_pntrs_[i]-&gt;setupGrids(arguments,min,max,nbins);</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          8 :     if(distribution_pntrs_[i]-&gt;getDimension()!=this-&gt;getDimension()) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :       plumed_merror(getName() + &quot;: all target distribution must have the same dimension&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span>            :     }</a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">          8 :     grid_pntrs_[i]=distribution_pntrs_[i]-&gt;getTargetDistGridPntr();</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :   }</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">          4 : }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         14 : void TD_ProductCombination::updateGrid() {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         42 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         28 :     distribution_pntrs_[i]-&gt;updateTargetDist();</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         28 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :   double norm = 0.0;</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">      11717 :   for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :     double value = 1.0;</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">      35109 :     for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">      23406 :       value *= grid_pntrs_[i]-&gt;getValue(l);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :     }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      11703 :     if(value&lt;0.0 &amp;&amp; !isTargetDistGridShiftedToZero()) {plumed_merror(getName()+&quot;: The target distribution function gives negative values. You should change the definition of the target distribution to avoid this. You can also use the SHIFT_TO_ZERO keyword to avoid this problem.&quot;);}</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">      11703 :     norm += integration_weights[l]*value;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      11703 :     targetDistGrid().setValue(l,value);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      11703 :     logTargetDistGrid().setValue(l,-std::log(value));</span></a>
+<a name="211"><span class="lineNum">     211 </span>            :   }</a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         14 :   if(norm&gt;0.0) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         14 :     targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 :   else if(!isTargetDistGridShiftedToZero()) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: The target distribution function cannot be normalized proberly. You should change the definition of the target distribution to avoid this. You can also use the SHIFT_TO_ZERO keyword to avoid this problem.&quot;);</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   }</a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         14 :   logTargetDistGrid().setMinToZero();</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         14 : }</span></a>
+<a name="221"><span class="lineNum">     221 </span>            : </a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          1 : void TD_ProductCombination::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          1 :   TargetDistribution::linkVesBias(vesbias_pntr_in);</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          3 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          2 :     distribution_pntrs_[i]-&gt;linkVesBias(vesbias_pntr_in);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          1 : }</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineNoCov">          0 : void TD_ProductCombination::linkAction(Action* action_pntr_in) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineNoCov">          0 :   TargetDistribution::linkAction(action_pntr_in);</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkAction(action_pntr_in);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   }</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineNoCov">          0 : void TD_ProductCombination::linkBiasGrid(Grid* bias_grid_pntr_in) {</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineNoCov">          0 :   TargetDistribution::linkBiasGrid(bias_grid_pntr_in);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkBiasGrid(bias_grid_pntr_in);</span></a>
+<a name="243"><span class="lineNum">     243 </span>            :   }</a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : </a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineNoCov">          0 : void TD_ProductCombination::linkBiasWithoutCutoffGrid(Grid* bias_withoutcutoff_grid_pntr_in) {</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineNoCov">          0 :   TargetDistribution::linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_in);</span></a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_in);</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : </a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">          1 : void TD_ProductCombination::linkFesGrid(Grid* fes_grid_pntr_in) {</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          1 :   TargetDistribution::linkFesGrid(fes_grid_pntr_in);</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">          3 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          2 :     distribution_pntrs_[i]-&gt;linkFesGrid(fes_grid_pntr_in);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">          1 : }</span></a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span>            : </a>
+<a name="263"><span class="lineNum">     263 </span>            : }</a>
+<a name="264"><span class="lineNum">     264 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ProductDistribution.cpp.func-sort-c.html b/coverage/ves/TD_ProductDistribution.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d790d71b22
--- /dev/null
+++ b/coverage/ves/TD_ProductDistribution.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ProductDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ProductDistribution.cpp<span style="font-size: 80%;"> (<a href="TD_ProductDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryLo">63.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">53.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_ProductDistribution.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#190">_ZN4PLMD3ves22TD_ProductDistribution10linkActionEPNS_6ActionE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#214">_ZN4PLMD3ves22TD_ProductDistribution11linkFesGridEPNS_4GridE</a></td>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#182">_ZN4PLMD3ves22TD_ProductDistribution11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#198">_ZN4PLMD3ves22TD_ProductDistribution12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#206">_ZN4PLMD3ves22TD_ProductDistribution25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#140">_ZNK4PLMD3ves22TD_ProductDistribution8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#101">_ZN4PLMD3ves12_GLOBAL__N_135TD_ProductDistributionRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#165">_ZN4PLMD3ves22TD_ProductDistribution10updateGridEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#146">_ZN4PLMD3ves22TD_ProductDistribution20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#113">_ZN4PLMD3ves22TD_ProductDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#104">_ZN4PLMD3ves22TD_ProductDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#101">_ZN4PLMD3ves12_GLOBAL__N_135TD_ProductDistributionRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#101">_ZN4PLMD3ves12_GLOBAL__N_135TD_ProductDistributionRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ProductDistribution.cpp.func.html b/coverage/ves/TD_ProductDistribution.cpp.func.html
new file mode 100644
index 0000000000..03b3a4c2da
--- /dev/null
+++ b/coverage/ves/TD_ProductDistribution.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ProductDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ProductDistribution.cpp<span style="font-size: 80%;"> (<a href="TD_ProductDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryLo">63.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">53.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_ProductDistribution.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#101">_ZN4PLMD3ves12_GLOBAL__N_135TD_ProductDistributionRegisterMe1036createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#101">_ZN4PLMD3ves12_GLOBAL__N_135TD_ProductDistributionRegisterMe103C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#101">_ZN4PLMD3ves12_GLOBAL__N_135TD_ProductDistributionRegisterMe103D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#190">_ZN4PLMD3ves22TD_ProductDistribution10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#165">_ZN4PLMD3ves22TD_ProductDistribution10updateGridEv</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#214">_ZN4PLMD3ves22TD_ProductDistribution11linkFesGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#182">_ZN4PLMD3ves22TD_ProductDistribution11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#198">_ZN4PLMD3ves22TD_ProductDistribution12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#104">_ZN4PLMD3ves22TD_ProductDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#146">_ZN4PLMD3ves22TD_ProductDistribution20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#206">_ZN4PLMD3ves22TD_ProductDistribution25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#113">_ZN4PLMD3ves22TD_ProductDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">15</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_ProductDistribution.cpp.gcov.html#140">_ZNK4PLMD3ves22TD_ProductDistribution8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_ProductDistribution.cpp.gcov.html b/coverage/ves/TD_ProductDistribution.cpp.gcov.html
new file mode 100644
index 0000000000..0e95e948ec
--- /dev/null
+++ b/coverage/ves/TD_ProductDistribution.cpp.gcov.html
@@ -0,0 +1,301 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_ProductDistribution.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_ProductDistribution.cpp<span style="font-size: 80%;"> (source / <a href="TD_ProductDistribution.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">49</td>
+            <td class="headerCovTableEntry">77</td>
+            <td class="headerCovTableEntryLo">63.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryLo">53.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace ves {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : //+PLUMEDOC VES_TARGETDIST TD_PRODUCT_DISTRIBUTION</a>
+<a name="35"><span class="lineNum">      35 </span>            : /*</a>
+<a name="36"><span class="lineNum">      36 </span>            : Target distribution given by a separable product of one-dimensional distributions (static or dynamic).</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : Employ a target distribution that is a separable product</a>
+<a name="39"><span class="lineNum">      39 </span>            : of one-dimensional distributions, defined as</a>
+<a name="40"><span class="lineNum">      40 </span>            : \f[</a>
+<a name="41"><span class="lineNum">      41 </span>            : p(\mathbf{s}) =</a>
+<a name="42"><span class="lineNum">      42 </span>            : \prod_{k}^{d} p_{k}(s_{k})</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f]</a>
+<a name="44"><span class="lineNum">      44 </span>            : where \f$d\f$ is the number of arguments used and \f$p_{k}(s_{k})\f$ is the</a>
+<a name="45"><span class="lineNum">      45 </span>            : one-dimensional distribution corresponding to the \f$k\f$-th argument.</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : Note the difference between this target distribution and the one defined in</a>
+<a name="48"><span class="lineNum">      48 </span>            : \ref TD_PRODUCT_COMBINATION. Here we have a separable distribution given as a</a>
+<a name="49"><span class="lineNum">      49 </span>            : product of one-dimensional distribution \f$p_{k}(s_{k})\f$.</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : The labels of the one-dimensional distributions \f$p_{k}(s_{k})\f$ to be</a>
+<a name="52"><span class="lineNum">      52 </span>            : used in the product distribution are given in the DISTRIBUTIONS keyword.</a>
+<a name="53"><span class="lineNum">      53 </span>            : Note that the order of the labels is very important.</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : It is assumed that all the distributions to be used in the product distribution</a>
+<a name="56"><span class="lineNum">      56 </span>            : are normalized. If that is not the case you need to</a>
+<a name="57"><span class="lineNum">      57 </span>            : normalize the distributions by using the NORMALIZE keyword.</a>
+<a name="58"><span class="lineNum">      58 </span>            : Here it does not matter if you normalize each distribution separately</a>
+<a name="59"><span class="lineNum">      59 </span>            : or the overall product, it will give the same results.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : The product distribution will be a dynamic target distribution if one or more</a>
+<a name="62"><span class="lineNum">      62 </span>            : of the distributions used is a dynamic distribution. Otherwise it will be a</a>
+<a name="63"><span class="lineNum">      63 </span>            : static distribution.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : \par Examples</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : In the following example we employ a uniform distribution for</a>
+<a name="68"><span class="lineNum">      68 </span>            : argument 1 and a Gaussian distribution for argument 2.</a>
+<a name="69"><span class="lineNum">      69 </span>            : \plumedfile</a>
+<a name="70"><span class="lineNum">      70 </span>            : target_uniform: TD_UNIFORM</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : target_Gaussian: TD_GAUSSIAN CENTER1=-2.0 SIGMA1=0.5</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : td_pd: TD_PRODUCT_DISTRIBUTION DISTRIBUTIONS=target_uniform,target_Gaussian</a>
+<a name="75"><span class="lineNum">      75 </span>            : \endplumedfile</a>
+<a name="76"><span class="lineNum">      76 </span>            : Note that order of the labels is important, using DISTRIBUTIONS=target_Gaussian,target_uniform</a>
+<a name="77"><span class="lineNum">      77 </span>            : would mean that we would employ a Gaussian distribution for argument 1 and a uniform</a>
+<a name="78"><span class="lineNum">      78 </span>            : distribution for argument 2, which would lead to completely different results.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : */</a>
+<a name="81"><span class="lineNum">      81 </span>            : //+ENDPLUMEDOC</a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : class TD_ProductDistribution: public TargetDistribution {</a>
+<a name="84"><span class="lineNum">      84 </span>            : private:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;TargetDistribution*&gt; distribution_pntrs_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   std::vector&lt;Grid*&gt; grid_pntrs_;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned int ndist_;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   void setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) override;</a>
+<a name="89"><span class="lineNum">      89 </span>            : public:</a>
+<a name="90"><span class="lineNum">      90 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="91"><span class="lineNum">      91 </span>            :   explicit TD_ProductDistribution(const ActionOptions&amp; ao);</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void updateGrid() override;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="94"><span class="lineNum">      94 </span>            :   //</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void linkVesBias(VesBias*) override;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   void linkAction(Action*) override;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   void linkBiasGrid(Grid*) override;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void linkBiasWithoutCutoffGrid(Grid*) override;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   void linkFesGrid(Grid*) override;</a>
+<a name="100"><span class="lineNum">     100 </span>            : };</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">      12519 : PLUMED_REGISTER_ACTION(TD_ProductDistribution,&quot;TD_PRODUCT_DISTRIBUTION&quot;)</span></a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+<a name="105"><span class="lineNum">     105 </span>            : </a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         17 : void TD_ProductDistribution::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         17 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         34 :   keys.add(&quot;compulsory&quot;,&quot;DISTRIBUTIONS&quot;,&quot;Labels of the one-dimensional target distribution actions for each argument to be used in the product distribution. Note that order of the labels is important.&quot;);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         17 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         17 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         17 :   keys.use(&quot;NORMALIZE&quot;);</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         17 : }</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         15 : TD_ProductDistribution::TD_ProductDistribution(const ActionOptions&amp; ao):</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         30 :   distribution_pntrs_(0),</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         15 :   grid_pntrs_(0),</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         30 :   ndist_(0)</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : {</a>
+<a name="121"><span class="lineNum">     121 </span>            :   std::vector&lt;std::string&gt; targetdist_labels;</a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         15 :   parseVector(&quot;DISTRIBUTIONS&quot;,targetdist_labels);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         15 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         30 :   distribution_pntrs_ = VesTools::getPointersFromLabels&lt;TargetDistribution*&gt;(targetdist_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         15 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword DISTRIBUTIONS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         45 :   for(unsigned int i=0; i&lt;distribution_pntrs_.size(); i++) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         30 :     if(distribution_pntrs_[i]-&gt;isDynamic()) {setDynamic();}</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         30 :     if(distribution_pntrs_[i]-&gt;fesGridNeeded()) {setFesGridNeeded();}</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         30 :     if(distribution_pntrs_[i]-&gt;biasGridNeeded()) {setBiasGridNeeded();}</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :   }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         15 :   ndist_ = distribution_pntrs_.size();</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">         15 :   grid_pntrs_.assign(ndist_,NULL);</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         15 :   setDimension(ndist_);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         15 :   checkRead();</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         15 : }</span></a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 : double TD_ProductDistribution::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_ProductDistribution&quot;);</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   return 0.0;</a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">         15 : void TD_ProductDistribution::setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp; arguments, const std::vector&lt;std::string&gt;&amp; min, const std::vector&lt;std::string&gt;&amp; max, const std::vector&lt;unsigned int&gt;&amp; nbins) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">         45 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         30 :     std::vector&lt;Value*&gt; arg1d(1);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         30 :     std::vector&lt;std::string&gt; min1d(1);</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">         30 :     std::vector&lt;std::string&gt; max1d(1);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         30 :     std::vector&lt;unsigned int&gt; nbins1d(1);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">         30 :     arg1d[0]=arguments[i];</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     min1d[0]=min[i];</a>
+<a name="156"><span class="lineNum">     156 </span>            :     max1d[0]=max[i];</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         30 :     nbins1d[0]=nbins[i];</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         30 :     distribution_pntrs_[i]-&gt;setupGrids(arg1d,min1d,max1d,nbins1d);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">         30 :     grid_pntrs_[i]=distribution_pntrs_[i]-&gt;getTargetDistGridPntr();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         30 :     if(distribution_pntrs_[i]-&gt;getDimension()!=1 || grid_pntrs_[i]-&gt;getDimension()!=1) {</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineNoCov">          0 :       plumed_merror(getName() + &quot;: all target distributions must be one dimensional&quot;);</span></a>
+<a name="162"><span class="lineNum">     162 </span>            :     }</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         30 :   }</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         15 : }</span></a>
+<a name="165"><span class="lineNum">     165 </span>            : </a>
+<a name="166"><span class="lineNum">     166 </span>            : </a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         15 : void TD_ProductDistribution::updateGrid() {</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         45 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         30 :     distribution_pntrs_[i]-&gt;updateTargetDist();</span></a>
+<a name="170"><span class="lineNum">     170 </span>            :   }</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">     153030 :   for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">     153015 :     std::vector&lt;unsigned int&gt; indices = targetDistGrid().getIndices(l);</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :     double value = 1.0;</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">     459045 :     for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">     306030 :       value *= grid_pntrs_[i]-&gt;getValue(indices[i]);</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :     }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     153015 :     targetDistGrid().setValue(l,value);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     153015 :     logTargetDistGrid().setValue(l,-std::log(value));</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   }</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         15 :   logTargetDistGrid().setMinToZero();</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         15 : }</span></a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 : void TD_ProductDistribution::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineNoCov">          0 :   TargetDistribution::linkVesBias(vesbias_pntr_in);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkVesBias(vesbias_pntr_in);</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineNoCov">          0 : void TD_ProductDistribution::linkAction(Action* action_pntr_in) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :   TargetDistribution::linkAction(action_pntr_in);</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkAction(action_pntr_in);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineNoCov">          0 : void TD_ProductDistribution::linkBiasGrid(Grid* bias_grid_pntr_in) {</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineNoCov">          0 :   TargetDistribution::linkBiasGrid(bias_grid_pntr_in);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkBiasGrid(bias_grid_pntr_in);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 : void TD_ProductDistribution::linkBiasWithoutCutoffGrid(Grid* bias_withoutcutoff_grid_pntr_in) {</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineNoCov">          0 :   TargetDistribution::linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_in);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkBiasWithoutCutoffGrid(bias_withoutcutoff_grid_pntr_in);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   }</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineNoCov">          0 : void TD_ProductDistribution::linkFesGrid(Grid* fes_grid_pntr_in) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :   TargetDistribution::linkFesGrid(fes_grid_pntr_in);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :   for(unsigned int i=0; i&lt;ndist_; i++) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :     distribution_pntrs_[i]-&gt;linkFesGrid(fes_grid_pntr_in);</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   }</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span>            : }</a>
+<a name="225"><span class="lineNum">     225 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Uniform.cpp.func-sort-c.html b/coverage/ves/TD_Uniform.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a840b67601
--- /dev/null
+++ b/coverage/ves/TD_Uniform.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_Uniform.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Uniform.cpp<span style="font-size: 80%;"> (<a href="TD_Uniform.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">98.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_Uniform.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#252">_ZN4PLMD3ves10TD_Uniform20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#204">_ZN4PLMD3ves10TD_UniformC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#192">_ZN4PLMD3ves12_GLOBAL__N_123TD_UniformRegisterMe1946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#195">_ZN4PLMD3ves10TD_Uniform16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">75</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#192">_ZN4PLMD3ves12_GLOBAL__N_123TD_UniformRegisterMe194C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#192">_ZN4PLMD3ves12_GLOBAL__N_123TD_UniformRegisterMe194D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#267">_ZNK4PLMD3ves10TD_Uniform8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">118654</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_Uniform.cpp.func.html b/coverage/ves/TD_Uniform.cpp.func.html
new file mode 100644
index 0000000000..a1d97fb282
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Uniform.cpp<span style="font-size: 80%;"> (<a href="TD_Uniform.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">98.2 %</td>
+          </tr>
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+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
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+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_Uniform.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#195">_ZN4PLMD3ves10TD_Uniform16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">75</td>
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+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#252">_ZN4PLMD3ves10TD_Uniform20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#204">_ZN4PLMD3ves10TD_UniformC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#192">_ZN4PLMD3ves12_GLOBAL__N_123TD_UniformRegisterMe1946createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#192">_ZN4PLMD3ves12_GLOBAL__N_123TD_UniformRegisterMe194C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#192">_ZN4PLMD3ves12_GLOBAL__N_123TD_UniformRegisterMe194D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_Uniform.cpp.gcov.html#267">_ZNK4PLMD3ves10TD_Uniform8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">118654</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/ves/TD_Uniform.cpp.gcov.html b/coverage/ves/TD_Uniform.cpp.gcov.html
new file mode 100644
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
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+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+    <tr>
+      <td width="100%">
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+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_Uniform.cpp<span style="font-size: 80%;"> (source / <a href="TD_Uniform.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">55</td>
+            <td class="headerCovTableEntry">56</td>
+            <td class="headerCovTableEntryHi">98.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : //+PLUMEDOC VES_TARGETDIST TD_UNIFORM</a>
+<a name="32"><span class="lineNum">      32 </span>            : /*</a>
+<a name="33"><span class="lineNum">      33 </span>            : Uniform target distribution (static).</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : Using this keyword you can define a uniform target distribution which is a</a>
+<a name="36"><span class="lineNum">      36 </span>            : product of one-dimensional distributions \f$p_{k}(s_{k})\f$ that are uniform</a>
+<a name="37"><span class="lineNum">      37 </span>            : over a given interval \f$[a_{k},b_{k}]\f$</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : \f[</a>
+<a name="40"><span class="lineNum">      40 </span>            : p_{k}(s_{k}) =</a>
+<a name="41"><span class="lineNum">      41 </span>            : \left \{\begin{array}{ll}</a>
+<a name="42"><span class="lineNum">      42 </span>            : \frac{1}{(b_{k}-a_{k})} &amp; \mathrm{if} \ a_{k} \leq s_{k} \leq b_{k} \\</a>
+<a name="43"><span class="lineNum">      43 </span>            : &amp;\\</a>
+<a name="44"><span class="lineNum">      44 </span>            : 0 &amp; \mathrm{otherwise}</a>
+<a name="45"><span class="lineNum">      45 </span>            : \end{array}\right .</a>
+<a name="46"><span class="lineNum">      46 </span>            : \f]</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : The overall distribution is then given as</a>
+<a name="49"><span class="lineNum">      49 </span>            : \f[</a>
+<a name="50"><span class="lineNum">      50 </span>            : p(\mathbf{s}) =</a>
+<a name="51"><span class="lineNum">      51 </span>            : \prod^{d}_{k} p_{k}(s_{k}) =</a>
+<a name="52"><span class="lineNum">      52 </span>            : \left\{\begin{array}{ll}</a>
+<a name="53"><span class="lineNum">      53 </span>            : \prod^{d}_{k} \frac{1}{(b_{k}-a_{k})}</a>
+<a name="54"><span class="lineNum">      54 </span>            : &amp; \mathrm{if} \ a_{k} \leq s_{k} \leq b_{k} \ \mathrm{for\ all}\ k \\</a>
+<a name="55"><span class="lineNum">      55 </span>            : \\</a>
+<a name="56"><span class="lineNum">      56 </span>            : 0 &amp; \mathrm{otherwise}</a>
+<a name="57"><span class="lineNum">      57 </span>            : \end{array}\right.</a>
+<a name="58"><span class="lineNum">      58 </span>            : \f]</a>
+<a name="59"><span class="lineNum">      59 </span>            : The distribution is thus uniform inside a rectangular for two arguments</a>
+<a name="60"><span class="lineNum">      60 </span>            : and a cube for a three arguments.</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : The limits of the intervals \f$ a_{k}\f$ and \f$ b_{k}\f$ are given</a>
+<a name="63"><span class="lineNum">      63 </span>            : with the MINIMA and MAXIMA keywords, respectively. If one or both of</a>
+<a name="64"><span class="lineNum">      64 </span>            : these keywords are missing the code should automatically detect the limits.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : It is also possible to use one-dimensional distributions</a>
+<a name="68"><span class="lineNum">      68 </span>            : that go smoothly to zero at the boundaries.</a>
+<a name="69"><span class="lineNum">      69 </span>            : This is done by employing a function with</a>
+<a name="70"><span class="lineNum">      70 </span>            : Gaussian switching functions at the boundaries \f$a_{k}\f$ and \f$b_{k}\f$</a>
+<a name="71"><span class="lineNum">      71 </span>            : \f[</a>
+<a name="72"><span class="lineNum">      72 </span>            : f_{k}(s_{k}) =</a>
+<a name="73"><span class="lineNum">      73 </span>            : \begin{cases}</a>
+<a name="74"><span class="lineNum">      74 </span>            : \exp\left(-\frac{(s_{k}-a_{k})^2}{2 \sigma^2_{a,k}}\right)</a>
+<a name="75"><span class="lineNum">      75 </span>            : &amp; \mathrm{if}\, s_{k} &lt; a_{k} \\</a>
+<a name="76"><span class="lineNum">      76 </span>            : \\</a>
+<a name="77"><span class="lineNum">      77 </span>            : 1 &amp; \mathrm{if}\, a_{k} \leq s_{k} \leq b_{k} \\</a>
+<a name="78"><span class="lineNum">      78 </span>            : \\</a>
+<a name="79"><span class="lineNum">      79 </span>            : \exp\left(-\frac{(s_{k}-b_{k})^2}{2 \sigma^2_{b,k}}\right)</a>
+<a name="80"><span class="lineNum">      80 </span>            : &amp; \mathrm{if}\, s_{k} &gt; b_{k}</a>
+<a name="81"><span class="lineNum">      81 </span>            : \end{cases}</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f]</a>
+<a name="83"><span class="lineNum">      83 </span>            : where the standard deviation parameters \f$\sigma_{a,k}\f$</a>
+<a name="84"><span class="lineNum">      84 </span>            : and \f$\sigma_{b,k}\f$ determine how quickly the switching functions</a>
+<a name="85"><span class="lineNum">      85 </span>            : goes to zero.</a>
+<a name="86"><span class="lineNum">      86 </span>            : The overall distribution is then normalized</a>
+<a name="87"><span class="lineNum">      87 </span>            : \f[</a>
+<a name="88"><span class="lineNum">      88 </span>            : p(\mathbf{s}) =</a>
+<a name="89"><span class="lineNum">      89 </span>            : \prod^{d}_{k} p_{k}(s_{k}) =</a>
+<a name="90"><span class="lineNum">      90 </span>            : \prod^{d}_{k} \frac{f(s_{k})}{\int d s_{k} \, f(s_{k})}</a>
+<a name="91"><span class="lineNum">      91 </span>            : \f]</a>
+<a name="92"><span class="lineNum">      92 </span>            : To use this option you need to provide the standard deviation</a>
+<a name="93"><span class="lineNum">      93 </span>            : parameters \f$\sigma_{a,k}\f$ and \f$\sigma_{b,k}\f$ by using the</a>
+<a name="94"><span class="lineNum">      94 </span>            : SIGMA_MINIMA and SIGMA_MAXIMA keywords, respectively. Giving a value of</a>
+<a name="95"><span class="lineNum">      95 </span>            : 0.0 means that the boundary is sharp, which is the default behavior.</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : \par Examples</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            : If one or both of the MINIMA or MAXIMA keywords are missing</a>
+<a name="105"><span class="lineNum">     105 </span>            : the code should automatically detect the limits not given.</a>
+<a name="106"><span class="lineNum">     106 </span>            : Therefore, if we consider a target distribution that is</a>
+<a name="107"><span class="lineNum">     107 </span>            : defined over an interval from 0.0 to 10.0 for the first</a>
+<a name="108"><span class="lineNum">     108 </span>            : argument and from 0.2 to 1.0 for the second argument are</a>
+<a name="109"><span class="lineNum">     109 </span>            : the following example</a>
+<a name="110"><span class="lineNum">     110 </span>            : \plumedfile</a>
+<a name="111"><span class="lineNum">     111 </span>            : td: TD_UNIFORM</a>
+<a name="112"><span class="lineNum">     112 </span>            : \endplumedfile</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : is equivalent to this one</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : \plumedfile</a>
+<a name="117"><span class="lineNum">     117 </span>            : TD_UNIFORM ...</a>
+<a name="118"><span class="lineNum">     118 </span>            :  MINIMA=0.0,0.2</a>
+<a name="119"><span class="lineNum">     119 </span>            :  MAXIMA=10.0,1.0</a>
+<a name="120"><span class="lineNum">     120 </span>            :  LABEL=td</a>
+<a name="121"><span class="lineNum">     121 </span>            :  ... TD_UNIFORM</a>
+<a name="122"><span class="lineNum">     122 </span>            : \endplumedfile</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : and this one</a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : \plumedfile</a>
+<a name="127"><span class="lineNum">     127 </span>            : td: TD_UNIFORM  MAXIMA=10.0,1.0</a>
+<a name="128"><span class="lineNum">     128 </span>            : \endplumedfile</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span>            : and also this one</a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span>            : \plumedfile</a>
+<a name="133"><span class="lineNum">     133 </span>            : td: TD_UNIFORM MINIMA=0.0,0,2</a>
+<a name="134"><span class="lineNum">     134 </span>            : \endplumedfile</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : We can also define a target distribution that goes smoothly to zero</a>
+<a name="138"><span class="lineNum">     138 </span>            : at the boundaries of the uniform distribution. In the following</a>
+<a name="139"><span class="lineNum">     139 </span>            : we consider an interval of 0 to 10 for the target distribution.</a>
+<a name="140"><span class="lineNum">     140 </span>            : The following input would result in a target distribution that</a>
+<a name="141"><span class="lineNum">     141 </span>            : would be uniform from 2 to 7 and then smoothly go to zero from</a>
+<a name="142"><span class="lineNum">     142 </span>            : 2 to 0 and from 7 to 10.</a>
+<a name="143"><span class="lineNum">     143 </span>            : \plumedfile</a>
+<a name="144"><span class="lineNum">     144 </span>            : TD_UNIFORM ...</a>
+<a name="145"><span class="lineNum">     145 </span>            :  MINIMA=2.0</a>
+<a name="146"><span class="lineNum">     146 </span>            :  MAXIMA=+7.0</a>
+<a name="147"><span class="lineNum">     147 </span>            :  SIGMA_MINIMA=0.5</a>
+<a name="148"><span class="lineNum">     148 </span>            :  SIGMA_MAXIMA=1.0</a>
+<a name="149"><span class="lineNum">     149 </span>            :  LABEL=td</a>
+<a name="150"><span class="lineNum">     150 </span>            : ... TD_UNIFORM</a>
+<a name="151"><span class="lineNum">     151 </span>            : \endplumedfile</a>
+<a name="152"><span class="lineNum">     152 </span>            : It is also possible to employ a smooth switching function for just one</a>
+<a name="153"><span class="lineNum">     153 </span>            : of the boundaries as shown here where the target distribution</a>
+<a name="154"><span class="lineNum">     154 </span>            : would be uniform from 0 to 7 and then smoothly go to zero from 7 to 10.</a>
+<a name="155"><span class="lineNum">     155 </span>            : \plumedfile</a>
+<a name="156"><span class="lineNum">     156 </span>            : TD_UNIFORM ...</a>
+<a name="157"><span class="lineNum">     157 </span>            :  MAXIMA=+7.0</a>
+<a name="158"><span class="lineNum">     158 </span>            :  SIGMA_MAXIMA=1.0</a>
+<a name="159"><span class="lineNum">     159 </span>            :  LABEL=td</a>
+<a name="160"><span class="lineNum">     160 </span>            : ... TD_UNIFORM</a>
+<a name="161"><span class="lineNum">     161 </span>            : \endplumedfile</a>
+<a name="162"><span class="lineNum">     162 </span>            : Furthermore, it is possible to employ a sharp boundary by</a>
+<a name="163"><span class="lineNum">     163 </span>            : using</a>
+<a name="164"><span class="lineNum">     164 </span>            : \plumedfile</a>
+<a name="165"><span class="lineNum">     165 </span>            : TD_UNIFORM ...</a>
+<a name="166"><span class="lineNum">     166 </span>            :  MAXIMA=+7.0</a>
+<a name="167"><span class="lineNum">     167 </span>            :  SIGMA_MAXIMA=0.0</a>
+<a name="168"><span class="lineNum">     168 </span>            :  LABEL=td</a>
+<a name="169"><span class="lineNum">     169 </span>            : ... TD_UNIFORM</a>
+<a name="170"><span class="lineNum">     170 </span>            : \endplumedfile</a>
+<a name="171"><span class="lineNum">     171 </span>            : or</a>
+<a name="172"><span class="lineNum">     172 </span>            : \plumedfile</a>
+<a name="173"><span class="lineNum">     173 </span>            : td: TD_UNIFORM MAXIMA=+7.0</a>
+<a name="174"><span class="lineNum">     174 </span>            : \endplumedfile</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : */</a>
+<a name="178"><span class="lineNum">     178 </span>            : //+ENDPLUMEDOC</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span>            : class TD_Uniform : public TargetDistribution {</a>
+<a name="181"><span class="lineNum">     181 </span>            :   std::vector&lt;double&gt; minima_;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   std::vector&lt;double&gt; maxima_;</a>
+<a name="183"><span class="lineNum">     183 </span>            :   std::vector&lt;double&gt; sigma_min_;</a>
+<a name="184"><span class="lineNum">     184 </span>            :   std::vector&lt;double&gt; sigma_max_;</a>
+<a name="185"><span class="lineNum">     185 </span>            :   double GaussianSwitchingFunc(const double, const double, const double) const;</a>
+<a name="186"><span class="lineNum">     186 </span>            :   void setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) override;</a>
+<a name="187"><span class="lineNum">     187 </span>            : public:</a>
+<a name="188"><span class="lineNum">     188 </span>            :   static void registerKeywords( Keywords&amp;);</a>
+<a name="189"><span class="lineNum">     189 </span>            :   explicit TD_Uniform(const ActionOptions&amp; ao);</a>
+<a name="190"><span class="lineNum">     190 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="191"><span class="lineNum">     191 </span>            : };</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      12577 : PLUMED_REGISTER_ACTION(TD_Uniform,&quot;TD_UNIFORM&quot;)</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         75 : void TD_Uniform::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         75 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        150 :   keys.add(&quot;optional&quot;,&quot;MINIMA&quot;,&quot;The minimum of the intervals where the target distribution is taken as uniform. You should give one value for each argument.&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        150 :   keys.add(&quot;optional&quot;,&quot;MAXIMA&quot;,&quot;The maximum of the intervals where the target distribution is taken as uniform. You should give one value for each argument.&quot;);</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        150 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MINIMA&quot;,&quot;The standard deviation parameters of the Gaussian switching functions for the minima of the intervals. You should give one value for each argument. Value of 0.0 means that switch is done without a smooth switching function, this is the default behavior.&quot;);</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">        150 :   keys.add(&quot;optional&quot;,&quot;SIGMA_MAXIMA&quot;,&quot;The standard deviation parameters of the Gaussian switching functions for the maximum of the intervals. You should give one value for each argument. Value of 0.0 means that switch is done without a smooth switching function, this is the default behavior.&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         75 : }</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         73 : TD_Uniform::TD_Uniform(const ActionOptions&amp; ao):</span></a>
+<a name="207"><span class="lineNum">     207 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        146 :   minima_(0),</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         73 :   maxima_(0),</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         73 :   sigma_min_(0),</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">        146 :   sigma_max_(0)</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : {</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         73 :   parseVector(&quot;MINIMA&quot;,minima_);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         73 :   parseVector(&quot;MAXIMA&quot;,maxima_);</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         73 :   parseVector(&quot;SIGMA_MINIMA&quot;,sigma_min_);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">        146 :   parseVector(&quot;SIGMA_MAXIMA&quot;,sigma_max_);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         73 :   if(minima_.size()==0 &amp;&amp; sigma_min_.size()&gt;0) {plumed_merror(getName()+&quot;: you cannot give SIGMA_MINIMA if MINIMA is not given&quot;);}</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         73 :   if(maxima_.size()==0 &amp;&amp; sigma_max_.size()&gt;0) {plumed_merror(getName()+&quot;: you cannot give SIGMA_MAXIMA if MAXIMA is not given&quot;);}</span></a>
+<a name="220"><span class="lineNum">     220 </span>            : </a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">         73 :   if(minima_.size()&gt;0 &amp;&amp; maxima_.size()&gt;0) {</span></a>
+<a name="222"><span class="lineNum">     222 </span>            :     // both MINIMA and MAXIMA given, do all checks</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">         58 :     if(minima_.size()!=maxima_.size()) {plumed_merror(getName()+&quot;: MINIMA and MAXIMA do not have the same number of values.&quot;);}</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">         58 :     setDimension(minima_.size());</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        122 :     for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         64 :       if(minima_[k]&gt;maxima_[k]) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :         plumed_merror(getName()+&quot;: error in MINIMA and MAXIMA keywords, one of the MINIMA values is larger than the corresponding MAXIMA values&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :       }</a>
+<a name="229"><span class="lineNum">     229 </span>            :     }</a>
+<a name="230"><span class="lineNum">     230 </span>            :   }</a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         15 :   else if(minima_.size()&gt;0 &amp;&amp; maxima_.size()==0) {</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :     // only MINIMA given, MAXIMA assigned later on.</a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">          1 :     setDimension(minima_.size());</span></a>
+<a name="234"><span class="lineNum">     234 </span>            :   }</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">         14 :   else if(maxima_.size()&gt;0 &amp;&amp; minima_.size()==0) {</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :     // only MAXIMA given, MINIMA assigned later on.</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          1 :     setDimension(maxima_.size());</span></a>
+<a name="238"><span class="lineNum">     238 </span>            :   }</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         13 :   else if(maxima_.size()==0 &amp;&amp; minima_.size()==0) {</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :     // neither MAXIMA nor MINIMA givenm, both assigned later on.</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         13 :     setDimension(0);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            :   }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">         73 :   if(sigma_min_.size()==0) {sigma_min_.assign(getDimension(),0.0);}</span></a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         73 :   if(sigma_max_.size()==0) {sigma_max_.assign(getDimension(),0.0);}</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         73 :   if(sigma_min_.size()!=getDimension()) {plumed_merror(getName()+&quot;: SIGMA_MINIMA has the wrong number of values&quot;);}</span></a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">         73 :   if(sigma_max_.size()!=getDimension()) {plumed_merror(getName()+&quot;: SIGMA_MAXIMA has the wrong number of values&quot;);}</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   //</a>
+<a name="249"><span class="lineNum">     249 </span>            :   setForcedNormalization();</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">         73 :   checkRead();</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">         73 : }</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">         73 : void TD_Uniform::setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp; arguments, const std::vector&lt;std::string&gt;&amp; min, const std::vector&lt;std::string&gt;&amp; max, const std::vector&lt;unsigned int&gt;&amp; nbins) {</span></a>
+<a name="255"><span class="lineNum">     255 </span>            : </a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">         73 :   if(minima_.size()==0) {</span></a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">         14 :     minima_.assign(getDimension(),0.0);</span></a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">         33 :     for(unsigned int k=0; k&lt;getDimension(); k++) {Tools::convert(min[k],minima_[k]);}</span></a>
+<a name="259"><span class="lineNum">     259 </span>            :   }</a>
+<a name="260"><span class="lineNum">     260 </span>            : </a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">         73 :   if(maxima_.size()==0) {</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         14 :     maxima_.assign(getDimension(),0.0);</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         33 :     for(unsigned int k=0; k&lt;getDimension(); k++) {Tools::convert(max[k],maxima_[k]);}</span></a>
+<a name="264"><span class="lineNum">     264 </span>            :   }</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         73 : }</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">     118654 : double TD_Uniform::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   //</a>
+<a name="271"><span class="lineNum">     271 </span>            :   double value = 1.0;</a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">     338719 :   for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="273"><span class="lineNum">     273 </span>            :     double tmp;</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">     220065 :     if(argument[k] &lt; minima_[k]) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      15379 :       tmp = GaussianSwitchingFunc(argument[k],minima_[k],sigma_min_[k]);</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     }</a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">     204686 :     else if(argument[k] &gt; maxima_[k]) {</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      15566 :       tmp = GaussianSwitchingFunc(argument[k],maxima_[k],sigma_max_[k]);</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :     }</a>
+<a name="280"><span class="lineNum">     280 </span>            :     else {</a>
+<a name="281"><span class="lineNum">     281 </span>            :       tmp = 1.0;</a>
+<a name="282"><span class="lineNum">     282 </span>            :     }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">     220065 :     value *= tmp;</span></a>
+<a name="284"><span class="lineNum">     284 </span>            :   }</a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">     118654 :   return value;</span></a>
+<a name="286"><span class="lineNum">     286 </span>            : }</a>
+<a name="287"><span class="lineNum">     287 </span>            : </a>
+<a name="288"><span class="lineNum">     288 </span>            : inline</a>
+<a name="289"><span class="lineNum">     289 </span>            : double TD_Uniform::GaussianSwitchingFunc(const double argument, const double center, const double sigma) const {</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">      30945 :   if(sigma&gt;0.0) {</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">      23278 :     double arg=(argument-center)/sigma;</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">      23278 :     return exp(-0.5*arg*arg);</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   }</a>
+<a name="294"><span class="lineNum">     294 </span>            :   else {</a>
+<a name="295"><span class="lineNum">     295 </span>            :     return 0.0;</a>
+<a name="296"><span class="lineNum">     296 </span>            :   }</a>
+<a name="297"><span class="lineNum">     297 </span>            : }</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            : </a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : }</a>
+<a name="305"><span class="lineNum">     305 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_VonMises.cpp.func-sort-c.html b/coverage/ves/TD_VonMises.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3937259b14
--- /dev/null
+++ b/coverage/ves/TD_VonMises.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_VonMises.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_VonMises.cpp<span style="font-size: 80%;"> (<a href="TD_VonMises.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntryHi">98.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_VonMises.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#125">_ZN4PLMD3ves11TD_VonMisesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_124TD_VonMisesRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#113">_ZN4PLMD3ves11TD_VonMises16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#209">_ZNK4PLMD3ves11TD_VonMises16getNormalizationEdd</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_124TD_VonMisesRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_124TD_VonMisesRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#190">_ZNK4PLMD3ves11TD_VonMises8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">31100</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#199">_ZNK4PLMD3ves11TD_VonMises16VonMisesDiagonalERKSt6vectorIdSaIdEES6_S6_S6_S6_</a></td>
+              <td class="coverFnHi">80319</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_VonMises.cpp.func.html b/coverage/ves/TD_VonMises.cpp.func.html
new file mode 100644
index 0000000000..691f417b2c
--- /dev/null
+++ b/coverage/ves/TD_VonMises.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_VonMises.cpp - functions</title>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_VonMises.cpp<span style="font-size: 80%;"> (<a href="TD_VonMises.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntryHi">98.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
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+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#113">_ZN4PLMD3ves11TD_VonMises16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#125">_ZN4PLMD3ves11TD_VonMisesC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_124TD_VonMisesRegisterMe1126createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_124TD_VonMisesRegisterMe112C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#110">_ZN4PLMD3ves12_GLOBAL__N_124TD_VonMisesRegisterMe112D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#199">_ZNK4PLMD3ves11TD_VonMises16VonMisesDiagonalERKSt6vectorIdSaIdEES6_S6_S6_S6_</a></td>
+              <td class="coverFnHi">80319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#209">_ZNK4PLMD3ves11TD_VonMises16getNormalizationEdd</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_VonMises.cpp.gcov.html#190">_ZNK4PLMD3ves11TD_VonMises8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">31100</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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diff --git a/coverage/ves/TD_VonMises.cpp.gcov.html b/coverage/ves/TD_VonMises.cpp.gcov.html
new file mode 100644
index 0000000000..52b21ed2a2
--- /dev/null
+++ b/coverage/ves/TD_VonMises.cpp.gcov.html
@@ -0,0 +1,315 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
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+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
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+  <link rel="stylesheet" type="text/css" href="../gcov.css">
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+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
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+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_VonMises.cpp<span style="font-size: 80%;"> (source / <a href="TD_VonMises.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">75</td>
+            <td class="headerCovTableEntry">76</td>
+            <td class="headerCovTableEntryHi">98.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Tools.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;iostream&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace ves {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : //+PLUMEDOC VES_TARGETDIST TD_VONMISES</a>
+<a name="37"><span class="lineNum">      37 </span>            : /*</a>
+<a name="38"><span class="lineNum">      38 </span>            : Target distribution given by a sum of Von Mises distributions (static).</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : Employ a target distribution that is given by a sum where each</a>
+<a name="41"><span class="lineNum">      41 </span>            : term is a product of one-dimensional</a>
+<a name="42"><span class="lineNum">      42 </span>            : [Von Mises distributions](https://en.wikipedia.org/wiki/Von_Mises_distribution),</a>
+<a name="43"><span class="lineNum">      43 </span>            : \f[</a>
+<a name="44"><span class="lineNum">      44 </span>            : p(\mathbf{s}) = \sum_{i} \, w_{i}</a>
+<a name="45"><span class="lineNum">      45 </span>            : \prod_{k}^{d}</a>
+<a name="46"><span class="lineNum">      46 </span>            : \frac{\exp\left(\kappa_{k,i} \, \cos (s_{k}-\mu_{k,i}) \right)}</a>
+<a name="47"><span class="lineNum">      47 </span>            : {2\pi I_{0}(\kappa_{k,i})}</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f]</a>
+<a name="49"><span class="lineNum">      49 </span>            : where \f$(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$</a>
+<a name="50"><span class="lineNum">      50 </span>            : are the centers of the distributions,</a>
+<a name="51"><span class="lineNum">      51 </span>            : \f$(\kappa_{1,i},\kappa_{2,i},\ldots,\kappa_{d,i})\f$</a>
+<a name="52"><span class="lineNum">      52 </span>            : are parameters that determine the extend of each distribution,</a>
+<a name="53"><span class="lineNum">      53 </span>            : and \f$I_{0}(x)\f$ is the modified Bessel function of order 0.</a>
+<a name="54"><span class="lineNum">      54 </span>            : The weights \f$w_{i}\f$ are normalized to 1, \f$\sum_{i}w_{i}=1\f$.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The Von Mises distribution is defined for periodic variables with a</a>
+<a name="57"><span class="lineNum">      57 </span>            : periodicity of \f$2\pi\f$ and is analogous to the Gaussian distribution.</a>
+<a name="58"><span class="lineNum">      58 </span>            : The parameter \f$ \sqrt{1/\kappa}\f$ is comparable to the standard deviation</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f$\sigma\f$ for the Gaussian distribution.</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : To use this target distribution you need to give the centers</a>
+<a name="62"><span class="lineNum">      62 </span>            : \f$(\mu_{1,i},\mu_{2,i},\ldots,\mu_{d,i})\f$ by</a>
+<a name="63"><span class="lineNum">      63 </span>            : using the numbered CENTER keywords and the &quot;standard deviations&quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            : \f$(\sqrt{1/\kappa_{1,i}},\sqrt{1/\kappa_{2,i}},\ldots,\sqrt{1/\kappa_{d,i}})\f$ using the numbered SIGMA keywords.</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : \par Examples</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span>            : Sum of two Von Mises distribution in one dimension that have equal weights</a>
+<a name="70"><span class="lineNum">      70 </span>            : as no weights are given.</a>
+<a name="71"><span class="lineNum">      71 </span>            : \plumedfile</a>
+<a name="72"><span class="lineNum">      72 </span>            : TD_VONMISES ...</a>
+<a name="73"><span class="lineNum">      73 </span>            :  CENTER1=+2.0 SIGMA1=0.6</a>
+<a name="74"><span class="lineNum">      74 </span>            :  CENTER2=-2.0 SIGMA2=0.7</a>
+<a name="75"><span class="lineNum">      75 </span>            :  LABEL=td</a>
+<a name="76"><span class="lineNum">      76 </span>            : ... TD_VONMISES</a>
+<a name="77"><span class="lineNum">      77 </span>            : \endplumedfile</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : Sum of two Von Mises distribution in two dimensions that have different weights.</a>
+<a name="80"><span class="lineNum">      80 </span>            : Note that the weights are automatically normalized to 1 such that</a>
+<a name="81"><span class="lineNum">      81 </span>            : specifying WEIGHTS=1.0,2.0 is equal to specifying WEIGHTS=0.33333,0.66667.</a>
+<a name="82"><span class="lineNum">      82 </span>            : \plumedfile</a>
+<a name="83"><span class="lineNum">      83 </span>            : TD_VONMISES ...</a>
+<a name="84"><span class="lineNum">      84 </span>            :  CENTER1=+2.0,+2.0 SIGMA1=0.6,0.7</a>
+<a name="85"><span class="lineNum">      85 </span>            :  CENTER2=-2.0,+2.0 SIGMA2=0.7,0.6</a>
+<a name="86"><span class="lineNum">      86 </span>            :  WEIGHTS=1.0,2.0</a>
+<a name="87"><span class="lineNum">      87 </span>            :  LABEL=td</a>
+<a name="88"><span class="lineNum">      88 </span>            : ... TD_VONMISES</a>
+<a name="89"><span class="lineNum">      89 </span>            : \endplumedfile</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : */</a>
+<a name="92"><span class="lineNum">      92 </span>            : //+ENDPLUMEDOC</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span>            : class TD_VonMises: public TargetDistribution {</a>
+<a name="95"><span class="lineNum">      95 </span>            :   // properties of the Gaussians</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; sigmas_;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; kappas_;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; centers_;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; normalization_;</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::vector&lt;double&gt; weights_;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::vector&lt;double&gt; periods_;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   unsigned int ncenters_;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   double VonMisesDiagonal(const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;, const std::vector&lt;double&gt;&amp;) const;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   double getNormalization(const double, const double) const;</a>
+<a name="105"><span class="lineNum">     105 </span>            : public:</a>
+<a name="106"><span class="lineNum">     106 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="107"><span class="lineNum">     107 </span>            :   explicit TD_VonMises(const ActionOptions&amp; ao);</a>
+<a name="108"><span class="lineNum">     108 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="109"><span class="lineNum">     109 </span>            : };</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">      12513 : PLUMED_REGISTER_ACTION(TD_VonMises,&quot;TD_VONMISES&quot;)</span></a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         11 : void TD_VonMises::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         11 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         22 :   keys.add(&quot;numbered&quot;,&quot;CENTER&quot;,&quot;The centers of the Von Mises distributions.&quot;);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         22 :   keys.add(&quot;numbered&quot;,&quot;SIGMA&quot;,&quot;The standard deviations of the Von Mises distributions.&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         22 :   keys.add(&quot;optional&quot;,&quot;WEIGHTS&quot;,&quot;The weights of the Von Mises distributions. Have to be as many as the number of centers given with the numbered CENTER keywords. If no weights are given the distributions are weighted equally. The weights are automatically normalized to 1.&quot;);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         22 :   keys.add(&quot;hidden&quot;,&quot;PERIODS&quot;,&quot;The periods for each of the dimensions. By default they are 2*pi for each dimension.&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         11 :   keys.use(&quot;WELLTEMPERED_FACTOR&quot;);</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         11 :   keys.use(&quot;SHIFT_TO_ZERO&quot;);</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   //keys.use(&quot;NORMALIZE&quot;);</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         11 : }</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : </a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">          9 : TD_VonMises::TD_VonMises(const ActionOptions&amp; ao):</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         18 :   sigmas_(0),</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">          9 :   centers_(0),</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">          9 :   normalization_(0),</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">          9 :   weights_(0),</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          9 :   periods_(0),</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">         18 :   ncenters_(0)</span></a>
+<a name="135"><span class="lineNum">     135 </span>            : {</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         13 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     std::vector&lt;double&gt; tmp_center;</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         44 :     if(!parseNumberedVector(&quot;CENTER&quot;,i,tmp_center) ) {break;}</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         13 :     centers_.push_back(tmp_center);</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         13 :   }</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         13 :   for(unsigned int i=1;; i++) {</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :     std::vector&lt;double&gt; tmp_sigma;</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         44 :     if(!parseNumberedVector(&quot;SIGMA&quot;,i,tmp_sigma) ) {break;}</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         13 :     sigmas_.push_back(tmp_sigma);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         13 :   }</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   //</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">          9 :   plumed_massert(centers_.size()==sigmas_.size(),&quot;there has to be an equal amount of CENTER and SIGMA keywords&quot;);</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          9 :   if(centers_.size()==0) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: CENTER and SIGMA keywords seem to be missing. Note that numbered keywords start at CENTER1 and SIGMA1.&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span>            :   //</a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">          9 :   setDimension(centers_[0].size());</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">          9 :   ncenters_ = centers_.size();</span></a>
+<a name="154"><span class="lineNum">     154 </span>            :   //</a>
+<a name="155"><span class="lineNum">     155 </span>            :   // check centers and sigmas</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         22 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">         13 :     if(centers_[i].size()!=getDimension()) {plumed_merror(getName()+&quot;: one of the CENTER keyword does not match the given dimension&quot;);}</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">         13 :     if(sigmas_[i].size()!=getDimension()) {plumed_merror(getName()+&quot;: one of the SIGMA keyword does not match the given dimension&quot;);}</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   }</a>
+<a name="160"><span class="lineNum">     160 </span>            :   //</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">          9 :   kappas_.resize(sigmas_.size());</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         22 :   for(unsigned int i=0; i&lt;sigmas_.size(); i++) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         13 :     kappas_[i].resize(sigmas_[i].size());</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">         32 :     for(unsigned int k=0; k&lt;kappas_[i].size(); k++) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         19 :       kappas_[i][k] = 1.0/(sigmas_[i][k]*sigmas_[i][k]);</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :     }</a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            :   //</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">         18 :   parseVector(&quot;WEIGHTS&quot;,weights_);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">          9 :   if(weights_.size()==0) {weights_.assign(centers_.size(),1.0);}</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">          9 :   if(centers_.size()!=weights_.size()) {plumed_merror(getName() + &quot;: there has to be as many weights given in WEIGHTS as numbered CENTER keywords&quot;);}</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   //</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          9 :   if(periods_.size()==0) {periods_.assign(getDimension(),2*pi);}</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         18 :   parseVector(&quot;PERIODS&quot;,periods_);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">          9 :   if(periods_.size()!=getDimension()) {plumed_merror(getName() + &quot;: the number of values given in PERIODS does not match the dimension of the distribution&quot;);}</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   //</a>
+<a name="177"><span class="lineNum">     177 </span>            :   double sum_weights=0.0;</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         22 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {sum_weights+=weights_[i];}</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">         22 :   for(unsigned int i=0; i&lt;weights_.size(); i++) {weights_[i]/=sum_weights;}</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :   //</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          9 :   normalization_.resize(ncenters_);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">         22 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         13 :     normalization_[i].resize(getDimension());</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         32 :     for(unsigned int k=0; k&lt;getDimension(); k++) {</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         19 :       normalization_[i][k] = getNormalization(kappas_[i][k],periods_[k]);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :     }</a>
+<a name="187"><span class="lineNum">     187 </span>            :   }</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">          9 :   checkRead();</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">          9 : }</span></a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">      31100 : double TD_VonMises::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="193"><span class="lineNum">     193 </span>            :   double value=0.0;</a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">      92400 :   for(unsigned int i=0; i&lt;ncenters_; i++) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">      61300 :     value+=weights_[i]*VonMisesDiagonal(argument, centers_[i], kappas_[i],periods_,normalization_[i]);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   }</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">      31100 :   return value;</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : }</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">      80319 : double TD_VonMises::VonMisesDiagonal(const std::vector&lt;double&gt;&amp; argument, const std::vector&lt;double&gt;&amp; center, const std::vector&lt;double&gt;&amp; kappa, const std::vector&lt;double&gt;&amp; periods, const std::vector&lt;double&gt;&amp; normalization) const {</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   double value = 1.0;</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">     220638 :   for(unsigned int k=0; k&lt;argument.size(); k++) {</span></a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">     140319 :     double arg = kappa[k]*cos( ((2*pi)/periods[k])*(argument[k]-center[k]) );</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">     140319 :     value*=normalization[k]*exp(arg);</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   }</a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">      80319 :   return value;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         19 : double TD_VonMises::getNormalization(const double kappa, const double period) const {</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :   //</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         19 :   std::vector&lt;double&gt; centers(1);</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         19 :   centers[0] = 0.0;</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         19 :   std::vector&lt;double&gt; kappas(1);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         19 :   kappas[0] = kappa;</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         19 :   std::vector&lt;double&gt; periods(1);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">         19 :   periods[0] = period;</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         19 :   std::vector&lt;double&gt; norm(1);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">         19 :   norm[0] = 1.0;</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :   //</a>
+<a name="222"><span class="lineNum">     222 </span>            :   const unsigned int nbins = 1001;</a>
+<a name="223"><span class="lineNum">     223 </span>            :   std::vector&lt;double&gt; points;</a>
+<a name="224"><span class="lineNum">     224 </span>            :   std::vector&lt;double&gt; weights;</a>
+<a name="225"><span class="lineNum">     225 </span>            :   double min = 0.0;</a>
+<a name="226"><span class="lineNum">     226 </span>            :   double max = period;</a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineCov">         19 :   GridIntegrationWeights::getOneDimensionalIntegrationPointsAndWeights(points,weights,nbins,min,max);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :   //</a>
+<a name="229"><span class="lineNum">     229 </span>            :   double sum = 0.0;</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">      19038 :   for(unsigned int l=0; l&lt;nbins; l++) {</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">      19019 :     std::vector&lt;double&gt; arg(1); arg[0]= points[l];</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">      19019 :     sum += weights[l] * VonMisesDiagonal(arg,centers,kappas,periods,norm);</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         38 :   return 1.0/sum;</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : }</a>
+<a name="239"><span class="lineNum">     239 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_WellTempered.cpp.func-sort-c.html b/coverage/ves/TD_WellTempered.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8cef3600d0
--- /dev/null
+++ b/coverage/ves/TD_WellTempered.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_WellTempered.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_WellTempered.cpp<span style="font-size: 80%;"> (<a href="TD_WellTempered.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TD_WellTempered.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#107">_ZN4PLMD3ves15TD_WellTemperedD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#138">_ZNK4PLMD3ves15TD_WellTempered8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#111">_ZN4PLMD3ves12_GLOBAL__N_128TD_WellTemperedRegisterMe1136createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#120">_ZN4PLMD3ves15TD_WellTemperedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#107">_ZN4PLMD3ves15TD_WellTemperedD0Ev</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#114">_ZN4PLMD3ves15TD_WellTempered16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#144">_ZN4PLMD3ves15TD_WellTempered10updateGridEv</a></td>
+              <td class="coverFnHi">319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#111">_ZN4PLMD3ves12_GLOBAL__N_128TD_WellTemperedRegisterMe113C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#111">_ZN4PLMD3ves12_GLOBAL__N_128TD_WellTemperedRegisterMe113D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TD_WellTempered.cpp.func.html b/coverage/ves/TD_WellTempered.cpp.func.html
new file mode 100644
index 0000000000..ec6d251749
--- /dev/null
+++ b/coverage/ves/TD_WellTempered.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_WellTempered.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_WellTempered.cpp<span style="font-size: 80%;"> (<a href="TD_WellTempered.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TD_WellTempered.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#111">_ZN4PLMD3ves12_GLOBAL__N_128TD_WellTemperedRegisterMe1136createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#111">_ZN4PLMD3ves12_GLOBAL__N_128TD_WellTemperedRegisterMe113C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#111">_ZN4PLMD3ves12_GLOBAL__N_128TD_WellTemperedRegisterMe113D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#144">_ZN4PLMD3ves15TD_WellTempered10updateGridEv</a></td>
+              <td class="coverFnHi">319</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#114">_ZN4PLMD3ves15TD_WellTempered16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">31</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#120">_ZN4PLMD3ves15TD_WellTemperedC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#107">_ZN4PLMD3ves15TD_WellTemperedD0Ev</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#107">_ZN4PLMD3ves15TD_WellTemperedD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TD_WellTempered.cpp.gcov.html#138">_ZNK4PLMD3ves15TD_WellTempered8getValueERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
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+
+</body>
+</html>
diff --git a/coverage/ves/TD_WellTempered.cpp.gcov.html b/coverage/ves/TD_WellTempered.cpp.gcov.html
new file mode 100644
index 0000000000..2415444b45
--- /dev/null
+++ b/coverage/ves/TD_WellTempered.cpp.gcov.html
@@ -0,0 +1,240 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TD_WellTempered.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TD_WellTempered.cpp<span style="font-size: 80%;"> (source / <a href="TD_WellTempered.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">90.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryMed">77.8 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC VES_TARGETDIST TD_WELLTEMPERED</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Well-tempered target distribution (dynamic).</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Use as a target distribution the well-tempered distribution \cite Barducci:2008</a>
+<a name="40"><span class="lineNum">      40 </span>            : given by</a>
+<a name="41"><span class="lineNum">      41 </span>            : \f[</a>
+<a name="42"><span class="lineNum">      42 </span>            : p(\mathbf{s}) =</a>
+<a name="43"><span class="lineNum">      43 </span>            : \frac{e^{-(\beta/\gamma) F(\mathbf{s})}}</a>
+<a name="44"><span class="lineNum">      44 </span>            : {\int d\mathbf{s}\, e^{-(\beta/\gamma) F(\mathbf{s})}} =</a>
+<a name="45"><span class="lineNum">      45 </span>            : \frac{[P_{0}(\mathbf{s})]^{1/\gamma}}</a>
+<a name="46"><span class="lineNum">      46 </span>            : {\int d\mathbf{s}\, [P_{0}(\mathbf{s})]^{1/\gamma}}</a>
+<a name="47"><span class="lineNum">      47 </span>            : \f]</a>
+<a name="48"><span class="lineNum">      48 </span>            : where \f$\gamma\f$ is a so-called bias factor and \f$P_{0}(\mathbf{s})\f$ is the</a>
+<a name="49"><span class="lineNum">      49 </span>            : unbiased canonical distribution of the CVs. This target distribution thus</a>
+<a name="50"><span class="lineNum">      50 </span>            : corresponds to a biased ensemble where, as compared to the unbiased one,</a>
+<a name="51"><span class="lineNum">      51 </span>            : the probability peaks have been broaden and the fluctuations of the CVs are</a>
+<a name="52"><span class="lineNum">      52 </span>            : enhanced.</a>
+<a name="53"><span class="lineNum">      53 </span>            : The value of the bias factor \f$\gamma\f$ determines by how much the fluctuations</a>
+<a name="54"><span class="lineNum">      54 </span>            : are enhanced.</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            : The well-tempered distribution can be view as sampling on</a>
+<a name="57"><span class="lineNum">      57 </span>            : an effective free energy surface \f$\tilde{F}(\mathbf{s}) = (1/\gamma) F(\mathbf{s})\f$</a>
+<a name="58"><span class="lineNum">      58 </span>            : which has largely the same metastable states as the original \f$F(\mathbf{s})\f$</a>
+<a name="59"><span class="lineNum">      59 </span>            : but with barriers that have been reduced by a factor of \f$\gamma\f$.</a>
+<a name="60"><span class="lineNum">      60 </span>            : Generally one should use a value of \f$\gamma\f$ that results in</a>
+<a name="61"><span class="lineNum">      61 </span>            : effective barriers on the order of few \f$k_{\mathrm{B}}T\f$</a>
+<a name="62"><span class="lineNum">      62 </span>            : such that thermal fluctuations can easily induce transitions</a>
+<a name="63"><span class="lineNum">      63 </span>            : between different metastable states.</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : At convergence the relationship between the bias potential and the free</a>
+<a name="66"><span class="lineNum">      66 </span>            : energy surface is given by</a>
+<a name="67"><span class="lineNum">      67 </span>            : \f[</a>
+<a name="68"><span class="lineNum">      68 </span>            : F(\mathbf{s}) = - \left(\frac{1}{1-\gamma^{-1}} \right) V(\mathbf{s})</a>
+<a name="69"><span class="lineNum">      69 </span>            : \f]</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : This target distribution depends directly on the free energy surface</a>
+<a name="72"><span class="lineNum">      72 </span>            : \f$F(\mathbf{s})\f$ which is quantity that we do not know a-priori and</a>
+<a name="73"><span class="lineNum">      73 </span>            : want to obtain. Therefore, this target distribution</a>
+<a name="74"><span class="lineNum">      74 </span>            : is iteratively updated \cite Valsson-JCTC-2015 according to</a>
+<a name="75"><span class="lineNum">      75 </span>            : \f[</a>
+<a name="76"><span class="lineNum">      76 </span>            : p^{(m+1)}(\mathbf{s}) =</a>
+<a name="77"><span class="lineNum">      77 </span>            : \frac{e^{-(\beta/\gamma) F^{(m+1)}(\mathbf{s})}}</a>
+<a name="78"><span class="lineNum">      78 </span>            : {\int d\mathbf{s}\, e^{-(\beta/\gamma) F^{(m+1)}(\mathbf{s})}}</a>
+<a name="79"><span class="lineNum">      79 </span>            : \f]</a>
+<a name="80"><span class="lineNum">      80 </span>            : where \f$F^{(m+1)}(\mathbf{s})\f$ is the current best estimate of the</a>
+<a name="81"><span class="lineNum">      81 </span>            : free energy surface obtained according to</a>
+<a name="82"><span class="lineNum">      82 </span>            : \f[</a>
+<a name="83"><span class="lineNum">      83 </span>            : F^{(m+1)}(\mathbf{s}) =</a>
+<a name="84"><span class="lineNum">      84 </span>            : - V^{(m+1)}(\mathbf{s}) - \frac{1}{\beta} \log p^{(m)}(\mathbf{s}) =</a>
+<a name="85"><span class="lineNum">      85 </span>            : - V^{(m+1)}(\mathbf{s}) + \frac{1}{\gamma} F^{(m)}(\mathbf{s})</a>
+<a name="86"><span class="lineNum">      86 </span>            : \f]</a>
+<a name="87"><span class="lineNum">      87 </span>            : The frequency of performing this update needs to be set in the</a>
+<a name="88"><span class="lineNum">      88 </span>            : optimizer used in the calculation. Normally it is sufficient</a>
+<a name="89"><span class="lineNum">      89 </span>            : to do it every 100-1000 bias update iterations.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \par Examples</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : Employ a well-tempered target distribution with a bias factor of 10</a>
+<a name="94"><span class="lineNum">      94 </span>            : \plumedfile</a>
+<a name="95"><span class="lineNum">      95 </span>            : td_welltemp: TD_WELLTEMPERED BIASFACTOR=10</a>
+<a name="96"><span class="lineNum">      96 </span>            : \endplumedfile</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : */</a>
+<a name="99"><span class="lineNum">      99 </span>            : //+ENDPLUMEDOC</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            : class TD_WellTempered: public TargetDistribution {</a>
+<a name="102"><span class="lineNum">     102 </span>            : private:</a>
+<a name="103"><span class="lineNum">     103 </span>            :   double bias_factor_;</a>
+<a name="104"><span class="lineNum">     104 </span>            : public:</a>
+<a name="105"><span class="lineNum">     105 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="106"><span class="lineNum">     106 </span>            :   explicit TD_WellTempered(const ActionOptions&amp; ao);</a>
+<a name="107"><span class="lineNum">     107 </span>            :   void updateGrid() override;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   double getValue(const std::vector&lt;double&gt;&amp;) const override;</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         29 :   ~TD_WellTempered() {}</span></a>
+<a name="110"><span class="lineNum">     110 </span>            : };</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : </a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">      12533 : PLUMED_REGISTER_ACTION(TD_WellTempered,&quot;TD_WELLTEMPERED&quot;)</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         31 : void TD_WellTempered::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         31 :   TargetDistribution::registerKeywords(keys);</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         62 :   keys.add(&quot;compulsory&quot;,&quot;BIASFACTOR&quot;,&quot;The bias factor used for the well-tempered distribution.&quot;);</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         31 : }</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         29 : TD_WellTempered::TD_WellTempered(const ActionOptions&amp; ao):</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   PLUMED_VES_TARGETDISTRIBUTION_INIT(ao),</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">         29 :   bias_factor_(0.0)</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : {</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         29 :   log.printf(&quot;  Well-tempered target distribution, see and cite &quot;);</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">         58 :   log &lt;&lt; plumed.cite(&quot;Valsson and Parrinello, J. Chem. Theory Comput. 11, 1996-2002 (2015)&quot;);</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         58 :   log &lt;&lt; plumed.cite(&quot;Barducci, Bussi, and Parrinello, Phys. Rev. Lett. 100, 020603 (2008)&quot;);</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         29 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         29 :   parse(&quot;BIASFACTOR&quot;,bias_factor_);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         29 :   if(bias_factor_&lt;=1.0) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;TD_WELLTEMPERED target distribution: the value of the bias factor doesn't make sense, it should be larger than 1.0&quot;);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   }</a>
+<a name="134"><span class="lineNum">     134 </span>            :   setDynamic();</a>
+<a name="135"><span class="lineNum">     135 </span>            :   setFesGridNeeded();</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         29 :   checkRead();</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         29 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 : double TD_WellTempered::getValue(const std::vector&lt;double&gt;&amp; argument) const {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;getValue not implemented for TD_WellTempered&quot;);</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :   return 0.0;</a>
+<a name="143"><span class="lineNum">     143 </span>            : }</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        319 : void TD_WellTempered::updateGrid() {</span></a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">        319 :   double beta_prime = getBeta()/bias_factor_;</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        319 :   plumed_massert(getFesGridPntr()!=NULL,&quot;the FES grid has to be linked to use TD_WellTempered!&quot;);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        638 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(getTargetDistGridPntr());</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   double norm = 0.0;</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">    1127896 :   for(Grid::index_t l=0; l&lt;targetDistGrid().getSize(); l++) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">    1127577 :     double value = beta_prime * getFesGridPntr()-&gt;getValue(l);</span></a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">    1127577 :     logTargetDistGrid().setValue(l,value);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">    1127577 :     value = exp(-value);</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">    1127577 :     norm += integration_weights[l]*value;</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">    1127577 :     targetDistGrid().setValue(l,value);</span></a>
+<a name="157"><span class="lineNum">     157 </span>            :   }</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        319 :   targetDistGrid().scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        319 :   logTargetDistGrid().setMinToZero();</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        319 : }</span></a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistModifer.h.func-sort-c.html b/coverage/ves/TargetDistModifer.h.func-sort-c.html
new file mode 100644
index 0000000000..9e714b2360
--- /dev/null
+++ b/coverage/ves/TargetDistModifer.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistModifer.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistModifer.h<span style="font-size: 80%;"> (<a href="TargetDistModifer.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TargetDistModifer.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistModifer.h.gcov.html#40">_ZNK4PLMD3ves19WellTemperedModifer25getModifedTargetDistValueEdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">21206</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistModifer.h.func.html b/coverage/ves/TargetDistModifer.h.func.html
new file mode 100644
index 0000000000..7b6bf64567
--- /dev/null
+++ b/coverage/ves/TargetDistModifer.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistModifer.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistModifer.h<span style="font-size: 80%;"> (<a href="TargetDistModifer.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TargetDistModifer.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistModifer.h.gcov.html#40">_ZNK4PLMD3ves19WellTemperedModifer25getModifedTargetDistValueEdRKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">21206</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistModifer.h.gcov.html b/coverage/ves/TargetDistModifer.h.gcov.html
new file mode 100644
index 0000000000..6a4c93f314
--- /dev/null
+++ b/coverage/ves/TargetDistModifer.h.gcov.html
@@ -0,0 +1,129 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistModifer.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistModifer.h<span style="font-size: 80%;"> (source / <a href="TargetDistModifer.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_TargetDistModifer_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_TargetDistModifer_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;vector&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cmath&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace ves {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class TargetDistModifer {</a>
+<a name="32"><span class="lineNum">      32 </span>            : public:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   virtual double getModifedTargetDistValue(const double targetdist_value, const std::vector&lt;double&gt;&amp; cv_values) const = 0;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   virtual ~TargetDistModifer() {}</a>
+<a name="35"><span class="lineNum">      35 </span>            : };</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : class WellTemperedModifer:public TargetDistModifer {</a>
+<a name="38"><span class="lineNum">      38 </span>            : private:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   double invbiasf_;</a>
+<a name="40"><span class="lineNum">      40 </span>            : public:</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          6 :   explicit WellTemperedModifer(double biasfactor):invbiasf_(1.0/biasfactor) {}</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      21206 :   double getModifedTargetDistValue(const double targetdist_value, const std::vector&lt;double&gt;&amp; cv_values) const override {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">      21206 :     return std::pow(targetdist_value,invbiasf_);</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   }</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            : }</a>
+<a name="51"><span class="lineNum">      51 </span>            : }</a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistribution.cpp.func-sort-c.html b/coverage/ves/TargetDistribution.cpp.func-sort-c.html
new file mode 100644
index 0000000000..4f6b98cd51
--- /dev/null
+++ b/coverage/ves/TargetDistribution.cpp.func-sort-c.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistribution.cpp<span style="font-size: 80%;"> (<a href="TargetDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntry">218</td>
+            <td class="headerCovTableEntryMed">87.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TargetDistribution.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#122">_ZN4PLMD3ves18TargetDistribution10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#127">_ZN4PLMD3ves18TargetDistribution12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#366">_ZN4PLMD3ves18TargetDistribution14checkNanAndInfEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#102">_ZN4PLMD3ves18TargetDistributionD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#361">_ZN4PLMD3ves18TargetDistribution22clearLogTargetDistGridEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#142">_ZN4PLMD3ves18TargetDistribution15setupBiasCutoffEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#132">_ZN4PLMD3ves18TargetDistribution25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#339">_ZN4PLMD3ves18TargetDistribution32setMinimumOfTargetDistGridToZeroEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#310">_ZN4PLMD3ves18TargetDistribution28applyTargetDistModiferToGridEPNS0_17TargetDistModiferE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
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+    <tr>
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+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#282">_ZN4PLMD3ves18TargetDistribution33updateBiasCutoffForTargetDistGridEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#209">_ZN4PLMD3ves18TargetDistribution27getMarginalDistributionGridEPNS_4GridERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#330">_ZN4PLMD3ves18TargetDistribution23updateLogTargetDistGridEv</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#137">_ZN4PLMD3ves18TargetDistribution11linkFesGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#116">_ZN4PLMD3ves18TargetDistribution11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#202">_ZN4PLMD3ves18TargetDistribution13normalizeGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#175">_ZN4PLMD3ves18TargetDistribution31calculateStaticDistributionGridEv</a></td>
+              <td class="coverFnHi">368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#104">_ZNK4PLMD3ves18TargetDistribution7getBetaEv</a></td>
+              <td class="coverFnHi">377</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#159">_ZN4PLMD3ves18TargetDistribution10setupGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#46">_ZN4PLMD3ves18TargetDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#102">_ZN4PLMD3ves18TargetDistributionD2Ev</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#110">_ZN4PLMD3ves18TargetDistribution12setDimensionEj</a></td>
+              <td class="coverFnHi">420</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#38">_ZN4PLMD3ves18TargetDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">441</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#243">_ZN4PLMD3ves18TargetDistribution16updateTargetDistEv</a></td>
+              <td class="coverFnHi">802</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#192">_ZN4PLMD3ves18TargetDistribution13integrateGridEPKNS_4GridE</a></td>
+              <td class="coverFnHi">901</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistribution.cpp.func.html b/coverage/ves/TargetDistribution.cpp.func.html
new file mode 100644
index 0000000000..2265a7014b
--- /dev/null
+++ b/coverage/ves/TargetDistribution.cpp.func.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistribution.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistribution.cpp<span style="font-size: 80%;"> (<a href="TargetDistribution.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntry">218</td>
+            <td class="headerCovTableEntryMed">87.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TargetDistribution.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#122">_ZN4PLMD3ves18TargetDistribution10linkActionEPNS_6ActionE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#159">_ZN4PLMD3ves18TargetDistribution10setupGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#238">_ZN4PLMD3ves18TargetDistribution11getMarginalERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaIS8_EE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#137">_ZN4PLMD3ves18TargetDistribution11linkFesGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">40</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#116">_ZN4PLMD3ves18TargetDistribution11linkVesBiasEPNS0_7VesBiasE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#127">_ZN4PLMD3ves18TargetDistribution12linkBiasGridEPNS_4GridE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#110">_ZN4PLMD3ves18TargetDistribution12setDimensionEj</a></td>
+              <td class="coverFnHi">420</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#192">_ZN4PLMD3ves18TargetDistribution13integrateGridEPKNS_4GridE</a></td>
+              <td class="coverFnHi">901</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#202">_ZN4PLMD3ves18TargetDistribution13normalizeGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#366">_ZN4PLMD3ves18TargetDistribution14checkNanAndInfEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#142">_ZN4PLMD3ves18TargetDistribution15setupBiasCutoffEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#38">_ZN4PLMD3ves18TargetDistribution16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">441</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#243">_ZN4PLMD3ves18TargetDistribution16updateTargetDistEv</a></td>
+              <td class="coverFnHi">802</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#361">_ZN4PLMD3ves18TargetDistribution22clearLogTargetDistGridEv</a></td>
+              <td class="coverFnHi">1</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#330">_ZN4PLMD3ves18TargetDistribution23updateLogTargetDistGridEv</a></td>
+              <td class="coverFnHi">29</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#132">_ZN4PLMD3ves18TargetDistribution25linkBiasWithoutCutoffGridEPNS_4GridE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#209">_ZN4PLMD3ves18TargetDistribution27getMarginalDistributionGridEPNS_4GridERKSt6vectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISA_EE</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#346">_ZN4PLMD3ves18TargetDistribution27readInRestartTargetDistGridERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#310">_ZN4PLMD3ves18TargetDistribution28applyTargetDistModiferToGridEPNS0_17TargetDistModiferE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#175">_ZN4PLMD3ves18TargetDistribution31calculateStaticDistributionGridEv</a></td>
+              <td class="coverFnHi">368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#339">_ZN4PLMD3ves18TargetDistribution32setMinimumOfTargetDistGridToZeroEv</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#282">_ZN4PLMD3ves18TargetDistribution33updateBiasCutoffForTargetDistGridEv</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#46">_ZN4PLMD3ves18TargetDistributionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#102">_ZN4PLMD3ves18TargetDistributionD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#102">_ZN4PLMD3ves18TargetDistributionD2Ev</a></td>
+              <td class="coverFnHi">407</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.cpp.gcov.html#104">_ZNK4PLMD3ves18TargetDistribution7getBetaEv</a></td>
+              <td class="coverFnHi">377</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistribution.cpp.gcov.html b/coverage/ves/TargetDistribution.cpp.gcov.html
new file mode 100644
index 0000000000..6aa9358e27
--- /dev/null
+++ b/coverage/ves/TargetDistribution.cpp.gcov.html
@@ -0,0 +1,464 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistribution.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistribution.cpp<span style="font-size: 80%;"> (source / <a href="TargetDistribution.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">190</td>
+            <td class="headerCovTableEntry">218</td>
+            <td class="headerCovTableEntryMed">87.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryMed">84.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;TargetDistModifer.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;GridIntegrationWeights.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;tools/Keywords.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;GridProjWeights.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace PLMD {</a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace ves {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        441 : void TargetDistribution::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        441 :   Action::registerKeywords(keys);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        882 :   keys.reserve(&quot;optional&quot;,&quot;WELLTEMPERED_FACTOR&quot;,&quot;Broaden the target distribution such that it is taken as [p(s)]^(1/gamma) where gamma is the well tempered factor given here. If this option is active the distribution will be automatically normalized.&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        882 :   keys.reserveFlag(&quot;SHIFT_TO_ZERO&quot;,false,&quot;Shift the minimum value of the target distribution to zero. This can for example be used to avoid negative values in the target distribution. If this option is active the distribution will be automatically normalized.&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        882 :   keys.reserveFlag(&quot;NORMALIZE&quot;,false,&quot;Renormalized the target distribution over the intervals on which it is defined to make sure that it is properly normalized to 1. In most cases this should not be needed as the target distributions should be normalized. The code will issue a warning (but still run) if this is needed for some reason.&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        441 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        407 : TargetDistribution::TargetDistribution(const ActionOptions&amp;ao):</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   Action(ao),</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        407 :   type_(static_targetdist),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        407 :   force_normalization_(false),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        407 :   check_normalization_(true),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        407 :   check_nonnegative_(true),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        407 :   check_nan_inf_(false),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        407 :   shift_targetdist_to_zero_(false),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        407 :   dimension_(0),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        814 :   grid_args_(0),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        407 :   action_pntr_(NULL),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        407 :   vesbias_pntr_(NULL),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        407 :   needs_bias_grid_(false),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        407 :   needs_bias_withoutcutoff_grid_(false),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        407 :   needs_fes_grid_(false),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        407 :   bias_grid_pntr_(NULL),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        407 :   bias_withoutcutoff_grid_pntr_(NULL),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        407 :   fes_grid_pntr_(NULL),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        407 :   static_grid_calculated(false),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        407 :   allow_bias_cutoff_(true),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        407 :   bias_cutoff_active_(false)</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : {</a>
+<a name="70"><span class="lineNum">      70 </span>            :   //</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        814 :   if(keywords.exists(&quot;WELLTEMPERED_FACTOR&quot;)) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        301 :     double welltempered_factor=0.0;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        301 :     parse(&quot;WELLTEMPERED_FACTOR&quot;,welltempered_factor);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :     //</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        301 :     if(welltempered_factor&gt;0.0) {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 :       auto pntr = Tools::make_unique&lt;WellTemperedModifer&gt;(welltempered_factor);</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          6 :       targetdist_modifer_pntrs_.emplace_back(std::move(pntr));</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          6 :     }</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        295 :     else if(welltempered_factor&lt;0.0) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: negative value in WELLTEMPERED_FACTOR does not make sense&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :     }</a>
+<a name="82"><span class="lineNum">      82 </span>            :   }</a>
+<a name="83"><span class="lineNum">      83 </span>            :   //</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        814 :   if(keywords.exists(&quot;SHIFT_TO_ZERO&quot;)) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        289 :     parseFlag(&quot;SHIFT_TO_ZERO&quot;,shift_targetdist_to_zero_);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">        289 :     if(shift_targetdist_to_zero_) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          3 :       if(bias_cutoff_active_) {plumed_merror(getName()+&quot;: using SHIFT_TO_ZERO with bias cutoff is not allowed.&quot;);}</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          3 :       check_nonnegative_=false;</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     }</a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            :   //</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        814 :   if(keywords.exists(&quot;NORMALIZE&quot;)) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        263 :     bool force_normalization=false;</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        263 :     parseFlag(&quot;NORMALIZE&quot;,force_normalization);</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        263 :     if(force_normalization) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          3 :       if(shift_targetdist_to_zero_) {plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: using NORMALIZE with SHIFT_TO_ZERO is not needed, the target distribution will be automatically normalized.&quot;);}</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :       setForcedNormalization();</a>
+<a name="98"><span class="lineNum">      98 </span>            :     }</a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        407 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        407 : TargetDistribution::~TargetDistribution() {</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        814 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        377 : double TargetDistribution::getBeta() const {</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        377 :   plumed_massert(vesbias_pntr_!=NULL,&quot;The VesBias has to be linked to use TargetDistribution::getBeta()&quot;);</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        377 :   return vesbias_pntr_-&gt;getBeta();</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : }</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        420 : void TargetDistribution::setDimension(const unsigned int dimension) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        420 :   plumed_massert(dimension_==0,&quot;setDimension: the dimension of the target distribution has already been set&quot;);</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        420 :   dimension_=dimension;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        420 : }</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         49 : void TargetDistribution::linkVesBias(VesBias* vesbias_pntr_in) {</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         49 :   vesbias_pntr_ = vesbias_pntr_in;</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         49 :   action_pntr_ = static_cast&lt;Action*&gt;(vesbias_pntr_in);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         49 : }</span></a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 : void TargetDistribution::linkAction(Action* action_pntr_in) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :   action_pntr_ = action_pntr_in;</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 : void TargetDistribution::linkBiasGrid(Grid* bias_grid_pntr_in) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :   bias_grid_pntr_ = bias_grid_pntr_in;</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : </a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          3 : void TargetDistribution::linkBiasWithoutCutoffGrid(Grid* bias_withoutcutoff_grid_pntr_in) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          3 :   bias_withoutcutoff_grid_pntr_ = bias_withoutcutoff_grid_pntr_in;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          3 : }</span></a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         40 : void TargetDistribution::linkFesGrid(Grid* fes_grid_pntr_in) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         40 :   fes_grid_pntr_ = fes_grid_pntr_in;</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">         40 : }</span></a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : </a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">          3 : void TargetDistribution::setupBiasCutoff() {</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">          3 :   if(!allow_bias_cutoff_) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: this target distribution does not support a bias cutoff&quot;);</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :   }</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">          3 :   if(targetdist_modifer_pntrs_.size()&gt;0) {</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: using a bias cutoff with a target distribution modifer like WELLTEMPERED_FACTOR is not allowed&quot;);</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   }</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">          3 :   bias_cutoff_active_=true;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   setBiasWithoutCutoffGridNeeded();</a>
+<a name="153"><span class="lineNum">     153 </span>            :   setDynamic();</a>
+<a name="154"><span class="lineNum">     154 </span>            :   // as the p(s) includes the derivative factor so normalization</a>
+<a name="155"><span class="lineNum">     155 </span>            :   // check can be misleading</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          3 :   check_normalization_=false;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          3 :   force_normalization_=false;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          3 : }</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        407 : void TargetDistribution::setupGrids(const std::vector&lt;Value*&gt;&amp; arguments, const std::vector&lt;std::string&gt;&amp; min, const std::vector&lt;std::string&gt;&amp; max, const std::vector&lt;unsigned int&gt;&amp; nbins) {</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        407 :   if(getDimension()==0) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         78 :     setDimension(arguments.size());</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span>            :   unsigned int dimension = getDimension();</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        407 :   plumed_massert(arguments.size()==dimension,&quot;TargetDistribution::setupGrids: mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        407 :   plumed_massert(min.size()==dimension,&quot;TargetDistribution::setupGrids: mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        407 :   plumed_massert(max.size()==dimension,&quot;TargetDistribution::setupGrids: mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        407 :   plumed_massert(nbins.size()==dimension,&quot;TargetDistribution::setupGrids: mismatch between number of values given for grid parameters&quot;);</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        407 :   grid_args_=arguments;</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        814 :   targetdist_grid_pntr_ =     Tools::make_unique&lt;Grid&gt;(&quot;targetdist&quot;,arguments,min,max,nbins,false,false);</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        814 :   log_targetdist_grid_pntr_ = Tools::make_unique&lt;Grid&gt;(&quot;log_targetdist&quot;,arguments,min,max,nbins,false,false);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">        407 :   setupAdditionalGrids(arguments,min,max,nbins);</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        407 : }</span></a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        368 : void TargetDistribution::calculateStaticDistributionGrid() {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        368 :   if(static_grid_calculated &amp;&amp; !bias_cutoff_active_) {return;}</span></a>
+<a name="179"><span class="lineNum">     179 </span>            :   // plumed_massert(isStatic(),&quot;this should only be used for static distributions&quot;);</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        348 :   plumed_massert(targetdist_grid_pntr_,&quot;the grids have not been setup using setupGrids&quot;);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        348 :   plumed_massert(log_targetdist_grid_pntr_,&quot;the grids have not been setup using setupGrids&quot;);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">     467955 :   for(Grid::index_t l=0; l&lt;targetdist_grid_pntr_-&gt;getSize(); l++)</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :   {</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">     467607 :     std::vector&lt;double&gt; argument = targetdist_grid_pntr_-&gt;getPoint(l);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">     467607 :     double value = getValue(argument);</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">     467607 :     targetdist_grid_pntr_-&gt;setValue(l,value);</span></a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">     467607 :     log_targetdist_grid_pntr_-&gt;setValue(l,-std::log(value));</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :   }</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">        348 :   log_targetdist_grid_pntr_-&gt;setMinToZero();</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        348 :   static_grid_calculated = true;</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : </a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">        901 : double TargetDistribution::integrateGrid(const Grid* grid_pntr) {</span></a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1802 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(grid_pntr);</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :   double sum = 0.0;</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">    2579140 :   for(Grid::index_t l=0; l&lt;grid_pntr-&gt;getSize(); l++) {</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">    2578239 :     sum += integration_weights[l]*grid_pntr-&gt;getValue(l);</span></a>
+<a name="199"><span class="lineNum">     199 </span>            :   }</a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">        901 :   return sum;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineCov">         90 : double TargetDistribution::normalizeGrid(Grid* grid_pntr) {</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         90 :   double normalization = TargetDistribution::integrateGrid(grid_pntr);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         90 :   grid_pntr-&gt;scaleAllValuesAndDerivatives(1.0/normalization);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         90 :   return normalization;</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">         28 : Grid TargetDistribution::getMarginalDistributionGrid(Grid* grid_pntr, const std::vector&lt;std::string&gt;&amp; args) {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         28 :   plumed_massert(grid_pntr-&gt;getDimension()&gt;1,&quot;doesn't make sense calculating the marginal distribution for a one-dimensional distribution&quot;);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         28 :   plumed_massert(args.size()&lt;grid_pntr-&gt;getDimension(),&quot;the number of arguments for the marginal distribution should be less than the dimension of the full distribution&quot;);</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   //</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         28 :   std::vector&lt;std::string&gt; argnames = grid_pntr-&gt;getArgNames();</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         28 :   std::vector&lt;unsigned int&gt; args_index(0);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         84 :   for(unsigned int i=0; i&lt;argnames.size(); i++) {</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">        112 :     for(unsigned int l=0; l&lt;args.size(); l++) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">         56 :       if(argnames[i]==args[l]) {args_index.push_back(i);}</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :     }</a>
+<a name="221"><span class="lineNum">     221 </span>            :   }</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">         28 :   plumed_massert(args.size()==args_index.size(),&quot;getMarginalDistributionGrid: problem with the arguments of the marginal&quot;);</span></a>
+<a name="223"><span class="lineNum">     223 </span>            :   //</a>
+<a name="224"><span class="lineNum">     224 </span>            :   auto Pw = Tools::make_unique&lt;MarginalWeight&gt;();</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         28 :   Grid proj_grid = grid_pntr-&gt;project(args,Pw.get());</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :   Pw.reset();</a>
+<a name="227"><span class="lineNum">     227 </span>            :   //</a>
+<a name="228"><span class="lineNum">     228 </span>            :   // scale with the bin volume used for the integral such that the</a>
+<a name="229"><span class="lineNum">     229 </span>            :   // marginals are proberly normalized to 1.0</a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">         28 :   double intVol = grid_pntr-&gt;getBinVolume();</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">         56 :   for(unsigned int l=0; l&lt;args_index.size(); l++) {</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         28 :     intVol/=grid_pntr-&gt;getDx()[args_index[l]];</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   }</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         28 :   proj_grid.scaleAllValuesAndDerivatives(intVol);</span></a>
+<a name="235"><span class="lineNum">     235 </span>            :   //</a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">         28 :   return proj_grid;</span></a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         56 : }</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          8 : Grid TargetDistribution::getMarginal(const std::vector&lt;std::string&gt;&amp; args) {</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">          8 :   return TargetDistribution::getMarginalDistributionGrid(targetdist_grid_pntr_.get(),args);</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : }</a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            : </a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        802 : void TargetDistribution::updateTargetDist() {</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   //</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        802 :   updateGrid();</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   //</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">        808 :   for(unsigned int i=0; i&lt;targetdist_modifer_pntrs_.size(); i++) {</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          6 :     applyTargetDistModiferToGrid(targetdist_modifer_pntrs_[i].get());</span></a>
+<a name="251"><span class="lineNum">     251 </span>            :   }</a>
+<a name="252"><span class="lineNum">     252 </span>            :   //</a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">        802 :   if(bias_cutoff_active_) {updateBiasCutoffForTargetDistGrid();}</span></a>
+<a name="254"><span class="lineNum">     254 </span>            :   //</a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        802 :   if(shift_targetdist_to_zero_ &amp;&amp; !(bias_cutoff_active_)) {setMinimumOfTargetDistGridToZero();}</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        802 :   if(force_normalization_ &amp;&amp; !(bias_cutoff_active_) ) {normalizeTargetDistGrid();}</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   //</a>
+<a name="258"><span class="lineNum">     258 </span>            :   // if(check_normalization_ &amp;&amp; !force_normalization_ &amp;&amp; !shift_targetdist_to_zero_){</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">        802 :   if(check_normalization_ &amp;&amp; !(bias_cutoff_active_)) {</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">        691 :     double normalization = integrateGrid(targetdist_grid_pntr_.get());</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :     const double normalization_thrshold = 0.1;</a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">        691 :     if(normalization &lt; 1.0-normalization_thrshold || normalization &gt; 1.0+normalization_thrshold) {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          9 :       std::string norm_str; Tools::convert(normalization,norm_str);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          9 :       std::string msg = &quot;the target distribution grid is not proberly normalized, integrating over the grid gives: &quot; + norm_str + &quot; - You can avoid this problem by using the NORMALIZE keyword&quot;;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          9 :       warning(msg);</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :     }</a>
+<a name="267"><span class="lineNum">     267 </span>            :   }</a>
+<a name="268"><span class="lineNum">     268 </span>            :   //</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        802 :   if(check_nonnegative_) {</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :     const double nonnegative_thrshold = -0.02;</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">        799 :     double grid_min_value = targetdist_grid_pntr_-&gt;getMinValue();</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">        799 :     if(grid_min_value&lt;nonnegative_thrshold) {</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineNoCov">          0 :       std::string grid_min_value_str; Tools::convert(grid_min_value,grid_min_value_str);</span></a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineNoCov">          0 :       std::string msg = &quot;the target distribution grid has negative values, the lowest value is: &quot; + grid_min_value_str + &quot; - You can avoid this problem by using the SHIFT_TO_ZERO keyword&quot;;</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineNoCov">          0 :       warning(msg);</span></a>
+<a name="276"><span class="lineNum">     276 </span>            :     }</a>
+<a name="277"><span class="lineNum">     277 </span>            :   }</a>
+<a name="278"><span class="lineNum">     278 </span>            :   //</a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">        802 :   if(check_nan_inf_) {checkNanAndInf();}</span></a>
+<a name="280"><span class="lineNum">     280 </span>            :   //</a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">        802 : }</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">         24 : void TargetDistribution::updateBiasCutoffForTargetDistGrid() {</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">         24 :   plumed_massert(vesbias_pntr_!=NULL,&quot;The VesBias has to be linked to use updateBiasCutoffForTargetDistGrid()&quot;);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">         24 :   plumed_massert(vesbias_pntr_-&gt;biasCutoffActive(),&quot;updateBiasCutoffForTargetDistGrid() should only be used if the bias cutoff is active&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :   // plumed_massert(targetdist_grid_pntr_!=NULL,&quot;the grids have not been setup using setupGrids&quot;);</a>
+<a name="288"><span class="lineNum">     288 </span>            :   // plumed_massert(log_targetdist_grid_pntr_!=NULL,&quot;the grids have not been setup using setupGrids&quot;);</a>
+<a name="289"><span class="lineNum">     289 </span><span class="lineCov">         24 :   plumed_massert(getBiasWithoutCutoffGridPntr()!=NULL,&quot;the bias without cutoff grid has to be linked&quot;);</span></a>
+<a name="290"><span class="lineNum">     290 </span>            :   //</a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         48 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(targetdist_grid_pntr_.get());</span></a>
+<a name="292"><span class="lineNum">     292 </span>            :   double norm = 0.0;</a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">       2624 :   for(Grid::index_t l=0; l&lt;targetdist_grid_pntr_-&gt;getSize(); l++)</span></a>
+<a name="294"><span class="lineNum">     294 </span>            :   {</a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">       2600 :     double value = targetdist_grid_pntr_-&gt;getValue(l);</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       2600 :     double bias = getBiasWithoutCutoffGridPntr()-&gt;getValue(l);</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">       2600 :     double deriv_factor_swf = 0.0;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">       2600 :     double swf = vesbias_pntr_-&gt;getBiasCutoffSwitchingFunction(bias,deriv_factor_swf);</span></a>
+<a name="299"><span class="lineNum">     299 </span>            :     // this comes from the p(s)</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineCov">       2600 :     value *= swf;</span></a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">       2600 :     norm += integration_weights[l]*value;</span></a>
+<a name="302"><span class="lineNum">     302 </span>            :     // this comes from the derivative of V(s)</a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">       2600 :     value *= deriv_factor_swf;</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">       2600 :     targetdist_grid_pntr_-&gt;setValue(l,value);</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :     // double log_value = log_targetdist_grid_pntr_-&gt;getValue(l) - std::log(swf);</a>
+<a name="306"><span class="lineNum">     306 </span>            :     // log_targetdist_grid_pntr_-&gt;setValue(l,log_value);</a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         24 :   targetdist_grid_pntr_-&gt;scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="309"><span class="lineNum">     309 </span>            :   // log_targetdist_grid_pntr_-&gt;setMinToZero();</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         24 : }</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          6 : void TargetDistribution::applyTargetDistModiferToGrid(TargetDistModifer* modifer_pntr) {</span></a>
+<a name="313"><span class="lineNum">     313 </span>            :   // plumed_massert(targetdist_grid_pntr_!=NULL,&quot;the grids have not been setup using setupGrids&quot;);</a>
+<a name="314"><span class="lineNum">     314 </span>            :   // plumed_massert(log_targetdist_grid_pntr_!=NULL,&quot;the grids have not been setup using setupGrids&quot;);</a>
+<a name="315"><span class="lineNum">     315 </span>            :   //</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">         12 :   std::vector&lt;double&gt; integration_weights = GridIntegrationWeights::getIntegrationWeights(targetdist_grid_pntr_.get());</span></a>
+<a name="317"><span class="lineNum">     317 </span>            :   double norm = 0.0;</a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">      21212 :   for(Grid::index_t l=0; l&lt;targetdist_grid_pntr_-&gt;getSize(); l++)</span></a>
+<a name="319"><span class="lineNum">     319 </span>            :   {</a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">      21206 :     double value = targetdist_grid_pntr_-&gt;getValue(l);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">      21206 :     std::vector&lt;double&gt; cv_values = targetdist_grid_pntr_-&gt;getPoint(l);</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      21206 :     value = modifer_pntr-&gt;getModifedTargetDistValue(value,cv_values);</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">      21206 :     norm += integration_weights[l]*value;</span></a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      21206 :     targetdist_grid_pntr_-&gt;setValue(l,value);</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">      21206 :     log_targetdist_grid_pntr_-&gt;setValue(l,-std::log(value));</span></a>
+<a name="326"><span class="lineNum">     326 </span>            :   }</a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          6 :   targetdist_grid_pntr_-&gt;scaleAllValuesAndDerivatives(1.0/norm);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          6 :   log_targetdist_grid_pntr_-&gt;setMinToZero();</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          6 : }</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">         29 : void TargetDistribution::updateLogTargetDistGrid() {</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">      44070 :   for(Grid::index_t l=0; l&lt;targetdist_grid_pntr_-&gt;getSize(); l++)</span></a>
+<a name="334"><span class="lineNum">     334 </span>            :   {</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      44041 :     log_targetdist_grid_pntr_-&gt;setValue(l,-std::log(targetdist_grid_pntr_-&gt;getValue(l)));</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   }</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">         29 :   log_targetdist_grid_pntr_-&gt;setMinToZero();</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         29 : }</span></a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          3 : void TargetDistribution::setMinimumOfTargetDistGridToZero() {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          3 :   targetDistGrid().setMinToZero();</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">          3 :   normalizeTargetDistGrid();</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          3 :   updateLogTargetDistGrid();</span></a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">          3 : }</span></a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          8 : void TargetDistribution::readInRestartTargetDistGrid(const std::string&amp; grid_fname) {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          8 :   plumed_massert(isDynamic(),&quot;this should only be used for dynamically updated target distributions!&quot;);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          8 :   IFile gridfile;</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          8 :   if(!gridfile.FileExist(grid_fname)) {</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: problem with reading previous target distribution when restarting, cannot find file &quot; + grid_fname);</span></a>
+<a name="353"><span class="lineNum">     353 </span>            :   }</a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          8 :   gridfile.open(grid_fname);</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         16 :   std::unique_ptr&lt;GridBase&gt; restart_grid = GridBase::create(&quot;targetdist&quot;,grid_args_,gridfile,false,false,false);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          8 :   if(restart_grid-&gt;getSize()!=targetdist_grid_pntr_-&gt;getSize()) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineNoCov">          0 :     plumed_merror(getName()+&quot;: problem with reading previous target distribution when restarting, the grid is not of the correct size!&quot;);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   }</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          8 :   VesTools::copyGridValues(restart_grid.get(),targetdist_grid_pntr_.get());</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">          8 :   updateLogTargetDistGrid();</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">          8 : }</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          1 : void TargetDistribution::clearLogTargetDistGrid() {</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          1 :   log_targetdist_grid_pntr_-&gt;clear();</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          1 : }</span></a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span>            : </a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineNoCov">          0 : void TargetDistribution::checkNanAndInf() {</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineNoCov">          0 :   for(Grid::index_t l=0; l&lt;targetdist_grid_pntr_-&gt;getSize(); l++)</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   {</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineNoCov">          0 :     double value = targetdist_grid_pntr_-&gt;getValue(l);</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     if(std::isnan(value) || std::isinf(value)) {</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :       std::string vs; Tools::convert(value,vs);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineNoCov">          0 :       std::vector&lt;double&gt; p = targetdist_grid_pntr_-&gt;getPoint(l);</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :       std::string ps; Tools::convert(p[0],ps);</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineNoCov">          0 :       ps = &quot;(&quot; + ps;</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineNoCov">          0 :       for(unsigned int k=1; k&lt;p.size(); k++) {</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 :         std::string t1; Tools::convert(p[k],t1);</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :         ps = ps + &quot;,&quot; + t1;</span></a>
+<a name="380"><span class="lineNum">     380 </span>            :       }</a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineNoCov">          0 :       ps = ps + &quot;)&quot;;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot;: problem with target distribution, the value at &quot; + ps + &quot; is &quot; + vs);</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     }</a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="386"><span class="lineNum">     386 </span>            : </a>
+<a name="387"><span class="lineNum">     387 </span>            : }</a>
+<a name="388"><span class="lineNum">     388 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistribution.h.func-sort-c.html b/coverage/ves/TargetDistribution.h.func-sort-c.html
new file mode 100644
index 0000000000..61a1643b69
--- /dev/null
+++ b/coverage/ves/TargetDistribution.h.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistribution.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistribution.h<span style="font-size: 80%;"> (<a href="TargetDistribution.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="TargetDistribution.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#177">_ZN4PLMD3ves18TargetDistribution5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#176">_ZN4PLMD3ves18TargetDistribution6updateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#178">_ZN4PLMD3ves18TargetDistribution9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#197">_ZN4PLMD3ves18TargetDistribution23normalizeTargetDistGridEv</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#106">_ZN4PLMD3ves18TargetDistribution20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">287</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#124">_ZN4PLMD3ves18TargetDistribution10updateGridEv</a></td>
+              <td class="coverFnHi">368</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistribution.h.func.html b/coverage/ves/TargetDistribution.h.func.html
new file mode 100644
index 0000000000..d19d5aca4a
--- /dev/null
+++ b/coverage/ves/TargetDistribution.h.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistribution.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistribution.h<span style="font-size: 80%;"> (<a href="TargetDistribution.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="TargetDistribution.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#124">_ZN4PLMD3ves18TargetDistribution10updateGridEv</a></td>
+              <td class="coverFnHi">368</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#106">_ZN4PLMD3ves18TargetDistribution20setupAdditionalGridsERKSt6vectorIPNS_5ValueESaIS4_EERKS2_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EESI_RKS2_IjSaIjEE</a></td>
+              <td class="coverFnHi">287</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#197">_ZN4PLMD3ves18TargetDistribution23normalizeTargetDistGridEv</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#177">_ZN4PLMD3ves18TargetDistribution5applyEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#176">_ZN4PLMD3ves18TargetDistribution6updateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="TargetDistribution.h.gcov.html#178">_ZN4PLMD3ves18TargetDistribution9calculateEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/TargetDistribution.h.gcov.html b/coverage/ves/TargetDistribution.h.gcov.html
new file mode 100644
index 0000000000..1f13a4b673
--- /dev/null
+++ b/coverage/ves/TargetDistribution.h.gcov.html
@@ -0,0 +1,285 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/TargetDistribution.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - TargetDistribution.h<span style="font-size: 80%;"> (source / <a href="TargetDistribution.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">18</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryMed">81.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_TargetDistribution_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_TargetDistribution_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;string&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;cmath&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;memory&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #define PLUMED_VES_TARGETDISTRIBUTION_INIT(ao) TargetDistribution(ao)</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : /**</a>
+<a name="37"><span class="lineNum">      37 </span>            : \ingroup INHERIT</a>
+<a name="38"><span class="lineNum">      38 </span>            : Abstract base class for implenting new target distributions.</a>
+<a name="39"><span class="lineNum">      39 </span>            : */</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class Action;</a>
+<a name="42"><span class="lineNum">      42 </span>            : class Grid;</a>
+<a name="43"><span class="lineNum">      43 </span>            : class Value;</a>
+<a name="44"><span class="lineNum">      44 </span>            : class Keywords;</a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : namespace ves {</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : class TargetDistModifer;</a>
+<a name="49"><span class="lineNum">      49 </span>            : class VesBias;</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span>            : class TargetDistribution :</a>
+<a name="52"><span class="lineNum">      52 </span>            :   public Action</a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span>            : private:</a>
+<a name="55"><span class="lineNum">      55 </span>            :   enum TargetDistType {</a>
+<a name="56"><span class="lineNum">      56 </span>            :     static_targetdist,</a>
+<a name="57"><span class="lineNum">      57 </span>            :     dynamic_targetdist</a>
+<a name="58"><span class="lineNum">      58 </span>            :   } type_;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   //</a>
+<a name="60"><span class="lineNum">      60 </span>            :   bool force_normalization_;</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool check_normalization_;</a>
+<a name="62"><span class="lineNum">      62 </span>            :   bool check_nonnegative_;</a>
+<a name="63"><span class="lineNum">      63 </span>            :   bool check_nan_inf_;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   bool shift_targetdist_to_zero_;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   // dimension of the distribution</a>
+<a name="66"><span class="lineNum">      66 </span>            :   unsigned int dimension_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   // grid parameters</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;Value*&gt; grid_args_;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   //</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::unique_ptr&lt;Grid&gt; targetdist_grid_pntr_;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   std::unique_ptr&lt;Grid&gt; log_targetdist_grid_pntr_;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   //</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;std::unique_ptr&lt;TargetDistModifer&gt;&gt; targetdist_modifer_pntrs_;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   //</a>
+<a name="75"><span class="lineNum">      75 </span>            :   Action* action_pntr_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   VesBias* vesbias_pntr_;</a>
+<a name="77"><span class="lineNum">      77 </span>            :   //</a>
+<a name="78"><span class="lineNum">      78 </span>            :   bool needs_bias_grid_;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   bool needs_bias_withoutcutoff_grid_;</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool needs_fes_grid_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   //</a>
+<a name="82"><span class="lineNum">      82 </span>            :   Grid* bias_grid_pntr_;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   Grid* bias_withoutcutoff_grid_pntr_;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   Grid* fes_grid_pntr_;</a>
+<a name="85"><span class="lineNum">      85 </span>            :   //</a>
+<a name="86"><span class="lineNum">      86 </span>            :   bool static_grid_calculated;</a>
+<a name="87"><span class="lineNum">      87 </span>            :   //</a>
+<a name="88"><span class="lineNum">      88 </span>            :   bool allow_bias_cutoff_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   bool bias_cutoff_active_;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   //</a>
+<a name="91"><span class="lineNum">      91 </span>            :   void calculateStaticDistributionGrid();</a>
+<a name="92"><span class="lineNum">      92 </span>            :   void updateBiasCutoffForTargetDistGrid();</a>
+<a name="93"><span class="lineNum">      93 </span>            :   void checkNanAndInf();</a>
+<a name="94"><span class="lineNum">      94 </span>            : protected:</a>
+<a name="95"><span class="lineNum">      95 </span>            :   void setStatic() {type_=static_targetdist;}</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         41 :   void setDynamic() {type_=dynamic_targetdist;}</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :   // set the that target distribution is normalized</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         80 :   void setForcedNormalization() {force_normalization_=true; check_normalization_=false;}</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   void unsetForcedNormalization() {force_normalization_=false; check_normalization_=true;};</a>
+<a name="100"><span class="lineNum">     100 </span>            :   //</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineNoCov">          0 :   void setBiasGridNeeded() {needs_bias_grid_=true;}</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          3 :   void setBiasWithoutCutoffGridNeeded() {needs_bias_withoutcutoff_grid_=true;}</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         38 :   void setFesGridNeeded() {needs_fes_grid_=true;}</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   //</a>
+<a name="105"><span class="lineNum">     105 </span>            :   VesBias* getPntrToVesBias() const;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   Action* getPntrToAction() const;</a>
+<a name="107"><span class="lineNum">     107 </span>            :   //</a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        287 :   virtual void setupAdditionalGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;) {}</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   //</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void normalizeTargetDistGrid();</a>
+<a name="111"><span class="lineNum">     111 </span>            :   //</a>
+<a name="112"><span class="lineNum">     112 </span>            :   Grid&amp; targetDistGrid() const {return *targetdist_grid_pntr_;}</a>
+<a name="113"><span class="lineNum">     113 </span>            :   Grid&amp; logTargetDistGrid() const {return *log_targetdist_grid_pntr_;}</a>
+<a name="114"><span class="lineNum">     114 </span>            :   //</a>
+<a name="115"><span class="lineNum">     115 </span>            :   Grid* getBiasGridPntr() const {return bias_grid_pntr_;}</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       2624 :   Grid* getBiasWithoutCutoffGridPntr() const {return bias_withoutcutoff_grid_pntr_;}</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">   11814078 :   Grid* getFesGridPntr() const {return fes_grid_pntr_;}</span></a>
+<a name="118"><span class="lineNum">     118 </span>            :   //</a>
+<a name="119"><span class="lineNum">     119 </span>            :   double getBeta() const;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   //</a>
+<a name="121"><span class="lineNum">     121 </span>            :   void applyTargetDistModiferToGrid(TargetDistModifer* modifer_pntr);</a>
+<a name="122"><span class="lineNum">     122 </span>            :   //</a>
+<a name="123"><span class="lineNum">     123 </span>            :   void setMinimumOfTargetDistGridToZero();</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void updateLogTargetDistGrid();</a>
+<a name="125"><span class="lineNum">     125 </span>            :   //</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        368 :   virtual void updateGrid() {calculateStaticDistributionGrid();}</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : public:</a>
+<a name="128"><span class="lineNum">     128 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="129"><span class="lineNum">     129 </span>            :   explicit TargetDistribution(const ActionOptions&amp;);</a>
+<a name="130"><span class="lineNum">     130 </span>            :   ~TargetDistribution();</a>
+<a name="131"><span class="lineNum">     131 </span>            :   //</a>
+<a name="132"><span class="lineNum">     132 </span>            :   bool isStatic() const {return type_==static_targetdist;}</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        602 :   bool isDynamic() const {return type_==dynamic_targetdist;}</span></a>
+<a name="134"><span class="lineNum">     134 </span>            :   // is the target distribution normalize or not</a>
+<a name="135"><span class="lineNum">     135 </span>            :   bool forcedNormalization() const {return force_normalization_;};</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       5194 :   bool isTargetDistGridShiftedToZero() const {return shift_targetdist_to_zero_;}</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :   //</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        466 :   bool biasGridNeeded() const {return needs_bias_grid_;}</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         45 :   bool biasWithoutCutoffGridNeeded() const {return needs_bias_withoutcutoff_grid_;}</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        466 :   bool fesGridNeeded()  const {return needs_fes_grid_;}</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :   //</a>
+<a name="142"><span class="lineNum">     142 </span>            :   void allowBiasCutoff() {allow_bias_cutoff_=true;}</a>
+<a name="143"><span class="lineNum">     143 </span>            :   void doNotAllowBiasCutoff() {allow_bias_cutoff_=false;}</a>
+<a name="144"><span class="lineNum">     144 </span>            :   bool isBiasCutoffAllowed() const {return allow_bias_cutoff_;}</a>
+<a name="145"><span class="lineNum">     145 </span>            :   bool biasCutoffActive() const {return bias_cutoff_active_;}</a>
+<a name="146"><span class="lineNum">     146 </span>            :   //</a>
+<a name="147"><span class="lineNum">     147 </span>            :   void setDimension(const unsigned int dimension);</a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">     506318 :   unsigned getDimension() const {return dimension_;}</span></a>
+<a name="149"><span class="lineNum">     149 </span>            :   //</a>
+<a name="150"><span class="lineNum">     150 </span>            :   virtual void linkVesBias(VesBias*);</a>
+<a name="151"><span class="lineNum">     151 </span>            :   virtual void linkAction(Action*);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   //</a>
+<a name="153"><span class="lineNum">     153 </span>            :   virtual void linkBiasGrid(Grid*);</a>
+<a name="154"><span class="lineNum">     154 </span>            :   virtual void linkBiasWithoutCutoffGrid(Grid*);</a>
+<a name="155"><span class="lineNum">     155 </span>            :   virtual void linkFesGrid(Grid*);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   //</a>
+<a name="157"><span class="lineNum">     157 </span>            :   void setupBiasCutoff();</a>
+<a name="158"><span class="lineNum">     158 </span>            :   //</a>
+<a name="159"><span class="lineNum">     159 </span>            :   Grid* getTargetDistGridPntr() const {return targetdist_grid_pntr_.get();}</a>
+<a name="160"><span class="lineNum">     160 </span>            :   Grid* getLogTargetDistGridPntr() const {return log_targetdist_grid_pntr_.get();}</a>
+<a name="161"><span class="lineNum">     161 </span>            :   //</a>
+<a name="162"><span class="lineNum">     162 </span>            :   void clearLogTargetDistGrid();</a>
+<a name="163"><span class="lineNum">     163 </span>            :   // calculate the target distribution itself</a>
+<a name="164"><span class="lineNum">     164 </span>            :   virtual double getValue(const std::vector&lt;double&gt;&amp;) const = 0;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   //</a>
+<a name="166"><span class="lineNum">     166 </span>            :   void setupGrids(const std::vector&lt;Value*&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;std::string&gt;&amp;, const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="167"><span class="lineNum">     167 </span>            :   //</a>
+<a name="168"><span class="lineNum">     168 </span>            :   Grid getMarginal(const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="169"><span class="lineNum">     169 </span>            :   //</a>
+<a name="170"><span class="lineNum">     170 </span>            :   void updateTargetDist();</a>
+<a name="171"><span class="lineNum">     171 </span>            :   //</a>
+<a name="172"><span class="lineNum">     172 </span>            :   void readInRestartTargetDistGrid(const std::string&amp;);</a>
+<a name="173"><span class="lineNum">     173 </span>            :   //</a>
+<a name="174"><span class="lineNum">     174 </span>            :   static double integrateGrid(const Grid*);</a>
+<a name="175"><span class="lineNum">     175 </span>            :   static double normalizeGrid(Grid*);</a>
+<a name="176"><span class="lineNum">     176 </span>            :   static Grid getMarginalDistributionGrid(Grid*, const std::vector&lt;std::string&gt;&amp;);</a>
+<a name="177"><span class="lineNum">     177 </span>            :   // empty standard action stuff</a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineNoCov">          0 :   void update() override {};</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineNoCov">          0 :   void apply() override {};</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineNoCov">          0 :   void calculate() override {};</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : };</a>
+<a name="182"><span class="lineNum">     182 </span>            : </a>
+<a name="183"><span class="lineNum">     183 </span>            : </a>
+<a name="184"><span class="lineNum">     184 </span>            : inline</a>
+<a name="185"><span class="lineNum">     185 </span>            : VesBias* TargetDistribution::getPntrToVesBias() const {</a>
+<a name="186"><span class="lineNum">     186 </span>            :   plumed_massert(vesbias_pntr_!=NULL,&quot;the VES bias has not been linked&quot;);</a>
+<a name="187"><span class="lineNum">     187 </span>            :   return vesbias_pntr_;</a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : inline</a>
+<a name="192"><span class="lineNum">     192 </span>            : Action* TargetDistribution::getPntrToAction() const {</a>
+<a name="193"><span class="lineNum">     193 </span>            :   plumed_massert(action_pntr_!=NULL,&quot;the action has not been linked&quot;);</a>
+<a name="194"><span class="lineNum">     194 </span>            :   return action_pntr_;</a>
+<a name="195"><span class="lineNum">     195 </span>            : }</a>
+<a name="196"><span class="lineNum">     196 </span>            : </a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            : inline</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         90 : void TargetDistribution::normalizeTargetDistGrid() {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         90 :   double normalization = normalizeGrid(targetdist_grid_pntr_.get());</span></a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">         90 :   if(normalization&lt;0.0) {plumed_merror(getName()+&quot;: something went wrong trying to normalize the target distribution, integrating over it gives a negative value.&quot;);}</span></a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         90 : }</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : </a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesBias.cpp.func-sort-c.html b/coverage/ves/VesBias.cpp.func-sort-c.html
new file mode 100644
index 0000000000..cf93b04c5e
--- /dev/null
+++ b/coverage/ves/VesBias.cpp.func-sort-c.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesBias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesBias.cpp<span style="font-size: 80%;"> (<a href="VesBias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">330</td>
+            <td class="headerCovTableEntry">432</td>
+            <td class="headerCovTableEntryMed">76.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
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+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesBias.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
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+              <td class="coverFnHi">567</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#549">_ZNK4PLMD3ves7VesBias19getIterationCounterEv</a></td>
+              <td class="coverFnHi">1005</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#722">_ZNK4PLMD3ves7VesBias30getBiasCutoffSwitchingFunctionEdRd</a></td>
+              <td class="coverFnHi">3263</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#413">_ZN4PLMD3ves7VesBias24updateGradientAndHessianEb</a></td>
+              <td class="coverFnHi">22810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#490">_ZN4PLMD3ves7VesBias20addToSampledAveragesERKSt6vectorIdSaIdEEj</a></td>
+              <td class="coverFnHi">23556</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
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diff --git a/coverage/ves/VesBias.cpp.func.html b/coverage/ves/VesBias.cpp.func.html
new file mode 100644
index 0000000000..6fe9d64c9b
--- /dev/null
+++ b/coverage/ves/VesBias.cpp.func.html
@@ -0,0 +1,252 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesBias.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesBias.cpp<span style="font-size: 80%;"> (<a href="VesBias.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">330</td>
+            <td class="headerCovTableEntry">432</td>
+            <td class="headerCovTableEntryMed">76.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesBias.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#652">_ZN4PLMD3ves7VesBias10setGridMaxERKSt6vectorIdSaIdEE</a></td>
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+              <td class="coverFnLo">0</td>
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+              <td class="coverFnHi">567</td>
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+              <td class="coverFnHi">90</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#235">_ZN4PLMD3ves7VesBiasD0Ev</a></td>
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+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#235">_ZN4PLMD3ves7VesBiasD2Ev</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#735">_ZNK4PLMD3ves7VesBias18useMultipleWalkersEv</a></td>
+              <td class="coverFnHi">567</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#549">_ZNK4PLMD3ves7VesBias19getIterationCounterEv</a></td>
+              <td class="coverFnHi">1005</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#752">_ZNK4PLMD3ves7VesBias23calculateReweightFactorEv</a></td>
+              <td class="coverFnLo">0</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#606">_ZNK4PLMD3ves7VesBias23getCoeffsSetLabelStringERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj</a></td>
+              <td class="coverFnHi">442</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#658">_ZNK4PLMD3ves7VesBias24getCurrentOutputFilenameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">383</td>
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+    <tr>
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+              <td class="coverFnHi">552</td>
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+              <td class="coverFnHi">3263</td>
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+    <tr>
+              <td class="coverFn"><a href="VesBias.cpp.gcov.html#670">_ZNK4PLMD3ves7VesBias34getCurrentTargetDistOutputFilenameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesBias.cpp.gcov.html b/coverage/ves/VesBias.cpp.gcov.html
new file mode 100644
index 0000000000..5682786901
--- /dev/null
+++ b/coverage/ves/VesBias.cpp.gcov.html
@@ -0,0 +1,837 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesBias.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesBias.cpp<span style="font-size: 80%;"> (source / <a href="VesBias.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">330</td>
+            <td class="headerCovTableEntry">432</td>
+            <td class="headerCovTableEntryMed">76.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntry">45</td>
+            <td class="headerCovTableEntryLo">60.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;FermiSwitchingFunction.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace PLMD {</a>
+<a name="40"><span class="lineNum">      40 </span>            : namespace ves {</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         90 : VesBias::VesBias(const ActionOptions&amp;ao):</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   Action(ao),</a>
+<a name="44"><span class="lineNum">      44 </span>            :   Bias(ao),</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         90 :   ncoeffssets_(0),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         90 :   sampled_averages(0),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         90 :   sampled_cross_averages(0),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         90 :   use_multiple_coeffssets_(false),</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         90 :   coeffs_fnames(0),</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         90 :   ncoeffs_total_(0),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         90 :   optimizer_pntr_(NULL),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         90 :   optimize_coeffs_(false),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         90 :   compute_hessian_(false),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         90 :   diagonal_hessian_(true),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         90 :   aver_counters(0),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         90 :   kbt_(0.0),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         90 :   targetdist_pntrs_(0),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         90 :   dynamic_targetdist_(false),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         90 :   grid_bins_(0),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         90 :   grid_min_(0),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         90 :   grid_max_(0),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         90 :   bias_filename_(&quot;&quot;),</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         90 :   fes_filename_(&quot;&quot;),</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         90 :   targetdist_filename_(&quot;&quot;),</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         90 :   coeffs_id_prefix_(&quot;c-&quot;),</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         90 :   bias_file_fmt_(&quot;14.9f&quot;),</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         90 :   fes_file_fmt_(&quot;14.9f&quot;),</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         90 :   targetdist_file_fmt_(&quot;14.9f&quot;),</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         90 :   targetdist_restart_file_fmt_(&quot;30.16e&quot;),</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">         90 :   filenames_have_iteration_number_(false),</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         90 :   bias_fileoutput_active_(false),</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         90 :   fes_fileoutput_active_(false),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         90 :   fesproj_fileoutput_active_(false),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         90 :   dynamic_targetdist_fileoutput_active_(false),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         90 :   static_targetdist_fileoutput_active_(true),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         90 :   bias_cutoff_active_(false),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         90 :   bias_cutoff_value_(0.0),</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         90 :   bias_current_max_value(0.0),</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         90 :   calc_reweightfactor_(false),</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">        270 :   optimization_threshold_(0.0)</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         90 :   log.printf(&quot;  VES bias, please read and cite &quot;);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        180 :   log &lt;&lt; plumed.cite(&quot;Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         90 :   log.printf(&quot;\n&quot;);</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : </a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         90 :   double temp=0.0;</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         90 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         90 :   if(temp&gt;0.0) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         90 :     kbt_=plumed.getAtoms().getKBoltzmann()*temp;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :   }</a>
+<a name="91"><span class="lineNum">      91 </span>            :   else {</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineNoCov">          0 :     kbt_=plumed.getAtoms().getKbT();</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :   }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">         90 :   if(kbt_&gt;0.0) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         90 :     log.printf(&quot;  KbT: %f\n&quot;,kbt_);</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span>            :   // NOTE: the check for that the temperature is given is done when linking the optimizer later on.</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;COEFFS&quot;)) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        180 :     parseVector(&quot;COEFFS&quot;,coeffs_fnames);</span></a>
+<a name="101"><span class="lineNum">     101 </span>            :   }</a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;GRID_BINS&quot;)) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        180 :     parseMultipleValues&lt;unsigned int&gt;(&quot;GRID_BINS&quot;,grid_bins_,getNumberOfArguments(),100);</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         90 :   if(keywords.exists(&quot;GRID_MIN&quot;) &amp;&amp; keywords.exists(&quot;GRID_MAX&quot;)) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :     parseMultipleValues(&quot;GRID_MIN&quot;,grid_min_,getNumberOfArguments());</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineNoCov">          0 :     parseMultipleValues(&quot;GRID_MAX&quot;,grid_max_,getNumberOfArguments());</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::vector&lt;std::string&gt; targetdist_labels;</a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;TARGET_DISTRIBUTION&quot;)) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">        180 :     parseVector(&quot;TARGET_DISTRIBUTION&quot;,targetdist_labels);</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         90 :     if(targetdist_labels.size()&gt;1) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :       plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: multiple target distribution labels not allowed&quot;);</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :   else if(keywords.exists(&quot;TARGET_DISTRIBUTIONS&quot;)) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :     parseVector(&quot;TARGET_DISTRIBUTIONS&quot;,targetdist_labels);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">         90 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">        180 :   targetdist_pntrs_ = VesTools::getPointersFromLabels&lt;TargetDistribution*&gt;(targetdist_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         90 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Problem with target distribution in &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        135 :   for(unsigned int i=0; i&lt;targetdist_pntrs_.size(); i++) {</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         45 :     targetdist_pntrs_[i]-&gt;linkVesBias(this);</span></a>
+<a name="129"><span class="lineNum">     129 </span>            :   }</a>
+<a name="130"><span class="lineNum">     130 </span>            : </a>
+<a name="131"><span class="lineNum">     131 </span>            : </a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         90 :   if(getNumberOfArguments()&gt;2) {</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :     disableStaticTargetDistFileOutput();</a>
+<a name="134"><span class="lineNum">     134 </span>            :   }</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;BIAS_FILE&quot;)) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        180 :     parse(&quot;BIAS_FILE&quot;,bias_filename_);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         90 :     if(bias_filename_.size()==0) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">        180 :       bias_filename_ = &quot;bias.&quot; + getLabel() + &quot;.data&quot;;</span></a>
+<a name="141"><span class="lineNum">     141 </span>            :     }</a>
+<a name="142"><span class="lineNum">     142 </span>            :   }</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;FES_FILE&quot;)) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        180 :     parse(&quot;FES_FILE&quot;,fes_filename_);</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         90 :     if(fes_filename_.size()==0) {</span></a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">        180 :       fes_filename_ = &quot;fes.&quot; + getLabel() + &quot;.data&quot;;</span></a>
+<a name="147"><span class="lineNum">     147 </span>            :     }</a>
+<a name="148"><span class="lineNum">     148 </span>            :   }</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;TARGETDIST_FILE&quot;)) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        180 :     parse(&quot;TARGETDIST_FILE&quot;,targetdist_filename_);</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">         90 :     if(targetdist_filename_.size()==0) {</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">        180 :       targetdist_filename_ = &quot;targetdist.&quot; + getLabel() + &quot;.data&quot;;</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :     }</a>
+<a name="154"><span class="lineNum">     154 </span>            :   }</a>
+<a name="155"><span class="lineNum">     155 </span>            :   //</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;BIAS_FILE_FMT&quot;)) {</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineNoCov">          0 :     parse(&quot;BIAS_FILE_FMT&quot;,bias_file_fmt_);</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :   }</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;FES_FILE_FMT&quot;)) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineNoCov">          0 :     parse(&quot;FES_FILE_FMT&quot;,fes_file_fmt_);</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;TARGETDIST_FILE_FMT&quot;)) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineNoCov">          0 :     parse(&quot;TARGETDIST_FILE_FMT&quot;,targetdist_file_fmt_);</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   }</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;TARGETDIST_RESTART_FILE_FMT&quot;)) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :     parse(&quot;TARGETDIST_RESTART_FILE_FMT&quot;,targetdist_restart_file_fmt_);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span>            : </a>
+<a name="169"><span class="lineNum">     169 </span>            :   //</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;BIAS_CUTOFF&quot;)) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         90 :     double cutoff_value=0.0;</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">         90 :     parse(&quot;BIAS_CUTOFF&quot;,cutoff_value);</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">         90 :     if(cutoff_value&lt;0.0) {</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;the value given in BIAS_CUTOFF doesn't make sense, it should be larger than 0.0&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            :     //</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">         90 :     if(cutoff_value&gt;0.0) {</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">          3 :       double fermi_lambda=10.0;</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :       parse(&quot;BIAS_CUTOFF_FERMI_LAMBDA&quot;,fermi_lambda);</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">          3 :       setupBiasCutoff(cutoff_value,fermi_lambda);</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          3 :       log.printf(&quot;  Employing a bias cutoff of %f (the lambda value for the Fermi switching function is %f), see and cite &quot;,cutoff_value,fermi_lambda);</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          6 :       log &lt;&lt; plumed.cite(&quot;McCarty, Valsson, Tiwary, and Parrinello, Phys. Rev. Lett. 115, 070601 (2015)&quot;);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :       log.printf(&quot;\n&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            :     }</a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;PROJ_ARG&quot;)) {</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :     std::vector&lt;std::string&gt; proj_arg;</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         90 :     for(int i=1;; i++) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">        212 :       if(!parseNumberedVector(&quot;PROJ_ARG&quot;,i,proj_arg)) {break;}</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :       // checks</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         16 :       if(proj_arg.size() &gt; (getNumberOfArguments()-1) ) {</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;PROJ_ARG must be a subset of ARG&quot;);</span></a>
+<a name="195"><span class="lineNum">     195 </span>            :       }</a>
+<a name="196"><span class="lineNum">     196 </span>            :       //</a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         32 :       for(unsigned int k=0; k&lt;proj_arg.size(); k++) {</span></a>
+<a name="198"><span class="lineNum">     198 </span>            :         bool found = false;</a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         24 :         for(unsigned int l=0; l&lt;getNumberOfArguments(); l++) {</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         24 :           if(proj_arg[k]==getPntrToArgument(l)-&gt;getName()) {</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :             found = true;</a>
+<a name="202"><span class="lineNum">     202 </span>            :             break;</a>
+<a name="203"><span class="lineNum">     203 </span>            :           }</a>
+<a name="204"><span class="lineNum">     204 </span>            :         }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         16 :         if(!found) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineNoCov">          0 :           std::string s1; Tools::convert(i,s1);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineNoCov">          0 :           std::string error = &quot;PROJ_ARG&quot; + s1 + &quot;: label &quot; + proj_arg[k] + &quot; is not among the arguments given in ARG&quot;;</span></a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineNoCov">          0 :           plumed_merror(error);</span></a>
+<a name="209"><span class="lineNum">     209 </span>            :         }</a>
+<a name="210"><span class="lineNum">     210 </span>            :       }</a>
+<a name="211"><span class="lineNum">     211 </span>            :       //</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">         16 :       projection_args_.push_back(proj_arg);</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         16 :     }</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         90 :   }</span></a>
+<a name="215"><span class="lineNum">     215 </span>            : </a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;CALC_REWEIGHT_FACTOR&quot;)) {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineNoCov">          0 :     parseFlag(&quot;CALC_REWEIGHT_FACTOR&quot;,calc_reweightfactor_);</span></a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineNoCov">          0 :     if(calc_reweightfactor_) {</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineNoCov">          0 :       addComponent(&quot;rct&quot;); componentIsNotPeriodic(&quot;rct&quot;);</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineNoCov">          0 :       updateReweightFactor();</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     }</a>
+<a name="222"><span class="lineNum">     222 </span>            :   }</a>
+<a name="223"><span class="lineNum">     223 </span>            : </a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">        180 :   if(keywords.exists(&quot;OPTIMIZATION_THRESHOLD&quot;)) {</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">         90 :     parse(&quot;OPTIMIZATION_THRESHOLD&quot;,optimization_threshold_);</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">         90 :     if(optimization_threshold_ &lt; 0.0) {</span></a>
+<a name="227"><span class="lineNum">     227 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;OPTIMIZATION_THRESHOLD should be a postive value&quot;);</span></a>
+<a name="228"><span class="lineNum">     228 </span>            :     }</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         90 :     if(optimization_threshold_!=0.0) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          1 :       log.printf(&quot;  Employing a threshold value of %e for optimization of localized basis functions.\n&quot;,optimization_threshold_);</span></a>
+<a name="231"><span class="lineNum">     231 </span>            :     }</a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         90 : }</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : </a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">         90 : VesBias::~VesBias() {</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">        180 : }</span></a>
+<a name="239"><span class="lineNum">     239 </span>            : </a>
+<a name="240"><span class="lineNum">     240 </span>            : </a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         92 : void VesBias::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         92 :   Bias::registerKeywords(keys);</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">        184 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;the system temperature - this is needed if the MD code does not pass the temperature to PLUMED.&quot;);</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   //</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;COEFFS&quot;,&quot;read in the coefficients from files.&quot;);</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   //</a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;TARGET_DISTRIBUTION&quot;,&quot;the label of the target distribution to be used.&quot;);</span></a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;TARGET_DISTRIBUTIONS&quot;,&quot;the label of the target distribution to be used. Here you are allows to use multiple labels.&quot;);</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :   //</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;GRID_BINS&quot;,&quot;the number of bins used for the grid. The default value is 100 bins per dimension.&quot;);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;GRID_MIN&quot;,&quot;the lower bounds used for the grid.&quot;);</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;GRID_MAX&quot;,&quot;the upper bounds used for the grid.&quot;);</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   //</a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">        184 :   keys.add(&quot;optional&quot;,&quot;BIAS_FILE&quot;,&quot;filename of the file on which the bias should be written out. By default it is bias.LABEL.data. Note that suffixes indicating the iteration number (iter-#) are added to the filename when optimizing coefficients.&quot;);</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">        184 :   keys.add(&quot;optional&quot;,&quot;FES_FILE&quot;,&quot;filename of the file on which the FES should be written out. By default it is fes.LABEL.data. Note that suffixes indicating the iteration number (iter-#) are added to the filename when optimizing coefficients.&quot;);</span></a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        184 :   keys.add(&quot;optional&quot;,&quot;TARGETDIST_FILE&quot;,&quot;filename of the file on which the target distribution should be written out. By default it is targetdist.LABEL.data. Note that suffixes indicating the iteration number (iter-#) are added to the filename when optimizing coefficients and the target distribution is dynamic.&quot;);</span></a>
+<a name="257"><span class="lineNum">     257 </span>            :   //</a>
+<a name="258"><span class="lineNum">     258 </span>            :   // keys.add(&quot;optional&quot;,&quot;BIAS_FILE_FMT&quot;,&quot;the format of the bias files, by default it is %14.9f.&quot;);</a>
+<a name="259"><span class="lineNum">     259 </span>            :   // keys.add(&quot;optional&quot;,&quot;FES_FILE_FMT&quot;,&quot;the format of the FES files, by default it is %14.9f.&quot;);</a>
+<a name="260"><span class="lineNum">     260 </span>            :   // keys.add(&quot;optional&quot;,&quot;TARGETDIST_FILE_FMT&quot;,&quot;the format of the target distribution files, by default it is %14.9f.&quot;);</a>
+<a name="261"><span class="lineNum">     261 </span>            :   // keys.add(&quot;hidden&quot;,&quot;TARGETDIST_RESTART_FILE_FMT&quot;,&quot;the format of the target distribution files that are used for restarting, by default it is %30.16e.&quot;);</a>
+<a name="262"><span class="lineNum">     262 </span>            :   //</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;BIAS_CUTOFF&quot;,&quot;cutoff the bias such that it only fills the free energy surface up to certain level F_cutoff, here you should give the value of the F_cutoff.&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        184 :   keys.reserve(&quot;optional&quot;,&quot;BIAS_CUTOFF_FERMI_LAMBDA&quot;,&quot;the lambda value used in the Fermi switching function for the bias cutoff (BIAS_CUTOFF), the default value is 10.0.&quot;);</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   //</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">        184 :   keys.reserve(&quot;numbered&quot;,&quot;PROJ_ARG&quot;,&quot;arguments for doing projections of the FES or the target distribution.&quot;);</span></a>
+<a name="267"><span class="lineNum">     267 </span>            :   //</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">        184 :   keys.reserveFlag(&quot;CALC_REWEIGHT_FACTOR&quot;,false,&quot;enable the calculation of the reweight factor c(t). You should also give a stride for updating the reweight factor in the optimizer by using the REWEIGHT_FACTOR_STRIDE keyword if the coefficients are updated.&quot;);</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        184 :   keys.add(&quot;optional&quot;,&quot;OPTIMIZATION_THRESHOLD&quot;,&quot;Threshold value to turn off optimization of localized basis functions.&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span>            : </a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">         92 : }</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">         92 : void VesBias::useInitialCoeffsKeywords(Keywords&amp; keys) {</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">         92 :   keys.use(&quot;COEFFS&quot;);</span></a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">         92 : }</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineCov">         92 : void VesBias::useTargetDistributionKeywords(Keywords&amp; keys) {</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">        184 :   plumed_massert(!keys.exists(&quot;TARGET_DISTRIBUTIONS&quot;),&quot;you cannot use both useTargetDistributionKeywords and useMultipleTargetDistributionKeywords&quot;);</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">         92 :   keys.use(&quot;TARGET_DISTRIBUTION&quot;);</span></a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">         92 : }</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            : </a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineNoCov">          0 : void VesBias::useMultipleTargetDistributionKeywords(Keywords&amp; keys) {</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   plumed_massert(!keys.exists(&quot;TARGET_DISTRIBUTION&quot;),&quot;you cannot use both useTargetDistributionKeywords and useMultipleTargetDistributionKeywords&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :   keys.use(&quot;TARGET_DISTRIBUTIONS&quot;);</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            : </a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineCov">         92 : void VesBias::useGridBinKeywords(Keywords&amp; keys) {</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">         92 :   keys.use(&quot;GRID_BINS&quot;);</span></a>
+<a name="293"><span class="lineNum">     293 </span><span class="lineCov">         92 : }</span></a>
+<a name="294"><span class="lineNum">     294 </span>            : </a>
+<a name="295"><span class="lineNum">     295 </span>            : </a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 : void VesBias::useGridLimitsKeywords(Keywords&amp; keys) {</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineNoCov">          0 :   keys.use(&quot;GRID_MIN&quot;);</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineNoCov">          0 :   keys.use(&quot;GRID_MAX&quot;);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            : </a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">         92 : void VesBias::useBiasCutoffKeywords(Keywords&amp; keys) {</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">         92 :   keys.use(&quot;BIAS_CUTOFF&quot;);</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">         92 :   keys.use(&quot;BIAS_CUTOFF_FERMI_LAMBDA&quot;);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">         92 : }</span></a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : </a>
+<a name="308"><span class="lineNum">     308 </span><span class="lineCov">         92 : void VesBias::useProjectionArgKeywords(Keywords&amp; keys) {</span></a>
+<a name="309"><span class="lineNum">     309 </span><span class="lineCov">         92 :   keys.use(&quot;PROJ_ARG&quot;);</span></a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">         92 : }</span></a>
+<a name="311"><span class="lineNum">     311 </span>            : </a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineNoCov">          0 : void VesBias::useReweightFactorKeywords(Keywords&amp; keys) {</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineNoCov">          0 :   keys.use(&quot;CALC_REWEIGHT_FACTOR&quot;);</span></a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineNoCov">          0 :   keys.addOutputComponent(&quot;rct&quot;,&quot;CALC_REWEIGHT_FACTOR&quot;,&quot;the reweight factor c(t).&quot;);</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="317"><span class="lineNum">     317 </span>            : </a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineNoCov">          0 : void VesBias::addCoeffsSet(const std::vector&lt;std::string&gt;&amp; dimension_labels,const std::vector&lt;unsigned int&gt;&amp; indices_shape) {</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineNoCov">          0 :   auto coeffs_pntr_tmp = Tools::make_unique&lt;CoeffsVector&gt;(&quot;coeffs&quot;,dimension_labels,indices_shape,comm,true);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineNoCov">          0 :   initializeCoeffs(std::move(coeffs_pntr_tmp));</span></a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="323"><span class="lineNum">     323 </span>            : </a>
+<a name="324"><span class="lineNum">     324 </span>            : </a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         90 : void VesBias::addCoeffsSet(std::vector&lt;Value*&gt;&amp; args,std::vector&lt;BasisFunctions*&gt;&amp; basisf) {</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         90 :   auto coeffs_pntr_tmp = Tools::make_unique&lt;CoeffsVector&gt;(&quot;coeffs&quot;,args,basisf,comm,true);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         90 :   initializeCoeffs(std::move(coeffs_pntr_tmp));</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         90 : }</span></a>
+<a name="329"><span class="lineNum">     329 </span>            : </a>
+<a name="330"><span class="lineNum">     330 </span>            : </a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineNoCov">          0 : void VesBias::addCoeffsSet(std::unique_ptr&lt;CoeffsVector&gt; coeffs_pntr_in) {</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineNoCov">          0 :   initializeCoeffs(std::move(coeffs_pntr_in));</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="334"><span class="lineNum">     334 </span>            : </a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         90 : void VesBias::initializeCoeffs(std::unique_ptr&lt;CoeffsVector&gt; coeffs_pntr_in) {</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   //</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         90 :   coeffs_pntr_in-&gt;linkVesBias(this);</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   //</a>
+<a name="340"><span class="lineNum">     340 </span>            :   std::string label;</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         90 :   if(!use_multiple_coeffssets_ &amp;&amp; ncoeffssets_==1) {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;you are not allowed to use multiple coefficient sets&quot;);</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   }</a>
+<a name="344"><span class="lineNum">     344 </span>            :   //</a>
+<a name="345"><span class="lineNum">     345 </span><span class="lineCov">        180 :   label = getCoeffsSetLabelString(&quot;coeffs&quot;,ncoeffssets_);</span></a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         90 :   coeffs_pntr_in-&gt;setLabels(label);</span></a>
+<a name="347"><span class="lineNum">     347 </span>            : </a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">         90 :   coeffs_pntrs_.emplace_back(std::move(coeffs_pntr_in));</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         90 :   auto aver_ps_tmp = Tools::make_unique&lt;CoeffsVector&gt;(*coeffs_pntrs_.back());</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        180 :   label = getCoeffsSetLabelString(&quot;targetdist_averages&quot;,ncoeffssets_);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         90 :   aver_ps_tmp-&gt;setLabels(label);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">         90 :   aver_ps_tmp-&gt;setValues(0.0);</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">         90 :   targetdist_averages_pntrs_.emplace_back(std::move(aver_ps_tmp));</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :   //</a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">         90 :   auto gradient_tmp = Tools::make_unique&lt;CoeffsVector&gt;(*coeffs_pntrs_.back());</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">        180 :   label = getCoeffsSetLabelString(&quot;gradient&quot;,ncoeffssets_);</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">         90 :   gradient_tmp-&gt;setLabels(label);</span></a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">         90 :   gradient_pntrs_.emplace_back(std::move(gradient_tmp));</span></a>
+<a name="359"><span class="lineNum">     359 </span>            :   //</a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineCov">        180 :   label = getCoeffsSetLabelString(&quot;hessian&quot;,ncoeffssets_);</span></a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">         90 :   auto hessian_tmp = Tools::make_unique&lt;CoeffsMatrix&gt;(label,coeffs_pntrs_.back().get(),comm,diagonal_hessian_);</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : </a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">         90 :   hessian_pntrs_.emplace_back(std::move(hessian_tmp));</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   //</a>
+<a name="365"><span class="lineNum">     365 </span>            :   std::vector&lt;double&gt; aver_sampled_tmp;</a>
+<a name="366"><span class="lineNum">     366 </span><span class="lineCov">         90 :   aver_sampled_tmp.assign(coeffs_pntrs_.back()-&gt;numberOfCoeffs(),0.0);</span></a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         90 :   sampled_averages.push_back(aver_sampled_tmp);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   //</a>
+<a name="369"><span class="lineNum">     369 </span>            :   std::vector&lt;double&gt; cross_aver_sampled_tmp;</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">         90 :   cross_aver_sampled_tmp.assign(hessian_pntrs_.back()-&gt;getSize(),0.0);</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         90 :   sampled_cross_averages.push_back(cross_aver_sampled_tmp);</span></a>
+<a name="372"><span class="lineNum">     372 </span>            :   //</a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         90 :   aver_counters.push_back(0);</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :   //</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">         90 :   ncoeffssets_++;</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">        180 : }</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">         90 : bool VesBias::readCoeffsFromFiles() {</span></a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         90 :   plumed_assert(ncoeffssets_&gt;0);</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">        180 :   plumed_massert(keywords.exists(&quot;COEFFS&quot;),&quot;you are not allowed to use this function as the COEFFS keyword is not enabled&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span>            :   bool read_coeffs = false;</a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">         90 :   if(coeffs_fnames.size()&gt;0) {</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          4 :     plumed_massert(coeffs_fnames.size()==ncoeffssets_,&quot;COEFFS keyword is of the wrong size&quot;);</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">          4 :     if(ncoeffssets_==1) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">          4 :       log.printf(&quot;  Read in coefficients from file &quot;);</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :     }</a>
+<a name="388"><span class="lineNum">     388 </span>            :     else {</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineNoCov">          0 :       log.printf(&quot;  Read in coefficients from files:\n&quot;);</span></a>
+<a name="390"><span class="lineNum">     390 </span>            :     }</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineCov">          8 :     for(unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="392"><span class="lineNum">     392 </span><span class="lineCov">          4 :       IFile ifile;</span></a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          4 :       ifile.link(*this);</span></a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">          4 :       ifile.open(coeffs_fnames[i]);</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">          8 :       if(!ifile.FieldExist(coeffs_pntrs_[i]-&gt;getDataLabel())) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :         std::string error_msg = &quot;Problem with reading coefficients from file &quot; + ifile.getPath() + &quot;: no field with name &quot; + coeffs_pntrs_[i]-&gt;getDataLabel() + &quot;\n&quot;;</span></a>
+<a name="397"><span class="lineNum">     397 </span><span class="lineNoCov">          0 :         plumed_merror(error_msg);</span></a>
+<a name="398"><span class="lineNum">     398 </span>            :       }</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          4 :       size_t ncoeffs_read = coeffs_pntrs_[i]-&gt;readFromFile(ifile,false,false);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          4 :       coeffs_pntrs_[i]-&gt;setIterationCounterAndTime(0,getTime());</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          4 :       if(ncoeffssets_==1) {</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          8 :         log.printf(&quot;%s (read %zu of %zu values)\n&quot;, ifile.getPath().c_str(),ncoeffs_read,coeffs_pntrs_[i]-&gt;numberOfCoeffs());</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :       }</a>
+<a name="404"><span class="lineNum">     404 </span>            :       else {</a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :         log.printf(&quot;   coefficient %u: %s (read %zu of %zu values)\n&quot;,i,ifile.getPath().c_str(),ncoeffs_read,coeffs_pntrs_[i]-&gt;numberOfCoeffs());</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :       }</a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          4 :       ifile.close();</span></a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">          4 :     }</span></a>
+<a name="409"><span class="lineNum">     409 </span>            :     read_coeffs = true;</a>
+<a name="410"><span class="lineNum">     410 </span>            :   }</a>
+<a name="411"><span class="lineNum">     411 </span><span class="lineCov">         90 :   return read_coeffs;</span></a>
+<a name="412"><span class="lineNum">     412 </span>            : }</a>
+<a name="413"><span class="lineNum">     413 </span>            : </a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">      22810 : void VesBias::updateGradientAndHessian(const bool use_mwalkers_mpi) {</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">      45620 :   for(unsigned int k=0; k&lt;ncoeffssets_; k++) {</span></a>
+<a name="417"><span class="lineNum">     417 </span>            :     //</a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">      22810 :     comm.Sum(sampled_averages[k]);</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      22810 :     comm.Sum(sampled_cross_averages[k]);</span></a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">      22810 :     if(use_mwalkers_mpi) {</span></a>
+<a name="421"><span class="lineNum">     421 </span>            :       double walker_weight=1.0;</a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">        120 :       if(aver_counters[k]==0) {walker_weight=0.0;}</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">        120 :       multiSimSumAverages(k,walker_weight);</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :     }</a>
+<a name="425"><span class="lineNum">     425 </span>            :     // NOTE: this assumes that all walkers have the same TargetDist, might change later on!!</a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">      22810 :     Gradient(k).setValues( TargetDistAverages(k) - sampled_averages[k] );</span></a>
+<a name="427"><span class="lineNum">     427 </span><span class="lineCov">      22810 :     Hessian(k) = computeCovarianceFromAverages(k);</span></a>
+<a name="428"><span class="lineNum">     428 </span><span class="lineCov">      22810 :     Hessian(k) *= getBeta();</span></a>
+<a name="429"><span class="lineNum">     429 </span>            : </a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">      22810 :     if(optimization_threshold_ != 0.0) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">        390 :       for(size_t c_id=0; c_id &lt; sampled_averages[k].size(); ++c_id) {</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">        380 :         if(fabs(sampled_averages[k][c_id]) &lt; optimization_threshold_) {</span></a>
+<a name="433"><span class="lineNum">     433 </span><span class="lineCov">        219 :           Gradient(k).setValue(c_id, 0.0);</span></a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineCov">        219 :           Hessian(k).setValue(c_id, c_id, 0.0);</span></a>
+<a name="435"><span class="lineNum">     435 </span>            :         }</a>
+<a name="436"><span class="lineNum">     436 </span>            :       }</a>
+<a name="437"><span class="lineNum">     437 </span>            :     }</a>
+<a name="438"><span class="lineNum">     438 </span>            :     //</a>
+<a name="439"><span class="lineNum">     439 </span>            :     Gradient(k).activate();</a>
+<a name="440"><span class="lineNum">     440 </span>            :     Hessian(k).activate();</a>
+<a name="441"><span class="lineNum">     441 </span>            :     //</a>
+<a name="442"><span class="lineNum">     442 </span>            :     // Check the total number of samples (from all walkers) and deactivate the Gradient and Hessian if it</a>
+<a name="443"><span class="lineNum">     443 </span>            :     // is zero</a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">      22810 :     unsigned int total_samples = aver_counters[k];</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">      22810 :     if(use_mwalkers_mpi) {</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">        120 :       if(comm.Get_rank()==0) {multi_sim_comm.Sum(total_samples);}</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">        120 :       comm.Bcast(total_samples,0);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            :     }</a>
+<a name="449"><span class="lineNum">     449 </span><span class="lineCov">      22810 :     if(total_samples==0) {</span></a>
+<a name="450"><span class="lineNum">     450 </span>            :       Gradient(k).deactivate();</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">         95 :       Gradient(k).clear();</span></a>
+<a name="452"><span class="lineNum">     452 </span>            :       Hessian(k).deactivate();</a>
+<a name="453"><span class="lineNum">     453 </span><span class="lineCov">         95 :       Hessian(k).clear();</span></a>
+<a name="454"><span class="lineNum">     454 </span>            :     }</a>
+<a name="455"><span class="lineNum">     455 </span>            :     //</a>
+<a name="456"><span class="lineNum">     456 </span>            :     std::fill(sampled_averages[k].begin(), sampled_averages[k].end(), 0.0);</a>
+<a name="457"><span class="lineNum">     457 </span>            :     std::fill(sampled_cross_averages[k].begin(), sampled_cross_averages[k].end(), 0.0);</a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">      22810 :     aver_counters[k]=0;</span></a>
+<a name="459"><span class="lineNum">     459 </span>            :   }</a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">      22810 : }</span></a>
+<a name="461"><span class="lineNum">     461 </span>            : </a>
+<a name="462"><span class="lineNum">     462 </span>            : </a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">        120 : void VesBias::multiSimSumAverages(const unsigned int c_id, const double walker_weight) {</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">        120 :   plumed_massert(walker_weight&gt;=0.0,&quot;the weight of the walker cannot be negative!&quot;);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">        120 :   if(walker_weight!=1.0) {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">       7860 :     for(size_t i=0; i&lt;sampled_averages[c_id].size(); i++) {</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">       7800 :       sampled_averages[c_id][i] *= walker_weight;</span></a>
+<a name="468"><span class="lineNum">     468 </span>            :     }</a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">       7860 :     for(size_t i=0; i&lt;sampled_cross_averages[c_id].size(); i++) {</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineCov">       7800 :       sampled_cross_averages[c_id][i] *= walker_weight;</span></a>
+<a name="471"><span class="lineNum">     471 </span>            :     }</a>
+<a name="472"><span class="lineNum">     472 </span>            :   }</a>
+<a name="473"><span class="lineNum">     473 </span>            :   //</a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">        120 :   if(comm.Get_rank()==0) {</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">        120 :     multi_sim_comm.Sum(sampled_averages[c_id]);</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">        120 :     multi_sim_comm.Sum(sampled_cross_averages[c_id]);</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">        120 :     double norm_weights = walker_weight;</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        120 :     multi_sim_comm.Sum(norm_weights);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        120 :     if(norm_weights&gt;0.0) {norm_weights=1.0/norm_weights;}</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">       8580 :     for(size_t i=0; i&lt;sampled_averages[c_id].size(); i++) {</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">       8460 :       sampled_averages[c_id][i] *= norm_weights;</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :     }</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">       8580 :     for(size_t i=0; i&lt;sampled_cross_averages[c_id].size(); i++) {</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">       8460 :       sampled_cross_averages[c_id][i] *= norm_weights;</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :     }</a>
+<a name="486"><span class="lineNum">     486 </span>            :   }</a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">        120 :   comm.Bcast(sampled_averages[c_id],0);</span></a>
+<a name="488"><span class="lineNum">     488 </span><span class="lineCov">        120 :   comm.Bcast(sampled_cross_averages[c_id],0);</span></a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">        120 : }</span></a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            : </a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">      23556 : void VesBias::addToSampledAverages(const std::vector&lt;double&gt;&amp; values, const unsigned int c_id) {</span></a>
+<a name="493"><span class="lineNum">     493 </span>            :   /*</a>
+<a name="494"><span class="lineNum">     494 </span>            :   use the following online equation to calculate the average and covariance</a>
+<a name="495"><span class="lineNum">     495 </span>            :   (see https://en.wikipedia.org/wiki/Algorithms_for_calculating_variance#Covariance)</a>
+<a name="496"><span class="lineNum">     496 </span>            :       xm[n+1] = xm[n] + (x[n+1]-xm[n])/(n+1)</a>
+<a name="497"><span class="lineNum">     497 </span>            :   */</a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineCov">      23556 :   double counter_dbl = static_cast&lt;double&gt;(aver_counters[c_id]);</span></a>
+<a name="499"><span class="lineNum">     499 </span>            :   size_t ncoeffs = numberOfCoeffs(c_id);</a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">      23556 :   std::vector&lt;double&gt; deltas(ncoeffs,0.0);</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">      23556 :   size_t stride = comm.Get_size();</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">      23556 :   size_t rank = comm.Get_rank();</span></a>
+<a name="503"><span class="lineNum">     503 </span>            :   // update average and diagonal part of Hessian</a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">    1830228 :   for(size_t i=rank; i&lt;ncoeffs; i+=stride) {</span></a>
+<a name="505"><span class="lineNum">     505 </span>            :     size_t midx = getHessianIndex(i,i,c_id);</a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">    1806672 :     deltas[i] = (values[i]-sampled_averages[c_id][i])/(counter_dbl+1); // (x[n+1]-xm[n])/(n+1)</span></a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">    1806672 :     sampled_averages[c_id][i] += deltas[i];</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">    1806672 :     sampled_cross_averages[c_id][midx] += (values[i]*values[i]-sampled_cross_averages[c_id][midx])/(counter_dbl+1);</span></a>
+<a name="509"><span class="lineNum">     509 </span>            :   }</a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">      23556 :   comm.Sum(deltas);</span></a>
+<a name="511"><span class="lineNum">     511 </span>            :   // update off-diagonal part of the Hessian</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">      23556 :   if(!diagonal_hessian_) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineNoCov">          0 :     for(size_t i=rank; i&lt;ncoeffs; i+=stride) {</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineNoCov">          0 :       for(size_t j=(i+1); j&lt;ncoeffs; j++) {</span></a>
+<a name="515"><span class="lineNum">     515 </span>            :         size_t midx = getHessianIndex(i,j,c_id);</a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineNoCov">          0 :         sampled_cross_averages[c_id][midx] += (values[i]*values[j]-sampled_cross_averages[c_id][midx])/(counter_dbl+1);</span></a>
+<a name="517"><span class="lineNum">     517 </span>            :       }</a>
+<a name="518"><span class="lineNum">     518 </span>            :     }</a>
+<a name="519"><span class="lineNum">     519 </span>            :   }</a>
+<a name="520"><span class="lineNum">     520 </span>            :   // NOTE: the MPI sum for sampled_averages and sampled_cross_averages is done later</a>
+<a name="521"><span class="lineNum">     521 </span><span class="lineCov">      23556 :   aver_counters[c_id] += 1;</span></a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">      23556 : }</span></a>
+<a name="523"><span class="lineNum">     523 </span>            : </a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineNoCov">          0 : void VesBias::setTargetDistAverages(const std::vector&lt;double&gt;&amp; coeffderivs_aver_ps, const unsigned int coeffs_id) {</span></a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineNoCov">          0 :   TargetDistAverages(coeffs_id) = coeffderivs_aver_ps;</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineNoCov">          0 :   TargetDistAverages(coeffs_id).setIterationCounterAndTime(this-&gt;getIterationCounter(),this-&gt;getTime());</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">        453 : void VesBias::setTargetDistAverages(const CoeffsVector&amp; coeffderivs_aver_ps, const unsigned int coeffs_id) {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        453 :   TargetDistAverages(coeffs_id).setValues( coeffderivs_aver_ps );</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        453 :   TargetDistAverages(coeffs_id).setIterationCounterAndTime(this-&gt;getIterationCounter(),this-&gt;getTime());</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">        453 : }</span></a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span>            : </a>
+<a name="537"><span class="lineNum">     537 </span><span class="lineNoCov">          0 : void VesBias::setTargetDistAveragesToZero(const unsigned int coeffs_id) {</span></a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineNoCov">          0 :   TargetDistAverages(coeffs_id).setAllValuesToZero();</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineNoCov">          0 :   TargetDistAverages(coeffs_id).setIterationCounterAndTime(this-&gt;getIterationCounter(),this-&gt;getTime());</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="541"><span class="lineNum">     541 </span>            : </a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">        175 : void VesBias::checkThatTemperatureIsGiven() {</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">        175 :   if(kbt_==0.0) {</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineNoCov">          0 :     std::string err_msg = &quot;VES bias &quot; + getLabel() + &quot; of type &quot; + getName() + &quot;: the temperature is needed so you need to give it using the TEMP keyword as the MD engine does not pass it to PLUMED.&quot;;</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineNoCov">          0 :     plumed_merror(err_msg);</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :   }</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        175 : }</span></a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineCov">       1005 : unsigned int VesBias::getIterationCounter() const {</span></a>
+<a name="552"><span class="lineNum">     552 </span>            :   unsigned int iteration = 0;</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">       1005 :   if(optimizeCoeffs()) {</span></a>
+<a name="554"><span class="lineNum">     554 </span>            :     iteration = getOptimizerPntr()-&gt;getIterationCounter();</a>
+<a name="555"><span class="lineNum">     555 </span>            :   }</a>
+<a name="556"><span class="lineNum">     556 </span>            :   else {</a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">        113 :     iteration = getCoeffsPntrs()[0]-&gt;getIterationCounter();</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :   }</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">       1005 :   return iteration;</span></a>
+<a name="560"><span class="lineNum">     560 </span>            : }</a>
+<a name="561"><span class="lineNum">     561 </span>            : </a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span><span class="lineCov">         85 : void VesBias::linkOptimizer(Optimizer* optimizer_pntr_in) {</span></a>
+<a name="564"><span class="lineNum">     564 </span>            :   //</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">         85 :   if(optimizer_pntr_==NULL) {</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">         85 :     optimizer_pntr_ = optimizer_pntr_in;</span></a>
+<a name="567"><span class="lineNum">     567 </span>            :   }</a>
+<a name="568"><span class="lineNum">     568 </span>            :   else {</a>
+<a name="569"><span class="lineNum">     569 </span><span class="lineNoCov">          0 :     std::string err_msg = &quot;VES bias &quot; + getLabel() + &quot; of type &quot; + getName() + &quot; has already been linked with optimizer &quot; + optimizer_pntr_-&gt;getLabel() + &quot; of type &quot; + optimizer_pntr_-&gt;getName() + &quot;. You cannot link two optimizer to the same VES bias.&quot;;</span></a>
+<a name="570"><span class="lineNum">     570 </span><span class="lineNoCov">          0 :     plumed_merror(err_msg);</span></a>
+<a name="571"><span class="lineNum">     571 </span>            :   }</a>
+<a name="572"><span class="lineNum">     572 </span><span class="lineCov">         85 :   checkThatTemperatureIsGiven();</span></a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         85 :   optimize_coeffs_ = true;</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         85 :   filenames_have_iteration_number_ = true;</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         85 : }</span></a>
+<a name="576"><span class="lineNum">     576 </span>            : </a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         82 : void VesBias::enableHessian(const bool diagonal_hessian) {</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">         82 :   compute_hessian_=true;</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">         82 :   diagonal_hessian_=diagonal_hessian;</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         82 :   sampled_cross_averages.clear();</span></a>
+<a name="582"><span class="lineNum">     582 </span><span class="lineCov">        164 :   for (unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="583"><span class="lineNum">     583 </span><span class="lineCov">         82 :     std::string label = getCoeffsSetLabelString(&quot;hessian&quot;,i);</span></a>
+<a name="584"><span class="lineNum">     584 </span><span class="lineCov">        164 :     hessian_pntrs_[i] = Tools::make_unique&lt;CoeffsMatrix&gt;(label,coeffs_pntrs_[i].get(),comm,diagonal_hessian_);</span></a>
+<a name="585"><span class="lineNum">     585 </span>            :     //</a>
+<a name="586"><span class="lineNum">     586 </span>            :     std::vector&lt;double&gt; cross_aver_sampled_tmp;</a>
+<a name="587"><span class="lineNum">     587 </span><span class="lineCov">         82 :     cross_aver_sampled_tmp.assign(hessian_pntrs_[i]-&gt;getSize(),0.0);</span></a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         82 :     sampled_cross_averages.push_back(cross_aver_sampled_tmp);</span></a>
+<a name="589"><span class="lineNum">     589 </span>            :   }</a>
+<a name="590"><span class="lineNum">     590 </span><span class="lineCov">         82 : }</span></a>
+<a name="591"><span class="lineNum">     591 </span>            : </a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineNoCov">          0 : void VesBias::disableHessian() {</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineNoCov">          0 :   compute_hessian_=false;</span></a>
+<a name="595"><span class="lineNum">     595 </span><span class="lineNoCov">          0 :   diagonal_hessian_=true;</span></a>
+<a name="596"><span class="lineNum">     596 </span><span class="lineNoCov">          0 :   sampled_cross_averages.clear();</span></a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineNoCov">          0 :   for (unsigned int i=0; i&lt;ncoeffssets_; i++) {</span></a>
+<a name="598"><span class="lineNum">     598 </span><span class="lineNoCov">          0 :     std::string label = getCoeffsSetLabelString(&quot;hessian&quot;,i);</span></a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineNoCov">          0 :     hessian_pntrs_[i] = Tools::make_unique&lt;CoeffsMatrix&gt;(label,coeffs_pntrs_[i].get(),comm,diagonal_hessian_);</span></a>
+<a name="600"><span class="lineNum">     600 </span>            :     //</a>
+<a name="601"><span class="lineNum">     601 </span>            :     std::vector&lt;double&gt; cross_aver_sampled_tmp;</a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineNoCov">          0 :     cross_aver_sampled_tmp.assign(hessian_pntrs_[i]-&gt;getSize(),0.0);</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineNoCov">          0 :     sampled_cross_averages.push_back(cross_aver_sampled_tmp);</span></a>
+<a name="604"><span class="lineNum">     604 </span>            :   }</a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="606"><span class="lineNum">     606 </span>            : </a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">        442 : std::string VesBias::getCoeffsSetLabelString(const std::string&amp; type, const unsigned int coeffs_id) const {</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">        442 :   std::string label_prefix = getLabel() + &quot;.&quot;;</span></a>
+<a name="610"><span class="lineNum">     610 </span><span class="lineCov">        442 :   std::string label_postfix = &quot;&quot;;</span></a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">        442 :   if(use_multiple_coeffssets_) {</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineNoCov">          0 :     Tools::convert(coeffs_id,label_postfix);</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineNoCov">          0 :     label_postfix = &quot;-&quot; + label_postfix;</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :   }</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">       1326 :   return label_prefix+type+label_postfix;</span></a>
+<a name="616"><span class="lineNum">     616 </span>            : }</a>
+<a name="617"><span class="lineNum">     617 </span>            : </a>
+<a name="618"><span class="lineNum">     618 </span>            : </a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">        567 : std::unique_ptr&lt;OFile&gt; VesBias::getOFile(const std::string&amp; filepath, const bool multi_sim_single_file, const bool enforce_backup) {</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">        567 :   auto ofile_pntr = Tools::make_unique&lt;OFile&gt;();</span></a>
+<a name="621"><span class="lineNum">     621 </span><span class="lineCov">        567 :   std::string fp = filepath;</span></a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">        567 :   ofile_pntr-&gt;link(*static_cast&lt;Action*&gt;(this));</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">        567 :   if(enforce_backup) {ofile_pntr-&gt;enforceBackup();}</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">        567 :   if(multi_sim_single_file) {</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         56 :     unsigned int r=0;</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         56 :     if(comm.Get_rank()==0) {r=multi_sim_comm.Get_rank();}</span></a>
+<a name="627"><span class="lineNum">     627 </span><span class="lineCov">         56 :     comm.Bcast(r,0);</span></a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         56 :     if(r&gt;0) {fp=&quot;/dev/null&quot;;}</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">        112 :     ofile_pntr-&gt;enforceSuffix(&quot;&quot;);</span></a>
+<a name="630"><span class="lineNum">     630 </span>            :   }</a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">        567 :   ofile_pntr-&gt;open(fp);</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">        567 :   return ofile_pntr;</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span>            : </a>
+<a name="636"><span class="lineNum">     636 </span><span class="lineNoCov">          0 : void VesBias::setGridBins(const std::vector&lt;unsigned int&gt;&amp; grid_bins_in) {</span></a>
+<a name="637"><span class="lineNum">     637 </span><span class="lineNoCov">          0 :   plumed_massert(grid_bins_in.size()==getNumberOfArguments(),&quot;the number of grid bins given doesn't match the number of arguments&quot;);</span></a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineNoCov">          0 :   grid_bins_=grid_bins_in;</span></a>
+<a name="639"><span class="lineNum">     639 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="640"><span class="lineNum">     640 </span>            : </a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineNoCov">          0 : void VesBias::setGridBins(const unsigned int nbins) {</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineNoCov">          0 :   std::vector&lt;unsigned int&gt; grid_bins_in(getNumberOfArguments(),nbins);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineNoCov">          0 :   grid_bins_=grid_bins_in;</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="646"><span class="lineNum">     646 </span>            : </a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineNoCov">          0 : void VesBias::setGridMin(const std::vector&lt;double&gt;&amp; grid_min_in) {</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineNoCov">          0 :   plumed_massert(grid_min_in.size()==getNumberOfArguments(),&quot;the number of lower bounds given for the grid doesn't match the number of arguments&quot;);</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineNoCov">          0 :   grid_min_=grid_min_in;</span></a>
+<a name="651"><span class="lineNum">     651 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="652"><span class="lineNum">     652 </span>            : </a>
+<a name="653"><span class="lineNum">     653 </span>            : </a>
+<a name="654"><span class="lineNum">     654 </span><span class="lineNoCov">          0 : void VesBias::setGridMax(const std::vector&lt;double&gt;&amp; grid_max_in) {</span></a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineNoCov">          0 :   plumed_massert(grid_max_in.size()==getNumberOfArguments(),&quot;the number of upper bounds given for the grid doesn't match the number of arguments&quot;);</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineNoCov">          0 :   grid_max_=grid_max_in;</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="658"><span class="lineNum">     658 </span>            : </a>
+<a name="659"><span class="lineNum">     659 </span>            : </a>
+<a name="660"><span class="lineNum">     660 </span><span class="lineCov">        383 : std::string VesBias::getCurrentOutputFilename(const std::string&amp; base_filename, const std::string&amp; suffix) const {</span></a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">        383 :   std::string filename = base_filename;</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">        383 :   if(suffix.size()&gt;0) {</span></a>
+<a name="663"><span class="lineNum">     663 </span><span class="lineCov">         82 :     filename = FileBase::appendSuffix(filename,&quot;.&quot;+suffix);</span></a>
+<a name="664"><span class="lineNum">     664 </span>            :   }</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">        383 :   if(filenamesIncludeIterationNumber()) {</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">        756 :     filename = FileBase::appendSuffix(filename,&quot;.&quot;+getIterationFilenameSuffix());</span></a>
+<a name="667"><span class="lineNum">     667 </span>            :   }</a>
+<a name="668"><span class="lineNum">     668 </span><span class="lineCov">        383 :   return filename;</span></a>
+<a name="669"><span class="lineNum">     669 </span>            : }</a>
+<a name="670"><span class="lineNum">     670 </span>            : </a>
+<a name="671"><span class="lineNum">     671 </span>            : </a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">        192 : std::string VesBias::getCurrentTargetDistOutputFilename(const std::string&amp; suffix) const {</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">        192 :   std::string filename = targetdist_filename_;</span></a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">        192 :   if(suffix.size()&gt;0) {</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">        204 :     filename = FileBase::appendSuffix(filename,&quot;.&quot;+suffix);</span></a>
+<a name="676"><span class="lineNum">     676 </span>            :   }</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">        192 :   if(filenamesIncludeIterationNumber() &amp;&amp; dynamicTargetDistribution()) {</span></a>
+<a name="678"><span class="lineNum">     678 </span><span class="lineCov">        348 :     filename = FileBase::appendSuffix(filename,&quot;.&quot;+getIterationFilenameSuffix());</span></a>
+<a name="679"><span class="lineNum">     679 </span>            :   }</a>
+<a name="680"><span class="lineNum">     680 </span><span class="lineCov">        192 :   return filename;</span></a>
+<a name="681"><span class="lineNum">     681 </span>            : }</a>
+<a name="682"><span class="lineNum">     682 </span>            : </a>
+<a name="683"><span class="lineNum">     683 </span>            : </a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">        552 : std::string VesBias::getIterationFilenameSuffix() const {</span></a>
+<a name="685"><span class="lineNum">     685 </span>            :   std::string iter_str;</a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">        552 :   Tools::convert(getIterationCounter(),iter_str);</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">        552 :   iter_str = &quot;iter-&quot; + iter_str;</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">        552 :   return iter_str;</span></a>
+<a name="689"><span class="lineNum">     689 </span>            : }</a>
+<a name="690"><span class="lineNum">     690 </span>            : </a>
+<a name="691"><span class="lineNum">     691 </span>            : </a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineNoCov">          0 : std::string VesBias::getCoeffsSetFilenameSuffix(const unsigned int coeffs_id) const {</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineNoCov">          0 :   std::string suffix = &quot;&quot;;</span></a>
+<a name="694"><span class="lineNum">     694 </span><span class="lineNoCov">          0 :   if(use_multiple_coeffssets_) {</span></a>
+<a name="695"><span class="lineNum">     695 </span><span class="lineNoCov">          0 :     Tools::convert(coeffs_id,suffix);</span></a>
+<a name="696"><span class="lineNum">     696 </span><span class="lineNoCov">          0 :     suffix = coeffs_id_prefix_ + suffix;</span></a>
+<a name="697"><span class="lineNum">     697 </span>            :   }</a>
+<a name="698"><span class="lineNum">     698 </span><span class="lineNoCov">          0 :   return suffix;</span></a>
+<a name="699"><span class="lineNum">     699 </span>            : }</a>
+<a name="700"><span class="lineNum">     700 </span>            : </a>
+<a name="701"><span class="lineNum">     701 </span>            : </a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">          3 : void VesBias::setupBiasCutoff(const double bias_cutoff_value, const double fermi_lambda) {</span></a>
+<a name="703"><span class="lineNum">     703 </span>            :   //</a>
+<a name="704"><span class="lineNum">     704 </span>            :   double fermi_exp_max = 100.0;</a>
+<a name="705"><span class="lineNum">     705 </span>            :   //</a>
+<a name="706"><span class="lineNum">     706 </span>            :   std::string str_bias_cutoff_value; VesTools::convertDbl2Str(bias_cutoff_value,str_bias_cutoff_value);</a>
+<a name="707"><span class="lineNum">     707 </span>            :   std::string str_fermi_lambda; VesTools::convertDbl2Str(fermi_lambda,str_fermi_lambda);</a>
+<a name="708"><span class="lineNum">     708 </span>            :   std::string str_fermi_exp_max; VesTools::convertDbl2Str(fermi_exp_max,str_fermi_exp_max);</a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">          6 :   std::string swfunc_keywords = &quot;FERMI R_0=&quot; + str_bias_cutoff_value + &quot; FERMI_LAMBDA=&quot; + str_fermi_lambda + &quot; FERMI_EXP_MAX=&quot; + str_fermi_exp_max;</span></a>
+<a name="710"><span class="lineNum">     710 </span>            :   //</a>
+<a name="711"><span class="lineNum">     711 </span><span class="lineCov">          3 :   std::string swfunc_errors=&quot;&quot;;</span></a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">          6 :   bias_cutoff_swfunc_pntr_ = Tools::make_unique&lt;FermiSwitchingFunction&gt;();</span></a>
+<a name="713"><span class="lineNum">     713 </span><span class="lineCov">          3 :   bias_cutoff_swfunc_pntr_-&gt;set(swfunc_keywords,swfunc_errors);</span></a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">          3 :   if(swfunc_errors.size()&gt;0) {</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;problem with setting up Fermi switching function: &quot; + swfunc_errors);</span></a>
+<a name="716"><span class="lineNum">     716 </span>            :   }</a>
+<a name="717"><span class="lineNum">     717 </span>            :   //</a>
+<a name="718"><span class="lineNum">     718 </span><span class="lineCov">          3 :   bias_cutoff_value_=bias_cutoff_value;</span></a>
+<a name="719"><span class="lineNum">     719 </span><span class="lineCov">          3 :   bias_cutoff_active_=true;</span></a>
+<a name="720"><span class="lineNum">     720 </span>            :   enableDynamicTargetDistribution();</a>
+<a name="721"><span class="lineNum">     721 </span><span class="lineCov">          3 : }</span></a>
+<a name="722"><span class="lineNum">     722 </span>            : </a>
+<a name="723"><span class="lineNum">     723 </span>            : </a>
+<a name="724"><span class="lineNum">     724 </span><span class="lineCov">       3263 : double VesBias::getBiasCutoffSwitchingFunction(const double bias, double&amp; deriv_factor) const {</span></a>
+<a name="725"><span class="lineNum">     725 </span><span class="lineCov">       3263 :   plumed_massert(bias_cutoff_active_,&quot;The bias cutoff is not active so you cannot call this function&quot;);</span></a>
+<a name="726"><span class="lineNum">     726 </span><span class="lineCov">       3263 :   double arg = -(bias-bias_current_max_value);</span></a>
+<a name="727"><span class="lineNum">     727 </span><span class="lineCov">       3263 :   double deriv=0.0;</span></a>
+<a name="728"><span class="lineNum">     728 </span><span class="lineCov">       3263 :   double value = bias_cutoff_swfunc_pntr_-&gt;calculate(arg,deriv);</span></a>
+<a name="729"><span class="lineNum">     729 </span>            :   // as FermiSwitchingFunction class has different behavior from normal SwitchingFunction class</a>
+<a name="730"><span class="lineNum">     730 </span>            :   // I was having problems with NaN as it was dividing with zero</a>
+<a name="731"><span class="lineNum">     731 </span>            :   // deriv *= arg;</a>
+<a name="732"><span class="lineNum">     732 </span><span class="lineCov">       3263 :   deriv_factor = value-bias*deriv;</span></a>
+<a name="733"><span class="lineNum">     733 </span><span class="lineCov">       3263 :   return value;</span></a>
+<a name="734"><span class="lineNum">     734 </span>            : }</a>
+<a name="735"><span class="lineNum">     735 </span>            : </a>
+<a name="736"><span class="lineNum">     736 </span>            : </a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">        567 : bool VesBias::useMultipleWalkers() const {</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :   bool use_mwalkers_mpi=false;</a>
+<a name="739"><span class="lineNum">     739 </span><span class="lineCov">        567 :   if(optimizeCoeffs() &amp;&amp; getOptimizerPntr()-&gt;useMultipleWalkers()) {</span></a>
+<a name="740"><span class="lineNum">     740 </span>            :     use_mwalkers_mpi=true;</a>
+<a name="741"><span class="lineNum">     741 </span>            :   }</a>
+<a name="742"><span class="lineNum">     742 </span><span class="lineCov">        567 :   return use_mwalkers_mpi;</span></a>
+<a name="743"><span class="lineNum">     743 </span>            : }</a>
+<a name="744"><span class="lineNum">     744 </span>            : </a>
+<a name="745"><span class="lineNum">     745 </span>            : </a>
+<a name="746"><span class="lineNum">     746 </span><span class="lineNoCov">          0 : void VesBias::updateReweightFactor() {</span></a>
+<a name="747"><span class="lineNum">     747 </span><span class="lineNoCov">          0 :   if(calc_reweightfactor_) {</span></a>
+<a name="748"><span class="lineNum">     748 </span><span class="lineNoCov">          0 :     double value = calculateReweightFactor();</span></a>
+<a name="749"><span class="lineNum">     749 </span><span class="lineNoCov">          0 :     getPntrToComponent(&quot;rct&quot;)-&gt;set(value);</span></a>
+<a name="750"><span class="lineNum">     750 </span>            :   }</a>
+<a name="751"><span class="lineNum">     751 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="752"><span class="lineNum">     752 </span>            : </a>
+<a name="753"><span class="lineNum">     753 </span>            : </a>
+<a name="754"><span class="lineNum">     754 </span><span class="lineNoCov">          0 : double VesBias::calculateReweightFactor() const {</span></a>
+<a name="755"><span class="lineNum">     755 </span><span class="lineNoCov">          0 :   plumed_merror(getName()+&quot; with label &quot;+getLabel()+&quot;: calculation of the reweight factor c(t) has not been implemented for this type of VES bias&quot;);</span></a>
+<a name="756"><span class="lineNum">     756 </span>            :   return 0.0;</a>
+<a name="757"><span class="lineNum">     757 </span>            : }</a>
+<a name="758"><span class="lineNum">     758 </span>            : </a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            : }</a>
+<a name="761"><span class="lineNum">     761 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesBias.h.func-sort-c.html b/coverage/ves/VesBias.h.func-sort-c.html
new file mode 100644
index 0000000000..4d906f4b6a
--- /dev/null
+++ b/coverage/ves/VesBias.h.func-sort-c.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesBias.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesBias.h<span style="font-size: 80%;"> (<a href="VesBias.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryLo">74.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">36.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesBias.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#281">_ZN4PLMD3ves7VesBias14writeFesToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#277">_ZN4PLMD3ves7VesBias15writeBiasToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#282">_ZN4PLMD3ves7VesBias18resetFesFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#280">_ZN4PLMD3ves7VesBias18setupFesFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#285">_ZN4PLMD3ves7VesBias18writeFesProjToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#382">_ZN4PLMD3ves7VesBias19parseMultipleValuesIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#278">_ZN4PLMD3ves7VesBias19resetBiasFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#276">_ZN4PLMD3ves7VesBias19setupBiasFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#289">_ZN4PLMD3ves7VesBias21writeTargetDistToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#286">_ZN4PLMD3ves7VesBias22resetFesProjFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#284">_ZN4PLMD3ves7VesBias22setupFesProjFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#290">_ZN4PLMD3ves7VesBias25resetTargetDistFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#202">_ZN4PLMD3ves7VesBias25updateTargetDistributionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#293">_ZN4PLMD3ves7VesBias25writeTargetDistProjToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#203">_ZN4PLMD3ves7VesBias26restartTargetDistributionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#294">_ZN4PLMD3ves7VesBias29resetTargetDistProjFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#292">_ZN4PLMD3ves7VesBias29setupTargetDistProjFileOutputEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#288">_ZN4PLMD3ves7VesBias25setupTargetDistFileOutputEv</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#382">_ZN4PLMD3ves7VesBias19parseMultipleValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS8_RSt6vectorIT_SaISC_EEj</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#382">_ZN4PLMD3ves7VesBias19parseMultipleValuesIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EEj</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#400">_ZN4PLMD3ves7VesBias19parseMultipleValuesIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EEjRKSC_</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#339">_ZNK4PLMD3ves7VesBias15applyBiasCutoffERdRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#346">_ZNK4PLMD3ves7VesBias15applyBiasCutoffERdRSt6vectorIdSaIdEES6_</a></td>
+              <td class="coverFnHi">663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#361">_ZNK4PLMD3ves7VesBias29computeCovarianceFromAveragesEj</a></td>
+              <td class="coverFnHi">22810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#313">_ZNK4PLMD3ves7VesBias7getBetaEv</a></td>
+              <td class="coverFnHi">23277</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesBias.h.func.html b/coverage/ves/VesBias.h.func.html
new file mode 100644
index 0000000000..08df83c8be
--- /dev/null
+++ b/coverage/ves/VesBias.h.func.html
@@ -0,0 +1,172 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesBias.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesBias.h<span style="font-size: 80%;"> (<a href="VesBias.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryLo">74.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">36.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesBias.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#281">_ZN4PLMD3ves7VesBias14writeFesToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#277">_ZN4PLMD3ves7VesBias15writeBiasToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#282">_ZN4PLMD3ves7VesBias18resetFesFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#280">_ZN4PLMD3ves7VesBias18setupFesFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#285">_ZN4PLMD3ves7VesBias18writeFesProjToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#382">_ZN4PLMD3ves7VesBias19parseMultipleValuesINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEbRKS8_RSt6vectorIT_SaISC_EEj</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#382">_ZN4PLMD3ves7VesBias19parseMultipleValuesIdEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EEj</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#382">_ZN4PLMD3ves7VesBias19parseMultipleValuesIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EEj</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#400">_ZN4PLMD3ves7VesBias19parseMultipleValuesIjEEbRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EEjRKSC_</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#278">_ZN4PLMD3ves7VesBias19resetBiasFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#276">_ZN4PLMD3ves7VesBias19setupBiasFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#289">_ZN4PLMD3ves7VesBias21writeTargetDistToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#286">_ZN4PLMD3ves7VesBias22resetFesProjFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#284">_ZN4PLMD3ves7VesBias22setupFesProjFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#290">_ZN4PLMD3ves7VesBias25resetTargetDistFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#288">_ZN4PLMD3ves7VesBias25setupTargetDistFileOutputEv</a></td>
+              <td class="coverFnHi">44</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#202">_ZN4PLMD3ves7VesBias25updateTargetDistributionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#293">_ZN4PLMD3ves7VesBias25writeTargetDistProjToFileEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#203">_ZN4PLMD3ves7VesBias26restartTargetDistributionsEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#294">_ZN4PLMD3ves7VesBias29resetTargetDistProjFileOutputEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#292">_ZN4PLMD3ves7VesBias29setupTargetDistProjFileOutputEv</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#339">_ZNK4PLMD3ves7VesBias15applyBiasCutoffERdRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">600</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#346">_ZNK4PLMD3ves7VesBias15applyBiasCutoffERdRSt6vectorIdSaIdEES6_</a></td>
+              <td class="coverFnHi">663</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#361">_ZNK4PLMD3ves7VesBias29computeCovarianceFromAveragesEj</a></td>
+              <td class="coverFnHi">22810</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesBias.h.gcov.html#313">_ZNK4PLMD3ves7VesBias7getBetaEv</a></td>
+              <td class="coverFnHi">23277</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesBias.h.gcov.html b/coverage/ves/VesBias.h.gcov.html
new file mode 100644
index 0000000000..26c8e9d8c5
--- /dev/null
+++ b/coverage/ves/VesBias.h.gcov.html
@@ -0,0 +1,491 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesBias.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesBias.h<span style="font-size: 80%;"> (source / <a href="VesBias.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">66</td>
+            <td class="headerCovTableEntry">89</td>
+            <td class="headerCovTableEntryLo">74.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">25</td>
+            <td class="headerCovTableEntryLo">36.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_VesBias_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_VesBias_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &lt;vector&gt;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &lt;string&gt;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &lt;cmath&gt;</a>
+<a name="36"><span class="lineNum">      36 </span>            : #include &lt;memory&gt;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : #define PLUMED_VES_VESBIAS_INIT(ao) Action(ao),VesBias(ao)</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : namespace PLMD {</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : class Value;</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : namespace ves {</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : class CoeffsVector;</a>
+<a name="48"><span class="lineNum">      48 </span>            : class CoeffsMatrix;</a>
+<a name="49"><span class="lineNum">      49 </span>            : class BasisFunctions;</a>
+<a name="50"><span class="lineNum">      50 </span>            : class Optimizer;</a>
+<a name="51"><span class="lineNum">      51 </span>            : class TargetDistribution;</a>
+<a name="52"><span class="lineNum">      52 </span>            : class FermiSwitchingFunction;</a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span>            : /**</a>
+<a name="55"><span class="lineNum">      55 </span>            : \ingroup INHERIT</a>
+<a name="56"><span class="lineNum">      56 </span>            : Abstract base class for implementing biases the extents the normal Bias.h class</a>
+<a name="57"><span class="lineNum">      57 </span>            : to include functions related to the variational approach.</a>
+<a name="58"><span class="lineNum">      58 </span>            : */</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            : class VesBias:</a>
+<a name="61"><span class="lineNum">      61 </span>            :   public bias::Bias</a>
+<a name="62"><span class="lineNum">      62 </span>            : {</a>
+<a name="63"><span class="lineNum">      63 </span>            : private:</a>
+<a name="64"><span class="lineNum">      64 </span>            :   unsigned int ncoeffssets_;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; coeffs_pntrs_;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; targetdist_averages_pntrs_;</a>
+<a name="67"><span class="lineNum">      67 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsVector&gt;&gt; gradient_pntrs_;</a>
+<a name="68"><span class="lineNum">      68 </span>            :   std::vector&lt;std::unique_ptr&lt;CoeffsMatrix&gt;&gt; hessian_pntrs_;</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; sampled_averages;</a>
+<a name="70"><span class="lineNum">      70 </span>            :   std::vector&lt;std::vector&lt;double&gt; &gt; sampled_cross_averages;</a>
+<a name="71"><span class="lineNum">      71 </span>            :   bool use_multiple_coeffssets_;</a>
+<a name="72"><span class="lineNum">      72 </span>            :   //</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;std::string&gt; coeffs_fnames;</a>
+<a name="74"><span class="lineNum">      74 </span>            :   //</a>
+<a name="75"><span class="lineNum">      75 </span>            :   size_t ncoeffs_total_;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   //</a>
+<a name="77"><span class="lineNum">      77 </span>            :   Optimizer* optimizer_pntr_;</a>
+<a name="78"><span class="lineNum">      78 </span>            :   bool optimize_coeffs_;</a>
+<a name="79"><span class="lineNum">      79 </span>            :   //</a>
+<a name="80"><span class="lineNum">      80 </span>            :   bool compute_hessian_;</a>
+<a name="81"><span class="lineNum">      81 </span>            :   bool diagonal_hessian_;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   //</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;unsigned int&gt; aver_counters;</a>
+<a name="84"><span class="lineNum">      84 </span>            :   //</a>
+<a name="85"><span class="lineNum">      85 </span>            :   double kbt_;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   //</a>
+<a name="87"><span class="lineNum">      87 </span>            :   std::vector&lt;TargetDistribution*&gt; targetdist_pntrs_;</a>
+<a name="88"><span class="lineNum">      88 </span>            :   bool dynamic_targetdist_;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   //</a>
+<a name="90"><span class="lineNum">      90 </span>            :   std::vector&lt;unsigned int&gt; grid_bins_;</a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;double&gt; grid_min_;</a>
+<a name="92"><span class="lineNum">      92 </span>            :   std::vector&lt;double&gt; grid_max_;</a>
+<a name="93"><span class="lineNum">      93 </span>            :   //</a>
+<a name="94"><span class="lineNum">      94 </span>            :   std::string bias_filename_;</a>
+<a name="95"><span class="lineNum">      95 </span>            :   std::string fes_filename_;</a>
+<a name="96"><span class="lineNum">      96 </span>            :   std::string targetdist_filename_;</a>
+<a name="97"><span class="lineNum">      97 </span>            :   std::string targetdist_averages_filename_;</a>
+<a name="98"><span class="lineNum">      98 </span>            :   std::string coeffs_id_prefix_;</a>
+<a name="99"><span class="lineNum">      99 </span>            :   //</a>
+<a name="100"><span class="lineNum">     100 </span>            :   std::string bias_file_fmt_;</a>
+<a name="101"><span class="lineNum">     101 </span>            :   std::string fes_file_fmt_;</a>
+<a name="102"><span class="lineNum">     102 </span>            :   std::string targetdist_file_fmt_;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::string targetdist_restart_file_fmt_;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   //</a>
+<a name="105"><span class="lineNum">     105 </span>            :   bool filenames_have_iteration_number_;</a>
+<a name="106"><span class="lineNum">     106 </span>            :   //</a>
+<a name="107"><span class="lineNum">     107 </span>            :   bool bias_fileoutput_active_;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   bool fes_fileoutput_active_;</a>
+<a name="109"><span class="lineNum">     109 </span>            :   bool fesproj_fileoutput_active_;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   bool dynamic_targetdist_fileoutput_active_;</a>
+<a name="111"><span class="lineNum">     111 </span>            :   bool static_targetdist_fileoutput_active_;</a>
+<a name="112"><span class="lineNum">     112 </span>            :   //</a>
+<a name="113"><span class="lineNum">     113 </span>            : </a>
+<a name="114"><span class="lineNum">     114 </span>            :   bool bias_cutoff_active_;</a>
+<a name="115"><span class="lineNum">     115 </span>            :   double bias_cutoff_value_;</a>
+<a name="116"><span class="lineNum">     116 </span>            :   double bias_current_max_value;</a>
+<a name="117"><span class="lineNum">     117 </span>            :   std::unique_ptr&lt;FermiSwitchingFunction&gt; bias_cutoff_swfunc_pntr_;</a>
+<a name="118"><span class="lineNum">     118 </span>            :   //</a>
+<a name="119"><span class="lineNum">     119 </span>            :   std::vector&lt; std::vector&lt;std::string&gt; &gt; projection_args_;</a>
+<a name="120"><span class="lineNum">     120 </span>            :   //</a>
+<a name="121"><span class="lineNum">     121 </span>            :   bool calc_reweightfactor_;</a>
+<a name="122"><span class="lineNum">     122 </span>            :   //</a>
+<a name="123"><span class="lineNum">     123 </span>            :   double optimization_threshold_;</a>
+<a name="124"><span class="lineNum">     124 </span>            : private:</a>
+<a name="125"><span class="lineNum">     125 </span>            :   void initializeCoeffs(std::unique_ptr&lt;CoeffsVector&gt;);</a>
+<a name="126"><span class="lineNum">     126 </span>            :   std::vector&lt;double&gt; computeCovarianceFromAverages(const unsigned int) const;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void multiSimSumAverages(const unsigned int, const double walker_weight=1.0);</a>
+<a name="128"><span class="lineNum">     128 </span>            : protected:</a>
+<a name="129"><span class="lineNum">     129 </span>            :   //</a>
+<a name="130"><span class="lineNum">     130 </span>            :   void checkThatTemperatureIsGiven();</a>
+<a name="131"><span class="lineNum">     131 </span>            :   //</a>
+<a name="132"><span class="lineNum">     132 </span>            :   void addCoeffsSet(const std::vector&lt;std::string&gt;&amp;,const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="133"><span class="lineNum">     133 </span>            :   void addCoeffsSet(std::vector&lt;Value*&gt;&amp;,std::vector&lt;BasisFunctions*&gt;&amp;);</a>
+<a name="134"><span class="lineNum">     134 </span>            :   void addCoeffsSet(std::unique_ptr&lt;CoeffsVector&gt;);</a>
+<a name="135"><span class="lineNum">     135 </span>            :   //</a>
+<a name="136"><span class="lineNum">     136 </span>            :   std::string getCoeffsSetLabelString(const std::string&amp;, const unsigned int coeffs_id = 0) const;</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void clearCoeffsPntrsVector() {coeffs_pntrs_.clear();}</a>
+<a name="138"><span class="lineNum">     138 </span>            :   void addToSampledAverages(const std::vector&lt;double&gt;&amp;, const unsigned int c_id = 0);</a>
+<a name="139"><span class="lineNum">     139 </span>            :   void setTargetDistAverages(const std::vector&lt;double&gt;&amp;, const unsigned int coeffs_id = 0);</a>
+<a name="140"><span class="lineNum">     140 </span>            :   void setTargetDistAverages(const CoeffsVector&amp;, const unsigned int coeffs_id= 0);</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void setTargetDistAveragesToZero(const unsigned int coeffs_id= 0);</a>
+<a name="142"><span class="lineNum">     142 </span>            :   //</a>
+<a name="143"><span class="lineNum">     143 </span>            :   bool readCoeffsFromFiles();</a>
+<a name="144"><span class="lineNum">     144 </span>            :   //</a>
+<a name="145"><span class="lineNum">     145 </span>            :   template&lt;class T&gt;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   bool parseMultipleValues(const std::string&amp;, std::vector&lt;T&gt;&amp;, unsigned int);</a>
+<a name="147"><span class="lineNum">     147 </span>            :   template&lt;class T&gt;</a>
+<a name="148"><span class="lineNum">     148 </span>            :   bool parseMultipleValues(const std::string&amp;, std::vector&lt;T&gt;&amp;, unsigned int, const T&amp;);</a>
+<a name="149"><span class="lineNum">     149 </span>            :   //</a>
+<a name="150"><span class="lineNum">     150 </span>            : public:</a>
+<a name="151"><span class="lineNum">     151 </span>            :   static void registerKeywords(Keywords&amp;);</a>
+<a name="152"><span class="lineNum">     152 </span>            :   explicit VesBias(const ActionOptions&amp;ao);</a>
+<a name="153"><span class="lineNum">     153 </span>            :   ~VesBias();</a>
+<a name="154"><span class="lineNum">     154 </span>            :   //</a>
+<a name="155"><span class="lineNum">     155 </span>            :   static void useInitialCoeffsKeywords(Keywords&amp;);</a>
+<a name="156"><span class="lineNum">     156 </span>            :   static void useTargetDistributionKeywords(Keywords&amp;);</a>
+<a name="157"><span class="lineNum">     157 </span>            :   static void useMultipleTargetDistributionKeywords(Keywords&amp;);</a>
+<a name="158"><span class="lineNum">     158 </span>            :   static void useGridBinKeywords(Keywords&amp;);</a>
+<a name="159"><span class="lineNum">     159 </span>            :   static void useGridLimitsKeywords(Keywords&amp;);</a>
+<a name="160"><span class="lineNum">     160 </span>            :   static void useBiasCutoffKeywords(Keywords&amp;);</a>
+<a name="161"><span class="lineNum">     161 </span>            :   static void useProjectionArgKeywords(Keywords&amp;);</a>
+<a name="162"><span class="lineNum">     162 </span>            :   static void useReweightFactorKeywords(Keywords&amp;);</a>
+<a name="163"><span class="lineNum">     163 </span>            :   //</a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        267 :   std::vector&lt;CoeffsVector*&gt; getCoeffsPntrs() const {return Tools::unique2raw(coeffs_pntrs_);}</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">         85 :   std::vector&lt;CoeffsVector*&gt; getTargetDistAveragesPntrs() const {return Tools::unique2raw(targetdist_averages_pntrs_);}</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">         85 :   std::vector&lt;CoeffsVector*&gt; getGradientPntrs()const {return Tools::unique2raw(gradient_pntrs_);}</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">         82 :   std::vector&lt;CoeffsMatrix*&gt; getHessianPntrs() const {return Tools::unique2raw(hessian_pntrs_);}</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">         93 :   std::vector&lt;TargetDistribution*&gt; getTargetDistributionPntrs() const {return targetdist_pntrs_;}</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :   //</a>
+<a name="170"><span class="lineNum">     170 </span>            :   CoeffsVector* getCoeffsPntr(const unsigned int coeffs_id = 0) const {return coeffs_pntrs_[coeffs_id].get();}</a>
+<a name="171"><span class="lineNum">     171 </span>            :   CoeffsVector* getTargetDistAveragesPntr(const unsigned int coeffs_id = 0) const {return targetdist_averages_pntrs_[coeffs_id].get();}</a>
+<a name="172"><span class="lineNum">     172 </span>            :   CoeffsVector* getGradientPntr(const unsigned int coeffs_id = 0)const {return gradient_pntrs_[coeffs_id].get();}</a>
+<a name="173"><span class="lineNum">     173 </span>            :   CoeffsMatrix* getHessianPntr(const unsigned int coeffs_id = 0) const {return hessian_pntrs_[coeffs_id].get();}</a>
+<a name="174"><span class="lineNum">     174 </span>            :   //</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">         90 :   unsigned int getNumberOfTargetDistributionPntrs() const {return targetdist_pntrs_.size();}</span></a>
+<a name="176"><span class="lineNum">     176 </span>            :   //</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">      22810 :   size_t numberOfCoeffs(const unsigned int coeffs_id = 0) const {return coeffs_pntrs_[coeffs_id]-&gt;numberOfCoeffs();}</span></a>
+<a name="178"><span class="lineNum">     178 </span>            :   size_t totalNumberOfCoeffs() const {return ncoeffs_total_;}</a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">          3 :   unsigned int numberOfCoeffsSets() const {return ncoeffssets_;}</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">         85 :   double getKbT() const {return kbt_;}</span></a>
+<a name="181"><span class="lineNum">     181 </span>            :   double getBeta() const;</a>
+<a name="182"><span class="lineNum">     182 </span>            :   //</a>
+<a name="183"><span class="lineNum">     183 </span>            :   CoeffsVector&amp; Coeffs(const unsigned int coeffs_id = 0) const {return *coeffs_pntrs_[coeffs_id];}</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        453 :   CoeffsVector&amp; TargetDistAverages(const unsigned int coeffs_id = 0) const {return *targetdist_averages_pntrs_[coeffs_id];}</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   CoeffsVector&amp; Gradient(const unsigned int coeffs_id = 0) const {return *gradient_pntrs_[coeffs_id];}</a>
+<a name="186"><span class="lineNum">     186 </span>            :   CoeffsMatrix&amp; Hessian(const unsigned int coeffs_id = 0) const {return *hessian_pntrs_[coeffs_id];}</a>
+<a name="187"><span class="lineNum">     187 </span>            :   //</a>
+<a name="188"><span class="lineNum">     188 </span>            :   size_t getCoeffsIndex(const std::vector&lt;unsigned int&gt;&amp; indices, const unsigned int coeffs_id = 0) const;</a>
+<a name="189"><span class="lineNum">     189 </span>            :   std::vector&lt;unsigned int&gt; getCoeffsIndices(const size_t index, const unsigned int coeffs_id = 0) const;</a>
+<a name="190"><span class="lineNum">     190 </span>            :   size_t getHessianIndex(const size_t index1, const size_t index2, const unsigned int coeffs_id = 0) const;</a>
+<a name="191"><span class="lineNum">     191 </span>            :   //</a>
+<a name="192"><span class="lineNum">     192 </span>            :   bool computeHessian() const {return compute_hessian_;}</a>
+<a name="193"><span class="lineNum">     193 </span>            :   bool diagonalHessian() const {return diagonal_hessian_;}</a>
+<a name="194"><span class="lineNum">     194 </span>            :   //</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1572 :   bool optimizeCoeffs() const {return optimize_coeffs_;}</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       1426 :   Optimizer* getOptimizerPntr() const {return optimizer_pntr_;}</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :   bool useMultipleWalkers() const;</a>
+<a name="198"><span class="lineNum">     198 </span>            :   //</a>
+<a name="199"><span class="lineNum">     199 </span>            :   unsigned int getIterationCounter() const;</a>
+<a name="200"><span class="lineNum">     200 </span>            :   //</a>
+<a name="201"><span class="lineNum">     201 </span>            :   void updateGradientAndHessian(const bool);</a>
+<a name="202"><span class="lineNum">     202 </span>            :   void clearGradientAndHessian() {};</a>
+<a name="203"><span class="lineNum">     203 </span>            :   //</a>
+<a name="204"><span class="lineNum">     204 </span><span class="lineNoCov">          0 :   virtual void updateTargetDistributions() {};</span></a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineNoCov">          0 :   virtual void restartTargetDistributions() {};</span></a>
+<a name="206"><span class="lineNum">     206 </span>            :   //</a>
+<a name="207"><span class="lineNum">     207 </span>            :   void linkOptimizer(Optimizer*);</a>
+<a name="208"><span class="lineNum">     208 </span>            :   void enableHessian(const bool diagonal_hessian=true);</a>
+<a name="209"><span class="lineNum">     209 </span>            :   void disableHessian();</a>
+<a name="210"><span class="lineNum">     210 </span>            :   //</a>
+<a name="211"><span class="lineNum">     211 </span>            :   void enableMultipleCoeffsSets() {use_multiple_coeffssets_=true;}</a>
+<a name="212"><span class="lineNum">     212 </span>            :   //</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         42 :   void enableDynamicTargetDistribution() {dynamic_targetdist_=true;}</span></a>
+<a name="214"><span class="lineNum">     214 </span>            :   void disableDynamicTargetDistribution() {dynamic_targetdist_=false;}</a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">        273 :   bool dynamicTargetDistribution() const {return dynamic_targetdist_;}</span></a>
+<a name="216"><span class="lineNum">     216 </span>            :   //</a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">         90 :   std::vector&lt;unsigned int&gt; getGridBins() const {return grid_bins_;}</span></a>
+<a name="218"><span class="lineNum">     218 </span>            :   void setGridBins(const std::vector&lt;unsigned int&gt;&amp;);</a>
+<a name="219"><span class="lineNum">     219 </span>            :   void setGridBins(const unsigned int);</a>
+<a name="220"><span class="lineNum">     220 </span>            :   std::vector&lt;double&gt; getGridMax() const {return grid_max_;}</a>
+<a name="221"><span class="lineNum">     221 </span>            :   void setGridMax(const std::vector&lt;double&gt;&amp;);</a>
+<a name="222"><span class="lineNum">     222 </span>            :   std::vector&lt;double&gt; getGridMin() const {return grid_min_;}</a>
+<a name="223"><span class="lineNum">     223 </span>            :   void setGridMin(const std::vector&lt;double&gt;&amp;);</a>
+<a name="224"><span class="lineNum">     224 </span>            :   //</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">        575 :   bool filenamesIncludeIterationNumber() const {return filenames_have_iteration_number_;}</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">          3 :   void enableIterationNumberInFilenames() {filenames_have_iteration_number_=true;}</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :   //</a>
+<a name="228"><span class="lineNum">     228 </span>            :   std::string getIterationFilenameSuffix() const;</a>
+<a name="229"><span class="lineNum">     229 </span>            :   std::string getCoeffsSetFilenameSuffix(const unsigned int coeffs_id) const;</a>
+<a name="230"><span class="lineNum">     230 </span>            :   std::string getCurrentOutputFilename(const std::string&amp;, const std::string&amp; suffix=&quot;&quot;) const;</a>
+<a name="231"><span class="lineNum">     231 </span>            :   std::string getBiasOutputFilename() const {return bias_filename_;}</a>
+<a name="232"><span class="lineNum">     232 </span>            :   std::string getCurrentBiasOutputFilename(const std::string&amp; suffix=&quot;&quot;) const;</a>
+<a name="233"><span class="lineNum">     233 </span>            :   std::string getFesOutputFilename() const {return fes_filename_;}</a>
+<a name="234"><span class="lineNum">     234 </span>            :   std::string getCurrentFesOutputFilename(const std::string&amp; suffix=&quot;&quot;) const;</a>
+<a name="235"><span class="lineNum">     235 </span>            :   std::string getTargetDistOutputFilename() const {return targetdist_filename_;}</a>
+<a name="236"><span class="lineNum">     236 </span>            :   std::string getCurrentTargetDistOutputFilename(const std::string&amp; suffix=&quot;&quot;) const;</a>
+<a name="237"><span class="lineNum">     237 </span>            :   //</a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">         83 :   void enableBiasFileOutput() {bias_fileoutput_active_=true;}</span></a>
+<a name="239"><span class="lineNum">     239 </span>            :   void disableBiasFileOutput() {bias_fileoutput_active_=false;}</a>
+<a name="240"><span class="lineNum">     240 </span>            :   bool isBiasFileOutputActive() const {return bias_fileoutput_active_;}</a>
+<a name="241"><span class="lineNum">     241 </span>            :   std::string getBiasFileFmt() const {return bias_file_fmt_;}</a>
+<a name="242"><span class="lineNum">     242 </span>            :   //</a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         83 :   void enableFesFileOutput() {fes_fileoutput_active_=true;}</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :   void disableFesFileOutput() {fes_fileoutput_active_=false;}</a>
+<a name="245"><span class="lineNum">     245 </span>            :   bool isFesFileOutputActive() const {return fes_fileoutput_active_;}</a>
+<a name="246"><span class="lineNum">     246 </span>            :   std::string getFesFileFmt() const {return fes_file_fmt_;}</a>
+<a name="247"><span class="lineNum">     247 </span>            :   //</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         17 :   void enableFesProjFileOutput() {fesproj_fileoutput_active_=true;}</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :   void disableFesFileProjOutput() {fesproj_fileoutput_active_=false;}</a>
+<a name="250"><span class="lineNum">     250 </span>            :   bool isFesProjFileOutputActive() const {return fesproj_fileoutput_active_;}</a>
+<a name="251"><span class="lineNum">     251 </span>            :   //</a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">         41 :   void enableDynamicTargetDistFileOutput() {dynamic_targetdist_fileoutput_active_=true;}</span></a>
+<a name="253"><span class="lineNum">     253 </span>            :   void disableDynamicTargetDistFileOutput() {dynamic_targetdist_fileoutput_active_=false;}</a>
+<a name="254"><span class="lineNum">     254 </span>            :   bool isDynamicTargetDistFileOutputActive() const {return dynamic_targetdist_fileoutput_active_;}</a>
+<a name="255"><span class="lineNum">     255 </span>            :   std::string getTargetDistFileFmt() const {return targetdist_file_fmt_;}</a>
+<a name="256"><span class="lineNum">     256 </span>            :   std::string getTargetDistRestartFileFmt() const {return targetdist_restart_file_fmt_;}</a>
+<a name="257"><span class="lineNum">     257 </span>            :   //</a>
+<a name="258"><span class="lineNum">     258 </span>            :   void enableStaticTargetDistFileOutput() {static_targetdist_fileoutput_active_=true;}</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">         46 :   void disableStaticTargetDistFileOutput() {static_targetdist_fileoutput_active_=false;}</span></a>
+<a name="260"><span class="lineNum">     260 </span><span class="lineCov">         50 :   bool isStaticTargetDistFileOutputActive() const {return static_targetdist_fileoutput_active_;}</span></a>
+<a name="261"><span class="lineNum">     261 </span>            :   //</a>
+<a name="262"><span class="lineNum">     262 </span>            :   std::vector&lt; std::vector&lt;std::string&gt; &gt; getProjectionArguments() const {return projection_args_;}</a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">         56 :   std::vector&lt;std::string&gt; getProjectionArgument(unsigned int i) const {return projection_args_[i];}</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">        122 :   unsigned int getNumberOfProjectionArguments() const {return projection_args_.size();}</span></a>
+<a name="265"><span class="lineNum">     265 </span>            :   //</a>
+<a name="266"><span class="lineNum">     266 </span>            :   void setupBiasCutoff(const double, const double);</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">    1498465 :   bool biasCutoffActive() const {return bias_cutoff_active_;}</span></a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">         45 :   double getBiasCutoffValue() const {return bias_cutoff_value_;}</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">        498 :   void setCurrentBiasMaxValue(const double max_value) {bias_current_max_value=max_value;}</span></a>
+<a name="270"><span class="lineNum">     270 </span>            :   double getCurrentBiasMaxValue() const {return bias_current_max_value;}</a>
+<a name="271"><span class="lineNum">     271 </span>            :   double getBiasCutoffSwitchingFunction(const double, double&amp;) const;</a>
+<a name="272"><span class="lineNum">     272 </span>            :   double getBiasCutoffSwitchingFunction(const double) const;</a>
+<a name="273"><span class="lineNum">     273 </span>            :   void applyBiasCutoff(double&amp;, std::vector&lt;double&gt;&amp;) const;</a>
+<a name="274"><span class="lineNum">     274 </span>            :   void applyBiasCutoff(double&amp;, std::vector&lt;double&gt;&amp;, std::vector&lt;double&gt;&amp;) const;</a>
+<a name="275"><span class="lineNum">     275 </span>            :   //</a>
+<a name="276"><span class="lineNum">     276 </span>            :   std::unique_ptr&lt;OFile&gt; getOFile(const std::string&amp; filename, const bool multi_sim_single_file=false, const bool enforce_backup=true);</a>
+<a name="277"><span class="lineNum">     277 </span>            :   //</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineNoCov">          0 :   virtual void setupBiasFileOutput() {};</span></a>
+<a name="279"><span class="lineNum">     279 </span><span class="lineNoCov">          0 :   virtual void writeBiasToFile() {};</span></a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineNoCov">          0 :   virtual void resetBiasFileOutput() {};</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   //</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineNoCov">          0 :   virtual void setupFesFileOutput() {};</span></a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineNoCov">          0 :   virtual void writeFesToFile() {};</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineNoCov">          0 :   virtual void resetFesFileOutput() {};</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   //</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   virtual void setupFesProjFileOutput() {};</span></a>
+<a name="287"><span class="lineNum">     287 </span><span class="lineNoCov">          0 :   virtual void writeFesProjToFile() {};</span></a>
+<a name="288"><span class="lineNum">     288 </span><span class="lineNoCov">          0 :   virtual void resetFesProjFileOutput() {};</span></a>
+<a name="289"><span class="lineNum">     289 </span>            :   //</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         44 :   virtual void setupTargetDistFileOutput() {};</span></a>
+<a name="291"><span class="lineNum">     291 </span><span class="lineNoCov">          0 :   virtual void writeTargetDistToFile() {};</span></a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineNoCov">          0 :   virtual void resetTargetDistFileOutput() {};</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :   //</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">          9 :   virtual void setupTargetDistProjFileOutput() {};</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineNoCov">          0 :   virtual void writeTargetDistProjToFile() {};</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineNoCov">          0 :   virtual void resetTargetDistProjFileOutput() {};</span></a>
+<a name="297"><span class="lineNum">     297 </span>            :   //</a>
+<a name="298"><span class="lineNum">     298 </span>            :   void updateReweightFactor();</a>
+<a name="299"><span class="lineNum">     299 </span>            :   virtual double calculateReweightFactor() const;</a>
+<a name="300"><span class="lineNum">     300 </span><span class="lineNoCov">          0 :   bool isReweightFactorCalculated() const {return calc_reweightfactor_;}</span></a>
+<a name="301"><span class="lineNum">     301 </span>            : };</a>
+<a name="302"><span class="lineNum">     302 </span>            : </a>
+<a name="303"><span class="lineNum">     303 </span>            : </a>
+<a name="304"><span class="lineNum">     304 </span>            : inline</a>
+<a name="305"><span class="lineNum">     305 </span>            : size_t VesBias::getCoeffsIndex(const std::vector&lt;unsigned int&gt;&amp; indices, const unsigned int coeffs_id) const {return coeffs_pntrs_[coeffs_id]-&gt;getIndex(indices);}</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            : inline</a>
+<a name="308"><span class="lineNum">     308 </span>            : std::vector&lt;unsigned int&gt; VesBias::getCoeffsIndices(const size_t index, const unsigned int coeffs_id) const {return coeffs_pntrs_[coeffs_id]-&gt;getIndices(index);}</a>
+<a name="309"><span class="lineNum">     309 </span>            : </a>
+<a name="310"><span class="lineNum">     310 </span>            : inline</a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">    3607712 : size_t VesBias::getHessianIndex(const size_t index1, const size_t index2, const unsigned int coeffs_id) const {return hessian_pntrs_[coeffs_id]-&gt;getMatrixIndex(index1,index2);}</span></a>
+<a name="312"><span class="lineNum">     312 </span>            : </a>
+<a name="313"><span class="lineNum">     313 </span>            : </a>
+<a name="314"><span class="lineNum">     314 </span>            : inline</a>
+<a name="315"><span class="lineNum">     315 </span><span class="lineCov">      23277 : double VesBias::getBeta() const {</span></a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">      23277 :   plumed_massert(kbt_!=0.0,&quot;you are requesting beta=1/(kB*T) when kB*T has not been defined. You need to give the temperature using the TEMP keyword as the MD engine does not pass it to PLUMED.&quot;);</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">      23277 :   return 1.0/kbt_;</span></a>
+<a name="318"><span class="lineNum">     318 </span>            : }</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span>            : </a>
+<a name="321"><span class="lineNum">     321 </span>            : inline</a>
+<a name="322"><span class="lineNum">     322 </span>            : std::string VesBias::getCurrentBiasOutputFilename(const std::string&amp; suffix) const {</a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">        178 :   return getCurrentOutputFilename(bias_filename_,suffix);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            : }</a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span>            : inline</a>
+<a name="328"><span class="lineNum">     328 </span>            : std::string VesBias::getCurrentFesOutputFilename(const std::string&amp; suffix) const {</a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">        205 :   return getCurrentOutputFilename(fes_filename_,suffix);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            : }</a>
+<a name="331"><span class="lineNum">     331 </span>            : </a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            : inline</a>
+<a name="334"><span class="lineNum">     334 </span>            : double VesBias::getBiasCutoffSwitchingFunction(const double bias) const {</a>
+<a name="335"><span class="lineNum">     335 </span>            :   double dummy=0.0;</a>
+<a name="336"><span class="lineNum">     336 </span>            :   return getBiasCutoffSwitchingFunction(bias,dummy);</a>
+<a name="337"><span class="lineNum">     337 </span>            : }</a>
+<a name="338"><span class="lineNum">     338 </span>            : </a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            : inline</a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">        600 : void VesBias::applyBiasCutoff(double&amp; bias, std::vector&lt;double&gt;&amp; forces) const {</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">        600 :   std::vector&lt;double&gt; dummy(0);</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">        600 :   applyBiasCutoff(bias,forces,dummy);</span></a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">        600 : }</span></a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span>            : </a>
+<a name="347"><span class="lineNum">     347 </span>            : inline</a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">        663 : void VesBias::applyBiasCutoff(double&amp; bias, std::vector&lt;double&gt;&amp; forces, std::vector&lt;double&gt;&amp; coeffsderivs_values) const {</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">        663 :   double deriv_factor_sf=0.0;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        663 :   double value_sf = getBiasCutoffSwitchingFunction(bias,deriv_factor_sf);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">        663 :   bias *= value_sf;</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">       1326 :   for(unsigned int i=0; i&lt;forces.size(); i++) {</span></a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">        663 :     forces[i] *= deriv_factor_sf;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            :   }</a>
+<a name="355"><span class="lineNum">     355 </span>            :   //</a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">       1398 :   for(unsigned int i=0; i&lt;coeffsderivs_values.size(); i++) {</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">        735 :     coeffsderivs_values[i] *= deriv_factor_sf;</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   }</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">        663 : }</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : </a>
+<a name="362"><span class="lineNum">     362 </span>            : inline</a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">      22810 : std::vector&lt;double&gt; VesBias::computeCovarianceFromAverages(const unsigned int c_id) const {</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :   size_t ncoeffs = numberOfCoeffs(c_id);</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">      22810 :   std::vector&lt;double&gt; covariance(sampled_cross_averages[c_id].size(),0.0);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   // diagonal part</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">    1823850 :   for(size_t i=0; i&lt;ncoeffs; i++) {</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :     size_t midx = getHessianIndex(i,i,c_id);</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">    1801040 :     covariance[midx] = sampled_cross_averages[c_id][midx] - sampled_averages[c_id][i]*sampled_averages[c_id][i];</span></a>
+<a name="370"><span class="lineNum">     370 </span>            :   }</a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">      22810 :   if(!diagonal_hessian_) {</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineNoCov">          0 :     for(size_t i=0; i&lt;ncoeffs; i++) {</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineNoCov">          0 :       for(size_t j=(i+1); j&lt;ncoeffs; j++) {</span></a>
+<a name="374"><span class="lineNum">     374 </span>            :         size_t midx = getHessianIndex(i,j,c_id);</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineNoCov">          0 :         covariance[midx] = sampled_cross_averages[c_id][midx] - sampled_averages[c_id][i]*sampled_averages[c_id][j];</span></a>
+<a name="376"><span class="lineNum">     376 </span>            :       }</a>
+<a name="377"><span class="lineNum">     377 </span>            :     }</a>
+<a name="378"><span class="lineNum">     378 </span>            :   }</a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineCov">      22810 :   return covariance;</span></a>
+<a name="380"><span class="lineNum">     380 </span>            : }</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span>            : </a>
+<a name="383"><span class="lineNum">     383 </span>            : template&lt;class T&gt;</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">        180 : bool VesBias::parseMultipleValues(const std::string&amp; keyword, std::vector&lt;T&gt;&amp; values, unsigned int nvalues) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">        180 :   plumed_assert(nvalues&gt;0);</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">        180 :   plumed_assert(values.size()==0);</span></a>
+<a name="387"><span class="lineNum">     387 </span>            :   bool identical_values=false;</a>
+<a name="388"><span class="lineNum">     388 </span>            :   //</a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">        180 :   parseVector(keyword,values);</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineCov">        180 :   if(values.size()==1 &amp;&amp; nvalues&gt;1) {</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :     values.resize(nvalues,values[0]);</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :     identical_values=true;</a>
+<a name="393"><span class="lineNum">     393 </span>            :   }</a>
+<a name="394"><span class="lineNum">     394 </span><span class="lineCov">        180 :   if(values.size()&gt;0 &amp;&amp; values.size()!=nvalues) {</span></a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineNoCov">          0 :     std::string s1; Tools::convert(nvalues,s1);</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;Error in &quot; + keyword + &quot; keyword: either give 1 common parameter value or &quot; + s1 + &quot; separate parameter values&quot;);</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">        180 :   return identical_values;</span></a>
+<a name="399"><span class="lineNum">     399 </span>            : }</a>
+<a name="400"><span class="lineNum">     400 </span>            : </a>
+<a name="401"><span class="lineNum">     401 </span>            : template&lt;class T&gt;</a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">         90 : bool VesBias::parseMultipleValues(const std::string&amp; keyword, std::vector&lt;T&gt;&amp; values, unsigned int nvalues, const T&amp; default_value) {</span></a>
+<a name="403"><span class="lineNum">     403 </span><span class="lineCov">         90 :   bool identical_values = parseMultipleValues(keyword,values,nvalues);</span></a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">         90 :   if(values.size()==0) {</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineNoCov">          0 :     values.resize(nvalues,default_value);</span></a>
+<a name="406"><span class="lineNum">     406 </span>            :     identical_values=true;</a>
+<a name="407"><span class="lineNum">     407 </span>            :   }</a>
+<a name="408"><span class="lineNum">     408 </span><span class="lineCov">         90 :   return identical_values;</span></a>
+<a name="409"><span class="lineNum">     409 </span>            : }</a>
+<a name="410"><span class="lineNum">     410 </span>            : </a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            : }</a>
+<a name="413"><span class="lineNum">     413 </span>            : }</a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesDeltaF.cpp.func-sort-c.html b/coverage/ves/VesDeltaF.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a633474805
--- /dev/null
+++ b/coverage/ves/VesDeltaF.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesDeltaF.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesDeltaF.cpp<span style="font-size: 80%;"> (<a href="VesDeltaF.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">346</td>
+            <td class="headerCovTableEntry">356</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesDeltaF.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#217">_ZN4PLMD3ves9VesDeltaFC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#178">_ZN4PLMD3ves12_GLOBAL__N_122VesDeltaFRegisterMe1806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#217">_ZN4PLMD3ves9VesDeltaFC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#180">_ZN4PLMD3ves9VesDeltaF16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#633">_ZN4PLMD3ves9VesDeltaF12update_alphaEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#586">_ZN4PLMD3ves9VesDeltaF17update_tg_and_rctEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#528">_ZN4PLMD3ves9VesDeltaF6updateEv</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#502">_ZN4PLMD3ves9VesDeltaF9calculateEv</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#178">_ZN4PLMD3ves12_GLOBAL__N_122VesDeltaFRegisterMe180C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#178">_ZN4PLMD3ves12_GLOBAL__N_122VesDeltaFRegisterMe180D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#710">_ZNK4PLMD3ves9VesDeltaF9get_indexEjj</a></td>
+              <td class="coverFnHi">4632</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesDeltaF.cpp.func.html b/coverage/ves/VesDeltaF.cpp.func.html
new file mode 100644
index 0000000000..4de574f7b4
--- /dev/null
+++ b/coverage/ves/VesDeltaF.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesDeltaF.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesDeltaF.cpp<span style="font-size: 80%;"> (<a href="VesDeltaF.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">346</td>
+            <td class="headerCovTableEntry">356</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesDeltaF.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#178">_ZN4PLMD3ves12_GLOBAL__N_122VesDeltaFRegisterMe1806createERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#178">_ZN4PLMD3ves12_GLOBAL__N_122VesDeltaFRegisterMe180C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#178">_ZN4PLMD3ves12_GLOBAL__N_122VesDeltaFRegisterMe180D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#633">_ZN4PLMD3ves9VesDeltaF12update_alphaEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#180">_ZN4PLMD3ves9VesDeltaF16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#586">_ZN4PLMD3ves9VesDeltaF17update_tg_and_rctEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#528">_ZN4PLMD3ves9VesDeltaF6updateEv</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#502">_ZN4PLMD3ves9VesDeltaF9calculateEv</a></td>
+              <td class="coverFnHi">804</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#217">_ZN4PLMD3ves9VesDeltaFC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">4</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#217">_ZN4PLMD3ves9VesDeltaFC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesDeltaF.cpp.gcov.html#710">_ZNK4PLMD3ves9VesDeltaF9get_indexEjj</a></td>
+              <td class="coverFnHi">4632</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesDeltaF.cpp.gcov.html b/coverage/ves/VesDeltaF.cpp.gcov.html
new file mode 100644
index 0000000000..2fbd9d559c
--- /dev/null
+++ b/coverage/ves/VesDeltaF.cpp.gcov.html
@@ -0,0 +1,797 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesDeltaF.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesDeltaF.cpp<span style="font-size: 80%;"> (source / <a href="VesDeltaF.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">346</td>
+            <td class="headerCovTableEntry">356</td>
+            <td class="headerCovTableEntryHi">97.2 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/Atoms.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/File.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : //#include &lt;algorithm&gt; //std::fill</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : //+PLUMEDOC VES_BIAS VES_DELTA_F</a>
+<a name="36"><span class="lineNum">      36 </span>            : /*</a>
+<a name="37"><span class="lineNum">      37 </span>            : Implementation of VES Delta F method</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : Implementation of VES\f$\Delta F\f$ method \cite Invernizzi2019vesdeltaf (step two only).</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : \warning</a>
+<a name="42"><span class="lineNum">      42 </span>            :   Notice that this is a stand-alone bias Action, it does not need any of the other VES module components</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            : First you should create some estimate of the local free energy basins of your system,</a>
+<a name="45"><span class="lineNum">      45 </span>            : using e.g. multiple \ref METAD short runs, and combining them with the \ref sum_hills utility.</a>
+<a name="46"><span class="lineNum">      46 </span>            : Once you have them, you can use this bias Action to perform the VES optimization part of the method.</a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span>            : These \f$N+1\f$ local basins are used to model the global free energy.</a>
+<a name="49"><span class="lineNum">      49 </span>            : In particular, given the conditional probabilities \f$P(\mathbf{s}|i)\propto e^{-\beta F_i(\mathbf{s})}\f$</a>
+<a name="50"><span class="lineNum">      50 </span>            : and the probabilities of being in a given basin \f$P_i\f$, we can write:</a>
+<a name="51"><span class="lineNum">      51 </span>            : \f[</a>
+<a name="52"><span class="lineNum">      52 </span>            :   e^{-\beta F(\mathbf{s})}\propto P(\mathbf{s})=\sum_{i=0}^N P(\mathbf{s}|i)P_i \, .</a>
+<a name="53"><span class="lineNum">      53 </span>            : \f]</a>
+<a name="54"><span class="lineNum">      54 </span>            : We use this free energy model and the chosen bias factor \f$\gamma\f$ to build the bias potential:</a>
+<a name="55"><span class="lineNum">      55 </span>            : \f$V(\mathbf{s})=-(1-1/\gamma)F(\mathbf{s})\f$.</a>
+<a name="56"><span class="lineNum">      56 </span>            : Or, more explicitly:</a>
+<a name="57"><span class="lineNum">      57 </span>            : \f[</a>
+<a name="58"><span class="lineNum">      58 </span>            :   V(\mathbf{s})=(1-1/\gamma)\frac{1}{\beta}\log\left[e^{-\beta F_0(\mathbf{s})}</a>
+<a name="59"><span class="lineNum">      59 </span>            :   +\sum_{i=1}^{N} e^{-\beta F_i(\mathbf{s})} e^{-\beta \alpha_i}\right] \, ,</a>
+<a name="60"><span class="lineNum">      60 </span>            : \f]</a>
+<a name="61"><span class="lineNum">      61 </span>            : where the parameters \f$\boldsymbol{\alpha}\f$ are the \f$N\f$ free energy differences (see below) from the \f$F_0\f$ basin.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            : By default the \f$F_i(\mathbf{s})\f$ are shifted so that \f$\min[F_i(\mathbf{s})]=0\f$ for all \f$i=\{0,...,N\}\f$.</a>
+<a name="64"><span class="lineNum">      64 </span>            : In this case the optimization parameters \f$\alpha_i\f$ are the difference in height between the minima of the basins.</a>
+<a name="65"><span class="lineNum">      65 </span>            : Using the keyword `NORMALIZE`, you can also decide to normalize the local free energies so that</a>
+<a name="66"><span class="lineNum">      66 </span>            : \f$\int d\mathbf{s}\, e^{-\beta F_i(\mathbf{s})}=1\f$.</a>
+<a name="67"><span class="lineNum">      67 </span>            : In this case the parameters will represent not the difference in height (which depends on the chosen CVs),</a>
+<a name="68"><span class="lineNum">      68 </span>            : but the actual free energy difference, \f$\alpha_i=\Delta F_i\f$.</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : However, as discussed in Ref. \cite Invernizzi2019vesdeltaf, a better estimate of \f$\Delta F_i\f$ should be obtained through the reweighting procedure.</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : \par Examples</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : The following performs the optimization of the free energy difference between two metastable basins:</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : \plumedfile</a>
+<a name="77"><span class="lineNum">      77 </span>            : cv: DISTANCE ATOMS=1,2</a>
+<a name="78"><span class="lineNum">      78 </span>            : ves: VES_DELTA_F ...</a>
+<a name="79"><span class="lineNum">      79 </span>            :   ARG=cv</a>
+<a name="80"><span class="lineNum">      80 </span>            :   TEMP=300</a>
+<a name="81"><span class="lineNum">      81 </span>            :   FILE_F0=fesA.data</a>
+<a name="82"><span class="lineNum">      82 </span>            :   FILE_F1=fesB.data</a>
+<a name="83"><span class="lineNum">      83 </span>            :   BIASFACTOR=10.0</a>
+<a name="84"><span class="lineNum">      84 </span>            :   M_STEP=0.1</a>
+<a name="85"><span class="lineNum">      85 </span>            :   AV_STRIDE=500</a>
+<a name="86"><span class="lineNum">      86 </span>            :   PRINT_STRIDE=100</a>
+<a name="87"><span class="lineNum">      87 </span>            : ...</a>
+<a name="88"><span class="lineNum">      88 </span>            : PRINT FMT=%g STRIDE=500 FILE=Colvar.data ARG=cv,ves.bias,ves.rct</a>
+<a name="89"><span class="lineNum">      89 </span>            : \endplumedfile</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : The local FES files can be obtained as described in Sec. 4.2 of Ref. \cite Invernizzi2019vesdeltaf, i.e. for example:</a>
+<a name="92"><span class="lineNum">      92 </span>            : - run 4 independent metad runs, all starting from basin A, and kill them as soon as they make the first transition (see e.g. \ref COMMITTOR)</a>
+<a name="93"><span class="lineNum">      93 </span>            : - \verbatim cat HILLS* &gt; all_HILLS \endverbatim</a>
+<a name="94"><span class="lineNum">      94 </span>            : - \verbatim plumed sum_hills --hills all_HILLS --outfile all_fesA.dat --mintozero --min 0 --max 1 --bin 100 \endverbatim</a>
+<a name="95"><span class="lineNum">      95 </span>            : - \verbatim awk -v n_rep=4 '{if($1!=&quot;#!&quot; &amp;&amp; $1!=&quot;&quot;) {for(i=1+(NF-1)/2; i&lt;=NF; i++) $i/=n_rep;} print $0}' all_fesA.dat &gt; fesA.data \endverbatim</a>
+<a name="96"><span class="lineNum">      96 </span>            : </a>
+<a name="97"><span class="lineNum">      97 </span>            : The header of both FES files must be identical, and should be similar to the following:</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : \auxfile{fesA.data}</a>
+<a name="100"><span class="lineNum">     100 </span>            : #! FIELDS cv file.free der_cv</a>
+<a name="101"><span class="lineNum">     101 </span>            : #! SET min_cv 0</a>
+<a name="102"><span class="lineNum">     102 </span>            : #! SET max_cv 1</a>
+<a name="103"><span class="lineNum">     103 </span>            : #! SET nbins_cv  100</a>
+<a name="104"><span class="lineNum">     104 </span>            : #! SET periodic_cv false</a>
+<a name="105"><span class="lineNum">     105 </span>            : 0 0 0</a>
+<a name="106"><span class="lineNum">     106 </span>            : \endauxfile</a>
+<a name="107"><span class="lineNum">     107 </span>            : \auxfile{fesB.data}</a>
+<a name="108"><span class="lineNum">     108 </span>            : #! FIELDS cv file.free der_cv</a>
+<a name="109"><span class="lineNum">     109 </span>            : #! SET min_cv 0</a>
+<a name="110"><span class="lineNum">     110 </span>            : #! SET max_cv 1</a>
+<a name="111"><span class="lineNum">     111 </span>            : #! SET nbins_cv  100</a>
+<a name="112"><span class="lineNum">     112 </span>            : #! SET periodic_cv false</a>
+<a name="113"><span class="lineNum">     113 </span>            : 0 0 0</a>
+<a name="114"><span class="lineNum">     114 </span>            : \endauxfile</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : */</a>
+<a name="117"><span class="lineNum">     117 </span>            : //+ENDPLUMEDOC</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span>            : class VesDeltaF : public bias::Bias {</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span>            : private:</a>
+<a name="122"><span class="lineNum">     122 </span>            :   double beta_;</a>
+<a name="123"><span class="lineNum">     123 </span>            :   unsigned NumParallel_;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   unsigned rank_;</a>
+<a name="125"><span class="lineNum">     125 </span>            :   unsigned NumWalkers_;</a>
+<a name="126"><span class="lineNum">     126 </span>            :   bool isFirstStep_;</a>
+<a name="127"><span class="lineNum">     127 </span>            :   bool afterCalculate_;</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : //prob</a>
+<a name="130"><span class="lineNum">     130 </span>            :   double tot_prob_;</a>
+<a name="131"><span class="lineNum">     131 </span>            :   std::vector&lt;double&gt; prob_;</a>
+<a name="132"><span class="lineNum">     132 </span>            :   std::vector&lt; std::vector&lt;double&gt; &gt; der_prob_;</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : //local basins</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::vector&lt; std::unique_ptr&lt;Grid&gt; &gt; grid_p_; //pointers because of GridBase::create</a>
+<a name="136"><span class="lineNum">     136 </span>            :   std::vector&lt;double&gt; norm_;</a>
+<a name="137"><span class="lineNum">     137 </span>            : </a>
+<a name="138"><span class="lineNum">     138 </span>            : //optimizer-related stuff</a>
+<a name="139"><span class="lineNum">     139 </span>            :   long long unsigned mean_counter_;</a>
+<a name="140"><span class="lineNum">     140 </span>            :   unsigned mean_weight_tau_;</a>
+<a name="141"><span class="lineNum">     141 </span>            :   unsigned alpha_size_;</a>
+<a name="142"><span class="lineNum">     142 </span>            :   unsigned sym_alpha_size_;</a>
+<a name="143"><span class="lineNum">     143 </span>            :   std::vector&lt;double&gt; mean_alpha_;</a>
+<a name="144"><span class="lineNum">     144 </span>            :   std::vector&lt;double&gt; inst_alpha_;</a>
+<a name="145"><span class="lineNum">     145 </span>            :   std::vector&lt;double&gt; past_increment2_;</a>
+<a name="146"><span class="lineNum">     146 </span>            :   double minimization_step_;</a>
+<a name="147"><span class="lineNum">     147 </span>            :   bool damping_off_;</a>
+<a name="148"><span class="lineNum">     148 </span>            : //'tg' -&gt; 'target distribution'</a>
+<a name="149"><span class="lineNum">     149 </span>            :   double inv_gamma_;</a>
+<a name="150"><span class="lineNum">     150 </span>            :   unsigned tg_counter_;</a>
+<a name="151"><span class="lineNum">     151 </span>            :   unsigned tg_stride_;</a>
+<a name="152"><span class="lineNum">     152 </span>            :   std::vector&lt;double&gt; tg_dV_dAlpha_;</a>
+<a name="153"><span class="lineNum">     153 </span>            :   std::vector&lt;double&gt; tg_d2V_dAlpha2_;</a>
+<a name="154"><span class="lineNum">     154 </span>            : //'av' -&gt; 'ensemble average'</a>
+<a name="155"><span class="lineNum">     155 </span>            :   unsigned av_counter_;</a>
+<a name="156"><span class="lineNum">     156 </span>            :   unsigned av_stride_;</a>
+<a name="157"><span class="lineNum">     157 </span>            :   std::vector&lt;double&gt; av_dV_dAlpha_;</a>
+<a name="158"><span class="lineNum">     158 </span>            :   std::vector&lt;double&gt; av_dV_dAlpha_prod_;</a>
+<a name="159"><span class="lineNum">     159 </span>            :   std::vector&lt;double&gt; av_d2V_dAlpha2_;</a>
+<a name="160"><span class="lineNum">     160 </span>            : //printing</a>
+<a name="161"><span class="lineNum">     161 </span>            :   unsigned print_stride_;</a>
+<a name="162"><span class="lineNum">     162 </span>            :   OFile alphaOfile_;</a>
+<a name="163"><span class="lineNum">     163 </span>            : //other</a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::vector&lt;double&gt; exp_alpha_;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   std::vector&lt;double&gt; prev_exp_alpha_;</a>
+<a name="166"><span class="lineNum">     166 </span>            :   double work_;</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            : //functions</a>
+<a name="169"><span class="lineNum">     169 </span>            :   void update_alpha();</a>
+<a name="170"><span class="lineNum">     170 </span>            :   void update_tg_and_rct();</a>
+<a name="171"><span class="lineNum">     171 </span>            :   inline unsigned get_index(const unsigned, const unsigned) const;</a>
+<a name="172"><span class="lineNum">     172 </span>            : </a>
+<a name="173"><span class="lineNum">     173 </span>            : public:</a>
+<a name="174"><span class="lineNum">     174 </span>            :   explicit VesDeltaF(const ActionOptions&amp;);</a>
+<a name="175"><span class="lineNum">     175 </span>            :   void calculate() override;</a>
+<a name="176"><span class="lineNum">     176 </span>            :   void update() override;</a>
+<a name="177"><span class="lineNum">     177 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="178"><span class="lineNum">     178 </span>            : };</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      12512 : PLUMED_REGISTER_ACTION(VesDeltaF,&quot;VES_DELTA_F&quot;)</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          6 : void VesDeltaF::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          6 :   Bias::registerKeywords(keys);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          6 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;TEMP&quot;,&quot;temperature is compulsory, but it can be sometimes fetched from the MD engine&quot;);</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : //local free energies</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">         12 :   keys.add(&quot;numbered&quot;,&quot;FILE_F&quot;,&quot;names of files containing local free energies and derivatives. &quot;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            :            &quot;The first one, FILE_F0, is used as reference for all the free energy differences.&quot;);</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         12 :   keys.reset_style(&quot;FILE_F&quot;,&quot;compulsory&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">         12 :   keys.addFlag(&quot;NORMALIZE&quot;,false,&quot;normalize all local free energies so that alpha will be (approx) Delta F&quot;);</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineCov">         12 :   keys.addFlag(&quot;NO_MINTOZERO&quot;,false,&quot;leave local free energies as provided, without shifting them to zero min&quot;);</span></a>
+<a name="192"><span class="lineNum">     192 </span>            : //target distribution</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;BIASFACTOR&quot;,&quot;0&quot;,&quot;the gamma bias factor used for well-tempered target p(s).&quot;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :            &quot; Set to 0 for non-tempered flat target&quot;);</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;TG_STRIDE&quot;,&quot;( default=1 ) number of AV_STRIDE between updates&quot;</span></a>
+<a name="196"><span class="lineNum">     196 </span>            :            &quot; of target p(s) and reweighing factor c(t)&quot;);</a>
+<a name="197"><span class="lineNum">     197 </span>            : //optimization</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;M_STEP&quot;,&quot;1.0&quot;,&quot;the mu step used for the Omega functional minimization&quot;);</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;AV_STRIDE&quot;,&quot;500&quot;,&quot;number of simulation steps between alpha updates&quot;);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;TAU_MEAN&quot;,&quot;exponentially decaying average for alpha (rescaled using AV_STRIDE).&quot;</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :            &quot; Should be used only in very specific cases&quot;);</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;INITIAL_ALPHA&quot;,&quot;( default=0 ) an initial guess for the bias potential parameter alpha&quot;);</span></a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         12 :   keys.addFlag(&quot;DAMPING_OFF&quot;,false,&quot;do not use an AdaGrad-like term to rescale M_STEP&quot;);</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : //output parameters file</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">         12 :   keys.add(&quot;compulsory&quot;,&quot;ALPHA_FILE&quot;,&quot;ALPHA&quot;,&quot;file name for output minimization parameters&quot;);</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;PRINT_STRIDE&quot;,&quot;( default=10 ) stride for printing to ALPHA_FILE&quot;);</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">         12 :   keys.add(&quot;optional&quot;,&quot;FMT&quot;,&quot;specify format for ALPHA_FILE&quot;);</span></a>
+<a name="208"><span class="lineNum">     208 </span>            : //debug flags</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         12 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;perform the calculation in serial even if multiple tasks are available&quot;);</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">         12 :   keys.addFlag(&quot;MULTIPLE_WALKERS&quot;,false,&quot;use multiple walkers connected via MPI for the optimization&quot;);</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          6 :   keys.use(&quot;RESTART&quot;);</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : //output components</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">          6 :   componentsAreNotOptional(keys);</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;rct&quot;,&quot;default&quot;,&quot;the reweighting factor c(t)&quot;);</span></a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">         12 :   keys.addOutputComponent(&quot;work&quot;,&quot;default&quot;,&quot;the work done by the bias in one AV_STRIDE&quot;);</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">          6 : }</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : </a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">          4 : VesDeltaF::VesDeltaF(const ActionOptions&amp;ao)</span></a>
+<a name="220"><span class="lineNum">     220 </span>            :   : PLUMED_BIAS_INIT(ao)</a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineCov">          4 :   , isFirstStep_(true)</span></a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">          4 :   , afterCalculate_(false)</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">          4 :   , mean_counter_(0)</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">          4 :   , av_counter_(0)</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">          4 :   , work_(0)</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : {</a>
+<a name="227"><span class="lineNum">     227 </span>            : //set beta</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">          4 :   const double Kb=plumed.getAtoms().getKBoltzmann();</span></a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">          4 :   double temp=0;</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">          4 :   parse(&quot;TEMP&quot;,temp);</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">          4 :   double KbT=Kb*temp;</span></a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">          4 :   if(KbT==0)</span></a>
+<a name="233"><span class="lineNum">     233 </span>            :   {</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineNoCov">          0 :     KbT=plumed.getAtoms().getKbT();</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :     plumed_massert(KbT&gt;0,&quot;your MD engine does not pass the temperature to plumed, you must specify it using TEMP&quot;);</span></a>
+<a name="236"><span class="lineNum">     236 </span>            :   }</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          4 :   beta_=1.0/KbT;</span></a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span>            : //initialize probability grids using local free energies</a>
+<a name="240"><span class="lineNum">     240 </span>            :   bool spline=true;</a>
+<a name="241"><span class="lineNum">     241 </span>            :   bool sparsegrid=false;</a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">          4 :   std::string funcl=&quot;file.free&quot;; //typical name given by sum_hills</span></a>
+<a name="243"><span class="lineNum">     243 </span>            : </a>
+<a name="244"><span class="lineNum">     244 </span>            :   std::vector&lt;std::string&gt; fes_names;</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">          8 :   for(unsigned n=0;; n++)//NB: here we start from FILE_F0 not from FILE_F1</span></a>
+<a name="246"><span class="lineNum">     246 </span>            :   {</a>
+<a name="247"><span class="lineNum">     247 </span>            :     std::string filename;</a>
+<a name="248"><span class="lineNum">     248 </span><span class="lineCov">         24 :     if(!parseNumbered(&quot;FILE_F&quot;,n,filename))</span></a>
+<a name="249"><span class="lineNum">     249 </span>            :       break;</a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">          8 :     fes_names.push_back(filename);</span></a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">          8 :     IFile gridfile;</span></a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">          8 :     gridfile.open(filename);</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">          8 :     auto g=GridBase::create(funcl,getArguments(),gridfile,sparsegrid,spline,true);</span></a>
+<a name="254"><span class="lineNum">     254 </span>            : // we assume this cannot be sparse. in case we want it to be sparse, some of the methods</a>
+<a name="255"><span class="lineNum">     255 </span>            : // that are available only in Grid should be ported to GridBase</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">          8 :     auto gg=dynamic_cast&lt;Grid*&gt;(g.get());</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : // if this throws, g is deleted</a>
+<a name="258"><span class="lineNum">     258 </span><span class="lineCov">          8 :     plumed_assert(gg);</span></a>
+<a name="259"><span class="lineNum">     259 </span>            : // release ownership in order to transfer it to emplaced pointer</a>
+<a name="260"><span class="lineNum">     260 </span>            :     g.release();</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">          8 :     grid_p_.emplace_back(gg);</span></a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">         16 :   }</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">          4 :   plumed_massert(grid_p_.size()&gt;1,&quot;at least 2 basins must be defined, starting from FILE_F0&quot;);</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">          4 :   alpha_size_=grid_p_.size()-1;</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">          4 :   sym_alpha_size_=alpha_size_*(alpha_size_+1)/2; //useful for symmetric matrix [alpha_size_]x[alpha_size_]</span></a>
+<a name="266"><span class="lineNum">     266 </span>            :   //check for consistency with first local free energy</a>
+<a name="267"><span class="lineNum">     267 </span><span class="lineCov">          8 :   for(unsigned n=1; n&lt;grid_p_.size(); n++)</span></a>
+<a name="268"><span class="lineNum">     268 </span>            :   {</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          8 :     std::string error_tag=&quot;FILE_F&quot;+std::to_string(n)+&quot; '&quot;+fes_names[n]+&quot;' not compatible with reference one, FILE_F0&quot;;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          4 :     plumed_massert(grid_p_[n]-&gt;getSize()==grid_p_[0]-&gt;getSize(),error_tag);</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          4 :     plumed_massert(grid_p_[n]-&gt;getMin()==grid_p_[0]-&gt;getMin(),error_tag);</span></a>
+<a name="272"><span class="lineNum">     272 </span><span class="lineCov">          4 :     plumed_massert(grid_p_[n]-&gt;getMax()==grid_p_[0]-&gt;getMax(),error_tag);</span></a>
+<a name="273"><span class="lineNum">     273 </span><span class="lineCov">          4 :     plumed_massert(grid_p_[n]-&gt;getBinVolume()==grid_p_[0]-&gt;getBinVolume(),error_tag);</span></a>
+<a name="274"><span class="lineNum">     274 </span>            :   }</a>
+<a name="275"><span class="lineNum">     275 </span>            : </a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">          4 :   bool no_mintozero=false;</span></a>
+<a name="277"><span class="lineNum">     277 </span><span class="lineCov">          4 :   parseFlag(&quot;NO_MINTOZERO&quot;,no_mintozero);</span></a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">          4 :   if(!no_mintozero)</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   {</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">          6 :     for(unsigned n=0; n&lt;grid_p_.size(); n++)</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">          4 :       grid_p_[n]-&gt;setMinToZero();</span></a>
+<a name="282"><span class="lineNum">     282 </span>            :   }</a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">          4 :   bool normalize=false;</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">          4 :   parseFlag(&quot;NORMALIZE&quot;,normalize);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">          4 :   norm_.resize(grid_p_.size(),0);</span></a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineCov">          4 :   std::vector&lt;double&gt; c_norm(grid_p_.size());</span></a>
+<a name="287"><span class="lineNum">     287 </span>            :   //convert the FESs to probability distributions</a>
+<a name="288"><span class="lineNum">     288 </span>            :   //NB: the spline interpolation will be done on the probability distributions, not on the given FESs</a>
+<a name="289"><span class="lineNum">     289 </span>            :   const unsigned ncv=getNumberOfArguments(); //just for ease</a>
+<a name="290"><span class="lineNum">     290 </span><span class="lineCov">         12 :   for(unsigned n=0; n&lt;grid_p_.size(); n++)</span></a>
+<a name="291"><span class="lineNum">     291 </span>            :   {</a>
+<a name="292"><span class="lineNum">     292 </span><span class="lineCov">        808 :     for(Grid::index_t t=0; t&lt;grid_p_[n]-&gt;getSize(); t++)</span></a>
+<a name="293"><span class="lineNum">     293 </span>            :     {</a>
+<a name="294"><span class="lineNum">     294 </span><span class="lineCov">        800 :       std::vector&lt;double&gt; der(ncv);</span></a>
+<a name="295"><span class="lineNum">     295 </span><span class="lineCov">        800 :       const double val=std::exp(-beta_*grid_p_[n]-&gt;getValueAndDerivatives(t,der));</span></a>
+<a name="296"><span class="lineNum">     296 </span><span class="lineCov">       1600 :       for(unsigned s=0; s&lt;ncv; s++)</span></a>
+<a name="297"><span class="lineNum">     297 </span><span class="lineCov">        800 :         der[s]*=-beta_*val;</span></a>
+<a name="298"><span class="lineNum">     298 </span><span class="lineCov">        800 :       grid_p_[n]-&gt;setValueAndDerivatives(t,val,der);</span></a>
+<a name="299"><span class="lineNum">     299 </span><span class="lineCov">        800 :       norm_[n]+=val;</span></a>
+<a name="300"><span class="lineNum">     300 </span>            :     }</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          8 :     c_norm[n]=1./beta_*std::log(norm_[n]);</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          8 :     if(normalize)</span></a>
+<a name="303"><span class="lineNum">     303 </span>            :     {</a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          4 :       grid_p_[n]-&gt;scaleAllValuesAndDerivatives(1./norm_[n]);</span></a>
+<a name="305"><span class="lineNum">     305 </span><span class="lineCov">          4 :       norm_[n]=1;</span></a>
+<a name="306"><span class="lineNum">     306 </span>            :     }</a>
+<a name="307"><span class="lineNum">     307 </span>            :   }</a>
+<a name="308"><span class="lineNum">     308 </span>            : </a>
+<a name="309"><span class="lineNum">     309 </span>            : //get target</a>
+<a name="310"><span class="lineNum">     310 </span><span class="lineCov">          4 :   double biasfactor=0;</span></a>
+<a name="311"><span class="lineNum">     311 </span><span class="lineCov">          4 :   parse(&quot;BIASFACTOR&quot;,biasfactor);</span></a>
+<a name="312"><span class="lineNum">     312 </span><span class="lineCov">          4 :   plumed_massert(biasfactor==0 || biasfactor&gt;1,&quot;BIASFACTOR must be zero (for uniform target) or greater than one&quot;);</span></a>
+<a name="313"><span class="lineNum">     313 </span><span class="lineCov">          4 :   if(biasfactor==0)</span></a>
+<a name="314"><span class="lineNum">     314 </span><span class="lineCov">          2 :     inv_gamma_=0;</span></a>
+<a name="315"><span class="lineNum">     315 </span>            :   else</a>
+<a name="316"><span class="lineNum">     316 </span><span class="lineCov">          2 :     inv_gamma_=1./biasfactor;</span></a>
+<a name="317"><span class="lineNum">     317 </span><span class="lineCov">          4 :   tg_counter_=0;</span></a>
+<a name="318"><span class="lineNum">     318 </span><span class="lineCov">          4 :   tg_stride_=1;</span></a>
+<a name="319"><span class="lineNum">     319 </span><span class="lineCov">          4 :   parse(&quot;TG_STRIDE&quot;,tg_stride_);</span></a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">          4 :   tg_dV_dAlpha_.resize(alpha_size_,0);</span></a>
+<a name="321"><span class="lineNum">     321 </span><span class="lineCov">          4 :   tg_d2V_dAlpha2_.resize(sym_alpha_size_,0);</span></a>
+<a name="322"><span class="lineNum">     322 </span>            : </a>
+<a name="323"><span class="lineNum">     323 </span>            : //setup optimization stuff</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">          4 :   minimization_step_=1;</span></a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">          4 :   parse(&quot;M_STEP&quot;,minimization_step_);</span></a>
+<a name="326"><span class="lineNum">     326 </span>            : </a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">          4 :   av_stride_=500;</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">          4 :   parse(&quot;AV_STRIDE&quot;,av_stride_);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">          4 :   av_dV_dAlpha_.resize(alpha_size_,0);</span></a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">          4 :   av_dV_dAlpha_prod_.resize(sym_alpha_size_,0);</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">          4 :   av_d2V_dAlpha2_.resize(sym_alpha_size_,0);</span></a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">          4 :   mean_weight_tau_=0;</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">          4 :   parse(&quot;TAU_MEAN&quot;,mean_weight_tau_);</span></a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">          4 :   if(mean_weight_tau_!=1) //set it to 1 for basic SGD</span></a>
+<a name="336"><span class="lineNum">     336 </span>            :   {</a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          4 :     plumed_massert((mean_weight_tau_==0 || mean_weight_tau_&gt;av_stride_),&quot;TAU_MEAN is rescaled with AV_STRIDE, so it has to be greater&quot;);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          4 :     mean_weight_tau_/=av_stride_; //this way you can look at the number of simulation steps to choose TAU_MEAN</span></a>
+<a name="339"><span class="lineNum">     339 </span>            :   }</a>
+<a name="340"><span class="lineNum">     340 </span>            : </a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">          8 :   parseVector(&quot;INITIAL_ALPHA&quot;,mean_alpha_);</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">          4 :   if(mean_alpha_.size()&gt;0)</span></a>
+<a name="343"><span class="lineNum">     343 </span>            :   {</a>
+<a name="344"><span class="lineNum">     344 </span><span class="lineCov">          2 :     plumed_massert(mean_alpha_.size()==alpha_size_,&quot;provide one INITIAL_ALPHA for each basin beyond the first one&quot;);</span></a>
+<a name="345"><span class="lineNum">     345 </span>            :   }</a>
+<a name="346"><span class="lineNum">     346 </span>            :   else</a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">          2 :     mean_alpha_.resize(alpha_size_,0);</span></a>
+<a name="348"><span class="lineNum">     348 </span><span class="lineCov">          4 :   inst_alpha_=mean_alpha_;</span></a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">          4 :   exp_alpha_.resize(alpha_size_);</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">          4 :     exp_alpha_[i]=std::exp(-beta_*mean_alpha_[i]);</span></a>
+<a name="352"><span class="lineNum">     352 </span><span class="lineCov">          4 :   prev_exp_alpha_=exp_alpha_;</span></a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">          4 :   damping_off_=false;</span></a>
+<a name="355"><span class="lineNum">     355 </span><span class="lineCov">          4 :   parseFlag(&quot;DAMPING_OFF&quot;,damping_off_);</span></a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">          4 :   if(damping_off_)</span></a>
+<a name="357"><span class="lineNum">     357 </span><span class="lineCov">          2 :     past_increment2_.resize(alpha_size_,1);</span></a>
+<a name="358"><span class="lineNum">     358 </span>            :   else</a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">          2 :     past_increment2_.resize(alpha_size_,0);</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            : //file printing options</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">          4 :   std::string alphaFileName(&quot;ALPHA&quot;);</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          4 :   parse(&quot;ALPHA_FILE&quot;,alphaFileName);</span></a>
+<a name="364"><span class="lineNum">     364 </span><span class="lineCov">          4 :   print_stride_=10;</span></a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">          8 :   parse(&quot;PRINT_STRIDE&quot;,print_stride_);</span></a>
+<a name="366"><span class="lineNum">     366 </span>            :   std::string fmt;</a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">          4 :   parse(&quot;FMT&quot;,fmt);</span></a>
+<a name="368"><span class="lineNum">     368 </span>            : </a>
+<a name="369"><span class="lineNum">     369 </span>            : //other flags, mainly for debugging</a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">          4 :   NumParallel_=comm.Get_size();</span></a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">          4 :   rank_=comm.Get_rank();</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">          4 :   bool serial=false;</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          4 :   parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          4 :   if(serial)</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :   {</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          2 :     log.printf(&quot; -- SERIAL: running without loop parallelization\n&quot;);</span></a>
+<a name="377"><span class="lineNum">     377 </span><span class="lineCov">          2 :     NumParallel_=1;</span></a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineCov">          2 :     rank_=0;</span></a>
+<a name="379"><span class="lineNum">     379 </span>            :   }</a>
+<a name="380"><span class="lineNum">     380 </span>            : </a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">          4 :   bool multiple_walkers=false;</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">          4 :   parseFlag(&quot;MULTIPLE_WALKERS&quot;,multiple_walkers);</span></a>
+<a name="383"><span class="lineNum">     383 </span><span class="lineCov">          4 :   if(!multiple_walkers)</span></a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineCov">          2 :     NumWalkers_=1;</span></a>
+<a name="385"><span class="lineNum">     385 </span>            :   else</a>
+<a name="386"><span class="lineNum">     386 </span>            :   {</a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">          2 :     if(comm.Get_rank()==0)//multi_sim_comm works well on first rank only</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">          2 :       NumWalkers_=multi_sim_comm.Get_size();</span></a>
+<a name="389"><span class="lineNum">     389 </span><span class="lineCov">          2 :     if(comm.Get_size()&gt;1) //if each walker has more than one processor update them all</span></a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :       comm.Bcast(NumWalkers_,0);</span></a>
+<a name="391"><span class="lineNum">     391 </span>            :   }</a>
+<a name="392"><span class="lineNum">     392 </span>            : </a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">          4 :   checkRead();</span></a>
+<a name="394"><span class="lineNum">     394 </span>            : </a>
+<a name="395"><span class="lineNum">     395 </span>            : //restart if needed</a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          4 :   if(getRestart())</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   {</a>
+<a name="398"><span class="lineNum">     398 </span><span class="lineCov">          2 :     IFile ifile;</span></a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">          2 :     ifile.link(*this);</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          2 :     if(NumWalkers_&gt;1)</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          4 :       ifile.enforceSuffix(&quot;&quot;);</span></a>
+<a name="402"><span class="lineNum">     402 </span><span class="lineCov">          2 :     if(ifile.FileExist(alphaFileName))</span></a>
+<a name="403"><span class="lineNum">     403 </span>            :     {</a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">          2 :       log.printf(&quot;  Restarting from: %s\n&quot;,alphaFileName.c_str());</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">          2 :       log.printf(&quot;    all options (also PRINT_STRIDE) must be consistent!\n&quot;);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">          2 :       log.printf(&quot;    any INITIAL_ALPHA will be overwritten\n&quot;);</span></a>
+<a name="407"><span class="lineNum">     407 </span><span class="lineCov">          2 :       ifile.open(alphaFileName);</span></a>
+<a name="408"><span class="lineNum">     408 </span>            :       double time;</a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">          2 :       std::vector&lt;double&gt; damping(alpha_size_);</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">         20 :       while(ifile.scanField(&quot;time&quot;,time)) //room for improvements: only last line is important</span></a>
+<a name="411"><span class="lineNum">     411 </span>            :       {</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">         16 :         for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="413"><span class="lineNum">     413 </span>            :         {</a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          8 :           const std::string index(std::to_string(i+1));</span></a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">          8 :           prev_exp_alpha_[i]=std::exp(-beta_*mean_alpha_[i]);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">         16 :           ifile.scanField(&quot;alpha_&quot;+index,mean_alpha_[i]);</span></a>
+<a name="417"><span class="lineNum">     417 </span><span class="lineCov">         16 :           ifile.scanField(&quot;auxiliary_&quot;+index,inst_alpha_[i]);</span></a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">         16 :           ifile.scanField(&quot;damping_&quot;+index,damping[i]);</span></a>
+<a name="419"><span class="lineNum">     419 </span>            :         }</a>
+<a name="420"><span class="lineNum">     420 </span><span class="lineCov">          8 :         ifile.scanField();</span></a>
+<a name="421"><span class="lineNum">     421 </span><span class="lineCov">          8 :         mean_counter_+=print_stride_;</span></a>
+<a name="422"><span class="lineNum">     422 </span>            :       }</a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">          4 :       for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="424"><span class="lineNum">     424 </span>            :       {</a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">          2 :         exp_alpha_[i]=std::exp(-beta_*mean_alpha_[i]);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">          2 :         past_increment2_[i]=damping[i]*damping[i];</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :       }</a>
+<a name="428"><span class="lineNum">     428 </span>            :       //sync all walkers and treads. Not sure is mandatory but is no harm</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">          2 :       comm.Barrier();</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">          2 :       if(comm.Get_rank()==0)</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">          2 :         multi_sim_comm.Barrier();</span></a>
+<a name="432"><span class="lineNum">     432 </span>            :     }</a>
+<a name="433"><span class="lineNum">     433 </span>            :     else</a>
+<a name="434"><span class="lineNum">     434 </span><span class="lineNoCov">          0 :       log.printf(&quot;  -- WARNING: restart requested, but no '%s' file found!\n&quot;,alphaFileName.c_str());</span></a>
+<a name="435"><span class="lineNum">     435 </span><span class="lineCov">          2 :   }</span></a>
+<a name="436"><span class="lineNum">     436 </span>            : </a>
+<a name="437"><span class="lineNum">     437 </span>            : //setup output file with Alpha values</a>
+<a name="438"><span class="lineNum">     438 </span><span class="lineCov">          4 :   alphaOfile_.link(*this);</span></a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">          4 :   if(NumWalkers_&gt;1)</span></a>
+<a name="440"><span class="lineNum">     440 </span>            :   {</a>
+<a name="441"><span class="lineNum">     441 </span><span class="lineCov">          2 :     if(comm.Get_rank()==0 &amp;&amp; multi_sim_comm.Get_rank()&gt;0)</span></a>
+<a name="442"><span class="lineNum">     442 </span>            :       alphaFileName=&quot;/dev/null&quot;; //only first walker writes on file</a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">          4 :     alphaOfile_.enforceSuffix(&quot;&quot;);</span></a>
+<a name="444"><span class="lineNum">     444 </span>            :   }</a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineCov">          4 :   alphaOfile_.open(alphaFileName);</span></a>
+<a name="446"><span class="lineNum">     446 </span><span class="lineCov">          4 :   if(fmt.length()&gt;0)</span></a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">          8 :     alphaOfile_.fmtField(&quot; &quot;+fmt);</span></a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            : //add other output components</a>
+<a name="450"><span class="lineNum">     450 </span><span class="lineCov">          8 :   addComponent(&quot;rct&quot;); componentIsNotPeriodic(&quot;rct&quot;);</span></a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">          8 :   addComponent(&quot;work&quot;); componentIsNotPeriodic(&quot;work&quot;);</span></a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            : //print some info</a>
+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          4 :   log.printf(&quot;  Temperature T: %g\n&quot;,1./(Kb*beta_));</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          4 :   log.printf(&quot;  Beta (1/Kb*T): %g\n&quot;,beta_);</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          4 :   log.printf(&quot;  Local free energy basins files and normalization constants:\n&quot;);</span></a>
+<a name="457"><span class="lineNum">     457 </span><span class="lineCov">         12 :   for(unsigned n=0; n&lt;grid_p_.size(); n++)</span></a>
+<a name="458"><span class="lineNum">     458 </span><span class="lineCov">          8 :     log.printf(&quot;    F_%d filename: %s  c_%d=%g\n&quot;,n,fes_names[n].c_str(),n,c_norm[n]);</span></a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">          4 :   if(no_mintozero)</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">          2 :     log.printf(&quot; -- NO_MINTOZERO: local free energies are not shifted to be zero at minimum\n&quot;);</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">          4 :   if(normalize)</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">          2 :     log.printf(&quot; -- NORMALIZE: F_n+=c_n, alpha=DeltaF\n&quot;);</span></a>
+<a name="463"><span class="lineNum">     463 </span><span class="lineCov">          4 :   log.printf(&quot;  Using target distribution with 1/gamma = %g\n&quot;,inv_gamma_);</span></a>
+<a name="464"><span class="lineNum">     464 </span><span class="lineCov">          4 :   log.printf(&quot;    and updated with stride %d\n&quot;,tg_stride_);</span></a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          4 :   log.printf(&quot;  Step for the minimization algorithm: %g\n&quot;,minimization_step_);</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">          4 :   log.printf(&quot;  Stride for the ensemble average: %d\n&quot;,av_stride_);</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          4 :   if(mean_weight_tau_&gt;1)</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          2 :     log.printf(&quot;  Exponentially decaying average with weight=tau/av_stride=%d\n&quot;,mean_weight_tau_);</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          4 :   if(mean_weight_tau_==1)</span></a>
+<a name="470"><span class="lineNum">     470 </span><span class="lineNoCov">          0 :     log.printf(&quot; +++ WARNING +++ setting TAU_MEAN=1 is equivalent to use simple SGD, without mean alpha nor hessian contribution\n&quot;);</span></a>
+<a name="471"><span class="lineNum">     471 </span><span class="lineCov">          4 :   log.printf(&quot;  Initial guess for alpha:\n&quot;);</span></a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">          8 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">          4 :     log.printf(&quot;    alpha_%d = %g\n&quot;,i+1,mean_alpha_[i]);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">          4 :   if(damping_off_)</span></a>
+<a name="475"><span class="lineNum">     475 </span><span class="lineCov">          2 :     log.printf(&quot; -- DAMPING_OFF: the minimization step will NOT become smaller as the simulation goes on\n&quot;);</span></a>
+<a name="476"><span class="lineNum">     476 </span><span class="lineCov">          4 :   log.printf(&quot;  Printing on file %s with stride %d\n&quot;,alphaFileName.c_str(),print_stride_);</span></a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">          4 :   if(serial)</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">          2 :     log.printf(&quot; -- SERIAL: running without loop parallelization\n&quot;);</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">          4 :   if(NumParallel_&gt;1)</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">          2 :     log.printf(&quot;  Using multiple threads per simulation: %d\n&quot;,NumParallel_);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">          4 :   if(multiple_walkers)</span></a>
+<a name="482"><span class="lineNum">     482 </span>            :   {</a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">          2 :     log.printf(&quot; -- MULTIPLE_WALKERS: multiple simulations will combine statistics for the optimization\n&quot;);</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          2 :     if(NumWalkers_&gt;1)</span></a>
+<a name="485"><span class="lineNum">     485 </span>            :     {</a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">          2 :       log.printf(&quot;    number of walkers: %d\n&quot;,NumWalkers_);</span></a>
+<a name="487"><span class="lineNum">     487 </span><span class="lineCov">          2 :       log.printf(&quot;    walker rank: %d\n&quot;,multi_sim_comm.Get_rank()); //only comm.Get_rank()=0 prints, so this is fine</span></a>
+<a name="488"><span class="lineNum">     488 </span>            :     }</a>
+<a name="489"><span class="lineNum">     489 </span>            :     else</a>
+<a name="490"><span class="lineNum">     490 </span><span class="lineNoCov">          0 :       log.printf(&quot; +++ WARNING +++ only one replica found: are you sure you are running MPI-connected simulations?\n&quot;);</span></a>
+<a name="491"><span class="lineNum">     491 </span>            :   }</a>
+<a name="492"><span class="lineNum">     492 </span><span class="lineCov">          4 :   log.printf(&quot; Bibliography &quot;);</span></a>
+<a name="493"><span class="lineNum">     493 </span><span class="lineCov">          8 :   log&lt;&lt;plumed.cite(&quot;Invernizzi and Parrinello, J. Chem. Theory Comput. 15, 2187-2194 (2019)&quot;);</span></a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">          8 :   log&lt;&lt;plumed.cite(&quot;Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)&quot;);</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">          4 :   if(inv_gamma_&gt;0)</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          4 :     log&lt;&lt;plumed.cite(&quot;Valsson and Parrinello, J. Chem. Theory Comput. 11, 1996-2002 (2015)&quot;);</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span>            : //last initializations</a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">          4 :   prob_.resize(grid_p_.size());</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">          4 :   der_prob_.resize(grid_p_.size(),std::vector&lt;double&gt;(getNumberOfArguments()));</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">          4 :   update_tg_and_rct();</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">          8 : }</span></a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">        804 : void VesDeltaF::calculate()</span></a>
+<a name="505"><span class="lineNum">     505 </span>            : {</a>
+<a name="506"><span class="lineNum">     506 </span>            : //get CVs</a>
+<a name="507"><span class="lineNum">     507 </span><span class="lineCov">        804 :   const unsigned ncv=getNumberOfArguments(); //just for ease</span></a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">        804 :   std::vector&lt;double&gt; cv(ncv);</span></a>
+<a name="509"><span class="lineNum">     509 </span><span class="lineCov">       1608 :   for(unsigned s=0; s&lt;ncv; s++)</span></a>
+<a name="510"><span class="lineNum">     510 </span><span class="lineCov">        804 :     cv[s]=getArgument(s);</span></a>
+<a name="511"><span class="lineNum">     511 </span>            : //get probabilities for each basin, and total one</a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">       2412 :   for(unsigned n=0; n&lt;grid_p_.size(); n++)</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">       1608 :     prob_[n]=grid_p_[n]-&gt;getValueAndDerivatives(cv,der_prob_[n]);</span></a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">        804 :   tot_prob_=prob_[0];</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">       1608 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">        804 :     tot_prob_+=prob_[i+1]*exp_alpha_[i];</span></a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            : //update bias and forces: V=-(1-inv_gamma_)*fes</a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">        804 :   setBias((1-inv_gamma_)/beta_*std::log(tot_prob_));</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">       1608 :   for(unsigned s=0; s&lt;ncv; s++)</span></a>
+<a name="521"><span class="lineNum">     521 </span>            :   {</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">        804 :     double dProb_dCV_s=der_prob_[0][s];</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">       1608 :     for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">        804 :       dProb_dCV_s+=der_prob_[i+1][s]*exp_alpha_[i];</span></a>
+<a name="525"><span class="lineNum">     525 </span><span class="lineCov">        804 :     setOutputForce(s,-(1-inv_gamma_)/beta_/tot_prob_*dProb_dCV_s);</span></a>
+<a name="526"><span class="lineNum">     526 </span>            :   }</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">        804 :   afterCalculate_=true;</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">        804 : }</span></a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">        804 : void VesDeltaF::update()</span></a>
+<a name="531"><span class="lineNum">     531 </span>            : {</a>
+<a name="532"><span class="lineNum">     532 </span>            : //skip first step to sync getTime() and av_counter_, as in METAD</a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        804 :   if(isFirstStep_)</span></a>
+<a name="534"><span class="lineNum">     534 </span>            :   {</a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">          4 :     isFirstStep_=false;</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">          4 :     return;</span></a>
+<a name="537"><span class="lineNum">     537 </span>            :   }</a>
+<a name="538"><span class="lineNum">     538 </span><span class="lineCov">        800 :   plumed_massert(afterCalculate_,&quot;VesDeltaF::update() must be called after VesDeltaF::calculate() to work properly&quot;);</span></a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">        800 :   afterCalculate_=false;</span></a>
+<a name="540"><span class="lineNum">     540 </span>            : </a>
+<a name="541"><span class="lineNum">     541 </span>            : //calculate derivatives for ensemble averages</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">        800 :   std::vector&lt;double&gt; dV_dAlpha(alpha_size_);</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">        800 :   std::vector&lt;double&gt; d2V_dAlpha2(sym_alpha_size_);</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">       1600 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">        800 :     dV_dAlpha[i]=-(1-inv_gamma_)/tot_prob_*prob_[i+1]*exp_alpha_[i];</span></a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">       1600 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="547"><span class="lineNum">     547 </span>            :   {</a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">        800 :     d2V_dAlpha2[get_index(i,i)]=-beta_*dV_dAlpha[i];</span></a>
+<a name="549"><span class="lineNum">     549 </span><span class="lineCov">       1600 :     for(unsigned j=i; j&lt;alpha_size_; j++)</span></a>
+<a name="550"><span class="lineNum">     550 </span><span class="lineCov">        800 :       d2V_dAlpha2[get_index(i,j)]-=beta_/(1-inv_gamma_)*dV_dAlpha[i]*dV_dAlpha[j];</span></a>
+<a name="551"><span class="lineNum">     551 </span>            :   }</a>
+<a name="552"><span class="lineNum">     552 </span>            : //update ensemble averages</a>
+<a name="553"><span class="lineNum">     553 </span><span class="lineCov">        800 :   av_counter_++;</span></a>
+<a name="554"><span class="lineNum">     554 </span><span class="lineCov">       1600 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="555"><span class="lineNum">     555 </span>            :   {</a>
+<a name="556"><span class="lineNum">     556 </span><span class="lineCov">        800 :     av_dV_dAlpha_[i]+=(dV_dAlpha[i]-av_dV_dAlpha_[i])/av_counter_;</span></a>
+<a name="557"><span class="lineNum">     557 </span><span class="lineCov">       1600 :     for(unsigned j=i; j&lt;alpha_size_; j++)</span></a>
+<a name="558"><span class="lineNum">     558 </span>            :     {</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">        800 :       const unsigned ij=get_index(i,j);</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">        800 :       av_dV_dAlpha_prod_[ij]+=(dV_dAlpha[i]*dV_dAlpha[j]-av_dV_dAlpha_prod_[ij])/av_counter_;</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">        800 :       av_d2V_dAlpha2_[ij]+=(d2V_dAlpha2[ij]-av_d2V_dAlpha2_[ij])/av_counter_;</span></a>
+<a name="562"><span class="lineNum">     562 </span>            :     }</a>
+<a name="563"><span class="lineNum">     563 </span>            :   }</a>
+<a name="564"><span class="lineNum">     564 </span>            : //update work</a>
+<a name="565"><span class="lineNum">     565 </span><span class="lineCov">        800 :   double prev_tot_prob=prob_[0];</span></a>
+<a name="566"><span class="lineNum">     566 </span><span class="lineCov">       1600 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="567"><span class="lineNum">     567 </span><span class="lineCov">        800 :     prev_tot_prob+=prob_[i+1]*prev_exp_alpha_[i];</span></a>
+<a name="568"><span class="lineNum">     568 </span><span class="lineCov">        800 :   work_+=(1-inv_gamma_)/beta_*std::log(tot_prob_/prev_tot_prob);</span></a>
+<a name="569"><span class="lineNum">     569 </span>            : </a>
+<a name="570"><span class="lineNum">     570 </span>            : //update coefficients</a>
+<a name="571"><span class="lineNum">     571 </span><span class="lineCov">        800 :   if(av_counter_==av_stride_)</span></a>
+<a name="572"><span class="lineNum">     572 </span>            :   {</a>
+<a name="573"><span class="lineNum">     573 </span><span class="lineCov">         16 :     update_alpha();</span></a>
+<a name="574"><span class="lineNum">     574 </span><span class="lineCov">         16 :     tg_counter_++;</span></a>
+<a name="575"><span class="lineNum">     575 </span><span class="lineCov">         16 :     if(tg_counter_==tg_stride_)</span></a>
+<a name="576"><span class="lineNum">     576 </span>            :     {</a>
+<a name="577"><span class="lineNum">     577 </span><span class="lineCov">         12 :       update_tg_and_rct();</span></a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">         12 :       tg_counter_=0;</span></a>
+<a name="579"><span class="lineNum">     579 </span>            :     }</a>
+<a name="580"><span class="lineNum">     580 </span>            :     //reset the ensemble averages</a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">         16 :     av_counter_=0;</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :     std::fill(av_dV_dAlpha_.begin(),av_dV_dAlpha_.end(),0);</a>
+<a name="583"><span class="lineNum">     583 </span>            :     std::fill(av_dV_dAlpha_prod_.begin(),av_dV_dAlpha_prod_.end(),0);</a>
+<a name="584"><span class="lineNum">     584 </span>            :     std::fill(av_d2V_dAlpha2_.begin(),av_d2V_dAlpha2_.end(),0);</a>
+<a name="585"><span class="lineNum">     585 </span>            :   }</a>
+<a name="586"><span class="lineNum">     586 </span>            : }</a>
+<a name="587"><span class="lineNum">     587 </span>            : </a>
+<a name="588"><span class="lineNum">     588 </span><span class="lineCov">         16 : void VesDeltaF::update_tg_and_rct()</span></a>
+<a name="589"><span class="lineNum">     589 </span>            : {</a>
+<a name="590"><span class="lineNum">     590 </span>            : //calculate target averages</a>
+<a name="591"><span class="lineNum">     591 </span><span class="lineCov">         16 :   double Z_0=norm_[0];</span></a>
+<a name="592"><span class="lineNum">     592 </span><span class="lineCov">         32 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="593"><span class="lineNum">     593 </span><span class="lineCov">         16 :     Z_0+=norm_[i+1]*exp_alpha_[i];</span></a>
+<a name="594"><span class="lineNum">     594 </span><span class="lineCov">         16 :   double Z_tg=0;</span></a>
+<a name="595"><span class="lineNum">     595 </span>            :   std::fill(tg_dV_dAlpha_.begin(),tg_dV_dAlpha_.end(),0);</a>
+<a name="596"><span class="lineNum">     596 </span>            :   std::fill(tg_d2V_dAlpha2_.begin(),tg_d2V_dAlpha2_.end(),0);</a>
+<a name="597"><span class="lineNum">     597 </span><span class="lineCov">       1116 :   for(Grid::index_t t=rank_; t&lt;grid_p_[0]-&gt;getSize(); t+=NumParallel_)</span></a>
+<a name="598"><span class="lineNum">     598 </span>            :   { //TODO can we recycle some code?</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">       1100 :     std::vector&lt;double&gt; prob(grid_p_.size());</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">       3300 :     for(unsigned n=0; n&lt;grid_p_.size(); n++)</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">       2200 :       prob[n]=grid_p_[n]-&gt;getValue(t);</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">       1100 :     double tot_prob=prob[0];</span></a>
+<a name="603"><span class="lineNum">     603 </span><span class="lineCov">       2200 :     for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="604"><span class="lineNum">     604 </span><span class="lineCov">       1100 :       tot_prob+=prob[i+1]*exp_alpha_[i];</span></a>
+<a name="605"><span class="lineNum">     605 </span><span class="lineCov">       1100 :     std::vector&lt;double&gt; dV_dAlpha(alpha_size_);</span></a>
+<a name="606"><span class="lineNum">     606 </span><span class="lineCov">       1100 :     std::vector&lt;double&gt; d2V_dAlpha2(sym_alpha_size_);</span></a>
+<a name="607"><span class="lineNum">     607 </span><span class="lineCov">       2200 :     for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="608"><span class="lineNum">     608 </span><span class="lineCov">       1100 :       dV_dAlpha[i]=-(1-inv_gamma_)/tot_prob*prob[i+1]*exp_alpha_[i];</span></a>
+<a name="609"><span class="lineNum">     609 </span><span class="lineCov">       2200 :     for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="610"><span class="lineNum">     610 </span>            :     {</a>
+<a name="611"><span class="lineNum">     611 </span><span class="lineCov">       1100 :       d2V_dAlpha2[get_index(i,i)]=-beta_*dV_dAlpha[i];</span></a>
+<a name="612"><span class="lineNum">     612 </span><span class="lineCov">       2200 :       for(unsigned j=i; j&lt;alpha_size_; j++)</span></a>
+<a name="613"><span class="lineNum">     613 </span><span class="lineCov">       1100 :         d2V_dAlpha2[get_index(i,j)]-=beta_/(1-inv_gamma_)*dV_dAlpha[i]*dV_dAlpha[j];</span></a>
+<a name="614"><span class="lineNum">     614 </span>            :     }</a>
+<a name="615"><span class="lineNum">     615 </span><span class="lineCov">       1100 :     const double unnorm_tg_p=std::pow(tot_prob,inv_gamma_);</span></a>
+<a name="616"><span class="lineNum">     616 </span><span class="lineCov">       1100 :     Z_tg+=unnorm_tg_p;</span></a>
+<a name="617"><span class="lineNum">     617 </span><span class="lineCov">       2200 :     for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="618"><span class="lineNum">     618 </span><span class="lineCov">       1100 :       tg_dV_dAlpha_[i]+=unnorm_tg_p*dV_dAlpha[i];</span></a>
+<a name="619"><span class="lineNum">     619 </span><span class="lineCov">       2200 :     for(unsigned ij=0; ij&lt;sym_alpha_size_; ij++)</span></a>
+<a name="620"><span class="lineNum">     620 </span><span class="lineCov">       1100 :       tg_d2V_dAlpha2_[ij]+=unnorm_tg_p*d2V_dAlpha2[ij];</span></a>
+<a name="621"><span class="lineNum">     621 </span>            :   }</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">         16 :   if(NumParallel_&gt;1)</span></a>
+<a name="623"><span class="lineNum">     623 </span>            :   {</a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">         10 :     comm.Sum(Z_tg);</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">         10 :     comm.Sum(tg_dV_dAlpha_);</span></a>
+<a name="626"><span class="lineNum">     626 </span><span class="lineCov">         10 :     comm.Sum(tg_d2V_dAlpha2_);</span></a>
+<a name="627"><span class="lineNum">     627 </span>            :   }</a>
+<a name="628"><span class="lineNum">     628 </span><span class="lineCov">         32 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="629"><span class="lineNum">     629 </span><span class="lineCov">         16 :     tg_dV_dAlpha_[i]/=Z_tg;</span></a>
+<a name="630"><span class="lineNum">     630 </span><span class="lineCov">         32 :   for(unsigned ij=0; ij&lt;sym_alpha_size_; ij++)</span></a>
+<a name="631"><span class="lineNum">     631 </span><span class="lineCov">         16 :     tg_d2V_dAlpha2_[ij]/=Z_tg;</span></a>
+<a name="632"><span class="lineNum">     632 </span><span class="lineCov">         16 :   getPntrToComponent(&quot;rct&quot;)-&gt;set(-1./beta_*std::log(Z_tg/Z_0)); //Z_tg is the best available estimate of Z_V</span></a>
+<a name="633"><span class="lineNum">     633 </span><span class="lineCov">         16 : }</span></a>
+<a name="634"><span class="lineNum">     634 </span>            : </a>
+<a name="635"><span class="lineNum">     635 </span><span class="lineCov">         16 : void VesDeltaF::update_alpha()</span></a>
+<a name="636"><span class="lineNum">     636 </span>            : {</a>
+<a name="637"><span class="lineNum">     637 </span>            : //combining the averages of multiple walkers</a>
+<a name="638"><span class="lineNum">     638 </span><span class="lineCov">         16 :   if(NumWalkers_&gt;1)</span></a>
+<a name="639"><span class="lineNum">     639 </span>            :   {</a>
+<a name="640"><span class="lineNum">     640 </span><span class="lineCov">          8 :     if(comm.Get_rank()==0) //sum only once: in the first rank of each walker</span></a>
+<a name="641"><span class="lineNum">     641 </span>            :     {</a>
+<a name="642"><span class="lineNum">     642 </span><span class="lineCov">          8 :       multi_sim_comm.Sum(av_dV_dAlpha_);</span></a>
+<a name="643"><span class="lineNum">     643 </span><span class="lineCov">          8 :       multi_sim_comm.Sum(av_dV_dAlpha_prod_);</span></a>
+<a name="644"><span class="lineNum">     644 </span><span class="lineCov">          8 :       multi_sim_comm.Sum(av_d2V_dAlpha2_);</span></a>
+<a name="645"><span class="lineNum">     645 </span><span class="lineCov">         16 :       for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="646"><span class="lineNum">     646 </span><span class="lineCov">          8 :         av_dV_dAlpha_[i]/=NumWalkers_;</span></a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">         16 :       for(unsigned ij=0; ij&lt;sym_alpha_size_; ij++)</span></a>
+<a name="648"><span class="lineNum">     648 </span>            :       {</a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          8 :         av_dV_dAlpha_prod_[ij]/=NumWalkers_;</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          8 :         av_d2V_dAlpha2_[ij]/=NumWalkers_;</span></a>
+<a name="651"><span class="lineNum">     651 </span>            :       }</a>
+<a name="652"><span class="lineNum">     652 </span>            :     }</a>
+<a name="653"><span class="lineNum">     653 </span><span class="lineCov">          8 :     if(comm.Get_size()&gt;1)//if there are more ranks for each walker, everybody has to know</span></a>
+<a name="654"><span class="lineNum">     654 </span>            :     {</a>
+<a name="655"><span class="lineNum">     655 </span><span class="lineNoCov">          0 :       comm.Bcast(av_dV_dAlpha_,0);</span></a>
+<a name="656"><span class="lineNum">     656 </span><span class="lineNoCov">          0 :       comm.Bcast(av_dV_dAlpha_prod_,0);</span></a>
+<a name="657"><span class="lineNum">     657 </span><span class="lineNoCov">          0 :       comm.Bcast(av_d2V_dAlpha2_,0);</span></a>
+<a name="658"><span class="lineNum">     658 </span>            :     }</a>
+<a name="659"><span class="lineNum">     659 </span>            :   }</a>
+<a name="660"><span class="lineNum">     660 </span>            :   //set work and reset it</a>
+<a name="661"><span class="lineNum">     661 </span><span class="lineCov">         16 :   getPntrToComponent(&quot;work&quot;)-&gt;set(work_);</span></a>
+<a name="662"><span class="lineNum">     662 </span><span class="lineCov">         16 :   work_=0;</span></a>
+<a name="663"><span class="lineNum">     663 </span>            : </a>
+<a name="664"><span class="lineNum">     664 </span>            : //build the gradient and the Hessian of the functional</a>
+<a name="665"><span class="lineNum">     665 </span><span class="lineCov">         16 :   std::vector&lt;double&gt; grad_omega(alpha_size_);</span></a>
+<a name="666"><span class="lineNum">     666 </span><span class="lineCov">         16 :   std::vector&lt;double&gt; hess_omega(sym_alpha_size_);</span></a>
+<a name="667"><span class="lineNum">     667 </span><span class="lineCov">         32 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="668"><span class="lineNum">     668 </span>            :   {</a>
+<a name="669"><span class="lineNum">     669 </span><span class="lineCov">         16 :     grad_omega[i]=tg_dV_dAlpha_[i]-av_dV_dAlpha_[i];</span></a>
+<a name="670"><span class="lineNum">     670 </span><span class="lineCov">         32 :     for(unsigned j=i; j&lt;alpha_size_; j++)</span></a>
+<a name="671"><span class="lineNum">     671 </span>            :     {</a>
+<a name="672"><span class="lineNum">     672 </span><span class="lineCov">         16 :       const unsigned ij=get_index(i,j);</span></a>
+<a name="673"><span class="lineNum">     673 </span><span class="lineCov">         16 :       hess_omega[ij]=beta_*(av_dV_dAlpha_prod_[ij]-av_dV_dAlpha_[i]*av_dV_dAlpha_[j])+tg_d2V_dAlpha2_[ij]-av_d2V_dAlpha2_[ij];</span></a>
+<a name="674"><span class="lineNum">     674 </span>            :     }</a>
+<a name="675"><span class="lineNum">     675 </span>            :   }</a>
+<a name="676"><span class="lineNum">     676 </span>            : //calculate the increment and update alpha</a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">         16 :   mean_counter_++;</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :   long long unsigned mean_weight=mean_counter_;</a>
+<a name="679"><span class="lineNum">     679 </span><span class="lineCov">         16 :   if(mean_weight_tau_&gt;0 &amp;&amp; mean_weight_tau_&lt;mean_counter_)</span></a>
+<a name="680"><span class="lineNum">     680 </span>            :     mean_weight=mean_weight_tau_;</a>
+<a name="681"><span class="lineNum">     681 </span><span class="lineCov">         16 :   std::vector&lt;double&gt; damping(alpha_size_);</span></a>
+<a name="682"><span class="lineNum">     682 </span><span class="lineCov">         32 :   for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="683"><span class="lineNum">     683 </span>            :   {</a>
+<a name="684"><span class="lineNum">     684 </span><span class="lineCov">         16 :     double increment_i=grad_omega[i];</span></a>
+<a name="685"><span class="lineNum">     685 </span><span class="lineCov">         32 :     for(unsigned j=0; j&lt;alpha_size_; j++)</span></a>
+<a name="686"><span class="lineNum">     686 </span><span class="lineCov">         16 :       increment_i+=hess_omega[get_index(i,j)]*(inst_alpha_[j]-mean_alpha_[j]);</span></a>
+<a name="687"><span class="lineNum">     687 </span><span class="lineCov">         16 :     if(!damping_off_)</span></a>
+<a name="688"><span class="lineNum">     688 </span><span class="lineCov">          8 :       past_increment2_[i]+=increment_i*increment_i;</span></a>
+<a name="689"><span class="lineNum">     689 </span><span class="lineCov">         16 :     damping[i]=std::sqrt(past_increment2_[i]);</span></a>
+<a name="690"><span class="lineNum">     690 </span><span class="lineCov">         16 :     prev_exp_alpha_[i]=std::exp(-beta_*mean_alpha_[i]);</span></a>
+<a name="691"><span class="lineNum">     691 </span><span class="lineCov">         16 :     inst_alpha_[i]-=minimization_step_/damping[i]*increment_i;</span></a>
+<a name="692"><span class="lineNum">     692 </span><span class="lineCov">         16 :     mean_alpha_[i]+=(inst_alpha_[i]-mean_alpha_[i])/mean_weight;</span></a>
+<a name="693"><span class="lineNum">     693 </span><span class="lineCov">         16 :     exp_alpha_[i]=std::exp(-beta_*mean_alpha_[i]);</span></a>
+<a name="694"><span class="lineNum">     694 </span>            :   }</a>
+<a name="695"><span class="lineNum">     695 </span>            : </a>
+<a name="696"><span class="lineNum">     696 </span>            : //update the Alpha file</a>
+<a name="697"><span class="lineNum">     697 </span><span class="lineCov">         16 :   if(mean_counter_%print_stride_==0)</span></a>
+<a name="698"><span class="lineNum">     698 </span>            :   {</a>
+<a name="699"><span class="lineNum">     699 </span><span class="lineCov">         16 :     alphaOfile_.printField(&quot;time&quot;,getTime());</span></a>
+<a name="700"><span class="lineNum">     700 </span><span class="lineCov">         32 :     for(unsigned i=0; i&lt;alpha_size_; i++)</span></a>
+<a name="701"><span class="lineNum">     701 </span>            :     {</a>
+<a name="702"><span class="lineNum">     702 </span><span class="lineCov">         16 :       const std::string index(std::to_string(i+1));</span></a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">         32 :       alphaOfile_.printField(&quot;alpha_&quot;+index,mean_alpha_[i]);</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">         32 :       alphaOfile_.printField(&quot;auxiliary_&quot;+index,inst_alpha_[i]);</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">         32 :       alphaOfile_.printField(&quot;damping_&quot;+index,damping[i]);</span></a>
+<a name="706"><span class="lineNum">     706 </span>            :     }</a>
+<a name="707"><span class="lineNum">     707 </span><span class="lineCov">         16 :     alphaOfile_.printField();</span></a>
+<a name="708"><span class="lineNum">     708 </span>            :   }</a>
+<a name="709"><span class="lineNum">     709 </span><span class="lineCov">         16 : }</span></a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            : //mapping of a [alpha_size_]x[alpha_size_] symmetric matrix into a vector of size sym_alpha_size_, useful for the communicator</a>
+<a name="712"><span class="lineNum">     712 </span><span class="lineCov">       4632 : inline unsigned VesDeltaF::get_index(const unsigned i, const unsigned j) const</span></a>
+<a name="713"><span class="lineNum">     713 </span>            : {</a>
+<a name="714"><span class="lineNum">     714 </span><span class="lineCov">       4632 :   if(i&lt;=j)</span></a>
+<a name="715"><span class="lineNum">     715 </span><span class="lineCov">       4632 :     return j+i*(alpha_size_-1)-i*(i-1)/2;</span></a>
+<a name="716"><span class="lineNum">     716 </span>            :   else</a>
+<a name="717"><span class="lineNum">     717 </span><span class="lineNoCov">          0 :     return get_index(j,i);</span></a>
+<a name="718"><span class="lineNum">     718 </span>            : }</a>
+<a name="719"><span class="lineNum">     719 </span>            : </a>
+<a name="720"><span class="lineNum">     720 </span>            : }</a>
+<a name="721"><span class="lineNum">     721 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesLinearExpansion.cpp.func-sort-c.html b/coverage/ves/VesLinearExpansion.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fcff94b9cc
--- /dev/null
+++ b/coverage/ves/VesLinearExpansion.cpp.func-sort-c.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesLinearExpansion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesLinearExpansion.cpp<span style="font-size: 80%;"> (<a href="VesLinearExpansion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesLinearExpansion.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#334">_ZN4PLMD3ves18VesLinearExpansionC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#407">_ZN4PLMD3ves18VesLinearExpansionD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#549">_ZNK4PLMD3ves18VesLinearExpansion23calculateReweightFactorEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#463">_ZN4PLMD3ves18VesLinearExpansion26restartTargetDistributionsEv</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#537">_ZN4PLMD3ves18VesLinearExpansion25writeTargetDistProjToFileEv</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#509">_ZN4PLMD3ves18VesLinearExpansion22setupFesProjFileOutputEv</a></td>
+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#504">_ZN4PLMD3ves18VesLinearExpansion18resetFesFileOutputEv</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#516">_ZN4PLMD3ves18VesLinearExpansion18writeFesProjToFileEv</a></td>
+              <td class="coverFnHi">36</td>
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+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#529">_ZN4PLMD3ves18VesLinearExpansion21writeTargetDistToFileEv</a></td>
+              <td class="coverFnHi">82</td>
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+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#334">_ZN4PLMD3ves18VesLinearExpansionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#407">_ZN4PLMD3ves18VesLinearExpansionD0Ev</a></td>
+              <td class="coverFnHi">90</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#407">_ZN4PLMD3ves18VesLinearExpansionD1Ev</a></td>
+              <td class="coverFnHi">90</td>
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+              <td class="coverFnHi">92</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#497">_ZN4PLMD3ves18VesLinearExpansion14writeFesToFileEv</a></td>
+              <td class="coverFnHi">169</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#475">_ZN4PLMD3ves18VesLinearExpansion15writeBiasToFileEv</a></td>
+              <td class="coverFnHi">173</td>
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+    <tr>
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+              <td class="coverFnHi">355</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#318">_ZN4PLMD3ves12_GLOBAL__N_131VesLinearExpansionRegisterMe320C2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#318">_ZN4PLMD3ves12_GLOBAL__N_131VesLinearExpansionRegisterMe320D2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#441">_ZN4PLMD3ves18VesLinearExpansion6updateEv</a></td>
+              <td class="coverFnHi">23750</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#411">_ZN4PLMD3ves18VesLinearExpansion9calculateEv</a></td>
+              <td class="coverFnHi">23750</td>
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+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesLinearExpansion.cpp.func.html b/coverage/ves/VesLinearExpansion.cpp.func.html
new file mode 100644
index 0000000000..18698db84e
--- /dev/null
+++ b/coverage/ves/VesLinearExpansion.cpp.func.html
@@ -0,0 +1,168 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesLinearExpansion.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesLinearExpansion.cpp<span style="font-size: 80%;"> (<a href="VesLinearExpansion.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesLinearExpansion.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
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+    <tr>
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+              <td class="coverFnHi">36</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#470">_ZN4PLMD3ves18VesLinearExpansion19setupBiasFileOutputEv</a></td>
+              <td class="coverFnHi">87</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#529">_ZN4PLMD3ves18VesLinearExpansion21writeTargetDistToFileEv</a></td>
+              <td class="coverFnHi">82</td>
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+    <tr>
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+              <td class="coverFnHi">17</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#457">_ZN4PLMD3ves18VesLinearExpansion25updateTargetDistributionsEv</a></td>
+              <td class="coverFnHi">355</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#537">_ZN4PLMD3ves18VesLinearExpansion25writeTargetDistProjToFileEv</a></td>
+              <td class="coverFnHi">13</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#463">_ZN4PLMD3ves18VesLinearExpansion26restartTargetDistributionsEv</a></td>
+              <td class="coverFnHi">8</td>
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+              <td class="coverFnHi">23750</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#411">_ZN4PLMD3ves18VesLinearExpansion9calculateEv</a></td>
+              <td class="coverFnHi">23750</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#334">_ZN4PLMD3ves18VesLinearExpansionC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">90</td>
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+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#334">_ZN4PLMD3ves18VesLinearExpansionC2ERKNS_13ActionOptionsE</a></td>
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+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#407">_ZN4PLMD3ves18VesLinearExpansionD1Ev</a></td>
+              <td class="coverFnHi">90</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#407">_ZN4PLMD3ves18VesLinearExpansionD2Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesLinearExpansion.cpp.gcov.html#549">_ZNK4PLMD3ves18VesLinearExpansion23calculateReweightFactorEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesLinearExpansion.cpp.gcov.html b/coverage/ves/VesLinearExpansion.cpp.gcov.html
new file mode 100644
index 0000000000..c2fbb929c7
--- /dev/null
+++ b/coverage/ves/VesLinearExpansion.cpp.gcov.html
@@ -0,0 +1,633 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesLinearExpansion.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesLinearExpansion.cpp<span style="font-size: 80%;"> (source / <a href="VesLinearExpansion.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">140</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntryHi">96.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">87.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesBias.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;LinearBasisSetExpansion.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;CoeffsVector.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;CoeffsMatrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;BasisFunctions.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Optimizer.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;TargetDistribution.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;bias/Bias.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;core/ActionRegister.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="35"><span class="lineNum">      35 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace PLMD {</a>
+<a name="39"><span class="lineNum">      39 </span>            : namespace ves {</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : //+PLUMEDOC VES_BIAS VES_LINEAR_EXPANSION</a>
+<a name="42"><span class="lineNum">      42 </span>            : /*</a>
+<a name="43"><span class="lineNum">      43 </span>            : Linear basis set expansion bias.</a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span>            : This VES bias action takes the bias potential to be a linear expansion</a>
+<a name="46"><span class="lineNum">      46 </span>            : in some basis set that is written as a product of one-dimensional basis functions.</a>
+<a name="47"><span class="lineNum">      47 </span>            : For example, for one CV the bias would be written as</a>
+<a name="48"><span class="lineNum">      48 </span>            : \f[</a>
+<a name="49"><span class="lineNum">      49 </span>            : V(s_{1};\boldsymbol{\alpha}) = \sum_{i_{1}} \alpha_{i_{1}} \, f_{i_{1}}(s_{1}),</a>
+<a name="50"><span class="lineNum">      50 </span>            : \f]</a>
+<a name="51"><span class="lineNum">      51 </span>            : while for two CVs it is written as</a>
+<a name="52"><span class="lineNum">      52 </span>            : \f[</a>
+<a name="53"><span class="lineNum">      53 </span>            : V(s_{1},s_{2};\boldsymbol{\alpha}) = \sum_{i_{1},i_{2}} \alpha_{i_{1},i_{2}} \, f_{i_{1}}(s_{1}) \, f_{i_{2}}(s_{2})</a>
+<a name="54"><span class="lineNum">      54 </span>            : \f]</a>
+<a name="55"><span class="lineNum">      55 </span>            : where \f$\boldsymbol{\alpha}\f$ is the set of expansion coefficients that</a>
+<a name="56"><span class="lineNum">      56 </span>            : are optimized within VES. With an appropriate choice of the basis functions</a>
+<a name="57"><span class="lineNum">      57 </span>            : it is possible to represent any generic free energy surface.</a>
+<a name="58"><span class="lineNum">      58 </span>            : The relationship between the bias and the free energy surface is given by</a>
+<a name="59"><span class="lineNum">      59 </span>            : \f[</a>
+<a name="60"><span class="lineNum">      60 </span>            : V(\mathbf{s}) = - F(\mathbf{s}) - \frac{1}{\beta} \log p(\mathbf{s}).</a>
+<a name="61"><span class="lineNum">      61 </span>            : \f]</a>
+<a name="62"><span class="lineNum">      62 </span>            : where \f$p(\mathbf{s})\f$ is the target distribution that is employed in the VES simulation.</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : \par Basis Functions</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span>            : Various one-dimensional basis functions are available in the VES code,</a>
+<a name="67"><span class="lineNum">      67 </span>            : see the complete list \ref ves_basisf &quot;here&quot;.</a>
+<a name="68"><span class="lineNum">      68 </span>            : At the current moment we recommend to use Legendre polynomials (\ref BF_LEGENDRE)</a>
+<a name="69"><span class="lineNum">      69 </span>            : for non-periodic CVs and Fourier basis functions (\ref BF_FOURIER)</a>
+<a name="70"><span class="lineNum">      70 </span>            : for periodic CV (e.g. dihedral angles).</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : To use basis functions within VES_LINEAR_EXPANSION you first need to</a>
+<a name="73"><span class="lineNum">      73 </span>            : define them in the input file before the VES_LINEAR_EXPANSION action and</a>
+<a name="74"><span class="lineNum">      74 </span>            : then give their labels using the BASIS_FUNCTIONS keyword.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span>            : \par Target Distributions</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : Various target distributions \f$p(\mathbf{s})\f$ are available in the VES code,</a>
+<a name="80"><span class="lineNum">      80 </span>            : see the complete list \ref ves_targetdist &quot;here&quot;.</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : To use a target distribution within VES_LINEAR_EXPANSION you first need to</a>
+<a name="83"><span class="lineNum">      83 </span>            : define it in the input file before the VES_LINEAR_EXPANSION action and</a>
+<a name="84"><span class="lineNum">      84 </span>            : then give its label using the TARGET_DISTRIBUTION keyword.</a>
+<a name="85"><span class="lineNum">      85 </span>            : The default behavior if no TARGET_DISTRIBUTION is given is to</a>
+<a name="86"><span class="lineNum">      86 </span>            : employ a uniform target distribution.</a>
+<a name="87"><span class="lineNum">      87 </span>            : </a>
+<a name="88"><span class="lineNum">      88 </span>            : Some target distribution, like the well-tempered one (\ref TD_WELLTEMPERED),</a>
+<a name="89"><span class="lineNum">      89 </span>            : are dynamic and need to be iteratively updated during the optimization.</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : \par Optimizer</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : In order to optimize the coefficients you will need to use VES_LINEAR_EXPANSION</a>
+<a name="94"><span class="lineNum">      94 </span>            : in combination with an optimizer, see the list of optimizers available in the</a>
+<a name="95"><span class="lineNum">      95 </span>            : VES code \ref ves_optimizer &quot;here&quot;. At the current moment we recommend to</a>
+<a name="96"><span class="lineNum">      96 </span>            : use the averaged stochastic gradient decent optimizer (\ref OPT_AVERAGED_SGD).</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span>            : The optimizer should be defined after the VES_LINEAR_EXPANSION action.</a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : \par Grid</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : Internally the code uses grids to calculate the basis set averages</a>
+<a name="103"><span class="lineNum">     103 </span>            : over the target distribution that is needed for the gradient. The same grid is</a>
+<a name="104"><span class="lineNum">     104 </span>            : also used for the output files (see next section).</a>
+<a name="105"><span class="lineNum">     105 </span>            : The size of the grid is determined by the GRID_BINS keyword. By default it has</a>
+<a name="106"><span class="lineNum">     106 </span>            : 100 grid points in each dimension, and generally this value should be sufficient.</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            : \par Outputting Free Energy Surfaces and Other Files</a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span>            : It is possible to output on-the-fly during the simulation the free energy surface</a>
+<a name="111"><span class="lineNum">     111 </span>            : estimated from the bias potential. How often this is done is specified within</a>
+<a name="112"><span class="lineNum">     112 </span>            : the \ref ves_optimizer &quot;optimizer&quot; by using the FES_OUTPUT keyword. The filename</a>
+<a name="113"><span class="lineNum">     113 </span>            : is specified by the FES_FILE keyword, but by default is it fes.LABEL.data,</a>
+<a name="114"><span class="lineNum">     114 </span>            : with an added suffix indicating</a>
+<a name="115"><span class="lineNum">     115 </span>            : the iteration number (iter-#).</a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span>            : For multi-dimensional case is it possible to also output projections of the</a>
+<a name="118"><span class="lineNum">     118 </span>            : free energy surfaces. The arguments for which to do these projections is</a>
+<a name="119"><span class="lineNum">     119 </span>            : specified using the numbered PROJ_ARG keywords. For these files a suffix</a>
+<a name="120"><span class="lineNum">     120 </span>            : indicating the projection (proj-#) will be added to the filenames.</a>
+<a name="121"><span class="lineNum">     121 </span>            : You will also need to specify the frequency of the output by using the</a>
+<a name="122"><span class="lineNum">     122 </span>            : FES_PROJ_OUTPUT keyword within the optimizer.</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : It is also possible to output the bias potential itself, for this the relevant</a>
+<a name="125"><span class="lineNum">     125 </span>            : keyword is BIAS_OUTPUT within the optimizer. The filename</a>
+<a name="126"><span class="lineNum">     126 </span>            : is specified by the BIAS_FILE keyword, but by default is it bias.LABEL.data,</a>
+<a name="127"><span class="lineNum">     127 </span>            : with an added suffix indicating the iteration number (iter-#).</a>
+<a name="128"><span class="lineNum">     128 </span>            : </a>
+<a name="129"><span class="lineNum">     129 </span>            : Furthermore is it possible to output the target distribution, and its projections</a>
+<a name="130"><span class="lineNum">     130 </span>            : (i.e. marginal distributions). The filenames of these files are specified with</a>
+<a name="131"><span class="lineNum">     131 </span>            : the TARGETDIST_FILE, but by default is it targetdist.LABEL.data. The</a>
+<a name="132"><span class="lineNum">     132 </span>            : logarithm of the target distribution will also be outputted to file that has the</a>
+<a name="133"><span class="lineNum">     133 </span>            : added suffix log. For static target distribution these files will be outputted in</a>
+<a name="134"><span class="lineNum">     134 </span>            : the beginning of the</a>
+<a name="135"><span class="lineNum">     135 </span>            : simulation while for dynamic ones you will need to specify the frequency</a>
+<a name="136"><span class="lineNum">     136 </span>            : of the output by using the TARGETDIST_OUTPUT and TARGETDIST_PROJ_OUTPUT</a>
+<a name="137"><span class="lineNum">     137 </span>            : keywords within the optimizer.</a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span>            : It is also possible to output free energy surfaces and bias in post processing</a>
+<a name="140"><span class="lineNum">     140 </span>            : by using the \ref VES_OUTPUT_FES action. However, be aware that this action</a>
+<a name="141"><span class="lineNum">     141 </span>            : does does not support dynamic target distribution (e.g. well-tempered).</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            : \par Static Bias</a>
+<a name="144"><span class="lineNum">     144 </span>            : </a>
+<a name="145"><span class="lineNum">     145 </span>            : It is also possible to use VES_LINEAR_EXPANSION as a static bias that uses</a>
+<a name="146"><span class="lineNum">     146 </span>            : previously obtained coefficients. In this case the coefficients should be</a>
+<a name="147"><span class="lineNum">     147 </span>            : read in from the coefficient file given in the COEFFS keyword.</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : \par Bias Cutoff</a>
+<a name="150"><span class="lineNum">     150 </span>            : </a>
+<a name="151"><span class="lineNum">     151 </span>            : It is possible to impose a cutoff on the bias potential using the procedure</a>
+<a name="152"><span class="lineNum">     152 </span>            : introduced in \cite McCarty-PRL-2015 such that the free energy surface</a>
+<a name="153"><span class="lineNum">     153 </span>            : is only flooded up to a certain value. The bias that results from this procedure</a>
+<a name="154"><span class="lineNum">     154 </span>            : can then be used as a static bias for obtaining kinetic rates.</a>
+<a name="155"><span class="lineNum">     155 </span>            : The value of the cutoff is given by the BIAS_CUTOFF keyword.</a>
+<a name="156"><span class="lineNum">     156 </span>            : To impose the cutoff the code uses a Fermi switching function \f$1/(1+e^{\lambda x})\f$</a>
+<a name="157"><span class="lineNum">     157 </span>            : where the parameter \f$\lambda\f$ controls how sharply the switchingfunction goes to zero.</a>
+<a name="158"><span class="lineNum">     158 </span>            : The default value is \f$\lambda=10\f$ but this can be changed by using the</a>
+<a name="159"><span class="lineNum">     159 </span>            : BIAS_CUTOFF_FERMI_LAMBDA keyword.</a>
+<a name="160"><span class="lineNum">     160 </span>            : </a>
+<a name="161"><span class="lineNum">     161 </span>            : \par Examples</a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : In the following example we run a VES_LINEAR_EXPANSION for one CV using</a>
+<a name="164"><span class="lineNum">     164 </span>            : a Legendre basis functions (\ref BF_LEGENDRE) and a uniform target</a>
+<a name="165"><span class="lineNum">     165 </span>            : distribution as no target distribution is specified. The coefficients</a>
+<a name="166"><span class="lineNum">     166 </span>            : are optimized using averaged stochastic gradient descent optimizer</a>
+<a name="167"><span class="lineNum">     167 </span>            : (\ref OPT_AVERAGED_SGD). Within the optimizer we specify that the</a>
+<a name="168"><span class="lineNum">     168 </span>            : FES should be outputted to file every 500 coefficients iterations (the</a>
+<a name="169"><span class="lineNum">     169 </span>            : FES_OUTPUT keyword).</a>
+<a name="170"><span class="lineNum">     170 </span>            : Parameters that are very specific to the problem at hand, like the</a>
+<a name="171"><span class="lineNum">     171 </span>            : order of the basis functions, the interval on which the</a>
+<a name="172"><span class="lineNum">     172 </span>            : basis functions are defined, and the step size used</a>
+<a name="173"><span class="lineNum">     173 </span>            : in the optimizer, are left unfilled.</a>
+<a name="174"><span class="lineNum">     174 </span>            : \plumedfile</a>
+<a name="175"><span class="lineNum">     175 </span>            : bf1: BF_LEGENDRE ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="178"><span class="lineNum">     178 </span>            :  ARG=d1</a>
+<a name="179"><span class="lineNum">     179 </span>            :  BASIS_FUNCTIONS=bf1</a>
+<a name="180"><span class="lineNum">     180 </span>            :  TEMP=__FILL__</a>
+<a name="181"><span class="lineNum">     181 </span>            :  GRID_BINS=200</a>
+<a name="182"><span class="lineNum">     182 </span>            :  LABEL=b1</a>
+<a name="183"><span class="lineNum">     183 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="184"><span class="lineNum">     184 </span>            : </a>
+<a name="185"><span class="lineNum">     185 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="186"><span class="lineNum">     186 </span>            :  BIAS=b1</a>
+<a name="187"><span class="lineNum">     187 </span>            :  STRIDE=1000</a>
+<a name="188"><span class="lineNum">     188 </span>            :  LABEL=o1</a>
+<a name="189"><span class="lineNum">     189 </span>            :  STEPSIZE=__FILL__</a>
+<a name="190"><span class="lineNum">     190 </span>            :  FES_OUTPUT=500</a>
+<a name="191"><span class="lineNum">     191 </span>            :  COEFFS_OUTPUT=10</a>
+<a name="192"><span class="lineNum">     192 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="193"><span class="lineNum">     193 </span>            : \endplumedfile</a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span>            : In the following example we employ VES_LINEAR_EXPANSION for two CVs,</a>
+<a name="196"><span class="lineNum">     196 </span>            : The first CV is periodic and therefore we employ a Fourier basis functions</a>
+<a name="197"><span class="lineNum">     197 </span>            : (\ref BF_LEGENDRE) while the second CV is non-periodic so we employ a</a>
+<a name="198"><span class="lineNum">     198 </span>            : Legendre polynomials as in the previous example. For the target distribution</a>
+<a name="199"><span class="lineNum">     199 </span>            : we employ a well-tempered target distribution (\ref TD_WELLTEMPERED), which is</a>
+<a name="200"><span class="lineNum">     200 </span>            : dynamic and needs to be iteratively updated with a stride that is given</a>
+<a name="201"><span class="lineNum">     201 </span>            : using the TARGETDIST_STRIDE within the optimizer.</a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : \plumedfile</a>
+<a name="204"><span class="lineNum">     204 </span>            : bf1: BF_FOURIER  ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="205"><span class="lineNum">     205 </span>            : bf2: BF_LEGENDRE ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="206"><span class="lineNum">     206 </span>            : </a>
+<a name="207"><span class="lineNum">     207 </span>            : td_wt: TD_WELLTEMPERED BIASFACTOR=10.0</a>
+<a name="208"><span class="lineNum">     208 </span>            : </a>
+<a name="209"><span class="lineNum">     209 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="210"><span class="lineNum">     210 </span>            :  ARG=cv1,cv2</a>
+<a name="211"><span class="lineNum">     211 </span>            :  BASIS_FUNCTIONS=bf1,bf2</a>
+<a name="212"><span class="lineNum">     212 </span>            :  TEMP=__FILL__</a>
+<a name="213"><span class="lineNum">     213 </span>            :  GRID_BINS=100</a>
+<a name="214"><span class="lineNum">     214 </span>            :  LABEL=b1</a>
+<a name="215"><span class="lineNum">     215 </span>            :  TARGET_DISTRIBUTION=td_wt</a>
+<a name="216"><span class="lineNum">     216 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="219"><span class="lineNum">     219 </span>            :  BIAS=b1</a>
+<a name="220"><span class="lineNum">     220 </span>            :  STRIDE=1000</a>
+<a name="221"><span class="lineNum">     221 </span>            :  LABEL=o1</a>
+<a name="222"><span class="lineNum">     222 </span>            :  STEPSIZE=__FILL__</a>
+<a name="223"><span class="lineNum">     223 </span>            :  FES_OUTPUT=500</a>
+<a name="224"><span class="lineNum">     224 </span>            :  COEFFS_OUTPUT=10</a>
+<a name="225"><span class="lineNum">     225 </span>            :  TARGETDIST_STRIDE=500</a>
+<a name="226"><span class="lineNum">     226 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="227"><span class="lineNum">     227 </span>            : \endplumedfile</a>
+<a name="228"><span class="lineNum">     228 </span>            : </a>
+<a name="229"><span class="lineNum">     229 </span>            : </a>
+<a name="230"><span class="lineNum">     230 </span>            : In the following example we employ a bias cutoff such that the bias</a>
+<a name="231"><span class="lineNum">     231 </span>            : only fills the free energy landscape up a certain level. In this case</a>
+<a name="232"><span class="lineNum">     232 </span>            : the target distribution is also dynamic and needs to iteratively updated.</a>
+<a name="233"><span class="lineNum">     233 </span>            : </a>
+<a name="234"><span class="lineNum">     234 </span>            : \plumedfile</a>
+<a name="235"><span class="lineNum">     235 </span>            : bf1: BF_LEGENDRE ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="236"><span class="lineNum">     236 </span>            : bf2: BF_LEGENDRE ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="239"><span class="lineNum">     239 </span>            :  ARG=cv1,cv2</a>
+<a name="240"><span class="lineNum">     240 </span>            :  BASIS_FUNCTIONS=bf1,bf2</a>
+<a name="241"><span class="lineNum">     241 </span>            :  TEMP=__FILL__</a>
+<a name="242"><span class="lineNum">     242 </span>            :  GRID_BINS=100</a>
+<a name="243"><span class="lineNum">     243 </span>            :  LABEL=b1</a>
+<a name="244"><span class="lineNum">     244 </span>            :  BIAS_CUTOFF=20.0</a>
+<a name="245"><span class="lineNum">     245 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span>            : OPT_AVERAGED_SGD ...</a>
+<a name="248"><span class="lineNum">     248 </span>            :  BIAS=b1</a>
+<a name="249"><span class="lineNum">     249 </span>            :  STRIDE=1000</a>
+<a name="250"><span class="lineNum">     250 </span>            :  LABEL=o1</a>
+<a name="251"><span class="lineNum">     251 </span>            :  STEPSIZE=__FILL__</a>
+<a name="252"><span class="lineNum">     252 </span>            :  FES_OUTPUT=500</a>
+<a name="253"><span class="lineNum">     253 </span>            :  COEFFS_OUTPUT=10</a>
+<a name="254"><span class="lineNum">     254 </span>            :  TARGETDIST_STRIDE=500</a>
+<a name="255"><span class="lineNum">     255 </span>            : ... OPT_AVERAGED_SGD</a>
+<a name="256"><span class="lineNum">     256 </span>            : \endplumedfile</a>
+<a name="257"><span class="lineNum">     257 </span>            : </a>
+<a name="258"><span class="lineNum">     258 </span>            : The optimized bias potential can then be used as a static bias for obtaining</a>
+<a name="259"><span class="lineNum">     259 </span>            : kinetics. For this you need read in the final coefficients from file</a>
+<a name="260"><span class="lineNum">     260 </span>            : (e.g. coeffs_final.data in this case) by using the</a>
+<a name="261"><span class="lineNum">     261 </span>            : COEFFS keyword (also, no optimizer should be defined in the input)</a>
+<a name="262"><span class="lineNum">     262 </span>            : \plumedfile</a>
+<a name="263"><span class="lineNum">     263 </span>            : bf1: BF_LEGENDRE ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="264"><span class="lineNum">     264 </span>            : bf2: BF_LEGENDRE ORDER=__FILL__ MINIMUM=__FILL__ MAXIMUM=__FILL__</a>
+<a name="265"><span class="lineNum">     265 </span>            : </a>
+<a name="266"><span class="lineNum">     266 </span>            : VES_LINEAR_EXPANSION ...</a>
+<a name="267"><span class="lineNum">     267 </span>            :  ARG=cv1,cv2</a>
+<a name="268"><span class="lineNum">     268 </span>            :  BASIS_FUNCTIONS=bf1,bf2</a>
+<a name="269"><span class="lineNum">     269 </span>            :  TEMP=__FILL__</a>
+<a name="270"><span class="lineNum">     270 </span>            :  GRID_BINS=100</a>
+<a name="271"><span class="lineNum">     271 </span>            :  LABEL=b1</a>
+<a name="272"><span class="lineNum">     272 </span>            :  BIAS_CUTOFF=20.0</a>
+<a name="273"><span class="lineNum">     273 </span>            :  COEFFS=coeffs_final.data</a>
+<a name="274"><span class="lineNum">     274 </span>            : ... VES_LINEAR_EXPANSION</a>
+<a name="275"><span class="lineNum">     275 </span>            : \endplumedfile</a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : */</a>
+<a name="280"><span class="lineNum">     280 </span>            : //+ENDPLUMEDOC</a>
+<a name="281"><span class="lineNum">     281 </span>            : </a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span>            : class VesLinearExpansion : public VesBias {</a>
+<a name="284"><span class="lineNum">     284 </span>            : private:</a>
+<a name="285"><span class="lineNum">     285 </span>            :   unsigned int nargs_;</a>
+<a name="286"><span class="lineNum">     286 </span>            :   std::vector&lt;BasisFunctions*&gt; basisf_pntrs_;</a>
+<a name="287"><span class="lineNum">     287 </span>            :   std::unique_ptr&lt;LinearBasisSetExpansion&gt; bias_expansion_pntr_;</a>
+<a name="288"><span class="lineNum">     288 </span>            :   size_t ncoeffs_;</a>
+<a name="289"><span class="lineNum">     289 </span>            :   Value* valueForce2_;</a>
+<a name="290"><span class="lineNum">     290 </span>            :   bool all_values_inside;</a>
+<a name="291"><span class="lineNum">     291 </span>            :   std::vector&lt;double&gt; bf_values;</a>
+<a name="292"><span class="lineNum">     292 </span>            :   bool bf_values_set;</a>
+<a name="293"><span class="lineNum">     293 </span>            : public:</a>
+<a name="294"><span class="lineNum">     294 </span>            :   explicit VesLinearExpansion(const ActionOptions&amp;);</a>
+<a name="295"><span class="lineNum">     295 </span>            :   ~VesLinearExpansion();</a>
+<a name="296"><span class="lineNum">     296 </span>            :   void calculate() override;</a>
+<a name="297"><span class="lineNum">     297 </span>            :   void update() override;</a>
+<a name="298"><span class="lineNum">     298 </span>            :   void updateTargetDistributions() override;</a>
+<a name="299"><span class="lineNum">     299 </span>            :   void restartTargetDistributions() override;</a>
+<a name="300"><span class="lineNum">     300 </span>            :   //</a>
+<a name="301"><span class="lineNum">     301 </span>            :   void setupBiasFileOutput() override;</a>
+<a name="302"><span class="lineNum">     302 </span>            :   void writeBiasToFile() override;</a>
+<a name="303"><span class="lineNum">     303 </span>            :   void resetBiasFileOutput() override;</a>
+<a name="304"><span class="lineNum">     304 </span>            :   //</a>
+<a name="305"><span class="lineNum">     305 </span>            :   void setupFesFileOutput() override;</a>
+<a name="306"><span class="lineNum">     306 </span>            :   void writeFesToFile() override;</a>
+<a name="307"><span class="lineNum">     307 </span>            :   void resetFesFileOutput() override;</a>
+<a name="308"><span class="lineNum">     308 </span>            :   //</a>
+<a name="309"><span class="lineNum">     309 </span>            :   void setupFesProjFileOutput() override;</a>
+<a name="310"><span class="lineNum">     310 </span>            :   void writeFesProjToFile() override;</a>
+<a name="311"><span class="lineNum">     311 </span>            :   //</a>
+<a name="312"><span class="lineNum">     312 </span>            :   void writeTargetDistToFile() override;</a>
+<a name="313"><span class="lineNum">     313 </span>            :   void writeTargetDistProjToFile() override;</a>
+<a name="314"><span class="lineNum">     314 </span>            :   //</a>
+<a name="315"><span class="lineNum">     315 </span>            :   double calculateReweightFactor() const override;</a>
+<a name="316"><span class="lineNum">     316 </span>            :   //</a>
+<a name="317"><span class="lineNum">     317 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="318"><span class="lineNum">     318 </span>            : };</a>
+<a name="319"><span class="lineNum">     319 </span>            : </a>
+<a name="320"><span class="lineNum">     320 </span><span class="lineCov">      12684 : PLUMED_REGISTER_ACTION(VesLinearExpansion,&quot;VES_LINEAR_EXPANSION&quot;)</span></a>
+<a name="321"><span class="lineNum">     321 </span>            : </a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">         92 : void VesLinearExpansion::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="323"><span class="lineNum">     323 </span><span class="lineCov">         92 :   VesBias::registerKeywords(keys);</span></a>
+<a name="324"><span class="lineNum">     324 </span>            :   //</a>
+<a name="325"><span class="lineNum">     325 </span><span class="lineCov">         92 :   VesBias::useInitialCoeffsKeywords(keys);</span></a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">         92 :   VesBias::useTargetDistributionKeywords(keys);</span></a>
+<a name="327"><span class="lineNum">     327 </span><span class="lineCov">         92 :   VesBias::useBiasCutoffKeywords(keys);</span></a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">         92 :   VesBias::useGridBinKeywords(keys);</span></a>
+<a name="329"><span class="lineNum">     329 </span><span class="lineCov">         92 :   VesBias::useProjectionArgKeywords(keys);</span></a>
+<a name="330"><span class="lineNum">     330 </span>            :   //</a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">         92 :   keys.use(&quot;ARG&quot;);</span></a>
+<a name="332"><span class="lineNum">     332 </span><span class="lineCov">        184 :   keys.add(&quot;compulsory&quot;,&quot;BASIS_FUNCTIONS&quot;,&quot;the label of the one dimensional basis functions that should be used.&quot;);</span></a>
+<a name="333"><span class="lineNum">     333 </span><span class="lineCov">        184 :   keys.addOutputComponent(&quot;force2&quot;,&quot;default&quot;,&quot;the instantaneous value of the squared force due to this bias potential.&quot;);</span></a>
+<a name="334"><span class="lineNum">     334 </span><span class="lineCov">         92 : }</span></a>
+<a name="335"><span class="lineNum">     335 </span>            : </a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">         90 : VesLinearExpansion::VesLinearExpansion(const ActionOptions&amp;ao):</span></a>
+<a name="337"><span class="lineNum">     337 </span>            :   PLUMED_VES_VESBIAS_INIT(ao),</a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">         90 :   nargs_(getNumberOfArguments()),</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">         90 :   basisf_pntrs_(0),</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">         90 :   valueForce2_(NULL),</span></a>
+<a name="341"><span class="lineNum">     341 </span><span class="lineCov">         90 :   all_values_inside(true),</span></a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineCov">         90 :   bf_values(0),</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineCov">         90 :   bf_values_set(false)</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : {</a>
+<a name="345"><span class="lineNum">     345 </span>            :   std::vector&lt;std::string&gt; basisf_labels;</a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">         90 :   parseMultipleValues(&quot;BASIS_FUNCTIONS&quot;,basisf_labels,nargs_);</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">         90 :   checkRead();</span></a>
+<a name="348"><span class="lineNum">     348 </span>            : </a>
+<a name="349"><span class="lineNum">     349 </span><span class="lineCov">         90 :   std::string error_msg = &quot;&quot;;</span></a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">        180 :   basisf_pntrs_ = VesTools::getPointersFromLabels&lt;BasisFunctions*&gt;(basisf_labels,plumed.getActionSet(),error_msg);</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">         90 :   if(error_msg.size()&gt;0) {plumed_merror(&quot;Error in keyword BASIS_FUNCTIONS of &quot;+getName()+&quot;: &quot;+error_msg);}</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   //</a>
+<a name="353"><span class="lineNum">     353 </span>            : </a>
+<a name="354"><span class="lineNum">     354 </span><span class="lineCov">         90 :   std::vector&lt;Value*&gt; args_pntrs = getArguments();</span></a>
+<a name="355"><span class="lineNum">     355 </span>            :   // check arguments and basis functions</a>
+<a name="356"><span class="lineNum">     356 </span>            :   // this is done to avoid some issues with integration of target distribution</a>
+<a name="357"><span class="lineNum">     357 </span>            :   // and periodic CVs, needs to be fixed later on.</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">        207 :   for(unsigned int i=0; i&lt;args_pntrs.size(); i++) {</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">        117 :     if(args_pntrs[i]-&gt;isPeriodic() &amp;&amp; !(basisf_pntrs_[i]-&gt;arePeriodic()) ) {</span></a>
+<a name="360"><span class="lineNum">     360 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;argument &quot;+args_pntrs[i]-&gt;getName()+&quot; is periodic while the basis functions &quot; + basisf_pntrs_[i]-&gt;getLabel()+ &quot; are not. You need to use the COMBINE action to remove the periodicity of the argument if you want to use these basis functions&quot;);</span></a>
+<a name="361"><span class="lineNum">     361 </span>            :     }</a>
+<a name="362"><span class="lineNum">     362 </span><span class="lineCov">        117 :     else if(!(args_pntrs[i]-&gt;isPeriodic()) &amp;&amp; basisf_pntrs_[i]-&gt;arePeriodic() ) {</span></a>
+<a name="363"><span class="lineNum">     363 </span><span class="lineCov">          1 :       log.printf(&quot;  warning: argument %s is not periodic while the basis functions %s used for it are periodic\n&quot;,args_pntrs[i]-&gt;getName().c_str(),basisf_pntrs_[i]-&gt;getLabel().c_str());</span></a>
+<a name="364"><span class="lineNum">     364 </span>            :     }</a>
+<a name="365"><span class="lineNum">     365 </span>            :   }</a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">         90 :   addCoeffsSet(args_pntrs,basisf_pntrs_);</span></a>
+<a name="368"><span class="lineNum">     368 </span><span class="lineCov">         90 :   ncoeffs_ = numberOfCoeffs();</span></a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">         90 :   bool coeffs_read = readCoeffsFromFiles();</span></a>
+<a name="370"><span class="lineNum">     370 </span>            : </a>
+<a name="371"><span class="lineNum">     371 </span><span class="lineCov">         90 :   checkThatTemperatureIsGiven();</span></a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">        180 :   bias_expansion_pntr_ = Tools::make_unique&lt;LinearBasisSetExpansion&gt;(getLabel(),getBeta(),comm,args_pntrs,basisf_pntrs_,getCoeffsPntr());</span></a>
+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">         90 :   bias_expansion_pntr_-&gt;linkVesBias(this);</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">         90 :   bias_expansion_pntr_-&gt;setGridBins(this-&gt;getGridBins());</span></a>
+<a name="375"><span class="lineNum">     375 </span>            :   //</a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">         90 :   bf_values.assign(ncoeffs_,0.0);</span></a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            : </a>
+<a name="380"><span class="lineNum">     380 </span><span class="lineCov">         90 :   if(getNumberOfTargetDistributionPntrs()==0) {</span></a>
+<a name="381"><span class="lineNum">     381 </span><span class="lineCov">         45 :     log.printf(&quot;  using an uniform target distribution: \n&quot;);</span></a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineCov">         45 :     bias_expansion_pntr_-&gt;setupUniformTargetDistribution();</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :     disableStaticTargetDistFileOutput();</a>
+<a name="384"><span class="lineNum">     384 </span>            :   }</a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineCov">         45 :   else if(getNumberOfTargetDistributionPntrs()==1) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineCov">         51 :     if(biasCutoffActive()) {getTargetDistributionPntrs()[0]-&gt;setupBiasCutoff();}</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineCov">         45 :     bias_expansion_pntr_-&gt;setupTargetDistribution(getTargetDistributionPntrs()[0]);</span></a>
+<a name="388"><span class="lineNum">     388 </span><span class="lineCov">         90 :     log.printf(&quot;  using target distribution of type %s with label %s \n&quot;,getTargetDistributionPntrs()[0]-&gt;getName().c_str(),getTargetDistributionPntrs()[0]-&gt;getLabel().c_str());</span></a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span>            :   else {</a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;problem with the TARGET_DISTRIBUTION keyword, either give no label or just one label.&quot;);</span></a>
+<a name="392"><span class="lineNum">     392 </span>            :   }</a>
+<a name="393"><span class="lineNum">     393 </span><span class="lineCov">         90 :   setTargetDistAverages(bias_expansion_pntr_-&gt;TargetDistAverages());</span></a>
+<a name="394"><span class="lineNum">     394 </span>            :   //</a>
+<a name="395"><span class="lineNum">     395 </span><span class="lineCov">         90 :   if(coeffs_read &amp;&amp; biasCutoffActive()) {</span></a>
+<a name="396"><span class="lineNum">     396 </span><span class="lineCov">          1 :     VesLinearExpansion::updateTargetDistributions();</span></a>
+<a name="397"><span class="lineNum">     397 </span>            :   }</a>
+<a name="398"><span class="lineNum">     398 </span>            :   //</a>
+<a name="399"><span class="lineNum">     399 </span><span class="lineCov">         90 :   if(coeffs_read) {</span></a>
+<a name="400"><span class="lineNum">     400 </span><span class="lineCov">          4 :     VesLinearExpansion::setupBiasFileOutput();</span></a>
+<a name="401"><span class="lineNum">     401 </span><span class="lineCov">          4 :     VesLinearExpansion::writeBiasToFile();</span></a>
+<a name="402"><span class="lineNum">     402 </span>            :   }</a>
+<a name="403"><span class="lineNum">     403 </span>            : </a>
+<a name="404"><span class="lineNum">     404 </span><span class="lineCov">        180 :   addComponent(&quot;force2&quot;); componentIsNotPeriodic(&quot;force2&quot;);</span></a>
+<a name="405"><span class="lineNum">     405 </span><span class="lineCov">         90 :   valueForce2_=getPntrToComponent(&quot;force2&quot;);</span></a>
+<a name="406"><span class="lineNum">     406 </span><span class="lineCov">         90 : }</span></a>
+<a name="407"><span class="lineNum">     407 </span>            : </a>
+<a name="408"><span class="lineNum">     408 </span>            : </a>
+<a name="409"><span class="lineNum">     409 </span><span class="lineCov">        180 : VesLinearExpansion::~VesLinearExpansion() {</span></a>
+<a name="410"><span class="lineNum">     410 </span><span class="lineCov">        270 : }</span></a>
+<a name="411"><span class="lineNum">     411 </span>            : </a>
+<a name="412"><span class="lineNum">     412 </span>            : </a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">      23750 : void VesLinearExpansion::calculate() {</span></a>
+<a name="414"><span class="lineNum">     414 </span>            : </a>
+<a name="415"><span class="lineNum">     415 </span><span class="lineCov">      23750 :   std::vector&lt;double&gt; cv_values(nargs_);</span></a>
+<a name="416"><span class="lineNum">     416 </span><span class="lineCov">      23750 :   std::vector&lt;double&gt; forces(nargs_);</span></a>
+<a name="417"><span class="lineNum">     417 </span>            : </a>
+<a name="418"><span class="lineNum">     418 </span><span class="lineCov">      60967 :   for(unsigned int k=0; k&lt;nargs_; k++) {</span></a>
+<a name="419"><span class="lineNum">     419 </span><span class="lineCov">      37217 :     cv_values[k]=getArgument(k);</span></a>
+<a name="420"><span class="lineNum">     420 </span>            :   }</a>
+<a name="421"><span class="lineNum">     421 </span>            : </a>
+<a name="422"><span class="lineNum">     422 </span><span class="lineCov">      23750 :   all_values_inside = true;</span></a>
+<a name="423"><span class="lineNum">     423 </span><span class="lineCov">      23750 :   double bias = bias_expansion_pntr_-&gt;getBiasAndForces(cv_values,all_values_inside,forces,bf_values);</span></a>
+<a name="424"><span class="lineNum">     424 </span><span class="lineCov">      23750 :   if(biasCutoffActive()) {</span></a>
+<a name="425"><span class="lineNum">     425 </span><span class="lineCov">         63 :     applyBiasCutoff(bias,forces,bf_values);</span></a>
+<a name="426"><span class="lineNum">     426 </span><span class="lineCov">         63 :     bf_values[0]=1.0;</span></a>
+<a name="427"><span class="lineNum">     427 </span>            :   }</a>
+<a name="428"><span class="lineNum">     428 </span>            :   double totalForce2 = 0.0;</a>
+<a name="429"><span class="lineNum">     429 </span><span class="lineCov">      23750 :   if(all_values_inside) {</span></a>
+<a name="430"><span class="lineNum">     430 </span><span class="lineCov">      60408 :     for(unsigned int k=0; k&lt;nargs_; k++) {</span></a>
+<a name="431"><span class="lineNum">     431 </span><span class="lineCov">      36852 :       setOutputForce(k,forces[k]);</span></a>
+<a name="432"><span class="lineNum">     432 </span><span class="lineCov">      36852 :       totalForce2 += forces[k]*forces[k];</span></a>
+<a name="433"><span class="lineNum">     433 </span>            :     }</a>
+<a name="434"><span class="lineNum">     434 </span>            :   }</a>
+<a name="435"><span class="lineNum">     435 </span>            : </a>
+<a name="436"><span class="lineNum">     436 </span><span class="lineCov">      23750 :   setBias(bias);</span></a>
+<a name="437"><span class="lineNum">     437 </span><span class="lineCov">      23750 :   valueForce2_-&gt;set(totalForce2);</span></a>
+<a name="438"><span class="lineNum">     438 </span>            : </a>
+<a name="439"><span class="lineNum">     439 </span><span class="lineCov">      23750 :   bf_values_set = true;</span></a>
+<a name="440"><span class="lineNum">     440 </span><span class="lineCov">      23750 : }</span></a>
+<a name="441"><span class="lineNum">     441 </span>            : </a>
+<a name="442"><span class="lineNum">     442 </span>            : </a>
+<a name="443"><span class="lineNum">     443 </span><span class="lineCov">      23750 : void VesLinearExpansion::update() {</span></a>
+<a name="444"><span class="lineNum">     444 </span><span class="lineCov">      23750 :   if(!bf_values_set) {</span></a>
+<a name="445"><span class="lineNum">     445 </span><span class="lineNoCov">          0 :     warning(&quot;VesLinearExpansion::update() is being called without calling VesLinearExpansion::calculate() first to calculate the basis function values. This can lead to incorrect behavior.&quot;);</span></a>
+<a name="446"><span class="lineNum">     446 </span>            :   }</a>
+<a name="447"><span class="lineNum">     447 </span><span class="lineCov">      23750 :   if(all_values_inside &amp;&amp; bf_values_set) {</span></a>
+<a name="448"><span class="lineNum">     448 </span><span class="lineCov">      23556 :     addToSampledAverages(bf_values);</span></a>
+<a name="449"><span class="lineNum">     449 </span>            :   }</a>
+<a name="450"><span class="lineNum">     450 </span>            :   std::fill(bf_values.begin(), bf_values.end(), 0.0);</a>
+<a name="451"><span class="lineNum">     451 </span><span class="lineCov">      23750 :   bf_values_set = false;</span></a>
+<a name="452"><span class="lineNum">     452 </span><span class="lineCov">      23750 : }</span></a>
+<a name="453"><span class="lineNum">     453 </span>            : </a>
+<a name="454"><span class="lineNum">     454 </span>            : </a>
+<a name="455"><span class="lineNum">     455 </span>            : </a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            : </a>
+<a name="458"><span class="lineNum">     458 </span>            : </a>
+<a name="459"><span class="lineNum">     459 </span><span class="lineCov">        355 : void VesLinearExpansion::updateTargetDistributions() {</span></a>
+<a name="460"><span class="lineNum">     460 </span><span class="lineCov">        355 :   bias_expansion_pntr_-&gt;updateTargetDistribution();</span></a>
+<a name="461"><span class="lineNum">     461 </span><span class="lineCov">        355 :   setTargetDistAverages(bias_expansion_pntr_-&gt;TargetDistAverages());</span></a>
+<a name="462"><span class="lineNum">     462 </span><span class="lineCov">        355 : }</span></a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            : </a>
+<a name="465"><span class="lineNum">     465 </span><span class="lineCov">          8 : void VesLinearExpansion::restartTargetDistributions() {</span></a>
+<a name="466"><span class="lineNum">     466 </span><span class="lineCov">         16 :   bias_expansion_pntr_-&gt;readInRestartTargetDistribution(getCurrentTargetDistOutputFilename());</span></a>
+<a name="467"><span class="lineNum">     467 </span><span class="lineCov">          8 :   bias_expansion_pntr_-&gt;restartTargetDistribution();</span></a>
+<a name="468"><span class="lineNum">     468 </span><span class="lineCov">          8 :   setTargetDistAverages(bias_expansion_pntr_-&gt;TargetDistAverages());</span></a>
+<a name="469"><span class="lineNum">     469 </span><span class="lineCov">          8 : }</span></a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            : </a>
+<a name="472"><span class="lineNum">     472 </span><span class="lineCov">         87 : void VesLinearExpansion::setupBiasFileOutput() {</span></a>
+<a name="473"><span class="lineNum">     473 </span><span class="lineCov">         87 :   bias_expansion_pntr_-&gt;setupBiasGrid(true);</span></a>
+<a name="474"><span class="lineNum">     474 </span><span class="lineCov">         87 : }</span></a>
+<a name="475"><span class="lineNum">     475 </span>            : </a>
+<a name="476"><span class="lineNum">     476 </span>            : </a>
+<a name="477"><span class="lineNum">     477 </span><span class="lineCov">        173 : void VesLinearExpansion::writeBiasToFile() {</span></a>
+<a name="478"><span class="lineNum">     478 </span><span class="lineCov">        173 :   bias_expansion_pntr_-&gt;updateBiasGrid();</span></a>
+<a name="479"><span class="lineNum">     479 </span><span class="lineCov">        519 :   auto ofile_pntr = getOFile(getCurrentBiasOutputFilename(),useMultipleWalkers());</span></a>
+<a name="480"><span class="lineNum">     480 </span><span class="lineCov">        173 :   bias_expansion_pntr_-&gt;writeBiasGridToFile(*ofile_pntr);</span></a>
+<a name="481"><span class="lineNum">     481 </span><span class="lineCov">        173 :   if(biasCutoffActive()) {</span></a>
+<a name="482"><span class="lineNum">     482 </span><span class="lineCov">          5 :     bias_expansion_pntr_-&gt;updateBiasWithoutCutoffGrid();</span></a>
+<a name="483"><span class="lineNum">     483 </span><span class="lineCov">         15 :     auto ofile_pntr2 = getOFile(getCurrentBiasOutputFilename(&quot;without-cutoff&quot;),useMultipleWalkers());</span></a>
+<a name="484"><span class="lineNum">     484 </span><span class="lineCov">          5 :     bias_expansion_pntr_-&gt;writeBiasWithoutCutoffGridToFile(*ofile_pntr2);</span></a>
+<a name="485"><span class="lineNum">     485 </span><span class="lineCov">          5 :   }</span></a>
+<a name="486"><span class="lineNum">     486 </span><span class="lineCov">        173 : }</span></a>
+<a name="487"><span class="lineNum">     487 </span>            : </a>
+<a name="488"><span class="lineNum">     488 </span>            : </a>
+<a name="489"><span class="lineNum">     489 </span><span class="lineCov">         36 : void VesLinearExpansion::resetBiasFileOutput() {</span></a>
+<a name="490"><span class="lineNum">     490 </span>            :   bias_expansion_pntr_-&gt;resetStepOfLastBiasGridUpdate();</a>
+<a name="491"><span class="lineNum">     491 </span><span class="lineCov">         36 : }</span></a>
+<a name="492"><span class="lineNum">     492 </span>            : </a>
+<a name="493"><span class="lineNum">     493 </span>            : </a>
+<a name="494"><span class="lineNum">     494 </span><span class="lineCov">         83 : void VesLinearExpansion::setupFesFileOutput() {</span></a>
+<a name="495"><span class="lineNum">     495 </span><span class="lineCov">         83 :   bias_expansion_pntr_-&gt;setupFesGrid();</span></a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">         83 : }</span></a>
+<a name="497"><span class="lineNum">     497 </span>            : </a>
+<a name="498"><span class="lineNum">     498 </span>            : </a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineCov">        169 : void VesLinearExpansion::writeFesToFile() {</span></a>
+<a name="500"><span class="lineNum">     500 </span><span class="lineCov">        169 :   bias_expansion_pntr_-&gt;updateFesGrid();</span></a>
+<a name="501"><span class="lineNum">     501 </span><span class="lineCov">        507 :   auto ofile_pntr = getOFile(getCurrentFesOutputFilename(),useMultipleWalkers());</span></a>
+<a name="502"><span class="lineNum">     502 </span><span class="lineCov">        169 :   bias_expansion_pntr_-&gt;writeFesGridToFile(*ofile_pntr);</span></a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">        169 : }</span></a>
+<a name="504"><span class="lineNum">     504 </span>            : </a>
+<a name="505"><span class="lineNum">     505 </span>            : </a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">         36 : void VesLinearExpansion::resetFesFileOutput() {</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :   bias_expansion_pntr_-&gt;resetStepOfLastFesGridUpdate();</a>
+<a name="508"><span class="lineNum">     508 </span><span class="lineCov">         36 : }</span></a>
+<a name="509"><span class="lineNum">     509 </span>            : </a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span><span class="lineCov">         17 : void VesLinearExpansion::setupFesProjFileOutput() {</span></a>
+<a name="512"><span class="lineNum">     512 </span><span class="lineCov">         17 :   if(getNumberOfProjectionArguments()&gt;0) {</span></a>
+<a name="513"><span class="lineNum">     513 </span><span class="lineCov">          8 :     bias_expansion_pntr_-&gt;setupFesProjGrid();</span></a>
+<a name="514"><span class="lineNum">     514 </span>            :   }</a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">         17 : }</span></a>
+<a name="516"><span class="lineNum">     516 </span>            : </a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span><span class="lineCov">         36 : void VesLinearExpansion::writeFesProjToFile() {</span></a>
+<a name="519"><span class="lineNum">     519 </span><span class="lineCov">         36 :   bias_expansion_pntr_-&gt;updateFesGrid();</span></a>
+<a name="520"><span class="lineNum">     520 </span><span class="lineCov">         72 :   for(unsigned int i=0; i&lt;getNumberOfProjectionArguments(); i++) {</span></a>
+<a name="521"><span class="lineNum">     521 </span>            :     std::string suffix;</a>
+<a name="522"><span class="lineNum">     522 </span><span class="lineCov">         36 :     Tools::convert(i+1,suffix);</span></a>
+<a name="523"><span class="lineNum">     523 </span><span class="lineCov">         36 :     suffix = &quot;proj-&quot; + suffix;</span></a>
+<a name="524"><span class="lineNum">     524 </span><span class="lineCov">         72 :     auto ofile_pntr = getOFile(getCurrentFesOutputFilename(suffix),useMultipleWalkers());</span></a>
+<a name="525"><span class="lineNum">     525 </span>            :     std::vector&lt;std::string&gt; args = getProjectionArgument(i);</a>
+<a name="526"><span class="lineNum">     526 </span><span class="lineCov">         36 :     bias_expansion_pntr_-&gt;writeFesProjGridToFile(args,*ofile_pntr);</span></a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">         36 :   }</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">         36 : }</span></a>
+<a name="529"><span class="lineNum">     529 </span>            : </a>
+<a name="530"><span class="lineNum">     530 </span>            : </a>
+<a name="531"><span class="lineNum">     531 </span><span class="lineCov">         82 : void VesLinearExpansion::writeTargetDistToFile() {</span></a>
+<a name="532"><span class="lineNum">     532 </span><span class="lineCov">        164 :   auto ofile1_pntr = getOFile(getCurrentTargetDistOutputFilename(),useMultipleWalkers());</span></a>
+<a name="533"><span class="lineNum">     533 </span><span class="lineCov">        164 :   auto ofile2_pntr = getOFile(getCurrentTargetDistOutputFilename(&quot;log&quot;),useMultipleWalkers());</span></a>
+<a name="534"><span class="lineNum">     534 </span><span class="lineCov">         82 :   bias_expansion_pntr_-&gt;writeTargetDistGridToFile(*ofile1_pntr);</span></a>
+<a name="535"><span class="lineNum">     535 </span><span class="lineCov">         82 :   bias_expansion_pntr_-&gt;writeLogTargetDistGridToFile(*ofile2_pntr);</span></a>
+<a name="536"><span class="lineNum">     536 </span><span class="lineCov">         82 : }</span></a>
+<a name="537"><span class="lineNum">     537 </span>            : </a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span><span class="lineCov">         13 : void VesLinearExpansion::writeTargetDistProjToFile() {</span></a>
+<a name="540"><span class="lineNum">     540 </span><span class="lineCov">         33 :   for(unsigned int i=0; i&lt;getNumberOfProjectionArguments(); i++) {</span></a>
+<a name="541"><span class="lineNum">     541 </span>            :     std::string suffix;</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">         20 :     Tools::convert(i+1,suffix);</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">         20 :     suffix = &quot;proj-&quot; + suffix;</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">         40 :     auto ofile_pntr = getOFile(getCurrentTargetDistOutputFilename(suffix),useMultipleWalkers());</span></a>
+<a name="545"><span class="lineNum">     545 </span>            :     std::vector&lt;std::string&gt; args = getProjectionArgument(i);</a>
+<a name="546"><span class="lineNum">     546 </span><span class="lineCov">         20 :     bias_expansion_pntr_-&gt;writeTargetDistProjGridToFile(args,*ofile_pntr);</span></a>
+<a name="547"><span class="lineNum">     547 </span><span class="lineCov">         20 :   }</span></a>
+<a name="548"><span class="lineNum">     548 </span><span class="lineCov">         13 : }</span></a>
+<a name="549"><span class="lineNum">     549 </span>            : </a>
+<a name="550"><span class="lineNum">     550 </span>            : </a>
+<a name="551"><span class="lineNum">     551 </span><span class="lineNoCov">          0 : double VesLinearExpansion::calculateReweightFactor() const {</span></a>
+<a name="552"><span class="lineNum">     552 </span><span class="lineNoCov">          0 :   return bias_expansion_pntr_-&gt;calculateReweightFactor();</span></a>
+<a name="553"><span class="lineNum">     553 </span>            : }</a>
+<a name="554"><span class="lineNum">     554 </span>            : </a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            : }</a>
+<a name="557"><span class="lineNum">     557 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesTools.cpp.func-sort-c.html b/coverage/ves/VesTools.cpp.func-sort-c.html
new file mode 100644
index 0000000000..643d90a338
--- /dev/null
+++ b/coverage/ves/VesTools.cpp.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesTools.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesTools.cpp<span style="font-size: 80%;"> (<a href="VesTools.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">92.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesTools.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.cpp.gcov.html#32">_ZN4PLMD3ves8VesTools14copyGridValuesEPNS_8GridBaseES3_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.cpp.gcov.html#45">_ZN4PLMD3ves8VesTools15getGridFileInfoERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS7_RSt6vectorIS7_SaIS7_EESE_SE_RSB_IbSaIbEERSB_IjSaIjEERb</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesTools.cpp.func.html b/coverage/ves/VesTools.cpp.func.html
new file mode 100644
index 0000000000..b8de36ce1c
--- /dev/null
+++ b/coverage/ves/VesTools.cpp.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesTools.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesTools.cpp<span style="font-size: 80%;"> (<a href="VesTools.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">92.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesTools.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.cpp.gcov.html#32">_ZN4PLMD3ves8VesTools14copyGridValuesEPNS_8GridBaseES3_</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.cpp.gcov.html#45">_ZN4PLMD3ves8VesTools15getGridFileInfoERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERS7_RSt6vectorIS7_SaIS7_EESE_SE_RSB_IbSaIbEERSB_IjSaIjEERb</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesTools.cpp.gcov.html b/coverage/ves/VesTools.cpp.gcov.html
new file mode 100644
index 0000000000..dada32eeb5
--- /dev/null
+++ b/coverage/ves/VesTools.cpp.gcov.html
@@ -0,0 +1,170 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesTools.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesTools.cpp<span style="font-size: 80%;"> (source / <a href="VesTools.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">35</td>
+            <td class="headerCovTableEntry">38</td>
+            <td class="headerCovTableEntryHi">92.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesTools.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/IFile.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace PLMD {</a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace ves {</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          8 : void VesTools::copyGridValues(GridBase* grid_pntr_orig, GridBase* grid_pntr_copy) {</span></a>
+<a name="35"><span class="lineNum">      35 </span>            :   // plumed_massert(grid_pntr_orig!=NULL,&quot;grid not defined&quot;);</a>
+<a name="36"><span class="lineNum">      36 </span>            :   // plumed_massert(grid_pntr_copy!=NULL,&quot;grid not defined&quot;);</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">          8 :   plumed_massert(grid_pntr_orig-&gt;getSize()==grid_pntr_copy-&gt;getSize(),&quot;the two grids are not of the same size&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">          8 :   plumed_massert(grid_pntr_orig-&gt;getDimension()==grid_pntr_copy-&gt;getDimension(),&quot;the two grids are not of the same dimension&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   //</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        808 :   for(Grid::index_t i=0; i&lt;grid_pntr_orig-&gt;getSize(); i++) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        800 :     double value = grid_pntr_orig-&gt;getValue(i);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        800 :     grid_pntr_copy-&gt;setValue(i,value);</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   }</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          8 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">          9 : unsigned int VesTools::getGridFileInfo(const std::string&amp; filepath, std::string&amp; grid_label, std::vector&lt;std::string&gt;&amp; arg_labels, std::vector&lt;std::string&gt;&amp; arg_min, std::vector&lt;std::string&gt;&amp; arg_max, std::vector&lt;bool&gt;&amp; arg_periodic, std::vector&lt;unsigned int&gt;&amp; arg_nbins, bool&amp; derivatives) {</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          9 :   IFile ifile; ifile.open(filepath);</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::vector&lt;std::string&gt; fields;</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          9 :   ifile.scanFieldList(fields);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">          9 :   ifile.allowIgnoredFields();</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          9 :   ifile.scanField();</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            :   unsigned int nargs=0;</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         31 :   for(unsigned int i=0; i&lt;fields.size(); i++) {</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         31 :     if(fields[i]==&quot;min_&quot;+fields[0]) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          9 :       derivatives = false;</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          9 :       nargs = i-1;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          9 :       break;</span></a>
+<a name="61"><span class="lineNum">      61 </span>            :     }</a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         22 :     else if(fields[i]==&quot;der_&quot;+fields[0]) {</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineNoCov">          0 :       derivatives = true;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 :       nargs = i-1;</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :       break;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :     }</a>
+<a name="67"><span class="lineNum">      67 </span>            :   }</a>
+<a name="68"><span class="lineNum">      68 </span>            : </a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          9 :   grid_label = fields[nargs];</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          9 :   arg_labels.assign(nargs,&quot;&quot;);</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          9 :   arg_min.assign(nargs,&quot;&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         18 :   arg_max.assign(nargs,&quot;&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :   arg_periodic.assign(nargs,false);</a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">          9 :   arg_nbins.assign(nargs,0);</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">         22 :   for(unsigned int i=0; i&lt;nargs; i++) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         13 :     arg_labels[i] = fields[i];</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         26 :     ifile.scanField(&quot;min_&quot;+arg_labels[i],arg_min[i]);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         26 :     ifile.scanField(&quot;max_&quot;+arg_labels[i],arg_max[i]);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :     std::string str_periodic;</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         26 :     ifile.scanField(&quot;periodic_&quot;+arg_labels[i],str_periodic);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         13 :     if(str_periodic==&quot;true&quot;) {arg_periodic[i]=true;}</span></a>
+<a name="83"><span class="lineNum">      83 </span>            :     int nbins;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         13 :     ifile.scanField(&quot;nbins_&quot;+arg_labels[i],nbins);</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         13 :     arg_nbins[i] = static_cast&lt;unsigned int&gt;(nbins);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          9 :   ifile.scanField();</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          9 :   ifile.close();</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">          9 :   return nargs;</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">          9 : }</span></a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : }</a>
+<a name="94"><span class="lineNum">      94 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesTools.h.func-sort-c.html b/coverage/ves/VesTools.h.func-sort-c.html
new file mode 100644
index 0000000000..7611a7993f
--- /dev/null
+++ b/coverage/ves/VesTools.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesTools.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesTools.h<span style="font-size: 80%;"> (<a href="VesTools.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryLo">65.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesTools.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#99">_ZN4PLMD3ves8VesTools21getPointersFromLabelsIPNS0_7VesBiasEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">82</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#99">_ZN4PLMD3ves8VesTools21getPointersFromLabelsIPNS0_14BasisFunctionsEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">163</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#56">_ZN4PLMD3ves8VesTools14convertDbl2StrEdRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj</a></td>
+              <td class="coverFnHi">167</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#90">_ZN4PLMD3ves8VesTools19getPointerFromLabelIPNS0_18TargetDistributionEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_9ActionSetERSB_</a></td>
+              <td class="coverFnHi">296</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#99">_ZN4PLMD3ves8VesTools21getPointersFromLabelsIPNS0_18TargetDistributionEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">417</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesTools.h.func.html b/coverage/ves/VesTools.h.func.html
new file mode 100644
index 0000000000..95a663f032
--- /dev/null
+++ b/coverage/ves/VesTools.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesTools.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesTools.h<span style="font-size: 80%;"> (<a href="VesTools.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryLo">65.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesTools.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#56">_ZN4PLMD3ves8VesTools14convertDbl2StrEdRNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEj</a></td>
+              <td class="coverFnHi">167</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#90">_ZN4PLMD3ves8VesTools19getPointerFromLabelIPNS0_18TargetDistributionEEET_RKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS_9ActionSetERSB_</a></td>
+              <td class="coverFnHi">296</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#99">_ZN4PLMD3ves8VesTools21getPointersFromLabelsIPNS0_14BasisFunctionsEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">163</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#99">_ZN4PLMD3ves8VesTools21getPointersFromLabelsIPNS0_18TargetDistributionEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">417</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesTools.h.gcov.html#99">_ZN4PLMD3ves8VesTools21getPointersFromLabelsIPNS0_7VesBiasEEESt6vectorIT_SaIS6_EERKS5_INSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESaISE_EERKNS_9ActionSetERSE_</a></td>
+              <td class="coverFnHi">82</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/VesTools.h.gcov.html b/coverage/ves/VesTools.h.gcov.html
new file mode 100644
index 0000000000..ecd7ce4646
--- /dev/null
+++ b/coverage/ves/VesTools.h.gcov.html
@@ -0,0 +1,216 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/VesTools.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - VesTools.h<span style="font-size: 80%;"> (source / <a href="VesTools.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryLo">65.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_ves_VesTools_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_ves_VesTools_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;sstream&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;iomanip&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;limits&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;vector&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class GridBase;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace ves {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : class VesTools {</a>
+<a name="41"><span class="lineNum">      41 </span>            : public:</a>
+<a name="42"><span class="lineNum">      42 </span>            :   // Convert double into a string with more digits</a>
+<a name="43"><span class="lineNum">      43 </span>            :   static void convertDbl2Str(const double value,std::string&amp; str, unsigned int precision);</a>
+<a name="44"><span class="lineNum">      44 </span>            :   static void convertDbl2Str(const double value,std::string&amp; str);</a>
+<a name="45"><span class="lineNum">      45 </span>            :   // get log2 of unsigned int</a>
+<a name="46"><span class="lineNum">      46 </span>            :   static unsigned int log2(unsigned value);</a>
+<a name="47"><span class="lineNum">      47 </span>            :   // copy grid values</a>
+<a name="48"><span class="lineNum">      48 </span>            :   static void copyGridValues(GridBase* grid_pntr_orig, GridBase* grid_pntr_copy);</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static unsigned int getGridFileInfo(const std::string&amp;, std::string&amp;, std::vector&lt;std::string&gt;&amp;, std::vector&lt;std::string&gt;&amp;, std::vector&lt;std::string&gt;&amp;, std::vector&lt;bool&gt;&amp;, std::vector&lt;unsigned int&gt;&amp;, bool&amp;);</a>
+<a name="50"><span class="lineNum">      50 </span>            :   //</a>
+<a name="51"><span class="lineNum">      51 </span>            :   template&lt;typename T&gt; static std::vector&lt;std::string&gt; getLabelsOfAvailableActions(const ActionSet&amp;);</a>
+<a name="52"><span class="lineNum">      52 </span>            :   template&lt;typename T&gt; static T getPointerFromLabel(const std::string&amp;, const ActionSet&amp;, std::string&amp;);</a>
+<a name="53"><span class="lineNum">      53 </span>            :   template&lt;typename T&gt; static std::vector&lt;T&gt; getPointersFromLabels(const std::vector&lt;std::string&gt;&amp;, const ActionSet&amp;, std::string&amp;);</a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span>            : };</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : inline</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        167 : void VesTools::convertDbl2Str(const double value,std::string&amp; str, unsigned int precision) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        167 :   std::ostringstream ostr;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        167 :   ostr&lt;&lt;std::setprecision(precision)&lt;&lt;value;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        167 :   str=ostr.str();</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        167 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : inline</a>
+<a name="66"><span class="lineNum">      66 </span>            : void VesTools::convertDbl2Str(const double value,std::string&amp; str) {</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned int precision = std::numeric_limits&lt;double&gt;::digits10 + 1;</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         88 :   convertDbl2Str(value,str,precision);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          9 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : inline</a>
+<a name="73"><span class="lineNum">      73 </span>            : unsigned int log2(unsigned value) {</a>
+<a name="74"><span class="lineNum">      74 </span>            :   unsigned int result = 0;</a>
+<a name="75"><span class="lineNum">      75 </span>            :   while(value &gt;&gt;= 1) result++;</a>
+<a name="76"><span class="lineNum">      76 </span>            :   return result;</a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : template&lt;typename T&gt;</a>
+<a name="81"><span class="lineNum">      81 </span>            : std::vector&lt;std::string&gt; VesTools::getLabelsOfAvailableActions(const ActionSet&amp; actionset) {</a>
+<a name="82"><span class="lineNum">      82 </span>            :   std::vector&lt;std::string&gt; avail_action_str(0);</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;T&gt; avail_action_pntrs = actionset.select&lt;T&gt;();</a>
+<a name="84"><span class="lineNum">      84 </span>            :   for(unsigned int i=0; i&lt;avail_action_pntrs.size(); i++) {</a>
+<a name="85"><span class="lineNum">      85 </span>            :     avail_action_str.push_back(avail_action_pntrs[i]-&gt;getLabel());</a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span>            :   return avail_action_str;</a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : template&lt;typename T&gt;</a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        296 : T VesTools::getPointerFromLabel(const std::string&amp; action_label, const ActionSet&amp; actionset, std::string&amp; error_msg) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        296 :   std::vector&lt;std::string&gt; action_labels(1);</span></a>
+<a name="94"><span class="lineNum">      94 </span>            :   action_labels[0] = action_label;</a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        296 :   std::vector&lt;T&gt; action_pntrs = getPointersFromLabels&lt;T&gt;(action_labels,actionset,error_msg);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">        592 :   return action_pntrs[0];</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        296 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : </a>
+<a name="100"><span class="lineNum">     100 </span>            : template&lt;typename T&gt;</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        662 : std::vector&lt;T&gt; VesTools::getPointersFromLabels(const std::vector&lt;std::string&gt;&amp; action_labels, const ActionSet&amp; actionset, std::string&amp; error_msg) {</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        662 :   std::vector&lt;T&gt; action_pntrs(action_labels.size(),NULL);</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   error_msg = &quot;&quot;;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        662 :   std::vector&lt;std::string&gt; missing(0);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       1350 :   for(unsigned int i=0; i&lt;action_labels.size(); i++) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">        688 :     action_pntrs[i] = actionset.selectWithLabel&lt;T&gt;(action_labels[i]);</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        688 :     if(action_pntrs[i]==NULL) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineNoCov">          0 :       missing.push_back(action_labels[i]);</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :     }</a>
+<a name="110"><span class="lineNum">     110 </span>            :   }</a>
+<a name="111"><span class="lineNum">     111 </span>            :   // error handling</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        662 :   if(missing.size()&gt;0) {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineNoCov">          0 :     if(missing.size()==1) {</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineNoCov">          0 :       error_msg = &quot;label &quot;+missing[0]+&quot; does not exist\n&quot;;</span></a>
+<a name="115"><span class="lineNum">     115 </span>            :     }</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineNoCov">          0 :     else if(missing.size()&gt;1) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineNoCov">          0 :       std::string tmp=&quot;&quot;;</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :       for(unsigned int j=0; j&lt;missing.size(); j++) {tmp +=missing[j]+&quot; &quot;;}</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineNoCov">          0 :       error_msg = &quot;labels &quot;+tmp+&quot;do not exist\n&quot;;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            :     }</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineNoCov">          0 :     std::vector&lt;T&gt; avail_action_pntrs = actionset.select&lt;T&gt;();</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineNoCov">          0 :     if(avail_action_pntrs.size()&gt;0) {</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :       error_msg += &quot;             Hint! the actions defined in the input file that can be used here are: \n&quot;;</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :       for(unsigned int i=0; i&lt;avail_action_pntrs.size(); i++) {</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineNoCov">          0 :         error_msg += &quot;             &quot; + avail_action_pntrs[i]-&gt;getName() + &quot; with label &quot; + avail_action_pntrs[i]-&gt;getLabel() + &quot;\n&quot;;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            :       }</a>
+<a name="127"><span class="lineNum">     127 </span>            :     }</a>
+<a name="128"><span class="lineNum">     128 </span>            :     else {</a>
+<a name="129"><span class="lineNum">     129 </span>            :       error_msg += &quot;             Hint! no actions defined in the input file that can be used here, they should be defined before this actions\n&quot;;</a>
+<a name="130"><span class="lineNum">     130 </span>            :     }</a>
+<a name="131"><span class="lineNum">     131 </span>            :   }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        662 :   return action_pntrs;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        662 : }</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : }</a>
+<a name="138"><span class="lineNum">     138 </span>            : }</a>
+<a name="139"><span class="lineNum">     139 </span>            : </a>
+<a name="140"><span class="lineNum">     140 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/WaveletCoeffs.cpp.func-sort-c.html b/coverage/ves/WaveletCoeffs.cpp.func-sort-c.html
new file mode 100644
index 0000000000..fb2d5e6b5a
--- /dev/null
+++ b/coverage/ves/WaveletCoeffs.cpp.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/WaveletCoeffs.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - WaveletCoeffs.cpp<span style="font-size: 80%;"> (<a href="WaveletCoeffs.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntry">150</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WaveletCoeffs.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletCoeffs.cpp.gcov.html#33">_ZN4PLMD3ves11WaveletGrid21getFilterCoefficientsEjbNS1_4TypeE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/WaveletCoeffs.cpp.func.html b/coverage/ves/WaveletCoeffs.cpp.func.html
new file mode 100644
index 0000000000..97d57961e4
--- /dev/null
+++ b/coverage/ves/WaveletCoeffs.cpp.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/WaveletCoeffs.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - WaveletCoeffs.cpp<span style="font-size: 80%;"> (<a href="WaveletCoeffs.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntry">150</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WaveletCoeffs.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletCoeffs.cpp.gcov.html#33">_ZN4PLMD3ves11WaveletGrid21getFilterCoefficientsEjbNS1_4TypeE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/WaveletCoeffs.cpp.gcov.html b/coverage/ves/WaveletCoeffs.cpp.gcov.html
new file mode 100644
index 0000000000..1e1dee6922
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+++ b/coverage/ves/WaveletCoeffs.cpp.gcov.html
@@ -0,0 +1,1058 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/WaveletCoeffs.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - WaveletCoeffs.cpp<span style="font-size: 80%;"> (source / <a href="WaveletCoeffs.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">145</td>
+            <td class="headerCovTableEntry">150</td>
+            <td class="headerCovTableEntryHi">96.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;WaveletGrid.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;algorithm&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace ves {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : // returns the filter coefficients, at the moment simply a lookup table (calculated with python script)</a>
+<a name="33"><span class="lineNum">      33 </span>            : // the coefficients are normalized such that their sum equals 2</a>
+<a name="34"><span class="lineNum">      34 </span>            : // lowpass coefficients are for the scaling function, highpass for the actual wavelets</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         49 : std::vector&lt;double&gt; WaveletGrid::getFilterCoefficients(const unsigned order, const bool lowpass, const Type type) {</span></a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::vector&lt;double&gt; h;</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         49 :   if (type == Type::db) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         24 :     switch(order) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          1 :     case 4:</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          2 :       h = { 3.2580342805129858252399799312116e-01,</span></a>
+<a name="41"><span class="lineNum">      41 </span>            :             1.0109457150918295109676137144561e+00,</a>
+<a name="42"><span class="lineNum">      42 </span>            :             8.9220013824675992175627925462322e-01,</a>
+<a name="43"><span class="lineNum">      43 </span>            :             -3.9575026235645245631378230655173e-02,</a>
+<a name="44"><span class="lineNum">      44 </span>            :             -2.6450716736904000825347793579567e-01,</a>
+<a name="45"><span class="lineNum">      45 </span>            :             4.3616300474177409352005696518972e-02,</a>
+<a name="46"><span class="lineNum">      46 </span>            :             4.6503601070981823162320267783798e-02,</a>
+<a name="47"><span class="lineNum">      47 </span>            :             -1.4986989330361497746446630685568e-02</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          1 :           };</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">          1 :     case 5:</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          2 :       h = { 2.2641898258355833140065271891217e-01,</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :             8.5394354270502825787758638398373e-01,</a>
+<a name="53"><span class="lineNum">      53 </span>            :             1.0243269442591973472644895082340e+00,</a>
+<a name="54"><span class="lineNum">      54 </span>            :             1.9576696134780988134416190860065e-01,</a>
+<a name="55"><span class="lineNum">      55 </span>            :             -3.4265671538293490661075679781788e-01,</a>
+<a name="56"><span class="lineNum">      56 </span>            :             -4.5601131883547744994000794349631e-02,</a>
+<a name="57"><span class="lineNum">      57 </span>            :             1.0970265864213350759381881971422e-01,</a>
+<a name="58"><span class="lineNum">      58 </span>            :             -8.8268001083581463378502363070766e-03,</a>
+<a name="59"><span class="lineNum">      59 </span>            :             -1.7791870101954165156454834573196e-02,</a>
+<a name="60"><span class="lineNum">      60 </span>            :             4.7174279390678596629582486343679e-03</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          1 :           };</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :     case 6:</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :       h = { 1.5774243200290161137644417976844e-01,</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :             6.9950381407523654075930608087219e-01,</a>
+<a name="66"><span class="lineNum">      66 </span>            :             1.0622637598817388226990487964940e+00,</a>
+<a name="67"><span class="lineNum">      67 </span>            :             4.4583132293003513435536433462403e-01,</a>
+<a name="68"><span class="lineNum">      68 </span>            :             -3.1998659889212388574009082731209e-01,</a>
+<a name="69"><span class="lineNum">      69 </span>            :             -1.8351806406029547158453851807280e-01,</a>
+<a name="70"><span class="lineNum">      70 </span>            :             1.3788809297474488579915430364053e-01,</a>
+<a name="71"><span class="lineNum">      71 </span>            :             3.8923209708329416234295905496765e-02,</a>
+<a name="72"><span class="lineNum">      72 </span>            :             -4.4663748330189156909852954413509e-02,</a>
+<a name="73"><span class="lineNum">      73 </span>            :             7.8325115229715134342741711392932e-04,</a>
+<a name="74"><span class="lineNum">      74 </span>            :             6.7560623629278858393032436424619e-03,</a>
+<a name="75"><span class="lineNum">      75 </span>            :             -1.5235338056025088393496957905882e-03</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          2 :           };</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          2 :       break;</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          1 :     case 7:</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">          2 :       h = { 1.1009943074562379694558700293783e-01,</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :             5.6079128362552554953879280219553e-01,</a>
+<a name="81"><span class="lineNum">      81 </span>            :             1.0311484916361983721344586228952e+00,</a>
+<a name="82"><span class="lineNum">      82 </span>            :             6.6437248221107991774658785288921e-01,</a>
+<a name="83"><span class="lineNum">      83 </span>            :             -2.0351382246269289488793674536282e-01,</a>
+<a name="84"><span class="lineNum">      84 </span>            :             -3.1683501128066671181926494682557e-01,</a>
+<a name="85"><span class="lineNum">      85 </span>            :             1.0084646500938766744415175935501e-01,</a>
+<a name="86"><span class="lineNum">      86 </span>            :             1.1400344515974307479933003151018e-01,</a>
+<a name="87"><span class="lineNum">      87 </span>            :             -5.3782452589690873945293958513503e-02,</a>
+<a name="88"><span class="lineNum">      88 </span>            :             -2.3439941564206586560592526780056e-02,</a>
+<a name="89"><span class="lineNum">      89 </span>            :             1.7749792379361528649184265304939e-02,</a>
+<a name="90"><span class="lineNum">      90 </span>            :             6.0751499540213742267535934615807e-04,</a>
+<a name="91"><span class="lineNum">      91 </span>            :             -2.5479047181873734281842835969201e-03,</a>
+<a name="92"><span class="lineNum">      92 </span>            :             5.0022685312249071977463987792589e-04</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          1 :           };</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">          2 :     case 8:</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">          4 :       h = { 7.6955622108152516025469935811998e-02,</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :             4.4246724715225010937658112197823e-01,</a>
+<a name="98"><span class="lineNum">      98 </span>            :             9.5548615042774787120549717656104e-01,</a>
+<a name="99"><span class="lineNum">      99 </span>            :             8.2781653242239250367617842130130e-01,</a>
+<a name="100"><span class="lineNum">     100 </span>            :             -2.2385735333760647947087818465661e-02,</a>
+<a name="101"><span class="lineNum">     101 </span>            :             -4.0165863278097890809448244908708e-01,</a>
+<a name="102"><span class="lineNum">     102 </span>            :             6.6819409243975983261898399234724e-04,</a>
+<a name="103"><span class="lineNum">     103 </span>            :             1.8207635684731554581716750362830e-01,</a>
+<a name="104"><span class="lineNum">     104 </span>            :             -2.4563901045696636543658186724315e-02,</a>
+<a name="105"><span class="lineNum">     105 </span>            :             -6.2350206650278829079159237380736e-02,</a>
+<a name="106"><span class="lineNum">     106 </span>            :             1.9772159296701483782721098236834e-02,</a>
+<a name="107"><span class="lineNum">     107 </span>            :             1.2368844819631834991424668146465e-02,</a>
+<a name="108"><span class="lineNum">     108 </span>            :             -6.8877192568836120845077175545157e-03,</a>
+<a name="109"><span class="lineNum">     109 </span>            :             -5.5400454895877760883027285387925e-04,</a>
+<a name="110"><span class="lineNum">     110 </span>            :             9.5522971129925185115872032781681e-04,</a>
+<a name="111"><span class="lineNum">     111 </span>            :             -1.6613726137322542978150274883831e-04</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :           };</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          2 :       break;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          1 :     case 9:</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :       h = { 5.3850349589325587074117862584899e-02,</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :             3.4483430381395580033299097522104e-01,</a>
+<a name="117"><span class="lineNum">     117 </span>            :             8.5534906435941493452190798052470e-01,</a>
+<a name="118"><span class="lineNum">     118 </span>            :             9.2954571436629451763877796111046e-01,</a>
+<a name="119"><span class="lineNum">     119 </span>            :             1.8836954950636755623527562875097e-01,</a>
+<a name="120"><span class="lineNum">     120 </span>            :             -4.1475176180187667274168461517547e-01,</a>
+<a name="121"><span class="lineNum">     121 </span>            :             -1.3695354902476589153970110146474e-01,</a>
+<a name="122"><span class="lineNum">     122 </span>            :             2.1006834227901241551883515512600e-01,</a>
+<a name="123"><span class="lineNum">     123 </span>            :             4.3452675461228981723671438430756e-02,</a>
+<a name="124"><span class="lineNum">     124 </span>            :             -9.5647264120193975500683336576913e-02,</a>
+<a name="125"><span class="lineNum">     125 </span>            :             3.5489281323312395211022618468633e-04,</a>
+<a name="126"><span class="lineNum">     126 </span>            :             3.1624165852511730567808712066835e-02,</a>
+<a name="127"><span class="lineNum">     127 </span>            :             -6.6796202262771747770742081229400e-03,</a>
+<a name="128"><span class="lineNum">     128 </span>            :             -6.0549605750901376935435571624566e-03,</a>
+<a name="129"><span class="lineNum">     129 </span>            :             2.6129672804944947123173548675368e-03,</a>
+<a name="130"><span class="lineNum">     130 </span>            :             3.2581467135218489857700907563753e-04,</a>
+<a name="131"><span class="lineNum">     131 </span>            :             -3.5632975902155574095264700673624e-04,</a>
+<a name="132"><span class="lineNum">     132 </span>            :             5.5645514034309739761618301967516e-05</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">          1 :           };</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">          4 :     case 10:</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">          8 :       h = { 3.7717157592241430663637657971776e-02,</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :             2.6612218279384214358884719331400e-01,</a>
+<a name="138"><span class="lineNum">     138 </span>            :             7.4557507148646740002817523418344e-01,</a>
+<a name="139"><span class="lineNum">     139 </span>            :             9.7362811073364052827372461251798e-01,</a>
+<a name="140"><span class="lineNum">     140 </span>            :             3.9763774176901656165483700533514e-01,</a>
+<a name="141"><span class="lineNum">     141 </span>            :             -3.5333620179411384665257855886011e-01,</a>
+<a name="142"><span class="lineNum">     142 </span>            :             -2.7710987872096615181050083265291e-01,</a>
+<a name="143"><span class="lineNum">     143 </span>            :             1.8012744853339432427041799655854e-01,</a>
+<a name="144"><span class="lineNum">     144 </span>            :             1.3160298710107026787241579768306e-01,</a>
+<a name="145"><span class="lineNum">     145 </span>            :             -1.0096657119677993064144061463594e-01,</a>
+<a name="146"><span class="lineNum">     146 </span>            :             -4.1659248087601748189445771686223e-02,</a>
+<a name="147"><span class="lineNum">     147 </span>            :             4.6969814097397283303436665846675e-02,</a>
+<a name="148"><span class="lineNum">     148 </span>            :             5.1004369678145037442229536850391e-03,</a>
+<a name="149"><span class="lineNum">     149 </span>            :             -1.5179002335856551370030231851160e-02,</a>
+<a name="150"><span class="lineNum">     150 </span>            :             1.9733253649632047886652852497491e-03,</a>
+<a name="151"><span class="lineNum">     151 </span>            :             2.8176865901946854600645941957282e-03,</a>
+<a name="152"><span class="lineNum">     152 </span>            :             -9.6994783985641268905103506980936e-04,</a>
+<a name="153"><span class="lineNum">     153 </span>            :             -1.6470900609077862271692471729523e-04,</a>
+<a name="154"><span class="lineNum">     154 </span>            :             1.3235436685110702815550143274237e-04,</a>
+<a name="155"><span class="lineNum">     155 </span>            :             -1.8758415627500432871534175038875e-05</a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          4 :           };</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">          4 :       break;</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">          1 :     case 11:</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">          2 :       h = { 2.6437729433313437304997606247525e-02,</span></a>
+<a name="160"><span class="lineNum">     160 </span>            :             2.0374153520190504962350530604454e-01,</a>
+<a name="161"><span class="lineNum">     161 </span>            :             6.3625434846077988382262446975801e-01,</a>
+<a name="162"><span class="lineNum">     162 </span>            :             9.6970753662635966740879212011350e-01,</a>
+<a name="163"><span class="lineNum">     163 </span>            :             5.8260559778060438951285959774395e-01,</a>
+<a name="164"><span class="lineNum">     164 </span>            :             -2.2949185235529601101234220550396e-01,</a>
+<a name="165"><span class="lineNum">     165 </span>            :             -3.8782098279100135629349210830696e-01,</a>
+<a name="166"><span class="lineNum">     166 </span>            :             9.3399738135533413863065277382702e-02,</a>
+<a name="167"><span class="lineNum">     167 </span>            :             2.1186617983636121809176700026001e-01,</a>
+<a name="168"><span class="lineNum">     168 </span>            :             -6.5732582904507175225461423906381e-02,</a>
+<a name="169"><span class="lineNum">     169 </span>            :             -9.3958631797504951754795854412805e-02,</a>
+<a name="170"><span class="lineNum">     170 </span>            :             4.4314509565959142589619546015456e-02,</a>
+<a name="171"><span class="lineNum">     171 </span>            :             2.9473489598288812874038455902337e-02,</a>
+<a name="172"><span class="lineNum">     172 </span>            :             -2.1729138108983869076551442844902e-02,</a>
+<a name="173"><span class="lineNum">     173 </span>            :             -4.7246879281915600545804778676029e-03,</a>
+<a name="174"><span class="lineNum">     174 </span>            :             6.9698350902376990032016657039549e-03,</a>
+<a name="175"><span class="lineNum">     175 </span>            :             -4.3641620618785245374129933004781e-04,</a>
+<a name="176"><span class="lineNum">     176 </span>            :             -1.2629255926067382322097731872645e-03,</a>
+<a name="177"><span class="lineNum">     177 </span>            :             3.5235487790788363191354926051702e-04,</a>
+<a name="178"><span class="lineNum">     178 </span>            :             7.6988477762888945306503363230632e-05,</a>
+<a name="179"><span class="lineNum">     179 </span>            :             -4.8981264369811758688493669167130e-05,</a>
+<a name="180"><span class="lineNum">     180 </span>            :             6.3558636358923973935959594872003e-06</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">          1 :           };</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">          3 :     case 12:</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          6 :       h = { 1.8543533036448515277649917720737e-02,</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :             1.5495010900239064577377234854794e-01,</a>
+<a name="186"><span class="lineNum">     186 </span>            :             5.3366075005107249662472668205737e-01,</a>
+<a name="187"><span class="lineNum">     187 </span>            :             9.2941934664592906756297452375293e-01,</a>
+<a name="188"><span class="lineNum">     188 </span>            :             7.2957365443751254208137879686547e-01,</a>
+<a name="189"><span class="lineNum">     189 </span>            :             -6.3305694196084630331888831733522e-02,</a>
+<a name="190"><span class="lineNum">     190 </span>            :             -4.4714385742734169548739942001703e-01,</a>
+<a name="191"><span class="lineNum">     191 </span>            :             -3.3628948114692740201103760000478e-02,</a>
+<a name="192"><span class="lineNum">     192 </span>            :             2.5806371934571636916899706193362e-01,</a>
+<a name="193"><span class="lineNum">     193 </span>            :             7.5795761219506355491071225571886e-03,</a>
+<a name="194"><span class="lineNum">     194 </span>            :             -1.3637561208887127861544286133721e-01,</a>
+<a name="195"><span class="lineNum">     195 </span>            :             1.5342987147736677697174023649040e-02,</a>
+<a name="196"><span class="lineNum">     196 </span>            :             5.8755309099664532190843146963743e-02,</a>
+<a name="197"><span class="lineNum">     197 </span>            :             -1.7279779228315594180598324669518e-02,</a>
+<a name="198"><span class="lineNum">     198 </span>            :             -1.8159669147498957303410449526382e-02,</a>
+<a name="199"><span class="lineNum">     199 </span>            :             9.4914929220922782115987814677283e-03,</a>
+<a name="200"><span class="lineNum">     200 </span>            :             3.1800108566658129814752609121342e-03,</a>
+<a name="201"><span class="lineNum">     201 </span>            :             -3.0822835767046288281412191878417e-03,</a>
+<a name="202"><span class="lineNum">     202 </span>            :             9.2562090856036967085468392113512e-06,</a>
+<a name="203"><span class="lineNum">     203 </span>            :             5.4963843249920504071409643742641e-04,</a>
+<a name="204"><span class="lineNum">     204 </span>            :             -1.2516371156799253796382265235820e-04,</a>
+<a name="205"><span class="lineNum">     205 </span>            :             -3.4282722782480915088738904206167e-05,</a>
+<a name="206"><span class="lineNum">     206 </span>            :             1.8069339114439924513354912560814e-05,</a>
+<a name="207"><span class="lineNum">     207 </span>            :             -2.1624340181021667700003892342853e-06</a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">          3 :           };</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">          3 :       break;</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">          1 :     case 13:</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">          2 :       h = { 1.3013782053568881749705532513417e-02,</span></a>
+<a name="212"><span class="lineNum">     212 </span>            :             1.1718349488016345516516736324775e-01,</a>
+<a name="213"><span class="lineNum">     213 </span>            :             4.4122943020981653106105113693047e-01,</a>
+<a name="214"><span class="lineNum">     214 </span>            :             8.6416347207619259584987503330922e-01,</a>
+<a name="215"><span class="lineNum">     215 </span>            :             8.3281561724389663314838117003092e-01,</a>
+<a name="216"><span class="lineNum">     216 </span>            :             1.2301639369613130703395853515758e-01,</a>
+<a name="217"><span class="lineNum">     217 </span>            :             -4.4543895786553527882389857950329e-01,</a>
+<a name="218"><span class="lineNum">     218 </span>            :             -1.7617810218390753118633540452720e-01,</a>
+<a name="219"><span class="lineNum">     219 </span>            :             2.5381750565052108026264932050253e-01,</a>
+<a name="220"><span class="lineNum">     220 </span>            :             1.0316537133807110460104183857766e-01,</a>
+<a name="221"><span class="lineNum">     221 </span>            :             -1.4963456864376814547945571121090e-01,</a>
+<a name="222"><span class="lineNum">     222 </span>            :             -3.7460263683081813923525515974688e-02,</a>
+<a name="223"><span class="lineNum">     223 </span>            :             7.9393209899753916514164586715196e-02,</a>
+<a name="224"><span class="lineNum">     224 </span>            :             3.3657890397617833827537126012430e-03,</a>
+<a name="225"><span class="lineNum">     225 </span>            :             -3.3702718379158690120700470060910e-02,</a>
+<a name="226"><span class="lineNum">     226 </span>            :             5.5492912148471726374587831287499e-03,</a>
+<a name="227"><span class="lineNum">     227 </span>            :             1.0260952934778005268823264373168e-02,</a>
+<a name="228"><span class="lineNum">     228 </span>            :             -3.9059323261223279077913872470162e-03,</a>
+<a name="229"><span class="lineNum">     229 </span>            :             -1.8606438898585472407204433054062e-03,</a>
+<a name="230"><span class="lineNum">     230 </span>            :             1.3185082588273093311126427096269e-03,</a>
+<a name="231"><span class="lineNum">     231 </span>            :             6.9652174801158197692090012775878e-05,</a>
+<a name="232"><span class="lineNum">     232 </span>            :             -2.3352765515756047508440229609761e-04,</a>
+<a name="233"><span class="lineNum">     233 </span>            :             4.3386003918454429126392440929649e-05,</a>
+<a name="234"><span class="lineNum">     234 </span>            :             1.4767119831443566670332347146033e-05,</a>
+<a name="235"><span class="lineNum">     235 </span>            :             -6.6473927339140924229086634933417e-06,</a>
+<a name="236"><span class="lineNum">     236 </span>            :             7.3822444322983881586676402353220e-07</a>
+<a name="237"><span class="lineNum">     237 </span><span class="lineCov">          1 :           };</span></a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">          1 :     case 14:</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">          2 :       h = { 9.1374508518302227644269919437647e-03,</span></a>
+<a name="241"><span class="lineNum">     241 </span>            :             8.8197087778947372282978278690280e-02,</a>
+<a name="242"><span class="lineNum">     242 </span>            :             3.6041270508674011496808020638127e-01,</a>
+<a name="243"><span class="lineNum">     243 </span>            :             7.8390652259161064385750705696410e-01,</a>
+<a name="244"><span class="lineNum">     244 </span>            :             8.9263441660919018438846705976175e-01,</a>
+<a name="245"><span class="lineNum">     245 </span>            :             3.0924705232209759309114360803505e-01,</a>
+<a name="246"><span class="lineNum">     246 </span>            :             -3.8422563537411602574422886391403e-01,</a>
+<a name="247"><span class="lineNum">     247 </span>            :             -3.0834597516857004118051577279402e-01,</a>
+<a name="248"><span class="lineNum">     248 </span>            :             1.9572038841513531015614546504366e-01,</a>
+<a name="249"><span class="lineNum">     249 </span>            :             1.9797436583701560897097238012066e-01,</a>
+<a name="250"><span class="lineNum">     250 </span>            :             -1.2268078015402955616153235496313e-01,</a>
+<a name="251"><span class="lineNum">     251 </span>            :             -1.0118550324745094470824113841445e-01,</a>
+<a name="252"><span class="lineNum">     252 </span>            :             7.8117093102298987283838016537629e-02,</a>
+<a name="253"><span class="lineNum">     253 </span>            :             3.8157473560976581938852802977635e-02,</a>
+<a name="254"><span class="lineNum">     254 </span>            :             -4.2688533533420329468821563523306e-02,</a>
+<a name="255"><span class="lineNum">     255 </span>            :             -7.9408791992275871984841018047518e-03,</a>
+<a name="256"><span class="lineNum">     256 </span>            :             1.8087074833128147927086004642661e-02,</a>
+<a name="257"><span class="lineNum">     257 </span>            :             -1.0553130151236629532401911646389e-03,</a>
+<a name="258"><span class="lineNum">     258 </span>            :             -5.4442114973955908763247890647108e-03,</a>
+<a name="259"><span class="lineNum">     259 </span>            :             1.5014579323156973956338022802015e-03,</a>
+<a name="260"><span class="lineNum">     260 </span>            :             1.0012931187669377956078742286650e-03,</a>
+<a name="261"><span class="lineNum">     261 </span>            :             -5.4706298624917549557056251074982e-04,</a>
+<a name="262"><span class="lineNum">     262 </span>            :             -5.9081947567055248949751539155884e-05,</a>
+<a name="263"><span class="lineNum">     263 </span>            :             9.7234313623187232453887185457120e-05,</a>
+<a name="264"><span class="lineNum">     264 </span>            :             -1.4619021425907697688093174470669e-05,</a>
+<a name="265"><span class="lineNum">     265 </span>            :             -6.2079802069149134127572231545145e-06,</a>
+<a name="266"><span class="lineNum">     266 </span>            :             2.4395108649265364349071390920320e-06,</a>
+<a name="267"><span class="lineNum">     267 </span>            :             -2.5273975810449469030721054638167e-07</a>
+<a name="268"><span class="lineNum">     268 </span><span class="lineCov">          1 :           };</span></a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">          1 :     case 15:</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">          2 :       h = { 6.4184610900818745565787892815024e-03,</span></a>
+<a name="272"><span class="lineNum">     272 </span>            :             6.6105143008711259033916007865628e-02,</a>
+<a name="273"><span class="lineNum">     273 </span>            :             2.9136174262291886227771442463563e-01,</a>
+<a name="274"><span class="lineNum">     274 </span>            :             6.9668653280553660689378148163087e-01,</a>
+<a name="275"><span class="lineNum">     275 </span>            :             9.1331770185222738156483046623180e-01,</a>
+<a name="276"><span class="lineNum">     276 </span>            :             4.7942198331894603224867523749708e-01,</a>
+<a name="277"><span class="lineNum">     277 </span>            :             -2.7323191454187872873049514055310e-01,</a>
+<a name="278"><span class="lineNum">     278 </span>            :             -4.0854168599855755772409793280531e-01,</a>
+<a name="279"><span class="lineNum">     279 </span>            :             9.2324037310499082464865239217033e-02,</a>
+<a name="280"><span class="lineNum">     280 </span>            :             2.6890806178955328764601517832489e-01,</a>
+<a name="281"><span class="lineNum">     281 </span>            :             -5.6096444852683710613483469842322e-02,</a>
+<a name="282"><span class="lineNum">     282 </span>            :             -1.5714873480744581679680038632796e-01,</a>
+<a name="283"><span class="lineNum">     283 </span>            :             4.7909516391089444764528337827869e-02,</a>
+<a name="284"><span class="lineNum">     284 </span>            :             7.7471397590875790140074741429999e-02,</a>
+<a name="285"><span class="lineNum">     285 </span>            :             -3.6440051225646634402988155443381e-02,</a>
+<a name="286"><span class="lineNum">     286 </span>            :             -2.9429855183644534899478628631186e-02,</a>
+<a name="287"><span class="lineNum">     287 </span>            :             2.1331881448689315322608806013704e-02,</a>
+<a name="288"><span class="lineNum">     288 </span>            :             7.2139038913583038159504923214627e-03,</a>
+<a name="289"><span class="lineNum">     289 </span>            :             -9.1750422042750877371641848867512e-03,</a>
+<a name="290"><span class="lineNum">     290 </span>            :             -3.4189530802674857664497087839095e-04,</a>
+<a name="291"><span class="lineNum">     291 </span>            :             2.7482751291413886653158815676079e-03,</a>
+<a name="292"><span class="lineNum">     292 </span>            :             -5.2818381052845782188537304691067e-04,</a>
+<a name="293"><span class="lineNum">     293 </span>            :             -5.0850204513539821755269132452781e-04,</a>
+<a name="294"><span class="lineNum">     294 </span>            :             2.2047093037207382386355458692151e-04,</a>
+<a name="295"><span class="lineNum">     295 </span>            :             3.6476384955660787364189329151642e-05,</a>
+<a name="296"><span class="lineNum">     296 </span>            :             -3.9786489133705268018015993591874e-05,</a>
+<a name="297"><span class="lineNum">     297 </span>            :             4.7559820825002058672348846657396e-06,</a>
+<a name="298"><span class="lineNum">     298 </span>            :             2.5615231760346128998698331941108e-06,</a>
+<a name="299"><span class="lineNum">     299 </span>            :             -8.9334206571767810297517772161191e-07,</a>
+<a name="300"><span class="lineNum">     300 </span>            :             8.6738807723125058175416435962690e-08</a>
+<a name="301"><span class="lineNum">     301 </span><span class="lineCov">          1 :           };</span></a>
+<a name="302"><span class="lineNum">     302 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="303"><span class="lineNum">     303 </span><span class="lineCov">          1 :     case 16:</span></a>
+<a name="304"><span class="lineNum">     304 </span><span class="lineCov">          2 :       h = { 4.5102394860307721408121395256785e-03,</span></a>
+<a name="305"><span class="lineNum">     305 </span>            :             4.9366963027983538914167382927189e-02,</a>
+<a name="306"><span class="lineNum">     306 </span>            :             2.3343614837332890554755238099460e-01,</a>
+<a name="307"><span class="lineNum">     307 </span>            :             6.0855408871050020724879914268968e-01,</a>
+<a name="308"><span class="lineNum">     308 </span>            :             9.0135796889724240088526130421087e-01,</a>
+<a name="309"><span class="lineNum">     309 </span>            :             6.2266445266940384506426653388189e-01,</a>
+<a name="310"><span class="lineNum">     310 </span>            :             -1.2692720787074832089480480590282e-01,</a>
+<a name="311"><span class="lineNum">     311 </span>            :             -4.6253736950318169451890071286471e-01,</a>
+<a name="312"><span class="lineNum">     312 </span>            :             -3.9482308578843897106658289430925e-02,</a>
+<a name="313"><span class="lineNum">     313 </span>            :             2.9866874362698586642395071066858e-01,</a>
+<a name="314"><span class="lineNum">     314 </span>            :             3.8664971797927487340285068739831e-02,</a>
+<a name="315"><span class="lineNum">     315 </span>            :             -1.8722533722795392518989388008777e-01,</a>
+<a name="316"><span class="lineNum">     316 </span>            :             -8.8243005420050348031058007336469e-03,</a>
+<a name="317"><span class="lineNum">     317 </span>            :             1.0737308432663163204612288836870e-01,</a>
+<a name="318"><span class="lineNum">     318 </span>            :             -1.0732430476938423918875642470994e-02,</a>
+<a name="319"><span class="lineNum">     319 </span>            :             -5.2168072309854519874594558359604e-02,</a>
+<a name="320"><span class="lineNum">     320 </span>            :             1.4563089924943300318416206096117e-02,</a>
+<a name="321"><span class="lineNum">     321 </span>            :             1.9790177710283740619701120522222e-02,</a>
+<a name="322"><span class="lineNum">     322 </span>            :             -9.8853733967658469899975060002362e-03,</a>
+<a name="323"><span class="lineNum">     323 </span>            :             -5.1537896658028692006836557482075e-03,</a>
+<a name="324"><span class="lineNum">     324 </span>            :             4.4236930891221213843489401540410e-03,</a>
+<a name="325"><span class="lineNum">     325 </span>            :             5.7685344236866427022891734566201e-04,</a>
+<a name="326"><span class="lineNum">     326 </span>            :             -1.3308057204323708866411379858619e-03,</a>
+<a name="327"><span class="lineNum">     327 </span>            :             1.6156190702488963770351582116547e-04,</a>
+<a name="328"><span class="lineNum">     328 </span>            :             2.4718649272750667844275596074510e-04,</a>
+<a name="329"><span class="lineNum">     329 </span>            :             -8.6317891212541529946146445784194e-05,</a>
+<a name="330"><span class="lineNum">     330 </span>            :             -1.9722154219490776696404113477179e-05,</a>
+<a name="331"><span class="lineNum">     331 </span>            :             1.6032385720093409830870612164944e-05,</a>
+<a name="332"><span class="lineNum">     332 </span>            :             -1.4758327456010213390660444285341e-06,</a>
+<a name="333"><span class="lineNum">     333 </span>            :             -1.0413783294645852350716365430916e-06,</a>
+<a name="334"><span class="lineNum">     334 </span>            :             3.2651137682251684123506938785264e-07,</a>
+<a name="335"><span class="lineNum">     335 </span>            :             -2.9830567125395646088604952733681e-08</a>
+<a name="336"><span class="lineNum">     336 </span><span class="lineCov">          1 :           };</span></a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">          1 :     case 17:</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">          2 :       h = { 3.1703938650899862738974377407430e-03,</span></a>
+<a name="340"><span class="lineNum">     340 </span>            :             3.6748896199244887594836939115339e-02,</a>
+<a name="341"><span class="lineNum">     341 </span>            :             1.8556589584340402176998452432599e-01,</a>
+<a name="342"><span class="lineNum">     342 </span>            :             5.2375501693137660463861493553850e-01,</a>
+<a name="343"><span class="lineNum">     343 </span>            :             8.6407970046528492780169017351000e-01,</a>
+<a name="344"><span class="lineNum">     344 </span>            :             7.3300918312113150232534053429845e-01,</a>
+<a name="345"><span class="lineNum">     345 </span>            :             3.8629201600176063524649805458466e-02,</a>
+<a name="346"><span class="lineNum">     346 </span>            :             -4.6431565514482092682513325598848e-01,</a>
+<a name="347"><span class="lineNum">     347 </span>            :             -1.7903908657682734983929151439952e-01,</a>
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+<a name="373"><span class="lineNum">     373 </span><span class="lineCov">          1 :           };</span></a>
+<a name="374"><span class="lineNum">     374 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">          1 :     case 18:</span></a>
+<a name="376"><span class="lineNum">     376 </span><span class="lineCov">          2 :       h = { 2.2292392894261341476647153569957e-03,</span></a>
+<a name="377"><span class="lineNum">     377 </span>            :             2.7278103162550408622433195660051e-02,</a>
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+<a name="410"><span class="lineNum">     410 </span>            :             4.3399892982154842698451632180406e-08,</a>
+<a name="411"><span class="lineNum">     411 </span>            :             -3.5467549197311356709477164192218e-09</a>
+<a name="412"><span class="lineNum">     412 </span><span class="lineCov">          1 :           };</span></a>
+<a name="413"><span class="lineNum">     413 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="414"><span class="lineNum">     414 </span><span class="lineCov">          1 :     case 19:</span></a>
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+<a name="416"><span class="lineNum">     416 </span>            :             2.0196523114657562170126681166948e-02,</a>
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+<a name="454"><span class="lineNum">     454 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="455"><span class="lineNum">     455 </span><span class="lineCov">          1 :     case 20:</span></a>
+<a name="456"><span class="lineNum">     456 </span><span class="lineCov">          2 :       h = { 1.1030209784697370036660180048216e-03,</span></a>
+<a name="457"><span class="lineNum">     457 </span>            :             1.4919096953433321622872753664524e-02,</a>
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+<a name="471"><span class="lineNum">     471 </span>            :             7.9651998921310210310942068190343e-03,</a>
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+<a name="483"><span class="lineNum">     483 </span>            :             -5.4462035854466845589266776883619e-04,</a>
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+<a name="491"><span class="lineNum">     491 </span>            :             3.7249313630534454078768497216345e-07,</a>
+<a name="492"><span class="lineNum">     492 </span>            :             2.8486815247482631938422053924332e-10,</a>
+<a name="493"><span class="lineNum">     493 </span>            :             -2.5665759353263497063665855347538e-08,</a>
+<a name="494"><span class="lineNum">     494 </span>            :             5.7362298926689411330572237329717e-09,</a>
+<a name="495"><span class="lineNum">     495 </span>            :             -4.2409952349582263523522284550586e-10</a>
+<a name="496"><span class="lineNum">     496 </span><span class="lineCov">          1 :           };</span></a>
+<a name="497"><span class="lineNum">     497 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="498"><span class="lineNum">     498 </span><span class="lineNoCov">          0 :     default:</span></a>
+<a name="499"><span class="lineNum">     499 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Specified order currently not implemented&quot;);</span></a>
+<a name="500"><span class="lineNum">     500 </span>            :     }</a>
+<a name="501"><span class="lineNum">     501 </span>            :   }</a>
+<a name="502"><span class="lineNum">     502 </span>            : </a>
+<a name="503"><span class="lineNum">     503 </span><span class="lineCov">         25 :   else if (type == Type::sym) {</span></a>
+<a name="504"><span class="lineNum">     504 </span><span class="lineCov">         25 :     switch(order) {</span></a>
+<a name="505"><span class="lineNum">     505 </span><span class="lineCov">          1 :     case 4:</span></a>
+<a name="506"><span class="lineNum">     506 </span><span class="lineCov">          2 :       h = { 4.55703458959498611258176481442206e-02,</span></a>
+<a name="507"><span class="lineNum">     507 </span>            :             -1.78247014416803885306084254125381e-02,</a>
+<a name="508"><span class="lineNum">     508 </span>            :             -1.40317624178845662408221528494323e-01,</a>
+<a name="509"><span class="lineNum">     509 </span>            :             4.21234534203536570284853723933338e-01,</a>
+<a name="510"><span class="lineNum">     510 </span>            :             1.13665824340874954678781705297297e+00,</a>
+<a name="511"><span class="lineNum">     511 </span>            :             7.03739068655225841197875524812844e-01,</a>
+<a name="512"><span class="lineNum">     512 </span>            :             -4.19109651250538992051097864077747e-02,</a>
+<a name="513"><span class="lineNum">     513 </span>            :             -1.07148901417882122522051702162571e-01</a>
+<a name="514"><span class="lineNum">     514 </span><span class="lineCov">          1 :           };</span></a>
+<a name="515"><span class="lineNum">     515 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="516"><span class="lineNum">     516 </span><span class="lineCov">          1 :     case 5:</span></a>
+<a name="517"><span class="lineNum">     517 </span><span class="lineCov">          2 :       h = { 2.76321529578600101617613660209827e-02,</span></a>
+<a name="518"><span class="lineNum">     518 </span>            :             -2.98424998687600064040115199759384e-02,</a>
+<a name="519"><span class="lineNum">     519 </span>            :             -2.47951362613500064790983401508129e-01,</a>
+<a name="520"><span class="lineNum">     520 </span>            :             2.34789231361400077546797149352642e-02,</a>
+<a name="521"><span class="lineNum">     521 </span>            :             8.96581648381840179418134084698977e-01,</a>
+<a name="522"><span class="lineNum">     522 </span>            :             1.02305296689210023508564972871682e+00,</a>
+<a name="523"><span class="lineNum">     523 </span>            :             2.81990696854580058516859253359144e-01,</a>
+<a name="524"><span class="lineNum">     524 </span>            :             -5.53441861167200052640247065482981e-02,</a>
+<a name="525"><span class="lineNum">     525 </span>            :             4.17468644215800155361506540430128e-02,</a>
+<a name="526"><span class="lineNum">     526 </span>            :             3.86547959548800140749946763207845e-02</a>
+<a name="527"><span class="lineNum">     527 </span><span class="lineCov">          1 :           };</span></a>
+<a name="528"><span class="lineNum">     528 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="529"><span class="lineNum">     529 </span><span class="lineCov">          2 :     case 6:</span></a>
+<a name="530"><span class="lineNum">     530 </span><span class="lineCov">          4 :       h = { -1.10318675093800024761270250905909e-02,</span></a>
+<a name="531"><span class="lineNum">     531 </span>            :             2.49992209278000017055876291749428e-03,</a>
+<a name="532"><span class="lineNum">     532 </span>            :             6.32505626598800080317985816691362e-02,</a>
+<a name="533"><span class="lineNum">     533 </span>            :             -2.97837512984400025473075146464907e-02,</a>
+<a name="534"><span class="lineNum">     534 </span>            :             -1.02724969861800033421594946503319e-01,</a>
+<a name="535"><span class="lineNum">     535 </span>            :             4.77904371332100064151404694712255e-01,</a>
+<a name="536"><span class="lineNum">     536 </span>            :             1.11389278392792001604050255991751e+00,</a>
+<a name="537"><span class="lineNum">     537 </span>            :             6.94457972956700086974990426824661e-01,</a>
+<a name="538"><span class="lineNum">     538 </span>            :             -6.83231215864800039971882483769150e-02,</a>
+<a name="539"><span class="lineNum">     539 </span>            :             -1.66863215411680032573826792940963e-01,</a>
+<a name="540"><span class="lineNum">     540 </span>            :             4.93661237184000057515165238442023e-03,</a>
+<a name="541"><span class="lineNum">     541 </span>            :             2.17847003265600018540038007586190e-02</a>
+<a name="542"><span class="lineNum">     542 </span><span class="lineCov">          2 :           };</span></a>
+<a name="543"><span class="lineNum">     543 </span><span class="lineCov">          2 :       break;</span></a>
+<a name="544"><span class="lineNum">     544 </span><span class="lineCov">          1 :     case 7:</span></a>
+<a name="545"><span class="lineNum">     545 </span><span class="lineCov">          2 :       h = { 1.45213947620201448696075630095947e-02,</span></a>
+<a name="546"><span class="lineNum">     546 </span>            :             5.67134268576005746986812283694235e-03,</a>
+<a name="547"><span class="lineNum">     547 </span>            :             -1.52463871896281522033689270756440e-01,</a>
+<a name="548"><span class="lineNum">     548 </span>            :             -1.98056706807362009614692510695022e-01,</a>
+<a name="549"><span class="lineNum">     549 </span>            :             4.08183939725744127091644486426958e-01,</a>
+<a name="550"><span class="lineNum">     550 </span>            :             1.08578270981199098699221394781489e+00,</a>
+<a name="551"><span class="lineNum">     551 </span>            :             7.58162601965387539237894998223055e-01,</a>
+<a name="552"><span class="lineNum">     552 </span>            :             2.46656594886402458222107725305250e-02,</a>
+<a name="553"><span class="lineNum">     553 </span>            :             -7.00782912221206977232412782541360e-02,</a>
+<a name="554"><span class="lineNum">     554 </span>            :             9.60147679356809641282310963106283e-02,</a>
+<a name="555"><span class="lineNum">     555 </span>            :             4.31554525820804293911869820021820e-02,</a>
+<a name="556"><span class="lineNum">     556 </span>            :             -1.78704316511401790912305642677893e-02,</a>
+<a name="557"><span class="lineNum">     557 </span>            :             -1.48122591460001472307705938646905e-03,</a>
+<a name="558"><span class="lineNum">     558 </span>            :             3.79265853420003790433256973813059e-03</a>
+<a name="559"><span class="lineNum">     559 </span><span class="lineCov">          1 :           };</span></a>
+<a name="560"><span class="lineNum">     560 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="561"><span class="lineNum">     561 </span><span class="lineCov">          2 :     case 8:</span></a>
+<a name="562"><span class="lineNum">     562 </span><span class="lineCov">          4 :       h = { 2.67279339279997366768393263214421e-03,</span></a>
+<a name="563"><span class="lineNum">     563 </span>            :             -4.28394300239995752879740287255572e-04,</a>
+<a name="564"><span class="lineNum">     564 </span>            :             -2.11456865283597902904766385745461e-02,</a>
+<a name="565"><span class="lineNum">     565 </span>            :             5.38638875375994745364760518668845e-03,</a>
+<a name="566"><span class="lineNum">     566 </span>            :             6.94904659111793138182022744331334e-02,</a>
+<a name="567"><span class="lineNum">     567 </span>            :             -3.84935212633396237058569511191308e-02,</a>
+<a name="568"><span class="lineNum">     568 </span>            :             -7.34625087607592708316417429159628e-02,</a>
+<a name="569"><span class="lineNum">     569 </span>            :             5.15398670373074963002579806925496e-01,</a>
+<a name="570"><span class="lineNum">     570 </span>            :             1.09910663053800905508694540912984e+00,</a>
+<a name="571"><span class="lineNum">     571 </span>            :             6.80745347188773330948663442541147e-01,</a>
+<a name="572"><span class="lineNum">     572 </span>            :             -8.66536154056391505484668869030429e-02,</a>
+<a name="573"><span class="lineNum">     573 </span>            :             -2.02648655285637996348313549788145e-01,</a>
+<a name="574"><span class="lineNum">     574 </span>            :             1.07586117504798947641653228401992e-02,</a>
+<a name="575"><span class="lineNum">     575 </span>            :             4.48236230436195592918835473028594e-02,</a>
+<a name="576"><span class="lineNum">     576 </span>            :             -7.66690896219992417716382337999903e-04,</a>
+<a name="577"><span class="lineNum">     577 </span>            :             -4.78345851149995348466914535379146e-03</a>
+<a name="578"><span class="lineNum">     578 </span><span class="lineCov">          2 :           };</span></a>
+<a name="579"><span class="lineNum">     579 </span><span class="lineCov">          2 :       break;</span></a>
+<a name="580"><span class="lineNum">     580 </span><span class="lineCov">          1 :     case 9:</span></a>
+<a name="581"><span class="lineNum">     581 </span><span class="lineCov">          2 :       h = { 1.51248730936219739386106031275858e-03,</span></a>
+<a name="582"><span class="lineNum">     582 </span>            :             -6.69141509131216294554989065801465e-04,</a>
+<a name="583"><span class="lineNum">     583 </span>            :             -1.45155785529446045012402777274474e-02,</a>
+<a name="584"><span class="lineNum">     584 </span>            :             1.25288962418580607921514413760633e-02,</a>
+<a name="585"><span class="lineNum">     585 </span>            :             8.77912515542808719049006072054908e-02,</a>
+<a name="586"><span class="lineNum">     586 </span>            :             -2.57864459294240427889022271301656e-02,</a>
+<a name="587"><span class="lineNum">     587 </span>            :             -2.70893783504461360678305936744437e-01,</a>
+<a name="588"><span class="lineNum">     588 </span>            :             4.98828309581242426706815251691296e-02,</a>
+<a name="589"><span class="lineNum">     589 </span>            :             8.73048407349484634210057265590876e-01,</a>
+<a name="590"><span class="lineNum">     590 </span>            :             1.01525979083351192144846208975650e+00,</a>
+<a name="591"><span class="lineNum">     591 </span>            :             3.37658923602252358797670694912085e-01,</a>
+<a name="592"><span class="lineNum">     592 </span>            :             -7.71721610974591964993152259921771e-02,</a>
+<a name="593"><span class="lineNum">     593 </span>            :             8.25140928710566164128170640879034e-04,</a>
+<a name="594"><span class="lineNum">     594 </span>            :             4.27444336024572976717728067796997e-02,</a>
+<a name="595"><span class="lineNum">     595 </span>            :             -1.63033512255879239893907595160272e-02,</a>
+<a name="596"><span class="lineNum">     596 </span>            :             -1.87693968364245344915275381936226e-02,</a>
+<a name="597"><span class="lineNum">     597 </span>            :             8.76502538903070420837904119792938e-04,</a>
+<a name="598"><span class="lineNum">     598 </span>            :             1.98119373648757883879523156167579e-03</a>
+<a name="599"><span class="lineNum">     599 </span><span class="lineCov">          1 :           };</span></a>
+<a name="600"><span class="lineNum">     600 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="601"><span class="lineNum">     601 </span><span class="lineCov">          5 :     case 10:</span></a>
+<a name="602"><span class="lineNum">     602 </span><span class="lineCov">         10 :       h = { -6.49589896781769724452837433403829e-04,</span></a>
+<a name="603"><span class="lineNum">     603 </span>            :             8.06612029979205351478896424133325e-05,</a>
+<a name="604"><span class="lineNum">     604 </span>            :             6.49572837868184205234456385369413e-03,</a>
+<a name="605"><span class="lineNum">     605 </span>            :             -1.13753531067373615109916684673408e-03,</a>
+<a name="606"><span class="lineNum">     606 </span>            :             -2.87862319438586915232303198308728e-02,</a>
+<a name="607"><span class="lineNum">     607 </span>            :             8.15281678377939578172828305469011e-03,</a>
+<a name="608"><span class="lineNum">     608 </span>            :             7.07035675622903064807545092662622e-02,</a>
+<a name="609"><span class="lineNum">     609 </span>            :             -4.52407723042161716286990724711359e-02,</a>
+<a name="610"><span class="lineNum">     610 </span>            :             -5.02565403406056709911808866309002e-02,</a>
+<a name="611"><span class="lineNum">     611 </span>            :             5.42813011102809772623345452302601e-01,</a>
+<a name="612"><span class="lineNum">     612 </span>            :             1.08825153073747227239209678373300e+00,</a>
+<a name="613"><span class="lineNum">     613 </span>            :             6.67071338429151339255440689157695e-01,</a>
+<a name="614"><span class="lineNum">     614 </span>            :             -1.00240215012934938410005258901947e-01,</a>
+<a name="615"><span class="lineNum">     615 </span>            :             -2.25558972319967215858227405078651e-01,</a>
+<a name="616"><span class="lineNum">     616 </span>            :             1.64188694163413528848138867033413e-02,</a>
+<a name="617"><span class="lineNum">     617 </span>            :             6.49509246029642689501670815843681e-02,</a>
+<a name="618"><span class="lineNum">     618 </span>            :             -2.07236392054689850042437093691206e-03,</a>
+<a name="619"><span class="lineNum">     619 </span>            :             -1.22206426340899319132882183680522e-02,</a>
+<a name="620"><span class="lineNum">     620 </span>            :             1.35245019942278199434962382419201e-04,</a>
+<a name="621"><span class="lineNum">     621 </span>            :             1.08917044724438603908733824709998e-03</a>
+<a name="622"><span class="lineNum">     622 </span><span class="lineCov">          5 :           };</span></a>
+<a name="623"><span class="lineNum">     623 </span><span class="lineCov">          5 :       break;</span></a>
+<a name="624"><span class="lineNum">     624 </span><span class="lineCov">          1 :     case 11:</span></a>
+<a name="625"><span class="lineNum">     625 </span><span class="lineCov">          2 :       h = { 6.91923233208036969968390828000793e-04,</span></a>
+<a name="626"><span class="lineNum">     626 </span>            :             1.56320234204571122593394050248605e-04,</a>
+<a name="627"><span class="lineNum">     627 </span>            :             -9.03626416328936338251409665645042e-03,</a>
+<a name="628"><span class="lineNum">     628 </span>            :             -2.83333713296809227427663913090328e-03,</a>
+<a name="629"><span class="lineNum">     629 </span>            :             6.08114528464804224294759649183106e-02,</a>
+<a name="630"><span class="lineNum">     630 </span>            :             4.98747296770196690829379804199561e-02,</a>
+<a name="631"><span class="lineNum">     631 </span>            :             -2.04498595618993084244152669270989e-01,</a>
+<a name="632"><span class="lineNum">     632 </span>            :             -2.89425585980639887839771517974441e-01,</a>
+<a name="633"><span class="lineNum">     633 </span>            :             3.36144293016675366203571684309281e-01,</a>
+<a name="634"><span class="lineNum">     634 </span>            :             1.03286175231250965111939876805991e+00,</a>
+<a name="635"><span class="lineNum">     635 </span>            :             8.08962653490911898224169362947578e-01,</a>
+<a name="636"><span class="lineNum">     636 </span>            :             1.37459287684679687391309244048898e-01,</a>
+<a name="637"><span class="lineNum">     637 </span>            :             -3.22902447410400722516143900975294e-02,</a>
+<a name="638"><span class="lineNum">     638 </span>            :             9.89621390609645434910390804361668e-02,</a>
+<a name="639"><span class="lineNum">     639 </span>            :             5.23788159925569485331209307332756e-02,</a>
+<a name="640"><span class="lineNum">     640 </span>            :             -3.40554527782290436532797173185827e-02,</a>
+<a name="641"><span class="lineNum">     641 </span>            :             -1.39412251318646231851294814418907e-02,</a>
+<a name="642"><span class="lineNum">     642 </span>            :             9.21005970815790518668730868512284e-03,</a>
+<a name="643"><span class="lineNum">     643 </span>            :             8.32056417857734271180392138234083e-04,</a>
+<a name="644"><span class="lineNum">     644 </span>            :             -2.45276429733504728117332582826293e-03,</a>
+<a name="645"><span class="lineNum">     645 </span>            :             -5.48653425032330071273514726648557e-05,</a>
+<a name="646"><span class="lineNum">     646 </span>            :             2.42851511636182730569100129969229e-04</a>
+<a name="647"><span class="lineNum">     647 </span><span class="lineCov">          1 :           };</span></a>
+<a name="648"><span class="lineNum">     648 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="649"><span class="lineNum">     649 </span><span class="lineCov">          3 :     case 12:</span></a>
+<a name="650"><span class="lineNum">     650 </span><span class="lineCov">          6 :       h = { -2.53238395868029360011308703803934e-04,</span></a>
+<a name="651"><span class="lineNum">     651 </span>            :             -2.56794013941539134206898387091655e-05,</a>
+<a name="652"><span class="lineNum">     652 </span>            :             3.32382276159138428939243681270455e-03,</a>
+<a name="653"><span class="lineNum">     653 </span>            :             4.35079685976638231084678842819358e-04,</a>
+<a name="654"><span class="lineNum">     654 </span>            :             -2.06331445793122500442784428287268e-02,</a>
+<a name="655"><span class="lineNum">     655 </span>            :             -3.68316511823289565938366330044573e-03,</a>
+<a name="656"><span class="lineNum">     656 </span>            :             8.17474545336821928342985188464809e-02,</a>
+<a name="657"><span class="lineNum">     657 </span>            :             2.16399291162249034214948295584691e-02,</a>
+<a name="658"><span class="lineNum">     658 </span>            :             -2.40940550666163183501922162577102e-01,</a>
+<a name="659"><span class="lineNum">     659 </span>            :             -1.10779056856021962396141589124454e-01,</a>
+<a name="660"><span class="lineNum">     660 </span>            :             6.54414642216806785590677009167848e-01,</a>
+<a name="661"><span class="lineNum">     661 </span>            :             1.07972249467402248157554822682869e+00,</a>
+<a name="662"><span class="lineNum">     662 </span>            :             5.64109951994629099658595805522054e-01,</a>
+<a name="663"><span class="lineNum">     663 </span>            :             -3.13422339595566742942445159769704e-02,</a>
+<a name="664"><span class="lineNum">     664 </span>            :             -5.06979026234183824395351791736175e-02,</a>
+<a name="665"><span class="lineNum">     665 </span>            :             6.95500589276436959051963526690088e-02,</a>
+<a name="666"><span class="lineNum">     666 </span>            :             1.06826589882294663985673466299886e-02,</a>
+<a name="667"><span class="lineNum">     667 </span>            :             -3.42532744974815631100462098856951e-02,</a>
+<a name="668"><span class="lineNum">     668 </span>            :             -1.99249856148396879348960730737872e-03,</a>
+<a name="669"><span class="lineNum">     669 </span>            :             1.04863447995954799790707667739298e-02,</a>
+<a name="670"><span class="lineNum">     670 </span>            :             2.54861210329473779345743622570808e-04,</a>
+<a name="671"><span class="lineNum">     671 </span>            :             -1.90884289542041446843811947076119e-03,</a>
+<a name="672"><span class="lineNum">     672 </span>            :             -1.60568790225561159679470990546690e-05,</a>
+<a name="673"><span class="lineNum">     673 </span>            :             1.58345524644348421491879541633807e-04</a>
+<a name="674"><span class="lineNum">     674 </span><span class="lineCov">          3 :           };</span></a>
+<a name="675"><span class="lineNum">     675 </span><span class="lineCov">          3 :       break;</span></a>
+<a name="676"><span class="lineNum">     676 </span><span class="lineCov">          1 :     case 13:</span></a>
+<a name="677"><span class="lineNum">     677 </span><span class="lineCov">          2 :       h = { 9.96028729759322644298977222909741e-05,</span></a>
+<a name="678"><span class="lineNum">     678 </span>            :             5.21920796195277043654989213017359e-05,</a>
+<a name="679"><span class="lineNum">     679 </span>            :             -1.02016329687258286949835817125631e-03,</a>
+<a name="680"><span class="lineNum">     680 </span>            :             5.84439592204865189864482211135055e-04,</a>
+<a name="681"><span class="lineNum">     681 </span>            :             8.02545515204910846207564389942490e-03,</a>
+<a name="682"><span class="lineNum">     682 </span>            :             -2.11063917638504251403364087025238e-03,</a>
+<a name="683"><span class="lineNum">     683 </span>            :             -2.93444878165318237539516132983408e-02,</a>
+<a name="684"><span class="lineNum">     684 </span>            :             2.49160343945351858696568569939700e-02,</a>
+<a name="685"><span class="lineNum">     685 </span>            :             1.31417253195061006776356293812569e-01,</a>
+<a name="686"><span class="lineNum">     686 </span>            :             1.24730209143528725235228193923831e-02,</a>
+<a name="687"><span class="lineNum">     687 </span>            :             -1.98682995060360217953743244834186e-01,</a>
+<a name="688"><span class="lineNum">     688 </span>            :             1.55889076380235497287785051412357e-01,</a>
+<a name="689"><span class="lineNum">     689 </span>            :             9.11551693535715079619308198743965e-01,</a>
+<a name="690"><span class="lineNum">     690 </span>            :             9.83923742598004968940017533896025e-01,</a>
+<a name="691"><span class="lineNum">     691 </span>            :             2.79596836052714847742350912085385e-01,</a>
+<a name="692"><span class="lineNum">     692 </span>            :             -1.75875078644905619151828091162315e-01,</a>
+<a name="693"><span class="lineNum">     693 </span>            :             -8.45001480790217585070678296688129e-02,</a>
+<a name="694"><span class="lineNum">     694 </span>            :             1.96045318821402025921685208231793e-02,</a>
+<a name="695"><span class="lineNum">     695 </span>            :             -2.43409385742523465268050131271593e-02,</a>
+<a name="696"><span class="lineNum">     696 </span>            :             -2.85908276815921014168964120472083e-02,</a>
+<a name="697"><span class="lineNum">     697 </span>            :             7.49018377371175360368571460867315e-03,</a>
+<a name="698"><span class="lineNum">     698 </span>            :             1.06436900199696239666113939392744e-02,</a>
+<a name="699"><span class="lineNum">     699 </span>            :             -2.41749708924265434154335374650202e-04,</a>
+<a name="700"><span class="lineNum">     700 </span>            :             -1.60663632304836349537491280159429e-03,</a>
+<a name="701"><span class="lineNum">     701 </span>            :             -5.05420462645238263775342157924086e-05,</a>
+<a name="702"><span class="lineNum">     702 </span>            :             9.64539648683696427926281824483112e-05</a>
+<a name="703"><span class="lineNum">     703 </span><span class="lineCov">          1 :           };</span></a>
+<a name="704"><span class="lineNum">     704 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="705"><span class="lineNum">     705 </span><span class="lineCov">          1 :     case 14:</span></a>
+<a name="706"><span class="lineNum">     706 </span><span class="lineCov">          2 :       h = { 6.31007638147709694776549271821864e-05,</span></a>
+<a name="707"><span class="lineNum">     707 </span>            :             2.73353579399835730078405920950857e-05,</a>
+<a name="708"><span class="lineNum">     708 </span>            :             -8.56674265589630994088832238730902e-04,</a>
+<a name="709"><span class="lineNum">     709 </span>            :             -1.03540533784965597756920485661425e-04,</a>
+<a name="710"><span class="lineNum">     710 </span>            :             6.41017395468853039969259199892804e-03,</a>
+<a name="711"><span class="lineNum">     711 </span>            :             1.43279913888553589278174182908288e-03,</a>
+<a name="712"><span class="lineNum">     712 </span>            :             -2.74913418748536537983273575491694e-02,</a>
+<a name="713"><span class="lineNum">     713 </span>            :             -3.34468414059296489937445073792333e-03,</a>
+<a name="714"><span class="lineNum">     714 </span>            :             9.87511620870536871441558446349518e-02,</a>
+<a name="715"><span class="lineNum">     715 </span>            :             3.66261337327129302132711075046245e-02,</a>
+<a name="716"><span class="lineNum">     716 </span>            :             -2.26270508787995705546336466795765e-01,</a>
+<a name="717"><span class="lineNum">     717 </span>            :             -8.21825286701456242388630357709189e-02,</a>
+<a name="718"><span class="lineNum">     718 </span>            :             6.72226282198253310973257157456828e-01,</a>
+<a name="719"><span class="lineNum">     719 </span>            :             1.07476870846271177484254621958826e+00,</a>
+<a name="720"><span class="lineNum">     720 </span>            :             5.56070925104528490656718986429041e-01,</a>
+<a name="721"><span class="lineNum">     721 </span>            :             -4.99473531504178586137854267690273e-02,</a>
+<a name="722"><span class="lineNum">     722 </span>            :             -8.15074892290164332298019189693150e-02,</a>
+<a name="723"><span class="lineNum">     723 </span>            :             5.29383812442578288726124924323813e-02,</a>
+<a name="724"><span class="lineNum">     724 </span>            :             6.05357014372925363032695855736165e-03,</a>
+<a name="725"><span class="lineNum">     725 </span>            :             -4.12896871319010858036868683029752e-02,</a>
+<a name="726"><span class="lineNum">     726 </span>            :             -3.89442565747022016384160103541490e-03,</a>
+<a name="727"><span class="lineNum">     727 </span>            :             1.41954425904793363893974245115714e-02,</a>
+<a name="728"><span class="lineNum">     728 </span>            :             5.18276140762161932271090414303671e-04,</a>
+<a name="729"><span class="lineNum">     729 </span>            :             -3.64788147216562339339440690366700e-03,</a>
+<a name="730"><span class="lineNum">     730 </span>            :             -8.89051363774028501323759554608728e-05,</a>
+<a name="731"><span class="lineNum">     731 </span>            :             5.63473132455830365457327690847933e-04,</a>
+<a name="732"><span class="lineNum">     732 </span>            :             1.58545584728775700955431815497576e-05,</a>
+<a name="733"><span class="lineNum">     733 </span>            :             -3.65985604352032339978313679740296e-05</a>
+<a name="734"><span class="lineNum">     734 </span><span class="lineCov">          1 :           };</span></a>
+<a name="735"><span class="lineNum">     735 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="736"><span class="lineNum">     736 </span><span class="lineCov">          1 :     case 15:</span></a>
+<a name="737"><span class="lineNum">     737 </span><span class="lineCov">          2 :       h = { 4.05323627037270219162362616671658e-05,</span></a>
+<a name="738"><span class="lineNum">     738 </span>            :             3.07137347973606144061961553681783e-05,</a>
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+<a name="743"><span class="lineNum">     743 </span>            :             -2.42838185667302274006740248069036e-02,</a>
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+<a name="746"><span class="lineNum">     746 </span>            :             9.67227466631194188195763672410976e-02,</a>
+<a name="747"><span class="lineNum">     747 </span>            :             -1.89584235398369660430262229056098e-01,</a>
+<a name="748"><span class="lineNum">     748 </span>            :             -2.78071663287250692153662612327025e-01,</a>
+<a name="749"><span class="lineNum">     749 </span>            :             3.45015366735401951547856924662483e-01,</a>
+<a name="750"><span class="lineNum">     750 </span>            :             1.02084020241597150935319859854644e+00,</a>
+<a name="751"><span class="lineNum">     751 </span>            :             8.18321122934300926310413615283323e-01,</a>
+<a name="752"><span class="lineNum">     752 </span>            :             1.57732464332277610985499904927565e-01,</a>
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+<a name="754"><span class="lineNum">     754 </span>            :             5.76086678570035190527498514256877e-02,</a>
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+<a name="762"><span class="lineNum">     762 </span>            :             1.51401068119577392884211874957145e-03,</a>
+<a name="763"><span class="lineNum">     763 </span>            :             7.79550547699306238926333922911738e-05,</a>
+<a name="764"><span class="lineNum">     764 </span>            :             -2.27210190383633081493211514079178e-04,</a>
+<a name="765"><span class="lineNum">     765 </span>            :             -1.04081406015788967609316320594992e-05,</a>
+<a name="766"><span class="lineNum">     766 </span>            :             1.37354357168879101134487813462570e-05</a>
+<a name="767"><span class="lineNum">     767 </span><span class="lineCov">          1 :           };</span></a>
+<a name="768"><span class="lineNum">     768 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="769"><span class="lineNum">     769 </span><span class="lineCov">          1 :     case 16:</span></a>
+<a name="770"><span class="lineNum">     770 </span><span class="lineCov">          2 :       h = { -1.52706527381910275756142503222890e-05,</span></a>
+<a name="771"><span class="lineNum">     771 </span>            :             -7.63177970130589524008421498102450e-06,</a>
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+<a name="776"><span class="lineNum">     776 </span>            :             9.81147588368609310793821975948958e-03,</a>
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+<a name="778"><span class="lineNum">     778 </span>            :             -3.52885288476778719024551378424803e-02,</a>
+<a name="779"><span class="lineNum">     779 </span>            :             -4.96427860935466733899312785638358e-03,</a>
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+<a name="788"><span class="lineNum">     788 </span>            :             -9.47283364442045167086448032023327e-02,</a>
+<a name="789"><span class="lineNum">     789 </span>            :             4.57258966692524679298337275668018e-02,</a>
+<a name="790"><span class="lineNum">     790 </span>            :             6.88619390233227712805330611445243e-03,</a>
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+<a name="794"><span class="lineNum">     794 </span>            :             1.01570512112273466515111053354303e-03,</a>
+<a name="795"><span class="lineNum">     795 </span>            :             -5.48843874201232484466572714154609e-03,</a>
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+<a name="797"><span class="lineNum">     797 </span>            :             1.20541159197261760899211324726821e-03,</a>
+<a name="798"><span class="lineNum">     798 </span>            :             3.97091116582507492704760820867449e-05,</a>
+<a name="799"><span class="lineNum">     799 </span>            :             -1.54759482169960371376535301912725e-04,</a>
+<a name="800"><span class="lineNum">     800 </span>            :             -4.40323369887264181395027801135811e-06,</a>
+<a name="801"><span class="lineNum">     801 </span>            :             8.81055997054166680230915392746383e-06</a>
+<a name="802"><span class="lineNum">     802 </span><span class="lineCov">          1 :           };</span></a>
+<a name="803"><span class="lineNum">     803 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="804"><span class="lineNum">     804 </span><span class="lineCov">          1 :     case 17:</span></a>
+<a name="805"><span class="lineNum">     805 </span><span class="lineCov">          2 :       h = { 5.36164168581481346588513137163545e-06,</span></a>
+<a name="806"><span class="lineNum">     806 </span>            :             -3.46866471633543758739618573239127e-06,</a>
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+<a name="810"><span class="lineNum">     810 </span>            :             8.25906783075320302753979939680562e-05,</a>
+<a name="811"><span class="lineNum">     811 </span>            :             -5.56114774235276932562443974461530e-03,</a>
+<a name="812"><span class="lineNum">     812 </span>            :             -2.69465339683962841130226983921148e-03,</a>
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+<a name="814"><span class="lineNum">     814 </span>            :             1.40756428708096667512528199495137e-02,</a>
+<a name="815"><span class="lineNum">     815 </span>            :             -2.55108531297768073575760183757666e-02,</a>
+<a name="816"><span class="lineNum">     816 </span>            :             -1.02695023497632355324871156199151e-02,</a>
+<a name="817"><span class="lineNum">     817 </span>            :             2.28520064519878510211903233084740e-02,</a>
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+<a name="819"><span class="lineNum">     819 </span>            :             -2.19310589964256619222027211435488e-01,</a>
+<a name="820"><span class="lineNum">     820 </span>            :             2.55321529059814311679588172410149e-01,</a>
+<a name="821"><span class="lineNum">     821 </span>            :             9.63770979824808082803144770878134e-01,</a>
+<a name="822"><span class="lineNum">     822 </span>            :             9.20252282282772893218236731627258e-01,</a>
+<a name="823"><span class="lineNum">     823 </span>            :             2.01381678415994358477547621077974e-01,</a>
+<a name="824"><span class="lineNum">     824 </span>            :             -1.67678964148070125395051377381606e-01,</a>
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+<a name="826"><span class="lineNum">     826 </span>            :             1.48145397031054587566600844183995e-01,</a>
+<a name="827"><span class="lineNum">     827 </span>            :             2.53200120416010171497944725160778e-02,</a>
+<a name="828"><span class="lineNum">     828 </span>            :             -4.70811260450583399239654625034746e-02,</a>
+<a name="829"><span class="lineNum">     829 </span>            :             -6.81539610621377002497300878758324e-03,</a>
+<a name="830"><span class="lineNum">     830 </span>            :             1.48243054824644532319055656444107e-02,</a>
+<a name="831"><span class="lineNum">     831 </span>            :             1.21165585310027278283240281808730e-03,</a>
+<a name="832"><span class="lineNum">     832 </span>            :             -3.87731534844140950796242961473581e-03,</a>
+<a name="833"><span class="lineNum">     833 </span>            :             -1.96069824769335180822404929301683e-04,</a>
+<a name="834"><span class="lineNum">     834 </span>            :             6.73160536609661666086756870441832e-04,</a>
+<a name="835"><span class="lineNum">     835 </span>            :             -1.91009105827510641166869231888370e-05,</a>
+<a name="836"><span class="lineNum">     836 </span>            :             -8.90063957100391663296648503411745e-05,</a>
+<a name="837"><span class="lineNum">     837 </span>            :             3.93169287554600132558258254733552e-06,</a>
+<a name="838"><span class="lineNum">     838 </span>            :             6.07736121570621208446468658470607e-06</a>
+<a name="839"><span class="lineNum">     839 </span><span class="lineCov">          1 :           };</span></a>
+<a name="840"><span class="lineNum">     840 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="841"><span class="lineNum">     841 </span><span class="lineCov">          1 :     case 18:</span></a>
+<a name="842"><span class="lineNum">     842 </span><span class="lineCov">          2 :       h = { -2.13992159246166473816484938919036e-06,</span></a>
+<a name="843"><span class="lineNum">     843 </span>            :             1.10977553385413026034323619173350e-06,</a>
+<a name="844"><span class="lineNum">     844 </span>            :             4.18005291525171048536493878522435e-05,</a>
+<a name="845"><span class="lineNum">     845 </span>            :             -1.39424713387653467029560910850350e-05,</a>
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+<a name="847"><span class="lineNum">     847 </span>            :             6.70565555942921202913289957514564e-05,</a>
+<a name="848"><span class="lineNum">     848 </span>            :             2.01961905200075380467650276727909e-03,</a>
+<a name="849"><span class="lineNum">     849 </span>            :             -2.66969918023956154402853702123366e-04,</a>
+<a name="850"><span class="lineNum">     850 </span>            :             -7.41018163371885089235613364166966e-03,</a>
+<a name="851"><span class="lineNum">     851 </span>            :             1.53836000238939262126092177851433e-03,</a>
+<a name="852"><span class="lineNum">     852 </span>            :             2.12306779452164293142679696302366e-02,</a>
+<a name="853"><span class="lineNum">     853 </span>            :             -4.61138867117545040580361970228296e-03,</a>
+<a name="854"><span class="lineNum">     854 </span>            :             -4.48485088469943032896125600927917e-02,</a>
+<a name="855"><span class="lineNum">     855 </span>            :             8.87835433253391509422769445336598e-03,</a>
+<a name="856"><span class="lineNum">     856 </span>            :             4.03469430616465660199843057398539e-02,</a>
+<a name="857"><span class="lineNum">     857 </span>            :             -1.04367839842760060098392216332286e-01,</a>
+<a name="858"><span class="lineNum">     858 </span>            :             -4.59344672605674214649340569849301e-02,</a>
+<a name="859"><span class="lineNum">     859 </span>            :             5.67783920692876864499964995047776e-01,</a>
+<a name="860"><span class="lineNum">     860 </span>            :             1.06579255093152891475938304211013e+00,</a>
+<a name="861"><span class="lineNum">     861 </span>            :             6.70293472647235155648104409920052e-01,</a>
+<a name="862"><span class="lineNum">     862 </span>            :             -7.35803422739719908962641170546704e-02,</a>
+<a name="863"><span class="lineNum">     863 </span>            :             -2.26186698989002510362666953369626e-01,</a>
+<a name="864"><span class="lineNum">     864 </span>            :             4.80771334803232336385647727183823e-02,</a>
+<a name="865"><span class="lineNum">     865 </span>            :             1.19104967186232965636882852322742e-01,</a>
+<a name="866"><span class="lineNum">     866 </span>            :             -7.18008269166581052089792791548462e-03,</a>
+<a name="867"><span class="lineNum">     867 </span>            :             -4.28861550987859954653380611944158e-02,</a>
+<a name="868"><span class="lineNum">     868 </span>            :             2.32353364582536326202188980971641e-03,</a>
+<a name="869"><span class="lineNum">     869 </span>            :             1.34380897535976585183137288481703e-02,</a>
+<a name="870"><span class="lineNum">     870 </span>            :             -5.81978733884339397529339432679762e-04,</a>
+<a name="871"><span class="lineNum">     871 </span>            :             -3.27230890166736818752690751921364e-03,</a>
+<a name="872"><span class="lineNum">     872 </span>            :             9.92958015089934567000418130788830e-05,</a>
+<a name="873"><span class="lineNum">     873 </span>            :             5.60266733289934543670030020479089e-04,</a>
+<a name="874"><span class="lineNum">     874 </span>            :             -1.98286778613536816145718894022210e-05,</a>
+<a name="875"><span class="lineNum">     875 </span>            :             -6.39885786401657284281838111716922e-05,</a>
+<a name="876"><span class="lineNum">     876 </span>            :             1.91614024625604985099780984414419e-06,</a>
+<a name="877"><span class="lineNum">     877 </span>            :             3.69479211060541101930730298330552e-06</a>
+<a name="878"><span class="lineNum">     878 </span><span class="lineCov">          1 :           };</span></a>
+<a name="879"><span class="lineNum">     879 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="880"><span class="lineNum">     880 </span><span class="lineCov">          1 :     case 19:</span></a>
+<a name="881"><span class="lineNum">     881 </span><span class="lineCov">          2 :       h = { 2.47619856876035267576182871684942e-06,</span></a>
+<a name="882"><span class="lineNum">     882 </span>            :             2.91655676074685013668191455038503e-06,</a>
+<a name="883"><span class="lineNum">     883 </span>            :             -3.98117220914099361156295031616281e-05,</a>
+<a name="884"><span class="lineNum">     884 </span>            :             -2.37890336748671808665862859033524e-05,</a>
+<a name="885"><span class="lineNum">     885 </span>            :             3.90632340413758891075474144471968e-04,</a>
+<a name="886"><span class="lineNum">     886 </span>            :             1.82868669835172258141334222791841e-04,</a>
+<a name="887"><span class="lineNum">     887 </span>            :             -2.41117792464671338789616861220111e-03,</a>
+<a name="888"><span class="lineNum">     888 </span>            :             -8.73874136465524497564827388629283e-04,</a>
+<a name="889"><span class="lineNum">     889 </span>            :             1.16845675580482498412404623877592e-02,</a>
+<a name="890"><span class="lineNum">     890 </span>            :             6.10848600213812192166740189236407e-03,</a>
+<a name="891"><span class="lineNum">     891 </span>            :             -3.91877120522209840269844960403134e-02,</a>
+<a name="892"><span class="lineNum">     892 </span>            :             -2.39118550567039567233962316095131e-02,</a>
+<a name="893"><span class="lineNum">     893 </span>            :             1.18896719019111141157907240994973e-01,</a>
+<a name="894"><span class="lineNum">     894 </span>            :             1.32414008615193368179063782008598e-01,</a>
+<a name="895"><span class="lineNum">     895 </span>            :             -1.64390631231593420391590143481153e-01,</a>
+<a name="896"><span class="lineNum">     896 </span>            :             -2.49745683326209749752777611320198e-01,</a>
+<a name="897"><span class="lineNum">     897 </span>            :             3.65243519237511582442579083362943e-01,</a>
+<a name="898"><span class="lineNum">     898 </span>            :             1.01760518334862726241851760278223e+00,</a>
+<a name="899"><span class="lineNum">     899 </span>            :             8.17620422715306993666217749705538e-01,</a>
+<a name="900"><span class="lineNum">     900 </span>            :             1.54185800478859824647059895141865e-01,</a>
+<a name="901"><span class="lineNum">     901 </span>            :             -9.54948528806143087654945134090667e-02,</a>
+<a name="902"><span class="lineNum">     902 </span>            :             1.26637042824246960626144442585428e-02,</a>
+<a name="903"><span class="lineNum">     903 </span>            :             9.92151969664582453201084888405603e-03,</a>
+<a name="904"><span class="lineNum">     904 </span>            :             -6.59532404097190189107280389180232e-02,</a>
+<a name="905"><span class="lineNum">     905 </span>            :             -3.20347562503009650192176138716604e-02,</a>
+<a name="906"><span class="lineNum">     906 </span>            :             2.23409529027087383479255322527024e-02,</a>
+<a name="907"><span class="lineNum">     907 </span>            :             1.12690735439448276589136099801181e-02,</a>
+<a name="908"><span class="lineNum">     908 </span>            :             -7.24389178390821321384951403388186e-03,</a>
+<a name="909"><span class="lineNum">     909 </span>            :             -1.64148228823170379275797614582189e-03,</a>
+<a name="910"><span class="lineNum">     910 </span>            :             3.00014804641317691172308634861565e-03,</a>
+<a name="911"><span class="lineNum">     911 </span>            :             2.25083469591080945247998923441912e-04,</a>
+<a name="912"><span class="lineNum">     912 </span>            :             -8.99106799594682343235163557437772e-04,</a>
+<a name="913"><span class="lineNum">     913 </span>            :             -6.52240895281959979666239202167333e-05,</a>
+<a name="914"><span class="lineNum">     914 </span>            :             1.63397150769660883320999467116508e-04,</a>
+<a name="915"><span class="lineNum">     915 </span>            :             1.25487584192582468661661745934488e-05,</a>
+<a name="916"><span class="lineNum">     916 </span>            :             -1.68015900652064169079266675588258e-05,</a>
+<a name="917"><span class="lineNum">     917 </span>            :             -9.14098333564239404867173867386132e-07,</a>
+<a name="918"><span class="lineNum">     918 </span>            :             7.76082610749008778884821136562211e-07</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineCov">          1 :           };</span></a>
+<a name="920"><span class="lineNum">     920 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineCov">          1 :     case 20:</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineNoCov">          0 :       h = { -8.95074013313225034112988621332052e-07,</span></a>
+<a name="923"><span class="lineNum">     923 </span>            :             -4.60567304495735576428397861289965e-07,</a>
+<a name="924"><span class="lineNum">     924 </span>            :             1.73767995228992186179835244264069e-05,</a>
+<a name="925"><span class="lineNum">     925 </span>            :             6.39991346364665771576834066292072e-06,</a>
+<a name="926"><span class="lineNum">     926 </span>            :             -1.66016418292479542555967197969835e-04,</a>
+<a name="927"><span class="lineNum">     927 </span>            :             -3.76400722545106348484143798938106e-05,</a>
+<a name="928"><span class="lineNum">     928 </span>            :             1.05728141728119568419630436295620e-03,</a>
+<a name="929"><span class="lineNum">     929 </span>            :             1.77400246424138069000625561599804e-04,</a>
+<a name="930"><span class="lineNum">     930 </span>            :             -4.90965140656484527736935774555604e-03,</a>
+<a name="931"><span class="lineNum">     931 </span>            :             -8.64263223121293565169576122997341e-04,</a>
+<a name="932"><span class="lineNum">     932 </span>            :             1.71926521880978698531006187977255e-02,</a>
+<a name="933"><span class="lineNum">     933 </span>            :             2.74159026446779826788335832077337e-03,</a>
+<a name="934"><span class="lineNum">     934 </span>            :             -5.00254525875804267887048126794980e-02,</a>
+<a name="935"><span class="lineNum">     935 </span>            :             -9.67845613584030449449979727205573e-03,</a>
+<a name="936"><span class="lineNum">     936 </span>            :             1.25751400487193104593686143743980e-01,</a>
+<a name="937"><span class="lineNum">     937 </span>            :             5.12665874779235433700286250768841e-02,</a>
+<a name="938"><span class="lineNum">     938 </span>            :             -2.27092007441644233578514899818401e-01,</a>
+<a name="939"><span class="lineNum">     939 </span>            :             -7.22498274381410260369662523771694e-02,</a>
+<a name="940"><span class="lineNum">     940 </span>            :             6.67496745413005965197328350768657e-01,</a>
+<a name="941"><span class="lineNum">     941 </span>            :             1.06230451808460291118763052509166e+00,</a>
+<a name="942"><span class="lineNum">     942 </span>            :             5.73932332635040842738760602514958e-01,</a>
+<a name="943"><span class="lineNum">     943 </span>            :             -4.21709558919741780980139367329684e-02,</a>
+<a name="944"><span class="lineNum">     944 </span>            :             -1.11714873948519005653068347783119e-01,</a>
+<a name="945"><span class="lineNum">     945 </span>            :             3.61746629928947835419528189504490e-02,</a>
+<a name="946"><span class="lineNum">     946 </span>            :             1.14879797113225934346303347410867e-02,</a>
+<a name="947"><span class="lineNum">     947 </span>            :             -4.47307789806269048837883417490957e-02,</a>
+<a name="948"><span class="lineNum">     948 </span>            :             -4.68650205569037543035237902699919e-03,</a>
+<a name="949"><span class="lineNum">     949 </span>            :             2.40473567441355992602147750858421e-02,</a>
+<a name="950"><span class="lineNum">     950 </span>            :             2.01254944419308181777217292562909e-03,</a>
+<a name="951"><span class="lineNum">     951 </span>            :             -9.34312323805295934231462950947389e-03,</a>
+<a name="952"><span class="lineNum">     952 </span>            :             -4.31706836813935599089092631786002e-04,</a>
+<a name="953"><span class="lineNum">     953 </span>            :             2.95428464804820467212720380700830e-03,</a>
+<a name="954"><span class="lineNum">     954 </span>            :             1.02049526041390444994726161009879e-04,</a>
+<a name="955"><span class="lineNum">     955 </span>            :             -6.99655419422072467026951780866284e-04,</a>
+<a name="956"><span class="lineNum">     956 </span>            :             -2.72718682941954995583092036248729e-05,</a>
+<a name="957"><span class="lineNum">     957 </span>            :             1.13037635169613691495625606986408e-04,</a>
+<a name="958"><span class="lineNum">     958 </span>            :             4.27893798113462174641198274005482e-06,</a>
+<a name="959"><span class="lineNum">     959 </span>            :             -1.11996683141520158823655969881905e-05,</a>
+<a name="960"><span class="lineNum">     960 </span>            :             -2.68922267421127013513505862526975e-07,</a>
+<a name="961"><span class="lineNum">     961 </span>            :             5.22627921716999034327578478598131e-07</a>
+<a name="962"><span class="lineNum">     962 </span><span class="lineCov">          1 :           };</span></a>
+<a name="963"><span class="lineNum">     963 </span><span class="lineCov">          1 :       break;</span></a>
+<a name="964"><span class="lineNum">     964 </span><span class="lineNoCov">          0 :     default:</span></a>
+<a name="965"><span class="lineNum">     965 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;Wavelets: Specified order currently not implemented&quot;);</span></a>
+<a name="966"><span class="lineNum">     966 </span>            :     }</a>
+<a name="967"><span class="lineNum">     967 </span>            :   }</a>
+<a name="968"><span class="lineNum">     968 </span>            : </a>
+<a name="969"><span class="lineNum">     969 </span>            :   // to get highpass: reverse order and inverse sign of every second</a>
+<a name="970"><span class="lineNum">     970 </span><span class="lineCov">         49 :   if (!lowpass) {</span></a>
+<a name="971"><span class="lineNum">     971 </span><span class="lineCov">          2 :     std::reverse(h.begin(), h.end());</span></a>
+<a name="972"><span class="lineNum">     972 </span><span class="lineCov">         22 :     for (unsigned i=1; i &lt; h.size(); i += 2) {</span></a>
+<a name="973"><span class="lineNum">     973 </span><span class="lineCov">         20 :       h[i] = -h[i];</span></a>
+<a name="974"><span class="lineNum">     974 </span>            :     }</a>
+<a name="975"><span class="lineNum">     975 </span>            :   }</a>
+<a name="976"><span class="lineNum">     976 </span>            : </a>
+<a name="977"><span class="lineNum">     977 </span><span class="lineCov">         49 :   return h;</span></a>
+<a name="978"><span class="lineNum">     978 </span>            : }</a>
+<a name="979"><span class="lineNum">     979 </span>            : </a>
+<a name="980"><span class="lineNum">     980 </span>            : </a>
+<a name="981"><span class="lineNum">     981 </span>            : }</a>
+<a name="982"><span class="lineNum">     982 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/WaveletGrid.cpp.func-sort-c.html b/coverage/ves/WaveletGrid.cpp.func-sort-c.html
new file mode 100644
index 0000000000..344ebc2b1e
--- /dev/null
+++ b/coverage/ves/WaveletGrid.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/WaveletGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - WaveletGrid.cpp<span style="font-size: 80%;"> (<a href="WaveletGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntryHi">99.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="WaveletGrid.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#230">_ZN4PLMD3ves11WaveletGrid12stringToTypeERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#237">_ZN4PLMD3ves11WaveletGrid12typeToStringB5cxx11ENS1_4TypeEb</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#211">_ZN4PLMD3ves11WaveletGrid16fillGridFromMapsERSt10unique_ptrINS_4GridESt14default_deleteIS3_EERKSt13unordered_mapINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEESt6vectorIdSaIdEESt4hashISE_ESt8equal_toISE_ESaISt4pairIKSE_SH_EEESS_</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#36">_ZN4PLMD3ves11WaveletGrid9setupGridEjjbNS1_4TypeE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#82">_ZN4PLMD3ves11WaveletGrid13setupMatricesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">49</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#124">_ZN4PLMD3ves11WaveletGrid14getEigenvectorERKNS_6MatrixIdEEd</a></td>
+              <td class="coverFnHi">94</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#101">_ZN4PLMD3ves11WaveletGrid17calcIntegerValuesERKNS_6MatrixIdEEi</a></td>
+              <td class="coverFnHi">94</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#158">_ZN4PLMD3ves11WaveletGrid7cascadeB5cxx11ERSt6vectorINS_6MatrixIdEESaIS4_EES7_RKS2_IdSaIdEEjjjb</a></td>
+              <td class="coverFnHi">94</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/WaveletGrid.cpp.func.html b/coverage/ves/WaveletGrid.cpp.func.html
new file mode 100644
index 0000000000..7b9b55246a
--- /dev/null
+++ b/coverage/ves/WaveletGrid.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/WaveletGrid.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - WaveletGrid.cpp<span style="font-size: 80%;"> (<a href="WaveletGrid.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntryHi">99.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="WaveletGrid.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#230">_ZN4PLMD3ves11WaveletGrid12stringToTypeERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">49</td>
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+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#124">_ZN4PLMD3ves11WaveletGrid14getEigenvectorERKNS_6MatrixIdEEd</a></td>
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+              <td class="coverFnHi">47</td>
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+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#101">_ZN4PLMD3ves11WaveletGrid17calcIntegerValuesERKNS_6MatrixIdEEi</a></td>
+              <td class="coverFnHi">94</td>
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+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#158">_ZN4PLMD3ves11WaveletGrid7cascadeB5cxx11ERSt6vectorINS_6MatrixIdEESaIS4_EES7_RKS2_IdSaIdEEjjjb</a></td>
+              <td class="coverFnHi">94</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="WaveletGrid.cpp.gcov.html#36">_ZN4PLMD3ves11WaveletGrid9setupGridEjjbNS1_4TypeE</a></td>
+              <td class="coverFnHi">47</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/WaveletGrid.cpp.gcov.html b/coverage/ves/WaveletGrid.cpp.gcov.html
new file mode 100644
index 0000000000..cb6dddf64e
--- /dev/null
+++ b/coverage/ves/WaveletGrid.cpp.gcov.html
@@ -0,0 +1,330 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves/WaveletGrid.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">ves</a> - WaveletGrid.cpp<span style="font-size: 80%;"> (source / <a href="WaveletGrid.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">105</td>
+            <td class="headerCovTableEntryHi">99.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2021 The VES code team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE-VES file at the root of this folder for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.ves-code.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of VES code module.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    The VES code module is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    The VES code module is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with the VES code module.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;WaveletGrid.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Grid.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;memory&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &lt;unordered_map&gt;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace ves {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : // construction of Wavelet grid according to the Daubechies-Lagarias method</a>
+<a name="37"><span class="lineNum">      37 </span>            : // see Strang, Nguyen &quot;Wavelets and Filter Banks&quot; chapter 6.3</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         47 : std::unique_ptr&lt;Grid&gt; WaveletGrid::setupGrid(const unsigned order, unsigned gridsize, const bool use_mother_wavelet, const Type type) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         47 :   plumed_assert(order&gt;=1) &lt;&lt; &quot;Wavelet order has to be a positive integer&quot;;</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   // calculate the grid properties of the scaling grid</a>
+<a name="41"><span class="lineNum">      41 </span>            :   // the range of the grid is from 0 to maxsupport</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         47 :   unsigned maxsupport = order*2 -1;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   // determine needed recursion depth for specified size</a>
+<a name="44"><span class="lineNum">      44 </span>            :   unsigned recursion_number = 0;</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        173 :   while (maxsupport*(1U&lt;&lt;recursion_number) &lt; gridsize) { recursion_number++; }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   // set &quot;true&quot; gridsize</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         47 :   unsigned bins_per_int = 1U&lt;&lt;recursion_number;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :   gridsize = maxsupport*bins_per_int;</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span>            :   // Filter coefficients</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         47 :   std::vector&lt;double&gt; h_coeffs = getFilterCoefficients(order, true, type);</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   // Vector with the Matrices M0 and M1 for the cascade</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         47 :   std::vector&lt;Matrix&lt;double&gt;&gt; h_Matvec = setupMatrices(h_coeffs);</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   std::vector&lt;Matrix&lt;double&gt;&gt; g_Matvec; // only filled if needed for wavelet</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span>            :   // get the values at integers</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         47 :   std::vector&lt;double&gt; values_at_integers = calcIntegerValues(h_Matvec[0], 0);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         47 :   std::vector&lt;double&gt; derivs_at_integers = calcIntegerValues(h_Matvec[0], 1);</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span>            :   std::string gridvarname; // stores the name of the grid variable</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         47 :   if (use_mother_wavelet) { // get the highpass filter coefficients as well</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :     std::vector&lt;double&gt; g_coeffs = getFilterCoefficients(order, false, type);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          4 :     g_Matvec = setupMatrices(g_coeffs);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          4 :     gridvarname = typeToString(type,true)+std::to_string(order)+&quot;_psi&quot;;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :   }</a>
+<a name="66"><span class="lineNum">      66 </span>            :   else {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         90 :     gridvarname = typeToString(type,true)+std::to_string(order)+&quot;_phi&quot;;</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            :   // Set up the grid with correct properties</a>
+<a name="71"><span class="lineNum">      71 </span>            :   auto grid = std::unique_ptr&lt;Grid&gt;(new Grid(gridvarname, {&quot;position&quot;}, {&quot;0&quot;},</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        517 :   {std::to_string(maxsupport)}, {gridsize}, false, true, {false}, {&quot;0.&quot;}, {&quot;0.&quot;}));</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         47 :   BinaryMap values = cascade(h_Matvec, g_Matvec, values_at_integers, recursion_number, bins_per_int, 0, use_mother_wavelet);</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         47 :   BinaryMap derivs = cascade(h_Matvec, g_Matvec, derivs_at_integers, recursion_number, bins_per_int, 1, use_mother_wavelet);</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : </a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         47 :   fillGridFromMaps(grid, values, derivs);</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         47 :   return grid;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         47 : }</span></a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         49 : std::vector&lt;Matrix&lt;double&gt;&gt; WaveletGrid::setupMatrices(const std::vector&lt;double&gt;&amp; coeffs) {</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   Matrix&lt;double&gt; M0, M1;</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         49 :   const int N = coeffs.size() -1;</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :   M0.resize(N,N); M1.resize(N,N);</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">       1108 :   for (int i = 0; i &lt; N; ++i) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      27644 :     for (int j = 0; j &lt; N; ++j) {</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">      26585 :       int shift = 2*i -j;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">      26585 :       if (0 &lt;= shift &amp;&amp; shift &lt;= N) {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">      13822 :         M0[i][j] = coeffs[2*i -j]; // normalization is already included in coeffs</span></a>
+<a name="93"><span class="lineNum">      93 </span>            :       }</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      26585 :       if (-1 &lt;= shift &amp;&amp; shift &lt;= N -1) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      13822 :         M1[i][j] = coeffs[2*i -j + 1];</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :       }</a>
+<a name="97"><span class="lineNum">      97 </span>            :     }</a>
+<a name="98"><span class="lineNum">      98 </span>            :   }</a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        196 :   return std::vector&lt;Matrix&lt;double&gt;&gt; {M0, M1};</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         94 : std::vector&lt;double&gt; WaveletGrid::calcIntegerValues(const Matrix&lt;double&gt; &amp;M, const int deriv) {</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   // corresponding eigenvalue of the matrix</a>
+<a name="105"><span class="lineNum">     105 </span>            :   double eigenvalue = std::pow(0.5, deriv);</a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; values = getEigenvector(M, eigenvalue);</span></a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span>            :   // normalization of the eigenvector</a>
+<a name="109"><span class="lineNum">     109 </span>            :   double normfactor = 0.;</a>
+<a name="110"><span class="lineNum">     110 </span>            :   // i=0 is always 0; for derivs &gt; 1 an additional factorial would have to be added</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">       2042 :   for (unsigned i=1; i&lt;values.size(); ++i) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">       1948 :     normfactor += values[i] * std::pow(-i, deriv);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">         94 :   normfactor = 1/normfactor;</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       2136 :   for (auto&amp; value : values) {</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">       2042 :     value *= normfactor;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   }</a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         94 :   return values;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : // maybe move this to the tools/matrix.h file?</a>
+<a name="124"><span class="lineNum">     124 </span>            : // this works reliably only for singular eigenvalues</a>
+<a name="125"><span class="lineNum">     125 </span>            : //</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         94 : std::vector&lt;double&gt; WaveletGrid::getEigenvector(const Matrix&lt;double&gt; &amp;A, const double eigenvalue) {</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   // mostly copied from tools/matrix.h</a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         94 :   int info, N = A.ncols(); // ncols == nrows</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; da(N*N);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; S(N);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; U(N*N);</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; VT(N*N);</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">         94 :   std::vector&lt;int&gt; iwork(8*N);</span></a>
+<a name="134"><span class="lineNum">     134 </span>            : </a>
+<a name="135"><span class="lineNum">     135 </span>            :   // Transfer the matrix to the local array and substract eigenvalue</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">      53862 :   for (int i=0; i&lt;N; ++i) for (int j=0; j&lt;N; ++j) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">      51726 :       da[i*N+j]=static_cast&lt;double&gt;( A(j,i) );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">      51726 :       if (i==j) da[i*N+j] -= eigenvalue;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :     }</a>
+<a name="140"><span class="lineNum">     140 </span>            : </a>
+<a name="141"><span class="lineNum">     141 </span>            :   // This optimizes the size of the work array used in lapack singular value decomposition</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">         94 :   int lwork=-1;</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; work(1);</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         94 :   plumed_lapack_dgesdd( &quot;A&quot;, &amp;N, &amp;N, da.data(), &amp;N, S.data(), U.data(), &amp;N, VT.data(), &amp;N, work.data(), &amp;lwork, iwork.data(), &amp;info );</span></a>
+<a name="145"><span class="lineNum">     145 </span>            : </a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Retrieve correct sizes for work and reallocate</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">         94 :   lwork=static_cast&lt;int&gt;(work[0]); work.resize(lwork);</span></a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            :   // This does the singular value decomposition</a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">         94 :   plumed_lapack_dgesdd( &quot;A&quot;, &amp;N, &amp;N, da.data(), &amp;N, S.data(), U.data(), &amp;N, VT.data(), &amp;N, work.data(), &amp;lwork, iwork.data(), &amp;info );</span></a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            :   // fill eigenvector with last column of VT</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">         94 :   std::vector&lt;double&gt; eigenvector(N);</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       2136 :   for (int i=0; i&lt;N; ++i) eigenvector[i] = VT[N-1 + i*N];</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">         94 :   return eigenvector;</span></a>
+<a name="157"><span class="lineNum">     157 </span>            : }</a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">         94 : WaveletGrid::BinaryMap WaveletGrid::cascade(std::vector&lt;Matrix&lt;double&gt;&gt;&amp; h_Matvec, std::vector&lt;Matrix&lt;double&gt;&gt;&amp; g_Matvec, const std::vector&lt;double&gt;&amp; values_at_integers, const unsigned recursion_number, const unsigned bins_per_int, const unsigned derivnum, const bool use_mother_wavelet) {</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   BinaryMap scaling_map, wavelet_map;</a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">         94 :   scaling_map.reserve(bins_per_int);</span></a>
+<a name="163"><span class="lineNum">     163 </span>            :   // vector to store the binary representation of all the decimal parts</a>
+<a name="164"><span class="lineNum">     164 </span>            :   std::vector&lt;std::string&gt; binary_vec;</a>
+<a name="165"><span class="lineNum">     165 </span>            :   // vector used as result of the matrix multiplications</a>
+<a name="166"><span class="lineNum">     166 </span>            :   std::vector&lt;double&gt; temp_values;</a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   // multiply matrices by 2 if derivatives are calculated (assumes ascending order)</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        188 :   if (derivnum != 0) for (auto&amp; M : h_Matvec) M *= 2;</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">         94 :   if (use_mother_wavelet) {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :     wavelet_map.reserve(bins_per_int);</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">          8 :     if (derivnum != 0) for (auto&amp; M : g_Matvec) M *= 2;</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   }</a>
+<a name="175"><span class="lineNum">     175 </span>            : </a>
+<a name="176"><span class="lineNum">     176 </span>            :   // fill the first two datasets by hand</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        282 :   scaling_map[&quot;0&quot;] = values_at_integers;</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">         94 :   mult(h_Matvec[1], values_at_integers, temp_values);</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        188 :   scaling_map[&quot;1&quot;] = temp_values;</span></a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">         94 :   if (use_mother_wavelet) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">          4 :     mult(g_Matvec[0], values_at_integers, temp_values);</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         12 :     wavelet_map[&quot;0&quot;] = temp_values;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">          4 :     mult(g_Matvec[1], values_at_integers, temp_values);</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">         12 :     wavelet_map[&quot;1&quot;] = temp_values;</span></a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   // now do the cascade</a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineCov">         94 :   binary_vec.emplace_back(&quot;1&quot;);</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">        252 :   for (unsigned i=1; i&lt;recursion_number; ++i) {</span></a>
+<a name="191"><span class="lineNum">     191 </span>            :     std::vector&lt;std::string&gt; new_binary_vec;</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">       1144 :     for (const auto&amp; binary : binary_vec) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">       2958 :       for (unsigned k=0; k&lt;2; ++k) {</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :         // prepend the new bit</a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       3944 :         std::string new_binary = std::to_string(k) + binary;</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       1972 :         mult(h_Matvec[k], scaling_map[binary], temp_values);</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       1972 :         scaling_map.insert(std::pair&lt;std::string, std::vector&lt;double&gt;&gt;(new_binary, temp_values));</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">       1972 :         if (use_mother_wavelet) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          8 :           mult(g_Matvec[k], scaling_map[binary], temp_values);</span></a>
+<a name="200"><span class="lineNum">     200 </span><span class="lineCov">         16 :           wavelet_map.insert(std::pair&lt;std::string, std::vector&lt;double&gt;&gt;(new_binary, temp_values));</span></a>
+<a name="201"><span class="lineNum">     201 </span>            :         }</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">       1972 :         new_binary_vec.push_back(new_binary);</span></a>
+<a name="203"><span class="lineNum">     203 </span>            :       }</a>
+<a name="204"><span class="lineNum">     204 </span>            :     }</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        158 :     binary_vec = new_binary_vec;</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        158 :   }</span></a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span><span class="lineCov">        188 :   return use_mother_wavelet ? wavelet_map : scaling_map;</span></a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">         94 : }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            : </a>
+<a name="212"><span class="lineNum">     212 </span>            : // Fill the Grid with the values of the unordered maps</a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">         47 : void WaveletGrid::fillGridFromMaps(std::unique_ptr&lt;Grid&gt;&amp; grid, const BinaryMap&amp; values_map, const BinaryMap&amp; derivs_map) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">         47 :   unsigned bins_per_int = values_map.size();</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   // this is somewhat complicated… not sure if the unordered_map way is the best way for c++</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">       1127 :   for (const auto&amp; value_iter : values_map) {</span></a>
+<a name="217"><span class="lineNum">     217 </span>            :     // get decimal of binary key</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       1080 :     unsigned decimal = std::stoi(value_iter.first, nullptr, 2);</span></a>
+<a name="219"><span class="lineNum">     219 </span>            :     // corresponding iterator of deriv</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       1080 :     auto deriv_iter = derivs_map.find(value_iter.first);</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     // calculate first grid element</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">       1080 :     unsigned first_grid_element = decimal * (bins_per_int &gt;&gt; value_iter.first.length());</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">      19480 :     for (unsigned i=0; i&lt;value_iter.second.size(); ++i) {</span></a>
+<a name="224"><span class="lineNum">     224 </span>            :       // derivative has to be passed as vector</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">      18400 :       std::vector&lt;double&gt; deriv {deriv_iter-&gt;second[i]};</span></a>
+<a name="226"><span class="lineNum">     226 </span><span class="lineCov">      18400 :       grid-&gt;setValueAndDerivatives(first_grid_element + bins_per_int*i, value_iter.second[i], deriv);</span></a>
+<a name="227"><span class="lineNum">     227 </span>            :     }</a>
+<a name="228"><span class="lineNum">     228 </span>            :   }</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">         47 : }</span></a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : </a>
+<a name="232"><span class="lineNum">     232 </span><span class="lineCov">         47 : WaveletGrid::Type WaveletGrid::stringToType(std::string&amp; type_str) {</span></a>
+<a name="233"><span class="lineNum">     233 </span><span class="lineCov">        188 :   std::unordered_map&lt;std::string, Type&gt; typemap = { {&quot;DAUBECHIES&quot;, Type::db}, {&quot;SYMLETS&quot;, Type::sym} };</span></a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">         47 :   try { return typemap.at(type_str); }</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineNoCov">          0 :   catch(const std::out_of_range&amp; e) {plumed_merror(&quot;The specified wavelet type &quot;+type_str+&quot; is not implemented.&quot;); }</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : </a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">         47 : std::string WaveletGrid::typeToString(Type type, bool abbrev) {</span></a>
+<a name="240"><span class="lineNum">     240 </span>            :   std::string type_str;</a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">         47 :   switch(type) {</span></a>
+<a name="242"><span class="lineNum">     242 </span><span class="lineCov">         23 :   case Type::db:</span></a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">         23 :     type_str = abbrev ? &quot;Db&quot; : &quot;DAUBECHIES&quot;;</span></a>
+<a name="244"><span class="lineNum">     244 </span>            :     break;</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">         24 :   case Type::sym:</span></a>
+<a name="246"><span class="lineNum">     246 </span><span class="lineCov">         24 :     type_str = abbrev ? &quot;Sym&quot; : &quot;SYMLETS&quot;;</span></a>
+<a name="247"><span class="lineNum">     247 </span>            :     break;</a>
+<a name="248"><span class="lineNum">     248 </span>            :   }</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">         47 :   return type_str;</span></a>
+<a name="250"><span class="lineNum">     250 </span>            : }</a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span>            : </a>
+<a name="253"><span class="lineNum">     253 </span>            : }</a>
+<a name="254"><span class="lineNum">     254 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/index-sort-f.html b/coverage/ves/index-sort-f.html
new file mode 100644
index 0000000000..dd6750c65d
--- /dev/null
+++ b/coverage/ves/index-sort-f.html
@@ -0,0 +1,723 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - ves</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5938</td>
+            <td class="headerCovTableEntry">7230</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">555</td>
+            <td class="headerCovTableEntry">788</td>
+            <td class="headerCovTableEntryLo">70.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridLinearInterpolation.h.gcov.html">GridLinearInterpolation.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">2 / 9</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsMatrix.cpp.gcov.html">CoeffsMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=29 height=10 alt="29.5%"><img src="../snow.png" width=71 height=10 alt="29.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">29.5&nbsp;%</td>
+      <td class="coverNumLo">105 / 356</td>
+      <td class="coverPerLo">25.3&nbsp;%</td>
+      <td class="coverNumLo">20 / 79</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesBias.h.gcov.html">VesBias.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="74.2%"><img src="../snow.png" width=26 height=10 alt="74.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">74.2&nbsp;%</td>
+      <td class="coverNumLo">66 / 89</td>
+      <td class="coverPerLo">36.0&nbsp;%</td>
+      <td class="coverNumLo">9 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FermiSwitchingFunction.cpp.gcov.html">FermiSwitchingFunction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=49 height=10 alt="49.3%"><img src="../snow.png" width=51 height=10 alt="49.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">49.3&nbsp;%</td>
+      <td class="coverNumLo">33 / 67</td>
+      <td class="coverPerLo">44.4&nbsp;%</td>
+      <td class="coverNumLo">4 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsVector.cpp.gcov.html">CoeffsVector.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=51 height=10 alt="50.7%"><img src="../snow.png" width=49 height=10 alt="50.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.7&nbsp;%</td>
+      <td class="coverNumLo">232 / 458</td>
+      <td class="coverPerLo">45.5&nbsp;%</td>
+      <td class="coverNumLo">45 / 99</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsBase.cpp.gcov.html">CoeffsBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=42 height=10 alt="42.2%"><img src="../snow.png" width=58 height=10 alt="42.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">42.2&nbsp;%</td>
+      <td class="coverNumLo">127 / 301</td>
+      <td class="coverPerLo">46.9&nbsp;%</td>
+      <td class="coverNumLo">15 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistribution.h.gcov.html">TargetDistribution.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ProductDistribution.cpp.gcov.html">TD_ProductDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=64 height=10 alt="63.6%"><img src="../snow.png" width=36 height=10 alt="63.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.6&nbsp;%</td>
+      <td class="coverNumLo">49 / 77</td>
+      <td class="coverPerLo">53.8&nbsp;%</td>
+      <td class="coverNumLo">7 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridLinearInterpolation.cpp.gcov.html">GridLinearInterpolation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="55.0%"><img src="../snow.png" width=45 height=10 alt="55.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.0&nbsp;%</td>
+      <td class="coverNumLo">66 / 120</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesBias.cpp.gcov.html">VesBias.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverNumLo">27 / 45</td>
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+      <td class="coverFile"><a href="OutputFesBias.cpp.gcov.html">OutputFesBias.cpp</a></td>
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+      <td class="coverPerMed">88.4&nbsp;%</td>
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+      <td class="coverNumLo">5 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_ProductCombination.cpp.gcov.html">TD_ProductCombination.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerLo">73.7&nbsp;%</td>
+      <td class="coverNumLo">56 / 76</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_LinearCombination.cpp.gcov.html">TD_LinearCombination.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">75.6&nbsp;%</td>
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+      <td class="coverNumLo">9 / 13</td>
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+      <td class="coverFile"><a href="OutputBasisFunctions.cpp.gcov.html">OutputBasisFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverNumLo">5 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="OutputTargetDistribution.cpp.gcov.html">OutputTargetDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverNumLo">5 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="BasisFunctions.h.gcov.html">BasisFunctions.h</a></td>
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+      <td class="coverPerHi">96.7&nbsp;%</td>
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+      <td class="coverNumMed">6 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_WellTempered.cpp.gcov.html">TD_WellTempered.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">90.6&nbsp;%</td>
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+      <td class="coverNumMed">7 / 9</td>
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+    <tr>
+      <td class="coverFile"><a href="BasisFunctions.cpp.gcov.html">BasisFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">87.7&nbsp;%</td>
+      <td class="coverNumMed">222 / 253</td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 21</td>
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+    <tr>
+      <td class="coverFile"><a href="LinearBasisSetExpansion.cpp.gcov.html">LinearBasisSetExpansion.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">88.7&nbsp;%</td>
+      <td class="coverNumMed">313 / 353</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
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+    <tr>
+      <td class="coverFile"><a href="Optimizer.cpp.gcov.html">Optimizer.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">682 / 762</td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistribution.cpp.gcov.html">TargetDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.2%"><img src="../snow.png" width=13 height=10 alt="87.2%"></td></tr></table>
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+      <td class="coverPerMed">87.2&nbsp;%</td>
+      <td class="coverNumMed">190 / 218</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">22 / 26</td>
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+    <tr>
+      <td class="coverFile"><a href="Opt_Dummy.cpp.gcov.html">Opt_Dummy.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="Opt_BachAveragedSGD.cpp.gcov.html">Opt_BachAveragedSGD.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
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+      <td class="coverPerHi">95.2&nbsp;%</td>
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+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html">Opt_RobbinsMonroSGD.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
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+      <td class="coverPerHi">96.0&nbsp;%</td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="Opt_Adam.cpp.gcov.html">Opt_Adam.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.2%"><img src="../snow.png" width=7 height=10 alt="93.2%"></td></tr></table>
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+      <td class="coverPerHi">93.2&nbsp;%</td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="VesLinearExpansion.cpp.gcov.html">VesLinearExpansion.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">140 / 145</td>
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+      <td class="coverNumMed">21 / 24</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_Multicanonical.cpp.gcov.html">TD_Multicanonical.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
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+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">198 / 205</td>
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+      <td class="coverNumMed">8 / 9</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_MultithermalMultibaric.cpp.gcov.html">TD_MultithermalMultibaric.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
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+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">148 / 152</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.h.gcov.html">Optimizer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
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+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">53 / 56</td>
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+      <td class="coverNumHi">9 / 10</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_Custom.cpp.gcov.html">TD_Custom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="86.7%"><img src="../snow.png" width=13 height=10 alt="86.7%"></td></tr></table>
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+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">78 / 90</td>
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+      <td class="coverNumHi">9 / 10</td>
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+    <tr>
+      <td class="coverFile"><a href="VesDeltaF.cpp.gcov.html">VesDeltaF.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
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+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">346 / 356</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsVector.h.gcov.html">CoeffsVector.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
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+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 4</td>
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+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsMatrix.h.gcov.html">CoeffsMatrix.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
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+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
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+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WaveletCoeffs.cpp.gcov.html">WaveletCoeffs.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
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+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">145 / 150</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistModifer.h.gcov.html">TargetDistModifer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsBase.h.gcov.html">CoeffsBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">33 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
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+    <tr>
+      <td class="coverFile"><a href="VesTools.cpp.gcov.html">VesTools.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">92.1&nbsp;%</td>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LinearBasisSetExpansion.h.gcov.html">LinearBasisSetExpansion.h</a></td>
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+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridIntegrationWeights.cpp.gcov.html">GridIntegrationWeights.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.6%"><img src="../snow.png" width=24 height=10 alt="75.6%"></td></tr></table>
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+      <td class="coverPerMed">75.6&nbsp;%</td>
+      <td class="coverNumMed">34 / 45</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridProjWeights.h.gcov.html">GridProjWeights.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesTools.h.gcov.html">VesTools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=66 height=10 alt="65.6%"><img src="../snow.png" width=34 height=10 alt="65.6%"></td></tr></table>
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+      <td class="coverPerLo">65.6&nbsp;%</td>
+      <td class="coverNumLo">21 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Chi.cpp.gcov.html">TD_Chi.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Grid.cpp.gcov.html">TD_Grid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.9%"><img src="../snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">56 / 59</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ChiSquared.cpp.gcov.html">TD_ChiSquared.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Exponential.cpp.gcov.html">TD_Exponential.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 27</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_GeneralizedNormal.cpp.gcov.html">TD_GeneralizedNormal.cpp</a></td>
+      <td class="coverBar" align="center">
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+      </td>
+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">64 / 70</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Powers.cpp.gcov.html">BF_Powers.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Uniform.cpp.gcov.html">TD_Uniform.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.2%"><img src="../snow.png" width=2 height=10 alt="98.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.2&nbsp;%</td>
+      <td class="coverNumHi">55 / 56</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Gaussians.cpp.gcov.html">BF_Gaussians.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html">TD_ExponentiallyModifiedGaussian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">58 / 64</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Legendre.cpp.gcov.html">BF_Legendre.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Chebyshev.cpp.gcov.html">BF_Chebyshev.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_CubicBsplines.cpp.gcov.html">BF_CubicBsplines.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">59 / 59</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html">TD_GeneralizedExtremeValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Combined.cpp.gcov.html">BF_Combined.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">64 / 66</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Wavelets.cpp.gcov.html">BF_Wavelets.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">119 / 119</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_VonMises.cpp.gcov.html">TD_VonMises.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.7%"><img src="../snow.png" width=1 height=10 alt="98.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.7&nbsp;%</td>
+      <td class="coverNumHi">75 / 76</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Gaussian.cpp.gcov.html">TD_Gaussian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">77 / 85</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Cosine.cpp.gcov.html">BF_Cosine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Fourier.cpp.gcov.html">BF_Fourier.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Custom.cpp.gcov.html">BF_Custom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.4%"><img src="../snow.png" width=18 height=10 alt="82.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">126 / 153</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WaveletGrid.cpp.gcov.html">WaveletGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.0%"><img src="../snow.png" width=1 height=10 alt="99.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.0&nbsp;%</td>
+      <td class="coverNumHi">104 / 105</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Sine.cpp.gcov.html">BF_Sine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MD_LinearExpansionPES.cpp.gcov.html">MD_LinearExpansionPES.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">326 / 336</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/index-sort-l.html b/coverage/ves/index-sort-l.html
new file mode 100644
index 0000000000..1d6558a268
--- /dev/null
+++ b/coverage/ves/index-sort-l.html
@@ -0,0 +1,723 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - ves</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5938</td>
+            <td class="headerCovTableEntry">7230</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">555</td>
+            <td class="headerCovTableEntry">788</td>
+            <td class="headerCovTableEntryLo">70.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsMatrix.h.gcov.html">CoeffsMatrix.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridLinearInterpolation.h.gcov.html">GridLinearInterpolation.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=22 height=10 alt="22.2%"><img src="../snow.png" width=78 height=10 alt="22.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">22.2&nbsp;%</td>
+      <td class="coverNumLo">2 / 9</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsMatrix.cpp.gcov.html">CoeffsMatrix.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=29 height=10 alt="29.5%"><img src="../snow.png" width=71 height=10 alt="29.5%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">29.5&nbsp;%</td>
+      <td class="coverNumLo">105 / 356</td>
+      <td class="coverPerLo">25.3&nbsp;%</td>
+      <td class="coverNumLo">20 / 79</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsBase.cpp.gcov.html">CoeffsBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=42 height=10 alt="42.2%"><img src="../snow.png" width=58 height=10 alt="42.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">42.2&nbsp;%</td>
+      <td class="coverNumLo">127 / 301</td>
+      <td class="coverPerLo">46.9&nbsp;%</td>
+      <td class="coverNumLo">15 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FermiSwitchingFunction.cpp.gcov.html">FermiSwitchingFunction.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=49 height=10 alt="49.3%"><img src="../snow.png" width=51 height=10 alt="49.3%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">49.3&nbsp;%</td>
+      <td class="coverNumLo">33 / 67</td>
+      <td class="coverPerLo">44.4&nbsp;%</td>
+      <td class="coverNumLo">4 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsVector.h.gcov.html">CoeffsVector.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=50 height=10 alt="50.0%"><img src="../snow.png" width=50 height=10 alt="50.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 4</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsVector.cpp.gcov.html">CoeffsVector.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=51 height=10 alt="50.7%"><img src="../snow.png" width=49 height=10 alt="50.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">50.7&nbsp;%</td>
+      <td class="coverNumLo">232 / 458</td>
+      <td class="coverPerLo">45.5&nbsp;%</td>
+      <td class="coverNumLo">45 / 99</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="GridLinearInterpolation.cpp.gcov.html">GridLinearInterpolation.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=55 height=10 alt="55.0%"><img src="../snow.png" width=45 height=10 alt="55.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">55.0&nbsp;%</td>
+      <td class="coverNumLo">66 / 120</td>
+      <td class="coverPerLo">55.6&nbsp;%</td>
+      <td class="coverNumLo">5 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ProductDistribution.cpp.gcov.html">TD_ProductDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=64 height=10 alt="63.6%"><img src="../snow.png" width=36 height=10 alt="63.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.6&nbsp;%</td>
+      <td class="coverNumLo">49 / 77</td>
+      <td class="coverPerLo">53.8&nbsp;%</td>
+      <td class="coverNumLo">7 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesTools.h.gcov.html">VesTools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=66 height=10 alt="65.6%"><img src="../snow.png" width=34 height=10 alt="65.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">65.6&nbsp;%</td>
+      <td class="coverNumLo">21 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ProductCombination.cpp.gcov.html">TD_ProductCombination.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.7%"><img src="../snow.png" width=26 height=10 alt="73.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.7&nbsp;%</td>
+      <td class="coverNumLo">56 / 76</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesBias.h.gcov.html">VesBias.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="74.2%"><img src="../snow.png" width=26 height=10 alt="74.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">74.2&nbsp;%</td>
+      <td class="coverNumLo">66 / 89</td>
+      <td class="coverPerLo">36.0&nbsp;%</td>
+      <td class="coverNumLo">9 / 25</td>
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+    <tr>
+      <td class="coverFile"><a href="GridIntegrationWeights.cpp.gcov.html">GridIntegrationWeights.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">75.6&nbsp;%</td>
+      <td class="coverNumMed">34 / 45</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_LinearCombination.cpp.gcov.html">TD_LinearCombination.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">75.6&nbsp;%</td>
+      <td class="coverNumMed">59 / 78</td>
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+      <td class="coverNumLo">9 / 13</td>
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+    <tr>
+      <td class="coverFile"><a href="VesBias.cpp.gcov.html">VesBias.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">76.4&nbsp;%</td>
+      <td class="coverNumMed">330 / 432</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">27 / 45</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistribution.h.gcov.html">TargetDistribution.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
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+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Custom.cpp.gcov.html">BF_Custom.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">126 / 153</td>
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+      <td class="coverNumHi">8 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_Custom.cpp.gcov.html">TD_Custom.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">86.7&nbsp;%</td>
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+      <td class="coverNumHi">9 / 10</td>
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+    <tr>
+      <td class="coverFile"><a href="TargetDistribution.cpp.gcov.html">TargetDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">87.2&nbsp;%</td>
+      <td class="coverNumMed">190 / 218</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">22 / 26</td>
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+    <tr>
+      <td class="coverFile"><a href="BasisFunctions.cpp.gcov.html">BasisFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">87.7&nbsp;%</td>
+      <td class="coverNumMed">222 / 253</td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 21</td>
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+    <tr>
+      <td class="coverFile"><a href="OutputFesBias.cpp.gcov.html">OutputFesBias.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">88.4&nbsp;%</td>
+      <td class="coverNumMed">61 / 69</td>
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+      <td class="coverNumLo">5 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LinearBasisSetExpansion.cpp.gcov.html">LinearBasisSetExpansion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="88.7%"><img src="../snow.png" width=11 height=10 alt="88.7%"></td></tr></table>
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+      <td class="coverPerMed">88.7&nbsp;%</td>
+      <td class="coverNumMed">313 / 353</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.cpp.gcov.html">Optimizer.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=90 height=10 alt="89.5%"><img src="../snow.png" width=10 height=10 alt="89.5%"></td></tr></table>
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+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">682 / 762</td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Gaussian.cpp.gcov.html">TD_Gaussian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
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+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">77 / 85</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_WellTempered.cpp.gcov.html">TD_WellTempered.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
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+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">29 / 32</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html">TD_ExponentiallyModifiedGaussian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">58 / 64</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_GeneralizedNormal.cpp.gcov.html">TD_GeneralizedNormal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.4%"><img src="../snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
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+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">64 / 70</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesTools.cpp.gcov.html">VesTools.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.1%"><img src="../snow.png" width=8 height=10 alt="92.1%"></td></tr></table>
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+      <td class="coverPerHi">92.1&nbsp;%</td>
+      <td class="coverNumHi">35 / 38</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Opt_Adam.cpp.gcov.html">Opt_Adam.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.2%"><img src="../snow.png" width=7 height=10 alt="93.2%"></td></tr></table>
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+      <td class="coverPerHi">93.2&nbsp;%</td>
+      <td class="coverNumHi">68 / 73</td>
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+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputTargetDistribution.cpp.gcov.html">OutputTargetDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
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+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">84 / 90</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Optimizer.h.gcov.html">Optimizer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.6%"><img src="../snow.png" width=5 height=10 alt="94.6%"></td></tr></table>
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+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">53 / 56</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Grid.cpp.gcov.html">TD_Grid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.9%"><img src="../snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">56 / 59</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Opt_BachAveragedSGD.cpp.gcov.html">Opt_BachAveragedSGD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
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+      <td class="coverPerHi">95.2&nbsp;%</td>
+      <td class="coverNumHi">60 / 63</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Opt_Dummy.cpp.gcov.html">Opt_Dummy.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.5%"><img src="../snow.png" width=5 height=10 alt="95.5%"></td></tr></table>
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+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LinearBasisSetExpansion.h.gcov.html">LinearBasisSetExpansion.h</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.5%"><img src="../snow.png" width=5 height=10 alt="95.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html">Opt_RobbinsMonroSGD.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
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+      <td class="coverPerHi">96.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 25</td>
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+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesLinearExpansion.cpp.gcov.html">VesLinearExpansion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">140 / 145</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">21 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Multicanonical.cpp.gcov.html">TD_Multicanonical.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
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+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">198 / 205</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WaveletCoeffs.cpp.gcov.html">WaveletCoeffs.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">145 / 150</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BasisFunctions.h.gcov.html">BasisFunctions.h</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
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+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">59 / 61</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Combined.cpp.gcov.html">BF_Combined.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
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+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">64 / 66</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MD_LinearExpansionPES.cpp.gcov.html">MD_LinearExpansionPES.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
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+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">326 / 336</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesDeltaF.cpp.gcov.html">VesDeltaF.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
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+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">346 / 356</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_MultithermalMultibaric.cpp.gcov.html">TD_MultithermalMultibaric.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">148 / 152</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OutputBasisFunctions.cpp.gcov.html">OutputBasisFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.2%"><img src="../snow.png" width=2 height=10 alt="98.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.2&nbsp;%</td>
+      <td class="coverNumHi">109 / 111</td>
+      <td class="coverPerLo">71.4&nbsp;%</td>
+      <td class="coverNumLo">5 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Uniform.cpp.gcov.html">TD_Uniform.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.2%"><img src="../snow.png" width=2 height=10 alt="98.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.2&nbsp;%</td>
+      <td class="coverNumHi">55 / 56</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_VonMises.cpp.gcov.html">TD_VonMises.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.7%"><img src="../snow.png" width=1 height=10 alt="98.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.7&nbsp;%</td>
+      <td class="coverNumHi">75 / 76</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
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+      <td class="coverBar" align="center">
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+      <td class="coverFile"><a href="GridProjWeights.h.gcov.html">GridProjWeights.h</a></td>
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+      <td class="coverFile"><a href="TD_Exponential.cpp.gcov.html">TD_Exponential.cpp</a></td>
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+    <tr>
+      <td class="coverFile"><a href="CoeffsBase.h.gcov.html">CoeffsBase.h</a></td>
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+      <td class="coverFile"><a href="BF_Powers.cpp.gcov.html">BF_Powers.cpp</a></td>
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+      <td class="coverFile"><a href="BF_Cosine.cpp.gcov.html">BF_Cosine.cpp</a></td>
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+      <td class="coverFile"><a href="BF_Chebyshev.cpp.gcov.html">BF_Chebyshev.cpp</a></td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Sine.cpp.gcov.html">BF_Sine.cpp</a></td>
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+      <td class="coverNumHi">36 / 36</td>
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+      <td class="coverNumHi">8 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Fourier.cpp.gcov.html">BF_Fourier.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html">TD_GeneralizedExtremeValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_Chi.cpp.gcov.html">TD_Chi.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ChiSquared.cpp.gcov.html">TD_ChiSquared.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Legendre.cpp.gcov.html">BF_Legendre.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Gaussians.cpp.gcov.html">BF_Gaussians.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_CubicBsplines.cpp.gcov.html">BF_CubicBsplines.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverNumHi">7 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Wavelets.cpp.gcov.html">BF_Wavelets.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">119 / 119</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/ves/index.html b/coverage/ves/index.html
new file mode 100644
index 0000000000..f3b4f595a4
--- /dev/null
+++ b/coverage/ves/index.html
@@ -0,0 +1,723 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - ves</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - ves</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">5938</td>
+            <td class="headerCovTableEntry">7230</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">555</td>
+            <td class="headerCovTableEntry">788</td>
+            <td class="headerCovTableEntryLo">70.4 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Chebyshev.cpp.gcov.html">BF_Chebyshev.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Combined.cpp.gcov.html">BF_Combined.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">64 / 66</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Cosine.cpp.gcov.html">BF_Cosine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_CubicBsplines.cpp.gcov.html">BF_CubicBsplines.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">59 / 59</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Custom.cpp.gcov.html">BF_Custom.cpp</a></td>
+      <td class="coverBar" align="center">
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+      </td>
+      <td class="coverPerMed">82.4&nbsp;%</td>
+      <td class="coverNumMed">126 / 153</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Fourier.cpp.gcov.html">BF_Fourier.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="BF_Gaussians.cpp.gcov.html">BF_Gaussians.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">53 / 53</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Legendre.cpp.gcov.html">BF_Legendre.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverNumHi">43 / 43</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Powers.cpp.gcov.html">BF_Powers.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Sine.cpp.gcov.html">BF_Sine.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">36 / 36</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BF_Wavelets.cpp.gcov.html">BF_Wavelets.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">119 / 119</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BasisFunctions.cpp.gcov.html">BasisFunctions.cpp</a></td>
+      <td class="coverBar" align="center">
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+      </td>
+      <td class="coverPerMed">87.7&nbsp;%</td>
+      <td class="coverNumMed">222 / 253</td>
+      <td class="coverPerMed">81.0&nbsp;%</td>
+      <td class="coverNumMed">17 / 21</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BasisFunctions.h.gcov.html">BasisFunctions.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">59 / 61</td>
+      <td class="coverPerMed">75.0&nbsp;%</td>
+      <td class="coverNumMed">6 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsBase.cpp.gcov.html">CoeffsBase.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=42 height=10 alt="42.2%"><img src="../snow.png" width=58 height=10 alt="42.2%"></td></tr></table>
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+      <td class="coverPerLo">42.2&nbsp;%</td>
+      <td class="coverNumLo">127 / 301</td>
+      <td class="coverPerLo">46.9&nbsp;%</td>
+      <td class="coverNumLo">15 / 32</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsBase.h.gcov.html">CoeffsBase.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">33 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
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+      <td class="coverNumLo">105 / 356</td>
+      <td class="coverPerLo">25.3&nbsp;%</td>
+      <td class="coverNumLo">20 / 79</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="CoeffsMatrix.h.gcov.html">CoeffsMatrix.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
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+      <td class="coverNumLo">0 / 1</td>
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+    <tr>
+      <td class="coverFile"><a href="CoeffsVector.cpp.gcov.html">CoeffsVector.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerLo">50.7&nbsp;%</td>
+      <td class="coverNumLo">232 / 458</td>
+      <td class="coverPerLo">45.5&nbsp;%</td>
+      <td class="coverNumLo">45 / 99</td>
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+    <tr>
+      <td class="coverFile"><a href="CoeffsVector.h.gcov.html">CoeffsVector.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">2 / 4</td>
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+      <td class="coverNumHi">0 / 0</td>
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+    <tr>
+      <td class="coverFile"><a href="FermiSwitchingFunction.cpp.gcov.html">FermiSwitchingFunction.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerLo">49.3&nbsp;%</td>
+      <td class="coverNumLo">33 / 67</td>
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+      <td class="coverNumLo">4 / 9</td>
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+    <tr>
+      <td class="coverFile"><a href="GridIntegrationWeights.cpp.gcov.html">GridIntegrationWeights.cpp</a></td>
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+      <td class="coverFile"><a href="GridLinearInterpolation.cpp.gcov.html">GridLinearInterpolation.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverNumLo">5 / 9</td>
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+    <tr>
+      <td class="coverFile"><a href="GridLinearInterpolation.h.gcov.html">GridLinearInterpolation.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverNumLo">0 / 1</td>
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+    <tr>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
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+      <td class="coverNumHi">4 / 4</td>
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+    <tr>
+      <td class="coverFile"><a href="LinearBasisSetExpansion.cpp.gcov.html">LinearBasisSetExpansion.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerMed">88.7&nbsp;%</td>
+      <td class="coverNumMed">313 / 353</td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">30 / 36</td>
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+    <tr>
+      <td class="coverFile"><a href="LinearBasisSetExpansion.h.gcov.html">LinearBasisSetExpansion.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">95.5&nbsp;%</td>
+      <td class="coverNumHi">21 / 22</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
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+    <tr>
+      <td class="coverFile"><a href="MD_LinearExpansionPES.cpp.gcov.html">MD_LinearExpansionPES.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
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+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">326 / 336</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
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+    <tr>
+      <td class="coverFile"><a href="Opt_Adam.cpp.gcov.html">Opt_Adam.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.2%"><img src="../snow.png" width=7 height=10 alt="93.2%"></td></tr></table>
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+      <td class="coverPerHi">93.2&nbsp;%</td>
+      <td class="coverNumHi">68 / 73</td>
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+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Opt_BachAveragedSGD.cpp.gcov.html">Opt_BachAveragedSGD.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.2%"><img src="../snow.png" width=5 height=10 alt="95.2%"></td></tr></table>
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+      <td class="coverPerHi">95.2&nbsp;%</td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="Opt_Dummy.cpp.gcov.html">Opt_Dummy.cpp</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">95.5&nbsp;%</td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="Opt_RobbinsMonroSGD.cpp.gcov.html">Opt_RobbinsMonroSGD.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.0%"><img src="../snow.png" width=4 height=10 alt="96.0%"></td></tr></table>
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+      <td class="coverPerHi">96.0&nbsp;%</td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="Optimizer.cpp.gcov.html">Optimizer.cpp</a></td>
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+      <td class="coverPerMed">89.5&nbsp;%</td>
+      <td class="coverNumMed">682 / 762</td>
+      <td class="coverPerMed">84.4&nbsp;%</td>
+      <td class="coverNumMed">27 / 32</td>
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+    <tr>
+      <td class="coverFile"><a href="Optimizer.h.gcov.html">Optimizer.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverPerHi">94.6&nbsp;%</td>
+      <td class="coverNumHi">53 / 56</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
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+    <tr>
+      <td class="coverFile"><a href="OutputBasisFunctions.cpp.gcov.html">OutputBasisFunctions.cpp</a></td>
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+      <td class="coverPerHi">98.2&nbsp;%</td>
+      <td class="coverNumHi">109 / 111</td>
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+      <td class="coverNumLo">5 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="OutputFesBias.cpp.gcov.html">OutputFesBias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=88 height=10 alt="88.4%"><img src="../snow.png" width=12 height=10 alt="88.4%"></td></tr></table>
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+      <td class="coverNumMed">61 / 69</td>
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+      <td class="coverNumLo">5 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="OutputTargetDistribution.cpp.gcov.html">OutputTargetDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.3%"><img src="../snow.png" width=7 height=10 alt="93.3%"></td></tr></table>
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+      <td class="coverPerHi">93.3&nbsp;%</td>
+      <td class="coverNumHi">84 / 90</td>
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+      <td class="coverNumLo">5 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="TD_Chi.cpp.gcov.html">TD_Chi.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ChiSquared.cpp.gcov.html">TD_ChiSquared.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">41 / 41</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Custom.cpp.gcov.html">TD_Custom.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="86.7%"><img src="../snow.png" width=13 height=10 alt="86.7%"></td></tr></table>
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+      <td class="coverPerMed">86.7&nbsp;%</td>
+      <td class="coverNumMed">78 / 90</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Exponential.cpp.gcov.html">TD_Exponential.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">27 / 27</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ExponentiallyModifiedGaussian.cpp.gcov.html">TD_ExponentiallyModifiedGaussian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
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+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">58 / 64</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Gaussian.cpp.gcov.html">TD_Gaussian.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
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+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">77 / 85</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_GeneralizedExtremeValue.cpp.gcov.html">TD_GeneralizedExtremeValue.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">39 / 39</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_GeneralizedNormal.cpp.gcov.html">TD_GeneralizedNormal.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="91.4%"><img src="../snow.png" width=9 height=10 alt="91.4%"></td></tr></table>
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+      <td class="coverPerHi">91.4&nbsp;%</td>
+      <td class="coverNumHi">64 / 70</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Grid.cpp.gcov.html">TD_Grid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="94.9%"><img src="../snow.png" width=5 height=10 alt="94.9%"></td></tr></table>
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+      <td class="coverPerHi">94.9&nbsp;%</td>
+      <td class="coverNumHi">56 / 59</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_LinearCombination.cpp.gcov.html">TD_LinearCombination.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="75.6%"><img src="../snow.png" width=24 height=10 alt="75.6%"></td></tr></table>
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+      <td class="coverPerMed">75.6&nbsp;%</td>
+      <td class="coverNumMed">59 / 78</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Multicanonical.cpp.gcov.html">TD_Multicanonical.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
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+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">198 / 205</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_MultithermalMultibaric.cpp.gcov.html">TD_MultithermalMultibaric.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.4%"><img src="../snow.png" width=3 height=10 alt="97.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.4&nbsp;%</td>
+      <td class="coverNumHi">148 / 152</td>
+      <td class="coverPerMed">88.9&nbsp;%</td>
+      <td class="coverNumMed">8 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ProductCombination.cpp.gcov.html">TD_ProductCombination.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="73.7%"><img src="../snow.png" width=26 height=10 alt="73.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">73.7&nbsp;%</td>
+      <td class="coverNumLo">56 / 76</td>
+      <td class="coverPerLo">69.2&nbsp;%</td>
+      <td class="coverNumLo">9 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_ProductDistribution.cpp.gcov.html">TD_ProductDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=64 height=10 alt="63.6%"><img src="../snow.png" width=36 height=10 alt="63.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">63.6&nbsp;%</td>
+      <td class="coverNumLo">49 / 77</td>
+      <td class="coverPerLo">53.8&nbsp;%</td>
+      <td class="coverNumLo">7 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_Uniform.cpp.gcov.html">TD_Uniform.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=98 height=10 alt="98.2%"><img src="../snow.png" width=2 height=10 alt="98.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.2&nbsp;%</td>
+      <td class="coverNumHi">55 / 56</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_VonMises.cpp.gcov.html">TD_VonMises.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="98.7%"><img src="../snow.png" width=1 height=10 alt="98.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">98.7&nbsp;%</td>
+      <td class="coverNumHi">75 / 76</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TD_WellTempered.cpp.gcov.html">TD_WellTempered.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=91 height=10 alt="90.6%"><img src="../snow.png" width=9 height=10 alt="90.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.6&nbsp;%</td>
+      <td class="coverNumHi">29 / 32</td>
+      <td class="coverPerMed">77.8&nbsp;%</td>
+      <td class="coverNumMed">7 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistModifer.h.gcov.html">TargetDistModifer.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistribution.cpp.gcov.html">TargetDistribution.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=87 height=10 alt="87.2%"><img src="../snow.png" width=13 height=10 alt="87.2%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">87.2&nbsp;%</td>
+      <td class="coverNumMed">190 / 218</td>
+      <td class="coverPerMed">84.6&nbsp;%</td>
+      <td class="coverNumMed">22 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="TargetDistribution.h.gcov.html">TargetDistribution.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="81.8%"><img src="../snow.png" width=18 height=10 alt="81.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">81.8&nbsp;%</td>
+      <td class="coverNumMed">18 / 22</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesBias.cpp.gcov.html">VesBias.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=76 height=10 alt="76.4%"><img src="../snow.png" width=24 height=10 alt="76.4%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">76.4&nbsp;%</td>
+      <td class="coverNumMed">330 / 432</td>
+      <td class="coverPerLo">60.0&nbsp;%</td>
+      <td class="coverNumLo">27 / 45</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesBias.h.gcov.html">VesBias.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=74 height=10 alt="74.2%"><img src="../snow.png" width=26 height=10 alt="74.2%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">74.2&nbsp;%</td>
+      <td class="coverNumLo">66 / 89</td>
+      <td class="coverPerLo">36.0&nbsp;%</td>
+      <td class="coverNumLo">9 / 25</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesDeltaF.cpp.gcov.html">VesDeltaF.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.2%"><img src="../snow.png" width=3 height=10 alt="97.2%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.2&nbsp;%</td>
+      <td class="coverNumHi">346 / 356</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesLinearExpansion.cpp.gcov.html">VesLinearExpansion.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.6%"><img src="../snow.png" width=3 height=10 alt="96.6%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.6&nbsp;%</td>
+      <td class="coverNumHi">140 / 145</td>
+      <td class="coverPerMed">87.5&nbsp;%</td>
+      <td class="coverNumMed">21 / 24</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesTools.cpp.gcov.html">VesTools.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.1%"><img src="../snow.png" width=8 height=10 alt="92.1%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.1&nbsp;%</td>
+      <td class="coverNumHi">35 / 38</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">2 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesTools.h.gcov.html">VesTools.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=66 height=10 alt="65.6%"><img src="../snow.png" width=34 height=10 alt="65.6%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">65.6&nbsp;%</td>
+      <td class="coverNumLo">21 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">5 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WaveletCoeffs.cpp.gcov.html">WaveletCoeffs.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="96.7%"><img src="../snow.png" width=3 height=10 alt="96.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.7&nbsp;%</td>
+      <td class="coverNumHi">145 / 150</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="WaveletGrid.cpp.gcov.html">WaveletGrid.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=99 height=10 alt="99.0%"><img src="../snow.png" width=1 height=10 alt="99.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">99.0&nbsp;%</td>
+      <td class="coverNumHi">104 / 105</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithAveraging.cpp.func-sort-c.html b/coverage/vesselbase/ActionWithAveraging.cpp.func-sort-c.html
new file mode 100644
index 0000000000..26eb7bae70
--- /dev/null
+++ b/coverage/vesselbase/ActionWithAveraging.cpp.func-sort-c.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithAveraging.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithAveraging.cpp<span style="font-size: 80%;"> (<a href="ActionWithAveraging.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntryHi">95.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithAveraging.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#192">_ZN4PLMD10vesselbase19ActionWithAveraging17performOperationsERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#128">_ZN4PLMD10vesselbase19ActionWithAveraging29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#41">_ZN4PLMD10vesselbase19ActionWithAveragingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#101">_ZNK4PLMD10vesselbase19ActionWithAveraging19ignoreNormalizationEv</a></td>
+              <td class="coverFnHi">53</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#194">_ZN4PLMD10vesselbase19ActionWithAveraging12runFinalJobsEv</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#106">_ZN4PLMD10vesselbase19ActionWithAveraging18setAveragingActionESt10unique_ptrINS0_15AveragingVesselESt14default_deleteIS3_EERKb</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#41">_ZN4PLMD10vesselbase19ActionWithAveragingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#30">_ZN4PLMD10vesselbase19ActionWithAveraging16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">93</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#190">_ZN4PLMD10vesselbase19ActionWithAveraging12clearAverageEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#123">_ZNK4PLMD10vesselbase19ActionWithAveraging21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">374</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#113">_ZN4PLMD10vesselbase19ActionWithAveraging12lockRequestsEv</a></td>
+              <td class="coverFnHi">1240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#118">_ZN4PLMD10vesselbase19ActionWithAveraging14unlockRequestsEv</a></td>
+              <td class="coverFnHi">1240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#132">_ZN4PLMD10vesselbase19ActionWithAveraging6updateEv</a></td>
+              <td class="coverFnHi">1258</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#178">_ZNK4PLMD10vesselbase19ActionWithAveraging11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">60010</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithAveraging.cpp.func.html b/coverage/vesselbase/ActionWithAveraging.cpp.func.html
new file mode 100644
index 0000000000..471eb1bc9e
--- /dev/null
+++ b/coverage/vesselbase/ActionWithAveraging.cpp.func.html
@@ -0,0 +1,128 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithAveraging.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithAveraging.cpp<span style="font-size: 80%;"> (<a href="ActionWithAveraging.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntryHi">95.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithAveraging.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#190">_ZN4PLMD10vesselbase19ActionWithAveraging12clearAverageEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#113">_ZN4PLMD10vesselbase19ActionWithAveraging12lockRequestsEv</a></td>
+              <td class="coverFnHi">1240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#194">_ZN4PLMD10vesselbase19ActionWithAveraging12runFinalJobsEv</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#118">_ZN4PLMD10vesselbase19ActionWithAveraging14unlockRequestsEv</a></td>
+              <td class="coverFnHi">1240</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#30">_ZN4PLMD10vesselbase19ActionWithAveraging16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">93</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#192">_ZN4PLMD10vesselbase19ActionWithAveraging17performOperationsERKb</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#106">_ZN4PLMD10vesselbase19ActionWithAveraging18setAveragingActionESt10unique_ptrINS0_15AveragingVesselESt14default_deleteIS3_EERKb</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#128">_ZN4PLMD10vesselbase19ActionWithAveraging29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#132">_ZN4PLMD10vesselbase19ActionWithAveraging6updateEv</a></td>
+              <td class="coverFnHi">1258</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#41">_ZN4PLMD10vesselbase19ActionWithAveragingC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#41">_ZN4PLMD10vesselbase19ActionWithAveragingC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">73</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#178">_ZNK4PLMD10vesselbase19ActionWithAveraging11performTaskERKjS3_RNS_10MultiValueE</a></td>
+              <td class="coverFnHi">60010</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#101">_ZNK4PLMD10vesselbase19ActionWithAveraging19ignoreNormalizationEv</a></td>
+              <td class="coverFnHi">53</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.cpp.gcov.html#123">_ZNK4PLMD10vesselbase19ActionWithAveraging21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">374</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+  </table>
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+</html>
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new file mode 100644
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+  <title>LCOV - plumed test coverage - vesselbase/ActionWithAveraging.cpp</title>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithAveraging.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithAveraging.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">104</td>
+            <td class="headerCovTableEntry">109</td>
+            <td class="headerCovTableEntryHi">95.4 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">14</td>
+            <td class="headerCovTableEntryMed">78.6 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithAveraging.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;analysis/DataCollectionObject.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;analysis/ReadAnalysisFrames.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;bias/ReweightBase.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace vesselbase {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         93 : void ActionWithAveraging::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         93 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys ); ActionAtomistic::registerKeywords( keys );</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         93 :   ActionWithArguments::registerKeywords( keys ); ActionWithValue::registerKeywords( keys ); ActionWithVessel::registerKeywords( keys );</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        186 :   keys.add(&quot;compulsory&quot;,&quot;STRIDE&quot;,&quot;1&quot;,&quot;the frequency with which the data should be collected and added to the quantity being averaged&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        186 :   keys.add(&quot;compulsory&quot;,&quot;CLEAR&quot;,&quot;0&quot;,&quot;the frequency with which to clear all the accumulated data.  The default value &quot;</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :            &quot;of 0 implies that all the data will be used and that the grid will never be cleared&quot;);</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        186 :   keys.add(&quot;optional&quot;,&quot;LOGWEIGHTS&quot;,&quot;list of actions that calculates log weights that should be used to weight configurations when calculating averages&quot;);</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        186 :   keys.add(&quot;compulsory&quot;,&quot;NORMALIZATION&quot;,&quot;true&quot;,&quot;This controls how the data is normalized it can be set equal to true, false or ndata.  The differences between these options are explained in the manual page for \\ref HISTOGRAM&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         93 :   keys.remove(&quot;NUMERICAL_DERIVATIVES&quot;);</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         93 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         73 : ActionWithAveraging::ActionWithAveraging( const ActionOptions&amp; ao ):</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   Action(ao),</a>
+<a name="45"><span class="lineNum">      45 </span>            :   ActionPilot(ao),</a>
+<a name="46"><span class="lineNum">      46 </span>            :   ActionAtomistic(ao),</a>
+<a name="47"><span class="lineNum">      47 </span>            :   ActionWithArguments(ao),</a>
+<a name="48"><span class="lineNum">      48 </span>            :   ActionWithValue(ao),</a>
+<a name="49"><span class="lineNum">      49 </span>            :   ActionWithVessel(ao),</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         73 :   myaverage(NULL),</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         73 :   activated(false),</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         73 :   my_analysis_object(NULL),</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         73 :   normalization(t),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         73 :   useRunAllTasks(false),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         73 :   clearstride(0),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         73 :   lweight(0),cweight(0)</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : {</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        146 :   if( keywords.exists(&quot;CLEAR&quot;) ) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         58 :     parse(&quot;CLEAR&quot;,clearstride);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         58 :     if( clearstride&gt;0 ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         12 :       if( clearstride%getStride()!=0 ) error(&quot;CLEAR parameter must be a multiple of STRIDE&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         12 :       log.printf(&quot;  clearing grid every %u steps \n&quot;,clearstride);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            :     }</a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         73 :   if( ActionWithAveraging::getNumberOfArguments()&gt;0 ) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         29 :     my_analysis_object=dynamic_cast&lt;analysis::AnalysisBase*&gt;( getPntrToArgument(0)-&gt;getPntrToAction() );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         38 :     for(unsigned i=1; i&lt;ActionWithAveraging::getNumberOfArguments(); i++) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          9 :       if( my_analysis_object &amp;&amp; my_analysis_object-&gt;getLabel()!=(getPntrToArgument(i)-&gt;getPntrToAction())-&gt;getLabel() ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineNoCov">          0 :         error(&quot;all arguments should be from one single analysis object&quot;);</span></a>
+<a name="70"><span class="lineNum">      70 </span>            :       }</a>
+<a name="71"><span class="lineNum">      71 </span>            :     }</a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         29 :     if( my_analysis_object ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          7 :       if( getStride()!=1 ) error(&quot;stride should not have been set when calculating average from analysis data&quot;);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          7 :       setStride(0); addDependency( my_analysis_object );</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :     }</a>
+<a name="76"><span class="lineNum">      76 </span>            :   }</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        146 :   if( keywords.exists(&quot;LOGWEIGHTS&quot;) ) {</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">        116 :     std::vector&lt;std::string&gt; wwstr; parseVector(&quot;LOGWEIGHTS&quot;,wwstr);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         58 :     if( wwstr.size()&gt;0 ) log.printf(&quot;  reweighting using weights from &quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         58 :     std::vector&lt;Value*&gt; arg( getArguments() );</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         66 :     for(unsigned i=0; i&lt;wwstr.size(); ++i) {</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">          8 :       ActionWithValue* val = plumed.getActionSet().selectWithLabel&lt;ActionWithValue*&gt;(wwstr[i]);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">          8 :       if( !val ) error(&quot;could not find value named&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :       bias::ReweightBase* iswham=dynamic_cast&lt;bias::ReweightBase*&gt;( val );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          8 :       if( iswham &amp;&amp; iswham-&gt;buildsWeightStore() ) error(&quot;to use wham you must gather data using COLLECT_FRAMES&quot;);</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">          8 :       weights.push_back( val-&gt;copyOutput(val-&gt;getLabel()) );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">          8 :       arg.push_back( val-&gt;copyOutput(val-&gt;getLabel()) );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">          8 :       log.printf(&quot;%s &quot;,wwstr[i].c_str() );</span></a>
+<a name="89"><span class="lineNum">      89 </span>            :     }</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         58 :     if( wwstr.size()&gt;0 ) log.printf(&quot;\n&quot;);</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         51 :     else log.printf(&quot;  weights are all equal to one\n&quot;);</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">         58 :     requestArguments( arg );</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">         58 :   }</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">        146 :   if( keywords.exists(&quot;NORMALIZATION&quot;) ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">        116 :     std::string normstr; parse(&quot;NORMALIZATION&quot;,normstr);</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">         58 :     if( normstr==&quot;true&quot; ) normalization=t;</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         35 :     else if( normstr==&quot;false&quot; ) normalization=f;</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         26 :     else if( normstr==&quot;ndata&quot; ) normalization=ndata;</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineNoCov">          0 :     else error(&quot;invalid instruction for NORMALIZATION flag should be true, false, or ndata&quot;);</span></a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">         73 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">         53 : bool ActionWithAveraging::ignoreNormalization() const {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         53 :   if( normalization==f ) return true;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            :   return false;</a>
+<a name="106"><span class="lineNum">     106 </span>            : }</a>
+<a name="107"><span class="lineNum">     107 </span>            : </a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         68 : void ActionWithAveraging::setAveragingAction( std::unique_ptr&lt;AveragingVessel&gt; av_vessel, const bool&amp; usetasks ) {</span></a>
+<a name="109"><span class="lineNum">     109 </span>            :   // cppcheck-suppress danglingLifetime</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         68 :   myaverage=av_vessel.get();</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">         68 :   addVessel( std::move(av_vessel) );</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">         68 :   useRunAllTasks=usetasks; resizeFunctions();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">         68 : }</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">       1240 : void ActionWithAveraging::lockRequests() {</span></a>
+<a name="116"><span class="lineNum">     116 </span>            :   ActionAtomistic::lockRequests();</a>
+<a name="117"><span class="lineNum">     117 </span>            :   ActionWithArguments::lockRequests();</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">       1240 : }</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">       1240 : void ActionWithAveraging::unlockRequests() {</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :   ActionAtomistic::unlockRequests();</a>
+<a name="122"><span class="lineNum">     122 </span>            :   ActionWithArguments::unlockRequests();</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">       1240 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        374 : unsigned ActionWithAveraging::getNumberOfQuantities() const {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        374 :   if( my_analysis_object ) return getNumberOfArguments()+2;</span></a>
+<a name="127"><span class="lineNum">     127 </span>            :   return 2;</a>
+<a name="128"><span class="lineNum">     128 </span>            : }</a>
+<a name="129"><span class="lineNum">     129 </span>            : </a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 : void ActionWithAveraging::calculateNumericalDerivatives(PLMD::ActionWithValue*) {</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :   error(&quot;not possible to compute numerical derivatives for this action&quot;);</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">       1258 : void ActionWithAveraging::update() {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">       1258 :   if( (clearstride!=1 &amp;&amp; getStep()==0) || (!onStep() &amp;&amp; !my_analysis_object) ) return;</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">       1177 :   if( my_analysis_object ) {</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">          7 :     analysis::ReadAnalysisFrames* myfram = dynamic_cast&lt;analysis::ReadAnalysisFrames*&gt;( my_analysis_object );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">          7 :     if( !activated &amp;&amp; !myfram &amp;&amp; !onStep() ) return ;</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">          7 :     else if( !activated &amp;&amp; !my_analysis_object-&gt;onStep() ) return ;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            :   // Clear if it is time to reset</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">       1177 :   if( myaverage ) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">       1176 :     if( myaverage-&gt;wasreset() ) clearAverage();</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span>            :   // Calculate the weight for all reweighting</a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       1177 :   if ( weights.size()&gt;0 &amp;&amp; !my_analysis_object ) {</span></a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">       3018 :     double sum=0; for(unsigned i=0; i&lt;weights.size(); ++i) sum+=weights[i]-&gt;get();</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1009 :     lweight=sum; cweight = exp( sum );</span></a>
+<a name="150"><span class="lineNum">     150 </span>            :   } else {</a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        168 :     lweight=0; cweight=1.0;</span></a>
+<a name="152"><span class="lineNum">     152 </span>            :   }</a>
+<a name="153"><span class="lineNum">     153 </span>            :   // Prepare the task list for averaging</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       1177 :   if( my_analysis_object ) {</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">       2115 :     for(unsigned i=getFullNumberOfTasks(); i&lt;my_analysis_object-&gt;getNumberOfDataPoints(); ++i) addTaskToList(i);</span></a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">          7 :     deactivateAllTasks(); cweight=0;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">       2115 :     for(unsigned i=0; i&lt;my_analysis_object-&gt;getNumberOfDataPoints(); ++i) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       2108 :       taskFlags[i]=1; cweight += my_analysis_object-&gt;getWeight(i);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :     }</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">          7 :     lockContributors();</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :   }</a>
+<a name="162"><span class="lineNum">     162 </span>            :   // Prepare to do the averaging</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       1177 :   prepareForAveraging();</span></a>
+<a name="164"><span class="lineNum">     164 </span>            :   // Run all the tasks (if required</a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       1177 :   if( my_analysis_object || useRunAllTasks ) runAllTasks();</span></a>
+<a name="166"><span class="lineNum">     166 </span>            :   // This the averaging if it is not done using task list</a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">       1032 :   else performOperations( true );</span></a>
+<a name="168"><span class="lineNum">     168 </span>            :   // Update the norm</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">       1177 :   double normt = cweight; if( !my_analysis_object &amp;&amp; normalization==ndata ) normt = 1;</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       1177 :   if( myaverage &amp;&amp; my_analysis_object ) myaverage-&gt;setNorm( normt );</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">       1170 :   else if( myaverage ) myaverage-&gt;setNorm( normt + myaverage-&gt;getNorm() );</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :   // Finish the averaging</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       1177 :   finishAveraging();</span></a>
+<a name="174"><span class="lineNum">     174 </span>            :   // By resetting here we are ensuring that the grid will be cleared at the start of the next step</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1177 :   if( myaverage ) {</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1176 :     if( getStride()==0 || (clearstride&gt;0 &amp;&amp; getStep()%clearstride==0) ) myaverage-&gt;reset();</span></a>
+<a name="177"><span class="lineNum">     177 </span>            :   }</a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : </a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">      60010 : void ActionWithAveraging::performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const {</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">      60010 :   if( my_analysis_object ) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       2108 :     const analysis::DataCollectionObject&amp; mystore=my_analysis_object-&gt;getStoredData( current, false );</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">       4216 :     for(unsigned i=0; i&lt;getNumberOfArguments(); ++i) myvals.setValue( 1+i, mystore.getArgumentValue( ActionWithArguments::getArguments()[i]-&gt;getName() ) );</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">       2108 :     myvals.setValue( 0, my_analysis_object-&gt;getWeight(current) );</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">       2108 :     if( normalization==f ) myvals.setValue( 1+getNumberOfArguments(), 1.0 ); else myvals.setValue( 1+getNumberOfArguments(), 1.0 / cweight );</span></a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">       2108 :     accumulateAverage( myvals );</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :   } else {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      57902 :     runTask( current, myvals );</span></a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineCov">      60010 : }</span></a>
+<a name="191"><span class="lineNum">     191 </span>            : </a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        102 : void ActionWithAveraging::clearAverage() { plumed_assert( myaverage-&gt;wasreset() ); myaverage-&gt;clear(); }</span></a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineNoCov">          0 : void ActionWithAveraging::performOperations( const bool&amp; from_update ) { plumed_error(); }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">         58 : void ActionWithAveraging::runFinalJobs() {</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">         58 :   if( my_analysis_object &amp;&amp; getStride()==0 ) { activated=true; update(); }</span></a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">         58 : }</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : }</a>
+<a name="201"><span class="lineNum">     201 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithAveraging.h.func-sort-c.html b/coverage/vesselbase/ActionWithAveraging.h.func-sort-c.html
new file mode 100644
index 0000000000..bd6d4084e9
--- /dev/null
+++ b/coverage/vesselbase/ActionWithAveraging.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithAveraging.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithAveraging.h<span style="font-size: 80%;"> (<a href="ActionWithAveraging.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithAveraging.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#98">_ZNK4PLMD10vesselbase19ActionWithAveraging7runTaskERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#115">_ZN4PLMD10vesselbase19ActionWithAveraging12getArgumentsEv</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#102">_ZN4PLMD10vesselbase19ActionWithAveraging15finishAveragingEv</a></td>
+              <td class="coverFnHi">76</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#82">_ZN4PLMD10vesselbase19ActionWithAveraging22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">271</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#92">_ZN4PLMD10vesselbase19ActionWithAveraging19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#100">_ZNK4PLMD10vesselbase19ActionWithAveraging17accumulateAverageERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">2108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#110">_ZNK4PLMD10vesselbase19ActionWithAveraging20getNumberOfArgumentsEv</a></td>
+              <td class="coverFnHi">145728</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithAveraging.h.func.html b/coverage/vesselbase/ActionWithAveraging.h.func.html
new file mode 100644
index 0000000000..34eb31d04f
--- /dev/null
+++ b/coverage/vesselbase/ActionWithAveraging.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithAveraging.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithAveraging.h<span style="font-size: 80%;"> (<a href="ActionWithAveraging.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithAveraging.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#115">_ZN4PLMD10vesselbase19ActionWithAveraging12getArgumentsEv</a></td>
+              <td class="coverFnHi">58</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#102">_ZN4PLMD10vesselbase19ActionWithAveraging15finishAveragingEv</a></td>
+              <td class="coverFnHi">76</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#92">_ZN4PLMD10vesselbase19ActionWithAveraging19prepareForAveragingEv</a></td>
+              <td class="coverFnHi">1022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#82">_ZN4PLMD10vesselbase19ActionWithAveraging22getNumberOfDerivativesEv</a></td>
+              <td class="coverFnHi">271</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#100">_ZNK4PLMD10vesselbase19ActionWithAveraging17accumulateAverageERNS_10MultiValueE</a></td>
+              <td class="coverFnHi">2108</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#110">_ZNK4PLMD10vesselbase19ActionWithAveraging20getNumberOfArgumentsEv</a></td>
+              <td class="coverFnHi">145728</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithAveraging.h.gcov.html#98">_ZNK4PLMD10vesselbase19ActionWithAveraging7runTaskERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithAveraging.h.gcov.html b/coverage/vesselbase/ActionWithAveraging.h.gcov.html
new file mode 100644
index 0000000000..78f40ff14c
--- /dev/null
+++ b/coverage/vesselbase/ActionWithAveraging.h.gcov.html
@@ -0,0 +1,212 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithAveraging.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithAveraging.h<span style="font-size: 80%;"> (source / <a href="ActionWithAveraging.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_ActionWithAveraging_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_ActionWithAveraging_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionPilot.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/MultiValue.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;analysis/AnalysisBase.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : #include &quot;AveragingVessel.h&quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace PLMD {</a>
+<a name="36"><span class="lineNum">      36 </span>            : namespace vesselbase {</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : /**</a>
+<a name="39"><span class="lineNum">      39 </span>            : \ingroup INHERIT</a>
+<a name="40"><span class="lineNum">      40 </span>            : This abstract base class should be used if you are writing some method that calculates an &quot;average&quot; from a set of</a>
+<a name="41"><span class="lineNum">      41 </span>            : trajectory frames.  Notice that we use the word average very broadly here and state that even dimensionality</a>
+<a name="42"><span class="lineNum">      42 </span>            : reduction algorithms calculate an &quot;average.&quot;  In other words, what we mean by average is that the method is going</a>
+<a name="43"><span class="lineNum">      43 </span>            : to take in data from each trajectory frame and only calculate the final quantity once a certain amount of data has</a>
+<a name="44"><span class="lineNum">      44 </span>            : been collected.</a>
+<a name="45"><span class="lineNum">      45 </span>            : */</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : class ActionWithAveraging :</a>
+<a name="48"><span class="lineNum">      48 </span>            :   public ActionPilot,</a>
+<a name="49"><span class="lineNum">      49 </span>            :   public ActionAtomistic,</a>
+<a name="50"><span class="lineNum">      50 </span>            :   public ActionWithArguments,</a>
+<a name="51"><span class="lineNum">      51 </span>            :   public ActionWithValue,</a>
+<a name="52"><span class="lineNum">      52 </span>            :   public ActionWithVessel</a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   friend class AveragingVessel;</a>
+<a name="55"><span class="lineNum">      55 </span>            : private:</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The vessel which is used to compute averages</a>
+<a name="57"><span class="lineNum">      57 </span>            :   AveragingVessel* myaverage;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The weights we are going to use for reweighting</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::vector&lt;Value*&gt; weights;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Are we accumulated the unormalized quantity</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool activated;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// An object in which analysis data has been stored</a>
+<a name="63"><span class="lineNum">      63 </span>            :   analysis::AnalysisBase* my_analysis_object;</a>
+<a name="64"><span class="lineNum">      64 </span>            :   enum {t,f,ndata} normalization;</a>
+<a name="65"><span class="lineNum">      65 </span>            : protected:</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// This ensures runAllTasks is used</a>
+<a name="67"><span class="lineNum">      67 </span>            :   bool useRunAllTasks;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// The frequency with which to clear the grid</a>
+<a name="69"><span class="lineNum">      69 </span>            :   unsigned clearstride;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// The current weight and its logarithm</a>
+<a name="71"><span class="lineNum">      71 </span>            :   double lweight, cweight;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Set the averaging action</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void setAveragingAction( std::unique_ptr&lt;AveragingVessel&gt; av_vessel, const bool&amp; usetasks );</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Check if we are using the normalization condition when calculating this quantity</a>
+<a name="75"><span class="lineNum">      75 </span>            :   bool noNormalization() const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Are we storing data then averaging</a>
+<a name="77"><span class="lineNum">      77 </span>            :   bool storeThenAverage() const ;</a>
+<a name="78"><span class="lineNum">      78 </span>            : public:</a>
+<a name="79"><span class="lineNum">      79 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="80"><span class="lineNum">      80 </span>            :   explicit ActionWithAveraging( const ActionOptions&amp; );</a>
+<a name="81"><span class="lineNum">      81 </span>            :   void lockRequests() override;</a>
+<a name="82"><span class="lineNum">      82 </span>            :   void unlockRequests() override;</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void calculateNumericalDerivatives(PLMD::ActionWithValue*) override;</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        271 :   unsigned getNumberOfDerivatives() override { return 0; }</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :   unsigned getNumberOfQuantities() const override;</a>
+<a name="86"><span class="lineNum">      86 </span>            :   unsigned getNumberOfArguments() const override;</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Overwrite ActionWithArguments getArguments() so that we don't return the bias</a>
+<a name="88"><span class="lineNum">      88 </span>            :   using ActionWithArguments::getArguments;</a>
+<a name="89"><span class="lineNum">      89 </span>            :   std::vector&lt;Value*&gt; getArguments();</a>
+<a name="90"><span class="lineNum">      90 </span>            :   void update() override;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// This does the clearing of the action</a>
+<a name="92"><span class="lineNum">      92 </span>            :   virtual void clearAverage();</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// This is done before the averaging comences</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       1022 :   virtual void prepareForAveraging() {}</span></a>
+<a name="95"><span class="lineNum">      95 </span>            : /// This does the averaging operation</a>
+<a name="96"><span class="lineNum">      96 </span>            :   virtual void performOperations( const bool&amp; from_update );</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Does the calculation</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void performTask( const unsigned&amp; task_index, const unsigned&amp; current, MultiValue&amp; myvals ) const override;</a>
+<a name="99"><span class="lineNum">      99 </span>            : ///</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineNoCov">          0 :   virtual void runTask( const unsigned&amp; current, MultiValue&amp; myvals ) const { plumed_error(); }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : ///</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">       2108 :   virtual void accumulateAverage( MultiValue&amp; myvals ) const {}</span></a>
+<a name="103"><span class="lineNum">     103 </span>            : /// This is done once the averaging is finished</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">         76 :   virtual void finishAveraging() {}</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : ///</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void runFinalJobs() override;</a>
+<a name="107"><span class="lineNum">     107 </span>            : ///</a>
+<a name="108"><span class="lineNum">     108 </span>            :   virtual bool ignoreNormalization() const ;</a>
+<a name="109"><span class="lineNum">     109 </span>            : };</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            : inline</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">     145728 : unsigned ActionWithAveraging::getNumberOfArguments() const {</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">        226 :   return ActionWithArguments::getNumberOfArguments() - weights.size();</span></a>
+<a name="114"><span class="lineNum">     114 </span>            : }</a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span>            : inline</a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         58 : std::vector&lt;Value*&gt; ActionWithAveraging::getArguments() {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">         58 :   std::vector&lt;Value*&gt; arg_vals( ActionWithArguments::getArguments() );</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         58 :   for(unsigned i=0; i&lt;weights.size(); ++i) arg_vals.erase(arg_vals.end()-1);</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">         58 :   return arg_vals;</span></a>
+<a name="121"><span class="lineNum">     121 </span>            : }</a>
+<a name="122"><span class="lineNum">     122 </span>            : </a>
+<a name="123"><span class="lineNum">     123 </span>            : inline</a>
+<a name="124"><span class="lineNum">     124 </span>            : bool ActionWithAveraging::noNormalization() const {</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         36 :   return normalization==f;</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span>            : inline</a>
+<a name="129"><span class="lineNum">     129 </span>            : bool ActionWithAveraging::storeThenAverage() const {</a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">        105 :   if( my_analysis_object ) return true;</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :   return false;</a>
+<a name="132"><span class="lineNum">     132 </span>            : }</a>
+<a name="133"><span class="lineNum">     133 </span>            : </a>
+<a name="134"><span class="lineNum">     134 </span>            : }</a>
+<a name="135"><span class="lineNum">     135 </span>            : }</a>
+<a name="136"><span class="lineNum">     136 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithInputVessel.cpp.func-sort-c.html b/coverage/vesselbase/ActionWithInputVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d236c6e736
--- /dev/null
+++ b/coverage/vesselbase/ActionWithInputVessel.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithInputVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithInputVessel.cpp<span style="font-size: 80%;"> (<a href="ActionWithInputVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryMed">86.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithInputVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#81">_ZN4PLMD10vesselbase21ActionWithInputVessel17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#36">_ZN4PLMD10vesselbase21ActionWithInputVesselC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#69">_ZN4PLMD10vesselbase21ActionWithInputVessel29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#43">_ZN4PLMD10vesselbase21ActionWithInputVessel12readArgumentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#36">_ZN4PLMD10vesselbase21ActionWithInputVesselC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#29">_ZN4PLMD10vesselbase21ActionWithInputVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithInputVessel.cpp.func.html b/coverage/vesselbase/ActionWithInputVessel.cpp.func.html
new file mode 100644
index 0000000000..34acd1107a
--- /dev/null
+++ b/coverage/vesselbase/ActionWithInputVessel.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithInputVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithInputVessel.cpp<span style="font-size: 80%;"> (<a href="ActionWithInputVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryMed">86.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithInputVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#43">_ZN4PLMD10vesselbase21ActionWithInputVessel12readArgumentERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#29">_ZN4PLMD10vesselbase21ActionWithInputVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">30</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#81">_ZN4PLMD10vesselbase21ActionWithInputVessel17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#69">_ZN4PLMD10vesselbase21ActionWithInputVessel29calculateNumericalDerivativesEPNS_15ActionWithValueE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#36">_ZN4PLMD10vesselbase21ActionWithInputVesselC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.cpp.gcov.html#36">_ZN4PLMD10vesselbase21ActionWithInputVesselC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">24</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithInputVessel.cpp.gcov.html b/coverage/vesselbase/ActionWithInputVessel.cpp.gcov.html
new file mode 100644
index 0000000000..e0d8ccf951
--- /dev/null
+++ b/coverage/vesselbase/ActionWithInputVessel.cpp.gcov.html
@@ -0,0 +1,164 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithInputVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithInputVessel.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithInputVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">37</td>
+            <td class="headerCovTableEntryMed">86.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithInputVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;BridgeVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/PlumedMain.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionSet.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace vesselbase {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         30 : void ActionWithInputVessel::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         60 :   keys.add(&quot;compulsory&quot;,&quot;DATA&quot;,&quot;certain actions in plumed work by calculating a list of variables and summing over them. &quot;</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :            &quot;This particular action can be used to calculate functions of these base variables or prints &quot;</a>
+<a name="34"><span class="lineNum">      34 </span>            :            &quot;them to a file. This keyword thus takes the label of one of those such variables as input.&quot;);</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         60 :   keys.reserve(&quot;compulsory&quot;,&quot;GRID&quot;,&quot;the action that creates the input grid you would like to use&quot;);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         30 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         24 : ActionWithInputVessel::ActionWithInputVessel(const ActionOptions&amp;ao):</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   Action(ao),</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         24 :   arguments(NULL),</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         24 :   myBridgeVessel(NULL)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : {</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         24 : }</span></a>
+<a name="44"><span class="lineNum">      44 </span>            : </a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         24 : void ActionWithInputVessel::readArgument( const std::string&amp; type ) {</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   std::string mlab;</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         96 :   if( keywords.exists(&quot;DATA&quot;) &amp;&amp; type!=&quot;grid&quot; ) parse(&quot;DATA&quot;,mlab);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         24 :   ActionWithVessel* mves= plumed.getActionSet().selectWithLabel&lt;ActionWithVessel*&gt;(mlab);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         24 :   if(!mves) error(&quot;action labelled &quot; +  mlab + &quot; does not exist or does not have vessels&quot;);</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         24 :   addDependency(mves);</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         24 :   ActionWithValue* aval=dynamic_cast&lt;ActionWithValue*&gt;( this );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         24 :   if(aval) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          2 :     if( aval-&gt;checkNumericalDerivatives() ) {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          1 :       ActionWithValue* aval2=dynamic_cast&lt;ActionWithValue*&gt;( mves );</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          1 :       plumed_assert( aval2 ); aval2-&gt;useNumericalDerivatives();</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :     }</a>
+<a name="58"><span class="lineNum">      58 </span>            :   }</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         24 :   if( type==&quot;bridge&quot; ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 :     ActionWithVessel* aves=dynamic_cast&lt;ActionWithVessel*&gt;( this );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          2 :     plumed_assert(aves); myBridgeVessel = mves-&gt;addBridgingVessel( aves );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :     arguments = dynamic_cast&lt;Vessel*&gt;( myBridgeVessel );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         22 :   } else  if( type==&quot;store&quot; ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         22 :     arguments = dynamic_cast&lt;Vessel*&gt;( mves-&gt;buildDataStashes( NULL ) );</span></a>
+<a name="66"><span class="lineNum">      66 </span>            :   } else {</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineNoCov">          0 :     plumed_error();</span></a>
+<a name="68"><span class="lineNum">      68 </span>            :   }</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         24 : }</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">          5 : void ActionWithInputVessel::calculateNumericalDerivatives( ActionWithValue* a ) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          5 :   if(!a) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          5 :     a=dynamic_cast&lt;ActionWithValue*&gt;(this);</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          5 :     plumed_massert(a,&quot;cannot compute numerical derivatives for an action without values&quot;);</span></a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          5 :   if( myBridgeVessel ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          5 :     myBridgeVessel-&gt;completeNumericalDerivatives();</span></a>
+<a name="78"><span class="lineNum">      78 </span>            :   } else {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineNoCov">          0 :     error(&quot;numerical derivatives are not implemented&quot;);</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">          5 : }</span></a>
+<a name="82"><span class="lineNum">      82 </span>            : </a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 : void ActionWithInputVessel::applyBridgeForces( const std::vector&lt;double&gt;&amp; bb ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :   plumed_dbg_assert( myBridgeVessel ); addBridgeForces( bb );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithInputVessel.h.func-sort-c.html b/coverage/vesselbase/ActionWithInputVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..13a64f90f8
--- /dev/null
+++ b/coverage/vesselbase/ActionWithInputVessel.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithInputVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithInputVessel.h<span style="font-size: 80%;"> (<a href="ActionWithInputVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithInputVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.h.gcov.html#57">_ZN4PLMD10vesselbase21ActionWithInputVessel15addBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithInputVessel.h.func.html b/coverage/vesselbase/ActionWithInputVessel.h.func.html
new file mode 100644
index 0000000000..b98cbc2050
--- /dev/null
+++ b/coverage/vesselbase/ActionWithInputVessel.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithInputVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithInputVessel.h<span style="font-size: 80%;"> (<a href="ActionWithInputVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithInputVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithInputVessel.h.gcov.html#57">_ZN4PLMD10vesselbase21ActionWithInputVessel15addBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithInputVessel.h.gcov.html b/coverage/vesselbase/ActionWithInputVessel.h.gcov.html
new file mode 100644
index 0000000000..181137e855
--- /dev/null
+++ b/coverage/vesselbase/ActionWithInputVessel.h.gcov.html
@@ -0,0 +1,146 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithInputVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithInputVessel.h<span style="font-size: 80%;"> (source / <a href="ActionWithInputVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryLo">66.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2014-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_ActionWithInputVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_ActionWithInputVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/Action.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace PLMD {</a>
+<a name="30"><span class="lineNum">      30 </span>            : namespace vesselbase {</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /**</a>
+<a name="33"><span class="lineNum">      33 </span>            : \ingroup MULTIINHERIT</a>
+<a name="34"><span class="lineNum">      34 </span>            : */</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class ActionWithInputVessel : public virtual Action {</a>
+<a name="37"><span class="lineNum">      37 </span>            : private:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   Vessel* arguments;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   BridgeVessel* myBridgeVessel;</a>
+<a name="40"><span class="lineNum">      40 </span>            : protected:</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// What type of arguments are we reading in</a>
+<a name="42"><span class="lineNum">      42 </span>            :   void readArgument( const std::string&amp; type );</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Return a pointer to specific argument</a>
+<a name="44"><span class="lineNum">      44 </span>            :   Vessel* getPntrToArgument();</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Add forces to arguments (used in apply)</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void addForcesOnArguments( const std::vector&lt;double&gt;&amp; forces );</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// Registers the list of keywords</a>
+<a name="49"><span class="lineNum">      49 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="50"><span class="lineNum">      50 </span>            :   explicit ActionWithInputVessel(const ActionOptions&amp;);</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         22 :   virtual ~ActionWithInputVessel() {}</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Calculate the numerical derivatives</a>
+<a name="53"><span class="lineNum">      53 </span>            : /// N.B. only pass an ActionWithValue to this routine if you know exactly what you</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// are doing.  The default will be correct for the vast majority of cases</a>
+<a name="55"><span class="lineNum">      55 </span>            :   virtual void calculateNumericalDerivatives( ActionWithValue* a=NULL );</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Apply forces from the bridge</a>
+<a name="57"><span class="lineNum">      57 </span>            :   void applyBridgeForces( const std::vector&lt;double&gt;&amp; bb );</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Apply forces from the bridge</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineNoCov">          0 :   virtual void addBridgeForces( const std::vector&lt;double&gt;&amp; bb ) {}</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : };</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : inline</a>
+<a name="63"><span class="lineNum">      63 </span>            : Vessel* ActionWithInputVessel::getPntrToArgument() {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         74 :   return arguments;</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : }</a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithVessel.cpp.func-sort-c.html b/coverage/vesselbase/ActionWithVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c966a1b526
--- /dev/null
+++ b/coverage/vesselbase/ActionWithVessel.cpp.func-sort-c.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithVessel.cpp<span style="font-size: 80%;"> (<a href="ActionWithVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">188</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#376">_ZN4PLMD10vesselbase16ActionWithVessel14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#380">_ZN4PLMD10vesselbase16ActionWithVessel17getVesselWithNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#49">_ZN4PLMD10vesselbase16ActionWithVesselC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#89">_ZN4PLMD10vesselbase16ActionWithVesselD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#89">_ZN4PLMD10vesselbase16ActionWithVesselD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#340">_ZNK4PLMD10vesselbase16ActionWithVessel27transformBridgedDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#126">_ZN4PLMD10vesselbase16ActionWithVessel17addBridgingVesselEPS1_</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#140">_ZN4PLMD10vesselbase16ActionWithVessel16buildDataStashesEPS1_</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#97">_ZN4PLMD10vesselbase16ActionWithVessel9addVesselERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_i</a></td>
+              <td class="coverFnHi">359</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#162">_ZN4PLMD10vesselbase16ActionWithVessel18readVesselKeywordsEv</a></td>
+              <td class="coverFnHi">417</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#108">_ZN4PLMD10vesselbase16ActionWithVessel9addVesselESt10unique_ptrINS0_6VesselESt14default_deleteIS3_EE</a></td>
+              <td class="coverFnHi">555</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#49">_ZN4PLMD10vesselbase16ActionWithVesselC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">570</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#89">_ZN4PLMD10vesselbase16ActionWithVesselD2Ev</a></td>
+              <td class="coverFnHi">570</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#35">_ZN4PLMD10vesselbase16ActionWithVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">796</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#197">_ZN4PLMD10vesselbase16ActionWithVessel16needsDerivativesEv</a></td>
+              <td class="coverFnHi">812</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#193">_ZN4PLMD10vesselbase16ActionWithVessel15resizeFunctionsEv</a></td>
+              <td class="coverFnHi">1375</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#209">_ZN4PLMD10vesselbase16ActionWithVessel16lockContributorsEv</a></td>
+              <td class="coverFnHi">3316</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#236">_ZN4PLMD10vesselbase16ActionWithVessel18deactivateAllTasksEv</a></td>
+              <td class="coverFnHi">3316</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#359">_ZN4PLMD10vesselbase16ActionWithVessel20getForcesFromVesselsERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">7222</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#260">_ZN4PLMD10vesselbase16ActionWithVessel11runAllTasksEv</a></td>
+              <td class="coverFnHi">19966</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#354">_ZN4PLMD10vesselbase16ActionWithVessel18finishComputationsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">22991</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#245">_ZN4PLMD10vesselbase16ActionWithVessel28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">22991</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#250">_ZN4PLMD10vesselbase16ActionWithVessel15getSizeOfBufferERj</a></td>
+              <td class="coverFnHi">23504</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#241">_ZNK4PLMD10vesselbase16ActionWithVessel21taskIsCurrentlyActiveERKj</a></td>
+              <td class="coverFnHi">213721</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#344">_ZN4PLMD10vesselbase16ActionWithVessel19calculateAllVesselsERKjRNS_10MultiValueES5_RSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">467194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#157">_ZN4PLMD10vesselbase16ActionWithVessel13addTaskToListERKj</a></td>
+              <td class="coverFnHi">12661369</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithVessel.cpp.func.html b/coverage/vesselbase/ActionWithVessel.cpp.func.html
new file mode 100644
index 0000000000..7d18a687ae
--- /dev/null
+++ b/coverage/vesselbase/ActionWithVessel.cpp.func.html
@@ -0,0 +1,176 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithVessel.cpp<span style="font-size: 80%;"> (<a href="ActionWithVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">188</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#260">_ZN4PLMD10vesselbase16ActionWithVessel11runAllTasksEv</a></td>
+              <td class="coverFnHi">19966</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#157">_ZN4PLMD10vesselbase16ActionWithVessel13addTaskToListERKj</a></td>
+              <td class="coverFnHi">12661369</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#376">_ZN4PLMD10vesselbase16ActionWithVessel14retrieveDomainERNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES8_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#250">_ZN4PLMD10vesselbase16ActionWithVessel15getSizeOfBufferERj</a></td>
+              <td class="coverFnHi">23504</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#193">_ZN4PLMD10vesselbase16ActionWithVessel15resizeFunctionsEv</a></td>
+              <td class="coverFnHi">1375</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#140">_ZN4PLMD10vesselbase16ActionWithVessel16buildDataStashesEPS1_</a></td>
+              <td class="coverFnHi">192</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#209">_ZN4PLMD10vesselbase16ActionWithVessel16lockContributorsEv</a></td>
+              <td class="coverFnHi">3316</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#197">_ZN4PLMD10vesselbase16ActionWithVessel16needsDerivativesEv</a></td>
+              <td class="coverFnHi">812</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">796</td>
+            </tr>
+    <tr>
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+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
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+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#236">_ZN4PLMD10vesselbase16ActionWithVessel18deactivateAllTasksEv</a></td>
+              <td class="coverFnHi">3316</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#354">_ZN4PLMD10vesselbase16ActionWithVessel18finishComputationsERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">22991</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#162">_ZN4PLMD10vesselbase16ActionWithVessel18readVesselKeywordsEv</a></td>
+              <td class="coverFnHi">417</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#344">_ZN4PLMD10vesselbase16ActionWithVessel19calculateAllVesselsERKjRNS_10MultiValueES5_RSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">467194</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#359">_ZN4PLMD10vesselbase16ActionWithVessel20getForcesFromVesselsERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">7222</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#245">_ZN4PLMD10vesselbase16ActionWithVessel28doJobsRequiredBeforeTaskListEv</a></td>
+              <td class="coverFnHi">22991</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#97">_ZN4PLMD10vesselbase16ActionWithVessel9addVesselERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_i</a></td>
+              <td class="coverFnHi">359</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#108">_ZN4PLMD10vesselbase16ActionWithVessel9addVesselESt10unique_ptrINS0_6VesselESt14default_deleteIS3_EE</a></td>
+              <td class="coverFnHi">555</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#49">_ZN4PLMD10vesselbase16ActionWithVesselC1ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#49">_ZN4PLMD10vesselbase16ActionWithVesselC2ERKNS_13ActionOptionsE</a></td>
+              <td class="coverFnHi">570</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#89">_ZN4PLMD10vesselbase16ActionWithVesselD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#89">_ZN4PLMD10vesselbase16ActionWithVesselD1Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#89">_ZN4PLMD10vesselbase16ActionWithVesselD2Ev</a></td>
+              <td class="coverFnHi">570</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#241">_ZNK4PLMD10vesselbase16ActionWithVessel21taskIsCurrentlyActiveERKj</a></td>
+              <td class="coverFnHi">213721</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.cpp.gcov.html#340">_ZNK4PLMD10vesselbase16ActionWithVessel27transformBridgedDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithVessel.cpp.gcov.html b/coverage/vesselbase/ActionWithVessel.cpp.gcov.html
new file mode 100644
index 0000000000..866e918ec0
--- /dev/null
+++ b/coverage/vesselbase/ActionWithVessel.cpp.gcov.html
@@ -0,0 +1,471 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithVessel.cpp<span style="font-size: 80%;"> (source / <a href="ActionWithVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">188</td>
+            <td class="headerCovTableEntry">201</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryMed">76.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ShortcutVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;BridgeVessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/OpenMP.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : #include &quot;tools/Stopwatch.h&quot;</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace PLMD {</a>
+<a name="35"><span class="lineNum">      35 </span>            : namespace vesselbase {</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        796 : void ActionWithVessel::registerKeywords(Keywords&amp; keys) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       1592 :   keys.add(&quot;hidden&quot;,&quot;TOL&quot;,&quot;this keyword can be used to speed up your calculation. When accumulating sums in which the individual &quot;</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :            &quot;terms are numbers in between zero and one it is assumed that terms less than a certain tolerance &quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :            &quot;make only a small contribution to the sum.  They can thus be safely ignored as can the the derivatives &quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            :            &quot;wrt these small quantities.&quot;);</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       1592 :   keys.add(&quot;hidden&quot;,&quot;MAXDERIVATIVES&quot;,&quot;The maximum number of derivatives that can be used when storing data.  This controls when &quot;</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :            &quot;we have to start using lowmem&quot;);</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       1592 :   keys.addFlag(&quot;SERIAL&quot;,false,&quot;do the calculation in serial.  Do not use MPI&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       1592 :   keys.addFlag(&quot;LOWMEM&quot;,false,&quot;lower the memory requirements&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1592 :   keys.addFlag(&quot;TIMINGS&quot;,false,&quot;output information on the timings of the various parts of the calculation&quot;);</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1592 :   keys.reserveFlag(&quot;HIGHMEM&quot;,false,&quot;use a more memory intensive version of this collective variable&quot;);</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        796 :   keys.add( vesselRegister().getKeywords() );</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        796 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        570 : ActionWithVessel::ActionWithVessel(const ActionOptions&amp;ao):</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   Action(ao),</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        570 :   serial(false),</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        570 :   lowmem(false),</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        570 :   noderiv(true),</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        570 :   actionIsBridged(false),</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        570 :   nactive_tasks(0),</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        570 :   dertime_can_be_off(false),</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        570 :   dertime(true),</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        570 :   contributorsAreUnlocked(false),</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">        570 :   weightHasDerivatives(false),</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">        570 :   mydata(NULL)</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        570 :   maxderivatives=309; parse(&quot;MAXDERIVATIVES&quot;,maxderivatives);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">       1677 :   if( keywords.exists(&quot;SERIAL&quot;) ) parseFlag(&quot;SERIAL&quot;,serial);</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         33 :   else serial=true;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        570 :   if(serial)log.printf(&quot;  doing calculation in serial\n&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       1140 :   if( keywords.exists(&quot;LOWMEM&quot;) ) {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       1076 :     plumed_assert( !keywords.exists(&quot;HIGHMEM&quot;) );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        538 :     parseFlag(&quot;LOWMEM&quot;,lowmem);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        538 :     if(lowmem) {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         29 :       log.printf(&quot;  lowering memory requirements\n&quot;);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         29 :       dertime_can_be_off=true;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            :     }</a>
+<a name="75"><span class="lineNum">      75 </span>            :   }</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       1140 :   if( keywords.exists(&quot;HIGHMEM&quot;) ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">         46 :     plumed_assert( !keywords.exists(&quot;LOWMEM&quot;) );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">         23 :     bool highmem; parseFlag(&quot;HIGHMEM&quot;,highmem);</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">         23 :     lowmem=!highmem;</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">         23 :     if(!lowmem) log.printf(&quot;  increasing the memory requirements\n&quot;);</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   }</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">        570 :   tolerance=nl_tolerance=epsilon;</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       1599 :   if( keywords.exists(&quot;TOL&quot;) ) parse(&quot;TOL&quot;,tolerance);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        570 :   if( tolerance&gt;epsilon) {</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">          6 :     log.printf(&quot; Ignoring contributions less than %f \n&quot;,tolerance);</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   }</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">        570 :   parseFlag(&quot;TIMINGS&quot;,timers);</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        570 :   stopwatch.start(); stopwatch.pause();</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">        570 : }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">        570 : ActionWithVessel::~ActionWithVessel() {</span></a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">        570 :   stopwatch.start(); stopwatch.stop();</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">        570 :   if(timers) {</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineNoCov">          0 :     log.printf(&quot;timings for action %s with label %s \n&quot;, getName().c_str(), getLabel().c_str() );</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineNoCov">          0 :     log&lt;&lt;stopwatch;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   }</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">        570 : }</span></a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">        359 : void ActionWithVessel::addVessel( const std::string&amp; name, const std::string&amp; input, const int numlab ) {</span></a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        359 :   VesselOptions da(name,&quot;&quot;,numlab,input,this);</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">        718 :   auto vv=vesselRegister().create(name,da);</span></a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        359 :   FunctionVessel* fv=dynamic_cast&lt;FunctionVessel*&gt;(vv.get());</span></a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        359 :   if( fv ) {</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        329 :     std::string mylabel=Vessel::transformName( name );</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">        329 :     plumed_massert( keywords.outputComponentExists(mylabel,false), &quot;a description of the value calculated by vessel &quot; + name + &quot; has not been added to the manual&quot;);</span></a>
+<a name="106"><span class="lineNum">     106 </span>            :   }</a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        359 :   addVessel(std::move(vv));</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">        359 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        555 : void ActionWithVessel::addVessel( std::unique_ptr&lt;Vessel&gt; vv_ptr ) {</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : </a>
+<a name="112"><span class="lineNum">     112 </span>            : // In the original code, the dynamically casted pointer was deleted here.</a>
+<a name="113"><span class="lineNum">     113 </span>            : // Now that vv_ptr is a unique_ptr, the object will be deleted automatically when</a>
+<a name="114"><span class="lineNum">     114 </span>            : // exiting this routine.</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">        555 :   if(dynamic_cast&lt;ShortcutVessel*&gt;(vv_ptr.get())) return;</span></a>
+<a name="116"><span class="lineNum">     116 </span>            : </a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        544 :   vv_ptr-&gt;checkRead();</span></a>
+<a name="118"><span class="lineNum">     118 </span>            : </a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">        544 :   StoreDataVessel* mm=dynamic_cast&lt;StoreDataVessel*&gt;( vv_ptr.get() );</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineCov">        544 :   if( mydata &amp;&amp; mm ) error(&quot;cannot have more than one StoreDataVessel in one action&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">        544 :   else if( mm ) mydata=mm;</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        413 :   else dertime_can_be_off=false;</span></a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span>            : // Ownership is transferred to functions</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        544 :   functions.emplace_back(std::move(vv_ptr));</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : }</a>
+<a name="127"><span class="lineNum">     127 </span>            : </a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">         46 : BridgeVessel* ActionWithVessel::addBridgingVessel( ActionWithVessel* tome ) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">         92 :   VesselOptions da(&quot;&quot;,&quot;&quot;,0,&quot;&quot;,this);</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         46 :   auto bv=Tools::make_unique&lt;BridgeVessel&gt;(da);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         46 :   bv-&gt;setOutputAction( tome );</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">         46 :   tome-&gt;actionIsBridged=true; dertime_can_be_off=false;</span></a>
+<a name="133"><span class="lineNum">     133 </span>            : // store this pointer in order to return it later.</a>
+<a name="134"><span class="lineNum">     134 </span>            : // notice that I cannot access this with functions.tail().get()</a>
+<a name="135"><span class="lineNum">     135 </span>            : // since functions contains pointers to a different class (Vessel)</a>
+<a name="136"><span class="lineNum">     136 </span>            :   auto toBeReturned=bv.get();</a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">         46 :   functions.emplace_back( std::move(bv) );</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">         46 :   resizeFunctions();</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">         46 :   return toBeReturned;</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         46 : }</span></a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">        192 : StoreDataVessel* ActionWithVessel::buildDataStashes( ActionWithVessel* actionThatUses ) {</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">        192 :   if(mydata) {</span></a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">         87 :     if( actionThatUses ) mydata-&gt;addActionThatUses( actionThatUses );</span></a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineCov">         87 :     return mydata;</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">        210 :   VesselOptions da(&quot;&quot;,&quot;&quot;,0,&quot;&quot;,this);</span></a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">        105 :   auto mm=Tools::make_unique&lt;StoreDataVessel&gt;(da);</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">        105 :   if( actionThatUses ) mm-&gt;addActionThatUses( actionThatUses );</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">        105 :   addVessel(std::move(mm));</span></a>
+<a name="152"><span class="lineNum">     152 </span>            : </a>
+<a name="153"><span class="lineNum">     153 </span>            :   // Make sure resizing of vessels is done</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        105 :   resizeFunctions();</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span><span class="lineCov">        105 :   return mydata;</span></a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        105 : }</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : </a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">   12661369 : void ActionWithVessel::addTaskToList( const unsigned&amp; taskCode ) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">   12661369 :   fullTaskList.push_back( taskCode ); taskFlags.push_back(0);</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">   12661369 :   plumed_assert( fullTaskList.size()==taskFlags.size() );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">   12661369 : }</span></a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        417 : void ActionWithVessel::readVesselKeywords() {</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :   // Set maxderivatives if it is too big</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        417 :   if( maxderivatives&gt;getNumberOfDerivatives() ) maxderivatives=getNumberOfDerivatives();</span></a>
+<a name="167"><span class="lineNum">     167 </span>            : </a>
+<a name="168"><span class="lineNum">     168 </span>            :   // Loop over all keywords find the vessels and create appropriate functions</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">      10136 :   for(unsigned i=0; i&lt;keywords.size(); ++i) {</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       9719 :     std::string thiskey,input; thiskey=keywords.getKeyword(i);</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :     // Check if this is a key for a vessel</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">       9719 :     if( vesselRegister().check(thiskey) ) {</span></a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       5526 :       plumed_assert( keywords.style(thiskey,&quot;vessel&quot;) );</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       2763 :       bool dothis=false; parseFlag(thiskey,dothis);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       2763 :       if(dothis) addVessel( thiskey, input );</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : </a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">       2763 :       parse(thiskey,input);</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">       2763 :       if(input.size()!=0) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        125 :         addVessel( thiskey, input );</span></a>
+<a name="180"><span class="lineNum">     180 </span>            :       } else {</a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       2638 :         for(unsigned i=1;; ++i) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">       2663 :           if( !parseNumbered(thiskey,i,input) ) break;</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">         25 :           std::string ss; Tools::convert(i,ss);</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">         25 :           addVessel( thiskey, input, i );</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :           input.clear();</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineCov">         25 :         }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            :       }</a>
+<a name="188"><span class="lineNum">     188 </span>            :     }</a>
+<a name="189"><span class="lineNum">     189 </span>            :   }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            :   // Make sure all vessels have had been resized at start</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">        417 :   if( functions.size()&gt;0 ) resizeFunctions();</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">        417 : }</span></a>
+<a name="194"><span class="lineNum">     194 </span>            : </a>
+<a name="195"><span class="lineNum">     195 </span><span class="lineCov">       1375 : void ActionWithVessel::resizeFunctions() {</span></a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineCov">       3548 :   for(unsigned i=0; i&lt;functions.size(); ++i) functions[i]-&gt;resize();</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineCov">       1375 : }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : </a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">        812 : void ActionWithVessel::needsDerivatives() {</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   // Turn on the derivatives and resize</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        812 :   noderiv=false; resizeFunctions();</span></a>
+<a name="202"><span class="lineNum">     202 </span>            :   // Setting contributors unlocked here ensures that link cells are ignored</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">        812 :   contributorsAreUnlocked=true; contributorsAreUnlocked=false;</span></a>
+<a name="204"><span class="lineNum">     204 </span>            :   // And turn on the derivatives in all actions on which we are dependent</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">       1110 :   for(unsigned i=0; i&lt;getDependencies().size(); ++i) {</span></a>
+<a name="206"><span class="lineNum">     206 </span><span class="lineCov">        298 :     ActionWithVessel* vv=dynamic_cast&lt;ActionWithVessel*&gt;( getDependencies()[i] );</span></a>
+<a name="207"><span class="lineNum">     207 </span><span class="lineCov">        298 :     if(vv) vv-&gt;needsDerivatives();</span></a>
+<a name="208"><span class="lineNum">     208 </span>            :   }</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">        812 : }</span></a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">       3316 : void ActionWithVessel::lockContributors() {</span></a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">       3316 :   nactive_tasks = 0;</span></a>
+<a name="213"><span class="lineNum">     213 </span><span class="lineCov">   18492791 :   for(unsigned i=0; i&lt;fullTaskList.size(); ++i) {</span></a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">   18489475 :     if( taskFlags[i]&gt;0 ) nactive_tasks++;</span></a>
+<a name="215"><span class="lineNum">     215 </span>            :   }</a>
+<a name="216"><span class="lineNum">     216 </span>            : </a>
+<a name="217"><span class="lineNum">     217 </span>            :   unsigned n=0;</a>
+<a name="218"><span class="lineNum">     218 </span><span class="lineCov">       3316 :   partialTaskList.resize( nactive_tasks );</span></a>
+<a name="219"><span class="lineNum">     219 </span><span class="lineCov">       3316 :   indexOfTaskInFullList.resize( nactive_tasks );</span></a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">   18492791 :   for(unsigned i=0; i&lt;fullTaskList.size(); ++i) {</span></a>
+<a name="221"><span class="lineNum">     221 </span>            :     // Deactivate sets inactive tasks to number not equal to zero</a>
+<a name="222"><span class="lineNum">     222 </span><span class="lineCov">   18489475 :     if( taskFlags[i]&gt;0 ) {</span></a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">    5482474 :       partialTaskList[n] = fullTaskList[i];</span></a>
+<a name="224"><span class="lineNum">     224 </span><span class="lineCov">    5482474 :       indexOfTaskInFullList[n]=i;</span></a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">    5482474 :       n++;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            :     }</a>
+<a name="227"><span class="lineNum">     227 </span>            :   }</a>
+<a name="228"><span class="lineNum">     228 </span>            :   plumed_dbg_assert( n==nactive_tasks );</a>
+<a name="229"><span class="lineNum">     229 </span><span class="lineCov">       8196 :   for(unsigned i=0; i&lt;functions.size(); ++i) {</span></a>
+<a name="230"><span class="lineNum">     230 </span><span class="lineCov">       4880 :     BridgeVessel* bb = dynamic_cast&lt;BridgeVessel*&gt;( functions[i].get() );</span></a>
+<a name="231"><span class="lineNum">     231 </span><span class="lineCov">       4880 :     if( bb ) bb-&gt;copyTaskFlags();</span></a>
+<a name="232"><span class="lineNum">     232 </span>            :   }</a>
+<a name="233"><span class="lineNum">     233 </span>            :   // Resize mydata to accommodate all active tasks</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">       3316 :   if( mydata ) mydata-&gt;resize();</span></a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">       3316 :   contributorsAreUnlocked=false;</span></a>
+<a name="236"><span class="lineNum">     236 </span><span class="lineCov">       3316 : }</span></a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span><span class="lineCov">       3316 : void ActionWithVessel::deactivateAllTasks() {</span></a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">       3316 :   contributorsAreUnlocked=true; nactive_tasks = 0;</span></a>
+<a name="240"><span class="lineNum">     240 </span><span class="lineCov">       3316 :   taskFlags.assign(taskFlags.size(),0);</span></a>
+<a name="241"><span class="lineNum">     241 </span><span class="lineCov">       3316 : }</span></a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span><span class="lineCov">     213721 : bool ActionWithVessel::taskIsCurrentlyActive( const unsigned&amp; index ) const {</span></a>
+<a name="244"><span class="lineNum">     244 </span><span class="lineCov">     213721 :   plumed_dbg_assert( index&lt;taskFlags.size() ); return (taskFlags[index]&gt;0);</span></a>
+<a name="245"><span class="lineNum">     245 </span>            : }</a>
+<a name="246"><span class="lineNum">     246 </span>            : </a>
+<a name="247"><span class="lineNum">     247 </span><span class="lineCov">      22991 : void ActionWithVessel::doJobsRequiredBeforeTaskList() {</span></a>
+<a name="248"><span class="lineNum">     248 </span>            :   // Do any preparatory stuff for functions</a>
+<a name="249"><span class="lineNum">     249 </span><span class="lineCov">      58260 :   for(unsigned j=0; j&lt;functions.size(); ++j) functions[j]-&gt;prepare();</span></a>
+<a name="250"><span class="lineNum">     250 </span><span class="lineCov">      22991 : }</span></a>
+<a name="251"><span class="lineNum">     251 </span>            : </a>
+<a name="252"><span class="lineNum">     252 </span><span class="lineCov">      23504 : unsigned ActionWithVessel::getSizeOfBuffer( unsigned&amp; bufsize ) {</span></a>
+<a name="253"><span class="lineNum">     253 </span><span class="lineCov">      59449 :   for(unsigned i=0; i&lt;functions.size(); ++i) functions[i]-&gt;setBufferStart( bufsize );</span></a>
+<a name="254"><span class="lineNum">     254 </span><span class="lineCov">      23504 :   if( buffer.size()!=bufsize ) buffer.resize( bufsize );</span></a>
+<a name="255"><span class="lineNum">     255 </span><span class="lineCov">      23504 :   if( mydata ) {</span></a>
+<a name="256"><span class="lineNum">     256 </span>            :     unsigned dsize=mydata-&gt;getSizeOfDerivativeList();</a>
+<a name="257"><span class="lineNum">     257 </span><span class="lineCov">       2554 :     if( der_list.size()!=dsize ) der_list.resize( dsize );</span></a>
+<a name="258"><span class="lineNum">     258 </span>            :   }</a>
+<a name="259"><span class="lineNum">     259 </span><span class="lineCov">      23504 :   return bufsize;</span></a>
+<a name="260"><span class="lineNum">     260 </span>            : }</a>
+<a name="261"><span class="lineNum">     261 </span>            : </a>
+<a name="262"><span class="lineNum">     262 </span><span class="lineCov">      19966 : void ActionWithVessel::runAllTasks() {</span></a>
+<a name="263"><span class="lineNum">     263 </span><span class="lineCov">      19966 :   plumed_massert( !contributorsAreUnlocked &amp;&amp; functions.size()&gt;0, &quot;you must have a call to readVesselKeywords somewhere&quot; );</span></a>
+<a name="264"><span class="lineNum">     264 </span><span class="lineCov">      19966 :   unsigned stride=comm.Get_size();</span></a>
+<a name="265"><span class="lineNum">     265 </span><span class="lineCov">      19966 :   unsigned rank=comm.Get_rank();</span></a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">      19966 :   if(serial) { stride=1; rank=0; }</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : </a>
+<a name="268"><span class="lineNum">     268 </span>            :   // Make sure jobs are done</a>
+<a name="269"><span class="lineNum">     269 </span><span class="lineCov">      19966 :   if(timers) stopwatch.start(&quot;1 Prepare Tasks&quot;);</span></a>
+<a name="270"><span class="lineNum">     270 </span><span class="lineCov">      19966 :   doJobsRequiredBeforeTaskList();</span></a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">      19966 :   if(timers) stopwatch.stop(&quot;1 Prepare Tasks&quot;);</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : </a>
+<a name="273"><span class="lineNum">     273 </span>            :   // Get number of threads for OpenMP</a>
+<a name="274"><span class="lineNum">     274 </span><span class="lineCov">      19966 :   unsigned nt=OpenMP::getNumThreads();</span></a>
+<a name="275"><span class="lineNum">     275 </span><span class="lineCov">      19966 :   if( nt*stride*2&gt;nactive_tasks || !threadSafe()) nt=1;</span></a>
+<a name="276"><span class="lineNum">     276 </span>            : </a>
+<a name="277"><span class="lineNum">     277 </span>            :   // Get size for buffer</a>
+<a name="278"><span class="lineNum">     278 </span><span class="lineCov">      19966 :   unsigned bsize=0, bufsize=getSizeOfBuffer( bsize );</span></a>
+<a name="279"><span class="lineNum">     279 </span>            :   // Clear buffer</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">      19966 :   buffer.assign( buffer.size(), 0.0 );</span></a>
+<a name="281"><span class="lineNum">     281 </span>            :   // Switch off calculation of derivatives in main loop</a>
+<a name="282"><span class="lineNum">     282 </span><span class="lineCov">      19966 :   if( dertime_can_be_off ) dertime=false;</span></a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">      19966 :   if(timers) stopwatch.start(&quot;2 Loop over tasks&quot;);</span></a>
+<a name="285"><span class="lineNum">     285 </span><span class="lineCov">      19966 :   #pragma omp parallel num_threads(nt)</span></a>
+<a name="286"><span class="lineNum">     286 </span>            :   {</a>
+<a name="287"><span class="lineNum">     287 </span>            :     std::vector&lt;double&gt; omp_buffer;</a>
+<a name="288"><span class="lineNum">     288 </span>            :     if( nt&gt;1 ) omp_buffer.resize( bufsize, 0.0 );</a>
+<a name="289"><span class="lineNum">     289 </span>            :     MultiValue myvals( getNumberOfQuantities(), getNumberOfDerivatives() );</a>
+<a name="290"><span class="lineNum">     290 </span>            :     MultiValue bvals( getNumberOfQuantities(), getNumberOfDerivatives() );</a>
+<a name="291"><span class="lineNum">     291 </span>            :     myvals.clearAll(); bvals.clearAll();</a>
+<a name="292"><span class="lineNum">     292 </span>            : </a>
+<a name="293"><span class="lineNum">     293 </span>            :     #pragma omp for nowait schedule(dynamic)</a>
+<a name="294"><span class="lineNum">     294 </span>            :     for(unsigned i=rank; i&lt;nactive_tasks; i+=stride) {</a>
+<a name="295"><span class="lineNum">     295 </span>            :       // Calculate the stuff in the loop for this action</a>
+<a name="296"><span class="lineNum">     296 </span>            :       performTask( indexOfTaskInFullList[i], partialTaskList[i], myvals );</a>
+<a name="297"><span class="lineNum">     297 </span>            : </a>
+<a name="298"><span class="lineNum">     298 </span>            :       // Check for conditions that allow us to just to skip the calculation</a>
+<a name="299"><span class="lineNum">     299 </span>            :       // the condition is that the weight of the contribution is low</a>
+<a name="300"><span class="lineNum">     300 </span>            :       // N.B. Here weights are assumed to be between zero and one</a>
+<a name="301"><span class="lineNum">     301 </span>            :       if( myvals.get(0)&lt;tolerance ) {</a>
+<a name="302"><span class="lineNum">     302 </span>            :         // Clear the derivatives</a>
+<a name="303"><span class="lineNum">     303 </span>            :         myvals.clearAll();</a>
+<a name="304"><span class="lineNum">     304 </span>            :         continue;</a>
+<a name="305"><span class="lineNum">     305 </span>            :       }</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :       // Now calculate all the functions</a>
+<a name="308"><span class="lineNum">     308 </span>            :       // If the contribution of this quantity is very small at neighbour list time ignore it</a>
+<a name="309"><span class="lineNum">     309 </span>            :       // until next neighbour list time</a>
+<a name="310"><span class="lineNum">     310 </span>            :       if( nt&gt;1 ) {</a>
+<a name="311"><span class="lineNum">     311 </span>            :         calculateAllVessels( indexOfTaskInFullList[i], myvals, bvals, omp_buffer, der_list );</a>
+<a name="312"><span class="lineNum">     312 </span>            :       } else {</a>
+<a name="313"><span class="lineNum">     313 </span>            :         calculateAllVessels( indexOfTaskInFullList[i], myvals, bvals, buffer, der_list );</a>
+<a name="314"><span class="lineNum">     314 </span>            :       }</a>
+<a name="315"><span class="lineNum">     315 </span>            : </a>
+<a name="316"><span class="lineNum">     316 </span>            :       // Clear the value</a>
+<a name="317"><span class="lineNum">     317 </span>            :       myvals.clearAll();</a>
+<a name="318"><span class="lineNum">     318 </span>            :     }</a>
+<a name="319"><span class="lineNum">     319 </span>            :     #pragma omp critical</a>
+<a name="320"><span class="lineNum">     320 </span>            :     if(nt&gt;1) for(unsigned i=0; i&lt;bufsize; ++i) buffer[i]+=omp_buffer[i];</a>
+<a name="321"><span class="lineNum">     321 </span>            :   }</a>
+<a name="322"><span class="lineNum">     322 </span><span class="lineCov">      19966 :   if(timers) stopwatch.stop(&quot;2 Loop over tasks&quot;);</span></a>
+<a name="323"><span class="lineNum">     323 </span>            :   // Turn back on derivative calculation</a>
+<a name="324"><span class="lineNum">     324 </span><span class="lineCov">      19966 :   dertime=true;</span></a>
+<a name="325"><span class="lineNum">     325 </span>            : </a>
+<a name="326"><span class="lineNum">     326 </span><span class="lineCov">      19966 :   if(timers) stopwatch.start(&quot;3 MPI gather&quot;);</span></a>
+<a name="327"><span class="lineNum">     327 </span>            :   // MPI Gather everything</a>
+<a name="328"><span class="lineNum">     328 </span><span class="lineCov">      19966 :   if( !serial &amp;&amp; buffer.size()&gt;0 ) comm.Sum( buffer );</span></a>
+<a name="329"><span class="lineNum">     329 </span>            :   // MPI Gather index stores</a>
+<a name="330"><span class="lineNum">     330 </span><span class="lineCov">      19966 :   if( mydata &amp;&amp; !lowmem &amp;&amp; !noderiv ) {</span></a>
+<a name="331"><span class="lineNum">     331 </span><span class="lineCov">        690 :     comm.Sum( der_list ); mydata-&gt;setActiveValsAndDerivatives( der_list );</span></a>
+<a name="332"><span class="lineNum">     332 </span>            :   }</a>
+<a name="333"><span class="lineNum">     333 </span>            :   // Update the elements that are makign contributions to the sum here</a>
+<a name="334"><span class="lineNum">     334 </span>            :   // this causes problems if we do it in prepare</a>
+<a name="335"><span class="lineNum">     335 </span><span class="lineCov">      19966 :   if(timers) stopwatch.stop(&quot;3 MPI gather&quot;);</span></a>
+<a name="336"><span class="lineNum">     336 </span>            : </a>
+<a name="337"><span class="lineNum">     337 </span><span class="lineCov">      19966 :   if(timers) stopwatch.start(&quot;4 Finishing computations&quot;);</span></a>
+<a name="338"><span class="lineNum">     338 </span><span class="lineCov">      19966 :   finishComputations( buffer );</span></a>
+<a name="339"><span class="lineNum">     339 </span><span class="lineCov">      19966 :   if(timers) stopwatch.stop(&quot;4 Finishing computations&quot;);</span></a>
+<a name="340"><span class="lineNum">     340 </span><span class="lineCov">      19966 : }</span></a>
+<a name="341"><span class="lineNum">     341 </span>            : </a>
+<a name="342"><span class="lineNum">     342 </span><span class="lineNoCov">          0 : void ActionWithVessel::transformBridgedDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) const {</span></a>
+<a name="343"><span class="lineNum">     343 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="344"><span class="lineNum">     344 </span>            : }</a>
+<a name="345"><span class="lineNum">     345 </span>            : </a>
+<a name="346"><span class="lineNum">     346 </span><span class="lineCov">     467194 : void ActionWithVessel::calculateAllVessels( const unsigned&amp; taskCode, MultiValue&amp; myvals, MultiValue&amp; bvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) {</span></a>
+<a name="347"><span class="lineNum">     347 </span><span class="lineCov">    1079096 :   for(unsigned j=0; j&lt;functions.size(); ++j) {</span></a>
+<a name="348"><span class="lineNum">     348 </span>            :     // Calculate returns a bool that tells us if this particular</a>
+<a name="349"><span class="lineNum">     349 </span>            :     // quantity is contributing more than the tolerance</a>
+<a name="350"><span class="lineNum">     350 </span><span class="lineCov">     611902 :     functions[j]-&gt;calculate( taskCode, functions[j]-&gt;transformDerivatives(taskCode, myvals, bvals), buffer, der_list );</span></a>
+<a name="351"><span class="lineNum">     351 </span><span class="lineCov">     611902 :     if( !actionIsBridged ) bvals.clearAll();</span></a>
+<a name="352"><span class="lineNum">     352 </span>            :   }</a>
+<a name="353"><span class="lineNum">     353 </span><span class="lineCov">     467194 :   return;</span></a>
+<a name="354"><span class="lineNum">     354 </span>            : }</a>
+<a name="355"><span class="lineNum">     355 </span>            : </a>
+<a name="356"><span class="lineNum">     356 </span><span class="lineCov">      22991 : void ActionWithVessel::finishComputations( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="357"><span class="lineNum">     357 </span>            :   // Set the final value of the function</a>
+<a name="358"><span class="lineNum">     358 </span><span class="lineCov">      58260 :   for(unsigned j=0; j&lt;functions.size(); ++j) functions[j]-&gt;finish( buffer );</span></a>
+<a name="359"><span class="lineNum">     359 </span><span class="lineCov">      22991 : }</span></a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span><span class="lineCov">       7222 : bool ActionWithVessel::getForcesFromVessels( std::vector&lt;double&gt;&amp; forcesToApply ) {</span></a>
+<a name="362"><span class="lineNum">     362 </span>            : #ifndef NDEBUG</a>
+<a name="363"><span class="lineNum">     363 </span>            :   if( forcesToApply.size()&gt;0 ) plumed_dbg_assert( forcesToApply.size()==getNumberOfDerivatives() );</a>
+<a name="364"><span class="lineNum">     364 </span>            : #endif</a>
+<a name="365"><span class="lineNum">     365 </span><span class="lineCov">       7222 :   if(tmpforces.size()!=forcesToApply.size() ) tmpforces.resize( forcesToApply.size() );</span></a>
+<a name="366"><span class="lineNum">     366 </span>            : </a>
+<a name="367"><span class="lineNum">     367 </span><span class="lineCov">       7222 :   forcesToApply.assign( forcesToApply.size(),0.0 );</span></a>
+<a name="368"><span class="lineNum">     368 </span>            :   bool wasforced=false;</a>
+<a name="369"><span class="lineNum">     369 </span><span class="lineCov">      21110 :   for(unsigned i=0; i&lt;getNumberOfVessels(); ++i) {</span></a>
+<a name="370"><span class="lineNum">     370 </span><span class="lineCov">      13888 :     if( (functions[i]-&gt;applyForce( tmpforces )) ) {</span></a>
+<a name="371"><span class="lineNum">     371 </span>            :       wasforced=true;</a>
+<a name="372"><span class="lineNum">     372 </span><span class="lineCov">     524255 :       for(unsigned j=0; j&lt;forcesToApply.size(); ++j) forcesToApply[j]+=tmpforces[j];</span></a>
+<a name="373"><span class="lineNum">     373 </span>            :     }</a>
+<a name="374"><span class="lineNum">     374 </span>            :   }</a>
+<a name="375"><span class="lineNum">     375 </span><span class="lineCov">       7222 :   return wasforced;</span></a>
+<a name="376"><span class="lineNum">     376 </span>            : }</a>
+<a name="377"><span class="lineNum">     377 </span>            : </a>
+<a name="378"><span class="lineNum">     378 </span><span class="lineNoCov">          0 : void ActionWithVessel::retrieveDomain( std::string&amp; min, std::string&amp; max ) {</span></a>
+<a name="379"><span class="lineNum">     379 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;If your function is periodic you need to add a retrieveDomain function so that ActionWithVessel can retrieve the domain&quot;);</span></a>
+<a name="380"><span class="lineNum">     380 </span>            : }</a>
+<a name="381"><span class="lineNum">     381 </span>            : </a>
+<a name="382"><span class="lineNum">     382 </span><span class="lineNoCov">          0 : Vessel* ActionWithVessel::getVesselWithName( const std::string&amp; mynam ) {</span></a>
+<a name="383"><span class="lineNum">     383 </span>            :   int target=-1;</a>
+<a name="384"><span class="lineNum">     384 </span><span class="lineNoCov">          0 :   for(unsigned i=0; i&lt;functions.size(); ++i) {</span></a>
+<a name="385"><span class="lineNum">     385 </span><span class="lineNoCov">          0 :     if( functions[i]-&gt;getName().find(mynam)!=std::string::npos ) {</span></a>
+<a name="386"><span class="lineNum">     386 </span><span class="lineNoCov">          0 :       if( target&lt;0 ) target=i;</span></a>
+<a name="387"><span class="lineNum">     387 </span><span class="lineNoCov">          0 :       else error(&quot;found more than one &quot; + mynam + &quot; object in action&quot;);</span></a>
+<a name="388"><span class="lineNum">     388 </span>            :     }</a>
+<a name="389"><span class="lineNum">     389 </span>            :   }</a>
+<a name="390"><span class="lineNum">     390 </span><span class="lineNoCov">          0 :   plumed_assert(target&gt;=0);</span></a>
+<a name="391"><span class="lineNum">     391 </span><span class="lineNoCov">          0 :   return functions[target].get();</span></a>
+<a name="392"><span class="lineNum">     392 </span>            : }</a>
+<a name="393"><span class="lineNum">     393 </span>            : </a>
+<a name="394"><span class="lineNum">     394 </span>            : }</a>
+<a name="395"><span class="lineNum">     395 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithVessel.h.func-sort-c.html b/coverage/vesselbase/ActionWithVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..563c8d8d6f
--- /dev/null
+++ b/coverage/vesselbase/ActionWithVessel.h.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithVessel.h<span style="font-size: 80%;"> (<a href="ActionWithVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ActionWithVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#184">_ZN4PLMD10vesselbase16ActionWithVessel17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#194">_ZNK4PLMD10vesselbase16ActionWithVessel15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#195">_ZNK4PLMD10vesselbase16ActionWithVessel26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#152">_ZNK4PLMD10vesselbase16ActionWithVessel10threadSafeEv</a></td>
+              <td class="coverFnHi">5214</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#214">_ZNK4PLMD10vesselbase16ActionWithVessel21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">196791</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#278">_ZNK4PLMD10vesselbase16ActionWithVessel28getPositionInCurrentTaskListERKj</a></td>
+              <td class="coverFnHi">224556</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithVessel.h.func.html b/coverage/vesselbase/ActionWithVessel.h.func.html
new file mode 100644
index 0000000000..0e35827152
--- /dev/null
+++ b/coverage/vesselbase/ActionWithVessel.h.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithVessel.h<span style="font-size: 80%;"> (<a href="ActionWithVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ActionWithVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#184">_ZN4PLMD10vesselbase16ActionWithVessel17applyBridgeForcesERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#152">_ZNK4PLMD10vesselbase16ActionWithVessel10threadSafeEv</a></td>
+              <td class="coverFnHi">5214</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#194">_ZNK4PLMD10vesselbase16ActionWithVessel15normalizeVectorERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#214">_ZNK4PLMD10vesselbase16ActionWithVessel21getNumberOfQuantitiesEv</a></td>
+              <td class="coverFnHi">196791</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#195">_ZNK4PLMD10vesselbase16ActionWithVessel26normalizeVectorDerivativesERNS_10MultiValueE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ActionWithVessel.h.gcov.html#278">_ZNK4PLMD10vesselbase16ActionWithVessel28getPositionInCurrentTaskListERKj</a></td>
+              <td class="coverFnHi">224556</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ActionWithVessel.h.gcov.html b/coverage/vesselbase/ActionWithVessel.h.gcov.html
new file mode 100644
index 0000000000..367424e39d
--- /dev/null
+++ b/coverage/vesselbase/ActionWithVessel.h.gcov.html
@@ -0,0 +1,367 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ActionWithVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ActionWithVessel.h<span style="font-size: 80%;"> (source / <a href="ActionWithVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryMed">83.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_ActionWithVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_ActionWithVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;core/ActionAtomistic.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;tools/DynamicList.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/MultiValue.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &lt;vector&gt;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;tools/ForwardDecl.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : class Value;</a>
+<a name="35"><span class="lineNum">      35 </span>            : class Stopwatch;</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span>            : namespace vesselbase {</a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span>            : class Vessel;</a>
+<a name="40"><span class="lineNum">      40 </span>            : class BridgeVessel;</a>
+<a name="41"><span class="lineNum">      41 </span>            : class StoreDataVessel;</a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span>            : /**</a>
+<a name="44"><span class="lineNum">      44 </span>            : \ingroup MULTIINHERIT</a>
+<a name="45"><span class="lineNum">      45 </span>            : This is used to create PLMD::Action objects that are computed by calculating the same function multiple</a>
+<a name="46"><span class="lineNum">      46 </span>            : times.  This is used in PLMD::MultiColvar.</a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : class ActionWithVessel : public virtual Action {</a>
+<a name="50"><span class="lineNum">      50 </span>            :   friend class Vessel;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   friend class ShortcutVessel;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   friend class FunctionVessel;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   friend class StoreDataVessel;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   friend class BridgeVessel;</a>
+<a name="55"><span class="lineNum">      55 </span>            :   friend class ActionWithInputVessel;</a>
+<a name="56"><span class="lineNum">      56 </span>            :   friend class OrderingVessel;</a>
+<a name="57"><span class="lineNum">      57 </span>            : private:</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Do all calculations in serial</a>
+<a name="59"><span class="lineNum">      59 </span>            :   bool serial;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Lower memory requirements</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool lowmem;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Are we skipping the calculation of the derivatives</a>
+<a name="63"><span class="lineNum">      63 </span>            :   bool noderiv;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// This tells plumed that this is used in a bridge</a>
+<a name="65"><span class="lineNum">      65 </span>            :   bool actionIsBridged;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// The maximum number of derivatives we can use before we need to invoke lowmem</a>
+<a name="67"><span class="lineNum">      67 </span>            :   unsigned maxderivatives;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// The tolerance on the accumulators</a>
+<a name="69"><span class="lineNum">      69 </span>            :   double tolerance;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Tolerance for quantities being put in neighbor lists</a>
+<a name="71"><span class="lineNum">      71 </span>            :   double nl_tolerance;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Pointers to the functions we are using on each value</a>
+<a name="73"><span class="lineNum">      73 </span>            :   std::vector&lt;std::unique_ptr&lt;Vessel&gt;&gt; functions;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Tempory storage for forces</a>
+<a name="75"><span class="lineNum">      75 </span>            :   std::vector&lt;double&gt; tmpforces;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Ths full list of tasks we have to perform</a>
+<a name="77"><span class="lineNum">      77 </span>            :   std::vector&lt;unsigned&gt; fullTaskList;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// The current number of active tasks</a>
+<a name="79"><span class="lineNum">      79 </span>            :   unsigned nactive_tasks;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// The indices of the tasks in the full list of tasks</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::vector&lt;unsigned&gt; indexOfTaskInFullList;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// The list of currently active tasks</a>
+<a name="83"><span class="lineNum">      83 </span>            :   std::vector&lt;unsigned&gt; partialTaskList;</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// The list of atoms involved in derivatives (we keep a copy here to avoid resizing)</a>
+<a name="85"><span class="lineNum">      85 </span>            :   std::vector&lt;unsigned&gt; der_list;</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// The buffer that we use (we keep a copy here to avoid resizing)</a>
+<a name="87"><span class="lineNum">      87 </span>            :   std::vector&lt;double&gt; buffer;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Do we want to output information on the timings of different parts of the calculation</a>
+<a name="89"><span class="lineNum">      89 </span>            :   bool timers;</a>
+<a name="90"><span class="lineNum">      90 </span>            :   ForwardDecl&lt;Stopwatch&gt; stopwatch_fwd;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// The stopwatch that times the different parts of the calculation</a>
+<a name="92"><span class="lineNum">      92 </span>            :   Stopwatch&amp; stopwatch=*stopwatch_fwd;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// These are used to minmise computational expense in complex functions</a>
+<a name="94"><span class="lineNum">      94 </span>            :   bool dertime_can_be_off;</a>
+<a name="95"><span class="lineNum">      95 </span>            : protected:</a>
+<a name="96"><span class="lineNum">      96 </span>            : /// This is also used to minimise computational expense in complex functions</a>
+<a name="97"><span class="lineNum">      97 </span>            :   bool dertime;</a>
+<a name="98"><span class="lineNum">      98 </span>            : /// The terms in the series are locked</a>
+<a name="99"><span class="lineNum">      99 </span>            :   bool contributorsAreUnlocked;</a>
+<a name="100"><span class="lineNum">     100 </span>            : /// Does the weight have derivatives</a>
+<a name="101"><span class="lineNum">     101 </span>            :   bool weightHasDerivatives;</a>
+<a name="102"><span class="lineNum">     102 </span>            : /// This is used for numerical derivatives of bridge variables</a>
+<a name="103"><span class="lineNum">     103 </span>            :   unsigned bridgeVariable;</a>
+<a name="104"><span class="lineNum">     104 </span>            : /// A pointer to the object that stores data</a>
+<a name="105"><span class="lineNum">     105 </span>            :   StoreDataVessel* mydata;</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// This list is used to update the neighbor list</a>
+<a name="107"><span class="lineNum">     107 </span>            :   std::vector&lt;unsigned&gt; taskFlags;</a>
+<a name="108"><span class="lineNum">     108 </span>            : /// Add a vessel to the list of vessels</a>
+<a name="109"><span class="lineNum">     109 </span>            :   void addVessel( const std::string&amp; name, const std::string&amp; input, const int numlab=0 );</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void addVessel( std::unique_ptr&lt;Vessel&gt; vv );</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// Add a bridging vessel to the list of vessels</a>
+<a name="112"><span class="lineNum">     112 </span>            :   BridgeVessel* addBridgingVessel( ActionWithVessel* tome );</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Complete the setup of this object (this routine must be called after construction of ActionWithValue)</a>
+<a name="114"><span class="lineNum">     114 </span>            :   void readVesselKeywords();</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Turn on the derivatives in the vessel</a>
+<a name="116"><span class="lineNum">     116 </span>            :   void needsDerivatives();</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Return the value of the tolerance</a>
+<a name="118"><span class="lineNum">     118 </span>            :   double getTolerance() const ;</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Return the value for the neighbor list tolerance</a>
+<a name="120"><span class="lineNum">     120 </span>            :   double getNLTolerance() const ;</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Calculate the values of all the vessels</a>
+<a name="122"><span class="lineNum">     122 </span>            :   void runAllTasks();</a>
+<a name="123"><span class="lineNum">     123 </span>            : /// Resize all the functions when the number of derivatives change</a>
+<a name="124"><span class="lineNum">     124 </span>            :   void resizeFunctions();</a>
+<a name="125"><span class="lineNum">     125 </span>            : /// This loops over all the vessels calculating them and also</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// sets all the element derivatives equal to zero</a>
+<a name="127"><span class="lineNum">     127 </span>            :   void calculateAllVessels( const unsigned&amp; taskCode, MultiValue&amp; myvals, MultiValue&amp; bvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list );</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// Retrieve the forces from all the vessels (used in apply)</a>
+<a name="129"><span class="lineNum">     129 </span>            :   bool getForcesFromVessels( std::vector&lt;double&gt;&amp; forcesToApply );</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// Is the calculation being done in serial</a>
+<a name="131"><span class="lineNum">     131 </span>            :   bool serialCalculation() const;</a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Are we using low memory</a>
+<a name="133"><span class="lineNum">     133 </span>            :   bool usingLowMem() const ;</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Set that we are using low memory</a>
+<a name="135"><span class="lineNum">     135 </span>            :   void setLowMemOption(const bool&amp; );</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Deactivate all the tasks in the task list</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void deactivateAllTasks();</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Get the size of the buffer</a>
+<a name="139"><span class="lineNum">     139 </span>            :   unsigned getSizeOfBuffer( unsigned&amp; bufsize );</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Add a task to the full list</a>
+<a name="141"><span class="lineNum">     141 </span>            :   void addTaskToList( const unsigned&amp; taskCode );</a>
+<a name="142"><span class="lineNum">     142 </span>            : public:</a>
+<a name="143"><span class="lineNum">     143 </span>            :   static void registerKeywords(Keywords&amp; keys);</a>
+<a name="144"><span class="lineNum">     144 </span>            :   explicit ActionWithVessel(const ActionOptions&amp;ao);</a>
+<a name="145"><span class="lineNum">     145 </span>            :   ~ActionWithVessel();</a>
+<a name="146"><span class="lineNum">     146 </span>            :   void lockContributors();</a>
+<a name="147"><span class="lineNum">     147 </span>            : /// Get the number of tasks that are currently active</a>
+<a name="148"><span class="lineNum">     148 </span>            :   unsigned getCurrentNumberOfActiveTasks() const ;</a>
+<a name="149"><span class="lineNum">     149 </span>            : /// Check whether or not a particular task is currently active</a>
+<a name="150"><span class="lineNum">     150 </span>            :   bool taskIsCurrentlyActive( const unsigned&amp; index ) const ;</a>
+<a name="151"><span class="lineNum">     151 </span>            : /// Are derivatives required for this quantity</a>
+<a name="152"><span class="lineNum">     152 </span>            :   bool derivativesAreRequired() const ;</a>
+<a name="153"><span class="lineNum">     153 </span>            : /// Is this action thread safe</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">       5214 :   virtual bool threadSafe() const { return true; }</span></a>
+<a name="155"><span class="lineNum">     155 </span>            : /// Finish running all the calculations</a>
+<a name="156"><span class="lineNum">     156 </span>            :   virtual void finishComputations( const std::vector&lt;double&gt;&amp; buffer );</a>
+<a name="157"><span class="lineNum">     157 </span>            : /// Are the base quantities periodic</a>
+<a name="158"><span class="lineNum">     158 </span>            :   virtual bool isPeriodic()=0;</a>
+<a name="159"><span class="lineNum">     159 </span>            : /// What are the domains of the base quantities</a>
+<a name="160"><span class="lineNum">     160 </span>            :   virtual void retrieveDomain( std::string&amp; min, std::string&amp; max);</a>
+<a name="161"><span class="lineNum">     161 </span>            : /// Get the number of derivatives for final calculated quantity</a>
+<a name="162"><span class="lineNum">     162 </span>            :   virtual unsigned getNumberOfDerivatives()=0;</a>
+<a name="163"><span class="lineNum">     163 </span>            : /// Get the number of quantities that are calculated during each task</a>
+<a name="164"><span class="lineNum">     164 </span>            :   virtual unsigned getNumberOfQuantities() const ;</a>
+<a name="165"><span class="lineNum">     165 </span>            : /// Get the number of vessels</a>
+<a name="166"><span class="lineNum">     166 </span>            :   unsigned getNumberOfVessels() const;</a>
+<a name="167"><span class="lineNum">     167 </span>            : /// Get a pointer to the ith vessel</a>
+<a name="168"><span class="lineNum">     168 </span>            :   Vessel* getPntrToVessel( const unsigned&amp; i );</a>
+<a name="169"><span class="lineNum">     169 </span>            : /// Do any jobs that are required before the task list is undertaken</a>
+<a name="170"><span class="lineNum">     170 </span>            :   virtual void doJobsRequiredBeforeTaskList();</a>
+<a name="171"><span class="lineNum">     171 </span>            : /// Get the full size of the taskList dynamic list</a>
+<a name="172"><span class="lineNum">     172 </span>            :   unsigned getFullNumberOfTasks() const ;</a>
+<a name="173"><span class="lineNum">     173 </span>            : /// Get the position of the ith active task in the full list</a>
+<a name="174"><span class="lineNum">     174 </span>            :   unsigned getPositionInFullTaskList( const unsigned&amp; ii ) const ;</a>
+<a name="175"><span class="lineNum">     175 </span>            : /// Get the code for the ii th task in the list</a>
+<a name="176"><span class="lineNum">     176 </span>            :   unsigned getTaskCode( const unsigned&amp; ii ) const ;</a>
+<a name="177"><span class="lineNum">     177 </span>            : /// Get the ith of the currently active tasks</a>
+<a name="178"><span class="lineNum">     178 </span>            :   unsigned getActiveTask( const unsigned&amp; ii ) const ;</a>
+<a name="179"><span class="lineNum">     179 </span>            : /// Calculate one of the functions in the distribution</a>
+<a name="180"><span class="lineNum">     180 </span>            :   virtual void performTask( const unsigned&amp;, const unsigned&amp;, MultiValue&amp; ) const=0;</a>
+<a name="181"><span class="lineNum">     181 </span>            : /// Do the task if we have a bridge</a>
+<a name="182"><span class="lineNum">     182 </span>            :   virtual void transformBridgedDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) const;</a>
+<a name="183"><span class="lineNum">     183 </span>            : /// Ensure that data required in other vessels is stored</a>
+<a name="184"><span class="lineNum">     184 </span>            :   StoreDataVessel* buildDataStashes( ActionWithVessel* actionThatUses );</a>
+<a name="185"><span class="lineNum">     185 </span>            : /// Apply forces from bridge vessel - this is rarely used - currently only in ActionVolume</a>
+<a name="186"><span class="lineNum">     186 </span><span class="lineNoCov">          0 :   virtual void applyBridgeForces( const std::vector&lt;double&gt;&amp; bb ) { plumed_error(); }</span></a>
+<a name="187"><span class="lineNum">     187 </span>            : /// These are overwritten in MultiColvarFunction</a>
+<a name="188"><span class="lineNum">     188 </span>            : //  virtual void activateIndexes( const unsigned&amp;, const unsigned&amp;, const std::vector&lt;unsigned&gt;&amp; ){}</a>
+<a name="189"><span class="lineNum">     189 </span>            : /// Return a particular named vessel</a>
+<a name="190"><span class="lineNum">     190 </span>            :   Vessel* getVesselWithName( const std::string&amp; mynam );</a>
+<a name="191"><span class="lineNum">     191 </span>            : /// Does the weight have derivatives</a>
+<a name="192"><span class="lineNum">     192 </span>            :   bool weightWithDerivatives() const ;</a>
+<a name="193"><span class="lineNum">     193 </span>            : /// Return the position in the current task list</a>
+<a name="194"><span class="lineNum">     194 </span>            :   unsigned getPositionInCurrentTaskList( const unsigned&amp; myind ) const ;</a>
+<a name="195"><span class="lineNum">     195 </span>            : /// These normalizes vectors and is used in StoreDataVessel</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :   virtual void normalizeVector( std::vector&lt;double&gt;&amp; vals ) const { plumed_error(); }</span></a>
+<a name="197"><span class="lineNum">     197 </span><span class="lineNoCov">          0 :   virtual void normalizeVectorDerivatives( MultiValue&amp; myvals ) const { plumed_error(); }</span></a>
+<a name="198"><span class="lineNum">     198 </span>            : };</a>
+<a name="199"><span class="lineNum">     199 </span>            : </a>
+<a name="200"><span class="lineNum">     200 </span>            : inline</a>
+<a name="201"><span class="lineNum">     201 </span>            : double ActionWithVessel::getTolerance() const {</a>
+<a name="202"><span class="lineNum">     202 </span><span class="lineCov">     698726 :   return tolerance;</span></a>
+<a name="203"><span class="lineNum">     203 </span>            : }</a>
+<a name="204"><span class="lineNum">     204 </span>            : </a>
+<a name="205"><span class="lineNum">     205 </span>            : inline</a>
+<a name="206"><span class="lineNum">     206 </span>            : double ActionWithVessel::getNLTolerance() const {</a>
+<a name="207"><span class="lineNum">     207 </span>            :   return nl_tolerance;</a>
+<a name="208"><span class="lineNum">     208 </span>            : }</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : inline</a>
+<a name="211"><span class="lineNum">     211 </span>            : unsigned ActionWithVessel::getNumberOfVessels() const {</a>
+<a name="212"><span class="lineNum">     212 </span><span class="lineCov">   12537462 :   return functions.size();</span></a>
+<a name="213"><span class="lineNum">     213 </span>            : }</a>
+<a name="214"><span class="lineNum">     214 </span>            : </a>
+<a name="215"><span class="lineNum">     215 </span>            : inline</a>
+<a name="216"><span class="lineNum">     216 </span><span class="lineCov">     196791 : unsigned ActionWithVessel::getNumberOfQuantities() const {</span></a>
+<a name="217"><span class="lineNum">     217 </span><span class="lineCov">     196791 :   return 2;</span></a>
+<a name="218"><span class="lineNum">     218 </span>            : }</a>
+<a name="219"><span class="lineNum">     219 </span>            : </a>
+<a name="220"><span class="lineNum">     220 </span>            : inline</a>
+<a name="221"><span class="lineNum">     221 </span>            : Vessel* ActionWithVessel::getPntrToVessel( const unsigned&amp; i ) {</a>
+<a name="222"><span class="lineNum">     222 </span>            :   plumed_dbg_assert( i&lt;functions.size() );</a>
+<a name="223"><span class="lineNum">     223 </span><span class="lineCov">       2502 :   return functions[i].get();</span></a>
+<a name="224"><span class="lineNum">     224 </span>            : }</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : inline</a>
+<a name="227"><span class="lineNum">     227 </span>            : unsigned ActionWithVessel::getFullNumberOfTasks() const {</a>
+<a name="228"><span class="lineNum">     228 </span><span class="lineCov">   15830326 :   return fullTaskList.size();</span></a>
+<a name="229"><span class="lineNum">     229 </span>            : }</a>
+<a name="230"><span class="lineNum">     230 </span>            : </a>
+<a name="231"><span class="lineNum">     231 </span>            : inline</a>
+<a name="232"><span class="lineNum">     232 </span>            : unsigned ActionWithVessel::getTaskCode( const unsigned&amp; ii ) const {</a>
+<a name="233"><span class="lineNum">     233 </span>            :   plumed_dbg_assert( ii&lt;fullTaskList.size() );</a>
+<a name="234"><span class="lineNum">     234 </span><span class="lineCov">    3509797 :   return fullTaskList[ii];</span></a>
+<a name="235"><span class="lineNum">     235 </span>            : }</a>
+<a name="236"><span class="lineNum">     236 </span>            : </a>
+<a name="237"><span class="lineNum">     237 </span>            : inline</a>
+<a name="238"><span class="lineNum">     238 </span>            : unsigned ActionWithVessel::getCurrentNumberOfActiveTasks() const {</a>
+<a name="239"><span class="lineNum">     239 </span><span class="lineCov">      29023 :   return nactive_tasks;</span></a>
+<a name="240"><span class="lineNum">     240 </span>            : }</a>
+<a name="241"><span class="lineNum">     241 </span>            : </a>
+<a name="242"><span class="lineNum">     242 </span>            : inline</a>
+<a name="243"><span class="lineNum">     243 </span>            : unsigned ActionWithVessel::getActiveTask( const unsigned&amp; ii ) const {</a>
+<a name="244"><span class="lineNum">     244 </span>            :   plumed_dbg_assert( ii&lt;nactive_tasks );</a>
+<a name="245"><span class="lineNum">     245 </span><span class="lineCov">      54936 :   return partialTaskList[ii];</span></a>
+<a name="246"><span class="lineNum">     246 </span>            : }</a>
+<a name="247"><span class="lineNum">     247 </span>            : </a>
+<a name="248"><span class="lineNum">     248 </span>            : inline</a>
+<a name="249"><span class="lineNum">     249 </span>            : unsigned ActionWithVessel::getPositionInFullTaskList( const unsigned&amp; ii ) const {</a>
+<a name="250"><span class="lineNum">     250 </span>            :   plumed_dbg_assert( ii&lt;nactive_tasks );</a>
+<a name="251"><span class="lineNum">     251 </span><span class="lineCov">      62238 :   return indexOfTaskInFullList[ii];</span></a>
+<a name="252"><span class="lineNum">     252 </span>            : }</a>
+<a name="253"><span class="lineNum">     253 </span>            : </a>
+<a name="254"><span class="lineNum">     254 </span>            : inline</a>
+<a name="255"><span class="lineNum">     255 </span>            : bool ActionWithVessel::serialCalculation() const {</a>
+<a name="256"><span class="lineNum">     256 </span><span class="lineCov">        454 :   return serial;</span></a>
+<a name="257"><span class="lineNum">     257 </span>            : }</a>
+<a name="258"><span class="lineNum">     258 </span>            : </a>
+<a name="259"><span class="lineNum">     259 </span>            : inline</a>
+<a name="260"><span class="lineNum">     260 </span>            : bool ActionWithVessel::usingLowMem() const {</a>
+<a name="261"><span class="lineNum">     261 </span><span class="lineCov">     867292 :   return lowmem;</span></a>
+<a name="262"><span class="lineNum">     262 </span>            : }</a>
+<a name="263"><span class="lineNum">     263 </span>            : </a>
+<a name="264"><span class="lineNum">     264 </span>            : inline</a>
+<a name="265"><span class="lineNum">     265 </span>            : void ActionWithVessel::setLowMemOption(const bool&amp; l) {</a>
+<a name="266"><span class="lineNum">     266 </span><span class="lineCov">         42 :   lowmem=l;</span></a>
+<a name="267"><span class="lineNum">     267 </span>            : }</a>
+<a name="268"><span class="lineNum">     268 </span>            : </a>
+<a name="269"><span class="lineNum">     269 </span>            : inline</a>
+<a name="270"><span class="lineNum">     270 </span>            : bool ActionWithVessel::derivativesAreRequired() const {</a>
+<a name="271"><span class="lineNum">     271 </span><span class="lineCov">     714800 :   return !noderiv;</span></a>
+<a name="272"><span class="lineNum">     272 </span>            : }</a>
+<a name="273"><span class="lineNum">     273 </span>            : </a>
+<a name="274"><span class="lineNum">     274 </span>            : inline</a>
+<a name="275"><span class="lineNum">     275 </span>            : bool ActionWithVessel::weightWithDerivatives() const {</a>
+<a name="276"><span class="lineNum">     276 </span><span class="lineCov">      13904 :   return weightHasDerivatives;</span></a>
+<a name="277"><span class="lineNum">     277 </span>            : }</a>
+<a name="278"><span class="lineNum">     278 </span>            : </a>
+<a name="279"><span class="lineNum">     279 </span>            : inline</a>
+<a name="280"><span class="lineNum">     280 </span><span class="lineCov">     224556 : unsigned ActionWithVessel::getPositionInCurrentTaskList( const unsigned&amp; myind ) const {</span></a>
+<a name="281"><span class="lineNum">     281 </span><span class="lineCov">     224556 :   if( nactive_tasks==fullTaskList.size() ) return myind;</span></a>
+<a name="282"><span class="lineNum">     282 </span>            : </a>
+<a name="283"><span class="lineNum">     283 </span><span class="lineCov">  253764165 :   for(unsigned i=0; i&lt;nactive_tasks; ++i) {</span></a>
+<a name="284"><span class="lineNum">     284 </span><span class="lineCov">  253764165 :     if( myind==indexOfTaskInFullList[i] ) return i;</span></a>
+<a name="285"><span class="lineNum">     285 </span>            :   }</a>
+<a name="286"><span class="lineNum">     286 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;requested task is not active&quot;);</span></a>
+<a name="287"><span class="lineNum">     287 </span>            : }</a>
+<a name="288"><span class="lineNum">     288 </span>            : </a>
+<a name="289"><span class="lineNum">     289 </span>            : }</a>
+<a name="290"><span class="lineNum">     290 </span>            : }</a>
+<a name="291"><span class="lineNum">     291 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AltMin.cpp.func-sort-c.html b/coverage/vesselbase/AltMin.cpp.func-sort-c.html
new file mode 100644
index 0000000000..82b1cc4156
--- /dev/null
+++ b/coverage/vesselbase/AltMin.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AltMin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AltMin.cpp<span style="font-size: 80%;"> (<a href="AltMin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AltMin.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#38">_ZN4PLMD10vesselbase12_GLOBAL__N_116AltMinRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#40">_ZN4PLMD10vesselbase6AltMin16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#61">_ZN4PLMD10vesselbase6AltMin16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#54">_ZN4PLMD10vesselbase6AltMinC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#70">_ZN4PLMD10vesselbase6AltMin14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#66">_ZNK4PLMD10vesselbase6AltMin13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#38">_ZN4PLMD10vesselbase12_GLOBAL__N_116AltMinRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#38">_ZN4PLMD10vesselbase12_GLOBAL__N_116AltMinRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#45">_ZN4PLMD10vesselbase6AltMin14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AltMin.cpp.func.html b/coverage/vesselbase/AltMin.cpp.func.html
new file mode 100644
index 0000000000..8dae3dc09f
--- /dev/null
+++ b/coverage/vesselbase/AltMin.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AltMin.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AltMin.cpp<span style="font-size: 80%;"> (<a href="AltMin.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AltMin.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#38">_ZN4PLMD10vesselbase12_GLOBAL__N_116AltMinRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#38">_ZN4PLMD10vesselbase12_GLOBAL__N_116AltMinRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#38">_ZN4PLMD10vesselbase12_GLOBAL__N_116AltMinRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#70">_ZN4PLMD10vesselbase6AltMin14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#45">_ZN4PLMD10vesselbase6AltMin14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#40">_ZN4PLMD10vesselbase6AltMin16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#61">_ZN4PLMD10vesselbase6AltMin16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#54">_ZN4PLMD10vesselbase6AltMinC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AltMin.cpp.gcov.html#66">_ZNK4PLMD10vesselbase6AltMin13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AltMin.cpp.gcov.html b/coverage/vesselbase/AltMin.cpp.gcov.html
new file mode 100644
index 0000000000..631da9541b
--- /dev/null
+++ b/coverage/vesselbase/AltMin.cpp.gcov.html
@@ -0,0 +1,153 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AltMin.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AltMin.cpp<span style="font-size: 80%;"> (source / <a href="AltMin.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntry">21</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : class AltMin : public vesselbase::FunctionVessel {</a>
+<a name="29"><span class="lineNum">      29 </span>            : private:</a>
+<a name="30"><span class="lineNum">      30 </span>            :   double beta;</a>
+<a name="31"><span class="lineNum">      31 </span>            : public:</a>
+<a name="32"><span class="lineNum">      32 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="34"><span class="lineNum">      34 </span>            :   explicit AltMin( const vesselbase::VesselOptions&amp; da );</a>
+<a name="35"><span class="lineNum">      35 </span>            :   std::string value_descriptor() override;</a>
+<a name="36"><span class="lineNum">      36 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double finalTransform( const double&amp; val, double&amp; dv ) override;</a>
+<a name="38"><span class="lineNum">      38 </span>            : };</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">      12506 : PLUMED_REGISTER_VESSEL(AltMin,&quot;ALT_MIN&quot;)</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">          2 : void AltMin::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          2 :   FunctionVessel::registerKeywords(keys);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BETA&quot;,&quot;the value of beta for the equation in the manual&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          2 : }</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       4168 : void AltMin::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;ALT_MIN&quot;,&quot;calculate the minimum value. &quot;</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :                &quot;To make this quantity continuous the minimum is calculated using &quot;</a>
+<a name="50"><span class="lineNum">      50 </span>            :                &quot;\\f$ \\textrm{min} = -\\frac{1}{\\beta} \\log \\sum_i \\exp\\left( -\\beta s_i \\right)  \\f$ &quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :                &quot;The value of \\f$\\beta\\f$ in this function is specified using (BETA=\\f$\\beta\\f$).&quot;);</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;altmin&quot;,&quot;ALT_MIN&quot;,&quot;the minimum value. This is calculated using the formula described in the description of the &quot;</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :                           &quot;keyword so as to make it continuous.&quot;);</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       4168 : }</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">          2 : AltMin::AltMin( const vesselbase::VesselOptions&amp; da ):</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          2 :   FunctionVessel(da)</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : {</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          2 :   if( getAction()-&gt;isPeriodic() ) error(&quot;MIN is not a meaningful option for periodic variables&quot;);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          2 :   parse(&quot;BETA&quot;,beta); usetol=true;</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 : }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 : std::string AltMin::value_descriptor() {</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          2 :   std::string str_beta; Tools::convert( beta, str_beta );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          4 :   return &quot;the minimum value. Beta is equal to &quot; + str_beta;</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         10 : double AltMin::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">         10 :   double f = exp( -beta*val ); dv = -beta*f; return f;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">          5 : double AltMin::finalTransform( const double&amp; val, double&amp; dv ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          5 :   dv = - 1.0 /(beta*val); return -std::log( val ) / beta;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AveragingVessel.cpp.func-sort-c.html b/coverage/vesselbase/AveragingVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..8e8d14e17d
--- /dev/null
+++ b/coverage/vesselbase/AveragingVessel.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AveragingVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AveragingVessel.cpp<span style="font-size: 80%;"> (<a href="AveragingVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AveragingVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#26">_ZN4PLMD10vesselbase15AveragingVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">69</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#52">_ZN4PLMD10vesselbase15AveragingVessel5resetEv</a></td>
+              <td class="coverFnHi">69</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#30">_ZN4PLMD10vesselbase15AveragingVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#40">_ZN4PLMD10vesselbase15AveragingVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">98</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#48">_ZN4PLMD10vesselbase15AveragingVessel5clearEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#56">_ZN4PLMD10vesselbase15AveragingVessel11setDataSizeERKj</a></td>
+              <td class="coverFnHi">216</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#44">_ZNK4PLMD10vesselbase15AveragingVessel8wasresetEv</a></td>
+              <td class="coverFnHi">1278</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AveragingVessel.cpp.func.html b/coverage/vesselbase/AveragingVessel.cpp.func.html
new file mode 100644
index 0000000000..c2659428c4
--- /dev/null
+++ b/coverage/vesselbase/AveragingVessel.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AveragingVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AveragingVessel.cpp<span style="font-size: 80%;"> (<a href="AveragingVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AveragingVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#56">_ZN4PLMD10vesselbase15AveragingVessel11setDataSizeERKj</a></td>
+              <td class="coverFnHi">216</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#26">_ZN4PLMD10vesselbase15AveragingVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">69</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#48">_ZN4PLMD10vesselbase15AveragingVessel5clearEv</a></td>
+              <td class="coverFnHi">102</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#52">_ZN4PLMD10vesselbase15AveragingVessel5resetEv</a></td>
+              <td class="coverFnHi">69</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#40">_ZN4PLMD10vesselbase15AveragingVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">98</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#30">_ZN4PLMD10vesselbase15AveragingVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">70</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.cpp.gcov.html#44">_ZNK4PLMD10vesselbase15AveragingVessel8wasresetEv</a></td>
+              <td class="coverFnHi">1278</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AveragingVessel.cpp.gcov.html b/coverage/vesselbase/AveragingVessel.cpp.gcov.html
new file mode 100644
index 0000000000..26e7f53ee5
--- /dev/null
+++ b/coverage/vesselbase/AveragingVessel.cpp.gcov.html
@@ -0,0 +1,140 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AveragingVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AveragingVessel.cpp<span style="font-size: 80%;"> (source / <a href="AveragingVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;AveragingVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithAveraging.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         69 : void AveragingVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         69 :   Vessel::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         69 : }</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         70 : AveragingVessel::AveragingVessel( const vesselbase::VesselOptions&amp; vo ):</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :   Vessel(vo),</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         70 :   wascleared(true)</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         70 :   if( getAction() ) {</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         68 :     ActionWithAveraging* myav = dynamic_cast&lt;ActionWithAveraging*&gt;( getAction() );</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         68 :     plumed_assert( myav ); unormalised = myav-&gt;ignoreNormalization();</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   }</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         70 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         98 : void AveragingVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">    1182011 :   wascleared=false; for(unsigned i=1; i&lt;data.size(); ++i) data[i]+=buffer[bufstart + i - 1];</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         98 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1278 : bool AveragingVessel::wasreset() const {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1278 :   return wascleared;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        102 : void AveragingVessel::clear() {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        102 :   plumed_assert( wascleared ); data.assign( data.size(), 0.0 );</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        102 : }</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : </a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         69 : void AveragingVessel::reset() {</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         69 :   wascleared=true;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         69 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        216 : void AveragingVessel::setDataSize( const unsigned&amp; size ) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        216 :   if( data.size()!=(1+size) ) data.resize( 1+size, 0 );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">        216 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AveragingVessel.h.func-sort-c.html b/coverage/vesselbase/AveragingVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..756bb28efa
--- /dev/null
+++ b/coverage/vesselbase/AveragingVessel.h.func-sort-c.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AveragingVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AveragingVessel.h<span style="font-size: 80%;"> (<a href="AveragingVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="AveragingVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.h.gcov.html#63">_ZN4PLMD10vesselbase15AveragingVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.h.gcov.html#79">_ZNK4PLMD10vesselbase15AveragingVessel14getDataElementERKj</a></td>
+              <td class="coverFnHi">7999387</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AveragingVessel.h.func.html b/coverage/vesselbase/AveragingVessel.h.func.html
new file mode 100644
index 0000000000..705f4f13bd
--- /dev/null
+++ b/coverage/vesselbase/AveragingVessel.h.func.html
@@ -0,0 +1,80 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AveragingVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AveragingVessel.h<span style="font-size: 80%;"> (<a href="AveragingVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="AveragingVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.h.gcov.html#63">_ZN4PLMD10vesselbase15AveragingVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="AveragingVessel.h.gcov.html#79">_ZNK4PLMD10vesselbase15AveragingVessel14getDataElementERKj</a></td>
+              <td class="coverFnHi">7999387</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/AveragingVessel.h.gcov.html b/coverage/vesselbase/AveragingVessel.h.gcov.html
new file mode 100644
index 0000000000..6c76451d42
--- /dev/null
+++ b/coverage/vesselbase/AveragingVessel.h.gcov.html
@@ -0,0 +1,177 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/AveragingVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - AveragingVessel.h<span style="font-size: 80%;"> (source / <a href="AveragingVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">2</td>
+            <td class="headerCovTableEntryLo">50.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2016-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_AveragingVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_AveragingVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace vesselbase {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : class AveragingVessel : public Vessel {</a>
+<a name="31"><span class="lineNum">      31 </span>            : private:</a>
+<a name="32"><span class="lineNum">      32 </span>            : /// The grid was recently cleared and bounds can be set</a>
+<a name="33"><span class="lineNum">      33 </span>            :   bool wascleared;</a>
+<a name="34"><span class="lineNum">      34 </span>            : /// Are we outputting unormalised data</a>
+<a name="35"><span class="lineNum">      35 </span>            :   bool unormalised;</a>
+<a name="36"><span class="lineNum">      36 </span>            : /// The data that is being averaged</a>
+<a name="37"><span class="lineNum">      37 </span>            :   std::vector&lt;double&gt; data;</a>
+<a name="38"><span class="lineNum">      38 </span>            : protected:</a>
+<a name="39"><span class="lineNum">      39 </span>            : /// Set the size of the data vector</a>
+<a name="40"><span class="lineNum">      40 </span>            :   void setDataSize( const unsigned&amp; size );</a>
+<a name="41"><span class="lineNum">      41 </span>            : /// Set an element of the data array</a>
+<a name="42"><span class="lineNum">      42 </span>            :   void setDataElement( const unsigned&amp; myelem, const double&amp; value );</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Add some value to an element of the data array</a>
+<a name="44"><span class="lineNum">      44 </span>            :   void addDataElement( const unsigned&amp; myelem, const double&amp; value );</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Get the value of one of the data element</a>
+<a name="46"><span class="lineNum">      46 </span>            :   double getDataElement( const unsigned&amp; myelem ) const ;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Are we averaging the data</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">     361786 :   bool noAverage() const { return unormalised; }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : public:</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// keywords</a>
+<a name="51"><span class="lineNum">      51 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Constructor</a>
+<a name="53"><span class="lineNum">      53 </span>            :   explicit AveragingVessel( const vesselbase::VesselOptions&amp; );</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Copy data from an accumulated buffer into the grid</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void finish( const std::vector&lt;double&gt;&amp; ) override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Was the grid cleared on the last step</a>
+<a name="57"><span class="lineNum">      57 </span>            :   bool wasreset() const ;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Clear all the data stored on the grid</a>
+<a name="59"><span class="lineNum">      59 </span>            :   virtual void clear();</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Reset the grid so that it is cleared at start of next time it is calculated</a>
+<a name="61"><span class="lineNum">      61 </span>            :   virtual void reset();</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Functions for dealing with normalisation constant</a>
+<a name="63"><span class="lineNum">      63 </span>            :   void setNorm( const double&amp; snorm );</a>
+<a name="64"><span class="lineNum">      64 </span>            :   double getNorm() const ;</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   bool applyForce(  std::vector&lt;double&gt;&amp; forces ) override { return false; }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : };</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span>            : inline</a>
+<a name="69"><span class="lineNum">      69 </span>            : void AveragingVessel::setDataElement( const unsigned&amp; myelem, const double&amp; value ) {</a>
+<a name="70"><span class="lineNum">      70 </span>            :   plumed_dbg_assert( myelem&lt;1+data.size() );</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     154208 :   wascleared=false; data[1+myelem]=value;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span>            : inline</a>
+<a name="75"><span class="lineNum">      75 </span>            : void AveragingVessel::addDataElement( const unsigned&amp; myelem, const double&amp; value ) {</a>
+<a name="76"><span class="lineNum">      76 </span>            :   plumed_dbg_assert( myelem&lt;1+data.size() );</a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">      58119 :   wascleared=false; data[1+myelem]+=value;</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            : inline</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">    7999387 : double AveragingVessel::getDataElement( const unsigned&amp; myelem ) const {</span></a>
+<a name="82"><span class="lineNum">      82 </span>            :   plumed_dbg_assert( myelem&lt;data.size()-1 );</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">    7999387 :   if( unormalised ) return data[1+myelem];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">    1851499 :   return data[1+myelem] / data[0];</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : inline</a>
+<a name="88"><span class="lineNum">      88 </span>            : void AveragingVessel::setNorm( const double&amp; snorm ) {</a>
+<a name="89"><span class="lineNum">      89 </span>            :   plumed_dbg_assert( data.size()&gt;0 );</a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1389 :   data[0]=snorm;</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         27 : }</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            : inline</a>
+<a name="94"><span class="lineNum">      94 </span>            : double AveragingVessel::getNorm() const {</a>
+<a name="95"><span class="lineNum">      95 </span>            :   plumed_dbg_assert( data.size()&gt;0 );</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     104745 :   return data[0];</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : }</a>
+<a name="98"><span class="lineNum">      98 </span>            : </a>
+<a name="99"><span class="lineNum">      99 </span>            : }</a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Between.cpp.func-sort-c.html b/coverage/vesselbase/Between.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d9a4a19a13
--- /dev/null
+++ b/coverage/vesselbase/Between.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Between.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Between.cpp<span style="font-size: 80%;"> (<a href="Between.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Between.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#72">_ZN4PLMD10vesselbase7Between9getCutoffEv</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#27">_ZN4PLMD10vesselbase12_GLOBAL__N_117BetweenRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#29">_ZN4PLMD10vesselbase7Between16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#63">_ZN4PLMD10vesselbase7Between16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#44">_ZN4PLMD10vesselbase7BetweenC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#27">_ZN4PLMD10vesselbase12_GLOBAL__N_117BetweenRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#27">_ZN4PLMD10vesselbase12_GLOBAL__N_117BetweenRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#35">_ZN4PLMD10vesselbase7Between14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#68">_ZNK4PLMD10vesselbase7Between13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">8224</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Between.cpp.func.html b/coverage/vesselbase/Between.cpp.func.html
new file mode 100644
index 0000000000..5baec49d9b
--- /dev/null
+++ b/coverage/vesselbase/Between.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Between.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Between.cpp<span style="font-size: 80%;"> (<a href="Between.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Between.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#27">_ZN4PLMD10vesselbase12_GLOBAL__N_117BetweenRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#27">_ZN4PLMD10vesselbase12_GLOBAL__N_117BetweenRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#27">_ZN4PLMD10vesselbase12_GLOBAL__N_117BetweenRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#35">_ZN4PLMD10vesselbase7Between14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#29">_ZN4PLMD10vesselbase7Between16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#63">_ZN4PLMD10vesselbase7Between16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#72">_ZN4PLMD10vesselbase7Between9getCutoffEv</a></td>
+              <td class="coverFnHi">60</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#44">_ZN4PLMD10vesselbase7BetweenC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Between.cpp.gcov.html#68">_ZNK4PLMD10vesselbase7Between13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">8224</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Between.cpp.gcov.html b/coverage/vesselbase/Between.cpp.gcov.html
new file mode 100644
index 0000000000..002883b28a
--- /dev/null
+++ b/coverage/vesselbase/Between.cpp.gcov.html
@@ -0,0 +1,155 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Between.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Between.cpp<span style="font-size: 80%;"> (source / <a href="Between.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntry">30</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Between.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace vesselbase {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">      12569 : PLUMED_REGISTER_VESSEL(Between,&quot;BETWEEN&quot;)</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         65 : void Between::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         65 :   FunctionVessel::registerKeywords( keys );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         65 :   HistogramBead::registerKeywords( keys );</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        130 :   keys.addFlag(&quot;NORM&quot;,false,&quot;calculate the fraction of values rather than the number&quot;);</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         65 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">       4168 : void Between::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;BETWEEN&quot;,&quot;calculate the number of values that are within a certain range. &quot;</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :                &quot;These quantities are calculated using kernel density estimation as described on &quot;</a>
+<a name="40"><span class="lineNum">      40 </span>            :                &quot;\\ref histogrambead.&quot;);</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;between&quot;,&quot;BETWEEN&quot;,&quot;the number/fraction of values within a certain range. This is calculated using one of the &quot;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :                           &quot;formula described in the description of the keyword so as to make it continuous. &quot;</a>
+<a name="43"><span class="lineNum">      43 </span>            :                           &quot;You can calculate this quantity multiple times using different parameters.&quot;);</a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       4168 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         65 : Between::Between( const VesselOptions&amp; da ) :</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         65 :   FunctionVessel(da)</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : {</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         65 :   usetol=true;</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         65 :   bool isPeriodic=getAction()-&gt;isPeriodic();</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   double min, max; std::string str_min, str_max;</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         65 :   if( isPeriodic ) {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          1 :     getAction()-&gt;retrieveDomain( str_min, str_max );</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          1 :     Tools::convert(str_min,min); Tools::convert(str_max,max);</span></a>
+<a name="55"><span class="lineNum">      55 </span>            :   }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        130 :   parseFlag(&quot;NORM&quot;,norm); std::string errormsg;</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         65 :   hist.set( getAllInput(),errormsg );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         65 :   if( !isPeriodic ) hist.isNotPeriodic();</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          1 :   else hist.isPeriodic( min, max );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         65 :   if( errormsg.size()!=0 ) error( errormsg );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         65 : }</span></a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         65 : std::string Between::value_descriptor() {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">         66 :   if(norm) return &quot;the fraction of values &quot; + hist.description();</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        128 :   return &quot;the number of values &quot; + hist.description();</span></a>
+<a name="68"><span class="lineNum">      68 </span>            : }</a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       8224 : double Between::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       8224 :   double f = hist.calculate(val, dv); return f;</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : </a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">         60 : double Between::getCutoff() {</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">         60 :   return std::numeric_limits&lt;double&gt;::max();</span></a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+<a name="77"><span class="lineNum">      77 </span>            : </a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/BridgeVessel.cpp.func-sort-c.html b/coverage/vesselbase/BridgeVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e1324ede6c
--- /dev/null
+++ b/coverage/vesselbase/BridgeVessel.cpp.func-sort-c.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/BridgeVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - BridgeVessel.cpp<span style="font-size: 80%;"> (<a href="BridgeVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BridgeVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#62">_ZN4PLMD10vesselbase12BridgeVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#53">_ZN4PLMD10vesselbase12BridgeVessel15setOutputActionEPNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#28">_ZN4PLMD10vesselbase12BridgeVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#105">_ZN4PLMD10vesselbase12BridgeVessel28completeNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#38">_ZN4PLMD10vesselbase12BridgeVessel6resizeEv</a></td>
+              <td class="coverFnHi">513</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#163">_ZN4PLMD10vesselbase12BridgeVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">795</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#179">_ZN4PLMD10vesselbase12BridgeVessel13copyTaskFlagsEv</a></td>
+              <td class="coverFnHi">795</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#70">_ZN4PLMD10vesselbase12BridgeVessel14setBufferStartERj</a></td>
+              <td class="coverFnHi">3025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#90">_ZN4PLMD10vesselbase12BridgeVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">3025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#66">_ZN4PLMD10vesselbase12BridgeVessel7prepareEv</a></td>
+              <td class="coverFnHi">3025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#185">_ZN4PLMD10vesselbase12BridgeVessel20getTemporyMultiValueEv</a></td>
+              <td class="coverFnHi">13042</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#74">_ZN4PLMD10vesselbase12BridgeVessel20transformDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">102743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#83">_ZNK4PLMD10vesselbase12BridgeVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">102743</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/BridgeVessel.cpp.func.html b/coverage/vesselbase/BridgeVessel.cpp.func.html
new file mode 100644
index 0000000000..8a25230929
--- /dev/null
+++ b/coverage/vesselbase/BridgeVessel.cpp.func.html
@@ -0,0 +1,124 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/BridgeVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - BridgeVessel.cpp<span style="font-size: 80%;"> (<a href="BridgeVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BridgeVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#163">_ZN4PLMD10vesselbase12BridgeVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">795</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#62">_ZN4PLMD10vesselbase12BridgeVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#179">_ZN4PLMD10vesselbase12BridgeVessel13copyTaskFlagsEv</a></td>
+              <td class="coverFnHi">795</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#70">_ZN4PLMD10vesselbase12BridgeVessel14setBufferStartERj</a></td>
+              <td class="coverFnHi">3025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#53">_ZN4PLMD10vesselbase12BridgeVessel15setOutputActionEPNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#185">_ZN4PLMD10vesselbase12BridgeVessel20getTemporyMultiValueEv</a></td>
+              <td class="coverFnHi">13042</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#74">_ZN4PLMD10vesselbase12BridgeVessel20transformDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">102743</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#105">_ZN4PLMD10vesselbase12BridgeVessel28completeNumericalDerivativesEv</a></td>
+              <td class="coverFnHi">65</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#90">_ZN4PLMD10vesselbase12BridgeVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">3025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#38">_ZN4PLMD10vesselbase12BridgeVessel6resizeEv</a></td>
+              <td class="coverFnHi">513</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#66">_ZN4PLMD10vesselbase12BridgeVessel7prepareEv</a></td>
+              <td class="coverFnHi">3025</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#28">_ZN4PLMD10vesselbase12BridgeVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">46</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="BridgeVessel.cpp.gcov.html#83">_ZNK4PLMD10vesselbase12BridgeVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">102743</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/BridgeVessel.cpp.gcov.html b/coverage/vesselbase/BridgeVessel.cpp.gcov.html
new file mode 100644
index 0000000000..5eb39f06fb
--- /dev/null
+++ b/coverage/vesselbase/BridgeVessel.cpp.gcov.html
@@ -0,0 +1,269 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/BridgeVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - BridgeVessel.cpp<span style="font-size: 80%;"> (source / <a href="BridgeVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">96</td>
+            <td class="headerCovTableEntry">99</td>
+            <td class="headerCovTableEntryHi">97.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">13</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;BridgeVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;tools/Matrix.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;core/ActionWithArguments.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace vesselbase {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         46 : BridgeVessel::BridgeVessel( const VesselOptions&amp; da ):</span></a>
+<a name="31"><span class="lineNum">      31 </span>            :   Vessel(da),</a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         46 :   inum(0),</span></a>
+<a name="33"><span class="lineNum">      33 </span>            : // in_normal_calculate(false)</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         46 :   myOutputAction(NULL),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">         46 :   myOutputValues(NULL),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         46 :   my_tmp_val(0,0)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : {</a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         46 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        513 : void BridgeVessel::resize() {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        513 :   if( myOutputAction-&gt;checkNumericalDerivatives() ) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         10 :     mynumerical_values.resize( getAction()-&gt;getNumberOfDerivatives()*myOutputValues-&gt;getNumberOfComponents() );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         10 :     inum=0;</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   }</a>
+<a name="45"><span class="lineNum">      45 </span>            :   // This bit ensures that we can store data in a bridge function if needs be</a>
+<a name="46"><span class="lineNum">      46 </span>            :   // Notice we need to resize der_list in the underlying action as this is called</a>
+<a name="47"><span class="lineNum">      47 </span>            :   // from a bridge</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        513 :   if( myOutputAction-&gt;mydata ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :     unsigned dsize=(myOutputAction-&gt;mydata)-&gt;getSizeOfDerivativeList();</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         12 :     if( getAction()-&gt;der_list.size()!=dsize ) getAction()-&gt;der_list.resize( dsize );</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :   }</a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">        513 :   unsigned tmp=0; resizeBuffer( myOutputAction-&gt;getSizeOfBuffer( tmp ) );</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        513 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         46 : void BridgeVessel::setOutputAction( ActionWithVessel* myact ) {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         46 :   ActionWithValue* checkme=dynamic_cast&lt;ActionWithValue*&gt;( getAction() );</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         46 :   plumed_massert( checkme, &quot;vessel in bridge must inherit from ActionWithValue&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span>            : </a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         46 :   myOutputAction=myact;</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         46 :   myOutputValues=dynamic_cast&lt;ActionWithValue*&gt;( myact );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         46 :   plumed_massert( myOutputValues, &quot;bridging vessel must inherit from ActionWithValue&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         46 : }</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineNoCov">          0 : std::string BridgeVessel::description() {</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;I shouldn't end up here&quot;);</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+<a name="67"><span class="lineNum">      67 </span>            : </a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       3025 : void BridgeVessel::prepare() {</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       3025 :   myOutputAction-&gt;doJobsRequiredBeforeTaskList();</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">       3025 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       3025 : void BridgeVessel::setBufferStart( unsigned&amp; start ) {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">       3025 :   myOutputAction-&gt;getSizeOfBuffer( start );</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       3025 : }</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">     102743 : MultiValue&amp; BridgeVessel::transformDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">     205022 :   if( outvals.getNumberOfValues()!=myOutputAction-&gt;getNumberOfQuantities() ||</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">     102279 :       outvals.getNumberOfDerivatives()!=myOutputAction-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">       2287 :     outvals.resize( myOutputAction-&gt;getNumberOfQuantities(), myOutputAction-&gt;getNumberOfDerivatives() );</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   }</a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">     102743 :   myOutputAction-&gt;transformBridgedDerivatives( current, invals, outvals );</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">     102743 :   return outvals;</span></a>
+<a name="83"><span class="lineNum">      83 </span>            : }</a>
+<a name="84"><span class="lineNum">      84 </span>            : </a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     102743 : void BridgeVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :   // in_normal_calculate=true;</a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">     102743 :   if( myvals.get(0)&lt;myOutputAction-&gt;getTolerance() ) return;</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      62508 :   myOutputAction-&gt;calculateAllVessels( current, myvals, myvals, buffer, der_list );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">      62508 :   return;</span></a>
+<a name="90"><span class="lineNum">      90 </span>            : }</a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+<a name="92"><span class="lineNum">      92 </span><span class="lineCov">       3025 : void BridgeVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">       3025 :   myOutputAction-&gt;finishComputations( buffer );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">       3025 :   if( myOutputAction-&gt;checkNumericalDerivatives() ) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">       1930 :     if ( inum&lt;mynumerical_values.size() ) {</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">       2160 :       for(int i=0; i&lt;myOutputValues-&gt;getNumberOfComponents(); ++i) {</span></a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">       1080 :         mynumerical_values[inum]=myOutputValues-&gt;getOutputQuantity(i);</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">       1080 :         inum++;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :       }</a>
+<a name="100"><span class="lineNum">     100 </span>            :       plumed_dbg_assert( inum&lt;=mynumerical_values.size() );</a>
+<a name="101"><span class="lineNum">     101 </span>            :     } else {</a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">        850 :       plumed_assert( inum==mynumerical_values.size() );</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :     }</a>
+<a name="104"><span class="lineNum">     104 </span>            :   }</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">       3025 : }</span></a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">         65 : void BridgeVessel::completeNumericalDerivatives() {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">         65 :   unsigned nextra = myOutputAction-&gt;getNumberOfDerivatives() - getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">         65 :   Matrix&lt;double&gt; tmpder( myOutputValues-&gt;getNumberOfComponents(), nextra );</span></a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">         65 :   ActionWithVessel* vval=dynamic_cast&lt;ActionWithVessel*&gt;( myOutputAction );</span></a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        785 :   for(unsigned i=0; i&lt;nextra; ++i) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        720 :     vval-&gt;bridgeVariable=i; getAction()-&gt;calculate();</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">       1440 :     for(int j=0; j&lt;myOutputValues-&gt;getNumberOfComponents(); ++j) tmpder(j,i) = myOutputValues-&gt;getOutputQuantity(j);</span></a>
+<a name="114"><span class="lineNum">     114 </span>            :   }</a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">         65 :   vval-&gt;bridgeVariable=nextra; getAction()-&gt;calculate();</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">         65 :   plumed_assert( inum==mynumerical_values.size() ); inum=0;  // Reset inum now that we have finished calling calculate</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">         65 :   std::vector&lt;double&gt; base( myOutputValues-&gt;getNumberOfComponents() );</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">        130 :   for(int j=0; j&lt;myOutputValues-&gt;getNumberOfComponents(); ++j) base[j] = myOutputValues-&gt;getOutputQuantity(j);</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : </a>
+<a name="120"><span class="lineNum">     120 </span>            :   const double delta=std::sqrt(epsilon);</a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">         65 :   ActionAtomistic* aa=dynamic_cast&lt;ActionAtomistic*&gt;( getAction() );</span></a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">         65 :   unsigned nvals=myOutputValues-&gt;getNumberOfComponents();</span></a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        130 :   for(unsigned j=0; j&lt;nvals; ++j) ( myOutputValues-&gt;copyOutput(j) )-&gt;clearDerivatives();</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">         65 :   if( aa ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">         65 :     ActionWithArguments* aarg=dynamic_cast&lt;ActionWithArguments*&gt;( getAction() );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        130 :     plumed_assert( !aarg ); Tensor box=aa-&gt;getBox();</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :     unsigned natoms=aa-&gt;getNumberOfAtoms();</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">        130 :     for(unsigned j=0; j&lt;nvals; ++j) {</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineCov">         65 :       double ref=( myOutputValues-&gt;copyOutput(j) )-&gt;get();</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">         65 :       if( ( myOutputValues-&gt;copyOutput(j) )-&gt;getNumberOfDerivatives()&gt;0 ) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">        560 :         for(unsigned i=0; i&lt;3*natoms; ++i) {</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">        495 :           double d=( mynumerical_values[i*nvals+j] - ref)/delta;</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        495 :           ( myOutputValues-&gt;copyOutput(j) )-&gt;addDerivative(i,d);</span></a>
+<a name="135"><span class="lineNum">     135 </span>            :         }</a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">         65 :         Tensor virial;</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        845 :         for(int i=0; i&lt;3; i++) for(int k=0; k&lt;3; k++) {</span></a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineCov">        585 :             virial(i,k)=( mynumerical_values[ nvals*(3*natoms + 3*i + k) + j ]-ref)/delta;</span></a>
+<a name="139"><span class="lineNum">     139 </span>            :           }</a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineCov">         65 :         virial=-matmul(box.transpose(),virial);</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">        845 :         for(int i=0; i&lt;3; i++) for(int k=0; k&lt;3; k++) ( myOutputValues-&gt;copyOutput(j) )-&gt;addDerivative(3*natoms+3*k+i,virial(k,i));</span></a>
+<a name="142"><span class="lineNum">     142 </span>            :       }</a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span>            :   } else {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;not implemented or tested yet&quot;);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            : //      unsigned nder=myOutputAction-&gt;getNumberOfDerivatives();</a>
+<a name="147"><span class="lineNum">     147 </span>            : //      for(unsigned j=0;j&lt;nvals;++j){</a>
+<a name="148"><span class="lineNum">     148 </span>            : //          double ref=( myOutputValues-&gt;copyOutput(j) )-&gt;get();</a>
+<a name="149"><span class="lineNum">     149 </span>            : //              for(unsigned i=0;i&lt;nder;++i){</a>
+<a name="150"><span class="lineNum">     150 </span>            : //                  double d=( mynumerical_values[i*nvals+j] - ref)/delta;</a>
+<a name="151"><span class="lineNum">     151 </span>            : //                  ( myOutputValues-&gt;copyOutput(j) )-&gt;addDerivative(i,d);</a>
+<a name="152"><span class="lineNum">     152 </span>            : //              }</a>
+<a name="153"><span class="lineNum">     153 </span>            : //          }</a>
+<a name="154"><span class="lineNum">     154 </span>            : //      }</a>
+<a name="155"><span class="lineNum">     155 </span>            :   }</a>
+<a name="156"><span class="lineNum">     156 </span>            :   // Add the derivatives wrt to the local quantities we are working with</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        130 :   for(unsigned j=0; j&lt;nvals; ++j) {</span></a>
+<a name="158"><span class="lineNum">     158 </span>            :     unsigned k=0;</a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">        785 :     for(unsigned i=getAction()-&gt;getNumberOfDerivatives(); i&lt;myOutputAction-&gt;getNumberOfDerivatives(); ++i) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">        720 :       ( myOutputValues-&gt;copyOutput(j) )-&gt;addDerivative( i, (tmpder(j,k)-base[j])/std::sqrt(epsilon) ); k++;</span></a>
+<a name="161"><span class="lineNum">     161 </span>            :     }</a>
+<a name="162"><span class="lineNum">     162 </span>            :   }</a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">         65 : }</span></a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        795 : bool BridgeVessel::applyForce( std::vector&lt;double&gt;&amp; outforces ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">        795 :   bool hasforce=false; outforces.assign(outforces.size(),0.0);</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">        795 :   unsigned ndertot = myOutputAction-&gt;getNumberOfDerivatives();</span></a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        795 :   unsigned nextra = ndertot - getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        795 :   std::vector&lt;double&gt; forces( ndertot ), eforces( nextra, 0.0 );</span></a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       1730 :   for(unsigned i=0; i&lt;myOutputAction-&gt;getNumberOfVessels(); ++i) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        935 :     if( ( myOutputAction-&gt;getPntrToVessel(i) )-&gt;applyForce( forces ) ) {</span></a>
+<a name="172"><span class="lineNum">     172 </span>            :       hasforce=true;</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">     260815 :       for(unsigned j=0; j&lt;outforces.size(); ++j) outforces[j]+=forces[j];</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">         94 :       for(unsigned j=0; j&lt;nextra; ++j) eforces[j]+=forces[ outforces.size()+j ];</span></a>
+<a name="175"><span class="lineNum">     175 </span>            :     }</a>
+<a name="176"><span class="lineNum">     176 </span>            :   }</a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">        795 :   if(hasforce) myOutputAction-&gt;applyBridgeForces( eforces );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        795 :   return hasforce;</span></a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">        795 : void BridgeVessel::copyTaskFlags() {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        795 :   myOutputAction-&gt;deactivateAllTasks();</span></a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">      89536 :   for(unsigned i=0; i&lt;getAction()-&gt;nactive_tasks; ++i) myOutputAction-&gt;taskFlags[ getAction()-&gt;indexOfTaskInFullList[i] ] = 1;</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        795 :   myOutputAction-&gt;lockContributors();</span></a>
+<a name="185"><span class="lineNum">     185 </span><span class="lineCov">        795 : }</span></a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">      13042 : MultiValue&amp; BridgeVessel::getTemporyMultiValue() {</span></a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">      13042 :   return my_tmp_val;</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+<a name="192"><span class="lineNum">     192 </span>            : }</a>
+<a name="193"><span class="lineNum">     193 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/BridgeVessel.h.func-sort-c.html b/coverage/vesselbase/BridgeVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..98a0fb36eb
--- /dev/null
+++ b/coverage/vesselbase/BridgeVessel.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/BridgeVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - BridgeVessel.h<span style="font-size: 80%;"> (<a href="BridgeVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="BridgeVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/BridgeVessel.h.func.html b/coverage/vesselbase/BridgeVessel.h.func.html
new file mode 100644
index 0000000000..38f6616ea8
--- /dev/null
+++ b/coverage/vesselbase/BridgeVessel.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/BridgeVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - BridgeVessel.h<span style="font-size: 80%;"> (<a href="BridgeVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="BridgeVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/BridgeVessel.h.gcov.html b/coverage/vesselbase/BridgeVessel.h.gcov.html
new file mode 100644
index 0000000000..42a1431450
--- /dev/null
+++ b/coverage/vesselbase/BridgeVessel.h.gcov.html
@@ -0,0 +1,167 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/BridgeVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - BridgeVessel.h<span style="font-size: 80%;"> (source / <a href="BridgeVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_BridgeVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_BridgeVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/MultiValue.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace vesselbase {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : /**</a>
+<a name="36"><span class="lineNum">      36 </span>            : \ingroup TOOLBOX</a>
+<a name="37"><span class="lineNum">      37 </span>            : This class allows you to calculate the vessel in one ActionWithVessel.  The user thinks</a>
+<a name="38"><span class="lineNum">      38 </span>            : it is created in a different Action however.  At the moment this is used for region</a>
+<a name="39"><span class="lineNum">      39 </span>            : */</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span>            : class BridgeVessel : public Vessel {</a>
+<a name="42"><span class="lineNum">      42 </span>            : private:</a>
+<a name="43"><span class="lineNum">      43 </span>            :   unsigned inum;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   // bool in_normal_calculate;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   std::vector&lt;double&gt; mynumerical_values;</a>
+<a name="46"><span class="lineNum">      46 </span>            :   ActionWithVessel* myOutputAction;</a>
+<a name="47"><span class="lineNum">      47 </span>            :   ActionWithValue* myOutputValues;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   // We create a tempory multivalue here so as to avoid vector resizing</a>
+<a name="49"><span class="lineNum">      49 </span>            :   MultiValue my_tmp_val;</a>
+<a name="50"><span class="lineNum">      50 </span>            : public:</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit BridgeVessel( const VesselOptions&amp; );</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// Does this have derivatives</a>
+<a name="53"><span class="lineNum">      53 </span>            :   bool hasDerivatives();</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Resize the quantities in the vessel</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void resize() override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Get the action that reads the command in</a>
+<a name="57"><span class="lineNum">      57 </span>            :   ActionWithVessel* getOutputAction();</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Setup the action we are outputting to</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void setOutputAction( ActionWithVessel* myOutputAction );</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Apply some force</a>
+<a name="61"><span class="lineNum">      61 </span>            :   bool applyForce( std::vector&lt;double&gt;&amp; forces ) override;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Should not be called</a>
+<a name="63"><span class="lineNum">      63 </span>            :   std::string description() override;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// Jobs to do before the task list starts</a>
+<a name="65"><span class="lineNum">      65 </span>            :   void prepare() override;</a>
+<a name="66"><span class="lineNum">      66 </span>            : /// Set the start of the buffer</a>
+<a name="67"><span class="lineNum">      67 </span>            :   void setBufferStart( unsigned&amp; start ) override;</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// This transforms the derivatives using the output value</a>
+<a name="69"><span class="lineNum">      69 </span>            :   MultiValue&amp; transformDerivatives( const unsigned&amp; current, MultiValue&amp; invals, MultiValue&amp; outvals ) override;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// Actually do the calculation</a>
+<a name="71"><span class="lineNum">      71 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_index ) const override;</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// Finish the calculation</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Calculate numerical derivatives</a>
+<a name="75"><span class="lineNum">      75 </span>            :   void completeNumericalDerivatives();</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Set the task flags in the bridged class the same as in the original class</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void copyTaskFlags();</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// Return a tempory multi value - we do this so as to avoid vector resizing</a>
+<a name="79"><span class="lineNum">      79 </span>            :   MultiValue&amp; getTemporyMultiValue();</a>
+<a name="80"><span class="lineNum">      80 </span>            : };</a>
+<a name="81"><span class="lineNum">      81 </span>            : </a>
+<a name="82"><span class="lineNum">      82 </span>            : inline</a>
+<a name="83"><span class="lineNum">      83 </span>            : ActionWithVessel* BridgeVessel::getOutputAction() {</a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">         70 :   return myOutputAction;</span></a>
+<a name="85"><span class="lineNum">      85 </span>            : }</a>
+<a name="86"><span class="lineNum">      86 </span>            : </a>
+<a name="87"><span class="lineNum">      87 </span>            : }</a>
+<a name="88"><span class="lineNum">      88 </span>            : }</a>
+<a name="89"><span class="lineNum">      89 </span>            : #endif</a>
+<a name="90"><span class="lineNum">      90 </span>            : </a>
+<a name="91"><span class="lineNum">      91 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/FunctionVessel.cpp.func-sort-c.html b/coverage/vesselbase/FunctionVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..0578fdd857
--- /dev/null
+++ b/coverage/vesselbase/FunctionVessel.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/FunctionVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - FunctionVessel.cpp<span style="font-size: 80%;"> (<a href="FunctionVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FunctionVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#74">_ZNK4PLMD10vesselbase14FunctionVessel13calcTransformERKdRd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#26">_ZN4PLMD10vesselbase14FunctionVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">329</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#30">_ZN4PLMD10vesselbase14FunctionVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">329</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#38">_ZN4PLMD10vesselbase14FunctionVessel6resizeEv</a></td>
+              <td class="coverFnHi">912</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#96">_ZN4PLMD10vesselbase14FunctionVessel14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">22778</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#78">_ZN4PLMD10vesselbase14FunctionVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">26616</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#50">_ZNK4PLMD10vesselbase14FunctionVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">244832</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/FunctionVessel.cpp.func.html b/coverage/vesselbase/FunctionVessel.cpp.func.html
new file mode 100644
index 0000000000..1e0eda377e
--- /dev/null
+++ b/coverage/vesselbase/FunctionVessel.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/FunctionVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - FunctionVessel.cpp<span style="font-size: 80%;"> (<a href="FunctionVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FunctionVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#96">_ZN4PLMD10vesselbase14FunctionVessel14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">22778</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#26">_ZN4PLMD10vesselbase14FunctionVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">329</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#78">_ZN4PLMD10vesselbase14FunctionVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">26616</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#38">_ZN4PLMD10vesselbase14FunctionVessel6resizeEv</a></td>
+              <td class="coverFnHi">912</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#30">_ZN4PLMD10vesselbase14FunctionVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">329</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#74">_ZNK4PLMD10vesselbase14FunctionVessel13calcTransformERKdRd</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="FunctionVessel.cpp.gcov.html#50">_ZNK4PLMD10vesselbase14FunctionVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">244832</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/FunctionVessel.cpp.gcov.html b/coverage/vesselbase/FunctionVessel.cpp.gcov.html
new file mode 100644
index 0000000000..3981d582d0
--- /dev/null
+++ b/coverage/vesselbase/FunctionVessel.cpp.gcov.html
@@ -0,0 +1,180 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/FunctionVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - FunctionVessel.cpp<span style="font-size: 80%;"> (source / <a href="FunctionVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">44</td>
+            <td class="headerCovTableEntry">46</td>
+            <td class="headerCovTableEntryHi">95.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        329 : void FunctionVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        329 :   ValueVessel::registerKeywords( keys );</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        329 : }</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        329 : FunctionVessel::FunctionVessel( const VesselOptions&amp; da ):</span></a>
+<a name="33"><span class="lineNum">      33 </span>            :   ValueVessel(da),</a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        329 :   norm(false),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        329 :   usetol(false)</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : {</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        329 :   diffweight=getAction()-&gt;weightHasDerivatives;</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        329 : }</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        912 : void FunctionVessel::resize() {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        912 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        540 :     unsigned nderivatives=getAction()-&gt;getNumberOfDerivatives();</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        540 :     getFinalValue()-&gt;resizeDerivatives( nderivatives );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        540 :     resizeBuffer( (1+nderivatives)*2 );</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        540 :     diffweight=getAction()-&gt;weightHasDerivatives;</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :   } else {</a>
+<a name="47"><span class="lineNum">      47 </span>            :     resizeBuffer(2);</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        372 :     diffweight=false;  // Don't need to worry about differentiable weights if no derivatives</span></a>
+<a name="49"><span class="lineNum">      49 </span>            :   }</a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        912 : }</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">     244832 : void FunctionVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">     244832 :   unsigned nderivatives=getFinalValue()-&gt;getNumberOfDerivatives();</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   double weight=myvals.get(0);</a>
+<a name="55"><span class="lineNum">      55 </span>            :   plumed_dbg_assert( weight&gt;=getTolerance() );</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            :   // This deals with the value</a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">     244832 :   double dval, f=calcTransform( myvals.get(mycomp), dval );</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">     244832 :   if( norm ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      82908 :     if( usetol &amp;&amp; weight&lt;getTolerance() ) return;</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      82908 :     buffer[bufstart+1+nderivatives] += weight;</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      82908 :     if( getAction()-&gt;derivativesAreRequired() &amp;&amp; diffweight ) myvals.chainRule( 0, 1, 1, 0, 1.0, bufstart, buffer );</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   }</a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     244832 :   double contr=weight*f;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     244832 :   if( usetol &amp;&amp; contr&lt;getTolerance() ) return;</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     239910 :   buffer[bufstart] += contr;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     239910 :   if( diffweight ) myvals.chainRule( 0, 0, 1, 0, f, bufstart, buffer );</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">     239910 :   if( getAction()-&gt;derivativesAreRequired() &amp;&amp; std::fabs(dval)&gt;0.0 ) myvals.chainRule( mycomp, 0, 1, 0, weight*dval, bufstart, buffer );</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span>            :   return;</a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineNoCov">          0 : double FunctionVessel::calcTransform( const double&amp;, double&amp; ) const {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineNoCov">          0 :   plumed_error();</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : }</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">      26616 : void FunctionVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">      26616 :   unsigned nderivatives=getFinalValue()-&gt;getNumberOfDerivatives();</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">      26616 :   if( norm &amp;&amp; diffweight ) {</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">       5114 :     double dv, val=finalTransform( buffer[bufstart], dv), weight=buffer[bufstart+1+nderivatives];</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">       5114 :     getFinalValue()-&gt;set( val / weight );</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">     417911 :     for(unsigned i=0; i&lt;nderivatives; ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">     412797 :       getFinalValue()-&gt;addDerivative( i, buffer[bufstart+1+i]/weight - val*buffer[bufstart+1+nderivatives+1+i]/(weight*weight) );</span></a>
+<a name="87"><span class="lineNum">      87 </span>            :     }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">      26616 :   } else if( norm ) {</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">       1227 :     double dv, val=finalTransform( buffer[bufstart], dv), weight=buffer[bufstart+1+nderivatives];</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">       1227 :     getFinalValue()-&gt;set( val / weight );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">     156783 :     for(unsigned i=0; i&lt;nderivatives; ++i) getFinalValue()-&gt;addDerivative( i, buffer[bufstart+1+i]/weight );</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   } else {</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">      20275 :     double dv, val=finalTransform( buffer[bufstart], dv); getFinalValue()-&gt;set( val );</span></a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">    1530087 :     for(unsigned i=0; i&lt;nderivatives; ++i) getFinalValue()-&gt;addDerivative( i, dv*buffer[bufstart+1+i] );</span></a>
+<a name="95"><span class="lineNum">      95 </span>            :   }</a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">      26616 : }</span></a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">      22778 : double FunctionVessel::finalTransform( const double&amp; val, double&amp; dv ) {</span></a>
+<a name="99"><span class="lineNum">      99 </span><span class="lineCov">      22778 :   dv=1.0; return val;</span></a>
+<a name="100"><span class="lineNum">     100 </span>            : }</a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span>            : }</a>
+<a name="103"><span class="lineNum">     103 </span>            : }</a>
+<a name="104"><span class="lineNum">     104 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/FunctionVessel.h.func-sort-c.html b/coverage/vesselbase/FunctionVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..b3a840db8d
--- /dev/null
+++ b/coverage/vesselbase/FunctionVessel.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/FunctionVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - FunctionVessel.h<span style="font-size: 80%;"> (<a href="FunctionVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="FunctionVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/FunctionVessel.h.func.html b/coverage/vesselbase/FunctionVessel.h.func.html
new file mode 100644
index 0000000000..2e52cc673f
--- /dev/null
+++ b/coverage/vesselbase/FunctionVessel.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/FunctionVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - FunctionVessel.h<span style="font-size: 80%;"> (<a href="FunctionVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="FunctionVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/FunctionVessel.h.gcov.html b/coverage/vesselbase/FunctionVessel.h.gcov.html
new file mode 100644
index 0000000000..a60257a7ad
--- /dev/null
+++ b/coverage/vesselbase/FunctionVessel.h.gcov.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/FunctionVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - FunctionVessel.h<span style="font-size: 80%;"> (source / <a href="FunctionVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_FunctionVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_FunctionVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ValueVessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace vesselbase {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /**</a>
+<a name="35"><span class="lineNum">      35 </span>            : \ingroup TOOLBOX</a>
+<a name="36"><span class="lineNum">      36 </span>            : Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel) to calculate</a>
+<a name="37"><span class="lineNum">      37 </span>            : functions of the form \f$\prod_k H_k[ \sum_j \prod_i g_i(x) ]\f$.  They should take in a series of values</a>
+<a name="38"><span class="lineNum">      38 </span>            : and return one single value.</a>
+<a name="39"><span class="lineNum">      39 </span>            : */</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 : class FunctionVessel : public ValueVessel {</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : protected:</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// Are the derivatives differentiable</a>
+<a name="44"><span class="lineNum">      44 </span>            :   bool diffweight;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Are we normalising by the weight</a>
+<a name="46"><span class="lineNum">      46 </span>            :   bool norm;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// Are we using the tolerance</a>
+<a name="48"><span class="lineNum">      48 </span>            :   bool usetol;</a>
+<a name="49"><span class="lineNum">      49 </span>            : public:</a>
+<a name="50"><span class="lineNum">      50 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="51"><span class="lineNum">      51 </span>            :   explicit FunctionVessel( const VesselOptions&amp; );</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// This does the resizing of the buffer</a>
+<a name="53"><span class="lineNum">      53 </span>            :   void resize() override;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// Do the calcualtion</a>
+<a name="55"><span class="lineNum">      55 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const override;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// Do any transformations of the value that are required</a>
+<a name="57"><span class="lineNum">      57 </span>            :   virtual double calcTransform( const double&amp; val, double&amp; df ) const ;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// Finish the calculation of the quantity</a>
+<a name="59"><span class="lineNum">      59 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// Finish with any transforms required</a>
+<a name="61"><span class="lineNum">      61 </span>            :   virtual double finalTransform( const double&amp; val, double&amp; dv );</a>
+<a name="62"><span class="lineNum">      62 </span>            : };</a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span>            : }</a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
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new file mode 100644
index 0000000000..073fbae53d
--- /dev/null
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+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Highest.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Highest.cpp<span style="font-size: 80%;"> (<a href="Highest.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Highest.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_117HighestRegisterMe6createERKNS0_13VesselOptionsE</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#37">_ZN4PLMD10vesselbase7Highest16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
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+              <td class="coverFn"><a href="Highest.cpp.gcov.html#51">_ZN4PLMD10vesselbase7Highest16value_descriptorB5cxx11Ev</a></td>
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+              <td class="coverFnHi">5</td>
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+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#55">_ZN4PLMD10vesselbase7Highest7compareERKdS3_</a></td>
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+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_117HighestRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
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+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_117HighestRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#41">_ZN4PLMD10vesselbase7Highest14reserveKeywordERNS_8KeywordsE</a></td>
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+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Highest.cpp.func.html b/coverage/vesselbase/Highest.cpp.func.html
new file mode 100644
index 0000000000..74bda4dad8
--- /dev/null
+++ b/coverage/vesselbase/Highest.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Highest.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Highest.cpp<span style="font-size: 80%;"> (<a href="Highest.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Highest.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_117HighestRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_117HighestRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_117HighestRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#41">_ZN4PLMD10vesselbase7Highest14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#37">_ZN4PLMD10vesselbase7Highest16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#51">_ZN4PLMD10vesselbase7Highest16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#55">_ZN4PLMD10vesselbase7Highest7compareERKdS3_</a></td>
+              <td class="coverFnHi">4047</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Highest.cpp.gcov.html#46">_ZN4PLMD10vesselbase7HighestC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Highest.cpp.gcov.html b/coverage/vesselbase/Highest.cpp.gcov.html
new file mode 100644
index 0000000000..af87c64e0b
--- /dev/null
+++ b/coverage/vesselbase/Highest.cpp.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Highest.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Highest.cpp<span style="font-size: 80%;"> (source / <a href="Highest.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OrderingVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : class Highest : public OrderingVessel {</a>
+<a name="29"><span class="lineNum">      29 </span>            : public:</a>
+<a name="30"><span class="lineNum">      30 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="31"><span class="lineNum">      31 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="32"><span class="lineNum">      32 </span>            :   explicit Highest( const VesselOptions&amp; da );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   std::string value_descriptor() override;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   bool compare( const double&amp;, const double&amp; ) override;</a>
+<a name="35"><span class="lineNum">      35 </span>            : };</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      12509 : PLUMED_REGISTER_VESSEL(Highest,&quot;HIGHEST&quot;)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          5 : void Highest::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          5 :   OrderingVessel::registerKeywords( keys );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          5 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       4168 : void Highest::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;HIGHEST&quot;,&quot;this flag allows you to recover the highest of these variables.&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;highest&quot;,&quot;HIGHEST&quot;,&quot;the highest of the quantities calculated by this action&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       4168 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          5 : Highest::Highest( const VesselOptions&amp; da ) :</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          5 :   OrderingVessel(da)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          5 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          5 : std::string Highest::value_descriptor() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          5 :   return &quot;the highest of the individual colvar values&quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       4047 : bool Highest::compare( const double&amp; val1, const double&amp; val2 ) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">       4047 :   return val1&gt;val2;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Histogram.cpp.func-sort-c.html b/coverage/vesselbase/Histogram.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c14c6d9a92
--- /dev/null
+++ b/coverage/vesselbase/Histogram.cpp.func-sort-c.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Histogram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Histogram.cpp<span style="font-size: 80%;"> (<a href="Histogram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Histogram.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#34">_ZN4PLMD10vesselbase12_GLOBAL__N_119HistogramRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#36">_ZN4PLMD10vesselbase9Histogram16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#49">_ZN4PLMD10vesselbase9HistogramC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#34">_ZN4PLMD10vesselbase12_GLOBAL__N_119HistogramRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#34">_ZN4PLMD10vesselbase12_GLOBAL__N_119HistogramRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#44">_ZN4PLMD10vesselbase9Histogram14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Histogram.cpp.func.html b/coverage/vesselbase/Histogram.cpp.func.html
new file mode 100644
index 0000000000..6c22b56d46
--- /dev/null
+++ b/coverage/vesselbase/Histogram.cpp.func.html
@@ -0,0 +1,96 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Histogram.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Histogram.cpp<span style="font-size: 80%;"> (<a href="Histogram.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Histogram.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#34">_ZN4PLMD10vesselbase12_GLOBAL__N_119HistogramRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#34">_ZN4PLMD10vesselbase12_GLOBAL__N_119HistogramRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#34">_ZN4PLMD10vesselbase12_GLOBAL__N_119HistogramRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#44">_ZN4PLMD10vesselbase9Histogram14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#36">_ZN4PLMD10vesselbase9Histogram16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Histogram.cpp.gcov.html#49">_ZN4PLMD10vesselbase9HistogramC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Histogram.cpp.gcov.html b/coverage/vesselbase/Histogram.cpp.gcov.html
new file mode 100644
index 0000000000..4fdd0012a3
--- /dev/null
+++ b/coverage/vesselbase/Histogram.cpp.gcov.html
@@ -0,0 +1,139 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Histogram.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Histogram.cpp<span style="font-size: 80%;"> (source / <a href="Histogram.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;tools/HistogramBead.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ShortcutVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace vesselbase {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Histogram : public ShortcutVessel {</a>
+<a name="30"><span class="lineNum">      30 </span>            : public:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="32"><span class="lineNum">      32 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   explicit Histogram( const VesselOptions&amp; da );</a>
+<a name="34"><span class="lineNum">      34 </span>            : };</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">      12515 : PLUMED_REGISTER_VESSEL(Histogram,&quot;HISTOGRAM&quot;)</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         11 : void Histogram::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         11 :   ShortcutVessel::registerKeywords( keys );</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         11 :   HistogramBead::registerKeywords( keys );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;NBINS&quot;,&quot;The number of equal width bins you want to divide the range into&quot;);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         22 :   keys.addFlag(&quot;NORM&quot;,false,&quot;calculate the fraction of values rather than the number&quot;);</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         22 :   keys.add(&quot;compulsory&quot;,&quot;COMPONENT&quot;,&quot;1&quot;,&quot;the component of the vector for which to calculate this quantity&quot;);</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         11 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       4168 : void Histogram::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;HISTOGRAM&quot;,&quot;calculate how many of the values fall in each of the bins of a histogram. &quot;</span></a>
+<a name="48"><span class="lineNum">      48 </span>            :                &quot;This shortcut allows you to calculates NBIN quantities like BETWEEN.&quot;);</a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       4168 : }</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         11 : Histogram::Histogram( const VesselOptions&amp; da ):</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         11 :   ShortcutVessel(da)</span></a>
+<a name="53"><span class="lineNum">      53 </span>            : {</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         22 :   bool norm; parseFlag(&quot;NORM&quot;,norm); std::string normstr=&quot;&quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         11 :   if(norm) normstr=&quot; NORM&quot;;</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         11 :   std::string compstr; parse(&quot;COMPONENT&quot;,compstr);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         22 :   normstr+=&quot; COMPONENT=&quot; + compstr;</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         11 :   std::vector&lt;std::string&gt; bins; HistogramBead::generateBins( getAllInput(), bins );</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         43 :   for(unsigned i=0; i&lt;bins.size(); ++i) addVessel(&quot;BETWEEN&quot;,bins[i] + normstr);</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         22 : }</span></a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/LessThan.cpp.func-sort-c.html b/coverage/vesselbase/LessThan.cpp.func-sort-c.html
new file mode 100644
index 0000000000..5715416dc1
--- /dev/null
+++ b/coverage/vesselbase/LessThan.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/LessThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - LessThan.cpp<span style="font-size: 80%;"> (<a href="LessThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="LessThan.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#59">_ZN4PLMD10vesselbase8LessThan9getCutoffEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#26">_ZN4PLMD10vesselbase12_GLOBAL__N_118LessThanRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#28">_ZN4PLMD10vesselbase8LessThan16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#51">_ZN4PLMD10vesselbase8LessThan16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#42">_ZN4PLMD10vesselbase8LessThanC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#26">_ZN4PLMD10vesselbase12_GLOBAL__N_118LessThanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#26">_ZN4PLMD10vesselbase12_GLOBAL__N_118LessThanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#33">_ZN4PLMD10vesselbase8LessThan14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#55">_ZNK4PLMD10vesselbase8LessThan13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">57355</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/LessThan.cpp.func.html b/coverage/vesselbase/LessThan.cpp.func.html
new file mode 100644
index 0000000000..0fb6ac432a
--- /dev/null
+++ b/coverage/vesselbase/LessThan.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/LessThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - LessThan.cpp<span style="font-size: 80%;"> (<a href="LessThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="LessThan.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#26">_ZN4PLMD10vesselbase12_GLOBAL__N_118LessThanRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#26">_ZN4PLMD10vesselbase12_GLOBAL__N_118LessThanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#26">_ZN4PLMD10vesselbase12_GLOBAL__N_118LessThanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#33">_ZN4PLMD10vesselbase8LessThan14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#28">_ZN4PLMD10vesselbase8LessThan16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#51">_ZN4PLMD10vesselbase8LessThan16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#59">_ZN4PLMD10vesselbase8LessThan9getCutoffEv</a></td>
+              <td class="coverFnHi">16</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#42">_ZN4PLMD10vesselbase8LessThanC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">59</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="LessThan.cpp.gcov.html#55">_ZNK4PLMD10vesselbase8LessThan13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">57355</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/LessThan.cpp.gcov.html b/coverage/vesselbase/LessThan.cpp.gcov.html
new file mode 100644
index 0000000000..02a94163b2
--- /dev/null
+++ b/coverage/vesselbase/LessThan.cpp.gcov.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/LessThan.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - LessThan.cpp<span style="font-size: 80%;"> (source / <a href="LessThan.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntry">22</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;LessThan.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">      12563 : PLUMED_REGISTER_VESSEL(LessThan,&quot;LESS_THAN&quot;)</span></a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         59 : void LessThan::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         59 :   FunctionVessel::registerKeywords( keys );</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">         59 :   SwitchingFunction::registerKeywords( keys );</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         59 : }</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       4168 : void LessThan::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;LESS_THAN&quot;,&quot;calculate the number of variables less than a certain target value. &quot;</span></a>
+<a name="37"><span class="lineNum">      37 </span>            :                &quot;This quantity is calculated using \\f$\\sum_i \\sigma(s_i)\\f$, where \\f$\\sigma(s)\\f$ &quot;</a>
+<a name="38"><span class="lineNum">      38 </span>            :                &quot;is a \\ref switchingfunction.&quot;);</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;lessthan&quot;,&quot;LESS_THAN&quot;,&quot;the number of values less than a target value. This is calculated using one of the &quot;</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :                           &quot;formula described in the description of the keyword so as to make it continuous. &quot;</a>
+<a name="41"><span class="lineNum">      41 </span>            :                           &quot;You can calculate this quantity multiple times using different parameters.&quot;);</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       4168 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         59 : LessThan::LessThan( const VesselOptions&amp; da ) :</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         59 :   FunctionVessel(da)</span></a>
+<a name="46"><span class="lineNum">      46 </span>            : {</a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         59 :   usetol=true;</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         59 :   if( getAction()-&gt;isPeriodic() ) error(&quot;LESS_THAN is not a meaningful option for periodic variables&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        118 :   std::string errormsg; sf.set( getAllInput(), errormsg );</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         59 :   if( errormsg.size()!=0 ) error( errormsg );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         59 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         59 : std::string LessThan::value_descriptor() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        118 :   return &quot;the number of values less than &quot; + sf.description();</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      57355 : double LessThan::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      57355 :   double f = sf.calculate(val, dv); dv*=val; return f;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         16 : double LessThan::getCutoff() {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         16 :   return sf.get_dmax();</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Lowest.cpp.func-sort-c.html b/coverage/vesselbase/Lowest.cpp.func-sort-c.html
new file mode 100644
index 0000000000..df162fef5c
--- /dev/null
+++ b/coverage/vesselbase/Lowest.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Lowest.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Lowest.cpp<span style="font-size: 80%;"> (<a href="Lowest.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Lowest.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_116LowestRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#37">_ZN4PLMD10vesselbase6Lowest16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#51">_ZN4PLMD10vesselbase6Lowest16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#46">_ZN4PLMD10vesselbase6LowestC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#55">_ZN4PLMD10vesselbase6Lowest7compareERKdS3_</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_116LowestRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_116LowestRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#41">_ZN4PLMD10vesselbase6Lowest14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Lowest.cpp.func.html b/coverage/vesselbase/Lowest.cpp.func.html
new file mode 100644
index 0000000000..b3faa481c7
--- /dev/null
+++ b/coverage/vesselbase/Lowest.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Lowest.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Lowest.cpp<span style="font-size: 80%;"> (<a href="Lowest.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Lowest.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_116LowestRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_116LowestRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_116LowestRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#41">_ZN4PLMD10vesselbase6Lowest14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#37">_ZN4PLMD10vesselbase6Lowest16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#51">_ZN4PLMD10vesselbase6Lowest16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#55">_ZN4PLMD10vesselbase6Lowest7compareERKdS3_</a></td>
+              <td class="coverFnHi">68</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Lowest.cpp.gcov.html#46">_ZN4PLMD10vesselbase6LowestC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Lowest.cpp.gcov.html b/coverage/vesselbase/Lowest.cpp.gcov.html
new file mode 100644
index 0000000000..14eb0d766c
--- /dev/null
+++ b/coverage/vesselbase/Lowest.cpp.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Lowest.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Lowest.cpp<span style="font-size: 80%;"> (source / <a href="Lowest.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OrderingVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : class Lowest : public OrderingVessel {</a>
+<a name="29"><span class="lineNum">      29 </span>            : public:</a>
+<a name="30"><span class="lineNum">      30 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="31"><span class="lineNum">      31 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="32"><span class="lineNum">      32 </span>            :   explicit Lowest( const VesselOptions&amp; da );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   std::string value_descriptor() override;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   bool compare( const double&amp;, const double&amp; ) override;</a>
+<a name="35"><span class="lineNum">      35 </span>            : };</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      12507 : PLUMED_REGISTER_VESSEL(Lowest,&quot;LOWEST&quot;)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">          3 : void Lowest::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">          3 :   OrderingVessel::registerKeywords( keys );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          3 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       4168 : void Lowest::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;LOWEST&quot;,&quot;this flag allows you to recover the lowest of these variables.&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;lowest&quot;,&quot;LOWEST&quot;,&quot;the lowest of the quantities calculated by this action&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       4168 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">          3 : Lowest::Lowest( const VesselOptions&amp; da ) :</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">          3 :   OrderingVessel(da)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">          3 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          3 : std::string Lowest::value_descriptor() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          3 :   return &quot;the lowest of the individual colvar values&quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         68 : bool Lowest::compare( const double&amp; val1, const double&amp; val2 ) {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         68 :   return val1&lt;val2;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Max.cpp.func-sort-c.html b/coverage/vesselbase/Max.cpp.func-sort-c.html
new file mode 100644
index 0000000000..c84f9efe21
--- /dev/null
+++ b/coverage/vesselbase/Max.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Max.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Max.cpp<span style="font-size: 80%;"> (<a href="Max.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Max.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MaxRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#41">_ZN4PLMD10vesselbase3Max16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#65">_ZN4PLMD10vesselbase3Max16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#56">_ZN4PLMD10vesselbase3MaxC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#74">_ZN4PLMD10vesselbase3Max14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#70">_ZNK4PLMD10vesselbase3Max13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MaxRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MaxRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#46">_ZN4PLMD10vesselbase3Max14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Max.cpp.func.html b/coverage/vesselbase/Max.cpp.func.html
new file mode 100644
index 0000000000..3792743149
--- /dev/null
+++ b/coverage/vesselbase/Max.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Max.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Max.cpp<span style="font-size: 80%;"> (<a href="Max.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Max.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MaxRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MaxRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MaxRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#74">_ZN4PLMD10vesselbase3Max14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">6</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#46">_ZN4PLMD10vesselbase3Max14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#41">_ZN4PLMD10vesselbase3Max16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#65">_ZN4PLMD10vesselbase3Max16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#56">_ZN4PLMD10vesselbase3MaxC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">3</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Max.cpp.gcov.html#70">_ZNK4PLMD10vesselbase3Max13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">13</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Max.cpp.gcov.html b/coverage/vesselbase/Max.cpp.gcov.html
new file mode 100644
index 0000000000..fb73b1962d
--- /dev/null
+++ b/coverage/vesselbase/Max.cpp.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Max.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Max.cpp<span style="font-size: 80%;"> (source / <a href="Max.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntry">23</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace vesselbase {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Max : public FunctionVessel {</a>
+<a name="30"><span class="lineNum">      30 </span>            : private:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   double beta;</a>
+<a name="32"><span class="lineNum">      32 </span>            : public:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="34"><span class="lineNum">      34 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="35"><span class="lineNum">      35 </span>            :   explicit Max( const VesselOptions&amp; da );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::string value_descriptor() override;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   double finalTransform( const double&amp; val, double&amp; dv ) override;</a>
+<a name="39"><span class="lineNum">      39 </span>            : };</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      12507 : PLUMED_REGISTER_VESSEL(Max,&quot;MAX&quot;)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          3 : void Max::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          3 :   FunctionVessel::registerKeywords( keys );</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          6 :   keys.add(&quot;compulsory&quot;,&quot;BETA&quot;,&quot;the value of beta for the equation in the manual&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          3 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       4168 : void Max::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;MAX&quot;,&quot;calculate the maximum value. &quot;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :                &quot;To make this quantity continuous the maximum is calculated using &quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :                &quot;\\f$ \\textrm{max} = \\beta \\log \\sum_i \\exp\\left( \\frac{s_i}{\\beta}\\right) \\f$ &quot;</a>
+<a name="52"><span class="lineNum">      52 </span>            :                &quot;The value of \\f$\\beta\\f$ in this function is specified using (BETA=\\f$\\beta\\f$)&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;max&quot;,&quot;MAX&quot;,&quot;the maximum value. This is calculated using the formula described in the description of the &quot;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :                           &quot;keyword so as to make it continuous.&quot;);</a>
+<a name="55"><span class="lineNum">      55 </span>            : </a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       4168 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          3 : Max::Max( const VesselOptions&amp; da ) :</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">          3 :   FunctionVessel(da)</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          3 :   if( getAction()-&gt;isPeriodic() ) error(&quot;max is not a meaningful option for periodic variables&quot;);</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">          3 :   parse(&quot;BETA&quot;,beta);</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : </a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          3 :   if( diffweight ) error(&quot;can't calculate max if weight is differentiable&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">          3 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          3 : std::string Max::value_descriptor() {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          3 :   std::string str_beta; Tools::convert( beta, str_beta );</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">          6 :   return &quot;the maximum value. Beta is equal to &quot; + str_beta;</span></a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         13 : double Max::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         13 :   double f = exp(val/beta); dv=f/beta; return f;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          6 : double Max::finalTransform( const double&amp; val, double&amp; dv ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          6 :   double dist=beta*std::log( val );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          6 :   dv = beta/val; return dist;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Mean.cpp.func-sort-c.html b/coverage/vesselbase/Mean.cpp.func-sort-c.html
new file mode 100644
index 0000000000..066ffb95d2
--- /dev/null
+++ b/coverage/vesselbase/Mean.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Mean.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Mean.cpp<span style="font-size: 80%;"> (<a href="Mean.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Mean.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#36">_ZN4PLMD10vesselbase12_GLOBAL__N_114MeanRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#38">_ZN4PLMD10vesselbase4Mean16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#55">_ZN4PLMD10vesselbase4Mean16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#48">_ZN4PLMD10vesselbase4MeanC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#36">_ZN4PLMD10vesselbase12_GLOBAL__N_114MeanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#36">_ZN4PLMD10vesselbase12_GLOBAL__N_114MeanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#42">_ZN4PLMD10vesselbase4Mean14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#59">_ZNK4PLMD10vesselbase4Mean13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">80199</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Mean.cpp.func.html b/coverage/vesselbase/Mean.cpp.func.html
new file mode 100644
index 0000000000..baa8674232
--- /dev/null
+++ b/coverage/vesselbase/Mean.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Mean.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Mean.cpp<span style="font-size: 80%;"> (<a href="Mean.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Mean.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#36">_ZN4PLMD10vesselbase12_GLOBAL__N_114MeanRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#36">_ZN4PLMD10vesselbase12_GLOBAL__N_114MeanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#36">_ZN4PLMD10vesselbase12_GLOBAL__N_114MeanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#42">_ZN4PLMD10vesselbase4Mean14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#38">_ZN4PLMD10vesselbase4Mean16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#55">_ZN4PLMD10vesselbase4Mean16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#48">_ZN4PLMD10vesselbase4MeanC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">84</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Mean.cpp.gcov.html#59">_ZNK4PLMD10vesselbase4Mean13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">80199</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Mean.cpp.gcov.html b/coverage/vesselbase/Mean.cpp.gcov.html
new file mode 100644
index 0000000000..7280bcbbc7
--- /dev/null
+++ b/coverage/vesselbase/Mean.cpp.gcov.html
@@ -0,0 +1,142 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Mean.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Mean.cpp<span style="font-size: 80%;"> (source / <a href="Mean.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntry">17</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace vesselbase {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Mean : public FunctionVessel {</a>
+<a name="30"><span class="lineNum">      30 </span>            : public:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="32"><span class="lineNum">      32 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   explicit Mean( const vesselbase::VesselOptions&amp; da );</a>
+<a name="34"><span class="lineNum">      34 </span>            :   std::string value_descriptor() override;</a>
+<a name="35"><span class="lineNum">      35 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="36"><span class="lineNum">      36 </span>            : };</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">      12588 : PLUMED_REGISTER_VESSEL(Mean,&quot;MEAN&quot;)</span></a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         84 : void Mean::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         84 :   FunctionVessel::registerKeywords(keys);</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         84 : }</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       4168 : void Mean::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;MEAN&quot;,&quot;take the mean of these variables.&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;mean&quot;,&quot;MEAN&quot;,&quot;the mean value. The output component can be referred to elsewhere in the input &quot;</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :                           &quot;file by using the label.mean&quot;);</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       4168 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         84 : Mean::Mean( const vesselbase::VesselOptions&amp; da ) :</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         84 :   FunctionVessel(da)</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : {</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         84 :   if( getAction()-&gt;isPeriodic() ) error(&quot;MEAN cannot be used with periodic variables&quot;);</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         84 :   norm=true;   // Makes sure we calculate the average</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">         84 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         84 : std::string Mean::value_descriptor() {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         84 :   return &quot;the mean value&quot;;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      80199 : double Mean::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      80199 :   dv=1.0; return val;</span></a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Min.cpp.func-sort-c.html b/coverage/vesselbase/Min.cpp.func-sort-c.html
new file mode 100644
index 0000000000..693c53c67b
--- /dev/null
+++ b/coverage/vesselbase/Min.cpp.func-sort-c.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Min.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Min.cpp<span style="font-size: 80%;"> (<a href="Min.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Min.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MinRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#41">_ZN4PLMD10vesselbase3Min16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#64">_ZN4PLMD10vesselbase3Min16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#55">_ZN4PLMD10vesselbase3MinC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#74">_ZN4PLMD10vesselbase3Min14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#69">_ZNK4PLMD10vesselbase3Min13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MinRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MinRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#46">_ZN4PLMD10vesselbase3Min14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Min.cpp.func.html b/coverage/vesselbase/Min.cpp.func.html
new file mode 100644
index 0000000000..88d2b4e9cc
--- /dev/null
+++ b/coverage/vesselbase/Min.cpp.func.html
@@ -0,0 +1,108 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Min.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Min.cpp<span style="font-size: 80%;"> (<a href="Min.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Min.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MinRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MinRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#39">_ZN4PLMD10vesselbase12_GLOBAL__N_113MinRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#74">_ZN4PLMD10vesselbase3Min14finalTransformERKdRd</a></td>
+              <td class="coverFnHi">5</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#46">_ZN4PLMD10vesselbase3Min14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#41">_ZN4PLMD10vesselbase3Min16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#64">_ZN4PLMD10vesselbase3Min16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#55">_ZN4PLMD10vesselbase3MinC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Min.cpp.gcov.html#69">_ZNK4PLMD10vesselbase3Min13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">10</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Min.cpp.gcov.html b/coverage/vesselbase/Min.cpp.gcov.html
new file mode 100644
index 0000000000..3db3448f88
--- /dev/null
+++ b/coverage/vesselbase/Min.cpp.gcov.html
@@ -0,0 +1,158 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Min.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Min.cpp<span style="font-size: 80%;"> (source / <a href="Min.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace vesselbase {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span>            : class Min : public FunctionVessel {</a>
+<a name="30"><span class="lineNum">      30 </span>            : private:</a>
+<a name="31"><span class="lineNum">      31 </span>            :   double beta;</a>
+<a name="32"><span class="lineNum">      32 </span>            : public:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="34"><span class="lineNum">      34 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="35"><span class="lineNum">      35 </span>            :   explicit Min( const VesselOptions&amp; da );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   std::string value_descriptor() override;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   double finalTransform( const double&amp; val, double&amp; dv ) override;</a>
+<a name="39"><span class="lineNum">      39 </span>            : };</a>
+<a name="40"><span class="lineNum">      40 </span>            : </a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">      12506 : PLUMED_REGISTER_VESSEL(Min,&quot;MIN&quot;)</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">          2 : void Min::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          2 :   FunctionVessel::registerKeywords( keys );</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          4 :   keys.add(&quot;compulsory&quot;,&quot;BETA&quot;,&quot;the value of beta for the equation in the manual&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          2 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       4168 : void Min::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;MIN&quot;,&quot;calculate the minimum value. &quot;</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :                &quot;To make this quantity continuous the minimum is calculated using &quot;</a>
+<a name="51"><span class="lineNum">      51 </span>            :                &quot;\\f$ \\textrm{min} = \\frac{\\beta}{ \\log \\sum_i \\exp\\left( \\frac{\\beta}{s_i} \\right) } \\f$ &quot;</a>
+<a name="52"><span class="lineNum">      52 </span>            :                &quot;The value of \\f$\\beta\\f$ in this function is specified using (BETA=\\f$\\beta\\f$)&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;min&quot;,&quot;MIN&quot;,&quot;the minimum value. This is calculated using the formula described in the description of the &quot;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :                           &quot;keyword so as to make it continuous.&quot;);</a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       4168 : }</span></a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">          2 : Min::Min( const VesselOptions&amp; da ) :</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          2 :   FunctionVessel(da)</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : {</a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">          2 :   if( getAction()-&gt;isPeriodic() ) error(&quot;min is not a meaningful option for periodic variables&quot;);</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">          2 :   parse(&quot;BETA&quot;,beta);</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">          2 :   if( diffweight ) error(&quot;can't calculate min if weight is differentiable&quot;);</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">          2 : }</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : </a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">          2 : std::string Min::value_descriptor() {</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">          2 :   std::string str_beta; Tools::convert( beta, str_beta );</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">          4 :   return &quot;the minimum value. Beta is equal to &quot; + str_beta;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">         10 : double Min::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">         10 :   double f = exp(beta/val); dv=f/(val*val);</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">         10 :   return f;</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : }</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          5 : double Min::finalTransform( const double&amp; val, double&amp; dv ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          5 :   double dist=beta/std::log( val );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          5 :   dv = dist*dist/val; return dist;</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : </a>
+<a name="81"><span class="lineNum">      81 </span>            : }</a>
+<a name="82"><span class="lineNum">      82 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Moments.cpp.func-sort-c.html b/coverage/vesselbase/Moments.cpp.func-sort-c.html
new file mode 100644
index 0000000000..d3547b87d2
--- /dev/null
+++ b/coverage/vesselbase/Moments.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Moments.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Moments.cpp<span style="font-size: 80%;"> (<a href="Moments.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">89.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Moments.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#49">_ZN4PLMD10vesselbase12_GLOBAL__N_117MomentsRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#100">_ZN4PLMD10vesselbase7Moments11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#51">_ZN4PLMD10vesselbase7Moments16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#71">_ZN4PLMD10vesselbase7MomentsC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#93">_ZN4PLMD10vesselbase7Moments6resizeEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#176">_ZN4PLMD10vesselbase7Moments10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">432</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#120">_ZN4PLMD10vesselbase7Moments6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#49">_ZN4PLMD10vesselbase12_GLOBAL__N_117MomentsRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#49">_ZN4PLMD10vesselbase12_GLOBAL__N_117MomentsRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#58">_ZN4PLMD10vesselbase7Moments14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#44">_ZNK4PLMD10vesselbase7Moments9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">6936</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Moments.cpp.func.html b/coverage/vesselbase/Moments.cpp.func.html
new file mode 100644
index 0000000000..449eda9ac9
--- /dev/null
+++ b/coverage/vesselbase/Moments.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Moments.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Moments.cpp<span style="font-size: 80%;"> (<a href="Moments.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">89.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Moments.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#49">_ZN4PLMD10vesselbase12_GLOBAL__N_117MomentsRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#49">_ZN4PLMD10vesselbase12_GLOBAL__N_117MomentsRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#49">_ZN4PLMD10vesselbase12_GLOBAL__N_117MomentsRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#176">_ZN4PLMD10vesselbase7Moments10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">432</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#100">_ZN4PLMD10vesselbase7Moments11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#58">_ZN4PLMD10vesselbase7Moments14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#51">_ZN4PLMD10vesselbase7Moments16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#120">_ZN4PLMD10vesselbase7Moments6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">822</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#93">_ZN4PLMD10vesselbase7Moments6resizeEv</a></td>
+              <td class="coverFnHi">28</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#71">_ZN4PLMD10vesselbase7MomentsC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Moments.cpp.gcov.html#44">_ZNK4PLMD10vesselbase7Moments9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">6936</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Moments.cpp.gcov.html b/coverage/vesselbase/Moments.cpp.gcov.html
new file mode 100644
index 0000000000..387bfb80ac
--- /dev/null
+++ b/coverage/vesselbase/Moments.cpp.gcov.html
@@ -0,0 +1,267 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Moments.cpp</title>
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+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Moments.cpp<span style="font-size: 80%;"> (source / <a href="Moments.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">82</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryMed">89.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace PLMD {</a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace vesselbase {</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : // This is not the most efficient implementation</a>
+<a name="31"><span class="lineNum">      31 </span>            : // The calculation of all the colvars is parallelized</a>
+<a name="32"><span class="lineNum">      32 </span>            : // but the loops for calculating moments are not</a>
+<a name="33"><span class="lineNum">      33 </span>            : // Feel free to reimplement this if you know how</a>
+<a name="34"><span class="lineNum">      34 </span>            : class Moments : public Vessel {</a>
+<a name="35"><span class="lineNum">      35 </span>            : private:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   unsigned mycomponent;</a>
+<a name="37"><span class="lineNum">      37 </span>            :   StoreDataVessel* mystash;</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::vector&lt;unsigned&gt; powers;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::vector&lt;Value*&gt; value_out;</a>
+<a name="40"><span class="lineNum">      40 </span>            : public:</a>
+<a name="41"><span class="lineNum">      41 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="42"><span class="lineNum">      42 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="43"><span class="lineNum">      43 </span>            :   explicit Moments( const vesselbase::VesselOptions&amp; da );</a>
+<a name="44"><span class="lineNum">      44 </span>            :   std::string description() override;</a>
+<a name="45"><span class="lineNum">      45 </span>            :   void resize() override;</a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       6936 :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const override {}</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="48"><span class="lineNum">      48 </span>            :   bool applyForce( std::vector&lt;double&gt;&amp; forces ) override;</a>
+<a name="49"><span class="lineNum">      49 </span>            : };</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">      12512 : PLUMED_REGISTER_VESSEL(Moments,&quot;MOMENTS&quot;)</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">          8 : void Moments::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">          8 :   Vessel::registerKeywords( keys );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">          8 :   keys.remove(&quot;LABEL&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">         16 :   keys.add(&quot;compulsory&quot;,&quot;COMPONENT&quot;,&quot;1&quot;,&quot;the component of the vector for which to calculate this quantity&quot;);</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">         16 :   keys.add(&quot;optional&quot;,&quot;MOMENTS&quot;,&quot;the list of moments that you would like to calculate&quot;);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">          8 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       4168 : void Moments::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       8336 :   keys.reserve(&quot;optional&quot;,&quot;MOMENTS&quot;,&quot;calculate the moments of the distribution of collective variables. &quot;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :                &quot;The mth moment of a distribution is calculated using \\f$\\frac{1}{N} \\sum_{i=1}^N ( s_i - \\overline{s} )^m \\f$, where \\f$\\overline{s}\\f$ is &quot;</a>
+<a name="63"><span class="lineNum">      63 </span>            :                &quot;the average for the distribution. The moments keyword takes a lists of integers as input or a range. Each integer is a value of \\f$m\\f$. The final &quot;</a>
+<a name="64"><span class="lineNum">      64 </span>            :                &quot;calculated values can be referenced using moment-\\f$m\\f$.  You can use the COMPONENT keyword in this action but the syntax is slightly different. &quot;</a>
+<a name="65"><span class="lineNum">      65 </span>            :                &quot;If you would like the second and third moments of the third component you would use MOMENTS={COMPONENT=3 MOMENTS=2-3}.  The moments would then be referred to &quot;</a>
+<a name="66"><span class="lineNum">      66 </span>            :                &quot;using the labels moment-3-2 and moment-3-3.  This syntax is also required if you are using numbered MOMENT keywords i.e. MOMENTS1, MOMENTS2...&quot;);</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">       8336 :   keys.reset_style(&quot;MOMENTS&quot;,&quot;vessel&quot;);</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;moment&quot;,&quot;MOMENTS&quot;,&quot;the central moments of the distribution of values. The second moment &quot;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :                           &quot;would be referenced elsewhere in the input file using &quot;</a>
+<a name="70"><span class="lineNum">      70 </span>            :                           &quot;&lt;em&gt;label&lt;/em&gt;.moment-2, the third as &lt;em&gt;label&lt;/em&gt;.moment-3, etc.&quot;);</a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">       4168 : }</span></a>
+<a name="72"><span class="lineNum">      72 </span>            : </a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">          8 : Moments::Moments( const vesselbase::VesselOptions&amp; da) :</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">          8 :   Vessel(da)</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : {</a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">          8 :   mystash = getAction()-&gt;buildDataStashes( NULL );</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">          8 :   ActionWithValue* a=dynamic_cast&lt;ActionWithValue*&gt;( getAction() );</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">          8 :   plumed_massert(a,&quot;cannot create passable values as base action does not inherit from ActionWithValue&quot;);</span></a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineCov">          8 :   std::vector&lt;std::string&gt; moments; std::string valstr = &quot;moment-&quot;;</span></a>
+<a name="81"><span class="lineNum">      81 </span><span class="lineCov">         24 :   parse(&quot;COMPONENT&quot;,mycomponent); parseVector(&quot;MOMENTS&quot;,moments);</span></a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">         10 :   if( getNumericalLabel()!=0 ) { std::string numstr; Tools::convert( mycomponent, numstr); valstr = &quot;moment-&quot; + numstr + &quot;-&quot;; }</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">         14 :   if( moments.size()==0 ) moments=Tools::getWords(getAllInput(),&quot;\t\n ,&quot;);</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">          8 :   Tools::interpretRanges(moments); unsigned nn;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">         20 :   for(unsigned i=0; i&lt;moments.size(); ++i) {</span></a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineCov">         24 :     a-&gt;addComponentWithDerivatives( valstr + moments[i] );</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineCov">         24 :     a-&gt;componentIsNotPeriodic( valstr + moments[i] );</span></a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">         12 :     value_out.push_back( a-&gt;copyOutput( a-&gt;getNumberOfComponents()-1 ) );</span></a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineCov">         12 :     Tools::convert( moments[i], nn );</span></a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         12 :     if( nn&lt;2 ) error(&quot;moments are only possible for m&gt;=2&quot; );</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         12 :     powers.push_back( nn ); std::string num; Tools::convert(powers[i],num);</span></a>
+<a name="92"><span class="lineNum">      92 </span>            :   }</a>
+<a name="93"><span class="lineNum">      93 </span><span class="lineCov">          8 : }</span></a>
+<a name="94"><span class="lineNum">      94 </span>            : </a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">         28 : void Moments::resize() {</span></a>
+<a name="96"><span class="lineNum">      96 </span>            :   resizeBuffer(0);</a>
+<a name="97"><span class="lineNum">      97 </span><span class="lineCov">         28 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">         56 :     for(unsigned i=0; i&lt;value_out.size(); ++i) value_out[i]-&gt;resizeDerivatives( getAction()-&gt;getNumberOfDerivatives() );</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   }</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">         28 : }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : </a>
+<a name="102"><span class="lineNum">     102 </span><span class="lineCov">          8 : std::string Moments::description() {</span></a>
+<a name="103"><span class="lineNum">     103 </span>            :   std::string descri, num;</a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">          8 :   Tools::convert(powers[0],num);</span></a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">          8 :   if( getNumericalLabel()==0 ) {</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">         12 :     descri = &quot;value &quot; + getAction()-&gt;getLabel() + &quot;.&quot; + &quot;moment-&quot; + num + &quot; contains the &quot; + num + &quot;th moment of the distribution&quot;;</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">          8 :     for(unsigned i=1; i&lt;powers.size(); ++i) {</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">          2 :       Tools::convert(powers[i],num);</span></a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">          4 :       descri = descri + &quot;\n  value &quot; + getAction()-&gt;getLabel() + &quot;.&quot; + &quot;moment-&quot; + num + &quot; contains the &quot; + num + &quot;th moment of the distribution&quot;;</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :     }</a>
+<a name="111"><span class="lineNum">     111 </span>            :   } else {</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">          2 :     std::string numlab; Tools::convert( mycomponent, numlab );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">          4 :     descri = &quot;value &quot; + getAction()-&gt;getLabel() + &quot;.&quot; + &quot;moment-&quot; + numlab + &quot;-&quot; + num + &quot; contains the &quot; + num + &quot;th moment for the distribution of component &quot; + numlab;</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">          4 :     for(unsigned i=1; i&lt;powers.size(); ++i) {</span></a>
+<a name="115"><span class="lineNum">     115 </span><span class="lineCov">          2 :       Tools::convert(powers[i],num);</span></a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">          4 :       descri = descri + &quot;\n  value &quot; + getAction()-&gt;getLabel() + &quot;.&quot; + &quot;moment-&quot; + numlab + &quot;-&quot; + num + &quot; contains the &quot; + num + &quot;th moment for the distribution of component &quot; + numlab;</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :     }</a>
+<a name="118"><span class="lineNum">     118 </span>            :   }</a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">          8 :   return descri;</span></a>
+<a name="120"><span class="lineNum">     120 </span>            : }</a>
+<a name="121"><span class="lineNum">     121 </span>            : </a>
+<a name="122"><span class="lineNum">     122 </span><span class="lineCov">        822 : void Moments::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="123"><span class="lineNum">     123 </span>            :   const double pi=3.141592653589793238462643383279502884197169399375105820974944592307;</a>
+<a name="124"><span class="lineNum">     124 </span>            :   unsigned nvals=getAction()-&gt;getFullNumberOfTasks();</a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        822 :   std::vector&lt;double&gt;  myvalues( getAction()-&gt;getNumberOfQuantities() );</span></a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">        822 :   double mean=0; Value myvalue;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineCov">        822 :   if( getAction()-&gt;isPeriodic() ) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :     std::string str_min, str_max; getAction()-&gt;retrieveDomain( str_min, str_max );</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :     double pfactor, min, max; Tools::convert(str_min,min); Tools::convert(str_max,max);</span></a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineNoCov">          0 :     pfactor = 2*pi / ( max-min ); myvalue.setDomain( str_min, str_max );</span></a>
+<a name="132"><span class="lineNum">     132 </span>            :     double sinsum=0, cossum=0, val;</a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;mystash-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineNoCov">          0 :       mystash-&gt;retrieveSequentialValue( i, false, myvalues );</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineNoCov">          0 :       val=pfactor*( myvalues[mycomponent] - min );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineNoCov">          0 :       sinsum+=std::sin(val); cossum+=std::cos(val);</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :     }</a>
+<a name="138"><span class="lineNum">     138 </span><span class="lineNoCov">          0 :     mean = 0.5 + std::atan2( sinsum / static_cast&lt;double&gt;( nvals ), cossum / static_cast&lt;double&gt;( nvals ) ) / (2*pi);</span></a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 :     mean = min + (max-min)*mean;</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :   } else {</a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineCov">       7758 :     for(unsigned i=0; i&lt;mystash-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">       6936 :       mystash-&gt;retrieveSequentialValue( i, false, myvalues ); mean+=myvalues[mycomponent];</span></a>
+<a name="143"><span class="lineNum">     143 </span>            :     }</a>
+<a name="144"><span class="lineNum">     144 </span><span class="lineCov">        822 :     mean/=static_cast&lt;double&gt;( nvals ); myvalue.setNotPeriodic();</span></a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span><span class="lineCov">       2056 :   for(unsigned npow=0; npow&lt;powers.size(); ++npow) {</span></a>
+<a name="148"><span class="lineNum">     148 </span>            :     double dev1=0;</a>
+<a name="149"><span class="lineNum">     149 </span><span class="lineCov">       1234 :     if( value_out[0]-&gt;getNumberOfDerivatives()&gt;0 ) {</span></a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">       4606 :       for(unsigned i=0; i&lt;mystash-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">       4172 :         mystash-&gt;retrieveSequentialValue( i, false, myvalues );</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">       4172 :         dev1+=pow( myvalue.difference( mean, myvalues[mycomponent] ), powers[npow] - 1 );</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :       }</a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">        434 :       dev1/=static_cast&lt;double&gt;( nvals );</span></a>
+<a name="155"><span class="lineNum">     155 </span>            :     }</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :     double moment=0;</a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       1234 :     MultiValue myvals( getAction()-&gt;getNumberOfQuantities(), getAction()-&gt;getNumberOfDerivatives() ); myvals.clearAll();</span></a>
+<a name="159"><span class="lineNum">     159 </span><span class="lineCov">      11006 :     for(unsigned i=0; i&lt;mystash-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">       9772 :       mystash-&gt;retrieveSequentialValue( i, false, myvalues );</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       9772 :       double tmp=myvalue.difference( mean, myvalues[mycomponent] );</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       9772 :       moment+=pow( tmp, powers[npow] );</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">       9772 :       if( value_out[npow]-&gt;getNumberOfDerivatives() ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">       4172 :         double pref=pow( tmp, powers[npow] - 1 ) - dev1;</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">       4172 :         mystash-&gt;retrieveDerivatives( i, false, myvals );</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     166880 :         for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :           unsigned jatom=myvals.getActiveIndex(j);</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">     162708 :           value_out[npow]-&gt;addDerivative(jatom, pref*myvals.getDerivative( mycomponent, jatom ) );</span></a>
+<a name="169"><span class="lineNum">     169 </span>            :         }</a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">       4172 :         myvals.clearAll();</span></a>
+<a name="171"><span class="lineNum">     171 </span>            :       }</a>
+<a name="172"><span class="lineNum">     172 </span>            :     }</a>
+<a name="173"><span class="lineNum">     173 </span><span class="lineCov">       1234 :     if( value_out[npow]-&gt;getNumberOfDerivatives()&gt;0 ) value_out[npow]-&gt;chainRule( powers[npow] / static_cast&lt;double&gt;( nvals ) );</span></a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">       1234 :     value_out[npow]-&gt;set( moment / static_cast&lt;double&gt;( nvals ) );</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">       1234 :   }</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">       1644 : }</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">        432 : bool Moments::applyForce( std::vector&lt;double&gt;&amp; forces ) {</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">        432 :   std::vector&lt;double&gt; tmpforce( forces.size() );</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        432 :   forces.assign(forces.size(),0.0); bool wasforced=false;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">       1276 :   for(unsigned i=0; i&lt;value_out.size(); ++i) {</span></a>
+<a name="182"><span class="lineNum">     182 </span><span class="lineCov">        844 :     if( value_out[i]-&gt;applyForce( tmpforce ) ) {</span></a>
+<a name="183"><span class="lineNum">     183 </span>            :       wasforced=true;</a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineNoCov">          0 :       for(unsigned j=0; j&lt;forces.size(); ++j) forces[j]+=tmpforce[j];</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :     }</a>
+<a name="186"><span class="lineNum">     186 </span>            :   }</a>
+<a name="187"><span class="lineNum">     187 </span><span class="lineCov">        432 :   return wasforced;</span></a>
+<a name="188"><span class="lineNum">     188 </span>            : }</a>
+<a name="189"><span class="lineNum">     189 </span>            : </a>
+<a name="190"><span class="lineNum">     190 </span>            : }</a>
+<a name="191"><span class="lineNum">     191 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/MoreThan.cpp.func-sort-c.html b/coverage/vesselbase/MoreThan.cpp.func-sort-c.html
new file mode 100644
index 0000000000..46e3f4120e
--- /dev/null
+++ b/coverage/vesselbase/MoreThan.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/MoreThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - MoreThan.cpp<span style="font-size: 80%;"> (<a href="MoreThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="MoreThan.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#40">_ZN4PLMD10vesselbase12_GLOBAL__N_118MoreThanRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#42">_ZN4PLMD10vesselbase8MoreThan16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#65">_ZN4PLMD10vesselbase8MoreThan16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#56">_ZN4PLMD10vesselbase8MoreThanC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#40">_ZN4PLMD10vesselbase12_GLOBAL__N_118MoreThanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#40">_ZN4PLMD10vesselbase12_GLOBAL__N_118MoreThanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#47">_ZN4PLMD10vesselbase8MoreThan14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#69">_ZNK4PLMD10vesselbase8MoreThan13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">19012</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/MoreThan.cpp.func.html b/coverage/vesselbase/MoreThan.cpp.func.html
new file mode 100644
index 0000000000..dc8e8baec4
--- /dev/null
+++ b/coverage/vesselbase/MoreThan.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/MoreThan.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - MoreThan.cpp<span style="font-size: 80%;"> (<a href="MoreThan.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="MoreThan.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#40">_ZN4PLMD10vesselbase12_GLOBAL__N_118MoreThanRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#40">_ZN4PLMD10vesselbase12_GLOBAL__N_118MoreThanRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#40">_ZN4PLMD10vesselbase12_GLOBAL__N_118MoreThanRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#47">_ZN4PLMD10vesselbase8MoreThan14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#42">_ZN4PLMD10vesselbase8MoreThan16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#65">_ZN4PLMD10vesselbase8MoreThan16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#56">_ZN4PLMD10vesselbase8MoreThanC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="MoreThan.cpp.gcov.html#69">_ZNK4PLMD10vesselbase8MoreThan13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">19012</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/MoreThan.cpp.gcov.html b/coverage/vesselbase/MoreThan.cpp.gcov.html
new file mode 100644
index 0000000000..aae1254113
--- /dev/null
+++ b/coverage/vesselbase/MoreThan.cpp.gcov.html
@@ -0,0 +1,152 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/MoreThan.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - MoreThan.cpp<span style="font-size: 80%;"> (source / <a href="MoreThan.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntry">20</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : </a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/SwitchingFunction.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace vesselbase {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : class MoreThan : public FunctionVessel {</a>
+<a name="32"><span class="lineNum">      32 </span>            : private:</a>
+<a name="33"><span class="lineNum">      33 </span>            :   SwitchingFunction sf;</a>
+<a name="34"><span class="lineNum">      34 </span>            : public:</a>
+<a name="35"><span class="lineNum">      35 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="36"><span class="lineNum">      36 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="37"><span class="lineNum">      37 </span>            :   explicit MoreThan( const VesselOptions&amp; da );</a>
+<a name="38"><span class="lineNum">      38 </span>            :   std::string value_descriptor() override;</a>
+<a name="39"><span class="lineNum">      39 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="40"><span class="lineNum">      40 </span>            : };</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      12536 : PLUMED_REGISTER_VESSEL(MoreThan,&quot;MORE_THAN&quot;)</span></a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         32 : void MoreThan::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         32 :   FunctionVessel::registerKeywords( keys );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         32 :   SwitchingFunction::registerKeywords( keys );</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">         32 : }</span></a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       4168 : void MoreThan::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;MORE_THAN&quot;,&quot;calculate the number of variables more than a certain target value. &quot;</span></a>
+<a name="51"><span class="lineNum">      51 </span>            :                &quot;This quantity is calculated using \\f$\\sum_i 1.0 - \\sigma(s_i)\\f$, where \\f$\\sigma(s)\\f$ &quot;</a>
+<a name="52"><span class="lineNum">      52 </span>            :                &quot;is a \\ref switchingfunction.&quot;);</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;morethan&quot;,&quot;MORE_THAN&quot;,&quot;the number of values more than a target value. This is calculated using one of the &quot;</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :                           &quot;formula described in the description of the keyword so as to make it continuous. &quot;</a>
+<a name="55"><span class="lineNum">      55 </span>            :                           &quot;You can calculate this quantity multiple times using different parameters.&quot;);</a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       4168 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">         32 : MoreThan::MoreThan( const VesselOptions&amp; da ) :</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">         32 :   FunctionVessel(da)</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : {</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         32 :   usetol=true;</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         32 :   if( getAction()-&gt;isPeriodic() ) error(&quot;more than is not a meaningful option for periodic variables&quot;);</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">         64 :   std::string errormsg; sf.set( getAllInput(), errormsg );</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">         32 :   if( errormsg.size()!=0 ) error( errormsg );</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">         32 : }</span></a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         32 : std::string MoreThan::value_descriptor() {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         64 :   return &quot;the number of values more than &quot; + sf.description();</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">      19012 : double MoreThan::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">      19012 :   double f = 1.0 - sf.calculate(val, dv); dv*=-val; return f;</span></a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : }</a>
+<a name="76"><span class="lineNum">      76 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/OrderingVessel.cpp.func-sort-c.html b/coverage/vesselbase/OrderingVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..ca2c466e7e
--- /dev/null
+++ b/coverage/vesselbase/OrderingVessel.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/OrderingVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - OrderingVessel.cpp<span style="font-size: 80%;"> (<a href="OrderingVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">96.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OrderingVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#27">_ZN4PLMD10vesselbase14OrderingVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#31">_ZN4PLMD10vesselbase14OrderingVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#46">_ZN4PLMD10vesselbase14OrderingVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#41">_ZN4PLMD10vesselbase14OrderingVessel6resizeEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/OrderingVessel.cpp.func.html b/coverage/vesselbase/OrderingVessel.cpp.func.html
new file mode 100644
index 0000000000..42cd6af001
--- /dev/null
+++ b/coverage/vesselbase/OrderingVessel.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/OrderingVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - OrderingVessel.cpp<span style="font-size: 80%;"> (<a href="OrderingVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">96.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OrderingVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#27">_ZN4PLMD10vesselbase14OrderingVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#46">_ZN4PLMD10vesselbase14OrderingVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">19</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#41">_ZN4PLMD10vesselbase14OrderingVessel6resizeEv</a></td>
+              <td class="coverFnHi">34</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.cpp.gcov.html#31">_ZN4PLMD10vesselbase14OrderingVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/OrderingVessel.cpp.gcov.html b/coverage/vesselbase/OrderingVessel.cpp.gcov.html
new file mode 100644
index 0000000000..2611b55060
--- /dev/null
+++ b/coverage/vesselbase/OrderingVessel.cpp.gcov.html
@@ -0,0 +1,147 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/OrderingVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - OrderingVessel.cpp<span style="font-size: 80%;"> (source / <a href="OrderingVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntry">27</td>
+            <td class="headerCovTableEntryHi">96.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;OrderingVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;core/ActionWithValue.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">          8 : void OrderingVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">          8 :   ValueVessel::registerKeywords( keys );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">          8 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">          8 : OrderingVessel::OrderingVessel( const VesselOptions&amp; da ) :</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">          8 :   ValueVessel(da)</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">          8 :   mydata = getAction()-&gt;buildDataStashes( NULL );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">         26 :   for(unsigned i=0; i&lt;getAction()-&gt;getNumberOfVessels(); ++i) {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         18 :     if( getAction()-&gt;getPntrToVessel(i)-&gt;getName()==getName() )</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineNoCov">          0 :       error(&quot;calculating lowest/highest value multiple times serves no purpose&quot;);</span></a>
+<a name="40"><span class="lineNum">      40 </span>            :   }</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">          8 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         34 : void OrderingVessel::resize() {</span></a>
+<a name="44"><span class="lineNum">      44 </span>            :   resizeBuffer( 0 );</a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">         34 :   if( getAction()-&gt;derivativesAreRequired() ) getFinalValue()-&gt;resizeDerivatives( getAction()-&gt;getNumberOfDerivatives() );</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">         34 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         19 : void OrderingVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         19 :   std::vector&lt;double&gt; values( getAction()-&gt;getNumberOfQuantities() );</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">         19 :   mydata-&gt;retrieveSequentialValue( 0, false, values );</span></a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">         19 :   double min=values[mycomp]; unsigned mini=getAction()-&gt;getPositionInFullTaskList(0);</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">       4134 :   for(unsigned i=1; i&lt;mydata-&gt;getNumberOfStoredValues(); ++i) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">       4115 :     mydata-&gt;retrieveSequentialValue( i, false, values );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">       4115 :     double newval = values[mycomp];</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">       4115 :     if( compare( newval, min ) ) { min=newval; mini=getAction()-&gt;getPositionInFullTaskList(i); }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            :   }</a>
+<a name="58"><span class="lineNum">      58 </span>            :   setOutputValue( min );</a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">         19 :   if( getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">         17 :     MultiValue myvals( getAction()-&gt;getNumberOfQuantities(), getAction()-&gt;getNumberOfDerivatives() );</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">         17 :     mydata-&gt;retrieveDerivatives( mini, false, myvals ); Value* fval=getFinalValue();</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">        551 :     for(unsigned i=0; i&lt;myvals.getNumberActive(); ++i) {</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :       unsigned ider=myvals.getActiveIndex(i);</a>
+<a name="65"><span class="lineNum">      65 </span>            :       fval-&gt;setDerivative( ider, myvals.getDerivative(mycomp,ider) );</a>
+<a name="66"><span class="lineNum">      66 </span>            :     }</a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">         17 :   }</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">         19 : }</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : </a>
+<a name="70"><span class="lineNum">      70 </span>            : }</a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/OrderingVessel.h.func-sort-c.html b/coverage/vesselbase/OrderingVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..8488dfa032
--- /dev/null
+++ b/coverage/vesselbase/OrderingVessel.h.func-sort-c.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/OrderingVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - OrderingVessel.h<span style="font-size: 80%;"> (<a href="OrderingVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="OrderingVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.h.gcov.html#40">_ZNK4PLMD10vesselbase14OrderingVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">2118</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/OrderingVessel.h.func.html b/coverage/vesselbase/OrderingVessel.h.func.html
new file mode 100644
index 0000000000..c42dcf1a9b
--- /dev/null
+++ b/coverage/vesselbase/OrderingVessel.h.func.html
@@ -0,0 +1,76 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/OrderingVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - OrderingVessel.h<span style="font-size: 80%;"> (<a href="OrderingVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="OrderingVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="OrderingVessel.h.gcov.html#40">_ZNK4PLMD10vesselbase14OrderingVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">2118</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/OrderingVessel.h.gcov.html b/coverage/vesselbase/OrderingVessel.h.gcov.html
new file mode 100644
index 0000000000..d583904924
--- /dev/null
+++ b/coverage/vesselbase/OrderingVessel.h.gcov.html
@@ -0,0 +1,126 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/OrderingVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - OrderingVessel.h<span style="font-size: 80%;"> (source / <a href="OrderingVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntry">1</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_OrderingVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_OrderingVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;ValueVessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace PLMD {</a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace vesselbase {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class OrderingVessel : public ValueVessel {</a>
+<a name="36"><span class="lineNum">      36 </span>            : private:</a>
+<a name="37"><span class="lineNum">      37 </span>            :   StoreDataVessel* mydata;</a>
+<a name="38"><span class="lineNum">      38 </span>            : public:</a>
+<a name="39"><span class="lineNum">      39 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="40"><span class="lineNum">      40 </span>            :   explicit OrderingVessel( const VesselOptions&amp; da );</a>
+<a name="41"><span class="lineNum">      41 </span>            :   void resize() override;</a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">       2118 :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const override {}</span></a>
+<a name="43"><span class="lineNum">      43 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="44"><span class="lineNum">      44 </span>            :   virtual bool compare( const double&amp;, const double&amp; )=0;</a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : #endif</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ShortcutVessel.cpp.func-sort-c.html b/coverage/vesselbase/ShortcutVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..1acc26ed52
--- /dev/null
+++ b/coverage/vesselbase/ShortcutVessel.cpp.func-sort-c.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ShortcutVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ShortcutVessel.cpp<span style="font-size: 80%;"> (<a href="ShortcutVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ShortcutVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.cpp.gcov.html#26">_ZN4PLMD10vesselbase14ShortcutVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.cpp.gcov.html#31">_ZN4PLMD10vesselbase14ShortcutVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.cpp.gcov.html#36">_ZN4PLMD10vesselbase14ShortcutVessel9addVesselERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ShortcutVessel.cpp.func.html b/coverage/vesselbase/ShortcutVessel.cpp.func.html
new file mode 100644
index 0000000000..88c07154bd
--- /dev/null
+++ b/coverage/vesselbase/ShortcutVessel.cpp.func.html
@@ -0,0 +1,84 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ShortcutVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ShortcutVessel.cpp<span style="font-size: 80%;"> (<a href="ShortcutVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ShortcutVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.cpp.gcov.html#26">_ZN4PLMD10vesselbase14ShortcutVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.cpp.gcov.html#36">_ZN4PLMD10vesselbase14ShortcutVessel9addVesselERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_</a></td>
+              <td class="coverFnHi">32</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.cpp.gcov.html#31">_ZN4PLMD10vesselbase14ShortcutVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">11</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ShortcutVessel.cpp.gcov.html b/coverage/vesselbase/ShortcutVessel.cpp.gcov.html
new file mode 100644
index 0000000000..9a7b3eb81b
--- /dev/null
+++ b/coverage/vesselbase/ShortcutVessel.cpp.gcov.html
@@ -0,0 +1,123 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ShortcutVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ShortcutVessel.cpp<span style="font-size: 80%;"> (source / <a href="ShortcutVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntry">12</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntry">3</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ShortcutVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         11 : void ShortcutVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         11 :   Vessel::registerKeywords( keys ); keys.remove(&quot;LABEL&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">         11 :   plumed_assert( keys.size()==0 );</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">         11 : }</span></a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">         11 : ShortcutVessel::ShortcutVessel( const VesselOptions&amp; da):</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">         11 :   Vessel(da)</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : {</a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">         11 : }</span></a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">         32 : void ShortcutVessel::addVessel( const std::string&amp; name, const std::string&amp; input ) {</span></a>
+<a name="39"><span class="lineNum">      39 </span>            :   unsigned numlab=1;</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         65 :   for(unsigned i=0; i&lt;(getAction()-&gt;functions).size(); ++i) {</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         33 :     if( (getAction()-&gt;functions[i])-&gt;getName()==name ) numlab++;</span></a>
+<a name="42"><span class="lineNum">      42 </span>            :   }</a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">         32 :   getAction()-&gt;addVessel( name, input, numlab );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">         32 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span>            : }</a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ShortcutVessel.h.func-sort-c.html b/coverage/vesselbase/ShortcutVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..f993d2eb70
--- /dev/null
+++ b/coverage/vesselbase/ShortcutVessel.h.func-sort-c.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ShortcutVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ShortcutVessel.h<span style="font-size: 80%;"> (<a href="ShortcutVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ShortcutVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#42">_ZN4PLMD10vesselbase14ShortcutVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#38">_ZN4PLMD10vesselbase14ShortcutVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#41">_ZN4PLMD10vesselbase14ShortcutVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#39">_ZN4PLMD10vesselbase14ShortcutVessel6resizeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#40">_ZNK4PLMD10vesselbase14ShortcutVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ShortcutVessel.h.func.html b/coverage/vesselbase/ShortcutVessel.h.func.html
new file mode 100644
index 0000000000..7e55f95a50
--- /dev/null
+++ b/coverage/vesselbase/ShortcutVessel.h.func.html
@@ -0,0 +1,92 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ShortcutVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ShortcutVessel.h<span style="font-size: 80%;"> (<a href="ShortcutVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ShortcutVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#42">_ZN4PLMD10vesselbase14ShortcutVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#38">_ZN4PLMD10vesselbase14ShortcutVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#41">_ZN4PLMD10vesselbase14ShortcutVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#39">_ZN4PLMD10vesselbase14ShortcutVessel6resizeEv</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ShortcutVessel.h.gcov.html#40">_ZNK4PLMD10vesselbase14ShortcutVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ShortcutVessel.h.gcov.html b/coverage/vesselbase/ShortcutVessel.h.gcov.html
new file mode 100644
index 0000000000..c9a5cb69cc
--- /dev/null
+++ b/coverage/vesselbase/ShortcutVessel.h.gcov.html
@@ -0,0 +1,126 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ShortcutVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ShortcutVessel.h<span style="font-size: 80%;"> (source / <a href="ShortcutVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">5</td>
+            <td class="headerCovTableEntryLo">0.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_ShortcutVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_ShortcutVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace vesselbase {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineNoCov">          0 : class ShortcutVessel : public Vessel {</span></a>
+<a name="35"><span class="lineNum">      35 </span>            : protected:</a>
+<a name="36"><span class="lineNum">      36 </span>            :   void addVessel( const std::string&amp; name, const std::string&amp; intput );</a>
+<a name="37"><span class="lineNum">      37 </span>            : public:</a>
+<a name="38"><span class="lineNum">      38 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="39"><span class="lineNum">      39 </span>            :   explicit ShortcutVessel( const VesselOptions&amp; );</a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineNoCov">          0 :   std::string description() override { return &quot;&quot;; }</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineNoCov">          0 :   void resize() override { plumed_error(); }</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineNoCov">          0 :   void calculate( const unsigned&amp; taskCode, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_index ) const override { plumed_error(); }</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineNoCov">          0 :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override { plumed_error(); }</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineNoCov">          0 :   bool applyForce( std::vector&lt;double&gt;&amp; forces ) override { plumed_error(); }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : };</a>
+<a name="46"><span class="lineNum">      46 </span>            : </a>
+<a name="47"><span class="lineNum">      47 </span>            : }</a>
+<a name="48"><span class="lineNum">      48 </span>            : }</a>
+<a name="49"><span class="lineNum">      49 </span>            : #endif</a>
+<a name="50"><span class="lineNum">      50 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/StoreDataVessel.cpp.func-sort-c.html b/coverage/vesselbase/StoreDataVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a740d69e34
--- /dev/null
+++ b/coverage/vesselbase/StoreDataVessel.cpp.func-sort-c.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/StoreDataVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - StoreDataVessel.cpp<span style="font-size: 80%;"> (<a href="StoreDataVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="StoreDataVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#25">_ZN4PLMD10vesselbase15StoreDataVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#40">_ZN4PLMD10vesselbase15StoreDataVessel17addActionThatUsesEPNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnHi">127</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#29">_ZN4PLMD10vesselbase15StoreDataVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">131</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#168">_ZN4PLMD10vesselbase15StoreDataVessel24resizeTemporyMultiValuesERKj</a></td>
+              <td class="coverFnHi">143</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#162">_ZN4PLMD10vesselbase15StoreDataVessel27setActiveValsAndDerivativesERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">690</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#44">_ZN4PLMD10vesselbase15StoreDataVessel6resizeEv</a></td>
+              <td class="coverFnHi">1643</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#156">_ZN4PLMD10vesselbase15StoreDataVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2542</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#70">_ZNK4PLMD10vesselbase15StoreDataVessel16storeDerivativesERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">5321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#172">_ZN4PLMD10vesselbase15StoreDataVessel20getTemporyMultiValueERKj</a></td>
+              <td class="coverFnHi">55063</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#61">_ZNK4PLMD10vesselbase15StoreDataVessel11storeValuesERKjRNS_10MultiValueERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">148022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#146">_ZNK4PLMD10vesselbase15StoreDataVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">148022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#119">_ZN4PLMD10vesselbase15StoreDataVessel19retrieveDerivativesERKjRKbRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">157983</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#114">_ZNK4PLMD10vesselbase15StoreDataVessel23retrieveWeightWithIndexERKj</a></td>
+              <td class="coverFnHi">330385</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#108">_ZNK4PLMD10vesselbase15StoreDataVessel22retrieveValueWithIndexERKjRKbRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1148018</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#101">_ZNK4PLMD10vesselbase15StoreDataVessel23retrieveSequentialValueERKjRKbRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1609805</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/StoreDataVessel.cpp.func.html b/coverage/vesselbase/StoreDataVessel.cpp.func.html
new file mode 100644
index 0000000000..6b7d75a541
--- /dev/null
+++ b/coverage/vesselbase/StoreDataVessel.cpp.func.html
@@ -0,0 +1,132 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/StoreDataVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - StoreDataVessel.cpp<span style="font-size: 80%;"> (<a href="StoreDataVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="StoreDataVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#25">_ZN4PLMD10vesselbase15StoreDataVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">26</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#40">_ZN4PLMD10vesselbase15StoreDataVessel17addActionThatUsesEPNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnHi">127</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#119">_ZN4PLMD10vesselbase15StoreDataVessel19retrieveDerivativesERKjRKbRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">157983</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#172">_ZN4PLMD10vesselbase15StoreDataVessel20getTemporyMultiValueERKj</a></td>
+              <td class="coverFnHi">55063</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#168">_ZN4PLMD10vesselbase15StoreDataVessel24resizeTemporyMultiValuesERKj</a></td>
+              <td class="coverFnHi">143</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#162">_ZN4PLMD10vesselbase15StoreDataVessel27setActiveValsAndDerivativesERKSt6vectorIjSaIjEE</a></td>
+              <td class="coverFnHi">690</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#156">_ZN4PLMD10vesselbase15StoreDataVessel6finishERKSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">2542</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#44">_ZN4PLMD10vesselbase15StoreDataVessel6resizeEv</a></td>
+              <td class="coverFnHi">1643</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#29">_ZN4PLMD10vesselbase15StoreDataVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">131</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#61">_ZNK4PLMD10vesselbase15StoreDataVessel11storeValuesERKjRNS_10MultiValueERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">148022</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#70">_ZNK4PLMD10vesselbase15StoreDataVessel16storeDerivativesERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">5321</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#108">_ZNK4PLMD10vesselbase15StoreDataVessel22retrieveValueWithIndexERKjRKbRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1148018</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#101">_ZNK4PLMD10vesselbase15StoreDataVessel23retrieveSequentialValueERKjRKbRSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">1609805</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#114">_ZNK4PLMD10vesselbase15StoreDataVessel23retrieveWeightWithIndexERKj</a></td>
+              <td class="coverFnHi">330385</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.cpp.gcov.html#146">_ZNK4PLMD10vesselbase15StoreDataVessel9calculateERKjRNS_10MultiValueERSt6vectorIdSaIdEERS6_IjSaIjEE</a></td>
+              <td class="coverFnHi">148022</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/StoreDataVessel.cpp.gcov.html b/coverage/vesselbase/StoreDataVessel.cpp.gcov.html
new file mode 100644
index 0000000000..c41bb17026
--- /dev/null
+++ b/coverage/vesselbase/StoreDataVessel.cpp.gcov.html
@@ -0,0 +1,255 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/StoreDataVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - StoreDataVessel.cpp<span style="font-size: 80%;"> (source / <a href="StoreDataVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">86</td>
+            <td class="headerCovTableEntry">92</td>
+            <td class="headerCovTableEntryHi">93.5 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;StoreDataVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace vesselbase {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">         26 : void StoreDataVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">         26 :   Vessel::registerKeywords(keys); keys.remove(&quot;LABEL&quot;);</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">         26 : }</span></a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineCov">        131 : StoreDataVessel::StoreDataVessel( const VesselOptions&amp; da ):</span></a>
+<a name="32"><span class="lineNum">      32 </span>            :   Vessel(da),</a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        131 :   max_lowmem_stash(3),</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        131 :   vecsize(0),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        131 :   nspace(0)</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : {</a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        131 :   ActionWithValue* myval=dynamic_cast&lt;ActionWithValue*&gt;( getAction() );</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        131 :   if( !myval ) hasderiv=false;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        131 :   else hasderiv=!myval-&gt;doNotCalculateDerivatives();</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">        131 : }</span></a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">        127 : void StoreDataVessel::addActionThatUses( ActionWithVessel* actionThatUses ) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        127 :   userActions.push_back( actionThatUses );</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        127 : }</span></a>
+<a name="45"><span class="lineNum">      45 </span>            : </a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       1643 : void StoreDataVessel::resize() {</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">       1643 :   if( getAction()-&gt;lowmem || !getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">       1066 :     nspace = 1;</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">       1066 :     active_der.resize( max_lowmem_stash * ( 1 + getAction()-&gt;getNumberOfDerivatives() ) );</span></a>
+<a name="50"><span class="lineNum">      50 </span>            :   } else {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        577 :     if( getAction()-&gt;getNumberOfDerivatives()&gt;getAction()-&gt;maxderivatives ) {</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineNoCov">          0 :       error(&quot;not enough memory to store derivatives for action &quot; + getAction()-&gt;getLabel() + &quot; use LOWMEM option&quot;);</span></a>
+<a name="53"><span class="lineNum">      53 </span>            :     }</a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        577 :     nspace = 1 + getAction()-&gt;maxderivatives;</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        577 :     active_der.resize( getNumberOfStoredValues() * ( 1 + getAction()-&gt;maxderivatives ) );</span></a>
+<a name="56"><span class="lineNum">      56 </span>            :   }</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">       1643 :   vecsize=getAction()-&gt;getNumberOfQuantities();</span></a>
+<a name="58"><span class="lineNum">      58 </span>            :   plumed_dbg_assert( vecsize&gt;0 );</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">       1643 :   resizeBuffer( getNumberOfStoredValues()*vecsize*nspace );</span></a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">       1643 :   local_buffer.resize( getNumberOfStoredValues()*vecsize*nspace );</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       1643 : }</span></a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">     148022 : void StoreDataVessel::storeValues( const unsigned&amp; myelem, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer ) const {</span></a>
+<a name="64"><span class="lineNum">      64 </span>            :   plumed_dbg_assert( vecsize&gt;0 );</a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">     148022 :   unsigned jelem = getAction()-&gt;getPositionInCurrentTaskList( myelem ); plumed_dbg_assert( jelem&lt;getNumberOfStoredValues() );</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     148022 :   unsigned ibuf = bufstart + jelem * vecsize * nspace;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">     898572 :   for(unsigned icomp=0; icomp&lt;vecsize; ++icomp) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">     750550 :     buffer[ibuf] += myvals.get(icomp); ibuf+=nspace;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            :   }</a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">     148022 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">       5321 : void StoreDataVessel::storeDerivatives( const unsigned&amp; myelem, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="73"><span class="lineNum">      73 </span>            :   plumed_dbg_assert( vecsize&gt;0 &amp;&amp; getAction()-&gt;derivativesAreRequired() &amp;&amp; myelem&lt;getAction()-&gt;getFullNumberOfTasks() );</a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">       5321 :   unsigned jelem = getAction()-&gt;getPositionInCurrentTaskList( myelem );</span></a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">       5321 :   if( getAction()-&gt;getFullNumberOfTasks()==getNumberOfStoredValues() ) {</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">       5321 :     der_list[jelem]=myvals.getNumberActive();</span></a>
+<a name="78"><span class="lineNum">      78 </span><span class="lineCov">       5321 :     unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );</span></a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">     193658 :     for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) { der_list[kder] = myvals.getActiveIndex(j); kder++; }</span></a>
+<a name="80"><span class="lineNum">      80 </span>            :   } else {</a>
+<a name="81"><span class="lineNum">      81 </span>            :     // This ensures that active indices are gathered correctly if</a>
+<a name="82"><span class="lineNum">      82 </span>            :     // we have multiple tasks contributing to a stored quantity</a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineNoCov">          0 :     unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineNoCov">          0 :     for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="85"><span class="lineNum">      85 </span>            :       bool found=false; unsigned jder = myvals.getActiveIndex(j);</a>
+<a name="86"><span class="lineNum">      86 </span><span class="lineNoCov">          0 :       for(unsigned k=0; k&lt;der_list[jelem]; ++k) {</span></a>
+<a name="87"><span class="lineNum">      87 </span><span class="lineNoCov">          0 :         if( der_list[kder+k]==jder ) { found=true; break; }</span></a>
+<a name="88"><span class="lineNum">      88 </span>            :       }</a>
+<a name="89"><span class="lineNum">      89 </span><span class="lineNoCov">          0 :       if(!found) { der_list[kder+der_list[jelem]]=jder; der_list[jelem]++; }</span></a>
+<a name="90"><span class="lineNum">      90 </span>            :     }</a>
+<a name="91"><span class="lineNum">      91 </span>            :   }</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   // Store the values of the components and the derivatives</a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      16071 :   for(unsigned icomp=0; icomp&lt;vecsize; ++icomp) {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      10750 :     unsigned ibuf = bufstart + jelem * ( vecsize*nspace ) + icomp*nspace + 1;</span></a>
+<a name="96"><span class="lineNum">      96 </span><span class="lineCov">     391636 :     for(unsigned j=0; j&lt;myvals.getNumberActive(); ++j) {</span></a>
+<a name="97"><span class="lineNum">      97 </span>            :       unsigned jder=myvals.getActiveIndex(j);</a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">     380886 :       buffer[ibuf] += myvals.getDerivative( icomp, jder ); ibuf++;</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :     }</a>
+<a name="100"><span class="lineNum">     100 </span>            :   }</a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       5321 : }</span></a>
+<a name="102"><span class="lineNum">     102 </span>            : </a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">    1609805 : void StoreDataVessel::retrieveSequentialValue( const unsigned&amp; jelem, const bool&amp; normed, std::vector&lt;double&gt;&amp; values ) const {</span></a>
+<a name="104"><span class="lineNum">     104 </span>            :   plumed_dbg_assert( values.size()==vecsize );</a>
+<a name="105"><span class="lineNum">     105 </span><span class="lineCov">    1609805 :   unsigned ibuf = jelem * vecsize * nspace;</span></a>
+<a name="106"><span class="lineNum">     106 </span><span class="lineCov">   11217468 :   for(unsigned i=0; i&lt;vecsize; ++i) { values[i]=local_buffer[ibuf]; ibuf+=nspace; }</span></a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">    1609805 :   if( normed &amp;&amp; values.size()&gt;2 ) getAction()-&gt;normalizeVector( values );</span></a>
+<a name="108"><span class="lineNum">     108 </span><span class="lineCov">    1609805 : }</span></a>
+<a name="109"><span class="lineNum">     109 </span>            : </a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">    1148018 : void StoreDataVessel::retrieveValueWithIndex( const unsigned&amp; myelem, const bool&amp; normed, std::vector&lt;double&gt;&amp; values ) const {</span></a>
+<a name="111"><span class="lineNum">     111 </span>            :   plumed_dbg_assert( values.size()==vecsize );</a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">    1148018 :   unsigned jelem = getStoreIndex( myelem );</span></a>
+<a name="113"><span class="lineNum">     113 </span><span class="lineCov">    1148018 :   retrieveSequentialValue( jelem, normed, values );</span></a>
+<a name="114"><span class="lineNum">     114 </span><span class="lineCov">    1148018 : }</span></a>
+<a name="115"><span class="lineNum">     115 </span>            : </a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">     330385 : double StoreDataVessel::retrieveWeightWithIndex( const unsigned&amp; myelem ) const {</span></a>
+<a name="117"><span class="lineNum">     117 </span>            :   plumed_dbg_assert( vecsize&gt;0 );</a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineCov">     330385 :   unsigned jelem = getStoreIndex( myelem ); unsigned ibuf = jelem * vecsize * nspace; return local_buffer[ibuf];</span></a>
+<a name="119"><span class="lineNum">     119 </span>            : }</a>
+<a name="120"><span class="lineNum">     120 </span>            : </a>
+<a name="121"><span class="lineNum">     121 </span><span class="lineCov">     157983 : void StoreDataVessel::retrieveDerivatives( const unsigned&amp; myelem, const bool&amp; normed, MultiValue&amp; myvals ) {</span></a>
+<a name="122"><span class="lineNum">     122 </span>            :   plumed_dbg_assert( myvals.getNumberOfValues()==vecsize &amp;&amp; myvals.getNumberOfDerivatives()==getAction()-&gt;getNumberOfDerivatives() );</a>
+<a name="123"><span class="lineNum">     123 </span>            : </a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineCov">     157983 :   myvals.clearAll();</span></a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">     157983 :   if( getAction()-&gt;lowmem ) {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">     101678 :     recalculateStoredQuantity( myelem, myvals );</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineCov">     101678 :     if( normed ) getAction()-&gt;normalizeVectorDerivatives( myvals );</span></a>
+<a name="128"><span class="lineNum">     128 </span>            :   } else {</a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineCov">      56305 :     unsigned jelem = getAction()-&gt;getPositionInCurrentTaskList( myelem );</span></a>
+<a name="130"><span class="lineNum">     130 </span>            :     // Retrieve the derivatives for elements 0 and 1 - weight and norm</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">     169383 :     for(unsigned icomp=0; icomp&lt;vecsize; ++icomp) {</span></a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineCov">     113078 :       unsigned ibuf = jelem * ( vecsize*nspace ) + icomp*nspace + 1;</span></a>
+<a name="133"><span class="lineNum">     133 </span><span class="lineCov">     113078 :       unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );</span></a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">     580640 :       for(unsigned j=0; j&lt;active_der[jelem]; ++j) {</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">     467562 :         myvals.addDerivative( icomp, active_der[kder], local_buffer[ibuf] );</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">     467562 :         kder++; ibuf++;</span></a>
+<a name="137"><span class="lineNum">     137 </span>            :       }</a>
+<a name="138"><span class="lineNum">     138 </span>            :     }</a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineCov">      56305 :     if( normed ) getAction()-&gt;normalizeVectorDerivatives( myvals );</span></a>
+<a name="140"><span class="lineNum">     140 </span>            :     // Now ensure appropriate parts of list are activated</a>
+<a name="141"><span class="lineNum">     141 </span>            :     myvals.emptyActiveMembers();</a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineCov">      56305 :     unsigned kder = getNumberOfStoredValues() + jelem * ( nspace - 1 );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">     280933 :     for(unsigned j=0; j&lt;active_der[jelem]; ++j) { myvals.putIndexInActiveArray( active_der[kder] ); kder++; }</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :     myvals.sortActiveList();</a>
+<a name="145"><span class="lineNum">     145 </span>            :   }</a>
+<a name="146"><span class="lineNum">     146 </span><span class="lineCov">     157983 : }</span></a>
+<a name="147"><span class="lineNum">     147 </span>            : </a>
+<a name="148"><span class="lineNum">     148 </span><span class="lineCov">     148022 : void StoreDataVessel::calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const {</span></a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span><span class="lineCov">     148022 :   if( myvals.get(0)&gt;epsilon ) {</span></a>
+<a name="151"><span class="lineNum">     151 </span><span class="lineCov">     148022 :     storeValues( current, myvals, buffer );</span></a>
+<a name="152"><span class="lineNum">     152 </span><span class="lineCov">     148022 :     if( !(getAction()-&gt;lowmem) &amp;&amp; getAction()-&gt;derivativesAreRequired() ) storeDerivatives( current, myvals, buffer, der_list );</span></a>
+<a name="153"><span class="lineNum">     153 </span>            :   }</a>
+<a name="154"><span class="lineNum">     154 </span>            : </a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">     148022 :   return;</span></a>
+<a name="156"><span class="lineNum">     156 </span>            : }</a>
+<a name="157"><span class="lineNum">     157 </span>            : </a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">       2542 : void StoreDataVessel::finish( const std::vector&lt;double&gt;&amp; buffer ) {</span></a>
+<a name="159"><span class="lineNum">     159 </span>            :   // Store the buffer locally</a>
+<a name="160"><span class="lineNum">     160 </span><span class="lineCov">    2186582 :   for(unsigned i=0; i&lt;local_buffer.size(); ++i) local_buffer[i]=buffer[bufstart+i];</span></a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">       2542 : }</span></a>
+<a name="162"><span class="lineNum">     162 </span>            : </a>
+<a name="163"><span class="lineNum">     163 </span>            : </a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        690 : void StoreDataVessel::setActiveValsAndDerivatives( const std::vector&lt;unsigned&gt;&amp; der_index ) {</span></a>
+<a name="165"><span class="lineNum">     165 </span><span class="lineCov">        690 :   if( !getAction()-&gt;lowmem &amp;&amp; getAction()-&gt;derivativesAreRequired() ) {</span></a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     228266 :     for(unsigned i=0; i&lt;der_index.size(); ++i) active_der[i]=der_index[i];</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :   }</a>
+<a name="168"><span class="lineNum">     168 </span><span class="lineCov">        690 : }</span></a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span><span class="lineCov">        143 : void StoreDataVessel::resizeTemporyMultiValues( const unsigned&amp; nvals ) {</span></a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">        416 :   for(unsigned i=0; i&lt;nvals; ++i) my_tmp_vals.push_back( MultiValue(0,0) );</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        143 : }</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">      55063 : MultiValue&amp; StoreDataVessel::getTemporyMultiValue( const unsigned&amp; ind ) {</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      55063 :   plumed_dbg_assert( ind&lt;my_tmp_vals.size() ); return my_tmp_vals[ind];</span></a>
+<a name="176"><span class="lineNum">     176 </span>            : }</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            : }</a>
+<a name="179"><span class="lineNum">     179 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/StoreDataVessel.h.func-sort-c.html b/coverage/vesselbase/StoreDataVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..65360591fc
--- /dev/null
+++ b/coverage/vesselbase/StoreDataVessel.h.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/StoreDataVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - StoreDataVessel.h<span style="font-size: 80%;"> (<a href="StoreDataVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="StoreDataVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#122">_ZN4PLMD10vesselbase15StoreDataVessel15activateIndicesEPNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#108">_ZN4PLMD10vesselbase15StoreDataVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#124">_ZN4PLMD10vesselbase15StoreDataVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">958</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#151">_ZNK4PLMD10vesselbase15StoreDataVessel19storedValueIsActiveERKj</a></td>
+              <td class="coverFnHi">65536</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#190">_ZN4PLMD10vesselbase15StoreDataVessel25recalculateStoredQuantityERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">101678</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#164">_ZNK4PLMD10vesselbase15StoreDataVessel23getNumberOfStoredValuesEv</a></td>
+              <td class="coverFnHi">632197</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#169">_ZNK4PLMD10vesselbase15StoreDataVessel13getStoreIndexERKj</a></td>
+              <td class="coverFnHi">1557091</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/StoreDataVessel.h.func.html b/coverage/vesselbase/StoreDataVessel.h.func.html
new file mode 100644
index 0000000000..35f3d8d86a
--- /dev/null
+++ b/coverage/vesselbase/StoreDataVessel.h.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/StoreDataVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - StoreDataVessel.h<span style="font-size: 80%;"> (<a href="StoreDataVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="StoreDataVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#124">_ZN4PLMD10vesselbase15StoreDataVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">958</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#108">_ZN4PLMD10vesselbase15StoreDataVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">128</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#122">_ZN4PLMD10vesselbase15StoreDataVessel15activateIndicesEPNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#190">_ZN4PLMD10vesselbase15StoreDataVessel25recalculateStoredQuantityERKjRNS_10MultiValueE</a></td>
+              <td class="coverFnHi">101678</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#169">_ZNK4PLMD10vesselbase15StoreDataVessel13getStoreIndexERKj</a></td>
+              <td class="coverFnHi">1557091</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#151">_ZNK4PLMD10vesselbase15StoreDataVessel19storedValueIsActiveERKj</a></td>
+              <td class="coverFnHi">65536</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="StoreDataVessel.h.gcov.html#164">_ZNK4PLMD10vesselbase15StoreDataVessel23getNumberOfStoredValuesEv</a></td>
+              <td class="coverFnHi">632197</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/StoreDataVessel.h.gcov.html b/coverage/vesselbase/StoreDataVessel.h.gcov.html
new file mode 100644
index 0000000000..517f8c7591
--- /dev/null
+++ b/coverage/vesselbase/StoreDataVessel.h.gcov.html
@@ -0,0 +1,286 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/StoreDataVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - StoreDataVessel.h<span style="font-size: 80%;"> (source / <a href="StoreDataVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">24</td>
+            <td class="headerCovTableEntry">26</td>
+            <td class="headerCovTableEntryHi">92.3 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">6</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryMed">85.7 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_StoreDataVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_StoreDataVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;cstddef&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : namespace PLMD {</a>
+<a name="32"><span class="lineNum">      32 </span>            : namespace vesselbase {</a>
+<a name="33"><span class="lineNum">      33 </span>            : </a>
+<a name="34"><span class="lineNum">      34 </span>            : /**</a>
+<a name="35"><span class="lineNum">      35 </span>            : \ingroup TOOLBOX</a>
+<a name="36"><span class="lineNum">      36 </span>            : Objects that inherit from FunctionVessel can be used (in tandem with PLMD::vesselbase::ActionWithVessel)</a>
+<a name="37"><span class="lineNum">      37 </span>            : to store values and derivatives for a set of scalars or vectors that are calculated by a</a>
+<a name="38"><span class="lineNum">      38 </span>            : PLMD::vesselbase::ActionWithVessel.  Functions of these stored quantities can then be calculated in a</a>
+<a name="39"><span class="lineNum">      39 </span>            : second step.</a>
+<a name="40"><span class="lineNum">      40 </span>            : */</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span>            : class StoreDataVessel : public Vessel {</a>
+<a name="43"><span class="lineNum">      43 </span>            :   friend class Moments;</a>
+<a name="44"><span class="lineNum">      44 </span>            : private:</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Do the quantities being stored in here need derivatives</a>
+<a name="46"><span class="lineNum">      46 </span>            :   bool hasderiv;</a>
+<a name="47"><span class="lineNum">      47 </span>            : /// What is the maximum number of vectors we are going to</a>
+<a name="48"><span class="lineNum">      48 </span>            : /// have to store when using lowmem option</a>
+<a name="49"><span class="lineNum">      49 </span>            :   unsigned max_lowmem_stash;</a>
+<a name="50"><span class="lineNum">      50 </span>            : /// The size of the vector we are computing</a>
+<a name="51"><span class="lineNum">      51 </span>            :   std::size_t vecsize;</a>
+<a name="52"><span class="lineNum">      52 </span>            : /// The amount of data per vector element</a>
+<a name="53"><span class="lineNum">      53 </span>            :   std::size_t nspace;</a>
+<a name="54"><span class="lineNum">      54 </span>            : /// The currently active values</a>
+<a name="55"><span class="lineNum">      55 </span>            : //  std::vector&lt;unsigned&gt; active_val;</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The active derivative elements</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::vector&lt;unsigned&gt; active_der;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The buffer</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::vector&lt;double&gt; local_buffer;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// The actions that are going to use the stored data</a>
+<a name="61"><span class="lineNum">      61 </span>            :   std::vector&lt;ActionWithVessel*&gt; userActions;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// We create a vector of tempory MultiValues here so as to avoid</a>
+<a name="63"><span class="lineNum">      63 </span>            : /// lots of vector resizing</a>
+<a name="64"><span class="lineNum">      64 </span>            :   unsigned tmp_index;</a>
+<a name="65"><span class="lineNum">      65 </span>            :   std::vector&lt;MultiValue&gt; my_tmp_vals;</a>
+<a name="66"><span class="lineNum">      66 </span>            : protected:</a>
+<a name="67"><span class="lineNum">      67 </span>            : /// Is the weight differentiable</a>
+<a name="68"><span class="lineNum">      68 </span>            :   bool weightHasDerivatives();</a>
+<a name="69"><span class="lineNum">      69 </span>            : /// Are we using low mem option</a>
+<a name="70"><span class="lineNum">      70 </span>            :   bool usingLowMem();</a>
+<a name="71"><span class="lineNum">      71 </span>            : /// Finish the setup of the storage object by setting how much</a>
+<a name="72"><span class="lineNum">      72 </span>            : /// data has to be stored</a>
+<a name="73"><span class="lineNum">      73 </span>            :   void completeSetup( const unsigned&amp;, const unsigned&amp; );</a>
+<a name="74"><span class="lineNum">      74 </span>            : /// Return value of nspace</a>
+<a name="75"><span class="lineNum">      75 </span>            :   unsigned getNumberOfDerivativeSpacesPerComponent() const ;</a>
+<a name="76"><span class="lineNum">      76 </span>            : /// Retrieve the values from the underlying ActionWithVessel</a>
+<a name="77"><span class="lineNum">      77 </span>            :   void storeValues( const unsigned&amp;, MultiValue&amp;, std::vector&lt;double&gt;&amp; ) const ;</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// This stores the data we get from the calculation</a>
+<a name="79"><span class="lineNum">      79 </span>            :   void storeDerivatives( const unsigned&amp;, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp;, std::vector&lt;unsigned&gt;&amp; ) const ;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// Get the ibuf'th local derivative value</a>
+<a name="81"><span class="lineNum">      81 </span>            :   double getLocalDerivative( const unsigned&amp; ibuf );</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// Set the ibuf'th local derivative value</a>
+<a name="83"><span class="lineNum">      83 </span>            :   void setLocalDerivative( const unsigned&amp; ibuf, const double&amp; val );</a>
+<a name="84"><span class="lineNum">      84 </span>            : public:</a>
+<a name="85"><span class="lineNum">      85 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="86"><span class="lineNum">      86 </span>            :   explicit StoreDataVessel( const VesselOptions&amp; );</a>
+<a name="87"><span class="lineNum">      87 </span>            : /// Get the number of values that have been stored</a>
+<a name="88"><span class="lineNum">      88 </span>            :   virtual unsigned getNumberOfStoredValues() const ;</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// Get the index to store a particular index inside</a>
+<a name="90"><span class="lineNum">      90 </span>            :   unsigned getStoreIndex( const unsigned&amp; ) const ;</a>
+<a name="91"><span class="lineNum">      91 </span>            : /// Get the true index of a quantity from the index it is stored in</a>
+<a name="92"><span class="lineNum">      92 </span>            :   unsigned getTrueIndex( const unsigned&amp; ) const ;</a>
+<a name="93"><span class="lineNum">      93 </span>            : /// Recalculate one of the base quantities</a>
+<a name="94"><span class="lineNum">      94 </span>            :   void recalculateStoredQuantity( const unsigned&amp; myelm, MultiValue&amp; myvals );</a>
+<a name="95"><span class="lineNum">      95 </span>            : /// Set a hard cutoff on the weight of an element</a>
+<a name="96"><span class="lineNum">      96 </span>            :   void setHardCutoffOnWeight( const double&amp; mytol );</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// Add an action that uses this data</a>
+<a name="98"><span class="lineNum">      98 </span>            :   void addActionThatUses( ActionWithVessel* actionThatUses );</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Return the number of components in the vector</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">       2094 :   unsigned getNumberOfComponents() const { return vecsize; }</span></a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Get the values of all the components in the vector</a>
+<a name="102"><span class="lineNum">     102 </span>            :   void retrieveSequentialValue( const unsigned&amp; myelem, const bool&amp; normed, std::vector&lt;double&gt;&amp; values ) const ;</a>
+<a name="103"><span class="lineNum">     103 </span>            :   void retrieveValueWithIndex( const unsigned&amp; myelem, const bool&amp; normed, std::vector&lt;double&gt;&amp; values ) const ;</a>
+<a name="104"><span class="lineNum">     104 </span>            :   double retrieveWeightWithIndex( const unsigned&amp; myelem ) const ;</a>
+<a name="105"><span class="lineNum">     105 </span>            : /// Get the derivatives for one of the components in the vector</a>
+<a name="106"><span class="lineNum">     106 </span>            :   void retrieveDerivatives( const unsigned&amp; myelem, const bool&amp; normed, MultiValue&amp; myvals );</a>
+<a name="107"><span class="lineNum">     107 </span>            : /// Do all resizing of data</a>
+<a name="108"><span class="lineNum">     108 </span>            :   void resize() override;</a>
+<a name="109"><span class="lineNum">     109 </span>            : ///</a>
+<a name="110"><span class="lineNum">     110 </span><span class="lineCov">        128 :   std::string description() override { return &quot;&quot;; }</span></a>
+<a name="111"><span class="lineNum">     111 </span>            : /// Get the number of derivatives for the ith value</a>
+<a name="112"><span class="lineNum">     112 </span>            :   unsigned getNumberOfDerivatives( const unsigned&amp; );</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Get the size of the derivative list</a>
+<a name="114"><span class="lineNum">     114 </span>            :   unsigned getSizeOfDerivativeList() const ;</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// This stores the data when not using lowmem</a>
+<a name="116"><span class="lineNum">     116 </span>            :   void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_index ) const override;</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Final step in gathering data</a>
+<a name="118"><span class="lineNum">     118 </span>            :   void finish( const std::vector&lt;double&gt;&amp; buffer ) override;</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Is a particular stored value active at the present time</a>
+<a name="120"><span class="lineNum">     120 </span>            :   bool storedValueIsActive( const unsigned&amp; iatom ) const ;</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Set the active values</a>
+<a name="122"><span class="lineNum">     122 </span>            :   void setActiveValsAndDerivatives( const std::vector&lt;unsigned&gt;&amp; der_index );</a>
+<a name="123"><span class="lineNum">     123 </span>            : /// Activate indexes (this is used at end of chain rule)</a>
+<a name="124"><span class="lineNum">     124 </span><span class="lineNoCov">          0 :   virtual void activateIndices( ActionWithVessel* ) {}</span></a>
+<a name="125"><span class="lineNum">     125 </span>            : /// Forces on vectors should always be applied elsewhere</a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        958 :   bool applyForce(std::vector&lt;double&gt;&amp;) override { return false; }</span></a>
+<a name="127"><span class="lineNum">     127 </span>            : ///  Get the number of data users</a>
+<a name="128"><span class="lineNum">     128 </span>            :   unsigned getNumberOfDataUsers() const ;</a>
+<a name="129"><span class="lineNum">     129 </span>            : /// Get one of the ith data user</a>
+<a name="130"><span class="lineNum">     130 </span>            :   ActionWithVessel* getDataUser( const unsigned&amp; );</a>
+<a name="131"><span class="lineNum">     131 </span>            : /// Set the number of tempory multivalues we need</a>
+<a name="132"><span class="lineNum">     132 </span>            :   void resizeTemporyMultiValues( const unsigned&amp; nvals );</a>
+<a name="133"><span class="lineNum">     133 </span>            : /// Return a tempory multi value - we do this so as to avoid vector resizing</a>
+<a name="134"><span class="lineNum">     134 </span>            :   MultiValue&amp; getTemporyMultiValue( const unsigned&amp; ind );</a>
+<a name="135"><span class="lineNum">     135 </span>            : };</a>
+<a name="136"><span class="lineNum">     136 </span>            : </a>
+<a name="137"><span class="lineNum">     137 </span>            : inline</a>
+<a name="138"><span class="lineNum">     138 </span>            : bool StoreDataVessel::weightHasDerivatives() {</a>
+<a name="139"><span class="lineNum">     139 </span>            :   return getAction()-&gt;weightHasDerivatives;</a>
+<a name="140"><span class="lineNum">     140 </span>            : }</a>
+<a name="141"><span class="lineNum">     141 </span>            : </a>
+<a name="142"><span class="lineNum">     142 </span>            : inline</a>
+<a name="143"><span class="lineNum">     143 </span>            : bool StoreDataVessel::usingLowMem() {</a>
+<a name="144"><span class="lineNum">     144 </span>            :   return getAction()-&gt;lowmem;</a>
+<a name="145"><span class="lineNum">     145 </span>            : }</a>
+<a name="146"><span class="lineNum">     146 </span>            : </a>
+<a name="147"><span class="lineNum">     147 </span>            : inline</a>
+<a name="148"><span class="lineNum">     148 </span>            : unsigned StoreDataVessel::getNumberOfDerivativeSpacesPerComponent() const {</a>
+<a name="149"><span class="lineNum">     149 </span>            :   return nspace;</a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+<a name="151"><span class="lineNum">     151 </span>            : </a>
+<a name="152"><span class="lineNum">     152 </span>            : inline</a>
+<a name="153"><span class="lineNum">     153 </span><span class="lineCov">      65536 : bool StoreDataVessel::storedValueIsActive( const unsigned&amp; iatom ) const {</span></a>
+<a name="154"><span class="lineNum">     154 </span><span class="lineCov">      65536 :   if( !getAction()-&gt;taskIsCurrentlyActive( iatom ) ) return false;</span></a>
+<a name="155"><span class="lineNum">     155 </span><span class="lineCov">      53771 :   unsigned jatom = getStoreIndex( iatom );</span></a>
+<a name="156"><span class="lineNum">     156 </span>            :   plumed_dbg_assert( jatom&lt;getNumberOfStoredValues() );</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">      53771 :   return local_buffer[jatom*vecsize*nspace]&gt;epsilon;</span></a>
+<a name="158"><span class="lineNum">     158 </span>            : }</a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            : inline</a>
+<a name="161"><span class="lineNum">     161 </span>            : unsigned StoreDataVessel::getSizeOfDerivativeList() const {</a>
+<a name="162"><span class="lineNum">     162 </span>            :   return active_der.size();</a>
+<a name="163"><span class="lineNum">     163 </span>            : }</a>
+<a name="164"><span class="lineNum">     164 </span>            : </a>
+<a name="165"><span class="lineNum">     165 </span>            : inline</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineCov">     632197 : unsigned StoreDataVessel::getNumberOfStoredValues() const {</span></a>
+<a name="167"><span class="lineNum">     167 </span><span class="lineCov">     632197 :   return getAction()-&gt;nactive_tasks;</span></a>
+<a name="168"><span class="lineNum">     168 </span>            : }</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            : inline</a>
+<a name="171"><span class="lineNum">     171 </span><span class="lineCov">    1557091 : unsigned StoreDataVessel::getStoreIndex( const unsigned&amp; ind ) const {</span></a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">    1557091 :   if( getAction()-&gt;nactive_tasks==getAction()-&gt;getFullNumberOfTasks() ) return ind;</span></a>
+<a name="173"><span class="lineNum">     173 </span>            : </a>
+<a name="174"><span class="lineNum">     174 </span>            :   // Binary search for required element - faster scaling than sequential search</a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">      64159 :   unsigned l=0, r=getAction()-&gt;nactive_tasks-1;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">     696300 :   for(unsigned i=0; i&lt;getAction()-&gt;nactive_tasks; ++i) {</span></a>
+<a name="177"><span class="lineNum">     177 </span><span class="lineCov">     696300 :     plumed_assert( l&lt;=r );</span></a>
+<a name="178"><span class="lineNum">     178 </span><span class="lineCov">     696300 :     unsigned m = std::floor( (l + r)/2 );</span></a>
+<a name="179"><span class="lineNum">     179 </span><span class="lineCov">     696300 :     if( ind==getAction()-&gt;indexOfTaskInFullList[m] ) return m;</span></a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">     632141 :     else if( getAction()-&gt;indexOfTaskInFullList[m]&lt;ind ) l=m+1;</span></a>
+<a name="181"><span class="lineNum">     181 </span><span class="lineCov">     302100 :     else if( getAction()-&gt;indexOfTaskInFullList[m]&gt;ind ) r=m-1;</span></a>
+<a name="182"><span class="lineNum">     182 </span>            :   }</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineNoCov">          0 :   plumed_merror(&quot;requested task is not active&quot;);</span></a>
+<a name="184"><span class="lineNum">     184 </span>            : }</a>
+<a name="185"><span class="lineNum">     185 </span>            : </a>
+<a name="186"><span class="lineNum">     186 </span>            : inline</a>
+<a name="187"><span class="lineNum">     187 </span>            : unsigned StoreDataVessel::getTrueIndex( const unsigned&amp; ind ) const {</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        300 :   return getAction()-&gt;indexOfTaskInFullList[ind];</span></a>
+<a name="189"><span class="lineNum">     189 </span>            : }</a>
+<a name="190"><span class="lineNum">     190 </span>            : </a>
+<a name="191"><span class="lineNum">     191 </span>            : inline</a>
+<a name="192"><span class="lineNum">     192 </span><span class="lineCov">     101678 : void StoreDataVessel::recalculateStoredQuantity( const unsigned&amp; myelem, MultiValue&amp; myvals ) {</span></a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineCov">     101678 :   getAction()-&gt;performTask( myelem, getAction()-&gt;getTaskCode(myelem), myvals );</span></a>
+<a name="194"><span class="lineNum">     194 </span><span class="lineCov">     101678 : }</span></a>
+<a name="195"><span class="lineNum">     195 </span>            : </a>
+<a name="196"><span class="lineNum">     196 </span>            : inline</a>
+<a name="197"><span class="lineNum">     197 </span>            : unsigned StoreDataVessel::getNumberOfDataUsers() const {</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        225 :   return userActions.size();</span></a>
+<a name="199"><span class="lineNum">     199 </span>            : }</a>
+<a name="200"><span class="lineNum">     200 </span>            : </a>
+<a name="201"><span class="lineNum">     201 </span>            : inline</a>
+<a name="202"><span class="lineNum">     202 </span>            : ActionWithVessel* StoreDataVessel::getDataUser( const unsigned&amp; idata ) {</a>
+<a name="203"><span class="lineNum">     203 </span><span class="lineCov">         49 :   plumed_dbg_assert( idata&lt;userActions.size() ); return userActions[idata];</span></a>
+<a name="204"><span class="lineNum">     204 </span>            : }</a>
+<a name="205"><span class="lineNum">     205 </span>            : </a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : }</a>
+<a name="208"><span class="lineNum">     208 </span>            : #endif</a>
+<a name="209"><span class="lineNum">     209 </span>            : </a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Sum.cpp.func-sort-c.html b/coverage/vesselbase/Sum.cpp.func-sort-c.html
new file mode 100644
index 0000000000..3e718efa3b
--- /dev/null
+++ b/coverage/vesselbase/Sum.cpp.func-sort-c.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Sum.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Sum.cpp<span style="font-size: 80%;"> (<a href="Sum.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Sum.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_113SumRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#37">_ZN4PLMD10vesselbase3Sum16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#51">_ZN4PLMD10vesselbase3Sum16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#46">_ZN4PLMD10vesselbase3SumC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_113SumRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_113SumRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#41">_ZN4PLMD10vesselbase3Sum14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#55">_ZNK4PLMD10vesselbase3Sum13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">60444</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Sum.cpp.func.html b/coverage/vesselbase/Sum.cpp.func.html
new file mode 100644
index 0000000000..5787ec3ca5
--- /dev/null
+++ b/coverage/vesselbase/Sum.cpp.func.html
@@ -0,0 +1,104 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Sum.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Sum.cpp<span style="font-size: 80%;"> (<a href="Sum.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Sum.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_113SumRegisterMe6createERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_113SumRegisterMeC2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#35">_ZN4PLMD10vesselbase12_GLOBAL__N_113SumRegisterMeD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#41">_ZN4PLMD10vesselbase3Sum14reserveKeywordERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#37">_ZN4PLMD10vesselbase3Sum16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#51">_ZN4PLMD10vesselbase3Sum16value_descriptorB5cxx11Ev</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#46">_ZN4PLMD10vesselbase3SumC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">57</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Sum.cpp.gcov.html#55">_ZNK4PLMD10vesselbase3Sum13calcTransformERKdRd</a></td>
+              <td class="coverFnHi">60444</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Sum.cpp.gcov.html b/coverage/vesselbase/Sum.cpp.gcov.html
new file mode 100644
index 0000000000..f57dcc65c6
--- /dev/null
+++ b/coverage/vesselbase/Sum.cpp.gcov.html
@@ -0,0 +1,138 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Sum.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Sum.cpp<span style="font-size: 80%;"> (source / <a href="Sum.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntry">15</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntry">8</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2013-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;FunctionVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace PLMD {</a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace vesselbase {</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : class Sum : public FunctionVessel {</a>
+<a name="29"><span class="lineNum">      29 </span>            : public:</a>
+<a name="30"><span class="lineNum">      30 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="31"><span class="lineNum">      31 </span>            :   static void reserveKeyword( Keywords&amp; keys );</a>
+<a name="32"><span class="lineNum">      32 </span>            :   explicit Sum( const VesselOptions&amp; da );</a>
+<a name="33"><span class="lineNum">      33 </span>            :   std::string value_descriptor() override;</a>
+<a name="34"><span class="lineNum">      34 </span>            :   double calcTransform( const double&amp; val, double&amp; dv ) const override;</a>
+<a name="35"><span class="lineNum">      35 </span>            : };</a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">      12561 : PLUMED_REGISTER_VESSEL(Sum,&quot;SUM&quot;)</span></a>
+<a name="38"><span class="lineNum">      38 </span>            : </a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">         57 : void Sum::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         57 :   FunctionVessel::registerKeywords( keys );</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         57 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">       4168 : void Sum::reserveKeyword( Keywords&amp; keys ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">       8336 :   keys.reserve(&quot;vessel&quot;,&quot;SUM&quot;,&quot;calculate the sum of all the quantities.&quot;);</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">       8336 :   keys.addOutputComponent(&quot;sum&quot;,&quot;SUM&quot;,&quot;the sum of values&quot;);</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">       4168 : }</span></a>
+<a name="47"><span class="lineNum">      47 </span>            : </a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">         57 : Sum::Sum( const VesselOptions&amp; da ) :</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">         57 :   FunctionVessel(da)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">         57 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">         57 : std::string Sum::value_descriptor() {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">         57 :   return &quot;the sum of all the values&quot;;</span></a>
+<a name="55"><span class="lineNum">      55 </span>            : }</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      60444 : double Sum::calcTransform( const double&amp; val, double&amp; dv ) const {</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      60444 :   dv=1.0; return val;</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span>            : }</a>
+<a name="62"><span class="lineNum">      62 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ValueVessel.cpp.func-sort-c.html b/coverage/vesselbase/ValueVessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..e411eb108c
--- /dev/null
+++ b/coverage/vesselbase/ValueVessel.cpp.func-sort-c.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ValueVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ValueVessel.cpp<span style="font-size: 80%;"> (<a href="ValueVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ValueVessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#53">_ZN4PLMD10vesselbase11ValueVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#25">_ZN4PLMD10vesselbase11ValueVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#30">_ZN4PLMD10vesselbase11ValueVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#59">_ZN4PLMD10vesselbase11ValueVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">11445</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ValueVessel.cpp.func.html b/coverage/vesselbase/ValueVessel.cpp.func.html
new file mode 100644
index 0000000000..fc08c6e3b1
--- /dev/null
+++ b/coverage/vesselbase/ValueVessel.cpp.func.html
@@ -0,0 +1,88 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ValueVessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ValueVessel.cpp<span style="font-size: 80%;"> (<a href="ValueVessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ValueVessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#59">_ZN4PLMD10vesselbase11ValueVessel10applyForceERSt6vectorIdSaIdEE</a></td>
+              <td class="coverFnHi">11445</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#53">_ZN4PLMD10vesselbase11ValueVessel11descriptionB5cxx11Ev</a></td>
+              <td class="coverFnHi">337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#25">_ZN4PLMD10vesselbase11ValueVessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">337</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="ValueVessel.cpp.gcov.html#30">_ZN4PLMD10vesselbase11ValueVesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">337</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ValueVessel.cpp.gcov.html b/coverage/vesselbase/ValueVessel.cpp.gcov.html
new file mode 100644
index 0000000000..7331a2388e
--- /dev/null
+++ b/coverage/vesselbase/ValueVessel.cpp.gcov.html
@@ -0,0 +1,148 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ValueVessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ValueVessel.cpp<span style="font-size: 80%;"> (source / <a href="ValueVessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntry">32</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;ValueVessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : </a>
+<a name="24"><span class="lineNum">      24 </span>            : namespace PLMD {</a>
+<a name="25"><span class="lineNum">      25 </span>            : namespace vesselbase {</a>
+<a name="26"><span class="lineNum">      26 </span>            : </a>
+<a name="27"><span class="lineNum">      27 </span><span class="lineCov">        337 : void ValueVessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="28"><span class="lineNum">      28 </span><span class="lineCov">        337 :   Vessel::registerKeywords( keys );</span></a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">        674 :   keys.add(&quot;compulsory&quot;,&quot;COMPONENT&quot;,&quot;1&quot;,&quot;the component of the vector for which to calculate this quantity&quot;);</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">        337 : }</span></a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineCov">        337 : ValueVessel::ValueVessel( const VesselOptions&amp; da ):</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        337 :   Vessel(da)</span></a>
+<a name="34"><span class="lineNum">      34 </span>            : {</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        674 :   parse(&quot;COMPONENT&quot;,mycomp);</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        337 :   ActionWithValue* a=dynamic_cast&lt;ActionWithValue*&gt;( getAction() );</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        337 :   plumed_massert(a,&quot;cannot create passable values as base action does not inherit from ActionWithValue&quot;);</span></a>
+<a name="38"><span class="lineNum">      38 </span>            :   int numval = getNumericalLabel();</a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        337 :   if( numval&lt;0 &amp;&amp; a-&gt;getNumberOfComponents()==0 ) {  // This allows us to make multicolvars pretend to be colvars - this is used in AlphaRMSD etc</span></a>
+<a name="40"><span class="lineNum">      40 </span><span class="lineCov">         36 :     a-&gt;addValueWithDerivatives();</span></a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">         36 :     a-&gt;setNotPeriodic();</span></a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">         36 :     final_value=a-&gt;copyOutput( a-&gt;getNumberOfComponents()-1 );</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        301 :   } else if( numval&lt;0 ) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">          4 :     final_value_ptr=Tools::make_unique&lt;Value&gt;();</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">          2 :     final_value=final_value_ptr.get();</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">          2 :     final_value-&gt;setNotPeriodic();</span></a>
+<a name="47"><span class="lineNum">      47 </span>            :   } else {</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        598 :     plumed_massert( !a-&gt;exists(getAction()-&gt;getLabel() + &quot;.&quot; + getLabel() ), &quot;you can't create the name multiple times&quot;);</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        299 :     a-&gt;addComponentWithDerivatives( getLabel() );</span></a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">        598 :     a-&gt;componentIsNotPeriodic( getLabel() );</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        299 :     final_value=a-&gt;copyOutput( a-&gt;getNumberOfComponents()-1 );</span></a>
+<a name="52"><span class="lineNum">      52 </span>            :   }</a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        337 : }</span></a>
+<a name="54"><span class="lineNum">      54 </span>            : </a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        337 : std::string ValueVessel::description() {</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        373 :   if( final_value-&gt;getName()==getAction()-&gt;getLabel() ) return &quot;value &quot; + getAction()-&gt;getLabel() + &quot; contains &quot; + value_descriptor();</span></a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">        301 :   std::string compstr; Tools::convert(mycomp,compstr);</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        602 :   return &quot;value &quot; + getAction()-&gt;getLabel() + &quot;.&quot; + getLabel() + &quot; is obtained by taking the &quot; + compstr + &quot;th component and finding &quot; + value_descriptor();</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : }</a>
+<a name="60"><span class="lineNum">      60 </span>            : </a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">      11445 : bool ValueVessel::applyForce( std::vector&lt;double&gt;&amp; forces ) {</span></a>
+<a name="62"><span class="lineNum">      62 </span><span class="lineCov">      11445 :   std::vector&lt;double&gt; tmpforce( forces.size() );</span></a>
+<a name="63"><span class="lineNum">      63 </span><span class="lineCov">      11445 :   forces.assign(forces.size(),0.0); bool wasforced=false;</span></a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">      11445 :   if( final_value-&gt;applyForce( tmpforce ) ) {</span></a>
+<a name="65"><span class="lineNum">      65 </span>            :     wasforced=true;</a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">     524318 :     for(unsigned j=0; j&lt;forces.size(); ++j) forces[j]+=tmpforce[j];</span></a>
+<a name="67"><span class="lineNum">      67 </span>            :   }</a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">      11445 :   return wasforced;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span>            : }</a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ValueVessel.h.func-sort-c.html b/coverage/vesselbase/ValueVessel.h.func-sort-c.html
new file mode 100644
index 0000000000..802b02d1d7
--- /dev/null
+++ b/coverage/vesselbase/ValueVessel.h.func-sort-c.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ValueVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ValueVessel.h<span style="font-size: 80%;"> (<a href="ValueVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="ValueVessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ValueVessel.h.func.html b/coverage/vesselbase/ValueVessel.h.func.html
new file mode 100644
index 0000000000..251ecf0685
--- /dev/null
+++ b/coverage/vesselbase/ValueVessel.h.func.html
@@ -0,0 +1,72 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ValueVessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ValueVessel.h<span style="font-size: 80%;"> (<a href="ValueVessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="ValueVessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/ValueVessel.h.gcov.html b/coverage/vesselbase/ValueVessel.h.gcov.html
new file mode 100644
index 0000000000..025be9231e
--- /dev/null
+++ b/coverage/vesselbase/ValueVessel.h.gcov.html
@@ -0,0 +1,150 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/ValueVessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - ValueVessel.h<span style="font-size: 80%;"> (source / <a href="ValueVessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntry">4</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntry">0</td>
+            <td class="headerCovTableEntryHi">-</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2015-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_ValueVessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_ValueVessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;memory&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : </a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;core/Value.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : namespace vesselbase {</a>
+<a name="35"><span class="lineNum">      35 </span>            : </a>
+<a name="36"><span class="lineNum">      36 </span>            : class ValueVessel : public Vessel {</a>
+<a name="37"><span class="lineNum">      37 </span>            : private:</a>
+<a name="38"><span class="lineNum">      38 </span>            : // unique pointer with the same scope as final_value</a>
+<a name="39"><span class="lineNum">      39 </span>            :   std::unique_ptr&lt;Value&gt; final_value_ptr;</a>
+<a name="40"><span class="lineNum">      40 </span>            : // this pointer either points to a non-owned Value or to final_value_ptr</a>
+<a name="41"><span class="lineNum">      41 </span>            :   Value* final_value;</a>
+<a name="42"><span class="lineNum">      42 </span>            : protected:</a>
+<a name="43"><span class="lineNum">      43 </span>            : /// The component that is being averaged/accumulated whatever</a>
+<a name="44"><span class="lineNum">      44 </span>            :   unsigned mycomp;</a>
+<a name="45"><span class="lineNum">      45 </span>            : /// Set the final value</a>
+<a name="46"><span class="lineNum">      46 </span>            :   void setOutputValue( const double&amp; val );</a>
+<a name="47"><span class="lineNum">      47 </span>            : public:</a>
+<a name="48"><span class="lineNum">      48 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="49"><span class="lineNum">      49 </span>            :   explicit ValueVessel( const VesselOptions&amp; da );</a>
+<a name="50"><span class="lineNum">      50 </span>            :   std::string description() override;</a>
+<a name="51"><span class="lineNum">      51 </span>            :   virtual std::string value_descriptor()=0;</a>
+<a name="52"><span class="lineNum">      52 </span>            :   bool applyForce( std::vector&lt;double&gt;&amp; forces ) override;</a>
+<a name="53"><span class="lineNum">      53 </span>            :   double getOutputValue() const ;</a>
+<a name="54"><span class="lineNum">      54 </span>            :   Value* getFinalValue() const ;</a>
+<a name="55"><span class="lineNum">      55 </span>            : };</a>
+<a name="56"><span class="lineNum">      56 </span>            : </a>
+<a name="57"><span class="lineNum">      57 </span>            : inline</a>
+<a name="58"><span class="lineNum">      58 </span>            : Value* ValueVessel::getFinalValue() const {</a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">    2406417 :   return final_value;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            : }</a>
+<a name="61"><span class="lineNum">      61 </span>            : </a>
+<a name="62"><span class="lineNum">      62 </span>            : inline</a>
+<a name="63"><span class="lineNum">      63 </span>            : double ValueVessel::getOutputValue() const {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">       3389 :   return final_value-&gt;get();</span></a>
+<a name="65"><span class="lineNum">      65 </span>            : }</a>
+<a name="66"><span class="lineNum">      66 </span>            : </a>
+<a name="67"><span class="lineNum">      67 </span>            : inline</a>
+<a name="68"><span class="lineNum">      68 </span>            : void ValueVessel::setOutputValue( const double&amp; val ) {</a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">       2079 :   final_value-&gt;set( val );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        251 : }</span></a>
+<a name="71"><span class="lineNum">      71 </span>            : </a>
+<a name="72"><span class="lineNum">      72 </span>            : }</a>
+<a name="73"><span class="lineNum">      73 </span>            : }</a>
+<a name="74"><span class="lineNum">      74 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Vessel.cpp.func-sort-c.html b/coverage/vesselbase/Vessel.cpp.func-sort-c.html
new file mode 100644
index 0000000000..a059fd0165
--- /dev/null
+++ b/coverage/vesselbase/Vessel.cpp.func-sort-c.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Vessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Vessel.cpp<span style="font-size: 80%;"> (<a href="Vessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Vessel.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#137">_ZN4PLMD10vesselbase6Vessel5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#88">_ZNK4PLMD10vesselbase6Vessel7getNameB5cxx11Ev</a></td>
+              <td class="coverFnHi">89</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#105">_ZN4PLMD10vesselbase6Vessel9parseFlagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERb</a></td>
+              <td class="coverFnHi">122</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#96">_ZN4PLMD10vesselbase6Vessel11getAllInputB5cxx11Ev</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#41">_ZN4PLMD10vesselbase13VesselOptionsC2ERKS1_RKNS_8KeywordsE</a></td>
+              <td class="coverFnHi">451</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#51">_ZN4PLMD10vesselbase6Vessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">451</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#123">_ZN4PLMD10vesselbase6Vessel9checkReadEv</a></td>
+              <td class="coverFnHi">544</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#31">_ZN4PLMD10vesselbase13VesselOptionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKjS9_PNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnHi">602</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#69">_ZN4PLMD10vesselbase6VesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#56">_ZN4PLMD10vesselbase6Vessel13transformNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">800</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#92">_ZNK4PLMD10vesselbase6Vessel8getLabelB5cxx11Ev</a></td>
+              <td class="coverFnHi">28589</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Vessel.cpp.func.html b/coverage/vesselbase/Vessel.cpp.func.html
new file mode 100644
index 0000000000..ea6c438c83
--- /dev/null
+++ b/coverage/vesselbase/Vessel.cpp.func.html
@@ -0,0 +1,116 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Vessel.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Vessel.cpp<span style="font-size: 80%;"> (<a href="Vessel.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Vessel.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#31">_ZN4PLMD10vesselbase13VesselOptionsC2ERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEES9_RKjS9_PNS0_16ActionWithVesselE</a></td>
+              <td class="coverFnHi">602</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#41">_ZN4PLMD10vesselbase13VesselOptionsC2ERKS1_RKNS_8KeywordsE</a></td>
+              <td class="coverFnHi">451</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#96">_ZN4PLMD10vesselbase6Vessel11getAllInputB5cxx11Ev</a></td>
+              <td class="coverFnHi">173</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#56">_ZN4PLMD10vesselbase6Vessel13transformNameERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">800</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#51">_ZN4PLMD10vesselbase6Vessel16registerKeywordsERNS_8KeywordsE</a></td>
+              <td class="coverFnHi">451</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#137">_ZN4PLMD10vesselbase6Vessel5errorERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#123">_ZN4PLMD10vesselbase6Vessel9checkReadEv</a></td>
+              <td class="coverFnHi">544</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#105">_ZN4PLMD10vesselbase6Vessel9parseFlagERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERb</a></td>
+              <td class="coverFnHi">122</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#69">_ZN4PLMD10vesselbase6VesselC2ERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#88">_ZNK4PLMD10vesselbase6Vessel7getNameB5cxx11Ev</a></td>
+              <td class="coverFnHi">89</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.cpp.gcov.html#92">_ZNK4PLMD10vesselbase6Vessel8getLabelB5cxx11Ev</a></td>
+              <td class="coverFnHi">28589</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Vessel.cpp.gcov.html b/coverage/vesselbase/Vessel.cpp.gcov.html
new file mode 100644
index 0000000000..4d52dc6125
--- /dev/null
+++ b/coverage/vesselbase/Vessel.cpp.gcov.html
@@ -0,0 +1,226 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Vessel.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Vessel.cpp<span style="font-size: 80%;"> (source / <a href="Vessel.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">64</td>
+            <td class="headerCovTableEntry">78</td>
+            <td class="headerCovTableEntryMed">82.1 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntry">11</td>
+            <td class="headerCovTableEntryHi">90.9 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &quot;tools/Communicator.h&quot;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &quot;tools/Log.h&quot;</a>
+<a name="27"><span class="lineNum">      27 </span>            : </a>
+<a name="28"><span class="lineNum">      28 </span>            : namespace PLMD {</a>
+<a name="29"><span class="lineNum">      29 </span>            : namespace vesselbase {</a>
+<a name="30"><span class="lineNum">      30 </span>            : </a>
+<a name="31"><span class="lineNum">      31 </span>            : Keywords VesselOptions::emptyKeys;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineCov">        602 : VesselOptions::VesselOptions(const std::string&amp; thisname, const std::string&amp; thislab, const unsigned&amp; nlab, const std::string&amp; params, ActionWithVessel* aa ):</span></a>
+<a name="34"><span class="lineNum">      34 </span><span class="lineCov">        602 :   myname(thisname),</span></a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">        602 :   mylabel(thislab),</span></a>
+<a name="36"><span class="lineNum">      36 </span><span class="lineCov">        602 :   numlab(nlab),</span></a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">        602 :   action(aa),</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">        602 :   keywords(emptyKeys),</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">        602 :   parameters(params)</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : {</a>
+<a name="41"><span class="lineNum">      41 </span><span class="lineCov">        602 : }</span></a>
+<a name="42"><span class="lineNum">      42 </span>            : </a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">        451 : VesselOptions::VesselOptions(const VesselOptions&amp; da, const Keywords&amp; keys ):</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">        451 :   myname(da.myname),</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">        451 :   mylabel(da.mylabel),</span></a>
+<a name="46"><span class="lineNum">      46 </span><span class="lineCov">        451 :   numlab(da.numlab),</span></a>
+<a name="47"><span class="lineNum">      47 </span><span class="lineCov">        451 :   action(da.action),</span></a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">        451 :   keywords(keys),</span></a>
+<a name="49"><span class="lineNum">      49 </span><span class="lineCov">        451 :   parameters(da.parameters)</span></a>
+<a name="50"><span class="lineNum">      50 </span>            : {</a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineCov">        451 : }</span></a>
+<a name="52"><span class="lineNum">      52 </span>            : </a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">        451 : void Vessel::registerKeywords( Keywords&amp; keys ) {</span></a>
+<a name="54"><span class="lineNum">      54 </span><span class="lineCov">        451 :   plumed_assert( keys.size()==0 );</span></a>
+<a name="55"><span class="lineNum">      55 </span><span class="lineCov">        902 :   keys.add(&quot;optional&quot;,&quot;LABEL&quot;,&quot;the label used to reference this particular quantity&quot;);</span></a>
+<a name="56"><span class="lineNum">      56 </span><span class="lineCov">        451 : }</span></a>
+<a name="57"><span class="lineNum">      57 </span>            : </a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">        800 : std::string Vessel::transformName( const std::string&amp; name ) {</span></a>
+<a name="59"><span class="lineNum">      59 </span><span class="lineCov">        800 :   std::string tlabel=name;</span></a>
+<a name="60"><span class="lineNum">      60 </span>            :   // Convert to lower case</a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       4637 :   std::transform( tlabel.begin(), tlabel.end(), tlabel.begin(), [](unsigned char c) { return std::tolower(c); } );</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   // Remove any underscore characters (as these are reserved)</a>
+<a name="63"><span class="lineNum">      63 </span>            :   for(unsigned i=0;; ++i) {</a>
+<a name="64"><span class="lineNum">      64 </span><span class="lineCov">        984 :     std::size_t num=tlabel.find_first_of(&quot;_&quot;);</span></a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        984 :     if( num==std::string::npos ) break;</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        184 :     tlabel.erase( tlabel.begin() + num, tlabel.begin() + num + 1 );</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        184 :   }</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        800 :   return tlabel;</span></a>
+<a name="69"><span class="lineNum">      69 </span>            : }</a>
+<a name="70"><span class="lineNum">      70 </span>            : </a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        603 : Vessel::Vessel( const VesselOptions&amp; da ):</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        603 :   myname(da.myname),</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineCov">        603 :   numlab(da.numlab),</span></a>
+<a name="74"><span class="lineNum">      74 </span><span class="lineCov">        603 :   action(da.action),</span></a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        603 :   line(Tools::getWords( da.parameters )),</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        603 :   keywords(da.keywords),</span></a>
+<a name="77"><span class="lineNum">      77 </span><span class="lineCov">        603 :   finished_read(false)</span></a>
+<a name="78"><span class="lineNum">      78 </span>            : {</a>
+<a name="79"><span class="lineNum">      79 </span><span class="lineCov">        603 :   if( da.mylabel.length()&gt;0) {</span></a>
+<a name="80"><span class="lineNum">      80 </span><span class="lineNoCov">          0 :     mylabel=da.mylabel;</span></a>
+<a name="81"><span class="lineNum">      81 </span>            :   } else {</a>
+<a name="82"><span class="lineNum">      82 </span><span class="lineCov">       1613 :     if( keywords.exists(&quot;LABEL&quot;) ) parse(&quot;LABEL&quot;,mylabel);</span></a>
+<a name="83"><span class="lineNum">      83 </span><span class="lineCov">        603 :     if( mylabel.length()==0 &amp;&amp; numlab&gt;=0 ) {</span></a>
+<a name="84"><span class="lineNum">      84 </span><span class="lineCov">        942 :       mylabel=transformName( myname ); std::string nn;</span></a>
+<a name="85"><span class="lineNum">      85 </span><span class="lineCov">        524 :       if(numlab&gt;0) { Tools::convert( numlab, nn ); mylabel =  mylabel + &quot;-&quot; + nn; }</span></a>
+<a name="86"><span class="lineNum">      86 </span>            :     }</a>
+<a name="87"><span class="lineNum">      87 </span>            :   }</a>
+<a name="88"><span class="lineNum">      88 </span><span class="lineCov">        603 : }</span></a>
+<a name="89"><span class="lineNum">      89 </span>            : </a>
+<a name="90"><span class="lineNum">      90 </span><span class="lineCov">         89 : std::string Vessel::getName() const {</span></a>
+<a name="91"><span class="lineNum">      91 </span><span class="lineCov">         89 :   return myname;</span></a>
+<a name="92"><span class="lineNum">      92 </span>            : }</a>
+<a name="93"><span class="lineNum">      93 </span>            : </a>
+<a name="94"><span class="lineNum">      94 </span><span class="lineCov">      28589 : std::string Vessel::getLabel() const {</span></a>
+<a name="95"><span class="lineNum">      95 </span><span class="lineCov">      28589 :   return mylabel;</span></a>
+<a name="96"><span class="lineNum">      96 </span>            : }</a>
+<a name="97"><span class="lineNum">      97 </span>            : </a>
+<a name="98"><span class="lineNum">      98 </span><span class="lineCov">        173 : std::string Vessel::getAllInput() {</span></a>
+<a name="99"><span class="lineNum">      99 </span>            :   std::string fullstring;</a>
+<a name="100"><span class="lineNum">     100 </span><span class="lineCov">        736 :   for(unsigned i=0; i&lt;line.size(); ++i) {</span></a>
+<a name="101"><span class="lineNum">     101 </span><span class="lineCov">       1126 :     fullstring = fullstring + &quot; &quot; + line[i];</span></a>
+<a name="102"><span class="lineNum">     102 </span>            :   }</a>
+<a name="103"><span class="lineNum">     103 </span><span class="lineCov">        173 :   line.clear(); line.resize(0);</span></a>
+<a name="104"><span class="lineNum">     104 </span><span class="lineCov">        173 :   return fullstring;</span></a>
+<a name="105"><span class="lineNum">     105 </span>            : }</a>
+<a name="106"><span class="lineNum">     106 </span>            : </a>
+<a name="107"><span class="lineNum">     107 </span><span class="lineCov">        122 : void Vessel::parseFlag(const std::string&amp;key, bool &amp; t) {</span></a>
+<a name="108"><span class="lineNum">     108 </span>            :   // Check keyword has been registered</a>
+<a name="109"><span class="lineNum">     109 </span><span class="lineCov">        122 :   plumed_massert(keywords.exists(key), &quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="110"><span class="lineNum">     110 </span>            :   // Check keyword is a flag</a>
+<a name="111"><span class="lineNum">     111 </span><span class="lineCov">        244 :   if(!keywords.style(key,&quot;nohtml&quot;)) {</span></a>
+<a name="112"><span class="lineNum">     112 </span><span class="lineCov">        244 :     plumed_massert(keywords.style(key,&quot;flag&quot;), &quot;keyword &quot; + key + &quot; is not a flag&quot;);</span></a>
+<a name="113"><span class="lineNum">     113 </span>            :   }</a>
+<a name="114"><span class="lineNum">     114 </span>            : </a>
+<a name="115"><span class="lineNum">     115 </span>            :   // Read in the flag otherwise get the default value from the keywords object</a>
+<a name="116"><span class="lineNum">     116 </span><span class="lineCov">        122 :   if(!Tools::parseFlag(line,key,t)) {</span></a>
+<a name="117"><span class="lineNum">     117 </span><span class="lineCov">        198 :     if( keywords.style(key,&quot;nohtml&quot;) ) {</span></a>
+<a name="118"><span class="lineNum">     118 </span><span class="lineNoCov">          0 :       t=false;</span></a>
+<a name="119"><span class="lineNum">     119 </span><span class="lineCov">         99 :     } else if ( !keywords.getLogicalDefault(key,t) ) {</span></a>
+<a name="120"><span class="lineNum">     120 </span><span class="lineNoCov">          0 :       plumed_merror(&quot;there is a flag with no logical default in a vessel - weird&quot;);</span></a>
+<a name="121"><span class="lineNum">     121 </span>            :     }</a>
+<a name="122"><span class="lineNum">     122 </span>            :   }</a>
+<a name="123"><span class="lineNum">     123 </span><span class="lineCov">        122 : }</span></a>
+<a name="124"><span class="lineNum">     124 </span>            : </a>
+<a name="125"><span class="lineNum">     125 </span><span class="lineCov">        544 : void Vessel::checkRead() {</span></a>
+<a name="126"><span class="lineNum">     126 </span><span class="lineCov">        544 :   if(!line.empty()) {</span></a>
+<a name="127"><span class="lineNum">     127 </span><span class="lineNoCov">          0 :     std::string msg=&quot;cannot understand the following words from input : &quot;;</span></a>
+<a name="128"><span class="lineNum">     128 </span><span class="lineNoCov">          0 :     for(unsigned i=0; i&lt;line.size(); i++) {</span></a>
+<a name="129"><span class="lineNum">     129 </span><span class="lineNoCov">          0 :       if(i&gt;0) msg = msg + &quot;, &quot;;</span></a>
+<a name="130"><span class="lineNum">     130 </span><span class="lineNoCov">          0 :       msg = msg + line[i];</span></a>
+<a name="131"><span class="lineNum">     131 </span>            :     }</a>
+<a name="132"><span class="lineNum">     132 </span><span class="lineNoCov">          0 :     error(msg);</span></a>
+<a name="133"><span class="lineNum">     133 </span>            :   }</a>
+<a name="134"><span class="lineNum">     134 </span><span class="lineCov">        544 :   finished_read=true;</span></a>
+<a name="135"><span class="lineNum">     135 </span><span class="lineCov">        544 :   std::string describe=description();</span></a>
+<a name="136"><span class="lineNum">     136 </span><span class="lineCov">        544 :   if( describe.length()&gt;0 &amp;&amp; action ) action-&gt;log.printf(&quot;  %s\n&quot;, describe.c_str() );</span></a>
+<a name="137"><span class="lineNum">     137 </span><span class="lineCov">        544 : }</span></a>
+<a name="138"><span class="lineNum">     138 </span>            : </a>
+<a name="139"><span class="lineNum">     139 </span><span class="lineNoCov">          0 : [[noreturn]] void Vessel::error( const std::string&amp; msg ) {</span></a>
+<a name="140"><span class="lineNum">     140 </span><span class="lineNoCov">          0 :   if( action ) {</span></a>
+<a name="141"><span class="lineNum">     141 </span><span class="lineNoCov">          0 :     action-&gt;log.printf(&quot;ERROR for keyword %s in action %s with label %s : %s \n \n&quot;,myname.c_str(), (action-&gt;getName()).c_str(), (action-&gt;getLabel()).c_str(), msg.c_str() );</span></a>
+<a name="142"><span class="lineNum">     142 </span><span class="lineNoCov">          0 :     if(finished_read) keywords.print( action-&gt;log );</span></a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;ERROR for keyword &quot; + myname + &quot; in action &quot;  + action-&gt;getName() + &quot; with label &quot; + action-&gt;getLabel() + &quot; : &quot; + msg );</span></a>
+<a name="144"><span class="lineNum">     144 </span>            :   } else {</a>
+<a name="145"><span class="lineNum">     145 </span><span class="lineNoCov">          0 :     plumed_merror(&quot;ERROR: &quot; + msg);</span></a>
+<a name="146"><span class="lineNum">     146 </span>            :   }</a>
+<a name="147"><span class="lineNum">     147 </span>            : }</a>
+<a name="148"><span class="lineNum">     148 </span>            : </a>
+<a name="149"><span class="lineNum">     149 </span>            : }</a>
+<a name="150"><span class="lineNum">     150 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Vessel.h.func-sort-c.html b/coverage/vesselbase/Vessel.h.func-sort-c.html
new file mode 100644
index 0000000000..66e013df6e
--- /dev/null
+++ b/coverage/vesselbase/Vessel.h.func-sort-c.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Vessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Vessel.h<span style="font-size: 80%;"> (<a href="Vessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">80.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="Vessel.h.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#129">_ZN4PLMD10vesselbase6VesselD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#155">_ZN4PLMD10vesselbase6Vessel5parseIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#170">_ZN4PLMD10vesselbase6Vessel11parseVectorIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#170">_ZN4PLMD10vesselbase6Vessel11parseVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_RSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">209</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#155">_ZN4PLMD10vesselbase6Vessel5parseIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">345</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#155">_ZN4PLMD10vesselbase6Vessel5parseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_RT_</a></td>
+              <td class="coverFnHi">528</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#129">_ZN4PLMD10vesselbase6VesselD2Ev</a></td>
+              <td class="coverFnHi">603</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#141">_ZN4PLMD10vesselbase6Vessel7prepareEv</a></td>
+              <td class="coverFnHi">26784</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#207">_ZN4PLMD10vesselbase6Vessel14setBufferStartERj</a></td>
+              <td class="coverFnHi">32920</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#212">_ZN4PLMD10vesselbase6Vessel20transformDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">509159</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Vessel.h.func.html b/coverage/vesselbase/Vessel.h.func.html
new file mode 100644
index 0000000000..331d94fd58
--- /dev/null
+++ b/coverage/vesselbase/Vessel.h.func.html
@@ -0,0 +1,112 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Vessel.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Vessel.h<span style="font-size: 80%;"> (<a href="Vessel.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">80.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Vessel.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#170">_ZN4PLMD10vesselbase6Vessel11parseVectorINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_RSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">209</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#170">_ZN4PLMD10vesselbase6Vessel11parseVectorIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERSt6vectorIT_SaISC_EE</a></td>
+              <td class="coverFnHi">36</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#207">_ZN4PLMD10vesselbase6Vessel14setBufferStartERj</a></td>
+              <td class="coverFnHi">32920</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#212">_ZN4PLMD10vesselbase6Vessel20transformDerivativesERKjRNS_10MultiValueES5_</a></td>
+              <td class="coverFnHi">509159</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#155">_ZN4PLMD10vesselbase6Vessel5parseINSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEEEvRKS8_RT_</a></td>
+              <td class="coverFnHi">528</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#155">_ZN4PLMD10vesselbase6Vessel5parseIdEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">9</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#155">_ZN4PLMD10vesselbase6Vessel5parseIjEEvRKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERT_</a></td>
+              <td class="coverFnHi">345</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#141">_ZN4PLMD10vesselbase6Vessel7prepareEv</a></td>
+              <td class="coverFnHi">26784</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#129">_ZN4PLMD10vesselbase6VesselD0Ev</a></td>
+              <td class="coverFnLo">0</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Vessel.h.gcov.html#129">_ZN4PLMD10vesselbase6VesselD2Ev</a></td>
+              <td class="coverFnHi">603</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/Vessel.h.gcov.html b/coverage/vesselbase/Vessel.h.gcov.html
new file mode 100644
index 0000000000..1e6cb399ac
--- /dev/null
+++ b/coverage/vesselbase/Vessel.h.gcov.html
@@ -0,0 +1,321 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/Vessel.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - Vessel.h<span style="font-size: 80%;"> (source / <a href="Vessel.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">29</td>
+            <td class="headerCovTableEntry">36</td>
+            <td class="headerCovTableEntryMed">80.6 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">9</td>
+            <td class="headerCovTableEntry">10</td>
+            <td class="headerCovTableEntryHi">90.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_vesselbase_Vessel_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_vesselbase_Vessel_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : #include &lt;string&gt;</a>
+<a name="26"><span class="lineNum">      26 </span>            : #include &lt;cstring&gt;</a>
+<a name="27"><span class="lineNum">      27 </span>            : #include &lt;vector&gt;</a>
+<a name="28"><span class="lineNum">      28 </span>            : #include &lt;algorithm&gt;</a>
+<a name="29"><span class="lineNum">      29 </span>            : #include &quot;tools/Exception.h&quot;</a>
+<a name="30"><span class="lineNum">      30 </span>            : #include &quot;tools/Keywords.h&quot;</a>
+<a name="31"><span class="lineNum">      31 </span>            : #include &quot;ActionWithVessel.h&quot;</a>
+<a name="32"><span class="lineNum">      32 </span>            : </a>
+<a name="33"><span class="lineNum">      33 </span>            : namespace PLMD {</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            : class Communicator;</a>
+<a name="36"><span class="lineNum">      36 </span>            : class Log;</a>
+<a name="37"><span class="lineNum">      37 </span>            : </a>
+<a name="38"><span class="lineNum">      38 </span>            : namespace vesselbase {</a>
+<a name="39"><span class="lineNum">      39 </span>            : </a>
+<a name="40"><span class="lineNum">      40 </span>            : /**</a>
+<a name="41"><span class="lineNum">      41 </span>            : \ingroup TOOLBOX</a>
+<a name="42"><span class="lineNum">      42 </span>            : Vessels are an important component of class PLMD::ActionWithVessel.  This class</a>
+<a name="43"><span class="lineNum">      43 </span>            : contains a large buffer array of doubles.  The various elements of this array</a>
+<a name="44"><span class="lineNum">      44 </span>            : can be accessed through vessels which are used to structure the elements of the</a>
+<a name="45"><span class="lineNum">      45 </span>            : double array.  As the buffer array is just a vector of doubles it can be easily</a>
+<a name="46"><span class="lineNum">      46 </span>            : mpi gathered or passed to another node.</a>
+<a name="47"><span class="lineNum">      47 </span>            : */</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            : //class ActionWithVessel;</a>
+<a name="50"><span class="lineNum">      50 </span>            : class Vessel;</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            : /// This class is used to pass the input to Vessels</a>
+<a name="53"><span class="lineNum">      53 </span>            : class VesselOptions {</a>
+<a name="54"><span class="lineNum">      54 </span>            :   friend class Vessel;</a>
+<a name="55"><span class="lineNum">      55 </span>            : private:</a>
+<a name="56"><span class="lineNum">      56 </span>            : /// The name of the particular vessel</a>
+<a name="57"><span class="lineNum">      57 </span>            :   std::string myname;</a>
+<a name="58"><span class="lineNum">      58 </span>            : /// The label for this particular vessel;</a>
+<a name="59"><span class="lineNum">      59 </span>            :   std::string mylabel;</a>
+<a name="60"><span class="lineNum">      60 </span>            : /// The numerical label for this vessel</a>
+<a name="61"><span class="lineNum">      61 </span>            :   int numlab;</a>
+<a name="62"><span class="lineNum">      62 </span>            : /// Pointer to ActionWithVessel that this if from</a>
+<a name="63"><span class="lineNum">      63 </span>            :   ActionWithVessel* action;</a>
+<a name="64"><span class="lineNum">      64 </span>            : /// The keywords</a>
+<a name="65"><span class="lineNum">      65 </span>            :   const Keywords&amp; keywords;</a>
+<a name="66"><span class="lineNum">      66 </span>            :   static Keywords emptyKeys;</a>
+<a name="67"><span class="lineNum">      67 </span>            : public:</a>
+<a name="68"><span class="lineNum">      68 </span>            : /// The parameters that are read into the function</a>
+<a name="69"><span class="lineNum">      69 </span>            :   std::string parameters;</a>
+<a name="70"><span class="lineNum">      70 </span>            : /// The constructor</a>
+<a name="71"><span class="lineNum">      71 </span>            :   VesselOptions( const std::string&amp; thisname, const std::string&amp; thislab, const unsigned&amp; nlab, const std::string&amp; params, ActionWithVessel* aa );</a>
+<a name="72"><span class="lineNum">      72 </span>            :   VesselOptions(const VesselOptions&amp; da, const Keywords&amp; keys );</a>
+<a name="73"><span class="lineNum">      73 </span>            : };</a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span>            : class Vessel {</a>
+<a name="76"><span class="lineNum">      76 </span>            :   friend class ActionWithVessel;</a>
+<a name="77"><span class="lineNum">      77 </span>            : private:</a>
+<a name="78"><span class="lineNum">      78 </span>            : /// The keyword for the vessel in the input file</a>
+<a name="79"><span class="lineNum">      79 </span>            :   std::string myname;</a>
+<a name="80"><span class="lineNum">      80 </span>            : /// The label for the vessel for referencing</a>
+<a name="81"><span class="lineNum">      81 </span>            :   std::string mylabel;</a>
+<a name="82"><span class="lineNum">      82 </span>            : /// The numerical label for this object</a>
+<a name="83"><span class="lineNum">      83 </span>            :   const int numlab;</a>
+<a name="84"><span class="lineNum">      84 </span>            : /// The action that this vessel is created within</a>
+<a name="85"><span class="lineNum">      85 </span>            :   ActionWithVessel* action;</a>
+<a name="86"><span class="lineNum">      86 </span>            : /// The number of elements in this vessel's buffered data</a>
+<a name="87"><span class="lineNum">      87 </span>            :   unsigned bufsize;</a>
+<a name="88"><span class="lineNum">      88 </span>            : /// Directive line.</a>
+<a name="89"><span class="lineNum">      89 </span>            : /// This line is progressively erased during vessel construction</a>
+<a name="90"><span class="lineNum">      90 </span>            : /// so as to check if all the present keywords are correct.</a>
+<a name="91"><span class="lineNum">      91 </span>            :   std::vector&lt;std::string&gt; line;</a>
+<a name="92"><span class="lineNum">      92 </span>            : /// The keywords</a>
+<a name="93"><span class="lineNum">      93 </span>            :   const PLMD::Keywords&amp; keywords;</a>
+<a name="94"><span class="lineNum">      94 </span>            : /// This just checks we have done checkRead</a>
+<a name="95"><span class="lineNum">      95 </span>            :   bool finished_read;</a>
+<a name="96"><span class="lineNum">      96 </span>            : protected:</a>
+<a name="97"><span class="lineNum">      97 </span>            : /// The start of this Vessel's buffer in buffer in the underlying ActionWithVessel</a>
+<a name="98"><span class="lineNum">      98 </span>            :   unsigned bufstart;</a>
+<a name="99"><span class="lineNum">      99 </span>            : /// Return the numerical label</a>
+<a name="100"><span class="lineNum">     100 </span>            :   int getNumericalLabel() const ;</a>
+<a name="101"><span class="lineNum">     101 </span>            : /// Report an error</a>
+<a name="102"><span class="lineNum">     102 </span>            :   [[noreturn]] void error(const std::string&amp; errmsg);</a>
+<a name="103"><span class="lineNum">     103 </span>            : /// Parse something from the input</a>
+<a name="104"><span class="lineNum">     104 </span>            :   template&lt;class T&gt;</a>
+<a name="105"><span class="lineNum">     105 </span>            :   void parse(const std::string&amp;key, T&amp;t);</a>
+<a name="106"><span class="lineNum">     106 </span>            : /// Parse one keyword as std::vector</a>
+<a name="107"><span class="lineNum">     107 </span>            :   template&lt;class T&gt;</a>
+<a name="108"><span class="lineNum">     108 </span>            :   void parseVector(const std::string&amp;key,std::vector&lt;T&gt;&amp;t);</a>
+<a name="109"><span class="lineNum">     109 </span>            : /// Parse one keyword as boolean flag</a>
+<a name="110"><span class="lineNum">     110 </span>            :   void parseFlag(const std::string&amp;key,bool&amp;t);</a>
+<a name="111"><span class="lineNum">     111 </span>            : /// This returns the whole input line (it is used for less_than/more_than/between)</a>
+<a name="112"><span class="lineNum">     112 </span>            :   std::string getAllInput();</a>
+<a name="113"><span class="lineNum">     113 </span>            : /// Return a pointer to the action we are working in</a>
+<a name="114"><span class="lineNum">     114 </span>            :   ActionWithVessel* getAction() const ;</a>
+<a name="115"><span class="lineNum">     115 </span>            : /// Return the value of the tolerance</a>
+<a name="116"><span class="lineNum">     116 </span>            :   double getTolerance() const ;</a>
+<a name="117"><span class="lineNum">     117 </span>            : /// Return the value of the neighbor list tolerance</a>
+<a name="118"><span class="lineNum">     118 </span>            :   double getNLTolerance() const ;</a>
+<a name="119"><span class="lineNum">     119 </span>            : /// Return the size of the buffer</a>
+<a name="120"><span class="lineNum">     120 </span>            :   unsigned getSizeOfBuffer() const ;</a>
+<a name="121"><span class="lineNum">     121 </span>            : /// Set the size of the data buffer</a>
+<a name="122"><span class="lineNum">     122 </span>            :   void resizeBuffer( const unsigned&amp; n );</a>
+<a name="123"><span class="lineNum">     123 </span>            : public:</a>
+<a name="124"><span class="lineNum">     124 </span>            : /// Reserve any keywords for this particular vessel</a>
+<a name="125"><span class="lineNum">     125 </span>            :   static void registerKeywords( Keywords&amp; keys );</a>
+<a name="126"><span class="lineNum">     126 </span>            : /// Convert the name to the label of the component</a>
+<a name="127"><span class="lineNum">     127 </span>            :   static std::string transformName( const std::string&amp; name );</a>
+<a name="128"><span class="lineNum">     128 </span>            : /// The constructor</a>
+<a name="129"><span class="lineNum">     129 </span>            :   explicit Vessel( const VesselOptions&amp; da );</a>
+<a name="130"><span class="lineNum">     130 </span>            : /// Virtual destructor needed for proper inheritance</a>
+<a name="131"><span class="lineNum">     131 </span><span class="lineCov">        603 :   virtual ~Vessel() {}</span></a>
+<a name="132"><span class="lineNum">     132 </span>            : /// Return the name</a>
+<a name="133"><span class="lineNum">     133 </span>            :   std::string getName() const ;</a>
+<a name="134"><span class="lineNum">     134 </span>            : /// Return the label</a>
+<a name="135"><span class="lineNum">     135 </span>            :   std::string getLabel() const ;</a>
+<a name="136"><span class="lineNum">     136 </span>            : /// Check that readin was fine</a>
+<a name="137"><span class="lineNum">     137 </span>            :   void checkRead();</a>
+<a name="138"><span class="lineNum">     138 </span>            : /// Return a description of the vessel contents</a>
+<a name="139"><span class="lineNum">     139 </span>            :   virtual std::string description()=0;</a>
+<a name="140"><span class="lineNum">     140 </span>            : /// Set the start of the buffer</a>
+<a name="141"><span class="lineNum">     141 </span>            :   virtual void setBufferStart( unsigned&amp; start );</a>
+<a name="142"><span class="lineNum">     142 </span>            : /// Do something before the loop</a>
+<a name="143"><span class="lineNum">     143 </span><span class="lineCov">      26784 :   virtual void prepare() {}</span></a>
+<a name="144"><span class="lineNum">     144 </span>            : /// This is replaced in bridges so we can transform the derivatives</a>
+<a name="145"><span class="lineNum">     145 </span>            :   virtual MultiValue&amp; transformDerivatives( const unsigned&amp; current, MultiValue&amp; myvals, MultiValue&amp; bvals );</a>
+<a name="146"><span class="lineNum">     146 </span>            : /// Calculate the part of the vessel that is done in the loop</a>
+<a name="147"><span class="lineNum">     147 </span>            :   virtual void calculate( const unsigned&amp; current, MultiValue&amp; myvals, std::vector&lt;double&gt;&amp; buffer, std::vector&lt;unsigned&gt;&amp; der_list ) const = 0;</a>
+<a name="148"><span class="lineNum">     148 </span>            : /// Complete the calculation once the loop is finished</a>
+<a name="149"><span class="lineNum">     149 </span>            :   virtual void finish( const std::vector&lt;double&gt;&amp; )=0;</a>
+<a name="150"><span class="lineNum">     150 </span>            : /// Reset the size of the buffers</a>
+<a name="151"><span class="lineNum">     151 </span>            :   virtual void resize()=0;</a>
+<a name="152"><span class="lineNum">     152 </span>            : /// Retrieve the forces on the quantities in the vessel</a>
+<a name="153"><span class="lineNum">     153 </span>            :   virtual bool applyForce( std::vector&lt;double&gt;&amp; forces )=0;</a>
+<a name="154"><span class="lineNum">     154 </span>            : };</a>
+<a name="155"><span class="lineNum">     155 </span>            : </a>
+<a name="156"><span class="lineNum">     156 </span>            : template&lt;class T&gt;</a>
+<a name="157"><span class="lineNum">     157 </span><span class="lineCov">        882 : void Vessel::parse(const std::string&amp;key, T&amp;t ) {</span></a>
+<a name="158"><span class="lineNum">     158 </span><span class="lineCov">        882 :   plumed_massert(keywords.exists(key),&quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="159"><span class="lineNum">     159 </span>            : </a>
+<a name="160"><span class="lineNum">     160 </span>            :   // Now try to read the keyword</a>
+<a name="161"><span class="lineNum">     161 </span><span class="lineCov">        882 :   bool found=Tools::parse(line,key,t); std::string def;</span></a>
+<a name="162"><span class="lineNum">     162 </span><span class="lineCov">       2015 :   if ( !found &amp;&amp; keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="163"><span class="lineNum">     163 </span><span class="lineCov">        365 :     if( keywords.getDefaultValue(key,def) ) {</span></a>
+<a name="164"><span class="lineNum">     164 </span><span class="lineCov">        365 :       plumed_massert( def.length()!=0 &amp;&amp; Tools::convertNoexcept(def,t), &quot;default value is dubious&quot;);</span></a>
+<a name="165"><span class="lineNum">     165 </span>            :     } else {</a>
+<a name="166"><span class="lineNum">     166 </span><span class="lineNoCov">          0 :       error(&quot;keyword &quot; + key + &quot; is comulsory for this vessel&quot;);</span></a>
+<a name="167"><span class="lineNum">     167 </span>            :     }</a>
+<a name="168"><span class="lineNum">     168 </span>            :   }</a>
+<a name="169"><span class="lineNum">     169 </span><span class="lineCov">        882 : }</span></a>
+<a name="170"><span class="lineNum">     170 </span>            : </a>
+<a name="171"><span class="lineNum">     171 </span>            : template&lt;class T&gt;</a>
+<a name="172"><span class="lineNum">     172 </span><span class="lineCov">        245 : void Vessel::parseVector(const std::string&amp;key,std::vector&lt;T&gt;&amp;t) {</span></a>
+<a name="173"><span class="lineNum">     173 </span>            :   // Check keyword has been registered</a>
+<a name="174"><span class="lineNum">     174 </span><span class="lineCov">        245 :   plumed_massert(keywords.exists(key), &quot;keyword &quot; + key + &quot; has not been registered&quot;);</span></a>
+<a name="175"><span class="lineNum">     175 </span><span class="lineCov">        245 :   unsigned size=t.size(); bool skipcheck=false;</span></a>
+<a name="176"><span class="lineNum">     176 </span><span class="lineCov">        245 :   if(size==0) skipcheck=true;</span></a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   // Now try to read the keyword</a>
+<a name="179"><span class="lineNum">     179 </span>            :   bool found; std::string def; T val;</a>
+<a name="180"><span class="lineNum">     180 </span><span class="lineCov">        245 :   found=Tools::parseVector(line,key,t);</span></a>
+<a name="181"><span class="lineNum">     181 </span>            : </a>
+<a name="182"><span class="lineNum">     182 </span>            :   // Check vectors size is correct (not if this is atoms or ARG)</a>
+<a name="183"><span class="lineNum">     183 </span><span class="lineCov">        490 :   if( !keywords.style(key,&quot;atoms&quot;) &amp;&amp; found ) {</span></a>
+<a name="184"><span class="lineNum">     184 </span><span class="lineCov">        237 :     if( !skipcheck &amp;&amp; t.size()!=size ) error(&quot;vector read in for keyword &quot; + key + &quot; has the wrong size&quot;);</span></a>
+<a name="185"><span class="lineNum">     185 </span>            :   }</a>
+<a name="186"><span class="lineNum">     186 </span>            : </a>
+<a name="187"><span class="lineNum">     187 </span>            :   // If it isn't read and it is compulsory see if a default value was specified</a>
+<a name="188"><span class="lineNum">     188 </span><span class="lineCov">        261 :   if ( !found &amp;&amp; keywords.style(key,&quot;compulsory&quot;) ) {</span></a>
+<a name="189"><span class="lineNum">     189 </span><span class="lineNoCov">          0 :     if( keywords.getDefaultValue(key,def) ) {</span></a>
+<a name="190"><span class="lineNum">     190 </span><span class="lineNoCov">          0 :       if( def.length()==0 || !Tools::convertNoexcept(def,val) ) {</span></a>
+<a name="191"><span class="lineNum">     191 </span><span class="lineNoCov">          0 :         plumed_merror(&quot;weird default value for keyword &quot; + key );</span></a>
+<a name="192"><span class="lineNum">     192 </span>            :       } else {</a>
+<a name="193"><span class="lineNum">     193 </span><span class="lineNoCov">          0 :         for(unsigned i=0; i&lt;t.size(); ++i) t[i]=val;</span></a>
+<a name="194"><span class="lineNum">     194 </span>            :       }</a>
+<a name="195"><span class="lineNum">     195 </span>            :     } else {</a>
+<a name="196"><span class="lineNum">     196 </span><span class="lineNoCov">          0 :       error(&quot;keyword &quot; + key + &quot; is compulsory&quot;);</span></a>
+<a name="197"><span class="lineNum">     197 </span>            :     }</a>
+<a name="198"><span class="lineNum">     198 </span><span class="lineCov">        245 :   } else if ( !found ) {</span></a>
+<a name="199"><span class="lineNum">     199 </span><span class="lineCov">          8 :     t.resize(0);</span></a>
+<a name="200"><span class="lineNum">     200 </span>            :   }</a>
+<a name="201"><span class="lineNum">     201 </span><span class="lineCov">        245 : }</span></a>
+<a name="202"><span class="lineNum">     202 </span>            : </a>
+<a name="203"><span class="lineNum">     203 </span>            : inline</a>
+<a name="204"><span class="lineNum">     204 </span>            : int Vessel::getNumericalLabel() const {</a>
+<a name="205"><span class="lineNum">     205 </span><span class="lineCov">        353 :   return numlab;</span></a>
+<a name="206"><span class="lineNum">     206 </span>            : }</a>
+<a name="207"><span class="lineNum">     207 </span>            : </a>
+<a name="208"><span class="lineNum">     208 </span>            : inline</a>
+<a name="209"><span class="lineNum">     209 </span><span class="lineCov">      32920 : void Vessel::setBufferStart( unsigned&amp; start ) {</span></a>
+<a name="210"><span class="lineNum">     210 </span><span class="lineCov">      32920 :   bufstart=start; start+=bufsize;</span></a>
+<a name="211"><span class="lineNum">     211 </span><span class="lineCov">      32920 : }</span></a>
+<a name="212"><span class="lineNum">     212 </span>            : </a>
+<a name="213"><span class="lineNum">     213 </span>            : inline</a>
+<a name="214"><span class="lineNum">     214 </span><span class="lineCov">     509159 : MultiValue&amp; Vessel::transformDerivatives( const unsigned&amp; current, MultiValue&amp; myvals, MultiValue&amp; bvals ) {</span></a>
+<a name="215"><span class="lineNum">     215 </span><span class="lineCov">     509159 :   return myvals;</span></a>
+<a name="216"><span class="lineNum">     216 </span>            : }</a>
+<a name="217"><span class="lineNum">     217 </span>            : </a>
+<a name="218"><span class="lineNum">     218 </span>            : inline</a>
+<a name="219"><span class="lineNum">     219 </span>            : void Vessel::resizeBuffer( const unsigned&amp; n ) {</a>
+<a name="220"><span class="lineNum">     220 </span><span class="lineCov">       2830 :   bufsize=n;</span></a>
+<a name="221"><span class="lineNum">     221 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            : inline</a>
+<a name="224"><span class="lineNum">     224 </span>            : double Vessel::getTolerance() const {</a>
+<a name="225"><span class="lineNum">     225 </span><span class="lineCov">     134266 :   return action-&gt;tolerance;</span></a>
+<a name="226"><span class="lineNum">     226 </span>            : }</a>
+<a name="227"><span class="lineNum">     227 </span>            : </a>
+<a name="228"><span class="lineNum">     228 </span>            : inline</a>
+<a name="229"><span class="lineNum">     229 </span>            : double Vessel::getNLTolerance() const {</a>
+<a name="230"><span class="lineNum">     230 </span>            :   return action-&gt;nl_tolerance;</a>
+<a name="231"><span class="lineNum">     231 </span>            : }</a>
+<a name="232"><span class="lineNum">     232 </span>            : </a>
+<a name="233"><span class="lineNum">     233 </span>            : inline</a>
+<a name="234"><span class="lineNum">     234 </span>            : ActionWithVessel* Vessel::getAction() const {</a>
+<a name="235"><span class="lineNum">     235 </span><span class="lineCov">    3907293 :   return action;</span></a>
+<a name="236"><span class="lineNum">     236 </span>            : }</a>
+<a name="237"><span class="lineNum">     237 </span>            : </a>
+<a name="238"><span class="lineNum">     238 </span>            : inline</a>
+<a name="239"><span class="lineNum">     239 </span>            : unsigned Vessel::getSizeOfBuffer() const {</a>
+<a name="240"><span class="lineNum">     240 </span>            :   return bufsize;</a>
+<a name="241"><span class="lineNum">     241 </span>            : }</a>
+<a name="242"><span class="lineNum">     242 </span>            : </a>
+<a name="243"><span class="lineNum">     243 </span>            : }</a>
+<a name="244"><span class="lineNum">     244 </span>            : }</a>
+<a name="245"><span class="lineNum">     245 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/VesselRegister.cpp.func-sort-c.html b/coverage/vesselbase/VesselRegister.cpp.func-sort-c.html
new file mode 100644
index 0000000000..9388192827
--- /dev/null
+++ b/coverage/vesselbase/VesselRegister.cpp.func-sort-c.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/VesselRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - VesselRegister.cpp<span style="font-size: 80%;"> (<a href="VesselRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><a href="VesselRegister.cpp.func.html"><img src="../updown.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></a></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#63">_ZN4PLMD10vesselbase14VesselRegister6createENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">359</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#73">_ZN4PLMD10vesselbase14VesselRegister11getKeywordsEv</a></td>
+              <td class="coverFnHi">796</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#27">_ZN4PLMD10vesselbase14VesselRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#58">_ZN4PLMD10vesselbase14VesselRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10078</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#48">_ZN4PLMD10vesselbase14VesselRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS0_6VesselESt14default_deleteIS9_EERKNS0_13VesselOptionsEEPFvRNS_8KeywordsEESL_</a></td>
+              <td class="coverFnHi">75024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#40">_ZN4PLMD10vesselbase14VesselRegister6removeEPFSt10unique_ptrINS0_6VesselESt14default_deleteIS3_EERKNS0_13VesselOptionsEE</a></td>
+              <td class="coverFnHi">75024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#35">_ZN4PLMD10vesselbase14vesselRegisterEv</a></td>
+              <td class="coverFnHi">160922</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/VesselRegister.cpp.func.html b/coverage/vesselbase/VesselRegister.cpp.func.html
new file mode 100644
index 0000000000..125dbf210f
--- /dev/null
+++ b/coverage/vesselbase/VesselRegister.cpp.func.html
@@ -0,0 +1,100 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/VesselRegister.cpp - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - VesselRegister.cpp<span style="font-size: 80%;"> (<a href="VesselRegister.cpp.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="VesselRegister.cpp.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
+    </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#73">_ZN4PLMD10vesselbase14VesselRegister11getKeywordsEv</a></td>
+              <td class="coverFnHi">796</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#48">_ZN4PLMD10vesselbase14VesselRegister3addENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEEPFSt10unique_ptrINS0_6VesselESt14default_deleteIS9_EERKNS0_13VesselOptionsEEPFvRNS_8KeywordsEESL_</a></td>
+              <td class="coverFnHi">75024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#58">_ZN4PLMD10vesselbase14VesselRegister5checkERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE</a></td>
+              <td class="coverFnHi">10078</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#63">_ZN4PLMD10vesselbase14VesselRegister6createENSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEERKNS0_13VesselOptionsE</a></td>
+              <td class="coverFnHi">359</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#40">_ZN4PLMD10vesselbase14VesselRegister6removeEPFSt10unique_ptrINS0_6VesselESt14default_deleteIS3_EERKNS0_13VesselOptionsEE</a></td>
+              <td class="coverFnHi">75024</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#27">_ZN4PLMD10vesselbase14VesselRegisterD2Ev</a></td>
+              <td class="coverFnHi">4168</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="VesselRegister.cpp.gcov.html#35">_ZN4PLMD10vesselbase14vesselRegisterEv</a></td>
+              <td class="coverFnHi">160922</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/VesselRegister.cpp.gcov.html b/coverage/vesselbase/VesselRegister.cpp.gcov.html
new file mode 100644
index 0000000000..ee353dea1d
--- /dev/null
+++ b/coverage/vesselbase/VesselRegister.cpp.gcov.html
@@ -0,0 +1,156 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase/VesselRegister.cpp</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">vesselbase</a> - VesselRegister.cpp<span style="font-size: 80%;"> (source / <a href="VesselRegister.cpp.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">28</td>
+            <td class="headerCovTableEntry">33</td>
+            <td class="headerCovTableEntryMed">84.8 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntry">7</td>
+            <td class="headerCovTableEntryHi">100.0 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2012-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #include &quot;VesselRegister.h&quot;</a>
+<a name="23"><span class="lineNum">      23 </span>            : #include &quot;Vessel.h&quot;</a>
+<a name="24"><span class="lineNum">      24 </span>            : #include &lt;iostream&gt;</a>
+<a name="25"><span class="lineNum">      25 </span>            : </a>
+<a name="26"><span class="lineNum">      26 </span>            : namespace PLMD {</a>
+<a name="27"><span class="lineNum">      27 </span>            : namespace vesselbase {</a>
+<a name="28"><span class="lineNum">      28 </span>            : </a>
+<a name="29"><span class="lineNum">      29 </span><span class="lineCov">       4168 : VesselRegister::~VesselRegister() {</span></a>
+<a name="30"><span class="lineNum">      30 </span><span class="lineCov">       4168 :   if(m.size()&gt;0) {</span></a>
+<a name="31"><span class="lineNum">      31 </span><span class="lineNoCov">          0 :     std::string names=&quot;&quot;;</span></a>
+<a name="32"><span class="lineNum">      32 </span><span class="lineNoCov">          0 :     for(const auto &amp; p : m) names+=p.first+&quot; &quot;;</span></a>
+<a name="33"><span class="lineNum">      33 </span><span class="lineNoCov">          0 :     std::cerr&lt;&lt;&quot;WARNING: Vessel &quot;+ names +&quot; has not been properly unregistered. This might lead to memory leak!!\n&quot;;</span></a>
+<a name="34"><span class="lineNum">      34 </span>            :   }</a>
+<a name="35"><span class="lineNum">      35 </span><span class="lineCov">       4168 : }</span></a>
+<a name="36"><span class="lineNum">      36 </span>            : </a>
+<a name="37"><span class="lineNum">      37 </span><span class="lineCov">     160922 : VesselRegister&amp; vesselRegister() {</span></a>
+<a name="38"><span class="lineNum">      38 </span><span class="lineCov">     160922 :   static VesselRegister ans;</span></a>
+<a name="39"><span class="lineNum">      39 </span><span class="lineCov">     160922 :   return ans;</span></a>
+<a name="40"><span class="lineNum">      40 </span>            : }</a>
+<a name="41"><span class="lineNum">      41 </span>            : </a>
+<a name="42"><span class="lineNum">      42 </span><span class="lineCov">      75024 : void VesselRegister::remove(creator_pointer f) {</span></a>
+<a name="43"><span class="lineNum">      43 </span><span class="lineCov">     475152 :   for(auto p=m.begin(); p!=m.end(); ++p) {</span></a>
+<a name="44"><span class="lineNum">      44 </span><span class="lineCov">     475152 :     if((*p).second==f) {</span></a>
+<a name="45"><span class="lineNum">      45 </span><span class="lineCov">      75024 :       m.erase(p); break;</span></a>
+<a name="46"><span class="lineNum">      46 </span>            :     }</a>
+<a name="47"><span class="lineNum">      47 </span>            :   }</a>
+<a name="48"><span class="lineNum">      48 </span><span class="lineCov">      75024 : }</span></a>
+<a name="49"><span class="lineNum">      49 </span>            : </a>
+<a name="50"><span class="lineNum">      50 </span><span class="lineCov">      75024 : void VesselRegister::add(std::string keyword,creator_pointer f,keyword_pointer k,keyword_pointer ik) {</span></a>
+<a name="51"><span class="lineNum">      51 </span><span class="lineNoCov">          0 :   plumed_massert(m.count(keyword)==0,&quot;keyword has already been registered&quot;);</span></a>
+<a name="52"><span class="lineNum">      52 </span><span class="lineCov">      75024 :   m.insert(std::pair&lt;std::string,creator_pointer&gt;(keyword,f));</span></a>
+<a name="53"><span class="lineNum">      53 </span><span class="lineCov">      75024 :   k( keywords );   // Store the keywords for all the things</span></a>
+<a name="54"><span class="lineNum">      54 </span>            :   // Store a pointer to the function that creates keywords</a>
+<a name="55"><span class="lineNum">      55 </span>            :   // A pointer is stored and not the keywords because all</a>
+<a name="56"><span class="lineNum">      56 </span>            :   // Vessels must be dynamically loaded before the actions.</a>
+<a name="57"><span class="lineNum">      57 </span><span class="lineCov">      75024 :   mk.insert(std::pair&lt;std::string,keyword_pointer&gt;(keyword,ik));</span></a>
+<a name="58"><span class="lineNum">      58 </span><span class="lineCov">      75024 : }</span></a>
+<a name="59"><span class="lineNum">      59 </span>            : </a>
+<a name="60"><span class="lineNum">      60 </span><span class="lineCov">      10078 : bool VesselRegister::check(const std::string &amp; key) {</span></a>
+<a name="61"><span class="lineNum">      61 </span><span class="lineCov">       3122 :   if( m.count(key)&gt;0 ) return true;</span></a>
+<a name="62"><span class="lineNum">      62 </span>            :   return false;</a>
+<a name="63"><span class="lineNum">      63 </span>            : }</a>
+<a name="64"><span class="lineNum">      64 </span>            : </a>
+<a name="65"><span class="lineNum">      65 </span><span class="lineCov">        359 : std::unique_ptr&lt;Vessel&gt; VesselRegister::create(std::string keyword, const VesselOptions&amp;da) {</span></a>
+<a name="66"><span class="lineNum">      66 </span><span class="lineCov">        359 :   std::unique_ptr&lt;Vessel&gt; df;</span></a>
+<a name="67"><span class="lineNum">      67 </span><span class="lineCov">        359 :   if(check(keyword)) {</span></a>
+<a name="68"><span class="lineNum">      68 </span><span class="lineCov">        359 :     Keywords keys; mk[keyword](keys);</span></a>
+<a name="69"><span class="lineNum">      69 </span><span class="lineCov">        359 :     VesselOptions nda( da,keys );</span></a>
+<a name="70"><span class="lineNum">      70 </span><span class="lineCov">        718 :     df=m[keyword](nda);</span></a>
+<a name="71"><span class="lineNum">      71 </span><span class="lineCov">        359 :   }</span></a>
+<a name="72"><span class="lineNum">      72 </span><span class="lineCov">        359 :   return df;</span></a>
+<a name="73"><span class="lineNum">      73 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="74"><span class="lineNum">      74 </span>            : </a>
+<a name="75"><span class="lineNum">      75 </span><span class="lineCov">        796 : Keywords VesselRegister::getKeywords() {</span></a>
+<a name="76"><span class="lineNum">      76 </span><span class="lineCov">        796 :   return keywords;</span></a>
+<a name="77"><span class="lineNum">      77 </span>            : }</a>
+<a name="78"><span class="lineNum">      78 </span>            : </a>
+<a name="79"><span class="lineNum">      79 </span>            : }</a>
+<a name="80"><span class="lineNum">      80 </span>            : }</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/index-sort-f.html b/coverage/vesselbase/index-sort-f.html
new file mode 100644
index 0000000000..992fca50af
--- /dev/null
+++ b/coverage/vesselbase/index-sort-f.html
@@ -0,0 +1,433 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - vesselbase</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1141</td>
+            <td class="headerCovTableEntry">1228</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntry">258</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputVessel.h.gcov.html">ActionWithInputVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ShortcutVessel.h.gcov.html">ShortcutVessel.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AveragingVessel.h.gcov.html">AveragingVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=90 height=10 alt="90.0%"><img src="../snow.png" width=10 height=10 alt="90.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVessel.h.gcov.html">ActionWithVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">20 / 24</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputVessel.cpp.gcov.html">ActionWithInputVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.5%"><img src="../snow.png" width=14 height=10 alt="86.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.5&nbsp;%</td>
+      <td class="coverNumMed">32 / 37</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVessel.cpp.gcov.html">ActionWithVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">188 / 201</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">20 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithAveraging.cpp.gcov.html">ActionWithAveraging.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.4%"><img src="../snow.png" width=5 height=10 alt="95.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.4&nbsp;%</td>
+      <td class="coverNumHi">104 / 109</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FunctionVessel.cpp.gcov.html">FunctionVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">44 / 46</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="StoreDataVessel.h.gcov.html">StoreDataVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">24 / 26</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithAveraging.h.gcov.html">ActionWithAveraging.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vessel.h.gcov.html">Vessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.6%"><img src="../snow.png" width=19 height=10 alt="80.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.6&nbsp;%</td>
+      <td class="coverNumMed">29 / 36</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vessel.cpp.gcov.html">Vessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.1%"><img src="../snow.png" width=18 height=10 alt="82.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">64 / 78</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgeVessel.cpp.gcov.html">BridgeVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 99</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FunctionVessel.h.gcov.html">FunctionVessel.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ValueVessel.h.gcov.html">ValueVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgeVessel.h.gcov.html">BridgeVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrderingVessel.h.gcov.html">OrderingVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ShortcutVessel.cpp.gcov.html">ShortcutVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ValueVessel.cpp.gcov.html">ValueVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrderingVessel.cpp.gcov.html">OrderingVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.3%"><img src="../snow.png" width=4 height=10 alt="96.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.3&nbsp;%</td>
+      <td class="coverNumHi">26 / 27</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Histogram.cpp.gcov.html">Histogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesselRegister.cpp.gcov.html">VesselRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AveragingVessel.cpp.gcov.html">AveragingVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Highest.cpp.gcov.html">Highest.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mean.cpp.gcov.html">Mean.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sum.cpp.gcov.html">Sum.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Lowest.cpp.gcov.html">Lowest.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoreThan.cpp.gcov.html">MoreThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Between.cpp.gcov.html">Between.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AltMin.cpp.gcov.html">AltMin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Min.cpp.gcov.html">Min.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LessThan.cpp.gcov.html">LessThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Max.cpp.gcov.html">Max.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Moments.cpp.gcov.html">Moments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.1%"><img src="../snow.png" width=11 height=10 alt="89.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.1&nbsp;%</td>
+      <td class="coverNumMed">82 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="StoreDataVessel.cpp.gcov.html">StoreDataVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.5%"><img src="../snow.png" width=7 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">86 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/index-sort-l.html b/coverage/vesselbase/index-sort-l.html
new file mode 100644
index 0000000000..2b2997fedf
--- /dev/null
+++ b/coverage/vesselbase/index-sort-l.html
@@ -0,0 +1,433 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - vesselbase</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1141</td>
+            <td class="headerCovTableEntry">1228</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntry">258</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FunctionVessel.h.gcov.html">FunctionVessel.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ShortcutVessel.h.gcov.html">ShortcutVessel.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 6</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 5</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputVessel.h.gcov.html">ActionWithInputVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=67 height=10 alt="66.7%"><img src="../snow.png" width=33 height=10 alt="66.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">2 / 3</td>
+      <td class="coverPerLo">0.0&nbsp;%</td>
+      <td class="coverNumLo">0 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vessel.h.gcov.html">Vessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.6%"><img src="../snow.png" width=19 height=10 alt="80.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.6&nbsp;%</td>
+      <td class="coverNumMed">29 / 36</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vessel.cpp.gcov.html">Vessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.1%"><img src="../snow.png" width=18 height=10 alt="82.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">64 / 78</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVessel.h.gcov.html">ActionWithVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=83 height=10 alt="83.3%"><img src="../snow.png" width=17 height=10 alt="83.3%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">83.3&nbsp;%</td>
+      <td class="coverNumMed">20 / 24</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">3 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesselRegister.cpp.gcov.html">VesselRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithInputVessel.cpp.gcov.html">ActionWithInputVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=86 height=10 alt="86.5%"><img src="../snow.png" width=14 height=10 alt="86.5%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">86.5&nbsp;%</td>
+      <td class="coverNumMed">32 / 37</td>
+      <td class="coverPerLo">66.7&nbsp;%</td>
+      <td class="coverNumLo">4 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Moments.cpp.gcov.html">Moments.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=89 height=10 alt="89.1%"><img src="../snow.png" width=11 height=10 alt="89.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">89.1&nbsp;%</td>
+      <td class="coverNumMed">82 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">11 / 11</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AveragingVessel.h.gcov.html">AveragingVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=90 height=10 alt="90.0%"><img src="../snow.png" width=10 height=10 alt="90.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+      <td class="coverPerLo">50.0&nbsp;%</td>
+      <td class="coverNumLo">1 / 2</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithAveraging.h.gcov.html">ActionWithAveraging.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="StoreDataVessel.h.gcov.html">StoreDataVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">24 / 26</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="StoreDataVessel.cpp.gcov.html">StoreDataVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.5%"><img src="../snow.png" width=7 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">86 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithVessel.cpp.gcov.html">ActionWithVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=94 height=10 alt="93.5%"><img src="../snow.png" width=6 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">188 / 201</td>
+      <td class="coverPerMed">76.9&nbsp;%</td>
+      <td class="coverNumMed">20 / 26</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithAveraging.cpp.gcov.html">ActionWithAveraging.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.4%"><img src="../snow.png" width=5 height=10 alt="95.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.4&nbsp;%</td>
+      <td class="coverNumHi">104 / 109</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="FunctionVessel.cpp.gcov.html">FunctionVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.7&nbsp;%</td>
+      <td class="coverNumHi">44 / 46</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrderingVessel.cpp.gcov.html">OrderingVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="96.3%"><img src="../snow.png" width=4 height=10 alt="96.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">96.3&nbsp;%</td>
+      <td class="coverNumHi">26 / 27</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgeVessel.cpp.gcov.html">BridgeVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=97 height=10 alt="97.0%"><img src="../snow.png" width=3 height=10 alt="97.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">97.0&nbsp;%</td>
+      <td class="coverNumHi">96 / 99</td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">12 / 13</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="OrderingVessel.h.gcov.html">OrderingVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="BridgeVessel.h.gcov.html">BridgeVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ValueVessel.h.gcov.html">ValueVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ShortcutVessel.cpp.gcov.html">ShortcutVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">12 / 12</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Highest.cpp.gcov.html">Highest.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sum.cpp.gcov.html">Sum.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Lowest.cpp.gcov.html">Lowest.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Mean.cpp.gcov.html">Mean.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Histogram.cpp.gcov.html">Histogram.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">6 / 6</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="MoreThan.cpp.gcov.html">MoreThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">20 / 20</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AltMin.cpp.gcov.html">AltMin.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">21 / 21</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="LessThan.cpp.gcov.html">LessThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">22 / 22</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="AveragingVessel.cpp.gcov.html">AveragingVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Max.cpp.gcov.html">Max.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">23 / 23</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Min.cpp.gcov.html">Min.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">24 / 24</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Between.cpp.gcov.html">Between.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">30 / 30</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 9</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ValueVessel.cpp.gcov.html">ValueVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/vesselbase/index.html b/coverage/vesselbase/index.html
new file mode 100644
index 0000000000..ca5c4da0dd
--- /dev/null
+++ b/coverage/vesselbase/index.html
@@ -0,0 +1,433 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - vesselbase</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - vesselbase</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">1141</td>
+            <td class="headerCovTableEntry">1228</td>
+            <td class="headerCovTableEntryHi">92.9 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">231</td>
+            <td class="headerCovTableEntry">258</td>
+            <td class="headerCovTableEntryMed">89.5 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithAveraging.cpp.gcov.html">ActionWithAveraging.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=95 height=10 alt="95.4%"><img src="../snow.png" width=5 height=10 alt="95.4%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">95.4&nbsp;%</td>
+      <td class="coverNumHi">104 / 109</td>
+      <td class="coverPerMed">78.6&nbsp;%</td>
+      <td class="coverNumMed">11 / 14</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ActionWithAveraging.h.gcov.html">ActionWithAveraging.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
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+      <td class="coverNumMed">6 / 7</td>
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+    <tr>
+      <td class="coverFile"><a href="ActionWithInputVessel.cpp.gcov.html">ActionWithInputVessel.cpp</a></td>
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+    <tr>
+      <td class="coverFile"><a href="ActionWithInputVessel.h.gcov.html">ActionWithInputVessel.h</a></td>
+      <td class="coverBar" align="center">
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+    <tr>
+      <td class="coverFile"><a href="ActionWithVessel.cpp.gcov.html">ActionWithVessel.cpp</a></td>
+      <td class="coverBar" align="center">
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+    <tr>
+      <td class="coverFile"><a href="ActionWithVessel.h.gcov.html">ActionWithVessel.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverFile"><a href="AltMin.cpp.gcov.html">AltMin.cpp</a></td>
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+      <td class="coverFile"><a href="AveragingVessel.cpp.gcov.html">AveragingVessel.cpp</a></td>
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+      <td class="coverFile"><a href="AveragingVessel.h.gcov.html">AveragingVessel.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverFile"><a href="Between.cpp.gcov.html">Between.cpp</a></td>
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+      <td class="coverFile"><a href="BridgeVessel.cpp.gcov.html">BridgeVessel.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=96 height=10 alt="95.7%"><img src="../snow.png" width=4 height=10 alt="95.7%"></td></tr></table>
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+    <tr>
+      <td class="coverFile"><a href="FunctionVessel.h.gcov.html">FunctionVessel.h</a></td>
+      <td class="coverBar" align="center">
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+      <td class="coverFile"><a href="Histogram.cpp.gcov.html">Histogram.cpp</a></td>
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+    <tr>
+      <td class="coverFile"><a href="LessThan.cpp.gcov.html">LessThan.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+    <tr>
+      <td class="coverFile"><a href="Lowest.cpp.gcov.html">Lowest.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverNumHi">8 / 8</td>
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+    <tr>
+      <td class="coverFile"><a href="Max.cpp.gcov.html">Max.cpp</a></td>
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+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
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+      <td class="coverFile"><a href="Mean.cpp.gcov.html">Mean.cpp</a></td>
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+      <td class="coverNumHi">17 / 17</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Min.cpp.gcov.html">Min.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverFile"><a href="Moments.cpp.gcov.html">Moments.cpp</a></td>
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+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverFile"><a href="OrderingVessel.cpp.gcov.html">OrderingVessel.cpp</a></td>
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+      <td class="coverFile"><a href="OrderingVessel.h.gcov.html">OrderingVessel.h</a></td>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">1 / 1</td>
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+    <tr>
+      <td class="coverFile"><a href="ShortcutVessel.cpp.gcov.html">ShortcutVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">3 / 3</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ShortcutVessel.h.gcov.html">ShortcutVessel.h</a></td>
+      <td class="coverBar" align="center">
+                <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../snow.png" width=100 height=10 alt="0.0%"></td></tr></table>
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+    <tr>
+      <td class="coverFile"><a href="StoreDataVessel.cpp.gcov.html">StoreDataVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=93 height=10 alt="93.5%"><img src="../snow.png" width=7 height=10 alt="93.5%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">93.5&nbsp;%</td>
+      <td class="coverNumHi">86 / 92</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
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+    <tr>
+      <td class="coverFile"><a href="StoreDataVessel.h.gcov.html">StoreDataVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=92 height=10 alt="92.3%"><img src="../snow.png" width=8 height=10 alt="92.3%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">92.3&nbsp;%</td>
+      <td class="coverNumHi">24 / 26</td>
+      <td class="coverPerMed">85.7&nbsp;%</td>
+      <td class="coverNumMed">6 / 7</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Sum.cpp.gcov.html">Sum.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">15 / 15</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">8 / 8</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ValueVessel.cpp.gcov.html">ValueVessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
+      </td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">32 / 32</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="ValueVessel.h.gcov.html">ValueVessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../emerald.png" width=100 height=10 alt="100.0%"></td></tr></table>
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+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">4 / 4</td>
+      <td class="coverPerHi">-</td>
+      <td class="coverNumHi">0 / 0</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Vessel.cpp.gcov.html">Vessel.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=82 height=10 alt="82.1%"><img src="../snow.png" width=18 height=10 alt="82.1%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">82.1&nbsp;%</td>
+      <td class="coverNumMed">64 / 78</td>
+      <td class="coverPerHi">90.9&nbsp;%</td>
+      <td class="coverNumHi">10 / 11</td>
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+    <tr>
+      <td class="coverFile"><a href="Vessel.h.gcov.html">Vessel.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=81 height=10 alt="80.6%"><img src="../snow.png" width=19 height=10 alt="80.6%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">80.6&nbsp;%</td>
+      <td class="coverNumMed">29 / 36</td>
+      <td class="coverPerHi">90.0&nbsp;%</td>
+      <td class="coverNumHi">9 / 10</td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="VesselRegister.cpp.gcov.html">VesselRegister.cpp</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../amber.png" width=85 height=10 alt="84.8%"><img src="../snow.png" width=15 height=10 alt="84.8%"></td></tr></table>
+      </td>
+      <td class="coverPerMed">84.8&nbsp;%</td>
+      <td class="coverNumMed">28 / 33</td>
+      <td class="coverPerHi">100.0&nbsp;%</td>
+      <td class="coverNumHi">7 / 7</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/wrapper/Plumed.h.func-sort-c.html b/coverage/wrapper/Plumed.h.func-sort-c.html
new file mode 100644
index 0000000000..39be5b1001
--- /dev/null
+++ b/coverage/wrapper/Plumed.h.func-sort-c.html
@@ -0,0 +1,1080 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - wrapper/Plumed.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">wrapper</a> - Plumed.h<span style="font-size: 80%;"> (<a href="Plumed.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">469</td>
+            <td class="headerCovTableEntryLo">52.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
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+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
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diff --git a/coverage/wrapper/Plumed.h.func.html b/coverage/wrapper/Plumed.h.func.html
new file mode 100644
index 0000000000..77ec3aa0e3
--- /dev/null
+++ b/coverage/wrapper/Plumed.h.func.html
@@ -0,0 +1,1080 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - wrapper/Plumed.h - functions</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">wrapper</a> - Plumed.h<span style="font-size: 80%;"> (<a href="Plumed.h.gcov.html">source</a> / functions)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
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+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">469</td>
+            <td class="headerCovTableEntryLo">52.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">252</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
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+
+  <center>
+  <table width="60%" cellpadding=1 cellspacing=1 border=0>
+    <tr><td><br></td></tr>
+    <tr>
+      <td width="80%" class="tableHead">Function Name <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function name" title="Sort by function name" border=0></span></td>
+      <td width="20%" class="tableHead">Hit count <span class="tableHeadSort"><a href="Plumed.h.func-sort-c.html"><img src="../updown.png" width=10 height=14 alt="Sort by hit count" title="Sort by hit count" border=0></a></span></td>
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+              <td class="coverFn"><a href="Plumed.h.gcov.html#3924">plumed_malloc</a></td>
+              <td class="coverFnHi">736225</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#3576">plumed_malloc_pimpl</a></td>
+              <td class="coverFnHi">737505</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#3469">plumed_retrieve_functions</a></td>
+              <td class="coverFnHi">715925</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#3356">plumed_search_symbols</a></td>
+              <td class="coverFnHi">8</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#3438">plumed_symbol_table_reexport</a></td>
+              <td class="coverFnHi">680225</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#3898">plumed_use_count</a></td>
+              <td class="coverFnHi">42</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#4057">plumed_v2c</a></td>
+              <td class="coverFnHi">2</td>
+            </tr>
+    <tr>
+              <td class="coverFn"><a href="Plumed.h.gcov.html#3887">plumed_valid</a></td>
+              <td class="coverFnHi">23</td>
+            </tr>
+  </table>
+  <br>
+  </center>
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/wrapper/Plumed.h.gcov.html b/coverage/wrapper/Plumed.h.gcov.html
new file mode 100644
index 0000000000..4ef640825b
--- /dev/null
+++ b/coverage/wrapper/Plumed.h.gcov.html
@@ -0,0 +1,4315 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - wrapper/Plumed.h</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - <a href="index.html">wrapper</a> - Plumed.h<span style="font-size: 80%;"> (source / <a href="Plumed.h.func-sort-c.html">functions</a>)</span></td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">469</td>
+            <td class="headerCovTableEntryLo">52.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">252</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <table cellpadding=0 cellspacing=0 border=0>
+    <tr>
+      <td><br></td>
+    </tr>
+    <tr>
+      <td>
+<pre class="sourceHeading">          Line data    Source code</pre>
+<pre class="source">
+<a name="1"><span class="lineNum">       1 </span>            : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++</a>
+<a name="2"><span class="lineNum">       2 </span>            :    Copyright (c) 2011-2023 The plumed team</a>
+<a name="3"><span class="lineNum">       3 </span>            :    (see the PEOPLE file at the root of the distribution for a list of names)</a>
+<a name="4"><span class="lineNum">       4 </span>            : </a>
+<a name="5"><span class="lineNum">       5 </span>            :    See http://www.plumed.org for more information.</a>
+<a name="6"><span class="lineNum">       6 </span>            : </a>
+<a name="7"><span class="lineNum">       7 </span>            :    This file is part of plumed, version 2.</a>
+<a name="8"><span class="lineNum">       8 </span>            : </a>
+<a name="9"><span class="lineNum">       9 </span>            :    plumed is free software: you can redistribute it and/or modify</a>
+<a name="10"><span class="lineNum">      10 </span>            :    it under the terms of the GNU Lesser General Public License as published by</a>
+<a name="11"><span class="lineNum">      11 </span>            :    the Free Software Foundation, either version 3 of the License, or</a>
+<a name="12"><span class="lineNum">      12 </span>            :    (at your option) any later version.</a>
+<a name="13"><span class="lineNum">      13 </span>            : </a>
+<a name="14"><span class="lineNum">      14 </span>            :    plumed is distributed in the hope that it will be useful,</a>
+<a name="15"><span class="lineNum">      15 </span>            :    but WITHOUT ANY WARRANTY; without even the implied warranty of</a>
+<a name="16"><span class="lineNum">      16 </span>            :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</a>
+<a name="17"><span class="lineNum">      17 </span>            :    GNU Lesser General Public License for more details.</a>
+<a name="18"><span class="lineNum">      18 </span>            : </a>
+<a name="19"><span class="lineNum">      19 </span>            :    You should have received a copy of the GNU Lesser General Public License</a>
+<a name="20"><span class="lineNum">      20 </span>            :    along with plumed.  If not, see &lt;http://www.gnu.org/licenses/&gt;.</a>
+<a name="21"><span class="lineNum">      21 </span>            : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */</a>
+<a name="22"><span class="lineNum">      22 </span>            : #ifndef __PLUMED_wrapper_Plumed_h</a>
+<a name="23"><span class="lineNum">      23 </span>            : #define __PLUMED_wrapper_Plumed_h</a>
+<a name="24"><span class="lineNum">      24 </span>            : </a>
+<a name="25"><span class="lineNum">      25 </span>            : /*</a>
+<a name="26"><span class="lineNum">      26 </span>            :   This header might be included more than once in order to provide</a>
+<a name="27"><span class="lineNum">      27 </span>            :   the declarations and the definitions. The guard is thus closed before the end of the file</a>
+<a name="28"><span class="lineNum">      28 </span>            :   (match this brace) {</a>
+<a name="29"><span class="lineNum">      29 </span>            :   and a new guard is added for the definitions.</a>
+<a name="30"><span class="lineNum">      30 </span>            : */</a>
+<a name="31"><span class="lineNum">      31 </span>            : </a>
+<a name="32"><span class="lineNum">      32 </span>            : /**</a>
+<a name="33"><span class="lineNum">      33 </span>            : \page ReferencePlumedH Reference for interfacing MD codes with PLUMED</a>
+<a name="34"><span class="lineNum">      34 </span>            : </a>
+<a name="35"><span class="lineNum">      35 </span>            :   Plumed.h and Plumed.c contain the external plumed interface, which is used to</a>
+<a name="36"><span class="lineNum">      36 </span>            :   integrate it with MD engines. This interface is very general, and is expected</a>
+<a name="37"><span class="lineNum">      37 </span>            :   not to change across plumed versions. Plumed.c also implements a dummy version</a>
+<a name="38"><span class="lineNum">      38 </span>            :   of the interface, so as to allow a code to be fully linked even if the plumed</a>
+<a name="39"><span class="lineNum">      39 </span>            :   library is not available yet. These files could be directly included in the official</a>
+<a name="40"><span class="lineNum">      40 </span>            :   host MD distribution. In this manner, it will be sufficient to link the plumed</a>
+<a name="41"><span class="lineNum">      41 </span>            :   library at link time (on all systems) or directly at runtime (on systems where</a>
+<a name="42"><span class="lineNum">      42 </span>            :   dynamic loading is enabled) to include plumed features.</a>
+<a name="43"><span class="lineNum">      43 </span>            : </a>
+<a name="44"><span class="lineNum">      44 </span>            :   Notice that in PLUMED 2.5 this interface has been rewritten in order to allow</a>
+<a name="45"><span class="lineNum">      45 </span>            :   more debugging features and a better behavior in multithread environments.</a>
+<a name="46"><span class="lineNum">      46 </span>            :   The interface is almost perfectly backward compatible, although it implements</a>
+<a name="47"><span class="lineNum">      47 </span>            :   a few additional functions. See more details below.</a>
+<a name="48"><span class="lineNum">      48 </span>            : </a>
+<a name="49"><span class="lineNum">      49 </span>            :   A further improvement has been made in PLUMED 2.8, where the interface has</a>
+<a name="50"><span class="lineNum">      50 </span>            :   been modified to allow dynamic type checking. See more details below.</a>
+<a name="51"><span class="lineNum">      51 </span>            : </a>
+<a name="52"><span class="lineNum">      52 </span>            :   Why is Plumed.c written in C and not C++? The reason is that the resulting Plumed.o</a>
+<a name="53"><span class="lineNum">      53 </span>            :   needs to be linked with the host MD code immediately (whereas the rest of plumed</a>
+<a name="54"><span class="lineNum">      54 </span>            :   could be linked a posteriori). Imagine the MD code is written in FORTRAN: when we</a>
+<a name="55"><span class="lineNum">      55 </span>            :   link the Plumed.o file we would like not to need any C++ library linked. In this</a>
+<a name="56"><span class="lineNum">      56 </span>            :   manner, we do not need to know which C++ compiler will be used to compile plumed.</a>
+<a name="57"><span class="lineNum">      57 </span>            :   The C++ library is only linked to the &quot;rest&quot; of plumed, which actually uses it.</a>
+<a name="58"><span class="lineNum">      58 </span>            :   Anyway, Plumed.c is written in such a manner to allow its compilation also in C++</a>
+<a name="59"><span class="lineNum">      59 </span>            :   (C++ is a bit stricter than C). This will</a>
+<a name="60"><span class="lineNum">      60 </span>            :   allow e.g. MD codes written in C++ to just incorporate Plumed.c (maybe renamed into</a>
+<a name="61"><span class="lineNum">      61 </span>            :   Plumed.cpp), without the need of configuring a plain C compiler.</a>
+<a name="62"><span class="lineNum">      62 </span>            : </a>
+<a name="63"><span class="lineNum">      63 </span>            :   Plumed interface can be used from C, C++ and FORTRAN. Everything concerning plumed</a>
+<a name="64"><span class="lineNum">      64 </span>            :   is hidden inside a single object type, which is described in C by a structure</a>
+<a name="65"><span class="lineNum">      65 </span>            :   (struct \ref plumed), in C++ by a class (PLMD::Plumed) and in FORTRAN by a</a>
+<a name="66"><span class="lineNum">      66 </span>            :   fixed-length string (CHARACTER(LEN=32)). Obviously C++ can use both struct</a>
+<a name="67"><span class="lineNum">      67 </span>            :   and class interfaces, but the second should be preferred since it will automatically take</a>
+<a name="68"><span class="lineNum">      68 </span>            :   care of objects constructions and destructions. The reference interface</a>
+<a name="69"><span class="lineNum">      69 </span>            :   is the C one, whereas FORTRAN and C++ interfaces are implemented as wrappers</a>
+<a name="70"><span class="lineNum">      70 </span>            :   around it.</a>
+<a name="71"><span class="lineNum">      71 </span>            :   In the C++ interface, all the routines are implemented as methods of PLMD::Plumed.</a>
+<a name="72"><span class="lineNum">      72 </span>            :   In the C and FORTRAN interfaces, all the routines are named plumed_*, to</a>
+<a name="73"><span class="lineNum">      73 </span>            :   avoid potential name clashes. Notice that the entire plumed library</a>
+<a name="74"><span class="lineNum">      74 </span>            :   is implemented in C++, and it is hidden inside the PLMD namespace.</a>
+<a name="75"><span class="lineNum">      75 </span>            : </a>
+<a name="76"><span class="lineNum">      76 </span>            :   Handlers to the plumed object can be converted among different representations,</a>
+<a name="77"><span class="lineNum">      77 </span>            :   to allow inter-operability among languages. In C, there are tools to convert</a>
+<a name="78"><span class="lineNum">      78 </span>            :   to/from FORTRAN, whereas in C++ there are tools to convert to/from FORTRAN and C.</a>
+<a name="79"><span class="lineNum">      79 </span>            : </a>
+<a name="80"><span class="lineNum">      80 </span>            :   These handlers only contain a pointer to the real structure, so that</a>
+<a name="81"><span class="lineNum">      81 </span>            :   when a plumed object is brought from one language to another,</a>
+<a name="82"><span class="lineNum">      82 </span>            :   it brings a reference to the same environment.</a>
+<a name="83"><span class="lineNum">      83 </span>            : </a>
+<a name="84"><span class="lineNum">      84 </span>            :   Moreover, to simplify life in all cases where a single Plumed object is</a>
+<a name="85"><span class="lineNum">      85 </span>            :   required for the entire simulation (which covers many of the practical</a>
+<a name="86"><span class="lineNum">      86 </span>            :   applications with conventional MD codes) it is possible to take advantage</a>
+<a name="87"><span class="lineNum">      87 </span>            :   of a global interface, which is implicitly referring to a unique global instance.</a>
+<a name="88"><span class="lineNum">      88 </span>            :   The global object should still be initialized and finalized properly.</a>
+<a name="89"><span class="lineNum">      89 </span>            :   This global object is obviously not usable in a multithread context. In addition,</a>
+<a name="90"><span class="lineNum">      90 </span>            :   it is difficult to use it in an exception-safe manner, so its usage in C++ is</a>
+<a name="91"><span class="lineNum">      91 </span>            :   allowed but discouraged.</a>
+<a name="92"><span class="lineNum">      92 </span>            : </a>
+<a name="93"><span class="lineNum">      93 </span>            :   As of PLUMED 2.5, the interface contains a reference counter that allows</a>
+<a name="94"><span class="lineNum">      94 </span>            :   for a better control of plumed initializations and deallocations.</a>
+<a name="95"><span class="lineNum">      95 </span>            :   This is particularly useful for the C++ interface that now</a>
+<a name="96"><span class="lineNum">      96 </span>            :   behaves similarly to a primitive shared pointer and can be thus copied.</a>
+<a name="97"><span class="lineNum">      97 </span>            :   In other languages, to use the reference counter correctly it is sufficient to</a>
+<a name="98"><span class="lineNum">      98 </span>            :   remember the following rule: for any `plumed_create*` call, there should be a corresponding</a>
+<a name="99"><span class="lineNum">      99 </span>            :   `plumed_finalize` call. More examples can be found below.</a>
+<a name="100"><span class="lineNum">     100 </span>            : </a>
+<a name="101"><span class="lineNum">     101 </span>            :   Notice that up to PLUMED 2.8 the reference counter was not thread safe. This is fixed</a>
+<a name="102"><span class="lineNum">     102 </span>            :   when using PLUMED&gt;=2.9 wrappers with a PLUMED&gt;=2.9 kernel.</a>
+<a name="103"><span class="lineNum">     103 </span>            : </a>
+<a name="104"><span class="lineNum">     104 </span>            :   The basic method to send a message to plumed is</a>
+<a name="105"><span class="lineNum">     105 </span>            : \verbatim</a>
+<a name="106"><span class="lineNum">     106 </span>            :   (C) plumed_cmd</a>
+<a name="107"><span class="lineNum">     107 </span>            :   (C++) PLMD::Plumed::cmd</a>
+<a name="108"><span class="lineNum">     108 </span>            :   (FORTRAN)  PLUMED_F_CMD</a>
+<a name="109"><span class="lineNum">     109 </span>            : \endverbatim</a>
+<a name="110"><span class="lineNum">     110 </span>            : </a>
+<a name="111"><span class="lineNum">     111 </span>            :   To initialize a plumed object, use:</a>
+<a name="112"><span class="lineNum">     112 </span>            : \verbatim</a>
+<a name="113"><span class="lineNum">     113 </span>            :   (C)        plumed_create</a>
+<a name="114"><span class="lineNum">     114 </span>            :   (C++)      (constructor of PLMD::Plumed)</a>
+<a name="115"><span class="lineNum">     115 </span>            :   (FORTRAN)  PLUMED_F_CREATE</a>
+<a name="116"><span class="lineNum">     116 </span>            : \endverbatim</a>
+<a name="117"><span class="lineNum">     117 </span>            : </a>
+<a name="118"><span class="lineNum">     118 </span>            :   As of PLUMED 2.5, you can also initialize a plumed object using the following functions,</a>
+<a name="119"><span class="lineNum">     119 </span>            :   that load a specific kernel. The function plumed_create_dlopen2 allows to specify options</a>
+<a name="120"><span class="lineNum">     120 </span>            :   for dlopen. The C++ version accepts an optional argument to this aim.</a>
+<a name="121"><span class="lineNum">     121 </span>            : \verbatim</a>
+<a name="122"><span class="lineNum">     122 </span>            :   (C)        plumed_create_dlopen or plumed_create_dlopen2</a>
+<a name="123"><span class="lineNum">     123 </span>            :   (C++)      PLMD::Plumed::dlopen</a>
+<a name="124"><span class="lineNum">     124 </span>            :   (FORTRAN)  PLUMED_F_CREATE_DLOPEN</a>
+<a name="125"><span class="lineNum">     125 </span>            : \endverbatim</a>
+<a name="126"><span class="lineNum">     126 </span>            : </a>
+<a name="127"><span class="lineNum">     127 </span>            :   As of PLUMED 2.8, you can also initialize a plumed object using the following function,</a>
+<a name="128"><span class="lineNum">     128 </span>            :   that loads a kernel from an already loaded shared library. It accepts a handler</a>
+<a name="129"><span class="lineNum">     129 </span>            :   returned by `dlopen`:</a>
+<a name="130"><span class="lineNum">     130 </span>            : \verbatim</a>
+<a name="131"><span class="lineNum">     131 </span>            :   (C)        plumed_create_dlsym</a>
+<a name="132"><span class="lineNum">     132 </span>            :   (C++)      PLMD::Plumed::dlsym</a>
+<a name="133"><span class="lineNum">     133 </span>            :   (FORTRAN not allowed)</a>
+<a name="134"><span class="lineNum">     134 </span>            : \endverbatim</a>
+<a name="135"><span class="lineNum">     135 </span>            : </a>
+<a name="136"><span class="lineNum">     136 </span>            :   To finalize a plumed object, use</a>
+<a name="137"><span class="lineNum">     137 </span>            : \verbatim</a>
+<a name="138"><span class="lineNum">     138 </span>            :   (C)        plumed_finalize</a>
+<a name="139"><span class="lineNum">     139 </span>            :   (C++)      (destructor of PLMD::Plumed)</a>
+<a name="140"><span class="lineNum">     140 </span>            :   (FORTRAN)  PLUMED_F_FINALIZE</a>
+<a name="141"><span class="lineNum">     141 </span>            : \endverbatim</a>
+<a name="142"><span class="lineNum">     142 </span>            : </a>
+<a name="143"><span class="lineNum">     143 </span>            :   To access to the global-object, use</a>
+<a name="144"><span class="lineNum">     144 </span>            : \verbatim</a>
+<a name="145"><span class="lineNum">     145 </span>            :   (C)        plumed_gcreate, plumed_gfinalize, plumed_gcmd</a>
+<a name="146"><span class="lineNum">     146 </span>            :   (C++)      PLMD::Plumed::gcreate, PLMD::Plumed::gfinalize, PLMD::Plumed::gcmd</a>
+<a name="147"><span class="lineNum">     147 </span>            :   (FORTRAN)  PLUMED_F_GCREATE, PLUMED_F_GFINALIZE, PLUMED_F_GCMD</a>
+<a name="148"><span class="lineNum">     148 </span>            : \endverbatim</a>
+<a name="149"><span class="lineNum">     149 </span>            : </a>
+<a name="150"><span class="lineNum">     150 </span>            :   To check if the global object has been initialized, use</a>
+<a name="151"><span class="lineNum">     151 </span>            : \verbatim</a>
+<a name="152"><span class="lineNum">     152 </span>            :   (C)        plumed_ginitialized</a>
+<a name="153"><span class="lineNum">     153 </span>            :   (C++)      PLMD::Plumed::ginitialized</a>
+<a name="154"><span class="lineNum">     154 </span>            :   (FORTRAN)  PLUMED_F_GINITIALIZED</a>
+<a name="155"><span class="lineNum">     155 </span>            : \endverbatim</a>
+<a name="156"><span class="lineNum">     156 </span>            : </a>
+<a name="157"><span class="lineNum">     157 </span>            :   Notice that when using runtime binding the plumed library might be not available.</a>
+<a name="158"><span class="lineNum">     158 </span>            :   In this case, plumed_create (and plumed_gcreate) will still succeed, but a subsequent</a>
+<a name="159"><span class="lineNum">     159 </span>            :   call to plumed_cmd (or plumed_gcmd) would exit. In order to avoid this</a>
+<a name="160"><span class="lineNum">     160 </span>            :   unpleasant situation you have two options.</a>
+<a name="161"><span class="lineNum">     161 </span>            : </a>
+<a name="162"><span class="lineNum">     162 </span>            :   First, you can check if plumed library is available before actually creating an object</a>
+<a name="163"><span class="lineNum">     163 </span>            :   using this function:</a>
+<a name="164"><span class="lineNum">     164 </span>            : \verbatim</a>
+<a name="165"><span class="lineNum">     165 </span>            :   (C)        plumed_installed</a>
+<a name="166"><span class="lineNum">     166 </span>            :   (C++)      PLMD::Plumed::installed</a>
+<a name="167"><span class="lineNum">     167 </span>            :   (FORTRAN)  PLUMED_F_INSTALLED</a>
+<a name="168"><span class="lineNum">     168 </span>            : \endverbatim</a>
+<a name="169"><span class="lineNum">     169 </span>            : </a>
+<a name="170"><span class="lineNum">     170 </span>            :   Alternatively, as of PLUMED 2.5, you can interrogate the just created plumed</a>
+<a name="171"><span class="lineNum">     171 </span>            :   object using the following function:</a>
+<a name="172"><span class="lineNum">     172 </span>            : \verbatim</a>
+<a name="173"><span class="lineNum">     173 </span>            :   (C)        plumed_valid</a>
+<a name="174"><span class="lineNum">     174 </span>            :   (C++)      PLMD::Plumed::valid</a>
+<a name="175"><span class="lineNum">     175 </span>            :   (FORTRAN)  PLUMED_F_VALID</a>
+<a name="176"><span class="lineNum">     176 </span>            : \endverbatim</a>
+<a name="177"><span class="lineNum">     177 </span>            : </a>
+<a name="178"><span class="lineNum">     178 </span>            :   If you want to create on purpose an invalid Plumed object (useful in C++ to postpone</a>
+<a name="179"><span class="lineNum">     179 </span>            :   the loading of the library) you can use `Plumed p(Plumed::makeInvalid());`.</a>
+<a name="180"><span class="lineNum">     180 </span>            : </a>
+<a name="181"><span class="lineNum">     181 </span>            :   To know if the global object is valid instead you should use the following function:</a>
+<a name="182"><span class="lineNum">     182 </span>            : \verbatim</a>
+<a name="183"><span class="lineNum">     183 </span>            :   (C)        plumed_gvalid</a>
+<a name="184"><span class="lineNum">     184 </span>            :   (C++)      PLMD::Plumed::gvalid</a>
+<a name="185"><span class="lineNum">     185 </span>            :   (FORTRAN)  PLUMED_F_GVALID</a>
+<a name="186"><span class="lineNum">     186 </span>            : \endverbatim</a>
+<a name="187"><span class="lineNum">     187 </span>            : </a>
+<a name="188"><span class="lineNum">     188 </span>            :   To convert handlers between different languages, use</a>
+<a name="189"><span class="lineNum">     189 </span>            : \verbatim</a>
+<a name="190"><span class="lineNum">     190 </span>            :   (C)        plumed_c2f                 (C to FORTRAN)</a>
+<a name="191"><span class="lineNum">     191 </span>            :   (C)        plumed_f2c                 (FORTRAN to C)</a>
+<a name="192"><span class="lineNum">     192 </span>            :   (C++)      Plumed(plumed) constructor (C to C++)</a>
+<a name="193"><span class="lineNum">     193 </span>            :   (C++)      operator plumed() cast     (C++ to C)</a>
+<a name="194"><span class="lineNum">     194 </span>            :   (C++)      Plumed(char*)  constructor (FORTRAN to C++)</a>
+<a name="195"><span class="lineNum">     195 </span>            :   (C++)      toFortran(char*)           (C++ to FORTRAN)</a>
+<a name="196"><span class="lineNum">     196 </span>            : \endverbatim</a>
+<a name="197"><span class="lineNum">     197 </span>            : </a>
+<a name="198"><span class="lineNum">     198 </span>            :   As of PLUMED 2.5, when using C or C++ we allow a user to explicitly store a plumed object as</a>
+<a name="199"><span class="lineNum">     199 </span>            :   a void pointer (indeed: that's the only thing contained in a plumed object).</a>
+<a name="200"><span class="lineNum">     200 </span>            :   This might be useful in case you do not want to include the Plumed.h header in some</a>
+<a name="201"><span class="lineNum">     201 </span>            :   of your headers. In order to convert to/from void pointers you can use the following functions</a>
+<a name="202"><span class="lineNum">     202 </span>            : \verbatim</a>
+<a name="203"><span class="lineNum">     203 </span>            :   (C)        plumed_v2c                 (void* to C)</a>
+<a name="204"><span class="lineNum">     204 </span>            :   (C)        plumed_c2v                 (C to void*)</a>
+<a name="205"><span class="lineNum">     205 </span>            :   (C++)      Plumed(void*) constructor  (void* to C++)</a>
+<a name="206"><span class="lineNum">     206 </span>            :   (C++)      toVoid()                   (C++ to void*)</a>
+<a name="207"><span class="lineNum">     207 </span>            : \endverbatim</a>
+<a name="208"><span class="lineNum">     208 </span>            :   Using the functions above is much safer than accessing directly the pointer contained in the \ref plumed struct</a>
+<a name="209"><span class="lineNum">     209 </span>            :   since, when compiling with debug options, it will check if the void pointer actually points to a plumed object.</a>
+<a name="210"><span class="lineNum">     210 </span>            : </a>
+<a name="211"><span class="lineNum">     211 </span>            :   As of PLUMED 2.5, we added a reference count. It is in practice possible</a>
+<a name="212"><span class="lineNum">     212 </span>            :   to create multiple `plumed` objects that refer to the same environment.</a>
+<a name="213"><span class="lineNum">     213 </span>            :   This is done using the following functions</a>
+<a name="214"><span class="lineNum">     214 </span>            : \verbatim</a>
+<a name="215"><span class="lineNum">     215 </span>            :   (C)        plumed_create_reference     (from a C object)</a>
+<a name="216"><span class="lineNum">     216 </span>            :   (C)        plumed_create_reference_f   (from a FORTRAN object)</a>
+<a name="217"><span class="lineNum">     217 </span>            :   (C)        plumed_create_reference_v   (from a void pointer)</a>
+<a name="218"><span class="lineNum">     218 </span>            :   (FORTRAN)  plumed_f_create_reference   (from a FORTRAN object)</a>
+<a name="219"><span class="lineNum">     219 </span>            : \endverbatim</a>
+<a name="220"><span class="lineNum">     220 </span>            :   In C++ references are managed automatically by constructors and destructor.</a>
+<a name="221"><span class="lineNum">     221 </span>            :   In addition, you can manually manage them (with care!) using incref() and decref().</a>
+<a name="222"><span class="lineNum">     222 </span>            : </a>
+<a name="223"><span class="lineNum">     223 </span>            :   The interface of the FORTRAN functions is very similar to that of the C functions</a>
+<a name="224"><span class="lineNum">     224 </span>            :   and is listed below:</a>
+<a name="225"><span class="lineNum">     225 </span>            : </a>
+<a name="226"><span class="lineNum">     226 </span>            : \verbatim</a>
+<a name="227"><span class="lineNum">     227 </span>            :   FORTRAN interface</a>
+<a name="228"><span class="lineNum">     228 </span>            :     SUBROUTINE PLUMED_F_CREATE(p)</a>
+<a name="229"><span class="lineNum">     229 </span>            :       CHARACTER(LEN=32), INTENT(OUT)   :: p</a>
+<a name="230"><span class="lineNum">     230 </span>            :     SUBROUTINE PLUMED_F_CREATE_DLOPEN(p,path)</a>
+<a name="231"><span class="lineNum">     231 </span>            :       CHARACTER(LEN=32), INTENT(OUT)   :: p</a>
+<a name="232"><span class="lineNum">     232 </span>            :       CHARACTER(LEN=*),  INTENT(IN)    :: path</a>
+<a name="233"><span class="lineNum">     233 </span>            :     SUBROUTINE PLUMED_F_CREATE_REFERENCE(p,r)</a>
+<a name="234"><span class="lineNum">     234 </span>            :       CHARACTER(LEN=32), INTENT(OUT)   :: p</a>
+<a name="235"><span class="lineNum">     235 </span>            :       CHARACTER(LEN=32), INTENT(IN)    :: r</a>
+<a name="236"><span class="lineNum">     236 </span>            :     SUBROUTINE PLUMED_F_CREATE_INVALID(p)</a>
+<a name="237"><span class="lineNum">     237 </span>            :       CHARACTER(LEN=32), INTENT(OUT)   :: p</a>
+<a name="238"><span class="lineNum">     238 </span>            :     SUBROUTINE PLUMED_F_CMD(p,key,val)</a>
+<a name="239"><span class="lineNum">     239 </span>            :       CHARACTER(LEN=32), INTENT(IN)    :: p</a>
+<a name="240"><span class="lineNum">     240 </span>            :       CHARACTER(LEN=*),  INTENT(IN)    :: key</a>
+<a name="241"><span class="lineNum">     241 </span>            :       UNSPECIFIED_TYPE,  INTENT(INOUT) :: val(*)</a>
+<a name="242"><span class="lineNum">     242 </span>            :     SUBROUTINE PLUMED_F_FINALIZE(p)</a>
+<a name="243"><span class="lineNum">     243 </span>            :       CHARACTER(LEN=32), INTENT(IN)    :: p</a>
+<a name="244"><span class="lineNum">     244 </span>            :     SUBROUTINE PLUMED_F_INSTALLED(i)</a>
+<a name="245"><span class="lineNum">     245 </span>            :       INTEGER,           INTENT(OUT)   :: i</a>
+<a name="246"><span class="lineNum">     246 </span>            :     SUBROUTINE PLUMED_F_VALID(p,i)</a>
+<a name="247"><span class="lineNum">     247 </span>            :       CHARACTER(LEN=32), INTENT(IN)    :: p</a>
+<a name="248"><span class="lineNum">     248 </span>            :       INTEGER,           INTENT(OUT)   :: i</a>
+<a name="249"><span class="lineNum">     249 </span>            :     SUBROUTINE PLUMED_F_USE_COUNT(p,i)</a>
+<a name="250"><span class="lineNum">     250 </span>            :       CHARACTER(LEN=32), INTENT(IN)    :: p</a>
+<a name="251"><span class="lineNum">     251 </span>            :       INTEGER,           INTENT(OUT)   :: i</a>
+<a name="252"><span class="lineNum">     252 </span>            :     SUBROUTINE PLUMED_F_GLOBAL(p)</a>
+<a name="253"><span class="lineNum">     253 </span>            :       CHARACTER(LEN=32), INTENT(OUT)   :: p</a>
+<a name="254"><span class="lineNum">     254 </span>            :     SUBROUTINE PLUMED_F_GINITIALIZED(i)</a>
+<a name="255"><span class="lineNum">     255 </span>            :       INTEGER,           INTENT(OUT)   :: i</a>
+<a name="256"><span class="lineNum">     256 </span>            :     SUBROUTINE PLUMED_F_GCREATE()</a>
+<a name="257"><span class="lineNum">     257 </span>            :     SUBROUTINE PLUMED_F_GCMD(key,val)</a>
+<a name="258"><span class="lineNum">     258 </span>            :       CHARACTER(LEN=*), INTENT(IN)     :: key</a>
+<a name="259"><span class="lineNum">     259 </span>            :       UNSPECIFIED_TYPE, INTENT(INOUT)  :: val(*)</a>
+<a name="260"><span class="lineNum">     260 </span>            :     SUBROUTINE PLUMED_F_GFINALIZE()</a>
+<a name="261"><span class="lineNum">     261 </span>            :     SUBROUTINE PLUMED_F_GVALID(i)</a>
+<a name="262"><span class="lineNum">     262 </span>            :       INTEGER,           INTENT(OUT)   :: i</a>
+<a name="263"><span class="lineNum">     263 </span>            : \endverbatim</a>
+<a name="264"><span class="lineNum">     264 </span>            : </a>
+<a name="265"><span class="lineNum">     265 </span>            :   Almost all C functions have a corresponding FORTRAN function.</a>
+<a name="266"><span class="lineNum">     266 </span>            :   As a simple mnemonic, if you know the name of the C function you can obtain the</a>
+<a name="267"><span class="lineNum">     267 </span>            :   corresponding FORTRAN subroutine by adding `F_` after the `PLUMED_` prefix.</a>
+<a name="268"><span class="lineNum">     268 </span>            :   In addition, all `plumed` objects are replaced by `CHARACTER(LEN=32)` objects</a>
+<a name="269"><span class="lineNum">     269 </span>            :   holding the same information. These pointers basically contain a text representation</a>
+<a name="270"><span class="lineNum">     270 </span>            :   of the stored pointer, that is suitable to be contained in a string.</a>
+<a name="271"><span class="lineNum">     271 </span>            :   Finally, whenever a C function returns a value,</a>
+<a name="272"><span class="lineNum">     272 </span>            :   the corresponding FORTRAN subroutine will have an additional `INTENT(OUT)` parameter</a>
+<a name="273"><span class="lineNum">     273 </span>            :   passed as the its last argument.</a>
+<a name="274"><span class="lineNum">     274 </span>            : </a>
+<a name="275"><span class="lineNum">     275 </span>            :   When you compile the FORTRAN interface, wrapper functions are added with several possible</a>
+<a name="276"><span class="lineNum">     276 </span>            :   name manglings, so you should not experience problems linking the plumed library with a FORTRAN file.</a>
+<a name="277"><span class="lineNum">     277 </span>            : </a>
+<a name="278"><span class="lineNum">     278 </span>            : \section ReferencePlumedH-exceptions Error handling</a>
+<a name="279"><span class="lineNum">     279 </span>            : </a>
+<a name="280"><span class="lineNum">     280 </span>            :   In case an error is detected by PLUMED, either because of some user error, some internal bug,</a>
+<a name="281"><span class="lineNum">     281 </span>            :   or some mistake in using the library, an exception will be thrown. The behavior is different depending if you use</a>
+<a name="282"><span class="lineNum">     282 </span>            :   PLUMED from C/FORTRAN or from C++.</a>
+<a name="283"><span class="lineNum">     283 </span>            : </a>
+<a name="284"><span class="lineNum">     284 </span>            :   First of all, notice that access to PLUMED goes through three functions:</a>
+<a name="285"><span class="lineNum">     285 </span>            :   - plumed_create: this, as of PLUMED 2.5, is guaranteed not to throw any exception. If there is a problem, it will</a>
+<a name="286"><span class="lineNum">     286 </span>            :     just return a plumed object containing a NULL pointer</a>
+<a name="287"><span class="lineNum">     287 </span>            :   - plumed_cmd: this function might throw exceptions.</a>
+<a name="288"><span class="lineNum">     288 </span>            :   - plumed_finalize: this is a destructor and is guaranteed not to throw any exception.</a>
+<a name="289"><span class="lineNum">     289 </span>            : </a>
+<a name="290"><span class="lineNum">     290 </span>            :   The following discussion concerns all the exceptions thrown by plumed_cmd.</a>
+<a name="291"><span class="lineNum">     291 </span>            : </a>
+<a name="292"><span class="lineNum">     292 </span>            :   If you use C/FORTRAN, you will basically have no way to intercept the exception and the program will just terminate.</a>
+<a name="293"><span class="lineNum">     293 </span>            : </a>
+<a name="294"><span class="lineNum">     294 </span>            :   If you use C++ and you are calling the C++ interface (e.g. \ref Plumed::cmd), as of PLUMED 2.5 we implemented a complete</a>
+<a name="295"><span class="lineNum">     295 </span>            :   remapping of the exceptions thrown by PLUMED.  This solves both the problems mentioned above. In particular:</a>
+<a name="296"><span class="lineNum">     296 </span>            :   - Instead of throwing an exception, PLUMED will return (using a \ref plumed_nothrow_handler) the details about the occurred error.</a>
+<a name="297"><span class="lineNum">     297 </span>            :   - An equivalent exception will be thrown within the inline PLUMED interface compiled with your MD code.</a>
+<a name="298"><span class="lineNum">     298 </span>            : </a>
+<a name="299"><span class="lineNum">     299 </span>            :   As a consequence, you will be able to combine different compilers and avoid stack unwinding in the C layer.</a>
+<a name="300"><span class="lineNum">     300 </span>            : </a>
+<a name="301"><span class="lineNum">     301 </span>            :   If you use C++ but you are calling the C interface (e.g. \ref plumed_cmd), then you might be</a>
+<a name="302"><span class="lineNum">     302 </span>            :   able to catch the exceptions thrown by PLUMED. Notice that all the exceptions thrown by PLUMED inherit from std::exception,</a>
+<a name="303"><span class="lineNum">     303 </span>            :   so you might want to catch it by reference. By default, as of PLUMED 2.8 \ref plumed_cmd is redefined as a macro and directly calls</a>
+<a name="304"><span class="lineNum">     304 </span>            :   the \ref Plumed::cmd interface, and thus behaves in an equivalent manner. With previous versions of this header</a>
+<a name="305"><span class="lineNum">     305 </span>            :   one could have encountered problems with stack unwinding performed during exception handling in the C layer.</a>
+<a name="306"><span class="lineNum">     306 </span>            : </a>
+<a name="307"><span class="lineNum">     307 </span>            :   Notice that, even if you use \ref Plumed::cmd, if you are loading a kernel &lt;=2.4 any exception generated by PLUMED will</a>
+<a name="308"><span class="lineNum">     308 </span>            :   leak through the C layer. This might lead to undefined behavior. If you are lucky (with some compiler it works!) and</a>
+<a name="309"><span class="lineNum">     309 </span>            :   the exception arrives to C, PLUMED will catch it and rethrow it as it would do if you were using a kernel &gt;=2.5.</a>
+<a name="310"><span class="lineNum">     310 </span>            : </a>
+<a name="311"><span class="lineNum">     311 </span>            :   The remapping of exceptions takes care of all the standard C++ exceptions plus all the exceptions raised within</a>
+<a name="312"><span class="lineNum">     312 </span>            :   PLUMED. Unexpected exceptions that are derived from std::exception will be rethrown as std::exception.</a>
+<a name="313"><span class="lineNum">     313 </span>            :   Notice that this implies some loss of information, since the original exception might have been of a different type.</a>
+<a name="314"><span class="lineNum">     314 </span>            :   However, it also implies that the virtual table of the original exception won't be needed anymore. This allows to</a>
+<a name="315"><span class="lineNum">     315 </span>            :   completely decouple the MD code from the PLUMED library.</a>
+<a name="316"><span class="lineNum">     316 </span>            : </a>
+<a name="317"><span class="lineNum">     317 </span>            : \section ReferencePlumedH-typesafe Typesafe interface</a>
+<a name="318"><span class="lineNum">     318 </span>            : </a>
+<a name="319"><span class="lineNum">     319 </span>            :   Starting with PLUMED 2.8, the `cmd` function of the C++ interface, and the similar function `gcmd`, can be called</a>
+<a name="320"><span class="lineNum">     320 </span>            :   with several interfaces and can perform a typechecking on the passed argument. In particular, the following</a>
+<a name="321"><span class="lineNum">     321 </span>            :   forms are now possible:</a>
+<a name="322"><span class="lineNum">     322 </span>            : \verbatim</a>
+<a name="323"><span class="lineNum">     323 </span>            :   cmd(&quot;string&quot;,value);        // by value</a>
+<a name="324"><span class="lineNum">     324 </span>            :   cmd(&quot;string&quot;,&amp;value);       // by pointer</a>
+<a name="325"><span class="lineNum">     325 </span>            :   cmd(&quot;string&quot;,&amp;value,nelem); // by pointer, specifying the number of elements of the passed array</a>
+<a name="326"><span class="lineNum">     326 </span>            :   cmd(&quot;string&quot;,&amp;value,shape); // by pointer, specifying the shape of the passed array</a>
+<a name="327"><span class="lineNum">     327 </span>            : \endverbati</a>
+<a name="328"><span class="lineNum">     328 </span>            :   The `nelem` and `shape` arguments are used by PLUMED to check that the user</a>
+<a name="329"><span class="lineNum">     329 </span>            :   provided enough elements. If nelem is provided, the check is done on the flatten array, whereas if shape</a>
+<a name="330"><span class="lineNum">     330 </span>            :   is passed a more thorough check is performed controlling each of the dimensions of the array.</a>
+<a name="331"><span class="lineNum">     331 </span>            :   In addition to this, the type of the pointer (or of the value) is checked at runtime.</a>
+<a name="332"><span class="lineNum">     332 </span>            : </a>
+<a name="333"><span class="lineNum">     333 </span>            :   All these checks are only implemented if the PLUMED library is recent (&gt;=2.8). However, it will still be</a>
+<a name="334"><span class="lineNum">     334 </span>            :   possible to load at runtime an older PLUMED library (&lt;=2.7). For this reason, it is still compulsory</a>
+<a name="335"><span class="lineNum">     335 </span>            :   to pass the correct types to the `cmd` function, also when the argument is passed by value.</a>
+<a name="336"><span class="lineNum">     336 </span>            :   Type conversions are only performed between pointers and only in ways compatible with</a>
+<a name="337"><span class="lineNum">     337 </span>            :   what is allowed in C++ (e.g., `const void*` cannot be converted to `void*`, but `void*` can</a>
+<a name="338"><span class="lineNum">     338 </span>            :   be converted to `const void*`).</a>
+<a name="339"><span class="lineNum">     339 </span>            : </a>
+<a name="340"><span class="lineNum">     340 </span>            :   Type checkes can be disabled in two ways:</a>
+<a name="341"><span class="lineNum">     341 </span>            :   - By compiling `Plumed.h` with `-D__PLUMED_WRAPPER_CXX_TYPESAFE=0`</a>
+<a name="342"><span class="lineNum">     342 </span>            :   - By setting `export PLUMED_TYPESAFE_IGNORE=yes` at runtime.</a>
+<a name="343"><span class="lineNum">     343 </span>            : </a>
+<a name="344"><span class="lineNum">     344 </span>            :   Typechecks are also enabled in the C interface (plumed_cmd). This function is replaced with a macro by default.</a>
+<a name="345"><span class="lineNum">     345 </span>            :   In particular:</a>
+<a name="346"><span class="lineNum">     346 </span>            :   - If the C interface is used in C++ code, it calls the C++ interface. Can be disabled with `-D__PLUMED_WRAPPER_CXX_BIND_C=0`.</a>
+<a name="347"><span class="lineNum">     347 </span>            :   - If the C interface is used in C code and compiled with a C11 compiler, it uses _Generic to pass type information.</a>
+<a name="348"><span class="lineNum">     348 </span>            :     Can be disabled using `-D__PLUMED_WRAPPER_C_TYPESAFE=0`.</a>
+<a name="349"><span class="lineNum">     349 </span>            : </a>
+<a name="350"><span class="lineNum">     350 </span>            : \section ReferencePlumedH-2-5 New in PLUMED 2.5</a>
+<a name="351"><span class="lineNum">     351 </span>            : </a>
+<a name="352"><span class="lineNum">     352 </span>            :   The wrappers in PLUMED 2.5 have been completely rewritten with several improvements.</a>
+<a name="353"><span class="lineNum">     353 </span>            :   The interface is almost perfectly backward compatible, although the behavior of C++ constructors</a>
+<a name="354"><span class="lineNum">     354 </span>            :   has been modified slightly.</a>
+<a name="355"><span class="lineNum">     355 </span>            :   In addition, a few new functions are introduced (explicitly marked in the documentation).</a>
+<a name="356"><span class="lineNum">     356 </span>            :   As a consequence, if your code uses some of the new functions, you will not be able</a>
+<a name="357"><span class="lineNum">     357 </span>            :   to link it directly with an older PLUMED library (though you will still be able to load</a>
+<a name="358"><span class="lineNum">     358 </span>            :   an older PLUMED library at runtime). In addition, the reference counter changes slightly</a>
+<a name="359"><span class="lineNum">     359 </span>            :   the behavior of the C++ methods used to interoperate with C and FORTRAN.</a>
+<a name="360"><span class="lineNum">     360 </span>            : </a>
+<a name="361"><span class="lineNum">     361 </span>            :   An important novelty is in the way the runtime loader is implemented.</a>
+<a name="362"><span class="lineNum">     362 </span>            :   In particular, the loader works also if the symbols of the main executable are not exported.</a>
+<a name="363"><span class="lineNum">     363 </span>            :   The proper functions from the kernel are indeed searched explicitly now using `dlsym`.</a>
+<a name="364"><span class="lineNum">     364 </span>            : </a>
+<a name="365"><span class="lineNum">     365 </span>            :   Some additional features can be enabled using suitable environment variables. In particular:</a>
+<a name="366"><span class="lineNum">     366 </span>            :   - `PLUMED_LOAD_DEBUG` can be set to report more information about the loading process.</a>
+<a name="367"><span class="lineNum">     367 </span>            :   - `PLUMED_LOAD_NAMESPACE` can be set to `LOCAL` to load the PLUMED kernel in a separate</a>
+<a name="368"><span class="lineNum">     368 </span>            :     namespace. The default is global namespace, which is the same behavior of PLUMED &lt;=2.4,</a>
+<a name="369"><span class="lineNum">     369 </span>            :     and is consistent with what happens when linking PLUMED as a shared library.</a>
+<a name="370"><span class="lineNum">     370 </span>            :   - `PLUMED_LOAD_NODEEPBIND` can be set to load the PLUMED kernel in not-deepbind mode. Deepbind</a>
+<a name="371"><span class="lineNum">     371 </span>            :     mode implies that the symbols defined in the library are preferred to other symbols with the same name.</a>
+<a name="372"><span class="lineNum">     372 </span>            :     Only works on systems supporting `RTLD_DEEPBIND` and is mostly for debugging purposes.</a>
+<a name="373"><span class="lineNum">     373 </span>            : </a>
+<a name="374"><span class="lineNum">     374 </span>            :   Another difference is that the implementation of the wrappers is now completely contained in the `Plumed.h`</a>
+<a name="375"><span class="lineNum">     375 </span>            :   file. You can see that the `Plumed.c` is much simpler now and just includes `Plumed.h`. With a similar</a>
+<a name="376"><span class="lineNum">     376 </span>            :   procedure you could compile the wrappers directly into your code making it unnecessary to link</a>
+<a name="377"><span class="lineNum">     377 </span>            :   the libplumedWrapper.a library. The corresponding macros are still subject to change and are not documented here.</a>
+<a name="378"><span class="lineNum">     378 </span>            : </a>
+<a name="379"><span class="lineNum">     379 </span>            :   As written above, the plumed object now implements a reference counter.  Consider the following example</a>
+<a name="380"><span class="lineNum">     380 </span>            : \verbatim</a>
+<a name="381"><span class="lineNum">     381 </span>            :   plumed p=plumed_create();</a>
+<a name="382"><span class="lineNum">     382 </span>            :   plumed_cmd(p,&quot;init&quot;,NULL);</a>
+<a name="383"><span class="lineNum">     383 </span>            :   plumed q=plumed_create_reference(p);</a>
+<a name="384"><span class="lineNum">     384 </span>            :   plumed_finalize(p);</a>
+<a name="385"><span class="lineNum">     385 </span>            : // at this stage, object q still exists</a>
+<a name="386"><span class="lineNum">     386 </span>            :   plumed_cmd(q,&quot;whatever&quot;,NULL);</a>
+<a name="387"><span class="lineNum">     387 </span>            :   plumed_finalize(q);</a>
+<a name="388"><span class="lineNum">     388 </span>            : // now plumed has been really finalized</a>
+<a name="389"><span class="lineNum">     389 </span>            : \endverbatim</a>
+<a name="390"><span class="lineNum">     390 </span>            : </a>
+<a name="391"><span class="lineNum">     391 </span>            :   In other words, every \ref plumed_create, \ref plumed_create_dlopen, \ref plumed_create_reference,</a>
+<a name="392"><span class="lineNum">     392 </span>            :   \ref plumed_create_reference_f, and \ref plumed_create_reference_v call must be matched by a \ref plumed_finalize.</a>
+<a name="393"><span class="lineNum">     393 </span>            :   Notice that in C++ whenever an object goes out of scope the reference counter</a>
+<a name="394"><span class="lineNum">     394 </span>            :   will be decreased. In addition, consider that conversion from C/FORTRAN/void* to C++ implies calling a C++ constructor, that</a>
+<a name="395"><span class="lineNum">     395 </span>            :   is increases the number of references by one. Converting from C++ to C/FORTRAN/void* instead does not call any constructor,</a>
+<a name="396"><span class="lineNum">     396 </span>            :   that is the number of references is unchanged.</a>
+<a name="397"><span class="lineNum">     397 </span>            : </a>
+<a name="398"><span class="lineNum">     398 </span>            :   The change in the behavior of C++ constructors means that the following code will behave in a backward incompatible manner:</a>
+<a name="399"><span class="lineNum">     399 </span>            : \verbatim</a>
+<a name="400"><span class="lineNum">     400 </span>            :   plumed p=plumed_create();</a>
+<a name="401"><span class="lineNum">     401 </span>            :   plumed_cmd(p,&quot;init&quot;,NULL);</a>
+<a name="402"><span class="lineNum">     402 </span>            :   Plumed q(p);</a>
+<a name="403"><span class="lineNum">     403 </span>            :   plumed_finalize(p);</a>
+<a name="404"><span class="lineNum">     404 </span>            : // at this stage, object q still exists with PLUMED 2.5</a>
+<a name="405"><span class="lineNum">     405 </span>            : // on the other hand, with PLUMED 2.4 object q refers to an</a>
+<a name="406"><span class="lineNum">     406 </span>            : // already finalized object</a>
+<a name="407"><span class="lineNum">     407 </span>            :   q.cmd(&quot;whatever&quot;,NULL);</a>
+<a name="408"><span class="lineNum">     408 </span>            : \endverbatim</a>
+<a name="409"><span class="lineNum">     409 </span>            : </a>
+<a name="410"><span class="lineNum">     410 </span>            :   Another difference is that the value of the variable `PLUMED_KERNEL` is read every time a new</a>
+<a name="411"><span class="lineNum">     411 </span>            :   plumed object is instantiated. So, you might even use it to load different plumed versions</a>
+<a name="412"><span class="lineNum">     412 </span>            :   simultaneously, although the preferred way to do this is using the function \ref plumed_create_dlopen.</a>
+<a name="413"><span class="lineNum">     413 </span>            :   Notice that if you want to load multiple versions simultaneously you should load them in a local namespace.</a>
+<a name="414"><span class="lineNum">     414 </span>            :   \ref plumed_create_dlopen does it automatically, whereas loading through env var `PLUMED_KERNEL` only does it if</a>
+<a name="415"><span class="lineNum">     415 </span>            :   you also set env var `PLUMED_NAMESPACE=LOCAL`.</a>
+<a name="416"><span class="lineNum">     416 </span>            : </a>
+<a name="417"><span class="lineNum">     417 </span>            :   Finally, a few functions have been added, namely:</a>
+<a name="418"><span class="lineNum">     418 </span>            :   - Functions to find if a plumed object is valid</a>
+<a name="419"><span class="lineNum">     419 </span>            :     (\ref plumed_valid(), \ref plumed_gvalid(), \ref PLMD::Plumed::valid(), and \ref PLMD::Plumed::gvalid()).</a>
+<a name="420"><span class="lineNum">     420 </span>            :   - Functions to create a plumed object based on the path of a specific kernel</a>
+<a name="421"><span class="lineNum">     421 </span>            :     (\ref plumed_create_dlopen() and \ref PLMD::Plumed::dlopen()).</a>
+<a name="422"><span class="lineNum">     422 </span>            :   - Functions to create a plumed object referencing to another one, implementing a reference counter</a>
+<a name="423"><span class="lineNum">     423 </span>            :     (\ref plumed_create_reference(), \ref plumed_create_reference_v(), \ref plumed_create_reference_f().</a>
+<a name="424"><span class="lineNum">     424 </span>            : </a>
+<a name="425"><span class="lineNum">     425 </span>            : */</a>
+<a name="426"><span class="lineNum">     426 </span>            : </a>
+<a name="427"><span class="lineNum">     427 </span>            : /* BEGINNING OF DECLARATIONS */</a>
+<a name="428"><span class="lineNum">     428 </span>            : </a>
+<a name="429"><span class="lineNum">     429 </span>            : /* SETTING DEFAULT VALUES FOR CONTROL MACROS */</a>
+<a name="430"><span class="lineNum">     430 </span>            : </a>
+<a name="431"><span class="lineNum">     431 </span>            : /*</a>
+<a name="432"><span class="lineNum">     432 </span>            :   1: make the C wrapper functions extern (default)</a>
+<a name="433"><span class="lineNum">     433 </span>            :   0: make the C wrapper functions static (C) or inline (C++)</a>
+<a name="434"><span class="lineNum">     434 </span>            : </a>
+<a name="435"><span class="lineNum">     435 </span>            :   If set to zero, it disables all functions that only make sense as extern, such as</a>
+<a name="436"><span class="lineNum">     436 </span>            :   Fortran wrappers, global objects, and plumed_kernel_register.</a>
+<a name="437"><span class="lineNum">     437 </span>            : </a>
+<a name="438"><span class="lineNum">     438 </span>            :   It can be set to zero to include multiple copies of the wrapper implementation without worrying</a>
+<a name="439"><span class="lineNum">     439 </span>            :   about duplicated symbols.</a>
+<a name="440"><span class="lineNum">     440 </span>            : </a>
+<a name="441"><span class="lineNum">     441 </span>            :   Notice that C++ wrappers are always inline. What this function controls is if the C wrappers</a>
+<a name="442"><span class="lineNum">     442 </span>            :   (called by the C++ wrappers) is inline or not. Also consider that if this header is compiled</a>
+<a name="443"><span class="lineNum">     443 </span>            :   with C++ and inline C wrappers, the C wrappers will be actually compiled with C++ linkage</a>
+<a name="444"><span class="lineNum">     444 </span>            :   in the root namespace.</a>
+<a name="445"><span class="lineNum">     445 </span>            : </a>
+<a name="446"><span class="lineNum">     446 </span>            :   Used both in declarations (to know which functions to declare) and definitions (to know which functions to define).</a>
+<a name="447"><span class="lineNum">     447 </span>            : */</a>
+<a name="448"><span class="lineNum">     448 </span>            : </a>
+<a name="449"><span class="lineNum">     449 </span>            : #ifndef __PLUMED_WRAPPER_EXTERN</a>
+<a name="450"><span class="lineNum">     450 </span>            : #define __PLUMED_WRAPPER_EXTERN 1</a>
+<a name="451"><span class="lineNum">     451 </span>            : #endif</a>
+<a name="452"><span class="lineNum">     452 </span>            : </a>
+<a name="453"><span class="lineNum">     453 </span>            : /*</a>
+<a name="454"><span class="lineNum">     454 </span>            :   1: emit global plumed object and related functions (default)</a>
+<a name="455"><span class="lineNum">     455 </span>            :   0: do not emit global plumed object and related functions</a>
+<a name="456"><span class="lineNum">     456 </span>            : </a>
+<a name="457"><span class="lineNum">     457 </span>            :   Used both in declarations (to know which functions to declare) and definitions (to know which functions to define).</a>
+<a name="458"><span class="lineNum">     458 </span>            : */</a>
+<a name="459"><span class="lineNum">     459 </span>            : </a>
+<a name="460"><span class="lineNum">     460 </span>            : #ifndef __PLUMED_WRAPPER_GLOBAL</a>
+<a name="461"><span class="lineNum">     461 </span>            : #define __PLUMED_WRAPPER_GLOBAL 1</a>
+<a name="462"><span class="lineNum">     462 </span>            : #endif</a>
+<a name="463"><span class="lineNum">     463 </span>            : </a>
+<a name="464"><span class="lineNum">     464 </span>            : /*</a>
+<a name="465"><span class="lineNum">     465 </span>            :   1: Enable typesafe C interface (default)</a>
+<a name="466"><span class="lineNum">     466 </span>            :   0: Disable typesafe C interface</a>
+<a name="467"><span class="lineNum">     467 </span>            : </a>
+<a name="468"><span class="lineNum">     468 </span>            :   Only used in declarations. Requires C11 _Generic and variadic macros, and so it is</a>
+<a name="469"><span class="lineNum">     469 </span>            :   disabled by default with C++ and pre C11 compilers.</a>
+<a name="470"><span class="lineNum">     470 </span>            : </a>
+<a name="471"><span class="lineNum">     471 </span>            :   https://mort.coffee/home/c-compiler-quirks/</a>
+<a name="472"><span class="lineNum">     472 </span>            : */</a>
+<a name="473"><span class="lineNum">     473 </span>            : </a>
+<a name="474"><span class="lineNum">     474 </span>            : #ifndef __PLUMED_WRAPPER_C_TYPESAFE</a>
+<a name="475"><span class="lineNum">     475 </span>            : #  if defined(__STDC_VERSION__)</a>
+<a name="476"><span class="lineNum">     476 </span>            : #    if ! defined(__cplusplus) &amp;&amp; __STDC_VERSION__ &gt;= 201112L</a>
+<a name="477"><span class="lineNum">     477 </span>            : #      if defined(__GNUC__) &amp;&amp; !defined(__clang__)</a>
+<a name="478"><span class="lineNum">     478 </span>            : #        if (__GNUC__ &gt;= 5 || (__GNUC__ == 4 &amp;&amp; __GNUC_MINOR__ &gt;= 9))</a>
+<a name="479"><span class="lineNum">     479 </span>            : #          define __PLUMED_WRAPPER_C_TYPESAFE 1</a>
+<a name="480"><span class="lineNum">     480 </span>            : #        endif</a>
+<a name="481"><span class="lineNum">     481 </span>            : #      else</a>
+<a name="482"><span class="lineNum">     482 </span>            : #        define __PLUMED_WRAPPER_C_TYPESAFE 1</a>
+<a name="483"><span class="lineNum">     483 </span>            : #      endif</a>
+<a name="484"><span class="lineNum">     484 </span>            : #    endif</a>
+<a name="485"><span class="lineNum">     485 </span>            : #  endif</a>
+<a name="486"><span class="lineNum">     486 </span>            : #  ifndef __PLUMED_WRAPPER_C_TYPESAFE</a>
+<a name="487"><span class="lineNum">     487 </span>            : #    define __PLUMED_WRAPPER_C_TYPESAFE 0</a>
+<a name="488"><span class="lineNum">     488 </span>            : #  endif</a>
+<a name="489"><span class="lineNum">     489 </span>            : #endif</a>
+<a name="490"><span class="lineNum">     490 </span>            : </a>
+<a name="491"><span class="lineNum">     491 </span>            : /*</a>
+<a name="492"><span class="lineNum">     492 </span>            :   1: Enable RTLD_DEEPBIND when possible (default)</a>
+<a name="493"><span class="lineNum">     493 </span>            :   0: Disable RTLD_DEEPBIND</a>
+<a name="494"><span class="lineNum">     494 </span>            : */</a>
+<a name="495"><span class="lineNum">     495 </span>            : </a>
+<a name="496"><span class="lineNum">     496 </span>            : #ifndef __PLUMED_WRAPPER_ENABLE_RTLD_DEEPBIND</a>
+<a name="497"><span class="lineNum">     497 </span>            : #define __PLUMED_WRAPPER_ENABLE_RTLD_DEEPBIND 1</a>
+<a name="498"><span class="lineNum">     498 </span>            : #endif</a>
+<a name="499"><span class="lineNum">     499 </span>            : </a>
+<a name="500"><span class="lineNum">     500 </span>            : /*</a>
+<a name="501"><span class="lineNum">     501 </span>            :   1: enable C++ wrapper (default)</a>
+<a name="502"><span class="lineNum">     502 </span>            :   0: disable C++ wrapper</a>
+<a name="503"><span class="lineNum">     503 </span>            : </a>
+<a name="504"><span class="lineNum">     504 </span>            :   Only used in declarations, but affects the scope of the C interface also in definitions.</a>
+<a name="505"><span class="lineNum">     505 </span>            : */</a>
+<a name="506"><span class="lineNum">     506 </span>            : </a>
+<a name="507"><span class="lineNum">     507 </span>            : #ifndef __PLUMED_WRAPPER_CXX</a>
+<a name="508"><span class="lineNum">     508 </span>            : #define __PLUMED_WRAPPER_CXX 1</a>
+<a name="509"><span class="lineNum">     509 </span>            : #endif</a>
+<a name="510"><span class="lineNum">     510 </span>            : </a>
+<a name="511"><span class="lineNum">     511 </span>            : /*</a>
+<a name="512"><span class="lineNum">     512 </span>            :   1: new headers such as cstdlib are included in C++ (default)</a>
+<a name="513"><span class="lineNum">     513 </span>            :   0: old headers such as stdlib.h are included in C++</a>
+<a name="514"><span class="lineNum">     514 </span>            : </a>
+<a name="515"><span class="lineNum">     515 </span>            :   Should only be set to zero when including the Plumed.h file in a file using the</a>
+<a name="516"><span class="lineNum">     516 </span>            :   old (stdlib.h) convention.</a>
+<a name="517"><span class="lineNum">     517 </span>            : </a>
+<a name="518"><span class="lineNum">     518 </span>            :   Used both in declarations and definitions.</a>
+<a name="519"><span class="lineNum">     519 </span>            : */</a>
+<a name="520"><span class="lineNum">     520 </span>            : </a>
+<a name="521"><span class="lineNum">     521 </span>            : #ifndef __PLUMED_WRAPPER_CXX_STD</a>
+<a name="522"><span class="lineNum">     522 </span>            : #define __PLUMED_WRAPPER_CXX_STD 1</a>
+<a name="523"><span class="lineNum">     523 </span>            : #endif</a>
+<a name="524"><span class="lineNum">     524 </span>            : </a>
+<a name="525"><span class="lineNum">     525 </span>            : /*</a>
+<a name="526"><span class="lineNum">     526 </span>            :   1: place C++ wrappers in an anonymous namespace</a>
+<a name="527"><span class="lineNum">     527 </span>            :   0: place C++ wrappers in the PLMD namespace (default)</a>
+<a name="528"><span class="lineNum">     528 </span>            : </a>
+<a name="529"><span class="lineNum">     529 </span>            :   It will make PLMD::Plumed a different class (though with the same name)</a>
+<a name="530"><span class="lineNum">     530 </span>            :   in each of the translation units in which `Plumed.h` is included.</a>
+<a name="531"><span class="lineNum">     531 </span>            : </a>
+<a name="532"><span class="lineNum">     532 </span>            :   Can be used to completey separate C++ implementations. However, it will make</a>
+<a name="533"><span class="lineNum">     533 </span>            :   it impossible to transfer Plumed objects between different translation units</a>
+<a name="534"><span class="lineNum">     534 </span>            :   without converting to a void* or plumed object.</a>
+<a name="535"><span class="lineNum">     535 </span>            : </a>
+<a name="536"><span class="lineNum">     536 </span>            :   Only used in declarations, but affects the scope of the C interface also in definitions.</a>
+<a name="537"><span class="lineNum">     537 </span>            : */</a>
+<a name="538"><span class="lineNum">     538 </span>            : </a>
+<a name="539"><span class="lineNum">     539 </span>            : #ifndef __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE</a>
+<a name="540"><span class="lineNum">     540 </span>            : #define __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE 0</a>
+<a name="541"><span class="lineNum">     541 </span>            : #endif</a>
+<a name="542"><span class="lineNum">     542 </span>            : </a>
+<a name="543"><span class="lineNum">     543 </span>            : </a>
+<a name="544"><span class="lineNum">     544 </span>            : /*</a>
+<a name="545"><span class="lineNum">     545 </span>            :   1: throw exceptions such as PLMD::Exception</a>
+<a name="546"><span class="lineNum">     546 </span>            :   0: throw exceptions such as PLMD::Plumed::Exception (default)</a>
+<a name="547"><span class="lineNum">     547 </span>            : </a>
+<a name="548"><span class="lineNum">     548 </span>            :   This is useful when including Plumed.h within the plumed library</a>
+<a name="549"><span class="lineNum">     549 </span>            :   in anonymous mode, to make sure that the exception types from the</a>
+<a name="550"><span class="lineNum">     550 </span>            :   library are used.</a>
+<a name="551"><span class="lineNum">     551 </span>            : */</a>
+<a name="552"><span class="lineNum">     552 </span>            : #ifndef __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS</a>
+<a name="553"><span class="lineNum">     553 </span>            : #define __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS 0</a>
+<a name="554"><span class="lineNum">     554 </span>            : #endif</a>
+<a name="555"><span class="lineNum">     555 </span>            : </a>
+<a name="556"><span class="lineNum">     556 </span>            : /*</a>
+<a name="557"><span class="lineNum">     557 </span>            :   1: make PLMD::Plumed class polymorphic (default)</a>
+<a name="558"><span class="lineNum">     558 </span>            :   0: make PLMD::Plumed class non-polymorphic</a>
+<a name="559"><span class="lineNum">     559 </span>            : </a>
+<a name="560"><span class="lineNum">     560 </span>            :   Only used in declarations.</a>
+<a name="561"><span class="lineNum">     561 </span>            : */</a>
+<a name="562"><span class="lineNum">     562 </span>            : </a>
+<a name="563"><span class="lineNum">     563 </span>            : #ifndef __PLUMED_WRAPPER_CXX_POLYMORPHIC</a>
+<a name="564"><span class="lineNum">     564 </span>            : #define __PLUMED_WRAPPER_CXX_POLYMORPHIC 1</a>
+<a name="565"><span class="lineNum">     565 </span>            : #endif</a>
+<a name="566"><span class="lineNum">     566 </span>            : </a>
+<a name="567"><span class="lineNum">     567 </span>            : /*</a>
+<a name="568"><span class="lineNum">     568 </span>            :   1: Enable typesafe interface (default)</a>
+<a name="569"><span class="lineNum">     569 </span>            :   0: Disable typesafe interface</a>
+<a name="570"><span class="lineNum">     570 </span>            : </a>
+<a name="571"><span class="lineNum">     571 </span>            :   Only used in declarations.</a>
+<a name="572"><span class="lineNum">     572 </span>            : */</a>
+<a name="573"><span class="lineNum">     573 </span>            : </a>
+<a name="574"><span class="lineNum">     574 </span>            : #ifndef __PLUMED_WRAPPER_CXX_TYPESAFE</a>
+<a name="575"><span class="lineNum">     575 </span>            : #define __PLUMED_WRAPPER_CXX_TYPESAFE 1</a>
+<a name="576"><span class="lineNum">     576 </span>            : #endif</a>
+<a name="577"><span class="lineNum">     577 </span>            : </a>
+<a name="578"><span class="lineNum">     578 </span>            : /*</a>
+<a name="579"><span class="lineNum">     579 </span>            :   1: Define macros plumed_cmd and plumed_gcmd to use the C++ interface (default).</a>
+<a name="580"><span class="lineNum">     580 </span>            :   0: Don't define macros plumed_cmd and plumed_gcmd.</a>
+<a name="581"><span class="lineNum">     581 </span>            : </a>
+<a name="582"><span class="lineNum">     582 </span>            :   Only used in declarations.</a>
+<a name="583"><span class="lineNum">     583 </span>            : */</a>
+<a name="584"><span class="lineNum">     584 </span>            : </a>
+<a name="585"><span class="lineNum">     585 </span>            : #ifndef __PLUMED_WRAPPER_CXX_BIND_C</a>
+<a name="586"><span class="lineNum">     586 </span>            : #define __PLUMED_WRAPPER_CXX_BIND_C 1</a>
+<a name="587"><span class="lineNum">     587 </span>            : #endif</a>
+<a name="588"><span class="lineNum">     588 </span>            : </a>
+<a name="589"><span class="lineNum">     589 </span>            : /*</a>
+<a name="590"><span class="lineNum">     590 </span>            :   1: Enable passing long long int</a>
+<a name="591"><span class="lineNum">     591 </span>            :   0: Disable passing long long int</a>
+<a name="592"><span class="lineNum">     592 </span>            : </a>
+<a name="593"><span class="lineNum">     593 </span>            :   Only used in declarations. Default is 0 in C++&lt;11 and 1 in C++&gt;=11</a>
+<a name="594"><span class="lineNum">     594 </span>            : */</a>
+<a name="595"><span class="lineNum">     595 </span>            : </a>
+<a name="596"><span class="lineNum">     596 </span>            : #ifndef __PLUMED_WRAPPER_CXX_LONGLONG</a>
+<a name="597"><span class="lineNum">     597 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="598"><span class="lineNum">     598 </span>            : #define __PLUMED_WRAPPER_CXX_LONGLONG 1</a>
+<a name="599"><span class="lineNum">     599 </span>            : #else</a>
+<a name="600"><span class="lineNum">     600 </span>            : #define __PLUMED_WRAPPER_CXX_LONGLONG 0</a>
+<a name="601"><span class="lineNum">     601 </span>            : #endif</a>
+<a name="602"><span class="lineNum">     602 </span>            : #endif</a>
+<a name="603"><span class="lineNum">     603 </span>            : </a>
+<a name="604"><span class="lineNum">     604 </span>            : /*</a>
+<a name="605"><span class="lineNum">     605 </span>            :   1: make the default constructor create an invalid object</a>
+<a name="606"><span class="lineNum">     606 </span>            :   0: make the default constructor create a valid object</a>
+<a name="607"><span class="lineNum">     607 </span>            : </a>
+<a name="608"><span class="lineNum">     608 </span>            :   Only for internal usage.</a>
+<a name="609"><span class="lineNum">     609 </span>            : */</a>
+<a name="610"><span class="lineNum">     610 </span>            : #ifndef __PLUMED_WRAPPER_CXX_DEFAULT_INVALID</a>
+<a name="611"><span class="lineNum">     611 </span>            : #define __PLUMED_WRAPPER_CXX_DEFAULT_INVALID 0</a>
+<a name="612"><span class="lineNum">     612 </span>            : #endif</a>
+<a name="613"><span class="lineNum">     613 </span>            : </a>
+<a name="614"><span class="lineNum">     614 </span>            : /*</a>
+<a name="615"><span class="lineNum">     615 </span>            :   Size of a buffer used to store message for exceptions with noexcept constructor.</a>
+<a name="616"><span class="lineNum">     616 </span>            :   Should typically hold short messages. Anyway, as long as the stack size stays within the correct</a>
+<a name="617"><span class="lineNum">     617 </span>            :   limits it does not seem to affect efficiency. Notice that there cannot be recursive calls of</a>
+<a name="618"><span class="lineNum">     618 </span>            :   PLMD::Plumed::cmd, so that it should be in practice irrelevant.</a>
+<a name="619"><span class="lineNum">     619 </span>            : */</a>
+<a name="620"><span class="lineNum">     620 </span>            : #ifndef __PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER</a>
+<a name="621"><span class="lineNum">     621 </span>            : #define __PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER 512</a>
+<a name="622"><span class="lineNum">     622 </span>            : #endif</a>
+<a name="623"><span class="lineNum">     623 </span>            : </a>
+<a name="624"><span class="lineNum">     624 </span>            : /*</a>
+<a name="625"><span class="lineNum">     625 </span>            :   1: enable nested exceptions (only with C++11) (default)</a>
+<a name="626"><span class="lineNum">     626 </span>            :   0: disable nested exceptions</a>
+<a name="627"><span class="lineNum">     627 </span>            : </a>
+<a name="628"><span class="lineNum">     628 </span>            :   For internal testing, used to mimic pre C++11 behavior on</a>
+<a name="629"><span class="lineNum">     629 </span>            :   nested exception.</a>
+<a name="630"><span class="lineNum">     630 </span>            : </a>
+<a name="631"><span class="lineNum">     631 </span>            :   Only used in declarations.</a>
+<a name="632"><span class="lineNum">     632 </span>            : */</a>
+<a name="633"><span class="lineNum">     633 </span>            : </a>
+<a name="634"><span class="lineNum">     634 </span>            : #ifndef __PLUMED_WRAPPER_CXX_ENABLE_NESTED_EXCEPTIONS</a>
+<a name="635"><span class="lineNum">     635 </span>            : #define __PLUMED_WRAPPER_CXX_ENABLE_NESTED_EXCEPTIONS 1</a>
+<a name="636"><span class="lineNum">     636 </span>            : #endif</a>
+<a name="637"><span class="lineNum">     637 </span>            : </a>
+<a name="638"><span class="lineNum">     638 </span>            : /*</a>
+<a name="639"><span class="lineNum">     639 </span>            :  By default, assume C++11 compliant library is not available.</a>
+<a name="640"><span class="lineNum">     640 </span>            : */</a>
+<a name="641"><span class="lineNum">     641 </span>            : </a>
+<a name="642"><span class="lineNum">     642 </span>            : #ifndef __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="643"><span class="lineNum">     643 </span>            : #define __PLUMED_WRAPPER_LIBCXX11 0</a>
+<a name="644"><span class="lineNum">     644 </span>            : #endif</a>
+<a name="645"><span class="lineNum">     645 </span>            : </a>
+<a name="646"><span class="lineNum">     646 </span>            : /* The following macros are just to define shortcuts */</a>
+<a name="647"><span class="lineNum">     647 </span>            : </a>
+<a name="648"><span class="lineNum">     648 </span>            : /* Simplify addition of extern &quot;C&quot; blocks.  */</a>
+<a name="649"><span class="lineNum">     649 </span>            : #ifdef __cplusplus</a>
+<a name="650"><span class="lineNum">     650 </span>            : #define __PLUMED_WRAPPER_EXTERN_C_BEGIN extern &quot;C&quot; {</a>
+<a name="651"><span class="lineNum">     651 </span>            : #define __PLUMED_WRAPPER_EXTERN_C_END }</a>
+<a name="652"><span class="lineNum">     652 </span>            : #else</a>
+<a name="653"><span class="lineNum">     653 </span>            : #define __PLUMED_WRAPPER_EXTERN_C_BEGIN</a>
+<a name="654"><span class="lineNum">     654 </span>            : #define __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="655"><span class="lineNum">     655 </span>            : #endif</a>
+<a name="656"><span class="lineNum">     656 </span>            : </a>
+<a name="657"><span class="lineNum">     657 </span>            : /* Without C++, stdlib functions should not be prepended with ::std:: */</a>
+<a name="658"><span class="lineNum">     658 </span>            : #ifndef __cplusplus</a>
+<a name="659"><span class="lineNum">     659 </span>            : #undef __PLUMED_WRAPPER_CXX_STD</a>
+<a name="660"><span class="lineNum">     660 </span>            : #define __PLUMED_WRAPPER_CXX_STD 0</a>
+<a name="661"><span class="lineNum">     661 </span>            : #endif</a>
+<a name="662"><span class="lineNum">     662 </span>            : </a>
+<a name="663"><span class="lineNum">     663 </span>            : /* Set prefix for stdlib functions */</a>
+<a name="664"><span class="lineNum">     664 </span>            : #if __PLUMED_WRAPPER_CXX_STD</a>
+<a name="665"><span class="lineNum">     665 </span>            : #define __PLUMED_WRAPPER_STD ::std::</a>
+<a name="666"><span class="lineNum">     666 </span>            : #else</a>
+<a name="667"><span class="lineNum">     667 </span>            : #define __PLUMED_WRAPPER_STD</a>
+<a name="668"><span class="lineNum">     668 </span>            : #endif</a>
+<a name="669"><span class="lineNum">     669 </span>            : </a>
+<a name="670"><span class="lineNum">     670 </span>            : /* Allow using noexcept, explicit, and override with C++11 compilers */</a>
+<a name="671"><span class="lineNum">     671 </span>            : #ifdef __cplusplus /*{*/</a>
+<a name="672"><span class="lineNum">     672 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="673"><span class="lineNum">     673 </span>            : #define __PLUMED_WRAPPER_CXX_NOEXCEPT noexcept</a>
+<a name="674"><span class="lineNum">     674 </span>            : #define __PLUMED_WRAPPER_CXX_NORETURN [[ noreturn ]]</a>
+<a name="675"><span class="lineNum">     675 </span>            : #define __PLUMED_WRAPPER_CXX_EXPLICIT explicit</a>
+<a name="676"><span class="lineNum">     676 </span>            : #define __PLUMED_WRAPPER_CXX_OVERRIDE override</a>
+<a name="677"><span class="lineNum">     677 </span>            : #define __PLUMED_WRAPPER_CXX_NULLPTR  nullptr</a>
+<a name="678"><span class="lineNum">     678 </span>            : #else</a>
+<a name="679"><span class="lineNum">     679 </span>            : #define __PLUMED_WRAPPER_CXX_NOEXCEPT throw()</a>
+<a name="680"><span class="lineNum">     680 </span>            : #define __PLUMED_WRAPPER_CXX_NORETURN</a>
+<a name="681"><span class="lineNum">     681 </span>            : #define __PLUMED_WRAPPER_CXX_EXPLICIT</a>
+<a name="682"><span class="lineNum">     682 </span>            : #define __PLUMED_WRAPPER_CXX_OVERRIDE</a>
+<a name="683"><span class="lineNum">     683 </span>            : #define __PLUMED_WRAPPER_CXX_NULLPTR  NULL</a>
+<a name="684"><span class="lineNum">     684 </span>            : #endif</a>
+<a name="685"><span class="lineNum">     685 </span>            : #else</a>
+<a name="686"><span class="lineNum">     686 </span>            : #define __PLUMED_WRAPPER_CXX_NOEXCEPT</a>
+<a name="687"><span class="lineNum">     687 </span>            : #define __PLUMED_WRAPPER_CXX_NORETURN</a>
+<a name="688"><span class="lineNum">     688 </span>            : #define __PLUMED_WRAPPER_CXX_EXPLICIT</a>
+<a name="689"><span class="lineNum">     689 </span>            : #define __PLUMED_WRAPPER_CXX_OVERRIDE</a>
+<a name="690"><span class="lineNum">     690 </span>            : #define __PLUMED_WRAPPER_CXX_NULLPTR  NULL</a>
+<a name="691"><span class="lineNum">     691 </span>            : #endif /*}*/</a>
+<a name="692"><span class="lineNum">     692 </span>            : </a>
+<a name="693"><span class="lineNum">     693 </span>            : /* static inline, for to avoid compiler warnings */</a>
+<a name="694"><span class="lineNum">     694 </span>            : #if defined(__cplusplus) || __STDC_VERSION__&gt;=199901L</a>
+<a name="695"><span class="lineNum">     695 </span>            : #define __PLUMED_WRAPPER_STATIC_INLINE static inline</a>
+<a name="696"><span class="lineNum">     696 </span>            : #else</a>
+<a name="697"><span class="lineNum">     697 </span>            : #define __PLUMED_WRAPPER_STATIC_INLINE static</a>
+<a name="698"><span class="lineNum">     698 </span>            : #endif</a>
+<a name="699"><span class="lineNum">     699 </span>            : </a>
+<a name="700"><span class="lineNum">     700 </span>            : /* Macros for anonymous namespace */</a>
+<a name="701"><span class="lineNum">     701 </span>            : #if __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE &amp;&amp; defined(__cplusplus) /*{*/</a>
+<a name="702"><span class="lineNum">     702 </span>            : #define __PLUMED_WRAPPER_ANONYMOUS_BEGIN namespace {</a>
+<a name="703"><span class="lineNum">     703 </span>            : #define __PLUMED_WRAPPER_ANONYMOUS_END }</a>
+<a name="704"><span class="lineNum">     704 </span>            : #else</a>
+<a name="705"><span class="lineNum">     705 </span>            : #define __PLUMED_WRAPPER_ANONYMOUS_BEGIN</a>
+<a name="706"><span class="lineNum">     706 </span>            : #define __PLUMED_WRAPPER_ANONYMOUS_END</a>
+<a name="707"><span class="lineNum">     707 </span>            : #endif /*}*/</a>
+<a name="708"><span class="lineNum">     708 </span>            : </a>
+<a name="709"><span class="lineNum">     709 </span>            : #if __PLUMED_WRAPPER_EXTERN /*{*/</a>
+<a name="710"><span class="lineNum">     710 </span>            : </a>
+<a name="711"><span class="lineNum">     711 </span>            : #define __PLUMED_WRAPPER_C_BEGIN __PLUMED_WRAPPER_EXTERN_C_BEGIN extern</a>
+<a name="712"><span class="lineNum">     712 </span>            : #define __PLUMED_WRAPPER_C_END __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="713"><span class="lineNum">     713 </span>            : #define __PLUMED_WRAPPER_INTERNALS_BEGIN __PLUMED_WRAPPER_EXTERN_C_BEGIN static</a>
+<a name="714"><span class="lineNum">     714 </span>            : #define __PLUMED_WRAPPER_INTERNALS_END __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="715"><span class="lineNum">     715 </span>            : </a>
+<a name="716"><span class="lineNum">     716 </span>            : #else</a>
+<a name="717"><span class="lineNum">     717 </span>            : </a>
+<a name="718"><span class="lineNum">     718 </span>            : #ifdef __cplusplus</a>
+<a name="719"><span class="lineNum">     719 </span>            : #define __PLUMED_WRAPPER_C_BEGIN  __PLUMED_WRAPPER_ANONYMOUS_BEGIN inline</a>
+<a name="720"><span class="lineNum">     720 </span>            : #define __PLUMED_WRAPPER_C_END __PLUMED_WRAPPER_ANONYMOUS_END</a>
+<a name="721"><span class="lineNum">     721 </span>            : #else</a>
+<a name="722"><span class="lineNum">     722 </span>            : #define __PLUMED_WRAPPER_C_BEGIN __PLUMED_WRAPPER_STATIC_INLINE</a>
+<a name="723"><span class="lineNum">     723 </span>            : #define __PLUMED_WRAPPER_C_END</a>
+<a name="724"><span class="lineNum">     724 </span>            : #endif</a>
+<a name="725"><span class="lineNum">     725 </span>            : </a>
+<a name="726"><span class="lineNum">     726 </span>            : #define __PLUMED_WRAPPER_INTERNALS_BEGIN __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="727"><span class="lineNum">     727 </span>            : #define __PLUMED_WRAPPER_INTERNALS_END __PLUMED_WRAPPER_C_END</a>
+<a name="728"><span class="lineNum">     728 </span>            : </a>
+<a name="729"><span class="lineNum">     729 </span>            : /* with an not-external interface, it does not make sense to define global functions */</a>
+<a name="730"><span class="lineNum">     730 </span>            : #undef __PLUMED_WRAPPER_GLOBAL</a>
+<a name="731"><span class="lineNum">     731 </span>            : #define __PLUMED_WRAPPER_GLOBAL 0</a>
+<a name="732"><span class="lineNum">     732 </span>            : </a>
+<a name="733"><span class="lineNum">     733 </span>            : #endif /*}*/</a>
+<a name="734"><span class="lineNum">     734 </span>            : </a>
+<a name="735"><span class="lineNum">     735 </span>            : #if __PLUMED_WRAPPER_CXX_STD</a>
+<a name="736"><span class="lineNum">     736 </span>            : #include &lt;cstddef&gt; /* size_t */</a>
+<a name="737"><span class="lineNum">     737 </span>            : #include &lt;cstring&gt; /* memcpy */</a>
+<a name="738"><span class="lineNum">     738 </span>            : #include &lt;cstdio&gt; /* fprintf */</a>
+<a name="739"><span class="lineNum">     739 </span>            : #include &lt;cstdlib&gt; /* abort */</a>
+<a name="740"><span class="lineNum">     740 </span>            : #include &lt;cassert&gt; /* assert */</a>
+<a name="741"><span class="lineNum">     741 </span>            : #else</a>
+<a name="742"><span class="lineNum">     742 </span>            : #include &lt;stddef.h&gt;</a>
+<a name="743"><span class="lineNum">     743 </span>            : #include &lt;string.h&gt;</a>
+<a name="744"><span class="lineNum">     744 </span>            : #include &lt;stdio.h&gt; /* FILE and fprintf */</a>
+<a name="745"><span class="lineNum">     745 </span>            : #include &lt;stdlib.h&gt; /* abort */</a>
+<a name="746"><span class="lineNum">     746 </span>            : #include &lt;limits.h&gt; /* CHAR_MIN */</a>
+<a name="747"><span class="lineNum">     747 </span>            : #include &lt;assert.h&gt; /* assert */</a>
+<a name="748"><span class="lineNum">     748 </span>            : #endif</a>
+<a name="749"><span class="lineNum">     749 </span>            : </a>
+<a name="750"><span class="lineNum">     750 </span>            : /**</a>
+<a name="751"><span class="lineNum">     751 </span>            :   This is an internal tool, to make sure that all malloc calls inside the</a>
+<a name="752"><span class="lineNum">     752 </span>            :   plumed library refer to the same implementation. When compiling with</a>
+<a name="753"><span class="lineNum">     753 </span>            :   __PLUMED_WRAPPER_DEBUG_REFCOUNT=1 it is possible to log</a>
+<a name="754"><span class="lineNum">     754 </span>            :   allocations and deallocations, so as to debug the wrappers.</a>
+<a name="755"><span class="lineNum">     755 </span>            : */</a>
+<a name="756"><span class="lineNum">     756 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="757"><span class="lineNum">     757 </span>            : void* plumed_malloc(__PLUMED_WRAPPER_STD size_t size);</a>
+<a name="758"><span class="lineNum">     758 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="759"><span class="lineNum">     759 </span>            : </a>
+<a name="760"><span class="lineNum">     760 </span>            : /**</a>
+<a name="761"><span class="lineNum">     761 </span>            :   This is an internal tool, to make sure that all free calls inside the</a>
+<a name="762"><span class="lineNum">     762 </span>            :   plumed library refer to the same implementation. When compiling with</a>
+<a name="763"><span class="lineNum">     763 </span>            :   __PLUMED_WRAPPER_DEBUG_REFCOUNT=1 it is possible to log</a>
+<a name="764"><span class="lineNum">     764 </span>            :   allocations and deallocations, so as to debug the wrappers.</a>
+<a name="765"><span class="lineNum">     765 </span>            : */</a>
+<a name="766"><span class="lineNum">     766 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="767"><span class="lineNum">     767 </span>            : void plumed_free(void* ptr);</a>
+<a name="768"><span class="lineNum">     768 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="769"><span class="lineNum">     769 </span>            : </a>
+<a name="770"><span class="lineNum">     770 </span>            : /**</a>
+<a name="771"><span class="lineNum">     771 </span>            :   \brief Main plumed object</a>
+<a name="772"><span class="lineNum">     772 </span>            : </a>
+<a name="773"><span class="lineNum">     773 </span>            :   This is an object containing a Plumed instance, which should be used in</a>
+<a name="774"><span class="lineNum">     774 </span>            :   the MD engine. It should first be initialized with plumed_create(),</a>
+<a name="775"><span class="lineNum">     775 </span>            :   then it communicates with the MD engine using plumed_cmd(). Finally,</a>
+<a name="776"><span class="lineNum">     776 </span>            :   before the termination, it should be deallocated with plumed_finalize().</a>
+<a name="777"><span class="lineNum">     777 </span>            :   Its interface is very simple and general, and is expected</a>
+<a name="778"><span class="lineNum">     778 </span>            :   not to change across plumed versions. See \ref ReferencePlumedH.</a>
+<a name="779"><span class="lineNum">     779 </span>            : */</a>
+<a name="780"><span class="lineNum">     780 </span>            : typedef struct {</a>
+<a name="781"><span class="lineNum">     781 </span>            :   /**</a>
+<a name="782"><span class="lineNum">     782 </span>            :     \private</a>
+<a name="783"><span class="lineNum">     783 </span>            :     \brief Void pointer holding the real PlumedMain structure</a>
+<a name="784"><span class="lineNum">     784 </span>            : </a>
+<a name="785"><span class="lineNum">     785 </span>            :     To maintain binary compatibility, we should not add members to this structure.</a>
+<a name="786"><span class="lineNum">     786 </span>            :     As of PLUMED 2.5, in order to add new components we do not store the pointer</a>
+<a name="787"><span class="lineNum">     787 </span>            :     to \ref PlumedMain here but rather a pointer to an intermediate private structure</a>
+<a name="788"><span class="lineNum">     788 </span>            :     that contains all the details.</a>
+<a name="789"><span class="lineNum">     789 </span>            :   */</a>
+<a name="790"><span class="lineNum">     790 </span>            :   void*p;</a>
+<a name="791"><span class="lineNum">     791 </span>            : } plumed;</a>
+<a name="792"><span class="lineNum">     792 </span>            : </a>
+<a name="793"><span class="lineNum">     793 </span>            : typedef struct {</a>
+<a name="794"><span class="lineNum">     794 </span>            :   void* ptr;</a>
+<a name="795"><span class="lineNum">     795 </span>            :   void (*handler)(void*,int,const char*,const void*);</a>
+<a name="796"><span class="lineNum">     796 </span>            : } plumed_nothrow_handler;</a>
+<a name="797"><span class="lineNum">     797 </span>            : </a>
+<a name="798"><span class="lineNum">     798 </span>            : /** \relates plumed</a>
+<a name="799"><span class="lineNum">     799 </span>            :     \brief Structure holding a typesafe pointer.</a>
+<a name="800"><span class="lineNum">     800 </span>            : */</a>
+<a name="801"><span class="lineNum">     801 </span>            : </a>
+<a name="802"><span class="lineNum">     802 </span>            : typedef struct {</a>
+<a name="803"><span class="lineNum">     803 </span>            :   /** Pointer to data */</a>
+<a name="804"><span class="lineNum">     804 </span>            :   const void* ptr;</a>
+<a name="805"><span class="lineNum">     805 </span>            :   /** Number of elements (in case pointing to an array) */</a>
+<a name="806"><span class="lineNum">     806 </span>            :   __PLUMED_WRAPPER_STD size_t nelem;</a>
+<a name="807"><span class="lineNum">     807 </span>            :   /** Shape (scanned up to a zero value is found) */</a>
+<a name="808"><span class="lineNum">     808 </span>            :   const __PLUMED_WRAPPER_STD size_t* shape;</a>
+<a name="809"><span class="lineNum">     809 </span>            :   /**</a>
+<a name="810"><span class="lineNum">     810 </span>            :     sum of:</a>
+<a name="811"><span class="lineNum">     811 </span>            :     sizeof(pointed data), up to 0x10000 (65536). 0 means size not checked</a>
+<a name="812"><span class="lineNum">     812 </span>            :     0x10000    * data type, up to 0xff (255)</a>
+<a name="813"><span class="lineNum">     813 </span>            :                0 not typechecked</a>
+<a name="814"><span class="lineNum">     814 </span>            :                1 void</a>
+<a name="815"><span class="lineNum">     815 </span>            :                2 nullptr</a>
+<a name="816"><span class="lineNum">     816 </span>            :                3 integral</a>
+<a name="817"><span class="lineNum">     817 </span>            :                4 floating point</a>
+<a name="818"><span class="lineNum">     818 </span>            :                5 FILE (size will not be computed as it might be incomplete)</a>
+<a name="819"><span class="lineNum">     819 </span>            :                &gt;5 not typechecked, reserved for future extensions</a>
+<a name="820"><span class="lineNum">     820 </span>            :     0x1000000  * 1 for unsigned (ignored)</a>
+<a name="821"><span class="lineNum">     821 </span>            :     0x2000000  * pointer/const type, up to 8</a>
+<a name="822"><span class="lineNum">     822 </span>            :                0 not typechecked</a>
+<a name="823"><span class="lineNum">     823 </span>            :                1 T (pass-by-value)</a>
+<a name="824"><span class="lineNum">     824 </span>            :                2 T       *</a>
+<a name="825"><span class="lineNum">     825 </span>            :                3 T const *</a>
+<a name="826"><span class="lineNum">     826 </span>            :                4 T       *       *</a>
+<a name="827"><span class="lineNum">     827 </span>            :                5 T       * const *</a>
+<a name="828"><span class="lineNum">     828 </span>            :                6 T const *       *</a>
+<a name="829"><span class="lineNum">     829 </span>            :                7 T const * const *</a>
+<a name="830"><span class="lineNum">     830 </span>            :     0x10000000 * 1 to forbid pointer copy (pointer copy is also forbidden for pass-by-value)</a>
+<a name="831"><span class="lineNum">     831 </span>            :     0x20000000 and higher bits are ignored, reserved for future extensions</a>
+<a name="832"><span class="lineNum">     832 </span>            :   */</a>
+<a name="833"><span class="lineNum">     833 </span>            :   __PLUMED_WRAPPER_STD size_t flags;</a>
+<a name="834"><span class="lineNum">     834 </span>            :   /** Optional information, not used yet  */</a>
+<a name="835"><span class="lineNum">     835 </span>            :   const void* opt;</a>
+<a name="836"><span class="lineNum">     836 </span>            : } plumed_safeptr;</a>
+<a name="837"><span class="lineNum">     837 </span>            : </a>
+<a name="838"><span class="lineNum">     838 </span>            : /**</a>
+<a name="839"><span class="lineNum">     839 </span>            :   Small structure that is only defined locally to retrieve errors.</a>
+<a name="840"><span class="lineNum">     840 </span>            : </a>
+<a name="841"><span class="lineNum">     841 </span>            :   It is supposed to be used in the C11/C++ plumed_cmd interface as follows:</a>
+<a name="842"><span class="lineNum">     842 </span>            : \verbatim</a>
+<a name="843"><span class="lineNum">     843 </span>            :   plumed p;</a>
+<a name="844"><span class="lineNum">     844 </span>            :   plumed_error error;</a>
+<a name="845"><span class="lineNum">     845 </span>            : </a>
+<a name="846"><span class="lineNum">     846 </span>            :   p=plumed_create();</a>
+<a name="847"><span class="lineNum">     847 </span>            : </a>
+<a name="848"><span class="lineNum">     848 </span>            :   plumed_cmd(p,&quot;setNatoms&quot;,10,&amp;error);</a>
+<a name="849"><span class="lineNum">     849 </span>            :   if(error.code) {</a>
+<a name="850"><span class="lineNum">     850 </span>            :     fprintf(errors,&quot;%d\n&quot;,error.code);</a>
+<a name="851"><span class="lineNum">     851 </span>            :     plumed_error_finalize(error); // make sure the error object is finalized!</a>
+<a name="852"><span class="lineNum">     852 </span>            :   }</a>
+<a name="853"><span class="lineNum">     853 </span>            :   // if no error was raised (error.code==0), it is not necessary to call plumed_error_finalize.</a>
+<a name="854"><span class="lineNum">     854 </span>            :   // but doing it is harmless</a>
+<a name="855"><span class="lineNum">     855 </span>            : </a>
+<a name="856"><span class="lineNum">     856 </span>            :   // no need to initialize error, it is written in the plumed_cmd function</a>
+<a name="857"><span class="lineNum">     857 </span>            :   plumed_cmd(p,&quot;init&quot;,&amp;error);</a>
+<a name="858"><span class="lineNum">     858 </span>            :   if(error.code) {</a>
+<a name="859"><span class="lineNum">     859 </span>            :     fprintf(errors,&quot;%d\n&quot;,error.code);</a>
+<a name="860"><span class="lineNum">     860 </span>            :     plumed_error_finalize(error); // make sure the error object is finalized!</a>
+<a name="861"><span class="lineNum">     861 </span>            :   }</a>
+<a name="862"><span class="lineNum">     862 </span>            : \endverbatim</a>
+<a name="863"><span class="lineNum">     863 </span>            : </a>
+<a name="864"><span class="lineNum">     864 </span>            :   The layout of this structure is subject to change, thus all the functions manipulating it</a>
+<a name="865"><span class="lineNum">     865 </span>            :   are defined as inline/static functions. In the future, we might reach some form</a>
+<a name="866"><span class="lineNum">     866 </span>            :   of ABI stability, and these functions might be moved below to the implementation</a>
+<a name="867"><span class="lineNum">     867 </span>            :   file.</a>
+<a name="868"><span class="lineNum">     868 </span>            : </a>
+<a name="869"><span class="lineNum">     869 </span>            :   Notice that there is a macro plumed_error() defined in the PLUMED source code</a>
+<a name="870"><span class="lineNum">     870 </span>            :   (at tools/Exception.h). There is no conflict with this type since C preprocessor</a>
+<a name="871"><span class="lineNum">     871 </span>            :   distinguishes macros and function-like macros.</a>
+<a name="872"><span class="lineNum">     872 </span>            : */</a>
+<a name="873"><span class="lineNum">     873 </span>            : typedef struct plumed_error {</a>
+<a name="874"><span class="lineNum">     874 </span>            :   /** code used for translating messages */</a>
+<a name="875"><span class="lineNum">     875 </span>            :   int code;</a>
+<a name="876"><span class="lineNum">     876 </span>            :   /** error code for system_error */</a>
+<a name="877"><span class="lineNum">     877 </span>            :   int error_code;</a>
+<a name="878"><span class="lineNum">     878 </span>            :   /** message */</a>
+<a name="879"><span class="lineNum">     879 </span>            :   const char* what;</a>
+<a name="880"><span class="lineNum">     880 </span>            :   /** the buffer containing the message to be deallocated */</a>
+<a name="881"><span class="lineNum">     881 </span>            :   char* what_buffer;</a>
+<a name="882"><span class="lineNum">     882 </span>            :   /** pointer to nested exception */</a>
+<a name="883"><span class="lineNum">     883 </span>            :   struct plumed_error* nested;</a>
+<a name="884"><span class="lineNum">     884 </span>            : } plumed_error;</a>
+<a name="885"><span class="lineNum">     885 </span>            : </a>
+<a name="886"><span class="lineNum">     886 </span>            : /** Initialize error (for internal usage) */</a>
+<a name="887"><span class="lineNum">     887 </span>            : __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_init(plumed_error* error) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="888"><span class="lineNum">     888 </span>            :   assert(error);</a>
+<a name="889"><span class="lineNum">     889 </span><span class="lineCov">      12959 :   error-&gt;code=0;</span></a>
+<a name="890"><span class="lineNum">     890 </span><span class="lineCov">      12959 :   error-&gt;error_code=0;</span></a>
+<a name="891"><span class="lineNum">     891 </span><span class="lineCov">      12959 :   error-&gt;what=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="892"><span class="lineNum">     892 </span><span class="lineCov">      12959 :   error-&gt;what_buffer=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="893"><span class="lineNum">     893 </span><span class="lineCov">      12959 :   error-&gt;nested=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="894"><span class="lineNum">     894 </span>            : }</a>
+<a name="895"><span class="lineNum">     895 </span>            : </a>
+<a name="896"><span class="lineNum">     896 </span>            : /** Finalize error - should be called when an error is raised to avoid leaks */</a>
+<a name="897"><span class="lineNum">     897 </span><span class="lineNoCov">          0 : __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_finalize(plumed_error error) __PLUMED_WRAPPER_CXX_NOEXCEPT {</span></a>
+<a name="898"><span class="lineNum">     898 </span><span class="lineNoCov">          0 :   if(!error.code) return;</span></a>
+<a name="899"><span class="lineNum">     899 </span><span class="lineNoCov">          0 :   if(error.nested) {</span></a>
+<a name="900"><span class="lineNum">     900 </span><span class="lineNoCov">          0 :     plumed_error_finalize(*error.nested);</span></a>
+<a name="901"><span class="lineNum">     901 </span><span class="lineNoCov">          0 :     plumed_free(error.nested);</span></a>
+<a name="902"><span class="lineNum">     902 </span>            :   }</a>
+<a name="903"><span class="lineNum">     903 </span><span class="lineNoCov">          0 :   if(error.what_buffer) {</span></a>
+<a name="904"><span class="lineNum">     904 </span><span class="lineNoCov">          0 :     plumed_free(error.what_buffer);</span></a>
+<a name="905"><span class="lineNum">     905 </span>            :   }</a>
+<a name="906"><span class="lineNum">     906 </span>            : }</a>
+<a name="907"><span class="lineNum">     907 </span>            : </a>
+<a name="908"><span class="lineNum">     908 </span>            : /** Access message - more robust than directly accessing what ptr, for future extensibility */</a>
+<a name="909"><span class="lineNum">     909 </span>            : __PLUMED_WRAPPER_STATIC_INLINE const char* plumed_error_what(plumed_error error) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="910"><span class="lineNum">     910 </span>            :   return error.what;</a>
+<a name="911"><span class="lineNum">     911 </span>            : }</a>
+<a name="912"><span class="lineNum">     912 </span>            : </a>
+<a name="913"><span class="lineNum">     913 </span>            : /** Set error to bad_alloc (for internal usage).</a>
+<a name="914"><span class="lineNum">     914 </span>            :     At variance with plumed_error_init, it also finalizes the error, possibly</a>
+<a name="915"><span class="lineNum">     915 </span>            :     deallocating any buffer.</a>
+<a name="916"><span class="lineNum">     916 </span>            : */</a>
+<a name="917"><span class="lineNum">     917 </span><span class="lineNoCov">          0 : __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_set_bad_alloc(plumed_error*error) {</span></a>
+<a name="918"><span class="lineNum">     918 </span>            :   assert(error);</a>
+<a name="919"><span class="lineNum">     919 </span><span class="lineNoCov">          0 :   plumed_error_finalize(*error);</span></a>
+<a name="920"><span class="lineNum">     920 </span>            :   plumed_error_init(error);</a>
+<a name="921"><span class="lineNum">     921 </span><span class="lineNoCov">          0 :   error-&gt;what=&quot;[msg erased due to allocation failure]&quot;;</span></a>
+<a name="922"><span class="lineNum">     922 </span><span class="lineNoCov">          0 :   error-&gt;code=11400;</span></a>
+<a name="923"><span class="lineNum">     923 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="924"><span class="lineNum">     924 </span>            : </a>
+<a name="925"><span class="lineNum">     925 </span>            : /** Recursive merge (for internal usage) */</a>
+<a name="926"><span class="lineNum">     926 </span>            : __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_recursive_merge(plumed_error* error,char*buffer,const char*join,__PLUMED_WRAPPER_STD size_t*len) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="927"><span class="lineNum">     927 </span>            :   if(error-&gt;nested) plumed_error_recursive_merge(error-&gt;nested,buffer,join,len);</a>
+<a name="928"><span class="lineNum">     928 </span>            :   __PLUMED_WRAPPER_STD strncat(buffer,plumed_error_what(*error),*len);</a>
+<a name="929"><span class="lineNum">     929 </span>            :   *len -= __PLUMED_WRAPPER_STD strlen(plumed_error_what(*error));</a>
+<a name="930"><span class="lineNum">     930 </span>            :   __PLUMED_WRAPPER_STD strncat(buffer,join,*len);</a>
+<a name="931"><span class="lineNum">     931 </span>            :   *len -= __PLUMED_WRAPPER_STD strlen(join);</a>
+<a name="932"><span class="lineNum">     932 </span>            : }</a>
+<a name="933"><span class="lineNum">     933 </span>            : </a>
+<a name="934"><span class="lineNum">     934 </span>            : /** Merge with nested exceptions */</a>
+<a name="935"><span class="lineNum">     935 </span>            : __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_merge_with_nested(plumed_error* error) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="936"><span class="lineNum">     936 </span>            :   __PLUMED_WRAPPER_STD size_t len;</a>
+<a name="937"><span class="lineNum">     937 </span>            :   __PLUMED_WRAPPER_STD size_t len_join;</a>
+<a name="938"><span class="lineNum">     938 </span>            :   /* The is temporarily holding the new message */</a>
+<a name="939"><span class="lineNum">     939 </span>            :   char* new_buffer;</a>
+<a name="940"><span class="lineNum">     940 </span>            :   /* This is the string used to concatenate messages */</a>
+<a name="941"><span class="lineNum">     941 </span>            :   const char* join=&quot;\n\nThe above exception was the direct cause of the following exception:\n&quot;;</a>
+<a name="942"><span class="lineNum">     942 </span>            :   /* This is used to iterate over the linked list of nested exceptions */</a>
+<a name="943"><span class="lineNum">     943 </span>            :   plumed_error*e;</a>
+<a name="944"><span class="lineNum">     944 </span>            : </a>
+<a name="945"><span class="lineNum">     945 </span>            :   /* If exception is not nested, nothing to do */</a>
+<a name="946"><span class="lineNum">     946 </span>            :   if(!error-&gt;nested) return;</a>
+<a name="947"><span class="lineNum">     947 </span>            : </a>
+<a name="948"><span class="lineNum">     948 </span>            :   /* Accumulate the total length of the concatenated message */</a>
+<a name="949"><span class="lineNum">     949 </span>            :   len_join=__PLUMED_WRAPPER_STD strlen(join);</a>
+<a name="950"><span class="lineNum">     950 </span>            :   e=error;</a>
+<a name="951"><span class="lineNum">     951 </span>            :   len=__PLUMED_WRAPPER_STD strlen(plumed_error_what(*e));</a>
+<a name="952"><span class="lineNum">     952 </span>            :   while(e-&gt;nested) {</a>
+<a name="953"><span class="lineNum">     953 </span>            :     e=e-&gt;nested;</a>
+<a name="954"><span class="lineNum">     954 </span>            :     len+=len_join+__PLUMED_WRAPPER_STD strlen(plumed_error_what(*e));</a>
+<a name="955"><span class="lineNum">     955 </span>            :   }</a>
+<a name="956"><span class="lineNum">     956 </span>            : </a>
+<a name="957"><span class="lineNum">     957 </span>            :   /* Allocate the new message */</a>
+<a name="958"><span class="lineNum">     958 </span>            :   new_buffer=(char*)plumed_malloc(len+1);</a>
+<a name="959"><span class="lineNum">     959 </span>            :   if(new_buffer) {</a>
+<a name="960"><span class="lineNum">     960 </span>            :     /* If allocation was successful, merge the messages */</a>
+<a name="961"><span class="lineNum">     961 </span>            :     new_buffer[0]='\0';</a>
+<a name="962"><span class="lineNum">     962 </span>            :     /* Notice that we have a forward linked list but we need to go through that in backward order</a>
+<a name="963"><span class="lineNum">     963 </span>            :        (inner to outer). To do that without allocating an additional array, we use a recursive</a>
+<a name="964"><span class="lineNum">     964 </span>            :        function.</a>
+<a name="965"><span class="lineNum">     965 </span>            :     */</a>
+<a name="966"><span class="lineNum">     966 </span>            :     assert(error-&gt;nested);</a>
+<a name="967"><span class="lineNum">     967 </span>            :     plumed_error_recursive_merge(error-&gt;nested,new_buffer,join,&amp;len);</a>
+<a name="968"><span class="lineNum">     968 </span>            :     __PLUMED_WRAPPER_STD strncat(new_buffer,plumed_error_what(*error),len);</a>
+<a name="969"><span class="lineNum">     969 </span>            :     len -= __PLUMED_WRAPPER_STD strlen(plumed_error_what(*error));</a>
+<a name="970"><span class="lineNum">     970 </span>            :     /* we keep track of length of buffer for safety */</a>
+<a name="971"><span class="lineNum">     971 </span>            :     assert(len==0);</a>
+<a name="972"><span class="lineNum">     972 </span>            :   }</a>
+<a name="973"><span class="lineNum">     973 </span>            :   error-&gt;what=new_buffer;</a>
+<a name="974"><span class="lineNum">     974 </span>            : </a>
+<a name="975"><span class="lineNum">     975 </span>            :   /* Deallocate the previous message */</a>
+<a name="976"><span class="lineNum">     976 </span>            :   if(error-&gt;what_buffer) plumed_free(error-&gt;what_buffer);</a>
+<a name="977"><span class="lineNum">     977 </span>            :   error-&gt;what_buffer=new_buffer;</a>
+<a name="978"><span class="lineNum">     978 </span>            : </a>
+<a name="979"><span class="lineNum">     979 </span>            :   /* Finalize the chain of nested exceptions */</a>
+<a name="980"><span class="lineNum">     980 </span>            :   plumed_error_finalize(*error-&gt;nested);</a>
+<a name="981"><span class="lineNum">     981 </span>            :   plumed_free(error-&gt;nested);</a>
+<a name="982"><span class="lineNum">     982 </span>            :   error-&gt;nested=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="983"><span class="lineNum">     983 </span>            : </a>
+<a name="984"><span class="lineNum">     984 </span>            :   if(!error-&gt;what) {</a>
+<a name="985"><span class="lineNum">     985 </span>            :     /* If allocation was not successful, reset to bad_alloc */</a>
+<a name="986"><span class="lineNum">     986 </span>            :     plumed_error_set_bad_alloc(error);</a>
+<a name="987"><span class="lineNum">     987 </span>            :   }</a>
+<a name="988"><span class="lineNum">     988 </span>            : }</a>
+<a name="989"><span class="lineNum">     989 </span>            : </a>
+<a name="990"><span class="lineNum">     990 </span>            : /** Rethrow error (calling abort) */</a>
+<a name="991"><span class="lineNum">     991 </span>            : __PLUMED_WRAPPER_CXX_NORETURN __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_rethrow(plumed_error h) {</a>
+<a name="992"><span class="lineNum">     992 </span>            :   if(h.nested) plumed_error_merge_with_nested(&amp;h);</a>
+<a name="993"><span class="lineNum">     993 </span>            :   __PLUMED_WRAPPER_STD fprintf(stderr,&quot;Terminate due to exception. Code: %d\n%s\n&quot;,h.code,plumed_error_what(h));</a>
+<a name="994"><span class="lineNum">     994 </span>            :   __PLUMED_WRAPPER_STD abort();</a>
+<a name="995"><span class="lineNum">     995 </span>            : }</a>
+<a name="996"><span class="lineNum">     996 </span>            : </a>
+<a name="997"><span class="lineNum">     997 </span>            : /** Callback (for internal usage) */</a>
+<a name="998"><span class="lineNum">     998 </span><span class="lineNoCov">          0 : __PLUMED_WRAPPER_STATIC_INLINE void plumed_error_set(void*ptr,int code,const char*what,const void* opt) __PLUMED_WRAPPER_CXX_NOEXCEPT {</span></a>
+<a name="999"><span class="lineNum">     999 </span>            :   plumed_error* error;</a>
+<a name="1000"><span class="lineNum">    1000 </span>            :   __PLUMED_WRAPPER_STD size_t len;</a>
+<a name="1001"><span class="lineNum">    1001 </span>            :   void*const* options;</a>
+<a name="1002"><span class="lineNum">    1002 </span>            : </a>
+<a name="1003"><span class="lineNum">    1003 </span>            :   error=(plumed_error*) ptr;</a>
+<a name="1004"><span class="lineNum">    1004 </span>            : </a>
+<a name="1005"><span class="lineNum">    1005 </span><span class="lineNoCov">          0 :   error-&gt;code=code;</span></a>
+<a name="1006"><span class="lineNum">    1006 </span><span class="lineNoCov">          0 :   error-&gt;error_code=0;</span></a>
+<a name="1007"><span class="lineNum">    1007 </span><span class="lineNoCov">          0 :   len=__PLUMED_WRAPPER_STD strlen(what);</span></a>
+<a name="1008"><span class="lineNum">    1008 </span><span class="lineNoCov">          0 :   error-&gt;what_buffer=(char*) plumed_malloc(len+1);</span></a>
+<a name="1009"><span class="lineNum">    1009 </span><span class="lineNoCov">          0 :   if(!error-&gt;what_buffer) {</span></a>
+<a name="1010"><span class="lineNum">    1010 </span><span class="lineNoCov">          0 :     plumed_error_set_bad_alloc(error);</span></a>
+<a name="1011"><span class="lineNum">    1011 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="1012"><span class="lineNum">    1012 </span>            :   }</a>
+<a name="1013"><span class="lineNum">    1013 </span>            : </a>
+<a name="1014"><span class="lineNum">    1014 </span>            :   __PLUMED_WRAPPER_STD strncpy(error-&gt;what_buffer,what,len+1);</a>
+<a name="1015"><span class="lineNum">    1015 </span><span class="lineNoCov">          0 :   error-&gt;what=error-&gt;what_buffer;</span></a>
+<a name="1016"><span class="lineNum">    1016 </span>            : </a>
+<a name="1017"><span class="lineNum">    1017 </span>            :   /* interpret optional arguments */</a>
+<a name="1018"><span class="lineNum">    1018 </span><span class="lineNoCov">          0 :   if(opt) {</span></a>
+<a name="1019"><span class="lineNum">    1019 </span>            :     options=(void*const*)opt;</a>
+<a name="1020"><span class="lineNum">    1020 </span><span class="lineNoCov">          0 :     while(*options) {</span></a>
+<a name="1021"><span class="lineNum">    1021 </span>            :       /* c: error code */</a>
+<a name="1022"><span class="lineNum">    1022 </span><span class="lineNoCov">          0 :       if(*((const char*)*options)=='c' &amp;&amp; *(options+1)) {</span></a>
+<a name="1023"><span class="lineNum">    1023 </span><span class="lineNoCov">          0 :         error-&gt;error_code=*((const int*)*(options+1));</span></a>
+<a name="1024"><span class="lineNum">    1024 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="1025"><span class="lineNum">    1025 </span>            :       }</a>
+<a name="1026"><span class="lineNum">    1026 </span><span class="lineNoCov">          0 :       options+=2;</span></a>
+<a name="1027"><span class="lineNum">    1027 </span>            :     }</a>
+<a name="1028"><span class="lineNum">    1028 </span>            :     options=(void*const*)opt;</a>
+<a name="1029"><span class="lineNum">    1029 </span><span class="lineNoCov">          0 :     while(*options) {</span></a>
+<a name="1030"><span class="lineNum">    1030 </span>            :       /* n: nested exception */</a>
+<a name="1031"><span class="lineNum">    1031 </span><span class="lineNoCov">          0 :       if(*((const char*)*options)=='n' &amp;&amp; *(options+1)) {</span></a>
+<a name="1032"><span class="lineNum">    1032 </span>            :         /* notice that once this is allocated it is guaranteed to be deallocated by the recursive destructor */</a>
+<a name="1033"><span class="lineNum">    1033 </span><span class="lineNoCov">          0 :         error-&gt;nested=(plumed_error*) plumed_malloc(sizeof(plumed_error));</span></a>
+<a name="1034"><span class="lineNum">    1034 </span>            :         /* this is if malloc fails */</a>
+<a name="1035"><span class="lineNum">    1035 </span><span class="lineNoCov">          0 :         if(!error-&gt;nested) {</span></a>
+<a name="1036"><span class="lineNum">    1036 </span><span class="lineNoCov">          0 :           plumed_error_set_bad_alloc(error);</span></a>
+<a name="1037"><span class="lineNum">    1037 </span><span class="lineNoCov">          0 :           break;</span></a>
+<a name="1038"><span class="lineNum">    1038 </span>            :         }</a>
+<a name="1039"><span class="lineNum">    1039 </span>            :         plumed_error_init((plumed_error*)error-&gt;nested);</a>
+<a name="1040"><span class="lineNum">    1040 </span>            :         /* plumed will make sure to only use this if it is not null */</a>
+<a name="1041"><span class="lineNum">    1041 </span><span class="lineNoCov">          0 :         *(void**)*(options+1)=error-&gt;nested;</span></a>
+<a name="1042"><span class="lineNum">    1042 </span><span class="lineNoCov">          0 :         break;</span></a>
+<a name="1043"><span class="lineNum">    1043 </span>            :       }</a>
+<a name="1044"><span class="lineNum">    1044 </span><span class="lineNoCov">          0 :       options+=2;</span></a>
+<a name="1045"><span class="lineNum">    1045 </span>            :     }</a>
+<a name="1046"><span class="lineNum">    1046 </span>            :   }</a>
+<a name="1047"><span class="lineNum">    1047 </span>            : }</a>
+<a name="1048"><span class="lineNum">    1048 </span>            : </a>
+<a name="1049"><span class="lineNum">    1049 </span>            : /** \relates plumed</a>
+<a name="1050"><span class="lineNum">    1050 </span>            :     \brief Constructor</a>
+<a name="1051"><span class="lineNum">    1051 </span>            : </a>
+<a name="1052"><span class="lineNum">    1052 </span>            :     Constructs a plumed object.</a>
+<a name="1053"><span class="lineNum">    1053 </span>            : </a>
+<a name="1054"><span class="lineNum">    1054 </span>            :     Notice that if you are linking against libplumedWrapper.a, if you are</a>
+<a name="1055"><span class="lineNum">    1055 </span>            :     using a code patched in runtime mode, or if you are including the `Plumed.c`</a>
+<a name="1056"><span class="lineNum">    1056 </span>            :     file directly in your code, this constructor might return an invalid plumed</a>
+<a name="1057"><span class="lineNum">    1057 </span>            :     object. In particular, this could happen if the `PLUMED_KERNEL` environment</a>
+<a name="1058"><span class="lineNum">    1058 </span>            :     variable is not set or set incorrectly. In order to detect an incorrect</a>
+<a name="1059"><span class="lineNum">    1059 </span>            :     plumed object you might use \ref plumed_valid() on the resulting object.</a>
+<a name="1060"><span class="lineNum">    1060 </span>            :     Alternatively, if you use \ref plumed_cmd() on an invalid plumed object the code will exit.</a>
+<a name="1061"><span class="lineNum">    1061 </span>            :     Also notice that to avoid memory leaks you should call \ref plumed_finalize()</a>
+<a name="1062"><span class="lineNum">    1062 </span>            :     to finalize a plumed object even if it is invalid:</a>
+<a name="1063"><span class="lineNum">    1063 </span>            : \verbatim</a>
+<a name="1064"><span class="lineNum">    1064 </span>            :   plumed p=plumed_create();</a>
+<a name="1065"><span class="lineNum">    1065 </span>            :   if(!plumed_valid(p)) {</a>
+<a name="1066"><span class="lineNum">    1066 </span>            : // this will happen if the PLUMED_KERNEL variable is not set correctly</a>
+<a name="1067"><span class="lineNum">    1067 </span>            :     plumed_finalize(p);</a>
+<a name="1068"><span class="lineNum">    1068 </span>            :     return whatever;</a>
+<a name="1069"><span class="lineNum">    1069 </span>            :   }</a>
+<a name="1070"><span class="lineNum">    1070 </span>            : \endverbatim</a>
+<a name="1071"><span class="lineNum">    1071 </span>            : </a>
+<a name="1072"><span class="lineNum">    1072 </span>            :     \return The constructed plumed object</a>
+<a name="1073"><span class="lineNum">    1073 </span>            : */</a>
+<a name="1074"><span class="lineNum">    1074 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1075"><span class="lineNum">    1075 </span>            : plumed plumed_create(void);</a>
+<a name="1076"><span class="lineNum">    1076 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1077"><span class="lineNum">    1077 </span>            : </a>
+<a name="1078"><span class="lineNum">    1078 </span>            : /** \relates plumed</a>
+<a name="1079"><span class="lineNum">    1079 </span>            :     \brief Constructor from path. Available as of PLUMED 2.5</a>
+<a name="1080"><span class="lineNum">    1080 </span>            : </a>
+<a name="1081"><span class="lineNum">    1081 </span>            :     It tries to construct a plumed object loading the kernel located at path.</a>
+<a name="1082"><span class="lineNum">    1082 </span>            :     Notice that it could leave the resulting object in an invalid state.</a>
+<a name="1083"><span class="lineNum">    1083 </span>            :     In order to detect an invalid</a>
+<a name="1084"><span class="lineNum">    1084 </span>            :     plumed object you might use \ref plumed_valid() on the resulting object.</a>
+<a name="1085"><span class="lineNum">    1085 </span>            :     Alternatively, if you use \ref plumed_cmd() on an invalid plumed object the code will exit.</a>
+<a name="1086"><span class="lineNum">    1086 </span>            : </a>
+<a name="1087"><span class="lineNum">    1087 </span>            :     Also notice that to avoid memory leaks you should call \ref plumed_finalize()</a>
+<a name="1088"><span class="lineNum">    1088 </span>            :     to finalize a plumed object even if it is invalid.</a>
+<a name="1089"><span class="lineNum">    1089 </span>            : \verbatim</a>
+<a name="1090"><span class="lineNum">    1090 </span>            :   plumed p=plumed_create(path);</a>
+<a name="1091"><span class="lineNum">    1091 </span>            :   if(!plumed_valid(p)) {</a>
+<a name="1092"><span class="lineNum">    1092 </span>            : // this will happen if the path argument is not set correctly</a>
+<a name="1093"><span class="lineNum">    1093 </span>            :     plumed_finalize(p);</a>
+<a name="1094"><span class="lineNum">    1094 </span>            :     return whatever;</a>
+<a name="1095"><span class="lineNum">    1095 </span>            :   }</a>
+<a name="1096"><span class="lineNum">    1096 </span>            : \endverbatim</a>
+<a name="1097"><span class="lineNum">    1097 </span>            : </a>
+<a name="1098"><span class="lineNum">    1098 </span>            :     \return The constructed plumed object</a>
+<a name="1099"><span class="lineNum">    1099 </span>            : */</a>
+<a name="1100"><span class="lineNum">    1100 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1101"><span class="lineNum">    1101 </span>            : plumed plumed_create_dlopen(const char*path);</a>
+<a name="1102"><span class="lineNum">    1102 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1103"><span class="lineNum">    1103 </span>            : </a>
+<a name="1104"><span class="lineNum">    1104 </span>            : </a>
+<a name="1105"><span class="lineNum">    1105 </span>            : /**</a>
+<a name="1106"><span class="lineNum">    1106 </span>            :   \brief Constructor from path. Available as of PLUMED 2.5</a>
+<a name="1107"><span class="lineNum">    1107 </span>            : </a>
+<a name="1108"><span class="lineNum">    1108 </span>            :   Same as \ref plumed_create_dlopen, but also allows to specify the mode for dlopen.</a>
+<a name="1109"><span class="lineNum">    1109 </span>            : </a>
+<a name="1110"><span class="lineNum">    1110 </span>            :   \warning</a>
+<a name="1111"><span class="lineNum">    1111 </span>            :   Use with care, since not all the possible modes work correctly with PLUMED.</a>
+<a name="1112"><span class="lineNum">    1112 </span>            : */</a>
+<a name="1113"><span class="lineNum">    1113 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1114"><span class="lineNum">    1114 </span>            : plumed plumed_create_dlopen2(const char*path,int mode);</a>
+<a name="1115"><span class="lineNum">    1115 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1116"><span class="lineNum">    1116 </span>            : </a>
+<a name="1117"><span class="lineNum">    1117 </span>            : /**</a>
+<a name="1118"><span class="lineNum">    1118 </span>            :   \brief Constructor from dlopen handle. Available as of PLUMED 2.8</a>
+<a name="1119"><span class="lineNum">    1119 </span>            : </a>
+<a name="1120"><span class="lineNum">    1120 </span>            :   Same as  \ref plumed_create_dlopen, but it acts on an already loaded library.</a>
+<a name="1121"><span class="lineNum">    1121 </span>            :   This allows to separate the library loading from the construction of the</a>
+<a name="1122"><span class="lineNum">    1122 </span>            :   plumed object. By using this function, the caller takes the responsibility</a>
+<a name="1123"><span class="lineNum">    1123 </span>            :   to later use dlclose on this handle.</a>
+<a name="1124"><span class="lineNum">    1124 </span>            : */</a>
+<a name="1125"><span class="lineNum">    1125 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1126"><span class="lineNum">    1126 </span>            : plumed plumed_create_dlsym(void* dlhandle);</a>
+<a name="1127"><span class="lineNum">    1127 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1128"><span class="lineNum">    1128 </span>            : </a>
+<a name="1129"><span class="lineNum">    1129 </span>            : /** \relates plumed</a>
+<a name="1130"><span class="lineNum">    1130 </span>            :     Create a new reference to an existing object, increasing its reference count. Available as of PLUMED 2.5</a>
+<a name="1131"><span class="lineNum">    1131 </span>            : </a>
+<a name="1132"><span class="lineNum">    1132 </span>            :     Use it to increase by one the reference count of a plumed object.</a>
+<a name="1133"><span class="lineNum">    1133 </span>            :     The resulting pointer might be identical to the one passed as an</a>
+<a name="1134"><span class="lineNum">    1134 </span>            :     argument, but the reference count will be incremented by one.</a>
+<a name="1135"><span class="lineNum">    1135 </span>            :     Notice that you should finalize the resulting object.</a>
+<a name="1136"><span class="lineNum">    1136 </span>            : \verbatim</a>
+<a name="1137"><span class="lineNum">    1137 </span>            :   plumed p1;</a>
+<a name="1138"><span class="lineNum">    1138 </span>            :   plumed p2;</a>
+<a name="1139"><span class="lineNum">    1139 </span>            :   p1=plumed_create();</a>
+<a name="1140"><span class="lineNum">    1140 </span>            :   p2=plumed_create_reference(p1);</a>
+<a name="1141"><span class="lineNum">    1141 </span>            :   plumed_finalize(p1);</a>
+<a name="1142"><span class="lineNum">    1142 </span>            : // now you can still use p2</a>
+<a name="1143"><span class="lineNum">    1143 </span>            :   plumed_cmd(p2,&quot;init&quot;,NULL);</a>
+<a name="1144"><span class="lineNum">    1144 </span>            :   plumed_finalize(p2);</a>
+<a name="1145"><span class="lineNum">    1145 </span>            : // now the underlying object is destroyed.</a>
+<a name="1146"><span class="lineNum">    1146 </span>            : \endverbatim</a>
+<a name="1147"><span class="lineNum">    1147 </span>            : </a>
+<a name="1148"><span class="lineNum">    1148 </span>            :     If the `p` object is invalid, also the returned object will be invalid.</a>
+<a name="1149"><span class="lineNum">    1149 </span>            : </a>
+<a name="1150"><span class="lineNum">    1150 </span>            :     \param p The plumed object that will be referenced to.</a>
+<a name="1151"><span class="lineNum">    1151 </span>            :     \return The constructed plumed object</a>
+<a name="1152"><span class="lineNum">    1152 </span>            : */</a>
+<a name="1153"><span class="lineNum">    1153 </span>            : </a>
+<a name="1154"><span class="lineNum">    1154 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1155"><span class="lineNum">    1155 </span>            : plumed plumed_create_reference(plumed p);</a>
+<a name="1156"><span class="lineNum">    1156 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1157"><span class="lineNum">    1157 </span>            : </a>
+<a name="1158"><span class="lineNum">    1158 </span>            : /** \relates plumed</a>
+<a name="1159"><span class="lineNum">    1159 </span>            :     \brief Create a new reference to an existing object passed as a void pointer, increasing its reference count. Available as of PLUMED 2.5</a>
+<a name="1160"><span class="lineNum">    1160 </span>            : </a>
+<a name="1161"><span class="lineNum">    1161 </span>            :   \return The constructed plumed object</a>
+<a name="1162"><span class="lineNum">    1162 </span>            : */</a>
+<a name="1163"><span class="lineNum">    1163 </span>            : </a>
+<a name="1164"><span class="lineNum">    1164 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1165"><span class="lineNum">    1165 </span>            : plumed plumed_create_reference_v(void*v);</a>
+<a name="1166"><span class="lineNum">    1166 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1167"><span class="lineNum">    1167 </span>            : </a>
+<a name="1168"><span class="lineNum">    1168 </span>            : /** \relates plumed</a>
+<a name="1169"><span class="lineNum">    1169 </span>            :     \brief Create a new reference to an existing object passed as a fortran string, increasing its reference count. Available as of PLUMED 2.5</a>
+<a name="1170"><span class="lineNum">    1170 </span>            : </a>
+<a name="1171"><span class="lineNum">    1171 </span>            :   \return The constructed plumed object</a>
+<a name="1172"><span class="lineNum">    1172 </span>            : */</a>
+<a name="1173"><span class="lineNum">    1173 </span>            : </a>
+<a name="1174"><span class="lineNum">    1174 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1175"><span class="lineNum">    1175 </span>            : plumed plumed_create_reference_f(const char*f);</a>
+<a name="1176"><span class="lineNum">    1176 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1177"><span class="lineNum">    1177 </span>            : </a>
+<a name="1178"><span class="lineNum">    1178 </span>            : /** \relates plumed</a>
+<a name="1179"><span class="lineNum">    1179 </span>            :     \brief Constructor as invalid. Available as of PLUMED 2.5</a>
+<a name="1180"><span class="lineNum">    1180 </span>            : </a>
+<a name="1181"><span class="lineNum">    1181 </span>            :    Can be used to create an object in the same state as if it was returned by</a>
+<a name="1182"><span class="lineNum">    1182 </span>            :    plumed_create_dlopen with an incorrect path (or plumed_create using runtime binding</a>
+<a name="1183"><span class="lineNum">    1183 </span>            :    and an incorrect PLUMED_KERNEL).</a>
+<a name="1184"><span class="lineNum">    1184 </span>            : </a>
+<a name="1185"><span class="lineNum">    1185 </span>            :    Can be used to initialize a plumed object to a well-defined state without explicitly</a>
+<a name="1186"><span class="lineNum">    1186 </span>            :    creating it. The resulting object can be checked later with \ref plumed_valid.</a>
+<a name="1187"><span class="lineNum">    1187 </span>            :    Consider the following example</a>
+<a name="1188"><span class="lineNum">    1188 </span>            : \verbatim</a>
+<a name="1189"><span class="lineNum">    1189 </span>            :     plumed p;</a>
+<a name="1190"><span class="lineNum">    1190 </span>            :     p=plumed_create_invalid();</a>
+<a name="1191"><span class="lineNum">    1191 </span>            : // at this point p is initialized to a well-defined (invalid) state.</a>
+<a name="1192"><span class="lineNum">    1192 </span>            :     setenv(&quot;PLUMED_KERNEL&quot;,&quot;/path/to/kernel/libplumedKernel.so&quot;,1);</a>
+<a name="1193"><span class="lineNum">    1193 </span>            :     plumed_finalize(p);</a>
+<a name="1194"><span class="lineNum">    1194 </span>            :     p=plumed_create();</a>
+<a name="1195"><span class="lineNum">    1195 </span>            : \endverbatim</a>
+<a name="1196"><span class="lineNum">    1196 </span>            : </a>
+<a name="1197"><span class="lineNum">    1197 </span>            :     \return The constructed plumed object</a>
+<a name="1198"><span class="lineNum">    1198 </span>            : */</a>
+<a name="1199"><span class="lineNum">    1199 </span>            : </a>
+<a name="1200"><span class="lineNum">    1200 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1201"><span class="lineNum">    1201 </span>            : plumed plumed_create_invalid();</a>
+<a name="1202"><span class="lineNum">    1202 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1203"><span class="lineNum">    1203 </span>            : </a>
+<a name="1204"><span class="lineNum">    1204 </span>            : /** \relates plumed</a>
+<a name="1205"><span class="lineNum">    1205 </span>            :     \brief Tells p to execute a command.</a>
+<a name="1206"><span class="lineNum">    1206 </span>            : </a>
+<a name="1207"><span class="lineNum">    1207 </span>            :     If the object is not valid (see \ref plumed_valid), this command will exit.</a>
+<a name="1208"><span class="lineNum">    1208 </span>            : </a>
+<a name="1209"><span class="lineNum">    1209 </span>            :     \param p The plumed object on which command is acting</a>
+<a name="1210"><span class="lineNum">    1210 </span>            :     \param key The name of the command to be executed</a>
+<a name="1211"><span class="lineNum">    1211 </span>            :     \param val The argument. It is declared as const to allow calls like plumed_cmd(p,&quot;A&quot;,&quot;B&quot;),</a>
+<a name="1212"><span class="lineNum">    1212 </span>            :                but for some choice of key it can change the content.</a>
+<a name="1213"><span class="lineNum">    1213 </span>            : </a>
+<a name="1214"><span class="lineNum">    1214 </span>            :     Notice that within PLUMED we use a const_cast to remove any const qualifier from the second</a>
+<a name="1215"><span class="lineNum">    1215 </span>            :     argument of \ref plumed_cmd.</a>
+<a name="1216"><span class="lineNum">    1216 </span>            : </a>
+<a name="1217"><span class="lineNum">    1217 </span>            :     In some cases val can be omitted: just pass a NULL pointer (in C++, val is optional and can be omitted,</a>
+<a name="1218"><span class="lineNum">    1218 </span>            :     or you can equivalently pass NULL or nullptr).</a>
+<a name="1219"><span class="lineNum">    1219 </span>            :     The set of possible keys is the real API of the plumed library, and will be expanded with time.</a>
+<a name="1220"><span class="lineNum">    1220 </span>            :     New commands will be added, but backward compatibility will be retained as long as possible.</a>
+<a name="1221"><span class="lineNum">    1221 </span>            : */</a>
+<a name="1222"><span class="lineNum">    1222 </span>            : </a>
+<a name="1223"><span class="lineNum">    1223 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1224"><span class="lineNum">    1224 </span>            : void plumed_cmd(plumed p,const char*key,const void*val);</a>
+<a name="1225"><span class="lineNum">    1225 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1226"><span class="lineNum">    1226 </span>            : </a>
+<a name="1227"><span class="lineNum">    1227 </span>            : /**</a>
+<a name="1228"><span class="lineNum">    1228 </span>            :   \relates plumed</a>
+<a name="1229"><span class="lineNum">    1229 </span>            :   \brief Same as \ref plumed_cmd, but does not throw exceptions.</a>
+<a name="1230"><span class="lineNum">    1230 </span>            : </a>
+<a name="1231"><span class="lineNum">    1231 </span>            :   This function is meant to be used when errors should be handled explicitly.</a>
+<a name="1232"><span class="lineNum">    1232 </span>            :   if an exception is raised within PLUMED, the function nothrow.handler() will</a>
+<a name="1233"><span class="lineNum">    1233 </span>            :   be called with arguments (nothrow.ptr,code,message,opt). This allows the C++ interface</a>
+<a name="1234"><span class="lineNum">    1234 </span>            :   to correctly rethrow exceptions, but might be used from C as well. opt can be used</a>
+<a name="1235"><span class="lineNum">    1235 </span>            :   to pass further information (not used yet).</a>
+<a name="1236"><span class="lineNum">    1236 </span>            : */</a>
+<a name="1237"><span class="lineNum">    1237 </span>            : </a>
+<a name="1238"><span class="lineNum">    1238 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1239"><span class="lineNum">    1239 </span>            : void plumed_cmd_nothrow(plumed p,const char*key,const void*val,plumed_nothrow_handler nothrow);</a>
+<a name="1240"><span class="lineNum">    1240 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1241"><span class="lineNum">    1241 </span>            : </a>
+<a name="1242"><span class="lineNum">    1242 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1243"><span class="lineNum">    1243 </span>            : void plumed_cmd_safe_nothrow(plumed p,const char*key,plumed_safeptr,plumed_nothrow_handler nothrow);</a>
+<a name="1244"><span class="lineNum">    1244 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1245"><span class="lineNum">    1245 </span>            : </a>
+<a name="1246"><span class="lineNum">    1246 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1247"><span class="lineNum">    1247 </span>            : void plumed_cmd_safe(plumed p,const char*key,plumed_safeptr);</a>
+<a name="1248"><span class="lineNum">    1248 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1249"><span class="lineNum">    1249 </span>            : </a>
+<a name="1250"><span class="lineNum">    1250 </span>            : /** \relates plumed</a>
+<a name="1251"><span class="lineNum">    1251 </span>            :     \brief Destructor.</a>
+<a name="1252"><span class="lineNum">    1252 </span>            : </a>
+<a name="1253"><span class="lineNum">    1253 </span>            :     It must be used for any object created using \ref plumed_create(),</a>
+<a name="1254"><span class="lineNum">    1254 </span>            :     even if the created object is not valid.</a>
+<a name="1255"><span class="lineNum">    1255 </span>            : </a>
+<a name="1256"><span class="lineNum">    1256 </span>            :     \param p The plumed object to be deallocated</a>
+<a name="1257"><span class="lineNum">    1257 </span>            : */</a>
+<a name="1258"><span class="lineNum">    1258 </span>            : </a>
+<a name="1259"><span class="lineNum">    1259 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1260"><span class="lineNum">    1260 </span>            : void plumed_finalize(plumed p);</a>
+<a name="1261"><span class="lineNum">    1261 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1262"><span class="lineNum">    1262 </span>            : </a>
+<a name="1263"><span class="lineNum">    1263 </span>            : /** \relates plumed</a>
+<a name="1264"><span class="lineNum">    1264 </span>            :     \brief Check if plumed is installed (for runtime binding).</a>
+<a name="1265"><span class="lineNum">    1265 </span>            : </a>
+<a name="1266"><span class="lineNum">    1266 </span>            :     Notice that this is equivalent to creating a dummy object and checking if it is valid.</a>
+<a name="1267"><span class="lineNum">    1267 </span>            : </a>
+<a name="1268"><span class="lineNum">    1268 </span>            : \verbatim</a>
+<a name="1269"><span class="lineNum">    1269 </span>            :   // this:</a>
+<a name="1270"><span class="lineNum">    1270 </span>            :   //int a=plumed_installed();</a>
+<a name="1271"><span class="lineNum">    1271 </span>            :   // is equivalent to this:</a>
+<a name="1272"><span class="lineNum">    1272 </span>            : </a>
+<a name="1273"><span class="lineNum">    1273 </span>            :   plumed p=plumed_create();</a>
+<a name="1274"><span class="lineNum">    1274 </span>            :   int a=plumed_valid(p);</a>
+<a name="1275"><span class="lineNum">    1275 </span>            :   plumed_finalize(p);</a>
+<a name="1276"><span class="lineNum">    1276 </span>            : </a>
+<a name="1277"><span class="lineNum">    1277 </span>            : \endverbatim</a>
+<a name="1278"><span class="lineNum">    1278 </span>            : </a>
+<a name="1279"><span class="lineNum">    1279 </span>            :     This function is mostly provided for compatibility with PLUMED 2.4, where \ref plumed_valid()</a>
+<a name="1280"><span class="lineNum">    1280 </span>            :     was not available. Using \ref plumed_valid() is now preferred since it creates a single object</a>
+<a name="1281"><span class="lineNum">    1281 </span>            :     instead of creating a dummy object that is then discarded.</a>
+<a name="1282"><span class="lineNum">    1282 </span>            : </a>
+<a name="1283"><span class="lineNum">    1283 </span>            :     \return 1 if plumed is installed, 0 otherwise</a>
+<a name="1284"><span class="lineNum">    1284 </span>            : */</a>
+<a name="1285"><span class="lineNum">    1285 </span>            : </a>
+<a name="1286"><span class="lineNum">    1286 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1287"><span class="lineNum">    1287 </span>            : int plumed_installed(void);</a>
+<a name="1288"><span class="lineNum">    1288 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1289"><span class="lineNum">    1289 </span>            : </a>
+<a name="1290"><span class="lineNum">    1290 </span>            : /** \relates plumed</a>
+<a name="1291"><span class="lineNum">    1291 </span>            :     \brief Check if plumed object is valid. Available as of PLUMED 2.5</a>
+<a name="1292"><span class="lineNum">    1292 </span>            : </a>
+<a name="1293"><span class="lineNum">    1293 </span>            :     It might return false if plumed is not available at runtime.</a>
+<a name="1294"><span class="lineNum">    1294 </span>            : </a>
+<a name="1295"><span class="lineNum">    1295 </span>            :     \return 1 if plumed is valid, 0 otherwise</a>
+<a name="1296"><span class="lineNum">    1296 </span>            : */</a>
+<a name="1297"><span class="lineNum">    1297 </span>            : </a>
+<a name="1298"><span class="lineNum">    1298 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1299"><span class="lineNum">    1299 </span>            : int plumed_valid(plumed p);</a>
+<a name="1300"><span class="lineNum">    1300 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1301"><span class="lineNum">    1301 </span>            : </a>
+<a name="1302"><span class="lineNum">    1302 </span>            : /** \relates plumed</a>
+<a name="1303"><span class="lineNum">    1303 </span>            :     \brief Returns the number of references to the underlying object. Available as of PLUMED 2.5.</a>
+<a name="1304"><span class="lineNum">    1304 </span>            : */</a>
+<a name="1305"><span class="lineNum">    1305 </span>            : </a>
+<a name="1306"><span class="lineNum">    1306 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1307"><span class="lineNum">    1307 </span>            : int plumed_use_count(plumed p);</a>
+<a name="1308"><span class="lineNum">    1308 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1309"><span class="lineNum">    1309 </span>            : </a>
+<a name="1310"><span class="lineNum">    1310 </span>            : </a>
+<a name="1311"><span class="lineNum">    1311 </span>            : /* routines to convert char handler from/to plumed objects */</a>
+<a name="1312"><span class="lineNum">    1312 </span>            : </a>
+<a name="1313"><span class="lineNum">    1313 </span>            : /** \related plumed</a>
+<a name="1314"><span class="lineNum">    1314 </span>            :     \brief Converts a C handler to a FORTRAN handler</a>
+<a name="1315"><span class="lineNum">    1315 </span>            : </a>
+<a name="1316"><span class="lineNum">    1316 </span>            :     \param p The C handler</a>
+<a name="1317"><span class="lineNum">    1317 </span>            :     \param c The FORTRAN handler (a char[32])</a>
+<a name="1318"><span class="lineNum">    1318 </span>            : </a>
+<a name="1319"><span class="lineNum">    1319 </span>            :     This function can be used to convert a plumed object created in C to</a>
+<a name="1320"><span class="lineNum">    1320 </span>            :     a plumed handler that can be used in FORTRAN. Notice that the reference counter</a>
+<a name="1321"><span class="lineNum">    1321 </span>            :     is not incremented. In other words, the FORTRAN object will be a weak reference.</a>
+<a name="1322"><span class="lineNum">    1322 </span>            :     If you later finalize the C handler, the FORTRAN handler will be invalid.</a>
+<a name="1323"><span class="lineNum">    1323 </span>            : \verbatim</a>
+<a name="1324"><span class="lineNum">    1324 </span>            : #include &lt;plumed/wrapper/Plumed.h&gt;</a>
+<a name="1325"><span class="lineNum">    1325 </span>            : int main(int argc,char*argv[]){</a>
+<a name="1326"><span class="lineNum">    1326 </span>            :   plumed p;</a>
+<a name="1327"><span class="lineNum">    1327 </span>            :   p=plumed_create();</a>
+<a name="1328"><span class="lineNum">    1328 </span>            :   char fortran_handler[32];</a>
+<a name="1329"><span class="lineNum">    1329 </span>            :   plumed_c2f(p,fortran_handler);</a>
+<a name="1330"><span class="lineNum">    1330 </span>            :   printf(&quot;DEBUG: this is a string representation for the plumed handler: %s\n&quot;,fortran_handler);</a>
+<a name="1331"><span class="lineNum">    1331 </span>            :   fortran_routine(fortran_handler);</a>
+<a name="1332"><span class="lineNum">    1332 </span>            :   plumed_finalize(p);</a>
+<a name="1333"><span class="lineNum">    1333 </span>            :   return 0;</a>
+<a name="1334"><span class="lineNum">    1334 </span>            : }</a>
+<a name="1335"><span class="lineNum">    1335 </span>            : \endverbatim</a>
+<a name="1336"><span class="lineNum">    1336 </span>            :   Here `fortran_routine` is a routine implemented in FORTRAN that manipulates the</a>
+<a name="1337"><span class="lineNum">    1337 </span>            :   fortran_handler.</a>
+<a name="1338"><span class="lineNum">    1338 </span>            : */</a>
+<a name="1339"><span class="lineNum">    1339 </span>            : </a>
+<a name="1340"><span class="lineNum">    1340 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1341"><span class="lineNum">    1341 </span>            : void   plumed_c2f(plumed p,char* c);</a>
+<a name="1342"><span class="lineNum">    1342 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1343"><span class="lineNum">    1343 </span>            : </a>
+<a name="1344"><span class="lineNum">    1344 </span>            : /** \related plumed</a>
+<a name="1345"><span class="lineNum">    1345 </span>            :     \brief Converts a FORTRAN handler to a C handler</a>
+<a name="1346"><span class="lineNum">    1346 </span>            :     \param c The FORTRAN handler (a char[32])</a>
+<a name="1347"><span class="lineNum">    1347 </span>            :     \return The C handler</a>
+<a name="1348"><span class="lineNum">    1348 </span>            : </a>
+<a name="1349"><span class="lineNum">    1349 </span>            :     This function can be used to convert a plumed object created in FORTRAN</a>
+<a name="1350"><span class="lineNum">    1350 </span>            :     to a plumed handler that can be used in C.  Notice that the reference counter</a>
+<a name="1351"><span class="lineNum">    1351 </span>            :     is not incremented. In other words, the C object will be a weak reference.</a>
+<a name="1352"><span class="lineNum">    1352 </span>            :     If you later finalize the FORTRAN handler, the C handler will be invalid.</a>
+<a name="1353"><span class="lineNum">    1353 </span>            : \verbatim</a>
+<a name="1354"><span class="lineNum">    1354 </span>            : void c_routine(char handler[32]){</a>
+<a name="1355"><span class="lineNum">    1355 </span>            :   plumed p;</a>
+<a name="1356"><span class="lineNum">    1356 </span>            :   p=plumed_f2c(handler);</a>
+<a name="1357"><span class="lineNum">    1357 </span>            :   plumed_cmd(p,&quot;init&quot;,NULL);</a>
+<a name="1358"><span class="lineNum">    1358 </span>            : }</a>
+<a name="1359"><span class="lineNum">    1359 </span>            : \endverbatim</a>
+<a name="1360"><span class="lineNum">    1360 </span>            :   Here `c_routine` is a C function that can be called from FORTRAN</a>
+<a name="1361"><span class="lineNum">    1361 </span>            :   and interact with the provided plumed handler.</a>
+<a name="1362"><span class="lineNum">    1362 </span>            : */</a>
+<a name="1363"><span class="lineNum">    1363 </span>            : </a>
+<a name="1364"><span class="lineNum">    1364 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1365"><span class="lineNum">    1365 </span>            : plumed plumed_f2c(const char* c);</a>
+<a name="1366"><span class="lineNum">    1366 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1367"><span class="lineNum">    1367 </span>            : </a>
+<a name="1368"><span class="lineNum">    1368 </span>            : /** \related plumed</a>
+<a name="1369"><span class="lineNum">    1369 </span>            :     \brief Converts a plumed object to a void pointer. Available as of PLUMED 2.5.</a>
+<a name="1370"><span class="lineNum">    1370 </span>            : </a>
+<a name="1371"><span class="lineNum">    1371 </span>            :     It returns a void pointer that can be converted back to a plumed object using \ref plumed_v2c.</a>
+<a name="1372"><span class="lineNum">    1372 </span>            :     When compiling without NDEBUG, it checks if the plumed object was properly created.</a>
+<a name="1373"><span class="lineNum">    1373 </span>            :     Notice that an invalid object (see \ref plumed_valid) can be converted to void* and back.</a>
+<a name="1374"><span class="lineNum">    1374 </span>            : </a>
+<a name="1375"><span class="lineNum">    1375 </span>            :     Can be used to store a reference to a plumed object without including the Plumed.h header.</a>
+<a name="1376"><span class="lineNum">    1376 </span>            : */</a>
+<a name="1377"><span class="lineNum">    1377 </span>            : </a>
+<a name="1378"><span class="lineNum">    1378 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1379"><span class="lineNum">    1379 </span>            : void* plumed_c2v(plumed p);</a>
+<a name="1380"><span class="lineNum">    1380 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1381"><span class="lineNum">    1381 </span>            : </a>
+<a name="1382"><span class="lineNum">    1382 </span>            : </a>
+<a name="1383"><span class="lineNum">    1383 </span>            : /** \related plumed</a>
+<a name="1384"><span class="lineNum">    1384 </span>            :     \brief Converts a void pointer to a plumed object. Available as of PLUMED 2.5.</a>
+<a name="1385"><span class="lineNum">    1385 </span>            : </a>
+<a name="1386"><span class="lineNum">    1386 </span>            :     It returns a plumed object from a void pointer obtained with \ref plumed_c2v.</a>
+<a name="1387"><span class="lineNum">    1387 </span>            :     When compiling without NDEBUG, it checks if the plumed object was properly created.</a>
+<a name="1388"><span class="lineNum">    1388 </span>            : </a>
+<a name="1389"><span class="lineNum">    1389 </span>            :     Can be used to store a reference to a plumed object without including the Plumed.h header.</a>
+<a name="1390"><span class="lineNum">    1390 </span>            : */</a>
+<a name="1391"><span class="lineNum">    1391 </span>            : </a>
+<a name="1392"><span class="lineNum">    1392 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="1393"><span class="lineNum">    1393 </span>            : plumed plumed_v2c(void*);</a>
+<a name="1394"><span class="lineNum">    1394 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="1395"><span class="lineNum">    1395 </span>            : </a>
+<a name="1396"><span class="lineNum">    1396 </span>            : #if ! defined( __cplusplus) /*{*/</a>
+<a name="1397"><span class="lineNum">    1397 </span>            : </a>
+<a name="1398"><span class="lineNum">    1398 </span>            : #if __PLUMED_WRAPPER_C_TYPESAFE /*{*/</a>
+<a name="1399"><span class="lineNum">    1399 </span>            : </a>
+<a name="1400"><span class="lineNum">    1400 </span>            : #define __PLUMED_WRAPPER_C_TYPESAFE_INNER(type_,typen_,flags_) \</a>
+<a name="1401"><span class="lineNum">    1401 </span>            :   static inline void plumed_cmdnse_ ## typen_(plumed p,const char*key,type_*ptr, size_t nelem, const size_t* shape,plumed_error* error) { \</a>
+<a name="1402"><span class="lineNum">    1402 </span>            :     plumed_safeptr safe; \</a>
+<a name="1403"><span class="lineNum">    1403 </span>            :     plumed_nothrow_handler nothrow; \</a>
+<a name="1404"><span class="lineNum">    1404 </span>            :     safe.ptr=ptr; \</a>
+<a name="1405"><span class="lineNum">    1405 </span>            :     safe.nelem=nelem; \</a>
+<a name="1406"><span class="lineNum">    1406 </span>            :     safe.shape=(const size_t*)shape; \</a>
+<a name="1407"><span class="lineNum">    1407 </span>            :     safe.flags=flags_; \</a>
+<a name="1408"><span class="lineNum">    1408 </span>            :     safe.opt=NULL; \</a>
+<a name="1409"><span class="lineNum">    1409 </span>            :     if(error) { \</a>
+<a name="1410"><span class="lineNum">    1410 </span>            :       plumed_error_init(error); \</a>
+<a name="1411"><span class="lineNum">    1411 </span>            :       nothrow.ptr=error; \</a>
+<a name="1412"><span class="lineNum">    1412 </span>            :       nothrow.handler=plumed_error_set; \</a>
+<a name="1413"><span class="lineNum">    1413 </span>            :       plumed_cmd_safe_nothrow(p,key,safe,nothrow); \</a>
+<a name="1414"><span class="lineNum">    1414 </span>            :     } else { \</a>
+<a name="1415"><span class="lineNum">    1415 </span>            :       plumed_cmd_safe(p,key,safe); \</a>
+<a name="1416"><span class="lineNum">    1416 </span>            :     } \</a>
+<a name="1417"><span class="lineNum">    1417 </span>            :   } \</a>
+<a name="1418"><span class="lineNum">    1418 </span>            :   static inline void plumed_cmdne_ ## typen_(plumed p,const char*key,type_*ptr, size_t nelem, plumed_error* error) { \</a>
+<a name="1419"><span class="lineNum">    1419 </span>            :     plumed_cmdnse_ ## typen_(p,key,ptr,nelem,NULL,error); \</a>
+<a name="1420"><span class="lineNum">    1420 </span>            :   } \</a>
+<a name="1421"><span class="lineNum">    1421 </span>            :   static inline void plumed_cmdse_ ## typen_(plumed p,const char*key,type_*ptr, const size_t* shape, plumed_error* error) { \</a>
+<a name="1422"><span class="lineNum">    1422 </span>            :     plumed_cmdnse_ ## typen_(p,key,ptr,0,shape,error); \</a>
+<a name="1423"><span class="lineNum">    1423 </span>            :   } \</a>
+<a name="1424"><span class="lineNum">    1424 </span>            :   static inline void plumed_cmdn_ ## typen_(plumed p,const char*key,type_*ptr, size_t nelem) { \</a>
+<a name="1425"><span class="lineNum">    1425 </span>            :     plumed_cmdnse_ ## typen_(p,key,ptr,nelem,NULL,NULL); \</a>
+<a name="1426"><span class="lineNum">    1426 </span>            :   } \</a>
+<a name="1427"><span class="lineNum">    1427 </span>            :   static inline void plumed_cmds_ ## typen_(plumed p,const char*key,type_*ptr, const size_t* shape) { \</a>
+<a name="1428"><span class="lineNum">    1428 </span>            :     plumed_cmdnse_ ## typen_(p,key,ptr,0,shape,NULL); \</a>
+<a name="1429"><span class="lineNum">    1429 </span>            :   } \</a>
+<a name="1430"><span class="lineNum">    1430 </span>            :   static inline void plumed_cmde_ ## typen_(plumed p,const char*key,type_*ptr, plumed_error* error) { \</a>
+<a name="1431"><span class="lineNum">    1431 </span>            :     plumed_cmdnse_ ## typen_(p,key,ptr,0,NULL,error); \</a>
+<a name="1432"><span class="lineNum">    1432 </span>            :   }</a>
+<a name="1433"><span class="lineNum">    1433 </span>            : </a>
+<a name="1434"><span class="lineNum">    1434 </span>            : #define __PLUMED_WRAPPER_C_TYPESAFE_OUTER(type,type_,code,size) \</a>
+<a name="1435"><span class="lineNum">    1435 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_INNER(type,             type_ ## _p,  size | (0x10000*(code)) | (0x2000000*2)) \</a>
+<a name="1436"><span class="lineNum">    1436 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_INNER(type const,       type_ ## _c,  size | (0x10000*(code)) | (0x2000000*3)) \</a>
+<a name="1437"><span class="lineNum">    1437 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_INNER(type*,            type_ ## _pp, size | (0x10000*(code)) | (0x2000000*4)) \</a>
+<a name="1438"><span class="lineNum">    1438 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_INNER(type*const,       type_ ## _pc, size | (0x10000*(code)) | (0x2000000*5)) \</a>
+<a name="1439"><span class="lineNum">    1439 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_INNER(type const*,      type_ ## _cp, size | (0x10000*(code)) | (0x2000000*6)) \</a>
+<a name="1440"><span class="lineNum">    1440 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_INNER(type const*const, type_ ## _cc, size | (0x10000*(code)) | (0x2000000*7))</a>
+<a name="1441"><span class="lineNum">    1441 </span>            : </a>
+<a name="1442"><span class="lineNum">    1442 </span>            : #define __PLUMED_WRAPPER_C_TYPESAFE_EMPTY(type,type_,code) __PLUMED_WRAPPER_C_TYPESAFE_OUTER(type,type_,code,0)</a>
+<a name="1443"><span class="lineNum">    1443 </span>            : </a>
+<a name="1444"><span class="lineNum">    1444 </span>            : #define __PLUMED_WRAPPER_C_TYPESAFE_SIZED(type,type_,code) \</a>
+<a name="1445"><span class="lineNum">    1445 </span>            :   __PLUMED_WRAPPER_C_TYPESAFE_OUTER(type,type_,code,sizeof(type)) \</a>
+<a name="1446"><span class="lineNum">    1446 </span>            :   static inline void plumed_cmdnse_ ## type_ ## _v(plumed p,const char*key,type val, size_t nelem, const size_t* shape, plumed_error* error) { \</a>
+<a name="1447"><span class="lineNum">    1447 </span>            :     plumed_safeptr safe; \</a>
+<a name="1448"><span class="lineNum">    1448 </span>            :     plumed_nothrow_handler nothrow; \</a>
+<a name="1449"><span class="lineNum">    1449 </span>            :     (void) nelem; \</a>
+<a name="1450"><span class="lineNum">    1450 </span>            :     (void) shape; \</a>
+<a name="1451"><span class="lineNum">    1451 </span>            :     safe.ptr=&amp;val; \</a>
+<a name="1452"><span class="lineNum">    1452 </span>            :     safe.nelem=1; \</a>
+<a name="1453"><span class="lineNum">    1453 </span>            :     safe.shape=NULL; \</a>
+<a name="1454"><span class="lineNum">    1454 </span>            :     safe.flags=sizeof(type) | (0x10000*(code)) | (0x2000000*1); \</a>
+<a name="1455"><span class="lineNum">    1455 </span>            :     safe.opt=NULL; \</a>
+<a name="1456"><span class="lineNum">    1456 </span>            :     if(error) { \</a>
+<a name="1457"><span class="lineNum">    1457 </span>            :       plumed_error_init(error); \</a>
+<a name="1458"><span class="lineNum">    1458 </span>            :       nothrow.ptr=error; \</a>
+<a name="1459"><span class="lineNum">    1459 </span>            :       nothrow.handler=plumed_error_set; \</a>
+<a name="1460"><span class="lineNum">    1460 </span>            :       plumed_cmd_safe_nothrow(p,key,safe,nothrow); \</a>
+<a name="1461"><span class="lineNum">    1461 </span>            :     } else { \</a>
+<a name="1462"><span class="lineNum">    1462 </span>            :       plumed_cmd_safe(p,key,safe); \</a>
+<a name="1463"><span class="lineNum">    1463 </span>            :     } \</a>
+<a name="1464"><span class="lineNum">    1464 </span>            :   } \</a>
+<a name="1465"><span class="lineNum">    1465 </span>            :   static inline void plumed_cmdne_ ## type_ ## _v(plumed p,const char*key,type val, size_t nelem, plumed_error* error) {  \</a>
+<a name="1466"><span class="lineNum">    1466 </span>            :     plumed_cmdnse_ ## type_ ## _v(p,key,val,nelem,NULL,error); \</a>
+<a name="1467"><span class="lineNum">    1467 </span>            :   } \</a>
+<a name="1468"><span class="lineNum">    1468 </span>            :   static inline void plumed_cmdse_ ## type_ ## _v(plumed p,const char*key,type val, const size_t* shape, plumed_error* error) {  \</a>
+<a name="1469"><span class="lineNum">    1469 </span>            :     plumed_cmdnse_ ## type_ ## _v(p,key,val,0,shape,error); \</a>
+<a name="1470"><span class="lineNum">    1470 </span>            :   } \</a>
+<a name="1471"><span class="lineNum">    1471 </span>            :   static inline void plumed_cmdn_ ## type_ ## _v(plumed p,const char*key,type val, size_t nelem) {  \</a>
+<a name="1472"><span class="lineNum">    1472 </span>            :     plumed_cmdnse_ ## type_ ## _v(p,key,val,nelem,NULL,NULL); \</a>
+<a name="1473"><span class="lineNum">    1473 </span>            :   } \</a>
+<a name="1474"><span class="lineNum">    1474 </span>            :   static inline void plumed_cmds_ ## type_ ## _v(plumed p,const char*key,type val, const size_t* shape) {  \</a>
+<a name="1475"><span class="lineNum">    1475 </span>            :     plumed_cmdnse_ ## type_ ## _v(p,key,val,0,shape,NULL); \</a>
+<a name="1476"><span class="lineNum">    1476 </span>            :   } \</a>
+<a name="1477"><span class="lineNum">    1477 </span>            :   static inline void plumed_cmde_ ## type_ ## _v(plumed p,const char*key,type val, plumed_error* error) {  \</a>
+<a name="1478"><span class="lineNum">    1478 </span>            :     plumed_cmdnse_ ## type_ ## _v(p,key,val,0,NULL,error); \</a>
+<a name="1479"><span class="lineNum">    1479 </span>            :   }</a>
+<a name="1480"><span class="lineNum">    1480 </span>            : </a>
+<a name="1481"><span class="lineNum">    1481 </span>            : #define __PLUMED_WRAPPER_C_GENERIC1(flavor,type,typen_) \</a>
+<a name="1482"><span class="lineNum">    1482 </span>            :     type: plumed_ ## flavor ## _ ## typen_,</a>
+<a name="1483"><span class="lineNum">    1483 </span>            : </a>
+<a name="1484"><span class="lineNum">    1484 </span>            : #define __PLUMED_WRAPPER_C_GENERIC_EMPTY(flavor,type,type_) \</a>
+<a name="1485"><span class="lineNum">    1485 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type*,             type_ ## _p) \</a>
+<a name="1486"><span class="lineNum">    1486 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type const*,       type_ ## _c) \</a>
+<a name="1487"><span class="lineNum">    1487 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type**,            type_ ## _pp) \</a>
+<a name="1488"><span class="lineNum">    1488 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type*const*,       type_ ## _pc) \</a>
+<a name="1489"><span class="lineNum">    1489 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type const**,      type_ ## _cp) \</a>
+<a name="1490"><span class="lineNum">    1490 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type const*const*, type_ ## _cc)</a>
+<a name="1491"><span class="lineNum">    1491 </span>            : </a>
+<a name="1492"><span class="lineNum">    1492 </span>            : #define __PLUMED_WRAPPER_C_GENERIC2(flavor,type,type_) \</a>
+<a name="1493"><span class="lineNum">    1493 </span>            :   __PLUMED_WRAPPER_C_GENERIC_EMPTY(flavor,type,type_) \</a>
+<a name="1494"><span class="lineNum">    1494 </span>            :   __PLUMED_WRAPPER_C_GENERIC1(flavor,type,             type_ ## _v)</a>
+<a name="1495"><span class="lineNum">    1495 </span>            : </a>
+<a name="1496"><span class="lineNum">    1496 </span>            : /// Here we create all the required instances</a>
+<a name="1497"><span class="lineNum">    1497 </span>            : /// 1: void</a>
+<a name="1498"><span class="lineNum">    1498 </span>            : /// 3: integral</a>
+<a name="1499"><span class="lineNum">    1499 </span>            : /// 4: floating</a>
+<a name="1500"><span class="lineNum">    1500 </span>            : /// 5: FILE</a>
+<a name="1501"><span class="lineNum">    1501 </span>            : /// 0x100: unsigned</a>
+<a name="1502"><span class="lineNum">    1502 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_EMPTY(void,void,1)</a>
+<a name="1503"><span class="lineNum">    1503 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(char,char,(CHAR_MIN==0)*0x100+3)</a>
+<a name="1504"><span class="lineNum">    1504 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(unsigned char,unsigned_char,0x100+3)</a>
+<a name="1505"><span class="lineNum">    1505 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(signed char,signed_char,0x100+3)</a>
+<a name="1506"><span class="lineNum">    1506 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(short,short,3)</a>
+<a name="1507"><span class="lineNum">    1507 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(unsigned short,unsigned_short,0x100+3)</a>
+<a name="1508"><span class="lineNum">    1508 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(int,int,3)</a>
+<a name="1509"><span class="lineNum">    1509 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(unsigned int,unsigned_int,0x100+3)</a>
+<a name="1510"><span class="lineNum">    1510 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(long,long,3)</a>
+<a name="1511"><span class="lineNum">    1511 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(unsigned long,unsigned_long,0x100+3)</a>
+<a name="1512"><span class="lineNum">    1512 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(long long,long_long,3)</a>
+<a name="1513"><span class="lineNum">    1513 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(unsigned long long,unsigned_long_long,0x100+3)</a>
+<a name="1514"><span class="lineNum">    1514 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(float,float,4)</a>
+<a name="1515"><span class="lineNum">    1515 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(double,double,4)</a>
+<a name="1516"><span class="lineNum">    1516 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_SIZED(long double,long_double,4)</a>
+<a name="1517"><span class="lineNum">    1517 </span>            : __PLUMED_WRAPPER_C_TYPESAFE_EMPTY(FILE,FILE,5)</a>
+<a name="1518"><span class="lineNum">    1518 </span>            : </a>
+<a name="1519"><span class="lineNum">    1519 </span>            : static inline void plumed_cmd_null_e(plumed p,const char*key,plumed_error* error,int ignore) {</a>
+<a name="1520"><span class="lineNum">    1520 </span>            :   (void) ignore;</a>
+<a name="1521"><span class="lineNum">    1521 </span>            :   plumed_cmde_void_p(p,key,NULL,error);</a>
+<a name="1522"><span class="lineNum">    1522 </span>            : }</a>
+<a name="1523"><span class="lineNum">    1523 </span>            : </a>
+<a name="1524"><span class="lineNum">    1524 </span>            : #define plumed_cmdnse_inner(flavor,val) _Generic((val), \</a>
+<a name="1525"><span class="lineNum">    1525 </span>            :     __PLUMED_WRAPPER_C_GENERIC_EMPTY(flavor,void,void) \</a>
+<a name="1526"><span class="lineNum">    1526 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,char,char) \</a>
+<a name="1527"><span class="lineNum">    1527 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,unsigned char,unsigned_char) \</a>
+<a name="1528"><span class="lineNum">    1528 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,signed char,signed_char) \</a>
+<a name="1529"><span class="lineNum">    1529 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,short,short) \</a>
+<a name="1530"><span class="lineNum">    1530 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,unsigned short,unsigned_short) \</a>
+<a name="1531"><span class="lineNum">    1531 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,int,int) \</a>
+<a name="1532"><span class="lineNum">    1532 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,unsigned int,unsigned_int) \</a>
+<a name="1533"><span class="lineNum">    1533 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,long,long) \</a>
+<a name="1534"><span class="lineNum">    1534 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,unsigned long,unsigned_long) \</a>
+<a name="1535"><span class="lineNum">    1535 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,long long,long_long) \</a>
+<a name="1536"><span class="lineNum">    1536 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,unsigned long long,unsigned_long_long) \</a>
+<a name="1537"><span class="lineNum">    1537 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,float,float) \</a>
+<a name="1538"><span class="lineNum">    1538 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,double,double) \</a>
+<a name="1539"><span class="lineNum">    1539 </span>            :     __PLUMED_WRAPPER_C_GENERIC2(flavor,long double,long_double) \</a>
+<a name="1540"><span class="lineNum">    1540 </span>            :     __PLUMED_WRAPPER_C_GENERIC_EMPTY(flavor,FILE,FILE) \</a>
+<a name="1541"><span class="lineNum">    1541 </span>            :     default: plumed_ ## flavor ## _void_c)</a>
+<a name="1542"><span class="lineNum">    1542 </span>            : </a>
+<a name="1543"><span class="lineNum">    1543 </span>            : #define plumed_cmd_2args(p,key) plumed_cmdnse_inner(cmdn,NULL) (p,key,NULL,0)</a>
+<a name="1544"><span class="lineNum">    1544 </span>            : </a>
+<a name="1545"><span class="lineNum">    1545 </span>            : #define plumed_cmd_3args(p,key,X) _Generic((X), \</a>
+<a name="1546"><span class="lineNum">    1546 </span>            :     plumed_error*: plumed_cmd_null_e, \</a>
+<a name="1547"><span class="lineNum">    1547 </span>            :     default:       plumed_cmdnse_inner(cmdn,X)) (p,key,X,0)</a>
+<a name="1548"><span class="lineNum">    1548 </span>            : </a>
+<a name="1549"><span class="lineNum">    1549 </span>            : /* ((X)+(size_t)0): for pointers, no op; for integers, convert to size_t */</a>
+<a name="1550"><span class="lineNum">    1550 </span>            : #define plumed_cmd_4args(p,key,val,X) _Generic(((X)+(size_t)0), \</a>
+<a name="1551"><span class="lineNum">    1551 </span>            :     const size_t *: plumed_cmdnse_inner(cmds,val), \</a>
+<a name="1552"><span class="lineNum">    1552 </span>            :     size_t *: plumed_cmdnse_inner(cmds,val), \</a>
+<a name="1553"><span class="lineNum">    1553 </span>            :     size_t: plumed_cmdnse_inner(cmdn,val), \</a>
+<a name="1554"><span class="lineNum">    1554 </span>            :     plumed_error*: plumed_cmdnse_inner(cmde,val) \</a>
+<a name="1555"><span class="lineNum">    1555 </span>            :     ) (p,key,val,X)</a>
+<a name="1556"><span class="lineNum">    1556 </span>            : </a>
+<a name="1557"><span class="lineNum">    1557 </span>            : /* ((X)+(size_t)0): for pointers, no op; for integers, convert to size_t */</a>
+<a name="1558"><span class="lineNum">    1558 </span>            : #define plumed_cmd_5args(p,key,val,X,error) _Generic(((X)+(size_t)0), \</a>
+<a name="1559"><span class="lineNum">    1559 </span>            :     const size_t *: plumed_cmdnse_inner(cmdse,val), \</a>
+<a name="1560"><span class="lineNum">    1560 </span>            :     size_t *: plumed_cmdnse_inner(cmdse,val), \</a>
+<a name="1561"><span class="lineNum">    1561 </span>            :     size_t: plumed_cmdnse_inner(cmdne,val) \</a>
+<a name="1562"><span class="lineNum">    1562 </span>            :     ) (p,key,val,X,error)</a>
+<a name="1563"><span class="lineNum">    1563 </span>            : </a>
+<a name="1564"><span class="lineNum">    1564 </span>            : #define __PLUMED_WRAPPER_C_GET_MACRO(_1,_2,_3,_4,_5,NAME,...) NAME</a>
+<a name="1565"><span class="lineNum">    1565 </span>            : #define plumed_cmd_c11(...) __PLUMED_WRAPPER_C_GET_MACRO(__VA_ARGS__, plumed_cmd_5args, plumed_cmd_4args, plumed_cmd_3args, plumed_cmd_2args)(__VA_ARGS__)</a>
+<a name="1566"><span class="lineNum">    1566 </span>            : </a>
+<a name="1567"><span class="lineNum">    1567 </span>            : #define plumed_gcmd_c11(...) plumed_cmd(plumed_global(),__VA_ARGS__)</a>
+<a name="1568"><span class="lineNum">    1568 </span>            : </a>
+<a name="1569"><span class="lineNum">    1569 </span>            : #define __PLUMED_WRAPPER_REDEFINE_CMD plumed_cmd_c11</a>
+<a name="1570"><span class="lineNum">    1570 </span>            : #define __PLUMED_WRAPPER_REDEFINE_GCMD plumed_gcmd_c11</a>
+<a name="1571"><span class="lineNum">    1571 </span>            : </a>
+<a name="1572"><span class="lineNum">    1572 </span>            : #endif /*}*/</a>
+<a name="1573"><span class="lineNum">    1573 </span>            : </a>
+<a name="1574"><span class="lineNum">    1574 </span>            : #endif /*}*/</a>
+<a name="1575"><span class="lineNum">    1575 </span>            : </a>
+<a name="1576"><span class="lineNum">    1576 </span>            : </a>
+<a name="1577"><span class="lineNum">    1577 </span>            : #if __PLUMED_WRAPPER_GLOBAL /*{*/</a>
+<a name="1578"><span class="lineNum">    1578 </span>            : </a>
+<a name="1579"><span class="lineNum">    1579 </span>            : /* Global C functions are always extern */</a>
+<a name="1580"><span class="lineNum">    1580 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN /*{*/</a>
+<a name="1581"><span class="lineNum">    1581 </span>            : </a>
+<a name="1582"><span class="lineNum">    1582 </span>            : /** \relates plumed</a>
+<a name="1583"><span class="lineNum">    1583 </span>            :     \brief Retrieves an handler to the global structure.</a>
+<a name="1584"><span class="lineNum">    1584 </span>            : </a>
+<a name="1585"><span class="lineNum">    1585 </span>            :   You can use this if you work on a code that uses the global structure and you want to</a>
+<a name="1586"><span class="lineNum">    1586 </span>            :   pass to a generic routine an handler to the same structure. E.g.</a>
+<a name="1587"><span class="lineNum">    1587 </span>            : </a>
+<a name="1588"><span class="lineNum">    1588 </span>            : \verbatim</a>
+<a name="1589"><span class="lineNum">    1589 </span>            :   plumed p=plumed_global();</a>
+<a name="1590"><span class="lineNum">    1590 </span>            :   some_routine(p);</a>
+<a name="1591"><span class="lineNum">    1591 </span>            : \endverbatim</a>
+<a name="1592"><span class="lineNum">    1592 </span>            : */</a>
+<a name="1593"><span class="lineNum">    1593 </span>            : extern</a>
+<a name="1594"><span class="lineNum">    1594 </span>            : plumed plumed_global(void);</a>
+<a name="1595"><span class="lineNum">    1595 </span>            : </a>
+<a name="1596"><span class="lineNum">    1596 </span>            : /** \relates plumed</a>
+<a name="1597"><span class="lineNum">    1597 </span>            :     \brief Check if the global interface has been initialized.</a>
+<a name="1598"><span class="lineNum">    1598 </span>            : </a>
+<a name="1599"><span class="lineNum">    1599 </span>            :     \return 1 if plumed has been initialized, 0 otherwise</a>
+<a name="1600"><span class="lineNum">    1600 </span>            : */</a>
+<a name="1601"><span class="lineNum">    1601 </span>            : extern</a>
+<a name="1602"><span class="lineNum">    1602 </span>            : int plumed_ginitialized(void);</a>
+<a name="1603"><span class="lineNum">    1603 </span>            : </a>
+<a name="1604"><span class="lineNum">    1604 </span>            : /** \relates plumed</a>
+<a name="1605"><span class="lineNum">    1605 </span>            :     \brief Constructor for the global interface.</a>
+<a name="1606"><span class="lineNum">    1606 </span>            : </a>
+<a name="1607"><span class="lineNum">    1607 </span>            :     \note Equivalent to plumed_create(), but initialize the static global plumed object</a>
+<a name="1608"><span class="lineNum">    1608 </span>            : */</a>
+<a name="1609"><span class="lineNum">    1609 </span>            : extern</a>
+<a name="1610"><span class="lineNum">    1610 </span>            : void plumed_gcreate(void);</a>
+<a name="1611"><span class="lineNum">    1611 </span>            : </a>
+<a name="1612"><span class="lineNum">    1612 </span>            : /** \relates plumed</a>
+<a name="1613"><span class="lineNum">    1613 </span>            :     \brief Tells to the global interface to execute a command.</a>
+<a name="1614"><span class="lineNum">    1614 </span>            : </a>
+<a name="1615"><span class="lineNum">    1615 </span>            :     \param key The name of the command to be executed</a>
+<a name="1616"><span class="lineNum">    1616 </span>            :     \param val The argument. It is declared as const to allow calls like plumed_gcmd(&quot;A&quot;,&quot;B&quot;),</a>
+<a name="1617"><span class="lineNum">    1617 </span>            :                but for some choice of key it can change the content</a>
+<a name="1618"><span class="lineNum">    1618 </span>            : </a>
+<a name="1619"><span class="lineNum">    1619 </span>            :     `plumed_gcmd(a,b);` is equivalent to `plumed_cmd(plumed_global(),a,b);`.</a>
+<a name="1620"><span class="lineNum">    1620 </span>            : */</a>
+<a name="1621"><span class="lineNum">    1621 </span>            : extern</a>
+<a name="1622"><span class="lineNum">    1622 </span>            : void plumed_gcmd(const char* key,const void* val);</a>
+<a name="1623"><span class="lineNum">    1623 </span>            : </a>
+<a name="1624"><span class="lineNum">    1624 </span>            : /** \relates plumed</a>
+<a name="1625"><span class="lineNum">    1625 </span>            :     \brief Tells to the global interface to execute a command.</a>
+<a name="1626"><span class="lineNum">    1626 </span>            : </a>
+<a name="1627"><span class="lineNum">    1627 </span>            :     \param key The name of the command to be executed</a>
+<a name="1628"><span class="lineNum">    1628 </span>            :     \param safe A safe pointer</a>
+<a name="1629"><span class="lineNum">    1629 </span>            : </a>
+<a name="1630"><span class="lineNum">    1630 </span>            :     `plumed_gcmd_safe(a,b);` is equivalent to `plumed_cmd_safe(plumed_global(),a,b);`.</a>
+<a name="1631"><span class="lineNum">    1631 </span>            : */</a>
+<a name="1632"><span class="lineNum">    1632 </span>            : extern</a>
+<a name="1633"><span class="lineNum">    1633 </span>            : void plumed_gcmd_safe(const char* key,plumed_safeptr);</a>
+<a name="1634"><span class="lineNum">    1634 </span>            : </a>
+<a name="1635"><span class="lineNum">    1635 </span>            : /** \relates plumed</a>
+<a name="1636"><span class="lineNum">    1636 </span>            :     \brief Destructor for the global interface.</a>
+<a name="1637"><span class="lineNum">    1637 </span>            : </a>
+<a name="1638"><span class="lineNum">    1638 </span>            :     `plumed_gfinalize(a,b);` is similar to `plumed_finalize(plumed_global(),a,b);`, but not completely</a>
+<a name="1639"><span class="lineNum">    1639 </span>            :     equivalent. In particular, plumed_gfinalize() also makes sure that the global object</a>
+<a name="1640"><span class="lineNum">    1640 </span>            :     is reset to its initial status. After calling it, \ref plumed_ginitialized() will thus return 0.</a>
+<a name="1641"><span class="lineNum">    1641 </span>            : */</a>
+<a name="1642"><span class="lineNum">    1642 </span>            : extern</a>
+<a name="1643"><span class="lineNum">    1643 </span>            : void plumed_gfinalize(void);</a>
+<a name="1644"><span class="lineNum">    1644 </span>            : </a>
+<a name="1645"><span class="lineNum">    1645 </span>            : /** \relates plumed</a>
+<a name="1646"><span class="lineNum">    1646 </span>            :     \brief Check if global plumed object is valid. Available as of PLUMED 2.5</a>
+<a name="1647"><span class="lineNum">    1647 </span>            : </a>
+<a name="1648"><span class="lineNum">    1648 </span>            :     It might return zero if plumed is not available at runtime.</a>
+<a name="1649"><span class="lineNum">    1649 </span>            : </a>
+<a name="1650"><span class="lineNum">    1650 </span>            :     \return 1 if plumed is valid, 0 otherwise.</a>
+<a name="1651"><span class="lineNum">    1651 </span>            : */</a>
+<a name="1652"><span class="lineNum">    1652 </span>            : extern</a>
+<a name="1653"><span class="lineNum">    1653 </span>            : int plumed_gvalid();</a>
+<a name="1654"><span class="lineNum">    1654 </span>            : </a>
+<a name="1655"><span class="lineNum">    1655 </span>            : __PLUMED_WRAPPER_EXTERN_C_END /*}*/</a>
+<a name="1656"><span class="lineNum">    1656 </span>            : </a>
+<a name="1657"><span class="lineNum">    1657 </span>            : #endif /*}*/</a>
+<a name="1658"><span class="lineNum">    1658 </span>            : </a>
+<a name="1659"><span class="lineNum">    1659 </span>            : #if defined( __cplusplus) &amp;&amp; __PLUMED_WRAPPER_CXX /*{*/</a>
+<a name="1660"><span class="lineNum">    1660 </span>            : </a>
+<a name="1661"><span class="lineNum">    1661 </span>            : #if __PLUMED_WRAPPER_CXX_STD</a>
+<a name="1662"><span class="lineNum">    1662 </span>            : #include &lt;cstdlib&gt; /* NULL getenv */</a>
+<a name="1663"><span class="lineNum">    1663 </span>            : #include &lt;cstddef&gt; /* nullptr_t */</a>
+<a name="1664"><span class="lineNum">    1664 </span>            : #include &lt;cstring&gt; /* strncat strlen */</a>
+<a name="1665"><span class="lineNum">    1665 </span>            : #include &lt;cassert&gt; /* assert */</a>
+<a name="1666"><span class="lineNum">    1666 </span>            : #include &lt;climits&gt; /* CHAR_MIN */</a>
+<a name="1667"><span class="lineNum">    1667 </span>            : #else</a>
+<a name="1668"><span class="lineNum">    1668 </span>            : #include &lt;stddef.h&gt;</a>
+<a name="1669"><span class="lineNum">    1669 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="1670"><span class="lineNum">    1670 </span>            : #include &lt;string.h&gt;</a>
+<a name="1671"><span class="lineNum">    1671 </span>            : #include &lt;assert.h&gt;</a>
+<a name="1672"><span class="lineNum">    1672 </span>            : #include &lt;limits.h&gt;</a>
+<a name="1673"><span class="lineNum">    1673 </span>            : #endif</a>
+<a name="1674"><span class="lineNum">    1674 </span>            : </a>
+<a name="1675"><span class="lineNum">    1675 </span>            : #include &lt;exception&gt; /* exception bad_exception */</a>
+<a name="1676"><span class="lineNum">    1676 </span>            : #include &lt;stdexcept&gt; /* runtime_error logic_error invalid_argument domain_error length_error out_of_range range_error overflow_error underflow_error */</a>
+<a name="1677"><span class="lineNum">    1677 </span>            : #include &lt;string&gt; /* string */</a>
+<a name="1678"><span class="lineNum">    1678 </span>            : #include &lt;ios&gt; /* iostream_category (C++11) ios_base::failure (C++11 and C++&lt;11) */</a>
+<a name="1679"><span class="lineNum">    1679 </span>            : #include &lt;new&gt; /* bad_alloc bad_array_new_length (C++11) */</a>
+<a name="1680"><span class="lineNum">    1680 </span>            : #include &lt;typeinfo&gt; /* bad_typeid bad_cast */</a>
+<a name="1681"><span class="lineNum">    1681 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1682"><span class="lineNum">    1682 </span>            : #include &lt;system_error&gt; /* system_error generic_category system_category */</a>
+<a name="1683"><span class="lineNum">    1683 </span>            : #include &lt;future&gt; /* future_category */</a>
+<a name="1684"><span class="lineNum">    1684 </span>            : #include &lt;memory&gt; /* bad_weak_ptr */</a>
+<a name="1685"><span class="lineNum">    1685 </span>            : #include &lt;functional&gt; /* bad_function_call */</a>
+<a name="1686"><span class="lineNum">    1686 </span>            : #endif</a>
+<a name="1687"><span class="lineNum">    1687 </span>            : </a>
+<a name="1688"><span class="lineNum">    1688 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="1689"><span class="lineNum">    1689 </span>            : #include &lt;array&gt; /* array */</a>
+<a name="1690"><span class="lineNum">    1690 </span>            : #include &lt;initializer_list&gt; /* initializer_list */</a>
+<a name="1691"><span class="lineNum">    1691 </span>            : #endif</a>
+<a name="1692"><span class="lineNum">    1692 </span>            : </a>
+<a name="1693"><span class="lineNum">    1693 </span>            : /* C++ interface is hidden in PLMD namespace (same as plumed library) */</a>
+<a name="1694"><span class="lineNum">    1694 </span>            : namespace PLMD {</a>
+<a name="1695"><span class="lineNum">    1695 </span>            : </a>
+<a name="1696"><span class="lineNum">    1696 </span>            : /* Optionally, it is further hidden in an anonymous namespace */</a>
+<a name="1697"><span class="lineNum">    1697 </span>            : </a>
+<a name="1698"><span class="lineNum">    1698 </span>            : __PLUMED_WRAPPER_ANONYMOUS_BEGIN /*{*/</a>
+<a name="1699"><span class="lineNum">    1699 </span>            : </a>
+<a name="1700"><span class="lineNum">    1700 </span>            : /**</a>
+<a name="1701"><span class="lineNum">    1701 </span>            :   Retrieve PLUMED_EXCEPTIONS_DEBUG (internal utility).</a>
+<a name="1702"><span class="lineNum">    1702 </span>            : </a>
+<a name="1703"><span class="lineNum">    1703 </span>            :   This function should not be used by external programs. It is defined</a>
+<a name="1704"><span class="lineNum">    1704 </span>            :   as inline static so that it can store a static variable (for quicker access)</a>
+<a name="1705"><span class="lineNum">    1705 </span>            :   without adding a unique global symbol to a library including this header file.</a>
+<a name="1706"><span class="lineNum">    1706 </span>            : */</a>
+<a name="1707"><span class="lineNum">    1707 </span><span class="lineNoCov">          0 : inline static bool PlumedGetenvExceptionsDebug() __PLUMED_WRAPPER_CXX_NOEXCEPT {</span></a>
+<a name="1708"><span class="lineNum">    1708 </span><span class="lineNoCov">          0 :   static const char* res=__PLUMED_WRAPPER_STD getenv(&quot;PLUMED_EXCEPTIONS_DEBUG&quot;);</span></a>
+<a name="1709"><span class="lineNum">    1709 </span><span class="lineNoCov">          0 :   return res;</span></a>
+<a name="1710"><span class="lineNum">    1710 </span>            : }</a>
+<a name="1711"><span class="lineNum">    1711 </span>            : </a>
+<a name="1712"><span class="lineNum">    1712 </span>            : /**</a>
+<a name="1713"><span class="lineNum">    1713 </span>            :   C++ wrapper for \ref plumed.</a>
+<a name="1714"><span class="lineNum">    1714 </span>            : </a>
+<a name="1715"><span class="lineNum">    1715 </span>            :   This class provides a C++ interface to PLUMED.</a>
+<a name="1716"><span class="lineNum">    1716 </span>            :   It only containts a \ref plumed object, but wraps it with a number of useful methods.</a>
+<a name="1717"><span class="lineNum">    1717 </span>            :   All methods are inlined so as to avoid the compilation of an extra c++ file.</a>
+<a name="1718"><span class="lineNum">    1718 </span>            : </a>
+<a name="1719"><span class="lineNum">    1719 </span>            : */</a>
+<a name="1720"><span class="lineNum">    1720 </span>            : </a>
+<a name="1721"><span class="lineNum">    1721 </span>            : class Plumed {</a>
+<a name="1722"><span class="lineNum">    1722 </span>            :   /**</a>
+<a name="1723"><span class="lineNum">    1723 </span>            :     C structure.</a>
+<a name="1724"><span class="lineNum">    1724 </span>            :   */</a>
+<a name="1725"><span class="lineNum">    1725 </span>            :   plumed main;</a>
+<a name="1726"><span class="lineNum">    1726 </span>            : </a>
+<a name="1727"><span class="lineNum">    1727 </span>            : private:</a>
+<a name="1728"><span class="lineNum">    1728 </span>            : </a>
+<a name="1729"><span class="lineNum">    1729 </span>            :   /**</a>
+<a name="1730"><span class="lineNum">    1730 </span>            :     This is an internal utility to dispatch exceptions based on the plumed_error object.</a>
+<a name="1731"><span class="lineNum">    1731 </span>            : </a>
+<a name="1732"><span class="lineNum">    1732 </span>            :     It takes information about the exception to be thrown by the passed h object</a>
+<a name="1733"><span class="lineNum">    1733 </span>            :     and use it to call function f() on the resulting exception. Notice that:</a>
+<a name="1734"><span class="lineNum">    1734 </span>            :     - this function does not consider if the error is nested.</a>
+<a name="1735"><span class="lineNum">    1735 </span>            :     - f should be a callable object, so that it can store information</a>
+<a name="1736"><span class="lineNum">    1736 </span>            :     - f operator() should be a template function so as to act based on the</a>
+<a name="1737"><span class="lineNum">    1737 </span>            :       type of its argument</a>
+<a name="1738"><span class="lineNum">    1738 </span>            : </a>
+<a name="1739"><span class="lineNum">    1739 </span>            :     New exceptions added here should be kept in sync with core/PlumedMainInitializer.cpp</a>
+<a name="1740"><span class="lineNum">    1740 </span>            : </a>
+<a name="1741"><span class="lineNum">    1741 </span>            :     Notice that this function also finalizes in place plumed_error h, so as to avoid</a>
+<a name="1742"><span class="lineNum">    1742 </span>            :     memory leaks.</a>
+<a name="1743"><span class="lineNum">    1743 </span>            :   */</a>
+<a name="1744"><span class="lineNum">    1744 </span>            :   template&lt;typename F&gt;</a>
+<a name="1745"><span class="lineNum">    1745 </span><span class="lineNoCov">          0 :   __PLUMED_WRAPPER_CXX_NORETURN static void exception_dispatch(plumed_error&amp;h,F f) {</span></a>
+<a name="1746"><span class="lineNum">    1746 </span>            :     /* this is required to make sure h is finalized when leaving this function */</a>
+<a name="1747"><span class="lineNum">    1747 </span>            :     finalize_plumed_error finalize(h);</a>
+<a name="1748"><span class="lineNum">    1748 </span>            :     /* grab the message */</a>
+<a name="1749"><span class="lineNum">    1749 </span>            :     const char* msg=plumed_error_what(h);</a>
+<a name="1750"><span class="lineNum">    1750 </span><span class="lineNoCov">          0 :     if(h.code==1) f(Plumed::Invalid(msg));</span></a>
+<a name="1751"><span class="lineNum">    1751 </span>            :     /* logic errors */</a>
+<a name="1752"><span class="lineNum">    1752 </span><span class="lineNoCov">          0 :     if(h.code&gt;=10100 &amp;&amp; h.code&lt;10200) {</span></a>
+<a name="1753"><span class="lineNum">    1753 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10105 &amp;&amp; h.code&lt;10110) f(::std::invalid_argument(msg));</span></a>
+<a name="1754"><span class="lineNum">    1754 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10110 &amp;&amp; h.code&lt;10115) f(::std::domain_error(msg));</span></a>
+<a name="1755"><span class="lineNum">    1755 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10115 &amp;&amp; h.code&lt;10120) f(::std::length_error(msg));</span></a>
+<a name="1756"><span class="lineNum">    1756 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10120 &amp;&amp; h.code&lt;10125) f(::std::out_of_range(msg));</span></a>
+<a name="1757"><span class="lineNum">    1757 </span><span class="lineNoCov">          0 :       f(::std::logic_error(msg));</span></a>
+<a name="1758"><span class="lineNum">    1758 </span>            :     }</a>
+<a name="1759"><span class="lineNum">    1759 </span>            :     /* runtime errors */</a>
+<a name="1760"><span class="lineNum">    1760 </span><span class="lineNoCov">          0 :     if(h.code&gt;=10200 &amp;&amp; h.code&lt;10300) {</span></a>
+<a name="1761"><span class="lineNum">    1761 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10205 &amp;&amp; h.code&lt;10210) f(::std::range_error(msg));</span></a>
+<a name="1762"><span class="lineNum">    1762 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10210 &amp;&amp; h.code&lt;10215) f(::std::overflow_error(msg));</span></a>
+<a name="1763"><span class="lineNum">    1763 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10215 &amp;&amp; h.code&lt;10220) f(::std::underflow_error(msg));</span></a>
+<a name="1764"><span class="lineNum">    1764 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1765"><span class="lineNum">    1765 </span>            :       if(h.code==10220) f(::std::system_error(h.error_code,::std::generic_category(),msg));</a>
+<a name="1766"><span class="lineNum">    1766 </span>            :       if(h.code==10221) f(::std::system_error(h.error_code,::std::system_category(),msg));</a>
+<a name="1767"><span class="lineNum">    1767 </span>            :       if(h.code==10222) f(::std::system_error(h.error_code,::std::iostream_category(),msg));</a>
+<a name="1768"><span class="lineNum">    1768 </span>            :       if(h.code==10223) f(::std::system_error(h.error_code,::std::future_category(),msg));</a>
+<a name="1769"><span class="lineNum">    1769 </span>            : #endif</a>
+<a name="1770"><span class="lineNum">    1770 </span><span class="lineNoCov">          0 :       if(h.code&gt;=10230 &amp;&amp; h.code&lt;10240) {</span></a>
+<a name="1771"><span class="lineNum">    1771 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1772"><span class="lineNum">    1772 </span>            : // These cases are probably useless as it looks like this should always be std::iostream_category</a>
+<a name="1773"><span class="lineNum">    1773 </span>            :         if(h.code==10230) f(::std::ios_base::failure(msg,::std::error_code(h.error_code,::std::generic_category())));</a>
+<a name="1774"><span class="lineNum">    1774 </span>            :         if(h.code==10231) f(::std::ios_base::failure(msg,::std::error_code(h.error_code,::std::system_category())));</a>
+<a name="1775"><span class="lineNum">    1775 </span>            :         if(h.code==10232) f(::std::ios_base::failure(msg,::std::error_code(h.error_code,::std::iostream_category())));</a>
+<a name="1776"><span class="lineNum">    1776 </span>            :         if(h.code==10233) f(::std::ios_base::failure(msg,::std::error_code(h.error_code,::std::future_category())));</a>
+<a name="1777"><span class="lineNum">    1777 </span>            : #endif</a>
+<a name="1778"><span class="lineNum">    1778 </span><span class="lineNoCov">          0 :         f(::std::ios_base::failure(msg));</span></a>
+<a name="1779"><span class="lineNum">    1779 </span>            :       }</a>
+<a name="1780"><span class="lineNum">    1780 </span><span class="lineNoCov">          0 :       f(::std::runtime_error(msg));</span></a>
+<a name="1781"><span class="lineNum">    1781 </span>            :     }</a>
+<a name="1782"><span class="lineNum">    1782 </span>            :     /* &quot;bad&quot; errors */</a>
+<a name="1783"><span class="lineNum">    1783 </span>            :     /* &quot;&lt; ::&quot; space required in C++ &lt; 11 */</a>
+<a name="1784"><span class="lineNum">    1784 </span><span class="lineNoCov">          0 :     if(h.code&gt;=11000 &amp;&amp; h.code&lt;11100) f(add_buffer_to&lt; ::std::bad_typeid&gt;(msg));</span></a>
+<a name="1785"><span class="lineNum">    1785 </span><span class="lineNoCov">          0 :     if(h.code&gt;=11100 &amp;&amp; h.code&lt;11200) f(add_buffer_to&lt; ::std::bad_cast&gt;(msg));</span></a>
+<a name="1786"><span class="lineNum">    1786 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1787"><span class="lineNum">    1787 </span>            :     if(h.code&gt;=11200 &amp;&amp; h.code&lt;11300) f(add_buffer_to&lt; ::std::bad_weak_ptr&gt;(msg));</a>
+<a name="1788"><span class="lineNum">    1788 </span>            :     if(h.code&gt;=11300 &amp;&amp; h.code&lt;11400) f(add_buffer_to&lt; ::std::bad_function_call&gt;(msg));</a>
+<a name="1789"><span class="lineNum">    1789 </span>            : #endif</a>
+<a name="1790"><span class="lineNum">    1790 </span><span class="lineNoCov">          0 :     if(h.code&gt;=11400 &amp;&amp; h.code&lt;11500) {</span></a>
+<a name="1791"><span class="lineNum">    1791 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1792"><span class="lineNum">    1792 </span>            :       if(h.code&gt;=11410 &amp;&amp; h.code&lt;11420) f(add_buffer_to&lt; ::std::bad_array_new_length&gt;(msg));</a>
+<a name="1793"><span class="lineNum">    1793 </span>            : #endif</a>
+<a name="1794"><span class="lineNum">    1794 </span><span class="lineNoCov">          0 :       f(add_buffer_to&lt; ::std::bad_alloc&gt;(msg));</span></a>
+<a name="1795"><span class="lineNum">    1795 </span>            :     }</a>
+<a name="1796"><span class="lineNum">    1796 </span><span class="lineNoCov">          0 :     if(h.code&gt;=11500 &amp;&amp; h.code&lt;11600) f(add_buffer_to&lt; ::std::bad_exception&gt;(msg));</span></a>
+<a name="1797"><span class="lineNum">    1797 </span>            :     /* lepton error */</a>
+<a name="1798"><span class="lineNum">    1798 </span><span class="lineNoCov">          0 :     if(h.code&gt;=19900 &amp;&amp; h.code&lt;20000) f(Plumed::LeptonException(msg));</span></a>
+<a name="1799"><span class="lineNum">    1799 </span>            :     /* plumed exceptions */</a>
+<a name="1800"><span class="lineNum">    1800 </span><span class="lineNoCov">          0 :     if(h.code&gt;=20000 &amp;&amp; h.code&lt;30000) {</span></a>
+<a name="1801"><span class="lineNum">    1801 </span>            :       /* debug - only raised with debug options */</a>
+<a name="1802"><span class="lineNum">    1802 </span><span class="lineNoCov">          0 :       if(h.code&gt;=20100 &amp;&amp; h.code&lt;20200) f(Plumed::ExceptionDebug(msg));</span></a>
+<a name="1803"><span class="lineNum">    1803 </span>            :       /* error - runtime check */</a>
+<a name="1804"><span class="lineNum">    1804 </span><span class="lineNoCov">          0 :       if(h.code&gt;=20200 &amp;&amp; h.code&lt;20300) f(Plumed::ExceptionError(msg));</span></a>
+<a name="1805"><span class="lineNum">    1805 </span>            :       /* error - type error */</a>
+<a name="1806"><span class="lineNum">    1806 </span><span class="lineNoCov">          0 :       if(h.code&gt;=20300 &amp;&amp; h.code&lt;20400) f(Plumed::ExceptionTypeError(msg));</span></a>
+<a name="1807"><span class="lineNum">    1807 </span><span class="lineNoCov">          0 :       f(Plumed::Exception(msg));</span></a>
+<a name="1808"><span class="lineNum">    1808 </span>            :     }</a>
+<a name="1809"><span class="lineNum">    1809 </span>            :     /* fallback for any other exception */</a>
+<a name="1810"><span class="lineNum">    1810 </span><span class="lineNoCov">          0 :     f(add_buffer_to&lt; ::std::exception&gt;(msg));</span></a>
+<a name="1811"><span class="lineNum">    1811 </span>            :   }</a>
+<a name="1812"><span class="lineNum">    1812 </span>            : </a>
+<a name="1813"><span class="lineNum">    1813 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_CXX_ENABLE_NESTED_EXCEPTIONS</a>
+<a name="1814"><span class="lineNum">    1814 </span>            :   /** Internal class used by exception_dispatch. */</a>
+<a name="1815"><span class="lineNum">    1815 </span>            :   class rethrow_nested {</a>
+<a name="1816"><span class="lineNum">    1816 </span>            :   public:</a>
+<a name="1817"><span class="lineNum">    1817 </span>            :     template&lt;typename E&gt;</a>
+<a name="1818"><span class="lineNum">    1818 </span>            :     __PLUMED_WRAPPER_CXX_NORETURN void operator()(const E&amp;e) {</a>
+<a name="1819"><span class="lineNum">    1819 </span><span class="lineNoCov">          0 :       std::throw_with_nested(e);</span></a>
+<a name="1820"><span class="lineNum">    1820 </span>            :     }</a>
+<a name="1821"><span class="lineNum">    1821 </span>            :   };</a>
+<a name="1822"><span class="lineNum">    1822 </span>            : #endif</a>
+<a name="1823"><span class="lineNum">    1823 </span>            : </a>
+<a name="1824"><span class="lineNum">    1824 </span>            :   /** Internal class used by exception_dispatch. */</a>
+<a name="1825"><span class="lineNum">    1825 </span>            :   class rethrow_not_nested {</a>
+<a name="1826"><span class="lineNum">    1826 </span>            :   public:</a>
+<a name="1827"><span class="lineNum">    1827 </span>            :     template&lt;typename E&gt;</a>
+<a name="1828"><span class="lineNum">    1828 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_NORETURN void operator()(const E&amp;e) {</span></a>
+<a name="1829"><span class="lineNum">    1829 </span><span class="lineNoCov">          0 :       throw e;</span></a>
+<a name="1830"><span class="lineNum">    1830 </span>            :     }</a>
+<a name="1831"><span class="lineNum">    1831 </span>            :   };</a>
+<a name="1832"><span class="lineNum">    1832 </span>            : </a>
+<a name="1833"><span class="lineNum">    1833 </span>            :   /** Internal class to simplify plumed_error finalization */</a>
+<a name="1834"><span class="lineNum">    1834 </span>            :   class finalize_plumed_error {</a>
+<a name="1835"><span class="lineNum">    1835 </span>            :     plumed_error&amp;e;</a>
+<a name="1836"><span class="lineNum">    1836 </span>            :     finalize_plumed_error(const finalize_plumed_error&amp;); //not implemented</a>
+<a name="1837"><span class="lineNum">    1837 </span>            :   public:</a>
+<a name="1838"><span class="lineNum">    1838 </span>            :     __PLUMED_WRAPPER_CXX_EXPLICIT finalize_plumed_error(plumed_error&amp;e):</a>
+<a name="1839"><span class="lineNum">    1839 </span>            :       e(e)</a>
+<a name="1840"><span class="lineNum">    1840 </span>            :     {}</a>
+<a name="1841"><span class="lineNum">    1841 </span>            :     ~finalize_plumed_error() {</a>
+<a name="1842"><span class="lineNum">    1842 </span><span class="lineNoCov">          0 :       plumed_error_finalize(e);</span></a>
+<a name="1843"><span class="lineNum">    1843 </span><span class="lineNoCov">          0 :       e.code=0; // make sure it's not finalized again</span></a>
+<a name="1844"><span class="lineNum">    1844 </span>            :     }</a>
+<a name="1845"><span class="lineNum">    1845 </span>            :   };</a>
+<a name="1846"><span class="lineNum">    1846 </span>            : </a>
+<a name="1847"><span class="lineNum">    1847 </span>            :   /**</a>
+<a name="1848"><span class="lineNum">    1848 </span>            :     Recursive function that rethrows an exception with all the nested ones.</a>
+<a name="1849"><span class="lineNum">    1849 </span>            : </a>
+<a name="1850"><span class="lineNum">    1850 </span>            :     In order to do so, we start throwing from the first exception that was originally thrown</a>
+<a name="1851"><span class="lineNum">    1851 </span>            :     and recursively throw the others using throw_with_nested.</a>
+<a name="1852"><span class="lineNum">    1852 </span>            : </a>
+<a name="1853"><span class="lineNum">    1853 </span>            :     plumed_error h is finalized at exit by the exception_dispatch function, to avoid memory leaks</a>
+<a name="1854"><span class="lineNum">    1854 </span>            :   */</a>
+<a name="1855"><span class="lineNum">    1855 </span><span class="lineNoCov">          0 :   __PLUMED_WRAPPER_CXX_NORETURN static void rethrow(plumed_error&amp;h) {</span></a>
+<a name="1856"><span class="lineNum">    1856 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_CXX_ENABLE_NESTED_EXCEPTIONS</a>
+<a name="1857"><span class="lineNum">    1857 </span>            :     /*</a>
+<a name="1858"><span class="lineNum">    1858 </span>            :       When using C++11 nested exceptions, we need to rethrow recursively</a>
+<a name="1859"><span class="lineNum">    1859 </span>            :     */</a>
+<a name="1860"><span class="lineNum">    1860 </span>            :     try {</a>
+<a name="1861"><span class="lineNum">    1861 </span><span class="lineNoCov">          0 :       if(h.nested) rethrow(*h.nested); /* recursive throw */</span></a>
+<a name="1862"><span class="lineNum">    1862 </span><span class="lineNoCov">          0 :     } catch(...) {</span></a>
+<a name="1863"><span class="lineNum">    1863 </span><span class="lineNoCov">          0 :       exception_dispatch(h,rethrow_nested());</span></a>
+<a name="1864"><span class="lineNum">    1864 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="1865"><span class="lineNum">    1865 </span><span class="lineNoCov">          0 :     exception_dispatch(h,rethrow_not_nested());</span></a>
+<a name="1866"><span class="lineNum">    1866 </span>            : #else</a>
+<a name="1867"><span class="lineNum">    1867 </span>            :     /*</a>
+<a name="1868"><span class="lineNum">    1868 </span>            :       When using C++&lt;11 exceptions, we merge the message and then throw the resulting exception</a>
+<a name="1869"><span class="lineNum">    1869 </span>            :     */</a>
+<a name="1870"><span class="lineNum">    1870 </span>            :     if(h.nested) plumed_error_merge_with_nested(&amp;h);</a>
+<a name="1871"><span class="lineNum">    1871 </span>            :     exception_dispatch(h,rethrow_not_nested());</a>
+<a name="1872"><span class="lineNum">    1872 </span>            : #endif</a>
+<a name="1873"><span class="lineNum">    1873 </span>            :   }</a>
+<a name="1874"><span class="lineNum">    1874 </span>            : </a>
+<a name="1875"><span class="lineNum">    1875 </span>            : public:</a>
+<a name="1876"><span class="lineNum">    1876 </span>            :   /**</a>
+<a name="1877"><span class="lineNum">    1877 </span>            :     This is a tool to rethrow an error as an exception and finalize the error.</a>
+<a name="1878"><span class="lineNum">    1878 </span>            : </a>
+<a name="1879"><span class="lineNum">    1879 </span>            :     In practice, this makes it possible to write a code like this:</a>
+<a name="1880"><span class="lineNum">    1880 </span>            :     ```</a>
+<a name="1881"><span class="lineNum">    1881 </span>            :     Plumed p;</a>
+<a name="1882"><span class="lineNum">    1882 </span>            :     plumed_error e;</a>
+<a name="1883"><span class="lineNum">    1883 </span>            :     // store error in e if something wrong happes</a>
+<a name="1884"><span class="lineNum">    1884 </span>            :     // notice that Plumed (C++) is implicitly converted to plumed (C) when calling plumed_cmd</a>
+<a name="1885"><span class="lineNum">    1885 </span>            :     plumed_cmd(p,&quot;init&quot;,&amp;e);</a>
+<a name="1886"><span class="lineNum">    1886 </span>            :     // do other things here</a>
+<a name="1887"><span class="lineNum">    1887 </span>            :     // then throw the exception</a>
+<a name="1888"><span class="lineNum">    1888 </span>            :     if(e.code) plumed_error_rethrow(e);</a>
+<a name="1889"><span class="lineNum">    1889 </span>            : </a>
+<a name="1890"><span class="lineNum">    1890 </span>            :     It should be used through the macro plumed_error_rethrow.</a>
+<a name="1891"><span class="lineNum">    1891 </span>            :     ```</a>
+<a name="1892"><span class="lineNum">    1892 </span>            :   */</a>
+<a name="1893"><span class="lineNum">    1893 </span>            :   __PLUMED_WRAPPER_CXX_NORETURN static void plumed_error_rethrow_cxx(plumed_error h) {</a>
+<a name="1894"><span class="lineNum">    1894 </span><span class="lineNoCov">          0 :     rethrow(h);</span></a>
+<a name="1895"><span class="lineNum">    1895 </span>            :   }</a>
+<a name="1896"><span class="lineNum">    1896 </span>            : </a>
+<a name="1897"><span class="lineNum">    1897 </span>            : private:</a>
+<a name="1898"><span class="lineNum">    1898 </span>            :   /**</a>
+<a name="1899"><span class="lineNum">    1899 </span>            :     Rethrow the current exception.</a>
+<a name="1900"><span class="lineNum">    1900 </span>            : </a>
+<a name="1901"><span class="lineNum">    1901 </span>            :     This is useful in order to handle an exception thrown by a kernel &lt;=2.4.</a>
+<a name="1902"><span class="lineNum">    1902 </span>            :     Only std exceptions are handled, though some of them are thrown as special</a>
+<a name="1903"><span class="lineNum">    1903 </span>            :     Plumed exceptions in order to be attached a message.</a>
+<a name="1904"><span class="lineNum">    1904 </span>            :   */</a>
+<a name="1905"><span class="lineNum">    1905 </span><span class="lineNoCov">          0 :   __PLUMED_WRAPPER_CXX_NORETURN static void rethrow() {</span></a>
+<a name="1906"><span class="lineNum">    1906 </span>            :     try {</a>
+<a name="1907"><span class="lineNum">    1907 </span><span class="lineNoCov">          0 :       throw;</span></a>
+<a name="1908"><span class="lineNum">    1908 </span><span class="lineNoCov">          0 :     } catch(const ::std::bad_exception &amp; e) {</span></a>
+<a name="1909"><span class="lineNum">    1909 </span><span class="lineNoCov">          0 :       throw add_buffer_to&lt; ::std::bad_exception&gt;(e.what());</span></a>
+<a name="1910"><span class="lineNum">    1910 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1911"><span class="lineNum">    1911 </span>            :     } catch(const ::std::bad_array_new_length &amp; e) {</a>
+<a name="1912"><span class="lineNum">    1912 </span>            :       throw add_buffer_to&lt; ::std::bad_array_new_length&gt;(e.what());</a>
+<a name="1913"><span class="lineNum">    1913 </span>            : #endif</a>
+<a name="1914"><span class="lineNum">    1914 </span><span class="lineNoCov">          0 :     } catch(const ::std::bad_alloc &amp; e) {</span></a>
+<a name="1915"><span class="lineNum">    1915 </span><span class="lineNoCov">          0 :       throw add_buffer_to&lt; ::std::bad_alloc&gt;(e.what());</span></a>
+<a name="1916"><span class="lineNum">    1916 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1917"><span class="lineNum">    1917 </span>            :     } catch(const ::std::bad_function_call &amp; e) {</a>
+<a name="1918"><span class="lineNum">    1918 </span>            :       throw add_buffer_to&lt; ::std::bad_function_call&gt;(e.what());</a>
+<a name="1919"><span class="lineNum">    1919 </span>            :     } catch(const ::std::bad_weak_ptr &amp; e) {</a>
+<a name="1920"><span class="lineNum">    1920 </span>            :       throw add_buffer_to&lt; ::std::bad_weak_ptr&gt;(e.what());</a>
+<a name="1921"><span class="lineNum">    1921 </span>            : #endif</a>
+<a name="1922"><span class="lineNum">    1922 </span><span class="lineNoCov">          0 :     } catch(const ::std::bad_cast &amp; e) {</span></a>
+<a name="1923"><span class="lineNum">    1923 </span><span class="lineNoCov">          0 :       throw add_buffer_to&lt; ::std::bad_cast&gt;(e.what());</span></a>
+<a name="1924"><span class="lineNum">    1924 </span><span class="lineNoCov">          0 :     } catch(const ::std::bad_typeid &amp; e) {</span></a>
+<a name="1925"><span class="lineNum">    1925 </span><span class="lineNoCov">          0 :       throw add_buffer_to&lt; ::std::bad_typeid&gt;(e.what());</span></a>
+<a name="1926"><span class="lineNum">    1926 </span>            :       // not implemented yet: std::regex_error</a>
+<a name="1927"><span class="lineNum">    1927 </span>            :       // we do not allow regex yet due to portability problems with gcc 4.8</a>
+<a name="1928"><span class="lineNum">    1928 </span>            :       // as soon as we transition to using &lt;regex&gt; it should be straightforward to add</a>
+<a name="1929"><span class="lineNum">    1929 </span><span class="lineNoCov">          0 :     } catch(const ::std::ios_base::failure &amp; e) {</span></a>
+<a name="1930"><span class="lineNum">    1930 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1931"><span class="lineNum">    1931 </span>            :       throw ::std::ios_base::failure(e.what(),e.code());</a>
+<a name="1932"><span class="lineNum">    1932 </span>            : #else</a>
+<a name="1933"><span class="lineNum">    1933 </span><span class="lineNoCov">          0 :       throw ::std::ios_base::failure(e.what());</span></a>
+<a name="1934"><span class="lineNum">    1934 </span>            : #endif</a>
+<a name="1935"><span class="lineNum">    1935 </span>            : #if __cplusplus &gt; 199711L &amp;&amp; __PLUMED_WRAPPER_LIBCXX11</a>
+<a name="1936"><span class="lineNum">    1936 </span>            :     } catch(const ::std::system_error &amp; e) {</a>
+<a name="1937"><span class="lineNum">    1937 </span>            :       throw ::std::system_error(e.code(),e.what());</a>
+<a name="1938"><span class="lineNum">    1938 </span>            : #endif</a>
+<a name="1939"><span class="lineNum">    1939 </span><span class="lineNoCov">          0 :     } catch(const ::std::underflow_error &amp;e) {</span></a>
+<a name="1940"><span class="lineNum">    1940 </span><span class="lineNoCov">          0 :       throw ::std::underflow_error(e.what());</span></a>
+<a name="1941"><span class="lineNum">    1941 </span><span class="lineNoCov">          0 :     } catch(const ::std::overflow_error &amp;e) {</span></a>
+<a name="1942"><span class="lineNum">    1942 </span><span class="lineNoCov">          0 :       throw ::std::overflow_error(e.what());</span></a>
+<a name="1943"><span class="lineNum">    1943 </span><span class="lineNoCov">          0 :     } catch(const ::std::range_error &amp;e) {</span></a>
+<a name="1944"><span class="lineNum">    1944 </span><span class="lineNoCov">          0 :       throw ::std::range_error(e.what());</span></a>
+<a name="1945"><span class="lineNum">    1945 </span><span class="lineNoCov">          0 :     } catch(const ::std::runtime_error &amp; e) {</span></a>
+<a name="1946"><span class="lineNum">    1946 </span><span class="lineNoCov">          0 :       throw ::std::runtime_error(e.what());</span></a>
+<a name="1947"><span class="lineNum">    1947 </span>            :       // not implemented yet: std::future_error</a>
+<a name="1948"><span class="lineNum">    1948 </span>            :       // not clear how useful it would be.</a>
+<a name="1949"><span class="lineNum">    1949 </span><span class="lineNoCov">          0 :     } catch(const ::std::out_of_range &amp; e) {</span></a>
+<a name="1950"><span class="lineNum">    1950 </span><span class="lineNoCov">          0 :       throw ::std::out_of_range(e.what());</span></a>
+<a name="1951"><span class="lineNum">    1951 </span><span class="lineNoCov">          0 :     } catch(const ::std::length_error &amp; e) {</span></a>
+<a name="1952"><span class="lineNum">    1952 </span><span class="lineNoCov">          0 :       throw ::std::length_error(e.what());</span></a>
+<a name="1953"><span class="lineNum">    1953 </span><span class="lineNoCov">          0 :     } catch(const ::std::domain_error &amp; e) {</span></a>
+<a name="1954"><span class="lineNum">    1954 </span><span class="lineNoCov">          0 :       throw ::std::domain_error(e.what());</span></a>
+<a name="1955"><span class="lineNum">    1955 </span><span class="lineNoCov">          0 :     } catch(const ::std::invalid_argument &amp; e) {</span></a>
+<a name="1956"><span class="lineNum">    1956 </span><span class="lineNoCov">          0 :       throw ::std::invalid_argument(e.what());</span></a>
+<a name="1957"><span class="lineNum">    1957 </span><span class="lineNoCov">          0 :     } catch(const ::std::logic_error &amp; e) {</span></a>
+<a name="1958"><span class="lineNum">    1958 </span><span class="lineNoCov">          0 :       throw ::std::logic_error(e.what());</span></a>
+<a name="1959"><span class="lineNum">    1959 </span><span class="lineNoCov">          0 :     } catch(const ::std::exception &amp; e) {</span></a>
+<a name="1960"><span class="lineNum">    1960 </span><span class="lineNoCov">          0 :       throw add_buffer_to&lt; ::std::exception&gt;(e.what());</span></a>
+<a name="1961"><span class="lineNum">    1961 </span><span class="lineNoCov">          0 :     } catch(...) {</span></a>
+<a name="1962"><span class="lineNum">    1962 </span><span class="lineNoCov">          0 :       throw add_buffer_to&lt; ::std::bad_exception&gt;(&quot;plumed could not translate exception&quot;);</span></a>
+<a name="1963"><span class="lineNum">    1963 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="1964"><span class="lineNum">    1964 </span>            :   }</a>
+<a name="1965"><span class="lineNum">    1965 </span>            : </a>
+<a name="1966"><span class="lineNum">    1966 </span>            : public:</a>
+<a name="1967"><span class="lineNum">    1967 </span>            : </a>
+<a name="1968"><span class="lineNum">    1968 </span>            : #if __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS</a>
+<a name="1969"><span class="lineNum">    1969 </span>            :   using Exception = PLMD::Exception;</a>
+<a name="1970"><span class="lineNum">    1970 </span>            : #else</a>
+<a name="1971"><span class="lineNum">    1971 </span>            :   /**</a>
+<a name="1972"><span class="lineNum">    1972 </span>            :     Base class used to rethrow PLUMED exceptions.</a>
+<a name="1973"><span class="lineNum">    1973 </span>            :   */</a>
+<a name="1974"><span class="lineNum">    1974 </span>            :   class Exception :</a>
+<a name="1975"><span class="lineNum">    1975 </span>            :     public ::std::exception</a>
+<a name="1976"><span class="lineNum">    1976 </span>            :   {</a>
+<a name="1977"><span class="lineNum">    1977 </span>            :     ::std::string msg;</a>
+<a name="1978"><span class="lineNum">    1978 </span>            :   public:</a>
+<a name="1979"><span class="lineNum">    1979 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT Exception(const char* msg): msg(msg) {}</span></a>
+<a name="1980"><span class="lineNum">    1980 </span><span class="lineNoCov">          0 :     const char* what() const __PLUMED_WRAPPER_CXX_NOEXCEPT __PLUMED_WRAPPER_CXX_OVERRIDE {return msg.c_str();}</span></a>
+<a name="1981"><span class="lineNum">    1981 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="1982"><span class="lineNum">    1982 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="1983"><span class="lineNum">    1983 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="1984"><span class="lineNum">    1984 </span>            :     ~Exception() throw() {}</a>
+<a name="1985"><span class="lineNum">    1985 </span>            : #endif</a>
+<a name="1986"><span class="lineNum">    1986 </span>            :   };</a>
+<a name="1987"><span class="lineNum">    1987 </span>            : #endif</a>
+<a name="1988"><span class="lineNum">    1988 </span>            : </a>
+<a name="1989"><span class="lineNum">    1989 </span>            : #if __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS</a>
+<a name="1990"><span class="lineNum">    1990 </span>            :   using ExceptionError = PLMD::ExceptionError;</a>
+<a name="1991"><span class="lineNum">    1991 </span>            : #else</a>
+<a name="1992"><span class="lineNum">    1992 </span>            :   /**</a>
+<a name="1993"><span class="lineNum">    1993 </span>            :     Used to rethrow a PLMD::ExceptionError</a>
+<a name="1994"><span class="lineNum">    1994 </span>            :   */</a>
+<a name="1995"><span class="lineNum">    1995 </span><span class="lineNoCov">          0 :   class ExceptionError :</span></a>
+<a name="1996"><span class="lineNum">    1996 </span>            :     public Exception {</a>
+<a name="1997"><span class="lineNum">    1997 </span>            :   public:</a>
+<a name="1998"><span class="lineNum">    1998 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT ExceptionError(const char* msg): Exception(msg) {}</span></a>
+<a name="1999"><span class="lineNum">    1999 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="2000"><span class="lineNum">    2000 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="2001"><span class="lineNum">    2001 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="2002"><span class="lineNum">    2002 </span>            :     ~ExceptionError() throw() {}</a>
+<a name="2003"><span class="lineNum">    2003 </span>            : #endif</a>
+<a name="2004"><span class="lineNum">    2004 </span>            :   };</a>
+<a name="2005"><span class="lineNum">    2005 </span>            : #endif</a>
+<a name="2006"><span class="lineNum">    2006 </span>            : </a>
+<a name="2007"><span class="lineNum">    2007 </span>            : #if __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS</a>
+<a name="2008"><span class="lineNum">    2008 </span>            :   using ExceptionDebug = PLMD::ExceptionDebug;</a>
+<a name="2009"><span class="lineNum">    2009 </span>            : #else</a>
+<a name="2010"><span class="lineNum">    2010 </span>            :   /**</a>
+<a name="2011"><span class="lineNum">    2011 </span>            :     Used to rethrow a PLMD::ExceptionDebug</a>
+<a name="2012"><span class="lineNum">    2012 </span>            :   */</a>
+<a name="2013"><span class="lineNum">    2013 </span><span class="lineNoCov">          0 :   class ExceptionDebug :</span></a>
+<a name="2014"><span class="lineNum">    2014 </span>            :     public Exception {</a>
+<a name="2015"><span class="lineNum">    2015 </span>            :   public:</a>
+<a name="2016"><span class="lineNum">    2016 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT ExceptionDebug(const char* msg): Exception(msg) {}</span></a>
+<a name="2017"><span class="lineNum">    2017 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="2018"><span class="lineNum">    2018 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="2019"><span class="lineNum">    2019 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="2020"><span class="lineNum">    2020 </span>            :     ~ExceptionDebug() throw() {}</a>
+<a name="2021"><span class="lineNum">    2021 </span>            : #endif</a>
+<a name="2022"><span class="lineNum">    2022 </span>            :   };</a>
+<a name="2023"><span class="lineNum">    2023 </span>            : #endif</a>
+<a name="2024"><span class="lineNum">    2024 </span>            : </a>
+<a name="2025"><span class="lineNum">    2025 </span>            :   /**</a>
+<a name="2026"><span class="lineNum">    2026 </span>            :     Thrown when trying to access an invalid plumed object</a>
+<a name="2027"><span class="lineNum">    2027 </span>            :   */</a>
+<a name="2028"><span class="lineNum">    2028 </span>            : </a>
+<a name="2029"><span class="lineNum">    2029 </span><span class="lineNoCov">          0 :   class Invalid :</span></a>
+<a name="2030"><span class="lineNum">    2030 </span>            :     public Exception {</a>
+<a name="2031"><span class="lineNum">    2031 </span>            :   public:</a>
+<a name="2032"><span class="lineNum">    2032 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT Invalid(const char* msg): Exception(msg) {}</span></a>
+<a name="2033"><span class="lineNum">    2033 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="2034"><span class="lineNum">    2034 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="2035"><span class="lineNum">    2035 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="2036"><span class="lineNum">    2036 </span>            :     ~Invalid() throw() {}</a>
+<a name="2037"><span class="lineNum">    2037 </span>            : #endif</a>
+<a name="2038"><span class="lineNum">    2038 </span>            :   };</a>
+<a name="2039"><span class="lineNum">    2039 </span>            : </a>
+<a name="2040"><span class="lineNum">    2040 </span>            : #if __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS</a>
+<a name="2041"><span class="lineNum">    2041 </span>            :   using ExceptionTypeError = PLMD::ExceptionTypeError;</a>
+<a name="2042"><span class="lineNum">    2042 </span>            : #else</a>
+<a name="2043"><span class="lineNum">    2043 </span>            :   /**</a>
+<a name="2044"><span class="lineNum">    2044 </span>            :     Thrown when a wrong pointer is passed to the PLUMED interface.</a>
+<a name="2045"><span class="lineNum">    2045 </span>            :   */</a>
+<a name="2046"><span class="lineNum">    2046 </span><span class="lineNoCov">          0 :   class ExceptionTypeError:</span></a>
+<a name="2047"><span class="lineNum">    2047 </span>            :     public Exception {</a>
+<a name="2048"><span class="lineNum">    2048 </span>            :   public:</a>
+<a name="2049"><span class="lineNum">    2049 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT ExceptionTypeError(const char* msg): Exception(msg) {}</span></a>
+<a name="2050"><span class="lineNum">    2050 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="2051"><span class="lineNum">    2051 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="2052"><span class="lineNum">    2052 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="2053"><span class="lineNum">    2053 </span>            :     ~ExceptionTypeError() throw() {}</a>
+<a name="2054"><span class="lineNum">    2054 </span>            : #endif</a>
+<a name="2055"><span class="lineNum">    2055 </span>            :   };</a>
+<a name="2056"><span class="lineNum">    2056 </span>            : #endif</a>
+<a name="2057"><span class="lineNum">    2057 </span>            : </a>
+<a name="2058"><span class="lineNum">    2058 </span>            : #if __PLUMED_WRAPPER_CXX_ANONYMOUS_NAMESPACE_PLMD_EXCEPTIONS</a>
+<a name="2059"><span class="lineNum">    2059 </span>            :   using LeptonException = PLMD::lepton::Exception;</a>
+<a name="2060"><span class="lineNum">    2060 </span>            : #else</a>
+<a name="2061"><span class="lineNum">    2061 </span>            :   /**</a>
+<a name="2062"><span class="lineNum">    2062 </span>            :     Class used to rethrow Lepton exceptions.</a>
+<a name="2063"><span class="lineNum">    2063 </span>            :   */</a>
+<a name="2064"><span class="lineNum">    2064 </span>            : </a>
+<a name="2065"><span class="lineNum">    2065 </span>            :   class LeptonException :</a>
+<a name="2066"><span class="lineNum">    2066 </span>            :     public ::std::exception</a>
+<a name="2067"><span class="lineNum">    2067 </span>            :   {</a>
+<a name="2068"><span class="lineNum">    2068 </span>            :     ::std::string msg;</a>
+<a name="2069"><span class="lineNum">    2069 </span>            :   public:</a>
+<a name="2070"><span class="lineNum">    2070 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT LeptonException(const char* msg): msg(msg) {}</span></a>
+<a name="2071"><span class="lineNum">    2071 </span><span class="lineNoCov">          0 :     const char* what() const __PLUMED_WRAPPER_CXX_NOEXCEPT __PLUMED_WRAPPER_CXX_OVERRIDE {return msg.c_str();}</span></a>
+<a name="2072"><span class="lineNum">    2072 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="2073"><span class="lineNum">    2073 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="2074"><span class="lineNum">    2074 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="2075"><span class="lineNum">    2075 </span>            :     ~LeptonException() throw() {}</a>
+<a name="2076"><span class="lineNum">    2076 </span>            : #endif</a>
+<a name="2077"><span class="lineNum">    2077 </span>            :   };</a>
+<a name="2078"><span class="lineNum">    2078 </span>            : #endif</a>
+<a name="2079"><span class="lineNum">    2079 </span>            : </a>
+<a name="2080"><span class="lineNum">    2080 </span>            : private:</a>
+<a name="2081"><span class="lineNum">    2081 </span>            :   /*</a>
+<a name="2082"><span class="lineNum">    2082 </span>            :     These exceptions are declared as private as they are not supposed to be</a>
+<a name="2083"><span class="lineNum">    2083 </span>            :     catched by value. they only exist to allow a buffer to be attached to</a>
+<a name="2084"><span class="lineNum">    2084 </span>            :     the std::exceptions that do not contain it already.</a>
+<a name="2085"><span class="lineNum">    2085 </span>            :     Notice that these exceptions are those whose constructor should never throw, and as</a>
+<a name="2086"><span class="lineNum">    2086 </span>            :     such they use a fixed size buffer.</a>
+<a name="2087"><span class="lineNum">    2087 </span>            :   */</a>
+<a name="2088"><span class="lineNum">    2088 </span>            : </a>
+<a name="2089"><span class="lineNum">    2089 </span>            :   template&lt;typename T&gt;</a>
+<a name="2090"><span class="lineNum">    2090 </span><span class="lineNoCov">          0 :   class add_buffer_to:</span></a>
+<a name="2091"><span class="lineNum">    2091 </span>            :     public T</a>
+<a name="2092"><span class="lineNum">    2092 </span>            :   {</a>
+<a name="2093"><span class="lineNum">    2093 </span>            :     char msg[__PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER]; \</a>
+<a name="2094"><span class="lineNum">    2094 </span>            :   public:</a>
+<a name="2095"><span class="lineNum">    2095 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_CXX_EXPLICIT add_buffer_to(const char * msg) __PLUMED_WRAPPER_CXX_NOEXCEPT {</span></a>
+<a name="2096"><span class="lineNum">    2096 </span><span class="lineNoCov">          0 :       this-&gt;msg[0]='\0';</span></a>
+<a name="2097"><span class="lineNum">    2097 </span><span class="lineNoCov">          0 :       __PLUMED_WRAPPER_STD strncat(this-&gt;msg,msg,__PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER-1);</span></a>
+<a name="2098"><span class="lineNum">    2098 </span><span class="lineNoCov">          0 :       this-&gt;msg[__PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER-1]='\0';</span></a>
+<a name="2099"><span class="lineNum">    2099 </span><span class="lineNoCov">          0 :       if(PlumedGetenvExceptionsDebug() &amp;&amp; __PLUMED_WRAPPER_STD strlen(msg) &gt; __PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER-1) __PLUMED_WRAPPER_STD fprintf(stderr,&quot;+++ WARNING: message will be truncated\n&quot;);</span></a>
+<a name="2100"><span class="lineNum">    2100 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="2101"><span class="lineNum">    2101 </span><span class="lineNoCov">          0 :     add_buffer_to(const add_buffer_to &amp; other) __PLUMED_WRAPPER_CXX_NOEXCEPT {</span></a>
+<a name="2102"><span class="lineNum">    2102 </span><span class="lineNoCov">          0 :       msg[0]='\0';</span></a>
+<a name="2103"><span class="lineNum">    2103 </span><span class="lineNoCov">          0 :       __PLUMED_WRAPPER_STD memcpy(msg,other.msg,__PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER);</span></a>
+<a name="2104"><span class="lineNum">    2104 </span>            :     }</a>
+<a name="2105"><span class="lineNum">    2105 </span>            :     add_buffer_to &amp; operator=(const add_buffer_to &amp; other) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2106"><span class="lineNum">    2106 </span>            :       if(this==&amp;other) return *this;</a>
+<a name="2107"><span class="lineNum">    2107 </span>            :       msg[0]='\0';</a>
+<a name="2108"><span class="lineNum">    2108 </span>            :       __PLUMED_WRAPPER_STD memcpy(msg,other.msg,__PLUMED_WRAPPER_CXX_EXCEPTION_BUFFER);</a>
+<a name="2109"><span class="lineNum">    2109 </span>            :       return *this;</a>
+<a name="2110"><span class="lineNum">    2110 </span>            :     }</a>
+<a name="2111"><span class="lineNum">    2111 </span><span class="lineNoCov">          0 :     const char* what() const __PLUMED_WRAPPER_CXX_NOEXCEPT __PLUMED_WRAPPER_CXX_OVERRIDE {return msg;}</span></a>
+<a name="2112"><span class="lineNum">    2112 </span>            : #if ! (__cplusplus &gt; 199711L)</a>
+<a name="2113"><span class="lineNum">    2113 </span>            :     /* Destructor should be declared in order to have the correct throw() before C++11 */</a>
+<a name="2114"><span class="lineNum">    2114 </span>            :     /* see https://stackoverflow.com/questions/50025862/why-is-the-stdexception-destructor-not-noexcept */</a>
+<a name="2115"><span class="lineNum">    2115 </span>            :     ~add_buffer_to() throw() {}</a>
+<a name="2116"><span class="lineNum">    2116 </span>            : #endif</a>
+<a name="2117"><span class="lineNum">    2117 </span>            :   };</a>
+<a name="2118"><span class="lineNum">    2118 </span>            : </a>
+<a name="2119"><span class="lineNum">    2119 </span>            : private:</a>
+<a name="2120"><span class="lineNum">    2120 </span>            :   /// Small class that wraps plumed_safeptr in order to make its initialization easier</a>
+<a name="2121"><span class="lineNum">    2121 </span>            :   class SafePtr {</a>
+<a name="2122"><span class="lineNum">    2122 </span>            :     /// non copyable (copy would require managing buffer, could be added in the future if needed)</a>
+<a name="2123"><span class="lineNum">    2123 </span>            :     SafePtr(const SafePtr&amp;);</a>
+<a name="2124"><span class="lineNum">    2124 </span>            :     /// non assignable (assignment would require managing buffer, could be added in the future if needed)</a>
+<a name="2125"><span class="lineNum">    2125 </span>            :     SafePtr&amp; operator=(SafePtr const&amp;);</a>
+<a name="2126"><span class="lineNum">    2126 </span>            :   public:</a>
+<a name="2127"><span class="lineNum">    2127 </span>            :     plumed_safeptr safe;</a>
+<a name="2128"><span class="lineNum">    2128 </span>            :     /// This buffer holds a copy of the data when they are passed by value.</a>
+<a name="2129"><span class="lineNum">    2129 </span>            :     /// The size is sufficient to hold any primitive type.</a>
+<a name="2130"><span class="lineNum">    2130 </span>            :     /// Notice that the buffer is required to enable conversions (e.g., passing a class that can be converted to int)</a>
+<a name="2131"><span class="lineNum">    2131 </span>            :     /// and, at the same time, allow the object to exist after SafePtr constructor has completed.</a>
+<a name="2132"><span class="lineNum">    2132 </span>            :     /// A perhaps cleaner implementation would require a base class containing</a>
+<a name="2133"><span class="lineNum">    2133 </span>            :     /// the plumed_safeptr object, derived classes depending on the</a>
+<a name="2134"><span class="lineNum">    2134 </span>            :     /// argument type as a template parameter, and overloaded functions</a>
+<a name="2135"><span class="lineNum">    2135 </span>            :     /// returning this derived class.</a>
+<a name="2136"><span class="lineNum">    2136 </span>            :     char buffer[32];</a>
+<a name="2137"><span class="lineNum">    2137 </span>            :     /// Default constructor, nullptr</a>
+<a name="2138"><span class="lineNum">    2138 </span>            :     SafePtr() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2139"><span class="lineNum">    2139 </span>            :       safe.ptr=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="2140"><span class="lineNum">    2140 </span>            :       safe.nelem=0;</a>
+<a name="2141"><span class="lineNum">    2141 </span>            :       safe.shape=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="2142"><span class="lineNum">    2142 </span>            :       safe.flags=0x10000*2;</a>
+<a name="2143"><span class="lineNum">    2143 </span>            :       safe.opt=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="2144"><span class="lineNum">    2144 </span>            :       buffer[0]='\0';</a>
+<a name="2145"><span class="lineNum">    2145 </span>            :     }</a>
+<a name="2146"><span class="lineNum">    2146 </span>            : </a>
+<a name="2147"><span class="lineNum">    2147 </span><span class="lineCov">        222 :     __PLUMED_WRAPPER_CXX_EXPLICIT SafePtr(const plumed_safeptr &amp; safe,__PLUMED_WRAPPER_STD size_t nelem=0, const __PLUMED_WRAPPER_STD size_t* shape=__PLUMED_WRAPPER_CXX_NULLPTR) __PLUMED_WRAPPER_CXX_NOEXCEPT {</span></a>
+<a name="2148"><span class="lineNum">    2148 </span><span class="lineCov">        222 :       this-&gt;safe=safe;</span></a>
+<a name="2149"><span class="lineNum">    2149 </span><span class="lineCov">        222 :       buffer[0]='\0';</span></a>
+<a name="2150"><span class="lineNum">    2150 </span>            :       if(nelem&gt;0) this-&gt;safe.nelem=nelem;</a>
+<a name="2151"><span class="lineNum">    2151 </span>            :       if(shape) this-&gt;safe.shape=const_cast&lt;__PLUMED_WRAPPER_STD size_t*&gt;(shape);</a>
+<a name="2152"><span class="lineNum">    2152 </span>            :     }</a>
+<a name="2153"><span class="lineNum">    2153 </span>            : </a>
+<a name="2154"><span class="lineNum">    2154 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="2155"><span class="lineNum">    2155 </span>            :     /// Construct from null</a>
+<a name="2156"><span class="lineNum">    2156 </span>            :     SafePtr(__PLUMED_WRAPPER_STD nullptr_t,__PLUMED_WRAPPER_STD size_t nelem, const __PLUMED_WRAPPER_STD size_t* shape) noexcept {</a>
+<a name="2157"><span class="lineNum">    2157 </span>            :       safe.ptr=nullptr;</a>
+<a name="2158"><span class="lineNum">    2158 </span>            :       safe.nelem=0;</a>
+<a name="2159"><span class="lineNum">    2159 </span>            :       safe.shape=nullptr;</a>
+<a name="2160"><span class="lineNum">    2160 </span>            :       safe.flags=0x10000*2;</a>
+<a name="2161"><span class="lineNum">    2161 </span>            :       safe.opt=nullptr;</a>
+<a name="2162"><span class="lineNum">    2162 </span>            :       buffer[0]='\0';</a>
+<a name="2163"><span class="lineNum">    2163 </span>            :       (void) nelem;</a>
+<a name="2164"><span class="lineNum">    2164 </span>            :       (void) shape;</a>
+<a name="2165"><span class="lineNum">    2165 </span>            :     }</a>
+<a name="2166"><span class="lineNum">    2166 </span>            : #endif</a>
+<a name="2167"><span class="lineNum">    2167 </span>            : </a>
+<a name="2168"><span class="lineNum">    2168 </span>            : /// Macro that generate a constructor with given type and flags</a>
+<a name="2169"><span class="lineNum">    2169 </span>            : #define __PLUMED_WRAPPER_SAFEPTR_INNER(type_,flags_) \</a>
+<a name="2170"><span class="lineNum">    2170 </span>            :   SafePtr(type_*ptr, __PLUMED_WRAPPER_STD size_t nelem, const __PLUMED_WRAPPER_STD size_t* shape) __PLUMED_WRAPPER_CXX_NOEXCEPT { \</a>
+<a name="2171"><span class="lineNum">    2171 </span>            :     safe.ptr=ptr; \</a>
+<a name="2172"><span class="lineNum">    2172 </span>            :     safe.nelem=nelem; \</a>
+<a name="2173"><span class="lineNum">    2173 </span>            :     safe.shape=const_cast&lt;__PLUMED_WRAPPER_STD size_t*&gt;(shape); \</a>
+<a name="2174"><span class="lineNum">    2174 </span>            :     safe.flags=flags_; \</a>
+<a name="2175"><span class="lineNum">    2175 </span>            :     safe.opt=__PLUMED_WRAPPER_CXX_NULLPTR; \</a>
+<a name="2176"><span class="lineNum">    2176 </span>            :     buffer[0]='\0'; \</a>
+<a name="2177"><span class="lineNum">    2177 </span>            :   }</a>
+<a name="2178"><span class="lineNum">    2178 </span>            : </a>
+<a name="2179"><span class="lineNum">    2179 </span>            : /// Macro that uses __PLUMED_WRAPPER_SAFEPTR_INNER to generate constructors with</a>
+<a name="2180"><span class="lineNum">    2180 </span>            : /// all possible pointer-const combinations</a>
+<a name="2181"><span class="lineNum">    2181 </span>            : #define __PLUMED_WRAPPER_SAFEPTR(type,code,size) \</a>
+<a name="2182"><span class="lineNum">    2182 </span>            :   __PLUMED_WRAPPER_SAFEPTR_INNER(type,             size | (0x10000*(code)) | (0x2000000*2)) \</a>
+<a name="2183"><span class="lineNum">    2183 </span>            :   __PLUMED_WRAPPER_SAFEPTR_INNER(type const,       size | (0x10000*(code)) | (0x2000000*3)) \</a>
+<a name="2184"><span class="lineNum">    2184 </span>            :   __PLUMED_WRAPPER_SAFEPTR_INNER(type*,            size | (0x10000*(code)) | (0x2000000*4)) \</a>
+<a name="2185"><span class="lineNum">    2185 </span>            :   __PLUMED_WRAPPER_SAFEPTR_INNER(type*const,       size | (0x10000*(code)) | (0x2000000*5)) \</a>
+<a name="2186"><span class="lineNum">    2186 </span>            :   __PLUMED_WRAPPER_SAFEPTR_INNER(type const*,      size | (0x10000*(code)) | (0x2000000*6)) \</a>
+<a name="2187"><span class="lineNum">    2187 </span>            :   __PLUMED_WRAPPER_SAFEPTR_INNER(type const*const, size | (0x10000*(code)) | (0x2000000*7))</a>
+<a name="2188"><span class="lineNum">    2188 </span>            : </a>
+<a name="2189"><span class="lineNum">    2189 </span>            : /// Macro that generates the constructors from empy types (those of which sizeof cannot be computed)</a>
+<a name="2190"><span class="lineNum">    2190 </span>            : #define __PLUMED_WRAPPER_SAFEPTR_EMPTY(type,code) __PLUMED_WRAPPER_SAFEPTR(type,code,0)</a>
+<a name="2191"><span class="lineNum">    2191 </span>            : </a>
+<a name="2192"><span class="lineNum">    2192 </span>            : /// Macro that generates the constructors from sized types (those of which sizeof can be computed).</a>
+<a name="2193"><span class="lineNum">    2193 </span>            : /// In addition to generating constructors with all pointer types, it generates a constructor to</a>
+<a name="2194"><span class="lineNum">    2194 </span>            : /// allow pass-by-value</a>
+<a name="2195"><span class="lineNum">    2195 </span>            : #define __PLUMED_WRAPPER_SAFEPTR_SIZED(type,code) \</a>
+<a name="2196"><span class="lineNum">    2196 </span>            :   __PLUMED_WRAPPER_SAFEPTR(type,code,sizeof(type)) \</a>
+<a name="2197"><span class="lineNum">    2197 </span>            :   SafePtr(type val, __PLUMED_WRAPPER_STD size_t nelem, const __PLUMED_WRAPPER_STD size_t* shape) __PLUMED_WRAPPER_CXX_NOEXCEPT { \</a>
+<a name="2198"><span class="lineNum">    2198 </span>            :     assert(sizeof(type)&lt;=32); \</a>
+<a name="2199"><span class="lineNum">    2199 </span>            :     (void) nelem; \</a>
+<a name="2200"><span class="lineNum">    2200 </span>            :     (void) shape; \</a>
+<a name="2201"><span class="lineNum">    2201 </span>            :     safe.ptr=buffer; \</a>
+<a name="2202"><span class="lineNum">    2202 </span>            :     safe.nelem=1; \</a>
+<a name="2203"><span class="lineNum">    2203 </span>            :     safe.shape=__PLUMED_WRAPPER_CXX_NULLPTR; \</a>
+<a name="2204"><span class="lineNum">    2204 </span>            :     safe.flags=sizeof(type) | (0x10000*(code)) | (0x2000000*1); \</a>
+<a name="2205"><span class="lineNum">    2205 </span>            :     safe.opt=__PLUMED_WRAPPER_CXX_NULLPTR; \</a>
+<a name="2206"><span class="lineNum">    2206 </span>            :     __PLUMED_WRAPPER_STD memcpy(buffer,&amp;val,sizeof(type)); \</a>
+<a name="2207"><span class="lineNum">    2207 </span>            :   }</a>
+<a name="2208"><span class="lineNum">    2208 </span>            : </a>
+<a name="2209"><span class="lineNum">    2209 </span>            : /// Here we create all the required instances</a>
+<a name="2210"><span class="lineNum">    2210 </span>            : /// 1: void</a>
+<a name="2211"><span class="lineNum">    2211 </span>            : /// 3: integral</a>
+<a name="2212"><span class="lineNum">    2212 </span>            : /// 4: floating</a>
+<a name="2213"><span class="lineNum">    2213 </span>            : /// 5: FILE</a>
+<a name="2214"><span class="lineNum">    2214 </span>            : /// 0x100: unsigned</a>
+<a name="2215"><span class="lineNum">    2215 </span><span class="lineCov">        338 :     __PLUMED_WRAPPER_SAFEPTR_EMPTY(void,1)</span></a>
+<a name="2216"><span class="lineNum">    2216 </span><span class="lineCov">       4133 :     __PLUMED_WRAPPER_SAFEPTR_SIZED(char,(CHAR_MIN==0)*0x100+3)</span></a>
+<a name="2217"><span class="lineNum">    2217 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(unsigned char,3)</a>
+<a name="2218"><span class="lineNum">    2218 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(signed char,0x100+3)</a>
+<a name="2219"><span class="lineNum">    2219 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(short,3)</a>
+<a name="2220"><span class="lineNum">    2220 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(unsigned short,0x100+3)</a>
+<a name="2221"><span class="lineNum">    2221 </span><span class="lineCov">       8266 :     __PLUMED_WRAPPER_SAFEPTR_SIZED(int,3)</span></a>
+<a name="2222"><span class="lineNum">    2222 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(unsigned int,0x100+3)</a>
+<a name="2223"><span class="lineNum">    2223 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(long,3)</a>
+<a name="2224"><span class="lineNum">    2224 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(unsigned long,0x100+3)</a>
+<a name="2225"><span class="lineNum">    2225 </span>            : #if __PLUMED_WRAPPER_CXX_LONGLONG</a>
+<a name="2226"><span class="lineNum">    2226 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(long long,3)</a>
+<a name="2227"><span class="lineNum">    2227 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(unsigned long long,0x100+3)</a>
+<a name="2228"><span class="lineNum">    2228 </span>            : #endif</a>
+<a name="2229"><span class="lineNum">    2229 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(float,4)</a>
+<a name="2230"><span class="lineNum">    2230 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(double,4)</a>
+<a name="2231"><span class="lineNum">    2231 </span>            :     __PLUMED_WRAPPER_SAFEPTR_SIZED(long double,4)</a>
+<a name="2232"><span class="lineNum">    2232 </span>            :     __PLUMED_WRAPPER_SAFEPTR_EMPTY(FILE,5)</a>
+<a name="2233"><span class="lineNum">    2233 </span>            : </a>
+<a name="2234"><span class="lineNum">    2234 </span>            :     /// Return the contained plumed_safeptr</a>
+<a name="2235"><span class="lineNum">    2235 </span>            :     plumed_safeptr get_safeptr() const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2236"><span class="lineNum">    2236 </span><span class="lineCov">      12959 :       return safe;</span></a>
+<a name="2237"><span class="lineNum">    2237 </span>            :     }</a>
+<a name="2238"><span class="lineNum">    2238 </span>            : </a>
+<a name="2239"><span class="lineNum">    2239 </span>            :   };</a>
+<a name="2240"><span class="lineNum">    2240 </span>            : </a>
+<a name="2241"><span class="lineNum">    2241 </span>            : public:</a>
+<a name="2242"><span class="lineNum">    2242 </span>            : </a>
+<a name="2243"><span class="lineNum">    2243 </span>            :   /**</a>
+<a name="2244"><span class="lineNum">    2244 </span>            :      Check if plumed is installed (for runtime binding)</a>
+<a name="2245"><span class="lineNum">    2245 </span>            :      \return true if plumed is installed, false otherwise</a>
+<a name="2246"><span class="lineNum">    2246 </span>            :      \note Equivalent to plumed_installed() but returns a bool</a>
+<a name="2247"><span class="lineNum">    2247 </span>            :   */</a>
+<a name="2248"><span class="lineNum">    2248 </span>            :   static bool installed() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2249"><span class="lineNum">    2249 </span>            :     return plumed_installed();</a>
+<a name="2250"><span class="lineNum">    2250 </span>            :   }</a>
+<a name="2251"><span class="lineNum">    2251 </span>            :   /**</a>
+<a name="2252"><span class="lineNum">    2252 </span>            :      Check if Plumed object is valid. Available as of PLUMED 2.5</a>
+<a name="2253"><span class="lineNum">    2253 </span>            :      \return true if plumed is valid, false otherwise</a>
+<a name="2254"><span class="lineNum">    2254 </span>            :      \note Equivalent to plumed_valid() but returns a bool</a>
+<a name="2255"><span class="lineNum">    2255 </span>            :   */</a>
+<a name="2256"><span class="lineNum">    2256 </span>            :   bool valid() const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2257"><span class="lineNum">    2257 </span>            :     return plumed_valid(main);</a>
+<a name="2258"><span class="lineNum">    2258 </span>            :   }</a>
+<a name="2259"><span class="lineNum">    2259 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="2260"><span class="lineNum">    2260 </span>            :   /**</a>
+<a name="2261"><span class="lineNum">    2261 </span>            :      Same as \ref valid(). Available as of PLUMED 2.5.</a>
+<a name="2262"><span class="lineNum">    2262 </span>            : </a>
+<a name="2263"><span class="lineNum">    2263 </span>            :   Allow code such as</a>
+<a name="2264"><span class="lineNum">    2264 </span>            :   \verbatim</a>
+<a name="2265"><span class="lineNum">    2265 </span>            :   Plumed p;</a>
+<a name="2266"><span class="lineNum">    2266 </span>            :   if(!p) raise_error();</a>
+<a name="2267"><span class="lineNum">    2267 </span>            :   p.cmd(&quot;init&quot;);</a>
+<a name="2268"><span class="lineNum">    2268 </span>            :   \endverbatim</a>
+<a name="2269"><span class="lineNum">    2269 </span>            : </a>
+<a name="2270"><span class="lineNum">    2270 </span>            :   In order to avoid ambiguous conversions, this is only allowed when compiling with C++11</a>
+<a name="2271"><span class="lineNum">    2271 </span>            :   where it is marked as explicit.</a>
+<a name="2272"><span class="lineNum">    2272 </span>            :   */</a>
+<a name="2273"><span class="lineNum">    2273 </span>            :   explicit</a>
+<a name="2274"><span class="lineNum">    2274 </span>            :   operator bool() const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2275"><span class="lineNum">    2275 </span>            :     return plumed_valid(main);</a>
+<a name="2276"><span class="lineNum">    2276 </span>            :   }</a>
+<a name="2277"><span class="lineNum">    2277 </span>            : #endif</a>
+<a name="2278"><span class="lineNum">    2278 </span>            : </a>
+<a name="2279"><span class="lineNum">    2279 </span>            :   /**</a>
+<a name="2280"><span class="lineNum">    2280 </span>            :      Returns the number of references to this object. Available as of PLUMED 2.5.</a>
+<a name="2281"><span class="lineNum">    2281 </span>            :     \note Equivalent to plumed_use_count()</a>
+<a name="2282"><span class="lineNum">    2282 </span>            :   */</a>
+<a name="2283"><span class="lineNum">    2283 </span>            :   int useCount() const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2284"><span class="lineNum">    2284 </span>            :     return plumed_use_count(main);</a>
+<a name="2285"><span class="lineNum">    2285 </span>            :   }</a>
+<a name="2286"><span class="lineNum">    2286 </span>            : </a>
+<a name="2287"><span class="lineNum">    2287 </span>            : #if __PLUMED_WRAPPER_GLOBAL /*{*/</a>
+<a name="2288"><span class="lineNum">    2288 </span>            :   /**</a>
+<a name="2289"><span class="lineNum">    2289 </span>            :      Check if global-plumed has been initialized</a>
+<a name="2290"><span class="lineNum">    2290 </span>            :      \return true if global plumed object (see global()) is initialized (i.e. if gcreate() has been</a>
+<a name="2291"><span class="lineNum">    2291 </span>            :              called), false otherwise.</a>
+<a name="2292"><span class="lineNum">    2292 </span>            :      \note Equivalent to plumed_ginitialized() but returns a bool</a>
+<a name="2293"><span class="lineNum">    2293 </span>            :   */</a>
+<a name="2294"><span class="lineNum">    2294 </span>            :   static bool ginitialized() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2295"><span class="lineNum">    2295 </span>            :     return plumed_ginitialized();</a>
+<a name="2296"><span class="lineNum">    2296 </span>            :   }</a>
+<a name="2297"><span class="lineNum">    2297 </span>            :   /**</a>
+<a name="2298"><span class="lineNum">    2298 </span>            :      Check if global-plumed is valid</a>
+<a name="2299"><span class="lineNum">    2299 </span>            :      \return true if global plumed object (see global()) is valid.</a>
+<a name="2300"><span class="lineNum">    2300 </span>            :      \note Equivalent to plumed_gvalid() but returns a bool</a>
+<a name="2301"><span class="lineNum">    2301 </span>            :   */</a>
+<a name="2302"><span class="lineNum">    2302 </span>            :   static bool gvalid() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2303"><span class="lineNum">    2303 </span>            :     return plumed_gvalid();</a>
+<a name="2304"><span class="lineNum">    2304 </span>            :   }</a>
+<a name="2305"><span class="lineNum">    2305 </span>            :   /**</a>
+<a name="2306"><span class="lineNum">    2306 </span>            :      Initialize global-plumed.</a>
+<a name="2307"><span class="lineNum">    2307 </span>            :      \warning Using the global objects in C++ is not recommended since they are difficult to use in</a>
+<a name="2308"><span class="lineNum">    2308 </span>            :               an exception safe manner. In particular, one should explicitly catch exceptions to</a>
+<a name="2309"><span class="lineNum">    2309 </span>            :               properly call gfinalize()</a>
+<a name="2310"><span class="lineNum">    2310 </span>            :      \note Equivalent to plumed_gcreate()</a>
+<a name="2311"><span class="lineNum">    2311 </span>            :   */</a>
+<a name="2312"><span class="lineNum">    2312 </span>            :   static void gcreate() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2313"><span class="lineNum">    2313 </span>            :     plumed_gcreate();</a>
+<a name="2314"><span class="lineNum">    2314 </span>            :   }</a>
+<a name="2315"><span class="lineNum">    2315 </span>            :   /**</a>
+<a name="2316"><span class="lineNum">    2316 </span>            :      Send a command to global-plumed</a>
+<a name="2317"><span class="lineNum">    2317 </span>            :       \param key The name of the command to be executed</a>
+<a name="2318"><span class="lineNum">    2318 </span>            :      \note Equivalent to plumed_gcmd()</a>
+<a name="2319"><span class="lineNum">    2319 </span>            :   */</a>
+<a name="2320"><span class="lineNum">    2320 </span>            :   static void gcmd(const char*key) {</a>
+<a name="2321"><span class="lineNum">    2321 </span>            :     global().cmd(key);</a>
+<a name="2322"><span class="lineNum">    2322 </span>            :   }</a>
+<a name="2323"><span class="lineNum">    2323 </span>            :   /**</a>
+<a name="2324"><span class="lineNum">    2324 </span>            :      Send a command to global-plumed</a>
+<a name="2325"><span class="lineNum">    2325 </span>            :       \param key The name of the command to be executed</a>
+<a name="2326"><span class="lineNum">    2326 </span>            :       \param val The argument.</a>
+<a name="2327"><span class="lineNum">    2327 </span>            :      \note Equivalent to plumed_gcmd()</a>
+<a name="2328"><span class="lineNum">    2328 </span>            :   */</a>
+<a name="2329"><span class="lineNum">    2329 </span>            :   template&lt;typename T&gt;</a>
+<a name="2330"><span class="lineNum">    2330 </span>            :   static void gcmd(const char*key,T val) {</a>
+<a name="2331"><span class="lineNum">    2331 </span>            :     global().cmd(key,val);</a>
+<a name="2332"><span class="lineNum">    2332 </span>            :   }</a>
+<a name="2333"><span class="lineNum">    2333 </span>            :   /**</a>
+<a name="2334"><span class="lineNum">    2334 </span>            :      Send a command to global-plumed</a>
+<a name="2335"><span class="lineNum">    2335 </span>            :       \param key The name of the command to be executed</a>
+<a name="2336"><span class="lineNum">    2336 </span>            :       \param val The argument.</a>
+<a name="2337"><span class="lineNum">    2337 </span>            :       \param nelem Number of elements in the passed array, for typechecking.</a>
+<a name="2338"><span class="lineNum">    2338 </span>            :      \note Equivalent to plumed_gcmd()</a>
+<a name="2339"><span class="lineNum">    2339 </span>            :   */</a>
+<a name="2340"><span class="lineNum">    2340 </span>            :   template&lt;typename T&gt;</a>
+<a name="2341"><span class="lineNum">    2341 </span>            :   static void gcmd(const char*key,T* val,__PLUMED_WRAPPER_STD size_t nelem) {</a>
+<a name="2342"><span class="lineNum">    2342 </span>            :     global().cmd(key,val,nelem);</a>
+<a name="2343"><span class="lineNum">    2343 </span>            :   }</a>
+<a name="2344"><span class="lineNum">    2344 </span>            : </a>
+<a name="2345"><span class="lineNum">    2345 </span>            :   /**</a>
+<a name="2346"><span class="lineNum">    2346 </span>            :      Send a command to global-plumed</a>
+<a name="2347"><span class="lineNum">    2347 </span>            :       \param key The name of the command to be executed</a>
+<a name="2348"><span class="lineNum">    2348 </span>            :       \param val The argument.</a>
+<a name="2349"><span class="lineNum">    2349 </span>            :       \param shape The shape of the argument.</a>
+<a name="2350"><span class="lineNum">    2350 </span>            :      \note Equivalent to plumed_gcmd()</a>
+<a name="2351"><span class="lineNum">    2351 </span>            :   */</a>
+<a name="2352"><span class="lineNum">    2352 </span>            :   template&lt;typename T&gt;</a>
+<a name="2353"><span class="lineNum">    2353 </span>            :   static void gcmd(const char*key,T* val, const __PLUMED_WRAPPER_STD size_t* shape) {</a>
+<a name="2354"><span class="lineNum">    2354 </span>            :     global().cmd(key,val,shape);</a>
+<a name="2355"><span class="lineNum">    2355 </span>            :   }</a>
+<a name="2356"><span class="lineNum">    2356 </span>            : </a>
+<a name="2357"><span class="lineNum">    2357 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="2358"><span class="lineNum">    2358 </span>            :   /**</a>
+<a name="2359"><span class="lineNum">    2359 </span>            :      Send a command to global-plumed</a>
+<a name="2360"><span class="lineNum">    2360 </span>            :       \param key The name of the command to be executed</a>
+<a name="2361"><span class="lineNum">    2361 </span>            :       \param val The argument.</a>
+<a name="2362"><span class="lineNum">    2362 </span>            :       \param shape The shape of the argument, in the form of an initialier_list (e.g., {10,3}).</a>
+<a name="2363"><span class="lineNum">    2363 </span>            :      \note Equivalent to plumed_gcmd()</a>
+<a name="2364"><span class="lineNum">    2364 </span>            :   */</a>
+<a name="2365"><span class="lineNum">    2365 </span>            :   template&lt;typename T&gt;</a>
+<a name="2366"><span class="lineNum">    2366 </span>            :   static void gcmd(const char*key,T* val, std::initializer_list&lt;std::size_t&gt; shape) {</a>
+<a name="2367"><span class="lineNum">    2367 </span>            :     global().cmd(key,val,shape);</a>
+<a name="2368"><span class="lineNum">    2368 </span>            :   }</a>
+<a name="2369"><span class="lineNum">    2369 </span>            : #endif</a>
+<a name="2370"><span class="lineNum">    2370 </span>            : </a>
+<a name="2371"><span class="lineNum">    2371 </span>            :   /**</a>
+<a name="2372"><span class="lineNum">    2372 </span>            :      Finalize global-plumed</a>
+<a name="2373"><span class="lineNum">    2373 </span>            :   */</a>
+<a name="2374"><span class="lineNum">    2374 </span>            :   static void gfinalize() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2375"><span class="lineNum">    2375 </span>            :     plumed_gfinalize();</a>
+<a name="2376"><span class="lineNum">    2376 </span>            :   }</a>
+<a name="2377"><span class="lineNum">    2377 </span>            :   /**</a>
+<a name="2378"><span class="lineNum">    2378 </span>            :      Returns the Plumed global object</a>
+<a name="2379"><span class="lineNum">    2379 </span>            : </a>
+<a name="2380"><span class="lineNum">    2380 </span>            :      Notice that the object is copied, thus increasing the reference counter of the</a>
+<a name="2381"><span class="lineNum">    2381 </span>            :      global object. In this manner, the global object will survive after a call to</a>
+<a name="2382"><span class="lineNum">    2382 </span>            :      \ref gfinalize() if the resulting object is still in scope.</a>
+<a name="2383"><span class="lineNum">    2383 </span>            : </a>
+<a name="2384"><span class="lineNum">    2384 </span>            :      \return The Plumed global object</a>
+<a name="2385"><span class="lineNum">    2385 </span>            :   */</a>
+<a name="2386"><span class="lineNum">    2386 </span>            :   static Plumed global() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2387"><span class="lineNum">    2387 </span>            :     return Plumed(plumed_global());</a>
+<a name="2388"><span class="lineNum">    2388 </span>            :   }</a>
+<a name="2389"><span class="lineNum">    2389 </span>            : #endif /*}*/</a>
+<a name="2390"><span class="lineNum">    2390 </span>            :   /**</a>
+<a name="2391"><span class="lineNum">    2391 </span>            :      Constructor.</a>
+<a name="2392"><span class="lineNum">    2392 </span>            : </a>
+<a name="2393"><span class="lineNum">    2393 </span>            :     Notice that when using runtime binding the constructed object might be</a>
+<a name="2394"><span class="lineNum">    2394 </span>            :     invalid. One might check it using the \ref valid() method.</a>
+<a name="2395"><span class="lineNum">    2395 </span>            : </a>
+<a name="2396"><span class="lineNum">    2396 </span>            :     \note Performs the same task a plumed_create()</a>
+<a name="2397"><span class="lineNum">    2397 </span>            :   */</a>
+<a name="2398"><span class="lineNum">    2398 </span><span class="lineCov">       4133 : Plumed()__PLUMED_WRAPPER_CXX_NOEXCEPT :</span></a>
+<a name="2399"><span class="lineNum">    2399 </span>            : #if __PLUMED_WRAPPER_CXX_DEFAULT_INVALID</a>
+<a name="2400"><span class="lineNum">    2400 </span>            :   main(plumed_create_invalid())</a>
+<a name="2401"><span class="lineNum">    2401 </span>            : #else</a>
+<a name="2402"><span class="lineNum">    2402 </span><span class="lineCov">       4133 :   main(plumed_create())</span></a>
+<a name="2403"><span class="lineNum">    2403 </span>            : #endif</a>
+<a name="2404"><span class="lineNum">    2404 </span>            :   {</a>
+<a name="2405"><span class="lineNum">    2405 </span>            :   }</a>
+<a name="2406"><span class="lineNum">    2406 </span>            : </a>
+<a name="2407"><span class="lineNum">    2407 </span>            :   /**</a>
+<a name="2408"><span class="lineNum">    2408 </span>            :      Clone a Plumed object from a FORTRAN char* handler.</a>
+<a name="2409"><span class="lineNum">    2409 </span>            : </a>
+<a name="2410"><span class="lineNum">    2410 </span>            :      \param c The FORTRAN handler (a char[32]).</a>
+<a name="2411"><span class="lineNum">    2411 </span>            : </a>
+<a name="2412"><span class="lineNum">    2412 </span>            :      The reference counter for the corresponding object will be increased</a>
+<a name="2413"><span class="lineNum">    2413 </span>            :      to make sure that the object will be available after plumed_f_finalize is called</a>
+<a name="2414"><span class="lineNum">    2414 </span>            :      if the created object is still in scope.</a>
+<a name="2415"><span class="lineNum">    2415 </span>            :   */</a>
+<a name="2416"><span class="lineNum">    2416 </span>            : __PLUMED_WRAPPER_CXX_EXPLICIT Plumed(const char*c)__PLUMED_WRAPPER_CXX_NOEXCEPT :</a>
+<a name="2417"><span class="lineNum">    2417 </span>            :   main(plumed_create_reference_f(c))</a>
+<a name="2418"><span class="lineNum">    2418 </span>            :   {</a>
+<a name="2419"><span class="lineNum">    2419 </span>            :   }</a>
+<a name="2420"><span class="lineNum">    2420 </span>            : </a>
+<a name="2421"><span class="lineNum">    2421 </span>            :   /**</a>
+<a name="2422"><span class="lineNum">    2422 </span>            :     Create a reference from a void* pointer. Available as of PLUMED 2.5.</a>
+<a name="2423"><span class="lineNum">    2423 </span>            :   */</a>
+<a name="2424"><span class="lineNum">    2424 </span>            : __PLUMED_WRAPPER_CXX_EXPLICIT Plumed(void*v)__PLUMED_WRAPPER_CXX_NOEXCEPT :</a>
+<a name="2425"><span class="lineNum">    2425 </span>            :   main(plumed_create_reference_v(v))</a>
+<a name="2426"><span class="lineNum">    2426 </span>            :   {</a>
+<a name="2427"><span class="lineNum">    2427 </span>            :   }</a>
+<a name="2428"><span class="lineNum">    2428 </span>            : </a>
+<a name="2429"><span class="lineNum">    2429 </span>            :   /**</a>
+<a name="2430"><span class="lineNum">    2430 </span>            :      Clone a Plumed object from a C plumed structure</a>
+<a name="2431"><span class="lineNum">    2431 </span>            : </a>
+<a name="2432"><span class="lineNum">    2432 </span>            :      \param p The C plumed structure.</a>
+<a name="2433"><span class="lineNum">    2433 </span>            : </a>
+<a name="2434"><span class="lineNum">    2434 </span>            :      The reference counter for the corresponding object will be increased</a>
+<a name="2435"><span class="lineNum">    2435 </span>            :      to make sure that the object will be available after plumed_finalize is called</a>
+<a name="2436"><span class="lineNum">    2436 </span>            :      if the created object is still in scope.</a>
+<a name="2437"><span class="lineNum">    2437 </span>            :   */</a>
+<a name="2438"><span class="lineNum">    2438 </span>            : __PLUMED_WRAPPER_CXX_EXPLICIT Plumed(plumed p)__PLUMED_WRAPPER_CXX_NOEXCEPT :</a>
+<a name="2439"><span class="lineNum">    2439 </span>            :   main(plumed_create_reference(p))</a>
+<a name="2440"><span class="lineNum">    2440 </span>            :   {</a>
+<a name="2441"><span class="lineNum">    2441 </span>            :   }</a>
+<a name="2442"><span class="lineNum">    2442 </span>            : </a>
+<a name="2443"><span class="lineNum">    2443 </span>            :   /** Copy constructor.</a>
+<a name="2444"><span class="lineNum">    2444 </span>            : </a>
+<a name="2445"><span class="lineNum">    2445 </span>            :     Takes a reference, incrementing the reference counter of the corresponding object.</a>
+<a name="2446"><span class="lineNum">    2446 </span>            :   */</a>
+<a name="2447"><span class="lineNum">    2447 </span>            : Plumed(const Plumed&amp; p)__PLUMED_WRAPPER_CXX_NOEXCEPT :</a>
+<a name="2448"><span class="lineNum">    2448 </span>            :   main(plumed_create_reference(p.main))</a>
+<a name="2449"><span class="lineNum">    2449 </span>            :   {</a>
+<a name="2450"><span class="lineNum">    2450 </span>            :   }</a>
+<a name="2451"><span class="lineNum">    2451 </span>            : </a>
+<a name="2452"><span class="lineNum">    2452 </span>            :   /** Assignment operator. Available as of PLUMED 2.5.</a>
+<a name="2453"><span class="lineNum">    2453 </span>            : </a>
+<a name="2454"><span class="lineNum">    2454 </span>            :     Takes a reference,incrementing the reference counter of the corresponding object.</a>
+<a name="2455"><span class="lineNum">    2455 </span>            :   */</a>
+<a name="2456"><span class="lineNum">    2456 </span>            :   Plumed&amp;operator=(const Plumed&amp;p) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2457"><span class="lineNum">    2457 </span>            :     if(this != &amp;p) {</a>
+<a name="2458"><span class="lineNum">    2458 </span>            : // the check is needed to avoid calling plumed_finalize on moved objects</a>
+<a name="2459"><span class="lineNum">    2459 </span>            :       if(main.p) plumed_finalize(main);</a>
+<a name="2460"><span class="lineNum">    2460 </span>            :       main=plumed_create_reference(p.main);</a>
+<a name="2461"><span class="lineNum">    2461 </span>            :     }</a>
+<a name="2462"><span class="lineNum">    2462 </span>            :     return *this;</a>
+<a name="2463"><span class="lineNum">    2463 </span>            :   }</a>
+<a name="2464"><span class="lineNum">    2464 </span>            : </a>
+<a name="2465"><span class="lineNum">    2465 </span>            :   /*</a>
+<a name="2466"><span class="lineNum">    2466 </span>            :     PLUMED &gt;= 2.4 requires a C++11 compiler.</a>
+<a name="2467"><span class="lineNum">    2467 </span>            :     Anyway, since Plumed.h file might be redistributed with other codes</a>
+<a name="2468"><span class="lineNum">    2468 </span>            :     and it should be possible to combine it with earlier PLUMED versions,</a>
+<a name="2469"><span class="lineNum">    2469 </span>            :     we here explicitly check if C+11 is available before enabling move semantics.</a>
+<a name="2470"><span class="lineNum">    2470 </span>            :   */</a>
+<a name="2471"><span class="lineNum">    2471 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="2472"><span class="lineNum">    2472 </span>            :   /** Move constructor. Available as of PLUMED 2.5.</a>
+<a name="2473"><span class="lineNum">    2473 </span>            :     Only if move semantics is enabled.</a>
+<a name="2474"><span class="lineNum">    2474 </span>            :   */</a>
+<a name="2475"><span class="lineNum">    2475 </span>            : Plumed(Plumed&amp;&amp;p)__PLUMED_WRAPPER_CXX_NOEXCEPT :</a>
+<a name="2476"><span class="lineNum">    2476 </span>            :   main(p.main)</a>
+<a name="2477"><span class="lineNum">    2477 </span>            :   {</a>
+<a name="2478"><span class="lineNum">    2478 </span>            :     p.main.p=nullptr;</a>
+<a name="2479"><span class="lineNum">    2479 </span>            :   }</a>
+<a name="2480"><span class="lineNum">    2480 </span>            :   /** Move assignment. Available as of PLUMED 2.5.</a>
+<a name="2481"><span class="lineNum">    2481 </span>            :     Only if move semantics is enabled.</a>
+<a name="2482"><span class="lineNum">    2482 </span>            :   */</a>
+<a name="2483"><span class="lineNum">    2483 </span>            :   Plumed&amp; operator=(Plumed&amp;&amp;p)__PLUMED_WRAPPER_CXX_NOEXCEPT  {</a>
+<a name="2484"><span class="lineNum">    2484 </span>            :     if(this != &amp;p) {</a>
+<a name="2485"><span class="lineNum">    2485 </span>            : // the check is needed to avoid calling plumed_finalize on moved objects</a>
+<a name="2486"><span class="lineNum">    2486 </span>            :       if(main.p) plumed_finalize(main);</a>
+<a name="2487"><span class="lineNum">    2487 </span>            :       main=p.main;</a>
+<a name="2488"><span class="lineNum">    2488 </span>            :       p.main.p=nullptr;</a>
+<a name="2489"><span class="lineNum">    2489 </span>            :     }</a>
+<a name="2490"><span class="lineNum">    2490 </span>            :     return *this;</a>
+<a name="2491"><span class="lineNum">    2491 </span>            :   }</a>
+<a name="2492"><span class="lineNum">    2492 </span>            : #endif</a>
+<a name="2493"><span class="lineNum">    2493 </span>            :   /**</a>
+<a name="2494"><span class="lineNum">    2494 </span>            :     Create a PLUMED object loading a specific kernel. Available as of PLUMED 2.5.</a>
+<a name="2495"><span class="lineNum">    2495 </span>            : </a>
+<a name="2496"><span class="lineNum">    2496 </span>            :     It returns an object created with \ref plumed_create_dlopen. The object is owned and</a>
+<a name="2497"><span class="lineNum">    2497 </span>            :     is then finalized in the destructor. It can be used as follows:</a>
+<a name="2498"><span class="lineNum">    2498 </span>            :   \verbatim</a>
+<a name="2499"><span class="lineNum">    2499 </span>            :     PLMD::Plumed p = PLMD::Plumed::dlopen(&quot;/path/to/libplumedKernel.so&quot;);</a>
+<a name="2500"><span class="lineNum">    2500 </span>            :   // or, equivalenty:</a>
+<a name="2501"><span class="lineNum">    2501 </span>            :   //    PLMD::Plumed p(PLMD::Plumed::dlopen(&quot;/path/to/libplumedKernel.so&quot;));</a>
+<a name="2502"><span class="lineNum">    2502 </span>            :     p.cmd(&quot;init&quot;);</a>
+<a name="2503"><span class="lineNum">    2503 </span>            :   \endverbatim</a>
+<a name="2504"><span class="lineNum">    2504 </span>            :     or, equivalently, as</a>
+<a name="2505"><span class="lineNum">    2505 </span>            :   \verbatim</a>
+<a name="2506"><span class="lineNum">    2506 </span>            :     auto p = PLMD::Plumed::dlopen(&quot;/path/to/libplumedKernel.so&quot;);</a>
+<a name="2507"><span class="lineNum">    2507 </span>            :     p.cmd(&quot;init&quot;);</a>
+<a name="2508"><span class="lineNum">    2508 </span>            :   \endverbatim</a>
+<a name="2509"><span class="lineNum">    2509 </span>            :   */</a>
+<a name="2510"><span class="lineNum">    2510 </span>            :   static Plumed dlopen(const char* path)__PLUMED_WRAPPER_CXX_NOEXCEPT  {</a>
+<a name="2511"><span class="lineNum">    2511 </span>            :     plumed p=plumed_create_dlopen(path);</a>
+<a name="2512"><span class="lineNum">    2512 </span>            :     Plumed pp(p);</a>
+<a name="2513"><span class="lineNum">    2513 </span>            :     plumed_finalize(p);</a>
+<a name="2514"><span class="lineNum">    2514 </span>            :     return pp;</a>
+<a name="2515"><span class="lineNum">    2515 </span>            :   }</a>
+<a name="2516"><span class="lineNum">    2516 </span>            : </a>
+<a name="2517"><span class="lineNum">    2517 </span>            :   /**</a>
+<a name="2518"><span class="lineNum">    2518 </span>            :     Create a PLUMED object loading a specific kernel. Available as of PLUMED 2.5.</a>
+<a name="2519"><span class="lineNum">    2519 </span>            : </a>
+<a name="2520"><span class="lineNum">    2520 </span>            :     Same as \ref dlopen(const char* path), but allows a dlopen mode to be chosen explicitly.</a>
+<a name="2521"><span class="lineNum">    2521 </span>            :   */</a>
+<a name="2522"><span class="lineNum">    2522 </span>            :   static Plumed dlopen(const char* path,int mode)__PLUMED_WRAPPER_CXX_NOEXCEPT  {</a>
+<a name="2523"><span class="lineNum">    2523 </span>            :     plumed p=plumed_create_dlopen2(path,mode);</a>
+<a name="2524"><span class="lineNum">    2524 </span>            :     Plumed pp(p);</a>
+<a name="2525"><span class="lineNum">    2525 </span>            :     plumed_finalize(p);</a>
+<a name="2526"><span class="lineNum">    2526 </span>            :     return pp;</a>
+<a name="2527"><span class="lineNum">    2527 </span>            :   }</a>
+<a name="2528"><span class="lineNum">    2528 </span>            :   /**</a>
+<a name="2529"><span class="lineNum">    2529 </span>            :     Create a PLUMED object loading from an already opened shared library. Available as of PLUMED 2.8.</a>
+<a name="2530"><span class="lineNum">    2530 </span>            : </a>
+<a name="2531"><span class="lineNum">    2531 </span>            :     Same as \ref dlopen(const char* path), but searches functions in an already loaded library.</a>
+<a name="2532"><span class="lineNum">    2532 </span>            :     See \ref plumed_create_dlsym.</a>
+<a name="2533"><span class="lineNum">    2533 </span>            :   */</a>
+<a name="2534"><span class="lineNum">    2534 </span>            :   static Plumed dlsym(void* dlhandle)__PLUMED_WRAPPER_CXX_NOEXCEPT  {</a>
+<a name="2535"><span class="lineNum">    2535 </span>            :     plumed p=plumed_create_dlsym(dlhandle);</a>
+<a name="2536"><span class="lineNum">    2536 </span>            :     Plumed pp(p);</a>
+<a name="2537"><span class="lineNum">    2537 </span>            :     plumed_finalize(p);</a>
+<a name="2538"><span class="lineNum">    2538 </span>            :     return pp;</a>
+<a name="2539"><span class="lineNum">    2539 </span>            :   }</a>
+<a name="2540"><span class="lineNum">    2540 </span>            : </a>
+<a name="2541"><span class="lineNum">    2541 </span>            :   /** Invalid constructor. Available as of PLUMED 2.5.</a>
+<a name="2542"><span class="lineNum">    2542 </span>            : </a>
+<a name="2543"><span class="lineNum">    2543 </span>            :     Can be used to initialize an invalid object. It might be useful to postpone</a>
+<a name="2544"><span class="lineNum">    2544 </span>            :     the initialization of a Plumed object. Consider the following case</a>
+<a name="2545"><span class="lineNum">    2545 </span>            :   \verbatim</a>
+<a name="2546"><span class="lineNum">    2546 </span>            :     Plumed p;</a>
+<a name="2547"><span class="lineNum">    2547 </span>            :     setenv(&quot;PLUMED_KERNEL&quot;,&quot;/path/to/kernel/libplumedKernel.so&quot;,1);</a>
+<a name="2548"><span class="lineNum">    2548 </span>            :     p.cmd(&quot;init&quot;)</a>
+<a name="2549"><span class="lineNum">    2549 </span>            :   \endverbatim</a>
+<a name="2550"><span class="lineNum">    2550 </span>            :     Here the `p` object will be initialized *before* the `PLUMED_KERNEL` env var has been set.</a>
+<a name="2551"><span class="lineNum">    2551 </span>            :     This can be particularly problematic if `p` is stored in some high level class.</a>
+<a name="2552"><span class="lineNum">    2552 </span>            :     The following case would do the job</a>
+<a name="2553"><span class="lineNum">    2553 </span>            :   \verbatim</a>
+<a name="2554"><span class="lineNum">    2554 </span>            :     Plumed p;</a>
+<a name="2555"><span class="lineNum">    2555 </span>            :     setenv(&quot;PLUMED_KERNEL&quot;,&quot;/path/to/kernel/libplumedKernel.so&quot;,1);</a>
+<a name="2556"><span class="lineNum">    2556 </span>            :     p=Plumed();</a>
+<a name="2557"><span class="lineNum">    2557 </span>            :     p.cmd(&quot;init&quot;)</a>
+<a name="2558"><span class="lineNum">    2558 </span>            :   \endverbatim</a>
+<a name="2559"><span class="lineNum">    2559 </span>            :     However, there will be some error reported related to the attempt to load the kernel</a>
+<a name="2560"><span class="lineNum">    2560 </span>            :     when `p` is initialized. The following solution is the optimal one:</a>
+<a name="2561"><span class="lineNum">    2561 </span>            :   \verbatim</a>
+<a name="2562"><span class="lineNum">    2562 </span>            :     Plumed p(Plumed::makeInvalid());</a>
+<a name="2563"><span class="lineNum">    2563 </span>            :     setenv(&quot;PLUMED_KERNEL&quot;,&quot;/path/to/kernel/libplumedKernel.so&quot;,1);</a>
+<a name="2564"><span class="lineNum">    2564 </span>            :     p=Plumed();</a>
+<a name="2565"><span class="lineNum">    2565 </span>            :     p.cmd(&quot;init&quot;)</a>
+<a name="2566"><span class="lineNum">    2566 </span>            :   \endverbatim</a>
+<a name="2567"><span class="lineNum">    2567 </span>            :   */</a>
+<a name="2568"><span class="lineNum">    2568 </span>            :   static Plumed makeInvalid() __PLUMED_WRAPPER_CXX_NOEXCEPT  {</a>
+<a name="2569"><span class="lineNum">    2569 </span>            :     plumed p=plumed_create_invalid();</a>
+<a name="2570"><span class="lineNum">    2570 </span>            :     Plumed pp(p);</a>
+<a name="2571"><span class="lineNum">    2571 </span>            :     plumed_finalize(p);</a>
+<a name="2572"><span class="lineNum">    2572 </span>            :     return pp;</a>
+<a name="2573"><span class="lineNum">    2573 </span>            :   }</a>
+<a name="2574"><span class="lineNum">    2574 </span>            : </a>
+<a name="2575"><span class="lineNum">    2575 </span>            :   /**</a>
+<a name="2576"><span class="lineNum">    2576 </span>            :     Create a valid PLMD::Plumed object.</a>
+<a name="2577"><span class="lineNum">    2577 </span>            : </a>
+<a name="2578"><span class="lineNum">    2578 </span>            :     Can be used to create a valid object e.g. when Plumed.h was compiled with</a>
+<a name="2579"><span class="lineNum">    2579 </span>            :     `-D__PLUMED_WRAPPER_CXX_DEFAULT_INVALID`. For internal usage.</a>
+<a name="2580"><span class="lineNum">    2580 </span>            :   */</a>
+<a name="2581"><span class="lineNum">    2581 </span>            : </a>
+<a name="2582"><span class="lineNum">    2582 </span>            :   static Plumed makeValid()__PLUMED_WRAPPER_CXX_NOEXCEPT  {</a>
+<a name="2583"><span class="lineNum">    2583 </span>            :     plumed p=plumed_create();</a>
+<a name="2584"><span class="lineNum">    2584 </span>            :     Plumed pp(p);</a>
+<a name="2585"><span class="lineNum">    2585 </span>            :     plumed_finalize(p);</a>
+<a name="2586"><span class="lineNum">    2586 </span>            :     return pp;</a>
+<a name="2587"><span class="lineNum">    2587 </span>            :   }</a>
+<a name="2588"><span class="lineNum">    2588 </span>            : </a>
+<a name="2589"><span class="lineNum">    2589 </span>            : </a>
+<a name="2590"><span class="lineNum">    2590 </span>            :   /**</a>
+<a name="2591"><span class="lineNum">    2591 </span>            :      Retrieve the C plumed structure for this object.</a>
+<a name="2592"><span class="lineNum">    2592 </span>            : </a>
+<a name="2593"><span class="lineNum">    2593 </span>            :      Notice that the resulting plumed structure is a weak reference and</a>
+<a name="2594"><span class="lineNum">    2594 </span>            :      should NOT be finalized, unless a new reference is explicitly added</a>
+<a name="2595"><span class="lineNum">    2595 </span>            :   \verbatim</a>
+<a name="2596"><span class="lineNum">    2596 </span>            :   Plumed p;</a>
+<a name="2597"><span class="lineNum">    2597 </span>            :   plumed c=p;</a>
+<a name="2598"><span class="lineNum">    2598 </span>            :   plumed_finalize(c); // &lt;- this is wrong</a>
+<a name="2599"><span class="lineNum">    2599 </span>            :   \endverbatim</a>
+<a name="2600"><span class="lineNum">    2600 </span>            :   \verbatim</a>
+<a name="2601"><span class="lineNum">    2601 </span>            :   Plumed p;</a>
+<a name="2602"><span class="lineNum">    2602 </span>            :   plumed c=plumed_create_reference(p);</a>
+<a name="2603"><span class="lineNum">    2603 </span>            :   plumed_finalize(c); // &lt;- this is right</a>
+<a name="2604"><span class="lineNum">    2604 </span>            :   \endverbatim</a>
+<a name="2605"><span class="lineNum">    2605 </span>            :   */</a>
+<a name="2606"><span class="lineNum">    2606 </span>            :   operator plumed()const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2607"><span class="lineNum">    2607 </span>            :     return main;</a>
+<a name="2608"><span class="lineNum">    2608 </span>            :   }</a>
+<a name="2609"><span class="lineNum">    2609 </span>            : </a>
+<a name="2610"><span class="lineNum">    2610 </span>            :   /**</a>
+<a name="2611"><span class="lineNum">    2611 </span>            :      Retrieve a FORTRAN handler for this object</a>
+<a name="2612"><span class="lineNum">    2612 </span>            :       \param c The FORTRAN handler (a char[32]).</a>
+<a name="2613"><span class="lineNum">    2613 </span>            :     Notice that the resulting plumed structure is a weak reference and</a>
+<a name="2614"><span class="lineNum">    2614 </span>            :     should NOT be finalized, unless a new reference is explicitly added.</a>
+<a name="2615"><span class="lineNum">    2615 </span>            :   */</a>
+<a name="2616"><span class="lineNum">    2616 </span>            :   void toFortran(char*c)const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2617"><span class="lineNum">    2617 </span>            :     plumed_c2f(main,c);</a>
+<a name="2618"><span class="lineNum">    2618 </span>            :   }</a>
+<a name="2619"><span class="lineNum">    2619 </span>            : </a>
+<a name="2620"><span class="lineNum">    2620 </span>            :   /**</a>
+<a name="2621"><span class="lineNum">    2621 </span>            :      Retrieve a void* handler for this object. Available as of PLUMED 2.5.</a>
+<a name="2622"><span class="lineNum">    2622 </span>            :     Notice that the resulting plumed structure is a weak reference and</a>
+<a name="2623"><span class="lineNum">    2623 </span>            :     should NOT be finalized, unless a new reference is explicitly added.</a>
+<a name="2624"><span class="lineNum">    2624 </span>            :   */</a>
+<a name="2625"><span class="lineNum">    2625 </span>            :   void* toVoid()const __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2626"><span class="lineNum">    2626 </span>            :     return plumed_c2v(main);</a>
+<a name="2627"><span class="lineNum">    2627 </span>            :   }</a>
+<a name="2628"><span class="lineNum">    2628 </span>            : </a>
+<a name="2629"><span class="lineNum">    2629 </span>            :   /**</a>
+<a name="2630"><span class="lineNum">    2630 </span>            :     Increase reference counter. Available as of PLUMED 2.5.</a>
+<a name="2631"><span class="lineNum">    2631 </span>            : </a>
+<a name="2632"><span class="lineNum">    2632 </span>            :     Using this method improperly might interfere with correct object construction</a>
+<a name="2633"><span class="lineNum">    2633 </span>            :     and destruction.</a>
+<a name="2634"><span class="lineNum">    2634 </span>            :     If you want to play with this, also try to compile using `-D__PLUMED_WRAPPER_DEBUG_REFCOUNT=1` and see what happens.</a>
+<a name="2635"><span class="lineNum">    2635 </span>            : </a>
+<a name="2636"><span class="lineNum">    2636 </span>            :     A possible usage is to transfer the ownership of a temporary</a>
+<a name="2637"><span class="lineNum">    2637 </span>            :     object when it is converted</a>
+<a name="2638"><span class="lineNum">    2638 </span>            :   \verbatim</a>
+<a name="2639"><span class="lineNum">    2639 </span>            :   plumed p=Plumed::dlopen(path).incref()</a>
+<a name="2640"><span class="lineNum">    2640 </span>            :   // without incref(), the just constructed object will be destroyed</a>
+<a name="2641"><span class="lineNum">    2641 </span>            :   // when the temporary object is deleted.</a>
+<a name="2642"><span class="lineNum">    2642 </span>            :   ... do stuff ...</a>
+<a name="2643"><span class="lineNum">    2643 </span>            :   plumed_finalize(p);</a>
+<a name="2644"><span class="lineNum">    2644 </span>            :   \endverbatim</a>
+<a name="2645"><span class="lineNum">    2645 </span>            : </a>
+<a name="2646"><span class="lineNum">    2646 </span>            :   */</a>
+<a name="2647"><span class="lineNum">    2647 </span>            :   Plumed&amp; incref() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2648"><span class="lineNum">    2648 </span>            :     plumed_create_reference(main);</a>
+<a name="2649"><span class="lineNum">    2649 </span>            :     return *this;</a>
+<a name="2650"><span class="lineNum">    2650 </span>            :   }</a>
+<a name="2651"><span class="lineNum">    2651 </span>            : </a>
+<a name="2652"><span class="lineNum">    2652 </span>            :   /**</a>
+<a name="2653"><span class="lineNum">    2653 </span>            :     Decrease reference counter. Available as of PLUMED 2.5.</a>
+<a name="2654"><span class="lineNum">    2654 </span>            : </a>
+<a name="2655"><span class="lineNum">    2655 </span>            :     Using this method improperly might interfere with correct object construction</a>
+<a name="2656"><span class="lineNum">    2656 </span>            :     and destruction.</a>
+<a name="2657"><span class="lineNum">    2657 </span>            :     If you want to play with this, also try to compile using `-D__PLUMED_WRAPPER_DEBUG_REFCOUNT=1` and see what happens.</a>
+<a name="2658"><span class="lineNum">    2658 </span>            :   */</a>
+<a name="2659"><span class="lineNum">    2659 </span>            :   Plumed&amp; decref() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2660"><span class="lineNum">    2660 </span>            : // calling decref on a moved plumed object should give an error, so we do not check if main.p!=NULL here:</a>
+<a name="2661"><span class="lineNum">    2661 </span>            :     plumed_finalize(main);</a>
+<a name="2662"><span class="lineNum">    2662 </span>            :     return *this;</a>
+<a name="2663"><span class="lineNum">    2663 </span>            :   }</a>
+<a name="2664"><span class="lineNum">    2664 </span>            : </a>
+<a name="2665"><span class="lineNum">    2665 </span>            : private:</a>
+<a name="2666"><span class="lineNum">    2666 </span>            : </a>
+<a name="2667"><span class="lineNum">    2667 </span>            :   /**</a>
+<a name="2668"><span class="lineNum">    2668 </span>            :     Private version of cmd. It is used here to avoid duplication of code between typesafe and not-typesafe versions</a>
+<a name="2669"><span class="lineNum">    2669 </span>            :   */</a>
+<a name="2670"><span class="lineNum">    2670 </span><span class="lineCov">      12959 :   static void cmd_priv(plumed main,const char*key, SafePtr*safe=__PLUMED_WRAPPER_CXX_NULLPTR, const void* unsafe=__PLUMED_WRAPPER_CXX_NULLPTR,plumed_error*error=__PLUMED_WRAPPER_CXX_NULLPTR) {</span></a>
+<a name="2671"><span class="lineNum">    2671 </span>            : </a>
+<a name="2672"><span class="lineNum">    2672 </span>            :     plumed_error error_cxx;</a>
+<a name="2673"><span class="lineNum">    2673 </span>            :     plumed_error_init(&amp;error_cxx);</a>
+<a name="2674"><span class="lineNum">    2674 </span>            : </a>
+<a name="2675"><span class="lineNum">    2675 </span>            :     plumed_nothrow_handler nothrow;</a>
+<a name="2676"><span class="lineNum">    2676 </span><span class="lineCov">      12959 :     if(error) {</span></a>
+<a name="2677"><span class="lineNum">    2677 </span>            :       plumed_error_init(error);</a>
+<a name="2678"><span class="lineNum">    2678 </span><span class="lineNoCov">          0 :       nothrow.ptr=error;</span></a>
+<a name="2679"><span class="lineNum">    2679 </span>            :     } else {</a>
+<a name="2680"><span class="lineNum">    2680 </span><span class="lineCov">      12959 :       nothrow.ptr=&amp;error_cxx;</span></a>
+<a name="2681"><span class="lineNum">    2681 </span>            :     }</a>
+<a name="2682"><span class="lineNum">    2682 </span><span class="lineCov">      12959 :     nothrow.handler=plumed_error_set;</span></a>
+<a name="2683"><span class="lineNum">    2683 </span>            : </a>
+<a name="2684"><span class="lineNum">    2684 </span>            :     try {</a>
+<a name="2685"><span class="lineNum">    2685 </span><span class="lineCov">      12959 :       if(safe) {</span></a>
+<a name="2686"><span class="lineNum">    2686 </span><span class="lineCov">      12959 :         plumed_cmd_safe_nothrow(main,key,safe-&gt;get_safeptr(),nothrow);</span></a>
+<a name="2687"><span class="lineNum">    2687 </span>            :       } else {</a>
+<a name="2688"><span class="lineNum">    2688 </span><span class="lineNoCov">          0 :         plumed_cmd_nothrow(main,key,unsafe,nothrow);</span></a>
+<a name="2689"><span class="lineNum">    2689 </span>            :       }</a>
+<a name="2690"><span class="lineNum">    2690 </span><span class="lineNoCov">          0 :     } catch (...) {</span></a>
+<a name="2691"><span class="lineNum">    2691 </span>            :       assert(error_cxx.code==0); /* no need to plumed_error_finalize here */</a>
+<a name="2692"><span class="lineNum">    2692 </span>            :       /*</a>
+<a name="2693"><span class="lineNum">    2693 </span>            :         When loading a kernel &lt;=2.4, plumed_cmd_nothrow could throw an exception.</a>
+<a name="2694"><span class="lineNum">    2694 </span>            :         If the exception is transmitted through the C interface and arrives here,</a>
+<a name="2695"><span class="lineNum">    2695 </span>            :         we translate it so as to free the virtual tables of the loaded kernel.</a>
+<a name="2696"><span class="lineNum">    2696 </span>            :       */</a>
+<a name="2697"><span class="lineNum">    2697 </span><span class="lineNoCov">          0 :       rethrow();</span></a>
+<a name="2698"><span class="lineNum">    2698 </span><span class="lineNoCov">          0 :     }</span></a>
+<a name="2699"><span class="lineNum">    2699 </span>            :     /* plumed_error_rethrow is finalizing */</a>
+<a name="2700"><span class="lineNum">    2700 </span><span class="lineCov">      12959 :     if(!error &amp;&amp; error_cxx.code!=0) plumed_error_rethrow_cxx(error_cxx);</span></a>
+<a name="2701"><span class="lineNum">    2701 </span><span class="lineCov">      12959 :   }</span></a>
+<a name="2702"><span class="lineNum">    2702 </span>            : </a>
+<a name="2703"><span class="lineNum">    2703 </span>            : public:</a>
+<a name="2704"><span class="lineNum">    2704 </span>            : </a>
+<a name="2705"><span class="lineNum">    2705 </span>            :   /**</a>
+<a name="2706"><span class="lineNum">    2706 </span>            :      Send a command to this plumed object</a>
+<a name="2707"><span class="lineNum">    2707 </span>            :       \param key The name of the command to be executed</a>
+<a name="2708"><span class="lineNum">    2708 </span>            :       \note Similar to \ref plumed_cmd(). It actually called \ref plumed_cmd_nothrow() and</a>
+<a name="2709"><span class="lineNum">    2709 </span>            :             rethrow any exception raised within PLUMED.</a>
+<a name="2710"><span class="lineNum">    2710 </span>            :   */</a>
+<a name="2711"><span class="lineNum">    2711 </span>            :   void cmd(const char*key) {</a>
+<a name="2712"><span class="lineNum">    2712 </span>            :     plumed_cmd_cxx(main,key);</a>
+<a name="2713"><span class="lineNum">    2713 </span>            :   }</a>
+<a name="2714"><span class="lineNum">    2714 </span>            : </a>
+<a name="2715"><span class="lineNum">    2715 </span>            :   /**</a>
+<a name="2716"><span class="lineNum">    2716 </span>            :      Send a command to this plumed object</a>
+<a name="2717"><span class="lineNum">    2717 </span>            :       \param key The name of the command to be executed</a>
+<a name="2718"><span class="lineNum">    2718 </span>            :       \param val The argument, passed by value.</a>
+<a name="2719"><span class="lineNum">    2719 </span>            :       \note Similar to \ref plumed_cmd(). It actually called \ref plumed_cmd_nothrow() and</a>
+<a name="2720"><span class="lineNum">    2720 </span>            :             rethrow any exception raised within PLUMED.</a>
+<a name="2721"><span class="lineNum">    2721 </span>            :       \note Unless one defines __PLUMED_WRAPPER_CXX_TYPESAFE=0 or PLUMED library is &lt;=2.7,</a>
+<a name="2722"><span class="lineNum">    2722 </span>            :              the type of the argument is checked.</a>
+<a name="2723"><span class="lineNum">    2723 </span>            :   */</a>
+<a name="2724"><span class="lineNum">    2724 </span>            :   template&lt;typename T&gt;</a>
+<a name="2725"><span class="lineNum">    2725 </span>            :   void cmd(const char*key,T val) {</a>
+<a name="2726"><span class="lineNum">    2726 </span><span class="lineCov">      12737 :     plumed_cmd_cxx(main,key,val);</span></a>
+<a name="2727"><span class="lineNum">    2727 </span><span class="lineCov">      12737 :   }</span></a>
+<a name="2728"><span class="lineNum">    2728 </span>            : </a>
+<a name="2729"><span class="lineNum">    2729 </span>            :   /**</a>
+<a name="2730"><span class="lineNum">    2730 </span>            :      Send a command to this plumed object</a>
+<a name="2731"><span class="lineNum">    2731 </span>            :       \param key The name of the command to be executed</a>
+<a name="2732"><span class="lineNum">    2732 </span>            :       \param val The argument, passed by pointer.</a>
+<a name="2733"><span class="lineNum">    2733 </span>            :       \param shape A zero-terminated array containing the shape of the data.</a>
+<a name="2734"><span class="lineNum">    2734 </span>            :       \note Similar to \ref plumed_cmd(). It actually called \ref plumed_cmd_nothrow() and</a>
+<a name="2735"><span class="lineNum">    2735 </span>            :             rethrow any exception raised within PLUMED.</a>
+<a name="2736"><span class="lineNum">    2736 </span>            :       \note Unless one defines __PLUMED_WRAPPER_CXX_TYPESAFE=0 or PLUMED library is &lt;=2.7,</a>
+<a name="2737"><span class="lineNum">    2737 </span>            :              the type of the argument is checked. If shape is passed, it is also</a>
+<a name="2738"><span class="lineNum">    2738 </span>            :              checked that PLUMED access only compatible indexes.</a>
+<a name="2739"><span class="lineNum">    2739 </span>            :   */</a>
+<a name="2740"><span class="lineNum">    2740 </span>            :   template&lt;typename T&gt;</a>
+<a name="2741"><span class="lineNum">    2741 </span>            :   void cmd(const char*key,T* val, const __PLUMED_WRAPPER_STD size_t* shape) {</a>
+<a name="2742"><span class="lineNum">    2742 </span>            :     plumed_cmd_cxx(main,key,val,shape);</a>
+<a name="2743"><span class="lineNum">    2743 </span>            :   }</a>
+<a name="2744"><span class="lineNum">    2744 </span>            : </a>
+<a name="2745"><span class="lineNum">    2745 </span>            : #if __cplusplus &gt; 199711L</a>
+<a name="2746"><span class="lineNum">    2746 </span>            :   /**</a>
+<a name="2747"><span class="lineNum">    2747 </span>            :      Send a command to this plumed object</a>
+<a name="2748"><span class="lineNum">    2748 </span>            :       \param key The name of the command to be executed</a>
+<a name="2749"><span class="lineNum">    2749 </span>            :       \param val The argument, passed by pointer.</a>
+<a name="2750"><span class="lineNum">    2750 </span>            :       \param shape The shape of the argument, in the form of an initialier_list (e.g., {10,3}).</a>
+<a name="2751"><span class="lineNum">    2751 </span>            :       \note Similar to \ref plumed_cmd(). It actually called \ref plumed_cmd_nothrow() and</a>
+<a name="2752"><span class="lineNum">    2752 </span>            :             rethrow any exception raised within PLUMED.</a>
+<a name="2753"><span class="lineNum">    2753 </span>            :       \note Unless one defines __PLUMED_WRAPPER_CXX_TYPESAFE=0 or PLUMED library is &lt;=2.7,</a>
+<a name="2754"><span class="lineNum">    2754 </span>            :              the type of the argument is checked. If shape is passed, it is also</a>
+<a name="2755"><span class="lineNum">    2755 </span>            :              checked that PLUMED access only compatible indexes.</a>
+<a name="2756"><span class="lineNum">    2756 </span>            :   */</a>
+<a name="2757"><span class="lineNum">    2757 </span>            :   template&lt;typename T&gt;</a>
+<a name="2758"><span class="lineNum">    2758 </span>            :   void cmd(const char*key,T* val, std::initializer_list&lt;std::size_t&gt; shape) {</a>
+<a name="2759"><span class="lineNum">    2759 </span>            :     if(shape.size()&gt;4) throw Plumed::ExceptionTypeError(&quot;Maximum shape size is 4&quot;);</a>
+<a name="2760"><span class="lineNum">    2760 </span>            :     std::array&lt;std::size_t,5&gt; shape_;</a>
+<a name="2761"><span class="lineNum">    2761 </span>            :     unsigned j=0;</a>
+<a name="2762"><span class="lineNum">    2762 </span>            :     for(auto i : shape) {</a>
+<a name="2763"><span class="lineNum">    2763 </span>            :       shape_[j]=i;</a>
+<a name="2764"><span class="lineNum">    2764 </span>            :       j++;</a>
+<a name="2765"><span class="lineNum">    2765 </span>            :     }</a>
+<a name="2766"><span class="lineNum">    2766 </span>            :     shape_[j]=0;</a>
+<a name="2767"><span class="lineNum">    2767 </span>            :     plumed_cmd_cxx(main,key,val,&amp;shape_[0]);</a>
+<a name="2768"><span class="lineNum">    2768 </span>            :   }</a>
+<a name="2769"><span class="lineNum">    2769 </span>            : #endif</a>
+<a name="2770"><span class="lineNum">    2770 </span>            :   /**</a>
+<a name="2771"><span class="lineNum">    2771 </span>            :      Send a command to this plumed object</a>
+<a name="2772"><span class="lineNum">    2772 </span>            :       \param key The name of the command to be executed</a>
+<a name="2773"><span class="lineNum">    2773 </span>            :       \param val The argument, passed by pointer.</a>
+<a name="2774"><span class="lineNum">    2774 </span>            :       \param nelem The number of elements passed.</a>
+<a name="2775"><span class="lineNum">    2775 </span>            :       \note Similar to \ref plumed_cmd(). It actually called \ref plumed_cmd_nothrow() and</a>
+<a name="2776"><span class="lineNum">    2776 </span>            :             rethrow any exception raised within PLUMED.</a>
+<a name="2777"><span class="lineNum">    2777 </span>            :       \note Unless one defines __PLUMED_WRAPPER_CXX_TYPESAFE=0 or PLUMED library is &lt;=2.7,</a>
+<a name="2778"><span class="lineNum">    2778 </span>            :              the type of the argument is checked.  nelem is used to check</a>
+<a name="2779"><span class="lineNum">    2779 </span>            :              the maximum index interpreting the array as flattened.</a>
+<a name="2780"><span class="lineNum">    2780 </span>            :   */</a>
+<a name="2781"><span class="lineNum">    2781 </span>            :   template&lt;typename T&gt;</a>
+<a name="2782"><span class="lineNum">    2782 </span>            :   void cmd(const char*key,T* val, __PLUMED_WRAPPER_STD size_t nelem) {</a>
+<a name="2783"><span class="lineNum">    2783 </span>            :     plumed_cmd_cxx(main,key,val,nelem);</a>
+<a name="2784"><span class="lineNum">    2784 </span>            :   }</a>
+<a name="2785"><span class="lineNum">    2785 </span>            : </a>
+<a name="2786"><span class="lineNum">    2786 </span>            :   /**</a>
+<a name="2787"><span class="lineNum">    2787 </span>            :      Destructor</a>
+<a name="2788"><span class="lineNum">    2788 </span>            : </a>
+<a name="2789"><span class="lineNum">    2789 </span>            :      It calls \ref plumed_finalize(). Notice that this is done also if the</a>
+<a name="2790"><span class="lineNum">    2790 </span>            :      constructor failed (that is, if it returned an invalid object). This allows</a>
+<a name="2791"><span class="lineNum">    2791 </span>            :      declaring Plumed objects also if PLUMED is actually not available, provided</a>
+<a name="2792"><span class="lineNum">    2792 </span>            :      one does not use the \ref cmd method.</a>
+<a name="2793"><span class="lineNum">    2793 </span>            : </a>
+<a name="2794"><span class="lineNum">    2794 </span>            :      Destructor is virtual so as to allow correct inheritance from Plumed object.</a>
+<a name="2795"><span class="lineNum">    2795 </span>            :   */</a>
+<a name="2796"><span class="lineNum">    2796 </span>            : #if __PLUMED_WRAPPER_CXX_POLYMORPHIC</a>
+<a name="2797"><span class="lineNum">    2797 </span>            :   virtual</a>
+<a name="2798"><span class="lineNum">    2798 </span>            : #endif</a>
+<a name="2799"><span class="lineNum">    2799 </span>            :   ~Plumed() __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2800"><span class="lineNum">    2800 </span>            : // the check is needed to avoid calling plumed_finalize on moved objects</a>
+<a name="2801"><span class="lineNum">    2801 </span><span class="lineCov">       4133 :     if(main.p) plumed_finalize(main);</span></a>
+<a name="2802"><span class="lineNum">    2802 </span><span class="lineCov">       4133 :   }</span></a>
+<a name="2803"><span class="lineNum">    2803 </span>            : </a>
+<a name="2804"><span class="lineNum">    2804 </span>            :   /**</a>
+<a name="2805"><span class="lineNum">    2805 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2806"><span class="lineNum">    2806 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2807"><span class="lineNum">    2807 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2808"><span class="lineNum">    2808 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2809"><span class="lineNum">    2809 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2810"><span class="lineNum">    2810 </span>            :   */</a>
+<a name="2811"><span class="lineNum">    2811 </span>            :   static void plumed_cmd_cxx(plumed p,const char*key,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2812"><span class="lineNum">    2812 </span>            : #if __PLUMED_WRAPPER_CXX_TYPESAFE</a>
+<a name="2813"><span class="lineNum">    2813 </span>            :     SafePtr s;</a>
+<a name="2814"><span class="lineNum">    2814 </span>            :     cmd_priv(p,key,&amp;s,__PLUMED_WRAPPER_CXX_NULLPTR,error);</a>
+<a name="2815"><span class="lineNum">    2815 </span>            : #else</a>
+<a name="2816"><span class="lineNum">    2816 </span>            :     cmd_priv(p,key,__PLUMED_WRAPPER_CXX_NULLPTR,__PLUMED_WRAPPER_CXX_NULLPTR,error);</a>
+<a name="2817"><span class="lineNum">    2817 </span>            : #endif</a>
+<a name="2818"><span class="lineNum">    2818 </span>            :   }</a>
+<a name="2819"><span class="lineNum">    2819 </span>            : </a>
+<a name="2820"><span class="lineNum">    2820 </span>            :   /**</a>
+<a name="2821"><span class="lineNum">    2821 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2822"><span class="lineNum">    2822 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2823"><span class="lineNum">    2823 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2824"><span class="lineNum">    2824 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2825"><span class="lineNum">    2825 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2826"><span class="lineNum">    2826 </span>            :   */</a>
+<a name="2827"><span class="lineNum">    2827 </span>            :   template&lt;typename T&gt;</a>
+<a name="2828"><span class="lineNum">    2828 </span><span class="lineCov">        222 :   static void plumed_cmd_cxx(plumed p,const char*key,T val,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</span></a>
+<a name="2829"><span class="lineNum">    2829 </span>            : #if __PLUMED_WRAPPER_CXX_TYPESAFE</a>
+<a name="2830"><span class="lineNum">    2830 </span>            :     SafePtr s(val,0,__PLUMED_WRAPPER_CXX_NULLPTR);</a>
+<a name="2831"><span class="lineNum">    2831 </span><span class="lineCov">        222 :     cmd_priv(p,key,&amp;s,__PLUMED_WRAPPER_CXX_NULLPTR,error);</span></a>
+<a name="2832"><span class="lineNum">    2832 </span>            : #else</a>
+<a name="2833"><span class="lineNum">    2833 </span>            :     cmd_priv(p,key,__PLUMED_WRAPPER_CXX_NULLPTR,&amp;val,error);</a>
+<a name="2834"><span class="lineNum">    2834 </span>            : #endif</a>
+<a name="2835"><span class="lineNum">    2835 </span><span class="lineCov">        222 :   }</span></a>
+<a name="2836"><span class="lineNum">    2836 </span>            : </a>
+<a name="2837"><span class="lineNum">    2837 </span>            :   /**</a>
+<a name="2838"><span class="lineNum">    2838 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2839"><span class="lineNum">    2839 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2840"><span class="lineNum">    2840 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2841"><span class="lineNum">    2841 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2842"><span class="lineNum">    2842 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2843"><span class="lineNum">    2843 </span>            :   */</a>
+<a name="2844"><span class="lineNum">    2844 </span>            :   template&lt;typename T&gt;</a>
+<a name="2845"><span class="lineNum">    2845 </span><span class="lineCov">      12737 :   static void plumed_cmd_cxx(plumed p,const char*key,T* val,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</span></a>
+<a name="2846"><span class="lineNum">    2846 </span>            : #if __PLUMED_WRAPPER_CXX_TYPESAFE</a>
+<a name="2847"><span class="lineNum">    2847 </span>            :     SafePtr s(val,0,__PLUMED_WRAPPER_CXX_NULLPTR);</a>
+<a name="2848"><span class="lineNum">    2848 </span><span class="lineCov">      12737 :     cmd_priv(p,key,&amp;s,__PLUMED_WRAPPER_CXX_NULLPTR,error);</span></a>
+<a name="2849"><span class="lineNum">    2849 </span>            : #else</a>
+<a name="2850"><span class="lineNum">    2850 </span>            :     cmd_priv(p,key,__PLUMED_WRAPPER_CXX_NULLPTR,val,error);</a>
+<a name="2851"><span class="lineNum">    2851 </span>            : #endif</a>
+<a name="2852"><span class="lineNum">    2852 </span><span class="lineCov">      12737 :   }</span></a>
+<a name="2853"><span class="lineNum">    2853 </span>            : </a>
+<a name="2854"><span class="lineNum">    2854 </span>            :   /**</a>
+<a name="2855"><span class="lineNum">    2855 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2856"><span class="lineNum">    2856 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2857"><span class="lineNum">    2857 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2858"><span class="lineNum">    2858 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2859"><span class="lineNum">    2859 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2860"><span class="lineNum">    2860 </span>            :   */</a>
+<a name="2861"><span class="lineNum">    2861 </span>            :   template&lt;typename T&gt;</a>
+<a name="2862"><span class="lineNum">    2862 </span>            :   static void plumed_cmd_cxx(plumed p,const char*key,T* val, __PLUMED_WRAPPER_STD size_t nelem,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2863"><span class="lineNum">    2863 </span>            : #if __PLUMED_WRAPPER_CXX_TYPESAFE</a>
+<a name="2864"><span class="lineNum">    2864 </span>            :     SafePtr s(val,nelem,__PLUMED_WRAPPER_CXX_NULLPTR);</a>
+<a name="2865"><span class="lineNum">    2865 </span>            :     cmd_priv(p,key,&amp;s,__PLUMED_WRAPPER_CXX_NULLPTR,error);</a>
+<a name="2866"><span class="lineNum">    2866 </span>            : #else</a>
+<a name="2867"><span class="lineNum">    2867 </span>            :     cmd_priv(p,key,__PLUMED_WRAPPER_CXX_NULLPTR,val,error);</a>
+<a name="2868"><span class="lineNum">    2868 </span>            : #endif</a>
+<a name="2869"><span class="lineNum">    2869 </span>            :   }</a>
+<a name="2870"><span class="lineNum">    2870 </span>            : </a>
+<a name="2871"><span class="lineNum">    2871 </span>            :   /**</a>
+<a name="2872"><span class="lineNum">    2872 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2873"><span class="lineNum">    2873 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2874"><span class="lineNum">    2874 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2875"><span class="lineNum">    2875 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2876"><span class="lineNum">    2876 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2877"><span class="lineNum">    2877 </span>            :   */</a>
+<a name="2878"><span class="lineNum">    2878 </span>            :   template&lt;typename T&gt;</a>
+<a name="2879"><span class="lineNum">    2879 </span>            :   static void plumed_cmd_cxx(plumed p,const char*key,T* val, const __PLUMED_WRAPPER_STD size_t* shape,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2880"><span class="lineNum">    2880 </span>            : #if __PLUMED_WRAPPER_CXX_TYPESAFE</a>
+<a name="2881"><span class="lineNum">    2881 </span>            :     SafePtr s(val,0,shape);</a>
+<a name="2882"><span class="lineNum">    2882 </span>            :     cmd_priv(p,key,&amp;s,__PLUMED_WRAPPER_CXX_NULLPTR,error);</a>
+<a name="2883"><span class="lineNum">    2883 </span>            : #else</a>
+<a name="2884"><span class="lineNum">    2884 </span>            :     cmd_priv(p,key,__PLUMED_WRAPPER_CXX_NULLPTR,val,error);</a>
+<a name="2885"><span class="lineNum">    2885 </span>            : #endif</a>
+<a name="2886"><span class="lineNum">    2886 </span>            :   }</a>
+<a name="2887"><span class="lineNum">    2887 </span>            : </a>
+<a name="2888"><span class="lineNum">    2888 </span>            : </a>
+<a name="2889"><span class="lineNum">    2889 </span>            : #if __PLUMED_WRAPPER_GLOBAL /*{*/</a>
+<a name="2890"><span class="lineNum">    2890 </span>            :   /**</a>
+<a name="2891"><span class="lineNum">    2891 </span>            :     \related Plumed</a>
+<a name="2892"><span class="lineNum">    2892 </span>            :     This function can be used to make plumed_gcmd behave as the C++ wrapper PLMD::Plumed::gcmd,</a>
+<a name="2893"><span class="lineNum">    2893 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2894"><span class="lineNum">    2894 </span>            :     To be used through the macro plumed_gcmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2895"><span class="lineNum">    2895 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2896"><span class="lineNum">    2896 </span>            :   */</a>
+<a name="2897"><span class="lineNum">    2897 </span>            : </a>
+<a name="2898"><span class="lineNum">    2898 </span>            :   /**</a>
+<a name="2899"><span class="lineNum">    2899 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2900"><span class="lineNum">    2900 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2901"><span class="lineNum">    2901 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2902"><span class="lineNum">    2902 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2903"><span class="lineNum">    2903 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2904"><span class="lineNum">    2904 </span>            :   */</a>
+<a name="2905"><span class="lineNum">    2905 </span>            :   static void plumed_gcmd_cxx(const char*key,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2906"><span class="lineNum">    2906 </span>            :     plumed_cmd_cxx(plumed_global(),key,error);</a>
+<a name="2907"><span class="lineNum">    2907 </span>            :   }</a>
+<a name="2908"><span class="lineNum">    2908 </span>            : </a>
+<a name="2909"><span class="lineNum">    2909 </span>            :   /**</a>
+<a name="2910"><span class="lineNum">    2910 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2911"><span class="lineNum">    2911 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2912"><span class="lineNum">    2912 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2913"><span class="lineNum">    2913 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2914"><span class="lineNum">    2914 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2915"><span class="lineNum">    2915 </span>            :   */</a>
+<a name="2916"><span class="lineNum">    2916 </span>            :   template&lt;typename T&gt;</a>
+<a name="2917"><span class="lineNum">    2917 </span>            :   static void plumed_gcmd_cxx(const char*key,T val,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2918"><span class="lineNum">    2918 </span>            :     plumed_cmd_cxx(plumed_global(),key,val,error);</a>
+<a name="2919"><span class="lineNum">    2919 </span>            :   }</a>
+<a name="2920"><span class="lineNum">    2920 </span>            : </a>
+<a name="2921"><span class="lineNum">    2921 </span>            :   /**</a>
+<a name="2922"><span class="lineNum">    2922 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2923"><span class="lineNum">    2923 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2924"><span class="lineNum">    2924 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2925"><span class="lineNum">    2925 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2926"><span class="lineNum">    2926 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2927"><span class="lineNum">    2927 </span>            :   */</a>
+<a name="2928"><span class="lineNum">    2928 </span>            :   template&lt;typename T&gt;</a>
+<a name="2929"><span class="lineNum">    2929 </span>            :   static void plumed_gcmd_cxx(const char*key,T val, __PLUMED_WRAPPER_STD size_t nelem,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2930"><span class="lineNum">    2930 </span>            :     plumed_cmd_cxx(plumed_global(),key,val,nelem,error);</a>
+<a name="2931"><span class="lineNum">    2931 </span>            :   }</a>
+<a name="2932"><span class="lineNum">    2932 </span>            : </a>
+<a name="2933"><span class="lineNum">    2933 </span>            :   /**</a>
+<a name="2934"><span class="lineNum">    2934 </span>            :     These functions can be used to make plumed_cmd behave as the C++ wrapper PLMD::Plumed::cmd,</a>
+<a name="2935"><span class="lineNum">    2935 </span>            :     namely implement typechecks and rethrowing exception.</a>
+<a name="2936"><span class="lineNum">    2936 </span>            :     To be used through the macro plumed_cmd (defined when __PLUMED_WRAPPER_CXX_BIND_C==1).</a>
+<a name="2937"><span class="lineNum">    2937 </span>            :     They are also used by the Plumed::cmd functions to avoid code duplication.</a>
+<a name="2938"><span class="lineNum">    2938 </span>            :     Available as of PLUMED 2.8.</a>
+<a name="2939"><span class="lineNum">    2939 </span>            :   */</a>
+<a name="2940"><span class="lineNum">    2940 </span>            :   template&lt;typename T&gt;</a>
+<a name="2941"><span class="lineNum">    2941 </span>            :   static void plumed_gcmd_cxx(const char*key,T val, const __PLUMED_WRAPPER_STD size_t* shape,plumed_error* error=__PLUMED_WRAPPER_CXX_NULLPTR) {</a>
+<a name="2942"><span class="lineNum">    2942 </span>            :     plumed_cmd_cxx(plumed_global(),key,val,shape,error);</a>
+<a name="2943"><span class="lineNum">    2943 </span>            :   }</a>
+<a name="2944"><span class="lineNum">    2944 </span>            : </a>
+<a name="2945"><span class="lineNum">    2945 </span>            : #endif /*}*/</a>
+<a name="2946"><span class="lineNum">    2946 </span>            : </a>
+<a name="2947"><span class="lineNum">    2947 </span>            : #if __PLUMED_WRAPPER_CXX_BIND_C /*{*/</a>
+<a name="2948"><span class="lineNum">    2948 </span>            : </a>
+<a name="2949"><span class="lineNum">    2949 </span>            : #define __PLUMED_WRAPPER_REDEFINE_CMD ::PLMD::Plumed::plumed_cmd_cxx</a>
+<a name="2950"><span class="lineNum">    2950 </span>            : </a>
+<a name="2951"><span class="lineNum">    2951 </span>            : #if __PLUMED_WRAPPER_GLOBAL /*{*/</a>
+<a name="2952"><span class="lineNum">    2952 </span>            : #define __PLUMED_WRAPPER_REDEFINE_GCMD ::PLMD::Plumed::plumed_gcmd_cxx</a>
+<a name="2953"><span class="lineNum">    2953 </span>            : #endif /*}*/</a>
+<a name="2954"><span class="lineNum">    2954 </span>            : </a>
+<a name="2955"><span class="lineNum">    2955 </span>            : #define __PLUMED_WRAPPER_REDEFINE_ERROR_RETHROW ::PLMD::Plumed::plumed_error_rethrow_cxx</a>
+<a name="2956"><span class="lineNum">    2956 </span>            : </a>
+<a name="2957"><span class="lineNum">    2957 </span>            : #endif /*}*/</a>
+<a name="2958"><span class="lineNum">    2958 </span>            : </a>
+<a name="2959"><span class="lineNum">    2959 </span>            : };</a>
+<a name="2960"><span class="lineNum">    2960 </span>            : </a>
+<a name="2961"><span class="lineNum">    2961 </span>            : /**</a>
+<a name="2962"><span class="lineNum">    2962 </span>            :   \related Plumed</a>
+<a name="2963"><span class="lineNum">    2963 </span>            :   Comparison operator. Available as of PLUMED 2.5.</a>
+<a name="2964"><span class="lineNum">    2964 </span>            : */</a>
+<a name="2965"><span class="lineNum">    2965 </span>            : inline</a>
+<a name="2966"><span class="lineNum">    2966 </span>            : bool operator==(const Plumed&amp;a,const Plumed&amp;b) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2967"><span class="lineNum">    2967 </span>            :   return a.toVoid()==b.toVoid();</a>
+<a name="2968"><span class="lineNum">    2968 </span>            : }</a>
+<a name="2969"><span class="lineNum">    2969 </span>            : </a>
+<a name="2970"><span class="lineNum">    2970 </span>            : /**</a>
+<a name="2971"><span class="lineNum">    2971 </span>            :   \related Plumed</a>
+<a name="2972"><span class="lineNum">    2972 </span>            :   Comparison operator. Available as of PLUMED 2.5.</a>
+<a name="2973"><span class="lineNum">    2973 </span>            : */</a>
+<a name="2974"><span class="lineNum">    2974 </span>            : inline</a>
+<a name="2975"><span class="lineNum">    2975 </span>            : bool operator!=(const Plumed&amp;a,const Plumed&amp;b) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2976"><span class="lineNum">    2976 </span>            :   return a.toVoid()!=b.toVoid();</a>
+<a name="2977"><span class="lineNum">    2977 </span>            : }</a>
+<a name="2978"><span class="lineNum">    2978 </span>            : </a>
+<a name="2979"><span class="lineNum">    2979 </span>            : /**</a>
+<a name="2980"><span class="lineNum">    2980 </span>            :   \related Plumed</a>
+<a name="2981"><span class="lineNum">    2981 </span>            :   Comparison operator. Available as of PLUMED 2.5.</a>
+<a name="2982"><span class="lineNum">    2982 </span>            : */</a>
+<a name="2983"><span class="lineNum">    2983 </span>            : inline</a>
+<a name="2984"><span class="lineNum">    2984 </span>            : bool operator&lt;=(const Plumed&amp;a,const Plumed&amp;b) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2985"><span class="lineNum">    2985 </span>            :   return a.toVoid()&lt;=b.toVoid();</a>
+<a name="2986"><span class="lineNum">    2986 </span>            : }</a>
+<a name="2987"><span class="lineNum">    2987 </span>            : </a>
+<a name="2988"><span class="lineNum">    2988 </span>            : /**</a>
+<a name="2989"><span class="lineNum">    2989 </span>            :   \related Plumed</a>
+<a name="2990"><span class="lineNum">    2990 </span>            :   Comparison operator. Available as of PLUMED 2.5.</a>
+<a name="2991"><span class="lineNum">    2991 </span>            : */</a>
+<a name="2992"><span class="lineNum">    2992 </span>            : inline</a>
+<a name="2993"><span class="lineNum">    2993 </span>            : bool operator&lt;(const Plumed&amp;a,const Plumed&amp;b) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="2994"><span class="lineNum">    2994 </span>            :   return a.toVoid()&lt;b.toVoid();</a>
+<a name="2995"><span class="lineNum">    2995 </span>            : }</a>
+<a name="2996"><span class="lineNum">    2996 </span>            : </a>
+<a name="2997"><span class="lineNum">    2997 </span>            : /**</a>
+<a name="2998"><span class="lineNum">    2998 </span>            :   \related Plumed</a>
+<a name="2999"><span class="lineNum">    2999 </span>            :   Comparison operator. Available as of PLUMED 2.5.</a>
+<a name="3000"><span class="lineNum">    3000 </span>            : */</a>
+<a name="3001"><span class="lineNum">    3001 </span>            : inline</a>
+<a name="3002"><span class="lineNum">    3002 </span>            : bool operator&gt;=(const Plumed&amp;a,const Plumed&amp;b) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="3003"><span class="lineNum">    3003 </span>            :   return a.toVoid()&gt;=b.toVoid();</a>
+<a name="3004"><span class="lineNum">    3004 </span>            : }</a>
+<a name="3005"><span class="lineNum">    3005 </span>            : </a>
+<a name="3006"><span class="lineNum">    3006 </span>            : /**</a>
+<a name="3007"><span class="lineNum">    3007 </span>            :   \related Plumed</a>
+<a name="3008"><span class="lineNum">    3008 </span>            :   Comparison operator. Available as of PLUMED 2.5.</a>
+<a name="3009"><span class="lineNum">    3009 </span>            : */</a>
+<a name="3010"><span class="lineNum">    3010 </span>            : inline</a>
+<a name="3011"><span class="lineNum">    3011 </span>            : bool operator&gt;(const Plumed&amp;a,const Plumed&amp;b) __PLUMED_WRAPPER_CXX_NOEXCEPT {</a>
+<a name="3012"><span class="lineNum">    3012 </span>            :   return a.toVoid()&gt;b.toVoid();</a>
+<a name="3013"><span class="lineNum">    3013 </span>            : }</a>
+<a name="3014"><span class="lineNum">    3014 </span>            : </a>
+<a name="3015"><span class="lineNum">    3015 </span>            : __PLUMED_WRAPPER_ANONYMOUS_END /*}*/</a>
+<a name="3016"><span class="lineNum">    3016 </span>            : </a>
+<a name="3017"><span class="lineNum">    3017 </span>            : }</a>
+<a name="3018"><span class="lineNum">    3018 </span>            : </a>
+<a name="3019"><span class="lineNum">    3019 </span>            : #endif /*}*/</a>
+<a name="3020"><span class="lineNum">    3020 </span>            : </a>
+<a name="3021"><span class="lineNum">    3021 </span>            : #endif /*}*/</a>
+<a name="3022"><span class="lineNum">    3022 </span>            : </a>
+<a name="3023"><span class="lineNum">    3023 </span>            : /* END OF DECLARATIONS */</a>
+<a name="3024"><span class="lineNum">    3024 </span>            : </a>
+<a name="3025"><span class="lineNum">    3025 </span>            : /*</a>
+<a name="3026"><span class="lineNum">    3026 </span>            : </a>
+<a name="3027"><span class="lineNum">    3027 </span>            :   1: emit implementation</a>
+<a name="3028"><span class="lineNum">    3028 </span>            :   0: do not emit implementation</a>
+<a name="3029"><span class="lineNum">    3029 </span>            : </a>
+<a name="3030"><span class="lineNum">    3030 </span>            :   Allows an implementation to be emitted together with the declarations.</a>
+<a name="3031"><span class="lineNum">    3031 </span>            : </a>
+<a name="3032"><span class="lineNum">    3032 </span>            :   Used to decide if definitions should be emitted. This macro could have a different</a>
+<a name="3033"><span class="lineNum">    3033 </span>            :   value when Plumed.h is reincluded. As a consequence, we map it to a local</a>
+<a name="3034"><span class="lineNum">    3034 </span>            :   macro (__PLUMED_WRAPPER_IMPLEMENTATION_) that is reset at the end of this file.</a>
+<a name="3035"><span class="lineNum">    3035 </span>            : */</a>
+<a name="3036"><span class="lineNum">    3036 </span>            : </a>
+<a name="3037"><span class="lineNum">    3037 </span>            : #ifdef __PLUMED_WRAPPER_IMPLEMENTATION</a>
+<a name="3038"><span class="lineNum">    3038 </span>            : #define __PLUMED_WRAPPER_IMPLEMENTATION_ __PLUMED_WRAPPER_IMPLEMENTATION</a>
+<a name="3039"><span class="lineNum">    3039 </span>            : #else</a>
+<a name="3040"><span class="lineNum">    3040 </span>            : #define __PLUMED_WRAPPER_IMPLEMENTATION_ 0</a>
+<a name="3041"><span class="lineNum">    3041 </span>            : #endif</a>
+<a name="3042"><span class="lineNum">    3042 </span>            : </a>
+<a name="3043"><span class="lineNum">    3043 </span>            : /* BEGINNING OF DEFINITIONS */</a>
+<a name="3044"><span class="lineNum">    3044 </span>            : </a>
+<a name="3045"><span class="lineNum">    3045 </span>            : #if __PLUMED_WRAPPER_IMPLEMENTATION_  /*{*/</a>
+<a name="3046"><span class="lineNum">    3046 </span>            : #ifndef __PLUMED_wrapper_Plumed_implementation /*{*/</a>
+<a name="3047"><span class="lineNum">    3047 </span>            : #define __PLUMED_wrapper_Plumed_implementation</a>
+<a name="3048"><span class="lineNum">    3048 </span>            : </a>
+<a name="3049"><span class="lineNum">    3049 </span>            : /*</a>
+<a name="3050"><span class="lineNum">    3050 </span>            :   the following macros only control the implementation</a>
+<a name="3051"><span class="lineNum">    3051 </span>            : */</a>
+<a name="3052"><span class="lineNum">    3052 </span>            : </a>
+<a name="3053"><span class="lineNum">    3053 </span>            : /*</a>
+<a name="3054"><span class="lineNum">    3054 </span>            :   1: enable the definition of plumed_symbol_table_reexport</a>
+<a name="3055"><span class="lineNum">    3055 </span>            :   0: does not enable the definition of plumed_symbol_table_reexport</a>
+<a name="3056"><span class="lineNum">    3056 </span>            : </a>
+<a name="3057"><span class="lineNum">    3057 </span>            :   This is only needed in the official plumed library to make</a>
+<a name="3058"><span class="lineNum">    3058 </span>            :   the symbol table available. This is a hack to reexport the function table</a>
+<a name="3059"><span class="lineNum">    3059 </span>            :   and is only needed when creating the library libplumed.so.</a>
+<a name="3060"><span class="lineNum">    3060 </span>            : */</a>
+<a name="3061"><span class="lineNum">    3061 </span>            : </a>
+<a name="3062"><span class="lineNum">    3062 </span>            : #ifndef __PLUMED_WRAPPER_REEXPORT_SYMBOL_TABLE</a>
+<a name="3063"><span class="lineNum">    3063 </span>            : #define __PLUMED_WRAPPER_REEXPORT_SYMBOL_TABLE 0</a>
+<a name="3064"><span class="lineNum">    3064 </span>            : #endif</a>
+<a name="3065"><span class="lineNum">    3065 </span>            : </a>
+<a name="3066"><span class="lineNum">    3066 </span>            : /*</a>
+<a name="3067"><span class="lineNum">    3067 </span>            :   1: write on stderr changes in reference counters</a>
+<a name="3068"><span class="lineNum">    3068 </span>            :   0: do not write changes in reference counters</a>
+<a name="3069"><span class="lineNum">    3069 </span>            : </a>
+<a name="3070"><span class="lineNum">    3070 </span>            :   Used for debugging.</a>
+<a name="3071"><span class="lineNum">    3071 </span>            : </a>
+<a name="3072"><span class="lineNum">    3072 </span>            :   Only used in definitions.</a>
+<a name="3073"><span class="lineNum">    3073 </span>            : */</a>
+<a name="3074"><span class="lineNum">    3074 </span>            : </a>
+<a name="3075"><span class="lineNum">    3075 </span>            : #ifndef __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3076"><span class="lineNum">    3076 </span>            : #define __PLUMED_WRAPPER_DEBUG_REFCOUNT 0</a>
+<a name="3077"><span class="lineNum">    3077 </span>            : #endif</a>
+<a name="3078"><span class="lineNum">    3078 </span>            : </a>
+<a name="3079"><span class="lineNum">    3079 </span>            : /*</a>
+<a name="3080"><span class="lineNum">    3080 </span>            :   1: emit plumed_kernel_register function (default)</a>
+<a name="3081"><span class="lineNum">    3081 </span>            :   0: do not emit plumed_kernel_register function</a>
+<a name="3082"><span class="lineNum">    3082 </span>            : </a>
+<a name="3083"><span class="lineNum">    3083 </span>            :   This function is only needed to avoid an extra warning when loading old (&lt;=2.4) kernels.</a>
+<a name="3084"><span class="lineNum">    3084 </span>            :   We might change its default in the future.</a>
+<a name="3085"><span class="lineNum">    3085 </span>            : </a>
+<a name="3086"><span class="lineNum">    3086 </span>            :   Used only in definitions.</a>
+<a name="3087"><span class="lineNum">    3087 </span>            : */</a>
+<a name="3088"><span class="lineNum">    3088 </span>            : </a>
+<a name="3089"><span class="lineNum">    3089 </span>            : #ifndef __PLUMED_WRAPPER_KERNEL_REGISTER</a>
+<a name="3090"><span class="lineNum">    3090 </span>            : #define __PLUMED_WRAPPER_KERNEL_REGISTER 1</a>
+<a name="3091"><span class="lineNum">    3091 </span>            : #endif</a>
+<a name="3092"><span class="lineNum">    3092 </span>            : </a>
+<a name="3093"><span class="lineNum">    3093 </span>            : /*</a>
+<a name="3094"><span class="lineNum">    3094 </span>            :   1: emit Fortran wrappers</a>
+<a name="3095"><span class="lineNum">    3095 </span>            :   0: do not emit Fortran wrappers (default)</a>
+<a name="3096"><span class="lineNum">    3096 </span>            : </a>
+<a name="3097"><span class="lineNum">    3097 </span>            :   Used only in definitions.</a>
+<a name="3098"><span class="lineNum">    3098 </span>            : */</a>
+<a name="3099"><span class="lineNum">    3099 </span>            : </a>
+<a name="3100"><span class="lineNum">    3100 </span>            : #ifndef __PLUMED_WRAPPER_FORTRAN</a>
+<a name="3101"><span class="lineNum">    3101 </span>            : #define __PLUMED_WRAPPER_FORTRAN 0</a>
+<a name="3102"><span class="lineNum">    3102 </span>            : #endif</a>
+<a name="3103"><span class="lineNum">    3103 </span>            : </a>
+<a name="3104"><span class="lineNum">    3104 </span>            : /*</a>
+<a name="3105"><span class="lineNum">    3105 </span>            :   With internal interface, it does not make sense to emit kernel register or fortran interfaces</a>
+<a name="3106"><span class="lineNum">    3106 </span>            : */</a>
+<a name="3107"><span class="lineNum">    3107 </span>            : </a>
+<a name="3108"><span class="lineNum">    3108 </span>            : #if ! __PLUMED_WRAPPER_EXTERN /*{*/</a>
+<a name="3109"><span class="lineNum">    3109 </span>            : #undef __PLUMED_WRAPPER_KERNEL_REGISTER</a>
+<a name="3110"><span class="lineNum">    3110 </span>            : #define __PLUMED_WRAPPER_KERNEL_REGISTER 0</a>
+<a name="3111"><span class="lineNum">    3111 </span>            : #undef __PLUMED_WRAPPER_FORTRAN</a>
+<a name="3112"><span class="lineNum">    3112 </span>            : #define __PLUMED_WRAPPER_FORTRAN 0</a>
+<a name="3113"><span class="lineNum">    3113 </span>            : #endif /*}*/</a>
+<a name="3114"><span class="lineNum">    3114 </span>            : </a>
+<a name="3115"><span class="lineNum">    3115 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="3116"><span class="lineNum">    3116 </span>            : #include &lt;dlfcn.h&gt; /* dlopen dlerror dlsym */</a>
+<a name="3117"><span class="lineNum">    3117 </span>            : #endif</a>
+<a name="3118"><span class="lineNum">    3118 </span>            : </a>
+<a name="3119"><span class="lineNum">    3119 </span>            : #if __PLUMED_WRAPPER_CXX_STD</a>
+<a name="3120"><span class="lineNum">    3120 </span>            : #include &lt;cstdio&gt;  /* fprintf */</a>
+<a name="3121"><span class="lineNum">    3121 </span>            : #include &lt;cstring&gt; /* memcpy strlen strncpy memcmp memmove strcmp memcpy */</a>
+<a name="3122"><span class="lineNum">    3122 </span>            : #include &lt;cassert&gt; /* assert */</a>
+<a name="3123"><span class="lineNum">    3123 </span>            : #include &lt;cstdlib&gt; /* getenv malloc free abort */</a>
+<a name="3124"><span class="lineNum">    3124 </span>            : #include &lt;climits&gt; /* CHAR_BIT */</a>
+<a name="3125"><span class="lineNum">    3125 </span>            : #else</a>
+<a name="3126"><span class="lineNum">    3126 </span>            : #include &lt;stdio.h&gt;</a>
+<a name="3127"><span class="lineNum">    3127 </span>            : #include &lt;string.h&gt;</a>
+<a name="3128"><span class="lineNum">    3128 </span>            : #include &lt;assert.h&gt;</a>
+<a name="3129"><span class="lineNum">    3129 </span>            : #include &lt;stdlib.h&gt;</a>
+<a name="3130"><span class="lineNum">    3130 </span>            : #include &lt;limits.h&gt;</a>
+<a name="3131"><span class="lineNum">    3131 </span>            : #endif</a>
+<a name="3132"><span class="lineNum">    3132 </span>            : </a>
+<a name="3133"><span class="lineNum">    3133 </span>            : /**</a>
+<a name="3134"><span class="lineNum">    3134 </span>            :   Function pointer to plumed_create</a>
+<a name="3135"><span class="lineNum">    3135 </span>            : */</a>
+<a name="3136"><span class="lineNum">    3136 </span>            : </a>
+<a name="3137"><span class="lineNum">    3137 </span>            : typedef void*(*plumed_create_pointer)(void);</a>
+<a name="3138"><span class="lineNum">    3138 </span>            : /**</a>
+<a name="3139"><span class="lineNum">    3139 </span>            :   Function pointer to plumed_cmd</a>
+<a name="3140"><span class="lineNum">    3140 </span>            : */</a>
+<a name="3141"><span class="lineNum">    3141 </span>            : typedef void(*plumed_cmd_pointer)(void*,const char*,const void*);</a>
+<a name="3142"><span class="lineNum">    3142 </span>            : </a>
+<a name="3143"><span class="lineNum">    3143 </span>            : /**</a>
+<a name="3144"><span class="lineNum">    3144 </span>            :   Function pointer to plumed_finalize</a>
+<a name="3145"><span class="lineNum">    3145 </span>            : */</a>
+<a name="3146"><span class="lineNum">    3146 </span>            : typedef void(*plumed_finalize_pointer)(void*);</a>
+<a name="3147"><span class="lineNum">    3147 </span>            : </a>
+<a name="3148"><span class="lineNum">    3148 </span>            : /**</a>
+<a name="3149"><span class="lineNum">    3149 </span>            :    Holder for plumedmain function pointers.</a>
+<a name="3150"><span class="lineNum">    3150 </span>            : */</a>
+<a name="3151"><span class="lineNum">    3151 </span>            : typedef struct {</a>
+<a name="3152"><span class="lineNum">    3152 </span>            :   plumed_create_pointer create;</a>
+<a name="3153"><span class="lineNum">    3153 </span>            :   plumed_cmd_pointer cmd;</a>
+<a name="3154"><span class="lineNum">    3154 </span>            :   plumed_finalize_pointer finalize;</a>
+<a name="3155"><span class="lineNum">    3155 </span>            : } plumed_plumedmain_function_holder;</a>
+<a name="3156"><span class="lineNum">    3156 </span>            : </a>
+<a name="3157"><span class="lineNum">    3157 </span>            : /**</a>
+<a name="3158"><span class="lineNum">    3158 </span>            :   Holder for plumed symbol table.</a>
+<a name="3159"><span class="lineNum">    3159 </span>            : </a>
+<a name="3160"><span class="lineNum">    3160 </span>            :   The table contains pointers to function exported from plumed. Functions can be added increasing the version number.</a>
+<a name="3161"><span class="lineNum">    3161 </span>            :   Notice that the default way to extend functionalities is by adding cmd strings. This is a last resort, and all new</a>
+<a name="3162"><span class="lineNum">    3162 </span>            :   functions should be explicitly motivated. Here's the addition:</a>
+<a name="3163"><span class="lineNum">    3163 </span>            : </a>
+<a name="3164"><span class="lineNum">    3164 </span>            :   version=2, cmd_nothrow.</a>
+<a name="3165"><span class="lineNum">    3165 </span>            : </a>
+<a name="3166"><span class="lineNum">    3166 </span>            :   This function accepts an extra argument `plumed_nothrow_handler*handler`.</a>
+<a name="3167"><span class="lineNum">    3167 </span>            :   In case an exception is thrown within plumed, it just calls `handler-&gt;handler(handler-&gt;ptr,code,message,opt)` and return.</a>
+<a name="3168"><span class="lineNum">    3168 </span>            :   An alternative would have been to install an error handler (with a call to cmd(&quot;setErrorHandler&quot;)). However, the cost</a>
+<a name="3169"><span class="lineNum">    3169 </span>            :   of doing it everytime Plumed::cmd is called is too high. On the other hand, installing it only at object construction</a>
+<a name="3170"><span class="lineNum">    3170 </span>            :   is very risky since and object created in that way would not report any error if manipulated from the C interface.</a>
+<a name="3171"><span class="lineNum">    3171 </span>            :   So, it looks like this is the only possibility.</a>
+<a name="3172"><span class="lineNum">    3172 </span>            : </a>
+<a name="3173"><span class="lineNum">    3173 </span>            :   version=3, cmd_safe and cmd_safe_nothrow</a>
+<a name="3174"><span class="lineNum">    3174 </span>            : </a>
+<a name="3175"><span class="lineNum">    3175 </span>            :   These are functions that accept a plumed_safeptr object, which can carry information about the passed type and size.</a>
+<a name="3176"><span class="lineNum">    3176 </span>            :   Since new information should be passed at every cmd call, this can only be obtained by adding new cmd calls.</a>
+<a name="3177"><span class="lineNum">    3177 </span>            : </a>
+<a name="3178"><span class="lineNum">    3178 </span>            :   version=4, thread-safe reference counter</a>
+<a name="3179"><span class="lineNum">    3179 </span>            : </a>
+<a name="3180"><span class="lineNum">    3180 </span>            :   These functions allow to access a thread-safe reference counter that is stored within the PlumedMain object.</a>
+<a name="3181"><span class="lineNum">    3181 </span>            :   This allows avoiding to enable atomic access also the C compiler used build Plumed.c. It's added here and not as a new</a>
+<a name="3182"><span class="lineNum">    3182 </span>            :   cmd since this is a very low-level functionality.</a>
+<a name="3183"><span class="lineNum">    3183 </span>            : */</a>
+<a name="3184"><span class="lineNum">    3184 </span>            : typedef struct {</a>
+<a name="3185"><span class="lineNum">    3185 </span>            :   /**</a>
+<a name="3186"><span class="lineNum">    3186 </span>            :     Version number.</a>
+<a name="3187"><span class="lineNum">    3187 </span>            : </a>
+<a name="3188"><span class="lineNum">    3188 </span>            :     Minimum value is 1.</a>
+<a name="3189"><span class="lineNum">    3189 </span>            :   */</a>
+<a name="3190"><span class="lineNum">    3190 </span>            :   int version;</a>
+<a name="3191"><span class="lineNum">    3191 </span>            :   /**</a>
+<a name="3192"><span class="lineNum">    3192 </span>            :     Pointers to standard plumed functions (create/cmd/finalize).</a>
+<a name="3193"><span class="lineNum">    3193 </span>            : </a>
+<a name="3194"><span class="lineNum">    3194 </span>            :     Always available.</a>
+<a name="3195"><span class="lineNum">    3195 </span>            :   */</a>
+<a name="3196"><span class="lineNum">    3196 </span>            :   plumed_plumedmain_function_holder functions;</a>
+<a name="3197"><span class="lineNum">    3197 </span>            :   /**</a>
+<a name="3198"><span class="lineNum">    3198 </span>            :     Pointer to a cmd function guaranteed not to throw exceptions.</a>
+<a name="3199"><span class="lineNum">    3199 </span>            : </a>
+<a name="3200"><span class="lineNum">    3200 </span>            :     Available with version&gt;=2.</a>
+<a name="3201"><span class="lineNum">    3201 </span>            :   */</a>
+<a name="3202"><span class="lineNum">    3202 </span>            :   void (*cmd_nothrow)(void*plumed,const char*key,const void*val,plumed_nothrow_handler);</a>
+<a name="3203"><span class="lineNum">    3203 </span>            :   /**</a>
+<a name="3204"><span class="lineNum">    3204 </span>            :     Pointer to a cmd function that accepts typeinfos.</a>
+<a name="3205"><span class="lineNum">    3205 </span>            : </a>
+<a name="3206"><span class="lineNum">    3206 </span>            :     Available with version&gt;=3.</a>
+<a name="3207"><span class="lineNum">    3207 </span>            :   */</a>
+<a name="3208"><span class="lineNum">    3208 </span>            :   void (*cmd_safe)(void*plumed,const char*key,plumed_safeptr);</a>
+<a name="3209"><span class="lineNum">    3209 </span>            : </a>
+<a name="3210"><span class="lineNum">    3210 </span>            :   /**</a>
+<a name="3211"><span class="lineNum">    3211 </span>            :     Pointer to a cmd function guaranteed not to throw exceptions and that accepts typeinfos.</a>
+<a name="3212"><span class="lineNum">    3212 </span>            : </a>
+<a name="3213"><span class="lineNum">    3213 </span>            :     Available with version&gt;=3.</a>
+<a name="3214"><span class="lineNum">    3214 </span>            :   */</a>
+<a name="3215"><span class="lineNum">    3215 </span>            :   void (*cmd_safe_nothrow)(void*plumed,const char*key,plumed_safeptr,plumed_nothrow_handler);</a>
+<a name="3216"><span class="lineNum">    3216 </span>            : </a>
+<a name="3217"><span class="lineNum">    3217 </span>            :   /**</a>
+<a name="3218"><span class="lineNum">    3218 </span>            :     Pointer to a function that increments the internal reference counter.</a>
+<a name="3219"><span class="lineNum">    3219 </span>            : </a>
+<a name="3220"><span class="lineNum">    3220 </span>            :     Available with version&gt;=4.</a>
+<a name="3221"><span class="lineNum">    3221 </span>            :   */</a>
+<a name="3222"><span class="lineNum">    3222 </span>            :   unsigned (*create_reference)(void*);</a>
+<a name="3223"><span class="lineNum">    3223 </span>            :   /**</a>
+<a name="3224"><span class="lineNum">    3224 </span>            :     Pointer to a function that decrements the internal reference counter.</a>
+<a name="3225"><span class="lineNum">    3225 </span>            : </a>
+<a name="3226"><span class="lineNum">    3226 </span>            :     Available with version&gt;=4.</a>
+<a name="3227"><span class="lineNum">    3227 </span>            :   */</a>
+<a name="3228"><span class="lineNum">    3228 </span>            :   unsigned (*delete_reference)(void*);</a>
+<a name="3229"><span class="lineNum">    3229 </span>            :   /**</a>
+<a name="3230"><span class="lineNum">    3230 </span>            :     Pointer to a function that returns the internal reference counter.</a>
+<a name="3231"><span class="lineNum">    3231 </span>            : </a>
+<a name="3232"><span class="lineNum">    3232 </span>            :     Available with version&gt;=4.</a>
+<a name="3233"><span class="lineNum">    3233 </span>            :   */</a>
+<a name="3234"><span class="lineNum">    3234 </span>            :   unsigned (*use_count)(void*);</a>
+<a name="3235"><span class="lineNum">    3235 </span>            : } plumed_symbol_table_type;</a>
+<a name="3236"><span class="lineNum">    3236 </span>            : </a>
+<a name="3237"><span class="lineNum">    3237 </span>            : /* Utility to convert function pointers to pointers, just for the sake of printing them */</a>
+<a name="3238"><span class="lineNum">    3238 </span>            : #define __PLUMED_CONVERT_FPTR(ptr,fptr) { ptr=__PLUMED_WRAPPER_CXX_NULLPTR; __PLUMED_WRAPPER_STD memcpy(&amp;ptr,&amp;fptr,(sizeof(fptr)&gt;sizeof(ptr)?sizeof(ptr):sizeof(fptr))); }</a>
+<a name="3239"><span class="lineNum">    3239 </span>            : </a>
+<a name="3240"><span class="lineNum">    3240 </span>            : #define __PLUMED_GETENV __PLUMED_WRAPPER_STD getenv</a>
+<a name="3241"><span class="lineNum">    3241 </span>            : #define __PLUMED_FPRINTF __PLUMED_WRAPPER_STD fprintf</a>
+<a name="3242"><span class="lineNum">    3242 </span>            : </a>
+<a name="3243"><span class="lineNum">    3243 </span>            : /**</a>
+<a name="3244"><span class="lineNum">    3244 </span>            :   Historically (PLUMED&lt;=2.4) register for plumedmain function pointers.</a>
+<a name="3245"><span class="lineNum">    3245 </span>            :   As of PLUMED&gt;=2.5, this function does not do anything except for reporting the attempt to register</a>
+<a name="3246"><span class="lineNum">    3246 </span>            :   something. It always returns NULL. The function should be here anyway to allow an incomplete</a>
+<a name="3247"><span class="lineNum">    3247 </span>            :   libplumedKernel (&lt;=2.4), expecting this function to be present, to be loaded correctly.</a>
+<a name="3248"><span class="lineNum">    3248 </span>            : */</a>
+<a name="3249"><span class="lineNum">    3249 </span>            : #if __PLUMED_WRAPPER_KERNEL_REGISTER</a>
+<a name="3250"><span class="lineNum">    3250 </span>            : /* Since it is only called from outside, it must be hardcoded to be extern */</a>
+<a name="3251"><span class="lineNum">    3251 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN /*{*/</a>
+<a name="3252"><span class="lineNum">    3252 </span>            : extern plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmain_function_holder*);</a>
+<a name="3253"><span class="lineNum">    3253 </span><span class="lineCov">         13 : plumed_plumedmain_function_holder* plumed_kernel_register(const plumed_plumedmain_function_holder* f) {</span></a>
+<a name="3254"><span class="lineNum">    3254 </span>            :   void* tmpptr;</a>
+<a name="3255"><span class="lineNum">    3255 </span><span class="lineCov">         13 :   if(f) {</span></a>
+<a name="3256"><span class="lineNum">    3256 </span><span class="lineCov">         13 :     if(__PLUMED_GETENV(&quot;PLUMED_LOAD_DEBUG&quot;)) {</span></a>
+<a name="3257"><span class="lineNum">    3257 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ Ignoring registration at %p (&quot;,(const void*)f);</span></a>
+<a name="3258"><span class="lineNum">    3258 </span>            :       __PLUMED_CONVERT_FPTR(tmpptr,f-&gt;create);</a>
+<a name="3259"><span class="lineNum">    3259 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;%p,&quot;,tmpptr);</span></a>
+<a name="3260"><span class="lineNum">    3260 </span>            :       __PLUMED_CONVERT_FPTR(tmpptr,f-&gt;cmd);</a>
+<a name="3261"><span class="lineNum">    3261 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;%p,&quot;,tmpptr);</span></a>
+<a name="3262"><span class="lineNum">    3262 </span>            :       __PLUMED_CONVERT_FPTR(tmpptr,f-&gt;finalize);</a>
+<a name="3263"><span class="lineNum">    3263 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;%p) +++\n&quot;,tmpptr);</span></a>
+<a name="3264"><span class="lineNum">    3264 </span>            :     }</a>
+<a name="3265"><span class="lineNum">    3265 </span>            :   }</a>
+<a name="3266"><span class="lineNum">    3266 </span><span class="lineCov">         13 :   return __PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3267"><span class="lineNum">    3267 </span>            : }</a>
+<a name="3268"><span class="lineNum">    3268 </span>            : __PLUMED_WRAPPER_EXTERN_C_END /*}*/</a>
+<a name="3269"><span class="lineNum">    3269 </span>            : #endif</a>
+<a name="3270"><span class="lineNum">    3270 </span>            : </a>
+<a name="3271"><span class="lineNum">    3271 </span>            : #if defined( __PLUMED_HAS_DLOPEN) /*{*/</a>
+<a name="3272"><span class="lineNum">    3272 </span>            : /**</a>
+<a name="3273"><span class="lineNum">    3273 </span>            : Try to dlopen a path with a given mode.</a>
+<a name="3274"><span class="lineNum">    3274 </span>            : If the dlopen command fails, it tries to strip the `Kernel` part of the name.</a>
+<a name="3275"><span class="lineNum">    3275 </span>            : </a>
+<a name="3276"><span class="lineNum">    3276 </span>            : This function is declared static (internal linkage) so that it is not visible from outside.</a>
+<a name="3277"><span class="lineNum">    3277 </span>            : It is first declared then defined to make sure it is a regular C static function.</a>
+<a name="3278"><span class="lineNum">    3278 </span>            : */</a>
+<a name="3279"><span class="lineNum">    3279 </span>            : </a>
+<a name="3280"><span class="lineNum">    3280 </span>            : __PLUMED_WRAPPER_INTERNALS_BEGIN</a>
+<a name="3281"><span class="lineNum">    3281 </span><span class="lineCov">          9 : void* plumed_attempt_dlopen(const char*path,int mode) {</span></a>
+<a name="3282"><span class="lineNum">    3282 </span>            :   char* pathcopy;</a>
+<a name="3283"><span class="lineNum">    3283 </span>            :   void* p;</a>
+<a name="3284"><span class="lineNum">    3284 </span>            :   char* pc;</a>
+<a name="3285"><span class="lineNum">    3285 </span>            :   __PLUMED_WRAPPER_STD size_t strlenpath;</a>
+<a name="3286"><span class="lineNum">    3286 </span>            :   FILE* fp;</a>
+<a name="3287"><span class="lineNum">    3287 </span>            :   pathcopy=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3288"><span class="lineNum">    3288 </span>            :   p=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3289"><span class="lineNum">    3289 </span>            :   pc=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3290"><span class="lineNum">    3290 </span>            :   strlenpath=0;</a>
+<a name="3291"><span class="lineNum">    3291 </span><span class="lineCov">          9 :   fp=__PLUMED_WRAPPER_STD fopen(path,&quot;r&quot;);</span></a>
+<a name="3292"><span class="lineNum">    3292 </span><span class="lineCov">          9 :   if(!fp) {</span></a>
+<a name="3293"><span class="lineNum">    3293 </span><span class="lineNoCov">          0 :     __PLUMED_FPRINTF(stderr,&quot;+++ File %s does not exist or cannot be read\n&quot;,path);</span></a>
+<a name="3294"><span class="lineNum">    3294 </span><span class="lineNoCov">          0 :     return __PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3295"><span class="lineNum">    3295 </span>            :   }</a>
+<a name="3296"><span class="lineNum">    3296 </span><span class="lineCov">          9 :   __PLUMED_WRAPPER_STD fclose(fp);</span></a>
+<a name="3297"><span class="lineNum">    3297 </span><span class="lineCov">          9 :   dlerror();</span></a>
+<a name="3298"><span class="lineNum">    3298 </span><span class="lineCov">          9 :   p=dlopen(path,mode);</span></a>
+<a name="3299"><span class="lineNum">    3299 </span><span class="lineCov">          9 :   if(!p) {</span></a>
+<a name="3300"><span class="lineNum">    3300 </span>            :     /*</a>
+<a name="3301"><span class="lineNum">    3301 </span>            :       Something went wrong. We try to remove &quot;Kernel&quot; string from the PLUMED_KERNEL variable</a>
+<a name="3302"><span class="lineNum">    3302 </span>            :       and load directly the shared library. Notice that this particular path is only expected</a>
+<a name="3303"><span class="lineNum">    3303 </span>            :       to be necessary when using PLUMED&lt;=2.4 and the symbols in the main executable are</a>
+<a name="3304"><span class="lineNum">    3304 </span>            :       not visible. All the other cases (either PLUMED&gt;=2.5 or symbols in the main executable visible)</a>
+<a name="3305"><span class="lineNum">    3305 </span>            :       should work correctly without entering here.</a>
+<a name="3306"><span class="lineNum">    3306 </span>            :     */</a>
+<a name="3307"><span class="lineNum">    3307 </span><span class="lineNoCov">          0 :     __PLUMED_FPRINTF(stderr,&quot;+++ An error occurred. Message from dlopen(): %s +++\n&quot;,dlerror());</span></a>
+<a name="3308"><span class="lineNum">    3308 </span><span class="lineNoCov">          0 :     strlenpath=__PLUMED_WRAPPER_STD strlen(path);</span></a>
+<a name="3309"><span class="lineNum">    3309 </span><span class="lineNoCov">          0 :     pathcopy=(char*) plumed_malloc(strlenpath+1);</span></a>
+<a name="3310"><span class="lineNum">    3310 </span><span class="lineNoCov">          0 :     if(!pathcopy) {</span></a>
+<a name="3311"><span class="lineNum">    3311 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ Allocation error +++\n&quot;);</span></a>
+<a name="3312"><span class="lineNum">    3312 </span><span class="lineNoCov">          0 :       __PLUMED_WRAPPER_STD abort();</span></a>
+<a name="3313"><span class="lineNum">    3313 </span>            :     }</a>
+<a name="3314"><span class="lineNum">    3314 </span>            :     __PLUMED_WRAPPER_STD strncpy(pathcopy,path,strlenpath+1);</a>
+<a name="3315"><span class="lineNum">    3315 </span><span class="lineNoCov">          0 :     pc=pathcopy+strlenpath-6;</span></a>
+<a name="3316"><span class="lineNum">    3316 </span><span class="lineNoCov">          0 :     while(pc&gt;=pathcopy &amp;&amp; __PLUMED_WRAPPER_STD memcmp(pc,&quot;Kernel&quot;,6)) pc--;</span></a>
+<a name="3317"><span class="lineNum">    3317 </span><span class="lineNoCov">          0 :     if(pc&gt;=pathcopy) {</span></a>
+<a name="3318"><span class="lineNum">    3318 </span><span class="lineNoCov">          0 :       __PLUMED_WRAPPER_STD memmove(pc, pc+6, __PLUMED_WRAPPER_STD strlen(pc)-5);</span></a>
+<a name="3319"><span class="lineNum">    3319 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ This error is expected if you are trying to load a kernel &lt;=2.4\n&quot;);</span></a>
+<a name="3320"><span class="lineNum">    3320 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ Trying %s +++\n&quot;,pathcopy);</span></a>
+<a name="3321"><span class="lineNum">    3321 </span><span class="lineNoCov">          0 :       fp=__PLUMED_WRAPPER_STD fopen(path,&quot;r&quot;);</span></a>
+<a name="3322"><span class="lineNum">    3322 </span><span class="lineNoCov">          0 :       if(!fp) {</span></a>
+<a name="3323"><span class="lineNum">    3323 </span><span class="lineNoCov">          0 :         __PLUMED_FPRINTF(stderr,&quot;+++ File %s does not exist or cannot be read\n&quot;,pathcopy);</span></a>
+<a name="3324"><span class="lineNum">    3324 </span><span class="lineNoCov">          0 :         plumed_free(pathcopy);</span></a>
+<a name="3325"><span class="lineNum">    3325 </span><span class="lineNoCov">          0 :         return __PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3326"><span class="lineNum">    3326 </span>            :       }</a>
+<a name="3327"><span class="lineNum">    3327 </span><span class="lineNoCov">          0 :       __PLUMED_WRAPPER_STD fclose(fp);</span></a>
+<a name="3328"><span class="lineNum">    3328 </span><span class="lineNoCov">          0 :       dlerror();</span></a>
+<a name="3329"><span class="lineNum">    3329 </span><span class="lineNoCov">          0 :       p=dlopen(pathcopy,mode);</span></a>
+<a name="3330"><span class="lineNum">    3330 </span><span class="lineNoCov">          0 :       if(!p) __PLUMED_FPRINTF(stderr,&quot;+++ An error occurred. Message from dlopen(): %s +++\n&quot;,dlerror());</span></a>
+<a name="3331"><span class="lineNum">    3331 </span>            :     }</a>
+<a name="3332"><span class="lineNum">    3332 </span><span class="lineNoCov">          0 :     plumed_free(pathcopy);</span></a>
+<a name="3333"><span class="lineNum">    3333 </span>            :   }</a>
+<a name="3334"><span class="lineNum">    3334 </span>            :   return p;</a>
+<a name="3335"><span class="lineNum">    3335 </span>            : }</a>
+<a name="3336"><span class="lineNum">    3336 </span>            : __PLUMED_WRAPPER_INTERNALS_END</a>
+<a name="3337"><span class="lineNum">    3337 </span>            : </a>
+<a name="3338"><span class="lineNum">    3338 </span>            : /**</a>
+<a name="3339"><span class="lineNum">    3339 </span>            :   Utility to search for a function.</a>
+<a name="3340"><span class="lineNum">    3340 </span>            : */</a>
+<a name="3341"><span class="lineNum">    3341 </span>            : #define __PLUMED_SEARCH_FUNCTION(tmpptr,handle,func,name,debug) \</a>
+<a name="3342"><span class="lineNum">    3342 </span>            :   if(!func) { \</a>
+<a name="3343"><span class="lineNum">    3343 </span>            :     tmpptr=dlsym(handle,name); \</a>
+<a name="3344"><span class="lineNum">    3344 </span>            :     if(tmpptr) { \</a>
+<a name="3345"><span class="lineNum">    3345 </span>            :       *(void **)(&amp;func)=tmpptr; \</a>
+<a name="3346"><span class="lineNum">    3346 </span>            :       if(debug) __PLUMED_FPRINTF(stderr,&quot;+++ %s found at %p +++\n&quot;,name,tmpptr); \</a>
+<a name="3347"><span class="lineNum">    3347 </span>            :     } else { \</a>
+<a name="3348"><span class="lineNum">    3348 </span>            :       if(debug) __PLUMED_FPRINTF(stderr,&quot;+++ Function %s not found\n&quot;,name); \</a>
+<a name="3349"><span class="lineNum">    3349 </span>            :     } \</a>
+<a name="3350"><span class="lineNum">    3350 </span>            :   }</a>
+<a name="3351"><span class="lineNum">    3351 </span>            : </a>
+<a name="3352"><span class="lineNum">    3352 </span>            : /**</a>
+<a name="3353"><span class="lineNum">    3353 </span>            : Search symbols in a dlopened library.</a>
+<a name="3354"><span class="lineNum">    3354 </span>            : </a>
+<a name="3355"><span class="lineNum">    3355 </span>            : This function is declared static (internal linkage) so that it is not visible from outside.</a>
+<a name="3356"><span class="lineNum">    3356 </span>            : */</a>
+<a name="3357"><span class="lineNum">    3357 </span>            : __PLUMED_WRAPPER_INTERNALS_BEGIN</a>
+<a name="3358"><span class="lineNum">    3358 </span><span class="lineCov">          9 : void plumed_search_symbols(void* handle, plumed_plumedmain_function_holder* f,plumed_symbol_table_type** table) {</span></a>
+<a name="3359"><span class="lineNum">    3359 </span>            :   plumed_plumedmain_function_holder functions;</a>
+<a name="3360"><span class="lineNum">    3360 </span>            :   plumed_symbol_table_type* table_ptr;</a>
+<a name="3361"><span class="lineNum">    3361 </span>            :   void* tmpptr;</a>
+<a name="3362"><span class="lineNum">    3362 </span>            :   char* debug;</a>
+<a name="3363"><span class="lineNum">    3363 </span>            :   functions.create=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3364"><span class="lineNum">    3364 </span>            :   functions.cmd=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3365"><span class="lineNum">    3365 </span>            :   functions.finalize=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3366"><span class="lineNum">    3366 </span>            :   table_ptr=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3367"><span class="lineNum">    3367 </span><span class="lineCov">          9 :   tmpptr=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3368"><span class="lineNum">    3368 </span>            :   /*</a>
+<a name="3369"><span class="lineNum">    3369 </span>            :     Notice that as of PLUMED 2.5 we ignore self registrations.</a>
+<a name="3370"><span class="lineNum">    3370 </span>            :     Pointers are searched in the form of a single pointer to a structure, which</a>
+<a name="3371"><span class="lineNum">    3371 </span>            :     is the standard way in PLUMED 2.5, as well as using alternative names used in</a>
+<a name="3372"><span class="lineNum">    3372 </span>            :     PLUMED 2.0 to 2.4 (e.g. plumedmain_create) and in some intermediate versions between</a>
+<a name="3373"><span class="lineNum">    3373 </span>            :     PLUMED 2.4 and 2.5 (e.g. plumed_plumedmain_create). The last chance is probably</a>
+<a name="3374"><span class="lineNum">    3374 </span>            :     unnecessary and might be removed at some point.</a>
+<a name="3375"><span class="lineNum">    3375 </span>            :   */</a>
+<a name="3376"><span class="lineNum">    3376 </span><span class="lineCov">          9 :   debug=__PLUMED_GETENV(&quot;PLUMED_LOAD_DEBUG&quot;);</span></a>
+<a name="3377"><span class="lineNum">    3377 </span><span class="lineCov">          9 :   table_ptr=(plumed_symbol_table_type*) dlsym(handle,&quot;plumed_symbol_table&quot;);</span></a>
+<a name="3378"><span class="lineNum">    3378 </span><span class="lineCov">          9 :   if(table_ptr) functions=table_ptr-&gt;functions;</span></a>
+<a name="3379"><span class="lineNum">    3379 </span><span class="lineCov">          9 :   if(debug) {</span></a>
+<a name="3380"><span class="lineNum">    3380 </span><span class="lineNoCov">          0 :     if(table_ptr) {</span></a>
+<a name="3381"><span class="lineNum">    3381 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ plumed_symbol_table version %i found at %p +++\n&quot;,table_ptr-&gt;version,(void*)table_ptr);</span></a>
+<a name="3382"><span class="lineNum">    3382 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ plumed_function_pointers found at %p (&quot;,(void*)&amp;table_ptr-&gt;functions);</span></a>
+<a name="3383"><span class="lineNum">    3383 </span>            :       __PLUMED_CONVERT_FPTR(tmpptr,functions.create);</a>
+<a name="3384"><span class="lineNum">    3384 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;%p,&quot;,tmpptr);</span></a>
+<a name="3385"><span class="lineNum">    3385 </span>            :       __PLUMED_CONVERT_FPTR(tmpptr,functions.cmd);</a>
+<a name="3386"><span class="lineNum">    3386 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;%p,&quot;,tmpptr);</span></a>
+<a name="3387"><span class="lineNum">    3387 </span>            :       __PLUMED_CONVERT_FPTR(tmpptr,functions.finalize);</a>
+<a name="3388"><span class="lineNum">    3388 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;%p) +++\n&quot;,tmpptr);</span></a>
+<a name="3389"><span class="lineNum">    3389 </span>            :     } else {</a>
+<a name="3390"><span class="lineNum">    3390 </span><span class="lineNoCov">          0 :       __PLUMED_FPRINTF(stderr,&quot;+++ plumed_symbol_table (available in PLUMED&gt;=2.5) not found, perhaps kernel is older +++\n&quot;);</span></a>
+<a name="3391"><span class="lineNum">    3391 </span>            :     }</a>
+<a name="3392"><span class="lineNum">    3392 </span>            :   }</a>
+<a name="3393"><span class="lineNum">    3393 </span>            :   /* only searches if they were not found already */</a>
+<a name="3394"><span class="lineNum">    3394 </span><span class="lineCov">          9 :   __PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.create,&quot;plumedmain_create&quot;,debug);</span></a>
+<a name="3395"><span class="lineNum">    3395 </span><span class="lineCov">          9 :   __PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.create,&quot;plumed_plumedmain_create&quot;,debug);</span></a>
+<a name="3396"><span class="lineNum">    3396 </span><span class="lineCov">          9 :   __PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.cmd,&quot;plumedmain_cmd&quot;,debug);</span></a>
+<a name="3397"><span class="lineNum">    3397 </span><span class="lineCov">          9 :   __PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.cmd,&quot;plumed_plumedmain_cmd&quot;,debug);</span></a>
+<a name="3398"><span class="lineNum">    3398 </span><span class="lineCov">          9 :   __PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.finalize,&quot;plumedmain_finalize&quot;,debug);</span></a>
+<a name="3399"><span class="lineNum">    3399 </span><span class="lineCov">          9 :   __PLUMED_SEARCH_FUNCTION(tmpptr,handle,functions.finalize,&quot;plumed_plumedmain_finalize&quot;,debug);</span></a>
+<a name="3400"><span class="lineNum">    3400 </span><span class="lineCov">          9 :   if(functions.create &amp;&amp; functions.cmd &amp;&amp; functions.finalize) {</span></a>
+<a name="3401"><span class="lineNum">    3401 </span><span class="lineCov">          9 :     if(debug) __PLUMED_FPRINTF(stderr,&quot;+++ PLUMED was loaded correctly +++\n&quot;);</span></a>
+<a name="3402"><span class="lineNum">    3402 </span><span class="lineCov">          9 :     *f=functions;</span></a>
+<a name="3403"><span class="lineNum">    3403 </span><span class="lineCov">          9 :     if(table) *table=table_ptr;</span></a>
+<a name="3404"><span class="lineNum">    3404 </span>            :   } else {</a>
+<a name="3405"><span class="lineNum">    3405 </span><span class="lineNoCov">          0 :     if(!functions.create) __PLUMED_FPRINTF(stderr,&quot;+++ Pointer to (plumed_)plumedmain_create not found +++\n&quot;);</span></a>
+<a name="3406"><span class="lineNum">    3406 </span><span class="lineNoCov">          0 :     if(!functions.cmd) __PLUMED_FPRINTF(stderr,&quot;+++ Pointer to (plumed_)plumedmain_cmd not found +++\n&quot;);</span></a>
+<a name="3407"><span class="lineNum">    3407 </span><span class="lineNoCov">          0 :     if(!functions.finalize) __PLUMED_FPRINTF(stderr,&quot;+++ Pointer to (plumed_)plumedmain_finalize not found +++\n&quot;);</span></a>
+<a name="3408"><span class="lineNum">    3408 </span><span class="lineNoCov">          0 :     f-&gt;create=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3409"><span class="lineNum">    3409 </span><span class="lineNoCov">          0 :     f-&gt;cmd=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3410"><span class="lineNum">    3410 </span><span class="lineNoCov">          0 :     f-&gt;finalize=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3411"><span class="lineNum">    3411 </span><span class="lineNoCov">          0 :     if(table) *table=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3412"><span class="lineNum">    3412 </span>            :   }</a>
+<a name="3413"><span class="lineNum">    3413 </span><span class="lineCov">          9 : }</span></a>
+<a name="3414"><span class="lineNum">    3414 </span>            : __PLUMED_WRAPPER_INTERNALS_END</a>
+<a name="3415"><span class="lineNum">    3415 </span>            : </a>
+<a name="3416"><span class="lineNum">    3416 </span>            : #endif /*}*/</a>
+<a name="3417"><span class="lineNum">    3417 </span>            : </a>
+<a name="3418"><span class="lineNum">    3418 </span>            : </a>
+<a name="3419"><span class="lineNum">    3419 </span>            : #if __PLUMED_WRAPPER_REEXPORT_SYMBOL_TABLE</a>
+<a name="3420"><span class="lineNum">    3420 </span>            : </a>
+<a name="3421"><span class="lineNum">    3421 </span>            : /*</a>
+<a name="3422"><span class="lineNum">    3422 </span>            :   Here is the case where plumed_symbol_table is</a>
+<a name="3423"><span class="lineNum">    3423 </span>            :   visible as extern. We first declare it (together with plumed_symbol_table_init) ...</a>
+<a name="3424"><span class="lineNum">    3424 </span>            : */</a>
+<a name="3425"><span class="lineNum">    3425 </span>            : </a>
+<a name="3426"><span class="lineNum">    3426 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN</a>
+<a name="3427"><span class="lineNum">    3427 </span>            : extern</a>
+<a name="3428"><span class="lineNum">    3428 </span>            : plumed_symbol_table_type plumed_symbol_table;</a>
+<a name="3429"><span class="lineNum">    3429 </span>            : __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="3430"><span class="lineNum">    3430 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN</a>
+<a name="3431"><span class="lineNum">    3431 </span>            : extern</a>
+<a name="3432"><span class="lineNum">    3432 </span>            : void plumed_symbol_table_init(void);</a>
+<a name="3433"><span class="lineNum">    3433 </span>            : __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="3434"><span class="lineNum">    3434 </span>            : </a>
+<a name="3435"><span class="lineNum">    3435 </span>            : /*</a>
+<a name="3436"><span class="lineNum">    3436 </span>            :   ... and then make available a function that returns the address</a>
+<a name="3437"><span class="lineNum">    3437 </span>            :   of the symbol table.</a>
+<a name="3438"><span class="lineNum">    3438 </span>            : */</a>
+<a name="3439"><span class="lineNum">    3439 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3440"><span class="lineNum">    3440 </span><span class="lineCov">     680225 : plumed_symbol_table_type* plumed_symbol_table_reexport() {</span></a>
+<a name="3441"><span class="lineNum">    3441 </span>            :   /* make sure the table is initialized */</a>
+<a name="3442"><span class="lineNum">    3442 </span><span class="lineCov">     680225 :   plumed_symbol_table_init();</span></a>
+<a name="3443"><span class="lineNum">    3443 </span><span class="lineCov">     720962 :   return &amp;plumed_symbol_table;</span></a>
+<a name="3444"><span class="lineNum">    3444 </span>            : }</a>
+<a name="3445"><span class="lineNum">    3445 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3446"><span class="lineNum">    3446 </span>            : </a>
+<a name="3447"><span class="lineNum">    3447 </span>            : #else</a>
+<a name="3448"><span class="lineNum">    3448 </span>            : </a>
+<a name="3449"><span class="lineNum">    3449 </span>            : /*</a>
+<a name="3450"><span class="lineNum">    3450 </span>            :   Here is the case where plumed_symbol_table is not</a>
+<a name="3451"><span class="lineNum">    3451 </span>            :   visible as extern. We thus assume that plumed_symbol_table_reexport is</a>
+<a name="3452"><span class="lineNum">    3452 </span>            :   available.</a>
+<a name="3453"><span class="lineNum">    3453 </span>            : */</a>
+<a name="3454"><span class="lineNum">    3454 </span>            : </a>
+<a name="3455"><span class="lineNum">    3455 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN</a>
+<a name="3456"><span class="lineNum">    3456 </span>            : extern plumed_symbol_table_type* plumed_symbol_table_reexport();</a>
+<a name="3457"><span class="lineNum">    3457 </span>            : __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="3458"><span class="lineNum">    3458 </span>            : #endif</a>
+<a name="3459"><span class="lineNum">    3459 </span>            : </a>
+<a name="3460"><span class="lineNum">    3460 </span>            : </a>
+<a name="3461"><span class="lineNum">    3461 </span>            : /*</a>
+<a name="3462"><span class="lineNum">    3462 </span>            :   Returns the global pointers, either those available at link time or those</a>
+<a name="3463"><span class="lineNum">    3463 </span>            :   found in the library loaded at PLUMED_KERNEL env var.</a>
+<a name="3464"><span class="lineNum">    3464 </span>            :   If plumed_symbol_table_ptr is not NULL, it is used to return a pointer to the symbol table</a>
+<a name="3465"><span class="lineNum">    3465 </span>            :   (if available).</a>
+<a name="3466"><span class="lineNum">    3466 </span>            :   Notice that problems can be detected checking if the functions have a NULL ptr.</a>
+<a name="3467"><span class="lineNum">    3467 </span>            :   On the other hand, the symbol table pointer might be NULL just because the plumed version is &lt;=2.4.</a>
+<a name="3468"><span class="lineNum">    3468 </span>            :   If handle is not NULL, it is used to return a dlopen handle that could be subsequently dlclosed.</a>
+<a name="3469"><span class="lineNum">    3469 </span>            : */</a>
+<a name="3470"><span class="lineNum">    3470 </span>            : __PLUMED_WRAPPER_INTERNALS_BEGIN</a>
+<a name="3471"><span class="lineNum">    3471 </span><span class="lineCov">     715925 : void plumed_retrieve_functions(plumed_plumedmain_function_holder* functions, plumed_symbol_table_type** plumed_symbol_table_ptr,void** handle) {</span></a>
+<a name="3472"><span class="lineNum">    3472 </span>            : #if ! __PLUMED_WRAPPER_LINK_RUNTIME</a>
+<a name="3473"><span class="lineNum">    3473 </span>            :   /*</a>
+<a name="3474"><span class="lineNum">    3474 </span>            :     Real interface, constructed using the symbol table obtained with plumed_symbol_table_reexport.</a>
+<a name="3475"><span class="lineNum">    3475 </span>            :     This makes the symbols hardcoded and independent of a mis-set PLUMED_KERNEL variable.</a>
+<a name="3476"><span class="lineNum">    3476 </span>            :   */</a>
+<a name="3477"><span class="lineNum">    3477 </span><span class="lineCov">     715925 :   plumed_symbol_table_type* ptr=plumed_symbol_table_reexport();</span></a>
+<a name="3478"><span class="lineNum">    3478 </span><span class="lineCov">     723689 :   if(plumed_symbol_table_ptr) *plumed_symbol_table_ptr=ptr;</span></a>
+<a name="3479"><span class="lineNum">    3479 </span><span class="lineCov">     723689 :   if(handle) *handle=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3480"><span class="lineNum">    3480 </span><span class="lineCov">     723689 :   if(functions) *functions=ptr-&gt;functions;</span></a>
+<a name="3481"><span class="lineNum">    3481 </span>            : #elif ! defined(__PLUMED_HAS_DLOPEN)</a>
+<a name="3482"><span class="lineNum">    3482 </span>            :   /*</a>
+<a name="3483"><span class="lineNum">    3483 </span>            :     When dlopen is not available, we hard code them to NULL</a>
+<a name="3484"><span class="lineNum">    3484 </span>            :   */</a>
+<a name="3485"><span class="lineNum">    3485 </span>            :   __PLUMED_FPRINTF(stderr,&quot;+++ PLUMED has been compiled without dlopen and without a static kernel +++\n&quot;);</a>
+<a name="3486"><span class="lineNum">    3486 </span>            :   plumed_plumedmain_function_holder g= {__PLUMED_WRAPPER_CXX_NULLPTR,__PLUMED_WRAPPER_CXX_NULLPTR,__PLUMED_WRAPPER_CXX_NULLPTR};</a>
+<a name="3487"><span class="lineNum">    3487 </span>            :   if(plumed_symbol_table_ptr) *plumed_symbol_table_ptr=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3488"><span class="lineNum">    3488 </span>            :   if(handle) *handle=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3489"><span class="lineNum">    3489 </span>            :   if(functions) *functions=g;</a>
+<a name="3490"><span class="lineNum">    3490 </span>            : #else</a>
+<a name="3491"><span class="lineNum">    3491 </span>            :   /*</a>
+<a name="3492"><span class="lineNum">    3492 </span>            :     On the other hand, for runtime binding, we use dlsym to find the relevant functions.</a>
+<a name="3493"><span class="lineNum">    3493 </span>            :   */</a>
+<a name="3494"><span class="lineNum">    3494 </span>            :   plumed_plumedmain_function_holder g;</a>
+<a name="3495"><span class="lineNum">    3495 </span>            :   /* search is done once and only once */</a>
+<a name="3496"><span class="lineNum">    3496 </span>            :   const char* path;</a>
+<a name="3497"><span class="lineNum">    3497 </span>            :   void* p;</a>
+<a name="3498"><span class="lineNum">    3498 </span>            :   char* debug;</a>
+<a name="3499"><span class="lineNum">    3499 </span>            :   int dlopenmode;</a>
+<a name="3500"><span class="lineNum">    3500 </span>            :   g.create=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3501"><span class="lineNum">    3501 </span>            :   g.cmd=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3502"><span class="lineNum">    3502 </span>            :   g.finalize=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3503"><span class="lineNum">    3503 </span>            :   path=__PLUMED_GETENV(&quot;PLUMED_KERNEL&quot;);</a>
+<a name="3504"><span class="lineNum">    3504 </span>            :   p=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3505"><span class="lineNum">    3505 </span>            :   debug=__PLUMED_GETENV(&quot;PLUMED_LOAD_DEBUG&quot;);</a>
+<a name="3506"><span class="lineNum">    3506 </span>            :   dlopenmode=0;</a>
+<a name="3507"><span class="lineNum">    3507 </span>            :   if(plumed_symbol_table_ptr) *plumed_symbol_table_ptr=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3508"><span class="lineNum">    3508 </span>            :   if(handle) *handle=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3509"><span class="lineNum">    3509 </span>            : #ifdef __PLUMED_DEFAULT_KERNEL</a>
+<a name="3510"><span class="lineNum">    3510 </span>            :   /*</a>
+<a name="3511"><span class="lineNum">    3511 </span>            :     This variable allows a default path for the kernel to be hardcoded.</a>
+<a name="3512"><span class="lineNum">    3512 </span>            :     Can be useful for hardcoding the predefined plumed location</a>
+<a name="3513"><span class="lineNum">    3513 </span>            :     still allowing the user to override this choice setting PLUMED_KERNEL.</a>
+<a name="3514"><span class="lineNum">    3514 </span>            :     The path should be chosen at compile time adding e.g.</a>
+<a name="3515"><span class="lineNum">    3515 </span>            :     -D__PLUMED_DEFAULT_KERNEL=/opt/local/lib/libplumed.dylib</a>
+<a name="3516"><span class="lineNum">    3516 </span>            :   */</a>
+<a name="3517"><span class="lineNum">    3517 </span>            :   /* This is required to add quotes */</a>
+<a name="3518"><span class="lineNum">    3518 </span>            : #define PLUMED_QUOTE_DIRECT(name) #name</a>
+<a name="3519"><span class="lineNum">    3519 </span>            : #define PLUMED_QUOTE(macro) PLUMED_QUOTE_DIRECT(macro)</a>
+<a name="3520"><span class="lineNum">    3520 </span>            :   if(! (path &amp;&amp; (*path) )) path=PLUMED_QUOTE(__PLUMED_DEFAULT_KERNEL);</a>
+<a name="3521"><span class="lineNum">    3521 </span>            : #endif</a>
+<a name="3522"><span class="lineNum">    3522 </span>            :   if(path &amp;&amp; (*path)) {</a>
+<a name="3523"><span class="lineNum">    3523 </span>            :     __PLUMED_FPRINTF(stderr,&quot;+++ Loading the PLUMED kernel runtime +++\n&quot;);</a>
+<a name="3524"><span class="lineNum">    3524 </span>            :     __PLUMED_FPRINTF(stderr,&quot;+++ PLUMED_KERNEL=\&quot;%s\&quot; +++\n&quot;,path);</a>
+<a name="3525"><span class="lineNum">    3525 </span>            :     if(debug) __PLUMED_FPRINTF(stderr,&quot;+++ Loading with mode RTLD_NOW&quot;);</a>
+<a name="3526"><span class="lineNum">    3526 </span>            :     dlopenmode=RTLD_NOW;</a>
+<a name="3527"><span class="lineNum">    3527 </span>            :     if(__PLUMED_GETENV(&quot;PLUMED_LOAD_NAMESPACE&quot;) &amp;&amp; !__PLUMED_WRAPPER_STD strcmp(__PLUMED_GETENV(&quot;PLUMED_LOAD_NAMESPACE&quot;),&quot;LOCAL&quot;)) {</a>
+<a name="3528"><span class="lineNum">    3528 </span>            :       dlopenmode=dlopenmode|RTLD_LOCAL;</a>
+<a name="3529"><span class="lineNum">    3529 </span>            :       if(debug) __PLUMED_FPRINTF(stderr,&quot;|RTLD_LOCAL&quot;);</a>
+<a name="3530"><span class="lineNum">    3530 </span>            :     } else {</a>
+<a name="3531"><span class="lineNum">    3531 </span>            :       dlopenmode=dlopenmode|RTLD_GLOBAL;</a>
+<a name="3532"><span class="lineNum">    3532 </span>            :       if(debug) __PLUMED_FPRINTF(stderr,&quot;|RTLD_GLOBAL&quot;);</a>
+<a name="3533"><span class="lineNum">    3533 </span>            :     }</a>
+<a name="3534"><span class="lineNum">    3534 </span>            : #ifdef RTLD_DEEPBIND</a>
+<a name="3535"><span class="lineNum">    3535 </span>            : #if __PLUMED_WRAPPER_ENABLE_RTLD_DEEPBIND</a>
+<a name="3536"><span class="lineNum">    3536 </span>            :     if(!__PLUMED_GETENV(&quot;PLUMED_LOAD_NODEEPBIND&quot;)) {</a>
+<a name="3537"><span class="lineNum">    3537 </span>            :       dlopenmode=dlopenmode|RTLD_DEEPBIND;</a>
+<a name="3538"><span class="lineNum">    3538 </span>            :       if(debug) __PLUMED_FPRINTF(stderr,&quot;|RTLD_DEEPBIND&quot;);</a>
+<a name="3539"><span class="lineNum">    3539 </span>            :     }</a>
+<a name="3540"><span class="lineNum">    3540 </span>            : #endif</a>
+<a name="3541"><span class="lineNum">    3541 </span>            : #endif</a>
+<a name="3542"><span class="lineNum">    3542 </span>            :     if(debug) __PLUMED_FPRINTF(stderr,&quot; +++\n&quot;);</a>
+<a name="3543"><span class="lineNum">    3543 </span>            :     p=plumed_attempt_dlopen(path,dlopenmode);</a>
+<a name="3544"><span class="lineNum">    3544 </span>            :     if(p) plumed_search_symbols(p,&amp;g,plumed_symbol_table_ptr);</a>
+<a name="3545"><span class="lineNum">    3545 </span>            :   }</a>
+<a name="3546"><span class="lineNum">    3546 </span>            :   if(handle) *handle=p;</a>
+<a name="3547"><span class="lineNum">    3547 </span>            :   if(functions) *functions=g;</a>
+<a name="3548"><span class="lineNum">    3548 </span>            : #endif</a>
+<a name="3549"><span class="lineNum">    3549 </span><span class="lineCov">     723689 : }</span></a>
+<a name="3550"><span class="lineNum">    3550 </span>            : __PLUMED_WRAPPER_INTERNALS_END</a>
+<a name="3551"><span class="lineNum">    3551 </span>            : </a>
+<a name="3552"><span class="lineNum">    3552 </span>            : /**</a>
+<a name="3553"><span class="lineNum">    3553 </span>            :   Implementation.</a>
+<a name="3554"><span class="lineNum">    3554 </span>            :   Small object used to store pointers directly into the plumed object defined in Plumed.h.</a>
+<a name="3555"><span class="lineNum">    3555 </span>            :   This allows avoiding the extra function call to plumed_retrieve_functions at every cmd,</a>
+<a name="3556"><span class="lineNum">    3556 </span>            :   at the cost of an extra indirection.</a>
+<a name="3557"><span class="lineNum">    3557 </span>            : */</a>
+<a name="3558"><span class="lineNum">    3558 </span>            : typedef struct {</a>
+<a name="3559"><span class="lineNum">    3559 </span>            :   /* allows errors with pointers to be found when debugging */</a>
+<a name="3560"><span class="lineNum">    3560 </span>            :   char magic[6];</a>
+<a name="3561"><span class="lineNum">    3561 </span>            :   /* reference count. this is only used with PLUMED&lt;=2.8. Later versions have an internal thread-safe reference counter. */</a>
+<a name="3562"><span class="lineNum">    3562 </span>            :   int refcount;</a>
+<a name="3563"><span class="lineNum">    3563 </span>            :   /* handler to dlopened library. NULL if there was no library opened */</a>
+<a name="3564"><span class="lineNum">    3564 </span>            :   void* dlhandle;</a>
+<a name="3565"><span class="lineNum">    3565 </span>            :   /* non zero if, upon destruction, the library should be dlclosed */</a>
+<a name="3566"><span class="lineNum">    3566 </span>            :   int dlclose;</a>
+<a name="3567"><span class="lineNum">    3567 </span>            :   /* 1 if path to kernel was taken from PLUMED_KERNEL var, 0 otherwise */</a>
+<a name="3568"><span class="lineNum">    3568 </span>            :   int used_plumed_kernel;</a>
+<a name="3569"><span class="lineNum">    3569 </span>            :   /* function pointers */</a>
+<a name="3570"><span class="lineNum">    3570 </span>            :   plumed_plumedmain_function_holder functions;</a>
+<a name="3571"><span class="lineNum">    3571 </span>            :   /* pointer to the symbol table. NULL if kernel &lt;=2.4 */</a>
+<a name="3572"><span class="lineNum">    3572 </span>            :   plumed_symbol_table_type* table;</a>
+<a name="3573"><span class="lineNum">    3573 </span>            :   /* pointer to plumed object */</a>
+<a name="3574"><span class="lineNum">    3574 </span>            :   void* p;</a>
+<a name="3575"><span class="lineNum">    3575 </span>            : } plumed_implementation;</a>
+<a name="3576"><span class="lineNum">    3576 </span>            : </a>
+<a name="3577"><span class="lineNum">    3577 </span>            : __PLUMED_WRAPPER_INTERNALS_BEGIN</a>
+<a name="3578"><span class="lineNum">    3578 </span><span class="lineCov">     737506 : plumed_implementation* plumed_malloc_pimpl() {</span></a>
+<a name="3579"><span class="lineNum">    3579 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3580"><span class="lineNum">    3580 </span>            :   /* allocate space for implementation object. this is free-ed in plumed_finalize(). */</a>
+<a name="3581"><span class="lineNum">    3581 </span><span class="lineCov">     737505 :   pimpl=(plumed_implementation*) plumed_malloc(sizeof(plumed_implementation));</span></a>
+<a name="3582"><span class="lineNum">    3582 </span><span class="lineCov">     732335 :   if(!pimpl) {</span></a>
+<a name="3583"><span class="lineNum">    3583 </span><span class="lineNoCov">          0 :     __PLUMED_FPRINTF(stderr,&quot;+++ Allocation error +++\n&quot;);</span></a>
+<a name="3584"><span class="lineNum">    3584 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_STD abort();</span></a>
+<a name="3585"><span class="lineNum">    3585 </span>            :   }</a>
+<a name="3586"><span class="lineNum">    3586 </span><span class="lineCov">     732335 :   __PLUMED_WRAPPER_STD memcpy(pimpl-&gt;magic,&quot;pLuMEd&quot;,6);</span></a>
+<a name="3587"><span class="lineNum">    3587 </span><span class="lineCov">     732335 :   pimpl-&gt;refcount=1;</span></a>
+<a name="3588"><span class="lineNum">    3588 </span>            : #if __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3589"><span class="lineNum">    3589 </span>            :   __PLUMED_FPRINTF(stderr,&quot;refcount: new at %p\n&quot;,(void*)pimpl);</a>
+<a name="3590"><span class="lineNum">    3590 </span>            : #endif</a>
+<a name="3591"><span class="lineNum">    3591 </span><span class="lineCov">     732335 :   pimpl-&gt;dlhandle=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3592"><span class="lineNum">    3592 </span><span class="lineCov">     732335 :   pimpl-&gt;dlclose=0;</span></a>
+<a name="3593"><span class="lineNum">    3593 </span><span class="lineCov">     732335 :   pimpl-&gt;used_plumed_kernel=0;</span></a>
+<a name="3594"><span class="lineNum">    3594 </span><span class="lineCov">     732335 :   pimpl-&gt;functions.create=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3595"><span class="lineNum">    3595 </span><span class="lineCov">     732335 :   pimpl-&gt;functions.cmd=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3596"><span class="lineNum">    3596 </span><span class="lineCov">     732335 :   pimpl-&gt;functions.finalize=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3597"><span class="lineNum">    3597 </span><span class="lineCov">     732335 :   pimpl-&gt;table=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3598"><span class="lineNum">    3598 </span><span class="lineCov">     732335 :   pimpl-&gt;p=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3599"><span class="lineNum">    3599 </span><span class="lineCov">     732335 :   return pimpl;</span></a>
+<a name="3600"><span class="lineNum">    3600 </span>            : }</a>
+<a name="3601"><span class="lineNum">    3601 </span>            : __PLUMED_WRAPPER_INTERNALS_END</a>
+<a name="3602"><span class="lineNum">    3602 </span>            : </a>
+<a name="3603"><span class="lineNum">    3603 </span>            : #ifndef NDEBUG</a>
+<a name="3604"><span class="lineNum">    3604 </span>            : </a>
+<a name="3605"><span class="lineNum">    3605 </span>            : __PLUMED_WRAPPER_INTERNALS_BEGIN</a>
+<a name="3606"><span class="lineNum">    3606 </span>            : int plumed_check_pimpl(plumed_implementation*pimpl) {</a>
+<a name="3607"><span class="lineNum">    3607 </span>            :   if(!pimpl) return 0;</a>
+<a name="3608"><span class="lineNum">    3608 </span>            :   if(__PLUMED_WRAPPER_STD memcmp(pimpl-&gt;magic,&quot;pLuMEd&quot;,6)) return 0;</a>
+<a name="3609"><span class="lineNum">    3609 </span>            :   return 1;</a>
+<a name="3610"><span class="lineNum">    3610 </span>            : }</a>
+<a name="3611"><span class="lineNum">    3611 </span>            : __PLUMED_WRAPPER_INTERNALS_END</a>
+<a name="3612"><span class="lineNum">    3612 </span>            : #endif</a>
+<a name="3613"><span class="lineNum">    3613 </span>            : </a>
+<a name="3614"><span class="lineNum">    3614 </span>            : /* C wrappers: */</a>
+<a name="3615"><span class="lineNum">    3615 </span>            : </a>
+<a name="3616"><span class="lineNum">    3616 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3617"><span class="lineNum">    3617 </span><span class="lineCov">     739580 : plumed plumed_create(void) {</span></a>
+<a name="3618"><span class="lineNum">    3618 </span>            :   /* returned object */</a>
+<a name="3619"><span class="lineNum">    3619 </span>            :   plumed p;</a>
+<a name="3620"><span class="lineNum">    3620 </span>            :   /* pointer to implementation */</a>
+<a name="3621"><span class="lineNum">    3621 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3622"><span class="lineNum">    3622 </span>            :   /* allocate space for implementation object. this is free-ed in plumed_finalize(). */</a>
+<a name="3623"><span class="lineNum">    3623 </span><span class="lineCov">     739580 :   pimpl=plumed_malloc_pimpl();</span></a>
+<a name="3624"><span class="lineNum">    3624 </span>            :   /* store pointers in pimpl */</a>
+<a name="3625"><span class="lineNum">    3625 </span><span class="lineCov">     729321 :   plumed_retrieve_functions(&amp;pimpl-&gt;functions,&amp;pimpl-&gt;table,&amp;pimpl-&gt;dlhandle);</span></a>
+<a name="3626"><span class="lineNum">    3626 </span>            : #if __PLUMED_WRAPPER_LINK_RUNTIME</a>
+<a name="3627"><span class="lineNum">    3627 </span>            :   /* note if PLUMED_KERNEL variable was used */</a>
+<a name="3628"><span class="lineNum">    3628 </span>            :   pimpl-&gt;used_plumed_kernel=1;</a>
+<a name="3629"><span class="lineNum">    3629 </span>            : #endif</a>
+<a name="3630"><span class="lineNum">    3630 </span>            :   /* note if handle should not be dlclosed */</a>
+<a name="3631"><span class="lineNum">    3631 </span><span class="lineCov">     746711 :   pimpl-&gt;dlclose=1;</span></a>
+<a name="3632"><span class="lineNum">    3632 </span><span class="lineCov">     746711 :   if(__PLUMED_GETENV(&quot;PLUMED_LOAD_DLCLOSE&quot;) &amp;&amp; !__PLUMED_WRAPPER_STD strcmp(__PLUMED_GETENV(&quot;PLUMED_LOAD_DLCLOSE&quot;),&quot;no&quot;)) pimpl-&gt;dlclose=0;</span></a>
+<a name="3633"><span class="lineNum">    3633 </span>            :   /* in case of failure, return */</a>
+<a name="3634"><span class="lineNum">    3634 </span>            :   /* the resulting object should be plumed_finalized, though you cannot use plumed_cmd */</a>
+<a name="3635"><span class="lineNum">    3635 </span><span class="lineCov">     799987 :   if(!pimpl-&gt;functions.create) {</span></a>
+<a name="3636"><span class="lineNum">    3636 </span>            :     /* store pimpl in returned object */</a>
+<a name="3637"><span class="lineNum">    3637 </span>            :     p.p=pimpl;</a>
+<a name="3638"><span class="lineNum">    3638 </span><span class="lineNoCov">          0 :     return p;</span></a>
+<a name="3639"><span class="lineNum">    3639 </span>            :   }</a>
+<a name="3640"><span class="lineNum">    3640 </span>            :   assert(pimpl-&gt;functions.cmd);</a>
+<a name="3641"><span class="lineNum">    3641 </span>            :   assert(pimpl-&gt;functions.finalize);</a>
+<a name="3642"><span class="lineNum">    3642 </span>            :   /* obtain object */</a>
+<a name="3643"><span class="lineNum">    3643 </span><span class="lineCov">     799987 :   pimpl-&gt;p=(*(pimpl-&gt;functions.create))();</span></a>
+<a name="3644"><span class="lineNum">    3644 </span>            :   /* notice: we do not assert pimpl-&gt;p since in principle it might be nullptr */</a>
+<a name="3645"><span class="lineNum">    3645 </span>            :   /* user might identify this using plumed_valid() */</a>
+<a name="3646"><span class="lineNum">    3646 </span>            :   /* store pimpl in returned object */</a>
+<a name="3647"><span class="lineNum">    3647 </span>            :   p.p=pimpl;</a>
+<a name="3648"><span class="lineNum">    3648 </span><span class="lineCov">     781904 :   return p;</span></a>
+<a name="3649"><span class="lineNum">    3649 </span>            : }</a>
+<a name="3650"><span class="lineNum">    3650 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3651"><span class="lineNum">    3651 </span>            : </a>
+<a name="3652"><span class="lineNum">    3652 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3653"><span class="lineNum">    3653 </span><span class="lineCov">          9 : plumed plumed_create_dlopen(const char*path) {</span></a>
+<a name="3654"><span class="lineNum">    3654 </span>            :   int dlopenmode;</a>
+<a name="3655"><span class="lineNum">    3655 </span>            :   /* plumed_create_dlopen always uses RTLD_LOCAL and, when possible, RTLD_DEEPBIND to allow multiple versions */</a>
+<a name="3656"><span class="lineNum">    3656 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="3657"><span class="lineNum">    3657 </span>            :   dlopenmode=RTLD_NOW|RTLD_LOCAL;</a>
+<a name="3658"><span class="lineNum">    3658 </span>            : #ifdef RTLD_DEEPBIND</a>
+<a name="3659"><span class="lineNum">    3659 </span>            : #if __PLUMED_WRAPPER_ENABLE_RTLD_DEEPBIND</a>
+<a name="3660"><span class="lineNum">    3660 </span><span class="lineCov">          9 :   if(!__PLUMED_GETENV(&quot;PLUMED_LOAD_NODEEPBIND&quot;)) dlopenmode=dlopenmode|RTLD_DEEPBIND;</span></a>
+<a name="3661"><span class="lineNum">    3661 </span>            : #endif</a>
+<a name="3662"><span class="lineNum">    3662 </span>            : #endif</a>
+<a name="3663"><span class="lineNum">    3663 </span>            : #else</a>
+<a name="3664"><span class="lineNum">    3664 </span>            :   dlopenmode=0;</a>
+<a name="3665"><span class="lineNum">    3665 </span>            : #endif</a>
+<a name="3666"><span class="lineNum">    3666 </span><span class="lineCov">          9 :   return plumed_create_dlopen2(path,dlopenmode);</span></a>
+<a name="3667"><span class="lineNum">    3667 </span>            : }</a>
+<a name="3668"><span class="lineNum">    3668 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3669"><span class="lineNum">    3669 </span>            : </a>
+<a name="3670"><span class="lineNum">    3670 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3671"><span class="lineNum">    3671 </span><span class="lineCov">          9 : plumed plumed_create_dlsym(void* dlhandle) {</span></a>
+<a name="3672"><span class="lineNum">    3672 </span>            :   /* returned object */</a>
+<a name="3673"><span class="lineNum">    3673 </span>            :   plumed p;</a>
+<a name="3674"><span class="lineNum">    3674 </span>            :   /* pointer to implementation */</a>
+<a name="3675"><span class="lineNum">    3675 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3676"><span class="lineNum">    3676 </span>            :   /* allocate space for implementation object. this is free-ed in plumed_finalize(). */</a>
+<a name="3677"><span class="lineNum">    3677 </span><span class="lineCov">          9 :   pimpl=plumed_malloc_pimpl();</span></a>
+<a name="3678"><span class="lineNum">    3678 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="3679"><span class="lineNum">    3679 </span><span class="lineCov">          9 :   pimpl-&gt;dlhandle=dlhandle;</span></a>
+<a name="3680"><span class="lineNum">    3680 </span><span class="lineCov">          9 :   plumed_search_symbols(pimpl-&gt;dlhandle,&amp;pimpl-&gt;functions,&amp;pimpl-&gt;table);</span></a>
+<a name="3681"><span class="lineNum">    3681 </span>            : #endif</a>
+<a name="3682"><span class="lineNum">    3682 </span><span class="lineCov">          9 :   if(!pimpl-&gt;functions.create) {</span></a>
+<a name="3683"><span class="lineNum">    3683 </span>            :     p.p=pimpl;</a>
+<a name="3684"><span class="lineNum">    3684 </span><span class="lineNoCov">          0 :     return p;</span></a>
+<a name="3685"><span class="lineNum">    3685 </span>            :   }</a>
+<a name="3686"><span class="lineNum">    3686 </span>            :   assert(pimpl-&gt;functions.cmd);</a>
+<a name="3687"><span class="lineNum">    3687 </span>            :   assert(pimpl-&gt;functions.finalize);</a>
+<a name="3688"><span class="lineNum">    3688 </span>            :   /* obtain object */</a>
+<a name="3689"><span class="lineNum">    3689 </span><span class="lineCov">          9 :   pimpl-&gt;p=(*(pimpl-&gt;functions.create))();</span></a>
+<a name="3690"><span class="lineNum">    3690 </span>            :   /* notice: we do not assert pimpl-&gt;p since in principle it might be nullptr */</a>
+<a name="3691"><span class="lineNum">    3691 </span>            :   /* user might identify this using plumed_valid() */</a>
+<a name="3692"><span class="lineNum">    3692 </span>            :   /* store pimpl in returned object */</a>
+<a name="3693"><span class="lineNum">    3693 </span>            :   p.p=pimpl;</a>
+<a name="3694"><span class="lineNum">    3694 </span><span class="lineCov">          9 :   return p;</span></a>
+<a name="3695"><span class="lineNum">    3695 </span>            : }</a>
+<a name="3696"><span class="lineNum">    3696 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3697"><span class="lineNum">    3697 </span>            : </a>
+<a name="3698"><span class="lineNum">    3698 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3699"><span class="lineNum">    3699 </span><span class="lineCov">          9 : plumed plumed_create_dlopen2(const char*path,int mode) {</span></a>
+<a name="3700"><span class="lineNum">    3700 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="3701"><span class="lineNum">    3701 </span>            :   /* returned object */</a>
+<a name="3702"><span class="lineNum">    3702 </span>            :   plumed p;</a>
+<a name="3703"><span class="lineNum">    3703 </span>            :   /* pointer to implementation */</a>
+<a name="3704"><span class="lineNum">    3704 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3705"><span class="lineNum">    3705 </span>            :   /* handler */</a>
+<a name="3706"><span class="lineNum">    3706 </span>            :   void* dlhandle;</a>
+<a name="3707"><span class="lineNum">    3707 </span>            :   dlhandle=__PLUMED_WRAPPER_CXX_NULLPTR;</a>
+<a name="3708"><span class="lineNum">    3708 </span><span class="lineCov">          9 :   if(path) dlhandle=plumed_attempt_dlopen(path,mode);</span></a>
+<a name="3709"><span class="lineNum">    3709 </span>            :   /* a NULL handle implies the file could not be loaded */</a>
+<a name="3710"><span class="lineNum">    3710 </span><span class="lineCov">          9 :   if(dlhandle) {</span></a>
+<a name="3711"><span class="lineNum">    3711 </span><span class="lineCov">          9 :     p=plumed_create_dlsym(dlhandle);</span></a>
+<a name="3712"><span class="lineNum">    3712 </span>            :     /* obtain pimpl */</a>
+<a name="3713"><span class="lineNum">    3713 </span><span class="lineCov">          9 :     pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3714"><span class="lineNum">    3714 </span>            :     /* make sure the handler is closed when plumed is finalized */</a>
+<a name="3715"><span class="lineNum">    3715 </span><span class="lineCov">          9 :     pimpl-&gt;dlclose=1;</span></a>
+<a name="3716"><span class="lineNum">    3716 </span><span class="lineCov">          9 :     return p;</span></a>
+<a name="3717"><span class="lineNum">    3717 </span>            :   }</a>
+<a name="3718"><span class="lineNum">    3718 </span>            : #else</a>
+<a name="3719"><span class="lineNum">    3719 </span>            :   (void) path;</a>
+<a name="3720"><span class="lineNum">    3720 </span>            :   (void) mode;</a>
+<a name="3721"><span class="lineNum">    3721 </span>            : #endif</a>
+<a name="3722"><span class="lineNum">    3722 </span><span class="lineNoCov">          0 :   return plumed_create_invalid();</span></a>
+<a name="3723"><span class="lineNum">    3723 </span>            : }</a>
+<a name="3724"><span class="lineNum">    3724 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3725"><span class="lineNum">    3725 </span>            : </a>
+<a name="3726"><span class="lineNum">    3726 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3727"><span class="lineNum">    3727 </span><span class="lineCov">    7597824 : plumed plumed_create_reference(plumed p) {</span></a>
+<a name="3728"><span class="lineNum">    3728 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3729"><span class="lineNum">    3729 </span>            :   /* obtain pimpl */</a>
+<a name="3730"><span class="lineNum">    3730 </span><span class="lineCov">    7597824 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3731"><span class="lineNum">    3731 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3732"><span class="lineNum">    3732 </span>            :   /* increase reference count */</a>
+<a name="3733"><span class="lineNum">    3733 </span>            :   /* with PLUMED &gt; 2.8, we can use an internal reference counter which is thread safe */</a>
+<a name="3734"><span class="lineNum">    3734 </span><span class="lineCov">    7597824 :   if(pimpl-&gt;p &amp;&amp; pimpl-&gt;table &amp;&amp; pimpl-&gt;table-&gt;version&gt;3) {</span></a>
+<a name="3735"><span class="lineNum">    3735 </span><span class="lineCov">    7524157 :     pimpl-&gt;table-&gt;create_reference(pimpl-&gt;p);</span></a>
+<a name="3736"><span class="lineNum">    3736 </span>            :   } else {</a>
+<a name="3737"><span class="lineNum">    3737 </span><span class="lineCov">      73667 :     pimpl-&gt;refcount++;</span></a>
+<a name="3738"><span class="lineNum">    3738 </span>            :   }</a>
+<a name="3739"><span class="lineNum">    3739 </span>            : #if __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3740"><span class="lineNum">    3740 </span>            :   __PLUMED_FPRINTF(stderr,&quot;refcount: increase at %p\n&quot;,(void*)pimpl);</a>
+<a name="3741"><span class="lineNum">    3741 </span>            : #endif</a>
+<a name="3742"><span class="lineNum">    3742 </span><span class="lineCov">    7645629 :   return p;</span></a>
+<a name="3743"><span class="lineNum">    3743 </span>            : }</a>
+<a name="3744"><span class="lineNum">    3744 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3745"><span class="lineNum">    3745 </span>            : </a>
+<a name="3746"><span class="lineNum">    3746 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3747"><span class="lineNum">    3747 </span><span class="lineCov">          2 : plumed plumed_create_reference_v(void*v) {</span></a>
+<a name="3748"><span class="lineNum">    3748 </span><span class="lineCov">          2 :   return plumed_create_reference(plumed_v2c(v));</span></a>
+<a name="3749"><span class="lineNum">    3749 </span>            : }</a>
+<a name="3750"><span class="lineNum">    3750 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3751"><span class="lineNum">    3751 </span>            : </a>
+<a name="3752"><span class="lineNum">    3752 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3753"><span class="lineNum">    3753 </span><span class="lineCov">          8 : plumed plumed_create_reference_f(const char*f) {</span></a>
+<a name="3754"><span class="lineNum">    3754 </span><span class="lineCov">          8 :   return plumed_create_reference(plumed_f2c(f));</span></a>
+<a name="3755"><span class="lineNum">    3755 </span>            : }</a>
+<a name="3756"><span class="lineNum">    3756 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3757"><span class="lineNum">    3757 </span>            : </a>
+<a name="3758"><span class="lineNum">    3758 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3759"><span class="lineNum">    3759 </span><span class="lineCov">          2 : plumed plumed_create_invalid() {</span></a>
+<a name="3760"><span class="lineNum">    3760 </span>            :   plumed p;</a>
+<a name="3761"><span class="lineNum">    3761 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3762"><span class="lineNum">    3762 </span><span class="lineCov">          2 :   pimpl=plumed_malloc_pimpl();</span></a>
+<a name="3763"><span class="lineNum">    3763 </span>            :   p.p=pimpl;</a>
+<a name="3764"><span class="lineNum">    3764 </span><span class="lineCov">          2 :   return p;</span></a>
+<a name="3765"><span class="lineNum">    3765 </span>            : }</a>
+<a name="3766"><span class="lineNum">    3766 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3767"><span class="lineNum">    3767 </span>            : </a>
+<a name="3768"><span class="lineNum">    3768 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3769"><span class="lineNum">    3769 </span><span class="lineCov">        357 : void plumed_cmd(plumed p,const char*key,const void*val) {</span></a>
+<a name="3770"><span class="lineNum">    3770 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3771"><span class="lineNum">    3771 </span>            :   /* obtain pimpl */</a>
+<a name="3772"><span class="lineNum">    3772 </span><span class="lineCov">        357 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3773"><span class="lineNum">    3773 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3774"><span class="lineNum">    3774 </span><span class="lineCov">        357 :   if(!pimpl-&gt;p) {</span></a>
+<a name="3775"><span class="lineNum">    3775 </span><span class="lineNoCov">          0 :     __PLUMED_FPRINTF(stderr,&quot;+++ ERROR: You are trying to use an invalid plumed object. +++\n&quot;);</span></a>
+<a name="3776"><span class="lineNum">    3776 </span><span class="lineNoCov">          0 :     if(pimpl-&gt;used_plumed_kernel) __PLUMED_FPRINTF(stderr,&quot;+++ Check your PLUMED_KERNEL environment variable. +++\n&quot;);</span></a>
+<a name="3777"><span class="lineNum">    3777 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_STD abort();</span></a>
+<a name="3778"><span class="lineNum">    3778 </span>            :   }</a>
+<a name="3779"><span class="lineNum">    3779 </span>            :   assert(pimpl-&gt;functions.create);</a>
+<a name="3780"><span class="lineNum">    3780 </span>            :   assert(pimpl-&gt;functions.cmd);</a>
+<a name="3781"><span class="lineNum">    3781 </span>            :   assert(pimpl-&gt;functions.finalize);</a>
+<a name="3782"><span class="lineNum">    3782 </span>            :   /* execute */</a>
+<a name="3783"><span class="lineNum">    3783 </span><span class="lineCov">        357 :   (*(pimpl-&gt;functions.cmd))(pimpl-&gt;p,key,val);</span></a>
+<a name="3784"><span class="lineNum">    3784 </span><span class="lineCov">        357 : }</span></a>
+<a name="3785"><span class="lineNum">    3785 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3786"><span class="lineNum">    3786 </span>            : </a>
+<a name="3787"><span class="lineNum">    3787 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3788"><span class="lineNum">    3788 </span><span class="lineCov">      14296 : void plumed_cmd_safe_nothrow(plumed p,const char*key,plumed_safeptr safe,plumed_nothrow_handler nothrow) {</span></a>
+<a name="3789"><span class="lineNum">    3789 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3790"><span class="lineNum">    3790 </span>            :   /* This is to allow caller to use a null handler to imply that handling is not done */</a>
+<a name="3791"><span class="lineNum">    3791 </span><span class="lineCov">      14296 :   if(!nothrow.handler) {</span></a>
+<a name="3792"><span class="lineNum">    3792 </span><span class="lineCov">         37 :     plumed_cmd_safe(p,key,safe);</span></a>
+<a name="3793"><span class="lineNum">    3793 </span><span class="lineCov">         37 :     return;</span></a>
+<a name="3794"><span class="lineNum">    3794 </span>            :   }</a>
+<a name="3795"><span class="lineNum">    3795 </span>            :   /* obtain pimpl */</a>
+<a name="3796"><span class="lineNum">    3796 </span><span class="lineCov">      14259 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3797"><span class="lineNum">    3797 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3798"><span class="lineNum">    3798 </span><span class="lineCov">      14259 :   if(!pimpl-&gt;p) {</span></a>
+<a name="3799"><span class="lineNum">    3799 </span><span class="lineNoCov">          0 :     if(pimpl-&gt;used_plumed_kernel) {</span></a>
+<a name="3800"><span class="lineNum">    3800 </span><span class="lineNoCov">          0 :       nothrow.handler(nothrow.ptr,1,&quot;You are trying to use plumed, but it is not available.\nCheck your PLUMED_KERNEL environment variable.&quot;,__PLUMED_WRAPPER_CXX_NULLPTR);</span></a>
+<a name="3801"><span class="lineNum">    3801 </span>            :     } else {</a>
+<a name="3802"><span class="lineNum">    3802 </span><span class="lineNoCov">          0 :       nothrow.handler(nothrow.ptr,1,&quot;You are trying to use plumed, but it is not available.&quot;,__PLUMED_WRAPPER_CXX_NULLPTR);</span></a>
+<a name="3803"><span class="lineNum">    3803 </span>            :     }</a>
+<a name="3804"><span class="lineNum">    3804 </span><span class="lineNoCov">          0 :     return;</span></a>
+<a name="3805"><span class="lineNum">    3805 </span>            :   }</a>
+<a name="3806"><span class="lineNum">    3806 </span>            :   assert(pimpl-&gt;functions.create);</a>
+<a name="3807"><span class="lineNum">    3807 </span>            :   assert(pimpl-&gt;functions.cmd);</a>
+<a name="3808"><span class="lineNum">    3808 </span>            :   assert(pimpl-&gt;functions.finalize);</a>
+<a name="3809"><span class="lineNum">    3809 </span>            :   /* execute */</a>
+<a name="3810"><span class="lineNum">    3810 </span><span class="lineCov">      14259 :   if(pimpl-&gt;table &amp;&amp; pimpl-&gt;table-&gt;version&gt;2) (*(pimpl-&gt;table-&gt;cmd_safe_nothrow))(pimpl-&gt;p,key,safe,nothrow);</span></a>
+<a name="3811"><span class="lineNum">    3811 </span><span class="lineNoCov">          0 :   else if(pimpl-&gt;table &amp;&amp; pimpl-&gt;table-&gt;version&gt;1) (*(pimpl-&gt;table-&gt;cmd_nothrow))(pimpl-&gt;p,key,safe.ptr,nothrow);</span></a>
+<a name="3812"><span class="lineNum">    3812 </span><span class="lineNoCov">          0 :   else (*(pimpl-&gt;functions.cmd))(pimpl-&gt;p,key,safe.ptr);</span></a>
+<a name="3813"><span class="lineNum">    3813 </span>            : }</a>
+<a name="3814"><span class="lineNum">    3814 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3815"><span class="lineNum">    3815 </span>            : </a>
+<a name="3816"><span class="lineNum">    3816 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3817"><span class="lineNum">    3817 </span><span class="lineNoCov">          0 : void plumed_cmd_nothrow(plumed p,const char*key,const void*val,plumed_nothrow_handler nothrow) {</span></a>
+<a name="3818"><span class="lineNum">    3818 </span>            :   plumed_safeptr safe;</a>
+<a name="3819"><span class="lineNum">    3819 </span><span class="lineNoCov">          0 :   safe.ptr=val;</span></a>
+<a name="3820"><span class="lineNum">    3820 </span><span class="lineNoCov">          0 :   safe.flags=0;</span></a>
+<a name="3821"><span class="lineNum">    3821 </span><span class="lineNoCov">          0 :   safe.nelem=0;</span></a>
+<a name="3822"><span class="lineNum">    3822 </span><span class="lineNoCov">          0 :   safe.shape=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3823"><span class="lineNum">    3823 </span><span class="lineNoCov">          0 :   safe.opt=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3824"><span class="lineNum">    3824 </span><span class="lineNoCov">          0 :   plumed_cmd_safe_nothrow(p,key,safe,nothrow);</span></a>
+<a name="3825"><span class="lineNum">    3825 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="3826"><span class="lineNum">    3826 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3827"><span class="lineNum">    3827 </span>            : </a>
+<a name="3828"><span class="lineNum">    3828 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3829"><span class="lineNum">    3829 </span><span class="lineCov">         95 : void plumed_cmd_safe(plumed p,const char*key,plumed_safeptr safe) {</span></a>
+<a name="3830"><span class="lineNum">    3830 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3831"><span class="lineNum">    3831 </span>            :   /* obtain pimpl */</a>
+<a name="3832"><span class="lineNum">    3832 </span><span class="lineCov">         95 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3833"><span class="lineNum">    3833 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3834"><span class="lineNum">    3834 </span><span class="lineCov">         95 :   if(!pimpl-&gt;p) {</span></a>
+<a name="3835"><span class="lineNum">    3835 </span><span class="lineNoCov">          0 :     __PLUMED_FPRINTF(stderr,&quot;+++ ERROR: You are trying to use an invalid plumed object. +++\n&quot;);</span></a>
+<a name="3836"><span class="lineNum">    3836 </span><span class="lineNoCov">          0 :     if(pimpl-&gt;used_plumed_kernel) __PLUMED_FPRINTF(stderr,&quot;+++ Check your PLUMED_KERNEL environment variable. +++\n&quot;);</span></a>
+<a name="3837"><span class="lineNum">    3837 </span><span class="lineNoCov">          0 :     __PLUMED_WRAPPER_STD abort();</span></a>
+<a name="3838"><span class="lineNum">    3838 </span>            :   }</a>
+<a name="3839"><span class="lineNum">    3839 </span>            :   assert(pimpl-&gt;functions.create);</a>
+<a name="3840"><span class="lineNum">    3840 </span>            :   assert(pimpl-&gt;functions.cmd);</a>
+<a name="3841"><span class="lineNum">    3841 </span>            :   assert(pimpl-&gt;functions.finalize);</a>
+<a name="3842"><span class="lineNum">    3842 </span>            :   /* execute */</a>
+<a name="3843"><span class="lineNum">    3843 </span><span class="lineCov">         95 :   if(pimpl-&gt;table &amp;&amp; pimpl-&gt;table-&gt;version&gt;2) (*(pimpl-&gt;table-&gt;cmd_safe))(pimpl-&gt;p,key,safe);</span></a>
+<a name="3844"><span class="lineNum">    3844 </span><span class="lineNoCov">          0 :   else (*(pimpl-&gt;functions.cmd))(pimpl-&gt;p,key,safe.ptr);</span></a>
+<a name="3845"><span class="lineNum">    3845 </span><span class="lineCov">         95 : }</span></a>
+<a name="3846"><span class="lineNum">    3846 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3847"><span class="lineNum">    3847 </span>            : </a>
+<a name="3848"><span class="lineNum">    3848 </span>            : </a>
+<a name="3849"><span class="lineNum">    3849 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3850"><span class="lineNum">    3850 </span><span class="lineCov">    8367497 : void plumed_finalize(plumed p) {</span></a>
+<a name="3851"><span class="lineNum">    3851 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3852"><span class="lineNum">    3852 </span>            :   /* obtain pimpl */</a>
+<a name="3853"><span class="lineNum">    3853 </span><span class="lineCov">    8367497 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3854"><span class="lineNum">    3854 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3855"><span class="lineNum">    3855 </span>            : #if __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3856"><span class="lineNum">    3856 </span>            :   __PLUMED_FPRINTF(stderr,&quot;refcount: decrease at %p\n&quot;,(void*)pimpl);</a>
+<a name="3857"><span class="lineNum">    3857 </span>            : #endif</a>
+<a name="3858"><span class="lineNum">    3858 </span>            :   /* with PLUMED &gt; 2.8, we can use an internal reference counter which is thread safe */</a>
+<a name="3859"><span class="lineNum">    3859 </span><span class="lineCov">    8367497 :   if(pimpl-&gt;p &amp;&amp; pimpl-&gt;table &amp;&amp; pimpl-&gt;table-&gt;version&gt;3) {</span></a>
+<a name="3860"><span class="lineNum">    3860 </span><span class="lineCov">    8331472 :     if(pimpl-&gt;table-&gt;delete_reference(pimpl-&gt;p)&gt;0) return;</span></a>
+<a name="3861"><span class="lineNum">    3861 </span>            :   } else {</a>
+<a name="3862"><span class="lineNum">    3862 </span><span class="lineCov">      36025 :     if(--pimpl-&gt;refcount&gt;0) return;</span></a>
+<a name="3863"><span class="lineNum">    3863 </span>            :   }</a>
+<a name="3864"><span class="lineNum">    3864 </span>            :   /* to allow finalizing an invalid plumed object, we only call</a>
+<a name="3865"><span class="lineNum">    3865 </span>            :      finalize if the object is valid */</a>
+<a name="3866"><span class="lineNum">    3866 </span><span class="lineCov">     777275 :   if(pimpl-&gt;p) {</span></a>
+<a name="3867"><span class="lineNum">    3867 </span>            :     assert(pimpl-&gt;functions.create);</a>
+<a name="3868"><span class="lineNum">    3868 </span>            :     assert(pimpl-&gt;functions.cmd);</a>
+<a name="3869"><span class="lineNum">    3869 </span>            :     assert(pimpl-&gt;functions.finalize);</a>
+<a name="3870"><span class="lineNum">    3870 </span>            :     /* finalize */</a>
+<a name="3871"><span class="lineNum">    3871 </span><span class="lineCov">     777273 :     (*(pimpl-&gt;functions.finalize))(pimpl-&gt;p);</span></a>
+<a name="3872"><span class="lineNum">    3872 </span>            :   }</a>
+<a name="3873"><span class="lineNum">    3873 </span>            : #ifdef __PLUMED_HAS_DLOPEN</a>
+<a name="3874"><span class="lineNum">    3874 </span>            :   /* dlclose library */</a>
+<a name="3875"><span class="lineNum">    3875 </span><span class="lineCov">     761329 :   if(pimpl-&gt;dlhandle &amp;&amp; pimpl-&gt;dlclose) {</span></a>
+<a name="3876"><span class="lineNum">    3876 </span><span class="lineCov">          9 :     if(__PLUMED_GETENV(&quot;PLUMED_LOAD_DEBUG&quot;)) __PLUMED_FPRINTF(stderr,&quot;+++ Unloading library\n&quot;);</span></a>
+<a name="3877"><span class="lineNum">    3877 </span><span class="lineCov">          9 :     dlclose(pimpl-&gt;dlhandle);</span></a>
+<a name="3878"><span class="lineNum">    3878 </span>            :   }</a>
+<a name="3879"><span class="lineNum">    3879 </span>            : #endif</a>
+<a name="3880"><span class="lineNum">    3880 </span>            : #if __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3881"><span class="lineNum">    3881 </span>            :   __PLUMED_FPRINTF(stderr,&quot;refcount: delete at %p\n&quot;,(void*)pimpl);</a>
+<a name="3882"><span class="lineNum">    3882 </span>            : #endif</a>
+<a name="3883"><span class="lineNum">    3883 </span>            :   /* free pimpl space */</a>
+<a name="3884"><span class="lineNum">    3884 </span><span class="lineCov">     761328 :   plumed_free(pimpl);</span></a>
+<a name="3885"><span class="lineNum">    3885 </span>            : }</a>
+<a name="3886"><span class="lineNum">    3886 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3887"><span class="lineNum">    3887 </span>            : </a>
+<a name="3888"><span class="lineNum">    3888 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3889"><span class="lineNum">    3889 </span><span class="lineCov">         23 : int plumed_valid(plumed p) {</span></a>
+<a name="3890"><span class="lineNum">    3890 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3891"><span class="lineNum">    3891 </span>            :   /* obtain pimpl */</a>
+<a name="3892"><span class="lineNum">    3892 </span><span class="lineCov">         23 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3893"><span class="lineNum">    3893 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3894"><span class="lineNum">    3894 </span><span class="lineCov">         24 :   if(pimpl-&gt;p) return 1;</span></a>
+<a name="3895"><span class="lineNum">    3895 </span><span class="lineCov">          2 :   else return 0;</span></a>
+<a name="3896"><span class="lineNum">    3896 </span>            : }</a>
+<a name="3897"><span class="lineNum">    3897 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3898"><span class="lineNum">    3898 </span>            : </a>
+<a name="3899"><span class="lineNum">    3899 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3900"><span class="lineNum">    3900 </span><span class="lineCov">         42 : int plumed_use_count(plumed p) {</span></a>
+<a name="3901"><span class="lineNum">    3901 </span>            :   plumed_implementation* pimpl;</a>
+<a name="3902"><span class="lineNum">    3902 </span>            :   /* obtain pimpl */</a>
+<a name="3903"><span class="lineNum">    3903 </span><span class="lineCov">         42 :   pimpl=(plumed_implementation*) p.p;</span></a>
+<a name="3904"><span class="lineNum">    3904 </span>            :   assert(plumed_check_pimpl(pimpl));</a>
+<a name="3905"><span class="lineNum">    3905 </span>            :   /* with PLUMED &gt; 2.8, we can use an internal reference counter which is thread safe */</a>
+<a name="3906"><span class="lineNum">    3906 </span><span class="lineCov">         42 :   if(pimpl-&gt;p &amp;&amp; pimpl-&gt;table &amp;&amp; pimpl-&gt;table-&gt;version&gt;3) {</span></a>
+<a name="3907"><span class="lineNum">    3907 </span><span class="lineCov">         42 :     return pimpl-&gt;table-&gt;use_count(pimpl-&gt;p);</span></a>
+<a name="3908"><span class="lineNum">    3908 </span>            :   } else {</a>
+<a name="3909"><span class="lineNum">    3909 </span><span class="lineNoCov">          0 :     return pimpl-&gt;refcount;</span></a>
+<a name="3910"><span class="lineNum">    3910 </span>            :   }</a>
+<a name="3911"><span class="lineNum">    3911 </span>            : }</a>
+<a name="3912"><span class="lineNum">    3912 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3913"><span class="lineNum">    3913 </span>            : </a>
+<a name="3914"><span class="lineNum">    3914 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3915"><span class="lineNum">    3915 </span><span class="lineCov">          9 : int plumed_installed(void) {</span></a>
+<a name="3916"><span class="lineNum">    3916 </span>            :   plumed p;</a>
+<a name="3917"><span class="lineNum">    3917 </span>            :   int result;</a>
+<a name="3918"><span class="lineNum">    3918 </span><span class="lineCov">          9 :   p=plumed_create();</span></a>
+<a name="3919"><span class="lineNum">    3919 </span><span class="lineCov">          9 :   result=plumed_valid(p);</span></a>
+<a name="3920"><span class="lineNum">    3920 </span><span class="lineCov">          9 :   plumed_finalize(p);</span></a>
+<a name="3921"><span class="lineNum">    3921 </span><span class="lineCov">          9 :   return result;</span></a>
+<a name="3922"><span class="lineNum">    3922 </span>            : }</a>
+<a name="3923"><span class="lineNum">    3923 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3924"><span class="lineNum">    3924 </span>            : </a>
+<a name="3925"><span class="lineNum">    3925 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3926"><span class="lineNum">    3926 </span><span class="lineCov">     736225 : void* plumed_malloc(__PLUMED_WRAPPER_STD size_t size) {</span></a>
+<a name="3927"><span class="lineNum">    3927 </span>            :   void* ptr;</a>
+<a name="3928"><span class="lineNum">    3928 </span><span class="lineCov">     736226 :   ptr=__PLUMED_WRAPPER_STD malloc(size);</span></a>
+<a name="3929"><span class="lineNum">    3929 </span>            : #if __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3930"><span class="lineNum">    3930 </span>            :   if(ptr) fprintf(stderr,&quot;plumed_malloc: %p\n&quot;,ptr);</a>
+<a name="3931"><span class="lineNum">    3931 </span>            : #endif</a>
+<a name="3932"><span class="lineNum">    3932 </span><span class="lineCov">     736225 :   return ptr;</span></a>
+<a name="3933"><span class="lineNum">    3933 </span>            : }</a>
+<a name="3934"><span class="lineNum">    3934 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3935"><span class="lineNum">    3935 </span>            : </a>
+<a name="3936"><span class="lineNum">    3936 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3937"><span class="lineNum">    3937 </span><span class="lineCov">     749031 : void plumed_free(void* ptr) {</span></a>
+<a name="3938"><span class="lineNum">    3938 </span><span class="lineCov">     749031 :   __PLUMED_WRAPPER_STD free(ptr);</span></a>
+<a name="3939"><span class="lineNum">    3939 </span>            : #if __PLUMED_WRAPPER_DEBUG_REFCOUNT</a>
+<a name="3940"><span class="lineNum">    3940 </span>            :   fprintf(stderr,&quot;plumed_free: %p\n&quot;,ptr);</a>
+<a name="3941"><span class="lineNum">    3941 </span>            : #endif</a>
+<a name="3942"><span class="lineNum">    3942 </span><span class="lineCov">     749032 : }</span></a>
+<a name="3943"><span class="lineNum">    3943 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="3944"><span class="lineNum">    3944 </span>            : </a>
+<a name="3945"><span class="lineNum">    3945 </span>            : #if __PLUMED_WRAPPER_GLOBAL /*{*/</a>
+<a name="3946"><span class="lineNum">    3946 </span>            : </a>
+<a name="3947"><span class="lineNum">    3947 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN</a>
+<a name="3948"><span class="lineNum">    3948 </span>            : </a>
+<a name="3949"><span class="lineNum">    3949 </span>            : /* we declare a Plumed_g_main object here, in such a way that it is always available */</a>
+<a name="3950"><span class="lineNum">    3950 </span>            : </a>
+<a name="3951"><span class="lineNum">    3951 </span>            : static plumed plumed_gmain= {__PLUMED_WRAPPER_CXX_NULLPTR};</a>
+<a name="3952"><span class="lineNum">    3952 </span>            : </a>
+<a name="3953"><span class="lineNum">    3953 </span><span class="lineCov">         41 : plumed plumed_global(void) {</span></a>
+<a name="3954"><span class="lineNum">    3954 </span><span class="lineCov">         41 :   return plumed_gmain;</span></a>
+<a name="3955"><span class="lineNum">    3955 </span>            : }</a>
+<a name="3956"><span class="lineNum">    3956 </span>            : </a>
+<a name="3957"><span class="lineNum">    3957 </span><span class="lineCov">         22 : void plumed_gcreate(void) {</span></a>
+<a name="3958"><span class="lineNum">    3958 </span>            :   /* should be created once */</a>
+<a name="3959"><span class="lineNum">    3959 </span>            :   assert(plumed_gmain.p==__PLUMED_WRAPPER_CXX_NULLPTR);</a>
+<a name="3960"><span class="lineNum">    3960 </span><span class="lineCov">         22 :   plumed_gmain=plumed_create();</span></a>
+<a name="3961"><span class="lineNum">    3961 </span><span class="lineCov">         22 : }</span></a>
+<a name="3962"><span class="lineNum">    3962 </span>            : </a>
+<a name="3963"><span class="lineNum">    3963 </span><span class="lineCov">         78 : void plumed_gcmd(const char*key,const void*val) {</span></a>
+<a name="3964"><span class="lineNum">    3964 </span><span class="lineCov">         78 :   plumed_cmd(plumed_gmain,key,val);</span></a>
+<a name="3965"><span class="lineNum">    3965 </span><span class="lineCov">         78 : }</span></a>
+<a name="3966"><span class="lineNum">    3966 </span>            : </a>
+<a name="3967"><span class="lineNum">    3967 </span>            : /* cppcheck-suppress passedByValue */</a>
+<a name="3968"><span class="lineNum">    3968 </span><span class="lineNoCov">          0 : void plumed_gcmd_safe(const char*key,plumed_safeptr safe) {</span></a>
+<a name="3969"><span class="lineNum">    3969 </span><span class="lineNoCov">          0 :   plumed_cmd_safe(plumed_gmain,key,safe);</span></a>
+<a name="3970"><span class="lineNum">    3970 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="3971"><span class="lineNum">    3971 </span>            : </a>
+<a name="3972"><span class="lineNum">    3972 </span><span class="lineCov">         22 : void plumed_gfinalize(void) {</span></a>
+<a name="3973"><span class="lineNum">    3973 </span><span class="lineCov">         22 :   plumed_finalize(plumed_gmain);</span></a>
+<a name="3974"><span class="lineNum">    3974 </span><span class="lineCov">         22 :   plumed_gmain.p=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="3975"><span class="lineNum">    3975 </span><span class="lineCov">         22 : }</span></a>
+<a name="3976"><span class="lineNum">    3976 </span>            : </a>
+<a name="3977"><span class="lineNum">    3977 </span><span class="lineCov">         24 : int plumed_ginitialized(void) {</span></a>
+<a name="3978"><span class="lineNum">    3978 </span><span class="lineCov">         24 :   if(plumed_gmain.p) return 1;</span></a>
+<a name="3979"><span class="lineNum">    3979 </span><span class="lineCov">         16 :   else        return 0;</span></a>
+<a name="3980"><span class="lineNum">    3980 </span>            : }</a>
+<a name="3981"><span class="lineNum">    3981 </span>            : </a>
+<a name="3982"><span class="lineNum">    3982 </span><span class="lineCov">          8 : int plumed_gvalid() {</span></a>
+<a name="3983"><span class="lineNum">    3983 </span>            :   assert(plumed_gmain.p);</a>
+<a name="3984"><span class="lineNum">    3984 </span><span class="lineCov">          8 :   return plumed_valid(plumed_gmain);</span></a>
+<a name="3985"><span class="lineNum">    3985 </span>            : }</a>
+<a name="3986"><span class="lineNum">    3986 </span>            : </a>
+<a name="3987"><span class="lineNum">    3987 </span>            : __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="3988"><span class="lineNum">    3988 </span>            : </a>
+<a name="3989"><span class="lineNum">    3989 </span>            : #endif /*}*/</a>
+<a name="3990"><span class="lineNum">    3990 </span>            : </a>
+<a name="3991"><span class="lineNum">    3991 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="3992"><span class="lineNum">    3992 </span><span class="lineCov">         56 : void plumed_c2f(plumed p,char*c) {</span></a>
+<a name="3993"><span class="lineNum">    3993 </span>            :   unsigned i;</a>
+<a name="3994"><span class="lineNum">    3994 </span>            :   unsigned char* cc;</a>
+<a name="3995"><span class="lineNum">    3995 </span>            :   /*</a>
+<a name="3996"><span class="lineNum">    3996 </span>            :     Convert the address stored in p.p into a proper FORTRAN string</a>
+<a name="3997"><span class="lineNum">    3997 </span>            :     made of only ASCII characters. For this to work, the two following</a>
+<a name="3998"><span class="lineNum">    3998 </span>            :     assertions should be satisfied:</a>
+<a name="3999"><span class="lineNum">    3999 </span>            :   */</a>
+<a name="4000"><span class="lineNum">    4000 </span>            :   assert(CHAR_BIT&lt;=12);</a>
+<a name="4001"><span class="lineNum">    4001 </span>            :   assert(sizeof(p.p)&lt;=16);</a>
+<a name="4002"><span class="lineNum">    4002 </span>            : </a>
+<a name="4003"><span class="lineNum">    4003 </span>            :   assert(c);</a>
+<a name="4004"><span class="lineNum">    4004 </span>            :   cc=(unsigned char*)&amp;p.p;</a>
+<a name="4005"><span class="lineNum">    4005 </span><span class="lineCov">        504 :   for(i=0; i&lt;sizeof(p.p); i++) {</span></a>
+<a name="4006"><span class="lineNum">    4006 </span>            :     /*</a>
+<a name="4007"><span class="lineNum">    4007 </span>            :       characters will range between '0' (ASCII 48) and 'o' (ASCII 111=48+63)</a>
+<a name="4008"><span class="lineNum">    4008 </span>            :     */</a>
+<a name="4009"><span class="lineNum">    4009 </span><span class="lineCov">        448 :     c[2*i]=cc[i]/64+48;</span></a>
+<a name="4010"><span class="lineNum">    4010 </span><span class="lineCov">        448 :     c[2*i+1]=cc[i]%64+48;</span></a>
+<a name="4011"><span class="lineNum">    4011 </span>            :   }</a>
+<a name="4012"><span class="lineNum">    4012 </span><span class="lineCov">        504 :   for(; i&lt;16; i++) {</span></a>
+<a name="4013"><span class="lineNum">    4013 </span><span class="lineCov">        448 :     c[2*i]=' ';</span></a>
+<a name="4014"><span class="lineNum">    4014 </span><span class="lineCov">        448 :     c[2*i+1]=' ';</span></a>
+<a name="4015"><span class="lineNum">    4015 </span>            :   }</a>
+<a name="4016"><span class="lineNum">    4016 </span><span class="lineCov">         56 : }</span></a>
+<a name="4017"><span class="lineNum">    4017 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="4018"><span class="lineNum">    4018 </span>            : </a>
+<a name="4019"><span class="lineNum">    4019 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="4020"><span class="lineNum">    4020 </span><span class="lineCov">        373 : plumed plumed_f2c(const char*c) {</span></a>
+<a name="4021"><span class="lineNum">    4021 </span>            :   plumed p;</a>
+<a name="4022"><span class="lineNum">    4022 </span>            :   unsigned i;</a>
+<a name="4023"><span class="lineNum">    4023 </span>            :   unsigned char* cc;</a>
+<a name="4024"><span class="lineNum">    4024 </span>            : </a>
+<a name="4025"><span class="lineNum">    4025 </span>            :   assert(CHAR_BIT&lt;=12);</a>
+<a name="4026"><span class="lineNum">    4026 </span>            :   assert(sizeof(p.p)&lt;=16);</a>
+<a name="4027"><span class="lineNum">    4027 </span>            : </a>
+<a name="4028"><span class="lineNum">    4028 </span>            :   assert(c);</a>
+<a name="4029"><span class="lineNum">    4029 </span>            : </a>
+<a name="4030"><span class="lineNum">    4030 </span>            :   /*</a>
+<a name="4031"><span class="lineNum">    4031 </span>            :      needed to avoid cppcheck warning on uninitialized p</a>
+<a name="4032"><span class="lineNum">    4032 </span>            :   */</a>
+<a name="4033"><span class="lineNum">    4033 </span><span class="lineCov">        373 :   p.p=__PLUMED_WRAPPER_CXX_NULLPTR;</span></a>
+<a name="4034"><span class="lineNum">    4034 </span>            :   cc=(unsigned char*)&amp;p.p;</a>
+<a name="4035"><span class="lineNum">    4035 </span><span class="lineCov">       3357 :   for(i=0; i&lt;sizeof(p.p); i++) {</span></a>
+<a name="4036"><span class="lineNum">    4036 </span>            :     assert(c[2*i]&gt;=48 &amp;&amp; c[2*i]&lt;48+64);</a>
+<a name="4037"><span class="lineNum">    4037 </span>            :     assert(c[2*i+1]&gt;=48 &amp;&amp; c[2*i+1]&lt;48+64);</a>
+<a name="4038"><span class="lineNum">    4038 </span>            :     /*</a>
+<a name="4039"><span class="lineNum">    4039 </span>            :       perform the reversed transform</a>
+<a name="4040"><span class="lineNum">    4040 </span>            :     */</a>
+<a name="4041"><span class="lineNum">    4041 </span><span class="lineCov">       2984 :     cc[i]=(c[2*i]-48)*64 + (c[2*i+1]-48);</span></a>
+<a name="4042"><span class="lineNum">    4042 </span>            :   }</a>
+<a name="4043"><span class="lineNum">    4043 </span><span class="lineCov">       3357 :   for(; i&lt;16; i++) {</span></a>
+<a name="4044"><span class="lineNum">    4044 </span>            :     assert(c[2*i]==' ');</a>
+<a name="4045"><span class="lineNum">    4045 </span>            :     assert(c[2*i+1]==' ');</a>
+<a name="4046"><span class="lineNum">    4046 </span>            :   }</a>
+<a name="4047"><span class="lineNum">    4047 </span><span class="lineCov">        373 :   return p;</span></a>
+<a name="4048"><span class="lineNum">    4048 </span>            : }</a>
+<a name="4049"><span class="lineNum">    4049 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="4050"><span class="lineNum">    4050 </span>            : </a>
+<a name="4051"><span class="lineNum">    4051 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="4052"><span class="lineNum">    4052 </span><span class="lineCov">          2 : void* plumed_c2v(plumed p) {</span></a>
+<a name="4053"><span class="lineNum">    4053 </span>            :   assert(plumed_check_pimpl((plumed_implementation*)p.p));</a>
+<a name="4054"><span class="lineNum">    4054 </span><span class="lineCov">          2 :   return p.p;</span></a>
+<a name="4055"><span class="lineNum">    4055 </span>            : }</a>
+<a name="4056"><span class="lineNum">    4056 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="4057"><span class="lineNum">    4057 </span>            : </a>
+<a name="4058"><span class="lineNum">    4058 </span>            : __PLUMED_WRAPPER_C_BEGIN</a>
+<a name="4059"><span class="lineNum">    4059 </span><span class="lineCov">          2 : plumed plumed_v2c(void* v) {</span></a>
+<a name="4060"><span class="lineNum">    4060 </span>            :   assert(plumed_check_pimpl((plumed_implementation*)v));</a>
+<a name="4061"><span class="lineNum">    4061 </span>            :   plumed p;</a>
+<a name="4062"><span class="lineNum">    4062 </span>            :   p.p=v;</a>
+<a name="4063"><span class="lineNum">    4063 </span><span class="lineCov">          2 :   return p;</span></a>
+<a name="4064"><span class="lineNum">    4064 </span>            : }</a>
+<a name="4065"><span class="lineNum">    4065 </span>            : __PLUMED_WRAPPER_C_END</a>
+<a name="4066"><span class="lineNum">    4066 </span>            : </a>
+<a name="4067"><span class="lineNum">    4067 </span>            : #if __PLUMED_WRAPPER_FORTRAN /*{*/</a>
+<a name="4068"><span class="lineNum">    4068 </span>            : </a>
+<a name="4069"><span class="lineNum">    4069 </span>            : /*</a>
+<a name="4070"><span class="lineNum">    4070 </span>            :   Fortran wrappers</a>
+<a name="4071"><span class="lineNum">    4071 </span>            :   These are just like the global C wrappers. They are</a>
+<a name="4072"><span class="lineNum">    4072 </span>            :   just defined here and not declared since they</a>
+<a name="4073"><span class="lineNum">    4073 </span>            :   should not be used from c/c++ anyway.</a>
+<a name="4074"><span class="lineNum">    4074 </span>            : </a>
+<a name="4075"><span class="lineNum">    4075 </span>            :   We use a macro that does the following:</a>
+<a name="4076"><span class="lineNum">    4076 </span>            :   - declare a static function named NAME_static</a>
+<a name="4077"><span class="lineNum">    4077 </span>            :   - declare a number of functions named NAME_ etc, with all possible</a>
+<a name="4078"><span class="lineNum">    4078 </span>            :     fortran mangling schemes (zero, one, or two underscores, lower and upper case)</a>
+<a name="4079"><span class="lineNum">    4079 </span>            :   - define the NAME_static function.</a>
+<a name="4080"><span class="lineNum">    4080 </span>            : </a>
+<a name="4081"><span class="lineNum">    4081 </span>            :   The static function is used basically as an inline function in a C-compatible manner.</a>
+<a name="4082"><span class="lineNum">    4082 </span>            : */</a>
+<a name="4083"><span class="lineNum">    4083 </span>            : </a>
+<a name="4084"><span class="lineNum">    4084 </span>            : #define __PLUMED_IMPLEMENT_FORTRAN(lower,upper,arg1,arg2) \</a>
+<a name="4085"><span class="lineNum">    4085 </span>            :   static void lower ## _static arg1; \</a>
+<a name="4086"><span class="lineNum">    4086 </span>            :   extern void lower      arg1 {lower ## _static arg2;} \</a>
+<a name="4087"><span class="lineNum">    4087 </span>            :   extern void lower ##_  arg1 {lower ## _static arg2;} \</a>
+<a name="4088"><span class="lineNum">    4088 </span>            :   extern void lower ##__ arg1 {lower ## _static arg2;} \</a>
+<a name="4089"><span class="lineNum">    4089 </span>            :   extern void upper      arg1 {lower ## _static arg2;} \</a>
+<a name="4090"><span class="lineNum">    4090 </span>            :   extern void upper ##_  arg1 {lower ## _static arg2;} \</a>
+<a name="4091"><span class="lineNum">    4091 </span>            :   extern void upper ##__ arg1 {lower ## _static arg2;} \</a>
+<a name="4092"><span class="lineNum">    4092 </span>            :   static void lower ## _static arg1</a>
+<a name="4093"><span class="lineNum">    4093 </span>            : </a>
+<a name="4094"><span class="lineNum">    4094 </span>            : /* FORTRAN wrappers would only make sense as extern &quot;C&quot; */</a>
+<a name="4095"><span class="lineNum">    4095 </span>            : </a>
+<a name="4096"><span class="lineNum">    4096 </span>            : __PLUMED_WRAPPER_EXTERN_C_BEGIN</a>
+<a name="4097"><span class="lineNum">    4097 </span>            : </a>
+<a name="4098"><span class="lineNum">    4098 </span><span class="lineCov">         36 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_create,PLUMED_F_CREATE,(char*c),(c)) {</span></a>
+<a name="4099"><span class="lineNum">    4099 </span><span class="lineCov">         18 :   plumed_c2f(plumed_create(),c);</span></a>
+<a name="4100"><span class="lineNum">    4100 </span><span class="lineCov">         18 : }</span></a>
+<a name="4101"><span class="lineNum">    4101 </span>            : </a>
+<a name="4102"><span class="lineNum">    4102 </span><span class="lineCov">         12 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_create_dlopen,PLUMED_F_CREATE_DLOPEN,(char*path,char*c),(path,c)) {</span></a>
+<a name="4103"><span class="lineNum">    4103 </span><span class="lineCov">          6 :   plumed_c2f(plumed_create_dlopen(path),c);</span></a>
+<a name="4104"><span class="lineNum">    4104 </span><span class="lineCov">          6 : }</span></a>
+<a name="4105"><span class="lineNum">    4105 </span>            : </a>
+<a name="4106"><span class="lineNum">    4106 </span><span class="lineCov">         12 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_create_reference,PLUMED_F_CREATE_REFERENCE,(char* r,char*c),(r,c)) {</span></a>
+<a name="4107"><span class="lineNum">    4107 </span><span class="lineCov">          6 :   plumed_c2f(plumed_create_reference_f(r),c);</span></a>
+<a name="4108"><span class="lineNum">    4108 </span><span class="lineCov">          6 : }</span></a>
+<a name="4109"><span class="lineNum">    4109 </span>            : </a>
+<a name="4110"><span class="lineNum">    4110 </span><span class="lineNoCov">          0 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_create_invalid,PLUMED_F_CREATE_INVALID,(char* c),(c)) {</span></a>
+<a name="4111"><span class="lineNum">    4111 </span><span class="lineNoCov">          0 :   plumed_c2f(plumed_create_invalid(),c);</span></a>
+<a name="4112"><span class="lineNum">    4112 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="4113"><span class="lineNum">    4113 </span>            : </a>
+<a name="4114"><span class="lineNum">    4114 </span><span class="lineCov">        558 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_cmd,PLUMED_F_CMD,(char*c,char*key,void*val),(c,key,val)) {</span></a>
+<a name="4115"><span class="lineNum">    4115 </span><span class="lineCov">        279 :   plumed_cmd(plumed_f2c(c),key,val);</span></a>
+<a name="4116"><span class="lineNum">    4116 </span><span class="lineCov">        279 : }</span></a>
+<a name="4117"><span class="lineNum">    4117 </span>            : </a>
+<a name="4118"><span class="lineNum">    4118 </span><span class="lineCov">         60 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_finalize,PLUMED_F_FINALIZE,(char*c),(c)) {</span></a>
+<a name="4119"><span class="lineNum">    4119 </span><span class="lineCov">         30 :   plumed_finalize(plumed_f2c(c));</span></a>
+<a name="4120"><span class="lineNum">    4120 </span><span class="lineCov">         30 : }</span></a>
+<a name="4121"><span class="lineNum">    4121 </span>            : </a>
+<a name="4122"><span class="lineNum">    4122 </span><span class="lineCov">         12 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_installed,PLUMED_F_INSTALLED,(int*i),(i)) {</span></a>
+<a name="4123"><span class="lineNum">    4123 </span>            :   assert(i);</a>
+<a name="4124"><span class="lineNum">    4124 </span><span class="lineCov">          6 :   *i=plumed_installed();</span></a>
+<a name="4125"><span class="lineNum">    4125 </span><span class="lineCov">          6 : }</span></a>
+<a name="4126"><span class="lineNum">    4126 </span>            : </a>
+<a name="4127"><span class="lineNum">    4127 </span>            : /* New in PLUMED 2.5 */</a>
+<a name="4128"><span class="lineNum">    4128 </span><span class="lineNoCov">          0 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_valid,PLUMED_F_VALID,(char*c,int*i),(c,i)) {</span></a>
+<a name="4129"><span class="lineNum">    4129 </span>            :   assert(i);</a>
+<a name="4130"><span class="lineNum">    4130 </span><span class="lineNoCov">          0 :   *i=plumed_valid(plumed_f2c(c));</span></a>
+<a name="4131"><span class="lineNum">    4131 </span><span class="lineNoCov">          0 : }</span></a>
+<a name="4132"><span class="lineNum">    4132 </span>            : </a>
+<a name="4133"><span class="lineNum">    4133 </span><span class="lineCov">         36 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_use_count,PLUMED_F_USE_COUNT,(char*c,int*i),(c,i)) {</span></a>
+<a name="4134"><span class="lineNum">    4134 </span>            :   assert(i);</a>
+<a name="4135"><span class="lineNum">    4135 </span><span class="lineCov">         18 :   *i=plumed_use_count(plumed_f2c(c));</span></a>
+<a name="4136"><span class="lineNum">    4136 </span><span class="lineCov">         18 : }</span></a>
+<a name="4137"><span class="lineNum">    4137 </span>            : </a>
+<a name="4138"><span class="lineNum">    4138 </span>            : /* New in PLUMED 2.8 */</a>
+<a name="4139"><span class="lineNum">    4139 </span>            : </a>
+<a name="4140"><span class="lineNum">    4140 </span>            : /* note: flags &amp; (~0x1ffffff) removes bits that are set here (code and size) */</a>
+<a name="4141"><span class="lineNum">    4141 </span>            : </a>
+<a name="4142"><span class="lineNum">    4142 </span>            : #define __PLUMED_IMPLEMENT_F_SAFEPTR_INNER(type,type_,size,code,suffix) \</a>
+<a name="4143"><span class="lineNum">    4143 </span>            : plumed_safeptr plumed_f_safeptr_ ## type_ ## suffix(void*val,__PLUMED_WRAPPER_STD size_t nelem,__PLUMED_WRAPPER_STD size_t*shape,__PLUMED_WRAPPER_STD size_t flags,void*opt) {\</a>
+<a name="4144"><span class="lineNum">    4144 </span>            :   plumed_safeptr safe; \</a>
+<a name="4145"><span class="lineNum">    4145 </span>            :   safe.ptr=val; \</a>
+<a name="4146"><span class="lineNum">    4146 </span>            :   safe.nelem=nelem; \</a>
+<a name="4147"><span class="lineNum">    4147 </span>            :   safe.shape=shape; \</a>
+<a name="4148"><span class="lineNum">    4148 </span>            :   safe.flags= (flags &amp; (~0x1ffffffu)) + 0x10000*code + size; \</a>
+<a name="4149"><span class="lineNum">    4149 </span>            :   safe.opt=opt; \</a>
+<a name="4150"><span class="lineNum">    4150 </span>            :   return safe; \</a>
+<a name="4151"><span class="lineNum">    4151 </span>            : }</a>
+<a name="4152"><span class="lineNum">    4152 </span>            : </a>
+<a name="4153"><span class="lineNum">    4153 </span>            : #define __PLUMED_IMPLEMENT_F_SAFEPTR(type,type_,size,code) \</a>
+<a name="4154"><span class="lineNum">    4154 </span>            :   __PLUMED_IMPLEMENT_F_SAFEPTR_INNER(type,type_,size,code,) \</a>
+<a name="4155"><span class="lineNum">    4155 </span>            :   __PLUMED_IMPLEMENT_F_SAFEPTR_INNER(type,type_,size,code,_scalar)</a>
+<a name="4156"><span class="lineNum">    4156 </span>            : </a>
+<a name="4157"><span class="lineNum">    4157 </span>            : #define __PLUMED_IMPLEMENT_F_SAFEPTR_EMPTY(type,type_,code) \</a>
+<a name="4158"><span class="lineNum">    4158 </span>            :         __PLUMED_IMPLEMENT_F_SAFEPTR(type,type_,0,code)</a>
+<a name="4159"><span class="lineNum">    4159 </span>            : </a>
+<a name="4160"><span class="lineNum">    4160 </span>            : #define __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(type,type_,code) \</a>
+<a name="4161"><span class="lineNum">    4161 </span>            :         __PLUMED_IMPLEMENT_F_SAFEPTR(type,type_,sizeof(type),code)</a>
+<a name="4162"><span class="lineNum">    4162 </span>            : </a>
+<a name="4163"><span class="lineNum">    4163 </span><span class="lineCov">         24 : __PLUMED_IMPLEMENT_F_SAFEPTR_EMPTY(void,ptr,0)</span></a>
+<a name="4164"><span class="lineNum">    4164 </span><span class="lineCov">          1 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(float,float,4)</span></a>
+<a name="4165"><span class="lineNum">    4165 </span><span class="lineCov">         19 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(double,double,4)</span></a>
+<a name="4166"><span class="lineNum">    4166 </span><span class="lineNoCov">          0 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(long double,long_double,4)</span></a>
+<a name="4167"><span class="lineNum">    4167 </span><span class="lineCov">         19 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(int,int,3)</span></a>
+<a name="4168"><span class="lineNum">    4168 </span><span class="lineNoCov">          0 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(short,short,3)</span></a>
+<a name="4169"><span class="lineNum">    4169 </span><span class="lineNoCov">          0 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(long,long,3)</span></a>
+<a name="4170"><span class="lineNum">    4170 </span><span class="lineCov">         20 : __PLUMED_IMPLEMENT_F_SAFEPTR_SIZED(char,char,3)</span></a>
+<a name="4171"><span class="lineNum">    4171 </span>            : </a>
+<a name="4172"><span class="lineNum">    4172 </span>            : #if __PLUMED_WRAPPER_GLOBAL /*{*/</a>
+<a name="4173"><span class="lineNum">    4173 </span>            : </a>
+<a name="4174"><span class="lineNum">    4174 </span><span class="lineCov">         48 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_global,PLUMED_F_GLOBAL,(char*c),(c)) {</span></a>
+<a name="4175"><span class="lineNum">    4175 </span><span class="lineCov">         24 :   plumed_c2f(plumed_gmain,c);</span></a>
+<a name="4176"><span class="lineNum">    4176 </span><span class="lineCov">         24 : }</span></a>
+<a name="4177"><span class="lineNum">    4177 </span>            : </a>
+<a name="4178"><span class="lineNum">    4178 </span><span class="lineCov">         36 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_ginitialized,PLUMED_F_GINITIALIZED,(int*i),(i)) {</span></a>
+<a name="4179"><span class="lineNum">    4179 </span>            :   assert(i);</a>
+<a name="4180"><span class="lineNum">    4180 </span><span class="lineCov">         18 :   *i=plumed_ginitialized();</span></a>
+<a name="4181"><span class="lineNum">    4181 </span><span class="lineCov">         18 : }</span></a>
+<a name="4182"><span class="lineNum">    4182 </span>            : </a>
+<a name="4183"><span class="lineNum">    4183 </span><span class="lineCov">         28 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_gcreate,PLUMED_F_GCREATE,(void),()) {</span></a>
+<a name="4184"><span class="lineNum">    4184 </span><span class="lineCov">         14 :   plumed_gcreate();</span></a>
+<a name="4185"><span class="lineNum">    4185 </span><span class="lineCov">         14 : }</span></a>
+<a name="4186"><span class="lineNum">    4186 </span>            : </a>
+<a name="4187"><span class="lineNum">    4187 </span><span class="lineCov">        156 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_gcmd,PLUMED_F_GCMD,(char*key,void*val),(key,val)) {</span></a>
+<a name="4188"><span class="lineNum">    4188 </span><span class="lineCov">         78 :   plumed_gcmd(key,val);</span></a>
+<a name="4189"><span class="lineNum">    4189 </span><span class="lineCov">         78 : }</span></a>
+<a name="4190"><span class="lineNum">    4190 </span>            : </a>
+<a name="4191"><span class="lineNum">    4191 </span><span class="lineCov">         28 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_gfinalize,PLUMED_F_GFINALIZE,(void),()) {</span></a>
+<a name="4192"><span class="lineNum">    4192 </span><span class="lineCov">         14 :   plumed_gfinalize();</span></a>
+<a name="4193"><span class="lineNum">    4193 </span><span class="lineCov">         14 : }</span></a>
+<a name="4194"><span class="lineNum">    4194 </span>            : </a>
+<a name="4195"><span class="lineNum">    4195 </span>            : /* New in PLUMED 2.5 */</a>
+<a name="4196"><span class="lineNum">    4196 </span><span class="lineCov">         12 : __PLUMED_IMPLEMENT_FORTRAN(plumed_f_gvalid,PLUMED_F_GVALID,(int*i),(i)) {</span></a>
+<a name="4197"><span class="lineNum">    4197 </span>            :   assert(i);</a>
+<a name="4198"><span class="lineNum">    4198 </span><span class="lineCov">          6 :   *i=plumed_gvalid();</span></a>
+<a name="4199"><span class="lineNum">    4199 </span><span class="lineCov">          6 : }</span></a>
+<a name="4200"><span class="lineNum">    4200 </span>            : </a>
+<a name="4201"><span class="lineNum">    4201 </span>            : #endif /*}*/</a>
+<a name="4202"><span class="lineNum">    4202 </span>            : </a>
+<a name="4203"><span class="lineNum">    4203 </span>            : __PLUMED_WRAPPER_EXTERN_C_END</a>
+<a name="4204"><span class="lineNum">    4204 </span>            : </a>
+<a name="4205"><span class="lineNum">    4205 </span>            : #endif /*}*/</a>
+<a name="4206"><span class="lineNum">    4206 </span>            : </a>
+<a name="4207"><span class="lineNum">    4207 </span>            : #endif /*}*/</a>
+<a name="4208"><span class="lineNum">    4208 </span>            : </a>
+<a name="4209"><span class="lineNum">    4209 </span>            : #endif /*}*/</a>
+<a name="4210"><span class="lineNum">    4210 </span>            : </a>
+<a name="4211"><span class="lineNum">    4211 </span>            : /* END OF DEFINITIONS */</a>
+<a name="4212"><span class="lineNum">    4212 </span>            : </a>
+<a name="4213"><span class="lineNum">    4213 </span>            : /* reset variable to allow it to be redefined upon re-inclusion */</a>
+<a name="4214"><span class="lineNum">    4214 </span>            : </a>
+<a name="4215"><span class="lineNum">    4215 </span>            : #undef __PLUMED_WRAPPER_IMPLEMENTATION_</a>
+<a name="4216"><span class="lineNum">    4216 </span>            : </a>
+<a name="4217"><span class="lineNum">    4217 </span>            : /* this macro is set in declarations */</a>
+<a name="4218"><span class="lineNum">    4218 </span>            : #ifdef __PLUMED_WRAPPER_REDEFINE_CMD</a>
+<a name="4219"><span class="lineNum">    4219 </span>            : #if defined(plumed_cmd)</a>
+<a name="4220"><span class="lineNum">    4220 </span>            : #undef plumed_cmd</a>
+<a name="4221"><span class="lineNum">    4221 </span>            : #endif</a>
+<a name="4222"><span class="lineNum">    4222 </span>            : #define plumed_cmd __PLUMED_WRAPPER_REDEFINE_CMD</a>
+<a name="4223"><span class="lineNum">    4223 </span>            : #endif</a>
+<a name="4224"><span class="lineNum">    4224 </span>            : </a>
+<a name="4225"><span class="lineNum">    4225 </span>            : /* this macro is set in declarations */</a>
+<a name="4226"><span class="lineNum">    4226 </span>            : #ifdef __PLUMED_WRAPPER_REDEFINE_GCMD</a>
+<a name="4227"><span class="lineNum">    4227 </span>            : #if defined(plumed_gcmd)</a>
+<a name="4228"><span class="lineNum">    4228 </span>            : #undef plumed_gcmd</a>
+<a name="4229"><span class="lineNum">    4229 </span>            : #endif</a>
+<a name="4230"><span class="lineNum">    4230 </span>            : #define plumed_gcmd __PLUMED_WRAPPER_REDEFINE_GCMD</a>
+<a name="4231"><span class="lineNum">    4231 </span>            : #endif</a>
+<a name="4232"><span class="lineNum">    4232 </span>            : </a>
+<a name="4233"><span class="lineNum">    4233 </span>            : /* this macro is set in declarations */</a>
+<a name="4234"><span class="lineNum">    4234 </span>            : #ifdef __PLUMED_WRAPPER_REDEFINE_ERROR_RETHROW</a>
+<a name="4235"><span class="lineNum">    4235 </span>            : #if defined(plumed_error_rethrow)</a>
+<a name="4236"><span class="lineNum">    4236 </span>            : #undef plumed_error_rethrow</a>
+<a name="4237"><span class="lineNum">    4237 </span>            : #endif</a>
+<a name="4238"><span class="lineNum">    4238 </span>            : #define plumed_error_rethrow __PLUMED_WRAPPER_REDEFINE_ERROR_RETHROW</a>
+<a name="4239"><span class="lineNum">    4239 </span>            : #endif</a>
+</pre>
+      </td>
+    </tr>
+  </table>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov" target="_parent">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/wrapper/index-sort-f.html b/coverage/wrapper/index-sort-f.html
new file mode 100644
index 0000000000..f7611d71bd
--- /dev/null
+++ b/coverage/wrapper/index-sort-f.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - wrapper</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - wrapper</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">469</td>
+            <td class="headerCovTableEntryLo">52.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">252</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Plumed.h.gcov.html">Plumed.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=53 height=10 alt="52.7%"><img src="../snow.png" width=47 height=10 alt="52.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.7&nbsp;%</td>
+      <td class="coverNumLo">247 / 469</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">144 / 252</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/wrapper/index-sort-l.html b/coverage/wrapper/index-sort-l.html
new file mode 100644
index 0000000000..5b013907c1
--- /dev/null
+++ b/coverage/wrapper/index-sort-l.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - wrapper</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - wrapper</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">469</td>
+            <td class="headerCovTableEntryLo">52.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">252</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><a href="index.html"><img src="../updown.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></a></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Plumed.h.gcov.html">Plumed.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=53 height=10 alt="52.7%"><img src="../snow.png" width=47 height=10 alt="52.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.7&nbsp;%</td>
+      <td class="coverNumLo">247 / 469</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">144 / 252</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/coverage/wrapper/index.html b/coverage/wrapper/index.html
new file mode 100644
index 0000000000..98d63b6d9d
--- /dev/null
+++ b/coverage/wrapper/index.html
@@ -0,0 +1,93 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">
+
+<html lang="en">
+
+<head>
+  <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
+  <title>LCOV - plumed test coverage - wrapper</title>
+  <link rel="stylesheet" type="text/css" href="../gcov.css">
+</head>
+
+<body>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="title">LCOV - code coverage report</td></tr>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+
+    <tr>
+      <td width="100%">
+        <table cellpadding=1 border=0 width="100%">
+          <tr>
+            <td width="10%" class="headerItem">Current view:</td>
+            <td width="35%" class="headerValue"><a href="../index.html">top level</a> - wrapper</td>
+            <td width="5%"></td>
+            <td width="15%"></td>
+            <td width="10%" class="headerCovTableHead">Hit</td>
+            <td width="10%" class="headerCovTableHead">Total</td>
+            <td width="15%" class="headerCovTableHead">Coverage</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Test:</td>
+            <td class="headerValue">plumed test coverage</td>
+            <td></td>
+            <td class="headerItem">Lines:</td>
+            <td class="headerCovTableEntry">247</td>
+            <td class="headerCovTableEntry">469</td>
+            <td class="headerCovTableEntryLo">52.7 %</td>
+          </tr>
+          <tr>
+            <td class="headerItem">Date:</td>
+            <td class="headerValue">2024-10-09 13:38:15</td>
+            <td></td>
+            <td class="headerItem">Functions:</td>
+            <td class="headerCovTableEntry">144</td>
+            <td class="headerCovTableEntry">252</td>
+            <td class="headerCovTableEntryLo">57.1 %</td>
+          </tr>
+          <tr><td><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+        </table>
+      </td>
+    </tr>
+
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+  </table>
+
+  <center>
+  <table width="80%" cellpadding=1 cellspacing=1 border=0>
+
+    <tr>
+      <td width="50%"><br></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+      <td width="10%"></td>
+    </tr>
+
+    <tr>
+      <td class="tableHead">Filename <span class="tableHeadSort"><img src="../glass.png" width=10 height=14 alt="Sort by name" title="Sort by name" border=0></span></td>
+      <td class="tableHead" colspan=3>Line Coverage <span class="tableHeadSort"><a href="index-sort-l.html"><img src="../updown.png" width=10 height=14 alt="Sort by line coverage" title="Sort by line coverage" border=0></a></span></td>
+      <td class="tableHead" colspan=2>Functions <span class="tableHeadSort"><a href="index-sort-f.html"><img src="../updown.png" width=10 height=14 alt="Sort by function coverage" title="Sort by function coverage" border=0></a></span></td>
+    </tr>
+    <tr>
+      <td class="coverFile"><a href="Plumed.h.gcov.html">Plumed.h</a></td>
+      <td class="coverBar" align="center">
+        <table border=0 cellspacing=0 cellpadding=1><tr><td class="coverBarOutline"><img src="../ruby.png" width=53 height=10 alt="52.7%"><img src="../snow.png" width=47 height=10 alt="52.7%"></td></tr></table>
+      </td>
+      <td class="coverPerLo">52.7&nbsp;%</td>
+      <td class="coverNumLo">247 / 469</td>
+      <td class="coverPerLo">57.1&nbsp;%</td>
+      <td class="coverNumLo">144 / 252</td>
+    </tr>
+  </table>
+  </center>
+  <br>
+
+  <table width="100%" border=0 cellspacing=0 cellpadding=0>
+    <tr><td class="ruler"><img src="../glass.png" width=3 height=3 alt=""></td></tr>
+    <tr><td class="versionInfo">Generated by: <a href="https://github.com/linux-test-project/lcov">LCOV version 1.16</a></td></tr>
+  </table>
+  <br>
+
+</body>
+</html>
diff --git a/index.html b/index.html
new file mode 100644
index 0000000000..cc4afdd80d
--- /dev/null
+++ b/index.html
@@ -0,0 +1,14 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.0 Transitional//EN">
+<html>
+<body>
+<title> Coverage scan </title>
+<h1> Coverage scan </h1>
+Here you can find coverage scan reports for PLUMED:
+<ul>
+  <li><a href=coverage/index.html>Standard coverage (excluding libraries)</a></li>
+  <li><a href=coverage-libs/index.html>Coverage for third-party libraries</a></li>
+</ul>
+The first one is equivalent to the one you will find on <a href="https://codecov.io/gh/plumed/plumed2">CodeCov</a> (if enabled).
+The second one only contains third-party libraries included in PLUMED.
+</body>
+</html>